Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold79
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: 4189514
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 5041 characters in sequence are not A, C, G, or T
File 22 of 26
Found at i:3063904 original size:9 final size:9
Alignment explanation
Indices: 3063892--3063945 Score: 51
Period size: 9 Copynumber: 6.3 Consensus size: 9
3063882 TTATTATAAT
3063892 TATATTTTA
1 TATATTTTA
3063901 TATATTTTA
1 TATATTTTA
*
3063910 TAT-TTATA
1 TATATTTTA
3063918 TA-ATTTTA
1 TATATTTTA
* *
3063926 AATATATTA
1 TATATTTTA
*
3063935 -ATAATTTA
1 TATATTTTA
3063943 TAT
1 TAT
3063946 TATATAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
8 17 0.47
9 19 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATATTTTA
Found at i:3063910 original size:16 final size:16
Alignment explanation
Indices: 3063891--3063973 Score: 62
Period size: 16 Copynumber: 5.0 Consensus size: 16
3063881 TTTATTATAA
3063891 TTATATTTTATATATT
1 TTATATTTTATATATT
3063907 TTATA-TTTATATAATT
1 TTATATTTTATAT-ATT
* *
3063923 TTAAATATATTA-ATAAT
1 TT--ATATTTTATATATT
* *
3063940 TTATATTATATAAATT
1 TTATATTTTATATATT
*
3063956 TTAAAATATTTATATATT
1 TT-ATAT-TTTATATATT
3063974 AAAAAAATAT
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
15 13 0.25
16 15 0.29
17 7 0.14
18 13 0.25
19 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATATTTTATATATT
Found at i:3063923 original size:25 final size:27
Alignment explanation
Indices: 3063895--3063945 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
3063885 TTATAATTAT
* *
3063895 ATTTTATATAT-TTTAT-ATTTATATA
1 ATTTTAAATATATTAATAATTTATATA
3063920 ATTTTAAATATATTAATAATTTATAT
1 ATTTTAAATATATTAATAATTTATAT
3063946 TATATAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 4 0.18
27 8 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
ATTTTAAATATATTAATAATTTATATA
Found at i:3063930 original size:27 final size:29
Alignment explanation
Indices: 3063900--3063973 Score: 82
Period size: 32 Copynumber: 2.5 Consensus size: 29
3063890 ATTATATTTT
3063900 ATATATTT-TATATTTATAT-AATTTTAA
1 ATATATTTATATATTTATATAAATTTTAA
*
3063927 ATATATTAATAATTTATATTATATAAATTTTAA
1 ATATATT--T-ATATAT-TTATATAAATTTTAA
3063960 A-ATATTTATATATT
1 ATATATTTATATATT
3063974 AAAAAAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
27 7 0.18
28 1 0.03
29 6 0.15
30 1 0.03
31 4 0.10
32 11 0.28
33 9 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
ATATATTTATATATTTATATAAATTTTAA
Found at i:3063955 original size:15 final size:16
Alignment explanation
Indices: 3063877--3063956 Score: 64
Period size: 15 Copynumber: 5.2 Consensus size: 16
3063867 ATTCGTGTAT
3063877 TTTAT-TTAT-TATAA
1 TTTATATTATATATAA
* *
3063891 -TTATATTTTATATAT
1 TTTATATTATATATAA
3063906 TTTATATT-TATATAA
1 TTTATATTATATATAA
*
3063921 TTT-TAAATATATTAATAA
1 TTTAT-ATTATA-T-ATAA
3063939 TTTATATTATATA-AA
1 TTTATATTATATATAA
3063954 TTT
1 TTT
3063957 TAAAATATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
13 4 0.08
14 4 0.08
15 20 0.38
16 10 0.19
17 2 0.04
18 12 0.23
19 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTATATTATATATAA
Found at i:3063969 original size:18 final size:18
Alignment explanation
Indices: 3063909--3063969 Score: 51
Period size: 20 Copynumber: 3.5 Consensus size: 18
3063899 TATATATTTT
3063909 ATATTTATATAATTTTAAA
1 ATATTTATA-AATTTTAAA
*
3063928 TATATTAAT-AA-TTT---
1 -ATATTTATAAATTTTAAA
3063942 ATATTATATAAATTTTAAA
1 ATATT-TATAAATTTTAAA
3063961 ATATTTATA
1 ATATTTATA
3063970 TATTAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
13 5 0.15
14 2 0.06
15 2 0.06
16 3 0.09
17 3 0.09
18 6 0.18
19 5 0.15
20 7 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATATTTATAAATTTTAAA
Found at i:3069120 original size:16 final size:16
Alignment explanation
Indices: 3069101--3069150 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 16
3069091 TAATATGAAT
3069101 ATATAAATATATTAAA
1 ATATAAATATATTAAA
3069117 ATATAAATATGATATGAAA
1 ATATAAATAT-AT-T-AAA
*
3069136 ATATTAAT-TATTAAA
1 ATATAAATATATTAAA
3069151 TTTAAAAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 3 0.10
16 11 0.37
17 4 0.13
18 2 0.07
19 10 0.33
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (16 bp):
ATATAAATATATTAAA
Found at i:3070180 original size:2 final size:2
Alignment explanation
Indices: 3070173--3070210 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3070163 CCTTTGGACT
3070173 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
3070211 ATAAAACTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3070387 original size:30 final size:29
Alignment explanation
Indices: 3070353--3070429 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
3070343 ATTTTAATAA
* *
3070353 ATTTTATTTGAATATAAGTT-AAAGATTAAT
1 ATTTTATTT-AATACAAATTAAAAG-TTAAT
3070383 ATTTTATTTAGATACAAATTAAAAGTTAAT
1 ATTTTATTTA-ATACAAATTAAAAGTTAAT
*
3070413 AATTTATTTAAATACAA
1 ATTTTATTT-AATACAA
3070430 GAAAAAATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 1 0.02
30 35 0.85
31 5 0.12
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (29 bp):
ATTTTATTTAATACAAATTAAAAGTTAAT
Found at i:3071108 original size:20 final size:17
Alignment explanation
Indices: 3071062--3071104 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
3071052 TTATAATTAA
*
3071062 ATTTAATTAAAAATATT
1 ATTTAATTAAAAATATG
3071079 ATTTTAATTAATAAATAATG
1 A-TTTAATTAA-AAAT-ATG
3071099 ATTTAA
1 ATTTAA
3071105 ATTAGAGGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 9 0.41
19 9 0.41
20 3 0.14
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
ATTTAATTAAAAATATG
Found at i:3073472 original size:17 final size:16
Alignment explanation
Indices: 3073450--3073482 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
3073440 TTTTTGCCCT
3073450 TTTTTTTAATAATTTTA
1 TTTTTTT-ATAATTTTA
3073467 TTTTTTTATAATTTTA
1 TTTTTTTATAATTTTA
3073483 GTTTGGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTTATAATTTTA
Found at i:3073939 original size:17 final size:17
Alignment explanation
Indices: 3073919--3073953 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3073909 TTAAAAAAAT
3073919 TAAAATATAATAT-AATA
1 TAAAA-ATAATATCAATA
3073936 TAAAAATAATATCAATA
1 TAAAAATAATATCAATA
3073953 T
1 T
3073954 GATATTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAAAATAATATCAATA
Found at i:3074403 original size:3 final size:3
Alignment explanation
Indices: 3074395--3074427 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3074385 TTCATTCACT
3074395 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3074428 TTAAATTCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3074627 original size:3 final size:3
Alignment explanation
Indices: 3074610--3074646 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
3074600 TGTGTGTTTT
*
3074610 TTA TTT TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3074647 TTGCAAGTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:3081077 original size:16 final size:16
Alignment explanation
Indices: 3081056--3081087 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3081046 GGAATCAAGT
3081056 TATGATATCCTTAATA
1 TATGATATCCTTAATA
3081072 TATGATATCCTTAATA
1 TATGATATCCTTAATA
3081088 CCTATATTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (16 bp):
TATGATATCCTTAATA
Found at i:3081817 original size:48 final size:48
Alignment explanation
Indices: 3081746--3081842 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
3081736 ATAGAAAGAG
3081746 AGTGCCTAACAAGTTAAAGATATAGATAAAAATCTTCGATGATCTAAA
1 AGTGCCTAACAAGTTAAAGATATAGATAAAAATCTTCGATGATCTAAA
3081794 AGTGCCTAACAAGTTAAAGATATAGATAAAAATCTTCGATGATCTAAA
1 AGTGCCTAACAAGTTAAAGATATAGATAAAAATCTTCGATGATCTAAA
3081842 A
1 A
3081843 TGCATCAAAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.27
Consensus pattern (48 bp):
AGTGCCTAACAAGTTAAAGATATAGATAAAAATCTTCGATGATCTAAA
Found at i:3090588 original size:31 final size:31
Alignment explanation
Indices: 3090521--3090589 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
3090511 TATTAATTTT
* * *
3090521 ATTTAAATTTATTCATATTTATAAATAAATA
1 ATTTAAATTTATCCAAATATATAAATAAATA
* *
3090552 ATTTAAATTTATCCAAATATATATATATATA
1 ATTTAAATTTATCCAAATATATAAATAAATA
*
3090583 TTTTAAA
1 ATTTAAA
3090590 AATATATATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (31 bp):
ATTTAAATTTATCCAAATATATAAATAAATA
Found at i:3090596 original size:19 final size:19
Alignment explanation
Indices: 3090572--3090610 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3090562 ATCCAAATAT
3090572 ATATATATATATTTTAAAA
1 ATATATATATATTTTAAAA
*
3090591 ATATATATATTTTTTAAAA
1 ATATATATATATTTTAAAA
3090610 A
1 A
3090611 AAACTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATATATATATTTTAAAA
Found at i:3091982 original size:13 final size:13
Alignment explanation
Indices: 3091964--3091993 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3091954 ATCTCACTGA
3091964 AAAGCCAAATTTC
1 AAAGCCAAATTTC
3091977 AAAGCCAAATTTC
1 AAAGCCAAATTTC
3091990 AAAG
1 AAAG
3091994 TTCATAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.50, C:0.20, G:0.10, T:0.20
Consensus pattern (13 bp):
AAAGCCAAATTTC
Found at i:3095118 original size:3 final size:3
Alignment explanation
Indices: 3095077--3095109 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3095067 GAAGCCTTAT
3095077 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3095110 CGCTTCTTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:3095668 original size:2 final size:2
Alignment explanation
Indices: 3095663--3095692 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3095653 TTTTTTGTTG
3095663 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3095693 TAACCAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3099680 original size:24 final size:24
Alignment explanation
Indices: 3099645--3099690 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
3099635 TATAATTAAA
*
3099645 TTAAAAATAATAATATTTTAATATT
1 TTAAAAATAATAA-AATTTAATATT
3099670 TTAAAAA-AATAAAATTTAATA
1 TTAAAAATAATAAAATTTAATA
3099691 AATGTATGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 5 0.25
25 7 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
TTAAAAATAATAAAATTTAATATT
Found at i:3102443 original size:3 final size:3
Alignment explanation
Indices: 3102437--3102465 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3102427 ATCTTTTTTT
3102437 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
3102466 AACGCGTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:3102866 original size:20 final size:20
Alignment explanation
Indices: 3102841--3102885 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3102831 TTATTAAAAT
3102841 AATATAATAAAATT-AATAAA
1 AATAT-ATAAAATTAAATAAA
* *
3102861 AATATATAAATTTAAATATA
1 AATATATAAAATTAAATAAA
3102881 AATAT
1 AATAT
3102886 TTTAACTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AATATATAAAATTAAATAAA
Found at i:3106541 original size:28 final size:28
Alignment explanation
Indices: 3106477--3106534 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
3106467 TTTGGCGATT
3106477 TTGCATATTGATATAAGTATTCCTTTTA
1 TTGCATATTGATATAAGTATTCCTTTTA
3106505 TTGCATATTGATATAAGTATTCCTTTTA
1 TTGCATATTGATATAAGTATTCCTTTTA
3106533 TT
1 TT
3106535 TTCTATTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.52
Consensus pattern (28 bp):
TTGCATATTGATATAAGTATTCCTTTTA
Found at i:3107315 original size:19 final size:21
Alignment explanation
Indices: 3107274--3107318 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
3107264 TACTTATATT
3107274 TTATATTTTTATGTATAATAA
1 TTATATTTTTATGTATAATAA
3107295 TTATATTTTTAT-TAT-ATAA
1 TTATATTTTTATGTATAATAA
3107314 TTATA
1 TTATA
3107319 AAAAAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 9 0.38
20 3 0.12
21 12 0.50
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTATATTTTTATGTATAATAA
Found at i:3109143 original size:2 final size:2
Alignment explanation
Indices: 3109136--3109180 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
3109126 AAATTAATAC
*
3109136 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3109177 TA TA
1 TA TA
3109181 AAAAAATTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3109240 original size:13 final size:13
Alignment explanation
Indices: 3109222--3109246 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3109212 AATAATATCA
3109222 AATTATTTAAAAT
1 AATTATTTAAAAT
3109235 AATTATTTAAAA
1 AATTATTTAAAA
3109247 ATTATAATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTATTTAAAAT
Found at i:3109495 original size:5 final size:5
Alignment explanation
Indices: 3109485--3109509 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3109475 TAAATGAGAA
3109485 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
3109510 CCATAGAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:3115094 original size:23 final size:22
Alignment explanation
Indices: 3115050--3115095 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
3115040 ATAATTTTTA
**
3115050 AAAATAATTTTATAAATTAATT
1 AAAATAATTTTATAAAAAAATT
*
3115072 AAAATAATTTTTTTAAAAAAATT
1 AAAATAA-TTTTATAAAAAAATT
3115095 A
1 A
3115096 TGATTTTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAATAATTTTATAAAAAAATT
Found at i:3118378 original size:3 final size:3
Alignment explanation
Indices: 3118372--3118399 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3118362 TCTGCTGCGG
3118372 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3118400 CTGCTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3118721 original size:17 final size:17
Alignment explanation
Indices: 3118699--3118752 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
3118689 AAATGTTAAT
3118699 TTATTTAATTTAAATTA
1 TTATTTAATTTAAATTA
* *
3118716 TTATTTAATAATAAA-AA
1 TTATTTAAT-TTAAATTA
3118733 TTATTTAAATTT-AATTA
1 TTATTT-AATTTAAATTA
3118750 TTA
1 TTA
3118753 AAATATAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
16 2 0.07
17 21 0.70
18 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTATTTAATTTAAATTA
Found at i:3118817 original size:7 final size:7
Alignment explanation
Indices: 3118807--3118866 Score: 52
Period size: 7 Copynumber: 8.3 Consensus size: 7
3118797 TAAAACAAAT
3118807 TTTAAAA
1 TTTAAAA
3118814 TTT-AAA
1 TTTAAAA
3118820 TTTAATTTAA
1 TTTAA---AA
3118830 TTT-AAA
1 TTTAAAA
*
3118836 TTTTAAA
1 TTTAAAA
*
3118843 TATAAAAA
1 T-TTAAAA
3118851 TTTAAAA
1 TTTAAAA
3118858 TTTAAAA
1 TTTAAAA
3118865 TT
1 TT
3118867 ACGAACATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
6 11 0.25
7 22 0.50
8 5 0.11
9 1 0.02
10 5 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
TTTAAAA
Found at i:3119430 original size:21 final size:21
Alignment explanation
Indices: 3119404--3119445 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3119394 TACAACATAA
3119404 ATGCTCCTCACTACTATTCTT
1 ATGCTCCTCACTACTATTCTT
*
3119425 ATGCTCTTCACTACTATTCTT
1 ATGCTCCTCACTACTATTCTT
3119446 TTTTAGTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.31, G:0.05, T:0.45
Consensus pattern (21 bp):
ATGCTCCTCACTACTATTCTT
Found at i:3128094 original size:2 final size:2
Alignment explanation
Indices: 3128089--3128121 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3128079 TAGTTGGTTT
3128089 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3128122 TGTTTGCTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3128300 original size:35 final size:36
Alignment explanation
Indices: 3128246--3128348 Score: 93
Period size: 38 Copynumber: 2.8 Consensus size: 36
3128236 ATGCATAAAA
*
3128246 AATATTATTATGAATATATAAATAATTATTTTTA-ATT
1 AATATTATT-T-AAAATATAAATAATTATTTTTATATT
* **
3128283 -TTATTAATTTAAAATATAAATTTTATATTTTTATATT
1 AATATT-ATTTAAAATATAAATAAT-TATTTTTATATT
*
3128320 AATATTTTTTAAAATTATAAATATATTAT
1 AATATTATTTAAAA-TATAAATA-ATTAT
3128349 AGATATAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
35 11 0.21
36 13 0.25
37 13 0.25
38 14 0.27
39 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (36 bp):
AATATTATTTAAAATATAAATAATTATTTTTATATT
Found at i:3128357 original size:17 final size:18
Alignment explanation
Indices: 3128335--3128374 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
3128325 TTTTTAAAAT
3128335 TATAAATATATTA-TAGA
1 TATAAATATATTAGTAGA
*
3128352 TATAAATATATTAGTATA
1 TATAAATATATTAGTAGA
3128370 TATAA
1 TATAA
3128375 TTTTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (18 bp):
TATAAATATATTAGTAGA
Found at i:3130212 original size:19 final size:19
Alignment explanation
Indices: 3130188--3130231 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
3130178 TGGTTGTCGA
*
3130188 GGTACTATTCACGTATACG
1 GGTACTATTCAAGTATACG
3130207 GGTACTATTCAAGTATACG
1 GGTACTATTCAAGTATACG
*
3130226 GTTACT
1 GGTACT
3130232 GTACACGTGA
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:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (19 bp):
GGTACTATTCAAGTATACG
Found at i:3134363 original size:34 final size:34
Alignment explanation
Indices: 3134297--3134480 Score: 228
Period size: 34 Copynumber: 5.4 Consensus size: 34
3134287 AAGTAGGAGA
* * *
3134297 ATTGTTGATTAAAT-AGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
3134330 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
3134364 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * * *
3134398 ATTATTGATTAAATGAGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
3134432 ATTGTTGACTAAATGGGAGATTTGGTATG-TTGCT
1 ATTGTTGATTAAATGGGAGATTTGGTA-GCTTACC
3134466 ATTGTTGATTAAATG
1 ATTGTTGATTAAATG
3134481 ATGGTTTTTA
Statistics
Matches: 129, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
33 13 0.10
34 115 0.89
35 1 0.01
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:3135256 original size:15 final size:15
Alignment explanation
Indices: 3135240--3135269 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
3135230 TAAAATAAAA
3135240 TTAAAATATATATAAT
1 TTAAAA-ATATATAAT
3135256 TTAAAAATATATAA
1 TTAAAAATATATAA
3135270 ACAGAAATTA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TTAAAAATATATAAT
Found at i:3136110 original size:23 final size:22
Alignment explanation
Indices: 3136071--3136118 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
3136061 CTCAATATTT
*
3136071 TATATATTTTATGTCATAATAA
1 TATATATTTTATATCATAATAA
* *
3136093 TATATTTTATTATATCATAATTA
1 TATATATT-TTATATCATAATAA
3136116 TAT
1 TAT
3136119 TTAAAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (22 bp):
TATATATTTTATATCATAATAA
Found at i:3136158 original size:29 final size:31
Alignment explanation
Indices: 3136090--3136235 Score: 99
Period size: 29 Copynumber: 4.7 Consensus size: 31
3136080 TATGTCATAA
*
3136090 TAATATATTTTATTATATCA--TAATTATATT
1 TAATATATTTTATTATATAATTTAATTATA-T
*
3136120 TAAAATATTTT-TTATATAATTTAATTATAT
1 TAATATATTTTATTATATAATTTAATTATAT
* *
3136150 TAATA-ATTTATATTATAAAATTT--TTAAAT
1 TAATATATTT-TATTATATAATTTAATTATAT
* * *
3136179 T-ATATATTTATATCGTATCATATTTTAATAATTT
1 TAATATATTT-TAT--TAT-ATAATTTAATTATAT
*
3136213 TATATATATTATATTTATATAAT
1 TA-ATATATTTTA-TTATATAAT
3136236 CATATTTAAA
Statistics
Matches: 91, Mismatches: 12, Indels: 23
0.72 0.10 0.18
Matches are distributed among these distances:
28 3 0.03
29 25 0.27
30 16 0.18
31 21 0.23
32 5 0.05
33 4 0.04
34 7 0.08
35 2 0.02
36 8 0.09
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (31 bp):
TAATATATTTTATTATATAATTTAATTATAT
Found at i:3136166 original size:31 final size:31
Alignment explanation
Indices: 3136090--3136172 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 31
3136080 TATGTCATAA
*
3136090 TAATATATTTTATTATATCA--TAATTATATT
1 TAATA-ATTTTATTATATAATTTAATTATATT
*
3136120 TAA-AATATTTTTTATATAATTTAATTATA-T
1 TAATAAT-TTTATTATATAATTTAATTATATT
*
3136150 TAATAATTTATATTATAAAATTT
1 TAATAATTT-TATTATATAATTT
3136173 TTAAATTATA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
28 2 0.05
29 11 0.25
30 9 0.20
31 22 0.50
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (31 bp):
TAATAATTTTATTATATAATTTAATTATATT
Found at i:3136242 original size:14 final size:15
Alignment explanation
Indices: 3136182--3136243 Score: 55
Period size: 14 Copynumber: 4.5 Consensus size: 15
3136172 TTTAAATTAT
*
3136182 ATATTTATATCGTATC
1 ATATTTATAT-ATATC
3136198 ATATTT-TA-ATA--
1 ATATTTATATATATC
*
3136209 AT-TTTATATATATT
1 ATATTTATATATATC
3136223 ATATTTATATA-ATC
1 ATATTTATATATATC
3136237 ATATTTA
1 ATATTTA
3136244 AAATTATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
10 3 0.08
11 4 0.10
12 3 0.08
13 2 0.05
14 11 0.28
15 10 0.26
16 6 0.15
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (15 bp):
ATATTTATATATATC
Found at i:3137173 original size:17 final size:15
Alignment explanation
Indices: 3137150--3137196 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
3137140 TAAATATATA
3137150 AATATATTAAAATTT
1 AATATATTAAAATTT
*
3137165 -ATATAATATAAATTATT
1 AATAT-AT-TAAAAT-TT
3137182 AATATATTAAAATTT
1 AATATATTAAAATTT
3137197 TAAAAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
14 4 0.15
15 4 0.15
16 10 0.38
17 4 0.15
18 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATATTAAAATTT
Found at i:3137199 original size:16 final size:16
Alignment explanation
Indices: 3137150--3137199 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 16
3137140 TAAATATATA
3137150 AATATATTAAAA-TTT
1 AATATATTAAAATTTT
*
3137165 -ATATAATATAAATTATT
1 AATATATTA-AAATT-TT
3137182 AATATATTAAAATTTT
1 AATATATTAAAATTTT
3137198 AA
1 AA
3137200 AAAATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 7 0.24
15 3 0.10
16 5 0.17
17 7 0.24
18 7 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AATATATTAAAATTTT
Found at i:3138857 original size:5 final size:5
Alignment explanation
Indices: 3138847--3138871 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3138837 AATAAATGGA
3138847 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
3138872 TTGATATGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:3139501 original size:47 final size:49
Alignment explanation
Indices: 3139450--3139566 Score: 143
Period size: 47 Copynumber: 2.4 Consensus size: 49
3139440 ATTATTATTT
*
3139450 AATAATAAGAATAATATTTTTATTTAAAATTA-ATTATAA-AATAT-ATA
1 AATAATAA-AATAATATTTTTATTTAAAATAATATTATAATAATATAATA
*** *
3139497 AATAATATTTTAAATATTTTTATTTAAAATAATATTTTAATAATATAATA
1 AATAATAAAAT-AATATTTTTATTTAAAATAATATTATAATAATATAATA
3139547 AATAATAAAATAAT-TTTTTA
1 AATAATAAAATAATATTTTTA
3139567 GATCAATTAT
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
46 1 0.02
47 26 0.45
48 12 0.21
49 8 0.14
50 11 0.19
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (49 bp):
AATAATAAAATAATATTTTTATTTAAAATAATATTATAATAATATAATA
Found at i:3142090 original size:20 final size:21
Alignment explanation
Indices: 3142059--3142109 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
3142049 ATTTTATAGT
3142059 TTATATTATATAAATTTTAAA
1 TTATATTATATAAATTTTAAA
* *
3142080 TTATA-TATATATATTTT-AT
1 TTATATTATATAAATTTTAAA
3142099 TTATATTATAT
1 TTATATTATAT
3142110 TATAATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 6 0.22
20 16 0.59
21 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATATTATATAAATTTTAAA
Found at i:3142105 original size:11 final size:11
Alignment explanation
Indices: 3142005--3142119 Score: 60
Period size: 11 Copynumber: 10.5 Consensus size: 11
3141995 TTTTGTTATG
3142005 TTATAATTATAT
1 TTAT-ATTATAT
* *
3142017 TTAAAATAT-T
1 TTATATTATAT
3142027 TTATATT-TAT
1 TTATATTATAT
*
3142037 TTAAATTATA-
1 TTATATTATAT
* *
3142047 ATATTTTATAGT
1 TTATATTATA-T
3142059 TTATATTATAT
1 TTATATTATAT
** * *
3142070 AAATTTTAAAT
1 TTATATTATAT
3142081 TATATATATATAT
1 T-TATAT-TATAT
3142094 TT-TATT-TAT
1 TTATATTATAT
*
3142103 ATTATATTATAA
1 -TTATATTATAT
3142115 TTATA
1 TTATA
3142120 ATAAAAAATT
Statistics
Matches: 75, Mismatches: 19, Indels: 19
0.66 0.17 0.17
Matches are distributed among these distances:
9 4 0.05
10 23 0.31
11 26 0.35
12 17 0.23
13 5 0.07
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (11 bp):
TTATATTATAT
Found at i:3145881 original size:2 final size:2
Alignment explanation
Indices: 3145874--3145908 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3145864 CTGAACTGCT
3145874 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
3145909 TATTTTGTGT
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:3148965 original size:15 final size:15
Alignment explanation
Indices: 3148925--3148970 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
3148915 CCAGATGGCC
* * *
3148925 GTTGCTGTTGCTGTT
1 GTTGATGTTGATGAT
*
3148940 GTTGTTGTTGATGAT
1 GTTGATGTTGATGAT
3148955 GTTGATGTTGATGAT
1 GTTGATGTTGATGAT
3148970 G
1 G
3148971 AGGATCAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.11, C:0.04, G:0.35, T:0.50
Consensus pattern (15 bp):
GTTGATGTTGATGAT
Found at i:3149642 original size:2 final size:2
Alignment explanation
Indices: 3149637--3149665 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3149627 TAAATGTGTG
3149637 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 T
3149666 CACTTTGAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3150236 original size:39 final size:39
Alignment explanation
Indices: 3150193--3150270 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
3150183 CAAGAGATAA
*
3150193 AATAACGTTTCGACATAAGTTGTGTTGTTCATCTAAATG
1 AATAACGTTTCGACATAAGTTGTATTGTTCATCTAAATG
* * * *
3150232 AATAACGTTTCGACGTAATTTTTATTGTTCATTTAAATG
1 AATAACGTTTCGACATAAGTTGTATTGTTCATCTAAATG
3150271 GAATCTAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (39 bp):
AATAACGTTTCGACATAAGTTGTATTGTTCATCTAAATG
Found at i:3151677 original size:2 final size:2
Alignment explanation
Indices: 3151670--3151703 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3151660 TTCACCTAAT
3151670 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
3151704 AATTAAAGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3153781 original size:18 final size:17
Alignment explanation
Indices: 3153760--3153796 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
3153750 ATTCATATGT
3153760 TATTTATATCATATAAAA
1 TATTTATAT-ATATAAAA
*
3153778 TATTTATATATATTAAA
1 TATTTATATATATAAAA
3153795 TA
1 TA
3153797 ATTAAACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
TATTTATATATATAAAA
Found at i:3153797 original size:22 final size:23
Alignment explanation
Indices: 3153754--3153797 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
3153744 TTTTAAATTC
* *
3153754 ATATGTTATTTATATCATATAAA
1 ATATGTTATATATATCAAATAAA
*
3153777 ATAT-TTATATATATTAAATAA
1 ATATGTTATATATATCAAATAA
3153798 TTAAACAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
ATATGTTATATATATCAAATAAA
Found at i:3153907 original size:20 final size:20
Alignment explanation
Indices: 3153884--3153973 Score: 60
Period size: 20 Copynumber: 4.2 Consensus size: 20
3153874 AAGTTATCAA
3153884 ATAAAATTAAAATAAATTAT
1 ATAAAATTAAAATAAATTAT
* *
3153904 ATAAATAATTATAA-AACTT-T
1 AT-AA-AATTAAAATAAATTAT
*
3153924 -TAAAATTATATAAAAAAGTTAT
1 ATAAAATTA-A-AATAAA-TTAT
3153946 CAAATAAAATTAAAATAAATTAT
1 ---ATAAAATTAAAATAAATTAT
3153969 ATAAA
1 ATAAA
3153974 TAATTATAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 22
0.67 0.06 0.27
Matches are distributed among these distances:
17 5 0.09
18 2 0.04
19 3 0.06
20 10 0.19
21 8 0.15
22 8 0.15
23 4 0.07
24 5 0.09
25 1 0.02
26 8 0.15
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.34
Consensus pattern (20 bp):
ATAAAATTAAAATAAATTAT
Found at i:3153915 original size:12 final size:13
Alignment explanation
Indices: 3153893--3153981 Score: 57
Period size: 12 Copynumber: 6.9 Consensus size: 13
3153883 AATAAAATTA
3153893 AAATAAATTATAT
1 AAATAAATTATAT
3153906 AAAT-AATTATA-
1 AAATAAATTATAT
3153917 AAACTTTTAAAATTATAT
1 AAA----T-AAATTATAT
*
3153935 AAA-AAAGTTAT-C
1 AAATAAA-TTATAT
*
3153947 AAATAAAAT-TA-
1 AAATAAATTATAT
3153958 AAATAAATTATAT
1 AAATAAATTATAT
3153971 AAAT-AATTATA
1 AAATAAATTATA
3153982 AAACTTTTAA
Statistics
Matches: 61, Mismatches: 3, Indels: 25
0.69 0.03 0.28
Matches are distributed among these distances:
11 12 0.20
12 23 0.38
13 15 0.25
15 1 0.02
17 7 0.11
18 3 0.05
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (13 bp):
AAATAAATTATAT
Found at i:3153939 original size:65 final size:65
Alignment explanation
Indices: 3153866--3153996 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
3153856 GTACACAATA
3153866 ATATAAAAAAGTTATCAAATAAAATTAAAATAAATTATATAAATAATTATAAAACTTTTAAAATT
1 ATATAAAAAAGTTATCAAATAAAATTAAAATAAATTATATAAATAATTATAAAACTTTTAAAATT
3153931 ATATAAAAAAGTTATCAAATAAAATTAAAATAAATTATATAAATAATTATAAAACTTTTAAAATT
1 ATATAAAAAAGTTATCAAATAAAATTAAAATAAATTATATAAATAATTATAAAACTTTTAAAATT
3153996 A
1 A
3153997 AATTAATTTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (65 bp):
ATATAAAAAAGTTATCAAATAAAATTAAAATAAATTATATAAATAATTATAAAACTTTTAAAATT
Found at i:3154823 original size:3 final size:3
Alignment explanation
Indices: 3154815--3154848 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3154805 TAAACTTTTA
3154815 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
3154849 ATTATTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:3154853 original size:3 final size:3
Alignment explanation
Indices: 3154847--3154874 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3154837 CTTCTTCTTC
3154847 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3154875 ATAAGATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3156486 original size:36 final size:40
Alignment explanation
Indices: 3156406--3156487 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 40
3156396 GAATTATTAT
* * *
3156406 ATAAATAAAAATATTTTTAATTTAATTATAAAATATTAAT
1 ATAAATAAAAATATTTTTAATATAATTATAAAATAATAAA
*
3156446 ATAAATATAAATA-TTTTAATAT-ATT-T-AAATAATAAA
1 ATAAATAAAAATATTTTTAATATAATTATAAAATAATAAA
3156482 ATAAAT
1 ATAAAT
3156488 TAATTTCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
36 14 0.37
37 1 0.03
38 3 0.08
39 8 0.21
40 12 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (40 bp):
ATAAATAAAAATATTTTTAATATAATTATAAAATAATAAA
Found at i:3157210 original size:26 final size:26
Alignment explanation
Indices: 3157181--3157251 Score: 92
Period size: 26 Copynumber: 2.7 Consensus size: 26
3157171 CCGAATTTGC
3157181 ACCATTAAGCTTGTACCTAAAG-TCGT
1 ACCATTAAGCTTGTACCTAAAGCT-GT
*
3157207 ACCATTCAAG-TTGTTCCTAAAGCTGT
1 ACCATT-AAGCTTGTACCTAAAGCTGT
*
3157233 ACCGTTAAGCTTGTACCTA
1 ACCATTAAGCTTGTACCTA
3157252 GTGTGCTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
25 3 0.08
26 32 0.82
27 4 0.10
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.32
Consensus pattern (26 bp):
ACCATTAAGCTTGTACCTAAAGCTGT
Found at i:3158462 original size:2 final size:2
Alignment explanation
Indices: 3158457--3158489 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3158447 TTTGCTTTTG
3158457 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3158490 GTGTCTAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3162202 original size:2 final size:2
Alignment explanation
Indices: 3162195--3162222 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3162185 CTAGCTCTTA
3162195 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
3162223 TTGTTAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3164077 original size:15 final size:14
Alignment explanation
Indices: 3164041--3164083 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
3164031 TTTTTTGTTT
3164041 TTTAAAGTATAAAA
1 TTTAAAGTATAAAA
*
3164055 TGTAAAAGTGATAAAA
1 T-TTAAAGT-ATAAAA
*
3164071 TTTAAAGAATAAA
1 TTTAAAGTATAAA
3164084 TTATACATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 6 0.25
15 11 0.46
16 7 0.29
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.30
Consensus pattern (14 bp):
TTTAAAGTATAAAA
Found at i:3166174 original size:12 final size:13
Alignment explanation
Indices: 3166149--3166198 Score: 59
Period size: 12 Copynumber: 3.8 Consensus size: 13
3166139 GTAAACCTCG
3166149 AAATATAATATAAA
1 AAATA-AATATAAA
3166163 AAATAAAT-TAAA
1 AAATAAATATAAA
3166175 AAAT-AATATAAA
1 AAATAAATATAAA
*
3166187 TATATAAATATA
1 -AAATAAATATA
3166199 TTAAAATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
11 3 0.09
12 12 0.38
13 6 0.19
14 11 0.34
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATAAATATAAA
Found at i:3166241 original size:24 final size:24
Alignment explanation
Indices: 3166179--3166241 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
3166169 ATTAAAAAAT
3166179 AATATAAATATATAAATATATTAA
1 AATATAAATATATAAATATATTAA
* *
3166203 AATTTATATAATATAAAT-TATTAA
1 AATATAAAT-ATATAAATATATTAA
*
3166227 AATATCAAATTTATA
1 AATAT-AAATATATA
3166242 TATAAAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
24 21 0.66
25 11 0.34
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
AATATAAATATATAAATATATTAA
Found at i:3166284 original size:23 final size:22
Alignment explanation
Indices: 3166258--3166316 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
3166248 AATAATTTAA
3166258 ATATAATTATAATATTAAAAAAT
1 ATATAATTATAATATT-AAAAAT
* * *
3166281 ATATAAATATGATATTAATAAT
1 ATATAATTATAATATTAAAAAT
* *
3166303 TTATTATTATAATA
1 ATATAATTATAATA
3166317 ATCGAAAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
ATATAATTATAATATTAAAAAT
Found at i:3166840 original size:14 final size:15
Alignment explanation
Indices: 3166811--3166847 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
3166801 ATTTTTATAT
3166811 ATAA-AAATTCATAA
1 ATAATAAATTCATAA
*
3166825 ATTATAAATT-ATAA
1 ATAATAAATTCATAA
3166839 ATAATAAAT
1 ATAATAAAT
3166848 ATTGATATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (15 bp):
ATAATAAATTCATAA
Found at i:3167264 original size:26 final size:27
Alignment explanation
Indices: 3167200--3167265 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 27
3167190 TAACATATAT
3167200 AAATATTTTAAAATTTTATATAATATTA
1 AAATA-TTTAAAATTTTATATAATATTA
* *
3167228 ATATA-TCAAAA-TTTATATAA-ATTTA
1 AAATATTTAAAATTTTATATAATA-TTA
3167253 AAATATTTAAAAT
1 AAATATTTAAAAT
3167266 ATAATTATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
24 1 0.03
25 16 0.52
26 10 0.32
28 4 0.13
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
AAATATTTAAAATTTTATATAATATTA
Found at i:3170241 original size:24 final size:25
Alignment explanation
Indices: 3170190--3170243 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
3170180 TAATATGGTA
* *
3170190 ACTTGCTGAATTCGGGGCTTAGTCC
1 ACTTGCTGAATTCGGGGCTCACTCC
*
3170215 ACTTGCTGAATT-GGGGCTCACTTC
1 ACTTGCTGAATTCGGGGCTCACTCC
3170239 ACTTG
1 ACTTG
3170244 GTTGATTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (25 bp):
ACTTGCTGAATTCGGGGCTCACTCC
Found at i:3172197 original size:15 final size:15
Alignment explanation
Indices: 3172149--3172201 Score: 65
Period size: 15 Copynumber: 3.5 Consensus size: 15
3172139 AATTAAATAT
3172149 ATTATTTTATTAAAA
1 ATTATTTTATTAAAA
*
3172164 ATTATATATTATT--AT
1 ATTAT-T-TTATTAAAA
3172179 ATTATTTTATTAAAA
1 ATTATTTTATTAAAA
3172194 ATTATTTT
1 ATTATTTT
3172202 TATAATTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
13 5 0.16
14 1 0.03
15 20 0.62
16 1 0.03
17 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTATTTTATTAAAA
Found at i:3173012 original size:25 final size:24
Alignment explanation
Indices: 3172988--3173034 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3172978 ATAATCTTAT
*
3172988 TATTA-ACAATAAAATTATTTTTTA
1 TATTACAC-ATAAAATAATTTTTTA
*
3173012 TATTACACATTAAATAATTTTTT
1 TATTACACATAAAATAATTTTTT
3173035 TAAAATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (24 bp):
TATTACACATAAAATAATTTTTTA
Found at i:3174870 original size:41 final size:41
Alignment explanation
Indices: 3174794--3174881 Score: 106
Period size: 41 Copynumber: 2.1 Consensus size: 41
3174784 TATTACATCA
* * * * *
3174794 TATAATATAATATTATAATTATTATTTTATAATTTAATTTT
1 TATAATATAATATTATAATAAATATATAATAATTTAATATT
*
3174835 TTTAATATAATATTATAATAAATATAATAAT-ATTTAATATT
1 TATAATATAATATTATAATAAATAT-ATAATAATTTAATATT
3174876 TATAAT
1 TATAAT
3174882 TATGATAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 36 0.92
42 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (41 bp):
TATAATATAATATTATAATAAATATATAATAATTTAATATT
Found at i:3177210 original size:42 final size:40
Alignment explanation
Indices: 3177151--3177238 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 40
3177141 TTGATTTCAG
3177151 TTTTAATTATAAAAAATTTTAATT-TAAATAATAATTAAATAT
1 TTTTAATTATAAAAAA-TTTAATTATAAATAAT-ATTAAAT-T
* * *
3177193 TTTTAATGTAT-ATAAATTTAATTATATATAATATTTAATT
1 TTTTAAT-TATAAAAAATTTAATTATAAATAATATTAAATT
3177233 TTTTAA
1 TTTTAA
3177239 AAAAATTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
40 7 0.17
41 13 0.32
42 18 0.44
43 3 0.07
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (40 bp):
TTTTAATTATAAAAAATTTAATTATAAATAATATTAAATT
Found at i:3177222 original size:16 final size:17
Alignment explanation
Indices: 3177201--3177232 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3177191 ATTTTTAATG
3177201 TATATAA-ATTTAATTA
1 TATATAATATTTAATTA
3177217 TATATAATATTTAATT
1 TATATAATATTTAATT
3177233 TTTTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATAATATTTAATTA
Found at i:3178445 original size:3 final size:3
Alignment explanation
Indices: 3178439--3178474 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3178429 CATTTTTTTA
3178439 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3178475 TAAAGTTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3179061 original size:72 final size:72
Alignment explanation
Indices: 3178956--3179097 Score: 232
Period size: 72 Copynumber: 2.0 Consensus size: 72
3178946 GGTCACATTT
*
3178956 TCATTGGTATATTGTTGCATCCATTGTACCTTACTACCAAAGAA-ATTATATATTTTTATTCTTA
1 TCATTGGTATATTATTGCATCCATTGTACCTTACTACCAAA-AAGATTATATATTTTTATTCTTA
3179020 CAATATAA
65 CAATATAA
* * *
3179028 TCATTGGTATGTTATTGCATCCATTGTATCTTACTGCCAAAAAGATTATATATTTTTATTCTTAC
1 TCATTGGTATATTATTGCATCCATTGTACCTTACTACCAAAAAGATTATATATTTTTATTCTTAC
3179093 AATAT
66 AATAT
3179098 GTATTTTCAT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
71 2 0.03
72 63 0.97
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (72 bp):
TCATTGGTATATTATTGCATCCATTGTACCTTACTACCAAAAAGATTATATATTTTTATTCTTAC
AATATAA
Found at i:3186465 original size:13 final size:13
Alignment explanation
Indices: 3186447--3186476 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3186437 GGGTTAAAAA
3186447 AATATTTATATTC
1 AATATTTATATTC
*
3186460 AATATTTATATTT
1 AATATTTATATTC
3186473 AATA
1 AATA
3186477 ATATTCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (13 bp):
AATATTTATATTC
Found at i:3192957 original size:25 final size:26
Alignment explanation
Indices: 3192904--3192960 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
3192894 TATTTTATAC
*
3192904 AAATA-TATATTTTTAAAAAAATTTA
1 AAATATTATATATTTAAAAAAATTTA
* *
3192929 AAATATTATATATTTATATAAATTT-
1 AAATATTATATATTTAAAAAAATTTA
3192954 AAATATT
1 AAATATT
3192961 TTAATAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 12 0.43
26 16 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
AAATATTATATATTTAAAAAAATTTA
Found at i:3192967 original size:18 final size:19
Alignment explanation
Indices: 3192936--3192972 Score: 51
Period size: 17 Copynumber: 2.0 Consensus size: 19
3192926 TTAAAATATT
3192936 ATATATTTATATAAATTTAA
1 ATATATTTATAT-AATTTAA
3192956 ATAT-TTTA-ATAATTTAA
1 ATATATTTATATAATTTAA
3192973 GCAATATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 7 0.41
18 2 0.12
19 4 0.24
20 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATATTTATATAATTTAA
Found at i:3193655 original size:14 final size:14
Alignment explanation
Indices: 3193636--3193668 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3193626 ATATTTTTTA
3193636 AAATTATATAATA-T
1 AAATTAT-TAATATT
3193650 AAATTATTAATATT
1 AAATTATTAATATT
3193664 AAATT
1 AAATT
3193669 TTATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AAATTATTAATATT
Found at i:3194168 original size:15 final size:15
Alignment explanation
Indices: 3194137--3194180 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 15
3194127 ATTATGTATC
3194137 AATTTATTATCAAATAA
1 AATTTATT-T-AAATAA
3194154 AATTTATTTAAATAA
1 AATTTATTTAAATAA
3194169 AATTTATATTAA
1 AATTTAT-TTAA
3194181 GTATATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 13 0.50
16 5 0.19
17 8 0.31
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTTATTTAAATAA
Found at i:3194372 original size:14 final size:14
Alignment explanation
Indices: 3194349--3194388 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
3194339 ATACATCATA
*
3194349 TTTAAATATTAAAT
1 TTTAATTATTAAAT
3194363 TTTAATTATT-AAT
1 TTTAATTATTAAAT
*
3194376 TTCAATTATTAAA
1 TTTAATTATTAAA
3194389 CACTATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTAATTATTAAAT
Found at i:3197657 original size:13 final size:13
Alignment explanation
Indices: 3197639--3197663 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3197629 TAAAAAATAT
3197639 ATATTTATATTTA
1 ATATTTATATTTA
3197652 ATATTTATATTT
1 ATATTTATATTT
3197664 GATTTCGACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATATTTATATTTA
Found at i:3198400 original size:16 final size:17
Alignment explanation
Indices: 3198366--3198410 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 17
3198356 AGCCTAACGT
3198366 TTTATT-TTAATAGTTA
1 TTTATTATTAATAGTTA
*
3198382 TTTTTTATTAATA-TTA
1 TTTATTATTAATAGTTA
3198398 TTTATTATTAATA
1 TTTATTATTAATA
3198411 ATGATAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 20 0.77
17 6 0.23
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTATTATTAATAGTTA
Found at i:3198444 original size:27 final size:25
Alignment explanation
Indices: 3198390--3198444 Score: 58
Period size: 27 Copynumber: 2.1 Consensus size: 25
3198380 TATTTTTTAT
*
3198390 TAATATTATTTATTATTAATAATGA
1 TAATATTATTTATTATTAATAATAA
*
3198415 TAATATTTATTTTATT-TATAATTATAA
1 TAATA-TTA-TTTATTAT-TAATAATAA
3198442 TAA
1 TAA
3198445 ACACCATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 5 0.20
26 4 0.16
27 16 0.64
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
TAATATTATTTATTATTAATAATAA
Found at i:3209709 original size:4 final size:4
Alignment explanation
Indices: 3209700--3209727 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
3209690 ACTGAAAAAA
3209700 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
3209728 GGTTCATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:3216186 original size:12 final size:12
Alignment explanation
Indices: 3216142--3216197 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
3216132 TTTTTATAAA
* *
3216142 AATAATATTTTT
1 AATAATATATAT
*
3216154 AA-AATATTTAT
1 AATAATATATAT
*
3216165 ATTCAATATATAT
1 AAT-AATATATAT
*
3216178 CATAATATATAT
1 AATAATATATAT
3216190 AATAATAT
1 AATAATAT
3216198 TATTATTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
11 9 0.25
12 18 0.50
13 9 0.25
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (12 bp):
AATAATATATAT
Found at i:3222057 original size:16 final size:16
Alignment explanation
Indices: 3222032--3222063 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3222022 ATTACTCATT
3222032 ATTTAAAATTTAATAA
1 ATTTAAAATTTAATAA
*
3222048 ATTTACAATTTAATAA
1 ATTTAAAATTTAATAA
3222064 GGTAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTTAAAATTTAATAA
Found at i:3222566 original size:22 final size:22
Alignment explanation
Indices: 3222524--3222566 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
3222514 ATTTTATTTT
* *
3222524 ATTAATATTTATATATTTTATA
1 ATTAATATTTAAATATATTATA
3222546 ATTAA-ATTTAAATATAATTAT
1 ATTAATATTTAAATAT-ATTAT
3222567 TTTTATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTAATATTTAAATATATTATA
Found at i:3222927 original size:2 final size:2
Alignment explanation
Indices: 3222920--3222953 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3222910 TTATAGTTTT
3222920 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
3222954 AAACAGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3223015 original size:2 final size:2
Alignment explanation
Indices: 3223010--3223056 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
3223000 CGAAAGAGAG
3223010 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
3223052 AT AT A
1 AT AT A
3223057 AATCTTCATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3223160 original size:15 final size:14
Alignment explanation
Indices: 3223140--3223187 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
3223130 ATGAAAAAAG
3223140 TAAAAATTTATATTT
1 TAAAAATTTATA-TT
*
3223155 TAAAAA-TAATATT
1 TAAAAATTTATATT
*
3223168 TAATAAATTTAAATT
1 TAA-AAATTTATATT
3223183 TAAAA
1 TAAAA
3223188 CTCAACTCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 5 0.18
14 9 0.32
15 14 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAAAAATTTATATT
Found at i:3231586 original size:13 final size:12
Alignment explanation
Indices: 3231568--3231606 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 12
3231558 GAAATTTTAT
3231568 AAAATAAATAATA
1 AAAATAAATAA-A
3231581 AAAATAAATAAA
1 AAAATAAATAAA
3231593 AGAAATAAAATAAA
1 A-AAAT-AAATAAA
3231607 GAAAGAAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 2 0.08
13 15 0.62
14 7 0.29
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (12 bp):
AAAATAAATAAA
Found at i:3231979 original size:3 final size:3
Alignment explanation
Indices: 3231966--3231995 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
3231956 AAGTTTACTC
3231966 ATA ATTA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA AT
3231996 TAAATAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:3232893 original size:36 final size:36
Alignment explanation
Indices: 3232838--3232923 Score: 106
Period size: 36 Copynumber: 2.4 Consensus size: 36
3232828 TTTTTATTCA
3232838 ATAATAAAATATTTATTTT-AAATTTAATTATAAACAT
1 ATAA-AAAATATTTATTTTAAAATTT-ATTATAAACAT
* *
3232875 ATAAAAAATATATT-TTTTAAAATTTTTTATTAACAT
1 ATAAAAAATAT-TTATTTTAAAATTTATTATAAACAT
3232911 ATAAAAAAT-TTTA
1 ATAAAAAATATTTA
3232924 AACTTTTGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
34 2 0.05
35 1 0.02
36 29 0.66
37 12 0.27
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (36 bp):
ATAAAAAATATTTATTTTAAAATTTATTATAAACAT
Found at i:3233930 original size:13 final size:14
Alignment explanation
Indices: 3233909--3233947 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
3233899 ATGAATATAA
3233909 ATATAATATATTTT
1 ATATAATATATTTT
*
3233923 -TATTATAT-TTTT
1 ATATAATATATTTT
3233935 ATATAATATATTT
1 ATATAATATATTT
3233948 GAAATTGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 4 0.19
13 14 0.67
14 3 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATATAATATATTTT
Found at i:3234705 original size:32 final size:31
Alignment explanation
Indices: 3234669--3234737 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 31
3234659 TTTTTATTAT
*
3234669 TTTTTTATTTGAAAATCCTACTAATTTTCTAC
1 TTTTTTATGTGAAAATCCTACTAATTTTC-AC
* * *
3234701 TTTTTAATGTGAAAATCCTATTAATTTTCCC
1 TTTTTTATGTGAAAATCCTACTAATTTTCAC
3234732 TTTTTT
1 TTTTTT
3234738 TTTTTCATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 6 0.19
32 26 0.81
ACGTcount: A:0.26, C:0.14, G:0.04, T:0.55
Consensus pattern (31 bp):
TTTTTTATGTGAAAATCCTACTAATTTTCAC
Found at i:3234736 original size:31 final size:32
Alignment explanation
Indices: 3234669--3234729 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
3234659 TTTTTATTAT
* *
3234669 TTTTTTATTTGAAAATCCTACTAATTTTCTAC
1 TTTTTAATGTGAAAATCCTACTAATTTTCTAC
*
3234701 TTTTTAATGTGAAAATCCTATTAATTTTC
1 TTTTTAATGTGAAAATCCTACTAATTTTC
3234730 CCTTTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.30, C:0.13, G:0.05, T:0.52
Consensus pattern (32 bp):
TTTTTAATGTGAAAATCCTACTAATTTTCTAC
Found at i:3235480 original size:14 final size:15
Alignment explanation
Indices: 3235451--3235488 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
3235441 TATTTATATA
3235451 TTTTTATAATTAATTT
1 TTTTTA-AATTAATTT
3235467 TTTTTAAATT-ATTT
1 TTTTTAAATTAATTT
*
3235481 TTATTAAA
1 TTTTTAAA
3235489 ATAGTAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.52
15 4 0.19
16 6 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTAAATTAATTT
Found at i:3239380 original size:2 final size:2
Alignment explanation
Indices: 3239373--3239400 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3239363 AATTAAACCC
3239373 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3239401 TTAAGATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3240894 original size:29 final size:32
Alignment explanation
Indices: 3240831--3240896 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 32
3240821 TTAATAATTT
3240831 TATTA-TTATTTTTTAATATATTTTAAAAAAA
1 TATTATTTATTTTTTAATATATTTTAAAAAAA
**
3240862 TATTATTTA-TTTTTAATA-A-TTTAATGAAA
1 TATTATTTATTTTTTAATATATTTTAAAAAAA
3240891 TATTAT
1 TATTAT
3240897 CATATATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 14 0.44
30 1 0.03
31 14 0.44
32 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (32 bp):
TATTATTTATTTTTTAATATATTTTAAAAAAA
Found at i:3246867 original size:94 final size:94
Alignment explanation
Indices: 3246638--3246878 Score: 320
Period size: 94 Copynumber: 2.5 Consensus size: 94
3246628 GAAGGGTGGA
* *
3246638 TGTTAGCCAGGAGCTAACACTCAACAAACCAAACAAGTCTGCATAAACACAGACATTATTACAGA
1 TGTTAGCCAGGAGCTAACACTC-ACAAACCAAACAAGTCTGCAGAAAGACAGACATTATTACAGA
* *
3246703 TAGTCAAACGAAAAACCATGGAGTTGGTGG
65 CAGTCAAACGAAAAACCATGGAGTTGATGG
* * * * *
3246733 TGTTAGCCAGGAGCTAACACTCACAAACCAGACAAATCTGCAGAAAGACGGACATTTTTACGGAC
1 TGTTAGCCAGGAGCTAACACTCACAAACCAAACAAGTCTGCAGAAAGACAGACATTATTACAGAC
* *
3246798 AGTCGAATGAAAAACCATGGAGTTGATGG
66 AGTCAAACGAAAAACCATGGAGTTGATGG
* * * * *
3246827 TGTTAGCCAGGAGCTAACAGTCACAACCCACACTAGTCTGCTGACAAGACAG
1 TGTTAGCCAGGAGCTAACACTCACAAACCAAACAAGTCTGCAGA-AAGACAG
3246879 TCAAATGAAT
Statistics
Matches: 127, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
94 99 0.78
95 28 0.22
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (94 bp):
TGTTAGCCAGGAGCTAACACTCACAAACCAAACAAGTCTGCAGAAAGACAGACATTATTACAGAC
AGTCAAACGAAAAACCATGGAGTTGATGG
Found at i:3247003 original size:79 final size:76
Alignment explanation
Indices: 3246817--3247024 Score: 239
Period size: 74 Copynumber: 2.7 Consensus size: 76
3246807 AAAAACCATG
*
3246817 GAGTTGATGGTGTTAGCCAGGAGCTAACAGTCACAACCCACACTAGTCTGCTGACAAGACAGTCA
1 GAGTTGGTGGTGTTAGCCAGGAGCTAACAGTCACAACCCACACTAGTCTGCTGACAAGACAGTCA
3246882 AATGAATAC--
66 AATGAATACAT
* * * * *
3246891 GA--TGGACTGATGTTAGCCAGGAGCTAACGGTCACAACTCC-TACTAGTTTTCATGACAAGACA
1 GAGTTGG--TGGTGTTAGCCAGGAGCTAACAGTCACAAC-CCACACTAGTCTGC-TGACAAGACA
3246953 GTCAAATGAATATCAT
62 GTCAAATGAATA-CAT
* *
3246969 GCAGTTGGTGGTGTTAGACAGGAGCTAACAGTCACAACCCACAAC-AGCCTGCTGAC
1 G-AGTTGGTGGTGTTAGCCAGGAGCTAACAGTCACAACCCAC-ACTAGTCTGCTGAC
3247025 TGACTGAAAA
Statistics
Matches: 109, Mismatches: 13, Indels: 20
0.77 0.09 0.14
Matches are distributed among these distances:
72 2 0.02
74 38 0.35
75 24 0.22
76 1 0.01
78 7 0.06
79 32 0.29
80 2 0.02
81 3 0.03
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (76 bp):
GAGTTGGTGGTGTTAGCCAGGAGCTAACAGTCACAACCCACACTAGTCTGCTGACAAGACAGTCA
AATGAATACAT
Found at i:3248661 original size:17 final size:17
Alignment explanation
Indices: 3248635--3248668 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3248625 ACATATATAT
*
3248635 ATATATATATATATTTA
1 ATATAAATATATATTTA
3248652 ATATAAATATATATTTA
1 ATATAAATATATATTTA
3248669 TTTTTTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATAAATATATATTTA
Found at i:3248681 original size:2 final size:2
Alignment explanation
Indices: 3248621--3248665 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
3248611 AGAGCGTCGA
* * *
3248621 AT AT AC AT AT AT AT AT AT AT AT AT AT AT TT A- AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3248662 AT AT
1 AT AT
3248666 TTATTTTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3251390 original size:25 final size:27
Alignment explanation
Indices: 3251341--3251393 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
3251331 ATCATTATAA
* *
3251341 ATTTTTAAAAATAAAATATTAATAATT
1 ATTTTAAAAAATAAAATAATAATAATT
3251368 ATTTTAAAAAATAAAA-AAT-ATAATT
1 ATTTTAAAAAATAAAATAATAATAATT
3251393 A
1 A
3251394 ACTATTATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 2 0.08
27 15 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
ATTTTAAAAAATAAAATAATAATAATT
Found at i:3251399 original size:29 final size:27
Alignment explanation
Indices: 3251341--3251399 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
3251331 ATCATTATAA
* * *
3251341 ATTTTTAAAAATAAAATATTAATAATT
1 ATTTTAAAAAATAAAAAATTAATAACT
3251368 ATTTTAAAAAATAAAAAATATAATTAACT
1 ATTTTAAAAAATAAAAAAT-TAA-TAACT
3251397 ATT
1 ATT
3251400 ATCATTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 17 0.63
28 3 0.11
29 7 0.26
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (27 bp):
ATTTTAAAAAATAAAAAATTAATAACT
Found at i:3252062 original size:6 final size:6
Alignment explanation
Indices: 3252051--3252078 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3252041 AATTTTTTAA
3252051 AAAATT AAAATT AAAATT AAAATT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAA
3252079 ATTTATTTAA
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:3253837 original size:61 final size:62
Alignment explanation
Indices: 3253701--3253826 Score: 182
Period size: 62 Copynumber: 2.0 Consensus size: 62
3253691 ACATGATGAA
* * * * *
3253701 TTAATAAGAAATTGAGATGTATCTATTATCATGCTATAATGTCTTATAAAAATTATTAAAAG
1 TTAATAAGAAATTGAAATGTATCTATTAACATGATATAATGTCCTATAAAAATAATTAAAAG
* *
3253763 TTAATAAGAAATTGAAATGTGTCTATTAACAT-ATTTAATGTCCTATAAAAATAATTAAAAG
1 TTAATAAGAAATTGAAATGTATCTATTAACATGATATAATGTCCTATAAAAATAATTAAAAG
3253824 TTA
1 TTA
3253827 TCTTTCAATT
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
61 28 0.49
62 29 0.51
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.38
Consensus pattern (62 bp):
TTAATAAGAAATTGAAATGTATCTATTAACATGATATAATGTCCTATAAAAATAATTAAAAG
Found at i:3253968 original size:10 final size:10
Alignment explanation
Indices: 3253931--3253973 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
3253921 AGAAAGGGTG
3253931 AAGAAAGAAAA
1 AAGAAA-AAAA
*
3253942 TAGAAAAATAA
1 AAGAAAAA-AA
3253953 AAGAAAAAAA
1 AAGAAAAAAA
*
3253963 AGGAAAAAAA
1 AAGAAAAAAA
3253973 A
1 A
3253974 TATTTTTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 14 0.50
11 14 0.50
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:3260551 original size:20 final size:20
Alignment explanation
Indices: 3260528--3260575 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
3260518 TCAAAAACTC
* * *
3260528 ATTTTATTATTTAAAATAAT
1 ATTTTATAAATTAAAAAAAT
* *
3260548 ATTTAAAAAATTAAAAAAAT
1 ATTTTATAAATTAAAAAAAT
3260568 ATTTTATA
1 ATTTTATA
3260576 CAAAATTTAT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTTTATAAATTAAAAAAAT
Found at i:3265345 original size:6 final size:6
Alignment explanation
Indices: 3265329--3265358 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
3265319 CACGGTCGCG
*
3265329 ACGGCT TCGGCT ACGGCT ACGGCT ACGGCT
1 ACGGCT ACGGCT ACGGCT ACGGCT ACGGCT
3265359 TCTGCTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.13, C:0.33, G:0.33, T:0.20
Consensus pattern (6 bp):
ACGGCT
Found at i:3265738 original size:21 final size:20
Alignment explanation
Indices: 3265695--3265734 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3265685 TTATATGGTA
**
3265695 AAAAAATATTTTTAAAAAAT
1 AAAAAATATGGTTAAAAAAT
*
3265715 AAAAAATATGGTTATAAAAT
1 AAAAAATATGGTTAAAAAAT
3265735 TAAATATAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
AAAAAATATGGTTAAAAAAT
Found at i:3265804 original size:40 final size:40
Alignment explanation
Indices: 3265734--3265821 Score: 124
Period size: 40 Copynumber: 2.1 Consensus size: 40
3265724 GGTTATAAAA
*
3265734 TTAAATATAAAAAAATATGAAATTTTTTAAATAAATAATTTT
1 TTAAA-ATAAAAAAATA-GAAATTTTTTAAATAAATAACTTT
3265776 TTAAAATAATAAAAATA-AAATTTTTTAAATAAATAACTTT
1 TTAAAATAA-AAAAATAGAAATTTTTTAAATAAATAACTTT
*
3265816 TAAAAA
1 TTAAAA
3265822 AATTATAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 27 0.63
41 4 0.09
42 12 0.28
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (40 bp):
TTAAAATAAAAAAATAGAAATTTTTTAAATAAATAACTTT
Found at i:3265877 original size:12 final size:11
Alignment explanation
Indices: 3265855--3265888 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
3265845 TACATAATTT
3265855 TTATAAAAATA
1 TTATAAAAATA
3265866 TTATATAAAATA
1 TTATA-AAAATA
3265878 TTA-AAAAATA
1 TTATAAAAATA
3265888 T
1 T
3265889 AAATATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.32
11 6 0.27
12 9 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TTATAAAAATA
Found at i:3268564 original size:2 final size:2
Alignment explanation
Indices: 3268559--3268590 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3268549 TTTTTTTTTT
3268559 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3268591 GAAGAATGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Done.