Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007744.1 Hibiscus syriacus cultivar Beakdansim tig00110007_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: 4276731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 16
Found at i:1237274 original size:20 final size:22
Alignment explanation
Indices: 1237236--1237275 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1237226 TGTTTGGCAG
1237236 AAAATCATCCCCAAACGACTCC
1 AAAATCATCCCCAAACGACTCC
1237258 AAAA-CATCCCC-AACGACT
1 AAAATCATCCCCAAACGACT
1237276 ATGCACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.42, C:0.40, G:0.05, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGACTCC
Found at i:1237538 original size:33 final size:33
Alignment explanation
Indices: 1237490--1237559 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
1237480 TTTTGTAAAG
* * * *
1237490 GGGAAATGTTCTAGTTGATCCCGTGAAAAGCTA
1 GGGAAAGGTTATAGTTGAGCCCGTGAAAAACTA
* *
1237523 GGGAAAGGTTATAGTTTAGCCCTTGAAAAACTA
1 GGGAAAGGTTATAGTTGAGCCCGTGAAAAACTA
1237556 GGGA
1 GGGA
1237560 GTTTGTAAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.26
Consensus pattern (33 bp):
GGGAAAGGTTATAGTTGAGCCCGTGAAAAACTA
Found at i:1238524 original size:305 final size:307
Alignment explanation
Indices: 1237970--1238581 Score: 1185
Period size: 305 Copynumber: 2.0 Consensus size: 307
1237960 CTTATTACTT
1237970 TGAAGATTTACCTATTATGGATTCACAACCGGTCAACAAGCCACCCTTCTTCAATGGAGAAAATT
1 TGAAGATTTACCTATTATGGATTCACAACCGGTCAACAAGCCACCCTTCTTCAATGGAGAAAATT
1238035 ATGCTCATTAGAAGAATAAGATGATATACTTTATTCGAGCCTACGATCTAGGAGCTTGGAACTCA
66 ATGCTCATTAGAAGAATAAGATGATATACTTTATTCGAGCCTACGATCTAGGAGCTTGGAACTCA
1238100 ATCATGTGGGGTTACTCCACTCCACCCGTGAATACAACGATTAGAGTAATGAAGAGAAGAAAAAT
131 ATCATGTGGGGTTACTCCACTCCACCCGTGAATACAACGATTAGAGTAATGAAGAGAAGAAAAAT
1238165 TTCCAGCTTAATTCCAAGGCTATACATATTCTATTTTGTGCTTTAGGCCCCAAACAAATATGGAA
196 TTCCAGCTTAATTCCAAGGCTATACATATTCTATTTTGTGCTTTAGGCCCCAAACAAATATGGAA
1238230 GAATATCCTCTTG-TCTACTGCC-AAGAGATTTAGGATAAGCTCCAA
261 GAATATCCTCTTGTTCTACTGCCAAAGAGATTTAGGATAAGCTCCAA
1238275 TGAAGATTTACCTATTATGGATTCACAACCGGTCAACAAGCCACCCTTCTTCAATGGAGAAAATT
1 TGAAGATTTACCTATTATGGATTCACAACCGGTCAACAAGCCACCCTTCTTCAATGGAGAAAATT
1238340 ATGCTCATTAGAAGAATAAGATGATATACTTTATTCGAGCCTACGATCTAGGAGCTTGGAACTCA
66 ATGCTCATTAGAAGAATAAGATGATATACTTTATTCGAGCCTACGATCTAGGAGCTTGGAACTCA
1238405 ATCATGTGGGGTTACTCCACTCCACCCGGTGAATACAACGATTAGAGTAATGAAGAGAAGAAAAA
131 ATCATGTGGGGTTACTCCACTCCACCC-GTGAATACAACGATTAGAGTAATGAAGAGAAGAAAAA
1238470 TTTCCAGCTTAATTCCAAGGCTATACATATTCTATTTTGTGCTTTAGG-CCCAAACAAATATGGA
195 TTTCCAGCTTAATTCCAAGGCTATACATATTCTATTTTGTGCTTTAGGCCCCAAACAAATATGGA
*
1238534 AGAATATCCTCTTGTTCTACTGCCAAAGATATTTAGGATAAGCTCCAA
260 AGAATATCCTCTTGTTCTACTGCCAAAGAGATTTAGGATAAGCTCCAA
1238582 GTCACTCATG
Statistics
Matches: 303, Mismatches: 1, Indels: 4
0.98 0.00 0.01
Matches are distributed among these distances:
305 187 0.62
306 94 0.31
307 22 0.07
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (307 bp):
TGAAGATTTACCTATTATGGATTCACAACCGGTCAACAAGCCACCCTTCTTCAATGGAGAAAATT
ATGCTCATTAGAAGAATAAGATGATATACTTTATTCGAGCCTACGATCTAGGAGCTTGGAACTCA
ATCATGTGGGGTTACTCCACTCCACCCGTGAATACAACGATTAGAGTAATGAAGAGAAGAAAAAT
TTCCAGCTTAATTCCAAGGCTATACATATTCTATTTTGTGCTTTAGGCCCCAAACAAATATGGAA
GAATATCCTCTTGTTCTACTGCCAAAGAGATTTAGGATAAGCTCCAA
Found at i:1240267 original size:83 final size:83
Alignment explanation
Indices: 1240110--1240270 Score: 191
Period size: 83 Copynumber: 1.9 Consensus size: 83
1240100 ATACTTTGAT
* * ** * * * *
1240110 TTTAAATGCAAATGATATCTCTCTAACAATTGATATCAAAATTTTAAATTTTTTGACCTAAATTT
1 TTTAAATGAAAATGATATATCTCTAACAATTGATATCAAAATTTTAAATAGTATAACATAAATTA
**
1240175 AAATGTTTATGCAATTAG
66 AAAACTTTATGCAATTAG
*
1240193 TTTAAATGAAAATGATATATCTCTAACAATTGATATCAAAATTTTCAAA-AGTATAACAT-TATT
1 TTTAAATGAAAATGATATATCTCTAACAATTGATATCAAAATTTT-AAATAGTATAACATAAATT
1240256 GAAAAACTTTATGCA
65 -AAAAACTTTATGCA
1240271 TATGCACTTA
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
82 3 0.05
83 59 0.91
84 3 0.05
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (83 bp):
TTTAAATGAAAATGATATATCTCTAACAATTGATATCAAAATTTTAAATAGTATAACATAAATTA
AAAACTTTATGCAATTAG
Found at i:1240647 original size:18 final size:18
Alignment explanation
Indices: 1240624--1240681 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
1240614 CAACAATTGA
*
1240624 TAACAATAGGTATCTTTT
1 TAACAATTGGTATCTTTT
1240642 TAACAATTGGTATCCTTTT
1 TAACAATTGGTAT-CTTTT
*
1240661 GTAAACAATTGGCATCTTTT
1 -T-AACAATTGGTATCTTTT
1240681 T
1 T
1240682 CATTAAACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 12 0.34
19 6 0.17
20 6 0.17
21 11 0.31
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (18 bp):
TAACAATTGGTATCTTTT
Found at i:1240933 original size:23 final size:23
Alignment explanation
Indices: 1240877--1240937 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
1240867 AAATATTAAG
* *
1240877 AGGTACCGATACCCC-TATGAAT
1 AGGTATCGATACCCCTTATAAAT
*
1240899 AGGTATCAATACCCCTTATAAAT
1 AGGTATCGATACCCCTTATAAAT
*
1240922 GGGTATCGATACCCCT
1 AGGTATCGATACCCCT
1240938 ACATGGGTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
22 13 0.39
23 20 0.61
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.26
Consensus pattern (23 bp):
AGGTATCGATACCCCTTATAAAT
Found at i:1241107 original size:20 final size:22
Alignment explanation
Indices: 1241069--1241108 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1241059 GTTTTGCAGA
1241069 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
1241091 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
1241109 GTACACAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:1241363 original size:33 final size:33
Alignment explanation
Indices: 1241322--1241392 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1241312 CTTTTATAAA
*
1241322 AGGGAAAGGTTATAGCTGATCCCGTGAAAAGCT
1 AGGGAAAGGTTATAGCTGATCCCGTGAAAAACT
* *
1241355 AGGGAAAGGTTATAGTTTATCCCGTGAAAAACT
1 AGGGAAAGGTTATAGCTGATCCCGTGAAAAACT
1241388 AGGGA
1 AGGGA
1241393 GTTGTAAAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.35, C:0.13, G:0.30, T:0.23
Consensus pattern (33 bp):
AGGGAAAGGTTATAGCTGATCCCGTGAAAAACT
Found at i:1245307 original size:17 final size:17
Alignment explanation
Indices: 1245285--1245343 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
1245275 ACTTTGACCA
1245285 AAAAGTTAAATTTTACG
1 AAAAGTTAAATTTTACG
** * *
1245302 AAAAGTCTTATGTTTTCCA
1 AAAAG--TTAAATTTTACG
1245321 AAAAGTTAAATTTTACG
1 AAAAGTTAAATTTTACG
1245338 AAAAGT
1 AAAAGT
1245344 CTTATTTTAT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
17 19 0.59
19 13 0.41
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (17 bp):
AAAAGTTAAATTTTACG
Found at i:1245350 original size:17 final size:17
Alignment explanation
Indices: 1245294--1245352 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
1245284 AAAAAGTTAA
1245294 ATTTTACGAAAAGTCTT
1 ATTTTACGAAAAGTCTT
* * *
1245311 ATGTTTTCCAAAAAGT-TAA
1 A--TTTTACGAAAAGTCT-T
1245330 ATTTTACGAAAAGTCTT
1 ATTTTACGAAAAGTCTT
1245347 ATTTTA
1 ATTTTA
1245353 TGTTTTTTGA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 18 0.56
18 2 0.06
19 12 0.38
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.42
Consensus pattern (17 bp):
ATTTTACGAAAAGTCTT
Found at i:1247162 original size:36 final size:38
Alignment explanation
Indices: 1247071--1247178 Score: 109
Period size: 36 Copynumber: 2.9 Consensus size: 38
1247061 GTATGAAGTC
* * *
1247071 TGCAGGTTCAGTTTTAATCAAGTTGGTAATTCCTTATA
1 TGCAGGTTCAGTTCTGATCAAGCTGGTAATTCCTTATA
* * *
1247109 T--AGGTTTAGCATC-GATC-AGCTGATAATTCCTTAT-
1 TGCAGGTTCAG-TTCTGATCAAGCTGGTAATTCCTTATA
*
1247143 TGCAGGTTCAGTTCTGATCAAGCAGGTAATTCCTTA
1 TGCAGGTTCAGTTCTGATCAAGCTGGTAATTCCTTA
1247179 CATAGGTTCA
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
34 1 0.02
35 17 0.31
36 21 0.38
37 15 0.27
38 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (38 bp):
TGCAGGTTCAGTTCTGATCAAGCTGGTAATTCCTTATA
Found at i:1247197 original size:72 final size:72
Alignment explanation
Indices: 1247071--1247212 Score: 187
Period size: 72 Copynumber: 2.0 Consensus size: 72
1247061 GTATGAAGTC
* ** * * * * *
1247071 TGCAGGTTCAGTTTTAATCAAGTTGGTAATTCCTTATATAGGTTTAGCATCGATCAGCT-GATAA
1 TGCAGGTTCAGTTCTAATCAAGCAGGTAATTCCTTACATAGGTTCAACACCGATCAACTAG-TAA
1247135 TTCCTTAT
65 TTCCTTAT
*
1247143 TGCAGGTTCAGTTCTGATCAAGCAGGTAATTCCTTACATAGGTTCAACACCGATCAACTAGTAAT
1 TGCAGGTTCAGTTCTAATCAAGCAGGTAATTCCTTACATAGGTTCAACACCGATCAACTAGTAAT
1247208 TCCTT
66 TCCTT
1247213 TATAGACTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
72 59 0.98
73 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (72 bp):
TGCAGGTTCAGTTCTAATCAAGCAGGTAATTCCTTACATAGGTTCAACACCGATCAACTAGTAAT
TCCTTAT
Found at i:1250901 original size:37 final size:38
Alignment explanation
Indices: 1250842--1251030 Score: 187
Period size: 37 Copynumber: 5.1 Consensus size: 38
1250832 TACTGATGGC
* *
1250842 TTTGCTTCAC-TACTC-TCAGTGAAGGTTTAAGATTGA
1 TTTGCTTCACTTACTCTTCGGTGAAGGCTTAAGATTGA
* *
1250878 TTTTCTTTA-TTACTCTTCGGTGAAGGCTTAAGATTGA
1 TTTGCTTCACTTACTCTTCGGTGAAGGCTTAAGATTGA
* *
1250915 TTTGCTTCACTT-CTCTTTGGTGAAGGCTTAAGA-TGG
1 TTTGCTTCACTTACTCTTCGGTGAAGGCTTAAGATTGA
* * * *
1250951 CTTGCTTCAC-TACTCTTCCGTGAAGGCTTTCTA-ATGGA
1 TTTGCTTCACTTACTCTTCGGTGAAGGC-TT-AAGATTGA
**
1250989 TTTGCTTCAC-TACTCTTTTGTGAAGGCTTAAGATTGA
1 TTTGCTTCACTTACTCTTCGGTGAAGGCTTAAGATTGA
*
1251026 CTTGC
1 TTTGC
1251031 CCCAATCTCA
Statistics
Matches: 125, Mismatches: 20, Indels: 15
0.78 0.12 0.09
Matches are distributed among these distances:
35 1 0.01
36 37 0.30
37 59 0.47
38 28 0.22
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (38 bp):
TTTGCTTCACTTACTCTTCGGTGAAGGCTTAAGATTGA
Found at i:1250938 original size:74 final size:75
Alignment explanation
Indices: 1250837--1251030 Score: 225
Period size: 74 Copynumber: 2.6 Consensus size: 75
1250827 AGGCTTACTG
* * * * * * * *
1250837 ATGGCTTTGCTTCACTACTC-TCAGTGAAGGTTTAAGATTGATTTTCTTTATTACTCTTCGGTGA
1 ATGGATTTGCTTCACTACTCTTTAGTGAAGGCTTAAGATTGACTTGCTTCACTACTCTTCCGTGA
1250901 AGGC-TT-AA
66 AGGCTTTCAA
* * * *
1250909 GATTGATTTGCTTCACTTCTCTTTGGTGAAGGCTTAAGA-TGGCTTGCTTCACTACTCTTCCGTG
1 -ATGGATTTGCTTCACTACTCTTTAGTGAAGGCTTAAGATTGACTTGCTTCACTACTCTTCCGTG
*
1250973 AAGGCTTTCTA
65 AAGGCTTTCAA
*
1250984 ATGGATTTGCTTCACTACTCTTTTGTGAAGGCTTAAGATTGACTTGC
1 ATGGATTTGCTTCACTACTCTTTAGTGAAGGCTTAAGATTGACTTGC
1251031 CCCAATCTCA
Statistics
Matches: 100, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
73 41 0.41
74 51 0.51
75 8 0.08
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.41
Consensus pattern (75 bp):
ATGGATTTGCTTCACTACTCTTTAGTGAAGGCTTAAGATTGACTTGCTTCACTACTCTTCCGTGA
AGGCTTTCAA
Found at i:1251019 original size:111 final size:111
Alignment explanation
Indices: 1250825--1251030 Score: 274
Period size: 111 Copynumber: 1.9 Consensus size: 111
1250815 ATCATGCTCG
* * * * *
1250825 GAAGGCTTACTGATGGCTTTGCTTCACTACTCTCAGTGAAGGTTTAAGATTGATTTTCTTTATTA
1 GAAGGCTTACAGATGGCTTTGCTTCACTACTCTCAGTGAAGGTTTAAGATGGATTTGCTTCACTA
*
1250890 CTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACTTCTCTTTGGT
66 CTCTTCGGTGAAGGCTTAAGATTGACTTGCTTCACTTCTCTTTGGT
* *
1250936 GAAGGCTTA-AGATGGC-TTGCTTCACTACTCTTCCGTGAAGGCTTTCTA-ATGGATTTGCTTCA
1 GAAGGCTTACAGATGGCTTTGCTTCACTACTC-TCAGTGAAGG-TTT-AAGATGGATTTGCTTCA
**
1250998 CTACTCTTTTGTGAAGGCTTAAGATTGACTTGC
63 CTACTCTTCGGTGAAGGCTTAAGATTGACTTGC
1251031 CCCAATCTCA
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
109 14 0.17
110 15 0.18
111 52 0.63
112 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.40
Consensus pattern (111 bp):
GAAGGCTTACAGATGGCTTTGCTTCACTACTCTCAGTGAAGGTTTAAGATGGATTTGCTTCACTA
CTCTTCGGTGAAGGCTTAAGATTGACTTGCTTCACTTCTCTTTGGT
Found at i:1259122 original size:75 final size:75
Alignment explanation
Indices: 1258991--1259429 Score: 603
Period size: 75 Copynumber: 5.9 Consensus size: 75
1258981 AGCAAAGATA
* * * * *
1258991 AGAAAATTTATCTCACTGGAGATAGTTTTTCTTAAAACAAACTTCGTCTTGCTTGAGACAATTTT
1 AGAAATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTT
* *
1259056 AACTCGATAC
66 CACTCGAAAC
* *
1259066 AGAGATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGATTGAGACAGTTTT
1 AGAAATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTT
1259131 CACTCGAAAC
66 CACTCGAAAC
* * *
1259141 ATAAATTTTATCTCACTTGAGATAGTTTTTCTTAAAACAATCTTCGTCTCGCTTGAGACA-TATT
1 AGAAATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGT-TT
1259205 TCACTCGAAAC
65 TCACTCGAAAC
* *
1259216 AGAGATTTTATCTCACTTGAGATTGTTTTT-TTAAAACAAACTTCATCTCGCTTGAGACAGTTTT
1 AGAAATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTT
1259280 CACTCGAAAC
66 CACTCGAAAC
* * ** * *
1259290 ATAAATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTGTCTTTCCTGAGATAGTTTT
1 AGAAATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTT
*
1259355 TACTCGAAAC
66 CACTCGAAAC
* * * * * *
1259365 AAGAAATTTTATCTCACTCGAGATTGTATTTCTTAAAACAAATTTCATCTCGCCTGAGAAAGTTT
1 -AGAAATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTT
1259430 CCCTTGAAAT
Statistics
Matches: 323, Mismatches: 37, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
74 69 0.21
75 199 0.62
76 55 0.17
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (75 bp):
AGAAATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTT
CACTCGAAAC
Found at i:1268376 original size:6 final size:6
Alignment explanation
Indices: 1268365--1270874 Score: 3848
Period size: 6 Copynumber: 421.2 Consensus size: 6
1268355 GGTGTACCTG
1268365 AGATAT AGATAT AGATAT AGATAT AGATATAT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AG--ATAT AGATAT AGATAT AGATAT
1268415 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1268463 AGATAT --ATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1268509 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AG--AT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1268555 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AG--AT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1268601 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
*
1268649 AGATAT AGATAT AGATAT AGATAT AGATAT AGACAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
*
1268697 AGACAT AGATAT AGATAT AGATAT AGATAT AGATAT AGAGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT --AGATAT AGATAT
* * *
1268747 AGAGAT AGAGAT AGAGAT AGATAT AGATAT AG--AT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1268793 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
*
1268841 AGATAT AGATAT AGATAT AGATAG AGATAT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1268889 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1268937 AGATAT AGATAT AGATAT AGATAT AG--AT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1268983 AGATAT AGATAT AGATAT AG--AT AGATAT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1269029 AGATAT AGATAT AGATAT AG--AT AGATAT AGATAT AG--AT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
* * * * * *
1269073 AGATAT AGATAT AGATAG AGATAG AGATAG AGATAG AGATAG AGATAG
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
* *
1269121 AGATAG AGATAG AGATAT AGATAT AGATAT AGAGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT --AGATAT AGATAT AGATAT
* *
1269171 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGAGATAG AGATAG
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT --AGATAT AGATAT
* * * * *
1269221 AGATAT AGAGAT AGAGAT --ATAG AGATAG AGATAG AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1269267 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1269315 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1269363 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1269411 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1269459 AGATAT AGATAT AGATAT AGATAGAT AGATAT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGAT--AT AGATAT AGATAT AGATAT AGATAT
* * * * *
1269509 AGATAT AGATAT AGATAT AGAGAT AGAGAT AGAGAT AGAGAT AGAGAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1269557 AGATAT AGAGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1 AGATAT --AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
* * * * * *
1269607 AGAGAT AGATAT AGAGAT AGAGAT AGAGAT --ATAG AGATAG AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
* * * *
1269653 AGAGAT AGAGAT AGAGAT AGAGAT AG--AT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1269699 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AG--AT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
* * *
1269745 AGATAT AGATAT AGATCT AGATCT AGATCT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1269793 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AG--AT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
* * * *
1269839 AGATAT AGATAT AGATAT AGATAT AGATAGAG AGAGAT AGAGAT AGAGAT
1 AGATAT AGATAT AGATAT AGATAT AGAT--AT AGATAT AGATAT AGATAT
* * * * * * *
1269889 AGAGAT AGATAT AGAGAT AGAGAT AGAGAT AGAGAT AGAGAT AGAGAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
* * * * * * * *
1269937 AGAGAT AGAGAT AGAGAT AGAGAT AGAGAT AGAGAT AGAGAT AGAGAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
* * * * * * *
1269985 AGAGAT AGAGAT AGAGAT AGAGAT AG--AT AGAGAT AGAGAT AGAGAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
*
1270031 AGATAT AGATAT AGATAT AGATAG AGATAT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1270079 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1270127 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
* * *
1270175 AGATAT AGATAT AGATAT AGATAT AGATAT AGAGATAG AGATAG AGATAG
1 AGATAT AGATAT AGATAT AGATAT AGATAT --AGATAT AGATAT AGATAT
* * * * *
1270225 AGATAG AGATAG AGATAG AGATAG AGATAG AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
*
1270273 AGATAT AGAGAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1270321 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1270369 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1270417 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1270465 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AG--AT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
* * *
1270511 AGATAT AGATAG AGATAG AGATAG AGATAT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
* * * *
1270559 AGAGATAT ATATAT AGATAT AGATAT AGATAT AGAGAT AGAGAT AGAGAT
1 --AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
* *
1270609 --ATAG AGATAG AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
*
1270655 GGATAT AGATAT AGATAT AGATAT AGATAT -GATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1270702 AGATAT AGATAT AGATAT AGATAT AG--AT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1270748 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1270796 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
1270844 AGATAT AGATAT AGATAT AGATAT AGATAT A
1 AGATAT AGATAT AGATAT AGATAT AGATAT A
1270875 TATAATTAAA
Statistics
Matches: 2402, Mismatches: 49, Indels: 106
0.94 0.02 0.04
Matches are distributed among these distances:
4 62 0.03
5 5 0.00
6 2285 0.95
8 50 0.02
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (6 bp):
AGATAT
Found at i:1270907 original size:3 final size:3
Alignment explanation
Indices: 1270899--1270924 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1270889 TAAAAAATTA
1270899 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1270925 CGATATATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1275982 original size:24 final size:23
Alignment explanation
Indices: 1275954--1276011 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
1275944 GATAGAGTGT
*
1275954 TTTCATAAAAAAACTCTAAAAGTA
1 TTTCA-AAAAAAACCCTAAAAGTA
* *
1275978 TTTCAGAAAAATCCCTAAAAGTA
1 TTTCAAAAAAAACCCTAAAAGTA
*
1276001 TTTCGAAAAAA
1 TTTCAAAAAAA
1276012 TCTTAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 24 0.83
24 5 0.17
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.28
Consensus pattern (23 bp):
TTTCAAAAAAAACCCTAAAAGTA
Found at i:1276011 original size:23 final size:22
Alignment explanation
Indices: 1275960--1276013 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
1275950 GTGTTTTCAT
* *
1275960 AAAAAAACTCTAAAAGTATTTC
1 AAAAAATCCCTAAAAGTATTTC
1275982 AGAAAAATCCCTAAAAGTATTTC
1 A-AAAAATCCCTAAAAGTATTTC
1276005 GAAAAAATC
1 -AAAAAATC
1276014 TTAAAAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 1 0.04
23 26 0.93
24 1 0.04
ACGTcount: A:0.54, C:0.15, G:0.07, T:0.24
Consensus pattern (22 bp):
AAAAAATCCCTAAAAGTATTTC
Found at i:1277002 original size:131 final size:132
Alignment explanation
Indices: 1276697--1277069 Score: 486
Period size: 131 Copynumber: 2.9 Consensus size: 132
1276687 TTTGTTCCAC
* * *
1276697 TGCTCTTTAGGGTAGATCAAATATGGAAACGTTGATTC--TCTCACTGCTCTTCAAGGTAGATTG
1 TGCTCTTTAGGGTAGATCAGATATGGAAACGTTGATTCATTC-CACTGCTTTTCAGGGTAGATTG
* * * * *
1276760 AATTGAGGCAAATTTGTTCCACTACTCCTCAAGGAAGATCAAATCTG--AAAAAGGAATTTGTTC
65 AATTGAGGTAGATTTGTTCCACTACTCCTCAAGGAAGATCAAATATGAAAAAAAGGAATATGCTC
**
1276823 TTT
130 CGT
* * * * * *
1276826 TGCTCTTCAAGGTAGATCAGATCTGGAAACGTTGATTCATTCCACTGTTTTTTAGGGAAGATTGA
1 TGCTCTTTAGGGTAGATCAGATATGGAAACGTTGATTCATTCCACTGCTTTTCAGGGTAGATTGA
* * * * * *
1276891 ATCGAGATAGATTTGTTCCATTGCTCCTCATGGAATATCAAATATGAAAAAAAGG-ATATGCTCC
66 ATTGAGGTAGATTTGTTCCACTACTCCTCAAGGAAGATCAAATATGAAAAAAAGGAATATGCTCC
1276955 GT
131 GT
*
1276957 TGCTCTTTAGGGTAGATTAGATATGGAAACGTTGATTCATTCCACTGCTTTTCAGGGTAGATTGA
1 TGCTCTTTAGGGTAGATCAGATATGGAAACGTTGATTCATTCCACTGCTTTTCAGGGTAGATTGA
*
1277022 ATTGAGGTAGATTTGTTCCACTACTCCTCAGGGAAGATCAAATATGAA
66 ATTGAGGTAGATTTGTTCCACTACTCCTCAAGGAAGATCAAATATGAA
1277070 GGTTTGGAAT
Statistics
Matches: 205, Mismatches: 35, Indels: 6
0.83 0.14 0.02
Matches are distributed among these distances:
129 34 0.17
130 55 0.27
131 109 0.53
132 7 0.03
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (132 bp):
TGCTCTTTAGGGTAGATCAGATATGGAAACGTTGATTCATTCCACTGCTTTTCAGGGTAGATTGA
ATTGAGGTAGATTTGTTCCACTACTCCTCAAGGAAGATCAAATATGAAAAAAAGGAATATGCTCC
GT
Found at i:1277232 original size:16 final size:17
Alignment explanation
Indices: 1277211--1277248 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
1277201 TTACTTTTCA
1277211 AAAATTTC-ATTTTCTG
1 AAAATTTCAATTTTCTG
1277227 AAAATTTCATATTTTCTG
1 AAAATTTCA-ATTTTCTG
1277245 AAAA
1 AAAA
1277249 ATATAAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
18 12 0.60
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (17 bp):
AAAATTTCAATTTTCTG
Found at i:1281204 original size:74 final size:74
Alignment explanation
Indices: 1281096--1281259 Score: 249
Period size: 74 Copynumber: 2.2 Consensus size: 74
1281086 TAAATAGGGA
* * *
1281096 GGTACCAATACCCCACATAGGATGTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAATAT
1 GGTACCGATA-CCCTCATAGGA-GTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAACAT
1281161 AATGCCAAATG
64 AATGCCAAATG
1281172 GGTACCGATATCCCTCATAGG-GTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAACATA
1 GGTACCGATA-CCCTCATAGGAGTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAACATA
* *
1281236 ATGCCCAGTG
65 ATGCCAAATG
1281246 GGTACCGATACCCT
1 GGTACCGATACCCT
1281260 TAGTCATTTA
Statistics
Matches: 82, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
73 4 0.05
74 60 0.73
76 18 0.22
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (74 bp):
GGTACCGATACCCTCATAGGAGTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAACATAA
TGCCAAATG
Found at i:1286962 original size:21 final size:20
Alignment explanation
Indices: 1286936--1287032 Score: 97
Period size: 20 Copynumber: 4.7 Consensus size: 20
1286926 TGTGCAATAG
1286936 GTATCGATACCCCTTTAACGT
1 GTATCGATACCCCTTTAA-GT
1286957 GTATCGATACCCTCTTTGAATGT
1 GTATCGATACCC-CTTT-AA-GT
* *
1286980 GTATCGATACCCCTATAAGA
1 GTATCGATACCCCTTTAAGT
* *
1287000 GTACCGATACCCCTATT-AGG
1 GTATCGATACCCCT-TTAAGT
*
1287020 GTACCGATACCCC
1 GTATCGATACCCC
1287033 CTGTCGGGTT
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
20 29 0.43
21 15 0.22
22 7 0.10
23 16 0.24
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
GTATCGATACCCCTTTAAGT
Found at i:1286985 original size:23 final size:21
Alignment explanation
Indices: 1286936--1287013 Score: 95
Period size: 23 Copynumber: 3.7 Consensus size: 21
1286926 TGTGCAATAG
1286936 GTATCGATACCCCTTTAACGT
1 GTATCGATACCCCTTTAACGT
*
1286957 GTATCGATACCCTCTTTGAATGT
1 GTATCGATACCC-CTTT-AACGT
* *
1286980 GTATCGATACCCCTATAA-GA
1 GTATCGATACCCCTTTAACGT
*
1287000 GTACCGATACCCCT
1 GTATCGATACCCCT
1287014 ATTAGGGTAC
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
20 14 0.27
21 14 0.27
22 7 0.14
23 16 0.31
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (21 bp):
GTATCGATACCCCTTTAACGT
Found at i:1287452 original size:19 final size:20
Alignment explanation
Indices: 1287425--1287465 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1287415 AAAATTATGA
*
1287425 TTTTGTTTAAAT-TGTTGTT
1 TTTTATTTAAATATGTTGTT
*
1287444 TTTTATTTAATTATGTTGTT
1 TTTTATTTAAATATGTTGTT
1287464 TT
1 TT
1287466 CATGAAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.17, C:0.00, G:0.12, T:0.71
Consensus pattern (20 bp):
TTTTATTTAAATATGTTGTT
Found at i:1287874 original size:28 final size:28
Alignment explanation
Indices: 1287834--1287890 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
1287824 TCTTCGAGTC
1287834 TTATAAAATTCGGGAAGAATGGATTCAT
1 TTATAAAATTCGGGAAGAATGGATTCAT
*
1287862 TTATAAAATTCGGGAAGAATGTATTCAT
1 TTATAAAATTCGGGAAGAATGGATTCAT
1287890 T
1 T
1287891 CTCTTCAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.35
Consensus pattern (28 bp):
TTATAAAATTCGGGAAGAATGGATTCAT
Found at i:1288984 original size:20 final size:21
Alignment explanation
Indices: 1288947--1288998 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
1288937 TTTTGTTTGT
* **
1288947 TTTGGATTTTTGTTTTGC-AA
1 TTTGGATGTTTGAATTGCTAA
**
1288967 TTTGGATGTTTGAATTGCTTG
1 TTTGGATGTTTGAATTGCTAA
1288988 TTTGGATGTTT
1 TTTGGATGTTT
1288999 ATTTTGATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.13, C:0.04, G:0.25, T:0.58
Consensus pattern (21 bp):
TTTGGATGTTTGAATTGCTAA
Found at i:1289862 original size:30 final size:30
Alignment explanation
Indices: 1289826--1289894 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
1289816 TTTCACACTA
* *
1289826 CAACGGCTCTAGCATCACCCAAATGATTCT
1 CAACGGCTATAACATCACCCAAATGATTCT
* *
1289856 CAACGGCTATAACGTCACCGAAATGATTCT
1 CAACGGCTATAACATCACCCAAATGATTCT
1289886 CAACGGCTA
1 CAACGGCTA
1289895 GAATCAATCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (30 bp):
CAACGGCTATAACATCACCCAAATGATTCT
Found at i:1300787 original size:33 final size:33
Alignment explanation
Indices: 1300750--1300813 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1300740 ATGCATAACA
*
1300750 GTGCATTATTGATAGAAATGAGCCATAAATGTG
1 GTGCATTATTGACAGAAATGAGCCATAAATGTG
* **
1300783 GTGCATTATTGGCAGAAATGTTCCATAAATG
1 GTGCATTATTGACAGAAATGAGCCATAAATG
1300814 AAAATGCATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.31
Consensus pattern (33 bp):
GTGCATTATTGACAGAAATGAGCCATAAATGTG
Found at i:1300852 original size:43 final size:44
Alignment explanation
Indices: 1300786--1300955 Score: 270
Period size: 44 Copynumber: 3.9 Consensus size: 44
1300776 AAATGTGGTG
* *
1300786 CATTATTGGCAGAAATGTTCCATAAATGAAAATGCATAACGGTA
1 CATTATTGGCAGAAAGGTGCCATAAATGAAAATGCATAACGGTA
* *
1300830 CATTA-TGGCAGAAAGGTGCCATAAATGAAAATGCATAATGGTG
1 CATTATTGGCAGAAAGGTGCCATAAATGAAAATGCATAACGGTA
*
1300873 CATTATTGGCAGAAAGGTGACATAAATGAAAATGCATAACGGTA
1 CATTATTGGCAGAAAGGTGCCATAAATGAAAATGCATAACGGTA
* *
1300917 CATTATTGGCAGAAAGATGCCATAAATGAAAATACATAA
1 CATTATTGGCAGAAAGGTGCCATAAATGAAAATGCATAA
1300956 TGATGCATTT
Statistics
Matches: 115, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
43 39 0.34
44 76 0.66
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (44 bp):
CATTATTGGCAGAAAGGTGCCATAAATGAAAATGCATAACGGTA
Found at i:1300873 original size:87 final size:88
Alignment explanation
Indices: 1300781--1300964 Score: 307
Period size: 87 Copynumber: 2.1 Consensus size: 88
1300771 GCCATAAATG
* **
1300781 TGGTGCATTATTGGCAGAAATGTTCCATAAATGAAAATGCATAACGGTACATTA-TGGCAGAAAG
1 TGGTGCATTATTGGCAGAAAGGTGACATAAATGAAAATGCATAACGGTACATTATTGGCAGAAAG
* *
1300845 GTGCCATAAATGAAAATGCATAA
66 ATGCCATAAATGAAAATACATAA
1300868 TGGTGCATTATTGGCAGAAAGGTGACATAAATGAAAATGCATAACGGTACATTATTGGCAGAAAG
1 TGGTGCATTATTGGCAGAAAGGTGACATAAATGAAAATGCATAACGGTACATTATTGGCAGAAAG
1300933 ATGCCATAAATGAAAATACATAA
66 ATGCCATAAATGAAAATACATAA
*
1300956 TGATGCATT
1 TGGTGCATT
1300965 TTGAAAAAAG
Statistics
Matches: 90, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
87 51 0.57
88 39 0.43
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.26
Consensus pattern (88 bp):
TGGTGCATTATTGGCAGAAAGGTGACATAAATGAAAATGCATAACGGTACATTATTGGCAGAAAG
ATGCCATAAATGAAAATACATAA
Found at i:1303973 original size:242 final size:236
Alignment explanation
Indices: 1303546--1304024 Score: 870
Period size: 242 Copynumber: 2.0 Consensus size: 236
1303536 ATGAGATCTA
1303546 CTGTTTCTCTTGGGGAGCATATGTGCTGCGTGTGAGAAGAAGAACGGGTCTATGCGATTATGCAT
1 CTGTTTCTCTTGGGGAGCATATGTGCTGCGTGTGAGAAGAAGAACGGGTCTATGCGATTATGCAT
1303611 TGACCACCGTCAGTTAAATAAAGTAACGATAAAGAAATTCCTCTTATGAGGATTGATGATATGTT
66 TGACCACCGTCAGTTAAATAAAGTAACGATAAAGAAATTCCTCTTATGAGGATTGATGATATGTT
1303676 CCATTAAATGACAGGCGTAACAGTGTTCTCTAAGATAGACCTGAGGTCGGGATACCGTCAATT-A
131 CCATTAAATGACAGGCGTAACAGTGTTCTCTAAGATAGACCTGAGGTCGGGATACCGTCAATTAA
1303740 AGATAAAAGAGGATGATATTTCAAGGACATCTTTTCGGACT
196 AGATAAAAGAGGATGATATTTCAAGGACATCTTTTCGGACT
*
1303781 CTGTTTCTCCTTGGGGAGCATATGTGCTGCTTGTGAGAAAGAAGAACGGGTCTATGCGATTATGC
1 CTGTTTCT-CTTGGGGAGCATATGTGCTGCGTGTGAG-AAGAAGAACGGGTCTATGCGATTATGC
1303846 ATTGACCACCGTCAGTTAAATAAAGTAACGATAAAGAAATAAATATCCTCTTATGAGGATTGATG
64 ATTGACCACCGTCAGTTAAATAAAGTAACGATAAAG----AAAT-TCCTCTTATGAGGATTGATG
*
1303911 ATATGTTCCATTAACTGACAGGCGTAACAGTGTTCTCTAAGATAGACCTGAGGTCGGGATACCGT
124 ATATGTTCCATTAAATGACAGGCGTAACAGTGTTCTCTAAGATAGACCTGAGGTCGGGATACCGT
1303976 CAATTAAAGATAAAAGAGGATGATATTTCAAGGACATCTTTTCGGACT
189 CAATTAAAGATAAAAGAGGATGATATTTCAAGGACATCTTTTCGGACT
1304024 C
1 C
1304025 GGTATGGACA
Statistics
Matches: 234, Mismatches: 2, Indels: 8
0.96 0.01 0.03
Matches are distributed among these distances:
235 8 0.03
236 27 0.12
237 63 0.27
241 4 0.02
242 89 0.38
243 43 0.18
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (236 bp):
CTGTTTCTCTTGGGGAGCATATGTGCTGCGTGTGAGAAGAAGAACGGGTCTATGCGATTATGCAT
TGACCACCGTCAGTTAAATAAAGTAACGATAAAGAAATTCCTCTTATGAGGATTGATGATATGTT
CCATTAAATGACAGGCGTAACAGTGTTCTCTAAGATAGACCTGAGGTCGGGATACCGTCAATTAA
AGATAAAAGAGGATGATATTTCAAGGACATCTTTTCGGACT
Found at i:1307835 original size:42 final size:44
Alignment explanation
Indices: 1307724--1307984 Score: 303
Period size: 42 Copynumber: 6.2 Consensus size: 44
1307714 CTCTAAAATT
* * *
1307724 AATGAAAATGCATAATGGTGTATTATTGGAAGAAAGGTGCCATA
1 AATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCCATA
*
1307768 AATGAAAATGCATAAC-GTGCA-TATTGGCAGAAAGGT-AC-TA
1 AATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCCATA
* *
1307808 GAATG-AAATGCATAACGGTGCATTATTGGTAGAAAAGTGCCATA
1 -AATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCCATA
* *
1307852 AATGAAAATGCATAAC-GTGCATTATT-GCATAAATGTGCCATA
1 AATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCCATA
**
1307894 AATGAAAATGCATAACGGTGC-TTATTGG-A-ATAATATGCCATA
1 AATGAAAATGCATAACGGTGCATTATTGGCAGA-AAGGTGCCATA
* * *
1307936 AAT-AAAATGCATAACGGTACATT-TTGGCAGAAATGTGCCACA
1 AATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCCATA
1307978 AATGAAA
1 AATGAAA
1307985 CTTAAATACA
Statistics
Matches: 190, Mismatches: 14, Indels: 27
0.82 0.06 0.12
Matches are distributed among these distances:
40 13 0.07
41 31 0.16
42 90 0.47
43 28 0.15
44 28 0.15
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (44 bp):
AATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCCATA
Found at i:1308689 original size:22 final size:23
Alignment explanation
Indices: 1308664--1308715 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
1308654 AATTAGCTAA
*
1308664 AATTAT-AAAATTATAAAT-AAAT
1 AATTATAAAAAATA-AAATAAAAT
1308686 AATT-TAAAAAATAAAATAAAAT
1 AATTATAAAAAATAAAATAAAAT
1308708 AATTATAA
1 AATTATAA
1308716 TTATAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 5 0.19
22 18 0.69
23 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
AATTATAAAAAATAAAATAAAAT
Found at i:1308721 original size:22 final size:22
Alignment explanation
Indices: 1308672--1308742 Score: 53
Period size: 22 Copynumber: 3.4 Consensus size: 22
1308662 AAAATTATAA
1308672 AATTAT-AAAT-AAATAATT-T
1 AATTATAAAATAAAATAATTAT
**
1308691 AAAAAATAAAATAAAATAATTAT
1 -AATTATAAAATAAAATAATTAT
**
1308714 AATTATAATAATACTAT-ATTAT
1 AATTATAA-AATAAAATAATTAT
1308736 -ATTATAA
1 AATTATAA
1308743 TATATACCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
20 4 0.10
21 11 0.27
22 19 0.46
23 7 0.17
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (22 bp):
AATTATAAAATAAAATAATTAT
Found at i:1310136 original size:21 final size:21
Alignment explanation
Indices: 1310112--1310168 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
1310102 AATCGTCGTG
* *
1310112 CCTCCGGCCACCATCGACGCT
1 CCTCCGGTCACCATCGACCCT
* *
1310133 CCTCAGGTCACCATCGTCCCT
1 CCTCCGGTCACCATCGACCCT
*
1310154 CCTCCGATCACCATC
1 CCTCCGGTCACCATC
1310169 ATCTCTCCTC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.16, C:0.51, G:0.14, T:0.19
Consensus pattern (21 bp):
CCTCCGGTCACCATCGACCCT
Found at i:1310176 original size:21 final size:21
Alignment explanation
Indices: 1310131--1310179 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1310121 ACCATCGACG
* *
1310131 CTCCTCAGGTCACCATCGTCC
1 CTCCTCAGATCACCATCATCC
* *
1310152 CTCCTCCGATCACCATCATCT
1 CTCCTCAGATCACCATCATCC
1310173 CTCCTCA
1 CTCCTCA
1310180 AGGCTTAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.16, C:0.49, G:0.08, T:0.27
Consensus pattern (21 bp):
CTCCTCAGATCACCATCATCC
Found at i:1319130 original size:16 final size:16
Alignment explanation
Indices: 1319109--1319153 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
1319099 AGACTGCTAT
1319109 GGGAGTAGCTTCATGG
1 GGGAGTAGCTTCATGG
1319125 GGGAGTAGCTTCATGG
1 GGGAGTAGCTTCATGG
*
1319141 GGAAGTAGCTTCA
1 GGGAGTAGCTTCA
1319154 CGGGTGGGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.22, C:0.13, G:0.40, T:0.24
Consensus pattern (16 bp):
GGGAGTAGCTTCATGG
Found at i:1321896 original size:15 final size:16
Alignment explanation
Indices: 1321873--1321906 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1321863 ATAAGTCCAT
1321873 AATAAAAATAAAT-AA
1 AATAAAAATAAATGAA
*
1321888 AATATAAATAAATGAA
1 AATAAAAATAAATGAA
1321904 AAT
1 AAT
1321907 TAAGCTAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
AATAAAAATAAATGAA
Found at i:1325506 original size:12 final size:12
Alignment explanation
Indices: 1325482--1325519 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1325472 TTTTTAAAAG
1325482 AAAA-TAAAATA
1 AAAACTAAAATA
*
1325493 AAAACTAAAGTA
1 AAAACTAAAATA
*
1325505 AAAACAAAAATA
1 AAAACTAAAATA
1325517 AAA
1 AAA
1325520 GAAAATGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 4 0.17
12 19 0.83
ACGTcount: A:0.79, C:0.05, G:0.03, T:0.13
Consensus pattern (12 bp):
AAAACTAAAATA
Found at i:1325670 original size:23 final size:24
Alignment explanation
Indices: 1325644--1325697 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 24
1325634 TATTTCAAAT
1325644 AAATA-TCTAAAAGAT-AATCCTAA
1 AAATATTC-AAAAGATAAATCCTAA
1325667 AAATATTCAAAAGATAAAATCCTAA
1 AAATATTCAAAAGAT-AAATCCTAA
1325692 ATAATA
1 A-AATA
1325698 GAAAATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
23 12 0.44
24 2 0.07
25 9 0.33
26 4 0.15
ACGTcount: A:0.59, C:0.11, G:0.04, T:0.26
Consensus pattern (24 bp):
AAATATTCAAAAGATAAATCCTAA
Found at i:1330545 original size:23 final size:24
Alignment explanation
Indices: 1330519--1330568 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
1330509 AATCAGAATT
* *
1330519 ATGCTTTCAAAT-AAGTAGTAAAC
1 ATGCTTTCAAATCAAGCAATAAAC
1330542 ATGCTTTCAAATCAAGCAATAAAC
1 ATGCTTTCAAATCAAGCAATAAAC
1330566 ATG
1 ATG
1330569 TTATAAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (24 bp):
ATGCTTTCAAATCAAGCAATAAAC
Found at i:1330586 original size:24 final size:24
Alignment explanation
Indices: 1330519--1330586 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
1330509 AATCAGAATT
* *
1330519 ATGCTTTCAAAT-AAGTAGTAAAC
1 ATGCTTTCAAATCAAGAAATAAAC
*
1330542 ATGCTTTCAAATCAAGCAATAAAC
1 ATGCTTTCAAATCAAGAAATAAAC
1330566 ATG-TTAT-AAATCAAAGAAATA
1 ATGCTT-TCAAATC-AAGAAATA
1330587 TTCATATCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
23 19 0.49
24 20 0.51
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (24 bp):
ATGCTTTCAAATCAAGAAATAAAC
Found at i:1333295 original size:22 final size:22
Alignment explanation
Indices: 1333270--1333313 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1333260 TTTCTTAACC
*
1333270 AGATCTCTTACTTTTATATTTA
1 AGATCTCTTACTTTCATATTTA
1333292 AGATCTCTTACTTTCATATTTA
1 AGATCTCTTACTTTCATATTTA
1333314 GACTAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.16, G:0.05, T:0.52
Consensus pattern (22 bp):
AGATCTCTTACTTTCATATTTA
Found at i:1340284 original size:15 final size:15
Alignment explanation
Indices: 1340264--1340292 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1340254 CTATTAGAAG
1340264 CCATAGACAAGTAAA
1 CCATAGACAAGTAAA
1340279 CCATAGACAAGTAA
1 CCATAGACAAGTAA
1340293 CAAAGTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.21, G:0.14, T:0.14
Consensus pattern (15 bp):
CCATAGACAAGTAAA
Found at i:1351204 original size:2 final size:2
Alignment explanation
Indices: 1351197--1351223 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1351187 ACTAAAGTAA
1351197 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 A
1351224 CTTAGGGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1351745 original size:21 final size:21
Alignment explanation
Indices: 1351703--1351745 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1351693 CAAAAATAAC
**
1351703 AATTATAAAAATCAGTGATTA
1 AATTATAAAAATCAAAGATTA
1351724 AATTATAAAATATCAAAG-TTA
1 AATTATAAAA-ATCAAAGATTA
1351745 A
1 A
1351746 TGAACATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.33
Consensus pattern (21 bp):
AATTATAAAAATCAAAGATTA
Found at i:1353038 original size:123 final size:123
Alignment explanation
Indices: 1352827--1353699 Score: 1203
Period size: 123 Copynumber: 7.1 Consensus size: 123
1352817 GTTGAATTGG
* *
1352827 GTCTGGAAATGTTGATGCCGCTTTATCTCCTTCTGCGATAGAGTCGAGCAAAAGGTTGAATAAGT
1 GTCTGGAAATGTTGATGCTGCTTTATCTCCTTCTGCGATAGAGTCGAGAAAAAGGTTGAATAAGT
* * * * *
1352892 TCTTCAGATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTATTATTATGAATTTCT
66 TCTTCAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAA-CTCT
* * *
1352951 -TCTGAAAATGTTGATGCTGCTTTATCTCCTTCTGCGATAAAGTCGAGAAAAAGGTTGTATAAGT
1 GTCTGGAAATGTTGATGCTGCTTTATCTCCTTCTGCGATAGAGTCGAGAAAAAGGTTGAATAAGT
* * * * *
1353015 TCTTCAGATTATGAATTTTTTCTTCCTCTTCAGATGACTTCTTCTTATTATGAACTCT
66 TCTTCAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCT
*
1353073 GTCTGGAAATGTTGATGCTGCTTTATCTCCTTCTGCGATAAAGTCGA-ACAAAAGGTTGAATAAG
1 GTCTGGAAATGTTGATGCTGCTTTATCTCCTTCTGCGATAGAGTCGAGA-AAAAGGTTGAATAAG
* *
1353137 TTCTTCAGATTATAAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTTCT
65 TTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAAC-TCT
* * * * *
1353197 -TGTGGAAATGTTGATGCTGCTTTATATCCTTCTGCGATAAAGTCGAGCAAAATGTTGAATAAGT
1 GTCTGGAAATGTTGATGCTGCTTTATCTCCTTCTGCGATAGAGTCGAGAAAAAGGTTGAATAAGT
*
1353261 TCTTCAGACTATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCTTATTACGAACTCT
66 TCTTCAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCT
* * * * *
1353319 GTCTGGAAATGGTT-CTGCTGCTCTATCTCCTTCTGTGATAGAGTCAAGCAAAAGGTTGAATAAG
1 GTCTGGAAAT-GTTGATGCTGCTTTATCTCCTTCTGCGATAGAGTCGAGAAAAAGGTTGAATAAG
* *
1353383 TTATTCAGACTATGAACTTCTTCTTCCTCTTCAGAGGAG---TTCTTATTACGAACTCT
65 TTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCT
* * *
1353439 GTCTGGAAATGGTT-ATGTTGCTCTATCTCCTTCTGCGATAGAGTCAAGTAAAAAGG-TGAATAA
1 GTCTGGAAAT-GTTGATGCTGCTTTATCTCCTTCTGCGATAGAGTCGAG-AAAAAGGTTGAATAA
* *
1353502 GTTCTTCAGACTATGAACTTCTTTTTCCTCTTCAGATGAGTTCTTCTTATTACGAGCTCT
64 GTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCT
* * * * * *
1353562 GTCTGGAAATGGTT-CTGCTGCTCTATCTCTTTCTACGATAGAGTCAAGTAAAAGGTTGAAT-AG
1 GTCTGGAAAT-GTTGATGCTGCTTTATCTCCTTCTGCGATAGAGTCGAGAAAAAGGTTGAATAAG
1353625 TTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCT
65 TTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACT-CT
*
1353685 -TCTAGAAATGTTGAT
1 GTCTGGAAATGTTGAT
1353700 CCATTGAGTG
Statistics
Matches: 683, Mismatches: 53, Indels: 28
0.89 0.07 0.04
Matches are distributed among these distances:
120 106 0.16
121 9 0.01
122 79 0.12
123 483 0.71
124 6 0.01
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (123 bp):
GTCTGGAAATGTTGATGCTGCTTTATCTCCTTCTGCGATAGAGTCGAGAAAAAGGTTGAATAAGT
TCTTCAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCT
Found at i:1354573 original size:54 final size:54
Alignment explanation
Indices: 1354491--1354626 Score: 209
Period size: 54 Copynumber: 2.5 Consensus size: 54
1354481 ACTGGTTCGT
* *
1354491 AAAACATTTTACAACACATTCATCCTTTCCTATGGCTTCTACCTAGATATTCAA
1 AAAACATTTGACAACACATTCATCCTTTCCTATGGCTTCTACCCAGATATTCAA
* * * **
1354545 AAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAGATGTTCGC
1 AAAACATTTGACAACACATTCATCCTTTCCTATGGCTTCTACCCAGATATTCAA
1354599 AAAACATTTGACAACACATTCATCCTTT
1 AAAACATTTGACAACACATTCATCCTTT
1354627 TATGTAGCTT
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 75 1.00
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.33
Consensus pattern (54 bp):
AAAACATTTGACAACACATTCATCCTTTCCTATGGCTTCTACCCAGATATTCAA
Found at i:1354637 original size:54 final size:53
Alignment explanation
Indices: 1354485--1354646 Score: 200
Period size: 54 Copynumber: 3.0 Consensus size: 53
1354475 ATAATCACTG
* * * *
1354485 GTTCGTAAAACATTTTACAACACATTCATCCTTTCCTATG-GCTTCTACCTAGAT
1 GTTCGAAAAACATTTGACAACACATTCATCCTTT--TATGTGCTTCTGCCCAGAT
* * **
1354539 ATTCAAAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAGAT
1 GTTCGAAAAACATTTGACAACACATTCATCCTTTTATGT-GCTTCTGCCCAGAT
*
1354593 GTTCGCAAAACATTTGACAACACATTCATCCTTTTATGTAGCTTCTGCCCAGAT
1 GTTCGAAAAACATTTGACAACACATTCATCCTTTTATGT-GCTTCTGCCCAGAT
1354647 TTCTCGTCAA
Statistics
Matches: 92, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
52 2 0.02
54 90 0.98
ACGTcount: A:0.28, C:0.27, G:0.11, T:0.34
Consensus pattern (53 bp):
GTTCGAAAAACATTTGACAACACATTCATCCTTTTATGTGCTTCTGCCCAGAT
Found at i:1356456 original size:72 final size:72
Alignment explanation
Indices: 1356325--1356460 Score: 200
Period size: 72 Copynumber: 1.9 Consensus size: 72
1356315 AAATAAAAGG
* * * *
1356325 CTAGCTGAATATTATCCATAAAGCTAGGTCTATTAACCAATTGCTTTAGGAGGACAACTCAAGCA
1 CTAGCTGAATATTATCCATAAAGCCAGGGCTATCAACCAATTGCTCTAGGAGGACAACTCAAGCA
1356390 TAACAGA
66 TAACAGA
* * * *
1356397 CTAGCTGAATATTATCTATAAAGCCGGGGCTATCAACCAATTGCTCTAGGGGGATAACTCAAGC
1 CTAGCTGAATATTATCCATAAAGCCAGGGCTATCAACCAATTGCTCTAGGAGGACAACTCAAGC
1356461 TTTATTGTAT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 56 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.26
Consensus pattern (72 bp):
CTAGCTGAATATTATCCATAAAGCCAGGGCTATCAACCAATTGCTCTAGGAGGACAACTCAAGCA
TAACAGA
Found at i:1358071 original size:20 final size:20
Alignment explanation
Indices: 1358026--1358074 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1358016 CACTTCTTCT
*
1358026 ATATTTTTCAGTCGTTGGGA
1 ATATTTTTCAGTCGTTCGGA
*
1358046 ATATTTTTCAGTTGTTCGGA
1 ATATTTTTCAGTCGTTCGGA
1358066 GA-ATTTTTC
1 -ATATTTTTC
1358075 CTTTTCAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.20, C:0.10, G:0.20, T:0.49
Consensus pattern (20 bp):
ATATTTTTCAGTCGTTCGGA
Found at i:1358666 original size:17 final size:16
Alignment explanation
Indices: 1358644--1358694 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
1358634 AAGTTAGAGC
*
1358644 AAAATGTATGAAAAATA
1 AAAATGAAT-AAAAATA
1358661 AAAATGAATAAAAATGA
1 AAAATGAATAAAAAT-A
*
1358678 GAAA-GAA-AAAAATA
1 AAAATGAATAAAAATA
1358692 AAA
1 AAA
1358695 TGGTTAGTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 3 0.10
15 6 0.20
16 9 0.30
17 12 0.40
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.16
Consensus pattern (16 bp):
AAAATGAATAAAAATA
Found at i:1358677 original size:23 final size:21
Alignment explanation
Indices: 1358651--1358694 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
1358641 AGCAAAATGT
*
1358651 ATGAAAAATAAAAATGAATAAAA
1 ATGAAAAAGAAAAA--AATAAAA
*
1358674 ATGAGAAAGAAAAAAATAAAA
1 ATGAAAAAGAAAAAAATAAAA
1358695 TGGTTAGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
23 12 0.63
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (21 bp):
ATGAAAAAGAAAAAAATAAAA
Found at i:1360010 original size:24 final size:24
Alignment explanation
Indices: 1359955--1360002 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1359945 AAAACTAAAT
1359955 AAATATTATTATTAAATCAATTTG
1 AAATATTATTATTAAATCAATTTG
*
1359979 AAATATTATTATTTAATCAATTTG
1 AAATATTATTATTAAATCAATTTG
1360003 TGAAATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATATTATTATTAAATCAATTTG
Found at i:1360281 original size:21 final size:21
Alignment explanation
Indices: 1360238--1360281 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1360228 TAAAAAATGA
**
1360238 AAATTATAAAAATCAGTGATT
1 AAATTATAAAAATCAAAGATT
1360259 AAATTATAAAATATCAAAG-TT
1 AAATTATAAAA-ATCAAAGATT
1360280 AA
1 AA
1360282 TGAACATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (21 bp):
AAATTATAAAAATCAAAGATT
Found at i:1360814 original size:106 final size:107
Alignment explanation
Indices: 1360629--1360841 Score: 419
Period size: 106 Copynumber: 2.0 Consensus size: 107
1360619 TTTTGTGCCA
1360629 ATTTTCCCTCATTGTGCATATTTCCTCTCTCTCTAAAATAGAGAGATGGAATTCTCTCTTCCCTC
1 ATTTTCCCTCATTGTGCATATTTCCTCTCTCTCTAAAATAGAGAGATGGAATTCTCTCTTCCCTC
1360694 TCCCTAGGTTTCCCTCGCCGGAAGGAAACCAGTC-CCGGCCG
66 TCCCTAGGTTTCCCTCGCCGGAAGGAAACCAGTCACCGGCCG
1360735 ATTTTCCCTCATTGTGCATATTTCCTCTCTCTCTAAAATAGAGAGATGGAATTCTCTCTTCCCTC
1 ATTTTCCCTCATTGTGCATATTTCCTCTCTCTCTAAAATAGAGAGATGGAATTCTCTCTTCCCTC
1360800 TCCCTAGGTTTCCCTCGCCGGAAGGAAACCAGTCACCGGCCG
66 TCCCTAGGTTTCCCTCGCCGGAAGGAAACCAGTCACCGGCCG
1360842 GCCGCATTCT
Statistics
Matches: 106, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
106 99 0.93
107 7 0.07
ACGTcount: A:0.20, C:0.32, G:0.17, T:0.31
Consensus pattern (107 bp):
ATTTTCCCTCATTGTGCATATTTCCTCTCTCTCTAAAATAGAGAGATGGAATTCTCTCTTCCCTC
TCCCTAGGTTTCCCTCGCCGGAAGGAAACCAGTCACCGGCCG
Found at i:1361578 original size:3 final size:3
Alignment explanation
Indices: 1361570--1361607 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
1361560 TATTTTTTAT
* *
1361570 TAA TAA TAA TAA CAA TAA TAA TAA TAA T-A TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1361608 AAAATAAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:1361613 original size:18 final size:21
Alignment explanation
Indices: 1361570--1361614 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
1361560 TATTTTTTAT
*
1361570 TAATAATAATAACAATAATAA
1 TAATAATAATAAAAATAATAA
1361591 TAATAAT-ATAAAAATAA-AA
1 TAATAATAATAAAAATAATAA
1361610 -AATAA
1 TAATAA
1361615 AAGGGACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 5 0.22
19 2 0.09
20 9 0.39
21 7 0.30
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
TAATAATAATAAAAATAATAA
Found at i:1366135 original size:137 final size:137
Alignment explanation
Indices: 1365766--1366147 Score: 480
Period size: 137 Copynumber: 2.8 Consensus size: 137
1365756 TTCCTTTTCA
* * * * *
1365766 TTGAGGAAGTTTGATTGTCTGAGAATGACACTACTTCTTCGCATTGAGGAGATTTGGTCAGTGGA
1 TTGAGGAAGTCTGATAGTCTGAGGATGACACTACTTCTTTGCATTGAGGAGATATGGTCAGTGGA
* * ** *
1365831 CAACATCATTCCTTCGTGTTGAGGACATCTAGTTGTATTTGGATAATTTGGAGACAACACGGTTC
66 CAACATCGTTCCTTCGTGTTGAGGACGTCTAGACGTATTTGGATAATTTAGAGACAACACGGTTC
1365896 CTTCGTG
131 CTTCGTG
* * *
1365903 TTGAGGAAGTCTGA-ATGTCTGAGGATGACACTGC-TCATTTGCATTGAGGATATATGGTCAGTA
1 TTGAGGAAGTCTGATA-GTCTGAGGATGACACTACTTC-TTTGCATTGAGGAGATATGGTCAGTG
* * * *
1365966 GATAACATCGTTCCTTCGTGTTGAGAAAGTCTAGACGTATTTGGATAATTTAGAGACAACATGGT
64 GACAACATCGTTCCTTCGTGTTGAGGACGTCTAGACGTATTTGGATAATTTAGAGACAACACGGT
1366031 TCCTTCGTG
129 TCCTTCGTG
* * * *
1366040 TTGAGGAAGTCTGATAGTCTGAGGATAACACTACTTCTTTGCATTTAGGAGATATGGTCGGCGGA
1 TTGAGGAAGTCTGATAGTCTGAGGATGACACTACTTCTTTGCATTGAGGAGATATGGTCAGTGGA
* * * * * * *
1366105 CGATATTGTTCATTCGTATTTAGGACGTCTAGCCGTATTTGGA
66 CAACATCGTTCCTTCGTGTTGAGGACGTCTAGACGTATTTGGA
1366148 GATAACATTG
Statistics
Matches: 207, Mismatches: 34, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
136 2 0.01
137 202 0.98
138 3 0.01
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (137 bp):
TTGAGGAAGTCTGATAGTCTGAGGATGACACTACTTCTTTGCATTGAGGAGATATGGTCAGTGGA
CAACATCGTTCCTTCGTGTTGAGGACGTCTAGACGTATTTGGATAATTTAGAGACAACACGGTTC
CTTCGTG
Found at i:1372311 original size:53 final size:53
Alignment explanation
Indices: 1372245--1372469 Score: 344
Period size: 53 Copynumber: 4.2 Consensus size: 53
1372235 GAACTCGAAT
*
1372245 AATCTTTAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCAC
1 AATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCAC
* * * *
1372298 AATCTTCATCAATCGCGTTTG-CCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CAC
* *
1372352 AATCTTCAACGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCAC
1 AATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCAC
* *
1372405 AATCTTCAACGATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCAC
1 AATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCAC
1372458 AATCTTCAACAA
1 AATCTTCAACAA
1372470 ATGGTTCGCT
Statistics
Matches: 155, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
52 27 0.17
53 82 0.53
54 20 0.13
55 26 0.17
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (53 bp):
AATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCAC
Found at i:1372645 original size:51 final size:51
Alignment explanation
Indices: 1372472--1372767 Score: 385
Period size: 51 Copynumber: 5.7 Consensus size: 51
1372462 TTCAACAAAT
* * *
1372472 GGTTCGCTCCCTATTTCTCTAGGGAGTATGGAACTCAGACATATTCTTCAAACG
1 GGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTC-GA-ACA-TCTTCAAACG
*
1372526 GGTTCGCTCCCCCTTTCTCTAGGGAGTATAGAACTCGAACATCTCTTCAAACG
1 GGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACA--TCTTCAAACG
* * *
1372579 GGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACG
1 GGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAAACG
* * * * * *
1372630 GGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGCATATCTTCACACG
1 GGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAAACG
* * *
1372681 GGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACCCGGACATCTTCAAACG
1 GGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAAACG
* *
1372732 GGTTTGCTCCCTCTTTCTCTAGGGAGTATGGAACTC
1 GGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTC
1372768 AAATAATCTT
Statistics
Matches: 219, Mismatches: 22, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
51 135 0.62
52 2 0.01
53 49 0.22
54 33 0.15
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (51 bp):
GGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAAACG
Found at i:1373207 original size:36 final size:36
Alignment explanation
Indices: 1373149--1373338 Score: 220
Period size: 36 Copynumber: 5.2 Consensus size: 36
1373139 ACTCTTCTGA
* * **
1373149 GAAGGCTTAAAATGGATCTGCTTCACTACTT-TTTGGT
1 GAAGGCTTAAGATGG-TTTGCTTCACTA-TTCTCCGGT
* * *
1373186 GAAGACTTAAGATGGTTTGCTTCACTACTCTCTGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
1373222 GAAGACTTATGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* * *
1373258 GAAGGCTTCAGATTGATTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* * *
1373294 GAAGGCTTCAGATGGTTTGCTTCACTATTCTTCGGC
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
1373330 GAAGGCTTA
1 GAAGGCTTA
1373339 GGATTGACTT
Statistics
Matches: 134, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
35 1 0.01
36 120 0.90
37 13 0.10
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (36 bp):
GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
Found at i:1374279 original size:122 final size:124
Alignment explanation
Indices: 1374057--1374353 Score: 422
Period size: 123 Copynumber: 2.4 Consensus size: 124
1374047 CAATAATTTT
* ** * *
1374057 CTTGGTCTGAATCTTTTCATCTC-ACATGACGTGGGTTTGGTTACGCCCCAACATTATCTTACAC
1 CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTCATGCCCCAACATTATCTTACAC
** * *
1374121 TGGTACGGGCCTTCAAATGCCCCATCACCTCAAATTGTAAGGCTCATTC-TCATGCCTC
66 TGGTACGGGCAATCAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTTAATGCCTC
* *
1374179 CTTGTTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTCATGCCCCAACATT-TCTTATAC
1 CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTCATGCCCCAACATTATCTTACAC
1374243 TGGTACGGG-AATCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTTAATGCCTC
66 TGGTACGGGCAATC-AAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTTAATGCCTC
* * * *
1374302 CTTGGTCTGAATCTTGTCTTCTCAACATGATGTGGGTTCATTCGTGCCCCAA
1 CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTCATGCCCCAA
1374354 ACATATCACA
Statistics
Matches: 156, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
121 2 0.01
122 72 0.46
123 82 0.53
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (124 bp):
CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTCATGCCCCAACATTATCTTACAC
TGGTACGGGCAATCAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTTAATGCCTC
Found at i:1375501 original size:28 final size:27
Alignment explanation
Indices: 1375444--1375506 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
1375434 TCCTTTTTTA
* *
1375444 TTTTCTTTTTCATTTCATTTTTTTTATC
1 TTTTC-TTTTCATTTCATATTTCTTATC
* *
1375472 TTTTCTTTTCCTTTCTATATTTCTTCTC
1 TTTTCTTTTCATTTC-ATATTTCTTATC
1375500 -TTTCTTT
1 TTTTCTTT
1375507 ATGATGTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 16 0.53
28 14 0.47
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (27 bp):
TTTTCTTTTCATTTCATATTTCTTATC
Found at i:1380562 original size:56 final size:57
Alignment explanation
Indices: 1380480--1380594 Score: 223
Period size: 56 Copynumber: 2.0 Consensus size: 57
1380470 TAACAAGATA
1380480 ACCTTAAGCCAAGCCTCTCTCGGAATCAAACCAACACTGCTCCCTCTAGACGCTCTG
1 ACCTTAAGCCAAGCCTCTCTCGGAATCAAACCAACACTGCTCCCTCTAGACGCTCTG
1380537 ACCTTAAGCC-AGCCTCTCTCGGAATCAAACCAACACTGCTCCCTCTAGACGCTCTG
1 ACCTTAAGCCAAGCCTCTCTCGGAATCAAACCAACACTGCTCCCTCTAGACGCTCTG
1380593 AC
1 AC
1380595 TCGTGATTCA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 48 0.83
57 10 0.17
ACGTcount: A:0.26, C:0.39, G:0.14, T:0.21
Consensus pattern (57 bp):
ACCTTAAGCCAAGCCTCTCTCGGAATCAAACCAACACTGCTCCCTCTAGACGCTCTG
Found at i:1382650 original size:28 final size:28
Alignment explanation
Indices: 1382592--1382646 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1382582 ATGTAGATAG
* **
1382592 GTAGAACATGCATGTATGTATGATGCAT
1 GTAGAACATACATGTATGTATGACACAT
*
1382620 GTAGAACATATATGTATGTAT-ACACAT
1 GTAGAACATACATGTATGTATGACACAT
1382647 TGTATGCATG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (28 bp):
GTAGAACATACATGTATGTATGACACAT
Found at i:1386597 original size:19 final size:19
Alignment explanation
Indices: 1386561--1386602 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1386551 TTTTAAAGAC
1386561 TTTT-ACAAAATAAATATA
1 TTTTAACAAAATAAATATA
* *
1386579 TTTTAACAAATTAATTATA
1 TTTTAACAAAATAAATATA
1386598 TTTTA
1 TTTTA
1386603 TCAATTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTTAACAAAATAAATATA
Found at i:1386615 original size:18 final size:19
Alignment explanation
Indices: 1386561--1386615 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 19
1386551 TTTTAAAGAC
* *
1386561 TTTT-ACAAAATAAATATA
1 TTTTAACAAATTAAGTATA
*
1386579 TTTTAACAAATTAATTATA
1 TTTTAACAAATTAAGTATA
* *
1386598 TTTTATC-AATTTAGTATA
1 TTTTAACAAATTAAGTATA
1386616 ATTGTATCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 13 0.42
19 18 0.58
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.47
Consensus pattern (19 bp):
TTTTAACAAATTAAGTATA
Found at i:1388881 original size:23 final size:24
Alignment explanation
Indices: 1388844--1388901 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 24
1388834 GGAGGATTCA
* * *
1388844 TCGGGCTCATTGAGTTCTAAGTCG
1 TCGGGTTCATCGAGTTATAAGTCG
**
1388868 T-GGGTTCATCGAGTTATGGGTCG
1 TCGGGTTCATCGAGTTATAAGTCG
1388891 TCGGGTTCATC
1 TCGGGTTCATC
1388902 TTGTCATCAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 18 0.64
24 10 0.36
ACGTcount: A:0.14, C:0.19, G:0.33, T:0.34
Consensus pattern (24 bp):
TCGGGTTCATCGAGTTATAAGTCG
Found at i:1392022 original size:2 final size:2
Alignment explanation
Indices: 1392015--1392059 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1392005 CATCGGTAAG
1392015 AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
1392056 AT AT
1 AT AT
1392060 CGATTTTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1398564 original size:16 final size:16
Alignment explanation
Indices: 1398540--1398571 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1398530 TATCGCCGAC
*
1398540 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
1398556 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
1398572 TGTGAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:1402554 original size:18 final size:16
Alignment explanation
Indices: 1402531--1402574 Score: 54
Period size: 15 Copynumber: 2.7 Consensus size: 16
1402521 AAAGAAAACT
*
1402531 AATAAAATTAAATTAAAA
1 AATAAAA-TAAAAT-AAA
1402549 AATAAAATAAAATAAA
1 AATAAAATAAAATAAA
1402565 AAT-AAATAAA
1 AATAAAATAAA
1402575 CTAATCAGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 7 0.28
16 6 0.24
17 5 0.20
18 7 0.28
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AATAAAATAAAATAAA
Found at i:1411133 original size:13 final size:13
Alignment explanation
Indices: 1411104--1411141 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1411094 TTACTAATGC
*
1411104 AAATTCTAAAC-A
1 AAATGCTAAACAA
1411116 AAATGCTAAACAA
1 AAATGCTAAACAA
*
1411129 AAATGCTCAACAA
1 AAATGCTAAACAA
1411142 CATATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.58, C:0.18, G:0.05, T:0.18
Consensus pattern (13 bp):
AAATGCTAAACAA
Found at i:1415600 original size:16 final size:18
Alignment explanation
Indices: 1415579--1415616 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
1415569 AAGTAATTAA
1415579 AATCTAAA-AATG-AAAG
1 AATCTAAACAATGTAAAG
1415595 AATCTAAACTAATGTAAAG
1 AATCTAAAC-AATGTAAAG
1415614 AAT
1 AAT
1415617 GACTTATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
18 4 0.21
19 7 0.37
ACGTcount: A:0.58, C:0.08, G:0.11, T:0.24
Consensus pattern (18 bp):
AATCTAAACAATGTAAAG
Found at i:1419256 original size:20 final size:20
Alignment explanation
Indices: 1419231--1419276 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1419221 TTGTAATTTT
1419231 GGAGAAATATGAAGATGAAA
1 GGAGAAATATGAAGATGAAA
1419251 GGAGAAATATGAAGATGAAA
1 GGAGAAATATGAAGATGAAA
*
1419271 TGAGAA
1 GGAGAA
1419277 CATTCTCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.30, T:0.15
Consensus pattern (20 bp):
GGAGAAATATGAAGATGAAA
Found at i:1423610 original size:138 final size:138
Alignment explanation
Indices: 1423411--1423730 Score: 380
Period size: 138 Copynumber: 2.3 Consensus size: 138
1423401 CCAAATTGAA
* * ***
1423411 AATTCTCC-TAAATTAAAGGA-TAACA-AAGAAATTAAAACTAAAACGGAGGCTCTAAACATTAA
1 AATTC-CCATAAATTAAAGGACTAA-ATATGAAATTAAACCTAAATTAGAGGCTCTAAACATTAA
*
1423473 CCTAACT-AATTTTAACCAATTATCGAATAAAATAATTAAAATGGAACCT-TAAGCAAAAGCAAG
64 CAT-ACTCAATTTTAACCAATTATCGAATAAAATAATTAAAATGGAACCTAT-AGCAAAAGCAAG
1423536 GACCAAACTAAG
127 GACCAAACTAAG
* **
1423548 AATTCCTATAAATTAAAGGACTAAATATGAAATTAAACCTAAATTAGAGGCTCTAATTATTAACA
1 AATTCCCATAAATTAAAGGACTAAATATGAAATTAAACCTAAATTAGAGGCTCTAAACATTAACA
* * * * ** * ** *
1423613 TAGTCCATTTTAGCCAATTATTGAATCGAATAATTAAAATGGAACCTATATCAAAAGTGATGACC
66 TACTCAATTTTAACCAATTATCGAATAAAATAATTAAAATGGAACCTATAGCAAAAGCAAGGACC
*
1423678 AAATTAAG
131 AAACTAAG
*
1423686 AATTCCCATAAATTAAAGGACTAAATATGAAATTAAGCCTAAATT
1 AATTCCCATAAATTAAAGGACTAAATATGAAATTAAACCTAAATT
1423731 CCATACAAAT
Statistics
Matches: 156, Mismatches: 22, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
136 1 0.01
137 20 0.13
138 134 0.86
139 1 0.01
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (138 bp):
AATTCCCATAAATTAAAGGACTAAATATGAAATTAAACCTAAATTAGAGGCTCTAAACATTAACA
TACTCAATTTTAACCAATTATCGAATAAAATAATTAAAATGGAACCTATAGCAAAAGCAAGGACC
AAACTAAG
Found at i:1425994 original size:42 final size:42
Alignment explanation
Indices: 1425943--1426024 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
1425933 AAGGACTTAT
*
1425943 CATCTTGCTCGAAAGA-TTGACAGATGACCCGAAGGATTTAAA
1 CATCATGCTCGAAAGACTT-ACAGATGACCCGAAGGATTTAAA
* *
1425985 CATCATGCTCGAAGGACTTACAGATGACCTGAAGGATTTA
1 CATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTA
1426025 CAAATTCGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 34 0.94
43 2 0.06
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (42 bp):
CATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAA
Found at i:1432422 original size:21 final size:19
Alignment explanation
Indices: 1432394--1432439 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
1432384 TCATTGAATC
1432394 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
1432414 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
1432433 ACTTAGT
1 A-TTAGT
1432440 AAGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:1450437 original size:25 final size:25
Alignment explanation
Indices: 1450403--1450456 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
1450393 GTGGTGTTCT
1450403 AAAACATGTGAATATATTTTTGTAC
1 AAAACATGTGAATATATTTTTGTAC
1450428 AAAACATGTGAATATATTTTTGTAC
1 AAAACATGTGAATATATTTTTGTAC
1450453 AAAA
1 AAAA
1450457 AATTTAGCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.37
Consensus pattern (25 bp):
AAAACATGTGAATATATTTTTGTAC
Found at i:1454080 original size:21 final size:20
Alignment explanation
Indices: 1454055--1454093 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1454045 CATCATGGTC
*
1454055 TTTGTGGAAGCCATGAAATCT
1 TTTGTCGAAGCCAT-AAATCT
*
1454076 TTTGTCGAGGCCATAAAT
1 TTTGTCGAAGCCATAAAT
1454094 TCCTGCAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.33
Consensus pattern (20 bp):
TTTGTCGAAGCCATAAATCT
Found at i:1473029 original size:6 final size:6
Alignment explanation
Indices: 1472973--1473030 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
1472963 TATCCTCCTC
* * ** * * *
1472973 ATCATC ATCAAT ATCATT ATCAAC ATCATC ATCATT GTCATT ATAATT
1 ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT
1473021 ATCATT ATCA
1 ATCATT ATCA
1473031 CAGTTCATTA
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.38, C:0.21, G:0.02, T:0.40
Consensus pattern (6 bp):
ATCATT
Found at i:1473164 original size:24 final size:23
Alignment explanation
Indices: 1473137--1473188 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
1473127 CAGCTCGTAT
*
1473137 AAATAGCACCGAAGTGCCGCATAGA
1 AAATA-CACCGAAGTGCCACATA-A
* *
1473162 AATTACACTGAAGTGCCACATAA
1 AAATACACCGAAGTGCCACATAA
1473185 AAAT
1 AAAT
1473189 GTCCCAAAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 4 0.17
24 15 0.65
25 4 0.17
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.17
Consensus pattern (23 bp):
AAATACACCGAAGTGCCACATAA
Found at i:1473235 original size:23 final size:23
Alignment explanation
Indices: 1473209--1473278 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
1473199 ACTACATAGT
*
1473209 AATGATCT-GAAGGACCGTGTAGA
1 AATG-TCTCGAAGGACCGCGTAGA
* *
1473232 AATGTCTCGAAGTACCACGTAGA
1 AATGTCTCGAAGGACCGCGTAGA
* *
1473255 ATTGTCTCGAAGGACCGCATAGA
1 AATGTCTCGAAGGACCGCGTAGA
1473278 A
1 A
1473279 CCCTCGACTC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
22 3 0.08
23 36 0.92
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (23 bp):
AATGTCTCGAAGGACCGCGTAGA
Found at i:1473426 original size:16 final size:16
Alignment explanation
Indices: 1473405--1473458 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
1473395 TTTTCACATT
1473405 TCACATATTCATATAA
1 TCACATATTCATATAA
*
1473421 TCACATAGTTCA-GT-A
1 TCACATA-TTCATATAA
**
1473436 TCACATAGACATATAA
1 TCACATATTCATATAA
1473452 TCACATA
1 TCACATA
1473459 AGTCCTTGTC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 2 0.06
15 9 0.29
16 16 0.52
17 4 0.13
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (16 bp):
TCACATATTCATATAA
Found at i:1474164 original size:15 final size:15
Alignment explanation
Indices: 1474144--1474172 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1474134 TTATGCATTA
1474144 GTATCGATACCCTTG
1 GTATCGATACCCTTG
1474159 GTATCGATACCCTT
1 GTATCGATACCCTT
1474173 CCTTTGGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (15 bp):
GTATCGATACCCTTG
Found at i:1479013 original size:23 final size:22
Alignment explanation
Indices: 1478929--1479013 Score: 64
Period size: 24 Copynumber: 3.6 Consensus size: 22
1478919 GGTAATTTAA
* * *
1478929 TAATAATATATAGTAAGTAGTAAA
1 TAATAATA-ATAATAAATAGT-AC
*
1478953 TAATAATAAGTAATAAATATTAC
1 TAATAATAA-TAATAAATAGTAC
*
1478976 TAATAATATTAAATAAATTAGTA-
1 TAATAATAAT-AATAAA-TAGTAC
1478999 TCAATAATAATAATA
1 T-AATAATAATAATA
1479014 TAAAATAGAC
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
22 1 0.02
23 21 0.42
24 28 0.56
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.35
Consensus pattern (22 bp):
TAATAATAATAATAAATAGTAC
Found at i:1480105 original size:47 final size:47
Alignment explanation
Indices: 1480049--1480495 Score: 725
Period size: 47 Copynumber: 9.5 Consensus size: 47
1480039 TTAACACATC
*
1480049 CATCCTTTCATGCATTTTAAATTATGGCATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
**
1480096 CATCCTTTCATATATTTTCAATTATGGCATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
* *
1480143 CATCCTTTCATGCATTTTCAATTATGACATCTTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
* *
1480190 CATCCTTTCATGCATTTTAAATTATGGCATCCTTTCATGTCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
* *
1480237 CATCCTTTCATGCATTTTCAATTATGGCATCTTTTCATGACTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
*
1480284 CATCCTTTCATGCATTTTAAATTATGGCATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
* *
1480331 CATCCTTTCATGCATTTTCAATTAT-GAATTCCATTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCA-TCCTTTCATGCCTTAATG
1480378 CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
** * *
1480425 CATATTTTCATGCATTTTCAAGTATGGCATTCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
*
1480472 CATCCTTTCATGCATTTTAAATTA
1 CATCCTTTCATGCATTTTCAATTA
1480496 CGAATTCAGT
Statistics
Matches: 368, Mismatches: 30, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
46 2 0.01
47 364 0.99
48 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.44
Consensus pattern (47 bp):
CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
Found at i:1480940 original size:22 final size:19
Alignment explanation
Indices: 1480892--1480962 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 19
1480882 GGATCCTCAG
* * *
1480892 TATCGATACCCCTACCACGG
1 TATCGATA-CCCTACTATGA
1480912 TATCGATACTACCATACTATGA
1 TATCGATAC--CC-TACTATGA
*
1480934 TATCGATACCCTATTATGA
1 TATCGATACCCTACTATGA
1480953 TATCGATACC
1 TATCGATACC
1480963 ATTTTTACAT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
19 18 0.41
20 10 0.23
21 2 0.05
22 14 0.32
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.30
Consensus pattern (19 bp):
TATCGATACCCTACTATGA
Found at i:1481010 original size:20 final size:20
Alignment explanation
Indices: 1480985--1481031 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1480975 TATTTTGAAA
*
1480985 TGGTATCAATAC-CTTCCCTT
1 TGGTATCAATACGC-CCCCTT
*
1481005 TGGTATCGATACGCCCCCTT
1 TGGTATCAATACGCCCCCTT
1481025 TGGTATC
1 TGGTATC
1481032 GATATTCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.17, C:0.30, G:0.17, T:0.36
Consensus pattern (20 bp):
TGGTATCAATACGCCCCCTT
Found at i:1486797 original size:38 final size:38
Alignment explanation
Indices: 1486755--1486873 Score: 127
Period size: 38 Copynumber: 3.1 Consensus size: 38
1486745 AGGGCATTAC
** *
1486755 ATAGTCCTTAGGAAGACGAGATTAAGGTTTCTAGGAAA
1 ATAGTCCTTAGGAAGAAAAGATTGAGGTTTCTAGGAAA
* * *
1486793 ATAGT--TTGAAGAAAGATAAGATTGAGATTTCTA-GAGAA
1 ATAGTCCTT--AGGAAGAAAAGATTGAGGTTTCTAGGA-AA
*
1486831 ATAGTCCTAAGGAAGAAAAGATTGAGGTTTCTAGGAAA
1 ATAGTCCTTAGGAAGAAAAGATTGAGGTTTCTAGGAAA
1486869 ATAGT
1 ATAGT
1486874 TTTCAGACAG
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
36 2 0.03
37 2 0.03
38 59 0.89
39 2 0.03
40 1 0.02
ACGTcount: A:0.41, C:0.07, G:0.25, T:0.27
Consensus pattern (38 bp):
ATAGTCCTTAGGAAGAAAAGATTGAGGTTTCTAGGAAA
Found at i:1487492 original size:15 final size:15
Alignment explanation
Indices: 1487472--1487503 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1487462 GACACAAATC
1487472 ATAAAATATGAGTTT
1 ATAAAATATGAGTTT
1487487 ATAAAATATGAGTTT
1 ATAAAATATGAGTTT
1487502 AT
1 AT
1487504 TGATTATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (15 bp):
ATAAAATATGAGTTT
Found at i:1489639 original size:41 final size:41
Alignment explanation
Indices: 1489588--1489670 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
1489578 TGATAAATGC
1489588 AATGCTGAAAGTGAAAATG-CAAAATGAAAAATAAAAAAGGT
1 AATGCTGAAAGTGAAAATGAC-AAATGAAAAATAAAAAAGGT
* *
1489629 AATGTTGAAAGTGAAAATGACAAATGAAAAATAAAGAAGGT
1 AATGCTGAAAGTGAAAATGACAAATGAAAAATAAAAAAGGT
1489670 A
1 A
1489671 TTAATTCCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
41 38 0.97
42 1 0.03
ACGTcount: A:0.58, C:0.04, G:0.20, T:0.18
Consensus pattern (41 bp):
AATGCTGAAAGTGAAAATGACAAATGAAAAATAAAAAAGGT
Found at i:1493216 original size:24 final size:24
Alignment explanation
Indices: 1493165--1493249 Score: 129
Period size: 24 Copynumber: 3.6 Consensus size: 24
1493155 TCGGGACAAA
*
1493165 TCTATGTGGCACTTCGGTG--TAT
1 TCTACGTGGCACTTCGGTGTATAT
1493187 TCTACGTGGCACTTCGGTGTATAT
1 TCTACGTGGCACTTCGGTGTATAT
**
1493211 TCTACGTGGCACTTCAATGTATAT
1 TCTACGTGGCACTTCGGTGTATAT
1493235 TCTACGTGGCACTTC
1 TCTACGTGGCACTTC
1493250 AACGCAAATT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
22 18 0.31
24 40 0.69
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (24 bp):
TCTACGTGGCACTTCGGTGTATAT
Found at i:1493250 original size:24 final size:24
Alignment explanation
Indices: 1493184--1493266 Score: 121
Period size: 24 Copynumber: 3.5 Consensus size: 24
1493174 CACTTCGGTG
**
1493184 TATTCTACGTGGCACTTCGGTGTA
1 TATTCTACGTGGCACTTCAATGTA
1493208 TATTCTACGTGGCACTTCAATGTA
1 TATTCTACGTGGCACTTCAATGTA
* *
1493232 TATTCTACGTGGCACTTCAACGCA
1 TATTCTACGTGGCACTTCAATGTA
*
1493256 AATTCTACGTG
1 TATTCTACGTG
1493267 ACAGTTTCAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (24 bp):
TATTCTACGTGGCACTTCAATGTA
Found at i:1495405 original size:105 final size:105
Alignment explanation
Indices: 1495213--1495424 Score: 383
Period size: 105 Copynumber: 2.0 Consensus size: 105
1495203 AGAAACATCG
1495213 TTGCTTGTGTGGTTCAGAACAGTCCAATGGTACTTGGGAGTTTCCTTCTCTCTAATACTTTTTAC
1 TTGCTTGTGTGGTTCAGAACAGTCCAATGGTACTTGGGAGTTTCCTTCTCTCTAATACTTTTTAC
1495278 TTATTTCAATATTATGGAAATGGGTTGTAA-CGAATGATA
66 TTATTTCAATATTATGGAAATGGGTTGTAACCGAATGATA
*
1495317 TTGCTTGTGTGGTTCAGAACAGTCCAATGGTTATTTGGGAGTTTCCTTCTCTCT-ATACTTTTTA
1 TTGCTTGTGTGGTTCAGAACAGTCCAATGG-TACTTGGGAGTTTCCTTCTCTCTAATACTTTTTA
1495381 CTTTATTTCAATATTATGGAAATGGGTTGTAACCGAATGATA
65 C-TTATTTCAATATTATGGAAATGGGTTGTAACCGAATGATA
1495423 TT
1 TT
1495425 TGTTAAACTT
Statistics
Matches: 104, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
104 41 0.39
105 52 0.50
106 11 0.11
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (105 bp):
TTGCTTGTGTGGTTCAGAACAGTCCAATGGTACTTGGGAGTTTCCTTCTCTCTAATACTTTTTAC
TTATTTCAATATTATGGAAATGGGTTGTAACCGAATGATA
Found at i:1503951 original size:2 final size:2
Alignment explanation
Indices: 1503903--1503934 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1503893 TATTTTTTGG
1503903 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
1503935 CACGTATGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1505291 original size:13 final size:12
Alignment explanation
Indices: 1505220--1505328 Score: 65
Period size: 13 Copynumber: 8.3 Consensus size: 12
1505210 AATAATGAAC
*
1505220 ATAAATAAATAAA
1 ATAAA-AAAAAAA
*
1505233 ATAAAGAAAACAA
1 ATAAA-AAAAAAA
*
1505246 ATAAACAAAAAGA
1 ATAAA-AAAAAAA
*
1505259 ATAAACAAAAAGAG
1 ATAAA-AAAAA-AA
1505273 ATAAAAAAAGAAA
1 ATAAAAAAA-AAA
1505286 ATAAAAGAAATAAA
1 ATAAAA-AAA-AAA
*
1505300 AGTAAAAAAACAA
1 A-TAAAAAAAAAA
** *
1505313 GGAAAAAAACAA
1 ATAAAAAAAAAA
1505325 ATAA
1 ATAA
1505329 GGAACTTGAT
Statistics
Matches: 77, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
12 12 0.16
13 44 0.57
14 16 0.21
15 5 0.06
ACGTcount: A:0.77, C:0.05, G:0.08, T:0.10
Consensus pattern (12 bp):
ATAAAAAAAAAA
Found at i:1505308 original size:22 final size:22
Alignment explanation
Indices: 1505226--1505300 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 22
1505216 GAACATAAAT
* *
1505226 AAATAAAATAAAGAAAA-CAAAT
1 AAATAAAA-AAAGAAAATAAAAG
* *
1505248 AAACAAAAAGAATAAACA-AAAAG
1 AAATAAAAA-AAGAAA-ATAAAAG
*
1505271 AGATAAAAAAAGAAAATAAAAG
1 AAATAAAAAAAGAAAATAAAAG
1505293 AAATAAAA
1 AAATAAAA
1505301 GTAAAAAAAC
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
21 2 0.05
22 29 0.69
23 11 0.26
ACGTcount: A:0.79, C:0.04, G:0.08, T:0.09
Consensus pattern (22 bp):
AAATAAAAAAAGAAAATAAAAG
Found at i:1505361 original size:16 final size:17
Alignment explanation
Indices: 1505342--1505376 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1505332 ACTTGATAAT
1505342 AATAGAAC-AAAAAATA
1 AATAGAACAAAAAAATA
*
1505358 AATATAACAAAAAAATA
1 AATAGAACAAAAAAATA
1505375 AA
1 AA
1505377 AAAAAAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.14
Consensus pattern (17 bp):
AATAGAACAAAAAAATA
Found at i:1505447 original size:17 final size:16
Alignment explanation
Indices: 1505369--1505447 Score: 61
Period size: 17 Copynumber: 4.7 Consensus size: 16
1505359 ATATAACAAA
1505369 AAAATAAAAAA-AAAG
1 AAAATAAAAAATAAAG
*
1505384 AGAAACAAATAAATATAAG
1 A-AAATAAA-AAATA-AAG
* *
1505403 GAAATAGAAAATAAATG
1 AAAATAAAAAATAAA-G
* *
1505420 AAGATAGAAAATAAAG
1 AAAATAAAAAATAAAG
1505436 CAAAATAAAAAA
1 -AAAATAAAAAA
1505448 AAGTAAAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
15 1 0.02
16 9 0.18
17 31 0.62
18 6 0.12
19 3 0.06
ACGTcount: A:0.73, C:0.03, G:0.11, T:0.13
Consensus pattern (16 bp):
AAAATAAAAAATAAAG
Found at i:1507645 original size:41 final size:41
Alignment explanation
Indices: 1507595--1507714 Score: 109
Period size: 41 Copynumber: 2.9 Consensus size: 41
1507585 ATCTAGAGTT
* * * *
1507595 GGCACGATATACTTCGTCTTTAAGTTGAAATCGTGGATGTG
1 GGCACGATATACTCCATCGTGAAGTTGAAATCGTGGATGTG
* * *
1507636 GGCATGATATCCTCCATCGTGGAGTTGAAATCGTGGACTTGTG
1 GGCACGATATACTCCATCGTGAAGTTGAAATCGTGGA--TGTG
* * *
1507679 GGTACGATATGCTCCGTTCG-G-AGTTGAAATCGTGGA
1 GGCACGATATACTCC-ATCGTGAAGTTGAAATCGTGGA
1507715 GGGCCCCTTC
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
41 30 0.46
42 15 0.23
43 17 0.26
44 3 0.05
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.31
Consensus pattern (41 bp):
GGCACGATATACTCCATCGTGAAGTTGAAATCGTGGATGTG
Found at i:1507712 original size:42 final size:40
Alignment explanation
Indices: 1507617--1507714 Score: 117
Period size: 42 Copynumber: 2.4 Consensus size: 40
1507607 TTCGTCTTTA
*
1507617 AGTTGAAATCGTGGATGTGGGCATGATATCCTCCATCGTGG
1 AGTTGAAATCGTGGATGTGGGCACGATATCCTCCATCG-GG
* * *
1507658 AGTTGAAATCGTGGACTTGTGGGTACGATATGCTCCGTTC-GG
1 AGTTGAAATCGTGGA--TGTGGGCACGATATCCTCC-ATCGGG
1507700 AGTTGAAATCGTGGA
1 AGTTGAAATCGTGGA
1507715 GGGCCCCTTC
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
41 15 0.30
42 17 0.34
43 16 0.32
44 2 0.04
ACGTcount: A:0.22, C:0.15, G:0.33, T:0.30
Consensus pattern (40 bp):
AGTTGAAATCGTGGATGTGGGCACGATATCCTCCATCGGG
Found at i:1519039 original size:17 final size:16
Alignment explanation
Indices: 1519008--1519046 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
1518998 CAAAATAAAT
1519008 ATAAAGGAAATAGAAA
1 ATAAAGGAAATAGAAA
*
1519024 ATAAATGAAGATAGAAA
1 ATAAAGGAA-ATAGAAA
1519041 ATAAAG
1 ATAAAG
1519047 CAAAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (16 bp):
ATAAAGGAAATAGAAA
Found at i:1519206 original size:39 final size:41
Alignment explanation
Indices: 1519163--1519247 Score: 97
Period size: 39 Copynumber: 2.1 Consensus size: 41
1519153 TAATAACGTA
* *
1519163 TAAATCAAATATAAAAAAT-ATGAAT-AATAA-AATAA-GAGT
1 TAAATAAAATACAAAAAATAAT-AATAAATAATAATAAGGA-T
*
1519202 TAAATAAAATACAAATAATAATAATAAATAATAATAAGGAT
1 TAAATAAAATACAAAAAATAATAATAAATAATAATAAGGAT
1519243 TAAAT
1 TAAAT
1519248 TGAAAGGAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
39 19 0.49
40 7 0.18
41 11 0.28
42 2 0.05
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (41 bp):
TAAATAAAATACAAAAAATAATAATAAATAATAATAAGGAT
Found at i:1520319 original size:18 final size:18
Alignment explanation
Indices: 1520292--1520341 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
1520282 ATAATAAGAA
1520292 ATATATATGAATATAT-T
1 ATATATATGAATATATAT
*
1520309 ATATAATATG-ATTTATAT
1 ATAT-ATATGAATATATAT
1520327 ATATTATAT-AATATA
1 ATA-TATATGAATATA
1520342 ATAACGTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
17 9 0.33
18 17 0.63
19 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (18 bp):
ATATATATGAATATATAT
Found at i:1520326 original size:14 final size:12
Alignment explanation
Indices: 1520295--1520341 Score: 62
Period size: 12 Copynumber: 3.9 Consensus size: 12
1520285 ATAAGAAATA
1520295 TATATGAATATAT
1 TATAT-AATATAT
1520308 TATATAATATGAT
1 TATATAATAT-AT
1520321 T-TAT-ATATAT
1 TATATAATATAT
1520331 TATATAATATA
1 TATATAATATA
1520342 ATAACGTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
12 13 0.42
13 8 0.26
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (12 bp):
TATATAATATAT
Found at i:1525260 original size:57 final size:58
Alignment explanation
Indices: 1525185--1525297 Score: 192
Period size: 57 Copynumber: 2.0 Consensus size: 58
1525175 GCACGCTCTA
* *
1525185 AAATATAAATATCCGATTATAAACCCTACAAAT-GGAATATCTGATTATAAACCCTAC
1 AAATAGAAATATCCGATTATAAACCCTACAAATAGAAATATCTGATTATAAACCCTAC
*
1525242 AAATAGAAATATCTGATTATAAACCCTACAAATAGAAATATCTGATTATAAACCCT
1 AAATAGAAATATCCGATTATAAACCCTACAAATAGAAATATCTGATTATAAACCCT
1525298 TATGTGAAGA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
57 31 0.60
58 21 0.40
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.28
Consensus pattern (58 bp):
AAATAGAAATATCCGATTATAAACCCTACAAATAGAAATATCTGATTATAAACCCTAC
Found at i:1525262 original size:29 final size:29
Alignment explanation
Indices: 1525185--1525297 Score: 192
Period size: 29 Copynumber: 3.9 Consensus size: 29
1525175 GCACGCTCTA
* *
1525185 AAATATAAATATCCGATTATAAACCCTAC
1 AAATAGAAATATCTGATTATAAACCCTAC
*
1525214 AAAT-GGAATATCTGATTATAAACCCTAC
1 AAATAGAAATATCTGATTATAAACCCTAC
1525242 AAATAGAAATATCTGATTATAAACCCTAC
1 AAATAGAAATATCTGATTATAAACCCTAC
1525271 AAATAGAAATATCTGATTATAAACCCT
1 AAATAGAAATATCTGATTATAAACCCT
1525298 TATGTGAAGA
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
28 25 0.32
29 54 0.68
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.28
Consensus pattern (29 bp):
AAATAGAAATATCTGATTATAAACCCTAC
Found at i:1527802 original size:40 final size:38
Alignment explanation
Indices: 1527739--1527942 Score: 114
Period size: 40 Copynumber: 5.6 Consensus size: 38
1527729 AAAAAGTATT
* *
1527739 TTTTTTAAAAAACTA-TATAATATAAATTTTTAAAAATG
1 TTTTTTAAAATATTATTAT-ATATAAATTTTTAAAAATG
* * * *
1527777 TTTTTTAAAACTATGTATTATATATAAAATTTCAAAACTA
1 TTTTTTAAAA-TAT-TATTATATATAAATTTTTAAAAATG
* *
1527817 TTTTTTTAAA-A--A--CTATAT-AATTTTTAAAAATG
1 TTTTTTAAAATATTATTATATATAAATTTTTAAAAATG
* *
1527849 TTTTTT-AAA-A--A--CTATAT-AATTTTCAAAAATG
1 TTTTTTAAAATATTATTATATATAAATTTTTAAAAATG
* *
1527880 -TTTTAAAAATTATATATTATATATAAGTTTTTAAAAATG
1 TTTTTTAAAA-TAT-TATTATATATAAATTTTTAAAAATG
**
1527919 TTTTCAAAAACTATATATTATATA
1 TTTTTTAAAA-TAT-TATTATATA
1527943 CGTTTTTTCA
Statistics
Matches: 134, Mismatches: 19, Indels: 24
0.76 0.11 0.14
Matches are distributed among these distances:
30 4 0.03
31 27 0.20
32 16 0.12
33 6 0.04
35 1 0.01
36 1 0.01
38 16 0.12
39 13 0.10
40 47 0.35
41 3 0.02
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (38 bp):
TTTTTTAAAATATTATTATATATAAATTTTTAAAAATG
Found at i:1527853 original size:31 final size:31
Alignment explanation
Indices: 1527818--1527895 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
1527808 TCAAAACTAT
*
1527818 TTTTTTAAAAACTATATAATTTTTAAAAATG
1 TTTTTTAAAAACTATATAATTTTCAAAAATG
1527849 TTTTTTAAAAACTATATAATTTTCAAAAATG
1 TTTTTTAAAAACTATATAATTTTCAAAAATG
*
1527880 --TTTTAAAAATTATATA
1 TTTTTTAAAAACTATATA
1527896 TTATATATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 15 0.33
31 30 0.67
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (31 bp):
TTTTTTAAAAACTATATAATTTTCAAAAATG
Found at i:1527896 original size:31 final size:30
Alignment explanation
Indices: 1527796--1527895 Score: 103
Period size: 31 Copynumber: 3.2 Consensus size: 30
1527786 ACTATGTATT
* *
1527796 ATATATAAAATTTCAAAACTATTTTTTTAAAAA
1 ATATAT-AATTTTCAAAA--ATGTTTTTAAAAA
* *
1527829 CTATATAATTTTTAAAAATGTTTTTTAAAAA
1 ATATATAATTTTCAAAAATG-TTTTTAAAAA
*
1527860 CTATATAATTTTCAAAAATG-TTTTAAAAA
1 ATATATAATTTTCAAAAATGTTTTTAAAAA
*
1527889 TTATATA
1 ATATATA
1527896 TTATATATAA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
29 15 0.25
30 2 0.03
31 29 0.48
32 9 0.15
33 5 0.08
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (30 bp):
ATATATAATTTTCAAAAATGTTTTTAAAAA
Found at i:1527934 original size:38 final size:38
Alignment explanation
Indices: 1527861--1527949 Score: 103
Period size: 38 Copynumber: 2.3 Consensus size: 38
1527851 TTTTAAAAAC
*
1527861 TATATAA-TTTTCAAAAATGTTTTAAAAAT-TATATATT
1 TATATAAGTTTTTAAAAATGTTTTAAAAATATATATA-T
*
1527898 ATATATAAGTTTTTAAAAATGTTTTCAAAAA-CTATATAT
1 -TATATAAGTTTTTAAAAATGTTTT-AAAAATATATATAT
*
1527937 TATATACGTTTTT
1 TATATAAGTTTTT
1527950 TCAAAAATCA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
38 19 0.41
39 16 0.35
40 11 0.24
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (38 bp):
TATATAAGTTTTTAAAAATGTTTTAAAAATATATATAT
Found at i:1527957 original size:40 final size:40
Alignment explanation
Indices: 1527861--1527942 Score: 125
Period size: 40 Copynumber: 2.1 Consensus size: 40
1527851 TTTTAAAAAC
*
1527861 TATATAA--TTTTCAAAAATGTTTTAAAAATTATATATTA
1 TATATAAGTTTTTCAAAAATGTTTTAAAAACTATATATTA
1527899 TATATAAGTTTTT-AAAAATGTTTTCAAAAACTATATATTA
1 TATATAAGTTTTTCAAAAATGTTTT-AAAAACTATATATTA
1527939 TATA
1 TATA
1527943 CGTTTTTTCA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
38 7 0.17
39 11 0.28
40 22 0.55
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (40 bp):
TATATAAGTTTTTCAAAAATGTTTTAAAAACTATATATTA
Found at i:1528279 original size:12 final size:12
Alignment explanation
Indices: 1528248--1528280 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1528238 TAGTAGTCAA
*
1528248 TCTCGGTCTTCT
1 TCTCGGTTTTCT
1528260 TCTCGGTTTTCT
1 TCTCGGTTTTCT
1528272 TCTCGGTTT
1 TCTCGGTTT
1528281 AAAGACCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.27, G:0.18, T:0.55
Consensus pattern (12 bp):
TCTCGGTTTTCT
Found at i:1528837 original size:35 final size:33
Alignment explanation
Indices: 1528800--1528939 Score: 118
Period size: 35 Copynumber: 3.9 Consensus size: 33
1528790 CTCGAAGGTC
*
1528800 TTTTGTTTCAAGAGAAACATTTTCAAAGGTTCTTCTTTT
1 TTTTGTTTCAAGAGAAACAATTTCAAAGG------TTTT
* *
1528839 ATTTTTGTGTTTCAAGAAAAACAATTTCAAAGATTTT
1 --TTTTGT-T-TCAAGAGAAACAATTTCAAAGGTTTT
*
1528876 TTTTGTGCTTCAAGAGAAGCAATTTCAAAGGTTTT
1 TTTTGT--TTCAAGAGAAACAATTTCAAAGGTTTT
* *
1528911 TTGTGTTTCAAGAGAAACAATCTCAAAGG
1 TTTTGTTTCAAGAGAAACAATTTCAAAGG
1528940 CGACCGATAA
Statistics
Matches: 86, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
33 21 0.24
35 34 0.40
36 1 0.01
37 4 0.05
41 6 0.07
42 1 0.01
43 19 0.22
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (33 bp):
TTTTGTTTCAAGAGAAACAATTTCAAAGGTTTT
Found at i:1528911 original size:33 final size:33
Alignment explanation
Indices: 1528840--1528939 Score: 137
Period size: 33 Copynumber: 3.0 Consensus size: 33
1528830 TCTTCTTTTA
* *
1528840 TTTTTGTGTTTCAAGAAAAACAATTTCAAAGATTT
1 TTTTTGTGTTTCAAGAGAAACAATTTCAAAG--GT
* *
1528875 TTTTTGTGCTTCAAGAGAAGCAATTTCAAAGGT
1 TTTTTGTGTTTCAAGAGAAACAATTTCAAAGGT
*
1528908 TTTTTGTGTTTCAAGAGAAACAATCTCAAAGG
1 TTTTTGTGTTTCAAGAGAAACAATTTCAAAGG
1528940 CGACCGATAA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 30 0.52
35 28 0.48
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (33 bp):
TTTTTGTGTTTCAAGAGAAACAATTTCAAAGGT
Found at i:1529770 original size:110 final size:106
Alignment explanation
Indices: 1529645--1529847 Score: 298
Period size: 110 Copynumber: 1.9 Consensus size: 106
1529635 TATTGTTTCA
* * * ** *
1529645 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGTTGTTTGTTGA
1 AGTCCAATATCCTTCGCTATGAAGTTGAAATTGACTCTGAATAAAACTGAAAAGTTATTTGTTG-
*
1529710 CAGTCAGTCGTCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTCG
65 -A-T-AGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTCG
1529755 AGTCCAATATCCTTCGCTATGAAGTTGAAATTGACTCTGAATAAAACTGAAAAGTTATTTGTTGA
1 AGTCCAATATCCTTCGCTATGAAGTTGAAATTGACTCTGAATAAAACTGAAAAGTTATTTGTTGA
*
1529820 TAGTCGCCCCTTCGCTGTGAAGTTGAGC
66 TAGTCGCCCCTTCACTGTGAAGTTGAGC
1529848 AACCACCATC
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
106 25 0.29
107 1 0.01
108 1 0.01
110 58 0.68
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (106 bp):
AGTCCAATATCCTTCGCTATGAAGTTGAAATTGACTCTGAATAAAACTGAAAAGTTATTTGTTGA
TAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTCG
Found at i:1535974 original size:40 final size:40
Alignment explanation
Indices: 1535910--1535986 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 40
1535900 AAACTACATA
* *
1535910 ATATAAATTTTTAAAAATATTTTTT-AAACTATATATTAT
1 ATATAAAATTTCAAAAATATTTTTTAAAACTATATATTAT
*
1535949 ATATAAAATTTCAAAACTATTTTTTTAAAAACTATATA
1 ATATAAAATTTCAAAAATA-TTTTTT-AAAACTATATA
1535987 ATTTTTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 16 0.50
40 6 0.19
42 10 0.31
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (40 bp):
ATATAAAATTTCAAAAATATTTTTTAAAACTATATATTAT
Done.