Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold59
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: 3999109
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 268233 characters in sequence are not A, C, G, or T
File 14 of 25
Found at i:2124057 original size:16 final size:16
Alignment explanation
Indices: 2124009--2124068 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
2123999 CATGAAAATA
2124009 ATAA-ATAAAAATAAT
1 ATAATATAAAAATAAT
2124024 -T-ATATGATAAAA-AAT
1 ATAATAT-A-AAAATAAT
2124039 ATAATATAAAAATAAT
1 ATAATATAAAAATAAT
* *
2124055 ATAAAATATAAATA
1 ATAATATAAAAATA
2124069 TTTTAAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
13 1 0.03
14 3 0.08
15 8 0.22
16 21 0.57
17 4 0.11
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (16 bp):
ATAATATAAAAATAAT
Found at i:2124075 original size:16 final size:16
Alignment explanation
Indices: 2124038--2124091 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
2124028 TGATAAAAAA
* * *
2124038 TATAATATAAAAATAA
1 TATAAAATATAAATAT
2124054 TATAAAATATAAATAT
1 TATAAAATATAAATAT
* * *
2124070 TTTAAAATTTATATAT
1 TATAAAATATAAATAT
2124086 TATAAA
1 TATAAA
2124092 CTATTAATTA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATAAAATATAAATAT
Found at i:2125322 original size:3 final size:3
Alignment explanation
Indices: 2125298--2125350 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
2125288 TTGAGTCCTA
* * *
2125298 ACT AC- ACT ACT GCT GCT GCT ACT ACT ACT ACT ACT ACT ACT ACT ACT
1 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT
2125345 ACT ACT
1 ACT ACT
2125351 CATTTTCTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.28, C:0.34, G:0.06, T:0.32
Consensus pattern (3 bp):
ACT
Found at i:2128089 original size:22 final size:22
Alignment explanation
Indices: 2128064--2128118 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 22
2128054 TATATTAATA
*
2128064 ATATA-ATTTAT-TTATAAATT
1 ATATATATTTATATAATAAATT
*
2128084 ATATATTTTTATATAAT-AATT
1 ATATATATTTATATAATAAATT
*
2128105 -TATATATTAATATA
1 ATATATATTTATATA
2128119 TATTTCATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 17 0.59
21 9 0.31
22 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATATATATTTATATAATAAATT
Found at i:2128119 original size:22 final size:22
Alignment explanation
Indices: 2128077--2128120 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2128067 TAATTTATTT
**
2128077 ATAAATTATATATTTTTATATA
1 ATAAATTATATATTAATATATA
*
2128099 ATAATTTATATATTAATATATA
1 ATAAATTATATATTAATATATA
2128121 TTTCATATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATAAATTATATATTAATATATA
Found at i:2128762 original size:18 final size:18
Alignment explanation
Indices: 2128739--2128777 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2128729 ATTAATTATT
2128739 ATATTTATATT-TTATTTA
1 ATATTTAT-TTATTATTTA
*
2128757 ATATTTATTTATTTTTTA
1 ATATTTATTTATTATTTA
2128775 ATA
1 ATA
2128778 AATTTATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATATTTATTTATTATTTA
Found at i:2129120 original size:16 final size:16
Alignment explanation
Indices: 2129096--2129128 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2129086 ACTTTATTTT
*
2129096 ATTATTTAATTTTAAA
1 ATTAATTAATTTTAAA
2129112 ATTAATTAATTTTAAA
1 ATTAATTAATTTTAAA
2129128 A
1 A
2129129 ATAAATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTAATTAATTTTAAA
Found at i:2129135 original size:17 final size:16
Alignment explanation
Indices: 2129101--2129140 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
2129091 ATTTTATTAT
*
2129101 TTAATTTTAAAATTAA
1 TTAATTTTAAAATAAA
2129117 TTAATTTTAAAAATAAA
1 TTAATTTT-AAAATAAA
*
2129134 TTTATTT
1 TTAATTT
2129141 AATTAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATTTTAAAATAAA
Found at i:2129157 original size:26 final size:25
Alignment explanation
Indices: 2129113--2129165 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
2129103 AATTTTAAAA
2129113 TTAATTAATTTTAAAAATAAATTTAT
1 TTAATTAATTTTAAAAAT-AATTTAT
** *
2129139 TTAATTAATTTTATCAATAGTTTAT
1 TTAATTAATTTTAAAAATAATTTAT
2129164 TT
1 TT
2129166 TAAAAATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (25 bp):
TTAATTAATTTTAAAAATAATTTAT
Found at i:2129332 original size:21 final size:21
Alignment explanation
Indices: 2129288--2129333 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2129278 ATTACACATA
* *
2129288 TTATATAATATATAATTATTT
1 TTATATAATATATAAATATAT
2129309 TTATATAATAATATAAATA-AT
1 TTATATAAT-ATATAAATATAT
2129330 TTAT
1 TTAT
2129334 TTTTTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATATAATATATAAATATAT
Found at i:2129584 original size:9 final size:10
Alignment explanation
Indices: 2129572--2129605 Score: 52
Period size: 11 Copynumber: 3.4 Consensus size: 10
2129562 TAATTATTTT
2129572 AATAAATA-A
1 AATAAATATA
2129581 AATAAATATA
1 AATAAATATA
2129591 ATATAAATATA
1 A-ATAAATATA
2129602 AATA
1 AATA
2129606 TTTAAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 8 0.35
10 5 0.22
11 10 0.43
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AATAAATATA
Found at i:2129621 original size:19 final size:19
Alignment explanation
Indices: 2129597--2129710 Score: 66
Period size: 19 Copynumber: 6.3 Consensus size: 19
2129587 TATAATATAA
*
2129597 ATATAAATATTTAAAATTT
1 ATATAAATATATAAAATTT
*
2129616 ATAT-AATA-CT-AAA-TT
1 ATATAAATATATAAAATTT
*
2129631 AT-TAATATATAAAAAATTT
1 ATATAA-ATATATAAAATTT
2129650 ATATAAATATA-AAATATTTT
1 ATATAAATATATAAA-A-TTT
* * *
2129670 AAATAAAT-TATAACA-TA
1 ATATAAATATATAAAATTT
*
2129687 ATA-AAATATAAAAAAATTT
1 ATATAAATAT-ATAAAATTT
2129706 ATATA
1 ATATA
2129711 CACAAATTAT
Statistics
Matches: 72, Mismatches: 10, Indels: 25
0.67 0.09 0.23
Matches are distributed among these distances:
14 1 0.01
15 5 0.07
16 10 0.14
17 5 0.07
18 14 0.19
19 21 0.29
20 16 0.22
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
ATATAAATATATAAAATTT
Found at i:2129628 original size:17 final size:16
Alignment explanation
Indices: 2129569--2129664 Score: 58
Period size: 17 Copynumber: 6.1 Consensus size: 16
2129559 ATATAATTAT
2129569 TTTA-ATAA-ATAAAA
1 TTTATATAATATAAAA
**
2129583 TAAATATAATAT-AAA
1 TTTATATAATATAAAA
* * *
2129598 TATAAAT-ATTTAAAA
1 TTTATATAATATAAAA
*
2129613 TTTATATAATACTAAAT
1 TTTATATAATA-TAAAA
*
2129630 TATTA-ATATATAAAAAA
1 T-TTATATA-ATATAAAA
2129647 TTTATATAAATATAAAA
1 TTTATAT-AATATAAAA
2129664 T
1 T
2129665 ATTTTAAATA
Statistics
Matches: 61, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
14 5 0.08
15 20 0.33
16 7 0.11
17 22 0.36
18 7 0.11
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (16 bp):
TTTATATAATATAAAA
Found at i:2129652 original size:34 final size:30
Alignment explanation
Indices: 2129586--2129710 Score: 93
Period size: 34 Copynumber: 4.2 Consensus size: 30
2129576 AATAAAATAA
**
2129586 ATATAATATAAATATAAATATTTAAAATTT
1 ATATAATATAAATATAAATATAAAAAATTT
2129616 ATATAATACTAAATTATTAATATATAAAAAATTT
1 ATATAATA-TAAA-TA-TAA-ATATAAAAAATTT
* *
2129650 ATATAAATATAAA-AT-ATTTTAAATAAA--T
1 ATAT-AATATAAATATAAATATAAA-AAATTT
*
2129678 -TATAACAT-AATA-AAATATAAAAAAATTT
1 ATATAATATAAATATAAATAT-AAAAAATTT
2129706 ATATA
1 ATATA
2129711 CACAAATTAT
Statistics
Matches: 76, Mismatches: 7, Indels: 25
0.70 0.06 0.23
Matches are distributed among these distances:
25 2 0.03
26 11 0.14
27 6 0.08
28 2 0.03
29 9 0.12
30 12 0.16
31 5 0.07
32 3 0.04
33 3 0.04
34 19 0.25
35 4 0.05
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (30 bp):
ATATAATATAAATATAAATATAAAAAATTT
Found at i:2129675 original size:20 final size:19
Alignment explanation
Indices: 2129637--2129682 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
2129627 AATTATTAAT
*
2129637 ATATAAAAAATTTATATAA
1 ATATAAAAAATTTAAATAA
*
2129656 ATATAAAATATTTTAAATAA
1 ATATAAAA-AATTTAAATAA
2129676 ATTATAA
1 A-TATAA
2129683 CATAATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 8 0.35
20 10 0.43
21 5 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATATAAAAAATTTAAATAA
Found at i:2129710 original size:29 final size:27
Alignment explanation
Indices: 2129634--2129710 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 27
2129624 CTAAATTATT
2129634 AATATATAAAAAATTTATATAAATATAA
1 AATATA-AAAAAATTTATATAAATATAA
* *
2129662 AATATTTTAAATAAA-TTATA-ACATAATAA
1 AATA---TAAAAAAATTTATATAAAT-ATAA
2129691 AATATAAAAAAATTTATATA
1 AATATAAAAAAATTTATATA
2129711 CACAAATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
26 7 0.17
27 5 0.12
28 8 0.20
29 13 0.32
30 5 0.12
31 2 0.05
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (27 bp):
AATATAAAAAAATTTATATAAATATAA
Found at i:2133251 original size:196 final size:199
Alignment explanation
Indices: 2132951--2133347 Score: 606
Period size: 196 Copynumber: 2.0 Consensus size: 199
2132941 CAACTATAGC
* * * *
2132951 TACATCTTGAAATTAGAAGTGTTGGGGTTTTGGTTTAAAAAAATTTTAAATTATCTATTGAGATT
1 TACAACTTGAAACTAGAAGTGTTAGGGTTGTGGTTTAAAAAAATTTTAAATTATCTATTGAGATT
* * *
2133016 TATTTTCAGTAATGGTTTAGTTTGTATATATTATTTATATTTATTGTTTATAATTAATAAAATAT
66 TATTTTCAGTAATGGTTTAATTTGTATATATTATTTATATTTATTATTTAAAATTAATAAAATAT
*
2133081 T-TAAAAATATTTTTATATTAATATTTATATATTTTATAATTAAAATTAAATTAAAATATTTTTT
131 TAT-AAAATATTTTTATATTAATATTTATATATTTTATAATTAAAATTAAATAAAAATA-TTTTT
2133145 AATTAT
194 AATTAT
* *
2133151 TACAACTTGAAACTAGAGGTGTTAGGG-TGTGGTTTAAAAAAATTTTAAA-T-TCTATTTAGATT
1 TACAACTTGAAACTAGAAGTGTTAGGGTTGTGGTTTAAAAAAATTTTAAATTATCTATTGAGATT
** *
2133213 TATTTTTTGT-ATGGTTTAATTTGTTTATATTATTTATATTTATTATTTAAAATTAATAAAATAT
66 TATTTTCAGTAATGGTTTAATTTGTATATATTATTTATATTTATTATTTAAAATTAATAAAATAT
* *
2133277 TATAAATTATTTTTATATTAATATTTATATATTTTATAATTATAATTAAATAAAAATATTTTTAA
131 TATAAAATATTTTTATATTAATATTTATATATTTTATAATTAAAATTAAATAAAAATATTTTTAA
2133342 TTAT
196 TTAT
2133346 TA
1 TA
2133348 ATAGAATCAT
Statistics
Matches: 181, Mismatches: 15, Indels: 7
0.89 0.07 0.03
Matches are distributed among these distances:
195 13 0.07
196 103 0.57
197 20 0.11
198 1 0.01
199 21 0.12
200 23 0.13
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (199 bp):
TACAACTTGAAACTAGAAGTGTTAGGGTTGTGGTTTAAAAAAATTTTAAATTATCTATTGAGATT
TATTTTCAGTAATGGTTTAATTTGTATATATTATTTATATTTATTATTTAAAATTAATAAAATAT
TATAAAATATTTTTATATTAATATTTATATATTTTATAATTAAAATTAAATAAAAATATTTTTAA
TTAT
Found at i:2133944 original size:20 final size:20
Alignment explanation
Indices: 2133915--2133960 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
2133905 ATATTTTTAA
* *
2133915 ATATATAAATTATATA-ATAT
1 ATATAAAAATAATATATAT-T
2133935 ATATAAAAATAATATATATT
1 ATATAAAAATAATATATATT
2133955 ATATAA
1 ATATAA
2133961 TTAAAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATAAAAATAATATATATT
Found at i:2133957 original size:22 final size:24
Alignment explanation
Indices: 2133925--2133968 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
2133915 ATATATAAAT
2133925 TATATAATATAT-A-TAAAAATAA
1 TATATAATATATAATTAAAAATAA
*
2133947 TATATATTATATAATTAAAAAT
1 TATATAATATATAATTAAAAAT
2133969 TAAATTGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 1 0.05
24 7 0.37
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
TATATAATATATAATTAAAAATAA
Found at i:2134345 original size:26 final size:25
Alignment explanation
Indices: 2134315--2134364 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2134305 AATTATTATA
* *
2134315 TATTTTATATTTAATAATATTTTTTT
1 TATTTTATA-TGAAAAATATTTTTTT
2134341 TATTTTATATGAAAAATATTTTTT
1 TATTTTATATGAAAAATATTTTTT
2134365 ATTCAGTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (25 bp):
TATTTTATATGAAAAATATTTTTTT
Found at i:2140633 original size:15 final size:15
Alignment explanation
Indices: 2140613--2140644 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2140603 TTTAATTACC
*
2140613 AATTATATCAAAATT
1 AATTATATAAAAATT
2140628 AATTATATAAAAATT
1 AATTATATAAAAATT
2140643 AA
1 AA
2140645 ATTGAACACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
AATTATATAAAAATT
Found at i:2143903 original size:27 final size:26
Alignment explanation
Indices: 2143865--2144029 Score: 127
Period size: 27 Copynumber: 6.3 Consensus size: 26
2143855 GTCCGCTTTC
*
2143865 GGCACCCTTCTTCGACGCCGGCGTTT
1 GGCACTCTTCTTCGACGCCGGCGTTT
* * * * *
2143891 GGCACTCATTCTTCCACTCCTGCCTTC
1 GGCACTC-TTCTTCGACGCCGGCGTTT
* *
2143918 GGCACTCTGTCGTCGAAGCCGGCGTTT
1 GGCACTCT-TCTTCGACGCCGGCGTTT
* * **
2143945 GGAACTC--CTTCGACTCCATCGTTT
1 GGCACTCTTCTTCGACGCCGGCGTTT
** * *
2143969 GGTGCTCCGTCTTCGACTCCGGCGTTT
1 GGCACT-CTTCTTCGACGCCGGCGTTT
*
2143996 GGCTCTCTGTCTTCGACGCCGGCGTTT
1 GGCACTCT-TCTTCGACGCCGGCGTTT
2144023 GGCACTC
1 GGCACTC
2144030 CGTCAACGCC
Statistics
Matches: 105, Mismatches: 28, Indels: 11
0.73 0.19 0.08
Matches are distributed among these distances:
24 16 0.15
25 1 0.01
26 8 0.08
27 80 0.76
ACGTcount: A:0.09, C:0.36, G:0.25, T:0.30
Consensus pattern (26 bp):
GGCACTCTTCTTCGACGCCGGCGTTT
Found at i:2152366 original size:15 final size:15
Alignment explanation
Indices: 2152336--2152382 Score: 60
Period size: 14 Copynumber: 3.1 Consensus size: 15
2152326 CTTATCATTA
2152336 AAATTTTATCTTAAAT
1 AAATTTTAT-TTAAAT
2152352 AAATTTTATTTAAAT
1 AAATTTTATTTAAAT
* *
2152367 -AATATTATTTTAAT
1 AAATTTTATTTAAAT
2152381 AA
1 AA
2152383 TAATTAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 12 0.43
15 7 0.25
16 9 0.32
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
AAATTTTATTTAAAT
Found at i:2152939 original size:19 final size:19
Alignment explanation
Indices: 2152895--2152947 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
2152885 CTTATTACAA
2152895 TAAT-TATATTTTATGTAT
1 TAATATATATTTTATGTAT
* *
2152913 T-ATCATATATTTTATTTTT
1 TAAT-ATATATTTTATGTAT
2152932 TAATATATATCTTTAT
1 TAATATATAT-TTTAT
2152948 ATAAATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 2 0.07
18 1 0.03
19 19 0.66
20 7 0.24
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (19 bp):
TAATATATATTTTATGTAT
Found at i:2152977 original size:24 final size:22
Alignment explanation
Indices: 2152931--2152996 Score: 60
Period size: 24 Copynumber: 2.8 Consensus size: 22
2152921 ATTTTATTTT
* * *
2152931 TTAATATATATCTTTATATAAA
1 TTAATATATATATTTAAAAAAA
2152953 TATAATATATAATATTTAAAAAAA
1 T-TAATATAT-ATATTTAAAAAAA
*
2152977 TTAAATATATTTATATTAAA
1 TT-AATATATATAT-TTAAA
2152997 TACATATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 1 0.03
23 12 0.33
24 23 0.64
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAATATATATATTTAAAAAAA
Found at i:2152996 original size:15 final size:16
Alignment explanation
Indices: 2152976--2153009 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2152966 ATTTAAAAAA
2152976 ATTAAAT-ATATTTAT
1 ATTAAATAATATTTAT
2152991 ATTAAATACATATTTAT
1 ATTAAATA-ATATTTAT
2153008 AT
1 AT
2153010 AACATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
17 10 0.59
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTAAATAATATTTAT
Found at i:2153279 original size:11 final size:12
Alignment explanation
Indices: 2153265--2153305 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
2153255 ATATTCAATA
2153265 AATATAA-AAAT
1 AATATAATAAAT
2153276 AATATAATAAAT
1 AATATAATAAAT
*
2153288 -ATAAAATAAAAT
1 AATATAAT-AAAT
2153300 AATATA
1 AATATA
2153306 TTTAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 13 0.52
12 8 0.32
13 4 0.16
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AATATAATAAAT
Found at i:2153286 original size:20 final size:19
Alignment explanation
Indices: 2153261--2153303 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
2153251 TGATATATTC
*
2153261 AATAAATATAAAAATAATAT
1 AATAAATAT-AAAATAAAAT
2153281 AATAAATATAAAATAAAAT
1 AATAAATATAAAATAAAAT
2153300 AATA
1 AATA
2153304 TATTTAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AATAAATATAAAATAAAAT
Found at i:2153312 original size:24 final size:24
Alignment explanation
Indices: 2153244--2153314 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 24
2153234 GTCCCATTAT
* *
2153244 TAAAATATGATATATTCAATA-AATA
1 TAAAATA--ATATATTAAATATAAAA
*
2153269 TAAAAATAATATAATAAATATAAAA
1 T-AAAATAATATATTAAATATAAAA
*
2153294 TAAAATAATATATTTAATATA
1 TAAAATAATATATTAAATATA
2153315 TGTATTATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
24 28 0.72
25 5 0.13
26 6 0.15
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (24 bp):
TAAAATAATATATTAAATATAAAA
Found at i:2153357 original size:10 final size:9
Alignment explanation
Indices: 2153299--2153359 Score: 58
Period size: 9 Copynumber: 7.1 Consensus size: 9
2153289 TAAAATAAAA
2153299 TAATATATT
1 TAATATATT
*
2153308 TAATATATG
1 TAATATATT
*
2153317 TATTATATT
1 TAATATATT
*
2153326 T-AT-TTTT
1 TAATATATT
2153333 TAA-AT-TT
1 TAATATATT
2153340 TAATATATT
1 TAATATATT
2153349 TAATAATATT
1 TAAT-ATATT
2153359 T
1 T
2153360 TATGTTTGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
7 9 0.21
8 5 0.12
9 22 0.52
10 6 0.14
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (9 bp):
TAATATATT
Found at i:2153907 original size:16 final size:17
Alignment explanation
Indices: 2153888--2153920 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2153878 ATGAAATTTA
2153888 AATTTATATAA-ATTAT
1 AATTTATATAATATTAT
*
2153904 AATTTTTATAATATTAT
1 AATTTATATAATATTAT
2153921 TATATCGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AATTTATATAATATTAT
Found at i:2154101 original size:17 final size:16
Alignment explanation
Indices: 2154058--2154104 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
2154048 TAAATTATTG
2154058 TAAATTTAAAATAATT
1 TAAATTTAAAATAATT
*
2154074 TAAACTTAAAATAATT
1 TAAATTTAAAATAATT
2154090 TAAATTTTAAAATAA
1 TAAA-TTTAAAATAA
2154105 ACATGTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 19 0.68
17 9 0.32
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAATTTAAAATAATT
Found at i:2154980 original size:20 final size:20
Alignment explanation
Indices: 2154951--2155001 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
2154941 GATTTACTTC
2154951 TATTTTTTTAAGTTGAGGTT
1 TATTTTTTTAAGTTGAGGTT
*
2154971 TATTTATTTAAGTTGAGGTT
1 TATTTTTTTAAGTTGAGGTT
*
2154991 GATTTTTTTAA
1 TATTTTTTTAA
2155002 TTTTTATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.59
Consensus pattern (20 bp):
TATTTTTTTAAGTTGAGGTT
Found at i:2157222 original size:23 final size:23
Alignment explanation
Indices: 2157192--2157236 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
2157182 TAATTAATTT
2157192 ATATAATTATTATTAAAAATAAA
1 ATATAATTATTATTAAAAATAAA
*
2157215 ATATAATTATTTTTAAAAATAA
1 ATATAATTATTATTAAAAATAA
2157237 TAAAATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATATAATTATTATTAAAAATAAA
Found at i:2160652 original size:43 final size:41
Alignment explanation
Indices: 2160597--2160687 Score: 98
Period size: 43 Copynumber: 2.2 Consensus size: 41
2160587 TAAAAATTAA
*
2160597 TTAATATATTATTTAT-AAT-AATAACAATATAAAATATTATAT
1 TTAATATATTATTCATCAATAAATAA-AATA-AAAATATTAT-T
* *
2160639 TTAAGTATTTTATTCATCAATAAATTAAATAAAAATATTATT
1 TTAA-TATATTATTCATCAATAAATAAAATAAAAATATTATT
2160681 TT-ATATA
1 TTAATATA
2160688 ATAATTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
40 3 0.07
41 1 0.02
42 7 0.17
43 20 0.48
44 7 0.17
45 4 0.10
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (41 bp):
TTAATATATTATTCATCAATAAATAAAATAAAAATATTATT
Found at i:2160746 original size:14 final size:15
Alignment explanation
Indices: 2160727--2160759 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2160717 GATTAACAAA
2160727 ATTTT-ATAAATATC
1 ATTTTAATAAATATC
*
2160741 ATTTTAATAAATATT
1 ATTTTAATAAATATC
2160756 ATTT
1 ATTT
2160760 GACATTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTTAATAAATATC
Found at i:2162662 original size:15 final size:15
Alignment explanation
Indices: 2162642--2162685 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
2162632 CATATTTTTA
2162642 TTATATTTATATATT
1 TTATATTTATATATT
*
2162657 TTATATTTAAATAATT
1 TTATATTTATAT-ATT
*
2162673 ATATATTT-TATAT
1 TTATATTTATATAT
2162686 AAATTTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 2 0.08
15 13 0.52
16 10 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATATTTATATATT
Found at i:2162688 original size:21 final size:22
Alignment explanation
Indices: 2162633--2162689 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
2162623 TATTTATATC
*
2162633 ATATTTT-TATT--ATATTTAT
1 ATATTTTATATTAAATAATTAT
2162652 ATATTTTATATTTAAATAATTAT
1 ATATTTTATA-TTAAATAATTAT
2162675 ATATTTTATA-TAAAT
1 ATATTTTATATTAAAT
2162690 TTTAATTTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 7 0.21
20 2 0.06
21 7 0.21
23 17 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTTTATATTAAATAATTAT
Found at i:2162851 original size:22 final size:23
Alignment explanation
Indices: 2162826--2162869 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
2162816 TAAATTCATA
*
2162826 TTATATTATGTTTT-AATTATTT
1 TTATATTATATTTTAAATTATTT
2162848 TTATATTATATTTTAAATTATT
1 TTATATTATATTTTAAATTATT
2162870 AAATTTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (23 bp):
TTATATTATATTTTAAATTATTT
Found at i:2162855 original size:11 final size:12
Alignment explanation
Indices: 2162826--2162868 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
2162816 TAAATTCATA
*
2162826 TTATATTATGTT
1 TTATATTATATT
2162838 TTA-ATTAT-TT
1 TTATATTATATT
2162848 TTATATTATATT
1 TTATATTATATT
*
2162860 TTAAATTAT
1 TTATATTAT
2162869 TAAATTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 5 0.18
11 10 0.36
12 13 0.46
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (12 bp):
TTATATTATATT
Found at i:2162890 original size:2 final size:2
Alignment explanation
Indices: 2162883--2162915 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2162873 TTTAATATTT
2162883 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
2162916 CTCACTTTCC
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:2163357 original size:17 final size:17
Alignment explanation
Indices: 2163325--2163358 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2163315 AGAGTTAAAC
2163325 ATTTTTATGTTGATAAT
1 ATTTTTATGTTGATAAT
2163342 ATTTTATATGTT-ATAAT
1 ATTTT-TATGTTGATAAT
2163359 TTATGTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (17 bp):
ATTTTTATGTTGATAAT
Found at i:2163826 original size:21 final size:19
Alignment explanation
Indices: 2163789--2163849 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
2163779 AGTGAATTTA
* *
2163789 ATTTAATTTTTAAATTAAT
1 ATTTTATTTTAAAATTAAT
*
2163808 TTTTTATATTATAAAATTAAAT
1 ATTTTAT-TT-TAAAATT-AAT
*
2163830 ATTTTATTTTTAAATTAAT
1 ATTTTATTTTAAAATTAAT
2163849 A
1 A
2163850 AAAAATATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 9 0.26
20 8 0.24
21 8 0.24
22 9 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTTATTTTAAAATTAAT
Found at i:2164177 original size:19 final size:21
Alignment explanation
Indices: 2164140--2164178 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2164130 AATTTAATTT
2164140 AAAAATTAAAATCACTATATA
1 AAAAATTAAAATCACTATATA
2164161 AAAAATTAAAA-CA-TATAT
1 AAAAATTAAAATCACTATAT
2164179 TTTATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 2 0.11
21 11 0.61
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAAATTAAAATCACTATATA
Found at i:2164193 original size:17 final size:17
Alignment explanation
Indices: 2164173--2164206 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
2164163 AAATTAAAAC
2164173 ATATATTTTAT--TTTA
1 ATATATTTTATAATTTA
2164188 ATATATTTTATAATTTA
1 ATATATTTTATAATTTA
2164205 AT
1 AT
2164207 TTAAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 11 0.65
17 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATATTTTATAATTTA
Found at i:2164523 original size:21 final size:21
Alignment explanation
Indices: 2164474--2164511 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2164464 CAATTTAACT
2164474 TAAAAT-A-ATATTTTTATAA
1 TAAAATAATATATTTTTATAA
2164493 TAAAATAATATATTTTTAT
1 TAAAATAATATATTTTTAT
2164512 TTAAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 1 0.06
21 10 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAAATAATATATTTTTATAA
Found at i:2164942 original size:21 final size:21
Alignment explanation
Indices: 2164916--2164955 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2164906 AGTTATATGA
2164916 TAAATAAATA-ATTAAAATATT
1 TAAATAAATATA-TAAAATATT
2164937 TAAATAAATATATAAAATA
1 TAAATAAATATATAAAATA
2164956 ATAAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAATAAATATATAAAATATT
Found at i:2168519 original size:15 final size:14
Alignment explanation
Indices: 2168492--2168527 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
2168482 GACGACTTTT
2168492 AATATAATTATATA
1 AATATAATTATATA
2168506 AATATAATTTATATA
1 AATATAA-TTATATA
*
2168521 TATATAA
1 AATATAA
2168528 AATATTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATATAATTATATA
Found at i:2168724 original size:9 final size:9
Alignment explanation
Indices: 2168701--2168753 Score: 56
Period size: 9 Copynumber: 5.7 Consensus size: 9
2168691 TTATTTGATA
2168701 ATAT-AAAT
1 ATATAAAAT
2168709 ATGATAAAAT
1 AT-ATAAAAT
2168719 ATAT-AAAT
1 ATATAAAAT
2168727 ATATTAAAATTT
1 ATA-TAAAA--T
2168739 ATATAAAAT
1 ATATAAAAT
2168748 ATATAA
1 ATATAA
2168754 TACTATAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
8 9 0.23
9 12 0.31
10 9 0.23
11 5 0.13
12 4 0.10
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (9 bp):
ATATAAAAT
Found at i:2168724 original size:18 final size:17
Alignment explanation
Indices: 2168701--2168765 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 17
2168691 TTATTTGATA
2168701 ATATAAATATGATAAAAT
1 ATATAAATAT-ATAAAAT
2168719 ATATAAATATATTAAAATTT
1 ATATAAATATA-TAAAA--T
*
2168739 ATATAAA-ATATATAAT
1 ATATAAATATATAAAAT
2168755 ACTATAAATAT
1 A-TATAAATAT
2168766 GATTATAGCA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
16 2 0.05
17 7 0.17
18 21 0.51
19 3 0.07
20 8 0.20
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (17 bp):
ATATAAATATATAAAAT
Found at i:2168762 original size:17 final size:18
Alignment explanation
Indices: 2168740--2168788 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
2168730 TTAAAATTTA
2168740 TATAAAATATATAATA-C
1 TATAAAATATATAATAGC
*
2168757 TAT-AAATATGATTATAGC
1 TATAAAATAT-ATAATAGC
2168775 -ATAAAATAATATAA
1 TATAAAAT-ATATAA
2168789 GTATGATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
16 6 0.23
17 10 0.38
18 8 0.31
19 2 0.08
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (18 bp):
TATAAAATATATAATAGC
Found at i:2169140 original size:17 final size:17
Alignment explanation
Indices: 2169118--2169150 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2169108 CTATAGACTT
2169118 AATAAT-TTATATATTTA
1 AATAATATT-TATATTTA
2169135 AATAATATTTATATTT
1 AATAATATTTATATTT
2169151 TTTACGTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AATAATATTTATATTTA
Found at i:2169292 original size:29 final size:29
Alignment explanation
Indices: 2169238--2169300 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
2169228 TATATTTATA
* *
2169238 TTATATTTTATATTAAATTTTAATAATTT
1 TTATATATTATATTAAATCTTAATAATTT
*
2169267 TTATATATTATATTTATATCTT-ATAATTT
1 TTATATATTATA-TTAAATCTTAATAATTT
*
2169296 ATATA
1 TTATA
2169301 ATGTGTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (29 bp):
TTATATATTATATTAAATCTTAATAATTT
Found at i:2169423 original size:6 final size:6
Alignment explanation
Indices: 2169412--2169438 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2169402 AAATTTTATG
2169412 TAAATT TAAATT TAAATT TAAATT TAA
1 TAAATT TAAATT TAAATT TAAATT TAA
2169439 TTTTTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TAAATT
Found at i:2170681 original size:14 final size:14
Alignment explanation
Indices: 2170662--2170703 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
2170652 ATTTTATGAG
*
2170662 TAATATATATTTAA
1 TAATATATATATAA
2170676 TAATATATATATAA
1 TAATATATATATAA
2170690 TAA-ATA-ATA-AA
1 TAATATATATATAA
2170701 TAA
1 TAA
2170704 ATTTTTTATC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 5 0.19
12 3 0.11
13 3 0.11
14 16 0.59
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATATATATATAA
Found at i:2170685 original size:18 final size:18
Alignment explanation
Indices: 2170664--2170698 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2170654 TTTATGAGTA
* *
2170664 ATATATATTTAATAATAT
1 ATATATAATAAATAATAT
2170682 ATATATAATAAATAATA
1 ATATATAATAAATAATA
2170699 AATAAATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATATAATAAATAATAT
Found at i:2170757 original size:39 final size:37
Alignment explanation
Indices: 2170705--2170789 Score: 93
Period size: 37 Copynumber: 2.2 Consensus size: 37
2170695 AATAAATAAA
*
2170705 TTTTTT-ATCTTTAAAATAATATATAAAATATTTAT-TAT
1 TTTTTTAAT-TTTAAAA-AATA-ATAAAATACTTATATAT
* *
2170743 TTTTATTAATTTTAAAAAATAATATATTACTTATATAT
1 TTTT-TTAATTTTAAAAAATAATAAAATACTTATATAT
2170781 TTTTTTAAT
1 TTTTTTAAT
2170790 GATATTAGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
37 15 0.37
38 15 0.37
39 9 0.22
40 2 0.05
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (37 bp):
TTTTTTAATTTTAAAAAATAATAAAATACTTATATAT
Found at i:2180569 original size:13 final size:13
Alignment explanation
Indices: 2180551--2180593 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 13
2180541 AAATTAATAC
2180551 TTTTTTTT-GTTT
1 TTTTTTTTCGTTT
2180563 TTTTTTTTCGTTT
1 TTTTTTTTCGTTT
*
2180576 TTTCTTTGCTCGTTT
1 TTT-TTT-TTCGTTT
2180591 TTT
1 TTT
2180594 CTCTCCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 8 0.30
13 7 0.26
14 3 0.11
15 9 0.33
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.81
Consensus pattern (13 bp):
TTTTTTTTCGTTT
Found at i:2180760 original size:21 final size:21
Alignment explanation
Indices: 2180735--2180774 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2180725 TCTGTGTAAT
* *
2180735 TTTTTTATTTTATTTATTTGA
1 TTTTTTAATTTATATATTTGA
2180756 TTTTTTAATTTATATATTT
1 TTTTTTAATTTATATATTT
2180775 ATGAGTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (21 bp):
TTTTTTAATTTATATATTTGA
Found at i:2181971 original size:13 final size:13
Alignment explanation
Indices: 2181953--2181983 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2181943 TATTTTTTAA
2181953 AATATTTATATAT
1 AATATTTATATAT
*
2181966 AATATTTATATTT
1 AATATTTATATAT
2181979 AATAT
1 AATAT
2181984 ATATTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
AATATTTATATAT
Found at i:2181997 original size:10 final size:11
Alignment explanation
Indices: 2181972--2182004 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
2181962 ATATAATATT
2181972 TATATTTAATA
1 TATATTTAATA
2181983 TATATTTAA-A
1 TATATTTAATA
2181993 TATATTTAATA
1 TATATTTAATA
2182004 T
1 T
2182005 TTAAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TATATTTAATA
Found at i:2182133 original size:15 final size:15
Alignment explanation
Indices: 2182073--2182134 Score: 65
Period size: 15 Copynumber: 4.1 Consensus size: 15
2182063 TTCATATATT
*
2182073 TATTTGATATTTATA
1 TATTTTATATTTATA
*
2182088 TATTTTAT-TATACTA
1 TATTTTATATTTA-TA
*
2182103 TA-ATTATATTTAATA
1 TATTTTATATTT-ATA
2182118 TATTTTATATTTATA
1 TATTTTATATTTATA
2182133 TA
1 TA
2182135 AAATTTGATA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
14 7 0.18
15 22 0.58
16 9 0.24
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (15 bp):
TATTTTATATTTATA
Found at i:2187616 original size:117 final size:117
Alignment explanation
Indices: 2187469--2187698 Score: 397
Period size: 117 Copynumber: 2.0 Consensus size: 117
2187459 AACAACAGCG
* * *
2187469 GCTTCTCTCAATTCTTCTTCGAGCATTTCAATTTTGGACTCCAATTCAATTTTGTTGTTGGAAGA
1 GCTTCTCTCAATTCTTCTTCAAGCATTTCAATTTTGGACTCCAATTCAACTTTGTTGTTGGAAAA
*
2187534 GCTATTTGCATTTTCTTCACTTTCAATACACGTATTATTTGTAGAACCATTA
66 GCTATTTGCATTTTCTTCACTTTCAATACACGTATCATTTGTAGAACCATTA
2187586 GCTTCTCTCAATTCTTCTTCAAGCATTTCAATTTTGGACTCCAATTCAACTTTGTTGTTGGAAAA
1 GCTTCTCTCAATTCTTCTTCAAGCATTTCAATTTTGGACTCCAATTCAACTTTGTTGTTGGAAAA
** *
2187651 GCTATTTGCATTTTCTTCACTTTCGTTACATGTATCATTTGTAGAACC
66 GCTATTTGCATTTTCTTCACTTTCAATACACGTATCATTTGTAGAACC
2187699 GTTATGAATC
Statistics
Matches: 106, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
117 106 1.00
ACGTcount: A:0.23, C:0.20, G:0.13, T:0.43
Consensus pattern (117 bp):
GCTTCTCTCAATTCTTCTTCAAGCATTTCAATTTTGGACTCCAATTCAACTTTGTTGTTGGAAAA
GCTATTTGCATTTTCTTCACTTTCAATACACGTATCATTTGTAGAACCATTA
Found at i:2191163 original size:18 final size:17
Alignment explanation
Indices: 2191140--2191199 Score: 50
Period size: 23 Copynumber: 3.2 Consensus size: 17
2191130 TTGTTGAAAT
2191140 TATTTTATATTATAATTA
1 TATTTTATATTA-AATTA
2191158 TATTTTAAATATTTTAAATATTA
1 TATTTT--ATA--TT-AA-ATTA
2191181 TATTTTA-ATTAAATTA
1 TATTTTATATTAAATTA
2191197 TAT
1 TAT
2191200 AATTATATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
16 7 0.19
17 2 0.06
18 8 0.22
20 4 0.11
21 1 0.03
22 3 0.08
23 11 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTTTATATTAAATTA
Found at i:2191222 original size:17 final size:15
Alignment explanation
Indices: 2191188--2191230 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
2191178 TTATATTTTA
*
2191188 ATTAAATTATATAATT
1 ATTAAATT-TAAAATT
2191204 ATATAATATTTAAAATT
1 AT-TAA-ATTTAAAATT
2191221 ATTAAATTTA
1 ATTAAATTTA
2191231 TTGATGCACG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 5 0.21
16 5 0.21
17 11 0.46
18 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTAAATTTAAAATT
Found at i:2192044 original size:18 final size:18
Alignment explanation
Indices: 2192021--2192074 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
2192011 TTTAATCATA
2192021 TAAATATAATATAAATAT
1 TAAATATAATATAAATAT
2192039 TAAATATAATATAAA-A-
1 TAAATATAATATAAATAT
2192055 TAAAT-TAAATATATAATAT
1 TAAATAT-AATATA-AATAT
2192074 T
1 T
2192075 TATATTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.03
16 11 0.34
17 3 0.09
18 16 0.50
19 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAATATAATATAAATAT
Found at i:2192051 original size:23 final size:23
Alignment explanation
Indices: 2192018--2192073 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
2192008 TTTTTTAATC
* *
2192018 ATATA-AATATAATATAAATATTA
1 ATATATAATATAAAATAAAT-TAA
2192041 A-ATATAATATAAAATAAATTAA
1 ATATATAATATAAAATAAATTAA
2192063 ATATATAATAT
1 ATATATAATAT
2192074 TTATATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 6 0.21
23 23 0.79
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
ATATATAATATAAAATAAATTAA
Found at i:2192065 original size:16 final size:16
Alignment explanation
Indices: 2192020--2192072 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
2192010 TTTTAATCAT
2192020 ATAAATATAATATAAA
1 ATAAATATAATATAAA
2192036 TATTAAATATAATATAAA
1 -A-TAAATATAATATAAA
*
2192054 ATAAAT-TAAATATATA
1 ATAAATAT-AATATAAA
2192070 ATA
1 ATA
2192073 TTTATATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
15 1 0.03
16 15 0.45
17 2 0.06
18 15 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAAATATAATATAAA
Found at i:2197544 original size:28 final size:28
Alignment explanation
Indices: 2197512--2197565 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
2197502 TAATTAAAAT
2197512 ATTTA-AAAAAATTTTAAACTGTAATTTA
1 ATTTATAAAAAATTTTAAACT-TAATTTA
* *
2197540 ATTTATACAAAATTTTAATCTTAATT
1 ATTTATAAAAAATTTTAAACTTAATT
2197566 AACCGTAGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (28 bp):
ATTTATAAAAAATTTTAAACTTAATTTA
Found at i:2199491 original size:23 final size:23
Alignment explanation
Indices: 2199438--2199492 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
2199428 ATTTTAAATT
* *
2199438 TATTAATATTTATATATATTTTA
1 TATTAATATGTAAATATATTTTA
*
2199461 TATAAATATGTAAATATATTTGTA
1 TATTAATATGTAAATATATTT-TA
2199485 T-TTAATAT
1 TATTAATAT
2199493 ATATAATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 24 0.89
24 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (23 bp):
TATTAATATGTAAATATATTTTA
Found at i:2199503 original size:14 final size:15
Alignment explanation
Indices: 2199459--2199531 Score: 51
Period size: 15 Copynumber: 4.9 Consensus size: 15
2199449 ATATATATTT
*
2199459 TATATAAATATGTAAA
1 TATATAAATAT-TTAA
***
2199475 TATATTTGTATTTAA
1 TATATAAATATTTAA
*
2199490 TATATATA-ATTTAA
1 TATATAAATATTTAA
*
2199504 AATTATAAATATTTAA
1 TA-TATAAATATTTAA
*
2199520 TATTTAAA-ATTT
1 TATATAAATATTT
2199532 TTAAAGATAA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
14 11 0.24
15 19 0.42
16 15 0.33
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (15 bp):
TATATAAATATTTAA
Found at i:2199657 original size:18 final size:18
Alignment explanation
Indices: 2199634--2199673 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2199624 TAAAAGATAA
*
2199634 AAATTTAATTAAAATATT
1 AAATTTAATTAAAAAATT
**
2199652 AAATTTTTTTAAAAAATT
1 AAATTTAATTAAAAAATT
2199670 AAAT
1 AAAT
2199674 AAATAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATTTAATTAAAAAATT
Found at i:2199670 original size:26 final size:27
Alignment explanation
Indices: 2199640--2199699 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
2199630 ATAAAAATTT
* *
2199640 AATTAAAAT-ATTAAATTTTTTTAAAA
1 AATTAAAATAAATAAAATTTTTTAAAA
2199666 AATT-AAATAAATAAAATTTTTTAAAA
1 AATTAAAATAAATAAAATTTTTTAAAA
2199692 AATTAAAA
1 AATTAAAA
2199700 ATTTGTCCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 4 0.13
26 23 0.77
27 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
AATTAAAATAAATAAAATTTTTTAAAA
Found at i:2201887 original size:24 final size:25
Alignment explanation
Indices: 2201829--2201890 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
2201819 TAGTATCTTT
2201829 TAATTTTTTTAAAATTAATTATTCACA
1 TAATTTTTTT--AATTAATTATTCACA
* *
2201856 T-ATATTTTTAATTTATTATT-ACA
1 TAATTTTTTTAATTAATTATTCACA
2201879 TAATTTTTTTAA
1 TAATTTTTTTAA
2201891 AAAAAATTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 4 0.13
24 19 0.61
26 7 0.23
27 1 0.03
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (25 bp):
TAATTTTTTTAATTAATTATTCACA
Found at i:2207101 original size:28 final size:28
Alignment explanation
Indices: 2207061--2207123 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
2207051 TTTTATATGA
2207061 TGATCAAAGCTGGAAAACAAACATCTGG
1 TGATCAAAGCTGGAAAACAAACATCTGG
*
2207089 TGATCAAAGCTGGAAAACAAACTTCTGG
1 TGATCAAAGCTGGAAAACAAACATCTGG
2207117 TGATCAA
1 TGATCAA
2207124 GAAAAGGCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21
Consensus pattern (28 bp):
TGATCAAAGCTGGAAAACAAACATCTGG
Found at i:2211328 original size:16 final size:16
Alignment explanation
Indices: 2211258--2211328 Score: 65
Period size: 16 Copynumber: 4.4 Consensus size: 16
2211248 TATGATTAAA
*
2211258 AAATTTTATATTTATAT
1 AAATTTTAAATTT-TAT
* *
2211275 AAATTTT-AATATAAT
1 AAATTTTAAATTTTAT
*
2211290 -AATATTTATATTTTAT
1 AAAT-TTTAAATTTTAT
2211306 AAATTTTAAATTTTAT
1 AAATTTTAAATTTTAT
*
2211322 ATATTTT
1 AAATTTT
2211329 GAGATAAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
14 3 0.07
15 5 0.12
16 25 0.58
17 10 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AAATTTTAAATTTTAT
Found at i:2219226 original size:12 final size:12
Alignment explanation
Indices: 2219209--2219233 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2219199 CATTAAAGTA
2219209 ATAAATTATTTT
1 ATAAATTATTTT
2219221 ATAAATTATTTT
1 ATAAATTATTTT
2219233 A
1 A
2219234 ATTTATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATAAATTATTTT
Found at i:2219513 original size:18 final size:18
Alignment explanation
Indices: 2219486--2219520 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2219476 TTAAATACAG
2219486 ATATAATATATGTATTAA
1 ATATAATATATGTATTAA
* *
2219504 ATATATTATATTTATTA
1 ATATAATATATGTATTA
2219521 TTTTATTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
ATATAATATATGTATTAA
Found at i:2220157 original size:21 final size:22
Alignment explanation
Indices: 2220128--2220172 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2220118 GTTAAATTTC
*
2220128 TAAACTTTAATTTTATAAAA-AA
1 TAAACTTTAAGTTTA-AAAATAA
2220150 TAAA-TTTAAGTTTAAAAATAA
1 TAAACTTTAAGTTTAAAAATAA
2220171 TA
1 TA
2220173 TATTAGATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 13 0.62
22 4 0.19
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAACTTTAAGTTTAAAAATAA
Found at i:2220390 original size:2 final size:2
Alignment explanation
Indices: 2220383--2220424 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2220373 TAGCTATGTT
2220383 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2220425 AACAAGCCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2220728 original size:2 final size:2
Alignment explanation
Indices: 2220721--2220763 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2220711 ATGATGATCC
2220721 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2220763 T
1 T
2220764 TTAATCAGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2220903 original size:10 final size:10
Alignment explanation
Indices: 2220890--2220929 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
2220880 TAGATTTATC
2220890 TTATTTATTT
1 TTATTTATTT
2220900 TTA-TTATTAT
1 TTATTTATT-T
2220910 TTATTTATTT
1 TTATTTATTT
*
2220920 TTATTAATTT
1 TTATTTATTT
2220930 ACAATAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 5 0.19
10 17 0.63
11 5 0.19
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (10 bp):
TTATTTATTT
Found at i:2220915 original size:20 final size:21
Alignment explanation
Indices: 2220885--2220925 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
2220875 TTTGATAGAT
2220885 TTATCTTATTTATTTTTATTA
1 TTATCTTATTTATTTTTATTA
2220906 TTAT-TTATTTATTTTTATTA
1 TTATCTTATTTATTTTTATTA
2220926 ATTTACAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (21 bp):
TTATCTTATTTATTTTTATTA
Found at i:2222017 original size:3 final size:3
Alignment explanation
Indices: 2222011--2222036 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2222001 ATAACATGTT
2222011 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
2222037 TTGTTAAATT
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:2222913 original size:23 final size:22
Alignment explanation
Indices: 2222869--2222916 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
2222859 GCTTATTTTG
* *
2222869 ATTATTTATTATTTATGTTTAA
1 ATTATTTAATATTTATGATTAA
*
2222891 ATTATTATAATATTTTTGATTAA
1 ATTATT-TAATATTTATGATTAA
2222914 ATT
1 ATT
2222917 TAATGTCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (22 bp):
ATTATTTAATATTTATGATTAA
Found at i:2223135 original size:44 final size:45
Alignment explanation
Indices: 2223049--2223134 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 45
2223039 AACTACCATT
*
2223049 TTTTATTTTAAAATTCAAAATTTTCGCAATGAAATAATTTTTTAA
1 TTTTATTTTAAAATCCAAAATTTTCGCAATGAAATAATTTTTTAA
* * *
2223094 TTTT-TTTT-AAATCCACAATTTTTGTAATGAAATAATTTTTT
1 TTTTATTTTAAAATCCAAAATTTTCGCAATGAAATAATTTTTT
2223135 TCATTAACAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 29 0.78
44 4 0.11
45 4 0.11
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (45 bp):
TTTTATTTTAAAATCCAAAATTTTCGCAATGAAATAATTTTTTAA
Found at i:2223574 original size:2 final size:2
Alignment explanation
Indices: 2223562--2223593 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2223552 TTATTTTGTT
*
2223562 TA TA CA 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
2223594 AGTATCATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2225844 original size:101 final size:101
Alignment explanation
Indices: 2225737--2225940 Score: 291
Period size: 101 Copynumber: 2.0 Consensus size: 101
2225727 ATGAACACCA
* * * *
2225737 AACTATTTCTACCACCATGCCTCATGCCATTAACAACAATCATAATTTCATGTATAACCACACAA
1 AACTATTTCTACCACCATGCCTCACGCCATTAAAAACAATAATAATTTCATGCATAACCACACAA
*
2225802 TGCTATAAACCTTGTGTCCAATTTATTAAACACATG
66 TGCTATAAACCTTGTGTCCAATTGATTAAACACATG
* * * * * *
2225838 AACTATTTCTTCCTCCATGCTTCACGCTATTAAAAACAATAATAATTTCTTGCATAACCAGACAA
1 AACTATTTCTACCACCATGCCTCACGCCATTAAAAACAATAATAATTTCATGCATAACCACACAA
* *
2225903 TGCTATAAACCTTGTGTTCAGTTGATTAAACACATG
66 TGCTATAAACCTTGTGTCCAATTGATTAAACACATG
2225939 AA
1 AA
2225941 ACATTCAATT
Statistics
Matches: 90, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
101 90 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (101 bp):
AACTATTTCTACCACCATGCCTCACGCCATTAAAAACAATAATAATTTCATGCATAACCACACAA
TGCTATAAACCTTGTGTCCAATTGATTAAACACATG
Found at i:2227582 original size:36 final size:33
Alignment explanation
Indices: 2227511--2227593 Score: 103
Period size: 36 Copynumber: 2.4 Consensus size: 33
2227501 GTTGCGTTGT
* **
2227511 TTTACAAGACAACTTTTACGTGTAAGTTATGTC
1 TTTACAAGACAACTTTTACATCAAAGTTATGTC
2227544 TTTACAAGACAACTTTTACAATACAAGAGTTATGTC
1 TTTACAAGACAACTTTTAC-AT-CAA-AGTTATGTC
*
2227580 TTTAAAAGACAACT
1 TTTACAAGACAACT
2227594 AATCAAGAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
33 19 0.44
34 1 0.02
35 1 0.02
36 22 0.51
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (33 bp):
TTTACAAGACAACTTTTACATCAAAGTTATGTC
Found at i:2233203 original size:2 final size:2
Alignment explanation
Indices: 2233196--2233250 Score: 60
Period size: 2 Copynumber: 28.0 Consensus size: 2
2233186 ACTCTGGCAA
*
2233196 AT AT AT AT CAT CT AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
2233237 AT AT GT AC AT AT AT
1 AT AT AT AT AT AT AT
2233251 GATACAAGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
1 2 0.05
2 40 0.91
3 2 0.05
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2236930 original size:11 final size:10
Alignment explanation
Indices: 2236889--2236939 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
2236879 ATAATTAACA
2236889 TAAATATATT
1 TAAATATATT
* *
2236899 T-AATTTTTT
1 TAAATATATT
*
2236908 TAAATATTTT
1 TAAATATATT
*
2236918 TATATCATATT
1 TAAAT-ATATT
2236929 TAAATATATT
1 TAAATATATT
2236939 T
1 T
2236940 TTGAATACCG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
9 7 0.21
10 18 0.55
11 8 0.24
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (10 bp):
TAAATATATT
Found at i:2238858 original size:26 final size:26
Alignment explanation
Indices: 2238807--2238860 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
2238797 TATTTTTTGA
* **
2238807 TATTTTAACTACTAACACTACTTTTT
1 TATTGTAACTACTAACACTAAGTTTT
2238833 TATTGTAA-TACTAAACACTAAGTTTT
1 TATTGTAACTACT-AACACTAAGTTTT
2238859 TA
1 TA
2238861 ACTATATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.35, C:0.15, G:0.04, T:0.46
Consensus pattern (26 bp):
TATTGTAACTACTAACACTAAGTTTT
Found at i:2240753 original size:20 final size:20
Alignment explanation
Indices: 2240730--2240774 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2240720 CTAATTTGAT
*
2240730 ATATTAAAAATTATGATATG
1 ATATTAAAAATTATAATATG
* *
2240750 ATATTAGAGATTATAATATG
1 ATATTAAAAATTATAATATG
2240770 ATATT
1 ATATT
2240775 TTTGTTTCGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (20 bp):
ATATTAAAAATTATAATATG
Found at i:2241438 original size:3 final size:3
Alignment explanation
Indices: 2241430--2241461 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2241420 ATTTAATAAA
*
2241430 TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2241462 ATCTTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2244239 original size:45 final size:46
Alignment explanation
Indices: 2244166--2244259 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 46
2244156 AACTTTTTAG
** *
2244166 GGTAATTAGAGAAAAAGGCAACGTGGAAAATAAGCAAGTATGCTAT
1 GGTAATTAGAGAAAAAGGCAAAATGGAAAATAAGCAACTATGCTAT
2244212 GGTAATTAGAG-AAAAGGCAAAATGGAAAATAAGCAACTATGCTAT
1 GGTAATTAGAGAAAAAGGCAAAATGGAAAATAAGCAACTATGCTAT
2244257 GGT
1 GGT
2244260 GAATAGATGA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 34 0.76
46 11 0.24
ACGTcount: A:0.46, C:0.09, G:0.26, T:0.20
Consensus pattern (46 bp):
GGTAATTAGAGAAAAAGGCAAAATGGAAAATAAGCAACTATGCTAT
Found at i:2247844 original size:13 final size:13
Alignment explanation
Indices: 2247826--2247850 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2247816 TATTCAAATT
2247826 TAAATATAAATAC
1 TAAATATAAATAC
2247839 TAAATATAAATA
1 TAAATATAAATA
2247851 TATTTAATTT
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAATATAAATAC
Found at i:2248339 original size:20 final size:20
Alignment explanation
Indices: 2248316--2248355 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2248306 AGTTATATTT
*
2248316 TATAAT-TTAATATTAATAAA
1 TATAATATTAA-ATAAATAAA
2248336 TATAATATTAAATAAATAAA
1 TATAATATTAAATAAATAAA
2248356 AAAAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TATAATATTAAATAAATAAA
Found at i:2248341 original size:15 final size:16
Alignment explanation
Indices: 2248323--2248353 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2248313 TTTTATAATT
2248323 TAATATT-AATAAATA
1 TAATATTAAATAAATA
2248338 TAATATTAAATAAATA
1 TAATATTAAATAAATA
2248354 AAAAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATATTAAATAAATA
Found at i:2248769 original size:24 final size:22
Alignment explanation
Indices: 2248711--2248770 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 22
2248701 GTTAAAACTG
*
2248711 TTAATTTACTATTTTGATTTTT
1 TTAATTTAATATTTTGATTTTT
2248733 TTAATAATTAATATTTATGATTATTT
1 TTAAT--TTAATATTT-TGATT-TTT
*
2248759 TTAATTAAATAT
1 TTAATTTAATAT
2248771 AATAATATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 5 0.16
24 14 0.44
25 5 0.16
26 8 0.25
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (22 bp):
TTAATTTAATATTTTGATTTTT
Found at i:2248781 original size:19 final size:19
Alignment explanation
Indices: 2248759--2248812 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
2248749 ATGATTATTT
2248759 TTAATTAAATATAATAATA
1 TTAATTAAATATAATAATA
* *
2248778 TTAATTATATATAATCATA
1 TTAATTAAATATAATAATA
* *
2248797 ATAAATATAATATAAT
1 TTAATTA-AATATAAT
2248813 TAAAAAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 22 0.76
20 7 0.24
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAATTAAATATAATAATA
Found at i:2248786 original size:15 final size:16
Alignment explanation
Indices: 2248762--2248812 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 16
2248752 ATTATTTTTA
2248762 ATTAAATATA-ATAAT
1 ATTAAATATATATAAT
*
2248777 ATTAATTATATATAAT
1 ATTAAATATATATAAT
2248793 CATAATAAATATAATATAAT
1 -AT--TAAATAT-ATATAAT
2248813 TAAAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 9 0.31
16 5 0.17
17 2 0.07
19 6 0.21
20 7 0.24
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTAAATATATATAAT
Found at i:2249222 original size:21 final size:21
Alignment explanation
Indices: 2249183--2249222 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2249173 CTAGATTTGT
* * *
2249183 AAAATTATTTTATTTTTTAAA
1 AAAATTATATTAATATTTAAA
2249204 AAAATTATATTAATATTTA
1 AAAATTATATTAATATTTA
2249223 TATATTTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AAAATTATATTAATATTTAAA
Found at i:2249284 original size:17 final size:17
Alignment explanation
Indices: 2249238--2249285 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
2249228 TTTATAATTC
2249238 AATTTAAA-TAAAAAAT
1 AATTTAAATTAAAAAAT
* *
2249254 ATTTTTATAATTAAACAAT
1 A-ATTTA-AATTAAAAAAT
2249273 AATTTAAATTAAA
1 AATTTAAATTAAA
2249286 TGAATTATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 1 0.04
17 11 0.42
18 6 0.23
19 8 0.31
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
AATTTAAATTAAAAAAT
Found at i:2249446 original size:17 final size:17
Alignment explanation
Indices: 2249424--2249462 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
2249414 ATGGATGATT
2249424 ATTAAAATTGTTCATGG
1 ATTAAAATTGTTCATGG
2249441 ATTAAAATTGTTCATGG
1 ATTAAAATTGTTCATGG
2249458 ATTAA
1 ATTAA
2249463 GTAGGTTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.41
Consensus pattern (17 bp):
ATTAAAATTGTTCATGG
Found at i:2249623 original size:27 final size:30
Alignment explanation
Indices: 2249593--2249653 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 30
2249583 ATTCACTTAT
*
2249593 ATTATATTTTT-TAA-AAATATAT-TTTTA
1 ATTAAATTTTTATAATAAATATATATTTTA
2249620 ATTAAATTTTTAATAATTAAATATATATTTTA
1 ATTAAATTTTT-ATAA-TAAATATATATTTTA
2249652 AT
1 AT
2249654 AAGCTTGTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 10 0.36
29 3 0.11
31 8 0.29
32 7 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
ATTAAATTTTTATAATAAATATATATTTTA
Found at i:2250414 original size:15 final size:15
Alignment explanation
Indices: 2250378--2250454 Score: 63
Period size: 15 Copynumber: 5.3 Consensus size: 15
2250368 GACATGATTT
2250378 TTATT-ATAAAAATA
1 TTATTAATAAAAATA
2250392 TT-TTAATAAATAA-A
1 TTATTAATAAA-AATA
*
2250406 TTATTAATAAAATTA
1 TTATTAATAAAAATA
* ** *
2250421 TTATTATTATTATTA
1 TTATTAATAAAAATA
2250436 TTATT-ATAAAAATAA
1 TTATTAATAAAAAT-A
2250451 TTAT
1 TTAT
2250455 ATAACTATAT
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
13 2 0.04
14 15 0.30
15 33 0.66
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTATTAATAAAAATA
Found at i:2250423 original size:3 final size:3
Alignment explanation
Indices: 2250417--2250442 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2250407 TATTAATAAA
2250417 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
2250443 AAAAATAATT
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):
ATT
Found at i:2250583 original size:17 final size:18
Alignment explanation
Indices: 2250548--2250588 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2250538 ATCTGTGTTA
2250548 ATTTTTTAAATAAATTTT
1 ATTTTTTAAATAAATTTT
**
2250566 ATTTTTTATTTAAA-TTT
1 ATTTTTTAAATAAATTTT
2250583 ATTTTT
1 ATTTTT
2250589 CATACTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTTTTAAATAAATTTT
Found at i:2251773 original size:28 final size:25
Alignment explanation
Indices: 2251717--2251776 Score: 68
Period size: 28 Copynumber: 2.3 Consensus size: 25
2251707 GTCTTGGCTT
*
2251717 TATGTTTTAAGATTGAAAAAACAAG
1 TATGTTTTAAAATTGAAAAAACAAG
2251742 TATGTTTTAATAATGTGATAAAAACATA-
1 TATGTTTTAA-AAT-TGA-AAAAACA-AG
2251770 TATGTTT
1 TATGTTT
2251777 AAGAATTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 10 0.33
26 2 0.07
27 3 0.10
28 14 0.47
29 1 0.03
ACGTcount: A:0.43, C:0.03, G:0.13, T:0.40
Consensus pattern (25 bp):
TATGTTTTAAAATTGAAAAAACAAG
Found at i:2252025 original size:19 final size:18
Alignment explanation
Indices: 2251979--2252029 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
2251969 AAAGTTGTTG
*
2251979 TTGCAATTAAATGTAGCT
1 TTGCAATTAAATGTAGCA
**
2251997 TTTAAATTAAATGTAGCAA
1 TTGCAATTAAATGTAGC-A
2252016 TTGCAATTAAATGT
1 TTGCAATTAAATGT
2252030 TACAATTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (18 bp):
TTGCAATTAAATGTAGCA
Found at i:2256768 original size:17 final size:17
Alignment explanation
Indices: 2256748--2256781 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2256738 AATTTTTTAA
2256748 TTATATT-TATATATTTT
1 TTATATTATA-ATATTTT
2256765 TTATATTATAATATTTT
1 TTATATTATAATATTTT
2256782 AATTATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATATTATAATATTTT
Found at i:2257192 original size:5 final size:5
Alignment explanation
Indices: 2257177--2257290 Score: 60
Period size: 5 Copynumber: 23.0 Consensus size: 5
2257167 TATATGTTTA
* * * *
2257177 TATAT TTTAT TATAT TATATT TAAAA TATTT TATAT T-T-T TATAAAT
1 TATAT TATAT TATAT TATA-T TATAT TATAT TATAT TATAT TAT--AT
* * * *
2257223 TTTAA TATAT TA-AT AAT-T TATAT TATAT TATAT TATAT T-TAAT TATTT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT-AT TATAT
*
2257271 TAT-T TATAT AATATT TATAT
1 TATAT TATAT TATA-T TATAT
2257291 AATCATATTT
Statistics
Matches: 81, Mismatches: 17, Indels: 22
0.68 0.14 0.18
Matches are distributed among these distances:
3 2 0.02
4 13 0.16
5 54 0.67
6 9 0.11
7 3 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:2257225 original size:41 final size:41
Alignment explanation
Indices: 2257160--2257287 Score: 114
Period size: 41 Copynumber: 3.0 Consensus size: 41
2257150 GGTATAAACT
* * *
2257160 AATAATTTATATGTTTATATATTTTATTATATTATATTTAA
1 AATATTTTATATTTTTATAAATTTTATTATATTATATTTAA
* *
2257201 AATATTTTATATTTTTATAAATTTTAATATATTAATAATTTAT
1 AATATTTTATATTTTTATAAATTTTATTATATT-AT-ATTTAA
* * *
2257244 ATTATATTATATTATATT-TAATTATTTTATTTATATAATATTTA
1 AATATTTTATATT-T-TTATAA--ATTTTA-TTATATTATATTTA
2257288 TATAATCATA
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
41 29 0.41
42 2 0.03
43 16 0.23
44 4 0.06
45 7 0.10
46 8 0.11
47 5 0.07
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (41 bp):
AATATTTTATATTTTTATAAATTTTATTATATTATATTTAA
Found at i:2257287 original size:15 final size:15
Alignment explanation
Indices: 2257228--2257314 Score: 56
Period size: 14 Copynumber: 5.7 Consensus size: 15
2257218 TAAATTTTAA
2257228 TATATTAATAATTTATAT
1 TATA-TAAT-ATTTAT-T
*
2257246 TATATTATATTATATT
1 TATATAATATT-TATT
*
2257262 TA-ATTAT-TTTATT
1 TATATAATATTTATT
*
2257275 TATATAATATTTATA
1 TATATAATATTTATT
*
2257290 TA-ATCATATTTAATAT
1 TATATAATATTT-AT-T
2257306 TATA-AATAT
1 TATATAATAT
2257315 AAATGTGATG
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
13 6 0.11
14 14 0.25
15 14 0.25
16 12 0.21
17 7 0.12
18 4 0.07
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (15 bp):
TATATAATATTTATT
Found at i:2257314 original size:30 final size:29
Alignment explanation
Indices: 2257176--2257314 Score: 96
Period size: 29 Copynumber: 4.8 Consensus size: 29
2257166 TTATATGTTT
*
2257176 ATATATTT-TATTATATTATATTTA-A-A
1 ATATATTTATATTATATAATATTTATATA
*
2257202 ATAT-TTTATATTTTTATAA-ATTTTAATATA
1 ATATATTTATA-TTATATAATA-TTT-ATATA
* * *
2257232 TTAATAATTTATATTATATTATATTATATTTA
1 AT-AT-ATTTATATTATATAATATT-TATATA
2257264 AT-TATTT-TATTTATATAATATTTATATA
1 ATATATTTATA-TTATATAATATTTATATA
2257292 ATCATATTTAATATTATA-AATAT
1 AT-ATATTT-ATATTATATAATAT
2257315 AAATGTGATG
Statistics
Matches: 88, Mismatches: 9, Indels: 28
0.70 0.07 0.22
Matches are distributed among these distances:
25 3 0.03
26 7 0.08
27 9 0.10
28 10 0.11
29 16 0.18
30 13 0.15
31 7 0.08
32 15 0.17
33 8 0.09
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.58
Consensus pattern (29 bp):
ATATATTTATATTATATAATATTTATATA
Found at i:2257727 original size:13 final size:12
Alignment explanation
Indices: 2257702--2257732 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
2257692 AATTTTAAAA
2257702 AATAAATATAAT
1 AATAAATATAAT
2257714 AATAAATAATAAT
1 AATAAAT-ATAAT
2257727 AATAAA
1 AATAAA
2257733 AATTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AATAAATATAAT
Found at i:2258027 original size:2 final size:2
Alignment explanation
Indices: 2258020--2258044 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2258010 GCCAAGGTCT
2258020 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 T
2258045 GATGTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2258933 original size:16 final size:14
Alignment explanation
Indices: 2258899--2258943 Score: 56
Period size: 13 Copynumber: 3.1 Consensus size: 14
2258889 ATTTTTATTT
2258899 AATAATTATATA-A
1 AATAATTATATATA
2258912 AATAATTATATATA
1 AATAATTATATATA
*
2258926 TAATTAATAATATATA
1 -AA-TAATTATATATA
2258942 AA
1 AA
2258944 AATAAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 12 0.43
14 1 0.04
15 4 0.14
16 11 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATAATTATATATA
Found at i:2258959 original size:16 final size:16
Alignment explanation
Indices: 2258898--2258957 Score: 61
Period size: 16 Copynumber: 3.7 Consensus size: 16
2258888 TATTTTTATT
2258898 TAATAATTATATAAAA
1 TAATAATTATATAAAA
* *
2258914 TAATTA-TATATATAAT
1 TAATAATTATATA-AAA
2258930 TAATAA-TATATAAAAA
1 TAATAATTATAT-AAAA
2258946 TAAATAATTATA
1 T-AATAATTATA
2258958 AATAAATACA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 6 0.17
16 20 0.56
17 6 0.17
18 4 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATAATTATATAAAA
Found at i:2264645 original size:14 final size:15
Alignment explanation
Indices: 2264626--2264655 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2264616 TTTATACAAG
2264626 AAATCAAAA-TAATC
1 AAATCAAAATTAATC
2264640 AAATCAAAATTAATC
1 AAATCAAAATTAATC
2264655 A
1 A
2264656 GTTTAGTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.63, C:0.13, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATCAAAATTAATC
Done.