Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009330.1 Hibiscus syriacus cultivar Beakdansim tig00113096_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: 1820295
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1369712 original size:23 final size:22
Alignment explanation
Indices: 1369662--1369714 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 22
1369652 TAGTAATTCA
*
1369662 ATTTCTATTTTTTAATATTTAAT
1 ATTT-TATTTTTTAATATTGAAT
1369685 ATTTTATTTTTTAATATATGAAT
1 ATTTTATTTTTTAATAT-TGAAT
1369708 ATTTTAT
1 ATTTTAT
1369715 ATTTAAACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 13 0.46
23 15 0.54
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
ATTTTATTTTTTAATATTGAAT
Found at i:1370501 original size:43 final size:42
Alignment explanation
Indices: 1370402--1370603 Score: 151
Period size: 43 Copynumber: 4.8 Consensus size: 42
1370392 TGTGAACCAA
* ** *
1370402 AAACGCCGCAATATGTAACGATATATAGCGGCGTTTG-A--AC
1 AAACGCCGCAATAGGT-TTGATATTTAGCGGCGTTTGTATTAC
* * *
1370442 AAACGCCACAACAGGTTGTGATATTTAGCGGCGTTTTTATTAC
1 AAACGCCGCAATAGGTT-TGATATTTAGCGGCGTTTGTATTAC
* * * *
1370485 AAACGCCGTAATAGGTTTGGAAATTTAGGGGCGTTTGTCTTAC
1 AAACGCCGCAATAGGTTT-GATATTTAGCGGCGTTTGTATTAC
* * ** *
1370528 AAACGCCGCAATATGTTTTGACA-TTACGCGAAGTTTGTCTTAC
1 AAACGCCGCAATA-GGTTTGATATTTA-GCGGCGTTTGTATTAC
* * *
1370571 AAACGCCGCAATAGGATCTGGTATATAGCGGCG
1 AAACGCCGCAATAGG-TTTGATATTTAGCGGCG
1370604 GTTTTAGGAT
Statistics
Matches: 126, Mismatches: 27, Indels: 15
0.75 0.16 0.09
Matches are distributed among these distances:
40 29 0.23
41 1 0.01
42 5 0.04
43 85 0.67
44 6 0.05
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (42 bp):
AAACGCCGCAATAGGTTTGATATTTAGCGGCGTTTGTATTAC
Found at i:1379047 original size:40 final size:39
Alignment explanation
Indices: 1378990--1379081 Score: 112
Period size: 40 Copynumber: 2.3 Consensus size: 39
1378980 TTATCTAAGT
* * * *
1378990 TTGTGGTGTTTTAAAAAAAAGCCTCTATACTTCCGATATA
1 TTGTGGCG-TTTAAAAAAAAACCTCTATACTGCAGATATA
*
1379030 TTGTGGCGTTTACAAAAAAAACCTCTATAGTGCAGATATA
1 TTGTGGCGTTTA-AAAAAAAACCTCTATACTGCAGATATA
*
1379070 TTGCGGCGTTTA
1 TTGTGGCGTTTA
1379082 GGTAAAAAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 4 0.09
40 41 0.91
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (39 bp):
TTGTGGCGTTTAAAAAAAAACCTCTATACTGCAGATATA
Found at i:1379091 original size:40 final size:40
Alignment explanation
Indices: 1379002--1379081 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
1378992 GTGGTGTTTT
* * *
1379002 AAAAAAAAGCCTCTATACTTCCGATATATTGTGGCGTTTAC
1 AAAAAAAA-CCTCTATACTGCAGATATATTGCGGCGTTTAC
*
1379043 AAAAAAAACCTCTATAGTGCAGATATATTGCGGCGTTTA
1 AAAAAAAACCTCTATACTGCAGATATATTGCGGCGTTTA
1379082 GGTAAAAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
40 27 0.77
41 8 0.23
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30
Consensus pattern (40 bp):
AAAAAAAACCTCTATACTGCAGATATATTGCGGCGTTTAC
Found at i:1379114 original size:42 final size:42
Alignment explanation
Indices: 1379066--1379164 Score: 130
Period size: 41 Copynumber: 2.4 Consensus size: 42
1379056 ATAGTGCAGA
*
1379066 TATATTGCGGCGTTTAGGTA-AAAAACGCCACTATTGTTCAAC
1 TATATTGCGGCGTTTA-GTAGAAAAACGCCACTATTATTCAAC
* * *
1379108 TCTATTGCGGCGTTT-GTAGAAAAATGCCTCTATTATTCAAC
1 TATATTGCGGCGTTTAGTAGAAAAACGCCACTATTATTCAAC
*
1379149 TATATTGTGGCGTTTA
1 TATATTGCGGCGTTTA
1379165 CATAACAAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
40 3 0.06
41 32 0.65
42 14 0.29
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.36
Consensus pattern (42 bp):
TATATTGCGGCGTTTAGTAGAAAAACGCCACTATTATTCAAC
Found at i:1379153 original size:83 final size:83
Alignment explanation
Indices: 1379065--1379277 Score: 222
Period size: 83 Copynumber: 2.6 Consensus size: 83
1379055 TATAGTGCAG
* * * *
1379065 ATATATTGCGGCGTTTAGGTAAAAAACGCCACTATTG-TT-CAACTCTATTGCGGCGTTTGTAGA
1 ATATATTGCGGCGTTTAGATAAAAAACGCCACTATAGATTAC-AC-CTATTGCGGCATTTGTACA
* *
1379128 AAAATGCCTCT-AT-TATTCAA
64 AAAATACCGCTAATGTA-T-AA
* * * * * *
1379148 CTATATTGTGGCGTTTACATAACAAACGCCTCCATAGATTACACCTATTGCGGCATTTGTACAAA
1 ATATATTGCGGCGTTTAGATAAAAAACGCCACTATAGATTACACCTATTGCGGCATTTGTACAAA
1379213 AATACCGCTAATGTATAA
66 AATACCGCTAATGTATAA
*
1379231 ATAT-TTGCGGCGTTT-GTTAAAAAAACGCCACTATAGATTACACCTAT
1 ATATATTGCGGCGTTTAGAT-AAAAAACGCCACTATAGATTACACCTAT
1379278 AGTCGCGTTT
Statistics
Matches: 106, Mismatches: 19, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
81 1 0.01
82 35 0.33
83 60 0.57
84 7 0.07
85 3 0.03
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (83 bp):
ATATATTGCGGCGTTTAGATAAAAAACGCCACTATAGATTACACCTATTGCGGCATTTGTACAAA
AATACCGCTAATGTATAA
Found at i:1379369 original size:83 final size:84
Alignment explanation
Indices: 1379229--1379393 Score: 183
Period size: 83 Copynumber: 2.0 Consensus size: 84
1379219 GCTAATGTAT
* * * * * *
1379229 AAATATTTGCGGCGTTTGTTAAAAAAACGCCACTATAGATTACACCTATAGTCGCGTTT-TT-AT
1 AAATATTTGCGACGTTTCTTAAAAAAACGCCACTATACAGTAAACATATAGTCGCGTTTATTGAT
*
1379292 AAAAACGCAGGAAAAGTAA
66 AAAAACGCAGCAAAAGTAA
* * *
1379311 AAATATTTTGCGACGTTTCTTTATAAAACGCCACTATACAGTAAACATATTG-CGGCGTTTATTG
1 AAATA-TTTGCGACGTTTCTTAAAAAAACGCCACTATACAGTAAACATATAGTC-GCGTTTATTG
* *
1379375 ATATAAACGCCGCAAAAGT
64 ATAAAAACGCAGCAAAAGT
1379394 CAGGTATATA
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
82 6 0.09
83 43 0.64
84 2 0.03
85 16 0.24
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (84 bp):
AAATATTTGCGACGTTTCTTAAAAAAACGCCACTATACAGTAAACATATAGTCGCGTTTATTGAT
AAAAACGCAGCAAAAGTAA
Found at i:1380997 original size:82 final size:80
Alignment explanation
Indices: 1380911--1381075 Score: 197
Period size: 80 Copynumber: 2.0 Consensus size: 80
1380901 TTTTTCGCAC
* ** * ** *
1380911 AAACGCCACTATAAACAATACTATTACGGTGTTTGTTTAGTAAACGCCGCTAAATTA-CTCTCTA
1 AAACGCCACTATAAACAA-ACTATAACGG-CATT-TTAAACAAACGCCGCTAAATTACCACTCTA
* *
1380975 TAGCGTCGTTTGTTGAAA
63 TAGAGGCGTTTGTTGAAA
* *
1380993 AAACGCCACTATAAACAACCTATAACGGCATTTTAAACAAACGCCGCTAAATTACCACTCTATTG
1 AAACGCCACTATAAACAAACTATAACGGCATTTTAAACAAACGCCGCTAAATTACCACTCTATAG
1381058 AGGCGTTTGTTGAAA
66 AGGCGTTTGTTGAAA
1381073 AAA
1 AAA
1381076 AACACTATAA
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
79 19 0.27
80 26 0.37
81 8 0.11
82 18 0.25
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (80 bp):
AAACGCCACTATAAACAAACTATAACGGCATTTTAAACAAACGCCGCTAAATTACCACTCTATAG
AGGCGTTTGTTGAAA
Found at i:1382936 original size:2 final size:2
Alignment explanation
Indices: 1382929--1382957 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1382919 GTCTATAAAG
1382929 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1382958 TATTTAGATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1384221 original size:23 final size:24
Alignment explanation
Indices: 1384170--1384221 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
1384160 ATATGTTTCA
*
1384170 AAAATAATAATTACTTAAAATATTT
1 AAAATAATAA-TACTTAAAATATTG
1384195 AAAATAATAA-AC-TAGAAATATTG
1 AAAATAATAATACTTA-AAATATTG
1384218 AAAA
1 AAAA
1384222 GTTTTACTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 2 0.08
23 13 0.52
25 10 0.40
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (24 bp):
AAAATAATAATACTTAAAATATTG
Found at i:1387169 original size:59 final size:59
Alignment explanation
Indices: 1387071--1387191 Score: 199
Period size: 59 Copynumber: 2.1 Consensus size: 59
1387061 TGAGGGCTGG
* **
1387071 TTAGAGTCATATTATCGAGTTTGCCTTTTCATTGTGACTAGG-AGAGTTCGATAGGACAC
1 TTAGAGCCATATTATCGAGTTTGCCTTTTCATTACGACTAGGAAG-GTTCGATAGGACAC
1387130 TTAGAGCCATATTATCGAGTTTGCCTTTTCATTACGACTAGGAAGGTTCGATAGGACAC
1 TTAGAGCCATATTATCGAGTTTGCCTTTTCATTACGACTAGGAAGGTTCGATAGGACAC
1387189 TTA
1 TTA
1387192 TCCATCTATT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 56 0.97
60 2 0.03
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (59 bp):
TTAGAGCCATATTATCGAGTTTGCCTTTTCATTACGACTAGGAAGGTTCGATAGGACAC
Found at i:1390244 original size:113 final size:114
Alignment explanation
Indices: 1390043--1390265 Score: 269
Period size: 113 Copynumber: 2.0 Consensus size: 114
1390033 GTTAAGAAAT
* *
1390043 ATTTTACGCTATTTAAACTTTCATTCATCAATGTAACAACTTACAATAGTCATTATCACTATACA
1 ATTTTACGCTATTCAAACTTTCATTCATCAATGTAACAACTTACAATAGTCATCATCACTATACA
** *
1390108 CTTGCATAAGTTAACATCTTTAGTCCCTAAACATC-A-TTGTCAAGATA
66 CTCACATAAGTTAACATCTTTAGTCCCCAAACATCAAGTTGTCAAGATA
* * * *
1390155 ATTTTACGCCTATTCAAACTTTCATTCAAT-AGTGTAATATA-TTGCAATAGTCATCATCATTAT
1 ATTTTACG-CTATTCAAACTTTCATTC-ATCAATGTAACA-ACTTACAATAGTCATCATCACTAT
*
1390218 ACACTCACATAAGTT--TATCTACTTAGTCCCCAAACATCAAGTTGTCAA
63 ACACTCACATAAGTTAACATCT--TTAGTCCCCAAACATCAAGTTGTCAA
1390266 ATTAAGACAT
Statistics
Matches: 94, Mismatches: 10, Indels: 11
0.82 0.09 0.10
Matches are distributed among these distances:
111 4 0.04
112 8 0.09
113 71 0.76
114 4 0.04
115 7 0.07
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.36
Consensus pattern (114 bp):
ATTTTACGCTATTCAAACTTTCATTCATCAATGTAACAACTTACAATAGTCATCATCACTATACA
CTCACATAAGTTAACATCTTTAGTCCCCAAACATCAAGTTGTCAAGATA
Found at i:1391233 original size:31 final size:31
Alignment explanation
Indices: 1391172--1391252 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 31
1391162 CGGGGCTTTT
* *
1391172 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-TCATCTCAGGGCCGCA
* *
1391204 GGGCCTACCCAAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAATCATCTCAGGGCCGCA
*
1391235 GAGCCTACCTAAGAATCA
1 GGGCCTACCTAAGAATCA
1391253 CATTAGGTCC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 28 0.67
32 14 0.33
ACGTcount: A:0.30, C:0.31, G:0.25, T:0.15
Consensus pattern (31 bp):
GGGCCTACCTAAGAATCATCTCAGGGCCGCA
Found at i:1399256 original size:22 final size:22
Alignment explanation
Indices: 1399229--1399277 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
1399219 TAAAGTATAA
1399229 GAATTAGATTTAGAACATGTTG
1 GAATTAGATTTAGAACATGTTG
1399251 GAATTAGATTTAGAACATGTTG
1 GAATTAGATTTAGAACATGTTG
1399273 GAATT
1 GAATT
1399278 TGAGTTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (22 bp):
GAATTAGATTTAGAACATGTTG
Found at i:1400353 original size:23 final size:23
Alignment explanation
Indices: 1400262--1400345 Score: 141
Period size: 23 Copynumber: 3.7 Consensus size: 23
1400252 ACATCTTATA
*
1400262 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
1400285 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
1400308 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
1400331 TGGCACTTCAGTGCA
1 TGGCACTTCGGTGCA
1400346 TTTATACGAG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.27
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1401737 original size:19 final size:19
Alignment explanation
Indices: 1401713--1401750 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1401703 ATGAAGGGCT
1401713 TATGCCCTAGATTGAAAGA
1 TATGCCCTAGATTGAAAGA
1401732 TATGCCCTAGATTGAAAGA
1 TATGCCCTAGATTGAAAGA
1401751 GATGTTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (19 bp):
TATGCCCTAGATTGAAAGA
Found at i:1411231 original size:24 final size:24
Alignment explanation
Indices: 1411204--1411262 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
1411194 ATGCACAGGT
1411204 AGTGCATCGATGCACACATTAAGG
1 AGTGCATCGATGCACACATTAAGG
1411228 AGTGCATCGATGCACACATTAAGG
1 AGTGCATCGATGCACACATTAAGG
1411252 AGTGCATCGAT
1 AGTGCATCGAT
1411263 ACACTGTAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.22
Consensus pattern (24 bp):
AGTGCATCGATGCACACATTAAGG
Found at i:1412483 original size:17 final size:17
Alignment explanation
Indices: 1412461--1412504 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
1412451 AAATTAAATA
*
1412461 TGACTTTTCGAAAATTT
1 TGACTTTTCAAAAATTT
1412478 TGACTTTTCAAAAATTT
1 TGACTTTTCAAAAATTT
1412495 TGACTTTTCA
1 TGACTTTTCA
1412505 GTCAAAGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.48
Consensus pattern (17 bp):
TGACTTTTCAAAAATTT
Found at i:1413616 original size:114 final size:117
Alignment explanation
Indices: 1413467--1413745 Score: 345
Period size: 119 Copynumber: 2.4 Consensus size: 117
1413457 AGTGTTACAC
* *
1413467 TACACTTGCATAA-TTAACCTCTTTAGTCCCCAAACATTAAAGTGTCAA-AATA-ATATT-ACGC
1 TACACTTGCATAAGTTAACCTCTTTAGTCCCCAAACATCAAAGTGTCAATAAGACATATTCACGC
*
1413528 TATTTAAACTTTC-ATCCATCAATGTAACATA-TTACAATAGTCATCATCATTA
66 TATTTAAA-TTTCGATCCATCAATGTAACA-ACTTACAATAGTCATCATCACTA
* * * * * *
1413580 TACACTCGTATAAGTTAACATCTTTAGTCCCCAAACATCAAAGTGACAAGTTAAGACATTTTCAT
1 TACACTTGCATAAGTTAACCTCTTTAGTCCCCAAACATCAAAGTGTCAA--TAAGACATATTCAC
* *
1413645 GCTATTTAAATTTCGATCCATCAATGTTACAACTTCCAATAGTCATCATCACTA
64 GCTATTTAAATTTCGATCCATCAATGTAACAACTTACAATAGTCATCATCACTA
* * * *
1413699 TACAGTTGCATAAGTTAACCTCTTTAATCTCTAAACATCAAAGTGTC
1 TACACTTGCATAAGTTAACCTCTTTAGTCCCCAAACATCAAAGTGTC
1413746 CATTAAAATT
Statistics
Matches: 139, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
113 11 0.08
114 32 0.23
117 3 0.02
118 9 0.06
119 84 0.60
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.34
Consensus pattern (117 bp):
TACACTTGCATAAGTTAACCTCTTTAGTCCCCAAACATCAAAGTGTCAATAAGACATATTCACGC
TATTTAAATTTCGATCCATCAATGTAACAACTTACAATAGTCATCATCACTA
Found at i:1421341 original size:14 final size:14
Alignment explanation
Indices: 1421322--1421352 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1421312 AAATAAACGG
1421322 GTTAACTCAGACGA
1 GTTAACTCAGACGA
*
1421336 GTTAACTTAGACGA
1 GTTAACTCAGACGA
1421350 GTT
1 GTT
1421353 GACATAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (14 bp):
GTTAACTCAGACGA
Found at i:1426340 original size:44 final size:44
Alignment explanation
Indices: 1426277--1426380 Score: 129
Period size: 44 Copynumber: 2.4 Consensus size: 44
1426267 TACACAGCAG
* * *
1426277 AGTGTATCAATGCACATTCAAAGAATGCATCGGTGCAAC-TTCAT
1 AGTGTATCGATGCACATTCAAAGAATGCATCAGTAC-ACTTTCAT
* * *
1426321 AGTGTATCGATGCATATTCAAGGGATGCATCAGTACACTTTCAT
1 AGTGTATCGATGCACATTCAAAGAATGCATCAGTACACTTTCAT
*
1426365 AGTGTATTGATGCACA
1 AGTGTATCGATGCACA
1426381 GTGCACAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 2 0.04
44 49 0.96
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (44 bp):
AGTGTATCGATGCACATTCAAAGAATGCATCAGTACACTTTCAT
Found at i:1431727 original size:65 final size:65
Alignment explanation
Indices: 1431635--1431809 Score: 180
Period size: 65 Copynumber: 2.7 Consensus size: 65
1431625 ATAAGACCTT
* * * * * * *
1431635 GTGCATCGATACACTTGG-TGTGCATCGGTACACTA-ATTATATTTGATGTTTTAA-AGGAGCCA
1 GTGCATCGATGCA--TGGTTGTGCATCGGTACACTAGAATACATTCGATGTTTCAATA-AAACCA
1431697 GGA
63 GGA
* *
1431700 GTGTATCGATGCATGGTTTGTGCATCGGTACA-TAGAATACATTCGATGTTTCAATAAAATCAGG
1 GTGCATCGATGCATGG-TTGTGCATCGGTACACTAGAATACATTCGATGTTTCAATAAAACCAGG
1431764 A
65 A
* *
1431765 GTGCATCGATGCATGGTTGTGCATCGGTACAC-AAAATGCATTCGA
1 GTGCATCGATGCATGGTTGTGCATCGGTACACTAGAATACATTCGA
1431810 ACTAGGGTGA
Statistics
Matches: 93, Mismatches: 12, Indels: 11
0.80 0.10 0.09
Matches are distributed among these distances:
63 3 0.03
64 28 0.30
65 61 0.66
66 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATGGTTGTGCATCGGTACACTAGAATACATTCGATGTTTCAATAAAACCAGGA
Found at i:1432933 original size:18 final size:18
Alignment explanation
Indices: 1432910--1432962 Score: 106
Period size: 18 Copynumber: 2.9 Consensus size: 18
1432900 AGTCATCAAC
1432910 TCAAAGAAGATGAACAAT
1 TCAAAGAAGATGAACAAT
1432928 TCAAAGAAGATGAACAAT
1 TCAAAGAAGATGAACAAT
1432946 TCAAAGAAGATGAACAA
1 TCAAAGAAGATGAACAA
1432963 CCAAAGAGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.57, C:0.11, G:0.17, T:0.15
Consensus pattern (18 bp):
TCAAAGAAGATGAACAAT
Found at i:1434206 original size:25 final size:25
Alignment explanation
Indices: 1434158--1434206 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1434148 AAAAATATAC
*
1434158 TAATTATATGTTTAATTTACAATTA
1 TAATTATAAGTTTAATTTACAATTA
*
1434183 TAATTATAAGTATTTATTTA-AATT
1 TAATTATAAGT-TTAATTTACAATT
1434207 TTGGATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (25 bp):
TAATTATAAGTTTAATTTACAATTA
Found at i:1434255 original size:2 final size:2
Alignment explanation
Indices: 1434244--1434332 Score: 171
Period size: 2 Copynumber: 45.0 Consensus size: 2
1434234 TAGTTGTTTC
1434244 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1434285 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1434327 TA TA TA
1 TA TA TA
1434333 GTGATTGAAA
Statistics
Matches: 86, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 85 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1437605 original size:21 final size:21
Alignment explanation
Indices: 1437563--1437607 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1437553 CGATAAAAAA
* *
1437563 TTACTTAAAATATTATTATTT
1 TTACTTAAAACATAATTATTT
1437584 TTACTTAAAACATCAATT-TTT
1 TTACTTAAAACAT-AATTATTT
1437605 TTA
1 TTA
1437608 ACATTTCTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (21 bp):
TTACTTAAAACATAATTATTT
Found at i:1445335 original size:18 final size:18
Alignment explanation
Indices: 1445312--1445346 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1445302 TTCCATCCGG
*
1445312 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1445330 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1445347 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1448915 original size:13 final size:13
Alignment explanation
Indices: 1448897--1448926 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1448887 ATGAATTCTG
1448897 AATTGATGTTATA
1 AATTGATGTTATA
1448910 AATTGATGTTATA
1 AATTGATGTTATA
1448923 AATT
1 AATT
1448927 ATGCAGAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (13 bp):
AATTGATGTTATA
Found at i:1453349 original size:14 final size:15
Alignment explanation
Indices: 1453320--1453354 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1453310 TCGTAGGACC
1453320 ACTACATCCTGAAGG
1 ACTACATCCTGAAGG
*
1453335 ACTACGTCC-GAAGG
1 ACTACATCCTGAAGG
1453349 ACTACA
1 ACTACA
1453355 ATACCCTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.34, C:0.29, G:0.20, T:0.17
Consensus pattern (15 bp):
ACTACATCCTGAAGG
Found at i:1453521 original size:13 final size:13
Alignment explanation
Indices: 1453485--1453538 Score: 51
Period size: 12 Copynumber: 4.3 Consensus size: 13
1453475 GTGTAACCAT
*
1453485 ATATTTCAT-TTC
1 ATATGTCATATTC
**
1453497 ATATCACATATTGC
1 ATATGTCATATT-C
1453511 ATAT-TCATATTC
1 ATATGTCATATTC
1453523 ATATGTCAT-TTC
1 ATATGTCATATTC
1453535 ATAT
1 ATAT
1453539 ATTCACATAG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
12 19 0.53
13 12 0.33
14 5 0.14
ACGTcount: A:0.31, C:0.17, G:0.04, T:0.48
Consensus pattern (13 bp):
ATATGTCATATTC
Found at i:1454012 original size:35 final size:36
Alignment explanation
Indices: 1453966--1454036 Score: 135
Period size: 35 Copynumber: 2.0 Consensus size: 36
1453956 TTCATTTAGG
1453966 GGGGAATCGATACCCCCCA-GGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAGGGGGGAATCTGTTCCC
1454001 GGGGAATCGATACCCCCCAGGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAGGGGGGAATCTGTTCCC
1454037 CCTGCACATA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 19 0.54
36 16 0.46
ACGTcount: A:0.20, C:0.31, G:0.32, T:0.17
Consensus pattern (36 bp):
GGGGAATCGATACCCCCCAGGGGGGAATCTGTTCCC
Found at i:1457738 original size:15 final size:15
Alignment explanation
Indices: 1457710--1457745 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1457700 TCGTAGGACC
*
1457710 ACTACATCCTGAAGG
1 ACTACATCCCGAAGG
*
1457725 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGG
1457740 ACTACA
1 ACTACA
1457746 ATACCCTCGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:1457917 original size:12 final size:13
Alignment explanation
Indices: 1457877--1457930 Score: 51
Period size: 12 Copynumber: 4.3 Consensus size: 13
1457867 GTGTAACCAT
*
1457877 ATATTTCATA-TC
1 ATATCTCATATTC
*
1457889 ATATCACATATTGC
1 ATATCTCATATT-C
1457903 ATAT-TCATATTC
1 ATATCTCATATTC
*
1457915 ATATGTCAT-TTC
1 ATATCTCATATTC
1457927 ATAT
1 ATAT
1457931 ATTCACATAG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
12 20 0.56
13 11 0.31
14 5 0.14
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (13 bp):
ATATCTCATATTC
Found at i:1468389 original size:21 final size:21
Alignment explanation
Indices: 1468350--1468391 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1468340 AACCAAATTC
*
1468350 AACACAAATCCAAATCCCATT
1 AACACAAATCCAAAACCCATT
1468371 AACACAAA-CCAAAAACCCATT
1 AACACAAATCC-AAAACCCATT
1468392 CAGCAAGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.52, C:0.33, G:0.00, T:0.14
Consensus pattern (21 bp):
AACACAAATCCAAAACCCATT
Found at i:1471108 original size:3 final size:3
Alignment explanation
Indices: 1471100--1471127 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1471090 GTAGGTTTTA
1471100 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1471128 TTTTTTTGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1474655 original size:3 final size:3
Alignment explanation
Indices: 1474647--1474671 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1474637 GTTGGTTTTA
1474647 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1474672 TTTTTTCGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1481647 original size:37 final size:37
Alignment explanation
Indices: 1481597--1482020 Score: 326
Period size: 37 Copynumber: 11.2 Consensus size: 37
1481587 AGTCGGACTC
*
1481597 AAGATCGATTTGCTTCACTACTCTTCGGTGAAGGCTT
1 AAGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTT
* * *
1481634 AAGATTGATTTGCTTCACTACTTTTTGGTGAAGGCTT
1 AAGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTT
* *
1481671 AAGAT-GATTTTGCTTCACCACTCTTTGGTGAAGGCTT
1 AAGATGGA-TTTGCTTCACTACTCTTCGGTGAAGGCTT
* *** *
1481708 AAGATCGCCCAAAGGACTT-AAT-CATCATGCTC-G-GAAGGCTT
1 AAGAT-G--GATTTG-CTTCACTAC-TC-T--TCGGTGAAGGCTT
* *
1481749 ATTGATGGATTTGCTTCACTACTCTTCCGTGAAGGCTT
1 A-AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTT
* * * *
1481787 ATGATGGATTTGCTTCACTACTTTTTGGTGAAGTCTT
1 AAGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTT
* *
1481824 AAGATGAATTTGCTTCACTACTCTTTGGTGAAGGCTT
1 AAGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTT
*** * *
1481861 AAGATGGCCCGGATGACTT-AATCACCATGCTT--G-GAAGGATT
1 AAGATGG---ATTTG-CTTCACT-A-C-T-CTTCGGTGAAGGCTT
* **
1481902 ACTGATGGATTTGCTTCACTACTCTTCCATGAAGGCTT
1 A-AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTT
*
1481940 ATGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTT
1 AAGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTT
* * * *
1481977 TAGATTGATTTGCTTTACTACTCTTTGGTGAAGGCTT
1 AAGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTT
1482014 AAGATGG
1 AAGATGG
1482021 CTCGGAGGAC
Statistics
Matches: 311, Mismatches: 48, Indels: 56
0.75 0.12 0.13
Matches are distributed among these distances:
35 3 0.01
36 5 0.02
37 215 0.69
38 25 0.08
39 11 0.04
40 9 0.03
41 27 0.09
42 11 0.04
43 2 0.01
44 3 0.01
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.36
Consensus pattern (37 bp):
AAGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTT
Found at i:1481881 original size:153 final size:153
Alignment explanation
Indices: 1481603--1482056 Score: 703
Period size: 153 Copynumber: 3.0 Consensus size: 153
1481593 ACTCAAGATC
* * *
1481603 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACTACTTTTTGGTGAAGG
1 GATTTGCTTCACTACTCTTCCGTGAAGGCTTATGATGGATTTGCTTCACTACTTTTTGGTGAAGG
* * * **
1481668 CTTAAGATGATTTTGCTTCACCACTCTTTGGTGAAGGCTTAAGATCGCCCAAAGGACTTAATCAT
66 CTTAAGATGAATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATGGCCCGGAGGACTTAATCAT
*
1481733 CATGCTCGGAAGGCTTATTGATG
131 CATGCTCGGAAGGCTTACTGATG
*
1481756 GATTTGCTTCACTACTCTTCCGTGAAGGCTTATGATGGATTTGCTTCACTACTTTTTGGTGAAGT
1 GATTTGCTTCACTACTCTTCCGTGAAGGCTTATGATGGATTTGCTTCACTACTTTTTGGTGAAGG
* *
1481821 CTTAAGATGAATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATGGCCCGGATGACTTAATCAC
66 CTTAAGATGAATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATGGCCCGGAGGACTTAATCAT
* *
1481886 CATGCTTGGAAGGATTACTGATG
131 CATGCTCGGAAGGCTTACTGATG
* * *
1481909 GATTTGCTTCACTACTCTTCCATGAAGGCTTATGATGGATTTGCTTCACTACTCTTCGGTGAAGG
1 GATTTGCTTCACTACTCTTCCGTGAAGGCTTATGATGGATTTGCTTCACTACTTTTTGGTGAAGG
* * *
1481974 CTTTAGATTG-ATTTGCTTTACTACTCTTTGGTGAAGGCTTAAGATGGCTCGGAGGACTTAATCA
66 CTTAAGA-TGAATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATGGCCCGGAGGACTTAATCA
*
1482038 TCATGCTCGGAAGACTTAC
130 TCATGCTCGGAAGGCTTAC
1482057 AAATGACCTG
Statistics
Matches: 274, Mismatches: 26, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
153 272 0.99
154 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (153 bp):
GATTTGCTTCACTACTCTTCCGTGAAGGCTTATGATGGATTTGCTTCACTACTTTTTGGTGAAGG
CTTAAGATGAATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATGGCCCGGAGGACTTAATCAT
CATGCTCGGAAGGCTTACTGATG
Found at i:1482262 original size:21 final size:21
Alignment explanation
Indices: 1482229--1482270 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1482219 ATGTGAAAAA
*
1482229 CATCCTGCCCGAATGACTTAT
1 CATCCTGCCCGAAAGACTTAT
* *
1482250 CATCTTGCTCGAAAGACTTAT
1 CATCCTGCCCGAAAGACTTAT
1482271 AGATGACTCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (21 bp):
CATCCTGCCCGAAAGACTTAT
Found at i:1482417 original size:214 final size:214
Alignment explanation
Indices: 1482026--1482463 Score: 693
Period size: 214 Copynumber: 2.0 Consensus size: 214
1482016 GATGGCTCGG
*
1482026 AGGACTTAATCATCATGCTCGGAAGACTTACAAATGACCTGAAGGATTTAAGCATCATGCTCGAA
1 AGGACTT-ATCATCATGCTCGAAAGACTTACAAATGACCTGAAGGATTTAAGCATCATGCTCGAA
* *
1482091 AGACTTACTGATGGGCCGAAGGACTTATAAATTTTTAAAATAGTTTACTGGATAAGAAACATTTC
65 AGACTTACTGATGGGCCGAAGGACTTATAAATTTTGAAAATAGTTTACTGGATAAGAAACATTTA
*
1482156 TTACTTTTCAAAAATTTTAAATTTCAAATTTAAATGAGAAACCTTTCTCATTTTTTGATAGACAT
130 TTACTTTTCAAAAATTTCAAATTTCAAATTTAAATGAGAAACCTTTCTCATTTTTTGATAGACAT
* *
1482221 GTGAAAAACATCCTGCCCGA
195 GTGAAAAACATCATGCCCAA
* * * *
1482241 ATGACTTATCATCTTGCTCGAAAGACTTATAGATGA-CTCGAAGGATTTAAGCATCATGCTCGAA
1 AGGACTTATCATCATGCTCGAAAGACTTACAAATGACCT-GAAGGATTTAAGCATCATGCTCGAA
* *
1482305 AGACTTACTGAT-GGCCTGAAGGACTTATAAATTTTGGAAATAGTTTACTAGG-TAAGAATCATT
65 AGACTTACTGATGGGCC-GAAGGACTTATAAATTTTGAAAATAGTTTACT-GGATAAGAAACATT
* *
1482368 TATTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAACCTTTCTCATTTTTTGATAGAC
128 TATTACTTTTCAAAAATTTCAAATTTCAAATTTAAATGAGAAACCTTTCTCATTTTTTGATAGAC
1482433 ATGTGAAAAACATCATGCCCAA
193 ATGTGAAAAACATCATGCCCAA
1482455 AGGACTTAT
1 AGGACTTAT
1482464 GGATAGCCCG
Statistics
Matches: 205, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
213 6 0.03
214 191 0.93
215 8 0.04
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (214 bp):
AGGACTTATCATCATGCTCGAAAGACTTACAAATGACCTGAAGGATTTAAGCATCATGCTCGAAA
GACTTACTGATGGGCCGAAGGACTTATAAATTTTGAAAATAGTTTACTGGATAAGAAACATTTAT
TACTTTTCAAAAATTTCAAATTTCAAATTTAAATGAGAAACCTTTCTCATTTTTTGATAGACATG
TGAAAAACATCATGCCCAA
Found at i:1482566 original size:151 final size:151
Alignment explanation
Indices: 1482292--1482573 Score: 415
Period size: 151 Copynumber: 1.9 Consensus size: 151
1482282 AGGATTTAAG
* * * *
1482292 CATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTATAAATTTTGGAAATAGTTTACTAGG
1 CATCATGCTCCAAAGACTTACTGATAGCCCGAAGGACTTATAAATTTTGGAAAAAGTTTACTAGG
* * * * *
1482357 TAAGAATCATTTATTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAACCTTTCTCATT
66 TAAGAAACATTTATTACTTTTCAAAAATTTAAATTTTCAGATTGAAATGAGAAACCTTTCCCATT
1482422 TTTTGATAGACATGTGAAAAA
131 TTTTGATAGACATGTGAAAAA
*
1482443 CATCATGC-CCAAAGGACTTA-TGGATAGCCCGAAGGACTTATAAATTTTGGAAAAATTTTACTA
1 CATCATGCTCCAAA-GACTTACT-GATAGCCCGAAGGACTTATAAATTTTGGAAAAAGTTTACTA
* * *
1482506 GGTAAGAAACCTTTCTTACTTTTCAAAAATTTAAATTTTCAGATTGGAATGAGAAACCTTTCCCA
64 GGTAAGAAACATTTATTACTTTTCAAAAATTTAAATTTTCAGATTGAAATGAGAAACCTTTCCCA
1482571 TTT
129 TTT
1482574 CATTTTTACT
Statistics
Matches: 116, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
150 5 0.04
151 111 0.96
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Consensus pattern (151 bp):
CATCATGCTCCAAAGACTTACTGATAGCCCGAAGGACTTATAAATTTTGGAAAAAGTTTACTAGG
TAAGAAACATTTATTACTTTTCAAAAATTTAAATTTTCAGATTGAAATGAGAAACCTTTCCCATT
TTTTGATAGACATGTGAAAAA
Found at i:1483320 original size:37 final size:37
Alignment explanation
Indices: 1483270--1483438 Score: 198
Period size: 37 Copynumber: 4.6 Consensus size: 37
1483260 TGGTCATGTC
* *
1483270 CCAAAGAGTAGTGAACCAAATCAATCTTAAGCCTTAA
1 CCAAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCA
* * *
1483307 CCAAAAAGTAGTGAAG-AAAGTCCATTTTAAGCCTTCA
1 CCAAAGAGTAGTGAAGCAAA-TCAATCTTAAGCCTTCA
* * * **
1483344 CGAAAGAGGAGTGAAACAAATC-ATCCCAAGCCTTCA
1 CCAAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCA
* *
1483380 CCGAAGAGTAGTGAAGCAAATCAATCTTAAGTCTTCA
1 CCAAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCA
*
1483417 CCGAAGAGTAGTGAAGCAAATC
1 CCAAAGAGTAGTGAAGCAAATC
1483439 CATCAATCTG
Statistics
Matches: 110, Mismatches: 19, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
36 32 0.29
37 75 0.68
38 3 0.03
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (37 bp):
CCAAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCA
Found at i:1483410 original size:73 final size:75
Alignment explanation
Indices: 1483272--1483438 Score: 198
Period size: 73 Copynumber: 2.3 Consensus size: 75
1483262 GTCATGTCCC
* ** * *
1483272 AAAGAGTAGTGAACCAAATCAATCTTAAGCCTTAACCAAAAAGTAGTGAAGAAAGTCCATTTTAA
1 AAAGAGTAGTGAAACAAATCAATCCCAAGCCTTAACCAAAAAGTAGTGAAGAAAGTCAATCTTAA
1483337 GCCTTCA-CG
66 GCCTTCACCG
* * * *
1483346 AAAGAGGAGTGAAACAAATC-ATCCCAAGCCTTCACCGAAGAGTAGTGAAGCAAA-TCAATCTTA
1 AAAGAGTAGTGAAACAAATCAATCCCAAGCCTTAACCAAAAAGTAGTGAAG-AAAGTCAATCTTA
*
1483409 AGTCTTCACCG
65 AGCCTTCACCG
*
1483420 -AAGAGTAGTGAAGCAAATC
1 AAAGAGTAGTGAAACAAATC
1483439 CATCAATCTG
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
73 56 0.71
74 23 0.29
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (75 bp):
AAAGAGTAGTGAAACAAATCAATCCCAAGCCTTAACCAAAAAGTAGTGAAGAAAGTCAATCTTAA
GCCTTCACCG
Found at i:1483610 original size:89 final size:87
Alignment explanation
Indices: 1483480--1483794 Score: 375
Period size: 88 Copynumber: 3.6 Consensus size: 87
1483470 ACACATGTCA
* *
1483480 CTCTTTTGCAAGATTTGATATTCCCTGAGTGACAACGGAACAAGTCTACCCCATATCTGATATTC
1 CTCTTTTCCAAGATTTGATATTCCCTGAGTGACAACAGAACAAGTCTACCCCATATCTGATATTC
* *
1483545 CCTGAGTGACAACGAAACAGGTC
66 CCTGAGTGACAGCGAAATA-GTC
* * * * * *
1483568 TCTCTTTTCCAAGATTTGATATTCCCTAACTGATAGCAGAACAAGTCT-GCTCATATCTGATATT
1 -CTCTTTTCCAAGATTTGATATTCCCTGAGTGACAACAGAACAAGTCTACCCCATATCTGATATT
*
1483632 CCCTGAGTGACAGCGGAATATGTC
65 CCCTGAGTGACAGCGAAATA-GTC
* * * * *
1483656 AATCTTTTCGAAGATTTGATATTCCCTGAGTGACAGCAGAACACGTCTACCCCAGATCTGATATT
1 -CTCTTTTCCAAGATTTGATATTCCCTGAGTGACAACAGAACAAGTCTACCCCATATCTGATATT
* *
1483721 CACTGAGTGACAGCGGAATATATTC
65 CCCTGAGTGACAGC-GAA-ATAGTC
* *
1483746 CTC-TTT-CAAGATTTGATATTCCCTTAGTGACAACGGAACAAGTCTACCC
1 CTCTTTTCCAAGATTTGATATTCCCTGAGTGACAACAGAACAAGTCTACCC
1483795 GATTCAATGG
Statistics
Matches: 192, Mismatches: 31, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
87 38 0.20
88 78 0.41
89 69 0.36
90 4 0.02
91 3 0.02
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (87 bp):
CTCTTTTCCAAGATTTGATATTCCCTGAGTGACAACAGAACAAGTCTACCCCATATCTGATATTC
CCTGAGTGACAGCGAAATAGTC
Found at i:1483664 original size:88 final size:89
Alignment explanation
Indices: 1483474--1483794 Score: 407
Period size: 89 Copynumber: 3.6 Consensus size: 89
1483464 GAAGTGACAC
* * *
1483474 ATGTCACTCTTTTGCAAGATTTGATATTCCCTGAGTGACAACGGAACAAGTCTACCCCATATCTG
1 ATGTCACTCTTTTCCAAGATTTGATATTCCCTGAGTGACAGCAGAACAAGTCTACCCCATATCTG
* * *
1483539 ATATTCCCTGAGTGACAACGAAAC
66 ATATTCCCTGAGTGACAGCGGAAT
* * * * * * *
1483563 AGGTCTCTCTTTTCCAAGATTTGATATTCCCTAACTGATAGCAGAACAAGTCT-GCTCATATCTG
1 ATGTCACTCTTTTCCAAGATTTGATATTCCCTGAGTGACAGCAGAACAAGTCTACCCCATATCTG
1483627 ATATTCCCTGAGTGACAGCGGAAT
66 ATATTCCCTGAGTGACAGCGGAAT
* * * *
1483651 ATGTCAATCTTTTCGAAGATTTGATATTCCCTGAGTGACAGCAGAACACGTCTACCCCAGATCTG
1 ATGTCACTCTTTTCCAAGATTTGATATTCCCTGAGTGACAGCAGAACAAGTCTACCCCATATCTG
*
1483716 ATATTCACTGAGTGACAGCGGAAT
66 ATATTCCCTGAGTGACAGCGGAAT
* * * *
1483740 ATATTC-CTC-TTT-CAAGATTTGATATTCCCTTAGTGACAACGGAACAAGTCTACCC
1 AT-GTCACTCTTTTCCAAGATTTGATATTCCCTGAGTGACAGCAGAACAAGTCTACCC
1483795 GATTCAATGG
Statistics
Matches: 198, Mismatches: 32, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
87 38 0.19
88 78 0.39
89 80 0.40
90 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (89 bp):
ATGTCACTCTTTTCCAAGATTTGATATTCCCTGAGTGACAGCAGAACAAGTCTACCCCATATCTG
ATATTCCCTGAGTGACAGCGGAAT
Found at i:1486046 original size:37 final size:37
Alignment explanation
Indices: 1485996--1486251 Score: 220
Period size: 37 Copynumber: 6.8 Consensus size: 37
1485986 CAAAATTAGA
1485996 CACTACTTTTCGGTGAAGGCTTAAGATGGATTTGCTT
1 CACTACTTTTCGGTGAAGGCTTAAGATGGATTTGCTT
*
1486033 CACTACTTTTCGGTGAAGGCTTAAGATGGATTTGTTT
1 CACTACTTTTCGGTGAAGGCTTAAGATGGATTTGCTT
1486070 CACTACTCTTT-GGTGAAGGCTTAAGATAGCCCGGA--TGACTT
1 CACTACT-TTTCGGTGAAGGCTTAAGAT-----GGATTTG-CTT
* ** * *
1486111 -AATCATCATACTC-G-GAAGGATTAGTGATGGATTTGCTT
1 CACT-A-C-TTTTCGGTGAAGGCTTA-AGATGGATTTGCTT
* * * * *
1486149 CACTGCTCTTCCGTGAAGGCTTATGATGGATTTACTT
1 CACTACTTTTCGGTGAAGGCTTAAGATGGATTTGCTT
* * *
1486186 CACTACTCTTCGGTGAAGGCTTTAGATTGATTTGCTT
1 CACTACTTTTCGGTGAAGGCTTAAGATGGATTTGCTT
*
1486223 CATTACTCTTT-GGTGAAGGCTTAAGATGG
1 CACTACT-TTTCGGTGAAGGCTTAAGATGG
1486252 CCCGGAGGAC
Statistics
Matches: 178, Mismatches: 23, Indels: 36
0.75 0.10 0.15
Matches are distributed among these distances:
36 3 0.02
37 130 0.73
38 16 0.09
39 4 0.02
40 4 0.02
41 11 0.06
42 9 0.05
43 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (37 bp):
CACTACTTTTCGGTGAAGGCTTAAGATGGATTTGCTT
Found at i:1486284 original size:22 final size:21
Alignment explanation
Indices: 1486254--1486328 Score: 57
Period size: 22 Copynumber: 3.5 Consensus size: 21
1486244 TAAGATGGCC
*
1486254 CGGAGGACTTAATCATCATGCT
1 CGGAAGACTTAA-CATCATGCT
*
1486276 CGGAAGACTT-ACA-GATGAC-
1 CGGAAGACTTAACATCATG-CT
* *
1486295 CTGAAAGATTTAAGCATCATGCT
1 C-GGAAGACTTAA-CATCATGCT
1486318 CGGAAGACTTA
1 CGGAAGACTTA
1486329 CTGATGGTCT
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
19 4 0.10
20 10 0.25
21 2 0.05
22 20 0.50
23 4 0.10
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (21 bp):
CGGAAGACTTAACATCATGCT
Found at i:1486490 original size:21 final size:21
Alignment explanation
Indices: 1486457--1486497 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1486447 ATGTGAAAAA
*
1486457 CATCCTGCCCGAAGGACTTAT
1 CATCCTGCCCGAAAGACTTAT
* *
1486478 CATCTTGCTCGAAAGACTTA
1 CATCCTGCCCGAAAGACTTA
1486498 CAGATGACCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (21 bp):
CATCCTGCCCGAAAGACTTAT
Found at i:1488869 original size:13 final size:13
Alignment explanation
Indices: 1488853--1488894 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
1488843 CAATTTCTTT
1488853 TTTTCTTCTTTTA
1 TTTTCTTCTTTTA
1488866 TTTTC-TCTTTTA
1 TTTTCTTCTTTTA
* *
1488878 TTTTCTTTTTTTC
1 TTTTCTTCTTTTA
1488891 TTTT
1 TTTT
1488895 TTTTCTACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 12 0.46
13 14 0.54
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTCTTCTTTTA
Found at i:1488894 original size:30 final size:30
Alignment explanation
Indices: 1488846--1488920 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
1488836 CTTGATTCAA
1488846 TTTCTT-TTTTTCTTCTTTTATTTTCT-CTTT
1 TTTCTTCTTTTT-TTCTTTT-TTTTCTACTTT
1488876 TATT-TTCTTTTTTTCTTTTTTTTCTACTTT
1 T-TTCTTCTTTTTTTCTTTTTTTTCTACTTT
1488906 TTTCTTCTTCTTTTT
1 TTTCTTCTT-TTTTT
1488921 GATGGATGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
29 8 0.20
30 20 0.50
31 12 0.30
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (30 bp):
TTTCTTCTTTTTTTCTTTTTTTTCTACTTT
Found at i:1488905 original size:12 final size:11
Alignment explanation
Indices: 1488850--1488920 Score: 60
Period size: 12 Copynumber: 6.4 Consensus size: 11
1488840 ATTCAATTTC
1488850 TTTTTTTCTTCT
1 TTTTTTTC-TCT
1488862 TTTATTTTCTCT
1 TTT-TTTTCTCT
*
1488874 TTTATTT-TC-
1 TTTTTTTCTCT
1488883 -TTTTTT-TCT
1 TTTTTTTCTCT
1488892 TTTTTTTCTACT
1 TTTTTTTCT-CT
1488904 TTTTTCTTCTTCT
1 TTTTT-TTC-TCT
1488917 TTTT
1 TTTT
1488921 GATGGATGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
8 7 0.14
10 8 0.16
11 4 0.08
12 16 0.32
13 14 0.28
14 1 0.02
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTTCTCT
Found at i:1488909 original size:19 final size:18
Alignment explanation
Indices: 1488846--1488911 Score: 59
Period size: 17 Copynumber: 3.8 Consensus size: 18
1488836 CTTGATTCAA
*
1488846 TTTCTTTTTTTC--TTCT
1 TTTCTTTTTTTCTTTTAT
* *
1488862 TTT-ATTTTCTCTTTTAT
1 TTTCTTTTTTTCTTTTAT
1488879 TTTCTTTTTTTCTTTT-T
1 TTTCTTTTTTTCTTTTAT
1488896 TTTCTACTTTTTTCTT
1 TTTCT--TTTTTTCTT
1488912 CTTCTTTTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
15 6 0.15
16 3 0.08
17 12 0.30
18 10 0.25
19 9 0.22
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTCTTTTTTTCTTTTAT
Found at i:1488917 original size:33 final size:33
Alignment explanation
Indices: 1488846--1488920 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
1488836 CTTGATTCAA
*
1488846 TTTCTTTTTTTCTTCTTTTATTTTCTCTTTTAT
1 TTTCTTTTTTTCTTCTTTTATTTACTCTTTTAT
* *
1488879 TTTCTTTTTTTCTT-TTTT-TTCTACTTTTTTCT
1 TTTCTTTTTTTCTTCTTTTATT-TACTCTTTTAT
1488911 TCTTCTTTTT
1 T-TTCTTTTT
1488921 GATGGATGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 2 0.05
32 13 0.35
33 22 0.59
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (33 bp):
TTTCTTTTTTTCTTCTTTTATTTACTCTTTTAT
Found at i:1490818 original size:28 final size:28
Alignment explanation
Indices: 1490778--1490837 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
1490768 GAGGCATTAA
1490778 CAACCTTTATATCTTTAATAGCTTCCTT
1 CAACCTTTATATCTTTAATAGCTTCCTT
1490806 CAACCTTTATATCTTTAATAGCTTCCTT
1 CAACCTTTATATCTTTAATAGCTTCCTT
1490834 CAAC
1 CAAC
1490838 AACTTGAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.27, C:0.27, G:0.03, T:0.43
Consensus pattern (28 bp):
CAACCTTTATATCTTTAATAGCTTCCTT
Found at i:1500278 original size:2 final size:2
Alignment explanation
Indices: 1500271--1500300 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1500261 TTTCCTTAAC
1500271 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1500301 CTTTTTCATA
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):
TA
Found at i:1502345 original size:73 final size:73
Alignment explanation
Indices: 1502257--1502405 Score: 280
Period size: 73 Copynumber: 2.0 Consensus size: 73
1502247 TATTTGTATA
1502257 GGAGAATTATGTTAAATTTTAAATATTTTAGGGTTTTAAGTCTTTTACTTCTGATATTGTGATGT
1 GGAGAATTATGTTAAATTTTAAATATTTTAGGGTTTTAAGTCTTTTACTTCTGATATTGTGATGT
1502322 TTACACTC
66 TTACACTC
* *
1502330 GGAGAATTATGTTAAATTTTAAATTTTTTAGGGTTTTAAGTCTTTTACTTCTGATATTTTGATGT
1 GGAGAATTATGTTAAATTTTAAATATTTTAGGGTTTTAAGTCTTTTACTTCTGATATTGTGATGT
1502395 TTACACTC
66 TTACACTC
1502403 GGA
1 GGA
1502406 TATTAAATTT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.27, C:0.08, G:0.17, T:0.48
Consensus pattern (73 bp):
GGAGAATTATGTTAAATTTTAAATATTTTAGGGTTTTAAGTCTTTTACTTCTGATATTGTGATGT
TTACACTC
Found at i:1504884 original size:21 final size:21
Alignment explanation
Indices: 1504852--1504900 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
1504842 ACTGCTGGAA
1504852 AATCGG-TTTGACCGGTTTTC
1 AATCGGTTTTGACCGGTTTTC
1504872 AATCGGTTTTGACCGGTTTTC
1 AATCGGTTTTGACCGGTTTTC
*
1504893 GATCGGTT
1 AATCGGTT
1504901 CGAACCAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.14, C:0.18, G:0.27, T:0.41
Consensus pattern (21 bp):
AATCGGTTTTGACCGGTTTTC
Found at i:1504953 original size:19 final size:20
Alignment explanation
Indices: 1504931--1504973 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
1504921 AAACCGGTTT
1504931 GACCGAT-CTGACCCGACCC
1 GACCGATACTGACCCGACCC
*
1504950 GACC-CTACTGACCCGACCC
1 GACCGATACTGACCCGACCC
1504969 GACCG
1 GACCG
1504974 TTGACCGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.21, C:0.49, G:0.21, T:0.09
Consensus pattern (20 bp):
GACCGATACTGACCCGACCC
Found at i:1512464 original size:14 final size:14
Alignment explanation
Indices: 1512447--1512475 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1512437 TTTGACCGGT
1512447 CTGACCCGACCCGA
1 CTGACCCGACCCGA
1512461 CTGACCCGACCCGA
1 CTGACCCGACCCGA
1512475 C
1 C
1512476 CGTTGACCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.52, G:0.21, T:0.07
Consensus pattern (14 bp):
CTGACCCGACCCGA
Found at i:1514945 original size:53 final size:53
Alignment explanation
Indices: 1514879--1514993 Score: 155
Period size: 53 Copynumber: 2.2 Consensus size: 53
1514869 TGTAACAGTA
* * *
1514879 AGGG-TTAAGGTTAAAGAAA-ATGAACAGAGATAGAAGATGAAGAGGCTTGGTTT
1 AGGGTTTAGGGTTAAA-AAAGATGAACAGAGATAGAAGATGAAAAGGCTAGG-TT
*
1514932 A-GGTTTAGGGTTAAAAAAGATGAACATAGATAGAAGATGAAAAGGCTAGGTT
1 AGGGTTTAGGGTTAAAAAAGATGAACAGAGATAGAAGATGAAAAGGCTAGGTT
1514984 AGGGTTTAGG
1 AGGGTTTAGG
1514994 ATTAGTGTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
52 8 0.15
53 47 0.85
ACGTcount: A:0.41, C:0.03, G:0.32, T:0.23
Consensus pattern (53 bp):
AGGGTTTAGGGTTAAAAAAGATGAACAGAGATAGAAGATGAAAAGGCTAGGTT
Found at i:1516613 original size:14 final size:15
Alignment explanation
Indices: 1516594--1516622 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1516584 TCAAGCATCT
1516594 AACAATCCA-AAACA
1 AACAATCCAGAAACA
1516608 AACAATCCAGAAACA
1 AACAATCCAGAAACA
1516623 TCAAAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.28, G:0.03, T:0.07
Consensus pattern (15 bp):
AACAATCCAGAAACA
Found at i:1518550 original size:20 final size:20
Alignment explanation
Indices: 1518525--1518576 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
1518515 GCCCGACTGA
1518525 TGCATCGATGCATGACCTTG
1 TGCATCGATGCATGACCTTG
1518545 TGCATCGATGCATGACCTTG
1 TGCATCGATGCATGACCTTG
1518565 TGCATCGATGCA
1 TGCATCGATGCA
1518577 CATTCAAGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (20 bp):
TGCATCGATGCATGACCTTG
Found at i:1518594 original size:23 final size:22
Alignment explanation
Indices: 1518564--1518643 Score: 92
Period size: 22 Copynumber: 3.6 Consensus size: 22
1518554 GCATGACCTT
1518564 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* *
1518586 CGTGCATCGGTGCA-ACTTC-ATG
1 -GTGCATCGATGCACA-TTCAAGG
*
1518608 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
1518630 ATGCATCGATGCAC
1 GTGCATCGATGCAC
1518644 TGTTAGGTGT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
21 14 0.30
22 18 0.38
23 15 0.32
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:1518619 original size:44 final size:42
Alignment explanation
Indices: 1518568--1518662 Score: 129
Period size: 44 Copynumber: 2.2 Consensus size: 42
1518558 GACCTTGTGC
* *
1518568 ATCGATGCACATTCAAGGCGTGCATCGGTGCAACT-TCATGGTGT
1 ATCGATGCACATTCAAGG-ATGCATCGATGC-ACTGTCA-GGTGT
*
1518612 ATCGATGCACATTCAAGGATGCATCGATGCACTGTTAGGTGT
1 ATCGATGCACATTCAAGGATGCATCGATGCACTGTCAGGTGT
1518654 ATCGATGCA
1 ATCGATGCA
1518663 TTAAGCACAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
42 17 0.36
43 12 0.26
44 18 0.38
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.27
Consensus pattern (42 bp):
ATCGATGCACATTCAAGGATGCATCGATGCACTGTCAGGTGT
Found at i:1518659 original size:20 final size:21
Alignment explanation
Indices: 1518568--1518662 Score: 79
Period size: 21 Copynumber: 4.4 Consensus size: 21
1518558 GACCTTGTGC
*
1518568 ATCGATGCACATTCAAGGCGTGC
1 ATCGATGCACATTCAA-G-GTGT
* *
1518591 ATCGGTGCA-ACTTCATGGTGT
1 ATCGATGCACA-TTCAAGGTGT
*
1518612 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACATTCAAGG-TGT
*
1518634 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
1518654 ATCGATGCA
1 ATCGATGCA
1518663 TTAAGCACAA
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
20 11 0.18
21 21 0.35
22 16 0.27
23 12 0.20
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.27
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:1524398 original size:26 final size:26
Alignment explanation
Indices: 1524365--1524430 Score: 132
Period size: 26 Copynumber: 2.5 Consensus size: 26
1524355 TGCACACACC
1524365 ATGCATCGATGCACTCAGTGCATTTG
1 ATGCATCGATGCACTCAGTGCATTTG
1524391 ATGCATCGATGCACTCAGTGCATTTG
1 ATGCATCGATGCACTCAGTGCATTTG
1524417 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1524431 AAGCCATGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (26 bp):
ATGCATCGATGCACTCAGTGCATTTG
Found at i:1524485 original size:45 final size:43
Alignment explanation
Indices: 1524383--1524497 Score: 124
Period size: 45 Copynumber: 2.6 Consensus size: 43
1524373 ATGCACTCAG
* * **
1524383 TGCATTTGATGCATCGATGCACTCAGTGCATTTGATGCATCGA
1 TGCACTTGATGCATCGATGCACTCTGTGCATTTGAAACATCGA
**
1524426 TGCACAAGCCATGCATCGATGCACTCTG-GCTATTTTGAAACATCGAA
1 TGCACTTG--ATGCATCGATGCACTCTGTGC-A-TTTGAAACATCG-A
1524473 TGCACTTGATGCATCGATGCACTCT
1 TGCACTTGATGCATCGATGCACTCT
1524498 TAGTGCACCG
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
43 5 0.08
44 2 0.03
45 35 0.59
46 10 0.17
47 7 0.12
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (43 bp):
TGCACTTGATGCATCGATGCACTCTGTGCATTTGAAACATCGA
Found at i:1524494 original size:17 final size:19
Alignment explanation
Indices: 1524466--1524514 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1524456 TATTTTGAAA
1524466 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1524484 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1524503 CACCGATGCACT
1 CATCGATGCACT
1524515 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1525285 original size:18 final size:18
Alignment explanation
Indices: 1525262--1525298 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1525252 GTTCAGGTTT
1525262 AGGTTCAAGTTTGGATTC
1 AGGTTCAAGTTTGGATTC
*
1525280 AGGTTCGAGTTTGGATTC
1 AGGTTCAAGTTTGGATTC
1525298 A
1 A
1525299 AGTTTAGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.30, T:0.38
Consensus pattern (18 bp):
AGGTTCAAGTTTGGATTC
Found at i:1525309 original size:18 final size:18
Alignment explanation
Indices: 1525269--1525311 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1525259 TTTAGGTTCA
*
1525269 AGTTTGGATTCAGGTTCG
1 AGTTTGGATTCAGGTTAG
*
1525287 AGTTTGGATTCAAGTTTAG
1 AGTTTGGATTC-AGGTTAG
1525306 -GTTTGG
1 AGTTTGG
1525312 GACCGGGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.19, C:0.07, G:0.33, T:0.42
Consensus pattern (18 bp):
AGTTTGGATTCAGGTTAG
Found at i:1525332 original size:6 final size:6
Alignment explanation
Indices: 1525323--1525383 Score: 52
Period size: 6 Copynumber: 10.2 Consensus size: 6
1525313 ACCGGGATTA
* * * * *
1525323 GGTTTG GGTTTG GTTTTA GGTTCG AGTTTA GGTTTG GGTTCT- GGTTTG
1 GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTT-TG GGTTTG
*
1525371 GGTTCG GGTTTG G
1 GGTTTG GGTTTG G
1525384 ATTCCAGTTA
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
5 1 0.02
6 39 0.95
7 1 0.02
ACGTcount: A:0.05, C:0.05, G:0.43, T:0.48
Consensus pattern (6 bp):
GGTTTG
Found at i:1526083 original size:61 final size:61
Alignment explanation
Indices: 1526011--1526140 Score: 215
Period size: 61 Copynumber: 2.1 Consensus size: 61
1526001 TTTAATTTTT
* * *
1526011 TTCAATTTAGTCCAAATTTAATGATGCAATGTATTGATTTAAGCTTCATATTTATAATTTG
1 TTCAATTTAGTCCAAATTTAATGATGCAATGTATTAATTTAAGCTTCATATTTAAAACTTG
* *
1526072 TTCAATTTAGTCCAAATTTAATGTTGCAATTTATTAATTTAAGCTTCATATTTAAAACTTG
1 TTCAATTTAGTCCAAATTTAATGATGCAATGTATTAATTTAAGCTTCATATTTAAAACTTG
1526133 TTCAATTT
1 TTCAATTT
1526141 GATCATTATA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (61 bp):
TTCAATTTAGTCCAAATTTAATGATGCAATGTATTAATTTAAGCTTCATATTTAAAACTTG
Found at i:1526246 original size:32 final size:30
Alignment explanation
Indices: 1526203--1526279 Score: 127
Period size: 32 Copynumber: 2.5 Consensus size: 30
1526193 AAATTAATAG
*
1526203 ATAGGTTATATATACTAATGAACTATATAAAT
1 ATAGTTTATATATACTAATG-ACTATAT-AAT
1526235 ATAGTTTATATATACTAATGACTATATAAT
1 ATAGTTTATATATACTAATGACTATATAAT
1526265 ATAGTTTATATATAC
1 ATAGTTTATATATAC
1526280 CATACACTCA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 18 0.41
31 7 0.16
32 19 0.43
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (30 bp):
ATAGTTTATATATACTAATGACTATATAAT
Found at i:1526276 original size:16 final size:16
Alignment explanation
Indices: 1526226--1526278 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
1526216 ACTAATGAAC
1526226 TATATA-AATATAGTT
1 TATATATAATATAGTT
*
1526241 TATATATACTA-A--T
1 TATATATAATATAGTT
*
1526254 GACTATATAATATAGTT
1 TA-TATATAATATAGTT
1526271 TATATATA
1 TATATATA
1526279 CCATACACTC
Statistics
Matches: 29, Mismatches: 4, Indels: 9
0.69 0.10 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.28
15 8 0.28
16 9 0.31
17 2 0.07
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (16 bp):
TATATATAATATAGTT
Found at i:1526476 original size:25 final size:25
Alignment explanation
Indices: 1526448--1526521 Score: 76
Period size: 27 Copynumber: 2.9 Consensus size: 25
1526438 TAGTAAATTA
* * *
1526448 TATAAGTATAAATTATATTATATAG
1 TATAAATATAAACTATAGTATATAG
* *
1526473 TATAAATATCAACTATAGTGTATAG
1 TATAAATATAAACTATAGTATATAG
*
1526498 TATATAAATATCAACTATAGTATA
1 --TATAAATATAAACTATAGTATA
1526522 GTTTATATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 20 0.49
27 21 0.51
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.39
Consensus pattern (25 bp):
TATAAATATAAACTATAGTATATAG
Found at i:1526522 original size:25 final size:25
Alignment explanation
Indices: 1526436--1526528 Score: 89
Period size: 25 Copynumber: 3.6 Consensus size: 25
1526426 CTTTGAATTA
* * * * *
1526436 TATAGTAAATTATATAAGTATAAAT
1 TATAGTATAGTATATAAATATCAAC
*
1526461 TATATTATA-TAGTATAAATATCAAC
1 TATAGTATAGTA-TATAAATATCAAC
1526486 TATAGTGTATAGTATATAAATATCAAC
1 TATA--GTATAGTATATAAATATCAAC
*
1526513 TATAGTATAGTTTATA
1 TATAGTATAGTATATA
1526529 TATAATTATA
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
24 2 0.04
25 32 0.56
27 21 0.37
28 2 0.04
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (25 bp):
TATAGTATAGTATATAAATATCAAC
Found at i:1526530 original size:27 final size:26
Alignment explanation
Indices: 1526473--1526528 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 26
1526463 TATTATATAG
1526473 TATAAATATCAACTATAGTGTATAGTA
1 TATAAATATCAACTATAG-GTATAGTA
*
1526500 TATAAATATCAACTATA-GTATAGTT
1 TATAAATATCAACTATAGGTATAGTA
1526525 TATA
1 TATA
1526529 TATAATTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 11 0.39
27 17 0.61
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (26 bp):
TATAAATATCAACTATAGGTATAGTA
Found at i:1526566 original size:15 final size:15
Alignment explanation
Indices: 1526546--1526583 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
1526536 ATAGTTTGTG
1526546 TAGTTTATATATATA
1 TAGTTTATATATATA
1526561 TAGTTT-T-TATATA
1 TAGTTTATATATATA
*
1526574 TAGTTCATAT
1 TAGTTTATAT
1526584 GTAACTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
13 11 0.55
14 2 0.10
15 7 0.35
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (15 bp):
TAGTTTATATATATA
Found at i:1526583 original size:26 final size:26
Alignment explanation
Indices: 1526553--1526627 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
1526543 GTGTAGTTTA
*
1526553 TATATATATAGTTTTTA-TATATAGT
1 TATATATATAGTATTTAGTATATAGT
* *
1526578 TCATATGTA-ACTATTTAGTATATAGT
1 T-ATATATATAGTATTTAGTATATAGT
* * *
1526604 TATATATGTAGTATATACTATATA
1 TATATATATAGTATTTAGTATATA
1526628 AATAGTTATA
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
25 12 0.31
26 27 0.69
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.49
Consensus pattern (26 bp):
TATATATATAGTATTTAGTATATAGT
Found at i:1526614 original size:66 final size:67
Alignment explanation
Indices: 1526543--1526735 Score: 175
Period size: 66 Copynumber: 2.9 Consensus size: 67
1526533 ATTATAGTTT
1526543 GTGTAGTTTATATATATATAGTTTTTATATATAGTTCATATGTAACTATTTAGTATATAGTTA-T
1 GTGTAGTTTATATATATATAGTTTTTATATATAGTTCATATGTAACTATTTAGTATATA-TTATT
1526607 ATA
65 ATA
* * ** * *
1526610 -TGTAGTATATACTATATA-AATAGTTATATATAGTTCATATGTAA--A-TTACTAAACTATTAT
1 GTGTAGTTTATA-TATATATAGTTTTTATATATAGTTCATATGTAACTATTTAGTATA-TATTAT
1526670 TATA
64 TATA
* * * * * *
1526674 GTTTACATAGTT-TATATATATAGTTTATACATATAGTTCATATCTAACTATATAGTATATAT
1 GTGTA-GT--TTATATATATATAGTTTTTATATATAGTTCATATGTAACTATTTAGTATATAT
1526736 AGTTTACATA
Statistics
Matches: 97, Mismatches: 18, Indels: 20
0.72 0.13 0.15
Matches are distributed among these distances:
63 9 0.09
64 7 0.07
65 3 0.03
66 40 0.41
67 28 0.29
68 1 0.01
69 4 0.04
70 5 0.05
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (67 bp):
GTGTAGTTTATATATATATAGTTTTTATATATAGTTCATATGTAACTATTTAGTATATATTATTA
TA
Found at i:1526698 original size:13 final size:13
Alignment explanation
Indices: 1526680--1526786 Score: 69
Period size: 13 Copynumber: 8.0 Consensus size: 13
1526670 TATAGTTTAC
1526680 ATAGTTTATATAT
1 ATAGTTTATATAT
*
1526693 ATAGTTTATACAT
1 ATAGTTTATATAT
* *
1526706 ATAGTTCATATCT
1 ATAGTTTATATAT
*
1526719 AACTA-TATAGTATAT
1 -A-TAGTTTA-TATAT
1526734 ATAGTTTACATATAGT
1 ATAGTTT--ATATA-T
*
1526750 ATAAGTTAATATAT
1 AT-AGTTTATATAT
*
1526764 ATTGTTTATA-AT
1 ATAGTTTATATAT
1526776 A-A-TTTATATAT
1 ATAGTTTATATAT
1526787 TACTATCTAT
Statistics
Matches: 73, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
10 6 0.08
11 2 0.03
12 3 0.04
13 30 0.41
14 9 0.12
15 15 0.21
16 4 0.05
17 4 0.05
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (13 bp):
ATAGTTTATATAT
Found at i:1526935 original size:17 final size:16
Alignment explanation
Indices: 1526882--1526950 Score: 59
Period size: 17 Copynumber: 4.0 Consensus size: 16
1526872 ATATATAGTT
*
1526882 TATATTAATAAATTATA
1 TATATTTAT-AATTATA
1526899 TA-ATTTATACATAATATA
1 TATATTTATA-AT--TATA
1526917 TATTATTTATAATTATA
1 TA-TATTTATAATTATA
*
1526934 TATAATATATAATTATA
1 TAT-ATTTATAATTATA
1526951 AGGTGTATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
15 1 0.02
16 8 0.18
17 20 0.45
18 6 0.14
19 2 0.05
20 7 0.16
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (16 bp):
TATATTTATAATTATA
Found at i:1526938 original size:26 final size:28
Alignment explanation
Indices: 1526897--1526949 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 28
1526887 TAATAAATTA
1526897 TATAATTTATACATAATATAT-ATTATT
1 TATAATTTATACATAATATATAATTATT
*
1526924 TATAA-TTATATATAATATATAATTAT
1 TATAATTTATACATAATATATAATTAT
1526950 AAGGTGTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (28 bp):
TATAATTTATACATAATATATAATTATT
Found at i:1526944 original size:11 final size:11
Alignment explanation
Indices: 1526841--1527034 Score: 73
Period size: 11 Copynumber: 17.6 Consensus size: 11
1526831 ACCTTAAACC
*
1526841 ATATATACTAT
1 ATATATAATAT
*
1526852 ATATATAA-AC
1 ATATATAATAT
* *
1526862 A-ATATAGTTT
1 ATATATAATAT
* *
1526872 ATATATAGTTT
1 ATATATAATAT
*
1526883 ATAT-TAATAA
1 ATATATAATAT
*
1526893 ATTATATAATTT
1 A-TATATAATAT
*
1526905 ATACATAATAT
1 ATATATAATAT
*
1526916 ATATTATTTATAATT
1 ATA-TA-TAAT-A-T
1526931 ATATATAATAT
1 ATATATAATAT
*
1526942 ATA-ATTATA-
1 ATATATAATAT
* *
1526951 AGGTGTATAATTT
1 A--TATATAATAT
1526964 ATATATAAT-T
1 ATATATAATAT
*
1526974 CATATATAATTT
1 -ATATATAATAT
1526986 ATATATAA-A-
1 ATATATAATAT
* *
1526995 CTATATAATTT
1 ATATATAATAT
*
1527006 ATAT-TAATAA
1 ATATATAATAT
* *
1527016 ACTATATAGTTT
1 A-TATATAATAT
1527028 ATATATA
1 ATATATA
1527035 GTTCAATAGT
Statistics
Matches: 136, Mismatches: 29, Indels: 36
0.68 0.14 0.18
Matches are distributed among these distances:
9 13 0.10
10 18 0.13
11 75 0.55
12 16 0.12
13 7 0.05
14 3 0.02
15 4 0.03
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (11 bp):
ATATATAATAT
Found at i:1526965 original size:81 final size:79
Alignment explanation
Indices: 1526875--1527023 Score: 187
Period size: 81 Copynumber: 1.9 Consensus size: 79
1526865 ATAGTTTATA
* *
1526875 TATAGTTTATAT-TAATAAATTATATAATTTATACATAATA-TATATTATTTATAATTATATATA
1 TATAATTTATATATAATAAA-TATATAATTTATACATAA-ACTATATAATTTAT-ATTA-ATA-A
1526938 A-TATATAATTATAAGGTG
61 ACTATATAATTATAAGGTG
** *
1526956 TATAATTTATATATAATTCATATATAATTTATATATAAACTATATAATTTATATTAATAAACTAT
1 TATAATTTATATATAATAAATATATAATTTATACATAAACTATATAATTTATATTAATAAACTAT
1527021 ATA
66 ATA
1527024 GTTTATATAT
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
78 2 0.03
79 9 0.15
80 5 0.08
81 39 0.65
82 5 0.08
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (79 bp):
TATAATTTATATATAATAAATATATAATTTATACATAAACTATATAATTTATATTAATAAACTAT
ATAATTATAAGGTG
Found at i:1526981 original size:22 final size:22
Alignment explanation
Indices: 1526840--1527034 Score: 102
Period size: 22 Copynumber: 8.9 Consensus size: 22
1526830 AACCTTAAAC
* *
1526840 CATATATACTATATATATAA-A
1 CATATATAATTTATATATAATA
* * *
1526861 CA-ATATAGTTTATATATAGTT
1 CATATATAATTTATATATAATA
* * *
1526882 TATATTAATAAATTATATAATTTATA
1 CATA-T-ATAATTTATAT-A-TAATA
*
1526908 CATA-ATATATATTATTTATAAT-
1 CATATATA-AT-TTATATATAATA
* * *
1526930 TATATATAATATATA-ATTATA
1 CATATATAATTTATATATAATA
* *
1526951 -AGGTGTATAATTTATATATAATT
1 CA--TATATAATTTATATATAATA
1526974 CATATATAATTTATATATAA-A
1 CATATATAATTTATATATAATA
1526995 C-TATATAATTTATAT-TAATA
1 CATATATAATTTATATATAATA
* *
1527015 AACTATATAGTTTATATATA
1 CA-TATATAATTTATATATA
1527035 GTTCAATAGT
Statistics
Matches: 130, Mismatches: 26, Indels: 34
0.68 0.14 0.18
Matches are distributed among these distances:
19 3 0.02
20 34 0.26
21 7 0.05
22 47 0.36
23 16 0.12
24 12 0.09
25 6 0.05
26 5 0.04
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (22 bp):
CATATATAATTTATATATAATA
Found at i:1527031 original size:42 final size:40
Alignment explanation
Indices: 1526872--1527034 Score: 145
Period size: 42 Copynumber: 4.0 Consensus size: 40
1526862 AATATAGTTT
* *
1526872 ATATATAGTTTATATTAATAAATTATATAATTTATACATAA
1 ATATATAATTTATATTAATAAA-TATATAATTTATATATAA
* *
1526913 TATATATTATTTATAATTATATATAATATATAA--T-TATA-AG
1 -ATATATAATTTAT-ATTA-ATA-AATATATAATTTATATATAA
* * **
1526953 GTGTATAATTTATATATAATTCATATATAATTTATATATAA
1 ATATATAATTTATAT-TAATAAATATATAATTTATATATAA
*
1526994 ACTATATAATTTATATTAATAAACTATATAGTTTATATATA
1 A-TATATAATTTATATTAATAAA-TATATAATTTATATATA
1527035 GTTCAATAGT
Statistics
Matches: 96, Mismatches: 15, Indels: 20
0.73 0.11 0.15
Matches are distributed among these distances:
37 8 0.08
38 4 0.04
39 13 0.14
40 5 0.05
41 9 0.09
42 41 0.43
43 4 0.04
44 10 0.10
45 2 0.02
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (40 bp):
ATATATAATTTATATTAATAAATATATAATTTATATATAA
Found at i:1527034 original size:55 final size:55
Alignment explanation
Indices: 1526965--1527100 Score: 152
Period size: 55 Copynumber: 2.5 Consensus size: 55
1526955 GTATAATTTA
*
1526965 TATATAATTCATATATAATTTATATATAAACTATATA-A-TTTATATTAATAAAC
1 TATATAATTTATATATAATTTATATATAAACTATATATAGTTTATATTAATAAAC
* * * ** *
1527018 TATATAGTTTATATATAGTTCA-ATAGTTCATTATATATAGTTTATATTAATAAAC
1 TATATAATTTATATATAATTTATATA-TAAACTATATATAGTTTATATTAATAAAC
* *
1527073 TATATAATTTCTATATATATATATATAT
1 TATATAATTTATATATA-ATTTATATAT
1527101 TATAATTATT
Statistics
Matches: 66, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
52 3 0.05
53 26 0.39
54 1 0.02
55 30 0.45
56 3 0.05
57 3 0.05
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (55 bp):
TATATAATTTATATATAATTTATATATAAACTATATATAGTTTATATTAATAAAC
Found at i:1527035 original size:11 final size:11
Alignment explanation
Indices: 1526863--1527099 Score: 93
Period size: 11 Copynumber: 21.5 Consensus size: 11
1526853 TATATAAACA
*
1526863 ATATAGTTTAT
1 ATATAATTTAT
*
1526874 ATATAGTTTAT
1 ATATAATTTAT
**
1526885 AT-TAATAAATT
1 ATATAATTTA-T
1526896 ATATAATTTAT
1 ATATAATTTAT
*
1526907 ACATAA--TAT
1 ATATAATTTAT
*
1526916 ATATTATTTAT
1 ATATAATTTAT
*
1526927 A-ATTATATATAAT
1 ATA-TA-AT-TTAT
1526940 ATATAATTATAAGGT
1 ATATAATT-T-A--T
*
1526955 GTATAATTTAT
1 ATATAATTTAT
*
1526966 ATATAATTCAT
1 ATATAATTTAT
1526977 ATATAATTTAT
1 ATATAATTTAT
1526988 ATATAA---ACT
1 ATATAATTTA-T
1526997 ATATAATTTAT
1 ATATAATTTAT
**
1527008 AT-TAATAAACT
1 ATATAATTTA-T
*
1527019 ATATAGTTTAT
1 ATATAATTTAT
* *
1527030 ATATAGTTCA-
1 ATATAATTTAT
*
1527040 ATAGTTCA-TTAT
1 ATA--TAATTTAT
*
1527052 ATATAGTTTAT
1 ATATAATTTAT
**
1527063 AT-TAATAAACT
1 ATATAATTTA-T
*
1527074 ATATAATTTCT
1 ATATAATTTAT
*
1527085 ATAT-ATATAT
1 ATATAATTTAT
1527095 ATATA
1 ATATA
1527100 TTATAATTAT
Statistics
Matches: 167, Mismatches: 34, Indels: 50
0.67 0.14 0.20
Matches are distributed among these distances:
8 1 0.01
9 14 0.08
10 26 0.16
11 86 0.51
12 22 0.13
13 8 0.05
14 2 0.01
15 8 0.05
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (11 bp):
ATATAATTTAT
Found at i:1530703 original size:14 final size:14
Alignment explanation
Indices: 1530663--1530704 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
1530653 TGTTTGGTTT
1530663 ATTTTCGTTATTTAA
1 ATTTT-GTTATTTAA
1530678 ATTTT-TACTATTTAA
1 ATTTTGT--TATTTAA
1530693 ATTTTGTTATTT
1 ATTTTGTTATTT
1530705 TAGTTTCCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 1 0.04
14 5 0.21
15 17 0.71
16 1 0.04
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (14 bp):
ATTTTGTTATTTAA
Found at i:1531554 original size:138 final size:138
Alignment explanation
Indices: 1531052--1531666 Score: 603
Period size: 139 Copynumber: 4.4 Consensus size: 138
1531042 GTCCCTAGAG
* *** * * * *
1531052 ATTTTAATTATTTGAATTGCATAATTGATTAAAATATTAATTTGGATTAATATTAGAGCCTTCAC
1 ATTTTAATTATTCGAATCAAATAATTGATTAAAAT-TGAA--TAGACTAATATTAGAGCCTTCAT
* * * * * * *
1531117 TTTAGGCCTAATTTTAAATTTAGTCCTTAAATTTAGGTGAATTCTTAATTTGATCCTCACTTTTA
63 TTTAGGCTTAATTTCAAACTTAGTCCTTAAATTTAGGAGAATTTTTAATTTGGTCCTCACTTTTG
1531182 CTCGAGGTTCC
128 CTCGAGGTTCC
* **
1531193 ATTTTAATTATTCGAATCAAATAATTGATTAAAATT-AATTAGGACTAATATTAGAGACAACATT
1 ATTTTAATTATTCGAATCAAATAATTGATTAAAATTGAA-TA-GACTAATATTAGAGCCTTCATT
* *
1531257 TTAGGCTTAATTTCACAA-TTAGTCCTTAAATTTAGGGGAATTTTTAATTTGGTCCTCGCTTTTG
64 TTAGGCTTAATTTCA-AACTTAGTCCTTAAATTTAGGAGAATTTTTAATTTGGTCCTCACTTTTG
*
1531321 CTCGAGGTTCT
128 CTCGAGGTTCC
* * * * * *
1531332 ATTTTAATCATTCGAATCAAATAATTGGTTAAAATTGATTAGGCTAATAATTAGAACCTCCATTT
1 ATTTTAATTATTCGAATCAAATAATTGATTAAAATTGAATAGACTAAT-ATTAGAGCCTTCATTT
* * * * * * *
1531397 TAGGTTTAATTTCACACTTAGTCTTTATATTTAGGAGAATTTTTTATTTGGTTCTCATTTTTGCT
65 TAGGCTTAATTTCAAACTTAGTCCTTAAATTTAGGAGAATTTTTAATTTGGTCCTCACTTTTGCT
* *
1531462 TGAGATTCC
130 CGAGGTTCC
* *
1531471 ATTTTAATTATTC-AAGTC-AATAATTGATTAAAATTGAATATATTAATATTTAGAGCCTTCATT
1 ATTTTAATTATTCGAA-TCAAATAATTGATTAAAATTGAATAGACTAATA-TTAGAGCCTTCATT
* * * * * * * *
1531534 TTAGGTTTAATTCCAAACTTAGTCCTTAAATCTATGAGAATTTTTGATTTGGTCCTCGCTTATGA
64 TTAGGCTTAATTTCAAACTTAGTCCTTAAATTTAGGAGAATTTTTAATTTGGTCCTCACTTTTGC
*
1531599 TCGAGGTTTC
129 TCGAGGTTCC
* * * * * * *
1531609 ATTTTGACTATTCGATTC-AATAATTCACTAGAAA-TGATTAGGATTAATATTAGAGCCT
1 ATTTTAATTATTCGAATCAAATAATTGATTA-AAATTGAATA-GACTAATATTAGAGCCT
1531667 ACACCTTTAG
Statistics
Matches: 396, Mismatches: 68, Indels: 23
0.81 0.14 0.05
Matches are distributed among these distances:
137 1 0.00
138 144 0.36
139 216 0.55
140 4 0.01
141 31 0.08
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.43
Consensus pattern (138 bp):
ATTTTAATTATTCGAATCAAATAATTGATTAAAATTGAATAGACTAATATTAGAGCCTTCATTTT
AGGCTTAATTTCAAACTTAGTCCTTAAATTTAGGAGAATTTTTAATTTGGTCCTCACTTTTGCTC
GAGGTTCC
Found at i:1532743 original size:25 final size:27
Alignment explanation
Indices: 1532715--1532772 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
1532705 TAAATTTGTT
1532715 TAAATAATTTAC-AAAT-A-ATTTAATA
1 TAAATAA-TTACTAAATAATATTTAATA
* *
1532740 TAAATGATTGCTAAATAATATTTAATA
1 TAAATAATTACTAAATAATATTTAATA
1532767 TAAATA
1 TAAATA
1532773 TTATTAATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 3 0.11
25 10 0.37
26 1 0.04
27 13 0.48
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (27 bp):
TAAATAATTACTAAATAATATTTAATA
Found at i:1533000 original size:65 final size:67
Alignment explanation
Indices: 1532925--1533062 Score: 165
Period size: 70 Copynumber: 2.0 Consensus size: 67
1532915 AAAATTATGA
* **
1532925 ACTAATTATGTAATTTAACCT-AAATACTA-ATATA-GGATTAAAATATAAATATTTAAAATTAA
1 ACTAAATATGTAATTTAACCTAAAATA-TATATATAGGGATTAAAATATAAATAAATAAAATTAA
1532987 AAG
65 AAG
* * *
1532990 ACTAAATATGTAATTTTACCTAAAATATATATATAGGCGGGGTTAAAATATAAATAAATGAAATT
1 ACTAAATATGTAATTTAACCTAAAATATATATATA---GGGATTAAAATATAAATAAATAAAATT
1533055 AAAAG
63 AAAAG
1533060 ACT
1 ACT
1533063 GAATTAAAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
65 21 0.34
66 10 0.16
70 30 0.49
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (67 bp):
ACTAAATATGTAATTTAACCTAAAATATATATATAGGGATTAAAATATAAATAAATAAAATTAAA
AG
Found at i:1534545 original size:45 final size:45
Alignment explanation
Indices: 1534490--1534599 Score: 184
Period size: 45 Copynumber: 2.4 Consensus size: 45
1534480 ACAGAATCTG
1534490 TTTCACTACTCTTCCATGAAAACAACTGAATGATTGAGAATATAA
1 TTTCACTACTCTTCCATGAAAACAACTGAATGATTGAGAATATAA
** * *
1534535 TTTCACTACTCTTCTTTGAAAACAATTGAATGATTGAGAATCTAA
1 TTTCACTACTCTTCCATGAAAACAACTGAATGATTGAGAATATAA
1534580 TTTCACTACTCTTCCATGAA
1 TTTCACTACTCTTCCATGAA
1534600 GATCAAACTC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (45 bp):
TTTCACTACTCTTCCATGAAAACAACTGAATGATTGAGAATATAA
Found at i:1534994 original size:22 final size:22
Alignment explanation
Indices: 1534949--1535001 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
1534939 TTTTCTGTTT
*
1534949 TTTGAAAAGAGAATCTATTATC
1 TTTGAAAAGAGAATCTATCATC
*
1534971 TTTGAAAAGAGAATCTATCGTC
1 TTTGAAAAGAGAATCTATCATC
1534993 TTTGCAAAA
1 TTTG-AAAA
1535002 TGTAGACATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (22 bp):
TTTGAAAAGAGAATCTATCATC
Found at i:1537905 original size:49 final size:49
Alignment explanation
Indices: 1537838--1537940 Score: 170
Period size: 49 Copynumber: 2.1 Consensus size: 49
1537828 TCATTTCTTC
*
1537838 TTTTTGCATACATACTTCATCCTCATTAGCTTTACCTTATCCTCCATTT
1 TTTTTCCATACATACTTCATCCTCATTAGCTTTACCTTATCCTCCATTT
* *
1537887 TTTTTCCATACATACTTCATTCTCCTTAGCTTTACCTTATCCTCCATTT
1 TTTTTCCATACATACTTCATCCTCATTAGCTTTACCTTATCCTCCATTT
*
1537936 GTTTT
1 TTTTT
1537941 GAAATTATCA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.18, C:0.28, G:0.04, T:0.50
Consensus pattern (49 bp):
TTTTTCCATACATACTTCATCCTCATTAGCTTTACCTTATCCTCCATTT
Found at i:1544874 original size:10 final size:10
Alignment explanation
Indices: 1544847--1544889 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
1544837 AGGAATATCT
1544847 ATACTCTTCC
1 ATACTCTTCC
1544857 ACT-CTCTTCC
1 A-TACTCTTCC
*
1544867 ATATTCTTCC
1 ATACTCTTCC
1544877 ATACTCTTCC
1 ATACTCTTCC
1544887 ATA
1 ATA
1544890 AGGTTCTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 1 0.03
10 27 0.93
11 1 0.03
ACGTcount: A:0.21, C:0.37, G:0.00, T:0.42
Consensus pattern (10 bp):
ATACTCTTCC
Found at i:1545030 original size:20 final size:20
Alignment explanation
Indices: 1544983--1545030 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
1544973 CTCCGGAATG
* *
1544983 TTCTAGAAAATTCTACACTT
1 TTCTAGAAAATTCTAAAATT
* * *
1545003 CTCCAGAAAGTTCTAAAATT
1 TTCTAGAAAATTCTAAAATT
1545023 TTCTAGAA
1 TTCTAGAA
1545031 CCTCTCCAAT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (20 bp):
TTCTAGAAAATTCTAAAATT
Found at i:1547629 original size:22 final size:22
Alignment explanation
Indices: 1547597--1547645 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
1547587 AAAATCTGTA
1547597 TGATC-GTATGACCGTTGACTT
1 TGATCGGTATGACCGTTGACTT
1547618 TGATCGGTATGACCGTTGACTT
1 TGATCGGTATGACCGTTGACTT
1547640 TGATCG
1 TGATCG
1547646 AAAAAGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (22 bp):
TGATCGGTATGACCGTTGACTT
Found at i:1551885 original size:12 final size:11
Alignment explanation
Indices: 1551862--1551899 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
1551852 TTTCGATGGA
1551862 TTTTGGTTGAT
1 TTTTGGTTGAT
1551873 TTTTGGATTGAT
1 TTTTGG-TTGAT
*
1551885 TGTTGGTTG-T
1 TTTTGGTTGAT
1551895 TTTTG
1 TTTTG
1551900 TGTTTGGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 5 0.21
11 9 0.38
12 10 0.42
ACGTcount: A:0.08, C:0.00, G:0.29, T:0.63
Consensus pattern (11 bp):
TTTTGGTTGAT
Found at i:1555769 original size:4 final size:4
Alignment explanation
Indices: 1555760--1555798 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
1555750 ATATAAAGAA
*
1555760 AAAT AAAT AAAT -AAT ATTAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAA
1555799 GGAATATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.10
4 25 0.81
5 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:1562454 original size:31 final size:31
Alignment explanation
Indices: 1562417--1562586 Score: 85
Period size: 30 Copynumber: 5.8 Consensus size: 31
1562407 CATATTAGAT
1562417 TTAAAGGACCAAAAATA-ACAAAAACAAAAAC
1 TTAAAGGACCAAAAATAGA-AAAAACAAAAAC
* * *
1562448 TTAAAGGA-CTAAAATAGAAAAAATAGAAAC
1 TTAAAGGACCAAAAATAGAAAAAACAAAAAC
* * **
1562478 TTAAGGGA-CTAAAATAG---TTA-AAAAAC
1 TTAAAGGACCAAAAATAGAAAAAACAAAAAC
** *
1562504 -TAAAGGGA-TTAAAATAGCAAAAACAAAAAC
1 TTAAA-GGACCAAAAATAGAAAAAACAAAAAC
* * * *
1562534 TTAAGGGA-CTAAAATAG-AAAAATAGAAAC
1 TTAAAGGACCAAAAATAGAAAAAACAAAAAC
* *
1562563 TTAAGGGA-CTAAAATAGCAAAAAA
1 TTAAAGGACCAAAAATAG-AAAAAA
1562587 ACTTAAAGGG
Statistics
Matches: 115, Mismatches: 15, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
25 3 0.03
26 16 0.14
27 1 0.01
29 28 0.24
30 50 0.43
31 17 0.15
ACGTcount: A:0.61, C:0.09, G:0.14, T:0.16
Consensus pattern (31 bp):
TTAAAGGACCAAAAATAGAAAAAACAAAAAC
Found at i:1562470 original size:30 final size:28
Alignment explanation
Indices: 1562417--1562657 Score: 199
Period size: 29 Copynumber: 8.5 Consensus size: 28
1562407 CATATTAGAT
* *
1562417 TTAAAGGACCAAAAATAACAAAAACAAAAAC
1 TTAAAGGA-CTAAAAT-AGAAAAA-AAAAAC
1562448 TTAAAGGACTAAAATAGAAAAAATAGAAAC
1 TTAAAGGACTAAAATAGAAAAAA-A-AAAC
* **
1562478 TTAAGGGACTAAAATAG--TTAAAAAAC
1 TTAAAGGACTAAAATAGAAAAAAAAAAC
*
1562504 -TAAAGGGATTAAAATAGCAAAAACAAAAAC
1 TTAAA-GGACTAAAATAG-AAAAA-AAAAAC
* *
1562534 TTAAGGGACTAAAATAGAAAAATAGAAAC
1 TTAAAGGACTAAAATAGAAAAA-AAAAAC
* *
1562563 TTAAGGGACTAAAATAG--CAAAAAAAC
1 TTAAAGGACTAAAATAGAAAAAAAAAAC
*
1562589 TTAAAGGGCT-AAATAG-AAAAAAAAAC
1 TTAAAGGACTAAAATAGAAAAAAAAAAC
* * * *
1562615 TTGAAGGACTAATATAGTAAAAAATAAAT
1 TTAAAGGACTAAAATAG-AAAAAAAAAAC
*
1562644 TTGAAGGACTAAAA
1 TTAAAGGACTAAAA
1562658 CAATAATTAA
Statistics
Matches: 174, Mismatches: 24, Indels: 26
0.78 0.11 0.12
Matches are distributed among these distances:
25 9 0.05
26 44 0.25
27 8 0.05
28 3 0.02
29 56 0.32
30 43 0.25
31 11 0.06
ACGTcount: A:0.60, C:0.09, G:0.14, T:0.17
Consensus pattern (28 bp):
TTAAAGGACTAAAATAGAAAAAAAAAAC
Found at i:1562503 original size:56 final size:56
Alignment explanation
Indices: 1562437--1562642 Score: 212
Period size: 56 Copynumber: 3.7 Consensus size: 56
1562427 AAAAATAACA
1562437 AAAACAAAAACTTAAAGGACTAAAATAGAAAAAATAGAAACTTAAGGGACTAAAATAG
1 AAAA-AAAAACTTAAAGGACTAAAATAGAAAAAATA-AAACTTAAGGGACTAAAATAG
** *
1562495 -TTAAAAAAC-TAAAGGGATTAAAATAGCAAAAACA-AAAACTTAAGGGACTAAAATAG
1 AAAAAAAAACTTAAA-GGACTAAAATAG-AAAAA-ATAAAACTTAAGGGACTAAAATAG
* *
1562551 AAAAATAGAAACTTAAGGGACTAAAATAG--CAAA-AAAACTTAAAGGG-CT-AAATAG
1 AAAAA-A-AAACTTAAAGGACTAAAATAGAAAAAATAAAACTT-AAGGGACTAAAATAG
* *
1562605 AAAAAAAAACTTGAAGGACTAATATAGTAAAAAATAAA
1 AAAAAAAAACTTAAAGGACTAAAATAG-AAAAAATAAA
1562643 TTTGAAGGAC
Statistics
Matches: 124, Mismatches: 12, Indels: 26
0.77 0.07 0.16
Matches are distributed among these distances:
52 18 0.15
53 1 0.01
54 11 0.09
55 17 0.14
56 48 0.39
57 9 0.07
58 2 0.02
59 15 0.12
60 3 0.02
ACGTcount: A:0.61, C:0.08, G:0.14, T:0.17
Consensus pattern (56 bp):
AAAAAAAAACTTAAAGGACTAAAATAGAAAAAATAAAACTTAAGGGACTAAAATAG
Found at i:1562525 original size:86 final size:86
Alignment explanation
Indices: 1562428--1562640 Score: 303
Period size: 86 Copynumber: 2.5 Consensus size: 86
1562418 TAAAGGACCA
*
1562428 AAAATAACAAAAACAAAAACTTAAAGGACTAAAATAGAAAAAATAGAAACTTAAGGGACTAAAAT
1 AAAATAGCAAAAACAAAAACTTAAAGGACTAAAATAGAAAAAATAGAAACTTAAGGGACTAAAAT
** *
1562493 AGTTAAAAAAC-TAAAGGGATT
66 AGCAAAAAAACTTAAAGGG-CT
*
1562514 AAAATAGCAAAAACAAAAACTTAAGGGACTAAAATAG-AAAAATAGAAACTTAAGGGACTAAAAT
1 AAAATAGCAAAAACAAAAACTTAAAGGACTAAAATAGAAAAAATAGAAACTTAAGGGACTAAAAT
1562578 AGCAAAAAAACTTAAAGGGCT
66 AGCAAAAAAACTTAAAGGGCT
* *
1562599 -AAATAG--AAAA-AAAAACTTGAAGGACTAATATAGTAAAAAATA
1 AAAATAGCAAAAACAAAAACTTAAAGGACTAAAATAG-AAAAAATA
1562641 AATTTGAAGG
Statistics
Matches: 116, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
81 20 0.17
82 4 0.03
83 7 0.06
84 6 0.05
85 37 0.32
86 42 0.36
ACGTcount: A:0.61, C:0.08, G:0.14, T:0.17
Consensus pattern (86 bp):
AAAATAGCAAAAACAAAAACTTAAAGGACTAAAATAGAAAAAATAGAAACTTAAGGGACTAAAAT
AGCAAAAAAACTTAAAGGGCT
Found at i:1563469 original size:25 final size:25
Alignment explanation
Indices: 1563435--1563483 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
1563425 TGTCATATGC
1563435 CAGCTGGATGACCTACTTCACGTGT
1 CAGCTGGATGACCTACTTCACGTGT
1563460 CAGCTGGATGACCTACTTCACGTG
1 CAGCTGGATGACCTACTTCACGTG
1563484 CAAGCATGCC
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:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (25 bp):
CAGCTGGATGACCTACTTCACGTGT
Found at i:1574149 original size:66 final size:66
Alignment explanation
Indices: 1573978--1574196 Score: 218
Period size: 66 Copynumber: 3.3 Consensus size: 66
1573968 TGAATAATGG
* * ** **
1573978 TTTCAAGGGAAACTGA-CTCAAA-GATG-ATGCTTCAAGAGAAGTTGTCTCAAGCAAGACAAAAT
1 TTTCAAGGGAAAC-AATCTCAAAGGATGTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAT
1574040 TCA
65 T-A
*
1574043 TTTCAA-GGAAACGATCTCAAA-GATGTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACT
1 TTTCAAGGGAAACAATCTCAAAGGATGTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-T
1574106 TA
65 TA
* * * *
1574108 TATCAAGGGAAACAATCTCAAAGGTTG-GTGTTTCATA-AGAAACTGACTCAAGGGAGACAAAAT
1 TTTCAAGGGAAACAATCTCAAAGGATGTATGTTTCA-AGAGAAACTGTCTCAAGGGAGACAAAA-
*
1574171 TTG
64 TTA
* *
1574174 TTTCAAGAGAAACAAACTCAAAG
1 TTTCAAGGGAAACAATCTCAAAG
1574197 ATTATAATTT
Statistics
Matches: 133, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
63 2 0.02
64 16 0.12
65 42 0.32
66 69 0.52
67 4 0.03
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (66 bp):
TTTCAAGGGAAACAATCTCAAAGGATGTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
A
Found at i:1574295 original size:36 final size:35
Alignment explanation
Indices: 1574254--1574346 Score: 107
Period size: 36 Copynumber: 2.6 Consensus size: 35
1574244 AGAAAAACAA
* * *
1574254 TGTCTCAAGTGAGACGAAATTTGTTTTGATAGAAAT
1 TGTCTCAAGAGAGACGAAATTTGTTTTGAAAG-AAC
* * *
1574290 TGTCTCAAGCGAGACAAAATTTGTTTTTAAAGAAC
1 TGTCTCAAGAGAGACGAAATTTGTTTTGAAAGAAC
1574325 TGTCTCAAGAGAGA-GAACATTT
1 TGTCTCAAGAGAGACGAA-ATTT
1574347 TATTTTTCCA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
34 2 0.04
35 19 0.39
36 28 0.57
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.32
Consensus pattern (35 bp):
TGTCTCAAGAGAGACGAAATTTGTTTTGAAAGAAC
Found at i:1575531 original size:34 final size:34
Alignment explanation
Indices: 1575493--1575592 Score: 109
Period size: 34 Copynumber: 3.0 Consensus size: 34
1575483 ATGCTTCTTA
*
1575493 TCTTTTTTCT-TTTGTGCTTTGCTTTGTTCTTTG
1 TCTTTTTTCTCTTTGTGCTTTGCTTTCTTCTTTG
** * *
1575526 CTCTTTTTTCTCTTTGCACTTTGTTTTTTTCTTTG
1 -TCTTTTTTCTCTTTGTGCTTTGCTTTCTTCTTTG
1575561 T-TTCTTTTCTCTTTGTG-TTT-CTTTCTTCTTTG
1 TCTT-TTTTCTCTTTGTGCTTTGCTTTCTTCTTTG
1575593 ATTTGATCAT
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
32 10 0.18
33 5 0.09
34 22 0.39
35 19 0.34
ACGTcount: A:0.01, C:0.18, G:0.11, T:0.70
Consensus pattern (34 bp):
TCTTTTTTCTCTTTGTGCTTTGCTTTCTTCTTTG
Found at i:1579220 original size:30 final size:30
Alignment explanation
Indices: 1579185--1579486 Score: 269
Period size: 30 Copynumber: 10.2 Consensus size: 30
1579175 TAAAAGACCA
*
1579185 AAAATAACAAAAACAGAAACTTAAAGGACT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
* * * *
1579215 AAAATAGTAAAACCAAAAACTTAAGGGACT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
* * * *
1579245 AAAATAGCAAAAATAGAAATTTAAAGAATT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
* * * *
1579275 AAAATAGCAAAAATAGAAAGTTAAGGGTCT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
* * * *
1579305 AAAACAACAAAAACAAAAACTTAAGGGACT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
* * *
1579335 AAAATAGCAAAAGCATAAACTTACAATG-CT
1 AAAATAGCAAAAACAGAAACTTA-AAGGACT
* *
1579365 AAACA-A-CAAAAAATAGAAACTTAAAGTACT
1 AAA-ATAGC-AAAAACAGAAACTTAAAGGACT
* * *
1579395 AAAATAGAAAAAACTGAAACTTAAAGGGCT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
* *
1579425 -AAATAGTAAAAACAAAAACTTAAAGGACT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
*
1579454 AAAATAGC--AAA-A-AAACTTAAAGAACT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
1579480 AAAATAG
1 AAAATAG
1579487 TAATTATAAA
Statistics
Matches: 219, Mismatches: 46, Indels: 18
0.77 0.16 0.06
Matches are distributed among these distances:
26 20 0.09
27 1 0.00
28 3 0.01
29 29 0.13
30 163 0.74
31 3 0.01
ACGTcount: A:0.60, C:0.11, G:0.12, T:0.17
Consensus pattern (30 bp):
AAAATAGCAAAAACAGAAACTTAAAGGACT
Found at i:1581461 original size:55 final size:55
Alignment explanation
Indices: 1581395--1581504 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
1581385 GGCCTTGAAG
1581395 AGTTCGTTAGTAAGAATCGGAGGAGCGGAAAGAGAGTTGGTTATGAGAACTTCAA
1 AGTTCGTTAGTAAGAATCGGAGGAGCGGAAAGAGAGTTGGTTATGAGAACTTCAA
1581450 AGTTCGTTAGTAAGAATCGGAGGAGCGGAAAGAGAGTTGGTTATGAGAACTTCAA
1 AGTTCGTTAGTAAGAATCGGAGGAGCGGAAAGAGAGTTGGTTATGAGAACTTCAA
1581505 TGACACTTAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.35, C:0.09, G:0.33, T:0.24
Consensus pattern (55 bp):
AGTTCGTTAGTAAGAATCGGAGGAGCGGAAAGAGAGTTGGTTATGAGAACTTCAA
Found at i:1592378 original size:17 final size:19
Alignment explanation
Indices: 1592341--1592378 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
1592331 TAATTAATTA
*
1592341 AATTATGCATTATAACTTT
1 AATTATGCATTATAACCTT
1592360 AATTATG-ATT-TAACCTT
1 AATTATGCATTATAACCTT
1592377 AA
1 AA
1592379 GACATTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 3 0.17
19 7 0.39
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (19 bp):
AATTATGCATTATAACCTT
Found at i:1596020 original size:24 final size:24
Alignment explanation
Indices: 1595992--1596071 Score: 81
Period size: 24 Copynumber: 3.3 Consensus size: 24
1595982 GATATATAAG
* * *
1595992 AAATCAGAACAGAATTCATAGCAT
1 AAATCAGAACAGAATTCAGAACAA
* * * *
1596016 AAATCAGAGCAAAATTCAGATCAG
1 AAATCAGAACAGAATTCAGAACAA
1596040 AAATCA-ATACAGAATTCAGAACAA
1 AAATCAGA-ACAGAATTCAGAACAA
1596064 AAATCAGA
1 AAATCAGA
1596072 TAAAACATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
23 1 0.02
24 43 0.96
25 1 0.02
ACGTcount: A:0.54, C:0.16, G:0.12, T:0.17
Consensus pattern (24 bp):
AAATCAGAACAGAATTCAGAACAA
Found at i:1596070 original size:12 final size:12
Alignment explanation
Indices: 1595990--1596071 Score: 60
Period size: 12 Copynumber: 6.8 Consensus size: 12
1595980 CGGATATATA
1595990 AGAAATCAGAAC
1 AGAAATCAGAAC
* * *
1596002 AGAATTCATAGC
1 AGAAATCAGAAC
* *
1596014 ATAAATCAGAGC
1 AGAAATCAGAAC
*
1596026 A-AAATTCAGATC
1 AGAAA-TCAGAAC
1596038 AGAAATCA-ATAC
1 AGAAATCAGA-AC
*
1596050 AGAATTCAGAAC
1 AGAAATCAGAAC
*
1596062 AAAAATCAGA
1 AGAAATCAGA
1596072 TAAAACATTC
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
11 4 0.07
12 47 0.85
13 4 0.07
ACGTcount: A:0.54, C:0.16, G:0.13, T:0.17
Consensus pattern (12 bp):
AGAAATCAGAAC
Found at i:1597168 original size:23 final size:24
Alignment explanation
Indices: 1597133--1597177 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1597123 TTTCGGTCAA
*
1597133 AGTCAATAGTCAATGGGTTGACTC
1 AGTCAATAGTCAATGAGTTGACTC
1597157 AGTCAA-AGTCAATGAGTTGAC
1 AGTCAATAGTCAATGAGTTGAC
1597178 ACGGTGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (24 bp):
AGTCAATAGTCAATGAGTTGACTC
Found at i:1598450 original size:20 final size:21
Alignment explanation
Indices: 1598413--1598455 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1598403 TCAAATGCGT
*
1598413 AAATAACAATAAACTAAATTA
1 AAATAACAACAAACTAAATTA
*
1598434 AAATAA-AACAAATTAAATTA
1 AAATAACAACAAACTAAATTA
1598454 AA
1 AA
1598456 TTTAAGGCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (21 bp):
AAATAACAACAAACTAAATTA
Found at i:1600812 original size:131 final size:131
Alignment explanation
Indices: 1600578--1600906 Score: 311
Period size: 131 Copynumber: 2.5 Consensus size: 131
1600568 TGCTTCGTTT
* * ** *
1600578 CTCTTCAGGGTAGATCAGATCTGGAAACATTGATTCACTTCACTGCTCTTCACGGAAGATTGAGT
1 CTCTTCAGGGTAGATCAAATATAAAAACATTGATTCACTTCACTGCTCTTCACGGAAGATTGAAT
** * * * * * *
1600643 CGAGACAGATTTATTCCACTGCCCTTCAGGGAAGATCAAATAT-GAGAAAGGGGATCTTCTCCAC
66 AAAGACAGATTTATTCCACTACCCATCAGGAAAGATCAAATATGGA-AAAAGGGATATGCTCCAC
1600707 TA
130 TA
* * * * *
1600709 CTCTTCAGGGTAGATCAAATATAAAAACATTGATTCACTTTATTGTTCTTTAGGGAAGATTGAAT
1 CTCTTCAGGGTAGATCAAATATAAAAACATTGATTCACTTCACTGCTCTTCACGGAAGATTGAAT
** * * * *
1600774 AAAGGTAGATTTGTTTCACTACTCATCAGGAAAGATCAAATCTGGAAAAAGGGATATGCTCCACT
66 AAAGACAGATTTATTCCACTACCCATCAGGAAAGATCAAATATGGAAAAAGGGATATGCTCCACT
*
1600839 G
131 A
* * * *** * *
1600840 CTCTTTAGGGTAGATTAGATCCGAAAACTTTGATTCACTCTACTACT-CTCTTCAAGGAAGATTG
1 CTCTTCAGGGTAGATCAAATATAAAAACATTGATTCACT-T-C-ACTGCTCTTCACGGAAGATTG
1600904 AAT
63 AAT
1600907 CGGGTTTGGT
Statistics
Matches: 157, Mismatches: 37, Indels: 6
0.79 0.19 0.03
Matches are distributed among these distances:
131 135 0.86
132 3 0.02
133 17 0.11
134 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (131 bp):
CTCTTCAGGGTAGATCAAATATAAAAACATTGATTCACTTCACTGCTCTTCACGGAAGATTGAAT
AAAGACAGATTTATTCCACTACCCATCAGGAAAGATCAAATATGGAAAAAGGGATATGCTCCACT
A
Found at i:1604752 original size:21 final size:21
Alignment explanation
Indices: 1604713--1604774 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
1604703 TTTAATCCCT
*
1604713 TTTTTGCTTACTA-TAAACCCC
1 TTTTTGCTCACTACT-AACCCC
1604734 TTTTTGCTCACTACTAA-CCC
1 TTTTTGCTCACTACTAACCCC
** *
1604754 AATTTGCTCACTACAAACCCC
1 TTTTTGCTCACTACTAACCCC
1604775 AAGATCTTAC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 17 0.49
21 17 0.49
22 1 0.03
ACGTcount: A:0.26, C:0.34, G:0.05, T:0.35
Consensus pattern (21 bp):
TTTTTGCTCACTACTAACCCC
Found at i:1604761 original size:20 final size:20
Alignment explanation
Indices: 1604736--1604773 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1604726 TAAACCCCTT
*
1604736 TTTGCTCACTACTAACCCAA
1 TTTGCTCACTACAAACCCAA
1604756 TTTGCTCACTACAAACCC
1 TTTGCTCACTACAAACCC
1604774 CAAGATCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.37, G:0.05, T:0.29
Consensus pattern (20 bp):
TTTGCTCACTACAAACCCAA
Found at i:1610820 original size:22 final size:22
Alignment explanation
Indices: 1610795--1610839 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1610785 ATAATATATC
1610795 ACAATCTCGGATATCTATAAAG
1 ACAATCTCGGATATCTATAAAG
*
1610817 ACAATCTCGGATATCTATGAAG
1 ACAATCTCGGATATCTATAAAG
1610839 A
1 A
1610840 TGATCATCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.27
Consensus pattern (22 bp):
ACAATCTCGGATATCTATAAAG
Done.