Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
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: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 7 of 79
Found at i:2359758 original size:9 final size:9
Alignment explanation
Indices: 2359744--2359774 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2359734 GTTAAACTAA
2359744 TCGAGTTAT
1 TCGAGTTAT
*
2359753 TCGAGTTAA
1 TCGAGTTAT
2359762 TCGAGTTAT
1 TCGAGTTAT
2359771 TCGA
1 TCGA
2359775 ATCAACTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:2359846 original size:9 final size:9
Alignment explanation
Indices: 2359829--2359865 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
2359819 TGAGTTTTCG
2359829 AATTCGAAT
1 AATTCGAAT
*
2359838 AACTCGAAT
1 AATTCGAAT
2359847 AATTCGAAT
1 AATTCGAAT
2359856 AATTCGAAT
1 AATTCGAAT
2359865 A
1 A
2359866 TCCAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:2367901 original size:16 final size:16
Alignment explanation
Indices: 2367866--2367901 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2367856 GGTCAGAATT
*
2367866 AAAATTTCAAATTTTA
1 AAAATTTCAAAATTTA
2367882 AAAATTTCAAAATTTGA
1 AAAATTTCAAAATTT-A
2367899 AAA
1 AAA
2367902 GTACAGGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.36
Consensus pattern (16 bp):
AAAATTTCAAAATTTA
Found at i:2368847 original size:4 final size:4
Alignment explanation
Indices: 2368838--2368889 Score: 50
Period size: 4 Copynumber: 13.0 Consensus size: 4
2368828 TAGGTAGCAT
* * * * * *
2368838 CATA CATA CATG CTTA CGTA CATA AATA CATA CATG CATG CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2368886 CATA
1 CATA
2368890 TATATATATG
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (4 bp):
CATA
Found at i:2368883 original size:24 final size:24
Alignment explanation
Indices: 2368839--2368885 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2368829 AGGTAGCATC
* *
2368839 ATACATACATGCTTACGTACATAA
1 ATACATACATGCATACATACATAA
*
2368863 ATACATACATGCATGCATACATA
1 ATACATACATGCATACATACATA
2368886 CATATATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (24 bp):
ATACATACATGCATACATACATAA
Found at i:2373948 original size:13 final size:13
Alignment explanation
Indices: 2373930--2373959 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2373920 ATTACATGCC
2373930 TGATGATTTTTGA
1 TGATGATTTTTGA
2373943 TGATGATTTTTGA
1 TGATGATTTTTGA
2373956 TGAT
1 TGAT
2373960 TGAATCTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.53
Consensus pattern (13 bp):
TGATGATTTTTGA
Found at i:2374378 original size:92 final size:92
Alignment explanation
Indices: 2374268--2374471 Score: 311
Period size: 92 Copynumber: 2.2 Consensus size: 92
2374258 TAATGTGGAG
* * *
2374268 CATGTACTCGATTGTGCATGAATGTTGGAAGCTGTTTTTCAGCTTGACATTCATGTATCTTCCAG
1 CATGCACTCGATTGTGCATGAATGTTGGAAGCTGTTTTTCAGCTAGACATTAATGTATCTTCCAG
*
2374333 ATTCAATGAAGCTACTTTAATA-AAGAA
66 ATTCAACGAAGCTACTTTAA-AGAAGAA
* * * *
2374360 CATGCACTCGATTGTGCATGAATTTTGGGAGTTGTTTTTTAGCTAGACATTAATGTATCTTCCAG
1 CATGCACTCGATTGTGCATGAATGTTGGAAGCTGTTTTTCAGCTAGACATTAATGTATCTTCCAG
2374425 ATTCAACGAAGCTACTTTAAAGAAGAA
66 ATTCAACGAAGCTACTTTAAAGAAGAA
*
2374452 CATGCACCCGATTGTGCATG
1 CATGCACTCGATTGTGCATG
2374472 TATTTTGAGA
Statistics
Matches: 102, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
91 1 0.01
92 101 0.99
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (92 bp):
CATGCACTCGATTGTGCATGAATGTTGGAAGCTGTTTTTCAGCTAGACATTAATGTATCTTCCAG
ATTCAACGAAGCTACTTTAAAGAAGAA
Found at i:2383612 original size:46 final size:46
Alignment explanation
Indices: 2383559--2383648 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
2383549 TTGCTATAAC
* *
2383559 TCAGTATGGTTTTCTTCACGGGAATACCATACCTACTTTTCACAAT
1 TCAGTATGGTTTTCTTCACGGAAATACCATACCTACATTTCACAAT
* *
2383605 TCAGTATGGTTTTCTTCACTGAAATATCATACCTACATTTCACA
1 TCAGTATGGTTTTCTTCACGGAAATACCATACCTACATTTCACA
2383649 CTTTGCCATG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (46 bp):
TCAGTATGGTTTTCTTCACGGAAATACCATACCTACATTTCACAAT
Found at i:2383747 original size:35 final size:35
Alignment explanation
Indices: 2383708--2383777 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
2383698 CCGAACGTAT
2383708 GTACTCAATCTTGCGTATCCCTTAATTTGAACTAA
1 GTACTCAATCTTGCGTATCCCTTAATTTGAACTAA
2383743 GTACTCAATCTTGCGTATCCCTTAATTTGAACTAA
1 GTACTCAATCTTGCGTATCCCTTAATTTGAACTAA
2383778 TAATCTAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (35 bp):
GTACTCAATCTTGCGTATCCCTTAATTTGAACTAA
Found at i:2383788 original size:35 final size:35
Alignment explanation
Indices: 2383712--2383789 Score: 131
Period size: 35 Copynumber: 2.2 Consensus size: 35
2383702 ACGTATGTAC
*
2383712 TCAATCTTGCGTATCCCTTAATTTGAACTAAGTAC
1 TCAATCTTGCGTATCCCTTAATTTGAACTAAGTAA
2383747 TCAATCTTGCGTATCCCTTAATTTGAACTAA-TAA
1 TCAATCTTGCGTATCCCTTAATTTGAACTAAGTAA
2383781 TCTAATCTT
1 TC-AATCTT
2383790 ATTCTCATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
34 4 0.10
35 37 0.90
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (35 bp):
TCAATCTTGCGTATCCCTTAATTTGAACTAAGTAA
Found at i:2384175 original size:14 final size:14
Alignment explanation
Indices: 2384156--2384184 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2384146 AACACCTTAT
2384156 CCAACCATTTTAGA
1 CCAACCATTTTAGA
2384170 CCAACCATTTTAGA
1 CCAACCATTTTAGA
2384184 C
1 C
2384185 TATTAAACAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.31, G:0.07, T:0.28
Consensus pattern (14 bp):
CCAACCATTTTAGA
Found at i:2384968 original size:16 final size:17
Alignment explanation
Indices: 2384922--2384969 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
2384912 AAATTCTTTT
*
2384922 TAAATAACAAAATTCAA
1 TAAATCACAAAATTCAA
*
2384939 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAA
*
2384956 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
2384970 TTCTAAATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 7 0.25
17 21 0.75
ACGTcount: A:0.56, C:0.17, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Found at i:2388214 original size:16 final size:16
Alignment explanation
Indices: 2388193--2388225 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2388183 AATGAGAAGA
2388193 AAAACTTT-GAATTGGT
1 AAAACTTTCG-ATTGGT
2388209 AAAACTTTCGATTGGT
1 AAAACTTTCGATTGGT
2388225 A
1 A
2388226 TAGGAGTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.94
17 1 0.06
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (16 bp):
AAAACTTTCGATTGGT
Found at i:2395069 original size:8 final size:9
Alignment explanation
Indices: 2395038--2395066 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
2395028 ATTTACACCC
2395038 TTTAAAATT
1 TTTAAAATT
2395047 TTTAAAATT
1 TTTAAAATT
2395056 TTTAAAATT
1 TTTAAAATT
2395065 TT
1 TT
2395067 AAATTAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTAAAATT
Found at i:2395463 original size:146 final size:147
Alignment explanation
Indices: 2395280--2395572 Score: 579
Period size: 146 Copynumber: 2.0 Consensus size: 147
2395270 CATTTAATAT
2395280 AAGAAAAAAATTTATATAATTATATACTAATTAATCAAAATATTTCAAATAATGTATCTATATTT
1 AAGAAAAAAATTTATATAATTATATACTAATTAATCAAAATATTTCAAATAATGTATCTATATTT
2395345 TAGTAATCTTAATATTTTTCAATTATGGATTAAATTTCTATTATGTTCTAATTTCCCTTAAATAC
66 TAGTAATCTTAATATTTTTCAATTATGGATTAAATTTCTATTATGTTCTAATTTCCCTTAAATAC
2395410 AAATATTATTTTAAGGA
131 AAATATTATTTTAAGGA
2395427 AAGAAAAAAA-TTATATAATTATATACTAATTAATCAAAATATTTCAAATAATGTATCTATATTT
1 AAGAAAAAAATTTATATAATTATATACTAATTAATCAAAATATTTCAAATAATGTATCTATATTT
2395491 TAGTAATCTTAATATTTTTCAATTATGGATTAAATTTCTATTATGTTCTAATTTCCCTTAAATAC
66 TAGTAATCTTAATATTTTTCAATTATGGATTAAATTTCTATTATGTTCTAATTTCCCTTAAATAC
2395556 AAATATTATTTTAAGGA
131 AAATATTATTTTAAGGA
2395573 GAAAGGATTG
Statistics
Matches: 146, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
146 136 0.93
147 10 0.07
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.44
Consensus pattern (147 bp):
AAGAAAAAAATTTATATAATTATATACTAATTAATCAAAATATTTCAAATAATGTATCTATATTT
TAGTAATCTTAATATTTTTCAATTATGGATTAAATTTCTATTATGTTCTAATTTCCCTTAAATAC
AAATATTATTTTAAGGA
Found at i:2419516 original size:31 final size:30
Alignment explanation
Indices: 2419480--2419551 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 30
2419470 GATTAAAACA
*
2419480 AAATTAAAGTTTTAAGTATACATTTGAACC
1 AAATTAAAGTTTTAAGTATACAATTGAACC
* * * * *
2419510 ACAATTAGAGTTTTATGTGTATAATTGCACC
1 A-AATTAAAGTTTTAAGTATACAATTGAACC
2419541 AAATTAAAGTT
1 AAATTAAAGTT
2419552 CATATGTACA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
30 10 0.29
31 24 0.71
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (30 bp):
AAATTAAAGTTTTAAGTATACAATTGAACC
Found at i:2440327 original size:63 final size:62
Alignment explanation
Indices: 2440248--2440376 Score: 168
Period size: 63 Copynumber: 2.1 Consensus size: 62
2440238 TCCTAAATAT
*** * * * *
2440248 AAAAAATTCAACAAATTTAGCCCTCATTGTTTACAAAATTTGTCATTTTAGTTCTAATTCTTA
1 AAAAAATTCAACAAATTTAGCCCTCAACATTTACAAAATTTATCAATTTAGTCCTAACTC-TA
* *
2440311 AAAAAATTCAATAAATTTGGCCCTCAACATTTACAAAATTTATCAATTTAGTCCTAACTCTA
1 AAAAAATTCAACAAATTTAGCCCTCAACATTTACAAAATTTATCAATTTAGTCCTAACTCTA
2440373 AAAA
1 AAAA
2440377 TAAAAAAAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
62 6 0.11
63 51 0.89
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (62 bp):
AAAAAATTCAACAAATTTAGCCCTCAACATTTACAAAATTTATCAATTTAGTCCTAACTCTA
Found at i:2441705 original size:2 final size:2
Alignment explanation
Indices: 2441698--2441729 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2441688 CTTTAAAGAG
2441698 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2441730 ATCTATGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2463034 original size:18 final size:18
Alignment explanation
Indices: 2463011--2463046 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2463001 TAATTTTGCG
2463011 TTTAATTTATAAAACACA
1 TTTAATTTATAAAACACA
2463029 TTTAATTTATAAAACACA
1 TTTAATTTATAAAACACA
2463047 GTTTGATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (18 bp):
TTTAATTTATAAAACACA
Found at i:2465653 original size:21 final size:18
Alignment explanation
Indices: 2465616--2465650 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2465606 GAAGAAAGAT
2465616 GGTGGGAAGAAAGATGAA
1 GGTGGGAAGAAAGATGAA
*
2465634 GGTGGGAAGAAGGATGA
1 GGTGGGAAGAAAGATGA
2465651 TGATAGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.49, T:0.11
Consensus pattern (18 bp):
GGTGGGAAGAAAGATGAA
Found at i:2469387 original size:14 final size:15
Alignment explanation
Indices: 2469368--2469397 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2469358 TTTAATATTA
2469368 ATTTAATTAT-TTTT
1 ATTTAATTATATTTT
2469382 ATTTAATTATATTTT
1 ATTTAATTATATTTT
2469397 A
1 A
2469398 ATGAGATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTAATTATATTTT
Found at i:2471253 original size:2 final size:2
Alignment explanation
Indices: 2471246--2471279 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2471236 TCAAACAATG
* *
2471246 TA TA TA TA TA TA TA TA TA TA TA TT TA TC TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2471280 CCATTCGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2472138 original size:18 final size:18
Alignment explanation
Indices: 2472115--2472152 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2472105 ATGTATAATG
2472115 AACTCAAATCATAAAAGT
1 AACTCAAATCATAAAAGT
2472133 AACTCAAATCATAAAAGT
1 AACTCAAATCATAAAAGT
2472151 AA
1 AA
2472153 AAACCAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.58, C:0.16, G:0.05, T:0.21
Consensus pattern (18 bp):
AACTCAAATCATAAAAGT
Found at i:2473650 original size:2 final size:2
Alignment explanation
Indices: 2473643--2473672 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2473633 AATAGTCAAC
2473643 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2473673 GTTGTTCGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2473993 original size:7 final size:7
Alignment explanation
Indices: 2473981--2474020 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
2473971 GATATAAGGT
2473981 TTAGGGG
1 TTAGGGG
2473988 TTAGGGG
1 TTAGGGG
*
2473995 TTAGGGA
1 TTAGGGG
*
2474002 TTAGGAG
1 TTAGGGG
2474009 TTAGGGG
1 TTAGGGG
2474016 TTAGG
1 TTAGG
2474021 AATTTAGGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.20, C:0.00, G:0.50, T:0.30
Consensus pattern (7 bp):
TTAGGGG
Found at i:2473998 original size:14 final size:14
Alignment explanation
Indices: 2473981--2474074 Score: 80
Period size: 14 Copynumber: 6.4 Consensus size: 14
2473971 GATATAAGGT
*
2473981 TTAGGGGTTAGGGG
1 TTAGGGGTTAGGAG
*
2473995 TTAGGGATTAGGAG
1 TTAGGGGTTAGGAG
*
2474009 TTAGGGGTTAGGAAT
1 TTAGGGGTTAGG-AG
* *
2474024 TTAGGGGCTAGAAGAT
1 TTAGGGGTTAG--GAG
*
2474040 TTAGGGGTTAGAAG
1 TTAGGGGTTAGGAG
* *
2474054 TTAGGGATTTAGGAT
1 TTAGGG-GTTAGGAG
2474069 TTAGGG
1 TTAGGG
2474075 TGTCAATTAA
Statistics
Matches: 65, Mismatches: 11, Indels: 7
0.78 0.13 0.08
Matches are distributed among these distances:
14 30 0.46
15 22 0.34
16 12 0.18
17 1 0.02
ACGTcount: A:0.26, C:0.01, G:0.43, T:0.31
Consensus pattern (14 bp):
TTAGGGGTTAGGAG
Found at i:2474011 original size:21 final size:21
Alignment explanation
Indices: 2473981--2474020 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2473971 GATATAAGGT
*
2473981 TTAGGGGTTAGGGGTTAGGGA
1 TTAGGAGTTAGGGGTTAGGGA
2474002 TTAGGAGTTAGGGGTTAGG
1 TTAGGAGTTAGGGGTTAGG
2474021 AATTTAGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.00, G:0.50, T:0.30
Consensus pattern (21 bp):
TTAGGAGTTAGGGGTTAGGGA
Found at i:2474043 original size:16 final size:16
Alignment explanation
Indices: 2474009--2474053 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
2473999 GGATTAGGAG
*
2474009 TTAGGGGTTAGGA-AT
1 TTAGGGGTTAGAAGAT
*
2474024 TTAGGGGCTAGAAGAT
1 TTAGGGGTTAGAAGAT
2474040 TTAGGGGTTAGAAG
1 TTAGGGGTTAGAAG
2474054 TTAGGGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.29, C:0.02, G:0.40, T:0.29
Consensus pattern (16 bp):
TTAGGGGTTAGAAGAT
Found at i:2474438 original size:23 final size:23
Alignment explanation
Indices: 2474407--2474462 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
2474397 ATTGGTGGAG
*
2474407 GGGGCTAGGAGATTTAGGG-GTTA
1 GGGGTTAGG-GATTTAGGGAGTTA
*
2474430 GGGGTTAGGGATTTAGGGATTTA
1 GGGGTTAGGGATTTAGGGAGTTA
*
2474453 GGGTTTAGGG
1 GGGGTTAGGG
2474463 TGTCAATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 9 0.31
23 20 0.69
ACGTcount: A:0.20, C:0.02, G:0.48, T:0.30
Consensus pattern (23 bp):
GGGGTTAGGGATTTAGGGAGTTA
Found at i:2474447 original size:8 final size:7
Alignment explanation
Indices: 2474419--2474463 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
2474409 GGCTAGGAGA
2474419 TTTAGGG
1 TTTAGGG
*
2474426 GTTAGGG
1 TTTAGGG
*
2474433 GTTAGGG
1 TTTAGGG
2474440 ATTTAGGG
1 -TTTAGGG
2474448 ATTTAGGG
1 -TTTAGGG
2474456 TTTAGGG
1 TTTAGGG
2474463 T
1 T
2474464 GTCAATTAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
7 21 0.60
8 14 0.40
ACGTcount: A:0.18, C:0.00, G:0.44, T:0.38
Consensus pattern (7 bp):
TTTAGGG
Found at i:2474775 original size:392 final size:387
Alignment explanation
Indices: 2474040--2474800 Score: 1310
Period size: 392 Copynumber: 2.0 Consensus size: 387
2474030 GCTAGAAGAT
2474040 TTAGGGGTTAGAAGTTAGGGATTTAGGATTTAGGGTGTCAATTAAGGGTACTACTCAAGTTAGGG
1 TTAGGGGTTAGAAGTTAGGGATTTAGGATTTAGGGTGTCAATTAAGGGTACTACTCAAGTTAGGG
2474105 GCTAGATTAATTAGTTTTATTAATTTATATATTAAATATGTTCTTATATGTTTGTAAATTATATA
66 GCTAGATTAATTAGTTTTATTAATTTATATATTAAATATGTTCTTATATGTTTGTAAATTATATA
*
2474170 ATAATAAATTTAATATTAAGTAGTGACCGTCCGGTTTTGTTTCTCCAAATTTTTGTCACTACTCT
131 ATAATAAATTTAATATTAAGTAGTGACCGTCCGGTTTCGTTTCTCCAAATTTTTGTCACTACTCT
2474235 ACAAAATCTGGTTCAGCCTTCTAATTTATAGTAGAAAGGATCGTTCTAAAAATATTTATTGATGA
196 ACAAAATCTGGTTCAGCCTTCTAATTTATAGTAGAAAGGATCGTTCTAAAAATATTTATTGATGA
* *
2474300 ACGACGGGATTTGGAGGGTTGGAAGCTAGCAGATGCCCCCTTTCGATATTTTGGCAATGTTCCTA
261 ACGACGAGATTTGGAGGGTTGGAAGCTAGCAGATGCCCCATTTCGATATTTTGGCAATGTTCCTA
* *
2474365 GGGCACCAATAGCACATGTCAAGAATCCTACAATTGGTGGAGGGGGCTAGGAGATTTAGGGG
326 GGGCACCAATAACACATGTCAAGAATCCTACAATTGGGGGAGGGGGCTAGGAGATTTAGGGG
* * *
2474427 TTAGGGGTTAGGGATTTAGGGATTTAGGGTTTAGGGTGTCAATTAAGGGTACTACTCAAGTTAGG
1 TTAGGGGTTA-GAAGTTAGGGATTTAGGATTTAGGGTGTCAATTAAGGGTACTACTCAAGTTAGG
2474492 GGCTAGATTAATTAGTTTTATTAATTTATATATTAAATATGTTCTTATATGTTTGTAAAATATAT
65 GGCTAGATTAATTAGTTTTATTAATTTATATATTAAATATGTTCTTATATGTTTGT-AAAT-TAT
* * **
2474557 AATAATTAATAAATTTAATATTAAGTAGTGACCG-CCTGGTTTCGTTTGTTTC-TCTTTTTGTCA
128 -ATAA-TAATAAATTTAATATTAAGTAGTGACCGTCC-GGTTTCGTTT-CTCCAAATTTTTGTCA
2474620 CTACTCTACAAAATCTGGTTCAGCCTTCTAATTTATAGTAGAAAGGATCGTTCTAAAAATATTTA
189 CTACTCTACAAAATCTGGTTCAGCCTTCTAATTTATAGTAGAAAGGATCGTTCTAAAAATATTTA
* *
2474685 TTGATGAATGACGAGATTTGGAGGGTTGGAAGCTAGCAGATGCCCCATTTCGGTATTTTGGCAAT
254 TTGATGAACGACGAGATTTGGAGGGTTGGAAGCTAGCAGATGCCCCATTTCGATATTTTGGCAAT
*
2474750 GTTCCTAGGGCACCGATAACACATGTCAAGAATCCTACAATTGGGGGAGGG
319 GTTCCTAGGGCACCAATAACACATGTCAAGAATCCTACAATTGGGGGAGGG
2474801 TTCGGTGATC
Statistics
Matches: 352, Mismatches: 15, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
387 10 0.03
388 107 0.30
389 4 0.01
390 3 0.01
391 6 0.02
392 220 0.62
393 2 0.01
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36
Consensus pattern (387 bp):
TTAGGGGTTAGAAGTTAGGGATTTAGGATTTAGGGTGTCAATTAAGGGTACTACTCAAGTTAGGG
GCTAGATTAATTAGTTTTATTAATTTATATATTAAATATGTTCTTATATGTTTGTAAATTATATA
ATAATAAATTTAATATTAAGTAGTGACCGTCCGGTTTCGTTTCTCCAAATTTTTGTCACTACTCT
ACAAAATCTGGTTCAGCCTTCTAATTTATAGTAGAAAGGATCGTTCTAAAAATATTTATTGATGA
ACGACGAGATTTGGAGGGTTGGAAGCTAGCAGATGCCCCATTTCGATATTTTGGCAATGTTCCTA
GGGCACCAATAACACATGTCAAGAATCCTACAATTGGGGGAGGGGGCTAGGAGATTTAGGGG
Found at i:2475621 original size:18 final size:19
Alignment explanation
Indices: 2475598--2475643 Score: 69
Period size: 17 Copynumber: 2.5 Consensus size: 19
2475588 AAATTAAACC
2475598 CTTTTTTTCTTTTTT-TTT
1 CTTTTTTTCTTTTTTCTTT
*
2475616 C-TTTTTCCTTTTTTCTTT
1 CTTTTTTTCTTTTTTCTTT
2475634 CTTTTTTTCT
1 CTTTTTTTCT
2475644 CTCTGCTGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 12 0.50
18 5 0.21
19 7 0.29
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (19 bp):
CTTTTTTTCTTTTTTCTTT
Found at i:2475965 original size:10 final size:10
Alignment explanation
Indices: 2475950--2476032 Score: 58
Period size: 10 Copynumber: 7.4 Consensus size: 10
2475940 AAAATTCTTT
2475950 TTCTTTTTTC
1 TTCTTTTTTC
2475960 TTCTTTTTTC
1 TTCTTTTTTC
2475970 TTTCCCCCTTTTTTC
1 -TT----CTTTTTTC
2475985 TTTCTTCTTCGTTC
1 -TTCTT-TT--TTC
* *
2475999 TTCCTTCTTC
1 TTCTTTTTTC
*
2476009 TTCCTTTTTC
1 TTCTTTTTTC
2476019 TTCTTTTTTC
1 TTCTTTTTTC
2476029 TTCT
1 TTCT
2476033 CCTTCGACAG
Statistics
Matches: 61, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
10 35 0.57
11 5 0.08
12 3 0.05
13 4 0.07
14 3 0.05
15 11 0.18
ACGTcount: A:0.00, C:0.29, G:0.01, T:0.70
Consensus pattern (10 bp):
TTCTTTTTTC
Found at i:2475992 original size:7 final size:7
Alignment explanation
Indices: 2475944--2476032 Score: 53
Period size: 7 Copynumber: 13.0 Consensus size: 7
2475934 TTTTAAAAAA
2475944 TTCTT-T
1 TTCTTCT
*
2475950 TTCTTTT
1 TTCTTCT
2475957 TTCTTCT
1 TTCTTCT
*
2475964 TTTTTCT
1 TTCTTCT
**
2475971 TTCCCCCT
1 TT-CTTCT
*
2475979 TTTTTCT
1 TTCTTCT
2475986 TTCTTC-
1 TTCTTCT
2475992 TTCGTTCT
1 TTC-TTCT
*
2476000 TCCTTC-
1 TTCTTCT
2476006 TTCTTCCT
1 TTCTT-CT
2476014 TT-TTC-
1 TTCTTCT
*
2476019 TTCTTTT
1 TTCTTCT
2476026 TTCTTCT
1 TTCTTCT
2476033 CCTTCGACAG
Statistics
Matches: 62, Mismatches: 13, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
5 2 0.03
6 15 0.24
7 37 0.60
8 8 0.13
ACGTcount: A:0.00, C:0.28, G:0.01, T:0.71
Consensus pattern (7 bp):
TTCTTCT
Found at i:2476171 original size:22 final size:22
Alignment explanation
Indices: 2476123--2476173 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
2476113 GCTCTCCCCC
* *
2476123 CTTTTCCTTTTTCTTTTTTCTT
1 CTTTTGCTCTTTCTTTTTTCTT
2476145 C-TTTGCTCTTTCTCTTTTTC-T
1 CTTTTGCTCTTTCT-TTTTTCTT
2476166 CTTTTGCT
1 CTTTTGCT
2476174 TGTTTTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.00, C:0.25, G:0.04, T:0.71
Consensus pattern (22 bp):
CTTTTGCTCTTTCTTTTTTCTT
Found at i:2477267 original size:11 final size:11
Alignment explanation
Indices: 2477247--2477279 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
2477237 ATTTATTGAC
*
2477247 TGTCAGTGAAT
1 TGTCAATGAAT
2477258 TGTCAATGAA-
1 TGTCAATGAAT
2477268 TGTCAATGAAT
1 TGTCAATGAAT
2477279 T
1 T
2477280 ATTAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.36
Consensus pattern (11 bp):
TGTCAATGAAT
Found at i:2477360 original size:13 final size:13
Alignment explanation
Indices: 2477314--2477405 Score: 96
Period size: 13 Copynumber: 6.9 Consensus size: 13
2477304 TATAACTTAC
2477314 ATTACTTAAATAT
1 ATTACTTAAATAT
* *
2477327 ATTAATTACTAAAAT
1 ATTACTTA--AATAT
2477342 -TTACTTAAATAT
1 ATTACTTAAATAT
*
2477354 ATTACTTAAATAC
1 ATTACTTAAATAT
* *
2477367 ATTACTTAACTAGA
1 ATTACTTAAATA-T
*
2477381 ATTTCTTAAATAT
1 ATTACTTAAATAT
2477394 ATTACTTAAATA
1 ATTACTTAAATA
2477406 CATGACTTAC
Statistics
Matches: 64, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
12 4 0.06
13 40 0.62
14 16 0.25
15 4 0.06
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (13 bp):
ATTACTTAAATAT
Found at i:2477389 original size:40 final size:40
Alignment explanation
Indices: 2477314--2477460 Score: 174
Period size: 40 Copynumber: 3.7 Consensus size: 40
2477304 TATAACTTAC
* *
2477314 ATTACTTAAATATATTAATTACTAAAATTTACTTAAATAT
1 ATTACTTAAATACATTACTTACTAAAATTTACTTAAATAT
*
2477354 ATTACTTAAATACATTACTTAACTAGAATTT-CTTAAATAT
1 ATTACTTAAATACATTACTT-ACTAAAATTTACTTAAATAT
* * **
2477394 ATTACTTAAATACATGACTTACTAAAATTAAAGT--ATAT
1 ATTACTTAAATACATTACTTACTAAAATTTACTTAAATAT
**
2477432 ATTACATTACTTACATTACTTACTAAAAT
1 ATTAC-TTAAATACATTACTTACTAAAAT
2477461 ATATTACCNN
Statistics
Matches: 93, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
38 9 0.10
39 28 0.30
40 47 0.51
41 9 0.10
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (40 bp):
ATTACTTAAATACATTACTTACTAAAATTTACTTAAATAT
Found at i:2477413 original size:13 final size:13
Alignment explanation
Indices: 2477311--2477414 Score: 86
Period size: 13 Copynumber: 7.8 Consensus size: 13
2477301 ATTTATAACT
2477311 TACATTACTTAAA
1 TACATTACTTAAA
* *
2477324 TATATTAATTACTAA
1 TACATTACTTA--AA
2477339 -A-ATTTACTTAAA
1 TACA-TTACTTAAA
*
2477351 TATATTACTTAAA
1 TACATTACTTAAA
*
2477364 TACATTACTTAAC
1 TACATTACTTAAA
* *
2477377 TAGAATTTCTTAAA
1 TA-CATTACTTAAA
*
2477391 TATATTACTTAAA
1 TACATTACTTAAA
*
2477404 TACATGACTTA
1 TACATTACTTA
2477415 CTAAAATTAA
Statistics
Matches: 73, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
12 2 0.03
13 51 0.70
14 18 0.25
15 2 0.03
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (13 bp):
TACATTACTTAAA
Found at i:2483157 original size:66 final size:65
Alignment explanation
Indices: 2483063--2483233 Score: 200
Period size: 66 Copynumber: 2.6 Consensus size: 65
2483053 GAGCAAATTA
* * * * *
2483063 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGATGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA
2483127 G
65 G
* *
2483128 CTACAACTAAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
2483193 G
65 G
* * * * *
2483194 CAGCAGCTTAAAGCAGATGCGGTAGCAAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
2483234 CGGCAGTGAG
Statistics
Matches: 90, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
65 2 0.02
66 84 0.93
67 4 0.04
ACGTcount: A:0.41, C:0.19, G:0.27, T:0.13
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:2483245 original size:21 final size:21
Alignment explanation
Indices: 2483224--2483316 Score: 96
Period size: 21 Copynumber: 4.4 Consensus size: 21
2483214 GGTAGCAAGA
** * *
2483224 GAAGCAGAGGCGGCAGTGAGA
1 GAAGCAGAGGCTACAGCGAGG
* *
2483245 GAAGTACAGGCTACAGCGAGG
1 GAAGCAGAGGCTACAGCGAGG
* * *
2483266 GAAACAGAGGCTAAAGTGAGG
1 GAAGCAGAGGCTACAGCGAGG
*
2483287 GAAGCAGAGGCTGCAGCGAGG
1 GAAGCAGAGGCTACAGCGAGG
2483308 GAAGCAGAG
1 GAAGCAGAG
2483317 CAGCGTCAAA
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.35, C:0.15, G:0.43, T:0.06
Consensus pattern (21 bp):
GAAGCAGAGGCTACAGCGAGG
Found at i:2483698 original size:43 final size:41
Alignment explanation
Indices: 2483635--2483721 Score: 95
Period size: 43 Copynumber: 2.1 Consensus size: 41
2483625 TAGTGGCGTT
*
2483635 TTTTTAAAAAACGCCACTAAAGGTGTTGG-CCTTTAGCGGCG
1 TTTTTAAAAAACGCCACTAAAGAT-TTGGTCCTTTAGCGGCG
* * * *
2483676 TTTTTAATAAAAGCTCCGCTAAAGATTTGGTTCTTTAGTGGCG
1 TTTTTAA-AAAA-CGCCACTAAAGATTTGGTCCTTTAGCGGCG
2483719 TTT
1 TTT
2483722 GTGGTCGAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
41 7 0.18
42 8 0.21
43 23 0.61
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (41 bp):
TTTTTAAAAAACGCCACTAAAGATTTGGTCCTTTAGCGGCG
Found at i:2483779 original size:43 final size:42
Alignment explanation
Indices: 2483732--2483827 Score: 129
Period size: 43 Copynumber: 2.3 Consensus size: 42
2483722 GTGGTCGAAG
* *
2483732 CGCCGCTAAAGACCTTAATCTTTAGCGACGCTTCTCGCAAAAA
1 CGCCGCTAAAGACCCTAATCTTTAGCGACGCTTC-CACAAAAA
* * * *
2483775 CGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTCCACTAAAG
1 CGCCGCTAAAGACCCTAATCTTTAGCGACGCTTCCACAAAAA
2483817 CGCCGCTAAAG
1 CGCCGCTAAAG
2483828 GTCTTAGTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
42 16 0.34
43 31 0.66
ACGTcount: A:0.27, C:0.32, G:0.20, T:0.21
Consensus pattern (42 bp):
CGCCGCTAAAGACCCTAATCTTTAGCGACGCTTCCACAAAAA
Found at i:2489008 original size:22 final size:22
Alignment explanation
Indices: 2488981--2489023 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2488971 AGTAAAAGAA
*
2488981 AAAAAAAAGTTAGCTCTTTCTG
1 AAAAAAAACTTAGCTCTTTCTG
*
2489003 AAAAAAGACTTAGCTCTTTCT
1 AAAAAAAACTTAGCTCTTTCT
2489024 ATCTCTATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.33
Consensus pattern (22 bp):
AAAAAAAACTTAGCTCTTTCTG
Found at i:2499306 original size:18 final size:18
Alignment explanation
Indices: 2499267--2499306 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2499257 AAATTAGGGC
*
2499267 TTTT-TTATTTTTTTAAA
1 TTTTATTATTTTTTGAAA
*
2499284 ATTTATTATTTTTTGAAA
1 TTTTATTATTTTTTGAAA
2499302 TTTTA
1 TTTTA
2499307 AAGATTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (18 bp):
TTTTATTATTTTTTGAAA
Found at i:2510237 original size:45 final size:45
Alignment explanation
Indices: 2510080--2510311 Score: 213
Period size: 44 Copynumber: 5.2 Consensus size: 45
2510070 GTACCAGCGT
* * * *
2510080 GAAGTAGATCAGAGATAACAAATCTT-CCTTTCCATACTGGTGGC
1 GAAGCAGATCAAAGATAACAGATCTTGCCTTCCCATACTGGTGGC
* * *** * *
2510124 AAAGCAGATCAAAGA-AAGCAGATCTTGTCTTCATGTACTGG-CGT
1 GAAGCAGATCAAAGATAA-CAGATCTTGCCTTCCCATACTGGTGGC
* *
2510168 GAAGTAGATCAGAGATAACAGATCTTGCCTTCCCATACTGGTGGC
1 GAAGCAGATCAAAGATAACAGATCTTGCCTTCCCATACTGGTGGC
* *** * *
2510213 GAAGCAGATCAAAGA-AAGCAGATCTTGTCTTCATGTACTGG-CGT
1 GAAGCAGATCAAAGATAA-CAGATCTTGCCTTCCCATACTGGTGGC
* * *
2510257 GAAGTAGATCAGAGATAATAGATCTTGCCTTCCCATACTGGTGGC
1 GAAGCAGATCAAAGATAACAGATCTTGCCTTCCCATACTGGTGGC
2510302 GAAGCAGATC
1 GAAGCAGATC
2510312 GAAGGAAAAA
Statistics
Matches: 143, Mismatches: 38, Indels: 13
0.74 0.20 0.07
Matches are distributed among these distances:
43 2 0.01
44 85 0.59
45 56 0.39
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (45 bp):
GAAGCAGATCAAAGATAACAGATCTTGCCTTCCCATACTGGTGGC
Found at i:2510243 original size:89 final size:89
Alignment explanation
Indices: 2510060--2510311 Score: 443
Period size: 89 Copynumber: 2.8 Consensus size: 89
2510050 ATAGCGGTTT
** * *
2510060 TTGTCTTCATGTACCAGCGTGAAGTAGATCAGAGATAACAAATCTT-CCTTTCCATACTGGTGGC
1 TTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGCCTTCCCATACTGGTGGC
*
2510124 AAAGCAGATCAAAGAAAGCAGATC
66 GAAGCAGATCAAAGAAAGCAGATC
2510148 TTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGCCTTCCCATACTGGTGGC
1 TTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGCCTTCCCATACTGGTGGC
2510213 GAAGCAGATCAAAGAAAGCAGATC
66 GAAGCAGATCAAAGAAAGCAGATC
*
2510237 TTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAATAGATCTTGCCTTCCCATACTGGTGGC
1 TTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGCCTTCCCATACTGGTGGC
2510302 GAAGCAGATC
66 GAAGCAGATC
2510312 GAAGGAAAAA
Statistics
Matches: 157, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
88 43 0.27
89 114 0.73
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.26
Consensus pattern (89 bp):
TTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGCCTTCCCATACTGGTGGC
GAAGCAGATCAAAGAAAGCAGATC
Found at i:2510589 original size:45 final size:44
Alignment explanation
Indices: 2510540--2510676 Score: 143
Period size: 45 Copynumber: 3.1 Consensus size: 44
2510530 AAAGATACCA
*
2510540 ATCTTATCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAG
1 ATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC-AAGAAAGCAG
*** * * *
2510585 ATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAGAGATTA-CAG
1 ATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCA-AGA-AAGCAG
* *
2510629 ATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAGCAG
1 ATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC-AAGAAAGCAG
2510674 ATC
1 ATC
2510677 AAAGAAAGCA
Statistics
Matches: 72, Mismatches: 15, Indels: 10
0.74 0.15 0.10
Matches are distributed among these distances:
43 1 0.01
44 34 0.47
45 36 0.50
46 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (44 bp):
ATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAGAAAGCAG
Found at i:2510647 original size:44 final size:45
Alignment explanation
Indices: 2510477--2510676 Score: 131
Period size: 44 Copynumber: 4.5 Consensus size: 45
2510467 NNNNNNNNNN
* *** * **
2510477 AGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG-CATGA
1 AGTAGATCGAAGAAAGCAGATCTTGCCTTCCCATACTGGTCGCGA
* * * * ** *
2510521 AATAGATCAAAAGATACCA-ATCTTATCTTCCCATACTGGTGGCGA
1 AGTAGATC-GAAGAAAGCAGATCTTGCCTTCCCATACTGGTCGCGA
* *** *
2510566 AGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACTGG-CGTGA
1 AGTAGATCGAAGAAAGCAGATCTTGCCTTCCCATACTGGTCGCGA
* *
2510610 AGTAGATC-AGAGATTA-CAGATCTTGCCTTCCCATACTGGTGGCGA
1 AGTAGATCGA-AGA-AAGCAGATCTTGCCTTCCCATACTGGTCGCGA
* *
2510655 AGCAGATCAAAGAAAGCAGATC
1 AGTAGATCGAAGAAAGCAGATC
2510677 AAAGAAAGCA
Statistics
Matches: 117, Mismatches: 31, Indels: 15
0.72 0.19 0.09
Matches are distributed among these distances:
43 1 0.01
44 63 0.54
45 52 0.44
46 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (45 bp):
AGTAGATCGAAGAAAGCAGATCTTGCCTTCCCATACTGGTCGCGA
Found at i:2510673 original size:14 final size:14
Alignment explanation
Indices: 2510654--2510690 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
2510644 ACTGGTGGCG
2510654 AAGCAGATCAAAGA
1 AAGCAGATCAAAGA
2510668 AAGCAGATCAAAGA
1 AAGCAGATCAAAGA
2510682 AAGCAGATC
1 AAGCAGATC
2510691 TTGTCTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.54, C:0.16, G:0.22, T:0.08
Consensus pattern (14 bp):
AAGCAGATCAAAGA
Found at i:2510797 original size:92 final size:92
Alignment explanation
Indices: 2510685--2511808 Score: 1584
Period size: 92 Copynumber: 12.4 Consensus size: 92
2510675 TCAAAGAAAG
* * *
2510685 CAGATCTTGTCTTCATGTACTGGTGTGAAGTAGATCAGAGATAATAGATCTTGCATTCCCATACT
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGCCTTCCCATACT
*
2510750 GGTGGAGAAGCAGATCGAAGGAAAAAT
66 GGTGGCGAAGCAGATCGAAGGAAAAAT
*
2510777 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATACCAGATCTTGCCTTCCCATACT
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGCCTTCCCATACT
2510842 GGTGGCGAAGCAGATCGAAGGAAAAAT
66 GGTGGCGAAGCAGATCGAAGGAAAAAT
*
2510869 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATACCAGATCTTGCCTTCCCATACT
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGCCTTCCCATACT
2510934 GGTGGCGAAGCAGATCGAAGGAAAAAT
66 GGTGGCGAAGCAGATCGAAGGAAAAAT
*
2510961 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATACCAGATCTTGCCTTCCCATACT
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGCCTTCCCATACT
2511026 GGTGGCGAAGCAGATCGAAGGAAAAAT
66 GGTGGCGAAGCAGATCGAAGGAAAAAT
*
2511053 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATACCAGATCTTGCCTTCCCATACT
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGCCTTCCCATACT
2511118 GGTGGCGAAGCAGATCGAAGGAAAAAT
66 GGTGGCGAAGCAGATCGAAGGAAAAAT
*
2511145 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATACCAGATCTTGCCTTCCCATACT
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGCCTTCCCATACT
* *
2511210 GGTGGCGAAGTAGATCGAAGGAAAAAA
66 GGTGGCGAAGCAGATCGAAGGAAAAAT
* * *
2511237 CAGATCTTGTCTTCATGTACTAGCGTGAAGTAGATCAGAGATACCAGATCTTGCCTTCACATACT
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGCCTTCCCATACT
*
2511302 GGTGGCGAAGCAGAT--AA--AAGAAAG
66 GGTGGCGAAGCAGATCGAAGGAA-AAAT
* * * *
2511326 CAGATATTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTATACT
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGCCTTCCCATACT
* * * *
2511391 AGTGGCGAAACAAATCGAA-G-AAAGT
66 GGTGGCGAAGCAGATCGAAGGAAAAAT
* * * *
2511416 -AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAAATCTTGTCTT-CCATACT
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGCCTTCCCATACT
* *
2511479 GGTAGCGAAGTAGATCGAAGGAAGAAA-
66 GGTGGCGAAGCAGATCGAAGGAA-AAAT
* * * * *
2511506 CAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAACAGATCGTGTCTTCCTATACT
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGCCTTCCCATACT
* * * *
2511571 AGTGGCGAAACAAATCGAA-G-AAAGT
66 GGTGGCGAAGCAGATCGAAGGAAAAAT
* * * *
2511596 -AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAAATCTTGTCTTCCCATACT
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGCCTTCCCATACT
* *
2511660 GGTGGCGAAGTAGATCGAAGGAAAAAG
66 GGTGGCGAAGCAGATCGAAGGAAAAAT
* * * * * * * *
2511687 CAGATCTTGTCTCCATGTATTAGCATGAAGTAGATCAAAGACAACAGATCTTGTCTCCCCATACT
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGCCTTCCCATACT
* * * *
2511752 GGTGGTGGAGTAGATCGAA-G-AGAA-
66 GGTGGCGAAGCAGATCGAAGGAAAAAT
*
2511776 CAGACCTTGTCTTCA--T--TGGCGTGAAGTAGATCA
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCA
2511809 AGCGCAGCAG
Statistics
Matches: 949, Mismatches: 70, Indels: 33
0.90 0.07 0.03
Matches are distributed among these distances:
85 15 0.02
87 1 0.00
88 22 0.02
89 216 0.23
90 10 0.01
91 62 0.07
92 623 0.66
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (92 bp):
CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAGAGATAACAGATCTTGCCTTCCCATACT
GGTGGCGAAGCAGATCGAAGGAAAAAT
Found at i:2519001 original size:11 final size:11
Alignment explanation
Indices: 2518976--2519005 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
2518966 TTGAATTGTT
2518976 TTTTTTAATGA
1 TTTTTTAATGA
2518987 -TTTTTAATGA
1 TTTTTTAATGA
2518997 TTTTTTAAT
1 TTTTTTAAT
2519006 CCAACCATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (11 bp):
TTTTTTAATGA
Found at i:2522573 original size:22 final size:22
Alignment explanation
Indices: 2522532--2522574 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2522522 TATCCAAATA
*
2522532 ATAACAACAAAATAGTAGCAAT
1 ATAACAACAAAATAGCAGCAAT
* *
2522554 ATAATAACAAAATGGCAGCAA
1 ATAACAACAAAATAGCAGCAA
2522575 AACAGTAGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.14, G:0.12, T:0.16
Consensus pattern (22 bp):
ATAACAACAAAATAGCAGCAAT
Found at i:2522971 original size:16 final size:16
Alignment explanation
Indices: 2522950--2522981 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2522940 TTGCTTCCAG
2522950 AGTAAATATTTAATTA
1 AGTAAATATTTAATTA
2522966 AGTAAATATTTAATTA
1 AGTAAATATTTAATTA
2522982 CTTTGACTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (16 bp):
AGTAAATATTTAATTA
Found at i:2526781 original size:25 final size:26
Alignment explanation
Indices: 2526752--2526806 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
2526742 GATTATAAGA
* *
2526752 TTTTAA-AAAATTATTATACTATT-AT
1 TTTTAATAAAATT-TTAAACCATTAAT
2526777 TTTTAATAAAATTTTAAACCATTAAT
1 TTTTAATAAAATTTTAAACCATTAAT
2526803 TTTT
1 TTTT
2526807 TTAATCACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (26 bp):
TTTTAATAAAATTTTAAACCATTAAT
Found at i:2531126 original size:40 final size:40
Alignment explanation
Indices: 2531071--2531151 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
2531061 GTGAGATAGG
2531071 AAAACCATTTGCATCCCAGAGTTATGATTTGATTGCTCAT
1 AAAACCATTTGCATCCCAGAGTTATGATTTGATTGCTCAT
2531111 AAAACCATTTGCATCCCAGAGTTATGATTTGATTGCTCAT
1 AAAACCATTTGCATCCCAGAGTTATGATTTGATTGCTCAT
2531151 A
1 A
2531152 CTTCTGATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.35
Consensus pattern (40 bp):
AAAACCATTTGCATCCCAGAGTTATGATTTGATTGCTCAT
Found at i:2542165 original size:24 final size:27
Alignment explanation
Indices: 2542135--2542185 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
2542125 CCACATCGTT
2542135 TCCTCCTCT-T-T-CTCCGCCGCCGCC
1 TCCTCCTCTGTCTGCTCCGCCGCCGCC
2542159 TCCTCCTCTGTCTGCTCCGCCGCCGCC
1 TCCTCCTCTGTCTGCTCCGCCGCCGCC
2542186 GCCGCCGCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 9 0.38
25 1 0.04
26 1 0.04
27 13 0.54
ACGTcount: A:0.00, C:0.57, G:0.16, T:0.27
Consensus pattern (27 bp):
TCCTCCTCTGTCTGCTCCGCCGCCGCC
Found at i:2543285 original size:14 final size:15
Alignment explanation
Indices: 2543266--2543294 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2543256 TTATTAAATG
2543266 AATGAATTA-AATAT
1 AATGAATTATAATAT
2543280 AATGAATTATAATAT
1 AATGAATTATAATAT
2543295 TTTTTTCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (15 bp):
AATGAATTATAATAT
Found at i:2543544 original size:17 final size:17
Alignment explanation
Indices: 2543522--2543556 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2543512 ACTTTTTTGT
2543522 AAAGTTAAAATGCCAAA
1 AAAGTTAAAATGCCAAA
**
2543539 AAAGTTATTATGCCAAA
1 AAAGTTAAAATGCCAAA
2543556 A
1 A
2543557 GAATATCATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.23
Consensus pattern (17 bp):
AAAGTTAAAATGCCAAA
Found at i:2549917 original size:21 final size:21
Alignment explanation
Indices: 2549876--2549921 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2549866 TTGGATTTTC
*
2549876 TTTGAAGAGAAAAATATTGGG
1 TTTGAAGAGAAAAATAATGGG
*
2549897 TTTGATGAG-AAAATCAATGGG
1 TTTGAAGAGAAAAAT-AATGGG
2549918 TTTG
1 TTTG
2549922 GAGGGAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.37, C:0.02, G:0.28, T:0.33
Consensus pattern (21 bp):
TTTGAAGAGAAAAATAATGGG
Found at i:2553551 original size:23 final size:23
Alignment explanation
Indices: 2553521--2553570 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
2553511 AATATGGGTT
2553521 GCTATGGACTATAGGAAGATTCG
1 GCTATGGACTATAGGAAGATTCG
2553544 GCTATGGACTATAGGAAGATTCG
1 GCTATGGACTATAGGAAGATTCG
2553567 GCTA
1 GCTA
2553571 AGGCATAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.26
Consensus pattern (23 bp):
GCTATGGACTATAGGAAGATTCG
Found at i:2554121 original size:42 final size:43
Alignment explanation
Indices: 2554054--2554214 Score: 166
Period size: 43 Copynumber: 3.8 Consensus size: 43
2554044 AATTTGAGAT
** * *
2554054 TTACGTGTAAGACCAGGTCTGGGACATTGGCGTCG-TATATAA
1 TTACGTGTAAGACCCTGTCTGGGACAGTGGCATCGTTATATAA
* * *
2554096 TTACGTGTAAGACCCTATCTAGGACAGTGGCATCGTTATTTAA
1 TTACGTGTAAGACCCTGTCTGGGACAGTGGCATCGTTATATAA
* * * *
2554139 TTACATGTAAGACCCTGTCTGGGACAGTGACATCGTTATTTGA
1 TTACGTGTAAGACCCTGTCTGGGACAGTGGCATCGTTATATAA
* *
2554182 TTACATGTAAGATCAC-GTCTGGGAC-GTTGGCAT
1 TTACGTGTAAGA-CCCTGTCTGGGACAG-TGGCAT
2554215 TGTACGAAAT
Statistics
Matches: 102, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
42 30 0.29
43 70 0.69
44 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (43 bp):
TTACGTGTAAGACCCTGTCTGGGACAGTGGCATCGTTATATAA
Found at i:2554202 original size:43 final size:41
Alignment explanation
Indices: 2554015--2554214 Score: 161
Period size: 43 Copynumber: 4.7 Consensus size: 41
2554005 TGTGATTTCG
* * *
2554015 TGTAAGATCACGTCTGGGACATTGGCATC-AATTTGAGATTTACG
1 TGTAAGA-CACGTCTGGGACAGTGGCATCGTATTT-A-A-TTACA
* * * * *
2554059 TGTAAGACCAGGTCTGGGACATTGGCGTCGTATATAATTACG
1 TGTAAGA-CACGTCTGGGACAGTGGCATCGTATTTAATTACA
* * *
2554101 TGTAAGACCCTATCTAGGACAGTGGCATCGTTATTTAATTACA
1 TGTAAGACAC-GTCTGGGACAGTGGCATCG-TATTTAATTACA
* * *
2554144 TGTAAGACCCTGTCTGGGACAGTGACATCGTTATTTGATTACA
1 TGTAAGACAC-GTCTGGGACAGTGGCATCG-TATTTAATTACA
2554187 TGTAAGATCACGTCTGGGAC-GTTGGCAT
1 TGTAAGA-CACGTCTGGGACAG-TGGCAT
2554215 TGTACGAAAT
Statistics
Matches: 132, Mismatches: 19, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
41 1 0.01
42 28 0.21
43 71 0.54
44 29 0.22
45 3 0.02
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (41 bp):
TGTAAGACACGTCTGGGACAGTGGCATCGTATTTAATTACA
Found at i:2554213 original size:86 final size:86
Alignment explanation
Indices: 2554015--2554214 Score: 194
Period size: 86 Copynumber: 2.3 Consensus size: 86
2554005 TGTGATTTCG
* *
2554015 TGTAAGATCACGTCTGGGACATTGGCATCAATTTGAGATTTACGTGTAAGACCAGGTCTGGGACA
1 TGTAAGATCACGTCTGGGACGTTGGCATCAATTTGAGATTTACATGTAAGACCAGGTCTGGGACA
* * * *
2554080 TTGGCGTCGTATATAATTACG
66 GTGACATCGTATATAATTACA
* * * * **
2554101 TGTAAGA-CCCTATCTAGGACAG-TGGCATCGTTATTT-A-A-TTACATGTAAGACCCTGTCTGG
1 TGTAAGATCAC-GTCTGGGAC-GTTGGCATC--AATTTGAGATTTACATGTAAGACCAGGTCTGG
* *
2554161 GACAGTGACATCGTTATTTGATTACA
62 GACAGTGACATCG-TATATAATTACA
2554187 TGTAAGATCACGTCTGGGACGTTGGCAT
1 TGTAAGATCACGTCTGGGACGTTGGCAT
2554215 TGTACGAAAT
Statistics
Matches: 90, Mismatches: 17, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
85 32 0.36
86 51 0.57
87 3 0.03
88 4 0.04
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (86 bp):
TGTAAGATCACGTCTGGGACGTTGGCATCAATTTGAGATTTACATGTAAGACCAGGTCTGGGACA
GTGACATCGTATATAATTACA
Found at i:2557627 original size:18 final size:17
Alignment explanation
Indices: 2557556--2557628 Score: 53
Period size: 18 Copynumber: 4.3 Consensus size: 17
2557546 TTAATTATTT
2557556 TTTAAAATTTTAAAAAA
1 TTTAAAATTTTAAAAAA
* *
2557573 TTCAAAAATTATAAAAAA
1 TT-TAAAATTTTAAAAAA
* **
2557591 --T-AATTTTTAAATACT
1 TTTAAAATTTTAAA-AAA
2557606 TTTAAAATTTTAAAAATA
1 TTTAAAATTTTAAAAA-A
2557624 TTTAA
1 TTTAA
2557629 TTACTAATGT
Statistics
Matches: 40, Mismatches: 10, Indels: 11
0.66 0.16 0.18
Matches are distributed among these distances:
14 8 0.20
15 1 0.03
17 4 0.10
18 27 0.68
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAAATTTTAAAAAA
Found at i:2560269 original size:6 final size:6
Alignment explanation
Indices: 2560260--2560290 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
2560250 AGAAACAGAA
2560260 GAGTTG GAGTTG GAGTTG GAGTTG GAGTTG G
1 GAGTTG GAGTTG GAGTTG GAGTTG GAGTTG G
2560291 TTATGATTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (6 bp):
GAGTTG
Found at i:2566258 original size:8 final size:8
Alignment explanation
Indices: 2566245--2566275 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
2566235 CAAGATAAAC
2566245 ATGTAATA
1 ATGTAATA
2566253 ATGTAATA
1 ATGTAATA
2566261 ATGTAATA
1 ATGTAATA
*
2566269 ATTTAAT
1 ATGTAAT
2566276 TATGAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (8 bp):
ATGTAATA
Found at i:2570598 original size:6 final size:6
Alignment explanation
Indices: 2570587--2570618 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
2570577 TTCTGAGAAT
2570587 GATAGG GATAGG GATAGG GATAGG GATAGG GA
1 GATAGG GATAGG GATAGG GATAGG GATAGG GA
2570619 CGGAGTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.50, T:0.16
Consensus pattern (6 bp):
GATAGG
Found at i:2580082 original size:22 final size:22
Alignment explanation
Indices: 2580040--2580082 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2580030 AATAGAATAA
*
2580040 ATTTAATATTAATTGTGAATTT
1 ATTTAATATTAATTGTAAATTT
*
2580062 ATTTAATTTTACATT-TAAATT
1 ATTTAATATTA-ATTGTAAATT
2580083 GTCAAATACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (22 bp):
ATTTAATATTAATTGTAAATTT
Found at i:2584487 original size:348 final size:347
Alignment explanation
Indices: 2583849--2584505 Score: 1206
Period size: 348 Copynumber: 1.9 Consensus size: 347
2583839 TGTGGTGAAG
*
2583849 AAGCAACTCTATTCTAAATTTTTGTACTGGCTTGAGGAGTCTGCTCTATTGTAGATTCTGGATTA
1 AAGCAACTCTATTCTAAATTTTTGTACTGGCTTGAGGAGTCGGCTCTATTGTAGATTCTGGATTA
*
2583914 ATCTGATGCTCCACCTACTTTTGATTTTCTTTATTGGAAGAGTCTTTAAGAGATAAGTTAGGTAG
66 ATCTGATGCTCCACCTACTTTTGATTTTCTTTATTGGAAGAGTCTTTAAGAGATAAATTAGGTAG
*
2583979 CATAATAATTTCATCAAAAACAATATCTCCGCTAATCATAACTTTTCTATTTTTAGGACACCATA
131 CATAATAATTTCATCAAAAACAATATCTCCGCTAATCATAAATTTTCTATTTTTAGGACACCATA
*
2584044 ACTTATACCCCTTTACACCAGCTTTATGACCAAGAAAAACATATTTAATAGATCTCGGTTCCAAT
196 ACTTATACCCATTTACACCAGCTTTATGACCAAGAAAAACATATTTAATAGATCTCGGTTCCAAT
2584109 TTTCCATTATCAACATGAGCATACGCAGGACACCCAAAGATCTATTAAATAGATCTCGGTTCCAT
261 TTTCCATTATCAACATGAGCATACGCAGGACACCCAAAGATCT-TTAAATAGATCTCGGTTCCAT
2584174 TGTAGATTAAAAAGATCTATTAA
325 TGTAGATTAAAAAGATCTATTAA
2584197 AAGCAACTCTATTCTAAATTTTTGTACTGGCTTGAGGAGTCGGCTCTATTGTAGATTCTGGATTA
1 AAGCAACTCTATTCTAAATTTTTGTACTGGCTTGAGGAGTCGGCTCTATTGTAGATTCTGGATTA
*
2584262 ATCTGATGCTCCACCTGCTTTTGATTTTCTTTATTGGAAGAGTCTTTAAGAGATAAATTAGGTAG
66 ATCTGATGCTCCACCTACTTTTGATTTTCTTTATTGGAAGAGTCTTTAAGAGATAAATTAGGTAG
* *
2584327 CATAATAGTTTCATCAAAAACAATATCTCTGCTAATCATAAATTTTCTATTTTTAGGACACCATA
131 CATAATAATTTCATCAAAAACAATATCTCCGCTAATCATAAATTTTCTATTTTTAGGACACCATA
* *
2584392 ACTTATACCCATTTATACCAGTTTTATGACCAAGAAAAACATATTTAATAGATCTCGGTTCCAAT
196 ACTTATACCCATTTACACCAGCTTTATGACCAAGAAAAACATATTTAATAGATCTCGGTTCCAAT
* *
2584457 TTTCCATTATCAACATGAGTATATGCAGGACACCCAAAGATCTTTAAAT
261 TTTCCATTATCAACATGAGCATACGCAGGACACCCAAAGATCTTTAAAT
2584506 TTTAATGGTC
Statistics
Matches: 298, Mismatches: 11, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
347 6 0.02
348 292 0.98
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (347 bp):
AAGCAACTCTATTCTAAATTTTTGTACTGGCTTGAGGAGTCGGCTCTATTGTAGATTCTGGATTA
ATCTGATGCTCCACCTACTTTTGATTTTCTTTATTGGAAGAGTCTTTAAGAGATAAATTAGGTAG
CATAATAATTTCATCAAAAACAATATCTCCGCTAATCATAAATTTTCTATTTTTAGGACACCATA
ACTTATACCCATTTACACCAGCTTTATGACCAAGAAAAACATATTTAATAGATCTCGGTTCCAAT
TTTCCATTATCAACATGAGCATACGCAGGACACCCAAAGATCTTTAAATAGATCTCGGTTCCATT
GTAGATTAAAAAGATCTATTAA
Found at i:2587702 original size:19 final size:19
Alignment explanation
Indices: 2587667--2587703 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2587657 TTTTAAAATG
**
2587667 TTTTTAAAATACTTTTTTA
1 TTTTTAAAATAAATTTTTA
2587686 TTTTTAAAATAAATTTTT
1 TTTTTAAAATAAATTTTT
2587704 GGTGTTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTAAAATAAATTTTTA
Found at i:2599614 original size:16 final size:17
Alignment explanation
Indices: 2599593--2599627 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2599583 AATTAATTTA
*
2599593 AATTAATTAATT-TCTC
1 AATTAAATAATTATCTC
2599609 AATTAAATAATTATCTC
1 AATTAAATAATTATCTC
2599626 AA
1 AA
2599628 CCCAATTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTAAATAATTATCTC
Found at i:2601412 original size:24 final size:23
Alignment explanation
Indices: 2601366--2601427 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
2601356 TGTCTTTCAC
2601366 AATTTTAGGG-TTTGTTTAGCTAA
1 AATTTTAGGGATTTGTTTAGCT-A
2601389 AATTTTAGGGATTTGTTT-GACTA
1 AATTTTAGGGATTTGTTTAG-CTA
*
2601412 AATTTTAGGCATTTGT
1 AATTTTAGGGATTTGT
2601428 CTTCCACAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
23 27 0.75
24 9 0.25
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.48
Consensus pattern (23 bp):
AATTTTAGGGATTTGTTTAGCTA
Found at i:2611432 original size:320 final size:321
Alignment explanation
Indices: 2610839--2611479 Score: 1275
Period size: 320 Copynumber: 2.0 Consensus size: 321
2610829 TATATTTAAA
2610839 AAATAGAATATATACACATATGATAGTGACAAATAGTTTTAATAAAAATAAAGAAAAATTGACAA
1 AAATAGAATATATACACATATGATAGTGACAAATAGTTTTAATAAAAATAAAGAAAAATTGACAA
2610904 AAAAAATTAATATATATATATGATATATGGAGAAACAATAAAAATGACGTGATGGTTATTAAATA
66 AAAAAATTAATATATATATATGATATATGGAGAAACAATAAAAATGACGTGATGGTTATTAAATA
2610969 AATAATTGACAAACTATAATATATGCAAAATTAAAATTAACAAACCTTTTATACGAAATCAATCC
131 AATAATTGACAAACTATAATATATGCAAAATTAAAATTAACAAACCTTTTATACGAAATCAATCC
2611034 TAATTTATTGATCAGAGATAAAATTAGTTAACGAAAATTATTCACTTTTCACCATTTAAATCCTC
196 TAATTTATTGATCAGAGATAAAATTAGTTAACGAAAATTATTCACTTTTCACCATTTAAATCCTC
2611099 GTATAAATTATTTCAAGTATGAGATTCATGAATAATTTTATTAATGAAAACTTATTTCCTT
261 GTATAAATTATTTCAAGTATGAGATTCATGAATAATTTTATTAATGAAAACTTATTTCCTT
2611160 AAATAGAATA-ATACACATATGATAGTGACAAATAGTTTTAATAAAAATAAAGAAAAATTGACAA
1 AAATAGAATATATACACATATGATAGTGACAAATAGTTTTAATAAAAATAAAGAAAAATTGACAA
2611224 AAAAAATTAATATATATATATGATATATGGAGAAACAATAAAAATGACGTGATGGTTATTAAATA
66 AAAAAATTAATATATATATATGATATATGGAGAAACAATAAAAATGACGTGATGGTTATTAAATA
2611289 AATAATTGACAAACTATAATATATGCAAAATTAAAATTAACAAACCTTTTATACGAAATCAATCC
131 AATAATTGACAAACTATAATATATGCAAAATTAAAATTAACAAACCTTTTATACGAAATCAATCC
2611354 TAATTTATTGATCAGAGATAAAATTAGTTAACGAAAATTATTCACTTTTCACCATTTAAATCCTC
196 TAATTTATTGATCAGAGATAAAATTAGTTAACGAAAATTATTCACTTTTCACCATTTAAATCCTC
2611419 GTATAAATTATTTCAAGTATGAGATTCATGAATAATTTTATTAATGAAAACTTATTTCCTT
261 GTATAAATTATTTCAAGTATGAGATTCATGAATAATTTTATTAATGAAAACTTATTTCCTT
2611480 TCTATAAAAC
Statistics
Matches: 320, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
320 310 0.97
321 10 0.03
ACGTcount: A:0.47, C:0.10, G:0.09, T:0.34
Consensus pattern (321 bp):
AAATAGAATATATACACATATGATAGTGACAAATAGTTTTAATAAAAATAAAGAAAAATTGACAA
AAAAAATTAATATATATATATGATATATGGAGAAACAATAAAAATGACGTGATGGTTATTAAATA
AATAATTGACAAACTATAATATATGCAAAATTAAAATTAACAAACCTTTTATACGAAATCAATCC
TAATTTATTGATCAGAGATAAAATTAGTTAACGAAAATTATTCACTTTTCACCATTTAAATCCTC
GTATAAATTATTTCAAGTATGAGATTCATGAATAATTTTATTAATGAAAACTTATTTCCTT
Found at i:2614246 original size:16 final size:16
Alignment explanation
Indices: 2614222--2614288 Score: 64
Period size: 18 Copynumber: 4.0 Consensus size: 16
2614212 ACGAATTATT
*
2614222 CCTCTCCCCCTCTCTC
1 CCTCCCCCCCTCTCTC
2614238 CCT-CCCCCCTCTCTC
1 CCTCCCCCCCTCTCTC
*
2614253 TCTCCCCCCATCTCTCTC
1 CCTCCCCCC--CTCTCTC
*
2614271 TCTCTCCCTCCCTCTCTC
1 -C-CTCCCCCCCTCTCTC
2614289 TCTCTATCTA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
15 13 0.31
16 8 0.19
18 14 0.33
20 7 0.17
ACGTcount: A:0.01, C:0.66, G:0.00, T:0.33
Consensus pattern (16 bp):
CCTCCCCCCCTCTCTC
Found at i:2614271 original size:20 final size:20
Alignment explanation
Indices: 2614231--2614293 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
2614221 TCCTCTCCCC
*
2614231 CTCTCTCCCTCCC-CCCTCT
1 CTCTCTCCCTCCCTCTCTCT
2614250 CTCTCTCCC-CCCATCTCTCT
1 CTCTCTCCCTCCC-TCTCTCT
2614270 CTCTCTCCCTCCCTCTCTCT
1 CTCTCTCCCTCCCTCTCTCT
2614290 CTCT
1 CTCT
2614294 ATCTATATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
18 3 0.08
19 9 0.22
20 25 0.62
21 3 0.08
ACGTcount: A:0.02, C:0.62, G:0.00, T:0.37
Consensus pattern (20 bp):
CTCTCTCCCTCCCTCTCTCT
Found at i:2614292 original size:16 final size:15
Alignment explanation
Indices: 2614223--2614288 Score: 80
Period size: 15 Copynumber: 4.3 Consensus size: 15
2614213 CGAATTATTC
2614223 CTCT-CCCCCTCTCT
1 CTCTCCCCCCTCTCT
*
2614237 CCCTCCCCCCTCTCT
1 CTCTCCCCCCTCTCT
2614252 CTCTCCCCCCATCTCT
1 CTCTCCCCCC-TCTCT
* *
2614268 CTCTCTCTCCCTCCCT
1 CTCTC-CCCCCTCTCT
2614284 CTCTC
1 CTCTC
2614289 TCTCTATCTA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
14 3 0.07
15 19 0.42
16 19 0.42
17 4 0.09
ACGTcount: A:0.02, C:0.65, G:0.00, T:0.33
Consensus pattern (15 bp):
CTCTCCCCCCTCTCT
Found at i:2616774 original size:51 final size:51
Alignment explanation
Indices: 2616698--2616862 Score: 251
Period size: 51 Copynumber: 3.3 Consensus size: 51
2616688 ACTTCTGATC
* *
2616698 AGTGACAAGTGATAAGTAGTAGCTTCAACTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATAAGTGACA
2616749 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATAAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATAAGTGACA
* * * * *
2616800 AGTGGCAAGTGATAAGTGGTAGCTT-AGCTACACTTATCTAATTAGGGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATAAGTGACA
*
2616850 AGTGATAAGTGAT
1 AGTGACAAGTGAT
2616863 CATACGTAAG
Statistics
Matches: 105, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 33 0.31
51 72 0.69
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.28
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATAAGTGACA
Found at i:2618585 original size:23 final size:23
Alignment explanation
Indices: 2618541--2618587 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
2618531 TTTAAAAATA
**
2618541 AAAAATAAATAAAAAAGCATTTT
1 AAAAATAAATAAAAAAAAATTTT
2618564 AAAAATAAA-AAAAATAAAATTTT
1 AAAAATAAATAAAAA-AAAATTTT
2618587 A
1 A
2618588 TTATATTCGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (23 bp):
AAAAATAAATAAAAAAAAATTTT
Found at i:2619523 original size:19 final size:20
Alignment explanation
Indices: 2619501--2619543 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2619491 CGGAAGAAAC
2619501 TTAT-AATT-TGTAATATTTT
1 TTATGAATTCTGTAAT-TTTT
*
2619520 TTATGAATTCTTTAATTTTT
1 TTATGAATTCTGTAATTTTT
2619540 TTAT
1 TTAT
2619544 TTATTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 12 0.57
21 5 0.24
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (20 bp):
TTATGAATTCTGTAATTTTT
Found at i:2620217 original size:28 final size:28
Alignment explanation
Indices: 2620164--2620218 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
2620154 TTGGCTTCAT
* *
2620164 TTTTTTATAAAAAAATATTTTATTTTTA
1 TTTTTAATAAAAAAAGATTTTATTTTTA
*
2620192 TTTTTAATAAAAAAAGACTTT-TTTTTA
1 TTTTTAATAAAAAAAGATTTTATTTTTA
2620219 ATTATAATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (28 bp):
TTTTTAATAAAAAAAGATTTTATTTTTA
Found at i:2620226 original size:27 final size:28
Alignment explanation
Indices: 2620170--2620226 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
2620160 TCATTTTTTT
* * * *
2620170 ATAAAAAAATATTTTATTTTTATTTTTA
1 ATAAAAAAAGACTTTATTTTTAATTATA
2620198 ATAAAAAAAGACTTT-TTTTTAATTATA
1 ATAAAAAAAGACTTTATTTTTAATTATA
2620225 AT
1 AT
2620227 TGAATTAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (28 bp):
ATAAAAAAAGACTTTATTTTTAATTATA
Found at i:2636600 original size:39 final size:39
Alignment explanation
Indices: 2636546--2636622 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
2636536 ACAATTACCA
*
2636546 AATTGCTATTAAACATATACATCAATCAGGGCACTATCG
1 AATTGCTATTAAACATATACATCAATCAGGACACTATCG
2636585 AATTGCTATTAAACATATACATCAATCAGGACACTATC
1 AATTGCTATTAAACATATACATCAATCAGGACACTATC
2636623 AAGTGGCGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (39 bp):
AATTGCTATTAAACATATACATCAATCAGGACACTATCG
Found at i:2643638 original size:84 final size:84
Alignment explanation
Indices: 2643491--2643650 Score: 207
Period size: 84 Copynumber: 1.9 Consensus size: 84
2643481 TTTTAGGGGT
* * * * *
2643491 TAAACTGTAATTTGATTATATATTAATTTATAACTTCTTTATTTAGAAGAGAATTGAATTGAAAA
1 TAAAATGTAATTTCATTATATATTAATTTATAACTTCTTTATTTAGAAGAGAACTAAAATGAAAA
2643556 TCTTTCATTTTGAAGGAGC
66 TCTTTCATTTTGAAGGAGC
* **
2643575 TAAAATGTAATTTCATTATATATTAATTTATAA-TTTTTCTATTTCTAAGA-AGACTAAAATGAA
1 TAAAATGTAATTTCATTATATATTAATTTATAACTTCTT-TATTTAGAAGAGA-ACTAAAATGAA
*
2643638 AATTTTTCATTTT
64 AATCTTTCATTTT
2643651 TGGGTACCAA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
83 5 0.08
84 60 0.92
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (84 bp):
TAAAATGTAATTTCATTATATATTAATTTATAACTTCTTTATTTAGAAGAGAACTAAAATGAAAA
TCTTTCATTTTGAAGGAGC
Found at i:2648506 original size:20 final size:20
Alignment explanation
Indices: 2648481--2648522 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
2648471 TCTTAGATAG
2648481 ATTTTTTTATTAAATTAAATT
1 ATTTTTTTATT-AATTAAATT
*
2648502 ATTTTTTTATTCATTAAATT
1 ATTTTTTTATTAATTAAATT
2648522 A
1 A
2648523 ATAGGATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTTTTATTAATTAAATT
Found at i:2649857 original size:21 final size:21
Alignment explanation
Indices: 2649832--2649880 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2649822 CAGAATTTAA
** *
2649832 AAATTAAATTTAAAAAGTATT
1 AAATTAAAAATAAAAAGTACT
*
2649853 AAATTAAAAATAAAAATTACT
1 AAATTAAAAATAAAAAGTACT
2649874 AAATTAA
1 AAATTAA
2649881 TAGAAATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
AAATTAAAAATAAAAAGTACT
Found at i:2666478 original size:33 final size:32
Alignment explanation
Indices: 2666340--2666500 Score: 115
Period size: 33 Copynumber: 4.8 Consensus size: 32
2666330 ACATTCGTAG
* *
2666340 TGCCATAACCCAGTTATGGTCTTATCATCAGAA
1 TGCCATAGCCCAGCTATGGTCTTA-CATCAGAA
* * * *
2666373 TGTCATAGCCCGGCTATGGTCTTACATATAAATA
1 TGCCATAGCCCAGCTATGGTCTTACAT-CAGA-A
* * * * * * * *
2666407 TTGCCATGGTCCAACCATGGTCTTACGGTTATAG
1 -TGCCATAGCCCAGCTATGGTCTTAC-ATCAGAA
* *
2666441 TGCCATAACCCAGTTATGGTCTTATCATCAGAA
1 TGCCATAGCCCAGCTATGGTCTTA-CATCAGAA
*
2666474 TGCCATAGCCCAGCTACGGTCTTACAT
1 TGCCATAGCCCAGCTATGGTCTTACAT
2666501 ATAAACACTG
Statistics
Matches: 95, Mismatches: 28, Indels: 11
0.71 0.21 0.08
Matches are distributed among these distances:
32 6 0.06
33 64 0.67
34 2 0.02
35 22 0.23
36 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (32 bp):
TGCCATAGCCCAGCTATGGTCTTACATCAGAA
Found at i:2666513 original size:101 final size:101
Alignment explanation
Indices: 2666328--2666566 Score: 390
Period size: 101 Copynumber: 2.4 Consensus size: 101
2666318 AATTCATCAT
* * * * *
2666328 TTACATTCGTAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGTCATAGCCCGGCTATGGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTACGGT
* *
2666393 CTTACATATAAATATTGCCATGGTCCAACCATGGTC
66 CTTACATATAAACACTGCCATGGTCCAACCATGGTC
2666429 TTACGGTT-ATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTACGG
1 TTAC-GTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTACGG
2666493 TCTTACATATAAACACTGCCATGGTCCAACCATGGTC
65 TCTTACATATAAACACTGCCATGGTCCAACCATGGTC
*
2666530 TTACGTTCATAGTGCCATAACCTAGTTATGGTCTTAT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTAT
2666567 TCCTCAATTC
Statistics
Matches: 128, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
100 3 0.02
101 123 0.96
102 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (101 bp):
TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTACGGT
CTTACATATAAACACTGCCATGGTCCAACCATGGTC
Found at i:2677960 original size:22 final size:22
Alignment explanation
Indices: 2677916--2677956 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2677906 ATAATACCAT
**
2677916 ATTAATAAGATTAAAATTATAA
1 ATTAATAAGATTAAAAAAATAA
2677938 ATTAATAA-ATTAAAAAAAT
1 ATTAATAAGATTAAAAAAAT
2677957 TAAAATTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (22 bp):
ATTAATAAGATTAAAAAAATAA
Found at i:2683073 original size:37 final size:36
Alignment explanation
Indices: 2683021--2683100 Score: 133
Period size: 37 Copynumber: 2.2 Consensus size: 36
2683011 AGGTTTCGAC
2683021 AACCTAATAGAAATTAATGAATTGATCAACAAATGG
1 AACCTAATAGAAATTAATGAATTGATCAACAAATGG
* *
2683057 AATCTAATTAGAAATTAATGAATTGATCAATAAATGG
1 AACCTAA-TAGAAATTAATGAATTGATCAACAAATGG
2683094 AACCTAA
1 AACCTAA
2683101 GCATCAAACA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
36 6 0.15
37 34 0.85
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (36 bp):
AACCTAATAGAAATTAATGAATTGATCAACAAATGG
Found at i:2684084 original size:24 final size:24
Alignment explanation
Indices: 2684040--2684091 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
2684030 TATACAGCCA
2684040 TGTGACAGCCTGTGTCTCAGGCCG
1 TGTGACAGCCTGTGTCTCAGGCCG
2684064 TGTGACAGTCTCTGT-TC-CAGGCCG
1 TGTGACAG-C-CTGTGTCTCAGGCCG
2684088 TGTG
1 TGTG
2684092 TACCTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 19 0.73
25 3 0.12
26 4 0.15
ACGTcount: A:0.12, C:0.27, G:0.33, T:0.29
Consensus pattern (24 bp):
TGTGACAGCCTGTGTCTCAGGCCG
Found at i:2686226 original size:79 final size:79
Alignment explanation
Indices: 2686132--2686277 Score: 256
Period size: 79 Copynumber: 1.8 Consensus size: 79
2686122 AGACGTGCCC
* *
2686132 ATATGCAGATAAAACATATCATAACATACTAGTTGCACATATAATTAACAGATCAAAACATGTTA
1 ATATGCAGATAAAACATATCAGAACATACTAGTTGCACATATAATTAACAGATCAAAACATGCTA
2686197 TTGGCATATTACCT
66 TTGGCATATTACCT
* *
2686211 ATATGCAGATAAAACATATCAGAACATACTAGTTGCACATATAGTTAATAGATCAAAACATGCTA
1 ATATGCAGATAAAACATATCAGAACATACTAGTTGCACATATAATTAACAGATCAAAACATGCTA
2686276 TT
66 TT
2686278 CGTATATTCG
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 63 1.00
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (79 bp):
ATATGCAGATAAAACATATCAGAACATACTAGTTGCACATATAATTAACAGATCAAAACATGCTA
TTGGCATATTACCT
Found at i:2702956 original size:3 final size:3
Alignment explanation
Indices: 2702948--2702994 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
2702938 TTCATTCTGT
2702948 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2702995 GCTTTGTTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2706501 original size:17 final size:16
Alignment explanation
Indices: 2706476--2706514 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
2706466 TGCTAATATT
*
2706476 TTAACTTATTTATAATA
1 TTAATTTATTTATAA-A
2706493 TTAATTTATTTATAAA
1 TTAATTTATTTATAAA
2706509 TTAATT
1 TTAATT
2706515 CAGTATACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAATTTATTTATAAA
Found at i:2706887 original size:14 final size:13
Alignment explanation
Indices: 2706859--2706892 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
2706849 TTATGTGTTG
2706859 TTATTATAATGTA
1 TTATTATAATGTA
*
2706872 TTATTCATATTGTA
1 TTATT-ATAATGTA
2706886 TTATTAT
1 TTATTAT
2706893 TTTATTGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.59
Consensus pattern (13 bp):
TTATTATAATGTA
Found at i:2710151 original size:3 final size:3
Alignment explanation
Indices: 2710145--2710180 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2710135 AAGAGTTTTT
2710145 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2710181 AAGATTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2720788 original size:30 final size:29
Alignment explanation
Indices: 2720745--2720802 Score: 107
Period size: 30 Copynumber: 2.0 Consensus size: 29
2720735 AAGGAAATAA
2720745 ATCCTAATTCCTAAGAATCAGTAATTGAT
1 ATCCTAATTCCTAAGAATCAGTAATTGAT
2720774 ATCCTAATTTCCTAAGAATCAGTAATTGA
1 ATCCTAA-TTCCTAAGAATCAGTAATTGA
2720803 GATTAGTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.34
Consensus pattern (29 bp):
ATCCTAATTCCTAAGAATCAGTAATTGAT
Found at i:2721171 original size:31 final size:31
Alignment explanation
Indices: 2721133--2721225 Score: 82
Period size: 31 Copynumber: 3.1 Consensus size: 31
2721123 ATTTCTTTAA
* * *
2721133 ATGTATATAATTGAATCAAAATTAAAGTTTC
1 ATGTATATAATTGAACCAAAATCAAAGTGTC
** * *
2721164 ATGTATATTTTTAAACCACAATCAAAGTGTC
1 ATGTATATAATTGAACCAAAATCAAAGTGTC
* * *
2721195 ATGTGTATAATTGTACC-AACTCAAAGT-TC
1 ATGTATATAATTGAACCAAAATCAAAGTGTC
2721224 AT
1 AT
2721226 ATATCAAATT
Statistics
Matches: 48, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 4 0.08
30 8 0.17
31 36 0.75
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.37
Consensus pattern (31 bp):
ATGTATATAATTGAACCAAAATCAAAGTGTC
Found at i:2730364 original size:20 final size:20
Alignment explanation
Indices: 2730339--2730383 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2730329 ATTGTTCGAA
2730339 TATCGATACCTATAAAAAAG
1 TATCGATACCTATAAAAAAG
* **
2730359 TATCGATACCTTTAATCAAG
1 TATCGATACCTATAAAAAAG
2730379 TATCG
1 TATCG
2730384 GTAAAATTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (20 bp):
TATCGATACCTATAAAAAAG
Found at i:2732592 original size:21 final size:21
Alignment explanation
Indices: 2732564--2732612 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
2732554 TTTGGTATGT
2732564 TTTG-ATGAGTTTTGAACTGG
1 TTTGAATGAGTTTTGAACTGG
2732584 TTTGAATGAGTTTTGAACTGG
1 TTTGAATGAGTTTTGAACTGG
2732605 TTTGAATG
1 TTTGAATG
2732613 TTGATATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.22, C:0.04, G:0.29, T:0.45
Consensus pattern (21 bp):
TTTGAATGAGTTTTGAACTGG
Found at i:2733751 original size:13 final size:13
Alignment explanation
Indices: 2733733--2733757 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2733723 TGGTGCCTAA
2733733 AAGCAATGTTGGC
1 AAGCAATGTTGGC
2733746 AAGCAATGTTGG
1 AAGCAATGTTGG
2733758 AGGATTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (13 bp):
AAGCAATGTTGGC
Found at i:2746150 original size:20 final size:20
Alignment explanation
Indices: 2746112--2746150 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
2746102 TAAAAAGATT
*
2746112 TTTTAAATTTAAATTTTATA
1 TTTTAAATTTAAATATTATA
2746132 TTTT-AATTTAAATAATTAT
1 TTTTAAATTTAAAT-ATTAT
2746151 TATGTAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTAAATTTAAATATTATA
Found at i:2746661 original size:59 final size:60
Alignment explanation
Indices: 2746547--2746672 Score: 209
Period size: 59 Copynumber: 2.1 Consensus size: 60
2746537 TTAACTTTAG
2746547 CATTAAAACGAGTTCCAAAAGTCAAATTTTCAATAGATTCTAATATTTCATTTACTTCAA
1 CATTAAAACGAGTTCCAAAAGTCAAATTTTCAATAGATTCTAATATTTCATTTACTTCAA
* * * *
2746607 CATTAAAACGAGTTCCAAAGGTCAAA-TTTCAATAGATTCTAATGTTTCATTTACTTTAG
1 CATTAAAACGAGTTCCAAAAGTCAAATTTTCAATAGATTCTAATATTTCATTTACTTCAA
2746666 CATTAAA
1 CATTAAA
2746673 GCATTCTGAA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
59 37 0.60
60 25 0.40
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.37
Consensus pattern (60 bp):
CATTAAAACGAGTTCCAAAAGTCAAATTTTCAATAGATTCTAATATTTCATTTACTTCAA
Found at i:2747716 original size:2 final size:2
Alignment explanation
Indices: 2747709--2747761 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
2747699 TCATCTGCAT
2747709 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2747751 AC AC AC AC AC A
1 AC AC AC AC AC A
2747762 GAGACATAAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2755647 original size:8 final size:8
Alignment explanation
Indices: 2755634--2755663 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
2755624 TTTTAAATTT
2755634 ATATTTAA
1 ATATTTAA
2755642 ATATTTAA
1 ATATTTAA
2755650 ATATTT-A
1 ATATTTAA
2755657 ATATTTA
1 ATATTTA
2755664 TTCTAGTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
ATATTTAA
Found at i:2755655 original size:16 final size:15
Alignment explanation
Indices: 2755634--2755663 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
2755624 TTTTAAATTT
2755634 ATATTTAAATATTTAA
1 ATATTT-AATATTTAA
2755650 ATATTTAATATTTA
1 ATATTTAATATTTA
2755664 TTCTAGTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTTAATATTTAA
Found at i:2768086 original size:14 final size:13
Alignment explanation
Indices: 2768067--2768105 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
2768057 AAATAATTCT
2768067 AAAAATTCAAAATA
1 AAAAATT-AAAATA
*
2768081 AAAAATTAATATA
1 AAAAATTAAAATA
2768094 AAAAATTTAAAA
1 AAAAA-TTAAAA
2768106 ATCGCACTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAAATTAAAATA
Found at i:2768098 original size:13 final size:14
Alignment explanation
Indices: 2768067--2768105 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
2768057 AAATAATTCT
2768067 AAAAATTCAAAATA
1 AAAAATTCAAAATA
*
2768081 AAAAATT-AATATA
1 AAAAATTCAAAATA
*
2768094 AAAAATTTAAAA
1 AAAAATTCAAAA
2768106 ATCGCACTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAAATTCAAAATA
Found at i:2775598 original size:28 final size:28
Alignment explanation
Indices: 2775541--2775601 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
2775531 AATTTTGTTA
* *
2775541 ATGTAATTATTATTATTATTATTTTCAT
1 ATGTAATTATTATTATTACTATTATCAT
2775569 ATGTAATTATTATT-TTAGCTATATAT-AT
1 ATGTAATTATTATTATTA-CTAT-TATCAT
2775597 ATGTA
1 ATGTA
2775602 TACTTGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 3 0.10
28 24 0.83
29 2 0.07
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.56
Consensus pattern (28 bp):
ATGTAATTATTATTATTACTATTATCAT
Found at i:2781723 original size:19 final size:20
Alignment explanation
Indices: 2781684--2781723 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2781674 TTCTAGGCCT
* *
2781684 TTGTAATATTTATTATTGCA
1 TTGTAATATTTAATATAGCA
2781704 TTGT-ATATTTAATATAGCA
1 TTGTAATATTTAATATAGCA
2781723 T
1 T
2781724 CACATCATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.53
Consensus pattern (20 bp):
TTGTAATATTTAATATAGCA
Found at i:2791978 original size:5 final size:5
Alignment explanation
Indices: 2791968--2792005 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
2791958 CGCCGTTACG
*
2791968 CTTCT CTTCT CTTCT CTTCT CTTCT CTTTT CTTCT CTT
1 CTTCT CTTCT CTTCT CTTCT CTTCT CTTCT CTTCT CTT
2792006 TGTTTTATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (5 bp):
CTTCT
Found at i:2792276 original size:13 final size:13
Alignment explanation
Indices: 2792258--2792284 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2792248 TGAAAGGGGA
2792258 TTTGATTTTGATT
1 TTTGATTTTGATT
2792271 TTTGATTTTGATT
1 TTTGATTTTGATT
2792284 T
1 T
2792285 GAGCAGCTTG
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:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (13 bp):
TTTGATTTTGATT
Found at i:2799156 original size:21 final size:21
Alignment explanation
Indices: 2799132--2799176 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2799122 TATTTTTTAG
2799132 ATATAAAATAATTA-AATATAA
1 ATAT-AAATAATTATAATATAA
* *
2799153 ATATTAATAATTATATTATAA
1 ATATAAATAATTATAATATAA
2799174 ATA
1 ATA
2799177 AAACACATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATATAAATAATTATAATATAA
Found at i:2799163 original size:20 final size:21
Alignment explanation
Indices: 2799138--2799176 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2799128 TTAGATATAA
2799138 AATAATTA-AATATAAATATT
1 AATAATTATAATATAAATATT
*
2799158 AATAATTATATTATAAATA
1 AATAATTATAATATAAATA
2799177 AAACACATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATAATTATAATATAAATATT
Found at i:2799373 original size:215 final size:216
Alignment explanation
Indices: 2799125--2799558 Score: 861
Period size: 215 Copynumber: 2.0 Consensus size: 216
2799115 TATATATTAT
2799125 TTTTTAGATATAAAATAATTAAATATAAATATTAATAATTATATTATAAATAAAACACATATTGA
1 TTTTTAGATATAAAATAATTAAATATAAATATTAATAATTATATTATAAATAAAACACATATTGA
2799190 ACAAAATAATTTTTAATATATGTTAATTGAACAATAAATAAGTTTTAAATGAGTTTTAAACAAAT
66 ACAAAATAATTTTTAATATATGTTAATTGAACAATAAATAAGTTTTAAATGAGTTTTAAACAAAT
2799255 ATAAACAAACTTGATCATAAAGATAAATGAATTGAATTATTCTTATTCGTATTTGGTCAATTTAA
131 ATAAACAAACTTGATCATAAAGATAAATGAATTGAATTATTCTTATTCGTATTTGGTCAATTTAA
2799320 TAAACAAGCCTCAAAATTTTA
196 TAAACAAGCCTCAAAATTTTA
2799341 TTTTTAGATA-AAAATAATTAAATATAAATATTAATAATTATATTATAAATAAAACACATATTGA
1 TTTTTAGATATAAAATAATTAAATATAAATATTAATAATTATATTATAAATAAAACACATATTGA
2799405 ACAAAATAATTTTTAATATATGTTAATTGAACAATAAATAAGTTTTAAATGAGTTTTAAACAAAT
66 ACAAAATAATTTTTAATATATGTTAATTGAACAATAAATAAGTTTTAAATGAGTTTTAAACAAAT
2799470 ATAAACAAACTTGATCATAAAGATAAATGAATTGAATTATTCTTATTCGTATTTGGTCAATTTAA
131 ATAAACAAACTTGATCATAAAGATAAATGAATTGAATTATTCTTATTCGTATTTGGTCAATTTAA
2799535 TAAACAAGCCTCAAAATTTTA
196 TAAACAAGCCTCAAAATTTTA
2799556 TTT
1 TTT
2799559 ATCCACAAGT
Statistics
Matches: 218, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
215 208 0.95
216 10 0.05
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (216 bp):
TTTTTAGATATAAAATAATTAAATATAAATATTAATAATTATATTATAAATAAAACACATATTGA
ACAAAATAATTTTTAATATATGTTAATTGAACAATAAATAAGTTTTAAATGAGTTTTAAACAAAT
ATAAACAAACTTGATCATAAAGATAAATGAATTGAATTATTCTTATTCGTATTTGGTCAATTTAA
TAAACAAGCCTCAAAATTTTA
Found at i:2799378 original size:20 final size:21
Alignment explanation
Indices: 2799353--2799391 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2799343 TTTAGATAAA
2799353 AATAATTA-AATATAAATATT
1 AATAATTATAATATAAATATT
*
2799373 AATAATTATATTATAAATA
1 AATAATTATAATATAAATA
2799392 AAACACATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATAATTATAATATAAATATT
Found at i:2802848 original size:9 final size:9
Alignment explanation
Indices: 2802836--2802949 Score: 54
Period size: 9 Copynumber: 11.8 Consensus size: 9
2802826 TATAAAGGTC
2802836 ATAAAAATT
1 ATAAAAATT
*
2802845 ATAAAAATC
1 ATAAAAATT
*
2802854 ATAAGAGATT
1 ATAA-AAATT
*
2802864 GTAAAAGA-T
1 ATAAAA-ATT
*
2802873 ATAAACAATC
1 ATAAA-AATT
*
2802883 ATAAATATT
1 ATAAAAATT
2802892 ATTAAAATATTTT
1 A-TAAAA-A--TT
2802905 ATACAAACA-T
1 ATA-AAA-ATT
2802915 ATAAAATATT
1 ATAAAA-ATT
2802925 -TAAAATATT
1 ATAAAA-ATT
*
2802934 ATAAAAGTT
1 ATAAAAATT
2802943 ATAAAAA
1 ATAAAAA
2802950 CTATTGAATT
Statistics
Matches: 80, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
9 43 0.54
10 27 0.34
11 1 0.01
12 2 0.03
13 7 0.09
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:2804381 original size:15 final size:15
Alignment explanation
Indices: 2804363--2804397 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2804353 AAAAGAAACA
* *
2804363 AAAACAAATTGAATG
1 AAAACAAATTAAAAG
2804378 AAAACAAATTAAAAG
1 AAAACAAATTAAAAG
2804393 AAAAC
1 AAAAC
2804398 CTAACAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.14
Consensus pattern (15 bp):
AAAACAAATTAAAAG
Found at i:2808902 original size:79 final size:81
Alignment explanation
Indices: 2808792--2808956 Score: 316
Period size: 79 Copynumber: 2.1 Consensus size: 81
2808782 TAATAAATTA
2808792 AAATATTTAGGGAATTCAATATGAAGGATAATTTAATTAATTTGTATTTAAATTTAAATAATAAT
1 AAATATTTAGGGAATTCAATATGAAGGATAATTTAATTAATTTGTATTTAAATTTAAATAATAAT
2808857 ACTTTGAATTTAATAG
66 ACTTTGAATTTAATAG
2808873 AAATA-TTAGGGAATT-AATATGAAGGATAATTTAATTAATTTGTATTTAAATTTAAATAATAAT
1 AAATATTTAGGGAATTCAATATGAAGGATAATTTAATTAATTTGTATTTAAATTTAAATAATAAT
2808936 ACTTTGAATTTAATAG
66 ACTTTGAATTTAATAG
2808952 AAATA
1 AAATA
2808957 ATAAACAAAT
Statistics
Matches: 84, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
79 69 0.82
80 10 0.12
81 5 0.06
ACGTcount: A:0.46, C:0.02, G:0.11, T:0.41
Consensus pattern (81 bp):
AAATATTTAGGGAATTCAATATGAAGGATAATTTAATTAATTTGTATTTAAATTTAAATAATAAT
ACTTTGAATTTAATAG
Found at i:2809471 original size:6 final size:6
Alignment explanation
Indices: 2809463--2809531 Score: 68
Period size: 6 Copynumber: 11.5 Consensus size: 6
2809453 AGACTGAGCC
* * *
2809463 TGAAGC TGAAGA TGAAGA TGAAGA TGAA-A GTGAAGA TGAGGA TGGAGA
1 TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA -TGAAGA TGAAGA TGAAGA
** *
2809511 TGGGGA TGAAGA TGAGGA TGA
1 TGAAGA TGAAGA TGAAGA TGA
2809532 CGAAGAAGAA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
5 1 0.02
6 51 0.96
7 1 0.02
ACGTcount: A:0.41, C:0.01, G:0.41, T:0.17
Consensus pattern (6 bp):
TGAAGA
Done.