Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008243.1 Hibiscus syriacus cultivar Beakdansim tig00110893_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: 10265705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 49
Found at i:1091021 original size:20 final size:21
Alignment explanation
Indices: 1090977--1091028 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1090967 ATAGTCAGTA
*
1090977 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1090998 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1091018 TCGCATTGCGA
1 TCGCATTGCGA
1091029 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1091915 original size:12 final size:12
Alignment explanation
Indices: 1091898--1091922 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1091888 ATATAATCCT
1091898 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1091910 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1091922 G
1 G
1091923 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1094234 original size:19 final size:19
Alignment explanation
Indices: 1094212--1094276 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
1094202 GGAAATTACT
1094212 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1094231 ATCGCAAT--G--A-GAAA
1 ATCGCAATGCGAAATGAAA
1094245 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1094264 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1094277 TTTAATTTCG
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 12 0.30
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 24 0.60
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1094246 original size:14 final size:14
Alignment explanation
Indices: 1094227--1094258 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1094217 AATGCGAAAT
1094227 GAAAATCGCAATGA
1 GAAAATCGCAATGA
*
1094241 GAAAATCGCAATGC
1 GAAAATCGCAATGA
1094255 GAAA
1 GAAA
1094259 TGAAAATCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.16, G:0.22, T:0.12
Consensus pattern (14 bp):
GAAAATCGCAATGA
Found at i:1094323 original size:33 final size:33
Alignment explanation
Indices: 1094272--1094361 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
1094262 AAATCGCAAC
* *
1094272 GCGAATTTAATTTCGCGTTGCGATTCTCTCATT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCATT
1094305 GCGATTTTCATTTCGCGTTGCGATTCTCTCATT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCATT
* *
1094338 GCAATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
1094362 AGTACTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.17, C:0.22, G:0.18, T:0.43
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCATT
Found at i:1094487 original size:14 final size:15
Alignment explanation
Indices: 1094468--1094504 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
1094458 CATCAATTAA
1094468 ACAAATCAA-CTTTT
1 ACAAATCAACCTTTT
1094482 ACAAAT-AACCTTTT
1 ACAAATCAACCTTTT
1094496 ACAAATCAA
1 ACAAATCAA
1094505 TTAAACAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.10
14 17 0.81
15 2 0.10
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (15 bp):
ACAAATCAACCTTTT
Found at i:1095925 original size:21 final size:21
Alignment explanation
Indices: 1095859--1095925 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1095849 GTGAATCGGG
1095859 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAATGGTGGGAGGGGA
* * * ** * *
1095879 CCTCTTTAACGATGACAGTGGC
1 -CTCTTGAATGGTGGGAGGGGA
1095901 CTCTTGAATGGTGGGAGGGGA
1 CTCTTGAATGGTGGGAGGGGA
1095922 CTCT
1 CTCT
1095926 CGAGGAATGA
Statistics
Matches: 31, Mismatches: 14, Indels: 2
0.66 0.30 0.04
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.18, G:0.36, T:0.27
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGGGGA
Found at i:1095944 original size:42 final size:42
Alignment explanation
Indices: 1095890--1096065 Score: 190
Period size: 42 Copynumber: 4.2 Consensus size: 42
1095880 CTCTTTAACG
* *
1095890 ATGACAGTGGCCTCTTGAATGGTGGGAGGGGACTCTCGAGGA
1 ATGACAGGGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGA
* * * * * * *
1095932 ATGATAGGGGCCTCTTCAACGATAGGAGTGGACTCTTGAGGG
1 ATGACAGGGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGA
* *
1095974 ATGACAGTGGCCTCTTGAACAGTGGGAGGGGACTCTCGAGGA
1 ATGACAGGGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGA
* * * * * * *
1096016 ATGATAGGGGCCTCTTCAACGATAGGAGTGGACTCTTGAGGG
1 ATGACAGGGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGA
1096058 ATGACAGG
1 ATGACAGG
1096066 CGAGTCGGTC
Statistics
Matches: 106, Mismatches: 28, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 106 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.22
Consensus pattern (42 bp):
ATGACAGGGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGA
Found at i:1096000 original size:84 final size:84
Alignment explanation
Indices: 1095889--1096064 Score: 334
Period size: 84 Copynumber: 2.1 Consensus size: 84
1095879 CCTCTTTAAC
**
1095889 GATGACAGTGGCCTCTTGAATGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACAGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1095954 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
1095973 GATGACAGTGGCCTCTTGAACAGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACAGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1096038 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
1096057 GATGACAG
1 GATGACAG
1096065 GCGAGTCGGT
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 90 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.22
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACAGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:1096452 original size:78 final size:79
Alignment explanation
Indices: 1096302--1096454 Score: 238
Period size: 78 Copynumber: 1.9 Consensus size: 79
1096292 AAGACAAAAC
1096302 AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGACAGCAACCGAA
1 AAAGACAAATACTAACTTCACAGTGTTAAAGAAT--A-AGTTTAGCAGAATTGACAGCAACCGAA
1096367 TAAATTTACTTCAACCA
63 TAAATTTACTTCAACCA
* *
1096384 AAAGACAAATACTAACTTCACAGTGTTAATA-AAT-AGTTTAGCAGTATTGGCAGCAACCGAATA
1 AAAGACAAATACTAACTTCACAGTGTTAA-AGAATAAGTTTAGCAGAATTGACAGCAACCGAATA
1096447 AATTTACT
65 AATTTACT
1096455 AAGCAATATA
Statistics
Matches: 68, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
78 35 0.51
82 32 0.47
83 1 0.01
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (79 bp):
AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAGTTTAGCAGAATTGACAGCAACCGAATAA
ATTTACTTCAACCA
Found at i:1098218 original size:33 final size:33
Alignment explanation
Indices: 1098164--1098251 Score: 117
Period size: 33 Copynumber: 2.6 Consensus size: 33
1098154 ACGAGATAAT
*
1098164 GAGAATCACAACGCGGAAATGACTA-C-TGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGTG--ACGA
*
1098198 GAGAATCGCAAGGCGAAATGACTATCGTGACGA
1 GAGAATCGCAACGCGAAATGACTATCGTGACGA
1098231 GAGAATCGCAACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
1098252 AAATCGCAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
33 34 0.69
34 13 0.27
35 2 0.04
ACGTcount: A:0.40, C:0.20, G:0.27, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGTGACGA
Found at i:1098258 original size:19 final size:19
Alignment explanation
Indices: 1098234--1098298 Score: 121
Period size: 19 Copynumber: 3.4 Consensus size: 19
1098224 GTGACGAGAG
*
1098234 AATCGCAACGCGAAATGAA
1 AATCGCAACACGAAATGAA
1098253 AATCGCAACACGAAATGAA
1 AATCGCAACACGAAATGAA
1098272 AATCGCAACACGAAATGAA
1 AATCGCAACACGAAATGAA
1098291 AATCGCAA
1 AATCGCAA
1098299 TGCGATTTTG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 45 1.00
ACGTcount: A:0.51, C:0.22, G:0.17, T:0.11
Consensus pattern (19 bp):
AATCGCAACACGAAATGAA
Found at i:1098332 original size:19 final size:19
Alignment explanation
Indices: 1098299--1098343 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1098289 AAAATCGCAA
*
1098299 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
1098318 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
1098337 TGCGATT
1 TGCGATT
1098344 CTCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:1098925 original size:20 final size:20
Alignment explanation
Indices: 1098897--1098949 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1098887 GCGCTATGTA
*
1098897 AATCGCGTTGCGAAAGTCAG
1 AATCACGTTGCGAAAGTCAG
1098917 AATCACGTTGCGAAAGTCAG
1 AATCACGTTGCGAAAGTCAG
* *
1098937 TATCTCGTTGCGA
1 AATCACGTTGCGA
1098950 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (20 bp):
AATCACGTTGCGAAAGTCAG
Found at i:1103133 original size:20 final size:20
Alignment explanation
Indices: 1103096--1103133 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1103086 CTTTCCTCGT
*
1103096 ACAACATAAACTATAAGAGC
1 ACAACATAAACTAGAAGAGC
1103116 ACAACA-AAACTTAGAAGA
1 ACAACATAAAC-TAGAAGA
1103134 TAATCATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.58, C:0.18, G:0.11, T:0.13
Consensus pattern (20 bp):
ACAACATAAACTAGAAGAGC
Found at i:1104070 original size:2 final size:2
Alignment explanation
Indices: 1104063--1104095 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1104053 CTGCTCAGGC
1104063 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 T
1104096 CAGAAAACAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1105354 original size:21 final size:21
Alignment explanation
Indices: 1105328--1105368 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1105318 GACTATCGTA
1105328 TTGCGATTTCCCAAATTCGCG
1 TTGCGATTTCCCAAATTCGCG
* *
1105349 TTGCGATTTTCCTAATTCGC
1 TTGCGATTTCCCAAATTCGC
1105369 AATGCGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.27, G:0.17, T:0.39
Consensus pattern (21 bp):
TTGCGATTTCCCAAATTCGCG
Found at i:1105374 original size:21 final size:21
Alignment explanation
Indices: 1105329--1105375 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1105319 ACTATCGTAT
**
1105329 TGCGATTTCCCAAATTCGCGT
1 TGCGATTTCCCAAATTCGCAA
* *
1105350 TGCGATTTTCCTAATTCGCAA
1 TGCGATTTCCCAAATTCGCAA
1105371 TGCGA
1 TGCGA
1105376 ATACGTAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TGCGATTTCCCAAATTCGCAA
Found at i:1105390 original size:20 final size:20
Alignment explanation
Indices: 1105365--1105587 Score: 349
Period size: 20 Copynumber: 11.1 Consensus size: 20
1105355 TTTTCCTAAT
1105365 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
1105385 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
1105406 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATACGTAAA
1105426 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1105446 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1105466 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
1105486 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1105506 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1105526 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1105546 TTGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1105566 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
1105586 TC
1 TC
1105588 ACAACGAGAT
Statistics
Matches: 186, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
19 1 0.01
20 169 0.91
21 16 0.09
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1108930 original size:20 final size:20
Alignment explanation
Indices: 1108905--1108994 Score: 128
Period size: 20 Copynumber: 4.5 Consensus size: 20
1108895 TTCATTTGAT
1108905 TATCGCAACGC-GAATATGAC
1 TATCGCAACGCGGAA-ATGAC
*
1108925 TATCGCAACACGGAAATGAC
1 TATCGCAACGCGGAAATGAC
* *
1108945 TATCGCAATGCGGAATTGAC
1 TATCGCAACGCGGAAATGAC
*
1108965 TATCGCAATGCGGAAATGAC
1 TATCGCAACGCGGAAATGAC
1108985 TATCGCAACG
1 TATCGCAACG
1108995 AGAGAATCGC
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 60 0.95
21 3 0.05
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.20
Consensus pattern (20 bp):
TATCGCAACGCGGAAATGAC
Found at i:1109023 original size:33 final size:33
Alignment explanation
Indices: 1108966--1109046 Score: 101
Period size: 33 Copynumber: 2.4 Consensus size: 33
1108956 GGAATTGACT
**
1108966 ATCGCAATGCGGAAATGACTATCGCAACGAG-AGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGTA-A
*
1109000 ATCGCAATGCGAAATTAAAATCGCAACGAGTAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGTAA
*
1109033 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
1109047 GTTTCGCGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
33 31 0.74
34 11 0.26
ACGTcount: A:0.42, C:0.21, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGTAA
Found at i:1109096 original size:34 final size:34
Alignment explanation
Indices: 1109053--1109148 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 34
1109043 GAAAGTTTCG
*
1109053 CGTTGCGATTTTCATTTTTGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
*
1109087 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
** *
1109120 CGTTGCGATAGTCATTTCCGCATTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
1109149 AGTCTGTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 29 0.52
34 27 0.48
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:1110736 original size:42 final size:42
Alignment explanation
Indices: 1110657--1110749 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
1110647 CCTCTTCAAC
* * *
1110657 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
1110699 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
1110741 GATGACAGG
1 GATGACAGG
1110750 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:1111247 original size:20 final size:20
Alignment explanation
Indices: 1111224--1111359 Score: 93
Period size: 20 Copynumber: 7.5 Consensus size: 20
1111214 GAAACTTAAA
1111224 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
1111244 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
1111264 ATCGCAA--CG-AGA-GA--
1 ATCGCAACGCGAAAATGACT
* **
1111278 ATCGCAATGCG-AAATGAAA
1 ATCGCAACGCGAAAATGACT
1111297 ATCGCAA--C-AACAA--A--
1 ATCGCAACGCGAA-AATGACT
1111311 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
1111331 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1111351 ATCGCAACG
1 ATCGCAACG
1111360 AGAGAATCGC
Statistics
Matches: 95, Mismatches: 7, Indels: 28
0.73 0.05 0.22
Matches are distributed among these distances:
14 14 0.15
16 10 0.11
17 8 0.08
18 5 0.05
19 7 0.07
20 51 0.54
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1111282 original size:34 final size:34
Alignment explanation
Indices: 1111244--1111337 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 34
1111234 GAAAATGACT
* * *
1111244 ATCGCAATGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGACTATCGCAACAACAAA
**
1111278 ATCGCAATGCG-AAATGAAAATCGCAACAACAAA
1 ATCGCAATGCGAAAATGACTATCGCAACAACAAA
*
1111311 ATCGCAACGCGAAAATGACTATCGCAA
1 ATCGCAATGCGAAAATGACTATCGCAA
1111338 TGCGAATTTG
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 27 0.53
34 24 0.47
ACGTcount: A:0.45, C:0.22, G:0.19, T:0.14
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGACTATCGCAACAACAAA
Found at i:1111430 original size:34 final size:35
Alignment explanation
Indices: 1111382--1111493 Score: 120
Period size: 34 Copynumber: 3.1 Consensus size: 35
1111372 TGCGATTTTC
*
1111382 ATTTCGCATTGCGATTCTTTCGTTGTGATAGTCAA
1 ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAA
1111417 ATTT-GCATTGCGATAGTCATTTTCGCATTGCGATAGTC-A
1 ATTTCGCATTGCGAT--TC--TTTCG--TTGCGATAGTCAA
* * *
1111456 TTTTCGCATTGCGATTCTCTCATTGCGATAGTCAA
1 ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAA
1111491 ATT
1 ATT
1111494 CGTATTACGA
Statistics
Matches: 64, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
34 21 0.33
35 7 0.11
36 5 0.08
38 7 0.11
39 4 0.06
40 20 0.31
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (35 bp):
ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAA
Found at i:1111433 original size:20 final size:20
Alignment explanation
Indices: 1111408--1111527 Score: 119
Period size: 20 Copynumber: 6.3 Consensus size: 20
1111398 CTTTCGTTGT
*
1111408 GATAGTCAAATTT-GCATTGC
1 GATAGTC-ATTTTCGCATTGC
1111428 GATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
1111448 GATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
*
1111468 GAT--TC----TCTCATTGC
1 GATAGTCATTTTCGCATTGC
** * *
1111482 GATAGTCAAATTCGTATTAC
1 GATAGTCATTTTCGCATTGC
*
1111502 GATAGTCATTTTCGCGTTGC
1 GATAGTCATTTTCGCATTGC
1111522 GATAGT
1 GATAGT
1111528 AAACTATTCT
Statistics
Matches: 83, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
14 11 0.13
16 2 0.02
18 2 0.02
19 4 0.05
20 64 0.77
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.38
Consensus pattern (20 bp):
GATAGTCATTTTCGCATTGC
Found at i:1111467 original size:74 final size:73
Alignment explanation
Indices: 1111366--1111527 Score: 225
Period size: 74 Copynumber: 2.2 Consensus size: 73
1111356 AACGAGAGAA
* ** * * * * *
1111366 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGTGATAGTCAAATTTGCATTGCGAT
1 TCGCATTGCGATAGTCATTTCGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTACGAT
1111431 AGTCATTT
66 AGTCATTT
*
1111439 TCGCATTGCGATAGTCATTTTCGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGTATTACGA
1 TCGCATTGCGATAGTCA-TTTCGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTACGA
1111504 TAGTCATTT
65 TAGTCATTT
*
1111513 TCGCGTTGCGATAGT
1 TCGCATTGCGATAGT
1111528 AAACTATTCT
Statistics
Matches: 78, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
73 14 0.18
74 64 0.82
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (73 bp):
TCGCATTGCGATAGTCATTTCGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTACGAT
AGTCATTT
Found at i:1111480 original size:54 final size:54
Alignment explanation
Indices: 1111422--1111524 Score: 161
Period size: 54 Copynumber: 1.9 Consensus size: 54
1111412 GTCAAATTTG
** *
1111422 CATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCGATTCTCT
1 CATTGCGATAGTCAAATTCGCATTACGATAGTCATTTTCGCATTGCGATTCTCT
* *
1111476 CATTGCGATAGTCAAATTCGTATTACGATAGTCATTTTCGCGTTGCGAT
1 CATTGCGATAGTCAAATTCGCATTACGATAGTCATTTTCGCATTGCGAT
1111525 AGTAAACTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.39
Consensus pattern (54 bp):
CATTGCGATAGTCAAATTCGCATTACGATAGTCATTTTCGCATTGCGATTCTCT
Found at i:1113397 original size:20 final size:20
Alignment explanation
Indices: 1113374--1113428 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1113364 CTGAAACTTT
1113374 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
1113394 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
** *
1113414 CTATCGCAACGCGAA
1 AAATCGCAACACGAA
1113429 TTTAACTATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.11
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:1113514 original size:20 final size:20
Alignment explanation
Indices: 1113489--1113535 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1113479 GATTCTCTTG
1113489 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
1113509 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
1113529 TTGCGAT
1 TTGCGAT
1113536 TCACTCGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:1114146 original size:20 final size:20
Alignment explanation
Indices: 1114123--1114215 Score: 123
Period size: 20 Copynumber: 4.7 Consensus size: 20
1114113 CGATAGTCAG
1114123 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1114143 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
1114163 AATCGCATTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
1114183 AATCGCGTTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1114203 ATTCGTATTGCGA
1 ATTCGCATTGCGA
1114216 ATTAGGAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1114169 original size:40 final size:40
Alignment explanation
Indices: 1114125--1114215 Score: 137
Period size: 40 Copynumber: 2.3 Consensus size: 40
1114115 ATAGTCAGAT
*
1114125 TCGCATTGCGATTTACGTATTCGCGTTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAATCGCGTTGCGATTTACGTAA
* * *
1114165 TCGCATTGTGATTTACGTAATCGCGTTGTGATTTACGTAT
1 TCGCATTGCGATTTACGTAATCGCGTTGCGATTTACGTAA
*
1114205 TCGTATTGCGA
1 TCGCATTGCGA
1114216 ATTAGGAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.40
Consensus pattern (40 bp):
TCGCATTGCGATTTACGTAATCGCGTTGCGATTTACGTAA
Found at i:1114247 original size:21 final size:21
Alignment explanation
Indices: 1114214--1114257 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1114204 TTCGTATTGC
1114214 GAATTAGGAAAATCGCAACGT
1 GAATTAGGAAAATCGCAACGT
* * *
1114235 GAATTTGGGAAATCGCAATGT
1 GAATTAGGAAAATCGCAACGT
1114256 GA
1 GA
1114258 TAGTCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.27, T:0.23
Consensus pattern (21 bp):
GAATTAGGAAAATCGCAACGT
Found at i:1116375 original size:21 final size:21
Alignment explanation
Indices: 1116303--1116375 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
1116293 TATGACATCT
1116303 CCACAGGGTTACATTCCTAGC
1 CCACAGGGTTACATTCCTAGC
* *
1116324 CCTCAGGTTTACATTCCTAGC
1 CCACAGGGTTACATTCCTAGC
* *
1116345 CCGCCA-GGTTACATGCCTAGC
1 CC-ACAGGGTTACATTCCTAGC
1116366 CCACAGGGTT
1 CCACAGGGTT
1116376 TTATAACACC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
20 2 0.05
21 40 0.91
22 2 0.05
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.25
Consensus pattern (21 bp):
CCACAGGGTTACATTCCTAGC
Found at i:1117082 original size:14 final size:14
Alignment explanation
Indices: 1117063--1117093 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1117053 ATTTATCCTT
1117063 AACATATACATTAA
1 AACATATACATTAA
1117077 AACATATACATTAA
1 AACATATACATTAA
1117091 AAC
1 AAC
1117094 CAACTTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (14 bp):
AACATATACATTAA
Found at i:1117331 original size:133 final size:133
Alignment explanation
Indices: 1117091--1117383 Score: 433
Period size: 133 Copynumber: 2.2 Consensus size: 133
1117081 TATACATTAA
* * * **
1117091 AACCAACTTATCACTTCACATTTATTCGTAAGAACTTGTCGGTTCTCATTCCATACAATTTCAAT
1 AACCAACTTATCACTTCACATTTATTCGTAAAAACATGTCGATGATCATTCCATACAATTTCAAT
* * * * *
1117156 GTCACAACCAACTTTTCACTTCACATTTATTCAATTTATCCATAAAAGTTTATCCAGTTTATTTA
66 GTCACAACCAACTTATCACTTCAAATTTATTCAATTTATCCATAAAAGTTTATCCAATATATTCA
1117221 AAC
131 AAC
*
1117224 ATCCAACTTATCACTTCACATTTATTCGTAAAAACATGTCGATGATCATTCCATACAATTTCAAT
1 AACCAACTTATCACTTCACATTTATTCGTAAAAACATGTCGATGATCATTCCATACAATTTCAAT
* * *
1117289 GTCACAACCAACTTATCACTTCAAATTTATTCAATTTATCCATAACATTTTATCTAATATATTCA
66 GTCACAACCAACTTATCACTTCAAATTTATTCAATTTATCCATAAAAGTTTATCCAATATATTCA
1117354 AAC
131 AAC
* * *
1117357 AAACAACTGATCAATTCACATTTATTC
1 AACCAACTTATCACTTCACATTTATTC
1117384 AATTTATCCA
Statistics
Matches: 142, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
133 142 1.00
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (133 bp):
AACCAACTTATCACTTCACATTTATTCGTAAAAACATGTCGATGATCATTCCATACAATTTCAAT
GTCACAACCAACTTATCACTTCAAATTTATTCAATTTATCCATAAAAGTTTATCCAATATATTCA
AAC
Found at i:1117386 original size:63 final size:63
Alignment explanation
Indices: 1117292--1117419 Score: 202
Period size: 63 Copynumber: 2.0 Consensus size: 63
1117282 TTTCAATGTC
* * * *
1117292 ACAACCAACTTATCACTTCAAATTTATTCAATTTATCCATAACATTTTATCTAATATATTCAA
1 ACAAACAACTGATCAATTCAAATTTATTCAATTTATCCATAACATTTTATCCAATATATTCAA
* *
1117355 ACAAACAACTGATCAATTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATTCAA
1 ACAAACAACTGATCAATTCAAATTTATTCAATTTATCCATAACATTTTATCCAATATATTCAA
1117418 AC
1 AC
1117420 TTCACATAAC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.40, C:0.21, G:0.01, T:0.38
Consensus pattern (63 bp):
ACAAACAACTGATCAATTCAAATTTATTCAATTTATCCATAACATTTTATCCAATATATTCAA
Found at i:1117893 original size:117 final size:117
Alignment explanation
Indices: 1117663--1118227 Score: 827
Period size: 117 Copynumber: 4.9 Consensus size: 117
1117653 AGAAATAATA
* * * *
1117663 GGTATTGACATGAATAGT--TCCCGGGGGACATGAGTGACATAATAGGGCAATAATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* * * * *
1117726 TCTAACAAAACAATCGAAGGCGCACCCTCGGGAACGCGTTTTCACCACTTTG
66 TCTGACAAAATAATGGAAGGCGCCCCCTCGGGAACGCGCTTTCACCACTTTG
* *
1117778 GGTACTGACATGAATAGTGCCCCCAAGGGACATGAGTGACATAATAGGGCAATAATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
*
1117843 TCTGACAAAATAATTGAAGGCGCCCCCTCGGGAACGCGCTTTCACCACTTTG
66 TCTGACAAAATAATGGAAGGCGCCCCCTCGGGAACGCGCTTTCACCACTTTG
*
1117895 GGTACTGACATGAATAGTGCCCCCGAGGGACATAAGTGACATAATAGGGCAATGATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
** *
1117960 TCTGACAAAATAATAAAAGGCGCGCCCTCGGGAACGCGCTTTCACCACTTTG
66 TCTGACAAAATAATGGAAGGCGCCCCCTCGGGAACGCGCTTTCACCACTTTG
* *
1118012 GGTACTGACATGAATAGTGCCCCCGAGGGATATGAGTGACATAATAGGGCAATGATAACATATTA
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* * * *
1118077 TCTGATAAAATAATGGAATGCGCGCCCC-CAGGAACACGCTTTCACCACTTTG
66 TCTGACAAAATAATGGAAGGCGC-CCCCTCGGGAACGCGCTTTCACCACTTTG
* * * *
1118129 GGTACTGACATGAATAGT-ACCCCGAGGGACATGAGTGACATAATAGGACAATGATAACATCTTA
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* *
1118193 TCTGATAAAATAATGGAA-GCGCCCCC-CAGGAACGC
66 TCTGACAAAATAATGGAAGGCGCCCCCTCGGGAACGC
1118228 ACCTTCACGT
Statistics
Matches: 417, Mismatches: 30, Indels: 7
0.92 0.07 0.02
Matches are distributed among these distances:
114 12 0.03
115 21 0.05
116 60 0.14
117 321 0.77
118 3 0.01
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (117 bp):
GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
TCTGACAAAATAATGGAAGGCGCCCCCTCGGGAACGCGCTTTCACCACTTTG
Found at i:1118011 original size:234 final size:232
Alignment explanation
Indices: 1117561--1118206 Score: 882
Period size: 234 Copynumber: 2.7 Consensus size: 232
1117551 AGTTCCTCGG
* *
1117561 GGGACATGTGTGACATAATAGGGCAAAAATAACATATTCTCTGACAAAATAA-TGAAAGGCGCGC
1 GGGACATGAGTGACATAATAGGGCAATAATAACATATTCTCTGACAAAATAATTG-AAGGCGCGC
* * * * *
1117625 CCCCGGGAACGCGCTTTCAACTCCCCTAAGAAATAATAGGTATTGACATGAATAGTTCCCGGGGG
65 CCCCGGGAACGCGCTTTC-A--CCACT------T--TGGGTACTGACATGAATAGTCCCCGAGGG
* * * **
1117690 ACATGAGTGACATAATAGGGCAATAATAACATATTCTCTAACAAAACAATCGAAGGCGCACCCTC
119 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATAAAAGGCGCACCCTC
*
1117755 GGGAACGCGTTTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCAA
184 GGGAACGCGCTTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCAA
1117804 GGGACATGAGTGACATAATAGGGCAATAATAACATATTCTCTGACAAAATAATTGAAGGCGC-CC
1 GGGACATGAGTGACATAATAGGGCAATAATAACATATTCTCTGACAAAATAATTGAAGGCGCGCC
*
1117868 CCTCGGGAACGCGCTTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGAGGGACATAAGTG
66 CC-CGGGAACGCGCTTTCACCACTTTGGGTACTGACATGAATAGT--CCCCGAGGGACATGAGTG
*
1117933 ACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATAAAAGGCGCGCCCTCGGGAACGCG
128 ACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATAAAAGGCGCACCCTCGGGAACGCG
*
1117998 CTTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGA
193 CTTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCAA
* * * * * *
1118038 GGGATATGAGTGACATAATAGGGCAATGATAACATATTATCTGATAAAATAATGGAATGCGCGCC
1 GGGACATGAGTGACATAATAGGGCAATAATAACATATTCTCTGACAAAATAATTGAAGGCGCGCC
* *
1118103 CCCAGGAACACGCTTTCACCACTTTGGGTACTGACATGAATAGTACCCCGAGGGACATGAGTGAC
66 CCCGGGAACGCGCTTTCACCACTTTGGGTACTGACATGAATAGT-CCCCGAGGGACATGAGTGAC
* * * *
1118168 ATAATAGGACAATGATAACATCTTATCTGATAAAATAAT
130 ATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1118207 GGAAGCGCCC
Statistics
Matches: 368, Mismatches: 30, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
232 18 0.05
233 54 0.15
234 209 0.57
235 4 0.01
240 4 0.01
242 5 0.01
243 72 0.20
244 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (232 bp):
GGGACATGAGTGACATAATAGGGCAATAATAACATATTCTCTGACAAAATAATTGAAGGCGCGCC
CCCGGGAACGCGCTTTCACCACTTTGGGTACTGACATGAATAGTCCCCGAGGGACATGAGTGACA
TAATAGGGCAATGATAACATATTCTCTGACAAAATAATAAAAGGCGCACCCTCGGGAACGCGCTT
TCACCACTTTGGGTACTGACATGAATAGTGCCCCCAA
Found at i:1121287 original size:26 final size:27
Alignment explanation
Indices: 1121230--1121281 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1121220 ATTAATATTC
*
1121230 TATTTAAATGAATGTTTTTGTTTCTAA
1 TATTTAAATGAATGTGTTTGTTTCTAA
1121257 TATTTAAATGTAAT-TGTTT-TTTCTA
1 TATTTAAATG-AATGTGTTTGTTTCTA
1121282 TAATTTCTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 6 0.26
27 14 0.61
28 3 0.13
ACGTcount: A:0.29, C:0.04, G:0.10, T:0.58
Consensus pattern (27 bp):
TATTTAAATGAATGTGTTTGTTTCTAA
Found at i:1122062 original size:60 final size:61
Alignment explanation
Indices: 1121994--1122110 Score: 148
Period size: 61 Copynumber: 1.9 Consensus size: 61
1121984 AAAAATACCA
* * * *
1121994 GCGTGGCA-TCCGACTCAGCAT-AACCCATATAAAGCGCGTCCCCGGGGATGCGCCTTACAC
1 GCGTGGCATTCC-AATCAGCATAAACCCAGATAAAGCGCATCCCCGGGGATGCACCTTACAC
* * *
1122054 GCGTGGCATTCCAATCAGCATAAAGCCAGGTAAAGTGCATCCCCGGGGATGCACCTT
1 GCGTGGCATTCCAATCAGCATAAACCCAGATAAAGCGCATCCCCGGGGATGCACCTT
1122111 TGTGCCACCT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
60 16 0.33
61 32 0.67
ACGTcount: A:0.25, C:0.32, G:0.26, T:0.18
Consensus pattern (61 bp):
GCGTGGCATTCCAATCAGCATAAACCCAGATAAAGCGCATCCCCGGGGATGCACCTTACAC
Found at i:1122268 original size:15 final size:15
Alignment explanation
Indices: 1122248--1122279 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1122238 GAGGTGAAAC
*
1122248 ATTATATTGTATTGT
1 ATTATATTATATTGT
1122263 ATTATATTATATTGT
1 ATTATATTATATTGT
1122278 AT
1 AT
1122280 GCAAAATCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.59
Consensus pattern (15 bp):
ATTATATTATATTGT
Found at i:1123771 original size:23 final size:22
Alignment explanation
Indices: 1123720--1123771 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
1123710 AAGTTTAGGA
* *
1123720 TTTAGAGTTTAAAATTTATAAG
1 TTTAGAATTTAAAATTTAAAAG
1123742 TTATAGAATTTAAAATTTTAAAAG
1 TT-TAGAATTTAAAA-TTTAAAAG
1123766 TTTAGA
1 TTTAGA
1123772 TTCAAATAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 2 0.08
23 15 0.58
24 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (22 bp):
TTTAGAATTTAAAATTTAAAAG
Found at i:1124958 original size:38 final size:39
Alignment explanation
Indices: 1124879--1124975 Score: 105
Period size: 38 Copynumber: 2.6 Consensus size: 39
1124869 GGGTTTTCGA
*
1124879 TCCACCCGACCCG-AC-CCAACCTAAACATTATACATCC
1 TCCACCCGACCCGAACTCCAACCAAAACATTATACATCC
* *
1124916 TCCACCCGACCCGAACTCGATCCAAAACA-TATACA-CC
1 TCCACCCGACCCGAACTCCAACCAAAACATTATACATCC
* *
1124953 TTCCACCCAACCCTAACT-CAACC
1 -TCCACCCGACCCGAACTCCAACC
1124976 CGCCTTTTGA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
37 18 0.36
38 23 0.46
39 9 0.18
ACGTcount: A:0.33, C:0.46, G:0.05, T:0.15
Consensus pattern (39 bp):
TCCACCCGACCCGAACTCCAACCAAAACATTATACATCC
Found at i:1126370 original size:3 final size:3
Alignment explanation
Indices: 1126362--1126395 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1126352 ATATATTCCA
*
1126362 TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1126396 GTCGTTGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1126492 original size:25 final size:25
Alignment explanation
Indices: 1126458--1126507 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1126448 CTAGATTAAG
* *
1126458 TAATGTAGAGGTTTATTATAGGACT
1 TAATGTAGAGGATTATTATAAGACT
1126483 TAATGTAGAGGATTATTATAAGACT
1 TAATGTAGAGGATTATTATAAGACT
1126508 GATCCTTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (25 bp):
TAATGTAGAGGATTATTATAAGACT
Found at i:1127306 original size:29 final size:29
Alignment explanation
Indices: 1127264--1127320 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
1127254 ATGGTTTTGG
*
1127264 GTAGGTCGCCAGGGCATCCCAGCGACATT
1 GTAGGTCACCAGGGCATCCCAGCGACATT
1127293 GTAGGTCACCAGGGCATCCCAGCGACAT
1 GTAGGTCACCAGGGCATCCCAGCGACAT
1127321 GCATGCTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.23, C:0.32, G:0.30, T:0.16
Consensus pattern (29 bp):
GTAGGTCACCAGGGCATCCCAGCGACATT
Found at i:1127434 original size:23 final size:23
Alignment explanation
Indices: 1127408--1127465 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
1127398 AATTCAACTG
1127408 CATTATTGCAGCACTTATTGTTA
1 CATTATTGCAGCACTTATTGTTA
* *
1127431 CATTATGGCAGCACTTATTGTTG
1 CATTATTGCAGCACTTATTGTTA
*
1127454 CATAATTGCAGC
1 CATTATTGCAGC
1127466 CCTTCAGCTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (23 bp):
CATTATTGCAGCACTTATTGTTA
Found at i:1127671 original size:8 final size:9
Alignment explanation
Indices: 1127641--1127678 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
1127631 GAGGTAAGTT
1127641 TTTTAATTA
1 TTTTAATTA
1127650 TTTTAATTA
1 TTTTAATTA
*
1127659 GTTT-ATTA
1 TTTTAATTA
1127667 TTTTAAATTA
1 TTTT-AATTA
1127677 TT
1 TT
1127679 AGTTTGTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 12 0.48
10 6 0.24
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTAATTA
Found at i:1127732 original size:4 final size:4
Alignment explanation
Indices: 1127715--1127744 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
1127705 AAACAATATT
*
1127715 TTAG TTAA TTAG TTAG TTAG TTAG TTAG TT
1 TTAG TTAG TTAG TTAG TTAG TTAG TTAG TT
1127745 TAAGGTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (4 bp):
TTAG
Found at i:1127763 original size:47 final size:49
Alignment explanation
Indices: 1127672--1127783 Score: 167
Period size: 47 Copynumber: 2.3 Consensus size: 49
1127662 TATTATTTTA
* *
1127672 AATTA-TTAGTTTGTTAGTTTATGGTTTAAGGTAAAACAATATTTTAGTT
1 AATTAGTTAGTTAGTTAGTTTA-GGTTTAAGGTAAAACAAAATTTTAGTT
1127721 AATTAGTTAGTTAGTTAG-TTA-GTTTAAGGTAAAACAAAATTTTAGTT
1 AATTAGTTAGTTAGTTAGTTTAGGTTTAAGGTAAAACAAAATTTTAGTT
*
1127768 AATTAGTTTGTTAGTT
1 AATTAGTTAGTTAGTT
1127784 TAAGTTATAT
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
47 40 0.68
49 8 0.14
50 11 0.19
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (49 bp):
AATTAGTTAGTTAGTTAGTTTAGGTTTAAGGTAAAACAAAATTTTAGTT
Found at i:1127914 original size:28 final size:27
Alignment explanation
Indices: 1127875--1127927 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
1127865 ATATTAAAAA
1127875 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
1127903 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
1127928 TAAATAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (27 bp):
AATAATTAATTAGTGTGTAGTTAGTCT
Found at i:1127933 original size:27 final size:29
Alignment explanation
Indices: 1127874--1127938 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
1127864 TATATTAAAA
1127874 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
1127903 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
1127929 AAATAGTTAA
1 AAATAATTAA
1127939 GTTATATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 16 0.50
28 15 0.47
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:1128169 original size:21 final size:21
Alignment explanation
Indices: 1128144--1128183 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1128134 GTTAATTAGT
1128144 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
1128165 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
1128184 CATATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:1128454 original size:28 final size:30
Alignment explanation
Indices: 1128365--1128460 Score: 112
Period size: 28 Copynumber: 3.3 Consensus size: 30
1128355 TAATTAATTT
* *
1128365 TTTAGTAG-TAAA-TTATAATTAAA-AATCG
1 TTTATTAGTTAAAGTTAT-ATTAAAGAATAG
* *
1128393 TTTATTAGTTTAAGTTATATTAAAGAATAT
1 TTTATTAGTTAAAGTTATATTAAAGAATAG
1128423 TTTATTAGTTAAAG-T-TATTAAAGAATAG
1 TTTATTAGTTAAAGTTATATTAAAGAATAG
1128451 TTTATTAGTT
1 TTTATTAGTT
1128461 GTTTAAGGGA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
28 29 0.49
29 10 0.17
30 20 0.34
ACGTcount: A:0.41, C:0.01, G:0.11, T:0.47
Consensus pattern (30 bp):
TTTATTAGTTAAAGTTATATTAAAGAATAG
Found at i:1129772 original size:23 final size:23
Alignment explanation
Indices: 1129744--1129788 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1129734 TTTAATTATT
*
1129744 ATTTAAATTAACTATATTATTTG
1 ATTTAAATCAACTATATTATTTG
* *
1129767 ATTTAAATCAATTTTATTATTT
1 ATTTAAATCAACTATATTATTT
1129789 TTGTAATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTTAAATCAACTATATTATTTG
Found at i:1129788 original size:18 final size:21
Alignment explanation
Indices: 1129738--1129787 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
1129728 GTTATTTTTA
*
1129738 ATTATTATTTAAATTAACTAT
1 ATTATTATTTAAATCAACTAT
* *
1129759 ATTATTTGATTTAAATCAATTTT
1 ATTA-TT-ATTTAAATCAACTAT
1129782 ATTATT
1 ATTATT
1129788 TTTGTAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 4 0.17
22 4 0.17
23 16 0.67
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTATTATTTAAATCAACTAT
Found at i:1130784 original size:11 final size:12
Alignment explanation
Indices: 1130757--1130789 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1130747 TATTATAATT
1130757 TCATTAGTAGTAA
1 TCATTAGTAG-AA
1130770 TCATTAGTA-AA
1 TCATTAGTAGAA
1130781 TCATTAGTA
1 TCATTAGTA
1130790 TTAAATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
13 9 0.45
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (12 bp):
TCATTAGTAGAA
Found at i:1130807 original size:21 final size:22
Alignment explanation
Indices: 1130777--1130821 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1130767 TAATCATTAG
* *
1130777 TAAATCATTAGTATTAAATAAT
1 TAAATCATTAATAATAAATAAT
*
1130799 TAAAT-ATTAATAATAAATCAT
1 TAAATCATTAATAATAAATAAT
1130820 TA
1 TA
1130822 TTAATAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAATCATTAATAATAAATAAT
Found at i:1130982 original size:14 final size:14
Alignment explanation
Indices: 1130961--1131367 Score: 234
Period size: 14 Copynumber: 31.1 Consensus size: 14
1130951 ATTAGTAATA
1130961 ATTATTAAATCATT
1 ATTATTAAATCATT
* *
1130975 AATATTAAATCAAT
1 ATTATTAAATCATT
*
1130989 ATTA-TAAA--ATC
1 ATTATTAAATCATT
*
1131000 ATTACTAAATC---
1 ATTATTAAATCATT
*
1131011 ATTATTAAACCATT
1 ATTATTAAATCATT
*
1131025 ACTATTAAATCATT
1 ATTATTAAATCATT
*
1131039 ATTA-T-AATTATT
1 ATTATTAAATCATT
1131051 ATTATTAAATCATT
1 ATTATTAAATCATT
1131065 ATTA-T---T-ATT
1 ATTATTAAATCATT
1131074 ATTATTAAATCATT
1 ATTATTAAATCATT
*
1131088 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1131100 ATTACTAAATCATT
1 ATTATTAAATCATT
*
1131114 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1131126 ATTATCAAATC---
1 ATTATTAAATCATT
*
1131137 ATTACTAAATCATT
1 ATTATTAAATCATT
* *
1131151 AAATATTAAA--ATC
1 -ATTATTAAATCATT
1131164 ATTATTAAATCATT
1 ATTATTAAATCATT
*
1131178 ATTA-T-AATGATT
1 ATTATTAAATCATT
1131190 ATTATTAAATCATT
1 ATTATTAAATCATT
*
1131204 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1131216 ATTACTAAATCATT
1 ATTATTAAATCATT
*
1131230 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1131242 ATTACTAAATCATT
1 ATTATTAAATCATT
*
1131256 ATTA-TAATTTCATT
1 ATTATTAA-ATCATT
* *
1131270 ACTAGT-AATC---
1 ATTATTAAATCATT
*
1131280 ATTAGTAAATCATT
1 ATTATTAAATCATT
* *
1131294 AGTATTAAATAATT
1 ATTATTAAATCATT
* * *
1131308 AAATATTAATAATAAATC
1 -ATTATT-A-AAT-CATT
* *
1131326 ATTATT-AATAATA
1 ATTATTAAATCATT
1131339 ATTATTAAATCATT
1 ATTATTAAATCATT
* *
1131353 AGTATCAAATCATT
1 ATTATTAAATCATT
1131367 A
1 A
1131368 AATATTTAAA
Statistics
Matches: 308, Mismatches: 45, Indels: 80
0.71 0.10 0.18
Matches are distributed among these distances:
9 7 0.02
10 7 0.02
11 27 0.09
12 72 0.23
13 33 0.11
14 137 0.44
15 13 0.04
16 1 0.00
17 8 0.03
18 3 0.01
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (14 bp):
ATTATTAAATCATT
Found at i:1131051 original size:3 final size:3
Alignment explanation
Indices: 1131036--1131130 Score: 61
Period size: 3 Copynumber: 32.7 Consensus size: 3
1131026 CTATTAAATC
* * * *
1131036 ATT ATT ATA ATT ATT ATT ATT A-A ATC ATT ATT ATT ATT ATT ATT A-A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * * *
1131082 ATC ATT ATT ATA ATG ATT ATT ACT A-A ATC ATT ATT ATA ATG ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1131129 AT
1 AT
1131131 CAAATCATTA
Statistics
Matches: 71, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
2 3 0.04
3 68 0.96
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (3 bp):
ATT
Found at i:1131058 original size:26 final size:26
Alignment explanation
Indices: 1130948--1131367 Score: 282
Period size: 26 Copynumber: 16.7 Consensus size: 26
1130938 TTATTCCATA
* *
1130948 ATTATTAGT-AATAATTATTA-AATC
1 ATTATTATTAAATCATTATTATAATC
* * *
1130972 ATTAATATTAAATCAATATTATAA-A
1 ATTATTATTAAATCATTATTATAATC
* * *
1130997 ATCATTACTAAATCATTATTA-AACC
1 ATTATTATTAAATCATTATTATAATC
* *
1131022 ATTACTATTAAATCATTATTATAATT
1 ATTATTATTAAATCATTATTATAATC
1131048 ATTATTATTAAATCATTATTAT--T-
1 ATTATTATTAAATCATTATTATAATC
*
1131071 ATTATTATTAAATCATTATTATAATG
1 ATTATTATTAAATCATTATTATAATC
* *
1131097 ATTATTACTAAATCATTATTATAATG
1 ATTATTATTAAATCATTATTATAATC
* *
1131123 ATTATTATCAAATCATTACTA-AATC
1 ATTATTATTAAATCATTATTATAATC
*
1131148 ATTAAATATTAAAATCATTATTA-AATC
1 ATT-ATTATT-AAATCATTATTATAATC
*
1131175 ATTATTA-T-AATGATTATTATTAAATC
1 ATTATTATTAAATCATTATTA-T-AATC
*
1131201 ATTATTA-T-AATGATTATTACTAAATC
1 ATTATTATTAAATCATTATTA-T-AATC
*
1131227 ATTATTA-T-AATGATTATTACTAAATC
1 ATTATTATTAAATCATTATTA-T-AATC
* *
1131253 ATTATTA-TAATTTCATTACTAGTAATC
1 ATTATTATTAA-ATCATTATTA-TAATC
* *
1131280 ---ATTAGTAAATCATTAGTATTAA--
1 ATTATTATTAAATCATTATTA-TAATC
*
1131302 A-TA--ATTAAAT-ATTAATAATAAATC
1 ATTATTATTAAATCATT-ATTAT-AATC
* *
1131326 ATTATTAAT-AATAATTATTA-AATC
1 ATTATTATTAAATCATTATTATAATC
* *
1131350 ATTAGTATCAAATCATTA
1 ATTATTATTAAATCATTA
1131368 AATATTTAAA
Statistics
Matches: 327, Mismatches: 43, Indels: 51
0.78 0.10 0.12
Matches are distributed among these distances:
21 4 0.01
22 10 0.03
23 32 0.10
24 37 0.11
25 64 0.20
26 144 0.44
27 28 0.09
28 8 0.02
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (26 bp):
ATTATTATTAAATCATTATTATAATC
Found at i:1131060 original size:90 final size:89
Alignment explanation
Indices: 1130948--1131308 Score: 300
Period size: 90 Copynumber: 4.0 Consensus size: 89
1130938 TTATTCCATA
* *
1130948 ATTATTAGT-AATAATTATTAAATCATTAATATTAAATCAATATTATAAAATCATTACTA-AATC
1 ATTATTA-TAAATCATTATTAAATCATTAATATTAAATCATTATTATAAAATCATTACTATAATC
* * *
1131011 ATTATTAAACCATTACTATTAAATC
65 ATTATTAAATCATTATTATTAAATG
* * * *
1131036 ATTATTATAATTATTATTATTAAATCA-T--TATT--ATTATTATTATTAAATCATTATTATAAT
1 ATTATTATAA--ATCATTATTAAATCATTAATATTAAATCATTATTATAAAATCATTACTATAAT
*
1131096 GATTATTACTAAATCATTATTA-T-AATG
64 CATTA-T--TAAATCATTATTATTAAATG
* *
1131123 ATTATTATCAAATCATTACTAAATCATTAAATATTAAAATCATTA-T-T-AAATCATTATTATAA
1 ATTATTAT-AAATCATTATTAAATCATT-AATATT-AAATCATTATTATAAAATCATTACTAT-A
*
1131185 TGATTATTATTAAATCATTATTA-T-AATG
62 --ATCATTATTAAATCATTATTATTAAATG
* * * **
1131213 ATTATTACTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATTTCATTACTAGTAA
1 ATTATTA-TAAATCATTATTA-AATCATTAATATTAAATCATTATTATAAAATCATTACTA-TAA
* * *
1131278 TCATTAGTAAATCATTAGTATTAAATA
63 TCATTATTAAATCATTATTATTAAATG
1131305 ATTA
1 ATTA
1131309 AATATTAATA
Statistics
Matches: 223, Mismatches: 24, Indels: 48
0.76 0.08 0.16
Matches are distributed among these distances:
85 20 0.09
86 20 0.09
87 18 0.08
88 11 0.05
89 21 0.09
90 90 0.40
91 11 0.05
92 19 0.09
93 13 0.06
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.45
Consensus pattern (89 bp):
ATTATTATAAATCATTATTAAATCATTAATATTAAATCATTATTATAAAATCATTACTATAATCA
TTATTAAATCATTATTATTAAATG
Found at i:1131201 original size:116 final size:113
Alignment explanation
Indices: 1131051--1131687 Score: 369
Period size: 116 Copynumber: 5.6 Consensus size: 113
1131041 TATAATTATT
1131051 ATTATTAAATCATTATTATTATTATTATTAAATCATTATTATAATGATTATTACTAAATCATTAT
1 ATTATTAAATCATTATTATTATTATTATTAAATCATTATTATAATGATTATTACTAAATCATTAT
1131116 TATAATGATTATTA-TCAAATCATTACTAAATCATTAAATATTAAAATC
66 TATAATGATTATTACT-AAATCATTACTAAATCATTAAATATTAAAATC
1131164 ATTATTAAATCATTATTATAATGATTATTATTAAATCATTATTATAATGATTATTACTAAATCAT
1 ATTATTAAATCATTATTAT--T-ATTATTATTAAATCATTATTATAATGATTATTACTAAATCAT
* * *
1131229 TATTATAATGATTATTACTAAATCATTATTATAATTTCATT-ACTAGT--AATC
63 TATTATAATGATTATTACTAAATCATTACTA-AA--TCATTAAATATTAAAATC
* * * * * * * *
1131280 ATTAGTAAATCATTAGTATTA-AATAATTAAAT-ATTAATAATAAATCATTATTAAT-AATAATT
1 ATTATTAAATCATTATTATTATTATTATTAAATCATT-ATTAT-AATGATTATTACTAAATCATT
* * *
1131342 ATTA-AATCATTAGTA-TCAAATCA-T--TAAAT-ATT---TA--AAAATT
64 ATTATAATGATTATTACT-AAATCATTACTAAATCATTAAATATTAAAATC
* * * * * * *
1131382 ATTAATAAAT--TTGACTATGTATAAAT-TTAAATTCGAGTAGTCCACACTTGTACACTCATTTG
1 ATTATTAAATCATT-ATTAT-TATTATTATTAAA-TC-A-T--T----A-TTATA-A-TGA-TTA
* * * * * * * * * * * *
1131444 TTA-TTATTCCATAATTATTAGTAATAATTATTAAATCATTAGT-ATTAAATAATTATTATAAAA
51 TTACTAAAT-CATTATTA-TAATGATTATTACTAAATCATTACTAAATCATTAAATA-T-TAAAA
*
1131507 TA
112 TC
* *
1131509 ATTACTAAATCATTATTAAATTATTACTATTAAATCATTATTATAATGATTATTACTAAATCATT
1 ATTATTAAATCATTATT--ATTATTATTATTAAATCATTATTATAATGATTATTACTAAATCATT
*
1131574 ATTATAATGATTATTA-TCAAATCATTACTAAATCATCAAATCATT-AAAT-
64 ATTATAATGATTATTACT-AAATCATTACTAAATCATTAAAT-ATTAAAATC
* * * *
1131623 ATTA--AAATCATTTTTAAATTATTATTA-TAATTTCATTATTACTAATCATTATTATTAAATCA
1 ATTATTAAATCATTATT--ATTATTATTATTAA-ATCATTATTA-TAATGATTATTACTAAATCA
1131685 TTA
62 TTA
1131688 AATATTAATA
Statistics
Matches: 413, Mismatches: 56, Indels: 110
0.71 0.10 0.19
Matches are distributed among these distances:
100 2 0.00
101 4 0.01
102 21 0.05
103 3 0.01
104 3 0.01
105 2 0.00
106 1 0.00
107 2 0.00
108 3 0.01
110 2 0.00
111 23 0.06
112 56 0.14
113 56 0.14
114 12 0.03
115 12 0.03
116 111 0.27
117 35 0.08
118 12 0.03
119 8 0.02
120 7 0.02
121 1 0.00
123 2 0.00
125 1 0.00
127 15 0.04
128 3 0.01
129 9 0.02
130 7 0.02
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (113 bp):
ATTATTAAATCATTATTATTATTATTATTAAATCATTATTATAATGATTATTACTAAATCATTAT
TATAATGATTATTACTAAATCATTACTAAATCATTAAATATTAAAATC
Found at i:1131315 original size:21 final size:22
Alignment explanation
Indices: 1131285--1131329 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1131275 TAATCATTAG
* *
1131285 TAAATCATTAGTATTAAATAAT
1 TAAATCATTAATAATAAATAAT
*
1131307 TAAAT-ATTAATAATAAATCAT
1 TAAATCATTAATAATAAATAAT
1131328 TA
1 TA
1131330 TTAATAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAATCATTAATAATAAATAAT
Found at i:1131491 original size:14 final size:14
Alignment explanation
Indices: 1131470--1131687 Score: 124
Period size: 14 Copynumber: 16.1 Consensus size: 14
1131460 ATTAGTAATA
1131470 ATTATTAAATCATT
1 ATTATTAAATCATT
* *
1131484 AGTATTAAATAATT
1 ATTATTAAATCATT
*
1131498 ATTA-TAAA--ATA
1 ATTATTAAATCATT
*
1131509 ATTACTAAATC---
1 ATTATTAAATCATT
*
1131520 ATTATTAAATTATT
1 ATTATTAAATCATT
*
1131534 ACTATTAAATCATT
1 ATTATTAAATCATT
*
1131548 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1131560 ATTACTAAATCATT
1 ATTATTAAATCATT
*
1131574 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1131586 ATTATCAAATCATT
1 ATTATTAAATCATT
*
1131600 ACTAAATCATCAAATCATT
1 A-T---T-ATTAAATCATT
*
1131619 AAATATTAAAATCA-T
1 -ATTATT-AAATCATT
*
1131634 -TT-TTAAATTATT
1 ATTATTAAATCATT
*
1131646 ATTA-TAATTTCATT
1 ATTATTAA-ATCATT
*
1131660 ATTACT-AATCATT
1 ATTATTAAATCATT
1131673 ATTATTAAATCATT
1 ATTATTAAATCATT
1131687 A
1 A
1131688 AATATTAATA
Statistics
Matches: 159, Mismatches: 22, Indels: 46
0.70 0.10 0.20
Matches are distributed among these distances:
11 20 0.13
12 27 0.17
13 23 0.14
14 64 0.40
15 5 0.03
16 7 0.04
18 1 0.01
19 11 0.07
20 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.45
Consensus pattern (14 bp):
ATTATTAAATCATT
Found at i:1131568 original size:26 final size:26
Alignment explanation
Indices: 1131457--1131600 Score: 145
Period size: 25 Copynumber: 5.7 Consensus size: 26
1131447 TTATTCCATA
* * *
1131457 ATTATTAGT-AATAATTATTA-AATC
1 ATTATTACTAAATCATTATTATAATG
* * * *
1131481 ATTAGTATTAAATAATTATTATAA-A
1 ATTATTACTAAATCATTATTATAATG
* *
1131506 ATAATTACTAAATCATTATTA-AATT
1 ATTATTACTAAATCATTATTATAATG
* *
1131531 ATTACTATTAAATCATTATTATAATG
1 ATTATTACTAAATCATTATTATAATG
1131557 ATTATTACTAAATCATTATTATAATG
1 ATTATTACTAAATCATTATTATAATG
1131583 ATTATTA-TCAAATCATTA
1 ATTATTACT-AAATCATTA
1131601 CTAAATCATC
Statistics
Matches: 101, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
24 9 0.09
25 47 0.47
26 45 0.45
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (26 bp):
ATTATTACTAAATCATTATTATAATG
Found at i:1131702 original size:49 final size:49
Alignment explanation
Indices: 1131636--1131931 Score: 388
Period size: 49 Copynumber: 6.1 Consensus size: 49
1131626 AAAATCATTT
* * *
1131636 TTAAATTATT-ATTATAATTTCATTATTACTAATCATTATTATTAAATCA
1 TTAAA-TATTAATAATAATTTCATTATTACTAATCATTACTATCAAATCA
*
1131685 TTAAATATTAATAATAATTTCATTGTTACTAATCATTACTATCAAATCA
1 TTAAATATTAATAATAATTTCATTATTACTAATCATTACTATCAAATCA
1131734 TTAAATATTAATAATAATTTCATTATTACTAATCATTACTA-CTAAATCA
1 TTAAATATTAATAATAATTTCATTATTACTAATCATTACTATC-AAATCA
* *
1131783 TTAAATATTAATAATATTTTCATTATTACTAATCATTACTACCAAATCA
1 TTAAATATTAATAATAATTTCATTATTACTAATCATTACTATCAAATCA
* * *
1131832 TTAAATATTAATAATAATTTCATTATTACTAATCATTATTA-AATAATTA
1 TTAAATATTAATAATAATTTCATTATTACTAATCATTACTATCA-AATCA
* * * *
1131881 TTATAATTTTAA-ATATAAATTCATTATTA--AATCATGATTATCAAATCA
1 TTA-AATATTAATA-ATAATTTCATTATTACTAATCATTACTATCAAATCA
1131929 TTA
1 TTA
1131932 CTAAATCAAA
Statistics
Matches: 225, Mismatches: 15, Indels: 15
0.88 0.06 0.06
Matches are distributed among these distances:
48 23 0.10
49 180 0.80
50 22 0.10
ACGTcount: A:0.44, C:0.10, G:0.01, T:0.45
Consensus pattern (49 bp):
TTAAATATTAATAATAATTTCATTATTACTAATCATTACTATCAAATCA
Found at i:1131850 original size:509 final size:501
Alignment explanation
Indices: 1130740--1131800 Score: 1375
Period size: 509 Copynumber: 2.1 Consensus size: 501
1130730 TTTTAGTATA
* * * *
1130740 AAATCATTATTATAATTTCATTAGTAGTAATCATTAGTAAATCATTAGTATTAAATAATTAAATA
1 AAATCATTATTATAA-TTCATTACTACTAATCATTAG-AAATCAATAATATTAAATAATTAAATA
*
1130805 TTAATAATAAATCATTATTAATAATAATTACAAAACATTAGTATCAAATCATTAAATATTTAAAA
64 TTAATAACAAATCATTATTAATAATAATTACAAAACATTAGTATCAAATCATTAAATATTTAAAA
1130870 ATCATTAATAAATTCGACTATGTATAAATTTAAATTCGAGTAGTCCACACTTGTACACTCATTTG
129 ATCATTAATAAATTCGACTATGTATAAATTTAAATTCGAGTAGTCCACACTTGTACACTCATTTG
*
1130935 TTATTATTCCATAATTATTAGTAATAATTATTAAATCATTAATATTAAATCAATATTATAAAATC
194 TTATTATTCCATAATTATTAGTAATAATTATTAAATCATTAATATTAAATCAATATTATAAAATA
* *
1131000 ATTACTAAATCATTATTAAACCATTACTATTAAATCATTATTATAATTATTATTATTAAATCATT
259 ATTACTAAATCATTATTAAACCATTACTATTAAATCATTATTATAATGATTATTACTAAATCATT
* * * * * *
1131065 ATTATTATTATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTA
324 ATTATTATTATTATCAAATCATTACTATAATCATAATCACTAAATCATTA-TATAATCATTATTA
* * *
1131130 TCAAATCATTACTAAATCATTAAATATTAAAATCATTATTAAATCATTATTATAATGATTATTAT
388 TCAAATCATTACTAAAT-ATTAAATATTAAAATCATTATTAAA-CATCATTATAATGATTAATAA
* * * *
1131195 TAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTACT
451 TAAATCATTATTATAATCATTACTACTAAATC--TATTATAATGATTAATAAT
* * *
1131248 AAATCATTATTATAATTTCATTACTAGTAATCATTAGTAAATCATTAGTATTAAATAATTAAATA
1 AAATCATTATTATAA-TTCATTACTACTAATCATTAG-AAATCAATAATATTAAATAATTAAATA
* * *
1131313 TTAATAATAAATCATTATTAATAATAATTATTAAATCATTAGTATCAAATCATTAAATATTTAAA
64 TTAATAACAAATCATTATTAATAATAATTA-CAAAACATTAGTATCAAATCATTAAATATTTAAA
* *
1131378 AATTATTAATAAATTTGACTATGTATAAATTTAAATTCGAGTAGTCCACACTTGTACACTCATTT
128 AATCATTAATAAATTCGACTATGTATAAATTTAAATTCGAGTAGTCCACACTTGTACACTCATTT
*
1131443 GTTATTATTCCATAATTATTAGTAATAATTATTAAATCATTAGTATTAAAT-AATTATTATAAAA
193 GTTATTATTCCATAATTATTAGTAATAATTATTAAATCATTAATATTAAATCAA-TATTATAAAA
**
1131507 TAATTACTAAATCATTATTAAATTATTACTATTAAATCATTATTATAATGATTATTACTAAATCA
257 TAATTACTAAATCATTATTAAACCATTACTATTAAATCATTATTATAATGATTATTACTAAATCA
*
1131572 TTATTATAATGATTATTATCAAATCATTACTA-AATCATCAAATCATTAAAT-ATTA-A-AATCA
322 TTATTAT--T-ATTATTATCAAATCATTACTATAATCAT--AATCACTAAATCATTATATAATCA
* * * * *
1131633 TT-TT-T-AAATTATTATTATAAT-TTCATTATTACTAATCATTATTATTAA-ATCATTA-AAT-
382 TTATTATCAAATCATTACTA-AATATTAAATATTA-AAATCATTATTA--AACATCATTATAATG
* *
1131691 ATTAATAATAATTTCATTGTTACTAATCATTACTA-TCAAATC-ATTA-AAT-ATTAATAAT
443 ATTAATAATAA-ATCATTATTA-TAATCATTACTACT-AAATCTATTATAATGATTAATAAT
* *
1131749 AATTTCATTATTACTAA-TCATTACTACTAAATCATTA-AATATTAATAATATT
1 AA-ATCATTATTA-TAATTCATTACTACT-AATCATTAGAA-ATCAATAATATT
1131801 TTCATTATTA
Statistics
Matches: 498, Mismatches: 37, Indels: 43
0.86 0.06 0.07
Matches are distributed among these distances:
500 2 0.00
501 28 0.06
502 20 0.04
503 7 0.01
504 9 0.02
505 20 0.04
506 42 0.08
507 4 0.01
508 100 0.20
509 228 0.46
510 1 0.00
511 6 0.01
512 23 0.05
513 8 0.02
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.43
Consensus pattern (501 bp):
AAATCATTATTATAATTCATTACTACTAATCATTAGAAATCAATAATATTAAATAATTAAATATT
AATAACAAATCATTATTAATAATAATTACAAAACATTAGTATCAAATCATTAAATATTTAAAAAT
CATTAATAAATTCGACTATGTATAAATTTAAATTCGAGTAGTCCACACTTGTACACTCATTTGTT
ATTATTCCATAATTATTAGTAATAATTATTAAATCATTAATATTAAATCAATATTATAAAATAAT
TACTAAATCATTATTAAACCATTACTATTAAATCATTATTATAATGATTATTACTAAATCATTAT
TATTATTATTATCAAATCATTACTATAATCATAATCACTAAATCATTATATAATCATTATTATCA
AATCATTACTAAATATTAAATATTAAAATCATTATTAAACATCATTATAATGATTAATAATAAAT
CATTATTATAATCATTACTACTAAATCTATTATAATGATTAATAAT
Found at i:1135741 original size:43 final size:48
Alignment explanation
Indices: 1135684--1135794 Score: 135
Period size: 50 Copynumber: 2.4 Consensus size: 48
1135674 GTTTAAAGAC
*
1135684 ACTAACAAATTAATTAATTATTTTTT-TAT-AT-T-TA-ATAACTTAA
1 ACTAACAAACTAATTAATTATTTTTTATATAATATATATATAACTTAA
* *
1135727 ACTAAGAAACTAATTAACTAATTTTTTATATAATATAATATATAACTTAA
1 ACTAACAAACTAATTAA-TTATTTTTTATATAATAT-ATATATAACTTAA
1135777 ACTAACAAACTAA-TAATT
1 ACTAACAAACTAATTAATT
1135795 TATACTAACA
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
43 15 0.27
44 8 0.14
45 3 0.05
46 2 0.04
47 1 0.02
48 1 0.02
49 5 0.09
50 21 0.38
ACGTcount: A:0.49, C:0.09, G:0.01, T:0.41
Consensus pattern (48 bp):
ACTAACAAACTAATTAATTATTTTTTATATAATATATATATAACTTAA
Found at i:1135801 original size:21 final size:21
Alignment explanation
Indices: 1135768--1135816 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1135758 AATATAATAT
1135768 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
1135789 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
1135810 ATTAACT
1 A-TAACT
1135817 AAATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:1138170 original size:23 final size:22
Alignment explanation
Indices: 1138127--1138193 Score: 80
Period size: 23 Copynumber: 3.0 Consensus size: 22
1138117 CTTGTGAGCA
*
1138127 CATAAATAAAAATAAACATATT
1 CATAAATAAAAATAAAAATATT
* *
1138149 CATAAATATTAAATAAATATATT
1 CATAAATA-AAAATAAAAATATT
*
1138172 CATGAATAAAAAATAAAAATAT
1 CATAAAT-AAAAATAAAAATAT
1138194 ATATTTACTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
22 8 0.21
23 29 0.76
24 1 0.03
ACGTcount: A:0.63, C:0.06, G:0.01, T:0.30
Consensus pattern (22 bp):
CATAAATAAAAATAAAAATATT
Found at i:1139244 original size:23 final size:23
Alignment explanation
Indices: 1139054--1139238 Score: 134
Period size: 23 Copynumber: 8.3 Consensus size: 23
1139044 TTTTACCTGT
*
1139054 TATATTGTAATAGGTAGCGCTTA
1 TATAATGTAATAGGTAGCGCTTA
*
1139077 TATAATGTAATAAGTAGCGCTTA
1 TATAATGTAATAGGTAGCGCTTA
1139100 TATAATGTAATAGGTAGCGCTTA
1 TATAATGTAATAGGTAGCGCTTA
** *
1139123 TATAATAAAATAGGTTA---ATTA
1 TATAATGTAATAGG-TAGCGCTTA
* ** * * *
1139144 CTAGAA-ACATTA-TTAAGCAC--A
1 -TATAATGTAATAGGT-AGCGCTTA
** * * *
1139165 -ATAACATATTAAGTACCGCTTA
1 TATAATGTAATAGGTAGCGCTTA
*
1139187 AATAATGTAATAGGTAGCGCTTA
1 TATAATGTAATAGGTAGCGCTTA
1139210 TATAATGTAATAGGTAGCGCTTA
1 TATAATGTAATAGGTAGCGCTTA
1139233 TATAAT
1 TATAAT
1139239 AAAATATGTT
Statistics
Matches: 129, Mismatches: 22, Indels: 22
0.75 0.13 0.13
Matches are distributed among these distances:
19 4 0.03
20 9 0.07
21 9 0.07
22 5 0.04
23 100 0.78
24 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (23 bp):
TATAATGTAATAGGTAGCGCTTA
Found at i:1139283 original size:110 final size:110
Alignment explanation
Indices: 1139071--1139272 Score: 352
Period size: 110 Copynumber: 1.8 Consensus size: 110
1139061 TAATAGGTAG
*
1139071 CGCTTATATAATGTAATAAGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAG
1 CGCTTAAATAATGTAATAAGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAG
1139136 GTTAATTACTAGAAACATTATTAAGCACAATAACATATTAAGTAC
66 GTTAATTACTAGAAACATTATTAAGCACAATAACATATTAAGTAC
* *
1139181 CGCTTAAATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAT
1 CGCTTAAATAATGTAATAAGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAG
*
1139246 GTTAATTACTGGAAACATT-TTCAAGCA
66 GTTAATTACTAGAAACATTATT-AAGCA
1139273 TTTCAACATA
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
109 2 0.02
110 85 0.98
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (110 bp):
CGCTTAAATAATGTAATAAGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAG
GTTAATTACTAGAAACATTATTAAGCACAATAACATATTAAGTAC
Found at i:1139744 original size:87 final size:86
Alignment explanation
Indices: 1139612--1139832 Score: 268
Period size: 87 Copynumber: 2.6 Consensus size: 86
1139602 TAACAAATTA
* ** *
1139612 AATAATTAACATATTTTATTATAT-CAC-TACTTATTATGTTATAT-AAGTGTTACATAATATAT
1 AATAATTAACATATTTTATTATATAAACATACTTATTACATTATATAAATTG-TACATAATATAT
** * *
1139674 TATTGTGTTTGATAATATTTTC
65 TATTGTACTTAATAATATTTCC
* * * *
1139696 GATAATTAACCTATTTTATTATATAAACGATACTTATTACACTATATAAATTGTACATAATATGT
1 AATAATTAACATATTTTATTATATAAAC-ATACTTATTACATTATATAAATTGTACATAATATAT
1139761 TATTGTACTTAATAATATTTCC
65 TATTGTACTTAATAATATTTCC
* *
1139783 AATAATTAACATATTTTATTATATAAATATTACCTATTACATTATATAAA
1 AATAATTAACATATTTTATTATATAAACA-TACTTATTACATTATATAAA
1139833 CGAAACCTAA
Statistics
Matches: 115, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
84 22 0.19
85 2 0.02
86 1 0.01
87 86 0.75
88 4 0.03
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.46
Consensus pattern (86 bp):
AATAATTAACATATTTTATTATATAAACATACTTATTACATTATATAAATTGTACATAATATATT
ATTGTACTTAATAATATTTCC
Found at i:1140485 original size:15 final size:15
Alignment explanation
Indices: 1140465--1140515 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
1140455 CTTCACGGCG
1140465 ACCACCTCCATATCC
1 ACCACCTCCATATCC
*
1140480 ACCACCACCATATCC
1 ACCACCTCCATATCC
*
1140495 TCCACCGCTACCATATCC
1 ACCA-C-CT-CCATATCC
1140513 ACC
1 ACC
1140516 TCCTTCACGG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 17 0.59
16 1 0.03
17 1 0.03
18 10 0.34
ACGTcount: A:0.27, C:0.53, G:0.02, T:0.18
Consensus pattern (15 bp):
ACCACCTCCATATCC
Found at i:1140498 original size:18 final size:18
Alignment explanation
Indices: 1140477--1140512 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1140467 CACCTCCATA
1140477 TCCACCACCACCATATCC
1 TCCACCACCACCATATCC
* *
1140495 TCCACCGCTACCATATCC
1 TCCACCACCACCATATCC
1140513 ACCTCCTTCA
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:0.25, C:0.53, G:0.03, T:0.19
Consensus pattern (18 bp):
TCCACCACCACCATATCC
Found at i:1151101 original size:14 final size:14
Alignment explanation
Indices: 1151082--1151115 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
1151072 AATCTGAAAG
1151082 CTTTTCTGAAATTT
1 CTTTTCTGAAATTT
1151096 CTTTTCTGAAATTT
1 CTTTTCTGAAATTT
1151110 CTTTTC
1 CTTTTC
1151116 ATTTTGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.59
Consensus pattern (14 bp):
CTTTTCTGAAATTT
Found at i:1161626 original size:13 final size:13
Alignment explanation
Indices: 1161592--1161618 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1161582 GGAATTGAAC
1161592 AACAACCAATCCA
1 AACAACCAATCCA
1161605 AACAACCAATCCA
1 AACAACCAATCCA
1161618 A
1 A
1161619 GCATCCAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.37, G:0.00, T:0.07
Consensus pattern (13 bp):
AACAACCAATCCA
Found at i:1163457 original size:14 final size:14
Alignment explanation
Indices: 1163438--1163465 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1163428 GATAAATCAG
1163438 TAGAAAGTTAACAA
1 TAGAAAGTTAACAA
1163452 TAGAAAGTTAACAA
1 TAGAAAGTTAACAA
1163466 ATCTATCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.14, T:0.21
Consensus pattern (14 bp):
TAGAAAGTTAACAA
Found at i:1164403 original size:69 final size:69
Alignment explanation
Indices: 1164322--1164459 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
1164312 CCAAAGATGC
1164322 AAAATTCTCAATAACCCAGAATTCAAAGAACCATTTTTCAACATAAAAAGATCAAAGGAAAGAAA
1 AAAATTCTCAATAACCCAGAATTCAAAGAACCATTTTTCAACATAAAAAGATCAAAGGAAAGAAA
1164387 AAAA
66 AAAA
1164391 AAAATTCTCAATAACCCAGAATTCAAAGAACCATTTTTCAACATAAAAAGATCAAAGGAAAGAAA
1 AAAATTCTCAATAACCCAGAATTCAAAGAACCATTTTTCAACATAAAAAGATCAAAGGAAAGAAA
1164456 AAAA
66 AAAA
1164460 CAACACACCA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.57, C:0.16, G:0.09, T:0.19
Consensus pattern (69 bp):
AAAATTCTCAATAACCCAGAATTCAAAGAACCATTTTTCAACATAAAAAGATCAAAGGAAAGAAA
AAAA
Found at i:1166278 original size:20 final size:20
Alignment explanation
Indices: 1166239--1166319 Score: 81
Period size: 20 Copynumber: 4.0 Consensus size: 20
1166229 AATATGTAAA
*
1166239 TCGCATTGCGATATTCCAAAT
1 TCGCATTGCGATAGT-CAAAT
*
1166260 TCGCGTTGCGATAGTCAAAT
1 TCGCATTGCGATAGTCAAAT
* **
1166280 TTGCAACGCGATAGTCAAAT
1 TCGCATTGCGATAGTCAAAT
** *
1166300 TCGCAACGCGAAAGTCAAAT
1 TCGCATTGCGATAGTCAAAT
1166320 GTTTTACGTG
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 39 0.75
21 13 0.25
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (20 bp):
TCGCATTGCGATAGTCAAAT
Found at i:1166377 original size:26 final size:26
Alignment explanation
Indices: 1166346--1166403 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
1166336 AATATTAATT
1166346 TCGCAACAAAAATGTAAACAGTATTA
1 TCGCAACAAAAATGTAAACAGTATTA
*
1166372 TCGCAACACAAATGTAAACAGTATTA
1 TCGCAACAAAAATGTAAACAGTATTA
1166398 TCGCAA
1 TCGCAA
1166404 ATCATCTCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (26 bp):
TCGCAACAAAAATGTAAACAGTATTA
Found at i:1166502 original size:22 final size:22
Alignment explanation
Indices: 1166477--1166529 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1166467 GCGACATCTG
*
1166477 TCCCTATCTCCGACGAAATTCA
1 TCCCTATCTCCGACGAAATCCA
* *
1166499 TCCCCATTTCCGACGAAATCCA
1 TCCCTATCTCCGACGAAATCCA
1166521 T--CTATCTCC
1 TCCCTATCTCC
1166530 ATCTCTCAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 6 0.23
22 20 0.77
ACGTcount: A:0.25, C:0.40, G:0.08, T:0.28
Consensus pattern (22 bp):
TCCCTATCTCCGACGAAATCCA
Found at i:1166856 original size:20 final size:20
Alignment explanation
Indices: 1166803--1166852 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1166793 GAAACTAAAA
1166803 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCATTT
*
1166823 TCGCGTTGAGATTTTCATTT
1 TCGCGTTGCGATTTTCATTT
1166843 T-GCGTTGCGA
1 TCGCGTTGCGA
1166853 ATTTAAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.46
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATTT
Found at i:1170412 original size:14 final size:14
Alignment explanation
Indices: 1170393--1170432 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1170383 TTTTGATTAA
1170393 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
** *
1170407 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
1170421 TTGATTTGTAAA
1 TTGATTTGTAAA
1170433 TAATAATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:1170425 original size:61 final size:65
Alignment explanation
Indices: 1170342--1170482 Score: 175
Period size: 61 Copynumber: 2.2 Consensus size: 65
1170332 TTTTACATTG
*
1170342 AAAGTTGATTTG-TTACAATTGATGAGGAAATAAGATTTA-TTTTTTG-A-TTAATTGATTTGTA
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTTTTTTGCATTTAATTGATTTGTA
* ** * *
1170403 AAAGTTGATTTGTTTA-ATTTGATTTGTAAATAATAATTATTTTTTTGCATGTTTAATTGATTTG
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTTTTTTGCA--TTTAATTGATTTG
1170467 TA
64 TA
1170469 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
1170483 GTTTCTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
61 29 0.43
62 10 0.15
63 1 0.01
66 28 0.41
ACGTcount: A:0.32, C:0.01, G:0.16, T:0.50
Consensus pattern (65 bp):
AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTTTTTTGCATTTAATTGATTTGTA
Found at i:1170608 original size:20 final size:20
Alignment explanation
Indices: 1170585--1170623 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1170575 GATTTTCGGT
*
1170585 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTATCGCG
1170605 TTGCGAATTTGACTATCGC
1 TTGCGAATTTGACTATCGC
1170624 ACCGCTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (20 bp):
TTGCGAATTTGACTATCGCG
Found at i:1171174 original size:18 final size:18
Alignment explanation
Indices: 1171151--1171187 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1171141 CGAAATTTAT
1171151 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1171169 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1171187 A
1 A
1171188 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1171608 original size:25 final size:25
Alignment explanation
Indices: 1171574--1171623 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1171564 ATTATTTTTC
*
1171574 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
*
1171599 CAAATAATGTACCCACAATAATGTT
1 CAAATAATGTACCCACAACAATGTT
1171624 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:1171618 original size:14 final size:13
Alignment explanation
Indices: 1171573--1171622 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
1171563 CATTATTTTT
1171573 CCAAATAATGTAC
1 CCAAATAATGTAC
*
1171586 CCATAACAATGT--
1 CCA-AATAATGTAC
*
1171598 TCAAATAATGTAC
1 CCAAATAATGTAC
1171611 CCACAATAATGT
1 CCA-AATAATGT
1171623 TTAATTGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
11 7 0.24
12 2 0.07
13 5 0.17
14 15 0.52
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (13 bp):
CCAAATAATGTAC
Found at i:1171864 original size:60 final size:60
Alignment explanation
Indices: 1171734--1171873 Score: 190
Period size: 60 Copynumber: 2.3 Consensus size: 60
1171724 AAATAAGCGT
* *
1171734 TGCGATAGTCAAATTCGCAACGCGAAAGTAAAATTCACAACGTGAAAGTAAAATTCGCAA
1 TGCGATAGTCAAATTCGCAACGCAAAAGTAAAATTCACAACGCGAAAGTAAAATTCGCAA
* * * * * * *
1171794 AGCAAAAGTCAAATTCGCAACGCAAAAGTCAAATTCACAACGCGAAAGTCAAATTTGCTA
1 TGCGATAGTCAAATTCGCAACGCAAAAGTAAAATTCACAACGCGAAAGTAAAATTCGCAA
*
1171854 TGCGATAGTCAAATTTGCAA
1 TGCGATAGTCAAATTCGCAA
1171874 TGCTTATTTC
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 67 1.00
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (60 bp):
TGCGATAGTCAAATTCGCAACGCAAAAGTAAAATTCACAACGCGAAAGTAAAATTCGCAA
Found at i:1171876 original size:20 final size:20
Alignment explanation
Indices: 1171735--1171873 Score: 152
Period size: 20 Copynumber: 7.0 Consensus size: 20
1171725 AATAAGCGTT
*
1171735 GCGATAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
* *
1171755 GCGAAAGTAAAATTCACAAC
1 GCGAAAGTCAAATTCGCAAC
* * *
1171775 GTGAAAGTAAAATTCGCAAA
1 GCGAAAGTCAAATTCGCAAC
*
1171795 GCAAAAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
* *
1171815 GCAAAAGTCAAATTCACAAC
1 GCGAAAGTCAAATTCGCAAC
* * *
1171835 GCGAAAGTCAAATTTGCTAT
1 GCGAAAGTCAAATTCGCAAC
* *
1171855 GCGATAGTCAAATTTGCAA
1 GCGAAAGTCAAATTCGCAA
1171874 TGCTTATTTC
Statistics
Matches: 101, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 101 1.00
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.20
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Found at i:1172186 original size:18 final size:18
Alignment explanation
Indices: 1172163--1172198 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1172153 AAGCCAGTTG
*
1172163 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1172181 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
1172199 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1174421 original size:24 final size:24
Alignment explanation
Indices: 1174394--1174446 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
1174384 CCATCACATC
*
1174394 ATCAAAATCCGCGTATTGATCAAG
1 ATCAAAATCCGCGTATTGACCAAG
* *
1174418 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGCGTATTGACCAAG
1174442 ATCAA
1 ATCAA
1174447 TTCGAATACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
ATCAAAATCCGCGTATTGACCAAG
Found at i:1175394 original size:20 final size:20
Alignment explanation
Indices: 1175345--1175398 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1175335 CGATTTACAT
1175345 ATTCGCGTTGCGAAATTGGA
1 ATTCGCGTTGCGAAATTGGA
* *
1175365 A-ACTGGGTTGCGAAATTGGA
1 ATTC-GCGTTGCGAAATTGGA
1175385 ATTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
1175399 TTTGAGATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (20 bp):
ATTCGCGTTGCGAAATTGGA
Found at i:1178535 original size:45 final size:45
Alignment explanation
Indices: 1178485--1178579 Score: 109
Period size: 45 Copynumber: 2.1 Consensus size: 45
1178475 TGGTGAATGA
* * * *
1178485 TCCCATGTTCATGCGCAATACCTCGCATAACTCTAAGCGGCATGG
1 TCCCATGGTCATGAGCAATACCTCGAATAACTCCAAGCGGCATGG
* ** * *
1178530 TCCCATGGTCATGAGCATTGTCTCGAATAGCTCCAAGCGGTATGG
1 TCCCATGGTCATGAGCAATACCTCGAATAACTCCAAGCGGCATGG
1178575 TCCCA
1 TCCCA
1178580 AGGTTATCAC
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.25
Consensus pattern (45 bp):
TCCCATGGTCATGAGCAATACCTCGAATAACTCCAAGCGGCATGG
Found at i:1185188 original size:28 final size:28
Alignment explanation
Indices: 1185144--1185210 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
1185134 AACAAGAAAC
*
1185144 TAAAAACATAATGAAAATAAAAAATATA
1 TAAAAAAATAATGAAAATAAAAAATATA
1185172 TAAATAAAATAAT-AAAATAAAAAATATA
1 TAAA-AAAATAATGAAAATAAAAAATATA
*
1185200 TATAAAAATAA
1 TAAAAAAATAA
1185211 AAATGTATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 7 0.19
28 22 0.61
29 7 0.19
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.24
Consensus pattern (28 bp):
TAAAAAAATAATGAAAATAAAAAATATA
Found at i:1185207 original size:13 final size:13
Alignment explanation
Indices: 1185160--1185207 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
1185150 CATAATGAAA
1185160 ATAAAAAATATAT
1 ATAAAAAATATAT
*
1185173 A-AATAAAATAATAAA
1 ATAA-AAAAT-AT-AT
1185188 ATAAAAAATATAT
1 ATAAAAAATATAT
1185201 ATAAAAA
1 ATAAAAA
1185208 TAAAAATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 2 0.07
13 14 0.48
14 4 0.14
15 7 0.24
16 2 0.07
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
ATAAAAAATATAT
Found at i:1185238 original size:41 final size:39
Alignment explanation
Indices: 1185163--1185290 Score: 116
Period size: 41 Copynumber: 3.1 Consensus size: 39
1185153 AATGAAAATA
** *
1185163 AAAAATATATAAATAA-AATAATAAAATAAAAAATATATAT
1 AAAAATA-ATAAATAATAATAATAAAATACTAAATATA-AC
*
1185203 AAAAATAA-AAATGTATAATTAATAAAATACTAAATAGTAAC
1 AAAAATAATAAAT-AATAA-TAATAAAATACTAAATA-TAAC
* *
1185244 AATAATAATAAATAATAAAAATAAATATACTAAATATTAAC
1 AAAAATAATAAATAATAATAATAAA-ATACTAAATA-TAAC
1185285 TAAAAA
1 -AAAAA
1185291 ATAGTAATAG
Statistics
Matches: 72, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
38 4 0.06
39 2 0.03
40 15 0.21
41 41 0.57
42 10 0.14
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (39 bp):
AAAAATAATAAATAATAATAATAAAATACTAAATATAAC
Found at i:1185255 original size:19 final size:19
Alignment explanation
Indices: 1185163--1185267 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 19
1185153 AATGAAAATA
1185163 AAAAATATATAAATAAAATAAT
1 AAAAATA-AT-AAT-AAATAAT
1185185 -AAAATAA-AA-AATATATAT
1 AAAAATAATAATAA-ATA-AT
* **
1185203 AAAAATAAAAATGTATAATT
1 AAAAATAATAATAAATAA-T
* * *
1185223 AATAA-AATACTAAATAGT
1 AAAAATAATAATAAATAAT
*
1185241 AACAATAATAATAAATAAT
1 AAAAATAATAATAAATAAT
1185260 AAAAATAA
1 AAAAATAA
1185268 ATATACTAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 17
0.69 0.13 0.18
Matches are distributed among these distances:
16 2 0.03
17 3 0.05
18 9 0.14
19 33 0.52
20 11 0.17
21 6 0.09
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAAATAATAATAAATAAT
Found at i:1185266 original size:16 final size:16
Alignment explanation
Indices: 1185177--1185267 Score: 62
Period size: 16 Copynumber: 5.4 Consensus size: 16
1185167 ATATATAAAT
1185177 AAAATAATAAAATAA-A
1 AAAATAAT-AAATAATA
1185193 AAATATATATAAA-AATA
1 AAA-ATA-ATAAATAATA
* *
1185210 AAAATGTATAATTAAT-
1 AAAAT-AATAAATAATA
* *
1185226 AAAATACTAAATAGTAA
1 AAAATAATAAATAAT-A
1185243 CAATAATAATAAATAATA
1 -AA-AATAATAAATAATA
1185261 AAAATAA
1 AAAATAA
1185268 ATATACTAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
15 6 0.10
16 21 0.36
17 15 0.26
18 5 0.09
19 11 0.19
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (16 bp):
AAAATAATAAATAATA
Found at i:1185277 original size:22 final size:22
Alignment explanation
Indices: 1185223--1185279 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 22
1185213 ATGTATAATT
* *
1185223 AATAAA-ATACTAAATAGTAAC
1 AATAAATATACTAAATAATAAA
1185244 AAT-AATA-A-TAAATAATAAA
1 AATAAATATACTAAATAATAAA
1185263 AATAAATATACTAAATA
1 AATAAATATACTAAATA
1185280 TTAACTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
19 12 0.40
20 7 0.23
21 5 0.17
22 6 0.20
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (22 bp):
AATAAATATACTAAATAATAAA
Found at i:1185392 original size:2 final size:2
Alignment explanation
Indices: 1185382--1185413 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1185372 CATAGAAAAA
1185382 AT AT A- 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
1185414 ATAGGAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1185470 original size:16 final size:17
Alignment explanation
Indices: 1185449--1185482 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
1185439 GAAAAATGAA
1185449 AAAAAATATAA-TAAAT
1 AAAAAATATAATTAAAT
1185465 AAAAAATATAATTAAAT
1 AAAAAATATAATTAAAT
1185482 A
1 A
1185483 TATATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAAAATATAATTAAAT
Found at i:1185935 original size:37 final size:37
Alignment explanation
Indices: 1185889--1185977 Score: 106
Period size: 37 Copynumber: 2.4 Consensus size: 37
1185879 GCTTGTGGAT
* * *
1185889 CTATCTTTAGGAGTTTAAATAATAGTAGAACTCTATC
1 CTATTTTTAGGAGTTTAAATAATAGCAAAACTCTATC
* ** * *
1185926 CTATTTTTAGGAGTTTGAATCCTAGCAAAATTTTATC
1 CTATTTTTAGGAGTTTAAATAATAGCAAAACTCTATC
1185963 CTATTTTTAGGAGTT
1 CTATTTTTAGGAGTT
1185978 GAATCTAGTA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (37 bp):
CTATTTTTAGGAGTTTAAATAATAGCAAAACTCTATC
Found at i:1186664 original size:103 final size:104
Alignment explanation
Indices: 1186479--1186677 Score: 294
Period size: 103 Copynumber: 1.9 Consensus size: 104
1186469 AGCATGTTCC
* * *
1186479 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAA
1 GAGTACAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAACCGAGAAATTGTTTGTTGACAA
1186544 CCAACCGTCCTTCGTTGTGAAGTTGAACTTGCGTGTCTG
66 CCAACCGTCCTTCGTTGTGAAGTTGAACTTGCGTGTCTG
* * ** *
1186583 GAGTACAATATCCTTCGTTGTGAAGTTGAAA-TGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTACAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAACCGAGAAATTGTTTGTTGACAA
*
1186647 -CAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
66 CCAACCGT-CCTTCGTTGTGAAGTTGAACTTG
1186678 TTTGTCGAGT
Statistics
Matches: 85, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
102 6 0.07
103 51 0.60
104 28 0.33
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.32
Consensus pattern (104 bp):
GAGTACAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAACCGAGAAATTGTTTGTTGACAA
CCAACCGTCCTTCGTTGTGAAGTTGAACTTGCGTGTCTG
Found at i:1187119 original size:102 final size:103
Alignment explanation
Indices: 1186851--1187157 Score: 422
Period size: 101 Copynumber: 3.1 Consensus size: 103
1186841 TTCGTTAAAT
* * * * *
1186851 TGTTTTCAAAGTTTATGTTT--GGAGAGACTGTCTCAAGGGAGAC--AA---TCGTTTCAAGGGA
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTGTTTCGAGGGA
* *
1186909 AACTATCTCAAGCGAGATAAAATTCATTTCAAGGG-AA
66 AACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
1186946 TGTTTTCAATGTTTATGTTTCAAGAGAAACTG--TCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT-TGTTTCGAGGG
*
1187009 AAACTATCTCAAGAGAGAAAAAAATCATTTCAAGGGAAA
65 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
1187048 TGTTTTCAATG-TTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTGTTTCGAGGGA
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTGTTTCGAGGGA
* * *
1187112 AACTATCTTAGGAGAG-AAAAATTAATTTCAAGGGAAA
66 AACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
1187149 TGTTTTCAA
1 TGTTTTCAA
1187158 GAGAAACTGT
Statistics
Matches: 189, Mismatches: 12, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
95 30 0.16
97 10 0.05
100 1 0.01
101 90 0.48
102 39 0.21
103 19 0.10
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (103 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTGTTTCGAGGGA
AACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
Found at i:1187350 original size:66 final size:71
Alignment explanation
Indices: 1187235--1187365 Score: 182
Period size: 66 Copynumber: 1.9 Consensus size: 71
1187225 AAAAAAACAG
* *
1187235 TGAGTGAAATGAAATGCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGACAAAT-TGTTTAAGAAA
1 TGAGTGAAATGAAATGCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAATATGTTTAAGAAA
1187299 CAATCT
66 CAATCT
* * *
1187305 TGAGTGAAAT-AAAT-C-TCTTTCGAG-AAAAACAGTCTCAAGTGAGACAATTATGTTTTAGAAA
1 TGAGTGAAATGAAATGCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAATATGTTTAAGAAA
1187366 AACAAATTGA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
66 21 0.38
67 19 0.35
68 1 0.02
69 4 0.07
70 10 0.18
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (71 bp):
TGAGTGAAATGAAATGCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAATATGTTTAAGAAA
CAATCT
Found at i:1188859 original size:177 final size:178
Alignment explanation
Indices: 1188473--1188984 Score: 743
Period size: 177 Copynumber: 2.9 Consensus size: 178
1188463 ATCAGGTATA
* * *
1188473 ACTGAAGGGTTCATCTCATCAC--AGTCTTTGACCTAACAAAAGCAGTGGAGCAAAGACCG-ATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* *
1188535 GCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCT-TTCATAAAGCCAGGGCTTTCGAGTT
66 GCAAGTGTCCGAGCAGTGTCATAG-TTTGAA-CTAATCTATTCATAAAGCCAGGGCTTTCGAGTT
1188598 TCCTCTATAACCAATTGCCTTAGTGG-ATAGCTCAGC-TTAGAGGGACAAATC
129 T-CTC--TAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* *
1188649 ACTGAAGGGTTCGTCTCATCACAAAGT-TTTGGCCTGACAAAAGCAGTGGTGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
1188713 CCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTT
66 GCAAGTGTCCGAGCAGTGTCATAGTTTGAAC-TAATCTATTCATAAAGCCAGGGCTTTCGAGTTT
1188778 CTCTAACCAATTGCCTTAGTGGAAT-GCTCAGCTTTAGAGGGACAAATC
130 CTCTAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
1188826 ACTGAAGGG-TCATCTCATCACAAAGTCTTTGGCCTGACAAAAGTAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
1188890 GCAAGTGTCCCAGCAGTGTCATAG-TTGAAC--ATCTATTCAT-AAG-CAGGGCTTTCGAGTTTC
66 GCAAGTGTCCGAGCAGTGTCATAGTTTGAACTAATCTATTCATAAAGCCAGGGCTTTCGAGTTTC
*
1188950 -CTATAACAA-TGCCTTAGTGGAATAGCTCAGCTTTA
131 TCTA-ACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
1188985 CGGATTAATT
Statistics
Matches: 311, Mismatches: 14, Indels: 27
0.88 0.04 0.08
Matches are distributed among these distances:
170 17 0.05
171 32 0.10
172 3 0.01
173 10 0.03
176 69 0.22
177 112 0.36
178 41 0.13
179 27 0.09
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (178 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCAAGTGTCCGAGCAGTGTCATAGTTTGAACTAATCTATTCATAAAGCCAGGGCTTTCGAGTTTC
TCTAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:1192390 original size:18 final size:18
Alignment explanation
Indices: 1192359--1192393 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1192349 TGCAGATTAT
1192359 GGAAATAAATAAAAGAGA
1 GGAAATAAATAAAAGAGA
1192377 GGAAA-AAATGAAAAGAG
1 GGAAATAAAT-AAAAGAG
1192394 TAGTAAGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.66, C:0.00, G:0.26, T:0.09
Consensus pattern (18 bp):
GGAAATAAATAAAAGAGA
Found at i:1193690 original size:25 final size:25
Alignment explanation
Indices: 1193662--1193715 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
1193652 ATAATGAAAT
* *
1193662 AAATAAATAGTATAAATAAAATA-AA
1 AAATAAAAAATATAAA-AAAATATAA
*
1193687 AAATAAAAAATATATAAAAATATAA
1 AAATAAAAAATATAAAAAAATATAA
1193712 AAAT
1 AAAT
1193716 GTATGTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (25 bp):
AAATAAAAAATATAAAAAAATATAA
Found at i:1193715 original size:18 final size:18
Alignment explanation
Indices: 1193658--1193715 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 18
1193648 AAACATAATG
* *
1193658 AAATAAATAAATAGTATAA
1 AAATATATAAA-AATATAA
*
1193677 ATAAAATA-AAAAATA-AA
1 A-AATATATAAAAATATAA
1193694 AAATATATAAAAATATAA
1 AAATATATAAAAATATAA
1193712 AAAT
1 AAAT
1193716 GTATGTATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
16 5 0.16
17 10 0.31
18 9 0.28
19 4 0.12
20 4 0.12
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
AAATATATAAAAATATAA
Found at i:1194443 original size:36 final size:35
Alignment explanation
Indices: 1194397--1194483 Score: 102
Period size: 35 Copynumber: 2.4 Consensus size: 35
1194387 GCTTGTAGAT
*
1194397 CTATCTTTAGGAGTTTAAATAATAGTAGAACTCTATC
1 CTAT-TTTAGGAGTTTAAATAATAGCA-AACTCTATC
* ** * *
1194434 CTATTTTAGGAGTTTTAATCCTAGCAAATTTTATC
1 CTATTTTAGGAGTTTAAATAATAGCAAACTCTATC
1194469 CTATTTTAGGAGTTT
1 CTATTTTAGGAGTTT
1194484 GAATCCTAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
35 22 0.50
36 18 0.41
37 4 0.09
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.44
Consensus pattern (35 bp):
CTATTTTAGGAGTTTAAATAATAGCAAACTCTATC
Found at i:1201155 original size:24 final size:23
Alignment explanation
Indices: 1201110--1201160 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
1201100 GTTCGTTAAC
* *
1201110 GTTCGTTTATATTGTTCATTTAT
1 GTTCGTTTACATCGTTCATTTAT
1201133 GTTCGTTTACATCCGTTCATTTAT
1 GTTCGTTTACAT-CGTTCATTTAT
1201157 GTTC
1 GTTC
1201161 ATTCATTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.16, C:0.16, G:0.14, T:0.55
Consensus pattern (23 bp):
GTTCGTTTACATCGTTCATTTAT
Found at i:1204257 original size:37 final size:39
Alignment explanation
Indices: 1204201--1204293 Score: 136
Period size: 37 Copynumber: 2.4 Consensus size: 39
1204191 GTTGTAAAAC
*
1204201 ATATTTGTTGAATTAATTATTAATAATATTAAAATTT-TAT
1 ATATTTGTTTAA--AATTATTAATAATATTAAAATTTCTAT
*
1204241 ATATTT-TTTAAAATTATTAATAATATTAATATTTCTAT
1 ATATTTGTTTAAAATTATTAATAATATTAAAATTTCTAT
1204279 ATATTTGTTTAAAAT
1 ATATTTGTTTAAAAT
1204294 ACAATATAAG
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
37 22 0.45
38 9 0.18
39 12 0.24
40 6 0.12
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (39 bp):
ATATTTGTTTAAAATTATTAATAATATTAAAATTTCTAT
Found at i:1205196 original size:6 final size:6
Alignment explanation
Indices: 1205185--1205236 Score: 77
Period size: 6 Copynumber: 8.7 Consensus size: 6
1205175 AACATACATT
* * *
1205185 AAGGAG AAGGAG AAGGAG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG
1205233 AAGG
1 AAGG
1205237 TTTATAAGTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:1206281 original size:101 final size:101
Alignment explanation
Indices: 1206106--1206309 Score: 372
Period size: 101 Copynumber: 2.0 Consensus size: 101
1206096 TCATGCATCA
* *
1206106 ATTATTGATGTATTATTGCAGATGTTGGAGGCCCGTGATTTCAACAATTATTGCCCAATTAATTG
1 ATTATTGATGCATTATTGCAGATGTTGGAGGCCCATGATTTCAACAATTATTGCCCAATTAATTG
1206171 AAGCAGTCGGGGCTTAATTTTTATATATAGGATATG
66 AAGCAGTCGGGGCTTAATTTTTATATATAGGATATG
* *
1206207 ATTATTGCTGCATTATTGCAGATGTTGGAGGCCCATGGTTTCAACAATTATTGCCCAATTAATTG
1 ATTATTGATGCATTATTGCAGATGTTGGAGGCCCATGATTTCAACAATTATTGCCCAATTAATTG
1206272 AAGCAGTCGGGGCTTAATTTTTATATATAGGATATG
66 AAGCAGTCGGGGCTTAATTTTTATATATAGGATATG
1206308 AT
1 AT
1206310 ATGGGATTAA
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
101 99 1.00
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (101 bp):
ATTATTGATGCATTATTGCAGATGTTGGAGGCCCATGATTTCAACAATTATTGCCCAATTAATTG
AAGCAGTCGGGGCTTAATTTTTATATATAGGATATG
Found at i:1206635 original size:42 final size:43
Alignment explanation
Indices: 1206550--1206636 Score: 106
Period size: 42 Copynumber: 2.0 Consensus size: 43
1206540 TTGATAGTTA
* ***
1206550 TATATTAAAAAATAATTAATTAGTTTGTTTGTTAGTCGTTAGT
1 TATATTAAAAAATAATTAATTAGTTTGTTAGTTAGTAAATAGT
*
1206593 TATA-TAAAAAATATTTAATTAGTTTG-TAGTTAGTTAAATAGT
1 TATATTAAAAAATAATTAATTAGTTTGTTAGTTAG-TAAATAGT
1206635 TA
1 TA
1206637 AGTTATATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
41 6 0.16
42 28 0.74
43 4 0.11
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.47
Consensus pattern (43 bp):
TATATTAAAAAATAATTAATTAGTTTGTTAGTTAGTAAATAGT
Done.