Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007884.1 Hibiscus syriacus cultivar Beakdansim tig00110264_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: 2814991
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 13
Found at i:1338857 original size:43 final size:42
Alignment explanation
Indices: 1338796--1338880 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 42
1338786 TTAGTTTTGT
* * * * *
1338796 CATTTGCTCTTTTGAATCATCTTGGAATTTTTTTTGCTTGATC
1 CATTTGCTCATTTGAATCACCCTGGAA-CTTTTTTACTTGATC
*
1338839 CATTTGTTCATTTGAATCACCCTGGAACTTTTTTACTTGATC
1 CATTTGCTCATTTGAATCACCCTGGAACTTTTTTACTTGATC
1338881 AATCATATCT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 13 0.36
43 23 0.64
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.49
Consensus pattern (42 bp):
CATTTGCTCATTTGAATCACCCTGGAACTTTTTTACTTGATC
Found at i:1339446 original size:43 final size:44
Alignment explanation
Indices: 1339365--1339447 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 44
1339355 CGGTGCATCA
* * *
1339365 AACAAAACTTTTACATGTAGGGGACATCTTTCAGTCCTAACTTC
1 AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTC
* *
1339409 AACAAAAC-TTTACATATAGGGGATAACTTTCCCTCCTAA
1 AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAA
1339448 TTTCTCTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
43 26 0.76
44 8 0.24
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (44 bp):
AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTC
Found at i:1341643 original size:2 final size:2
Alignment explanation
Indices: 1341636--1341707 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
1341626 ATTTAAACAA
1341636 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
1341678 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
1341708 TTGTATGACT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1341838 original size:21 final size:21
Alignment explanation
Indices: 1341814--1341853 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1341804 AGTGACTAAA
*
1341814 ATAAATAAAAT-TAAGAATAAC
1 ATAAACAAAATGTAA-AATAAC
1341835 ATAAACAAAATGTAAAATA
1 ATAAACAAAATGTAAAATA
1341854 TCAAAGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (21 bp):
ATAAACAAAATGTAAAATAAC
Found at i:1343033 original size:3 final size:3
Alignment explanation
Indices: 1343027--1343083 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
1343017 ATTATTTTTT
** * *
1343027 TAA TAA TAA TAA TTTT TAA TAA TAA TAA TAC TAA TATT TAA TAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
1343074 TAA TAA TAA T
1 TAA TAA TAA T
1343084 TTTAAATAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:1343044 original size:16 final size:16
Alignment explanation
Indices: 1343023--1343055 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1343013 ATTTATTATT
1343023 TTTTTAATAATAATAA
1 TTTTTAATAATAATAA
1343039 TTTTTAATAATAATAA
1 TTTTTAATAATAATAA
1343055 T
1 T
1343056 ACTAATATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTTAATAATAATAA
Found at i:1343052 original size:22 final size:22
Alignment explanation
Indices: 1343027--1343092 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
1343017 ATTATTTTTT
1343027 TAATAATAATAATTTTTAATAA
1 TAATAATAATAATTTTTAATAA
* *
1343049 TAATAATACTAATATTTAATAA
1 TAATAATAATAATTTTTAATAA
*
1343071 TAATAATAATAATTTTAAATAA
1 TAATAATAATAATTTTTAATAA
1343093 ATAAAAAGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TAATAATAATAATTTTTAATAA
Found at i:1343092 original size:16 final size:15
Alignment explanation
Indices: 1343024--1343088 Score: 64
Period size: 16 Copynumber: 4.4 Consensus size: 15
1343014 TTTATTATTT
1343024 TTTTAATAATAATAA
1 TTTTAATAATAATAA
1343039 TTTTTAATAATAATAA
1 -TTTTAATAATAATAA
** *
1343055 TACTAATATTTAATAA
1 TTTTAATA-ATAATAA
1343071 ---TAATAATAATAA
1 TTTTAATAATAATAA
1343083 TTTTAA
1 TTTTAA
1343089 ATAAATAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
12 6 0.15
13 5 0.12
15 9 0.22
16 21 0.51
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
TTTTAATAATAATAA
Found at i:1345563 original size:22 final size:22
Alignment explanation
Indices: 1345538--1345579 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1345528 TTATAACTTT
1345538 TAAAAAAAAATTATTTTAAAAA
1 TAAAAAAAAATTATTTTAAAAA
**
1345560 TAAAAAATTATTATTTTAAA
1 TAAAAAAAAATTATTTTAAA
1345580 CCCCAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAAAAAAAATTATTTTAAAAA
Found at i:1348730 original size:15 final size:15
Alignment explanation
Indices: 1348710--1348746 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
1348700 TTATCGAGTT
1348710 AAGTACTAATCCTTA
1 AAGTACTAATCCTTA
1348725 AAGTACTAATCCTTA
1 AAGTACTAATCCTTA
1348740 AAGTACT
1 AAGTACT
1348747 TTCTCATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (15 bp):
AAGTACTAATCCTTA
Found at i:1353214 original size:12 final size:12
Alignment explanation
Indices: 1353197--1353255 Score: 62
Period size: 10 Copynumber: 5.6 Consensus size: 12
1353187 CTTGGTGCAT
1353197 GGATGCACATCA
1 GGATGCACATCA
1353209 GGATG--CATC-
1 GGATGCACATCA
1353218 -GATGCACATCA
1 GGATGCACATCA
1353229 GGATG--CATC-
1 GGATGCACATCA
1353238 -GATGCACATCA
1 GGATGCACATCA
1353249 GGATGCA
1 GGATGCA
1353256 TCGATGCACT
Statistics
Matches: 39, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
8 8 0.21
10 16 0.41
12 15 0.38
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.19
Consensus pattern (12 bp):
GGATGCACATCA
Found at i:1353221 original size:20 final size:20
Alignment explanation
Indices: 1353192--1353264 Score: 137
Period size: 20 Copynumber: 3.6 Consensus size: 20
1353182 GCAGCCTTGG
*
1353192 TGCATGGATGCACATCAGGA
1 TGCATCGATGCACATCAGGA
1353212 TGCATCGATGCACATCAGGA
1 TGCATCGATGCACATCAGGA
1353232 TGCATCGATGCACATCAGGA
1 TGCATCGATGCACATCAGGA
1353252 TGCATCGATGCAC
1 TGCATCGATGCAC
1353265 TAATTGCATT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.29, C:0.25, G:0.26, T:0.21
Consensus pattern (20 bp):
TGCATCGATGCACATCAGGA
Found at i:1357990 original size:17 final size:18
Alignment explanation
Indices: 1357962--1357995 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1357952 ATTAATAGAT
1357962 AAGGATATAAAAATAATA
1 AAGGATATAAAAATAATA
1357980 AAGGATA-AAAAATAAT
1 AAGGATATAAAAATAAT
1357996 TGAAGGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.21
Consensus pattern (18 bp):
AAGGATATAAAAATAATA
Found at i:1358763 original size:2 final size:2
Alignment explanation
Indices: 1358756--1358801 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1358746 ATTTAAACAA
1358756 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
1358798 AT AT
1 AT AT
1358802 TTGTATGACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1358932 original size:21 final size:21
Alignment explanation
Indices: 1358908--1358947 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1358898 AGTGACTAAA
*
1358908 ATAAATAAAAT-TAAGAATAAC
1 ATAAACAAAATGTAA-AATAAC
1358929 ATAAACAAAATGTAAAATA
1 ATAAACAAAATGTAAAATA
1358948 TCAAAGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (21 bp):
ATAAACAAAATGTAAAATAAC
Found at i:1360117 original size:3 final size:3
Alignment explanation
Indices: 1360111--1360190 Score: 90
Period size: 3 Copynumber: 26.3 Consensus size: 3
1360101 ATTATTTTTT
** *
1360111 TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TTTT TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA
* *
1360156 TAA TAA TAC TAA TATT TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA T
1360191 TTTAAATAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.03
3 59 0.92
4 3 0.05
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:1360158 original size:22 final size:22
Alignment explanation
Indices: 1360111--1360195 Score: 122
Period size: 22 Copynumber: 4.0 Consensus size: 22
1360101 ATTATTTTTT
1360111 TAATAATAATAATAATA--TAA
1 TAATAATAATAATAATATTTAA
*
1360131 TAATAATAATAATAATTTTTAA
1 TAATAATAATAATAATATTTAA
* *
1360153 TGATAATAATACTAATATTTAA
1 TAATAATAATAATAATATTTAA
1360175 TAATAATAATAATAAT-TTTAA
1 TAATAATAATAATAATATTTAA
1360196 ATAAATAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
20 16 0.28
21 5 0.09
22 36 0.63
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (22 bp):
TAATAATAATAATAATATTTAA
Found at i:1361231 original size:3 final size:3
Alignment explanation
Indices: 1361223--1361302 Score: 151
Period size: 3 Copynumber: 26.7 Consensus size: 3
1361213 TTTTTATCCA
1361223 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1361271 TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1361303 AATATATATT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1361314 original size:11 final size:11
Alignment explanation
Indices: 1361298--1361329 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
1361288 TTATTATTAT
1361298 TATTAAATATA
1 TATTAAATATA
1361309 TATTAAATATA
1 TATTAAATATA
1361320 TATATAAATA
1 TAT-TAAATA
1361330 AATAATTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATTAAATATA
Found at i:1361822 original size:13 final size:13
Alignment explanation
Indices: 1361804--1361828 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1361794 AGAGAGACGG
1361804 AGAGAAAAAAAAC
1 AGAGAAAAAAAAC
1361817 AGAGAAAAAAAA
1 AGAGAAAAAAAA
1361829 AGATATACTA
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:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (13 bp):
AGAGAAAAAAAAC
Found at i:1374487 original size:16 final size:16
Alignment explanation
Indices: 1374461--1374505 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1374451 TTTGAATACA
*
1374461 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
1374478 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
1374493 ATTCAATTTATTT
1 ATTCAATTTATTT
1374506 TTGGAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:1376217 original size:83 final size:83
Alignment explanation
Indices: 1375244--1376215 Score: 1528
Period size: 83 Copynumber: 11.7 Consensus size: 83
1375234 CATTAACTGA
1375244 AAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACA
1 AAGATGAATTTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CA
1375307 GAA-CAATCATTGAATTTAG
64 GAACCAATCATTGAATTTAG
*
1375326 AAGATAAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
1375390 AACCAATCATTGAATTTAG
65 AACCAATCATTGAATTTAG
* * * * *
1375409 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGTAGA
1 AAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1375474 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
*
1375492 AAGATGAATTTGCTCATAGCATCTTCTGGAAGTGCTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
1375556 AA-CAATCATTGAATTTAG
65 AACCAATCATTGAATTTAG
1375574 AAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
*
1375638 AATCAATCATTGAATTTAG
65 AACCAATCATTGAATTTAG
1375657 AAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
1375721 AACCAATCATTGAATTTAG
65 AACCAATCATTGAATTTAG
* * * * ** *
1375740 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGACCTGGTTAAGTAGA
1 AAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
**
1375805 ACCAATCATTGAATTGGG
66 ACCAATCATTGAATTTAG
* *
1375823 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
1 AAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1375888 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
* * * *
1375906 AAGATGAATTTGTTAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
1 AAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
**
1375971 ACCAATCATTGAATTGGG
66 ACCAATCATTGAATTTAG
* * *
1375989 AAGATGAATATGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
1 AAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
**
1376054 ACCAATCATTGAATTGGG
66 ACCAATCATTGAATTTAG
* *
1376072 AAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGA
1 AAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1376137 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
* *
1376155 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 AAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1376216 TAAGAACTAC
Statistics
Matches: 832, Mismatches: 52, Indels: 11
0.93 0.06 0.01
Matches are distributed among these distances:
82 147 0.18
83 680 0.82
84 5 0.01
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (83 bp):
AAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
ACCAATCATTGAATTTAG
Found at i:1377049 original size:113 final size:113
Alignment explanation
Indices: 1376873--1377493 Score: 879
Period size: 113 Copynumber: 5.5 Consensus size: 113
1376863 TGGATTGACA
* * *
1376873 TTTCAAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGA
1 TTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * *
1376938 AGAATTTGTTCAACCTTCTGCCT-AATTCTATCACTTGATAGATCAGCT
66 AGAATTTGTTCAACCTTTTGCCTGAATTC-ATCACTTGATGGATCATCT
*
1376986 TTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGA
1 TTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * *
1377051 AGAATTTGTTCAACCTGTTACCTGAATTCATCACTTGATGGATTATCT
66 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCATCT
1377099 TTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
** * *
1377164 AGAATTTGTTCAACCTTTTTTCTGAATTCATCAAATTGATGGATTATCT
66 AGAATTTGTTCAACCTTTTGCCTGAATTCATC-ACTTGATGGATCATCT
1377213 TTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * * * *
1377278 AGAACTTGTTCAATCTTTTGCTTGAATTCATCATTTGATGGATCAACA
66 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCATCT
* *
1377326 TTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1 TTTCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* * * * *
1377390 GAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCATTTGATGGATCATCA
62 GAGAAGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCATCT
** * *
1377442 TCCCCAGCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-AGAAGAA
1 TTTCCAG-AGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
1377494 TTTATTCAAT
Statistics
Matches: 470, Mismatches: 30, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
112 3 0.01
113 234 0.50
114 125 0.27
115 2 0.00
116 87 0.19
117 17 0.04
118 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (113 bp):
TTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCATCT
Found at i:1377306 original size:227 final size:225
Alignment explanation
Indices: 1376854--1377493 Score: 890
Period size: 227 Copynumber: 2.8 Consensus size: 225
1376844 ATTCAAATCT
* *
1376854 ATCATTTGATGGATTGACATTTCAAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATT-ACATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* * * * *
1376919 GAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTCTGCCT-AATTCTATCACTTGATAGATCA
65 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTC-ATCAATTGATGGATCA
*
1376983 GCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
129 TCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
*
1377048 AGAAGAATTTGTTCAACCTGTTACCTGAATTC
194 AGAAGAACTTGTTCAACCTGTTACCTGAATTC
* *
1377080 ATCACTTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATTA-CATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
1377145 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTTCTGAATTCATCAAATTGATGGATTA
65 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATC-AATTGATGGATCA
*
1377210 TCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
129 TCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
* * * *
1377275 AGAAGAACTTGTTCAATCTTTTGCTTGAATTC
194 AGAAGAACTTGTTCAACCTGTTACCTGAATTC
* * *
1377307 ATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 ATCATTTGATGGAT-TACATTTCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGAA
* * * * *
1377371 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCATTTGATGGA
61 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATCAATTGATGGA
* ** * *
1377436 TCATCATCCCCAGCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-AGAAGAA
126 TCATCTTTTCCAG-AGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
1377494 TTTATTCAAT
Statistics
Matches: 370, Mismatches: 35, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
225 1 0.00
226 103 0.28
227 142 0.38
228 1 0.00
229 26 0.07
230 97 0.26
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (225 bp):
ATCATTTGATGGATTACATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATCAATTGATGGATCATC
TTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAG
AAGAACTTGTTCAACCTGTTACCTGAATTC
Found at i:1377637 original size:3 final size:3
Alignment explanation
Indices: 1377629--1377697 Score: 115
Period size: 3 Copynumber: 23.7 Consensus size: 3
1377619 TTTTTATCCA
1377629 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1377677 CA- TAT TAT TAT TAT TA- TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
1377698 AATATATATT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 3 0.05
3 59 0.95
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1377705 original size:11 final size:11
Alignment explanation
Indices: 1377691--1377722 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
1377681 TTATTATTAT
1377691 TATATTAAATA
1 TATATTAAATA
1377702 TATATTAAATA
1 TATATTAAATA
1377713 TATA-TAAATA
1 TATATTAAATA
1377723 AATAATTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATATTAAATA
Found at i:1378023 original size:13 final size:13
Alignment explanation
Indices: 1378005--1378036 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1377995 AGAAGCTCCA
1378005 ACGCCAGCCGTCC
1 ACGCCAGCCGTCC
1378018 ACGCCAGCCGTCC
1 ACGCCAGCCGTCC
1378031 ACGCCA
1 ACGCCA
1378037 TGGCTACGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.19, C:0.53, G:0.22, T:0.06
Consensus pattern (13 bp):
ACGCCAGCCGTCC
Found at i:1382898 original size:24 final size:24
Alignment explanation
Indices: 1382816--1382887 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
1382806 AACGAAAGAT
* * * *
1382816 ATCAGATATCAAAATAGAATTCAA
1 ATCAGATATCAGAACAGAATCCAG
* *
1382840 ATCAAATATCAGAACATAATCCAG
1 ATCAGATATCAGAACAGAATCCAG
*
1382864 ATCAGAAATCAGAACAGAATCCAG
1 ATCAGATATCAGAACAGAATCCAG
1382888 GTCATGTATC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.51, C:0.18, G:0.11, T:0.19
Consensus pattern (24 bp):
ATCAGATATCAGAACAGAATCCAG
Found at i:1388812 original size:20 final size:20
Alignment explanation
Indices: 1388787--1388873 Score: 165
Period size: 20 Copynumber: 4.3 Consensus size: 20
1388777 TTGGTACATG
*
1388787 GATGCACAGCAGGATGCATC
1 GATGCACATCAGGATGCATC
1388807 GATGCACATCAGGATGCATC
1 GATGCACATCAGGATGCATC
1388827 GATGCACATCAGGATGCATC
1 GATGCACATCAGGATGCATC
1388847 GATGCACATCAGGATGCATC
1 GATGCACATCAGGATGCATC
1388867 GATGCAC
1 GATGCAC
1388874 TAATTGCATT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.18
Consensus pattern (20 bp):
GATGCACATCAGGATGCATC
Found at i:1388822 original size:12 final size:12
Alignment explanation
Indices: 1388786--1388864 Score: 65
Period size: 10 Copynumber: 7.6 Consensus size: 12
1388776 CTTGGTACAT
*
1388786 GGATGCACAGCA
1 GGATGCACATCA
1388798 GGATG--CATC-
1 GGATGCACATCA
1388807 -GATGCACATCA
1 GGATGCACATCA
1388818 GGATG--CATC-
1 GGATGCACATCA
1388827 -GATGCACATCA
1 GGATGCACATCA
1388838 GGATG--CATC-
1 GGATGCACATCA
1388847 -GATGCACATCA
1 GGATGCACATCA
1388858 GGATGCA
1 GGATGCA
1388865 TCGATGCACT
Statistics
Matches: 54, Mismatches: 1, Indels: 24
0.68 0.01 0.30
Matches are distributed among these distances:
8 12 0.22
10 23 0.43
12 19 0.35
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.18
Consensus pattern (12 bp):
GGATGCACATCA
Found at i:1388950 original size:23 final size:23
Alignment explanation
Indices: 1388920--1388994 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
1388910 ATGGTACATC
1388920 GATGCACTAGTAGCAGGTGCATG
1 GATGCACTAGTAGCAGGTGCATG
1388943 GATGCACTAGTAGCAGGTGCATG
1 GATGCACTAGTAGCAGGTGCATG
* *
1388966 GATGCACT-GCAG-GGGTGCATG
1 GATGCACTAGTAGCAGGTGCATG
*
1388987 AATGCACT
1 GATGCACT
1388995 TTGACACCCT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
21 15 0.31
22 3 0.06
23 31 0.63
ACGTcount: A:0.25, C:0.19, G:0.35, T:0.21
Consensus pattern (23 bp):
GATGCACTAGTAGCAGGTGCATG
Found at i:1392052 original size:20 final size:20
Alignment explanation
Indices: 1392023--1392115 Score: 123
Period size: 20 Copynumber: 4.7 Consensus size: 20
1392013 GCAGCCTTGG
*
1392023 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
* * *
1392043 TGCATCGATGCATAGTAGTA
1 TGCATCGATGCACAGCAGGA
* *
1392063 TGCATCGATGCACAACATGA
1 TGCATCGATGCACAGCAGGA
*
1392083 TGCATCGATGCACATCAGGA
1 TGCATCGATGCACAGCAGGA
1392103 TGCATCGATGCAC
1 TGCATCGATGCAC
1392116 TAATTGCATT
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.22
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:1392160 original size:20 final size:20
Alignment explanation
Indices: 1392135--1392192 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
1392125 TCGAAATAGA
1392135 GTGCATGGATGCACTA-CATG
1 GTGCATGGATGCACTAGCA-G
*
1392155 GTGCATCGATGCACTAGTGGCAG
1 GTGCATGGATGCACTA---GCAG
1392178 GTGCATGGATGCACT
1 GTGCATGGATGCACT
1392193 GTAGGGGTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 15 0.47
23 15 0.47
24 2 0.06
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.24
Consensus pattern (20 bp):
GTGCATGGATGCACTAGCAG
Found at i:1393051 original size:23 final size:23
Alignment explanation
Indices: 1393025--1393069 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1393015 CACCACAGCT
*
1393025 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
1393048 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1393070 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:1393308 original size:149 final size:149
Alignment explanation
Indices: 1393048--1393351 Score: 590
Period size: 149 Copynumber: 2.0 Consensus size: 149
1393038 CGAAGTGCCC
* *
1393048 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1393113 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATA
1393178 CATATGTCTCGAAGAACCG
131 CATATGTCTCGAAGAACCG
1393197 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1393262 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATA
1393327 CATATGTCTCGAAGAACCG
131 CATATGTCTCGAAGAACCG
1393346 CGTAGA
1 CGTAGA
1393352 CCCTTGACTC
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATA
CATATGTCTCGAAGAACCG
Found at i:1393999 original size:2 final size:2
Alignment explanation
Indices: 1393992--1394021 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1393982 TCTCTTAGAC
1393992 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
1394022 TCACATGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1399119 original size:33 final size:33
Alignment explanation
Indices: 1399081--1399194 Score: 126
Period size: 33 Copynumber: 3.5 Consensus size: 33
1399071 AATGTATGTA
1399081 TATATGTATGTATGTATATGGAGAGAAGAAGCC
1 TATATGTATGTATGTATATGGAGAGAAGAAGCC
* * * * *
1399114 TATATGTATGTATGTCATGCATGCATATATGTA---
1 TATATGTATGTATGT-AT--ATGGAGAGAAGAAGCC
*
1399147 TATATCTATGTATGTATATGGAGAGAAGAAGCC
1 TATATGTATGTATGTATATGGAGAGAAGAAGCC
1399180 TATATGTATGTATGT
1 TATATGTATGTATGT
1399195 CATGCATGCA
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
30 8 0.13
32 2 0.03
33 43 0.68
34 2 0.03
36 8 0.13
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (33 bp):
TATATGTATGTATGTATATGGAGAGAAGAAGCC
Found at i:1399161 original size:66 final size:65
Alignment explanation
Indices: 1399060--1399256 Score: 294
Period size: 66 Copynumber: 3.0 Consensus size: 65
1399050 CCAACATATC
* *
1399060 ATGT-ATGCATGAATGTATGTATATATGTATGTATGTATATGGAGAGAAGAAGCCTATATGTATG
1 ATGTCATGCATGCATATATGTATATAT-TATGTATGTATATGGAGAGAAGAAGCCTATATGTATG
1399124 T
65 T
1399125 ATGTCATGCATGCATATATGTATATATCTATGTATGTATATGGAGAGAAGAAGCCTATATGTATG
1 ATGTCATGCATGCATATATGTATATAT-TATGTATGTATATGGAGAGAAGAAGCCTATATGTATG
1399190 T
65 T
*
1399191 ATGTCATGCATGCATATATG--TATA-TATGTATGCATATGGAGAGATGGAGAAGCCTATATGTA
1 ATGTCATGCATGCATATATGTATATATTATGTATGTATATGGAGAGA---AGAAGCCTATATGTA
1399253 TGT
63 TGT
1399256 A
1 A
1399257 ATATGGCAAT
Statistics
Matches: 124, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
62 19 0.15
64 4 0.03
65 23 0.19
66 78 0.63
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.36
Consensus pattern (65 bp):
ATGTCATGCATGCATATATGTATATATTATGTATGTATATGGAGAGAAGAAGCCTATATGTATGT
Found at i:1399225 original size:20 final size:21
Alignment explanation
Indices: 1399186--1399227 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1399176 AGCCTATATG
*
1399186 TATGTATGTCATGCATGCATA
1 TATGTATATCATGCATGCATA
*
1399207 TATGTATAT-ATGTATGCATA
1 TATGTATATCATGCATGCATA
1399227 T
1 T
1399228 GGAGAGATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.43
Consensus pattern (21 bp):
TATGTATATCATGCATGCATA
Found at i:1401320 original size:85 final size:84
Alignment explanation
Indices: 1401174--1401345 Score: 272
Period size: 85 Copynumber: 2.0 Consensus size: 84
1401164 ATCATATATC
*
1401174 TAACGATTATGAAAACAAAAGCTAAAATATTGAGATATTCTAAAATAATATAAAAATAATATATA
1 TAACGAATATGAAAACAAAAGCTAAAATATTGAGATATTCTAAAATAATATAAAAATAATATATA
* *
1401239 TCTAAAAATATTCTTAAAA
66 TATAAAAATATTCATAAAA
* * *
1401258 TAACGAATATGAAAACAAAATCTAAAATGTTGAGATTATTCTAAAATACTATAAAAATAATATAT
1 TAACGAATATGAAAACAAAAGCTAAAATATTGAGA-TATTCTAAAATAATATAAAAATAATATAT
*
1401323 ATATATAAATATTCATAAAA
65 ATATAAAAATATTCATAAAA
1401343 TAA
1 TAA
1401346 TTTAAATATT
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
84 32 0.40
85 48 0.60
ACGTcount: A:0.56, C:0.07, G:0.06, T:0.31
Consensus pattern (84 bp):
TAACGAATATGAAAACAAAAGCTAAAATATTGAGATATTCTAAAATAATATAAAAATAATATATA
TATAAAAATATTCATAAAA
Found at i:1401818 original size:23 final size:23
Alignment explanation
Indices: 1401771--1401819 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1401761 AATAACATAT
**
1401771 TAGGTAACACTAATATAATGTAA
1 TAGGTAACACTAATATAATAAAA
* *
1401794 TAGGTAGCACTTATATAATAAAA
1 TAGGTAACACTAATATAATAAAA
1401817 TAG
1 TAG
1401820 ATTAATTACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (23 bp):
TAGGTAACACTAATATAATAAAA
Found at i:1401946 original size:23 final size:23
Alignment explanation
Indices: 1401920--1402002 Score: 67
Period size: 23 Copynumber: 3.6 Consensus size: 23
1401910 ATCAAGCACA
*
1401920 ATAACATATTAGGTAACGATTAT
1 ATAACATAATAGGTAACGATTAT
** * *
1401943 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAACGATTAT
* * * *
1401966 ATAACGTAATAAGTAGCGCTTAT
1 ATAACATAATAGGTAACGATTAT
* *
1401989 ATAATAAAATAGGT
1 ATAACATAATAGGT
1402003 TAATTATTTA
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAACGATTAT
Found at i:1401965 original size:158 final size:158
Alignment explanation
Indices: 1401759--1402273 Score: 618
Period size: 158 Copynumber: 3.1 Consensus size: 158
1401749 ATTATTAAAT
* *
1401759 ACAATAACATATTAGGTAAC-ACTAATATAATGTAATAGGTAGCACTTATATAATAAAATAGATT
1 ACAATAACATATTAGGTAACGA-TTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGATT
* *
1401823 AATTACTTAAATTGTTATTACAACATATTAGGTAAACACCTAAAATGTTATCAATGATAACATAA
65 AATTAATTAAATTGTTATTACAACATATTAGGTAAACACCTAAAATGTTATCAAAGATAACATAA
*
1401888 CCGGTTAATTACTAGAAACATTATCAAGC
130 CCGGTTAATTACTAGAAACATTATAAAGC
1401917 ACAATAACATATTAGGTAACGATTATATAATGTAATAGGTAGCGCTTATATAACGTAATAAGTAG
1 ACAATAACATATTAGGTAACGATTATATAATGTAATAGGTAGCGCTTATATAA--TAA-AA-TA-
* *
1401982 CGCTTATATAATAAAATAGGTTAATTATTTAATTTGTTATTATAACATATTAGGTAAACGCCTAA
61 -G---AT-TAAT----TA----A-TTA---AA-TTGTTATTACAACATATTAGGTAAACACCTAA
* *
1402047 AATGTTACCAAAGATAACATAACCGGTTAATTACTGGAAACATTATAAAGC
108 AATGTTATCAAAGATAACATAACCGGTTAATTACTAGAAACATTATAAAGC
* * * * * *
1402098 ACAATAATATATTAGGTAGCGCTTATATAACGTAATAAGTAGCGCTTATATAATAAAATAGGTTA
1 ACAATAACATATTAGGTAACGATTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGATTA
* * * *
1402163 ATTATTTAATTTGTTATTACAACATATTAGGTAAACACTTAAAATGTTATCAAGGATAACATAAC
66 ATTAATTAAATTGTTATTACAACATATTAGGTAAACACCTAAAATGTTATCAAAGATAACATAAC
*
1402228 CGGTTAATTACTCGAAACATTATAAAGC
131 CGGTTAATTACTAGAAACATTATAAAGC
*
1402256 ATAATAACATATTAGGTA
1 ACAATAACATATTAGGTA
1402274 GTGCTTATGT
Statistics
Matches: 308, Mismatches: 25, Indels: 48
0.81 0.07 0.13
Matches are distributed among these distances:
158 142 0.46
159 2 0.01
160 3 0.01
161 2 0.01
162 5 0.02
164 1 0.00
167 4 0.01
168 4 0.01
171 4 0.01
172 3 0.01
175 1 0.00
177 5 0.02
178 2 0.01
179 3 0.01
180 2 0.01
181 125 0.41
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (158 bp):
ACAATAACATATTAGGTAACGATTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGATTA
ATTAATTAAATTGTTATTACAACATATTAGGTAAACACCTAAAATGTTATCAAAGATAACATAAC
CGGTTAATTACTAGAAACATTATAAAGC
Found at i:1401991 original size:25 final size:23
Alignment explanation
Indices: 1401939--1401992 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
1401929 TAGGTAACGA
* *
1401939 TTATATAATGTAATAGGTAGCGC
1 TTATATAACGTAATAAGTAGCGC
1401962 TTATATAACGTAATAAGTAGCGC
1 TTATATAACGTAATAAGTAGCGC
1401985 TTATATAA
1 TTATATAA
1401993 TAAAATAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (23 bp):
TTATATAACGTAATAAGTAGCGC
Found at i:1402112 original size:181 final size:181
Alignment explanation
Indices: 1401783--1402150 Score: 583
Period size: 181 Copynumber: 2.0 Consensus size: 181
1401773 GGTAACACTA
* *
1401783 ATATAATGTAATAGGTAGCACTTATATAATAAAATAGATTAATTACTTAAATTGTTATTACAACA
1 ATATAACGTAATAAGTAGCACTTATATAATAAAATAGATTAATTACTTAAATTGTTATTACAACA
* * *
1401848 TATTAGGTAAACACCTAAAATGTTATCAATGATAACATAACCGGTTAATTACTAGAAACATTATC
66 TATTAGGTAAACACCTAAAATGTTACCAAAGATAACATAACCGGTTAATTACTAGAAACATTATA
* *
1401913 AAGCACAATAACATATTAGGTAACGATTATATAATGTAATAGGTAGCGCTT
131 AAGCACAATAACATATTAGGTAACGATTATATAACGTAATAAGTAGCGCTT
* * * * *
1401964 ATATAACGTAATAAGTAGCGCTTATATAATAAAATAGGTTAATTATTTAATTTGTTATTATAACA
1 ATATAACGTAATAAGTAGCACTTATATAATAAAATAGATTAATTACTTAAATTGTTATTACAACA
* *
1402029 TATTAGGTAAACGCCTAAAATGTTACCAAAGATAACATAACCGGTTAATTACTGGAAACATTATA
66 TATTAGGTAAACACCTAAAATGTTACCAAAGATAACATAACCGGTTAATTACTAGAAACATTATA
* * *
1402094 AAGCACAATAATATATTAGGTAGCGCTTATATAACGTAATAAGTAGCGCTT
131 AAGCACAATAACATATTAGGTAACGATTATATAACGTAATAAGTAGCGCTT
1402145 ATATAA
1 ATATAA
1402151 TAAAATAGGT
Statistics
Matches: 170, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
181 170 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (181 bp):
ATATAACGTAATAAGTAGCACTTATATAATAAAATAGATTAATTACTTAAATTGTTATTACAACA
TATTAGGTAAACACCTAAAATGTTACCAAAGATAACATAACCGGTTAATTACTAGAAACATTATA
AAGCACAATAACATATTAGGTAACGATTATATAACGTAATAAGTAGCGCTT
Found at i:1402127 original size:23 final size:23
Alignment explanation
Indices: 1402101--1402157 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
1402091 ATAAAGCACA
* *
1402101 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAAGTAGCGCTTAT
**
1402124 ATAACGTAATAAGTAGCGCTTAT
1 ATAATATAATAAGTAGCGCTTAT
*
1402147 ATAATAAAATA
1 ATAATATAATA
1402158 GGTTAATTAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (23 bp):
ATAATATAATAAGTAGCGCTTAT
Found at i:1402490 original size:74 final size:72
Alignment explanation
Indices: 1402365--1402612 Score: 300
Period size: 73 Copynumber: 3.4 Consensus size: 72
1402355 AAAATTTAAA
* * * *
1402365 CTACTTATTACATTAAAATACATACCGGTTTTTTTTAAAATTGTTAATAATGTAAACGGTAAAAA
1 CTACCTATTACATTAAAATACTTACCGG-TTTTTTTAAAGTTGCTAATAATGTAAACGGTAAAAA
1402430 AAATAGACG
65 AAATAG-CG
* * * *
1402439 CTGCCTATTACATTAAAATACTTACCAGTTTTTTTGAAAGTTGCTATTAATGTAAACGGTAAAAG
1 CTACCTATTACATTAAAATACTTACCGGTTTTTTT-AAAGTTGCTAATAATGTAAACGGTAAAAA
* *
1402504 AAATGGTG
65 AAATAGCG
* **
1402512 CTACCTATTACATTAAAATA-TCTACCGGTTTTTTTAAGGTTGCTAATAATGTAAACAATAAAAA
1 CTACCTATTACATTAAAATACT-TACCGGTTTTTTTAAAGTTGCTAATAATGTAAACGGTAAAAA
*
1402576 AAATATGCA
65 AAATA-GCG
* *
1402585 CTACCTATTACATTAAACTACCTACCGG
1 CTACCTATTACATTAAAATACTTACCGG
1402613 ATATGTTGAA
Statistics
Matches: 148, Mismatches: 22, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
72 29 0.20
73 65 0.44
74 54 0.36
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.34
Consensus pattern (72 bp):
CTACCTATTACATTAAAATACTTACCGGTTTTTTTAAAGTTGCTAATAATGTAAACGGTAAAAAA
AATAGCG
Found at i:1402889 original size:112 final size:112
Alignment explanation
Indices: 1402692--1403174 Score: 733
Period size: 112 Copynumber: 4.3 Consensus size: 112
1402682 TAGCGCTTAT
*
1402692 AAAGTATCGATATTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
1 AAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
1402757 ACCAGTTTCATTATGACAAAACCGGTAAAGAACTACCTGATATGTTG
66 ACCAGTTTCATTATGACAAAACCGGTAAAGAACTACCTGATATGTTG
* **
1402804 AAAGTATCGACACTTTATAAAAATGTATTAATACTTTACAATATAACAGGTAAAAATATGACAAA
1 AAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
* * * *
1402869 ATCATTTTCATTATGACAAAACCGGTAAATAGCTACCTGATATGTTG
66 ACCAGTTTCATTATGACAAAACCGGTAAAGAACTACCTGATATGTTG
*
1402916 AAAGTATCGATACTTTTTATAAAAATGTATCGATACTTTACAATATAACATGTAAAAAATATGAC
1 AAAGTATCGATAC--TTTATAAAAATGTATCGATACTTTACAATATAACAGGT-AAAAATATGAC
1402981 AAAACCAGTTTCATTATGACAAAACCGGTAAAGAACTACCTGATATGTTG
63 AAAACCAGTTTCATTATGACAAAACCGGTAAAGAACTACCTGATATGTTG
* * *
1403031 AAAGTAT--AGA---TATAAAAATGTATTGATACTTTACAATATAACATGTAAAAATATGACAAA
1 AAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
*
1403091 ACCAGTTTCATTATGACAAAACCGATAAAGAACTACCTGATATGTTG
66 ACCAGTTTCATTATGACAAAACCGGTAAAGAACTACCTGATATGTTG
* * * ** *
1403138 AAAGTATAGATATTTTTTGTACATGTATCGATACTTT
1 AAAGTATCGATACTTTATAAAAATGTATCGATACTTT
1403175 GTTGAAAGTT
Statistics
Matches: 338, Mismatches: 25, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
107 67 0.20
108 35 0.10
109 2 0.01
112 133 0.39
113 2 0.01
114 35 0.10
115 64 0.19
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.31
Consensus pattern (112 bp):
AAAGTATCGATACTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAA
ACCAGTTTCATTATGACAAAACCGGTAAAGAACTACCTGATATGTTG
Found at i:1403114 original size:222 final size:222
Alignment explanation
Indices: 1402692--1403174 Score: 776
Period size: 222 Copynumber: 2.2 Consensus size: 222
1402682 TAGCGCTTAT
1402692 AAAGTATCGATA-TTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAA
1 AAAGTATCGATATTTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAA
1402756 AACCAGTTTCATTATGACAAAACCGGTAAAGAACTACCTGATATGTTGAAAGTATCGACACTTTA
66 AACCAGTTTCATTATGACAAAACCGGTAAAGAACTACCTGATATGTTGAAAGTATC-ACA--TTA
* *
1402821 TAAAAATGTATTAATACTTTACAATATAACAGGTAAAAATATGACAAAATCATTTTCATTATGAC
128 TAAAAATGTATTAATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGAC
* * *
1402886 AAAACCGGTAAATAGCTACCTGATATGTTG
193 AAAACCGATAAAGAACTACCTGATATGTTG
*
1402916 AAAGTATCGATACTTTTTATAAAAATGTATCGATACTTTACAATATAACATGTAAAAAATATGAC
1 AAAGTATCGATA-TTTTTATAAAAATGTATCGATACTTTACAATATAACAGGT-AAAAATATGAC
*
1402981 AAAACCAGTTTCATTATGACAAAACCGGTAAAGAACTACCTGATATGTTGAAAGTAT-AGA-TAT
64 AAAACCAGTTTCATTATGACAAAACCGGTAAAGAACTACCTGATATGTTGAAAGTATCACATTAT
* *
1403044 AAAAATGTATTGATACTTTACAATATAACATGTAAAAATATGACAAAACCAGTTTCATTATGACA
129 AAAAATGTATTAATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACA
1403109 AAACCGATAAAGAACTACCTGATATGTTG
194 AAACCGATAAAGAACTACCTGATATGTTG
* ** *
1403138 AAAGTATAGATATTTTT-TGTACATGTATCGATACTTT
1 AAAGTATCGATATTTTTATAAAAATGTATCGATACTTT
1403175 GTTGAAAGTT
Statistics
Matches: 243, Mismatches: 13, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
220 17 0.07
221 5 0.02
222 101 0.42
224 12 0.05
225 2 0.01
226 38 0.16
227 68 0.28
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.31
Consensus pattern (222 bp):
AAAGTATCGATATTTTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAA
AACCAGTTTCATTATGACAAAACCGGTAAAGAACTACCTGATATGTTGAAAGTATCACATTATAA
AAATGTATTAATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAA
ACCGATAAAGAACTACCTGATATGTTG
Found at i:1408510 original size:2 final size:2
Alignment explanation
Indices: 1408503--1408528 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1408493 GAATTTCATA
1408503 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
1408529 TGTGAAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1408682 original size:14 final size:14
Alignment explanation
Indices: 1408646--1408672 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1408636 ATACCGTGTA
1408646 AATAAAATATTATT
1 AATAAAATATTATT
1408660 AATAAAATATTAT
1 AATAAAATATTAT
1408673 ATGAAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATAAAATATTATT
Found at i:1410536 original size:19 final size:19
Alignment explanation
Indices: 1410512--1410553 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1410502 AGATTTACAC
1410512 AGAATAGTTAAATTATGTT
1 AGAATAGTTAAATTATGTT
1410531 AGAATAGTTAAATTATGTT
1 AGAATAGTTAAATTATGTT
1410550 AGAA
1 AGAA
1410554 ACTTTGACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.17, T:0.38
Consensus pattern (19 bp):
AGAATAGTTAAATTATGTT
Found at i:1410733 original size:28 final size:28
Alignment explanation
Indices: 1410687--1410751 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
1410677 CGGCAAGGTC
* ***
1410687 GACCATATATCATTCAGGCGGTATAACT
1 GACCATATATCAATCAGGCAACATAACT
* *
1410715 GACCATATATCAATGAGGCAACATAGCT
1 GACCATATATCAATCAGGCAACATAACT
1410743 GACCATATA
1 GACCATATA
1410752 ATAGAACTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.25
Consensus pattern (28 bp):
GACCATATATCAATCAGGCAACATAACT
Found at i:1418355 original size:13 final size:13
Alignment explanation
Indices: 1418337--1418365 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1418327 AATGATAAGA
1418337 TAATTAAAGAAAC
1 TAATTAAAGAAAC
1418350 TAATTAAAGAAAC
1 TAATTAAAGAAAC
1418363 TAA
1 TAA
1418366 ATGAATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.24
Consensus pattern (13 bp):
TAATTAAAGAAAC
Found at i:1418916 original size:30 final size:29
Alignment explanation
Indices: 1418876--1418984 Score: 119
Period size: 30 Copynumber: 3.7 Consensus size: 29
1418866 TGGAAAATAA
**
1418876 TTTACGTAAAATGGGTTACCTAAAAATTAT
1 TTTACGTAAAATGAATTACCT-AAAATTAT
* **
1418906 TTTACTTAAAATGAATTAAATGAAAATTAAT
1 TTTACGTAAAATGAATTACCT-AAAATT-AT
* *
1418937 TTTACGTCAAATGAATTACCTAAAATTGT
1 TTTACGTAAAATGAATTACCTAAAATTAT
*
1418966 TTTACGTAAAATGACTTAC
1 TTTACGTAAAATGAATTAC
1418985 ATTTTCTAGA
Statistics
Matches: 65, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
29 18 0.28
30 28 0.43
31 19 0.29
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (29 bp):
TTTACGTAAAATGAATTACCTAAAATTAT
Found at i:1418937 original size:60 final size:59
Alignment explanation
Indices: 1418868--1418979 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 59
1418858 GGTTTTTTTG
** *
1418868 GAAAATAA-TTTACGTAAAATGGGTTACCTAAAAATTATTTTACTTAAAATGAATTAAAT
1 GAAAATAATTTTACGTAAAATGAATTACCT-AAAATTATTTTACGTAAAATGAATTAAAT
* *
1418927 GAAAATTAATTTTACGTCAAATGAATTACCTAAAATTGTTTTACGTAAAATGA
1 GAAAA-TAATTTTACGTAAAATGAATTACCTAAAATTATTTTACGTAAAATGA
1418980 CTTACATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
59 5 0.11
60 23 0.50
61 18 0.39
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.36
Consensus pattern (59 bp):
GAAAATAATTTTACGTAAAATGAATTACCTAAAATTATTTTACGTAAAATGAATTAAAT
Found at i:1418949 original size:31 final size:29
Alignment explanation
Indices: 1418898--1418979 Score: 101
Period size: 31 Copynumber: 2.8 Consensus size: 29
1418888 GGGTTACCTA
*
1418898 AAAATTATTTTACTTAAAATGAATTAAAT
1 AAAATTATTTTACGTAAAATGAATTAAAT
* **
1418927 GAAAATTAATTTTACGTCAAATGAATTACCT
1 -AAAATT-ATTTTACGTAAAATGAATTAAAT
*
1418958 AAAATTGTTTTACGTAAAATGA
1 AAAATTATTTTACGTAAAATGA
1418980 CTTACATTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 14 0.31
30 12 0.27
31 19 0.42
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.38
Consensus pattern (29 bp):
AAAATTATTTTACGTAAAATGAATTAAAT
Found at i:1419289 original size:19 final size:19
Alignment explanation
Indices: 1419267--1419306 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1419257 AATATAATTC
1419267 TAAATT-AGTATATTAATAT
1 TAAATTCAGTA-ATTAATAT
*
1419286 TAAATTCATTAATTAATAT
1 TAAATTCAGTAATTAATAT
1419305 TA
1 TA
1419307 CTCATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (19 bp):
TAAATTCAGTAATTAATAT
Found at i:1419533 original size:11 final size:10
Alignment explanation
Indices: 1419514--1419566 Score: 58
Period size: 11 Copynumber: 5.4 Consensus size: 10
1419504 ATTAATATTT
1419514 TATTGAAATAA
1 TATT-AAATAA
1419525 TATT-AA-AA
1 TATTAAATAA
1419533 TATTAAATAAA
1 TATTAAAT-AA
1419544 TATTAAATAA
1 TATTAAATAA
*
1419554 -ATAAAATAA
1 TATTAAATAA
1419563 TATT
1 TATT
1419567 TTTTTAGTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
8 6 0.17
9 12 0.33
10 4 0.11
11 14 0.39
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (10 bp):
TATTAAATAA
Found at i:1419545 original size:19 final size:19
Alignment explanation
Indices: 1419514--1419550 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1419504 ATTAATATTT
1419514 TATTGAAATAATATTAAAA
1 TATTGAAATAATATTAAAA
1419533 TATT-AAATAAATATTAAA
1 TATTGAAAT-AATATTAAA
1419551 TAAATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
TATTGAAATAATATTAAAA
Found at i:1419558 original size:19 final size:18
Alignment explanation
Indices: 1419519--1419566 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
1419509 TATTTTATTG
*
1419519 AAATAATATTAAAATATT
1 AAATAATATTAAAATAAT
1419537 AAATAAATATT-AAATAAAT
1 AAAT-AATATTAAAAT-AAT
1419556 AAAATAATATT
1 -AAATAATATT
1419567 TTTTTAGTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 8 0.31
19 14 0.54
20 4 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATAATATTAAAATAAT
Found at i:1426785 original size:21 final size:20
Alignment explanation
Indices: 1426751--1426789 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1426741 GAGTTTATTT
1426751 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAA-TTTGAAACA
1426772 TCATTTTT-ATATTTGAAA
1 TCATTTTTCA-ATTTGAAA
1426790 AACAATTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.51
Consensus pattern (20 bp):
TCATTTTTCAATTTGAAACA
Found at i:1430559 original size:37 final size:37
Alignment explanation
Indices: 1430471--1430559 Score: 92
Period size: 37 Copynumber: 2.4 Consensus size: 37
1430461 ATCGGGCCGG
1430471 TATATATATAT-ATTTAAATTAAATATATAAAAATTA
1 TATATATATATAATTTAAATTAAATATATAAAAATTA
* * * * * *
1430507 TATATATTTTTTAATTT-AATTTAATTTATTAATATTA
1 TATATA-TATATAATTTAAATTAAATATATAAAAATTA
1430544 TATATATATAATAATT
1 TATATATAT-ATAATT
1430560 ATTTTTAATA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
36 8 0.19
37 30 0.71
38 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (37 bp):
TATATATATATAATTTAAATTAAATATATAAAAATTA
Found at i:1433408 original size:2 final size:2
Alignment explanation
Indices: 1433396--1433468 Score: 130
Period size: 2 Copynumber: 37.0 Consensus size: 2
1433386 TACTGTGTAC
*
1433396 AT AT AT GT AT AT AT AT A- 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
1433437 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
1433469 GAAAACCTTG
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.01
2 67 0.99
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1433826 original size:11 final size:11
Alignment explanation
Indices: 1433810--1433834 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1433800 TGCTAACTCA
1433810 GGTGACACGGT
1 GGTGACACGGT
1433821 GGTGACACGGT
1 GGTGACACGGT
1433832 GGT
1 GGT
1433835 ATGTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.16, G:0.48, T:0.20
Consensus pattern (11 bp):
GGTGACACGGT
Found at i:1434409 original size:15 final size:15
Alignment explanation
Indices: 1434358--1434410 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
1434348 TAAAAAATAA
*
1434358 TTAATTAATAA-ATT
1 TTAATAAATAATATT
* *
1434372 TAAATAAATAATAAT
1 TTAATAAATAATATT
*
1434387 TTATATAAATATTATT
1 TTA-ATAAATAATATT
1434403 TTAATAAA
1 TTAATAAA
1434411 AAAATAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 9 0.29
15 9 0.29
16 13 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAATAAATAATATT
Found at i:1435065 original size:19 final size:19
Alignment explanation
Indices: 1435024--1435065 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1435014 ATTATTTAAT
**
1435024 TATTTATATATTTTAAATT
1 TATTTATATATTTTAAAAA
1435043 TATTTATAT-TTGTTAAAAA
1 TATTTATATATT-TTAAAAA
1435062 TATT
1 TATT
1435066 AAACATTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TATTTATATATTTTAAAAA
Found at i:1442035 original size:17 final size:17
Alignment explanation
Indices: 1442013--1442051 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
1442003 TAGCATTGCT
1442013 TGTAGCATTGTTCATGC
1 TGTAGCATTGTTCATGC
*
1442030 TGTAGCATTGTTCATGT
1 TGTAGCATTGTTCATGC
1442047 TGTAG
1 TGTAG
1442052 AATTCATCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.13, G:0.26, T:0.44
Consensus pattern (17 bp):
TGTAGCATTGTTCATGC
Found at i:1449963 original size:44 final size:45
Alignment explanation
Indices: 1449846--1449969 Score: 187
Period size: 45 Copynumber: 2.8 Consensus size: 45
1449836 TATAAAATCT
*
1449846 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
1449891 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTTCCTATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
1449936 CTTGCCA-TTATTCCATAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
1449970 GCATGGTTAC
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
44 26 0.36
45 47 0.64
ACGTcount: A:0.29, C:0.23, G:0.07, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:1454052 original size:6 final size:6
Alignment explanation
Indices: 1454036--1454132 Score: 67
Period size: 6 Copynumber: 16.3 Consensus size: 6
1454026 TCTCTCATTT
* * * *
1454036 TTTTCTC TTTTTC -TTTTC TTTCTC GTTTTC -ATTT- TTTTTC TTCTTC
1 TTTT-TC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
* * * *
1454082 GTTTTC ATTTTC ATTTTC TTTTTC TATTTTTC TTCTTC TTTTT- TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC --TTTTTC TTTTTC TTTTTC TTTTTC
1454131 TT
1 TT
1454133 CTTATAATAT
Statistics
Matches: 72, Mismatches: 12, Indels: 13
0.74 0.12 0.13
Matches are distributed among these distances:
5 16 0.22
6 46 0.64
7 4 0.06
8 6 0.08
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.75
Consensus pattern (6 bp):
TTTTTC
Found at i:1454057 original size:17 final size:15
Alignment explanation
Indices: 1454033--1454132 Score: 60
Period size: 17 Copynumber: 6.1 Consensus size: 15
1454023 TCATCTCTCA
1454033 TTTTTTTCTCTTTTTC
1 TTTTTTT-TCTTTTTC
*
1454049 TTTTCTTTCTCGTTTTC
1 TTTT-TTT-TCTTTTTC
*
1454066 ATTTTTTTTCTTCTTC
1 -TTTTTTTTCTTTTTC
*
1454082 GTTTTCATTTTCATTTTC
1 -TTTT--TTTTCTTTTTC
1454100 TTTTTCTATT-TTTCTTC
1 TTTTT-T-TTCTTT-TTC
*
1454117 TTCTTTTT-TTTTTC
1 TTTTTTTTCTTTTTC
1454131 TT
1 TT
1454133 CTTATAATAT
Statistics
Matches: 69, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
14 5 0.07
15 6 0.09
16 18 0.26
17 27 0.39
18 13 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTTTTTTCTTTTTC
Found at i:1454059 original size:28 final size:29
Alignment explanation
Indices: 1454015--1454106 Score: 86
Period size: 28 Copynumber: 3.2 Consensus size: 29
1454005 AAGTGAAATA
*
1454015 TTTTT-TTTTCATCTCTCATTTT-TTTCTC
1 TTTTTCTTTTCATTTCTCATTTTCTTT-TC
* *
1454043 TTTTTCTTTTC-TTTCTCGTTTTCATTT-
1 TTTTTCTTTTCATTTCTCATTTTCTTTTC
*
1454070 TTTTTCTTCTTCGTTT-TCATTTTCATTTTC
1 TTTTTCTT-TTCATTTCTCATTTTC-TTTTC
1454100 TTTTTCT
1 TTTTTCT
1454107 ATTTTTCTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
27 8 0.15
28 25 0.47
29 13 0.25
30 7 0.13
ACGTcount: A:0.05, C:0.20, G:0.02, T:0.73
Consensus pattern (29 bp):
TTTTTCTTTTCATTTCTCATTTTCTTTTC
Found at i:1454077 original size:22 final size:24
Alignment explanation
Indices: 1454044--1454102 Score: 88
Period size: 22 Copynumber: 2.5 Consensus size: 24
1454034 TTTTTTCTCT
1454044 TTTTCTTTTCTTTC-TCGTTTTCA
1 TTTTCTTTTCTTTCTTCGTTTTCA
1454067 TTTT-TTTTC-TTCTTCGTTTTCA
1 TTTTCTTTTCTTTCTTCGTTTTCA
1454089 TTTTCATTTTCTTT
1 TTTTC-TTTTCTTT
1454103 TTCTATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 4 0.12
24 5 0.16
25 2 0.06
ACGTcount: A:0.05, C:0.19, G:0.03, T:0.73
Consensus pattern (24 bp):
TTTTCTTTTCTTTCTTCGTTTTCA
Found at i:1454131 original size:14 final size:14
Alignment explanation
Indices: 1454095--1454135 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1454085 TTCATTTTCA
* *
1454095 TTTTCTTTTTCTAT
1 TTTTCTTCTTCTTT
1454109 TTTTCTTCTTCTTT
1 TTTTCTTCTTCTTT
*
1454123 TTTTTTTCTTCTT
1 TTTTCTTCTTCTT
1454136 ATAATATATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTCTTCTTCTTT
Found at i:1454133 original size:17 final size:17
Alignment explanation
Indices: 1454015--1454135 Score: 77
Period size: 18 Copynumber: 6.9 Consensus size: 17
1454005 AAGTGAAATA
* *
1454015 TTTTTTTTTCATCTCTCA
1 TTTTTTTTTCTTCT-TCT
* *
1454033 TTTTTTTCTCTTTTTCT
1 TTTTTTTTTCTTCTTCT
* *
1454050 TTTCTTTCTCGTT-TTC-
1 TTTTTTTTTC-TTCTTCT
*
1454066 ATTTTTTTTCTTCTTCGT
1 TTTTTTTTTCTTCTTC-T
**
1454084 TTTCATTTTCATT-TTCTT
1 TTTTTTTTTC-TTCTTC-T
1454102 TTTCTATTTTTCTTCTTCT
1 TTT-T-TTTTTCTTCTTCT
1454121 TTTTTTTTTCTTCTT
1 TTTTTTTTTCTTCTT
1454136 ATAATATATG
Statistics
Matches: 81, Mismatches: 14, Indels: 17
0.72 0.12 0.15
Matches are distributed among these distances:
15 2 0.02
16 10 0.12
17 25 0.31
18 28 0.35
19 8 0.10
20 8 0.10
ACGTcount: A:0.05, C:0.19, G:0.02, T:0.74
Consensus pattern (17 bp):
TTTTTTTTTCTTCTTCT
Found at i:1462185 original size:23 final size:23
Alignment explanation
Indices: 1462150--1462217 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
1462140 CATATTATAT
*
1462150 GGCACTTCAGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
1462173 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
1462196 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
1462218 AGCTGTGATG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:1471372 original size:2 final size:2
Alignment explanation
Indices: 1471367--1471402 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1471357 ACACACACAC
1471367 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
1471403 CAGTTTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1481134 original size:9 final size:9
Alignment explanation
Indices: 1481122--1481170 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
1481112 TTTTTTCGAG
1481122 TTCTTTTTC
1 TTCTTTTTC
1481131 TTCTTTTT-
1 TTCTTTTTC
*
1481139 TT-TTTTTT
1 TTCTTTTTC
1481147 TTCTTTTTTC
1 TTC-TTTTTC
1481157 GTT-TTTTTC
1 -TTCTTTTTC
1481166 TTCTT
1 TTCTT
1481171 CTTTTTTCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
7 5 0.15
8 6 0.18
9 16 0.47
10 5 0.15
11 2 0.06
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (9 bp):
TTCTTTTTC
Found at i:1481137 original size:22 final size:19
Alignment explanation
Indices: 1481125--1481175 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 19
1481115 TTTCGAGTTC
1481125 TTTTTCTTCTTTTTT--TT
1 TTTTTCTTCTTTTTTCGTT
1481142 TTTTT-TTCTTTTTTCGTT
1 TTTTTCTTCTTTTTTCGTT
1481160 TTTTTCTTCTTCTTTT
1 TTTTTCTTCTT-TTTT
1481176 TTCAAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 9 0.30
17 5 0.17
18 7 0.23
19 5 0.17
20 4 0.13
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (19 bp):
TTTTTCTTCTTTTTTCGTT
Found at i:1481161 original size:8 final size:7
Alignment explanation
Indices: 1481125--1481178 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
1481115 TTTCGAGTTC
1481125 TTTTTCT
1 TTTTTCT
*
1481132 TCTTT-T
1 TTTTTCT
1481138 TTTTT-T
1 TTTTTCT
1481144 TTTTTCT
1 TTTTTCT
1481151 TTTTTCGT
1 TTTTTC-T
1481159 TTTTT-T
1 TTTTTCT
*
1481165 CTTCTTCT
1 -TTTTTCT
1481173 TTTTTC
1 TTTTTC
1481179 AAAATTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
6 12 0.31
7 20 0.51
8 7 0.18
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (7 bp):
TTTTTCT
Found at i:1482145 original size:3 final size:3
Alignment explanation
Indices: 1482137--1482269 Score: 203
Period size: 3 Copynumber: 43.7 Consensus size: 3
1482127 TTTATCCATT
*
1482137 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** *
1482185 GCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
*
1482231 TTA TTA TTA ATA TTA TATA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TT
1482270 TAATAAATAA
Statistics
Matches: 118, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
3 113 0.96
4 5 0.04
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1483557 original size:19 final size:19
Alignment explanation
Indices: 1483519--1483554 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1483509 CAATTTAGTC
1483519 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
1483538 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
1483555 TAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:1483629 original size:16 final size:15
Alignment explanation
Indices: 1483608--1483640 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1483598 AAATATTTTG
*
1483608 ATATATAT-TCATAA
1 ATATATATATAATAA
1483622 ATATATATATAATAA
1 ATATATATATAATAA
1483637 ATAT
1 ATAT
1483641 TAATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATATATATAATAA
Found at i:1494943 original size:1 final size:1
Alignment explanation
Indices: 1494937--1494977 Score: 64
Period size: 1 Copynumber: 41.0 Consensus size: 1
1494927 ATTATGCTTG
* *
1494937 AAAAAAAAAAAAAAAGAAAAAAAAAAAAAGAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1494978 GGGGTCAAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.95, C:0.00, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:1494958 original size:13 final size:14
Alignment explanation
Indices: 1494939--1494977 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
1494929 TATGCTTGAA
1494939 AAAAAAAAAAAAAG
1 AAAAAAAAAAAAAG
1494953 AAAAAAAAAAAAAG
1 AAAAAAAAAAAAAG
1494967 AAAAAAAAAAA
1 AAAAAAAAAAA
1494978 GGGGTCAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.95, C:0.00, G:0.05, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAG
Found at i:1496024 original size:52 final size:52
Alignment explanation
Indices: 1495919--1496634 Score: 1283
Period size: 52 Copynumber: 13.7 Consensus size: 52
1495909 TATGTGCTCA
*
1495919 ATAGCATCTTCTGGAAGTGTTCTTTGAAGTTATCTGATCTGATTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTG-AGTTATCTGATCTGGTTGGACAGAAC
*
1495972 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
1496024 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* *
1496076 ATAGCACCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
1496128 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
1496180 ATAGCATCTTCTGGAAGTGTTTCTTTGAGTTATCTGATCTGATTGGACAGAAC
1 ATAGCATCTTCTGGAAGTG-TTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
1496233 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1496285 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GATCAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAAC
1496337 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GATCAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAAC
1496389 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1496441 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1496493 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* *
1496545 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATGGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
1496597 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1496635 CGAAGAAGTG
Statistics
Matches: 646, Mismatches: 14, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
51 2 0.00
52 566 0.88
53 78 0.12
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.37
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:1497389 original size:113 final size:113
Alignment explanation
Indices: 1497191--1497863 Score: 1139
Period size: 113 Copynumber: 5.9 Consensus size: 113
1497181 AAAAGATTCA
* *
1497191 AATTCATCATTTGATGGATCATCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1497256 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
*
1497304 AATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1497369 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
*
1497417 AATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1497482 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* * * *
1497530 AATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * *
1497595 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* * * *
1497643 AATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * *
1497708 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTA
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
** *
1497756 AATTCATCATTTGATGGATCAACATGGCCAAAGAAAGTTCATGAATGAGAAGAACTCATCTGAAG
1 AATTCATCATTTGATGGATCAACATTTCCAGAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAG
*
1497821 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
1497864 GTTTGATATC
Statistics
Matches: 533, Mismatches: 26, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
113 470 0.88
114 63 0.12
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (113 bp):
AATTCATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
Found at i:1498168 original size:3 final size:3
Alignment explanation
Indices: 1498160--1498289 Score: 197
Period size: 3 Copynumber: 42.7 Consensus size: 3
1498150 TTTATCCATT
* **
1498160 TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA GCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1498208 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
*
1498254 TTA TTA ATA TTA TATA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TT
1498290 TAATAAATAA
Statistics
Matches: 115, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
3 110 0.96
4 5 0.04
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1499579 original size:19 final size:19
Alignment explanation
Indices: 1499541--1499576 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1499531 CAATTTAGTC
1499541 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
1499560 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
1499577 TAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:1499651 original size:16 final size:15
Alignment explanation
Indices: 1499630--1499662 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1499620 AAATATTTTG
*
1499630 ATATATAT-TCATAA
1 ATATATATATAATAA
1499644 ATATATATATAATAA
1 ATATATATATAATAA
1499659 ATAT
1 ATAT
1499663 TAATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATATATATAATAA
Found at i:1501597 original size:2 final size:2
Alignment explanation
Indices: 1501590--1501618 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1501580 TTTTTAAAAC
1501590 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1501619 CCCTCATCCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1501819 original size:24 final size:24
Alignment explanation
Indices: 1501792--1501879 Score: 86
Period size: 24 Copynumber: 3.7 Consensus size: 24
1501782 ATAAAAACAT
*
1501792 AATCCAAGTCAAGTATCAAATCAA
1 AATCCAGGTCAAGTATCAAATCAA
** * *
1501816 AATCCAGGTCAAGTATCCGATTAG
1 AATCCAGGTCAAGTATCAAATCAA
** *
1501840 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCAAATCAA
* *
1501864 AATTCAGGTCATGTAT
1 AATCCAGGTCAAGTAT
1501880 TATAATAGAA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCAAATCAA
Found at i:1501889 original size:48 final size:48
Alignment explanation
Indices: 1501792--1501889 Score: 106
Period size: 48 Copynumber: 2.0 Consensus size: 48
1501782 ATAAAAACAT
* *
1501792 AATCCAAGTCAAGTATCAAATCAAAATCCAGGTCAAGTATCCGATTAG
1 AATCCAAGTCAAGTATCAAATCAAAATCCAGGTCAAGTATCAGAATAG
* ** * * * * *
1501840 AATCCAGGTCAAGTATCCGATCAGAATTCAGGTCATGTATTATAATAG
1 AATCCAAGTCAAGTATCAAATCAAAATCCAGGTCAAGTATCAGAATAG
1501888 AA
1 AA
1501890 ATCAAATCGG
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (48 bp):
AATCCAAGTCAAGTATCAAATCAAAATCCAGGTCAAGTATCAGAATAG
Found at i:1503508 original size:413 final size:413
Alignment explanation
Indices: 1502741--1503570 Score: 1651
Period size: 413 Copynumber: 2.0 Consensus size: 413
1502731 TACTCACTTA
1502741 AATTATGTTCCATTACTTTTAAAGGTAGTCCAATACCTATGCTTATTTGGATTCCTTAATTAATC
1 AATTATGTTCCATTACTTTTAAAGGTAGTCCAATACCTATGCTTATTTGGATTCCTTAATTAATC
1502806 CAAGATATTTACTTAGTTTAGGCCATAAGGTTATTTTGGTAATTTTGGTGTTCAGATTTATTACA
66 CAAGATATTTACTTAGTTTAGGCCATAAGGTTATTTTGGTAATTTTGGTGTTCAGATTTATTACA
1502871 TTCATTTCATAGCTCGATGATATCCAATCATTTCTGAGCTTGGTGATATTCTTGGGTCATTTCCA
131 TTCATTTCATAGCTCGATGATATCCAATCATTTCTGAGCTTGGTGATATTCTTGGGTCATTTCCA
*
1502936 TTACAGGGGTATTCTGGTCATTCTACAGATCCGATGTATTTCAATCATTTCCTTCTATCCTGTCT
196 TTACAGGGGTATTCTGGTCATTCTACAGATCCGATGTATTTCAATCATTTCCTTCTATCCTATCT
1503001 TATTATTTAATACCAACTTATCATCTATTTCAGTCCCTTCGAACAATTCTGATAAAAGAGCACCC
261 TATTATTTAATACCAACTTATCATCTATTTCAGTCCCTTCGAACAATTCTGATAAAAGAGCACCC
1503066 CCGATAATTTGTTATTCAGGTATTTACTCGTATCTTGGATATTTTCAGGTCAAATGCCTTCTCAA
326 CCGATAATTTGTTATTCAGGTATTTACTCGTATCTTGGATATTTTCAGGTCAAATGCCTTCTCAA
1503131 ATTTTTACCAACGGAATATCAAG
391 ATTTTTACCAACGGAATATCAAG
1503154 AATTATGTTCCATTACTTTTAAAGGTAGTCCAATACCTATGCTTATTTGGATTCCTTAATTAATC
1 AATTATGTTCCATTACTTTTAAAGGTAGTCCAATACCTATGCTTATTTGGATTCCTTAATTAATC
1503219 CAAGATATTTACTTAGTTTAGGCCATAAGGTTATTTTGGTAATTTTGGTGTTCAGATTTATTACA
66 CAAGATATTTACTTAGTTTAGGCCATAAGGTTATTTTGGTAATTTTGGTGTTCAGATTTATTACA
1503284 TTCATTTCATAGCTCGATGATATCCAATCATTTCTGAGCTTGGTGATATTCTTGGGTCATTTCCA
131 TTCATTTCATAGCTCGATGATATCCAATCATTTCTGAGCTTGGTGATATTCTTGGGTCATTTCCA
1503349 TTACAGGGGTATTCTGGTCATTCTACAGATCCGATGTATTTCAATCATTTCCTTCTATCCTATCT
196 TTACAGGGGTATTCTGGTCATTCTACAGATCCGATGTATTTCAATCATTTCCTTCTATCCTATCT
1503414 TATTATTTAATACCAACTTATCATCTATTTCAGTCCCTTCGAACAATTCTGATAAAAGAGCACCC
261 TATTATTTAATACCAACTTATCATCTATTTCAGTCCCTTCGAACAATTCTGATAAAAGAGCACCC
1503479 CCGATAATTTGTTATTCAGGTATTTACTCGTATCTTGGATATTTTCAGGTCAAATGCCTTCTCAA
326 CCGATAATTTGTTATTCAGGTATTTACTCGTATCTTGGATATTTTCAGGTCAAATGCCTTCTCAA
1503544 ATTTTTACCAACGGAATATCAAG
391 ATTTTTACCAACGGAATATCAAG
1503567 AATT
1 AATT
1503571 TTTTTTCACT
Statistics
Matches: 416, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
413 416 1.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (413 bp):
AATTATGTTCCATTACTTTTAAAGGTAGTCCAATACCTATGCTTATTTGGATTCCTTAATTAATC
CAAGATATTTACTTAGTTTAGGCCATAAGGTTATTTTGGTAATTTTGGTGTTCAGATTTATTACA
TTCATTTCATAGCTCGATGATATCCAATCATTTCTGAGCTTGGTGATATTCTTGGGTCATTTCCA
TTACAGGGGTATTCTGGTCATTCTACAGATCCGATGTATTTCAATCATTTCCTTCTATCCTATCT
TATTATTTAATACCAACTTATCATCTATTTCAGTCCCTTCGAACAATTCTGATAAAAGAGCACCC
CCGATAATTTGTTATTCAGGTATTTACTCGTATCTTGGATATTTTCAGGTCAAATGCCTTCTCAA
ATTTTTACCAACGGAATATCAAG
Found at i:1511162 original size:2 final size:2
Alignment explanation
Indices: 1511151--1511203 Score: 50
Period size: 2 Copynumber: 30.5 Consensus size: 2
1511141 TTAAAACAAT
1511151 TA TA -A TA TA TA T- TA -A TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1511189 -A TA -A TA -A TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA T
1511204 GTATGATGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
1 8 0.19
2 35 0.81
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1511170 original size:8 final size:9
Alignment explanation
Indices: 1511151--1511203 Score: 65
Period size: 10 Copynumber: 5.9 Consensus size: 9
1511141 TTAAAACAAT
1511151 TATAATATA
1 TATAATATA
1511160 TATTAATATA
1 TA-TAATATA
1511170 TATATATATA
1 TATA-ATATA
*
1511180 TATATTATA
1 TATAATATA
1511189 -ATAATA-A
1 TATAATATA
1511196 TATAATAT
1 TATAATAT
1511204 GTATGATGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 1 0.03
8 11 0.29
9 8 0.21
10 18 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TATAATATA
Found at i:1511174 original size:6 final size:6
Alignment explanation
Indices: 1511151--1511203 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 6
1511141 TTAAAACAAT
1511151 TATA-A TATATA T-TA-A TATATA TATATA TATATA T-TATA -ATA-A
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
1511193 TA-ATA TA-ATA T
1 TATATA TATATA T
1511204 GTATGATGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
4 4 0.10
5 22 0.52
6 16 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
TATATA
Found at i:1511224 original size:24 final size:25
Alignment explanation
Indices: 1511197--1511254 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 25
1511187 TAATAATAAT
1511197 ATAATATGTATG-ATGAATAT-TATG
1 ATAATAT-TATGCATGAATATATATG
* * *
1511221 ATAACATTATGCATGTATATATATT
1 ATAATATTATGCATGAATATATATG
1511246 ATAAT-TTAT
1 ATAATATTAT
1511255 ATTATATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 4 0.14
24 17 0.61
25 7 0.25
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.45
Consensus pattern (25 bp):
ATAATATTATGCATGAATATATATG
Found at i:1511945 original size:42 final size:42
Alignment explanation
Indices: 1511871--1511951 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
1511861 AACACTCGTA
*
1511871 GCAATAAAGCGCGCCCCCTGAATCGCACTATACGCTGATTAC
1 GCAATAAAGCGCGCCCCCTGAATCGCAATATACGCTGATTAC
* *
1511913 GCAATAAAGCGCGCCCCCTG-CTCCGCAATATACGGTGAT
1 GCAATAAAGCGCGCCCCCTGAAT-CGCAATATACGCTGAT
1511952 CTGGCACTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 1 0.03
42 34 0.97
ACGTcount: A:0.27, C:0.33, G:0.21, T:0.19
Consensus pattern (42 bp):
GCAATAAAGCGCGCCCCCTGAATCGCAATATACGCTGATTAC
Found at i:1515885 original size:24 final size:24
Alignment explanation
Indices: 1515863--1515908 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1515853 TCGCTGTCAT
*
1515863 CATCATCGTCGTCGTCGTCGTCAC
1 CATCATCATCGTCGTCGTCGTCAC
*
1515887 CATCATCATCGTTGTCGTCGTC
1 CATCATCATCGTCGTCGTCGTC
1515909 GTCCTGAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.13, C:0.35, G:0.20, T:0.33
Consensus pattern (24 bp):
CATCATCATCGTCGTCGTCGTCAC
Found at i:1515897 original size:27 final size:27
Alignment explanation
Indices: 1515860--1515911 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
1515850 TCATCGCTGT
1515860 CATCATCATCGTCGTCGTCGTCGTCAC
1 CATCATCATCGTCGTCGTCGTCGTCAC
*
1515887 CATCATCATCGTTGTCGTCGTCGTC
1 CATCATCATCGTCGTCGTCGTCGTC
1515912 CTGAGCAGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.13, C:0.35, G:0.19, T:0.33
Consensus pattern (27 bp):
CATCATCATCGTCGTCGTCGTCGTCAC
Found at i:1516287 original size:18 final size:18
Alignment explanation
Indices: 1516261--1516301 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1516251 TACAGACGAT
1516261 TGCGGCATCATATATGGA
1 TGCGGCATCATATATGGA
* *
1516279 TGCGTCATCATATATGGT
1 TGCGGCATCATATATGGA
1516297 TGCGG
1 TGCGG
1516302 TGGCTACTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.32
Consensus pattern (18 bp):
TGCGGCATCATATATGGA
Found at i:1517976 original size:111 final size:111
Alignment explanation
Indices: 1517782--1518114 Score: 612
Period size: 111 Copynumber: 3.0 Consensus size: 111
1517772 ATTACAAAAA
* *
1517782 TTAATTCTTACTCTAATAATCATGCATTTAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1517847 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
1517893 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1517958 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
1518004 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* * *
1518069 AATTAAAACGTTAAAATGTTACCATATCAGCAAAGTATAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
1518115 ATGATTTCCA
Statistics
Matches: 216, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 216 1.00
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:1518415 original size:50 final size:49
Alignment explanation
Indices: 1518361--1518516 Score: 124
Period size: 50 Copynumber: 3.1 Consensus size: 49
1518351 CCCCCTGCAC
1518361 CGCGCTATACCCCACGTGTCAGATACCCAGGTATAGCGCGGATCAGGGGG
1 CGCGCTATA-CCCACGTGTCAGATACCCAGGTATAGCGCGGATCAGGGGG
* * ** *
1518411 CGCGCTATATCCACGTGGCATCAGAT-CACC--GTATATCGCGGGGCAGGGTG
1 CGCGCTATACCCACGT-G--TCAGATAC-CCAGGTATAGCGCGGATCAGGGGG
* ** *
1518461 CGCGCTATACCCACGTGGC-GCCA-AATCAGCGTATAGCGCGGTTCAGGGGG
1 CGCGCTATACCCACGTGTCAG--ATACCCAG-GTATAGCGCGGATCAGGGGG
1518511 CGCGCT
1 CGCGCT
1518517 TTACTGCTAC
Statistics
Matches: 83, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
46 1 0.01
47 2 0.02
48 1 0.01
49 7 0.08
50 63 0.76
51 1 0.01
52 8 0.10
ACGTcount: A:0.20, C:0.30, G:0.33, T:0.17
Consensus pattern (49 bp):
CGCGCTATACCCACGTGTCAGATACCCAGGTATAGCGCGGATCAGGGGG
Found at i:1518735 original size:23 final size:24
Alignment explanation
Indices: 1518690--1518739 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 24
1518680 ATCTTTTATA
1518690 TATATTTTAAAATTTTAAGTTAAAT
1 TATATTTTAAAATTTTAAGTT-AAT
1518715 TATA-TTT-AAATTATTAA-TTAAT
1 TATATTTTAAAATT-TTAAGTTAAT
1518737 TAT
1 TAT
1518740 TACATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.25
23 7 0.29
24 7 0.29
25 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
TATATTTTAAAATTTTAAGTTAAT
Found at i:1518754 original size:41 final size:43
Alignment explanation
Indices: 1518709--1518789 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
1518699 AAATTTTAAG
*
1518709 TTAAATTATA-TT-TAAAT-TATTAATTAATTATTACATAAAAA
1 TTAAATTAAATTTATAAATATATTAATTAATT-TTACATAAAAA
* *
1518750 TTAAATTAAATTTATAAATATTTTAATTAATTTTATATAA
1 TTAAATTAAATTTATAAATATATTAATTAATTTTACATAA
1518790 TTTAATAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 9 0.26
42 2 0.06
43 12 0.35
44 11 0.32
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (43 bp):
TTAAATTAAATTTATAAATATATTAATTAATTTTACATAAAAA
Found at i:1521521 original size:45 final size:45
Alignment explanation
Indices: 1521457--1521543 Score: 165
Period size: 45 Copynumber: 1.9 Consensus size: 45
1521447 ATATGACCAA
*
1521457 AATCACAATTCCACCATTTATAAAGCCTTTAATCTATTTTCTACT
1 AATCACAATTCCACCATTTATAAAGCCTTTAATCTATGTTCTACT
1521502 AATCACAATTCCACCATTTATAAAGCCTTTAATCTATGTTCT
1 AATCACAATTCCACCATTTATAAAGCCTTTAATCTATGTTCT
1521544 CTTCACTCTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.39
Consensus pattern (45 bp):
AATCACAATTCCACCATTTATAAAGCCTTTAATCTATGTTCTACT
Found at i:1528995 original size:68 final size:67
Alignment explanation
Indices: 1528915--1529050 Score: 254
Period size: 68 Copynumber: 2.0 Consensus size: 67
1528905 ATATCACAAA
1528915 ATAAGAATGTATTAAAAATATTTTTACAATCATATTTAAAAAGTTGAGATACGTTAATTATAATA
1 ATAAGAATGTATTAAAAATATTTTTACAATCATATTTAAAAAGTTGAGATACGTTAATTAT-ATA
1528980 TAT
65 TAT
*
1528983 ATAAGAATGTATTAAAAATATTTTTACAATCATATTTAAAAAGTTGAGGTACGTTAATTATATAT
1 ATAAGAATGTATTAAAAATATTTTTACAATCATATTTAAAAAGTTGAGATACGTTAATTATATAT
1529048 AT
66 AT
1529050 A
1 A
1529051 GATAGATAGA
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
67 7 0.10
68 60 0.90
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (67 bp):
ATAAGAATGTATTAAAAATATTTTTACAATCATATTTAAAAAGTTGAGATACGTTAATTATATAT
AT
Found at i:1535368 original size:5 final size:5
Alignment explanation
Indices: 1535355--1535385 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
1535345 TTTTTTTTTT
1535355 TGGGTG TGGGG TGGGG TGGGG TGGGG TGGGG
1 TGGG-G TGGGG TGGGG TGGGG TGGGG TGGGG
1535386 CAAGGTTCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.84
6 4 0.16
ACGTcount: A:0.00, C:0.00, G:0.77, T:0.23
Consensus pattern (5 bp):
TGGGG
Found at i:1538967 original size:42 final size:42
Alignment explanation
Indices: 1538905--1538994 Score: 144
Period size: 42 Copynumber: 2.1 Consensus size: 42
1538895 CGCTTGACAC
*
1538905 ATCTTTATTTTATGTACAAGTAAAGATGTTATTTTCTTAAAT
1 ATCTTTATTTTATGTACAAGTAAAGATGTTATTTTCCTAAAT
* *
1538947 ATCTTTATTTTATGTTCAAGTAAAGATTTTATTTTCCTAAAT
1 ATCTTTATTTTATGTACAAGTAAAGATGTTATTTTCCTAAAT
*
1538989 CTCTTT
1 ATCTTT
1538995 TTTGAATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (42 bp):
ATCTTTATTTTATGTACAAGTAAAGATGTTATTTTCCTAAAT
Found at i:1542188 original size:25 final size:25
Alignment explanation
Indices: 1542154--1542202 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
1542144 GTTTACTTCA
1542154 GAATGATTAAGGTCCTGAATGATTT
1 GAATGATTAAGGTCCTGAATGATTT
1542179 GAATGATTAAGGTCCTGAATGATT
1 GAATGATTAAGGTCCTGAATGATT
1542203 CAAATGCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35
Consensus pattern (25 bp):
GAATGATTAAGGTCCTGAATGATTT
Found at i:1542208 original size:25 final size:25
Alignment explanation
Indices: 1542150--1542208 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 25
1542140 GTTTGTTTAC
1542150 TTCAGAATGATTAAGGTCCTGAATGA
1 TTCA-AATGATTAAGGTCCTGAATGA
**
1542176 TTTGAATGATTAAGGTCCTGAATGA
1 TTCAAATGATTAAGGTCCTGAATGA
1542201 TTCAAATG
1 TTCAAATG
1542209 CTAAATGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 27 0.93
26 2 0.07
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (25 bp):
TTCAAATGATTAAGGTCCTGAATGA
Found at i:1542741 original size:37 final size:37
Alignment explanation
Indices: 1542689--1542792 Score: 145
Period size: 37 Copynumber: 2.8 Consensus size: 37
1542679 ATTTTCGTCC
1542689 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
* * *
1542726 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
* * * *
1542763 TACTAAGATTTAAATTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
1542793 CCACAAGCAC
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.31
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
Found at i:1543187 original size:18 final size:17
Alignment explanation
Indices: 1543148--1543190 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1543138 ATTATATGGA
1543148 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
1543164 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
1543182 TATTATTAT
1 TATTATTAT
1543191 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:1543342 original size:18 final size:17
Alignment explanation
Indices: 1543311--1543356 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
1543301 AATTATTACT
*
1543311 TTACTATTTTTTTTATC
1 TTACTATTTATTTTATC
1543328 TTACTTATTTATTTTAT-
1 TTAC-TATTTATTTTATC
1543345 TTA-T-TTTATTTT
1 TTACTATTTATTTT
1543357 TTCCCTTGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 8 0.30
15 1 0.04
17 7 0.26
18 11 0.41
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.74
Consensus pattern (17 bp):
TTACTATTTATTTTATC
Found at i:1547751 original size:183 final size:183
Alignment explanation
Indices: 1547443--1547979 Score: 977
Period size: 183 Copynumber: 2.9 Consensus size: 183
1547433 ATTAAATCCG
*
1547443 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGTAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1547508 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
1547573 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
*
1547626 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAAATCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
1547691 ATAGATTATGTTCAAACTATGACACTGCTCGGATACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
1547756 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
*
1547809 TAAAGCTGAGCTATTCCACTAAGGTAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** *
1547874 ATAGATTACATTCAAA-TCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
1547938 TTTGTCAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
1547980 TAAACCTGAT
Statistics
Matches: 341, Mismatches: 12, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
182 1 0.00
183 340 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:1549201 original size:36 final size:36
Alignment explanation
Indices: 1549161--1549277 Score: 90
Period size: 36 Copynumber: 3.1 Consensus size: 36
1549151 ATACTTTGTC
1549161 TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
1 TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
** * * ** * * *
1549197 TCACTCAAGATTATTTTTCTTAAAACAAGATTTGTC
1 TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
* * *
1549233 TCGCTTGAGACCGTTTTCACTCGAAAGAAGGCATTTCATT
1 TCACTTGAGACTGTTTT-TCTCGAAAGAA-G-ATTT-ATT
1549273 TCACT
1 TCACT
1549278 CAAGGTTATT
Statistics
Matches: 55, Mismatches: 22, Indels: 4
0.68 0.27 0.05
Matches are distributed among these distances:
36 38 0.69
37 7 0.13
38 1 0.02
39 4 0.07
40 5 0.09
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (36 bp):
TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
Found at i:1549215 original size:72 final size:75
Alignment explanation
Indices: 1549120--1549303 Score: 220
Period size: 72 Copynumber: 2.5 Consensus size: 75
1549110 ATGCAGATGA
* * * * *
1549120 TTATCTCACTCAA-ATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTC
1 TTATTTCACTCAAGA-TTATTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCGTTTTCACTC
1549182 GAAAGAA-G-AT
64 GAAAGAAGGCAT
*
1549192 TTATTTCACTCAAGATTATTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGA
1 TTATTTCACTCAAGATTATTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
1549257 AAGAAGGCAT
66 AAGAAGGCAT
* *
1549267 TTCATTTCACTCAAGGTTATTTTT-TT-AAAGAAGATTT
1 TT-ATTTCACTCAAGATTATTTTTCTTAAAACAAGATTT
1549304 TATCTTGCTT
Statistics
Matches: 98, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
71 1 0.01
72 49 0.50
73 11 0.11
74 11 0.11
75 6 0.06
76 20 0.20
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (75 bp):
TTATTTCACTCAAGATTATTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
AAGAAGGCAT
Found at i:1549354 original size:39 final size:39
Alignment explanation
Indices: 1549311--1549446 Score: 112
Period size: 39 Copynumber: 3.2 Consensus size: 39
1549301 TTTTATCTTG
1549311 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
* * * *
1549350 CTTGAGACAGTTTCTCTTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTC
1 CTTGAGATAGTTTCCCTCG-AAACA--------G-AA--AATTTTGTCTC-C
1549402 C-TGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1549440 CTTGAGA
1 CTTGAGA
1549447 CAGATTCTCT
Statistics
Matches: 75, Mismatches: 8, Indels: 28
0.68 0.07 0.25
Matches are distributed among these distances:
38 2 0.03
39 31 0.41
40 5 0.07
41 2 0.03
42 1 0.01
48 1 0.01
49 2 0.03
50 5 0.07
51 24 0.32
52 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (39 bp):
CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
Found at i:1549532 original size:105 final size:104
Alignment explanation
Indices: 1549366--1549684 Score: 509
Period size: 105 Copynumber: 3.1 Consensus size: 104
1549356 ACAGTTTCTC
* *
1549366 TTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
*
1549431 TTTGTCTCCCTTGAGACAGATTCTCTTGAAACATAAACA
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
*
1549470 TTGAAAACATTTCCCTTGAAATGATTTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
1 TTGAAAACATTTCCCTTGAAATGA-ATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
1549535 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
65 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * * *
1549575 TTGAAAACATTTCCATTGAAATGAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G--AAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
** *
1549637 TTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
1549676 TTGAAAACA
1 TTGAAAACA
1549685 ATTTAACGAA
Statistics
Matches: 202, Mismatches: 12, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
101 48 0.24
103 1 0.00
104 53 0.26
105 100 0.50
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.36
Consensus pattern (104 bp):
TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Done.