Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 8 of 255
Found at i:2394039 original size:22 final size:22
Alignment explanation
Indices: 2394023--2394076 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
2394013 ATTTTTTTTA
2394023 AATATTTATATTATTTTAATTT
1 AATATTTATATTATTTTAATTT
*
2394045 AATATTTATA--ATTTT-ATAT
1 AATATTTATATTATTTTAATTT
2394064 AAT-TTTAT-TTATT
1 AATATTTATATTATT
2394077 AATTTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.17
19 9 0.31
20 5 0.17
22 10 0.34
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
AATATTTATATTATTTTAATTT
Found at i:2394074 original size:14 final size:14
Alignment explanation
Indices: 2394025--2394087 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 14
2394015 TTTTTTTAAA
*
2394025 TATTTATATTATTT
1 TATTTATATAATTT
2394039 TAATTTA-AT-ATTT
1 T-ATTTATATAATTT
2394052 ATAATTTTATATAATTT
1 -T-A-TTTATATAATTT
2394069 TATTTAT-TAATTT
1 TATTTATATAATTT
*
2394082 TTTTTA
1 TATTTA
2394088 CATAGACATC
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
13 15 0.35
14 11 0.26
15 10 0.23
16 3 0.07
17 4 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTATATAATTT
Found at i:2394081 original size:13 final size:12
Alignment explanation
Indices: 2394033--2394087 Score: 53
Period size: 13 Copynumber: 4.6 Consensus size: 12
2394023 AATATTTATA
2394033 TTATTT-TAATT
1 TTATTTATAATT
2394044 TAATATTTATAATT
1 T--TATTTATAATT
2394058 TTA--TATAATT
1 TTATTTATAATT
2394068 TTATTTATTAATT
1 TTATTTA-TAATT
*
2394081 TTTTTTA
1 TTATTTA
2394088 CATAGACATC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
10 10 0.27
11 1 0.03
12 4 0.11
13 16 0.43
14 6 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTATTTATAATT
Found at i:2394480 original size:19 final size:19
Alignment explanation
Indices: 2394437--2394481 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
2394427 GGACTAAATG
* *
2394437 TTGGTAGATATTTTATCTG
1 TTGGTGGATATTTTATCTC
2394456 TTGGTGGATATTTTATCTC
1 TTGGTGGATATTTTATCTC
2394475 TTGGTGG
1 TTGGTGG
2394482 TTGATTTGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.16, C:0.07, G:0.27, T:0.51
Consensus pattern (19 bp):
TTGGTGGATATTTTATCTC
Found at i:2398876 original size:40 final size:40
Alignment explanation
Indices: 2398803--2398878 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
2398793 AAAACAAATA
*
2398803 TTAAAACAAGAAACAAATAAAAATGATATTAAAAAAATTC
1 TTAAAACAAGAAACAAATAAAAATGATAATAAAAAAATTC
* * *
2398843 TTAAAACAATACACAAATTGAAAAT-ATAATAAAAAA
1 TTAAAACAAGAAACAAA-TAAAAATGATAATAAAAAA
2398879 TGATTATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 25 0.81
41 6 0.19
ACGTcount: A:0.66, C:0.08, G:0.04, T:0.22
Consensus pattern (40 bp):
TTAAAACAAGAAACAAATAAAAATGATAATAAAAAAATTC
Found at i:2407466 original size:11 final size:10
Alignment explanation
Indices: 2407430--2407494 Score: 55
Period size: 10 Copynumber: 6.5 Consensus size: 10
2407420 TTTTAGAAAA
2407430 TTTTA-AATT
1 TTTTATAATT
*
2407439 TTTGA-AATT
1 TTTTATAATT
2407448 TCTTTATATATT
1 T-TTTATA-ATT
2407460 TTTTATAATT
1 TTTTATAATT
**
2407470 TTTT-TGAAAA
1 TTTTAT-AATT
2407480 TTTTATAATT
1 TTTTATAATT
2407490 TTTTA
1 TTTTA
2407495 AAAGATATGA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
9 10 0.22
10 23 0.51
11 8 0.18
12 4 0.09
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.65
Consensus pattern (10 bp):
TTTTATAATT
Found at i:2407713 original size:14 final size:14
Alignment explanation
Indices: 2407694--2407723 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2407684 TGACTCAAAT
2407694 AATTCAAATAACTC
1 AATTCAAATAACTC
*
2407708 AATTCAATTAACTC
1 AATTCAAATAACTC
2407722 AA
1 AA
2407724 AATTTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (14 bp):
AATTCAAATAACTC
Found at i:2408023 original size:15 final size:15
Alignment explanation
Indices: 2408005--2408040 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2407995 ACGAATCGAA
*
2408005 TCGAGTCAAAAAATT
1 TCGAGTCAAAAAATG
*
2408020 TCGAGTCAAATAATG
1 TCGAGTCAAAAAATG
2408035 TCGAGT
1 TCGAGT
2408041 TAACGAATCC
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:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (15 bp):
TCGAGTCAAAAAATG
Found at i:2410674 original size:12 final size:12
Alignment explanation
Indices: 2410641--2410674 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2410631 TTCCCTGTAA
*
2410641 AATAGTAAAAAT
1 AATAGTAAAGAT
*
2410653 AATAATAAAGAT
1 AATAGTAAAGAT
2410665 AATAGTAAAG
1 AATAGTAAAG
2410675 GGGAAGTAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (12 bp):
AATAGTAAAGAT
Found at i:2411636 original size:27 final size:26
Alignment explanation
Indices: 2411606--2411668 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
2411596 GGATAATTAA
2411606 AATAAAATCCTAAAATTAAATAATCCT
1 AATAAAATCCTAAAATT-AATAATCCT
* * * *
2411633 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCCTAAAATTAATAATCCT
2411660 AATATAAAT
1 AATA-AAAT
2411669 AAAATGGAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 19 0.66
28 10 0.34
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (26 bp):
AATAAAATCCTAAAATTAATAATCCT
Found at i:2411655 original size:15 final size:15
Alignment explanation
Indices: 2411635--2411664 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2411625 ATAATCCTAA
*
2411635 TAATTATCTTAATAT
1 TAATTATCCTAATAT
2411650 TAATTATCCTAATAT
1 TAATTATCCTAATAT
2411665 AAATAAAATG
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):
TAATTATCCTAATAT
Found at i:2412186 original size:9 final size:9
Alignment explanation
Indices: 2412172--2412204 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
2412162 ATTAATATAA
2412172 TTTTTTTTC
1 TTTTTTTTC
2412181 --TTTTTTC
1 TTTTTTTTC
2412188 TTTTTTTTC
1 TTTTTTTTC
2412197 TTTTTTTT
1 TTTTTTTT
2412205 TATAGAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.32
9 15 0.68
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:2412191 original size:16 final size:16
Alignment explanation
Indices: 2412172--2412202 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2412162 ATTAATATAA
2412172 TTTTTTTTCTTTTTTC
1 TTTTTTTTCTTTTTTC
2412188 TTTTTTTTCTTTTTT
1 TTTTTTTTCTTTTTT
2412203 TTTATAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (16 bp):
TTTTTTTTCTTTTTTC
Found at i:2412403 original size:96 final size:97
Alignment explanation
Indices: 2412230--2412408 Score: 288
Period size: 96 Copynumber: 1.9 Consensus size: 97
2412220 TAATTTATTT
* * *
2412230 ATTTTTACTTAAGAATATATTGAACCTTTGGACGCGAAGAGAGATGACAGCCAAGCACCCCACCC
1 ATTTTTACCTAAGAACATATCGAACCTTTGGACGCGAAGAGAGATGACAGCCAAGCACCCCACCC
2412295 CAGTTACTCAGCCCAACATACTCCTGATTTTG
66 CAGTTACTCAGCCCAACATACTCCTGATTTTG
* *
2412327 ATTTTT-CCTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCTCACCC
1 ATTTTTACCTAAGAACATATCGAACCTTTGGACGCGAAGAGAGATGACAGCCAAGCACCCCACCC
**
2412391 GGGTTACTCAGCCCAACA
66 CAGTTACTCAGCCCAACA
2412409 CATTCTTAGA
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
96 69 0.92
97 6 0.08
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.23
Consensus pattern (97 bp):
ATTTTTACCTAAGAACATATCGAACCTTTGGACGCGAAGAGAGATGACAGCCAAGCACCCCACCC
CAGTTACTCAGCCCAACATACTCCTGATTTTG
Found at i:2413162 original size:18 final size:17
Alignment explanation
Indices: 2413131--2413181 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
2413121 AATATCTGAA
*
2413131 AATAATAAATAATAAAAT
1 AATAA-AAAAAATAAAAT
2413149 AATAAGAAAAAATAAAAT
1 AATAA-AAAAAATAAAAT
*
2413167 AA-AATAAAAATAAAA
1 AATAAAAAAAATAAAA
2413182 ATTGGGTTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
16 10 0.33
17 2 0.07
18 18 0.60
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (17 bp):
AATAAAAAAAATAAAAT
Found at i:2413176 original size:11 final size:11
Alignment explanation
Indices: 2413134--2413181 Score: 53
Period size: 11 Copynumber: 4.2 Consensus size: 11
2413124 ATCTGAAAAT
2413134 AATAAATAATAA
1 AATAAA-AATAA
*
2413146 AATAATAAGAAAA
1 AATAA-AA-ATAA
2413159 AAT-AAAATAA
1 AATAAAAATAA
2413169 AATAAAAATAA
1 AATAAAAATAA
2413180 AA
1 AA
2413182 ATTGGGTTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
10 6 0.19
11 11 0.35
12 7 0.23
13 7 0.23
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:2418667 original size:12 final size:12
Alignment explanation
Indices: 2418634--2418667 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2418624 TTCCCTGTAA
*
2418634 AATAGTAAAAAT
1 AATAGTAAAGAT
*
2418646 AATAATAAAGAT
1 AATAGTAAAGAT
2418658 AATAGTAAAG
1 AATAGTAAAG
2418668 GGGAAGTAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (12 bp):
AATAGTAAAGAT
Found at i:2419624 original size:27 final size:26
Alignment explanation
Indices: 2419594--2419656 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 26
2419584 GGATAATTAA
2419594 AATAAAATCCTAAAATTAAATAATCCT
1 AATAAAATCCTAAAATTAAATAA-CCT
* * * *
2419621 AATAATTATCTTAATATTAATTAACCT
1 AATAA-AATCCTAAAATTAAATAACCT
2419648 AATATAAAT
1 AATA-AAAT
2419657 AAAATGGAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 14 0.48
28 15 0.52
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (26 bp):
AATAAAATCCTAAAATTAAATAACCT
Found at i:2425646 original size:18 final size:17
Alignment explanation
Indices: 2425621--2425666 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
2425611 ATTCTGTTAT
*
2425621 TTATTTATTTATTATTA
1 TTATTTATTTACTATTA
*
2425638 TTATGTTATTTACTGTTA
1 TTAT-TTATTTACTATTA
2425656 TTATTATATTT
1 TTATT-TATTT
2425667 TTTTGCATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (17 bp):
TTATTTATTTACTATTA
Found at i:2425940 original size:17 final size:16
Alignment explanation
Indices: 2425908--2425945 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
2425898 ATATTGTATT
2425908 TATATATATTATTATG
1 TATATATATTATTATG
*
2425924 TATATATTTTAATTATG
1 TATATATATT-ATTATG
2425941 TATAT
1 TATAT
2425946 TTCTAATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (16 bp):
TATATATATTATTATG
Found at i:2425963 original size:19 final size:19
Alignment explanation
Indices: 2425939--2425976 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2425929 ATTTTAATTA
*
2425939 TGTATATTTCTAATATCAT
1 TGTATATTTCTAACATCAT
2425958 TGTATATTTCTAACATCAT
1 TGTATATTTCTAACATCAT
2425977 CATTATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.13, G:0.05, T:0.50
Consensus pattern (19 bp):
TGTATATTTCTAACATCAT
Found at i:2426093 original size:13 final size:12
Alignment explanation
Indices: 2426050--2426094 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
2426040 TCGTTTCTAA
2426050 TATATATGTGTAT
1 TATATATGT-TAT
* *
2426063 CATATATGTTTT
1 TATATATGTTAT
2426075 TATATATGTTAT
1 TATATATGTTAT
2426087 GTATATAT
1 -TATATAT
2426095 CTTTAGTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 12 0.44
13 15 0.56
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56
Consensus pattern (12 bp):
TATATATGTTAT
Found at i:2426099 original size:23 final size:25
Alignment explanation
Indices: 2426050--2426099 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 25
2426040 TCGTTTCTAA
* *
2426050 TATATATGTGTATCATATATGTTTT
1 TATATATGTGTATCATATATATCTT
*
2426075 TATATATGT-TAT-GTATATATCTT
1 TATATATGTGTATCATATATATCTT
2426098 TA
1 TA
2426100 GTATTATTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 10 0.45
24 3 0.14
25 9 0.41
ACGTcount: A:0.30, C:0.04, G:0.10, T:0.56
Consensus pattern (25 bp):
TATATATGTGTATCATATATATCTT
Found at i:2426467 original size:21 final size:21
Alignment explanation
Indices: 2426443--2426494 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
2426433 ACTATTATTT
* *
2426443 TATTTATTTTTATTCCTAGTA
1 TATTTATTTTTAATACTAGTA
*
2426464 TATTT-TTTATTAATATTAGTA
1 TATTTATTT-TTAATACTAGTA
*
2426485 TATGTATTTT
1 TATTTATTTT
2426495 ATTATACGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 3 0.12
21 19 0.76
22 3 0.12
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (21 bp):
TATTTATTTTTAATACTAGTA
Found at i:2429045 original size:14 final size:14
Alignment explanation
Indices: 2429026--2429052 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2429016 AGCGTTTGAT
2429026 CGAATTGAGTGAAC
1 CGAATTGAGTGAAC
2429040 CGAATTGAGTGAA
1 CGAATTGAGTGAA
2429053 AAATTTTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.30, T:0.22
Consensus pattern (14 bp):
CGAATTGAGTGAAC
Found at i:2429340 original size:10 final size:10
Alignment explanation
Indices: 2429325--2429353 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2429315 TCTCAAAATT
2429325 ATTATTTTAA
1 ATTATTTTAA
2429335 ATTATTTTAA
1 ATTATTTTAA
2429345 ATT-TTTTAA
1 ATTATTTTAA
2429354 CTTTCTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTATTTTAA
Found at i:2429402 original size:18 final size:18
Alignment explanation
Indices: 2429379--2429432 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
2429369 TTTAGAATTT
2429379 ATTTTTGAAAATTTTATA
1 ATTTTTGAAAATTTTATA
* **
2429397 ATTTTTTAAAA-AATATA
1 ATTTTTGAAAATTTTATA
* *
2429414 AATTTTGAAATTTTTATA
1 ATTTTTGAAAATTTTATA
2429432 A
1 A
2429433 ATATTTTGAG
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (18 bp):
ATTTTTGAAAATTTTATA
Found at i:2432379 original size:22 final size:21
Alignment explanation
Indices: 2432354--2432407 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
2432344 ATTTTTTAAA
*
2432354 AATATTTATATTATTTTAATTT
1 AATATTTATATTATTTT-ATAT
2432376 AATATTTATA--ATTTTATAT
1 AATATTTATATTATTTTATAT
2432395 AAT-TTTAT-TTATT
1 AATATTTATATTATT
2432408 AATTTTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.17
19 9 0.31
20 5 0.17
22 10 0.34
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
AATATTTATATTATTTTATAT
Found at i:2432405 original size:14 final size:14
Alignment explanation
Indices: 2432356--2432417 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 14
2432346 TTTTTAAAAA
*
2432356 TATTTATATTATTT
1 TATTTATATAATTT
2432370 TAATTTA-AT-ATTT
1 T-ATTTATATAATTT
2432383 ATAATTTTATATAATTT
1 -T-A-TTTATATAATTT
2432400 TATTTAT-TAATTT
1 TATTTATATAATTT
2432413 T-TTTA
1 TATTTA
2432418 CATATACATC
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
12 4 0.09
13 11 0.26
14 11 0.26
15 10 0.23
16 3 0.07
17 4 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTTATATAATTT
Found at i:2433760 original size:19 final size:19
Alignment explanation
Indices: 2433736--2433793 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
2433726 ACTTAACATA
2433736 ATAATATTTTATAAGTAAT
1 ATAATATTTTATAAGTAAT
*
2433755 ATAATA----ATAA--CAT
1 ATAATATTTTATAAGTAAT
2433768 AATAATATTTTATAAGTAAT
1 -ATAATATTTTATAAGTAAT
2433788 ATAATA
1 ATAATA
2433794 ATATATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
13 2 0.07
14 6 0.20
15 4 0.13
18 4 0.13
19 12 0.40
20 2 0.07
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.41
Consensus pattern (19 bp):
ATAATATTTTATAAGTAAT
Found at i:2433768 original size:33 final size:33
Alignment explanation
Indices: 2433729--2433796 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
2433719 ATAGGGTACT
2433729 TAACATAATAATATTTTATAAGTAATATAATAA
1 TAACATAATAATATTTTATAAGTAATATAATAA
2433762 TAACATAATAATATTTTATAAGTAATATAATAA
1 TAACATAATAATATTTTATAAGTAATATAATAA
2433795 TA
1 TA
2433797 TATATAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (33 bp):
TAACATAATAATATTTTATAAGTAATATAATAA
Found at i:2439421 original size:5 final size:5
Alignment explanation
Indices: 2439407--2439436 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
2439397 ATGGAAATTA
2439407 AAAAT AAAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAA
2439437 CTCACCCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:2445402 original size:31 final size:31
Alignment explanation
Indices: 2445364--2445481 Score: 182
Period size: 31 Copynumber: 3.8 Consensus size: 31
2445354 ACAAATGACA
* *
2445364 AGTGAAAAGTGGTAGCTTCTGCTACTTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
2445395 AGTGAAAATTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
2445426 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
2445457 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
2445482 AAGTGACAAG
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 79 1.00
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:2445581 original size:47 final size:46
Alignment explanation
Indices: 2445511--2445758 Score: 155
Period size: 49 Copynumber: 5.3 Consensus size: 46
2445501 TATAAGACCA
* * * * *
2445511 TGGGATATGGTATCGGTGTGATATATGCTACTGTATAAGACCATATC
1 TGGGATATGGCATCAGTGAGATATATGATAC-GTATAAGACCATAGC
* * * *
2445558 TGGGATATGACATCAGTGAGATATGTGATTCGTGTAAGACCATAGC
1 TGGGATATGGCATCAGTGAGATATATGATACGTATAAGACCATAGC
* * * * * *
2445604 TGGGTTATGGCATCGATATGTGATATGTGATTACGTGTAAGACCATAAC
1 TGGGATATGGCATC-A-GTGAGATATATGA-TACGTATAAGACCATAGC
* * * * * *
2445653 TGGGCTATGGCATCGATATGTGATATGTGATTACGTGTAAGACCATAGT
1 TGGGATATGGCATC-A-GTGAGATATATGA-TACGTATAAGACCATAGC
* * * *
2445702 TGGGCTATGGCATC-----GATATATGAATATGTGTAAGACCATAGA
1 TGGGATATGGCATCAGTGAGATATATG-ATACGTATAAGACCATAGC
*
2445744 TGGGCTATGGCATCA
1 TGGGATATGGCATCA
2445759 TTATGTAAAG
Statistics
Matches: 175, Mismatches: 21, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
42 37 0.21
43 1 0.01
46 25 0.14
47 25 0.14
48 11 0.06
49 76 0.43
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (46 bp):
TGGGATATGGCATCAGTGAGATATATGATACGTATAAGACCATAGC
Found at i:2445647 original size:49 final size:49
Alignment explanation
Indices: 2445546--2445757 Score: 264
Period size: 49 Copynumber: 4.5 Consensus size: 49
2445536 TGCTACTGTA
* * * * *
2445546 TAAGACCATATCTGGGATATGACATC-A-GTGAGATATGTGATT-CGTG
1 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTACGTG
*
2445592 TAAGACCATAGCTGGGTTATGGCATCGATATGTGATATGTGATTACGTG
1 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTACGTG
*
2445641 TAAGACCATAACTGGGCTATGGCATCGATATGTGATATGTGATTACGTG
1 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTACGTG
* *
2445690 TAAGACCATAGTTGGGCTATGGCATCGATATATGA-A--T-A-T--GTG
1 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTACGTG
*
2445732 TAAGACCATAGATGGGCTATGGCATC
1 TAAGACCATAGCTGGGCTATGGCATC
2445758 ATTATGTAAA
Statistics
Matches: 152, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
42 28 0.18
44 1 0.01
45 1 0.01
46 24 0.16
47 1 0.01
48 14 0.09
49 83 0.55
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (49 bp):
TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTACGTG
Found at i:2445733 original size:42 final size:42
Alignment explanation
Indices: 2445687--2445801 Score: 162
Period size: 42 Copynumber: 2.7 Consensus size: 42
2445677 ATGTGATTAC
*
2445687 GTGTAAGACCATAGTTGGGCTATGGCATCGATATATG-AATAT
1 GTGTAAGACCATAGTTGGGCTATGGCATCGAT-TATGAAAGAT
*
2445729 GTGTAAGACCATAGATGGGCTATGGCATC-ATTATGTAAAGAT
1 GTGTAAGACCATAGTTGGGCTATGGCATCGATTATG-AAAGAT
**
2445771 GTGTAAGACCATAGTTGAACTATGGCATCGA
1 GTGTAAGACCATAGTTGGGCTATGGCATCGA
2445802 GAAAACGAAG
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
40 4 0.06
41 2 0.03
42 58 0.89
43 1 0.02
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (42 bp):
GTGTAAGACCATAGTTGGGCTATGGCATCGATTATGAAAGAT
Found at i:2448386 original size:14 final size:14
Alignment explanation
Indices: 2448367--2448417 Score: 66
Period size: 14 Copynumber: 3.5 Consensus size: 14
2448357 AGAAAGAGAT
2448367 GAGAAGATAGAAAA
1 GAGAAGATAGAAAA
*
2448381 GAGAAGAAACGAAATA
1 GAGAAGATA-GAAA-A
*
2448397 GAGAAGATAGAAAT
1 GAGAAGATAGAAAA
2448411 GAGAAGA
1 GAGAAGA
2448418 AACAAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 15 0.47
15 8 0.25
16 9 0.28
ACGTcount: A:0.61, C:0.02, G:0.29, T:0.08
Consensus pattern (14 bp):
GAGAAGATAGAAAA
Found at i:2448401 original size:30 final size:30
Alignment explanation
Indices: 2448367--2448426 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
2448357 AGAAAGAGAT
*
2448367 GAGAAGATAGAAAAGAGAAGAAACGAAATA
1 GAGAAGATAGAAAAGAGAAGAAACAAAATA
*
2448397 GAGAAGATAGAAATGAGAAGAAACAAAATA
1 GAGAAGATAGAAAAGAGAAGAAACAAAATA
2448427 AAAAAAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.63, C:0.03, G:0.25, T:0.08
Consensus pattern (30 bp):
GAGAAGATAGAAAAGAGAAGAAACAAAATA
Found at i:2448569 original size:10 final size:10
Alignment explanation
Indices: 2448532--2448567 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
2448522 AAAGAAGAAA
2448532 AAAATGGAAG
1 AAAATGGAAG
2448542 AAAATGGAAG
1 AAAATGGAAG
2448552 AAAAT-GAAGG
1 AAAATGGAA-G
2448562 AAAATG
1 AAAATG
2448568 AAAAAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 3 0.12
10 21 0.88
ACGTcount: A:0.61, C:0.00, G:0.28, T:0.11
Consensus pattern (10 bp):
AAAATGGAAG
Found at i:2450321 original size:18 final size:19
Alignment explanation
Indices: 2450298--2450334 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2450288 CGTTTATGCT
*
2450298 ATAATAGTT-TAATTTTAC
1 ATAATAATTATAATTTTAC
2450316 ATAATAATTATAATTTTAC
1 ATAATAATTATAATTTTAC
2450335 TTTTATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (19 bp):
ATAATAATTATAATTTTAC
Found at i:2451142 original size:20 final size:20
Alignment explanation
Indices: 2451104--2451143 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2451094 TCGTTATGAA
*
2451104 ATTATTAAAAACATAAAAAT
1 ATTATTAAAAAAATAAAAAT
*
2451124 ATTATTAAAAAAATTAAAAT
1 ATTATTAAAAAAATAAAAAT
2451144 TATGTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
ATTATTAAAAAAATAAAAAT
Found at i:2451414 original size:19 final size:19
Alignment explanation
Indices: 2451361--2451414 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
2451351 TATAGAAATC
2451361 AATTTTTAATAAAATTTTAT
1 AATTTTTAAT-AAATTTTAT
** *
2451381 GGTTTTTAATTAATTTTAAT
1 AATTTTTAATAAATTTT-AT
2451401 AATTTTT-ATAAATT
1 AATTTTTAATAAATT
2451415 AGTTTTTTTC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (19 bp):
AATTTTTAATAAATTTTAT
Found at i:2451473 original size:23 final size:22
Alignment explanation
Indices: 2451426--2451476 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
2451416 GTTTTTTTCT
* *
2451426 AATTTTTTTATGATTTTTAATA
1 AATTTTTTTATAAATTTTAATA
2451448 AATTATTTTTATAAATTTT-ATGA
1 AATT-TTTTTATAAATTTTAAT-A
2451471 AATTTT
1 AATTTT
2451477 ATTGTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (22 bp):
AATTTTTTTATAAATTTTAATA
Found at i:2454159 original size:18 final size:18
Alignment explanation
Indices: 2454138--2454249 Score: 90
Period size: 17 Copynumber: 6.4 Consensus size: 18
2454128 AAGTTTTTTT
*
2454138 AACACGGGAATTTTTGAA
1 AACACGAGAATTTTTGAA
*
2454156 AACACGAGAA--TTTGTA
1 AACACGAGAATTTTTGAA
* *
2454172 AACACGAAAATTTTAG-A
1 AACACGAGAATTTTTGAA
* *
2454189 AACATGAAAATTTTT-AA
1 AACACGAGAATTTTTGAA
* *
2454206 AACACGACATTTTTTTTG-A
1 AACACGAGA--ATTTTTGAA
*
2454225 AACACGGGAATTTTTGAA
1 AACACGAGAATTTTTGAA
2454243 AACACGA
1 AACACGA
2454250 ATTTTTTTTA
Statistics
Matches: 74, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
16 14 0.19
17 28 0.38
18 19 0.26
19 13 0.18
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (18 bp):
AACACGAGAATTTTTGAA
Found at i:2454169 original size:16 final size:16
Alignment explanation
Indices: 2454150--2454212 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
2454140 CACGGGAATT
*
2454150 TTTGAAAACACGAGAA
1 TTTGAAAACACGAAAA
*
2454166 TTTGTAAACACGAAAA
1 TTTGAAAACACGAAAA
* *
2454182 TTTTAGAAACATGAAAA
1 TTTGA-AAACACGAAAA
*
2454199 TTTTTAAAACACGA
1 -TTTGAAAACACGA
2454213 CATTTTTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
16 17 0.44
17 17 0.44
18 5 0.13
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.27
Consensus pattern (16 bp):
TTTGAAAACACGAAAA
Found at i:2454208 original size:17 final size:17
Alignment explanation
Indices: 2454115--2454250 Score: 80
Period size: 17 Copynumber: 7.9 Consensus size: 17
2454105 GTATTTCTTT
* *
2454115 TTTTTTAAA-ACGAAAG
1 TTTTTAAAACACGAAAA
** **
2454131 TTTTTTTAACACGGGAA
1 TTTTTAAAACACGAAAA
*
2454148 TTTTTGAAAACACGAGAA
1 TTTTT-AAAACACGAAAA
*
2454166 TTTGT-AAACACGAAAA
1 TTTTTAAAACACGAAAA
*
2454182 -TTTTAGAAACATGAAAA
1 TTTTTA-AAACACGAAAA
**
2454199 TTTTTAAAACACGACATTT
1 TTTTTAAAACACGA-A-AA
* **
2454218 TTTTTGAAACACGGGAA
1 TTTTTAAAACACGAAAA
2454235 TTTTTGAAAACACGAA
1 TTTTT-AAAACACGAA
2454251 TTTTTTTTAT
Statistics
Matches: 90, Mismatches: 22, Indels: 14
0.71 0.17 0.11
Matches are distributed among these distances:
15 3 0.03
16 18 0.20
17 31 0.34
18 26 0.29
19 12 0.13
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:2454219 original size:16 final size:16
Alignment explanation
Indices: 2454115--2454255 Score: 72
Period size: 18 Copynumber: 8.3 Consensus size: 16
2454105 GTATTTCTTT
*
2454115 TTTTTTAAA-ACGAAA
1 TTTTTAAAACACGAAA
** *
2454130 GTTTTTTTAACACGGGAA
1 -TTTTTAAAACAC-GAAA
2454148 TTTTTGAAAACACGAGAA
1 TTTTT-AAAACACGA-AA
*
2454166 TTTGT-AAACACGAAA
1 TTTTTAAAACACGAAA
* *
2454181 ATTTTAGAAACATGAAAA
1 TTTTTA-AAACACG-AAA
*
2454199 TTTTTAAAACACGACATTT
1 TTTTTAAAACACGA-A--A
* *
2454218 TTTTTGAAACACGGGAA
1 TTTTTAAAACAC-GAAA
2454235 TTTTTGAAAACACG-AA
1 TTTTT-AAAACACGAAA
2454251 TTTTT
1 TTTTT
2454256 TTTATTCACG
Statistics
Matches: 97, Mismatches: 16, Indels: 24
0.71 0.12 0.18
Matches are distributed among these distances:
15 5 0.05
16 24 0.25
17 27 0.28
18 28 0.29
19 12 0.12
20 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Consensus pattern (16 bp):
TTTTTAAAACACGAAA
Found at i:2454227 original size:19 final size:19
Alignment explanation
Indices: 2454199--2454285 Score: 74
Period size: 19 Copynumber: 4.7 Consensus size: 19
2454189 AACATGAAAA
* *
2454199 TTTTTAAAACACGACATTT
1 TTTTTGAAACACGAGATTT
* *
2454218 TTTTTGAAACACGGGA--A
1 TTTTTGAAACACGAGATTT
2454235 TTTTTGAAAACACGA-ATTT
1 TTTTTG-AAACACGAGATTT
** *
2454254 TTTTT-ATTCACGAGAATT
1 TTTTTGAAACACGAGATTT
2454272 TTTTTGAAACACGA
1 TTTTTGAAACACGA
2454286 TTTTTCTTTA
Statistics
Matches: 52, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
17 13 0.25
18 15 0.29
19 24 0.46
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (19 bp):
TTTTTGAAACACGAGATTT
Found at i:2454276 original size:37 final size:35
Alignment explanation
Indices: 2454155--2454296 Score: 114
Period size: 36 Copynumber: 4.1 Consensus size: 35
2454145 GAATTTTTGA
* ** **
2454155 AAACACGAGAA--TTTGTAAACACGAAAATTTTAG
1 AAACACGAGAATTTTTGAAAACACGAATTTTTTTT
* *
2454188 AAACATGAAAATTTTT-AAAACACGACATTTTTTTT
1 AAACACGAGAATTTTTGAAAACACGA-ATTTTTTTT
*
2454223 GAAACACGGGAATTTTTGAAAACACGAATTTTTTTT
1 -AAACACGAGAATTTTTGAAAACACGAATTTTTTTT
**
2454259 ATTCACGAGAATTTTTTTG-AAACACG-ATTTTTCTTT
1 AAACACGAGAA--TTTTTGAAAACACGAATTTTT-TTT
2454295 AA
1 AA
2454297 CAAATACCGT
Statistics
Matches: 87, Mismatches: 14, Indels: 13
0.76 0.12 0.11
Matches are distributed among these distances:
33 9 0.10
34 8 0.09
35 22 0.25
36 33 0.38
37 15 0.17
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (35 bp):
AAACACGAGAATTTTTGAAAACACGAATTTTTTTT
Found at i:2454889 original size:10 final size:10
Alignment explanation
Indices: 2454876--2454929 Score: 56
Period size: 10 Copynumber: 5.2 Consensus size: 10
2454866 TTAATTACTT
2454876 TTTTTCTTTC
1 TTTTTCTTTC
2454886 TTTTTCTTTC
1 TTTTTCTTTC
2454896 TCTTTT-TTTC
1 T-TTTTCTTTC
*
2454906 TTTCTTTTTTC
1 TTT-TTCTTTC
*
2454917 TTCTTCTCTTC
1 TTTTTCT-TTC
2454928 TT
1 TT
2454930 CTTGTCTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
9 2 0.05
10 21 0.55
11 15 0.39
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:2454895 original size:14 final size:13
Alignment explanation
Indices: 2454874--2454926 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 13
2454864 TTTTAATTAC
2454874 TTTT-TTTCTTTCT
1 TTTTCTTTCTTT-T
2454887 TTTTCTTTCTCTTT
1 TTTTCTTTCT-TTT
2454901 TTTTCTTTCTTTT
1 TTTTCTTTCTTTT
2454914 TTCTTCTTCTCTT
1 TT-TTCTT-TCTT
2454927 CTTCTTGTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
13 9 0.25
14 21 0.58
15 6 0.17
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTCTTTCTTTT
Found at i:2455513 original size:29 final size:29
Alignment explanation
Indices: 2455480--2455580 Score: 80
Period size: 30 Copynumber: 3.4 Consensus size: 29
2455470 TGTAATTTTT
2455480 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGATTAAAATGAAATTTAA
* * * *
2455509 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGAT-TAAAATGAAATTTAA
* * *
2455539 AGAAAGTTTAAGAGTCAAAATGAAATTT-A
1 AGAAAATTTAGGA-TTAAAATGAAATTTAA
*
2455568 GGAAAAGTTTAGG
1 AGAAAA-TTTAGG
2455581 GGTCAAAATG
Statistics
Matches: 55, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
29 14 0.25
30 40 0.73
31 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.22, T:0.30
Consensus pattern (29 bp):
AGAAAATTTAGGATTAAAATGAAATTTAA
Found at i:2455535 original size:30 final size:30
Alignment explanation
Indices: 2455495--2455596 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
2455485 ATTTAGGATT
*
2455495 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * * *
2455525 TAAGTGAAATTTAAAGAAAGTTTAAGAGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
2455555 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
2455585 AAAATGCAATTT
1 AAAATGAAATTT
2455597 TTATTTTTTA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 2 0.03
30 58 0.97
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:2455617 original size:14 final size:15
Alignment explanation
Indices: 2455592--2455626 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
2455582 GTCAAAATGC
*
2455592 AATTTTTATTTTTTA
1 AATTTTTATTTTTGA
2455607 AATTTTT-TTTTTGA
1 AATTTTTATTTTTGA
2455621 AATTTT
1 AATTTT
2455627 GAAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
AATTTTTATTTTTGA
Found at i:2456053 original size:54 final size:54
Alignment explanation
Indices: 2455868--2456183 Score: 509
Period size: 54 Copynumber: 5.9 Consensus size: 54
2455858 CACGTGAGCC
* * *
2455868 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCGA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT--AA
*
2455923 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAG--A--AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
* *
2455973 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
2456027 AAGGCTCAACTCACCTCTCGCAATATG-GTTGATTTTTGAAAAACAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
2456080 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
*
2456134 AAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
2456184 CTGAAAAGTA
Statistics
Matches: 247, Mismatches: 8, Indels: 13
0.92 0.03 0.05
Matches are distributed among these distances:
50 47 0.19
52 1 0.00
53 51 0.21
54 104 0.42
55 38 0.15
56 6 0.02
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (54 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
Found at i:2456105 original size:107 final size:106
Alignment explanation
Indices: 2455868--2456183 Score: 505
Period size: 107 Copynumber: 3.0 Consensus size: 106
2455858 CACGTGAGCC
* * *
2455868 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCGAAAGGCTCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT--AAAAGGCTCAA
*
2455932 CTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAG--AAA
64 CTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAAAA
* *
2455973 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATTAAAAGGCTCAACT
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACT
2456038 CACCTCTCGCAATATG-GTTGATTTTTGAAAAACAGAAATTAA
66 CACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA--AA
2456080 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACT
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACT
*
2456145 CATCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
66 CACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
2456184 CTGAAAAGTA
Statistics
Matches: 196, Mismatches: 9, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
103 18 0.09
104 28 0.14
105 38 0.19
106 10 0.05
107 80 0.41
108 22 0.11
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (106 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACT
CACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAAAA
Found at i:2456298 original size:13 final size:14
Alignment explanation
Indices: 2456270--2456302 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
2456260 TTTTTGAAAC
2456270 ACAGAAATTAAAAA
1 ACAGAAATTAAAAA
2456284 ACAGAAATT-AAAA
1 ACAGAAATTAAAAA
2456297 ACAGAA
1 ACAGAA
2456303 TTTGAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.70, C:0.09, G:0.09, T:0.12
Consensus pattern (14 bp):
ACAGAAATTAAAAA
Found at i:2456310 original size:14 final size:14
Alignment explanation
Indices: 2456263--2456310 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
2456253 ATTTTTTTTT
*
2456263 TTGAAACACAGAAA
1 TTGAAAAACAGAAA
*
2456277 TTAAAAAACAGAAA
1 TTGAAAAACAGAAA
*
2456291 TT-AAAAACAGAAT
1 TTGAAAAACAGAAA
2456304 TTGAAAA
1 TTGAAAA
2456311 GACCTCAGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 12 0.40
14 18 0.60
ACGTcount: A:0.62, C:0.08, G:0.10, T:0.19
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:2456442 original size:85 final size:87
Alignment explanation
Indices: 2456298--2456462 Score: 210
Period size: 87 Copynumber: 1.9 Consensus size: 87
2456288 AAATTAAAAA
* *
2456298 CAGAATTTGAAAAGACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTACAATATGAGTT-GA
1 CAGAAATTGAAAAGACCTCAGCG-GTGGCCTGAGACTCAACTCACCTCTCACAATATGAGTTAGA
*
2456362 TTTGAAAAGTAGAATTAGTAAAG
65 TTTGAAAAGCAGAATTAGTAAAG
* * * *
2456385 CAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCATCTCTCGCAATATGAGTTAAG
1 CAGAAATTGAAAAGACCTCAGCGGTGGCC-TGAGACTCAACTCACCTCTCACAATATGAGTT-AG
*
2456448 TTTTGAAAAGCAGAA
64 ATTTGAAAAGCAGAA
2456463 ATTGAAAATA
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
84 3 0.04
85 30 0.45
87 34 0.51
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (87 bp):
CAGAAATTGAAAAGACCTCAGCGGTGGCCTGAGACTCAACTCACCTCTCACAATATGAGTTAGAT
TTGAAAAGCAGAATTAGTAAAG
Found at i:2456500 original size:73 final size:73
Alignment explanation
Indices: 2456381--2456758 Score: 606
Period size: 73 Copynumber: 5.2 Consensus size: 73
2456371 TAGAATTAGT
* * *
2456381 AAAGCAGAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCATCTCTCGCAATATGAGTT-
1 AAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
2456445 AAGTTTTGA
66 AA-TTTTGA
*
2456454 AAAGCAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
1 AAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
2456519 AATTTTGA
66 AATTTTGA
*
2456527 AAA-CA-AAGATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTT
1 AAAGCAGAA-ATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTT
2456590 GAATTTTGA
65 GAATTTTGA
* *
2456599 GAAGCAGAAATTGAAAATACATCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
1 AAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
2456664 AATTTTGA
66 AATTTTGA
*
2456672 AAA-CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
1 AAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
2456736 -ATTTTGA
66 AATTTTGA
* *
2456743 AAAACAAAAATT-AAAA
1 AAAGCAGAAATTGAAAA
2456759 GGCTTAACTC
Statistics
Matches: 286, Mismatches: 14, Indels: 12
0.92 0.04 0.04
Matches are distributed among these distances:
71 15 0.05
72 132 0.46
73 135 0.47
74 4 0.01
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (73 bp):
AAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
AATTTTGA
Found at i:2456573 original size:72 final size:72
Alignment explanation
Indices: 2456385--2456758 Score: 594
Period size: 72 Copynumber: 5.2 Consensus size: 72
2456375 ATTAGTAAAG
* * *
2456385 CAGAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCATCTCTCGCAATATGAGTT-AAGT
1 CAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA-T
2456449 TTTGAAAA
65 TTTGAAAA
*
2456457 GCAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAT
1 -CAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAT
2456522 TTTGAAAA
65 TTTGAAAA
*
2456530 CA-AAGATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAT
1 CAGAA-ATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAT
*
2456594 TTTGAGAAG
65 TTTGA-AAA
*
2456603 CAGAAATTGAAAATACATCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
1 CAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
2456668 TTGAAAA
66 TTGAAAA
*
2456675 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG-ATT
1 CAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
2456739 TTGAAAAA
66 TTG-AAAA
*
2456747 CAAAAATT-AAAA
1 CAGAAATTGAAAA
2456759 GGCTTAACTC
Statistics
Matches: 282, Mismatches: 14, Indels: 12
0.92 0.05 0.04
Matches are distributed among these distances:
71 11 0.04
72 136 0.48
73 131 0.46
74 4 0.01
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (72 bp):
CAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
TTGAAAA
Found at i:2456636 original size:145 final size:145
Alignment explanation
Indices: 2456385--2456758 Score: 621
Period size: 145 Copynumber: 2.6 Consensus size: 145
2456375 ATTAGTAAAG
* * * *
2456385 CAGAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCATCTCTCGCAATATGAGTT-AAGT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA-T
* *
2456449 TTTGAAAAGCAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
65 TTTGAAAAGCAGAAATTGAAAATACATCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
2456514 AGTTGAATTTTGAAAA
130 AGTTGAATTTTGAAAA
2456530 CA-AAGATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAT
1 CAGAA-ATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAT
*
2456594 TTTGAGAAGCAGAAATTGAAAATACATCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
65 TTTGAAAAGCAGAAATTGAAAATACATCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATG
2456659 AGTTGAATTTTGAAAA
130 AGTTGAATTTTGAAAA
2456675 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG-ATT
1 CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
* *
2456739 TTGAAAAACAAAAATT-AAAA
66 TTGAAAAGCAGAAATTGAAAA
2456759 GGCTTAACTC
Statistics
Matches: 216, Mismatches: 10, Indels: 8
0.92 0.04 0.03
Matches are distributed among these distances:
143 4 0.02
144 18 0.08
145 190 0.88
146 4 0.02
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (145 bp):
CAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATT
TTGAAAAGCAGAAATTGAAAATACATCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGA
GTTGAATTTTGAAAA
Found at i:2456853 original size:122 final size:125
Alignment explanation
Indices: 2456633--2457433 Score: 423
Period size: 145 Copynumber: 6.0 Consensus size: 125
2456623 ACGTGTCTTG
** * * * *
2456633 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTCAATTTTGAAAACAGAAACTAAAAATACCTCAACG
2456698 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG-ATTTTGAAAAACAAAAATTAAA
66 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AAAACAAAAATTAAA
* * *
2456758 AGGCTTAACTCACCTCTCGCAATATGAG-TCAA-TTT-AAAACATAAACTAAAAATACCTCAATG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTCAATTTTGAAAACAGAAACTAAAAATACCTCAACG
*
2456820 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAA
66 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATT-AAA
* * * * * * * * * **
2456881 TTA-CCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGA
1 --AGGCTCAAC---TC---A-CCTC-TCGCA-ATAT-G-AGT-TCA----ATTTTGAAAA-CAGA
* * * *
2456945 AATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTAAATTTTGA
47 AACTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGA
* *
2457010 GAAGCAGAAATTGAAA
112 -AAACAAAAATT-AAA
** * * * * * * * * **
2457026 ATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAA
1 A-GGCTCAAC---TC---A-CCTC-TCGCA-ATAT-G-AGT-TCA----ATTTTGAAAA-CAGAA
* * *
2457091 ATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAA
48 ACTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAA
*
2457156 AACAAAGATTGAAA
113 AACAAAAATT-AAA
* * * * * * * * * **
2457170 TTA-CCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAG
1 --AGGCTCAAC---TC---A-CCTC-TCGCA-ATAT-G-AGT-TCA----ATTTTGAAAA--CAG
* * *
2457234 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTTATTTCTCGCAATATGAGTTGAATTTTG
46 AAACTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG
2457299 AAAAACAAAAATTAAA
111 -AAAACAAAAATTAAA
* * *
2457315 AGGCTTAACTCACCTCTCGCAATATGAG-TCAA-TTT-AAAACATAAACTAAAAATACCTCAATG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTCAATTTTGAAAACAGAAACTAAAAATACCTCAACG
*
2457377 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATT
66 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATT
2457434 GAAATTACCT
Statistics
Matches: 593, Mismatches: 51, Indels: 67
0.83 0.07 0.09
Matches are distributed among these distances:
122 82 0.14
123 75 0.13
124 8 0.01
125 29 0.05
126 3 0.01
127 3 0.01
130 1 0.00
131 5 0.01
132 3 0.01
133 3 0.01
134 2 0.00
135 3 0.01
136 3 0.01
137 5 0.01
138 1 0.00
141 3 0.01
142 3 0.01
143 5 0.01
144 136 0.23
145 208 0.35
146 12 0.02
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (125 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTCAATTTTGAAAACAGAAACTAAAAATACCTCAACG
TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTAAA
Found at i:2456900 original size:72 final size:72
Alignment explanation
Indices: 2456758--2457311 Score: 909
Period size: 72 Copynumber: 7.7 Consensus size: 72
2456748 AAAAATTAAA
* ** * * * * * *
2456758 AGGCTTAACTCACCTCTCGCAATATGAG-TCAA-TTT-AAAACATAAACTAAAAATACCTCAATG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
2456820 TGTCTTG
66 TGTCTTG
2456827 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
2456892 TGTCTTG
66 TGTCTTG
2456899 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
2456964 TGTCTTG
66 TGTCTTG
* * *
2456971 AGGCTCAACTCATTTCTCGCAATATGAGTTAAATTTTGAGAAGCAGAAATTGAAAATACCTCAAC
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGA-AAACAGAAATTGAAATTACCTCAAC
2457036 GTGTCTTG
65 GTGTCTTG
2457044 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
2457109 TGTCTTG
66 TGTCTTG
2457116 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACA-AAGATTGAAATTACCTCAAC
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAA-ATTGAAATTACCTCAAC
2457180 GTGTCTTG
65 GTGTCTTG
*
2457188 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAATACCTCAAC
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAGAAATTGAAATTACCTCAAC
2457253 GTGTCTTG
65 GTGTCTTG
* *
2457261 AGGCTCAACTTATTTCTCGCAATATGAGTTGAATTTTGAAAAACAAAAATT
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATT
2457312 AAAAGGCTTA
Statistics
Matches: 459, Mismatches: 18, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
69 25 0.05
70 3 0.01
71 5 0.01
72 281 0.61
73 139 0.30
74 6 0.01
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (72 bp):
AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
TGTCTTG
Found at i:2457074 original size:145 final size:144
Alignment explanation
Indices: 2456758--2458209 Score: 909
Period size: 145 Copynumber: 9.8 Consensus size: 144
2456748 AAAAATTAAA
* ** * * * * *
2456758 AGGCTTAACTCACCTCTCGCAATATGAG-TCAA-TTT-AAAACATAAACTAAAAATACCTCAATG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAACG
2456820 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTAC
66 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTAC
2456885 CTCAACGTGTCTTG
131 CTCAACGTGTCTTG
*
2456899 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAACG
* * *
2456964 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTAAATTTTGAGAAGCAGAAATTGAAAATA
66 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGA-AAACAGAAATTGAAATTA
2457029 CCTCAACGTGTCTTG
130 CCTCAACGTGTCTTG
*
2457044 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAACG
2457109 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACA-AAGATTGAAATTA
66 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAA-ATTGAAATTA
2457173 CCTCAACGTGTCTTG
130 CCTCAACGTGTCTTG
2457188 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAATACCTCAAC
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAGAAATTGAAAATACCTCAAC
* * *
2457253 GTGTCTTGAGGCTCAACTTATTTCTCGCAATATGAGTTGAATTTTGAAAAACAAAAATTAAAAGG
65 GTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATTGAAA--
* * *
2457318 CTTAACTC-ACCTCTCGCAATATG
127 -TTACCTCAACGTGT--C--T-TG
* * ** ** *** * * * * ** **
2457341 AGTCAATTTAAAACATAAACTAAAAATACCTCAATGTG--TCTTGAGGCTCAACTCATTTCTCGC
1 AGGC---TCAACTCAT-TTCTCGCAATA--TGAGT-TGAATTTTGA----AAACAGAAAT-T-G-
* ** * ** ** * * * * ** ** *** *
2457404 AATATGAGTTGAA--T-T-TTGAAAACAGAAATTGAAATTAC-CTCAACGTGTCTTG-AGGCTCA
52 AAAAT-ACCTCAACGTGTCTTG-AGGC-TCAACT--CATTTCTCGCAATATGAGTTGAATTTTGA
* * * * * * **
2457463 ACTAATTTCTCGCAATATGAGTTGAATT--TTGAGAAGCAGAAATTG
112 A--AA---C-AGAAAT-TGA----AATTACCTCA-ACG-TG-TCTTG
*** * * * * *** * ** * * * *
2457508 AAAAT-ACCTTAACGTGTCTTG-AGGCTCAACT-CATTTCTCGCAATA-TG-AGTTGAATTTTGA
1 AGGCTCAAC-T--CATTTCTCGCAATATGAGTTGAATTT-T-G-AAAACAGAAATTGAA-----A
* ** ** ** * * * * *** * ** * *
2457568 A-AACAGAAATTGAAATT-A-CCTCAA--CGTGTCTTG-AGGCTCAACT-CATTTCTCGCAATA-
55 ATACCTCAACGTG-TCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTT-T-G-AAAAC
* * * ***** ***** *
2457625 TG-AGTTGAATTTTGAAAAACAAAAATTAAA
116 AGAAATTGAAATTACCTCAACGTGTCTT--G
* ** * * * * * *
2457655 AGGCTTAACTCACCTCTCGAAATATGAG-TCAA-TTT-AAAACATAAACTAAAAATACCTCAATG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAACG
2457717 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAATTTTGAAAACAGAAATTGAAATTA
66 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG-AATTTTGAAAACAGAAATTGAAATTA
2457782 CCTCAACGTGTCTTG
130 CCTCAACGTGTCTTG
* *
2457797 AGGCTCAACTCATTTCTCGCAATATGAGTTGACTTTTGAGAAGCAGAAATTGAAAATACCTCAAC
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGA-AAACAGAAATTGAAAATACCTCAAC
2457862 GTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTA
65 GTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTA
2457927 CCTCAACGTGTCTTG
130 CCTCAACGTGTCTTG
*
2457942 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAACG
2458007 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACA-AAGATTGAAATTA
66 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAA-ATTGAAATTA
2458071 CCTCAACGTGTCTTG
130 CCTCAACGTGTCTTG
2458086 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAATACCTCAAC
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAGAAATTGAAAATACCTCAAC
* * *
2458151 GTGTCTTGAGGCTCAACTCATTTCTCGCAGTATGAGTTGAGTTTTGAAAAACAAAAATT
65 GTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATT
2458210 AAAAGGCTTA
Statistics
Matches: 1014, Mismatches: 197, Indels: 195
0.72 0.14 0.14
Matches are distributed among these distances:
138 4 0.00
139 7 0.01
140 5 0.00
141 28 0.03
142 36 0.04
143 19 0.02
144 297 0.29
145 368 0.36
146 88 0.09
147 8 0.01
148 7 0.01
149 6 0.01
150 4 0.00
151 2 0.00
152 2 0.00
153 5 0.00
156 14 0.01
157 9 0.01
158 6 0.01
159 10 0.01
160 5 0.00
161 11 0.01
162 15 0.01
163 9 0.01
164 20 0.02
165 11 0.01
166 2 0.00
167 4 0.00
168 5 0.00
169 2 0.00
170 3 0.00
173 2 0.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (144 bp):
AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAACG
TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTAC
CTCAACGTGTCTTG
Found at i:2457181 original size:217 final size:217
Alignment explanation
Indices: 2456758--2457311 Score: 947
Period size: 217 Copynumber: 2.6 Consensus size: 217
2456748 AAAAATTAAA
* ** * * * * *
2456758 AGGCTTAACTCACCTCTCGCAATATGAG-TCAA-TTT-AAAA-CATAAACTAAAAATACCTCAAT
1 AGGCTCAACTCATTTCTCGCAATATGAGTTAAATTTTGAAAAGCAGAAATTGAAAATACCTCAAC
2456819 GTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTA
66 GTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTA
2456884 CCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATT
131 CCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATT
2456949 GAAATTACCTCAACGTGTCTTG
196 GAAATTACCTCAACGTGTCTTG
*
2456971 AGGCTCAACTCATTTCTCGCAATATGAGTTAAATTTTGAGAAGCAGAAATTGAAAATACCTCAAC
1 AGGCTCAACTCATTTCTCGCAATATGAGTTAAATTTTGAAAAGCAGAAATTGAAAATACCTCAAC
2457036 GTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTA
66 GTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTA
2457101 CCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACA-AAGAT
131 CCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAA-AT
2457165 TGAAATTACCTCAACGTGTCTTG
195 TGAAATTACCTCAACGTGTCTTG
*
2457188 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAATACCTCAAC
1 AGGCTCAACTCATTTCTCGCAATATGAGTTAAATTTTGAAAAGCAGAAATTGAAAATACCTCAAC
* *
2457253 GTGTCTTGAGGCTCAACTTATTTCTCGCAATATGAGTTGAATTTTGAAAAACAAAAATT
66 GTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATT
2457312 AAAAGGCTTA
Statistics
Matches: 322, Mismatches: 13, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
213 25 0.08
214 3 0.01
215 3 0.01
216 5 0.02
217 275 0.85
218 11 0.03
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (217 bp):
AGGCTCAACTCATTTCTCGCAATATGAGTTAAATTTTGAAAAGCAGAAATTGAAAATACCTCAAC
GTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTA
CCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATT
GAAATTACCTCAACGTGTCTTG
Found at i:2457411 original size:123 final size:126
Alignment explanation
Indices: 2457188--2457433 Score: 365
Period size: 123 Copynumber: 2.0 Consensus size: 126
2457178 ACGTGTCTTG
** * * *
2457188 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAATACCTCAAC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTCAATTTTGAAAAGCAGAAACTAAAAATACCTCAAC
*
2457253 GTGTCTTGAGGCTCAACTTATTTCTCGCAATATGAGTTGAATTTTGAAAAACAAAAATTAAA
66 GTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AAAACAAAAATTAAA
* * *
2457315 AGGCTTAACTCACCTCTCGCAATATGAG-TCAA-TTT-AAAA-CATAAACTAAAAATACCTCAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTCAATTTTGAAAAGCAGAAACTAAAAATACCTCAAC
*
2457376 GTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATT
66 GTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATT
2457434 GAAATTACCT
Statistics
Matches: 109, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
122 11 0.10
123 63 0.58
124 4 0.04
125 3 0.03
126 3 0.03
127 25 0.23
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.30
Consensus pattern (126 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTCAATTTTGAAAAGCAGAAACTAAAAATACCTCAAC
GTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTAAA
Found at i:2457537 original size:73 final size:72
Alignment explanation
Indices: 2457315--2457655 Score: 510
Period size: 72 Copynumber: 4.8 Consensus size: 72
2457305 AAAAATTAAA
* ** * * * * *
2457315 AGGCTTAACTCACCTCTCGCAATATGAG-TCAA-TTT-AAAACATAAACTAAAAATACCTCAATG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAACG
2457377 TGTCTTG
66 TGTCTTG
*
2457384 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAACG
2457449 TGTCTTG
66 TGTCTTG
* * *
2457456 AGGCTCAACTAATTTCTCGCAATATGAGTTGAATTTTGAGAAGCAGAAATTGAAAATACCTTAAC
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGA-AAACAGAAATTGAAAATACCTCAAC
2457521 GTGTCTTG
65 GTGTCTTG
*
2457529 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAACG
2457594 TGTCTTG
66 TGTCTTG
*
2457601 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAACAAAAATT-AAAA
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATTGAAAA
2457656 GGCTTAACTC
Statistics
Matches: 248, Mismatches: 19, Indels: 7
0.91 0.07 0.03
Matches are distributed among these distances:
69 25 0.10
70 3 0.01
71 3 0.01
72 138 0.56
73 79 0.32
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (72 bp):
AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAACG
TGTCTTG
Found at i:2457751 original size:123 final size:126
Alignment explanation
Indices: 2457529--2458599 Score: 629
Period size: 123 Copynumber: 8.0 Consensus size: 126
2457519 ACGTGTCTTG
** * * * * *
2457529 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
1 AGGCTCAACTCACCTCTCGAAATATGAGTTCAATTTTGAAAACAGAAACTAAAAATACCTCAACG
2457594 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG-AATTTTGAAAAACAAAAATTAAA
66 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAATTTTG-AAAACAAAAATTAAA
* * *
2457655 AGGCTTAACTCACCTCTCGAAATATGAG-TCAA-TTT-AAAACATAAACTAAAAATACCTCAATG
1 AGGCTCAACTCACCTCTCGAAATATGAGTTCAATTTTGAAAACAGAAACTAAAAATACCTCAACG
*
2457717 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAATTTTGAAAACAGAAATTGAAA
66 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAATTTTGAAAACAAAAATT-AAA
* * ** * * *
2457779 TTA-CCTCAACGTGTCTTGAGGCTCAACTC-ATTTCTCGCAATATGAGTTGACTTTTGAGAAGCA
1 --AGGCTCAAC---TC---A--C-C-TCTCGA--AAT----A--TGAGTTCAATTTTGA-AAACA
* *
2457842 GAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG-AATTT
45 GAAACTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAATTT
*
2457906 TGAAAACAGAAATTGAAA
110 TGAAAACAAAAATT-AAA
* * ** *
2457924 TTA-CCTCAACGTGTCTTGAGGCTCAACTC-ATTTCTCGCAATATGAGTTGAATTTTGAAAACAG
1 --AGGCTCAAC---TC---A--C-C-TCTCGA--AAT----A--TGAGTTCAATTTTGAAAACAG
* * *
2457987 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG-AATTTT
46 AAACTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAATTTT
*
2458051 GAAAACAAAGATTGAAA
111 GAAAACAAAAATT-AAA
* * ** *
2458068 TTA-CCTCAACGTGTCTTGAGGCTCAACTC-ATTTCTCGCAATATGAGTTGAATTTTGAAAAGCA
1 --AGGCTCAAC---TC---A--C-C-TCTCGA--AAT----A--TGAGTTCAATTTTGAAAA-CA
* * * *
2458131 GAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAGTATGAGTTG-AGTTT
45 GAAACTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAATTT
2458195 TGAAAAACAAAAATTAAA
110 TG-AAAACAAAAATTAAA
* * * *
2458213 AGGCTTAACTCACCTCTCGCAATATGAG-TCAA-TTT-AAAACATAAACTAAAAATACCTCAATG
1 AGGCTCAACTCACCTCTCGAAATATGAGTTCAATTTTGAAAACAGAAACTAAAAATACCTCAACG
*
2458275 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG-AGTTTTGAAAAACAAAAATTAAA
66 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAATTTTG-AAAACAAAAATTAAA
* * * **
2458336 AGGCTTAACTCACCTCTCGCAATATGAG-TCAA-TTT-AAAACATAAACTAAAAATACCTCGGCG
1 AGGCTCAACTCACCTCTCGAAATATGAGTTCAATTTTGAAAACAGAAACTAAAAATACCTCAACG
* ** * *
2458398 TGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG--ATTTTGAAAAAAGTAGAAATTAAA
66 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAATTTTGAAAACA--A-AAATTAAA
* * * * * * *
2458460 AGGTTCAACCCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAACAGGAATTGAA
1 AGGCTCAACTCACCTCTCGAAATATGAGTTCAATTTTG-AAAAC----A--G---A--AACTAAA
** ** *
2458525 AATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAATA
54 AATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAATT-TTGAAAACA
*
2458590 GAAATTAAA
118 AAAATTAAA
2458599 A
1 A
2458600 TTACCTCAGC
Statistics
Matches: 824, Mismatches: 70, Indels: 89
0.84 0.07 0.09
Matches are distributed among these distances:
121 5 0.01
122 5 0.01
123 244 0.30
124 50 0.06
125 13 0.02
126 31 0.04
127 4 0.00
128 7 0.01
129 1 0.00
131 1 0.00
132 1 0.00
133 2 0.00
134 5 0.01
135 4 0.00
136 2 0.00
137 1 0.00
138 1 0.00
139 58 0.07
140 1 0.00
141 4 0.00
142 12 0.01
143 3 0.00
144 151 0.18
145 148 0.18
146 70 0.08
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (126 bp):
AGGCTCAACTCACCTCTCGAAATATGAGTTCAATTTTGAAAACAGAAACTAAAAATACCTCAACG
TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAAATTTTGAAAACAAAAATTAAA
Found at i:2457957 original size:72 final size:72
Alignment explanation
Indices: 2457655--2458209 Score: 884
Period size: 72 Copynumber: 7.7 Consensus size: 72
2457645 AAAAATTAAA
* ** * * * * * * *
2457655 AGGCTTAACTCACCTCTCGAAATATGAG-TCAA-TTT-AAAACATAAACTAAAAATACCTCAATG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
2457717 TGTCTTG
66 TGTCTTG
2457724 AGGCTCAACTCATTTCTCGCAATATGAGTTGAAATTTTGAAAACAGAAATTGAAATTACCTCAAC
1 AGGCTCAACTCATTTCTCGCAATATGAGTTG-AATTTTGAAAACAGAAATTGAAATTACCTCAAC
2457789 GTGTCTTG
65 GTGTCTTG
* * *
2457797 AGGCTCAACTCATTTCTCGCAATATGAGTTGACTTTTGAGAAGCAGAAATTGAAAATACCTCAAC
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGA-AAACAGAAATTGAAATTACCTCAAC
2457862 GTGTCTTG
65 GTGTCTTG
2457870 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
2457935 TGTCTTG
66 TGTCTTG
2457942 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
2458007 TGTCTTG
66 TGTCTTG
2458014 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACA-AAGATTGAAATTACCTCAAC
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAA-ATTGAAATTACCTCAAC
2458078 GTGTCTTG
65 GTGTCTTG
*
2458086 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAATACCTCAAC
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAGAAATTGAAATTACCTCAAC
2458151 GTGTCTTG
65 GTGTCTTG
* * *
2458159 AGGCTCAACTCATTTCTCGCAGTATGAGTTGAGTTTTGAAAAACAAAAATT
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATT
2458210 AAAAGGCTTA
Statistics
Matches: 457, Mismatches: 20, Indels: 14
0.93 0.04 0.03
Matches are distributed among these distances:
69 24 0.05
70 1 0.00
71 4 0.01
72 224 0.49
73 198 0.43
74 6 0.01
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (72 bp):
AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
TGTCTTG
Found at i:2458766 original size:122 final size:126
Alignment explanation
Indices: 2458544--2458775 Score: 328
Period size: 122 Copynumber: 1.9 Consensus size: 126
2458534 ACGTGTCTTG
* * * * *
2458544 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAATAGAAATTAAAATTACCTCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTCA-TATCTTGAAAACAGAAACTAAAAATACCTCAG
*
2458609 CGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTGAAAAACAAATATTAAA
65 CGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTGAAAAACAAATATTAAA
* * *
2458671 AGGCTTAACTCACCTCTCGCAATATGAG-TCA-AT-TT-AAAACATAAACTAAAAATACCTCGGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTCATATCTTGAAAACAGAAACTAAAAATACCTCAGC
* *
2458732 GTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT
66 GTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAATTGATTTT
2458776 TTTTTAATTT
Statistics
Matches: 94, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
122 62 0.66
123 2 0.02
124 1 0.01
126 2 0.02
127 27 0.29
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (126 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTCATATCTTGAAAACAGAAACTAAAAATACCTCAGC
GTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTGAAAAACAAATATTAAA
Found at i:2464815 original size:18 final size:18
Alignment explanation
Indices: 2464794--2464905 Score: 90
Period size: 17 Copynumber: 6.4 Consensus size: 18
2464784 AAGTTTTTTT
*
2464794 AACACGGGAATTTTTGAA
1 AACACGAGAATTTTTGAA
*
2464812 AACACGAGAA--TTTGTA
1 AACACGAGAATTTTTGAA
* *
2464828 AACACGAAAATTTTAG-A
1 AACACGAGAATTTTTGAA
* *
2464845 AACATGAAAATTTTT-AA
1 AACACGAGAATTTTTGAA
* *
2464862 AACACGACATTTTTTTTG-A
1 AACACGAGA--ATTTTTGAA
*
2464881 AACACGGGAATTTTTGAA
1 AACACGAGAATTTTTGAA
2464899 AACACGA
1 AACACGA
2464906 ATTTTTTTAT
Statistics
Matches: 74, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
16 14 0.19
17 28 0.38
18 19 0.26
19 13 0.18
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (18 bp):
AACACGAGAATTTTTGAA
Found at i:2464825 original size:16 final size:16
Alignment explanation
Indices: 2464806--2464868 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
2464796 CACGGGAATT
*
2464806 TTTGAAAACACGAGAA
1 TTTGAAAACACGAAAA
*
2464822 TTTGTAAACACGAAAA
1 TTTGAAAACACGAAAA
* *
2464838 TTTTAGAAACATGAAAA
1 TTTGA-AAACACGAAAA
*
2464855 TTTTTAAAACACGA
1 -TTTGAAAACACGA
2464869 CATTTTTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
16 17 0.44
17 17 0.44
18 5 0.13
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.27
Consensus pattern (16 bp):
TTTGAAAACACGAAAA
Found at i:2464864 original size:17 final size:17
Alignment explanation
Indices: 2464771--2464906 Score: 80
Period size: 17 Copynumber: 7.9 Consensus size: 17
2464761 GTATTTCTTT
* *
2464771 TTTTTTAAA-ACGAAAG
1 TTTTTAAAACACGAAAA
** **
2464787 TTTTTTTAACACGGGAA
1 TTTTTAAAACACGAAAA
*
2464804 TTTTTGAAAACACGAGAA
1 TTTTT-AAAACACGAAAA
*
2464822 TTTGT-AAACACGAAAA
1 TTTTTAAAACACGAAAA
*
2464838 -TTTTAGAAACATGAAAA
1 TTTTTA-AAACACGAAAA
**
2464855 TTTTTAAAACACGACATTT
1 TTTTTAAAACACGA-A-AA
* **
2464874 TTTTTGAAACACGGGAA
1 TTTTTAAAACACGAAAA
2464891 TTTTTGAAAACACGAA
1 TTTTT-AAAACACGAA
2464907 TTTTTTTATT
Statistics
Matches: 90, Mismatches: 22, Indels: 14
0.71 0.17 0.11
Matches are distributed among these distances:
15 3 0.03
16 18 0.20
17 31 0.34
18 26 0.29
19 12 0.13
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:2464875 original size:16 final size:16
Alignment explanation
Indices: 2464771--2464911 Score: 72
Period size: 18 Copynumber: 8.3 Consensus size: 16
2464761 GTATTTCTTT
*
2464771 TTTTTTAAA-ACGAAA
1 TTTTTAAAACACGAAA
** *
2464786 GTTTTTTTAACACGGGAA
1 -TTTTTAAAACAC-GAAA
2464804 TTTTTGAAAACACGAGAA
1 TTTTT-AAAACACGA-AA
*
2464822 TTTGT-AAACACGAAA
1 TTTTTAAAACACGAAA
* *
2464837 ATTTTAGAAACATGAAAA
1 TTTTTA-AAACACG-AAA
*
2464855 TTTTTAAAACACGACATTT
1 TTTTTAAAACACGA-A--A
* *
2464874 TTTTTGAAACACGGGAA
1 TTTTTAAAACAC-GAAA
2464891 TTTTTGAAAACACG-AA
1 TTTTT-AAAACACGAAA
2464907 TTTTT
1 TTTTT
2464912 TTATTCACGA
Statistics
Matches: 97, Mismatches: 16, Indels: 24
0.71 0.12 0.18
Matches are distributed among these distances:
15 5 0.05
16 24 0.25
17 27 0.28
18 28 0.29
19 12 0.12
20 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Consensus pattern (16 bp):
TTTTTAAAACACGAAA
Found at i:2464883 original size:19 final size:18
Alignment explanation
Indices: 2464855--2464940 Score: 70
Period size: 18 Copynumber: 4.8 Consensus size: 18
2464845 AACATGAAAA
* *
2464855 TTTTTAAAACACGACATTT
1 TTTTTGAAACACGAGA-TT
* *
2464874 TTTTTGAAACACGGGA-A
1 TTTTTGAAACACGAGATT
2464891 TTTTTGAAAACACGA-ATT
1 TTTTTG-AAACACGAGATT
**
2464909 TTTTT-ATTCACGAGAATT
1 TTTTTGAAACACGAG-ATT
2464927 TTTTTGAAACACGA
1 TTTTTGAAACACGA
2464941 TTTTTCTTTA
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
16 6 0.12
17 7 0.13
18 20 0.38
19 19 0.37
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (18 bp):
TTTTTGAAACACGAGATT
Found at i:2464893 original size:53 final size:53
Alignment explanation
Indices: 2464802--2464940 Score: 124
Period size: 53 Copynumber: 2.7 Consensus size: 53
2464792 TTAACACGGG
* * *
2464802 AATTTTTGAAAACACGAGAA--TTTGT-AAACACGAAAATTTTAG-AAACATGAA
1 AATTTTT-AAAACACGACAATTTTTTTGAAACACGAAAATTTTAGAAAACACG-A
* ** *
2464853 AATTTTTAAAACACGACATTTTTTTTGAAACACGGGAATTTTTGAAAACACGA
1 AATTTTTAAAACACGACAATTTTTTTGAAACACGAAAATTTTAGAAAACACGA
* * ** *
2464906 ATTTTTTTATTCACGAGAATTTTTTTGAAACACGA
1 AATTTTTAAAACACGACAATTTTTTTGAAACACGA
2464941 TTTTTCTTTA
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
50 10 0.14
51 7 0.10
52 4 0.06
53 43 0.61
54 6 0.09
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.35
Consensus pattern (53 bp):
AATTTTTAAAACACGACAATTTTTTTGAAACACGAAAATTTTAGAAAACACGA
Found at i:2465533 original size:11 final size:11
Alignment explanation
Indices: 2465517--2465543 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2465507 GTTTTTATTT
2465517 TTTTTAATTAC
1 TTTTTAATTAC
2465528 TTTTTAATTAC
1 TTTTTAATTAC
2465539 TTTTT
1 TTTTT
2465544 TTCTTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTTAATTAC
Found at i:2465554 original size:10 final size:10
Alignment explanation
Indices: 2465541--2465594 Score: 56
Period size: 10 Copynumber: 5.2 Consensus size: 10
2465531 TTAATTACTT
2465541 TTTTTCTTTC
1 TTTTTCTTTC
2465551 TTTTTCTTTC
1 TTTTTCTTTC
2465561 TCTTTT-TTTC
1 T-TTTTCTTTC
*
2465571 TTTCTTTTTTC
1 TTT-TTCTTTC
*
2465582 TTCTTCTCTTC
1 TTTTTCT-TTC
2465593 TT
1 TT
2465595 CTTGTCTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
9 2 0.05
10 21 0.55
11 15 0.39
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:2465560 original size:14 final size:13
Alignment explanation
Indices: 2465539--2465591 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 13
2465529 TTTTAATTAC
2465539 TTTT-TTTCTTTCT
1 TTTTCTTTCTTT-T
2465552 TTTTCTTTCTCTTT
1 TTTTCTTTCT-TTT
2465566 TTTTCTTTCTTTT
1 TTTTCTTTCTTTT
2465579 TTCTTCTTCTCTT
1 TT-TTCTT-TCTT
2465592 CTTCTTGTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
13 9 0.25
14 21 0.58
15 6 0.17
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTCTTTCTTTT
Found at i:2466178 original size:29 final size:29
Alignment explanation
Indices: 2466145--2466245 Score: 80
Period size: 30 Copynumber: 3.4 Consensus size: 29
2466135 TGTAATTTTT
2466145 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGATTAAAATGAAATTTAA
* * * *
2466174 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGAT-TAAAATGAAATTTAA
* * *
2466204 AGAAAGTTTAAGAGTCAAAATGAAATTT-A
1 AGAAAATTTAGGA-TTAAAATGAAATTTAA
*
2466233 GGAAAAGTTTAGG
1 AGAAAA-TTTAGG
2466246 GGTCAAAATG
Statistics
Matches: 55, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
29 14 0.25
30 40 0.73
31 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.22, T:0.30
Consensus pattern (29 bp):
AGAAAATTTAGGATTAAAATGAAATTTAA
Found at i:2466200 original size:30 final size:30
Alignment explanation
Indices: 2466160--2466261 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
2466150 ATTTAGGATT
*
2466160 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * * *
2466190 TAAGTGAAATTTAAAGAAAGTTTAAGAGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
2466220 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
2466250 AAAATGCAATTT
1 AAAATGAAATTT
2466262 TTATTTTTAA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 2 0.03
30 58 0.97
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:2466282 original size:14 final size:15
Alignment explanation
Indices: 2466257--2466291 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
2466247 GTCAAAATGC
2466257 AATTTTTATTTTTAA
1 AATTTTTATTTTTAA
*
2466272 AATTTTT-TTTTTGA
1 AATTTTTATTTTTAA
2466286 AATTTT
1 AATTTT
2466292 GAAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
AATTTTTATTTTTAA
Found at i:2466704 original size:15 final size:16
Alignment explanation
Indices: 2466674--2466706 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2466664 TTTTTAAGAA
2466674 AAAATATTAAAAAAAG
1 AAAATATTAAAAAAAG
*
2466690 AAAAT-TTAGAAAAAG
1 AAAATATTAAAAAAAG
2466705 AA
1 AA
2466707 TTTTATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (16 bp):
AAAATATTAAAAAAAG
Found at i:2467698 original size:19 final size:19
Alignment explanation
Indices: 2467674--2467711 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2467664 TTTTTTCTTC
*
2467674 GTTTTGATTTATGTGATAA
1 GTTTTGATCTATGTGATAA
2467693 GTTTTGATCTATGTGATAA
1 GTTTTGATCTATGTGATAA
2467712 CGTGACACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.50
Consensus pattern (19 bp):
GTTTTGATCTATGTGATAA
Found at i:2468249 original size:114 final size:113
Alignment explanation
Indices: 2468021--2468317 Score: 348
Period size: 114 Copynumber: 2.6 Consensus size: 113
2468011 TCAAGTTGAG
* *
2468021 AAAGTTGTCAAGTTTAGGGACTAAATGTTGACTTATCCCTAATTTTGTGTAAAAAAATTAGGTGA
1 AAAGTTGCCAAGTTTAGGG-CTAAATGTTGACTTATCCCTAATTTTGTAT-AAAAAATTAGGTGA
* * * *
2468086 TAATATGTCATAATCTCATAGTGTCATGTCAACATAGGACCAAGTTGGGA
64 TAATATGTCACAATCTCATAATGTCATGTCAACATAGGACAAAATTGGGA
* * * * * *
2468136 AAATTTGCCAAGTTTAGGGCTAAATGTTGACTTATTCCTAA-CTTGTATAAAAATTTAGTTGATG
1 AAAGTTGCCAAGTTTAGGGCTAAATGTTGACTTATCCCTAATTTTGTATAAAAAATTAGGTGATA
* *
2468200 ATGA-GTCACAATCTCATAATGTTATGTCATCATAGGAACTAAAATTGGGA
66 AT-ATGTCACAATCTCATAATGTCATGTCAACATAGG-AC-AAAATTGGGA
** *
2468250 AAAGTTGCCAAG-TTAGAGATTAAATGTTGAATTATCCCTAATTTTGTATAAAAAAAATTAGGTG
1 AAAGTTGCCAAGTTTAG-GGCTAAATGTTGACTTATCCCTAATTTTGTAT--AAAAAATTAGGTG
2468314 ATAA
63 ATAA
2468318 CGTGTAATAA
Statistics
Matches: 152, Mismatches: 23, Indels: 12
0.81 0.12 0.06
Matches are distributed among these distances:
112 43 0.28
113 12 0.08
114 60 0.39
115 23 0.15
117 14 0.09
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (113 bp):
AAAGTTGCCAAGTTTAGGGCTAAATGTTGACTTATCCCTAATTTTGTATAAAAAATTAGGTGATA
ATATGTCACAATCTCATAATGTCATGTCAACATAGGACAAAATTGGGA
Found at i:2474771 original size:3 final size:3
Alignment explanation
Indices: 2474763--2474788 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2474753 CCGACCACCG
2474763 TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TC
2474789 GAGCTCCACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
TCC
Found at i:2477877 original size:29 final size:30
Alignment explanation
Indices: 2477824--2477903 Score: 99
Period size: 29 Copynumber: 2.6 Consensus size: 30
2477814 ATATTAAAAT
* *
2477824 TATATATGAATTATAATTTAATGTGCAATTG
1 TATATATGAATTTTGATTT-ATGTGCAATTG
* *
2477855 TATATATGAATTTTGATTT-TGTGTAATTT
1 TATATATGAATTTTGATTTATGTGCAATTG
2477884 TATATATGAATTTTTGATTT
1 TATATATGAA-TTTTGATTT
2477904 GATATAATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 18 0.41
30 9 0.20
31 17 0.39
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.54
Consensus pattern (30 bp):
TATATATGAATTTTGATTTATGTGCAATTG
Found at i:2477912 original size:30 final size:29
Alignment explanation
Indices: 2477823--2477914 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 29
2477813 AATATTAAAA
* * **
2477823 TTATATATGAATTATAATTTAATGTGCAATT
1 TTATATATGAATTTTGATTT--TGTATAATT
* *
2477854 GTATATATGAATTTTGATTTTGTGTAATT
1 TTATATATGAATTTTGATTTTGTATAATT
2477883 TTATATATGAATTTTTGA-TTTGATATAATT
1 TTATATATGAA-TTTTGATTTTG-TATAATT
2477913 TT
1 TT
2477915 TGTAATTTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
29 22 0.42
30 14 0.26
31 17 0.32
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.54
Consensus pattern (29 bp):
TTATATATGAATTTTGATTTTGTATAATT
Found at i:2480520 original size:19 final size:20
Alignment explanation
Indices: 2480498--2480542 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
2480488 ACAAAATAAA
*
2480498 CAAAATAATTT-TTAAAATT-
1 CAAAAT-ATTTATAAAAATTC
2480517 CAAAATATTTATAAAAATTC
1 CAAAATATTTATAAAAATTC
2480537 CAAAAT
1 CAAAAT
2480543 TTATACTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 13 0.57
20 6 0.26
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.36
Consensus pattern (20 bp):
CAAAATATTTATAAAAATTC
Found at i:2482020 original size:45 final size:46
Alignment explanation
Indices: 2481957--2482043 Score: 106
Period size: 45 Copynumber: 1.9 Consensus size: 46
2481947 TCTAAACTAA
* *
2481957 AAAAAACTTAATGTTATTTACTTTGAAATAAAA-AATAAAATAATT
1 AAAAAACTTAATCTTATTTACTTTAAAATAAAATAATAAAATAATT
** *
2482002 AAAAAA-TGTAATCTTATTTGTTTTAAAATAAAATAATTAAAT
1 AAAAAACT-TAATCTTATTTACTTTAAAATAAAATAATAAAAT
2482044 TAAATTTGGG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
44 1 0.03
45 27 0.77
46 7 0.20
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (46 bp):
AAAAAACTTAATCTTATTTACTTTAAAATAAAATAATAAAATAATT
Found at i:2492846 original size:118 final size:118
Alignment explanation
Indices: 2492682--2492911 Score: 379
Period size: 118 Copynumber: 1.9 Consensus size: 118
2492672 TATTTCCGGT
* *
2492682 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
1 TAGCGGAGTTTTACCCAACACGTCAAACAACCTTTTGACGCAAAGTAGAATGACAACCCAAGCAC
* *
2492747 CCTACCCCGGTTACTCAGTCAGTCACGATTTGAGCCATACTCATAACCTCGGC
66 CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCCATACTCATAACCTCGGC
****
2492800 TAGCGGAGTTTTACTTGTCACGTCAAACAACCTTTTGACGCAAAGTAGAATGACAACCCAAGCAC
1 TAGCGGAGTTTTACCCAACACGTCAAACAACCTTTTGACGCAAAGTAGAATGACAACCCAAGCAC
*
2492865 CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCTATACTCATAAC
66 CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCCATACTCATAAC
2492912 AATGGAAAAC
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
118 103 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (118 bp):
TAGCGGAGTTTTACCCAACACGTCAAACAACCTTTTGACGCAAAGTAGAATGACAACCCAAGCAC
CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCCATACTCATAACCTCGGC
Found at i:2493739 original size:42 final size:42
Alignment explanation
Indices: 2493693--2493808 Score: 160
Period size: 42 Copynumber: 2.8 Consensus size: 42
2493683 GGGATTCTAT
* * *
2493693 GGCTGAAATAGGACTGTTTGGCTGCAGGGATATGACATTCTG
1 GGCTGGAATAGAACTGTTTGGCAGCAGGGATATGACATTCTG
* * *
2493735 GGCTGGAATAAAACTGTTTGGCAGCAGGGATATGGCATTTTG
1 GGCTGGAATAGAACTGTTTGGCAGCAGGGATATGACATTCTG
* *
2493777 GGCTGGAATAGAACTGTTTGGCACCATGGATA
1 GGCTGGAATAGAACTGTTTGGCAGCAGGGATA
2493809 GGGTTGCTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.26, C:0.14, G:0.33, T:0.28
Consensus pattern (42 bp):
GGCTGGAATAGAACTGTTTGGCAGCAGGGATATGACATTCTG
Found at i:2493927 original size:7 final size:7
Alignment explanation
Indices: 2493915--2493966 Score: 67
Period size: 7 Copynumber: 7.9 Consensus size: 7
2493905 AAATAAAATA
2493915 AAATAAT
1 AAATAAT
2493922 AAATAAT
1 AAATAAT
2493929 AAATAAT
1 AAATAAT
2493936 AAA-AGA-
1 AAATA-AT
2493942 AAATAAT
1 AAATAAT
2493949 AAATAA-
1 AAATAAT
2493955 AAATAA-
1 AAATAAT
2493961 AAATAA
1 AAATAA
2493967 AGATTGGGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
6 17 0.40
7 25 0.60
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (7 bp):
AAATAAT
Found at i:2493939 original size:27 final size:26
Alignment explanation
Indices: 2493906--2493967 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 26
2493896 ATTTAACTAA
2493906 AATAAAATAAAATAATAAATAATAAAT
1 AATAAAATAAAATAATAAATAA-AAAT
*
2493933 AATAAAAGAAAATAATAAATAAAAAT
1 AATAAAATAAAATAATAAATAAAAAT
2493959 -A-AAAATAAA
1 AATAAAATAAA
2493968 GATTGGGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
24 7 0.21
25 1 0.03
26 4 0.12
27 21 0.64
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (26 bp):
AATAAAATAAAATAATAAATAAAAAT
Found at i:2498396 original size:5 final size:5
Alignment explanation
Indices: 2498382--2498413 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
2498372 TTGTGTGTTC
2498382 TTTA- TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
2498414 TCACAGTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:2514261 original size:20 final size:21
Alignment explanation
Indices: 2514225--2514269 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
2514215 CATAAATTAT
*
2514225 TAAAATATTCATTTAATTACA
1 TAAAATATTCATCTAATTACA
*
2514246 TAAAATATT-ATCTAATTACG
1 TAAAATATTCATCTAATTACA
2514266 TAAA
1 TAAA
2514270 TCAGTATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (21 bp):
TAAAATATTCATCTAATTACA
Found at i:2518000 original size:6 final size:6
Alignment explanation
Indices: 2517991--2518027 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
2517981 TCCCACCCGG
*
2517991 TCCCTC TCCCTC TCCCTC TCCCTC TCCCTT TCCCTC T
1 TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC T
2518028 GCACCGTCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (6 bp):
TCCCTC
Found at i:2518192 original size:6 final size:6
Alignment explanation
Indices: 2518181--2518226 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
2518171 GCCTTCACCT
2518181 CCCACA CCCACA CCCACA CCCACA CCCACA CCCACA CCCACA CCCA
1 CCCACA CCCACA CCCACA CCCACA CCCACA CCCACA CCCACA CCCA
2518227 AGTGGAACAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCACA
Found at i:2528417 original size:14 final size:15
Alignment explanation
Indices: 2528405--2528486 Score: 58
Period size: 15 Copynumber: 4.9 Consensus size: 15
2528395 TGCTCTTTAC
2528405 TTTTTTTATTTTATA
1 TTTTTTTATTTTATA
2528420 TTTTTTTAAATAAATTGTATA
1 TTTTTTT--AT---TT-TATA
*
2528441 TTTTATTAGTTTTATA
1 TTTTTTTA-TTTTATA
2528457 -TTTTTTATTTTATA
1 TTTTTTTATTTTATA
*
2528471 GTTTTTATAATTTTAT
1 -TTTTT-TTATTTTAT
2528487 TTTAGGATAA
Statistics
Matches: 54, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
14 7 0.13
15 13 0.24
16 8 0.15
17 12 0.22
19 1 0.02
20 3 0.06
21 10 0.19
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.70
Consensus pattern (15 bp):
TTTTTTTATTTTATA
Found at i:2528475 original size:22 final size:23
Alignment explanation
Indices: 2528439--2528490 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
2528429 ATAAATTGTA
*
2528439 TATTTTATTAG-TTTTATATTTTT
1 TATTTTATTAGTTTTTATA-ATTT
2528462 TATTTTA-TAGTTTTTATAATTT
1 TATTTTATTAGTTTTTATAATTT
2528484 TATTTTA
1 TATTTTA
2528491 GGATAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 13 0.48
23 14 0.52
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (23 bp):
TATTTTATTAGTTTTTATAATTT
Found at i:2529038 original size:16 final size:14
Alignment explanation
Indices: 2529009--2529060 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
2528999 GAAGAGAATG
2529009 AAAAAT-AAAGAAA
1 AAAAATAAAAGAAA
2529022 AAAAATAAAAGTTAAA
1 AAAAATAAAAG--AAA
*
2529038 AAATATAAAAGAAA
1 AAAAATAAAAGAAA
*
2529052 AAAATTAAA
1 AAAAATAAA
2529061 TTACTCAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
13 6 0.18
14 14 0.42
16 13 0.39
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (14 bp):
AAAAATAAAAGAAA
Found at i:2542435 original size:137 final size:136
Alignment explanation
Indices: 2542052--2542445 Score: 442
Period size: 136 Copynumber: 2.9 Consensus size: 136
2542042 TTAAATTTAC
* * * * * *
2542052 TTTGATTTTTCGATTAATCAAGTTGAGTTAATATTATAAGTTAATTTAGTATCAA-TTAAAAATT
1 TTTGATTTTTCGATTAATCAAGCTGAGTTAGTATCACAAGTTAATTTGGTATCAACTGAAAAA-T
* * ** * * * * *
2542116 TTAAAA-CCTGAATTTTTTTAGTTTATTTCTTTAAATAAATTTATAATTTGTTTTAAATTAGATA
65 TTAAAATACTAAAAGTTTTTAATTTATGTCTTTAAATAATTTTATAATTTTTTTTAAATCAGATA
2542180 ATTTTGA
130 ATTTTGA
* * * *
2542187 CTTTGATTTTTCGATTATTCAAGCTGAATT-GATATCACAAGTTAATTTGATACCAACTGAAAAG
1 -TTTGATTTTTCGATTAATCAAGCTGAGTTAG-TATCACAAGTTAATTTGGTATCAACTGAAAA-
* * * *
2542251 A-TT-AAATACTAAAAGTTTTTAATTTATGTCATCAGATAATTTCATAATTTATTTTTAAATCAG
63 ATTTAAAATACTAAAAGTTTTTAATTTATGTCTTTAAATAATTTTATAATTT-TTTTTAAATCAG
*
2542314 ATAGTTTTG-
127 ATAATTTTGA
* * *
2542323 TTCTGATTTTTCTATCAATCAAGCCGAGTTAGTATCACAAGTTAATTTGGTATCAACTGAAAAAT
1 TT-TGATTTTTCGATTAATCAAGCTGAGTTAGTATCACAAGTTAATTTGGTATCAACTGAAAAAT
2542388 TTAAAATACTAAAAGTTTTTAATTTATGTCTTTAAATAATTTTATAA-TTTTTTTAAAT
65 TTAAAATACTAAAAGTTTTTAATTTATGTCTTTAAATAATTTTATAATTTTTTTTAAAT
2542446 TAAATAAATT
Statistics
Matches: 214, Mismatches: 35, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
135 15 0.07
136 134 0.63
137 64 0.30
138 1 0.00
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (136 bp):
TTTGATTTTTCGATTAATCAAGCTGAGTTAGTATCACAAGTTAATTTGGTATCAACTGAAAAATT
TAAAATACTAAAAGTTTTTAATTTATGTCTTTAAATAATTTTATAATTTTTTTTAAATCAGATAA
TTTTGA
Found at i:2550969 original size:23 final size:23
Alignment explanation
Indices: 2550938--2550988 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
2550928 CAAACCAGTA
2550938 CATGGTGAAATACACGCCACCTC
1 CATGGTGAAATACACGCCACCTC
*
2550961 TATGGTGAAATACACGCCACCTC
1 CATGGTGAAATACACGCCACCTC
2550984 CATGG
1 CATGG
2550989 GCAACAATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (23 bp):
CATGGTGAAATACACGCCACCTC
Found at i:2553260 original size:20 final size:21
Alignment explanation
Indices: 2553237--2553284 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
2553227 ATTCAAATTG
2553237 AAATACTAAAATTCAAGAT-A
1 AAATACTAAAATTCAAGATAA
* *
2553257 AAAT-CTTGAAATTCAGGATAA
1 AAATAC-TAAAATTCAAGATAA
2553278 AAATACT
1 AAATACT
2553285 GATGTGGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 1 0.04
20 15 0.65
21 6 0.26
22 1 0.04
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.27
Consensus pattern (21 bp):
AAATACTAAAATTCAAGATAA
Found at i:2556070 original size:137 final size:138
Alignment explanation
Indices: 2555890--2556208 Score: 398
Period size: 137 Copynumber: 2.3 Consensus size: 138
2555880 ACTTAAATTT
* * *
2555890 ACTTTGATTTTTCAATTAATCAAGCTAAATTAGTATCATAAGTTAATTTGATATCAACT-AAAAG
1 ACTTTGATTTTTCGATTAATCAAGCTGAATTAGTATCATAAGTTAATTTGATACCAACTGAAAAG
* * * * * * *
2555954 TTTTAAAAATTAAAATTTTTTTAATTTGTATCTTTAAATAAACTT-ATAATTTG-TTTTAAATTA
66 -ATTAAAAACTAAAA-GTTTTTAATTTATATCATCAAAT-AACTTCATAATTTGTTTTTAAATAA
2556017 GATAG-TTTCG
128 GATAGTTTTCG
* *
2556027 ACTTTGATTTTTCGATTAATCAAGCTGAATT-GATATCAAAAGTTAATTTGATACCAATTGAAAA
1 ACTTTGATTTTTCGATTAATCAAGCTGAATTAG-TATCATAAGTTAATTTGATACCAACTGAAAA
* * *
2556091 GATTAAATACTAAAAGTTTTTAATTTATGTCATCAAATAATTTCATAATTTGTTTTTAAATAAGA
65 GATTAAAAACTAAAAGTTTTTAATTTATATCATCAAATAACTTCATAATTTGTTTTTAAATAAGA
*
2556156 TAGTTTTTG
130 TAGTTTTCG
* *
2556165 -CTTTGATTTTTTGATTAATCAAGCTGAGTTAGTATCATAAGTTA
1 ACTTTGATTTTTCGATTAATCAAGCTGAATTAGTATCATAAGTTA
2556209 CAAAAAAATT
Statistics
Matches: 157, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
135 4 0.03
136 27 0.17
137 116 0.74
138 10 0.06
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (138 bp):
ACTTTGATTTTTCGATTAATCAAGCTGAATTAGTATCATAAGTTAATTTGATACCAACTGAAAAG
ATTAAAAACTAAAAGTTTTTAATTTATATCATCAAATAACTTCATAATTTGTTTTTAAATAAGAT
AGTTTTCG
Found at i:2556569 original size:20 final size:21
Alignment explanation
Indices: 2556532--2556570 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2556522 CATGTGACAC
2556532 ATTAAATATTTAATTTATATA
1 ATTAAATATTTAATTTATATA
*
2556553 ATTAAAT-TTTCATTTATA
1 ATTAAATATTTAATTTATA
2556571 ATTAATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTAAATATTTAATTTATATA
Found at i:2556965 original size:19 final size:20
Alignment explanation
Indices: 2556930--2556979 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2556920 CTTTTAAATA
*
2556930 TAAATAAA-CTTAATA-TTT
1 TAAATAAATCTAAATATTTT
2556948 TAAATAAATCTAAATATTTT
1 TAAATAAATCTAAATATTTT
2556968 TAAATAAATCTA
1 TAAATAAATCTA
2556980 CTTTTATGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 8 0.28
19 6 0.21
20 15 0.52
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAATAAATCTAAATATTTT
Found at i:2557145 original size:34 final size:37
Alignment explanation
Indices: 2557076--2557149 Score: 100
Period size: 38 Copynumber: 2.1 Consensus size: 37
2557066 GTAAGAATAG
*
2557076 GAAAGATATATAATATATTCCTAAATATATGCCTAAAA
1 GAAAGATATACAATATATT-CTAAATATATGCCTAAAA
*
2557114 GAAAGATATACAATATATT-TAGATAT-T-CCTAAAA
1 GAAAGATATACAATATATTCTAAATATATGCCTAAAA
2557148 GA
1 GA
2557150 TAATATCCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 9 0.26
35 1 0.03
36 6 0.18
38 18 0.53
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.31
Consensus pattern (37 bp):
GAAAGATATACAATATATTCTAAATATATGCCTAAAA
Found at i:2562620 original size:41 final size:41
Alignment explanation
Indices: 2562561--2562642 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
2562551 ATTAACAAGA
*
2562561 GATGCTATAGCTTCTAGTTTAATGAATTCACTTTAAAATGC
1 GATGCTATAGCTTATAGTTTAATGAATTCACTTTAAAATGC
2562602 GATGCTATAGCTTATAGTTTAATGAATTCACTTTAAAATGC
1 GATGCTATAGCTTATAGTTTAATGAATTCACTTTAAAATGC
2562643 AAATGTTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (41 bp):
GATGCTATAGCTTATAGTTTAATGAATTCACTTTAAAATGC
Found at i:2570595 original size:18 final size:18
Alignment explanation
Indices: 2570562--2570597 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2570552 TTATATATCG
* *
2570562 TTATTATTAGTCTTTTTA
1 TTATTATTACTATTTTTA
2570580 TTATTATTACTATTTTTA
1 TTATTATTACTATTTTTA
2570598 ATAAATATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.67
Consensus pattern (18 bp):
TTATTATTACTATTTTTA
Found at i:2572985 original size:18 final size:18
Alignment explanation
Indices: 2572944--2572985 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2572934 ATACATCTAT
*
2572944 AAAATAATAGTATTAATA
1 AAAATAATAGGATTAATA
*
2572962 ACAATAATAAGGATT-ATA
1 AAAATAAT-AGGATTAATA
2572980 AAAATA
1 AAAATA
2572986 CATACATGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AAAATAATAGGATTAATA
Found at i:2573346 original size:20 final size:19
Alignment explanation
Indices: 2573323--2573370 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
2573313 ACTACTTCAC
2573323 AAATATAT-ATACATATACTA
1 AAATATATAATA-ATATA-TA
2573343 AAATATACATAATAATATATA
1 AAATAT--ATAATAATATATA
2573364 AAATATA
1 AAATATA
2573371 ATATTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
19 1 0.04
20 6 0.24
21 8 0.32
22 7 0.28
23 3 0.12
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATATATAATAATATATA
Found at i:2573440 original size:28 final size:30
Alignment explanation
Indices: 2573404--2573475 Score: 92
Period size: 32 Copynumber: 2.4 Consensus size: 30
2573394 TATATGAAAA
*
2573404 ATATATATATAATATAATATTAATAAAAATAC
1 ATATATATATAATA-CATATTAA-AAAAATAC
* *
2573436 ATATATATGTAATACATATTAAAAGAATAC
1 ATATATATATAATACATATTAAAAAAATAC
2573466 ATATA-ATATA
1 ATATATATATA
2573476 CATATATTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 4 0.11
30 12 0.33
31 7 0.19
32 13 0.36
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (30 bp):
ATATATATATAATACATATTAAAAAAATAC
Found at i:2573442 original size:30 final size:29
Alignment explanation
Indices: 2573406--2573481 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 29
2573396 TATGAAAAAT
2573406 ATATATATAATATAATATTAATAAAAATAC
1 ATATATATAATATAATATTAA-AAAAATAC
* *
2573436 ATATATATGTAATA-CATATTAAAAGAATAC
1 ATATATA--TAATATAATATTAAAAAAATAC
2573466 ATATAATATACATATA
1 ATAT-ATATA-ATATA
2573482 TTTCAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
29 2 0.05
30 21 0.55
31 10 0.26
32 5 0.13
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.36
Consensus pattern (29 bp):
ATATATATAATATAATATTAAAAAAATAC
Found at i:2573476 original size:26 final size:27
Alignment explanation
Indices: 2573401--2573480 Score: 83
Period size: 26 Copynumber: 2.9 Consensus size: 27
2573391 TGATATATGA
*
2573401 AAAATATATATATAATATA-ATATTAAT
1 AAAA-ATACATATAATATACATATTAAT
2573428 AAAAATACATATATATGTAATACATATTAA-
1 AAAAATACATATA-A--T-ATACATATTAAT
*
2573458 AAGAATACATATAATATACATAT
1 AAAAATACATATAATATACATAT
2573481 ATTTCAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
26 16 0.35
27 6 0.13
29 2 0.04
30 15 0.33
31 7 0.15
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (27 bp):
AAAAATACATATAATATACATATTAAT
Found at i:2573546 original size:2 final size:2
Alignment explanation
Indices: 2573539--2573564 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2573529 TTACATAAAG
2573539 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
2573565 AATAATGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2575004 original size:37 final size:36
Alignment explanation
Indices: 2574955--2575028 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 36
2574945 TGATTAGGGT
*
2574955 TAGGGTGGTTAGGGTATTGGGTATGGGTTAGTGGGC
1 TAGGGTGGTTAGGGTAGTGGGTATGGGTTAGTGGGC
* *
2574991 TAGGTTGGTTTAGGTTAGTGGGTATGGGTTAGTGGGC
1 TAGGGTGG-TTAGGGTAGTGGGTATGGGTTAGTGGGC
2575028 T
1 T
2575029 TCTGAATTGG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 7 0.21
37 27 0.79
ACGTcount: A:0.14, C:0.03, G:0.47, T:0.36
Consensus pattern (36 bp):
TAGGGTGGTTAGGGTAGTGGGTATGGGTTAGTGGGC
Found at i:2575780 original size:37 final size:37
Alignment explanation
Indices: 2575736--2575901 Score: 305
Period size: 37 Copynumber: 4.5 Consensus size: 37
2575726 CACTTGTCCC
2575736 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
2575773 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
*
2575810 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
* *
2575847 TGATCAGATAAGTGTAGCCACTTATCACTTTGTCTCT
1 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
2575884 TGATCAGATAAGTGTAGC
1 TGATCAGATAAGTGTAGC
2575902 TAAAGCTATC
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 127 1.00
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.37
Consensus pattern (37 bp):
TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
Found at i:2575944 original size:52 final size:52
Alignment explanation
Indices: 2575865--2576231 Score: 470
Period size: 52 Copynumber: 7.2 Consensus size: 52
2575855 TAAGTGTAGC
* * **
2575865 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTAT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
2575918 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* *
2575970 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
** *
2576016 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* *
2576068 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* * *
2576114 CACTTTCCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* ** *
2576166 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
2576218 CACTTTGTCACTTG
1 CACTTT-TCACTTG
2576232 ATCAGAAGTA
Statistics
Matches: 278, Mismatches: 23, Indels: 26
0.85 0.07 0.08
Matches are distributed among these distances:
46 83 0.30
49 3 0.01
52 177 0.64
53 15 0.05
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
Done.