Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008522.1 Hibiscus syriacus cultivar Beakdansim tig00111390_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: 1416293
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 8
Found at i:528599 original size:9 final size:10
Alignment explanation
Indices: 528563--528599 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
528553 TTACTTGAAG
528563 ATGA-AAAAA
1 ATGAGAAAAA
528572 ATGAGAAAAA
1 ATGAGAAAAA
528582 ATGAGAAAAA
1 ATGAGAAAAA
528592 ATGA-AAAA
1 ATGAGAAAA
528600 GAAAAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 8 0.30
10 19 0.70
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (10 bp):
ATGAGAAAAA
Found at i:528662 original size:35 final size:32
Alignment explanation
Indices: 528595--528668 Score: 87
Period size: 35 Copynumber: 2.2 Consensus size: 32
528585 AGAAAAAATG
*
528595 AAAAAGAAAAAAAAGATAAAGAAGAAAGAAGA
1 AAAAAGAAAAAAAACATAAAGAAGAAAGAAGA
*
528627 AAAAATGAAAACAAAACATAAAAGATGAATA-AAGA
1 AAAAA-GAAAA-AAAACAT-AAAGAAGAA-AGAAGA
528662 AAAAAGA
1 AAAAAGA
528669 TGAATAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
32 5 0.14
33 5 0.14
34 8 0.22
35 17 0.47
36 1 0.03
ACGTcount: A:0.76, C:0.03, G:0.15, T:0.07
Consensus pattern (32 bp):
AAAAAGAAAAAAAACATAAAGAAGAAAGAAGA
Found at i:529978 original size:53 final size:53
Alignment explanation
Indices: 529909--530326 Score: 516
Period size: 53 Copynumber: 7.8 Consensus size: 53
529899 GTGAAGCAAA
* * *
529909 AGAAGATTGTTTGAGTTTTACTCCCTGAAGAAAGAGGGAGTGAACCCGTAGGC
1 AGAAGATTGTTCGAGTTTTACTCCCTGAAGAAAGAGAGAGAGAACCCGTAGGC
* * * *
529962 TGAAGATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGAGAG-CAACCCATAGGC
1 AGAAGATTGTTCGAGTT-TTACTCCCTGAAGAAAGAGAGAGAGAACCCGTAGGC
* * * * *
530015 AAAAGATTGTTCGAGTTCTACTTCCTGGAGAAAGAGAGAGCGAACCCGTAGGC
1 AGAAGATTGTTCGAGTTTTACTCCCTGAAGAAAGAGAGAGAGAACCCGTAGGC
* * *
530068 AGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAAAGAGTGAACCCGTAGGC
1 AGAAGATTGTTCGAGTTTTACTCCCTGAAGAAAGAGAGAGAGAACCCGTAGGC
* * *
530121 AGAAGATTGTTCGAGTTATACTCCCTCAAGAAAGAGAGAGAGAACCTGTAGGC
1 AGAAGATTGTTCGAGTTTTACTCCCTGAAGAAAGAGAGAGAGAACCCGTAGGC
* * * * ** *
530174 AGAAGATTGTTTGAGTTCTTACTCCTTGAAGCAAGAGAGAGAAAACTTGTAGGT
1 AGAAGATTGTTCGAGTT-TTACTCCCTGAAGAAAGAGAGAGAGAACCCGTAGGC
* *
530228 AGAAGATTGTTCGAGTTCTACTCCCT-AAGGCAAGAGAGAGAGAACCCGTAGGC
1 AGAAGATTGTTCGAGTTTTACTCCCTGAA-GAAAGAGAGAGAGAACCCGTAGGC
* * *
530281 AGAAGATTGTTCGAGTTCTTACTCCCTGAAGCAAGATAGAGCGAAC
1 AGAAGATTGTTCGAGTT-TTACTCCCTGAAGAAAGAGAGAGAGAAC
530327 TCGTTCACAG
Statistics
Matches: 317, Mismatches: 42, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
52 21 0.07
53 206 0.65
54 88 0.28
55 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.23
Consensus pattern (53 bp):
AGAAGATTGTTCGAGTTTTACTCCCTGAAGAAAGAGAGAGAGAACCCGTAGGC
Found at i:530381 original size:107 final size:107
Alignment explanation
Indices: 529909--530326 Score: 581
Period size: 106 Copynumber: 3.9 Consensus size: 107
529899 GTGAAGCAAA
* * * * *
529909 AGAAGATTGTTTGAGTTTTACTCCCTGAAGAAAGAGGGAGTGAACCCGTAGGCTGAAGATTGTTC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGAGAACCCGTAGGCAGAAGATTGTTC
*
529974 GAGTTCTTACTCCCTGAAGCAAGAGAGAGC-AACCCATAGGC
66 GAGTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
* * * *
530015 AAAAGATTGTTCGAGTTCTACTTCCTGGAGAAAGAGAGAGCGAACCCGTAGGCAGAAGATTGTTC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGAGAACCCGTAGGCAGAAGATTGTTC
* * *
530080 GAGTTC-TACTCCCTGAAGAAAGAAAGAGTGAACCCGTAGGC
66 GAGTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
* * * *
530121 AGAAGATTGTTCGAGTTATACTCCCTCAAGAAAGAGAGAGAGAACCTGTAGGCAGAAGATTGTTT
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGAGAACCCGTAGGCAGAAGATTGTTC
* ** ** *
530186 GAGTTCTTACTCCTTGAAGCAAGAGAGAGAAAACTTGTAGGT
66 GAGTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
*
530228 AGAAGATTGTTCGAGTTCTACTCCCT-AAGGCAAGAGAGAGAGAACCCGTAGGCAGAAGATTGTT
1 AGAAGATTGTTCGAGTTCTACTCCCTGAA-GAAAGAGAGAGAGAACCCGTAGGCAGAAGATTGTT
*
530292 CGAGTTCTTACTCCCTGAAGCAAGATAGAGCGAAC
65 CGAGTTCTTACTCCCTGAAGCAAGAGAGAGCGAAC
530327 TCGTTCACAG
Statistics
Matches: 273, Mismatches: 36, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
105 20 0.07
106 138 0.51
107 115 0.42
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.23
Consensus pattern (107 bp):
AGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGAGAACCCGTAGGCAGAAGATTGTTC
GAGTTCTTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAGGC
Found at i:536649 original size:21 final size:20
Alignment explanation
Indices: 536598--536657 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 20
536588 AAACCCGACG
*
536598 AGTGTATCGATACACATTCA
1 AGTGTATCGATACATATTCA
*
536618 AGAAATATATCGATACATATTCA
1 AG---TGTATCGATACATATTCA
536641 TAGTGTATCGATACATA
1 -AGTGTATCGATACATA
536658 GCGAGGGTGC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 2 0.06
21 13 0.39
23 16 0.48
24 2 0.06
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (20 bp):
AGTGTATCGATACATATTCA
Found at i:551831 original size:184 final size:184
Alignment explanation
Indices: 551564--551977 Score: 632
Period size: 184 Copynumber: 2.2 Consensus size: 184
551554 GACACCATTT
** * *
551564 ACTCGAGATTGGATTTCAACTTCACGAAAAAGGATATCCAACTCAAAGCCAATTTGGTTAAACAA
1 ACTCGAGATTGGATTTCAACTTCACGATGAAGGATATCCAACTCAAAGCCAATTTGATGAAACAA
* *
551629 CCATTCGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAATGGG-
66 CCATTCGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAAAGAACGGGC
*
551693 TCATCCACGATTTCAACTTCACGACGAAGGATATCGTTCCCACCAGCAACATACA
131 T-ATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAACATACA
551748 ACTCGAGATTGGATTTCAACTTCACGATGAAGGATATCCAACTCAAAGCCAATTTGATGAAACAA
1 ACTCGAGATTGGATTTCAACTTCACGATGAAGGATATCCAACTCAAAGCCAATTTGATGAAACAA
* * * * ** *
551813 CCCTTGGATTTTAACTTCACGATGAAGGATATCCAATTTGAGGCTCAGCTTCACAAAGAACGGGC
66 CCATTCGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAAAGAACGGGC
* *
551878 TATCCACGATTTTAACTTCACGACGAAGGATATCGTGCCCACCAGCAACATTCA
131 TATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAACATACA
* ** *
551932 TCTTTAGATTGGATTTCAACTTCACGATGAAGGATATCCAATTCAA
1 ACTCGAGATTGGATTTCAACTTCACGATGAAGGATATCCAACTCAA
551978 GGCTAAACTT
Statistics
Matches: 209, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
184 208 1.00
185 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (184 bp):
ACTCGAGATTGGATTTCAACTTCACGATGAAGGATATCCAACTCAAAGCCAATTTGATGAAACAA
CCATTCGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAAAGAACGGGC
TATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAACATACA
Found at i:552122 original size:124 final size:124
Alignment explanation
Indices: 551816--552113 Score: 398
Period size: 124 Copynumber: 2.4 Consensus size: 124
551806 GAAACAACCC
* ** * * *
551816 TTGGATTTTAACTTCACGATGAAGGATATCCAATTTGAGGCTCAGCTTCACAAAGAACGGGCTAT
1 TTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAAAGAATGGGCCAT
* * * * * * * *
551881 CCACGATTTTAACTTCACGACGAAGGATATCGTGCCCACCAGCAACATTCATCTTTAGA
66 CCACGATTTGAACTTCACAACGAAGGATATCATACCCACCAGAAACATACAACTCTAGA
* *
551940 TTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTAAACTTCACAACGAATGGGCCAT
1 TTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAAAGAATGGGCCAT
* *
552005 CCATGATTTGAACTTCACAACGAAGGATATCATACCCACCAGAAATATACAACTCTAGA
66 CCACGATTTGAACTTCACAACGAAGGATATCATACCCACCAGAAACATACAACTCTAGA
** * *
552064 TTGGATTTCAACTTCATAATGAAGGATATCCAATGCAAAGCTCAACTTCA
1 TTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCA
552114 GAGTGAATGA
Statistics
Matches: 151, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
124 151 1.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (124 bp):
TTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAAAGAATGGGCCAT
CCACGATTTGAACTTCACAACGAAGGATATCATACCCACCAGAAACATACAACTCTAGA
Found at i:553827 original size:25 final size:25
Alignment explanation
Indices: 553799--553913 Score: 65
Period size: 26 Copynumber: 4.3 Consensus size: 25
553789 TATTATACAC
553799 TATTTTTATTTTTATTTTTTTATAT
1 TATTTTTATTTTTATTTTTTTATAT
* *
553824 TATTTATT-TTTTTAATATTTTTAGTTT
1 TATTT-TTATTTTT-ATTTTTTTA-TAT
* *
553851 TAGTTTATTATTATTATTTTGTTTGTTTAT
1 TA-TTT-TTATTTTTA-TTT-TTT-TATAT
*
553881 TATTATTATTTCGTT-TATTTTTTAT-T
1 TATTTTTATTT--TTAT-TTTTTTATAT
553907 TATTTTT
1 TATTTTT
553914 TTCTAATGTT
Statistics
Matches: 69, Mismatches: 10, Indels: 21
0.69 0.10 0.21
Matches are distributed among these distances:
25 10 0.14
26 17 0.25
27 6 0.09
28 16 0.23
29 10 0.14
30 9 0.13
31 1 0.01
ACGTcount: A:0.20, C:0.01, G:0.04, T:0.75
Consensus pattern (25 bp):
TATTTTTATTTTTATTTTTTTATAT
Found at i:553831 original size:17 final size:16
Alignment explanation
Indices: 553801--553870 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 16
553791 TTATACACTA
553801 TTTT-TATTTTTATTT
1 TTTTATATTTTTATTT
553816 TTTTATATTATTTATTT
1 TTTTATATT-TTTATTT
553833 TTTTAATATTTTTAGTTT
1 TTTT-ATATTTTTA-TTT
*
553851 TAGTTTATTATTATTATTT
1 T--TTTA-TATTTTTATTT
553870 T
1 T
553871 GTTTGTTTAT
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
15 4 0.09
16 4 0.09
17 15 0.32
18 9 0.19
19 5 0.11
20 10 0.21
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTATATTTTTATTT
Found at i:553878 original size:22 final size:22
Alignment explanation
Indices: 553853--553915 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
553843 TTTAGTTTTA
553853 GTTTATTATTATTATTTTGTTT
1 GTTTATTATTATTATTTTGTTT
*
553875 GTTTATTATTATTATTTCGTTT
1 GTTTATTATTATTATTTTGTTT
* * *
553897 ATTTTTTATTTATTTTTTT
1 GTTTATTA-TTATTATTTT
553916 CTAATGTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
22 27 0.77
23 8 0.23
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.75
Consensus pattern (22 bp):
GTTTATTATTATTATTTTGTTT
Found at i:553907 original size:16 final size:16
Alignment explanation
Indices: 553861--553907 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
553851 TAGTTTATTA
*
553861 TTATTATTTTGTTTGT
1 TTATTATTTTATTTGT
553877 TTATTATTATTATTTCGT
1 TTATTATT-TTATTT-GT
553895 TTATT-TTTTATTT
1 TTATTATTTTATTT
553908 ATTTTTTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 14 0.50
17 7 0.25
18 7 0.25
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.74
Consensus pattern (16 bp):
TTATTATTTTATTTGT
Found at i:553963 original size:3 final size:3
Alignment explanation
Indices: 553955--554010 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
553945 ATATCACCAT
*
553955 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
554003 TTA TTA TT
1 TTA TTA TT
554011 TTTTTGTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:554117 original size:19 final size:19
Alignment explanation
Indices: 554084--554204 Score: 75
Period size: 19 Copynumber: 5.8 Consensus size: 19
554074 CGCTATATTA
* *
554084 TTTTCTTATTCTTTATTTT
1 TTTTCTTTTTATTTATTTT
554103 TTTTCTTTTTATTTAGGTTCCTT
1 TTTTCTTTTTATTTA--TT--TT
*
554126 TTTTCTATTTAATTTCATTATGT
1 TTTTCT-TTTTATTT-ATT-T-T
*
554149 TTTTCTTTGT-TTTATTTTT
1 TTTTCTTTTTATTTA-TTTT
554168 TTTTCCTTTTTA-TTATTTT
1 TTTT-CTTTTTATTTATTTT
*
554187 GTTTTGTCTTTTATTTAT
1 -TTTTCT-TTTTATTTAT
554205 GTTAGCATTT
Statistics
Matches: 81, Mismatches: 8, Indels: 24
0.72 0.07 0.21
Matches are distributed among these distances:
19 23 0.28
20 19 0.23
21 11 0.14
22 3 0.04
23 17 0.21
24 7 0.09
25 1 0.01
ACGTcount: A:0.12, C:0.09, G:0.05, T:0.74
Consensus pattern (19 bp):
TTTTCTTTTTATTTATTTT
Found at i:554176 original size:20 final size:20
Alignment explanation
Indices: 554146--554198 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
554136 AATTTCATTA
554146 TGTTTTTCTTTGTT-TTATTT
1 TGTTTTTCTTT-TTATTATTT
554166 T-TTTTTCCTTTTTATTATTT
1 TGTTTTT-CTTTTTATTATTT
554186 TGTTTTGTCTTTT
1 TGTTTT-TCTTTT
554199 ATTTATGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 7 0.24
20 12 0.41
21 9 0.31
22 1 0.03
ACGTcount: A:0.06, C:0.08, G:0.08, T:0.79
Consensus pattern (20 bp):
TGTTTTTCTTTTTATTATTT
Found at i:554246 original size:25 final size:24
Alignment explanation
Indices: 554212--554258 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
554202 TATGTTAGCA
* *
554212 TTTCATTTATTTTGTTTATTTTTAT
1 TTTCACTTATTTT-ATTATTTTTAT
554237 TTTCACTTATTTTATTATTTTT
1 TTTCACTTATTTTATTATTTTT
554259 CCTTATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.74
Consensus pattern (24 bp):
TTTCACTTATTTTATTATTTTTAT
Found at i:556855 original size:13 final size:13
Alignment explanation
Indices: 556837--556882 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
556827 TTCTTAAATA
556837 GTGAACAGTACCC
1 GTGAACAGTACCC
* *
556850 GTGAACAGTAACA
1 GTGAACAGTACCC
556863 GTGAACAGTACCC
1 GTGAACAGTACCC
*
556876 ATGAACA
1 GTGAACA
556883 TTATGGATGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (13 bp):
GTGAACAGTACCC
Found at i:557438 original size:47 final size:45
Alignment explanation
Indices: 557370--557542 Score: 222
Period size: 47 Copynumber: 3.8 Consensus size: 45
557360 ATAAAATCTT
*
557370 TTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* *
557415 TTACCATTTAAATTCCATAAGCTCATAAGCTTATTTTATACAAAATAC
1 TTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTA-CCAAAATAC
* * *
557463 TTACCATTTAATCTCATAAGCTCGTAAGCTTTATTTTACCCATATAC
1 TTACCATTTATTC-CATAAGCTCGTAAGC-TTATTTTACCAAAATAC
* *
557510 TTGCCA-TTATTCCAAAAGCTCGTAAGCTTATTT
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTT
557543 GTATGCTTAC
Statistics
Matches: 112, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
44 6 0.05
45 23 0.21
46 8 0.07
47 50 0.45
48 25 0.22
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
Found at i:557702 original size:40 final size:40
Alignment explanation
Indices: 557650--557808 Score: 291
Period size: 40 Copynumber: 4.0 Consensus size: 40
557640 GTAGTGCTAT
557650 ACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTAC
1 ACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTAC
* *
557690 ATATAAGGTCGTGCCCACCATATACATCGAAGTGTATTAC
1 ACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTAC
557730 ACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTAC
1 ACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTAC
*
557770 ACATAAGGTCGTGCCCACCATATACATCGAAGTGTATTA
1 ACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTA
557809 TAAACCTGTG
Statistics
Matches: 114, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 114 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (40 bp):
ACATAAGGTCGTGCCCACCATATACACCGAAGTGTATTAC
Found at i:559873 original size:30 final size:30
Alignment explanation
Indices: 559812--559890 Score: 74
Period size: 30 Copynumber: 2.7 Consensus size: 30
559802 ATTTGTAATA
* * *
559812 TTTCCAAAA-TTACATTTTGGTCCCTAAAC
1 TTTCCAAAATTTATAATTTGATCCCTAAAC
*
559841 TTTCCAAAATTTATACTTTGATCACC-AAAC
1 TTTCCAAAATTTATAATTTGATC-CCTAAAC
*
559871 TTTATC-AAATTTATAATTTG
1 TTT-CCAAAATTTATAATTTG
559891 GTCATTAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
29 9 0.21
30 30 0.71
31 3 0.07
ACGTcount: A:0.34, C:0.19, G:0.05, T:0.42
Consensus pattern (30 bp):
TTTCCAAAATTTATAATTTGATCCCTAAAC
Found at i:565467 original size:21 final size:22
Alignment explanation
Indices: 565443--565493 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
565433 TTTATTATAA
*
565443 TTATATTTTCATTT-ATATTTT
1 TTATATTTTAATTTGATATTTT
*
565464 TTATAATTTAATTTGATATTTT
1 TTATATTTTAATTTGATATTTT
565486 TATATATT
1 T-TATATT
565494 AAAATATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 12 0.48
22 8 0.32
23 5 0.20
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
TTATATTTTAATTTGATATTTT
Found at i:567776 original size:19 final size:18
Alignment explanation
Indices: 567749--567784 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
567739 AACTTTATCT
*
567749 TTAATTTCTTGTTATTTC
1 TTAATTTCTTATTATTTC
567767 TTAATATTCTTATTATTT
1 TTAAT-TTCTTATTATTT
567785 GTGCAATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.22, C:0.08, G:0.03, T:0.67
Consensus pattern (18 bp):
TTAATTTCTTATTATTTC
Found at i:568949 original size:86 final size:84
Alignment explanation
Indices: 568833--569016 Score: 217
Period size: 84 Copynumber: 2.2 Consensus size: 84
568823 ATTTTGTTGA
* * *
568833 CAGATAGCCCTTCTTGCCTCAAGCTATGCTGTAAATTTTATT-TACCTCTGAGCTAAATGTAATA
1 CAGATAGCCCTTCTCGACTCAACCTATGCTGTAAA---TATTGTACCTCTGAGCTAAATGTAATA
568897 GAACTCGAAGGTCTTTGGATGG
63 GAACTCGAAGGTCTTTGGATGG
* * * * * * *
568919 CAGATAGCCCTTCTCGACTTAACCTCTGCTGTAAATATTGTGCCTTTGAGCTGAGTGTAATCGAA
1 CAGATAGCCCTTCTCGACTCAACCTATGCTGTAAATATTGTACCTCTGAGCTAAATGTAATAGAA
* *
568984 CTCGAAGGTCTTTTGTTGG
66 CTCGAAGGTCTTTGGATGG
*
569003 CAGATAACCCTTCT
1 CAGATAGCCCTTCT
569017 AGCCTTGAGT
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
83 4 0.05
84 50 0.60
86 30 0.36
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (84 bp):
CAGATAGCCCTTCTCGACTCAACCTATGCTGTAAATATTGTACCTCTGAGCTAAATGTAATAGAA
CTCGAAGGTCTTTGGATGG
Found at i:568985 original size:84 final size:84
Alignment explanation
Indices: 568881--569166 Score: 324
Period size: 84 Copynumber: 3.4 Consensus size: 84
568871 TATTTACCTC
* * * * * * * *
568881 TGAGCTAAATGTAATAGAACTCGAAGGTCTTTGGATGGCAGATAGCCCTTCTCGACTTAACCTCT
1 TGAGCTAAGTGTAATCGAACTCGAAGGTCTTTGGATGGCAGATAACCCTTCTAGCCTTGAGCTAT
*
568946 GCTGTAAAT-ATTGTGCCTT
66 GCTGCAAATGA-TGTGCCTT
* * * *
568965 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
1 TGAGCTAAGTGTAATCGAACTCGAAGGTCTTTGGATGGCAGATAACCCTTCTAGCCTTGAGCTAT
569030 GCTGCAAATGATGTGCCTT
66 GCTGCAAATGATGTGCCTT
* * * * * *
569049 GGAGCTGAGTGTAATCGAACTCGAATGT-TTTGTATTGGCAGATAACTCTTCTTGCCTTGAGCTA
1 TGAGCTAAGTGTAATCGAACTCGAAGGTCTTTGGA-TGGCAGATAACCCTTCTAGCCTTGAGCTA
* *
569113 TGTTGCAAATGATGTGTCTT
65 TGCTGCAAATGATGTGCCTT
* * *
569133 TGAGCTAAGCGTAGTCGAACTCAAAGGTCTTTGG
1 TGAGCTAAGTGTAATCGAACTCGAAGGTCTTTGG
569167 GTTTCAAGAG
Statistics
Matches: 169, Mismatches: 30, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
83 3 0.02
84 161 0.95
85 5 0.03
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (84 bp):
TGAGCTAAGTGTAATCGAACTCGAAGGTCTTTGGATGGCAGATAACCCTTCTAGCCTTGAGCTAT
GCTGCAAATGATGTGCCTT
Found at i:569227 original size:30 final size:31
Alignment explanation
Indices: 569153--569328 Score: 167
Period size: 30 Copynumber: 5.4 Consensus size: 31
569143 GTAGTCGAAC
** *
569153 TCAAAGGTCTTTGGGTTTCAAGAGAAACACTT
1 TCAAAGGT-TTTTTGTTTCAAGAGAAACAATT
569185 TCAAAGGGTTTTTT-TTTCAAGAGAAACAATT
1 TCAAA-GGTTTTTTGTTTCAAGAGAAACAATT
* *
569216 TCAAAGGTTTTTGTGTTTCAAGAGAAGCATTT
1 TCAAAGGTTTTT-TGTTTCAAGAGAAACAATT
* *
569248 TCAATGTTTTTTTTTTTTTGAGTTTCAAGAGAAACAATT
1 TCAAAG------GTTTTTT--GTTTCAAGAGAAACAATT
*
569287 TCAAAGG-TTTGTGTTTCAAGAGAAACAATT
1 TCAAAGGTTTTTTGTTTCAAGAGAAACAATT
569317 TCAAAGGTTTTT
1 TCAAAGGTTTTT
569329 GTTGACAGAT
Statistics
Matches: 119, Mismatches: 13, Indels: 25
0.76 0.08 0.16
Matches are distributed among these distances:
30 32 0.27
31 25 0.21
32 32 0.27
33 3 0.03
37 1 0.01
38 5 0.04
39 21 0.18
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.40
Consensus pattern (31 bp):
TCAAAGGTTTTTTGTTTCAAGAGAAACAATT
Found at i:569260 original size:63 final size:64
Alignment explanation
Indices: 569153--569322 Score: 184
Period size: 63 Copynumber: 2.6 Consensus size: 64
569143 GTAGTCGAAC
* *
569153 TCAAAGGTCTTTGGGTTTCAAGAGAAACACTTTCAAAG-GGTTTTTT-TTTCAAGAGAAACAATT
1 TCAAAGGT-TTTGTGTTTCAAGAGAAACAATTTCAAAGTGGTTTTTTGTTTCAAGAGAAACAATT
* * * **
569216 TCAAAGGTTTTTGTGTTTCAAGAGAAGCATTTTCAATGTTTTTTTTTTTTTGAGTTTCAAGAGAA
1 TCAAAGG-TTTTGTGTTTCAAGAGAAACAATTTCAAAG----TGGTTTTTT--GTTTCAAGAGAA
569281 ACAATT
59 ACAATT
569287 TCAAAGG-TTTGTGTTTCAAGAGAAACAATTTCAAAG
1 TCAAAGGTTTTGTGTTTCAAGAGAAACAATTTCAAAG
569323 GTTTTTGTTG
Statistics
Matches: 89, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
63 32 0.36
64 1 0.01
68 6 0.07
69 26 0.29
71 24 0.27
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (64 bp):
TCAAAGGTTTTGTGTTTCAAGAGAAACAATTTCAAAGTGGTTTTTTGTTTCAAGAGAAACAATT
Found at i:569752 original size:164 final size:163
Alignment explanation
Indices: 569317--569822 Score: 710
Period size: 164 Copynumber: 3.1 Consensus size: 163
569307 AGAAACAATT
*
569317 TCAAAGGTTTTTGTTGACAGATAACCCTTCTAACCTTGAGTTATACTGTAAATGATGTGCCCTCG
1 TCAAAGGTCTTTGTTGACAGATAACCCTTCT-ACCTTGAGTTATACTGTAAATGATGTGCCCTCG
* * * *
569382 GAGCTGAGTATAATCGAACTCGGGGGA-CTTTGGCAGATAGCCCTTTTCTACTTGAGCTATGTTG
65 GAGCTGAGTATAATCGAACTC-GGGGATCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTG
569446 CAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
129 CAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
* * * * * * * *
569481 TCGAAGGTCTTTGGTTGGCAGATAACTCTTCTCAACTTAAGTTATACTGCAAATGATATACCCTC
1 TCAAAGGTCTTT-GTTGACAGATAACCCTTCT-ACCTTGAGTTATACTGTAAATGATGTGCCCTC
* * * *
569546 GGAGCTGAGTGTAATCAAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCCATGCTG
64 GGAGCTGAGTATAATCGAACTCGGGGATCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTG
* * * *
569611 TAAATGATGTGCCGTT-GAACTGAGTGTAATCGAAC
129 CAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAAC
* * **
569646 TCAAAGGTCTTTATTGACATATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCG
1 TCAAAGGTCTTTGTTGACAGATAACCCTTCTA-CCTTGAGTTATACTGTAAATGATGTGCCCTCG
569711 GAGCTGAGTATAATCGAACTCGGGGATCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
65 GAGCTGAGTATAATCGAACTCGGGGATCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
569776 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
130 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
*
569810 TCGAAGGTCTTTG
1 TCAAAGGTCTTTG
569823 GTTGGCAACT
Statistics
Matches: 293, Mismatches: 44, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
163 3 0.01
164 153 0.52
165 135 0.46
166 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (163 bp):
TCAAAGGTCTTTGTTGACAGATAACCCTTCTACCTTGAGTTATACTGTAAATGATGTGCCCTCGG
AGCTGAGTATAATCGAACTCGGGGATCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
AATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
Found at i:569957 original size:186 final size:186
Alignment explanation
Indices: 569643--570015 Score: 746
Period size: 186 Copynumber: 2.0 Consensus size: 186
569633 AGTGTAATCG
569643 AACTCAAAGGTCTTTATTGACATATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCC
1 AACTCAAAGGTCTTTATTGACATATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCC
569708 TCGGAGCTGAGTATAATCGAACTCGGGGATCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
66 TCGGAGCTGAGTATAATCGAACTCGGGGATCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
569773 TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGC
131 TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGC
569829 AACTCAAAGGTCTTTATTGACATATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCC
1 AACTCAAAGGTCTTTATTGACATATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCC
569894 TCGGAGCTGAGTATAATCGAACTCGGGGATCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
66 TCGGAGCTGAGTATAATCGAACTCGGGGATCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
569959 TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGC
131 TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGC
570015 A
1 A
570016 GATAACCCCT
Statistics
Matches: 187, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
186 187 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (186 bp):
AACTCAAAGGTCTTTATTGACATATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCC
TCGGAGCTGAGTATAATCGAACTCGGGGATCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGC
Found at i:570042 original size:84 final size:83
Alignment explanation
Indices: 569829--570339 Score: 505
Period size: 84 Copynumber: 6.2 Consensus size: 83
569819 TTTGGTTGGC
* * * * * * * * *
569829 AACTCAAAGGTCTTTATTGACATATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCC
1 AACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CC
* ** *
569894 TCGGAGCTGAGTATAATCG
65 TTGGAGCTGAGCGTAGTCG
* * *
569913 AACTCG-GGGATC--T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
1 AACTCGAAGG-TCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC
569974 TTGGAGCTGAGCGTAGTCG
65 TTGGAGCTGAGCGTAGTCG
* * *
569993 AACTCGAAGGTCTTTGGTTGGCAGATAACCCCTCTCGACTTAAGTTATGCTACAAATGATATGCC
1 AACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC
570058 TTGGAGCTGAGCGTAGTCG
65 TTGGAGCTGAGCGTAGTCG
* ** * * * * * *
570077 AACTCGAAGGTCTTTTGGTCACAGATAACCCTCCTAGCCTTGAGTTATGTTGTAAATGATGTGCC
1 AACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-C
* * * *
570142 CTCGAAGCTGAGTGTAATCG
64 CTTGGAGCTGAGCGTAGTCG
* * * *
570162 AACTCGAGGGTC--T-TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAAAGATGCGCCT
1 AACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCT
*
570224 TGGAGTTGAGCGTAGTCG
66 TGGAGCTGAGCGTAGTCG
* * *
570242 AACTCGAAAGTCTTTGTTGGCAGATAACCCTTCTCAACTTAAGTTATGCTGTAAATGATGTGCCC
1 AACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CC
* * ** *
570307 TCGAAGCTGAATGTAATCG
65 TTGGAGCTGAGCGTAGTCG
*
570326 AACTCGAGGGTCTT
1 AACTCGAAGGTCTT
570340 AAAAAATGGC
Statistics
Matches: 345, Mismatches: 70, Indels: 24
0.79 0.16 0.05
Matches are distributed among these distances:
80 51 0.15
81 73 0.21
82 4 0.01
83 43 0.12
84 143 0.41
85 31 0.09
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (83 bp):
AACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCT
TGGAGCTGAGCGTAGTCG
Found at i:570298 original size:164 final size:165
Alignment explanation
Indices: 569926--570339 Score: 537
Period size: 164 Copynumber: 2.5 Consensus size: 165
569916 TCGGGGATCT
* * * * * * * *
569926 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCAACTTAAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAA
* * * *
569990 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCCTCTCGACTTAAGTTATGCTACAAATGATAT
66 TCGAACTCGAGGGTC--T--TTGGCAGATAACCCCTCTCGACTTAAGCTATGCTACAAAAGATAC
*
570055 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
127 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAAGTCTTTTG
* ** * * * *
570094 GTCACAGATAACCCTCCT-AGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTA
1 TTGGCAGATAACCCTTCTCA-ACTTAAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTA
* * *
570158 ATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAAAGATGCGCC
65 ATCGAACTCGAGGGTCTTTGGCAGATAACCCCTCTCGACTTAAGCTATGCTACAAAAGATACGCC
*
570223 TTGGAGTTGAGCGTAGTCGAACTCGAAAGTC-TTTG
130 TTGGAGCTGAGCGTAGTCGAACTCGAAAGTCTTTTG
*
570258 TTGGCAGATAACCCTTCTCAACTTAAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAATGTAA
1 TTGGCAGATAACCCTTCTCAACTTAAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAA
570323 TCGAACTCGAGGGTCTT
66 TCGAACTCGAGGGTCTT
570340 AAAAAATGGC
Statistics
Matches: 211, Mismatches: 32, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
164 76 0.36
165 72 0.34
167 1 0.00
168 34 0.16
169 28 0.13
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (165 bp):
TTGGCAGATAACCCTTCTCAACTTAAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAA
TCGAACTCGAGGGTCTTTGGCAGATAACCCCTCTCGACTTAAGCTATGCTACAAAAGATACGCCT
TGGAGCTGAGCGTAGTCGAACTCGAAAGTCTTTTG
Found at i:570329 original size:249 final size:249
Alignment explanation
Indices: 569852--570339 Score: 773
Period size: 249 Copynumber: 2.0 Consensus size: 249
569842 TTATTGACAT
* *
569852 ATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGGAGCTGAGTATAATCGAACT
1 ATAACCCTCCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTATAATCGAACT
* * *
569917 CGGGGATCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCT
66 CGGGGATCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAAAGATGCGCCTTGGAGCT
* *
569982 GAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCCTCTCGACTTAAGTTATGCTACA
131 GAGCGTAGTCGAACTCGAAAGTCTTTGGTTGGCAGATAACCCCTCTCAACTTAAGTTATGCTACA
* * * *
570047 AATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAG
196 AATGATATGCCTCGAAGCTGAACGTAATCGAACTCGAAGGTCTTTTGGTCACAG
*
570101 ATAACCCTCCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
1 ATAACCCTCCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTATAATCGAACT
*
570166 CGAGGG-TCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAAAGATGCGCCTTGGAGT
66 CG-GGGATCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAAAGATGCGCCTTGGAGC
* **
570230 TGAGCGTAGTCGAACTCGAAAGTCTTT-GTTGGCAGATAACCCTTCTCAACTTAAGTTATGCTGT
130 TGAGCGTAGTCGAACTCGAAAGTCTTTGGTTGGCAGATAACCCCTCTCAACTTAAGTTATGCTAC
* * *
570294 AAATGATGTGCCCTCGAAGCTGAATGTAATCGAACTCGAGGGTCTT
195 AAATGATATG-CCTCGAAGCTGAACGTAATCGAACTCGAAGGTCTT
570340 AAAAAATGGC
Statistics
Matches: 218, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
248 42 0.19
249 173 0.79
250 3 0.01
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (249 bp):
ATAACCCTCCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTATAATCGAACT
CGGGGATCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAAAGATGCGCCTTGGAGCT
GAGCGTAGTCGAACTCGAAAGTCTTTGGTTGGCAGATAACCCCTCTCAACTTAAGTTATGCTACA
AATGATATGCCTCGAAGCTGAACGTAATCGAACTCGAAGGTCTTTTGGTCACAG
Found at i:573215 original size:23 final size:22
Alignment explanation
Indices: 573173--573215 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
573163 CCTGTAACTG
573173 TTTGATTTTCTCCTTCATCTTC
1 TTTGATTTTCTCCTTCATCTTC
573195 TTTGATTTGTCAT-CTTCATCT
1 TTTGATTT-TC-TCCTTCATCT
573216 AAATCTGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 10 0.53
24 1 0.05
ACGTcount: A:0.12, C:0.23, G:0.07, T:0.58
Consensus pattern (22 bp):
TTTGATTTTCTCCTTCATCTTC
Found at i:579404 original size:13 final size:13
Alignment explanation
Indices: 579386--579420 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
579376 CTCAATACGC
*
579386 GTCATAAATGTGT
1 GTCATAAATGCGT
579399 GTCATAAATGCGT
1 GTCATAAATGCGT
*
579412 GTCAAAAAT
1 GTCATAAAT
579421 ACGCTTCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.31
Consensus pattern (13 bp):
GTCATAAATGCGT
Found at i:579696 original size:58 final size:59
Alignment explanation
Indices: 579592--579712 Score: 145
Period size: 58 Copynumber: 2.1 Consensus size: 59
579582 CTTTGTGGCT
* *
579592 TCTTTTATAACAAATCCTTGATTTAACAAAAGCCACAAGTTCAAAACATTTAT-TCTTA
1 TCTTTTATAACAAATCCTTAATTTAACAAAAGCCACAAGTTCAAAACATTTATCCCTTA
* * ** * ** *
579650 TCTTTTATAACAAATTCTTAATTTAATAAGGGTCATTAGTTTAAAACATTTATCCCTTA
1 TCTTTTATAACAAATCCTTAATTTAACAAAAGCCACAAGTTCAAAACATTTATCCCTTA
579709 TCTT
1 TCTT
579713 ATCCTTGATT
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
58 44 0.85
59 8 0.15
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.41
Consensus pattern (59 bp):
TCTTTTATAACAAATCCTTAATTTAACAAAAGCCACAAGTTCAAAACATTTATCCCTTA
Found at i:592456 original size:2 final size:2
Alignment explanation
Indices: 592449--592510 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
592439 CATCCTTTAA
592449 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
592491 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
592511 TAAGTACAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:599715 original size:10 final size:10
Alignment explanation
Indices: 599702--599744 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
599692 TCGAAGTAAG
599702 AAGAAGAAAA
1 AAGAAGAAAA
**
599712 AAGAAGAGGA
1 AAGAAGAAAA
*
599722 AAGAAAAAAA
1 AAGAAGAAAA
599732 AAGAA-AAAA
1 AAGAAGAAAA
599741 AAGA
1 AAGA
599745 GGGATTGATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
9 8 0.29
10 20 0.71
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AAGAAGAAAA
Found at i:600238 original size:9 final size:9
Alignment explanation
Indices: 600212--600318 Score: 53
Period size: 9 Copynumber: 12.0 Consensus size: 9
600202 GAAAAAAACG
*
600212 GAAAAGAAG
1 GAAAAGAAA
600221 GAAAAGAAA
1 GAAAAGAAA
600230 GAAAAGAAA
1 GAAAAGAAA
*
600239 -ACAAGAAA
1 GAAAAGAAA
* *
600247 CAAGAGAAA
1 GAAAAGAAA
*
600256 -AAGAGAAAA
1 GAAAAG-AAA
* *
600265 GGAAA-AAG
1 GAAAAGAAA
*
600273 GAAAAAAAA
1 GAAAAGAAA
600282 GGAAAAGGAAA
1 -GAAAA-GAAA
*
600293 -AAAA-AAG
1 GAAAAGAAA
*
600300 GAAAAAAAA
1 GAAAAGAAA
600309 GAAAGAGAAA
1 GAAA-AGAAA
600319 ATGAAAGGAG
Statistics
Matches: 76, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
7 2 0.03
8 22 0.29
9 38 0.50
10 11 0.14
11 3 0.04
ACGTcount: A:0.75, C:0.02, G:0.23, T:0.00
Consensus pattern (9 bp):
GAAAAGAAA
Found at i:600239 original size:23 final size:23
Alignment explanation
Indices: 600212--600325 Score: 60
Period size: 23 Copynumber: 4.8 Consensus size: 23
600202 GAAAAAAACG
600212 GAAAAGAAGGAAAAGAAAGAAAA
1 GAAAAGAAGGAAAAGAAAGAAAA
* * *
600235 GAAAACAAGAAACAAGAGA-AAAA
1 GAAAAGAAGGAA-AAGAAAGAAAA
* *
600258 GAGAA-AAGGAAAAAGGAAAAAAAA
1 GAAAAGAAGG-AAAA-GAAAGAAAA
600282 GGAAAAGGAA--AAAA-AAAGGAAAA
1 -GAAAA-GAAGGAAAAGAAA-GAAAA
600305 -AAAAGAAAGAGAAAATGAAAG
1 GAAAAG-AAG-GAAAA-GAAAG
600326 GAGAAAAAAG
Statistics
Matches: 69, Mismatches: 8, Indels: 26
0.67 0.08 0.25
Matches are distributed among these distances:
20 1 0.01
21 6 0.09
22 8 0.12
23 27 0.39
24 17 0.25
25 5 0.07
26 3 0.04
27 2 0.03
ACGTcount: A:0.74, C:0.02, G:0.24, T:0.01
Consensus pattern (23 bp):
GAAAAGAAGGAAAAGAAAGAAAA
Found at i:600281 original size:17 final size:18
Alignment explanation
Indices: 600261--600305 Score: 76
Period size: 17 Copynumber: 2.6 Consensus size: 18
600251 AGAAAAAGAG
600261 AAAAGGAAAAAGG-AAAA
1 AAAAGGAAAAAGGAAAAA
600278 AAAAGG-AAAAGGAAAAA
1 AAAAGGAAAAAGGAAAAA
600295 AAAAGGAAAAA
1 AAAAGGAAAAA
600306 AAAGAAAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.23
17 16 0.62
18 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (18 bp):
AAAAGGAAAAAGGAAAAA
Found at i:600288 original size:30 final size:29
Alignment explanation
Indices: 600205--600324 Score: 106
Period size: 30 Copynumber: 4.1 Consensus size: 29
600195 CATTAGAGAA
*
600205 AAAAACGG-AAAAGAAGGAAAAGAAAGAAAAG
1 AAAAA-GGAAAAAAAAGGAAAAG--AGAAAAG
* * * *
600236 AAAACAAGAAACAAGAGAAAAAGAGAAAAGG
1 AAAA-AGGAAAAAAAAGGAAAAGAGAAAA-G
600267 AAAAAGGAAAAAAAAGGAAAAG-GAAAA-
1 AAAAAGGAAAAAAAAGGAAAAGAGAAAAG
600294 AAAAAGGAAAAAAAA-G-AAAGAGAAAATG
1 AAAAAGGAAAAAAAAGGAAAAGAGAAAA-G
600322 AAA
1 AAA
600325 GGAGAAAAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
25 4 0.05
26 6 0.08
27 15 0.20
28 3 0.04
29 5 0.07
30 20 0.27
31 10 0.14
32 11 0.15
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.01
Consensus pattern (29 bp):
AAAAAGGAAAAAAAAGGAAAAGAGAAAAG
Found at i:600298 original size:11 final size:11
Alignment explanation
Indices: 600284--600308 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
600274 AAAAAAAAGG
600284 AAAAGGAAAAA
1 AAAAGGAAAAA
600295 AAAAGGAAAAA
1 AAAAGGAAAAA
600306 AAA
1 AAA
600309 GAAAGAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAGGAAAAA
Found at i:600305 original size:27 final size:27
Alignment explanation
Indices: 600255--600335 Score: 94
Period size: 26 Copynumber: 3.0 Consensus size: 27
600245 AACAAGAGAA
600255 AAAGAGAAAAGGAAAAAGGAAAAAAAAGG
1 AAAGAGAAAA--AAAAAGGAAAAAAAAGG
600284 AAA-AGGAAAAAAAAAGGAAAAAAAA-G
1 AAAGA-GAAAAAAAAAGGAAAAAAAAGG
** *
600310 AAAGAGAAAATGAAAGGAGAAAAAAG
1 AAAGAGAAAAAAAAAGGAAAAAAAAG
600336 AAATTGAATC
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
26 21 0.46
27 16 0.35
28 1 0.02
29 8 0.17
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.01
Consensus pattern (27 bp):
AAAGAGAAAAAAAAAGGAAAAAAAAGG
Found at i:600329 original size:13 final size:12
Alignment explanation
Indices: 600255--600338 Score: 54
Period size: 10 Copynumber: 7.2 Consensus size: 12
600245 AACAAGAGAA
*
600255 AAAGAGAAAAGG
1 AAAGAGAAAAAG
*
600267 AAAAAGGAAAAA-
1 AAAGA-GAAAAAG
*
600279 AAAG-GAAAAGG
1 AAAGAGAAAAAG
600290 AAA-A-AAAAAG
1 AAAGAGAAAAAG
*
600300 GAA-A-AAAAAG
1 AAAGAGAAAAAG
*
600310 AAAGAGAAAATG
1 AAAGAGAAAAAG
600322 AAAGGAGAAAAAAG
1 AAA-GAG-AAAAAG
600336 AAA
1 AAA
600339 TTGAATCAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
10 21 0.38
11 4 0.07
12 15 0.27
13 8 0.14
14 8 0.14
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (12 bp):
AAAGAGAAAAAG
Found at i:602784 original size:90 final size:89
Alignment explanation
Indices: 602505--602787 Score: 494
Period size: 90 Copynumber: 3.1 Consensus size: 89
602495 AGCATGATGC
* *
602505 GTAAGACCTTCGGGCCATCCATAAGACCTTCAGTGCAAGATGTTTTCAAATGAGATTTTAGAAAC
1 GTAAGTCCTTC-GGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAAC
602570 TAAGCCTTCGGGGGTTTCTTGATTT
65 TAAGCCTTCGGGGGTTTCTTGATTT
*
602595 GTAAGTCATTCGGCCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAAC
1 GTAAGTCCTTCGG-CCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAAC
602660 TAAGCCTTCGGGGGTTTCTTGATTT
65 TAAGCCTTCGGGGGTTTCTTGATTT
602685 GTAAGTCCTTCGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAAGAAAC
1 GTAAGTCCTTCGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTT-AGAAAC
602750 TAAGCCTTCGGGGGTTTCTTGATTT
65 TAAGCCTTCGGGGGTTTCTTGATTT
* *
602775 TTAAATCCTTCGG
1 GTAAGTCCTTCGG
602788 GTCATCTGTA
Statistics
Matches: 185, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
89 47 0.25
90 138 0.75
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (89 bp):
GTAAGTCCTTCGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAACT
AAGCCTTCGGGGGTTTCTTGATTT
Found at i:606491 original size:137 final size:137
Alignment explanation
Indices: 606225--606866 Score: 763
Period size: 137 Copynumber: 4.7 Consensus size: 137
606215 ATATTTTAGG
* * * * * * *
606225 TTTAGACCTTCAATCTAGGGGAATTTTTAATTTGGTCATCG-TTTATGCTCGTGGTTCAATTTTA
1 TTTAGTCCTTTAATTTAGGGG-ATTCTTAATTTGGTCCTCGCTTT-TGCTCGAGGTTCCATTTTA
* *
606289 ATTATTCGATTC-ATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTCCATTTTAGGCTT
64 ATTATTCGATTCAATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTCCACTTTAGACTT
606353 AATTTCATA
129 AATTTCATA
606362 CTTT-GTCCTTTAATTTAGGGGATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAA
1 -TTTAGTCCTTTAATTTAGGGGATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAA
** * * * * *
606426 TTATTCGACCCAATAATTGGTTAAAATGGACCAGATTAATAGTTAGAGTCTCCATTTTAGACTTA
65 TTATTCGATTCAATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTCCACTTTAGACTTA
*
606491 ACTTCATA
130 ATTTCATA
* * * * *
606499 -TTAGTCCTTAAATTTAGGGGAATTCTTAATTTGGTCCACACCTTTGCTCAAGGTTCCATTTTAA
1 TTTAGTCCTTTAATTTAGGGG-ATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAA
* * * * *
606563 TTATTCGATTCGATAATTGGCTAAAATGGACTAGGTTAATAATTAGAGACTCCACTATAGGCTTA
65 TTATTCGATTCAATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTCCACTTTAGACTTA
606628 ATTTTCATA
130 A-TTTCATA
* * *
606637 TTTAGTCCTTTAATTTAGGAGAATTTTTAATTTGGTCATCGCTTTTGCTCGAGGTTCCATTTTAA
1 TTTAGTCCTTTAATTTAGG-GGATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAA
** * * * * *
606702 TTATTCGACCCAATAATTGATTAAAATGGATTATGTTAATAATTAGAACCTTCACTTTAGTA-TT
65 TTATTCGATTCAATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTCCACTTTAG-ACTT
*
606766 AATTTCATT
129 AATTTCATA
* ** * * ** *
606775 TTTAGTTCTTTGTTTTAGAGGAATTCTTAATTTGGTCCTTGCTTTTGCTTTATGTTCCATTTTAA
1 TTTAGTCCTTTAATTTAG-GGGATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAA
606840 TTATTCGATTCAATAATTGGTTAAAAT
65 TTATTCGATTCAATAATTGGTTAAAAT
606867 TAGTTAGATT
Statistics
Matches: 430, Mismatches: 65, Indels: 18
0.84 0.13 0.04
Matches are distributed among these distances:
135 2 0.00
136 60 0.14
137 166 0.39
138 93 0.22
139 108 0.25
140 1 0.00
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.43
Consensus pattern (137 bp):
TTTAGTCCTTTAATTTAGGGGATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAAT
TATTCGATTCAATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTCCACTTTAGACTTAA
TTTCATA
Found at i:606907 original size:276 final size:274
Alignment explanation
Indices: 606277--607001 Score: 835
Period size: 276 Copynumber: 2.6 Consensus size: 274
606267 TTATGCTCGT
*
606277 GGTTCAATTTTAATTATTCGATTCATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTCC
1 GGTTCCATTTTAATTATTCGATTCATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTCC
* *
606342 ATTTTAGGCTTAATTTCATACTTT-GTCCTTTAATTTAGG-GGATTCTTAATTTGGTCCTCGCTT
66 ATTTTAGGCTTAATTTCATA-TTTAGTCCTTTAATTTAGGAGAATTCTTAATTTGGTCATCGCTT
* *
606405 TTGCTCGAGGTTCCATTTTAATTATTCGACCCAATAATTGGTTAAAATGGACCAGATTAATAGTT
130 TTGCTCGAGGTTCCATTTTAATTATTCGACCCAATAATTGATTAAAATGGACCAGATTAATAATT
** * *
606470 AGAGTCTCCATTTTAGACTTAACTTCATATTAGTCCTTAAATTTAGGGGAATTCTTAATTTGGTC
195 AGAACCTCCACTTTAGACTTAACTTCATATTAGTCCTTAAATTTAGAGGAATTCTTAATTTGGTC
606535 CACACCTTTGCTCAA
260 CACACCTTTGCTCAA
* *
606550 GGTTCCATTTTAATTATTCGATTCGATAATTGGCTAAAATGGACTAGGTTAATAATTAGAGACTC
1 GGTTCCATTTTAATTATTCGATTC-ATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTC
* * *
606615 CACTATAGGCTTAATTTTCATATTTAGTCCTTTAATTTAGGAGAATTTTTAATTTGGTCATCGCT
65 CATTTTAGGCTTAA-TTTCATATTTAGTCCTTTAATTTAGGAGAATTCTTAATTTGGTCATCGCT
**
606680 TTTGCTCGAGGTTCCATTTTAATTATTCGACCCAATAATTGATTAAAATGGATTATG-TTAATAA
129 TTTGCTCGAGGTTCCATTTTAATTATTCGACCCAATAATTGATTAAAATGGACCA-GATTAATAA
* * * * ***
606744 TTAGAACCTTCACTTTAGTA-TTAATTTCATTTTTAGTTCTTTGTTTTAGAGGAATTCTTAATTT
193 TTAGAACCTCCACTTTAG-ACTTAACTTCA-TATTAGTCCTTAAATTTAGAGGAATTCTTAATTT
*** * **
606808 GGTCCTTGCTTTTGCTTTA
256 GGTCCACACCTTTGCTCAA
* * * *
606827 TGTTCCATTTTAATTATTCGATTCAATAATTGGTTAAAAT-TAGTTAGATTAAT-ATT-GAGGCC
1 GGTTCCATTTTAATTATTCGATTC-ATAATTGGTTAAAATGGA-CTAGGTTAATAATTAGA-GCC
** * ** * *
606889 TCCATTTTAGTTTTAATTTCA-CTTTAGTTGTTTAATTTAGGA-ACATTC--AATTTGATTC-TT
63 TCCATTTTAGGCTTAATTTCATATTTAGTCCTTTAATTTAGGAGA-ATTCTTAATTTG-GTCATC
* ** * * *
606949 GCTTTTATGTTCGAGGTTTTATTTTGATTATTCGACTCAATAATTTATTAAAA
126 GC-TTT-TGCTCGAGGTTCCATTTTAATTATTCGACCCAATAATTGATTAAAA
607002 ATAATTTGGA
Statistics
Matches: 387, Mismatches: 52, Indels: 25
0.83 0.11 0.05
Matches are distributed among these distances:
272 9 0.02
273 29 0.07
274 114 0.29
275 29 0.07
276 118 0.30
277 88 0.23
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.44
Consensus pattern (274 bp):
GGTTCCATTTTAATTATTCGATTCATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTCC
ATTTTAGGCTTAATTTCATATTTAGTCCTTTAATTTAGGAGAATTCTTAATTTGGTCATCGCTTT
TGCTCGAGGTTCCATTTTAATTATTCGACCCAATAATTGATTAAAATGGACCAGATTAATAATTA
GAACCTCCACTTTAGACTTAACTTCATATTAGTCCTTAAATTTAGAGGAATTCTTAATTTGGTCC
ACACCTTTGCTCAA
Found at i:612819 original size:137 final size:138
Alignment explanation
Indices: 612456--613093 Score: 695
Period size: 138 Copynumber: 4.7 Consensus size: 138
612446 GATTTTAGGT
* * * ** *
612456 TTAGTCCTTCAATTTAGGGGAATTTTTAATTTAGTTATC-GTTTATGCTCGAGGTTCCATTTTAA
1 TTAGTCCTTTAATTTAGGGGAATTCTTAATTTGGTCCTCACTTT-TGCTCGAGGTTCCATTTTAA
* *
612520 TTATTTGATTC-ATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTCTATTTTAGGCTTA
65 TTATTCGACTCAATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTCTATTTTAGGCTTA
612584 ATTTCATAC
130 ATTTCATAC
* * ** *
612593 TTAGTCCTTTAATTTAGGGG---GCTTAATTTGGTCATTGCTTTTGCTCGAGGTTACATTTTAAT
1 TTAGTCCTTTAATTTAGGGGAATTCTTAATTTGGTCCTCACTTTTGCTCGAGGTTCCATTTTAAT
* * ** *
612655 TATTC-AGCCCAATAATTGGTTAAAATGGACCAGGTTAATAATTAGATTCTCTATTTTAGACTTA
66 TATTCGA-CTCAATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTCTATTTTAGGCTTA
612719 ATTTCATA-
130 ATTTCATAC
* * *
612727 TGA-TTCTTTAACTTTAGGGGAATTCTTAATTTGGTCCTTGC-CTTTT-CTCAAGGTTCCATTTT
1 TTAGTCCTTTAA-TTTAGGGGAATTCTTAATTTGGTCC-T-CACTTTTGCTCGAGGTTCCATTTT
* * * * * * * * *
612789 AATTATTCGATTTAATTATTGGCTAAAATGGACTAGGTTAATAATTAAAGACTCCACTATAGGCT
63 AATTATTCGACTCAATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTCTATTTTAGGCT
*
612854 TAATTTCATAT
128 TAATTTCATAC
* * * * * * *
612865 TTAGTCCTTTAATTTAGGAGAATTTTTAATTTGATTCTCATTTTTGCTCGATGTTCCACTTTAAT
1 TTAGTCCTTTAATTTAGGGGAATTCTTAATTTGGTCCTCACTTTTGCTCGAGGTTCCATTTTAAT
* * * * *
612930 TATTCGGCCCAATTATTGGTTAAAATGGACTATGTTAATAATTAGAGCCTGC-ATTTTAGGCTTC
66 TATTCGACTCAATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCT-CTATTTTAGGCTTA
**
612994 ATTTCATTT
130 ATTTCATAC
* * * *
613003 TTAGTCCTTTAATTTAGAGGAATTCTTAATTTGGTCCTCTCTTTTGCTCTATGTTCCATTTTAAT
1 TTAGTCCTTTAATTTAGGGGAATTCTTAATTTGGTCCTCACTTTTGCTCGAGGTTCCATTTTAAT
*
613068 TATTCGATTCAATAATTGGTTAAAAT
66 TATTCGACTCAATAATTGGTTAAAAT
613094 TAGTTAGATT
Statistics
Matches: 416, Mismatches: 70, Indels: 29
0.81 0.14 0.06
Matches are distributed among these distances:
133 8 0.02
134 46 0.11
135 60 0.14
136 1 0.00
137 110 0.26
138 183 0.44
139 8 0.02
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.45
Consensus pattern (138 bp):
TTAGTCCTTTAATTTAGGGGAATTCTTAATTTGGTCCTCACTTTTGCTCGAGGTTCCATTTTAAT
TATTCGACTCAATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTCTATTTTAGGCTTAA
TTTCATAC
Found at i:612944 original size:138 final size:137
Alignment explanation
Indices: 612455--613223 Score: 677
Period size: 138 Copynumber: 5.6 Consensus size: 137
612445 AGATTTTAGG
* * * * *
612455 TTTAGTCCTTCAATTTAGGGGAATTTTTAATTT-AGTTATCGTTTATGCTCGAGGTTCCATTTTA
1 TTTAGTCCTTTAATTTAGGAGAATTCTTAATTTGA-TTCTC-TTTTTGCTCGAGGTTCCATTTTA
* *
612519 ATTATTTGATTC-ATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTCTATTTTAGGCTT
64 ATTATTCGATTCAATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTCCATTTTAGGCTT
612583 AATTTCATA
129 AATTTCATA
* ** * *
612592 CTTAGTCCTTTAATTTAGG-G--GGCTTAATTTG-GTCAT-TGCTTTTGCTCGAGGTTACATTTT
1 TTTAGTCCTTTAATTTAGGAGAATTCTTAATTTGATTC-TCT--TTTTGCTCGAGGTTCCATTTT
** * ** * *
612652 AATTATTC-AGCCCAATAATTGGTTAAAATGGACCAGGTTAATAATTAGATTCTCTATTTTAGAC
63 AATTATTCGA-TTCAATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTCCATTTTAGGC
612716 TTAATTTCATA
127 TTAATTTCATA
* * * * * * *
612727 -TGA-TTCTTTAACTTTAGGGGAATTCTTAATTTGGTCCTTGCCTTTT-CTCAAGGTTCCATTTT
1 TTTAGTCCTTTAA-TTTAGGAGAATTCTTAATTTGATTC-T-CTTTTTGCTCGAGGTTCCATTTT
* * * * * * *
612789 AATTATTCGATTTAATTATTGGCTAAAATGGACTAGGTTAATAATTAAAGACTCCACTATAGGCT
63 AATTATTCGATTCAATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTCCATTTTAGGCT
612854 TAATTTCATA
128 TAATTTCATA
* * *
612864 TTTAGTCCTTTAATTTAGGAGAATTTTTAATTTGATTCTCATTTTTGCTCGATGTTCCACTTTAA
1 TTTAGTCCTTTAATTTAGGAGAATTCTTAATTTGATTCTC-TTTTTGCTCGAGGTTCCATTTTAA
*** * * * *
612929 TTATTCGGCCCAATTATTGGTTAAAATGGACTATGTTAATAATTAGAGCCTGCATTTTAGGCTTC
65 TTATTCGATTCAATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTCCATTTTAGGCTTA
*
612994 ATTTCATT
130 ATTTCATA
* * * *
613002 TTTAGTCCTTTAATTTA-GAGGAATTCTTAATTTGGTCCTCTCTTTTGCTCTATGTTCCATTTTA
1 TTTAGTCCTTTAATTTAGGA-GAATTCTTAATTTGATTCTCT-TTTTGCTCGAGGTTCCATTTTA
* * * * * * ***
613066 ATTATTCGATTCAATAATTGGTTAAAAT-TAGTTAGATTAATATTTAAAGGCTCCATTTTATTTT
64 ATTATTCGATTCAATAATTGGTTAAAATGGA-CTAGGTTAATAATTAGAGCCTCCATTTTAGGCT
*
613130 TAATTTCA-C
128 TAATTTCATA
** * * * *
613139 TTTAGTTGTTTAATTTAGGA-ACATTTTTTATTTGATTCTCACTTTTATGCTTGAGGTTTCATTT
1 TTTAGTCCTTTAATTTAGGAGA-ATTCTTAATTTGATTCT--CTTTT-TGCTCGAGGTTCCATTT
* * *
613203 TGATTATTCGACTCAGTAATT
62 TAATTATTCGATTCAATAATT
613224 TATTAAAAAT
Statistics
Matches: 509, Mismatches: 97, Indels: 50
0.78 0.15 0.08
Matches are distributed among these distances:
132 1 0.00
133 9 0.02
134 43 0.08
135 58 0.11
136 3 0.01
137 137 0.27
138 218 0.43
139 40 0.08
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (137 bp):
TTTAGTCCTTTAATTTAGGAGAATTCTTAATTTGATTCTCTTTTTGCTCGAGGTTCCATTTTAAT
TATTCGATTCAATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTCCATTTTAGGCTTAA
TTTCATA
Found at i:612969 original size:275 final size:276
Alignment explanation
Indices: 612458--613212 Score: 802
Period size: 275 Copynumber: 2.8 Consensus size: 276
612448 TTTTAGGTTT
* * * * * *
612458 AGTCCTTCAATTTAGGGGAATTTTTAATTTAGT--TATCGTTTATGCTCGAGGTTCCATTTTAAT
1 AGTCCTTTAATTTAGAGGAATTCTTAATTTGGTCCTCTC-TTT-TGCTCAAGGTTCCATTTTAAT
* * * * *
612521 TATTTGA-TTCATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTCTATTTTAGGCTTAA
64 TATTCGATTTAATAATTGGTTAAAATGGACTAGGTTAATAATTAAAGACTCCATTTTAGGCTTAA
* *** * ***
612585 TTTCATACTTAGTCCTTTAATTTAGG-G--GGCTTAATTTG-GTCATTGCTTTTGCTCGAGGTTA
129 TTTCATATTTAGTCCTTTAATTTAGGAGAATTTTTAATTTGATTC-TCATTTTTGCTCGAGGTTA
* **
612646 CATTTTAATTATTCAGCCCAATAATTGGTTAAAATGGACCAGGTTAATAATTAGATTCT-CTATT
193 CATTTTAATTATTCGGCCCAATAATTGGTTAAAATGGACCAGGTTAATAATTAGAGCCTGC-ATT
612710 TTAGACTTAATTTCA-TATG
257 TTAGACTTAATTTCATTATG
* *
612729 A-TTCTTTAACTTTAGGGGAATTCTTAATTTGGTCCT-TGCCTTTT-CTCAAGGTTCCATTTTAA
1 AGTCCTTTAA-TTTAGAGGAATTCTTAATTTGGTCCTCT--CTTTTGCTCAAGGTTCCATTTTAA
* * * *
612791 TTATTCGATTTAATTATTGGCTAAAATGGACTAGGTTAATAATTAAAGACTCCACTATAGGCTTA
63 TTATTCGATTTAATAATTGGTTAAAATGGACTAGGTTAATAATTAAAGACTCCATTTTAGGCTTA
* *
612856 ATTTCATATTTAGTCCTTTAATTTAGGAGAATTTTTAATTTGATTCTCATTTTTGCTCGATGTTC
128 ATTTCATATTTAGTCCTTTAATTTAGGAGAATTTTTAATTTGATTCTCATTTTTGCTCGAGGTTA
* * * *
612921 CACTTTAATTATTCGGCCCAATTATTGGTTAAAATGGACTATGTTAATAATTAGAGCCTGCATTT
193 CATTTTAATTATTCGGCCCAATAATTGGTTAAAATGGACCAGGTTAATAATTAGAGCCTGCATTT
* * * *
612986 TAGGCTTCATTTCATTTTT
258 TAGACTTAATTTCATTATG
* *
613005 AGTCCTTTAATTTAGAGGAATTCTTAATTTGGTCCTCTCTTTTGCTCTATGTTCCATTTTAATTA
1 AGTCCTTTAATTTAGAGGAATTCTTAATTTGGTCCTCTCTTTTGCTCAAGGTTCCATTTTAATTA
* * * * * * ***
613070 TTCGATTCAATAATTGGTTAAAAT-TAGTTAGATTAATATTTAAAGGCTCCATTTTATTTTTAAT
66 TTCGATTTAATAATTGGTTAAAATGGA-CTAGGTTAATAATTAAAGACTCCATTTTAGGCTTAAT
* ** * *
613134 TTCA-CTTTAGTTGTTTAATTTAGGA-ACATTTTTTATTTGATTCTCACTTTTATGCTTGAGGTT
130 TTCATATTTAGTCCTTTAATTTAGGAGA-ATTTTTAATTTGATTCTCA-TTTT-TGCTCGAGGTT
* *
613197 TCATTTTGATTATTCG
192 ACATTTTAATTATTCG
613213 ACTCAGTAAT
Statistics
Matches: 404, Mismatches: 61, Indels: 32
0.81 0.12 0.06
Matches are distributed among these distances:
270 6 0.01
271 46 0.11
272 76 0.19
273 5 0.01
274 2 0.00
275 132 0.33
276 107 0.26
277 30 0.07
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.46
Consensus pattern (276 bp):
AGTCCTTTAATTTAGAGGAATTCTTAATTTGGTCCTCTCTTTTGCTCAAGGTTCCATTTTAATTA
TTCGATTTAATAATTGGTTAAAATGGACTAGGTTAATAATTAAAGACTCCATTTTAGGCTTAATT
TCATATTTAGTCCTTTAATTTAGGAGAATTTTTAATTTGATTCTCATTTTTGCTCGAGGTTACAT
TTTAATTATTCGGCCCAATAATTGGTTAAAATGGACCAGGTTAATAATTAGAGCCTGCATTTTAG
ACTTAATTTCATTATG
Found at i:614552 original size:20 final size:21
Alignment explanation
Indices: 614527--614567 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
614517 TCTCATTTAT
614527 TTTGTTACTTGA-TTTGTATG
1 TTTGTTACTTGATTTTGTATG
* *
614547 TTTGTTATTTTATTTTGTATG
1 TTTGTTACTTGATTTTGTATG
614568 AACATCACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.15, C:0.02, G:0.17, T:0.66
Consensus pattern (21 bp):
TTTGTTACTTGATTTTGTATG
Found at i:621871 original size:241 final size:239
Alignment explanation
Indices: 621394--621889 Score: 674
Period size: 241 Copynumber: 2.1 Consensus size: 239
621384 CAGGCTATCT
* * *
621394 ATAAGACCTTCGGGCAAGATGCTTTCACATGATATTTATGAAAAATGAGAAAGCGATTTTCAAAG
1 ATAAGTCCTTCGAGCAAGATGCTTTCACATGATATTTATGAAAAATGAGAAAGCAATTTTCAAAG
*
621459 TTTCTTATTTAATATTTTCAAAAAATAAATTTTTAAAAAGTAAAAAAGTGATTTCCAAAGTTTCT
66 TTTCTCATTTAATATTTTCAAAAAATAAATTTTTAAAAAGTAAAAAAGTGATTTCCAAAGTTTCT
* * * *
621524 TACCTAGTAGACTATTTCCAAAATTACTAAGTCCTTCGAGTCATCAGTAAGTCTTTCAAACATGA
131 TACCAAGCAGACTATTTCCAAAATTACTAAGTCCTTAGAGCCATCAGTAAGTCTTTCAAACATGA
** *
621589 TGATTAAATCCTCCGGGTCATCTGTCAGCCTTTCAAGCAAGATG
196 TGATTAAATCCTCCAAGTCATCTGTCAACCTTTCAAGCAAGATG
* * *
621633 GTAAGTCCTTCGAGCAAGATGCTTTCATATGATATTTTTTGAAAAATGAGAAAGCAATTTTCAAA
1 ATAAGTCCTTCGAGCAAGATGCTTTCACATGATA-TTTATGAAAAATGAGAAAGCAATTTTCAAA
* * * *
621698 GTTTCTCATTTAATATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAA-TCGATTTTCAAAGTT
65 GTTTCTCATTTAATATTTTCAAAAAAT-AAATTTTTAAAAAGTAAAAAAGT-GATTTCCAAAGTT
* ** * *
621762 TCTTACCAAGCAGACTATTTCTAAAATTGGTAAGTCCTTTAG-GCCATCAGTAAGTCTTTCGAGC
128 TCTTACCAAGCAGACTATTTCCAAAATTACTAAGTCC-TTAGAGCCATCAGTAAGTCTTTCAAAC
* * * *
621826 ATGATGATTAAATCCTTCAATTCATTTGTCAATCTTT-AGAGCAAGATG
192 ATGATGATTAAATCCTCCAAGTCATCTGTCAACCTTTCA-AGCAAGATG
*
621874 ATAAGTTCTTCGAGCA
1 ATAAGTCCTTCGAGCA
621890 TCTATAAGAT
Statistics
Matches: 223, Mismatches: 29, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
239 30 0.13
240 55 0.25
241 135 0.61
242 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (239 bp):
ATAAGTCCTTCGAGCAAGATGCTTTCACATGATATTTATGAAAAATGAGAAAGCAATTTTCAAAG
TTTCTCATTTAATATTTTCAAAAAATAAATTTTTAAAAAGTAAAAAAGTGATTTCCAAAGTTTCT
TACCAAGCAGACTATTTCCAAAATTACTAAGTCCTTAGAGCCATCAGTAAGTCTTTCAAACATGA
TGATTAAATCCTCCAAGTCATCTGTCAACCTTTCAAGCAAGATG
Found at i:622004 original size:3 final size:3
Alignment explanation
Indices: 621998--622035 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
621988 CAACAACAAC
621998 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
622036 CAAAAAATAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:622233 original size:28 final size:28
Alignment explanation
Indices: 622201--622263 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
622191 TGTATAGAGG
622201 CAGATCATTTGATTGAAAGATGGATTAA
1 CAGATCATTTGATTGAAAGATGGATTAA
622229 CAGATCATTTGATTGAAAGATGGATTAA
1 CAGATCATTTGATTGAAAGATGGATTAA
*
622257 CAAATCA
1 CAGATCA
622264 ATAGAAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (28 bp):
CAGATCATTTGATTGAAAGATGGATTAA
Found at i:624904 original size:138 final size:138
Alignment explanation
Indices: 624531--625235 Score: 660
Period size: 137 Copynumber: 5.1 Consensus size: 138
624521 AAATTTTAGG
* * * * * *
624531 TTTAGTCCTTCAATTTAGTGGAATTATTAATTTGGTCATC-CCTTATGCTCGAGGTTCAATTTTA
1 TTTAGTCATTTAATTTAGGGGAATTCTTAATTTGGTCCTCGCCTT-TGCTCGAGGTTCCATTTTA
** * * * * *
624595 ATTATTCGATTCAATAATTGGTTAAAATGGACTATGTTAATAATTAAAGCCTCTATTTTCTGCTT
65 ATTATTCGACCCAATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTCCACTTTATGCTT
*
624660 AATTTTATA
130 AATTTCATA
** * * * *
624669 TTTAGTCATGCAATTTAGGGG-ATTCTTAATGTGGTCCTCAG-TTTTGCTCGAGGTTCCAATATA
1 TTTAGTCATTTAATTTAGGGGAATTCTTAATTTGGTCCTC-GCCTTTGCTCGAGGTTCCATTTTA
* * * * *
624732 ATTATTTGACCCAATAATTGGTTAAAATGTACTAGGTTAATAAGTAGAGACTCCATTTTATGCTT
65 ATTATTCGACCCAATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTCCACTTTATGCTT
624797 AATTTCATA
130 AATTTCATA
* * * * * ** *
624806 TTTAATCGTTAAATTTAGGGGAATACTTCATTTACTTCTCGCCTTTGC-CGGAGGTTCCATTTTA
1 TTTAGTCATTTAATTTAGGGGAATTCTTAATTTGGTCCTCGCCTTTGCTC-GAGGTTCCATTTTA
**** **
624870 ATTATTCGATTTGATAATT-GTCTAAAATGGACTAGGTTAATAATTAGAGCCTCCACCGTA-GAC
65 ATTATTCGACCCAATAATTGGT-TAAAATGGACTAGGTTAATAATTAGAGCCTCCACTTTATG-C
624933 TTAATTTCATA
128 TTAATTTCATA
* * * * * *
624944 TTTAGTCATTTATTTTAAGGGAATT-TTTATTTGGTTCTCGTCTTTGCTTGAGGTTCCATTTTAA
1 TTTAGTCATTTAATTTAGGGGAATTCTTAATTTGGTCCTCGCCTTTGCTCGAGGTTCCATTTTAA
* * ** *
625008 TTATTCGACCCAATAATTGGTTAAAA-AGACTAGGTTAATAATTATAGCCTCCACTTTGGGTTTA
66 TTATTCGACCCAATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTCCACTTTATGCTTA
*
625072 ATTTCATT
131 ATTTCATA
* * * *
625080 TTTAGTCATTTACTTTAGGGAAATTCTTAATTCGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAA
1 TTTAGTCATTTAATTTAGGGGAATTCTTAATTTGGTCCTCGCCTTTGCTCGAGGTTCCATTTTAA
* ** * * * * * * *
625145 TTATTCAATTCAATAATTGGTTAAAAT-TAGTTAGATTAATATTTAGAGCCTCTATTTTAAT-TT
66 TTATTCGACCCAATAATTGGTTAAAATGGA-CTAGGTTAATAATTAGAGCCTCCACTTT-ATGCT
*
625208 TAATTTCA-C
129 TAATTTCATA
625217 TTTAGTTC-TTTAATTTAGG
1 TTTAG-TCATTTAATTTAGG
625236 AAAGATTTTG
Statistics
Matches: 462, Mismatches: 90, Indels: 31
0.79 0.15 0.05
Matches are distributed among these distances:
136 59 0.13
137 241 0.52
138 162 0.35
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (138 bp):
TTTAGTCATTTAATTTAGGGGAATTCTTAATTTGGTCCTCGCCTTTGCTCGAGGTTCCATTTTAA
TTATTCGACCCAATAATTGGTTAAAATGGACTAGGTTAATAATTAGAGCCTCCACTTTATGCTTA
ATTTCATA
Found at i:625213 original size:274 final size:271
Alignment explanation
Indices: 624542--625310 Score: 753
Period size: 275 Copynumber: 2.8 Consensus size: 271
624532 TTAGTCCTTC
* * * * *
624542 AATTTAGTGGAATTATTAATTTGGTCATCCCTTATGCTCGAGGTTCAATTTTAATTATTCGATTC
1 AATTTAG-GGAATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAATTATTCGATTC
* * *
624607 AATAATTGGTTAAAATGGACTATGTTAATAATTAAAGCCTCTATTTT-CTGCTTAATTTTATATT
65 AATAATTGGTTAAAATGGACTA-GTTAATAATTAGAGCCTCTATTTTAAT-CTTAATTTCATATT
** * * * * * *
624671 TAGTCATGCAATTTAGGGGATTCTTAATGTGGTCCTCAGTTTTGCTCGAGGTTCCAATATAATTA
128 TAGTCATTTAATTTAGGGAATT-TTAATTTGGTTCTC-GTTTTGCTTGAGGTTCCATTTTAATTA
* * * *
624736 TTTGACCCAATAATTGGTTAAAATGTACTAGGTTAATAAGTAGAGACTCCATTTTATGCTTAATT
191 TTCGACCCAATAATTGGTTAAAAAGTACTAGGTTAATAAGTAGAGACTCCACTTTAGGCTTAATT
*
624801 TCATATTTAATCGTTA
256 TCATATTTAATCATTA
* * ** * *
624817 AATTTAGGGGAATACTTCATTTACTTCTCGCCTTTGC-CGGAGGTTCCATTTTAATTATTCGATT
1 AATTTA-GGGAATTCTTAATTTGGTCCTCGCTTTTGCTC-GAGGTTCCATTTTAATTATTCGATT
** * ***
624881 TGATAATT-GTCTAAAATGGACTAGGTTAATAATTAGAGCCTCCACCGTAGA-CTTAATTTCATA
64 CAATAATTGGT-TAAAATGGACTA-GTTAATAATTAGAGCCTCTATTTTA-ATCTTAATTTCATA
* *
624944 TTTAGTCATTTATTTTAAGGGAATTTTTATTTGGTTCTCGTCTTTGCTTGAGGTTCCATTTTAAT
126 TTTAGTCATTTAATTT-AGGGAATTTTAATTTGGTTCTCGT-TTTGCTTGAGGTTCCATTTTAAT
* * * * *
625009 TATTCGACCCAATAATTGGTTAAAAAG-ACTAGGTTAATAATTATAGCCTCCACTTTGGGTTTAA
189 TATTCGACCCAATAATTGGTTAAAAAGTACTAGGTTAATAAGTAGAGACTCCACTTTAGGCTTAA
* * *
625073 TTTCATTTTTAGTCATTT
254 TTTCATATTTAATCATTA
* * *
625091 ACTTTAGGGAAATTCTTAATTCGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAATTATTCAATTC
1 AATTTAGGG-AATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAATTATTCGATTC
* * * * *
625156 AATAATTGGTTAAAAT-TAGTTAGATTAATATTTAGAGCCTCTATTTTAATTTTAATTTCA-CTT
65 AATAATTGGTTAAAATGGA-CTAG-TTAATAATTAGAGCCTCTATTTTAATCTTAATTTCATATT
* * * ** *
625219 TAGTTC-TTTAATTTAGGAAAGATTTTGATTTGGTTCTCGCTTTTATTCTTGAGGTTTTATTTTG
128 TAG-TCATTTAATTTAGG-GA-ATTTTAATTTGGTTCTCG--TTT-TGCTTGAGGTTCCATTTTA
* **
625283 ATTATTCGACTCAATAATTTATTAAAAA
187 ATTATTCGACCCAATAATTGGTTAAAAA
625311 TGATTTGGAT
Statistics
Matches: 401, Mismatches: 74, Indels: 37
0.78 0.14 0.07
Matches are distributed among these distances:
272 3 0.01
273 19 0.05
274 159 0.40
275 171 0.43
276 49 0.12
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (271 bp):
AATTTAGGGAATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAATTATTCGATTCA
ATAATTGGTTAAAATGGACTAGTTAATAATTAGAGCCTCTATTTTAATCTTAATTTCATATTTAG
TCATTTAATTTAGGGAATTTTAATTTGGTTCTCGTTTTGCTTGAGGTTCCATTTTAATTATTCGA
CCCAATAATTGGTTAAAAAGTACTAGGTTAATAAGTAGAGACTCCACTTTAGGCTTAATTTCATA
TTTAATCATTA
Found at i:625341 original size:139 final size:137
Alignment explanation
Indices: 624576--625351 Score: 462
Period size: 137 Copynumber: 5.6 Consensus size: 137
624566 TCATCCCTTA
* * *
624576 TGCTCGAGGTTCAATTTTAATTATTCGATTCAATAATTGGTT-AAAATGGACTAT-G-TTAATAA
1 TGCTTGAGGTTCCATTTTAATTATTCGACTCAATAATTGGTTAAAAAT-GACT-TGGATTAAT-A
* * * * * ** ** *
624638 TTAAAGCCTCTATTTT-CTGCTTAATTTTATATTTAGTCATGCAATTTAGG-GGATTCTTAATGT
63 TTAGAGCCTC-ATTTTAGT-TTTAATTTCATCTTTAGTCATTTAATTTAGGAAAATT-TTAATTT
*
624701 GGTCCTCAG--TTT
125 GGTTCTC-GCTTTT
* * * * * * *
624713 TGCTCGAGGTTCCAATATAATTATTTGACCCAATAATTGGTT-AAAATGTACTAGG-TTAATAAG
1 TGCTTGAGGTTCCATTTTAATTATTCGACTCAATAATTGGTTAAAAATG-ACTTGGATTAAT-AT
* * * * * * ** * * *
624776 TAGAGACTCCATTTTA-TGCTTAATTTCATATTTAATCGTTAAATTTAGGGGAATACTTCATTTA
64 TAGAGCCT-CATTTTAGT-TTTAATTTCATCTTTAGTCATTTAATTTAGGAAAAT-TTTAATTTG
* *
624840 CTTCTCGC-CTT
126 GTTCTCGCTTTT
** * ** *
624851 TGCCGGAGGTTCCATTTTAATTATTCGATTTGATAATT-GTCT-AAAATGGACTAGG-TTAATAA
1 TGCTTGAGGTTCCATTTTAATTATTCGACTCAATAATTGGT-TAAAAAT-GACTTGGATTAAT-A
*** ** * * * *
624913 TTAGAGCCTCCACCGTAGACTTAATTTCATATTTAGTCATTTATTTTAAGG-GAATTTTTATTTG
63 TTAGAGCCT-CATTTTAGTTTTAATTTCATCTTTAGTCATTTAATTT-AGGAAAATTTTAATTTG
*
624977 GTTCTCG-TCTT
126 GTTCTCGCTTTT
* *
624988 TGCTTGAGGTTCCATTTTAATTATTCGACCCAATAATTGGTTAAAAA-GACTAGG-TTAATAATT
1 TGCTTGAGGTTCCATTTTAATTATTCGACTCAATAATTGGTTAAAAATGACTTGGATTAAT-ATT
* * * * * * * *
625051 ATAGCCTCCACTTTGGGTTTAATTTCATTTTTAGTCATTTACTTTAGGGAAATTCTTAATTCGGT
65 AGAGCCT-CATTTTAGTTTTAATTTCATCTTTAGTCATTTAATTTAGGAAAATT-TTAATTTGGT
*
625116 CCTCGC-TTT
128 TCTCGCTTTT
* * * * * *
625125 TGCTCGAGGTTCCATTTTAATTATTCAATTCAATAATTGGTT-AAAATTAGTTAGATTAATATTT
1 TGCTTGAGGTTCCATTTTAATTATTCGACTCAATAATTGGTTAAAAATGACTTGGATTAATA-TT
* *
625189 AGAGCCTCTATTTTAATTTTAATTTCA-CTTTAGTTC-TTTAATTTAGGAAAGATTTTGATTTGG
65 AGAGCCTC-ATTTTAGTTTTAATTTCATCTTTAG-TCATTTAATTTAGGAAA-ATTTTAATTTGG
625252 TTCTCGCTTTT
127 TTCTCGCTTTT
* ** * ** *
625263 ATTCTTGAGGTTTTATTTTGATTATTCGACTCAATAATTTATTAAAAATGATTTGGATTAATATT
1 -TGCTTGAGGTTCCATTTTAATTATTCGACTCAATAATTGGTTAAAAATGACTTGGATTAATATT
*
625328 AGAGCTTACATTTTTAGTTTTAAT
65 AGAGCCT-CA-TTTTAGTTTTAAT
625352 CTCCTAGGTT
Statistics
Matches: 513, Mismatches: 98, Indels: 53
0.77 0.15 0.08
Matches are distributed among these distances:
135 3 0.01
136 62 0.12
137 229 0.45
138 144 0.28
139 46 0.09
140 29 0.06
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (137 bp):
TGCTTGAGGTTCCATTTTAATTATTCGACTCAATAATTGGTTAAAAATGACTTGGATTAATATTA
GAGCCTCATTTTAGTTTTAATTTCATCTTTAGTCATTTAATTTAGGAAAATTTTAATTTGGTTCT
CGCTTTT
Found at i:630108 original size:20 final size:19
Alignment explanation
Indices: 630083--630125 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
630073 ATAAGTATAG
*
630083 TATGAATATATAATTTTAAT
1 TATGAACATAT-ATTTTAAT
*
630103 TATGAACATGTATTTTAAT
1 TATGAACATATATTTTAAT
630122 TATG
1 TATG
630126 GATCGGAGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (19 bp):
TATGAACATATATTTTAAT
Found at i:653015 original size:21 final size:21
Alignment explanation
Indices: 652977--653022 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
652967 AATCAAAATT
*
652977 TGAATCCTTAACCATGAACTA
1 TGAATCCTAAACCATGAACTA
* * *
652998 TGAATCCTAAATCTTGAACTC
1 TGAATCCTAAACCATGAACTA
653019 TGAA
1 TGAA
653023 CTAATATTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (21 bp):
TGAATCCTAAACCATGAACTA
Found at i:654355 original size:60 final size:60
Alignment explanation
Indices: 654291--654452 Score: 193
Period size: 60 Copynumber: 2.7 Consensus size: 60
654281 TAAGACGTTA
** **
654291 CTTTGTTGAGTC-CTTTAACTATTAAAAGTTACAAAATGGTCCTTTGACTATATGAG-ATTG
1 CTTTGTTGAGTCTC-TCGACTATTAAAAGTTACAAAATGGTCCAATGACTATA-GAGCATTG
* * * * *
654351 CTTTGTTGAGTCTCTCGACTATTAAAGGTTACAAAATAGTCCAATGATTATAGAGCTTTTT
1 CTTTGTTGAGTCTCTCGACTATTAAAAGTTACAAAATGGTCCAATGACTATAGAGC-ATTG
*
654412 TTTTGTTGAGTCTCTCGACTATTAAAAGTTACAAAATGGTC
1 CTTTGTTGAGTCTCTCGACTATTAAAAGTTACAAAATGGTC
654453 ACCCAACTAT
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
59 3 0.03
60 43 0.49
61 41 0.47
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.40
Consensus pattern (60 bp):
CTTTGTTGAGTCTCTCGACTATTAAAAGTTACAAAATGGTCCAATGACTATAGAGCATTG
Found at i:657953 original size:20 final size:20
Alignment explanation
Indices: 657930--657975 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
657920 AAACTTAAAT
*
657930 TCGCAACACGAAAATGAAAA
1 TCGCAACACAAAAATGAAAA
**
657950 TCGCAATGCAAAAATGAAAA
1 TCGCAACACAAAAATGAAAA
657970 TCGCAA
1 TCGCAA
657976 TGCGATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.52, C:0.20, G:0.15, T:0.13
Consensus pattern (20 bp):
TCGCAACACAAAAATGAAAA
Found at i:657976 original size:20 final size:20
Alignment explanation
Indices: 657940--657978 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
657930 TCGCAACACG
657940 AAAATGAAAATCGCAATGCA
1 AAAATGAAAATCGCAATGCA
657960 AAAATGAAAATCGCAATGC
1 AAAATGAAAATCGCAATGC
657979 GATTTTAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAATGAAAATCGCAATGCA
Found at i:657998 original size:19 final size:20
Alignment explanation
Indices: 657976--658015 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
657966 AAAATCGCAA
657976 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCAGTTTCGCGT
*
657995 TGCGATTTTCATTTTCGCGT
1 TGCGATTTTCAGTTTCGCGT
658015 T
1 T
658016 TTTATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.10, C:0.17, G:0.23, T:0.50
Consensus pattern (20 bp):
TGCGATTTTCAGTTTCGCGT
Found at i:658222 original size:24 final size:24
Alignment explanation
Indices: 658194--658241 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
658184 ATATGTTATC
658194 CTTTTAAATGTTTATATAGGTGCT
1 CTTTTAAATGTTTATATAGGTGCT
658218 CTTTTAAATGTTTATATAGGTGCT
1 CTTTTAAATGTTTATATAGGTGCT
658242 TACTTCTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.50
Consensus pattern (24 bp):
CTTTTAAATGTTTATATAGGTGCT
Found at i:659826 original size:21 final size:21
Alignment explanation
Indices: 659785--659828 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
659775 TTGTGCATGG
*
659785 CGTGATGAGGTACGGTCTTTA
1 CGTGATGAGGTAAGGTCTTTA
*
659806 CGTGGTGAGGTAGAGGT-TTTA
1 CGTGATGAGGTA-AGGTCTTTA
659827 CG
1 CG
659829 CAATGACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.18, C:0.11, G:0.39, T:0.32
Consensus pattern (21 bp):
CGTGATGAGGTAAGGTCTTTA
Found at i:660204 original size:21 final size:21
Alignment explanation
Indices: 660176--660294 Score: 123
Period size: 21 Copynumber: 5.7 Consensus size: 21
660166 GATTCACTTG
*
660176 TCATCGTTCAAGAGGCCTCTC
1 TCATCGTTCAAGAGGCCCCTC
* * *
660197 -CTATCGTTCAAAAGGCCCATA
1 TC-ATCGTTCAAGAGGCCCCTC
*
660218 TCATCCTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
660239 TCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
* *
660260 TCATCGTTCAAGAGGTCCCGC
1 TCATCGTTCAAGAGGCCCCTC
* *
660281 CCACCGTTCAAGAG
1 TCATCGTTCAAGAG
660295 CCCGATTCAT
Statistics
Matches: 79, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
20 1 0.01
21 77 0.97
22 1 0.01
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:660292 original size:42 final size:41
Alignment explanation
Indices: 660174--660294 Score: 143
Period size: 42 Copynumber: 2.9 Consensus size: 41
660164 CTGATTCACT
* * *
660174 TGTCATCGTTCAAGAGGCCTCTCCTATCGTTCAAAAGGCCCA
1 TGTCATCGTTCAAGAGGCC-CTCCCACCGTTCAAGAGGCCCA
* * * *
660216 TATCATCCTTCAAGAGGCCCCTCTCACCGTTCAAGAGGCCCC
1 TGTCATCGTTCAAGAGG-CCCTCCCACCGTTCAAGAGGCCCA
*
660258 TGTCATCGTTCAAGAGGTCCCGCCCACCGTTCAAGAG
1 TGTCATCGTTCAAGAGG-CCCTCCCACCGTTCAAGAG
660295 CCCGATTCAT
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 64 0.97
43 2 0.03
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.23
Consensus pattern (41 bp):
TGTCATCGTTCAAGAGGCCCTCCCACCGTTCAAGAGGCCCA
Found at i:661739 original size:63 final size:64
Alignment explanation
Indices: 661636--661799 Score: 253
Period size: 63 Copynumber: 2.6 Consensus size: 64
661626 GTACACTTTG
661636 TTTT-CTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTAATGAGGAAATAA-GAAT-TAT
1 TTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTAATGAGGAAATAATGAATAT-T
* * * **
661698 TTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCATATT
1 TTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTAATGAGGAAATAATGAATATT
661762 TTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
661800 GTTTTAAATT
Statistics
Matches: 94, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
62 4 0.04
63 48 0.51
64 41 0.44
65 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.16, T:0.52
Consensus pattern (64 bp):
TTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTAATGAGGAAATAATGAATATT
Found at i:661908 original size:20 final size:20
Alignment explanation
Indices: 661857--661901 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
661847 AAGGTACACT
*
661857 TTCGCAACGTGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
661877 TTCGCAACGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
661897 TTCGC
1 TTCGC
661902 GTTGCGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
TTCGCAACGCGAAAGTCAAA
Found at i:662269 original size:18 final size:18
Alignment explanation
Indices: 662231--662269 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
662221 GTGGTTAGGA
*
662231 TTTTGATTTTGATTGCGT
1 TTTTGATTTTGATTGCCT
*
662249 TTTTGATTTTGATTTCCT
1 TTTTGATTTTGATTGCCT
662267 TTT
1 TTT
662270 GCTTGGCACC
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:0.10, C:0.08, G:0.15, T:0.67
Consensus pattern (18 bp):
TTTTGATTTTGATTGCCT
Found at i:665314 original size:16 final size:15
Alignment explanation
Indices: 665292--665330 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
665282 GAAATAATTG
665292 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
665308 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
665323 AAAAATTA
1 AAAAATTA
665331 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:665570 original size:20 final size:20
Alignment explanation
Indices: 665547--665680 Score: 69
Period size: 20 Copynumber: 6.6 Consensus size: 20
665537 CAAAATTCAC
*
665547 GTTGCGAATTTAGAAATCGA
1 GTTGCGAATTTGGAAATCGA
* * *
665567 GTTGTGAAATT-GAAATTCAGT
1 GTTGCGAATTTGGAAA-TC-GA
665588 GTTGCGAATTTGGAAAATCGCA
1 GTTGCGAATTTGG-AAATCG-A
* ** * *
665610 -ATGCG-ATTTATATATTCGC
1 GTTGCGAATTTGGA-AATCGA
665629 GTTGCGAATTTGGAAA-CTGA
1 GTTGCGAATTTGGAAATC-GA
* ** *
665649 GTTGCGAAATTGGAGTTCGC
1 GTTGCGAATTTGGAAATCGA
665669 GTTGCGAATTTG
1 GTTGCGAATTTG
665681 TTGGTCATTT
Statistics
Matches: 83, Mismatches: 21, Indels: 20
0.67 0.17 0.16
Matches are distributed among these distances:
19 6 0.07
20 50 0.60
21 21 0.25
22 3 0.04
23 3 0.04
ACGTcount: A:0.28, C:0.11, G:0.27, T:0.34
Consensus pattern (20 bp):
GTTGCGAATTTGGAAATCGA
Found at i:665583 original size:40 final size:40
Alignment explanation
Indices: 665487--665603 Score: 128
Period size: 40 Copynumber: 2.9 Consensus size: 40
665477 ACTAAAACCT
* *
665487 GTTGTGAAATTAAAATTCGTGTTGCGAA-TTCGAAAATCGA
1 GTTGTGAAATTAAAATTCATGTTGCGAATTTAG-AAATCGA
** ** *
665527 GTTGCAAAAACAAAATTCACGTTGCGAATTTAGAAATCGA
1 GTTGTGAAATTAAAATTCATGTTGCGAATTTAGAAATCGA
* *
665567 GTTGTGAAATTGAAATTCAGTGTTGCGAATTTGGAAA
1 GTTGTGAAATTAAAATTCA-TGTTGCGAATTTAGAAA
665604 ATCGCAATGC
Statistics
Matches: 61, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
40 43 0.70
41 18 0.30
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (40 bp):
GTTGTGAAATTAAAATTCATGTTGCGAATTTAGAAATCGA
Found at i:674647 original size:24 final size:24
Alignment explanation
Indices: 674620--674681 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 24
674610 TTTTTTTTGA
674620 ATCCTCTTATGTTTTTTTCCAGGT
1 ATCCTCTTATGTTTTTTTCCAGGT
*
674644 ATCCTC---TGTATTTTTTCTAGGT
1 ATCCTCTTATGT-TTTTTTCCAGGT
674666 ATCCTCTGTAT-TTTTT
1 ATCCTCT-TATGTTTTT
674682 CTATCCGAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
21 3 0.09
22 17 0.53
24 10 0.31
25 1 0.03
26 1 0.03
ACGTcount: A:0.13, C:0.19, G:0.11, T:0.56
Consensus pattern (24 bp):
ATCCTCTTATGTTTTTTTCCAGGT
Found at i:674683 original size:22 final size:22
Alignment explanation
Indices: 674632--674684 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
674622 CCTCTTATGT
*
674632 TTTTTTCCAGGTATCCTCTGTA
1 TTTTTTCTAGGTATCCTCTGTA
674654 TTTTTTCTAGGTATCCTCTGTA
1 TTTTTTCTAGGTATCCTCTGTA
674676 TTTTTTCTA
1 TTTTTTCTA
674685 TCCGAATGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.13, C:0.19, G:0.11, T:0.57
Consensus pattern (22 bp):
TTTTTTCTAGGTATCCTCTGTA
Found at i:675879 original size:11 final size:12
Alignment explanation
Indices: 675857--675882 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
675847 GAAAAAACTG
675857 AAAAATGAAAAA
1 AAAAATGAAAAA
675869 AAAAATGAAAAA
1 AAAAATGAAAAA
675881 AA
1 AA
675883 TGTGATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAAATGAAAAA
Found at i:677765 original size:28 final size:29
Alignment explanation
Indices: 677717--677771 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
677707 TTAGATTAGA
*
677717 TAAATATAATAATTTTGTATAT-AATATT
1 TAAATATAACAATTTTGTATATCAATATT
*
677745 TAAATAT-ACAATTATTTTATATCAATA
1 TAAATATAACAATT-TTGTATATCAATA
677772 ATAATTTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.22
28 14 0.61
29 4 0.17
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (29 bp):
TAAATATAACAATTTTGTATATCAATATT
Found at i:678084 original size:29 final size:29
Alignment explanation
Indices: 678051--678108 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
678041 TTACTGTATT
678051 ATGTTATTACCTAAAATTCAATATTTAAC
1 ATGTTATTACCTAAAATTCAATATTTAAC
678080 ATGTTATTACCTAAAATTCAATATTTAAC
1 ATGTTATTACCTAAAATTCAATATTTAAC
678109 CATACGATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.14, G:0.03, T:0.41
Consensus pattern (29 bp):
ATGTTATTACCTAAAATTCAATATTTAAC
Found at i:679940 original size:3 final size:3
Alignment explanation
Indices: 679932--680011 Score: 115
Period size: 3 Copynumber: 26.0 Consensus size: 3
679922 TGTAATACTT
*
679932 TAA TAA TAA TAA TAA TAA TAA TAA TACT TAA TAA TATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TA-A TAA TAA TAA
* *
679979 TAA TAA TGA TAA TGA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
680012 GTAAGACTAG
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
3 64 0.93
4 5 0.07
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:680265 original size:20 final size:20
Alignment explanation
Indices: 680242--680305 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
680232 AAAACATCCT
* *
680242 ACCCTGAGGTTTTACATATG
1 ACCCGGAGGTTTTACAAATG
*
680262 ACCCGGAGATTTTACAAATG
1 ACCCGGAGGTTTTACAAATG
*
680282 ACCCGGAGGTTTTACAAATC
1 ACCCGGAGGTTTTACAAATG
680302 ACCC
1 ACCC
680306 AGAGTCTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.27
Consensus pattern (20 bp):
ACCCGGAGGTTTTACAAATG
Found at i:680393 original size:139 final size:139
Alignment explanation
Indices: 680143--680419 Score: 446
Period size: 139 Copynumber: 2.0 Consensus size: 139
680133 AAAACATCCT
*
680143 ACCCGGAGGTTTTACAAATGACCCAGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTTGA
1 ACCCGGAGGTTTTACAAATCACCCAGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTTGA
* * * * *
680208 AAATCGCTTTCTTATTTTCATGCGAAAACATCCTACCCTGAGGTTTTACATATGACCCGGAGATT
66 AAATCACTTTCTCATTTTCATGCGAAAACATCATACCCTGAGGTTTTACAGATGACCCAGAGATT
680273 TTACAAATG
131 TTACAAATG
** * *
680282 ACCCGGAGGTTTTACAAATCACCCAGAGTCTTTACTTTTCTAGAACATTAAATGAGAAATTTTGA
1 ACCCGGAGGTTTTACAAATCACCCAGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTTGA
* *
680347 AAATCACTTTCTCATTTTCATGCGAAAACATCATACCTTGAGGTTTTACAGATGACCCAGAGGTT
66 AAATCACTTTCTCATTTTCATGCGAAAACATCATACCCTGAGGTTTTACAGATGACCCAGAGATT
680412 TTACAAAT
131 TTACAAAT
680420 TCGTGGGAAA
Statistics
Matches: 126, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
139 126 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (139 bp):
ACCCGGAGGTTTTACAAATCACCCAGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTTGA
AAATCACTTTCTCATTTTCATGCGAAAACATCATACCCTGAGGTTTTACAGATGACCCAGAGATT
TTACAAATG
Found at i:689128 original size:20 final size:20
Alignment explanation
Indices: 689087--689129 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
689077 AGTTTTCATG
*
689087 AAACAACATAATTAAATCAA
1 AAACAACATAATTAAATAAA
*
689107 AAACAACA-ATTTACAATAAA
1 AAACAACATAATTA-AATAAA
689127 AAA
1 AAA
689130 GTTTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.67, C:0.14, G:0.00, T:0.19
Consensus pattern (20 bp):
AAACAACATAATTAAATAAA
Found at i:689579 original size:23 final size:22
Alignment explanation
Indices: 689552--689628 Score: 79
Period size: 21 Copynumber: 3.5 Consensus size: 22
689542 CACTCTTGAG
689552 TGTATCGATACACATTCAAGGAA
1 TGTATCGATACACATTCAAGG-A
*
689575 TGTATCGGTACACATTCATA-G-
1 TGTATCGATACACATTCA-AGGA
* * *
689596 TGTATCGATACATA-GCGAGGA
1 TGTATCGATACACATTCAAGGA
689617 TGTATCGATACA
1 TGTATCGATACA
689629 TAGGTATCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
19 1 0.02
20 2 0.04
21 24 0.52
23 18 0.39
24 1 0.02
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.29
Consensus pattern (22 bp):
TGTATCGATACACATTCAAGGA
Found at i:689601 original size:21 final size:20
Alignment explanation
Indices: 689550--689607 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 20
689540 TACACTCTTG
689550 AGTGTATCGATACACATTCA
1 AGTGTATCGATACACATTCA
*
689570 AGGAATGTATCGGTACACATTCA
1 A-G--TGTATCGATACACATTCA
689593 TAGTGTATCGATACA
1 -AGTGTATCGATACA
689608 TAGCGAGGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 1 0.03
21 12 0.38
23 18 0.56
24 1 0.03
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (20 bp):
AGTGTATCGATACACATTCA
Found at i:695932 original size:19 final size:19
Alignment explanation
Indices: 695904--695969 Score: 114
Period size: 19 Copynumber: 3.5 Consensus size: 19
695894 GCAATGTAAG
*
695904 CAAAAGAAATTAATATAAA
1 CAAAATAAATTAATATAAA
695923 CAAAATAAATTAATATAAA
1 CAAAATAAATTAATATAAA
695942 CAAAATAAATTAATATAAA
1 CAAAATAAATTAATATAAA
*
695961 CAAATTAAA
1 CAAAATAAA
695970 GCCAAAATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 45 1.00
ACGTcount: A:0.68, C:0.06, G:0.02, T:0.24
Consensus pattern (19 bp):
CAAAATAAATTAATATAAA
Found at i:698482 original size:3 final size:3
Alignment explanation
Indices: 698476--698599 Score: 143
Period size: 3 Copynumber: 42.0 Consensus size: 3
698466 TGTAATAATT
*
698476 TAA TAA TAA TAA TAA TAA TAA TAA TACT TAA TAA TATA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TA-A TAA TAA TAA
* *
698522 T-A TAA TAA TAA TAG TAG T-A TAA TATA TAA TAA T-A TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
698564 TAA TAA TAA TATA TAA TAA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
698600 GTAAAACCGG
Statistics
Matches: 107, Mismatches: 4, Indels: 20
0.82 0.03 0.15
Matches are distributed among these distances:
2 11 0.10
3 85 0.79
4 11 0.10
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:698527 original size:53 final size:48
Alignment explanation
Indices: 698468--698599 Score: 164
Period size: 50 Copynumber: 2.7 Consensus size: 48
698458 TCAGGTCTTG
* *
698468 TAATAATTTAATAATAATAATAATAATAATAATACT-TAATAATATATAA
1 TAATAATATAATAATAATAATAATAATAATAATAATATAA-AATA-ATAA
*
698517 T-ATAATATAATAATAATAGTAGTATAATATATAATAATATAAAATAATAA
1 TAATAATATAATAATAATAATA--ATAATA-ATAATAATATAAAATAATAA
698567 TAATAATAT-ATAATAATAAT-ATAATAATAATAA
1 TAATAATATAATAATAATAATAATAATAATAATAA
698600 GTAAAACCGG
Statistics
Matches: 74, Mismatches: 4, Indels: 13
0.81 0.04 0.14
Matches are distributed among these distances:
46 7 0.09
47 6 0.08
48 18 0.24
49 1 0.01
50 21 0.28
51 18 0.24
52 3 0.04
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.37
Consensus pattern (48 bp):
TAATAATATAATAATAATAATAATAATAATAATAATATAAAATAATAA
Found at i:698544 original size:34 final size:34
Alignment explanation
Indices: 698476--698599 Score: 152
Period size: 32 Copynumber: 3.7 Consensus size: 34
698466 TGTAATAATT
698476 TAATAATAATAATAATAATAATAATACTTAATAATATA
1 TAATAATAAT-ATAATAATAATAATA--T-ATAATATA
*
698514 TAAT-ATAATATAATAATAATAGTAGTAT-A-ATA
1 TAATAATAATATAATAATAATAATA-TATAATATA
698546 T-ATAATAATATAA-AATAATAATA-ATAATATA
1 TAATAATAATATAATAATAATAATATATAATATA
698577 TAATAATAATATAATAATAATAA
1 TAATAATAATATAATAATAATAA
698600 GTAAAACCGG
Statistics
Matches: 78, Mismatches: 3, Indels: 15
0.81 0.03 0.16
Matches are distributed among these distances:
29 2 0.03
30 1 0.01
31 15 0.19
32 25 0.32
33 9 0.12
34 2 0.03
35 1 0.01
36 14 0.18
37 5 0.06
38 4 0.05
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (34 bp):
TAATAATAATATAATAATAATAATATATAATATA
Found at i:699953 original size:29 final size:29
Alignment explanation
Indices: 699893--699963 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
699883 ATTCATATCA
**
699893 AATATATTAATATTTTAAAATAATTAAAAT
1 AATATATT-ATATACTAAAATAATTAAAAT
* * *
699923 AATATATTATATACTAATATATTTATAAT
1 AATATATTATATACTAAAATAATTAAAAT
*
699952 AATTTATTATAT
1 AATATATTATAT
699964 TTTTATAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
29 27 0.77
30 8 0.23
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (29 bp):
AATATATTATATACTAAAATAATTAAAAT
Found at i:699968 original size:11 final size:11
Alignment explanation
Indices: 699937--699979 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
699927 TATTATATAC
*
699937 TAATATATTTA
1 TAATATTTTTA
*
699948 TAATA-ATTTA
1 TAATATTTTTA
*
699958 TTATATTTTTA
1 TAATATTTTTA
699969 TAATATTTTTA
1 TAATATTTTTA
699980 AAAATTAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TAATATTTTTA
Found at i:705621 original size:85 final size:84
Alignment explanation
Indices: 705517--705735 Score: 201
Period size: 85 Copynumber: 2.6 Consensus size: 84
705507 ATACAATCAC
* * * *
705517 GACACACGAATGTGTGTCATCTTT-TTTAATGACGTG-TGCTTCAATGACACGCAATGTAAGTCA
1 GACACACAAATATGTGTCAT-TTTATTT-ATGACG-GAGGCTTCAATGACACGCAATGCAAGTCA
* * **
705580 TAAATGTGTGTCTTAAATTTAT
63 TAAATGCGCGTAATAAATTTAT
* **
705602 GACACACAAATATGTGTCATTTTCATTTATGACGGAGGCTTCAATGACGCGCAATGCGCGTCATA
1 GACACACAAATATGTGTCATTTT-ATTTATGACGGAGGCTTCAATGACACGCAATGCAAGTCATA
*
705667 AATGCGCGTAATAGATTTAT
65 AATGCGCGTAATAAATTTAT
* ** * *
705687 GACACACAATTGCGTGTCATTTGAGATTTAT-ATCGGTGGCTTCAATGAC
1 GACACACAAATATGTGTCATTT--TATTTATGA-CGGAGGCTTCAATGAC
705736 GTGTATTTGT
Statistics
Matches: 111, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
84 4 0.04
85 83 0.75
86 24 0.22
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (84 bp):
GACACACAAATATGTGTCATTTTATTTATGACGGAGGCTTCAATGACACGCAATGCAAGTCATAA
ATGCGCGTAATAAATTTAT
Found at i:706245 original size:13 final size:13
Alignment explanation
Indices: 706227--706253 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
706217 CAATACGTTC
706227 CGAGCAAAATAGG
1 CGAGCAAAATAGG
706240 CGAGCAAAATAGG
1 CGAGCAAAATAGG
706253 C
1 C
706254 CGTGATATAA
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:0.44, C:0.19, G:0.30, T:0.07
Consensus pattern (13 bp):
CGAGCAAAATAGG
Found at i:706739 original size:30 final size:29
Alignment explanation
Indices: 706689--706755 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 29
706679 GGCTTCCTCA
706689 AAATTTTAAAAATTACAATTTAGAT-CCTT
1 AAATTTTAAAAATTACAATTT-GATCCCTT
*
706718 AAATTTTCAAAAAATT-TAATTTGATCCCCTT
1 AAATTTT--AAAAATTACAATTTGAT-CCCTT
706749 AAATTTT
1 AAATTTT
706756 TTAGAAATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 5 0.15
31 18 0.55
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.43
Consensus pattern (29 bp):
AAATTTTAAAAATTACAATTTGATCCCTT
Found at i:713298 original size:8 final size:8
Alignment explanation
Indices: 713285--713348 Score: 50
Period size: 8 Copynumber: 8.6 Consensus size: 8
713275 ATTTACAAAA
713285 AAATAATT
1 AAATAATT
713293 AAAT-A--
1 AAATAATT
713298 AAAT-ATT
1 AAATAATT
*
713305 AAAAAATT
1 AAATAATT
*
713313 AAATACTT
1 AAATAATT
713321 AAATAAATT
1 AAAT-AATT
*
713330 AAA-AATA
1 AAATAATT
713337 AAAT-ATT
1 AAATAATT
713344 AAATA
1 AAATA
713349 TAATAAAAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
5 5 0.11
7 16 0.36
8 17 0.39
9 6 0.14
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (8 bp):
AAATAATT
Found at i:713307 original size:12 final size:12
Alignment explanation
Indices: 713284--713353 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 12
713274 TATTTACAAA
713284 AAAATAATTAAAT
1 AAAAT-ATTAAAT
713297 AAAATATTAAAAAAT
1 AAAATATT---AAAT
*
713312 TAAATACTTAAAT
1 AAAATA-TTAAAT
* *
713325 AAATTA-AAAAT
1 AAAATATTAAAT
713336 AAAATATTAAAT
1 AAAATATTAAAT
*
713348 ATAATA
1 AAAATA
713354 AAAGATACCT
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
11 9 0.20
12 12 0.27
13 13 0.29
15 9 0.20
16 2 0.04
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATATTAAAT
Found at i:713323 original size:24 final size:24
Alignment explanation
Indices: 713296--713356 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
713286 AATAATTAAA
*
713296 TAAA-ATATTAAAAAATTAAATACT
1 TAAATATATTAAAAAATAAAATA-T
*
713320 TAAATAAATT-AAAAATAAAATAT
1 TAAATATATTAAAAAATAAAATAT
*
713343 TAAATATAATAAAA
1 TAAATATATTAAAA
713357 GATACCTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
23 9 0.29
24 18 0.58
25 4 0.13
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (24 bp):
TAAATATATTAAAAAATAAAATAT
Found at i:714608 original size:18 final size:18
Alignment explanation
Indices: 714568--714619 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
714558 TAAATCATCT
714568 TTTTAATTAATAAATATAG
1 TTTT-ATTAATAAATATAG
* *
714587 TTTTTTTAATAAATCTTA-
1 TTTTATTAATAAAT-ATAG
*
714605 TTTTATTATTAAATA
1 TTTTATTAATAAATA
714620 ATGTTAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 21 0.78
19 6 0.22
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTTATTAATAAATATAG
Found at i:715588 original size:37 final size:35
Alignment explanation
Indices: 715547--715636 Score: 117
Period size: 37 Copynumber: 2.5 Consensus size: 35
715537 ATCTCGATGA
* *
715547 GATGAATCAGTCGGTAGTTGGATTTATCATCCTAGTG
1 GATGAA-CAGTCGGTAATTGGATTTATCATCC-AATG
*
715584 GATGAACCAGTCTGTAATTGGATTTATCATCCAATG
1 GATGAA-CAGTCGGTAATTGGATTTATCATCCAATG
715620 GATGAACTAGTCGGTAA
1 GATGAAC-AGTCGGTAA
715637 ACTAGTCACT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
35 1 0.02
36 17 0.36
37 29 0.62
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.32
Consensus pattern (35 bp):
GATGAACAGTCGGTAATTGGATTTATCATCCAATG
Found at i:716400 original size:27 final size:27
Alignment explanation
Indices: 716336--716403 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
716326 TCAACAATCG
* *
716336 AAGTCAATGGCCAACAATTAAGGGTCG
1 AAGTCAATGGTCAACAATTAAGGGTCA
*
716363 AAGTCAATGGTCAACAGTTAAGGGTCA
1 AAGTCAATGGTCAACAATTAAGGGTCA
716390 AAGTCAATGGTCAA
1 AAGTCAATGGTCAA
716404 GGGGTCAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.21
Consensus pattern (27 bp):
AAGTCAATGGTCAACAATTAAGGGTCA
Found at i:716403 original size:13 final size:13
Alignment explanation
Indices: 716358--716403 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
716348 AACAATTAAG
*
716358 GGTCGAAGTCAAT
1 GGTCAAAGTCAAT
* *
716371 GGTCAACAGTTAAG
1 GGTCAA-AGTCAAT
716385 GGTCAAAGTCAAT
1 GGTCAAAGTCAAT
716398 GGTCAA
1 GGTCAA
716404 GGGGTCAAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (13 bp):
GGTCAAAGTCAAT
Found at i:717301 original size:2 final size:2
Alignment explanation
Indices: 717294--717333 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
717284 AGATTAAGAT
717294 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
717334 GGTTTTGTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:718235 original size:22 final size:22
Alignment explanation
Indices: 718205--718247 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
718195 CTATTGACCG
*
718205 TTGATCGGTCTGACAGTTGACT
1 TTGACCGGTCTGACAGTTGACT
*
718227 TTGACCGGTCTGACCGTTGAC
1 TTGACCGGTCTGACAGTTGAC
718248 CATTAACTTT
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:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (22 bp):
TTGACCGGTCTGACAGTTGACT
Found at i:718860 original size:27 final size:27
Alignment explanation
Indices: 718830--718908 Score: 133
Period size: 27 Copynumber: 2.9 Consensus size: 27
718820 TACTTTGGTT
*
718830 GGGTAAAATT-TCAAAAATACCCTTATG
1 GGGTAAAATTAT-GAAAATACCCTTATG
718857 GGGTAAAATTATGAAAATACCCTTATG
1 GGGTAAAATTATGAAAATACCCTTATG
718884 GGGTAAAATTATGAAAATACCCTTA
1 GGGTAAAATTATGAAAATACCCTTA
718909 AGTTGTAGGA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 49 0.98
28 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (27 bp):
GGGTAAAATTATGAAAATACCCTTATG
Found at i:719617 original size:35 final size:35
Alignment explanation
Indices: 719577--719713 Score: 116
Period size: 35 Copynumber: 3.9 Consensus size: 35
719567 AAGTCTCTGC
*
719577 AGGTTCAGCTCAATCAAACTGGTAATTCCTTATAT
1 AGGTTCAGCTCAATCAAACTGGTAATTCCTTAAAT
* ***
719612 AGGTTCAGGC-CGATCAAACTGGTAATTCCTTACGGC
1 AGGTTCA-GCTCAATCAAACTGGTAATTCCTTA-AAT
* * * * *
719648 ATGTTTAGCTCGATCAAATTGGTAATTCGTTAAAT
1 AGGTTCAGCTCAATCAAACTGGTAATTCCTTAAAT
* * * *
719683 AGGTTCAG-ACAATCGAGCTAGTAATTCCTTA
1 AGGTTCAGCTCAATCAAACTGGTAATTCCTTA
719714 CGGATCTAAG
Statistics
Matches: 79, Mismatches: 20, Indels: 7
0.75 0.19 0.07
Matches are distributed among these distances:
34 16 0.20
35 36 0.46
36 27 0.34
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (35 bp):
AGGTTCAGCTCAATCAAACTGGTAATTCCTTAAAT
Found at i:719675 original size:71 final size:70
Alignment explanation
Indices: 719583--719716 Score: 178
Period size: 71 Copynumber: 1.9 Consensus size: 70
719573 CTGCAGGTTC
* * * *
719583 AGCTCAATCAAACTGGTAATTCCTTATATAGGTTCAGGCCGATCAAACTGGTAATTCCTTACGGC
1 AGCTCAATCAAACTGGTAATTCCTTAAATAGGTTCA-GACAATCAAACTAGTAATTCCTTACGGC
719648 ATGTTT
65 ATGTTT
* * * * *
719654 AGCTCGATCAAATTGGTAATTCGTTAAATAGGTTCAGACAATCGAGCTAGTAATTCCTTACGG
1 AGCTCAATCAAACTGGTAATTCCTTAAATAGGTTCAGACAATCAAACTAGTAATTCCTTACGG
719717 ATCTAAGGTG
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
70 22 0.41
71 32 0.59
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (70 bp):
AGCTCAATCAAACTGGTAATTCCTTAAATAGGTTCAGACAATCAAACTAGTAATTCCTTACGGCA
TGTTT
Found at i:724338 original size:17 final size:18
Alignment explanation
Indices: 724313--724351 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
724303 AACTATTTTT
*
724313 AATTAAAAAATT-TATTA
1 AATTAAAAAATTCTAATA
*
724330 AATTCAAAAATTCTAATA
1 AATTAAAAAATTCTAATA
724348 AATT
1 AATT
724352 TCAGTTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTAAAAAATTCTAATA
Found at i:725275 original size:3 final size:3
Alignment explanation
Indices: 725267--725378 Score: 77
Period size: 3 Copynumber: 36.7 Consensus size: 3
725257 TTTATTACTA
* * * *
725267 ATT ATT ATT ATCT ATT GTA ATT ACT ATT ATT AATT ATT ATT ATT AGT
1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT
* **
725314 AAT ATT ATT ATTT ATT -TT AATT ACC ATT ATT AATT ATT ATT A-T ATT
1 ATT ATT ATT A-TT ATT ATT -ATT ATT ATT ATT -ATT ATT ATT ATT ATT
**
725360 -TT ATT ACA ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT AT
725379 ATTTAATATA
Statistics
Matches: 84, Mismatches: 17, Indels: 16
0.72 0.15 0.14
Matches are distributed among these distances:
2 6 0.07
3 64 0.76
4 14 0.17
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:725304 original size:22 final size:22
Alignment explanation
Indices: 725269--725351 Score: 78
Period size: 22 Copynumber: 3.6 Consensus size: 22
725259 TATTACTAAT
*
725269 TATTATT-ATCTATTGTAATTAC
1 TATTATTAAT-TATTTTAATTAC
* *
725291 TATTATTAATTATTATTATTAGTAA
1 TATTATTAATTATT-TTA--ATTAC
*
725316 TATTATTATTTATTTTAATTAC
1 TATTATTAATTATTTTAATTAC
*
725338 CATTATTAATTATT
1 TATTATTAATTATT
725352 ATTATATTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
22 26 0.53
23 4 0.08
24 3 0.06
25 16 0.33
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (22 bp):
TATTATTAATTATTTTAATTAC
Found at i:725335 original size:47 final size:48
Alignment explanation
Indices: 725258--725356 Score: 155
Period size: 47 Copynumber: 2.1 Consensus size: 48
725248 TGTTACAGGT
*
725258 TTATTACTAATTATTATTATCTATTGTAATTACTATTATTAATTATTA
1 TTATTACTAATTATTATTATCTATTGTAATTACCATTATTAATTATTA
* * *
725306 TTATTAGTAA-TATTATTATTTATTTTAATTACCATTATTAATTATTA
1 TTATTACTAATTATTATTATCTATTGTAATTACCATTATTAATTATTA
725353 TTAT
1 TTAT
725357 ATTTTATTAC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
47 38 0.81
48 9 0.19
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (48 bp):
TTATTACTAATTATTATTATCTATTGTAATTACCATTATTAATTATTA
Found at i:725365 original size:29 final size:28
Alignment explanation
Indices: 725316--725383 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 28
725306 TTATTAGTAA
*
725316 TATTATTATTTATTTTAATTACCATTAT
1 TATTATTATTTATTTTAATTACAATTAT
725344 TAATTATTATTATATTTT-ATTACAATTAT
1 T-ATTATTATT-TATTTTAATTACAATTAT
725373 TATTA-TATTTA
1 TATTATTATTTA
725384 ATATAGTAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
26 2 0.05
27 4 0.11
28 5 0.14
29 20 0.54
30 6 0.16
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (28 bp):
TATTATTATTTATTTTAATTACAATTAT
Found at i:725376 original size:47 final size:46
Alignment explanation
Indices: 725273--725376 Score: 118
Period size: 47 Copynumber: 2.2 Consensus size: 46
725263 ACTAATTATT
* **
725273 ATTATCTATTGTAATTACTATTATTAATTATTATTATTAGTAATATT
1 ATTAT-TATTGTAATTACCATTATTAATTATTATTATTAGTAATACA
* ** *
725320 ATTATTTATTTTAATTACCATTATTAATTATTATTATATTTTATTACA
1 ATTA-TTATTGTAATTACCATTATTAATTATTATTAT-TAGTAATACA
725368 ATTATTATT
1 ATTATTATT
725377 ATATTTAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
47 38 0.79
48 10 0.21
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.58
Consensus pattern (46 bp):
ATTATTATTGTAATTACCATTATTAATTATTATTATTAGTAATACA
Found at i:726087 original size:17 final size:17
Alignment explanation
Indices: 726030--726093 Score: 83
Period size: 17 Copynumber: 3.7 Consensus size: 17
726020 TGTTTATGAG
*
726030 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-CA
726048 GGAATTGGAATCTGTCA
1 GGAATTGGAATCTGTCA
** *
726065 TAAATTAGAATCTGTCA
1 GGAATTGGAATCTGTCA
726082 GGAATTGGAATC
1 GGAATTGGAATC
726094 CAATTCCATA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 24 0.62
18 15 0.38
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.30
Consensus pattern (17 bp):
GGAATTGGAATCTGTCA
Found at i:727674 original size:20 final size:20
Alignment explanation
Indices: 727649--727758 Score: 174
Period size: 20 Copynumber: 5.7 Consensus size: 20
727639 TTTGGTTCAC
727649 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
*
727669 GGAATGTAATATTACCAGTG
1 GGAATGTAAGATTACCAGTG
727689 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
*
727709 GGAATGTAAGATTATCA--G
1 GGAATGTAAGATTACCAGTG
727727 GGAA--TAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
727745 GGAATGTAAGATTA
1 GGAATGTAAGATTA
727759 TCAGGGAATA
Statistics
Matches: 82, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
16 10 0.12
18 10 0.12
20 62 0.76
ACGTcount: A:0.37, C:0.08, G:0.28, T:0.26
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:727736 original size:16 final size:16
Alignment explanation
Indices: 727715--727773 Score: 73
Period size: 16 Copynumber: 3.4 Consensus size: 16
727705 AGTGGGAATG
727715 TAAGATTATCAGGGAA
1 TAAGATTATCAGGGAA
*
727731 TAAGATTACCAGTGGGAA
1 TAAGATTATCA--GGGAA
727749 TGTAAGATTATCAGGGAA
1 --TAAGATTATCAGGGAA
727767 TAAGATT
1 TAAGATT
727774 GCTGAGAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
16 17 0.46
18 10 0.27
20 10 0.27
ACGTcount: A:0.41, C:0.07, G:0.25, T:0.27
Consensus pattern (16 bp):
TAAGATTATCAGGGAA
Found at i:727742 original size:36 final size:36
Alignment explanation
Indices: 727655--727773 Score: 184
Period size: 36 Copynumber: 3.2 Consensus size: 36
727645 TCACGGAATG
* *
727655 TAAGATTACCAGTGGGAATGTAATATTACCAGTGGGAA
1 TAAGATTACCAGTGGGAATGTAAGATTATCA--GGGAA
727693 TGTAAGATTACCAGTGGGAATGTAAGATTATCAGGGAA
1 --TAAGATTACCAGTGGGAATGTAAGATTATCAGGGAA
727731 TAAGATTACCAGTGGGAATGTAAGATTATCAGGGAA
1 TAAGATTACCAGTGGGAATGTAAGATTATCAGGGAA
727767 TAAGATT
1 TAAGATT
727774 GCTGAGAATG
Statistics
Matches: 77, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
36 43 0.56
38 5 0.06
40 29 0.38
ACGTcount: A:0.38, C:0.08, G:0.27, T:0.27
Consensus pattern (36 bp):
TAAGATTACCAGTGGGAATGTAAGATTATCAGGGAA
Found at i:735328 original size:130 final size:131
Alignment explanation
Indices: 735023--735362 Score: 441
Period size: 131 Copynumber: 2.6 Consensus size: 131
735013 ATAATTTTAA
* * * *
735023 GAGAGAAAATGATAATATCTAATTATTTCCAATCTAGAATAAATGACCTTTCATTCCTTAAAACA
1 GAGAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCA
* * * *
735088 ACCATTTATTACTCAGATCGAAATGAAGAGATATTACAACTCCATCTTAAAAATCAATATCGATT
66 ATCATTTATTACTCAGATCGAAATGAAGAGATATCACAACTCCACCTTAAAAATCAATATCAATT
735153 C
131 C
* * * * *
735154 GAGCGAAAACGATAATATCTAATGATTTCCAATCGAGAATAAATGGCCTCTCATACATTAAAGCA
1 GAGAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCA
* * * ** * * *
735219 TTCATTTATTGCTCCA-ATCGAAATGAAGATATATCATTATTCCCCCTTAAAAAT-AATATTAAT
66 ATCATTTATTACT-CAGATCGAAATGAAGAGATATCACAACTCCACCTTAAAAATCAATATCAAT
735282 TC
130 TC
* * *
735284 GAGAGAAAATGGTAATATCGAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCA
735349 ATCATTTATTACTC
66 ATCATTTATTACTC
735363 TAACCTAAAT
Statistics
Matches: 177, Mismatches: 31, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
129 1 0.01
130 77 0.44
131 97 0.55
132 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (131 bp):
GAGAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCA
ATCATTTATTACTCAGATCGAAATGAAGAGATATCACAACTCCACCTTAAAAATCAATATCAATT
C
Found at i:738023 original size:265 final size:265
Alignment explanation
Indices: 737534--738596 Score: 1289
Period size: 265 Copynumber: 4.0 Consensus size: 265
737524 GTCGAGAAAT
* * * * * *
737534 GTTGACTCATTCCAGTGTTCTTCAAGGAAGATTTAATCGAGGTAGACTTGTTCAACTGTAACTCA
1 GTTGATTCATTCTA-TGTTCTTCAGGGAAGATTGAATCAAGGTAGACTTGTTCCACTGTAACTCA
*
737599 GGGAAGATTAAATCTCGAAAGAGAGGGATCTGTTCCGCTTCTTCTTGAGGGAAAATCATATCTGG
65 GGGAAGATTAAATCTCGAAAGAGAGGGATCTGTTCCGCTTCTTCTTGAGGGAAAATCAGATCTGG
* * *
737664 GGATGTTGATTCATTCCATTGTTCTCCAGGAAAGATTGAATCGAGGCAGACTTGTTCCACTGTTA
130 GGACGTTGATTCATTCCACTATTCTCCAGGAAAGATTGAATCGAGGCAGACTTGTTCCACTGTTA
* *
737729 CTCAGGGAATATCAAATCTTGAAAGAGGGATCTGTTTTGCTTCTTCTTGAGGAAAAATTAGATCT
195 CTCAGGGAATATCAAATCTTGAAAGAGGAATCTATTTTGCTTCTTCTTGAGGAAAAATTAGATCT
737794 AGGGAC
260 AGGGAC
*
737800 GTTGATTCATTCTATTGTTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTT-CACTGTAACTCA
1 GTTGATTCATTCTA-TGTTCTTCAGGGAAGATTGAATCAAGGTAGACTTGTTCCACTGTAACTCA
*
737864 GGGAAGATTAAATCTCGAAAGAGAGGGATCTGTTCCGCTTCTTCTTGAGGGAAAATCATATCTGG
65 GGGAAGATTAAATCTCGAAAGAGAGGGATCTGTTCCGCTTCTTCTTGAGGGAAAATCAGATCTGG
* * *
737929 GGATGTTGATTCATTCCATTGTTCTCCAGGAAAGATTGAATCGAGGCAGACTTGTTCCACTGTTA
130 GGACGTTGATTCATTCCACTATTCTCCAGGAAAGATTGAATCGAGGCAGACTTGTTCCACTGTTA
* *
737994 CTCAGGGAATATCAAATCTTGAAAGAGGGATCTGTTTTGCTTCTTCTTGAGGAAAAATTAGATCT
195 CTCAGGGAATATCAAATCTTGAAAGAGGAATCTATTTTGCTTCTTCTTGAGGAAAAATTAGATCT
738059 AGGGAC
260 AGGGAC
* * * * *
738065 GTTG---------A-------CAGGGAAGATTGAATCAAAGAAGACTTGTTCCATTGTTACTTAG
1 GTTGATTCATTCTATGTTCTTCAGGGAAGATTGAATCAAGGTAGACTTGTTCCACTGTAACTCAG
* * * * * *
738114 GGAAGATTAAATATTGAAAGAGAGGGACCTATTCCGCTTCTTCTTGAAGGAAAATCAGATCTGAG
66 GGAAGATTAAATCTCGAAAGAGAGGGATCTGTTCCGCTTCTTCTTGAGGGAAAATCAGATCTGGG
* * *
738179 AACGTTGATTCATTCCACTATTCTCCAGGGAAGATTGAATCGAGGCAAACTTGTTCCACTGTTAC
131 GACGTTGATTCATTCCACTATTCTCCAGGAAAGATTGAATCGAGGCAGACTTGTTCCACTGTTAC
* *
738244 TCAGGGAATATCAAATATTGAAAGAGATGAATCTATTTTGCTTATTCTTGAGGGAAAAATTAGAT
196 TCAGGGAATATCAAATCTTGAAAGAG--GAATCTATTTTGCTTCTTCTTGA-GGAAAAATTAGAT
* *
738309 TTTGGGAC
258 CTAGGGAC
* ** * * *
738317 GTTGATTCATTCTACTATTCTTCAGGGAAGATTGAATCAAGGCGGTCTTGTTCCGCTGTTACTCA
1 GTTGATTCATTCTA-TGTTCTTCAGGGAAGATTGAATCAAGGTAGACTTGTTCCACTGTAACTCA
* * * * * * * * * *
738382 GGGAATATCAAATCTTGAACGAGTGGGATCTGTTCCACTTTTTATTGAGGGAAAATCAGATATAG
65 GGGAAGATTAAATCTCGAAAGAGAGGGATCTGTTCCGCTTCTTCTTGAGGGAAAATCAGATCTGG
* * * * * * *
738447 GGACATTGATTTATTCCACTATTCTTCAGGGAATATTGAATTGAGGCGGACTTGTTCCACTGTTA
130 GGACGTTGATTCATTCCACTATTCTCCAGGAAAGATTGAATCGAGGCAGACTTGTTCCACTGTTA
* * * * * * *
738512 TTTAGGGAAGATCAAATCTTGAAAGA-GAATGACATATTCTACTTCTTCTTGAGGGAAAATCAGA
195 CTCAGGGAATATCAAATCTTGAAAGAGGAAT--C-TATTTTGCTTCTTCTTGAGGAAAAATTAGA
* *
738576 TATGGGGAC
257 TCTAGGGAC
*
738585 ATTGATTCATTC
1 GTTGATTCATTC
738597 CACTATTTTT
Statistics
Matches: 701, Mismatches: 72, Indels: 46
0.86 0.09 0.06
Matches are distributed among these distances:
248 27 0.04
249 152 0.22
251 20 0.03
252 23 0.03
256 1 0.00
261 1 0.00
265 216 0.31
266 51 0.07
268 29 0.04
269 181 0.26
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (265 bp):
GTTGATTCATTCTATGTTCTTCAGGGAAGATTGAATCAAGGTAGACTTGTTCCACTGTAACTCAG
GGAAGATTAAATCTCGAAAGAGAGGGATCTGTTCCGCTTCTTCTTGAGGGAAAATCAGATCTGGG
GACGTTGATTCATTCCACTATTCTCCAGGAAAGATTGAATCGAGGCAGACTTGTTCCACTGTTAC
TCAGGGAATATCAAATCTTGAAAGAGGAATCTATTTTGCTTCTTCTTGAGGAAAAATTAGATCTA
GGGAC
Found at i:738259 original size:249 final size:250
Alignment explanation
Indices: 737822--738321 Score: 743
Period size: 249 Copynumber: 2.0 Consensus size: 250
737812 TATTGTTCTT
* * * *
737822 CAGGGAAGATTGAATCGAGGTAGACTTGTTCACTGTAACTCAGGGAAGATTAAATCTCGAAAGAG
1 CAGGGAAGATTGAATCAAAGAAGACTTGTTCACTGTAACTCAGGGAAGATTAAATATCGAAAGAG
* * * * * * * * *
737887 AGGGATCTGTTCCGCTTCTTCTTGAGGGAAAATCATATCTGGGGATGTTGATTCATTCCATTGTT
66 AGGGACCTATTCCGCTTCTTCTTGAAGGAAAATCAGATCTGAGAACGTTGATTCATTCCACTATT
* *
737952 CTCCAGGAAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAA
131 CTCCAGGAAAGATTGAATCGAGGCAAACTTGTTCCACTGTTACTCAGGGAATATCAAATATTGAA
* * *
738017 AGAG-GGATCTGTTTTGCTTCTTCTTGA-GGAAAAATTAGATCTAGGGACGTTGA
196 AGAGAGAATCTATTTTGCTTATTCTTGAGGGAAAAATTAGATCTAGGGACGTTGA
* * * *
738070 CAGGGAAGATTGAATCAAAGAAGACTTGTTCCATTGTTACTTAGGGAAGATTAAATATTGAAAGA
1 CAGGGAAGATTGAATCAAAGAAGACTTGTT-CACTGTAACTCAGGGAAGATTAAATATCGAAAGA
738135 GAGGGACCTATTCCGCTTCTTCTTGAAGGAAAATCAGATCTGAGAACGTTGATTCATTCCACTAT
65 GAGGGACCTATTCCGCTTCTTCTTGAAGGAAAATCAGATCTGAGAACGTTGATTCATTCCACTAT
*
738200 TCTCCAGGGAAGATTGAATCGAGGCAAACTTGTTCCACTGTTACTCAGGGAATATCAAATATTGA
130 TCTCCAGGAAAGATTGAATCGAGGCAAACTTGTTCCACTGTTACTCAGGGAATATCAAATATTGA
* *
738265 AAGAGATGAATCTATTTTGCTTATTCTTGAGGGAAAAATTAGATTTTGGGACGTTGA
195 AAGAGA-GAATCTATTTTGCTTATTCTTGAGGGAAAAATTAGATCTAGGGACGTTGA
738322 TTCATTCTAC
Statistics
Matches: 223, Mismatches: 25, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
248 27 0.12
249 152 0.68
251 20 0.09
252 24 0.11
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (250 bp):
CAGGGAAGATTGAATCAAAGAAGACTTGTTCACTGTAACTCAGGGAAGATTAAATATCGAAAGAG
AGGGACCTATTCCGCTTCTTCTTGAAGGAAAATCAGATCTGAGAACGTTGATTCATTCCACTATT
CTCCAGGAAAGATTGAATCGAGGCAAACTTGTTCCACTGTTACTCAGGGAATATCAAATATTGAA
AGAGAGAATCTATTTTGCTTATTCTTGAGGGAAAAATTAGATCTAGGGACGTTGA
Found at i:738501 original size:134 final size:133
Alignment explanation
Indices: 738070--738617 Score: 594
Period size: 134 Copynumber: 4.1 Consensus size: 133
738060 GGGACGTTGA
* * ** * * *
738070 CAGGGAAGATTGAATCAAAGAAGACTTGTTCCATTGTTACTTAGGGAAGATTAAATATTGAAAGA
1 CAGGGAAGATTGAATCGAGGCGGACTTGTTCCACTGTTACTCAGGGAAGATCAAATATTGAAAGA
* * * * * *
738135 GAGGGACCTATTCCGCTTCTTCTTGAAGGAAAATCAGATCTGAGAACGTTGATTCATTCCACTAT
66 GAGGGATCTATTCCACTTCTTCTTGAGGGAAAATCAGATATG-GGACATTGATTCATTCCACTAT
*
738200 TCTC
130 TCTT
** *
738204 CAGGGAAGATTGAATCGAGGCAAACTTGTTCCACTGTTACTCAGGGAATATCAAATATTGAAAGA
1 CAGGGAAGATTGAATCGAGGCGGACTTGTTCCACTGTTACTCAGGGAAGATCAAATATTGAAAGA
* * *** * * * * *
738269 GATGAATCTATTTTGCTTATTCTTGAGGGAAAAATTAGATTTTGGGACGTTGATTCATTCTACTA
66 GAGGGATCTATTCCACTTCTTCTTGAGGG-AAAATCAGA-TATGGGACATTGATTCATTCCACTA
738334 TTCTT
129 TTCTT
* * * * * *
738339 CAGGGAAGATTGAATCAAGGCGGTCTTGTTCCGCTGTTACTCAGGGAATATCAAATCTTGAACGA
1 CAGGGAAGATTGAATCGAGGCGGACTTGTTCCACTGTTACTCAGGGAAGATCAAATATTGAAAGA
* * * * *
738404 GTGGGATCTGTTCCACTTTTTATTGAGGGAAAATCAGATATAGGGACATTGATTTATTCCACTAT
66 GAGGGATCTATTCCACTTCTTCTTGAGGGAAAATCAGATAT-GGGACATTGATTCATTCCACTAT
738469 TCTT
130 TCTT
* * * * *
738473 CAGGGAATATTGAATTGAGGCGGACTTGTTCCACTGTTATTTAGGGAAGATCAAATCTTGAAAGA
1 CAGGGAAGATTGAATCGAGGCGGACTTGTTCCACTGTTACTCAGGGAAGATCAAATATTGAAAGA
** *
738538 GAATGA-CATATTCTACTTCTTCTTGAGGGAAAATCAGATATGGGGACATTGATTCATTCCACTA
66 GAGGGATC-TATTCCACTTCTTCTTGAGGGAAAATCAGATAT-GGGACATTGATTCATTCCACTA
*
738602 TTTTT
129 TTCTT
* *
738607 CAAGAAAGATT
1 CAGGGAAGATT
738618 AAATTGATTT
Statistics
Matches: 347, Mismatches: 63, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
133 3 0.01
134 232 0.67
135 109 0.31
136 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (133 bp):
CAGGGAAGATTGAATCGAGGCGGACTTGTTCCACTGTTACTCAGGGAAGATCAAATATTGAAAGA
GAGGGATCTATTCCACTTCTTCTTGAGGGAAAATCAGATATGGGACATTGATTCATTCCACTATT
CTT
Found at i:738563 original size:269 final size:267
Alignment explanation
Indices: 738070--738617 Score: 659
Period size: 269 Copynumber: 2.0 Consensus size: 267
738060 GGGACGTTGA
* * *
738070 CAGGGAAGATTGAATCAAAGAAGACTTGTTCCATTGTTACTTAGGGAAGATTAAATATTGAAAGA
1 CAGGGAAGATTGAATCAAAGAAGACTTGTTCCACTGTTACTCAGGGAAGATCAAATATTGAAAGA
* * * *
738135 GAGGGACCTATTCCGCTTCTTCTTGAAGGAAAATCAGATCTGAGAACGTTGATTCATTCCACTAT
66 GAGGGACCTATTCCACTTCTTATTGAAGGAAAATCAGATATGAGAACATTGATTCATTCCACTAT
*
738200 TCTCCAGGGAAGATTGAATCGAGGCAAACTTGTTCCACTGTTACTCAGGGAATATCAAATATTGA
131 TCTCCAGGGAAGATTGAATCGAGGCAAACTTGTTCCACTGTTACTCAGGGAAGATCAAATATTGA
* * * * * * *
738265 AAGAGATGAATCTATTTTGCTTATTCTTGAGGGAAAAATTAGATTTTGGGACGTTGATTCATTCT
196 AAGAGATGAA-CTATTCTACTTATTCTTGAGGG-AAAATCAGATATGGGGACATTGATTCATTCC
738330 ACTATTCTT
259 ACTATTCTT
* ** * * * * *
738339 CAGGGAAGATTGAATCAAGGCGGTCTTGTTCCGCTGTTACTCAGGGAATATCAAATCTTGAACGA
1 CAGGGAAGATTGAATCAAAGAAGACTTGTTCCACTGTTACTCAGGGAAGATCAAATATTGAAAGA
* * * * * * *
738404 GTGGGATCTGTTCCACTTTTTATTGAGGGAAAATCAGATAT-AGGGACATTGATTTATTCCACTA
66 GAGGGACCTATTCCACTTCTTATTGAAGGAAAATCAGATATGA-GAACATTGATTCATTCCACTA
* * * ** * * *
738468 TTCTTCAGGGAATATTGAATTGAGGCGGACTTGTTCCACTGTTATTTAGGGAAGATCAAATCTTG
130 TTCTCCAGGGAAGATTGAATCGAGGCAAACTTGTTCCACTGTTACTCAGGGAAGATCAAATATTG
*
738533 AAAGAGAATG-ACATATTCTACTTCTTCTTGAGGGAAAATCAGATATGGGGACATTGATTCATTC
195 AAAGAG-ATGAAC-TATTCTACTTATTCTTGAGGGAAAATCAGATATGGGGACATTGATTCATTC
*
738597 CACTATTTTT
258 CACTATTCTT
* *
738607 CAAGAAAGATT
1 CAGGGAAGATT
738618 AAATTGATTT
Statistics
Matches: 234, Mismatches: 42, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
268 45 0.19
269 186 0.79
270 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (267 bp):
CAGGGAAGATTGAATCAAAGAAGACTTGTTCCACTGTTACTCAGGGAAGATCAAATATTGAAAGA
GAGGGACCTATTCCACTTCTTATTGAAGGAAAATCAGATATGAGAACATTGATTCATTCCACTAT
TCTCCAGGGAAGATTGAATCGAGGCAAACTTGTTCCACTGTTACTCAGGGAAGATCAAATATTGA
AAGAGATGAACTATTCTACTTATTCTTGAGGGAAAATCAGATATGGGGACATTGATTCATTCCAC
TATTCTT
Found at i:742518 original size:164 final size:164
Alignment explanation
Indices: 742247--742576 Score: 660
Period size: 164 Copynumber: 2.0 Consensus size: 164
742237 AAATCGCATC
742247 ATGATTCCTAAAATTAAGGCAAGTCTGGTTATTAGGCACAATAACTGATTAGACAAATTTATGCT
1 ATGATTCCTAAAATTAAGGCAAGTCTGGTTATTAGGCACAATAACTGATTAGACAAATTTATGCT
742312 AGGGGAAGAATGTTATCAGCCTTAATAAATGAATACCATTTTCAACTTTGCATCTGTAATGATTT
66 AGGGGAAGAATGTTATCAGCCTTAATAAATGAATACCATTTTCAACTTTGCATCTGTAATGATTT
742377 TTAAATTAAATAAAGTTCAAACTTAAAATTTCCA
131 TTAAATTAAATAAAGTTCAAACTTAAAATTTCCA
742411 ATGATTCCTAAAATTAAGGCAAGTCTGGTTATTAGGCACAATAACTGATTAGACAAATTTATGCT
1 ATGATTCCTAAAATTAAGGCAAGTCTGGTTATTAGGCACAATAACTGATTAGACAAATTTATGCT
742476 AGGGGAAGAATGTTATCAGCCTTAATAAATGAATACCATTTTCAACTTTGCATCTGTAATGATTT
66 AGGGGAAGAATGTTATCAGCCTTAATAAATGAATACCATTTTCAACTTTGCATCTGTAATGATTT
742541 TTAAATTAAATAAAGTTCAAACTTAAAATTTCCA
131 TTAAATTAAATAAAGTTCAAACTTAAAATTTCCA
742575 AT
1 AT
742577 TCTAAATATA
Statistics
Matches: 166, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
164 166 1.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34
Consensus pattern (164 bp):
ATGATTCCTAAAATTAAGGCAAGTCTGGTTATTAGGCACAATAACTGATTAGACAAATTTATGCT
AGGGGAAGAATGTTATCAGCCTTAATAAATGAATACCATTTTCAACTTTGCATCTGTAATGATTT
TTAAATTAAATAAAGTTCAAACTTAAAATTTCCA
Found at i:745569 original size:26 final size:25
Alignment explanation
Indices: 745533--745588 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 25
745523 CTGTAATGCT
*
745533 TACACATAAGGTTGTGCCCACCATAA
1 TACACATAAGGTCGTGCCCACCAT-A
745559 TACACATAAGGTCGTGCCCACCATA
1 TACACATAAGGTCGTGCCCACCATA
745584 TACAC
1 TACAC
745589 CTAGTGTCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 6 0.21
26 23 0.79
ACGTcount: A:0.34, C:0.30, G:0.14, T:0.21
Consensus pattern (25 bp):
TACACATAAGGTCGTGCCCACCATA
Done.