Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 111 of 328
Found at i:31289241 original size:45 final size:45
Alignment explanation
Indices: 31289191--31289281 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
31289181 CCAAAAAATG
*
31289191 TGTCACATACATCATGAACTCAGACCATAACTCAATGAGTTCAGA
1 TGTCACATACATCATGAACTCAGACCACAACTCAATGAGTTCAGA
**
31289236 TGTCACATATGTCATGAACTCAGACCACAACTCAATGAGTTCAGA
1 TGTCACATACATCATGAACTCAGACCACAACTCAATGAGTTCAGA
31289281 T
1 T
31289282 CACATAATTC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.25
Consensus pattern (45 bp):
TGTCACATACATCATGAACTCAGACCACAACTCAATGAGTTCAGA
Found at i:31289279 original size:21 final size:21
Alignment explanation
Indices: 31289210--31289285 Score: 55
Period size: 21 Copynumber: 3.5 Consensus size: 21
31289200 CATCATGAAC
*
31289210 TCAGACCATAACTCAATGAGT
1 TCAGACCACAACTCAATGAGT
* * **
31289231 TCAGATGTCACATATGTC-ATGAAC
1 TCAGA--CCACA-A-CTCAATGAGT
31289255 TCAGACCACAACTCAATGAGT
1 TCAGACCACAACTCAATGAGT
*
31289276 TCAGATCACA
1 TCAGACCACA
31289286 TAATTCCTAG
Statistics
Matches: 40, Mismatches: 10, Indels: 10
0.67 0.17 0.17
Matches are distributed among these distances:
20 2 0.05
21 19 0.47
22 4 0.10
23 3 0.08
24 10 0.25
25 2 0.05
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (21 bp):
TCAGACCACAACTCAATGAGT
Found at i:31291863 original size:40 final size:40
Alignment explanation
Indices: 31291784--31291960 Score: 225
Period size: 40 Copynumber: 4.5 Consensus size: 40
31291774 CGGATGATAA
* * * * *
31291784 CCGGACTAAGATCTGAAGGCATTCGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * * *
31291824 CCGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
*
31291864 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
31291904 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
31291944 CC-GGCTAA-ATCCCGAAG
1 CCGGGCTAAGA-CCCGAAG
31291961 ATGCTTGGGT
Statistics
Matches: 119, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.01
39 15 0.13
40 101 0.85
41 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:31294843 original size:34 final size:33
Alignment explanation
Indices: 31294805--31294874 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 33
31294795 AGCCCCTTTT
31294805 TTTCAATAACAGTCG-CAGCCTGGGCCCGAGCCCA
1 TTTCAATAACAGT-GACAGCCT-GGCCCGAGCCCA
* * *
31294839 TTTCAGTAACAGTGACAGTCTGGCCTGAGCCCA
1 TTTCAATAACAGTGACAGCCTGGCCCGAGCCCA
31294872 TTT
1 TTT
31294875 TAGTACAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 15 0.47
34 17 0.53
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.24
Consensus pattern (33 bp):
TTTCAATAACAGTGACAGCCTGGCCCGAGCCCA
Found at i:31294874 original size:33 final size:34
Alignment explanation
Indices: 31294805--31294879 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 34
31294795 AGCCCCTTTT
*
31294805 TTTCAATAACAGTCGCAGCCTGGGCCCGAGCCCA
1 TTTCAGTAACAGTCGCAGCCTGGGCCCGAGCCCA
* *
31294839 TTTCAGTAACAGT-GACAGTCT-GGCCTGAGCCCA
1 TTTCAGTAACAGTCG-CAGCCTGGGCCCGAGCCCA
*
31294872 TTTTAGTA
1 TTTCAGTA
31294880 CAATATGCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 19 0.53
34 17 0.47
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (34 bp):
TTTCAGTAACAGTCGCAGCCTGGGCCCGAGCCCA
Found at i:31295907 original size:22 final size:22
Alignment explanation
Indices: 31295872--31295915 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
31295862 TAGGAATTAG
*
31295872 GGTGTGTCGTTTTCTCT-TTTT
1 GGTGTGTCATTTTCTCTCTTTT
31295893 GGTGTAGTCATTTTCTCTCTTTT
1 GGTGT-GTCATTTTCTCTCTTTT
31295916 CTTTTCCAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.05, C:0.16, G:0.20, T:0.59
Consensus pattern (22 bp):
GGTGTGTCATTTTCTCTCTTTT
Found at i:31297137 original size:20 final size:19
Alignment explanation
Indices: 31297124--31297178 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
31297114 ATGACTGATG
31297124 TGATATGCACATGATATGTA
1 TGATATGCACATGATATG-A
31297144 TGATATGCACATGATATGTA
1 TGATATGCACATGATATG-A
*
31297164 TGAAATGCACATGAT
1 TGATATGCACATGAT
31297179 GAATTCATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (19 bp):
TGATATGCACATGATATGA
Found at i:31297140 original size:11 final size:11
Alignment explanation
Indices: 31297124--31297178 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
31297114 ATGACTGATG
31297124 TGATATGCACA
1 TGATATGCACA
*
31297135 TGATATG--TA
1 TGATATGCACA
31297144 TGATATGCACA
1 TGATATGCACA
*
31297155 TGATATG--TA
1 TGATATGCACA
*
31297164 TGAAATGCACA
1 TGATATGCACA
31297175 TGAT
1 TGAT
31297179 GAATTCATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (11 bp):
TGATATGCACA
Found at i:31297257 original size:26 final size:26
Alignment explanation
Indices: 31297228--31297332 Score: 151
Period size: 26 Copynumber: 4.1 Consensus size: 26
31297218 AAGGAAGTGC
31297228 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
31297254 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* *
31297280 AAAAGGGCTTATGCCCCTGATTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
31297306 AAAAGGGCTT-TGCCCTAGTTT-TTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
31297330 AAA
1 AAA
31297333 GAGGCTAGGC
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
24 6 0.09
25 8 0.11
26 56 0.80
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:31300487 original size:20 final size:20
Alignment explanation
Indices: 31300462--31300501 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
31300452 AGTTGATGCA
31300462 GAAAGGTTGTGAGGCGTAGT
1 GAAAGGTTGTGAGGCGTAGT
31300482 GAAAGGTTGTGAGGCGTAGT
1 GAAAGGTTGTGAGGCGTAGT
31300502 TGGCTTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.45, T:0.25
Consensus pattern (20 bp):
GAAAGGTTGTGAGGCGTAGT
Found at i:31305253 original size:20 final size:20
Alignment explanation
Indices: 31305219--31305274 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
31305209 GATACGTGGG
31305219 ATATGATAT--ACATGAT-T
1 ATATGATATGCACATGATAT
31305236 CATATGATATGCACATGATAT
1 -ATATGATATGCACATGATAT
* *
31305257 GTATGAAATGCACATGAT
1 ATATGATATGCACATGAT
31305275 GAATTCATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.27
20 23 0.70
21 1 0.03
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (20 bp):
ATATGATATGCACATGATAT
Found at i:31305402 original size:52 final size:51
Alignment explanation
Indices: 31305324--31305459 Score: 206
Period size: 52 Copynumber: 2.7 Consensus size: 51
31305314 GAGGAAGTGC
31305324 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGGTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTT-TGCCCCAGGTTACCG
* *
31305376 AAAAGGGCTTATGCCCCTGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGGTTACCG
*
31305427 AAAAGGGATT-TGCCCCAG-TTATT-AAAAGAGGCT
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAG-GGCT
31305460 AGGCCTCCAG
Statistics
Matches: 79, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
48 5 0.06
49 9 0.11
50 7 0.09
51 23 0.29
52 35 0.44
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.26
Consensus pattern (51 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGGTTACCG
Found at i:31305422 original size:25 final size:26
Alignment explanation
Indices: 31305324--31305459 Score: 172
Period size: 26 Copynumber: 5.3 Consensus size: 26
31305314 GAGGAAGTGC
31305324 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* **
31305350 AAAAGGGCTTATGCCCCAGGTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
31305376 AAAAGGGCTTATGCCCCTGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
31305402 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
31305427 AAAAGGGATT-TGCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
31305450 AAAAGAGGCT
1 AAAAG-GGCT
31305460 AGGCCTCCAG
Statistics
Matches: 95, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
23 5 0.05
24 6 0.06
25 29 0.31
26 55 0.58
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.26
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:31314170 original size:20 final size:20
Alignment explanation
Indices: 31314145--31314186 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
31314135 CATAATGAAC
31314145 ATAACCTTGCATTTTATCAA
1 ATAACCTTGCATTTTATCAA
31314165 ATAACCTTGCATTTTATCAA
1 ATAACCTTGCATTTTATCAA
31314185 AT
1 AT
31314187 CTCTTAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.40
Consensus pattern (20 bp):
ATAACCTTGCATTTTATCAA
Found at i:31318832 original size:31 final size:31
Alignment explanation
Indices: 31318794--31318857 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
31318784 CCTTTTCATA
31318794 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
31318825 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
31318856 TT
1 TT
31318858 ACTGTAAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:31319157 original size:25 final size:24
Alignment explanation
Indices: 31319051--31319171 Score: 183
Period size: 24 Copynumber: 5.0 Consensus size: 24
31319041 TGTTTATCAT
*
31319051 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
31319076 ATAACTGGGGCA-AAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
31319099 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
31319123 ATAACTGGGGCATAAGCCCTTTATC
1 ATAACTGGGGCATAAGCCCTTT-TA
31319148 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
31319172 CACTTCCTCC
Statistics
Matches: 90, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
23 18 0.20
24 41 0.46
25 31 0.34
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:31319165 original size:49 final size:47
Alignment explanation
Indices: 31319051--31319171 Score: 181
Period size: 49 Copynumber: 2.5 Consensus size: 47
31319041 TGTTTATCAT
*
31319051 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAGCCCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAGCCCTTTTA
*
31319099 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTATC
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCA-AAGCCCTTT-TA
31319148 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
31319172 CACTTCCTCC
Statistics
Matches: 68, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
47 22 0.32
48 21 0.31
49 25 0.37
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (47 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAGCCCTTTTA
Found at i:31319245 original size:20 final size:20
Alignment explanation
Indices: 31319220--31319286 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
31319210 TTACGAATAC
31319220 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
31319240 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* * * *
31319260 GTCATATGCATACCGTACAT
1 ATCATGTGCATATCATACAT
*
31319280 AACATGT
1 ATCATGT
31319287 TTATCAAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:31324325 original size:36 final size:36
Alignment explanation
Indices: 31324278--31324350 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
31324268 CTTTCGAGAG
*
31324278 TAAGAGCAACTGGCTCTAGGTTGATTAATTGAAATT
1 TAAGAGCAACTGACTCTAGGTTGATTAATTGAAATT
*
31324314 TAAGAGCAACTGACTCTAGGTTGATTAATTGGAATT
1 TAAGAGCAACTGACTCTAGGTTGATTAATTGAAATT
31324350 T
1 T
31324351 CTTTCTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.34
Consensus pattern (36 bp):
TAAGAGCAACTGACTCTAGGTTGATTAATTGAAATT
Found at i:31325801 original size:20 final size:21
Alignment explanation
Indices: 31325776--31325814 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
31325766 ACTCAATCAA
*
31325776 AATTTTCTCT-TTTTTTATAT
1 AATTTTATCTCTTTTTTATAT
31325796 AATTTTATCTCTTTTTTAT
1 AATTTTATCTCTTTTTTAT
31325815 TTTTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (21 bp):
AATTTTATCTCTTTTTTATAT
Found at i:31326804 original size:23 final size:23
Alignment explanation
Indices: 31326773--31326829 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
31326763 AGTTCAAAAT
* *
31326773 AAAAA-AAAAAACAAATAACA-AG
1 AAAAATAAAAAACAAA-AAAATAA
*
31326795 AAAAATAAAATACAAAAAAATAA
1 AAAAATAAAAAACAAAAAAATAA
31326818 AAAAATAAAAAA
1 AAAAATAAAAAA
31326830 ACATAAAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 8 0.28
23 21 0.72
ACGTcount: A:0.84, C:0.05, G:0.02, T:0.09
Consensus pattern (23 bp):
AAAAATAAAAAACAAAAAAATAA
Found at i:31326805 original size:33 final size:33
Alignment explanation
Indices: 31326768--31326838 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
31326758 AGTAAAGTTC
*
31326768 AAAATA-AAAAAAA-AAACAAATAACAAGAAAAAT
1 AAAATACAAAAAAATAAAAAAATAA-AA-AAAAAT
*
31326801 AAAATACAAAAAAATAAAAAAATAAAAAAACAT
1 AAAATACAAAAAAATAAAAAAATAAAAAAAAAT
31326834 AAAAT
1 AAAAT
31326839 CTAAATAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 16 0.47
34 9 0.26
35 9 0.26
ACGTcount: A:0.82, C:0.06, G:0.01, T:0.11
Consensus pattern (33 bp):
AAAATACAAAAAAATAAAAAAATAAAAAAAAAT
Found at i:31326835 original size:10 final size:9
Alignment explanation
Indices: 31326768--31326837 Score: 58
Period size: 8 Copynumber: 8.0 Consensus size: 9
31326758 AGTAAAGTTC
31326768 AAAAT-AAA
1 AAAATAAAA
31326776 AAAA-AAAA
1 AAAATAAAA
* *
31326784 CAAATAACA
1 AAAATAAAA
* *
31326793 AGAA-AAAT
1 AAAATAAAA
31326801 AAAATACAAA
1 AAAATA-AAA
31326811 AAAAT-AAA
1 AAAATAAAA
31326819 AAAATAAAA
1 AAAATAAAA
31326828 AAACATAAAA
1 AAA-ATAAAA
31326838 TCTAAATAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
8 23 0.48
9 12 0.25
10 13 0.27
ACGTcount: A:0.83, C:0.06, G:0.01, T:0.10
Consensus pattern (9 bp):
AAAATAAAA
Found at i:31331975 original size:9 final size:9
Alignment explanation
Indices: 31331961--31331995 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
31331951 GCTCTTGGTT
31331961 GAAAACCTA
1 GAAAACCTA
*
31331970 GAAAACCCA
1 GAAAACCTA
31331979 -AAAACCTA
1 GAAAACCTA
31331987 GAAAACCTA
1 GAAAACCTA
31331996 CAATCTTGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.57, C:0.26, G:0.09, T:0.09
Consensus pattern (9 bp):
GAAAACCTA
Found at i:31332475 original size:22 final size:22
Alignment explanation
Indices: 31332445--31332524 Score: 106
Period size: 22 Copynumber: 3.6 Consensus size: 22
31332435 ACAGGATCAT
31332445 ACTTTAGTGCCTCTGTACTTGC
1 ACTTTAGTGCCTCTGTACTTGC
* * *
31332467 ATTTTAGTGCCTTTGTACTTGT
1 ACTTTAGTGCCTCTGTACTTGC
*
31332489 ACTTTAGTGCCTCTGTATTTGC
1 ACTTTAGTGCCTCTGTACTTGC
**
31332511 ACTACAGTGCCTCT
1 ACTTTAGTGCCTCT
31332525 ACTAGTATTT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.44
Consensus pattern (22 bp):
ACTTTAGTGCCTCTGTACTTGC
Found at i:31341540 original size:29 final size:29
Alignment explanation
Indices: 31341479--31341603 Score: 128
Period size: 29 Copynumber: 4.3 Consensus size: 29
31341469 GAGTCTACAT
* * * *
31341479 ACATGCATATGGCCCATTAAG-CCTAATC
1 ACATTCATATGGACCATTAGGCCCAAATC
* *
31341507 TCATTCATATGGACCGTTAGGCCCAAATC
1 ACATTCATATGGACCATTAGGCCCAAATC
* *
31341536 ACATTCGTAT-GACCCATTAGGCCCAAATT
1 ACATTCATATGGA-CCATTAGGCCCAAATC
* *
31341565 ACATTCATACGGCCCATTAGGCCCAAATC
1 ACATTCATATGGACCATTAGGCCCAAATC
*
31341594 ACAATCATAT
1 ACATTCATAT
31341604 ACATACTTTC
Statistics
Matches: 78, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
28 18 0.23
29 59 0.76
30 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.26
Consensus pattern (29 bp):
ACATTCATATGGACCATTAGGCCCAAATC
Found at i:31343023 original size:14 final size:13
Alignment explanation
Indices: 31343003--31343039 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
31342993 AATATTTGAT
31343003 TTGTTCTTAATTA
1 TTGTTCTTAATTA
31343016 TGTGTTCTTAATTA
1 T-TGTTCTTAATTA
31343030 TTGTT-TTAAT
1 TTGTTCTTAAT
31343040 ATTTTAGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.22
13 5 0.22
14 13 0.57
ACGTcount: A:0.22, C:0.05, G:0.11, T:0.62
Consensus pattern (13 bp):
TTGTTCTTAATTA
Found at i:31346208 original size:19 final size:19
Alignment explanation
Indices: 31346173--31346210 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
31346163 TTGCAATTTA
*
31346173 AATTTTTATTTTCTTTTCT
1 AATTTTTATTTTATTTTCT
31346192 AATTTTTCA-TTTATTTTCT
1 AATTTTT-ATTTTATTTTCT
31346211 TCTGACAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (19 bp):
AATTTTTATTTTATTTTCT
Found at i:31352344 original size:9 final size:8
Alignment explanation
Indices: 31352325--31352355 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
31352315 TATTTGTTCT
31352325 AAAAAAT-
1 AAAAAATA
31352332 AAAAAATA
1 AAAAAATA
31352340 AAAAAATA
1 AAAAAATA
31352348 AAAAAATA
1 AAAAAATA
31352356 TTTCATTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAAAATA
Found at i:31358141 original size:29 final size:29
Alignment explanation
Indices: 31358075--31358198 Score: 162
Period size: 29 Copynumber: 4.3 Consensus size: 29
31358065 GAGTCTACAT
* * *
31358075 ACATACATATGGCCCACTAGG--CTAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
* * *
31358102 TCATTCATATGGCCCATTTGGCCTAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
*
31358131 ACATTCGTATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
*
31358160 ACATTCATACGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
31358189 ACATTCATAT
1 ACATTCATAT
31358199 ACATGCTTTC
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
27 17 0.21
29 65 0.79
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.27
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAAATC
Found at i:31360485 original size:16 final size:17
Alignment explanation
Indices: 31360464--31360496 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
31360454 CACATTGAAG
31360464 TGTTTT-TTGAAAACCA
1 TGTTTTATTGAAAACCA
31360480 TGTTTTCATTGAAAACC
1 TGTTTT-ATTGAAAACC
31360497 CTTCTTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (17 bp):
TGTTTTATTGAAAACCA
Found at i:31361870 original size:27 final size:27
Alignment explanation
Indices: 31361837--31361952 Score: 99
Period size: 27 Copynumber: 4.3 Consensus size: 27
31361827 CAAAATAGTC
* * *
31361837 ATTTTACCCTACAGGGGTATTTCGGTA
1 ATTTTACACTACAAGGGTATTTCAGTA
31361864 ATTTTACACTACAAGGGTATTTCAGTA
1 ATTTTACACTACAAGGGTATTTCAGTA
* *** *
31361891 ATTTTACA-AATTGGGGGTATTTCAATA
1 ATTTTACACTA-CAAGGGTATTTCAGTA
* ****
31361918 ATTTTACAATTTGCGGGTATTTCAGTA
1 ATTTTACACTACAAGGGTATTTCAGTA
31361945 ATTTTACA
1 ATTTTACA
31361953 AACTGGGGGT
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
26 1 0.01
27 74 0.99
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (27 bp):
ATTTTACACTACAAGGGTATTTCAGTA
Found at i:31361974 original size:81 final size:81
Alignment explanation
Indices: 31361889--31362041 Score: 229
Period size: 81 Copynumber: 1.9 Consensus size: 81
31361879 GGTATTTCAG
* ** *
31361889 TAATTTTACAAATTGGGGGTATTTCAATAATTTTAC-AATTTGCGGGTATTTC-AGTAATTTTAC
1 TAATTTTACAAATTGAGGGTATTTCAATAATTTTACAAACCTG-GAGTATTTCGA-TAATTTTAC
*
31361952 AAACTGGGGGTATTTTGA
64 AAACCGGGGGTATTTTGA
31361970 TAATTTTACAAATTGAGGGTATTTCAATAATTTTACAAACCTGGAGTATTTCGATAATTTTACAA
1 TAATTTTACAAATTGAGGGTATTTCAATAATTTTACAAACCTGGAGTATTTCGATAATTTTACAA
31362035 ACCGGGG
66 ACCGGGG
31362042 TCTTAACGAC
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
81 60 0.92
82 5 0.08
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.39
Consensus pattern (81 bp):
TAATTTTACAAATTGAGGGTATTTCAATAATTTTACAAACCTGGAGTATTTCGATAATTTTACAA
ACCGGGGGTATTTTGA
Found at i:31362034 original size:54 final size:54
Alignment explanation
Indices: 31361850--31362035 Score: 241
Period size: 54 Copynumber: 3.4 Consensus size: 54
31361840 TTACCCTACA
* * ** *
31361850 GGGGTATTTCGGTAATTTTAC-ACTACAAGGGTATTTCAGTAATTTTACAAATTG
1 GGGGTATTTCGATAATTTTACAAAT-TGAGGGTATTTCAGTAATTTTACAAACTG
* * *
31361904 GGGGTATTTCAATAATTTTACAATTTGCGGGTATTTCAGTAATTTTACAAACTG
1 GGGGTATTTCGATAATTTTACAAATTGAGGGTATTTCAGTAATTTTACAAACTG
* *
31361958 GGGGTATTTTGATAATTTTACAAATTGAGGGTATTTCAATAATTTTACAAACCT-
1 GGGGTATTTCGATAATTTTACAAATTGAGGGTATTTCAGTAATTTTACAAA-CTG
*
31362012 GGAGTATTTCGATAATTTTACAAA
1 GGGGTATTTCGATAATTTTACAAA
31362036 CCGGGGTCTT
Statistics
Matches: 116, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
54 112 0.97
55 4 0.03
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (54 bp):
GGGGTATTTCGATAATTTTACAAATTGAGGGTATTTCAGTAATTTTACAAACTG
Found at i:31362036 original size:27 final size:26
Alignment explanation
Indices: 31361850--31362042 Score: 183
Period size: 27 Copynumber: 7.2 Consensus size: 26
31361840 TTACCCTACA
* * *
31361850 GGGGTATTTCGGTAATTTTACACTACA
1 GGGGTATTTCGATAATTTTACA-AACT
* *
31361877 AGGGTATTTC-AGTAATTTTACAAATT
1 GGGGTATTTCGA-TAATTTTACAAACT
* **
31361903 GGGGGTATTTCAATAATTTTACAATTT
1 -GGGGTATTTCGATAATTTTACAAACT
31361930 GCGGGTATTTC-AGTAATTTTACAAACT
1 G-GGGTATTTCGA-TAATTTTACAAACT
* *
31361957 GGGGGTATTTTGATAATTTTACAAATT
1 -GGGGTATTTCGATAATTTTACAAACT
*
31361984 GAGGGTATTTCAATAATTTTACAAACCT
1 G-GGGTATTTCGATAATTTTACAAA-CT
* *
31362012 GGAGTATTTCGATAATTTTACAAACC
1 GGGGTATTTCGATAATTTTACAAACT
31362038 GGGGT
1 GGGGT
31362043 CTTAACGACC
Statistics
Matches: 139, Mismatches: 18, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
26 9 0.06
27 125 0.90
28 5 0.04
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.39
Consensus pattern (26 bp):
GGGGTATTTCGATAATTTTACAAACT
Found at i:31375162 original size:21 final size:19
Alignment explanation
Indices: 31375125--31375179 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 19
31375115 ATTAGAATGT
*
31375125 AAAAAATTAAATTAAAATA
1 AAAAAATTAAATCAAAATA
31375144 AAAAATATTAAAATCAAAATA
1 AAAAA-ATT-AAATCAAAATA
**
31375165 AAAAAGCTAAATCAA
1 AAAAAATTAAATCAA
31375180 TAAAAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 12 0.39
20 4 0.13
21 15 0.48
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (19 bp):
AAAAAATTAAATCAAAATA
Found at i:31375583 original size:21 final size:21
Alignment explanation
Indices: 31375554--31375596 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
31375544 TTCGAAAGTA
31375554 AAAGAAATTGACTCTAGGTTG
1 AAAGAAATTGACTCTAGGTTG
*
31375575 AAAGCAATTGACTCTAGGTTG
1 AAAGAAATTGACTCTAGGTTG
31375596 A
1 A
31375597 TTAATTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (21 bp):
AAAGAAATTGACTCTAGGTTG
Found at i:31377874 original size:40 final size:39
Alignment explanation
Indices: 31377746--31377888 Score: 187
Period size: 39 Copynumber: 3.6 Consensus size: 39
31377736 AATGTTCGAG
*
31377746 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
31377785 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
31377824 TGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
31377864 CCATAACCGGGCTATGTCCCGAAGG
1 TGATATCCGGGCTAAG-CCCGAAGG
31377889 TGTTTTGAAC
Statistics
Matches: 92, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 52 0.57
40 40 0.43
ACGTcount: A:0.23, C:0.22, G:0.31, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:31381015 original size:13 final size:14
Alignment explanation
Indices: 31380997--31381027 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
31380987 GTTAAAATTG
31380997 TAAATT-AGTAAAA
1 TAAATTAAGTAAAA
31381010 TAAATTAAGTAAAA
1 TAAATTAAGTAAAA
31381024 TAAA
1 TAAA
31381028 GAAAACCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (14 bp):
TAAATTAAGTAAAA
Found at i:31382679 original size:24 final size:25
Alignment explanation
Indices: 31382652--31382707 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
31382642 AGGCCTTTTA
* *
31382652 ATATGTTG-TGTATAATTGTCATT-T
1 ATATGTTGTTGT-GAATTGGCATTAT
31382676 ATATGCTTGTTGTGAATTGGCATTAT
1 ATATG-TTGTTGTGAATTGGCATTAT
31382702 ATATGT
1 ATATGT
31382708 CAAATGGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 5 0.19
25 13 0.48
26 9 0.33
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.50
Consensus pattern (25 bp):
ATATGTTGTTGTGAATTGGCATTAT
Found at i:31385708 original size:29 final size:29
Alignment explanation
Indices: 31385675--31385806 Score: 140
Period size: 29 Copynumber: 4.6 Consensus size: 29
31385665 GTGACGAGAT
*
31385675 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* *
31385704 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* * ***
31385733 TGGCACTAAGTGTGCGAGCTCGAAGGGCA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* * * *
31385762 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ACA
31385791 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
31385807 AAATCGAGTA
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
28 2 0.02
29 86 0.98
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATACA
Found at i:31393394 original size:29 final size:29
Alignment explanation
Indices: 31393361--31393492 Score: 140
Period size: 29 Copynumber: 4.6 Consensus size: 29
31393351 GTGACGAGAT
*
31393361 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* *
31393390 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* * ***
31393419 TGGCACTAAGTGTGCGAGCTCGAAGGGCA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* * * *
31393448 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ACA
31393477 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
31393493 AAATCGAGTA
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
28 2 0.02
29 86 0.98
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATACA
Found at i:31399540 original size:39 final size:40
Alignment explanation
Indices: 31399492--31399686 Score: 215
Period size: 38 Copynumber: 5.0 Consensus size: 40
31399482 GCTACTCGTT
* * * **
31399492 CAAACGCCTTCGGGACATAGCCCGGTTATGGTAAC-CGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATCATAACTCGCA
* *
31399531 CAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATCATAACTCGCA
*
31399571 CAATTGCCTTC-GG-CTTAGCCCGGATATCATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATCATAACTCGCA
* * *
31399609 CGATTGCCTTCGGG-CTTAG-CCGGATATCACAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATCATAACTCGCA
* * *
31399647 -AATTGCCTTCGGG-CTTAGCCCGGATATCACAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATCATAACTCGCA
31399685 CA
1 CA
31399687 TTCATACACA
Statistics
Matches: 138, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
37 17 0.12
38 69 0.50
39 38 0.28
40 14 0.10
ACGTcount: A:0.25, C:0.31, G:0.21, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATCATAACTCGCA
Found at i:31399605 original size:38 final size:39
Alignment explanation
Indices: 31399527--31399686 Score: 245
Period size: 38 Copynumber: 4.2 Consensus size: 39
31399517 TTATGGTAAC
* *
31399527 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
*
31399567 CGCACAATTGCCTTC-GGCTTAGCCCGGATATCATAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
31399605 CGCACGATTGCCTTCGGGCTTAG-CCGGATATCACAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
31399643 CGCA-AATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
31399681 CGCACA
1 CGCACA
31399687 TTCATACACA
Statistics
Matches: 110, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
37 17 0.15
38 69 0.63
39 10 0.09
40 14 0.13
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:31399642 original size:76 final size:78
Alignment explanation
Indices: 31399497--31399686 Score: 253
Period size: 76 Copynumber: 2.5 Consensus size: 78
31399487 TCGTTCAAAC
* * **
31399497 GCCTTCGGGACATAGCCCGGTTATGGTAAC-CGCACAAATGCCTTCGGGACTTAACCCGGATATC
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATC
31399561 ACAACTCGCACAATT
65 ACAACTCGCA-AATT
* * *
31399576 GCCTTC-GGCTTAGCCCGGATATCATAACTCGCACGATTGCCTTCGGG-CTT-AGCCGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATCA
31399638 CAACTCGCAAATT
66 CAACTCGCAAATT
* *
31399651 GCCTTCGGGCTTAGCCCGGATATCACAATTCGCACA
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACA
31399687 TTCATACACA
Statistics
Matches: 99, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
75 10 0.10
76 46 0.46
77 19 0.19
78 18 0.18
79 6 0.06
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.23
Consensus pattern (78 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATCA
CAACTCGCAAATT
Found at i:31402142 original size:29 final size:29
Alignment explanation
Indices: 31402108--31402169 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
31402098 TCGCACACCC
*
31402108 AGTGCCGTAAATTTCCAGCATGCACACTT
1 AGTGCCATAAATTTCCAGCATGCACACTT
*
31402137 AGTGCCATATATTTCCAGCATGCACACTT
1 AGTGCCATAAATTTCCAGCATGCACACTT
31402166 AGTG
1 AGTG
31402170 GCCACATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (29 bp):
AGTGCCATAAATTTCCAGCATGCACACTT
Found at i:31410030 original size:57 final size:58
Alignment explanation
Indices: 31409969--31410098 Score: 165
Period size: 57 Copynumber: 2.3 Consensus size: 58
31409959 ATTTAAGCCC
* * * *
31409969 GCACACATAGTGCCATACCCTTCGAGC-TCGCACACCCAGTGCCGTA-ATTTCCAGCAT
1 GCACACTTAGTGCCATACACTTCCAGCAT-GCACACCCAGTGCCATATATTTCCAGCAT
* * **
31410026 GCACACTTAGTGCCATATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATACACTTCCAGCATGCACACCCAGTGCCATATATTTCCAGCAT
31410084 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
31410099 ATCTCGTCAC
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
57 36 0.57
58 27 0.43
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.25
Consensus pattern (58 bp):
GCACACTTAGTGCCATACACTTCCAGCATGCACACCCAGTGCCATATATTTCCAGCAT
Found at i:31410055 original size:29 final size:29
Alignment explanation
Indices: 31409940--31410098 Score: 171
Period size: 29 Copynumber: 5.5 Consensus size: 29
31409930 ACTCGATTTC
* * **
31409940 GCACACTTAGTGCCATGTGATTT-AAGCCC
1 GCACACTTAGTGCCATAT-ATTTCCAGCAT
* *** *
31409969 GCACACATAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
31409997 CGCACACCCAGTGCCGTA-ATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
31410026 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
31410055 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
31410084 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
31410099 ATCTCGTCAC
Statistics
Matches: 110, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
28 22 0.20
29 88 0.80
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:31417030 original size:49 final size:50
Alignment explanation
Indices: 31416970--31417098 Score: 165
Period size: 50 Copynumber: 2.6 Consensus size: 50
31416960 TCAAGTAGAT
31416970 GCCATGTCCCAGACATGGTCTTACACTGACTATCA-AAATC-GAGGCCGAC
1 GCCATGTCCCAGACATGGTCTTACACTGACTATCACAAATCTG-GGCCGAC
* * * *
31417019 GCCATGTCCCAGACATGGTCTTACACT-AGCTCTCACATATCTGTGCCGAT
1 GCCATGTCCCAGACATGGTCTTACACTGA-CTATCACAAATCTGGGCCGAC
* *
31417069 GCCATTTCCCAGACATGGTCTTACATTGAC
1 GCCATGTCCCAGACATGGTCTTACACTGAC
31417099 ACTTCTATAG
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
48 1 0.01
49 32 0.46
50 35 0.50
51 2 0.03
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.26
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACACTGACTATCACAAATCTGGGCCGAC
Found at i:31417287 original size:48 final size:47
Alignment explanation
Indices: 31416914--31417327 Score: 278
Period size: 48 Copynumber: 8.8 Consensus size: 47
31416904 CATAGGGTAT
* * * *
31416914 AATGCCGATGCCATGTCCCAAACATGGTTTTACATTGGCTCATCCATC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCTATC
** * * *
31416962 AA-GTAGATGCCATGTCCCAGACATGGTCTTACACTGACTATCAAAATC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC--TATC
* * * *
31417010 GAGGCCGACGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT--C-TATC
** * * * *
31417060 TGTGCCGATGCCATTTCCCAGACATGGTCTTACATTGACACTTCTAT-
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCTATC
* * * * * * *
31417107 AGGTACCAATTCCATGTCCCAGACATGGTCTTATACTGGCACATCT-TG
1 A-ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCTATC
* * * * *
31417155 TA-CCCGATG-CATGTCCTAGACAT-GTCGTACACTGGCT-TACATCTC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-C-TATC
* * * * *
31417200 GAGGCCAATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCGTTTC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC-TATC
31417246 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC-AT-
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCTATC
31417291 AATGTGGCCGATG-CATGTCCCAGACAT-GTCTTACACT
1 AA--T-GCCGATGCCATGTCCCAGACATGGTCTTACACT
31417328 AGCACACTAA
Statistics
Matches: 291, Mismatches: 57, Indels: 38
0.75 0.15 0.10
Matches are distributed among these distances:
42 1 0.00
43 1 0.00
44 12 0.04
45 17 0.06
46 58 0.20
47 62 0.21
48 68 0.23
49 34 0.12
50 36 0.12
51 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (47 bp):
AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCTATC
Found at i:31417305 original size:94 final size:94
Alignment explanation
Indices: 31416967--31417330 Score: 322
Period size: 94 Copynumber: 3.9 Consensus size: 94
31416957 CCATCAAGTA
* * * *
31416967 GATGCCATGTCCCAGACATGGTCTTACACTGACTATCAAAATCGAGGCCGACGCCATGTCCCAGA
1 GATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATAATCGAGGCCAATG-CATGTCCCAGA
* *
31417032 CATGGTCTTACACTAGCTCTCACATATCTGTGCC
65 CATGGTCTTACACTAGCTCT--C-TTTC-ATGCC
* * * *
31417066 GATGCCATTTCCCAGACATGGTCTTACATTGACACTTC-T-AT--AGGTACCAATTCCATGTCCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACTC-TCATAATCGAGG--CCAA-TGCATGTCCC
* * * *
31417127 AGACATGGTCTTATACTGGCACATCTTGT-A-CCC
62 AGACATGGTCTTACACTAGCTC-TCTT-TCATGCC
* * * *
31417160 GATG-CATGTCCTAGACAT-GTCGTACACTGGCT-TACAT-CTCGAGGCCAATGCATGTCCCAGA
1 GATGCCATGTCCCAGACATGGTCTTACACTGACTCT-CATAATCGAGGCCAATGCATGTCCCAGA
31417221 CAT-GTCTTACACTAGCTCTCGTTTCAATGCC
65 CATGGTCTTACACTAGCTCTC-TTTC-ATGCC
* * *
31417252 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGCCGATGCATGTCCCAGAC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATAATCGAGGCCAATGCATGTCCCAGAC
31417316 AT-GTCTTACACTAGC
66 ATGGTCTTACACTAGC
31417331 ACACTAATAA
Statistics
Matches: 216, Mismatches: 31, Indels: 41
0.75 0.11 0.14
Matches are distributed among these distances:
89 3 0.01
90 15 0.07
91 17 0.08
92 22 0.10
93 25 0.12
94 60 0.28
95 2 0.01
96 4 0.02
97 2 0.01
98 32 0.15
99 32 0.15
100 2 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (94 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATAATCGAGGCCAATGCATGTCCCAGAC
ATGGTCTTACACTAGCTCTCTTTCATGCC
Found at i:31443252 original size:40 final size:40
Alignment explanation
Indices: 31443168--31443259 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
31443158 CTCGGTATCG
*
31443168 CACACTTAGTGCATCATATAGCCAAAGCTATTCCAATCCG
1 CACACTTAGTGCATCATATAGCCAAAGCTATTCCAATCCA
** * **
31443208 CACACTTAGTGCATTTTATAGCCGAAGCTATTTTACAT-CA
1 CACACTTAGTGCATCATATAGCCAAAGCTATTCCA-ATCCA
31443248 CACACTTAGTGC
1 CACACTTAGTGC
31443260 CTAACATAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 43 0.96
41 2 0.04
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.29
Consensus pattern (40 bp):
CACACTTAGTGCATCATATAGCCAAAGCTATTCCAATCCA
Found at i:31445767 original size:28 final size:27
Alignment explanation
Indices: 31445733--31445802 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
31445723 AACTTACATG
*
31445733 GCGAACCACCAGTTCGCCAAACAAACTA
1 GCGAACC-CCAGCTCGCCAAACAAACTA
* * *
31445761 GCGAACCCTAGCTCGCCAAATAGACTA
1 GCGAACCCCAGCTCGCCAAACAAACTA
*
31445788 GAGAACCCCTAGCTC
1 GCGAACCCC-AGCTC
31445803 ACTAAATAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 23 0.66
28 12 0.34
ACGTcount: A:0.34, C:0.36, G:0.17, T:0.13
Consensus pattern (27 bp):
GCGAACCCCAGCTCGCCAAACAAACTA
Found at i:31445779 original size:27 final size:28
Alignment explanation
Indices: 31445746--31445802 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
31445736 AACCACCAGT
*
31445746 TCGCCAAACAAACTAGCGAA-CCCTAGC
1 TCGCCAAACAAACTAGAGAACCCCTAGC
* *
31445773 TCGCCAAATAGACTAGAGAACCCCTAGC
1 TCGCCAAACAAACTAGAGAACCCCTAGC
31445801 TC
1 TC
31445803 ACTAAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 17 0.65
28 9 0.35
ACGTcount: A:0.35, C:0.35, G:0.16, T:0.14
Consensus pattern (28 bp):
TCGCCAAACAAACTAGAGAACCCCTAGC
Found at i:31445821 original size:28 final size:29
Alignment explanation
Indices: 31445749--31445821 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 29
31445739 CACCAGTTCG
* *
31445749 CCAAACAAACTAG-CGAA-CCCTAGCTCG
1 CCAAATAAACTAGACGAACCCCTAGCTCA
*
31445776 CCAAATAGACTAGA-GAACCCCTAGCTCA
1 CCAAATAAACTAGACGAACCCCTAGCTCA
*
31445804 CTAAATAAACT-GACGAAC
1 CCAAATAAACTAGACGAAC
31445822 ATGACTTTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
27 16 0.42
28 22 0.58
ACGTcount: A:0.41, C:0.32, G:0.14, T:0.14
Consensus pattern (29 bp):
CCAAATAAACTAGACGAACCCCTAGCTCA
Found at i:31447893 original size:28 final size:29
Alignment explanation
Indices: 31447826--31447926 Score: 125
Period size: 28 Copynumber: 3.5 Consensus size: 29
31447816 ATAGTGAATC
*
31447826 CGCACACTTAGTGCTATATACATTC-AGCT
1 CGCACACTTAGTGCTATATA-ATTCAAACT
31447855 CGCACACTTAGTGCTATATAA-TCAAACT
1 CGCACACTTAGTGCTATATAATTCAAACT
* * * *
31447883 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA-TTCAAACT
31447913 CGCACACTTAGTGC
1 CGCACACTTAGTGC
31447927 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 23 0.36
29 20 0.31
30 19 0.30
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATAATTCAAACT
Found at i:31455649 original size:28 final size:29
Alignment explanation
Indices: 31455582--31455682 Score: 125
Period size: 28 Copynumber: 3.5 Consensus size: 29
31455572 ATAGTGAATC
*
31455582 CGCACACTTAGTGCTATATACATTC-AGCT
1 CGCACACTTAGTGCTATATA-ATTCAAACT
31455611 CGCACACTTAGTGCTATATAA-TCAAACT
1 CGCACACTTAGTGCTATATAATTCAAACT
* * * *
31455639 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA-TTCAAACT
31455669 CGCACACTTAGTGC
1 CGCACACTTAGTGC
31455683 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 23 0.36
29 20 0.31
30 19 0.30
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATAATTCAAACT
Found at i:31457273 original size:18 final size:18
Alignment explanation
Indices: 31457259--31457294 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
31457249 AAACTAAACT
31457259 TTCTTGTTTAACTAAGAA
1 TTCTTGTTTAACTAAGAA
*
31457277 TTCTTGTTTGACTAAGAA
1 TTCTTGTTTAACTAAGAA
31457295 ACAAATACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (18 bp):
TTCTTGTTTAACTAAGAA
Found at i:31459357 original size:14 final size:13
Alignment explanation
Indices: 31459325--31459358 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
31459315 GACAGAATAA
31459325 TTTTTTATTTTTC
1 TTTTTTATTTTTC
*
31459338 TTTTTTCATTTTTT
1 TTTTTT-ATTTTTC
31459352 TTTTTTA
1 TTTTTTA
31459359 CACTTTTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTATTTTTC
Found at i:31465904 original size:123 final size:123
Alignment explanation
Indices: 31465745--31466228 Score: 950
Period size: 123 Copynumber: 3.9 Consensus size: 123
31465735 TAGAATCCAG
*
31465745 CTTCCTCTTATTTGAAGAAAATTTTTCCTTAATGTCACTTGAATCCAACTTCACAACATCATCAT
1 CTTCCTCTTATTTGAAGACAATTTTTCCTTAATGTCACTTGAATCCAACTTCACAACATCATCAT
*
31465810 CACTATGTGTGTATTTCTTACATTCAACAGAATCCTCCATAATTGCACTTGAATCCCT
66 CACTATGTGTGCATTTCTTACATTCAACAGAATCCTCCATAATTGCACTTGAATCCCT
31465868 CTTCCTCTTATTTGAAGACAATTTTTCCTTAATGTCACTTGAATCCAACTTCACAACATCATCAT
1 CTTCCTCTTATTTGAAGACAATTTTTCCTTAATGTCACTTGAATCCAACTTCACAACATCATCAT
31465933 CACTATGTGTGCATTTCTTACATTCAACAGAATCCTCCATAATTGCACTTGAATCCCT
66 CACTATGTGTGCATTTCTTACATTCAACAGAATCCTCCATAATTGCACTTGAATCCCT
31465991 CTTCCTCTTATTTGAAGACAATTTTTCCTTAATGTCACTTGAATCCAACTTCACAACATCATCAT
1 CTTCCTCTTATTTGAAGACAATTTTTCCTTAATGTCACTTGAATCCAACTTCACAACATCATCAT
31466056 CACTATGTGTGCATTTCTTACATTCAACAGAATCCTCCATAATTGCACTTGAATCCCT
66 CACTATGTGTGCATTTCTTACATTCAACAGAATCCTCCATAATTGCACTTGAATCCCT
31466114 CTTCCTCTTATTTGAAGACAATTTTTCCTTAATGTCACTTGAATCCAACTTCACAACATCATCAT
1 CTTCCTCTTATTTGAAGACAATTTTTCCTTAATGTCACTTGAATCCAACTTCACAACATCATCAT
31466179 CACTATGTGTGCATTTCTTACATTCAACAGAATCCTCCATAATTGCACTT
66 CACTATGTGTGCATTTCTTACATTCAACAGAATCCTCCATAATTGCACTT
31466229 TTCACCTCAT
Statistics
Matches: 359, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
123 359 1.00
ACGTcount: A:0.29, C:0.26, G:0.08, T:0.37
Consensus pattern (123 bp):
CTTCCTCTTATTTGAAGACAATTTTTCCTTAATGTCACTTGAATCCAACTTCACAACATCATCAT
CACTATGTGTGCATTTCTTACATTCAACAGAATCCTCCATAATTGCACTTGAATCCCT
Found at i:31472662 original size:64 final size:65
Alignment explanation
Indices: 31472594--31472714 Score: 183
Period size: 65 Copynumber: 1.9 Consensus size: 65
31472584 ATGTATAATT
* * *
31472594 TGCAAGAAAA-TAAACATACTT-AAAATATCATAAAAATGCCAAAATAACACCAACTTATTATTT
1 TGCAAGAAAACGAAACATACTTAAAAACAACAT-AAAATGCCAAAATAACACCAACTTATTATTT
31472657 A
65 A
*
31472658 TGCAAGAAAACGAAACATACTTAAAAACAACATAAAATGCTAAAATAACACCAACTT
1 TGCAAGAAAACGAAACATACTTAAAAACAACATAAAATGCCAAAATAACACCAACTT
31472715 TTCTAATGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
64 10 0.20
65 33 0.65
66 8 0.16
ACGTcount: A:0.55, C:0.17, G:0.06, T:0.22
Consensus pattern (65 bp):
TGCAAGAAAACGAAACATACTTAAAAACAACATAAAATGCCAAAATAACACCAACTTATTATTTA
Found at i:31477707 original size:43 final size:43
Alignment explanation
Indices: 31477644--31477765 Score: 151
Period size: 44 Copynumber: 2.8 Consensus size: 43
31477634 GTACAACGCT
*
31477644 AATGTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCC
1 AATGTCCCAGACGTGGTCTTACATGTAATCATATATCGATGCC
* * *
31477687 ACTGTCCTAGACAG-GGTCTTACACT-TAAATCATAAATCGATGCC
1 AATGTCCCAGAC-GTGGTCTTACA-TGT-AATCATATATCGATGCC
*
31477731 AATGTCCCAGACGTGGTCCTACATG-AATCATATAT
1 AATGTCCCAGACGTGGTCTTACATGTAATCATATAT
31477766 AAGAATCCTA
Statistics
Matches: 66, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
42 9 0.14
43 22 0.33
44 35 0.53
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (43 bp):
AATGTCCCAGACGTGGTCTTACATGTAATCATATATCGATGCC
Found at i:31478892 original size:13 final size:13
Alignment explanation
Indices: 31478874--31478898 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31478864 TCAAACGATA
31478874 AAATTTTCACACG
1 AAATTTTCACACG
31478887 AAATTTTCACAC
1 AAATTTTCACAC
31478899 ATATAAATTA
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:31479195 original size:32 final size:32
Alignment explanation
Indices: 31479154--31479217 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
31479144 AGAGATTTTC
31479154 TTATTTCTTAATTCTTTAACCTCACTATCTAA
1 TTATTTCTTAATTCTTTAACCTCACTATCTAA
31479186 TTATTTCTTAATTCTTTAACCTCACTATCTAA
1 TTATTTCTTAATTCTTTAACCTCACTATCTAA
31479218 AATTCAGATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.22, G:0.00, T:0.50
Consensus pattern (32 bp):
TTATTTCTTAATTCTTTAACCTCACTATCTAA
Found at i:31487776 original size:29 final size:29
Alignment explanation
Indices: 31487735--31487794 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
31487725 ACTAATTAAA
*
31487735 TTAATTAATCTAAAATAACCTAACGAAAT
1 TTAATTAACCTAAAATAACCTAACGAAAT
* * *
31487764 TTAATTAACCTAAGATATCCTAATGAAAT
1 TTAATTAACCTAAAATAACCTAACGAAAT
31487793 TT
1 TT
31487795 CCTGTTCCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.35
Consensus pattern (29 bp):
TTAATTAACCTAAAATAACCTAACGAAAT
Found at i:31488399 original size:17 final size:16
Alignment explanation
Indices: 31488373--31488404 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
31488363 AAGAAATGAT
31488373 AAAATAAAAATTAAAG
1 AAAATAAAAATTAAAG
31488389 AAAACTAAAAATTAAA
1 AAAA-TAAAAATTAAA
31488405 AGTATGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAATAAAAATTAAAG
Found at i:31494080 original size:39 final size:39
Alignment explanation
Indices: 31494026--31494216 Score: 301
Period size: 39 Copynumber: 4.9 Consensus size: 39
31494016 AATGTTCGAG
31494026 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
* **
31494065 TGATACCCGGGCTAAGCCCGAAGGCAATTGTATGAGCTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
31494104 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
* * *
31494143 TGATACCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
* *
31494182 TGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCG
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCG
31494217 GGTTACCATA
Statistics
Matches: 139, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 122 0.88
40 17 0.12
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.22
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGCTA
Found at i:31495687 original size:29 final size:29
Alignment explanation
Indices: 31495645--31495717 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
31495635 CGGAGTGTTA
* *
31495645 CACTAAGTTTGCGAAGTAAAATTATCGAG
1 CACTAAGTGTGCGAAGTAAAACTATCGAG
31495674 CACTAAGTGTGCGAAGTAAAACTATCGAG
1 CACTAAGTGTGCGAAGTAAAACTATCGAG
31495703 CACTAAGTGTGCGAA
1 CACTAAGTGTGCGAA
31495718 TACAACAAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.23
Consensus pattern (29 bp):
CACTAAGTGTGCGAAGTAAAACTATCGAG
Found at i:31506068 original size:6 final size:6
Alignment explanation
Indices: 31506057--31506258 Score: 361
Period size: 6 Copynumber: 33.8 Consensus size: 6
31506047 GCCATGTTCA
31506057 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
31506105 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
31506153 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
* * * *
31506201 TATATC TATATC TATATC TATATA TTTAAC -ATATT TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
31506248 TATATC TATAT
1 TATATC TATAT
31506259 ATTTAACATA
Statistics
Matches: 187, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
5 2 0.01
6 185 0.99
ACGTcount: A:0.34, C:0.15, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATC
Found at i:31508307 original size:28 final size:27
Alignment explanation
Indices: 31508259--31508316 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
31508249 AATGAATCGA
* * *
31508259 CTAGTCCGATACTTTGTTTTTCCTTTAT
1 CTAGTCCGATACTTCGCTTTT-CTTAAT
31508287 CTAGATCCGA-ACTTCGCTTTTCTTAAT
1 CTAG-TCCGATACTTCGCTTTTCTTAAT
31508314 CTA
1 CTA
31508317 AATAATATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 8 0.31
28 13 0.50
29 5 0.19
ACGTcount: A:0.19, C:0.24, G:0.10, T:0.47
Consensus pattern (27 bp):
CTAGTCCGATACTTCGCTTTTCTTAAT
Found at i:31516924 original size:28 final size:29
Alignment explanation
Indices: 31516857--31516957 Score: 125
Period size: 28 Copynumber: 3.5 Consensus size: 29
31516847 ATAGTGAATC
*
31516857 CGCACACTTAGTGCTATATACATTC-AGCT
1 CGCACACTTAGTGCTATATA-ATTCAAACT
31516886 CGCACACTTAGTGCTATATAA-TCAAACT
1 CGCACACTTAGTGCTATATAATTCAAACT
* * * *
31516914 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA-TTCAAACT
31516944 CGCACACTTAGTGC
1 CGCACACTTAGTGC
31516958 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 23 0.36
29 20 0.31
30 19 0.30
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATAATTCAAACT
Found at i:31524608 original size:28 final size:29
Alignment explanation
Indices: 31524541--31524641 Score: 125
Period size: 28 Copynumber: 3.5 Consensus size: 29
31524531 ATAGTGAATC
*
31524541 CGCACACTTAGTGCTATATACATTC-AGCT
1 CGCACACTTAGTGCTATATA-ATTCAAACT
31524570 CGCACACTTAGTGCTATATAA-TCAAACT
1 CGCACACTTAGTGCTATATAATTCAAACT
* * * *
31524598 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA-TTCAAACT
31524628 CGCACACTTAGTGC
1 CGCACACTTAGTGC
31524642 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 23 0.36
29 20 0.31
30 19 0.30
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATAATTCAAACT
Found at i:31530478 original size:16 final size:16
Alignment explanation
Indices: 31530457--31530489 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
31530447 GTAAGCTAAC
31530457 TTAGCTTAGTAAGCCT
1 TTAGCTTAGTAAGCCT
31530473 TTAGCTTAGTAAGCCT
1 TTAGCTTAGTAAGCCT
31530489 T
1 T
31530490 AAGGAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (16 bp):
TTAGCTTAGTAAGCCT
Found at i:31533728 original size:39 final size:39
Alignment explanation
Indices: 31533674--31533836 Score: 272
Period size: 39 Copynumber: 4.2 Consensus size: 39
31533664 TGTGTATGAA
*
31533674 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
31533713 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* *
31533752 CGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* *
31533791 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
31533831 TGTGCG
1 TGTGCG
31533837 GTTACCATAA
Statistics
Matches: 116, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
39 99 0.85
40 17 0.15
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.25
Consensus pattern (39 bp):
TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:31533862 original size:39 final size:39
Alignment explanation
Indices: 31533674--31533866 Score: 262
Period size: 39 Copynumber: 4.9 Consensus size: 39
31533664 TGTGTATGAA
* *
31533674 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
*
31533713 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
*
31533752 CGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
31533791 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGCAAT
** * *
31533831 TGTGCG-GTTACCATAACCGGGCTATGTCCCGAAGGC
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGC
31533867 GTTTGAACGA
Statistics
Matches: 140, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
39 123 0.88
40 17 0.12
ACGTcount: A:0.23, C:0.22, G:0.32, T:0.24
Consensus pattern (39 bp):
TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:31539915 original size:29 final size:29
Alignment explanation
Indices: 31539881--31540012 Score: 140
Period size: 29 Copynumber: 4.6 Consensus size: 29
31539871 TACTCGATTT
** * *
31539881 CGCACACTTAGTGCCATGCGATTT-AAGCC
1 CGCACACTTAGTGCCAT-ATATTTCCAGCA
* **** * *
31539910 CGCACACATAGTGCCATGCCCTTCGAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
31539939 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
31539968 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
31539997 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
31540013 ATCTCGTCAC
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
28 2 0.02
29 84 0.98
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:31547628 original size:29 final size:29
Alignment explanation
Indices: 31547594--31547725 Score: 140
Period size: 29 Copynumber: 4.6 Consensus size: 29
31547584 TACTCGATTT
** * *
31547594 CGCACACTTAGTGCCATGCGATTT-AAGCC
1 CGCACACTTAGTGCCAT-ATATTTCCAGCA
* **** * *
31547623 CGCACACATAGTGCCATGCCCTTCGAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
31547652 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
31547681 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
31547710 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
31547726 ATCTCGTCAC
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
28 2 0.02
29 84 0.98
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:31554637 original size:16 final size:19
Alignment explanation
Indices: 31554616--31554654 Score: 57
Period size: 16 Copynumber: 2.2 Consensus size: 19
31554606 ATCAAGGTTC
31554616 ATTTAATT-TA-TTC-ACT
1 ATTTAATTCTACTTCTACT
31554632 ATTTAATTCTACTTCTACT
1 ATTTAATTCTACTTCTACT
31554651 ATTT
1 ATTT
31554655 TTAGTGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 8 0.40
17 2 0.10
18 3 0.15
19 7 0.35
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTAATTCTACTTCTACT
Found at i:31556777 original size:71 final size:71
Alignment explanation
Indices: 31556691--31556854 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
31556681 CGATTTGTCT
31556691 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
31556756 CTTTCA
66 CTTTCA
31556762 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
31556827 CTTTCA
66 CTTTCA
31556833 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
31556855 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:31556892 original size:71 final size:70
Alignment explanation
Indices: 31556691--31556888 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
31556681 CGATTTGTCT
* * * *
31556691 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
31556756 CTTTCA
65 CTTTCA
* * * *
31556762 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
31556827 CTTTCA
65 CTTTCA
* *
31556833 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
31556889 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:31564349 original size:71 final size:71
Alignment explanation
Indices: 31564263--31564426 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
31564253 CGATTTGTCT
31564263 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
31564328 CTTTCA
66 CTTTCA
31564334 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
31564399 CTTTCA
66 CTTTCA
31564405 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
31564427 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:31564464 original size:71 final size:70
Alignment explanation
Indices: 31564263--31564460 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
31564253 CGATTTGTCT
* * * *
31564263 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
31564328 CTTTCA
65 CTTTCA
* * * *
31564334 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
31564399 CTTTCA
65 CTTTCA
* *
31564405 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
31564461 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:31572815 original size:90 final size:95
Alignment explanation
Indices: 31572655--31572877 Score: 248
Period size: 93 Copynumber: 2.4 Consensus size: 95
31572645 CCTCATCGAG
* * * * *
31572655 GCCGATGCCATAT-CTCAGACATGGTCTTACACTAGTTCTTGCATATCCATG-TCGATACCATGT
1 GCCGATGCCATGTCCT-AGACATGGTCTTACACT-G-GCTTACATATCGAGGCT-GATACCATGT
* *
31572718 CCTGGACATGGT-TTACACTGACA-T-GTCTC-GT
62 CCCGGACAT-GTCTTACACTGACACTCGTCTCAAT
31572749 AGCCGATG-CATGTCCTAGACAT-GTCTTACACTGGCTTACATATCGAGGCTGATA-CATGTCCC
1 -GCCGATGCCATGTCCTAGACATGGTCTTACACTGGCTTACATATCGAGGCTGATACCATGTCCC
*
31572811 GGACATGTCTTACACTGGCACTCGTCTCAAT
65 GGACATGTCTTACACTGACACTCGTCTCAAT
*
31572842 GTCGATGCCATGTCCTAGACATGGTCTTACACTGGC
1 GCCGATGCCATGTCCTAGACATGGTCTTACACTGGC
31572878 ACACAAATTA
Statistics
Matches: 111, Mismatches: 9, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
89 2 0.02
90 23 0.21
91 16 0.14
92 13 0.12
93 25 0.23
94 23 0.21
95 9 0.08
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (95 bp):
GCCGATGCCATGTCCTAGACATGGTCTTACACTGGCTTACATATCGAGGCTGATACCATGTCCCG
GACATGTCTTACACTGACACTCGTCTCAAT
Found at i:31589190 original size:12 final size:13
Alignment explanation
Indices: 31589173--31589210 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
31589163 ATCCTGGAAT
31589173 ATTAAG-ACAAGA
1 ATTAAGAACAAGA
*
31589185 ATTAAGAACACATA
1 ATTAAGAACA-AGA
31589199 ATTAAGAACAAG
1 ATTAAGAACAAG
31589211 TCAAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 6 0.27
13 4 0.18
14 12 0.55
ACGTcount: A:0.58, C:0.11, G:0.13, T:0.18
Consensus pattern (13 bp):
ATTAAGAACAAGA
Found at i:31590885 original size:12 final size:12
Alignment explanation
Indices: 31590868--31590892 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31590858 CAAAAATGTA
31590868 AAAATCATCAAG
1 AAAATCATCAAG
31590880 AAAATCATCAAG
1 AAAATCATCAAG
31590892 A
1 A
31590893 TCACTTACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAATCATCAAG
Found at i:31594847 original size:40 final size:41
Alignment explanation
Indices: 31594797--31594933 Score: 152
Period size: 40 Copynumber: 3.4 Consensus size: 41
31594787 ATATATATAA
* *
31594797 ATGGCACTTAGTGTGCGATTTGAGATAGCTTCGGCTAT-AT
1 ATGGCACTTAGTGTGCGATTTAAAATAGCTTCGGCTATGAT
* * * *
31594837 ATGGCACTTAGTATGCTATTCAAAATAGCTTCAGCTATGA-
1 ATGGCACTTAGTGTGCGATTTAAAATAGCTTCGGCTATGAT
* * * *
31594877 AAGGCACTTAGTGTGCGAGATTAAAATAGCTTTGGCTATGTT
1 ATGGCACTTAGTGTGCGA-TTTAAAATAGCTTCGGCTATGAT
*
31594919 TTGGCACTTAGTGTG
1 ATGGCACTTAGTGTG
31594934 TGAGAATTCG
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
40 47 0.60
41 18 0.23
42 13 0.17
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (41 bp):
ATGGCACTTAGTGTGCGATTTAAAATAGCTTCGGCTATGAT
Found at i:31596194 original size:20 final size:19
Alignment explanation
Indices: 31596165--31596207 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
31596155 TGTGCCCCTT
31596165 GTTTGAGAAAAGCTTTC-TAA
1 GTTTGAGAAAA--TTTCTTAA
*
31596185 GTTTGTGAAAATTTCTTAA
1 GTTTGAGAAAATTTCTTAA
31596204 GTTT
1 GTTT
31596208 TCGGTTTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 4 0.19
19 7 0.33
20 10 0.48
ACGTcount: A:0.30, C:0.07, G:0.19, T:0.44
Consensus pattern (19 bp):
GTTTGAGAAAATTTCTTAA
Found at i:31596951 original size:167 final size:167
Alignment explanation
Indices: 31596675--31596985 Score: 532
Period size: 167 Copynumber: 1.9 Consensus size: 167
31596665 AATGAAACAC
*
31596675 AAAGTAGGGGCGTTTTGGTCTACACAATTGAACGTGAAGCTCAGGAACGTTAGCTAACCTATAGT
1 AAAGTAGGGGCGTTTTGGTCTACACAATTGAACGTGAAGCTCAGGAACATTAGCTAACCTATAGT
* *
31596740 TAAACATGACAGCTACCTAAAAGCTATAAATAGGCTTCTTTGGCACAGATTATGGAAACATTTCA
66 TAAACATGACAGCTACCTAAAAGCTATAAATAGGCTCCTTTGGCACACATTATGGAAACATTTCA
31596805 TTAGCTTAGATTCTATAAATAGCTGTAAATAAGCTAT
131 TTAGCTTAGATTCTATAAATAGCTGTAAATAAGCTAT
* * **
31596842 AAAGTAGGGGCGTTTTGGTCTACACAATTGAGCTTGAAGCTTGGGAACATTAGCTAACCTATAGT
1 AAAGTAGGGGCGTTTTGGTCTACACAATTGAACGTGAAGCTCAGGAACATTAGCTAACCTATAGT
** *
31596907 TAAGGATGATAGCTACCTAAAAGCTATAAATAGGCTCCTTTGGCACACATTATGGAAACATTTCA
66 TAAACATGACAGCTACCTAAAAGCTATAAATAGGCTCCTTTGGCACACATTATGGAAACATTTCA
31596972 TTAGCTTAGATTCT
131 TTAGCTTAGATTCT
31596986 CTCATTAGGT
Statistics
Matches: 134, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
167 134 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (167 bp):
AAAGTAGGGGCGTTTTGGTCTACACAATTGAACGTGAAGCTCAGGAACATTAGCTAACCTATAGT
TAAACATGACAGCTACCTAAAAGCTATAAATAGGCTCCTTTGGCACACATTATGGAAACATTTCA
TTAGCTTAGATTCTATAAATAGCTGTAAATAAGCTAT
Found at i:31606192 original size:30 final size:30
Alignment explanation
Indices: 31606158--31606218 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
31606148 TCCTTAACTC
31606158 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
31606188 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
31606218 A
1 A
31606219 GGCTCGGAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:31610576 original size:30 final size:30
Alignment explanation
Indices: 31610542--31610602 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
31610532 TCCTTAACTC
31610542 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
31610572 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
31610602 A
1 A
31610603 GGCTCAGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:31621813 original size:80 final size:80
Alignment explanation
Indices: 31621729--31621877 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
31621719 TATGGTAACC
* * * *
31621729 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
31621793 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
31621809 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
31621874 CCGG
66 CCGG
31621878 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:31621819 original size:40 final size:38
Alignment explanation
Indices: 31621770--31621877 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
31621760 ATCACGATTT
*
31621770 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
31621810 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
31621850 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
31621878 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:31627419 original size:30 final size:30
Alignment explanation
Indices: 31627383--31627513 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
31627373 GACAAGATTG
* * * * *
31627383 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
31627413 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
31627441 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
31627471 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
31627500 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
31627514 GATTCACTAT
Statistics
Matches: 92, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 20 0.22
30 46 0.50
31 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:31627474 original size:58 final size:58
Alignment explanation
Indices: 31627383--31627513 Score: 174
Period size: 58 Copynumber: 2.2 Consensus size: 58
31627373 GACAAGATTG
* * * * * *
31627383 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTG-ATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAG-CTGAAATATATA
*
31627441 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTG-AAATATATA
31627500 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
31627514 GATTCACTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
57 2 0.03
58 41 0.64
59 21 0.33
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (58 bp):
GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTGAAATATATA
Found at i:31635372 original size:30 final size:30
Alignment explanation
Indices: 31635336--31635466 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
31635326 GACAAGATTG
* * * * *
31635336 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
31635366 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
31635394 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
31635424 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
31635453 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
31635467 GATTCACTAT
Statistics
Matches: 92, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 20 0.22
30 46 0.50
31 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:31635427 original size:58 final size:58
Alignment explanation
Indices: 31635336--31635466 Score: 174
Period size: 58 Copynumber: 2.2 Consensus size: 58
31635326 GACAAGATTG
* * * * * *
31635336 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTG-ATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAG-CTGAAATATATA
*
31635394 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTG-AAATATATA
31635453 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
31635467 GATTCACTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
57 2 0.03
58 41 0.64
59 21 0.33
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (58 bp):
GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTGAAATATATA
Found at i:31641004 original size:80 final size:80
Alignment explanation
Indices: 31640920--31641067 Score: 181
Period size: 80 Copynumber: 1.9 Consensus size: 80
31640910 TATGGTAACC
* * * *
31640920 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
31640984 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
31641000 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
31641065 CCG
66 CCG
31641068 TTATAATTTC
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 55 0.98
ACGTcount: A:0.23, C:0.30, G:0.24, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:31641052 original size:40 final size:39
Alignment explanation
Indices: 31640961--31641067 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 39
31640951 ATCACGATTT
*
31640961 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATAGAATGACTA
*
31641001 GCACGAATGCCTTCGGGTCTTAGCCCGGAT-GTA-GCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATAGAATG--ACTA
*
31641041 GCACAATTGCCTTCGGGTCTTAACCCG
1 GCACAA-TGCCTTCGGGTCTTAGCCCG
31641068 TTATAATTTC
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 55 0.92
ACGTcount: A:0.21, C:0.30, G:0.25, T:0.23
Consensus pattern (39 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTA
Found at i:31643998 original size:17 final size:17
Alignment explanation
Indices: 31643976--31644015 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
31643966 ATCACTTACC
*
31643976 GTGTGTCACGCAC-AGCT
1 GTGTGTCACACACGA-CT
31643993 GTGTGTCACACACGACT
1 GTGTGTCACACACGACT
31644010 GTGTGT
1 GTGTGT
31644016 TAGCCCGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.17, C:0.25, G:0.30, T:0.28
Consensus pattern (17 bp):
GTGTGTCACACACGACT
Found at i:31644939 original size:19 final size:20
Alignment explanation
Indices: 31644915--31644957 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
31644905 GTCCCAAAGC
*
31644915 CATTCAA-TTTATACAATGT
1 CATTCAACTTAATACAATGT
*
31644934 CATTCAACTTAATTCAATGT
1 CATTCAACTTAATACAATGT
31644954 CATT
1 CATT
31644958 TAATCAGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.42
Consensus pattern (20 bp):
CATTCAACTTAATACAATGT
Found at i:31646535 original size:30 final size:30
Alignment explanation
Indices: 31646499--31646560 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
31646489 CCTTTTCATA
31646499 TTTCATAATTCATAACACTGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGCCGAAGCCT
* ** *
31646529 TTTCATATTTCATATTACTGGGCGAAGCCT
1 TTTCATAATTCATAACACTGGCCGAAGCCT
31646559 TT
1 TT
31646561 ACTGTAAACG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.37
Consensus pattern (30 bp):
TTTCATAATTCATAACACTGGCCGAAGCCT
Found at i:31646809 original size:26 final size:27
Alignment explanation
Indices: 31646773--31646849 Score: 119
Period size: 23 Copynumber: 3.0 Consensus size: 27
31646763 GCCTAGCCTC
31646773 TTTTAATAACTGGGGCA-AAGCCCTTT
1 TTTTAATAACTGGGGCATAAGCCCTTT
31646799 TTTTAATAACTGGGGCATAAGCCC---
1 TTTTAATAACTGGGGCATAAGCCCTTT
31646823 -TTTAATAACTGGGGCATAAGCCCTTT
1 TTTTAATAACTGGGGCATAAGCCCTTT
31646849 T
1 T
31646850 GCACTTCCTC
Statistics
Matches: 46, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
23 23 0.50
26 17 0.37
27 6 0.13
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.34
Consensus pattern (27 bp):
TTTTAATAACTGGGGCATAAGCCCTTT
Found at i:31646921 original size:9 final size:9
Alignment explanation
Indices: 31646907--31646963 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
31646897 ATCTCGTGTG
31646907 CATATCATA
1 CATATCATA
31646916 CATATCATGTA
1 CATATCA--TA
31646927 CATATCATA
1 CATATCATA
** *
31646936 CATGCCATGTG
1 CATATCA--TA
31646947 CATATCATA
1 CATATCATA
31646956 CATATCAT
1 CATATCAT
31646964 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.33
Consensus pattern (9 bp):
CATATCATA
Found at i:31646930 original size:20 final size:20
Alignment explanation
Indices: 31646907--31646965 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
31646897 ATCTCGTGTG
31646907 CATATCATACATATCATGTA
1 CATATCATACATATCATGTA
** *
31646927 CATATCATACATGCCATGTG
1 CATATCATACATATCATGTA
31646947 CATATCATACATATCATGT
1 CATATCATACATATCATGT
31646966 TTATCAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.34
Consensus pattern (20 bp):
CATATCATACATATCATGTA
Found at i:31647030 original size:25 final size:25
Alignment explanation
Indices: 31647002--31647049 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
31646992 ATATATAAAC
* * *
31647002 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
31647027 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
31647050 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:31653840 original size:40 final size:40
Alignment explanation
Indices: 31653775--31654018 Score: 303
Period size: 40 Copynumber: 6.1 Consensus size: 40
31653765 CGGAATACAA
* ** * * *
31653775 CCGGATATAACCACACGCACGAATGCCCTCGGGTCTTAGC
1 CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
*
31653815 CCGGATATAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
31653855 CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
31653895 CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
* * * * *
31653935 CCGGATATAGTC-ACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATA-ACAACTTGCACAAATGCCTTCGGGTATTAGC
** * * *
31653975 CCGGATATAATTACTAGCATAAATGTCTTCGGG-ACTTAGC
1 CCGGATATAACAACTTGCACAAATGCCTTCGGGTA-TTAGC
31654015 CCGG
1 CCGG
31654019 GTATCATTCA
Statistics
Matches: 182, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
40 181 0.99
41 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
Found at i:31654173 original size:64 final size:64
Alignment explanation
Indices: 31654105--31654293 Score: 142
Period size: 64 Copynumber: 3.0 Consensus size: 64
31654095 GAACACAAAC
31654105 ATATCACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACAT
1 ATATCACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACAT
* * * * *** * *** * ** * *
31654169 ATATCAATA--ATCATTACACATCCATATTTCATTTTC-GTTA-C--T--AAGGCTCAAACACAA
1 ATATCACTAGCATAATTGC-CTTCGGGACTT-A-GCCCGGGTACCATTCAAATACTCATACACAC
*
31654226 AC
63 AT
31654228 ATATCACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACAT
1 ATATCACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACAT
31654292 AT
1 AT
31654294 GTCAATAATC
Statistics
Matches: 80, Mismatches: 34, Indels: 22
0.59 0.25 0.16
Matches are distributed among these distances:
58 1 0.01
59 24 0.30
60 7 0.09
61 7 0.09
62 7 0.09
63 7 0.09
64 26 0.32
65 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (64 bp):
ATATCACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACAT
Found at i:31654206 original size:123 final size:123
Alignment explanation
Indices: 31653987--31654325 Score: 597
Period size: 123 Copynumber: 2.8 Consensus size: 123
31653977 GGATATAATT
* * * * * * *
31653987 ACTAGCATAAATGTCTTCGGGACTTAGCCCGGGTATCATTCAATTGCTCATGCACACATAAATCA
1 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
*
31654052 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCGAACACAAACATATC
66 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
31654110 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
1 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
31654175 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
66 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
*
31654233 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATGTCA
1 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
31654298 ATAATCATTACACATCCATATTTCATTT
66 ATAATCATTACACATCCATATTTCATTT
31654326 CACATAATTC
Statistics
Matches: 207, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
123 207 1.00
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.30
Consensus pattern (123 bp):
ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
Found at i:31660916 original size:40 final size:40
Alignment explanation
Indices: 31660851--31661094 Score: 294
Period size: 40 Copynumber: 6.1 Consensus size: 40
31660841 CTGAATACAA
* ** * * *
31660851 CCGGATATAACCACACGCACGAATGCCCTCGGGTCTTAGC
1 CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
*
31660891 CCGGATATAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
31660931 CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
31660971 CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
* * * * * *
31661011 TCGGATATAGTC-ACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATA-ACAACTTGCACAAATGCCTTCGGGTATTAGC
** * * *
31661051 CCGGATATAATTACTAGCATAAATGTCTTCGGG-ACTTAGC
1 CCGGATATAACAACTTGCACAAATGCCTTCGGGTA-TTAGC
31661091 CCGG
1 CCGG
31661095 GTATCATTCA
Statistics
Matches: 180, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
40 179 0.99
41 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.25
Consensus pattern (40 bp):
CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
Found at i:31661282 original size:123 final size:123
Alignment explanation
Indices: 31661063--31661401 Score: 597
Period size: 123 Copynumber: 2.8 Consensus size: 123
31661053 GGATATAATT
* * * * * * **
31661063 ACTAGCATAAATGTCTTCGGGACTTAGCCCGGGTATCATTCAATTGCTCATGCACACATAAATCA
1 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATGTCA
*
31661128 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCGAACACAAACATATC
66 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
31661186 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATGTCA
1 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATGTCA
31661251 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
66 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
31661309 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATGTCA
1 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATGTCA
31661374 ATAATCATTACACATCCATATTTCATTT
66 ATAATCATTACACATCCATATTTCATTT
31661402 CACATAATTC
Statistics
Matches: 207, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
123 207 1.00
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.30
Consensus pattern (123 bp):
ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATGTCA
ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
Found at i:31664896 original size:29 final size:30
Alignment explanation
Indices: 31664863--31664923 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
31664853 CCTTTTCATA
31664863 TTTCATAATTCATAACACT-GCCGAAGCCT
1 TTTCATAATTCATAACACTGGCCGAAGCCT
* ** *
31664892 TTTCATATTTCATATTACTGGGCGAAGCCT
1 TTTCATAATTCATAACACTGGCCGAAGCCT
31664922 TT
1 TT
31664924 ACTGTAAACG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (30 bp):
TTTCATAATTCATAACACTGGCCGAAGCCT
Found at i:31665192 original size:23 final size:24
Alignment explanation
Indices: 31665116--31665234 Score: 172
Period size: 24 Copynumber: 4.9 Consensus size: 24
31665106 GCTTTATCAT
*
31665116 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
31665141 ATAACTGGGGCA-AAGCCCTTTTTTA
1 ATAACTGGGGCATAAGCCC--TTTTA
31665166 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
31665189 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
31665213 ATAACTGGGGCATAAGCCCTTT
1 ATAACTGGGGCATAAGCCCTTT
31665235 GCACTTCCTC
Statistics
Matches: 88, Mismatches: 1, Indels: 11
0.88 0.01 0.11
Matches are distributed among these distances:
23 24 0.27
24 33 0.38
25 25 0.28
26 6 0.07
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:31665223 original size:47 final size:47
Alignment explanation
Indices: 31665137--31665234 Score: 171
Period size: 47 Copynumber: 2.1 Consensus size: 47
31665127 CCTAGCCTCT
31665137 TTTAATAACTGGGGCAAAGCCCTTTTTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCAAAGCCC-TTTTTAATAACTGGGGCATAAGCCC
31665185 TTTAATAACTGGGGCATAAGCCC-TTTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCA-AAGCCCTTTTTAATAACTGGGGCATAAGCCC
31665232 TTT
1 TTT
31665235 GCACTTCCTC
Statistics
Matches: 49, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
47 27 0.55
48 16 0.33
49 6 0.12
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (47 bp):
TTTAATAACTGGGGCAAAGCCCTTTTTAATAACTGGGGCATAAGCCC
Found at i:31665306 original size:9 final size:9
Alignment explanation
Indices: 31665292--31665348 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
31665282 ATCTCGTGTG
31665292 CATATCATA
1 CATATCATA
*
31665301 CATATCATGTG
1 CATATCA--TA
31665312 CATATCATA
1 CATATCATA
* *
31665321 CATGTCATGTG
1 CATATCA--TA
31665332 CATATCATA
1 CATATCATA
31665341 CATATCAT
1 CATATCAT
31665349 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:31665311 original size:20 final size:20
Alignment explanation
Indices: 31665288--31665350 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
31665278 GAACATCTCG
31665288 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
31665308 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
31665328 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
31665348 TGT
1 TGT
31665351 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:31665415 original size:25 final size:25
Alignment explanation
Indices: 31665387--31665434 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
31665377 ATATATAAAC
* * *
31665387 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
31665412 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
31665435 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:31672933 original size:29 final size:30
Alignment explanation
Indices: 31672900--31672961 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
31672890 CCTTTTCATA
31672900 TTTCATAATTCATAACACTGGG-GAAGCCT
1 TTTCATAATTCATAACACTGGGCGAAGCCT
* **
31672929 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGG-CGAAGCCT
31672960 TT
1 TT
31672962 ACTGTAAACG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 19 0.68
31 9 0.32
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (30 bp):
TTTCATAATTCATAACACTGGGCGAAGCCT
Found at i:31673199 original size:23 final size:24
Alignment explanation
Indices: 31673154--31673272 Score: 172
Period size: 24 Copynumber: 5.0 Consensus size: 24
31673144 GCTTTATCAT
* *
31673154 ATAACTGGAGGCCT-AGCCTTTTTA
1 ATAACTGG-GGCATAAGCCCTTTTA
31673178 ATAACTGGGGCA-AAGCCCTTTTTTA
1 ATAACTGGGGCATAAGCCC--TTTTA
31673203 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
31673226 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
31673250 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
31673273 GCACTTCCTC
Statistics
Matches: 88, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
23 30 0.34
24 35 0.40
25 17 0.19
26 6 0.07
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:31673260 original size:47 final size:47
Alignment explanation
Indices: 31673174--31673271 Score: 171
Period size: 47 Copynumber: 2.1 Consensus size: 47
31673164 GCCTAGCCTT
31673174 TTTAATAACTGGGGCAAAGCCCTTTTTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCAAAGCCC-TTTTTAATAACTGGGGCATAAGCCC
31673222 TTTAATAACTGGGGCATAAGCCC-TTTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCA-AAGCCCTTTTTAATAACTGGGGCATAAGCCC
31673269 TTT
1 TTT
31673272 TGCACTTCCT
Statistics
Matches: 49, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
47 27 0.55
48 16 0.33
49 6 0.12
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (47 bp):
TTTAATAACTGGGGCAAAGCCCTTTTTAATAACTGGGGCATAAGCCC
Found at i:31673344 original size:9 final size:9
Alignment explanation
Indices: 31673330--31673386 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
31673320 ATCTCGTGTG
31673330 CATATCATA
1 CATATCATA
*
31673339 CATATCATGTG
1 CATATCA--TA
31673350 CATATCATA
1 CATATCATA
* *
31673359 CATGTCATGTG
1 CATATCA--TA
31673370 CATATCATA
1 CATATCATA
31673379 CATATCAT
1 CATATCAT
31673387 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Done.