Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008310.1 Hibiscus syriacus cultivar Beakdansim tig00111000_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: 3887810
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 15
Found at i:832368 original size:7 final size:7
Alignment explanation
Indices: 832319--832359 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
832309 TAAAAAGAAA
832319 AAAAAAG
1 AAAAAAG
832326 AAAAAAG
1 AAAAAAG
832333 AAAAAAG
1 AAAAAAG
* *
832340 GAAAAGG
1 AAAAAAG
832347 AAAAAAG
1 AAAAAAG
832354 AAAAAA
1 AAAAAA
832360 AAAGAAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:837004 original size:22 final size:22
Alignment explanation
Indices: 836978--837057 Score: 133
Period size: 22 Copynumber: 3.6 Consensus size: 22
836968 TACATCTACA
836978 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
837000 CTCTTCAAAGATGATAGATTTT
1 CTCTTCAAAGATGATAGATTCT
*
837022 CTCTTCAAATATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
837044 CTTTTCAAAGATGA
1 CTCTTCAAAGATGA
837058 ACGCTTAATT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:837778 original size:45 final size:45
Alignment explanation
Indices: 837714--838405 Score: 1127
Period size: 45 Copynumber: 15.4 Consensus size: 45
837704 CTATTTCCCA
* *
837714 CATCTATAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTAGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
837759 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
*
837805 CAT-TGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
* *
837850 CATCTGTAAGTCTTTCAGTGCATGATGTTTTCAAAAACCTTTGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
* *
837896 CATCTGTAAGCCCTTCAATGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
837941 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTTGAGC
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
837986 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
838031 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
838076 CATCTGTAAGTCCTTTAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
838121 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
838166 CATCTGTAAGTCCTTCAGTGCATGATATTTTCAAAACCTACGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
838211 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTCCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
838256 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
838301 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * * *
838346 CATCTGTAAGCCCTTCAGTGAATGATGTTTTCAAAGCCTTCGGGC
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
838391 CATTTGTAAG-CCTTC
1 CATCTGTAAGTCCTTC
838406 CGAGCAAGAT
Statistics
Matches: 607, Mismatches: 38, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
44 5 0.01
45 519 0.86
46 83 0.14
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (45 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:838596 original size:3 final size:3
Alignment explanation
Indices: 838588--838668 Score: 90
Period size: 3 Copynumber: 26.7 Consensus size: 3
838578 TTTCATATAG
* ** *
838588 TTA TTA TTA TTA TTA TGA TTA TTA AAA TTA TTA TTT TTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* * *
838634 TTA TTA TTA ATA TTA TTA CTA TTA ATA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
838669 TAAAAATAAT
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
3 60 0.95
4 3 0.05
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:840076 original size:26 final size:26
Alignment explanation
Indices: 840045--840095 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
840035 AAATAATATT
* * *
840045 TATTTATTTTATTTCTATTAAAATCC
1 TATTTAATATATTACTATTAAAATCC
*
840071 TATTTAATATATTACTTTTAAAATC
1 TATTTAATATATTACTATTAAAATC
840096 ATTTTAAATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (26 bp):
TATTTAATATATTACTATTAAAATCC
Found at i:840226 original size:21 final size:22
Alignment explanation
Indices: 840188--840231 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
840178 TTTTAAATAA
840188 AAATAAATATTTTACTTT-TAT
1 AAATAAATATTTTACTTTATAT
*
840209 AAATAAATCTATTT-CTTTATAT
1 AAATAAATAT-TTTACTTTATAT
840231 A
1 A
840232 TTTATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATAAATATTTTACTTTATAT
Found at i:840813 original size:18 final size:18
Alignment explanation
Indices: 840792--840829 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
840782 CCCTTAGGTA
840792 TCAATACCCTAATTAGAT
1 TCAATACCCTAATTAGAT
**
840810 TCAATGTCCTAATTAGAT
1 TCAATACCCTAATTAGAT
840828 TC
1 TC
840830 GATGTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37
Consensus pattern (18 bp):
TCAATACCCTAATTAGAT
Found at i:840853 original size:18 final size:18
Alignment explanation
Indices: 840801--840854 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
840791 ATCAATACCC
* **
840801 TAATTAGATTCAATGTCC
1 TAATTAGATTCGATGTTT
840819 TAATTAGATTCGATGTTT
1 TAATTAGATTCGATGTTT
840837 TAATTAGATTCGATGTTT
1 TAATTAGATTCGATGTTT
840855 ACTGGTATCG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (18 bp):
TAATTAGATTCGATGTTT
Found at i:846365 original size:20 final size:19
Alignment explanation
Indices: 846322--846370 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
846312 GATGCAAGTA
846322 GTATCGATACTAAGAGGGG
1 GTATCGATACTAAGAGGGG
* * *
846341 GTATCAATACTATGAGGATG
1 GTATCGATACTAAGAGG-GG
846361 GTATCGATAC
1 GTATCGATAC
846371 CATTGATAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.27
Consensus pattern (19 bp):
GTATCGATACTAAGAGGGG
Found at i:846874 original size:54 final size:53
Alignment explanation
Indices: 846787--847130 Score: 463
Period size: 54 Copynumber: 6.4 Consensus size: 53
846777 TTATGTGTAC
* *
846787 TACATGCACTATGTGCGCAACCCACGAAATTCATCATGAGTTGATGAACAACCG
1 TACAGGCACTATGTGTGCAACCCAC-AAATTCATCATGAGTTGATGAACAACCG
**
846841 TACAGGCACTATGTGTGCAACCCACATAATTCATCATGAGTTGATGAACAGTCG
1 TACAGGCACTATGTGTGCAACCCACA-AATTCATCATGAGTTGATGAACAACCG
* *
846895 TACAGGCACTATGTGTGCAACCCACGGAATTCATCATGAGTTGATAAACAACCG
1 TACAGGCACTATGTGTGCAACCCAC-AAATTCATCATGAGTTGATGAACAACCG
* *
846949 TACAGTCACTATGTGTGCAACCCACGAAATTCATCAATGAGTTGACGAACAACCG
1 TACAGGCACTATGTGTGCAACCCAC-AAATTCATC-ATGAGTTGATGAACAACCG
* * *
847004 TACAGGAACTATGTGTGCAACCCACATAATTCATCATGTGTTGATGAACGACCG
1 TACAGGCACTATGTGTGCAACCCACA-AATTCATCATGAGTTGATGAACAACCG
* * * * *
847058 TACAAGCACTATGTGTGTAACCCACAGAATTCATCATGTGTTGATGAACGATCG
1 TACAGGCACTATGTGTGCAACCCACA-AATTCATCATGAGTTGATGAACAACCG
* *
847112 TATAGGCACTACGTGTGCA
1 TACAGGCACTATGTGTGCA
847131 TCTTAATAAA
Statistics
Matches: 260, Mismatches: 26, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
53 1 0.00
54 211 0.81
55 48 0.18
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.24
Consensus pattern (53 bp):
TACAGGCACTATGTGTGCAACCCACAAATTCATCATGAGTTGATGAACAACCG
Found at i:847069 original size:163 final size:162
Alignment explanation
Indices: 846787--847130 Score: 519
Period size: 163 Copynumber: 2.1 Consensus size: 162
846777 TTATGTGTAC
* * * *
846787 TACATGCACTATGTGCGCAACCCACGAAATTCATCATGAGTTGATGAACAACCGTACAGGCACTA
1 TACAGGCACTATGTGTGCAACCCACGAAATTCATCATGAGTTGACGAACAACCGTACAGGAACTA
* *
846852 TGTGTGCAACCCACATAATTCATCATGAGTTGATGAACAGTCGTACAGGCACTATGTGTGCAACC
66 TGTGTGCAACCCACATAATTCATCATGAGTTGATGAACAGCCGTACAAGCACTATGTGTGCAACC
*
846917 CACGGAATTCATCATGAGTTGATAAACAACCG
131 CACAGAATTCATCATGAGTTGATAAACAACCG
*
846949 TACAGTCACTATGTGTGCAACCCACGAAATTCATCAATGAGTTGACGAACAACCGTACAGGAACT
1 TACAGGCACTATGTGTGCAACCCACGAAATTCATC-ATGAGTTGACGAACAACCGTACAGGAACT
* *
847014 ATGTGTGCAACCCACATAATTCATCATGTGTTGATGAAC-GACCGTACAAGCACTATGTGTGTAA
65 ATGTGTGCAACCCACATAATTCATCATGAGTTGATGAACAG-CCGTACAAGCACTATGTGTGCAA
* * * *
847078 CCCACAGAATTCATCATGTGTTGATGAACGATCG
129 CCCACAGAATTCATCATGAGTTGATAAACAACCG
* *
847112 TATAGGCACTACGTGTGCA
1 TACAGGCACTATGTGTGCA
847131 TCTTAATAAA
Statistics
Matches: 163, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
162 33 0.20
163 130 0.80
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.24
Consensus pattern (162 bp):
TACAGGCACTATGTGTGCAACCCACGAAATTCATCATGAGTTGACGAACAACCGTACAGGAACTA
TGTGTGCAACCCACATAATTCATCATGAGTTGATGAACAGCCGTACAAGCACTATGTGTGCAACC
CACAGAATTCATCATGAGTTGATAAACAACCG
Found at i:849087 original size:23 final size:23
Alignment explanation
Indices: 849054--849141 Score: 115
Period size: 23 Copynumber: 3.9 Consensus size: 23
849044 AATTTTTGTA
* *
849054 TTTGTGACACATTTATCTATGCC
1 TTTGTGGCACATTTATCTCTGCC
*
849077 TTTGTGGCACATTTATCTCTGTC
1 TTTGTGGCACATTTATCTCTGCC
* *
849100 TTTGTGGTACATTT-TCTCTGCT
1 TTTGTGGCACATTTATCTCTGCC
*
849122 TTTGTGGCACATTTTTCTCT
1 TTTGTGGCACATTTATCTCT
849142 AATTGTCGGT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
22 19 0.33
23 38 0.67
ACGTcount: A:0.14, C:0.20, G:0.16, T:0.50
Consensus pattern (23 bp):
TTTGTGGCACATTTATCTCTGCC
Found at i:854938 original size:3 final size:3
Alignment explanation
Indices: 854930--854955 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
854920 GTCTACAAAA
854930 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
854956 CATCATGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:856746 original size:17 final size:17
Alignment explanation
Indices: 856724--856770 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
856714 GCTGACCAAT
*
856724 TTTTGTCTTAAAAACTA
1 TTTTGTCTTAAAAACGA
856741 TTTTGTCTTAAAAACGA
1 TTTTGTCTTAAAAACGA
856758 TTTT-TCCTTAAAA
1 TTTTGT-CTTAAAA
856771 TTGTTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 1 0.04
17 27 0.96
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.47
Consensus pattern (17 bp):
TTTTGTCTTAAAAACGA
Found at i:859692 original size:23 final size:22
Alignment explanation
Indices: 859653--859720 Score: 79
Period size: 23 Copynumber: 3.2 Consensus size: 22
859643 AGATCAAATC
* *
859653 AAAACAGAGAGAAAAGCAAAGA
1 AAAAAAGAGAAAAAAGCAAAGA
859675 AAAAAAGAGAAAATAAGCAAAGA
1 AAAAAAGAGAAAA-AAGCAAAGA
*
859698 AAAAAA-A-TAAAAA-CAAAGA
1 AAAAAAGAGAAAAAAGCAAAGA
859717 AAAA
1 AAAA
859721 TAGGGCAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
19 10 0.24
20 2 0.05
21 3 0.07
22 12 0.29
23 15 0.36
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.03
Consensus pattern (22 bp):
AAAAAAGAGAAAAAAGCAAAGA
Found at i:859719 original size:10 final size:10
Alignment explanation
Indices: 859662--859720 Score: 50
Period size: 10 Copynumber: 5.7 Consensus size: 10
859652 CAAAACAGAG
*
859662 AGAAAAGCAA
1 AGAAAAACAA
859672 AGAAAAA-AA
1 AGAAAAACAA
859681 GAGAAAATAAGCAA
1 -AG-AAA-AA-CAA
859695 AGAAAAA-AA
1 AGAAAAACAA
*
859704 ATAAAAACAA
1 AGAAAAACAA
859714 AGAAAAA
1 AGAAAAA
859721 TAGGGCAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
9 10 0.25
10 16 0.40
11 5 0.12
12 5 0.12
13 2 0.05
14 2 0.05
ACGTcount: A:0.78, C:0.05, G:0.14, T:0.03
Consensus pattern (10 bp):
AGAAAAACAA
Found at i:861164 original size:50 final size:50
Alignment explanation
Indices: 861098--861193 Score: 156
Period size: 50 Copynumber: 1.9 Consensus size: 50
861088 CTCTTTAAAC
* *
861098 ATCATATTTGAGTCGTTTCCCTTGACATGAATTTTGTCTCTCTTGAAATA
1 ATCATATTTGAGTCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAAATA
* *
861148 ATCATCTTTGATTCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGA
1 ATCATATTTGAGTCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGA
861194 CACAGTTTCC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.45
Consensus pattern (50 bp):
ATCATATTTGAGTCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAAATA
Found at i:861378 original size:66 final size:65
Alignment explanation
Indices: 861136--861434 Score: 288
Period size: 66 Copynumber: 4.6 Consensus size: 65
861126 GAATTTTGTC
* * * * *
861136 TCTCTTGAAATAATCATCTTTGA-TTCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGACACAGT
1 TCTCTTGAAACACTCATCTTTGAGTTCGTTTCCCTTGAAAC-AATTTTGTCTCCCTTGAGAAAGT
861200 T
65 T
* * * * * * *
861201 TCCCTTGAAA-AATCATTTTTGAGTTTGTTTCTCTTGAAACAA-ATTGTCTCCCTTGAGATAGTT
1 TCTCTTGAAACACTCATCTTTGAGTTCGTTTCCCTTGAAACAATTTTGTCTCCCTTGAGAAAGTT
** ** * *
861264 TCTCTTGAAACACAAATCTTTGAGTTAATTTCCCTTGAAACAAGTTTTGTATCCCTTGAGAAATT
1 TCTCTTGAAACACTCATCTTTGAGTTCGTTTCCCTTGAAACAA-TTTTGTCTCCCTTGAGAAAGT
861329 T
65 T
* * * * *
861330 TCTCTTGAAACACCCACCTTTGAGATCGTTTCCCTTGAAATGAATTTTGTCTCACTTGA-AACAG
1 TCTCTTGAAACACTCATCTTTGAGTTCGTTTCCCTTGAAA-CAATTTTGTCTCCCTTGAGAA-AG
861394 TT
64 TT
861396 TC-CATTGAAACA-TCATCTTTGAG-TCTGTTTCCCTTGAAA
1 TCTC-TTGAAACACTCATCTTTGAGTTC-GTTTCCCTTGAAA
861435 TAAATCCCTA
Statistics
Matches: 194, Mismatches: 32, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
63 26 0.13
64 40 0.21
65 49 0.25
66 77 0.40
67 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (65 bp):
TCTCTTGAAACACTCATCTTTGAGTTCGTTTCCCTTGAAACAATTTTGTCTCCCTTGAGAAAGTT
Found at i:861860 original size:3 final size:3
Alignment explanation
Indices: 861852--861901 Score: 73
Period size: 3 Copynumber: 16.3 Consensus size: 3
861842 TCTACAAAAA
* *
861852 ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATTT ATT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
861898 ATT A
1 ATT A
861902 CATCTTATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:862119 original size:19 final size:18
Alignment explanation
Indices: 862081--862120 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
862071 GCCCAATAAG
*
862081 AGGATCCAGACCCTACCC
1 AGGATCCAGACCCGACCC
*
862099 AGGATCCAGAACCCGATCC
1 AGGATCCAG-ACCCGACCC
862118 AGG
1 AGG
862121 CCCATCAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.30, C:0.38, G:0.23, T:0.10
Consensus pattern (18 bp):
AGGATCCAGACCCGACCC
Found at i:866225 original size:10 final size:10
Alignment explanation
Indices: 866210--866295 Score: 55
Period size: 10 Copynumber: 9.2 Consensus size: 10
866200 TTTTTTGTTC
866210 ATGTTCGTTT
1 ATGTTCGTTT
866220 ATGTTCGTGTT
1 ATGTTCGT-TT
* *
866231 CAT-TTATGTTC
1 -ATGTT-CGTTT
*
866242 GTGTTCGTTT
1 ATGTTCGTTT
866252 ATGTTCG---
1 ATGTTCGTTT
866259 -TGTTCGTTT
1 ATGTTCGTTT
866268 ATGTTCG---
1 ATGTTCGTTT
866275 -TGTTCGTTT
1 ATGTTCGTTT
866284 ATGTTCGTTT
1 ATGTTCGTTT
866294 AT
1 AT
866296 TTATTAAATG
Statistics
Matches: 58, Mismatches: 6, Indels: 24
0.66 0.07 0.27
Matches are distributed among these distances:
6 12 0.21
10 35 0.60
11 7 0.12
12 4 0.07
ACGTcount: A:0.09, C:0.12, G:0.22, T:0.57
Consensus pattern (10 bp):
ATGTTCGTTT
Found at i:866230 original size:16 final size:16
Alignment explanation
Indices: 866205--866291 Score: 156
Period size: 16 Copynumber: 5.4 Consensus size: 16
866195 GGGTTTTTTT
*
866205 TGTTCATGTTCGTTTA
1 TGTTCGTGTTCGTTTA
*
866221 TGTTCGTGTTCATTTA
1 TGTTCGTGTTCGTTTA
866237 TGTTCGTGTTCGTTTA
1 TGTTCGTGTTCGTTTA
866253 TGTTCGTGTTCGTTTA
1 TGTTCGTGTTCGTTTA
866269 TGTTCGTGTTCGTTTA
1 TGTTCGTGTTCGTTTA
866285 TGTTCGT
1 TGTTCGT
866292 TTATTTATTA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 68 1.00
ACGTcount: A:0.08, C:0.13, G:0.23, T:0.56
Consensus pattern (16 bp):
TGTTCGTGTTCGTTTA
Found at i:873778 original size:21 final size:21
Alignment explanation
Indices: 873746--873786 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
873736 ATTCTCTGCA
873746 TCTTCTTCTTCCTCCTCCTCC
1 TCTTCTTCTTCCTCCTCCTCC
*
873767 TCTTACTT-TTCCTCTTCCTC
1 TCTT-CTTCTTCCTCCTCCTC
873787 TTCTCCGCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.02, C:0.46, G:0.00, T:0.51
Consensus pattern (21 bp):
TCTTCTTCTTCCTCCTCCTCC
Found at i:876213 original size:13 final size:12
Alignment explanation
Indices: 876185--876235 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
876175 ACAATATTTT
876185 TATTAAAA-TAA
1 TATTAAAATTAA
876196 TATTAAAATTATA
1 TATTAAAATTA-A
*
876209 TATTAATATTAA
1 TATTAAAATTAA
876221 -ATATATAAATTAA
1 TAT-TA-AAATTAA
876234 TA
1 TA
876236 ATATTTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
11 10 0.30
12 5 0.15
13 17 0.52
14 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TATTAAAATTAA
Found at i:876217 original size:19 final size:19
Alignment explanation
Indices: 876188--876235 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
876178 ATATTTTTAT
*
876188 TAAAATAATATTAAA-ATTA
1 TAAATTAATATTAAATA-TA
*
876207 TATATTAATATTAAATATA
1 TAAATTAATATTAAATATA
876226 TAAATTAATA
1 TAAATTAATA
876236 ATATTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 24 0.96
20 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAATTAATATTAAATATA
Found at i:881931 original size:14 final size:14
Alignment explanation
Indices: 881906--881991 Score: 63
Period size: 14 Copynumber: 6.3 Consensus size: 14
881896 TAATTTATCT
**
881906 AATATTATTTATTCC
1 AATATTA-TTATTAA
881921 AATATTATTATTAA
1 AATATTATTATTAA
881935 AATATTA-TATCTAA
1 AATATTATTAT-TAA
* *
881949 AAT-TT-TAATAAA
1 AATATTATTATTAA
* *
881961 AATATTAATATTAT
1 AATATTATTATTAA
*
881975 TATATT-TTATTAA
1 AATATTATTATTAA
881988 AATA
1 AATA
881992 AAAATATTAT
Statistics
Matches: 55, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
12 5 0.09
13 17 0.31
14 26 0.47
15 7 0.13
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (14 bp):
AATATTATTATTAA
Found at i:881995 original size:33 final size:34
Alignment explanation
Indices: 881955--882082 Score: 111
Period size: 35 Copynumber: 3.7 Consensus size: 34
881945 CTAAAATTTT
*
881955 AATAAAAATATTAATATTATTATAT-TTTATTAA
1 AATAAAAATATTAATATTATTAAATATTTATTAA
881988 AATAAAAATATT-ATAATTATATTAAATATTTATTAA
1 AATAAAAATATTAAT-A-T-TATTAAATATTTATTAA
* *
882024 AAT-AAAA-ATTATATATTATTAAGTATATTAATTACT
1 AATAAAAATATTA-ATATTATTAA--ATATTTATTA-A
* * *
882060 TATTAAAATAATAATATTATTAA
1 AATAAAAATATTAATATTATTAA
882083 TCTAATAAAA
Statistics
Matches: 79, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
32 2 0.03
33 19 0.24
34 5 0.06
35 21 0.27
36 15 0.19
37 14 0.18
38 3 0.04
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (34 bp):
AATAAAAATATTAATATTATTAAATATTTATTAA
Found at i:882052 original size:42 final size:43
Alignment explanation
Indices: 881995--882079 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 43
881985 TAAAATAAAA
* *
881995 ATATTATAATTATATTAAATATTTATTAAAATAA-AA-ATTAT
1 ATATTATAAGTATATTAAATACTTATTAAAATAATAATATTAT
*
882036 ATATTATTAAGTATATTAATTACTTATTAAAATAATAATATTAT
1 ATATTA-TAAGTATATTAAATACTTATTAAAATAATAATATTAT
882080 TAATCTAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 6 0.16
42 25 0.66
43 2 0.05
44 5 0.13
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (43 bp):
ATATTATAAGTATATTAAATACTTATTAAAATAATAATATTAT
Found at i:882088 original size:17 final size:17
Alignment explanation
Indices: 882036--882090 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
882026 TAAAAATTAT
*
882036 ATATTATTAAGTATATTA
1 ATATTATTAA-TATAATA
*
882054 ATTACTTATTAAAATAATA
1 A-TA-TTATTAATATAATA
*
882073 ATATTATTAATCTAATA
1 ATATTATTAATATAATA
882090 A
1 A
882091 AATTTATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 13 0.42
18 3 0.10
19 8 0.26
20 7 0.23
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (17 bp):
ATATTATTAATATAATA
Found at i:885084 original size:24 final size:24
Alignment explanation
Indices: 885057--885103 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
885047 CACCACAGCT
885057 CGTATAAAT-TGCAACGAAGTGCCG
1 CGTA-AAATATGCAACGAAGTGCCG
* *
885081 CGTAGAATATGCAATGAAGTGCC
1 CGTAAAATATGCAACGAAGTGCC
885104 ACATAGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (24 bp):
CGTAAAATATGCAACGAAGTGCCG
Found at i:885110 original size:24 final size:23
Alignment explanation
Indices: 885066--885115 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
885056 TCGTATAAAT
* *
885066 TGCAACGAAGTGCCGCGTAGAATA
1 TGCAACGAAGTGCCACATAGAA-A
*
885090 TGCAATGAAGTGCCACATAGAAA
1 TGCAACGAAGTGCCACATAGAAA
885113 TGC
1 TGC
885116 CCGGAAGGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.18
Consensus pattern (23 bp):
TGCAACGAAGTGCCACATAGAAA
Found at i:885149 original size:23 final size:23
Alignment explanation
Indices: 885123--885203 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
885113 TGCCCGGAAG
* * *
885123 GACCACATAGTATTGTCCCGAAA
1 GACCACGTAGAATTGTCCCGAAT
* * *
885146 GACCGCGTAGAAATATCCCGAAT
1 GACCACGTAGAATTGTCCCGAAT
885169 GACCACGTAGAATTGTCCCGAAT
1 GACCACGTAGAATTGTCCCGAAT
*
885192 GACCGCGTAGAA
1 GACCACGTAGAA
885204 CCCTCGACTC
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.19
Consensus pattern (23 bp):
GACCACGTAGAATTGTCCCGAAT
Found at i:886373 original size:3 final size:3
Alignment explanation
Indices: 886365--886389 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
886355 CCACGGCTAA
886365 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
886390 GAAATACACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:887534 original size:21 final size:21
Alignment explanation
Indices: 887504--887559 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
887494 CTATATACAG
*
887504 AGGTATCGATACCTATGCCAA
1 AGGTACCGATACCTATGCCAA
887525 AGGTACCGATACCTATGCCAA
1 AGGTACCGATACCTATGCCAA
887546 AGGTACCGATACCT
1 AGGTACCGATACCT
887560 CTTGTGTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (21 bp):
AGGTACCGATACCTATGCCAA
Found at i:887744 original size:21 final size:21
Alignment explanation
Indices: 887719--887769 Score: 67
Period size: 16 Copynumber: 2.7 Consensus size: 21
887709 TATACAGGTA
887719 GTACCGATACCCATTGAAGAG
1 GTACCGATACCCATTGAAGAG
887740 GTA-C----CCCATTGAAGAG
1 GTACCGATACCCATTGAAGAG
887756 GTACCGATACCCAT
1 GTACCGATACCCAT
887770 ACGCTCCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
16 15 0.60
17 1 0.04
20 1 0.04
21 8 0.32
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (21 bp):
GTACCGATACCCATTGAAGAG
Found at i:891790 original size:19 final size:19
Alignment explanation
Indices: 891766--891809 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
891756 TAAGAAGTGG
891766 CACGACAAAATACAGTTGC
1 CACGACAAAATACAGTTGC
* *
891785 CACGACAAAATGCGGTTGC
1 CACGACAAAATACAGTTGC
891804 CACGAC
1 CACGAC
891810 TTTTTCATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.30, G:0.20, T:0.14
Consensus pattern (19 bp):
CACGACAAAATACAGTTGC
Found at i:894320 original size:19 final size:20
Alignment explanation
Indices: 894277--894315 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
894267 AAAACACAAG
894277 ATTTTTCAAAAAAAAAATAA
1 ATTTTTCAAAAAAAAAATAA
* *
894297 ATTTTTTAAATAAAAAATA
1 ATTTTTCAAAAAAAAAATA
894316 GTTTTGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
ATTTTTCAAAAAAAAAATAA
Found at i:896319 original size:17 final size:18
Alignment explanation
Indices: 896286--896322 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
896276 TTTAAGATTT
896286 TATATTCGATTCAAAATTA
1 TATATTCGATT-AAAATTA
896305 TATATTCGATT-AAATTA
1 TATATTCGATTAAAATTA
896322 T
1 T
896323 TCGAATATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
19 11 0.61
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (18 bp):
TATATTCGATTAAAATTA
Found at i:909554 original size:21 final size:21
Alignment explanation
Indices: 909517--909556 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
909507 CCCCCTTTGA
*
909517 AGGGGAACTGATTCCCCCTAC
1 AGGGGAACTGATACCCCCTAC
909538 AGGGGAA-TCGATACCCCCT
1 AGGGGAACT-GATACCCCCT
909557 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.17
Consensus pattern (21 bp):
AGGGGAACTGATACCCCCTAC
Found at i:914840 original size:3 final size:3
Alignment explanation
Indices: 914806--914858 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
914796 CGAACCTGAA
* * **
914806 AAT AAT -AT AAT ATT AAT AAC AAT AGC AAT AAT AAT AAT AAT AAT ATAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
914854 AAT AA
1 AAT AA
914859 ATATATATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:914943 original size:17 final size:18
Alignment explanation
Indices: 914921--914963 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
914911 AAAGTATATA
914921 ATGTATATTT-CAAAACT
1 ATGTATATTTCCAAAACT
* *
914938 ATGTATGTTTCCAAAATT
1 ATGTATATTTCCAAAACT
*
914956 ATATATAT
1 ATGTATAT
914964 ATATATATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (18 bp):
ATGTATATTTCCAAAACT
Found at i:914983 original size:24 final size:22
Alignment explanation
Indices: 914950--915040 Score: 92
Period size: 23 Copynumber: 3.9 Consensus size: 22
914940 GTATGTTTCC
*
914950 AAAATTATATATATATATATATT
1 AAAAATATA-ATATATATATATT
*
914973 AAAATTTATATATATATATATATT
1 AAAA-ATATA-ATATATATATATT
* *
914997 AAAAAATATAACATATATATTTTT
1 -AAAAATATAATATATATA-TATT
*
915021 AAACATATAATATATATATA
1 AAAAATATAATATATATATA
915041 CTCCAAAACT
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
22 1 0.02
23 28 0.47
24 26 0.44
25 4 0.07
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAAATATAATATATATATATT
Found at i:915015 original size:2 final size:2
Alignment explanation
Indices: 914955--914995 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
914945 TTTCCAAAAT
* *
914955 TA TA TA TA TA TA TA TA T- TA -A AA TT 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 TA
914995 T
1 T
914996 TAAAAAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:915016 original size:23 final size:23
Alignment explanation
Indices: 914950--915040 Score: 101
Period size: 24 Copynumber: 3.9 Consensus size: 23
914940 GTATGTTTCC
*
914950 AAAATTATATATATATATATATTA
1 AAAAATATA-ATATATATATATTA
**
914974 AAATTTATATATATATATATATTA
1 AAAAATATA-ATATATATATATTA
* * *
914998 AAAAATATAACATATATATTTTT
1 AAAAATATAATATATATATATTA
*
915021 AAACATATAATATATATATA
1 AAAAATATAATATATATATA
915041 CTCCAAAACT
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
23 28 0.48
24 30 0.52
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
AAAAATATAATATATATATATTA
Found at i:915106 original size:18 final size:18
Alignment explanation
Indices: 915083--915126 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
915073 TATATACACC
* *
915083 ATAATAATTCATATTTAT
1 ATAATAATACATAATTAT
915101 ATAAT-ATACATAATTAT
1 ATAATAATACATAATTAT
*
915118 ATTATAATA
1 ATAATAATA
915127 TTAAAATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATAATACATAATTAT
Found at i:919682 original size:2 final size:2
Alignment explanation
Indices: 919675--919703 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
919665 TCAATCTACA
919675 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
919704 AATTTACGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:919882 original size:13 final size:13
Alignment explanation
Indices: 919861--919915 Score: 74
Period size: 13 Copynumber: 4.2 Consensus size: 13
919851 AATGACACAC
*
919861 AATGAGCGTCATA
1 AATGCGCGTCATA
919874 AATGCGCGTCATA
1 AATGCGCGTCATA
* *
919887 AATGTGTGTCATA
1 AATGCGCGTCATA
*
919900 AATGCGCGTTATA
1 AATGCGCGTCATA
919913 AAT
1 AAT
919916 TTATGACGCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:919890 original size:26 final size:26
Alignment explanation
Indices: 919861--919915 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
919851 AATGACACAC
919861 AATGAGCGTCATAAATGCGCGTCATA
1 AATGAGCGTCATAAATGCGCGTCATA
* * *
919887 AATGTGTGTCATAAATGCGCGTTATA
1 AATGAGCGTCATAAATGCGCGTCATA
919913 AAT
1 AAT
919916 TTATGACGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (26 bp):
AATGAGCGTCATAAATGCGCGTCATA
Found at i:921104 original size:15 final size:15
Alignment explanation
Indices: 921086--921115 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
921076 AAATAAGAAT
921086 TAAAAAGAATCATTA
1 TAAAAAGAATCATTA
*
921101 TAAAAAGAATTATTA
1 TAAAAAGAATCATTA
921116 GTCTAGGGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (15 bp):
TAAAAAGAATCATTA
Found at i:921919 original size:18 final size:18
Alignment explanation
Indices: 921881--921918 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
921871 ATAATATGAC
921881 AAATAAACAAATAAACTA
1 AAATAAACAAATAAACTA
921899 AAAT-AACAAGATAAA-TA
1 AAATAAACAA-ATAAACTA
921916 AAA
1 AAA
921919 ACACCAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.74, C:0.08, G:0.03, T:0.16
Consensus pattern (18 bp):
AAATAAACAAATAAACTA
Found at i:928365 original size:13 final size:13
Alignment explanation
Indices: 928347--928385 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
928337 TGTATTAAGT
928347 GATGATACTCTTG
1 GATGATACTCTTG
928360 GATGATACTCTTG
1 GATGATACTCTTG
928373 GATGATACT-TTG
1 GATGATACTCTTG
928385 G
1 G
928386 CAACACCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 4 0.15
13 22 0.85
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (13 bp):
GATGATACTCTTG
Found at i:929717 original size:25 final size:24
Alignment explanation
Indices: 929661--929775 Score: 112
Period size: 23 Copynumber: 4.9 Consensus size: 24
929651 CACCGAAGTT
*
929661 CCACATAG-ATTTGTACCGAAGGA
1 CCACATAGAATTTGTCCCGAAGGA
* * * *
929684 TCGCGTAGAAATTTGTCCTGAAGGA
1 CCACATAG-AATTTGTCCCGAAGGA
*
929709 CCACATAGAATTT-TCCCCAAGGA
1 CCACATAGAATTTGTCCCGAAGGA
*
929732 CCACATAGAA-TTGTCCCGAATGA
1 CCACATAGAATTTGTCCCGAAGGA
* *
929755 CCACATAG-TTTTGTTCCGAAG
1 CCACATAGAATTTGTCCCGAAG
929776 AAGACTTGAA
Statistics
Matches: 73, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
22 2 0.03
23 48 0.66
24 5 0.07
25 18 0.25
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.25
Consensus pattern (24 bp):
CCACATAGAATTTGTCCCGAAGGA
Found at i:936151 original size:2 final size:2
Alignment explanation
Indices: 936144--936180 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
936134 TGTTATACGG
*
936144 AT AT AT AT AT AT AT AT AT AT AT AT GAT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
936181 GGATTGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:941409 original size:184 final size:185
Alignment explanation
Indices: 941100--941474 Score: 603
Period size: 184 Copynumber: 2.0 Consensus size: 185
941090 ATAAAAATTA
941100 AATA-TTTGTAATTAAAAAAACAGTTTCTAATTAATTTAAATAATATATAATTATAAAATAAAAA
1 AATATTTTGTAATTAAAAAAACAGTTTCTAATTAATTTAAATAATATATAATTATAAAATAAAAA
*
941164 TTTTATATAAATTTTTTAATTAATTAATATTGATTAAGGTTTAAAAGCTATTAGATCTTAAATTA
66 TTTTATATAAAATTTTTAATTAATTAATATTGATTAAGGTTTAAAAGCTATTAGATCTTAAATTA
941229 TTAATTAAGTTTTAAATAGTTTGGGCTGAGCTCATATGTTATATATAATATATAT
131 TTAATTAAGTTTTAAATAGTTTGGGCTGAGCTCATATGTTATATATAATATATAT
*
941284 AATATTTTTTAATT-AAAAAACAGTTTAC-AATTAATTTAAATAATATATAATTATAAAATAAAA
1 AATATTTTGTAATTAAAAAAACAGTTT-CTAATTAATTTAAATAATATATAATTATAAAATAAAA
* * * * *
941347 ATTTTATATAAAATTTTTAATTATTTTATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATT
65 ATTTTATATAAAATTTTTAATTAATTAATATTGATTAAGGTTTAAAAGCTATTAGATCTTAAATT
** * * *
941412 ATTAATTGGGTTTTAAATGGTTTGGGTTGAGCTCATATGTTATATATAATATATTT
130 ATTAATTAAGTTTTAAATAGTTTGGGCTGAGCTCATATGTTATATATAATATATAT
*
941468 AAAATTT
1 AATATTT
941475 AATTTCGGTT
Statistics
Matches: 176, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
184 167 0.95
185 9 0.05
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (185 bp):
AATATTTTGTAATTAAAAAAACAGTTTCTAATTAATTTAAATAATATATAATTATAAAATAAAAA
TTTTATATAAAATTTTTAATTAATTAATATTGATTAAGGTTTAAAAGCTATTAGATCTTAAATTA
TTAATTAAGTTTTAAATAGTTTGGGCTGAGCTCATATGTTATATATAATATATAT
Found at i:942006 original size:2 final size:2
Alignment explanation
Indices: 942001--942039 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
941991 TCTTGTGTGA
942001 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
942040 CCTAAGTTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:942092 original size:2 final size:2
Alignment explanation
Indices: 942085--942113 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
942075 TTAGACTCAG
942085 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
942114 CTTTAGTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:943334 original size:3 final size:3
Alignment explanation
Indices: 943326--943356 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
943316 TTTTCCCATT
943326 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
943357 TTTAAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:943346 original size:14 final size:14
Alignment explanation
Indices: 943327--943355 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
943317 TTTCCCATTT
943327 TATTATTATTATTA
1 TATTATTATTATTA
943341 TATTATTATTATTA
1 TATTATTATTATTA
943355 T
1 T
943356 TTTTAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:943472 original size:15 final size:16
Alignment explanation
Indices: 943452--943481 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
943442 TACCTGATCC
943452 AAGCCCAA-ACCCGAG
1 AAGCCCAAGACCCGAG
943467 AAGCCCAAGACCCGA
1 AAGCCCAAGACCCGA
943482 AAACCCTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.40, G:0.20, T:0.00
Consensus pattern (16 bp):
AAGCCCAAGACCCGAG
Found at i:948997 original size:28 final size:29
Alignment explanation
Indices: 948954--949020 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 29
948944 ATATTAATAA
948954 AATAT-TTATAACTAATATTAAAATAATT
1 AATATATTATAACTAATATTAAAATAATT
* *
948982 -ATATATTATAATTAATATTAATATAATT
1 AATATATTATAACTAATATTAAAATAATT
*
949010 AATATAATATA
1 AATATATTATA
949021 GTTTATAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 4 0.12
28 21 0.62
29 9 0.26
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (29 bp):
AATATATTATAACTAATATTAAAATAATT
Found at i:949013 original size:43 final size:43
Alignment explanation
Indices: 948960--949050 Score: 105
Period size: 43 Copynumber: 2.1 Consensus size: 43
948950 ATAAAATATT
*
948960 TATAACTAATATTAAAATAA-TTAT-ATATTATAATTAATATTAA
1 TATAACTAATA-TAAAATAATTTATAAT-TTATAATTAAAATTAA
* * * *
949003 TATAATTAATATAATATAGTTTATAATTTGTAATTAAAATTAA
1 TATAACTAATATAAAATAATTTATAATTTATAATTAAAATTAA
949046 TATAA
1 TATAA
949051 AATATAGTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
42 6 0.15
43 33 0.80
44 2 0.05
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (43 bp):
TATAACTAATATAAAATAATTTATAATTTATAATTAAAATTAA
Found at i:949056 original size:29 final size:30
Alignment explanation
Indices: 949024--949097 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 30
949014 TAATATAGTT
*
949024 TATAATTTGT-AATTAAAATTAATATAAAA
1 TATAATTTATAAATTAAAATTAATATAAAA
* * *
949053 TATAGTTTATAAAATTAATATTAATATAAAC
1 TATAATTTAT-AAATTAAAATTAATATAAAA
949084 TAT-ATGTTATAAAT
1 TATAAT-TTATAAAT
949098 ATATAGTATA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
29 8 0.22
30 5 0.14
31 24 0.65
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (30 bp):
TATAATTTATAAATTAAAATTAATATAAAA
Found at i:949076 original size:31 final size:31
Alignment explanation
Indices: 949034--949217 Score: 144
Period size: 31 Copynumber: 5.7 Consensus size: 31
949024 TATAATTTGT
* *
949034 AATTAAAATTAATATAAAATATAGTTTATAA
1 AATTAATATTAATATAAATTATAGTTTATAA
*
949065 AATTAATATTAATATAAACTATA-TGTTATAA
1 AATTAATATTAATATAAATTATAGT-TTATAA
* *
949096 ATATATAGTATAGTT--TATAAATTATAGTTAATAT
1 A-AT-TA--ATA-TTAATATAAATTATAGTTTATAA
*
949130 AATTAATATTAATAT--AGTATAGTTTATAA
1 AATTAATATTAATATAAATTATAGTTTATAA
* * *
949159 ACTATATACTATATTAATATAAATTATAGTTAAGAT
1 A--AT-TA--ATATTAATATAAATTATAGTTTATAA
*
949195 AATTAACATTAATATAAATTATA
1 AATTAATATTAATATAAATTATA
949218 TAGTACATTA
Statistics
Matches: 124, Mismatches: 13, Indels: 32
0.73 0.08 0.19
Matches are distributed among these distances:
29 14 0.11
30 4 0.03
31 50 0.40
32 6 0.05
33 6 0.05
34 27 0.22
35 4 0.03
36 13 0.10
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (31 bp):
AATTAATATTAATATAAATTATAGTTTATAA
Found at i:949076 original size:65 final size:65
Alignment explanation
Indices: 948939--949211 Score: 228
Period size: 65 Copynumber: 4.3 Consensus size: 65
948929 ATCCGTATAA
* * * * *
948939 AATTTATATTAATA-AA-ATA-TTTATAACTA-ATATTAAAA-TAATTATATATTATAATTAATA
1 AATTAATATTAATATAATATAGTTTATAAATATATACTAAAATTAA-TATAAATTATAGTTAATA
948999 TT
65 -T
* * * * *
949001 AA-T-ATAATTAATATAATATAGTTTAT-AATTTGTAATTAAAATTAATATAAAATATAGTTTAT
1 AATTAAT-ATTAATATAATATAGTTTATAAATATAT-ACTAAAATTAATATAAATTATAGTTAAT
*
949063 AA
64 AT
* * *
949065 AATTAATATTAATATAAACTATA-TGTTATAAATATATAGTATAGTT--TATAAATTATAGTTAA
1 AATTAATATTAATAT-AA-TATAGT-TTATAAATATATACTAAAATTAATATAAATTATAGTTAA
949127 TAT
63 TAT
* * *
949130 AATTAATATTAATATAGTATAGTTTATAAACTATATACT-ATATTAATATAAATTATAGTTAAGA
1 AATTAATATTAATATAATATAGTTTATAAA-TATATACTAAAATTAATATAAATTATAGTTAATA
949194 T
65 T
*
949195 AATTAACATTAATATAA
1 AATTAATATTAATATAA
949212 ATTATATAGT
Statistics
Matches: 170, Mismatches: 24, Indels: 31
0.76 0.11 0.14
Matches are distributed among these distances:
60 2 0.01
61 8 0.05
62 4 0.02
63 18 0.11
64 17 0.10
65 94 0.55
66 8 0.05
67 14 0.08
68 5 0.03
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (65 bp):
AATTAATATTAATATAATATAGTTTATAAATATATACTAAAATTAATATAAATTATAGTTAATAT
Found at i:949107 original size:20 final size:19
Alignment explanation
Indices: 949090--949188 Score: 60
Period size: 20 Copynumber: 4.7 Consensus size: 19
949080 AAACTATATG
949090 TTATAAATATATAGTATAGT
1 TTATAAAT-TATAGTATAGT
949110 TTATAAATTATAGTTAATA-T
1 TTATAAATTATAG-T-ATAGT
949130 AATTAATATTAA-TATAGTATAGT
1 --TT-ATA--AATTATAGTATAGT
*
949153 TTATAAACTATATACTATA-T
1 TTATAAA-T-TATAGTATAGT
949173 TAATATAAATTATAGT
1 T--TATAAATTATAGT
949189 TAAGATAATT
Statistics
Matches: 64, Mismatches: 2, Indels: 26
0.70 0.02 0.28
Matches are distributed among these distances:
18 2 0.03
19 5 0.08
20 20 0.31
21 14 0.22
22 11 0.17
23 5 0.08
24 5 0.08
25 2 0.03
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.45
Consensus pattern (19 bp):
TTATAAATTATAGTATAGT
Found at i:949147 original size:43 final size:40
Alignment explanation
Indices: 949098--949188 Score: 119
Period size: 43 Copynumber: 2.2 Consensus size: 40
949088 TGTTATAAAT
* *
949098 ATATAGTATAGTTTATAAATTATAGTTAATATAATTAATATTA
1 ATATAGTATAGTTTATAAACTATA--TAATAT-ATTAATATAA
*
949141 ATATAGTATAGTTTATAAACTATATACTATATTAATATAA
1 ATATAGTATAGTTTATAAACTATATAATATATTAATATAA
949181 ATTATAGT
1 A-TATAGT
949189 TAAGATAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 10 0.23
41 11 0.25
43 23 0.52
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (40 bp):
ATATAGTATAGTTTATAAACTATATAATATATTAATATAA
Found at i:949152 original size:29 final size:29
Alignment explanation
Indices: 949118--949210 Score: 78
Period size: 29 Copynumber: 3.0 Consensus size: 29
949108 GTTTATAAAT
949118 TATAGTTAATATAATTAATATTAATATAG
1 TATAGTTAATATAATTAATATTAATATAG
* * *
949147 TATAGTTTATAAACTATATACTATATTAATATAAAT
1 TATAGTTAATATA--AT-TA--ATATTAATAT--AG
* *
949183 TATAGTTAAGATAATTAACATTAATATA
1 TATAGTTAATATAATTAATATTAATATA
949211 AATTATATAG
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
29 12 0.24
31 11 0.22
32 2 0.04
33 2 0.04
34 12 0.24
36 11 0.22
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (29 bp):
TATAGTTAATATAATTAATATTAATATAG
Found at i:949175 original size:130 final size:132
Alignment explanation
Indices: 948980--949252 Score: 315
Period size: 130 Copynumber: 2.1 Consensus size: 132
948970 ATTAAAATAA
* ** * *
948980 TTATATATTATAATTAATATTAATATAATTAATATAATATAGTTTATAATTTGTAATTAAAATTA
1 TTATAAATTATAATTAATATTAATATAATTAATATAATATAGTTTATAAACTATAACTAAAATTA
* * * * * *
949045 ATATAAAATATAGTTTATAAAATTAATATTAATATAAACTATAT-GT-TATAAATATATAGTATA
66 ATATAAAATATAGTTAAGAAAATTAACATTAATATAAACTATATAGTACATAAATATAAACTATA
949108 GT
131 GT
* * *
949110 TTATAAATTATAGTTAATA-TAAT-TAATATTAATATAGTATAGTTTATAAACTATATACT-ATA
1 TTATAAATTATAATTAATATTAATAT-A-ATTAATATAATATAGTTTATAAACTATA-ACTAAAA
* * * *
949172 TTAATATAAATTATAGTTAAGATAATTAACATTAATATAAATTATATAGTACATTAATATAAACT
63 TTAATATAAAATATAGTTAAGAAAATTAACATTAATATAAACTATATAGTACATAAATATAAACT
949237 ATAGT
128 ATAGT
949242 TTAT-AATTATA
1 TTATAAATTATA
949253 TACTATAGGT
Statistics
Matches: 120, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
128 1 0.01
129 5 0.04
130 84 0.70
131 11 0.09
132 19 0.16
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (132 bp):
TTATAAATTATAATTAATATTAATATAATTAATATAATATAGTTTATAAACTATAACTAAAATTA
ATATAAAATATAGTTAAGAAAATTAACATTAATATAAACTATATAGTACATAAATATAAACTATA
GT
Found at i:949342 original size:18 final size:19
Alignment explanation
Indices: 949320--949639 Score: 152
Period size: 18 Copynumber: 17.4 Consensus size: 19
949310 AACTATAGGT
949320 TACATATATAGTTTATATA
1 TACATATATAGTTTATATA
949339 -ACATATAAATAGATTGTATATA
1 TACATAT--ATAG-TT-TATATA
**
949361 TACATATACTA---TAGGT-
1 TACATATA-TAGTTTATATA
*
949377 TATATATATAGTTTATATA
1 TACATATATAGTTTATATA
***
949396 TACATATACTA-TAGGT-TA
1 TACATATA-TAGTTTATATA
*
949414 TATATATATAGTTTATATA
1 TACATATATAGTTTATATA
* *
949433 TATTATACATAGTTTATATA
1 TA-CATATATAGTTTATATA
* * *
949453 TACTACACATAGTTTATACA
1 TAC-ATATATAGTTTATATA
*
949473 TACATGTACTATATAGTTTACATA
1 TAC----A-TATATAGTTTATATA
*
949497 TAC-TATATAG--TCTATA
1 TACATATATAGTTTATATA
*
949513 TAC-TATATAGGTTATATA
1 TACATATATAGTTTATATA
*
949531 TAC-TA-AT-G--AACTATA
1 TACATATATAGTTTA-TATA
*
949546 TA-ATATATAGTTTACATA
1 TACATATATAGTTTATATA
949564 TAC-TATATAGTTTATATA
1 TACATATATAGTTTATATA
*
949582 TAC-TA-AT-G--AACTATA
1 TACATATATAGTTTA-TATA
949597 TA-ATATATAGTTTATATA
1 TACATATATAGTTTATATA
*
949615 TA-TTATATAGTTTATATA
1 TACATATATAGTTTATATA
949633 TA-ATATA
1 TACATATA
949640 GTATAAATTA
Statistics
Matches: 235, Mismatches: 32, Indels: 69
0.70 0.10 0.21
Matches are distributed among these distances:
14 2 0.01
15 18 0.08
16 27 0.11
17 11 0.05
18 88 0.37
19 15 0.06
20 41 0.17
21 3 0.01
22 8 0.03
23 8 0.03
24 14 0.06
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (19 bp):
TACATATATAGTTTATATA
Found at i:949350 original size:20 final size:22
Alignment explanation
Indices: 949327--949384 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
949317 GGTTACATAT
949327 ATAGTTTATATA-ACATATA-A
1 ATAGTTTATATATACATATACA
*
949347 ATAGATTGTATATATACATATACT
1 ATAG-TT-TATATATACATATACA
*
949371 ATAGGTTATATATA
1 ATAGTTTATATATA
949385 TAGTTTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 4 0.12
21 2 0.06
22 14 0.44
23 8 0.25
24 4 0.12
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (22 bp):
ATAGTTTATATATACATATACA
Found at i:949362 original size:2 final size:2
Alignment explanation
Indices: 949355--949684 Score: 51
Period size: 2 Copynumber: 159.0 Consensus size: 2
949345 AAATAGATTG
* ** *
949355 TA TA TA TA CA TA TA CTA TA GG T- TA TA TA TA TA GTT 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 TA
* ** *
949398 CA TA TA CTA TA GG T- TA TA TA TA TA TA GTT TA TA TA TA T- TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * * * * * * *
949440 CA TA GTT TA TA TA TA CTA CA CA TA GTT TA TA CA TA CA TG TA CTA
1 TA TA -TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA -TA
* * * **
949484 TA TA GTT TA CA TA TA CTA TA TA GTC TA TA TA CTA TA TA GG T- TA
1 TA TA -TA TA TA TA TA -TA TA TA -TA TA TA TA -TA TA TA TA TA TA
* *
949527 TA TA TA CTA -A TGA -A CTA TA TA -A TA TA TA GTT TA CA TA TA CTA
1 TA TA TA -TA TA T-A TA -TA TA TA TA TA TA TA -TA TA TA TA TA -TA
* *
949569 TA TA GTT TA TA TA TA CTA -A TGA -A CTA TA TA -A TA TA TA GTT TA
1 TA TA -TA TA TA TA TA -TA TA T-A TA -TA TA TA TA TA TA TA -TA TA
* *
949611 TA TA TA T- TA TA TA GTT TA TA TA TA -A TA TA GTA TA AA T- TA T-
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* *
949651 TT TA TA TA GTA TA TA AA TA TCA -A CTA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA T-A TA -TA TA TA TA TA
949685 GTTCATTTGT
Statistics
Matches: 234, Mismatches: 52, Indels: 84
0.63 0.14 0.23
Matches are distributed among these distances:
1 15 0.06
2 181 0.77
3 38 0.16
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (2 bp):
TA
Found at i:949372 original size:57 final size:59
Alignment explanation
Indices: 949311--949421 Score: 172
Period size: 57 Copynumber: 1.9 Consensus size: 59
949301 TTGTTTATAA
*
949311 ACTATAGGTTACATATATAGTTTATATA-ACATATA-AATAGATTGTATATATACATAT
1 ACTATAGGTTACATATATAGTTTATATATACATATACAATAGATTATATATATACATAT
* * *
949368 ACTATAGGTTATATATATAGTTTATATATACATATACTATAGGTTATATATATA
1 ACTATAGGTTACATATATAGTTTATATATACATATACAATAGATTATATATATA
949422 TAGTTTATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
57 27 0.56
58 7 0.15
59 14 0.29
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.42
Consensus pattern (59 bp):
ACTATAGGTTACATATATAGTTTATATATACATATACAATAGATTATATATATACATAT
Found at i:949374 original size:24 final size:21
Alignment explanation
Indices: 949323--949505 Score: 72
Period size: 24 Copynumber: 8.2 Consensus size: 21
949313 TATAGGTTAC
949323 ATATATAGTTTATATA-ACAT
1 ATATATAGTTTATATATACAT
*
949343 ATAAATAGATTGTATATATACAT
1 ATATATAG-TT-TATATATACAT
**
949366 ATACTATAGGTTATATATATAGTTT
1 ATA-TATA-GTT-TATATATA-CAT
** *
949391 ATATATA-CATATACTATAGGTTAT
1 ATATATAGTTTATA-TATA---CAT
*
949415 ATATATA-TAGTT-TATATATATT
1 ATATATAGT--TTATATATACA-T
*
949437 ATACATAGTTTATATATAC-T
1 ATATATAGTTTATATATACAT
* * *
949457 ACACATAGTTTATACATACATGT
1 ATATATAGTTTATATATACA--T
*
949480 ACTATATAGTTTACATATAC-T
1 A-TATATAGTTTATATATACAT
949501 ATATA
1 ATATA
949506 GTCTATATAC
Statistics
Matches: 126, Mismatches: 19, Indels: 36
0.70 0.10 0.20
Matches are distributed among these distances:
20 29 0.23
21 12 0.10
22 23 0.18
23 10 0.08
24 44 0.35
25 7 0.06
26 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.44
Consensus pattern (21 bp):
ATATATAGTTTATATATACAT
Found at i:949396 original size:37 final size:35
Alignment explanation
Indices: 949341--949454 Score: 151
Period size: 37 Copynumber: 3.2 Consensus size: 35
949331 TTTATATAAC
*
949341 ATATAAATAGATTGTATATATACATATACTATAGGTT
1 ATATATATAG-TT-TATATATACATATACTATAGGTT
949378 ATATATATAGTTTATATATACATATACTATAGGTTAT
1 ATATATATAGTTTATATATACATATACTATAGG-T-T
* *
949415 ATATATATAGTTTATATATA-TTATAC-ATAGTTT
1 ATATATATAGTTTATATATACATATACTATAGGTT
949448 ATATATA
1 ATATATA
949455 CTACACATAG
Statistics
Matches: 72, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
33 8 0.11
34 1 0.01
35 25 0.35
36 8 0.11
37 30 0.42
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (35 bp):
ATATATATAGTTTATATATACATATACTATAGGTT
Found at i:949408 original size:22 final size:21
Alignment explanation
Indices: 949378--949419 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
949368 ACTATAGGTT
*
949378 ATATATATAGTTTATATATAC
1 ATATATATAGGTTATATATAC
949399 ATATACTATAGGTTATATATA
1 ATATA-TATAGGTTATATATA
949420 TATAGTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
ATATATATAGGTTATATATAC
Found at i:949430 original size:22 final size:21
Alignment explanation
Indices: 949383--949470 Score: 69
Period size: 20 Copynumber: 4.2 Consensus size: 21
949373 AGGTTATATA
*
949383 TATAGTTTATATATACATA-TAC
1 TATAG-TTATATATACATAGT-T
*
949405 TATAGGTTATATATATATAGTT
1 TATA-GTTATATATACATAGTT
949427 TATA--TATATTATACATAGTT
1 TATAGTTATA-TATACATAGTT
*
949447 TATA--TATACTACACATAGTT
1 TATAGTTATA-TATACATAGTT
949467 TATA
1 TATA
949471 CATACATGTA
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.07
20 32 0.55
22 20 0.34
23 2 0.03
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (21 bp):
TATAGTTATATATACATAGTT
Found at i:949454 original size:15 final size:16
Alignment explanation
Indices: 949399--949439 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
949389 TTATATATAC
949399 ATATACTATAGGTTAT
1 ATATACTATAGGTTAT
*
949415 ATATA-TATAGTTTAT
1 ATATACTATAGGTTAT
*
949430 ATATATTATA
1 ATATACTATA
949440 CATAGTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (16 bp):
ATATACTATAGGTTAT
Found at i:949573 original size:51 final size:50
Alignment explanation
Indices: 949494--949634 Score: 221
Period size: 51 Copynumber: 2.8 Consensus size: 50
949484 TATAGTTTAC
* * *
949494 ATATACTATATAGTCT-ATATACTATATAGGTTATATATACTAATGAACT
1 ATATAATATATAGTTTAATATACTATATAGTTTATATATACTAATGAACT
949543 ATATAATATATAGTTTACATATACTATATAGTTTATATATACTAATGAACT
1 ATATAATATATAGTTTA-ATATACTATATAGTTTATATATACTAATGAACT
*
949594 ATATAATATATAGTTTATATATATTATATAGTTTATATATA
1 ATATAATATATAGTTTA-ATATACTATATAGTTTATATATA
949635 ATATAGTATA
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
49 14 0.16
51 71 0.84
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (50 bp):
ATATAATATATAGTTTAATATACTATATAGTTTATATATACTAATGAACT
Found at i:949612 original size:9 final size:9
Alignment explanation
Indices: 949600--949632 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
949590 AACTATATAA
949600 TATATAGTT
1 TATATAGTT
949609 TATATA-TAT
1 TATATAGT-T
949618 TATATAGTT
1 TATATAGTT
949627 TATATA
1 TATATA
949633 TAATATAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.05
9 20 0.91
10 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (9 bp):
TATATAGTT
Found at i:950063 original size:216 final size:216
Alignment explanation
Indices: 949689--950146 Score: 772
Period size: 216 Copynumber: 2.1 Consensus size: 216
949679 TATATAGTTC
*
949689 ATTTGTAATTTTATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATATGAAATTGACCCAT
1 ATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATATGAAATTGACCCAT
* *
949754 ACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
66 ACTTATTACTTAATTATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
* *
949819 TTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATATGTGTT
131 TTTTGTATTAATATCAACATCACAATTTAAAATTATTTCGATTTGATCCATCATCAATATGTGTT
*
949884 GTTTAATTAATTTAAAATTTT
196 GTCTAATTAATTTAAAATTTT
* * *
949905 ATTTGTAATTTCATATTTGTTCAATTTAGTCCTCTAAATTTTATTTGTATATGAAATTGATCCAT
1 ATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATATGAAATTGACCCAT
* *
949970 ACTTTTTACTTAATTATATTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
66 ACTTATTACTTAATTATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
* *
950035 TTTTGTATTAATATCAGCATCACAATTTAAAATTATTTCGATTTGATCCATCATCAATGTGTGTT
131 TTTTGTATTAATATCAACATCACAATTTAAAATTATTTCGATTTGATCCATCATCAATATGTGTT
* *
950100 GTCTAATTTATTTAAATTTTT
196 GTCTAATTAATTTAAAATTTT
*
950121 ATTTGTGATTTCATATTTGTTCAATT
1 ATTTGTAATTTCATATTTGTTCAATT
950147 GAATTCTTAA
Statistics
Matches: 226, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
216 226 1.00
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.50
Consensus pattern (216 bp):
ATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATATGAAATTGACCCAT
ACTTATTACTTAATTATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
TTTTGTATTAATATCAACATCACAATTTAAAATTATTTCGATTTGATCCATCATCAATATGTGTT
GTCTAATTAATTTAAAATTTT
Found at i:951389 original size:31 final size:32
Alignment explanation
Indices: 951352--951444 Score: 134
Period size: 31 Copynumber: 2.8 Consensus size: 32
951342 GATGTTTGAT
951352 TCTTTACAACAGGGCTATTGCCATGGATG-AC
1 TCTTTACAACAGGGCTATTGCCATGGATGTAC
*
951383 TCTTTACAACAGGGCTATTGCCATGGATGTTTTAT
1 TCTTTACAACAGGGCTATTGCCATGGATG---TAC
*
951418 TCTTTATAACAGGGCTATTGCCATGGA
1 TCTTTACAACAGGGCTATTGCCATGGA
951445 CGTTTGATTC
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
31 29 0.52
35 27 0.48
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (32 bp):
TCTTTACAACAGGGCTATTGCCATGGATGTAC
Found at i:951429 original size:35 final size:35
Alignment explanation
Indices: 951339--951460 Score: 171
Period size: 35 Copynumber: 3.6 Consensus size: 35
951329 TACTCAAGCA
951339 ATGGATGTTTGATTCTTTACAACAGGGCTATTGCC
1 ATGGATGTTTGATTCTTTACAACAGGGCTATTGCC
*
951374 ATGGA----TGACTCTTTACAACAGGGCTATTGCC
1 ATGGATGTTTGATTCTTTACAACAGGGCTATTGCC
* *
951405 ATGGATGTTTTATTCTTTATAACAGGGCTATTGCC
1 ATGGATGTTTGATTCTTTACAACAGGGCTATTGCC
* *
951440 ATGGACGTTTGATTCCTTACA
1 ATGGATGTTTGATTCTTTACA
951461 GCTTGTTACA
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
31 30 0.40
35 45 0.60
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (35 bp):
ATGGATGTTTGATTCTTTACAACAGGGCTATTGCC
Found at i:954345 original size:19 final size:18
Alignment explanation
Indices: 954323--954359 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
954313 ATTAGTGTTT
954323 TTTTAAATATATTTTTAAA
1 TTTTAAATA-ATTTTTAAA
*
954342 TTTTTAATAATTTTTAAA
1 TTTTAAATAATTTTTAAA
954360 AAAAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTAAATAATTTTTAAA
Found at i:956508 original size:5 final size:5
Alignment explanation
Indices: 956462--956539 Score: 102
Period size: 5 Copynumber: 14.4 Consensus size: 5
956452 GGATGTCGGT
956462 CGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC CGACC CGACC
1 CGACC -CGACC -CGACC -CGACC -CGACC -CGACC -CGACC CGACC CGACC
956513 CGACC CGACC CGACC CGACC CGACC CG
1 CGACC CGACC CGACC CGACC CGACC CG
956540 GGACGGACGG
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 37 0.51
6 35 0.49
ACGTcount: A:0.26, C:0.55, G:0.19, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:957312 original size:19 final size:20
Alignment explanation
Indices: 957275--957313 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
957265 TGCGATTTTG
957275 GACTATCGCAACGCGAACTTC
1 GACTATCGCAAC-CGAACTTC
957296 GACTATCGCAA-CGAACTT
1 GACTATCGCAACCGAACTT
957314 GAAATAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
21 11 0.61
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.21
Consensus pattern (20 bp):
GACTATCGCAACCGAACTTC
Found at i:957753 original size:23 final size:24
Alignment explanation
Indices: 957696--957753 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
957686 AATTATTTAT
* *
957696 TATATTTTAA-ACTATTAAAATAA
1 TATATTTTAATAGTAATAAAATAA
* *
957719 TATGTTTT-ATAGTAATAAAA-AG
1 TATATTTTAATAGTAATAAAATAA
957741 TATATTTTAATAG
1 TATATTTTAATAG
957754 CATGAACCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.45
Consensus pattern (24 bp):
TATATTTTAATAGTAATAAAATAA
Found at i:958998 original size:48 final size:47
Alignment explanation
Indices: 958946--959039 Score: 136
Period size: 47 Copynumber: 2.0 Consensus size: 47
958936 AGGTTGAATT
958946 AAGAAAATTAACAAATGTTAAAAGAAA-AAAATAAAAATAAAATAAATG
1 AAGAAAA-TAACAAATGTTAAAAGAAATAAAATAAAAAT-AAATAAATG
** *
958994 AAGAAAATATTAAATTTTAAAAGAAATAAAATAAAAATAAATAAAT
1 AAGAAAATAACAAATGTTAAAAGAAATAAAATAAAAATAAATAAAT
959040 AAAAGGGAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
47 24 0.57
48 18 0.43
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.22
Consensus pattern (47 bp):
AAGAAAATAACAAATGTTAAAAGAAATAAAATAAAAATAAATAAATG
Found at i:960371 original size:20 final size:21
Alignment explanation
Indices: 960348--960401 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
960338 TATAATATAA
960348 TAATAAAAAATAAAAAATAT-
1 TAATAAAAAATAAAAAATATG
** * *
960368 TAATGTAATATAAAAACTATG
1 TAATAAAAAATAAAAAATATG
960389 TAATAAAATAATA
1 TAATAAAA-AATA
960402 TGTTTTCAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
20 16 0.64
21 6 0.24
22 3 0.12
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (21 bp):
TAATAAAAAATAAAAAATATG
Found at i:960500 original size:35 final size:35
Alignment explanation
Indices: 960454--960626 Score: 179
Period size: 35 Copynumber: 4.9 Consensus size: 35
960444 AAAAAACCAT
*
960454 TTTTAGAAACTATATTA-TATATGTTTTCAAAACCG
1 TTTTAAAAACTATA-TACTATATGTTTTCAAAACCG
* * **
960489 TTTTAAAAACTATATATTATACGTTTTCAAAACTAT
1 TTTTAAAAACTATATACTATATGTTTTCAAAAC-CG
***
960525 TTTTAAAAAGCTATATACTATAT-TTTTCAAAATTA
1 TTTTAAAAA-CTATATACTATATGTTTTCAAAACCG
* * *
960560 TCTGAAAAACTATATACTACATGTTTTCAAAACCG
1 TTTTAAAAACTATATACTATATGTTTTCAAAACCG
* * *
960595 TTTTAAAAACTATATATTTTACGTTTTCAAAA
1 TTTTAAAAACTATATACTATATGTTTTCAAAA
960627 GTAAGTTTCC
Statistics
Matches: 113, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
34 14 0.12
35 70 0.62
36 18 0.16
37 11 0.10
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (35 bp):
TTTTAAAAACTATATACTATATGTTTTCAAAACCG
Found at i:960552 original size:71 final size:69
Alignment explanation
Indices: 960446--960626 Score: 184
Period size: 71 Copynumber: 2.6 Consensus size: 69
960436 ACGTTTAAAA
* * * * * *
960446 AAAACCATTTTTAGAAACTATATTATATATGTTTTCAAAACCGTTTTAAAAACTATATATTATAC
1 AAAA-CATTTTTAAAAACTATA-TATATATGTTTTCAAAACCATCTGAAAAACTATATACTACAC
960511 GTTTTC
64 GTTTTC
**
960517 AAAACTATTTTTAAAAAGCTATATACTATAT-TTTTCAAAATTATCTGAAAAACTATATACTACA
1 AAAAC-ATTTTTAAAAA-CTATATA-TATATGTTTTCAAAACCATCTGAAAAACTATATACTACA
*
960581 TGTTTTC
63 CGTTTTC
** * *
960588 AAAACCGTTTTAAAAACTATATATTTTACGTTTTCAAAA
1 AAAACATTTTTAAAAACTATATA-TATATGTTTTCAAAA
960627 GTAAGTTTCC
Statistics
Matches: 92, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
69 10 0.11
70 19 0.21
71 53 0.58
72 10 0.11
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.41
Consensus pattern (69 bp):
AAAACATTTTTAAAAACTATATATATATGTTTTCAAAACCATCTGAAAAACTATATACTACACGT
TTTC
Found at i:960691 original size:2 final size:2
Alignment explanation
Indices: 960684--960718 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
960674 GAAATTACTT
960684 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
960719 TAAAATAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:969122 original size:4 final size:4
Alignment explanation
Indices: 969113--969333 Score: 75
Period size: 4 Copynumber: 52.2 Consensus size: 4
969103 AATGTAATGA
* *
969113 AAAT AAAT AAAAT AAAA AAAT AAAT GAAAT AAAT AAGAT AAAAT AAAG
1 AAAT AAAT -AAAT AAAT AAAT AAAT -AAAT AAAT AA-AT -AAAT AAAT
* *
969161 AAA- ATAA- AAAT AAAAT AAAGAT AAAT AAA- GAGT AAAT AAAAT AAAT
1 AAAT A-AAT AAAT -AAAT -AA-AT AAAT AAAT AAAT AAAT -AAAT AAAT
* *
969207 -AAT AAAGAT AAAG AGAAT AAA- AAA- AATAA AAAT AAAT ATAAT -AAT
1 AAAT -AA-AT AAAT A-AAT AAAT AAAT AA-AT AAAT AAAT A-AAT AAAT
* * * *
969252 AAAG ATAT AAA- AAAT ACTAAT AATAT ACAT ATAAT AAAT AAAT AAAA
1 AAAT AAAT AAAT AAAT A--AAT AA-AT AAAT A-AAT AAAT AAAT AAAT
*
969299 AGGAAT AAAGT -AA- AAAT AAAG AAAT AAAAT AAAT A
1 A--AAT AAA-T AAAT AAAT AAAT AAAT -AAAT AAAT A
969334 TAAAGGAGAT
Statistics
Matches: 168, Mismatches: 20, Indels: 58
0.68 0.08 0.24
Matches are distributed among these distances:
3 20 0.12
4 88 0.52
5 47 0.28
6 13 0.08
ACGTcount: A:0.72, C:0.01, G:0.06, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:969126 original size:9 final size:9
Alignment explanation
Indices: 969112--969337 Score: 119
Period size: 9 Copynumber: 23.9 Consensus size: 9
969102 AAATGTAATG
969112 AAAATAAAT
1 AAAATAAAT
969121 AAAATAAA-
1 AAAATAAAT
969129 AAAATAAAT
1 AAAATAAAT
*
969138 GAAATAAAT
1 AAAATAAAT
*
969147 AAGATAAAAT
1 AAAAT-AAAT
969157 AAAGA-AAAT
1 AAA-ATAAAT
969166 AAAAATAAAAT
1 -AAAAT-AAAT
969177 AAAGATAAAT
1 AAA-ATAAAT
969187 AAAGAGTAAAT
1 AAA-A-TAAAT
969198 AAAATAAAT
1 AAAATAAAT
*
969207 AATAA-AGAT
1 AA-AATAAAT
*
969216 AAAGA-GAAT
1 AAA-ATAAAT
*
969225 AAAAAAAAT
1 AAAATAAAT
969234 AAAAATAAAT
1 -AAAATAAAT
*
969244 ATAAT-AAT
1 AAAATAAAT
969252 AAAGATATAA-
1 AAA-ATA-AAT
969262 AAAATACTAAT
1 AAAATA--AAT
* *
969273 AATATACAT
1 AAAATAAAT
*
969282 ATAATAAAT
1 AAAATAAAT
969291 -AAATAAA-
1 AAAATAAAT
969298 AAGGAATAAAGT
1 AA--AATAAA-T
969310 AAAAATAAA-
1 -AAAATAAAT
*
969319 GAAATAAAAT
1 AAAAT-AAAT
969329 AAATATAAA
1 AAA-ATAAA
969338 GGAGATAAAA
Statistics
Matches: 172, Mismatches: 19, Indels: 51
0.71 0.08 0.21
Matches are distributed among these distances:
8 26 0.15
9 65 0.38
10 49 0.28
11 30 0.17
13 2 0.01
ACGTcount: A:0.73, C:0.01, G:0.06, T:0.20
Consensus pattern (9 bp):
AAAATAAAT
Found at i:969172 original size:6 final size:6
Alignment explanation
Indices: 969161--969264 Score: 54
Period size: 6 Copynumber: 16.7 Consensus size: 6
969151 TAAAATAAAG
*
969161 AAAATA AAAAT- AAAATA AAGATA AATAA-A GAGTAAAT- AAAATA AATAATA
1 AAAATA AAAATA AAAATA AAAATA AA-AATA -A--AAATA AAAATA AA-AATA
* * * * *
969211 AAGATA AAGAGA ATAAA-A AAAATA AAAATA AATATA ATAATA AAGATATA
1 AAAATA AAAATA A-AAATA AAAATA AAAATA AAAATA AAAATA AA-A-ATA
969261 AAAA
1 AAAA
969265 ATACTAATAA
Statistics
Matches: 77, Mismatches: 9, Indels: 24
0.70 0.08 0.22
Matches are distributed among these distances:
5 12 0.16
6 44 0.57
7 13 0.17
8 7 0.09
9 1 0.01
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:969175 original size:11 final size:11
Alignment explanation
Indices: 969117--969408 Score: 70
Period size: 11 Copynumber: 25.6 Consensus size: 11
969107 TAATGAAAAT
969117 AAATAAAATAA
1 AAATAAAATAA
* *
969128 AAAAATAAAT-G
1 AAATA-AAATAA
969139 AAAT-AAAT-A
1 AAATAAAATAA
*
969148 AGATAAAAT--
1 AAATAAAATAA
*
969157 AAAGAAAATAA
1 AAATAAAATAA
969168 AAATAAAATAA
1 AAATAAAATAA
*
969179 AGAT-AAATAA
1 AAATAAAATAA
*
969189 AGAGT-AAAT-A
1 A-AATAAAATAA
969199 AAATAAATAATAA
1 AAAT-AA-AATAA
* *
969212 AGATAAAGAGAA
1 AAATAAA-ATAA
*
969224 TAAAAAAAATAA
1 -AAATAAAATAA
969236 AAATAAATATAA
1 AAATAAA-ATAA
*
969248 TAATAAAGATATA
1 AAATAAA-ATA-A
*
969261 AAA-AATACTAA
1 AAATAA-AATAA
*
969272 TAATATACATATAA
1 -AA-ATA-AAATAA
*
969286 TAAATAAATAAAA
1 -AAATAAA-ATAA
*
969299 AGGAATAAAGTAA
1 A--AATAAAATAA
*
969312 AAATAAAGAAATA
1 AAATAAA-ATA-A
969325 AAATAAATATAA
1 AAATAAA-ATAA
* * *
969337 AGGAGATAA-AA
1 A-AATAAAATAA
**
969348 AAATAAGGTAA
1 AAATAAAATAA
*
969359 AAATAAAA-AG
1 AAATAAAATAA
*
969369 GAATAAAA-ATA
1 AAATAAAATA-A
*
969380 AAAT-AAAGAA
1 AAATAAAATAA
*
969390 AAAGAAAATAAA
1 AAATAAAAT-AA
969402 AAATAAA
1 AAATAAA
969409 GAATATATAT
Statistics
Matches: 203, Mismatches: 49, Indels: 57
0.66 0.16 0.18
Matches are distributed among these distances:
9 16 0.08
10 31 0.15
11 58 0.29
12 48 0.24
13 36 0.18
14 13 0.06
15 1 0.00
ACGTcount: A:0.73, C:0.01, G:0.08, T:0.18
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:969241 original size:42 final size:42
Alignment explanation
Indices: 969194--969338 Score: 115
Period size: 42 Copynumber: 3.5 Consensus size: 42
969184 AATAAAGAGT
969194 AAATAAAATAAATAATAAAGATAAAGAGAATAAAAAAAATAA
1 AAATAAAATAAATAATAAAGATAAAGAGAATAAAAAAAATAA
* ** * *
969236 AAAT-AAATATAATAATAAAGATATAA-AAAATACTAATAATAT
1 AAATAAAATA-AATAATAAAGATA-AAGAGAATAAAAAAAATAA
* * *
969278 ACATATAATAAATAA-ATA-A-AAAG-GAATAAAGTAAAAATAAA
1 AAATAAAATAAATAATAAAGATAAAGAGAATAAA--AAAAAT-AA
969319 GAAATAAAATAAAT-ATAAAG
1 -AAATAAAATAAATAATAAAG
969339 GAGATAAAAA
Statistics
Matches: 77, Mismatches: 16, Indels: 19
0.69 0.14 0.17
Matches are distributed among these distances:
38 6 0.08
39 1 0.01
40 6 0.08
41 9 0.12
42 49 0.64
43 6 0.08
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.21
Consensus pattern (42 bp):
AAATAAAATAAATAATAAAGATAAAGAGAATAAAAAAAATAA
Found at i:969264 original size:33 final size:32
Alignment explanation
Indices: 969118--969299 Score: 92
Period size: 35 Copynumber: 5.5 Consensus size: 32
969108 AATGAAAATA
969118 AATAAAATA-AAAAAAT--AAATGAAATA-AAT
1 AATAAAATATAAAAAATAAAAAT-AAATATAAT
*
969147 AAGATAAAATA-AAGAAAATAAAAATAAAATAAAGAT
1 -A-ATAAAATATAA-AAAATAAAAAT-AAATATA-AT
*
969183 AAATAAAGAGTA-AATAAAATAAATAATAAAGAT-A-
1 -AATAAA-A-TATAA-AAAATAAA-AATAAATATAAT
* * *
969217 AAGAGAATAAAAAAAATAAAAATAAATATAAT
1 AATAAAATATAAAAAATAAAAATAAATATAAT
** *
969249 AATAAAGATATAAAAAATACTAATAATATACATAT
1 AATAAA-ATATAAAAAATAAAAATAA-ATATA-AT
*
969284 AATAAATAAATAAAAA
1 AATAAA-ATATAAAAA
969300 GGAATAAAGT
Statistics
Matches: 122, Mismatches: 15, Indels: 25
0.75 0.09 0.15
Matches are distributed among these distances:
30 9 0.07
31 21 0.17
32 12 0.10
33 20 0.16
34 13 0.11
35 23 0.19
36 5 0.04
37 16 0.13
38 3 0.02
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.21
Consensus pattern (32 bp):
AATAAAATATAAAAAATAAAAATAAATATAAT
Found at i:969312 original size:19 final size:18
Alignment explanation
Indices: 969284--969353 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 18
969274 ATATACATAT
969284 AATAAATAAATAAAAAGG
1 AATAAATAAATAAAAAGG
*
969302 AATAAAGTAAA-AATAAAGA
1 AATAAA-TAAATAA-AAAGG
*
969321 AATAAAATAAATATAAAGG
1 AAT-AAATAAATAAAAAGG
*
969340 AGATAAAAAAATAA
1 A-ATAAATAAATAA
969354 GGTAAAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
18 8 0.19
19 28 0.67
20 6 0.14
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (18 bp):
AATAAATAAATAAAAAGG
Found at i:969345 original size:28 final size:26
Alignment explanation
Indices: 969313--969408 Score: 88
Period size: 27 Copynumber: 3.5 Consensus size: 26
969303 ATAAAGTAAA
*
969313 AATAAAGAAATAAAATAAATATAAAGG
1 AATAAA-AAATAAAATAAATAAAAAGG
969340 AGATAAAAAAATAAGGTAA-AAATAAAAAGG
1 A-AT-AAAAAATAA---AATAAATAAAAAGG
* *
969370 AAT-AAAAATAAAATAAAGAAAAAGAA
1 AATAAAAAATAAAATAAATAAAAAG-G
969396 AATAAAAAATAAA
1 AATAAAAAATAAA
969409 GAATATATAT
Statistics
Matches: 58, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
24 2 0.03
25 9 0.16
26 3 0.05
27 18 0.31
28 8 0.14
29 5 0.09
30 11 0.19
31 2 0.03
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.15
Consensus pattern (26 bp):
AATAAAAAATAAAATAAATAAAAAGG
Found at i:969366 original size:16 final size:16
Alignment explanation
Indices: 969347--969400 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 16
969337 AGGAGATAAA
969347 AAAATAAGGTAAAAAT
1 AAAATAAGGTAAAAAT
969363 -AAA-AAGGAATAAAAAT
1 AAAATAAGG--TAAAAAT
* *
969379 AAAATAAAG-AAAAAG
1 AAAATAAGGTAAAAAT
969394 AAAATAA
1 AAAATAA
969401 AAAATAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 4 0.12
15 15 0.47
16 7 0.22
17 3 0.09
18 3 0.09
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (16 bp):
AAAATAAGGTAAAAAT
Found at i:970722 original size:2 final size:2
Alignment explanation
Indices: 970715--970750 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
970705 CTGTAAAATA
970715 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
970751 GTTCGTCATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:971667 original size:65 final size:64
Alignment explanation
Indices: 971528--971706 Score: 242
Period size: 65 Copynumber: 2.8 Consensus size: 64
971518 GTGAAGTTGA
*
971528 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAAT-C--C--AAGTATTGTTTCACCAAATTG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCATCTTAAGTA-AGTTTCACCAAATTG
* *
971588 GCTTTGAGTTGGATATCCTTTGTTGTGAAGTCGAAATCCGATCTTAAGTAAGTTTCACCAAATTG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCC-ATCTTAAGTAAGTTTCACCAAATTG
* * *
971653 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTAAAATCCAATCTTGATTAAGTT
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCC-ATCTTAAGTAAGTT
971707 ATGTTGCTTC
Statistics
Matches: 104, Mismatches: 9, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
60 35 0.34
61 1 0.01
64 1 0.01
65 62 0.60
66 5 0.05
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.39
Consensus pattern (64 bp):
GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCATCTTAAGTAAGTTTCACCAAATTG
Found at i:971909 original size:6 final size:6
Alignment explanation
Indices: 971898--971925 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
971888 TTCAGCAAAT
971898 TAAAGA TAAAGA TAAAGA TAAAGA TAAA
1 TAAAGA TAAAGA TAAAGA TAAAGA TAAA
971926 ATGCAATGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (6 bp):
TAAAGA
Found at i:976857 original size:8 final size:8
Alignment explanation
Indices: 976844--976868 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
976834 AGATGCAAGA
976844 ATGGATGC
1 ATGGATGC
976852 ATGGATGC
1 ATGGATGC
976860 ATGGATGC
1 ATGGATGC
976868 A
1 A
976869 CTTTGACACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.36, T:0.24
Consensus pattern (8 bp):
ATGGATGC
Found at i:977010 original size:30 final size:30
Alignment explanation
Indices: 976953--977012 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
976943 AACTTTGAAT
976953 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
976983 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
977013 CTTAAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:978320 original size:19 final size:20
Alignment explanation
Indices: 978277--978324 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
978267 TCTAAATCCT
*
978277 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
978297 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
978316 TTTTCAAAA
1 TTTTCAAAA
978325 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:979996 original size:64 final size:64
Alignment explanation
Indices: 979883--980092 Score: 203
Period size: 64 Copynumber: 3.2 Consensus size: 64
979873 TGCACTAAGA
* * *
979883 GTGCATCGATGCATGAAGTGCATTCGATGTTTGAA--AAAT-AGCCTGGTGCATCGATGCATGGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAG---AGTGCATCGATGCATGGA
979945 TT
63 TT
* * **
979947 GTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCAGAGTGCATCGATGCATGGAGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGGATT
* * * * * *
980011 GTGCATTGGTGCATGGAATTCATTCGATGTTTCAATTTATTCATTGA-TGCATCGATGCATGGTA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCA--GAGTGCATCGATGCATGG-A
980075 TT
63 TT
*
980077 GATGCATCGGTGCATG
1 G-TGCATCGATGCATG
980093 CCTTTGAAAA
Statistics
Matches: 122, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
64 84 0.69
65 15 0.12
66 8 0.07
67 15 0.12
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGGATT
Found at i:980013 original size:19 final size:19
Alignment explanation
Indices: 979989--980027 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
979979 TAATTAAATC
979989 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
* *
980008 AGAGTGCATTGGTGCATGG
1 AGAGTGCATCGATGCATGG
980027 A
1 A
980028 ATTCATTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.38, T:0.23
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:980077 original size:21 final size:21
Alignment explanation
Indices: 980053--980092 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
980043 CAATTTATTC
980053 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
980074 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
980093 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:982600 original size:24 final size:23
Alignment explanation
Indices: 982529--982608 Score: 94
Period size: 24 Copynumber: 3.5 Consensus size: 23
982519 CATGGTCTTG
*
982529 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGGGA
* *
982552 TGCATCGGTG--CA-TCATGCGGA
1 TGCATCGATGCACATTCAAG-GGA
982573 TGCATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
982597 TGCATCGATGCA
1 TGCATCGATGCA
982609 TTGTTAAGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
20 4 0.09
21 13 0.28
23 11 0.23
24 17 0.36
25 2 0.04
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.23
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:982621 original size:44 final size:42
Alignment explanation
Indices: 982506--982628 Score: 122
Period size: 44 Copynumber: 2.8 Consensus size: 42
982496 AAAACCCGAC
* *
982506 GGATGCATCGATGCATGGTCTTGTGCATCGATGCACATTCAAG
1 GGATGCATCGATGCATTGT-TAGTGCATCGATGCACATTCAAG
* * **
982549 GCATGCATCGGTGCATCATG-CGGATGCATCGATGCACATTCAAAG
1 GGATGCATCGATGCAT--TGTTAG-TGCATCGATGCACATTC-AAG
*
982594 GGATGCATCGATGCATTGTTAAGTGCATCGGTGCA
1 GGATGCATCGATGCATTGTT-AGTGCATCGATGCA
982629 TTAAGAACAA
Statistics
Matches: 64, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
43 17 0.27
44 28 0.44
45 19 0.30
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (42 bp):
GGATGCATCGATGCATTGTTAGTGCATCGATGCACATTCAAG
Found at i:988614 original size:4 final size:4
Alignment explanation
Indices: 988605--988711 Score: 73
Period size: 4 Copynumber: 26.8 Consensus size: 4
988595 AATGTAATGA
*
988605 AAAT AAAT AAAAT AAA- AAAT AAA- AAAC AAAT GAAAT AAAT AAGAT AAGAT
1 AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AA-AT AA-AT
* * * *
988655 AAAGA AAAT AAAA AAAT -AA- AAAT AAAT AAA- GAGT AAAT AAAAT AAAT
1 AAA-T AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT
988702 -AAT AAAT AAA
1 AAAT AAAT AAA
988712 ATGAAAATGA
Statistics
Matches: 83, Mismatches: 9, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
3 14 0.17
4 45 0.54
5 24 0.29
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:988617 original size:5 final size:5
Alignment explanation
Indices: 988604--988901 Score: 65
Period size: 5 Copynumber: 57.8 Consensus size: 5
988594 AAATGTAATG
* * *
988604 AAAAT -AAAT AAAAT AAAAAAT AAAAA ACAAAT GAAAT -AAAT AAGAT
1 AAAAT AAAAT AAAAT --AAAAT AAAAT A-AAAT AAAAT AAAAT AAAAT
* *
988650 AAGAT -AAAG AAAAT -AAA- AAAAT AAAA- ATAAAT AAAGAGT -AAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT AAA-A-T AAAAT
* *
988693 AAAAT -AAAT AATAAAT AAAAT GAAAAT GAAAAT GAAA- GAAAT AAAAAT
1 AAAAT AAAAT -A-AAAT AAAAT -AAAAT -AAAAT AAAAT AAAAT -AAAAT
* *
988741 AAAA- ATAAAG AAAAT AATAAT ATATATAT ATATAT ATAAAT -AAAT AAAA-
1 AAAAT A-AAAT AAAAT AA-AAT A-A-A-AT A-AAAT A-AAAT AAAAT AAAAT
* * *
988790 ACAGGAAT AAAGT AAAA- ATAAA- GAAAT AAAAT AAATAT AAAGGAG ATAAA-
1 A-A--AAT AAAAT AAAAT A-AAAT AAAAT AAAAT AAA-AT AAA--AT A-AAAT
** * * *
988840 AAAAT AAGGT AAAGAT AAAA- AAAAA AAAAA AAAAT AAAAT -ACAT AAAAT
1 AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
*
988889 -ACAT AAAAT AAAA
1 AAAAT AAAAT AAAA
988902 AATAAAGAAT
Statistics
Matches: 227, Mismatches: 27, Indels: 78
0.68 0.08 0.23
Matches are distributed among these distances:
4 49 0.22
5 107 0.47
6 45 0.20
7 18 0.08
8 8 0.04
ACGTcount: A:0.73, C:0.01, G:0.07, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:988635 original size:27 final size:26
Alignment explanation
Indices: 988604--988903 Score: 107
Period size: 27 Copynumber: 11.0 Consensus size: 26
988594 AAATGTAATG
988604 AAAATAAATAAAATAAAAAATAAAAA
1 AAAATAAATAAAATAAAAAATAAAAA
*
988630 ACAAATGAAAT-AAATAAGATAAGAT-AAAG
1 A-AAAT-AAATAAAATAA-A-AA-ATAAAAA
988659 AAAATAAA-AAAAT-AAAAATAAATAA
1 AAAATAAATAAAATAAAAAATAAA-AA
* * * *
988684 AGAGTAAATAAAATAAATAAT-AAAT
1 AAAATAAATAAAATAAAAAATAAAAA
988709 AAAATGAAAATGAAAATGAAAGAAATAAAAATA
1 AAAAT--AAAT-AAAAT-AAA-AAAT-AAAA-A
* * * *
988742 AAAATAAAGAAAAT-AATAATATATA
1 AAAATAAATAAAATAAAAAATAAAAA
* * * * *
988767 TATATATATATAAATAAATAA-AAACA
1 AAAATAAATA-AAATAAAAAATAAAAA
**
988793 GGAATAAAGTAAAAATAAAGAAATAAAATA
1 AAAATAAA-T-AAAATAAA-AAATAAAA-A
* ** * **
988823 AATATAAAGGAGATAAAAAAATAAGGTA
1 AAAATAAATAAAAT-AAAAAATAA-AAA
*
988851 AAGATAAA-AAAA-AAAAAA-AAAAA
1 AAAATAAATAAAATAAAAAATAAAAA
*
988874 TAAAATACATAAAATACATAAAATAAAAA
1 -AAAATAAATAAAATA-A-AAAATAAAAA
988903 A
1 A
988904 TAAAGAATAT
Statistics
Matches: 200, Mismatches: 41, Indels: 64
0.66 0.13 0.21
Matches are distributed among these distances:
23 3 0.01
24 12 0.06
25 29 0.14
26 23 0.12
27 45 0.22
28 41 0.20
29 20 0.10
30 16 0.08
31 3 0.01
32 3 0.01
33 5 0.03
ACGTcount: A:0.73, C:0.01, G:0.07, T:0.18
Consensus pattern (26 bp):
AAAATAAATAAAATAAAAAATAAAAA
Found at i:988668 original size:6 final size:6
Alignment explanation
Indices: 988666--988749 Score: 50
Period size: 6 Copynumber: 13.5 Consensus size: 6
988656 AAGAAAATAA
*
988666 AAAAAT AAAAAT --AAAT AAAGAGT AAATAA- AATAAAT AATAAAT -AAAAT
1 AAAAAT AAAAAT AAAAAT AAA-AAT AAA-AAT AA-AAAT AA-AAAT AAAAAT
* *
988714 GAAAAT GAAAAT GAAAGAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT --AA-AAAT AAAAAT AAAAAT AAA
988750 GAAAATAATA
Statistics
Matches: 65, Mismatches: 4, Indels: 18
0.75 0.05 0.21
Matches are distributed among these distances:
4 4 0.06
5 4 0.06
6 36 0.55
7 16 0.25
8 1 0.02
9 4 0.06
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:988756 original size:63 final size:61
Alignment explanation
Indices: 988648--988830 Score: 168
Period size: 63 Copynumber: 3.0 Consensus size: 61
988638 AATAAATAAG
*
988648 ATAAGATAAA-GAAAATAAAAAAATAAAAAT--AAATAAAGAGTAAATAAAATAAATAATAAAT
1 ATAA-ATAAATGAAAATAAAGAAATAAAAATAAAAATAAAGA--AAATAAAATAAATAATAAAT
988709 A-AAATGAAAATGAAAATGAAAGAAATAAAAATAAAAATAAAGAAAATAATAATATATATATATA
1 ATAAAT--AAATGAAAAT-AAAGAAATAAAAATAAAAATAAAGAAAATAA-AATA-A-ATA-ATA
*
988773 TAT
59 AAT
* * *
988776 ATAAATAAAT-AAAA-ACAGGAAT-AAAGTAAAAATAAAG-AAATAAAATAAAT-ATAAA
1 ATAAATAAATGAAAATAAAGAAATAAAAATAAAAATAAAGAAAATAAAATAAATAATAAA
988831 GGAGATAAAA
Statistics
Matches: 105, Mismatches: 6, Indels: 27
0.76 0.04 0.20
Matches are distributed among these distances:
56 4 0.04
58 2 0.02
59 3 0.03
60 6 0.06
61 10 0.10
62 20 0.19
63 25 0.24
64 4 0.04
65 14 0.13
66 7 0.07
67 6 0.06
68 4 0.04
ACGTcount: A:0.72, C:0.01, G:0.07, T:0.21
Consensus pattern (61 bp):
ATAAATAAATGAAAATAAAGAAATAAAAATAAAAATAAAGAAAATAAAATAAATAATAAAT
Found at i:988819 original size:19 final size:19
Alignment explanation
Indices: 988659--988910 Score: 120
Period size: 21 Copynumber: 12.6 Consensus size: 19
988649 TAAGATAAAG
*
988659 AAAATAAAAAAATAAAAATA
1 AAAATAAAGAAAT-AAAATA
*
988679 AATAA-AGAGTAAATAAAATA
1 AA-AATAAAG-AAATAAAATA
* *
988699 AATAATAAATAAAATGAAAATG
1 AA-AATAAA-GAAAT-AAAATA
988721 AAAATGAAAGAAATAAAAATA
1 AAAAT-AAAGAAAT-AAAATA
988742 AAAATAAAGAAAATAATAATA
1 AAAATAAAG-AAATAA-AATA
* * * * *
988763 TATATATATATATATAAATA
1 AAAATAAAGAAATA-AAATA
* * *
988783 AATAAAAACAGGAATAAAGTA
1 AA-AATAA-AGAAATAAAATA
988804 AAAATAAAGAAATAAAATA
1 AAAATAAAGAAATAAAATA
* *
988823 AATATAAAGGAGATAAAA-A
1 AAAATAAA-GAAATAAAATA
988842 AATAAGGTAAAGATAA-AAAA-A
1 AA-AA--TAAAGA-AATAAAATA
*
988863 AAAA-AAAAAAATAAAATA
1 AAAATAAAGAAATAAAATA
* * * *
988881 CATA-AAATACATAAAATAA
1 AAAATAAAGAAATAAAAT-A
988900 AAAATAAAGAA
1 AAAATAAAGAA
988911 TATATATATA
Statistics
Matches: 175, Mismatches: 37, Indels: 40
0.69 0.15 0.16
Matches are distributed among these distances:
16 2 0.01
17 8 0.05
18 14 0.08
19 23 0.13
20 49 0.28
21 60 0.34
22 19 0.11
ACGTcount: A:0.73, C:0.01, G:0.07, T:0.19
Consensus pattern (19 bp):
AAAATAAAGAAATAAAATA
Found at i:991094 original size:65 final size:63
Alignment explanation
Indices: 990952--991130 Score: 240
Period size: 65 Copynumber: 2.8 Consensus size: 63
990942 GTGAAGTTGA
* *
990952 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTT-AA-A-AT-TCAAGTATTGTTTCACCAAATTG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTAAATACATCTTAAGTA-AGTTTCACCAAATTG
991012 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATACGATCTTAAGTAAGTTTCACCAAATTG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTT-AAATAC-ATCTTAAGTAAGTTTCACCAAATTG
* * *
991077 GCTTTGAGTTGGATATCCTTCATTGTGAAGTTAAAATCCAATCTTGAGTAAGTT
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTT-AAATAC-ATCTTAAGTAAGTT
991131 GTGTTACTTC
Statistics
Matches: 106, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
60 32 0.30
62 2 0.02
63 1 0.01
65 65 0.61
66 6 0.06
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (63 bp):
GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTAAATACATCTTAAGTAAGTTTCACCAAATTG
Found at i:992075 original size:66 final size:65
Alignment explanation
Indices: 991947--992076 Score: 147
Period size: 66 Copynumber: 2.0 Consensus size: 65
991937 TTCTTATTTA
* * * * *
991947 TTTTTCTATTTTTTTTCTTTTCTTTTTCAATTTAGGGCCTCCTTTCGGGTTTTTACCCTAAGCGT
1 TTTTTCTATTTTTTTTCTTTTCTTCTTCAACTTAGGGCCTCCTCTCGGGTTTTCACCATAAGCGT
* * *
992012 TTTTTCTTTTTTTTTTTCCTTTTCTTCTTCAACTTAGATG-C-CCTCTCGGGTTTTCATCATAAG
1 TTTTTC-TATTTTTTTT-CTTTTCTTCTTCAACTTAG-GGCCTCCTCTCGGGTTTTCACCATAAG
992075 CG
63 CG
992077 AAGTATTTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
65 6 0.11
66 29 0.54
67 18 0.33
68 1 0.02
ACGTcount: A:0.12, C:0.22, G:0.12, T:0.55
Consensus pattern (65 bp):
TTTTTCTATTTTTTTTCTTTTCTTCTTCAACTTAGGGCCTCCTCTCGGGTTTTCACCATAAGCGT
Found at i:1002256 original size:4 final size:4
Alignment explanation
Indices: 1002247--1002471 Score: 87
Period size: 4 Copynumber: 55.2 Consensus size: 4
1002237 AATGTAATGA
* *
1002247 AAAT AAAT AAAAT AAA- AAAT AAAA AAAC AAAT GAAAT AAAT AAGAT AAGAT
1 AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AA-AT AA-AT
* * * *
1002298 AAAGA AAAT AAAA AAAT AAAGAT AAAT AAA- AAGT AAAT AAAAT AAAG
1 AAA-T AAAT AAAT AAAT -AA-AT AAAT AAAT AAAT AAAT -AAAT AAAT
* * * *
1002345 ATAC AGA- AAAT AAAAT AAAAT AAAT -AA- AAAT AAAG AAAT -AA- AAAT
1 AAAT AAAT AAAT -AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * *
1002390 AAAG AAA- ATAAT -AAT AATAT ACAT ATAAT AAAT AAAT AAAT AAA- AACAG
1 AAAT AAAT A-AAT AAAT AA-AT AAAT A-AAT AAAT AAAT AAAT AAAT AA-AT
* *
1002439 GAAT AAAGT -AA- AAAT AAAG AAAT AAAAT AAAT A
1 AAAT AAA-T AAAT AAAT AAAT AAAT -AAAT AAAT A
1002472 TAAAGGAAAT
Statistics
Matches: 171, Mismatches: 24, Indels: 52
0.69 0.10 0.21
Matches are distributed among these distances:
3 23 0.13
4 97 0.57
5 49 0.29
6 2 0.01
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.18
Consensus pattern (4 bp):
AAAT
Done.