Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004693.1 Hibiscus syriacus cultivar Beakdansim tig00010533_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: 2620943
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 8 of 12
Found at i:1616176 original size:22 final size:22
Alignment explanation
Indices: 1616133--1616177 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1616123 CGATAAAAAA
* *
1616133 TTACTTAAAACATTATTATTTT
1 TTACCTAAAACATTAATATTTT
*
1616155 TTACCTAAAACATTAATGTTTT
1 TTACCTAAAACATTAATATTTT
1616177 T
1 T
1616178 CAACATTTCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.51
Consensus pattern (22 bp):
TTACCTAAAACATTAATATTTT
Found at i:1618434 original size:2 final size:2
Alignment explanation
Indices: 1618427--1618459 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1618417 CTCAAAATTA
1618427 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 A
1618460 ATTATGAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1624238 original size:11 final size:11
Alignment explanation
Indices: 1624224--1624248 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1624214 AAATTAATTT
1624224 TAAAATTTAAA
1 TAAAATTTAAA
1624235 TAAAATTTAAA
1 TAAAATTTAAA
1624246 TAA
1 TAA
1624249 TAAGATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TAAAATTTAAA
Found at i:1624243 original size:18 final size:18
Alignment explanation
Indices: 1624210--1624245 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1624200 GTGTTTTACT
* *
1624210 ATTTAAATTAATTTTAAA
1 ATTTAAATAAAATTTAAA
1624228 ATTTAAATAAAATTTAAA
1 ATTTAAATAAAATTTAAA
1624246 TAATAAGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTAAATAAAATTTAAA
Found at i:1625956 original size:67 final size:66
Alignment explanation
Indices: 1625885--1626015 Score: 190
Period size: 67 Copynumber: 2.0 Consensus size: 66
1625875 ATCTTTAATG
*
1625885 TTAATAAAAATTAACTTTTAATAAAAATAAATTTATCAAAAATATTTAATTTCAGTTCAAATATA
1 TTAATAAAAAATAACTTTTAATAAAAATAAATTTAT-AAAAATATTTAATTTCAGTTCAAATATA
1625950 TT
65 TT
* ** * * *
1625952 TTAATAAAAAATAACTTTTAATATAAATTTATTTATTAAAATATTTAATTTTAGTTCATATATA
1 TTAATAAAAAATAACTTTTAATAAAAATAAATTTATAAAAATATTTAATTTCAGTTCAAATATA
1626016 AAATAATAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
66 25 0.44
67 32 0.56
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.45
Consensus pattern (66 bp):
TTAATAAAAAATAACTTTTAATAAAAATAAATTTATAAAAATATTTAATTTCAGTTCAAATATAT
T
Found at i:1626023 original size:66 final size:67
Alignment explanation
Indices: 1625886--1626029 Score: 182
Period size: 66 Copynumber: 2.2 Consensus size: 67
1625876 TCTTTAATGT
* *
1625886 TAATAAAAATTAACTTTTAATAAAAATAAATTTATCAAAAATATTTAATTTCAGTTCAAATATAT
1 TAATAAAAAATAACTTTTAATAAAAATAAATTTATCAAAAATATTTAATTTCAGTTCAAATATAA
**
1625951 TT
66 AA
* ** * * *
1625953 TAATAAAAAATAACTTTTAATATAAATTTATTTAT-TAAAATATTTAATTTTAGTTCATATATAA
1 TAATAAAAAATAACTTTTAATAAAAATAAATTTATCAAAAATATTTAATTTCAGTTCAAATATAA
1626017 AA
66 AA
*
1626019 TAATAATAAAT
1 TAATAAAAAAT
1626030 TTAATGGGTA
Statistics
Matches: 66, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
66 35 0.53
67 31 0.47
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (67 bp):
TAATAAAAAATAACTTTTAATAAAAATAAATTTATCAAAAATATTTAATTTCAGTTCAAATATAA
AA
Found at i:1632983 original size:17 final size:17
Alignment explanation
Indices: 1632963--1632996 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1632953 CGGATCTATC
1632963 AACGAGTCAAGTCGGTT
1 AACGAGTCAAGTCGGTT
* *
1632980 AACGTGTCCAGTCGGTT
1 AACGAGTCAAGTCGGTT
1632997 CGATCCACAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (17 bp):
AACGAGTCAAGTCGGTT
Found at i:1634268 original size:43 final size:40
Alignment explanation
Indices: 1634199--1634296 Score: 117
Period size: 43 Copynumber: 2.4 Consensus size: 40
1634189 ATCTAAATAA
*
1634199 TAAT-TATTAATTTATTAATAAATAATAAAAATAATAGGTTAAC
1 TAATATATT-ATTTTTTAATAAATAAT-AAAATAATA--TTAAC
* *
1634242 TAATATATTATTTTTTAATAAATAATAAAATATTATTAAT
1 TAATATATTATTTTTTAATAAATAATAAAATAATATTAAC
1634282 TAATAATATTATTTT
1 TAAT-ATATTATTTT
1634297 AATACAAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
40 8 0.16
41 10 0.20
42 8 0.16
43 20 0.40
44 4 0.08
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (40 bp):
TAATATATTATTTTTTAATAAATAATAAAATAATATTAAC
Found at i:1634298 original size:18 final size:18
Alignment explanation
Indices: 1634250--1634300 Score: 50
Period size: 21 Copynumber: 2.7 Consensus size: 18
1634240 ACTAATATAT
1634250 TATT-TTTTAATAAATAA
1 TATTATTTTAATAAATAA
* *
1634267 TAAAATATTATTAATTAATAA
1 T--ATTATT-TTAATAAATAA
1634288 TATTATTTTAATA
1 TATTATTTTAATA
1634301 CAAAAAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
17 1 0.04
18 5 0.19
19 7 0.27
20 2 0.08
21 11 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTATTTTAATAAATAA
Found at i:1634681 original size:6 final size:6
Alignment explanation
Indices: 1634642--1634679 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
1634632 GTCGTTGTTC
1634642 TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTT-CA TTT
1 TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTT
1634680 TCTTCTTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.16, C:0.29, G:0.00, T:0.55
Consensus pattern (6 bp):
TTTCCA
Found at i:1635447 original size:30 final size:31
Alignment explanation
Indices: 1635411--1635484 Score: 98
Period size: 30 Copynumber: 2.4 Consensus size: 31
1635401 TTTAAATAGT
* *
1635411 TATTATTTTTTATTAATAT-AT-TTATGTAAA
1 TATTATTTTTTATTAAAATAATATTATAT-AA
1635441 TATTATTTTTTATTAAAATAATATTATATAA
1 TATTATTTTTTATTAAAATAATATTATATAA
1635472 TATTATTTATTTA
1 TATTATTT-TTTA
1635485 GAATTATTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 18 0.46
31 12 0.31
32 9 0.23
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (31 bp):
TATTATTTTTTATTAAAATAATATTATATAA
Found at i:1637236 original size:21 final size:21
Alignment explanation
Indices: 1637206--1637253 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1637196 GCAGGGGTAC
* *
1637206 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
1637227 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
1637248 ATGCCA
1 ATGCCA
1637254 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:1637283 original size:21 final size:21
Alignment explanation
Indices: 1637257--1637350 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
1637247 TATGCCATCT
* *
1637257 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
1637278 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
1637299 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
1637320 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
1637341 CCGCAGGGTT
1 CCGCAGGGTT
1637351 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:1637932 original size:33 final size:34
Alignment explanation
Indices: 1637885--1637969 Score: 118
Period size: 33 Copynumber: 2.5 Consensus size: 34
1637875 AATACAACTT
1637885 ATATTATTCGAAATTTAAAATAAAAATAAAAATA
1 ATATTATTCGAAATTTAAAATAAAAATAAAAATA
* * * *
1637919 ATATTATTC-AAATTTAAATTTAAAATATAAATT
1 ATATTATTCGAAATTTAAAATAAAAATAAAAATA
*
1637952 ATAGTATTCGAAATTTAA
1 ATATTATTCGAAATTTAA
1637970 CATTAAATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
33 28 0.62
34 17 0.38
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (34 bp):
ATATTATTCGAAATTTAAAATAAAAATAAAAATA
Found at i:1637976 original size:34 final size:33
Alignment explanation
Indices: 1637871--1637976 Score: 124
Period size: 34 Copynumber: 3.2 Consensus size: 33
1637861 ATAAATGTTT
* *
1637871 TTAAAATACAACTTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
1637905 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
1637937 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
1637972 TTAAA
1 TTAAA
1637977 TTTCAACTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.41
34 32 0.52
35 1 0.02
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:1646361 original size:34 final size:34
Alignment explanation
Indices: 1646322--1646388 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
1646312 CAAAAAAAAG
1646322 ATAAATTTTAAATATTTACTTTTTATTTAATTAT
1 ATAAATTTTAAATATTTACTTTTTATTTAATTAT
1646356 ATAAATTTTAAATATTTACTTTTTATTTAATTA
1 ATAAATTTTAAATATTTACTTTTTATTTAATTA
1646389 AACCTATTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (34 bp):
ATAAATTTTAAATATTTACTTTTTATTTAATTAT
Found at i:1646384 original size:19 final size:19
Alignment explanation
Indices: 1646328--1646385 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 19
1646318 AAAGATAAAT
1646328 TTTAAATATTTACTTTTTA
1 TTTAAATATTTACTTTTTA
* ***
1646347 TTT-AAT-TATA-TAAAT-
1 TTTAAATATTTACTTTTTA
1646362 TTTAAATATTTACTTTTTA
1 TTTAAATATTTACTTTTTA
1646381 TTTAA
1 TTTAA
1646386 TTAAACCTAT
Statistics
Matches: 27, Mismatches: 8, Indels: 8
0.63 0.19 0.19
Matches are distributed among these distances:
15 3 0.11
16 5 0.19
17 6 0.22
18 5 0.19
19 8 0.30
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTAAATATTTACTTTTTA
Found at i:1647899 original size:13 final size:13
Alignment explanation
Indices: 1647862--1647903 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
1647852 TGAAAATTAA
1647862 ATTTATAAAAAAA-
1 ATTTA-AAAAAAAT
1647875 A-TTAAAAAAAAT
1 ATTTAAAAAAAAT
1647887 ATTTAAAAAAAAT
1 ATTTAAAAAAAAT
1647900 ATTT
1 ATTT
1647904 TGCCGATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 7 0.26
12 4 0.15
13 16 0.59
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
ATTTAAAAAAAAT
Found at i:1658307 original size:257 final size:257
Alignment explanation
Indices: 1657748--1658332 Score: 788
Period size: 257 Copynumber: 2.2 Consensus size: 257
1657738 ATTTTTATTC
*
1657748 AATATATGAATTAGAAACCCGACCCGACACGACTCAAAATAATAAAAAATTATTTTTATTCAATA
1 AATATATGAATTAGAAACCCGA--C--C-CGACTCGAAATAATAAAAAATTATTTTTATTCAATA
* *
1657813 AAAACATTGACTTAATTGAAAAAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAAT
61 AAAACAATGACTTAATTGAAAAAAAAATTATATAGAGAGGGGTATTATTGTAATTATTCCTAAAT
* * *
1657878 ATATAAGGTAAAATTATATTTTTTTTCGGGTCGGTCCGATTTTTTTCACCCTAAACCCGACCCGA
126 ATATAAGGTAAAATTATATATATTTTC--GTCGGTCCGATATTTTTCACCCTAAACCCGACCCGA
* *
1657943 CTCGACCCGAATATCACACTTAAAAAACCTGACTCGACCTGAACAAAATAAAGTTTCACCCGACC
189 CCCGACCCGAATATCACACTTAAAAAA-C--ACTCGACCCGAACAAAATAAAGTTTCACCCGACC
1658008 CGAACCG
251 CGAACCG
* * * *
1658015 AATATATGAATTATAAATCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTCAATAAAAGC
1 AATATATGAATTAGAAACCCGACCCGACTCGAAATAATAAAAAATTATTTTTATTCAATAAAAAC
* *
1658080 AATGACTTAATTG-AAAATATA-TATATAGAGAGGGGTATTATTGTAATTATTCCTAAATATATA
66 AATGACTTAATTGAAAAAAAAATTATATAGAGAGGGGTATTATTGTAATTATTCCTAAATATATA
* * * *
1658143 AGGTAAAGTTATATATATTTTC-T-GGTCGGATATTTTTCACCCTAAACTCGAGCTCGACCCGAC
131 AGGTAAAATTATATATATTTTCGTCGGTCCGATATTTTTCACCCTAAACCCGA-CCCGACCCGAC
*
1658206 CCGAATATCACACTTAAAAAA-AC-CGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAC
195 CCGAATATCACACTTAAAAAACACTCGACCCGAACAAAATAAAGTTTCACCCGACCCGA----A-
1658269 CCG
255 CCG
1658272 AATATATGAATTAGAAACCCGACCCGACTCGAAATAATAAACAAA-TATTTTTTATTCAATA
1 AATATATGAATTAGAAACCCGACCCGACTCGAAATAATAAA-AAATTA-TTTTTATTCAATA
1658333 TATGAATAAG
Statistics
Matches: 288, Mismatches: 22, Indels: 25
0.86 0.07 0.07
Matches are distributed among these distances:
252 32 0.11
253 2 0.01
256 26 0.09
257 74 0.26
258 16 0.06
260 60 0.21
261 6 0.02
262 50 0.17
263 1 0.00
265 1 0.00
267 20 0.07
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.29
Consensus pattern (257 bp):
AATATATGAATTAGAAACCCGACCCGACTCGAAATAATAAAAAATTATTTTTATTCAATAAAAAC
AATGACTTAATTGAAAAAAAAATTATATAGAGAGGGGTATTATTGTAATTATTCCTAAATATATA
AGGTAAAATTATATATATTTTCGTCGGTCCGATATTTTTCACCCTAAACCCGACCCGACCCGACC
CGAATATCACACTTAAAAAACACTCGACCCGAACAAAATAAAGTTTCACCCGACCCGAACCG
Found at i:1659155 original size:13 final size:14
Alignment explanation
Indices: 1659126--1659185 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
1659116 ATAATAAAAA
* *
1659126 AAATAAAAATAATT
1 AAATACAAACAATT
1659140 AAATACAAAC-ATT
1 AAATACAAACAATT
*
1659153 AAATACAAACGA-T
1 AAATACAAACAATT
*
1659166 ACAATTCAAACAATT
1 A-AATACAAACAATT
1659181 AAATA
1 AAATA
1659186 ATAAAAATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
13 15 0.39
14 21 0.55
15 2 0.05
ACGTcount: A:0.63, C:0.12, G:0.02, T:0.23
Consensus pattern (14 bp):
AAATACAAACAATT
Found at i:1672035 original size:24 final size:24
Alignment explanation
Indices: 1672008--1672068 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
1671998 GAGTGTTAAT
1672008 CATGCATACATGTGAAAGAACATA
1 CATGCATACATGTGAAAGAACATA
*
1672032 CATGCATACATATGAAAGAACATA
1 CATGCATACATGTGAAAGAACATA
1672056 CATGCATACATGT
1 CATGCATACATGT
1672069 TAATCATTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.23
Consensus pattern (24 bp):
CATGCATACATGTGAAAGAACATA
Found at i:1676169 original size:60 final size:57
Alignment explanation
Indices: 1676074--1676236 Score: 141
Period size: 60 Copynumber: 2.7 Consensus size: 57
1676064 TCCTTATTTC
* * * *
1676074 AAATTAGTCCCTAAATTTTTAGATATTTAAATTTCAGCCTAAAACTATGACTATCATTCT
1 AAATTAGTCCCAAAATTTTGA-ATATTTCATTTTCA-CCTAAAACTATGA-TATCATTCT
* * * *
1676134 AAATTAGTCCTCAAAATTTTGAACATTTCATTTTCATCAACAAACTATGATTTCATTCT
1 AAATTAGTCC-CAAAATTTTGAATATTTCATTTTCACCTA-AAACTATGATATCATTCT
*
1676193 AAATT-GATCCCCAAACTTTTTGAATATTTCAATTTT-ATCCTAAA
1 AAATTAG-T-CCCAAA-ATTTTGAATATTTC-ATTTTCA-CCTAAA
1676237 TTATATGTAT
Statistics
Matches: 84, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
58 1 0.01
59 20 0.24
60 47 0.56
61 16 0.19
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.40
Consensus pattern (57 bp):
AAATTAGTCCCAAAATTTTGAATATTTCATTTTCACCTAAAACTATGATATCATTCT
Found at i:1678824 original size:21 final size:21
Alignment explanation
Indices: 1678782--1678825 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1678772 CGATAAAAAA
*
1678782 TTACCTAAAAAATTATTATTT
1 TTACCTAAAAAATTAATATTT
* * *
1678803 TTACTTAAAATATTAATGTTT
1 TTACCTAAAAAATTAATATTT
1678824 TT
1 TT
1678826 TAATATTTCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (21 bp):
TTACCTAAAAAATTAATATTT
Found at i:1678931 original size:27 final size:27
Alignment explanation
Indices: 1678868--1678932 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
1678858 AACTTGATAG
*
1678868 AAAAA-AATAA-AATACCAAAACTAAT
1 AAAAATAATAATAATAACAAAACTAAT
* *
1678893 AAAACGT-CTAATAATAACAAAACTAAT
1 AAAA-ATAATAATAATAACAAAACTAAT
1678920 AAAAATAATAATA
1 AAAAATAATAATA
1678933 TTTTTAATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
25 4 0.13
26 4 0.13
27 23 0.74
ACGTcount: A:0.68, C:0.11, G:0.02, T:0.20
Consensus pattern (27 bp):
AAAAATAATAATAATAACAAAACTAAT
Found at i:1680699 original size:57 final size:57
Alignment explanation
Indices: 1680631--1680758 Score: 238
Period size: 57 Copynumber: 2.2 Consensus size: 57
1680621 GTCAGGTTAC
*
1680631 CATTTTGTAACTTTAATAGTTGGAGACTCAATAAAACAACATTATATAGTCGGTGAT
1 CATTTTGTAACTTTAATAGTTGAAGACTCAATAAAACAACATTATATAGTCGGTGAT
*
1680688 CATTTTGTAACTTTAATAGTTGAAGACTCAATAAAGCAACATTATATAGTCGGTGAT
1 CATTTTGTAACTTTAATAGTTGAAGACTCAATAAAACAACATTATATAGTCGGTGAT
1680745 CATTTTGTAACTTT
1 CATTTTGTAACTTT
1680759 CGATAATCAT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 69 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (57 bp):
CATTTTGTAACTTTAATAGTTGAAGACTCAATAAAACAACATTATATAGTCGGTGAT
Found at i:1681643 original size:21 final size:21
Alignment explanation
Indices: 1681601--1681644 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1681591 CGATAAAAAA
*
1681601 TTACCTAAAAAATTATTATTT
1 TTACCTAAAAAATTAATATTT
* * *
1681622 TTACTTAAAATATTAATGTTT
1 TTACCTAAAAAATTAATATTT
1681643 TT
1 TT
1681645 TAATATTTCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (21 bp):
TTACCTAAAAAATTAATATTT
Found at i:1681750 original size:27 final size:27
Alignment explanation
Indices: 1681687--1681751 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
1681677 AACTTGATAG
*
1681687 AAAAA-AATAA-AATACCAAAACTAAT
1 AAAAATAATAATAATAACAAAACTAAT
* *
1681712 AAAACGT-CTAATAATAACAAAACTAAT
1 AAAA-ATAATAATAATAACAAAACTAAT
1681739 AAAAATAATAATA
1 AAAAATAATAATA
1681752 TTTTTAATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
25 4 0.13
26 4 0.13
27 23 0.74
ACGTcount: A:0.68, C:0.11, G:0.02, T:0.20
Consensus pattern (27 bp):
AAAAATAATAATAATAACAAAACTAAT
Found at i:1683514 original size:57 final size:57
Alignment explanation
Indices: 1683447--1683574 Score: 229
Period size: 57 Copynumber: 2.2 Consensus size: 57
1683437 GTCAGGTTAC
*
1683447 CATTTTGTAACTTTAATAGTTGGAGACTCAATAAAACAACATTATATAGTCGGTGAT
1 CATTTTGTAACTTTAATAGTTGAAGACTCAATAAAACAACATTATATAGTCGGTGAT
*
1683504 CATTTTGTAACTTTAATAGTTGAAGACTCAATAAAGCAACATTATATAGTCGGTGAT
1 CATTTTGTAACTTTAATAGTTGAAGACTCAATAAAACAACATTATATAGTCGGTGAT
*
1683561 CGTTTTGTAACTTT
1 CATTTTGTAACTTT
1683575 CGATAATTAT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 68 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (57 bp):
CATTTTGTAACTTTAATAGTTGAAGACTCAATAAAACAACATTATATAGTCGGTGAT
Found at i:1684674 original size:20 final size:19
Alignment explanation
Indices: 1684649--1684702 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
1684639 GCGAAATAAA
1684649 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
1684669 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
1684689 AATCGCAACGCGAT
1 AATCGCAACGCGAT
1684703 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:1684713 original size:21 final size:20
Alignment explanation
Indices: 1684689--1684806 Score: 71
Period size: 20 Copynumber: 5.8 Consensus size: 20
1684679 CAGTTCCCAG
1684689 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
*
1684709 GAATCGCAATGCGA-TA-GTACA
1 -AATCGCAACGCGATTATG-A-A
** * * *
1684730 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTAT-GAA
*
1684752 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGATTATGAA
* **
1684772 AATCGCAACGTGAACAT-ATA
1 AATCGCAACGCGATTATGA-A
1684792 AATCGCAACGCGATT
1 AATCGCAACGCGATT
1684807 CTGACTATCA
Statistics
Matches: 74, Mismatches: 16, Indels: 15
0.70 0.15 0.14
Matches are distributed among these distances:
19 2 0.03
20 34 0.46
21 34 0.46
22 3 0.04
23 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.22
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:1684777 original size:20 final size:20
Alignment explanation
Indices: 1684752--1685027 Score: 218
Period size: 20 Copynumber: 13.7 Consensus size: 20
1684742 GATTTTCCAG
** *
1684752 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGTA
* **
1684772 AATCGCAACGTGAA-CATATA
1 AATCGCAACGCGAATC-CGTA
* *
1684792 AATCGCAACGCGATTCTG-A
1 AATCGCAACGCGAATCCGTA
* * * *
1684811 CTATCACAACGAGTATCCGTAA
1 -AATCGCAACGCGAATCCGT-A
*
1684833 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
1684853 AATCGCAATGAC-AATACGTAA
1 AATCGCAACG-CGAATCCGT-A
*
1684874 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
1684894 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
1684914 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATCCGTA
* *
1684934 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* * *
1684954 AATCGTAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
1684974 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCGT-A
*
1684995 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
1685015 AATCGCAACGCGA
1 AATCGCAACGCGA
1685028 TTTTTAAAGC
Statistics
Matches: 200, Mismatches: 45, Indels: 22
0.75 0.17 0.08
Matches are distributed among these distances:
19 1 0.00
20 148 0.74
21 50 0.25
22 1 0.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:1684856 original size:81 final size:81
Alignment explanation
Indices: 1684752--1685024 Score: 297
Period size: 81 Copynumber: 3.4 Consensus size: 81
1684742 GATTTTCCAG
* ** * * *
1684752 AATCGCAACGCGAATATGAAAATCGCAACGTGAACATATAAATCGCAACGCG-ATTC-TGACTAT
1 AATCGCAACGCGTATCCGTAAATCGCAACGTGAACATATAAATCGCAACGCGTATCCGT-A-AAT
* * *
1684815 CACAACGAGTATCCGTAA
64 CGCAACGAGAATACGTAA
1684833 AATCGCAACGCGTATCCGTAAATCGCAA--TG-ACAATACGTAAAATCGCAACGCGTATCCGTAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGTGAAC-ATA--T-AAATCGCAACGCGTATCCGTAA
1684895 ATCGCAACGAGAATACGT-A
62 ATCGCAACGAGAATACGTAA
* * * ** * *
1684914 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAATCGTAATGCGTATCCGTAAATCG
1 AATCGCAACGCGTATCCGTAAATCGCAACGTGAACATATAAATCGCAACGCGTATCCGTAAATCG
*
1684979 CAACGACAATACGTAA
66 CAACGAGAATACGTAA
1684995 AATCGCAACGCGTATCCGTAAATCGCAACG
1 AATCGCAACGCGTATCCGTAAATCGCAACG
1685025 CGATTTTTAA
Statistics
Matches: 164, Mismatches: 18, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
78 2 0.01
79 5 0.03
80 37 0.23
81 84 0.51
82 28 0.17
83 6 0.04
84 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (81 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGTGAACATATAAATCGCAACGCGTATCCGTAAATCG
CAACGAGAATACGTAA
Found at i:1684928 original size:40 final size:41
Alignment explanation
Indices: 1684817--1685024 Score: 330
Period size: 41 Copynumber: 5.1 Consensus size: 41
1684807 CTGACTATCA
* *
1684817 CAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAAATCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
* *
1684858 CAATGACAATACGTAAAATCGCAACGCGTATCCGTAAATCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
*
1684899 CAACGAGAATACGT-AAATCGCAACGCGTATCTGTAAATCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
* *
1684939 CAACGAGAATACGT-AAATCGTAATGCGTATCCGTAAATCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
*
1684979 CAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
1685020 CAACG
1 CAACG
1685025 CGATTTTTAA
Statistics
Matches: 153, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 75 0.49
41 78 0.51
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (41 bp):
CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
Found at i:1685609 original size:20 final size:20
Alignment explanation
Indices: 1685584--1685691 Score: 105
Period size: 19 Copynumber: 5.5 Consensus size: 20
1685574 TTCTAAATTT
* *
1685584 AAAATCGTAACATGAAAATG
1 AAAATCGCAACACGAAAATG
*
1685604 AAAATCGCAACACGAAAATT
1 AAAATCGCAACACGAAAATG
**
1685624 ACTATCGCAACGA-GAGAAATG
1 AAAATCGCAAC-ACGA-AAATG
* *
1685645 AAAATCGCAACGCG-AAATT
1 AAAATCGCAACACGAAAATG
*
1685664 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
1685683 AAAATCGCA
1 AAAATCGCA
1685692 TTGTGATTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
19 31 0.42
20 28 0.38
21 15 0.20
ACGTcount: A:0.50, C:0.19, G:0.17, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:1685674 original size:40 final size:40
Alignment explanation
Indices: 1685582--1685691 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 40
1685572 GTTTCTAAAT
*
1685582 TTAAAATCGTAACATGA-AAATGAAAATCGCAACACGAAAA
1 TTAAAATCGCAACA-GAGAAATGAAAATCGCAACACGAAAA
** *
1685622 TTACTATCGCAACGAGAGAAATGAAAATCGCAACGCG-AAA
1 TTAAAATCGCAAC-AGAGAAATGAAAATCGCAACACGAAAA
*
1685662 TTAAAATCGCAAC-GCGAAATGAAAATCGCA
1 TTAAAATCGCAACAGAGAAATGAAAATCGCA
1685692 TTGTGATTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
38 16 0.26
40 26 0.43
41 19 0.31
ACGTcount: A:0.49, C:0.18, G:0.16, T:0.16
Consensus pattern (40 bp):
TTAAAATCGCAACAGAGAAATGAAAATCGCAACACGAAAA
Found at i:1685718 original size:19 final size:18
Alignment explanation
Indices: 1685696--1685784 Score: 59
Period size: 19 Copynumber: 5.2 Consensus size: 18
1685686 ATCGCATTGT
1685696 GATTTTCCTTTCGCGTTGC
1 GATTTT-CTTTCGCGTTGC
*
1685715 GA--TTC--TCTCGTTGC
1 GATTTTCTTTCGCGTTGC
* *
1685729 GATTTTAATTTCGCATTGC
1 GATTTT-CTTTCGCGTTGC
*
1685748 GA--TTC--TCTCGTTGC
1 GATTTTCTTTCGCGTTGC
1685762 GATTTTCATTTCGCGTTGC
1 GATTTTC-TTTCGCGTTGC
1685781 GATT
1 GATT
1685785 CTCTCGTTGC
Statistics
Matches: 52, Mismatches: 8, Indels: 20
0.65 0.10 0.25
Matches are distributed among these distances:
14 19 0.37
16 6 0.12
17 4 0.08
19 23 0.44
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.46
Consensus pattern (18 bp):
GATTTTCTTTCGCGTTGC
Found at i:1685728 original size:14 final size:14
Alignment explanation
Indices: 1685709--1685797 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
1685699 TTTCCTTTCG
1685709 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
1685723 CGTTGCGATTTTAATTT
1 CGTTGCGA--TT-CTCT
1685740 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
*
1685756 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1685775 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1685789 CGTTGCGAT
1 CGTTGCGAT
1685798 AGTCATTTCC
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 25 0.42
16 9 0.15
17 9 0.15
19 16 0.27
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1685741 original size:33 final size:33
Alignment explanation
Indices: 1685696--1685846 Score: 194
Period size: 33 Copynumber: 4.4 Consensus size: 33
1685686 ATCGCATTGT
*
1685696 GATTTTCCTTTCGCGTTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
* *
1685729 GATTTTAATTTCGCATTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
1685762 GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
**
1685795 GATAGTCATTTCCGCGTTGCGATAGTCATTCTCTCGTTGC
1 GATTTTCATTT-CGCGTTGC----G--ATTCTCTCGTTGC
1685835 GATTTTCATTTC
1 GATTTTCATTTC
1685847 AACCAAAAGA
Statistics
Matches: 102, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
33 70 0.69
34 8 0.08
38 1 0.01
39 1 0.01
40 22 0.22
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (33 bp):
GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
Found at i:1685844 original size:20 final size:20
Alignment explanation
Indices: 1685782--1685837 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
1685772 TCGCGTTGCG
1685782 ATTCTCTCGTTGCGATAGTC
1 ATTCTCTCGTTGCGATAGTC
*
1685802 ATT-TCCGCGTTGCGATAGTC
1 ATTCT-CTCGTTGCGATAGTC
1685822 ATTCTCTCGTTGCGAT
1 ATTCTCTCGTTGCGAT
1685838 TTTCATTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATAGTC
Found at i:1687754 original size:94 final size:91
Alignment explanation
Indices: 1687548--1687829 Score: 408
Period size: 94 Copynumber: 3.1 Consensus size: 91
1687538 TAGATTGCTT
* * *
1687548 AGTAAATTTATTCGGTTGCTGCCAATACGGCTAAACTGTTTATTC-TT-ACTGTGAAGTTAGTAT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACTGTGAAGTTAGTAT
1687611 TTGTCTTTTGATTTT-TCTTTTGGTTGA
66 TTGTC-TTTG-TTTTGTCTTTTGGTTGA
*
1687638 AGTAAATTTATTCGGTTGCTGCCAATTTTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT-A-ACTGTGAAGTTAGT
1687703 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
64 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * *
1687732 AGTAAATTTGTTCGGTTACTGCCAATTCTGCTAAACTGTGTATTCTTTAGTACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTA--ACTGTGAAGTTAGT
*
1687797 ATTTGTCTTTGTTTTGTATTTTGGTTGA
64 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
1687825 AGTAA
1 AGTAA
1687830 TGCAATCCAT
Statistics
Matches: 175, Mismatches: 10, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
90 41 0.23
91 2 0.01
92 4 0.02
93 22 0.13
94 106 0.61
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.48
Consensus pattern (91 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACTGTGAAGTTAGTAT
TTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:1687954 original size:33 final size:33
Alignment explanation
Indices: 1687917--1687996 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
1687907 AAAAATGACT
* * *
1687917 ATCGCAACGAGAAATAAAAATCGCAATGAGAGA
1 ATCGCAACGAGAAATAAAAATCGCAACGACAAA
*
1687950 ATCGCAACGTA-AAATGAAAATCGCAACGACAAA
1 ATCGCAACG-AGAAATAAAAATCGCAACGACAAA
*
1687983 ATCGCAACGCGAAA
1 ATCGCAACGAGAAA
1687997 CTATAATCGC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
33 39 0.98
34 1 0.03
ACGTcount: A:0.50, C:0.20, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGAGAAATAAAAATCGCAACGACAAA
Found at i:1688104 original size:25 final size:20
Alignment explanation
Indices: 1688039--1688127 Score: 151
Period size: 20 Copynumber: 4.5 Consensus size: 20
1688029 GCGATTATCT
1688039 CATTGCGATAGTCATTTTTG
1 CATTGCGATAGTCATTTTTG
1688059 CATTGCGATAGTCATTTTTG
1 CATTGCGATAGTCATTTTTG
*
1688079 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTTG
*
1688099 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTTG
*
1688119 CGTTGCGAT
1 CATTGCGAT
1688128 TTTAAGTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (20 bp):
CATTGCGATAGTCATTTTTG
Found at i:1688652 original size:18 final size:19
Alignment explanation
Indices: 1688613--1688654 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
1688603 CTCACCTGTC
1688613 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
1688634 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
1688652 ATC
1 ATC
1688655 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:1688708 original size:42 final size:42
Alignment explanation
Indices: 1688609--1688718 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 42
1688599 CCGACTCACC
* * * **
1688609 TGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCCC
1 TGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCAA
* **
1688651 TATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCAA
1 TGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCAA
*
1688693 TGTCATCGTTGAAGAGGT-CCCTCCCA
1 TGTCATCGTTCAAGA-GTCCCCTCCCA
1688719 ACATTCTAGA
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
41 2 0.04
42 50 0.93
43 2 0.04
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (42 bp):
TGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCAA
Found at i:1690094 original size:14 final size:14
Alignment explanation
Indices: 1690075--1690110 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1690065 ATTGTTTAAT
1690075 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1690089 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1690103 TGATTTGT
1 TGATTTGT
1690111 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1690269 original size:19 final size:19
Alignment explanation
Indices: 1690245--1690324 Score: 98
Period size: 19 Copynumber: 4.4 Consensus size: 19
1690235 GCAACGAGAG
1690245 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1690264 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
1690283 AATCTCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
1690297 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
1690317 AATCGCAA
1 AATCGCAA
1690325 CATGAAATTA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 2 0.04
18 3 0.06
19 26 0.51
20 8 0.16
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1690281 original size:52 final size:54
Alignment explanation
Indices: 1690212--1690325 Score: 169
Period size: 52 Copynumber: 2.1 Consensus size: 54
1690202 AAAACAGACT
**
1690212 ATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGCAATGCG-AAATGAAA
1 ATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
* * *
1690265 ATCGCAATGC-GAAATGAAAATCTCAACGAGTGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
1690318 ATCGCAAC
1 ATCGCAAC
1690326 ATGAAATTAG
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
52 30 0.56
53 24 0.44
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (54 bp):
ATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
Found at i:1690398 original size:33 final size:34
Alignment explanation
Indices: 1690341--1690436 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 34
1690331 ATTAGTTTCG
1690341 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
*
1690375 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
** *
1690408 CGTTGCGATAGTCATTTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
1690437 AGTCAATTCC
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 30 0.53
34 27 0.47
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:1690433 original size:20 final size:20
Alignment explanation
Indices: 1690408--1690501 Score: 127
Period size: 20 Copynumber: 4.7 Consensus size: 20
1690398 GCGATTCTCT
*
1690408 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
*
1690428 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
1690448 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
1690468 TGTTGTGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
1690488 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
1690502 AATGAATGTC
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 62 0.97
21 2 0.03
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:1692944 original size:24 final size:24
Alignment explanation
Indices: 1692917--1692970 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1692907 CTGAAAAATC
* *
1692917 ATCAAAATCTGAGTATTGATCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1692941 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1692965 ATCAAA
1 ATCAAA
1692971 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1693845 original size:20 final size:19
Alignment explanation
Indices: 1693832--1693918 Score: 111
Period size: 20 Copynumber: 4.4 Consensus size: 19
1693822 CAGAATCTCG
*
1693832 TTGCGATTTACAGATTCGCA
1 TTGCGATTTAC-GAATCGCA
*
1693852 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACG-AATCGCA
1693872 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACG-AATCGCA
*
1693892 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACG-AATCGCA
1693912 TTGCGAT
1 TTGCGAT
1693919 AGTCAGAATC
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
19 1 0.02
20 63 0.98
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.38
Consensus pattern (19 bp):
TTGCGATTTACGAATCGCA
Found at i:1693891 original size:40 final size:40
Alignment explanation
Indices: 1693832--1693937 Score: 153
Period size: 40 Copynumber: 2.6 Consensus size: 40
1693822 CAGAATCTCG
*
1693832 TTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTACAGAATCGCATTGCGATTTACGTATTCGCA
1693872 TTGCGATTTAC-GTAATCGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTACAG-AATCGCATTGCGATTTACGTATTCGCA
* *
1693912 TTGCGATAGT-CAGAATCGCGTTGCGA
1 TTGCGAT-TTACAGAATCGCATTGCGA
1693938 ATCTGGAAAC
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
39 1 0.02
40 57 0.95
41 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (40 bp):
TTGCGATTTACAGAATCGCATTGCGATTTACGTATTCGCA
Found at i:1693991 original size:20 final size:20
Alignment explanation
Indices: 1693968--1694100 Score: 176
Period size: 20 Copynumber: 6.5 Consensus size: 20
1693958 TACCGGAGAT
1693968 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1693988 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
1694008 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1694028 CGCGTTGCGATTTTACGTATT
1 CGCGTTGCGA-TTTACGGATA
**
1694049 TTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
1694069 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
1694090 CTCGTTGCGAT
1 CGCGTTGCGAT
1694101 AGTCAGAATC
Statistics
Matches: 96, Mismatches: 15, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
20 61 0.64
21 35 0.36
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1694055 original size:41 final size:41
Alignment explanation
Indices: 1693970--1694100 Score: 228
Period size: 41 Copynumber: 3.2 Consensus size: 41
1693960 CCGGAGATCG
1693970 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
1694010 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
1694051 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
1694092 CGTTGCGAT
1 CGTTGCGAT
1694101 AGTCAGAATC
Statistics
Matches: 86, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
40 28 0.33
41 58 0.67
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:1702330 original size:2 final size:2
Alignment explanation
Indices: 1702323--1702359 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1702313 CTAATAACTT
1702323 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1702360 TATTTTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1705022 original size:42 final size:42
Alignment explanation
Indices: 1704963--1705047 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
1704953 AGGAAACGAA
1704963 CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCACACAC
1 CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCACACAC
* *
1705005 CAGAGCTTTGGAAATCAAGCTAGTTAAGAGTGCATCTCACAC
1 CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCACACAC
1705047 C
1 C
1705048 GGTGAGATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.21
Consensus pattern (42 bp):
CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCACACAC
Found at i:1714673 original size:7 final size:7
Alignment explanation
Indices: 1714638--1714671 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1714628 AATTTGGATG
1714638 AAATGTC
1 AAATGTC
1714645 AAATGTC
1 AAATGTC
1714652 AAATGTC
1 AAATGTC
* *
1714659 AAAAGTT
1 AAATGTC
1714666 AAATGT
1 AAATGT
1714672 TATATTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.29
Consensus pattern (7 bp):
AAATGTC
Found at i:1715341 original size:3 final size:3
Alignment explanation
Indices: 1715333--1715386 Score: 74
Period size: 3 Copynumber: 17.3 Consensus size: 3
1715323 CGGGTCTTTT
1715333 TTA TTA TTA TT- TATA TTA TTTA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA T-TA TTA -TTA TTA TTA TTA TTA TTA TTA -TTA TTA
1715380 TTA TTA T
1 TTA TTA T
1715387 GTTTATTAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.02
3 39 0.83
4 7 0.15
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1715361 original size:22 final size:22
Alignment explanation
Indices: 1715333--1715394 Score: 92
Period size: 22 Copynumber: 2.8 Consensus size: 22
1715323 CGGGTCTTTT
1715333 TTATTATTATTTATATTATTTA
1 TTATTATTATTTATATTATTTA
1715355 TTATTATTA-TTATTATTATTTA
1 TTATTATTATTTA-TATTATTTA
1715377 TTATTATTATGTT-TATTA
1 TTATTATTAT-TTATATTA
1715395 ATTACATATT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
21 3 0.08
22 32 0.86
24 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (22 bp):
TTATTATTATTTATATTATTTA
Found at i:1715385 original size:19 final size:19
Alignment explanation
Indices: 1715332--1715386 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1715322 CCGGGTCTTT
1715332 TTTATTATTATT-TATATTA
1 TTTATTATTATTAT-TATTA
1715351 TTTATTATTATTATTATTA
1 TTTATTATTATTATTATTA
1715370 -TTATTTATTATTATTAT
1 TTTA-TTATTATTATTAT
1715387 GTTTATTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.09
19 30 0.88
20 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTATTATTATTATTATTA
Found at i:1715392 original size:19 final size:18
Alignment explanation
Indices: 1715332--1715394 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
1715322 CCGGGTCTTT
*
1715332 TTTATTATTATTTATATTA
1 TTTATTATTA-TTATTTTA
1715351 TTTATTATTATTATTATTA
1 TTTATTATTATTATT-TTA
* *
1715370 -TTATTTATTATTATTATG
1 TTTA-TTATTATTATTTTA
1715388 TTTATTA
1 TTTATTA
1715395 ATTACATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
18 11 0.29
19 27 0.71
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTATTATTATTATTTTA
Found at i:1715531 original size:25 final size:25
Alignment explanation
Indices: 1715502--1715573 Score: 119
Period size: 25 Copynumber: 2.9 Consensus size: 25
1715492 ACCAACCCAT
1715502 CAGATTAGGGTTTCAAACCCTAAAA
1 CAGATTAGGGTTTCAAACCCTAAAA
1715527 CAGATTAGGGTTTCAAACCCTAAAA
1 CAGATTAGGGTTTCAAACCCTAAAA
* *
1715552 CAAATTAGGGTTT-TAACCCTAA
1 CAGATTAGGGTTTCAAACCCTAA
1715574 TCCCCTAACT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
24 8 0.18
25 37 0.82
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.26
Consensus pattern (25 bp):
CAGATTAGGGTTTCAAACCCTAAAA
Found at i:1715746 original size:29 final size:29
Alignment explanation
Indices: 1715704--1715761 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1715694 CGTATCTGAT
1715704 GAACGCATCAACAACAGTGACCAAAATCC
1 GAACGCATCAACAACAGTGACCAAAATCC
1715733 GAACGCATCAACAACAGTGACCAAAATCC
1 GAACGCATCAACAACAGTGACCAAAATCC
1715762 CTCAAACAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.31, G:0.14, T:0.10
Consensus pattern (29 bp):
GAACGCATCAACAACAGTGACCAAAATCC
Found at i:1717566 original size:22 final size:22
Alignment explanation
Indices: 1717541--1717584 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1717531 TCAAACGATG
*
1717541 CAATGTGTGTTATTTTAAGTGA
1 CAATGTATGTTATTTTAAGTGA
* * *
1717563 CAATTTATTTTATTTTATGTGA
1 CAATGTATGTTATTTTAAGTGA
1717585 ATGTAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (22 bp):
CAATGTATGTTATTTTAAGTGA
Found at i:1718359 original size:42 final size:42
Alignment explanation
Indices: 1718300--1718384 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
1718290 AGGAAACGAA
1718300 CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCGCACAC
1 CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCGCACAC
* *
1718342 CAGAGCTTTGGAAATCAAGCTAGTTAAGAGTGCATCTCACAC
1 CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCGCACAC
1718384 C
1 C
1718385 GGTGAGATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.21
Consensus pattern (42 bp):
CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCGCACAC
Found at i:1727975 original size:7 final size:7
Alignment explanation
Indices: 1727940--1727973 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1727930 AATTTGGATG
1727940 AAATGTC
1 AAATGTC
1727947 AAATGTC
1 AAATGTC
1727954 AAATGTC
1 AAATGTC
* *
1727961 AAAAGTT
1 AAATGTC
1727968 AAATGT
1 AAATGT
1727974 TATATTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.29
Consensus pattern (7 bp):
AAATGTC
Found at i:1728642 original size:3 final size:3
Alignment explanation
Indices: 1728634--1728683 Score: 75
Period size: 3 Copynumber: 16.3 Consensus size: 3
1728624 CGGGTCTTTT
1728634 TTA TTA TTA TT- TATA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
1728680 TTA T
1 TTA T
1728684 GTTTATTAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.02
3 39 0.89
4 4 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1728828 original size:25 final size:25
Alignment explanation
Indices: 1728799--1728870 Score: 119
Period size: 25 Copynumber: 2.9 Consensus size: 25
1728789 ACCAACCCAT
1728799 CAGATTAGGGTTTCAAACCCTAAAA
1 CAGATTAGGGTTTCAAACCCTAAAA
1728824 CAGATTAGGGTTTCAAACCCTAAAA
1 CAGATTAGGGTTTCAAACCCTAAAA
* *
1728849 CAAATTAGGGTTT-TAACCCTAA
1 CAGATTAGGGTTTCAAACCCTAA
1728871 TCCCCTAACT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
24 8 0.18
25 37 0.82
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.26
Consensus pattern (25 bp):
CAGATTAGGGTTTCAAACCCTAAAA
Found at i:1729043 original size:29 final size:29
Alignment explanation
Indices: 1729001--1729058 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1728991 CGTATCTGAT
1729001 GAACGCATCAACAACAGTGACCAAAATCC
1 GAACGCATCAACAACAGTGACCAAAATCC
1729030 GAACGCATCAACAACAGTGACCAAAATCC
1 GAACGCATCAACAACAGTGACCAAAATCC
1729059 CTCAAACAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.31, G:0.14, T:0.10
Consensus pattern (29 bp):
GAACGCATCAACAACAGTGACCAAAATCC
Found at i:1730856 original size:22 final size:22
Alignment explanation
Indices: 1730831--1730874 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1730821 TCAAACGATG
*
1730831 CAATGTGTGTTATTTTAAGTGA
1 CAATGTATGTTATTTTAAGTGA
* * *
1730853 CAATTTATTTTATTTTATGTGA
1 CAATGTATGTTATTTTAAGTGA
1730875 ATGTAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (22 bp):
CAATGTATGTTATTTTAAGTGA
Found at i:1731649 original size:42 final size:42
Alignment explanation
Indices: 1731590--1731674 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
1731580 AGGAAACGAA
1731590 CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCGCACAC
1 CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCGCACAC
* *
1731632 CAGAGCTTTGGAAATCAAGCTAGTTAAGAGTGCATCTCACAC
1 CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCGCACAC
1731674 C
1 C
1731675 GGTGAGATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.21
Consensus pattern (42 bp):
CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCGCACAC
Found at i:1739016 original size:2 final size:2
Alignment explanation
Indices: 1739009--1739034 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1738999 TTGTTTAACC
1739009 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1739035 TCTTTTCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1739916 original size:181 final size:181
Alignment explanation
Indices: 1739612--1739950 Score: 660
Period size: 181 Copynumber: 1.9 Consensus size: 181
1739602 TTTACTTACC
* *
1739612 CCTATTCTTACCATCAACGTGGTGAGGTATAGAGTCAAAATAAAACTTTATGAGTTAAATATAAA
1 CCTATTCTCACCATCAACGTGGTGAGGGATAGAGTCAAAATAAAACTTTATGAGTTAAATATAAA
1739677 TAAGAATATAATGATTGTCAGAGTTTAATTATTAAGCTATCAATTTAAAGTAGAGAGGGTTATAA
66 TAAGAATATAATGATTGTCAGAGTTTAATTATTAAGCTATCAATTTAAAGTAGAGAGGGTTATAA
1739742 TCTAATTTTTATAATCCTGAAATTTAAAACCATGGTTATAACTCCCTCTCA
131 TCTAATTTTTATAATCCTGAAATTTAAAACCATGGTTATAACTCCCTCTCA
1739793 CCTATTCTCACCATCAACGTGGTGAGGGATAGAGTCAAAATAAAACTTTATGAGTTAAATATAAA
1 CCTATTCTCACCATCAACGTGGTGAGGGATAGAGTCAAAATAAAACTTTATGAGTTAAATATAAA
1739858 TAAGAATATAATGATTGTCAGAGTTTAATTATTAAGCTATCAATTTAAAGTAGAGAGGGTTATAA
66 TAAGAATATAATGATTGTCAGAGTTTAATTATTAAGCTATCAATTTAAAGTAGAGAGGGTTATAA
1739923 TCTAATTTTTATAATCCTGAAATTTAAA
131 TCTAATTTTTATAATCCTGAAATTTAAA
1739951 GGGACCTAAA
Statistics
Matches: 156, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
181 156 1.00
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (181 bp):
CCTATTCTCACCATCAACGTGGTGAGGGATAGAGTCAAAATAAAACTTTATGAGTTAAATATAAA
TAAGAATATAATGATTGTCAGAGTTTAATTATTAAGCTATCAATTTAAAGTAGAGAGGGTTATAA
TCTAATTTTTATAATCCTGAAATTTAAAACCATGGTTATAACTCCCTCTCA
Found at i:1740874 original size:26 final size:27
Alignment explanation
Indices: 1740821--1740874 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
1740811 ATAATTTTAA
*
1740821 AATTTTAAAAATAAATTCAAATTTAAT
1 AATTTTAAAAATAAATTCAAATTAAAT
* * *
1740848 AATTTTAATAAT-AGTTCAAGTTAAAT
1 AATTTTAAAAATAAATTCAAATTAAAT
1740874 A
1 A
1740875 TTAGTTTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (27 bp):
AATTTTAAAAATAAATTCAAATTAAAT
Found at i:1743998 original size:36 final size:36
Alignment explanation
Indices: 1743957--1744030 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 36
1743947 ATATGTTGAT
* **
1743957 TTAATTTTGAGGGGATGGCATGGTTTAATTTAAATA
1 TTAATTTTGAGGGGATGACATAATTTAATTTAAATA
* * *
1743993 TTAATTTTTAGGTGATGATATAATTTAATTTAAATA
1 TTAATTTTGAGGGGATGACATAATTTAATTTAAATA
1744029 TT
1 TT
1744031 TTTTGATGGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (36 bp):
TTAATTTTGAGGGGATGACATAATTTAATTTAAATA
Found at i:1745483 original size:2 final size:2
Alignment explanation
Indices: 1745476--1745502 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1745466 TATTGATGAT
1745476 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1745503 TTGTTTGTCC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1746540 original size:60 final size:60
Alignment explanation
Indices: 1746367--1746546 Score: 175
Period size: 60 Copynumber: 3.0 Consensus size: 60
1746357 TATAATTTAG
* * * * * ***
1746367 GATGAAATTGAAATATTTAAAAAGTTTAGGGACCAATTTAGAATGAAGATTATAGTTTGGG
1 GATGAAATTGAAATGTTT-AAAAGTTTAAGGACTAATTTAGAATGGAGATCATAGTTTAAA
* * * *
1746428 GATGAAAATGAAATGTTCAAAAGTCTAAGGACTAATTTAGAAT-GATAGTCATAGTTTAAA
1 GATGAAATTGAAATGTTTAAAAGTTTAAGGACTAATTTAGAATGGAGA-TCATAGTTTAAA
* * * *
1746488 GATGGAATTAAAATGTTTAAAAGTTTATGGACTAATTT-GAAATGGAGATCATAGATTAA
1 GATGAAATTGAAATGTTTAAAAGTTTAAGGACTAATTTAG-AATGGAGATCATAGTTTAA
1746547 GGACATATGA
Statistics
Matches: 96, Mismatches: 20, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
59 3 0.03
60 75 0.78
61 18 0.19
ACGTcount: A:0.43, C:0.04, G:0.21, T:0.32
Consensus pattern (60 bp):
GATGAAATTGAAATGTTTAAAAGTTTAAGGACTAATTTAGAATGGAGATCATAGTTTAAA
Found at i:1753798 original size:111 final size:111
Alignment explanation
Indices: 1753666--1753999 Score: 668
Period size: 111 Copynumber: 3.0 Consensus size: 111
1753656 AAATACAATA
1753666 TCACCAAAAATGTTTATAGCCTATGTCACATAAGCCTCAAGGATTTCTCCCTTCAAGGTTGGTTT
1 TCACCAAAAATGTTTATAGCCTATGTCACATAAGCCTCAAGGATTTCTCCCTTCAAGGTTGGTTT
1753731 TGTATTTTGATGTACCTGGAATGAGCAAAACGAAGTGATATTTATG
66 TGTATTTTGATGTACCTGGAATGAGCAAAACGAAGTGATATTTATG
1753777 TCACCAAAAATGTTTATAGCCTATGTCACATAAGCCTCAAGGATTTCTCCCTTCAAGGTTGGTTT
1 TCACCAAAAATGTTTATAGCCTATGTCACATAAGCCTCAAGGATTTCTCCCTTCAAGGTTGGTTT
1753842 TGTATTTTGATGTACCTGGAATGAGCAAAACGAAGTGATATTTATG
66 TGTATTTTGATGTACCTGGAATGAGCAAAACGAAGTGATATTTATG
1753888 TCACCAAAAATGTTTATAGCCTATGTCACATAAGCCTCAAGGATTTCTCCCTTCAAGGTTGGTTT
1 TCACCAAAAATGTTTATAGCCTATGTCACATAAGCCTCAAGGATTTCTCCCTTCAAGGTTGGTTT
1753953 TGTATTTTGATGTACCTGGAATGAGCAAAACGAAGTGATATTTATG
66 TGTATTTTGATGTACCTGGAATGAGCAAAACGAAGTGATATTTATG
1753999 T
1 T
1754000 GACAATTTTG
Statistics
Matches: 223, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 223 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (111 bp):
TCACCAAAAATGTTTATAGCCTATGTCACATAAGCCTCAAGGATTTCTCCCTTCAAGGTTGGTTT
TGTATTTTGATGTACCTGGAATGAGCAAAACGAAGTGATATTTATG
Found at i:1765066 original size:24 final size:24
Alignment explanation
Indices: 1765038--1765141 Score: 93
Period size: 24 Copynumber: 4.3 Consensus size: 24
1765028 AAATATTTTA
* *
1765038 TCTGATTTCTGACTTGAATTTTGT
1 TCTGATTTCTGACCTGAATTCTGT
*
1765062 TCTGA-TACATGACCTGAATTCTGT
1 TCTGATTTC-TGACCTGAATTCTGT
* * *
1765086 TTTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGACCTGAATTCTGT
* * **
1765110 TATGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGACCTGAATTCTGT
*
1765134 TTTGATTT
1 TCTGATTT
1765142 ATGATATATC
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
23 2 0.03
24 61 0.94
25 2 0.03
ACGTcount: A:0.18, C:0.13, G:0.17, T:0.51
Consensus pattern (24 bp):
TCTGATTTCTGACCTGAATTCTGT
Found at i:1765095 original size:12 final size:12
Alignment explanation
Indices: 1765080--1765141 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
1765070 ATGACCTGAA
1765080 TTCTGTTTTGAT
1 TTCTGTTTTGAT
* *
1765092 TTCTGATCTGGA-
1 TTCTG-TTTTGAT
*
1765104 TTCTGTTATGAT
1 TTCTGTTTTGAT
* * *
1765116 ATCTGTTCTGAA
1 TTCTGTTTTGAT
1765128 TTCTGTTTTGAT
1 TTCTGTTTTGAT
1765140 TT
1 TT
1765142 ATGATATATC
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
11 3 0.08
12 30 0.81
13 4 0.11
ACGTcount: A:0.15, C:0.11, G:0.18, T:0.56
Consensus pattern (12 bp):
TTCTGTTTTGAT
Found at i:1765096 original size:48 final size:48
Alignment explanation
Indices: 1765040--1765146 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 48
1765030 ATATTTTATC
* *
1765040 TGATTTCTGA-CTTGAATTTTGTTCTGATA-CATGACCTGAATTCTGTTT
1 TGATTTCTGATC-TGAATTCTGTTATGATATC-TGACCTGAATTCTGTTT
* **
1765088 TGATTTCTGATCTGGATTCTGTTATGATATCTGTTCTGAATTCTGTTT
1 TGATTTCTGATCTGAATTCTGTTATGATATCTGACCTGAATTCTGTTT
*
1765136 TGATTTATGAT
1 TGATTTCTGAT
1765147 ATATCCGTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
48 49 0.96
49 2 0.04
ACGTcount: A:0.20, C:0.12, G:0.18, T:0.50
Consensus pattern (48 bp):
TGATTTCTGATCTGAATTCTGTTATGATATCTGACCTGAATTCTGTTT
Found at i:1767254 original size:13 final size:13
Alignment explanation
Indices: 1767236--1767263 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1767226 GTTACAACCC
1767236 GACCCGACCCGTT
1 GACCCGACCCGTT
1767249 GACCCGACCCGTT
1 GACCCGACCCGTT
1767262 GA
1 GA
1767264 TCGTTGGCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.18, C:0.43, G:0.25, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1769030 original size:24 final size:23
Alignment explanation
Indices: 1769003--1769067 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 23
1768993 ATTTCCGACT
1769003 TGAATTCTGTTCTGATACATGACC
1 TGAATTCTGTTCTGATAC-TGACC
* * *
1769027 TGAATTCTGTTTTGATTTCTGATC
1 TGAATTCTGTTCTGA-TACTGACC
1769051 TGAATTCTGTTCTGATA
1 TGAATTCTGTTCTGATA
1769068 TCTATTTTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 1 0.03
24 32 0.91
25 2 0.06
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (23 bp):
TGAATTCTGTTCTGATACTGACC
Found at i:1769046 original size:12 final size:12
Alignment explanation
Indices: 1769026--1769083 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
1769016 GATACATGAC
*
1769026 CTGAATTCTGTT
1 CTGATTTCTGTT
* *
1769038 TTGATTTCTGAT
1 CTGATTTCTGTT
*
1769050 CTGAATTCTGTT
1 CTGATTTCTGTT
* *
1769062 CTGATATCTATT
1 CTGATTTCTGTT
*
1769074 TTGATTTCTG
1 CTGATTTCTG
1769084 ATATCTCCGT
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.17, C:0.14, G:0.16, T:0.53
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:1770251 original size:263 final size:263
Alignment explanation
Indices: 1769784--1770316 Score: 1066
Period size: 263 Copynumber: 2.0 Consensus size: 263
1769774 CTCCGGTGGC
1769784 CCTAATGTGACATTCCAGATTGGATCGAGTTATCCGCATCGGTCTGAGGGGGTTACAGATCGTGT
1 CCTAATGTGACATTCCAGATTGGATCGAGTTATCCGCATCGGTCTGAGGGGGTTACAGATCGTGT
1769849 ACTACTTTTGTTCGGAGTGAGACTGGTGCTCAGTATATCTCTCAGACAGACCCATTTCGCGAGGT
66 ACTACTTTTGTTCGGAGTGAGACTGGTGCTCAGTATATCTCTCAGACAGACCCATTTCGCGAGGT
1769914 GTATTCCTTGTGTACTATATATATATTCTTCTCTAAGGTTCTAATGTTAAGTCTGGTTCAACATC
131 GTATTCCTTGTGTACTATATATATATTCTTCTCTAAGGTTCTAATGTTAAGTCTGGTTCAACATC
1769979 CGAATCTCGTCTACCTGATCGGATATTGTGCAGACGGGGATCAAAGAATTTAAATTTATGAATAT
196 CGAATCTCGTCTACCTGATCGGATATTGTGCAGACGGGGATCAAAGAATTTAAATTTATGAATAT
1770044 ATG
261 ATG
1770047 CCTAATGTGACATTCCAGATTGGATCGAGTTATCCGCATCGGTCTGAGGGGGTTACAGATCGTGT
1 CCTAATGTGACATTCCAGATTGGATCGAGTTATCCGCATCGGTCTGAGGGGGTTACAGATCGTGT
1770112 ACTACTTTTGTTCGGAGTGAGACTGGTGCTCAGTATATCTCTCAGACAGACCCATTTCGCGAGGT
66 ACTACTTTTGTTCGGAGTGAGACTGGTGCTCAGTATATCTCTCAGACAGACCCATTTCGCGAGGT
1770177 GTATTCCTTGTGTACTATATATATATTCTTCTCTAAGGTTCTAATGTTAAGTCTGGTTCAACATC
131 GTATTCCTTGTGTACTATATATATATTCTTCTCTAAGGTTCTAATGTTAAGTCTGGTTCAACATC
1770242 CGAATCTCGTCTACCTGATCGGATATTGTGCAGACGGGGATCAAAGAATTTAAATTTATGAATAT
196 CGAATCTCGTCTACCTGATCGGATATTGTGCAGACGGGGATCAAAGAATTTAAATTTATGAATAT
1770307 ATG
261 ATG
1770310 CCTAATG
1 CCTAATG
1770317 GATCTTTGGA
Statistics
Matches: 270, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
263 270 1.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (263 bp):
CCTAATGTGACATTCCAGATTGGATCGAGTTATCCGCATCGGTCTGAGGGGGTTACAGATCGTGT
ACTACTTTTGTTCGGAGTGAGACTGGTGCTCAGTATATCTCTCAGACAGACCCATTTCGCGAGGT
GTATTCCTTGTGTACTATATATATATTCTTCTCTAAGGTTCTAATGTTAAGTCTGGTTCAACATC
CGAATCTCGTCTACCTGATCGGATATTGTGCAGACGGGGATCAAAGAATTTAAATTTATGAATAT
ATG
Found at i:1771938 original size:12 final size:12
Alignment explanation
Indices: 1771921--1771954 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1771911 TTTCCATGAC
*
1771921 CTACCACTACTA
1 CTACCACCACTA
1771933 CTACCACCACTA
1 CTACCACCACTA
1771945 CTACCACCAC
1 CTACCACCAC
1771955 CAACAATACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (12 bp):
CTACCACCACTA
Found at i:1771943 original size:15 final size:15
Alignment explanation
Indices: 1771923--1771956 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1771913 TCCATGACCT
*
1771923 ACCACTACTACTACC
1 ACCACTACTACCACC
1771938 ACCACTACTACCACC
1 ACCACTACTACCACC
1771953 ACCA
1 ACCA
1771957 ACAATACCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.50, G:0.00, T:0.15
Consensus pattern (15 bp):
ACCACTACTACCACC
Found at i:1772845 original size:6 final size:6
Alignment explanation
Indices: 1772838--1772876 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
1772828 TTCCATATCT
* *
1772838 ATCCCT ATCCCT ATCCCA ATCCCA ATCCCA ATCCCA ATC
1 ATCCCA ATCCCA ATCCCA ATCCCA ATCCCA ATCCCA ATC
1772877 AATAACGTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.28, C:0.49, G:0.00, T:0.23
Consensus pattern (6 bp):
ATCCCA
Found at i:1781889 original size:30 final size:30
Alignment explanation
Indices: 1781855--1781920 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
1781845 TATATATTAT
* *
1781855 TTATATTATTAAAATTTTTATTATT-TTTA-A
1 TTATAATATT-AAATTTTAATT-TTATTTATA
1781885 TTATAATATTAAATTTTAATTTTATTTATA
1 TTATAATATTAAATTTTAATTTTATTTATA
1781915 TTATAA
1 TTATAA
1781921 AACTGCTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 2 0.06
29 14 0.44
30 16 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
TTATAATATTAAATTTTAATTTTATTTATA
Found at i:1783395 original size:2 final size:2
Alignment explanation
Indices: 1783388--1783415 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1783378 ATATGTAAAG
1783388 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
1783416 GTCTAATTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1787140 original size:21 final size:20
Alignment explanation
Indices: 1787054--1787211 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
1787044 AAATGACCAA
**
1787054 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* * *
1787073 AAAAATCGCAACGCGATCTC
1 CAAAATCGCAACGCGATTTT
* ** *
1787093 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1787113 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1787134 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1787155 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
1787175 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1787196 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1787212 ACACATAAAT
Statistics
Matches: 103, Mismatches: 30, Indels: 11
0.72 0.21 0.08
Matches are distributed among these distances:
19 16 0.16
20 41 0.40
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1787204 original size:20 final size:20
Alignment explanation
Indices: 1787179--1787371 Score: 246
Period size: 20 Copynumber: 9.6 Consensus size: 20
1787169 GATTTTCCAG
* ** *
1787179 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1787199 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1787219 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1787239 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1787259 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1787279 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1787299 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1787319 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
1787340 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1787360 AATCGCAACGCG
1 AATCGCAACGCG
1787372 ATTTTTAAAG
Statistics
Matches: 151, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 131 0.87
21 19 0.13
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1787790 original size:33 final size:33
Alignment explanation
Indices: 1787751--1787821 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1787741 TTCACTTAGA
1787751 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1787784 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1787817 TTTCA
1 TTTCA
1787822 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1787927 original size:21 final size:20
Alignment explanation
Indices: 1787901--1787974 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 20
1787891 TGCAGAAGAG
1787901 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
1787922 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
1787942 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
1787964 TCGCAACGAGA
1 TCGCAACGAGA
1787975 GAATCGCAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 10 0.22
21 25 0.56
22 10 0.22
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:1787981 original size:14 final size:14
Alignment explanation
Indices: 1787962--1788018 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1787952 GAAAAATGAA
1787962 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
1787976 AATCGCAACGCGAAATAAA
1 AATCGCAA--CG--A-GAG
1787995 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1788009 AATCGCAACG
1 AATCGCAACG
1788019 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1787998 original size:33 final size:33
Alignment explanation
Indices: 1787955--1788034 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
1787945 GCAACGAGAA
*
1787955 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATAAAAATCGCAACGAGAGAATCGCAACGCG
1787988 AAATAAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATAAAAATCGCAACGAGAGAATCGCAACGCG
**
1788021 AAACCAAAATCGCA
1 AAATAAAAATCGCA
1788035 TTGCGATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.49, C:0.23, G:0.20, T:0.09
Consensus pattern (33 bp):
AAATAAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:1788086 original size:21 final size:21
Alignment explanation
Indices: 1788060--1788124 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
1788050 CGCGTTGTGA
1788060 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1788081 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1788101 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
1788122 TTC
1 TTC
1788125 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1788121 original size:20 final size:20
Alignment explanation
Indices: 1788059--1788122 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
1788049 TCGCGTTGTG
1788059 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
1788079 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
1788100 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
1788120 ATT
1 ATT
1788123 TCAACCAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.12, C:0.25, G:0.16, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1789968 original size:93 final size:93
Alignment explanation
Indices: 1789809--1790124 Score: 623
Period size: 93 Copynumber: 3.4 Consensus size: 93
1789799 TAGATTGCTT
*
1789809 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1789874 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1789902 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1789967 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1789995 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1790060 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1790088 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1790125 AATACCCTGA
Statistics
Matches: 222, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 222 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1790259 original size:14 final size:14
Alignment explanation
Indices: 1790240--1790296 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1790230 CGAAACTTAA
1790240 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1790254 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1790273 AATCGCAACGACAG
1 AATCGCAACGAGAG
1790287 AATCGCAACG
1 AATCGCAACG
1790297 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1790278 original size:19 final size:18
Alignment explanation
Indices: 1790254--1790345 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 18
1790244 GCAACGAGAG
1790254 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
1790273 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
1790287 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
*
1790306 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAAGAA
*
1790320 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
1790339 AATCGCA
1 AATCGCA
1790346 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 7 0.12
17 6 0.10
18 1 0.02
19 26 0.43
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:1790280 original size:33 final size:33
Alignment explanation
Indices: 1790222--1790345 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
1790212 TAGTTTACTT
* * *
1790222 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
**
1790256 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
1790289 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
1790322 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
1790346 TTGCGATTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:1790322 original size:14 final size:14
Alignment explanation
Indices: 1790271--1790329 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
1790261 ACGCGAAATG
1790271 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1790285 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
1790304 AAAATCGCAACGAC
1 AAAATCGCAACGAC
1790318 AAAATCGCAACG
1 AAAATCGCAACG
1790330 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1790363 original size:19 final size:19
Alignment explanation
Indices: 1790341--1790513 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
1790331 GAAACCAAAA
*
1790341 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1790360 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1790374 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1790393 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1790409 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* **
1790426 TCACGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
1790445 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
1790464 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
1790483 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1790503 TCGTGTTGCGA
1 TCGCGTTGCGA
1790514 AAGTAAACTA
Statistics
Matches: 125, Mismatches: 18, Indels: 21
0.76 0.11 0.13
Matches are distributed among these distances:
14 17 0.14
16 8 0.06
17 8 0.06
19 80 0.64
20 12 0.10
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1790382 original size:14 final size:14
Alignment explanation
Indices: 1790363--1790419 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1790353 TTTCATTTCG
1790363 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1790377 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
1790394 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
1790410 CGTTGCGATT
1 CGTTGCGATT
1790420 TTCATTTCAC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1790452 original size:38 final size:37
Alignment explanation
Indices: 1790341--1790513 Score: 164
Period size: 33 Copynumber: 4.8 Consensus size: 37
1790331 GAAACCAAAA
*
1790341 TCGCATTGCGATTTTCATTTCGCGTTGCGATTC----
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTGTT
* *
1790374 TCTCGTTGCGATTTTCATTTCGCATTGCGATTCTG--
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTGTT
* *
1790409 T--CGTTGCGATTTTCATTTCACGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCT-GTT
** * *
1790445 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCT-GTT
* *
1790483 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
1790514 AAGTAAACTA
Statistics
Matches: 116, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
33 58 0.50
34 1 0.01
35 1 0.01
36 1 0.01
38 44 0.38
39 11 0.09
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (37 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTGTT
Found at i:1792458 original size:14 final size:14
Alignment explanation
Indices: 1792439--1792474 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1792429 ATTGTTTAAT
1792439 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1792453 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1792467 TGATTTGT
1 TGATTTGT
1792475 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1792649 original size:20 final size:19
Alignment explanation
Indices: 1792581--1792659 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 19
1792571 AAAAATGACT
1792581 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1792600 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1792614 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1792633 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1792653 ATCGCAA
1 ATCGCAA
1792660 CGAGAGAATC
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 20 0.38
20 16 0.31
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1792696 original size:19 final size:19
Alignment explanation
Indices: 1792668--1793000 Score: 410
Period size: 19 Copynumber: 18.7 Consensus size: 19
1792658 AACGAGAGAA
*
1792668 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1792687 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1792706 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT
*
1792726 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
1792743 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1792760 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1792779 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1792795 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1792812 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1792831 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1792847 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1792864 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1792883 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1792899 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1792916 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1792935 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1792954 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
1792972 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
1792988 TCGCATTGCGATT
1 TCGCATTGCGATT
1793001 CTCTCGTTGC
Statistics
Matches: 276, Mismatches: 11, Indels: 54
0.81 0.03 0.16
Matches are distributed among these distances:
14 35 0.13
16 28 0.10
17 28 0.10
18 4 0.01
19 135 0.49
20 46 0.17
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1792770 original size:33 final size:33
Alignment explanation
Indices: 1792674--1792876 Score: 187
Period size: 33 Copynumber: 5.8 Consensus size: 33
1792664 AGAATCGCAA
*
1792674 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--T
1792713 TGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
1792747 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
1792785 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
1792818 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1792851 TGCGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
1792877 TTCATTTCGC
Statistics
Matches: 139, Mismatches: 13, Indels: 30
0.76 0.07 0.16
Matches are distributed among these distances:
31 9 0.06
32 5 0.04
33 48 0.35
34 15 0.11
35 5 0.04
36 6 0.04
37 4 0.03
38 11 0.08
39 17 0.12
40 19 0.14
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:1792799 original size:52 final size:52
Alignment explanation
Indices: 1792692--1793014 Score: 521
Period size: 52 Copynumber: 6.2 Consensus size: 52
1792682 TCATTTCGCA
1792692 TTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
1792746 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1792798 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1792850 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1792902 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG
*
1792958 CATTGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1793007 TTGCGATT
1 TTGCGATT
1793015 GTAATTTCCG
Statistics
Matches: 260, Mismatches: 3, Indels: 19
0.92 0.01 0.07
Matches are distributed among these distances:
47 8 0.03
49 2 0.01
50 2 0.01
51 3 0.01
52 166 0.64
53 43 0.17
54 18 0.07
55 3 0.01
56 3 0.01
58 12 0.05
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1793022 original size:33 final size:33
Alignment explanation
Indices: 1792765--1793014 Score: 256
Period size: 33 Copynumber: 7.2 Consensus size: 33
1792755 TCATTTCGCA
1792765 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1792798 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
1792834 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
1792869 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1792902 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
1792938 CATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
1792974 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1793007 TTGCGATT
1 TTGCGATT
1793015 GTAATTTCCG
Statistics
Matches: 180, Mismatches: 18, Indels: 38
0.76 0.08 0.16
Matches are distributed among these distances:
31 9 0.05
32 6 0.03
33 83 0.46
34 14 0.08
35 8 0.04
36 10 0.06
37 5 0.03
38 23 0.13
39 13 0.07
40 9 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1795316 original size:12 final size:12
Alignment explanation
Indices: 1795299--1795323 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1795289 TCTTCGGGGA
1795299 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1795311 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1795323 C
1 C
1795324 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1795532 original size:24 final size:24
Alignment explanation
Indices: 1795498--1795544 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1795488 CTGAAACATC
1795498 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1795522 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1795545 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1796265 original size:20 final size:20
Alignment explanation
Indices: 1796237--1796445 Score: 226
Period size: 20 Copynumber: 10.4 Consensus size: 20
1796227 AAATTTCAGT
* * *
1796237 GTTGTGATTTACGGATTCTC
1 GTTGCGATTTACGGATACGC
*
1796257 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1796277 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1796297 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1796317 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1796337 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1796357 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1796377 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
1796397 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
1796417 GTTGTGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
1796437 GTTGCGATT
1 GTTGCGATT
1796446 CTTGAAAATC
Statistics
Matches: 163, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
19 3 0.02
20 157 0.96
21 3 0.02
ACGTcount: A:0.19, C:0.17, G:0.27, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1798313 original size:56 final size:57
Alignment explanation
Indices: 1798247--1798353 Score: 157
Period size: 57 Copynumber: 1.9 Consensus size: 57
1798237 AGTGCATCGA
1798247 TGCATAAAATGCATTCGATG-TTTCA-AAATAGC-CGGAGTGCATCGATGCATGGCTGG
1 TGCATAAAATGCATTCGATGTTTTCATAAA-A-CTCGGAGTGCATCGATGCATGGCTGG
* *
1798303 TGCATCAAATGCATTCGATGTTTTCATAAAACTCTGAGTGCATCGATGCAT
1 TGCATAAAATGCATTCGATGTTTTCATAAAACTCGGAGTGCATCGATGCAT
1798354 AGTATGTGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
56 20 0.43
57 23 0.50
58 3 0.07
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (57 bp):
TGCATAAAATGCATTCGATGTTTTCATAAAACTCGGAGTGCATCGATGCATGGCTGG
Found at i:1798902 original size:2 final size:2
Alignment explanation
Indices: 1798895--1798941 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1798885 TAGCCAATTG
1798895 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1798937 AT AT A
1 AT AT A
1798942 AATAGCTTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1803842 original size:57 final size:56
Alignment explanation
Indices: 1803722--1803832 Score: 136
Period size: 57 Copynumber: 2.0 Consensus size: 56
1803712 AGAGTGCATC
* *
1803722 GATGCATAAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCT
1 GATGCATCAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATAGCT
* **
1803778 GGTGCATCAAATGCATTCGATGTTTTCATAAA-A-CTTTGAGTGCATCGATGCATAG
1 GATGCATCAAATGCATTCGATG-TTTCA-AAATAGC-CAGAGTGCATCGATGCATAG
1803833 TATATGCATC
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
56 21 0.45
57 23 0.49
58 3 0.06
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.30
Consensus pattern (56 bp):
GATGCATCAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATAGCT
Found at i:1805733 original size:20 final size:21
Alignment explanation
Indices: 1805701--1805753 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
1805691 ATGGAAATGA
*
1805701 TTTGGTTTT-AAAAG-AAAAT
1 TTTGATTTTGAAAAGCAAAAT
1805720 TTTGATTTTGAAAAGCAAAAT
1 TTTGATTTTGAAAAGCAAAAT
**
1805741 GAT-ATTTTGAAAA
1 TTTGATTTTGAAAA
1805754 TTGATTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 8 0.28
20 15 0.52
21 6 0.21
ACGTcount: A:0.43, C:0.02, G:0.15, T:0.40
Consensus pattern (21 bp):
TTTGATTTTGAAAAGCAAAAT
Found at i:1806294 original size:21 final size:21
Alignment explanation
Indices: 1806237--1806297 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
1806227 TGGTTGAAAC
*
1806237 TTTTCTTCTTCATTTTCTGTT
1 TTTTCTTCTTAATTTTCTGTT
* *
1806258 TCTTTGTTATTAATTTT-TGTT
1 T-TTTCTTCTTAATTTTCTGTT
*
1806279 ATTTTCTTCTTGATTTTCT
1 -TTTTCTTCTTAATTTTCT
1806298 CTCGTCAATC
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
21 17 0.55
22 14 0.45
ACGTcount: A:0.10, C:0.13, G:0.07, T:0.70
Consensus pattern (21 bp):
TTTTCTTCTTAATTTTCTGTT
Done.