Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000295.1 Hibiscus syriacus cultivar Beakdansim tig00000541_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2017499
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 7 of 9
Found at i:1266195 original size:17 final size:17
Alignment explanation
Indices: 1266173--1266216 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
1266163 TATGGAATTG
1266173 GATTTCAATTTCTGACA
1 GATTTCAATTTCTGACA
1266190 GATTTCAATTTCTGACA
1 GATTTCAATTTCTGACA
1266207 GATTTCAATT
1 GATTTCAATT
1266217 CCTTCACAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (17 bp):
GATTTCAATTTCTGACA
Found at i:1266227 original size:18 final size:17
Alignment explanation
Indices: 1266173--1266236 Score: 83
Period size: 17 Copynumber: 3.7 Consensus size: 17
1266163 TATGGAATTG
*
1266173 GATTTCAATTTCTGACA
1 GATTTCAATTCCTGACA
*
1266190 GATTTCAATTTCTGACA
1 GATTTCAATTCCTGACA
*
1266207 GATTTCAATTCCTTCACA
1 GATTTCAATTCC-TGACA
*
1266225 GATTCCAATTCC
1 GATTTCAATTCC
1266237 CTCAGAAACA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
17 28 0.65
18 15 0.35
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.39
Consensus pattern (17 bp):
GATTTCAATTCCTGACA
Found at i:1269034 original size:23 final size:22
Alignment explanation
Indices: 1268987--1269054 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
1268977 ATATAATATC
*
1268987 ATATATTATTGTAATA-TAATTAA
1 ATATATTATTATAATATTAA--AA
1269010 ATATATTATTATAATATTGAAAA
1 ATATATTATTATAATATT-AAAA
* *
1269033 ATATAATATTATATTATTAAAA
1 ATATATTATTATAATATTAAAA
1269055 TTATTAATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
22 4 0.10
23 33 0.82
24 1 0.03
25 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (22 bp):
ATATATTATTATAATATTAAAA
Found at i:1269054 original size:21 final size:21
Alignment explanation
Indices: 1269000--1269097 Score: 71
Period size: 23 Copynumber: 4.6 Consensus size: 21
1268990 TATTATTGTA
* *
1269000 ATATAATT-AAATATATTATT
1 ATATTATTAAAATATAATATT
*
1269020 ATAATATTGAAAAATATAATATT
1 ATATTATT--AAAATATAATATT
*
1269043 ATATTATTAAAATTATTAATAAAT
1 ATATTATTAAAA-TA-TAAT-ATT
1269067 ATATT-TTAATAATA-AATATT
1 ATATTATTAA-AATATAATATT
1269087 -T-TTATTAAAAT
1 ATATTATTAAAAT
1269098 GGTAGTAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
18 5 0.08
19 5 0.08
20 8 0.12
21 7 0.11
22 2 0.03
23 28 0.44
24 9 0.14
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (21 bp):
ATATTATTAAAATATAATATT
Found at i:1269079 original size:17 final size:16
Alignment explanation
Indices: 1269059--1269090 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1269049 TTAAAATTAT
1269059 TAATAAATATATTTTAA
1 TAATAAATAT-TTTTAA
1269076 TAATAAATATTTTTA
1 TAATAAATATTTTTA
1269091 TTAAAATGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATAAATATTTTTAA
Found at i:1270346 original size:3 final size:3
Alignment explanation
Indices: 1270338--1270367 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1270328 CTATCGATCA
*
1270338 ATC ATC ATC ATC ATC ATC ATT ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1270368 CGCTGCCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:1271776 original size:51 final size:51
Alignment explanation
Indices: 1271671--1271777 Score: 128
Period size: 51 Copynumber: 2.1 Consensus size: 51
1271661 AGATTTATTG
* * * *
1271671 TTTTATTAGGAATTAAGATTGAGTTAAAACATTATTCTTAGTTTATTATTA
1 TTTTATTAGGAATTAAGATAGAATTAAAACATTATTCTTAGTTCATTATAA
* *
1271722 TTTTATTAGGAATTAGGATAGAATTGAAACATTATAT-TTA-TTCATTAGTAA
1 TTTTATTAGGAATTAAGATAGAATTAAAACATTAT-TCTTAGTTCATTA-TAA
1271773 TTTTA
1 TTTTA
1271778 CAACAAGGAC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
50 6 0.12
51 41 0.85
52 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.48
Consensus pattern (51 bp):
TTTTATTAGGAATTAAGATAGAATTAAAACATTATTCTTAGTTCATTATAA
Found at i:1273143 original size:51 final size:51
Alignment explanation
Indices: 1272997--1273167 Score: 260
Period size: 51 Copynumber: 3.4 Consensus size: 51
1272987 ATCATTTATC
* * * *
1272997 CCATAAGCTCGTAAGC-T-TA--TTTTACTAAAATACTTACCGTTTAAAATT
1 CCATAAGCTCGTAAGCTTATATTTTTTTCCAATATACTTACCATTT-AAATT
1273045 CCATAAGCTCGTAAGCTTATATTTTTTTTCCAATATACTTACCATTTAAATT
1 CCATAAGCTCGTAAGCTTATA-TTTTTTTCCAATATACTTACCATTTAAATT
1273097 CCATAAGCTCGTAAGCTTATATTTTTTTCCAATATACTTACCATTTAAATT
1 CCATAAGCTCGTAAGCTTATATTTTTTTCCAATATACTTACCATTTAAATT
1273148 CCATAAGCTCGTAAGCTTAT
1 CCATAAGCTCGTAAGCTTAT
1273168 TTTACCCATA
Statistics
Matches: 114, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
48 16 0.14
49 1 0.01
50 2 0.02
51 50 0.44
52 26 0.23
53 19 0.17
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (51 bp):
CCATAAGCTCGTAAGCTTATATTTTTTTCCAATATACTTACCATTTAAATT
Found at i:1273362 original size:40 final size:40
Alignment explanation
Indices: 1273318--1273439 Score: 244
Period size: 40 Copynumber: 3.0 Consensus size: 40
1273308 ACCGTAGTGC
1273318 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1273358 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1273398 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1273438 TA
1 TA
1273440 TAAACCTGCA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1276086 original size:2 final size:2
Alignment explanation
Indices: 1276079--1276164 Score: 172
Period size: 2 Copynumber: 43.0 Consensus size: 2
1276069 TCATGCGTAC
1276079 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1276121 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1276163 AT
1 AT
1276165 CGTGAGTTAT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1276626 original size:11 final size:12
Alignment explanation
Indices: 1276599--1276625 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1276589 CATGGCAACT
1276599 AAAATTAATACA
1 AAAATTAATACA
1276611 AAAATTAATACA
1 AAAATTAATACA
1276623 AAA
1 AAA
1276626 TACGGGACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAATTAATACA
Found at i:1277797 original size:21 final size:19
Alignment explanation
Indices: 1277773--1277815 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1277763 AGTAATAATC
*
1277773 ATAATAATAATACTATAGTAT
1 ATAATAATAA-A-TATAATAT
1277794 ATAATAATAAATATAATAT
1 ATAATAATAAATATAATAT
1277813 ATA
1 ATA
1277816 TTTTAATCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.48
20 1 0.05
21 10 0.48
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (19 bp):
ATAATAATAAATATAATAT
Found at i:1277816 original size:21 final size:21
Alignment explanation
Indices: 1277765--1277816 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
1277755 ATGATATTAG
1277765 TAATA-ATCATAATAATAATAC
1 TAATATAT-ATAATAATAATAC
1277786 T-ATAGTATATAATAATAAATA-
1 TAATA-TATATAATAAT-AATAC
1277807 TAATATATAT
1 TAATATATAT
1277817 TTTAATCCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
20 3 0.11
21 15 0.56
22 9 0.33
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (21 bp):
TAATATATATAATAATAATAC
Found at i:1278079 original size:110 final size:110
Alignment explanation
Indices: 1277942--1278353 Score: 666
Period size: 110 Copynumber: 3.7 Consensus size: 110
1277932 TCGTTGGATT
1277942 GAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCGTGGATGAGTTCTTCTCATTATGAACTCT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCGTGGATGAGTTCTTCTCATTATGAACTCT
* * * * * * *
1278007 TCACTGAAAATATTGAGT-CACCTATTTCTGTGGTGGACTTGAAAG
66 CCATTGGAAATGTTGA-TCCATCTCTTTCTGTGATGGACTTGAAAG
*
1278052 GAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCGTGTATGAGTTCTTCTCATTATGAACTCT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCGTGGATGAGTTCTTCTCATTATGAACTCT
*
1278117 CCATTGGAAATGTTGATCCATCTCTTTCTGTGATGGTCTTGAAAG
66 CCATTGGAAATGTTGATCCATCTCTTTCTGTGATGGACTTGAAAG
*
1278162 GAACAAGTTCTTCTCATTATGAACTTATTCTCTCTCGTGGATGAGTTCTTCTCATTATGAACTCT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCGTGGATGAGTTCTTCTCATTATGAACTCT
1278227 CCATTGGAAATGTTGATCCATCTCTTTCTGTGATGGACTTGAAAG
66 CCATTGGAAATGTTGATCCATCTCTTTCTGTGATGGACTTGAAAG
* *
1278272 GAACAAGTTCTTCTCATTATGAACTTCTTCTC-CTTCTGTCGGATGAGTTATTCTCATTAGGAAC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCTC-TC-GT-GGATGAGTTCTTCTCATTATGAAC
1278336 TCTCCATTGGAAATGTTG
63 TCTCCATTGGAAATGTTG
1278354 GTTCACCTCA
Statistics
Matches: 283, Mismatches: 15, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
109 2 0.01
110 239 0.84
111 2 0.01
112 40 0.14
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.39
Consensus pattern (110 bp):
GAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCGTGGATGAGTTCTTCTCATTATGAACTCT
CCATTGGAAATGTTGATCCATCTCTTTCTGTGATGGACTTGAAAG
Found at i:1279179 original size:13 final size:13
Alignment explanation
Indices: 1279161--1279228 Score: 58
Period size: 13 Copynumber: 5.5 Consensus size: 13
1279151 CGAACACTCC
1279161 TTTTTCTCTTCAT
1 TTTTTCTCTTCAT
1279174 TTTTTCTCTT--T
1 TTTTTCTCTTCAT
1279185 TTTTT-TCTT--T
1 TTTTTCTCTTCAT
*
1279195 TTTCTT-TTTTCAT
1 TTT-TTCTCTTCAT
*
1279208 TTTTTCTTTTTCAT
1 TTTTTC-TCTTCAT
1279222 TTTTTCT
1 TTTTTCT
1279229 TTTTCTTCAA
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
10 8 0.16
11 11 0.22
12 2 0.04
13 15 0.31
14 13 0.27
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTCTCTTCAT
Found at i:1279195 original size:7 final size:7
Alignment explanation
Indices: 1279173--1279232 Score: 72
Period size: 7 Copynumber: 8.7 Consensus size: 7
1279163 TTTCTCTTCA
1279173 TTTTTTC
1 TTTTTTC
*
1279180 -TCTTT-
1 TTTTTTC
1279185 TTTTTTC
1 TTTTTTC
1279192 TTTTTTC
1 TTTTTTC
1279199 TTTTTTC
1 TTTTTTC
1279206 ATTTTTTC
1 -TTTTTTC
1279214 -TTTTTC
1 TTTTTTC
1279220 ATTTTTTC
1 -TTTTTTC
1279228 TTTTT
1 TTTTT
1279233 CTTCAAGCAT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
6 14 0.30
7 19 0.41
8 13 0.28
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTTC
Found at i:1279213 original size:22 final size:21
Alignment explanation
Indices: 1279185--1279232 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 21
1279175 TTTTCTCTTT
1279185 TTTTTTCTTTTTTC-TTTTTTC
1 TTTTTTC-TTTTTCATTTTTTC
1279206 ATTTTTTCTTTTTCATTTTTTC
1 -TTTTTTCTTTTTCATTTTTTC
1279228 TTTTT
1 TTTTT
1279233 CTTCAAGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTTTTCTTTTTCATTTTTTC
Found at i:1279231 original size:13 final size:13
Alignment explanation
Indices: 1279161--1279231 Score: 64
Period size: 14 Copynumber: 5.8 Consensus size: 13
1279151 CGAACACTCC
*
1279161 TTTTTCTCTTCAT
1 TTTTTCTTTTCAT
1279174 TTTTTCTCTTT--T
1 TTTTTCT-TTTCAT
1279186 TTTTTC-TTT--T
1 TTTTTCTTTTCAT
*
1279196 TTCTT-TTTTCAT
1 TTTTTCTTTTCAT
1279208 TTTTTCTTTTTCAT
1 TTTTTC-TTTTCAT
1279222 TTTTTCTTTT
1 TTTTTCTTTT
1279232 TCTTCAAGCA
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
10 11 0.22
12 12 0.24
13 11 0.22
14 15 0.31
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCTTTTCAT
Found at i:1291316 original size:2 final size:2
Alignment explanation
Indices: 1291309--1291342 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1291299 TATAATACCA
1291309 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1291343 TAGACACATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1292883 original size:13 final size:13
Alignment explanation
Indices: 1292828--1292899 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 13
1292818 GTTGGCCTGA
1292828 ATAA-AATATAA-
1 ATAATAATATAAT
*
1292839 ATAA-AATGATATT
1 ATAATAAT-ATAAT
1292852 AGTAATAATCAT-A-
1 A-TAATAAT-ATAAT
*
1292865 ATAATAATATAGT
1 ATAATAATATAAT
1292878 ATAATAATA-AAT
1 ATAATAATATAAT
1292890 ATAAT-ATATA
1 ATAATAATATA
1292900 TTTTAATCCC
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
11 12 0.24
12 18 0.37
13 11 0.22
14 3 0.06
15 5 0.10
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (13 bp):
ATAATAATATAAT
Found at i:1292887 original size:22 final size:22
Alignment explanation
Indices: 1292838--1292897 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 22
1292828 ATAAAATATA
*
1292838 AATAAAATGATATTAGTAATAAT
1 AATAAAATAATA-TAGTAATAAT
*
1292861 CATAATAATAATATAGT-ATAAT
1 AATAA-AATAATATAGTAATAAT
1292883 AATAAATATAATATA
1 AATAAA-ATAATATA
1292898 TATTTTAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 1 0.03
22 17 0.53
23 8 0.25
24 6 0.19
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (22 bp):
AATAAAATAATATAGTAATAAT
Found at i:1297804 original size:51 final size:51
Alignment explanation
Indices: 1297687--1297876 Score: 261
Period size: 51 Copynumber: 3.8 Consensus size: 51
1297677 TTTTACTAAA
*
1297687 ATACTTACCGTTTAAAATTCCATAAGCTCGTAAGCTTATATTTTTTTTCCAAT
1 ATACTTACCATTT-AAATTCCATAAGCTCGTAAGCTTATA-TTTTTTTCCAAT
1297740 ATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTTTTCCAAT
1 ATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTTTTCCAAT
* *
1297791 ATACTTACCATTTAAATTCCATAAGCTCGTAAGC-T-TA--TTTTACCCAT
1 ATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTTTTCCAAT
* *
1297838 ATACTTGCCA-TT--ATTCCAAAAGCTCGTAAGCTTAT-TTTT
1 ATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTT
1297877 ATGCTTACCA
Statistics
Matches: 128, Mismatches: 5, Indels: 14
0.87 0.03 0.10
Matches are distributed among these distances:
44 18 0.14
45 1 0.01
46 3 0.02
47 19 0.15
49 2 0.02
50 1 0.01
51 46 0.36
52 26 0.20
53 12 0.09
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.42
Consensus pattern (51 bp):
ATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTTTTCCAAT
Found at i:1297863 original size:44 final size:46
Alignment explanation
Indices: 1297649--1297875 Score: 226
Period size: 51 Copynumber: 4.7 Consensus size: 46
1297639 AAATCCCTTT
* * * *
1297649 CCATTT-ATCCCATAAGCTCGTAATCTTATTTTACTAAAATACTTA
1 CCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTA
* *
1297694 CCGTTTAAAATTCCATAAGCTCGTAAGCTTATATTTTTTTTCCAATATACTTA
1 CCATTT--AATTCCATAAGCTCGTAAGC-T-TA---TTTTACCAATATACTTA
*
1297747 CCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTTTTCCAATATACTTA
1 CCATTT-AATTCCATAAGCTCGTAAGC-T-TA--TTTTACCAATATACTTA
* *
1297798 CCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATACTTG
1 CCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTA
*
1297845 CCA-TT-ATTCCAAAAGCTCGTAAGCTTATTTT
1 CCATTTAATTCCATAAGCTCGTAAGCTTATTTT
1297876 TATGCTTACC
Statistics
Matches: 163, Mismatches: 11, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
44 25 0.15
45 5 0.03
46 2 0.01
47 17 0.10
48 17 0.10
49 3 0.02
50 3 0.02
51 46 0.28
52 26 0.16
53 19 0.12
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (46 bp):
CCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTA
Found at i:1297888 original size:39 final size:40
Alignment explanation
Indices: 1297790--1297888 Score: 101
Period size: 44 Copynumber: 2.3 Consensus size: 40
1297780 TTTTTTCCAA
*
1297790 TATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCC
1 TATACTTACCA-TT--ATTCCAAAAGCTCGTAAGCTTATTTT---C
*
1297836 ATATACTTGCCATTATTCCAAAAGCTCGTAAGCTTATTTT-
1 -TATACTTACCATTATTCCAAAAGCTCGTAAGCTTATTTTC
*
1297876 TATGCTTACCATT
1 TATACTTACCATT
1297889 TATTAAGCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
39 11 0.23
44 25 0.52
46 2 0.04
47 10 0.21
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.40
Consensus pattern (40 bp):
TATACTTACCATTATTCCAAAAGCTCGTAAGCTTATTTTC
Found at i:1298023 original size:40 final size:40
Alignment explanation
Indices: 1297979--1298100 Score: 244
Period size: 40 Copynumber: 3.0 Consensus size: 40
1297969 ACCGTAGTGC
1297979 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1298019 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1298059 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1298099 TA
1 TA
1298101 TAAACCTGCA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1300726 original size:2 final size:2
Alignment explanation
Indices: 1300719--1300801 Score: 159
Period size: 2 Copynumber: 42.0 Consensus size: 2
1300709 TAATCATTAC
1300719 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1300760 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1300802 CGTGATTATA
Statistics
Matches: 80, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 79 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1300880 original size:2 final size:2
Alignment explanation
Indices: 1300873--1300921 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
1300863 GCTATAACCA
1300873 AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1300914 AT AT AT AT
1 AT AT AT AT
1300922 TAGACACATA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1301171 original size:46 final size:46
Alignment explanation
Indices: 1301121--1301213 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
1301111 AAGATATCAT
1301121 GTTAAATTCAAATAAAGAAAAGATTTGAACTAGTGACCAAAATACA
1 GTTAAATTCAAATAAAGAAAAGATTTGAACTAGTGACCAAAATACA
1301167 GTTAAATTCAAATAAAGAAAAGATTTGAACTAGTGACCAAAATACA
1 GTTAAATTCAAATAAAGAAAAGATTTGAACTAGTGACCAAAATACA
1301213 G
1 G
1301214 GAAAGCAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.52, C:0.11, G:0.14, T:0.24
Consensus pattern (46 bp):
GTTAAATTCAAATAAAGAAAAGATTTGAACTAGTGACCAAAATACA
Found at i:1301325 original size:12 final size:13
Alignment explanation
Indices: 1301298--1301338 Score: 82
Period size: 13 Copynumber: 3.2 Consensus size: 13
1301288 CATGGCAACT
1301298 AAAATTAATACAA
1 AAAATTAATACAA
1301311 AAAATTAATACAA
1 AAAATTAATACAA
1301324 AAAATTAATACAA
1 AAAATTAATACAA
1301337 AA
1 AA
1301339 TACGAGACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (13 bp):
AAAATTAATACAA
Found at i:1302501 original size:21 final size:21
Alignment explanation
Indices: 1302477--1302520 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1302467 AGTAATAATC
1302477 ATAATAAT-AATACTATAGTAT
1 ATAATAATAAATACTATA-TAT
*
1302498 ATAATAATAAATATTATATAT
1 ATAATAATAAATACTATATAT
1302519 AT
1 AT
1302521 TTTAATCCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
ATAATAATAAATACTATATAT
Found at i:1307685 original size:52 final size:52
Alignment explanation
Indices: 1307600--1307785 Score: 264
Period size: 51 Copynumber: 3.7 Consensus size: 52
1307590 TTTTACTAAA
*
1307600 ATACTTACCGTTTAAAATTCCATAAGCTCGTAAGCTTATATTTTTTTCCCAAT
1 ATACTTACCATTT-AAATTCCATAAGCTCGTAAGCTTATATTTTTTTCCCAAT
1307653 ATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTTTT-CCAAT
1 ATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTTTTCCCAAT
*
1307704 ATACTTACCATTTAAATTCCATAAGCTCGTAAGC-T-TA--TTTTACCC-AT
1 ATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTTTTCCCAAT
* *
1307751 ATACTTGCCA-TT--ATTCCAAAAGCTCGTAAGCTTAT
1 ATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTAT
1307786 TTGTATGCTT
Statistics
Matches: 126, Mismatches: 4, Indels: 13
0.88 0.03 0.09
Matches are distributed among these distances:
44 18 0.14
45 1 0.01
46 3 0.02
47 15 0.12
48 2 0.02
49 2 0.02
50 1 0.01
51 39 0.31
52 33 0.26
53 12 0.10
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.40
Consensus pattern (52 bp):
ATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTTTTCCCAAT
Found at i:1307717 original size:51 final size:49
Alignment explanation
Indices: 1307558--1307785 Score: 258
Period size: 51 Copynumber: 4.7 Consensus size: 49
1307548 TATAAAATCC
* * *
1307558 CTTACCATTT--ATCCCATAAGCTCGTAAGC-T-TATTTTACTAAAATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTACCAATATA
* *
1307603 CTTACCGTTTAAAATTCCATAAGCTCGTAAGCTTATATTTTTTTCCCAATATA
1 CTTACCATTT-AAATTCCATAAGCTCGTAAGCTTATA---TTTTACCAATATA
*
1307656 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTTTTCCAATATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATA--TTTTACCAATATA
*
1307707 CTTACCATTTAAATTCCATAAGCTCGTAAGC-T-TATTTTACCCATATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTACCAATATA
* *
1307754 CTTGCCA-TT--ATTCCAAAAGCTCGTAAGCTTAT
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTAT
1307786 TTGTATGCTT
Statistics
Matches: 162, Mismatches: 11, Indels: 19
0.84 0.06 0.10
Matches are distributed among these distances:
44 18 0.11
45 10 0.06
46 3 0.02
47 17 0.10
48 18 0.11
49 3 0.02
50 3 0.02
51 45 0.28
52 26 0.16
53 19 0.12
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.39
Consensus pattern (49 bp):
CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTACCAATATA
Found at i:1307737 original size:103 final size:95
Alignment explanation
Indices: 1307558--1307785 Score: 275
Period size: 95 Copynumber: 2.3 Consensus size: 95
1307548 TATAAAATCC
* * *
1307558 CTTACCATTTATCCCATAAGCTCGTAAGC-T-TATTTTACTAAAATACTTACCGTTTAAAATTCC
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATATTTTACCAAAATACTTACCATTTAAAATTCC
*
1307621 ATAAGCTCGTAAGCTTATATTTTTTTCCCAATATA
66 ATAAGCTCGTAAGC-T-TA--TTTTACCC-ATATA
* *
1307656 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATATTTTTTTCCAATATACTTACCATTT-AAA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATA--TTTTACCAAAATACTTACCATTTAAAA
1307720 TTCCATAAGCTCGTAAGCTTATTTTACCCATATA
62 TTCCATAAGCTCGTAAGCTTATTTTACCCATATA
* *
1307754 CTTGCCA-TTATTCCAAAAGCTCGTAAGCTTAT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTAT
1307786 TTGTATGCTT
Statistics
Matches: 116, Mismatches: 8, Indels: 15
0.83 0.06 0.11
Matches are distributed among these distances:
95 22 0.19
97 2 0.02
98 21 0.18
99 7 0.06
100 18 0.16
101 3 0.03
102 3 0.03
103 21 0.18
104 19 0.16
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.39
Consensus pattern (95 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATATTTTACCAAAATACTTACCATTTAAAATTCC
ATAAGCTCGTAAGCTTATTTTACCCATATA
Found at i:1307936 original size:40 final size:40
Alignment explanation
Indices: 1307892--1308013 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
1307882 ACCGTAGTGC
1307892 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1307932 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
1307972 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1308012 TA
1 TA
1308014 TATACCTGCA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1311334 original size:290 final size:290
Alignment explanation
Indices: 1310807--1311392 Score: 1068
Period size: 290 Copynumber: 2.0 Consensus size: 290
1310797 GGTCATACCG
* * *
1310807 AAATAATGGGGGCACTTTAGAAAGTTCGCAAGGATCAGGAATTAAGGAACATCTTGATGACCATG
1 AAATAACGGGGGCACTTTAGAAAGTTCGCAAGGATCAAGAATTAAGGAACATATTGATGACCATG
1310872 AAAGCCTTGAAAATCTGAGGCAAAGCTAACCCAAATTAACCAATCAATCTTGACACTTGTTAAAG
66 AAAGCCTTGAAAATCTGAGGCAAAGCTAACCCAAATTAACCAATCAATCTTGACACTTGTTAAAG
*
1310937 ACTATAATTTTTGGGGATAAAACAAAATGAGAGATTGAATTATTTGATATTCAATGAACTGATTA
131 ACTATAATTTTTGGGGAAAAAACAAAATGAGAGATTGAATTATTTGATATTCAATGAACTGATTA
1311002 TTTGTTTTAATTGTGAGTCTAAAGTAAGGGCACCATTTTTCTTTTCTTAACACTCTGCATCAAAC
196 TTTGTTTTAATTGTGAGTCTAAAGTAAGGGCACCATTTTTCTTTTCTTAACACTCTGCATCAAAC
1311067 -TTTTTTTACATTTTTGAAAAAAAA-AGAGAA
261 TTTTTTTTACA-TTTTGAAAAAAAATA-AGAA
1311097 AAATAACGGGGGCACTTTAGAAAGTTCGCAAGGATCAAGAATTAAGGAACATATTGATGACCATG
1 AAATAACGGGGGCACTTTAGAAAGTTCGCAAGGATCAAGAATTAAGGAACATATTGATGACCATG
* *
1311162 AAAGCCTTTAAAATCTGAGGCAAAGCTAACCCAAATTAATCAATCAATCTTGACACTTGTTAAAG
66 AAAGCCTTGAAAATCTGAGGCAAAGCTAACCCAAATTAACCAATCAATCTTGACACTTGTTAAAG
*
1311227 ACTATAATTTTTGGGGAAAAAACAAAATGATAGATTGAATTATTTGATATTCAATGAACTGATTA
131 ACTATAATTTTTGGGGAAAAAACAAAATGAGAGATTGAATTATTTGATATTCAATGAACTGATTA
1311292 TTTGTTTTAATTGTGAGTCTAAAGTAAGGGCACCATTTTTCTTTTCTTAACACTCTGCATCAAAC
196 TTTGTTTTAATTGTGAGTCTAAAGTAAGGGCACCATTTTTCTTTTCTTAACACTCTGCATCAAAC
1311357 TTTTTTTTTACATTTTGAAAAAAAATAAGAA
261 -TTTTTTTTACATTTTGAAAAAAAATAAGAA
1311388 AAATA
1 AAATA
1311393 TTTTCGAACA
Statistics
Matches: 286, Mismatches: 7, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
290 253 0.88
291 22 0.08
292 11 0.04
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.32
Consensus pattern (290 bp):
AAATAACGGGGGCACTTTAGAAAGTTCGCAAGGATCAAGAATTAAGGAACATATTGATGACCATG
AAAGCCTTGAAAATCTGAGGCAAAGCTAACCCAAATTAACCAATCAATCTTGACACTTGTTAAAG
ACTATAATTTTTGGGGAAAAAACAAAATGAGAGATTGAATTATTTGATATTCAATGAACTGATTA
TTTGTTTTAATTGTGAGTCTAAAGTAAGGGCACCATTTTTCTTTTCTTAACACTCTGCATCAAAC
TTTTTTTTACATTTTGAAAAAAAATAAGAA
Found at i:1312559 original size:43 final size:43
Alignment explanation
Indices: 1312506--1312759 Score: 373
Period size: 43 Copynumber: 5.9 Consensus size: 43
1312496 GAGCCTGCAA
* ** *
1312506 AAACGGTAAGGTCTTACCCTTGCACATAGCAAAAAAGCCTAGG
1 AAACGGTAAGGTCTTATCCTTGCACATAGCAAAGGAGCCTGGG
* * * *
1312549 AAACGGTAAGGTTTTATCCTTGGACCTAGCAAATGAGCCTGGG
1 AAACGGTAAGGTCTTATCCTTGCACATAGCAAAGGAGCCTGGG
* *
1312592 AAACGGTAAGGTCTTATCCTTGAACATATCAAAGGAGCCTGGG
1 AAACGGTAAGGTCTTATCCTTGCACATAGCAAAGGAGCCTGGG
* *
1312635 AAATGGTAAGGTCTTATCCTTGCACATAGCATAGGAGCCTGGG
1 AAACGGTAAGGTCTTATCCTTGCACATAGCAAAGGAGCCTGGG
*
1312678 AAACGGTAAGGTCTTATCCTTGCGCATAGCAAAGGAGCCTGGG
1 AAACGGTAAGGTCTTATCCTTGCACATAGCAAAGGAGCCTGGG
* *
1312721 AAACGGTAAGGTCTTATCCTTGCACATAGAAAATGAGCC
1 AAACGGTAAGGTCTTATCCTTGCACATAGCAAAGGAGCC
1312760 CGCGGTAAGG
Statistics
Matches: 189, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 189 1.00
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (43 bp):
AAACGGTAAGGTCTTATCCTTGCACATAGCAAAGGAGCCTGGG
Found at i:1317781 original size:3 final size:3
Alignment explanation
Indices: 1317775--1317809 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
1317765 ACGACGATAT
* *
1317775 TTA TTA TTA TTA TTC TTA TTC TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1317810 TATTTATAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1318180 original size:2 final size:2
Alignment explanation
Indices: 1318173--1318226 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1318163 TACCTATTTA
1318173 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1318215 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1318227 TTTATTGATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1327736 original size:48 final size:48
Alignment explanation
Indices: 1327668--1327807 Score: 187
Period size: 48 Copynumber: 3.0 Consensus size: 48
1327658 TAGAGCTCAA
*
1327668 CCTCCACTTCCTAGCATGCCAACATTGCCTACCATGCAATCCATCCCT
1 CCTCCACTTCCTAGCATGCCAACATTGCCTACCATGCCATCCATCCCT
* * *
1327716 CCTCCACTTCCTAGCATGCCAACAATGGCAACCATGCCATCCATCCCT
1 CCTCCACTTCCTAGCATGCCAACATTGCCTACCATGCCATCCATCCCT
* * * *
1327764 -CT--GCTTCCTAACATGCTAACATTGCCTACCATGCCATTCATCCC
1 CCTCCACTTCCTAGCATGCCAACATTGCCTACCATGCCATCCATCCC
1327808 CACAATACCA
Statistics
Matches: 81, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
45 35 0.43
47 2 0.02
48 44 0.54
ACGTcount: A:0.24, C:0.42, G:0.09, T:0.25
Consensus pattern (48 bp):
CCTCCACTTCCTAGCATGCCAACATTGCCTACCATGCCATCCATCCCT
Found at i:1328478 original size:21 final size:22
Alignment explanation
Indices: 1328433--1328544 Score: 108
Period size: 21 Copynumber: 5.3 Consensus size: 22
1328423 TCTCTTGATG
* * *
1328433 AAAAGATTAAATCCTTTT-ATG
1 AAAAGGTTAAGTCCTTTTCATT
*
1328454 AAAAGGTTAAG-CCTTTTCATC
1 AAAAGGTTAAGTCCTTTTCATT
* *
1328475 AAAAGGATAAGT-CTTTTAATT
1 AAAAGGTTAAGTCCTTTTCATT
*
1328496 GAAAGGTTAAGTCC-TTTCATT
1 AAAAGGTTAAGTCCTTTTCATT
*
1328517 GAAAGGTTAAGTCC-TTTCATT
1 AAAAGGTTAAGTCCTTTTCATT
*
1328538 GAAAGGT
1 AAAAGGT
1328545 CTTAACCCTT
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
20 6 0.08
21 72 0.91
22 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (22 bp):
AAAAGGTTAAGTCCTTTTCATT
Found at i:1328501 original size:42 final size:42
Alignment explanation
Indices: 1328455--1328544 Score: 119
Period size: 42 Copynumber: 2.1 Consensus size: 42
1328445 CCTTTTATGA
*
1328455 AAAGGTTAAG-CCTTTTCATCAAAAGGATAAGTCTTTTAATTG
1 AAAGGTTAAGTCC-TTTCATCAAAAGGATAAGTCCTTTAATTG
** * *
1328497 AAAGGTTAAGTCCTTTCATTGAAAGGTTAAGTCCTTTCATTG
1 AAAGGTTAAGTCCTTTCATCAAAAGGATAAGTCCTTTAATTG
1328539 AAAGGT
1 AAAGGT
1328545 CTTAACCCTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 40 0.95
43 2 0.05
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (42 bp):
AAAGGTTAAGTCCTTTCATCAAAAGGATAAGTCCTTTAATTG
Found at i:1328985 original size:3 final size:3
Alignment explanation
Indices: 1328979--1329027 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
1328969 TAATATATGT
* *
1328979 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1329027 T
1 T
1329028 CTCGGATTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1334087 original size:20 final size:20
Alignment explanation
Indices: 1334058--1334096 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1334048 AGAGCTCATA
*
1334058 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
1334078 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
1334097 ATGGTTGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:1339870 original size:20 final size:22
Alignment explanation
Indices: 1339825--1339882 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
1339815 GCATGGATAG
1339825 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
1339849 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
1339869 TGTATCGATGCACT
1 TGCATCGATGCACT
1339883 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:1344462 original size:29 final size:30
Alignment explanation
Indices: 1344430--1344490 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
1344420 TATTTCAAGA
* *
1344430 TAACTACTAACTTTTATTT-T-ATTGCATAT
1 TAACCACTAACATTTATTTATCATTG-ATAT
*
1344459 TAACCACTGACATTTATTTATCATTGATAT
1 TAACCACTAACATTTATTTATCATTGATAT
1344489 TA
1 TA
1344491 GATTCGACCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 16 0.59
30 7 0.26
31 4 0.15
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.48
Consensus pattern (30 bp):
TAACCACTAACATTTATTTATCATTGATAT
Found at i:1344803 original size:15 final size:16
Alignment explanation
Indices: 1344769--1344803 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1344759 ATTCTTGTTA
1344769 TTTAAATTTATGCACT
1 TTTAAATTTATGCACT
1344785 TTTAAATTTATGC-CT
1 TTTAAATTTATGCACT
1344800 TTTA
1 TTTA
1344804 TTTTCTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.29, C:0.11, G:0.06, T:0.54
Consensus pattern (16 bp):
TTTAAATTTATGCACT
Found at i:1347059 original size:48 final size:48
Alignment explanation
Indices: 1346985--1347207 Score: 251
Period size: 48 Copynumber: 4.7 Consensus size: 48
1346975 AACCAGGAGT
* * *
1346985 GGCACCTTTCTGCCAAAATGCACCGTTATATATTTAAGTTTCATTTGC
1 GGCACCTTTCTGCCAAAATGCACCGTTATACATTTAATTTTCATTAGC
* * *
1347033 GGTACCTTTATGCCAAAATGCACCGTTATGCATTTAATTTTCATTAGC
1 GGCACCTTTCTGCCAAAATGCACCGTTATACATTTAATTTTCATTAGC
* * *
1347081 GGCACCTTTCTGCCAAAATGCACCCTTATACATTTAATTTTTATTAGT
1 GGCACCTTTCTGCCAAAATGCACCGTTATACATTTAATTTTCATTAGC
* * * *
1347129 GGCACATTTCTGCCAAAATGCACAGTTATGC-----ATTTTCATTTA-T
1 GGCACCTTTCTGCCAAAATGCACCGTTATACATTTAATTTTCA-TTAGC
* *
1347172 GGCACCTTTCTGCCAATAATGCACTGTTATGCATTT
1 GGCACCTTTCTGCCAA-AATGCACCGTTATACATTT
1347208 TCATTTATGG
Statistics
Matches: 150, Mismatches: 19, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
43 22 0.15
44 17 0.11
48 111 0.74
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (48 bp):
GGCACCTTTCTGCCAAAATGCACCGTTATACATTTAATTTTCATTAGC
Found at i:1347207 original size:44 final size:43
Alignment explanation
Indices: 1347128--1347259 Score: 203
Period size: 44 Copynumber: 3.0 Consensus size: 43
1347118 TTTTTATTAG
*
1347128 TGGCACATTTCTGCCAA-AATGCACAGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCAC-GTTATGCATTTTCATTTA
1347171 TGGCACCTTTCTGCCAATAATGCACTGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCAC-GTTATGCATTTTCATTTA
* *
1347215 TGGCACCTTTTTACCAATAATGCAACGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGC-ACGTTATGCATTTTCATTTA
1347259 T
1 T
1347260 TCATTAATTT
Statistics
Matches: 83, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
43 16 0.19
44 65 0.78
45 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (43 bp):
TGGCACCTTTCTGCCAATAATGCACGTTATGCATTTTCATTTA
Found at i:1361640 original size:20 final size:21
Alignment explanation
Indices: 1361602--1361640 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1361592 CATCAAGGTC
1361602 TTTGTTGAGGCCATGAAATCT
1 TTTGTTGAGGCCATGAAATCT
*
1361623 TTTGTTGAGTCCAT-AAAT
1 TTTGTTGAGGCCATGAAAT
1361641 TCCTGCAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.41
Consensus pattern (21 bp):
TTTGTTGAGGCCATGAAATCT
Found at i:1364202 original size:2 final size:2
Alignment explanation
Indices: 1364195--1364274 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
1364185 GAATAGCCGG
1364195 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1364237 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1364275 TGTAGAGCTT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1364718 original size:21 final size:23
Alignment explanation
Indices: 1364694--1364739 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
1364684 ATAGTTCCCC
*
1364694 TTCTTATCTAAGG-TTCT-TATA
1 TTCTCATCTAAGGTTTCTATATA
*
1364715 TTCTCATGTAAGGTTTCTATATA
1 TTCTCATCTAAGGTTTCTATATA
1364738 TT
1 TT
1364740 ATAGAACTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
22 4 0.19
23 6 0.29
ACGTcount: A:0.24, C:0.13, G:0.11, T:0.52
Consensus pattern (23 bp):
TTCTCATCTAAGGTTTCTATATA
Found at i:1365183 original size:85 final size:85
Alignment explanation
Indices: 1365040--1365236 Score: 254
Period size: 85 Copynumber: 2.3 Consensus size: 85
1365030 ATCACACCAC
* * * * *
1365040 ACGAATGTGTGTCATCTT-TTTTAATGACGTGTGCTTCAATGACACGCAATGTAAGTCATACATG
1 ACGAATGTGTGTCGTCTTCATTT-ATGACGGGGGCTTCAATGACACGCAATGTAAGTCATAAATG
* *
1365104 CGTGTCATAAATTTATGACAA
65 CGCGTCATAAATTTATAACAA
** *
1365125 ACGAATGTGTGTCGTCTTCATTTATGACGGGGGCTTCAATGATGCGCAATG-AGCGTCATAAATG
1 ACGAATGTGTGTCGTCTTCATTTATGACGGGGGCTTCAATGACACGCAATGTA-AGTCATAAATG
* *
1365189 TGCGTCATAAATTTATAACAC
65 CGCGTCATAAATTTATAACAA
1365210 ACGAATGTGTGTCGTCTTCATTTATGA
1 ACGAATGTGTGTCGTCTTCATTTATGA
1365237 TGCACAATTG
Statistics
Matches: 98, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
84 1 0.01
85 94 0.96
86 3 0.03
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (85 bp):
ACGAATGTGTGTCGTCTTCATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCATAAATGC
GCGTCATAAATTTATAACAA
Found at i:1369439 original size:48 final size:43
Alignment explanation
Indices: 1369368--1369595 Score: 233
Period size: 44 Copynumber: 5.0 Consensus size: 43
1369358 AAACTAGGAG
*
1369368 TGGCACCTTTCTGCCAAAATGCACCGTTATGTATTTAAGTTTCATTTA
1 TGGCACCTTTCTGCCAAAATGCACCGTTATGCA--T---TTTCATTTA
*
1369416 TGGCACCTTTCTGCCAAAATGCACCATTATGCATTTAATTTTCA-TTA
1 TGGCACCTTTCTGCCAAAATGCACCGTTATGC-----ATTTTCATTTA
** *
1369463 GTGGCACCTTTCTATCAAAATGCACTGTTATGCATTTTCATTTA
1 -TGGCACCTTTCTGCCAAAATGCACCGTTATGCATTTTCATTTA
* * *
1369507 TGGCACTTTTCTGCCAATAATGTATCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAA-AATGCACCGTTATGCATTTTCATTTA
* **
1369551 TGGCACCTTTTTGCCAATAATGCAATGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAA-AATGCACCGTTATGCATTTTCATTTA
1369595 T
1 T
1369596 TCATTAATTT
Statistics
Matches: 155, Mismatches: 17, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
43 21 0.14
44 66 0.43
47 3 0.02
48 63 0.41
51 1 0.01
53 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (43 bp):
TGGCACCTTTCTGCCAAAATGCACCGTTATGCATTTTCATTTA
Found at i:1369594 original size:88 final size:87
Alignment explanation
Indices: 1369366--1369595 Score: 230
Period size: 96 Copynumber: 2.5 Consensus size: 87
1369356 TTAAACTAGG
* ** *
1369366 AGTGGCACCTTTCTGCCAAAATGCACCGTTATGTATTTAAGTTTCATTTATGGCACCTTTCTGCC
1 AGTGGCACCTTTCTACCAAAATGCAATGTTATGCA--T---TTTCATTTATGGCACCTTTCTGCC
1369431 AAAATGCACCATTATGCATTTAATTTTCATT
61 AAAATGCACCATTATGC---T-ATTTTCATT
* * *
1369462 AGTGGCACCTTTCTATCAAAATGCACTGTTATGCATTTTCATTTATGGCACTTTTCTGCCAATAA
1 AGTGGCACCTTTCTACCAAAATGCAATGTTATGCATTTTCATTTATGGCACCTTTCTGCCAA-AA
* * *
1369527 TGTATCGTTATGC-ATTTTCATTT
65 TGCACCATTATGCTATTTTCA-TT
* *
1369550 A-TGGCACCTTTTTGCCAATAATGCAATGTTATGCATTTTCATTTAT
1 AGTGGCACCTTTCTACCAA-AATGCAATGTTATGCATTTTCATTTAT
1369596 TCATTAATTT
Statistics
Matches: 119, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
87 21 0.18
88 29 0.24
91 25 0.21
92 12 0.10
94 1 0.01
96 31 0.26
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.41
Consensus pattern (87 bp):
AGTGGCACCTTTCTACCAAAATGCAATGTTATGCATTTTCATTTATGGCACCTTTCTGCCAAAAT
GCACCATTATGCTATTTTCATT
Found at i:1372001 original size:24 final size:24
Alignment explanation
Indices: 1371969--1372022 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
1371959 TTTGATCCAA
1371969 TTCCAATGACCTATGAGGAATTAC
1 TTCCAATGACCTATGAGGAATTAC
1371993 TTCCAATGACCTATGAGGAATTAC
1 TTCCAATGACCTATGAGGAATTAC
1372017 TTCCAA
1 TTCCAA
1372023 CACTGGTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (24 bp):
TTCCAATGACCTATGAGGAATTAC
Found at i:1373256 original size:11 final size:10
Alignment explanation
Indices: 1373231--1373286 Score: 60
Period size: 10 Copynumber: 5.3 Consensus size: 10
1373221 AACAAAGGAA
*
1373231 AAAGAAAAGG
1 AAAGAAAAAG
1373241 AAAAGGAAAAAG
1 -AAA-GAAAAAG
1373253 AAAGAAAAAG
1 AAAGAAAAAG
1373263 AAAAGAAAAAG
1 -AAAGAAAAAG
1373274 AAA-AAGAAAG
1 AAAGAA-AAAG
1373284 AAA
1 AAA
1373287 ACAAATCAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
9 2 0.05
10 17 0.41
11 16 0.39
12 6 0.15
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:1373258 original size:22 final size:21
Alignment explanation
Indices: 1373231--1373287 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
1373221 AACAAAGGAA
*
1373231 AAAGAAAAGGAAAAGGAAAAAG
1 AAAGAAAAAGAAAA-GAAAAAG
1373253 AAAGAAAAAGAAAAGAAAAAG
1 AAAGAAAAAGAAAAGAAAAAG
1373274 AAA-AAGAAAGAAAA
1 AAAGAA-AAAGAAAA
1373288 CAAATCAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 2 0.06
21 18 0.55
22 13 0.39
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (21 bp):
AAAGAAAAAGAAAAGAAAAAG
Found at i:1373270 original size:27 final size:28
Alignment explanation
Indices: 1373224--1373282 Score: 59
Period size: 28 Copynumber: 2.1 Consensus size: 28
1373214 GAAAATAAAC
*
1373224 AAAGGAAAAAGAAAAGGAAAAGGAAAAAG-
1 AAAGGAAAAAGAAAAAG-AAA-GAAAAAGA
*
1373253 AAA-GAAAAAGAAAAGAAAAAGAAAAAGA
1 AAAGGAAAAAGAAAA-AGAAAGAAAAAGA
1373281 AA
1 AA
1373283 GAAAACAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
27 7 0.27
28 16 0.62
29 3 0.12
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (28 bp):
AAAGGAAAAAGAAAAAGAAAGAAAAAGA
Found at i:1373280 original size:6 final size:6
Alignment explanation
Indices: 1373228--1373282 Score: 71
Period size: 6 Copynumber: 9.7 Consensus size: 6
1373218 ATAAACAAAG
* *
1373228 GAAAAA GAAAAG GAAAAG GAAAAA G--AAA GAAAAA G-AAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
1373273 GAAAAA GAAA
1 GAAAAA GAAA
1373283 GAAAACAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
4 4 0.09
5 5 0.11
6 35 0.80
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:1373283 original size:27 final size:28
Alignment explanation
Indices: 1373228--1373287 Score: 104
Period size: 27 Copynumber: 2.2 Consensus size: 28
1373218 ATAAACAAAG
*
1373228 GAAAAAGAAAAGGAAAAGGAAAAAGAAA
1 GAAAAAGAAAAGGAAAAAGAAAAAGAAA
1373256 GAAAAAGAAAA-GAAAAAGAAAAAGAAA
1 GAAAAAGAAAAGGAAAAAGAAAAAGAAA
1373283 GAAAA
1 GAAAA
1373288 CAAATCAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 20 0.65
28 11 0.35
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (28 bp):
GAAAAAGAAAAGGAAAAAGAAAAAGAAA
Found at i:1376751 original size:98 final size:98
Alignment explanation
Indices: 1376565--1377119 Score: 719
Period size: 98 Copynumber: 5.7 Consensus size: 98
1376555 TTTCTCGAAG
* * * * *
1376565 CAAAATTGATCTCACTTGATATAGTTTTCCTGAAAACAAATTTCATCTCGCTTGAGACAGTTTTC
1 CAAAATTGATCTCACTTGAGATTGTTTTCCTAAAAACAAATTTCGTCTCGCTTGAGACAATTTTC
*
1376630 CTTTGAAAACACAAATTTA-TTTTGCACTTGAAA
66 C-TTCAAAACACAAATTTATTTTTGCACTTGAAA
* * * * *
1376663 CAAAATTGATCTCACTTGAGATTGTTTTCCTAAAAATAAATTTTGTATCGTTTAAGACAATTTTC
1 CAAAATTGATCTCACTTGAGATTGTTTTCCTAAAAACAAATTTCGTCTCGCTTGAGACAATTTTC
* *
1376728 CTTTAAAACAAAAATTTATTTTTGCACTTGAAA
66 CTTCAAAACACAAATTTATTTTTGCACTTGAAA
* * *
1376761 CAAAATTGATCCCACTTGAGATTGTTTTCCTAAAAACAAAATTT-GTCTCCCTTGAGACAGTTTT
1 CAAAATTGATCTCACTTGAGATTGTTTTCCTAAAAAC-AAATTTCGTCTCGCTTGAGACAATTTT
*
1376825 CATTCAAAACACAAATTTATTTTTGCACTTGAAA
65 CCTTCAAAACACAAATTTATTTTTGCACTTGAAA
* * *
1376859 CAAAATTGATCTCACTTGATATTGTTTTCCTAAAAACAAATTTCGTCTCGCTTGAGATATTTTTC
1 CAAAATTGATCTCACTTGAGATTGTTTTCCTAAAAACAAATTTCGTCTCGCTTGAGACAATTTTC
*
1376924 CTTCGAAACACAAATTTATTTTTGCACTTGAAA
66 CTTCAAAACACAAATTTATTTTTGCACTTGAAA
* * *
1376957 CAAAATTGATCTCACTTGAGATTGTTTTCCTAAAAACAAATTTCATCTCGCTAGAGAC-AGTTTC
1 CAAAATTGATCTCACTTGAGATTGTTTTCCTAAAAACAAATTTCGTCTCGCTTGAGACAATTTTC
*
1377021 C--CAAAA-AAAAATTTGAAATTGTTT-CACTTGAAA
66 CTTCAAAACACAAATTT---ATT-TTTGCACTTGAAA
* * * ** * *
1377054 CAAAATTGATCTCATTTGAAATTGTTTTTCTAAAAACAAATTTTATCTCGCTTGAAAGAATTTTC
1 CAAAATTGATCTCACTTGAGATTGTTTTCCTAAAAACAAATTTCGTCTCGCTTGAGACAATTTTC
1377119 C
66 C
1377120 CTTGAAATGC
Statistics
Matches: 404, Mismatches: 45, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
94 7 0.02
95 4 0.01
97 89 0.22
98 298 0.74
99 6 0.01
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (98 bp):
CAAAATTGATCTCACTTGAGATTGTTTTCCTAAAAACAAATTTCGTCTCGCTTGAGACAATTTTC
CTTCAAAACACAAATTTATTTTTGCACTTGAAA
Found at i:1376943 original size:24 final size:24
Alignment explanation
Indices: 1376916--1376963 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1376906 TCGCTTGAGA
1376916 TATTTTT-C-CTTCGAAACACAAATT
1 TATTTTTGCACTT-GAAACA-AAATT
1376940 TATTTTTGCACTTGAAACAAAATT
1 TATTTTTGCACTTGAAACAAAATT
1376964 GATCTCACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 12 0.55
25 7 0.32
26 3 0.14
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (24 bp):
TATTTTTGCACTTGAAACAAAATT
Found at i:1377091 original size:36 final size:36
Alignment explanation
Indices: 1377031--1377102 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
1377021 CCAAAAAAAA
**
1377031 ATTTGAAATTGTTTCACTTGAAACAAAATTGATCTC
1 ATTTGAAATTGTTTCACTAAAAACAAAATTGATCTC
** * *
1377067 ATTTGAAATTGTTTTTCTAAAAACAAATTTTATCTC
1 ATTTGAAATTGTTTCACTAAAAACAAAATTGATCTC
1377103 GCTTGAAAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.43
Consensus pattern (36 bp):
ATTTGAAATTGTTTCACTAAAAACAAAATTGATCTC
Found at i:1377109 original size:36 final size:36
Alignment explanation
Indices: 1377033--1377110 Score: 84
Period size: 36 Copynumber: 2.2 Consensus size: 36
1377023 AAAAAAAAAT
** *
1377033 TTGAAATTGTTTCACTTGAAACAAAATTGATCTCAT
1 TTGAAATTGTTTCACTAAAAACAAAATTGATCTCAC
** * * *
1377069 TTGAAATTGTTTTTCTAAAAACAAATTTTATCTCGC
1 TTGAAATTGTTTCACTAAAAACAAAATTGATCTCAC
1377105 TTGAAA
1 TTGAAA
1377111 GAATTTTCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (36 bp):
TTGAAATTGTTTCACTAAAAACAAAATTGATCTCAC
Found at i:1377593 original size:40 final size:41
Alignment explanation
Indices: 1377549--1377636 Score: 101
Period size: 43 Copynumber: 2.1 Consensus size: 41
1377539 CCTCAACACG
1377549 AAGGA-CATATGTCATCCACATAC-CAGA-TCTCCTCAACGTA
1 AAGGAGCA-ATGTCATCCACATACACAGACT-TCCTCAACGTA
* *
1377589 AAGGAGCAGTGTCATCCTCATACAATCAGACTTCCTCAACGTA
1 AAGGAGCAATGTCATCCACATAC-A-CAGACTTCCTCAACGTA
1377632 AAGGA
1 AAGGA
1377637 ACTATGTTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
40 18 0.44
41 2 0.05
43 20 0.49
44 1 0.02
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (41 bp):
AAGGAGCAATGTCATCCACATACACAGACTTCCTCAACGTA
Found at i:1381386 original size:33 final size:33
Alignment explanation
Indices: 1381337--1381404 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
1381327 ACCTAGCACA
* *
1381337 TATGGTGGATATGACCTTATGTATCATACGAAT
1 TATGGTGGACACGACCTTATGTATCATACGAAT
* *
1381370 TATGGTGGACACGACCTTATGTGTCATACGGAT
1 TATGGTGGACACGACCTTATGTATCATACGAAT
1381403 TA
1 TA
1381405 CCACTACGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.34
Consensus pattern (33 bp):
TATGGTGGACACGACCTTATGTATCATACGAAT
Found at i:1381551 original size:45 final size:44
Alignment explanation
Indices: 1381482--1381588 Score: 151
Period size: 45 Copynumber: 2.4 Consensus size: 44
1381472 TGGTATATGG
* * *
1381482 TTATGGAATAATGGCAAGTGTATTGGTAAAATAAGCTTACAAGC
1 TTATGGAAAAATGGTAAGTATATTGGTAAAATAAGCTTACAAGC
*
1381526 TTATGGAACAAATGGTAAGTATATTGGTAAACTAAGCTTACAAGC
1 TTATGGAA-AAATGGTAAGTATATTGGTAAAATAAGCTTACAAGC
*
1381571 TTATGGGATAAATGGTAA
1 TTAT-GGAAAAATGGTAA
1381589 AAGATTTTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
44 8 0.14
45 45 0.80
46 3 0.05
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.30
Consensus pattern (44 bp):
TTATGGAAAAATGGTAAGTATATTGGTAAAATAAGCTTACAAGC
Found at i:1382103 original size:20 final size:21
Alignment explanation
Indices: 1382080--1382125 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
1382070 TCACGGGTAT
1382080 TGTTCACT-CTTACTGTTCAC
1 TGTTCACTACTTACTGTTCAC
*
1382100 TGTT-ACTATTTACTGTTCAC
1 TGTTCACTACTTACTGTTCAC
*
1382120 TATTCA
1 TGTTCA
1382126 TAAAAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 3 0.14
20 18 0.82
21 1 0.05
ACGTcount: A:0.20, C:0.24, G:0.09, T:0.48
Consensus pattern (21 bp):
TGTTCACTACTTACTGTTCAC
Found at i:1386944 original size:33 final size:33
Alignment explanation
Indices: 1386902--1386965 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
1386892 AGCACAGATT
1386902 GTGGACACGACCTTATGTGTCATACGAATTATG
1 GTGGACACGACCTTATGTGTCATACGAATTATG
*
1386935 GTGGACACGACCTTATGTGTCATACGGATTA
1 GTGGACACGACCTTATGTGTCATACGAATTA
1386966 GCACTACGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.30
Consensus pattern (33 bp):
GTGGACACGACCTTATGTGTCATACGAATTATG
Found at i:1387113 original size:45 final size:45
Alignment explanation
Indices: 1387053--1387150 Score: 151
Period size: 45 Copynumber: 2.2 Consensus size: 45
1387043 GTTATGGAAT
* *
1387053 AATGGCAAGTGTATTGGTAAAATAAGCTTACGAGCTTATAGAACA
1 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATAGAACA
* * *
1387098 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGGATA
1 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATAGAACA
1387143 AATGGTAA
1 AATGGTAA
1387151 AAGATTTTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (45 bp):
AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATAGAACA
Found at i:1388323 original size:20 final size:20
Alignment explanation
Indices: 1388258--1388327 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
1388248 CCTCTTCATG
*
1388258 AGGTATCGATACCAAAAGGGT
1 AGGTATCGATACCATAA-GGT
1388279 A-GTATCGATACCAT---G-
1 AGGTATCGATACCATAAGGT
1388294 -GGTA-CTGATACCATAAGGT
1 AGGTATC-GATACCATAAGGT
1388313 AGGTATCGATACCAT
1 AGGTATCGATACCAT
1388328 TTTGGAAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 17
0.69 0.02 0.29
Matches are distributed among these distances:
14 1 0.03
15 11 0.28
16 1 0.03
18 1 0.03
20 24 0.60
21 2 0.05
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.24
Consensus pattern (20 bp):
AGGTATCGATACCATAAGGT
Found at i:1388987 original size:21 final size:20
Alignment explanation
Indices: 1388963--1389018 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 20
1388953 TATGTAATCA
*
1388963 TTTGGAACATATATGCGGTTC
1 TTTGGAACATATAT-CGGTCC
*
1388984 TTTGAGACACATAT-TTGGTCC
1 TTTG-GA-ACATATATCGGTCC
*
1389005 TTTGGAATATATAT
1 TTTGGAACATATAT
1389019 ATAGTCCTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 5 0.17
20 3 0.10
21 12 0.41
22 3 0.10
23 6 0.21
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (20 bp):
TTTGGAACATATATCGGTCC
Found at i:1389060 original size:23 final size:23
Alignment explanation
Indices: 1389034--1389164 Score: 104
Period size: 23 Copynumber: 5.7 Consensus size: 23
1389024 CCTTAAGGAG
*
1389034 ATTTCTATGTGGTACTTCAGG-AC
1 ATTTCTATGTGGCACTTC-GGTAC
* *
1389057 ATTT-TATATGGCACTTCGGTGC
1 ATTTCTATGTGGCACTTCGGTAC
* *
1389079 ATTTCTACGTGGCACTTCGGTGC
1 ATTTCTATGTGGCACTTCGGTAC
** *
1389102 ATTTCTATGTGATACTTCGGTGC
1 ATTTCTATGTGGCACTTCGGTAC
* ** * **
1389125 ATTTCTACGCAGCACTTCAGTGT
1 ATTTCTATGTGGCACTTCGGTAC
*
1389148 ATTTCTACGTGGCACTT
1 ATTTCTATGTGGCACTT
1389165 TAGTGCATTT
Statistics
Matches: 89, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
21 2 0.02
22 16 0.18
23 71 0.80
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.39
Consensus pattern (23 bp):
ATTTCTATGTGGCACTTCGGTAC
Found at i:1389169 original size:23 final size:23
Alignment explanation
Indices: 1389065--1389174 Score: 139
Period size: 23 Copynumber: 4.8 Consensus size: 23
1389055 ACATTTTATA
1389065 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
1389088 TGGCACTTCGGTGCATTTCTATG
1 TGGCACTTCGGTGCATTTCTACG
**
1389111 TGATACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
** * *
1389134 CAGCACTTCAGTGTATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
**
1389157 TGGCACTTTAGTGCATTT
1 TGGCACTTCGGTGCATTT
1389175 TATACGAGTT
Statistics
Matches: 73, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 73 1.00
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:1392087 original size:14 final size:14
Alignment explanation
Indices: 1392070--1392118 Score: 89
Period size: 14 Copynumber: 3.5 Consensus size: 14
1392060 ATTTTCTTTA
1392070 TTTAATTTCAGTCC
1 TTTAATTTCAGTCC
*
1392084 TTTAATTTCAGTGC
1 TTTAATTTCAGTCC
1392098 TTTAATTTCAGTCC
1 TTTAATTTCAGTCC
1392112 TTTAATT
1 TTTAATT
1392119 ATTACGCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.22, C:0.16, G:0.08, T:0.53
Consensus pattern (14 bp):
TTTAATTTCAGTCC
Found at i:1392877 original size:11 final size:11
Alignment explanation
Indices: 1392861--1392887 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1392851 GGTACGAGAT
1392861 AAAATTAATTC
1 AAAATTAATTC
1392872 AAAATTAATTC
1 AAAATTAATTC
1392883 AAAAT
1 AAAAT
1392888 CCTACTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (11 bp):
AAAATTAATTC
Found at i:1408532 original size:17 final size:17
Alignment explanation
Indices: 1408485--1408534 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
1408475 TTTTTTAGTG
*
1408485 ATTTATTTAATAATTTT
1 ATTTATTTAATTATTTT
* *
1408502 AATTGTTTAA-TATTTT
1 ATTTATTTAATTATTTT
*
1408518 ATTTAATTAATTATTTT
1 ATTTATTTAATTATTTT
1408535 TGCAGATATA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
ATTTATTTAATTATTTT
Found at i:1410777 original size:13 final size:13
Alignment explanation
Indices: 1410736--1410779 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
1410726 TATTTAGTAC
*
1410736 TTTTTATTGTAGT
1 TTTTTATTGTAAT
* * *
1410749 TGTTTATTGGACT
1 TTTTTATTGTAAT
1410762 TTTTTATTGTAAT
1 TTTTTATTGTAAT
1410775 TTTTT
1 TTTTT
1410780 TTATTATTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.16, C:0.02, G:0.14, T:0.68
Consensus pattern (13 bp):
TTTTTATTGTAAT
Found at i:1415898 original size:64 final size:63
Alignment explanation
Indices: 1415830--1416059 Score: 212
Period size: 64 Copynumber: 3.6 Consensus size: 63
1415820 TTGGAACACT
* ***
1415830 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
** * * **
1415894 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATATTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGAT-GTTTGAAAATAGCC
* * * * * *
1415958 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAAT-TC
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATAGC
*
1416021 A
63 C
* *
1416022 TCGATGCATCGATGCATGGACTGATGCATCGGTGCATG
1 T-GATGCATCGATGCATGGAGTG-TGCATCGATGCATG
1416060 CCTTTGAATA
Statistics
Matches: 136, Mismatches: 24, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
63 4 0.03
64 69 0.51
65 63 0.46
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:1415982 original size:19 final size:19
Alignment explanation
Indices: 1415958--1416008 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1415948 GAAAATATTC
1415958 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1415977 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
1415996 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
1416009 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1416050 original size:65 final size:63
Alignment explanation
Indices: 1415852--1416059 Score: 210
Period size: 65 Copynumber: 3.2 Consensus size: 63
1415842 GCACCAAGTG
* *
1415852 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGATGCATCGATGCATGG-CTTG
1 TGCATCGATGCATGAAATGCATTCGATG-TTGAAAAAT-TCATGATGCATCGATGCATGGAC-TG
1415916 -
63 A
* *
1415916 TGCATCGATGCATCAAATGCATTCGATATTTTGAAAATATTCA-GAGTGCATCGATGCATGGA--
1 TGCATCGATGCATGAAATGCATTCG--ATGTTGAAAA-ATTCATGA-TGCATCGATGCATGGACT
1415978 GA
62 GA
* * * *
1415980 GTGCATCGGTGCATGGAATGCATTCGATGTTCAATTAATTCATCGATGCATCGATGCATGGACTG
1 -TGCATCGATGCATGAAATGCATTCGATGTTGAA-AAATTCAT-GATGCATCGATGCATGGACTG
1416045 A
63 A
*
1416046 TGCATCGGTGCATG
1 TGCATCGATGCATG
1416060 CCTTTGAATA
Statistics
Matches: 122, Mismatches: 10, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
63 12 0.10
64 43 0.35
65 61 0.50
66 6 0.05
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (63 bp):
TGCATCGATGCATGAAATGCATTCGATGTTGAAAAATTCATGATGCATCGATGCATGGACTGA
Found at i:1420143 original size:14 final size:14
Alignment explanation
Indices: 1420126--1420178 Score: 63
Period size: 14 Copynumber: 3.7 Consensus size: 14
1420116 AAGTCAACGG
1420126 GTTGACTC-GAACGA
1 GTTGACTCAG-ACGA
* *
1420140 GTTGACCCAGACGG
1 GTTGACTCAGACGA
1420154 GTTGACTCAGACAGA
1 GTTGACTCAGAC-GA
1420169 GTTGACTCAG
1 GTTGACTCAG
1420179 TGACTGGGTC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 21 0.64
15 12 0.36
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (14 bp):
GTTGACTCAGACGA
Found at i:1423695 original size:80 final size:81
Alignment explanation
Indices: 1423425--1423696 Score: 397
Period size: 81 Copynumber: 3.4 Consensus size: 81
1423415 GGGGCCTATA
* *
1423425 GGCCTACCCAAGGATATCCTTAGATCCGTAGGG-TACCTTAAGCACACAACAAAAAGAGAACCAA
1 GGCCTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTTAAGCACACAAC-AAAAGGGAACCAA
* *
1423489 CATAAGGATATACCTTG
65 CCTAAGGATATGCCTTG
*
1423506 GGTCTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTTAAGCACACAACAAAAGGGAACCAAC
1 GGCCTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTTAAGCACACAACAAAAGGGAACCAAC
1423571 CTAAGGATATGCCTTG
66 CTAAGGATATGCCTTG
* * * *
1423587 GGCCTACCCCAGGGCATCCTTAGATCCGTAGGGTTACCTTATGCACACAGC-AAAGGGAACCAAC
1 GGCCTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTTAAGCACACAACAAAAGGGAACCAAC
1423651 CTAAGGATATGCCTTGG
66 CTAAGGATATGCCTT-G
* * *
1423668 GGCCTACCCAA-GATATTCTTAGGTCCGTA
1 GGCCTACCCAAGGACATCCTTAGATCCGTA
1423697 AAGACTTACA
Statistics
Matches: 174, Mismatches: 15, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
80 42 0.24
81 115 0.66
82 17 0.10
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.20
Consensus pattern (81 bp):
GGCCTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTTAAGCACACAACAAAAGGGAACCAAC
CTAAGGATATGCCTTG
Found at i:1426646 original size:21 final size:21
Alignment explanation
Indices: 1426620--1426664 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1426610 ACTTCCCCAC
*
1426620 GCGTAGGGGGCGGCATGTGGG
1 GCGTAGGGGGCGGCACGTGGG
1426641 GCGTAGGGGGCGGCACGTGGG
1 GCGTAGGGGGCGGCACGTGGG
1426662 GCG
1 GCG
1426665 AGTACGGCGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.09, C:0.18, G:0.62, T:0.11
Consensus pattern (21 bp):
GCGTAGGGGGCGGCACGTGGG
Found at i:1427099 original size:199 final size:199
Alignment explanation
Indices: 1426759--1427156 Score: 787
Period size: 199 Copynumber: 2.0 Consensus size: 199
1426749 GGTTCACAAT
1426759 TTTGAACGGTGGAGAGCTCGATTCCGAAATGTCGAAAACTTTGACTTTCTCACCCCTCCACGCGC
1 TTTGAACGGTGGAGAGCTCGATTCCGAAATGTCGAAAACTTTGACTTTCTCACCCCTCCACGCGC
1426824 CGGCGACGACAGAGAAACGGAGAACACCGGTGGACTCGAAACGATGCAAGGAACACAATGGTGTG
66 CGGCGACGACAGAGAAACGGAGAACACCGGTGGACTCGAAACGATGCAAGGAACACAATGGTGTG
*
1426889 GGAGGTGTCAAAAGCGGATGGCTGGATCGACGTGAATCGACGAAAAACCAACAAAAATAGAGTTA
131 GGAGGTGTCAAAAACGGATGGCTGGATCGACGTGAATCGACGAAAAACCAACAAAAATAGAGTTA
1426954 AAAC
196 AAAC
1426958 TTTGAACGGTGGAGAGCTCGATTCCGAAATGTCGAAAACTTTGACTTTCTCACCCCTCCACGCGC
1 TTTGAACGGTGGAGAGCTCGATTCCGAAATGTCGAAAACTTTGACTTTCTCACCCCTCCACGCGC
1427023 CGGCGACGACAGAGAAACGGAGAACACCGGTGGACTCGAAACGATGCAAGGAACACAATGGTGTG
66 CGGCGACGACAGAGAAACGGAGAACACCGGTGGACTCGAAACGATGCAAGGAACACAATGGTGTG
1427088 GGAGGTGTCAAAAACGGATGGCTGGATCGACGTGAATCGACGAAAAACCAACAAAAATAGAGTTA
131 GGAGGTGTCAAAAACGGATGGCTGGATCGACGTGAATCGACGAAAAACCAACAAAAATAGAGTTA
1427153 AAAC
196 AAAC
1427157 CGACGATACT
Statistics
Matches: 198, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
199 198 1.00
ACGTcount: A:0.34, C:0.22, G:0.27, T:0.17
Consensus pattern (199 bp):
TTTGAACGGTGGAGAGCTCGATTCCGAAATGTCGAAAACTTTGACTTTCTCACCCCTCCACGCGC
CGGCGACGACAGAGAAACGGAGAACACCGGTGGACTCGAAACGATGCAAGGAACACAATGGTGTG
GGAGGTGTCAAAAACGGATGGCTGGATCGACGTGAATCGACGAAAAACCAACAAAAATAGAGTTA
AAAC
Found at i:1429807 original size:15 final size:16
Alignment explanation
Indices: 1429781--1429815 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1429771 TTTATTTGTA
1429781 AAAATGTATGTTAATT
1 AAAATGTATGTTAATT
*
1429797 AAAAT-TATGTTTATT
1 AAAATGTATGTTAATT
1429812 AAAA
1 AAAA
1429816 CAAATAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (16 bp):
AAAATGTATGTTAATT
Found at i:1430330 original size:13 final size:13
Alignment explanation
Indices: 1430312--1430338 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1430302 GAATTATATC
1430312 TGTTAAATCCATA
1 TGTTAAATCCATA
1430325 TGTTAAATCCATA
1 TGTTAAATCCATA
1430338 T
1 T
1430339 ATAATTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
TGTTAAATCCATA
Found at i:1434554 original size:15 final size:15
Alignment explanation
Indices: 1434525--1434572 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
1434515 CAATTTGAAC
*
1434525 CGAACTGAGTCAACT
1 CGAACTGAGTAAACT
1434540 CGAAC-GAAGTAAACT
1 CGAACTG-AGTAAACT
*
1434555 CGAACTGAGTCAACT
1 CGAACTGAGTAAACT
1434570 CGA
1 CGA
1434573 CCCTATTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 1 0.03
15 27 0.93
16 1 0.03
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.17
Consensus pattern (15 bp):
CGAACTGAGTAAACT
Found at i:1435280 original size:27 final size:28
Alignment explanation
Indices: 1435222--1435283 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
1435212 TTTATAATAT
* *
1435222 ATTTTTTAGCATGATCTCTAAATATTGT
1 ATTTTTTAACATGATCTCTAAATATTGG
*
1435250 ATTTTTTAATATGAT-TCTAAAT-TATGG
1 ATTTTTTAACATGATCTCTAAATAT-TGG
1435277 ATTTTTT
1 ATTTTTT
1435284 CATGTTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 1 0.03
27 16 0.53
28 13 0.43
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.55
Consensus pattern (28 bp):
ATTTTTTAACATGATCTCTAAATATTGG
Found at i:1438975 original size:14 final size:16
Alignment explanation
Indices: 1438958--1438998 Score: 59
Period size: 14 Copynumber: 2.7 Consensus size: 16
1438948 CAGGTAACAA
1438958 TCAATGGGTCAA-A-G
1 TCAATGGGTCAACATG
1438972 TCAATGGGTCAACATG
1 TCAATGGGTCAACATG
*
1438988 ACAATGGGTCA
1 TCAATGGGTCA
1438999 GGTTAAACTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 12 0.50
15 1 0.04
16 11 0.46
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.22
Consensus pattern (16 bp):
TCAATGGGTCAACATG
Found at i:1440858 original size:19 final size:18
Alignment explanation
Indices: 1440815--1440866 Score: 86
Period size: 18 Copynumber: 2.8 Consensus size: 18
1440805 GTAAAATGAA
1440815 TAAATAAATGATTTTGATTT
1 TAAA-AAAT-ATTTTGATTT
1440835 TAAAAAATATTTTGATTT
1 TAAAAAATATTTTGATTT
1440853 TAAAAAATATTTTG
1 TAAAAAATATTTTG
1440867 GGAGTCGCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 24 0.75
19 4 0.12
20 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (18 bp):
TAAAAAATATTTTGATTT
Found at i:1441566 original size:3 final size:3
Alignment explanation
Indices: 1441558--1441587 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1441548 TATATGACTA
1441558 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1441588 TAAATATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1442316 original size:21 final size:20
Alignment explanation
Indices: 1442289--1442337 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1442279 TATTTATTAT
1442289 TTTTTTTTATTTTAACTTG-
1 TTTTTTTTATTTTAACTTGC
1442308 TTGTTTTTTATTTTAACTTGC
1 TT-TTTTTTATTTTAACTTGC
1442329 TTTTTTTTA
1 TTTTTTTTA
1442338 ATCTCCTACT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.14, C:0.06, G:0.06, T:0.73
Consensus pattern (20 bp):
TTTTTTTTATTTTAACTTGC
Found at i:1443191 original size:137 final size:139
Alignment explanation
Indices: 1443038--1443378 Score: 442
Period size: 137 Copynumber: 2.5 Consensus size: 139
1443028 ATTTCTTCAG
* *
1443038 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTATCATTGTGAACTTCTTCTGGAAATATTG
1 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTGTGAACTTCTTCTGGAAATGTTG
* * ** *
1443103 ATCCTCAAAAGAGG-T-GTCGTTGATTCAACTTCATATG-TGATGAATTAAGGC-AAGGTTGAAG
66 ATCCTCAAAAGAGGTTCGTCGTTCATTCAACTTCATA-GATGATGAATCAA-GCTAAGGTCAAAC
1443164 AAGTTCTTCTC
129 AAGTTCTTCTC
* * *
1443175 ATTATGAACTTCTTCTTCCTTTTCAGATGAGTTCTTCTCATTATGAAC-TC-TCTGAAAATGTTG
1 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTGTGAACTTCTTCTGGAAATGTTG
* ** * * * *
1443238 ATCCTCCAGGGAGGTTCTTCTTTCATTTAACTTCATAGATGATGAATCAAGCTAAGGTCAAACAT
66 ATCCTCAAAAGAGGTTCGTCGTTCATTCAACTTCATAGATGATGAATCAAGCTAAGGTCAAACAA
1443303 GTTCTTCTC
131 GTTCTTCTC
* * *
1443312 ATTATGAACTTCTTATTCCTCTTCAGATAAGTTCTTCTCATTGTGAACTTCTTTTGGAAATGTTG
1 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTGTGAACTTCTTCTGGAAATGTTG
1443377 AT
66 AT
1443379 GCTGATCTAT
Statistics
Matches: 175, Mismatches: 23, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
135 22 0.13
136 6 0.03
137 132 0.75
138 2 0.01
139 13 0.07
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (139 bp):
ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTGTGAACTTCTTCTGGAAATGTTG
ATCCTCAAAAGAGGTTCGTCGTTCATTCAACTTCATAGATGATGAATCAAGCTAAGGTCAAACAA
GTTCTTCTC
Found at i:1443510 original size:123 final size:123
Alignment explanation
Indices: 1443298--1443624 Score: 494
Period size: 123 Copynumber: 2.7 Consensus size: 123
1443288 GCTAAGGTCA
* * * *
1443298 AACATGTTCTTCTCATTATGAACTTCTTATTCCTCTTCAGATAAGTTCTTCTCATTGTGAACTTC
1 AACAAGTTCTTCTCATTATGAACTTCTTATTCCTTTTCAGATGAGTTCTTCTCATTATGAACTTC
*
1443363 TTTTGGAAATGTTGATGCTGATCTATCTCCTTCTGTAATAGAATAGAGAAAAAGGTTG
66 TTTTGGAAATGTTGATGCTGATCTATCTCCTTCTGTAATACAATAGAGAAAAAGGTTG
* * *
1443421 AACAAGTTCTTCTTATTATGAACTTTTTCTTCCTTTTCAGATGAGTTCTTCTCATTATGAACTTC
1 AACAAGTTCTTCTCATTATGAACTTCTTATTCCTTTTCAGATGAGTTCTTCTCATTATGAACTTC
* * * * *
1443486 TTTTGGAAATGCTGATGCTGATCTATCTTCTTCTGTGATACAATTGAGCAAAAGGTTG
66 TTTTGGAAATGTTGATGCTGATCTATCTCCTTCTGTAATACAATAGAGAAAAAGGTTG
*
1443544 AACAAGTTCTTCTCATTATGAACTTCTTATTCCTCTTT-ATATGAGTTCTTCTCATTATGAACTT
1 AACAAGTTCTTCTCATTATGAACTTCTTATTCCT-TTTCAGATGAGTTCTTCTCATTATGAACTT
* *
1443608 CCTATGGAAATGTTGAT
65 CTTTTGGAAATGTTGAT
1443625 CCATCGAGTG
Statistics
Matches: 183, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
123 180 0.98
124 3 0.02
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (123 bp):
AACAAGTTCTTCTCATTATGAACTTCTTATTCCTTTTCAGATGAGTTCTTCTCATTATGAACTTC
TTTTGGAAATGTTGATGCTGATCTATCTCCTTCTGTAATACAATAGAGAAAAAGGTTG
Found at i:1443724 original size:37 final size:36
Alignment explanation
Indices: 1443663--1443862 Score: 166
Period size: 36 Copynumber: 5.5 Consensus size: 36
1443653 AGTGAAACTG
* ** *
1443663 TCTCAAGCGAGACGAATCTTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGATAAATTTTGTTTTAAGAAAAACAA
* ** **
1443699 TCTCAAGTGAGATAAATTGTTGTTTTGAGTGAAACTG
1 TCTCAAGTGAGATAAATT-TTGTTTTAAGAAAAACAA
* * * **
1443736 TCTCAAGCGAGACAAATTTTGCTTTAAGAAAATTAA
1 TCTCAAGTGAGATAAATTTTGTTTTAAGAAAAACAA
* ** **
1443772 TCTCAAGTGAGATAAATTGTTGTTTTGAGTGAAACTG
1 TCTCAAGTGAGATAAATT-TTGTTTTAAGAAAAACAA
* *** *
1443809 TCTCAAGCGAGACGTAGTTTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGATAAATTTTGTTTTAAGAAAAACAA
1443845 TCTCAAGTGAGATAAATT
1 TCTCAAGTGAGATAAATT
1443863 ATTATTTGAA
Statistics
Matches: 118, Mismatches: 44, Indels: 4
0.71 0.27 0.02
Matches are distributed among these distances:
36 66 0.56
37 52 0.44
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (36 bp):
TCTCAAGTGAGATAAATTTTGTTTTAAGAAAAACAA
Found at i:1443762 original size:73 final size:73
Alignment explanation
Indices: 1443653--1443862 Score: 357
Period size: 73 Copynumber: 2.9 Consensus size: 73
1443643 TTCTGTTTCT
*
1443653 AGTGAAACTGTCTCAAGCGAGACGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
1 AGTGAAACTGTCTCAAGCGAGACGAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
1443718 TTGTTTTG
66 TTGTTTTG
* * **
1443726 AGTGAAACTGTCTCAAGCGAGACAAATTTTGCTTTAAGAAAATTAATCTCAAGTGAGATAAATTG
1 AGTGAAACTGTCTCAAGCGAGACGAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
1443791 TTGTTTTG
66 TTGTTTTG
* *
1443799 AGTGAAACTGTCTCAAGCGAGACGTAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATT
1 AGTGAAACTGTCTCAAGCGAGACGAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATT
1443863 ATTATTTGAA
Statistics
Matches: 126, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 126 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (73 bp):
AGTGAAACTGTCTCAAGCGAGACGAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
TTGTTTTG
Found at i:1444630 original size:22 final size:22
Alignment explanation
Indices: 1444553--1444631 Score: 131
Period size: 22 Copynumber: 3.6 Consensus size: 22
1444543 AATAAAGCTT
*
1444553 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
1444575 TCATCTTTAAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
1444597 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
1444619 TCATATTTGAAGA
1 TCATCTTTGAAGA
1444632 ATGTAGATGT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:1452026 original size:43 final size:44
Alignment explanation
Indices: 1451962--1452047 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 44
1451952 CTGTGCATCA
* * * *
1451962 AACAAAACTTTTACATGTAGGGGACAGCTTTCAGTCCTAACTTC
1 AACAAAACTATTACATATAGGGGACAACTTTCACTCCTAACTTC
* *
1452006 AACAAAAC-ATTACATATAGGGGATAACTTTCCCTCCTAACTT
1 AACAAAACTATTACATATAGGGGACAACTTTCACTCCTAACTT
1452048 ATCTAAAGCC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 28 0.78
44 8 0.22
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (44 bp):
AACAAAACTATTACATATAGGGGACAACTTTCACTCCTAACTTC
Found at i:1452562 original size:36 final size:36
Alignment explanation
Indices: 1452502--1452570 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
1452492 TCTTACCGTA
* *
1452502 GAATGCTTTTGGTATCAATCTAACAGGATCTTTCTG
1 GAATACTTTTGGTATCAATATAACAGGATCTTTCTG
*
1452538 GAATACTTTTGGTATTAATATAACAGGATCTTT
1 GAATACTTTTGGTATCAATATAACAGGATCTTT
1452571 GTGTGCATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (36 bp):
GAATACTTTTGGTATCAATATAACAGGATCTTTCTG
Found at i:1453447 original size:15 final size:16
Alignment explanation
Indices: 1453421--1453461 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
1453411 TTTAATATCT
1453421 AAAA-ATAA-AATAAA
1 AAAATATAATAATAAA
*
1453435 AACAT-TAATAATAAA
1 AAAATATAATAATAAA
1453450 AAAATATAATAA
1 AAAATATAATAA
1453462 ATATTATAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 6 0.27
15 10 0.45
16 6 0.27
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAATATAATAATAAA
Found at i:1453467 original size:26 final size:25
Alignment explanation
Indices: 1453420--1453480 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
1453410 ATTTAATATC
*
1453420 TAAAAATAAAATAAAAACATTAATAA-
1 TAAAAA-AATATAAAAACATT-ATAAG
*
1453446 TAAAAAAATATAATAAATATTATAAG
1 TAAAAAAATATAA-AAACATTATAAG
*
1453472 TAATAAAAT
1 TAAAAAAAT
1453481 TTTTGAAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 10 0.33
26 20 0.67
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (25 bp):
TAAAAAAATATAAAAACATTATAAG
Found at i:1456171 original size:14 final size:14
Alignment explanation
Indices: 1456152--1456183 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1456142 TCCTTTGATA
*
1456152 CCATCAAATGTAGC
1 CCATCAAATGTAAC
1456166 CCATCAAATGTAAC
1 CCATCAAATGTAAC
1456180 CCAT
1 CCAT
1456184 TATCGATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.31, G:0.09, T:0.22
Consensus pattern (14 bp):
CCATCAAATGTAAC
Found at i:1456693 original size:46 final size:46
Alignment explanation
Indices: 1456621--1456716 Score: 147
Period size: 46 Copynumber: 2.1 Consensus size: 46
1456611 ATTGGAAATT
* * *
1456621 ACCATCATGTAAATTGGTATTTGGATTTATCATCCGGTAAGGATGC
1 ACCAACATGTAAATCGGTAATTGGATTTATCATCCGGTAAGGATGC
* *
1456667 ACCAACATGTATATCGGTAATTGGATTTATCATCTGGTAAGGATGC
1 ACCAACATGTAAATCGGTAATTGGATTTATCATCCGGTAAGGATGC
1456713 ACCA
1 ACCA
1456717 GCCTATATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (46 bp):
ACCAACATGTAAATCGGTAATTGGATTTATCATCCGGTAAGGATGC
Found at i:1459870 original size:13 final size:13
Alignment explanation
Indices: 1459861--1459895 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
1459851 TGAGCCACTA
1459861 AGTCGAGCCACCG
1 AGTCGAGCCACCG
*
1459874 AGCCGAGCCACCG
1 AGTCGAGCCACCG
1459887 AGTCGAGCC
1 AGTCGAGCC
1459896 GAGCCGCTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.23, C:0.40, G:0.31, T:0.06
Consensus pattern (13 bp):
AGTCGAGCCACCG
Found at i:1459911 original size:18 final size:18
Alignment explanation
Indices: 1459871--1459919 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1459861 AGTCGAGCCA
*
1459871 CCGAGCCGAGCCACCGAG
1 CCGAGCCGAGCCGCCGAG
* *
1459889 TCGAGCCGAGCCGCTGAG
1 CCGAGCCGAGCCGCCGAG
*
1459907 CCGAGCCAAGCCG
1 CCGAGCCGAGCCG
1459920 ACCAAGCCTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.20, C:0.41, G:0.35, T:0.04
Consensus pattern (18 bp):
CCGAGCCGAGCCGCCGAG
Found at i:1462663 original size:30 final size:30
Alignment explanation
Indices: 1462577--1462682 Score: 133
Period size: 31 Copynumber: 3.5 Consensus size: 30
1462567 TTAATGTAAC
* * *
1462577 TCTTGAGTAGGCCCCGTGGCCCTTAGATCAT
1 TCTTGGGTAGG-CCCGTGGCCCTGAGATCTT
*
1462608 TCTTGGGTAGG-CCATGCGACCCTGAGATCTT
1 TCTTGGGTAGGCCCGTG-G-CCCTGAGATCTT
*
1462639 TCTTGGGTAGGCCCGTGGCCCTGAGAACTT
1 TCTTGGGTAGGCCCGTGGCCCTGAGATCTT
1462669 TCTTGGGTAGGCCC
1 TCTTGGGTAGGCCC
1462683 ATAGGCCCCA
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
29 4 0.06
30 26 0.39
31 32 0.48
32 4 0.06
ACGTcount: A:0.14, C:0.27, G:0.30, T:0.28
Consensus pattern (30 bp):
TCTTGGGTAGGCCCGTGGCCCTGAGATCTT
Found at i:1467574 original size:62 final size:62
Alignment explanation
Indices: 1467452--1467592 Score: 158
Period size: 62 Copynumber: 2.3 Consensus size: 62
1467442 ATCATACATA
* * * * * * * *
1467452 GGTAGGCTTTGCGGCCCTGGGATTTTTATTGGGTAGGCCCTGTAGCCCTGATATCATTCTTT
1 GGTAGGCTATACGGCCCTGAGATCTTTATTGGGTAGGCCCTGTAGCCCTAAGAACATTCTTG
* * * *
1467514 GGTAGGCTATACGGCTCTGAGATCTTTCTTGGGTAGGCCCTGTGGCCCTAAGAACTTTCTTG
1 GGTAGGCTATACGGCCCTGAGATCTTTATTGGGTAGGCCCTGTAGCCCTAAGAACATTCTTG
1467576 GGTAGGCTCATA-GGCCC
1 GGTAGGCT-ATACGGCCC
1467593 CAAGATGCTC
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
62 62 0.95
63 3 0.05
ACGTcount: A:0.15, C:0.23, G:0.30, T:0.33
Consensus pattern (62 bp):
GGTAGGCTATACGGCCCTGAGATCTTTATTGGGTAGGCCCTGTAGCCCTAAGAACATTCTTG
Found at i:1467592 original size:31 final size:31
Alignment explanation
Indices: 1467508--1467597 Score: 85
Period size: 31 Copynumber: 2.9 Consensus size: 31
1467498 CCTGATATCA
* * * *
1467508 TTCTTTGGTAGGCT-ATACGGCTCTGAGATCT
1 TTCTTGGGTAGGCTCATA-GGCCCTAAGAACT
* *
1467539 TTCTTGGGTAGGC-CCTGTGGCCCTAAGAACT
1 TTCTTGGGTAGGCTCAT-AGGCCCTAAGAACT
*
1467570 TTCTTGGGTAGGCTCATAGGCCCCAAGA
1 TTCTTGGGTAGGCTCATAGGCCCTAAGA
1467598 TGCTCTCTTA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
31 45 0.96
32 2 0.04
ACGTcount: A:0.18, C:0.23, G:0.28, T:0.31
Consensus pattern (31 bp):
TTCTTGGGTAGGCTCATAGGCCCTAAGAACT
Found at i:1470410 original size:62 final size:62
Alignment explanation
Indices: 1470313--1470436 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
1470303 AAACAGTTAT
1470313 GATAGCGCTCTGGTTGTCAGAAACTTGATTAGAAGTCAAACGAACCACTTGTTCTCTAAGAC
1 GATAGCGCTCTGGTTGTCAGAAACTTGATTAGAAGTCAAACGAACCACTTGTTCTCTAAGAC
1470375 GATAGCGCTCTGGTTGTCAGAAACTTGATTAGAAGTCAAACGAACCACTTGTTCTCTAAGAC
1 GATAGCGCTCTGGTTGTCAGAAACTTGATTAGAAGTCAAACGAACCACTTGTTCTCTAAGAC
1470437 ATAATGAAGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (62 bp):
GATAGCGCTCTGGTTGTCAGAAACTTGATTAGAAGTCAAACGAACCACTTGTTCTCTAAGAC
Found at i:1478718 original size:23 final size:23
Alignment explanation
Indices: 1478688--1478744 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
1478678 AAAGTAAAAT
1478688 TCAAAGTCAACGGGTTGACTCGG
1 TCAAAGTCAACGGGTTGACTCGG
*
1478711 TCAAAGTCAACGGGTTGACTTGG
1 TCAAAGTCAACGGGTTGACTCGG
1478734 TCAAAGTCAAC
1 TCAAAGTCAAC
1478745 AGTTAACAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (23 bp):
TCAAAGTCAACGGGTTGACTCGG
Found at i:1482538 original size:24 final size:24
Alignment explanation
Indices: 1482511--1482562 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1482501 AACGGATATA
*
1482511 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
1482535 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
1482559 TCAA
1 TCAA
1482563 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:1482563 original size:24 final size:24
Alignment explanation
Indices: 1482527--1482645 Score: 120
Period size: 24 Copynumber: 5.0 Consensus size: 24
1482517 ATCAAAACAT
*
1482527 AAATCAGGTCAAGTATCATATCAG
1 AAATCAGGTCAAGTATCAGATCAG
*
1482551 AAATCAGGTCAAGTAACAGATCAG
1 AAATCAGGTCAAGTATCAGATCAG
*
1482575 -AATCCAAGTCAAGTATCAGATCAG
1 AAAT-CAGGTCAAGTATCAGATCAG
* *
1482599 -AATCTATGTC-AGATATTAGATCAG
1 AAATC-AGGTCAAG-TATCAGATCAG
*
1482623 -AATCCATGTCAAGTATCAGATCA
1 AAAT-CAGGTCAAGTATCAGATCA
1482646 TAATTCAAAT
Statistics
Matches: 83, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.07
24 74 0.89
25 3 0.04
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (24 bp):
AAATCAGGTCAAGTATCAGATCAG
Found at i:1482620 original size:48 final size:48
Alignment explanation
Indices: 1482534--1482645 Score: 147
Period size: 48 Copynumber: 2.3 Consensus size: 48
1482524 CATAAATCAG
*
1482534 GTCAAGTATCATATCAGAAATCAGGTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAAATCAGGTCAAGTAACAGATCAGAATCCAA
* ** *
1482582 GTCAAGTATCAGATCAG-AATCTATGTC-AGATATTAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAAATC-AGGTCAAG-TAACAGATCAGAATCCAA
1482630 GTCAAGTATCAGATCA
1 GTCAAGTATCAGATCA
1482646 TAATTCAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
47 6 0.11
48 51 0.89
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAAATCAGGTCAAGTAACAGATCAGAATCCAA
Found at i:1485178 original size:18 final size:18
Alignment explanation
Indices: 1485152--1485191 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1485142 AACGGTCAAT
* *
1485152 GGGTCAACGGGTCGGGTC
1 GGGTAAACGGGTAGGGTC
1485170 GGGTAAACGGGTAGGGTC
1 GGGTAAACGGGTAGGGTC
1485188 GGGT
1 GGGT
1485192 TATGACCGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.53, T:0.17
Consensus pattern (18 bp):
GGGTAAACGGGTAGGGTC
Found at i:1487597 original size:15 final size:16
Alignment explanation
Indices: 1487577--1487607 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1487567 TCACAAACAT
1487577 AATTTGTTTA-TAAAA
1 AATTTGTTTATTAAAA
1487592 AATTTGTTTATTAAAA
1 AATTTGTTTATTAAAA
1487608 CAAATAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (16 bp):
AATTTGTTTATTAAAA
Found at i:1490758 original size:24 final size:24
Alignment explanation
Indices: 1490742--1490838 Score: 122
Period size: 24 Copynumber: 4.0 Consensus size: 24
1490732 CAGAAAATAA
* *
1490742 AACATAATTCAGATCAGATATCAT
1 AACATAATTCAGATCAGAAATCAG
* * * *
1490766 AACAGAATCCAGGTCAGGAATCAG
1 AACATAATTCAGATCAGAAATCAG
*
1490790 AACAAAATTCAGATCAGAAATCAG
1 AACATAATTCAGATCAGAAATCAG
*
1490814 AACATAATTCAAATCAGAAATCAG
1 AACATAATTCAGATCAGAAATCAG
1490838 A
1 A
1490839 TAAAACATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.20
Consensus pattern (24 bp):
AACATAATTCAGATCAGAAATCAG
Found at i:1490813 original size:12 final size:12
Alignment explanation
Indices: 1490750--1490839 Score: 58
Period size: 12 Copynumber: 7.5 Consensus size: 12
1490740 AAAACATAAT
*
1490750 TCAGATCAGATA
1 TCAGATCAGAAA
* *
1490762 TCATAACAG-AA
1 TCAGATCAGAAA
* *
1490773 TCCAGGTCAGGAA
1 T-CAGATCAGAAA
*
1490786 TCAGAACA-AAA
1 TCAGATCAGAAA
1490797 TTCAGATCAGAAA
1 -TCAGATCAGAAA
* * *
1490810 TCAGAACATAAT
1 TCAGATCAGAAA
*
1490822 TCAAATCAGAAA
1 TCAGATCAGAAA
1490834 TCAGAT
1 TCAGAT
1490840 AAAACATTCA
Statistics
Matches: 56, Mismatches: 18, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
11 4 0.07
12 46 0.82
13 6 0.11
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (12 bp):
TCAGATCAGAAA
Found at i:1493206 original size:20 final size:20
Alignment explanation
Indices: 1493177--1493214 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1493167 GTCAAGACAA
*
1493177 CGGGTCGGGTCGAGTCAAAC
1 CGGGTAGGGTCGAGTCAAAC
*
1493197 CGGGTAGGGTCGGGTCAA
1 CGGGTAGGGTCGAGTCAA
1493215 CGGGTTTGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.21, G:0.45, T:0.16
Consensus pattern (20 bp):
CGGGTAGGGTCGAGTCAAAC
Found at i:1496393 original size:12 final size:12
Alignment explanation
Indices: 1496376--1496445 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
1496366 ACGGAGATAT
*
1496376 CAGAAATCAAAA
1 CAGAAATCAGAA
* *
1496388 CAGAAATCATAT
1 CAGAAATCAGAA
*
1496400 CAGATATCAGAA
1 CAGAAATCAGAA
*
1496412 CAG-AATCCAGAT
1 CAGAAAT-CAGAA
1496424 CAGAAATCAGAA
1 CAGAAATCAGAA
*
1496436 CAGAATTCAG
1 CAGAAATCAG
1496446 GTTATGTATC
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.89
13 3 0.06
ACGTcount: A:0.51, C:0.19, G:0.14, T:0.16
Consensus pattern (12 bp):
CAGAAATCAGAA
Done.