Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004433.1 Hibiscus syriacus cultivar Beakdansim tig00009719_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: 137031
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:85 original size:39 final size:39
Alignment explanation
Indices: 26--171 Score: 127
Period size: 39 Copynumber: 3.6 Consensus size: 39
16 AGATTCTCAA
** *
26 GAAAATAAATTCAATGATTTATTTTCTTTTACAAGATAG
1 GAAAATAAATTCAACAATTTATTTCCTTTTACAAGATAG
* * * *
65 GAAAATAAATTTAACAATTTATTCCCTTTTACAA-ACAT
1 GAAAATAAATTCAACAATTTATTTCCTTTTACAAGATAG
* *
103 GAAAAT-AA-TCAAACAATTTATTTCCTTTTAAAATAGAATCATAA
1 GAAAATAAATTC-AACAATTTATTTCCTTTT-ACA-AG----ATAG
147 GAAAATAAATTCAACAATTTATTTC
1 GAAAATAAATTCAACAATTTATTTC
172 TTTATTCAAA
Statistics
Matches: 85, Mismatches: 12, Indels: 14
0.77 0.11 0.13
Matches are distributed among these distances:
36 1 0.01
37 19 0.22
38 10 0.12
39 30 0.35
44 8 0.09
45 15 0.18
46 2 0.02
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (39 bp):
GAAAATAAATTCAACAATTTATTTCCTTTTACAAGATAG
Found at i:130 original size:37 final size:39
Alignment explanation
Indices: 42--132 Score: 114
Period size: 37 Copynumber: 2.4 Consensus size: 39
32 AAATTCAATG
* * **
42 ATTTATTTTCTTTTACAAGATAGGAAAATAAATTTAACA
1 ATTTATTTCCTTTTACAAGACAGGAAAATAAATCAAACA
* *
81 ATTTATTCCCTTTTACAA-ACATGAAAAT-AATCAAACA
1 ATTTATTTCCTTTTACAAGACAGGAAAATAAATCAAACA
118 ATTTATTTCCTTTTA
1 ATTTATTTCCTTTTA
133 AAATAGAATC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 21 0.47
38 8 0.18
39 16 0.36
ACGTcount: A:0.41, C:0.13, G:0.04, T:0.42
Consensus pattern (39 bp):
ATTTATTTCCTTTTACAAGACAGGAAAATAAATCAAACA
Found at i:464 original size:59 final size:59
Alignment explanation
Indices: 292--574 Score: 312
Period size: 57 Copynumber: 4.9 Consensus size: 59
282 AATCATCCAC
* * * * * * *
292 GATTCTCAA-TAACATAAATTCGATAAT-TA-TTTTCCTGACAAAATTAAAATCATTCAA
1 GATTCTCAAGGAA-ATAAATTCAACAATCTATTTTTCCTTACAAAGTTAGAATCATTTAA
* * *
349 GATTC-CAAAGAAATAAATTCAACAATTTATTTTT--TTACAAAGTTATAATCATTTAA
1 GATTCTCAAGGAAATAAATTCAACAATCTATTTTTCCTTACAAAGTTAGAATCATTTAA
* * *
405 GATTCTCAAGGAAACAAATTCAACAATCTATTTTTCCTTATAAAGTTATAATCATTTAA
1 GATTCTCAAGGAAATAAATTCAACAATCTATTTTTCCTTACAAAGTTAGAATCATTTAA
* * *
464 GATTCACAAGGAAATAAATTC-ACAACCTA-TTTTCCTTACAAAGTTAGAATCATTAAA
1 GATTCTCAAGGAAATAAATTCAACAATCTATTTTTCCTTACAAAGTTAGAATCATTTAA
* * * * *
521 GATTCTCAATGAAATAAATTTAACTATTTATTTTTCCTTACGAAGTTAGAATCA
1 GATTCTCAAGGAAATAAATTCAACAATCTATTTTTCCTTACAAAGTTAGAATCA
575 ACACAAGATT
Statistics
Matches: 194, Mismatches: 24, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
56 38 0.20
57 78 0.40
58 16 0.08
59 62 0.32
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.36
Consensus pattern (59 bp):
GATTCTCAAGGAAATAAATTCAACAATCTATTTTTCCTTACAAAGTTAGAATCATTTAA
Found at i:515 original size:116 final size:115
Alignment explanation
Indices: 321--574 Score: 321
Period size: 116 Copynumber: 2.2 Consensus size: 115
311 TCGATAATTA
* * ** *
321 TTTTCCTGACAAAATTAAAATCATTCAAGATTCCAAAGAAATAAATTCAACAATTTATTTTTTTA
1 TTTTCCTTACAAAGTTAAAATCATTCAAGATTCCAAAGAAATAAATTCAACAACCTATTTTCTTA
* *
386 CAAAGTTATAATCATTTAAGATTCTCAAGGAAACAAATTCAACAATCTAT
66 CAAAGTTAGAATCATTAAAGATTCTCAAGGAAACAAATTCAACAATCTAT
* * * *
436 TTTTCCTTATAAAGTTATAATCATTTAAGATTCACAAGGAAATAAATTC-ACAACCTATTTTCCT
1 TTTTCCTTACAAAGTTAAAATCATTCAAGATTC-CAAAGAAATAAATTCAACAACCTATTTT-CT
* * * * *
500 TACAAAGTTAGAATCATTAAAGATTCTCAATGAAATAAATTTAACTATTTAT
64 TACAAAGTTAGAATCATTAAAGATTCTCAAGGAAACAAATTCAACAATCTAT
* *
552 TTTTCCTTACGAAGTTAGAATCA
1 TTTTCCTTACAAAGTTAAAATCA
575 ACACAAGATT
Statistics
Matches: 118, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
115 38 0.32
116 80 0.68
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.37
Consensus pattern (115 bp):
TTTTCCTTACAAAGTTAAAATCATTCAAGATTCCAAAGAAATAAATTCAACAACCTATTTTCTTA
CAAAGTTAGAATCATTAAAGATTCTCAAGGAAACAAATTCAACAATCTAT
Found at i:609 original size:57 final size:58
Alignment explanation
Indices: 359--610 Score: 135
Period size: 57 Copynumber: 4.4 Consensus size: 58
349 GATTCCAAAG
* * * * *** *
359 AAATAAATTCAACAATTTATTTTT--TTACAAAGTTATAATCATTTAAGATTCTCAAGG
1 AAATAAAATAAACCATTTATTTTTCCTTACAAAGTTAGAATCAACAAAGATTCTCAA-T
* * * * * * * *** * *
416 AAACAAATTCAACAATCTATTTTTCCTTATAAAGTTATAATCATTTAAGATTCACAAGG
1 AAATAAAATAAACCATTTATTTTTCCTTACAAAGTTAGAATCAACAAAGATTCTCAA-T
* **
475 AAATAAATTCACAACC---TA-TTTTCCTTACAAAGTTAGAATCATTAAAGATTCTCAAT
1 AAATAAAAT-A-AACCATTTATTTTTCCTTACAAAGTTAGAATCAACAAAGATTCTCAAT
* * * *
531 GAAATAAATTTAACTATTTATTTTTCCTTACGAAGTTAGAATCAACACAAGATTCT-AAT
1 -AAATAAAATAAACCATTTATTTTTCCTTACAAAGTTAGAATCAACA-AAGATTCTCAAT
590 -AATAAAATAAATCCA-TTATTT
1 AAATAAAATAAA-CCATTTATTT
611 CTTTATGTTA
Statistics
Matches: 164, Mismatches: 20, Indels: 22
0.80 0.10 0.11
Matches are distributed among these distances:
55 3 0.02
57 79 0.48
58 6 0.04
59 65 0.40
60 8 0.05
61 3 0.02
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (58 bp):
AAATAAAATAAACCATTTATTTTTCCTTACAAAGTTAGAATCAACAAAGATTCTCAAT
Found at i:829 original size:44 final size:44
Alignment explanation
Indices: 736--834 Score: 137
Period size: 44 Copynumber: 2.2 Consensus size: 44
726 TTACCAACCC
*
736 AATAATCAAAAGGAACTAATCATTTGATTTTAATTTTCACAATT
1 AATAATCAAAAGGAACTAATCATTTGATTTTAACTTTCACAATT
* * * *
780 CATAATCGAAAGGAACTAATCCTTTGATTTT-ACTTTGACAATCT
1 AATAATCAAAAGGAACTAATCATTTGATTTTAACTTTCACAAT-T
824 AATAATCAAAA
1 AATAATCAAAA
835 ACTTGGATCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 9 0.19
44 38 0.81
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.35
Consensus pattern (44 bp):
AATAATCAAAAGGAACTAATCATTTGATTTTAACTTTCACAATT
Found at i:3380 original size:18 final size:18
Alignment explanation
Indices: 3357--3391 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3347 TATTCGATTA
3357 AATAAT-TTGAATAGAAAC
1 AATAATATT-AATAGAAAC
3375 AATAATATTAATAGAAA
1 AATAATATTAATAGAAA
3392 TAAGTTGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.60, C:0.03, G:0.09, T:0.29
Consensus pattern (18 bp):
AATAATATTAATAGAAAC
Found at i:8192 original size:29 final size:29
Alignment explanation
Indices: 8159--8250 Score: 96
Period size: 30 Copynumber: 3.1 Consensus size: 29
8149 CTTAAATTTT
* *
8159 GTTTAGTGACTAAAATATAAGTTTTAAAA
1 GTTTAGTGACTAAAATATAAATTTGAAAA
** * *
8188 GTTTAGTGGTTAAAATAAAAACTTTGAAAC
1 GTTTAGTGACTAAAATATAAA-TTTGAAAA
8218 GTTTA-TGGACTAAAATTATAAATTTGAAAA
1 GTTTAGT-GACTAAAA-TATAAATTTGAAAA
8248 GTT
1 GTT
8251 ATATATTTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
29 18 0.36
30 27 0.54
31 5 0.10
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.37
Consensus pattern (29 bp):
GTTTAGTGACTAAAATATAAATTTGAAAA
Found at i:14321 original size:18 final size:19
Alignment explanation
Indices: 14280--14321 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
14270 TTTAATTTTG
*
14280 ATTATTTTTATATTACTAT
1 ATTATTTATATATTACTAT
*
14299 A-TATTTATATATT-TTAT
1 ATTATTTATATATTACTAT
14316 ATTATT
1 ATTATT
14322 ATTAGTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 4 0.20
18 15 0.75
19 1 0.05
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTATTTATATATTACTAT
Found at i:14643 original size:139 final size:138
Alignment explanation
Indices: 14470--14738 Score: 393
Period size: 136 Copynumber: 1.9 Consensus size: 138
14460 TTATTTAGTT
*
14470 TTTTTTTATTATTATATACATATTTTTTTCCTCCCTCTCATATTTAGCTATTATATATATATGGT
1 TTTTTCTATTATTATATACATATTTTTTTCCTCCCTCTCATATTTAGCTA-TAT-TATATATGG-
* *
14535 TAAT-ATTATTATATGTTTTTACTAACTTTATTTATTTTACTTTATACGCTA-TA-TTTACATTT
63 TAATGA-TATTATATGTTCTTACTAACTTTATTTATTCTACTTTATACGCTATTATTTTACATTT
14597 TTATTTTTATAA
127 TTATTTTTATAA
*
14609 TTTTTCTATTATTAT-TATATATATTTTTTCCTCCCTCTCATATTTAGCTATATTATATATGGTA
1 TTTTTCTATTATTATATACATAT-TTTTTTCCTCCCTCTCATATTTAGCTATATTATATATGGTA
* * * *
14673 TTGATATTCTATGTTCTTATTAATTTTATTTATTCTACTTTATACGCTATTATTTTACATTTTTA
65 ATGATATTATATGTTCTTACTAACTTTATTTATTCTACTTTATACGCTATTATTTTACATTTTTA
14738 T
130 T
14739 ATATGTACAT
Statistics
Matches: 118, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
136 43 0.36
137 12 0.10
138 22 0.19
139 41 0.35
ACGTcount: A:0.26, C:0.12, G:0.04, T:0.58
Consensus pattern (138 bp):
TTTTTCTATTATTATATACATATTTTTTTCCTCCCTCTCATATTTAGCTATATTATATATGGTAA
TGATATTATATGTTCTTACTAACTTTATTTATTCTACTTTATACGCTATTATTTTACATTTTTAT
TTTTATAA
Found at i:14751 original size:139 final size:139
Alignment explanation
Indices: 14470--14756 Score: 386
Period size: 139 Copynumber: 2.1 Consensus size: 139
14460 TTATTTAGTT
*
14470 TTTTTTTATTATTATATACATATTTTTTTCCTCCCTCTCATATTTAGCTATTATATATATATGGT
1 TTTTTCTATTATTATATACATATTTTTTTCCTCCCTCTCATATTTAGCTATTATATATATATGGT
* *
14535 TAATATTATTATATGTTTTTACTAACTTTATTTATTTTACTTTATACGCTATATTTACATTTTTA
66 TAATATTATTATATGTTCTTACTAACTTTATTTATTCTACTTTATACGCTATATTTACATTTTTA
* *
14600 TTTTTATAA
131 TATATATAA
*
14609 TTTTTCTATTATTAT-TATATATATTTTTTCCTCCCTCTCATATTTAGCTA-TAT-TATATATGG
1 TTTTTCTATTATTATATACATAT-TTTTTTCCTCCCTCTCATATTTAGCTATTATATATATATGG
* * * *
14671 -TATTGA-TATTCTATGTTCTTATTAATTTTATTTATTCTACTTTATACGCTATTATTTTACATT
65 TTAAT-ATTATTATATGTTCTTACTAACTTTATTTATTCTACTTTATACGCTA-TA-TTTACATT
*
14734 TTTATATATGTACA
127 TTTATATATATA-A
14748 TTTTATCTA
1 TTTT-TCTA
14757 ACTCTCATTA
Statistics
Matches: 131, Mismatches: 11, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
136 43 0.33
137 12 0.09
138 26 0.20
139 46 0.35
140 4 0.03
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.58
Consensus pattern (139 bp):
TTTTTCTATTATTATATACATATTTTTTTCCTCCCTCTCATATTTAGCTATTATATATATATGGT
TAATATTATTATATGTTCTTACTAACTTTATTTATTCTACTTTATACGCTATATTTACATTTTTA
TATATATAA
Found at i:17584 original size:2 final size:2
Alignment explanation
Indices: 17577--17619 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
17567 AAAATACGAA
*
17577 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17619 A
1 A
17620 GTTATTTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19228 original size:6 final size:6
Alignment explanation
Indices: 19217--19246 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
19207 CGAATCTATA
*
19217 AATTTT AATTTT AATTTT AATTTC AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT
19247 CTCAATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (6 bp):
AATTTT
Found at i:25277 original size:43 final size:43
Alignment explanation
Indices: 25224--25438 Score: 225
Period size: 43 Copynumber: 5.0 Consensus size: 43
25214 ACGAAAGGGT
* *
25224 CATCCGCGATTTCAACTCCACAACGGAGGATATCGTACCCACG
1 CATCCGCGATTTCAACTCCACGACGGAGGATATCGTACCCACA
* **
25267 CATCTGCGATTTCAACTCCACGATAGAGGATATCGTACCCACA
1 CATCCGCGATTTCAACTCCACGACGGAGGATATCGTACCCACA
* * * * * *
25310 CATCCACAATTTCAACTCCATGATGGAGGATATCGTACCAACG
1 CATCCGCGATTTCAACTCCACGACGGAGGATATCGTACCCACA
* * * *
25353 GATCCGTGATTTCAACTCCACGACGGAGGATATTGTGCCCACA
1 CATCCGCGATTTCAACTCCACGACGGAGGATATCGTACCCACA
** * * * *
25396 CATCCATGGTTTCAACTTCACGACGAAGGGA-ATCGTACACACA
1 CATCCGCGATTTCAACTCCACGACGGA-GGATATCGTACCCACA
25439 AGCAACATAC
Statistics
Matches: 141, Mismatches: 30, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
43 138 0.98
44 3 0.02
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.22
Consensus pattern (43 bp):
CATCCGCGATTTCAACTCCACGACGGAGGATATCGTACCCACA
Found at i:25868 original size:66 final size:66
Alignment explanation
Indices: 25786--26022 Score: 210
Period size: 66 Copynumber: 3.5 Consensus size: 66
25776 TCCACGATTT
*
25786 CAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACA-TAAACTTTGAAAACATTTCCCTTGAA
1 CAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATTAAACTTTGAAAACATTTCCCTTGAA
25850 A
66 A
* * * * *
25851 CAAAATTTTGTCTCCCTTGAGACAGTTTTTCTTAAAACCAGATTTTATCTCGCTT-AAGACAATT
1 C-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAA-C--A-TTAAACT---TTGAAAAC-ATT
25915 TCCCTTGAAA
57 TCCCTTGAAA
* * ** * * * *
25925 CTAATTTTGTCTCCCTCGAGACAGTTTCT-TATGAAACACCAAACTTTGAGATCGTTTCCCTTAA
1 CAAATTTTGTCTCCCTTGAGACAGTTTCTCT-TGAAACATTAAACTTTGAAAACATTTCCCTTGA
25989 AA
65 AA
** *
25991 CAAATTTTGTCTCTTTTGAAACAGTTTCTCTT
1 CAAATTTTGTCTCCCTTGAGACAGTTTCTCTT
26023 AAAGCATCAT
Statistics
Matches: 135, Mismatches: 24, Indels: 25
0.73 0.13 0.14
Matches are distributed among these distances:
65 1 0.01
66 70 0.52
67 4 0.03
69 4 0.03
70 1 0.01
71 4 0.03
72 2 0.01
73 33 0.24
74 16 0.12
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38
Consensus pattern (66 bp):
CAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATTAAACTTTGAAAACATTTCCCTTGAA
A
Found at i:25947 original size:36 final size:36
Alignment explanation
Indices: 25838--25952 Score: 113
Period size: 37 Copynumber: 3.1 Consensus size: 36
25828 CTTTGAAAAC
25838 ATTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACA
1 ATTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACA
* ** * * * * *
25875 GTTTTTCTTAAAACCAGATTTTATCTCGCTTAAGACA
1 ATTTCCCTTGAAA-CAAATTTTGTCTCCCTTGAGACA
* *
25912 ATTTCCCTTGAAACTAATTTTGTCTCCCTCGAGACA
1 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
*
25948 GTTTC
1 ATTTC
25953 TTATGAAACA
Statistics
Matches: 58, Mismatches: 19, Indels: 3
0.73 0.24 0.04
Matches are distributed among these distances:
36 21 0.36
37 36 0.62
38 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.38
Consensus pattern (36 bp):
ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
Found at i:25960 original size:36 final size:36
Alignment explanation
Indices: 25854--25961 Score: 96
Period size: 36 Copynumber: 3.0 Consensus size: 36
25844 CTTGAAACAA
25854 AATTTTGTCTCCCTTGAGACAGTTTTTCTTA--AAACC
1 AATTTTGTCTCCCTTGAGACAG--TTTCTTATGAAACC
* * * * * *
25890 AGATTTTATCTCGCTTAAGACAATTTCCCT-TGAAACT
1 A-ATTTTGTCTCCCTTGAGACAGTTT-CTTATGAAACC
*
25927 AATTTTGTCTCCCTCGAGACAGTTTCTTATGAAAC
1 AATTTTGTCTCCCTTGAGACAGTTTCTTATGAAAC
25962 ACCAAACTTT
Statistics
Matches: 55, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
35 5 0.09
36 28 0.51
37 22 0.40
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (36 bp):
AATTTTGTCTCCCTTGAGACAGTTTCTTATGAAACC
Found at i:26274 original size:40 final size:39
Alignment explanation
Indices: 26213--26344 Score: 140
Period size: 40 Copynumber: 3.2 Consensus size: 39
26203 TGGTCTACCG
26213 TCCTCATCACGTAGGAACCGTGTCATCCTTCGACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCATCCTT-GACCAGATC
* * *
26253 TTCTCATCACGTAGGAGCCGTGTCAACCTTGGATAACCAG-TC
1 TCCTCATCACGTAGGAACCGTGTCATCCTT-G---ACCAGATC
* * *
26295 ATCCTCAACACGTAGGAACCGTGTTATCCCTTGACTAGATC
1 -TCCTCATCACGTAGGAACCGTGTCAT-CCTTGACCAGATC
26336 TCCTCATCA
1 TCCTCATCA
26345 AGTAAGAGTC
Statistics
Matches: 75, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
40 40 0.53
41 2 0.03
42 2 0.03
43 27 0.36
44 4 0.05
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (39 bp):
TCCTCATCACGTAGGAACCGTGTCATCCTTGACCAGATC
Found at i:26300 original size:131 final size:131
Alignment explanation
Indices: 26061--26322 Score: 380
Period size: 131 Copynumber: 2.0 Consensus size: 131
26051 TGAAACCATT
* *
26061 ATCCCTAATGATGGTCTGCCATCCTCATCATGTAGGAACCGTGTCATCCCTAGACCAGATCTCCT
1 ATCCCTAATGATGGTCTACCATCCTCATCACGTAGGAACCGTGTCATCCCTAGACCAGATCTCCT
* * * * * * *
26126 TATTACGTATGAGCCGTGTCAACCTTAGATAATCAGTCGTCCTCATCACATAGGAATCGCGTTAT
66 CATCACGTAGGAGCCGTGTCAACCTTAGATAACCAGTCATCCTCAACACATAGGAACCGCGTTAT
26191 C
131 C
* * * *
26192 ATCCCTAATGATGGTCTACCGTCCTCATCACGTAGGAACCGTGTCATCCTTCGACCAGATCTTCT
1 ATCCCTAATGATGGTCTACCATCCTCATCACGTAGGAACCGTGTCATCCCTAGACCAGATCTCCT
* * *
26257 CATCACGTAGGAGCCGTGTCAACCTTGGATAACCAGTCATCCTCAACACGTAGGAACCGTGTTAT
66 CATCACGTAGGAGCCGTGTCAACCTTAGATAACCAGTCATCCTCAACACATAGGAACCGCGTTAT
26322 C
131 C
26323 CCTTGACTAG
Statistics
Matches: 115, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
131 115 1.00
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27
Consensus pattern (131 bp):
ATCCCTAATGATGGTCTACCATCCTCATCACGTAGGAACCGTGTCATCCCTAGACCAGATCTCCT
CATCACGTAGGAGCCGTGTCAACCTTAGATAACCAGTCATCCTCAACACATAGGAACCGCGTTAT
C
Found at i:26308 original size:43 final size:40
Alignment explanation
Indices: 26213--26362 Score: 133
Period size: 40 Copynumber: 3.7 Consensus size: 40
26203 TGGTCTACCG
*
26213 TCCTCATCACGTAGGAACCGTGTCATCCTTCGACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCAACCTTCGACCAGATC
* * *
26253 TTCTCATCACGTAGGAGCCGTGTCAACCTTGGATAACCAG-TC
1 TCCTCATCACGTAGGAACCGTGTCAACCTTCG---ACCAGATC
* * * *
26295 ATCCTCAACACGTAGGAACCGTGTTATCCCTT-GACTAGATC
1 -TCCTCATCACGTAGGAACCGTGTCA-ACCTTCGACCAGATC
* * **
26336 TCCTCATCAAGTAAGAGTCGTGTCAAC
1 TCCTCATCACGTAGGAACCGTGTCAAC
26363 TTTAGATAAC
Statistics
Matches: 87, Mismatches: 17, Indels: 13
0.74 0.15 0.11
Matches are distributed among these distances:
39 1 0.01
40 51 0.59
41 2 0.02
42 2 0.02
43 27 0.31
44 4 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACCGTGTCAACCTTCGACCAGATC
Found at i:26402 original size:83 final size:84
Alignment explanation
Indices: 26210--26405 Score: 270
Period size: 83 Copynumber: 2.4 Consensus size: 84
26200 TGATGGTCTA
* * * *
26210 CCGTCCTCATCACGTAGGAACCGTGTCAT-CCTTCGACCAGATCTTCTCATCACGTAGGAGCCGT
1 CCGTCCTCATCACGTAGGAACCGTGTTATCCCTTCGACCAGATCTCCTCATCAAGTAAGAGCCGT
*
26274 GTCAACCTTGGATAACCAG
66 GTCAACCTTAGATAACCAG
* * * * *
26293 TCATCCTCAACACGTAGGAACCGTGTTATCCCTT-GACTAGATCTCCTCATCAAGTAAGAGTCGT
1 CCGTCCTCATCACGTAGGAACCGTGTTATCCCTTCGACCAGATCTCCTCATCAAGTAAGAGCCGT
*
26357 GTCAACTTTAGATAACCAG
66 GTCAACCTTAGATAACCAG
*
26376 CCGTCCTCATCACGTAGGAACTGTGTTATC
1 CCGTCCTCATCACGTAGGAACCGTGTTATC
26406 GTCCTTAGAC
Statistics
Matches: 97, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
83 93 0.96
84 4 0.04
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.27
Consensus pattern (84 bp):
CCGTCCTCATCACGTAGGAACCGTGTTATCCCTTCGACCAGATCTCCTCATCAAGTAAGAGCCGT
GTCAACCTTAGATAACCAG
Found at i:31349 original size:9 final size:10
Alignment explanation
Indices: 31335--31379 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
31325 TATAGCTTAT
31335 ATATTTTTTA
1 ATATTTTTTA
31345 A-A-TTTTTA
1 ATATTTTTTA
31353 ATATTTTTTA
1 ATATTTTTTA
*
31363 ATACATTTTTA
1 ATA-TTTTTTA
31374 ATATTT
1 ATATTT
31380 ATTTTTTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
8 7 0.23
9 2 0.07
10 12 0.40
11 9 0.30
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (10 bp):
ATATTTTTTA
Found at i:31356 original size:18 final size:21
Alignment explanation
Indices: 31335--31379 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
31325 TATAGCTTAT
31335 ATATTTTTT-A-A-ATTTTTA
1 ATATTTTTTAATACATTTTTA
31353 ATATTTTTTAATACATTTTTA
1 ATATTTTTTAATACATTTTTA
31374 ATATTT
1 ATATTT
31380 ATTTTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.38
19 1 0.04
20 1 0.04
21 13 0.54
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
ATATTTTTTAATACATTTTTA
Found at i:31403 original size:24 final size:25
Alignment explanation
Indices: 31354--31399 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
31344 AAATTTTTAA
*
31354 TATTTTTTAATACATTTTTAATATT
1 TATTTTTTAATACATTTTGAATATT
31379 TATTTTTT-ATAC-TTTTGAATA
1 TATTTTTTAATACATTTTGAATA
31400 ATTTTGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 4 0.20
25 8 0.40
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.63
Consensus pattern (25 bp):
TATTTTTTAATACATTTTGAATATT
Found at i:31413 original size:33 final size:34
Alignment explanation
Indices: 31346--31420 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
31336 TATTTTTTAA
* * * * *
31346 ATTTTTAATATTTTTTAATACATTTTTAATATTT
1 ATTTTTTATACTTTTGAATACATTTTGAAAATTT
31380 ATTTTTTATACTTTTGAATA-ATTTTGAAAATTT
1 ATTTTTTATACTTTTGAATACATTTTGAAAATTT
31413 ATATTTTT
1 AT-TTTTT
31421 GTTAAAGATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 13 0.37
34 22 0.63
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (34 bp):
ATTTTTTATACTTTTGAATACATTTTGAAAATTT
Found at i:36164 original size:114 final size:114
Alignment explanation
Indices: 35935--36150 Score: 297
Period size: 114 Copynumber: 1.9 Consensus size: 114
35925 ATGGTTATGT
* * *
35935 TATTGCCAAAGTGGGCAACCAAACTGTTATTGCTGGCAACAACTTGGCTGCTAATACAGTGACTA
1 TATTGCCAAAGCGAGCAACCAAACTGTTATTGATGGCAACAACTTGGCTGCTAATACAGTGACTA
* * * *
36000 ATGGGGCTTGTTATGGGAACTCATATGCTATTTCAATATCAGGAGAGGC
66 ATGGGGCTTGTTATGGGAACTCAGATGATATTCCAATATCAGAAGAGGC
* * * * * *
36049 TATTGCTAAAGCGAGCAACCATACTGTTATTGATGGTAGCAACTTGGCTTCTAATTCAGTGACTA
1 TATTGCCAAAGCGAGCAACCAAACTGTTATTGATGGCAACAACTTGGCTGCTAATACAGTGACTA
* *
36114 ATGGGGCTTGTTCTGGGAACTCAGGTGATATTCCAAT
66 ATGGGGCTTGTTATGGGAACTCAGATGATATTCCAAT
36151 GTCAAATGGG
Statistics
Matches: 88, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
114 88 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (114 bp):
TATTGCCAAAGCGAGCAACCAAACTGTTATTGATGGCAACAACTTGGCTGCTAATACAGTGACTA
ATGGGGCTTGTTATGGGAACTCAGATGATATTCCAATATCAGAAGAGGC
Found at i:41253 original size:22 final size:22
Alignment explanation
Indices: 41228--41276 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
41218 TTAAATTTAC
41228 ATTTGTTTACATTTATTTATTT
1 ATTTGTTTACATTTATTTATTT
* ** *
41250 ATTTATTTATGTTTCTTTATTT
1 ATTTGTTTACATTTATTTATTT
*
41272 GTTTG
1 ATTTG
41277 GTTAAAATTA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.04, G:0.08, T:0.69
Consensus pattern (22 bp):
ATTTGTTTACATTTATTTATTT
Found at i:41669 original size:34 final size:34
Alignment explanation
Indices: 41610--41676 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
41600 TTCTTTAGAG
*
41610 TTGTTTTCTCCTTTTTATCAAGAGAGAA-TTGTCA
1 TTGTTTTCTCCTTTTGATC-AGAGAGAAGTTGTCA
41644 TTGTTTTCTCCTTGTTAGATC-GAGAGAAGTTGT
1 TTGTTTTCTCCTT-TT-GATCAGAGAGAAGTTGT
41677 AATTCATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 20 0.69
35 6 0.21
36 3 0.10
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.46
Consensus pattern (34 bp):
TTGTTTTCTCCTTTTGATCAGAGAGAAGTTGTCA
Found at i:53932 original size:2 final size:2
Alignment explanation
Indices: 53925--53985 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
53915 GGTGCCGAAG
53925 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
53967 CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT C
53986 GACACAAAAC
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:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:60761 original size:15 final size:16
Alignment explanation
Indices: 60741--60777 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
60731 CCGACCCGAC
60741 CCGTTGAAC-AGTTGA
1 CCGTTGAACTAGTTGA
*
60756 CCGTTG-ACTCGTTGA
1 CCGTTGAACTAGTTGA
60771 CCGTTGA
1 CCGTTGA
60778 CCGGCGTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 2 0.11
15 17 0.89
ACGTcount: A:0.19, C:0.24, G:0.27, T:0.30
Consensus pattern (16 bp):
CCGTTGAACTAGTTGA
Found at i:60768 original size:8 final size:7
Alignment explanation
Indices: 60741--60780 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
60731 CCGACCCGAC
60741 CCGTTGAA
1 CCGTTG-A
*
60749 CAGTTGA
1 CCGTTGA
60756 CCGTTGA
1 CCGTTGA
60763 CTCGTTGA
1 C-CGTTGA
60771 CCGTTGA
1 CCGTTGA
60778 CCG
1 CCG
60781 GCGTTGACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
7 17 0.59
8 12 0.41
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.28
Consensus pattern (7 bp):
CCGTTGA
Found at i:63259 original size:24 final size:24
Alignment explanation
Indices: 63232--63336 Score: 81
Period size: 24 Copynumber: 4.4 Consensus size: 24
63222 AAATATTTTA
63232 TCTGATTTCCGA-CTTGAATTATGT
1 TCTGATTTCCGATC-TGAATTATGT
* *
63256 TCTGA-TACATC-ACCTGAATTATGT
1 TCTGATTTC--CGATCTGAATTATGT
* * *
63280 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCCGATCTGAATTATGT
* * *
63304 TCTGATATCTGATCTGAATTCTGT
1 TCTGATTTCCGATCTGAATTATGT
*
63328 TTTGATTTC
1 TCTGATTTC
63337 TGATATCTCC
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
23 2 0.03
24 60 0.91
25 4 0.06
ACGTcount: A:0.20, C:0.17, G:0.16, T:0.47
Consensus pattern (24 bp):
TCTGATTTCCGATCTGAATTATGT
Found at i:63284 original size:12 final size:12
Alignment explanation
Indices: 63269--63338 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
63259 GATACATCAC
*
63269 CTGAATTATGTT
1 CTGAATTCTGTT
* *
63281 CTGATTTCTGAT
1 CTGAATTCTGTT
*
63293 CTGGATTCTGTT
1 CTGAATTCTGTT
*
63305 CTG-ATATCTGAT
1 CTGAAT-TCTGTT
63317 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
63329 TTGATTTCTG
1 CTGAATTCTG
63339 ATATCTCCGT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.91
13 2 0.04
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.50
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:63288 original size:48 final size:48
Alignment explanation
Indices: 63232--63336 Score: 115
Period size: 48 Copynumber: 2.2 Consensus size: 48
63222 AAATATTTTA
63232 TCTGATTTCCGA-CTTGAATTATGTTCTGATA-CATCACCTGAATTATGT
1 TCTGATTTCCGATC-TGAATTATGTTCTGATATC-TCACCTGAATTATGT
* * * * * *
63280 TCTGATTTCTGATCTGGATTCTGTTCTGATATCTGATCTGAATTCTGT
1 TCTGATTTCCGATCTGAATTATGTTCTGATATCTCACCTGAATTATGT
*
63328 TTTGATTTC
1 TCTGATTTC
63337 TGATATCTCC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
48 46 0.96
49 2 0.04
ACGTcount: A:0.20, C:0.17, G:0.16, T:0.47
Consensus pattern (48 bp):
TCTGATTTCCGATCTGAATTATGTTCTGATATCTCACCTGAATTATGT
Found at i:63338 original size:24 final size:24
Alignment explanation
Indices: 63269--63340 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
63259 GATACATCAC
*
63269 CTGAATTATGTTCTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
* *
63293 CTGGATTCTGTTCTGATATCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
*
63317 CTGAATTCTGTTTTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
63341 ATCTCCGTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.50
Consensus pattern (24 bp):
CTGAATTCTGTTCTGATTTCTGAT
Found at i:63508 original size:2 final size:2
Alignment explanation
Indices: 63501--63555 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
63491 GATGGGGGTG
63501 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
63543 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
63556 GTTTTAAATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:64780 original size:39 final size:36
Alignment explanation
Indices: 64613--64839 Score: 152
Period size: 35 Copynumber: 6.2 Consensus size: 36
64603 TATATAGTTT
* * *
64613 TTTTAAAACGTTTTTGAAAACTTATATACAATATATAAG
1 TTTTAAAACATTTTGGAAAA-TT-TATATAATATAT-AG
* *
64652 TTTTAAAACATTTTGG-AAA-TTATGTAGTATATAG
1 TTTTAAAACATTTTGGAAAATTTATATAATATATAG
* * *
64686 TTTTGAAATCATTTT-GAAAATATA-AT-ATATAT-T
1 TTTT-AAAACATTTTGGAAAATTTATATAATATATAG
64719 TTTTAAAAAAACATTTTGGGAAAATTTATATAATATATAG
1 TTTT---AAAACATTTT-GGAAAATTTATATAATATATAG
*
64759 TTTTAACAAAACATTTTGGAAAACTTATAT-A-ATAT--
1 TTTT---AAAACATTTTGGAAAATTTATATAATATATAG
* *
64794 TTTTAAAATCATTTTTTGAAAA-CTATATAATATATAG
1 TTTTAAAA-CA-TTTTGGAAAATTTATATAATATATAG
64831 TTTTGAAAA
1 TTTT-AAAA
64840 TGTTTTTATA
Statistics
Matches: 153, Mismatches: 18, Indels: 35
0.74 0.09 0.17
Matches are distributed among these distances:
32 4 0.03
33 11 0.07
34 22 0.14
35 39 0.25
36 3 0.02
37 16 0.10
38 10 0.07
39 32 0.21
40 16 0.10
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (36 bp):
TTTTAAAACATTTTGGAAAATTTATATAATATATAG
Found at i:64936 original size:5 final size:5
Alignment explanation
Indices: 64920--64960 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
64910 ATTATTAATA
* * *
64920 TTTAT TTCAT TTTAT TTTAT TTTAT TTCAT TTCAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT T
64961 AACTTAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (5 bp):
TTTAT
Found at i:64943 original size:20 final size:20
Alignment explanation
Indices: 64920--64960 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
64910 ATTATTAATA
*
64920 TTTATTTCATTTTATTTTAT
1 TTTATTTCATTTCATTTTAT
64940 TTTATTTCATTTCATTTTAT
1 TTTATTTCATTTCATTTTAT
64960 T
1 T
64961 AACTTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTATTTCATTTCATTTTAT
Found at i:69665 original size:20 final size:22
Alignment explanation
Indices: 69630--69673 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
69620 TCACCACTTA
*
69630 ATTATTTAACTATTTTATTTTT
1 ATTATTTAACTATTTTAATTTT
69652 ATTATTT-A-TATTTTAATTTT
1 ATTATTTAACTATTTTAATTTT
69672 AT
1 AT
69674 CAATTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 1 0.05
22 7 0.33
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (22 bp):
ATTATTTAACTATTTTAATTTT
Found at i:72743 original size:5 final size:5
Alignment explanation
Indices: 72735--72760 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
72725 TTTTTTTATT
72735 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
72761 GAAACATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:78090 original size:19 final size:19
Alignment explanation
Indices: 78068--78112 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
78058 TGACGAAAAT
* * *
78068 AAAAGAGTAATAGTAATGG
1 AAAAGAGAAAGAGTAATGC
*
78087 AAAAAAGAAAGAGTAATGC
1 AAAAGAGAAAGAGTAATGC
78106 AAAAGAG
1 AAAAGAG
78113 GAAAAACCAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.60, C:0.02, G:0.24, T:0.13
Consensus pattern (19 bp):
AAAAGAGAAAGAGTAATGC
Found at i:81334 original size:2 final size:2
Alignment explanation
Indices: 81327--81351 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
81317 ACATGTTAAA
81327 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
81352 ATTTAATTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:82467 original size:43 final size:43
Alignment explanation
Indices: 82375--82660 Score: 156
Period size: 43 Copynumber: 6.4 Consensus size: 43
82365 GTTAAAGTTC
* *
82375 GCGGCGTTTTTTTAAACTAAAAACGCCGCAATA-G-GTAACGATATATA
1 GCGGCGTTTTTTT-AAC---AAACGCCGCAATATGTGTTA--ATATTTA
82422 GCGGCGTTTTTTTAACAAACGCCGCAATATGTGTTAATATTTA
1 GCGGCGTTTTTTTAACAAACGCCGCAATATGTGTTAATATTTA
* * * * *
82465 GCGACGTTTTTATCACAAACGCCGCAATAAGTGTTGATATTTA
1 GCGGCGTTTTTTTAACAAACGCCGCAATATGTGTTAATATTTA
* * * ** *
82508 GAGGCGTTTTTTTATGA-AAATGCCGCTAA-AAG-GTCTGGTATATA
1 GCGGCGTTTTTTTA--ACAAACGCCGC-AATATGTGT-TAATATTTA
* * * ** *
82552 ACAGCATTTTTAGGATACAAACGCCGCAATATGTGTTAATATTTG
1 GCGGCGTTTTT-TTA-ACAAACGCCGCAATATGTGTTAATATTTA
* * *
82597 GCGGTGTTTTTTTTGATACAAACGCCGCTAA-ATGTATGACATA-TT-
1 GCGGCG-TTTTTTT-A-ACAAACGCCGC-AATATGTGTTA-ATATTTA
*
82642 GCGGCGTTTTTTTTACAAA
1 GCGGCGTTTTTTTAACAAA
82661 AGTCGCTAAA
Statistics
Matches: 188, Mismatches: 37, Indels: 33
0.73 0.14 0.13
Matches are distributed among these distances:
42 5 0.03
43 69 0.37
44 36 0.19
45 29 0.15
46 31 0.16
47 18 0.10
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (43 bp):
GCGGCGTTTTTTTAACAAACGCCGCAATATGTGTTAATATTTA
Found at i:82653 original size:46 final size:46
Alignment explanation
Indices: 82565--82655 Score: 107
Period size: 46 Copynumber: 2.0 Consensus size: 46
82555 GCATTTTTAG
* * *
82565 GATACAAACGCCGCAATATGTGTTAATATTTGGCGGTGTTTTTTTT
1 GATACAAACGCCGCAATATGTATGAATATTCGGCGGTGTTTTTTTT
*
82611 GATACAAACGCCGCTAA-ATGTATGACATATT--GCGGCGTTTTTTTT
1 GATACAAACGCCGC-AATATGTATGA-ATATTCGGCGGTGTTTTTTTT
82656 ACAAAAGTCG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
45 13 0.32
46 20 0.50
47 7 0.17
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.38
Consensus pattern (46 bp):
GATACAAACGCCGCAATATGTATGAATATTCGGCGGTGTTTTTTTT
Found at i:86104 original size:31 final size:31
Alignment explanation
Indices: 86024--86145 Score: 154
Period size: 31 Copynumber: 3.9 Consensus size: 31
86014 GAGTTTTATG
* *
86024 AATGACGCGTCCTAGGGAACACACCTCCCTTG
1 AATGACGCGTCTTAGGGAACACACCT-CCTTT
* * *
86056 AATGACACGTCTCAGGGAACGCACCTCCTTT
1 AATGACGCGTCTTAGGGAACACACCTCCTTT
*
86087 AATGGCGCGTCTTAGGGAACACACCTCCTTT
1 AATGACGCGTCTTAGGGAACACACCTCCTTT
* * *
86118 AATGGCGCGTCGTAGGGAACGCACCTCC
1 AATGACGCGTCTTAGGGAACACACCTCC
86146 CATGCCCGAT
Statistics
Matches: 79, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
31 57 0.72
32 22 0.28
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.20
Consensus pattern (31 bp):
AATGACGCGTCTTAGGGAACACACCTCCTTT
Found at i:99442 original size:19 final size:19
Alignment explanation
Indices: 99418--99460 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
99408 GGCTGAAAAT
*
99418 CGGTTTGACCGGTTTT-GAC
1 CGGTTTGACC-ATTTTCGAC
99437 CGGTTTGACCATTTTCGAC
1 CGGTTTGACCATTTTCGAC
99456 CGGTT
1 CGGTT
99461 CGAATCGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.12, C:0.23, G:0.28, T:0.37
Consensus pattern (19 bp):
CGGTTTGACCATTTTCGAC
Found at i:106731 original size:10 final size:9
Alignment explanation
Indices: 106708--106748 Score: 55
Period size: 10 Copynumber: 4.3 Consensus size: 9
106698 GTGGCTGAAA
106708 ACCGGTTTG
1 ACCGGTTTG
106717 ACCGGTTTCG
1 ACCGGTTT-G
106727 ACCGGTTTG
1 ACCGGTTTG
*
106736 AACCGGTCTG
1 -ACCGGTTTG
106746 ACC
1 ACC
106749 CGACCCGACC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 12 0.41
10 17 0.59
ACGTcount: A:0.15, C:0.29, G:0.29, T:0.27
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:106748 original size:19 final size:19
Alignment explanation
Indices: 106708--106748 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
106698 GTGGCTGAAA
*
106708 ACCGGTTTGACCGGTTTCG
1 ACCGGTTTGACCGGTCTCG
106727 ACCGGTTTGAACCGGTCT-G
1 ACCGGTTTG-ACCGGTCTCG
106746 ACC
1 ACC
106749 CGACCCGACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.15, C:0.29, G:0.29, T:0.27
Consensus pattern (19 bp):
ACCGGTTTGACCGGTCTCG
Found at i:108436 original size:7 final size:7
Alignment explanation
Indices: 108424--108493 Score: 51
Period size: 7 Copynumber: 10.3 Consensus size: 7
108414 AAAGAAGGGG
108424 AGAAGAA
1 AGAAGAA
108431 AGAAGAGA
1 AGAAGA-A
108439 A-AAG-A
1 AGAAGAA
*
108444 GGAAGAA
1 AGAAGAA
108451 AGAAGAGA
1 AGAAGA-A
*
108459 A-AAGAG
1 AGAAGAA
108465 A-AAGAA
1 AGAAGAA
108471 AGAAG-A
1 AGAAGAA
*
108477 ACAAGAA
1 AGAAGAA
108484 GAGAAGAA
1 -AGAAGAA
108492 AG
1 AG
108494 TTAAAGTTAG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
5 1 0.02
6 14 0.28
7 25 0.50
8 10 0.20
ACGTcount: A:0.67, C:0.01, G:0.31, T:0.00
Consensus pattern (7 bp):
AGAAGAA
Found at i:108448 original size:20 final size:20
Alignment explanation
Indices: 108425--108476 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
108415 AAGAAGGGGA
108425 GAAGAAAGAAGAGAAAAGAG
1 GAAGAAAGAAGAGAAAAGAG
108445 GAAGAAAGAAGAGAAAAGAG
1 GAAGAAAGAAGAGAAAAGAG
*
108465 AAAGAAAGAAGA
1 GAAGAAAGAAGA
108477 ACAAGAAGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (20 bp):
GAAGAAAGAAGAGAAAAGAG
Found at i:108452 original size:10 final size:10
Alignment explanation
Indices: 108424--108477 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
108414 AAAGAAGGGG
108424 AGAAGAAAGA
1 AGAAGAAAGA
108434 AG-AGAAAAGA
1 AGAAG-AAAGA
*
108444 GGAAGAAAGA
1 AGAAGAAAGA
108454 AG-AGAAA-A
1 AGAAGAAAGA
108462 GAGAAAGAAAGA
1 -AG-AAGAAAGA
108474 AGAA
1 AGAA
108478 CAAGAAGAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
8 1 0.03
9 9 0.25
10 16 0.44
11 9 0.25
12 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (10 bp):
AGAAGAAAGA
Found at i:108475 original size:27 final size:28
Alignment explanation
Indices: 108409--108491 Score: 82
Period size: 27 Copynumber: 2.9 Consensus size: 28
108399 CACCGGGAGT
**
108409 GAAAGAAAGAAGGGGAGAAGA-AAGAAGA
1 GAAAGAAAGAA-GAAAGAAGAGAAGAAGA
*
108437 GAAA-AGAGGAAGAAAGAAGAGAA-AAGA
1 GAAAGA-AAGAAGAAAGAAGAGAAGAAGA
108464 GAAAGAAAGAAGAACAAGAAGAGAAGAA
1 GAAAGAAAGAAG-A-AAGAAGAGAAGAA
108492 AGTTAAAGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
27 21 0.47
28 12 0.27
29 10 0.22
30 2 0.04
ACGTcount: A:0.65, C:0.01, G:0.34, T:0.00
Consensus pattern (28 bp):
GAAAGAAAGAAGAAAGAAGAGAAGAAGA
Found at i:108843 original size:17 final size:18
Alignment explanation
Indices: 108818--108856 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
108808 TGTAGATTTT
*
108818 TTTAGATTAAAT-TAATG
1 TTTAGATTAAATGTAATC
*
108835 TTTATATTAAATGTAATC
1 TTTAGATTAAATGTAATC
108853 TTTA
1 TTTA
108857 AATTGAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (18 bp):
TTTAGATTAAATGTAATC
Found at i:111027 original size:17 final size:17
Alignment explanation
Indices: 111002--111038 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
110992 CATAAGTAAA
*
111002 TATTTTTTAATAAATTTT
1 TATTTTTAAAT-AATTTT
111020 TATTTTTAAATAATTTT
1 TATTTTTAAATAATTTT
111037 TA
1 TA
111039 CCTTAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTTTTAAATAATTTT
Found at i:111401 original size:121 final size:120
Alignment explanation
Indices: 111248--111618 Score: 460
Period size: 121 Copynumber: 3.0 Consensus size: 120
111238 ATTCGAAGAT
* *
111248 TAAATTAATTTTAATTTATTAAAATTAGGACTAAATTGATAGAATCTATAAGTGAAAGTGAAAAA
1 TAAATTAATTTTAATTTATTAAAATTAGGACTAAATTGATAGAATATATAAGT-AAAGTGACAAA
* *
111313 ATGTGTAATTATATCAATTTTATTAAACTCTAAAACTTAAGATGAGATAAAATATA
65 ATGTGTAATTATATCAATTTTATTAAATTTTAAAACTTAAGATGAGATAAAATATA
** * *
111369 TAAATTTTTTTTAATTT-TTAAAATTTACGACTAAATTGATAGAATATAAAAGTATAAGTGACAA
1 TAAATTAATTTTAATTTATTAAAA-TTAGGACTAAATTGATAGAATATATAAGTA-AAGTGACAA
* * * * *
111433 AATAT-AACACTATATC-ATTTTCATTAAATTTTAAAATTTAAGATGGGGTGAGATAAAAAAATA
64 AATGTGTA-ATTATATCAATTTT-ATTAAATTTTAAAACTTAAGA-----TGAGAT-AAAATATA
* *
111496 TAAATTAATTTTAATTTATTAAAATTAGGACTAAATTGATAGAATATATAAGTCAAATTGACCAA
1 TAAATTAATTTTAATTTATTAAAATTAGGACTAAATTGATAGAATATATAAGT-AAAGTGACAAA
* *
111561 ATGTGTAATTATATCAATTTGATTAAATTTTAAAAGTTAAGATGAGATAAAATATA
65 ATGTGTAATTATATCAATTTTATTAAATTTTAAAACTTAAGATGAGATAAAATATA
111617 TA
1 TA
111619 TTATGTTTTT
Statistics
Matches: 211, Mismatches: 25, Indels: 28
0.80 0.09 0.11
Matches are distributed among these distances:
120 13 0.06
121 87 0.41
122 6 0.03
126 6 0.03
127 87 0.41
128 12 0.06
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (120 bp):
TAAATTAATTTTAATTTATTAAAATTAGGACTAAATTGATAGAATATATAAGTAAAGTGACAAAA
TGTGTAATTATATCAATTTTATTAAATTTTAAAACTTAAGATGAGATAAAATATA
Found at i:111803 original size:19 final size:22
Alignment explanation
Indices: 111749--111794 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 22
111739 ATTTTTAAAG
111749 TTAAAATACATAAATTATTATA
1 TTAAAATACATAAATTATTATA
111771 TTAAAAAATACATAAATTATTATA
1 TT--AAAATACATAAATTATTATA
111795 AAATACATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 2 0.09
24 20 0.91
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (22 bp):
TTAAAATACATAAATTATTATA
Found at i:114261 original size:12 final size:12
Alignment explanation
Indices: 114243--114283 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
114233 ACTATACGGT
114243 ATGAACAATACC
1 ATGAACAATACC
* *
114255 TTGAACAGTA--
1 ATGAACAATACC
114265 ATGAACAATACC
1 ATGAACAATACC
114277 ATGAACA
1 ATGAACA
114284 GTGCTACATT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
10 8 0.35
12 15 0.65
ACGTcount: A:0.49, C:0.20, G:0.12, T:0.20
Consensus pattern (12 bp):
ATGAACAATACC
Found at i:114271 original size:22 final size:22
Alignment explanation
Indices: 114243--114285 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
114233 ACTATACGGT
*
114243 ATGAACAATACCTTGAACAGTA
1 ATGAACAATACCATGAACAGTA
114265 ATGAACAATACCATGAACAGT
1 ATGAACAATACCATGAACAGT
114286 GCTACATTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.19, G:0.14, T:0.21
Consensus pattern (22 bp):
ATGAACAATACCATGAACAGTA
Found at i:114309 original size:21 final size:21
Alignment explanation
Indices: 114285--114325 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
114275 CCATGAACAG
* *
114285 TGCTACATTGTACCGATGCAC
1 TGCTACAGTATACCGATGCAC
114306 TGCTACAGTATACCGATGCA
1 TGCTACAGTATACCGATGCA
114326 AAAAAACATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (21 bp):
TGCTACAGTATACCGATGCAC
Found at i:114377 original size:21 final size:21
Alignment explanation
Indices: 114348--114387 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
114338 ATATAAATTA
*
114348 TGTATCGATGCACTACTACAG
1 TGTACCGATGCACTACTACAG
*
114369 TGTACCGATGCACTGCTAC
1 TGTACCGATGCACTACTAC
114388 TGCTACAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.28
Consensus pattern (21 bp):
TGTACCGATGCACTACTACAG
Found at i:116936 original size:15 final size:15
Alignment explanation
Indices: 116916--116946 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
116906 ACATATATAA
116916 TTTAATTACCTAGAC
1 TTTAATTACCTAGAC
116931 TTTAATTACCTAGAC
1 TTTAATTACCTAGAC
116946 T
1 T
116947 ATCAAAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.42
Consensus pattern (15 bp):
TTTAATTACCTAGAC
Found at i:118788 original size:29 final size:29
Alignment explanation
Indices: 118746--118811 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 29
118736 GGAACATATA
* **
118746 AATAGTTGGAGGACAACTTTGTAACTTTT
1 AATAGTCGGAGGACAACTTTACAACTTTT
*
118775 AATAGTCGGAGGACCACTTTACAACTTTT
1 AATAGTCGGAGGACAACTTTACAACTTTT
118804 AATAGTCG
1 AATAGTCG
118812 AGATACTCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (29 bp):
AATAGTCGGAGGACAACTTTACAACTTTT
Found at i:127837 original size:24 final size:24
Alignment explanation
Indices: 127791--127903 Score: 172
Period size: 24 Copynumber: 4.7 Consensus size: 24
127781 TATAAAAAAA
* * *
127791 ATAAACGAGCTTATCAATTAACTT
1 ATAAACGAGCTTCTAAATGAACTT
* *
127815 ATAAACAAGTTTCTAAATGAACTT
1 ATAAACGAGCTTCTAAATGAACTT
127839 ATAAACGAGCTTCTAAATGAACTT
1 ATAAACGAGCTTCTAAATGAACTT
*
127863 ATAAATGAGCTTCTAAATGAACTT
1 ATAAACGAGCTTCTAAATGAACTT
127887 ATAAACGAGCTTCTAAA
1 ATAAACGAGCTTCTAAA
127904 CAAGATTGTT
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 80 1.00
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (24 bp):
ATAAACGAGCTTCTAAATGAACTT
Found at i:127904 original size:12 final size:12
Alignment explanation
Indices: 127825--127903 Score: 86
Period size: 12 Copynumber: 6.6 Consensus size: 12
127815 ATAAACAAGT
127825 TTCTAAATGAAC
1 TTCTAAATGAAC
* * *
127837 TTATAAACGAGC
1 TTCTAAATGAAC
127849 TTCTAAATGAAC
1 TTCTAAATGAAC
* *
127861 TTATAAATGAGC
1 TTCTAAATGAAC
127873 TTCTAAATGAAC
1 TTCTAAATGAAC
* * *
127885 TTATAAACGAGC
1 TTCTAAATGAAC
127897 TTCTAAA
1 TTCTAAA
127904 CAAGATTGTT
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 53 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (12 bp):
TTCTAAATGAAC
Found at i:136692 original size:34 final size:34
Alignment explanation
Indices: 136645--136730 Score: 145
Period size: 34 Copynumber: 2.4 Consensus size: 34
136635 TTTTTTGGTT
136645 TGGTTATTGCCATCACGAGTGGCCAAGAAATCTGG
1 TGGTTA-TGCCATCACGAGTGGCCAAGAAATCTGG
136680 TGGTTATGCCATCACGAGTGGCCAAGAAATCTGG
1 TGGTTATGCCATCACGAGTGGCCAAGAAATCTGG
136714 TGGTTATATGCCATCAC
1 TGG-T-TATGCCATCAC
136731 TCTTTGCTCC
Statistics
Matches: 49, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
34 31 0.63
35 7 0.14
36 11 0.22
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (34 bp):
TGGTTATGCCATCACGAGTGGCCAAGAAATCTGG
Done.