Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008826.1 Hibiscus syriacus cultivar Beakdansim tig00112000_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: 3884024
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 18
Found at i:2864811 original size:20 final size:21
Alignment explanation
Indices: 2864786--2864826 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2864776 GTTGAGGTCG
2864786 TTTCTAACCG-TTGGGGATGA
1 TTTCTAACCGTTTGGGGATGA
*
2864806 TTTCTAGCCGTTTGGGGATGA
1 TTTCTAACCGTTTGGGGATGA
2864827 AATCTCTGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.17, C:0.15, G:0.32, T:0.37
Consensus pattern (21 bp):
TTTCTAACCGTTTGGGGATGA
Found at i:2868305 original size:20 final size:21
Alignment explanation
Indices: 2868280--2868318 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2868270 GTTGTGACCG
*
2868280 TTTCTAGCTG-TTGGGGATAA
1 TTTCTAGCCGTTTGGGGATAA
2868300 TTTCTAGCCGTTTGGGGAT
1 TTTCTAGCCGTTTGGGGAT
2868319 GAAATCTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.15, C:0.13, G:0.31, T:0.41
Consensus pattern (21 bp):
TTTCTAGCCGTTTGGGGATAA
Found at i:2870091 original size:18 final size:16
Alignment explanation
Indices: 2870057--2870094 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
2870047 AAATTAATCG
2870057 AAAT-TATTAATTATT
1 AAATATATTAATTATT
2870072 AAATATATTATATATATT
1 AAATATATTA-AT-TATT
2870090 AAATA
1 AAATA
2870095 CATATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 5 0.25
17 2 0.10
18 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATATATTAATTATT
Found at i:2875359 original size:22 final size:22
Alignment explanation
Indices: 2875317--2875372 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
2875307 GTTTACATAC
* *
2875317 GAGTATCGATA-TTCCCCCTTA
1 GAGTATCAATACTTACCCCTTA
*
2875338 GAGTATCATTACTTACCCCTTA
1 GAGTATCAATACTTACCCCTTA
2875360 GAGTATCAATACT
1 GAGTATCAATACT
2875373 CACTTGGGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 9 0.30
22 21 0.70
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (22 bp):
GAGTATCAATACTTACCCCTTA
Found at i:2877843 original size:20 final size:19
Alignment explanation
Indices: 2877818--2877865 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
2877808 TCTAAATTAT
**
2877818 TTTTCAAAATTTTATTTTG
1 TTTTCAAAATCCTATTTTG
*
2877837 ATTTTCATAATCCTATTTTG
1 -TTTTCAAAATCCTATTTTG
*
2877857 CTTTCAAAA
1 TTTTCAAAA
2877866 GAAAATCATT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.54
Consensus pattern (19 bp):
TTTTCAAAATCCTATTTTG
Found at i:2894814 original size:104 final size:104
Alignment explanation
Indices: 2894698--2894921 Score: 290
Period size: 104 Copynumber: 2.2 Consensus size: 104
2894688 CAATCTATTT
* * * * *
2894698 GACACAATTATCAATATAAATTGCGATGAATTT-TTTGACACTAAAAATATATTTTGTGACCATC
1 GACACTATTATCAATAGAAATTGCGATAAATTTATTTAACACTAAAAATATATTTTGTGACCACC
*
2894762 AATATTGTCACACTAAGTATTTTTTAGTGACCAAATG-TC
66 AATATTGTCACACTAAGT-GTTTTTAGTGACCAAATGTTC
* * * * *
2894801 TGATACTATTATCAATAGAAATTGTGATAAATTTATTTAACATTGAAAGTATATTTTGTGACCAC
1 -GACACTATTATCAATAGAAATTGCGATAAATTTATTTAACACTAAAAATATATTTTGTGACCAC
* *
2894866 CAATGTTGTCACACTAAGTGTTTTTAGTGACTAAATGTTC
65 CAATATTGTCACACTAAGTGTTTTTAGTGACCAAATGTTC
*
2894906 GACACTATTAGCAATA
1 GACACTATTATCAATA
2894922 ACTCTGTCAC
Statistics
Matches: 103, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
104 58 0.56
105 45 0.44
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (104 bp):
GACACTATTATCAATAGAAATTGCGATAAATTTATTTAACACTAAAAATATATTTTGTGACCACC
AATATTGTCACACTAAGTGTTTTTAGTGACCAAATGTTC
Found at i:2895726 original size:42 final size:42
Alignment explanation
Indices: 2895679--2895784 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 42
2895669 TTCACTTCAA
**
2895679 TAGTGATAAAAATTATT-TGCGTCACAAATCATCAACTAAGAC
1 TAGTGATAAAAACAATTAT-CGTCACAAATCATCAACTAAGAC
* *
2895721 TAGTGATAGAAACAATTATCGTTACAAATCATCAACTAAGAC
1 TAGTGATAAAAACAATTATCGTCACAAATCATCAACTAAGAC
*
2895763 TAGTGACAAAAACAATTTATCG
1 TAGTGATAAAAACAA-TTATCG
2895785 CAAATCGCCA
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
42 49 0.88
43 7 0.12
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.27
Consensus pattern (42 bp):
TAGTGATAAAAACAATTATCGTCACAAATCATCAACTAAGAC
Found at i:2898084 original size:22 final size:23
Alignment explanation
Indices: 2898058--2898100 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
2898048 CTGTTTCATG
2898058 AGTTCGGA-TTTG-TGTGTTTTGT
1 AGTTC-GATTTTGCTGTGTTTTGT
2898080 AGTTCGATTTTGCTGTGTTTT
1 AGTTCGATTTTGCTGTGTTTT
2898101 TTTTGTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 2 0.11
22 9 0.47
23 8 0.42
ACGTcount: A:0.09, C:0.07, G:0.28, T:0.56
Consensus pattern (23 bp):
AGTTCGATTTTGCTGTGTTTTGT
Found at i:2900016 original size:29 final size:27
Alignment explanation
Indices: 2899970--2900029 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
2899960 TTACGGAATG
2899970 AAACGTTAGACACCAAACTAGAACGAAA
1 AAACGTTAGACACCAAACTAGAAC-AAA
* * *
2899998 TAAACGTTAGTCACTAAACTGGAACAAA
1 -AAACGTTAGACACCAAACTAGAACAAA
2900026 AAAC
1 AAAC
2900030 AGACGTTGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 4 0.14
28 3 0.11
29 21 0.75
ACGTcount: A:0.52, C:0.20, G:0.13, T:0.15
Consensus pattern (27 bp):
AAACGTTAGACACCAAACTAGAACAAA
Found at i:2907174 original size:13 final size:13
Alignment explanation
Indices: 2907125--2907182 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 13
2907115 ACCTTCAATT
2907125 AAATAATTA-TTA
1 AAATAATTATTTA
2907137 AATATACATT-TTATA
1 AA-ATA-ATTATT-TA
2907152 AAATTAATTATTTA
1 AAA-TAATTATTTA
2907166 AAATAATTATATTA
1 AAATAATTAT-TTA
2907180 AAA
1 AAA
2907183 ATTTAAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
12 2 0.05
13 10 0.26
14 19 0.49
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (13 bp):
AAATAATTATTTA
Found at i:2907181 original size:28 final size:28
Alignment explanation
Indices: 2907128--2907182 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
2907118 TTCAATTAAA
*
2907128 TAATTATTAAATATACATTTTATAAAAT
1 TAATTATTAAATATACATTATATAAAAT
2907156 TAATTATTTAAA-ATA-ATTATATTAAAA
1 TAATTA-TTAAATATACATTATA-TAAAA
2907183 ATTTAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 5 0.21
28 14 0.58
29 5 0.21
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (28 bp):
TAATTATTAAATATACATTATATAAAAT
Found at i:2911406 original size:18 final size:19
Alignment explanation
Indices: 2911376--2911426 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
2911366 CTAATAAAAA
2911376 AATAACAAATAAAAAAATA-
1 AATAA-AAATAAAAAAATAG
*
2911395 AA-AAAAAGTAAAAACATAG
1 AATAAAAA-TAAAAAAATAG
2911414 AATAAAAATAAAA
1 AATAAAAATAAAA
2911427 TAAACATAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 3 0.11
18 11 0.39
19 9 0.32
20 5 0.18
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.14
Consensus pattern (19 bp):
AATAAAAATAAAAAAATAG
Found at i:2911408 original size:8 final size:8
Alignment explanation
Indices: 2911368--2911400 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
2911358 TAATAAACCT
2911368 AATAAAAA
1 AATAAAAA
*
2911376 AAT-AACA
1 AATAAAAA
2911383 AATAAAAA
1 AATAAAAA
2911391 AATAAAAA
1 AATAAAAA
2911399 AA
1 AA
2911401 AGTAAAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (8 bp):
AATAAAAA
Found at i:2914011 original size:13 final size:13
Alignment explanation
Indices: 2913993--2914017 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2913983 GGTCAAAGGA
2913993 AGTCAACGGTCAC
1 AGTCAACGGTCAC
2914006 AGTCAACGGTCA
1 AGTCAACGGTCA
2914018 ACGGTCGGGT
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:0.28, G:0.24, T:0.16
Consensus pattern (13 bp):
AGTCAACGGTCAC
Found at i:2914030 original size:5 final size:5
Alignment explanation
Indices: 2914020--2914057 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
2914010 AACGGTCAAC
* *
2914020 GGTCG GGTCG GGTCG GGT-A AGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
2914058 AAACCGATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
4 2 0.07
5 26 0.93
ACGTcount: A:0.05, C:0.18, G:0.55, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:2921021 original size:5 final size:5
Alignment explanation
Indices: 2921011--2921053 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
2921001 AACGGTCAAC
* *
2921011 GGTCG GGTCG GGTCG GGTCG GGTC- AGTCG GGTTG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
2921054 AGACCGGTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
4 3 0.09
5 30 0.91
ACGTcount: A:0.02, C:0.19, G:0.56, T:0.23
Consensus pattern (5 bp):
GGTCG
Found at i:2921041 original size:14 final size:15
Alignment explanation
Indices: 2921011--2921049 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
2921001 AACGGTCAAC
*
2921011 GGTCGGGTCGGGTCG
1 GGTCGGGTCGAGTCG
2921026 GGTCGGGTC-AGTCG
1 GGTCGGGTCGAGTCG
*
2921040 GGTTGGGTCG
1 GGTCGGGTCG
2921050 GGTCAGACCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.03, C:0.18, G:0.56, T:0.23
Consensus pattern (15 bp):
GGTCGGGTCGAGTCG
Found at i:2921041 original size:19 final size:19
Alignment explanation
Indices: 2921017--2921055 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2921007 CAACGGTCGG
2921017 GTCGGGTCGGGTCGGGTCA
1 GTCGGGTCGGGTCGGGTCA
*
2921036 GTCGGGTTGGGTCGGGTCA
1 GTCGGGTCGGGTCGGGTCA
2921055 G
1 G
2921056 ACCGGTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.05, C:0.18, G:0.54, T:0.23
Consensus pattern (19 bp):
GTCGGGTCGGGTCGGGTCA
Found at i:2921074 original size:19 final size:19
Alignment explanation
Indices: 2921052--2921109 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
2921042 TTGGGTCGGG
*
2921052 TCAGACCGGTCATACCGGT
1 TCAGACCGGTCAAACCGGT
* *
2921071 TCAGACCAGTCAAACCGGC
1 TCAGACCGGTCAAACCGGT
2921090 TC-GAACCGGTCAAACCGGT
1 TCAG-ACCGGTCAAACCGGT
2921109 T
1 T
2921110 TCCAGCCCTC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
18 1 0.03
19 32 0.97
ACGTcount: A:0.26, C:0.33, G:0.24, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:2921098 original size:10 final size:9
Alignment explanation
Indices: 2921050--2921108 Score: 55
Period size: 9 Copynumber: 6.3 Consensus size: 9
2921040 GGTTGGGTCG
*
2921050 GGTCAGACC
1 GGTCAAACC
*
2921059 GGTCATACC
1 GGTCAAACC
*
2921068 GGTTCAGACC
1 GG-TCAAACC
*
2921078 AGTCAAACC
1 GGTCAAACC
*
2921087 GGCTCGAACC
1 GG-TCAAACC
2921097 GGTCAAACC
1 GGTCAAACC
2921106 GGT
1 GGT
2921109 TTCCAGCCCT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
9 26 0.63
10 15 0.37
ACGTcount: A:0.25, C:0.32, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:2922302 original size:39 final size:39
Alignment explanation
Indices: 2922257--2922893 Score: 934
Period size: 39 Copynumber: 16.3 Consensus size: 39
2922247 CAAGTGAAAT
*
2922257 AAATCTTCTGTTTAGAGTGAAACTATCTCAAGCGAGATA
1 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATA
* ** * *
2922296 ATATCTTCAATTTTGAGTGAAACTATCTCAAGAGAGATA
1 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATA
* * *
2922335 AAATATTCTATTTTGAGTGAAACTATCTCAAGCGAGATA
1 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATA
*
2922374 AAATCTTCTGTTTCGAGTGAAACTATATCAAGCGAGATA
1 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATA
*
2922413 AAATATTCTGTTTCGAGTGAAACTTATCTCAAGCGAGATA
1 AAATCTTCTGTTTCGAGTGAAAC-TATCTCAAGCGAGATA
* *
2922453 AAATATTCTGTTTCGAGTGAAACTATCTCAAGAGAGATA
1 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATA
* * *
2922492 AAATATTATGTTTCAAGTGAAACTATCTCAAGCGAGATA
1 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATA
* * *
2922531 AAATATTCTGTTT-GAGTGAAACAAATCTCGAGCGAGATA
1 AAATCTTCTGTTTCGAGTGAAAC-TATCTCAAGCGAGATA
**
2922570 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGTAAGATA
1 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATA
*
2922609 AAATCTTTTGTTTCGAGTGAAACTATCTCAAGCGAGATA
1 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATA
* ** * * *
2922648 AAATCTTCTATTTAAATTGAAATTATCTTAAGCGAGATA
1 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATA
2922687 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATA
1 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATA
* *
2922726 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGATAAA
1 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATA
* *
2922765 AAATATTCTGTTTCAAGTGAAACTATCTCAAGCGAGATA
1 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATA
* *
2922804 AAATCTTCTGTTTTGAGTGAAACTATCTCAAGCAAGATA
1 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATA
*
2922843 AAATCTTCTGTTTCGAATGAAACTATCTCAAGCGAGATA
1 AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATA
2922882 AAATCTTCTGTT
1 AAATCTTCTGTT
2922894 AAAAACAATC
Statistics
Matches: 538, Mismatches: 57, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
38 8 0.01
39 483 0.90
40 47 0.09
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (39 bp):
AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATA
Found at i:2922703 original size:20 final size:20
Alignment explanation
Indices: 2922680--2922742 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
2922670 TTATCTTAAG
2922680 CGAGATAAAATCTTCTGTTT
1 CGAGATAAAATCTTCTGTTT
* ****
2922700 CGAG-TGAAA-CTATCTCAAG
1 CGAGATAAAATCT-TCTGTTT
2922719 CGAGATAAAATCTTCTGTTT
1 CGAGATAAAATCTTCTGTTT
2922739 CGAG
1 CGAG
2922743 TGAAACTATC
Statistics
Matches: 30, Mismatches: 10, Indels: 6
0.65 0.22 0.13
Matches are distributed among these distances:
18 2 0.07
19 11 0.37
20 15 0.50
21 2 0.07
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (20 bp):
CGAGATAAAATCTTCTGTTT
Found at i:2922981 original size:73 final size:76
Alignment explanation
Indices: 2922894--2923066 Score: 244
Period size: 76 Copynumber: 2.3 Consensus size: 76
2922884 ATCTTCTGTT
* * ** *
2922894 AAAAACAATCTTGAGTGAAATGAAATGT-CTTTTTTTAGT-AAAACTGTCTCAAGCAAGACAAAT
1 AAAAACAATCTTGAGTGAAATGAAATATCCTCTTTCGAGTAAAAACTGTCTCAAGCAAGAAAAAT
*
2922957 CTT-TTTTATG
66 CTTGTTTTAAG
* * *
2922967 AAAAACAATATTGAGTGAAATGAAATATCCTCTTTCGAGTAAAAACTTTCTCAAGCGAGAAAAAT
1 AAAAACAATCTTGAGTGAAATGAAATATCCTCTTTCGAGTAAAAACTGTCTCAAGCAAGAAAAAT
2923032 CTTGTTTTAAG
66 CTTGTTTTAAG
2923043 AAAAACAATCTTGAGTGAAATGAA
1 AAAAACAATCTTGAGTGAAATGAA
2923067 TTTTCTGTAT
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
73 26 0.30
74 8 0.09
75 24 0.28
76 29 0.33
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.31
Consensus pattern (76 bp):
AAAAACAATCTTGAGTGAAATGAAATATCCTCTTTCGAGTAAAAACTGTCTCAAGCAAGAAAAAT
CTTGTTTTAAG
Found at i:2923057 original size:76 final size:72
Alignment explanation
Indices: 2922853--2923066 Score: 243
Period size: 76 Copynumber: 2.9 Consensus size: 72
2922843 AAATCTTCTG
* * *
2922853 TTTCGAATGAAACTATCTCAAGCGAGATAAAATCTTCTGTT--AAAAACAATCTTGAGTGAAATG
1 TTTCGAGTAAAACTATCTCAAGCGAGA-AAAATCTT-TTTTAGAAAAACAATCTTGAGTGAAATG
* *
2922916 AAATGTCTT
64 AAATATCTC
** * * * *
2922925 TTTTTAGTAAAACTGTCTCAAGCAAGACAAATCTTTTTTATGAAAAACAATATTGAGTGAAATGA
1 TTTCGAGTAAAACTATCTCAAGCGAGAAAAATCTTTTTTA-GAAAAACAATCTTGAGTGAAATGA
2922990 AATATCCTC
65 AATAT-CTC
*
2922999 TTTCGAGTAAAAACTTTCTCAAGCGAGAAAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAAT
1 TTTCGAGT-AAAACTATCTCAAGCGAGAAAAATCTT-TTTT-AGAAAAACAATCTTGAGTGAAAT
2923064 GAA
63 GAA
2923067 TTTTCTGTAT
Statistics
Matches: 118, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
70 3 0.03
71 7 0.06
72 21 0.18
73 26 0.22
74 8 0.07
75 24 0.20
76 28 0.24
77 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (72 bp):
TTTCGAGTAAAACTATCTCAAGCGAGAAAAATCTTTTTTAGAAAAACAATCTTGAGTGAAATGAA
ATATCTC
Found at i:2925863 original size:29 final size:30
Alignment explanation
Indices: 2925804--2925863 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
2925794 AAGACACGAG
*
2925804 ACAAGACAAACAGAAATCAAGTCAGTAGAA
1 ACAAGACAAAAAGAAATCAAGTCAGTAGAA
* *
2925834 ACAAGACAAAAAG-AATCAAGTTAGTTGAA
1 ACAAGACAAAAAGAAATCAAGTCAGTAGAA
2925863 A
1 A
2925864 TGATTAGTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.57, C:0.13, G:0.17, T:0.13
Consensus pattern (30 bp):
ACAAGACAAAAAGAAATCAAGTCAGTAGAA
Found at i:2927740 original size:13 final size:13
Alignment explanation
Indices: 2927701--2927752 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
2927691 ATAAAACAAT
*
2927701 AACAAATAATAAA
1 AACAAAAAATAAA
*
2927714 AATAAAAAAGTAAA
1 AACAAAAAA-TAAA
*
2927728 AACAAAGAATAAA
1 AACAAAAAATAAA
*
2927741 AA-ATAAAATAAA
1 AACAAAAAATAAA
2927753 CATAAGTACA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
12 8 0.25
13 13 0.41
14 11 0.34
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.13
Consensus pattern (13 bp):
AACAAAAAATAAA
Found at i:2930595 original size:43 final size:43
Alignment explanation
Indices: 2930492--2930596 Score: 129
Period size: 43 Copynumber: 2.4 Consensus size: 43
2930482 TTATTTCTGT
* * **
2930492 ATGGGGTCCTCTACAGAGGGTAATATCTGCATCATGTTTCTAC
1 ATGGGATCCTCTACGGAGGGTAATATCCCCATCATGTTTCTAC
* * *
2930535 ATGTGATCCTCTACGGAGGGTAATATCCCCGTCATGTTTCTAT
1 ATGGGATCCTCTACGGAGGGTAATATCCCCATCATGTTTCTAC
* *
2930578 TTGGGATCCTCTTCGGAGG
1 ATGGGATCCTCTACGGAGG
2930597 ACTATCTCCC
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (43 bp):
ATGGGATCCTCTACGGAGGGTAATATCCCCATCATGTTTCTAC
Found at i:2930607 original size:43 final size:43
Alignment explanation
Indices: 2930493--2930623 Score: 120
Period size: 43 Copynumber: 3.0 Consensus size: 43
2930483 TATTTCTGTA
* * * ** **
2930493 TGGGGTCCTCTACAGAGGGTAATATCTGCATCATGTTTCTACA
1 TGGGATCCTCTACGGAGGCTAATATCCCCATCATGTTTCTATT
* * *
2930536 TGTGATCCTCTACGGAGGGTAATATCCCCGTCATGTTTCTATT
1 TGGGATCCTCTACGGAGGCTAATATCCCCATCATGTTTCTATT
* * *
2930579 TGGGATCCTCTTCGGAGGACT-ATCTCCCCATCTTGATTTCTATT
1 TGGGATCCTCTACGGAGG-CTAATATCCCCATCATG-TTTCTATT
2930623 T
1 T
2930624 CTGACTAGGA
Statistics
Matches: 72, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
43 62 0.86
44 10 0.14
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.37
Consensus pattern (43 bp):
TGGGATCCTCTACGGAGGCTAATATCCCCATCATGTTTCTATT
Found at i:2932617 original size:29 final size:31
Alignment explanation
Indices: 2932578--2932637 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
2932568 AAATTTTGAA
*
2932578 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
2932607 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
2932638 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:2935970 original size:22 final size:22
Alignment explanation
Indices: 2935945--2935994 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
2935935 CGTGTTGCTC
2935945 TTGGTTCGGGTTAATTTCAATT
1 TTGGTTCGGGTTAATTTCAATT
*
2935967 TTGGTTCGGGTTAATTTCGATT
1 TTGGTTCGGGTTAATTTCAATT
2935989 TTGGTT
1 TTGGTT
2935995 GATTTCGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.14, C:0.08, G:0.26, T:0.52
Consensus pattern (22 bp):
TTGGTTCGGGTTAATTTCAATT
Found at i:2935994 original size:16 final size:16
Alignment explanation
Indices: 2935975--2936005 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2935965 TTTTGGTTCG
2935975 GGTTAATTTCGATTTT
1 GGTTAATTTCGATTTT
*
2935991 GGTTGATTTCGATTT
1 GGTTAATTTCGATTT
2936006 CGCTAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.06, G:0.23, T:0.55
Consensus pattern (16 bp):
GGTTAATTTCGATTTT
Found at i:2938284 original size:27 final size:27
Alignment explanation
Indices: 2938241--2938320 Score: 90
Period size: 27 Copynumber: 3.0 Consensus size: 27
2938231 AAATAATATT
*
2938241 AAATAAATC-AAAGAAAAACATAAAAA
1 AAATAAATCAAAAGAAAAAAATAAAAA
* *
2938267 TAATAAATCAAAATAAAAAAATAAAAA
1 AAATAAATCAAAAGAAAAAAATAAAAA
* * *
2938294 AAAAAAATCAAAGGAAAAGAAAGAAAA
1 AAATAAATCAAAAGAAAA-AAATAAAA
2938321 TACAAAATAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 8 0.18
27 29 0.66
28 7 0.16
ACGTcount: A:0.78, C:0.05, G:0.06, T:0.11
Consensus pattern (27 bp):
AAATAAATCAAAAGAAAAAAATAAAAA
Found at i:2938300 original size:21 final size:21
Alignment explanation
Indices: 2938262--2938301 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2938252 AGAAAAACAT
* **
2938262 AAAAATAATAAATCAAAATAA
1 AAAAATAAAAAAAAAAAATAA
2938283 AAAAATAAAAAAAAAAAAT
1 AAAAATAAAAAAAAAAAAT
2938302 CAAAGGAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (21 bp):
AAAAATAAAAAAAAAAAATAA
Found at i:2938311 original size:14 final size:14
Alignment explanation
Indices: 2938245--2938305 Score: 56
Period size: 13 Copynumber: 4.6 Consensus size: 14
2938235 AATATTAAAT
*
2938245 AAATC-AAAGAAAA
1 AAATCAAAAAAAAA
* * *
2938258 ACAT-AAAAATAAT
1 AAATCAAAAAAAAA
*
2938271 AAATCAAAATAAAA
1 AAATCAAAAAAAAA
2938285 AAAT-AAAAAAAAA
1 AAATCAAAAAAAAA
2938298 AAATCAAA
1 AAATCAAA
2938306 GGAAAAGAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
13 23 0.64
14 13 0.36
ACGTcount: A:0.79, C:0.07, G:0.02, T:0.13
Consensus pattern (14 bp):
AAATCAAAAAAAAA
Found at i:2938405 original size:5 final size:5
Alignment explanation
Indices: 2938382--2938441 Score: 63
Period size: 5 Copynumber: 12.0 Consensus size: 5
2938372 GGGAAAAAGG
2938382 TAAAA TAATAGA T-AAA TAAAA TAAAA TAAAA TAAAA -AACAA -AAAA
1 TAAAA TAA-A-A TAAAA TAAAA TAAAA TAAAA TAAAA TAA-AA TAAAA
*
2938427 AAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA
2938442 AATAATTAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
4 6 0.12
5 39 0.80
6 2 0.04
7 2 0.04
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.17
Consensus pattern (5 bp):
TAAAA
Found at i:2938452 original size:11 final size:12
Alignment explanation
Indices: 2938395--2938446 Score: 72
Period size: 12 Copynumber: 4.5 Consensus size: 12
2938385 AATAATAGAT
2938395 AAATAAAAT--A
1 AAATAAAATAAA
2938405 AAATAAAATAAA
1 AAATAAAATAAA
* *
2938417 AAACAAAAAAAA
1 AAATAAAATAAA
2938429 AAATAAAATAAA
1 AAATAAAATAAA
2938441 AAATAA
1 AAATAA
2938447 TTAAAATTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
10 9 0.25
12 27 0.75
ACGTcount: A:0.85, C:0.02, G:0.00, T:0.13
Consensus pattern (12 bp):
AAATAAAATAAA
Found at i:2946147 original size:31 final size:29
Alignment explanation
Indices: 2946112--2946175 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
2946102 GAGTTGCTCA
**
2946112 CGAGCTTCAGTTCAGGATTTCGAGTTCGAGT
1 CGAGCTTCA-TTCAAAATTTCGAG-TCGAGT
*
2946143 CGAGCTTCATTTAAAATTTCGAGTCGAGT
1 CGAGCTTCATTCAAAATTTCGAGTCGAGT
2946172 CGAG
1 CGAG
2946176 TCAGCAATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 10 0.33
30 11 0.37
31 9 0.30
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (29 bp):
CGAGCTTCATTCAAAATTTCGAGTCGAGT
Found at i:2948969 original size:27 final size:27
Alignment explanation
Indices: 2948928--2948979 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
2948918 ACCAACGGAC
* *
2948928 TAAATTTGATCTATAAATTTTAAATCT
1 TAAATTTAATATATAAATTTTAAATCT
*
2948955 TAAATTTAATATATAATTTTTAAAT
1 TAAATTTAATATATAAATTTTAAAT
2948980 GTATAACCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (27 bp):
TAAATTTAATATATAAATTTTAAATCT
Found at i:2949120 original size:18 final size:18
Alignment explanation
Indices: 2949097--2949135 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2949087 GTTTTTTCAT
* *
2949097 TTAAATTTTTTATTATTA
1 TTAAATTTATTATTAATA
2949115 TTAAATTTATTATTAATA
1 TTAAATTTATTATTAATA
2949133 TTA
1 TTA
2949136 TTATTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTAAATTTATTATTAATA
Found at i:2949160 original size:27 final size:25
Alignment explanation
Indices: 2949107--2949179 Score: 112
Period size: 27 Copynumber: 2.8 Consensus size: 25
2949097 TTAAATTTTT
2949107 TATTATTATTAAAT-TTATTATTAA
1 TATTATTATTAAATATTATTATTAA
2949131 TATTATTATTAAATATTATTATTAGTA
1 TATTATTATTAAATATTATTATTA--A
2949158 TATTATTATTAAATAATTATTA
1 TATTATTATTAAAT-ATTATTA
2949180 CAAGCCCAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
24 14 0.31
25 9 0.20
27 15 0.33
28 7 0.16
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (25 bp):
TATTATTATTAAATATTATTATTAA
Found at i:2949179 original size:3 final size:3
Alignment explanation
Indices: 2949106--2949168 Score: 58
Period size: 3 Copynumber: 21.0 Consensus size: 3
2949096 TTTAAATTTT
* * *
2949106 TTA TTA TTA TTA -AA TTTA TTA TTA ATA TTA TTA TTAA ATA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
*
2949152 TTA GTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
2949169 AATAATTATT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
2 3 0.06
3 43 0.88
4 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:2953679 original size:7 final size:7
Alignment explanation
Indices: 2953644--2953684 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
2953634 TTTTCATACA
2953644 TGCATTT
1 TGCATTT
2953651 T-CATTT
1 TGCATTT
2953657 TGCATCTT
1 TGCAT-TT
2953665 TGCATTT
1 TGCATTT
*
2953672 TTCATTT
1 TGCATTT
2953679 TGCATT
1 TGCATT
2953685 CATACTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 6 0.20
7 17 0.57
8 7 0.23
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.59
Consensus pattern (7 bp):
TGCATTT
Found at i:2956249 original size:10 final size:9
Alignment explanation
Indices: 2956230--2956268 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
2956220 TCCAGCAAAG
2956230 AAAGAAAAAA
1 AAAG-AAAAA
2956240 AAAGAGAAAA
1 AAAGA-AAAA
*
2956250 AAAGAAAAG
1 AAAGAAAAA
2956259 AAAGAAAAA
1 AAAGAAAAA
2956268 A
1 A
2956269 TTGTATCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 13 0.50
10 13 0.50
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:2956251 original size:9 final size:8
Alignment explanation
Indices: 2956226--2956268 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
2956216 CTCATCCAGC
2956226 AAAGAAAGA
1 AAAGAAA-A
2956235 AAA-AAAA
1 AAAGAAAA
*
2956242 AGAGAAAA
1 AAAGAAAA
2956250 AAAGAAAA
1 AAAGAAAA
2956258 GAAAGAAAA
1 -AAAGAAAA
2956267 AA
1 AA
2956269 TTGTATCAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
7 3 0.10
8 16 0.53
9 11 0.37
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:2956252 original size:13 final size:12
Alignment explanation
Indices: 2956230--2956268 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
2956220 TCCAGCAAAG
2956230 AAAGAAAAAAAA
1 AAAGAAAAAAAA
*
2956242 AGAGAAAAAAAGA
1 AAAGAAAAAAA-A
2956255 AAAGAAAGAAAAA
1 AAAGAAA-AAAAA
2956268 A
1 A
2956269 TTGTATCAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 10 0.43
13 9 0.39
14 4 0.17
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAA
Found at i:2958585 original size:93 final size:93
Alignment explanation
Indices: 2958426--2958607 Score: 346
Period size: 93 Copynumber: 2.0 Consensus size: 93
2958416 AATAAGAAGA
* *
2958426 CTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGATTTGGTATGAACTCCAAAAT
1 CTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTCGTATGAACTCCAAAAT
2958491 CAATCATTGGATTTGAAAGATGAATAGG
66 CAATCATTGGATTTGAAAGATGAATAGG
2958519 CTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTCGTATGAACTCCAAAAT
1 CTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTCGTATGAACTCCAAAAT
2958584 CAATCATTGGATTTGAAAGATGAA
66 CAATCATTGGATTTGAAAGATGAA
2958608 ATTTGCTCAT
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 87 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.36
Consensus pattern (93 bp):
CTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTCGTATGAACTCCAAAAT
CAATCATTGGATTTGAAAGATGAATAGG
Found at i:2958718 original size:115 final size:115
Alignment explanation
Indices: 2958516--2958722 Score: 328
Period size: 115 Copynumber: 1.8 Consensus size: 115
2958506 AAAGATGAAT
* *
2958516 AGGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTCGTATGAACTCCAA
1 AGGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTCGTAGGAACCCCAA
*
2958581 AATCAATCATTGGATTTGAAAGATGAAATTTGCTCATAGTAGAAATAAGG
66 AATCAATCATTGGAATTGAAAGATGAAATTTGCTCATAGTAGAAATAAGG
*
2958631 AGGCTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGA-TTCGGTAGGAACCCCA
1 AGGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTC-GTAGGAACCCCA
* *
2958695 GAA-CTGATCATTGGAATTGAAAGATGAA
65 AAATC-AATCATTGGAATTGAAAGATGAA
2958723 CTGCATGACC
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
114 4 0.05
115 80 0.95
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (115 bp):
AGGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTCGTAGGAACCCCAA
AATCAATCATTGGAATTGAAAGATGAAATTTGCTCATAGTAGAAATAAGG
Found at i:2960874 original size:54 final size:54
Alignment explanation
Indices: 2960789--2960904 Score: 178
Period size: 54 Copynumber: 2.1 Consensus size: 54
2960779 ATTTCAATGA
* ***
2960789 TTACGAACATCTGAGCAGAAACTACAAGAAAGGATGAATGTGTTGTCAAATGTT
1 TTACGAACATCTGAGCAGAAACCACAAGAAAGGATGAATGCACTGTCAAATGTT
* *
2960843 TTACGAACATCTGAGCAGAAGCCACAGGAAAGGATGAATGCACTGTCAAATGTT
1 TTACGAACATCTGAGCAGAAACCACAAGAAAGGATGAATGCACTGTCAAATGTT
2960897 TTACGAAC
1 TTACGAAC
2960905 CTGCTATTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.23
Consensus pattern (54 bp):
TTACGAACATCTGAGCAGAAACCACAAGAAAGGATGAATGCACTGTCAAATGTT
Found at i:2961263 original size:22 final size:22
Alignment explanation
Indices: 2961232--2961283 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
2961222 ATCTAAACTC
*
2961232 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
2961254 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
2961276 TTCAAAGA
1 TTCAAAGA
2961284 AGAAAACTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:2962264 original size:75 final size:76
Alignment explanation
Indices: 2961963--2962727 Score: 1057
Period size: 76 Copynumber: 10.0 Consensus size: 76
2961953 ACTATTTCCC
2961963 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
2962028 AAGCCTTCGGG
66 AAGCCTTCGGG
2962039 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
2962104 AAGCCTTCGAG
66 AAGCCTTCGGG
2962115 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
2962180 AAGCCTTCGGG
66 AAGCCTTCGGG
2962191 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
2962255 AAGCCTTCGGG
66 AAGCCTTCGGG
*
2962266 TTATCTGTAAGTCCTTCAGTGCATG-TGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
2962329 AAGCCTTCGGG
66 AAGCCTTCGGG
2962340 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-
2962405 AAAAGCCTTCGGG
65 -AAAGCCTTCGGG
* * * * * ** * ** *** * *
2962418 AGC-TTTTTGATGT-TTTCAAAGCCT--TCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTC
1 -TCATCTGT-AAGTCCTTCAGTGCATGAT-GTTTC--CAAAAAG-CCTTC-G-GGA-GCT-TTT-
** *******
2962479 AAAAAAAAAAAAAAGCCTTCGGG
55 -TGATGTTTTCAAAGCCTTCGGG
2962502 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
2962567 AAGCCTTC-GG
66 AAGCCTTCGGG
2962577 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTC-GGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
2962640 AAGCCTTCGGG
66 AAGCCTTCGGG
* *
2962651 TCATCTGTAAGCCCTTCA-TGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-
2962715 AAAAGCCTTCGGG
65 -AAAGCCTTCGGG
2962728 AGCTTTTTGA
Statistics
Matches: 610, Mismatches: 54, Indels: 49
0.86 0.08 0.07
Matches are distributed among these distances:
73 42 0.07
74 112 0.18
75 126 0.21
76 224 0.37
77 15 0.02
78 25 0.04
79 10 0.02
80 7 0.01
81 2 0.00
82 7 0.01
83 10 0.02
84 25 0.04
85 3 0.00
86 2 0.00
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (76 bp):
TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
AAGCCTTCGGG
Found at i:2962398 original size:31 final size:31
Alignment explanation
Indices: 2962363--2962446 Score: 145
Period size: 31 Copynumber: 2.8 Consensus size: 31
2962353 CTTCAGTGCA
*
2962363 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
1 TGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
2962394 TGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
1 TGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
2962425 TGATGTTTTC--AAAGCCTTCGGG
1 TGATGTTTTCAAAAAGCCTTCGGG
2962447 TCATCTGTAA
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
29 12 0.23
31 40 0.77
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (31 bp):
TGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
Found at i:2962416 original size:107 final size:107
Alignment explanation
Indices: 2962288--2962832 Score: 480
Period size: 107 Copynumber: 5.2 Consensus size: 107
2962278 CCTTCAGTGC
*
2962288 ATGTGTTTCCAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTC
1 ATGT-TTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTC
2962353 CTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
65 CTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
2962396 ATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCC
1 ATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCC
******** * *
2962461 TTCAGTGCATGATGTTT-CAAAAA-AAAAAAAAAGC-CTTCG
66 TTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
* ** *** * * * ** *** * * * *
2962500 -GGTCATCTGTAAGTCCTTC-AGTGCATGATG-T-TTCCAAAAAGCCTTCGGGAGC-TTTTTGAT
1 ATGTTTTCAAAAAG-CCTTCGGGAGCTTTTTGATGTT-TTCAAAGCCTTCGGG-TCATCTGT-AA
* ** * *** * *** ***
2962560 GT-TTTCAAAGCCTTCGGTCAT-CTGTAAGTCCTTC---AG-TGCATG
62 GTCCTTCAGTGCATGATGT-TTCCAAAAAG-CCTTCGGGAGCTTTTTG
* *
2962602 ATG-TTTCCAAAAGCCTTC-GGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCC
1 ATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCC
2962665 TTCA-TGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
66 TTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
*
2962706 ATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCC
1 ATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCC
2962771 TTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
66 TTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
2962813 ATGTTTTC--AAAGCCTTCGGG
1 ATGTTTTCAAAAAGCCTTCGGG
2962833 TCATCTGTAA
Statistics
Matches: 331, Mismatches: 85, Indels: 45
0.72 0.18 0.10
Matches are distributed among these distances:
100 6 0.02
101 25 0.08
102 53 0.16
103 26 0.08
104 14 0.04
105 28 0.08
106 54 0.16
107 121 0.37
108 4 0.01
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.35
Consensus pattern (107 bp):
ATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCC
TTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG
Found at i:2962501 original size:55 final size:55
Alignment explanation
Indices: 2962435--2962539 Score: 201
Period size: 55 Copynumber: 1.9 Consensus size: 55
2962425 TGATGTTTTC
2962435 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCAAAAAAAAAAA
1 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCAAAAAAAAAAA
*
2962490 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAA
1 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCAAAAAA
2962540 GCCTTCGGGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (55 bp):
AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCAAAAAAAAAAA
Found at i:2962708 original size:31 final size:31
Alignment explanation
Indices: 2962673--2962756 Score: 145
Period size: 31 Copynumber: 2.8 Consensus size: 31
2962663 CCTTCATGCA
2962673 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
2962704 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
2962735 TGATGTTTTC--AAAGCCTTCGGG
1 TGATGTTTCCAAAAAGCCTTCGGG
2962757 TCATCTGTAA
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
29 12 0.23
31 40 0.77
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (31 bp):
TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
Found at i:2962740 original size:106 final size:106
Alignment explanation
Indices: 2962600--2962832 Score: 418
Period size: 106 Copynumber: 2.2 Consensus size: 106
2962590 CTTCAGTGCA
2962600 TGATGTTTCCAAAAGCCTTC-GGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCC
1 TGATGTTTCCAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCC
2962664 CTTCA-TGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
66 CTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
2962704 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGC
2962769 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
65 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
2962811 TGATGTTTTC-AAAGCCTTCGGG
1 TGATGTTTCCAAAAGCCTTCGGG
2962833 TCATCTGTAA
Statistics
Matches: 124, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
104 10 0.08
105 22 0.18
106 48 0.39
107 44 0.35
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (106 bp):
TGATGTTTCCAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCC
CTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
Found at i:2962791 original size:76 final size:76
Alignment explanation
Indices: 2962704--2962899 Score: 374
Period size: 76 Copynumber: 2.6 Consensus size: 76
2962694 GGGAGCTTTT
*
2962704 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGC
2962769 CCTTCAGTGCA
66 CCTTCAGTGCA
2962780 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGC
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGC
2962845 CCTTCAGTGCA
66 CCTTCAGTGCA
*
2962856 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCCAAA
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
2962900 AAGCCTTTGG
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 118 1.00
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (76 bp):
TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGC
CCTTCAGTGCA
Found at i:2962817 original size:386 final size:385
Alignment explanation
Indices: 2962103--2962975 Score: 1164
Period size: 386 Copynumber: 2.3 Consensus size: 385
2962093 TGATGTTTTC
2962103 AAAGCCTTCGAGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTT
1 AAAGCCTTCGAGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTT
2962168 TTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTT
66 TTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTT
* *
2962233 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTTATCTGTAAGTCCTTCAGTGCATGTGTTTCC
131 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGTGTTTCC
* * **
2962298 AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
196 AAAAGCCTTCGGGAGCTTTTTGATGTTTCCAAAGCCTTCGGGGCATCTGTAAGTCCTTCAAAGCA
* * *** *
2962363 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGA
261 TGAGGTATCCAAAAAGCCTTC--GAGCTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGA
*
2962428 TGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCAAAAAAAAAAA
324 TGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCAAAAAAAAAAA
*
2962490 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTT
1 AAAGCCTTCGAGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTT
2962555 TTGATGTTTTCAAAGCCTTC-GGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTT
66 TTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTT
2962619 C-GGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCA-TGCATGATGTTTC
131 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG-TGTTTC
* * * *
2962682 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATGT-TTTC
195 C-AAAAGCCTTCGGGAGCTTTTTGATGTTTCC--AAAGCCTTCGGG-GCATCTGT-AAGTCCTTC
* ***
2962745 AAAGCCTTCG-GGTCAT-CTGTAAGTCCTTC-AG-TGCATGATGTTTCCAAAAAGCCTTCGGGAG
255 AAAG-CAT-GAGGT-ATCCAAAAAG-CCTTCGAGCTGCATGATGTTTCCAAAAAGCCTTCGGGAG
2962806 CTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTC------
316 CTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCAAAAAA
*
2962865 --CAA
381 AAAAA
* *
2962868 AAAGCCTTCG-G------G--AG--CTT---T--TTGATGTTTCCAAAAAGCCTTTGGGAGCTTT
1 AAAGCCTTCGAGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTT
* *
2962917 TTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
66 TTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
2962976 CATTTCCATC
Statistics
Matches: 448, Mismatches: 27, Indels: 46
0.86 0.05 0.09
Matches are distributed among these distances:
362 49 0.11
363 36 0.08
364 1 0.00
367 3 0.01
369 2 0.00
371 1 0.00
377 1 0.00
378 12 0.03
384 6 0.01
385 54 0.12
386 158 0.35
387 86 0.19
388 20 0.04
389 12 0.03
390 7 0.02
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (385 bp):
AAAGCCTTCGAGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTT
TTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAGCCTT
CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGTGTTTCC
AAAAGCCTTCGGGAGCTTTTTGATGTTTCCAAAGCCTTCGGGGCATCTGTAAGTCCTTCAAAGCA
TGAGGTATCCAAAAAGCCTTCGAGCTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG
TTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCAAAAAAAAAAA
Found at i:2962891 original size:31 final size:31
Alignment explanation
Indices: 2962856--2962939 Score: 136
Period size: 31 Copynumber: 2.8 Consensus size: 31
2962846 CTTCAGTGCA
2962856 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
2962887 TGATGTTTCCAAAAAGCCTTTGGGAGCTTTT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
2962918 TGATGTTTTC--AAAGCCTTCGGG
1 TGATGTTTCCAAAAAGCCTTCGGG
2962940 TCATCTGTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
29 11 0.22
31 39 0.78
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (31 bp):
TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
Found at i:2962891 original size:107 final size:107
Alignment explanation
Indices: 2962780--2962975 Score: 374
Period size: 107 Copynumber: 1.8 Consensus size: 107
2962770 CTTCAGTGCA
2962780 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGC
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGC
2962845 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
66 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
2962887 TGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGC
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGC
*
2962952 CCTTCAGTGCATGATGTTTTCAAA
66 CCTTCAGTGCATGATGTTTCCAAA
2962976 CATTTCCATC
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 87 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (107 bp):
TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGC
CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
Found at i:2962903 original size:183 final size:181
Alignment explanation
Indices: 2962525--2962975 Score: 843
Period size: 183 Copynumber: 2.5 Consensus size: 181
2962515 CTTCAGTGCA
2962525 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTC-GGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
2962589 CCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTC
66 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTC
2962653 ATCTGTAAGCCCTTCATGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
131 ATCTGTAAGCCCTTCATGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
2962704 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
2962769 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
66 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTC-GGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
2962834 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
130 CATCTGTAAGCCCTTCA-TGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
* *
2962887 TGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGC
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
*
2962952 CCTTCAGTGCATGATGTTTTCAAA
66 CCTTCAGTGCATGATGTTTCCAAA
2962976 CATTTCCATC
Statistics
Matches: 265, Mismatches: 3, Indels: 4
0.97 0.01 0.01
Matches are distributed among these distances:
179 50 0.19
180 35 0.13
181 10 0.04
182 49 0.18
183 121 0.46
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (181 bp):
TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTC
ATCTGTAAGCCCTTCATGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
Found at i:2963110 original size:3 final size:3
Alignment explanation
Indices: 2963102--2963174 Score: 69
Period size: 3 Copynumber: 24.0 Consensus size: 3
2963092 TTTAAATTTT
* *
2963102 TTA TTA TTA TTA -AA TTTA TTA TTA TTA TTA TTA TTAA ATA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
* *
2963148 TTA GTA -TA TTA TTA TTAA TAA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA
2963175 CAAGCCCAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
2 3 0.05
3 50 0.86
4 5 0.09
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:2963116 original size:18 final size:18
Alignment explanation
Indices: 2963093--2963164 Score: 74
Period size: 18 Copynumber: 4.0 Consensus size: 18
2963083 CATTTTTCAT
*
2963093 TTAAATTTTTTATTATTA
1 TTAAATTTATTATTATTA
2963111 TTAAATTTATTATTATTA
1 TTAAATTTATTATTATTA
* * *
2963129 TTATTATTAAATATTATTA
1 TTA-AATTTATTATTATTA
* *
2963148 TT-AGTATATTATTATTA
1 TTAAATTTATTATTATTA
2963165 ATAATTATTA
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
17 10 0.23
18 20 0.45
19 14 0.32
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (18 bp):
TTAAATTTATTATTATTA
Found at i:2963129 original size:24 final size:25
Alignment explanation
Indices: 2963102--2963174 Score: 103
Period size: 27 Copynumber: 2.8 Consensus size: 25
2963092 TTTAAATTTT
2963102 TTATTATTATTAAATTTATTATTA-
1 TTATTATTATTAAATTTATTATTAG
2963126 TTATTATTATTAAATATTATTATTAG
1 TTATTATTATTAAAT-TTATTATTAG
*
2963152 TATATTATTATTAATAATTATTA
1 T-TATTATTATTAA-ATTTATTA
2963175 CAAGCCCAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
24 15 0.34
25 9 0.20
26 1 0.02
27 18 0.41
28 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (25 bp):
TTATTATTATTAAATTTATTATTAG
Found at i:2963671 original size:43 final size:43
Alignment explanation
Indices: 2963599--2963693 Score: 106
Period size: 41 Copynumber: 2.2 Consensus size: 43
2963589 GAATCCTGCA
*
2963599 AAAAAAAAAAAAGAGGCGGAGAACGACAACAAACAA-AA-CAG
1 AAAAAAAAAAAACAGGCGGAGAACGACAACAAACAACAACCAG
* *
2963640 AAAAAAAAAAGACAGG-GAGAGATACGAACAACAACCAACAACCAG
1 AAAAAAAAAAAACAGGCG-GAGA-ACG-ACAACAAACAACAACCAG
*
2963685 AACAAAAAA
1 AAAAAAAAA
2963694 GGAAAAAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
40 1 0.02
41 18 0.40
42 3 0.07
43 10 0.22
44 2 0.04
45 11 0.24
ACGTcount: A:0.65, C:0.17, G:0.17, T:0.01
Consensus pattern (43 bp):
AAAAAAAAAAAACAGGCGGAGAACGACAACAAACAACAACCAG
Found at i:2965171 original size:2 final size:2
Alignment explanation
Indices: 2965164--2965189 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2965154 TTATTTTAAA
2965164 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2965190 TCACATCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2965747 original size:2 final size:2
Alignment explanation
Indices: 2965740--2965767 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2965730 TAAATTATTA
2965740 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2965768 TCAAACTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2968045 original size:2 final size:2
Alignment explanation
Indices: 2967999--2968037 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2967989 TTGTAGCAAC
2967999 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2968038 CTTATATACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2971744 original size:22 final size:22
Alignment explanation
Indices: 2971716--2971761 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
2971706 AAGTAATACT
2971716 AAGGCTCGCGTCGTTGTCTATC
1 AAGGCTCGCGTCGTTGTCTATC
2971738 AAGGCTCGCGTCGTTGTCTATC
1 AAGGCTCGCGTCGTTGTCTATC
2971760 AA
1 AA
2971762 CCAAAGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.30
Consensus pattern (22 bp):
AAGGCTCGCGTCGTTGTCTATC
Found at i:2971843 original size:2 final size:2
Alignment explanation
Indices: 2971836--2971876 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2971826 TAAAATTTTA
2971836 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2971877 AACATATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2972950 original size:37 final size:37
Alignment explanation
Indices: 2972909--2973016 Score: 171
Period size: 37 Copynumber: 2.9 Consensus size: 37
2972899 TTGTGGATCC
* *
2972909 TATTTTTAGGAGTTTGAATCATAGTAGAACTCTATTA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
* *
2972946 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTATCC
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
*
2972983 TATTTTTAGGAGTTTGAATCATAGTAAAAGTCTA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTA
2973017 ACGTTATGTT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (37 bp):
TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
Found at i:2974340 original size:110 final size:110
Alignment explanation
Indices: 2974154--2974660 Score: 789
Period size: 110 Copynumber: 4.6 Consensus size: 110
2974144 TTGTGTCGCT
* * * *
2974154 TCGAGTTCAATATCCTTCGCTGTGAAGTTGAAATTAACTCTGAATAAAACTAAAAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
*
2974219 TGACAGCCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
*
2974264 TCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* *
2974329 TGACAGTCAGTCGCCCCTTCACTGTGAAGTTGAGTTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
** * *
2974374 TCGAGTTTAATATCCTTTGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* * * *
2974439 TGAAATTCAGTCGCCCATTCGCTGTGAAGTTGAGCTTGTTTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* * *
2974484 TCGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTATTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* * * * *
2974549 TGATAGTTAGTCACCCCTTCGATGTGAAGTTGAGGTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
*
2974594 TCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
2974659 TG
66 TG
2974661 TCATTCAACT
Statistics
Matches: 361, Mismatches: 36, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
110 361 1.00
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (110 bp):
TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
Found at i:2976316 original size:14 final size:13
Alignment explanation
Indices: 2976307--2976365 Score: 59
Period size: 13 Copynumber: 4.4 Consensus size: 13
2976297 TTTTTCTTTG
2976307 TTTTTGTTTCTCT
1 TTTTTGTTTCTCT
2976320 TTTTTGTTTTCTCT
1 TTTTTG-TTTCTCT
2976334 TTGCTTT-TTTCTTCT
1 TT--TTTGTTTC-TCT
*
2976349 TCTTT-TTTCTCT
1 TTTTTGTTTCTCT
2976361 TTTTT
1 TTTTT
2976366 CTTTTTATTC
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
12 7 0.17
13 13 0.32
14 13 0.32
15 4 0.10
16 3 0.08
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.78
Consensus pattern (13 bp):
TTTTTGTTTCTCT
Found at i:2976325 original size:13 final size:12
Alignment explanation
Indices: 2976296--2976365 Score: 59
Period size: 14 Copynumber: 5.2 Consensus size: 12
2976286 TTTTCTTCAA
*
2976296 TTTTTTCTTTGTT
1 TTTTTTCTCT-TT
2976309 TTTGTTTCTCTTTT
1 TTT-TTTCTC-TTT
2976323 TTGTTTTCTCTTT
1 TT-TTTTCTCTTT
*
2976336 GCTTTTTTCTTCTTC
1 --TTTTTTC-TCTTT
2976351 TTTTTTCTCTTT
1 TTTTTTCTCTTT
2976363 TTT
1 TTT
2976366 CTTTTTATTC
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
12 7 0.15
13 13 0.27
14 20 0.42
15 8 0.17
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.79
Consensus pattern (12 bp):
TTTTTTCTCTTT
Found at i:2976327 original size:19 final size:18
Alignment explanation
Indices: 2976307--2976376 Score: 59
Period size: 20 Copynumber: 3.6 Consensus size: 18
2976297 TTTTTCTTTG
*
2976307 TTTTTGTTTCTCTTTTTTG
1 TTTTT-TTTCTCTTTTTTC
*
2976326 TTTTCTCTTTGCTTTTTTCTTC
1 TTTT-T-TTT-CTCTTTT-TTC
2976348 TTCTTTTTTCTCTTTTTTC
1 TT-TTTTTTCTCTTTTTTC
*
2976367 TTTTTATTCT
1 TTTTTTTTCT
2976377 TATTGGATCT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
18 7 0.17
19 9 0.21
20 10 0.24
21 9 0.21
22 5 0.12
23 2 0.05
ACGTcount: A:0.01, C:0.17, G:0.04, T:0.77
Consensus pattern (18 bp):
TTTTTTTTCTCTTTTTTC
Found at i:2976371 original size:7 final size:7
Alignment explanation
Indices: 2976296--2976371 Score: 50
Period size: 7 Copynumber: 10.7 Consensus size: 7
2976286 TTTTCTTCAA
2976296 TTTTTTC
1 TTTTTTC
2976303 TTTGTTT-
1 TTT-TTTC
*
2976310 TTGTTTC
1 TTTTTTC
2976317 TCTTTTT-
1 T-TTTTTC
*
2976324 TGTTTTC
1 TTTTTTC
* *
2976331 TCTTTGC
1 TTTTTTC
2976338 TTTTTTC
1 TTTTTTC
2976345 TTCTTCTT-
1 TT-TT-TTC
*
2976353 TTTTCTC
1 TTTTTTC
2976360 TTTTTTC
1 TTTTTTC
2976367 TTTTT
1 TTTTT
2976372 ATTCTTATTG
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
6 8 0.15
7 32 0.60
8 11 0.21
9 2 0.04
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (7 bp):
TTTTTTC
Found at i:2979441 original size:26 final size:26
Alignment explanation
Indices: 2979399--2979448 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
2979389 AAAGGTAAGA
*
2979399 AAGAAATAAATAAATTAAATTAAAATG
1 AAGAAATAAACAAATTAAA-TAAAATG
2979426 AAGAAA-AAACAAATTAAATAAAA
1 AAGAAATAAACAAATTAAATAAAA
2979449 GATAAGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 11 0.50
27 6 0.27
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (26 bp):
AAGAAATAAACAAATTAAATAAAATG
Found at i:2979455 original size:26 final size:27
Alignment explanation
Indices: 2979395--2979455 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
2979385 ATAAAAAGGT
* *
2979395 AAGA-AAGAAATAAATAAATTAAATTA
1 AAGATAAGAAATAAACAAATTAAATAA
2979421 AA-ATGAAGAAA-AAACAAATTAAATAA
1 AAGAT-AAGAAATAAACAAATTAAATAA
2979447 AAGATAAGA
1 AAGATAAGA
2979456 TAAAGAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
25 1 0.03
26 21 0.70
27 8 0.27
ACGTcount: A:0.70, C:0.02, G:0.10, T:0.18
Consensus pattern (27 bp):
AAGATAAGAAATAAACAAATTAAATAA
Found at i:2979508 original size:21 final size:20
Alignment explanation
Indices: 2979484--2979545 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
2979474 AATAGTAAGT
2979484 AAAATAAATAAATAAAATATA
1 AAAATAAATAAATAAAATA-A
* *
2979505 AAAA-AATATAAAAAAGAAGAA
1 AAAATAA-ATAAATAA-AATAA
*
2979526 AAAATATATAAATAAAATAA
1 AAAATAAATAAATAAAATAA
2979546 TAATAAAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
20 6 0.18
21 23 0.70
22 4 0.12
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (20 bp):
AAAATAAATAAATAAAATAA
Found at i:2979519 original size:19 final size:20
Alignment explanation
Indices: 2979483--2979537 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
2979473 AAATAGTAAG
*
2979483 TAAAATAAATA-AATAAAATA
1 TAAAA-AAATATAATAAAAGA
2979503 TAAAAAAATATAA-AAAAGA
1 TAAAAAAATATAATAAAAGA
2979522 -AGAAAAAATAT-ATAAA
1 TA-AAAAAATATAATAAA
2979538 TAAAATAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 2 0.06
19 22 0.71
20 7 0.23
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (20 bp):
TAAAAAAATATAATAAAAGA
Found at i:2979541 original size:35 final size:35
Alignment explanation
Indices: 2979502--2979570 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
2979492 TAAATAAAAT
2979502 ATAAAAAAAT-ATAAAAAAG-AAGAAAAAATATATAA
1 ATAAAAAAATAAT-AAAAAGTAA-AAAAAATATATAA
* *
2979537 ATAAAATAATAATAAAAAGTAAAAATAATATATA
1 ATAAAAAAATAATAAAAAGTAAAAAAAATATATA
2979571 TATATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 26 0.87
36 4 0.13
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (35 bp):
ATAAAAAAATAATAAAAAGTAAAAAAAATATATAA
Found at i:2979568 original size:33 final size:32
Alignment explanation
Indices: 2979499--2979568 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
2979489 AAATAAATAA
2979499 AATATAAAAAAATATAAAAAAGAAGAAAAAAT
1 AATATAAAAAAATATAAAAAAGAAGAAAAAAT
* *
2979531 -ATATAAATAAAATAATAATAAA-AAGTAAAAAT
1 AATATAAA-AAAAT-ATAAAAAAGAAGAAAAAAT
2979563 AATATA
1 AATATA
2979569 TATATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
31 7 0.21
32 14 0.42
33 12 0.36
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.21
Consensus pattern (32 bp):
AATATAAAAAAATATAAAAAAGAAGAAAAAAT
Found at i:2979571 original size:2 final size:2
Alignment explanation
Indices: 2979564--2979672 Score: 130
Period size: 2 Copynumber: 54.5 Consensus size: 2
2979554 AGTAAAAATA
* * * * * *
2979564 AT AT AT AT AT AT AT AT AT AT AT AA AT AA AA AC AT A- AA AA AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* *
2979606 AA AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2979648 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 A
2979673 AATTAATAAA
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.01
2 93 0.98
3 1 0.01
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (2 bp):
AT
Found at i:2979777 original size:24 final size:26
Alignment explanation
Indices: 2979708--2979779 Score: 71
Period size: 24 Copynumber: 2.9 Consensus size: 26
2979698 TAGCATATAT
* *
2979708 ATATATATATATGTAAAAAAATAAAA
1 ATATATACAAATGTAAAAAAATAAAA
*
2979734 ATATATACTAAA-GT-AAAAAA-GAAA
1 ATATATAC-AAATGTAAAAAAATAAAA
*
2979758 ATGTATA-AAATGTAAAAAAATA
1 ATATATACAAATGTAAAAAAATA
2979780 TTACATGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
22 3 0.08
23 2 0.05
24 15 0.41
25 6 0.16
26 9 0.24
27 2 0.05
ACGTcount: A:0.65, C:0.01, G:0.07, T:0.26
Consensus pattern (26 bp):
ATATATACAAATGTAAAAAAATAAAA
Found at i:2979800 original size:7 final size:8
Alignment explanation
Indices: 2979786--2979815 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
2979776 AATATTACAT
2979786 GAAAAAAA
1 GAAAAAAA
2979794 GAAAAAAA
1 GAAAAAAA
2979802 GAAAAAAA
1 GAAAAAAA
2979810 GAAAAA
1 GAAAAA
2979816 TAACAAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (8 bp):
GAAAAAAA
Found at i:2980344 original size:37 final size:37
Alignment explanation
Indices: 2980294--2980401 Score: 162
Period size: 37 Copynumber: 2.9 Consensus size: 37
2980284 TTGTGGATCC
*
2980294 TATTTTTAGGAGTTTGAATCCTAGTAGAACTCTATCA
1 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTATCA
*
2980331 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTATCC
1 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTATCA
* ** *
2980368 TATTTTTAAGAGTTTGAATTATAGTAAAAGTCTA
1 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTA
2980402 ACGTTATGTT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (37 bp):
TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTATCA
Found at i:2986755 original size:3 final size:3
Alignment explanation
Indices: 2986747--2986771 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2986737 ATATTTATTA
2986747 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
2986772 TTTATAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2988097 original size:21 final size:21
Alignment explanation
Indices: 2988073--2988114 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2988063 CAAAATTCCA
2988073 GGTTAATTT-AGGTTCAGATCG
1 GGTTAATTTCA-GTTCAGATCG
2988094 GGTTAATTTCAGTTCAGATCG
1 GGTTAATTTCAGTTCAGATCG
2988115 ATGTTAGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (21 bp):
GGTTAATTTCAGTTCAGATCG
Found at i:2989091 original size:23 final size:23
Alignment explanation
Indices: 2989057--2989148 Score: 121
Period size: 23 Copynumber: 4.0 Consensus size: 23
2989047 CACCACATCT
*
2989057 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
2989080 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
* * *
2989103 TGTAGAAATGCAACGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
2989126 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
2989149 TATAAGGTTG
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.32, C:0.24, G:0.27, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:2992416 original size:23 final size:24
Alignment explanation
Indices: 2992360--2992406 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
2992350 CAAACAATGA
2992360 AGGGAATTATCTTTTGTAATTTTT
1 AGGGAATTATCTTTTGTAATTTTT
*
2992384 AGGGAATTATCTTTT-TCATTTTT
1 AGGGAATTATCTTTTGTAATTTTT
2992407 TAGTAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.23, C:0.06, G:0.15, T:0.55
Consensus pattern (24 bp):
AGGGAATTATCTTTTGTAATTTTT
Found at i:3009885 original size:64 final size:65
Alignment explanation
Indices: 3009816--3009978 Score: 229
Period size: 65 Copynumber: 2.5 Consensus size: 65
3009806 TGGTGCACTA
* * * *
3009816 AGTGTGCATCAATGCATAAAATGCATTCGATGTTTTGAAT-AAGCCTAAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATAAAATGCATTTGATGTTTTCAATAAAACCTAAGTGCATCGATGCATGG
* * *
3009880 TGTGTGCATCGATGCATAAAATGCATTTGATGTTTTCATTAAAACCTGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATAAAATGCATTTGATGTTTTCAATAAAACCTAAGTGCATCGATGCATGG
* * *
3009945 AGAGTGCATCGATGTATAAACTGCATTTGATGTT
1 AGTGTGCATCGATGCATAAAATGCATTTGATGTT
3009979 CAATTTATTC
Statistics
Matches: 87, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
64 35 0.40
65 52 0.60
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (65 bp):
AGTGTGCATCGATGCATAAAATGCATTTGATGTTTTCAATAAAACCTAAGTGCATCGATGCATGG
Found at i:3024417 original size:19 final size:20
Alignment explanation
Indices: 3024370--3024418 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
3024360 TATTCCAGTA
*
3024370 GTATCGATACTAACCCTTGG
1 GTATCAATACTAACCCTTGG
* * *
3024390 GTATTAATACTCACCCTT-T
1 GTATCAATACTAACCCTTGG
3024409 GTATCAATAC
1 GTATCAATAC
3024419 AAAAATAGCA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (20 bp):
GTATCAATACTAACCCTTGG
Found at i:3028375 original size:19 final size:19
Alignment explanation
Indices: 3028320--3028378 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
3028310 GCATTGGGTG
* *
3028320 ATGAATTTGAAAGTAAGCT
1 ATGAATATGAAAGTAAGTT
* * *
3028339 ATGAATCTAAAATTAAGTT
1 ATGAATATGAAAGTAAGTT
3028358 ATGAATATGAAAGTAAGTT
1 ATGAATATGAAAGTAAGTT
3028377 AT
1 AT
3028379 AATTCAGAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.34
Consensus pattern (19 bp):
ATGAATATGAAAGTAAGTT
Found at i:3028448 original size:13 final size:13
Alignment explanation
Indices: 3028430--3028468 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
3028420 GTAAATGAAT
*
3028430 ATGAAAGTGAAAG
1 ATGAAAATGAAAG
*
3028443 ATGAAAATGAAAT
1 ATGAAAATGAAAG
3028456 ATGAAATATGAAA
1 ATGAAA-ATGAAA
3028469 TTTCTGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 17 0.74
14 6 0.26
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (13 bp):
ATGAAAATGAAAG
Found at i:3028459 original size:7 final size:7
Alignment explanation
Indices: 3028427--3028469 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
3028417 TATGTAAATG
3028427 AATATGA
1 AATATGA
*
3028434 AA-GTGA
1 AATATGA
*
3028440 AAGATGA
1 AATATGA
3028447 AA-ATGA
1 AATATGA
3028453 AATATGA
1 AATATGA
3028460 AATATGA
1 AATATGA
3028467 AAT
1 AAT
3028470 TTCTGAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 11 0.34
7 21 0.66
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.23
Consensus pattern (7 bp):
AATATGA
Found at i:3030588 original size:21 final size:22
Alignment explanation
Indices: 3030556--3030638 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 22
3030546 ATAATTTACA
3030556 CCGAACTG-CCACATA-TTTTTC
1 CCGAA-TGACCACATAGTTTTTC
**
3030577 CTAAATGACCACATAGTTTTGTC
1 CCGAATGACCACATAGTTTT-TC
* *
3030600 CCGAAGGACCACATAGGATTTTC
1 CCGAATGACCACATA-GTTTTTC
3030623 CCGAATGACCACATAG
1 CCGAATGACCACATAG
3030639 AACCCTCAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
20 2 0.04
21 10 0.20
22 5 0.10
23 30 0.59
24 4 0.08
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.27
Consensus pattern (22 bp):
CCGAATGACCACATAGTTTTTC
Found at i:3031219 original size:22 final size:20
Alignment explanation
Indices: 3031172--3031226 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
3031162 TCCAACGCAG
*
3031172 TAGTATCGGTACCTCTCCTA
1 TAGTATCGATACCTCTCCTA
3031192 TAGTATCGATACCTCTCCTCTA
1 TAGTATCGATACCTCT-C-CTA
*
3031214 TGGTATCGATACC
1 TAGTATCGATACC
3031227 CCCATTAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 15 0.48
21 1 0.03
22 15 0.48
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.35
Consensus pattern (20 bp):
TAGTATCGATACCTCTCCTA
Found at i:3033453 original size:3 final size:3
Alignment explanation
Indices: 3033445--3033474 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3033435 GCAAGTCTGC
3033445 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3033475 CAATGAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3033659 original size:3 final size:3
Alignment explanation
Indices: 3033651--3033687 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3033641 CAATAAATGC
3033651 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3033688 ACCCTTAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3033973 original size:13 final size:13
Alignment explanation
Indices: 3033934--3033988 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
3033924 AAAAGAACCA
3033934 AAATGATTATTTT
1 AAATGATTATTTT
*** *
3033947 AACCCATAATTTTT
1 AAATGATTA-TTTT
3033961 AAATGATTATTTT
1 AAATGATTATTTT
*
3033974 AAATAATTATTTT
1 AAATGATTATTTT
3033987 AA
1 AA
3033989 CCCATAATTT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
13 23 0.72
14 9 0.28
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (13 bp):
AAATGATTATTTT
Found at i:3033985 original size:27 final size:27
Alignment explanation
Indices: 3033934--3033986 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
3033924 AAAAGAACCA
* *
3033934 AAATGATTATTTTAACCCATAATTTTT
1 AAATGATTATTTTAAACAATAATTTTT
* *
3033961 AAATGATTATTTTAAATAATTATTTT
1 AAATGATTATTTTAAACAATAATTTT
3033987 AACCCATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.51
Consensus pattern (27 bp):
AAATGATTATTTTAAACAATAATTTTT
Found at i:3034183 original size:262 final size:267
Alignment explanation
Indices: 3033703--3034189 Score: 664
Period size: 262 Copynumber: 1.8 Consensus size: 267
3033693 TAACATTTAC
* * *
3033703 TTAAATAATTATTCTAACCTATAATTTTTTAAGATTTTAATATTTCATTTGGGTAAAAAGGACAC
1 TTAAATAATTATTCTAACCCATAATTTTTAAAGATTTTAATAATTCATTTGGGTAAAAAGGACAC
* *
3033768 ACTATATAGATGAAAATCATTAGTCATCAAACGTTAATACTTTAATTAGAGATTTTTGTCCCAAA
66 AC--TATAGAT-AAAACCATTAGTCATCAAACGTTAATACTCTAATTAGAGATTTTTGTCCCAAA
* ** * * **
3033833 ATGAACTATTAGGATCAAAATGTTTCAAAAAGGAATAAAGACTAAAGTGATTATTTAGTTGAATG
128 ATGAACTATTAGGACCAAAATACTTCAAAAAAGAATAAAGACTAAAGTGACTATTTAGTCAAATG
*
3033898 CATTGGGACTAAAATACTT-AAAAAATAAAAGAACCAAAATGATTATTTTAACCCATAATTTTTA
193 CATCGGGACTAAAATACTTAAAAAAATAAAAGAACCAAAATGATTATTTTAACCCATAATTTTTA
3033962 AATGATTATT
258 AATGATTATT
* * *
3033972 TTAAATAATTATTTTAACCCATAATTTTTAAAGATTTTAATAATTCATTTTGGGTAAAAATGTCA
1 TTAAATAATTATTCTAACCCATAATTTTTAAAGATTTTAATAATTCA-TTTGGGTAAAAAGGACA
* * * * *
3034037 C-C-A-A-AT-AAACCGTTAGTCATCAAACGTTATTGCTCTAATTTGATATTTTTGTCCCAAAAT
65 CACTATAGATAAAACCATTAGTCATCAAACGTTAATACTCTAATTAGAGATTTTTGTCCCAAAAT
* *
3034097 GAACTATTAGGGCCAAAATACTTCAAAAAAGAATAAAGGCTAAAGTGACTA-TTAGTCAAATGCA
130 GAACTATTAGGACCAAAATACTTCAAAAAAGAATAAAGACTAAAGTGACTATTTAGTCAAATGCA
*
3034161 TCGGGACTAAAATTCTTTAAAAAAATAAA
195 TCGGGACTAAAATAC-TTAAAAAAATAAA
3034190 GCCAAAACGA
Statistics
Matches: 191, Mismatches: 24, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
261 24 0.13
262 93 0.49
263 10 0.05
264 2 0.01
265 1 0.01
266 1 0.01
269 44 0.23
270 16 0.08
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.35
Consensus pattern (267 bp):
TTAAATAATTATTCTAACCCATAATTTTTAAAGATTTTAATAATTCATTTGGGTAAAAAGGACAC
ACTATAGATAAAACCATTAGTCATCAAACGTTAATACTCTAATTAGAGATTTTTGTCCCAAAATG
AACTATTAGGACCAAAATACTTCAAAAAAGAATAAAGACTAAAGTGACTATTTAGTCAAATGCAT
CGGGACTAAAATACTTAAAAAAATAAAAGAACCAAAATGATTATTTTAACCCATAATTTTTAAAT
GATTATT
Found at i:3036938 original size:15 final size:14
Alignment explanation
Indices: 3036908--3036950 Score: 61
Period size: 15 Copynumber: 3.0 Consensus size: 14
3036898 ACCTCATAAT
3036908 TTTTAAT-TATTTA
1 TTTTAATATATTTA
3036921 TTTTAATATATATTA
1 TTTTAATATAT-TTA
3036936 TTTTAACTATATTTA
1 TTTTAA-TATATTTA
3036951 AACTTTTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 7 0.26
14 3 0.11
15 12 0.44
16 5 0.19
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTAATATATTTA
Found at i:3037867 original size:2 final size:2
Alignment explanation
Indices: 3037860--3037905 Score: 83
Period size: 2 Copynumber: 22.5 Consensus size: 2
3037850 TGAAGTTTTG
3037860 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
3037903 AT A
1 AT A
3037906 GAATTTATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3039559 original size:20 final size:20
Alignment explanation
Indices: 3039536--3039579 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
3039526 GTCACAACCC
*
3039536 GACCCGACCCGTTGACCGTT
1 GACCCGACACGTTGACCGTT
3039556 GACCCGACACGTTGACCGTT
1 GACCCGACACGTTGACCGTT
3039576 GACC
1 GACC
3039580 GGCGTTGACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.39, G:0.25, T:0.18
Consensus pattern (20 bp):
GACCCGACACGTTGACCGTT
Found at i:3040922 original size:18 final size:18
Alignment explanation
Indices: 3040896--3040931 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3040886 TCGAAAGGAC
*
3040896 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
3040914 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
3040932 CGGATGAAAG
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:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:3045443 original size:20 final size:21
Alignment explanation
Indices: 3045416--3045462 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
3045406 ATAACTCGAT
*
3045416 TCAAATTTA-AAAATTTTAAG
1 TCAAATTTATAAAATTATAAG
*
3045436 TTAAATTTATAAAATTATAAG
1 TCAAATTTATAAAATTATAAG
3045457 TCAAAT
1 TCAAAT
3045463 CAATTCAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (21 bp):
TCAAATTTATAAAATTATAAG
Found at i:3045644 original size:31 final size:31
Alignment explanation
Indices: 3045609--3045668 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
3045599 ATTTAAACTT
3045609 CATATAGTATCCAACAAATATTATTTTTTTA
1 CATATAGTATCCAACAAATATTATTTTTTTA
* *
3045640 CATATAGTATCTAACAAATGTTATTTTTT
1 CATATAGTATCCAACAAATATTATTTTTT
3045669 AATATCTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.47
Consensus pattern (31 bp):
CATATAGTATCCAACAAATATTATTTTTTTA
Found at i:3047690 original size:20 final size:19
Alignment explanation
Indices: 3047652--3047689 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
3047642 ACTTGAGTTC
3047652 TTATTTTCTATATATTATA
1 TTATTTTCTATATATTATA
3047671 TTATTTT-TATATATTATA
1 TTATTTTCTATATATTATA
3047689 T
1 T
3047690 AGTTCATATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
TTATTTTCTATATATTATA
Found at i:3049103 original size:22 final size:21
Alignment explanation
Indices: 3049071--3049155 Score: 66
Period size: 22 Copynumber: 3.9 Consensus size: 21
3049061 AAATCTATAT
*
3049071 ATAAAAAAATTAATAA-ACCAA
1 ATAAAAAAATTAA-AATAACAA
3049092 ATAAAAATAATTAAAATAACAA
1 ATAAAAA-AATTAAAATAACAA
* *
3049114 ATAAATAAATAAAACAATAACAAA
1 ATAAAAAAAT-TAA-AATAAC-AA
*
3049138 ATCATAAAAA-TAAAATAA
1 AT-AAAAAAATTAAAATAA
3049156 ACATACATTC
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
21 12 0.23
22 23 0.44
23 8 0.15
24 4 0.08
25 5 0.10
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (21 bp):
ATAAAAAAATTAAAATAACAA
Found at i:3049117 original size:16 final size:15
Alignment explanation
Indices: 3049090--3049127 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3049080 TTAATAAACC
*
3049090 AAATAAAAATAATTA
1 AAATAAAAATAAATA
3049105 AAATAACAAATAAAT-
1 AAATAA-AAATAAATA
3049120 AAATAAAA
1 AAATAAAA
3049128 CAATAACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 12 0.57
16 7 0.33
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (15 bp):
AAATAAAAATAAATA
Found at i:3052167 original size:5 final size:5
Alignment explanation
Indices: 3052157--3052214 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
3052147 AACGGTCAAC
* *
3052157 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
3052206 GGTCG GGTC
1 GGTCG GGTC
3052215 AGACCAGTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.07, C:0.22, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:3052178 original size:22 final size:22
Alignment explanation
Indices: 3052150--3052214 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
3052140 AACGGTCAAC
3052150 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
3052172 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
3052194 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
3052215 AGACCAGTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:3052269 original size:29 final size:30
Alignment explanation
Indices: 3052236--3052311 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 30
3052226 ACCGATTCAG
*
3052236 ACCGGTCAAACCGGTTTGAACTGGTTG-AA
1 ACCGGTCAAACCGGTTTGAACCGGTTGAAA
**
3052265 ACCGGTCAAACCGGTCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTTGAACCGGTTGAAA
*
3052295 ACCGGTTAAACCGGTTT
1 ACCGGTCAAACCGGTTT
3052312 CCAGCAGCCA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 24 0.60
30 16 0.40
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (30 bp):
ACCGGTCAAACCGGTTTGAACCGGTTGAAA
Found at i:3052288 original size:10 final size:9
Alignment explanation
Indices: 3052211--3052309 Score: 54
Period size: 9 Copynumber: 10.3 Consensus size: 9
3052201 GGTCGGGTCG
*
3052211 GGTCAGACC
1 GGTCAAACC
*
3052220 AGTCAAACC
1 GGTCAAACC
* *
3052229 GATTCAGACC
1 G-GTCAAACC
3052239 GGTCAAACC
1 GGTCAAACC
** *
3052248 GGTTTGAACT
1 GG-TCAAACC
*
3052258 GGTTGAAACC
1 GG-TCAAACC
3052268 GGTCAAACC
1 GGTCAAACC
3052277 GGTCAGAACC
1 GGTCA-AACC
*
3052287 GGTTGAAAACC
1 GG-T-CAAACC
*
3052298 GGTTAAACC
1 GGTCAAACC
3052307 GGT
1 GGT
3052310 TTCCAGCAGC
Statistics
Matches: 69, Mismatches: 16, Indels: 10
0.73 0.17 0.11
Matches are distributed among these distances:
9 34 0.49
10 27 0.39
11 7 0.10
12 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.18
Consensus pattern (9 bp):
GGTCAAACC
Found at i:3052288 original size:19 final size:19
Alignment explanation
Indices: 3052211--3052309 Score: 60
Period size: 19 Copynumber: 5.2 Consensus size: 19
3052201 GGTCGGGTCG
*
3052211 GGTCAG-ACCAGTCAAACC
1 GGTCAGAACCGGTCAAACC
*
3052229 GATTCAG-ACCGGTCAAACC
1 G-GTCAGAACCGGTCAAACC
** * *
3052248 GGTTTGAACTGGTTGAAACC
1 GGTCAGAACCGG-TCAAACC
3052268 GGTCA-AACCGGTCAGAACC
1 GGTCAGAACCGGTCA-AACC
* * *
3052287 GGTTGAAAACCGGTTAAACC
1 GG-TCAGAACCGGTCAAACC
3052307 GGT
1 GGT
3052310 TTCCAGCAGC
Statistics
Matches: 62, Mismatches: 13, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
18 5 0.08
19 32 0.52
20 17 0.27
21 8 0.13
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.18
Consensus pattern (19 bp):
GGTCAGAACCGGTCAAACC
Found at i:3052308 original size:20 final size:21
Alignment explanation
Indices: 3052272--3052310 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3052262 GAAACCGGTC
3052272 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
*
3052293 AAACCGGTTA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
3052311 TCCAGCAGCC
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:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:3052310 original size:9 final size:9
Alignment explanation
Indices: 3052236--3052310 Score: 60
Period size: 9 Copynumber: 7.8 Consensus size: 9
3052226 ACCGATTCAG
*
3052236 ACCGGTCAA
1 ACCGGTTAA
*
3052245 ACCGGTTTGA
1 ACCGG-TTAA
*
3052255 ACTGGTTGAA
1 ACCGGTT-AA
*
3052265 ACCGGTCAA
1 ACCGGTTAA
*
3052274 ACCGGTCAGA
1 ACCGGTTA-A
3052284 ACCGGTTGAAA
1 ACCGGTT--AA
3052295 ACCGGTTAA
1 ACCGGTTAA
3052304 ACCGGTT
1 ACCGGTT
3052311 TCCAGCAGCC
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
9 26 0.48
10 19 0.35
11 8 0.15
12 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (9 bp):
ACCGGTTAA
Found at i:3059488 original size:16 final size:16
Alignment explanation
Indices: 3059467--3059504 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
3059457 CAACGGTCAA
3059467 CGGTCAACGGTCGGGT
1 CGGTCAACGGTCGGGT
3059483 CGGTCAACGGTCGGGT
1 CGGTCAACGGTCGGGT
3059499 CAGGTC
1 C-GGTC
3059505 GGGTCAACGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.13, C:0.26, G:0.42, T:0.18
Consensus pattern (16 bp):
CGGTCAACGGTCGGGT
Found at i:3059499 original size:12 final size:12
Alignment explanation
Indices: 3059480--3059521 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
3059470 TCAACGGTCG
3059480 GGTC-GGTCAAC
1 GGTCGGGTCAAC
3059491 GGTCGGGTC-A-
1 GGTCGGGTCAAC
3059501 GGTCGGGTCAAC
1 GGTCGGGTCAAC
3059513 GGTCGGGTC
1 GGTCGGGTC
3059522 GGGTCAGACC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 9 0.32
11 6 0.21
12 13 0.46
ACGTcount: A:0.12, C:0.24, G:0.45, T:0.19
Consensus pattern (12 bp):
GGTCGGGTCAAC
Found at i:3059512 original size:22 final size:21
Alignment explanation
Indices: 3059460--3059526 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 21
3059450 AGAAAGTCAA
*
3059460 CGGTCAACGGTCAACGGTCGGGT
1 CGGTCAACGGTC--GGGTCGGGT
*
3059483 CGGTCAACGGTCGGGTCAGGT
1 CGGTCAACGGTCGGGTCGGGT
3059504 CGGGTCAACGGTCGGGTCGGGT
1 C-GGTCAACGGTCGGGTCGGGT
3059526 C
1 C
3059527 AGACCGGTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
21 8 0.20
22 20 0.50
23 12 0.30
ACGTcount: A:0.13, C:0.25, G:0.43, T:0.18
Consensus pattern (21 bp):
CGGTCAACGGTCGGGTCGGGT
Done.