Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold221
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: 2539808
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 17 of 19
Found at i:2168748 original size:10 final size:10
Alignment explanation
Indices: 2168703--2168769 Score: 55
Period size: 10 Copynumber: 6.5 Consensus size: 10
2168693 TAAAATAAAA
2168703 TAAA-TAATT
1 TAAATTAATT
* *
2168712 TAAATAAACT
1 TAAATTAATT
*
2168722 TAATATAAATT
1 TAA-ATTAATT
2168733 TAAATTAATT
1 TAAATTAATT
*
2168743 TAAATTTAATA
1 TAAA-TTAATT
*
2168754 TAATTTAATT
1 TAAATTAATT
2168764 TCAAAT
1 T-AAAT
2168770 GATTTAAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
9 4 0.09
10 22 0.48
11 20 0.43
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (10 bp):
TAAATTAATT
Found at i:2168885 original size:16 final size:16
Alignment explanation
Indices: 2168864--2168925 Score: 81
Period size: 16 Copynumber: 3.8 Consensus size: 16
2168854 ATTTAAGTTC
2168864 TAAATTTAAAA-ATATT
1 TAAATTTAAAATA-ATT
*
2168880 TTAATTTAAAAATAATT
1 TAAATTT-AAAATAATT
*
2168897 TAAAATTAAAATAATT
1 TAAATTTAAAATAATT
2168913 TAAATTTAAAATA
1 TAAATTTAAAATA
2168926 TATTAATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
16 27 0.68
17 12 0.30
18 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTTAAAATAATT
Found at i:2172280 original size:23 final size:23
Alignment explanation
Indices: 2172254--2172329 Score: 55
Period size: 23 Copynumber: 3.2 Consensus size: 23
2172244 CATCTTTGCC
2172254 TCATGTACTGTATTATCCTTTCT
1 TCATGTACTGTATTATCCTTTCT
** * * * *
2172277 TCATCAAAATTTTTTCTAT-CTTTGCC
1 TCAT--GTACTGTAT-TATCCTTT-CT
2172303 TCATGTACTGTATTATCCTTTCT
1 TCATGTACTGTATTATCCTTTCT
2172326 TCAT
1 TCAT
2172330 CAAAATTTTT
Statistics
Matches: 36, Mismatches: 12, Indels: 10
0.62 0.21 0.17
Matches are distributed among these distances:
23 12 0.33
24 8 0.22
25 8 0.22
26 8 0.22
ACGTcount: A:0.20, C:0.22, G:0.07, T:0.51
Consensus pattern (23 bp):
TCATGTACTGTATTATCCTTTCT
Found at i:2172308 original size:49 final size:49
Alignment explanation
Indices: 2172245--2172342 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
2172235 TTTTGATAAC
2172245 ATCTTTGCCTCATGTACTGTATTATCCTTTCTTCATCAAAATTTTTTCT
1 ATCTTTGCCTCATGTACTGTATTATCCTTTCTTCATCAAAATTTTTTCT
2172294 ATCTTTGCCTCATGTACTGTATTATCCTTTCTTCATCAAAATTTTTTCT
1 ATCTTTGCCTCATGTACTGTATTATCCTTTCTTCATCAAAATTTTTTCT
2172343 TAAACTTGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.20, C:0.22, G:0.06, T:0.51
Consensus pattern (49 bp):
ATCTTTGCCTCATGTACTGTATTATCCTTTCTTCATCAAAATTTTTTCT
Found at i:2174477 original size:28 final size:27
Alignment explanation
Indices: 2174434--2174508 Score: 69
Period size: 28 Copynumber: 2.6 Consensus size: 27
2174424 TATCAAAATC
* *
2174434 ATATTATATAAAAATTTAATATATTTAT
1 ATATTATATTATAATTTAATA-ATTTAT
* *
2174462 ATATTATATTATAATTATATTAATTTTT
1 ATATTATATTATAATT-TAATAATTTAT
*
2174490 ATGTTATATCATATAATTT
1 ATATTATAT--TATAATTT
2174509 TATTCTATCA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 27 0.69
29 5 0.13
30 7 0.18
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (27 bp):
ATATTATATTATAATTTAATAATTTAT
Found at i:2178273 original size:18 final size:17
Alignment explanation
Indices: 2178245--2178379 Score: 84
Period size: 16 Copynumber: 8.0 Consensus size: 17
2178235 TTTTAGTGTT
2178245 ATATTTGTATATTTTATA
1 ATATTT-TATATTTTATA
*
2178263 ATATTATTATA-TTTAAA
1 ATATT-TTATATTTTATA
2178280 ATATTTTATATTTATATA
1 ATATTTTATATTT-TATA
*
2178298 A-ATTTTA-A-TATATTA
1 ATATTTTATATTTTA-TA
*
2178313 ATAATTTATATTTTATA
1 ATATTTTATATTTTATA
* * * *
2178330 A-ATCTTAAAATATATA
1 ATATTTTATATTTTATA
* *
2178346 ATCATGTTATATATT-TA
1 AT-ATTTTATATTTTATA
* *
2178363 ATATTATATATATTATA
1 ATATTTTATATTTTATA
2178380 TTTATATAAT
Statistics
Matches: 90, Mismatches: 17, Indels: 21
0.70 0.13 0.16
Matches are distributed among these distances:
14 2 0.02
15 4 0.04
16 32 0.36
17 28 0.31
18 23 0.26
19 1 0.01
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (17 bp):
ATATTTTATATTTTATA
Found at i:2178290 original size:16 final size:16
Alignment explanation
Indices: 2178245--2178293 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
2178235 TTTTAGTGTT
*
2178245 ATATTTGTATATTTTATA
1 ATATTT-TATA-TTTAAA
2178263 ATATTATTATATTTAAA
1 ATATT-TTATATTTAAA
2178280 ATATTTTATATTTA
1 ATATTTTATATTTA
2178294 TATAAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 9 0.31
17 10 0.34
18 9 0.31
19 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
ATATTTTATATTTAAA
Found at i:2178304 original size:27 final size:27
Alignment explanation
Indices: 2178253--2178342 Score: 69
Period size: 27 Copynumber: 3.1 Consensus size: 27
2178243 TTATATTTGT
*
2178253 ATATTTTATAATATTAT-TATA-TTTAAA
1 ATATTTTAT-AT-TTATATAAATTTTAAA
2178280 ATATTTTATATTTATATAAATTTTAATA
1 ATATTTTATATTTATATAAATTTTAA-A
*
2178308 TATTAATAATTTATATTT-TATAAATCTTAAA
1 -A-T-AT--TTTATATTTATATAAATTTTAAA
2178339 ATAT
1 ATAT
2178343 ATAATCATGT
Statistics
Matches: 53, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
25 4 0.08
26 5 0.09
27 14 0.26
28 3 0.06
29 2 0.04
30 2 0.04
31 3 0.06
32 11 0.21
33 9 0.17
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (27 bp):
ATATTTTATATTTATATAAATTTTAAA
Found at i:2178321 original size:33 final size:33
Alignment explanation
Indices: 2178279--2178362 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 33
2178269 TTATATTTAA
* * *
2178279 AATATTTTATATTTATATAAATTTTAATATAT-T
1 AATAATTTATATTT-TATAAATCTTAAAATATAT
2178312 AATAATTTATATTTTATAAATCTTAAAATATAT
1 AATAATTTATATTTTATAAATCTTAAAATATAT
*
2178345 AATCATGTTATATATTTA
1 AATAAT-TTATAT-TTTA
2178363 ATATTATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
32 15 0.34
33 19 0.43
34 6 0.14
35 4 0.09
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.52
Consensus pattern (33 bp):
AATAATTTATATTTTATAAATCTTAAAATATAT
Found at i:2178342 original size:34 final size:31
Alignment explanation
Indices: 2178252--2178386 Score: 87
Period size: 33 Copynumber: 4.2 Consensus size: 31
2178242 GTTATATTTG
* * * *
2178252 TATATTTTATAATATTATTATATTTAAAATATTT
1 TATATTTTATAA-A-T-TTAAATATATAATAATT
*
2178286 TATATTTATATAAATTTTAATATATTAATAATT
1 TATATTT-TATAAATTTAAATATA-TAATAATT
*
2178319 TATATTTTATAAATCTTAAAATATATAATCATGT
1 TATATTTTATAAAT-TT-AAATATATAATAAT-T
* * *
2178353 TATATATT-T-AATATTATATATATTAT-ATT
1 TATATTTTATAAAT-TTAAATATATAATAATT
2178382 TATAT
1 TATAT
2178387 AATAGTGTAT
Statistics
Matches: 85, Mismatches: 11, Indels: 15
0.77 0.10 0.14
Matches are distributed among these distances:
29 6 0.07
30 2 0.02
31 9 0.11
32 18 0.21
33 23 0.27
34 22 0.26
35 5 0.06
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (31 bp):
TATATTTTATAAATTTAAATATATAATAATT
Found at i:2178345 original size:23 final size:23
Alignment explanation
Indices: 2178293--2178345 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
2178283 TTTTATATTT
* *
2178293 ATATAAATTTTAATATATTAATA
1 ATATATATTTTAAAATATTAATA
* *
2178316 ATTTATATTTTATAAATCTTAA-A
1 ATATATATTTTA-AAATATTAATA
2178339 ATATATA
1 ATATATA
2178346 ATCATGTTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
ATATATATTTTAAAATATTAATA
Found at i:2181425 original size:22 final size:22
Alignment explanation
Indices: 2181397--2181442 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
2181387 CTGAGGATAG
2181397 TTTATGTGCATACCTCATTACT
1 TTTATGTGCATACCTCATTACT
*
2181419 TTTATGTGCATACCTCATTGCT
1 TTTATGTGCATACCTCATTACT
2181441 TT
1 TT
2181443 CATATTGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.22, G:0.11, T:0.48
Consensus pattern (22 bp):
TTTATGTGCATACCTCATTACT
Found at i:2186620 original size:3 final size:3
Alignment explanation
Indices: 2186607--2186652 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
2186597 GCTCAGCTCA
**
2186607 TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC GCC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
2186653 TTTTTTTGGA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:2189722 original size:3 final size:3
Alignment explanation
Indices: 2189714--2189755 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
2189704 CTCCAGTTAA
2189714 AAT AAT 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 AAT AAT
2189756 CTTGTTTTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2192823 original size:22 final size:21
Alignment explanation
Indices: 2192798--2192848 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
2192788 AATTTAATGA
2192798 TTTATTCAAATATTTTAAATAG
1 TTTATTCAAAT-TTTTAAATAG
* *
2192820 TTTATAATTAAATTTTTAAATAT
1 TTTAT--TCAAATTTTTAAATAG
2192843 TTTATT
1 TTTATT
2192849 GATAAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 1 0.04
22 5 0.20
23 14 0.56
24 5 0.20
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTATTCAAATTTTTAAATAG
Found at i:2192940 original size:13 final size:14
Alignment explanation
Indices: 2192922--2192950 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2192912 ATTAAACTTA
2192922 TTTAATT-ATTATT
1 TTTAATTAATTATT
2192935 TTTAATTAATTATT
1 TTTAATTAATTATT
2192949 TT
1 TT
2192951 AAAAATCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTAATTAATTATT
Found at i:2196577 original size:10 final size:10
Alignment explanation
Indices: 2196562--2196715 Score: 60
Period size: 10 Copynumber: 15.7 Consensus size: 10
2196552 AAATAAATAA
2196562 AATATAAAAT
1 AATATAAAAT
*
2196572 AATATAATAT
1 AATATAAAAT
*
2196582 AATATAATAT
1 AATATAAAAT
2196592 AAATATATAAAT
1 -AATATA-AAAT
2196604 -ATAT-AAAT
1 AATATAAAAT
* *
2196612 ATTTTAAAATT
1 AATATAAAA-T
* *
2196623 TATATAATAT
1 AATATAAAAT
2196633 AA-ATTAATAA-
1 AATA-TAA-AAT
2196643 AATATTAAAAT
1 AATA-TAAAAT
* *
2196654 -TTAT-ATA-
1 AATATAAAAT
2196661 AATATAAAAT
1 AATATAAAAT
*
2196671 AA-ATTAAAT
1 AATATAAAAT
2196680 ATATATAATAA-
1 A-ATATAA-AAT
**
2196691 AATATACTA-
1 AATATAAAAT
2196700 AATATAAAAT
1 AATATAAAAT
2196710 AA-ATAA
1 AATATAA
2196716 TTTAATAATA
Statistics
Matches: 108, Mismatches: 20, Indels: 33
0.67 0.12 0.20
Matches are distributed among these distances:
8 9 0.08
9 25 0.23
10 47 0.44
11 22 0.20
12 5 0.05
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (10 bp):
AATATAAAAT
Found at i:2196680 original size:34 final size:34
Alignment explanation
Indices: 2196588--2196713 Score: 114
Period size: 39 Copynumber: 3.6 Consensus size: 34
2196578 ATATAATATA
*
2196588 ATATAAATATATAAATATA-TAAATATTTTAAAATTT
1 ATATAAATATA-AAATAAATTAAATA--TTAAAATTT
* *
2196624 ATAT-AATAT-AAATTAATAAAATATTAAAATTT
1 ATATAAATATAAAATAAATTAAATATTAAAATTT
**
2196656 ATATAAATATAAAATAAATTAAATATATATAATAAAAT
1 ATATAAATATAAAATAAATT-AA-ATAT-TAA-AATTT
2196694 ATACTAAATATAAAATAAAT
1 ATA-TAAATATAAAATAAAT
2196714 AATTTAATAA
Statistics
Matches: 75, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
32 13 0.17
33 10 0.13
34 12 0.16
35 7 0.09
36 8 0.11
37 3 0.04
38 6 0.08
39 16 0.21
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (34 bp):
ATATAAATATAAAATAAATTAAATATTAAAATTT
Found at i:2196708 original size:56 final size:55
Alignment explanation
Indices: 2196551--2196709 Score: 162
Period size: 56 Copynumber: 2.8 Consensus size: 55
2196541 TGATGATTAC
* * *
2196551 AAAATAAATAAAATATAAAATAATATAATATAATATAATAT-AAA-TATATAAATAT
1 AAAATAAATTAAATAT-ATATAATAAAATATAATA-AATATAAAATTATATAAATAT
** *
2196606 ATAAATATTTTAAAATTTATATAATATAAAT-TAATAAAATATTAAAATTTATATAAATAT
1 A-AAATAAATT-AAATATATATAATA-AAATATAAT-AAATA-TAAAA-TTATATAAATAT
*
2196666 AAAATAAATTAAATATATATAATAAAATATACTAAATATAAAAT
1 AAAATAAATTAAATATATATAATAAAATATAATAAATATAAAAT
2196710 AAATAATTTA
Statistics
Matches: 85, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
55 2 0.02
56 26 0.31
57 19 0.22
58 19 0.22
59 7 0.08
60 12 0.14
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (55 bp):
AAAATAAATTAAATATATATAATAAAATATAATAAATATAAAATTATATAAATAT
Found at i:2197196 original size:2 final size:2
Alignment explanation
Indices: 2197189--2197222 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2197179 ATAGAATGAG
2197189 CT CT CT 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 CT CT CT
2197223 GTGTGAGATG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2203784 original size:36 final size:36
Alignment explanation
Indices: 2203744--2203812 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
2203734 AGACTAAAAC
*
2203744 TTTTTAATGACTGTTAAATTTATAAGTGATTATGTA
1 TTTTTAATGACTGTTAAATTTATAAGTAATTATGTA
*
2203780 TTTTTAATGACTGTTAAATTTATGAGTAATTAT
1 TTTTTAATGACTGTTAAATTTATAAGTAATTAT
2203813 TTAAATATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (36 bp):
TTTTTAATGACTGTTAAATTTATAAGTAATTATGTA
Found at i:2203800 original size:18 final size:18
Alignment explanation
Indices: 2203744--2203800 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
2203734 AGACTAAAAC
2203744 TTTTTAATGACTGTTAAA
1 TTTTTAATGACTGTTAAA
* **
2203762 TTTATAAGTGA-T-TATGTA
1 TTTTTAA-TGACTGT-TAAA
2203780 TTTTTAATGACTGTTAAA
1 TTTTTAATGACTGTTAAA
2203798 TTT
1 TTT
2203801 ATGAGTAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
17 4 0.14
18 21 0.72
19 4 0.14
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.53
Consensus pattern (18 bp):
TTTTTAATGACTGTTAAA
Found at i:2203863 original size:63 final size:65
Alignment explanation
Indices: 2203757--2203897 Score: 171
Period size: 63 Copynumber: 2.2 Consensus size: 65
2203747 TTAATGACTG
* * * * *
2203757 TTAAATTTATAAGTGATTATGTATTTTTAATGACTGTTAAATTTATGAGTAATTATTTAAATATT
1 TTAAATTTATAAGTAATTATGTA-TTTTAATAACTATTAAATTTATAAGTAATTATATAAA-ATT
2203822 CA
64 CA
* **
2203824 TTAAATTTATAAGTAATT-T-TA-TTTAATAATTATTAAATTTATAAGTAATTATATCTAATTCA
1 TTAAATTTATAAGTAATTATGTATTTTAATAACTATTAAATTTATAAGTAATTATATAAAATTCA
2203886 TTAAATTTATAA
1 TTAAATTTATAA
2203898 TCAATATCAA
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
62 17 0.26
63 29 0.44
65 2 0.03
66 1 0.02
67 17 0.26
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (65 bp):
TTAAATTTATAAGTAATTATGTATTTTAATAACTATTAAATTTATAAGTAATTATATAAAATTCA
Found at i:2203864 original size:32 final size:32
Alignment explanation
Indices: 2203757--2203897 Score: 121
Period size: 32 Copynumber: 4.4 Consensus size: 32
2203747 TTAATGACTG
* * * *
2203757 TTAAATTTATAAGTGATTATGTATTTTTAATGACTG
1 TTAAATTTATAAGTAATT-T-TA--TTTAATAATTA
*
2203793 TTAAATTTATGAGTAA--TTATTTAA-ATATTCA
1 TTAAATTTATAAGTAATTTTATTTAATA-ATT-A
2203824 TTAAATTTATAAGTAATTTTATTTAATAATTA
1 TTAAATTTATAAGTAATTTTATTTAATAATTA
* * *
2203856 TTAAATTTATAAGTAATTATATCTAAT--TCA
1 TTAAATTTATAAGTAATTTTATTTAATAATTA
2203886 TTAAATTTATAA
1 TTAAATTTATAA
2203898 TCAATATCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 16
0.78 0.08 0.14
Matches are distributed among these distances:
30 21 0.23
31 15 0.16
32 28 0.31
33 12 0.13
34 1 0.01
36 14 0.15
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (32 bp):
TTAAATTTATAAGTAATTTTATTTAATAATTA
Found at i:2205984 original size:2 final size:2
Alignment explanation
Indices: 2205979--2206020 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
2205969 ATATATATAT
2205979 AG AG AG AG AG AG AG AG AG AG AG -G AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2206020 A
1 A
2206021 CTTGAATAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2206393 original size:3 final size:3
Alignment explanation
Indices: 2206385--2206416 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2206375 ATTACTTTAT
2206385 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2206417 TGATGTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2207730 original size:2 final size:2
Alignment explanation
Indices: 2207723--2207768 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2207713 TCAACCTTCA
2207723 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
2207765 AT AT
1 AT AT
2207769 GTATTTTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2208083 original size:14 final size:14
Alignment explanation
Indices: 2208045--2208089 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
2208035 ATAATATAAC
2208045 ATATGTA-ATA-AT
1 ATATGTATATATAT
2208057 AGTAT-TATAATATAT
1 A-TATGTAT-ATATAT
2208072 ATATGTATATATAT
1 ATATGTATATATAT
2208086 ATAT
1 ATAT
2208090 ATAATTCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 3 0.11
13 3 0.11
14 16 0.57
15 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (14 bp):
ATATGTATATATAT
Found at i:2208523 original size:26 final size:25
Alignment explanation
Indices: 2208494--2208556 Score: 81
Period size: 26 Copynumber: 2.5 Consensus size: 25
2208484 ATATATTTAA
*
2208494 ATATTTTTATTTAATTAATAAAATAT
1 ATATTTTTATTTAATAAAT-AAATAT
* *
2208520 ATATTTTTATTTTATAAATAAATTT
1 ATATTTTTATTTAATAAATAAATAT
*
2208545 AAATTTTTATTT
1 ATATTTTTATTT
2208557 TAAAATTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
25 16 0.48
26 17 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATATTTTTATTTAATAAATAAATAT
Found at i:2208542 original size:25 final size:26
Alignment explanation
Indices: 2208494--2208562 Score: 88
Period size: 25 Copynumber: 2.7 Consensus size: 26
2208484 ATATATTTAA
* *
2208494 ATATTTTTATTTAATTAATAAAATAT
1 ATATTTTTATTTTATAAATAAAATAT
*
2208520 ATATTTTTATTTTATAAAT-AAATTT
1 ATATTTTTATTTTATAAATAAAATAT
*
2208545 AAATTTTTATTTTA-AAAT
1 ATATTTTTATTTTATAAAT
2208563 TTTAAAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.10
25 18 0.46
26 17 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
ATATTTTTATTTTATAAATAAAATAT
Found at i:2208618 original size:39 final size:38
Alignment explanation
Indices: 2208526--2208620 Score: 108
Period size: 38 Copynumber: 2.6 Consensus size: 38
2208516 ATATATATTT
* * *
2208526 TTATTTTATA-AATAA-ATTTAAATTTTTATTTTAAAA
1 TTATTATATATAATAATATTTAAAATTATATTTTAAAA
*
2208562 TT-TTA-AAATAATAAATATATTAAAATTATATTTTAAAA
1 TTATTATATATAAT-AATAT-TTAAAATTATATTTTAAAA
2208600 TTATTATATATAATAATATTT
1 TTATTATATATAATAATATTT
2208621 TTATTCAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
34 2 0.04
35 5 0.10
36 4 0.08
37 2 0.04
38 21 0.44
39 8 0.17
40 6 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (38 bp):
TTATTATATATAATAATATTTAAAATTATATTTTAAAA
Found at i:2208708 original size:31 final size:30
Alignment explanation
Indices: 2208660--2208734 Score: 71
Period size: 31 Copynumber: 2.4 Consensus size: 30
2208650 TTTTACTCAA
* *
2208660 ATAAA-ATTATAATTTTTAGATAAAAATAATT
1 ATAAATATTA-AAATTTTA-ATAAAAATAAAT
* * *
2208691 ATAAATATTAAAATTTTAATTATATTAAAT
1 ATAAATATTAAAATTTTAATAAAAATAAAT
2208721 ATAAATTATTAAAA
1 ATAAA-TATTAAAA
2208735 ATAATTAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 13 0.35
31 20 0.54
32 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (30 bp):
ATAAATATTAAAATTTTAATAAAAATAAAT
Found at i:2208741 original size:24 final size:25
Alignment explanation
Indices: 2208680--2208745 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 25
2208670 AATTTTTAGA
2208680 TAAAAATAATTATAAATATTAAAATTT
1 TAAAAATAA-T-TAAATATTAAAATTT
**
2208707 TAATTAT-ATTAAATA-T-AAATTAT
1 TAAAAATAATTAAATATTAAAATT-T
2208730 TAAAAATAATTAAATA
1 TAAAAATAATTAAATA
2208746 AATTCTATAC
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
22 5 0.15
23 7 0.21
24 14 0.42
25 1 0.03
26 1 0.03
27 5 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
TAAAAATAATTAAATATTAAAATTT
Found at i:2209137 original size:2 final size:2
Alignment explanation
Indices: 2209130--2209154 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2209120 AATTGGGATT
2209130 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
2209155 TTGGTTAAGT
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:2210010 original size:25 final size:27
Alignment explanation
Indices: 2209982--2210032 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2209972 TAAATTTGAT
2209982 AATTA-ATATTTAATAT-ATTAAAAGA
1 AATTACATATTTAATATCATTAAAAGA
*
2210007 AATTACTTTATTTAATATCATTAAAA
1 AATTAC-ATATTTAATATCATTAAAA
2210033 AGAATCATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
27 10 0.45
28 7 0.32
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (27 bp):
AATTACATATTTAATATCATTAAAAGA
Found at i:2210193 original size:19 final size:20
Alignment explanation
Indices: 2210144--2210194 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
2210134 ATAATAATAA
*
2210144 TAAAA-TATAAAATTTTTCT
1 TAAAATTATATAATTTTTCT
*
2210163 TATAAATAATATAATTTTT-T
1 TA-AAATTATATAATTTTTCT
2210183 TAAAATTATATA
1 TAAAATTATATA
2210195 TTCACATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 11 0.41
20 6 0.22
21 10 0.37
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAAATTATATAATTTTTCT
Found at i:2210195 original size:21 final size:22
Alignment explanation
Indices: 2210143--2210195 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
2210133 AATAATAATA
*
2210143 ATAAA-ATATAAAATTTTTCTT
1 ATAAATATATATAATTTTTCTT
2210164 ATAAATA-ATATAATTTTT-TT
1 ATAAATATATATAATTTTTCTT
2210184 A-AAATTATATAT
1 ATAAA-TATATAT
2210196 TCACATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 3 0.11
20 5 0.18
21 19 0.68
22 1 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAAATATATATAATTTTTCTT
Found at i:2225482 original size:21 final size:21
Alignment explanation
Indices: 2225452--2225507 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
2225442 TTATTATTAT
2225452 TTTAAA-TAATAAAATAAAAA
1 TTTAAATTAATAAAATAAAAA
** **
2225472 TTTAAATTAATTTAATTTAAA
1 TTTAAATTAATAAAATAAAAA
*
2225493 TTTAAATTAAAAAAA
1 TTTAAATTAATAAAA
2225508 ATAGATCGTG
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TTTAAATTAATAAAATAAAAA
Found at i:2226978 original size:11 final size:11
Alignment explanation
Indices: 2226962--2227029 Score: 68
Period size: 11 Copynumber: 6.2 Consensus size: 11
2226952 ATATACTTAA
*
2226962 TTATATCATAT
1 TTATATTATAT
*
2226973 TTATATTATTT
1 TTATATTATAT
2226984 TTATATTATA-
1 TTATATTATAT
* *
2226994 TTATATTTTAA
1 TTATATTATAT
2227005 TTAT-TTATAT
1 TTATATTATAT
2227015 TATATAATTATAT
1 T-TAT-ATTATAT
2227028 TT
1 TT
2227030 TAAATTATCT
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
10 14 0.30
11 25 0.53
12 1 0.02
13 7 0.15
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (11 bp):
TTATATTATAT
Found at i:2226981 original size:5 final size:5
Alignment explanation
Indices: 2226961--2227028 Score: 61
Period size: 5 Copynumber: 13.6 Consensus size: 5
2226951 AATATACTTA
* * *
2226961 ATTAT ATCAT ATTTAT ATTATT TTTAT ATTAT ATTAT ATTTT AATTAT
1 ATTAT ATTAT A-TTAT ATTA-T ATTAT ATTAT ATTAT ATTAT -ATTAT
2227009 -TTAT ATTAT A-TA- ATTAT ATT
1 ATTAT ATTAT ATTAT ATTAT ATT
2227029 TTAAATTATC
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
3 1 0.02
4 8 0.16
5 30 0.59
6 12 0.24
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (5 bp):
ATTAT
Found at i:2226991 original size:27 final size:25
Alignment explanation
Indices: 2226946--2227019 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 25
2226936 ATAATAATAA
*
2226946 ATTTTAATATACTTA-ATTATATCAT
1 ATTTTAAT-TATTTATATTATATCAT
*
2226971 A-TTTATATTATTTTTATATTATATTAT
1 ATTTTA-ATTA--TTTATATTATATCAT
2226998 ATTTTAATTATTTATATTATAT
1 ATTTTAATTATTTATATTATAT
2227020 AATTATATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
24 6 0.14
25 15 0.36
26 3 0.07
27 14 0.33
28 4 0.10
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (25 bp):
ATTTTAATTATTTATATTATATCAT
Found at i:2227025 original size:28 final size:27
Alignment explanation
Indices: 2226961--2227037 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 27
2226951 AATATACTTA
* *
2226961 ATTATATCATA-TTTATATTATTTTTAT
1 ATTATATTATATTTTA-ATTATTTATAT
2226988 ATTATATTATATTTTAATTATTTATAT
1 ATTATATTATATTTTAATTATTTATAT
2227015 -TATATAATTATATTTTAAATTAT
1 AT-TAT-ATTATATTTT-AATTAT
2227038 CTAATTTAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
26 1 0.02
27 23 0.52
28 14 0.32
29 6 0.14
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (27 bp):
ATTATATTATATTTTAATTATTTATAT
Found at i:2227031 original size:20 final size:20
Alignment explanation
Indices: 2226969--2227043 Score: 57
Period size: 20 Copynumber: 3.6 Consensus size: 20
2226959 TAATTATATC
2226969 ATATT-TAT-ATTAT-TTTT
1 ATATTATATAATTATATTTT
*
2226986 ATATTATATTATATTTTAATTATTT
1 ATATTATA-TA-ATTAT-A-T-TTT
2227011 ATATTATATAATTATATTTT
1 ATATTATATAATTATATTTT
* *
2227031 AAATTATCTAATT
1 ATATTATATAATT
2227044 TAGTTTTAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
17 5 0.11
18 2 0.04
19 1 0.02
20 14 0.30
21 5 0.11
22 1 0.02
23 4 0.09
24 3 0.07
25 11 0.24
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (20 bp):
ATATTATATAATTATATTTT
Found at i:2227050 original size:20 final size:20
Alignment explanation
Indices: 2227008--2227052 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2226998 ATTTTAATTA
*
2227008 TTTATATTATATAATTATAT
1 TTTAAATTATATAATTATAT
*
2227028 TTTAAATTATCTAATT-TAGT
1 TTTAAATTATATAATTATA-T
2227048 TTTAA
1 TTTAA
2227053 CTCATAGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTAAATTATATAATTATAT
Found at i:2227334 original size:26 final size:26
Alignment explanation
Indices: 2227247--2227344 Score: 63
Period size: 26 Copynumber: 3.5 Consensus size: 26
2227237 TACTTAATTT
* *
2227247 AATAATTTATATTAT-AATTATATTAA
1 AATAATTTATATTATAAATTTTA-AAA
* * *
2227273 AATATTTTATATTTATATAAATTTAATTTATT
1 AATAATTTATA-TTATA-AATTTTAA---A-A
2227305 AATAATTTATATTATAAATTTTAAAA
1 AATAATTTATATTATAAATTTTAAAA
*
2227331 AATATTTTTATATT
1 AATA-ATTTATATT
2227345 TTATTAATAA
Statistics
Matches: 55, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
26 14 0.25
27 13 0.24
29 5 0.09
30 7 0.13
31 6 0.11
32 10 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
AATAATTTATATTATAAATTTTAAAA
Found at i:2227347 original size:20 final size:22
Alignment explanation
Indices: 2227322--2227372 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
2227312 TATATTATAA
*
2227322 ATTTTA-AAAAATATTTTTA-T
1 ATTTTATAAAAATATTTTAATT
*
2227342 ATTTTATTAATAATATTTTAATT
1 ATTTTA-TAAAAATATTTTAATT
2227365 ATTTTATA
1 ATTTTATA
2227373 TATATTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 6 0.23
22 13 0.50
23 7 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTTTATAAAAATATTTTAATT
Found at i:2227787 original size:14 final size:14
Alignment explanation
Indices: 2227768--2227795 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2227758 CAAATAATGC
2227768 TTAAAATTAAAATT
1 TTAAAATTAAAATT
2227782 TTAAAATTAAAATT
1 TTAAAATTAAAATT
2227796 AATAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAATTAAAATT
Found at i:2227793 original size:20 final size:21
Alignment explanation
Indices: 2227768--2227808 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
2227758 CAAATAATGC
2227768 TTAAAATTAA-AATTTTAAAA
1 TTAAAATTAATAATTTTAAAA
2227788 TTAAAATTAATAATTTTAAAA
1 TTAAAATTAATAATTTTAAAA
2227809 ATATATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAAAATTAATAATTTTAAAA
Found at i:2227861 original size:24 final size:23
Alignment explanation
Indices: 2227807--2227892 Score: 79
Period size: 22 Copynumber: 3.7 Consensus size: 23
2227797 ATAATTTTAA
* * *
2227807 AAATATATT-ATATATAATATAA
1 AAATATATTAAAATATAAAATAT
2227829 AAATA-ATTAAAATATAAAATTAT
1 AAATATATTAAAATATAAAA-TAT
*
2227852 AAATATATTAAAATTTATATAATAT
1 AAATATATTAAAA--TATAAAATAT
*
2227877 TAAT-TATTAAAATATA
1 AAATATATTAAAATATA
2227893 TTAAAATTTA
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
21 3 0.06
22 17 0.31
23 7 0.13
24 15 0.28
25 6 0.11
26 6 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATATATTAAAATATAAAATAT
Found at i:2227958 original size:13 final size:13
Alignment explanation
Indices: 2227940--2227979 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
2227930 ATATTATATT
2227940 ATAAAAAAATTTA
1 ATAAAAAAATTTA
2227953 ATAAAAAAATATTA
1 ATAAAAAAAT-TTA
*
2227967 AAATAAAAAATTT
1 ATA-AAAAAATTT
2227980 TATTTTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 10 0.42
14 7 0.29
15 7 0.29
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
ATAAAAAAATTTA
Found at i:2228904 original size:25 final size:26
Alignment explanation
Indices: 2228860--2228910 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
2228850 TTATATTTTA
* *
2228860 TTTATATAAATTATACATA-TTAAAT
1 TTTAAATAAATTACACATATTTAAAT
*
2228885 TTTAAATAAATTACATATATTTAAAT
1 TTTAAATAAATTACACATATTTAAAT
2228911 CATATATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (26 bp):
TTTAAATAAATTACACATATTTAAAT
Found at i:2230501 original size:28 final size:26
Alignment explanation
Indices: 2230477--2230529 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2230467 ATGATATATA
2230477 TATTTAAATATAAATATAAAAATATAAT
1 TATTT-AAT-TAAATATAAAAATATAAT
**
2230505 TATTTAATTATGTATAAAAATATAA
1 TATTTAATTAAATATAAAAATATAA
2230530 AAATTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 15 0.65
27 3 0.13
28 5 0.22
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (26 bp):
TATTTAATTAAATATAAAAATATAAT
Found at i:2231118 original size:2 final size:2
Alignment explanation
Indices: 2231113--2231137 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2231103 TTTGACACTT
2231113 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
2231138 GAGGAAGGAA
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:2231578 original size:20 final size:24
Alignment explanation
Indices: 2231550--2231597 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
2231540 CGATTAAATT
2231550 TAATATATT-TT-T-TAA-TTATA
1 TAATATATTATTATGTAATTTATA
*
2231570 TAATTTATTATTATGTAATTTATA
1 TAATATATTATTATGTAATTTATA
2231594 TAAT
1 TAAT
2231598 GTAAATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 8 0.35
21 2 0.09
22 1 0.04
23 3 0.13
24 9 0.39
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
TAATATATTATTATGTAATTTATA
Found at i:2231717 original size:18 final size:20
Alignment explanation
Indices: 2231667--2231719 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
2231657 TTTAAAAATT
*
2231667 TTAATAAA-ATAATATAAAA
1 TTAATAAATATTATATAAAA
2231686 TTAATAAATATTATATAAAA
1 TTAATAAATATTATATAAAA
*
2231706 TTTA-AAAT-TTATAT
1 TTAATAAATATTATAT
2231720 TTTAAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 6 0.19
19 12 0.39
20 13 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAATAAATATTATATAAAA
Found at i:2234116 original size:7 final size:8
Alignment explanation
Indices: 2234090--2234115 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2234080 TATCAAGATG
2234090 AAATAAAA
1 AAATAAAA
2234098 AAATAAAA
1 AAATAAAA
2234106 AAATAAAA
1 AAATAAAA
2234114 AA
1 AA
2234116 TGAAACGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAATAAAA
Found at i:2235616 original size:2 final size:2
Alignment explanation
Indices: 2235609--2235636 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2235599 AATTTTTAAA
2235609 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
2235637 GAGAATGAAA
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:2238724 original size:13 final size:13
Alignment explanation
Indices: 2238708--2238733 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2238698 ATATTAATAA
2238708 AAAAATTTTATTT
1 AAAAATTTTATTT
2238721 AAAAATTTTATTT
1 AAAAATTTTATTT
2238734 TTATAATGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAAAATTTTATTT
Found at i:2238876 original size:15 final size:15
Alignment explanation
Indices: 2238856--2238915 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
2238846 AGTAAGATTC
*
2238856 TTTAAATTTAATAAT
1 TTTAAATATAATAAT
*
2238871 TTTAAATATAATACT
1 TTTAAATATAATAAT
* *
2238886 AATTATAATTTAATAAT
1 -TTTA-AATATAATAAT
2238903 TTTAAATATAATA
1 TTTAAATATAATA
2238916 TAATTATAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
15 21 0.58
16 6 0.17
17 9 0.25
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTAAATATAATAAT
Found at i:2238923 original size:31 final size:32
Alignment explanation
Indices: 2238860--2238931 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
2238850 AGATTCTTTA
2238860 AATTTAATAATTTTAAATATAATACTAATTAT
1 AATTTAATAATTTTAAATATAATACTAATTAT
2238892 AATTTAATAATTTTAAATATAATA-TAATTAT
1 AATTTAATAATTTTAAATATAATACTAATTAT
2238923 AATTTAATA
1 AATTTAATA
2238932 TAAAAATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 16 0.40
32 24 0.60
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (32 bp):
AATTTAATAATTTTAAATATAATACTAATTAT
Found at i:2238932 original size:16 final size:16
Alignment explanation
Indices: 2238879--2238951 Score: 69
Period size: 16 Copynumber: 4.5 Consensus size: 16
2238869 ATTTTAAATA
2238879 TAATACTAATTATAATT
1 TAATA-TAATTATAATT
* *
2238896 T-A-ATAATTTTAAATA
1 TAATATAATTAT-AATT
2238911 TAATATAATTATAATT
1 TAATATAATTATAATT
**
2238927 TAATATAAAAATAATT
1 TAATATAATTATAATT
2238943 TAAATATAA
1 T-AATATAA
2238952 AATATTAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
14 6 0.13
15 5 0.11
16 20 0.43
17 15 0.33
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATATAATTATAATT
Found at i:2239010 original size:33 final size:33
Alignment explanation
Indices: 2238937--2239010 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 33
2238927 TAATATAAAA
*
2238937 ATAATTTAAATATAAAATATTAATTTTTAAAATT
1 ATAATATAAATATAAAATATT-ATTTTTAAAATT
* * *
2238971 -TTATATAAATATATAATATT-TTTATTATAATT
1 ATAATATAAATATAAAATATTATTT-TTAAAATT
2239003 ATAATATA
1 ATAATATA
2239011 TAAAAAATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
31 3 0.09
32 7 0.21
33 23 0.70
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (33 bp):
ATAATATAAATATAAAATATTATTTTTAAAATT
Found at i:2239011 original size:22 final size:21
Alignment explanation
Indices: 2238969--2239009 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
2238959 ATTTTTAAAA
2238969 TTTTATATAAATATATAATAT
1 TTTTATATAAATATATAATAT
2238990 TTTTAT-TATAAT-TATAATAT
1 TTTTATATA-AATATATAATAT
2239010 ATAAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTATATAAATATATAATAT
Found at i:2239040 original size:18 final size:19
Alignment explanation
Indices: 2238997--2239033 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
2238987 TATTTTTATT
2238997 ATAATTATAATATATAAAAA
1 ATAA-TATAATATATAAAAA
2239017 ATAATATAA-ATATAAAA
1 ATAATATAATATATAAAA
2239034 TAAAATAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAATATAATATATAAAAA
Found at i:2239892 original size:27 final size:27
Alignment explanation
Indices: 2239862--2239922 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
2239852 TAAAAAAATT
*
2239862 ATAAATATTAAAATTAAAATTTAT-TAA
1 ATAAATATTAAAAGT-AAATTTATATAA
* *
2239889 ATAAATTTTTAAAAGTATATTTATATAA
1 ATAAA-TATTAAAAGTAAATTTATATAA
2239917 ATAAAT
1 ATAAAT
2239923 TGAATTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 13 0.45
28 16 0.55
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (27 bp):
ATAAATATTAAAAGTAAATTTATATAA
Found at i:2239902 original size:28 final size:28
Alignment explanation
Indices: 2239869--2239923 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
2239859 ATTATAAATA
*
2239869 TTAAAATTAAAATTTAT-TAAATAAATTT
1 TTAAAAGT-AAATTTATATAAATAAATTT
*
2239897 TTAAAAGTATATTTATATAAATAAATT
1 TTAAAAGTAAATTTATATAAATAAATT
2239924 GAATTATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (28 bp):
TTAAAAGTAAATTTATATAAATAAATTT
Found at i:2240332 original size:16 final size:15
Alignment explanation
Indices: 2240301--2240360 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 15
2240291 TCAGTTACAT
*
2240301 TATTTATTTATTAAA
1 TATTTATTTATAAAA
2240316 TATTTATTTTATAAAA
1 TATTTA-TTTATAAAA
2240332 TA---ATTTATTAAAA
1 TATTTATTTA-TAAAA
2240345 -ATTTATTTTATAAAA
1 TATTTA-TTTATAAAA
2240360 T
1 T
2240361 TTTGAAATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
12 5 0.14
13 6 0.16
15 12 0.32
16 14 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTTATTTATAAAA
Found at i:2240337 original size:28 final size:28
Alignment explanation
Indices: 2240306--2240360 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
2240296 TACATTATTT
*
2240306 ATTTATTAAATATTTATTTTATAAAATA
1 ATTTATTAAAAATTTATTTTATAAAATA
2240334 ATTTATTAAAAATTTATTTTATAAAAT
1 ATTTATTAAAAATTTATTTTATAAAAT
2240361 TTTGAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
ATTTATTAAAAATTTATTTTATAAAATA
Found at i:2240358 original size:15 final size:16
Alignment explanation
Indices: 2240302--2240359 Score: 56
Period size: 15 Copynumber: 4.0 Consensus size: 16
2240292 CAGTTACATT
*
2240302 ATTTA-TTTATTAAAT
1 ATTTATTTTATTAAAA
2240317 ATTTATTTTA-T-AAA
1 ATTTATTTTATTAAAA
*
2240331 A--TAATTTATTAAAA
1 ATTTATTTTATTAAAA
2240345 ATTTATTTTA-TAAAA
1 ATTTATTTTATTAAAA
2240360 TTTTGAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
12 6 0.17
13 1 0.03
14 7 0.20
15 11 0.31
16 10 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTATTTTATTAAAA
Found at i:2240420 original size:19 final size:19
Alignment explanation
Indices: 2240398--2240495 Score: 87
Period size: 20 Copynumber: 5.2 Consensus size: 19
2240388 TTTTCATTAA
*
2240398 ATAAATATTTTAATATTTT
1 ATAAAAATTTTAATATTTT
* *
2240417 AT-AAAA-TATAAAATTATT
1 ATAAAAATTTTAATATT-TT
* *
2240435 -TTAAAATTTTAAATTTTTT
1 ATAAAAATTTT-AATATTTT
*
2240454 ATAAAAATTTTAAATTTTTT
1 ATAAAAATTTT-AATATTTT
2240474 ATAAAAATTTTAA-ATTTT
1 ATAAAAATTTTAATATTTT
2240492 ATAA
1 ATAA
2240496 TTTATTAAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
17 8 0.12
18 17 0.26
19 8 0.12
20 33 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATAAAAATTTTAATATTTT
Found at i:2240441 original size:18 final size:17
Alignment explanation
Indices: 2240412--2240454 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
2240402 ATATTTTAAT
*
2240412 ATTTTATAAAATATAAA
1 ATTTTTTAAAATATAAA
* *
2240429 ATTATTTTAAAATTTTAA
1 ATT-TTTTAAAATATAAA
2240447 ATTTTTTA
1 ATTTTTTA
2240455 TAAAAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTTTAAAATATAAA
Found at i:2241329 original size:18 final size:17
Alignment explanation
Indices: 2241302--2241339 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
2241292 AACCCTCGCC
*
2241302 CTCCTCTTCATCTTCAT
1 CTCCTCTTCATCATCAT
2241319 CTCCTTCTTCATCATCAT
1 CTCC-TCTTCATCATCAT
2241337 CTC
1 CTC
2241340 GTGGTGGCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.13, C:0.42, G:0.00, T:0.45
Consensus pattern (17 bp):
CTCCTCTTCATCATCAT
Found at i:2243573 original size:78 final size:78
Alignment explanation
Indices: 2243454--2243687 Score: 396
Period size: 78 Copynumber: 3.0 Consensus size: 78
2243444 TTTGAAATAA
* * ** * * *
2243454 TAAAAAAAAGTTATAGATATTGAAATTCAAACTTCGTATATGATAAATGTTATCCATATAAACTA
1 TAAAAAAAA-TTACAGATATTAAAATTTGAATTTCGGATATGATGAATGTTATCCATATAAACTA
2243519 ATTGAAATAAGTTT
65 ATTGAAATAAGTTT
2243533 TAAAAAAAATTACAGATATTAAAATTTGAATTTCGGATATGATGAATGTTATCCATATAAACTAA
1 TAAAAAAAATTACAGATATTAAAATTTGAATTTCGGATATGATGAATGTTATCCATATAAACTAA
2243598 TTGAAATAAGTTT
66 TTGAAATAAGTTT
2243611 TAAAAAAAATTACAGATATTAAAATTTGAATTTCGGATATGATGAATGTTATCCATATAAACTAA
1 TAAAAAAAATTACAGATATTAAAATTTGAATTTCGGATATGATGAATGTTATCCATATAAACTAA
2243676 TTGAAATAAGTT
66 TTGAAATAAGTT
2243688 CTAATTAAAA
Statistics
Matches: 148, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
78 139 0.94
79 9 0.06
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (78 bp):
TAAAAAAAATTACAGATATTAAAATTTGAATTTCGGATATGATGAATGTTATCCATATAAACTAA
TTGAAATAAGTTT
Found at i:2245896 original size:54 final size:54
Alignment explanation
Indices: 2245814--2245920 Score: 169
Period size: 54 Copynumber: 2.0 Consensus size: 54
2245804 AAGAGAGGTC
* *
2245814 CTTAGGTTCAAATCGAGAGAGGCGCAAGAGGACAATACCTTAATACCTTTGATA
1 CTTAGGTTCAAATCGAGAGAGCCACAAGAGGACAATACCTTAATACCTTTGATA
* * *
2245868 CTTAGGTTCGAATTGAGAGAGCCACAAGATGACAATACCTTAATACCTTTGAT
1 CTTAGGTTCAAATCGAGAGAGCCACAAGAGGACAATACCTTAATACCTTTGAT
2245921 GCAAGTGCAC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.26
Consensus pattern (54 bp):
CTTAGGTTCAAATCGAGAGAGCCACAAGAGGACAATACCTTAATACCTTTGATA
Found at i:2248121 original size:2 final size:2
Alignment explanation
Indices: 2248116--2248181 Score: 80
Period size: 2 Copynumber: 33.5 Consensus size: 2
2248106 CTACACACAT
* * * *
2248116 TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA TA TA TA TG TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2248158 TA TA TA TA TA TA TA TG TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2248182 GCAAGTAAGT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2248145 original size:18 final size:18
Alignment explanation
Indices: 2248122--2248181 Score: 99
Period size: 18 Copynumber: 3.5 Consensus size: 18
2248112 ACATTATATA
2248122 TATATATATATATGTATG
1 TATATATATATATGTATG
2248140 TATATATATATATGTATG
1 TATATATATATATGTATG
2248158 TATATATATATA--TATG
1 TATATATATATATGTATG
2248174 TAT-TATAT
1 TATATATAT
2248182 GCAAGTAAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.12
16 7 0.17
18 30 0.71
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (18 bp):
TATATATATATATGTATG
Found at i:2248237 original size:2 final size:2
Alignment explanation
Indices: 2248232--2248277 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
2248222 CTACACACAT
* * *
2248232 TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA TA TA TA TG TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2248273 TA TA T
1 TA TA T
2248278 GCAAGTAAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2248248 original size:96 final size:95
Alignment explanation
Indices: 2248140--2248357 Score: 377
Period size: 96 Copynumber: 2.3 Consensus size: 95
2248130 TATATGTATG
*
2248140 TATATATATATATGTATGTATATATATATATATGTATTATATGCAAGTAAGTTATCTAAAGGATG
1 TATATATATATAT-TATGTATATATATATATATGTATTATATGCAAGTAAGTTATCTAAAAGATG
2248205 GAAGAAATTGATCATTGCTACACACATTATA
65 GAAGAAATTGATCATTGCTACACACATTATA
2248236 TATATATATATA-TATGTATGTATATATATATATGTATTATATGCAAGTAAGTTATCTAAAAGAT
1 TATATATATATATTATGTA--TATATATATATATGTATTATATGCAAGTAAGTTATCTAAAAGAT
2248300 GGAAGAAATTGATCATTGCTACACACATTATA
64 GGAAGAAATTGATCATTGCTACACACATTATA
2248332 TATATATATATATATATGTAT-TATAT
1 TATATATATATAT-TATGTATATATAT
2248358 GCAAGTAAGT
Statistics
Matches: 117, Mismatches: 1, Indels: 9
0.92 0.01 0.07
Matches are distributed among these distances:
94 6 0.05
95 5 0.04
96 100 0.85
98 6 0.05
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.40
Consensus pattern (95 bp):
TATATATATATATTATGTATATATATATATATGTATTATATGCAAGTAAGTTATCTAAAAGATGG
AAGAAATTGATCATTGCTACACACATTATA
Found at i:2248261 original size:18 final size:17
Alignment explanation
Indices: 2248238--2248277 Score: 71
Period size: 18 Copynumber: 2.3 Consensus size: 17
2248228 ACATTATATA
2248238 TATATATATATATGTAT
1 TATATATATATATGTAT
2248255 GTATATATATATATGTAT
1 -TATATATATATATGTAT
2248273 TATAT
1 TATAT
2248278 GCAAGTAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (17 bp):
TATATATATATATGTAT
Found at i:2248381 original size:80 final size:76
Alignment explanation
Indices: 2248256--2248439 Score: 314
Period size: 80 Copynumber: 2.4 Consensus size: 76
2248246 TATATGTATG
2248256 TATATATATATATGTATTATATGCAAGTAAGTTATCTAAAAGATGGAAGAAATTGATCATTGCTA
1 TATATATATATATGTATTATATGCAAGTAAGTTATCTAAAAGATGGAAGAAATTGATCATTGCTA
2248321 CACACATTATATATA
66 CACAC---AT-TATA
*
2248336 TATATATATATATGTATTATATGCAAGTAAGTTATCTAAAGGATGGAAGAAATTGATCATTGCTA
1 TATATATATATATGTATTATATGCAAGTAAGTTATCTAAAAGATGGAAGAAATTGATCATTGCTA
*
2248401 CACGCATTATA
66 CACACATTATA
2248412 TATATATATATATGTATTATATGCAAGT
1 TATATATATATATGTATTATATGCAAGT
2248440 GTGGTTTTTT
Statistics
Matches: 102, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
76 32 0.31
77 2 0.02
80 68 0.67
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.38
Consensus pattern (76 bp):
TATATATATATATGTATTATATGCAAGTAAGTTATCTAAAAGATGGAAGAAATTGATCATTGCTA
CACACATTATA
Found at i:2250633 original size:29 final size:30
Alignment explanation
Indices: 2250570--2250641 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
2250560 TTAATCATAA
* *
2250570 AAATTTAAATAATAATTTTTATTATAATAT
1 AAATTTAAATTATTATTTTTATTATAATAT
*
2250600 AAA-TTAAGATTATTATTTTATATT-TATTAT
1 AAATTTAA-ATTATTATTTT-TATTATAATAT
2250630 -AATTTAAATTAT
1 AAATTTAAATTAT
2250642 GATTATTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
29 11 0.31
30 21 0.58
31 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (30 bp):
AAATTTAAATTATTATTTTTATTATAATAT
Found at i:2251058 original size:11 final size:10
Alignment explanation
Indices: 2251042--2251088 Score: 53
Period size: 11 Copynumber: 4.6 Consensus size: 10
2251032 ATTTTATGTT
2251042 TTTATATCATA
1 TTTATAT-ATA
2251053 TTTATATATA
1 TTTATATATA
2251063 TTT-TAATTATA
1 TTTAT-A-TATA
2251074 TTTA-ATATA
1 TTTATATATA
2251083 TTTATA
1 TTTATA
2251089 AATTTTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
9 9 0.28
10 9 0.28
11 14 0.44
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTATATATA
Found at i:2251139 original size:20 final size:22
Alignment explanation
Indices: 2251097--2251142 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
2251087 TAAATTTTTT
*
2251097 TATAAAATAATAATTAATATTA
1 TATAAAATAATAATAAATATTA
*
2251119 TATAAAAT-TTAATAAAT-TTA
1 TATAAAATAATAATAAATATTA
2251139 TATA
1 TATA
2251143 TTATATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 7 0.32
22 8 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TATAAAATAATAATAAATATTA
Found at i:2251186 original size:24 final size:25
Alignment explanation
Indices: 2251141--2251203 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 25
2251131 TAAATTTATA
* * *
2251141 TATTATATTATTTTTTATATCATAT
1 TATTATAATATTTTTCATATCACAT
*
2251166 T-TTAATTATATTTTTCA-ATCACAT
1 TATT-ATAATATTTTTCATATCACAT
2251190 TATTATAATATTTT
1 TATTATAATATTTT
2251204 AACTTTTGCT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
24 18 0.58
25 13 0.42
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.60
Consensus pattern (25 bp):
TATTATAATATTTTTCATATCACAT
Found at i:2263930 original size:16 final size:19
Alignment explanation
Indices: 2263911--2263946 Score: 51
Period size: 16 Copynumber: 2.1 Consensus size: 19
2263901 TTAATAAAAA
2263911 TATTAA-AA-TATAT-TTT
1 TATTAATAATTATATATTT
2263927 TATTAATAATTATATATTT
1 TATTAATAATTATATATTT
2263946 T
1 T
2263947 TATAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
16 6 0.35
17 2 0.12
18 5 0.29
19 4 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTAATAATTATATATTT
Found at i:2263943 original size:22 final size:22
Alignment explanation
Indices: 2263916--2263978 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 22
2263906 AAAAATATTA
2263916 AAATATATTTTTATTAATAATT
1 AAATATATTTTTATTAATAATT
2263938 --ATATATTTTTA-TAATTAAATTT
1 AAATATATTTTTATTAA-T-AA-TT
2263960 AAATAATATTTTTATTAAT
1 AAAT-ATATTTTTATTAAT
2263979 TAAATAACGA
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
19 3 0.09
20 12 0.35
21 2 0.06
22 2 0.06
24 2 0.06
25 10 0.29
26 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AAATATATTTTTATTAATAATT
Found at i:2267122 original size:2 final size:2
Alignment explanation
Indices: 2267115--2267146 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2267105 GAATTTAAGA
2267115 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
2267147 CAATACGAAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2268092 original size:27 final size:27
Alignment explanation
Indices: 2268062--2268113 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2268052 AATAATTATA
*
2268062 TTTAAAATATT-TTATATTTATATTAAT
1 TTTAAAATATTAATA-ATTTATATTAAT
*
2268089 TTTAATATATTAATAATTTATATTA
1 TTTAAAATATTAATAATTTATATTA
2268114 TATAAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TTTAAAATATTAATAATTTATATTAAT
Found at i:2268099 original size:14 final size:15
Alignment explanation
Indices: 2268079--2268125 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 15
2268069 TATTTTATAT
2268079 TTATATTAATTTTAA
1 TTATATTAATTTTAA
2268094 -TATATTAATAATTTATA
1 TTATATTAAT--TTTA-A
*
2268111 TTATATAAATTTTAA
1 TTATATTAATTTTAA
2268126 AAATATATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
14 9 0.33
15 1 0.04
16 8 0.30
17 1 0.04
18 8 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATATTAATTTTAA
Found at i:2268124 original size:16 final size:17
Alignment explanation
Indices: 2268057--2268199 Score: 59
Period size: 17 Copynumber: 8.5 Consensus size: 17
2268047 AAATTAATAA
*
2268057 TTATATT-TAAAATATT
1 TTATATTATATAATATT
*
2268073 TTATATT-TATATTAATT
1 TTATATTATATAAT-ATT
*
2268090 TTA-A-TATATTAATAAT
1 TTATATTATA-TAATATT
2268106 TTATATTATATAA-ATT
1 TTATATTATATAATATT
** * * *
2268122 TTA-AAAATATATTCGTA
1 TTATATTATATAAT-ATT
* *
2268139 TCATATTATATTATAATT
1 TTATATTATATAAT-ATT
*
2268157 TTATTATTTTAT-ATATT
1 TTA-TATTATATAATATT
*
2268174 TTAT-TTATATTTATATT
1 TTATATTATA-TAATATT
*
2268191 TAATATTAT
1 TTATATTAT
2268200 TATATTTACT
Statistics
Matches: 93, Mismatches: 22, Indels: 22
0.68 0.16 0.16
Matches are distributed among these distances:
15 11 0.12
16 26 0.28
17 30 0.32
18 19 0.20
19 7 0.08
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (17 bp):
TTATATTATATAATATT
Found at i:2268168 original size:21 final size:22
Alignment explanation
Indices: 2268144--2268207 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 22
2268134 TCGTATCATA
2268144 TTATATTATAATTTTA-T-TAT
1 TTATATTATAATTTTATTATAT
2268164 TT-TA-TAT-ATTTTATTTATAT
1 TTATATTATAATTTTA-TTATAT
*
2268184 TTATATT-TAATATTATTATAT
1 TTATATTATAATTTTATTATAT
2268205 TTA
1 TTA
2268208 CTTTCAACTT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
17 6 0.16
18 3 0.08
19 3 0.08
20 7 0.19
21 12 0.32
22 6 0.16
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TTATATTATAATTTTATTATAT
Found at i:2268175 original size:9 final size:9
Alignment explanation
Indices: 2268149--2268189 Score: 50
Period size: 8 Copynumber: 4.7 Consensus size: 9
2268139 TCATATTATA
2268149 TTATA-ATT
1 TTATATATT
2268157 TTAT-TATT
1 TTATATATT
2268165 TTATATATT
1 TTATATATT
*
2268174 TTATTTATAT
1 TTATATAT-T
2268184 TTATAT
1 TTATAT
2268190 TTAATATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 11 0.39
9 11 0.39
10 6 0.21
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTATATATT
Found at i:2268186 original size:27 final size:27
Alignment explanation
Indices: 2268142--2268207 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
2268132 ATTCGTATCA
*
2268142 TATTATA-TTATAATTTTATTATTTTATA-
1 TATTATATTTAT-A-TTTA-TATTTAATAT
*
2268170 TATTTTATTTATATTTATATTTAATAT
1 TATTATATTTATATTTATATTTAATAT
2268197 TATTATATTTA
1 TATTATATTTA
2268208 CTTTCAACTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
26 8 0.24
27 14 0.42
28 7 0.21
29 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (27 bp):
TATTATATTTATATTTATATTTAATAT
Found at i:2268538 original size:25 final size:25
Alignment explanation
Indices: 2268492--2268550 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
2268482 TAGTAAAAAA
* *
2268492 TAAATTTAATTTTTATGCTTGAATT
1 TAAATTTAATTTTTATACTTGAACT
* * *
2268517 TAAATTTAATTTTTGTATTTGAGCT
1 TAAATTTAATTTTTATACTTGAACT
2268542 TAAATTTAA
1 TAAATTTAA
2268551 ATTAAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.54
Consensus pattern (25 bp):
TAAATTTAATTTTTATACTTGAACT
Found at i:2269576 original size:10 final size:10
Alignment explanation
Indices: 2269561--2269630 Score: 61
Period size: 10 Copynumber: 6.9 Consensus size: 10
2269551 TTAAAAGTAT
2269561 TATAAATTTA
1 TATAAATTTA
*
2269571 TATAAATTTT
1 TATAAATTTA
* **
2269581 TATATATCAA
1 TATAAATTTA
* *
2269591 TAATTTATTTTA
1 T-A-TAAATTTA
2269603 TATAAATTT-
1 TATAAATTTA
2269612 TATAAATTTA
1 TATAAATTTA
2269622 TATAAATTT
1 TATAAATTT
2269631 TTTACATGAT
Statistics
Matches: 45, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
9 9 0.20
10 30 0.67
11 2 0.04
12 4 0.09
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (10 bp):
TATAAATTTA
Found at i:2269615 original size:51 final size:52
Alignment explanation
Indices: 2269560--2269664 Score: 151
Period size: 52 Copynumber: 2.0 Consensus size: 52
2269550 GTTAAAAGTA
* * *
2269560 TTATAAATTTATATAAA-TTTTTATAT-ATCAATAATTTATTTTATATAAATT
1 TTATAAATTTATATAAATTTTTTACATGAT-AATAACTTATTTTATACAAATT
*
2269611 TTATAAATTTATATAAATTTTTTACATGATAATAACTTATTTTATGCAAATT
1 TTATAAATTTATATAAATTTTTTACATGATAATAACTTATTTTATACAAATT
2269663 TT
1 TT
2269665 GATACGTTCG
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
51 17 0.35
52 29 0.60
53 2 0.04
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (52 bp):
TTATAAATTTATATAAATTTTTTACATGATAATAACTTATTTTATACAAATT
Found at i:2269632 original size:20 final size:19
Alignment explanation
Indices: 2269560--2269631 Score: 68
Period size: 19 Copynumber: 4.1 Consensus size: 19
2269550 GTTAAAAGTA
2269560 TTATAAATTTATATAAATT
1 TTATAAATTTATATAAATT
* *
2269579 TT-TATATATCA-AT-AA-T
1 TTATAAAT-TTATATAAATT
2269595 TTAT---TTTATATAAATT
1 TTATAAATTTATATAAATT
2269611 TTATAAATTTATATAAATT
1 TTATAAATTTATATAAATT
2269630 TT
1 TT
2269632 TTACATGATA
Statistics
Matches: 42, Mismatches: 3, Indels: 16
0.69 0.05 0.26
Matches are distributed among these distances:
13 2 0.05
14 3 0.07
15 2 0.05
16 8 0.19
17 3 0.07
18 6 0.14
19 18 0.43
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATAAATTTATATAAATT
Found at i:2269634 original size:32 final size:32
Alignment explanation
Indices: 2269567--2269634 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 32
2269557 GTATTATAAA
* *
2269567 TTTATATAAATTTTTATATATCAATAATTTAT
1 TTTATATAAATTTTTAAATATCAATAAATTAT
*
2269599 TTTATATAAATTTTATAAAT-TTATATAAATT-T
1 TTTATATAAATTTT-TAAATATCA-ATAAATTAT
2269631 TTTA
1 TTTA
2269635 CATGATAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
32 21 0.68
33 10 0.32
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (32 bp):
TTTATATAAATTTTTAAATATCAATAAATTAT
Found at i:2269828 original size:21 final size:21
Alignment explanation
Indices: 2269791--2269840 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2269781 TCATAATAAT
* *
2269791 TTAATTTTAATTCTAAATTTA
1 TTAATTTAAATTCTAAATTAA
2269812 TTAATTTAAATAT-TAAATTAA
1 TTAATTTAAAT-TCTAAATTAA
*
2269833 TAAATTTA
1 TTAATTTA
2269841 TTACAACCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TTAATTTAAATTCTAAATTAA
Found at i:2271434 original size:24 final size:24
Alignment explanation
Indices: 2271390--2271436 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
2271380 ATAAATAAAA
**
2271390 TATATAAATTTTTTAAAATTTATT
1 TATATAAATTTTAAAAAATTTATT
2271414 TATA-AAATTTTAAAAATATTTAT
1 TATATAAATTTTAAAAA-ATTTAT
2271437 ATTAGATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TATATAAATTTTAAAAAATTTATT
Found at i:2274419 original size:12 final size:11
Alignment explanation
Indices: 2274387--2274416 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
2274377 AATAGATCGC
2274387 TATTATTATTTT
1 TATTATTA-TTT
2274399 TATTATTATTT
1 TATTATTATTT
2274410 TATTATT
1 TATTATT
2274417 TATAATCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TATTATTATTT
Found at i:2275502 original size:6 final size:6
Alignment explanation
Indices: 2275416--2275503 Score: 56
Period size: 6 Copynumber: 14.2 Consensus size: 6
2275406 TATAATTACG
* * * *
2275416 ATATAA ATATATA TATATAA ATATAT A-AT-A ATTTTA ATATAA TTAGTAA
1 ATATAA ATATA-A -ATATAA ATATAA ATATAA ATATAA ATATAA ATA-TAA
*
2275465 ATAT-A ATAATTAT ATATATA ATATAA ATATAA ATATAA A
1 ATATAA AT-A-TAA ATATA-A ATATAA ATATAA ATATAA A
2275504 AATTATGAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
4 1 0.02
5 6 0.09
6 36 0.56
7 14 0.22
8 7 0.11
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (6 bp):
ATATAA
Found at i:2278316 original size:2 final size:2
Alignment explanation
Indices: 2278309--2278339 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2278299 TAAGGAAGAA
2278309 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2278340 CCTCAATGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2280066 original size:5 final size:5
Alignment explanation
Indices: 2280041--2280152 Score: 50
Period size: 5 Copynumber: 21.8 Consensus size: 5
2280031 TTTATCGAAA
* * *
2280041 TTAAT TTGAAT CTAA- TTAAT TTAAT TTAAAT TTAAT TAAAT TTAAAA
1 TTAAT TT-AAT TTAAT TTAAT TTAAT TT-AAT TTAAT TTAAT TT-AAT
* * ** * * *
2280088 TTAAA ATAAT TT-AT AAAAT TTAAT TTAAAT CTAA- TCAAT ATAAAT TTAAAT
1 TTAAT TTAAT TTAAT TTAAT TTAAT TT-AAT TTAAT TTAAT -TTAAT TT-AAT
*
2280139 TTAAT TAAAT TTAA
1 TTAAT TTAAT TTAA
2280153 AATTAAAATA
Statistics
Matches: 79, Mismatches: 19, Indels: 18
0.68 0.16 0.16
Matches are distributed among these distances:
4 7 0.09
5 46 0.58
6 26 0.33
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (5 bp):
TTAAT
Found at i:2280066 original size:20 final size:21
Alignment explanation
Indices: 2280041--2280152 Score: 86
Period size: 21 Copynumber: 5.2 Consensus size: 21
2280031 TTTATCGAAA
*
2280041 TTAATTTGAATCTAATT-AAT
1 TTAATTTAAATCTAATTAAAT
*
2280061 TTAATTTAAATTTAATTAAAT
1 TTAATTTAAATCTAATTAAAT
* *
2280082 TTAAAATTAAA-ATAATTTATAAAAT
1 TT-AATTTAAATCTAA--T-T-AAAT
*
2280107 TTAATTTAAATCTAA-TCAAT
1 TTAATTTAAATCTAATTAAAT
* *
2280127 ATAAATTTAAATTTAATTAAAT
1 -TTAATTTAAATCTAATTAAAT
2280149 TTAA
1 TTAA
2280153 AATTAAAATA
Statistics
Matches: 72, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
20 18 0.25
21 25 0.35
22 11 0.15
23 1 0.01
24 8 0.11
25 9 0.12
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (21 bp):
TTAATTTAAATCTAATTAAAT
Found at i:2280074 original size:6 final size:6
Alignment explanation
Indices: 2280058--2280159 Score: 56
Period size: 6 Copynumber: 17.3 Consensus size: 6
2280048 GAATCTAATT
* * *
2280058 AATTT- AATTTA AATTT- AA-TTA AATTTA AAATTA AA-ATA ATTTATAA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATT-T-A
* *
2280104 AATTT- AATTTA AATCTAATC AATATA AATTTA AATTT- AA-TTA AATTTA
1 AATTTA AATTTA AAT-T--TA AATTTA AATTTA AATTTA AATTTA AATTTA
*
2280152 AAATTA AA
1 AATTTA AA
2280160 ATAGTTCACG
Statistics
Matches: 75, Mismatches: 10, Indels: 23
0.69 0.09 0.21
Matches are distributed among these distances:
4 4 0.05
5 21 0.28
6 39 0.52
7 3 0.04
8 4 0.05
9 4 0.05
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:2280153 original size:16 final size:16
Alignment explanation
Indices: 2280056--2280158 Score: 84
Period size: 16 Copynumber: 6.2 Consensus size: 16
2280046 TTGAATCTAA
*
2280056 TTAATTTAATTTAAAT
1 TTAATTAAATTTAAAT
2280072 TTAATTAAATTTAAAAT
1 TTAATTAAATTT-AAAT
* * *
2280089 TAAAATAATTTATAAAAT
1 TTAATTAAATT-T-AAAT
*
2280107 TTAATTTAAATCT-AA-
1 TTAA-TTAAATTTAAAT
*
2280122 TCAATATAAATTTAAAT
1 TTAAT-TAAATTTAAAT
*
2280139 TTAATTAAATTTAAAA
1 TTAATTAAATTTAAAT
2280155 TTAA
1 TTAA
2280159 AATAGTTCAC
Statistics
Matches: 69, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
14 1 0.01
15 9 0.13
16 29 0.42
17 16 0.23
18 10 0.14
19 4 0.06
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAATTAAATTTAAAT
Found at i:2280178 original size:67 final size:65
Alignment explanation
Indices: 2280038--2280167 Score: 197
Period size: 67 Copynumber: 2.0 Consensus size: 65
2280028 CAGTTTATCG
* * * *
2280038 AAATTAATTTGAATCTAATTAATTTAATTTAAATTTAATTAAATTTAAAATTAAAATAATTTATA
1 AAATTAATTTAAATCTAATCAATTAAATTTAAATTTAATTAAATTTAAAATTAAAATAATTCATA
*
2280103 AAATTTAATTTAAATCTAATCAATATAAATTTAAATTTAATTAAATTTAAAATTAAAATAGTTCA
1 AAA-TTAATTTAAATCTAATCAAT-TAAATTTAAATTTAATTAAATTTAAAATTAAAATAATTCA
2280168 CGTAAATTAA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
65 3 0.05
66 18 0.31
67 37 0.64
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (65 bp):
AAATTAATTTAAATCTAATCAATTAAATTTAAATTTAATTAAATTTAAAATTAAAATAATTCATA
Found at i:2280434 original size:19 final size:18
Alignment explanation
Indices: 2280410--2280449 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
2280400 AGATTAAATA
2280410 ATTTATATATTTATATTAT
1 ATTTATATATTT-TATTAT
2280429 ATTTATATATTTTATTAT
1 ATTTATATATTTTATTAT
2280447 ATT
1 ATT
2280450 ATAATCATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTATATATTTTATTAT
Found at i:2280512 original size:25 final size:26
Alignment explanation
Indices: 2280453--2280512 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 26
2280443 TTATATTATA
* *
2280453 ATCATGTTTAAAGTATTTTAATTTAT
1 ATCATATTTAAAGTATTTTAATTCAT
* * *
2280479 AT-ATTTTTAAATTATTTT-ATTCGT
1 ATCATATTTAAAGTATTTTAATTCAT
2280503 ATCATATTTA
1 ATCATATTTA
2280513 TATAATTATG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 6 0.21
25 20 0.71
26 2 0.07
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (26 bp):
ATCATATTTAAAGTATTTTAATTCAT
Found at i:2282172 original size:5 final size:5
Alignment explanation
Indices: 2282152--2282186 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
2282142 CAAATATCGA
2282152 AAAAGG AAAA- AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAA-G AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
2282187 GATGATTGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.14
5 20 0.71
6 4 0.14
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:2283374 original size:3 final size:3
Alignment explanation
Indices: 2283355--2283388 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2283345 CTCAACGATC
* *
2283355 TCT TGT TCT TGT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
2283389 TATCTTCGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.26, G:0.06, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:2284375 original size:16 final size:17
Alignment explanation
Indices: 2284351--2284388 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2284341 CGAACGTGAG
*
2284351 TATTAAATAT-AATATA
1 TATTTAATATAAATATA
2284367 TATTTAATATAAATATA
1 TATTTAATATAAATATA
2284384 TATTT
1 TATTT
2284389 TTTAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTTAATATAAATATA
Found at i:2284461 original size:17 final size:17
Alignment explanation
Indices: 2284439--2284473 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2284429 TATTTATATT
2284439 TAAATA-TATATCGAATA
1 TAAATAGTATAT-GAATA
2284456 TAAATAGTATATGAATA
1 TAAATAGTATATGAATA
2284473 T
1 T
2284474 TTTAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.37
Consensus pattern (17 bp):
TAAATAGTATATGAATA
Found at i:2286196 original size:2 final size:2
Alignment explanation
Indices: 2286189--2286219 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2286179 TTTCTTTAGC
2286189 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 T
2286220 TACTTTTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2286371 original size:31 final size:30
Alignment explanation
Indices: 2286324--2286382 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
2286314 ATATTTTATG
* *
2286324 TTTTTATATATTTTGATATGTTAATATAGA
1 TTTTTATAAATTTTGATATATTAATATAGA
*
2286354 TTTTATATAAATTTTGATATATTTATATA
1 TTTT-TATAAATTTTGATATATTAATATA
2286383 TTCATATTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (30 bp):
TTTTTATAAATTTTGATATATTAATATAGA
Found at i:2287428 original size:19 final size:19
Alignment explanation
Indices: 2287395--2287448 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
2287385 ATATAAATTA
2287395 AATTAATTT-TAATTTTTTT
1 AATTAATTTAT-ATTTTTTT
*
2287414 ATATT-ATTTATATTTATTT
1 A-ATTAATTTATATTTTTTT
*
2287433 AATTAAGTTATATTTT
1 AATTAATTTATATTTT
2287449 ATATTTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 3 0.10
19 22 0.76
20 4 0.14
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
AATTAATTTATATTTTTTT
Found at i:2287603 original size:22 final size:22
Alignment explanation
Indices: 2287559--2287614 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
2287549 ATAGATATAC
2287559 TTATATTATTAAATTTAATTAA
1 TTATATTATTAAATTTAATTAA
2287581 TTAT-TTATTAAAATATTAA-TAA
1 TTATATTATT-AAAT-TTAATTAA
*
2287603 TATATAATATTA
1 T-TATATTATTA
2287615 TAAAAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 5 0.17
22 12 0.41
23 8 0.28
24 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATATTATTAAATTTAATTAA
Found at i:2287668 original size:136 final size:137
Alignment explanation
Indices: 2287480--2287759 Score: 481
Period size: 136 Copynumber: 2.1 Consensus size: 137
2287470 TTTAAAATTT
* *
2287480 AAAATATTTAATGAATTTTTAATTTAAAAATTTTTAATTATTAAATCAATTTAAAATTATATGTA
1 AAAATATTTAATGAATTTTTAATCTAAAAATTTTTAATTATTAAATCAATTTAAAATTACATGTA
*
2287545 CATAATAGATATACTTATATTATTAAATTTAATTAATTATTTATTAAAATATTAATAATATATAA
66 CATAATAAATATACTTATATTATTAAATTTAATTAATTATTTATTAAAATATTAATAATATATAA
2287610 TATTATA
131 TATTATA
*
2287617 AAAATTTTTAATGAATTTTTAATCT-AAAATTTTTAATTATTAAATCAATTTAAAATTACATGTA
1 AAAATATTTAATGAATTTTTAATCTAAAAATTTTTAATTATTAAATCAATTTAAAATTACATGTA
* * * *
2287681 CATAATAAATATATTTATATTATTAAATTTAATTATTTATTTATTAAAATGTTAATGATATATAA
66 CATAATAAATATACTTATATTATTAAATTTAATTAATTATTTATTAAAATATTAATAATATATAA
2287746 TATTATA
131 TATTATA
2287753 AAAATAT
1 AAAATAT
2287760 ATAAAATTAA
Statistics
Matches: 134, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
136 111 0.83
137 23 0.17
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (137 bp):
AAAATATTTAATGAATTTTTAATCTAAAAATTTTTAATTATTAAATCAATTTAAAATTACATGTA
CATAATAAATATACTTATATTATTAAATTTAATTAATTATTTATTAAAATATTAATAATATATAA
TATTATA
Found at i:2287725 original size:68 final size:67
Alignment explanation
Indices: 2287508--2287728 Score: 202
Period size: 68 Copynumber: 3.3 Consensus size: 67
2287498 TTAATTTAAA
* *
2287508 AATTTTTAATTATTAAATCAATTTAAAATTATATGTACATAATAGATATACTTATATTATTAAAT
1 AATTTTTAATTATTAAATCAATTTAAAATTATATGTACATAATAAATATATTTATATTATTAAAT
2287573 TT
66 TT
* * * * * * *
2287575 AATTAATTATTTATT-AA--AATATTAATAA-TATAT-AATATTATAAAAATTTTTAATGAATT-
1 AATT-TTTAATTATTAAATCAAT-TTAA-AATTATATGTACATAATAAATATATTT-AT--ATTA
* *
2287634 TTTAATCTAA
60 TTAAAT-T-T
*
2287644 AATTTTTAATTATTAAATCAATTTAAAATTACATGTACATAATAAATATATTTATATTATTAAAT
1 AATTTTTAATTATTAAATCAATTTAAAATTATATGTACATAATAAATATATTTATATTATTAAAT
2287709 TT
66 TT
*
2287711 AATTATTTATTTATTAAA
1 AATT-TTTAATTATTAAA
2287729 ATGTTAATGA
Statistics
Matches: 117, Mismatches: 22, Indels: 29
0.70 0.13 0.17
Matches are distributed among these distances:
65 14 0.12
66 11 0.09
67 17 0.15
68 36 0.31
69 13 0.11
70 10 0.09
71 16 0.14
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (67 bp):
AATTTTTAATTATTAAATCAATTTAAAATTATATGTACATAATAAATATATTTATATTATTAAAT
TT
Done.