Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 180 of 193
Found at i:56270825 original size:15 final size:16
Alignment explanation
Indices: 56270805--56270838 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
56270795 AATCTTTTAA
56270805 AAATTATAAAAAT-AT
1 AAATTATAAAAATAAT
*
56270820 AAATTATTAAAATAAT
1 AAATTATAAAAATAAT
56270836 AAA
1 AAA
56270839 ATTACATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATAAT
Found at i:56271018 original size:23 final size:23
Alignment explanation
Indices: 56270992--56271035 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
56270982 TATGAGTAAA
*
56270992 ATCAAATTTA-AATATATAAATAC
1 ATCAAATTAACAATAT-TAAATAC
*
56271015 ATCAGATTAACAATATTAAAT
1 ATCAAATTAACAATATTAAAT
56271036 GCACTACAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (23 bp):
ATCAAATTAACAATATTAAATAC
Found at i:56274923 original size:23 final size:20
Alignment explanation
Indices: 56274880--56274923 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 20
56274870 ACAACCATCA
*
56274880 TACATTATAATTAAATTTAT
1 TACATTATAAATAAATTTAT
56274900 TACATTATTAAATATAATTATAT
1 TACATTA-TAAATA-AATT-TAT
56274923 T
1 T
56274924 TTTTTATACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 7 0.35
21 5 0.25
22 4 0.20
23 4 0.20
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
TACATTATAAATAAATTTAT
Found at i:56276543 original size:92 final size:92
Alignment explanation
Indices: 56276362--56276545 Score: 237
Period size: 93 Copynumber: 2.0 Consensus size: 92
56276352 ATTAAATTCC
* * ** *
56276362 TTTTTTTTACACTCGATTGAGCACTTGAACTTTTAAAATGCATAAAAAAAATTCTCAAACTTCTT
1 TTTTTTTTACACTCAATTGAGCACTTGAACTTTTAAAATACATAAAAAAAACCCTCAAAATTCTT
56276427 AAAAAAAAAAACAATTAAGCCCTTGCT
66 AAAAAAAAAAACAATTAAGCCCTTGCT
* * * * *
56276454 TTTTTTTCTCCACTCAATTGGGTACTTGAA-TTTTCAAAATACATCAAAAAAACCCTCAAAATTT
1 TTTTTTT-TACACTCAATTGAGCACTTGAACTTTT-AAAATACATAAAAAAAACCCTCAAAATTC
*
56276518 TTCAAAAAAAAAA-AATTAAGCCCTTGCT
64 TTAAAAAAAAAAACAATTAAGCCCTTGCT
56276546 CTTATTAAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
92 26 0.33
93 53 0.67
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (92 bp):
TTTTTTTTACACTCAATTGAGCACTTGAACTTTTAAAATACATAAAAAAAACCCTCAAAATTCTT
AAAAAAAAAAACAATTAAGCCCTTGCT
Found at i:56276709 original size:21 final size:22
Alignment explanation
Indices: 56276683--56276729 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
56276673 AAAAAATTGT
56276683 AAAATTTTATAGAAAT-CAT-AA
1 AAAATTTTATA-AAATGCATCAA
56276704 AAAA-TTTATAAAATGCATCAA
1 AAAATTTTATAAAATGCATCAA
56276725 AAAAT
1 AAAAT
56276730 CTCTTTAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 4 0.17
20 9 0.39
21 10 0.43
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (22 bp):
AAAATTTTATAAAATGCATCAA
Found at i:56276711 original size:20 final size:21
Alignment explanation
Indices: 56276683--56276729 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
56276673 AAAAAATTGT
*
56276683 AAAATTTTATAGAAAT-CAT-A
1 AAAAATTTATA-AAATGCATCA
56276703 AAAAATTTATAAAATGCATCA
1 AAAAATTTATAAAATGCATCA
56276724 AAAAAT
1 AAAAAT
56276730 CTCTTTAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 4 0.17
20 13 0.54
21 7 0.29
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (21 bp):
AAAAATTTATAAAATGCATCA
Found at i:56276986 original size:19 final size:19
Alignment explanation
Indices: 56276964--56277033 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
56276954 TTCTCACGAC
56276964 TTTATAAAATTTTATGATT
1 TTTATAAAATTTTATGATT
*
56276983 TTTAT---ATTTCTATATATT
1 TTTATAAAATTT-TAT-GATT
** *
56277001 TTTATAATTTTTTACGATT
1 TTTATAAAATTTTATGATT
56277020 TTTATAAAATTTTA
1 TTTATAAAATTTTA
56277034 CAATTTTTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
16 4 0.10
17 3 0.08
18 8 0.20
19 20 0.50
20 2 0.05
21 3 0.08
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTATAAAATTTTATGATT
Found at i:56276986 original size:57 final size:57
Alignment explanation
Indices: 56276916--56277063 Score: 178
Period size: 57 Copynumber: 2.6 Consensus size: 57
56276906 TATAATTTTT
* *
56276916 TTTTACAA-ATTTTATATTTCTTTATATTTTGTATAATTTTCTCACGA-CTTTATAAAA
1 TTTTACAATTTTTTATATTTCTATATATTTT-TATAATTTT-TCACGATCTTTATAAAA
** * *
56276973 TTTTATGA-TTTTTATATTTCTATATATTTTTATAATTTTTTACGATTTTTATAAAA
1 TTTTACAATTTTTTATATTTCTATATATTTTTATAATTTTTCACGATCTTTATAAAA
*
56277029 TTTTACAATTTTTTATATTTTCTA-CTATTTTTATA
1 TTTTACAATTTTTTATA-TTTCTATATATTTTTATA
56277064 TTTGTTTTCT
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
55 5 0.06
56 24 0.30
57 44 0.56
58 6 0.08
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (57 bp):
TTTTACAATTTTTTATATTTCTATATATTTTTATAATTTTTCACGATCTTTATAAAA
Found at i:56276991 original size:8 final size:8
Alignment explanation
Indices: 56276973--56277066 Score: 53
Period size: 10 Copynumber: 10.2 Consensus size: 8
56276963 CTTTATAAAA
56276973 TTTTATGAT
1 TTTTAT-AT
56276982 TTTTATAT
1 TTTTATAT
56276990 TTCTATATAT
1 TT-T-TATAT
56277000 TTTTATAATT
1 TTTTAT-A-T
*
56277010 TTTTACGAT
1 TTTTA-TAT
*
56277019 TTTTATAAAA
1 TTTTAT--AT
*
56277029 TTTTACAATT
1 TTTTA-TA-T
56277039 TTTTATAT
1 TTTTATAT
56277047 TTTCTACTAT
1 TTT-TA-TAT
56277057 TTTTATAT
1 TTTTATAT
56277065 TT
1 TT
56277067 GTTTTCTAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 23
0.70 0.06 0.24
Matches are distributed among these distances:
8 16 0.24
9 21 0.31
10 31 0.46
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (8 bp):
TTTTATAT
Found at i:56276998 original size:29 final size:28
Alignment explanation
Indices: 56276964--56277049 Score: 102
Period size: 29 Copynumber: 3.1 Consensus size: 28
56276954 TTCTCACGAC
*
56276964 TTTATAAAATTTTATGA-TTTTTATATT
1 TTTATAAAATTTTATAATTTTTTATATT
* * * *
56276991 TCTATATATTTTTATAATTTTTTACGATT
1 TTTATAAAATTTTATAATTTTTTA-TATT
*
56277020 TTTATAAAATTTTACAATTTTTTATATT
1 TTTATAAAATTTTATAATTTTTTATATT
56277048 TT
1 TT
56277050 CTACTATTTT
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
27 13 0.28
28 11 0.23
29 23 0.49
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.63
Consensus pattern (28 bp):
TTTATAAAATTTTATAATTTTTTATATT
Found at i:56277012 original size:10 final size:10
Alignment explanation
Indices: 56276999--56277090 Score: 57
Period size: 10 Copynumber: 9.4 Consensus size: 10
56276989 TTTCTATATA
56276999 TTTTTATAAT
1 TTTTTATAAT
**
56277009 TTTTTACGA-
1 TTTTTATAAT
*
56277018 TTTTTATAAA
1 TTTTTATAAT
* *
56277028 ATTTTACAAT
1 TTTTTATAAT
56277038 TTTTTAT-AT
1 TTTTTATAAT
*
56277047 TTTCTACT-A-
1 TTTTTA-TAAT
*
56277056 TTTTTATATT
1 TTTTTATAAT
*
56277066 TGTTTTCTAAT
1 T-TTTTATAAT
*
56277077 TTTTAATAAT
1 TTTTTATAAT
56277087 TTTT
1 TTTT
56277091 AATTAAAATT
Statistics
Matches: 61, Mismatches: 16, Indels: 10
0.70 0.18 0.11
Matches are distributed among these distances:
8 1 0.02
9 19 0.31
10 33 0.54
11 8 0.13
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.65
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:56277034 original size:19 final size:19
Alignment explanation
Indices: 56276964--56277063 Score: 64
Period size: 19 Copynumber: 5.3 Consensus size: 19
56276954 TTCTCACGAC
*
56276964 TTTATAAAATTTTATGATT
1 TTTATAAAATTTTACGATT
**
56276983 TTTAT---ATTTCTATATATT
1 TTTATAAAATTT-TA-CGATT
**
56277001 TTTATAATTTTTTACGATT
1 TTTATAAAATTTTACGATT
*
56277020 TTTATAAAATTTTACAATT
1 TTTATAAAATTTTACGATT
* * *
56277039 TTT-TATATTTTCTACTATT
1 TTTATAAAATTT-TACGATT
56277058 TTTATA
1 TTTATA
56277064 TTTGTTTTCT
Statistics
Matches: 63, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
16 4 0.06
17 2 0.03
18 14 0.22
19 36 0.57
20 4 0.06
21 3 0.05
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTATAAAATTTTACGATT
Found at i:56277081 original size:20 final size:18
Alignment explanation
Indices: 56276980--56277066 Score: 70
Period size: 18 Copynumber: 4.7 Consensus size: 18
56276970 AAATTTTATG
*
56276980 ATTTTTATA-TTTCTATAT
1 ATTTTTATATTTTCTA-CT
* *
56276998 ATTTTTATAATTTTTTACG
1 ATTTTTAT-ATTTTCTACT
* *
56277017 ATTTTTATAAAATTT-TACA
1 ATTTTTAT--ATTTTCTACT
56277036 ATTTTTTATATTTTCTACT
1 A-TTTTTATATTTTCTACT
56277055 ATTTTTATATTT
1 ATTTTTATATTT
56277067 GTTTTCTAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
18 23 0.40
19 17 0.30
20 17 0.30
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (18 bp):
ATTTTTATATTTTCTACT
Found at i:56281375 original size:100 final size:100
Alignment explanation
Indices: 56281174--56281356 Score: 278
Period size: 100 Copynumber: 1.8 Consensus size: 100
56281164 TATTTAACTG
* * *
56281174 TTTTATTTAAGCATTTCATATAATTGATTTAAATAATTTATTTTTATTTAAACATTTAATATACA
1 TTTTATTTAAACATTTCATATAAATGACTTAAATAATTTATTTTTATTTAAACATTTAATATACA
* *
56281239 TATCAAATTTGTTCGATTGAAAAAATAAATCTTTC
66 TATCAAATTTGTTCCAGTGAAAAAATAAATCTTTC
* * *
56281274 TTTTATTTAAACATTTTATATAAATGACTTAAATTATTT-TATTTTATTTAAACATTTAATATTC
1 TTTTATTTAAACATTTCATATAAATGACTTAAATAATTTAT-TTTTATTTAAACATTTAATATAC
56281338 ATATCAAATTTGTTCCAGT
65 ATATCAAATTTGTTCCAGT
56281357 AAGAAATTTC
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
99 1 0.01
100 73 0.99
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (100 bp):
TTTTATTTAAACATTTCATATAAATGACTTAAATAATTTATTTTTATTTAAACATTTAATATACA
TATCAAATTTGTTCCAGTGAAAAAATAAATCTTTC
Found at i:56289316 original size:30 final size:26
Alignment explanation
Indices: 56289246--56289316 Score: 63
Period size: 30 Copynumber: 2.6 Consensus size: 26
56289236 GATAAAAAAA
*
56289246 TAAAAAAT-AAAAAATATTAAATTAT
1 TAAAAATTAAAAAAATATTAAATTAT
**
56289271 TAAATTTTAATAAAAACTATTTAAATTTAT
1 TAAAAATTAA-AAAAA-TA-TTAAA-TTAT
56289301 TAAAAATTAGAAAAAA
1 TAAAAATTA-AAAAAA
56289317 ATAAAAATCG
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
25 5 0.14
26 1 0.03
27 5 0.14
28 2 0.06
29 5 0.14
30 16 0.46
31 1 0.03
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (26 bp):
TAAAAATTAAAAAAATATTAAATTAT
Found at i:56289404 original size:20 final size:20
Alignment explanation
Indices: 56289379--56289438 Score: 79
Period size: 19 Copynumber: 3.0 Consensus size: 20
56289369 ATTTTATAAG
56289379 TCGTAAAAAAATTATAGAAAA
1 TCGTAAAAAAATTATA-AAAA
* *
56289400 T-GTAAAAAAAATATAAAAT
1 TCGTAAAAAAATTATAAAAA
56289419 TCG-AAAAAAATTATAAAAA
1 TCGTAAAAAAATTATAAAAA
56289438 T
1 T
56289439 TATCGTACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 19 0.56
20 14 0.41
21 1 0.03
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (20 bp):
TCGTAAAAAAATTATAAAAA
Found at i:56289439 original size:20 final size:20
Alignment explanation
Indices: 56289381--56289439 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
56289371 TTTATAAGTC
56289381 GTAAAAAAATTATAGAAAA-T
1 GTAAAAAAATTATA-AAAATT
*
56289401 GTAAAAAAAATAT-AAAATT
1 GTAAAAAAATTATAAAAATT
56289420 CG-AAAAAAATTATAAAAATT
1 -GTAAAAAAATTATAAAAATT
56289440 ATCGTACTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 4 0.12
19 11 0.32
20 19 0.56
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (20 bp):
GTAAAAAAATTATAAAAATT
Found at i:56294895 original size:15 final size:15
Alignment explanation
Indices: 56294875--56294907 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
56294865 TAATGCTTTC
56294875 AACCCGACTCAAATT
1 AACCCGACTCAAATT
56294890 AACCCGACTCAAATT
1 AACCCGACTCAAATT
56294905 AAC
1 AAC
56294908 GAGACCGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.42, C:0.33, G:0.06, T:0.18
Consensus pattern (15 bp):
AACCCGACTCAAATT
Found at i:56298174 original size:15 final size:15
Alignment explanation
Indices: 56298154--56298184 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
56298144 AACACAGCCT
56298154 CATTCATTTTATTTC
1 CATTCATTTTATTTC
56298169 CATTCATTTTATTTC
1 CATTCATTTTATTTC
56298184 C
1 C
56298185 TTAAAAGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (15 bp):
CATTCATTTTATTTC
Found at i:56298425 original size:16 final size:16
Alignment explanation
Indices: 56298404--56298435 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
56298394 ACAAACTTAG
56298404 TTATGTGTCTTAAGAT
1 TTATGTGTCTTAAGAT
56298420 TTATGTGTCTTAAGAT
1 TTATGTGTCTTAAGAT
56298436 CATTGACGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (16 bp):
TTATGTGTCTTAAGAT
Found at i:56301441 original size:9 final size:9
Alignment explanation
Indices: 56301427--56301456 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
56301417 CACAATTGTC
56301427 TTTTTTTAT
1 TTTTTTTAT
56301436 TTTTTTTAT
1 TTTTTTTAT
*
56301445 TTCTTTTAT
1 TTTTTTTAT
56301454 TTT
1 TTT
56301457 CCATCTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:56313866 original size:52 final size:52
Alignment explanation
Indices: 56313783--56313886 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 52
56313773 AGTATCCAAA
* *
56313783 TTTATAATAACCAAGTTTATTAAATTATACAATACCCTATACATACAAACAC
1 TTTACAATAACCAAGTTAATTAAATTATACAATACCCTATACATACAAACAC
* *
56313835 TTTACAATAATCAAGTTAATTAAATTATACAATACCCTATACATGCAAACAC
1 TTTACAATAACCAAGTTAATTAAATTATACAATACCCTATACATACAAACAC
56313887 ATTAATCATT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (52 bp):
TTTACAATAACCAAGTTAATTAAATTATACAATACCCTATACATACAAACAC
Found at i:56316104 original size:28 final size:28
Alignment explanation
Indices: 56316073--56316164 Score: 96
Period size: 28 Copynumber: 3.2 Consensus size: 28
56316063 TCGGGGTTAC
56316073 AAATGGGATTTAGGGAAATTTGAGGGTA
1 AAATGGGATTTAGGGAAATTTGAGGGTA
* * * *
56316101 AAATGGTAATTTTAGTGAAA-TCGAGGTTAA
1 AAATGG-GA-TTTAGGGAAATTTGAGGGT-A
* *
56316131 AAATGGGATTTAGGGAAGTTTAAGGGTA
1 AAATGGGATTTAGGGAAATTTGAGGGTA
56316159 AAATGG
1 AAATGG
56316165 TAATTTTTGA
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
28 21 0.42
29 13 0.26
30 16 0.32
ACGTcount: A:0.38, C:0.01, G:0.32, T:0.29
Consensus pattern (28 bp):
AAATGGGATTTAGGGAAATTTGAGGGTA
Found at i:56316121 original size:30 final size:31
Alignment explanation
Indices: 56316081--56316210 Score: 105
Period size: 29 Copynumber: 4.4 Consensus size: 31
56316071 ACAAATGGGA
56316081 TTTAGGGAAATTTGAGGGT-AAAATGGTAAT
1 TTTAGGGAAATTTGAGGGTAAAAATGGTAAT
* * * *
56316111 TTTAGTGAAA-TCGAGGTTAAAAATGG-GA-
1 TTTAGGGAAATTTGAGGGTAAAAATGGTAAT
* *
56316139 TTTAGGGAAGTTTAAGGGT-AAAATGGTAAT
1 TTTAGGGAAATTTGAGGGTAAAAATGGTAAT
* *
56316169 TTT--TGAAAGTTTTAGGGTAAAAAT-GTAAT
1 TTTAGGGAAA-TTTGAGGGTAAAAATGGTAAT
**
56316198 TTTTTGGAAATTT
1 TTTAGGGAAATTT
56316211 TGGGGTCAAA
Statistics
Matches: 78, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
28 18 0.23
29 29 0.37
30 27 0.35
31 4 0.05
ACGTcount: A:0.36, C:0.01, G:0.26, T:0.37
Consensus pattern (31 bp):
TTTAGGGAAATTTGAGGGTAAAAATGGTAAT
Found at i:56316135 original size:58 final size:58
Alignment explanation
Indices: 56316041--56316171 Score: 208
Period size: 58 Copynumber: 2.2 Consensus size: 58
56316031 ACCCGGGGGC
* * * *
56316041 AAAATGGTAGATTTTGGTGAAATCGGGGTTACAAATGGGATTTAGGGAAATTTGAGGGT
1 AAAATGGTA-ATTTTAGTGAAATCGAGGTTAAAAATGGGATTTAGGGAAATTTAAGGGT
*
56316100 AAAATGGTAATTTTAGTGAAATCGAGGTTAAAAATGGGATTTAGGGAAGTTTAAGGGT
1 AAAATGGTAATTTTAGTGAAATCGAGGTTAAAAATGGGATTTAGGGAAATTTAAGGGT
56316158 AAAATGGTAATTTT
1 AAAATGGTAATTTT
56316172 TGAAAGTTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
58 58 0.87
59 9 0.13
ACGTcount: A:0.36, C:0.02, G:0.30, T:0.32
Consensus pattern (58 bp):
AAAATGGTAATTTTAGTGAAATCGAGGTTAAAAATGGGATTTAGGGAAATTTAAGGGT
Found at i:56316141 original size:29 final size:30
Alignment explanation
Indices: 56316041--56316141 Score: 93
Period size: 29 Copynumber: 3.4 Consensus size: 30
56316031 ACCCGGGGGC
* *
56316041 AAAATGGTAGATTTTGGTGAAATCGGGGTTA
1 AAAATGGT-GATTTTAGTGAAATCGAGGTTA
* * * *
56316072 CAAATGG-GA-TTTAGGGAAATTTGAGGGT-
1 AAAATGGTGATTTTAGTGAAA-TCGAGGTTA
*
56316100 AAAATGGTAATTTTAGTGAAATCGAGGTTA
1 AAAATGGTGATTTTAGTGAAATCGAGGTTA
56316130 AAAATGG-GATTT
1 AAAATGGTGATTT
56316142 AGGGAAGTTT
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
28 14 0.26
29 18 0.33
30 16 0.30
31 6 0.11
ACGTcount: A:0.36, C:0.03, G:0.30, T:0.32
Consensus pattern (30 bp):
AAAATGGTGATTTTAGTGAAATCGAGGTTA
Found at i:56316222 original size:30 final size:30
Alignment explanation
Indices: 56316154--56316294 Score: 164
Period size: 30 Copynumber: 4.7 Consensus size: 30
56316144 GGAAGTTTAA
*
56316154 GGGT-AAAATGGTAATTTTT-GAAAGTTTTA
1 GGGTCAAAAT-GTAATTTTTGGAAAGTTTTG
*
56316183 GGGTAAAAATGTAATTTTTTGGAAA-TTTTG
1 GGGTCAAAATGTAA-TTTTTGGAAAGTTTTG
* *
56316213 GGGTCAAAATATGA-TTTTGGAAAAGTTTTG
1 GGGTCAAAATGTAATTTTTGG-AAAGTTTTG
*
56316243 GGGTCAAAATGTAATTTTTAGAAAGTTTTG
1 GGGTCAAAATGTAATTTTTGGAAAGTTTTG
* *
56316273 GGGTTAAAATGTAATTTCTGGA
1 GGGTCAAAATGTAATTTTTGGA
56316295 CAATTTAGGG
Statistics
Matches: 96, Mismatches: 10, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.06
29 11 0.11
30 70 0.73
31 9 0.09
ACGTcount: A:0.33, C:0.02, G:0.25, T:0.40
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTTGGAAAGTTTTG
Found at i:56317103 original size:23 final size:24
Alignment explanation
Indices: 56317048--56317111 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 24
56317038 GTTCAAGGTA
56317048 TGGTTTCTTCTCTTTTCTTCCCTTT
1 TGGTTT-TTCTCTTTTCTTCCCTTT
* *
56317073 T-TTGTTTTCT-TTTTCTTTCCTTT
1 TGGT-TTTTCTCTTTTCTTCCCTTT
56317096 TGGTTTTTCTCATTTT
1 TGGTTTTTCTC-TTTT
56317112 TTAAAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
23 19 0.59
24 6 0.19
25 7 0.22
ACGTcount: A:0.02, C:0.20, G:0.08, T:0.70
Consensus pattern (24 bp):
TGGTTTTTCTCTTTTCTTCCCTTT
Found at i:56317427 original size:28 final size:27
Alignment explanation
Indices: 56317374--56317429 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 27
56317364 AATTCCCTTT
*
56317374 TTTATTATTTTATTATCATTATTATTA
1 TTTATTATTTTAATATCATTATTATTA
56317401 TTTATTATTATTAATATCA-TATTTATTA
1 TTTATTATT-TTAATATCATTA-TTATTA
56317429 T
1 T
56317430 GAAACCTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 11 0.42
28 15 0.58
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTATTATTTTAATATCATTATTATTA
Found at i:56317429 original size:3 final size:3
Alignment explanation
Indices: 56317375--56317413 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
56317365 ATTCCCTTTT
*
56317375 TTA TTA TT- TTA TTA TCA TTA TTA TTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
56317414 ATATCATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:56318145 original size:6 final size:6
Alignment explanation
Indices: 56318128--56318186 Score: 61
Period size: 6 Copynumber: 10.0 Consensus size: 6
56318118 TTAATTTTAT
* *
56318128 TTTAAA TTTAAA TTTAAA -GTAAA TCTAAA TAATTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA TTTAAA TTTAAA
56318177 --TAAA TTTAAA
1 TTTAAA TTTAAA
56318187 ATCAATTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
4 4 0.09
5 4 0.09
6 32 0.71
8 5 0.11
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:56318150 original size:11 final size:10
Alignment explanation
Indices: 56318136--56318196 Score: 54
Period size: 11 Copynumber: 5.9 Consensus size: 10
56318126 ATTTTAAATT
56318136 TAAATTTAAA
1 TAAATTTAAA
*
56318146 GTAAATCTAAA
1 -TAAATTTAAA
56318157 T-AA-TTAAA
1 TAAATTTAAA
56318165 TTTAAATTTAAA
1 --TAAATTTAAA
56318177 TAAATTTAAAA
1 TAAATTT-AAA
*
56318188 TCAATTTAA
1 TAAATTTAA
56318197 CTCCAAATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
8 4 0.10
9 2 0.05
10 11 0.26
11 20 0.48
12 5 0.12
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (10 bp):
TAAATTTAAA
Found at i:56318165 original size:31 final size:30
Alignment explanation
Indices: 56318129--56318186 Score: 98
Period size: 31 Copynumber: 1.9 Consensus size: 30
56318119 TAATTTTATT
56318129 TTAAATTTAAATTTAAAGTAAATCTAAATAA
1 TTAAATTTAAATTTAAA-TAAATCTAAATAA
*
56318160 TTAAATTTAAATTTAAATAAATTTAAA
1 TTAAATTTAAATTTAAATAAATCTAAA
56318187 ATCAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (30 bp):
TTAAATTTAAATTTAAATAAATCTAAATAA
Found at i:56318574 original size:52 final size:52
Alignment explanation
Indices: 56318512--56318669 Score: 173
Period size: 52 Copynumber: 3.3 Consensus size: 52
56318502 TTATCCAGCT
56318512 TTACTTCAATTTCAAGAGGATAGGAAAATGACGTTGATGCTTCGTCTTACTC
1 TTACTTCAATTTCAAGAGGATAGGAAAATGACGTTGATGCTTCGTCTTACTC
* * *
56318564 TTACTTCAATTTC---A-GA-AGGACGAA-GGC-TTG-T--TT--TC-CAGCT-
1 TTACTTCAATTTCAAGAGGATAGGA-AAATGACGTTGATGCTTCGTCTTA-CTC
56318604 TTACTTCAATTTCAAGAGGATAGGAAAATGACGTTGATGCTTCGTCTTACTC
1 TTACTTCAATTTCAAGAGGATAGGAAAATGACGTTGATGCTTCGTCTTACTC
56318656 TTACTTCAATTTCA
1 TTACTTCAATTTCA
56318670 GAAGGACGAA
Statistics
Matches: 84, Mismatches: 6, Indels: 32
0.69 0.05 0.26
Matches are distributed among these distances:
40 14 0.17
41 4 0.05
43 3 0.04
44 4 0.05
45 7 0.08
46 6 0.07
47 7 0.08
48 4 0.05
49 3 0.04
51 4 0.05
52 28 0.33
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTACTTCAATTTCAAGAGGATAGGAAAATGACGTTGATGCTTCGTCTTACTC
Found at i:56318610 original size:92 final size:92
Alignment explanation
Indices: 56318453--56318710 Score: 480
Period size: 92 Copynumber: 2.8 Consensus size: 92
56318443 AAAAGTAGAT
* *
56318453 TTGATGCTTCATTTTACTCTTACTTCAATTTCAGAAGGACGAAGGCTTGTTATCCAGCTTTACTT
1 TTGATGCTTCGTCTTACTCTTACTTCAATTTCAGAAGGACGAAGGCTTGTTATCCAGCTTTACTT
56318518 CAATTTCAAGAGGATAGGAAAATGACG
66 CAATTTCAAGAGGATAGGAAAATGACG
*
56318545 TTGATGCTTCGTCTTACTCTTACTTCAATTTCAGAAGGACGAAGGCTTGTTTTCCAGCTTTACTT
1 TTGATGCTTCGTCTTACTCTTACTTCAATTTCAGAAGGACGAAGGCTTGTTATCCAGCTTTACTT
56318610 CAATTTCAAGAGGATAGGAAAATGACG
66 CAATTTCAAGAGGATAGGAAAATGACG
*
56318637 TTGATGCTTCGTCTTACTCTTACTTCAATTTCAGAAGGACGAAGGCTTGTTATCTAGCTTTACTT
1 TTGATGCTTCGTCTTACTCTTACTTCAATTTCAGAAGGACGAAGGCTTGTTATCCAGCTTTACTT
56318702 CAATTTCAA
66 CAATTTCAA
56318711 AGGGATGACG
Statistics
Matches: 161, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 161 1.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (92 bp):
TTGATGCTTCGTCTTACTCTTACTTCAATTTCAGAAGGACGAAGGCTTGTTATCCAGCTTTACTT
CAATTTCAAGAGGATAGGAAAATGACG
Found at i:56318734 original size:31 final size:31
Alignment explanation
Indices: 56318696--56318806 Score: 114
Period size: 31 Copynumber: 3.4 Consensus size: 31
56318686 TTATCTAGCT
56318696 TTACTTCAATTTCAAAGGGATGACGTTGCTC
1 TTACTTCAATTTCAAAGGGATGACGTTGCTC
** * * *
56318727 TTACTTCAATTTCAAAGATAAAGACGTGTTATCCAC
1 TTACTTCAATTTCAAAG-GGATGAC--G-T-TGCTC
*
56318763 TTTACTTCAATTTCAAGGGGATGACGTTGCTC
1 -TTACTTCAATTTCAAAGGGATGACGTTGCTC
56318795 TTACTTCAATTT
1 TTACTTCAATTT
56318807 TAGAGATAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
31 29 0.46
32 7 0.11
33 1 0.02
34 2 0.03
35 1 0.02
36 7 0.11
37 16 0.25
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (31 bp):
TTACTTCAATTTCAAAGGGATGACGTTGCTC
Found at i:56318778 original size:68 final size:68
Alignment explanation
Indices: 56318653--56319489 Score: 1125
Period size: 68 Copynumber: 11.9 Consensus size: 68
56318643 CTTCGTCTTA
** * * * * *
56318653 CTCTTACTTCAATTTCAGAAGGACGAAGGCTTGTTATCTAGCTTTACTTCAATTTCAAAGGGATG
1 CTCTTACTTCAATTTCAG-A-GATAAAGACGTGTTATCCA-CTCTACTTCAATTTCAAGGGGATG
56318718 ACGTTG
63 ACGTTG
* *
56318724 CTCTTACTTCAATTTCAAAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGGGGATGACG
1 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
56318789 TTG
66 TTG
*
56318792 CTCTTACTTCAATTTTAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATAGGA
1 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGAT--G-
*
56318857 AATGATCTTG
63 -ACG---TTG
* * * * *
56318867 CACTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATGAC
1 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA-CTCTACTTCAATTTCAAGGGGATGAC
*
56318932 ATTG
65 GTTG
56318936 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
1 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
56319001 TTG
66 TTG
56319004 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
1 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
56319069 TTG
66 TTG
*
56319072 CTCTTACTTCAATTTTAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATAGGA
1 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGAT--G-
*
56319137 AATGATCTTG
63 -ACG---TTG
* * * * *
56319147 CACTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATGAC
1 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA-CTCTACTTCAATTTCAAGGGGATGAC
*
56319212 ATTG
65 GTTG
56319216 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
1 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
56319281 TTG
66 TTG
*
56319284 CTCTTACTTCATTTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
1 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
56319349 TTG
66 TTG
56319352 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCGAGCAGTCAGG
1 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTC-A--AG---GG
* * *
56319417 AAAAGATCTTTG
59 -GATGA-CGTTG
* * * *
56319429 CTCTTACTTCAATTTCAAAGATGAAGACTTGTTATCCACTCTACTTCAATTTCAAGCGGAT
1 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGAT
56319490 TGGAAATGAT
Statistics
Matches: 689, Mismatches: 52, Indels: 52
0.87 0.07 0.07
Matches are distributed among these distances:
68 372 0.54
69 107 0.16
70 5 0.01
71 17 0.02
72 8 0.01
73 2 0.00
74 2 0.00
75 77 0.11
76 61 0.09
77 38 0.06
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (68 bp):
CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
TTG
Found at i:56318939 original size:212 final size:204
Alignment explanation
Indices: 56318653--56319489 Score: 1111
Period size: 212 Copynumber: 4.0 Consensus size: 204
56318643 CTTCGTCTTA
** * * * *
56318653 CTCTTACTTCAATTTCAGAAGGACGAAGGCTTGTTATCTAGCTTTACTTCAATTTCAA-AGGGAT
1 CTCTTACTTCAATTTCAG-A-GATAAAGACGTGTTATCCA-CTCTACTTCAATTTCAAGA-GGAT
* *
56318717 GACGTTGCTCTTACTTCAATTTCAAAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGGG
62 GACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGG
*
56318782 GATGACGTTGCTCTTACTTCAATTTTAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAA
127 GATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAA
*
56318847 GGGGATAGGAAATGATCTTG
192 GGGGAT--G--ACG---TTG
* * * *
56318867 CACTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATGAC
1 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA-CTCTACTTCAATTTCAAGAGGATGAC
*
56318932 ATTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGAT
65 GTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGAT
56318997 GACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGG
130 GACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGG
56319062 GATGACGTTG
195 GATGACGTTG
*
56319072 CTCTTACTTCAATTTTAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATAGGA
1 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAA---G--AGG-
* * * *
56319137 AATGATC-TTGCACTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTC
60 -ATGA-CGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA-CTCTACTTCAATTTC
* *
56319201 AAGAGGATGACATTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAAT
122 AAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAAT
56319266 TTCAAGGGGATGACGTTG
187 TTCAAGGGGATGACGTTG
* *
56319284 CTCTTACTTCATTTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
1 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACG
56319349 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCGAGCAGTC
66 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTC-A--AG--
* * * * * *
56319414 AGGAAAAGATCTTTGCTCTTACTTCAATTTCAAAGATGAAGACTTGTTATCCACTCTACTTCAAT
125 -GG-GATGA-CGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAAT
*
56319479 TTCAAGCGGAT
187 TTCAAGGGGAT
56319490 TGGAAATGAT
Statistics
Matches: 566, Mismatches: 37, Indels: 41
0.88 0.06 0.06
Matches are distributed among these distances:
204 17 0.03
205 92 0.16
206 2 0.00
207 3 0.01
208 4 0.01
209 4 0.01
210 1 0.00
211 43 0.08
212 320 0.57
213 63 0.11
214 17 0.03
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (204 bp):
CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACG
TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
ACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGG
ATGACGTTG
Found at i:56318946 original size:31 final size:31
Alignment explanation
Indices: 56318908--56319368 Score: 161
Period size: 31 Copynumber: 13.5 Consensus size: 31
56318898 ATATCCAGCT
*
56318908 TTACTTCAATTTCAAGAGGATGACATTGCTC
1 TTACTTCAATTTCAAGAGGATGACGTTGCTC
** * * *
56318939 TTACTTCAATTTCAGAGATAAAGACGTGTTATCCAC
1 TTACTTCAATTTCA-AGAGGATGAC--G-T-TGCTC
*
56318975 TCTACTTCAATTTCAAGGGGATGACGTTGCTC
1 T-TACTTCAATTTCAAGAGGATGACGTTGCTC
** * * *
56319007 TTACTTCAATTTCAGAGATAAAGACGTGTTATCCAC
1 TTACTTCAATTTCA-AGAGGATGAC--G-T-TGCTC
*
56319043 TCTACTTCAATTTCAAGGGGATGACGTTGCTC
1 T-TACTTCAATTTCAAGAGGATGACGTTGCTC
* ** * * *
56319075 TTACTTCAATTTTAGAGATAAAGACGTGTTATCCAC
1 TTACTTCAATTTCA-AGAGGATGAC--G-T-TGCTC
*
56319111 TCTACTTCAATTTCAAGGGGATAGGAAATGATC-TTGCAC
1 T-TACTTCAATTTCAA---G--AGG--ATGA-CGTTGCTC
** *
56319150 TTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCT-
1 TTACTTCAATTTCA-AGAGGATGAC--G-T-T---GCTC
*
56319188 TTACTTCAATTTCAAGAGGATGACATTGCTC
1 TTACTTCAATTTCAAGAGGATGACGTTGCTC
** * * *
56319219 TTACTTCAATTTCAGAGATAAAGACGTGTTATCCAC
1 TTACTTCAATTTCA-AGAGGATGAC--G-T-TGCTC
*
56319255 TCTACTTCAATTTCAAGGGGATGACGTTGCTC
1 T-TACTTCAATTTCAAGAGGATGACGTTGCTC
* ** * * *
56319287 TTACTTCATTTTCAGAGATAAAGACGTGTTATCCAC
1 TTACTTCAATTTCA-AGAGGATGAC--G-T-TGCTC
*
56319323 TCTACTTCAATTTCAAGGGGATGACGTTGCTC
1 T-TACTTCAATTTCAAGAGGATGACGTTGCTC
56319355 TTACTTCAATTTCA
1 TTACTTCAATTTCA
56319369 GAGATAAAGA
Statistics
Matches: 312, Mismatches: 70, Indels: 96
0.65 0.15 0.20
Matches are distributed among these distances:
30 3 0.01
31 79 0.25
32 51 0.16
33 5 0.02
34 9 0.03
35 6 0.02
36 47 0.15
37 70 0.22
38 27 0.09
39 9 0.03
40 1 0.00
41 1 0.00
43 3 0.01
44 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (31 bp):
TTACTTCAATTTCAAGAGGATGACGTTGCTC
Found at i:56319008 original size:280 final size:280
Alignment explanation
Indices: 56318653--56319489 Score: 1417
Period size: 280 Copynumber: 3.0 Consensus size: 280
56318643 CTTCGTCTTA
** * * * * *
56318653 CTCTTACTTCAATTTCAGAAGGACGAAGGCTTGTTATCTAGCTTTACTTCAATTTCAAAGGGATG
1 CTCTTACTTCAATTTCAG-A-GATAAAGACGTGTTATCCA-CTCTACTTCAATTTCAAGGGGATG
* *
56318718 ACGTTGCTCTTACTTCAATTTCAAAGATAAAGACGTGTTATCCACTTTACTTCAATTTCAAGGGG
63 ACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGG
56318783 ATGACGTTGCTCTTACTTCAATTTTAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAG
128 ATGACGTTGCTCTTACTTCAATTTTAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAG
56318848 GGGATAGGAAATGATCTTGCACTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACT
193 GGGATAGGAAATGATCTTGCACTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACT
56318913 TCAATTTCAAGAGGATGACATTG
258 TCAATTTCAAGAGGATGACATTG
56318936 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
1 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
56319001 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
66 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
56319066 ACGTTGCTCTTACTTCAATTTTAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGG
131 ACGTTGCTCTTACTTCAATTTTAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGG
56319131 ATAGGAAATGATCTTGCACTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCA
196 ATAGGAAATGATCTTGCACTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCA
56319196 ATTTCAAGAGGATGACATTG
261 ATTTCAAGAGGATGACATTG
56319216 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
1 CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
*
56319281 TTGCTCTTACTTCATTTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
66 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
* * **
56319346 ACGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCGAGCA
131 ACGTTGCTCTTACTTCAATTTTAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGG
* * * * * *
56319411 G-TCAGGAAAAGATCTTTGCTCTTACTTCAATTTCAAAGATGAAGACTTGTTATCCA-CTCTACT
195 GAT-AGGAAATGATC-TTGCACTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACT
*
56319474 TCAATTTCAAGCGGAT
258 TCAATTTCAAGAGGAT
56319490 TGGAAATGAT
Statistics
Matches: 530, Mismatches: 21, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
280 410 0.77
281 64 0.12
282 38 0.07
283 18 0.03
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (280 bp):
CTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
ACGTTGCTCTTACTTCAATTTTAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGG
ATAGGAAATGATCTTGCACTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCA
ATTTCAAGAGGATGACATTG
Found at i:56331293 original size:28 final size:28
Alignment explanation
Indices: 56331262--56331353 Score: 87
Period size: 28 Copynumber: 3.2 Consensus size: 28
56331252 TCGGGGTTAT
56331262 AAATGGGATTTAGGGAAATTTGAGGGTA
1 AAATGGGATTTAGGGAAATTTGAGGGTA
* * * *
56331290 AAATGGTAATTTTAGTGAAA-TCGAGGTTAA
1 AAATGG-GA-TTTAGGGAAATTTGAGGGT-A
* * *
56331320 AAATGAGATTTAGGGAAGTTTGGGGGTA
1 AAATGGGATTTAGGGAAATTTGAGGGTA
56331348 AAATGG
1 AAATGG
56331354 TAATTTTTGA
Statistics
Matches: 48, Mismatches: 12, Indels: 8
0.71 0.18 0.12
Matches are distributed among these distances:
28 20 0.42
29 13 0.27
30 15 0.31
ACGTcount: A:0.37, C:0.01, G:0.33, T:0.29
Consensus pattern (28 bp):
AAATGGGATTTAGGGAAATTTGAGGGTA
Found at i:56331310 original size:30 final size:30
Alignment explanation
Indices: 56331270--56331566 Score: 194
Period size: 30 Copynumber: 10.1 Consensus size: 30
56331260 ATAAATGGGA
56331270 TTTAGGGAAA-TTTGAGGGT-AAAATGGTAAT
1 TTTA-GGAAAGTTTGAGGGTAAAAAT-GTAAT
* *
56331300 TTTAGTGAAA--TCGAGGTTAAAAATG-AGA-
1 TTTAG-GAAAGTTTGAGGGTAAAAATGTA-AT
* *
56331328 TTTAGGGAAGTTTGGGGGT-AAAATGGTAAT
1 TTTAGGAAAGTTTGAGGGTAAAAAT-GTAAT
* *
56331358 TTT-TGAAAGTTTTAGGGTAAAAATGTAAT
1 TTTAGGAAAGTTTGAGGGTAAAAATGTAAT
* * *
56331387 TTTTGGAAATTTTG-GGGTTAAAATGTAAT
1 TTTAGGAAAGTTTGAGGGTAAAAATGTAAT
* *
56331416 TTT-GGAAAAGTTTTAGGGTCAAAATGTAAT
1 TTTAGG-AAAGTTTGAGGGTAAAAATGTAAT
* *
56331446 TTT-GGAAAAGTTTTG-GAGTCAAAATGTAATT
1 TTTAGG-AAAG-TTTGAGGGTAAAAATGTAA-T
* * *
56331477 TTTA-AAAAGTTTTG-GGGTCAAAATATAAT
1 TTTAGGAAAG-TTTGAGGGTAAAAATGTAAT
* *
56331506 TTT-GGAAAAGTTTAAGGGTCAAAATGTAAT
1 TTTAGG-AAAGTTTGAGGGTAAAAATGTAAT
* * *
56331536 TTTA-GAAAGTTTTAGGGTCAAAATATAAT
1 TTTAGGAAAGTTTGAGGGTAAAAATGTAAT
56331565 TT
1 TT
56331567 CTAGACAATT
Statistics
Matches: 221, Mismatches: 27, Indels: 39
0.77 0.09 0.14
Matches are distributed among these distances:
27 3 0.01
28 13 0.06
29 89 0.40
30 109 0.49
31 7 0.03
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (30 bp):
TTTAGGAAAGTTTGAGGGTAAAAATGTAAT
Found at i:56331320 original size:29 final size:29
Alignment explanation
Indices: 56331230--56331321 Score: 89
Period size: 29 Copynumber: 3.1 Consensus size: 29
56331220 ACCCGGGGGC
* *
56331230 AAAATGGTAGATTTTGGTGAAATCGGGGTT
1 AAAATGGTA-ATTTTAGTGAAATCGAGGTT
* * * *
56331260 ATAAATGG-GA-TTTAGGGAAATTTGAGGGT
1 A-AAATGGTAATTTTAGTGAAA-TCGAGGTT
56331289 AAAATGGTAATTTTAGTGAAATCGAGGTT
1 AAAATGGTAATTTTAGTGAAATCGAGGTT
56331318 AAAA
1 AAAA
56331322 ATGAGATTTA
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
28 14 0.29
29 18 0.38
30 10 0.21
31 6 0.12
ACGTcount: A:0.37, C:0.02, G:0.29, T:0.32
Consensus pattern (29 bp):
AAAATGGTAATTTTAGTGAAATCGAGGTT
Found at i:56331324 original size:58 final size:58
Alignment explanation
Indices: 56331230--56331360 Score: 199
Period size: 58 Copynumber: 2.2 Consensus size: 58
56331220 ACCCGGGGGC
* * * *
56331230 AAAATGGTAGATTTTGGTGAAATCGGGGTTATAAATGGGATTTAGGGAAATTTGAGGGT
1 AAAATGGTA-ATTTTAGTGAAATCGAGGTTAAAAATGAGATTTAGGGAAATTTGAGGGT
* *
56331289 AAAATGGTAATTTTAGTGAAATCGAGGTTAAAAATGAGATTTAGGGAAGTTTGGGGGT
1 AAAATGGTAATTTTAGTGAAATCGAGGTTAAAAATGAGATTTAGGGAAATTTGAGGGT
56331347 AAAATGGTAATTTT
1 AAAATGGTAATTTT
56331361 TGAAAGTTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
58 57 0.86
59 9 0.14
ACGTcount: A:0.35, C:0.02, G:0.31, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTAGTGAAATCGAGGTTAAAAATGAGATTTAGGGAAATTTGAGGGT
Found at i:56331428 original size:59 final size:59
Alignment explanation
Indices: 56331335--56331566 Score: 299
Period size: 60 Copynumber: 3.9 Consensus size: 59
56331325 AGATTTAGGG
* * *
56331335 AAGTTTGGGGGT-AAAATGGTAATTTTTGAAAGTTTTAGGGTAAAAATGTAATTTTTGG-A
1 AAGTTTTGGGGTCAAAAT-GTAATTTTTGAAAGTTTTAGGGTCAAAATATAA-TTTTGGAA
* * *
56331394 AA-TTTTGGGGTTAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTTG-AAAGTTTTAGGGTCAAAATATAATTTTGGAA
* * *
56331453 AAGTTTTGGAGTCAAAATGTAATTTTTAAAAAGTTTTGGGGTCAAAATATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTT-GAAAGTTTTAGGGTCAAAATATAATTTTGGAA
** *
56331513 AAGTTTAAGGGTCAAAATGTAATTTTAGAAAGTTTTAGGGTCAAAATATAATTT
1 AAGTTTTGGGGTCAAAATGTAATTTTTGAAAGTTTTAGGGTCAAAATATAATTT
56331567 CTAGACAATT
Statistics
Matches: 153, Mismatches: 15, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
58 23 0.15
59 57 0.37
60 73 0.48
ACGTcount: A:0.37, C:0.02, G:0.22, T:0.38
Consensus pattern (59 bp):
AAGTTTTGGGGTCAAAATGTAATTTTTGAAAGTTTTAGGGTCAAAATATAATTTTGGAA
Found at i:56331578 original size:29 final size:29
Alignment explanation
Indices: 56331343--56331571 Score: 223
Period size: 30 Copynumber: 7.7 Consensus size: 29
56331333 GGAAGTTTGG
*
56331343 GGGT-AAAATGGTAATTTTTG-AAAGTTTTA
1 GGGTCAAAAT-GTAATTTTAGAAAAG-TTTA
* * * * *
56331372 GGGTAAAAATGTAATTTTTGGAAATTTTG
1 GGGTCAAAATGTAATTTTAGAAAAGTTTA
* *
56331401 GGGTTAAAATGTAATTTTGGAAAAGTTTTA
1 GGGTCAAAATGTAATTTTAGAAAAG-TTTA
* *
56331431 GGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGTCAAAATGTAATTTTAGAAAAGTTTA
*
56331460 GGAGTCAAAATGTAATTTTTA-AAAAGTTTTG
1 GG-GTCAAAATGTAA-TTTTAGAAAAG-TTTA
* *
56331491 GGGTCAAAATATAATTTTGGAAAAGTTTAA
1 GGGTCAAAATGTAATTTTAGAAAAGTTT-A
56331521 GGGTCAAAATGTAATTTTAG-AAAGTTTTA
1 GGGTCAAAATGTAATTTTAGAAAAG-TTTA
*
56331550 GGGTCAAAATATAATTTCTAGA
1 GGGTCAAAATGTAATTT-TAGA
56331572 CAATTTAAGG
Statistics
Matches: 172, Mismatches: 17, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
29 71 0.41
30 92 0.53
31 9 0.05
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.38
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTAGAAAAGTTTA
Found at i:56331581 original size:59 final size:59
Alignment explanation
Indices: 56331343--56331566 Score: 276
Period size: 59 Copynumber: 3.8 Consensus size: 59
56331333 GGAAGTTTGG
* * * **
56331343 GGGT-AAAATGGTAATTTTTGAAAGTTTTAGGGTAAAAATGTAATTTTTGG-AAA-TTTTG
1 GGGTCAAAAT-GTAATTTTAGAAAGTTTTAGGGTCAAAATATAA-TTTTGGAAAAGTTTAA
* * * *
56331401 GGGTTAAAATGTAATTTTGGAAAAGTTTTAGGGTCAAAATGTAATTTTGGAAAAGTTT-T
1 GGGTCAAAATGTAATTTTAG-AAAGTTTTAGGGTCAAAATATAATTTTGGAAAAGTTTAA
* *
56331460 GGAGTCAAAATGTAATTTTTAAAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTAA
1 GG-GTCAAAATGTAA-TTTTAGAAAGTTTTAGGGTCAAAATATAATTTTGGAAAAGTTTAA
56331521 GGGTCAAAATGTAATTTTAGAAAGTTTTAGGGTCAAAATATAATTT
1 GGGTCAAAATGTAATTTTAGAAAGTTTTAGGGTCAAAATATAATTT
56331567 CTAGACAATT
Statistics
Matches: 148, Mismatches: 11, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
58 19 0.13
59 62 0.42
60 61 0.41
61 6 0.04
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (59 bp):
GGGTCAAAATGTAATTTTAGAAAGTTTTAGGGTCAAAATATAATTTTGGAAAAGTTTAA
Found at i:56332691 original size:28 final size:27
Alignment explanation
Indices: 56332638--56332693 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 27
56332628 AATTCCTTTT
*
56332638 TTTATTATTTTATTATCATTATTATTA
1 TTTATTATTTTAATATCATTATTATTA
56332665 TTTATTATTATTAATATCA-TATTTATTA
1 TTTATTATT-TTAATATCATTA-TTATTA
56332693 T
1 T
56332694 GAAACCTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 11 0.42
28 15 0.58
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTATTATTTTAATATCATTATTATTA
Found at i:56332693 original size:3 final size:3
Alignment explanation
Indices: 56332639--56332677 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
56332629 ATTCCTTTTT
*
56332639 TTA TTA TT- TTA TTA TCA TTA TTA TTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
56332678 ATATCATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:56333408 original size:6 final size:6
Alignment explanation
Indices: 56333391--56333449 Score: 61
Period size: 6 Copynumber: 10.0 Consensus size: 6
56333381 TTAATTTTAT
* *
56333391 TTTAAA TTTAAA TTTAAA -GTAAA TCTAAA TAATTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA TTTAAA TTTAAA
56333440 --TAAA TTTAAA
1 TTTAAA TTTAAA
56333450 ATCAATTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
4 4 0.09
5 4 0.09
6 32 0.71
8 5 0.11
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:56333413 original size:11 final size:10
Alignment explanation
Indices: 56333399--56333459 Score: 54
Period size: 11 Copynumber: 5.9 Consensus size: 10
56333389 ATTTTAAATT
56333399 TAAATTTAAA
1 TAAATTTAAA
*
56333409 GTAAATCTAAA
1 -TAAATTTAAA
56333420 T-AA-TTAAA
1 TAAATTTAAA
56333428 TTTAAATTTAAA
1 --TAAATTTAAA
56333440 TAAATTTAAAA
1 TAAATTT-AAA
*
56333451 TCAATTTAA
1 TAAATTTAA
56333460 CTCCAAATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
8 4 0.10
9 2 0.05
10 11 0.26
11 20 0.48
12 5 0.12
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (10 bp):
TAAATTTAAA
Found at i:56333428 original size:31 final size:30
Alignment explanation
Indices: 56333392--56333449 Score: 98
Period size: 31 Copynumber: 1.9 Consensus size: 30
56333382 TAATTTTATT
56333392 TTAAATTTAAATTTAAAGTAAATCTAAATAA
1 TTAAATTTAAATTTAAA-TAAATCTAAATAA
*
56333423 TTAAATTTAAATTTAAATAAATTTAAA
1 TTAAATTTAAATTTAAATAAATCTAAA
56333450 ATCAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (30 bp):
TTAAATTTAAATTTAAATAAATCTAAATAA
Found at i:56334265 original size:6 final size:6
Alignment explanation
Indices: 56334254--56334303 Score: 54
Period size: 6 Copynumber: 9.0 Consensus size: 6
56334244 ATCAAATCAT
* *
56334254 TTTAAA TTTAAA TTT--A -TTAAA TTTAAA TTTAGA TTT-AA TATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
56334298 TTTAAA
1 TTTAAA
56334304 ATTATTATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
3 2 0.06
4 1 0.03
5 4 0.11
6 29 0.81
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:56334275 original size:15 final size:15
Alignment explanation
Indices: 56334255--56334284 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
56334245 TCAAATCATT
56334255 TTAAATTTAAATTTA
1 TTAAATTTAAATTTA
56334270 TTAAATTTAAATTTA
1 TTAAATTTAAATTTA
56334285 GATTTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAAATTTAAATTTA
Found at i:56334279 original size:21 final size:23
Alignment explanation
Indices: 56334254--56334303 Score: 77
Period size: 21 Copynumber: 2.3 Consensus size: 23
56334244 ATCAAATCAT
56334254 TTTAAATTTAAATTT-AT-TAAA
1 TTTAAATTTAAATTTAATATAAA
*
56334275 TTTAAATTTAGATTTAATATAAA
1 TTTAAATTTAAATTTAATATAAA
56334298 TTTAAA
1 TTTAAA
56334304 ATTATTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 14 0.54
22 2 0.08
23 10 0.38
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TTTAAATTTAAATTTAATATAAA
Found at i:56334299 original size:17 final size:17
Alignment explanation
Indices: 56334277--56334319 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
56334267 TTATTAAATT
* *
56334277 TAAATTTAGATTTAATA
1 TAAATTTAAAATTAATA
*
56334294 TAAATTTAAAATTATTA
1 TAAATTTAAAATTAATA
56334311 TAAATTTAA
1 TAAATTTAA
56334320 TTAAATGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
TAAATTTAAAATTAATA
Found at i:56334925 original size:19 final size:19
Alignment explanation
Indices: 56334901--56334941 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
56334891 AGGTCTTCTG
56334901 TATATTAAGTGTATAATAA
1 TATATTAAGTGTATAATAA
* * *
56334920 TATATTTATTGTATATTAA
1 TATATTAAGTGTATAATAA
56334939 TAT
1 TAT
56334942 TTACCTCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (19 bp):
TATATTAAGTGTATAATAA
Found at i:56335101 original size:15 final size:15
Alignment explanation
Indices: 56335081--56335112 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
56335071 AATTTTTTAG
56335081 TAATAATAATAGCAA
1 TAATAATAATAGCAA
*
56335096 TAATAATAATATCAA
1 TAATAATAATAGCAA
56335111 TA
1 TA
56335113 GCATTAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.31
Consensus pattern (15 bp):
TAATAATAATAGCAA
Found at i:56336224 original size:30 final size:28
Alignment explanation
Indices: 56336182--56336252 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 28
56336172 GGACTGTCTG
* *
56336182 AAAAGTACATTTTGGCCCCAAAACTTTTT
1 AAAATTACATTTT-ACCCCAAAACTTTTT
*
56336211 AAAATTACTATTTTACCCCTAAACTTTTT
1 AAAATTAC-ATTTTACCCCAAAACTTTTT
*
56336240 AAAATTCCATTTT
1 AAAATTACATTTT
56336253 TAATCCCGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 5 0.14
29 27 0.73
30 5 0.14
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (28 bp):
AAAATTACATTTTACCCCAAAACTTTTT
Found at i:56336283 original size:59 final size:58
Alignment explanation
Indices: 56336211--56336405 Score: 198
Period size: 59 Copynumber: 3.3 Consensus size: 58
56336201 AAAACTTTTT
*
56336211 AAAATTACTATTTTACCCCTAAACTTTTTAAAATTCCATTTTTAATCCCGATTTCACCA
1 AAAATTACCATTTTACCCCTAAA-TTTTTAAAATTCCATTTTTAATCCCGATTTCACCA
* * * * ** *
56336270 AAAATTACCATTTTACCCTTAAATTTTCTAATATTTCATTTCT-ATCCTTAATTTCATC-
1 AAAATTACCATTTTACCCCTAAATTTT-TAAAATTCCATTTTTAATCC-CGATTTCACCA
* ** * * *
56336328 AAAATTACCATTCTACCACCCGAATTTCTAAAAATCCCA-TTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACC-CCTAAATTT-TTAAAATTCCATTTTTAATCCCGATTTCACCA
56336387 AAAATTACCATTTTACCCC
1 AAAATTACCATTTTACCCC
56336406 CGAACTTCTA
Statistics
Matches: 108, Mismatches: 22, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
58 36 0.33
59 71 0.66
60 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.38
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCTAAATTTTTAAAATTCCATTTTTAATCCCGATTTCACCA
Found at i:56336360 original size:29 final size:28
Alignment explanation
Indices: 56336319--56336418 Score: 85
Period size: 30 Copynumber: 3.4 Consensus size: 28
56336309 TTCTATCCTT
*
56336319 AATTTCATCAAAATTACCATTCTACCACCCG
1 AATTTC-T-AAAATTACCATTTTACC-CCCG
* * *
56336350 AATTTCTAAAAATCCCATTTTAACCCCG
1 AATTTCTAAAATTACCATTTTACCCCCG
*
56336378 -ATTTCACCAAAAATTACCATTTTACCCCCG
1 AATTT---CTAAAATTACCATTTTACCCCCG
*
56336408 AACTTCTAAAA
1 AATTTCTAAAA
56336419 ATCTCGTTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
27 4 0.07
28 9 0.16
29 13 0.24
30 20 0.36
31 9 0.16
ACGTcount: A:0.37, C:0.30, G:0.03, T:0.30
Consensus pattern (28 bp):
AATTTCTAAAATTACCATTTTACCCCCG
Found at i:56336419 original size:29 final size:29
Alignment explanation
Indices: 56336319--56336420 Score: 100
Period size: 29 Copynumber: 3.4 Consensus size: 29
56336309 TTCTATCCTT
* *
56336319 AATTTCATCAAAATTACCATTCTACCACCCG
1 AATTTC-TAAAAATTACCATTTTACC-CCCG
* *
56336350 AATTTCTAAAAA-TCCCATTTTAACCCCG
1 AATTTCTAAAAATTACCATTTTACCCCCG
*
56336378 -ATTTCACCAAAAATTACCATTTTACCCCCG
1 AATTT--CTAAAAATTACCATTTTACCCCCG
*
56336408 AACTTCTAAAAAT
1 AATTTCTAAAAAT
56336421 CTCGTTTTTG
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
27 4 0.07
28 4 0.07
29 22 0.38
30 19 0.33
31 9 0.16
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.30
Consensus pattern (29 bp):
AATTTCTAAAAATTACCATTTTACCCCCG
Found at i:56336448 original size:117 final size:118
Alignment explanation
Indices: 56336240--56336456 Score: 271
Period size: 117 Copynumber: 1.8 Consensus size: 118
56336230 TAAACTTTTT
* * ** * * *
56336240 AAAATTCCATTTTTAATCCCGATTTCACCAAAAATTACCATTTTACCCTTAAATTTTCTAATATT
1 AAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAATCTTCTAAAATC
* *
56336305 TCATTTCTATCCTTAATTTCATCAAAATTACCATTCTACCACCCGAATTTCTA
66 TCATTTCTATCCTTAATTTAACCAAAATTACCATTCTACCACCCGAATTTCTA
*
56336358 AAAATCCCA-TTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAA-CTTCTAAAAAT
1 AAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAATCTTCT-AAAAT
* *
56336421 CTCGTTTTTGAT-C-TAATTTAAACCAAAATTACCATT
65 CTCATTTCT-ATCCTTAATTT-AACCAAAATTACCATT
56336457 TTGCCATCGG
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
116 10 0.12
117 64 0.76
118 10 0.12
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (118 bp):
AAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAATCTTCTAAAATC
TCATTTCTATCCTTAATTTAACCAAAATTACCATTCTACCACCCGAATTTCTA
Found at i:56339610 original size:31 final size:34
Alignment explanation
Indices: 56339554--56339623 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 34
56339544 CCGAAGGTCC
56339554 GCCCGAAAAATGGGAGGATTTGGATAAAAATAT-AG
1 GCCCGAAAAAT-GGAGGATTTGGATAAAAA-ATGAG
56339589 GCCCGAAAAAT-G-GG-TTTGGATAAAAAATGAG
1 GCCCGAAAAATGGAGGATTTGGATAAAAAATGAG
56339620 GCCC
1 GCCC
56339624 ATTTTTCTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
30 2 0.06
31 18 0.53
32 2 0.06
33 1 0.03
35 11 0.32
ACGTcount: A:0.40, C:0.13, G:0.29, T:0.19
Consensus pattern (34 bp):
GCCCGAAAAATGGAGGATTTGGATAAAAAATGAG
Found at i:56339778 original size:22 final size:20
Alignment explanation
Indices: 56339737--56339800 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
56339727 TGGTGCTTTT
56339737 TTTTTTTACTGTTTTGGTTG
1 TTTTTTTACTGTTTTGGTTG
* *
56339757 TTGTTTTTGCTTTTTTGTGTTG
1 TT-TTTTTACTGTTTTG-GTTG
*
56339779 -TTTTTTACTATTTTGGTT-
1 TTTTTTTACTGTTTTGGTTG
56339797 TTTT
1 TTTT
56339801 ATTGTTTTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
19 6 0.16
20 14 0.38
21 13 0.35
22 4 0.11
ACGTcount: A:0.05, C:0.05, G:0.17, T:0.73
Consensus pattern (20 bp):
TTTTTTTACTGTTTTGGTTG
Found at i:56339799 original size:16 final size:16
Alignment explanation
Indices: 56339778--56339812 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
56339768 TTTTTGTGTT
56339778 GTTTTTTACTATTTTG
1 GTTTTTTACTATTTTG
* *
56339794 GTTTTTTATTGTTTTG
1 GTTTTTTACTATTTTG
56339810 GTT
1 GTT
56339813 GCTGTTTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.03, G:0.17, T:0.71
Consensus pattern (16 bp):
GTTTTTTACTATTTTG
Found at i:56339807 original size:57 final size:60
Alignment explanation
Indices: 56339738--56339853 Score: 157
Period size: 57 Copynumber: 2.0 Consensus size: 60
56339728 GGTGCTTTTT
*
56339738 TTTTTTACTGTTTTGGTTGTTGTTTT-TGCTTTTTTG-TGTT-GTTTTTTACTATTTTGG
1 TTTTTTACTGTTTTGGTTGCTGTTTTCTGCTTTTTTGTTGTTAGTTTTTTACTATTTTGG
* * * *
56339795 TTTTTTATTGTTTTGGTTGCTGTTTTCGTGTTTTTTTGTTGTTATTTTTTTGCTATTTT
1 TTTTTTACTGTTTTGGTTGCTGTTTTC-TGCTTTTTTGTTGTTAGTTTTTTACTATTTT
56339854 TATTGTTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
57 24 0.48
59 9 0.18
60 4 0.08
61 13 0.26
ACGTcount: A:0.05, C:0.05, G:0.18, T:0.72
Consensus pattern (60 bp):
TTTTTTACTGTTTTGGTTGCTGTTTTCTGCTTTTTTGTTGTTAGTTTTTTACTATTTTGG
Found at i:56339820 original size:28 final size:28
Alignment explanation
Indices: 56339738--56339834 Score: 74
Period size: 28 Copynumber: 3.4 Consensus size: 28
56339728 GGTGCTTTTT
* * *
56339738 TTTTTTACTGTTTTGGTTGTTGTTTTTGCT
1 TTTTTTATTGTTTTGGTTGCTG-TTTTG-G
* * *
56339768 TTTTTGTGTTGTTTT--TTACTATTTTGG
1 TTTTT-TATTGTTTTGGTTGCTGTTTTGG
*
56339795 TTTTTTATTGTTTTGGTTGCTGTTTTCG
1 TTTTTTATTGTTTTGGTTGCTGTTTTGG
56339823 TGTTTTT-TTGTT
1 T-TTTTTATTGTT
56339835 GTTATTTTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
26 8 0.15
27 5 0.09
28 20 0.38
29 8 0.15
30 5 0.09
31 7 0.13
ACGTcount: A:0.04, C:0.05, G:0.20, T:0.71
Consensus pattern (28 bp):
TTTTTTATTGTTTTGGTTGCTGTTTTGG
Found at i:56339837 original size:11 final size:11
Alignment explanation
Indices: 56339823--56339903 Score: 56
Period size: 11 Copynumber: 7.1 Consensus size: 11
56339813 GCTGTTTTCG
56339823 TGTTTTTTTGT
1 TGTTTTTTTGT
56339834 TGTTATTTTT-T
1 TGTT-TTTTTGT
* *
56339845 TGCTATTTTTAT
1 TG-TTTTTTTGT
*
56339857 TGTTTTTAATGT
1 TGTTTTT-TTGT
**
56339869 TGTTTTGCTGT
1 TGTTTTTTTGT
*
56339880 TGTTTGTTTGT
1 TGTTTTTTTGT
*
56339891 TATTTTTGTTGT
1 TGTTTTT-TTGT
56339903 T
1 T
56339904 TGAATGTTAT
Statistics
Matches: 54, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
11 32 0.59
12 22 0.41
ACGTcount: A:0.07, C:0.02, G:0.17, T:0.73
Consensus pattern (11 bp):
TGTTTTTTTGT
Found at i:56339837 original size:31 final size:30
Alignment explanation
Indices: 56339737--56339837 Score: 86
Period size: 31 Copynumber: 3.4 Consensus size: 30
56339727 TGGTGCTTTT
* *
56339737 TTTTTTTACTGTTTTGGTTGTTGTTTT-TG
1 TTTTTTTATTGTTTTGGTTGCTGTTTTGTG
* * *
56339766 CTTTTTTGTGTTGTTTT--TTACTATTTTG-G
1 -TTTTTT-TATTGTTTTGGTTGCTGTTTTGTG
56339795 -TTTTTTATTGTTTTGGTTGCTGTTTTCGTG
1 TTTTTTTATTGTTTTGGTTGCTGTTTT-GTG
*
56339825 TTTTTTTGTTGTT
1 TTTTTTTATTGTT
56339838 ATTTTTTTGC
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
26 8 0.15
27 5 0.09
28 8 0.15
29 9 0.16
30 7 0.13
31 18 0.33
ACGTcount: A:0.04, C:0.05, G:0.20, T:0.71
Consensus pattern (30 bp):
TTTTTTTATTGTTTTGGTTGCTGTTTTGTG
Found at i:56339896 original size:43 final size:43
Alignment explanation
Indices: 56339823--56339904 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
56339813 GCTGTTTTCG
* * *
56339823 TGTTTTTTTGTTGTTATTTTTTTGCTATTTTTATTGTTTTTAA
1 TGTTGTTTTGCTGTTATTTGTTTGCTATTTTTATTGTTTTTAA
* * *
56339866 TGTTGTTTTGCTGTTGTTTGTTTGTTATTTTTGTTGTTT
1 TGTTGTTTTGCTGTTATTTGTTTGCTATTTTTATTGTTT
56339905 GAATGTTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.07, C:0.02, G:0.17, T:0.73
Consensus pattern (43 bp):
TGTTGTTTTGCTGTTATTTGTTTGCTATTTTTATTGTTTTTAA
Found at i:56339902 original size:20 final size:20
Alignment explanation
Indices: 56339848--56339917 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
56339838 ATTTTTTTGC
* *
56339848 TATTTTTATTGTTTTTAATGT
1 TATTTTTGTTG-TTTGAATGT
* **
56339869 TGTTTTGCTGTTGTTTGTTTGT
1 TATTTT--TGTTGTTTGAATGT
56339891 TATTTTTGTTGTTTGAATGT
1 TATTTTTGTTGTTTGAATGT
56339911 TATTTTT
1 TATTTTT
56339918 TTATGCGTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
20 19 0.49
21 5 0.13
22 11 0.28
23 4 0.10
ACGTcount: A:0.11, C:0.01, G:0.17, T:0.70
Consensus pattern (20 bp):
TATTTTTGTTGTTTGAATGT
Found at i:56340940 original size:2 final size:2
Alignment explanation
Indices: 56340935--56340959 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56340925 AAAAAAAAAT
56340935 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 T
56340960 TTAATTTAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56341066 original size:16 final size:16
Alignment explanation
Indices: 56341045--56341077 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
56341035 GAGTCTTCTC
56341045 AAGTAGGAGCATTCAA
1 AAGTAGGAGCATTCAA
*
56341061 AAGTAGGAGCGTTCAA
1 AAGTAGGAGCATTCAA
56341077 A
1 A
56341078 CGGTTAATCA
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:0.42, C:0.12, G:0.27, T:0.18
Consensus pattern (16 bp):
AAGTAGGAGCATTCAA
Found at i:56348713 original size:9 final size:9
Alignment explanation
Indices: 56348678--56348730 Score: 51
Period size: 8 Copynumber: 6.3 Consensus size: 9
56348668 GTATTCTATA
*
56348678 TTTAGAATT
1 TTTATAATT
*
56348687 TTTAGAATT
1 TTTATAATT
*
56348696 TGTAT--TT
1 TTTATAATT
56348703 TTTATAA-T
1 TTTATAATT
56348711 TTTATAATT
1 TTTATAATT
56348720 TTT-TAATT
1 TTTATAATT
56348728 TTT
1 TTT
56348731 TCATGACACG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
7 6 0.16
8 16 0.42
9 16 0.42
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (9 bp):
TTTATAATT
Found at i:56350482 original size:24 final size:24
Alignment explanation
Indices: 56350422--56350483 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
56350412 AAAAATTTTA
56350422 AAAATTATTAATAAACTTTATTATT
1 AAAATTA-TAATAAACTTTATTATT
* * *
56350447 AAAATAAGAATAAAGTTTATTA-T
1 AAAATTATAATAAACTTTATTATT
56350470 AATAATTATAATAA
1 AA-AATTATAATAA
56350484 TTAAATACAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 3 0.10
24 22 0.71
25 6 0.19
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (24 bp):
AAAATTATAATAAACTTTATTATT
Found at i:56365547 original size:58 final size:58
Alignment explanation
Indices: 56365462--56365576 Score: 196
Period size: 58 Copynumber: 2.0 Consensus size: 58
56365452 AAAGGAGTTG
*
56365462 TTTATGAGTGTTATTTAGGAATAAAATTATATTTGGGTTTAAAAATATTTGGGTTTAA
1 TTTATGAGTGTTATTTAAGAATAAAATTATATTTGGGTTTAAAAATATTTGGGTTTAA
*
56365520 TTTATGAGTGTT-TTTGAAGAATGAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
1 TTTATGAGTGTTATTT-AAGAATAAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
56365577 GTTTGTTGAT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
57 3 0.06
58 51 0.94
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (58 bp):
TTTATGAGTGTTATTTAAGAATAAAATTATATTTGGGTTTAAAAATATTTGGGTTTAA
Found at i:56369775 original size:27 final size:28
Alignment explanation
Indices: 56369718--56369776 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
56369708 AGATTTGAAC
**
56369718 TTAAAATGTTTAAAATTAACTTGTTGAT
1 TTAAAATGTTTAAAATTAACTTACTGAT
* * *
56369746 TTAAAA-GTTTAAATTTAAGTTACTGTT
1 TTAAAATGTTTAAAATTAACTTACTGAT
56369773 TTAA
1 TTAA
56369777 GTTGTTAGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.47
Consensus pattern (28 bp):
TTAAAATGTTTAAAATTAACTTACTGAT
Found at i:56372565 original size:69 final size:69
Alignment explanation
Indices: 56372454--56372672 Score: 294
Period size: 69 Copynumber: 3.0 Consensus size: 69
56372444 AAAGTAGTTA
56372454 AAATCACAATGTGAACCAAAGGAATTTTTAAAACATCAATAAAAAGGAAGACTGTATTCTTAATG
1 AAATCACAATGTGAACCAAAGGAATTTTTAAAACATCAATAAAAAGGAAGACTGTATTCTTAATG
56372519 AATG
66 AATG
* * *
56372523 AAATCACAATGTGAACCAACGGAAGTTTTAAAACATCAATAAAAAGGAAGACTGGATTCTTAATG
1 AAATCACAATGTGAACCAAAGGAATTTTTAAAACATCAATAAAAAGGAAGACTGTATTC-T--T-
56372588 AATGAAAGTAG
62 AATG-AA-T-G
** *
56372599 TTAAAATCACAATGTGAACCAAAGGAATTTTTAAAACATCAATAAAAAGGAAGACAATAATCTTA
1 ---AAATCACAATGTGAACCAAAGGAATTTTTAAAACATCAATAAAAAGGAAGACTGTATTCTTA
56372664 ATGAATG
63 ATGAATG
56372671 AA
1 AA
56372673 CGATGTACGT
Statistics
Matches: 131, Mismatches: 9, Indels: 20
0.82 0.06 0.12
Matches are distributed among these distances:
69 58 0.44
70 1 0.01
72 2 0.02
73 5 0.04
74 4 0.03
75 5 0.04
76 2 0.02
78 1 0.01
79 53 0.40
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.24
Consensus pattern (69 bp):
AAATCACAATGTGAACCAAAGGAATTTTTAAAACATCAATAAAAAGGAAGACTGTATTCTTAATG
AATG
Found at i:56372663 original size:79 final size:79
Alignment explanation
Indices: 56372523--56372672 Score: 246
Period size: 79 Copynumber: 1.9 Consensus size: 79
56372513 TTAATGAATG
* ** *
56372523 AAATCACAATGTGAACCAACGGAAGTTTTAAAACATCAATAAAAAGGAAGACTGGATTCTTAATG
1 AAATCACAATGTGAACCAAAGGAAGTTTTAAAACATCAATAAAAAGGAAGACAAGAATCTTAATG
56372588 AATGAAAGTAGTTA
66 AATGAAAGTAGTTA
* *
56372602 AAATCACAATGTGAACCAAAGGAATTTTTAAAACATCAATAAAAAGGAAGACAATAATCTTAATG
1 AAATCACAATGTGAACCAAAGGAAGTTTTAAAACATCAATAAAAAGGAAGACAAGAATCTTAATG
56372667 AATGAA
66 AATGAA
56372673 CGATGTACGT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 65 1.00
ACGTcount: A:0.50, C:0.11, G:0.15, T:0.23
Consensus pattern (79 bp):
AAATCACAATGTGAACCAAAGGAAGTTTTAAAACATCAATAAAAAGGAAGACAAGAATCTTAATG
AATGAAAGTAGTTA
Found at i:56394075 original size:22 final size:23
Alignment explanation
Indices: 56394050--56394098 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
56394040 GTAACAAAAT
*
56394050 TAATAAT-AAAACAATAATTATA
1 TAATAATCAAAACAATAATAATA
*
56394072 TAAT-ATCCAAACAATAATAATA
1 TAATAATCAAAACAATAATAATA
*
56394094 AAATA
1 TAATA
56394099 GTATTAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (23 bp):
TAATAATCAAAACAATAATAATA
Found at i:56395178 original size:21 final size:20
Alignment explanation
Indices: 56395152--56395195 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
56395142 CTTAATTTTT
56395152 AAAAAATT-TAAAAATTCATAA
1 AAAAAATTAT-AAAATT-ATAA
56395173 AAAAAATTATAAAATTATAA
1 AAAAAATTATAAAATTATAA
56395193 AAA
1 AAA
56395196 TTATTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.32
21 14 0.64
22 1 0.05
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAAAATTATAAAATTATAA
Found at i:56395205 original size:20 final size:20
Alignment explanation
Indices: 56395157--56395219 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
56395147 TTTTTAAAAA
* **
56395157 ATTTAAAAATTCATAAAAAAA
1 ATTTTAAAATT-ATAAAAATT
*
56395178 ATTATAAAATTATAAAAATT
1 ATTTTAAAATTATAAAAATT
*
56395198 ATTTTAAAAGTA-AAAGAATT
1 ATTTTAAAATTATAAA-AATT
56395218 AT
1 AT
56395220 AAATAATAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
19 3 0.09
20 23 0.66
21 9 0.26
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (20 bp):
ATTTTAAAATTATAAAAATT
Found at i:56399909 original size:9 final size:9
Alignment explanation
Indices: 56399895--56399933 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
56399885 CAATTAACTT
56399895 TATTTAAAA
1 TATTTAAAA
56399904 TATTTAAAA
1 TATTTAAAA
56399913 TATTTAAAA
1 TATTTAAAA
*
56399922 TAATT-AAA
1 TATTTAAAA
56399930 TATT
1 TATT
56399934 AATTATAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
8 6 0.21
9 22 0.79
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
TATTTAAAA
Found at i:56400865 original size:22 final size:22
Alignment explanation
Indices: 56400821--56400887 Score: 57
Period size: 21 Copynumber: 3.0 Consensus size: 22
56400811 ATGTAATATT
* *
56400821 TATATCAAGTATATAATTCAAATA
1 TATAT-AATTATAT-ATTTAAATA
*
56400845 TATATAATTATATATTTAAATT
1 TATATAATTATATATTTAAATA
*
56400867 TATA-AATGT-TATATTTTAATA
1 TATATAAT-TATATATTTAAATA
56400888 CAGTTTAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
21 13 0.35
22 12 0.32
23 7 0.19
24 5 0.14
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (22 bp):
TATATAATTATATATTTAAATA
Found at i:56402725 original size:16 final size:16
Alignment explanation
Indices: 56402690--56402731 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
56402680 TATATTTTTT
*
56402690 ATATAATATAAATTAA
1 ATATTATATAAATTAA
56402706 ATATTATATAAA-TAA
1 ATATTATATAAATTAA
56402721 CATATT-TATAA
1 -ATATTATATAA
56402732 TTTTTGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATTATATAAATTAA
Found at i:56403641 original size:6 final size:6
Alignment explanation
Indices: 56403630--56403656 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
56403620 TATGAGATAC
56403630 GAGAGT GAGAGT GAGAGT GAGAGT GAG
1 GAGAGT GAGAGT GAGAGT GAGAGT GAG
56403657 TTTGAATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.52, T:0.15
Consensus pattern (6 bp):
GAGAGT
Found at i:56405040 original size:42 final size:42
Alignment explanation
Indices: 56404971--56405063 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
56404961 ATCGTGTACC
* * *
56404971 AGACTGTGTAATTCACTAACTTGGGTCACAC-AGCCATGTCAT
1 AGACCGTGTAACTCACTAACTTAGGTCACACGA-CCATGTCAT
* * * *
56405013 AGACCGTGTAACTCAGTGACTTAGGTCACACGATCGTGTCAT
1 AGACCGTGTAACTCACTAACTTAGGTCACACGACCATGTCAT
56405055 AGACCGTGT
1 AGACCGTGT
56405064 GCCAGACTGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 42 0.98
43 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.27
Consensus pattern (42 bp):
AGACCGTGTAACTCACTAACTTAGGTCACACGACCATGTCAT
Found at i:56407707 original size:22 final size:20
Alignment explanation
Indices: 56407663--56407719 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 20
56407653 TTATATTTTT
* *
56407663 AAAAAATTATAAAAATTTCTAA
1 AAAAAATT-TAAAAATATAT-A
56407685 AAAAAATTCTAAAAATATATA
1 AAAAAATT-TAAAAATATATA
*
56407706 AAGAAATTTAAAAA
1 AAAAAATTTAAAAA
56407720 AATGAATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.19
21 8 0.26
22 17 0.55
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (20 bp):
AAAAAATTTAAAAATATATA
Found at i:56410768 original size:14 final size:15
Alignment explanation
Indices: 56410738--56410771 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
56410728 TTGAGAGAGG
*
56410738 TAATTTTTTTATTTT
1 TAATTTTTTTATATT
56410753 TAATTTTTTTA-ATT
1 TAATTTTTTTATATT
56410767 TAATT
1 TAATT
56410772 ATTAGTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TAATTTTTTTATATT
Found at i:56410905 original size:10 final size:10
Alignment explanation
Indices: 56410890--56410917 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
56410880 TTGTTGTTGT
56410890 TTTTAATTTA
1 TTTTAATTTA
56410900 TTTTAATTTA
1 TTTTAATTTA
56410910 TTTTAATT
1 TTTTAATT
56410918 ATTCTAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTAATTTA
Found at i:56411126 original size:141 final size:139
Alignment explanation
Indices: 56410780--56411143 Score: 391
Period size: 141 Copynumber: 2.5 Consensus size: 139
56410770 TTATTAGTTT
* * * *
56410780 AGTTTAGTTTAGTTTAATGTATATGATTTGTTTGTTACAATTTTTTTTGTTTAGTAGAATAAATT
1 AGTTTAGTTTAGTTTAATGTTTATGATTTG-TT-ATA-AA-TTTTTTTGTTTAGTAGAGTAGATT
* * *
56410845 AAAGTGAAAAGAAAGCTAAAAGAAAGTTAATTTTGTTGTTGTTGTTTTTAATTTATTTTAATTTA
62 AAAG-GAAAAGAAAGCTAAAAGAAAGGTAA-TTTGTTGTTGTTGTTTTAAATTTATTTTAAATTA
56410910 TTTTAATTATTCTAA
125 TTTTAATTATTCTAA
56410925 AGTTTAGTTTAGTTTAATGAATGATTATGATTTGTTAT-AATTTTTTTGTTTAGTAGAGTAGATT
1 AGTTTAGTTTAGTTTAATG--T--TTATGATTTGTTATAAATTTTTTTGTTTAGTAGAGTAGATT
* * *
56410989 AAAGGAAAAAAAAGTTAAAAAGAGAGGTAA-TT-TTGTTGTTGTTTTAAATTTATTTTAAAATTA
62 AAAGGAAAAGAAAGCT-AAAAGAAAGGTAATTTGTTGTTGTTGTTTTAAATTTATTTT-AAATTA
56411052 TTTT-ATT-TT-TAA
125 TTTTAATTATTCTAA
* * *
56411064 TTA-TTATAAAGTTTAGTTTAATGTTTATGATATGTTATAAATTTTTTTCGTTTAATACAGTAGA
1 --AGTT-T--AGTTTAGTTTAATGTTTATGATTTGTTATAAATTTTTTT-GTTTAGTAGAGTAGA
*
56411128 TTAAAGGGAAAGAAAG
60 TTAAAGGAAAAGAAAG
56411144 GCAGGTAATG
Statistics
Matches: 191, Mismatches: 15, Indels: 30
0.81 0.06 0.13
Matches are distributed among these distances:
139 16 0.08
140 13 0.07
141 56 0.29
142 11 0.06
143 24 0.13
144 37 0.19
145 21 0.11
147 2 0.01
148 2 0.01
149 9 0.05
ACGTcount: A:0.35, C:0.01, G:0.15, T:0.48
Consensus pattern (139 bp):
AGTTTAGTTTAGTTTAATGTTTATGATTTGTTATAAATTTTTTTGTTTAGTAGAGTAGATTAAAG
GAAAAGAAAGCTAAAAGAAAGGTAATTTGTTGTTGTTGTTTTAAATTTATTTTAAATTATTTTAA
TTATTCTAA
Found at i:56411275 original size:24 final size:22
Alignment explanation
Indices: 56411217--56411276 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 22
56411207 GTAATTATTA
56411217 TAAATTATTTGTTTAGTTTAATG
1 TAAATTATTT-TTTAGTTTAATG
**
56411240 TTTATGTGATTTTTTAGTTATAAATG
1 TAAAT-T-ATTTTTTAGTT-T-AATG
56411266 TAAATTATTTT
1 TAAATTATTTT
56411277 GTTATTTGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
23 3 0.10
24 13 0.45
25 6 0.21
26 7 0.24
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (22 bp):
TAAATTATTTTTTAGTTTAATG
Found at i:56411412 original size:43 final size:41
Alignment explanation
Indices: 56411365--56411455 Score: 98
Period size: 44 Copynumber: 2.2 Consensus size: 41
56411355 CATTGTTTTG
*
56411365 TTGTTAT-TTATTTATT-TTAAAGTTATTTTGTTTTTAATTAAAT
1 TTGTTATGTGATTTATTATTAAA-TT-TTTTGTTTTT-ATT-AAT
*
56411408 TTGTTTATGTGATTTGTTATTAAATTTTTTGTTTTTATTAAT
1 TTG-TTATGTGATTTATTATTAAATTTTTTGTTTTTATTAAT
56411450 TT-TTAT
1 TTGTTAT
56411456 CGAAATAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
40 4 0.09
42 5 0.12
43 6 0.14
44 14 0.33
45 9 0.21
46 5 0.12
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (41 bp):
TTGTTATGTGATTTATTATTAAATTTTTTGTTTTTATTAAT
Found at i:56416753 original size:30 final size:27
Alignment explanation
Indices: 56416719--56416929 Score: 97
Period size: 30 Copynumber: 7.2 Consensus size: 27
56416709 CAAAATAGTA
56416719 ATTTTTGTTGAAATCGGGGTCGAAAATGGG
1 ATTTTTG-TGAAATCGGGGT--AAAATGGG
* *
56416749 A-TTTTGGGAAGTTCGAGGGTAAAATGGG
1 ATTTTTGTGAA-ATCG-GGGTAAAATGGG
56416777 TATTTTTGGTGAAATCGGGGTTAAAAATGGG
1 -ATTTTT-GTGAAATCGGGG-T-AAAATGGG
* * * *
56416808 A-TTTTGGGAAGTTTGGGGGTAAAATGGTA
1 ATTTTTGTGAA--ATCGGGGTAAAATGG-G
* * *
56416837 ATTTTTGGTAAAATTGAGGTTAAAAT-GG
1 ATTTTT-GTGAAATCG-GGGTAAAATGGG
* *
56416865 AATTTTG-GAAAGTTCAGGGGTAAAATGGTA
1 ATTTTTGTGAAA--TC-GGGGTAAAATGG-G
*
56416895 ATTTTTGATGAAATCGGGGTTAAAAATGGA
1 ATTTTTG-TGAAATCGGGG-T-AAAATGGG
56416925 ATTTT
1 ATTTT
56416930 AGAAAGTTCA
Statistics
Matches: 139, Mismatches: 20, Indels: 44
0.68 0.10 0.22
Matches are distributed among these distances:
26 3 0.02
27 1 0.01
28 36 0.26
29 27 0.19
30 46 0.33
31 22 0.16
32 4 0.03
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.35
Consensus pattern (27 bp):
ATTTTTGTGAAATCGGGGTAAAATGGG
Found at i:56416889 original size:58 final size:59
Alignment explanation
Indices: 56416705--56416959 Score: 327
Period size: 59 Copynumber: 4.3 Consensus size: 59
56416695 TGGATGCCCG
* * * ** * *
56416705 GGGGCAAAATAGTAATTTTTGTTGAAATCGGGGTCGAAAATGGGATTTTGGGAAGTTC-
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCA
* * **
56416763 GAGGGTAAAATGGGT-ATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGGAAGTTTG
1 G-GGGTAAAAT-GGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCA
* * *
56416823 GGGGTAAAATGGTAATTTTTGGTAAAATTGAGGTT-AAAATGGAATTTTGGAAAGTTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCA
* *
56416881 GGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCA
56416940 GGGGTAAAATGGTAATTTTT
1 GGGGTAAAATGGTAATTTTT
56416960 AAATAGTCCA
Statistics
Matches: 174, Mismatches: 18, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
58 54 0.31
59 117 0.67
60 3 0.02
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.33
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCA
Found at i:56416889 original size:117 final size:118
Alignment explanation
Indices: 56416703--56416959 Score: 340
Period size: 117 Copynumber: 2.2 Consensus size: 118
56416693 TTTGGATGCC
* * * * * * *
56416703 CGGGGGCAAAATAGTAATTTTTGTTGAAATCGGGGTCGAAAATGGGATTTTGGGAAGTTCGAGGG
1 CGGGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTCGAAAATGGAATTTTGGAAAGTTCGAGGG
* * * *
56416768 TAAAATGGGT-ATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGGAAGTT
66 TAAAAT-GGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTT
* * *
56416821 TGGGGGTAAAATGGTAATTTTTGGTAAAATTGAGGT-TAAAATGGAATTTTGGAAAGTTC-AGGG
1 CGGGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTCGAAAATGGAATTTTGGAAAGTTCGA-GG
56416884 GTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTT
65 GTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTT
*
56416938 CAGGGGTAAAATGGTAATTTTT
1 CGGGGGTAAAATGGTAATTTTT
56416960 AAATAGTCCA
Statistics
Matches: 121, Mismatches: 16, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
116 4 0.03
117 88 0.73
118 29 0.24
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (118 bp):
CGGGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTCGAAAATGGAATTTTGGAAAGTTCGAGGG
TAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTT
Found at i:56416956 original size:29 final size:29
Alignment explanation
Indices: 56416823--56416958 Score: 122
Period size: 28 Copynumber: 4.7 Consensus size: 29
56416813 GGGAAGTTTG
* * *
56416823 GGGGTAAAATGGTAATTTTTGGTAAAATTGA
1 GGGGTAAAATGGTAA-TTTTAG-AAAGTTCA
* *
56416854 -GGTTAAAATGG-AATTTTGGAAAGTTCA
1 GGGGTAAAATGGTAATTTTAGAAAGTTCA
56416881 GGGGTAAAATGGTAATTTTTGATGAAA--TC-
1 GGGGTAAAATGGTAA-TTTT-A-GAAAGTTCA
56416910 GGGGTTAAAAATGG-AATTTTAGAAAGTTCA
1 GGGG-T-AAAATGGTAATTTTAGAAAGTTCA
56416940 GGGGTAAAATGGTAATTTT
1 GGGGTAAAATGGTAATTTT
56416959 TAAATAGTCC
Statistics
Matches: 89, Mismatches: 5, Indels: 24
0.75 0.04 0.20
Matches are distributed among these distances:
27 10 0.11
28 24 0.27
29 21 0.24
30 23 0.26
31 7 0.08
32 4 0.04
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTAGAAAGTTCA
Found at i:56416972 original size:30 final size:29
Alignment explanation
Indices: 56416823--56416960 Score: 117
Period size: 30 Copynumber: 4.7 Consensus size: 29
56416813 GGGAAGTTTG
* * *
56416823 GGGGTAAAATGGTAATTTTTGGTAAAATTGA
1 GGGGTAAAATGG-AATTTTTAG-AAAGTTCA
* *
56416854 -GGTTAAAATGGAA-TTTTGGAAAGTTCA
1 GGGGTAAAATGGAATTTTTAGAAAGTTCA
56416881 GGGGTAAAATGGTAATTTTTGATGAAA--TC-
1 GGGGTAAAATGG-AATTTTT-A-GAAAGTTCA
56416910 GGGGTTAAAAATGGAA-TTTTAGAAAGTTCA
1 GGGG-T-AAAATGGAATTTTTAGAAAGTTCA
56416940 GGGGTAAAATGGTAATTTTTA
1 GGGGTAAAATGG-AATTTTTA
56416961 AATAGTCCAG
Statistics
Matches: 90, Mismatches: 5, Indels: 25
0.75 0.04 0.21
Matches are distributed among these distances:
27 10 0.11
28 24 0.27
29 17 0.19
30 28 0.31
31 7 0.08
32 4 0.04
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (29 bp):
GGGGTAAAATGGAATTTTTAGAAAGTTCA
Found at i:56418791 original size:17 final size:18
Alignment explanation
Indices: 56418769--56418816 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
56418759 TTATCTGGAC
*
56418769 ATTT-AATTTTATTTTAA
1 ATTTAAATTTTATATTAA
56418786 ATTTAAATTTT-TATTAA
1 ATTTAAATTTTATATTAA
*
56418803 GTTTAAATTTTATA
1 ATTTAAATTTTATA
56418817 AAAACTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 19 0.70
18 8 0.30
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
ATTTAAATTTTATATTAA
Found at i:56420629 original size:15 final size:15
Alignment explanation
Indices: 56420609--56420643 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
56420599 AGTAACAAAC
56420609 CATGTGTATATAACT
1 CATGTGTATATAACT
56420624 CATGTGTATATAACT
1 CATGTGTATATAACT
56420639 CATGT
1 CATGT
56420644 ACTTTGATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (15 bp):
CATGTGTATATAACT
Found at i:56432556 original size:2 final size:2
Alignment explanation
Indices: 56432549--56432582 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
56432539 TCTACTGTTT
56432549 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
56432583 GGTTTTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:56436447 original size:24 final size:22
Alignment explanation
Indices: 56436394--56436455 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 22
56436384 AAAACTATAT
*
56436394 AATAATTCATAAAAATTTATAAA
1 AATAATTC-TAAAAATTAATAAA
*
56436417 AAT-ATTCTAAAAATTAAAATTAA
1 AATAATTCTAAAAATT--AATAAA
*
56436440 AATAATTCTAACAATT
1 AATAATTCTAAAAATT
56436456 TTACAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 8 0.24
22 4 0.12
23 10 0.30
24 11 0.33
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (22 bp):
AATAATTCTAAAAATTAATAAA
Found at i:56436671 original size:28 final size:26
Alignment explanation
Indices: 56436591--56436700 Score: 78
Period size: 28 Copynumber: 4.0 Consensus size: 26
56436581 TTTTATAAAT
* * *
56436591 AATTGCAATATTT-TTATTTTTTTATAA
1 AATTGAAATATTTATTAATATTTT-T-A
* * *
56436618 AATTTAAATATTTTCTTAATGTTTTTA
1 AATTGAAATA-TTTATTAATATTTTTA
*
56436645 ATTTTGGAAATATTTATTAATATTTTTGA
1 A-ATT-GAAATATTTATTAATATTTTT-A
*
56436674 AATTGAATTGATTTATTAATATTTTTA
1 AATTGAAAT-ATTTATTAATATTTTTA
56436701 TAAATTTTAA
Statistics
Matches: 67, Mismatches: 10, Indels: 12
0.75 0.11 0.13
Matches are distributed among these distances:
27 15 0.22
28 37 0.55
29 15 0.22
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (26 bp):
AATTGAAATATTTATTAATATTTTTA
Found at i:56439016 original size:18 final size:19
Alignment explanation
Indices: 56438976--56439060 Score: 56
Period size: 19 Copynumber: 4.7 Consensus size: 19
56438966 ATAAATTCTT
* * * *
56438976 TTTATAATTTATTAGATTT
1 TTTATAATTTTTTATAATA
56438995 TTTAT-ATTTTTTATAATA
1 TTTATAATTTTTTATAATA
* *
56439013 TTTATAAGTTTATATCAAT-
1 TTTATAATTTTTTAT-AATA
56439032 TTT-T-A-TTTTT-TAATA
1 TTTATAATTTTTTATAATA
56439047 TTTAATAATTTTTT
1 TTT-ATAATTTTTT
56439061 TCTTATTTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
14 3 0.06
15 4 0.08
16 4 0.08
17 2 0.04
18 16 0.31
19 20 0.38
20 3 0.06
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTATAATTTTTTATAATA
Found at i:56444736 original size:2 final size:2
Alignment explanation
Indices: 56444729--56444758 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
56444719 AAACAAAATC
56444729 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
56444759 TAGATTGTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56449158 original size:24 final size:24
Alignment explanation
Indices: 56449097--56449159 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
56449087 TAGACTAATA
* *
56449097 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* ** *
56449121 AAAGTTTATTTGAAACAATTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
56449145 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
56449160 GATTATTTCT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:56451108 original size:24 final size:24
Alignment explanation
Indices: 56451081--56451131 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
56451071 AGTTTGACTC
*
56451081 AAACAAATAAACAGAGTTTATTTG
1 AAACAAATAAACAGAGTTTAATTG
* *
56451105 AAACAATTAAATAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
56451129 AAA
1 AAA
56451132 GATTATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:56456662 original size:14 final size:15
Alignment explanation
Indices: 56456643--56456672 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
56456633 TTGGTAACTA
56456643 AATA-TTTTAATTTT
1 AATATTTTTAATTTT
56456657 AATATTTTTAATTTT
1 AATATTTTTAATTTT
56456672 A
1 A
56456673 TAATATTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
AATATTTTTAATTTT
Found at i:56462947 original size:24 final size:24
Alignment explanation
Indices: 56462920--56462968 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
56462910 TCTCACTTAC
56462920 TAAAAT-AAAAAAATATAAACAAAA
1 TAAAATCAAAAAAA-ATAAACAAAA
* *
56462944 TAAAATCAAAGAAAATAAATAAAA
1 TAAAATCAAAAAAAATAAACAAAA
56462968 T
1 T
56462969 CTGATTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (24 bp):
TAAAATCAAAAAAAATAAACAAAA
Found at i:56463803 original size:15 final size:15
Alignment explanation
Indices: 56463783--56463841 Score: 118
Period size: 15 Copynumber: 3.9 Consensus size: 15
56463773 TAAATTATTT
56463783 AAAATGATTTTTATC
1 AAAATGATTTTTATC
56463798 AAAATGATTTTTATC
1 AAAATGATTTTTATC
56463813 AAAATGATTTTTATC
1 AAAATGATTTTTATC
56463828 AAAATGATTTTTAT
1 AAAATGATTTTTAT
56463842 TTTTAAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (15 bp):
AAAATGATTTTTATC
Found at i:56474426 original size:18 final size:19
Alignment explanation
Indices: 56474381--56474426 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
56474371 ATTGACTAAA
*
56474381 AAAT-TATAAAAAATATTT
1 AAATATATAAAAAATATTC
* *
56474399 AAAAAAATAAAAAA-ATTC
1 AAATATATAAAAAATATTC
56474417 AAATATATAA
1 AAATATATAA
56474427 TGAAGTACAC
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (19 bp):
AAATATATAAAAAATATTC
Found at i:56492741 original size:26 final size:26
Alignment explanation
Indices: 56492707--56492760 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
56492697 CACTATATTC
*
56492707 TAATGTTTACATATT-TAATATTTAAT
1 TAATGTTTAAATATTAT-ATATTTAAT
* *
56492733 TAATTTTTAAATATTATATTTTTAAT
1 TAATGTTTAAATATTATATATTTAAT
56492759 TA
1 TA
56492761 TAACGTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (26 bp):
TAATGTTTAAATATTATATATTTAAT
Found at i:56492949 original size:17 final size:18
Alignment explanation
Indices: 56492917--56492960 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
56492907 TTTTTAACTA
*
56492917 ATAATTATAATTTAAAT-T
1 ATAATTAT-TTTTAAATGT
*
56492935 CTAATTATTTTTAAATGT
1 ATAATTATTTTTAAATGT
56492953 ATAATTAT
1 ATAATTAT
56492961 CATCATTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
ATAATTATTTTTAAATGT
Found at i:56493264 original size:20 final size:20
Alignment explanation
Indices: 56493227--56493264 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
56493217 CAAAATTGCC
*
56493227 TAAATAATATTTTGATTATA
1 TAAATAATATTTAGATTATA
56493247 TAAAT-ATATTTAGTATTA
1 TAAATAATATTTAG-ATTA
56493265 GTTATTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
TAAATAATATTTAGATTATA
Found at i:56494100 original size:23 final size:24
Alignment explanation
Indices: 56494054--56494100 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
56494044 AAATTGCTCT
*
56494054 TCAAAATTTAAAAAAATATAAAAA
1 TCAAAATTAAAAAAAATATAAAAA
*
56494078 TCAAAATTAAAAAAAATCTAAAA
1 TCAAAATTAAAAAAAATATAAAA
56494101 GTTTTCTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.23
Consensus pattern (24 bp):
TCAAAATTAAAAAAAATATAAAAA
Found at i:56495771 original size:23 final size:23
Alignment explanation
Indices: 56495745--56495886 Score: 120
Period size: 23 Copynumber: 6.4 Consensus size: 23
56495735 AGTGCTGGGC
56495745 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
56495768 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
*
56495787 -AC--TGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
** *
56495807 ATTAGAGAGCACACGAAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
* * * *
56495831 TAACAAAGAGCACATACAGTGCTG
1 -AACAGAGAGCACACAAAGTGCTA
*
56495855 AACAGAG-GCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
56495877 AACAGAGAGC
1 AACAGAGAGC
56495887 GCGCAAGTGT
Statistics
Matches: 92, Mismatches: 17, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
16 10 0.11
18 3 0.03
19 1 0.01
20 1 0.01
21 1 0.01
22 20 0.22
23 39 0.42
24 1 0.01
25 16 0.17
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:56495805 original size:39 final size:39
Alignment explanation
Indices: 56495751--56495825 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
56495741 GGGCAACAGA
*
56495751 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
** *
56495790 GAGCACACAAAGTGCTAATTAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
56495826 GCTAATAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:56495895 original size:22 final size:22
Alignment explanation
Indices: 56495792--56495883 Score: 78
Period size: 22 Copynumber: 4.0 Consensus size: 22
56495782 AAAGTACTGA
* **
56495792 GCACACAAAGTGCTAATTAGAG
1 GCACACACAGTGCTAAACAGAG
*
56495814 AGCACACGA-AGTGCTAATAACAAAG
1 -GCACAC-ACAGTGCT-A-AACAGAG
* *
56495839 AGCACATACAGTGCTGAACAGAG
1 -GCACACACAGTGCTAAACAGAG
56495862 GCACACACAGTGCTAAACAGAG
1 GCACACACAGTGCTAAACAGAG
56495884 AGCGCGCAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
22 20 0.35
23 18 0.32
24 3 0.05
25 16 0.28
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (22 bp):
GCACACACAGTGCTAAACAGAG
Found at i:56500696 original size:18 final size:18
Alignment explanation
Indices: 56500669--56500708 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
56500659 TATCAAGGAA
*
56500669 ATATACATTTATATATAT
1 ATATACATTTATATACAT
* *
56500687 ATATATATTTGTATACAT
1 ATATACATTTATATACAT
56500705 ATAT
1 ATAT
56500709 TTGATAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (18 bp):
ATATACATTTATATACAT
Done.