Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007984.1 Hibiscus syriacus cultivar Beakdansim tig00110429_pilon, whole genome shotgun sequence
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: 12923621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 65
Found at i:143743 original size:18 final size:16
Alignment explanation
Indices: 143700--143761 Score: 63
Period size: 18 Copynumber: 3.6 Consensus size: 16
143690 CATGTACCTG
143700 AAAAATAAAA-AAAAT
1 AAAAATAAAATAAAAT
*
143715 AAAAACAAAAATAAATCAT
1 AAAAA-TAAAATAAA--AT
143734 AAAAATAAAATTGAAAAT
1 AAAAATAAAA-T-AAAAT
143752 AAAAATAAAA
1 AAAAATAAAA
143762 ATTAAACAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
15 5 0.13
16 4 0.10
17 3 0.08
18 16 0.41
19 8 0.21
20 3 0.08
ACGTcount: A:0.79, C:0.03, G:0.02, T:0.16
Consensus pattern (16 bp):
AAAAATAAAATAAAAT
Found at i:143787 original size:6 final size:6
Alignment explanation
Indices: 143709--143763 Score: 65
Period size: 6 Copynumber: 9.0 Consensus size: 6
143699 GAAAAATAAA
* * * *
143709 AAAAAT AAAAAC AAAAAT AAATCAT AAAAAT AAAATT GAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAA-AAT AAAAAT AAAAAT AAAAAT AAAAAT
143758 AAAAAT
1 AAAAAT
143764 TAAACAAACG
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
6 35 0.88
7 5 0.12
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:150387 original size:86 final size:85
Alignment explanation
Indices: 150282--150456 Score: 280
Period size: 86 Copynumber: 2.0 Consensus size: 85
150272 ATAAAGAAAA
*
150282 TAAATCCTAATTAAAATACTTAAAACTATTTAAACTAAAATACCTAAAACAAAGGTAAGATAAAA
1 TAAATCCTAATTAAAATACTTAAAACTATTTAAACTAAAATACCTAAAAC--AGATAAGATAAAA
* *
150347 TATAATATTTAAAA-AAAATCC
64 AAAAATATTTAAAATAAAATCC
*
150368 TAAATCCTAATTAAAATACTTAAAACTATTTAAACTATAATACCTAAAACAGATAAGATAAAAAA
1 TAAATCCTAATTAAAATACTTAAAACTATTTAAACTAAAATACCTAAAACAGATAAGATAAAAAA
*
150433 AAATATTTAAAATAATATCC
66 AAATATTTAAAATAAAATCC
150453 TAAA
1 TAAA
150457 AGATGAGTTT
Statistics
Matches: 83, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
84 24 0.29
85 10 0.12
86 49 0.59
ACGTcount: A:0.57, C:0.11, G:0.03, T:0.29
Consensus pattern (85 bp):
TAAATCCTAATTAAAATACTTAAAACTATTTAAACTAAAATACCTAAAACAGATAAGATAAAAAA
AAATATTTAAAATAAAATCC
Found at i:170114 original size:31 final size:32
Alignment explanation
Indices: 170039--170114 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
170029 TCAGGTCTGC
* *
170039 GAGCCTACCCAAGACAATTCCTGGGGCCACTA
1 GAGCCTACCCAAGAAAATTCCTAGGGCCACTA
*
170071 -AGGCTTACCCAAGAAAATT-CTCAGGGCCA-TA
1 GA-GCCTACCCAAGAAAATTCCT-AGGGCCACTA
170102 GAGCCTACCCAAG
1 GAGCCTACCCAAG
170115 GCTCGACTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
31 15 0.41
32 22 0.59
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.16
Consensus pattern (32 bp):
GAGCCTACCCAAGAAAATTCCTAGGGCCACTA
Found at i:170365 original size:16 final size:16
Alignment explanation
Indices: 170344--170381 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
170334 TACATTTCAG
*
170344 TAAATCCAGAATCAAC
1 TAAATCCAAAATCAAC
*
170360 TAAATCCAAAATCAGC
1 TAAATCCAAAATCAAC
170376 TAAATC
1 TAAATC
170382 ATACAATAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.24, G:0.05, T:0.21
Consensus pattern (16 bp):
TAAATCCAAAATCAAC
Found at i:171215 original size:29 final size:28
Alignment explanation
Indices: 171147--171386 Score: 202
Period size: 29 Copynumber: 8.2 Consensus size: 28
171137 ACAGAATTAA
* *
171147 TTACGAAACTAACACCATTTTAAAAAATAT
1 TTACAAAACTAACACCCTTTT--AAAATAT
*
171177 TTACGTAAA-TAACACCCTTTTAGAAATAT
1 TTAC-AAAACTAACACCCTTTTA-AAATAT
* *
171206 TTACAAAAATATCA-CCTTGTTAAAAATAT
1 TTACAAAACTAACACCCTT-TT-AAAATAT
* * *
171235 TTACGAAACTAGCACCTTTTTAACAATAT
1 TTACAAAACTAACACCCTTTTAA-AATAT
*
171264 TTACGAAACTAACA-CCTTCTTAACAATAT
1 TTACAAAACTAACACCCTT-TTAA-AATAT
*
171293 TTACAAAACTAACACCTTTTTAACAATAT
1 TTACAAAACTAACACCCTTTTAA-AATAT
*
171322 TTACAAAACTAACA-CCTTCTTAACAAAAT
1 TTACAAAACTAACACCCTT-TTAA-AATAT
* *
171351 TTACGAAACTAACA-CCTTTACAAAAATAT
1 TTACAAAACTAACACCCTTT--TAAAATAT
171380 TTACAAA
1 TTACAAA
171387 CATACCACCA
Statistics
Matches: 180, Mismatches: 18, Indels: 25
0.81 0.08 0.11
Matches are distributed among these distances:
28 17 0.09
29 136 0.76
30 24 0.13
31 3 0.02
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (28 bp):
TTACAAAACTAACACCCTTTTAAAATAT
Found at i:171263 original size:58 final size:58
Alignment explanation
Indices: 171147--171395 Score: 281
Period size: 58 Copynumber: 4.3 Consensus size: 58
171137 ACAGAATTAA
* * *
171147 TTACGAAACTAACACCATT-TTAAAAAATATTTACGTAAA-TAACACCCTTTTAGA-AATAT
1 TTACAAAAATAACACC-TTCTT-AAAAATATTTACG-AAACTAACACCTTTTTA-ACAATAT
* * *
171206 TTACAAAAATATCACCTTGTTAAAAATATTTACGAAACTAGCACCTTTTTAACAATAT
1 TTACAAAAATAACACCTTCTTAAAAATATTTACGAAACTAACACCTTTTTAACAATAT
* * * *
171264 TTACGAAACTAACACCTTCTTAACAATATTTACAAAACTAACACCTTTTTAACAATAT
1 TTACAAAAATAACACCTTCTTAAAAATATTTACGAAACTAACACCTTTTTAACAATAT
* ** *
171322 TTACAAAACTAACACCTTCTTAACAAA-ATTTACGAAACTAACACCTTTACAAAAATAT
1 TTACAAAAATAACACCTTCTTAA-AAATATTTACGAAACTAACACCTTTTTAACAATAT
* *
171380 TTACAAACATACCACC
1 TTACAAAAATAACACC
171396 ATAACCGAAA
Statistics
Matches: 165, Mismatches: 21, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
57 4 0.02
58 144 0.87
59 17 0.10
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.31
Consensus pattern (58 bp):
TTACAAAAATAACACCTTCTTAAAAATATTTACGAAACTAACACCTTTTTAACAATAT
Found at i:171299 original size:87 final size:85
Alignment explanation
Indices: 171147--171395 Score: 302
Period size: 87 Copynumber: 2.8 Consensus size: 85
171137 ACAGAATTAA
* *
171147 TTACGAAACTAACACCATTTTAAAAAATATTTACGTAAA-TAACACCCTTTTAGAAATATTTACA
1 TTACGAAACTAACACC-TTTTTAACAATATTTACG-AAACTAACA-CCTTTTA-AAATATTTACA
*
171211 AAAATATCACCTTGTTAAAAATAT
62 AAAATAACACCTTGTTAAAAATAT
*
171235 TTACGAAACTAGCACCTTTTTAACAATATTTACGAAACTAACACCTTCTTAACAATATTTACAAA
1 TTACGAAACTAACACCTTTTTAACAATATTTACGAAACTAACACCTT-TTAA-AATATTTACAAA
* * *
171300 ACTAACACCTTTTTAACAATAT
64 AATAACACCTTGTTAAAAATAT
* * * *
171322 TTACAAAACTAACACCTTCTTAACAAAATTTACGAAACTAACACCTTTACAAAAATATTTACAAA
1 TTACGAAACTAACACCTTTTTAACAATATTTACGAAACTAACACCTTT--TAAAATATTTACAAA
* *
171387 CATACCACC
64 AATAACACC
171396 ATAACCGAAA
Statistics
Matches: 141, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
86 9 0.06
87 115 0.82
88 17 0.12
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.31
Consensus pattern (85 bp):
TTACGAAACTAACACCTTTTTAACAATATTTACGAAACTAACACCTTTTAAAATATTTACAAAAA
TAACACCTTGTTAAAAATAT
Found at i:171478 original size:58 final size:59
Alignment explanation
Indices: 171372--171499 Score: 177
Period size: 58 Copynumber: 2.2 Consensus size: 59
171362 ACACCTTTAC
* * * * *
171372 AAAAATATTTACAAACATACCACCATAACCGAAATTAATTACGTATTAGTCATTCTTTT
1 AAAAATATTTACAAAAATACCACCATAACAGAAATTAATTACATATTAGTCACTCTATT
* *
171431 AAAACTATTTACAAAAATAGCACCATAA-AGAAATTAATTACATATTAGTCACTCTATT
1 AAAAATATTTACAAAAATACCACCATAACAGAAATTAATTACATATTAGTCACTCTATT
*
171489 AAAATTATTTA
1 AAAAATATTTA
171500 TCAACAATCT
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
58 36 0.59
59 25 0.41
ACGTcount: A:0.46, C:0.16, G:0.05, T:0.34
Consensus pattern (59 bp):
AAAAATATTTACAAAAATACCACCATAACAGAAATTAATTACATATTAGTCACTCTATT
Found at i:174728 original size:16 final size:16
Alignment explanation
Indices: 174707--174744 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
174697 TACATTTCAG
*
174707 TAAATCCAGAATCAA-C
1 TAAATCCAAAAT-AAGC
174723 TAAATCCAAAATAAGC
1 TAAATCCAAAATAAGC
174739 TAAATC
1 TAAATC
174745 ATACAATAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 2 0.10
16 18 0.90
ACGTcount: A:0.53, C:0.21, G:0.05, T:0.21
Consensus pattern (16 bp):
TAAATCCAAAATAAGC
Found at i:175541 original size:29 final size:29
Alignment explanation
Indices: 175511--175776 Score: 312
Period size: 29 Copynumber: 9.1 Consensus size: 29
175501 ACAGAACTAA
* *
175511 TTACGAAACTAACACCCTTTTAAAAAAAAT
1 TTACGAAACTAACACCCTTTT-AACAATAT
175541 TTACGTAAA-TAACACCCTTTTAGA-AATAT
1 TTACG-AAACTAACACCCTTTTA-ACAATAT
*
175570 TTACGAAA-TAACACCTTTTTAACAATAT
1 TTACGAAACTAACACCCTTTTAACAATAT
* *
175598 TTATGAAACTAACACCTTTTTAACAATAT
1 TTACGAAACTAACACCCTTTTAACAATAT
175627 TTACGAAACTAACA-CCTTCTTAACAATAT
1 TTACGAAACTAACACCCTT-TTAACAATAT
*
175656 TTATGAAACTAACA-CCTTCTTAACAATAT
1 TTACGAAACTAACACCCTT-TTAACAATAT
* **
175685 TTACAAAACTAACACATTTTTAACAATAT
1 TTACGAAACTAACACCCTTTTAACAATAT
*
175714 TTACAAAACTAACA-CCTTCTTAACAATAT
1 TTACGAAACTAACACCCTT-TTAACAATAT
*
175743 TTACGAAACTAACA-CCTTTACTAAAAATAT
1 TTACGAAACTAACACCCTTT--TAACAATAT
175773 TTAC
1 TTAC
175777 AAAAATACCA
Statistics
Matches: 213, Mismatches: 14, Indels: 18
0.87 0.06 0.07
Matches are distributed among these distances:
27 1 0.00
28 33 0.15
29 144 0.68
30 32 0.15
31 3 0.01
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.33
Consensus pattern (29 bp):
TTACGAAACTAACACCCTTTTAACAATAT
Found at i:175640 original size:58 final size:58
Alignment explanation
Indices: 175511--175776 Score: 351
Period size: 58 Copynumber: 4.6 Consensus size: 58
175501 ACAGAACTAA
* * *
175511 TTACGAAACTAACACCCTTTTAAAAAAAATTTACGTAAA-TAACACCCTT-TTAGA-AATAT
1 TTACGAAACTAACA-CCTTTTTAACAATATTTACG-AAACTAACA-CCTTCTTA-ACAATAT
* *
175570 TTACGAAA-TAACACCTTTTTAACAATATTTATGAAACTAACACCTTTTTAACAATAT
1 TTACGAAACTAACACCTTTTTAACAATATTTACGAAACTAACACCTTCTTAACAATAT
* *
175627 TTACGAAACTAACACCTTCTTAACAATATTTATGAAACTAACACCTTCTTAACAATAT
1 TTACGAAACTAACACCTTTTTAACAATATTTACGAAACTAACACCTTCTTAACAATAT
* * *
175685 TTACAAAACTAACACATTTTTAACAATATTTACAAAACTAACACCTTCTTAACAATAT
1 TTACGAAACTAACACCTTTTTAACAATATTTACGAAACTAACACCTTCTTAACAATAT
* *
175743 TTACGAAACTAACACCTTTACTAAAAATATTTAC
1 TTACGAAACTAACACCTTT-TTAACAATATTTAC
175777 AAAAATACCA
Statistics
Matches: 187, Mismatches: 15, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
56 8 0.04
57 37 0.20
58 122 0.65
59 20 0.11
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.33
Consensus pattern (58 bp):
TTACGAAACTAACACCTTTTTAACAATATTTACGAAACTAACACCTTCTTAACAATAT
Found at i:175679 original size:87 final size:87
Alignment explanation
Indices: 175511--175760 Score: 355
Period size: 87 Copynumber: 2.9 Consensus size: 87
175501 ACAGAACTAA
* * *
175511 TTACGAAACTAACACCCTTTTAAAAAAAATTTACGTAAA-TAACACCCTT-TTAGA-AATATTTA
1 TTACGAAACTAACA-CCTTTTTAACAATATTTACG-AAACTAACA-CCTTCTTA-ACAATATTTA
*
175573 CGAAA-TAACACCTTTTTAACAATAT
62 CGAAACTAACACCTTCTTAACAATAT
* *
175598 TTATGAAACTAACACCTTTTTAACAATATTTACGAAACTAACACCTTCTTAACAATATTTATGAA
1 TTACGAAACTAACACCTTTTTAACAATATTTACGAAACTAACACCTTCTTAACAATATTTACGAA
175663 ACTAACACCTTCTTAACAATAT
66 ACTAACACCTTCTTAACAATAT
* * *
175685 TTACAAAACTAACACATTTTTAACAATATTTACAAAACTAACACCTTCTTAACAATATTTACGAA
1 TTACGAAACTAACACCTTTTTAACAATATTTACGAAACTAACACCTTCTTAACAATATTTACGAA
175750 ACTAACACCTT
66 ACTAACACCTT
175761 TACTAAAAAT
Statistics
Matches: 148, Mismatches: 11, Indels: 8
0.89 0.07 0.05
Matches are distributed among these distances:
85 8 0.05
86 37 0.25
87 103 0.70
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.33
Consensus pattern (87 bp):
TTACGAAACTAACACCTTTTTAACAATATTTACGAAACTAACACCTTCTTAACAATATTTACGAA
ACTAACACCTTCTTAACAATAT
Found at i:175827 original size:59 final size:59
Alignment explanation
Indices: 175764--175893 Score: 197
Period size: 59 Copynumber: 2.2 Consensus size: 59
175754 ACACCTTTAC
* ** *
175764 TAAAAATATTTACAAAAATACCACCATAACCGAAATTAATTACGTATTAGTCATTCTTT
1 TAAAACTATTTACAAAAATACCACCATAACAAAAATTAATTACGTATTAGTCACTCTTT
* * *
175823 TAAAACTATTTACAAAAATAGCAGCATAACAAAAATTAATTACTTATTAGTCACTCTTT
1 TAAAACTATTTACAAAAATACCACCATAACAAAAATTAATTACGTATTAGTCACTCTTT
175882 TAAAACTATTTA
1 TAAAACTATTTA
175894 TCAACAATCT
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 64 1.00
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (59 bp):
TAAAACTATTTACAAAAATACCACCATAACAAAAATTAATTACGTATTAGTCACTCTTT
Found at i:176389 original size:20 final size:20
Alignment explanation
Indices: 176361--176400 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
176351 TCACTTCAAT
*
176361 TTTTTTTCATAGTGCTATTA
1 TTTTATTCATAGTGCTATTA
176381 TTTTATTCATAGTGCTATTA
1 TTTTATTCATAGTGCTATTA
176401 GATATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.57
Consensus pattern (20 bp):
TTTTATTCATAGTGCTATTA
Found at i:176892 original size:7 final size:7
Alignment explanation
Indices: 176869--176933 Score: 53
Period size: 7 Copynumber: 9.1 Consensus size: 7
176859 TATTATGCTT
176869 AAAAGAAA
1 AAAAG-AA
176877 AAAAGAA
1 AAAAGAA
176884 AGAAA-AA
1 A-AAAGAA
176891 AGAAA-AA
1 A-AAAGAA
*
176898 GAAAGAA
1 AAAAGAA
*
176905 AAATGAA
1 AAAAGAA
*
176912 AAATGAA
1 AAAAGAA
176919 AAAAGAA
1 AAAAGAA
*
176926 AAATGAA
1 AAAAGAA
176933 A
1 A
176934 TGAAAGTGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
6 3 0.06
7 39 0.78
8 8 0.16
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (7 bp):
AAAAGAA
Found at i:176896 original size:17 final size:17
Alignment explanation
Indices: 176876--176919 Score: 70
Period size: 17 Copynumber: 2.5 Consensus size: 17
176866 CTTAAAAGAA
176876 AAAAAGAAAGAAAAAAG
1 AAAAAGAAAGAAAAAAG
*
176893 AAAAAGAAAGAAAAATG
1 AAAAAGAAAGAAAAAAG
176910 AAAAATGAAA
1 AAAAA-GAAA
176920 AAAGAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 21 0.84
18 4 0.16
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.05
Consensus pattern (17 bp):
AAAAAGAAAGAAAAAAG
Found at i:176899 original size:25 final size:25
Alignment explanation
Indices: 176870--176928 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
176860 ATTATGCTTA
176870 AAAGAAAAAAAGAAAGAAAAAAG-AA
1 AAAGAAAAAAA-AAAGAAAAAAGAAA
* * *
176895 AAAGAAAGAAAAATGAAAAATGAAA
1 AAAGAAAAAAAAAAGAAAAAAGAAA
176920 AAAGAAAAA
1 AAAGAAAAA
176929 TGAAATGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 9 0.31
25 20 0.69
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.03
Consensus pattern (25 bp):
AAAGAAAAAAAAAAGAAAAAAGAAA
Found at i:176921 original size:14 final size:14
Alignment explanation
Indices: 176869--176933 Score: 61
Period size: 14 Copynumber: 5.1 Consensus size: 14
176859 TATTATGCTT
176869 AAAAGAAAAA--AA
1 AAAAGAAAAATGAA
* *
176881 GAAAGAAAAAAG-A
1 AAAAGAAAAATGAA
176894 AAAAG--AAA-GAA
1 AAAAGAAAAATGAA
*
176905 AAATGAAAAATGAA
1 AAAAGAAAAATGAA
176919 AAAAGAAAAATGAA
1 AAAAGAAAAATGAA
176933 A
1 A
176934 TGAAAGTGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 1 0.02
11 8 0.19
12 9 0.21
13 8 0.19
14 17 0.40
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (14 bp):
AAAAGAAAAATGAA
Found at i:176946 original size:7 final size:7
Alignment explanation
Indices: 176902--176933 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
176892 GAAAAAGAAA
176902 GAAAAAT
1 GAAAAAT
176909 GAAAAAT
1 GAAAAAT
*
176916 GAAAAAA
1 GAAAAAT
176923 GAAAAAT
1 GAAAAAT
176930 GAAA
1 GAAA
176934 TGAAAGTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (7 bp):
GAAAAAT
Found at i:178138 original size:58 final size:58
Alignment explanation
Indices: 178075--178470 Score: 648
Period size: 58 Copynumber: 6.8 Consensus size: 58
178065 ATGGCACTAA
*
178075 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACCTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* **
178133 GTGTGCAAAAATTTAAGAAATTCATACTAAGTGTATGAATTTTAGTATTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* *
178191 GTGTGCAAAAATTTAAGAAATTCATACTAAGTGTATGCATTTCCGTATTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
178249 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
178307 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGAATTGGGCATTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
** *
178365 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTTGTATTGGGCTCTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * * *
178423 TTGTGCAAAAAGTTAAGAGATTCATAATAAGTGTATGAATTTCTGTAT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
178471 GGGAAATATG
Statistics
Matches: 318, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 318 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.36
Consensus pattern (58 bp):
GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
Found at i:182983 original size:26 final size:26
Alignment explanation
Indices: 182935--182985 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
182925 TGAATTTTCG
*
182935 TATTGAGCACTTTGTGTGAAAAAATT
1 TATTGAGCACTTTGTGTCAAAAAATT
*
182961 TATTGGGCACTTTGTGTCCAAAAAA
1 TATTGAGCACTTTGTGT-CAAAAAA
182986 GTTAAGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (26 bp):
TATTGAGCACTTTGTGTCAAAAAATT
Found at i:183076 original size:45 final size:45
Alignment explanation
Indices: 183007--183095 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
182997 CATACTAAGT
* *
183007 GTATGAATTTTCGTATTGGGCACTTTGTGTGCAAAAAGTTAAGAA
1 GTATGAATTTCCGTATTGGCCACTTTGTGTGCAAAAAGTTAAGAA
183052 GTATGAATTTCCGTATTGGCCACTTTGTGTGCAAAAAGTTAAGA
1 GTATGAATTTCCGTATTGGCCACTTTGTGTGCAAAAAGTTAAGA
183096 GATTCATACT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (45 bp):
GTATGAATTTCCGTATTGGCCACTTTGTGTGCAAAAAGTTAAGAA
Found at i:184191 original size:23 final size:23
Alignment explanation
Indices: 184161--184207 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
184151 AGCTACGATC
*
184161 AATGATATAAAGTAAAACATATA
1 AATGATATAAAATAAAACATATA
*
184184 AATGATATAAAATAAATCATATA
1 AATGATATAAAATAAAACATATA
184207 A
1 A
184208 TAAAAATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (23 bp):
AATGATATAAAATAAAACATATA
Found at i:185300 original size:20 final size:20
Alignment explanation
Indices: 185234--185306 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
185224 AATTCATTTT
185234 GGGTATCGATACC-TAG-ATG
1 GGGTATCGATACCATAGTA-G
*
185253 GGGTATCGGTACCATAGCATAG
1 GGGTATCGATACCATAG--TAG
*
185275 GGGTATCGATACCATAGTAA
1 GGGTATCGATACCATAGTAG
185295 GGGTATCGATAC
1 GGGTATCGATAC
185307 TAGGCTATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
19 12 0.26
20 17 0.36
22 17 0.36
23 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (20 bp):
GGGTATCGATACCATAGTAG
Found at i:185964 original size:45 final size:45
Alignment explanation
Indices: 185915--186134 Score: 253
Period size: 45 Copynumber: 4.9 Consensus size: 45
185905 AAAGGATGCC
*
185915 AGAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATATT
1 AGAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACT
* * *
185960 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAACGTATGCT
1 AGAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACT
* * * *
186005 AGAGTTGAAATGTATACGGGTACATTCTCAACATAAAAGGTATACT
1 AGAGTTGAAATGCATATGGGTACATTATCAACAGAAAA-GTATACT
* * * * *
186051 ATG-GTTGAAATGTATATGGGTACATTATCCACATAGAAGTATAGT
1 A-GAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACT
* * ** *
186096 AGAGTTTAAATGTATATGGGTGTATTATCAACCGAAAAG
1 AGAGTTGAAATGCATATGGGTACATTATCAACAGAAAAG
186135 ATGTTATAGT
Statistics
Matches: 149, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
44 1 0.01
45 109 0.73
46 38 0.26
47 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (45 bp):
AGAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACT
Found at i:186099 original size:91 final size:90
Alignment explanation
Indices: 185910--186134 Score: 267
Period size: 91 Copynumber: 2.5 Consensus size: 90
185900 GCATGAAAGG
* * *
185910 ATGCCAGAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATATTAGAGTTGAAATGCAT
1 ATGCTAGAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAGAGTTGAAATGCAT
*
185975 ATGGGTGCATTATCAACAGAAACGT
66 ATGGGTACATTATCAACAGAAACGT
* * * *
186000 ATGCTAGAGTTGAAATGTATACGGGTACATTCTCAACATAAAAGGTATACTATG-GTTGAAATGT
1 ATGCTAGAGTTGAAATGTATATGGGTACATTATCAACAGAAAA-GTATACTA-GAGTTGAAATGC
* *
186064 ATATGGGTACATTATCCACATAGAA-GT
64 ATATGGGTACATTATCAACAGA-AACGT
* ** *
186091 ATAG-TAGAGTTTAAATGTATATGGGTGTATTATCAACCGAAAAG
1 AT-GCTAGAGTTGAAATGTATATGGGTACATTATCAACAGAAAAG
186135 ATGTTATAGT
Statistics
Matches: 114, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
90 39 0.34
91 71 0.62
92 4 0.04
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (90 bp):
ATGCTAGAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTAGAGTTGAAATGCAT
ATGGGTACATTATCAACAGAAACGT
Found at i:187202 original size:29 final size:29
Alignment explanation
Indices: 187169--187253 Score: 98
Period size: 30 Copynumber: 2.9 Consensus size: 29
187159 CAAAATATAT
*
187169 AACTTTTAAAATTTACATTTTTGTCATTA
1 AACTTTTAAAATTTACATTTTGGTCATTA
* * * *
187198 AACTTTTACAATTTTATACTTTGGCCATTA
1 AACTTTTA-AAATTTACATTTTGGTCATTA
* *
187228 AACTTTCAAAACTTACATTTTGGTCA
1 AACTTTTAAAATTTACATTTTGGTCA
187254 CTACCAAAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
29 21 0.48
30 23 0.52
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.46
Consensus pattern (29 bp):
AACTTTTAAAATTTACATTTTGGTCATTA
Found at i:188497 original size:22 final size:22
Alignment explanation
Indices: 188467--188509 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
188457 AATATGACTA
*
188467 AAACATGTAATGTGTGGTTTAG
1 AAACATGTAATGTGGGGTTTAG
*
188489 AAACTTGTAATGTGGGGTTTA
1 AAACATGTAATGTGGGGTTTA
188510 AAATGAAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.05, G:0.28, T:0.37
Consensus pattern (22 bp):
AAACATGTAATGTGGGGTTTAG
Found at i:194233 original size:26 final size:26
Alignment explanation
Indices: 194197--194251 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
194187 TATCTCAACA
194197 GATACACTCAGTGCATTTGATGCATC
1 GATACACTCAGTGCATTTGATGCATC
194223 GATACACTCAGTGCATTTGATGCATC
1 GATACACTCAGTGCATTTGATGCATC
194249 GAT
1 GAT
194252 GCACAAGCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (26 bp):
GATACACTCAGTGCATTTGATGCATC
Found at i:200056 original size:23 final size:22
Alignment explanation
Indices: 199975--200056 Score: 78
Period size: 23 Copynumber: 3.6 Consensus size: 22
199965 ACACTTAACA
199975 GTGCATCGATGCAACCCTTTGAAT
1 GTGCATCGATGC-ACCC-TTGAAT
* *
199999 GTGCATCGATACACCAC--GAAG
1 GTGCATCGATGCACC-CTTGAAT
* *
200020 GTGTACCGATGCACGCCTTGAAT
1 GTGCATCGATGCAC-CCTTGAAT
200043 GTGCATCGATGCAC
1 GTGCATCGATGCAC
200057 AAGGACATGC
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
21 15 0.33
22 1 0.02
23 18 0.39
24 12 0.26
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.23
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:202662 original size:26 final size:26
Alignment explanation
Indices: 202632--202691 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
202622 GAACATCAAA
202632 TGCATTTTATGCATCGATACACTCAG
1 TGCATTTTATGCATCGATACACTCAG
* *
202658 TGCATTTGATGCATCGATGCACTCAG
1 TGCATTTTATGCATCGATACACTCAG
202684 -GCTATTTT
1 TGC-ATTTT
202692 GAATCATCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 2 0.07
26 28 0.93
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (26 bp):
TGCATTTTATGCATCGATACACTCAG
Found at i:220244 original size:20 final size:20
Alignment explanation
Indices: 220219--220271 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
220209 AACTTGAAAA
220219 TGGTATCGATACTATACCCT
1 TGGTATCGATACTATACCCT
220239 TGGTATCGATACTATACCCT
1 TGGTATCGATACTATACCCT
220259 TGGTATCGATACT
1 TGGTATCGATACT
220272 CCCATTTCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.36
Consensus pattern (20 bp):
TGGTATCGATACTATACCCT
Found at i:221726 original size:30 final size:30
Alignment explanation
Indices: 221692--221759 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 30
221682 AAAATTACAT
* *
221692 TTTTGGTCC-TTAAACTTTTGC-AAATTTATA
1 TTTTGGACCATTAAAC-TTT-CAAAACTTATA
221722 TTTT-GACCATTAAACTTTCAAAACTTATA
1 TTTTGGACCATTAAACTTTCAAAACTTATA
221751 TTTT-GACCA
1 TTTTGGACCA
221760 CTACCCAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 1 0.03
29 23 0.68
30 10 0.29
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.46
Consensus pattern (30 bp):
TTTTGGACCATTAAACTTTCAAAACTTATA
Found at i:222489 original size:13 final size:13
Alignment explanation
Indices: 222471--222497 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
222461 TAAAAACACA
222471 TGCTTCCCCTCCC
1 TGCTTCCCCTCCC
222484 TGCTTCCCCTCCC
1 TGCTTCCCCTCCC
222497 T
1 T
222498 TGCCCTCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.59, G:0.07, T:0.33
Consensus pattern (13 bp):
TGCTTCCCCTCCC
Found at i:224226 original size:22 final size:22
Alignment explanation
Indices: 224151--224220 Score: 95
Period size: 22 Copynumber: 3.2 Consensus size: 22
224141 TACGTATTTA
* *
224151 TGAACAGTAATGAACAATATCG
1 TGAATAGTAATGAACAATACCG
*
224173 TGAATAGTAATGAACAATACCA
1 TGAATAGTAATGAACAATACCG
* *
224195 TGAATAGTGATGAACAGTACCG
1 TGAATAGTAATGAACAATACCG
224217 TGAA
1 TGAA
224221 AAGTGAACAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.23
Consensus pattern (22 bp):
TGAATAGTAATGAACAATACCG
Found at i:224777 original size:44 final size:44
Alignment explanation
Indices: 224662--225145 Score: 745
Period size: 44 Copynumber: 11.0 Consensus size: 44
224652 CCATTTAATC
* * * *
224662 CATAAGCTAGTAAGCTTATTTTACCAATATACTTACCATTAAATC
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTA-TAATTT
* * * *
224707 CCTAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTATTC
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
* * * *
224751 CATAAGATCGTAAGCTTATTTTACCAATATACTTACCATTATTC
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
*
224795 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATGATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
* *
224839 CATAAGCTCGTAAACTTATTTTACCCATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
*
224883 CATAATCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
224927 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
* *
224971 CATAAGCTCGTAAGCTTATTTTACCAATATACATACTACAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
* * *
225015 CATAACCTCGTAAGTTTATTTTACCAATATACATACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
225059 CATAAGCTCGTAAGCTTA-TTTACCAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
* *
225102 CAAAAGCTCGTAAGCTTATTTTACTAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
225146 GCATCACTGG
Statistics
Matches: 411, Mismatches: 27, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
43 41 0.10
44 334 0.81
45 36 0.09
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.40
Consensus pattern (44 bp):
CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
Found at i:225306 original size:59 final size:58
Alignment explanation
Indices: 225222--225716 Score: 328
Period size: 59 Copynumber: 8.4 Consensus size: 58
225212 TATACAATTC
* * * * *
225222 GTATAATTTCCTTATAATATTAGCACTCTCAGTGCTCTATCTGGAATAT-CATATACTTA
1 GTATGATTTCCTTATCATTTTAGCACTCTAAGTGCTCTATATGGAA-ATCCATATA-TTA
* * * * *
225281 ATATGATTTCCTTCTCATTTTAGCACACGAAGTGC-CTAT-TCGAGAATCC--ATATTA
1 GTATGATTTCCTTATCATTTTAGCACTCTAAGTGCTCTATATGGA-AATCCATATATTA
* * * * *
225336 GTATGA-TTCCTTTACCATTTTAGCACAT-GAAGTGCCCTAT-TCGAGAATCCATACCATTA
1 GTATGATTTCC-TTATCATTTTAGCAC-TCTAAGTGCTCTATATGGA-AATCCATA-TATTA
* * * * *
225395 GTATGA-TCCCTTTACCATTTTTAGCACAT-GAAGTGCCCTATATGAAAATCCATACTATTA
1 GTATGATTTCC-TTATCA-TTTTAGCAC-TCTAAGTGCTCTATATGGAAATCCATA-TATTA
* * * * * * * * *
225455 GTATGATTTCCTTATCCTTGTAGCACCCTTAGTGCTTTTTTTGAAAATCCATACACTTA
1 GTATGATTTCCTTATCATTTTAGCACTCTAAGTGCTCTATATGGAAATCCATATA-TTA
* * * *
225514 GTATGATTCCCTTACCATTTTAGCACATATAA-TGCTCTATCTGGAAATCCATATATTCA
1 GTATGATTTCCTTATCATTTTAGCAC-TCTAAGTGCTCTATATGGAAATCCATATATT-A
* * * * * * * *
225573 ATATGATTTCCTTATCATTTTACCACACTCAGTGCTCCATATGGAAATACATACACTCA
1 GTATGATTTCCTTATCATTTTAGCACTCTAAGTGCTCTATATGGAAATCCATATA-TTA
* * * * * * * *
225632 ATATGATTTCCTTATCATTTTAGTACACTCAGTGCTCCATAAGGAAATTCATACATTCA
1 GTATGATTTCCTTATCATTTTAGCACTCTAAGTGCTCTATATGGAAATCCATATATT-A
225691 GTATGATTTCCTTATCATTTTAGCAC
1 GTATGATTTCCTTATCATTTTAGCAC
225717 ATATAGTGCC
Statistics
Matches: 357, Mismatches: 61, Indels: 36
0.79 0.13 0.08
Matches are distributed among these distances:
54 4 0.01
55 28 0.08
56 17 0.05
57 5 0.01
58 13 0.04
59 236 0.66
60 49 0.14
61 5 0.01
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (58 bp):
GTATGATTTCCTTATCATTTTAGCACTCTAAGTGCTCTATATGGAAATCCATATATTA
Found at i:225607 original size:118 final size:117
Alignment explanation
Indices: 225218--225717 Score: 391
Period size: 118 Copynumber: 4.3 Consensus size: 117
225208 AGTTTATACA
* * * * * * * *
225218 ATTC-GTATAATTTCCTTATAATATTAGCACTCTCAGTGCTCTATCTGGAATAT-CATATACTTA
1 ATTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATAT-GAAAATCCATACACTTA
* * * *
225281 ATATGATTTCCTT-CTCATTTTAGCACACGAAGTGC-CTAT-TCGAGAATCC--AT
65 GTATGATTCCCTTAC-CATTTTAGCACA-TAAGTGCTCTATATGGA-AATCCATAT
* * *
225332 ATT-AGTATGA-TTCCTTTACCATTTTAGCACA-TGAAGTGC-CC-TATTCGAGAATCCATAC-C
1 ATTCAGTATGATTTCC-TTATCATTTTAGCACACT-CAGTGCTCCATA-T-GAAAATCCATACAC
* *
225391 ATTAGTATGA-TCCCTTTACCATTTTTAGCACATGAAGTGCCCTATATGAAAATCCATACT
62 -TTAGTATGATTCCC-TTACCA-TTTTAGCACAT-AAGTGCTCTATATGGAAATCCATA-T
* * * * *** *
225451 ATT-AGTATGATTTCCTTATCCTTGTAGCACCCTTAGTGCTTTTTTTGAAAATCCATACACTTAG
1 ATTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGAAAATCCATACACTTAG
* *
225515 TATGATTCCCTTACCATTTTAGCACATATAATGCTCTATCTGGAAATCCATAT
66 TATGATTCCCTTACCATTTTAGCACATA-AGTGCTCTATATGGAAATCCATAT
* * * * * *
225568 ATTCAATATGATTTCCTTATCATTTTACCACACTCAGTGCTCCATATGGAAATACATACACTCAA
1 ATTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGAAAATCCATACACTTAG
* * * * * * * *
225633 TATGATTTCCTTATCATTTTAGTACACTCAGTGCTCCATAAGGAAATTCATAC
66 TATGATTCCCTTACCATTTTAGCACA-TAAGTGCTCTATATGGAAATCCATAT
225686 ATTCAGTATGATTTCCTTATCATTTTAGCACA
1 ATTCAGTATGATTTCCTTATCATTTTAGCACA
225718 TATAGTGCCA
Statistics
Matches: 306, Mismatches: 56, Indels: 44
0.75 0.14 0.11
Matches are distributed among these distances:
112 1 0.00
113 15 0.05
114 41 0.13
115 17 0.06
116 9 0.03
117 7 0.02
118 149 0.49
119 55 0.18
120 11 0.04
121 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38
Consensus pattern (117 bp):
ATTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGAAAATCCATACACTTAG
TATGATTCCCTTACCATTTTAGCACATAAGTGCTCTATATGGAAATCCATAT
Found at i:229034 original size:16 final size:16
Alignment explanation
Indices: 229013--229062 Score: 91
Period size: 16 Copynumber: 3.1 Consensus size: 16
229003 TTGCATTCCC
229013 TTAACCCTAGCACATA
1 TTAACCCTAGCACATA
229029 TTAACCCTAGCACATA
1 TTAACCCTAGCACATA
*
229045 TTAACCCTAACACATA
1 TTAACCCTAGCACATA
229061 TT
1 TT
229063 CTAATAATCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.38, C:0.30, G:0.04, T:0.28
Consensus pattern (16 bp):
TTAACCCTAGCACATA
Found at i:229239 original size:25 final size:25
Alignment explanation
Indices: 229189--229242 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
229179 ATGTTTTTCT
* *
229189 TAATTAATTTATATAATAATATATA
1 TAATTAATTTATAAAATAATAAATA
229214 TAATTAATTT-TAAAATAATAAA-A
1 TAATTAATTTATAAAATAATAAATA
229237 T-ATTAA
1 TAATTAA
229243 ATTAAATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 5 0.19
23 2 0.07
24 10 0.37
25 10 0.37
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TAATTAATTTATAAAATAATAAATA
Found at i:229239 original size:27 final size:24
Alignment explanation
Indices: 229188--229247 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 24
229178 TATGTTTTTC
* *
229188 TTAATTAATTTATATAATAATATA
1 TTAATTAATTTAAATAATAAAATA
229212 TATAATTAATTTTAAAATAATAAAATA
1 T-TAATTAA-TTT-AAATAATAAAATA
229239 TTAAATTAA
1 TT-AATTAA
229248 ATAACCCTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 1 0.03
25 7 0.23
26 4 0.13
27 18 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TTAATTAATTTAAATAATAAAATA
Found at i:229270 original size:16 final size:16
Alignment explanation
Indices: 229249--229281 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
229239 TTAAATTAAA
*
229249 TAACCCTAGCACATAT
1 TAACCCTAACACATAT
229265 TAACCCTAACACATAT
1 TAACCCTAACACATAT
229281 T
1 T
229282 CTAATAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.30, G:0.03, T:0.27
Consensus pattern (16 bp):
TAACCCTAACACATAT
Found at i:229409 original size:219 final size:219
Alignment explanation
Indices: 229030--229470 Score: 873
Period size: 219 Copynumber: 2.0 Consensus size: 219
229020 TAGCACATAT
229030 TAACCCTAGCACATATTAACCCTAACACATATTCTAATAATCAACCCAAACCAATAGCCCAACTC
1 TAACCCTAGCACATATTAACCCTAACACATATTCTAATAATCAACCCAAACCAATAGCCCAACTC
*
229095 TAATATTTTTTATTTATAACATGCCTATTAGAGCTCCTTTTACTTGTTTTAAATCAAAAGTACAA
66 TAATATGTTTTATTTATAACATGCCTATTAGAGCTCCTTTTACTTGTTTTAAATCAAAAGTACAA
229160 TATTTTTTATAATATCTTTATGTTTTTCTTAATTAATTTATATAATAATATATATAATTAATTTT
131 TATTTTTTATAATATCTTTATGTTTTTCTTAATTAATTTATATAATAATATATATAATTAATTTT
229225 AAAATAATAAAATATTAAATTAAA
196 AAAATAATAAAATATTAAATTAAA
229249 TAACCCTAGCACATATTAACCCTAACACATATTCTAATAATCAACCCAAACCAATAGCCCAACTC
1 TAACCCTAGCACATATTAACCCTAACACATATTCTAATAATCAACCCAAACCAATAGCCCAACTC
229314 TAATATGTTTTATTTATAACATGCCTATTAGAGCTCCTTTTACTTGTTTTAAATCAAAAGTACAA
66 TAATATGTTTTATTTATAACATGCCTATTAGAGCTCCTTTTACTTGTTTTAAATCAAAAGTACAA
229379 TATTTTTTATAATATCTTTATGTTTTTCTTAATTAATTTATATAATAATATATATAATTAATTTT
131 TATTTTTTATAATATCTTTATGTTTTTCTTAATTAATTTATATAATAATATATATAATTAATTTT
229444 AAAATAATAAAATATTAAATTAAA
196 AAAATAATAAAATATTAAATTAAA
229468 TAA
1 TAA
229471 TATTTACTGA
Statistics
Matches: 221, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
219 221 1.00
ACGTcount: A:0.41, C:0.15, G:0.04, T:0.40
Consensus pattern (219 bp):
TAACCCTAGCACATATTAACCCTAACACATATTCTAATAATCAACCCAAACCAATAGCCCAACTC
TAATATGTTTTATTTATAACATGCCTATTAGAGCTCCTTTTACTTGTTTTAAATCAAAAGTACAA
TATTTTTTATAATATCTTTATGTTTTTCTTAATTAATTTATATAATAATATATATAATTAATTTT
AAAATAATAAAATATTAAATTAAA
Found at i:229458 original size:25 final size:25
Alignment explanation
Indices: 229408--229461 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
229398 ATGTTTTTCT
* *
229408 TAATTAATTTATATAATAATATATA
1 TAATTAATTTATAAAATAATAAATA
229433 TAATTAATTT-TAAAATAATAAA-A
1 TAATTAATTTATAAAATAATAAATA
229456 T-ATTAA
1 TAATTAA
229462 ATTAAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 5 0.19
23 2 0.07
24 10 0.37
25 10 0.37
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TAATTAATTTATAAAATAATAAATA
Found at i:229458 original size:27 final size:24
Alignment explanation
Indices: 229407--229466 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 24
229397 TATGTTTTTC
* *
229407 TTAATTAATTTATATAATAATATA
1 TTAATTAATTTAAATAATAAAATA
229431 TATAATTAATTTTAAAATAATAAAATA
1 T-TAATTAA-TTT-AAATAATAAAATA
229458 TTAAATTAA
1 TT-AATTAA
229467 ATAATATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 1 0.03
25 7 0.23
26 4 0.13
27 18 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TTAATTAATTTAAATAATAAAATA
Found at i:236229 original size:26 final size:26
Alignment explanation
Indices: 236198--236249 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
236188 TTTTAGTTTT
*
236198 ATTTATTAATGAGTTGATGT-ATTATA
1 ATTTATTAAT-AGTGGATGTGATTATA
236224 ATTTATTAATAGTGGATGTGATTATA
1 ATTTATTAATAGTGGATGTGATTATA
236250 TATCCATAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (26 bp):
ATTTATTAATAGTGGATGTGATTATA
Found at i:236639 original size:57 final size:57
Alignment explanation
Indices: 236576--236700 Score: 223
Period size: 57 Copynumber: 2.2 Consensus size: 57
236566 AAGATTAGTT
*
236576 TATATTAAAATGATTTAATACAATTAATGTTAATTAGATTTTATTAATGAAATAAAG
1 TATATTAAAATGATTTAATACAATTAATGTTAATTAGATTTTATTAATGAAATAAAC
* *
236633 TATATTAAAATGATTTAATACAATTAATGTTAATTAGATTTTATTAATTAAGTAAAC
1 TATATTAAAATGATTTAATACAATTAATGTTAATTAGATTTTATTAATGAAATAAAC
236690 TATATTAAAAT
1 TATATTAAAAT
236701 TTAATGTTAA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 65 1.00
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.43
Consensus pattern (57 bp):
TATATTAAAATGATTTAATACAATTAATGTTAATTAGATTTTATTAATGAAATAAAC
Found at i:244994 original size:17 final size:17
Alignment explanation
Indices: 244969--245003 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
244959 GCACGACCCG
* *
244969 CCTGCCCGACCCGTTGA
1 CCTGACCGAACCGTTGA
244986 CCTGACCGAACCGTTGA
1 CCTGACCGAACCGTTGA
245003 C
1 C
245004 TTGGTCAGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (17 bp):
CCTGACCGAACCGTTGA
Found at i:246683 original size:24 final size:24
Alignment explanation
Indices: 246617--246674 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
246607 ATGAGTGCTA
246617 GACGAGGTCGTCGGCCTAGCCATG
1 GACGAGGTCGTCGGCCTAGCCATG
246641 GACGAGGTCGTCGGCCTAGCCATG
1 GACGAGGTCGTCGGCCTAGCCATG
*
246665 GGCGAGGTCG
1 GACGAGGTCG
246675 ATCTGCTAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.16, C:0.28, G:0.41, T:0.16
Consensus pattern (24 bp):
GACGAGGTCGTCGGCCTAGCCATG
Found at i:254286 original size:2 final size:2
Alignment explanation
Indices: 254279--254303 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
254269 GTCTGTTGTA
254279 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
254304 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:262210 original size:19 final size:19
Alignment explanation
Indices: 262186--262236 Score: 93
Period size: 19 Copynumber: 2.6 Consensus size: 19
262176 TTGAACAGTG
262186 GGGGGAATCGGTACCCCCT
1 GGGGGAATCGGTACCCCCT
262205 GGGGGAATCGGTACCCCCT
1 GGGGGAATCGGTACCCCCT
262224 GAGGGGAATCGGT
1 G-GGGGAATCGGT
262237 TCCCTCCAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 20 0.65
20 11 0.35
ACGTcount: A:0.18, C:0.25, G:0.41, T:0.16
Consensus pattern (19 bp):
GGGGGAATCGGTACCCCCT
Found at i:263432 original size:27 final size:27
Alignment explanation
Indices: 263400--263456 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
263390 GATCATCGTC
263400 AGCTTCTGGTGGAGCTCGTGAAGAACT
1 AGCTTCTGGTGGAGCTCGTGAAGAACT
263427 AGCTTCTGGTGGAGCTCGTGAAGAACT
1 AGCTTCTGGTGGAGCTCGTGAAGAACT
263454 AGC
1 AGC
263457 ACCCGGAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (27 bp):
AGCTTCTGGTGGAGCTCGTGAAGAACT
Found at i:265018 original size:19 final size:18
Alignment explanation
Indices: 264990--265028 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
264980 AAAACCAGAA
*
264990 CCCCAGGGGGTATCGATT
1 CCCCAGGGGGAATCGATT
*
265008 CCCCTAGGGGGAATCGGTT
1 CCCC-AGGGGGAATCGATT
265027 CC
1 CC
265029 TCTTCAAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.15, C:0.31, G:0.33, T:0.21
Consensus pattern (18 bp):
CCCCAGGGGGAATCGATT
Found at i:278240 original size:16 final size:17
Alignment explanation
Indices: 278218--278255 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
278208 GTGAAAGTTT
* *
278218 TGAAAAGTATATGAAAA
1 TGAAAAGAATATAAAAA
278235 -GAAAAGAATATAAAAA
1 TGAAAAGAATATAAAAA
278251 TGAAA
1 TGAAA
278256 TATGAACGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (17 bp):
TGAAAAGAATATAAAAA
Found at i:285490 original size:21 final size:22
Alignment explanation
Indices: 285464--285508 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
285454 GATTACAAAT
285464 AGGGAACCGA-TACCCTGCTAC
1 AGGGAACCGATTACCCTGCTAC
*
285485 AGGGAACCGATTCCCCTGCTAC
1 AGGGAACCGATTACCCTGCTAC
285507 AG
1 AG
285509 TACTGCTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.27, C:0.33, G:0.24, T:0.16
Consensus pattern (22 bp):
AGGGAACCGATTACCCTGCTAC
Found at i:286100 original size:24 final size:24
Alignment explanation
Indices: 286071--286134 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
286061 CTCATATAAA
286071 TTGCACCGAAGTGCCACGTAGAAT
1 TTGCACCGAAGTGCCACGTAGAAT
*
286095 TTGCACCGAAGTGCCGCGTAGAAT
1 TTGCACCGAAGTGCCACGTAGAAT
*
286119 TTGCACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
286135 TATAAGATTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.22
Consensus pattern (24 bp):
TTGCACCGAAGTGCCACGTAGAAT
Found at i:286754 original size:26 final size:25
Alignment explanation
Indices: 286714--286789 Score: 66
Period size: 26 Copynumber: 3.0 Consensus size: 25
286704 TCATATGCTT
* *
286714 CACATGCATTACATAT-ATCACATA
1 CACATACATTTCATATAATCACATA
286738 GCACATATCATTTCATATAATCA-AGTA
1 -CACATA-CATTTCATATAATCACA-TA
* *
286765 TACATACATTTCATATCATTCACAT
1 CACATACATTTCATAT-AATCACAT
286790 CCTTATAATC
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
25 15 0.36
26 20 0.48
27 7 0.17
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.34
Consensus pattern (25 bp):
CACATACATTTCATATAATCACATA
Found at i:287186 original size:21 final size:21
Alignment explanation
Indices: 287160--287199 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
287150 TTTTTCATTT
287160 AGGGGGAATCGATACCCCCCC
1 AGGGGGAATCGATACCCCCCC
*
287181 AGGGGGAATCGGTACCCCC
1 AGGGGGAATCGATACCCCC
287200 TGCATAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.35, G:0.33, T:0.10
Consensus pattern (21 bp):
AGGGGGAATCGATACCCCCCC
Found at i:291320 original size:20 final size:18
Alignment explanation
Indices: 291283--291321 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
291273 GGGAAAATAA
*
291283 TTTTTTTTTATTTGTTTC
1 TTTTTTTTTATTTATTTC
291301 TTTTTCTTTTATTTTATTTC
1 TTTTT-TTTTA-TTTATTTC
291321 T
1 T
291322 GATTTTAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 5 0.28
20 8 0.44
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.82
Consensus pattern (18 bp):
TTTTTTTTTATTTATTTC
Found at i:301840 original size:30 final size:31
Alignment explanation
Indices: 301777--301847 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
301767 CTATGCATTA
* *
301777 AGTACCTAAATTATAAGTTTTGGACCGTTTT
1 AGTACCTAAAATATAAGTTTTGGACCATTTT
* *
301808 AGTATCTAAAATATAAGTTTTGG-TCATTTT
1 AGTACCTAAAATATAAGTTTTGGACCATTTT
*
301838 AGTGCCTAAA
1 AGTACCTAAA
301848 CATTTAATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 13 0.38
31 21 0.62
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.41
Consensus pattern (31 bp):
AGTACCTAAAATATAAGTTTTGGACCATTTT
Found at i:303310 original size:11 final size:11
Alignment explanation
Indices: 303296--303320 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
303286 AATTTAGTCA
303296 TAATTTTAATT
1 TAATTTTAATT
303307 TAATTTTAATT
1 TAATTTTAATT
303318 TAA
1 TAA
303321 CAATCCAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TAATTTTAATT
Found at i:303913 original size:66 final size:71
Alignment explanation
Indices: 303843--303985 Score: 197
Period size: 76 Copynumber: 2.0 Consensus size: 71
303833 AATATAATTT
303843 ATTTAGTACATTTGTTTCAAC-A-AT-TATA-TG-TGTGTGTGTGAAATAATAGAAAACACAATA
1 ATTTAGTACATTTGTTTCAACAATATATATAGTGATGTGTGTGTGAAATAATAGAAAACACAATA
303903 TATATA
66 TATATA
*
303909 ATTTAGTAGATTTGTTTCAACAATTATATATATGTGTGTATGTGTGTGTGAAATAATAGAAAACA
1 ATTTAGTACATTTGTTTCAACAA-TATATATA---GTG-ATGTGTGTGTGAAATAATAGAAAACA
303974 CAATATATATA
61 CAATATATATA
303985 A
1 A
303986 GAGTTTACAA
Statistics
Matches: 66, Mismatches: 1, Indels: 10
0.86 0.01 0.13
Matches are distributed among these distances:
66 20 0.30
67 1 0.02
69 2 0.03
70 4 0.06
74 2 0.03
76 37 0.56
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.38
Consensus pattern (71 bp):
ATTTAGTACATTTGTTTCAACAATATATATAGTGATGTGTGTGTGAAATAATAGAAAACACAATA
TATATA
Found at i:304766 original size:20 final size:20
Alignment explanation
Indices: 304737--304774 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
304727 TCTAAAAACA
* *
304737 CAAGGTAGTATCGGTACTAC
1 CAAGGGAGTATCGATACTAC
304757 CAAGGGAGTATCGATACT
1 CAAGGGAGTATCGATACT
304775 TCCCAAACCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (20 bp):
CAAGGGAGTATCGATACTAC
Found at i:306206 original size:20 final size:21
Alignment explanation
Indices: 306169--306207 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
306159 CTAATTATTT
**
306169 TTTTTTATTTTTTTATTAAAG
1 TTTTTTATTTTTAAATTAAAG
306190 TTTTTTA-TTTTAAATTAA
1 TTTTTTATTTTTAAATTAA
306208 TCTCTAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (21 bp):
TTTTTTATTTTTAAATTAAAG
Found at i:306220 original size:20 final size:20
Alignment explanation
Indices: 306197--306237 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
306187 AAGTTTTTTA
*
306197 TTTTAAATTAATCTCTAAAT
1 TTTTAAATTAATATCTAAAT
306217 TTTTAAATTAATATCTAAAT
1 TTTTAAATTAATATCTAAAT
306237 T
1 T
306238 AATAGAGCGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTAAATTAATATCTAAAT
Found at i:307129 original size:6 final size:6
Alignment explanation
Indices: 307118--307185 Score: 50
Period size: 6 Copynumber: 11.7 Consensus size: 6
307108 GTTCAAATTC
* * * * *
307118 GAGTTT GAGTTT GAGCTT GAG-TC GAGTTC GAGTTT GAGCTT GAG-TC
1 GAGTTT GAGTTT GAGTTT GAGTTT GAGTTT GAGTTT GAGTTT GAGTTT
* * *
307164 CAGTTC GAGTTT GAGCTT GAGT
1 GAGTTT GAGTTT GAGTTT GAGT
307186 CGAGTTCGAG
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
5 7 0.14
6 43 0.86
ACGTcount: A:0.18, C:0.12, G:0.34, T:0.37
Consensus pattern (6 bp):
GAGTTT
Found at i:307150 original size:23 final size:23
Alignment explanation
Indices: 307116--307200 Score: 143
Period size: 23 Copynumber: 3.7 Consensus size: 23
307106 AGGTTCAAAT
*
307116 TCGAGTTTGAGTTTGAGCTTGAG
1 TCGAGTTCGAGTTTGAGCTTGAG
307139 TCGAGTTCGAGTTTGAGCTTGAG
1 TCGAGTTCGAGTTTGAGCTTGAG
*
307162 TCCAGTTCGAGTTTGAGCTTGAG
1 TCGAGTTCGAGTTTGAGCTTGAG
*
307185 TCGAGTTCGAGCTTGA
1 TCGAGTTCGAGTTTGA
307201 ATCGAGCTCA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.18, C:0.14, G:0.33, T:0.35
Consensus pattern (23 bp):
TCGAGTTCGAGTTTGAGCTTGAG
Found at i:307171 original size:29 final size:29
Alignment explanation
Indices: 307115--307184 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
307105 TAGGTTCAAA
* **
307115 TTCGAGTTTGAGTTTGAGCTTGAGTCGAG
1 TTCGAGTTTGAGCTTGAGCTCCAGTCGAG
307144 TTCGAGTTTGAGCTTGAG-TCCAGTTCGAG
1 TTCGAGTTTGAGCTTGAGCTCCAG-TCGAG
* *
307173 TTTGAGCTTGAG
1 TTCGAGTTTGAG
307185 TCGAGTTCGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 32 0.91
ACGTcount: A:0.17, C:0.13, G:0.33, T:0.37
Consensus pattern (29 bp):
TTCGAGTTTGAGCTTGAGCTCCAGTCGAG
Found at i:307188 original size:17 final size:17
Alignment explanation
Indices: 307168--307206 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
307158 TGAGTCCAGT
* *
307168 TCGAGTTTGAGCTTGAG
1 TCGAGTTCGAGCTTGAA
307185 TCGAGTTCGAGCTTGAA
1 TCGAGTTCGAGCTTGAA
307202 TCGAG
1 TCGAG
307207 CTCAAAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (17 bp):
TCGAGTTCGAGCTTGAA
Found at i:308115 original size:37 final size:37
Alignment explanation
Indices: 308021--308125 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
308011 CATTTTCGTC
308021 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
308058 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* ** * * *
308095 CTATTATTATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
308126 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:308678 original size:19 final size:19
Alignment explanation
Indices: 308580--308679 Score: 67
Period size: 22 Copynumber: 4.7 Consensus size: 19
308570 TCAATTGATT
308580 TTTTTATACTATATATTATTA
1 TTTTTATA-TATAT-TTATTA
* *
308601 TTATATATGCATATATTTTTTA
1 TT-TTTAT--ATATATTTATTA
308623 TTTATT-TATATTCATTTGATTA
1 TTT-TTATATA-T-ATTT-ATTA
308645 TTTTTTAATACTATATTTATTA
1 -TTTTT-ATA-TATATTTATTA
308667 TTTTTATATATAT
1 TTTTTATATATAT
308680 ATATACCTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 24
0.70 0.04 0.26
Matches are distributed among these distances:
19 8 0.12
20 4 0.06
21 13 0.20
22 21 0.33
23 12 0.19
24 4 0.06
25 2 0.03
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTTATATATATTTATTA
Found at i:308827 original size:25 final size:26
Alignment explanation
Indices: 308788--308850 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 26
308778 TATGTATACT
308788 TTTATATTTGGTTTATATATTTAT-TTAA
1 TTTATATTT--TTTATATATTTATATT-A
* *
308816 TTT-TATTTTTTATTTGTTTATATTA
1 TTTATATTTTTTATATATTTATATTA
308841 TTTATATTTT
1 TTTATATTTT
308851 CATATTACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
25 15 0.48
26 8 0.26
27 5 0.16
28 3 0.10
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (26 bp):
TTTATATTTTTTATATATTTATATTA
Found at i:308839 original size:17 final size:18
Alignment explanation
Indices: 308792--308845 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 18
308782 TATACTTTTA
*
308792 TATTTGGTTTATA-TATT
1 TATTTAGTTTATATTATT
* *
308809 TATTTAATTT-TATTTTT
1 TATTTAGTTTATATTATT
308826 TATTT-GTTTATATTATT
1 TATTTAGTTTATATTATT
308843 TAT
1 TAT
308846 ATTTTCATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
16 5 0.17
17 25 0.83
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (18 bp):
TATTTAGTTTATATTATT
Found at i:308855 original size:17 final size:16
Alignment explanation
Indices: 308803--308857 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
308793 ATTTGGTTTA
308803 TATATTTATTTA-ATTT
1 TATA-TTATTTATATTT
*
308819 TAT-TT-TTTATTTGTT
1 TATATTATTTATAT-TT
308834 TATATTATTTATATTT
1 TATATTATTTATATTT
308850 TCATATTA
1 T-ATATTA
308858 CTATCATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
13 4 0.12
14 3 0.09
15 5 0.16
16 8 0.25
17 12 0.38
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (16 bp):
TATATTATTTATATTT
Found at i:308942 original size:4 final size:4
Alignment explanation
Indices: 308927--308956 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
308917 TATTTTTTAA
308927 TATT TCATT TATT TATT TATT TATT TATT T
1 TATT T-ATT TATT TATT TATT TATT TATT T
308957 TCCCTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:311100 original size:2 final size:2
Alignment explanation
Indices: 311093--311125 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
311083 TGTTAGAAAT
311093 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
311126 CAGTCATGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:317843 original size:2 final size:2
Alignment explanation
Indices: 317836--317870 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
317826 GCCATTTAAT
317836 TA TA TA TA TA TA TA TA TA T- TA TA TA -A TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
317871 TATGAGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:317864 original size:14 final size:13
Alignment explanation
Indices: 317834--317873 Score: 52
Period size: 11 Copynumber: 3.4 Consensus size: 13
317824 ATGCCATTTA
317834 ATTATATATATAT
1 ATTATATATATAT
317847 A-TATATAT-TAT
1 ATTATATATATAT
317858 A-TA-ATATATAT
1 ATTATATATATAT
317869 ATTAT
1 ATTAT
317874 GAGAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.17
11 10 0.42
12 9 0.38
13 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTATATATATAT
Found at i:317866 original size:16 final size:17
Alignment explanation
Indices: 317838--317873 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
317828 CATTTAATTA
317838 TATATATATATATATAT
1 TATATATATATATATAT
317855 TATATA-ATATATATAT
1 TATATATATATATATAT
317871 TAT
1 TAT
317874 GAGAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:318347 original size:138 final size:138
Alignment explanation
Indices: 318061--318322 Score: 379
Period size: 138 Copynumber: 1.9 Consensus size: 138
318051 GTTACAAAAC
* *
318061 TTGTCACTATATAACATTTTTGCACCAAAAAATAGGAAGAAATATTTCTAATAGTATAAGTTTTC
1 TTGTTACTATATAACATTTTTGCACCAAAAAATAGGAAGAAATAGTTCTAATAGTATAAGTTTTC
318126 ATAATGATTAAAATATACAATACAAAAATAATTAATTACAAAAAAACTTAAATTTTATTAATTAC
66 ATAATGATTAAAATATACAATACAAAAATAATTAATTACAAAAAAACTTAAATTTTATTAATTAC
318191 AATATATT
131 AATATATT
* * * *
318199 TTGTTACTATATAACTTTTTTG-ACACTAAAAATA-GAGAGAAATGGTTCTGATAGTATAA-TTT
1 TTGTTACTATATAACATTTTTGCAC-CAAAAAATAGGA-AGAAATAGTTCTAATAGTATAAGTTT
* * * *
318261 TTATAATGATTAAAATATATAAGTATAAAAATAATTAATTAC-AAAAAACTTGAATTTTATTA
64 TCATAATGATTAAAATATACAA-TACAAAAATAATTAATTACAAAAAAACTTAAATTTTATTA
318323 TTTGATGTGA
Statistics
Matches: 111, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
137 46 0.41
138 65 0.59
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.38
Consensus pattern (138 bp):
TTGTTACTATATAACATTTTTGCACCAAAAAATAGGAAGAAATAGTTCTAATAGTATAAGTTTTC
ATAATGATTAAAATATACAATACAAAAATAATTAATTACAAAAAAACTTAAATTTTATTAATTAC
AATATATT
Found at i:318686 original size:29 final size:29
Alignment explanation
Indices: 318644--318707 Score: 128
Period size: 29 Copynumber: 2.2 Consensus size: 29
318634 TTCATCGAAT
318644 AAATTTTCAGAACATTGCTATCCTCTTCA
1 AAATTTTCAGAACATTGCTATCCTCTTCA
318673 AAATTTTCAGAACATTGCTATCCTCTTCA
1 AAATTTTCAGAACATTGCTATCCTCTTCA
318702 AAATTT
1 AAATTT
318708 GCAATGATCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (29 bp):
AAATTTTCAGAACATTGCTATCCTCTTCA
Found at i:326184 original size:419 final size:419
Alignment explanation
Indices: 325406--326245 Score: 1500
Period size: 419 Copynumber: 2.0 Consensus size: 419
325396 TTTCCAGACT
* * * * * *
325406 TAGTGGTAAAACGAGTGCATTCTGTATTTTTTTATTATTTGGTTATGGTTGGAGATATGGGCATG
1 TAGTGGTAAAACGAGCGCATTCTGCATTGTTTTATTATTTGGTCATGGTTGGAGACATGGGCACG
* *
325471 ACTCTGGGCATGACACGGTTTGACGTGGCAGTTTCTAAAAGGTCCAGTCAGCGACGGTTTCTAGA
66 ACTCTGGGCATGACACGGTTTGACATGGCAGTTTCTAAAAGGTCCAGTCAGCGACGATTTCTAGA
*
325536 AGATCTACTCATCGCGCCTTCTGGAAGATGGACGGGCAGAGTTGCATTAGGAGACTTATTTAGAG
131 AGATCTACTCATCGCGCCTTCTGGAAGATGGACGAGCAGAGTTGCATTAGGAGACTTATTTAGAG
*
325601 TTTGAATTTAGGAAAAAATTTATCTTTAGGATTATTTTACTTTAATTTCTTTGTTTATCCTTAGG
196 TTTGAATTTAGGAAAAAAATTATCTTTAGGATTATTTTACTTTAATTTCTTTGTTTATCCTTAGG
325666 CTTTGAGAGGCTATAAATACCCTCTTGGGTAAGCCTAAACTCACATCTCAGATTACAATTCTCTT
261 CTTTGAGAGGCTATAAATACCCTCTTGGGTAAGCCTAAACTCACATCTCAGATTACAATTCTCTT
325731 ATTCTTTCTAGTTTTATTAAAGCTTTCTCTTTTATTTTACTTTTCAAGTTTTTCATTTTTATTTT
326 ATTCTTTCTAGTTTTATTAAAGCTTTCTCTTTTATTTTACTTTTCAAGTTTTTCATTTTTATTTT
*
325796 ATTTTCAAGCTTGTTTTTAATATACTAAG
391 ATTTTCAAGCTTGTTTTTAATATACAAAG
*
325825 TAGTGGTAAAACGGGCGCATTCTGCATTGTTTTATTATTTGGTCATGGTTGGAGACATGGGCACG
1 TAGTGGTAAAACGAGCGCATTCTGCATTGTTTTATTATTTGGTCATGGTTGGAGACATGGGCACG
* * *
325890 ACTTTGGGCATGACACGGTTTGACATGGCAGTTTCTAGAAGGTCCAGTCAGCGATGATTTCTAGA
66 ACTCTGGGCATGACACGGTTTGACATGGCAGTTTCTAAAAGGTCCAGTCAGCGACGATTTCTAGA
325955 AGATCTACTCATCGCGCCTTCTGGAAGATGGACGAGCAGAGTTGCATTAGGAGACTTATTTAGAG
131 AGATCTACTCATCGCGCCTTCTGGAAGATGGACGAGCAGAGTTGCATTAGGAGACTTATTTAGAG
*
326020 TTTGAATTTAGGAAAAAAATTATCTTTAGGATTATTTTATTTTAATTTCTTTGTTTATCCTTAGG
196 TTTGAATTTAGGAAAAAAATTATCTTTAGGATTATTTTACTTTAATTTCTTTGTTTATCCTTAGG
**
326085 CTTTGAGAGGCTATAAATACCCTCTTTTGTAAGCCTAAACTCACATCTCAGATTACAATTCTCTT
261 CTTTGAGAGGCTATAAATACCCTCTTGGGTAAGCCTAAACTCACATCTCAGATTACAATTCTCTT
* *
326150 CTTCTTTCTAGTTTTATTAAAGCTTTCTCTTTTATTTTACTTTTCAAGTTTTTCATTTTTCTTTT
326 ATTCTTTCTAGTTTTATTAAAGCTTTCTCTTTTATTTTACTTTTCAAGTTTTTCATTTTTATTTT
326215 ATTTTCAAGCTTGTTTTTAATATACAAAG
391 ATTTTCAAGCTTGTTTTTAATATACAAAG
326244 TA
1 TA
326246 TGACTTTTGT
Statistics
Matches: 401, Mismatches: 20, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
419 401 1.00
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (419 bp):
TAGTGGTAAAACGAGCGCATTCTGCATTGTTTTATTATTTGGTCATGGTTGGAGACATGGGCACG
ACTCTGGGCATGACACGGTTTGACATGGCAGTTTCTAAAAGGTCCAGTCAGCGACGATTTCTAGA
AGATCTACTCATCGCGCCTTCTGGAAGATGGACGAGCAGAGTTGCATTAGGAGACTTATTTAGAG
TTTGAATTTAGGAAAAAAATTATCTTTAGGATTATTTTACTTTAATTTCTTTGTTTATCCTTAGG
CTTTGAGAGGCTATAAATACCCTCTTGGGTAAGCCTAAACTCACATCTCAGATTACAATTCTCTT
ATTCTTTCTAGTTTTATTAAAGCTTTCTCTTTTATTTTACTTTTCAAGTTTTTCATTTTTATTTT
ATTTTCAAGCTTGTTTTTAATATACAAAG
Found at i:329970 original size:19 final size:19
Alignment explanation
Indices: 329946--329996 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
329936 GAATCAAAAT
329946 ATGGTACTGATACCCTCAA
1 ATGGTACTGATACCCTCAA
*
329965 ATGGTACTAATACCCTCAA
1 ATGGTACTGATACCCTCAA
*
329984 ATGGTACCGATAC
1 ATGGTACTGATAC
329997 TACTATATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (19 bp):
ATGGTACTGATACCCTCAA
Found at i:333607 original size:65 final size:65
Alignment explanation
Indices: 333463--333622 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
333453 TGCACCAAGT
* * * *
333463 GTGCATCGATGCATAAAATGCATTCGATG-TTTGAAAATAGCCTGAGTGCATCGATGCATGACTT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAAAGCCTGAGTGCATCGATGCATGACTA
*
333527 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAATCC-GAGTGCATCGATGCATGGA-
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAAAAGCCTGAGTGCATCGATGCAT-GAC
333590 TA
64 TA
* *
333592 GTGCATCGGTACATCAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
333623 CAATTAATTC
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
64 28 0.33
65 50 0.58
66 8 0.09
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAAAGCCTGAGTGCATCGATGCATGACTA
Found at i:333658 original size:20 final size:20
Alignment explanation
Indices: 333633--333670 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
333623 CAATTAATTC
333633 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
*
333653 ATTGATGCATCGGTGCAT
1 ATTGATGCATCGATGCAT
333671 ACCTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:333662 original size:65 final size:64
Alignment explanation
Indices: 333462--333666 Score: 204
Period size: 65 Copynumber: 3.2 Consensus size: 64
333452 GTGCACCAAG
* * * * * *
333462 TGTGCATCGATGCATAAAATGCATTCGATGTTTGA-AAATAGCCTGAGTGCATCGATGCAT-GAC
1 TGTGCATCGGTACATCAAATGCATTCGATGTTTCATAAAAATCC-GAGTGCATCGATGCATGGA-
333525 T
64 T
* *
333526 TGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAATCCGAGTGCATCGATGCATGGAT
1 TGTGCATCGGTACATCAAATGCATTCGATG-TTTCATAAAAATCCGAGTGCATCGATGCATGGAT
* ** *
333591 AGTGCATCGGTACATCAAATGCATTCGATG-TTCA-ATTAATTC-ATTGATGCATCGATGCATGG
1 TGTGCATCGGTACATCAAATGCATTCGATGTTTCATAAAAATCCGA--G-TGCATCGATGCATGG
333653 AT
63 AT
333655 TGATGCATCGGT
1 TG-TGCATCGGT
333667 GCATACCTTT
Statistics
Matches: 123, Mismatches: 11, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
61 1 0.01
62 5 0.04
63 5 0.04
64 47 0.38
65 57 0.46
66 8 0.07
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (64 bp):
TGTGCATCGGTACATCAAATGCATTCGATGTTTCATAAAAATCCGAGTGCATCGATGCATGGAT
Found at i:334738 original size:21 final size:21
Alignment explanation
Indices: 334704--334747 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
334694 CCGGAGGAGG
*
334704 AGGAGGAGCACGAGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
*
334725 AGGAGCAGCTCGAGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
334746 AG
1 AG
334748 CTCCCGGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.16, G:0.36, T:0.07
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAACT
Found at i:335571 original size:21 final size:21
Alignment explanation
Indices: 335547--335589 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
335537 ATAATAGGCC
**
335547 ATTAGGAGATTGAGGAACGGG
1 ATTAGGAGAGGGAGGAACGGG
*
335568 ATTAGGAGGGGGAGGAACGGG
1 ATTAGGAGAGGGAGGAACGGG
335589 A
1 A
335590 GGACAGTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.49, T:0.14
Consensus pattern (21 bp):
ATTAGGAGAGGGAGGAACGGG
Found at i:336310 original size:23 final size:22
Alignment explanation
Indices: 336280--336360 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 22
336270 CATGGCCTTT
336280 ATGCATCGATGCATATTCAAGG
1 ATGCATCGATGCATATTCAAGG
* * *
336302 CATGCATCGGTGCATCTTC-ATG
1 -ATGCATCGATGCATATTCAAGG
*
336324 ATGCATCGATGCACATTCAAAGGG
1 ATGCATCGATGCATATTC-AA-GG
336348 ATGCATCGATGCA
1 ATGCATCGATGCA
336361 CTGACAAGTG
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
21 15 0.31
22 2 0.04
23 17 0.35
24 14 0.29
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.26
Consensus pattern (22 bp):
ATGCATCGATGCATATTCAAGG
Found at i:336376 original size:44 final size:44
Alignment explanation
Indices: 336280--336380 Score: 116
Period size: 44 Copynumber: 2.3 Consensus size: 44
336270 CATGGCCTTT
* * * *
336280 ATGCATCGATGCATATTCAAGGCATGCATCGGTGCATCTTCATG
1 ATGCATCGATGCACATTCAAGGCATGCATCGATGCATCTACAAG
*
336324 ATGCATCGATGCACATTCAAAGGGATGCATCGATGCA-CTGACAAG
1 ATGCATCGATGCACATTC-AAGGCATGCATCGATGCATCT-ACAAG
*
336369 -TGTATCGATGCA
1 ATGCATCGATGCA
336381 TTAAGCACAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
44 30 0.61
45 19 0.39
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.26
Consensus pattern (44 bp):
ATGCATCGATGCACATTCAAGGCATGCATCGATGCATCTACAAG
Found at i:340215 original size:22 final size:21
Alignment explanation
Indices: 340173--340212 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
340163 GAGTTTGTTT
*
340173 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
340194 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
340213 ACAATTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:342342 original size:20 final size:20
Alignment explanation
Indices: 342317--342354 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
342307 CAATTAATTC
342317 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
*
342337 ATTGATGCATCGGTGCAT
1 ATTGATGCATCGATGCAT
342355 ACCTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:342347 original size:65 final size:65
Alignment explanation
Indices: 342146--342355 Score: 225
Period size: 65 Copynumber: 3.2 Consensus size: 65
342136 GTGCACCAAG
* * *
342146 TGTGCATCGATGCATAAAATGCATTCGATGTTTGAA-AATAGACTGAGTGCATCGATGCAT-GAC
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTCAATAATAAATTGAGTGCATCGATGCATGGA-
342209 T
65 T
* *
342210 TGTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAA-AAATCCGAGTGCATCGATGCATGG
1 TGTGCATCGATGCATAAAATGCATTCGATG-TTTCAATAATAAAT-TGAGTGCATCGATGCATGG
342273 AT
64 AT
* * * * **
342275 AGCGCATCGGTGCATGAAATGCATTCGATG-TTCAATTAATTCATTGA-TGCATCGATGCATGGA
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTCAA-TAATAAATTGAGTGCATCGATGCATGGA
342338 T
65 T
*
342339 TGATGCATCGGTGCATA
1 TG-TGCATCGATGCATA
342356 CCTTTGAAAA
Statistics
Matches: 123, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
63 3 0.02
64 51 0.41
65 65 0.53
66 4 0.03
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.30
Consensus pattern (65 bp):
TGTGCATCGATGCATAAAATGCATTCGATGTTTCAATAATAAATTGAGTGCATCGATGCATGGAT
Found at i:345394 original size:13 final size:12
Alignment explanation
Indices: 345354--345395 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
345344 TTTCACAACA
345354 AGCTCGTTTATG
1 AGCTCGTTTATG
* *
345366 AGCTCATTTATA
1 AGCTCGTTTATG
345378 AGCTCGTTTTATG
1 AGCTCG-TTTATG
345391 AGCTC
1 AGCTC
345396 ATTCATTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (12 bp):
AGCTCGTTTATG
Found at i:345754 original size:23 final size:23
Alignment explanation
Indices: 345728--345794 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
345718 ACATATGCAT
345728 AACATATTCAT-AACATATAAACG
1 AACATATTCATGAACAT-TAAACG
* *
345751 AACACATTCATGAACATTAAATG
1 AACATATTCATGAACATTAAACG
* * *
345774 AACATGTTCACGAACAATAAA
1 AACATATTCATGAACATTAAA
345795 ATGTAATACC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
23 32 0.86
24 5 0.14
ACGTcount: A:0.51, C:0.18, G:0.07, T:0.24
Consensus pattern (23 bp):
AACATATTCATGAACATTAAACG
Found at i:350177 original size:25 final size:25
Alignment explanation
Indices: 350149--350217 Score: 120
Period size: 25 Copynumber: 2.8 Consensus size: 25
350139 TTCAACAAAT
*
350149 CTCTTCATCAAAAGGTCTTTCTTAA
1 CTCTTCATCGAAAGGTCTTTCTTAA
*
350174 CTCTTCATCGAAATGTCTTTCTTAA
1 CTCTTCATCGAAAGGTCTTTCTTAA
350199 CTCTTCATCGAAAGGTCTT
1 CTCTTCATCGAAAGGTCTT
350218 AACATTTCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.41
Consensus pattern (25 bp):
CTCTTCATCGAAAGGTCTTTCTTAA
Found at i:353074 original size:21 final size:21
Alignment explanation
Indices: 353026--353067 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
353016 TCCAACAAAT
353026 ATCTTCATCAAAAGGTCTTAA
1 ATCTTCATCAAAAGGTCTTAA
353047 ATCTTCATCAAAAGGTCTTAA
1 ATCTTCATCAAAAGGTCTTAA
353068 CCTTTCAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (21 bp):
ATCTTCATCAAAAGGTCTTAA
Found at i:356652 original size:22 final size:21
Alignment explanation
Indices: 356622--356684 Score: 72
Period size: 22 Copynumber: 3.0 Consensus size: 21
356612 TTTCATGAAA
* *
356622 AAAATGTTAAGCCCTTTCATC
1 AAAAGGTTAAGTCCTTTCATC
* *
356643 AAAAGAGTTAAGTCTTTTAATC
1 AAAAG-GTTAAGTCCTTTCATC
*
356665 AAAAGGTTAAGTTCTTTCAT
1 AAAAGGTTAAGTCCTTTCAT
356685 TGAAAGGTCT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 16 0.47
22 18 0.53
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (21 bp):
AAAAGGTTAAGTCCTTTCATC
Found at i:359539 original size:21 final size:22
Alignment explanation
Indices: 359492--359564 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
359482 ATGTTTAATA
*
359492 TTTTCATGAAAAA-ATGTTAAGCC
1 TTTTCAT-AAAAAGA-GTTAAGTC
*
359515 CTTTCATAAAAAGAGTTAAGTC
1 TTTTCATAAAAAGAGTTAAGTC
* *
359537 TTTTAATCAAAAG-GTTAAGT-
1 TTTTCATAAAAAGAGTTAAGTC
359557 TATTTCAT
1 T-TTTCAT
359565 TGAAAGATCT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.02
21 12 0.29
22 22 0.52
23 7 0.17
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.38
Consensus pattern (22 bp):
TTTTCATAAAAAGAGTTAAGTC
Found at i:365230 original size:20 final size:20
Alignment explanation
Indices: 365186--365227 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
365176 TACTATGATG
*
365186 GAATTTGATGTTAGAATGTT
1 GAATTTGATGTTAGAATGGT
*
365206 GAATTTGGTGTTAGAA-GGT
1 GAATTTGATGTTAGAATGGT
365225 GAA
1 GAA
365228 ATTGGATCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (20 bp):
GAATTTGATGTTAGAATGGT
Found at i:365232 original size:19 final size:20
Alignment explanation
Indices: 365194--365232 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
365184 TGGAATTTGA
* *
365194 TGTTAGAATGTTGAATTTGG
1 TGTTAGAATGGTGAAATTGG
365214 TGTTAGAA-GGTGAAATTGG
1 TGTTAGAATGGTGAAATTGG
365233 ATCATTATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.28, C:0.00, G:0.33, T:0.38
Consensus pattern (20 bp):
TGTTAGAATGGTGAAATTGG
Found at i:366837 original size:50 final size:49
Alignment explanation
Indices: 366752--366847 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 49
366742 ATGAAAATAA
* * * * *
366752 AATATGAAAGTTCTGAAATGTGTCTGAATGAAAAATAGATCATGAAAGTG
1 AATATGAAAGCTCTAAAATGTATCTAAATGAAAAATAAAT-ATGAAAGTG
366802 AATATGAAAGCTCTAAAATGTATCTCAAATG-AAAATAAATATGAAA
1 AATATGAAAGCTCTAAAATGTATCT-AAATGAAAAATAAATATGAAA
366848 TGATTATTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
49 6 0.15
50 30 0.75
51 4 0.10
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.27
Consensus pattern (49 bp):
AATATGAAAGCTCTAAAATGTATCTAAATGAAAAATAAATATGAAAGTG
Found at i:371349 original size:12 final size:11
Alignment explanation
Indices: 371320--371368 Score: 53
Period size: 12 Copynumber: 4.2 Consensus size: 11
371310 GAAGGGGGAG
371320 GGAGAGAAAGA
1 GGAGAGAAAGA
371331 GGCAGAGAAAGA
1 GG-AGAGAAAGA
*
371343 GTGAGAGAGAGA
1 G-GAGAGAAAGA
*
371355 TGGAGAGAGAGA
1 -GGAGAGAAAGA
371367 GG
1 GG
371369 GGTAGGGGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
11 4 0.12
12 28 0.82
13 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.49, T:0.04
Consensus pattern (11 bp):
GGAGAGAAAGA
Found at i:371457 original size:8 final size:8
Alignment explanation
Indices: 371441--371509 Score: 50
Period size: 8 Copynumber: 8.2 Consensus size: 8
371431 GAGGGCAAGG
*
371441 GAGATGGA
1 GAGAGGGA
371449 GAGAGGGA
1 GAGAGGGA
*
371457 GAGCGGGGGA
1 GA--GAGGGA
*
371467 GAAAGGG-
1 GAGAGGGA
371474 GAGAGGGAAA
1 GAGAGGG--A
*
371484 GAGAAGGA
1 GAGAGGGA
*
371492 GAGTGGGA
1 GAGAGGGA
371500 GAGAGGGA
1 GAGAGGGA
371508 GA
1 GA
371510 TATATGTTTA
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
7 6 0.13
8 28 0.60
10 13 0.28
ACGTcount: A:0.38, C:0.01, G:0.58, T:0.03
Consensus pattern (8 bp):
GAGAGGGA
Found at i:372140 original size:28 final size:28
Alignment explanation
Indices: 372089--372142 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
372079 GTGTTGTAGC
*
372089 ATTTATGCCACTGAACTTTCATTTTTAT
1 ATTTATGCCACTGAACTTACATTTTTAT
* * *
372117 ATTTATGGCATTGAACTTAGATTTTT
1 ATTTATGCCACTGAACTTACATTTTT
372143 GTTTCAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.50
Consensus pattern (28 bp):
ATTTATGCCACTGAACTTACATTTTTAT
Found at i:372479 original size:33 final size:31
Alignment explanation
Indices: 372442--372518 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 31
372432 GATTTTGATA
372442 TATTTTTAAAATTTTAATTGTATTTTAGT-ATTT
1 TATTTTTAAAA-TTTAATTG--TTTTAGTAATTT
*
372475 TATTTTTTAGTAATTTAATTGTTTTAGTAATTT
1 TA-TTTTTA-AAATTTAATTGTTTTAGTAATTT
372508 TATATTTTAAA
1 TAT-TTTTAAA
372519 GTATTTGAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
32 9 0.24
33 13 0.34
34 14 0.37
35 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (31 bp):
TATTTTTAAAATTTAATTGTTTTAGTAATTT
Found at i:372501 original size:17 final size:17
Alignment explanation
Indices: 372454--372507 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
372444 TTTTTAAAAT
372454 TTTAATTGTATTTTAGT-A
1 TTTAATTG--TTTTAGTAA
*
372472 TTTTATT-TTTTAGTAA
1 TTTAATTGTTTTAGTAA
372488 TTTAATTGTTTTAGTAA
1 TTTAATTGTTTTAGTAA
372505 TTT
1 TTT
372508 TATATTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 7 0.22
16 7 0.22
17 12 0.38
18 6 0.19
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (17 bp):
TTTAATTGTTTTAGTAA
Found at i:373823 original size:51 final size:51
Alignment explanation
Indices: 373747--373847 Score: 150
Period size: 51 Copynumber: 2.0 Consensus size: 51
373737 CTGGATCTGT
* * *
373747 CTGCATAGAATGCTCGCCCTACTTCCT-TAGGTGGATCATGTTAAATCTTCG
1 CTGCATAGAACGCTCGCCCTACTTCCTGT-GGTGGATCATGGTAAACCTTCG
*
373798 CTGCATAGAACGCTGGCCCTACTTCCTGTGGTGGATCATGGTAAACCTTC
1 CTGCATAGAACGCTCGCCCTACTTCCTGTGGTGGATCATGGTAAACCTTC
373848 ATCTCAAATG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 44 0.98
52 1 0.02
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.31
Consensus pattern (51 bp):
CTGCATAGAACGCTCGCCCTACTTCCTGTGGTGGATCATGGTAAACCTTCG
Found at i:386354 original size:23 final size:22
Alignment explanation
Indices: 386308--386351 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
386298 GGTCTCCAAA
386308 ATAGTAGAACCTTGCTTTTTTT
1 ATAGTAGAACCTTGCTTTTTTT
386330 ATAGTAGAACCTTGCTTTTTTT
1 ATAGTAGAACCTTGCTTTTTTT
386352 TATTGAGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.50
Consensus pattern (22 bp):
ATAGTAGAACCTTGCTTTTTTT
Found at i:389201 original size:26 final size:26
Alignment explanation
Indices: 389171--389265 Score: 190
Period size: 26 Copynumber: 3.7 Consensus size: 26
389161 TATGGAAAAC
389171 ATGTTTATTCACTTTTACTGTTTTAT
1 ATGTTTATTCACTTTTACTGTTTTAT
389197 ATGTTTATTCACTTTTACTGTTTTAT
1 ATGTTTATTCACTTTTACTGTTTTAT
389223 ATGTTTATTCACTTTTACTGTTTTAT
1 ATGTTTATTCACTTTTACTGTTTTAT
389249 ATGTTTATTCACTTTTA
1 ATGTTTATTCACTTTTA
389266 TTGAAAACTT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 69 1.00
ACGTcount: A:0.20, C:0.12, G:0.07, T:0.61
Consensus pattern (26 bp):
ATGTTTATTCACTTTTACTGTTTTAT
Found at i:389522 original size:14 final size:14
Alignment explanation
Indices: 389500--389529 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
389490 ATTTATTTGT
*
389500 TTGATTAATGTGTA
1 TTGAGTAATGTGTA
389514 TTGAGTAATGTGTA
1 TTGAGTAATGTGTA
389528 TT
1 TT
389530 CTCACTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (14 bp):
TTGAGTAATGTGTA
Found at i:392120 original size:2 final size:2
Alignment explanation
Indices: 392113--392159 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
392103 CTTTTAAAAC
392113 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
392155 AT AT A
1 AT AT A
392160 CCTCCATCCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:392346 original size:12 final size:12
Alignment explanation
Indices: 392329--392387 Score: 66
Period size: 12 Copynumber: 4.9 Consensus size: 12
392319 CAAAAATCAA
392329 AACAGAATTCAG
1 AACAGAATTCAG
392341 AACAG-ATATCAG
1 AACAGAAT-TCAG
*
392353 AACAGAATCCAG
1 AACAGAATTCAG
* *
392365 ATCAGAAATCAG
1 AACAGAATTCAG
*
392377 AACAAAATTCA
1 AACAGAATTCA
392388 AGTCATGTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 2 0.05
12 34 0.89
13 2 0.05
ACGTcount: A:0.53, C:0.19, G:0.14, T:0.15
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:392356 original size:24 final size:24
Alignment explanation
Indices: 392324--392411 Score: 99
Period size: 24 Copynumber: 3.7 Consensus size: 24
392314 GATATCAAAA
* *
392324 ATCAAAACAGAATTCAGAACAGAT
1 ATCAGAACAGAATTCAGATCAGAT
* *
392348 ATCAGAACAGAATCCAGATCAGAA
1 ATCAGAACAGAATTCAGATCAGAT
*
392372 ATCAGAACAAAATTCA-AGTCATG-T
1 ATCAGAACAGAATTCAGA-TCA-GAT
392396 ATCAGAACAGAATTCA
1 ATCAGAACAGAATTCA
392412 AGTCGAAAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
23 1 0.02
24 52 0.96
25 1 0.02
ACGTcount: A:0.50, C:0.18, G:0.14, T:0.18
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGATCAGAT
Found at i:392386 original size:48 final size:48
Alignment explanation
Indices: 392317--392425 Score: 116
Period size: 48 Copynumber: 2.3 Consensus size: 48
392307 AAACAGAGAT
*
392317 ATCAAAAATCAAAACAGAATTC-AGAACA-GATATCAGAACAGAATCCAG
1 ATCAAAAATCAAAACAAAATTCAAG-ACATG-TATCAGAACAGAATCCAG
* * * *
392365 ATCAGAAATCAGAACAAAATTCAAGTCATGTATCAGAACAGAATTCA-
1 ATCAAAAATCAAAACAAAATTCAAGACATGTATCAGAACAGAATCCAG
*
392412 AGTCGAAAATCAAA
1 A-TCAAAAATCAAA
392426 TAAAATATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
47 1 0.02
48 46 0.92
49 3 0.06
ACGTcount: A:0.52, C:0.17, G:0.13, T:0.17
Consensus pattern (48 bp):
ATCAAAAATCAAAACAAAATTCAAGACATGTATCAGAACAGAATCCAG
Found at i:394841 original size:30 final size:29
Alignment explanation
Indices: 394806--394919 Score: 88
Period size: 30 Copynumber: 3.9 Consensus size: 29
394796 TTATACAAAT
* *
394806 AGCACCCAAACAGAATTTAATTCCCAGAAC
1 AGCACCAAAACAGAA-TTAATTACCAGAAC
** *
394836 AGCACCAAAATTGAATTAATTACCAGAAT
1 AGCACCAAAACAGAATTAATTACCAGAAC
* * * *
394865 AGCACAAAAAACCA-AATTATTTACCAAAAT
1 AGCAC-CAAAA-CAGAATTAATTACCAGAAC
*
394895 AGCACCAAAATC-GAATTATTTACCA
1 AGCACCAAAA-CAGAATTAATTACCA
394920 AAATATCATC
Statistics
Matches: 69, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
29 34 0.49
30 35 0.51
ACGTcount: A:0.48, C:0.23, G:0.08, T:0.21
Consensus pattern (29 bp):
AGCACCAAAACAGAATTAATTACCAGAAC
Found at i:394944 original size:29 final size:29
Alignment explanation
Indices: 394836--394924 Score: 115
Period size: 29 Copynumber: 3.0 Consensus size: 29
394826 TTCCCAGAAC
* * *
394836 AGCACCAAAATTGAATTAATTACCAGAAT
1 AGCACCAAAATCGAATTATTTACCAAAAT
* * *
394865 AGCACAAAAAACCAAATTATTTACCAAAAT
1 AGCAC-CAAAATCGAATTATTTACCAAAAT
394895 AGCACCAAAATCGAATTATTTACCAAAAT
1 AGCACCAAAATCGAATTATTTACCAAAAT
394924 A
1 A
394925 TCATCAGTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 27 0.54
30 23 0.46
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (29 bp):
AGCACCAAAATCGAATTATTTACCAAAAT
Found at i:396226 original size:64 final size:64
Alignment explanation
Indices: 396147--396286 Score: 156
Period size: 64 Copynumber: 2.2 Consensus size: 64
396137 CGGATCTTGA
* * * *
396147 CAGGTCGGGTAAAATCGGATACAGGTCA-AGTCAGGTAAATTTGACACCAGATCCAGGTCGGGTT
1 CAGGTCAGGTCAAATCAG-TACAGGTCATAGTCAGGTAAATTTGACACCAGATCCAGATCGGGTT
* * * ** **
396211 CAGGTCAGGTCAAATCAGTTCGGGTTATTTTCAGGTCGATTTGACACCAGATCCAGATCGGGTT
1 CAGGTCAGGTCAAATCAGTACAGGTCATAGTCAGGTAAATTTGACACCAGATCCAGATCGGGTT
*
396275 CAGGTTAGGTCA
1 CAGGTCAGGTCA
396287 TTTTCAGTTC
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
63 6 0.10
64 57 0.90
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (64 bp):
CAGGTCAGGTCAAATCAGTACAGGTCATAGTCAGGTAAATTTGACACCAGATCCAGATCGGGTT
Found at i:397001 original size:13 final size:13
Alignment explanation
Indices: 396985--397119 Score: 81
Period size: 13 Copynumber: 9.3 Consensus size: 13
396975 AATATAAGTT
396985 TATATATATAAAC
1 TATATATATAAAC
396998 TATATTTATATTATAAAC
1 --TA--TATA-TATAAAC
*
397016 TATATAATTATTATAAG
1 TATAT-A-TA-TA-AAC
*
397033 TTATATATATAAAT
1 T-ATATATATAAAC
* * *
397047 TATGTTTATATGAAT
1 TA--TATATATAAAC
*
397062 TATATATATGAAC
1 TATATATATAAAC
397075 TATATATATAAAC
1 TATATATATAAAC
*
397088 TATATATGTAAAC
1 TATATATATAAAC
397101 TATATATGTATAAAC
1 TATATA--TATAAAC
397116 TATA
1 TATA
397120 AAAATTATAT
Statistics
Matches: 100, Mismatches: 9, Indels: 22
0.76 0.07 0.17
Matches are distributed among these distances:
13 40 0.40
14 6 0.06
15 29 0.29
16 6 0.06
17 8 0.08
18 11 0.11
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (13 bp):
TATATATATAAAC
Done.