Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold267
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: 2306539
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 499 characters in sequence are not A, C, G, or T
File 8 of 15
Found at i:1146375 original size:107 final size:105
Alignment explanation
Indices: 1146211--1146633 Score: 317
Period size: 107 Copynumber: 4.0 Consensus size: 105
1146201 TTCTATAATC
*
1146211 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACTCCGATTTTA-TTCC-AAAAACACCAATTT-TTCACAATCGGGGATACTCC
1146276 AACCCCGTTAATCATCGGGGATACTCCAACCCCGTAATTTTCGA
63 AACCCCGTTAATCATCGGGGATACTCCAACCCCGT-ATTTTCGA
* * *
1146320 GGGGATACTCCAACTCCGGTTTTA-TCGCTAAAACACTAATTTTTCCACAATCGGGGATACTCCA
1 GGGGATACTCCAACTCCGATTTTATTC-CAAAAACACCAATTTTT-CACAATCGGGGATACTCCA
** * ** * * * ** *
1146384 ATCCTGGTTTTATTTTC---AAAACGCCAATTTTCC-T-TTAATC--
64 A-CCCCG-TTAATCATCGGGGATACTCCAA--CCCCGTATT-TTCGA
* *
1146424 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTA-TTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAA
* * * *
1146489 CCTCGATATTTCATCGGGGATACTCCAACCCCGTTACTTTCGA
65 CCCCGTTA-ATCATCGGGGATACTCCAACCCCG-TATTTTCGA
* ** * * *** * * *
1146532 GGGGATACTCCAACCCCGGCTTTATTCCTAAAATATTGATTTCTCATAATTGGGGATACTCCAAC
1 GGGGATACTCCAACTCCGATTTTATTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
** *
1146597 CCCGTT-ATTTTCGAAGGGATACTCCAATCCCG-ATTTT
66 CCCGTTAATCATCG--GGGATACTCCAACCCCGTATTTT
1146634 TTTTTCTAAT
Statistics
Matches: 243, Mismatches: 51, Indels: 44
0.72 0.15 0.13
Matches are distributed among these distances:
102 1 0.00
103 7 0.03
104 44 0.18
105 24 0.10
106 23 0.09
107 89 0.37
108 27 0.11
109 28 0.12
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.31
Consensus pattern (105 bp):
GGGGATACTCCAACTCCGATTTTATTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
CCCGTTAATCATCGGGGATACTCCAACCCCGTATTTTCGA
Found at i:1146509 original size:28 final size:30
Alignment explanation
Indices: 1146473--1146549 Score: 99
Period size: 28 Copynumber: 2.7 Consensus size: 30
1146463 ATTTTTCACA
* *
1146473 ATCGAGGATACTCCAACCTCGATA-TTTC-
1 ATCGGGGATACTCCAACCCCGATACTTTCG
*
1146501 ATCGGGGATACTCCAACCCCGTTACTTTCG
1 ATCGGGGATACTCCAACCCCGATACTTTCG
1146531 A--GGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
1146550 GCTTTATTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 39 0.89
29 4 0.09
30 1 0.02
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.23
Consensus pattern (30 bp):
ATCGGGGATACTCCAACCCCGATACTTTCG
Found at i:1146518 original size:212 final size:212
Alignment explanation
Indices: 1146148--1146596 Score: 629
Period size: 212 Copynumber: 2.1 Consensus size: 212
1146138 AGTTTATCAA
* * *
1146148 TTCTCCACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGG
1 TTCTCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGG
* *
1146213 GGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAA
66 GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAA
* * * *
1146278 CCCCGTTAATCATCGGGGATACTCCAACCCCGTAATTTTCGAGGGGATACTCCAACTCCGGTTTT
131 CCCCGATAATCATCGGGGATACTCCAACCCCGTAACTTTCGAGGGGATACTCCAACCCCGGCTTT
1146343 A-TCGCTAAAACACTAAT
196 ATTC-CTAAAACACTAAT
* * * *
1146360 TTTTCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC
1 TTCTCCACAATCGGGGATACTCCAACTCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATC
*
1146424 GGGGATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCC
64 GGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCC
* * *
1146487 AACCTCGATATTTCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACCCCGGC
129 AACCCCGATA-ATCATCGGGGATACTCCAACCCCGTAACTTTCGAGGGGATACTCCAACCCCGGC
* * *
1146552 TTTATTCCTAAAATATTGAT
193 TTTATTCCTAAAACACTAAT
* *
1146572 TTCT-CATAATTGGGGATACTCCAAC
1 TTCTCCACAATCGGGGATACTCCAAC
1146597 CCCGTTATTT
Statistics
Matches: 209, Mismatches: 23, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
211 48 0.23
212 124 0.59
213 37 0.18
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (212 bp):
TTCTCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGG
GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAA
CCCCGATAATCATCGGGGATACTCCAACCCCGTAACTTTCGAGGGGATACTCCAACCCCGGCTTT
ATTCCTAAAACACTAAT
Found at i:1146652 original size:79 final size:78
Alignment explanation
Indices: 1146503--1146705 Score: 239
Period size: 79 Copynumber: 2.6 Consensus size: 78
1146493 GATATTTCAT
* *
1146503 CGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGCTTTATTCCT-AAATAT
* * *
1146568 TGATTTCTCATAAT
65 CGATTTCTCACAAC
* * ** * *
1146582 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTTTTTTTTCT-AATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCG-GCTTTATTCCTAAAT-A
1146646 TCGATTTCTCACAAC
64 TCGATTTCTCACAAC
* *
1146661 CGGGGATACTCCAGCCCCGTTATTTTC-AAGGGAACACTCCAACCC
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCC
1146706 TGTTATTATC
Statistics
Matches: 106, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
78 8 0.08
79 91 0.86
80 7 0.07
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGCTTTATTCCTAAATATC
GATTTCTCACAAC
Found at i:1152924 original size:55 final size:55
Alignment explanation
Indices: 1152840--1153337 Score: 606
Period size: 55 Copynumber: 8.9 Consensus size: 55
1152830 CTTTTTCTTT
* *
1152840 TCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGGGCAGGACGCCTC
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTC
* *
1152895 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTT
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTC
* *
1152950 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTT
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTC
* * *
1153005 TTAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGTAGGACGCCTTTTC
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCC---TC
* ** **
1153063 TTTTAAAGCCCACACAAGTTGGTGGCA-CCTCCAGTCCTCAAAGAGTGGGACGCCTTTTC
1 --TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCC---TC
* *
1153122 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACACCTC
1 --TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTC
* *
1153179 TTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACGCCTC
1 TCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCCTC
* * * *
1153234 TTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGTAGGACGCCTT
1 TCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCCTC
** * ** * *
1153289 TCAAAGCCCACACGTGTTTGTGGCATTTTTTACTCCTCAATGAGCAGGA
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA
1153338 TACACTTTAT
Statistics
Matches: 400, Mismatches: 35, Indels: 16
0.89 0.08 0.04
Matches are distributed among these distances:
54 3 0.01
55 291 0.73
56 3 0.01
57 2 0.00
58 1 0.00
59 54 0.14
60 46 0.12
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (55 bp):
TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTC
Found at i:1154187 original size:19 final size:19
Alignment explanation
Indices: 1154163--1154230 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1154153 AATTCAACGA
1154163 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1154182 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1154197 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1154214 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1154231 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1154201 original size:32 final size:32
Alignment explanation
Indices: 1154165--1154227 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1154155 TTCAACGATT
*
1154165 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1154197 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1154228 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1154202 original size:13 final size:13
Alignment explanation
Indices: 1154184--1154208 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1154174 ACATAAGTTT
1154184 TGTATCGATACAA
1 TGTATCGATACAA
1154197 TGTATCGATACA
1 TGTATCGATACA
1154209 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1154288 original size:13 final size:13
Alignment explanation
Indices: 1154270--1154295 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1154260 CATTTTTCTG
1154270 TGTATCGATACAT
1 TGTATCGATACAT
1154283 TGTATCGATACAT
1 TGTATCGATACAT
1154296 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1154292 original size:33 final size:33
Alignment explanation
Indices: 1154250--1154316 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1154240 GCCAAGGAAA
***
1154250 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1154283 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1154316 T
1 T
1154317 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1156729 original size:51 final size:53
Alignment explanation
Indices: 1156660--1157000 Score: 194
Period size: 52 Copynumber: 6.5 Consensus size: 53
1156650 AGTTTATCAA
* * * * *
1156660 TTCTCCACAATCGAGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
1156711 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
* * * *** * *
1156765 TTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAACCCCGT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC-CAAAAACACCAA-----T
* * * *
1156823 TAT-TTC-CGA--GGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAAT
1 T-TCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAAT
* * **
1156872 TT-TTCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTT-TAAAAATGCCAATT
1 TTCTT-CACAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAA-T
* *
1156925 TTCCTT--TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAAT
1 TT-CTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
*
1156977 TT-TTCACAATCGAGGATACTCCAA
1 TTCTTCACAATCGGGGATACTCCAA
1157001 TCTCGATATT
Statistics
Matches: 223, Mismatches: 38, Indels: 57
0.70 0.12 0.18
Matches are distributed among these distances:
48 3 0.01
49 3 0.01
50 6 0.03
51 35 0.16
52 76 0.34
53 34 0.15
54 33 0.15
55 22 0.10
57 5 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:1156844 original size:28 final size:27
Alignment explanation
Indices: 1156777--1156845 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
1156767 CTTCACAATC
**
1156777 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCAGA
* *
1156804 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTA-ATCAGA
1156832 GGGGATACTCCAAC
1 GGGGATACTCCAAC
1156846 TCCGGTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.25, C:0.32, G:0.22, T:0.22
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCAGA
Found at i:1156887 original size:107 final size:104
Alignment explanation
Indices: 1156723--1157116 Score: 314
Period size: 107 Copynumber: 3.7 Consensus size: 104
1156713 TTCTATAATC
*
1156723 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACTCCGATTTTA-TTCC-AAAAACACCAATTT-TTCACAATCGGGGATACTCC
1156788 AACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGA
63 AACCCCGTT-ATCATCGGGGATACTCCAACCCCGTTA-TTCCGA
* * *
1156832 GGGGATACTCCAACTCCGGTTTTA-TCGCTAAAACACTAATTTTTCCACAATCGGGGATACTCCA
1 GGGGATACTCCAACTCCGATTTTATTC-CAAAAACACCAATTTTT-CACAATCGGGGATACTCCA
** * **** * * ** * *
1156896 ATCCTGGTT-TTAT-TTTAAAAATGCCAATTTTCCTTTAAT-C--
64 A-CCCCGTTATCATCGGGGATACT-CCAA--CCCCGTTATTCCGA
* *
1156936 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTA-TTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAA
* * *
1157001 TCTCGATATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
65 CCCCG-T-TATCATCGGGGATACTCCAACCCCGTTA-TTCCGA
* ** * * *** * * *
1157044 GGGGATACTCCAACCCCGGCTTTATTCCTAAAATATTGATTTCTCATAATTGGGGATACTCCAAC
1 GGGGATACTCCAACTCCGATTTTATTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
1157109 CCCGTTAT
66 CCCGTTAT
1157117 TTTCGAAGGG
Statistics
Matches: 220, Mismatches: 49, Indels: 36
0.72 0.16 0.12
Matches are distributed among these distances:
103 3 0.01
104 48 0.22
105 21 0.10
106 21 0.10
107 73 0.33
108 32 0.15
109 22 0.10
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (104 bp):
GGGGATACTCCAACTCCGATTTTATTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
CCCGTTATCATCGGGGATACTCCAACCCCGTTATTCCGA
Found at i:1157030 original size:212 final size:212
Alignment explanation
Indices: 1156660--1157108 Score: 611
Period size: 212 Copynumber: 2.1 Consensus size: 212
1156650 AGTTTATCAA
* * * *
1156660 TTCTCCACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGG
1 TTCTCCACAATCGGGGATACTCCAACTCCGATTTTATTTTAAAAACACCAATTTTCTATAATCGG
* *
1156725 GGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAA
66 GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAA
* * * *
1156790 CCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACTCCGGTTTT
131 CCCCGATAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
1156855 A-TCGCTAAAACACTAAT
196 ATTC-CTAAAACACTAAT
* * ** *
1156872 TTTTCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTAAAAATGCCAATTTTCCTTTAATC
1 TTCTCCACAATCGGGGATACTCCAACTCC-GATTTTATTTTAAAAACACCAATTTT-CTATAATC
*
1156936 GGGGATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCC
64 GGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCC
* * *
1156999 AATCTCGATATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGC
129 AACCCCGATA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGC
* * *
1157064 TTTATTCCTAAAATATTGAT
193 TTTATTCCTAAAACACTAAT
* *
1157084 TTCT-CATAATTGGGGATACTCCAAC
1 TTCTCCACAATCGGGGATACTCCAAC
1157109 CCCGTTATTT
Statistics
Matches: 207, Mismatches: 25, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
211 47 0.23
212 123 0.59
213 37 0.18
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (212 bp):
TTCTCCACAATCGGGGATACTCCAACTCCGATTTTATTTTAAAAACACCAATTTTCTATAATCGG
GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAA
CCCCGATAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
ATTCCTAAAACACTAAT
Found at i:1157164 original size:79 final size:78
Alignment explanation
Indices: 1157015--1157217 Score: 221
Period size: 79 Copynumber: 2.6 Consensus size: 78
1157005 GATATTTCAT
* * *
1157015 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGCTTTATTCCT-AAATAT
* * *
1157080 TGATTTCTCATAAT
65 CGATTTCTCACAAC
* * * ** * *
1157094 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTTCAATCCCGATTTTTTTTTCT-AATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCG-GCTTTATTCCTAAAT-A
1157158 TCGATTTCTCACAAC
64 TCGATTTCTCACAAC
* *
1157173 CGGGGATACTCCAGCCCCGTTATTTTC-AAGGGAACACTCCAACCC
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCC
1157218 TTTTATTATC
Statistics
Matches: 103, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
78 8 0.08
79 88 0.85
80 7 0.07
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGCTTTATTCCTAAATATC
GATTTCTCACAAC
Found at i:1163442 original size:55 final size:55
Alignment explanation
Indices: 1163358--1163855 Score: 606
Period size: 55 Copynumber: 8.9 Consensus size: 55
1163348 CTTTTTCTTT
* *
1163358 TCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGGGCAGGACGCCTC
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTC
* * *
1163413 TCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACACCTT
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTC
* *
1163468 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTT
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTC
* * *
1163523 TTAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGTAGGACGCCTTTTC
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCC---TC
* ** **
1163581 TTTTAAAGCCCACACAAGTTGGTGGCA-CCTCCAGTCCTCAAAGAGTGGGACGCCTTTTC
1 --TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCC---TC
*
1163640 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
1 --TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTC
* *
1163697 TTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACGCCTC
1 TCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCCTC
* * * *
1163752 TTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGTAGGACGCCTT
1 TCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCCTC
** * ** * *
1163807 TCAAAGCCCACACGTGTTTGTGGCATTTTTTACTCCTCAATGAGCAGGA
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA
1163856 TACACTTTAT
Statistics
Matches: 402, Mismatches: 33, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
54 3 0.01
55 292 0.73
56 3 0.01
57 2 0.00
58 1 0.00
59 54 0.13
60 47 0.12
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (55 bp):
TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTC
Found at i:1164705 original size:19 final size:19
Alignment explanation
Indices: 1164681--1164748 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1164671 AATTCAACGA
1164681 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1164700 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1164715 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1164732 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1164749 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1164719 original size:32 final size:32
Alignment explanation
Indices: 1164683--1164745 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1164673 TTCAACGATT
*
1164683 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1164715 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1164746 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1164720 original size:13 final size:13
Alignment explanation
Indices: 1164702--1164726 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1164692 ACATAAGTTT
1164702 TGTATCGATACAA
1 TGTATCGATACAA
1164715 TGTATCGATACA
1 TGTATCGATACA
1164727 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1164806 original size:13 final size:13
Alignment explanation
Indices: 1164788--1164813 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1164778 CATTTTTCTG
1164788 TGTATCGATACAT
1 TGTATCGATACAT
1164801 TGTATCGATACAT
1 TGTATCGATACAT
1164814 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1164810 original size:33 final size:33
Alignment explanation
Indices: 1164768--1164834 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1164758 GCCAAGGAAA
***
1164768 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1164801 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1164834 T
1 T
1164835 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1167244 original size:51 final size:53
Alignment explanation
Indices: 1167175--1167516 Score: 198
Period size: 52 Copynumber: 6.5 Consensus size: 53
1167165 AGTTTATCAA
* * * * *
1167175 TTCTCCACAATCGAGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
1167226 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
* * * * * *
1167280 TTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAAC-CCCAT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC---CA-A---AAACACCAAT
* * * *
1167338 TAT-TTC-CGA--GGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAAT
1 T-TCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAAT
* * *
1167387 TT-TTCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTC-AAAACGCCAATT
1 TTCTT-CACAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAA-T
* *
1167440 TTCCTT--TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAAT
1 TT-CTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
1167492 TT-TTCACAATCGAGGATACTACAAC
1 TTCTTCACAATCGGGGATACTCCAAC
1167517 CTCGTTATTT
Statistics
Matches: 225, Mismatches: 35, Indels: 61
0.70 0.11 0.19
Matches are distributed among these distances:
48 6 0.03
49 5 0.02
50 6 0.03
51 36 0.16
52 79 0.35
53 26 0.12
54 26 0.12
55 23 0.10
56 1 0.00
57 5 0.02
58 8 0.04
59 4 0.02
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:1167359 original size:28 final size:27
Alignment explanation
Indices: 1167292--1167360 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
1167282 CTTCACAATC
* **
1167292 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCATTAATCAGA
* *
1167319 GGGGATACTCCAACCCCATTATTTCCGA
1 GGGGATACTCCAACCCCATTA-ATCAGA
1167347 GGGGATACTCCAAC
1 GGGGATACTCCAAC
1167361 TCCGGTTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 20 0.56
28 16 0.44
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.22
Consensus pattern (27 bp):
GGGGATACTCCAACCCCATTAATCAGA
Found at i:1167402 original size:107 final size:105
Alignment explanation
Indices: 1167238--1167630 Score: 323
Period size: 107 Copynumber: 3.7 Consensus size: 105
1167228 TTCTATAATC
*
1167238 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACTCCGATTTTA-TTCC-AAAAACACCAATTT-TTCACAATCGGGGATACTCC
1167303 AACCCCGTTAATCATCGGGGATACTCCAACCCCATTATTTCCGA
63 AACCCCGTTAATCATCGGGGATACTCCAACCCCATTA-TTCCGA
* * *
1167347 GGGGATACTCCAACTCCGGTTTTA-TCGCTAAAACACTAATTTTTCCACAATCGGGGATACTCCA
1 GGGGATACTCCAACTCCGATTTTATTC-CAAAAACACCAATTTTT-CACAATCGGGGATACTCCA
** * ** * * * ** * *
1167411 ATCCTGGTTTTATTTTC---AAAACGCCAATTTTCCTTTAAT-C--
64 A-CCCCG-TTAATCATCGGGGATACTCCAA--CCCCATTATTCCGA
* * *
1167451 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTACAA
1 GGGGATACTCCAACTCCGATTTTA-TTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAA
* * *
1167516 CCTCGTTATTTCATCGGGGATACTCCAACCCTATTACTTCCGA
65 CCCCGTTA-ATCATCGGGGATACTCCAACCCCATTA-TTCCGA
* ** * * *** * * *
1167559 GGGGATACTCCAACCCCGGCTTTATTCCTAAAATATTGATTTCTCATAATTGGGGATACTCCAAC
1 GGGGATACTCCAACTCCGATTTTATTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
1167624 CCCGTTA
66 CCCGTTA
1167631 TTTTCGAAGG
Statistics
Matches: 220, Mismatches: 48, Indels: 34
0.73 0.16 0.11
Matches are distributed among these distances:
102 2 0.01
103 7 0.03
104 45 0.20
105 15 0.07
106 20 0.09
107 73 0.33
108 30 0.14
109 28 0.13
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (105 bp):
GGGGATACTCCAACTCCGATTTTATTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
CCCGTTAATCATCGGGGATACTCCAACCCCATTATTCCGA
Found at i:1167545 original size:212 final size:212
Alignment explanation
Indices: 1167175--1167623 Score: 629
Period size: 212 Copynumber: 2.1 Consensus size: 212
1167165 AGTTTATCAA
* * *
1167175 TTCTCCACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGG
1 TTCTCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGG
* * *
1167240 GGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAA
66 GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTACAA
* * *
1167305 CCCCGTTAATCATCGGGGATACTCCAACCCCATTATTTCCGAGGGGATACTCCAACTCCGGTTTT
131 CCCCGTTAATCATCGGGGATACTCCAACCCCATTACTTCCGAGGGGATACTCCAACCCCGGCTTT
1167370 A-TCGCTAAAACACTAAT
196 ATTC-CTAAAACACTAAT
* * * *
1167387 TTTTCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC
1 TTCTCCACAATCGGGGATACTCCAACTCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATC
*
1167451 GGGGATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTAC
64 GGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTAC
* * *
1167514 AACCTCGTTATTTCATCGGGGATACTCCAACCCTATTACTTCCGAGGGGATACTCCAACCCCGGC
129 AACCCCGTTA-ATCATCGGGGATACTCCAACCCCATTACTTCCGAGGGGATACTCCAACCCCGGC
* * *
1167579 TTTATTCCTAAAATATTGAT
193 TTTATTCCTAAAACACTAAT
* *
1167599 TTCT-CATAATTGGGGATACTCCAAC
1 TTCTCCACAATCGGGGATACTCCAAC
1167624 CCCGTTATTT
Statistics
Matches: 209, Mismatches: 23, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
211 48 0.23
212 124 0.59
213 37 0.18
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (212 bp):
TTCTCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGG
GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTACAA
CCCCGTTAATCATCGGGGATACTCCAACCCCATTACTTCCGAGGGGATACTCCAACCCCGGCTTT
ATTCCTAAAACACTAAT
Found at i:1169403 original size:22 final size:22
Alignment explanation
Indices: 1169351--1169403 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
1169341 TGTCCGCAAC
*
1169351 AAAACATATGTTTTGGGAATTT
1 AAAACATCTGTTTTGGGAATTT
*
1169373 AAAATATCTGTTTTGGGAATTT
1 AAAACATCTGTTTTGGGAATTT
1169395 AAAACATCT
1 AAAACATCT
1169404 AAAAGTACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.40
Consensus pattern (22 bp):
AAAACATCTGTTTTGGGAATTT
Found at i:1170839 original size:15 final size:15
Alignment explanation
Indices: 1170821--1170855 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1170811 CAAGTCAACT
1170821 TCATCATTATCATCA
1 TCATCATTATCATCA
*
1170836 TCATCATTATCTTCA
1 TCATCATTATCATCA
1170851 TCATC
1 TCATC
1170856 TTTGATGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (15 bp):
TCATCATTATCATCA
Found at i:1172346 original size:13 final size:13
Alignment explanation
Indices: 1172328--1172356 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1172318 CAATTCTTCA
1172328 TGTATCGATACAT
1 TGTATCGATACAT
1172341 TGTATCGATACAT
1 TGTATCGATACAT
1172354 TGT
1 TGT
1172357 TCCATGTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1172350 original size:33 final size:33
Alignment explanation
Indices: 1172308--1172372 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1172298 TTTGGGACAA
1172308 TGTATCGATACAATTCTT-CATGTATCGATACAT
1 TGTATCGATAC-ATTCTTCCATGTATCGATACAT
*
1172341 TGTATCGATACATTGTTCCATGTATCGATACA
1 TGTATCGATACATTCTTCCATGTATCGATACA
1172373 AATAGTGGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 5 0.17
33 25 0.83
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Consensus pattern (33 bp):
TGTATCGATACATTCTTCCATGTATCGATACAT
Found at i:1172495 original size:20 final size:19
Alignment explanation
Indices: 1172402--1172494 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 19
1172392 CTACGAGTTT
1172402 TATGTATCGATACAAATGTG-
1 TATGTATCGATAC-AATG-GA
*
1172422 TATGTATCGATACAATGAA
1 TATGTATCGATACAATGGA
* *
1172441 CATGTATCGATACCAA-GCA
1 TATGTATCGATA-CAATGGA
*
1172460 TAATGTATCGATACATCTGGA
1 T-ATGTATCGATACA-ATGGA
1172481 TATGTATCGATACA
1 TATGTATCGATACA
1172495 TTCAAGGGTT
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
19 19 0.31
20 40 0.65
21 3 0.05
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (19 bp):
TATGTATCGATACAATGGA
Found at i:1177555 original size:13 final size:13
Alignment explanation
Indices: 1177537--1177561 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1177527 ACATAAGTGT
1177537 TGTATCGATACAA
1 TGTATCGATACAA
1177550 TGTATCGATACA
1 TGTATCGATACA
1177562 TAATACATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1177637 original size:13 final size:13
Alignment explanation
Indices: 1177619--1177643 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1177609 GCCAAGAAAA
1177619 TGTATCGATACAT
1 TGTATCGATACAT
1177632 TGTATCGATACA
1 TGTATCGATACA
1177644 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1177694 original size:52 final size:52
Alignment explanation
Indices: 1177652--1177780 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
1177642 CACTGATCTT
*
1177652 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* *
1177704 TGTATCGATACATACAGGCAAATTTGCTCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
1177756 TGTATCGATACATGCAGGTAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1177781 TCATATTTCG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:1179234 original size:78 final size:78
Alignment explanation
Indices: 1179118--1179323 Score: 225
Period size: 78 Copynumber: 2.6 Consensus size: 78
1179108 GAGATAATAA
* * * * * * *
1179118 CGGGGTTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-A
*
1179183 -TTAGAAAAAAAAT
65 TTTAGAAAAAAAAC
* * *
1179196 CGGGATTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-
* * * *
1179261 TTTGGGAATAAAGC
65 TTTAGAAAAAAAAC
* * *
1179275 CGGGGTTAGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
1179324 GAAATAACGA
Statistics
Matches: 105, Mismatches: 21, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
77 1 0.01
78 53 0.50
79 51 0.49
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTAGAAAAAAAAC
Found at i:1179315 original size:28 final size:28
Alignment explanation
Indices: 1179275--1179346 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
1179265 GGAATAAAGC
* ** *
1179275 CGGGGTTAGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1179303 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1179331 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
1179347 TCGATTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:1179394 original size:52 final size:51
Alignment explanation
Indices: 1179334--1179713 Score: 395
Period size: 52 Copynumber: 7.3 Consensus size: 51
1179324 GAAATAACGA
* * * *
1179334 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGT-GTTTTGGAAATAAAACCGG
* * * *
1179386 AGTTGGAGTATCCTCGATTAAAG-GGAAAATTAGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT---GTGAAAAATTAGTGTTTTGGAAATAAAACCGG
* *
1179439 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGT-GAAAAATTAGTGTTTTGGAAATAAAACCGG
* * * *
1179491 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGT-GTTTTGGAAATAAAACCGG
* * * *
1179543 AGTTGGAGTATCCCCGATTAAAG-GGAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT---GTGAAAAATTAGTGTTTTGGAAATAAAACCGG
* * *
1179596 GGTTGAAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGT-GAAAAATTAGTGTTTTGGAAATAAAACCGG
* * * * * ** *
1179648 GGTTAGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCAG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAACCGG
1179699 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
1179714 TCGGAAATAA
Statistics
Matches: 274, Mismatches: 43, Indels: 23
0.81 0.13 0.07
Matches are distributed among these distances:
50 2 0.01
51 46 0.17
52 139 0.51
53 66 0.24
54 19 0.07
55 2 0.01
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAACCGG
Found at i:1179459 original size:105 final size:101
Alignment explanation
Indices: 1179334--1179711 Score: 382
Period size: 105 Copynumber: 3.6 Consensus size: 101
1179324 GAAATAACGA
* * * * *
1179334 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGT-GTTTTGGAAATAAAACCGGGGTTGGAGTATCC
*
1179399 TCGATTAAAGGGAAAATTAGTGTTTTGAAAATAAAACCGG
65 TCGATT---GGAAAAATTAGTGTTTTGAAAATAAAACCGG
* *
1179439 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGGGGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATTGT-GAAAAATTAGTGTTTTGGAAATAAAACCGGGGTTGGAGTATCC
* * * *
1179504 TCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
65 TCGATTG-GAAAAATTAGT-GTTTTGAAAATAAAACCGG
* * * * *
1179543 AGTTGGAGTATCCCCGATTAAAG-GGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGAAGTAT
1 GGTTGGAGTATCCCCGATT---GTGAAAAATTAGTGTTTTGGAAATAAAACCGGGGTTGGAGTAT
* *
1179607 CCCCGATTGTGGAAAAATTAGTGTTTT-AGCAATAAAACCGG
63 CCTCGA-T-TGGAAAAATTAGTGTTTTGA-AAATAAAACCGG
* * * * * ** *
1179648 GGTTAGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCAGGGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAACCGGGGTTGGAGTATCC
1179712 CCTCGGAAAT
Statistics
Matches: 225, Mismatches: 38, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
102 1 0.00
103 42 0.19
104 34 0.15
105 124 0.55
106 21 0.09
107 3 0.01
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (101 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAACCGGGGTTGGAGTATCCT
CGATTGGAAAAATTAGTGTTTTGAAAATAAAACCGG
Found at i:1179516 original size:157 final size:157
Alignment explanation
Indices: 1179334--1179713 Score: 647
Period size: 157 Copynumber: 2.4 Consensus size: 157
1179324 GAAATAACGA
1179334 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCC
1 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCC
* *
1179399 TCGATTAAAGGGAAAATTAGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAA
66 CCGATTAAAGGGAAAATTAGTGTTTTGAAAATAAAACCGGGGTTGAAGTATCCCCGATTGTGGAA
1179464 AAATTAGTGTTTTAGCAATAAAACCGG
131 AAATTAGTGTTTTAGCAATAAAACCGG
1179491 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCC
1 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCC
*
1179556 CCGATTAAAGGGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGAAGTATCCCCGATTGTGGAA
66 CCGATTAAAGGGAAAATTAGTGTTTTGAAAATAAAACCGGGGTTGAAGTATCCCCGATTGTGGAA
1179621 AAATTAGTGTTTTAGCAATAAAACCGG
131 AAATTAGTGTTTTAGCAATAAAACCGG
* * * *** *
1179648 GGTTAGAGTATCCCCGATTATGAAAAATCAATA-TTTTGGAAATAAAGTCAGG-GTTGGAGTATC
1 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATC-GGAGTTGGAGTATC
1179711 CCC
65 CCC
1179714 TCGGAAATAA
Statistics
Matches: 212, Mismatches: 10, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
156 29 0.14
157 183 0.86
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (157 bp):
GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCC
CCGATTAAAGGGAAAATTAGTGTTTTGAAAATAAAACCGGGGTTGAAGTATCCCCGATTGTGGAA
AAATTAGTGTTTTAGCAATAAAACCGG
Found at i:1180653 original size:19 final size:19
Alignment explanation
Indices: 1180629--1180720 Score: 166
Period size: 19 Copynumber: 4.8 Consensus size: 19
1180619 TAGTAGCTAA
1180629 TTATGTATCGATACAATAC
1 TTATGTATCGATACAATAC
1180648 TTATGTATCGATACAATAC
1 TTATGTATCGATACAATAC
1180667 TTATGTATCGATACAATAC
1 TTATGTATCGATACAATAC
* *
1180686 TTATGTATCGATACAACAT
1 TTATGTATCGATACAATAC
1180705 TTATGTATCGATACAA
1 TTATGTATCGATACAA
1180721 ATCGCTGAAA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 71 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (19 bp):
TTATGTATCGATACAATAC
Found at i:1180800 original size:21 final size:21
Alignment explanation
Indices: 1180776--1180833 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
1180766 ACATTTGTAG
*
1180776 AATGTATTGATACATTCCACA
1 AATGTATCGATACATTCCACA
*
1180797 AATGTATCGATACATTCTACA
1 AATGTATCGATACATTCCACA
1180818 AATGTATCGATACATT
1 AATGTATCGATACATT
1180834 TGGATAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.34
Consensus pattern (21 bp):
AATGTATCGATACATTCCACA
Found at i:1181867 original size:61 final size:61
Alignment explanation
Indices: 1181553--1182807 Score: 1451
Period size: 61 Copynumber: 21.2 Consensus size: 61
1181543 ATAAAGTGTA
*** *
1181553 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT-----G-AAAGGCG
1 TCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
* * * *
1181608 TCCTGCTCTTTGAGGA-TTGAAAGGTGCCACCAACTTGTATGGGCTTT--AA-G---AGGTG
1 TCCTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
* * *
1181663 TCCTGCTTTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAAGCG
1 TCCTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
* * *
1181723 TCCCGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTATGGGCTTT------AAAAGGCA
1 TCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
* *
1181778 TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCG
1 TCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
* *
1181839 TCCTGCTCTTTGAGGATTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
*
1181900 TCCTGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGGGTGGGCTTT-AAAGGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
* ** * * * *
1181959 TCCCGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGTG
1 TCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
* *
1182020 TCTTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
* *
1182081 TCCTGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGGGTGGGATTT-AAAGGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
* * * *
1182140 TCCCGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCG
1 TCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
* * *
1182201 TCCTGCTCTTTGAGGATTGGGAAGTGCCACAAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
* *
1182262 TCTTGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGGGTGGGCTTT-AAAGGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
* * * *
1182321 TCCCGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCG
1 TCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
* *
1182382 TCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGC-TT----CG-AAAGGGG
1 TCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
* * * * * *
1182437 TCCTACTCTTTGGGGACT-GAAAGGTGCCAGCAACTTGTGTGGGCTTTGAAAA-GAAAAAGCA
1 TCCTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCG
* *
1182498 TCCTGCTCTTTGAGGACT--AAAGGTGCCACCAACTTGGGTGGGCTTTAAAA-GAAAAGGCG
1 TCCTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
*
1182557 TCCCGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCG
1 TCCTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
* * * * * *
1182616 TCCCGCTATTTAAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCG
1 TCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
* * *
1182677 TCCTACTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGC-TT----CG-AAAGGGG
1 TCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
* * * * *
1182732 TCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
1182793 TCCTGCTCTTTGAGG
1 TCCTGCTCTTTGAGG
1182808 GCTAAAAAGC
Statistics
Matches: 1039, Mismatches: 115, Indels: 86
0.84 0.09 0.07
Matches are distributed among these distances:
54 10 0.01
55 218 0.21
56 7 0.01
57 4 0.00
59 178 0.17
60 233 0.22
61 389 0.37
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (61 bp):
TCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
Found at i:1182029 original size:181 final size:181
Alignment explanation
Indices: 1181552--1182807 Score: 1575
Period size: 181 Copynumber: 7.1 Consensus size: 181
1181542 AATAAAGTGT
* * *
1181552 ATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT----G-AAAGGCGTCCT
1 ATCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAGGAAAAGGCGTCCT
* * * * *
1181612 GCTCTTTGAGGATTGAAAGGTGCCACCAACTTGTATGGGCTTT----A-AG-AGGTGTCCTGCTT
65 GCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCGTCCTGCTC
* *
1181671 TTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAAGC
130 TTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* * * *
1181722 GTCCCGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTATGGGCTTT-----AAAAGGCATCC
1 ATCCTGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGTGTGGGCTTTAAAGGAAAAGGCGTCC
* *
1181781 TGCTCTTTGAGGACT-AGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTGC
64 TGCTCTTTGAGGACTGA-AAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCGTCCTGC
*
1181845 TCTTTGAGGATTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
128 TCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* *
1181899 ATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAGGAAAAGGCGTCCCG
1 ATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAGGAAAAGGCGTCCTG
* * *
1181964 CTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGTGTCTTGCTCT
66 CTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCGTCCTGCTCT
1182029 TTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
131 TTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* * *
1182080 ATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGATTTAAAGGAAAAGGCGTCCCG
1 ATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAGGAAAAGGCGTCCTG
*
1182145 CTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTGCTC
66 CTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCGTCCTGCTC
* *
1182209 TTTGAGGATTGGGAAGTGCCACAAACTTGTGTGGGCTTTAAAAGGAAAAGGC
130 TTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* * *
1182261 ATCTTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAGGAAAAGGCGTCCCG
1 ATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAGGAAAAGGCGTCCTG
*
1182326 CTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTGCTC
66 CTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCGTCCTGCTC
**
1182390 TTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTCGAAAGG----GG-
130 TTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* * * * * *
1182437 -TCCTACTCTTTGGGGACTGAAAGGTGCCAGCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCC
1 ATCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAGGAAAAGGCGTCC
* * * *
1182501 TGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGGGTGGGCTTT-AAAAGAAAAGGCGTCCCGCT
64 TGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCGTCCTGCT
1182564 CTTTGAGGACT--GAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGC
129 CTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* * * * ** *
1182615 GTCCCGCTATTTAAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCC
1 ATCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTT-AAAGGAAAAGGCGTCC
* ** * *
1182680 TACTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGC-TT----CGA-AAGGGGTCCTGCT
64 TGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCGTCCTGCT
* * * *
1182739 CTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAAGC
129 CTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
1182792 ATCCTGCTCTTTGAGG
1 ATCCTGCTCTTTGAGG
1182808 GCTAAAAAGC
Statistics
Matches: 967, Mismatches: 86, Indels: 59
0.87 0.08 0.05
Matches are distributed among these distances:
169 1 0.00
170 86 0.09
171 2 0.00
173 4 0.00
174 26 0.03
175 73 0.08
176 149 0.15
177 77 0.08
179 65 0.07
180 22 0.02
181 456 0.47
182 6 0.01
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (181 bp):
ATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAGGAAAAGGCGTCCTG
CTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCGTCCTGCTCT
TTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
Found at i:1182784 original size:29 final size:29
Alignment explanation
Indices: 1182700--1182784 Score: 72
Period size: 29 Copynumber: 3.0 Consensus size: 29
1182690 GGACTGGGAA
*
1182700 GTGCCACCAACTTGTGTGGGCTTCGAAAG
1 GTGCCACCAACTTGTGTGGGCTTTGAAAG
* ** *
1182729 GGGTCCTGC-TCTT-TG-GGGAC--TGAAAG
1 GTG-CCACCAACTTGTGTGGG-CTTTGAAAG
1182755 GTGCCACCAACTTGTGTGGGCTTTGAAAG
1 GTGCCACCAACTTGTGTGGGCTTTGAAAG
1182784 G
1 G
1182785 AAAAAGCATC
Statistics
Matches: 40, Mismatches: 9, Indels: 14
0.63 0.14 0.22
Matches are distributed among these distances:
25 3 0.08
26 10 0.25
27 6 0.15
28 6 0.15
29 12 0.30
30 3 0.08
ACGTcount: A:0.19, C:0.21, G:0.34, T:0.26
Consensus pattern (29 bp):
GTGCCACCAACTTGTGTGGGCTTTGAAAG
Found at i:1183175 original size:21 final size:21
Alignment explanation
Indices: 1183142--1183182 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1183132 CTAAGTAAAA
1183142 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
1183163 ATAC-TATTGGTATCAATACA
1 ATACGTATT-GTATCAATACA
1183183 CAAGGTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.37
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:1183264 original size:19 final size:19
Alignment explanation
Indices: 1183222--1183271 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1183212 ACCCTGAAAA
*
1183222 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TCAAAT
1183242 GTATCGATACACA-CAATAT
1 GTATCGATACACATCAA-AT
1183261 GTATCGATACA
1 GTATCGATACA
1183272 GGACATTGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 2 0.07
19 13 0.46
20 13 0.46
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATCAAAT
Found at i:1183321 original size:53 final size:53
Alignment explanation
Indices: 1183241--1183430 Score: 344
Period size: 53 Copynumber: 3.6 Consensus size: 53
1183231 CACATTTAAA
* *
1183241 TGTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATT
1 TGTATCGATACACACAATATGTATCGATACAGGTCTTTGGCAGTAGCCAAATT
* *
1183294 TGTATCGATACACACAATATGTATCGATATAGGTTTTTGGCAGTAGCCAAATT
1 TGTATCGATACACACAATATGTATCGATACAGGTCTTTGGCAGTAGCCAAATT
1183347 TGTATCGATACACACAATATGTATCGATACAGGTCTTTGGCAGTAGCCAAATT
1 TGTATCGATACACACAATATGTATCGATACAGGTCTTTGGCAGTAGCCAAATT
1183400 TGTATCGATACACACAATATGTATCGATACA
1 TGTATCGATACACACAATATGTATCGATACA
1183431 TTGGCAGTAG
Statistics
Matches: 131, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 131 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (53 bp):
TGTATCGATACACACAATATGTATCGATACAGGTCTTTGGCAGTAGCCAAATT
Found at i:1187331 original size:13 final size:13
Alignment explanation
Indices: 1187313--1187337 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1187303 TTTTCCAGAT
1187313 TGTATCGATACAA
1 TGTATCGATACAA
1187326 TGTATCGATACA
1 TGTATCGATACA
1187338 TTACTTCAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1188635 original size:56 final size:56
Alignment explanation
Indices: 1188573--1188687 Score: 212
Period size: 56 Copynumber: 2.1 Consensus size: 56
1188563 TCAAATTATA
*
1188573 GGTTACGATCTTTGATGAAACGGAGAGTATGATGGATCAACGACCTTGTGATAATT
1 GGTTACGATCTTTAATGAAACGGAGAGTATGATGGATCAACGACCTTGTGATAATT
*
1188629 GGTTACGATCTTTAATGAAACGGAGAGTATGATGGATCAATGACCTTGTGATAATT
1 GGTTACGATCTTTAATGAAACGGAGAGTATGATGGATCAACGACCTTGTGATAATT
1188685 GGT
1 GGT
1188688 AAGATCATAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.31
Consensus pattern (56 bp):
GGTTACGATCTTTAATGAAACGGAGAGTATGATGGATCAACGACCTTGTGATAATT
Found at i:1189023 original size:21 final size:21
Alignment explanation
Indices: 1188990--1189030 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1188980 CTAAGTAAAA
1188990 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
1189011 ATAC-TATTGGTATCAATACA
1 ATACGTATT-GTATCAATACA
1189031 CAAGGTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.37
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:1189112 original size:19 final size:19
Alignment explanation
Indices: 1189070--1189172 Score: 69
Period size: 19 Copynumber: 5.6 Consensus size: 19
1189060 ACCCTGAAAA
*
1189070 GTATCGATACACATTTAA-AT
1 GTATCGATACACA--CAATAT
1189090 GTATCGATACACACAATAT
1 GTATCGATACACACAATAT
*
1189109 GTATCGATACAGGAC-AT-T
1 GTATCGATACA-CACAATAT
* *
1189127 G--GC-AGTAGC-CA-AATTT
1 GTATCGA-TA-CACACAATAT
1189143 GTATCGATACACACAATAT
1 GTATCGATACACACAATAT
1189162 GTATCGATACA
1 GTATCGATACA
1189173 GGTCTTTGGT
Statistics
Matches: 66, Mismatches: 6, Indels: 23
0.69 0.06 0.24
Matches are distributed among these distances:
15 4 0.06
16 5 0.08
17 2 0.03
18 9 0.14
19 31 0.47
20 15 0.23
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (19 bp):
GTATCGATACACACAATAT
Found at i:1189169 original size:53 final size:53
Alignment explanation
Indices: 1189089--1189225 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
1189079 CACATTTAAA
1189089 TGTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATT
1 TGTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATT
* * *
1189142 TGTATCGATACACACAATATGTATCGATACAGGTCTTTGGTAGTAGCCAAATT
1 TGTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATT
1189195 TGTATCGATACACACAATATGTATCGATACA
1 TGTATCGATACACACAATATGTATCGATACA
1189226 TTGGCAGTAG
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 81 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (53 bp):
TGTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATT
Found at i:1189268 original size:10 final size:10
Alignment explanation
Indices: 1189249--1189279 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1189239 AATCTCATTT
1189249 TCACTGTTCA
1 TCACTGTTCA
*
1189259 TCACTATTCA
1 TCACTGTTCA
1189269 TCACTGTTCA
1 TCACTGTTCA
1189279 T
1 T
1189280 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:1189301 original size:21 final size:22
Alignment explanation
Indices: 1189267--1189322 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
1189257 CATCACTATT
1189267 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
1189289 CATCACT-TTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
1189310 CATCACTGTTCAT
1 CATCACTGTTCAT
1189323 CGTTGTTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.38
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:1189413 original size:13 final size:13
Alignment explanation
Indices: 1189395--1189432 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1189385 TCACTATTCA
*
1189395 TGTATCGATACAT
1 TGTATCGATACAG
1189408 TGTATCGATACAG
1 TGTATCGATACAG
*
1189421 TATATCGATACA
1 TGTATCGATACA
1189433 CTATAAATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1189437 original size:13 final size:13
Alignment explanation
Indices: 1189397--1189437 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
1189387 ACTATTCATG
* *
1189397 TATCGATACATTG
1 TATCGATACACTA
*
1189410 TATCGATACAGTA
1 TATCGATACACTA
1189423 TATCGATACACTA
1 TATCGATACACTA
1189436 TA
1 TA
1189438 AATAGTATCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (13 bp):
TATCGATACACTA
Found at i:1190952 original size:1 final size:1
Alignment explanation
Indices: 1190941--1190996 Score: 58
Period size: 1 Copynumber: 56.0 Consensus size: 1
1190931 CTTAAGCAGA
* * * * * *
1190941 TTTTTTCTTTTTTTTTGTTTTGTTTTTTGTTTTTTTTTCTTTTTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1190997 GAAGAGAATG
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.05, G:0.05, T:0.89
Consensus pattern (1 bp):
T
Found at i:1190966 original size:11 final size:10
Alignment explanation
Indices: 1190941--1190996 Score: 67
Period size: 10 Copynumber: 5.3 Consensus size: 10
1190931 CTTAAGCAGA
1190941 TTTTTTCTTT
1 TTTTTTCTTT
*
1190951 TTTTTTGTTTT
1 TTTTTT-CTTT
*
1190962 GTTTTTTGTTT
1 -TTTTTTCTTT
1190973 TTTTTTCTTTT
1 TTTTTTC-TTT
1190984 TTTTTTCTTT
1 TTTTTTCTTT
1190994 TTT
1 TTT
1190997 GAAGAGAATG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
10 18 0.45
11 16 0.40
12 6 0.15
ACGTcount: A:0.00, C:0.05, G:0.05, T:0.89
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:1190966 original size:12 final size:11
Alignment explanation
Indices: 1190948--1190996 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
1190938 AGATTTTTTC
1190948 TTTTTTTTTGT
1 TTTTTTTTTGT
1190959 TTTGTTTTTTG-
1 TTT-TTTTTTGT
*
1190970 TTTTTTTTTCT
1 TTTTTTTTTGT
*
1190981 TTTTTTTTTCT
1 TTTTTTTTTGT
1190992 TTTTT
1 TTTTT
1190997 GAAGAGAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
10 6 0.17
11 22 0.63
12 7 0.20
ACGTcount: A:0.00, C:0.04, G:0.06, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:1190966 original size:22 final size:21
Alignment explanation
Indices: 1190941--1190996 Score: 85
Period size: 22 Copynumber: 2.6 Consensus size: 21
1190931 CTTAAGCAGA
*
1190941 TTTTTTCTTTTTTTTTGTTTT
1 TTTTTTCTTTTTTTTTCTTTT
*
1190962 GTTTTTTGTTTTTTTTTCTTTT
1 -TTTTTTCTTTTTTTTTCTTTT
1190984 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
1190997 GAAGAGAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 12 0.39
22 19 0.61
ACGTcount: A:0.00, C:0.05, G:0.05, T:0.89
Consensus pattern (21 bp):
TTTTTTCTTTTTTTTTCTTTT
Found at i:1205764 original size:28 final size:28
Alignment explanation
Indices: 1205708--1205778 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
1205698 GGAATAAAGC
* *
1205708 CGGGGTTGGAGTAT-TCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCTCCATC-GAAATAA
1205736 CGGGGTTGGAGTATCTCCGAT-GAAATAA
1 CGGGGTTGGAGTATCTCC-ATCGAAATAA
*
1205764 CGAGGTTGGAGTATC
1 CGGGGTTGGAGTATC
1205779 CTCGATTGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 34 0.89
29 3 0.08
30 1 0.03
ACGTcount: A:0.24, C:0.15, G:0.35, T:0.25
Consensus pattern (28 bp):
CGGGGTTGGAGTATCTCCATCGAAATAA
Found at i:1205830 original size:52 final size:51
Alignment explanation
Indices: 1205767--1205989 Score: 241
Period size: 52 Copynumber: 4.3 Consensus size: 51
1205757 GAAATAACGA
* * *
1205767 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGT-GTTTTGGAAATAAAATCGG
* * * *
1205819 AGTTGGAGTATCCCCGATTAAAG-GGAAAATTGGTGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATT---GTGAAAAATTAGTGTTTTGGAAATAAAATCGG
* * *
1205872 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGT-GAAAAATTAGTGTTTTGGAAATAAAATCGG
* * * * * *
1205924 GGTTGGAGTATCCCCGATTATGAAAACTCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCGG
*
1205975 GTTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
1205990 TCGGAAATAA
Statistics
Matches: 144, Mismatches: 22, Indels: 11
0.81 0.12 0.06
Matches are distributed among these distances:
50 1 0.01
51 36 0.25
52 61 0.42
53 35 0.24
54 10 0.07
55 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCGG
Found at i:1206008 original size:28 final size:27
Alignment explanation
Indices: 1205972--1206046 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 27
1205962 GAAATAAAGT
* **
1205972 CGGGTTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGAGG-AATAA
* *
1206000 CGGGGTTGGAGTATCCCCGATGATTAA
1 CGGGGTTGGAGTATCCCCGAGGAATAA
1206027 CGGGGTTGGAGTATCCCCGA
1 CGGGGTTGGAGTATCCCCGA
1206047 TTGTGAAGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 24 0.57
28 18 0.43
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.24
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCGAGGAATAA
Found at i:1211492 original size:52 final size:51
Alignment explanation
Indices: 1211414--1211562 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 51
1211404 CGAAATATGA
1211414 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
1211466 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
* **
1211518 AAATTTTCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
1211563 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:1211569 original size:13 final size:13
Alignment explanation
Indices: 1211551--1211575 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1211541 CAAAGATCAG
1211551 TGTATCGATACAA
1 TGTATCGATACAA
1211564 TGTATCGATACA
1 TGTATCGATACA
1211576 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1211653 original size:33 final size:33
Alignment explanation
Indices: 1211616--1211682 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1211606 AGTAGCTTAA
1211616 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1211649 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1211682 A
1 A
1211683 AATCATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1211656 original size:13 final size:13
Alignment explanation
Indices: 1211638--1211662 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1211628 CAAAAAAATA
1211638 TGTATCGATACAT
1 TGTATCGATACAT
1211651 TGTATCGATACA
1 TGTATCGATACA
1211663 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1212688 original size:52 final size:52
Alignment explanation
Indices: 1212556--1212819 Score: 294
Period size: 52 Copynumber: 5.2 Consensus size: 52
1212546 GAAAAGTGAT
* * * * * * *
1212556 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGTTGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG-G-A
* * * *
1212610 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
*
1212663 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
1212715 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* ** *
1212758 AAAGGTGCCAATGTGCTGATTCAAGGTTAGCTACATTGGACTTAAAGATGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
1212810 AAAGGTGCCA
1 AAAGGTGCCA
1212820 CCGACTTGTG
Statistics
Matches: 180, Mismatches: 20, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
43 37 0.21
44 1 0.01
46 1 0.01
49 1 0.01
51 1 0.01
52 93 0.52
53 6 0.03
54 5 0.03
55 35 0.19
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
Found at i:1212776 original size:43 final size:43
Alignment explanation
Indices: 1212715--1212804 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
1212705 TAAAGATGGG
*
1212715 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* **
1212758 AAAGGTGCCAATGTGCTGATTCAAGGTTAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
1212801 AAAG
1 AAAG
1212805 ATGGAAAAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:1212849 original size:30 final size:30
Alignment explanation
Indices: 1212808--1213286 Score: 392
Period size: 30 Copynumber: 16.1 Consensus size: 30
1212798 CTTAAAGATG
* **
1212808 GAAAA-GGTGCCACCGACTTGTGGGCTTCG
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
*
1212837 GAAAAGGGTGCCACTGATTTGTGGGC-TTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
*
1212866 G--AAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
*
1212894 --AAAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
***
1212922 GAAAAATATGCCACTGACTTGTGGGCTTTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
*
1212952 GAAAAGGGTGCCACTAACTTGTGGGCTTTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
*
1212982 --AAAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
***
1213010 GAAAAATATGCCACTGACTTGTGGGCTTTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
* ***
1213040 GAAAAGGGTGCCACTAACTTGTGGGCTGAAAAA
1 GAAAAGGGTGCCACTGACTTGTGGGCT---TTT
* * * * **
1213073 GAAAAAGAGTGCTA-TAGAGTTGTGAGCTTACAAAA
1 G-AAAAGGGTGCCACT-GACTTGTGGGCTT----TT
* * * * *
1213108 GAAAAAGAGTGCCACGGAGTTGTGGACTTTG
1 G-AAAAGGGTGCCACTGACTTGTGGGCTTTT
* * **
1213139 GAAAA-GATGCCACCGACTTGTGGGCTTCG
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
*
1213168 GAAAAGGGTGCCACTGATTTGTGGGC-TTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
*
1213197 G--AAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
***
1213225 GAAAAAAATGCCACTGACTTGTGGGC-TTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
*** *
1213254 GAAAAAAATGCCACTGACTTGTGGACTTTT
1 GAAAAGGGTGCCACTGACTTGTGGGCTTTT
1213284 GAA
1 GAA
1213287 GGGTGATGAA
Statistics
Matches: 374, Mismatches: 54, Indels: 43
0.79 0.11 0.09
Matches are distributed among these distances:
27 42 0.11
28 60 0.16
29 60 0.16
30 164 0.44
31 1 0.00
33 2 0.01
34 19 0.05
35 26 0.07
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (30 bp):
GAAAAGGGTGCCACTGACTTGTGGGCTTTT
Found at i:1212992 original size:58 final size:59
Alignment explanation
Indices: 1212810--1213286 Score: 359
Period size: 58 Copynumber: 8.0 Consensus size: 59
1212800 TAAAGATGGA
* ** *
1212810 AAAGG-TGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
*
1212867 -AAGGTTGCCACTGACTTGTGGGCTTTT--AAAGGTTGCCACTGACTTGTGGGCTTTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
** *
1212923 AAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTT-
1 AAAGGT-TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
***
1212982 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
* * *** * * * *
1213041 AAAAGGGTGCCACTAACTTGTGGGCTGAAAAAGAAAAAGAGTGCTA-TAGAGTTGTGAGCTTACA
1 -AAAGGTTGCCACTGACTTGTGGGCT---TTTG-AAAAGGGTGCCACT-GACTTGTGGGCTT---
**
1213105 AAAG
57 -TTG
* * * * * * **
1213109 AAAAAGAG-TGCCACGGAGTTGTGGACTTTGGAAAA-GATGCCACCGACTTGTGGGCTTCGG
1 --AAAG-GTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
* * *
1213169 AAAAGGGTGCCACTGATTTGTGGGC-TTTG--AAGGTTGCCACTGACTTGTGGGCTTTTG
1 -AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
*** *** *
1213226 AAAAAAATGCCACTGACTTGTGGGC-TTTGAAAAAAATGCCACTGACTTGTGGACTTTTG
1 -AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
1213285 AA
1 AA
1213287 GGGTGATGAA
Statistics
Matches: 337, Mismatches: 59, Indels: 47
0.76 0.13 0.11
Matches are distributed among these distances:
55 22 0.07
56 10 0.03
57 68 0.20
58 76 0.23
59 48 0.14
60 50 0.15
63 2 0.01
64 34 0.10
65 4 0.01
66 1 0.00
68 1 0.00
69 20 0.06
70 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (59 bp):
AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
Found at i:1212998 original size:88 final size:88
Alignment explanation
Indices: 1212810--1213066 Score: 405
Period size: 88 Copynumber: 3.0 Consensus size: 88
1212800 TAAAGATGGA
* ** *** *
1212810 AAAGG-TGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG--AAGG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGG
* *
1212871 TTGCCACTGACTTGTGGGCTTTT
66 GTGCCACTAACTTGTGGGCTTTT
1212894 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGG
1212959 GTGCCACTAACTTGTGGGCTTTT
66 GTGCCACTAACTTGTGGGCTTTT
1212982 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGG
1213047 GTGCCACTAACTTGTGGGCT
66 GTGCCACTAACTTGTGGGCT
1213067 GAAAAAGAAA
Statistics
Matches: 160, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
84 5 0.03
85 41 0.26
86 4 0.03
88 110 0.69
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (88 bp):
AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGG
GTGCCACTAACTTGTGGGCTTTT
Found at i:1213209 original size:27 final size:27
Alignment explanation
Indices: 1213117--1213288 Score: 119
Period size: 29 Copynumber: 6.0 Consensus size: 27
1213107 AGAAAAAGAG
* * * *
1213117 TGCCACGGAGTTGTGGACTTTGGAAAAGA
1 TGCCACTGACTTGTGGGCTTT-G-AAGGA
* * *
1213146 TGCCACCGACTTGTGGGCTTCGGAAAAGGG
1 TGCCACTGACTTGTGGGCTT-TG--AAGGA
* *
1213176 TGCCACTGATTTGTGGGCTTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTGAAGGA
**
1213203 TGCCACTGACTTGTGGGCTTTTGAAAAAAA
1 TGCCACTGACTTGTGGGC-TTTG--AAGGA
**
1213233 TGCCACTGACTTGTGGGCTTTGAAAAAAA
1 TGCCACTGACTTGTGGGCTTTG--AAGGA
*
1213262 TGCCACTGACTTGTGGACTTTTGAAGG
1 TGCCACTGACTTGTGGGC-TTTGAAGG
1213289 GTGATGAATG
Statistics
Matches: 120, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
27 21 0.17
28 6 0.05
29 47 0.39
30 46 0.38
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.28
Consensus pattern (27 bp):
TGCCACTGACTTGTGGGCTTTGAAGGA
Found at i:1214707 original size:1 final size:1
Alignment explanation
Indices: 1214703--1214809 Score: 79
Period size: 1 Copynumber: 107.0 Consensus size: 1
1214693 CCGGACCCCC
* * * * * * * * *
1214703 TTTTTTTGTTTTTGTTTGTTTTTTTATTGTTTTTGTTTTTTTTGTTTTTTGTTTTTTTTTTGTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** ** * *
1214768 TTTCATTTTTTTCGTTTTTTTTTGTTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1214810 GGAGGACGCC
Statistics
Matches: 78, Mismatches: 28, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 78 1.00
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.86
Consensus pattern (1 bp):
T
Found at i:1214724 original size:18 final size:17
Alignment explanation
Indices: 1214703--1214807 Score: 97
Period size: 18 Copynumber: 5.9 Consensus size: 17
1214693 CCGGACCCCC
1214703 TTTTTTTGTTTTTGTTTG
1 TTTTTTTGTTTTT-TTTG
* *
1214721 TTTTTTTATTGTTTTTG
1 TTTTTTTGTTTTTTTTG
*
1214738 TTTTTTTTGTTTTTTGTTT
1 -TTTTTTTGTTTTTT-TTG
*
1214757 TTTTTTTGTTTTTTCAT-
1 TTTTTTTGTTTTTT-TTG
*
1214774 TTTTTTCGTTTTTTTTTG
1 TTTTTTTG-TTTTTTTTG
1214792 TTTTTTT-TTTGTTTTT
1 TTTTTTTGTTT-TTTTT
1214808 TTGGAGGACG
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
16 3 0.04
17 17 0.24
18 50 0.69
19 2 0.03
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.86
Consensus pattern (17 bp):
TTTTTTTGTTTTTTTTG
Found at i:1214732 original size:11 final size:10
Alignment explanation
Indices: 1214703--1214809 Score: 110
Period size: 10 Copynumber: 10.5 Consensus size: 10
1214693 CCGGACCCCC
1214703 TTTTTTTGTT
1 TTTTTTTGTT
*
1214713 TTTGTTTGTT
1 TTTTTTTGTT
1214723 TTTTTATTGTT
1 TTTTT-TTGTT
*
1214734 TTTGTTTTTTT
1 TTT-TTTTGTT
1214745 TGTTTTTTG-T
1 T-TTTTTTGTT
1214755 TTTTTTT-TT
1 TTTTTTTGTT
* **
1214764 GTTTTTTCAT
1 TTTTTTTGTT
*
1214774 TTTTTTCGTT
1 TTTTTTTGTT
1214784 TTTTTTTGTTT
1 TTTTTTTG-TT
1214795 TTTTTTTGTT
1 TTTTTTTGTT
1214805 TTTTT
1 TTTTT
1214810 GGAGGACGCC
Statistics
Matches: 80, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
9 13 0.16
10 36 0.45
11 27 0.34
12 4 0.05
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.86
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:1214739 original size:27 final size:27
Alignment explanation
Indices: 1214705--1214808 Score: 106
Period size: 27 Copynumber: 3.8 Consensus size: 27
1214695 GGACCCCCTT
1214705 TTTTTGTTTTTGTTTGTTTTTT-TATTG
1 TTTTTGTTTTT-TTTGTTTTTTGTATTG
* *
1214732 TTTTTGTTTTTTTTGTTTTTTGTTTTT
1 TTTTTGTTTTTTTTGTTTTTTGTATTG
* *
1214759 TTTTTGTTTTTTCATT-TTTTTCGT-TTT
1 TTTTTGTTTTTT--TTGTTTTTTGTATTG
1214786 TTTTTGTTTTTTTTTTGTTTTTT
1 TTTTTG--TTTTTTTTGTTTTTT
1214809 TGGAGGACGC
Statistics
Matches: 67, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
26 10 0.15
27 37 0.55
28 12 0.18
29 8 0.12
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.86
Consensus pattern (27 bp):
TTTTTGTTTTTTTTGTTTTTTGTATTG
Found at i:1214751 original size:44 final size:43
Alignment explanation
Indices: 1214703--1214809 Score: 139
Period size: 44 Copynumber: 2.5 Consensus size: 43
1214693 CCGGACCCCC
*
1214703 TTTTTTTGTTTTTGTTTGTTTTTTTATTGTTTTT-GTTTTTTTT
1 TTTTTTTGTTTTTGTTTGTTTTTTCATT-TTTTTCGTTTTTTTT
* *
1214746 GTTTTTTGTTTTTTTTTTGTTTTTTCATTTTTTTCGTTTTTTTT
1 TTTTTTTG-TTTTTGTTTGTTTTTTCATTTTTTTCGTTTTTTTT
*
1214790 TGTTTTT-TTTTTGTTT-TTTT
1 TTTTTTTGTTTTTGTTTGTTTT
1214810 GGAGGACGCC
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
41 4 0.07
42 8 0.14
43 12 0.21
44 32 0.57
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.86
Consensus pattern (43 bp):
TTTTTTTGTTTTTGTTTGTTTTTTCATTTTTTTCGTTTTTTTT
Found at i:1224513 original size:10 final size:10
Alignment explanation
Indices: 1224498--1224524 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1224488 ATGTATCAAG
1224498 CAAAAACAAA
1 CAAAAACAAA
1224508 CAAAAACAAA
1 CAAAAACAAA
1224518 CAAAAAC
1 CAAAAAC
1224525 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:1228739 original size:52 final size:51
Alignment explanation
Indices: 1228661--1228809 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 51
1228651 CGAAATATGA
1228661 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
1228713 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
* **
1228765 AAATTTTCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
1228810 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:1228816 original size:13 final size:13
Alignment explanation
Indices: 1228798--1228822 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1228788 CAAAGATCAG
1228798 TGTATCGATACAA
1 TGTATCGATACAA
1228811 TGTATCGATACA
1 TGTATCGATACA
1228823 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1228900 original size:33 final size:33
Alignment explanation
Indices: 1228863--1228929 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1228853 AGTAGCTTAA
1228863 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1228896 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1228929 A
1 A
1228930 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1228903 original size:13 final size:13
Alignment explanation
Indices: 1228885--1228909 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1228875 CAAAAAAATA
1228885 TGTATCGATACAT
1 TGTATCGATACAT
1228898 TGTATCGATACA
1 TGTATCGATACA
1228910 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1229938 original size:52 final size:52
Alignment explanation
Indices: 1229806--1230017 Score: 208
Period size: 52 Copynumber: 4.2 Consensus size: 52
1229796 GAAAAGTGAT
* * * * * * * *
1229806 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGCTGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-G-A
* * *
1229860 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
*
1229913 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
* *
1229956 AAAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAAGATGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
1230008 AAAGGTGCCA
1 AAAGGTGCCA
1230018 CCGACTTGTG
Statistics
Matches: 130, Mismatches: 18, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
43 38 0.29
44 1 0.01
46 1 0.01
49 1 0.01
51 1 0.01
52 42 0.32
53 6 0.05
54 5 0.04
55 35 0.27
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
Found at i:1229974 original size:43 final size:43
Alignment explanation
Indices: 1229913--1230002 Score: 153
Period size: 43 Copynumber: 2.1 Consensus size: 43
1229903 TAAAGATGGA
*
1229913 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
1229956 AAAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
1229999 AAAG
1 AAAG
1230003 ATGGAAAAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:1230236 original size:34 final size:35
Alignment explanation
Indices: 1230198--1230272 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
1230188 TGCCACTAAC
*
1230198 TTGTGGGCTGA-AAAAGAAAAAGAGTGCTATA-GAG
1 TTGTGGGCTGACAAAAGAAAAAGAGTGCCA-AGGAG
* *
1230232 TTGTGAGCTTACAAAAGAAAAAGAGTGCCAAGGAG
1 TTGTGGGCTGACAAAAGAAAAAGAGTGCCAAGGAG
1230267 TTGTGG
1 TTGTGG
1230273 ACTTTGGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
34 10 0.29
35 25 0.71
ACGTcount: A:0.39, C:0.08, G:0.32, T:0.21
Consensus pattern (35 bp):
TTGTGGGCTGACAAAAGAAAAAGAGTGCCAAGGAG
Found at i:1230369 original size:57 final size:58
Alignment explanation
Indices: 1230267--1230426 Score: 187
Period size: 57 Copynumber: 2.7 Consensus size: 58
1230257 TGCCAAGGAG
* * * ** ***
1230267 TTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGAT
1 TTGTGGGCTTT-GAAAAAATGCCACTGACTTGTGGGCTTTTGAAAAAAATGCCACTGAT
***
1230326 TTGTGGGCTTTG-AAGGTTGCCACTGACTTGTGGGCTTTTGAAAAAAATGCCACTGAT
1 TTGTGGGCTTTGAAAAAATGCCACTGACTTGTGGGCTTTTGAAAAAAATGCCACTGAT
*
1230383 TTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGGACTTTTGAA
1 TTGTGGGCTTTG-AAAAAATGCCACTGACTTGTGGGCTTTTGAA
1230427 GGGTGATGAA
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
57 49 0.57
58 1 0.01
59 36 0.42
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (58 bp):
TTGTGGGCTTTGAAAAAATGCCACTGACTTGTGGGCTTTTGAAAAAAATGCCACTGAT
Found at i:1230425 original size:30 final size:30
Alignment explanation
Indices: 1230007--1230426 Score: 304
Period size: 30 Copynumber: 14.0 Consensus size: 30
1229997 TTAAAGATGG
* * **
1230007 AAAAGGTGCCACCGACTTGTGGGCTTCGGA
1 AAAAGATGCCACTGACTTGTGGGCTTTTGA
* * *
1230037 AAAGGGTGCCACTGATTTGTGGGC-TTTG-
1 AAAAGATGCCACTGACTTGTGGGCTTTTGA
* *
1230065 -AAGGTTGCCACTGACTTGTGGGCTTTT--
1 AAAAGATGCCACTGACTTGTGGGCTTTTGA
* *
1230092 AAAGGTTGCCACTGACTTGTGGGCTTTTGA
1 AAAAGATGCCACTGACTTGTGGGCTTTTGA
*
1230122 AAAATATGCCACTGACTTGTGGGCTTTTGA
1 AAAAGATGCCACTGACTTGTGGGCTTTTGA
*
1230152 AAAATATGCCACTGACTTGTGGGCTTTTGA
1 AAAAGATGCCACTGACTTGTGGGCTTTTGA
* * * ***
1230182 AAAGGGTGCCACTAACTTGTGGGCTGAAAAAGA
1 AAAAGATGCCACTGACTTGTGGGCT---TTTGA
* * * **
1230215 AAAAGAGTGCTA-TAGAGTTGTGAGCTTACAAAAGA
1 AAAAGA-TGCCACT-GACTTGTGGGCTT----TTGA
** * * *
1230250 AAAAGAGTGCCAAGGAGTTGTGGAC-TTTGG
1 AAAAGA-TGCCACTGACTTGTGGGCTTTTGA
* **
1230280 AAAAGATGCCACCGACTTGTGGGCTTCGGA
1 AAAAGATGCCACTGACTTGTGGGCTTTTGA
* * *
1230310 AAAGGGTGCCACTGATTTGTGGGC-TTTG-
1 AAAAGATGCCACTGACTTGTGGGCTTTTGA
* *
1230338 -AAGGTTGCCACTGACTTGTGGGCTTTTGA
1 AAAAGATGCCACTGACTTGTGGGCTTTTGA
* *
1230367 AAAAAATGCCACTGATTTGTGGGC-TTTGA
1 AAAAGATGCCACTGACTTGTGGGCTTTTGA
* *
1230396 AAAAAATGCCACTGACTTGTGGACTTTTGA
1 AAAAGATGCCACTGACTTGTGGGCTTTTGA
1230426 A
1 A
1230427 GGGTGATGAA
Statistics
Matches: 319, Mismatches: 52, Indels: 38
0.78 0.13 0.09
Matches are distributed among these distances:
27 42 0.13
28 34 0.11
29 45 0.14
30 153 0.48
33 7 0.02
34 14 0.04
35 24 0.08
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (30 bp):
AAAAGATGCCACTGACTTGTGGGCTTTTGA
Found at i:1231868 original size:1 final size:1
Alignment explanation
Indices: 1231864--1231987 Score: 104
Period size: 1 Copynumber: 124.0 Consensus size: 1
1231854 CCGGACCCCC
* * * * * * * *
1231864 TTTTTTGTTTTTGTTTGTTTTTTTATTGTTTTTGTTTTTTTTTTTGTTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* ** ** * * *
1231929 TTTGTTTTTTTCATTTTTTTCGTTTTTTTTTTGTTTTGTTTTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1231988 GGAGGACGCC
Statistics
Matches: 93, Mismatches: 30, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 93 1.00
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.87
Consensus pattern (1 bp):
T
Found at i:1231909 original size:29 final size:28
Alignment explanation
Indices: 1231864--1231987 Score: 129
Period size: 29 Copynumber: 4.5 Consensus size: 28
1231854 CCGGACCCCC
*
1231864 TTTTTTG--TTTTTGTTTGTTTTTTTAT
1 TTTTTTGTTTTTTTTTTTGTTTTTTTAT
1231890 TGTTTTTGTTTTTTTTTTTG----TTT-T
1 T-TTTTTGTTTTTTTTTTTGTTTTTTTAT
1231914 TTTTTTGTTTTTTTTTTTGTTTTTTTCAT
1 TTTTTTGTTTTTTTTTTTGTTTTTTT-AT
*
1231943 TTTTTTCG-TTTTTTTTTTGTTTTGTTTTTT
1 TTTTTT-GTTTTTTTTTTTG-TTT-TTTTAT
1231973 TTTTTTGTTTTTTTT
1 TTTTTTGTTTTTTTT
1231988 GGAGGACGCC
Statistics
Matches: 83, Mismatches: 2, Indels: 22
0.78 0.02 0.21
Matches are distributed among these distances:
23 18 0.22
24 2 0.02
25 3 0.04
26 1 0.01
27 9 0.11
29 28 0.34
30 18 0.22
31 4 0.05
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.87
Consensus pattern (28 bp):
TTTTTTGTTTTTTTTTTTGTTTTTTTAT
Found at i:1231955 original size:52 final size:53
Alignment explanation
Indices: 1231864--1231985 Score: 164
Period size: 52 Copynumber: 2.3 Consensus size: 53
1231854 CCGGACCCCC
*
1231864 TTTTTTG--TTTTTGTTTGTTTTTTTATTGTTTTTGTTTTTTTTTTTGTTTT-
1 TTTTTTGTTTTTTTTTTTGTTTTTTTATTGTTTTTGTTTTTTTTTTTGTTTTG
1231914 TTTTTTGTTTTTTTTTTTGTTTTTTTCATT-TTTTTCG-TTTTTTTTTTGTTTTG
1 TTTTTTGTTTTTTTTTTTGTTTTTTT-ATTGTTTTT-GTTTTTTTTTTTGTTTTG
*
1231967 TTTTTTTTTTTTGTTTTTT
1 TTTTTTGTTTTT-TTTTTT
1231986 TTGGAGGACG
Statistics
Matches: 64, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
50 7 0.11
52 36 0.56
53 15 0.23
54 6 0.09
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.87
Consensus pattern (53 bp):
TTTTTTGTTTTTTTTTTTGTTTTTTTATTGTTTTTGTTTTTTTTTTTGTTTTG
Found at i:1240520 original size:54 final size:51
Alignment explanation
Indices: 1240462--1240735 Score: 226
Period size: 54 Copynumber: 5.1 Consensus size: 51
1240452 TCTTTAACTC
* * * *
1240462 GATAGAAGTGACTAGGTGTCACTGGATGGGATGTCGTTGTGGCGATCAAGATTT
1 GATAGGAGTGACTTGGTGTCACT-GAT--GATGTCATTGTGGCGATCAAAATTT
* * * *
1240516 GATAGGGGTGACTTGGTGTCACTAAAGATGATGTCATTATGGCAAAT-GAAATTT
1 GATAGGAGTGACTTGGTGTCACT---GATGATGTCATTGTGGC-GATCAAAATTT
* * * * *
1240570 GATAGAAGTGACTTGGTGTCACTAAGGATGATGCCTTTGTAGTGATCAAAATTT
1 GATAGGAGTGACTTGGTGTCACT---GATGATGTCATTGTGGCGATCAAAATTT
* * * * *
1240624 GATAGGATTGACTTGGTTTCACTAAAGTTGATGCCATGGTGGCGATCAAAATTT
1 GATAGGAGTGACTTGGTGTCACT---GATGATGTCATTGTGGCGATCAAAATTT
*
1240678 GATAGGAGTGACTTGGTGTCACTGAGGATGATGCTATTGTGGCGATCAAAATTT
1 GATAGGAGTGACTTGGTGTCACTGATGATG-T-C-ATTGTGGCGATCAAAATTT
1240732 GATA
1 GATA
1240736 CAAAAGATTT
Statistics
Matches: 179, Mismatches: 34, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
51 5 0.03
53 3 0.02
54 166 0.93
55 2 0.01
56 3 0.02
ACGTcount: A:0.28, C:0.11, G:0.29, T:0.32
Consensus pattern (51 bp):
GATAGGAGTGACTTGGTGTCACTGATGATGTCATTGTGGCGATCAAAATTT
Found at i:1240656 original size:108 final size:106
Alignment explanation
Indices: 1240462--1240735 Score: 327
Period size: 108 Copynumber: 2.5 Consensus size: 106
1240452 TCTTTAACTC
* * * *
1240462 GATAGAAGTGACTAGGTGTCACT-GGATGGGATGTCGTTGTGGCGATCAAGATTTGATAGGGGTG
1 GATAGAAGTGACTTGGTGTCACTAGGAT--GATG-CTTTGTGGCGATCAAAATTTGATAGGAGTG
* * *
1240526 ACTTGGTGTCACTAAAGATGATGTCATTATGGCAAAT-GAAATTT
63 ACTTGGTGTCACTAAAGATGATGCCATGATGGC-AATCAAAATTT
* * *
1240570 GATAGAAGTGACTTGGTGTCACTAAGGATGATGCCTTTGTAGTGATCAAAATTTGATAGGATTGA
1 GATAGAAGTGACTTGGTGTCACT-AGGATGATG-CTTTGTGGCGATCAAAATTTGATAGGAGTGA
* * * *
1240635 CTTGGTTTCACTAAAGTTGATGCCATGGTGGCGATCAAAATTT
64 CTTGGTGTCACTAAAGATGATGCCATGATGGCAATCAAAATTT
*
1240678 GATAGGAGTGACTTGGTGTCACTGAGGATGATGCTATTGTGGCGATCAAAATTTGATA
1 GATAGAAGTGACTTGGTGTCACT-AGGATGATGCT-TTGTGGCGATCAAAATTTGATA
1240736 CAAAAGATTT
Statistics
Matches: 143, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
107 4 0.03
108 135 0.94
110 4 0.03
ACGTcount: A:0.28, C:0.11, G:0.29, T:0.32
Consensus pattern (106 bp):
GATAGAAGTGACTTGGTGTCACTAGGATGATGCTTTGTGGCGATCAAAATTTGATAGGAGTGACT
TGGTGTCACTAAAGATGATGCCATGATGGCAATCAAAATTT
Found at i:1240780 original size:162 final size:161
Alignment explanation
Indices: 1240500--1240832 Score: 379
Period size: 162 Copynumber: 2.1 Consensus size: 161
1240490 GGATGTCGTT
* * *
1240500 GTGGCGATCAAGATTTGATAGGGGTGACTTGGTGTCACTAAAGATGATGTCATTATGGCAAATGA
1 GTGGCGATCAAAATTTGATAGGAGTGACTTGGTGTCACTAAAGATGATGTCATTATGGCAAATAA
* ** * * * ** *
1240565 AATTTGATAGAAGTGACTTGGTGTCACTAAGGATGATGCCTTTGTAGTGATCAAAATTTGATAGG
66 AATTTGATACAAAAGACTTGGTATCACTAACGATAATGCCTAAGTAGTGATCAAAATTCGATAGG
* * * *
1240630 ATTGACTTGGTTTCACTAAAGTTGATG-CCATG
131 AGTGACTTGGTGTCACTAAA-ATGATGCCCA-A
* * * *
1240662 GTGGCGATCAAAATTTGATAGGAGTGACTTGGTGTCACTGAGGATGATG-CTATTGTGGC-GATC
1 GTGGCGATCAAAATTTGATAGGAGTGACTTGGTGTCACTAAAGATGATGTC-ATTATGGCAAAT-
* *
1240725 AAAATTTGATACAAAAGATTTAGG-ATCACTAACTATAATGCCTAAGT-GATGATCAAAATTCGA
64 AAAATTTGATACAAAAGACTT-GGTATCACTAACGATAATGCCTAAGTAG-TGATCAAAATTCGA
1240788 TAGGAGTGACTTGGTGTCACTAAAATGATGCCCAA
127 TAGGAGTGACTTGGTGTCACTAAAATGATGCCCAA
1240823 GTGGCGATCA
1 GTGGCGATCA
1240833 GAGTTGTGGA
Statistics
Matches: 144, Mismatches: 22, Indels: 11
0.81 0.12 0.06
Matches are distributed among these distances:
161 19 0.13
162 123 0.85
163 2 0.01
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (161 bp):
GTGGCGATCAAAATTTGATAGGAGTGACTTGGTGTCACTAAAGATGATGTCATTATGGCAAATAA
AATTTGATACAAAAGACTTGGTATCACTAACGATAATGCCTAAGTAGTGATCAAAATTCGATAGG
AGTGACTTGGTGTCACTAAAATGATGCCCAA
Found at i:1240809 original size:54 final size:55
Alignment explanation
Indices: 1240498--1240819 Score: 266
Period size: 54 Copynumber: 6.0 Consensus size: 55
1240488 TGGGATGTCG
* * * * *
1240498 TTGTGGCGATCAAGATTTGATAGGGGTGACTTGGTGTCACTAAAGATGATGTC-A
1 TTGTGACGATCAAAATTTGATAGGAGTGACTTGGTGTCACTAAGGATGATGCCTA
* * * * *
1240552 TTATGGCAAAT-GAAATTTGATAGAAGTGACTTGGTGTCACTAAGGATGATGCCT-
1 TTGTGAC-GATCAAAATTTGATAGGAGTGACTTGGTGTCACTAAGGATGATGCCTA
* * * * *
1240606 TTGT-AGTGATCAAAATTTGATAGGATTGACTTGGTTTCACTAAAGTTGATGCC-A
1 TTGTGA-CGATCAAAATTTGATAGGAGTGACTTGGTGTCACTAAGGATGATGCCTA
* * *
1240660 TGGTGGCGATCAAAATTTGATAGGAGTGACTTGGTGTCACTGAGGATGATG-CTA
1 TTGTGACGATCAAAATTTGATAGGAGTGACTTGGTGTCACTAAGGATGATGCCTA
* ** ** * * ** *
1240714 TTGTGGCGATCAAAATTTGATACAAAAGATTTAGG-ATCACTAACTATAATGCCTA
1 TTGTGACGATCAAAATTTGATAGGAGTGACTT-GGTGTCACTAAGGATGATGCCTA
* * * *
1240769 -AGTGATGATCAAAATTCGATAGGAGTGACTTGGTGTCACTAA-AATGATGCC
1 TTGTGACGATCAAAATTTGATAGGAGTGACTTGGTGTCACTAAGGATGATGCC
1240820 CAAGTGGCGA
Statistics
Matches: 209, Mismatches: 49, Indels: 21
0.75 0.18 0.08
Matches are distributed among these distances:
53 12 0.06
54 190 0.91
55 7 0.03
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (55 bp):
TTGTGACGATCAAAATTTGATAGGAGTGACTTGGTGTCACTAAGGATGATGCCTA
Found at i:1253454 original size:13 final size:13
Alignment explanation
Indices: 1253436--1253461 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1253426 TACACAAAGT
1253436 ATGTATCGATACA
1 ATGTATCGATACA
1253449 ATGTATCGATACA
1 ATGTATCGATACA
1253462 CAAAAAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1253480 original size:34 final size:32
Alignment explanation
Indices: 1253418--1253482 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1253408 TAGCCAAACT
**
1253418 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAATGTATCGATACAA
1253450 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACAC-AAAAAA-TGTATCGATACA
1253483 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.45
33 4 0.14
34 12 0.41
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCGATACAA
Found at i:1256980 original size:15 final size:15
Alignment explanation
Indices: 1256960--1256990 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1256950 TAAAAATGTC
*
1256960 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1256975 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1256990 C
1 C
1256991 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1261645 original size:13 final size:13
Alignment explanation
Indices: 1261627--1261652 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1261617 TACACAAAGT
1261627 ATGTATCGATACA
1 ATGTATCGATACA
1261640 ATGTATCGATACA
1 ATGTATCGATACA
1261653 CAAAAAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1261671 original size:34 final size:32
Alignment explanation
Indices: 1261609--1261673 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1261599 TAACCAAACT
**
1261609 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAATGTATCGATACAA
1261641 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACAC-AAAAAA-TGTATCGATACA
1261674 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.45
33 4 0.14
34 12 0.41
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCGATACAA
Found at i:1272167 original size:16 final size:15
Alignment explanation
Indices: 1272142--1272172 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1272132 TTAAATAAAA
1272142 TTTTTATTTTTATTT
1 TTTTTATTTTTATTT
1272157 TTTTATATTTTTATTT
1 TTTT-TATTTTTATTT
1272173 AAAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTATTTTTATTT
Found at i:1272309 original size:20 final size:21
Alignment explanation
Indices: 1272284--1272323 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1272274 TTCTGTTACT
*
1272284 ATAAAA-TCAAGATTTTTTAA
1 ATAAAAGTCAAAATTTTTTAA
*
1272304 ATAAAAGTTAAAATTTTTTA
1 ATAAAAGTCAAAATTTTTTA
1272324 TTTAATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (21 bp):
ATAAAAGTCAAAATTTTTTAA
Found at i:1272332 original size:33 final size:33
Alignment explanation
Indices: 1272295--1272360 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
1272285 TAAAATCAAG
*
1272295 ATTTTTTAAA-TAAAAGTTA-AAATTTTTTATTTA
1 ATTTTTAAAAGTAAAA-TTATAAA-TTTTTATTTA
1272328 ATTTTTAAAAGTAAAATTATAAATTTTTATTTA
1 ATTTTTAAAAGTAAAATTATAAATTTTTATTTA
1272361 TATAATTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 22 0.73
34 8 0.27
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (33 bp):
ATTTTTAAAAGTAAAATTATAAATTTTTATTTA
Found at i:1272736 original size:17 final size:20
Alignment explanation
Indices: 1272696--1272736 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
1272686 TATAATTAAA
1272696 ATTATTAAAATTTGAATTTG
1 ATTATTAAAATTTGAATTTG
1272716 ATTA-TAAAATTT-AATTT-
1 ATTATTAAAATTTGAATTTG
1272733 ATTA
1 ATTA
1272737 ATATTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.19
18 5 0.24
19 8 0.38
20 4 0.19
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
ATTATTAAAATTTGAATTTG
Found at i:1272744 original size:10 final size:10
Alignment explanation
Indices: 1272729--1272832 Score: 53
Period size: 9 Copynumber: 10.7 Consensus size: 10
1272719 ATAAAATTTA
1272729 ATTTATTAAT
1 ATTTATTAAT
1272739 ATTTA-T-AT
1 ATTTATTAAT
1272747 A-TTATTAA-
1 ATTTATTAAT
1272755 ATATTATTTAAT
1 AT-TTA-TTAAT
* *
1272767 TTTTATTAAAA
1 ATTTATT-AAT
1272778 ATTTCATTAA-
1 ATTT-ATTAAT
*
1272788 ATATATT-AT
1 ATTTATTAAT
*
1272797 TTTTATTAA-
1 ATTTATTAAT
**
1272806 ATTTAAAAAT
1 ATTTATTAAT
1272816 ATTTTATTAAT
1 A-TTTATTAAT
1272827 -TTTATT
1 ATTTATT
1272833 TTTTTCTGAG
Statistics
Matches: 71, Mismatches: 11, Indels: 25
0.66 0.10 0.23
Matches are distributed among these distances:
7 3 0.04
8 6 0.08
9 22 0.31
10 15 0.21
11 21 0.30
12 4 0.06
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (10 bp):
ATTTATTAAT
Found at i:1274519 original size:16 final size:16
Alignment explanation
Indices: 1274487--1274539 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 16
1274477 GTTTATTTTA
1274487 ATAATTTATATTATAAAT
1 ATAA-TTAT-TTATAAAT
*
1274505 A-AAGTTATTTTTAAAAT
1 ATAA-TTATTTAT-AAAT
1274522 ATAATTATTTATAAAT
1 ATAATTATTTATAAAT
1274538 AT
1 AT
1274540 TTAATATCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 9 0.30
17 18 0.60
18 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
ATAATTATTTATAAAT
Found at i:1276213 original size:24 final size:24
Alignment explanation
Indices: 1276186--1276232 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1276176 AATGAACATC
*
1276186 TAAAAAAT-GATTAGTGAAATATTA
1 TAAAAAATAG-TTAGTAAAATATTA
1276210 TAAAAAATAGTTAGTAAAATATT
1 TAAAAAATAGTTAGTAAAATATT
1276233 CGAAATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (24 bp):
TAAAAAATAGTTAGTAAAATATTA
Found at i:1281182 original size:21 final size:21
Alignment explanation
Indices: 1281156--1281195 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1281146 AAAATTAAGA
1281156 AACAAAAATAAGGAACAAAGG
1 AACAAAAATAAGGAACAAAGG
1281177 AACAAAAATAAGGAACAAA
1 AACAAAAATAAGGAACAAA
1281196 AATAAGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.70, C:0.10, G:0.15, T:0.05
Consensus pattern (21 bp):
AACAAAAATAAGGAACAAAGG
Found at i:1289662 original size:21 final size:21
Alignment explanation
Indices: 1289638--1289677 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1289628 TCCTGTATCG
1289638 ATACATTTCAGACATGTATTA
1 ATACATTTCAGACATGTATTA
*
1289659 ATACATTTTAGACATGTAT
1 ATACATTTCAGACATGTAT
1289678 CGATATATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (21 bp):
ATACATTTCAGACATGTATTA
Found at i:1289816 original size:161 final size:164
Alignment explanation
Indices: 1289526--1289826 Score: 473
Period size: 161 Copynumber: 1.8 Consensus size: 164
1289516 AATTGCCTGC
* * * *
1289526 ATGTATCGATACATTTGGGTCAAAAACCCAGAATGTATCGATACAATGAAAAATGTATCGATACA
1 ATGTATCAACACATTTGAGTCAAAAACCCAAAATGTATCGATACAATGAAAAA--TATCGATACA
* *
1289591 TTTTTCTTTTCAGAATGTAAAATTTGCTTCGAAATGGTCCTGTATCGATACATTTCAGACATGTA
64 TTTTTATTTTCAGAATGCAAAATTTGCTTCGAAATGGTCCTGTATCGATACATTTCAGACATGTA
*
1289656 TTAATACATTTTAGACATGTATCGATATATTGAAGA
129 TCAATACATTTTAGACATGTATCGATATATTGAAGA
1289692 ATGTATCAACACATTTGAGTCAAAAACCCAAAATGTATCGATACAATG-AAAA-ATCGATACA-T
1 ATGTATCAACACATTTGAGTCAAAAACCCAAAATGTATCGATACAATGAAAAATATCGATACATT
* * *
1289754 TTTATTTTCAGAATGCAAAATTTGCTTCGATATGGTCTTGTATCGATACATTTCATACATGTATC
66 TTTATTTTCAGAATGCAAAATTTGCTTCGAAATGGTCCTGTATCGATACATTTCAGACATGTATC
1289819 AATACATT
131 AATACATT
1289827 CACTTATGTG
Statistics
Matches: 125, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
161 68 0.54
162 9 0.07
165 4 0.03
166 44 0.35
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.35
Consensus pattern (164 bp):
ATGTATCAACACATTTGAGTCAAAAACCCAAAATGTATCGATACAATGAAAAATATCGATACATT
TTTATTTTCAGAATGCAAAATTTGCTTCGAAATGGTCCTGTATCGATACATTTCAGACATGTATC
AATACATTTTAGACATGTATCGATATATTGAAGA
Found at i:1289835 original size:20 final size:20
Alignment explanation
Indices: 1289812--1289850 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1289802 CATTTCATAC
1289812 ATGTATCAATACATTCACTT
1 ATGTATCAATACATTCACTT
*
1289832 ATGTGTCAATACATTCACT
1 ATGTATCAATACATTCACT
1289851 CATTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (20 bp):
ATGTATCAATACATTCACTT
Found at i:1293274 original size:20 final size:19
Alignment explanation
Indices: 1293249--1293306 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 19
1293239 AAAAATCTAG
1293249 AATGTATTGATACATTGATA
1 AATGTATTGATACATTG-TA
*
1293269 AATGTATAGATACAATTGTA
1 AATGTATTGATAC-ATTGTA
1293289 AGCATGTATTGATACATT
1 A--ATGTATTGATACATT
1293307 TCCTTTCCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 15 0.45
21 7 0.21
22 11 0.33
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.38
Consensus pattern (19 bp):
AATGTATTGATACATTGTA
Found at i:1293377 original size:20 final size:21
Alignment explanation
Indices: 1293352--1293405 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
1293342 CATTTTAGGC
*
1293352 ATGTATTGATACATTCACT-T
1 ATGTATCGATACATTCACTAT
*
1293372 ATGTATCGATACATTTACTAT
1 ATGTATCGATACATTCACTAT
*
1293393 TTGTATCGATACA
1 ATGTATCGATACA
1293406 AATTGTAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATTCACTAT
Found at i:1296082 original size:37 final size:37
Alignment explanation
Indices: 1296041--1296118 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
1296031 GATGTATTAT
* * * *
1296041 TTGTTCTTAGTCATGTATGTTGAATTTGTTTTATTTG
1 TTGTTCTTAGCCATGCATGTTGAATTTATTTTATTTA
* *
1296078 TTGTTCTTGGCCATGCATGTTGAATTTATTTTTTTTA
1 TTGTTCTTAGCCATGCATGTTGAATTTATTTTATTTA
1296115 TTGT
1 TTGT
1296119 AGGCTGTACA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.15, C:0.08, G:0.18, T:0.59
Consensus pattern (37 bp):
TTGTTCTTAGCCATGCATGTTGAATTTATTTTATTTA
Found at i:1297321 original size:55 final size:55
Alignment explanation
Indices: 1297240--1297368 Score: 159
Period size: 55 Copynumber: 2.3 Consensus size: 55
1297230 TTATGGTCTT
* * ** * **
1297240 AATAAAGGTGACTTGGAGTCACTTGCCATTGTGGTGAGTAGATTTTTGAGGTTTC
1 AATAAAGATGACTTGGTGTCACTTGCCATTGTGGCAAGTAAAACTTTGAGGTTTC
* *
1297295 AATGAAGATGACTTGGTGTCATTTGCCATTGTGGCAAGTAAAACTTTGAGGTTTC
1 AATAAAGATGACTTGGTGTCACTTGCCATTGTGGCAAGTAAAACTTTGAGGTTTC
* *
1297350 AATAAAGGTGACTTAGTGT
1 AATAAAGATGACTTGGTGT
1297369 TACATTGCAT
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 62 1.00
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.35
Consensus pattern (55 bp):
AATAAAGATGACTTGGTGTCACTTGCCATTGTGGCAAGTAAAACTTTGAGGTTTC
Found at i:1302947 original size:52 final size:52
Alignment explanation
Indices: 1302862--1302986 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
1302852 ATATGAAAAG
* *
1302862 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
1302914 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
1302966 TTTCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1302987 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:1302999 original size:52 final size:51
Alignment explanation
Indices: 1302862--1303006 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
1302852 ATATGAAAAG
*
1302862 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
1302914 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
1302966 TTTCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1303007 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 82 0.98
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:1303013 original size:13 final size:13
Alignment explanation
Indices: 1302995--1303019 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1302985 CAAAGATCAG
1302995 TGTATCGATACAA
1 TGTATCGATACAA
1303008 TGTATCGATACA
1 TGTATCGATACA
1303020 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1303097 original size:33 final size:33
Alignment explanation
Indices: 1303060--1303192 Score: 185
Period size: 33 Copynumber: 4.0 Consensus size: 33
1303050 AGTAGCTTAA
*
1303060 ATTGTATCGATATAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1303093 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1303126 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1303159 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1303192 A
1 A
1303193 AATCGTTGAA
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 95 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1303100 original size:13 final size:13
Alignment explanation
Indices: 1303082--1303172 Score: 56
Period size: 13 Copynumber: 5.9 Consensus size: 13
1303072 TAAAAAAATA
1303082 TGTATCGATACAT
1 TGTATCGATACAT
1303095 TGTATCGATACAAAAAAAT
1 TGTATCGATAC------AT
1303114 ATGTATCGATACAT
1 -TGTATCGATACAT
1303128 TGTATCGATACAACATTTT
1 TGTATCGAT---ACA---T
1303147 ATGTATCGATACAT
1 -TGTATCGATACAT
1303161 TGTATCGATACA
1 TGTATCGATACA
1303173 ACATTTTATG
Statistics
Matches: 64, Mismatches: 0, Indels: 28
0.70 0.00 0.30
Matches are distributed among these distances:
13 32 0.50
14 3 0.05
16 3 0.05
17 3 0.05
19 3 0.05
20 20 0.31
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1303120 original size:20 final size:19
Alignment explanation
Indices: 1303058--1303126 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 19
1303048 GTAGTAGCTT
*
1303058 AAATTGTATCGATATAAAA
1 AAATTGTATCGATACAAAA
1303077 AAATATGTATCGATAC----
1 AAAT-TGTATCGATACAAAA
1303093 --ATTGTATCGATACAAAA
1 AAATTGTATCGATACAAAA
1303110 AAATATGTATCGATACA
1 AAAT-TGTATCGATACA
1303127 TTGTATCGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 15
0.72 0.02 0.26
Matches are distributed among these distances:
13 11 0.27
14 2 0.05
19 6 0.15
20 22 0.54
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.30
Consensus pattern (19 bp):
AAATTGTATCGATACAAAA
Done.