Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold154
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: 1945843
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 156 characters in sequence are not A, C, G, or T
File 8 of 12
Found at i:1030451 original size:13 final size:12
Alignment explanation
Indices: 1030435--1030547 Score: 59
Period size: 12 Copynumber: 8.4 Consensus size: 12
1030425 TTATATTTTA
1030435 TATTTAAATATAT
1 TATTTAAA-ATAT
1030448 TATTTAAAATTAAT
1 TATTTAAAA-T-AT
1030462 ATCATGTATAAAATA-
1 -T-AT-T-TAAAATAT
1030477 TATTTTATAAATAT
1 TA-TTTA-AAATAT
1030491 TATTTTACATATTATAT
1 TA-TTTA-A-A--ATAT
1030508 T-TTTAAAATAT
1 TATTTAAAATAT
*
1030519 TATTTTAAATAT
1 TATTTAAAATAT
* *
1030531 AATTCAAAATAT
1 TATTTAAAATAT
1030543 TATTT
1 TATTT
1030548 TAGTAAAATT
Statistics
Matches: 80, Mismatches: 7, Indels: 27
0.70 0.06 0.24
Matches are distributed among these distances:
11 5 0.06
12 24 0.30
13 17 0.21
14 13 0.16
15 6 0.08
16 3 0.04
17 7 0.09
18 5 0.06
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (12 bp):
TATTTAAAATAT
Found at i:1030507 original size:28 final size:25
Alignment explanation
Indices: 1030472--1030549 Score: 88
Period size: 28 Copynumber: 3.0 Consensus size: 25
1030462 ATCATGTATA
1030472 AAATATATTTTATAAATATTATTTT
1 AAATATATTTTATAAATATTATTTT
1030497 ACATATTATATTTT-TAAAATATTATTTT
1 A-A-A-TATATTTTAT-AAATATTATTTT
* *
1030525 AAATATAATTCA-AAATATTATTTT
1 AAATATATTTTATAAATATTATTTT
1030549 A
1 A
1030550 GTAAAATTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
24 13 0.28
25 7 0.15
26 2 0.04
27 3 0.07
28 21 0.46
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (25 bp):
AAATATATTTTATAAATATTATTTT
Found at i:1030530 original size:12 final size:12
Alignment explanation
Indices: 1030484--1030549 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
1030474 ATATATTTTA
1030484 TAAATATTATTT
1 TAAATATTATTT
*
1030496 TACATATTATATTTT
1 TAAATA-T-TA-TTT
1030511 TAAAATATTATTT
1 T-AAATATTATTT
* *
1030524 TAAATATAATTC
1 TAAATATTATTT
*
1030536 AAAATATTATTT
1 TAAATATTATTT
1030548 TA
1 TA
1030550 GTAAAATTGA
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
12 24 0.57
13 5 0.12
14 4 0.10
15 5 0.12
16 4 0.10
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (12 bp):
TAAATATTATTT
Found at i:1031364 original size:15 final size:16
Alignment explanation
Indices: 1031344--1031451 Score: 78
Period size: 17 Copynumber: 6.5 Consensus size: 16
1031334 ATAATTTCTA
1031344 AAATTTTATATATA-T
1 AAATTTTATATATATT
1031359 AAATTTT-TATATATT
1 AAATTTTATATATATT
*
1031374 AATAATTTATATTATATT
1 AA-ATTTTATA-TATATT
*
1031392 AAATTTAATATAT-TT
1 AAATTTTATATATATT
* *
1031407 ATATATTAATATTATATTT
1 AAAT-TTTATA-TATA-TT
*
1031426 ATATTTTTATATTATATT
1 A-AATTTTATA-TATATT
*
1031444 ATATTTTA
1 AAATTTTA
1031452 CTTGTGCCGT
Statistics
Matches: 75, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
14 6 0.08
15 15 0.20
16 13 0.17
17 16 0.21
18 11 0.15
19 13 0.17
20 1 0.01
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AAATTTTATATATATT
Found at i:1031366 original size:16 final size:16
Alignment explanation
Indices: 1031342--1031404 Score: 67
Period size: 16 Copynumber: 3.9 Consensus size: 16
1031332 CAATAATTTC
1031342 TAAAATTTTATATATA
1 TAAAATTTTATATATA
*
1031358 TAAATTTTTATATAT-
1 TAAAATTTTATATATA
1031373 TAATAA-TTTATATTATA
1 TAA-AATTTTATA-TATA
* *
1031390 TTAAATTTAATATAT
1 TAAAATTTTATATAT
1031405 TTATATATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
15 9 0.23
16 23 0.59
17 7 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TAAAATTTTATATATA
Found at i:1031371 original size:14 final size:15
Alignment explanation
Indices: 1031344--1031404 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
1031334 ATAATTTCTA
1031344 AAATTTTATATATAT
1 AAATTTTATATATAT
1031359 AAATTTT-TATATATT
1 AAATTTTATATATA-T
*
1031374 AATAATTTATATTATATT
1 AA-ATTTTATA-TATA-T
*
1031392 AAATTTAATATAT
1 AAATTTTATATAT
1031405 TTATATATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
14 6 0.15
15 10 0.26
16 7 0.18
17 8 0.21
18 8 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
AAATTTTATATATAT
Found at i:1031390 original size:5 final size:5
Alignment explanation
Indices: 1031368--1031448 Score: 68
Period size: 5 Copynumber: 17.2 Consensus size: 5
1031358 TAAATTTTTA
* * *
1031368 TATAT TA-AT AAT-T TATAT TATAT TAAAT T-TAA TATAT T-TA- TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1031413 TAATAT TATATT TATAT T-T-T TATAT TATAT TATAT T
1 T-ATAT TATA-T TATAT TATAT TATAT TATAT TATAT T
1031449 TTACTTGTGC
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
3 3 0.05
4 14 0.23
5 34 0.56
6 10 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:1031415 original size:16 final size:16
Alignment explanation
Indices: 1031348--1031418 Score: 52
Period size: 16 Copynumber: 4.9 Consensus size: 16
1031338 TTTCTAAAAT
*
1031348 TTTATATATATAA-ATT
1 TTTATATAT-TAATATA
1031364 TTTATATATTAATA-A
1 TTTATATATTAATATA
1031379 -TT-TATA-T--TATA
1 TTTATATATTAATATA
*
1031390 -TTAAAT-TTAATATA
1 TTTATATATTAATATA
1031404 TTTATATATTAATAT
1 TTTATATATTAATAT
1031419 TATATTTATA
Statistics
Matches: 44, Mismatches: 3, Indels: 16
0.70 0.05 0.25
Matches are distributed among these distances:
10 2 0.05
11 3 0.07
12 4 0.09
13 4 0.09
14 6 0.14
15 8 0.18
16 17 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTATATATTAATATA
Found at i:1031422 original size:19 final size:19
Alignment explanation
Indices: 1031364--1031447 Score: 75
Period size: 19 Copynumber: 4.4 Consensus size: 19
1031354 TATATAAATT
1031364 TTTATATATTAATAATT-TA
1 TTTATATATTAAT-ATTATA
* *
1031383 TATTATAT-TAAATTTAATATA
1 T-TTATATATTAA--TATTATA
1031404 TTTATATATTAATATTATA
1 TTTATATATTAATATTATA
* *
1031423 TTTATATTTTTATATTATA
1 TTTATATATTAATATTATA
1031442 -TTATAT
1 TTTATAT
1031448 TTTACTTGTG
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
18 6 0.11
19 27 0.50
20 14 0.26
21 7 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTATATATTAATATTATA
Found at i:1031437 original size:33 final size:33
Alignment explanation
Indices: 1031352--1031448 Score: 99
Period size: 33 Copynumber: 2.8 Consensus size: 33
1031342 TAAAATTTTA
* *
1031352 TATATATAAATTTTTATATATTA-ATAATTTATAT
1 TATATTTAAATTTTTATAT-TTATAT-ATTAATAT
*
1031386 TATA-TTAAATTTAATATATTTATATATTAATAT
1 TATATTTAAATTT-TTATATTTATATATTAATAT
*
1031419 TATATTTATATTTTTATATTATATTATATT
1 TATATTTAAATTTTTATATT-TA-TATATT
1031449 TTACTTGTGC
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
33 27 0.51
34 20 0.38
35 6 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (33 bp):
TATATTTAAATTTTTATATTTATATATTAATAT
Found at i:1034198 original size:11 final size:11
Alignment explanation
Indices: 1034178--1034206 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1034168 AAAATATAAA
1034178 AATAAT-ATTT
1 AATAATAATTT
1034188 AATAATAATTT
1 AATAATAATTT
1034199 AATAATAA
1 AATAATAA
1034207 ATAGTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AATAATAATTT
Found at i:1034250 original size:26 final size:28
Alignment explanation
Indices: 1034170--1034258 Score: 78
Period size: 29 Copynumber: 3.2 Consensus size: 28
1034160 AGTATTTGAA
*
1034170 AATATAAA-AATAATATTTAATAA-TAATTT
1 AATATAAATAGTAATATTT--TAAGT-ATTT
*
1034199 AATAATAAATAGTATTATTTTAAGTATTT
1 AAT-ATAAATAGTAATATTTTAAGTATTT
* *
1034228 AATATTAATA-TAATATTTT-AGTATTA
1 AATATAAATAGTAATATTTTAAGTATTT
1034254 AATAT
1 AATAT
1034259 CATTATTAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
26 11 0.21
27 8 0.15
28 6 0.12
29 13 0.25
30 6 0.12
31 8 0.15
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (28 bp):
AATATAAATAGTAATATTTTAAGTATTT
Found at i:1034918 original size:19 final size:20
Alignment explanation
Indices: 1034879--1034918 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1034869 AGTAATATAG
1034879 AAATAATCTTTCTCTCGTGAT
1 AAATAATCTTTCTCTC-TGAT
*
1034900 AAATAATGTTTCTCT-TGAT
1 AAATAATCTTTCTCTCTGAT
1034919 GTGTTTCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
21 14 0.78
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (20 bp):
AAATAATCTTTCTCTCTGAT
Found at i:1035189 original size:19 final size:20
Alignment explanation
Indices: 1035160--1035206 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1035150 TTCGTTGAAG
*
1035160 TTTCAAATGACCGTTAGAGC
1 TTTCAAGTGACCGTTAGAGC
* *
1035180 TTT-AAGTGACTGTTAGGGC
1 TTTCAAGTGACCGTTAGAGC
1035199 TTTCAAGT
1 TTTCAAGT
1035207 ATTGATACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (20 bp):
TTTCAAGTGACCGTTAGAGC
Found at i:1035967 original size:20 final size:20
Alignment explanation
Indices: 1035938--1035991 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1035928 CGACCACTAC
*
1035938 TTGTAGCGATACAT-AGGACA
1 TTGTATCGATACATGAGGA-A
*
1035958 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGAGGAA
1035978 TTGTATCGATACAT
1 TTGTATCGATACAT
1035992 TGCTTGTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 28 0.90
21 3 0.10
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (20 bp):
TTGTATCGATACATGAGGAA
Found at i:1039167 original size:131 final size:131
Alignment explanation
Indices: 1038932--1039181 Score: 446
Period size: 131 Copynumber: 1.9 Consensus size: 131
1038922 TTAGTTATCA
* *
1038932 TAGTTCCCTTTCTCAAGTTTCATTGTATGTGTTTTTAAACATTTTAATGCTGGAATCTTTTAGGT
1 TAGTTCCCTTTCTCAAGTTTCATTGTATGTGTTTGTAAACATTTTAATGCTGGAATCCTTTAGGT
*
1038997 AGTTAAAATGTTTCATACATGATGTTATTGCTATGACTTTTATGTGTTTCATGCATGATGTTACC
66 AGTTAAAATGTTTCATACATGATGTTATTGCTATAACTTTTATGTGTTTCATGCATGATGTTACC
1039062 G
131 G
* * *
1039063 TAGTTCCCTTTTTCAAGTTTCATTGTATGTGTTTGTAAACATTTTGATGTTGGAATCCTTTAGGT
1 TAGTTCCCTTTCTCAAGTTTCATTGTATGTGTTTGTAAACATTTTAATGCTGGAATCCTTTAGGT
1039128 AGTTAAAATGTTTCATACATGATGTTATTGCTATAACTTTTATGTGTTTCATGC
66 AGTTAAAATGTTTCATACATGATGTTATTGCTATAACTTTTATGTGTTTCATGC
1039182 GATTCCCTTT
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
131 113 1.00
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (131 bp):
TAGTTCCCTTTCTCAAGTTTCATTGTATGTGTTTGTAAACATTTTAATGCTGGAATCCTTTAGGT
AGTTAAAATGTTTCATACATGATGTTATTGCTATAACTTTTATGTGTTTCATGCATGATGTTACC
G
Found at i:1041615 original size:22 final size:22
Alignment explanation
Indices: 1041590--1041631 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1041580 AAAAAAATAT
1041590 ATTTT-ATATAATAAAATTTAAA
1 ATTTTAAT-TAATAAAATTTAAA
*
1041612 ATTTTAATTAATTAAATTTA
1 ATTTTAATTAATAAAATTTA
1041632 TATTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTTTAATTAATAAAATTTAAA
Found at i:1041690 original size:37 final size:36
Alignment explanation
Indices: 1041596--1041691 Score: 103
Period size: 37 Copynumber: 2.7 Consensus size: 36
1041586 ATATATTTTA
*
1041596 TATAATAAAATTTAA-A-ATTTTAATTAATTAAATT
1 TATATTAAAATTTAATATATTTTAATTAATTAAATT
* *
1041630 TATATTAAAAATT-ATATCA-TTTAATTACAATTATATT
1 TATATTAAAATTTAATAT-ATTTTAATT--AATTAAATT
1041667 T-TATTAAAATTTAATATATTTTAAT
1 TATATTAAAATTTAATATATTTTAAT
1041692 ATTATTTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
33 1 0.02
34 12 0.24
35 7 0.14
36 12 0.24
37 19 0.37
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (36 bp):
TATATTAAAATTTAATATATTTTAATTAATTAAATT
Found at i:1042363 original size:33 final size:33
Alignment explanation
Indices: 1042306--1042373 Score: 79
Period size: 31 Copynumber: 2.1 Consensus size: 33
1042296 TATAAAATAT
*
1042306 AATAATATTTATATATTTTTATAATTATTT-AA
1 AATAATATTTATATATTTTTATAATAATTTGAA
1042338 AATAA-ATTTAT-TATTATTTAAATAATAATTTGAA
1 AATAATATTTATATATT-TTT--ATAATAATTTGAA
1042372 AA
1 AA
1042374 GATTTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
30 4 0.13
31 9 0.29
32 5 0.16
33 9 0.29
34 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (33 bp):
AATAATATTTATATATTTTTATAATAATTTGAA
Found at i:1042655 original size:20 final size:21
Alignment explanation
Indices: 1042619--1042657 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1042609 TATTTTTATT
1042619 TAAAATTAATTATAAAATATA
1 TAAAATTAATTATAAAATATA
1042640 TAAATATTAA-TA-AAAATA
1 TAAA-ATTAATTATAAAATA
1042658 ATATTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 6 0.35
22 5 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAAATTAATTATAAAATATA
Found at i:1050130 original size:31 final size:31
Alignment explanation
Indices: 1050092--1050168 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
1050082 TTAAAAAATT
**
1050092 AAATATTAATTTTTTAATAT-TTATAATTTTA
1 AAATATTAATTTTTTAATATATT-TAATTAAA
** *
1050123 AAATATTAACATTTTAATATATTTTATTAAA
1 AAATATTAATTTTTTAATATATTTAATTAAA
1050154 AAGATATTAATTTTT
1 AA-ATATTAATTTTT
1050169 AAAAAATATA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
31 25 0.68
32 12 0.32
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (31 bp):
AAATATTAATTTTTTAATATATTTAATTAAA
Found at i:1050180 original size:16 final size:17
Alignment explanation
Indices: 1050138--1050183 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
1050128 TTAACATTTT
*
1050138 AATATATTTTATTAAAA
1 AATATAATTTATTAAAA
1050155 AGATATTAATTT-TTAAAA
1 A-ATA-TAATTTATTAAAA
1050173 AATATAATTTA
1 AATATAATTTA
1050184 AATATTCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 6 0.24
17 4 0.16
18 10 0.40
19 5 0.20
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
AATATAATTTATTAAAA
Found at i:1051663 original size:19 final size:20
Alignment explanation
Indices: 1051618--1051663 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
1051608 GGTTGAATAA
1051618 AGATATATTTAACATAAGTT
1 AGATATATTTAACATAAGTT
*
1051638 A-AAATATTT-ACA-AAGTAT
1 AGATATATTTAACATAAGT-T
1051656 AGATATAT
1 AGATATAT
1051664 ACTTTAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
17 4 0.18
18 5 0.23
19 12 0.55
20 1 0.05
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.37
Consensus pattern (20 bp):
AGATATATTTAACATAAGTT
Found at i:1057734 original size:2 final size:2
Alignment explanation
Indices: 1057729--1057763 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1057719 CTCTCTCTCT
1057729 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1057764 TCCACCATGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1061287 original size:3 final size:3
Alignment explanation
Indices: 1061279--1061305 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1061269 ATTTATCAAT
1061279 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1061306 ATGGAGTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1062343 original size:19 final size:19
Alignment explanation
Indices: 1062319--1062356 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1062309 TTGAATTCAG
* *
1062319 AAAATTAGAAAGAACTAAA
1 AAAATTAAAAAAAACTAAA
1062338 AAAATTAAAAAAAACTAAA
1 AAAATTAAAAAAAACTAAA
1062357 TTGTTTGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (19 bp):
AAAATTAAAAAAAACTAAA
Found at i:1062998 original size:10 final size:9
Alignment explanation
Indices: 1062963--1062994 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
1062953 AAGATAAAAT
1062963 AATTTTTTA
1 AATTTTTTA
1062972 AATTTTTTA
1 AATTTTTTA
*
1062981 AATTATTTA
1 AATTTTTTA
1062990 AATTT
1 AATTT
1062995 ATTTTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
AATTTTTTA
Found at i:1063088 original size:25 final size:26
Alignment explanation
Indices: 1063054--1063102 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
1063044 ATAAATTTTA
*
1063054 TTTAATATTTTAATAAAT-TATAAAT
1 TTTAATATTTAAATAAATATATAAAT
* *
1063079 TTTATTATTTAAATTAATATATAA
1 TTTAATATTTAAATAAATATATAA
1063103 TTAATTCATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
TTTAATATTTAAATAAATATATAAAT
Found at i:1063810 original size:12 final size:12
Alignment explanation
Indices: 1063789--1063819 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1063779 ATGATTATTT
1063789 AAAAAAAAAAAG
1 AAAAAAAAAAAG
*
1063801 AAAAAGAAAAAG
1 AAAAAAAAAAAG
1063813 AAAAAAA
1 AAAAAAA
1063820 GATGGACCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:1064135 original size:19 final size:17
Alignment explanation
Indices: 1064086--1064122 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
1064076 AAAATTGCTC
1064086 AATATAAAAAT---ATT
1 AATATAAAAATAAAATT
1064100 AATATAAAAATAAAATT
1 AATATAAAAATAAAATT
1064117 AATATA
1 AATATA
1064123 TGAAATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.55
17 9 0.45
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AATATAAAAATAAAATT
Found at i:1065188 original size:36 final size:36
Alignment explanation
Indices: 1065147--1065221 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 36
1065137 TAATTTTATC
* *
1065147 AATTAAGATTTCCTTTAAAAGCTCGACAAAAAGTCT
1 AATTAAGATTTCATTTAAAAGCTCGACAAAAAATCT
* *
1065183 AATTAAGATTTCATTTACAAGCTCGATAAAAAATCT
1 AATTAAGATTTCATTTAAAAGCTCGACAAAAAATCT
1065219 AAT
1 AAT
1065222 CATAAAATGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (36 bp):
AATTAAGATTTCATTTAAAAGCTCGACAAAAAATCT
Found at i:1066516 original size:13 final size:14
Alignment explanation
Indices: 1066488--1066529 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1066478 AAATTTATTT
1066488 ATAAATATAAATAA
1 ATAAATATAAATAA
*
1066502 ATAAATAT-GATAA
1 ATAAATATAAATAA
*
1066515 ATAAAAAATAAATAA
1 AT-AAATATAAATAA
1066530 CATGTGTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 6 0.26
14 13 0.57
15 4 0.17
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (14 bp):
ATAAATATAAATAA
Found at i:1067115 original size:24 final size:23
Alignment explanation
Indices: 1067083--1067133 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1067073 GGGTAAAGAG
1067083 AAAAAGAGAAAAAAAAAAAAGAAA
1 AAAAAGAG-AAAAAAAAAAAGAAA
* * *
1067107 AAAAAGAGAGAAAAGAAAGGAAA
1 AAAAAGAGAAAAAAAAAAAGAAA
1067130 AAAA
1 AAAA
1067134 TTATCACTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (23 bp):
AAAAAGAGAAAAAAAAAAAGAAA
Found at i:1067118 original size:13 final size:12
Alignment explanation
Indices: 1067083--1067133 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
1067073 GGGTAAAGAG
1067083 AAAAAGAGAAAA
1 AAAAAGAGAAAA
*
1067095 AAAAA-AAAGAAA
1 AAAAAGAGA-AAA
1067107 AAAAAGAGAGAAA
1 AAAAAGAGA-AAA
*
1067120 AGAAAG-GAAAA
1 AAAAAGAGAAAA
1067131 AAA
1 AAA
1067134 TTATCACTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
11 7 0.21
12 15 0.45
13 11 0.33
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAAGAGAAAA
Found at i:1068944 original size:20 final size:20
Alignment explanation
Indices: 1068921--1068962 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1068911 CTAATCTAAC
* *
1068921 TTAATTTAAATTACTATTTA
1 TTAATTAAAAGTACTATTTA
*
1068941 TTAATTAAAAGTATTATTTA
1 TTAATTAAAAGTACTATTTA
1068961 TT
1 TT
1068963 TAAATAATCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (20 bp):
TTAATTAAAAGTACTATTTA
Found at i:1072368 original size:2 final size:2
Alignment explanation
Indices: 1072363--1072396 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1072353 GTTCACATCC
1072363 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1072397 CACTATTGCC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1073029 original size:51 final size:51
Alignment explanation
Indices: 1072974--1073079 Score: 203
Period size: 51 Copynumber: 2.1 Consensus size: 51
1072964 ATAATGATAA
*
1072974 AAATGAATGGCCTGAATTTTAAAATTTAAATTCATTAAATTTAAATACCAT
1 AAATGAATGGCCTGAATTTTAAAATTTAAATTCATTAAATTTAAAAACCAT
1073025 AAATGAATGGCCTGAATTTTAAAATTTAAATTCATTAAATTTAAAAACCAT
1 AAATGAATGGCCTGAATTTTAAAATTTAAATTCATTAAATTTAAAAACCAT
1073076 AAAT
1 AAAT
1073080 TTAAATTCAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (51 bp):
AAATGAATGGCCTGAATTTTAAAATTTAAATTCATTAAATTTAAAAACCAT
Found at i:1073080 original size:30 final size:31
Alignment explanation
Indices: 1073044--1073132 Score: 144
Period size: 30 Copynumber: 2.9 Consensus size: 31
1073034 GCCTGAATTT
1073044 TAAAATTTAAATTCATTAAATTTAAAAACCA
1 TAAAATTTAAATTCATTAAATTTAAAAACCA
* *
1073075 T-AAATTTAAATTCATAAAATTTAAATACCA
1 TAAAATTTAAATTCATTAAATTTAAAAACCA
1073105 TAAAATTTAAATTCATTAAAATTTAAAA
1 TAAAATTTAAATTCATT-AAATTTAAAA
1073133 TTTATCTTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
30 28 0.54
31 15 0.29
32 9 0.17
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (31 bp):
TAAAATTTAAATTCATTAAATTTAAAAACCA
Found at i:1073108 original size:16 final size:15
Alignment explanation
Indices: 1073044--1073131 Score: 106
Period size: 16 Copynumber: 5.7 Consensus size: 15
1073034 GCCTGAATTT
1073044 TAAAATTTAAATTCA
1 TAAAATTTAAATTCA
* **
1073059 TTAAATTTAAAAACCA
1 TAAAATTT-AAATTCA
1073075 T-AAATTTAAATTCA
1 TAAAATTTAAATTCA
*
1073089 TAAAATTTAAATACCA
1 TAAAATTTAAAT-TCA
1073105 TAAAATTTAAATTCA
1 TAAAATTTAAATTCA
1073120 TTAAAATTTAAA
1 -TAAAATTTAAA
1073132 ATTTATCTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
14 6 0.10
15 25 0.40
16 31 0.50
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAAATTTAAATTCA
Found at i:1076258 original size:13 final size:13
Alignment explanation
Indices: 1076240--1076281 Score: 84
Period size: 13 Copynumber: 3.2 Consensus size: 13
1076230 CATTATTCAA
1076240 TGTATCGATACAT
1 TGTATCGATACAT
1076253 TGTATCGATACAT
1 TGTATCGATACAT
1076266 TGTATCGATACAT
1 TGTATCGATACAT
1076279 TGT
1 TGT
1076282 TCTTTGTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1091827 original size:23 final size:21
Alignment explanation
Indices: 1091807--1091846 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1091797 AGTCACATTT
1091807 TTTCT-AAATGTATCGATACA
1 TTTCTCAAATGTATCGATACA
*
1091827 TTTCTCGAATGTATCGATAC
1 TTTCTCAAATGTATCGATAC
1091847 GAGATCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (21 bp):
TTTCTCAAATGTATCGATACA
Found at i:1091966 original size:91 final size:91
Alignment explanation
Indices: 1091811--1092008 Score: 324
Period size: 91 Copynumber: 2.2 Consensus size: 91
1091801 ACATTTTTTC
* *
1091811 TAAATGTATCGATACATTTCTCGAATGTATCGATACGAGATCTCAACAGTCAAAAATTTTAAATT
1 TAAATGTATCGATACATTTCTCGAATGTATCGATACGAGATCCCAACAGTCAAAAATTTCAAATT
1091876 TTTACAATTTGTATCGATACAAATAG
66 TTTACAATTTGTATCGATACAAATAG
* * *
1091902 TAAATGTATCGATACATTTCTTGAATGTATCGATACGAGGTCCCAACGGTCAAAAATTTCAAATT
1 TAAATGTATCGATACATTTCTCGAATGTATCGATACGAGATCCCAACAGTCAAAAATTTCAAATT
* * *
1091967 TTTACAATTTTTATTGATTCAAATAG
66 TTTACAATTTGTATCGATACAAATAG
1091993 TAAATGTATCGATACA
1 TAAATGTATCGATACA
1092009 ATGTATCGAT
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 99 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (91 bp):
TAAATGTATCGATACATTTCTCGAATGTATCGATACGAGATCCCAACAGTCAAAAATTTCAAATT
TTTACAATTTGTATCGATACAAATAG
Found at i:1092013 original size:13 final size:13
Alignment explanation
Indices: 1091995--1092021 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1091985 TCAAATAGTA
1091995 AATGTATCGATAC
1 AATGTATCGATAC
1092008 AATGTATCGATAC
1 AATGTATCGATAC
1092021 A
1 A
1092022 TGCCTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1092135 original size:20 final size:20
Alignment explanation
Indices: 1092070--1092123 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1092060 GGAAAAGAAA
*
1092070 TGTATCGATACCTTTACTAT
1 TGTATCGATACATTTACTAT
*
1092090 TGTATCGATATATTTACTAT
1 TGTATCGATACATTTACTAT
1092110 TGTATCGATACATT
1 TGTATCGATACATT
1092124 ATTCATTGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.46
Consensus pattern (20 bp):
TGTATCGATACATTTACTAT
Found at i:1094176 original size:20 final size:20
Alignment explanation
Indices: 1094099--1094176 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 20
1094089 TTTTACCCAG
* *
1094099 ATGTATCGATATATTTTTTCA
1 ATGTATCGATACA-TTCTTCA
* * *
1094120 ATATATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
*
1094140 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTCTTCA
1094160 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
1094177 GTCTTTTTAC
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
19 1 0.02
20 33 0.72
21 12 0.26
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:1108073 original size:8 final size:8
Alignment explanation
Indices: 1108060--1108124 Score: 57
Period size: 8 Copynumber: 8.6 Consensus size: 8
1108050 TACACCTAAA
1108060 AAAAAAAC
1 AAAAAAAC
1108068 AAAAAAAC
1 AAAAAAAC
1108076 -AAAAAA-
1 AAAAAAAC
1108082 AAAAAAAC
1 AAAAAAAC
*
1108090 AAGAAAAC
1 AAAAAAAC
* *
1108098 CAAGAAA-
1 AAAAAAAC
* *
1108105 AAAATAGC
1 AAAAAAAC
1108113 AAAAAAA-
1 AAAAAAAC
1108120 AAAAA
1 AAAAA
1108125 CAGAAAGGGG
Statistics
Matches: 44, Mismatches: 10, Indels: 7
0.72 0.16 0.11
Matches are distributed among these distances:
7 20 0.45
8 24 0.55
ACGTcount: A:0.85, C:0.09, G:0.05, T:0.02
Consensus pattern (8 bp):
AAAAAAAC
Found at i:1108085 original size:22 final size:22
Alignment explanation
Indices: 1108057--1108124 Score: 84
Period size: 23 Copynumber: 3.1 Consensus size: 22
1108047 CTTTACACCT
1108057 AAAAAAAAAACAAAAAAACAAA
1 AAAAAAAAAACAAAAAAACAAA
* *
1108079 AAAAAAAAAACAAGAAAACCAAG
1 AAAAAAAAAACAA-AAAAACAAA
* *
1108102 AAAAAAATAGCAAAAAAA-AAA
1 AAAAAAAAAACAAAAAAACAAA
1108123 AA
1 AA
1108125 CAGAAAGGGG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
21 4 0.10
22 17 0.44
23 18 0.46
ACGTcount: A:0.85, C:0.09, G:0.04, T:0.01
Consensus pattern (22 bp):
AAAAAAAAAACAAAAAAACAAA
Found at i:1109396 original size:28 final size:28
Alignment explanation
Indices: 1109342--1110516 Score: 1453
Period size: 28 Copynumber: 41.5 Consensus size: 28
1109332 ATGTTCATCC
*
1109342 CTTTCAAAGCCCACAAGTCAGCGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1109370 CTTTCCAAAGCCCACGAGTCAGT-GCAC-
1 CTTT-CAAAGCCCACAAGTCAGTGGCACT
* * *
1109397 CTTTTTAAAGCCCATAAGTCAGTGGCACA
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
1109426 CCTTCGAAGCCCACAAGTTAGTGGCACA
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1109454 CTTTTCAAAGCCCACAAGTCAGT-GCACC
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
*
1109482 CTTTCAAAGCCCATAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1109510 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
* *
1109539 CATTTCAAAGCCCAAAAGTCAGTGGCACC
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
1109568 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1109596 CTTTCAAAGCCCATAAGTTAGTGGCA-T
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
1109623 CCTTTCAAAGCCCACAAGTCAGTGGCAC-
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1109651 CTAGTCAAAGCCCACAAGTCAGTGGCACT
1 CT-TTCAAAGCCCACAAGTCAGTGGCACT
1109680 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1109708 CTTTTCGAAGCCCACAAGTCAGTGGCACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
* *
1109737 CTTTTCGAAGCCCACAAGTTAGTGGCACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
1109766 CTTTTCAAAG-CC-CAAGTCAGTGGCA-T
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
* *
1109792 CCTTTCAAAGCCCACTAGTCAGTGGCACC
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1109821 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1109849 CTTTCAAAGCCCACTAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1109877 CTTTTCAAAGCCTACAAGTTAGTGGCACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
*
1109906 CTTTTCAAAGCCCACAAGTTAGTGGCA-T
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
* *
1109934 CCTTTCAAAGCCCACTAGTCAGTGGCACC
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1109963 CCTTCAAAGCCCACTAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1109991 CTTTCAAAGCCCACCAGTTAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1110019 CTTTCAAAGCCCACGAGTCAATGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1110047 TTTTCAAAGCCCACAAGTCAGTGGCA-T
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1110074 CCTTTCAAAGCCTACGAGTCAGTGGCACT
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1110103 TTTTTAAAGCCCACAAGTCAGTGGCA-T
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1110130 CCTTTCAAAGCCTACAAGTCAGTGGCAC-
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1110158 CTTTTCAAAGCCCGCAAGTTAGTGGCACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
1110187 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
*
1110216 CTTTTCAAAGCCTACAAGTCAGTGGCACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
* *
1110245 CTTTTAAAAGCCCACAAGTCAGTGGCACC
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
*
1110274 CTTTCAAAGCCCATAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1110302 CTTTCAAGGCCCACAAGTCAGTGGTACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
1110330 CTTTTAAAGCCCACAAGTCAGTGGCACTGT
1 CTTTCAAAGCCCACAAGTCAGTGGCAC--T
* *
1110360 TTTTC-AAGCCCACGAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1110387 TTTTCAAAGCCCACAAGTTAGTGGCA-T
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1110414 CCTTTCAAAGCCTACAAGTCAATGGCAC-
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
1110442 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1110471 CTTTTCAAAGCCCACAAGCCAATGGTAACT
1 C-TTTCAAAGCCCACAAGTCAGTGG-CACT
*
1110501 CTTTTCAAAACCCACA
1 C-TTTCAAAGCCCACA
1110517 CGTGTCGGTG
Statistics
Matches: 1016, Mismatches: 98, Indels: 64
0.86 0.08 0.05
Matches are distributed among these distances:
26 9 0.01
27 65 0.06
28 590 0.58
29 330 0.32
30 22 0.02
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (28 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:1111195 original size:20 final size:20
Alignment explanation
Indices: 1111118--1111195 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 20
1111108 TTTTACCCAG
* *
1111118 ATGTATCGATATATTTTTTCA
1 ATGTATCGATACA-TTCTTCA
* * *
1111139 ATATATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
*
1111159 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTCTTCA
1111179 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
1111196 GTCTTTTTAC
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
19 1 0.02
20 33 0.72
21 12 0.26
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:1118350 original size:51 final size:51
Alignment explanation
Indices: 1118284--1118401 Score: 152
Period size: 50 Copynumber: 2.3 Consensus size: 51
1118274 TTAAAAATAA
1118284 CGGGGTTGGAGTATCCCCGATGGTGAGAAA-TCGATATTTTGAAAATAAAAAT
1 CGGGGTTGGAGTATCCCCGATGGTGA-AAAGTCGATATTTTGAAAAT-AAAAT
* * *
1118336 -GGGGTTGGAGTAT-CCTGATGGTGAAAAGTTGATATTTTGGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATGGTGAAAAGTCGATATTTTGAAAATAAAAT
* *
1118385 CAGGGTTAGAGTATCCC
1 CGGGGTTGGAGTATCCC
1118402 TTCAAAAATA
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
49 8 0.14
50 35 0.60
51 15 0.26
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.29
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATGGTGAAAAGTCGATATTTTGAAAATAAAAT
Found at i:1118382 original size:129 final size:129
Alignment explanation
Indices: 1118238--1118479 Score: 346
Period size: 129 Copynumber: 1.9 Consensus size: 129
1118228 GAAAAATTTA
* * *
1118238 ATATTTTGGAGATAAAAACGGGGTTAGAGTATCCCCTT-AAAAATAACGGGGTTGGAGTATCCCC
1 ATATTTTGGAAATAAAAACAGGGTTAGAGTAT-CCCTTCAAAAATAACGGGGTTAGAGTATCCCC
* *
1118302 GATGGT-GAGAAATCGATATTTTGAAAATAAAAAT-GGGGTTGGAGTATCCTGATGGTGAAAAGT
65 GATGGTGGA-AAATCGATATTTTAAAAAT-AAAATCGAGGTTGGAGTATCCTGATGGTGAAAAGT
1118365 TG
128 TG
* * *
1118367 ATATTTTGGAAATAAAATCAGGGTTAGAGTATCCCTTCAAAAATAACGGGGTTAGAGTATCTCTG
1 ATATTTTGGAAATAAAAACAGGGTTAGAGTATCCCTTCAAAAATAACGGGGTTAGAGTATCCCCG
* *
1118432 ATGGTGGAAAATCGATGTTTTAAAAATAAAATCGAGGTTTGAGTATCC
66 ATGGTGGAAAATCGATATTTTAAAAATAAAATCGAGGTTGGAGTATCC
1118480 CCTAAAGAAT
Statistics
Matches: 100, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
128 10 0.10
129 88 0.88
130 2 0.02
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.29
Consensus pattern (129 bp):
ATATTTTGGAAATAAAAACAGGGTTAGAGTATCCCTTCAAAAATAACGGGGTTAGAGTATCCCCG
ATGGTGGAAAATCGATATTTTAAAAATAAAATCGAGGTTGGAGTATCCTGATGGTGAAAAGTTG
Found at i:1118459 original size:79 final size:77
Alignment explanation
Indices: 1118336--1118700 Score: 369
Period size: 79 Copynumber: 4.6 Consensus size: 77
1118326 AAATAAAAAT
* * ** *
1118336 GGGGTTGGAGTATCCTGATGGT-GAAAAGTTGATATTTTGGAAATAAAATCAGGGTTAGAGTATC
1 GGGGTTGGAGTATCCTGATGGTGGAAAA-TCGATGTTTTAAAAATAAAATCAGGGTTGGAGTATC
*
1118400 CCTTCAAAAATAAC
65 CCCT-AAAAATAAC
* *
1118414 GGGGTTAGAGTATCTCTGATGGTGGAAAATCGATGTTTTAAAAATAAAATC-GAGGTTTGAGTAT
1 GGGGTTGGAGTATC-CTGATGGTGGAAAATCGATGTTTTAAAAATAAAATCAG-GGTTGGAGTAT
1118478 CCCCTAAAGAATAAC
64 CCCCTAAA-AATAAC
* *
1118493 GGGGTTGGAGTATCCTCGATGGTGGAAAATC-AGTGTTTTCAAAATAAAATTAGGGTTGGAGTAT
1 GGGGTTGGAGTATCCT-GATGGTGGAAAATCGA-TGTTTTAAAAATAAAATCAGGGTTGGAGTAT
* *
1118557 CCCCTCGAAAATAAT
64 CCCCT-AAAAATAAC
* * * *
1118572 GAGGTTGAAGTATCCCCGATGGTGGAAAATCGATGTTTTGGAAAAA-AAAATCGGGGTTGGAGTA
1 GGGGTTGGAGTAT-CCTGATGGTGGAAAATCGATGTTTT--AAAAATAAAATCAGGGTTGGAGTA
* **
1118636 TCCCCTTGAAAATAGT
63 TCCCC-TAAAAATAAC
* * * * *
1118652 AGAGTTGGAGTATCCCCGATGGTGGAAAATCGATATTTTAGAAATAAAA
1 GGGGTTGGAGTAT-CCTGATGGTGGAAAATCGATGTTTTAAAAATAAAA
1118701 ACATCAATGA
Statistics
Matches: 247, Mismatches: 26, Indels: 27
0.82 0.09 0.09
Matches are distributed among these distances:
78 24 0.10
79 144 0.58
80 74 0.30
81 5 0.02
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (77 bp):
GGGGTTGGAGTATCCTGATGGTGGAAAATCGATGTTTTAAAAATAAAATCAGGGTTGGAGTATCC
CCTAAAAATAAC
Found at i:1118568 original size:158 final size:159
Alignment explanation
Indices: 1118336--1118700 Score: 433
Period size: 158 Copynumber: 2.3 Consensus size: 159
1118326 AAATAAAAAT
* **
1118336 GGGGTTGGAGTATCCT-GATGGT-GAAAAGT-TGATATTTTGGAAATAAAATCAGGGTTAGAGTA
1 GGGGTTGGAGTATCCTCGATGGTGGAAAA-TCAGATATTTTCAAAATAAAATCAGGGTTAGAGTA
* * * *
1118398 TCCCTTCAAAAATAACGGGGTT-AGAGTATCTCTGATGGTGGAAAATCGATGTTTT-AAAAATAA
65 TCCCCTCAAAAATAACGAGGTTGA-AGTATCCCCGATGGTGGAAAATCGATGTTTTGAAAAA-AA
*
1118461 AATCGAGGTTTGAGTATCCCC-TAAAGAATAAC
128 AATCGAGGTTGGAGTATCCCCTTAAA-AATAAC
* * *
1118493 GGGGTTGGAGTATCCTCGATGGTGGAAAATCAG-TGTTTTCAAAATAAAATTAGGGTTGGAGTAT
1 GGGGTTGGAGTATCCTCGATGGTGGAAAATCAGATATTTTCAAAATAAAATCAGGGTTAGAGTAT
* *
1118557 CCCCTCGAAAATAATGAGGTTGAAGTATCCCCGATGGTGGAAAATCGATGTTTTGGAAAAAAAAA
66 CCCCTCAAAAATAACGAGGTTGAAGTATCCCCGATGGTGGAAAATCGATGTTTT-GAAAAAAAAA
* * **
1118622 TCGGGGTTGGAGTATCCCCTTGAAAATAGT
130 TCGAGGTTGGAGTATCCCCTTAAAAATAAC
* * *
1118652 AGAGTTGGAGTATCCCCGATGGTGGAAAATC-GATATTTT-AGAAATAAAA
1 GGGGTTGGAGTATCCTCGATGGTGGAAAATCAGATATTTTCA-AAATAAAA
1118701 ACATCAATGA
Statistics
Matches: 178, Mismatches: 21, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
157 16 0.09
158 81 0.46
159 73 0.41
160 8 0.04
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (159 bp):
GGGGTTGGAGTATCCTCGATGGTGGAAAATCAGATATTTTCAAAATAAAATCAGGGTTAGAGTAT
CCCCTCAAAAATAACGAGGTTGAAGTATCCCCGATGGTGGAAAATCGATGTTTTGAAAAAAAAAT
CGAGGTTGGAGTATCCCCTTAAAAATAAC
Found at i:1121139 original size:51 final size:51
Alignment explanation
Indices: 1121044--1121179 Score: 186
Period size: 51 Copynumber: 2.7 Consensus size: 51
1121034 AAAAATGTCT
* * **
1121044 GAATGTATCGATACATTG-AAAATGTACCGATACATCTGTTTTAAAAC-CTA
1 GAATGTATCGATACAATGAAAAATGTATCGATACATCTGGGTTAAAACTC-A
*
1121094 GAATGTATGGATACAATGAAAAATGTATCGATACATCTGGGTTAAAACTCA
1 GAATGTATCGATACAATGAAAAATGTATCGATACATCTGGGTTAAAACTCA
* *
1121145 AAATGTATCGATACAATGAAAAATGTATCAATACA
1 GAATGTATCGATACAATGAAAAATGTATCGATACA
1121180 AATAGTATAT
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
50 16 0.21
51 59 0.78
52 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (51 bp):
GAATGTATCGATACAATGAAAAATGTATCGATACATCTGGGTTAAAACTCA
Found at i:1121827 original size:12 final size:12
Alignment explanation
Indices: 1121810--1121835 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1121800 AATTATTAAG
1121810 ATATAAAAATTA
1 ATATAAAAATTA
1121822 ATATAAAAATTA
1 ATATAAAAATTA
1121834 AT
1 AT
1121836 TTTAATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATATAAAAATTA
Found at i:1126358 original size:16 final size:18
Alignment explanation
Indices: 1126326--1126367 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
1126316 AGTAATTAAT
1126326 TTTTATATATGAATGT-A
1 TTTTATATATGAATGTAA
*
1126343 TTTTAT-TATGATTGTAA
1 TTTTATATATGAATGTAA
1126360 TTTTATAT
1 TTTTATAT
1126368 GGTTATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 8 0.36
17 13 0.59
18 1 0.05
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.60
Consensus pattern (18 bp):
TTTTATATATGAATGTAA
Found at i:1126368 original size:16 final size:16
Alignment explanation
Indices: 1126331--1126379 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1126321 TTAATTTTTA
*
1126331 TATATGAATGT-ATTT
1 TATATGATTGTAATTT
1126346 TATTATGATTGTAATTT
1 TA-TATGATTGTAATTT
* *
1126363 TATATGGTTATAATTT
1 TATATGATTGTAATTT
1126379 T
1 T
1126380 TTTTAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 2 0.07
16 21 0.72
17 6 0.21
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (16 bp):
TATATGATTGTAATTT
Found at i:1130902 original size:90 final size:91
Alignment explanation
Indices: 1130746--1130912 Score: 282
Period size: 90 Copynumber: 1.8 Consensus size: 91
1130736 AGATATATTG
* * *
1130746 ATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAAAATGTATCGATACATTGAAGAAT
1 ATACATTGAAAAATATATCAATACATCTGGGTAAAAAGACAAAATGTATCGATACATTGAAAAAT
*
1130811 GTATTGATACATTCATACATGTATCA
66 GTATCGATACATTCATACATGTATCA
*
1130837 ATACATTGAAAAATATATCAATATATCTGGGT-AAAAGACAAAATGTATCGATACATTGAAAAAT
1 ATACATTGAAAAATATATCAATACATCTGGGTAAAAAGACAAAATGTATCGATACATTGAAAAAT
1130901 GTATCGATACAT
66 GTATCGATACAT
1130913 CTGGGTAAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
90 42 0.59
91 29 0.41
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.29
Consensus pattern (91 bp):
ATACATTGAAAAATATATCAATACATCTGGGTAAAAAGACAAAATGTATCGATACATTGAAAAAT
GTATCGATACATTCATACATGTATCA
Found at i:1130925 original size:24 final size:20
Alignment explanation
Indices: 1130786--1130912 Score: 83
Period size: 20 Copynumber: 5.8 Consensus size: 20
1130776 GTAAAAAGAC
1130786 AAAATGTATCGATACATTGA
1 AAAATGTATCGATACATTGA
* * *
1130806 AGAATGTATTGATACATTCA
1 AAAATGTATCGATACATTGA
* * *
1130826 TACATGTATCAATACATTGA
1 AAAATGTATCGATACATTGA
* * *
1130846 AAAATATATCAATATATCTGGGTAAAAGA
1 AAAATGTATCGATACA--T---T----GA
1130875 CAAAATGTATCGATACATTGA
1 -AAAATGTATCGATACATTGA
1130896 AAAATGTATCGATACAT
1 AAAATGTATCGATACAT
1130913 CTGGGTAAAA
Statistics
Matches: 81, Mismatches: 16, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
20 60 0.74
21 2 0.02
22 1 0.01
25 2 0.02
28 1 0.01
29 2 0.02
30 13 0.16
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (20 bp):
AAAATGTATCGATACATTGA
Found at i:1132338 original size:22 final size:21
Alignment explanation
Indices: 1132298--1132338 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1132288 ATATTTTGTT
* *
1132298 TAAATTTAATTATATAATATA
1 TAAATTTAATAATAAAATATA
1132319 TAAATATTAATAATAAAATA
1 TAAAT-TTAATAATAAAATA
1132339 ATTTTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATTTAATAATAAAATATA
Found at i:1133775 original size:2 final size:2
Alignment explanation
Indices: 1133768--1133794 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1133758 TAGATCCCTC
1133768 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 A
1133795 AAAGAATCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1134632 original size:44 final size:43
Alignment explanation
Indices: 1134540--1134633 Score: 104
Period size: 44 Copynumber: 2.2 Consensus size: 43
1134530 TTGTTAATTT
*
1134540 TTTTAAATTTAAATTAAGTGTTGTAATAATTTAATTATTTTAAA
1 TTTTAAATTTAAATTAAGTGTTGTAATAATTT-ATTAATTTAAA
* *
1134584 -TTTAATATTTAAATTATG-GATTGTAATAGCTTT-TTAATTTAAA
1 TTTTAA-ATTTAAATTAAGTG-TTGTAATA-ATTTATTAATTTAAA
1134627 TTTTAAA
1 TTTTAAA
1134634 AATAATTAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
43 16 0.37
44 24 0.56
45 3 0.07
ACGTcount: A:0.39, C:0.01, G:0.07, T:0.52
Consensus pattern (43 bp):
TTTTAAATTTAAATTAAGTGTTGTAATAATTTATTAATTTAAA
Found at i:1134685 original size:14 final size:14
Alignment explanation
Indices: 1134648--1134698 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
1134638 ATTAGAGATT
*
1134648 ATAACTTAAATTAA
1 ATAAATTAAATTAA
** *
1134662 A-AGTTTAAATTAT
1 ATAAATTAAATTAA
1134675 ATAAATTAAATTAA
1 ATAAATTAAATTAA
*
1134689 ATATATTAAA
1 ATAAATTAAA
1134699 ATAATTAACA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
13 10 0.34
14 19 0.66
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (14 bp):
ATAAATTAAATTAA
Found at i:1134773 original size:28 final size:27
Alignment explanation
Indices: 1134713--1134773 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 27
1134703 TTAACAAAAT
1134713 ATAA-TTTAAATAAAAATTTTTACTATA
1 ATAATTTTAAATAAAAATTTTTA-TATA
1134740 ATTAATTTTAAATGAAATAATTTTT-TATA
1 A-TAATTTTAAAT-AAA-AATTTTTATATA
1134769 ATAAT
1 ATAAT
1134774 AAAAACTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
27 1 0.03
28 7 0.23
29 12 0.40
30 3 0.10
31 7 0.23
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
ATAATTTTAAATAAAAATTTTTATATA
Found at i:1134818 original size:19 final size:19
Alignment explanation
Indices: 1134790--1134835 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
1134780 TATTATTATA
* *
1134790 TTTA-TAATAATATTATCT
1 TTTATTAATAATATAATAT
1134808 TTTATTAATAATATAATAT
1 TTTATTAATAATATAATAT
1134827 TTTATTAAT
1 TTTATTAAT
1134836 TTTAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTATTAATAATATAATAT
Found at i:1135613 original size:87 final size:87
Alignment explanation
Indices: 1135467--1135634 Score: 223
Period size: 87 Copynumber: 1.9 Consensus size: 87
1135457 ATTGAATTAA
*
1135467 AACTTGACTTACTTTAATTTTAGTCTTCCCAAGTTTCCACTTATATTTACTCTAATTTTCCACAA
1 AACTTGACTTACTTTAATTTTAGTCTTCCCAAGTTTCCACTTACATTTACTCTAATTTTCCACAA
*
1135532 TCTCACACACATTATGAACTAG
66 TATCACACACATTATGAACTAG
* * * * *
1135554 AACTTGACTTACTTTATTTTTAGTC-TCACCAAGTTTCCACATT-CGTTTGCTTTAATTTTCTAC
1 AACTTGACTTACTTTAATTTTAGTCTTC-CCAAGTTTCCAC-TTACATTTACTCTAATTTTCCAC
* *
1135617 ATTATCACACGCATTATG
64 AATATCACACACATTATG
1135635 CTCCAAAACA
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
86 2 0.03
87 66 0.94
88 2 0.03
ACGTcount: A:0.27, C:0.23, G:0.07, T:0.42
Consensus pattern (87 bp):
AACTTGACTTACTTTAATTTTAGTCTTCCCAAGTTTCCACTTACATTTACTCTAATTTTCCACAA
TATCACACACATTATGAACTAG
Found at i:1138649 original size:38 final size:38
Alignment explanation
Indices: 1138607--1138694 Score: 144
Period size: 37 Copynumber: 2.3 Consensus size: 38
1138597 AATATTATAG
*
1138607 AAAATTAAAGTAAATGTATG-TGGAAACTTGAGGAGACT
1 AAAATTAAAGTAAATGTA-GCTGGAAACTTAAGGAGACT
1138645 AAAATTAAAGT-AATGTAGCTGGAAACTTAAGGAGACT
1 AAAATTAAAGTAAATGTAGCTGGAAACTTAAGGAGACT
1138682 AAAATTAAAGTAA
1 AAAATTAAAGTAA
1138695 GTCAATTTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
36 1 0.02
37 34 0.72
38 12 0.26
ACGTcount: A:0.49, C:0.06, G:0.20, T:0.25
Consensus pattern (38 bp):
AAAATTAAAGTAAATGTAGCTGGAAACTTAAGGAGACT
Found at i:1141151 original size:2 final size:2
Alignment explanation
Indices: 1141144--1141173 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1141134 CCTATATGTG
1141144 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
1141174 AATGATTTAC
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:1143690 original size:91 final size:90
Alignment explanation
Indices: 1143553--1143747 Score: 345
Period size: 91 Copynumber: 2.2 Consensus size: 90
1143543 ATACTAAGCA
1143553 ATATGTATCGATACATCTAGGTGTGTATCGATACTTTTTAGGGTTTTAACCTTTGTAACTTAAGT
1 ATATGTATCGATACATCTAGGTGTGTATCGATACTTTTTAGGGTTTTAACCTTTGTAACTTAAGT
*
1143618 CAACCTTTATGTACCGATACAAATAC
66 CAA-ATTTATGTACCGATACAAATAC
* *
1143644 ATATGTATCGATACATCTAGGTGTGTATCGATACTTTTTAGGGTTTTAACCTTTGTAGCTTGAGT
1 ATATGTATCGATACATCTAGGTGTGTATCGATACTTTTTAGGGTTTTAACCTTTGTAACTTAAGT
*
1143709 CAAATTTATGTACTGATACAAATAC
66 CAAATTTATGTACCGATACAAATAC
1143734 ATATGTATCGATAC
1 ATATGTATCGATAC
1143748 TTTGGATTAT
Statistics
Matches: 100, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
90 34 0.34
91 66 0.66
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (90 bp):
ATATGTATCGATACATCTAGGTGTGTATCGATACTTTTTAGGGTTTTAACCTTTGTAACTTAAGT
CAAATTTATGTACCGATACAAATAC
Found at i:1144563 original size:18 final size:18
Alignment explanation
Indices: 1144540--1144585 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 18
1144530 CAATAAACAA
1144540 GCATTCATGTAGAATATT
1 GCATTCATGTAGAATATT
1144558 GCATTCATGT---ATATT
1 GCATTCATGTAGAATATT
1144573 GCATTCATGTAGA
1 GCATTCATGTAGA
1144586 GAATATCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 15 0.60
18 10 0.40
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.39
Consensus pattern (18 bp):
GCATTCATGTAGAATATT
Found at i:1158244 original size:14 final size:13
Alignment explanation
Indices: 1158221--1158254 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1158211 CCTTCGTACC
1158221 AAAAAA-ACAAATA
1 AAAAAAGACAAA-A
1158234 AAAAAAGACAAAA
1 AAAAAAGACAAAA
1158247 AAAAAAGA
1 AAAAAAGA
1158255 AAGGTCTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.85, C:0.06, G:0.06, T:0.03
Consensus pattern (13 bp):
AAAAAAGACAAAA
Found at i:1159462 original size:13 final size:13
Alignment explanation
Indices: 1159425--1159463 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
1159415 CCTTTTGCCA
*
1159425 TTTGTCAAGAAAT
1 TTTGTCAAGAACT
1159438 TATTGTCAAGAACT
1 T-TTGTCAAGAACT
*
1159452 TTTGTCTAGAAC
1 TTTGTCAAGAAC
1159464 ATTCATCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (13 bp):
TTTGTCAAGAACT
Found at i:1159516 original size:28 final size:28
Alignment explanation
Indices: 1159476--1159889 Score: 387
Period size: 28 Copynumber: 14.8 Consensus size: 28
1159466 TCATCTCTTG
*
1159476 AAAGCCCACAAGTCAGTGGTATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
1159504 AAAGCCCACAAGTCAGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
* * * *
1159532 AAAACCCAAAAGTTAGTGGCATCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
*
1159560 AAAGCCCACAAGTTAGTGGCAT-CTCTTC
1 AAAGCCCACAAGTCAGTGGCATCCT-TTC
* * *
1159588 AAAGCCTATAGGTCAGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
*
1159616 AAAGCCCACAAGTCAGCGGCAT-CTCTTC
1 AAAGCCCACAAGTCAGTGGCATCCT-TTC
1159644 AAAG-CCACAAGTCAGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
* * *
1159671 AAAGTCCACAAGTCAGTGGTATCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
* * * * *
1159699 ACAGCTCATAGGTCAGCGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
* * *
1159727 AAAGTCCACAAGTCAGTGGCACCCTTTT
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
* *
1159755 TAATCCCACAAGTCAGTGGCA-CCTTTCC
1 AAAGCCCACAAGTCAGTGGCATCCTTT-C
* * * *
1159783 AAAGCTCACAAG-CAAGCGACA-CTCTTTT
1 AAAGCCCACAAGTC-AGTGGCATC-CTTTC
* *
1159811 TAAGCCCACAAGTC-GATGGCA-CCCTTC
1 AAAGCCCACAAGTCAG-TGGCATCCTTTC
* *
1159838 -CAGCCCACAAGTCAGTGGCAACTCTTTTC
1 AAAGCCCACAAGTCAGTGGC-A-TCCTTTC
*
1159867 AAAGTCCACACAAGTCGGTGGCA
1 AAAG-CC-CACAAGTCAGTGGCA
1159890 ACATTTTTCA
Statistics
Matches: 313, Mismatches: 56, Indels: 31
0.78 0.14 0.08
Matches are distributed among these distances:
26 16 0.05
27 38 0.12
28 230 0.73
29 11 0.04
30 2 0.01
31 3 0.01
32 13 0.04
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.24
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCATCCTTTC
Found at i:1159915 original size:31 final size:31
Alignment explanation
Indices: 1159843--1159964 Score: 115
Period size: 32 Copynumber: 3.8 Consensus size: 31
1159833 CCTTCCAGCC
*
1159843 CACAAGTCAGTGGCAAC-TCTTTTCAAAGTCCA
1 CACAAGTCAGTGGCAACAT-TTTTC-AAGCCCA
*
1159875 CACAAGTCGGTGGCAACATTTTTCAAGCCCA
1 CACAAGTCAGTGGCAACATTTTTCAAGCCCA
* *
1159906 CACAGGTCGGTGGC-ACTTATTTTT-AGAGGCCCA
1 CACAAGTCAGTGGCAAC--ATTTTTCA-A-GCCCA
**
1159939 CACAAGTCAGTGGCAACCCTTTTCAA
1 CACAAGTCAGTGGCAACATTTTTCAA
1159965 AACATCACTT
Statistics
Matches: 76, Mismatches: 7, Indels: 14
0.78 0.07 0.14
Matches are distributed among these distances:
30 2 0.03
31 20 0.26
32 33 0.43
33 19 0.25
34 2 0.03
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (31 bp):
CACAAGTCAGTGGCAACATTTTTCAAGCCCA
Found at i:1160951 original size:20 final size:20
Alignment explanation
Indices: 1160909--1160962 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
1160899 TTTTACCCAG
* * *
1160909 ATGTATCGATACTTTTTTCA
1 ATGTATCGATACATGTATCA
*
1160929 ATGTATCGATACATGTATGA
1 ATGTATCGATACATGTATCA
*
1160949 ATGTATCAATACAT
1 ATGTATCGATACAT
1160963 TCTGTCTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATGTATCA
Found at i:1160972 original size:70 final size:71
Alignment explanation
Indices: 1160859--1161013 Score: 213
Period size: 71 Copynumber: 2.2 Consensus size: 71
1160849 TTTTACCGAG
* * * * * * *
1160859 ATGTATCGATACATTTTTCAATGTGTCGAGATATTCTGTC-TTTTACCCAGATGTATCGATACTT
1 ATGTATCGATACATGTATCAATGTATCAAGACATTCTGTCTTTTTACCCAGATGTATCAATACAT
1160923 TTTTCA
66 TTTTCA
* * *
1160929 ATGTATCGATACATGTATGAATGTATCAATACATTCTGTCTTTTTATCCAGATGTATCAATACAT
1 ATGTATCGATACATGTATCAATGTATCAAGACATTCTGTCTTTTTACCCAGATGTATCAATACAT
1160994 TTTTCA
66 TTTTCA
1161000 ATGTATCGATACAT
1 ATGTATCGATACAT
1161014 CTAGTTAAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
70 33 0.45
71 41 0.55
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (71 bp):
ATGTATCGATACATGTATCAATGTATCAAGACATTCTGTCTTTTTACCCAGATGTATCAATACAT
TTTTCA
Found at i:1172700 original size:51 final size:51
Alignment explanation
Indices: 1172634--1172734 Score: 168
Period size: 51 Copynumber: 2.0 Consensus size: 51
1172624 TGTTCAATTA
1172634 GGTCTCTTTACCAACTTTTTCCATGAAATTGTTTCTTCTAATGCATTCTAT
1 GGTCTCTTTACCAACTTTTTCCATGAAATTGTTTCTTCTAATGCATTCTAT
* *
1172685 GGTC-CTTCTACCAACTTTTTCCGTGACATTGTTTCTTCTAATGCATTCTA
1 GGTCTCTT-TACCAACTTTTTCCATGAAATTGTTTCTTCTAATGCATTCTA
1172735 AACCTTGAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
50 3 0.06
51 44 0.94
ACGTcount: A:0.20, C:0.24, G:0.11, T:0.46
Consensus pattern (51 bp):
GGTCTCTTTACCAACTTTTTCCATGAAATTGTTTCTTCTAATGCATTCTAT
Found at i:1173640 original size:16 final size:16
Alignment explanation
Indices: 1173619--1173650 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1173609 GCTCTCTTCA
1173619 CCATCAATATTTATCG
1 CCATCAATATTTATCG
1173635 CCATCAATATTTATCG
1 CCATCAATATTTATCG
1173651 TGATTGACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (16 bp):
CCATCAATATTTATCG
Found at i:1174211 original size:1 final size:1
Alignment explanation
Indices: 1174205--1174229 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1174195 GCAAACCCTG
1174205 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
1174230 CAACCCTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1177621 original size:38 final size:38
Alignment explanation
Indices: 1177577--1177651 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
1177567 TCTTCATGCA
1177577 CATTGACAAATGTGTCACAAGACCCAAAAAATCATGGT
1 CATTGACAAATGTGTCACAAGACCCAAAAAATCATGGT
1177615 CATTGACAAATGTGTCACAAGACCCAAAAAATCATGG
1 CATTGACAAATGTGTCACAAGACCCAAAAAATCATGG
1177652 CTCAAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.20
Consensus pattern (38 bp):
CATTGACAAATGTGTCACAAGACCCAAAAAATCATGGT
Found at i:1181036 original size:6 final size:6
Alignment explanation
Indices: 1181025--1181057 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1181015 GGCGCAGTGG
*
1181025 TTTGGT TTTGGT TTTGGA TTTGGT TTTGGT TTT
1 TTTGGT TTTGGT TTTGGT TTTGGT TTTGGT TTT
1181058 TAGATCTGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.03, C:0.00, G:0.30, T:0.67
Consensus pattern (6 bp):
TTTGGT
Found at i:1181165 original size:5 final size:5
Alignment explanation
Indices: 1181152--1181184 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
1181142 TGGTTCCAAT
*
1181152 GTCTT GTCTC GTCTC GTCTC GTCTC GTCTC GTC
1 GTCTC GTCTC GTCTC GTCTC GTCTC GTCTC GTC
1181185 GGATTTCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.36, G:0.21, T:0.42
Consensus pattern (5 bp):
GTCTC
Found at i:1183284 original size:20 final size:20
Alignment explanation
Indices: 1183261--1183301 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1183251 ACTTGCATGT
1183261 TATCTCACATATGCTTCTAA
1 TATCTCACATATGCTTCTAA
1183281 TATCTCACATATGCTTCTAA
1 TATCTCACATATGCTTCTAA
1183301 T
1 T
1183302 TTTGTGGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.41
Consensus pattern (20 bp):
TATCTCACATATGCTTCTAA
Found at i:1184063 original size:2 final size:2
Alignment explanation
Indices: 1184056--1184090 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1184046 TTAGTTAATT
*
1184056 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1184091 GCTACTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1184686 original size:21 final size:20
Alignment explanation
Indices: 1184660--1184698 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1184650 AGATCAAAAC
1184660 CCTAGAAAGTATTGATACACA
1 CCTAG-AAGTATTGATACACA
*
1184681 CCTAGATGTATTGATACA
1 CCTAGAAGTATTGATACA
1184699 TGTTCTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (20 bp):
CCTAGAAGTATTGATACACA
Found at i:1184795 original size:10 final size:10
Alignment explanation
Indices: 1184780--1184805 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1184770 TTGATATAAT
1184780 ACTGTTCATC
1 ACTGTTCATC
1184790 ACTGTTCATC
1 ACTGTTCATC
1184800 ACTGTT
1 ACTGTT
1184806 AATGTATCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.27, G:0.12, T:0.42
Consensus pattern (10 bp):
ACTGTTCATC
Found at i:1184816 original size:14 final size:14
Alignment explanation
Indices: 1184797--1184827 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1184787 ATCACTGTTC
1184797 ATCACTGTTAATGT
1 ATCACTGTTAATGT
*
1184811 ATCACTGTTCATGT
1 ATCACTGTTAATGT
1184825 ATC
1 ATC
1184828 GATACATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (14 bp):
ATCACTGTTAATGT
Found at i:1185222 original size:15 final size:15
Alignment explanation
Indices: 1185202--1185246 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
1185192 CATTGTAGAG
1185202 GTTTATTTAGTTTGT
1 GTTTATTTAGTTTGT
1185217 GTTTATTTA-TTT-T
1 GTTTATTTAGTTTGT
* *
1185230 CTTTA-TAAGTTTGT
1 GTTTATTTAGTTTGT
1185244 GTT
1 GTT
1185247 CAACCTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
12 2 0.08
13 8 0.32
14 6 0.24
15 9 0.36
ACGTcount: A:0.16, C:0.02, G:0.16, T:0.67
Consensus pattern (15 bp):
GTTTATTTAGTTTGT
Found at i:1192971 original size:28 final size:28
Alignment explanation
Indices: 1192931--1193344 Score: 405
Period size: 28 Copynumber: 14.8 Consensus size: 28
1192921 TCATCTCTTG
*
1192931 AAAGCCCACAAGTCAGTGGTATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
1192959 AAAGCCCACAAGTCAGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
* * * *
1192987 AAAACCCAAAAGTTAGTGGCATCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
*
1193015 AAAGCCCACAAGTTAGTGGCAT-CTCTTC
1 AAAGCCCACAAGTCAGTGGCATCCT-TTC
* * *
1193043 AAAGCCTATAGGTCAGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
*
1193071 AAAGCCCACAAGTCAGCGGCAT-CTCTTC
1 AAAGCCCACAAGTCAGTGGCATCCT-TTC
1193099 AAAG-CCACAAGTCAGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
* *
1193126 AAAGTCCACAAGTCAGTGGCATCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
* * *
1193154 AAAGCTCATAGGTCAGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
* * *
1193182 AAAGTCCACAAGTCAGTGGCACCCTTTT
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
* * *
1193210 TAATCCCTCAAGTCAGTGGCA-CCTTTCC
1 AAAGCCCACAAGTCAGTGGCATCCTTT-C
* * * *
1193238 AAAGCTCACAAG-CAAGCGACA-CTCTTTT
1 AAAGCCCACAAGTC-AGTGGCATC-CTTTC
* *
1193266 TAAGCCCACAAGTC-GATGGCA-CCCTTC
1 AAAGCCCACAAGTCAG-TGGCATCCTTTC
* *
1193293 -CAGCCCACAAGTCAGTGGCACCTCTTTTC
1 AAAGCCCACAAGTCAGTGGCA--TCCTTTC
*
1193322 AAAGTCCACACAAGTCGGTGGCA
1 AAAG-CC-CACAAGTCAGTGGCA
1193345 ACATTTTTCA
Statistics
Matches: 317, Mismatches: 52, Indels: 30
0.79 0.13 0.08
Matches are distributed among these distances:
26 17 0.05
27 37 0.12
28 234 0.74
29 11 0.03
30 2 0.01
31 2 0.01
32 14 0.04
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCATCCTTTC
Found at i:1193165 original size:111 final size:112
Alignment explanation
Indices: 1192922--1193249 Score: 412
Period size: 111 Copynumber: 2.9 Consensus size: 112
1192912 CTAGAACATT
* * * * *
1192922 CATCTCTTGAAAGCCCACAAGTCAGTGGTATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTC
1 CATCTCTTCAAAGCCTATAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTC
* * *
1192987 AAAACCCAAAAGTTAGTGGCATCTTTTCAAAGCCCACAAGTTAGTGG
66 AAAACCCAAAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGG
*
1193034 CATCTCTTCAAAGCCTATAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGCGGCAT-CTCTT
1 CATCTCTTCAAAGCCTATAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCT-TT
* * *
1193098 C-AAAGCCACAAGTCAGTGGCATCCTTTCAAAGTCCACAAGTCAGTGG
65 CAAAACCCAAAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGG
* * *
1193145 CATCTTTTCAAAG-CTCATAGGTCAGTGGCATCCTTTCAAAGTCCACAAGTCAGTGGCACCCTTT
1 CATCTCTTCAAAGCCT-ATAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTT
** * ** *
1193209 TTAATCCCTCAAGTCAGTGGCA-CCTTTCCAAAGCTCACAAG
65 CAAAACCCAAAAGTCAGTGGCATCCTTT-CAAAGCCCACAAG
1193250 CAAGCGACAC
Statistics
Matches: 189, Mismatches: 22, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
110 2 0.01
111 101 0.53
112 86 0.46
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (112 bp):
CATCTCTTCAAAGCCTATAGGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTC
AAAACCCAAAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGG
Found at i:1193370 original size:31 final size:31
Alignment explanation
Indices: 1193298--1193419 Score: 113
Period size: 32 Copynumber: 3.8 Consensus size: 31
1193288 CCTTCCAGCC
* * *
1193298 CACAAGTCAGTGGC-ACCTCTTTTCAAAGTCCA
1 CACAAGTCGGTGGCAACAT-TTTTC-AAGCCCA
1193330 CACAAGTCGGTGGCAACATTTTTCAAGCCCA
1 CACAAGTCGGTGGCAACATTTTTCAAGCCCA
* *
1193361 CACAGGTCGGTGGC-ACTTATTTTTAAAGGCCCA
1 CACAAGTCGGTGGCAAC--ATTTTTCAA-GCCCA
* **
1193394 CACAAGTCAGTGGCAACCCTTTTCAA
1 CACAAGTCGGTGGCAACATTTTTCAA
1193420 AACATCACTT
Statistics
Matches: 75, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
30 2 0.03
31 19 0.25
32 32 0.43
33 20 0.27
34 2 0.03
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.25
Consensus pattern (31 bp):
CACAAGTCGGTGGCAACATTTTTCAAGCCCA
Found at i:1193398 original size:64 final size:61
Alignment explanation
Indices: 1192937--1193419 Score: 174
Period size: 56 Copynumber: 8.4 Consensus size: 61
1192927 CTTGAAAGCC
* * *
1192937 CACAAGTCAGTGGTATC-C-TTTCAAAGCCCACAAGTCAGTGGCATCC---TTTCAAAACCCA
1 CACAAGTCAGTGGCAACACTTTTC-AAGCCCACAAGTCAGTGGCA-CCTATTTTCAAAGCCCA
* * * * *
1192995 -A-AAGTTAGTGGC-A-TCTTTTCAAAGCCCACAAGTTAGTGGCA--TCTCTTCAAAG-CC-
1 CACAAGTCAGTGGCAACACTTTTC-AAGCCCACAAGTCAGTGGCACCTATTTTCAAAGCCCA
* * * * * * *
1193049 TATAGGTCAGTGGCATC-C-TTTCAAAGCCCACAAGTCAGCGGCA--TCTCTTCAAAG--C-
1 CACAAGTCAGTGGCAACACTTTTC-AAGCCCACAAGTCAGTGGCACCTATTTTCAAAGCCCA
* * * *
1193104 CACAAGTCAGTGGCATC-C-TTTCAAAGTCCACAAGTCAGTGGCA--TCTTTTCAAAG--CT
1 CACAAGTCAGTGGCAACACTTTTC-AAGCCCACAAGTCAGTGGCACCTATTTTCAAAGCCCA
* * * * *
1193160 CATAGGTCAGTGGCATC-C-TTTCAAAGTCCACAAGTCAGTGGCACCCT-TTTT--AA-TCC-
1 CACAAGTCAGTGGCAACACTTTTC-AAGCCCACAAGTCAGTGGCA-CCTATTTTCAAAGCCCA
* * * * *
1193216 CTCAAGTCAGTGGC-AC-CTTTCCAAAGCTCACAAG-CAAGCGACACTCT-TTTT--AAG-CC-
1 CACAAGTCAGTGGCAACACTTTTC-AAGCCCACAAGTC-AGTGGCAC-CTATTTTCAAAGCCCA
* * * *
1193272 CACAAGTC-GATGGC-AC-C-CTTCCAGCCCACAAGTCAGTGGCACCTCTTTTCAAAGTCCA
1 CACAAGTCAG-TGGCAACACTTTTCAAGCCCACAAGTCAGTGGCACCTATTTTCAAAGCCCA
* * * * *
1193330 CACAAGTCGGTGGCAACATTTTTCAAGCCCACACAGGTCGGTGGCACTTATTTTTAAAGGCCCA
1 CACAAGTCAGTGGCAACACTTTTCAAGCCCACA-A-GTCAGTGGCACCTATTTTCAAA-GCCCA
*
1193394 CACAAGTCAGTGGCAACCCTTTTCAA
1 CACAAGTCAGTGGCAACACTTTTCAA
1193420 AACATCACTT
Statistics
Matches: 346, Mismatches: 46, Indels: 60
0.77 0.10 0.13
Matches are distributed among these distances:
53 2 0.01
54 19 0.05
55 62 0.18
56 181 0.52
57 5 0.01
58 16 0.05
59 4 0.01
61 11 0.03
62 1 0.00
63 18 0.05
64 27 0.08
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (61 bp):
CACAAGTCAGTGGCAACACTTTTCAAGCCCACAAGTCAGTGGCACCTATTTTCAAAGCCCA
Found at i:1193407 original size:33 final size:31
Alignment explanation
Indices: 1193298--1193408 Score: 116
Period size: 31 Copynumber: 3.5 Consensus size: 31
1193288 CCTTCCAGCC
* * *
1193298 CACAAGTCAGTGGCACCTCTTTTCAAAGTCCA
1 CACAAGTCAGTGGCA-CTATTTTTAAAGCCCA
* *
1193330 CACAAGTCGGTGGCAAC-ATTTTTCAAGCCCA
1 CACAAGTCAGTGGC-ACTATTTTTAAAGCCCA
* *
1193361 CACAGGTCGGTGGCACTTATTTTTAAAGGCCCA
1 CACAAGTCAGTGGCAC-TATTTTTAAA-GCCCA
1193394 CACAAGTCAGTGGCA
1 CACAAGTCAGTGGCA
1193409 ACCCTTTTCA
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
30 2 0.03
31 23 0.35
32 22 0.33
33 19 0.29
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (31 bp):
CACAAGTCAGTGGCACTATTTTTAAAGCCCA
Found at i:1194390 original size:20 final size:20
Alignment explanation
Indices: 1194365--1194418 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1194355 TTTTACCTAG
* * *
1194365 ATGTATCGATACTTTTTTCA
1 ATGTATCGATACATGTATCA
*
1194385 ATGTATCGATACATGTATGA
1 ATGTATCGATACATGTATCA
1194405 ATGTATCGATACAT
1 ATGTATCGATACAT
1194419 TCTGTCTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATGTATCA
Found at i:1194428 original size:70 final size:71
Alignment explanation
Indices: 1194315--1194469 Score: 215
Period size: 71 Copynumber: 2.2 Consensus size: 71
1194305 TTTTACCGAG
* * * * * *
1194315 ATGTATCGATACATTTTTCAATGTGTCGAGATATTCTGTC-TTTTA-CCTAGATGTATCGATACT
1 ATGTATCGATACATGTATCAATGTATCGAGACATTCTGTCTTTTTATCC-AGATGTATCAATACA
1194378 TTTTTCA
65 TTTTTCA
* *
1194385 ATGTATCGATACATGTATGAATGTATCGATACATTCTGTCTTTTTATCCAGATGTATCAATACAT
1 ATGTATCGATACATGTATCAATGTATCGAGACATTCTGTCTTTTTATCCAGATGTATCAATACAT
1194450 TTTTCA
66 TTTTCA
1194456 ATGTATCGATACAT
1 ATGTATCGATACAT
1194470 CTAGTTAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
70 34 0.45
71 39 0.52
72 2 0.03
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (71 bp):
ATGTATCGATACATGTATCAATGTATCGAGACATTCTGTCTTTTTATCCAGATGTATCAATACAT
TTTTCA
Found at i:1200541 original size:13 final size:13
Alignment explanation
Indices: 1200523--1200548 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1200513 TACACAAAGT
1200523 ATGTATCGATACA
1 ATGTATCGATACA
1200536 ATGTATCGATACA
1 ATGTATCGATACA
1200549 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1200546 original size:32 final size:33
Alignment explanation
Indices: 1200505--1200568 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1200495 TAGCCAAACT
**
1200505 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1200537 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1200569 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1211050 original size:38 final size:38
Alignment explanation
Indices: 1211001--1211075 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
1210991 TCTTCATGCA
*
1211001 CATTGACAAATGCGTCACAAGACCCAAAAAATCATGGT
1 CATTGAAAAATGCGTCACAAGACCCAAAAAATCATGGT
*
1211039 CATTGAAAAATGTGTCACAAGACCCAAAAAATCATGG
1 CATTGAAAAATGCGTCACAAGACCCAAAAAATCATGG
1211076 CTCAAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.44, C:0.21, G:0.16, T:0.19
Consensus pattern (38 bp):
CATTGAAAAATGCGTCACAAGACCCAAAAAATCATGGT
Found at i:1216683 original size:20 final size:20
Alignment explanation
Indices: 1216660--1216700 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1216650 ACTTGCATGT
1216660 TATCTCACATATGCTTCTAA
1 TATCTCACATATGCTTCTAA
1216680 TATCTCACATATGCTTCTAA
1 TATCTCACATATGCTTCTAA
1216700 T
1 T
1216701 TTTGTGGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.41
Consensus pattern (20 bp):
TATCTCACATATGCTTCTAA
Found at i:1217463 original size:2 final size:2
Alignment explanation
Indices: 1217456--1217482 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1217446 TTAGTTAATT
1217456 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 T
1217483 TTATCTGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1220535 original size:18 final size:18
Alignment explanation
Indices: 1220512--1220557 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1220502 CCTCGCAATC
*
1220512 CTGGGATTTGTGGTATTG
1 CTGGGATTTGTGGGATTG
*
1220530 CTGGGATTTTTGGGATTG
1 CTGGGATTTGTGGGATTG
*
1220548 CCGGGATTTG
1 CTGGGATTTG
1220558 GATTTTTGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.11, C:0.09, G:0.39, T:0.41
Consensus pattern (18 bp):
CTGGGATTTGTGGGATTG
Found at i:1220545 original size:9 final size:9
Alignment explanation
Indices: 1220531--1220610 Score: 64
Period size: 9 Copynumber: 9.6 Consensus size: 9
1220521 GTGGTATTGC
1220531 TGGGATTTT
1 TGGGATTTT
**
1220540 TGGGATTGC
1 TGGGATTTT
*
1220549 CGGGA--TT
1 TGGGATTTT
1220556 T-GGATTTT
1 TGGGATTTT
*
1220564 TGGGATTGT
1 TGGGATTTT
*
1220573 GGGGA--TT
1 TGGGATTTT
1220580 T-GGATTTT
1 TGGGATTTT
1220588 TGGGATTTT
1 TGGGATTTT
*
1220597 TGGAATTTT
1 TGGGATTTT
1220606 TGGGA
1 TGGGA
1220611 AGCGTAAAGT
Statistics
Matches: 53, Mismatches: 12, Indels: 12
0.69 0.16 0.16
Matches are distributed among these distances:
6 6 0.11
7 1 0.02
8 6 0.11
9 40 0.75
ACGTcount: A:0.14, C:0.03, G:0.38, T:0.46
Consensus pattern (9 bp):
TGGGATTTT
Found at i:1220604 original size:24 final size:24
Alignment explanation
Indices: 1220533--1220594 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
1220523 GGTATTGCTG
*
1220533 GGATTTTTGGGATTGCCGGGATTT
1 GGATTTTTGGGATTGTCGGGATTT
*
1220557 GGATTTTTGGGATTGTGGGGATTT
1 GGATTTTTGGGATTGTCGGGATTT
1220581 GGATTTTTGGGATT
1 GGATTTTTGGGATT
1220595 TTTGGAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.13, C:0.03, G:0.39, T:0.45
Consensus pattern (24 bp):
GGATTTTTGGGATTGTCGGGATTT
Found at i:1220814 original size:84 final size:84
Alignment explanation
Indices: 1220706--1220892 Score: 243
Period size: 84 Copynumber: 2.2 Consensus size: 84
1220696 TCCAGTGCCT
* ** * * *
1220706 CCATTTCCAATGCCTTCACCTTCACCATATCCAATATTACCTGGT-CCTGATCCAATTCCATAAC
1 CCATTTCCAATGCCTTCACATTCACCATATCCAATACCACCT-GTCCCTAATCCAATACCACAAC
* *
1220770 AATGTCTAT-GACCACTTCCC
65 AATGTCCATAG-CCACTTCCA
* *
1220790 CCATTTCTAATGCCTTCACATTCACCATATCCAATACCACCTGTCCCTAATCCAATACCACAACC
1 CCATTTCCAATGCCTTCACATTCACCATATCCAATACCACCTGTCCCTAATCCAATACCACAACA
*
1220855 ATGTCCATAGCCAGTTCCA
66 ATGTCCATAGCCACTTCCA
1220874 CCATTTCCAATGCCTTCAC
1 CCATTTCCAATGCCTTCAC
1220893 CATAGCCAAT
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
83 2 0.02
84 86 0.97
85 1 0.01
ACGTcount: A:0.27, C:0.37, G:0.06, T:0.29
Consensus pattern (84 bp):
CCATTTCCAATGCCTTCACATTCACCATATCCAATACCACCTGTCCCTAATCCAATACCACAACA
ATGTCCATAGCCACTTCCA
Found at i:1225616 original size:36 final size:35
Alignment explanation
Indices: 1225552--1225623 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 35
1225542 AGATAAGAAC
*
1225552 CTCCCTATCTTTTCACGGACTAAAATAGAACATCT
1 CTCCCTATCTTTTCAAGGACTAAAATAGAACATCT
* *
1225587 CTCCCTATCTTTTTCAAAGG-CTAAGATAGAACCTCT
1 CTCCCTATC-TTTTC-AAGGACTAAAATAGAACATCT
1225623 C
1 C
1225624 AATCACTTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 9 0.28
36 20 0.62
37 3 0.09
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (35 bp):
CTCCCTATCTTTTCAAGGACTAAAATAGAACATCT
Found at i:1226100 original size:20 final size:20
Alignment explanation
Indices: 1226075--1226126 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1226065 GTTGAGCTCA
1226075 ATGTATCGATACTATTCACC
1 ATGTATCGATACTATTCACC
*
1226095 ATGTATTGATACTATTCACC
1 ATGTATCGATACTATTCACC
1226115 ATGTATCGATAC
1 ATGTATCGATAC
1226127 ATGAACAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACTATTCACC
Found at i:1226182 original size:24 final size:24
Alignment explanation
Indices: 1226123--1226183 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
1226113 CCATGTATCG
* *
1226123 ATACATGAACAATGATGAATAATG
1 ATACATGAACAGTGATGAATAATA
*
1226147 ATACATGAACAGTGATGAATAGTA
1 ATACATGAACAGTGATGAATAATA
*
1226171 ATACATAAACAGT
1 ATACATGAACAGT
1226184 AATATATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.25
Consensus pattern (24 bp):
ATACATGAACAGTGATGAATAATA
Found at i:1227148 original size:32 final size:31
Alignment explanation
Indices: 1227111--1227179 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 31
1227101 TATTTTGTAA
*
1227111 CTAATACCAAAAGTTTATGCAAGCTCTCC-CC
1 CTAATA-CAAAAGTTTATGCAAACTCTCCTCC
* *
1227142 CTTAATA-TAAATTTTATGCAAACTCTCCTCC
1 C-TAATACAAAAGTTTATGCAAACTCTCCTCC
1227173 CTAATAC
1 CTAATAC
1227180 GTTCTCACCC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
30 23 0.72
31 4 0.12
32 5 0.16
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.32
Consensus pattern (31 bp):
CTAATACAAAAGTTTATGCAAACTCTCCTCC
Found at i:1229408 original size:21 final size:21
Alignment explanation
Indices: 1229384--1229441 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
1229374 TTTATTAGTT
*
1229384 AACTCA-TCATTTTCATTTTGC
1 AACTCATTCATTTTC-TTTTCC
1229405 AACTCATTTC-TTTTCTTTTCC
1 AACTCA-TTCATTTTCTTTTCC
1229426 AACTCATTCATTTTCT
1 AACTCATTCATTTTCT
1229442 CCTCTAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 3 0.09
21 23 0.70
22 5 0.15
23 2 0.06
ACGTcount: A:0.21, C:0.26, G:0.02, T:0.52
Consensus pattern (21 bp):
AACTCATTCATTTTCTTTTCC
Found at i:1231082 original size:32 final size:34
Alignment explanation
Indices: 1231037--1231126 Score: 107
Period size: 36 Copynumber: 2.7 Consensus size: 34
1231027 CAATACTATC
1231037 TTTC-AAGGCTAAGATAGAAACCTCT-CTATC-T
1 TTTCAAAGGCTAAGATAGAAACCTCTCCTATCTT
** *
1231068 TTTCACGGGCTAAGATAGAACCTCTCTCCCTATCTT
1 TTTCAAAGGCTAAGATAGAAAC-CTCT-CCTATCTT
1231104 TTTCAAAGGCTAAGATA-AAACCT
1 TTTCAAAGGCTAAGATAGAAACCT
1231127 TTCAATTACT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
31 4 0.08
32 14 0.29
33 4 0.08
34 2 0.04
35 8 0.17
36 16 0.33
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.31
Consensus pattern (34 bp):
TTTCAAAGGCTAAGATAGAAACCTCTCCTATCTT
Found at i:1231614 original size:14 final size:14
Alignment explanation
Indices: 1231594--1231646 Score: 79
Period size: 14 Copynumber: 3.8 Consensus size: 14
1231584 ATGTATCGAA
* *
1231594 ACATGAAAAATGAT
1 ACATGAACAGTGAT
*
1231608 GCATGAACAGTGAT
1 ACATGAACAGTGAT
1231622 ACATGAACAGTGAT
1 ACATGAACAGTGAT
1231636 ACATGAACAGT
1 ACATGAACAGT
1231647 AATGTATCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.21
Consensus pattern (14 bp):
ACATGAACAGTGAT
Found at i:1239231 original size:69 final size:68
Alignment explanation
Indices: 1239108--1239258 Score: 225
Period size: 69 Copynumber: 2.2 Consensus size: 68
1239098 CCTCTGAAGA
*
1239108 GATACTCCAACCCCATTTTTAAACTCATCAAAATTTAAATCTCATTTTGTCCAAATTATCATTGT
1 GATACTCCAA-CCCATTTTTAAACTCATCAAAATTTAAATCTCATTTTGACCAAATTATCATT-T
1239173 T-GGG
64 TCGGG
*
1239177 GATACTCCAACCC-TGTTTTAAACTCATCAAAATTTAAAGTCTTATTTTGACCAAATTATCATTT
1 GATACTCCAACCCAT-TTTTAAACTCATCAAAATTTAAA-TCTCATTTTGACCAAATTATCATTT
1239241 TCGGG
64 TCGGG
*
1239246 GATACTCTAACCC
1 GATACTCCAACCC
1239259 CATTCCTCTG
Statistics
Matches: 76, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
67 1 0.01
68 28 0.37
69 47 0.62
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (68 bp):
GATACTCCAACCCATTTTTAAACTCATCAAAATTTAAATCTCATTTTGACCAAATTATCATTTTC
GGG
Found at i:1239991 original size:16 final size:16
Alignment explanation
Indices: 1239970--1240005 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
1239960 AAATGATCGA
1239970 TGGTGACTCCAAATCT
1 TGGTGACTCCAAATCT
1239986 TGGTGACTCCAAATCT
1 TGGTGACTCCAAATCT
1240002 TGGT
1 TGGT
1240006 CACTTCATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (16 bp):
TGGTGACTCCAAATCT
Found at i:1246768 original size:33 final size:32
Alignment explanation
Indices: 1246726--1246790 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1246716 CACACCCAGA
* *
1246726 TGTATCGATACATGCTGCTTTGTATTGATACAT
1 TGTATCGATACATG-TGCATTGTATCGATACAT
*
1246759 TGTATCGATACATGTTCATTGTATCGATACAT
1 TGTATCGATACATGTGCATTGTATCGATACAT
1246791 GGCCAAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (32 bp):
TGTATCGATACATGTGCATTGTATCGATACAT
Found at i:1246802 original size:21 final size:19
Alignment explanation
Indices: 1246756--1246812 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1246746 TGTATTGATA
**
1246756 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGGC
1246775 CATTGTATCGATACATGGC
1 CATTGTATCGATACATGGC
*
1246794 CAAATTGTATCCATACATG
1 C--ATTGTATCGATACATG
1246813 AAACTAGCAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 18 0.55
21 15 0.45
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (19 bp):
CATTGTATCGATACATGGC
Found at i:1246878 original size:13 final size:13
Alignment explanation
Indices: 1246857--1246887 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1246847 GGATACATGG
*
1246857 TACAATGTATCGA
1 TACATTGTATCGA
1246870 TACATTGTATCGA
1 TACATTGTATCGA
1246883 TACAT
1 TACAT
1246888 GAAGAAATGT
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:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:1246885 original size:33 final size:32
Alignment explanation
Indices: 1246841--1246907 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 32
1246831 CTATCACTAT
*
1246841 TTGTATGGATACATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
1246874 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
1246907 T
1 T
1246908 AGCATGTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:1250061 original size:29 final size:28
Alignment explanation
Indices: 1250000--1250250 Score: 281
Period size: 29 Copynumber: 8.6 Consensus size: 28
1249990 CATTAATACT
* *
1250000 ACCCTTTTCAAAGCACACATGTCA-TGGC
1 ACCC-TTTCAAAGCCCACAAGTCAGTGGC
* *
1250028 ACCCTTTCAAATCCCACAAGTTAGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGC
1250056 AACCCTTTTCAAAGCCCACAAGTCAGTGGC
1 -ACCC-TTTCAAAGCCCACAAGTCAGTGGC
*
1250086 ACTCTTTTCAAAGCCCACAAGTCAGTGGC
1 AC-CCTTTCAAAGCCCACAAGTCAGTGGC
* *
1250115 ACTCTTTTCAAAGCCCACAAGTCAGTAGC
1 AC-CCTTTCAAAGCCCACAAGTCAGTGGC
* *
1250144 ACCATTTTCAAAGCCCACATGTCAGTGGC
1 ACC-CTTTCAAAGCCCACAAGTCAGTGGC
* *
1250173 ACCCTTTCAAAGCCCATAAGTCAATGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGC
*
1250201 ACCCTTTCAAAGCCCACACAAGT-TGATGGC
1 ACCCTTTCAAAG-CC-CACAAGTCAG-TGGC
1250231 ACCCTTCTCAAAAGCCCACA
1 ACCCTT-TC-AAAGCCCACA
1250251 CAAGTTGATG
Statistics
Matches: 196, Mismatches: 17, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
27 15 0.08
28 42 0.21
29 88 0.45
30 43 0.22
31 4 0.02
32 4 0.02
ACGTcount: A:0.30, C:0.33, G:0.15, T:0.22
Consensus pattern (28 bp):
ACCCTTTCAAAGCCCACAAGTCAGTGGC
Found at i:1251473 original size:20 final size:20
Alignment explanation
Indices: 1251401--1251475 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
1251391 TTTTACCCAG
*
1251401 ATGTATTGATAC-TTTTTTCA
1 ATGTATCGATACATTTTTT-A
* * *
1251421 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTTA
1251441 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTTTTTA
1251461 ATGTATCGATACATT
1 ATGTATCGATACATT
1251476 CTGCTTTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 44 0.94
21 3 0.06
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (20 bp):
ATGTATCGATACATTTTTTA
Found at i:1254191 original size:17 final size:15
Alignment explanation
Indices: 1254171--1254220 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 15
1254161 TTAGGTAAAA
1254171 AAGAAAGAAAGAAGATG
1 AAGAAAGAAAGAA-A-G
1254188 AAG-AAGAAAGAAAG
1 AAGAAAGAAAGAAAG
*
1254202 AA-AAAGAAA-AAAA
1 AAGAAAGAAAGAAAG
1254215 AAGAAA
1 AAGAAA
1254221 AAAATATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 5 0.17
14 12 0.40
15 1 0.03
16 9 0.30
17 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (15 bp):
AAGAAAGAAAGAAAG
Done.