Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001826.1 Hibiscus syriacus cultivar Beakdansim tig00003694_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 88639
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:8906 original size:23 final size:23
Alignment explanation
Indices: 8876--8954 Score: 74
Period size: 21 Copynumber: 3.6 Consensus size: 23
8866 GCATGGCCTT
8876 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* * * *
8899 GTGCATCGGTGTACCTTC-ATG-
1 GTGCATCGATGCACATTCAAGGA
* *
8920 GTGTATCGATGTACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
*
8943 -TGCATTGATGCA
1 GTGCATCGATGCA
8955 TTGTTAGGTG
Statistics
Matches: 43, Mismatches: 11, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
21 15 0.35
22 13 0.30
23 15 0.35
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:14877 original size:65 final size:62
Alignment explanation
Indices: 14802--14968 Score: 203
Period size: 65 Copynumber: 2.6 Consensus size: 62
14792 TTCAAAATAG
*
14802 CCTGAGTGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTTAATGTTTTC-ATTATA
1 CCTGAGTGCATCGATGCATGG-TTGTGCATCGATGCATCAAATGCATTCAATG--TTCAATTAT-
14866 T
62 T
* * *
14867 CCTGAGTGCATCGATGCATGGTATGTGCATAGATGCATAAAATGCATTCGATGTTCAATTATT
1 CCTGAGTGCATCGATGCATGGT-TGTGCATCGATGCATCAAATGCATTCAATGTTCAATTATT
* *
14930 CATG-GTGCATCGATGCATGGATTGGTGCATCGGTGCATC
1 CCTGAGTGCATCGATGCATGG-TT-GTGCATCGATGCATC
14969 CGTGCATCCC
Statistics
Matches: 90, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
62 17 0.19
63 20 0.22
64 6 0.07
65 47 0.52
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.34
Consensus pattern (62 bp):
CCTGAGTGCATCGATGCATGGTTGTGCATCGATGCATCAAATGCATTCAATGTTCAATTATT
Found at i:16412 original size:35 final size:35
Alignment explanation
Indices: 16346--16413 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
16336 TACAGTAAGG
**
16346 CCCTGAGCACAAAGCCGAGGAGCCTGTAAGTAAAA
1 CCCTGAGCACAAAGCCGAGGAGCCTCCAAGTAAAA
**
16381 CCCTGAGCACAAAGCCGTTGAGCCTCCAAGTAA
1 CCCTGAGCACAAAGCCGAGGAGCCTCCAAGTAA
16414 TCTTCCTCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.34, C:0.29, G:0.24, T:0.13
Consensus pattern (35 bp):
CCCTGAGCACAAAGCCGAGGAGCCTCCAAGTAAAA
Found at i:16523 original size:24 final size:23
Alignment explanation
Indices: 16490--16581 Score: 103
Period size: 24 Copynumber: 3.9 Consensus size: 23
16480 ACATAATTCA
* *
16490 AGGTAAGTATCATATCAGAATCC
1 AGGTCAGTATCAGATCAGAATCC
16513 AGGTCATGTATCAGATCAGAATCC
1 AGGTCA-GTATCAGATCAGAATCC
* * *
16537 ATGTCAATATCAGATCAGAATCT
1 AGGTCAGTATCAGATCAGAATCC
* *
16560 AGGTCAGGTATCATAACAGAAT
1 AGGTCA-GTATCAGATCAGAAT
16582 TCAAATCAGA
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
23 25 0.43
24 33 0.57
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.26
Consensus pattern (23 bp):
AGGTCAGTATCAGATCAGAATCC
Found at i:19077 original size:13 final size:13
Alignment explanation
Indices: 19059--19090 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
19049 CAACGGTTAA
19059 CGGGTCAACGAGT
1 CGGGTCAACGAGT
*
19072 CGGGTCAACGGGT
1 CGGGTCAACGAGT
19085 CGGGTC
1 CGGGTC
19091 GAGTTGTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.25, G:0.44, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGAGT
Found at i:19915 original size:45 final size:45
Alignment explanation
Indices: 19866--19965 Score: 137
Period size: 45 Copynumber: 2.2 Consensus size: 45
19856 CTTTTTGATA
* * * **
19866 TTTTCAAAAACTTCAGGTCATCTGTAAGCCCTTCAGTGCATTATG
1 TTTTCAAAAACTTCAGGTCATCTATAAGACCTGCAGTGCAGGATG
* *
19911 TTTTCAAAATCTTCGGGTCATCTATAAGACCTGCAGTGCAGGATG
1 TTTTCAAAAACTTCAGGTCATCTATAAGACCTGCAGTGCAGGATG
19956 TTTTCAAAAA
1 TTTTCAAAAA
19966 GCCTTCGGGA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (45 bp):
TTTTCAAAAACTTCAGGTCATCTATAAGACCTGCAGTGCAGGATG
Found at i:20036 original size:45 final size:45
Alignment explanation
Indices: 19982--20140 Score: 237
Period size: 45 Copynumber: 3.5 Consensus size: 45
19972 GGGAGCTTTT
* ** *
19982 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTTCAGTGCA
* *
20027 TGATGTTTTCAAAACCTTCGGGCCATCCATAAGACCTTCAATGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTTCAGTGCA
*
20072 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTTCAGTGCA
20117 TGATGTTTTCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
20141 AGCTTTTTGA
Statistics
Matches: 103, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
45 91 0.88
46 4 0.04
47 8 0.08
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTTCAGTGCA
Found at i:20037 original size:121 final size:121
Alignment explanation
Indices: 19823--20093 Score: 447
Period size: 121 Copynumber: 2.3 Consensus size: 121
19813 GTACGCCCTT
19823 CAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAAACTTCAGGTCATC
1 CAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAAACTTCAGGTCATC
* * * *
19888 TGTAAGCCCTTCAGTGCATTATGTTTTCAAAATCTTCGGGTCATCTATAAGACCTG
66 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGCCATCCATAAGACCTG
* * *
19944 CAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATC
1 CAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAAACTTCAGGTCATC
*
20009 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGCCATCCATAAGACCTT
66 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGCCATCCATAAGACCTG
*
20065 CAATGCATGATGTTTTC-AAAA-CCTTCGGG
1 CAGTGCATGATGTTTTCAAAAAGCCTTCGGG
20094 TCATCCATAA
Statistics
Matches: 140, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
119 8 0.06
120 4 0.03
121 128 0.91
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (121 bp):
CAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAAACTTCAGGTCATC
TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGCCATCCATAAGACCTG
Found at i:20140 original size:166 final size:165
Alignment explanation
Indices: 19861--20304 Score: 676
Period size: 166 Copynumber: 2.7 Consensus size: 165
19851 GGGAGCTTTT
* * * *
19861 TGATATTTTCAAAAACTTCAGGTCATCTGTAAGCCCTTCAGTGCATTATGTTTTCAAAATCTTCG
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAG-CCTTCAGTGCATAATGTTTTCAAAACCTTCG
*
19926 GGTCATCTATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTT
65 GGTCATCTATAAGACCTGCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTT
*
19991 CAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
130 CAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCA
* * ** * *
20027 TGATGTTTTCAAAACCTTCGGGCCATCCATAAGACCTTCAATGCATGATGTTTTCAAAACCTTCG
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAG-CCTTCAGTGCATAATGTTTTCAAAACCTTCG
*
20092 GGTCATCCATAAGACCTGCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTT
65 GGTCATCTATAAGACCTGCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTT
*
20157 CAAAACCTTCAGTTCATCTGTAAGCCCTTCAGTGCA
130 CAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCA
*
20193 TGATATTTTCAAAACCTTCGGATCATCTGTAAGCTCTTCAGTGCATAATGTTTTCAAAACCTTCG
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGC-CTTCAGTGCATAATGTTTTCAAAACCTTCG
* * * *
20258 GGTCATCTGTAAGCCCTTCAGTGCATGATATTTTC-AAAA-CCTTCGGG
65 GGTCATCTATAAGACCTGCAGTGCATGATGTTTTCAAAAAGCCTTCGGG
20305 TCATCTGTAA
Statistics
Matches: 251, Mismatches: 26, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
164 8 0.03
165 5 0.02
166 238 0.95
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (165 bp):
TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCTTCAGTGCATAATGTTTTCAAAACCTTCGG
GTCATCTATAAGACCTGCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTC
AAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:20157 original size:121 final size:119
Alignment explanation
Indices: 20027--20259 Score: 306
Period size: 121 Copynumber: 1.9 Consensus size: 119
20017 CTTCAGTGCA
* * *
20027 TGATGTTTTCAAAACCTTCGGGCCATCCATAAGACCTTCAATGCATGATGTTTTCAAAACCTTCG
1 TGATATTTTCAAAACCTTCAGGCCATCCATAAGACCTTCAATGCATGATATTTTCAAAACCTTCG
* *
20092 GGTCATCCATAAGAC-CTGCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
66 GATCATCCATAAG-CTCTGCAGTGCATAATGTTTTC-AAAA-CCTTCGGGAGCTTTT
** ** * *
20148 TGATATTTTCAAAACCTTCAGTTCATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAACCTTCG
1 TGATATTTTCAAAACCTTCAGGCCATCCATAAGACCTTCAATGCATGATATTTTCAAAACCTTCG
** *
20213 GATCATCTGTAAGCTCTTCAGTGCATAATGTTTTCAAAACCTTCGGG
66 GATCATCCATAAGCTCTGCAGTGCATAATGTTTTCAAAACCTTCGGG
20260 TCATCTGTAA
Statistics
Matches: 97, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
119 8 0.08
120 5 0.05
121 84 0.87
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (119 bp):
TGATATTTTCAAAACCTTCAGGCCATCCATAAGACCTTCAATGCATGATATTTTCAAAACCTTCG
GATCATCCATAAGCTCTGCAGTGCATAATGTTTTCAAAACCTTCGGGAGCTTTT
Found at i:20197 original size:45 final size:45
Alignment explanation
Indices: 20148--20335 Score: 288
Period size: 45 Copynumber: 4.2 Consensus size: 45
20138 GGGAGCTTTT
* *
20148 TGATATTTTCAAAACCTTCAGTTCATCTGTAAGCCCTTCAGTGCA
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
20193 TGATATTTTCAAAACCTTCGGATCATCTGTAAGCTCTTCAGTGCA
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
20238 TAATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
20283 TGATATTTTCAAAACCTTCGGGTCATCTGTAA-CCCTTTAGTACA
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
20327 TGATGTTTT
1 TGATATTTT
20336 TAGGACCTCT
Statistics
Matches: 131, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
44 18 0.14
45 113 0.86
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (45 bp):
TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:20203 original size:76 final size:74
Alignment explanation
Indices: 20072--20213 Score: 194
Period size: 76 Copynumber: 1.9 Consensus size: 74
20062 CTTCAATGCA
* * *
20072 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCATGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAACCTTCAGGTCATCCATAAGACCTGCAGTGCATGATATTTTC-AAAA-CCTT
20137 CGGGAGCTTTT
64 CGGGAGCTTTT
* ** * *
20148 TGATATTTTCAAAACCTTCAGTTCATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAACCTTCG
1 TGATATTTTCAAAACCTTCAGGTCATCCATAAGACCTGCAGTGCATGATATTTTCAAAACCTTCG
20213 G
66 G
20214 ATCATCTGTA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
74 7 0.12
75 4 0.07
76 47 0.81
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.35
Consensus pattern (74 bp):
TGATATTTTCAAAACCTTCAGGTCATCCATAAGACCTGCAGTGCATGATATTTTCAAAACCTTCG
GGAGCTTTT
Found at i:20496 original size:3 final size:3
Alignment explanation
Indices: 20488--20558 Score: 79
Period size: 3 Copynumber: 23.0 Consensus size: 3
20478 TCATTTCGTT
** *
20488 TTA TTA TTA TTA TTA AAA ATA TTA TTA TTA TTA TTA TTA TTA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
* *
20534 TTA TATA TTA TTG TTT TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA
20559 AATAAATAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
3 53 0.90
4 6 0.10
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:28597 original size:18 final size:16
Alignment explanation
Indices: 28560--28608 Score: 71
Period size: 16 Copynumber: 2.9 Consensus size: 16
28550 TTTTCAGATT
28560 CAGATTCCAATTCCCA
1 CAGATTCCAATTCCCA
28576 CAGATTCCAATTCCTTCA
1 CAGATTCCAATTCC--CA
*
28594 CAGATTTCAATTCCC
1 CAGATTCCAATTCCC
28609 TTAGAAACAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 15 0.50
18 15 0.50
ACGTcount: A:0.29, C:0.35, G:0.06, T:0.31
Consensus pattern (16 bp):
CAGATTCCAATTCCCA
Found at i:32920 original size:2 final size:2
Alignment explanation
Indices: 32913--32968 Score: 57
Period size: 2 Copynumber: 29.5 Consensus size: 2
32903 AAGTTATGAC
*
32913 AT AT AT AT AT AT -T AT A- AT -T AC AT AT AT AT ACT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
*
32952 AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
32969 GAGCATACAT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
1 4 0.09
2 39 0.87
3 2 0.04
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:33142 original size:2 final size:2
Alignment explanation
Indices: 33063--33130 Score: 52
Period size: 2 Copynumber: 34.0 Consensus size: 2
33053 TGTGTGTGTG
*
33063 TA TA TA TA TA TA TA TA -A GTA TA TA -A GTA TA TA CA TA TA TGA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA T-A
* * *
33104 TA TA TA TA CA TG TA TA -A CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33131 CATAAGTATA
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
1 3 0.06
2 46 0.87
3 4 0.08
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (2 bp):
TA
Found at i:33142 original size:23 final size:23
Alignment explanation
Indices: 33103--33162 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 23
33093 TACATATATG
33103 ATATAT-ATACAT--GTATA-AC
1 ATATATCATACATAAGTATATAC
33122 ATATAT-ATACATAAGTATATAC
1 ATATATCATACATAAGTATATAC
**
33144 ATGCATCATACATAAGTAT
1 ATATATCATACATAAGTAT
33163 TGTAACACCC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.34
21 5 0.14
22 6 0.17
23 12 0.34
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.35
Consensus pattern (23 bp):
ATATATCATACATAAGTATATAC
Found at i:33263 original size:17 final size:17
Alignment explanation
Indices: 33222--33265 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
33212 TGTATATACT
*
33222 TATGTATATATATTATA
1 TATGTATATATATCATA
* * *
33239 CATTTATATATGTCATA
1 TATGTATATATATCATA
33256 TATGTATATA
1 TATGTATATA
33266 CTTATATATA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.50
Consensus pattern (17 bp):
TATGTATATATATCATA
Found at i:33330 original size:15 final size:15
Alignment explanation
Indices: 33305--33343 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
33295 TAAATTATTA
*
33305 CATATATATATACAT
1 CATACATATATACAT
33320 GCATA-ATATATACAT
1 -CATACATATATACAT
33335 CATACATAT
1 CATACATAT
33344 TTTATAACTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.18
15 14 0.64
16 4 0.18
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.36
Consensus pattern (15 bp):
CATACATATATACAT
Found at i:34384 original size:2 final size:2
Alignment explanation
Indices: 34379--34412 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
34369 CATTTTGTGC
34379 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34413 TTTTTGTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:35173 original size:61 final size:61
Alignment explanation
Indices: 35077--35196 Score: 188
Period size: 61 Copynumber: 2.0 Consensus size: 61
35067 GACGCATCGA
* *
35077 GGACAACATCGTGTTATAGGAGGAACCCAACTTAGGGACATGGAGAAAATGAAGCTTGTCG
1 GGACAACATCGTGTCATAGGAGAAACCCAACTTAGGGACATGGAGAAAATGAAGCTTGTCG
* *
35138 GGACAACA-CTGTGTCATGGGAGAAACCCGACTTAGGGACATGGAGAAAATGAAGCTTGT
1 GGACAACATC-GTGTCATAGGAGAAACCCAACTTAGGGACATGGAGAAAATGAAGCTTGT
35197 AAAATTTGAC
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
60 1 0.02
61 53 0.98
ACGTcount: A:0.34, C:0.17, G:0.30, T:0.19
Consensus pattern (61 bp):
GGACAACATCGTGTCATAGGAGAAACCCAACTTAGGGACATGGAGAAAATGAAGCTTGTCG
Found at i:35312 original size:14 final size:13
Alignment explanation
Indices: 35280--35336 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 13
35270 ATTAGCACCT
*
35280 TTTTGCATTTGTA
1 TTTTGCATTTGCA
35293 -TTTGCACTTTGCA
1 TTTTGCA-TTTGCA
35306 TTTTGCATTTTGCA
1 TTTTGCA-TTTGCA
*
35320 TTTTTGCGTTTGC-
1 -TTTTGCATTTGCA
35333 TTTT
1 TTTT
35337 TATATTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
12 10 0.26
13 5 0.13
14 17 0.45
15 6 0.16
ACGTcount: A:0.11, C:0.14, G:0.16, T:0.60
Consensus pattern (13 bp):
TTTTGCATTTGCA
Found at i:35326 original size:8 final size:7
Alignment explanation
Indices: 35280--35323 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
35270 ATTAGCACCT
35280 TTTTGCA
1 TTTTGCA
*
35287 -TTTGTA
1 TTTTGCA
35293 -TTTGCA
1 TTTTGCA
*
35299 CTTTGCA
1 TTTTGCA
35306 TTTTGCA
1 TTTTGCA
35313 TTTTGCA
1 TTTTGCA
35320 TTTT
1 TTTT
35324 TGCGTTTGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
6 10 0.30
7 23 0.70
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (7 bp):
TTTTGCA
Found at i:41241 original size:45 final size:44
Alignment explanation
Indices: 41080--41260 Score: 154
Period size: 45 Copynumber: 4.1 Consensus size: 44
41070 AGACCAACAT
* * *
41080 AGCATATCCACTTTTCTAGATTTGATCTTCCCTAAAGAGTAGTGG
1 AGCATAT-CATTTTTCTAGATTTGATCTTCCCTAAAGAGCAATGG
* * * **
41125 AGCAAATC-TATCTC-A-ATTCAATCTTCCCTAAAGAGCAATGG
1 AGCATATCATTTTTCTAGATTTGATCTTCCCTAAAGAGCAATGG
* * * * *
41166 AGTGAATAAT-TTTTTTCCAGATCTGATCTTCCCTGAAGAGCAATGG
1 A--GCAT-ATCATTTTTCTAGATTTGATCTTCCCTAAAGAGCAATGG
* *
41212 AGCATATCCATTTTTCTAGATTTGATCTTCCTTGAAGAGCAATGG
1 AGCATAT-CATTTTTCTAGATTTGATCTTCCCTAAAGAGCAATGG
41257 AGCA
1 AGCA
41261 GATCTAACTC
Statistics
Matches: 107, Mismatches: 21, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
41 23 0.21
42 1 0.01
43 7 0.07
44 10 0.09
45 43 0.40
46 23 0.21
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (44 bp):
AGCATATCATTTTTCTAGATTTGATCTTCCCTAAAGAGCAATGG
Found at i:41320 original size:132 final size:131
Alignment explanation
Indices: 40913--41328 Score: 435
Period size: 132 Copynumber: 3.2 Consensus size: 131
40903 AGATCACCTC
* * * * * * *
40913 ATTTTCCAGATCTGATCTTCCCTGGAGAGTAATAAAACAAATCCTTTTTTTCCAGATTTGATC-T
1 ATTTTTCAGATCTGATCTTCCCTGAAGAGCAATAAAGCATATCC-ATTTTTCTAGATTTGATCTT
* * * *
40977 CCTCTAAAGAGCAGT-GAGCAAATCTACCCCGATTCAATCTTCCCCAAAGAATAGTGGAGTGAAT
65 CCT-TAAAGAGCAGTGGAGCAAATCTAACTCGATTCAATCTTCCCTAAAGAGTAGTGGAGTGAA-
41041 TAAA
128 TAAA
* * ** * * * *
41045 ATTTTTCAGATATGATATTCATTGAAGACCAACATAGCATATCCACTTTTCTAGATTTGATCTTC
1 ATTTTTCAGATCTGATCTTCCCTGAAGAGCAATAAAGCATATCCATTTTTCTAGATTTGATCTTC
* * * * * *
41110 CCTAAAGAGTAGTGGAGCAAATCTATCTCAATTCAATCTTCCCTAAAGAGCAATGGAGTGAATAA
66 CTTAAAGAGCAGTGGAGCAAATCTAACTCGATTCAATCTTCCCTAAAGAGTAGTGGAGTGAATAA
*
41175 T
131 A
* **
41176 TTTTTTCCAGATCTGATCTTCCCTGAAGAGCAATGGAGCATATCCATTTTTCTAGATTTGATCTT
1 ATTTTT-CAGATCTGATCTTCCCTGAAGAGCAATAAAGCATATCCATTTTTCTAGATTTGATCTT
* * *
41241 CCTTGAAGAGCAATGGAGCAGATCTAACTCGATTCAATCTTCCCTGAAA-AGTAGTGGAGTGAAT
65 CCTTAAAGAGCAGTGGAGCAAATCTAACTCGATTCAATCTTCCCT-AAAGAGTAGTGGAGTGAAT
41305 CAAAA
129 --AAA
* *
41310 AATTTT-AGATCTAATCTTC
1 ATTTTTCAGATCTGATCTTC
41329 ATTGAGTAGA
Statistics
Matches: 230, Mismatches: 48, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
131 33 0.14
132 188 0.82
133 3 0.01
134 6 0.03
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (131 bp):
ATTTTTCAGATCTGATCTTCCCTGAAGAGCAATAAAGCATATCCATTTTTCTAGATTTGATCTTC
CTTAAAGAGCAGTGGAGCAAATCTAACTCGATTCAATCTTCCCTAAAGAGTAGTGGAGTGAATAA
A
Found at i:41627 original size:14 final size:14
Alignment explanation
Indices: 41608--41634 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41598 ATCTCACTTG
41608 AAATTTGTTTTACA
1 AAATTTGTTTTACA
41622 AAATTTGTTTTAC
1 AAATTTGTTTTAC
41635 TTAAAGTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.52
Consensus pattern (14 bp):
AAATTTGTTTTACA
Found at i:42333 original size:21 final size:21
Alignment explanation
Indices: 42285--42334 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
42275 ATTACTATCT
42285 CAATGCGATTTTCCAATTTCG
1 CAATGCGATTTTCCAATTTCG
**
42306 CGTTGCGATTTTCCCAA-TTCG
1 CAATGCGATTTT-CCAATTTCG
42327 CAATGCGA
1 CAATGCGA
42335 ATAAGTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (21 bp):
CAATGCGATTTTCCAATTTCG
Found at i:42367 original size:21 final size:21
Alignment explanation
Indices: 42324--42437 Score: 83
Period size: 21 Copynumber: 5.5 Consensus size: 21
42314 TTTTCCCAAT
* *
42324 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTAGAAAA
*
42344 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTAGAAAA
* **
42365 TCGCAATGCG-ATACT-GACTA
1 TCGCAATGCGAAT-TTAGAAAA
* * *
42385 TCGCAACGCG-ATAATACAAAA
1 TCGCAATGCGAAT-TTAGAAAA
* *
42406 TCACAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTAGAAAA
42427 TCGCAATGCGA
1 TCGCAATGCGA
42438 TATTGACTAT
Statistics
Matches: 73, Mismatches: 17, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
20 30 0.41
21 41 0.56
22 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTTAGAAAA
Found at i:42375 original size:62 final size:60
Alignment explanation
Indices: 42324--42462 Score: 163
Period size: 62 Copynumber: 2.3 Consensus size: 60
42314 TTTTCCCAAT
* * * *
42324 TCGCAATGCGAATAAGT-AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTA
1 TCGCAACGCG-ATAA-TAAAATCACAATGCGAATTTGGAAAATCGCAATGCGATACTCACAA
* * *
42385 TCGCAACGCGATAATACAAAATCACAATGCGAATTTGGAAAATCGCAATGCGATATTGACTA
1 TCGCAACGCGATAAT--AAAATCACAATGCGAATTTGGAAAATCGCAATGCGATACTCACAA
*
42447 TCGCAATGCGATAATA
1 TCGCAACGCGATAATA
42463 CAAAATCGCA
Statistics
Matches: 71, Mismatches: 4, Indels: 7
0.87 0.05 0.09
Matches are distributed among these distances:
59 1 0.01
60 5 0.07
61 9 0.13
62 56 0.79
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (60 bp):
TCGCAACGCGATAATAAAATCACAATGCGAATTTGGAAAATCGCAATGCGATACTCACAA
Found at i:42451 original size:20 final size:20
Alignment explanation
Indices: 42426--42580 Score: 93
Period size: 20 Copynumber: 7.7 Consensus size: 20
42416 AATTTGGAAA
*
42426 ATCGCAATGCGATATTGACT
1 ATCGCAACGCGATATTGACT
* * *
42446 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATATTGAC--T
*
42467 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATATTGACT
* * ** *
42487 TTCGCAATGTTATACTGACT
1 ATCGCAACGCGATATTGACT
*
42507 TTCGCAACGCGAT-TCTGACT
1 ATCGCAACGCGATAT-TGACT
* *
42527 TTCGCAACGCAAT-TCTGACT
1 ATCGCAACGCGATAT-TGACT
* *
42547 TTCGCAACGAGAT-TCTGACT
1 ATCGCAACGCGATAT-TGACT
*
42567 ATCGCAACGAGATA
1 ATCGCAACGCGATA
42581 ATACATGATC
Statistics
Matches: 113, Mismatches: 17, Indels: 9
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.02
20 95 0.84
21 14 0.12
22 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (20 bp):
ATCGCAACGCGATATTGACT
Found at i:42463 original size:62 final size:62
Alignment explanation
Indices: 42341--42478 Score: 240
Period size: 62 Copynumber: 2.2 Consensus size: 62
42331 GCGAATAAGT
42341 AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGATAATACA
1 AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGATAATACA
* * *
42403 AAATCACAATGCGAATTTGGAAAATCGCAATGCGATATTGACTATCGCAATGCGATAATACA
1 AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGATAATACA
*
42465 AAATCGCAACGCGA
1 AAATCGCAATGCGA
42479 TACTGACTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 71 1.00
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (62 bp):
AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGATAATACA
Found at i:42472 original size:21 final size:21
Alignment explanation
Indices: 42361--42480 Score: 88
Period size: 21 Copynumber: 5.8 Consensus size: 21
42351 GCGAATTTGG
*
42361 AAAATCGCAATGCGATACTGAC
1 AAAATCGCAATGCGATAAT-AC
* *
42383 --TATCGCAACGCGATAATAC
1 AAAATCGCAATGCGATAATAC
* * **
42402 AAAATCACAATGCGA-ATTTGG
1 AAAATCGCAATGCGATA-ATAC
*
42423 AAAATCGCAATGCGATATTGAC
1 AAAATCGCAATGCGATAAT-AC
*
42445 --TATCGCAATGCGATAATAC
1 AAAATCGCAATGCGATAATAC
*
42464 AAAATCGCAACGCGATA
1 AAAATCGCAATGCGATA
42481 CTGACTTTCG
Statistics
Matches: 75, Mismatches: 16, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
19 4 0.05
20 30 0.40
21 40 0.53
22 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.21
Consensus pattern (21 bp):
AAAATCGCAATGCGATAATAC
Found at i:42525 original size:40 final size:40
Alignment explanation
Indices: 42468--42575 Score: 153
Period size: 40 Copynumber: 2.7 Consensus size: 40
42458 TAATACAAAA
* * **
42468 TCGCAACGCGATACTGACTTTCGCAATGTTATACTGACTT
1 TCGCAACGCGATTCTGACTTTCGCAACGCAATACTGACTT
*
42508 TCGCAACGCGATTCTGACTTTCGCAACGCAATTCTGACTT
1 TCGCAACGCGATTCTGACTTTCGCAACGCAATACTGACTT
* *
42548 TCGCAACGAGATTCTGACTATCGCAACG
1 TCGCAACGCGATTCTGACTTTCGCAACG
42576 AGATAATACA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.29
Consensus pattern (40 bp):
TCGCAACGCGATTCTGACTTTCGCAACGCAATACTGACTT
Found at i:43347 original size:24 final size:24
Alignment explanation
Indices: 43320--43373 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
43310 GTATTCGAAA
*
43320 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
43344 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
43368 TTTGAT
1 TTTGAT
43374 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:43565 original size:12 final size:12
Alignment explanation
Indices: 43548--43572 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43538 ATATAATCCT
43548 GAAGAAGAAAAA
1 GAAGAAGAAAAA
43560 GAAGAAGAAAAA
1 GAAGAAGAAAAA
43572 G
1 G
43573 TCCCTGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:45917 original size:19 final size:20
Alignment explanation
Indices: 45875--45929 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
45865 CAATCATCTT
*
45875 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGCGGA
45895 AATGACTATCGCAATC-C-GA
1 AATGACTATCGCAA-CGCGGA
**
45914 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
45930 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 1 0.03
19 14 0.47
20 14 0.47
21 1 0.03
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (20 bp):
AATGACTATCGCAACGCGGA
Found at i:45948 original size:33 final size:33
Alignment explanation
Indices: 45902--46028 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
45892 GGAAATGACT
*
45902 ATCGCAATCCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
45935 ATCGCAATGCGAAATGAAAATCGCAACAACAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
45968 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
46001 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
46029 CGAATTTAGT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:45958 original size:19 final size:18
Alignment explanation
Indices: 45882--46032 Score: 85
Period size: 19 Copynumber: 8.7 Consensus size: 18
45872 CTTAATGTCT
**
45882 ATCGCAACGCGGAAATGACT
1 ATCGCAA-GC-GAAATGAAA
*
45902 ATCGCAATCCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
45921 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
45935 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
45954 ATCGCAA-C-AACA-G--A
1 ATCGCAAGCGAA-ATGAAA
45968 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
45987 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
46001 ATCGCAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
46020 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
46033 TTTAGTTTCG
Statistics
Matches: 103, Mismatches: 10, Indels: 37
0.69 0.07 0.25
Matches are distributed among these distances:
14 25 0.24
15 4 0.04
16 9 0.09
17 9 0.09
18 4 0.04
19 44 0.43
20 8 0.08
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:46070 original size:19 final size:19
Alignment explanation
Indices: 46028--46104 Score: 85
Period size: 19 Copynumber: 4.3 Consensus size: 19
46018 AAATCGCAAC
* *
46028 GCGAATTTAGTTTCGTGTT
1 GCGATTTTAGTTTCGCGTT
46047 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
46066 GCGATTTT-G--T--CGTT
1 GCGATTTTAGTTTCGCGTT
46080 GCGATTTTCA-TTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
46099 GCGATT
1 GCGATT
46105 CTCTCGTTAC
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
14 12 0.24
16 1 0.02
17 1 0.02
18 1 0.02
19 35 0.70
ACGTcount: A:0.12, C:0.16, G:0.26, T:0.47
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:46086 original size:33 final size:33
Alignment explanation
Indices: 46044--46169 Score: 200
Period size: 33 Copynumber: 3.8 Consensus size: 33
46034 TTAGTTTCGT
* *
46044 GTTGCGATTTT-AGTTTCGCGTTGCGATTTTGTC
1 GTTGCGATTTTCA-TTTCGCGTTGCGATTCTCTC
46077 GTTGCGATTTTCATTTCGCGTTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCGTTGCGATTCTCTC
*
46110 GTTACGATTTTCATTTCGCGTTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCGTTGCGATTCTCTC
*
46143 GTTGCGATTTTCATTTCGCATTGCGAT
1 GTTGCGATTTTCATTTCGCGTTGCGAT
46170 AGTCATTTTT
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
33 86 0.99
34 1 0.01
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.46
Consensus pattern (33 bp):
GTTGCGATTTTCATTTCGCGTTGCGATTCTCTC
Found at i:46136 original size:19 final size:19
Alignment explanation
Indices: 46038--46169 Score: 89
Period size: 19 Copynumber: 7.7 Consensus size: 19
46028 GCGAATTTAG
*
46038 TTTCGTGTTGCGATTTT-A
1 TTTCGCGTTGCGATTTTCA
46056 GTTTCGCGTTGCGA-TTT--
1 -TTTCGCGTTGCGATTTTCA
*
46073 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
46090 TTTCGCGTTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
* *
46106 --TCTCGTTACGATTTTCA
1 TTTCGCGTTGCGATTTTCA
46123 TTTCGCGTTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
*
46139 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
46156 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
46170 AGTCATTTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
14 27 0.31
15 3 0.03
16 8 0.09
17 8 0.09
18 3 0.03
19 39 0.44
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:46147 original size:14 final size:14
Alignment explanation
Indices: 46095--46151 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
46085 TTTCATTTCG
46095 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
46109 CGTTACGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
46128 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
46142 CGTTGCGATT
1 CGTTGCGATT
46152 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:46295 original size:14 final size:14
Alignment explanation
Indices: 46276--46312 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
46266 CATCAATTAA
46276 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
46290 ACAAATCATCTTTT
1 ACAAATCAACTTTT
46304 ACAAATCAA
1 ACAAATCAA
46313 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:47697 original size:21 final size:21
Alignment explanation
Indices: 47668--47748 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
47658 GAATGGTGGG
*
47668 AGGGACCTCTTCAACGATGAC
1 AGGGGCCTCTTCAACGATGAC
* * * **
47689 AGTGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTCAACGATGAC
* * *
47710 AGGGGACTC-TCAAGGAATGAT
1 AGGGGCCTCTTCAACG-ATGAC
47731 AGGGGCCTCTTCAACGAT
1 AGGGGCCTCTTCAACGAT
47749 AGGAGTGGAC
Statistics
Matches: 43, Mismatches: 15, Indels: 4
0.69 0.24 0.06
Matches are distributed among these distances:
20 4 0.09
21 34 0.79
22 5 0.12
ACGTcount: A:0.25, C:0.22, G:0.32, T:0.21
Consensus pattern (21 bp):
AGGGGCCTCTTCAACGATGAC
Found at i:47738 original size:42 final size:41
Alignment explanation
Indices: 47653--47761 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 41
47643 GTGAATCGGG
* *
47653 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCAACGATGACAGGGGC
* *
47695 CTCTTGAACGGTGGGAGGGGACTCTCAAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCAACG-ATGACAGGGGC
* * * *
47737 CTCTTCAACGATAGGAGTGGACTCT
1 CTCTTGAACGGTGGGAGGGGACTCT
47762 TGAGGGATGA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
41 5 0.09
42 48 0.84
43 4 0.07
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCAACGATGACAGGGGC
Found at i:48325 original size:94 final size:94
Alignment explanation
Indices: 48164--48468 Score: 476
Period size: 94 Copynumber: 3.3 Consensus size: 94
48154 GAATAGTTTC
** * *
48164 AATTGGCAGCAAATGAACAAATTTACTTTCAACCAAAAGATAAAACAAAGAAAAATACTAACTTC
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
48229 ACAGTGTTAAAGAATACACAGTTTAGCAG
66 ACAGTGTTAAAGAATACACAGTTTAGCAG
*
48258 AATTGGCAGCAACCGAACAAATTTACTTTCAGCCAAAAGACAAAACAAAGACAAATACTAACTTC
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
48323 ACAGTGTTAAAGAATACACAGTTTAGCAG
66 ACAGTGTTAAAGAATACACAGTTTAGCAG
* *
48352 AATTGGCAGTAACCGAATAAATTTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTT
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTT
*
48416 CACAGTGTT----AATAAACAGTTTAGCAG
65 CACAGTGTTAAAGAATACACAGTTTAGCAG
* *
48442 TATTGGCAGCAACCGAATAAATTTACT
1 AATTGGCAGCAACCGAACAAATTTACT
48469 AAGCAATCTA
Statistics
Matches: 198, Mismatches: 11, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
90 40 0.20
93 18 0.09
94 140 0.71
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (94 bp):
AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
ACAGTGTTAAAGAATACACAGTTTAGCAG
Found at i:50250 original size:33 final size:33
Alignment explanation
Indices: 50189--50287 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
50179 AGAGAATGAA
**
50189 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGAAAATCGCAACGAGAG
*
50223 AATCGCAACGCGAAATGAAAATTGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
50256 AATCGCAACGCGAAATGAAAATCGCAACGAGA
1 AATCGCAACGCGAAATGAAAATCGCAACGAGA
50288 AATGAAAATC
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 50 0.82
34 11 0.18
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:50251 original size:19 final size:19
Alignment explanation
Indices: 50161--50306 Score: 123
Period size: 19 Copynumber: 8.1 Consensus size: 19
50151 TCTTTTGGTT
* *
50161 GAAATGAAAATCACAACGA
1 GAAATGAAAATCGCAACGC
50180 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
50200 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
50218 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
50234 GAAATGAAAATTGCAA--C
1 GAAATGAAAATCGCAACGC
*
50251 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
50267 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
50286 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
50305 GA
1 GA
50307 TAGTCATATT
Statistics
Matches: 101, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
14 18 0.18
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 42 0.42
20 27 0.27
21 2 0.02
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:50325 original size:20 final size:20
Alignment explanation
Indices: 50313--50530 Score: 129
Period size: 20 Copynumber: 10.7 Consensus size: 20
50303 GCGATAGTCA
*
50313 TATTCGCATTGCGATTTGCG
1 TATTCGCATTGCGATTTACG
* * *
50333 TATTCGCGTTGCGATTTTCC
1 TATTCGCATTGCGATTTACG
*
50353 TAATTCGCATTGCGATTTACT
1 T-ATTCGCATTGCGATTTACG
*
50374 TAATCGCATTGCGATTTACG
1 TATTCGCATTGCGATTTACG
* *
50394 TATTCGCATTGCGAATTATG
1 TATTCGCATTGCGATTTACG
* * ** *
50414 AAAATCGCAACGCGA-ATACG
1 -TATTCGCATTGCGATTTACG
* * * *
50434 TAAATCGCAATGCGAATTAGG
1 T-ATTCGCATTGCGATTTACG
* *
50455 AAAATT-GCATTGCGATAGT-CAG
1 --TATTCGCATTGCGAT-TTAC-G
* *
50477 TA-TCGCATTGCGATTTTCCA
1 TATTCGCATTGCGA-TTTACG
* *
50497 AATTCGCATTGCGATTTACT
1 TATTCGCATTGCGATTTACG
50517 TATTCGCATTGCGA
1 TATTCGCATTGCGA
50531 ATTGGGAAAA
Statistics
Matches: 152, Mismatches: 34, Indels: 24
0.72 0.16 0.11
Matches are distributed among these distances:
19 1 0.01
20 96 0.63
21 51 0.34
22 4 0.03
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (20 bp):
TATTCGCATTGCGATTTACG
Found at i:50360 original size:41 final size:40
Alignment explanation
Indices: 50313--50530 Score: 127
Period size: 41 Copynumber: 5.3 Consensus size: 40
50303 GCGATAGTCA
* * * *
50313 TATTCGCATTGCGATTTGCGTATTCGCGTTGCGATTTTCC
1 TATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACC
* *
50353 TAATTCGCATTGCGATTTACTTAATCGCATTGCGATTTACG
1 T-ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACC
* * * ** * *
50394 TATTCGCATTGCGAATTATGAAAATCGCAACGCGA-ATACG
1 TATTCGCATTGCGATTTACG-TAATCGCATTGCGATTTACC
* * * * * * * *
50434 TAAATCGCAATGCGAATTAGGAAAATTGCATTGCGATAGT-CAG
1 T-ATTCGCATTGCGATTTACG-TAATCGCATTGCGAT-TTAC-C
* ** *
50477 TA-TCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACT
1 TATTCGCATTGCGATTTACGTAA-TCGCATTGCGATTTACC
50517 TATTCGCATTGCGA
1 TATTCGCATTGCGA
50531 ATTGGGAAAA
Statistics
Matches: 141, Mismatches: 28, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
40 28 0.20
41 108 0.77
42 2 0.01
43 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (40 bp):
TATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACC
Found at i:50422 original size:61 final size:60
Alignment explanation
Indices: 50316--50530 Score: 166
Period size: 61 Copynumber: 3.5 Consensus size: 60
50306 ATAGTCATAT
* * * * * * *
50316 TCGCATTGCGATTTGCGTATTCGCGTTGCGATTTTCCTAATTCGCATTGCGATTTACTTAA
1 TCGCATTGCGATTTACGTATTCGCATTGCGATTAT-CAAAATCGCAATGCGATTTACTAAA
* * *
50377 TCGCATTGCGATTTACGTATTCGCATTGCGAATTATGAAAATCGCAACGCGA-ATACGTAAA
1 TCGCATTGCGATTTACGTATTCGCATTGCG-ATTATCAAAATCGCAATGCGATTTAC-TAAA
* * * * ** * * *
50438 TCGCAATGCGAATTAGGAAAATT-GCATTGCGA-TAGTCAGTATCGCATTGCGATTTTCCAAA
1 TCGCATTGCGATTTACG--TATTCGCATTGCGATTA-TCAAAATCGCAATGCGATTTACTAAA
*
50499 TTCGCATTGCGATTTACTTATTCGCATTGCGA
1 -TCGCATTGCGATTTACGTATTCGCATTGCGA
50531 ATTGGGAAAA
Statistics
Matches: 119, Mismatches: 27, Indels: 16
0.73 0.17 0.10
Matches are distributed among these distances:
60 8 0.07
61 81 0.68
62 27 0.23
63 3 0.03
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (60 bp):
TCGCATTGCGATTTACGTATTCGCATTGCGATTATCAAAATCGCAATGCGATTTACTAAA
Found at i:66368 original size:19 final size:19
Alignment explanation
Indices: 66346--66389 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
66336 TTCATTAGGC
*
66346 TATGAATCT-AAAATTAAAT
1 TATGAATATGAAAA-TAAAT
*
66365 TATGAATATGAAAATAAGT
1 TATGAATATGAAAATAAAT
66384 TATGAA
1 TATGAA
66390 GTTGGAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.34
Consensus pattern (19 bp):
TATGAATATGAAAATAAAT
Found at i:66492 original size:13 final size:13
Alignment explanation
Indices: 66460--66508 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
66450 ATGAGTTGTA
*
66460 AAAATGAATG-TG
1 AAAATGAAAGATG
*
66472 AAAGTGAAAGATG
1 AAAATGAAAGATG
*
66485 AAAATGAAATATG
1 AAAATGAAAGATG
66498 AAATATGAAAG
1 AAA-ATGAAAG
66509 TTCTCGAATG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
12 8 0.27
13 16 0.53
14 6 0.20
ACGTcount: A:0.57, C:0.00, G:0.22, T:0.20
Consensus pattern (13 bp):
AAAATGAAAGATG
Found at i:70968 original size:20 final size:21
Alignment explanation
Indices: 70930--70970 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
70920 AGACACACGG
70930 TACAAGACACTAGAGTGTATA
1 TACAAGACACTAGAGTGTATA
*
70951 TACAAGACACT-TAGTGTATA
1 TACAAGACACTAGAGTGTATA
70971 AGGTGGGCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (21 bp):
TACAAGACACTAGAGTGTATA
Found at i:71099 original size:17 final size:15
Alignment explanation
Indices: 71077--71112 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
71067 TGGAAATATT
71077 TTATAATTATAATTATA
1 TTATAATTA-AATTA-A
71094 TTATAATTAAATTAA
1 TTATAATTAAATTAA
71109 TTAT
1 TTAT
71113 GGAAATATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 5 0.26
17 9 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATAATTAAATTAA
Found at i:76036 original size:19 final size:20
Alignment explanation
Indices: 76000--76037 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
75990 ATCGACATCA
76000 ACCCTTGAGTATCAGTACCC
1 ACCCTTGAGTATCAGTACCC
*
76020 ACCCTTG-GTATCGGTACC
1 ACCCTTGAGTATCAGTACC
76038 AAATTTGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.21, C:0.34, G:0.18, T:0.26
Consensus pattern (20 bp):
ACCCTTGAGTATCAGTACCC
Found at i:80843 original size:21 final size:20
Alignment explanation
Indices: 80805--80851 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
80795 AATTAAACTT
* *
80805 AAAAAATAAAATCCAAATAA
1 AAAAAATAAAAACAAAATAA
80825 ATAAAAATAAAAACAAAATTAA
1 A-AAAAATAAAAACAAAA-TAA
80847 AAAAA
1 AAAAA
80852 GAAAGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 18 0.78
22 4 0.17
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (20 bp):
AAAAAATAAAAACAAAATAA
Done.