Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold5
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: 1536239
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.33
Warning! 124408 characters in sequence are not A, C, G, or T
File 12 of 14
Found at i:1355457 original size:18 final size:19
Alignment explanation
Indices: 1355434--1355469 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1355424 TATAATTAAA
1355434 TTAAATA-AAAATAATTTT
1 TTAAATATAAAATAATTTT
*
1355452 TTAAATATATAATAATTT
1 TTAAATATAAAATAATTT
1355470 AAGTCAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAAATATAAAATAATTTT
Found at i:1355933 original size:3 final size:3
Alignment explanation
Indices: 1355925--1355963 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
1355915 TAACTTTTAC
*
1355925 ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1355964 TGGACTTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1363727 original size:45 final size:45
Alignment explanation
Indices: 1363668--1363757 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 45
1363658 GGATTAATAA
* * *
1363668 CATCAATTTAATCGAGAACAT-ATAGGTCTGTTGGATCAATAACAT
1 CATCAATTTAATCGAGAA-ATGATAGGTCCGATGCATCAATAACAT
*
1363713 CATCAATTTAATCGAGAATTGATAGGTCCGATGCATCAATAACAT
1 CATCAATTTAATCGAGAAATGATAGGTCCGATGCATCAATAACAT
1363758 ATAAGGAACT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 1 0.03
45 39 0.98
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.30
Consensus pattern (45 bp):
CATCAATTTAATCGAGAAATGATAGGTCCGATGCATCAATAACAT
Found at i:1364484 original size:3 final size:3
Alignment explanation
Indices: 1364476--1364518 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1364466 TCTTTAAATA
1364476 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1364519 GATTTAGCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1365568 original size:24 final size:24
Alignment explanation
Indices: 1365540--1365627 Score: 72
Period size: 24 Copynumber: 3.7 Consensus size: 24
1365530 ATTTATAGTG
*
1365540 ATTATAAATATAATAAAAATTATA
1 ATTATAAATATAATAAAAATTAAA
* * * *
1365564 ATTATCAATTAAAATAAATATAAAA
1 ATTAT-AAATATAATAAAAATTAAA
* * *
1365589 AATAAAAAT-TAATAAAAAATTAGA
1 ATTATAAATATAAT-AAAAATTAAA
1365613 ATTATAAA-ATAATAA
1 ATTATAAATATAATAA
1365628 TAATAATATC
Statistics
Matches: 47, Mismatches: 14, Indels: 7
0.69 0.21 0.10
Matches are distributed among these distances:
23 5 0.11
24 25 0.53
25 17 0.36
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (24 bp):
ATTATAAATATAATAAAAATTAAA
Found at i:1365605 original size:17 final size:16
Alignment explanation
Indices: 1365582--1365627 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
1365572 TTAAAATAAA
1365582 TATAAAAAATAAAAAT
1 TATAAAAAATAAAAAT
* *
1365598 TAATAAAAAATTAGAAT
1 T-ATAAAAAATAAAAAT
1365615 TATAAAATAATAA
1 TATAAAA-AATAA
1365628 TAATAATATC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
TATAAAAAATAAAAAT
Found at i:1365814 original size:5 final size:6
Alignment explanation
Indices: 1365800--1365824 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1365790 CAAATTAAAG
1365800 AAAATA AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA A
1365825 CAGTGAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:1368303 original size:26 final size:25
Alignment explanation
Indices: 1368269--1368320 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
1368259 TTTTTATTTT
* *
1368269 AAATAAAAATTTTATTTATATTAAAA
1 AAATAAAAAATTTATTTA-AGTAAAA
*
1368295 AAATTAAAAATTTATTTAAGTAAAA
1 AAATAAAAAATTTATTTAAGTAAAA
1368320 A
1 A
1368321 TTAAATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
AAATAAAAAATTTATTTAAGTAAAA
Found at i:1368307 original size:22 final size:22
Alignment explanation
Indices: 1368282--1368325 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1368272 TAAAAATTTT
1368282 ATTTATATTAA-AAAAATTAAAA
1 ATTTAT-TTAAGAAAAATTAAAA
1368304 ATTTATTTAAGTAAAAATTAAA
1 ATTTATTTAAG-AAAAATTAAA
1368326 TTAAAATCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 6 0.30
23 10 0.50
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
ATTTATTTAAGAAAAATTAAAA
Found at i:1368327 original size:28 final size:28
Alignment explanation
Indices: 1368267--1368371 Score: 76
Period size: 28 Copynumber: 3.8 Consensus size: 28
1368257 AATTTTTATT
*
1368267 TTAAA-TAAAAATTTTATTTATA-TTAAAA
1 TTAAATTAAAAA-TTTATTTA-AGTAAAAA
1368295 --AAATTAAAAATTTATTTAAGTAAAAA
1 TTAAATTAAAAATTTATTTAAGTAAAAA
* **
1368321 TTAAATT-AAAATCTGATTTAAGTGTAAA
1 TTAAATTAAAAAT-TTATTTAAGTAAAAA
* *
1368349 TTAAAATATAACAATTTGTTTAA
1 TT-AAAT-TAAAAATTTATTTAA
1368372 ACGTAATAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
25 1 0.02
26 16 0.26
27 11 0.18
28 19 0.31
29 4 0.06
30 7 0.11
31 4 0.06
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (28 bp):
TTAAATTAAAAATTTATTTAAGTAAAAA
Found at i:1369419 original size:16 final size:17
Alignment explanation
Indices: 1369384--1369421 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1369374 TATAAATTCT
* *
1369384 AATAATATATTTACATA
1 AATATTATACTTACATA
1369401 AATATTATACTTA-ATA
1 AATATTATACTTACATA
1369417 AATAT
1 AATAT
1369422 GGTATTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
AATATTATACTTACATA
Found at i:1369873 original size:30 final size:29
Alignment explanation
Indices: 1369830--1369896 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
1369820 TTATTAGATA
1369830 TTTAAAAA-TATTT-AATAAAAATATTAAG
1 TTTAAAAATTATTTAAATAAAAA-ATTAAG
* *
1369858 TTTAAAAATTAATTTAAATAAAAAATTTAT
1 TTTAAAAATT-ATTTAAATAAAAAATTAAG
1369888 TTTAAAAAT
1 TTTAAAAAT
1369897 GAGCTTAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 8 0.24
29 1 0.03
30 17 0.50
31 8 0.24
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (29 bp):
TTTAAAAATTATTTAAATAAAAAATTAAG
Found at i:1370867 original size:24 final size:23
Alignment explanation
Indices: 1370830--1370885 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
1370820 TTATTAAAAT
*
1370830 AAATATCAAATTAT-TGATTATTA
1 AAATATTAAATTATCT-ATTATTA
1370853 AAATATTAAAGTTATCTATTATTA
1 AAATATTAAA-TTATCTATTATTA
*
1370877 AATTATTAA
1 AAATATTAA
1370886 TATTTTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 9 0.31
24 19 0.66
25 1 0.03
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (23 bp):
AAATATTAAATTATCTATTATTA
Found at i:1370897 original size:14 final size:13
Alignment explanation
Indices: 1370883--1370934 Score: 61
Period size: 14 Copynumber: 3.9 Consensus size: 13
1370873 ATTAAATTAT
*
1370883 TAATATTTTAATAT
1 TAATA-TTTAATAA
*
1370897 TAATAATT-ATAA
1 TAATATTTAATAA
1370909 TAATATTTTAATAA
1 TAATA-TTTAATAA
1370923 TAATATTTAATA
1 TAATATTTAATA
1370935 CTAAGAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 8 0.24
13 11 0.33
14 14 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAATATTTAATAA
Found at i:1370914 original size:26 final size:24
Alignment explanation
Indices: 1370883--1370934 Score: 77
Period size: 26 Copynumber: 2.1 Consensus size: 24
1370873 ATTAAATTAT
*
1370883 TAATATTTTAATATTAATAATTATAA
1 TAATATTTTAATAATAAT-ATT-TAA
1370909 TAATATTTTAATAATAATATTTAA
1 TAATATTTTAATAATAATATTTAA
1370933 TA
1 TA
1370935 CTAAGAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 5 0.20
25 3 0.12
26 17 0.68
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TAATATTTTAATAATAATATTTAA
Found at i:1371304 original size:16 final size:16
Alignment explanation
Indices: 1371266--1371324 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
1371256 TATGTATGTT
* *
1371266 TAATAATAAACAAAATA
1 TAATATTAAA-AAATTA
1371283 TAAATATTAAAAAATTA
1 T-AATATTAAAAAATTA
1371300 TAATATTAAAATAATT-
1 TAATATTAAAA-AATTA
*
1371316 TAATTTTAA
1 TAATATTAA
1371325 TTTAATATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
16 18 0.49
17 11 0.30
18 8 0.22
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATATTAAAAAATTA
Found at i:1371385 original size:21 final size:21
Alignment explanation
Indices: 1371336--1371388 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
1371326 TTAATATTTT
1371336 TAAAATATTTTTAAATTAAAAA
1 TAAAATATTTTT-AATTAAAAA
* *
1371358 TTAAATATTTTT-ATTAACAA
1 TAAAATATTTTTAATTAAAAA
1371378 TAATAATATTT
1 TAA-AATATTT
1371389 AATCCAAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.33
21 7 0.26
22 11 0.41
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAAATATTTTTAATTAAAAA
Found at i:1372659 original size:21 final size:19
Alignment explanation
Indices: 1372633--1372673 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1372623 TATTTTTATA
*
1372633 TATTTTATTATATATTTAAAT
1 TATTTTA-TAT-TATATAAAT
1372654 TATTTTATATTATATAAAT
1 TATTTTATATTATATAAAT
1372673 T
1 T
1372674 TTAATTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 3 0.16
21 7 0.37
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTTTATATTATATAAAT
Found at i:1372831 original size:26 final size:25
Alignment explanation
Indices: 1372787--1372839 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
1372777 TATTTAATTT
* *
1372787 TTAAAATTTTTTACATATATTTTAAA
1 TTAAAATTTTATACATATA-ATTAAA
**
1372813 TTAAAATTTTATATTTATAATTAAA
1 TTAAAATTTTATACATATAATTAAA
1372838 TT
1 TT
1372840 TAATTAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
TTAAAATTTTATACATATAATTAAA
Found at i:1372979 original size:18 final size:18
Alignment explanation
Indices: 1372958--1373015 Score: 53
Period size: 20 Copynumber: 3.0 Consensus size: 18
1372948 TTAATATATT
1372958 AAATTTTATATAAATAAA
1 AAATTTTATATAAATAAA
* *
1372976 AAATTTTAAATATAATTATA
1 AAATTTT--ATATAAATAAA
*
1372996 AAATAATTATATAATATAAA
1 AAAT-TTTATATAA-ATAAA
1373016 TATATAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
18 7 0.23
19 6 0.19
20 16 0.52
21 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATTTTATATAAATAAA
Found at i:1373470 original size:12 final size:12
Alignment explanation
Indices: 1373453--1373518 Score: 75
Period size: 12 Copynumber: 5.7 Consensus size: 12
1373443 GATTTGTTTA
1373453 ATATTTATGAAT
1 ATATTTATGAAT
*
1373465 ATATTT-TTAAT
1 ATATTTATGAAT
1373476 -TATTTATGAAT
1 ATATTTATGAAT
*
1373487 ATATTTGAT-TAT
1 ATATTT-ATGAAT
*
1373499 ATATTTATAAAT
1 ATATTTATGAAT
1373511 ATATTTAT
1 ATATTTAT
1373519 TTAGAGTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
10 5 0.11
11 10 0.22
12 29 0.63
13 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (12 bp):
ATATTTATGAAT
Found at i:1373503 original size:24 final size:22
Alignment explanation
Indices: 1373439--1373516 Score: 95
Period size: 24 Copynumber: 3.4 Consensus size: 22
1373429 AAAATGAATA
*
1373439 AATAGATTTGTTTAATATTTATG
1 AATATATTTG-TTAATATTTATG
1373462 AATATATTT-TTAATTATTTATG
1 AATATATTTGTTAA-TATTTATG
*
1373484 AATATATTTGATTATATATTTATA
1 AATATATTTG-TTA-ATATTTATG
1373508 AATATATTT
1 AATATATTT
1373517 ATTTAGAGTT
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
21 4 0.08
22 17 0.35
23 8 0.16
24 19 0.39
25 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.55
Consensus pattern (22 bp):
AATATATTTGTTAATATTTATG
Found at i:1374351 original size:27 final size:28
Alignment explanation
Indices: 1374251--1374352 Score: 73
Period size: 27 Copynumber: 3.5 Consensus size: 28
1374241 TATTTTATAT
* *
1374251 TTATATAAATTTTAATATATTAATAATTAATA
1 TTATATAAA-TTTAAAATA-T-ATATTTAA-A
* *
1374283 TAATATAAAATTTAAAATATATATTTACA
1 TTATAT-AAATTTAAAATATATATTTAAA
** *
1374312 TTATATATTTTTATAAT-TATATTTAAAA
1 TTATATAAATTTAAAATATATATTT-AAA
1374340 TTA-ATAAATTTAA
1 TTATATAAATTTAA
1374353 TTTGATTCCA
Statistics
Matches: 56, Mismatches: 12, Indels: 9
0.73 0.16 0.12
Matches are distributed among these distances:
27 14 0.25
28 13 0.23
29 6 0.11
30 6 0.11
31 1 0.02
32 13 0.23
33 3 0.05
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (28 bp):
TTATATAAATTTAAAATATATATTTAAA
Found at i:1374637 original size:23 final size:21
Alignment explanation
Indices: 1374609--1374665 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
1374599 ATTTTTTTAA
1374609 TTTTAAATAAAAAAATTGTAAAT
1 TTTTAAA-AAAAAAATT-TAAAT
*
1374632 TTTTAAAATAAAAATTTAAAT
1 TTTTAAAAAAAAAATTTAAAT
*
1374653 TATTTTAAAAAAA
1 T-TTTAAAAAAAA
1374666 TTAATACTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.20
22 17 0.57
23 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
TTTTAAAAAAAAAATTTAAAT
Found at i:1374804 original size:18 final size:18
Alignment explanation
Indices: 1374783--1374821 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1374773 AGATTGTTTA
1374783 ATTAAA-AATAAATTATAT
1 ATTAAATAATAAA-TATAT
*
1374801 ATTAAATATTAAATATAT
1 ATTAAATAATAAATATAT
1374819 ATT
1 ATT
1374822 TTGAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTAAATAATAAATATAT
Found at i:1374831 original size:19 final size:20
Alignment explanation
Indices: 1374791--1374834 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
1374781 TAATTAAAAA
1374791 TAAAT-TATATATTAAATAT
1 TAAATATATATATTAAATAT
* *
1374810 TAAATATATATTTTGAAT-T
1 TAAATATATATATTAAATAT
1374829 TAAATA
1 TAAATA
1374835 AGTATTAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TAAATATATATATTAAATAT
Found at i:1375002 original size:19 final size:19
Alignment explanation
Indices: 1374975--1375013 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1374965 TTTTAATTTT
* *
1374975 TAATATTTACTGAATTTAA
1 TAATATTTAATCAATTTAA
*
1374994 TAATTTTTAATCAATTTAA
1 TAATATTTAATCAATTTAA
1375013 T
1 T
1375014 TTGATATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (19 bp):
TAATATTTAATCAATTTAA
Found at i:1375224 original size:42 final size:42
Alignment explanation
Indices: 1375167--1375248 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
1375157 CTTTATTTAC
*
1375167 ATGATAAGGATAAAATTGAATAAGTAAAAAAAAAAA-AAAACT
1 ATGATAAGGACAAAATTGAA-AAGTAAAAAAAAAAAGAAAACT
*
1375209 ATGATGAGGACAAAATTGAAAAGTAAAAAAAAAAAGAAAA
1 ATGATAAGGACAAAATTGAAAAGTAAAAAAAAAAAGAAAA
1375249 AGGCCACATC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 15 0.41
42 22 0.59
ACGTcount: A:0.67, C:0.02, G:0.15, T:0.16
Consensus pattern (42 bp):
ATGATAAGGACAAAATTGAAAAGTAAAAAAAAAAAGAAAACT
Found at i:1375638 original size:14 final size:13
Alignment explanation
Indices: 1375606--1375639 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1375596 AATTTTAATT
1375606 TTATTAAATTTTA
1 TTATTAAATTTTA
*
1375619 TCATTAAATTTTTA
1 TTATTAAA-TTTTA
1375633 TTATTAA
1 TTATTAA
1375640 TAAATTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (13 bp):
TTATTAAATTTTA
Found at i:1375643 original size:17 final size:16
Alignment explanation
Indices: 1375595--1375674 Score: 67
Period size: 16 Copynumber: 5.0 Consensus size: 16
1375585 CAAAGTTATA
*
1375595 AAATTTTAATT-TTATT
1 AAATTTT-ATTATTAAT
*
1375611 AAATTTTATCATT-A-
1 AAATTTTATTATTAAT
*
1375625 AATTTTTATTATTAAT
1 AAATTTTATTATTAAT
*
1375641 AAATTATATTATTATAT
1 AAATTTTATTATTA-AT
*
1375658 TAATTTTATTATATAAT
1 AAATTTTATTAT-TAAT
1375675 TTTAATAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
14 11 0.22
15 3 0.06
16 21 0.41
17 14 0.27
18 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (16 bp):
AAATTTTATTATTAAT
Found at i:1375644 original size:30 final size:29
Alignment explanation
Indices: 1375595--1375654 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
1375585 CAAAGTTATA
* *
1375595 AAATTTTAATTTTATTAAATTTTATCATT
1 AAATTTTAATTTTAATAAATTATATCATT
* *
1375624 AAATTTTTATTATTAATAAATTATATTATT
1 AAATTTTAATT-TTAATAAATTATATCATT
1375654 A
1 A
1375655 TATTAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (29 bp):
AAATTTTAATTTTAATAAATTATATCATT
Found at i:1375674 original size:13 final size:14
Alignment explanation
Indices: 1375649--1375678 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1375639 ATAAATTATA
1375649 TTATTATATTAATT
1 TTATTATATTAATT
1375663 TTATTATA-TAATT
1 TTATTATATTAATT
1375676 TTA
1 TTA
1375679 ATAAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTATTATATTAATT
Found at i:1376615 original size:31 final size:31
Alignment explanation
Indices: 1376553--1376617 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
1376543 TTTTAAAATA
* *
1376553 TCTATTTATTGATATTATATTTATATTATTT
1 TCTATTTATTGATATTACATTTATATCATTT
* * * *
1376584 TCTATTTATTGGTGTTACGTTTGTATCATTT
1 TCTATTTATTGATATTACATTTATATCATTT
1376615 TCT
1 TCT
1376618 TATGTTTTGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.22, C:0.08, G:0.09, T:0.62
Consensus pattern (31 bp):
TCTATTTATTGATATTACATTTATATCATTT
Found at i:1376654 original size:11 final size:12
Alignment explanation
Indices: 1376629--1376657 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1376619 ATGTTTTGTA
1376629 ATATTTTATATT
1 ATATTTTATATT
1376641 ATATTTTA-ATT
1 ATATTTTATATT
1376652 ATATTT
1 ATATTT
1376658 AGTATCCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
ATATTTTATATT
Found at i:1377179 original size:19 final size:19
Alignment explanation
Indices: 1377098--1377180 Score: 57
Period size: 19 Copynumber: 4.5 Consensus size: 19
1377088 TTAAAAAATT
*
1377098 TAATTGTAAAAATATAAAAA
1 TAATT-TAAAAATTTAAAAA
* *
1377118 T-ATTT-TAAATTTATAAA
1 TAATTTAAAAATTTAAAAA
* *
1377135 TCAAGTT--AAATTTAAATA
1 T-AATTTAAAAATTTAAAAA
*
1377153 TAAATTAAAAATTTAAAAA
1 TAATTTAAAAATTTAAAAA
*
1377172 TATTTTAAA
1 TAATTTAAA
1377181 TAATAATACA
Statistics
Matches: 49, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
17 14 0.29
18 11 0.22
19 23 0.47
20 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (19 bp):
TAATTTAAAAATTTAAAAA
Found at i:1377949 original size:16 final size:16
Alignment explanation
Indices: 1377924--1377954 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1377914 TGACTATAAA
1377924 TTCGAATCATTTTAGT
1 TTCGAATCATTTTAGT
*
1377940 TTCGAGTCATTTTAG
1 TTCGAATCATTTTAG
1377955 ATTAAATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.13, G:0.16, T:0.48
Consensus pattern (16 bp):
TTCGAATCATTTTAGT
Found at i:1378594 original size:39 final size:40
Alignment explanation
Indices: 1378551--1378630 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 40
1378541 GATGATGTAA
*
1378551 TAATCCAGACTC-GAGAACTTTCATGCAGGATTTAAATAG
1 TAATCCAGACTCAGAGAACTTTCATACAGGATTTAAATAG
1378590 TAATCCAGACTCGAGAGAACTTTCATACAGGATTTAAATAG
1 TAATCCAGACTC-AGAGAACTTTCATACAGGATTTAAATAG
1378631 CAGTCATTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
39 12 0.32
41 26 0.68
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (40 bp):
TAATCCAGACTCAGAGAACTTTCATACAGGATTTAAATAG
Found at i:1385693 original size:25 final size:27
Alignment explanation
Indices: 1385663--1385734 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 27
1385653 ATGTAATAAA
1385663 AAATTAATAAAATTTTATATT-T-AAT
1 AAATTAATAAAATTTTATATTATCAAT
*
1385688 ATATTAAT-AAATTTATATATTATCAAT
1 AAATTAATAAAATTT-TATATTATCAAT
*
1385715 AAAATAA-AAAATTTTA-ATTA
1 AAATTAATAAAATTTTATATTA
1385735 AATTATATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 6 0.15
25 17 0.43
26 3 0.08
27 14 0.35
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (27 bp):
AAATTAATAAAATTTTATATTATCAAT
Found at i:1386822 original size:28 final size:28
Alignment explanation
Indices: 1386790--1386844 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
1386780 TCTCAATTAT
1386790 GTTCATTTATTAATAAAAAAATCAAAAA
1 GTTCATTTATTAATAAAAAAATCAAAAA
*
1386818 GTTCATTTATTAATAAAAAAGTCAAAA
1 GTTCATTTATTAATAAAAAAATCAAAA
1386845 TTAAATCATA
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:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (28 bp):
GTTCATTTATTAATAAAAAAATCAAAAA
Found at i:1391755 original size:2 final size:2
Alignment explanation
Indices: 1391748--1391777 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1391738 TACAAAAATC
1391748 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
1391778 AAATTATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1392998 original size:31 final size:31
Alignment explanation
Indices: 1392960--1393022 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
1392950 TTTTTTATCC
1392960 ATGAGCTATAACTTTTTTTATATAAAAAATA
1 ATGAGCTATAACTTTTTTTATATAAAAAATA
1392991 ATGAGCTATAACTTTTTTTATATAAAAAATA
1 ATGAGCTATAACTTTTTTTATATAAAAAATA
1393022 A
1 A
1393023 CGATTTATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.41
Consensus pattern (31 bp):
ATGAGCTATAACTTTTTTTATATAAAAAATA
Found at i:1399025 original size:5 final size:5
Alignment explanation
Indices: 1399015--1399042 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1399005 GGGTACAAAG
1399015 AAACC AAACC AAACC AAACC AAACC AAA
1 AAACC AAACC AAACC AAACC AAACC AAA
1399043 GGCACTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.64, C:0.36, G:0.00, T:0.00
Consensus pattern (5 bp):
AAACC
Found at i:1399662 original size:15 final size:14
Alignment explanation
Indices: 1399635--1399664 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1399625 AATTTGTTTT
1399635 TAATATTTATATTA
1 TAATATTTATATTA
1399649 TAATATTATATATTA
1 TAATATT-TATATTA
1399664 T
1 T
1399665 TTAAATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TAATATTTATATTA
Found at i:1399693 original size:18 final size:18
Alignment explanation
Indices: 1399660--1399716 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 18
1399650 AATATTATAT
1399660 ATTATTTAA-ATAATAAAA
1 ATTATTTAATAT-ATAAAA
1399678 ATTATTTAATATATAAAA
1 ATTATTTAATATATAAAA
*
1399696 ATATAAAATTAATATATAAAA
1 AT-T--ATTTAATATATAAAA
1399717 TATAATTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 17 0.50
19 3 0.09
21 14 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATTATTTAATATATAAAA
Found at i:1399707 original size:21 final size:20
Alignment explanation
Indices: 1399683--1399721 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1399673 TAAAAATTAT
1399683 TTAATATATAAAAATATAAAA
1 TTAATATAT-AAAATATAAAA
1399704 TTAATATATAAAATATAA
1 TTAATATATAAAATATAA
1399722 TTATAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TTAATATATAAAATATAAAA
Found at i:1399714 original size:13 final size:14
Alignment explanation
Indices: 1399696--1399731 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
1399686 ATATATAAAA
1399696 ATATAAAAT-TAAT
1 ATATAAAATATAAT
1399709 ATATAAAATATAAT
1 ATATAAAATATAAT
1399723 -TATAAAATA
1 ATATAAAATA
1399732 GATCAGATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
ATATAAAATATAAT
Found at i:1399876 original size:19 final size:18
Alignment explanation
Indices: 1399852--1399889 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1399842 TATTTATATT
1399852 TTTTTAAATATTAAATAAA
1 TTTTTAAAT-TTAAATAAA
1399871 TTTTTAAATTTAAATAAA
1 TTTTTAAATTTAAATAAA
1399889 T
1 T
1399890 AAATCAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTTAAATTTAAATAAA
Found at i:1399899 original size:26 final size:25
Alignment explanation
Indices: 1399854--1399905 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
1399844 TTTATATTTT
* *
1399854 TTTAAATATTAAATAAATTTTTAAA
1 TTTAAATAATAAATAAATTTATAAA
*
1399879 TTTAAATAAATAAATCAATTTATAAA
1 TTTAAAT-AATAAATAAATTTATAAA
1399905 T
1 T
1399906 ATTTTTAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
TTTAAATAATAAATAAATTTATAAA
Found at i:1400368 original size:20 final size:20
Alignment explanation
Indices: 1400345--1400393 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1400335 TATTTATATA
*
1400345 ATAATTTAAAAATATATAAT
1 ATAATATAAAAATATATAAT
**
1400365 ATAATATAATTATATATAAT
1 ATAATATAAAAATATATAAT
1400385 -TATATATAA
1 ATA-ATATAA
1400394 GTATTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATAATATAAAAATATATAAT
Found at i:1400373 original size:10 final size:10
Alignment explanation
Indices: 1400356--1400393 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
1400346 TAATTTAAAA
1400356 ATATATAA-T
1 ATATATAATT
1400365 ATAATATAATT
1 AT-ATATAATT
1400376 ATATATAATT
1 ATATATAATT
1400386 ATATATAA
1 ATATATAA
1400394 GTATTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 2 0.07
10 22 0.81
11 3 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
ATATATAATT
Found at i:1400829 original size:15 final size:15
Alignment explanation
Indices: 1400809--1400838 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1400799 TTGTCTGAAA
1400809 AAATAACTTTTCATT
1 AAATAACTTTTCATT
*
1400824 AAATAATTTTTCATT
1 AAATAACTTTTCATT
1400839 TTTTATCTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
AAATAACTTTTCATT
Found at i:1401147 original size:21 final size:21
Alignment explanation
Indices: 1401123--1401162 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1401113 TAAATAAAAT
1401123 TTTTATAATT-TAAATATTTTA
1 TTTTATAATTAT-AATATTTTA
1401144 TTTTATAATTATAATATTT
1 TTTTATAATTATAATATTT
1401163 AAAATATAAT
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTATAATTATAATATTTTA
Found at i:1403600 original size:2 final size:2
Alignment explanation
Indices: 1403595--1403643 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1403585 ACAATGTGTG
1403595 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
1403637 TA TA TA T
1 TA TA TA T
1403644 TAAGAAAGGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1404289 original size:24 final size:25
Alignment explanation
Indices: 1404240--1404295 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
1404230 TCAACTTATG
* * *
1404240 TTATAATT-AATATATTATTTTTATA
1 TTAT-ATTAAATATATGATATTGATA
1404265 TT-TATTAAATATATGATATTGATA
1 TTATATTAAATATATGATATTGATA
1404289 TTATATT
1 TTATATT
1404296 TTGTATCCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 3 0.12
24 17 0.65
25 6 0.23
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (25 bp):
TTATATTAAATATATGATATTGATA
Found at i:1405002 original size:25 final size:25
Alignment explanation
Indices: 1404967--1405022 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
1404957 CATCCTCCAT
*
1404967 AATTCACAATTATATATAATTAAAG
1 AATTCAAAATTATATATAATTAAAG
1404992 AATTCAAAATTATATATAATTAAAG
1 AATTCAAAATTATATATAATTAAAG
1405017 AATTCA
1 AATTCA
1405023 TAAGTTCGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.36
Consensus pattern (25 bp):
AATTCAAAATTATATATAATTAAAG
Found at i:1405583 original size:23 final size:21
Alignment explanation
Indices: 1405557--1405599 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
1405547 ATTTTATTTT
1405557 TAAAAATTAAACTCGATTTGAGA
1 TAAAAATTAAACT--ATTTGAGA
* *
1405580 TAAACATTTAACTATTTGAG
1 TAAAAATTAAACTATTTGAG
1405600 CTCACTCGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
23 11 0.61
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (21 bp):
TAAAAATTAAACTATTTGAGA
Found at i:1406703 original size:13 final size:13
Alignment explanation
Indices: 1406685--1406715 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1406675 ATCTTTTTTA
1406685 AATATTTATATTT
1 AATATTTATATTT
*
1406698 AATATTTATGTTT
1 AATATTTATATTT
1406711 AATAT
1 AATAT
1406716 ATTTTATGTA
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:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:1407060 original size:2 final size:2
Alignment explanation
Indices: 1407053--1407087 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1407043 TATGTATTAA
*
1407053 AT AT AT AT AT AT AT AT AT AT TT A- 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
1407088 TTGAATCCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1407081 original size:15 final size:15
Alignment explanation
Indices: 1407061--1407089 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1407051 AAATATATAT
1407061 ATATATATATATTTA
1 ATATATATATATTTA
1407076 ATATATATATATTT
1 ATATATATATATTT
1407090 GAATCCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATATATATATTTA
Found at i:1407518 original size:23 final size:22
Alignment explanation
Indices: 1407492--1407534 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1407482 AATATTAAAA
1407492 TAAAAATAGTTTTTTAAATTTTT
1 TAAAAATA-TTTTTTAAATTTTT
* *
1407515 TAAAATTATTTTTTGAATTT
1 TAAAAATATTTTTTAAATTT
1407535 AAAAACATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (22 bp):
TAAAAATATTTTTTAAATTTTT
Found at i:1407718 original size:43 final size:43
Alignment explanation
Indices: 1407671--1407756 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
1407661 TTTTTCTTAC
*
1407671 ATGTCCGTACCTATCTTAAACATATT-TCATTATGTCAAAACTA
1 ATGTCCGTACCTATCTTAAACATATTCT-ATTACGTCAAAACTA
1407714 ATGTCCGTACCTATCTTAAACATATTCTATTACGTCAAAACTA
1 ATGTCCGTACCTATCTTAAACATATTCTATTACGTCAAAACTA
1407757 TATTTGTACT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
43 40 0.98
44 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.36
Consensus pattern (43 bp):
ATGTCCGTACCTATCTTAAACATATTCTATTACGTCAAAACTA
Found at i:1409969 original size:5 final size:5
Alignment explanation
Indices: 1409948--1409982 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
1409938 TAAATTTTTT
1409948 ATTTAA ATTTAA ATTTA ATTTA ATTTA ATTTA ATT
1 ATTT-A ATTT-A ATTTA ATTTA ATTTA ATTTA ATT
1409983 AGTTTAGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 19 0.66
6 10 0.34
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
ATTTA
Found at i:1410061 original size:33 final size:32
Alignment explanation
Indices: 1409997--1410076 Score: 83
Period size: 33 Copynumber: 2.5 Consensus size: 32
1409987 TAGATTATTT
1409997 ATATTTATTATTTATAATTAATTAAAAAT-AA
1 ATATTTATTATTTATAATTAATTAAAAATAAA
* *
1410028 ATATTTATATATTTTATAATTAAATT-TATATAAA
1 ATATTTAT-TA-TTTATAATT-AATTAAAAATAAA
* *
1410062 ATATTTTTTAATTAT
1 ATATTTATTATTTAT
1410077 TAAATATTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
31 8 0.20
32 6 0.15
33 14 0.34
34 13 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (32 bp):
ATATTTATTATTTATAATTAATTAAAAATAAA
Found at i:1410237 original size:14 final size:15
Alignment explanation
Indices: 1410218--1410260 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
1410208 ATTATAATTG
*
1410218 TATTTAAAATTTT-A
1 TATTTAATATTTTGA
1410232 TATTTATATATTTTGA
1 TATTTA-ATATTTTGA
1410248 TATATTAATATTT
1 TAT-TTAATATTT
1410261 AATAATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 6 0.24
15 6 0.24
16 10 0.40
17 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
TATTTAATATTTTGA
Found at i:1410293 original size:17 final size:18
Alignment explanation
Indices: 1410247--1410293 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
1410237 ATATATTTTG
* *
1410247 ATATATTAATATTTAATA
1 ATATATAAATTTTTAATA
1410265 ATATATAAATTTTTAA-A
1 ATATATAAATTTTTAATA
* *
1410282 ATTTATATATTT
1 ATATATAAATTT
1410294 ATATTATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATATAAATTTTTAATA
Found at i:1411159 original size:21 final size:22
Alignment explanation
Indices: 1411135--1411182 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
1411125 TTAAAAAAAT
* *
1411135 TTAATTAAATAATTATTT-TTA
1 TTAATTAAATAAATATTTAATA
* *
1411156 TTAAATATATAAATATTTAATA
1 TTAATTAAATAAATATTTAATA
1411178 TTAAT
1 TTAAT
1411183 ATTATTAAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAATTAAATAAATATTTAATA
Found at i:1411280 original size:18 final size:18
Alignment explanation
Indices: 1411240--1411283 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1411230 AACATAATAA
1411240 TAATATTATATTTTTATC
1 TAATATTATATTTTTATC
* *
1411258 AAATATTATATTTTTATT
1 TAATATTATATTTTTATC
1411276 TAATATTA
1 TAATATTA
1411284 AATATTATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
TAATATTATATTTTTATC
Found at i:1411318 original size:20 final size:19
Alignment explanation
Indices: 1411275--1411344 Score: 62
Period size: 19 Copynumber: 3.9 Consensus size: 19
1411265 ATATTTTTAT
*
1411275 TTAATA-TTAAATATTATA
1 TTAATATTTAAATATAATA
*
1411293 TCAATATTTAAATAATAATA
1 TTAATATTTAAAT-ATAATA
*
1411313 TTAATA-TAAAATAT-ATA
1 TTAATATTTAAATATAATA
1411330 TT--TATTTAAAT-TAAT
1 TTAATATTTAAATATAAT
1411345 TTTTTAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
15 3 0.07
16 7 0.16
17 5 0.12
18 7 0.16
19 11 0.26
20 10 0.23
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATATTTAAATATAATA
Found at i:1411838 original size:20 final size:20
Alignment explanation
Indices: 1411815--1411870 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
1411805 TTATTTAATT
1411815 TTAAAAAAATTAAATATAAA
1 TTAAAAAAATTAAATATAAA
* * *
1411835 TTAAATAATTTTAATATTAAA
1 TTAAAAAAATTAAATA-TAAA
1411856 -T--AAAAATTAAATATA
1 TTAAAAAAATTAAATATA
1411871 GTAAGTATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
17 2 0.07
18 9 0.31
20 14 0.48
21 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TTAAAAAAATTAAATATAAA
Found at i:1411868 original size:38 final size:35
Alignment explanation
Indices: 1411796--1411870 Score: 105
Period size: 38 Copynumber: 2.1 Consensus size: 35
1411786 TTTGATTAGT
* *
1411796 TAAATTAAATTATTTAATTTTAAAAAAATTAAATA
1 TAAATTAAATAATTTAATTTAAAAAAAATTAAATA
1411831 TAAATTAAATAATTTTAATATTAAATAAAAATTAAATA
1 TAAATTAAATAA-TTTAAT-TTAAA-AAAAATTAAATA
1411869 TA
1 TA
1411871 GTAAGTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
35 11 0.31
36 6 0.17
37 4 0.11
38 14 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (35 bp):
TAAATTAAATAATTTAATTTAAAAAAAATTAAATA
Found at i:1411879 original size:27 final size:27
Alignment explanation
Indices: 1411823--1411879 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
1411813 TTTTAAAAAA
* **
1411823 ATTAAATATAAATTAAATAATTTTAAT
1 ATTAAATAAAAATTAAATAATAGTAAT
1411850 ATTAAATAAAAATTAAAT-ATAGTAAGT
1 ATTAAATAAAAATTAAATAATAGTAA-T
1411877 ATT
1 ATT
1411880 TAATTAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (27 bp):
ATTAAATAAAAATTAAATAATAGTAAT
Found at i:1412488 original size:15 final size:15
Alignment explanation
Indices: 1412470--1412505 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1412460 ATGCATCTAC
*
1412470 TTTATATTTTTATTA
1 TTTATATTTATATTA
1412485 TTTATATTTATATTA
1 TTTATATTTATATTA
*
1412500 TATATA
1 TTTATA
1412506 AAATTTTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTATATTTATATTA
Found at i:1413497 original size:2 final size:2
Alignment explanation
Indices: 1413490--1413533 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1413480 CCAAGCGCAA
1413490 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
1413532 AT
1 AT
1413534 CAAGTAATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1413996 original size:35 final size:34
Alignment explanation
Indices: 1413931--1414000 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 34
1413921 TGAATTATTA
* * *
1413931 TATAATAATAAAAAATATTTATATTTAAATTTAAT
1 TATAAAAATAAAAAATATTAATA-TTAAAATTAAT
1413966 TATAAAAATATAAAAATATTAATA-TAAAATTAAT
1 TATAAAAATA-AAAAATATTAATATTAAAATTAAT
1414000 T
1 T
1414001 TAACAATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 10 0.32
35 9 0.29
36 12 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (34 bp):
TATAAAAATAAAAAATATTAATATTAAAATTAAT
Found at i:1416581 original size:20 final size:21
Alignment explanation
Indices: 1416545--1416591 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
1416535 ATAATAATAA
* *
1416545 ATTTT-AATTTTATAAT-ATT
1 ATTTTAAATTATAAAATAATT
1416564 ATTTTAAATTATAAAATAATT
1 ATTTTAAATTATAAAATAATT
1416585 -TTTTAAA
1 ATTTTAAA
1416592 AATTAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.21
20 16 0.67
21 3 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTTAAATTATAAAATAATT
Found at i:1416585 original size:18 final size:19
Alignment explanation
Indices: 1416530--1416586 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 19
1416520 ACTATCAATA
* *
1416530 TTAATATAATAATA-AATT
1 TTAATATTATAAAATAATT
* * *
1416548 TTAATTTTATAATATTATT
1 TTAATATTATAAAATAATT
1416567 TTAA-ATTATAAAATAATT
1 TTAATATTATAAAATAATT
1416585 TT
1 TT
1416587 TTAAAAATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 25 0.78
19 7 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAATATTATAAAATAATT
Found at i:1416797 original size:32 final size:32
Alignment explanation
Indices: 1416761--1416826 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
1416751 TATCAATATC
* *
1416761 AATATCAATAT-AATAATAAATTTTAATTTTTT
1 AATATCAATATAAATAATAAA-ATAAATTTTTT
*
1416793 AATATTAATATAAATAATAAAATAAATTTTTT
1 AATATCAATATAAATAATAAAATAAATTTTTT
1416825 AA
1 AA
1416827 AATAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 21 0.70
33 9 0.30
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (32 bp):
AATATCAATATAAATAATAAAATAAATTTTTT
Found at i:1416921 original size:236 final size:226
Alignment explanation
Indices: 1416462--1416921 Score: 597
Period size: 236 Copynumber: 2.0 Consensus size: 226
1416452 TTTTAAATCA
*
1416462 ATTTGAGTATAATTTTATAAAATTTTATTTAGATAATAAAATTGATTTATTTAATTCAACTATCA
1 ATTTGAGTATAATTTTATAAAATTTTATTTAAATAATAAAATTGATTTATTTAATTCAACTATCA
* * * *
1416527 ATATTAATATAATAATAAATTTTAATTTTATAATATTATTTTAAATTATAAAATAATTTTTTAAA
66 ATATCAATATAATAATAAATTTTAATTTTATAATATTAATATAAATAATAAAATAATTTTTTAAA
* * *
1416592 AATTAAAAAAATTCAACTCGGATTGAACTATAAACATCTCTATTTTATTTGTTTTACTCATTTAA
131 AATAAAAAAAATTCAACTCGAATTCAACTATAAACATCTCTATTTTATTTGTTTTACTCATTTAA
1416657 AGCAACCTCAACAAGAATAGGATTAATAGGG
196 AGCAACCTCAACAAGAATAGGATTAATAGGG
* *
1416688 ATTTGAGTATAATTTTTTTAAAATTATTATTTAAATAATAAAAATATTTTTATTTAATTTAATTA
1 ATTTGAGTATAA-TTTTATAAAATT-TTATTTAAATAAT--AAA-A--TTGATTT-ATTTAA-T-
*
1416753 TCAA-TATCAATATCAATATAATAATAAATTTTAATTTTTTAATATTAATATAAATAATAAAATA
56 TCAACTATCAATATCAATATAATAATAAATTTTAATTTTATAATATTAATATAAATAATAAAAT-
* *
1416817 AATTTTTT-AAAATAAAAAAAATTTCAAGCT-GAATTCAACTATAAAC-CCTTCTATTTTATTTT
120 AATTTTTTAAAAATAAAAAAAA-TTCAA-CTCGAATTCAACTATAAACATC-TCTATTTTATTTG
* * * *
1416879 TTTTACTTATTTAAAGGAACC-CTAACAAGAGTAGGGTTAATAG
182 TTTTACTCATTTAAAGCAACCTC-AACAAGAATAGGATTAATAG
1416922 AGAATTCAGA
Statistics
Matches: 202, Mismatches: 17, Indels: 20
0.85 0.07 0.08
Matches are distributed among these distances:
226 12 0.06
227 11 0.05
228 12 0.06
230 3 0.01
231 1 0.00
233 6 0.03
234 6 0.03
235 69 0.34
236 80 0.40
237 2 0.01
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (226 bp):
ATTTGAGTATAATTTTATAAAATTTTATTTAAATAATAAAATTGATTTATTTAATTCAACTATCA
ATATCAATATAATAATAAATTTTAATTTTATAATATTAATATAAATAATAAAATAATTTTTTAAA
AATAAAAAAAATTCAACTCGAATTCAACTATAAACATCTCTATTTTATTTGTTTTACTCATTTAA
AGCAACCTCAACAAGAATAGGATTAATAGGG
Found at i:1417710 original size:16 final size:16
Alignment explanation
Indices: 1417691--1417749 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
1417681 AAAAATTATG
1417691 AAAAATTAAAATATTT
1 AAAAATTAAAATATTT
* * *
1417707 AAAAAAT-ATATGTTT
1 AAAAATTAAAATATTT
*
1417722 -AAAATAATAAATATTT
1 AAAAATTA-AAATATTT
1417738 AAAAATATAAAA
1 AAAAAT-TAAAA
1417750 ATAATAAAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 7
0.67 0.17 0.15
Matches are distributed among these distances:
14 4 0.13
15 6 0.19
16 12 0.39
17 8 0.26
18 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
AAAAATTAAAATATTT
Found at i:1418026 original size:11 final size:11
Alignment explanation
Indices: 1418010--1418076 Score: 55
Period size: 11 Copynumber: 5.8 Consensus size: 11
1418000 TAAATTTATT
1418010 TATAAAAATAA
1 TATAAAAATAA
*
1418021 TAT-AAATTAA
1 TATAAAAATAA
1418031 TATAAAAATAA
1 TATAAAAATAA
* *
1418042 TATTTTAATAATAT
1 TA---TAAAAATAA
1418056 TATAAATAATAA
1 TATAAA-AATAA
*
1418068 AATAAAAAT
1 TATAAAAAT
1418077 TTAAATTTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
10 9 0.20
11 17 0.39
12 9 0.20
14 9 0.20
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TATAAAAATAA
Found at i:1418075 original size:37 final size:36
Alignment explanation
Indices: 1418006--1418076 Score: 90
Period size: 35 Copynumber: 1.9 Consensus size: 36
1417996 TATTTAAATT
*
1418006 TATTTATAAAAATAATATAAATTAATATAAAAATAA
1 TATTTATAAAAATAATATAAATTAAAATAAAAATAA
* *
1418042 TATTT-TAATAATATTATAAATAATAAAATAAAAAT
1 TATTTATAAAAATAATATAAAT--TAAAATAAAAAT
1418077 TTAAATTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
35 14 0.47
36 5 0.17
37 11 0.37
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (36 bp):
TATTTATAAAAATAATATAAATTAAAATAAAAATAA
Found at i:1418376 original size:18 final size:17
Alignment explanation
Indices: 1418355--1418408 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
1418345 AATAAAAAAG
1418355 TATAAATATTTTAAAATT
1 TATAAATA-TTTAAAATT
*
1418373 TAT--ATA-ATAAAATT
1 TATAAATATTTAAAATT
*
1418387 TATTAATATATTAAAATT
1 TATAAATAT-TTAAAATT
1418405 TATA
1 TATA
1418409 TAAAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
14 10 0.34
16 6 0.21
18 13 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATAAATATTTAAAATT
Found at i:1418396 original size:20 final size:21
Alignment explanation
Indices: 1418373--1418440 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 21
1418363 TTTTAAAATT
1418373 TATATAATAAAATTTAT-TAA
1 TATATAATAAAATTTATATAA
1418393 TATAT--TAAAATTTATATAA
1 TATATAATAAAATTTATATAA
*
1418412 -AAATAA-AAAATTTAAATATAA
1 TATATAATAAAATTT--ATATAA
1418433 T-TATAATA
1 TATATAATA
1418441 TAATAAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
18 13 0.33
19 10 0.26
20 5 0.13
21 10 0.26
22 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TATATAATAAAATTTATATAA
Found at i:1418432 original size:21 final size:22
Alignment explanation
Indices: 1418398--1418458 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 22
1418388 ATTAATATAT
1418398 TAAAATTT--ATATAAAAATAA
1 TAAAATTTAAATATAAAAATAA
**
1418418 -AAAATTTAAATATAATTATAA
1 TAAAATTTAAATATAAAAATAA
* *
1418439 TATAA-TAAAATATAAAAATA
1 TAAAATTTAAATATAAAAATA
1418459 TAATATAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 7 0.22
21 22 0.69
22 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
TAAAATTTAAATATAAAAATAA
Found at i:1418444 original size:5 final size:5
Alignment explanation
Indices: 1418426--1418466 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
1418416 AAAAAATTTA
*
1418426 AATAT AATTAT AATAT AATAA AATAT AA-A- AATAT AATAT AA
1 AATAT AA-TAT AATAT AATAT AATAT AATAT AATAT AATAT AA
1418467 ATACGAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
3 2 0.06
4 2 0.06
5 22 0.71
6 5 0.16
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (5 bp):
AATAT
Found at i:1418469 original size:29 final size:28
Alignment explanation
Indices: 1418374--1418469 Score: 76
Period size: 27 Copynumber: 3.5 Consensus size: 28
1418364 TTTAAAATTT
* * *
1418374 ATATAATA-AAATTTATTAATATATTAAA
1 ATATAATATAAATATAATAAAATA-TAAA
* * *
1418402 AT-TTATATAAAAATAA-AAAAT-TTAA
1 ATATAATATAAATATAATAAAATATAAA
1418427 ATATAAT-TATAATATAATAAAATATAAAA
1 ATATAATATA-AATATAATAAAATAT-AAA
1418456 ATATAATATAAATA
1 ATATAATATAAATA
1418470 CGAATTATTA
Statistics
Matches: 52, Mismatches: 9, Indels: 13
0.70 0.12 0.18
Matches are distributed among these distances:
25 7 0.13
26 9 0.17
27 13 0.25
28 8 0.15
29 13 0.25
30 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
ATATAATATAAATATAATAAAATATAAA
Found at i:1418909 original size:6 final size:6
Alignment explanation
Indices: 1418898--1418965 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 6
1418888 TCAAAATTGA
*
1418898 TATATT TATA-T TATATT TATATAT TAT-TAT TATA-T TATAAT TATATT
1 TATATT TATATT TATATT TATAT-T TATAT-T TATATT TATATT TATATT
**
1418945 TA-AAA TAT-TT TATATT TATAT
1 TATATT TATATT TATATT TATAT
1418966 AAATTTTAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
5 16 0.31
6 31 0.61
7 4 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (6 bp):
TATATT
Found at i:1418914 original size:11 final size:11
Alignment explanation
Indices: 1418898--1419004 Score: 57
Period size: 11 Copynumber: 10.1 Consensus size: 11
1418888 TCAAAATTGA
1418898 TATATTTATAT
1 TATATTTATAT
1418909 TATATTTATA-
1 TATATTTATAT
*
1418919 TAT-TAT-TAT
1 TATATTTATAT
1418928 TATA-TTATAAT
1 TATATTTAT-AT
* *
1418939 TATATTTAAAA
1 TATATTTATAT
1418950 TAT-TTTATATT
1 TATATTTATA-T
** *
1418961 TATATAAATTT
1 TATATTTATAT
* * *
1418972 TAAAATAAT-T
1 TATATTTATAT
1418982 ATATATTTATAT
1 -TATATTTATAT
1418994 TATA-TTATAT
1 TATATTTATAT
1419004 T
1 T
1419005 TTAATTATTT
Statistics
Matches: 72, Mismatches: 15, Indels: 19
0.68 0.14 0.18
Matches are distributed among these distances:
8 2 0.03
9 6 0.08
10 17 0.24
11 40 0.56
12 7 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1419762 original size:35 final size:36
Alignment explanation
Indices: 1419695--1419762 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 36
1419685 TACTTACATA
* *
1419695 AAAAATATATAATAAGATTTATATATTTAATATTTT
1 AAAAATATATAATAAGATATATAAATTTAATATTTT
* *
1419731 AAAAATATA-ATTATGATATATAAATTTAATAT
1 AAAAATATATAATAAGATATATAAATTTAATAT
1419763 AAAAATATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 19 0.68
36 9 0.32
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (36 bp):
AAAAATATATAATAAGATATATAAATTTAATATTTT
Found at i:1419796 original size:27 final size:24
Alignment explanation
Indices: 1419733--1419796 Score: 56
Period size: 27 Copynumber: 2.4 Consensus size: 24
1419723 AATATTTTAA
*
1419733 AAATATAATTATGATATATAAATTT
1 AAATATAA-TATGATATATAAATCT
*
1419758 AATATAAAAATATGAATATATAAATAGCT
1 AA-AT-ATAATATG-ATATATAAAT--CT
1419787 AAATATAATA
1 AAATATAATA
1419797 ACTATTAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
25 2 0.06
26 6 0.19
27 18 0.58
28 2 0.06
29 3 0.10
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.36
Consensus pattern (24 bp):
AAATATAATATGATATATAAATCT
Found at i:1420084 original size:25 final size:24
Alignment explanation
Indices: 1420052--1420156 Score: 112
Period size: 25 Copynumber: 4.4 Consensus size: 24
1420042 AATTTAATAT
1420052 AATT-ATATAATATAAAAAATTAA
1 AATTAATATAATATAAAAAATTAA
*
1420075 AATATAATATTAA-ATAAAAATTTATA
1 AAT-TAATA-TAATATAAAAAATTA-A
1420101 AATT-ATATAATATAAAAAATTAA
1 AATTAATATAATATAAAAAATTAA
* *
1420124 AATATTATATAATAT-AAATA-TAA
1 AAT-TAATATAATATAAAAAATTAA
1420147 AATTAATATA
1 AATTAATATA
1420157 TTAAAATTTA
Statistics
Matches: 71, Mismatches: 4, Indels: 15
0.79 0.04 0.17
Matches are distributed among these distances:
22 6 0.08
23 16 0.23
24 19 0.27
25 23 0.32
26 7 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
AATTAATATAATATAAAAAATTAA
Found at i:1420111 original size:49 final size:51
Alignment explanation
Indices: 1420041--1420141 Score: 163
Period size: 49 Copynumber: 2.0 Consensus size: 51
1420031 TAATAATTTT
1420041 AAATTTAATATAATTATATAATATAAAAAATTAAAATATAATATTAA-ATAA
1 AAATTTAATATAATTATATAATATAAAAAATTAAAATATAATA-TAATATAA
*
1420092 AAATTT-ATA-AATTATATAATATAAAAAATTAAAATATTATATAATATAA
1 AAATTTAATATAATTATATAATATAAAAAATTAAAATATAATATAATATAA
1420141 A
1 A
1420142 TATAAAATTA
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
48 3 0.06
49 36 0.75
50 3 0.06
51 6 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (51 bp):
AAATTTAATATAATTATATAATATAAAAAATTAAAATATAATATAATATAA
Found at i:1420145 original size:36 final size:36
Alignment explanation
Indices: 1420097--1420178 Score: 110
Period size: 36 Copynumber: 2.2 Consensus size: 36
1420087 AATAAAAATT
*
1420097 TATAAATTATATAATATAAAAAATTAAAATATTATATAA
1 TATAAA-TATAAAAT-TAAAAAATTAAAAT-TTATATAA
* *
1420136 TATAAATATAAAATTAATATATTAAAATTTATATAA
1 TATAAATATAAAATTAAAAAATTAAAATTTATATAA
1420172 TATAAAT
1 TATAAAT
1420179 TATTAATTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
36 15 0.38
37 12 0.30
38 7 0.17
39 6 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (36 bp):
TATAAATATAAAATTAAAAAATTAAAATTTATATAA
Found at i:1420157 original size:29 final size:29
Alignment explanation
Indices: 1420076--1420266 Score: 114
Period size: 29 Copynumber: 6.6 Consensus size: 29
1420066 AAAAATTAAA
* *
1420076 ATATAATATTAAATA-AAAATTTATAAATT
1 ATATAATA-TAAATATAAAATTAATATATT
*
1420105 ATATAATAT--A-A-AAAATTAAAATATT
1 ATATAATATAAATATAAAATTAATATATT
1420130 ATATAATATAAATATAAAATTAATATATT
1 ATATAATATAAATATAAAATTAATATATT
*
1420159 A-A-AATTTATATAATATAAATTATTAATTTATT
1 ATATAA--TATA-AATATAAA--ATTAATATATT
* * * * * *
1420191 AAATTTATATAAATATATAA-TATTTTA-A
1 ATA-TAATATAAATATAAAATTAATATATT
* *
1420219 ATATAATTATAATATATAAAAATAATATA-A
1 ATATAA-TATAA-ATATAAAATTAATATATT
*
1420249 ATATGATATAAATATAAA
1 ATATAATATAAATATAAA
1420267 TTATTTTATT
Statistics
Matches: 132, Mismatches: 15, Indels: 31
0.74 0.08 0.17
Matches are distributed among these distances:
25 21 0.16
26 1 0.01
27 5 0.04
28 17 0.13
29 44 0.33
30 20 0.15
32 18 0.14
33 5 0.04
35 1 0.01
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (29 bp):
ATATAATATAAATATAAAATTAATATATT
Found at i:1420157 original size:49 final size:49
Alignment explanation
Indices: 1420048--1420180 Score: 154
Period size: 49 Copynumber: 2.8 Consensus size: 49
1420038 TTTAAATTTA
1420048 ATAT-AATTATATAATATAAAAAATTAAAATATAATATTAAATAAAAAT
1 ATATAAATTATATAATATAAAAAATTAAAATATAATATTAAATAAAAAT
* * *
1420096 TTATAAATTATATAATATAAAAAATTAAAATATTATA-T-AATATAAAT
1 ATATAAATTATATAATATAAAAAATTAAAATATAATATTAAATAAAAAT
* *
1420143 ATA-AAATTA-AT-ATATTAAAATTTATATAATATAA-ATTA
1 ATATAAATTATATAATATAAAAAATTA-A-AATATAATATTA
1420181 TTAATTTATT
Statistics
Matches: 73, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
44 11 0.15
45 4 0.05
46 13 0.18
47 10 0.14
48 4 0.05
49 31 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (49 bp):
ATATAAATTATATAATATAAAAAATTAAAATATAATATTAAATAAAAAT
Found at i:1420160 original size:37 final size:33
Alignment explanation
Indices: 1420091--1420223 Score: 116
Period size: 32 Copynumber: 3.9 Consensus size: 33
1420081 ATATTAAATA
*
1420091 AAAATTTATA-AATTATATAATATA--AA-AAATT
1 AAAATTTATATAA-TATA-AATATATTAATATATT
1420122 AAAATATTATATAATATAAATATAAAATTAATATATT
1 AAAAT-TTATATAATATAAATAT---ATTAATATATT
*
1420159 AAAATTTATATAATATAAAT-TATTAATTTATT
1 AAAATTTATATAATATAAATATATTAATATATT
*
1420191 -AAATTTATATAAATATATAATATTTTAAATATA
1 AAAATTTATAT-AATATA-AATATATT-AATATA
1420224 ATTATAATAT
Statistics
Matches: 86, Mismatches: 4, Indels: 20
0.78 0.04 0.18
Matches are distributed among these distances:
31 20 0.23
32 25 0.29
33 5 0.06
34 4 0.05
35 6 0.07
36 17 0.20
37 9 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (33 bp):
AAAATTTATATAATATAAATATATTAATATATT
Found at i:1420191 original size:32 final size:30
Alignment explanation
Indices: 1420099--1420207 Score: 116
Period size: 30 Copynumber: 3.6 Consensus size: 30
1420089 TAAAAATTTA
* *
1420099 TAAA-TTATATAATATAAAAAATTAAAATAT
1 TAAATTTATATAA-ATATAAAATTAATATAT
* *
1420129 TATA-TAATATAAATATAAAATTAATATAT
1 TAAATTTATATAAATATAAAATTAATATAT
*
1420158 TAAAATTTATAT-AATATAAATTATTAATTTAT
1 T-AAATTTATATAAATATAAA--ATTAATATAT
1420190 TAAATTTATATAAATATA
1 TAAATTTATATAAATATA
1420208 TAATATTTTA
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
29 16 0.24
30 20 0.30
31 15 0.22
32 16 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
TAAATTTATATAAATATAAAATTAATATAT
Found at i:1420211 original size:26 final size:26
Alignment explanation
Indices: 1420166--1420274 Score: 80
Period size: 26 Copynumber: 4.0 Consensus size: 26
1420156 ATTAAAATTT
1420166 ATATAATATAAAT-TATTAAT-TTATTAA
1 ATAT-ATATAAATATA-TAATATT-TTAA
*
1420193 ATTTATATAAATATATAATATTTTAA
1 ATATATATAAATATATAATATTTTAA
* * *
1420219 ATATAATTATAATATATAAAAATAATATAA
1 ATAT-A-TATAA-ATAT-ATAATATTTTAA
1420249 ATATGATATAAATATA-AATTATTTTA
1 ATAT-ATATAAATATATAA-TATTTTA
1420275 TTTAATTCTT
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
26 21 0.31
27 14 0.21
28 9 0.13
29 9 0.13
30 14 0.21
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (26 bp):
ATATATATAAATATATAATATTTTAA
Found at i:1420223 original size:22 final size:21
Alignment explanation
Indices: 1420197--1420265 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 21
1420187 TATTAAATTT
*
1420197 ATATAAATATATAATATTTTAA
1 ATAT-AATATATAATATTATAA
1420219 ATATAAT-TATAATA-TATAA
1 ATATAATATATAATATTATAA
*
1420238 AAATAATATA-AATATGATATAA
1 ATATAATATATAATAT--TATAA
1420260 ATATAA
1 ATATAA
1420266 ATTATTTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 14 0.35
20 9 0.22
21 3 0.08
22 14 0.35
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (21 bp):
ATATAATATATAATATTATAA
Found at i:1420249 original size:46 final size:47
Alignment explanation
Indices: 1420120--1420252 Score: 121
Period size: 46 Copynumber: 2.8 Consensus size: 47
1420110 ATATAAAAAA
* * *
1420120 TTAAA-AT-ATTAT-ATAATATAAATATAAAATTAATATATTAAAATT
1 TTAAATATAATTATAAT-ATATAAAAATAATATAAATATATTAAAATT
* * * * *
1420165 TATATAATATAAATTATTAATTTATTAAATTTATATAAATATA-TAATATT
1 T-TA-AATAT-AATTA-TAATATATAAAAATAATATAAATATATTAAAATT
1420215 TTAAATATAATTATAATATATAAAAATAATATAAATAT
1 TTAAATATAATTATAATATATAAAAATAATATAAATAT
1420253 GATATAAATA
Statistics
Matches: 69, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
45 1 0.01
46 23 0.33
47 7 0.10
48 7 0.10
49 2 0.03
50 11 0.16
51 16 0.23
52 2 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (47 bp):
TTAAATATAATTATAATATATAAAAATAATATAAATATATTAAAATT
Found at i:1420415 original size:25 final size:26
Alignment explanation
Indices: 1420386--1420436 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
1420376 TTTTGTTAAC
*
1420386 ATATAAAA-TATATATATTT-ATATTA
1 ATATAAAATTAAAT-TATTTCATATTA
1420411 ATATAAAATTAAATTATTTCATATTA
1 ATATAAAATTAAATTATTTCATATTA
1420437 TATTATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
ATATAAAATTAAATTATTTCATATTA
Found at i:1420509 original size:21 final size:21
Alignment explanation
Indices: 1420451--1420509 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
1420441 ATAATTTTTT
1420451 ATATAATTA-ATATTTTAATA
1 ATATAATTATATATTTTAATA
*
1420471 A-ATTAATTAT-TAAATTTAATA
1 ATA-TAATTATAT-ATTTTAATA
*
1420492 ATATAATTATATTTTTTA
1 ATATAATTATATATTTTA
1420510 TACACATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
19 1 0.03
20 8 0.26
21 20 0.65
22 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATAATTATATATTTTAATA
Found at i:1420622 original size:22 final size:23
Alignment explanation
Indices: 1420597--1420644 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
1420587 AAATTTTTAT
1420597 ATTAAA-TAATAAAAATATAAA-A
1 ATTAAATTAA-AAAAATATAAATA
*
1420619 ATTAAATTAAATAAATATAAATA
1 ATTAAATTAAAAAAATATAAATA
1420642 ATT
1 ATT
1420645 TAAAATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
ATTAAATTAAAAAAATATAAATA
Found at i:1420658 original size:24 final size:21
Alignment explanation
Indices: 1420597--1420659 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 21
1420587 AAATTTTTAT
*
1420597 ATTAAATAATAAAAATATAAAA
1 ATTAAATTA-AAAAATATAAAA
1420619 ATTAAATTAAATAAATATAAATA
1 ATTAAATTAAA-AAATATAAA-A
*
1420642 ATTTAAAATTATAAAATA
1 A-TT-AAATTAAAAAATA
1420660 CTGATAACTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 2 0.06
22 17 0.49
23 2 0.06
24 7 0.20
25 7 0.20
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATTAAATTAAAAAATATAAAA
Found at i:1420881 original size:2 final size:2
Alignment explanation
Indices: 1420874--1420904 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1420864 ACCTACTTTT
1420874 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1420905 TTCTTCTTTC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1425213 original size:23 final size:23
Alignment explanation
Indices: 1425160--1425215 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
1425150 GTCAGTGATT
*
1425160 TAAAAA-AATAAAAATATGTATA
1 TAAAAATAATTAAAATATGTATA
*
1425182 TCAAAATAATTAAAATATG-ATA
1 TAAAAATAATTAAAATATGTATA
1425204 TAAAATATAATT
1 TAAAA-ATAATT
1425216 TTAACATGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.41
23 17 0.59
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAAAATAATTAAAATATGTATA
Found at i:1425406 original size:28 final size:31
Alignment explanation
Indices: 1425355--1425429 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
1425345 TATAATATTT
*
1425355 TAAATATGAT-TATAAT-TAAAAAAA-TGATA
1 TAAATATGATATA-AATAAAAAAAAATTGATA
1425384 TAAA-ATGATATAAATAAAAAAAAAATTGATA
1 TAAATATGATATAAAT-AAAAAAAAATTGATA
*
1425415 TAAATGTGATATAAA
1 TAAATATGATATAAA
1425430 AAATTGATGG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
28 8 0.21
29 6 0.15
30 7 0.18
31 9 0.23
32 9 0.23
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (31 bp):
TAAATATGATATAAATAAAAAAAAATTGATA
Found at i:1425703 original size:20 final size:21
Alignment explanation
Indices: 1425660--1425703 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
1425650 CTCAGGGTTT
* *
1425660 TTTAAATAAAGATTTTATATA
1 TTTAAATAAAGATTATATAGA
*
1425681 TTTAAATTAA-ATTATATAGA
1 TTTAAATAAAGATTATATAGA
1425701 TTT
1 TTT
1425704 TATTTGAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (21 bp):
TTTAAATAAAGATTATATAGA
Found at i:1425705 original size:21 final size:22
Alignment explanation
Indices: 1425659--1425705 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
1425649 TCTCAGGGTT
* *
1425659 TTTTAAATAAAGATTTTATATA
1 TTTTAAATAAAGATTATATAGA
*
1425681 -TTTAAATTAA-ATTATATAGA
1 TTTTAAATAAAGATTATATAGA
1425701 TTTTA
1 TTTTA
1425706 TTTGAATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (22 bp):
TTTTAAATAAAGATTATATAGA
Found at i:1426179 original size:19 final size:19
Alignment explanation
Indices: 1426157--1426206 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
1426147 AAATTTGTTA
*
1426157 ATTTAAAAATTATTTTATT
1 ATTTAAAAATTATTTTAAT
*
1426176 ATTTAAAAATAATTTTAAT
1 ATTTAAAAATTATTTTAAT
*
1426195 A-TTAAAATTTAT
1 ATTTAAAAATTAT
1426207 ATATTTTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 9 0.33
19 18 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTTAAAAATTATTTTAAT
Found at i:1426194 original size:36 final size:35
Alignment explanation
Indices: 1426154--1426266 Score: 97
Period size: 36 Copynumber: 3.2 Consensus size: 35
1426144 ATTAAATTTG
1426154 TTAATTTAAAAATTATTTTATTATTTAAAAATAATT
1 TTAATTTAAAAATT-TTTTATTATTTAAAAATAATT
* * * *
1426190 TTAATATT-AAAA-TTTATA-TATTTTATAATTATAT
1 TTAAT-TTAAAAATTTTTTATTATTTAAAAATAAT-T
* * *
1426224 TTAAATAAAAATATTTTTTATTAATTAAATAATAATT
1 TTAATTTAAAA-ATTTTTTATTATTTAAA-AATAATT
1426261 TTAATT
1 TTAATT
1426267 AAATCAAATC
Statistics
Matches: 58, Mismatches: 12, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
33 12 0.21
34 12 0.21
35 2 0.03
36 14 0.24
37 13 0.22
38 5 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (35 bp):
TTAATTTAAAAATTTTTTATTATTTAAAAATAATT
Found at i:1426237 original size:27 final size:24
Alignment explanation
Indices: 1426207--1426255 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 24
1426197 TAAAATTTAT
1426207 ATATTTTATAATTATATTTAAATAAAA
1 ATATTTT-TAATTA-A-TTAAATAAAA
*
1426234 ATATTTTTTATTAATTAAATAA
1 ATATTTTTAATTAATTAAATAA
1426256 TAATTTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 8 0.38
25 1 0.05
26 5 0.24
27 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
ATATTTTTAATTAATTAAATAAAA
Found at i:1426245 original size:21 final size:20
Alignment explanation
Indices: 1426214--1426275 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
1426204 TATATATTTT
*
1426214 ATAATTATATTTAAATAAA-A
1 ATAATTTTA-TTAAATAAATA
* *
1426234 ATATTTTTTATTAATTAAATA
1 ATA-ATTTTATTAAATAAATA
1426255 ATAATTTTAATTAAATCAAAT
1 ATAATTTT-ATTAAAT-AAAT
1426276 CGAGTAAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
20 15 0.45
21 14 0.42
22 4 0.12
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAATTTTATTAAATAAATA
Found at i:1426506 original size:21 final size:23
Alignment explanation
Indices: 1426475--1426538 Score: 87
Period size: 21 Copynumber: 2.9 Consensus size: 23
1426465 ATAATTATAC
*
1426475 GTTATAAATATAATATAAATTAT
1 GTTAAAAATATAATATAAATTAT
*
1426498 -TT-AAAATATGATATAAATTAT
1 GTTAAAAATATAATATAAATTAT
*
1426519 GTTAAAAAAATAATATAAAT
1 GTTAAAAATATAATATAAAT
1426539 ATAAAATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 17 0.49
22 4 0.11
23 14 0.40
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (23 bp):
GTTAAAAATATAATATAAATTAT
Found at i:1426575 original size:27 final size:27
Alignment explanation
Indices: 1426481--1426575 Score: 85
Period size: 28 Copynumber: 3.7 Consensus size: 27
1426471 ATACGTTATA
1426481 AATATAATATAAATTATTT-----AA-
1 AATATAATATAAATTATTTAAAAAAAT
*
1426502 AATATGATATAAATTATGTTAAAAAAAT
1 AATATAATATAAATTAT-TTAAAAAAAT
* *
1426530 AATATAAATATAAAATATTTAAAAAATT
1 AATAT-AATATAAATTATTTAAAAAAAT
* *
1426558 TATATAATATCAATTATT
1 AATATAATATAAATTATT
1426576 AATATATTAA
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
21 16 0.27
22 2 0.03
27 13 0.22
28 18 0.31
29 10 0.17
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (27 bp):
AATATAATATAAATTATTTAAAAAAAT
Found at i:1426856 original size:18 final size:17
Alignment explanation
Indices: 1426833--1426866 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1426823 ACACGATTAT
1426833 AATATAACAAAATATATA
1 AATATAACAAAA-ATATA
*
1426851 AATATAATAAAAATAT
1 AATATAACAAAAATAT
1426867 TGAATTATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
AATATAACAAAAATATA
Found at i:1427007 original size:18 final size:20
Alignment explanation
Indices: 1426971--1427007 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
1426961 GTGTTTTGAC
*
1426971 ATATTATTTTAAATTTATAA
1 ATATTATTTTAAATATATAA
1426991 ATATT-TTTT-AATATATA
1 ATATTATTTTAAATATATA
1427008 TTTATAGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 7 0.44
19 4 0.25
20 5 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATTATTTTAAATATATAA
Found at i:1427080 original size:2 final size:2
Alignment explanation
Indices: 1427073--1427114 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
1427063 TATACTTTCC
* *
1427073 AT AT AT AT AT AT AT TT AT AT CT AT AT A- 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
1427114 A
1 A
1427115 AAATGTTAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1427961 original size:27 final size:27
Alignment explanation
Indices: 1427931--1428018 Score: 73
Period size: 27 Copynumber: 3.4 Consensus size: 27
1427921 ATTAATATTT
1427931 ATATATTTATAATTAAATTTAAATAAA
1 ATATATTTATAATTAAATTTAAATAAA
*
1427958 ATATATTT-TTATT-AA-TTAAATAATA
1 ATATATTTATAATTAAATTTAAATAA-A
* * *
1427983 ATTTAAATTAT--TTAAATCTAAATAAA
1 ATAT-ATTTATAATTAAATTTAAATAAA
1428009 A-A-ATTTATAA
1 ATATATTTATAA
1428019 CTGGTCTGGC
Statistics
Matches: 48, Mismatches: 6, Indels: 16
0.69 0.09 0.23
Matches are distributed among these distances:
23 5 0.10
24 8 0.17
25 8 0.17
26 11 0.23
27 16 0.33
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (27 bp):
ATATATTTATAATTAAATTTAAATAAA
Found at i:1428909 original size:32 final size:31
Alignment explanation
Indices: 1428853--1428957 Score: 95
Period size: 32 Copynumber: 3.1 Consensus size: 31
1428843 TAAAGTATTA
1428853 TATATATTTATATAAATTTTAATATATTAATAATT
1 TATATA-TTATAT--ATTTTAATATATT-ATAATT
1428888 TATATATTATATATTTTAATATATTTATATATT
1 TATATATTATATATTTTAATATA-TTATA-ATT
* *
1428921 T-TGTATTATATTTATTTTATATTATATTTTAATT
1 TATATATTATA--TATTTTA-A-TATATTATAATT
1428955 TAT
1 TAT
1428958 TTCAAGCCAT
Statistics
Matches: 61, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
32 22 0.36
33 6 0.10
34 17 0.28
35 12 0.20
36 4 0.07
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (31 bp):
TATATATTATATATTTTAATATATTATAATT
Done.