Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008136.1 Corchorus capsularis cultivar CVL-1 contig08157, 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: 112207
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--61 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
43 TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC T
62 TTTTCCTTAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:4167 original size:31 final size:31
Alignment explanation
Indices: 4098--4260 Score: 137
Period size: 31 Copynumber: 5.5 Consensus size: 31
4088 TCCTTTTGTT
* * * **
4098 CACGTGGCATGCCACGTGCCATTTTTTGAAA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* *
4129 CATGTGGCATGCCACGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* *
4160 CACGTGGCGTGACATGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* *
4191 CA--T---GTGGCAC--G--ACTTTTTGATA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* *
4213 CATGTGGCGTGCCACATGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
*
4244 CACGTGGCGTGTCACGT
1 CACGTGGCGTGCCACGT
4261 CGGACACCGT
Statistics
Matches: 106, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
22 12 0.11
24 2 0.02
26 5 0.05
27 6 0.06
29 2 0.02
31 79 0.75
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.33
Consensus pattern (31 bp):
CACGTGGCGTGCCACGTGTCACTTTTTGGTA
Found at i:4233 original size:53 final size:53
Alignment explanation
Indices: 4149--4251 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
4139 GCCACGTGTC
* ** *
4149 ACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGATACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
* *
4202 ACTTTTTGATACATGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGC
1 ACTTTTTGATACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGC
4252 GTGTCACGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.36
Consensus pattern (53 bp):
ACTTTTTGATACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
Found at i:9741 original size:117 final size:119
Alignment explanation
Indices: 9602--9835 Score: 366
Period size: 118 Copynumber: 2.0 Consensus size: 119
9592 ATCTTATTTT
9602 AGCAAACTGTTTTTCTTCTTAAATTTTAGGAATTATGC-AGCCAACC-TTTTTTATAAACCAAAT
1 AGCAAACTGTTTTTCTTCTTAAATTTTAGGAATTATGCAAG-CAACCGTTTTTTATAAACCAAAT
*
9665 GCTATAATCAGAAATAGGAAATTCAGTTTTATGAGAAGTAGGAAACGTGAGTAGC
65 GCTATAATCAGAAATAGGAAATTCAGTTTTATGACAAGTAGGAAACGTGAGTAGC
* * *
9720 AGCAAACT-TTTTTCTTCTTAAATTTTAGGAATTATGCAAGCAACCGTTTTTTGTATATCAAATG
1 AGCAAACTGTTTTTCTTCTTAAATTTTAGGAATTATGCAAGCAACCGTTTTTTATAAACCAAATG
* * * *
9784 CTATAATCAGAAATGGGAATTTGAGTTTTATGACAAGTGGGAAACGTGAGTA
66 CTATAATCAGAAATAGGAAATTCAGTTTTATGACAAGTAGGAAACGTGAGTA
9836 AAGAGAAATA
Statistics
Matches: 106, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
117 34 0.32
118 72 0.68
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (119 bp):
AGCAAACTGTTTTTCTTCTTAAATTTTAGGAATTATGCAAGCAACCGTTTTTTATAAACCAAATG
CTATAATCAGAAATAGGAAATTCAGTTTTATGACAAGTAGGAAACGTGAGTAGC
Found at i:9903 original size:19 final size:20
Alignment explanation
Indices: 9879--9925 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
9869 GATACTTCTT
9879 AGAGAT-TAAA-AAAGGATAA
1 AGAGATATAAATAAAGG-TAA
9898 AGAGATGATAAATAAAGGTAA
1 AGAGAT-ATAAATAAAGGTAA
9919 AGA-ATAT
1 AGAGATAT
9926 GAATTAATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 8 0.32
20 2 0.08
21 10 0.40
22 5 0.20
ACGTcount: A:0.60, C:0.00, G:0.21, T:0.19
Consensus pattern (20 bp):
AGAGATATAAATAAAGGTAA
Found at i:10636 original size:17 final size:17
Alignment explanation
Indices: 10614--10649 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
10604 GCCAACACTA
10614 AAGTAAAACTCTTTGTT
1 AAGTAAAACTCTTTGTT
10631 AAGTAAAACTCTTTGTT
1 AAGTAAAACTCTTTGTT
10648 AA
1 AA
10650 TAACTCTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (17 bp):
AAGTAAAACTCTTTGTT
Found at i:11070 original size:19 final size:19
Alignment explanation
Indices: 11046--11082 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
11036 CATGGTTGAT
11046 ACCTGTAATTAACCAACAC
1 ACCTGTAATTAACCAACAC
*
11065 ACCTGTAGTTAACCAACA
1 ACCTGTAATTAACCAACA
11083 GAGACTCATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.08, T:0.22
Consensus pattern (19 bp):
ACCTGTAATTAACCAACAC
Found at i:12195 original size:20 final size:20
Alignment explanation
Indices: 12170--12207 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12160 AAAAAAAAAC
12170 CCCCTTATTGATAAAGTTAA
1 CCCCTTATTGATAAAGTTAA
*
12190 CCCCTTATTGGTAAAGTT
1 CCCCTTATTGATAAAGTT
12208 TACATGTAAG
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:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (20 bp):
CCCCTTATTGATAAAGTTAA
Found at i:16978 original size:38 final size:38
Alignment explanation
Indices: 16927--17014 Score: 176
Period size: 38 Copynumber: 2.3 Consensus size: 38
16917 TTAAAGCATC
16927 TTAAACTTGCTTATTGCAAAGGATTTACTCACTCAGGA
1 TTAAACTTGCTTATTGCAAAGGATTTACTCACTCAGGA
16965 TTAAACTTGCTTATTGCAAAGGATTTACTCACTCAGGA
1 TTAAACTTGCTTATTGCAAAGGATTTACTCACTCAGGA
17003 TTAAACTTGCTT
1 TTAAACTTGCTT
17015 GTTTCTAAGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (38 bp):
TTAAACTTGCTTATTGCAAAGGATTTACTCACTCAGGA
Found at i:17254 original size:12 final size:12
Alignment explanation
Indices: 17237--17262 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17227 TTTTCGGTAC
17237 TAGCTAGAAAGT
1 TAGCTAGAAAGT
17249 TAGCTAGAAAGT
1 TAGCTAGAAAGT
17261 TA
1 TA
17263 AAGGGAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (12 bp):
TAGCTAGAAAGT
Found at i:17831 original size:28 final size:28
Alignment explanation
Indices: 17788--17867 Score: 92
Period size: 27 Copynumber: 2.9 Consensus size: 28
17778 GCATTAGGGT
* *
17788 CACCCAA-GGGTATTTTGGTCATTTTCG
1 CACCCAAGGGGCATTTTGGTCATTTTCA
*
17815 CACCCAAGGGGCATTTTGGTCATTTTTA
1 CACCCAAGGGGCATTTTGGTCATTTTCA
** *
17843 CA-CTTAGGGGCATTTTAGTCATTTT
1 CACCCAAGGGGCATTTTGGTCATTTT
17868 TTAGTTCACC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 27 0.59
28 19 0.41
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (28 bp):
CACCCAAGGGGCATTTTGGTCATTTTCA
Found at i:18441 original size:26 final size:26
Alignment explanation
Indices: 18412--18497 Score: 79
Period size: 29 Copynumber: 3.3 Consensus size: 26
18402 AGTATTGCAA
18412 TTCTTTTTTACACAAGTAATAGATTC
1 TTCTTTTTTACACAAGTAATAGATTC
* * * *
18438 TTCTTTTTCTATAAACAAGTATTACAATC
1 TTC-TTTT-T-TACACAAGTAATAGATTC
*
18467 --C-TTTTTACACAAATAATAGATTC
1 TTCTTTTTTACACAAGTAATAGATTC
18490 TTCTTTTT
1 TTCTTTTT
18498 CTATAAACAA
Statistics
Matches: 45, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
23 13 0.29
24 1 0.02
25 4 0.09
26 7 0.16
27 5 0.11
28 1 0.02
29 14 0.31
ACGTcount: A:0.31, C:0.16, G:0.05, T:0.48
Consensus pattern (26 bp):
TTCTTTTTTACACAAGTAATAGATTC
Found at i:18484 original size:52 final size:53
Alignment explanation
Indices: 18402--18537 Score: 229
Period size: 52 Copynumber: 2.6 Consensus size: 53
18392 TTTATCATTT
* * *
18402 AGTATTGCAATTCTTTTTTACACAAGTAATAGATTCTTCTTTTTCTATAAACA
1 AGTATTACAATTCCTTTTTACACAAATAATAGATTCTTCTTTTTCTATAAACA
18455 AGTATTACAA-TCCTTTTTACACAAATAATAGATTCTTCTTTTTCTATAAACA
1 AGTATTACAATTCCTTTTTACACAAATAATAGATTCTTCTTTTTCTATAAACA
*
18507 AATATTACAATTCCTTTTTACACAAATAATA
1 AGTATTACAATTCCTTTTTACACAAATAATA
18538 AACTCACTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
52 49 0.63
53 29 0.37
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.43
Consensus pattern (53 bp):
AGTATTACAATTCCTTTTTACACAAATAATAGATTCTTCTTTTTCTATAAACA
Found at i:18510 original size:26 final size:26
Alignment explanation
Indices: 18429--18510 Score: 64
Period size: 25 Copynumber: 3.2 Consensus size: 26
18419 TTACACAAGT
18429 AATAGATTCTTCTTTTTCTATAAACA
1 AATAGATTCTTCTTTTTCTATAAACA
* * * *
18455 AGT--ATTACAATCCTTTTTAC-ACAAA-T
1 AATAGATT-C--TTCTTTTT-CTATAAACA
18481 AATAGATTCTTCTTTTTCTATAAACA
1 AATAGATTCTTCTTTTTCTATAAACA
18507 AATA
1 AATA
18511 TTACAATTCC
Statistics
Matches: 40, Mismatches: 8, Indels: 16
0.62 0.12 0.25
Matches are distributed among these distances:
24 4 0.10
25 12 0.30
26 8 0.20
27 12 0.30
28 4 0.10
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (26 bp):
AATAGATTCTTCTTTTTCTATAAACA
Found at i:18531 original size:24 final size:24
Alignment explanation
Indices: 18452--18534 Score: 62
Period size: 29 Copynumber: 3.3 Consensus size: 24
18442 TTTTCTATAA
*
18452 ACAAGTATTACAA-TCCTTTTTAC
1 ACAAATATTACAATTCCTTTTTAC
* * *
18475 ACAAATAATA-GATTCTTCTTTTTCTATAA
1 ACAAATATTACAATTC--C--TTT-T-TAC
18504 ACAAATATTACAATTCCTTTTTAC
1 ACAAATATTACAATTCCTTTTTAC
18528 ACAAATA
1 ACAAATA
18535 ATAAACTCAC
Statistics
Matches: 45, Mismatches: 7, Indels: 15
0.67 0.10 0.22
Matches are distributed among these distances:
22 1 0.02
23 10 0.22
24 9 0.20
25 2 0.04
26 3 0.07
27 3 0.07
28 2 0.04
29 11 0.24
30 4 0.09
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (24 bp):
ACAAATATTACAATTCCTTTTTAC
Found at i:21014 original size:19 final size:19
Alignment explanation
Indices: 20990--21036 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
20980 GAGTAATTAG
20990 TAAATAAAGATTTAACCTT
1 TAAATAAAGATTTAACCTT
*
21009 TAAATAGAGATTTAACCTT
1 TAAATAAAGATTTAACCTT
*
21028 TGAATAAAG
1 TAAATAAAG
21037 GATTGTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.34
Consensus pattern (19 bp):
TAAATAAAGATTTAACCTT
Found at i:21020 original size:50 final size:51
Alignment explanation
Indices: 20861--21014 Score: 211
Period size: 51 Copynumber: 3.0 Consensus size: 51
20851 CATCTTTGGG
20861 TAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAGATTTAACCTTTGAA
1 TAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAGATTTAACCTTTGAA
** * * * * ** *
20912 TAAAAGATTGTTTTTTTA-AGTAATTGGTAAATAAAAATGTCATATTTGAG
1 TAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAGATTTAACCTTTGAA
*
20962 TAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAGATTTAACCTTTAAA
1 TAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAGATTTAACCTTTGAA
21013 TA
1 TA
21015 GAGATTTAAC
Statistics
Matches: 83, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
50 41 0.49
51 42 0.51
ACGTcount: A:0.44, C:0.03, G:0.14, T:0.39
Consensus pattern (51 bp):
TAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAGATTTAACCTTTGAA
Found at i:21050 original size:120 final size:120
Alignment explanation
Indices: 20889--21141 Score: 452
Period size: 120 Copynumber: 2.1 Consensus size: 120
20879 GAGTAATTAG
*
20889 TAAATAAAGATTTAACCTTTGAATAAAAGATTGTTTTTTTAAGTAATTGGTAAATAAAAATGTCA
1 TAAATAAAGATTTAACCTTTGAATAAAAGATTGTTTTTTTAAATAATTGGTAAATAAAAATGTCA
20954 TATTTGAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAGATTTAACCTT
66 TATTTGAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAGATTTAACCTT
* *
21009 TAAATAGAGATTTAACCTTTGAATAAAGGATTGTTTTTTTAAATAATTGGTAAATAAAAATGTCA
1 TAAATAAAGATTTAACCTTTGAATAAAAGATTGTTTTTTTAAATAATTGGTAAATAAAAATGTCA
*
21074 TCTTTGAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAGATTTAACCTT
66 TATTTGAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAGATTTAACCTT
*
21129 TGAATAAAAGATT
1 TAAAT-AAAGATT
21142 GAATTTTTAA
Statistics
Matches: 126, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
120 120 0.95
121 6 0.05
ACGTcount: A:0.43, C:0.04, G:0.14, T:0.39
Consensus pattern (120 bp):
TAAATAAAGATTTAACCTTTGAATAAAAGATTGTTTTTTTAAATAATTGGTAAATAAAAATGTCA
TATTTGAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAGATTTAACCTT
Found at i:21063 original size:50 final size:50
Alignment explanation
Indices: 21009--21167 Score: 210
Period size: 50 Copynumber: 3.2 Consensus size: 50
20999 ATTTAACCTT
* * ** * *
21009 TAAATAGAGATTTAACCTTTGAATAAAGGATTGTTTTTTTAAATAATTGG
1 TAAATAAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTAG
* * * * *
21059 TAAATAAAAATGTCATCTTTGAGTAAAAGATTGAATTTTTAGAGTAATTAG
1 TAAATAAAGATTTAACCTTTGAATAAAAGATTGAATTTTTA-AGTAATTAG
21110 TAAATAAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTAG
1 TAAATAAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTAG
21160 TAAATAAA
1 TAAATAAA
21168 ATGTCATTTT
Statistics
Matches: 92, Mismatches: 16, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
50 49 0.53
51 43 0.47
ACGTcount: A:0.44, C:0.04, G:0.14, T:0.38
Consensus pattern (50 bp):
TAAATAAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTAG
Found at i:21115 original size:51 final size:50
Alignment explanation
Indices: 21025--21217 Score: 210
Period size: 50 Copynumber: 3.8 Consensus size: 50
21015 GAGATTTAAC
* ** * *
21025 CTTTGAATAAAGGATTGTTTTTTTAAATAATTGGTAAATAAAAATGTCAT
1 CTTTGAATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAAATGTCAT
* * * * *
21075 CTTTGAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAGATTTAAC
1 CTTTGAATAAAAGATTGAATTTTTA-AGTAATTAGTAAATAAAAATGTCAT
21126 CTTTGAATAAAAGATTGAATTTTTAAGTAATTAGTAAAT-AAAATGTCAT
1 CTTTGAATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAAATGTCAT
* * * **
21175 TTTTGAAATAGAAG-TGTGAACTTTTAAGCCATTAGTAAATAAA
1 CTTTG-AATAAAAGAT-TGAATTTTTAAGTAATTAGTAAATAAA
21218 TTGATTAGTT
Statistics
Matches: 119, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
49 11 0.09
50 63 0.53
51 45 0.38
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (50 bp):
CTTTGAATAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAAATGTCAT
Found at i:21184 original size:120 final size:117
Alignment explanation
Indices: 20932--21169 Score: 311
Period size: 120 Copynumber: 2.0 Consensus size: 117
20922 TTTTTTTAAG
20932 TAATTGGTAAATAAAAATGTCATATTTGAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAA
1 TAATTGGTAAATAAAAATGTCATATTTGAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAA
* * * *** *
20997 AGATTTAACCTTTAAATAGAGATTTAACCTTTGAATAAAGGATTGTTTTTTTAAA
66 AGATTTAACCTTTAAATAAAGATTGAA-CTTT--ATAAAGAATTGTTAAATAAAA
*
21052 TAATTGGTAAATAAAAATGTCATCTTTGAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAA
1 TAATTGGTAAATAAAAATGTCATATTTGAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAA
* *
21117 AGATTTAACCTTTGAATAAAAGATTGAA-TTT-TTAAGTAATTAG-TAAATAAAA
66 AGATTTAACCTTTAAAT-AAAGATTGAACTTTATAAAG-AATT-GTTAAATAAAA
21169 T
1 T
21170 GTCATTTTTG
Statistics
Matches: 105, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
116 4 0.04
117 9 0.09
118 1 0.01
119 3 0.03
120 80 0.76
121 8 0.08
ACGTcount: A:0.44, C:0.04, G:0.14, T:0.38
Consensus pattern (117 bp):
TAATTGGTAAATAAAAATGTCATATTTGAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAA
AGATTTAACCTTTAAATAAAGATTGAACTTTATAAAGAATTGTTAAATAAAA
Found at i:21233 original size:101 final size:101
Alignment explanation
Indices: 21009--21217 Score: 271
Period size: 101 Copynumber: 2.1 Consensus size: 101
20999 ATTTAACCTT
* * ** *
21009 TAAATAGAGATTTAACCTTTGAATAAAGGATTGTTTTTTTAAATAATTGGTAAATAAAAATGTCA
1 TAAATAAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAATAATTAGTAAATAAAAATGTCA
* * *
21074 TCTTTGAGTAAAAGATTGAATTTTTAGAGTAATTAG
66 TCTTTGAATAAAAGATTGAACTTTTAGAGCAATTAG
*
21110 TAAATAAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTAGTAAAT-AAAATGTCA
1 TAAATAAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAATAATTAGTAAATAAAAATGTCA
* * *
21174 TTTTTGAAATAGAAG-TGTGAACTTTTA-AGCCATTAG
66 TCTTTG-AATAAAAGAT-TGAACTTTTAGAGCAATTAG
21210 TAAATAAA
1 TAAATAAA
21218 TTGATTAGTT
Statistics
Matches: 94, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
100 30 0.32
101 64 0.68
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (101 bp):
TAAATAAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAATAATTAGTAAATAAAAATGTCA
TCTTTGAATAAAAGATTGAACTTTTAGAGCAATTAG
Found at i:32470 original size:24 final size:25
Alignment explanation
Indices: 32424--32475 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
32414 AATACAATTG
* *
32424 CCAAGCCCAACAGGAAATTAAAACC
1 CCAAGCCCAACAAGAAATAAAAACC
* *
32449 CCAA-CCCAACAAGATATAAAAATC
1 CCAAGCCCAACAAGAAATAAAAACC
32473 CCA
1 CCA
32476 CTCAATGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.50, C:0.33, G:0.08, T:0.10
Consensus pattern (25 bp):
CCAAGCCCAACAAGAAATAAAAACC
Found at i:33069 original size:12 final size:13
Alignment explanation
Indices: 33052--33080 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
33042 AAAGGTCACG
33052 TTTTC-TCTTTTT
1 TTTTCTTCTTTTT
33064 TTTTCTTCTTTTT
1 TTTTCTTCTTTTT
33077 TTTT
1 TTTT
33081 ACCCCTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTCTTCTTTTT
Found at i:35757 original size:60 final size:60
Alignment explanation
Indices: 35664--35780 Score: 225
Period size: 60 Copynumber: 1.9 Consensus size: 60
35654 GTGATATAAG
35664 CACCAAAGTTCAGAAATTCCCTATCCAACAGACTCCCACTTATCATTGCAGCTAACTGGC
1 CACCAAAGTTCAGAAATTCCCTATCCAACAGACTCCCACTTATCATTGCAGCTAACTGGC
*
35724 CACCAAAGTTCAGAAATTCCCTATGCAACAGACTCCCACTTATCATTGCAGCTAACT
1 CACCAAAGTTCAGAAATTCCCTATCCAACAGACTCCCACTTATCATTGCAGCTAACT
35781 AGCCCTTCTG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.32, C:0.32, G:0.11, T:0.24
Consensus pattern (60 bp):
CACCAAAGTTCAGAAATTCCCTATCCAACAGACTCCCACTTATCATTGCAGCTAACTGGC
Found at i:38062 original size:26 final size:26
Alignment explanation
Indices: 38033--38101 Score: 79
Period size: 25 Copynumber: 2.6 Consensus size: 26
38023 AATTTAATAT
*
38033 ATTTTAAATTTTAAAAACTATAATTA
1 ATTTTAAATTTTAAAAAATATAATTA
38059 A-TTTAAGA-TTTAAAAAATATAATTA
1 ATTTTAA-ATTTTAAAAAATATAATTA
*
38084 ATTTATATATATTTAAAA
1 ATTT-TAAAT-TTTAAAA
38102 TTATTTACTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
25 22 0.61
26 5 0.14
27 2 0.06
28 7 0.19
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (26 bp):
ATTTTAAATTTTAAAAAATATAATTA
Found at i:38838 original size:1 final size:1
Alignment explanation
Indices: 38828--38864 Score: 65
Period size: 1 Copynumber: 37.0 Consensus size: 1
38818 TTTAGGGTGG
*
38828 TTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
38865 GCGTCAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:39320 original size:13 final size:13
Alignment explanation
Indices: 39302--39329 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
39292 ATAGTTGACA
39302 ATTAATTATATTT
1 ATTAATTATATTT
39315 ATTAATTATATTT
1 ATTAATTATATTT
39328 AT
1 AT
39330 ATTTATTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTAATTATATTT
Found at i:44207 original size:106 final size:106
Alignment explanation
Indices: 44033--44296 Score: 372
Period size: 107 Copynumber: 2.5 Consensus size: 106
44023 AATTTTTCTA
* ** * * *
44033 ACCCTTAAAATAAAATTTTAATTTTAATTT-TGACAAAACTTAGTG-AATTAATTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTAGGGCTAAACTTAGTGAAATTAATTATATATTTTA
*
44096 TTTCTAAAACCCTATAACAAT-ATTATTAATTATGGAATTT
66 TTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
* * * *
44136 ACTCTTAAAATAAAAAATAAAATTTTAATTTAGGGCTAAACTTAGTGAAATTAGTTTTGTATTTT
1 ACCCTTAAAAT-AAAAATAAAATTTTAATTTAGGGCTAAACTTAGTGAAATTAATTATATATTTT
*
44201 ATTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
65 ATTTCTAAAACCCTATAACAAT-AATTATTAATTATGAAATTT
*
44244 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTAGGGCTAAACTTAGTGAAATTAA
44297 GGCTAAATTT
Statistics
Matches: 141, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
103 10 0.07
104 16 0.11
105 12 0.09
106 36 0.26
107 40 0.28
108 27 0.19
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (106 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTAGGGCTAAACTTAGTGAAATTAATTATATATTTTA
TTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
Found at i:44559 original size:15 final size:15
Alignment explanation
Indices: 44541--44576 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
44531 TTAACCGGTG
44541 AAACCGGGACCGGCA
1 AAACCGGGACCGGCA
44556 AAACCGGGACCGGCA
1 AAACCGGGACCGGCA
44571 AAACCG
1 AAACCG
44577 CTAATTATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.36, C:0.33, G:0.31, T:0.00
Consensus pattern (15 bp):
AAACCGGGACCGGCA
Found at i:45469 original size:21 final size:21
Alignment explanation
Indices: 45442--45495 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
45432 ACCGACAGTT
45442 TTATTATATATAAAAATAATA
1 TTATTATATATAAAAATAATA
* * *
45463 TTGTTAT-TATTAATACTAATA
1 TTATTATATA-TAAAAATAATA
*
45484 TTAATATATATA
1 TTATTATATATA
45496 TATATTATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
20 2 0.08
21 22 0.85
22 2 0.08
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
TTATTATATATAAAAATAATA
Found at i:45582 original size:20 final size:22
Alignment explanation
Indices: 45559--45599 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
45549 CTCTTTTCTT
45559 ATTTCTCTCT-CTTC-CTCTCG
1 ATTTCTCTCTCCTTCTCTCTCG
*
45579 ATTTCTTTCTCCTTCTCTCTC
1 ATTTCTCTCTCCTTCTCTCTC
45600 CTCCAGTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 4 0.22
22 5 0.28
ACGTcount: A:0.05, C:0.39, G:0.02, T:0.54
Consensus pattern (22 bp):
ATTTCTCTCTCCTTCTCTCTCG
Found at i:46373 original size:37 final size:36
Alignment explanation
Indices: 46255--46360 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
46245 GATTAAACTC
* *
46255 TTTATTGACTCCACTTAATTACCCTGAATTAAGCCT
1 TTTATTGACGCTACTTAATTACCCTGAATTAAGCCT
46291 TTTATTGACGCTACTTAATTACCCTGAATTAAGCCTT
1 TTTATTGACGCTACTTAATTACCCTGAATTAAGCC-T
*
46328 TTTATTGACGTTACTTAATTACCCTGAATTAAG
1 TTTATTGACGCTACTTAATTACCCTGAATTAAG
46361 TCCCTAACTT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
36 33 0.50
37 33 0.50
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (36 bp):
TTTATTGACGCTACTTAATTACCCTGAATTAAGCCT
Found at i:46395 original size:37 final size:37
Alignment explanation
Indices: 46354--46697 Score: 286
Period size: 37 Copynumber: 9.2 Consensus size: 37
46344 AATTACCCTG
46354 AATTAAGTCCCTAACT-TGACTTAATTTCCTTCCTTGA
1 AATTAAGTCCCTAACTCT-ACTTAATTTCCTTCCTTGA
* * *
46391 AATTAAGTCCTTAACTCTACTTAATTCCCTTCCTTGG
1 AATTAAGTCCCTAACTCTACTTAATTTCCTTCCTTGA
* *
46428 AATCAAGT--C---CTCTACTTAATTTCATTCCTTGA
1 AATTAAGTCCCTAACTCTACTTAATTTCCTTCCTTGA
* * *
46460 AATTAAGTCCTTAACTCTACTTAATTCCCCTTCCTTGG
1 AATTAAGTCCCTAACTCTACTTAATT-TCCTTCCTTGA
* * * * * *
46498 AATCAAGTCCTTTACTCTACTAAATTCCCTTCCTTGG
1 AATTAAGTCCCTAACTCTACTTAATTTCCTTCCTTGA
* * * *
46535 AATCAAGTCCCTTACTCTACTTAATTCCCTTCCTTGG
1 AATTAAGTCCCTAACTCTACTTAATTTCCTTCCTTGA
* *
46572 AACTAAGTCCCTAACTCTACTTAATTTCCTTCATTGA
1 AATTAAGTCCCTAACTCTACTTAATTTCCTTCCTTGA
*** * * *
46609 AATTAAGTTTGTGTTTTACTTTACCTAATTTCCTTCCTTGA
1 AATTAA----GTCCCTAACTCTACTTAATTTCCTTCCTTGA
** ** *
46650 AATTAAGTTTATGCTTTCTTTACTTAATTTCCTTCCTTGA
1 AATTAAG--T-CCCTAACTCTACTTAATTTCCTTCCTTGA
46690 AATTAAGT
1 AATTAAGT
46698 TTGTGCTTTA
Statistics
Matches: 256, Mismatches: 37, Indels: 27
0.80 0.12 0.08
Matches are distributed among these distances:
32 27 0.11
37 134 0.52
38 33 0.13
39 1 0.00
40 31 0.12
41 30 0.12
ACGTcount: A:0.25, C:0.25, G:0.08, T:0.42
Consensus pattern (37 bp):
AATTAAGTCCCTAACTCTACTTAATTTCCTTCCTTGA
Found at i:46539 original size:107 final size:108
Alignment explanation
Indices: 46354--46616 Score: 343
Period size: 107 Copynumber: 2.4 Consensus size: 108
46344 AATTACCCTG
* * *
46354 AATTAAGTCCCTAACT-TGACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCTACTTAATTC
1 AATTAAGTCCCTAACTCT-ACTTAATTCCCTTCCTTGAAATCAAGTCCTTAACTCTACTAAATTC
*
46418 CCTTCCTTGGAATCAAGT-C-CTCTACTTAATTTCATTCCTTGA
65 CCTTCCTTGGAATCAAGTCCTCTCTACTTAATTCCATTCCTTGA
* * *
46460 AATTAAGTCCTTAACTCTACTTAATTCCCCTTCCTTGGAATCAAGTCCTTTACTCTACTAAATTC
1 AATTAAGTCCCTAACTCTACTTAATT-CCCTTCCTTGAAATCAAGTCCTTAACTCTACTAAATTC
* *
46525 CCTTCCTTGGAATCAAGTCCCTTACTCTACTTAATTCCCTTCCTTGG
65 CCTTCCTTGGAATCAAGT-CC-T-CTCTACTTAATTCCATTCCTTGA
* * * *
46572 AACTAAGTCCCTAACTCTACTTAATTTCCTTCATTGAAATTAAGT
1 AATTAAGTCCCTAACTCTACTTAATTCCCTTCCTTGAAATCAAGT
46617 TTGTGTTTTA
Statistics
Matches: 135, Mismatches: 15, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
106 23 0.17
107 52 0.39
109 1 0.01
111 15 0.11
112 44 0.33
ACGTcount: A:0.26, C:0.27, G:0.08, T:0.39
Consensus pattern (108 bp):
AATTAAGTCCCTAACTCTACTTAATTCCCTTCCTTGAAATCAAGTCCTTAACTCTACTAAATTCC
CTTCCTTGGAATCAAGTCCTCTCTACTTAATTCCATTCCTTGA
Found at i:46545 original size:19 final size:19
Alignment explanation
Indices: 46487--46547 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
46477 TACTTAATTC
46487 CCCTTCCTTGGAATCAAGT
1 CCCTTCCTTGGAATCAAGT
* * * * *
46506 CCTTTACTCT--ACTAAATT
1 CCCTTCCT-TGGAATCAAGT
46524 CCCTTCCTTGGAATCAAGT
1 CCCTTCCTTGGAATCAAGT
46543 CCCTT
1 CCCTT
46548 ACTCTACTTA
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
17 1 0.03
18 11 0.38
19 16 0.55
20 1 0.03
ACGTcount: A:0.21, C:0.33, G:0.10, T:0.36
Consensus pattern (19 bp):
CCCTTCCTTGGAATCAAGT
Found at i:46640 original size:41 final size:41
Alignment explanation
Indices: 46593--46861 Score: 358
Period size: 41 Copynumber: 6.7 Consensus size: 41
46583 TAACTCTACT
* *
46593 TAATTTCCTTCATTGAAATTAAGTTTGTGTTTTACTTTACC
1 TAATTTCCTTCCTTGAAATTAAGTTTGTGCTTTACTTTACC
* *
46634 TAATTTCCTTCCTTGAAATTAAGTTTATGCTTT-CTTTACT
1 TAATTTCCTTCCTTGAAATTAAGTTTGTGCTTTACTTTACC
46674 TAATTTCCTTCCTTGAAATTAAGTTTGTGCTTTACTTTACC
1 TAATTTCCTTCCTTGAAATTAAGTTTGTGCTTTACTTTACC
* *
46715 TAATTTCCTTCCCTGAAATTAAGTTTGTGCTTTGCTTTACC
1 TAATTTCCTTCCTTGAAATTAAGTTTGTGCTTTACTTTACC
* *
46756 TAATTTCCTTCAC-TGAAATTAAGTATGTGC-TTACTTTACT
1 TAATTTCCTTC-CTTGAAATTAAGTTTGTGCTTTACTTTACC
* *
46796 TAA-TTAC--CC-TG-AATTAAGTCTGTGCTTGT-CTTTACC
1 TAATTTCCTTCCTTGAAATTAAGTTTGTGCTT-TACTTTACC
*
46832 TAATTTCCTTCCTTGAAATTAAGTCTGTGC
1 TAATTTCCTTCCTTGAAATTAAGTTTGTGC
46862 CTATCCTTAC
Statistics
Matches: 204, Mismatches: 15, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
35 13 0.06
36 13 0.06
37 5 0.02
39 5 0.02
40 51 0.25
41 116 0.57
42 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.47
Consensus pattern (41 bp):
TAATTTCCTTCCTTGAAATTAAGTTTGTGCTTTACTTTACC
Found at i:46694 original size:81 final size:79
Alignment explanation
Indices: 46593--46860 Score: 357
Period size: 81 Copynumber: 3.4 Consensus size: 79
46583 TAACTCTACT
*
46593 TAATTTCCTTCATTGAAATTAAGTTTGTGTTTTACTTTACCTAATTTCCTTCCTTGAAATTAAGT
1 TAATTTCCTTCCTTGAAATTAAGTTTGTG-TTTACTTTACCTAATTTCCTTCC-TGAAATTAAGT
* *
46658 TTATGCTTTCTTTACT
64 TTGTGCTTTCTTTACC
46674 TAATTTCCTTCCTTGAAATTAAGTTTGTGCTTTACTTTACCTAATTTCCTTCCCTGAAATTAAGT
1 TAATTTCCTTCCTTGAAATTAAGTTTGTG-TTTACTTTACCTAATTTCCTT-CCTGAAATTAAGT
46739 TTGTGCTTTGCTTTACC
64 TTGTGCTTT-CTTTACC
* * * * *
46756 TAATTTCCTTCAC-TGAAATTAAGTATGTGCTTACTTTACTTAA-TTAC--CCTG-AATTAAGTC
1 TAATTTCCTTC-CTTGAAATTAAGTTTGTGTTTACTTTACCTAATTTCCTTCCTGAAATTAAGTT
46816 TGTGCTTGTCTTTACC
65 TGTGCTT-TCTTTACC
*
46832 TAATTTCCTTCCTTGAAATTAAGTCTGTG
1 TAATTTCCTTCCTTGAAATTAAGTTTGTG
46861 CCTATCCTTA
Statistics
Matches: 172, Mismatches: 10, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
75 1 0.01
76 48 0.28
77 5 0.03
80 3 0.02
81 80 0.47
82 34 0.20
83 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.47
Consensus pattern (79 bp):
TAATTTCCTTCCTTGAAATTAAGTTTGTGTTTACTTTACCTAATTTCCTTCCTGAAATTAAGTTT
GTGCTTTCTTTACC
Found at i:46739 original size:122 final size:117
Alignment explanation
Indices: 46593--46861 Score: 371
Period size: 122 Copynumber: 2.3 Consensus size: 117
46583 TAACTCTACT
* *
46593 TAATTTCCTTCATTGAAATTAAGTTTGTGTTTTACTTTACCTAATTTCCTTC-CTTGAAATTAAG
1 TAATTTCCTTCCTTGAAATTAAGTTTGTGCTTTACTTTACCTAATTTCCTTCAC-TGAAATTAAG
* * * *
46657 TTTATGCTTTCTTTACTTAATTTCCTTCCTTGAAATTAAGTTTGTGCTT-TACTTTACC
65 TATATGCTTACTTTACTTAA-TTAC--CC-TG-AATTAAGTCTGTGCTTGT-CTTTACC
* *
46715 TAATTTCCTTCCCTGAAATTAAGTTTGTGCTTTGCTTTACCTAATTTCCTTCACTGAAATTAAGT
1 TAATTTCCTTCCTTGAAATTAAGTTTGTGCTTTACTTTACCTAATTTCCTTCACTGAAATTAAGT
*
46780 ATGTGCTTACTTTACTTAATTACCCTGAATTAAGTCTGTGCTTGTCTTTACC
66 ATATGCTTACTTTACTTAATTACCCTGAATTAAGTCTGTGCTTGTCTTTACC
*
46832 TAATTTCCTTCCTTGAAATTAAGTCTGTGC
1 TAATTTCCTTCCTTGAAATTAAGTTTGTGC
46862 CTATCCTTAC
Statistics
Matches: 134, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
117 50 0.37
118 3 0.02
119 2 0.01
121 3 0.02
122 75 0.56
123 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.47
Consensus pattern (117 bp):
TAATTTCCTTCCTTGAAATTAAGTTTGTGCTTTACTTTACCTAATTTCCTTCACTGAAATTAAGT
ATATGCTTACTTTACTTAATTACCCTGAATTAAGTCTGTGCTTGTCTTTACC
Found at i:46927 original size:37 final size:37
Alignment explanation
Indices: 46874--47606 Score: 770
Period size: 37 Copynumber: 19.5 Consensus size: 37
46864 ATCCTTACCT
* *
46874 TTTAACTGTTTTTACTTAATTACCCTGAATTAAGTCC
1 TTTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
*
46911 TTCAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
1 TTTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
**
46948 -TTAACTGCTTTTACTTAATTGTCCTGAATTAAGTT-
1 TTTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
** *
46983 TTTAACTGCTTTTACTTAATTGTCCTAAATTAAGTTC
1 TTTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
* * *
47020 -TTAATTGTTCTTTACTTAATTACTCTGAATTAAGTTC
1 TTTAACTGCT-TTTACTTAATTACCCTGAATTAAGTTC
* * * *
47057 TTTGACCG-TGTTTACTTAATTTCCCTGAATTAAGCTC
1 TTTAACTGCT-TTTACTTAATTACCCTGAATTAAGTTC
* * * *
47094 ATTTGACTGCTTTTACCTT-ATTTCCTTGAATTAAGAT-
1 -TTTAACTGCTTTTA-CTTAATTACCCTGAATTAAGTTC
* * *
47131 TTTGACTGACTATGTTTACTTTTCTTAATTGCCCTGAATTAAGAT-
1 TTTAACTG-C--T-TTTA-----CTTAATTACCCTGAATTAAGTTC
* ** *
47176 TTTGACTATTTTTACTTAATTACCCTGAATTAAGTTT
1 TTTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
* *
47213 TTTACCTGCTTTTACTTAATTGCCCTGAATTAAGTTC
1 TTTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
*
47250 -TTAACTGCTCCTTTACTTAACTACCCTGAATTAAGTTC
1 TTTAACTGCT--TTTACTTAATTACCCTGAATTAAGTTC
* * * *
47288 CTTACCTGCTTTTACTTAATTGCCCTGAATTAGGTTC
1 TTTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
* *
47325 -TTAACCTGCTTCTTTACTTAACTACCCCGAATTAAGTTC
1 TTTAA-CTGC-T-TTTACTTAATTACCCTGAATTAAGTTC
* *
47364 TTTACCTGCTTTTACTTAATTGCCCTGAATTAAGTTC
1 TTTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
**
47401 -TTAACCTGCTTTTACTTAATCGCCCTGAATTAAGTTC
1 TTTAA-CTGCTTTTACTTAATTACCCTGAATTAAGTTC
47438 -TTAACTTGCTTTTACTTAATTACCCTGAATTAAGTTC
1 TTTAAC-TGCTTTTACTTAATTACCCTGAATTAAGTTC
*
47475 TTTAACTGCTCTTACTTAATTACCCTGAATTAAGTTC
1 TTTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
*
47512 TTTAACTGCTCTTACTTAATTACCCTGAATTAAGTTC
1 TTTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
* * *
47549 TTTGACTAG-TTTTACTTAATTTCCATGAATTAAGTTC
1 TTTAACT-GCTTTTACTTAATTACCCTGAATTAAGTTC
* *
47586 TTTAGCTGCTCTTTTCTTAAT
1 TTTAACTGCT-TTTACTTAAT
47607 CACCATGGAT
Statistics
Matches: 602, Mismatches: 64, Indels: 59
0.83 0.09 0.08
Matches are distributed among these distances:
36 117 0.19
37 334 0.55
38 73 0.12
39 40 0.07
40 7 0.01
41 4 0.01
42 1 0.00
44 3 0.00
45 23 0.04
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.46
Consensus pattern (37 bp):
TTTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
Found at i:47689 original size:41 final size:40
Alignment explanation
Indices: 47598--47741 Score: 207
Period size: 41 Copynumber: 3.5 Consensus size: 40
47588 TAGCTGCTCT
* * * **
47598 TTTCTTAATCACCATGGATTAAAACTTTAACTAATTTGAC
1 TTTCTTAATCGCCCTGGATTAAAACCTTAACTTGTTTGAC
47638 TTTCTTAATCGCCCTGGATTAAAACCTTAACTGTGTTTGAC
1 TTTCTTAATCGCCCTGGATTAAAACCTTAACT-TGTTTGAC
47679 TTTCTTAATCGCCCTGGATTAAAACCTTAACTATGTTTGAC
1 TTTCTTAATCGCCCTGGATTAAAACCTTAACT-TGTTTGAC
* *
47720 CTTCTTAATCGCCCTAGATTAA
1 TTTCTTAATCGCCCTGGATTAA
47742 GACTTTACTT
Statistics
Matches: 95, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 29 0.31
41 66 0.69
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (40 bp):
TTTCTTAATCGCCCTGGATTAAAACCTTAACTTGTTTGAC
Found at i:56027 original size:19 final size:19
Alignment explanation
Indices: 56000--56038 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
55990 TGTAAGTTTG
56000 TTTCATTTTTATTTT-TCAA
1 TTTCATTTTT-TTTTCTCAA
*
56019 TTTCTTTTTTTTTTCTCAA
1 TTTCATTTTTTTTTCTCAA
56038 T
1 T
56039 CTTAATTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTCATTTTTTTTTCTCAA
Found at i:61638 original size:15 final size:14
Alignment explanation
Indices: 61604--61638 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
61594 GAGGGAAGTA
61604 GGAGGAAAGAAATG
1 GGAGGAAAGAAATG
61618 GTGAGGAAAGAAAATG
1 G-GAGGAAAG-AAATG
61634 GGAGG
1 GGAGG
61639 GAAATACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.05
15 12 0.63
16 6 0.32
ACGTcount: A:0.46, C:0.00, G:0.46, T:0.09
Consensus pattern (14 bp):
GGAGGAAAGAAATG
Found at i:63679 original size:11 final size:10
Alignment explanation
Indices: 63652--63678 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
63642 ATTTGACCTC
63652 TTTTTTTCTT
1 TTTTTTTCTT
63662 TTTTTTTCTT
1 TTTTTTTCTT
63672 TTTTTTT
1 TTTTTTT
63679 TTTCATATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:64022 original size:60 final size:60
Alignment explanation
Indices: 63929--64109 Score: 344
Period size: 60 Copynumber: 3.0 Consensus size: 60
63919 TAGAAATGCG
*
63929 CTTGCAACAGTTAAAAGTTCTGAAGTTATTAGTGATGCAGGAACACCATCTGTGGAGCCA
1 CTTGCAACAGTTACAAGTTCTGAAGTTATTAGTGATGCAGGAACACCATCTGTGGAGCCA
63989 CTTGCAACAGTTACAAGTTCTGAAGTTATTAGTGATGCAGGAACACCATCTGTGGAGCCA
1 CTTGCAACAGTTACAAGTTCTGAAGTTATTAGTGATGCAGGAACACCATCTGTGGAGCCA
*
64049 CTTGCAACAGTTACAAGTTCTGAAGTTATTAGTGATGCAGGAACACCCTCTGTGGAGCCA
1 CTTGCAACAGTTACAAGTTCTGAAGTTATTAGTGATGCAGGAACACCATCTGTGGAGCCA
64109 C
1 C
64110 CTTTTGAGCT
Statistics
Matches: 119, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 119 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (60 bp):
CTTGCAACAGTTACAAGTTCTGAAGTTATTAGTGATGCAGGAACACCATCTGTGGAGCCA
Found at i:73656 original size:11 final size:11
Alignment explanation
Indices: 73640--73671 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
73630 TGGGGTGTAT
73640 TCCCGTCCCCG
1 TCCCGTCCCCG
73651 TCCCGTCCCCG
1 TCCCGTCCCCG
*
73662 TCCCCTCCCC
1 TCCCGTCCCC
73672 CGGCGGGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.69, G:0.12, T:0.19
Consensus pattern (11 bp):
TCCCGTCCCCG
Found at i:73934 original size:13 final size:13
Alignment explanation
Indices: 73901--73936 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 13
73891 TAGTAAATAT
73901 TTATTTATTAGTA
1 TTATTTATTAGTA
73914 -TA--TATTAGTA
1 TTATTTATTAGTA
73924 TTATTTATTAGTA
1 TTATTTATTAGTA
73937 AAACATATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
10 8 0.40
11 2 0.10
12 2 0.10
13 8 0.40
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (13 bp):
TTATTTATTAGTA
Found at i:77138 original size:440 final size:438
Alignment explanation
Indices: 76304--77243 Score: 1619
Period size: 440 Copynumber: 2.1 Consensus size: 438
76294 CCCACTCTTA
* * *
76304 ATAAACAAATCATTTTTTCCTGATTTATTTATCAAATGATCCCTATACTTTTATGTTTTATGCTA
1 ATAAACAAATCATTTTTTTCTGGTTTATTTATCAAATGAT-CCTATACTTTTATGCTTTATGCTA
* *
76369 TTTAGTGCCTCATAATTTCTGGGTTGGACGATTGAACGTTTGGGTTTTAATTCTTTTATTTTTTT
65 TTTAGTGCCTCACAATTTCTGGGTTGGACGATTGAACGTTTCGGTTTTAATTCTTTTATTTTTTT
* *
76434 GTTTTCTTGTCCGATGAAGGTGATTCAAGTATCTATTAATAGGTAATTTCATTATCTACAACTTC
130 GTTTTCTTGTCCGATGAAGGTGATCCAAGTATCTATTAATAGGTAATTTCATGATCTACAACTTC
76499 CATGAAGGACTCAGAAGCCAATTTTAATGTTTTGATTCTAAAAAATGCTTCTGAAATTTTATGGT
195 CATGAAGGACTCAGAAGCCAATTTTAATGTTTTGATTCTAAAAAATGCTTCTGAAATTTTATGGT
* *
76564 CTCGATTGCCGGTCTATCTAATATTGTATAATTTTCGGTCCACTTGTCCGATTGAGGTTGTTCAA
260 CTAGATTGCCGGTCTATCTAATATTGTATAATTTTCGGTCCACTTGTCCGATTGAAGTTGTTCAA
* * * *
76629 GTGTCGGTTAAAAGGTTATTGGGTGATCTACGGCTTTCATTAAGGGCCTAAAAACTGAATTTGAT
325 GTGTCAGTTAAAACGTTATTGGGTGATCTACGACTTTCATTAAGGGCCTAAAAACTGAATTTAAT
* *
76694 TAATGAGTTTCGTGGAGGGTTCAAGAGGAAATTTTTATGTTTGGTCTCC
390 TAATGAGTTTCGTGAAGGATTCAAGAGGAAATTTTTATGTTTGGTCTCC
*
76743 ATAAACAAATCATTTTTTTCGTGGTTTATTTATCAAATGATACCTATACTTTTATGCTTTATGTT
1 ATAAACAAATCATTTTTTTC-TGGTTTATTTATCAAATGAT-CCTATACTTTTATGCTTTATGCT
76808 ATTTAGTGCCTCACAATTTCTGGGTTGGACGATTGAACGTTTCGGTTTTAATTCTTTTATTTTTT
64 ATTTAGTGCCTCACAATTTCTGGGTTGGACGATTGAACGTTTCGGTTTTAATTCTTTTATTTTTT
* *
76873 TGTTTTCTTGTCCGATGAAGGTGATCCAAGTGTCTATTGATAGGTAATTTCATGATCTACAACTT
129 TGTTTTCTTGTCCGATGAAGGTGATCCAAGTATCTATTAATAGGTAATTTCATGATCTACAACTT
* *
76938 CCATGAAGGACTTAGAAGCCAATTTTAATGTTTTGATTCTAAAAAATGCTTTTGAAATTTTATGG
194 CCATGAAGGACTCAGAAGCCAATTTTAATGTTTTGATTCTAAAAAATGCTTCTGAAATTTTATGG
* *
77003 TTTAGATTGCCGGTCTATCTAATATTGTATAATTTTCGGTCTACTTGTCCGATTGAAGTTGTTCA
259 TCTAGATTGCCGGTCTATCTAATATTGTATAATTTTCGGTCCACTTGTCCGATTGAAGTTGTTCA
* *
77068 AGTGTCAGTTAAAACGTTATTGTGTGATCTACGACTTTCATTAAGGGCCTGAAAACTGAATTTAA
324 AGTGTCAGTTAAAACGTTATTGGGTGATCTACGACTTTCATTAAGGGCCTAAAAACTGAATTTAA
77133 TTAATGAGTTTCGTGAAGGATTCAAGAGGAAATTTTTATGTTTGGTCTCC
389 TTAATGAGTTTCGTGAAGGATTCAAGAGGAAATTTTTATGTTTGGTCTCC
*
77183 ATAAACAAATCATTTTTTTCTGGTTTATTTATCAAAGGATCTCTATACTTTTATGCTTTAT
1 ATAAACAAATCATTTTTTTCTGGTTTATTTATCAAATGATC-CTATACTTTTATGCTTTAT
77244 TTGTAAGTGA
Statistics
Matches: 473, Mismatches: 26, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
438 1 0.00
439 57 0.12
440 415 0.88
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (438 bp):
ATAAACAAATCATTTTTTTCTGGTTTATTTATCAAATGATCCTATACTTTTATGCTTTATGCTAT
TTAGTGCCTCACAATTTCTGGGTTGGACGATTGAACGTTTCGGTTTTAATTCTTTTATTTTTTTG
TTTTCTTGTCCGATGAAGGTGATCCAAGTATCTATTAATAGGTAATTTCATGATCTACAACTTCC
ATGAAGGACTCAGAAGCCAATTTTAATGTTTTGATTCTAAAAAATGCTTCTGAAATTTTATGGTC
TAGATTGCCGGTCTATCTAATATTGTATAATTTTCGGTCCACTTGTCCGATTGAAGTTGTTCAAG
TGTCAGTTAAAACGTTATTGGGTGATCTACGACTTTCATTAAGGGCCTAAAAACTGAATTTAATT
AATGAGTTTCGTGAAGGATTCAAGAGGAAATTTTTATGTTTGGTCTCC
Found at i:77597 original size:1 final size:1
Alignment explanation
Indices: 77586--77624 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
77576 TCTCTATTAT
* **
77586 AAAAAAGAAAAAGCAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
77625 CTCCCTACAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.92, C:0.03, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:81500 original size:17 final size:17
Alignment explanation
Indices: 81478--81511 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
81468 AGCTAATTTT
81478 TATGTTTCATGAACCAC
1 TATGTTTCATGAACCAC
81495 TATGTTTCATGAACCAC
1 TATGTTTCATGAACCAC
81512 AAAGATCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (17 bp):
TATGTTTCATGAACCAC
Found at i:81809 original size:64 final size:64
Alignment explanation
Indices: 81705--81825 Score: 217
Period size: 65 Copynumber: 1.9 Consensus size: 64
81695 TATTCAACAT
81705 TGGGGAAATTTTGAAAAAAAAAAATCACTGAGGAAGTTAGGTACATTGTTAGACAACCAAAACGC
1 TGGGGAAATTTTGAAAAAAAAAAATCACTGAGGAAGTTAGGTA-ATTGTTAGACAACCAAAACGC
*
81770 TGGGGAAATTTTGAAAAAAAAAAA-CGCTGAGGAAGTTAGGTAATTGTTAGACAACC
1 TGGGGAAATTTTGAAAAAAAAAAATCACTGAGGAAGTTAGGTAATTGTTAGACAACC
81826 TAACTTCATT
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
63 14 0.25
64 17 0.31
65 24 0.44
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.22
Consensus pattern (64 bp):
TGGGGAAATTTTGAAAAAAAAAAATCACTGAGGAAGTTAGGTAATTGTTAGACAACCAAAACGC
Found at i:85417 original size:2 final size:2
Alignment explanation
Indices: 85410--85444 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
85400 ATTTAAAAAC
*
85410 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
85445 GTTCTCCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:86824 original size:71 final size:71
Alignment explanation
Indices: 86708--86852 Score: 290
Period size: 71 Copynumber: 2.0 Consensus size: 71
86698 TAATTACTGA
86708 AACAAGAATGTTTGGAAACCAAGGATTTCAGGCTAGACATTCAATGGGATTCCCAGCAAGCACTT
1 AACAAGAATGTTTGGAAACCAAGGATTTCAGGCTAGACATTCAATGGGATTCCCAGCAAGCACTT
86773 CCATAG
66 CCATAG
86779 AACAAGAATGTTTGGAAACCAAGGATTTCAGGCTAGACATTCAATGGGATTCCCAGCAAGCACTT
1 AACAAGAATGTTTGGAAACCAAGGATTTCAGGCTAGACATTCAATGGGATTCCCAGCAAGCACTT
86844 CCATAG
66 CCATAG
86850 AAC
1 AAC
86853 CAGACGATTA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 74 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (71 bp):
AACAAGAATGTTTGGAAACCAAGGATTTCAGGCTAGACATTCAATGGGATTCCCAGCAAGCACTT
CCATAG
Found at i:87292 original size:82 final size:82
Alignment explanation
Indices: 87155--87321 Score: 316
Period size: 82 Copynumber: 2.0 Consensus size: 82
87145 TTGGTTGACT
*
87155 TTATATTCATTTACTTTTGGTTTTGATTTAGAGAAATTAAACTTGAAGCATGTAAAGTTTTGGTT
1 TTATATTCATTTACTTTTGGTTTTGATTCAGAGAAATTAAACTTGAAGCATGTAAAGTTTTGGTT
87220 TAAATTTTGATTTAGAG
66 TAAATTTTGATTTAGAG
*
87237 TTATATTCATTTGCTTTTGGTTTTGATTCAGAGAAATTAAACTTGAAGCATGTAAAGTTTTGGTT
1 TTATATTCATTTACTTTTGGTTTTGATTCAGAGAAATTAAACTTGAAGCATGTAAAGTTTTGGTT
87302 TAAATTTTGATTTAGAG
66 TAAATTTTGATTTAGAG
87319 TTA
1 TTA
87322 ATTTGATGTT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 83 1.00
ACGTcount: A:0.30, C:0.05, G:0.17, T:0.47
Consensus pattern (82 bp):
TTATATTCATTTACTTTTGGTTTTGATTCAGAGAAATTAAACTTGAAGCATGTAAAGTTTTGGTT
TAAATTTTGATTTAGAG
Found at i:94412 original size:22 final size:24
Alignment explanation
Indices: 94374--94437 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 24
94364 CAACATTACC
*
94374 AAAAA-AAA-AAAAAAAAACAAAAG
1 AAAAAGAAAGAAAGAAAAA-AAAAG
*
94397 AAGAAG-AAG-AAGAAAAAAAAAG
1 AAAAAGAAAGAAAGAAAAAAAAAG
94419 AAAAAGAAAGAAAGAAAAA
1 AAAAAGAAAGAAAGAAAAA
94438 GAAGCACTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 10 0.29
23 16 0.47
24 8 0.24
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (24 bp):
AAAAAGAAAGAAAGAAAAAAAAAG
Found at i:94423 original size:33 final size:33
Alignment explanation
Indices: 94376--94441 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
94366 ACATTACCAA
*
94376 AAAAAAAAAAAAAAACAAAAG-AAGAAGAAGAAG
1 AAAAAAAAAAAAAAA-AAAAGAAAGAAAAAGAAG
* *
94409 AAAAAAAAAGAAAAAGAAAGAAAGAAAAAGAAG
1 AAAAAAAAAAAAAAAAAAAGAAAGAAAAAGAAG
94442 CACTCAATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 4 0.14
33 25 0.86
ACGTcount: A:0.82, C:0.02, G:0.17, T:0.00
Consensus pattern (33 bp):
AAAAAAAAAAAAAAAAAAAGAAAGAAAAAGAAG
Found at i:94423 original size:36 final size:35
Alignment explanation
Indices: 94374--94441 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
94364 CAACATTACC
*
94374 AAAAAAAAAAAAAA-AAACAAAAGAAGAAGAAGAAG
1 AAAAAAAAAAAAAAGAAA-AAAAGAAAAAGAAGAAG
*
94409 AAAAAAAAAGAAAAAGAAAGAAAGAAAAAGAAG
1 AAAAAAAAA-AAAAAGAAAAAAAGAAAAAGAAG
94442 CACTCAATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
35 9 0.31
36 17 0.59
37 3 0.10
ACGTcount: A:0.82, C:0.01, G:0.16, T:0.00
Consensus pattern (35 bp):
AAAAAAAAAAAAAAGAAAAAAAGAAAAAGAAGAAG
Found at i:94434 original size:14 final size:13
Alignment explanation
Indices: 94374--94440 Score: 61
Period size: 14 Copynumber: 5.2 Consensus size: 13
94364 CAACATTACC
94374 AAAAAA-AAAAA-
1 AAAAAAGAAAAAG
*
94385 AAAAAA-CAAAAG
1 AAAAAAGAAAAAG
94397 AAGAAGAAGAAGAAA-
1 AA-AA-AAGAA-AAAG
94412 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
94425 AAAGAAAGAAAAAG
1 AAA-AAAGAAAAAG
94439 AA
1 AA
94441 GCACTCAATG
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
11 10 0.21
12 5 0.11
13 10 0.21
14 16 0.34
15 3 0.06
16 3 0.06
ACGTcount: A:0.84, C:0.01, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:94438 original size:6 final size:6
Alignment explanation
Indices: 94374--94440 Score: 52
Period size: 6 Copynumber: 11.3 Consensus size: 6
94364 CAACATTACC
* * *
94374 AAAAA- AAAAA- AAAAAA ACAAAAG AAGAAG AAGAAG -AAAA- AAAAAG
1 AAAAAG AAAAAG AAAAAG A-AAAAG AAAAAG AAAAAG AAAAAG AAAAAG
94419 AAAAAG AAAGAAAG AAAAAG AA
1 AAAAAG -AA-AAAG AAAAAG AA
94441 GCACTCAATG
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
5 17 0.32
6 23 0.43
7 9 0.17
8 4 0.08
ACGTcount: A:0.84, C:0.01, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:94438 original size:10 final size:10
Alignment explanation
Indices: 94392--94440 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
94382 AAAAAAAAAC
94392 AAAAG-AAGA
1 AAAAGAAAGA
*
94401 AGAAG-AAGA
1 AAAAGAAAGA
*
94410 AAAAAAAAGA
1 AAAAGAAAGA
94420 AAAAGAAAGA
1 AAAAGAAAGA
94430 AAGAA-AAAGA
1 AA-AAGAAAGA
94440 A
1 A
94441 GCACTCAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
9 11 0.32
10 21 0.62
11 2 0.06
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
AAAAGAAAGA
Found at i:101120 original size:19 final size:19
Alignment explanation
Indices: 101096--101132 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
101086 CGCGGGCGGG
101096 AAGAGAGAGAAACAAAGAC
1 AAGAGAGAGAAACAAAGAC
* *
101115 AAGAGAGATAAGCAAAGA
1 AAGAGAGAGAAACAAAGA
101133 AGATTGTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.08, G:0.27, T:0.03
Consensus pattern (19 bp):
AAGAGAGAGAAACAAAGAC
Found at i:105328 original size:2 final size:2
Alignment explanation
Indices: 105323--105353 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
105313 TATATATATA
105323 TG TG TG TG TG TG TG TG TG TG TG TG TG T- TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
105354 CCAAAAAGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:107331 original size:2 final size:2
Alignment explanation
Indices: 107320--107357 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
107310 ATATTAATAC
*
107320 TA TA -A TA TA TA TA TA TA TA TA TA TC TA TA CTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
107358 AAAGTACGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:107819 original size:15 final size:16
Alignment explanation
Indices: 107795--107838 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
107785 CTAAATTGAC
107795 ATTATTAAAATTTATTA
1 ATTA-TAAAATTTATTA
* *
107812 TTTA-AAAATTAATTA
1 ATTATAAAATTTATTA
107827 ATTATAAAATTT
1 ATTATAAAATTT
107839 TAATTTAGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
15 13 0.59
16 6 0.27
17 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTATAAAATTTATTA
Found at i:108116 original size:19 final size:20
Alignment explanation
Indices: 108089--108126 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
108079 TACTATTATT
108089 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
108109 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
108127 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:108320 original size:22 final size:22
Alignment explanation
Indices: 108292--108376 Score: 93
Period size: 22 Copynumber: 3.9 Consensus size: 22
108282 TGTCTCTATG
108292 TGGTTATCAAAATTTCATAAGT
1 TGGTTATCAAAATTTCATAAGT
* * * *
108314 TGGTTATTATAATTTCATGAGG
1 TGGTTATCAAAATTTCATAAGT
108336 TGGTTA-CAAGAATTTCAT-AGT
1 TGGTTATCAA-AATTTCATAAGT
*
108357 ATGGTTACCAAAATTTCATA
1 -TGGTTATCAAAATTTCATA
108377 TGATCAAGTT
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
21 3 0.06
22 46 0.88
23 3 0.06
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.40
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGT
Found at i:108372 original size:44 final size:44
Alignment explanation
Indices: 108291--108375 Score: 111
Period size: 44 Copynumber: 1.9 Consensus size: 44
108281 TTGTCTCTAT
** *
108291 GTGGTTATCAAAATTTCATAAGTTGGTTATTATAATTTCATGAG
1 GTGGTTATCAAAATTTCATAAGTTGGTTACCAAAATTTCATGAG
108335 GTGGTTA-CAAGAATTTCAT-AGTATGGTTACCAAAATTTCAT
1 GTGGTTATCAA-AATTTCATAAGT-TGGTTACCAAAATTTCAT
108376 ATGATCAAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 6 0.17
44 30 0.83
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (44 bp):
GTGGTTATCAAAATTTCATAAGTTGGTTACCAAAATTTCATGAG
Found at i:108578 original size:22 final size:22
Alignment explanation
Indices: 108466--108858 Score: 110
Period size: 22 Copynumber: 17.7 Consensus size: 22
108456 ATCAAAGAGA
* *
108466 TTATCAAAATGTCATAGTGTGC
1 TTATCAAAATTTCATAGTGTGG
* *
108488 TTAACAAAATTTCATTAG-GAGG
1 TTATCAAAATTTCA-TAGTGTGG
* * *
108510 TTA-CTAATATTTCAT-GCGGAGG
1 TTATC-AAAATTTCATAG-TGTGG
*
108532 TTATCAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATAGTGTGG
108554 TTATCAAAATTTCATA-TGAAT-G
1 TTATCAAAATTTCATAGTG--TGG
* *
108576 TTATAAAAGTCTCAATTTCATA-AG-GAG
1 TTAT-CAA-----AATTTCATAGTGTG-G
* * * **
108603 -CACCAAAATTTGATAG-AAGG
1 TTATCAAAATTTCATAGTGTGG
* * *
108623 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGTGTGG
* *
108644 TTATCGAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAGTG-T-GG
*** *
108668 ATTATCAAAATTT-ATAGAAAGA
1 -TTATCAAAATTTCATAGTGTGG
*
108690 TTATCAAAATTTCATAGTCTTGG
1 TTATCAAAATTTCATAGT-GTGG
* * *
108713 -TATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGTGTGG
* * * *
108734 TTATCAAAATTACGTAATGTGA
1 TTATCAAAATTTCATAGTGTGG
* ** *
108756 TTATCAGAATTTCATAAAGGGG
1 TTATCAAAATTTCATAGTGTGG
* * * ** *
108778 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAGTGTGG
* *
108800 TTATCAAAATTTCATAGAGAGG
1 TTATCAAAATTTCATAGTGTGG
* * * *
108822 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGTGG
108844 TTA-CAAAAATTTCAT
1 TTATC-AAAATTTCAT
108859 GGTGGTATTT
Statistics
Matches: 275, Mismatches: 68, Indels: 56
0.69 0.17 0.14
Matches are distributed among these distances:
20 19 0.07
21 28 0.10
22 187 0.68
23 10 0.04
24 6 0.02
25 13 0.05
26 1 0.00
27 1 0.00
28 10 0.04
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGG
Found at i:108692 original size:21 final size:22
Alignment explanation
Indices: 108606--108706 Score: 91
Period size: 21 Copynumber: 4.6 Consensus size: 22
108596 TAAGGAGCAC
* *
108606 CAAAATTTGATAG-AAGGTTAT
1 CAAAATTTCATAGAAAGATTAT
* **
108627 C-AAATCTCATAGAGTGATTAT
1 CAAAATTTCATAGAAAGATTAT
* *
108648 CGAAATTTCATAGAGATCGGATTAT
1 CAAAATTTCATAGA-A--AGATTAT
108673 CAAAATTT-ATAGAAAGATTAT
1 CAAAATTTCATAGAAAGATTAT
108694 CAAAATTTCATAG
1 CAAAATTTCATAG
108707 TCTTGGTATC
Statistics
Matches: 64, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
20 9 0.14
21 21 0.33
22 15 0.23
23 1 0.02
24 5 0.08
25 13 0.20
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.33
Consensus pattern (22 bp):
CAAAATTTCATAGAAAGATTAT
Found at i:108761 original size:44 final size:43
Alignment explanation
Indices: 108667--108857 Score: 129
Period size: 44 Copynumber: 4.4 Consensus size: 43
108657 ATAGAGATCG
* * * * *
108667 GATTATCAAAATTT-ATAGAAAGATTATCAAAATTTCATAGTCTT
1 GATTATCAAAATTTCAAAG-GAGGTTATCAAAATTTCATAAT-GT
* * *
108711 G-GTATCAAAATTTCAAAGCGAGGTTATCAAAATTACGTAATGT
1 GATTATCAAAATTTCAAAG-GAGGTTATCAAAATTTCATAATGT
* * * * * *
108754 GATTATCAGAATTTCATAAAGG-GGTCAACAAAATTTTATAAAGA
1 GATTATCAAAATTTC--AAAGGAGGTTATCAAAATTTCATAATGT
* * * *
108798 GGTTATCAAAATTTCATAGAGAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCAAAG-GAGGTTATCAAAATTTCATAATGT
108842 GATTA-CAAAAATTTCA
1 GATTATC-AAAATTTCA
108858 TGGTGGTATT
Statistics
Matches: 111, Mismatches: 29, Indels: 14
0.72 0.19 0.09
Matches are distributed among these distances:
42 3 0.03
43 15 0.14
44 88 0.79
45 1 0.01
46 4 0.04
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (43 bp):
GATTATCAAAATTTCAAAGGAGGTTATCAAAATTTCATAATGT
Found at i:108988 original size:22 final size:22
Alignment explanation
Indices: 108941--109517 Score: 214
Period size: 22 Copynumber: 26.6 Consensus size: 22
108931 TTATGGAGTA
* *
108941 ATCAAAATTTCA-A-GGAGGAT
1 ATCAAAATTTCATATGAAGGTT
108961 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
**
108983 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATA-TGAAGGTT
* * *
109005 TTCAAAATTTCATAAGAGGGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
109027 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATATGAAGGT-T
* * * *
109049 ATCAAAATATCATAGGGAGATT
1 ATCAAAATTTCATATGAAGGTT
*
109071 AACAAAATTTCATAATG-AGGTT
1 ATCAAAATTTCAT-ATGAAGGTT
** * *
109093 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
*
109115 ATCAAAA--T--T-TGTA-GTT
1 ATCAAAATTTCATATGAAGGTT
* * *
109131 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
109153 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATATGAAGG-TT
* *
109176 ATCAAAATTTTATAGGAAGGTTT
1 ATCAAAATTTCATATGAAGG-TT
* *
109199 ATTAAAATCTCATAGTG-AGGTT
1 ATCAAAATTTCATA-TGAAGGTT
* * *
109221 ATCACAATTTCATAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
* * *
109243 ATCAAAATTTCAGAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
*
109265 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATATGAAGGTT
* * * **
109287 TTTAAATTTTCATA-GCGTGGTT
1 ATCAAAATTTCATATG-AAGGTT
* * *
109309 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* * **
109331 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATA-TGAAGGTT
*
109354 ATC-AAATTTCATTAGGAA-GTT
1 ATCAAAATTTCA-TATGAAGGTT
109375 ATCAAAATTTCATATTG-AGGTCT
1 ATCAAAATTTCATA-TGAAGGT-T
* * * * *
109398 -TCAAAATTCCTTAGGGAGCTT
1 ATCAAAATTTCATATGAAGGTT
*
109419 AACAAAATTTC--AT-AAGGTT
1 ATCAAAATTTCATATGAAGGTT
** * * **
109438 AAAAAAAATTAATAAAAAGGTT
1 ATCAAAATTTCATATGAAGGTT
* * * **
109460 CTCGAAATTCCATA-GTATCGTT
1 ATCAAAATTTCATATG-AAGGTT
* *
109482 ATTAAAATTTCATAGGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
109504 ATCAAAATTTCATA
1 ATCAAAATTTCATA
109518 ATGGGATCAT
Statistics
Matches: 419, Mismatches: 102, Indels: 70
0.71 0.17 0.12
Matches are distributed among these distances:
16 9 0.02
17 2 0.00
18 2 0.00
19 12 0.03
20 15 0.04
21 25 0.06
22 292 0.70
23 61 0.15
24 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATATGAAGGTT
Found at i:109017 original size:44 final size:44
Alignment explanation
Indices: 108960--109517 Score: 266
Period size: 44 Copynumber: 12.8 Consensus size: 44
108950 TCAAGGAGGA
*
108960 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTAGT
* * *
109004 TTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTATGTAG-
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGT-T-TAGT
* * * * * *
109049 -ATCAAAATATCATAGGGAGATTAACAAAATTTCATA-ATGAGGT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTA-GT
** *
109092 TATCAAAAAATCATAGGGAGGTTATCAAAA-TT--T-G--TAGT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTAGT
* * * * **
109130 TATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAG-GGAGGTT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTA-G-T
* * * *
109175 TATCAAAATTTTATAGGAAGGTTTATTAAAATCTCATAG-TGAGGT
1 TATCAAAATTTCATAGGAAGG-TTATCAAAATTTCATAGTTTA-GT
* * * * *
109220 TATCACAATTTCATAGTG-TGATTATCAAAATTTCAGAGTGT-GAT
1 TATCAAAATTTCATAG-GAAGGTTATCAAAATTTCATAGTTTAG-T
* * * ** *
109264 TA-CTAACAA-TTCATATGG-AGGTTTTTAAATTTTCATAGCGTGGT
1 TATC-AA-AATTTCATA-GGAAGGTTATCAAAATTTCATAGTTTAGT
* * * * *
109308 TATCAATATATCATATGG-AGGTTATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-GGAAGGTTATCAAAATTTCATAGT-TTAGT
*
109353 TATC-AAATTTCATTAGGAA-GTTATCAAAATTTCATA-TTGAGGT
1 TATCAAAATTTCA-TAGGAAGGTTATCAAAATTTCATAGTTTA-GT
* * * * *
109396 CT-TCAAAATTCCTTAGGGAGCTTAACAAAATTTCATA----AGGT
1 -TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTA-GT
** * * ** * * * * *
109437 TAAAAAAAATTAATAAAAAGGTTCTCGAAATTCCATAGTATCGT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTAGT
*
109481 TATTAAAATTTCATAGGAAGGTTATCAAAATTTCATA
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
109518 ATGGGATCAT
Statistics
Matches: 387, Mismatches: 92, Indels: 70
0.70 0.17 0.13
Matches are distributed among these distances:
38 26 0.07
39 3 0.01
40 1 0.00
41 28 0.07
42 4 0.01
43 16 0.04
44 236 0.61
45 51 0.13
46 22 0.06
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (44 bp):
TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTAGT
Found at i:109739 original size:30 final size:32
Alignment explanation
Indices: 109685--109750 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
109675 AACTTTATGT
* *
109685 TTTCCGATTGTACCCTTATTTTT-AAAATATA
1 TTTCCAATTGTACCCTTATTTTTAAAAACATA
109716 TTTCCAATTGTACCCTT-TTTTTAAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAAACATA
109747 TTTC
1 TTTC
109751 TGAATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.48
Consensus pattern (32 bp):
TTTCCAATTGTACCCTTATTTTTAAAAACATA
Found at i:109944 original size:37 final size:37
Alignment explanation
Indices: 109874--109969 Score: 122
Period size: 38 Copynumber: 2.6 Consensus size: 37
109864 AATTTGACTT
109874 TTTGTTTCCAACGTCCTATTTAATTTTCCCTTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATTTTCCCTTTTGTC
** * *
109911 TTTGTTTCCAATCGTTGTATTTAATTTTGCTTTTTGT-
1 TTTGTTTCCAA-CGTCCTATTTAATTTTCCCTTTTGTC
*
109948 TTTCGTTTTCAACGTCCTATTT
1 TTT-GTTTCCAACGTCCTATTT
109970 GGGCTTAGAT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
37 22 0.44
38 28 0.56
ACGTcount: A:0.14, C:0.19, G:0.10, T:0.57
Consensus pattern (37 bp):
TTTGTTTCCAACGTCCTATTTAATTTTCCCTTTTGTC
Found at i:110048 original size:22 final size:20
Alignment explanation
Indices: 110023--110141 Score: 85
Period size: 22 Copynumber: 5.5 Consensus size: 20
110013 TGGATGATCC
110023 AATTTCAAAGCACGGTTATCAA
1 AATTTCAAAG-A-GGTTATCAA
* * *
110045 AATTACATAATGTGATTATCAA
1 AATTTCA-AA-GAGGTTATCAA
* *
110067 AATTTCATAGAGGGGTTAACAA
1 AATTTCA-A-AGAGGTTATCAA
*
110089 AATTTTATAGAGAGGTTATCAA
1 AATTTCA-A-AGAGGTTATCAA
110111 AATTTCATAAAGAGGTTATCAA
1 AATTTC--AAAGAGGTTATCAA
*
110133 ATTTTCAAA
1 AATTTCAAA
110142 ATATGATTAC
Statistics
Matches: 80, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
20 3 0.04
22 71 0.89
23 4 0.05
24 2 0.03
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (20 bp):
AATTTCAAAGAGGTTATCAA
Found at i:110162 original size:44 final size:44
Alignment explanation
Indices: 110036--110163 Score: 125
Period size: 44 Copynumber: 2.9 Consensus size: 44
110026 TTCAAAGCAC
* * * * * *
110036 GGTTATCAAAATTACATAATGTGATTATCAAAATTTCATAGAGG
1 GGTTATCAAATTTTCAAAATATGATTATCAAAATTTCATAAAGA
* * * *
110080 GGTTAACAAAATTTT-ATAGAGA-GGTTATCAAAATTTCATAAAGA
1 GGTTATC-AAATTTTCA-AAATATGATTATCAAAATTTCATAAAGA
*
110124 GGTTATCAAATTTTCAAAATATGATTACCAAAATTTCATA
1 GGTTATCAAATTTTCAAAATATGATTATCAAAATTTCATA
110164 GTGGTATTTC
Statistics
Matches: 65, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
43 10 0.15
44 49 0.75
45 6 0.09
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.34
Consensus pattern (44 bp):
GGTTATCAAATTTTCAAAATATGATTATCAAAATTTCATAAAGA
Found at i:110292 original size:22 final size:22
Alignment explanation
Indices: 110264--110425 Score: 138
Period size: 22 Copynumber: 7.5 Consensus size: 22
110254 TCAGGGAGGA
110264 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* **
110286 TATCAAATTTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
110308 TATCAAAATTTC--AT-AAGGT
1 TATCAAAATTTCATATGAAGGT
* *
110327 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * *
110348 ATATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
110371 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
110393 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATATGAAGGT
110415 TATCAAAATTT
1 TATCAAAATTT
110426 GTAGTTATTA
Statistics
Matches: 112, Mismatches: 19, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
18 1 0.01
19 15 0.13
20 1 0.01
21 6 0.05
22 82 0.73
23 7 0.06
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:110313 original size:44 final size:44
Alignment explanation
Indices: 110264--110817 Score: 178
Period size: 44 Copynumber: 12.8 Consensus size: 44
110254 TCAGGGAGGA
* *
110264 TATCAAAATTTCATATGAAGGTTATCAAATTTTCATAGTTTAGT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTAGT
*
110308 TATCAAAATTTCAT---AAGGTTATCAAAATTTCATAGTAT-GT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTAGT
* * * * *
110348 ATATCAAAATTTCATAGGGAGATTAACAAAATTTCATA-ATGAGGT
1 -TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTA-GT
** *
110393 TATCAAAAAATCATAGGGAGGTTATCAAAA-TT--T-G--TAGT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTAGT
* * * * **
110431 TATTAAGATTTCAT--G-AGGTTATCAAAATTTTACAG-GGAGTTT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTAG--T
* * **
110473 TATCAAAATTTTATTGGAAGGTTTATCAAAATTTCATAG-CGAGGT
1 TATCAAAATTTCATAGGAAGG-TTATCAAAATTTCATAGTTTA-GT
* * * * * *
110518 TATC-ACA-TTCATAGTATGATTATCAAAATTTCAGAGTGT-GAT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTAG-T
* * * * ** *** *
110560 TACTGACAA-TTCATATGG-AGGTTTTTAACTTTTCATAACGTGGT
1 TA-TCAAAATTTCATA-GGAAGGTTATCAAAATTTCATAGTTTAGT
* * * *
110604 TATCAATATATCATATGG-AGGTTATCAACATCTT-ATAGTGTTGGT
1 TATCAAAATTTCATA-GGAAGGTTATCAAAAT-TTCATAGT-TTAGT
** * * *
110649 TATTGAAATTTCATTTGGAA-GTTATTAAAACTTT-ATAG-TGAGGT
1 TATCAAAATTTCA-TAGGAAGGTTATCAAAA-TTTCATAGTTTA-GT
* * * * *
110693 CT-TCAAAATTCCTTAGGGAGGTTAAT-AAAATTTCATAAG-ATGGT
1 -TATCAAAATTTCATAGGAAGGTT-ATCAAAATTTCAT-AGTTTAGT
** ** * * * *
110737 TAAAAAAAATTT-ATAAAAAGGTTCTCGAAATTTCATAGTATCGT
1 T-ATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTAGT
**
110781 TATTGAAATTTCATAGGAAGGTTATCAAAATTTCATA
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
110818 AAGATGTCAT
Statistics
Matches: 376, Mismatches: 92, Indels: 84
0.68 0.17 0.15
Matches are distributed among these distances:
35 12 0.03
36 3 0.01
38 12 0.03
39 2 0.01
40 4 0.01
41 38 0.10
42 31 0.08
43 32 0.09
44 167 0.44
45 54 0.14
46 20 0.05
47 1 0.00
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (44 bp):
TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTTTAGT
Found at i:110353 original size:63 final size:65
Alignment explanation
Indices: 110259--110425 Score: 180
Period size: 63 Copynumber: 2.6 Consensus size: 65
110249 AAATTTCAGG
* * ** *
110259 GAGGATATCAAAATTTCATATGAAGGTTATCAAATTTTCATAGTTTAG-TTATCAAAATTTCAT-
1 GAGGTTATCAAAATTTCATATGAAGGTTATCAAAATTTCATAG-GGAGATTAACAAAATTTCATA
110322 A
65 A
* *
110323 -AGGTTATCAAAATTTCATA-GTATGTATATCAAAATTTCATAGGGAGATTAACAAAATTTCATA
1 GAGGTTATCAAAATTTCATATGAAGGT-TATCAAAATTTCATAGGGAGATTAACAAAATTTCATA
110386 A
65 A
** * *
110387 TGAGGTTATCAAAAAATCATAGGGAGGTTATCAAAATTT
1 -GAGGTTATCAAAATTTCATATGAAGGTTATCAAAATTT
110426 GTAGTTATTA
Statistics
Matches: 86, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
62 6 0.07
63 47 0.55
64 1 0.01
66 28 0.33
67 4 0.05
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.35
Consensus pattern (65 bp):
GAGGTTATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGGGAGATTAACAAAATTTCATAA
Found at i:110479 original size:23 final size:23
Alignment explanation
Indices: 110449--110506 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
110439 TTTCATGAGG
* *
110449 TTATCAAAATTTTACAGGGAGTT
1 TTATCAAAATTTTACAGGAAGGT
**
110472 TTATCAAAATTTTATTGGAAGGT
1 TTATCAAAATTTTACAGGAAGGT
110495 TTATCAAAATTT
1 TTATCAAAATTT
110507 CATAGCGAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (23 bp):
TTATCAAAATTTTACAGGAAGGT
Found at i:110517 original size:23 final size:21
Alignment explanation
Indices: 110258--110522 Score: 120
Period size: 22 Copynumber: 12.5 Consensus size: 21
110248 GAAATTTCAG
* *
110258 GGAGGATATCAAAATTTCATA
1 GGAGGTTATCAAAATTTTATA
*
110279 TGAAGGTTATC-AAATTTTCATA
1 -GGAGGTTATCAAAATTTT-ATA
* *
110301 GTTTA-GTTATCAAAATTTCATA
1 G--GAGGTTATCAAAATTTTATA
*
110323 --AGGTTATCAAAATTTCATA
1 GGAGGTTATCAAAATTTTATA
* * *
110342 GTATGTATATCAAAATTTCATA
1 GGAGGT-TATCAAAATTTTATA
* * *
110364 GGGAGATTAACAAAATTTCATAA
1 -GGAGGTTATCAAAATTTTAT-A
* ** *
110387 TGAGGTTATCAAAAAATCATA
1 GGAGGTTATCAAAATTTTATA
110408 GGGAGGTTATCAAAA--TT-T-
1 -GGAGGTTATCAAAATTTTATA
* * * *
110426 GTA-GTTATTAAGATTTCAT-
1 GGAGGTTATCAAAATTTTATA
*
110445 -GAGGTTATCAAAATTTTACA
1 GGAGGTTATCAAAATTTTATA
* *
110465 GGGAGTTTTATCAAAATTTTATT
1 -GGAG-GTTATCAAAATTTTATA
*
110488 GGAAGGTTTATCAAAATTTCATA
1 GG-AGG-TTATCAAAATTTTATA
110511 GCGAGGTTATCA
1 G-GAGGTTATCA
110523 CATTCATAGT
Statistics
Matches: 189, Mismatches: 32, Indels: 44
0.71 0.12 0.17
Matches are distributed among these distances:
16 8 0.04
17 2 0.01
18 3 0.02
19 31 0.16
20 1 0.01
21 11 0.06
22 87 0.46
23 45 0.24
24 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (21 bp):
GGAGGTTATCAAAATTTTATA
Found at i:110530 original size:123 final size:122
Alignment explanation
Indices: 110304--110548 Score: 262
Period size: 123 Copynumber: 2.0 Consensus size: 122
110294 TTTCATAGTT
* * *
110304 TAGTTATCAAAATTTCATAAGGTTATCAAAATTTCATAGTATGTATATCAAAATTTCATAGGGAG
1 TAGTTATCAAAATTTCATAAGGTTATCAAAATTTCACAGGATGTATATCAAAATTTCATAGGAAG
* *
110369 ATTAACAAAATTTCATAATGAGGTTATCAAAAAATCATAGGGA-GGTTATCAAAATTTG
66 ATTAACAAAATTTCATAACGAGGTTATC-AAAAATCATA-GGATGATTATCAAAATTTG
* * * * * * *
110427 TAGTTATTAAGATTTCATGAGGTTATCAAAATTTTACAGGGA-GTTTTATCAAAATTTTATTGGA
1 TAGTTATCAAAATTTCATAAGGTTATCAAAATTTCACA-GGATG-TATATCAAAATTTCATAGGA
* * * * * *
110491 AGGTTTATCAAAATTTCATAGCGAGGTTATC-ACATTCATAGTATGATTATCAAAATTT
64 A-GATTAACAAAATTTCATAACGAGGTTATCAAAAATCATAGGATGATTATCAAAATTT
110549 CAGAGTGTGA
Statistics
Matches: 100, Mismatches: 18, Indels: 8
0.79 0.14 0.06
Matches are distributed among these distances:
122 2 0.02
123 54 0.54
124 19 0.19
125 25 0.25
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (122 bp):
TAGTTATCAAAATTTCATAAGGTTATCAAAATTTCACAGGATGTATATCAAAATTTCATAGGAAG
ATTAACAAAATTTCATAACGAGGTTATCAAAAATCATAGGATGATTATCAAAATTTG
Found at i:110559 original size:22 final size:22
Alignment explanation
Indices: 110495--110561 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
110485 ATTGGAAGGT
* * *
110495 TTATCAAAATTTCATAGCGAGG
1 TTATCAAAATTTCATAGTGTGA
* *
110517 TTATC-ACA-TTCATAGTATGA
1 TTATCAAAATTTCATAGTGTGA
*
110537 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCATAGTGTGA
110559 TTA
1 TTA
110562 CTGACAATTC
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
20 13 0.37
21 4 0.11
22 18 0.51
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGA
Found at i:110737 original size:22 final size:22
Alignment explanation
Indices: 110712--110823 Score: 61
Period size: 22 Copynumber: 5.0 Consensus size: 22
110702 TCCTTAGGGA
110712 GGTTAATAAAATTTCATAAGAT
1 GGTTAATAAAATTTCATAAGAT
* * *
110734 GGTTAAAAAAAATTT-ATAAAAA
1 GGTT-AATAAAATTTCATAAGAT
* *
110756 GGTT-CTCGAAATTTCAT-AGTAT
1 GGTTAAT-AAAATTTCATAAG-AT
* * * * *
110778 CGTTATTGAAATTTCATAGGAA
1 GGTTAATAAAATTTCATAAGAT
110800 GGTT-ATCAAAATTTCATAAAGAT
1 GGTTAAT-AAAATTTCAT-AAGAT
110823 G
1 G
110824 TCATAAAAAT
Statistics
Matches: 65, Mismatches: 17, Indels: 15
0.67 0.18 0.15
Matches are distributed among these distances:
21 8 0.12
22 42 0.65
23 15 0.23
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.35
Consensus pattern (22 bp):
GGTTAATAAAATTTCATAAGAT
Found at i:110856 original size:39 final size:41
Alignment explanation
Indices: 110802--110898 Score: 137
Period size: 40 Copynumber: 2.4 Consensus size: 41
110792 CATAGGAAGG
* *
110802 TTATCAAAATTTCATAAAG-ATGTCAT-AAAAATAGTGTAA
1 TTATCATAATTTCATAAAGAAGGTCATAAAAAATAGTGTAA
*
110841 TTATCATAATTTCAT-AAGAAGGTTATAAAAAATAGTGTAA
1 TTATCATAATTTCATAAAGAAGGTCATAAAAAATAGTGTAA
*
110881 TTATCATAATTTAATAAA
1 TTATCATAATTTCATAAA
110899 AAAGTTATCA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
38 3 0.06
39 19 0.37
40 27 0.53
41 2 0.04
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (41 bp):
TTATCATAATTTCATAAAGAAGGTCATAAAAAATAGTGTAA
Found at i:110984 original size:2 final size:2
Alignment explanation
Indices: 110977--111001 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
110967 CTAATATTAG
110977 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
111002 TAAGCAACTG
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
Done.