Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 54 of 310
Found at i:16676124 original size:158 final size:157
Alignment explanation
Indices: 16675833--16676147 Score: 531
Period size: 158 Copynumber: 2.0 Consensus size: 157
16675823 AGATCTAGCC
* * * * **
16675833 CATTTTGATAGTTAATATAATTTAAGGTCATCATGATAAGTTATAAATCGAAACCCAATTAAAAA
1 CATTTTGACAGTTAATATAATTTAAGATCATCATGATAAGTTATAAATCAAAACCAAAAAAAAAA
* *
16675898 TAATCATAAGCGGCCTTATTACATAACAAAACCCAAATCATCAAAGTAAAGAAAATTGAAGTCTA
66 TAATCATAAGCGGCCATATTACATAACAAAACCCAAATCATCAAAGTAAAGAAAATTGAAGTCCA
16675963 AATCACCAGAAGAAATCCATATTGCAG
131 AATCACCAGAAGAAATCCATATTGCAG
16675990 CATTTTGACAGTTAATATAATTTAAGATCATCATGATAAGTTATAAATCAAAACCTAAAAAAAAA
1 CATTTTGACAGTTAATATAATTTAAGATCATCATGATAAGTTATAAATCAAAACC-AAAAAAAAA
* *
16676055 ATAATTATAAGTGGCCATATTACATAACAAAACCCAAATCATCAAAGTAAAGAAAATTGAAGTCC
65 ATAATCATAAGCGGCCATATTACATAACAAAACCCAAATCATCAAAGTAAAGAAAATTGAAGTCC
16676120 AAATCACCAGAAGAAATCCATATTGCAG
130 AAATCACCAGAAGAAATCCATATTGCAG
16676148 AACGAGTGGC
Statistics
Matches: 147, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
157 52 0.35
158 95 0.65
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.26
Consensus pattern (157 bp):
CATTTTGACAGTTAATATAATTTAAGATCATCATGATAAGTTATAAATCAAAACCAAAAAAAAAA
TAATCATAAGCGGCCATATTACATAACAAAACCCAAATCATCAAAGTAAAGAAAATTGAAGTCCA
AATCACCAGAAGAAATCCATATTGCAG
Found at i:16676550 original size:28 final size:27
Alignment explanation
Indices: 16676495--16676579 Score: 102
Period size: 27 Copynumber: 3.1 Consensus size: 27
16676485 AGCATGGCTG
* *
16676495 CCAGA-ACAGATAATGTGACAGAGTCA
1 CCAGATACAGATAATGTGGCAGAGCCA
16676521 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGATACAGATAAT-GTGGCAGAGCCA
* *
16676549 CCAGAT-CAGATAATTATGGCATAGCCA
1 CCAGATACAGATAA-TGTGGCAGAGCCA
16676576 CCAG
1 CCAG
16676580 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
26 5 0.10
27 30 0.58
28 17 0.33
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (27 bp):
CCAGATACAGATAATGTGGCAGAGCCA
Found at i:16683493 original size:19 final size:19
Alignment explanation
Indices: 16683469--16683510 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
16683459 ATTTTTCCAT
16683469 AAAAATATTA-AAAATAAGA
1 AAAAATA-TAGAAAATAAGA
*
16683488 AAAAATATAGAAAATTAGA
1 AAAAATATAGAAAATAAGA
16683507 AAAA
1 AAAA
16683511 TAAAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (19 bp):
AAAAATATAGAAAATAAGA
Found at i:16683526 original size:25 final size:24
Alignment explanation
Indices: 16683487--16683540 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
16683477 TAAAAATAAG
16683487 AAAAAATATAGAAAATTAGAAAAAT
1 AAAAAATATAGAAAATTA-AAAAAT
16683512 AAAAAATATTA-AAAATTAAAAAAT
1 AAAAAATA-TAGAAAATTAAAAAAT
*
16683536 GAAAA
1 AAAAA
16683541 TTGATATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 10 0.37
25 15 0.56
26 2 0.07
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (24 bp):
AAAAAATATAGAAAATTAAAAAAT
Found at i:16683551 original size:25 final size:24
Alignment explanation
Indices: 16683468--16683559 Score: 76
Period size: 27 Copynumber: 3.5 Consensus size: 24
16683458 TATTTTTCCA
* *
16683468 TAAAAATATTAAAAATAAGAAAAAAT
1 TAAAAAT-TAAAAAATAA-AAAATAT
16683494 ATAGAAAATTAGAAAAATAAAAAATAT
1 -TA-AAAATTA-AAAAATAAAAAATAT
* *
16683521 TAAAAATTAAAAAATGAAAATTGAT
1 TAAAAATTAAAAAATAAAAAAT-AT
16683546 ATAAAAATATAAAA
1 -TAAAAAT-TAAAA
16683560 TTAACAAAAC
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
24 11 0.20
25 9 0.16
26 9 0.16
27 14 0.25
28 13 0.23
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (24 bp):
TAAAAATTAAAAAATAAAAAATAT
Found at i:16683559 original size:7 final size:8
Alignment explanation
Indices: 16683467--16683559 Score: 57
Period size: 9 Copynumber: 10.8 Consensus size: 8
16683457 ATATTTTTCC
16683467 ATAAAAAT
1 ATAAAAAT
16683475 ATTAAAAAT
1 A-TAAAAAT
*
16683484 AAGAAAAAAT
1 -A-TAAAAAT
16683494 ATAGAAAATT
1 ATA-AAAA-T
*
16683504 AGAAAAAT
1 ATAAAAAT
16683512 A-AAAAAT
1 ATAAAAAT
16683519 ATTAAAAAT
1 A-TAAAAAT
16683528 -TAAAAA-
1 ATAAAAAT
16683534 ATGAAAATTGAT
1 AT-AAAA---AT
16683546 ATAAAAAT
1 ATAAAAAT
16683554 ATAAAA
1 ATAAAA
16683560 TTAACAAAAC
Statistics
Matches: 69, Mismatches: 4, Indels: 24
0.71 0.04 0.25
Matches are distributed among these distances:
7 14 0.20
8 16 0.23
9 22 0.32
10 10 0.14
11 5 0.07
12 2 0.03
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (8 bp):
ATAAAAAT
Found at i:16684005 original size:28 final size:27
Alignment explanation
Indices: 16683966--16684191 Score: 80
Period size: 28 Copynumber: 8.1 Consensus size: 27
16683956 TTTATGTTTT
* *
16683966 TTTTATACTTTTTATA-TGTTTATATAA
1 TTTTATAATTTTTATATTCTTTATA-AA
*
16683993 TTTTAGTAATTTTAATATTCTTTATAAA
1 TTTTA-TAATTTTTATATTCTTTATAAA
*
16684021 TTTTAATAATTTATTATTATTTTTTA-AGAA
1 TTTT-ATAATTT-TTA-TATTCTTTATA-AA
* * *
16684051 TTATAATACATTTTTCTAAT-TTTA-AATA
1 TT-TTATA-ATTTTTATATTCTTTATAA-A
* *
16684079 TTTTAAATAAGTTTTATTAAT-TTTATAAA
1 TTTT--ATAATTTTTA-TATTCTTTATAAA
*
16684108 TTCTTGTATAATTTATTAGATT-TTTAT--A
1 -T-TT-TATAATTT-TTATATTCTTTATAAA
* * *
16684136 TTTTATAA-TTTTAAATT-TATATCAA
1 TTTTATAATTTTTATATTCTTTATAAA
*
16684161 TTTTAATATTTTTTATATT-TTT-TAAA
1 TTTT-ATAATTTTTATATTCTTTATAAA
16684187 GTTTT
1 -TTTT
16684192 TTTTAAGAAT
Statistics
Matches: 157, Mismatches: 20, Indels: 44
0.71 0.09 0.20
Matches are distributed among these distances:
23 10 0.06
24 2 0.01
25 10 0.06
26 8 0.05
27 22 0.14
28 35 0.22
29 26 0.17
30 33 0.21
31 10 0.06
32 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (27 bp):
TTTTATAATTTTTATATTCTTTATAAA
Found at i:16684006 original size:19 final size:18
Alignment explanation
Indices: 16683984--16684032 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
16683974 TTTTTATATG
16683984 TTTATATAATTTTAGT-AAT
1 TTTA-ATAATTTTA-TAAAT
*
16684003 TTTAATATTCTTTATAAAT
1 TTTAATAAT-TTTATAAAT
16684022 TTTAATAATTT
1 TTTAATAATTT
16684033 ATTATTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (18 bp):
TTTAATAATTTTATAAAT
Found at i:16684031 original size:9 final size:9
Alignment explanation
Indices: 16683984--16684149 Score: 56
Period size: 9 Copynumber: 17.6 Consensus size: 9
16683974 TTTTTATATG
16683984 TTTATATAAT
1 TTTA-ATAAT
*
16683994 TTTAGTAAT
1 TTTAATAAT
16684003 TTTAAT-AT
1 TTTAATAAT
*
16684011 TCTTTATAAAT
1 T-TTAAT-AAT
16684022 TTTAATAATT
1 TTTAATAA-T
* *
16684032 TATTATTATTT
1 T-TTAATA-AT
*
16684043 TTTAAGAAT
1 TTTAATAAT
*
16684052 TATAATACAT
1 TTTAATA-AT
**
16684062 TTTTCTAAT
1 TTTAATAAT
16684071 TTTAA-ATAT
1 TTTAATA-AT
16684080 TTTAAATAAGT
1 TTT-AATAA-T
*
16684091 TTTATTAAT
1 TTTAATAAT
16684100 TTT-ATAAAT
1 TTTAAT-AAT
*
16684109 TCTTGTATAA-
1 T-TT-AATAAT
*
16684119 TTTATTAGAT
1 TTTAATA-AT
*
16684129 TTTTAT-AT
1 TTTAATAAT
16684137 TTT-ATAAT
1 TTTAATAAT
16684145 TTTAA
1 TTTAA
16684150 ATTTATATCA
Statistics
Matches: 115, Mismatches: 22, Indels: 39
0.65 0.12 0.22
Matches are distributed among these distances:
7 2 0.02
8 17 0.15
9 43 0.37
10 34 0.30
11 17 0.15
12 2 0.02
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (9 bp):
TTTAATAAT
Found at i:16688461 original size:13 final size:14
Alignment explanation
Indices: 16688425--16688461 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
16688415 TATGTCTATA
*
16688425 TATTTTAAA-AATT
1 TATTTTAAATTATT
16688438 TATTTTAAATTATT
1 TATTTTAAATTATT
16688452 TA-TTTAAATT
1 TATTTTAAATT
16688462 TAAAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTTTAAATTATT
Found at i:16688487 original size:32 final size:32
Alignment explanation
Indices: 16688428--16688489 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
16688418 GTCTATATAT
** *
16688428 TTTAAAAATTTATTTTAAATTATTTATTTAAA
1 TTTAAAAATTTATCATAAAATATTTATTTAAA
16688460 TTTAAAAA-TTATCATAAAATATATTATTTA
1 TTTAAAAATTTATCATAAAATAT-TTATTTA
16688490 TCTTAACATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 11 0.42
32 15 0.58
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (32 bp):
TTTAAAAATTTATCATAAAATATTTATTTAAA
Found at i:16691939 original size:87 final size:87
Alignment explanation
Indices: 16691837--16691997 Score: 286
Period size: 87 Copynumber: 1.9 Consensus size: 87
16691827 TTTATTCAAA
** *
16691837 CTAGAGGAGGGAATAAATATTTTATTACCTTCATTGATGATAGTACAAAATATTGCTATGTATAT
1 CTAGAGGAGAAAATAAATATTTTATTACCTTCATTGATGATAGTACAAAATATTGCTATATATAT
16691902 TTGCTTAAAAGCAAAGGTGAAG
66 TTGCTTAAAAGCAAAGGTGAAG
*
16691924 CTAGAGGAGAAAATAAATATTTTATTACCTTCATTGATGTTAGTACAAAATATTGCTATATATAT
1 CTAGAGGAGAAAATAAATATTTTATTACCTTCATTGATGATAGTACAAAATATTGCTATATATAT
16691989 TTGCTTAAA
66 TTGCTTAAA
16691998 GGAAATATGA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (87 bp):
CTAGAGGAGAAAATAAATATTTTATTACCTTCATTGATGATAGTACAAAATATTGCTATATATAT
TTGCTTAAAAGCAAAGGTGAAG
Found at i:16695105 original size:14 final size:13
Alignment explanation
Indices: 16695086--16695122 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
16695076 TTTAAATTCC
16695086 AATTATATTAGGAT
1 AATTAT-TTAGGAT
*
16695100 AATTATTAAGGAT
1 AATTATTTAGGAT
16695113 AATTATTTAG
1 AATTATTTAG
16695123 ATTTAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (13 bp):
AATTATTTAGGAT
Found at i:16695157 original size:10 final size:10
Alignment explanation
Indices: 16695137--16695195 Score: 57
Period size: 10 Copynumber: 5.9 Consensus size: 10
16695127 AATTTTAGTT
*
16695137 TTTATATTTA
1 TTTATCTTTA
*
16695147 TTTATCCTTA
1 TTTATCTTTA
*
16695157 TTTTTCTTTA
1 TTTATCTTTA
*
16695167 ATTATCTTTA
1 TTTATCTTTA
*
16695177 TTTAAT-TATA
1 TTT-ATCTTTA
16695187 TTTATCTTT
1 TTTATCTTT
16695196 TAGAATTTAA
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
9 2 0.05
10 34 0.89
11 2 0.05
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:16696564 original size:46 final size:46
Alignment explanation
Indices: 16696514--16696686 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
16696504 TGGTTGAGCA
16696514 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
16696560 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
16696605 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
16696653 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
16696687 GGGGCGGGTT
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:16696670 original size:93 final size:93
Alignment explanation
Indices: 16696511--16696681 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
16696501 GGATGGTTGA
* *
16696511 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
16696576 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
16696604 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
16696669 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
16696682 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:16707057 original size:21 final size:22
Alignment explanation
Indices: 16707031--16707100 Score: 92
Period size: 21 Copynumber: 3.3 Consensus size: 22
16707021 TTTATTTTTA
16707031 TTTATTTTTCTTATTTTA-TAT
1 TTTATTTTTCTTATTTTATTAT
*
16707052 TTTATTTTAC-TATTTTATTAT
1 TTTATTTTTCTTATTTTATTAT
*
16707073 TTTATTATT-TTATTTTATTAT
1 TTTATTTTTCTTATTTTATTAT
*
16707094 ATTATTT
1 TTTATTT
16707101 ATTTTTGGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 7 0.17
21 35 0.83
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTATTTTTCTTATTTTATTAT
Found at i:16707065 original size:8 final size:8
Alignment explanation
Indices: 16707053--16707100 Score: 60
Period size: 8 Copynumber: 5.8 Consensus size: 8
16707043 ATTTTATATT
16707053 TTATTTTA
1 TTATTTTA
*
16707061 CTATTTTA
1 TTATTTTA
16707069 TTATTTTA
1 TTATTTTA
16707077 TTATTTTA
1 TTATTTTA
*
16707085 TTTTATTATA
1 --TTATTTTA
16707095 TTATTT
1 TTATTT
16707101 ATTTTTGGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
8 27 0.79
10 7 0.21
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (8 bp):
TTATTTTA
Found at i:16707065 original size:13 final size:13
Alignment explanation
Indices: 16707026--16707100 Score: 73
Period size: 13 Copynumber: 5.6 Consensus size: 13
16707016 CAACCTTTAT
*
16707026 TTTTA-TTTATTT
1 TTTTATTTTATTA
16707038 TTCTTATTTTA-TA
1 TT-TTATTTTATTA
*
16707051 TTTTATTTTACTATT
1 TTTTATTTTA-T-TA
16707066 TTATTATTTTATTA
1 TT-TTATTTTATTA
16707080 TTTTATTTTATTA
1 TTTTATTTTATTA
*
16707093 TATTATTT
1 TTTTATTT
16707101 ATTTTTGGAT
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
12 10 0.19
13 24 0.45
14 7 0.13
15 4 0.08
16 8 0.15
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTATTTTATTA
Found at i:16709287 original size:26 final size:26
Alignment explanation
Indices: 16709258--16709443 Score: 120
Period size: 26 Copynumber: 7.3 Consensus size: 26
16709248 AAACGAAACA
*
16709258 AAATAATATGTAAAGCAATTTAAAGT
1 AAATAATATGTAAAGCAATTTAAAAT
* ** *
16709284 AAATAAGA--TAAAATAATTTAAGAT
1 AAATAATATGTAAAGCAATTTAAAAT
* * *
16709308 AAATAATAAGTAAA-AAAATTAAAAT
1 AAATAATATGTAAAGCAATTTAAAAT
** *
16709333 AAATAATATACAATGCAATTTAAAAT
1 AAATAATATGTAAAGCAATTTAAAAT
* * *
16709359 AAATAATATATATAA-TACTTTAAAAT
1 AAATAATATGTA-AAGCAATTTAAAAT
*
16709385 AACAT-ATA---AAAG-AGTTTAAAAT
1 AA-ATAATATGTAAAGCAATTTAAAAT
**
16709407 AAATAATATGTAAAAATAAATTTAAAAT
1 AAATAATATGT--AAAGCAATTTAAAAT
16709435 AAATAATAT
1 AAATAATAT
16709444 ACAAAACAAA
Statistics
Matches: 125, Mismatches: 22, Indels: 24
0.73 0.13 0.14
Matches are distributed among these distances:
21 2 0.02
22 16 0.13
23 1 0.01
24 19 0.15
25 18 0.14
26 45 0.36
27 6 0.05
28 18 0.14
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (26 bp):
AAATAATATGTAAAGCAATTTAAAAT
Found at i:16709335 original size:25 final size:27
Alignment explanation
Indices: 16709285--16709340 Score: 80
Period size: 25 Copynumber: 2.1 Consensus size: 27
16709275 ATTTAAAGTA
* *
16709285 AATAAGATAAAATAATTTAAGATAAAT
1 AATAAGATAAAATAAATTAAAATAAAT
16709312 AATAAG-TAAAA-AAATTAAAATAAAT
1 AATAAGATAAAATAAATTAAAATAAAT
16709337 AATA
1 AATA
16709341 TACAATGCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 16 0.59
26 5 0.19
27 6 0.22
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (27 bp):
AATAAGATAAAATAAATTAAAATAAAT
Found at i:16709384 original size:22 final size:22
Alignment explanation
Indices: 16709359--16709408 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
16709349 AATTTAAAAT
* * *
16709359 AAATAATATATATAATACTTTA
1 AAATAACATATAAAAGACTTTA
*
16709381 AAATAACATATAAAAGAGTTTA
1 AAATAACATATAAAAGACTTTA
16709403 AAATAA
1 AAATAA
16709409 ATAATATGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (22 bp):
AAATAACATATAAAAGACTTTA
Found at i:16709454 original size:21 final size:20
Alignment explanation
Indices: 16709430--16709477 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
16709420 AAATAAATTT
16709430 AAAATAAATA-ATATACAAAA
1 AAAATAAA-AGATATACAAAA
*
16709450 CAAAATAAAAGATATACATAA
1 -AAAATAAAAGATATACAAAA
16709471 AAAATAA
1 AAAATAA
16709478 TTCGAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.19
Consensus pattern (20 bp):
AAAATAAAAGATATACAAAA
Found at i:16709565 original size:25 final size:25
Alignment explanation
Indices: 16709537--16709611 Score: 98
Period size: 25 Copynumber: 3.0 Consensus size: 25
16709527 GGATAATAGT
*
16709537 TTAAAATACATAATATATGAAAAAC
1 TTAAAATAAATAATATATGAAAAAC
*
16709562 TTAAAATAAATAATA-ATGAAACAAT
1 TTAAAATAAATAATATATGAAA-AAC
*
16709587 TTAAAATAAATAATATGAGGAAAAA
1 TTAAAATAAATAATAT-ATGAAAAA
16709612 AGGTTTAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
24 6 0.14
25 31 0.70
26 2 0.05
27 5 0.11
ACGTcount: A:0.63, C:0.04, G:0.07, T:0.27
Consensus pattern (25 bp):
TTAAAATAAATAATATATGAAAAAC
Found at i:16711333 original size:45 final size:44
Alignment explanation
Indices: 16711269--16711384 Score: 115
Period size: 45 Copynumber: 2.6 Consensus size: 44
16711259 CCATGATTTG
* ** * *
16711269 TAGCTTCTATCTATTCCACTGTAACTTCAAGGAAATGAGATTTGC
1 TAGCTTCAATCTGCTCCACTGTAACTTCAAGGAAATAAGA-CTGC
* * * * * * *
16711314 TATCTTCAGTTTGCTCCACTGCAACTTCAGGGAGATAAGACTGG
1 TAGCTTCAATCTGCTCCACTGTAACTTCAAGGAAATAAGACTGC
16711358 TAGCTTCAATCTGCTCCACTGTAACTT
1 TAGCTTCAATCTGCTCCACTGTAACTT
16711385 TAGAGAGATA
Statistics
Matches: 55, Mismatches: 16, Indels: 1
0.76 0.22 0.01
Matches are distributed among these distances:
44 25 0.45
45 30 0.55
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (44 bp):
TAGCTTCAATCTGCTCCACTGTAACTTCAAGGAAATAAGACTGC
Found at i:16711367 original size:143 final size:142
Alignment explanation
Indices: 16711184--16711548 Score: 493
Period size: 143 Copynumber: 2.5 Consensus size: 142
16711174 TTTCAACCTA
* * *
16711184 CTCCACTGCAACTTCAGAGAGATAAAGA-TTGTGGCTTCAATCTGCTTCACTGTAACTTCAGGTA
1 CTCCACTGCAACTTCAGGGAGAT-AAGACTGGTGGCTTCAATCTGCTCCACTGTAACTTCAGG-A
* * * * *
16711248 GATAAGATCCGCCATGATTTGTAGCTTCT-ATCTATTCCACTGTAACTTCAAGGAAATGAGAT-T
64 GATAAGATTCGCCATAATTTGTAGCTT-TAATCTATTCCACTGCAACGTCAAGGAAATAAGATCT
16711311 TGCTATCTTCAGTTTG
128 T-CTATCTTCAGTTTG
* *
16711327 CTCCACTGCAACTTCAGGGAGATAAGACTGGTAGCTTCAATCTGCTCCACTGTAACTTTAGAGAG
1 CTCCACTGCAACTTCAGGGAGATAAGACTGGTGGCTTCAATCTGCTCCACTGTAACTTCAG-GAG
* * * *
16711392 ATAAGGTTTGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGTCAGGGAAATAAGATCTTC
65 ATAAGATTCGCCATAATTTGTAGCTTTAATCTATTCCACTGCAACGTCAAGGAAATAAGATCTTC
* *
16711457 TATTTTTAGTTTG
130 TATCTTCAGTTTG
* *
16711470 CTCCGCTGCAACTTCAGGGAGATAAGACTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGGAG
1 CTCCACTGCAACTTCAGGGAGATAAGACTGGTGGCTTCAATCTGCTCCACTGTAACTTCA-GGAG
16711535 ATAAGATTCGCCAT
65 ATAAGATTCGCCAT
16711549 TATAACTTCA
Statistics
Matches: 195, Mismatches: 22, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
142 5 0.03
143 186 0.95
144 4 0.02
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (142 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTGGTGGCTTCAATCTGCTCCACTGTAACTTCAGGAGA
TAAGATTCGCCATAATTTGTAGCTTTAATCTATTCCACTGCAACGTCAAGGAAATAAGATCTTCT
ATCTTCAGTTTG
Found at i:16711377 original size:44 final size:44
Alignment explanation
Indices: 16711325--16711540 Score: 171
Period size: 44 Copynumber: 4.7 Consensus size: 44
16711315 ATCTTCAGTT
16711325 TGCTCCACTGCAACTTCAGGGAGATAAGACTGGTAGCTTCAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTGGTAGCTTCAATC
* * * * * *
16711369 TGCTCCACTGTAACTTTAGAGAGATAAGGTTTGCCATAATTTGTAGCTTTAATC
1 TGCTCCACTGCAACTTCAGGGAGATAA-----G-----ACTGGTAGCTTCAATC
* * * ** ** * * *
16711423 TGTTCCACTGCAACGTCAGGGAAATAAGATCTTCTATTTTTAGTT
1 TGCTCCACTGCAACTTCAGGGAGATAAGA-CTGGTAGCTTCAATC
* *
16711468 TGCTCCGCTGCAACTTCAGGGAGATAAGACTGGTGGCTTCAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTGGTAGCTTCAATC
16711512 TGCTCCACTGCAACTTCAGGGAGATAAGA
1 TGCTCCACTGCAACTTCAGGGAGATAAGA
16711541 TTCGCCATTA
Statistics
Matches: 130, Mismatches: 31, Indels: 22
0.71 0.17 0.12
Matches are distributed among these distances:
44 60 0.46
45 34 0.26
49 2 0.02
54 34 0.26
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (44 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGACTGGTAGCTTCAATC
Found at i:16716157 original size:12 final size:12
Alignment explanation
Indices: 16716140--16716170 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
16716130 GCCAATTGCT
16716140 CTTGCATTTGTG
1 CTTGCATTTGTG
*
16716152 CTTGCATTTGTT
1 CTTGCATTTGTG
16716164 CTTGCAT
1 CTTGCAT
16716171 CTCCTTCTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.19, G:0.19, T:0.52
Consensus pattern (12 bp):
CTTGCATTTGTG
Found at i:16716347 original size:19 final size:20
Alignment explanation
Indices: 16716323--16716367 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
16716313 TTGTGACATT
*
16716323 CAATGCATATG-ATGAAATG
1 CAATGCAGATGCATGAAATG
16716342 CAATGCAGATGCATGAAATG
1 CAATGCAGATGCATGAAATG
16716362 -AATGCA
1 CAATGCA
16716368 AAAAGAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.22
Consensus pattern (20 bp):
CAATGCAGATGCATGAAATG
Found at i:16720525 original size:21 final size:22
Alignment explanation
Indices: 16720507--16720547 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
16720497 CATTAATATT
16720507 ATAAATATAGTA-AATAATACG
1 ATAAATATAGTACAATAATACG
16720528 ATAAATATAGTACAATAATA
1 ATAAATATAGTACAATAATA
16720548 ATACAATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (22 bp):
ATAAATATAGTACAATAATACG
Found at i:16720804 original size:20 final size:21
Alignment explanation
Indices: 16720784--16720833 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
16720774 AATTGTCAAA
16720784 TACATTAAAAACAAATAAAAT
1 TACATTAAAAACAAATAAAAT
* *
16720805 TACA-TCATAACAAATAAAAT
1 TACATTAAAAACAAATAAAAT
16720825 TACATTAAA
1 TACATTAAA
16720834 CTAAACAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.26
Consensus pattern (21 bp):
TACATTAAAAACAAATAAAAT
Found at i:16720956 original size:114 final size:108
Alignment explanation
Indices: 16720790--16721007 Score: 303
Period size: 114 Copynumber: 2.0 Consensus size: 108
16720780 CAAATACATT
* * * * *
16720790 AAAAACAAATAAAATTACATCATAACAAATAAAATTACATTAAACTAAACAAATAATTTATAACC
1 AAAAACAAAAAAAATTACATCATAAAAAATAAAATAACACTAAACTAAACAAACAATTTATAACC
*
16720855 TAATGATAAATTACTAACAAAATAACTTT-AAAATAATTTTAA
66 TAATAATAAATTACTAACAAAATAACTTTAAAAATAATTTTAA
*
16720897 AAAACACAAAAAAAATTACATTCATAAAAAAATCACAATAAACACTAAACTAAAGACAAACAATT
1 AAAA-ACAAAAAAAATTACA-TCAT-AAAAAAT-AAAAT-AACACTAAACT-AA-ACAAACAATT
16720962 TATAACCTAATAATAAATTACTAACAAAATAACTTTAAAAATAATT
59 TATAACCTAATAATAAATTACTAACAAAATAACTTTAAAAATAATT
16721008 AATTTTTTTT
Statistics
Matches: 96, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
107 4 0.04
108 14 0.15
109 4 0.04
110 6 0.06
111 4 0.04
112 9 0.09
113 2 0.02
114 44 0.46
115 9 0.09
ACGTcount: A:0.60, C:0.13, G:0.01, T:0.26
Consensus pattern (108 bp):
AAAAACAAAAAAAATTACATCATAAAAAATAAAATAACACTAAACTAAACAAACAATTTATAACC
TAATAATAAATTACTAACAAAATAACTTTAAAAATAATTTTAA
Found at i:16721021 original size:105 final size:105
Alignment explanation
Indices: 16720912--16721106 Score: 345
Period size: 105 Copynumber: 1.9 Consensus size: 105
16720902 ACAAAAAAAA
*
16720912 TTACATTCATAAAAAAATCACAATAAACACTAAACTAAAGACAAACAATTTATAACCTAATAATA
1 TTACATTCATAAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATAATA
*
16720977 AATTACTAACAAAATAACTTTAAAAATAATTAATTTTTTT
66 AATTACAAACAAAATAACTTTAAAAATAATTAATTTTTTT
* * *
16721017 TTACATTCATAAAAAATTCACAATAAACACTAAATTAAACACAAACAATTTATAACCTAATCATA
1 TTACATTCATAAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATAATA
16721082 AATTACAAACAAAATAACTTTAAAA
66 AATTACAAACAAAATAACTTTAAAA
16721107 CAATTTTTAA
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
105 85 1.00
ACGTcount: A:0.55, C:0.15, G:0.01, T:0.29
Consensus pattern (105 bp):
TTACATTCATAAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATAATA
AATTACAAACAAAATAACTTTAAAAATAATTAATTTTTTT
Found at i:16721137 original size:105 final size:104
Alignment explanation
Indices: 16720904--16721137 Score: 324
Period size: 105 Copynumber: 2.2 Consensus size: 104
16720894 TAAAAAACAC
*
16720904 AAAAAAAATTACATTCATAAAAAAATCACAATAAACACTAAACTAAAGACAAACAATTTATAACC
1 AAAAAAAATTACATTCATAAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACC
*
16720969 TAATAATAAATTACTAACAAAATAACTTTAAAAATAATT
66 TAATAATAAATTACAAACAAAATAACTTTAAAAATAATT
****** * *
16721008 AATTTTTTTTTACATTCATAAAAAATTCACAATAAACACTAAATTAAACACAAACAATTTATAAC
1 AA-AAAAAATTACATTCATAAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAAC
* **
16721073 CTAATCATAAATTACAAACAAAATAACTTTAAAACAATTTTT
65 CTAATAATAAATTACAAACAAAATAACTTT-AAA-AATAATT
16721115 AAAAAAAATTACATTCATAAAAA
1 AAAAAAAATTACATTCATAAAAA
16721138 GTCACGAAAT
Statistics
Matches: 108, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
104 2 0.02
105 81 0.75
106 18 0.17
107 7 0.06
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (104 bp):
AAAAAAAATTACATTCATAAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACC
TAATAATAAATTACAAACAAAATAACTTTAAAAATAATT
Found at i:16721239 original size:25 final size:27
Alignment explanation
Indices: 16721194--16721253 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
16721184 AAAAAAAACA
* *
16721194 TAAAAAAATAACTAATCCCTTCT-ACT
1 TAAAAAAATAACTAATACCTTCTAAAT
* *
16721220 TAAAAAAATTACTAA-ACCTTTTAAAT
1 TAAAAAAATAACTAATACCTTCTAAAT
16721246 TAAAAAAA
1 TAAAAAAA
16721254 AACATTAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 5 0.17
26 24 0.83
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (27 bp):
TAAAAAAATAACTAATACCTTCTAAAT
Found at i:16721297 original size:4 final size:4
Alignment explanation
Indices: 16721280--16721313 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
16721270 AAACATACCT
*
16721280 TTTC TTTT TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
16721314 CCTCTCCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTC
Found at i:16727892 original size:25 final size:25
Alignment explanation
Indices: 16727858--16727914 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
16727848 TATCCCTTGG
16727858 TTAGG-CAATACTTAGGATAACAAA
1 TTAGGACAATACTTAGGATAACAAA
* *
16727882 TTAGGACAATACTTATGATAGCAAA
1 TTAGGACAATACTTAGGATAACAAA
*
16727907 TTATGACA
1 TTAGGACA
16727915 GTTGAAGTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 5 0.17
25 24 0.83
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (25 bp):
TTAGGACAATACTTAGGATAACAAA
Found at i:16737694 original size:6 final size:6
Alignment explanation
Indices: 16737641--16737708 Score: 59
Period size: 6 Copynumber: 11.5 Consensus size: 6
16737631 AGGAAGTCTA
* * * * *
16737641 AAAACAT AACAAT AAACAT AAAAAT AGAAAT AAAACT AAAACT AAAAAT
1 AAAA-AT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
*
16737690 AAAAA- CAAAAT -AAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAA
16737709 GAGACTCAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
5 9 0.18
6 38 0.76
7 3 0.06
ACGTcount: A:0.75, C:0.09, G:0.01, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:16739544 original size:15 final size:14
Alignment explanation
Indices: 16739518--16739569 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
16739508 AATAAAGAAG
*
16739518 AATAAGAAATAAAT
1 AATAAAAAATAAAT
*
16739532 ATTAATAAAAT-AAT
1 AATAA-AAAATAAAT
16739546 AATAAAAACATAAAT
1 AATAAAAA-ATAAAT
16739561 AAATAAAAA
1 -AATAAAAA
16739570 TTAGGGAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 3 0.10
14 13 0.42
15 7 0.23
16 8 0.26
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (14 bp):
AATAAAAAATAAAT
Found at i:16749361 original size:27 final size:27
Alignment explanation
Indices: 16749331--16749508 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
16749321 ATATTGAGCC
* *
16749331 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
16749358 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
16749385 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
16749413 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
16749440 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
16749467 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
16749494 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
16749509 GTACAATTTA
Statistics
Matches: 129, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 104 0.81
28 25 0.19
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:16749470 original size:82 final size:81
Alignment explanation
Indices: 16749352--16749507 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
16749342 TGCTATATAA
* *
16749352 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
16749417 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
16749434 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
16749498 CACTTAGTGC
65 CACTTAGTGC
16749508 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:16754544 original size:21 final size:21
Alignment explanation
Indices: 16754474--16754544 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
16754464 CATATATATC
*
16754474 ATGAACTCAAACCACAACTCA
1 ATGAACTCAGACCACAACTCA
** * *
16754495 ATGAGTTCGGATGCCACATATATC-
1 ATGAACTCAGA--CCACA-A-CTCA
16754519 ATGAACTCAGACCACAACTCA
1 ATGAACTCAGACCACAACTCA
16754540 ATGAA
1 ATGAA
16754545 TTTAGATCAC
Statistics
Matches: 36, Mismatches: 9, Indels: 10
0.65 0.16 0.18
Matches are distributed among these distances:
20 2 0.06
21 13 0.36
22 5 0.14
23 5 0.14
24 9 0.25
25 2 0.06
ACGTcount: A:0.41, C:0.27, G:0.13, T:0.20
Consensus pattern (21 bp):
ATGAACTCAGACCACAACTCA
Found at i:16756664 original size:28 final size:28
Alignment explanation
Indices: 16756624--16756680 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
16756614 CAATATAAGA
16756624 ACATAATTTGAAGTTTATGTGATTGTTG
1 ACATAATTTGAAGTTTATGTGATTGTTG
16756652 ACATAATTTGAAGTTTATGTGATTGTTG
1 ACATAATTTGAAGTTTATGTGATTGTTG
16756680 A
1 A
16756681 TGTTAACACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.04, G:0.21, T:0.46
Consensus pattern (28 bp):
ACATAATTTGAAGTTTATGTGATTGTTG
Found at i:16756998 original size:19 final size:20
Alignment explanation
Indices: 16756976--16757013 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16756966 ATTAAAAAAG
16756976 ATAAAAAT-AACTTTTTTTT
1 ATAAAAATAAACTTTTTTTT
*
16756995 ATAAAATTAAACTTTTTTT
1 ATAAAAATAAACTTTTTTT
16757014 AAAAGAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (20 bp):
ATAAAAATAAACTTTTTTTT
Found at i:16773349 original size:128 final size:128
Alignment explanation
Indices: 16773157--16773411 Score: 492
Period size: 128 Copynumber: 2.0 Consensus size: 128
16773147 TTTTGTTTCA
*
16773157 TTAAAGTTAAGTATATTTTTGGTATATGAGTAAGTGTATATCATGTACGTATTTATGTTTTGAGA
1 TTAAAGTTAAGTAAATTTTTGGTATATGAGTAAGTGTATATCATGTACGTATTTATGTTTTGAGA
16773222 TGGCCGAATATAAATGGAAAAGTTTACATTAGACTTATATTAAGGATGTAGTCATAAAATACT
66 TGGCCGAATATAAATGGAAAAGTTTACATTAGACTTATATTAAGGATGTAGTCATAAAATACT
*
16773285 TTAAGGTTAAGTAAATTTTTGGTATATGAGTAAGTGTATATCATGTACGTATTTATGTTTTGAGA
1 TTAAAGTTAAGTAAATTTTTGGTATATGAGTAAGTGTATATCATGTACGTATTTATGTTTTGAGA
16773350 TGGCCGAATATAAATGGAAAAGTTTACATTAGACTTATATTAAGGATGTAGTCATAAAATAC
66 TGGCCGAATATAAATGGAAAAGTTTACATTAGACTTATATTAAGGATGTAGTCATAAAATAC
16773412 ATATATACCA
Statistics
Matches: 125, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 125 1.00
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.38
Consensus pattern (128 bp):
TTAAAGTTAAGTAAATTTTTGGTATATGAGTAAGTGTATATCATGTACGTATTTATGTTTTGAGA
TGGCCGAATATAAATGGAAAAGTTTACATTAGACTTATATTAAGGATGTAGTCATAAAATACT
Found at i:16774529 original size:45 final size:45
Alignment explanation
Indices: 16774465--16774595 Score: 167
Period size: 45 Copynumber: 3.0 Consensus size: 45
16774455 GTTGTACAGT
* *
16774465 ATTATTCGGGCCTTGGAGCCTAGCAGGCTATAATGCTGGTGAAAC
1 ATTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAAC
* * *
16774510 ATTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGAT
1 ATTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAAC
* * * *
16774555 ATTTTTTGGGCC-TCGAGCCTAGCAGGC-AAAATGACGGTGAA
1 ATTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAA
16774596 TAAATTCGGG
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
43 11 0.14
44 14 0.18
45 51 0.67
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (45 bp):
ATTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAAC
Found at i:16781579 original size:99 final size:99
Alignment explanation
Indices: 16781404--16781605 Score: 377
Period size: 99 Copynumber: 2.0 Consensus size: 99
16781394 TTCAGGAAAA
*
16781404 ACATCCGGGTATTCACAAACCACCGGCACAGATTCGGGTTTCTTTTCTAATTCTTTGTCATCAAG
1 ACATCCGGGTATTCACAAACCACCGGCACAGATTCGGGTTTCTTTTCTAACTCTTTGTCATCAAG
*
16781469 TACATATGCAAGGTATGCTTCGCACCCTTTTCTT
66 TACATACGCAAGGTATGCTTCGCACCCTTTTCTT
*
16781503 ACATCCGGGTATTCACAAACCACCGTCACAGATTCGGGTTTCTTTTCTAACTCTTTGTCATCAAG
1 ACATCCGGGTATTCACAAACCACCGGCACAGATTCGGGTTTCTTTTCTAACTCTTTGTCATCAAG
16781568 TACATACGCAAGGTATGCTTCGCACCCTTTTCTT
66 TACATACGCAAGGTATGCTTCGCACCCTTTTCTT
16781602 ACAT
1 ACAT
16781606 ATTTCTGGGC
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 100 1.00
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.34
Consensus pattern (99 bp):
ACATCCGGGTATTCACAAACCACCGGCACAGATTCGGGTTTCTTTTCTAACTCTTTGTCATCAAG
TACATACGCAAGGTATGCTTCGCACCCTTTTCTT
Found at i:16791665 original size:40 final size:40
Alignment explanation
Indices: 16791569--16791736 Score: 221
Period size: 40 Copynumber: 4.2 Consensus size: 40
16791559 CTCGTTCAAG
* * * *
16791569 TGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AA
1 TGCCTTCGGGACATAACCCGGATTTAATAACTCGCACGAA
*
16791608 TGCCTTCGGGACATAACCCGGATTTAACAACTCGCACGAA
1 TGCCTTCGGGACATAACCCGGATTTAATAACTCGCACGAA
*
16791648 TGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAA
1 TGCCTTCGGGACATAACCCGGATTTAATAACTCGCACGAA
* * * * *
16791688 TGCCTTTGGGACTTAACCCGGATTTAGTATCTCGCACAAA
1 TGCCTTCGGGACATAACCCGGATTTAATAACTCGCACGAA
*
16791728 GGCCTTCGG
1 TGCCTTCGG
16791737 ATCTTAGTCC
Statistics
Matches: 115, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 32 0.28
40 83 0.72
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
TGCCTTCGGGACATAACCCGGATTTAATAACTCGCACGAA
Found at i:16791749 original size:80 final size:79
Alignment explanation
Indices: 16791570--16791789 Score: 217
Period size: 80 Copynumber: 2.8 Consensus size: 79
16791560 TCGTTCAAGT
* * * *
16791570 GCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATTTAA
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCACACAATGCCTTCGGGACATAACCCGGATTTAA
* *
16791635 CAACTCGCACGAAT
66 CAACTCGCACAAAG
* * *
16791649 GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTTGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTAATAACTCACAC-AATGCCTTCGGGACATAACCCGGATTTA
** *
16791714 GTATCTCGCACAAAG
65 ACAACTCGCACAAAG
** * * * * * * *
16791729 GCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGA-CTTAACCCGGATTTAATAACTCA-CACAATGCCTTCGGGACATAACCCGGA
16791790 CAGCATTCAA
Statistics
Matches: 116, Mismatches: 22, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
79 34 0.29
80 79 0.68
81 3 0.03
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
GCCTTCGGGACTTAACCCGGATTTAATAACTCACACAATGCCTTCGGGACATAACCCGGATTTAA
CAACTCGCACAAAG
Found at i:16791798 original size:41 final size:41
Alignment explanation
Indices: 16791721--16791798 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
16791711 TTAGTATCTC
* * *
16791721 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
16791762 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
16791799 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:16798264 original size:45 final size:44
Alignment explanation
Indices: 16798027--16798415 Score: 178
Period size: 45 Copynumber: 8.8 Consensus size: 44
16798017 TTGTAGCTTT
* * ** * * *
16798027 AATCTGCTCTACTACAACTTCAGAAAGATAAGATTTGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGA-TCGCCATCTTC
** * * * **
16798072 AGGCTGCTCCACTGCAACTTCAGGTAGATAAGACTTGTAAT-TTC
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGA-TCGCCATCTTC
* * * * * * **
16798116 GACCTGCCCCACTGCAACTTTAGGGGGATAAGAT--TTATGGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATCGCCAT--CTTC
* * * * **** *
16798160 AATCTACTCCACTACAACTTTAGGGAGATAAGAT-GGTGGCTTA
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATCGCCATCTTC
*
16798203 AATCTGCTCCACTGCAACTTCAGGGAGACAATATTCGCCATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGA-TCGCCATCTTC
* * * * * *
16798248 GATTTGCTCCACTGCAACTTTAGGGAGACAAGATCTACAATCTTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATC-GCCATC-TTC
* ** * * **** *
16798294 AACCTATTCCACTACAACTT-AGGGAGATAAGAT-GGTGGCTTA
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATCGCCATCTTC
* * *
16798336 AATTTGCTCCACTACAACTTCAGGGAGACAAGATTCGCCGTCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGA-TCGCCATCTTC
* * *
16798381 GATCTGCTCCATTGTAACTTCAGGGAGACAAGATC
1 AATCTGCTCCACTGCAACTTCAGGGAGACAAGATC
16798416 TACAATCTTT
Statistics
Matches: 262, Mismatches: 71, Indels: 23
0.74 0.20 0.06
Matches are distributed among these distances:
41 3 0.01
42 18 0.07
43 44 0.17
44 66 0.25
45 115 0.44
46 16 0.06
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGGGAGACAAGATCGCCATCTTC
Found at i:16798338 original size:133 final size:132
Alignment explanation
Indices: 16798075--16798454 Score: 460
Period size: 133 Copynumber: 2.9 Consensus size: 132
16798065 TATCTTCAGG
* * * ** * * *
16798075 CTGCTCCACTGCAACTTCAGGTAGATAAGACTT-GTAAT-TTCGACCTGCCCCACTGCAACTTTA
1 CTGCTCCACTACAACTTCAGGGAGACAAGA-TTCGCCATCTTCGATCTGCTCCACTGCAACTTCA
* * * *** * * *
16798138 GGGGGATAAGATTTA-TGGCTTCAATCTACTCCACTACAACTTTAGGGAGATAAGATGGTGGCTT
65 GGGAGACAAGATCTACAATCTTTAACCTAATCCACTACAAC-TTAGGGAGATAAGATGGTGGCTT
16798202 AAAT
129 AAAT
* * * *
16798206 CTGCTCCACTGCAACTTCAGGGAGACAATATTCGCCATCTTCGATTTGCTCCACTGCAACTTTAG
1 CTGCTCCACTACAACTTCAGGGAGACAAGATTCGCCATCTTCGATCTGCTCCACTGCAACTTCAG
*
16798271 GGAGACAAGATCTACAATCTTTTAACCTATTCCACTACAACTTAGGGAGATAAGATGGTGGCTTA
66 GGAGACAAGATCTACAATC-TTTAACCTAATCCACTACAACTTAGGGAGATAAGATGGTGGCTTA
16798336 AAT
130 AAT
* * * *
16798339 TTGCTCCACTACAACTTCAGGGAGACAAGATTCGCCGTCTTCGATCTGCTCCATTGTAACTTCAG
1 CTGCTCCACTACAACTTCAGGGAGACAAGATTCGCCATCTTCGATCTGCTCCACTGCAACTTCAG
* *
16798404 GGAGACAAGATCTACAATCTTTAGCCTAATCCACTACAATTTAGGGAGATA
66 GGAGACAAGATCTACAATCTTTAACCTAATCCACTACAACTTAGGGAGATA
16798455 GGGCTTGTGA
Statistics
Matches: 217, Mismatches: 28, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
130 2 0.01
131 30 0.14
132 63 0.29
133 104 0.48
134 18 0.08
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (132 bp):
CTGCTCCACTACAACTTCAGGGAGACAAGATTCGCCATCTTCGATCTGCTCCACTGCAACTTCAG
GGAGACAAGATCTACAATCTTTAACCTAATCCACTACAACTTAGGGAGATAAGATGGTGGCTTAA
AT
Found at i:16798630 original size:64 final size:64
Alignment explanation
Indices: 16798529--16798656 Score: 229
Period size: 64 Copynumber: 2.0 Consensus size: 64
16798519 TCATGTATCA
*
16798529 ATGCTTATGCCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGATCCTAACTAGATGTG
1 ATGCTTATGCCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGATCCTAACTAGATGTG
* *
16798593 ATGCTTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
1 ATGCTTATGCCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGATCCTAACTAGATGTG
16798657 TTATTATATG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (64 bp):
ATGCTTATGCCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGATCCTAACTAGATGTG
Found at i:16803933 original size:64 final size:64
Alignment explanation
Indices: 16803852--16804036 Score: 205
Period size: 67 Copynumber: 2.9 Consensus size: 64
16803842 AAGACATTAT
* *
16803852 TATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATA
1 TATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATA
* * * * *
16803916 TATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGA
1 TATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGA
16803981 TA
63 TA
* * * *
16803983 AAT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 TATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
16804037 CGAACTATAT
Statistics
Matches: 100, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 26 0.26
66 21 0.21
67 33 0.33
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.24
Consensus pattern (64 bp):
TATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATA
Found at i:16807184 original size:43 final size:43
Alignment explanation
Indices: 16807123--16807234 Score: 170
Period size: 43 Copynumber: 2.6 Consensus size: 43
16807113 ACCGCATTAC
* *
16807123 GCCTGCTGGGCATGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* * *
16807166 GCGTGCTATGCACGAAGGCCCGAATACACATCACCGGCACTAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
16807209 GCCTGCTAGGCACGAAGGCACGAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
16807235 TAATACCAGC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 61 1.00
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.12
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:16812390 original size:64 final size:64
Alignment explanation
Indices: 16812235--16812493 Score: 202
Period size: 68 Copynumber: 3.9 Consensus size: 64
16812225 TGGATAATAC
* ** * ** * *
16812235 AGATAGTATGTAGCTAGGTCACATGTATGGTGCTGGGTGCACATCATGT-GTACAAGAGAGCTAC
1 AGATA-TATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAG-ACAAGAGAGCTAC
16812299 AAG
64 --G
* *
16812302 ACATTATTATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTAC
1 AGA-TA-TATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTAC
16812367 G
64 G
* * * * * * *
16812368 GGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACATCATGTAGACAAGAGAGCTA
1 AGATATATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTA
16812433 CG
63 CG
* * * *
16812435 AGATAAAT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 AGATATATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
16812494 CGAACTATAT
Statistics
Matches: 154, Mismatches: 31, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
62 1 0.01
63 18 0.12
64 26 0.17
65 2 0.01
66 23 0.15
67 34 0.22
68 49 0.32
69 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (64 bp):
AGATATATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACG
Found at i:16819967 original size:26 final size:25
Alignment explanation
Indices: 16819912--16819973 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
16819902 AATAAACATT
* ** *
16819912 AAACAAAATAATTTATAATAGTAAC
1 AAACAAAATAATTTAAAATAAAAAA
*
16819937 TAACAAAATAACTTTAAAATAAAAAA
1 AAACAAAATAA-TTTAAAATAAAAAA
*
16819963 AAACAACATAA
1 AAACAAAATAA
16819974 AAATAACAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
25 10 0.34
26 19 0.66
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.23
Consensus pattern (25 bp):
AAACAAAATAATTTAAAATAAAAAA
Found at i:16823912 original size:5 final size:5
Alignment explanation
Indices: 16823902--16823933 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
16823892 TTGTGTGTTC
16823902 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
16823934 TCACAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:16823916 original size:9 final size:9
Alignment explanation
Indices: 16823902--16823932 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
16823892 TTGTGTGTTC
16823902 TTTATTTTA
1 TTTATTTTA
16823911 TTTATTTTA
1 TTTATTTTA
16823920 TTTTATTTTA
1 -TTTATTTTA
16823930 TTT
1 TTT
16823933 TTCACAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:16833324 original size:93 final size:93
Alignment explanation
Indices: 16833216--16833387 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
16833206 GCCCATAAGT
* * *
16833216 GAACTCGAACTCAACTCAACGAGCTCGGGCGTTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
16833281 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* *
16833309 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
16833374 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
16833388 CAAATATCCC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:16833383 original size:46 final size:46
Alignment explanation
Indices: 16833208--16833383 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
16833198 TGTAACCCGC
* * * *
16833208 CCATAAGTGAACTCGAACTCAACTCAACGAGCTCGGGCGTTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
16833254 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
16833300 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
16833347 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
16833384 TGCCCAAATA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 2 0.02
46 69 0.63
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:16833402 original size:46 final size:45
Alignment explanation
Indices: 16833259--16833389 Score: 133
Period size: 47 Copynumber: 2.8 Consensus size: 45
16833249 TGCATCCATA
* *
16833259 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA--TACATC-C
* * * *
16833307 --TCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-A
1 AGT-GAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCATACATCC
16833352 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA
16833390 AATATCCCAG
Statistics
Matches: 70, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
44 5 0.07
46 29 0.41
47 32 0.46
49 4 0.06
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCC
Found at i:16836119 original size:24 final size:25
Alignment explanation
Indices: 16836092--16836138 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
16836082 GAAAAATCAG
16836092 AACCCT-ATGTCAAAAGACAGACGA
1 AACCCTCATGTCAAAAGACAGACGA
* * *
16836116 AACCTTCGTGTCAAAGGACAGAC
1 AACCCTCATGTCAAAAGACAGAC
16836139 CTGATTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 5 0.26
25 14 0.74
ACGTcount: A:0.40, C:0.26, G:0.19, T:0.15
Consensus pattern (25 bp):
AACCCTCATGTCAAAAGACAGACGA
Found at i:16838342 original size:22 final size:23
Alignment explanation
Indices: 16838305--16838347 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
16838295 ATTATTCTTA
*
16838305 ATTTTTATGAACTTTTTAATTTT
1 ATTTTTATGAACTTTTAAATTTT
*
16838328 ATTTTTAT-AATTTTTAAATT
1 ATTTTTATGAACTTTTAAATT
16838348 ATTTGTTGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (23 bp):
ATTTTTATGAACTTTTAAATTTT
Found at i:16838544 original size:24 final size:25
Alignment explanation
Indices: 16838501--16838548 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
16838491 TGAAAGGTTG
*
16838501 ATGACCAAATTTAACTAAAAAAATA
1 ATGACCAAATTTAACAAAAAAAATA
*
16838526 ATGATCAAA-TTAACAAAAAAAAT
1 ATGACCAAATTTAACAAAAAAAAT
16838549 TGTTAATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.62, C:0.10, G:0.04, T:0.23
Consensus pattern (25 bp):
ATGACCAAATTTAACAAAAAAAATA
Found at i:16843489 original size:666 final size:668
Alignment explanation
Indices: 16842306--16844050 Score: 2681
Period size: 667 Copynumber: 2.6 Consensus size: 668
16842296 TTGAGTTGAT
*
16842306 AAATTACCAAACTAG-AAACATTAAACAAATGTTGAATTAAAAATCCA-CGCATCAATAACTATT
1 AAATTACCAAACTAGCAAA-ATTAAACAAATGTTGAATTAAAAA-CAAGCGCATCAATAACTATT
* * *
16842369 CAAGAA-AAAAAACGAGCTTCTTCTCAAAATATGAAATTGACTGTCCAAACTCAATCAACAAATA
64 CAAGAACAAAAAA-GAGCTTCTTCTCAAAATATGAAATTGACTATTCAAGCTCAATCAACAAATA
* * **
16842433 ACTAATTAATAATCAATATTTTTGTTTTCTCTTTTTTTATCTAAAATTATAAGAAATAATTTAGC
128 ACTAATTAATAATCAATA---TTATTTTCT-TTTTCTTATCTAAAACAATAAGAAATAATTTAGC
* * * *
16842498 AAATCAAATAGAAGAGCATAGTTAGGCAACTAATCAAATCAAATATTGAC-AAAAAGGAGTCAAT
189 AAATCAAACAAAAGAGCATAGTTAGGCAACTAACCAAATCAAATATCGACAAAAAAGGAGTCAAT
* * *
16842562 AAAATAAGAAAAGTCACAACGAAAAAAAATGGGTTATGGTTAACATTAATGGGCTAATCAAGAAA
254 AAAATGAGAAGAGTCACAACGAAAAAAAATGGGTTATGGTTAACATTAATGGGTTAATCAAGAAA
* * * *
16842627 CGGGATGTTTGGTTTAACGGGGTTCACTAAGGGTTAATTAAAAAGGGTGCCTTTTTATGAGATAA
319 CGGGATGTTAGGTTTAACGGGGTTCACTAAGGGTTAATTAAAAAGGGAGGCTTTTTATGGGATAA
* *
16842692 GTGTGTTAAAACCTAAGTGCCTTTATCATCTTAGTATATCAAATCAAAGGTGTGGTCTCGACATG
384 GTGGGTTAAAACCTAAGTGCCTTTATCATCTTAGTATACCAAATCAAAGGTGTGGTCTCGACATG
*
16842757 CATAATCGAAATAAGTTCTAAAATAACAAATCAAGTTGACATACTCAAAACCAACAACAAAATGA
449 CATAATCGAAATAAGTTCTAAAATAACAAATCAAGTTGACACACTCAAAACCAACAACAAAATGA
*
16842822 GCATGAAAATGTATGCCCTAAAGGCTTAAAATCTCAC-AAAAAATCATGGTTTTGATGTCAAACT
514 GCATGAAAATGTATGCCCTAAAGGCTTAAAATCTCACAAAAAAATCATGGTTTTAATGTCAAACT
* *
16842886 TACAAATTTAAAACTTCAAAATAATACCTCAATTCAGGGAAACAGCCTAAAAAATTTTAATTCTA
579 TACAAATTTAAAACTTCAAAATAATACCTCAATTCAAGGAAACAACCTAAAAAATTTTAATTCTA
16842951 AAAATAACTTATCATGTTTGACTAG
644 AAAATAACTTATCATGTTTGACTAG
* *
16842976 AAATTATCAAACTAGCAAAATTAAACAAATGTTGAATTAAAAACAAGCGCATCAATATCTATTCA
1 AAATTACCAAACTAGCAAAATTAAACAAATGTTGAATTAAAAACAAGCGCATCAATAACTATTCA
* *
16843041 AGAACAAAAATGAGCTTCTTCTCAAAATATGAAATTGACTATTCAAGCTCAATCAACAAATTACT
66 AGAACAAAAAAGAGCTTCTTCTCAAAATATGAAATTGACTATTCAAGCTCAATCAACAAATAACT
*
16843106 AATTAATAATCAATATTATTTTCATTTTTCTTATCTATAACAATAAGAAATAATTTAGCAAATCA
131 AATTAATAATCAATATTATTTTC-TTTTTCTTATCTAAAACAATAAGAAATAATTTAGCAAATCA
* * ** * *
16843171 AACATAAGAGTATAACTAGGCAACTAACCAAATCAAATATCAACAAAAAATGAGTCAATAAAATG
195 AACAAAAGAGCATAGTTAGGCAACTAACCAAATCAAATATCGACAAAAAAGGAGTCAATAAAATG
* *
16843236 AGAAGAGTCACAACGAAAAAAAATGGGTTATGGTT-ACATTAACGAGTTAATCAAGAAACGGGAT
260 AGAAGAGTCACAACGAAAAAAAATGGGTTATGGTTAACATTAATGGGTTAATCAAGAAACGGGAT
* * *
16843300 GTTAGGTTTAACGGGTTTCACTAAGGGTTAAATAAAAAGAGAGGC-TTTTATGGGATAAGTGGGT
325 GTTAGGTTTAACGGGGTTCACTAAGGGTTAATTAAAAAGGGAGGCTTTTTATGGGATAAGTGGGT
16843364 TAAAACCTAAGTGCCTTTATCATCTTAGTATACCAAATCAAAGGTGTGGTCTCGACATGCATAAT
390 TAAAACCTAAGTGCCTTTATCATCTTAGTATACCAAATCAAAGGTGTGGTCTCGACATGCATAAT
* * * * * *
16843429 CGAAGTAAGTTCTAGAATAACAAGTCAAGTTGACACACAT-ATAACCAACGATAAAATGAGCATG
455 CGAAATAAGTTCTAAAATAACAAATCAAGTTGACACAC-TCAAAACCAACAACAAAATGAGCATG
*
16843493 AAAATGTATGCCCTAAAGGCTTAAAATCTCACAAAAAAATCATGGTTTTAATGTCAAACTTGCAA
519 AAAATGTATGCCCTAAAGGCTTAAAATCTCACAAAAAAATCATGGTTTTAATGTCAAACTTACAA
* *
16843558 ATTTAAAACTTCAAGATAATACCTCAATTCAAGGAAACAACCTAAAAAATTTTAATTTTAAAAAT
584 ATTTAAAACTTCAAAATAATACCTCAATTCAAGGAAACAACCTAAAAAATTTTAATTCTAAAAAT
16843623 AACTTATCATGTTTGACTAG
649 AACTTATCATGTTTGACTAG
* *
16843643 AAATTACCAAACTAGCAAAATTAAACAAATGTTGAATTAAAAACAAGCGCATCGATAACTATTGA
1 AAATTACCAAACTAGCAAAATTAAACAAATGTTGAATTAAAAACAAGCGCATCAATAACTATTCA
* * *
16843708 AGAACAAAAAAGAGCTTCTTCTCAGAATATGAAATTGACTATTCAAGCTCGATTAACAAATAACT
66 AGAACAAAAAAGAGCTTCTTCTCAAAATATGAAATTGACTATTCAAGCTCAATCAACAAATAACT
* * * * * *
16843773 AATTGATAATC--GA-TA-TTT-TTTTTCTTATTTAGAGCAATAAGAAATAATTCAGCAAATCAA
131 AATTAATAATCAATATTATTTTCTTTTTCTTATCTAAAACAATAAGAAATAATTTAGCAAATCAA
* * * * *
16843833 ACAAAAGAGCATAGTTGGGCAACTAACAAAATCAAATGTCGACAAAAAGGGAGTCAATAAAACGA
196 ACAAAAGAGCATAGTTAGGCAACTAACCAAATCAAATATCGACAAAAAAGGAGTCAATAAAATGA
* *
16843898 GATGAGTCACAAC-TAAAAAAATGGGTTATGGTTAACATTAATGGGTTAATCAAGAAACGGGATG
261 GAAGAGTCACAACGAAAAAAAATGGGTTATGGTTAACATTAATGGGTTAATCAAGAAACGGGATG
*
16843962 TTAGGTTTAACGGGGTTCACTAAGGGTTAATTAAAAAGGGAGGCTTTTTATGGGATAAGGGGGTT
326 TTAGGTTTAACGGGGTTCACTAAGGGTTAATTAAAAAGGGAGGCTTTTTATGGGATAAGTGGGTT
*
16844027 AAAACCTAAGTGTCTTTATCATCT
391 AAAACCTAAGTGCCTTTATCATCT
16844051 GATGCGATCC
Statistics
Matches: 982, Mismatches: 84, Indels: 26
0.90 0.08 0.02
Matches are distributed among these distances:
660 19 0.02
661 173 0.18
662 42 0.04
663 3 0.00
664 2 0.00
665 1 0.00
666 168 0.17
667 387 0.39
668 53 0.05
669 2 0.00
670 124 0.13
671 8 0.01
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.28
Consensus pattern (668 bp):
AAATTACCAAACTAGCAAAATTAAACAAATGTTGAATTAAAAACAAGCGCATCAATAACTATTCA
AGAACAAAAAAGAGCTTCTTCTCAAAATATGAAATTGACTATTCAAGCTCAATCAACAAATAACT
AATTAATAATCAATATTATTTTCTTTTTCTTATCTAAAACAATAAGAAATAATTTAGCAAATCAA
ACAAAAGAGCATAGTTAGGCAACTAACCAAATCAAATATCGACAAAAAAGGAGTCAATAAAATGA
GAAGAGTCACAACGAAAAAAAATGGGTTATGGTTAACATTAATGGGTTAATCAAGAAACGGGATG
TTAGGTTTAACGGGGTTCACTAAGGGTTAATTAAAAAGGGAGGCTTTTTATGGGATAAGTGGGTT
AAAACCTAAGTGCCTTTATCATCTTAGTATACCAAATCAAAGGTGTGGTCTCGACATGCATAATC
GAAATAAGTTCTAAAATAACAAATCAAGTTGACACACTCAAAACCAACAACAAAATGAGCATGAA
AATGTATGCCCTAAAGGCTTAAAATCTCACAAAAAAATCATGGTTTTAATGTCAAACTTACAAAT
TTAAAACTTCAAAATAATACCTCAATTCAAGGAAACAACCTAAAAAATTTTAATTCTAAAAATAA
CTTATCATGTTTGACTAG
Found at i:16844513 original size:11 final size:11
Alignment explanation
Indices: 16844497--16844525 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
16844487 TATAAAAATT
16844497 TTCTATTAAAA
1 TTCTATTAAAA
16844508 TTCTATTAAAA
1 TTCTATTAAAA
16844519 TTC-ATTA
1 TTCTATTA
16844526 TCAAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.48
Consensus pattern (11 bp):
TTCTATTAAAA
Found at i:16845210 original size:23 final size:23
Alignment explanation
Indices: 16845184--16845412 Score: 104
Period size: 23 Copynumber: 10.3 Consensus size: 23
16845174 TTCTAGCAAC
* *
16845184 TAAACTCTTCAATTTGCAATACTT
1 TAAACACTTCAATTTACAATA-TT
* * *
16845208 AAAACACTTTAATTTACAACATT
1 TAAACACTTCAATTTACAATATT
* * *
16845231 TAAGCACTTCAATTTACAGTGTT
1 TAAACACTTCAATTTACAATATT
* **
16845254 TAAACACTTCAATTTGCAGCACTT
1 TAAACACTTCAATTTACAATA-TT
* *
16845278 T-AACA-TCTCAATTAACAACATT
1 TAAACACT-TCAATTTACAATATT
* * * **
16845300 TATATAATTCAA-TTACAGCGA-T
1 TAAACACTTCAATTTACA-ATATT
*
16845322 AAAACA-TCTCAATTT-C------
1 TAAACACT-TCAATTTACAATATT
*
16845338 TAGACACTTCAATTTACAATATT
1 TAAACACTTCAATTTACAATATT
**
16845361 TAAACACTTCAATTTACAGCATT
1 TAAACACTTCAATTTACAATATT
* **
16845384 TAAACACTTCAATTTGCAGCATT
1 TAAACACTTCAATTTACAATATT
16845407 TAAACA
1 TAAACA
16845413 ACAGTAGCCA
Statistics
Matches: 158, Mismatches: 32, Indels: 31
0.71 0.14 0.14
Matches are distributed among these distances:
16 11 0.07
17 2 0.01
21 1 0.01
22 17 0.11
23 107 0.68
24 20 0.13
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.35
Consensus pattern (23 bp):
TAAACACTTCAATTTACAATATT
Found at i:16849221 original size:40 final size:40
Alignment explanation
Indices: 16849150--16849258 Score: 166
Period size: 40 Copynumber: 2.8 Consensus size: 40
16849140 TGCAAAATTT
* *
16849150 TTAGCGGCGTTTGTT-CAAAGCGTCGCTAAAGATCGAGCA
1 TTAGCGGCGTTTGTTAAAAAGCGCCGCTAAAGATCGAGCA
*
16849189 TTAGCGGCGTTTGTTAAAAAGCGCCACTAAAGATCGAGCA
1 TTAGCGGCGTTTGTTAAAAAGCGCCGCTAAAGATCGAGCA
* *
16849229 TTAGCGGTGTTTTTTAAAAAGCGCCGCTAA
1 TTAGCGGCGTTTGTTAAAAAGCGCCGCTAA
16849259 TGCCACTAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 15 0.24
40 48 0.76
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (40 bp):
TTAGCGGCGTTTGTTAAAAAGCGCCGCTAAAGATCGAGCA
Found at i:16849851 original size:21 final size:22
Alignment explanation
Indices: 16849822--16849862 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
16849812 CTTGTAGTTT
16849822 TTAATTAGCTCAATTAAGTTCA
1 TTAATTAGCTCAATTAAGTTCA
16849844 TTAA-TAGCTCAATTAAGTT
1 TTAATTAGCTCAATTAAGTT
16849863 GAGTGTGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (22 bp):
TTAATTAGCTCAATTAAGTTCA
Found at i:16853256 original size:20 final size:19
Alignment explanation
Indices: 16853230--16853269 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
16853220 ATATGAATAT
16853230 AAAAAAATAAGATAGGGAA
1 AAAAAAATAAGATAGGGAA
16853249 ANAAAAAATAAGATAGGGAA
1 A-AAAAAATAAGATAGGGAA
16853269 A
1 A
16853270 GAAGTGAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.68, C:0.00, G:0.20, T:0.10
Consensus pattern (19 bp):
AAAAAAATAAGATAGGGAA
Found at i:16860162 original size:21 final size:20
Alignment explanation
Indices: 16860138--16860189 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
16860128 GAGTCTGCAG
16860138 AAAAAGTAAAAAAAACAAAAA
1 AAAAAG-AAAAAAAACAAAAA
*
16860159 AAAAAGAAAGAAAAAGAAAAA
1 AAAAAGAAA-AAAAACAAAAA
*
16860180 GAAAAGAAAA
1 AAAAAGAAAA
16860190 TTGGGAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.85, C:0.02, G:0.12, T:0.02
Consensus pattern (20 bp):
AAAAAGAAAAAAAACAAAAA
Found at i:16860172 original size:12 final size:11
Alignment explanation
Indices: 16860145--16860189 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
16860135 CAGAAAAAGT
*
16860145 AAAAAAAACAA
1 AAAAAAAAGAA
16860156 AAAAAAAAG-A
1 AAAAAAAAGAA
*
16860166 AAGAAAAAGAA
1 AAAAAAAAGAA
*
16860177 AAAGAAAAGAA
1 AAAAAAAAGAA
16860188 AA
1 AA
16860190 TTGGGAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 9 0.31
11 20 0.69
ACGTcount: A:0.87, C:0.02, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:16860173 original size:16 final size:17
Alignment explanation
Indices: 16860154--16860189 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
16860144 TAAAAAAAAC
16860154 AAAAAAAAAAG-AAAGA
1 AAAAAAAAAAGAAAAGA
*
16860170 AAAAGAAAAAGAAAAGA
1 AAAAAAAAAAGAAAAGA
16860187 AAA
1 AAA
16860190 TTGGGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAGAAAAGA
Found at i:16860184 original size:11 final size:10
Alignment explanation
Indices: 16860138--16860189 Score: 61
Period size: 10 Copynumber: 5.0 Consensus size: 10
16860128 GAGTCTGCAG
16860138 AAAAAGTAAAA
1 AAAAAG-AAAA
16860149 AAAACA-AAAA
1 AAAA-AGAAAA
*
16860159 AAAAAGAAAG
1 AAAAAGAAAA
16860169 AAAAAGAAAA
1 AAAAAGAAAA
16860179 AGAAAAGAAAA
1 A-AAAAGAAAA
16860190 TTGGGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
9 1 0.03
10 21 0.58
11 13 0.36
12 1 0.03
ACGTcount: A:0.85, C:0.02, G:0.12, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:16860203 original size:6 final size:6
Alignment explanation
Indices: 16860136--16860189 Score: 51
Period size: 6 Copynumber: 9.0 Consensus size: 6
16860126 AAGAGTCTGC
*
16860136 AGAAAA AGTAAAA A-AAACA A-AAAA AAAAGAA AGAAAA AGAAAA AG-AAA
1 AGAAAA AG-AAAA AGAAA-A AGAAAA AGAA-AA AGAAAA AGAAAA AGAAAA
16860184 AGAAAA
1 AGAAAA
16860190 TTGGGAAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
5 10 0.24
6 22 0.52
7 10 0.24
ACGTcount: A:0.83, C:0.02, G:0.13, T:0.02
Consensus pattern (6 bp):
AGAAAA
Found at i:16862965 original size:55 final size:55
Alignment explanation
Indices: 16862897--16863205 Score: 618
Period size: 55 Copynumber: 5.6 Consensus size: 55
16862887 AGGTACGTAC
16862897 GAGATTCATACGAGTATTAAAAAGGGAAGTATTTAATGAATTCACATGTATGTAT
1 GAGATTCATACGAGTATTAAAAAGGGAAGTATTTAATGAATTCACATGTATGTAT
16862952 GAGATTCATACGAGTATTAAAAAGGGAAGTATTTAATGAATTCACATGTATGTAT
1 GAGATTCATACGAGTATTAAAAAGGGAAGTATTTAATGAATTCACATGTATGTAT
16863007 GAGATTCATACGAGTATTAAAAAGGGAAGTATTTAATGAATTCACATGTATGTAT
1 GAGATTCATACGAGTATTAAAAAGGGAAGTATTTAATGAATTCACATGTATGTAT
16863062 GAGATTCATACGAGTATTAAAAAGGGAAGTATTTAATGAATTCACATGTATGTAT
1 GAGATTCATACGAGTATTAAAAAGGGAAGTATTTAATGAATTCACATGTATGTAT
16863117 GAGATTCATACGAGTATTAAAAAGGGAAGTATTTAATGAATTCACATGTATGTAT
1 GAGATTCATACGAGTATTAAAAAGGGAAGTATTTAATGAATTCACATGTATGTAT
16863172 GAGATTCATACGAGTATTAAAAAGGGAAGTATTT
1 GAGATTCATACGAGTATTAAAAAGGGAAGTATTT
16863206 CATCAGGGAT
Statistics
Matches: 254, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 254 1.00
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.32
Consensus pattern (55 bp):
GAGATTCATACGAGTATTAAAAAGGGAAGTATTTAATGAATTCACATGTATGTAT
Found at i:16872597 original size:43 final size:44
Alignment explanation
Indices: 16872543--16872714 Score: 174
Period size: 43 Copynumber: 4.0 Consensus size: 44
16872533 AATTACCGAG
*
16872543 ATGTGATTACATGTAAGACCATGT-TCGGGACATTGGCATTGTAT
1 ATGTGATTACATGTAAGACCATGTCT-GGGACATTGGCATCGTAT
* * *
16872587 -TGTGGTTACATGTAAGATCATGTCTGGGACATTGTCATCGT-T
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
* *** *
16872629 ATATGATTTTGTGTAAGACCATGTCTAGGACATTGGCATCG-AT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
* * * * *
16872672 GTGTGATAACATGTAAGACCATATCTGGGATA-TGGCATTGTAT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
16872715 GATCTATATA
Statistics
Matches: 102, Mismatches: 22, Indels: 9
0.77 0.17 0.07
Matches are distributed among these distances:
42 8 0.08
43 93 0.91
44 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (44 bp):
ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
Found at i:16872932 original size:107 final size:107
Alignment explanation
Indices: 16872746--16872959 Score: 410
Period size: 107 Copynumber: 2.0 Consensus size: 107
16872736 TATCCTTAAC
16872746 GATTCTGAAGGGTTCAACGGGAAAAGTCAAGTTGAGAAAGAATATGTGAACGAGTTAAGTGATTC
1 GATTCTGAAGGGTTCAACGGGAAAAGTCAAGTTGAGAAAGAATATGTGAACGAGTTAAGTGATTC
16872811 AGGTACGTACAAGATTCATACAAGTATTAAAAATAGAAGTAT
66 AGGTACGTACAAGATTCATACAAGTATTAAAAATAGAAGTAT
* *
16872853 GATTCTGAAGGGTTCAATGGGAAAAGTCAAGTTGAGAAAGAATATGTGAACGATTTAAGTGATTC
1 GATTCTGAAGGGTTCAACGGGAAAAGTCAAGTTGAGAAAGAATATGTGAACGAGTTAAGTGATTC
16872918 AGGTACGTACAAGATTCATACAAGTATTAAAAATAGAAGTAT
66 AGGTACGTACAAGATTCATACAAGTATTAAAAATAGAAGTAT
16872960 TTGATGAATT
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 105 1.00
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.26
Consensus pattern (107 bp):
GATTCTGAAGGGTTCAACGGGAAAAGTCAAGTTGAGAAAGAATATGTGAACGAGTTAAGTGATTC
AGGTACGTACAAGATTCATACAAGTATTAAAAATAGAAGTAT
Found at i:16878843 original size:50 final size:50
Alignment explanation
Indices: 16878711--16878908 Score: 252
Period size: 50 Copynumber: 3.9 Consensus size: 50
16878701 TAAGACGATT
* * * * *
16878711 TTAGGTCACTTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAGC
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT-GG
* * * * *
16878762 TTCGATCACATGTGTAGTACTGAGTGAAGGCTACTACGTGTATCAGATGG
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGG
* * *
16878812 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTG
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGG
* *
16878862 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA
16878909 GAGCTTCGGT
Statistics
Matches: 125, Mismatches: 22, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
50 86 0.69
51 39 0.31
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (50 bp):
TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGG
Found at i:16878847 original size:101 final size:100
Alignment explanation
Indices: 16878711--16878897 Score: 275
Period size: 101 Copynumber: 1.9 Consensus size: 100
16878701 TAAGACGATT
* * ** *
16878711 TTAGGTCACTTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAGCTTCGATCACATGTG
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAAATAG-TTAGATCACATGTG
*
16878776 TAGTACTGAGTGAAGGCTACTACGTGTATCAGATGG
65 TAGTACTAAGTGAAGGCTACTACGTGTATCAGATGG
* * *
16878812 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAAATTGTTAGGTCACATGTGT
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAAATAGTTAGATCACATGTGT
*
16878877 AGTACTAAGTGCAGGCTACTA
66 AGTACTAAGTGAAGGCTACTA
16878898 TGCGTACCAG
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
100 32 0.42
101 44 0.58
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (100 bp):
TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAAATAGTTAGATCACATGTGT
AGTACTAAGTGAAGGCTACTACGTGTATCAGATGG
Found at i:16879898 original size:17 final size:19
Alignment explanation
Indices: 16879862--16879907 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
16879852 TGATTTTATT
*
16879862 AATCATAATATAATATATA
1 AATCATAATATAAAATATA
16879881 AATCAT-AT-TAAAATATA
1 AATCATAATATAAAATATA
16879898 AATCAATAAT
1 AATC-ATAAT
16879908 GAACCTCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 12 0.50
18 4 0.17
19 8 0.33
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATCATAATATAAAATATA
Found at i:16888359 original size:17 final size:19
Alignment explanation
Indices: 16888323--16888368 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
16888313 TGATTTTATT
*
16888323 AATCATAATATAATATATA
1 AATCATAATATAAAATATA
16888342 AATCAT-AT-TAAAATATA
1 AATCATAATATAAAATATA
16888359 AATCAATAAT
1 AATC-ATAAT
16888369 GAACCTCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 12 0.50
18 4 0.17
19 8 0.33
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATCATAATATAAAATATA
Found at i:16891403 original size:49 final size:49
Alignment explanation
Indices: 16891331--16892280 Score: 1732
Period size: 49 Copynumber: 19.5 Consensus size: 49
16891321 TATCACAGTT
* *
16891331 ATACACTTCCAC-TTCCATGACATTGGCCATTCGGCCTTATCACATATAC
1 ATACACTTTCACATT-CATCACATTGGCCATTCGGCCTTATCACATATAC
16891380 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
16891429 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
16891478 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
16891527 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
16891576 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
16891625 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
16891674 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
16891723 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
16891772 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
16891821 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
16891870 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
16891919 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
16891968 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
16892017 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
16892066 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
* *
16892115 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATGTGC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
* *
16892164 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTAGCACACA-A-
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
* * * *
16892211 ATGCA-TGTTCACATTCATCACATTTGCCATTCGGCCTTAGCTCATAT--
1 ATACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
* *
16892258 ATACACATTCACATCCATCACAT
1 ATACACTTTCACATTCATCACAT
16892281 AAAATCCTAA
Statistics
Matches: 882, Mismatches: 15, Indels: 10
0.97 0.02 0.01
Matches are distributed among these distances:
46 1 0.00
47 59 0.07
49 820 0.93
50 2 0.00
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (49 bp):
ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
Found at i:16896981 original size:44 final size:44
Alignment explanation
Indices: 16896929--16897016 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
16896919 ATTTATTCTC
16896929 ATGAAAAGACTGAGCATTCAGAGCATTTGAGAAT-GATTTTACAG
1 ATGAAAAGACTGAGCATTCAGAGCATTTGAGAATAG-TTTTACAG
16896973 ATGAAAAGACTGAGCATTCAGAGCATTTGAGAATAGTTTTACAG
1 ATGAAAAGACTGAGCATTCAGAGCATTTGAGAATAGTTTTACAG
16897017 TTTTTGAGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
44 42 0.98
45 1 0.02
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (44 bp):
ATGAAAAGACTGAGCATTCAGAGCATTTGAGAATAGTTTTACAG
Found at i:16900364 original size:53 final size:53
Alignment explanation
Indices: 16900187--16900393 Score: 200
Period size: 53 Copynumber: 3.8 Consensus size: 53
16900177 ATTAGGGTTT
* * * *
16900187 AAGGATACCAAGTAAGACCATGCCAAGGCATGG-AATTGGTAAGTTTTACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAA-TGGTAAG-TTCATAAGGC
* * * * * * *
16900241 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAACTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGGC
** * * * *
16900296 AAAAATCCCATGTAAGACCATGCCAAGGCATTGCAATGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
* *
16900349 AAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
16900394 TGAAAGGGAA
Statistics
Matches: 118, Mismatches: 32, Indels: 7
0.75 0.20 0.04
Matches are distributed among these distances:
53 44 0.37
54 35 0.30
55 39 0.33
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
Found at i:16903472 original size:39 final size:39
Alignment explanation
Indices: 16903429--16903814 Score: 548
Period size: 39 Copynumber: 10.0 Consensus size: 39
16903419 GTGTGAGATA
* * *
16903429 TATATCCGGGCTAATTCCCGAAGGCGTTTGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
*
16903468 TATATTCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
* *
16903507 TATATCTGGGCTAAGTCCTGAAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
16903546 TATATCCGGG-TAAGTCCCGAAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
* *
16903584 TATATCTGGGCTAAGTCCTGAAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
16903623 TATATCCGGG-TAAGTCCCGAAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
* *
16903661 TATATCTGGGCTAAGTCCTGAAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
16903700 TATATCCGGG-TAAGTCCCGAAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
* * ** *
16903738 TATATCTGGGTTAAGTCCCGAAGGC-TTTATGCTGGTAT
1 TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
* * * *
16903776 TAGATCCGGGCTTAAAGTCCCGCATGCATT-GTGGTGGTG
1 TATATCCGGGC-T-AAGTCCCGAAGGCATTCGTGCTGGTG
16903815 ATTGAATTTG
Statistics
Matches: 312, Mismatches: 29, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
38 126 0.40
39 167 0.54
40 17 0.05
41 2 0.01
ACGTcount: A:0.18, C:0.19, G:0.31, T:0.32
Consensus pattern (39 bp):
TATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGT
Found at i:16903589 original size:77 final size:77
Alignment explanation
Indices: 16903429--16903785 Score: 590
Period size: 77 Copynumber: 4.6 Consensus size: 77
16903419 GTGTGAGATA
* * * * * *
16903429 TATATCCGGGCTAATTCCCGAAGGCGTTTGTGCTGGTGTTATATTCGGGCTAAGTCCCGAAGGCA
1 TATATCTGGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTTATATCCGGG-TAAGTCCCGAAGGCA
16903494 TTCGTGCTGGTGT
65 TTCGTGCTGGTGT
16903507 TATATCTGGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTTATATCCGGGTAAGTCCCGAAGGCAT
1 TATATCTGGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTTATATCCGGGTAAGTCCCGAAGGCAT
16903572 TCGTGCTGGTGT
66 TCGTGCTGGTGT
16903584 TATATCTGGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTTATATCCGGGTAAGTCCCGAAGGCAT
1 TATATCTGGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTTATATCCGGGTAAGTCCCGAAGGCAT
16903649 TCGTGCTGGTGT
66 TCGTGCTGGTGT
16903661 TATATCTGGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTTATATCCGGGTAAGTCCCGAAGGCAT
1 TATATCTGGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTTATATCCGGGTAAGTCCCGAAGGCAT
16903726 TCGTGCTGGTGT
66 TCGTGCTGGTGT
* * ** * *
16903738 TATATCTGGGTTAAGTCCCGAAGGC-TTTATGCTGGTATTAGATCCGGG
1 TATATCTGGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTTATATCCGGG
16903786 CTTAAAGTCC
Statistics
Matches: 267, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
76 19 0.07
77 205 0.77
78 43 0.16
ACGTcount: A:0.18, C:0.19, G:0.31, T:0.32
Consensus pattern (77 bp):
TATATCTGGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTTATATCCGGGTAAGTCCCGAAGGCAT
TCGTGCTGGTGT
Found at i:16907509 original size:40 final size:40
Alignment explanation
Indices: 16907403--16907531 Score: 134
Period size: 40 Copynumber: 3.2 Consensus size: 40
16907393 ACTCGAATTC
** *
16907403 TCGCACACTAAGTGCCAATACATAGCTGAAGCTAT-TACAATA
1 TCGCACACTAAGTGCC-ATACATAGCCAAAGCTATCT-CGA-A
* * * * *
16907445 TCACACACTAAGTGCTATATATAGCCAAAGCGATCTGGAA
1 TCGCACACTAAGTGCCATACATAGCCAAAGCTATCTCGAA
* *
16907485 TCGCACACTAAGTGCCATACATAGCCAACGCTATCTTGAA
1 TCGCACACTAAGTGCCATACATAGCCAAAGCTATCTCGAA
16907525 TCGCACA
1 TCGCACA
16907532 ATATGTGACA
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
40 42 0.58
41 15 0.21
42 15 0.21
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (40 bp):
TCGCACACTAAGTGCCATACATAGCCAAAGCTATCTCGAA
Found at i:16909217 original size:28 final size:28
Alignment explanation
Indices: 16909184--16909282 Score: 107
Period size: 28 Copynumber: 3.5 Consensus size: 28
16909174 ATGAATATAT
*
16909184 GCACTATGTGTGCGAGATTAGTAACCGA
1 GCACTATGTGTGCGAAATTAGTAACCGA
*
16909212 ACACTATGTGTGCGAAATCGGGT-GTAA--G-
1 GCACTATGTGTGCGAAAT----TAGTAACCGA
*
16909240 GCACTATGTGTGCGAAATTATTAACCGA
1 GCACTATGTGTGCGAAATTAGTAACCGA
16909268 GCACTATGTGTGCGA
1 GCACTATGTGTGCGA
16909283 GATCGAGTGT
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
24 1 0.02
25 3 0.05
27 1 0.02
28 48 0.81
29 1 0.02
31 4 0.07
32 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.26
Consensus pattern (28 bp):
GCACTATGTGTGCGAAATTAGTAACCGA
Found at i:16909273 original size:56 final size:56
Alignment explanation
Indices: 16909184--16909307 Score: 194
Period size: 56 Copynumber: 2.2 Consensus size: 56
16909174 ATGAATATAT
* *
16909184 GCACTATGTGTGCGAGATTAGTAACCGAACACTATGTGTGCGAAATCGGGTGTAAG
1 GCACTATGTGTGCGAAATTAGTAACCGAACACTATGTGTGCGAAATCGAGTGTAAG
* * *
16909240 GCACTATGTGTGCGAAATTATTAACCGAGCACTATGTGTGCGAGATCGAGTGTAAG
1 GCACTATGTGTGCGAAATTAGTAACCGAACACTATGTGTGCGAAATCGAGTGTAAG
*
16909296 GCACTGTGTGTG
1 GCACTATGTGTG
16909308 TGCAAAATTA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.27
Consensus pattern (56 bp):
GCACTATGTGTGCGAAATTAGTAACCGAACACTATGTGTGCGAAATCGAGTGTAAG
Found at i:16909299 original size:28 final size:28
Alignment explanation
Indices: 16909213--16909307 Score: 106
Period size: 28 Copynumber: 3.4 Consensus size: 28
16909203 AGTAACCGAA
*
16909213 CACTATGTGTGCGAAATCGGGTGTAAGG
1 CACTATGTGTGCGAAATCGAGTGTAAGG
*
16909241 CACTATGTGTGCGAAAT-TA-T-TAACCGAG
1 CACTATGTGTGCGAAATCGAGTGTAA--G-G
*
16909269 CACTATGTGTGCGAGATCGAGTGTAAGG
1 CACTATGTGTGCGAAATCGAGTGTAAGG
*
16909297 CACTGTGTGTG
1 CACTATGTGTG
16909308 TGCAAAATTA
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
25 3 0.05
26 1 0.02
27 1 0.02
28 45 0.80
29 2 0.04
30 1 0.02
31 3 0.05
ACGTcount: A:0.25, C:0.16, G:0.32, T:0.27
Consensus pattern (28 bp):
CACTATGTGTGCGAAATCGAGTGTAAGG
Found at i:16911480 original size:44 final size:44
Alignment explanation
Indices: 16911417--16911504 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
16911407 GGACGAGAGC
* *
16911417 AGGAATTTCTATTAAGCAACGATCATCAACGGACTCTCGAGCTA
1 AGGAATTTCTATTAAGCAACAACCATCAACGGACTCTCGAGCTA
16911461 AGGAATTTCTATTAAGCAACAACCATCAACGGACTCTCGAGCTA
1 AGGAATTTCTATTAAGCAACAACCATCAACGGACTCTCGAGCTA
16911505 CTTCAGTTGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (44 bp):
AGGAATTTCTATTAAGCAACAACCATCAACGGACTCTCGAGCTA
Found at i:16916885 original size:28 final size:26
Alignment explanation
Indices: 16916853--16916954 Score: 100
Period size: 28 Copynumber: 3.7 Consensus size: 26
16916843 ATAAATATAT
16916853 GCACTATGTGTGCGAGATTAGTAATTGA
1 GCACTATGTGTGCGAGATTAGTAA--GA
16916881 GCACTATGTGTGCGAGATCGGGT-GTAAG-
1 GCACTATGTGTGCGAGAT----TAGTAAGA
* *
16916909 GCACTATGTGTGCGAAATTATTAACCGA
1 GCACTATGTGTGCGAGATTAGTAA--GA
16916937 GCACTATGTGTGCGAGAT
1 GCACTATGTGTGCGAGAT
16916955 CGGGTGTAAG
Statistics
Matches: 63, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
24 1 0.02
25 3 0.05
27 1 0.02
28 52 0.83
29 1 0.02
31 4 0.06
32 1 0.02
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.28
Consensus pattern (26 bp):
GCACTATGTGTGCGAGATTAGTAAGA
Found at i:16916920 original size:56 final size:56
Alignment explanation
Indices: 16916853--16916976 Score: 203
Period size: 56 Copynumber: 2.2 Consensus size: 56
16916843 ATAAATATAT
* **
16916853 GCACTATGTGTGCGAGATTAGTAATTGAGCACTATGTGTGCGAGATCGGGTGTAAG
1 GCACTATGTGTGCGAAATTAGTAACCGAGCACTATGTGTGCGAGATCGGGTGTAAG
*
16916909 GCACTATGTGTGCGAAATTATTAACCGAGCACTATGTGTGCGAGATCGGGTGTAAG
1 GCACTATGTGTGCGAAATTAGTAACCGAGCACTATGTGTGCGAGATCGGGTGTAAG
*
16916965 GCACTGTGTGTG
1 GCACTATGTGTG
16916977 TGCAAAATTA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.28
Consensus pattern (56 bp):
GCACTATGTGTGCGAAATTAGTAACCGAGCACTATGTGTGCGAGATCGGGTGTAAG
Found at i:16916968 original size:28 final size:28
Alignment explanation
Indices: 16916881--16916976 Score: 108
Period size: 28 Copynumber: 3.4 Consensus size: 28
16916871 TAGTAATTGA
16916881 GCACTATGTGTGCGAGATCGGGTGTAAG
1 GCACTATGTGTGCGAGATCGGGTGTAAG
* **
16916909 GCACTATGTGTGCGAAAT--TAT-TAACCG
1 GCACTATGTGTGCGAGATCGGGTGTAA--G
16916936 AGCACTATGTGTGCGAGATCGGGTGTAAG
1 -GCACTATGTGTGCGAGATCGGGTGTAAG
*
16916965 GCACTGTGTGTG
1 GCACTATGTGTG
16916977 TGCAAAATTA
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
25 3 0.05
26 1 0.02
27 1 0.02
28 45 0.82
29 1 0.02
30 1 0.02
31 3 0.05
ACGTcount: A:0.23, C:0.16, G:0.34, T:0.27
Consensus pattern (28 bp):
GCACTATGTGTGCGAGATCGGGTGTAAG
Found at i:16917737 original size:248 final size:248
Alignment explanation
Indices: 16917299--16917789 Score: 973
Period size: 248 Copynumber: 2.0 Consensus size: 248
16917289 TGTGCACTCG
16917299 GAACTACTACCGAAGTCATCGCACTTATCGTCAACTTTTTGGTATCTTTAAAGAAGCTTTAAGTT
1 GAACTACTACCGAAGTCATCGCACTTATCGTCAACTTTTTGGTATCTTTAAAGAAGCTTTAAGTT
16917364 TTAAATTTGGCATGTATAGGATAGACGAAACTAATAAAGTGAGTTTTGTATTTTTGAGTAATGTA
66 TTAAATTTGGCATGTATAGGATAGACGAAACTAATAAAGTGAGTTTTGTATTTTTGAGTAATGTA
*
16917429 ATTATCTTTTTGATGAGCCATACGAAAATGGCACACAATCTAGTTTTGTGACTTTAAAATGTTAA
131 ATTATCTTTTTGATAAGCCATACGAAAATGGCACACAATCTAGTTTTGTGACTTTAAAATGTTAA
16917494 ATATTTTGATAACTAGCATGCGTAATATGAATGAATCGTATCTACTTTGCTCA
196 ATATTTTGATAACTAGCATGCGTAATATGAATGAATCGTATCTACTTTGCTCA
16917547 GAACTACTACCGAAGTCATCGCACTTATCGTCAACTTTTTGGTATCTTTAAAGAAGCTTTAAGTT
1 GAACTACTACCGAAGTCATCGCACTTATCGTCAACTTTTTGGTATCTTTAAAGAAGCTTTAAGTT
16917612 TTAAATTTGGCATGTATAGGATAGACGAAACTAATAAAGTGAGTTTTGTATTTTTGAGTAATGTA
66 TTAAATTTGGCATGTATAGGATAGACGAAACTAATAAAGTGAGTTTTGTATTTTTGAGTAATGTA
16917677 ATTATCTTTTTGATAAGCCATACGAAAATGGCACACAATCTAGTTTTGTGACTTTAAAATGTTAA
131 ATTATCTTTTTGATAAGCCATACGAAAATGGCACACAATCTAGTTTTGTGACTTTAAAATGTTAA
16917742 ATATTTTGATAACTAGCATGCGTAATATGAATGAATCGTATCTACTTT
196 ATATTTTGATAACTAGCATGCGTAATATGAATGAATCGTATCTACTTT
16917790 TTGTATATAA
Statistics
Matches: 242, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
248 242 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (248 bp):
GAACTACTACCGAAGTCATCGCACTTATCGTCAACTTTTTGGTATCTTTAAAGAAGCTTTAAGTT
TTAAATTTGGCATGTATAGGATAGACGAAACTAATAAAGTGAGTTTTGTATTTTTGAGTAATGTA
ATTATCTTTTTGATAAGCCATACGAAAATGGCACACAATCTAGTTTTGTGACTTTAAAATGTTAA
ATATTTTGATAACTAGCATGCGTAATATGAATGAATCGTATCTACTTTGCTCA
Found at i:16918596 original size:16 final size:17
Alignment explanation
Indices: 16918575--16918606 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
16918565 AATTTAGCCT
16918575 AAAATTTACA-ATTTGG
1 AAAATTTACACATTTGG
16918591 AAAATTTACACATTTG
1 AAAATTTACACATTTG
16918607 CCCCTAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (17 bp):
AAAATTTACACATTTGG
Found at i:16921315 original size:14 final size:15
Alignment explanation
Indices: 16921280--16921323 Score: 63
Period size: 14 Copynumber: 2.9 Consensus size: 15
16921270 CATTAGGGGC
16921280 AAATGTGTAAATTTGCA
1 AAAT-TGTAAATTT-CA
16921297 AAATTGTAAATTT-A
1 AAATTGTAAATTTCA
16921311 AAATTGTAAATTT
1 AAATTGTAAATTT
16921324 TAGGCTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.52
16 9 0.33
17 4 0.15
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.41
Consensus pattern (15 bp):
AAATTGTAAATTTCA
Found at i:16921609 original size:40 final size:40
Alignment explanation
Indices: 16921565--16921788 Score: 202
Period size: 40 Copynumber: 5.5 Consensus size: 40
16921555 TGACAAATCA
*
16921565 GCTATATGTGGCACTTAGTGTGCGATTCGAA-ATAGCTTCG
1 GCTATATATGGCACTTAGTGTGCGATTC-AAGATAGCTTCG
16921605 GCTATATATGGCACTTAGTGTGCAAGA-TCAAGATAGCTTCG
1 GCTATATATGGCACTTAGTGTGC--GATTCAAGATAGCTTCG
* * *
16921646 GCTATGTATGGCACTTAATGTGCGATTCAAGATAGCTTTG
1 GCTATATATGGCACTTAGTGTGCGATTCAAGATAGCTTCG
* ** * * * *
16921686 GCTATGTATAACACTTAGTGCGTGATTCGAGATAGCTACG
1 GCTATATATGGCACTTAGTGTGCGATTCAAGATAGCTTCG
* ** * * *
16921726 GATATATAACGCACTTAGTGTGTGAGATT-AAAATAGCTTCA
1 GCTATATATGGCACTTA--GTGTGCGATTCAAGATAGCTTCG
* *
16921767 GCTATGTATTGACACTTAGTGT
1 GCTATATA-TGGCACTTAGTGT
16921789 ACAAGAATTC
Statistics
Matches: 149, Mismatches: 28, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
39 2 0.01
40 85 0.57
41 46 0.31
42 16 0.11
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (40 bp):
GCTATATATGGCACTTAGTGTGCGATTCAAGATAGCTTCG
Found at i:16928739 original size:17 final size:18
Alignment explanation
Indices: 16928717--16928750 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16928707 CACATTAAAT
16928717 TGTTTT-AGTGAAAACCG
1 TGTTTTCAGTGAAAACCG
*
16928734 TGTTTTCATTGAAAACC
1 TGTTTTCAGTGAAAACC
16928751 CTTCTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (18 bp):
TGTTTTCAGTGAAAACCG
Found at i:16930091 original size:8 final size:8
Alignment explanation
Indices: 16930078--16930120 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
16930068 GTAGCCAAAC
16930078 TTTCGGCT
1 TTTCGGCT
*
16930086 TTTCGGCG
1 TTTCGGCT
*
16930094 TTTCAGCT
1 TTTCGGCT
*
16930102 TTTCGGCA
1 TTTCGGCT
*
16930110 TTTCTGCT
1 TTTCGGCT
16930118 TTT
1 TTT
16930121 GCCGATACAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.05, C:0.23, G:0.21, T:0.51
Consensus pattern (8 bp):
TTTCGGCT
Found at i:16930102 original size:16 final size:16
Alignment explanation
Indices: 16930078--16930120 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
16930068 GTAGCCAAAC
* *
16930078 TTTCGGCTTTTCGGCG
1 TTTCAGCTTTTCGGCA
16930094 TTTCAGCTTTTCGGCA
1 TTTCAGCTTTTCGGCA
*
16930110 TTTCTGCTTTT
1 TTTCAGCTTTT
16930121 GCCGATACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.05, C:0.23, G:0.21, T:0.51
Consensus pattern (16 bp):
TTTCAGCTTTTCGGCA
Found at i:16931376 original size:16 final size:16
Alignment explanation
Indices: 16931352--16931383 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
16931342 AAGTTCAGGA
*
16931352 TTTCGGGATTTTTGGG
1 TTTCAGGATTTTTGGG
16931368 TTTCAGGATTTTTGGG
1 TTTCAGGATTTTTGGG
16931384 GCGTTACATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.06, G:0.34, T:0.50
Consensus pattern (16 bp):
TTTCAGGATTTTTGGG
Found at i:16936998 original size:23 final size:24
Alignment explanation
Indices: 16936923--16937010 Score: 90
Period size: 24 Copynumber: 3.7 Consensus size: 24
16936913 CTATATAACG
* **
16936923 GGAAGCTCA-TAAGAGCCATTATTG
1 GGAAGCTCACAAAGAGCCA-TATCA
* *
16936947 GGAAGTTCACAAAGAACCATATCA
1 GGAAGCTCACAAAGAGCCATATCA
* *
16936971 AGAAGCTCACGAAGAGCC-TATCA
1 GGAAGCTCACAAAGAGCCATATCA
16936994 GGAAGCTCACAAAGAGC
1 GGAAGCTCACAAAGAGC
16937011 AATGTAACGG
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
23 20 0.38
24 25 0.48
25 7 0.13
ACGTcount: A:0.40, C:0.22, G:0.23, T:0.16
Consensus pattern (24 bp):
GGAAGCTCACAAAGAGCCATATCA
Found at i:16943415 original size:47 final size:47
Alignment explanation
Indices: 16942231--16943379 Score: 1947
Period size: 47 Copynumber: 24.3 Consensus size: 47
16942221 CAGCCAAGAG
* * * *
16942231 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
* * * * *
16942278 AGTGTATGTATATATGTAATAAGGTCTAATAGCCGATGTGATGAATGTGAA
1 A--G--TGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
16942329 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
* *
16942376 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
* * * *
16942423 AGTGTATGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTA--TATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
16942472 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
16942519 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
16942566 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
16942613 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
16942660 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
16942707 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
16942754 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
16942801 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
16942848 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
16942895 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
16942942 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
16942989 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
16943036 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
16943083 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
16943130 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
* *
16943177 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
* * * * *
16943224 AGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
* * * * *
16943271 AGTGTATATATGTGATAAGGCCTAATGGCCGATGCGATGAATGTGAA
1 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
* * * * *
16943318 AGTGTATATATGTGTTAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
*
16943365 AGTGTATATATGTGA
1 AGTGTATATGTGTGA
16943380 CAGGGCCGAG
Statistics
Matches: 1070, Mismatches: 26, Indels: 12
0.97 0.02 0.01
Matches are distributed among these distances:
47 980 0.92
49 47 0.04
51 43 0.04
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.29
Consensus pattern (47 bp):
AGTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
Found at i:16943605 original size:37 final size:37
Alignment explanation
Indices: 16943549--16943627 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
16943539 CCGAGCTCTA
* * *
16943549 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
* *
16943586 AAGACCCTATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
16943623 AAGAC
1 AAGAC
16943628 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:16945527 original size:43 final size:43
Alignment explanation
Indices: 16945479--16945577 Score: 198
Period size: 43 Copynumber: 2.3 Consensus size: 43
16945469 TTGGTTTTCA
16945479 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
16945522 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
16945565 GCACTAAGTGTGC
1 GCACTAAGTGTGC
16945578 AGGCTTGAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.23, C:0.15, G:0.34, T:0.27
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:16945598 original size:29 final size:29
Alignment explanation
Indices: 16945563--16945636 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
16945553 GTTGTGAGAT
*
16945563 TGGCACTAAGTGTGC-AGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGA-G-TTGAAAGTACA
*
16945592 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
16945621 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
16945637 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 5 0.12
29 35 0.85
30 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:16946078 original size:40 final size:40
Alignment explanation
Indices: 16945955--16946190 Score: 226
Period size: 40 Copynumber: 5.9 Consensus size: 40
16945945 TCGAATGATG
** *
16945955 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGA-TATA
* * ** * * *
16945995 TCCGGACTAAGACCCGAAG-GCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA-TATA
*
16946035 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
*
16946075 TCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* ** * * * *
16946115 TCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTATG
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* * *
16946155 TCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
16946191 CGTGTATTCG
Statistics
Matches: 162, Mismatches: 32, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
40 144 0.89
41 18 0.11
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
Found at i:16949440 original size:47 final size:47
Alignment explanation
Indices: 16949382--16949776 Score: 610
Period size: 47 Copynumber: 8.4 Consensus size: 47
16949372 CAGCCTAGAG
16949382 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
16949429 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * *
16949476 ACTGTATATGTGTGATGAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * *
16949523 AGTGTATATGTGTGATAAGGCCTAATAGCCGAGGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
16949570 AGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
16949617 AGTGTATATATGTGATAAGGCCTAATGGCCGATGCGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
16949664 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * * *
16949711 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTAATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
16949758 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
16949777 TCCCGAAAGG
Statistics
Matches: 321, Mismatches: 27, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 321 1.00
ACGTcount: A:0.32, C:0.10, G:0.30, T:0.28
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:16949951 original size:37 final size:37
Alignment explanation
Indices: 16949895--16949973 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
16949885 CCGAGCTCTA
* * *
16949895 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
* *
16949932 AAGACCCGATAACTTCGTGTGTAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
16949969 AAGAC
1 AAGAC
16949974 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:16961675 original size:29 final size:29
Alignment explanation
Indices: 16961600--16961688 Score: 128
Period size: 29 Copynumber: 3.1 Consensus size: 29
16961590 CACATACCTG
*
16961600 TATATGGTCCATTAGGCCC-AATCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
16961628 TATA-GGCCCATTAGGCCCAAATCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
* * *
16961656 TATATGGCCCATCAGACCCAATTCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
16961685 TATA
1 TATA
16961689 GTCATGATCA
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
27 13 0.24
28 17 0.31
29 25 0.45
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.29
Consensus pattern (29 bp):
TATATGGCCCATTAGGCCCAAATCACATT
Found at i:16961922 original size:16 final size:16
Alignment explanation
Indices: 16961901--16961951 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
16961891 ATAGTCAAAC
16961901 TTTCGGCTTTTCAGCA
1 TTTCGGCTTTTCAGCA
16961917 TTTCGGCTTTTCAGCA
1 TTTCGGCTTTTCAGCA
* *
16961933 TTTCGACTTTTCGGCA
1 TTTCGGCTTTTCAGCA
16961949 TTT
1 TTT
16961952 TGACTTTTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.47
Consensus pattern (16 bp):
TTTCGGCTTTTCAGCA
Found at i:16961956 original size:16 final size:16
Alignment explanation
Indices: 16961901--16961959 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
16961891 ATAGTCAAAC
*
16961901 TTTCGGCTTTTCAGCA
1 TTTCGACTTTTCAGCA
*
16961917 TTTCGGCTTTTCAGCA
1 TTTCGACTTTTCAGCA
*
16961933 TTTCGACTTTTCGGCA
1 TTTCGACTTTTCAGCA
*
16961949 TTTTGACTTTT
1 TTTCGACTTTT
16961960 GCCGATCTAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.12, C:0.22, G:0.17, T:0.49
Consensus pattern (16 bp):
TTTCGACTTTTCAGCA
Found at i:16972758 original size:25 final size:25
Alignment explanation
Indices: 16972730--16972785 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
16972720 CTATGATCGA
**
16972730 TAAGCTCCTCCTGAGCT-GATAACAG
1 TAAGCTCCTAATGAGCTGGA-AACAG
16972755 TAAGCT-CTAATGAGCTGGAAACAG
1 TAAGCTCCTAATGAGCTGGAAACAG
16972779 TAAGCTC
1 TAAGCTC
16972786 TGACAAGCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 19 0.70
25 8 0.30
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.23
Consensus pattern (25 bp):
TAAGCTCCTAATGAGCTGGAAACAG
Found at i:16972794 original size:24 final size:24
Alignment explanation
Indices: 16972742--16972819 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
16972732 AGCTCCTCCT
*
16972742 GAGCT-GATAACAGTAAGCTCTAAT
1 GAGCTGGA-AACAGTAAGCTCTAAC
*
16972766 GAGCTGGAAACAGTAAGCTCTGAC
1 GAGCTGGAAACAGTAAGCTCTAAC
* * ** *
16972790 AAGCTGGGATTAGTAAGCTCTTAC
1 GAGCTGGAAACAGTAAGCTCTAAC
16972814 GAGCTG
1 GAGCTG
16972820 ATATATCGGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
24 43 0.96
25 2 0.04
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (24 bp):
GAGCTGGAAACAGTAAGCTCTAAC
Found at i:16973962 original size:28 final size:28
Alignment explanation
Indices: 16973929--16973997 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
16973919 TGTGAATCTT
* * * * *
16973929 GCACTAAGTTTGTGAGTGTGATTATTGA
1 GCACTAAGTGTGCGAGTGTAAATATCGA
*
16973957 GCACTAAGTGTGCGAGTTTAAATATCGA
1 GCACTAAGTGTGCGAGTGTAAATATCGA
16973985 GCACTAAGTGTGC
1 GCACTAAGTGTGC
16973998 AAACTATATA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTGTAAATATCGA
Found at i:16986489 original size:29 final size:29
Alignment explanation
Indices: 16986447--16986515 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
16986437 ATAGAGATCA
16986447 CCACAAAGGC-TTTCCTCTCTAGA-GTTTG
1 CCACAAAGGCATTTCCTCTC-AGAGGTTTG
* * *
16986475 CCACAGAGGCATTTCGTTTCAGAGGTTTG
1 CCACAAAGGCATTTCCTCTCAGAGGTTTG
*
16986504 CCATAAAGGCAT
1 CCACAAAGGCAT
16986516 CCTTTTCATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 12 0.35
29 22 0.65
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.29
Consensus pattern (29 bp):
CCACAAAGGCATTTCCTCTCAGAGGTTTG
Found at i:16986926 original size:50 final size:50
Alignment explanation
Indices: 16986841--16986939 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 50
16986831 CCTGTAGATC
* * * * **
16986841 TTTCCATGTGATGCCATAGCCCACCTGTTATGGTCTTGTACGATATGGTG
1 TTTCCATATGACGCCATAGCCCACCTGCTACGGTCTTACACGATATGGTG
16986891 TTTCCATATGACGCCATAGCCCA-CTAGCTACGGTCTTACACGATATGGT
1 TTTCCATATGACGCCATAGCCCACCT-GCTACGGTCTTACACGATATGGT
16986940 CCTTTCAGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
49 2 0.05
50 40 0.95
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.32
Consensus pattern (50 bp):
TTTCCATATGACGCCATAGCCCACCTGCTACGGTCTTACACGATATGGTG
Done.