Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004002.1 Hibiscus syriacus cultivar Beakdansim tig00008724_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: 56069
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:13036 original size:75 final size:76
Alignment explanation
Indices: 12942--13164 Score: 257
Period size: 76 Copynumber: 3.0 Consensus size: 76
12932 GATTAAACTC
*
12942 AAGTTTTAGAATAATATTTTAAATATTATATTTTATCTTT-GA-ATTTTAGTTTAAATAGGTTTT
1 AAGTTTTAGAATATTATTTTAAATATTATATTTTAT-TTTAGATATTTTAGTTTAAATAGGTTTT
13005 AGTATTTTAATT
65 AGTATTTTAATT
* * * *
13017 AAGTTTTAGGATATTATTTT-TATATTTTATCTTTGTTTTAGATATTTTAGTTTAAATAGGTTTT
1 AAGTTTTAGAATATTATTTTAAATATTATAT-TTTATTTTAGATATTTTAGTTTAAATAGGTTTT
*
13081 AGTATTTTGATT
65 AGTATTTTAATT
* * * *
13093 AGGATTTAGAATATTATTTTAAATA-T-TA--TT-TTTTAGGTATTTTAGTTTAAATA-TTTTTA
1 AAGTTTTAGAATATTATTTTAAATATTATATTTTATTTTAGATATTTTAGTTTAAATAGGTTTT-
*
13152 AGTGTTTTAATT
65 AGTATTTTAATT
13164 A
1 A
13165 GGATTTAAGA
Statistics
Matches: 129, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
70 4 0.03
71 33 0.26
72 2 0.02
74 11 0.09
75 26 0.20
76 50 0.39
77 3 0.02
ACGTcount: A:0.31, C:0.01, G:0.11, T:0.57
Consensus pattern (76 bp):
AAGTTTTAGAATATTATTTTAAATATTATATTTTATTTTAGATATTTTAGTTTAAATAGGTTTTA
GTATTTTAATT
Found at i:19023 original size:28 final size:28
Alignment explanation
Indices: 18983--19052 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
18973 GATAGCACTT
* *
18983 CTTGCTTCGAGCTATGTTGTAAGTTTTA
1 CTTGCCTCGAGCTATGCTGTAAGTTTTA
19011 CTTGCCTCGAGCTATGCTGTAAGTTTTA
1 CTTGCCTCGAGCTATGCTGTAAGTTTTA
*
19039 TTTGCCTCTGAGCT
1 CTTGCCTC-GAGCT
19053 GAATGTAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
28 33 0.87
29 5 0.13
ACGTcount: A:0.16, C:0.20, G:0.21, T:0.43
Consensus pattern (28 bp):
CTTGCCTCGAGCTATGCTGTAAGTTTTA
Found at i:19059 original size:28 final size:27
Alignment explanation
Indices: 18983--19060 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 27
18973 GATAGCACTT
* *
18983 CTTGCTTCGAGCTATGTTGTAAGTTTTA
1 CTTGCCTCGAGCTA-GATGTAAGTTTTA
*
19011 CTTGCCTCGAGCTATGCTGTAAGTTTTA
1 CTTGCCTCGAGCTA-GATGTAAGTTTTA
*
19039 TTTGCCTCTGAGCT-GAATGTAA
1 CTTGCCTC-GAGCTAG-ATGTAA
19061 TTGAACTCGA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
27 1 0.02
28 38 0.86
29 5 0.11
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (27 bp):
CTTGCCTCGAGCTAGATGTAAGTTTTA
Found at i:19221 original size:84 final size:84
Alignment explanation
Indices: 19043--19322 Score: 239
Period size: 84 Copynumber: 3.4 Consensus size: 84
19033 GTTTTATTTG
* * * * * *
19043 CCTCTGAGCTGAATGTAATTGAACTCGAATGTCTTTGGATGGCAGATAACCGTTCTCGACTTAAG
1 CCTC-GAGCTGAGTGTAATCGAACTCGAAGGTATTTGGATGGCAGATAACCCTTCTAGACTTAAG
* *
19108 TTATGCTGCAAATGTTGTGC
65 TTATGATGCAAATGATGTGC
* * * * *
19128 CTTTGAGCTGAGTGTAATCGAACTCGAAGGTATTT-GTTGGCAGATAACCCTTCTAGCCTTGAGT
1 CCTCGAGCTGAGTGTAATCGAACTCGAAGGTATTTGGATGGCAGATAACCCTTCTAGACTTAAGT
* *
19192 TATGATGTAAATGATGTTC
66 TATGATGCAAATGATGTGC
* * * * * *
19211 CCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTT---T-GCAAATAGCCATTCTCGACTTAA-
1 CCTCG-AGCTGAGTGTAATCGAACTCGAAGGTATTTGGATGGCAGATAACCCTTCTAGACTTAAG
* * *
19271 TCTATGCTGCAAATAATATGC
65 T-TATGATGCAAATGATGTGC
* * * *
19292 CTTAGAGCTGAGCGTAGTCGAACTCGAAGGT
1 CCTCGAGCTGAGTGTAATCGAACTCGAAGGT
19323 CTTTATGTTT
Statistics
Matches: 158, Mismatches: 35, Indels: 9
0.78 0.17 0.04
Matches are distributed among these distances:
80 24 0.15
81 34 0.22
82 1 0.01
83 42 0.27
84 55 0.35
85 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (84 bp):
CCTCGAGCTGAGTGTAATCGAACTCGAAGGTATTTGGATGGCAGATAACCCTTCTAGACTTAAGT
TATGATGCAAATGATGTGC
Found at i:19365 original size:33 final size:33
Alignment explanation
Indices: 19328--19407 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
19318 AAGGTCTTTA
* *
19328 TGTTTCAAGAGAAACATTTTCAAAGGTTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTGG
19361 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTGG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTGG
19394 TGTTTCAAGAGAAA
1 TGTTTCAAGAGAAA
19408 ATGTCTCTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.38
Consensus pattern (33 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTTTGG
Found at i:19495 original size:67 final size:67
Alignment explanation
Indices: 19361--19585 Score: 213
Period size: 67 Copynumber: 3.2 Consensus size: 67
19351 AGGTTTTTTG
* * * * *
19361 TGTTTCAAGAGAAACA-ATTTCAAAGGTTTTTGGTGTTTCAAGAGAAAATGTCTCTAGGGAGGCA
1 TGTTTCAAGAGAAACATA-TTCAAAGG---TTGTTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
19425 AAATTT
62 AAATTT
19431 TGTTTCAAGAGAAACATATTCAAAGGTTGTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
1 TGTTTCAAGAGAAACATATTCAAAGGTTGTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
19496 TT
66 TT
* **
19498 TGTTTCAAGGGAAAC-TATCTCGAGAGAGACAAAAT-TTGTTTCAAGAGAAACTGTCTCAAGAGA
1 TGTTTCAAGAGAAACATAT-TC-A-A-AG----GTTGTTGTTTCAAGAGAAACTGTCTCAAGAGA
*
19561 GACAAAACTT
58 GACAAAATTT
* * *
19571 AGTTCCAAAAGAAAC
1 TGTTTCAAGAGAAAC
19586 TGTCTCAAGG
Statistics
Matches: 133, Mismatches: 13, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
66 3 0.02
67 52 0.39
68 1 0.01
69 1 0.01
70 26 0.20
71 1 0.01
73 48 0.36
74 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (67 bp):
TGTTTCAAGAGAAACATATTCAAAGGTTGTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
TT
Found at i:19548 original size:36 final size:36
Alignment explanation
Indices: 19460--19795 Score: 409
Period size: 36 Copynumber: 9.4 Consensus size: 36
19450 TCAAAGGTTG
*
19460 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-T
* *
19497 TTGTTTCAAGGGAAACTATCTCGAGAGAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
*
19533 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-T
* * ** *
19570 TAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
* * *
19606 TTGTTTCAAGGAAAACATAT-TC-A-A-AG----ATT
1 TTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAAT
* *
19635 TTATTTCAAGGGAAACTGTCTCAAGAGAGAAAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
*
19671 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACC
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-T
* *
19708 TTGTTTCAAGGGAAATTATCTCAAGAGAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
*
19744 TTGTTTCAAGGGAAACTGTCTCAAGAGAAACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
*
19780 TTGTTTCAAGAGAAAC
1 TTGTTTCAAGGGAAAC
19796 AAAATTTGTT
Statistics
Matches: 256, Mismatches: 32, Indels: 23
0.82 0.10 0.07
Matches are distributed among these distances:
28 2 0.01
29 18 0.07
30 1 0.00
31 1 0.00
32 2 0.01
33 2 0.01
35 1 0.00
36 130 0.51
37 99 0.39
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (36 bp):
TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
Found at i:19554 original size:73 final size:73
Alignment explanation
Indices: 19460--19795 Score: 406
Period size: 73 Copynumber: 4.7 Consensus size: 73
19450 TCAAAGGTTG
* *
19460 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTATCTCGAGAGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAGAGA
19525 GACAAAAT
66 GACAAAAT
* * ** * *
19533 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAGAGA
19598 GACAAAAT
66 GACAAAAT
* * * *
19606 TTGTTTCAAG-GAAAACATAT-TC-A-A-AG-----ATTTTATTTCAAGGGAAACTGTCTCAAGA
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAGA
*
19661 GAGAAAAAAT
64 GAGACAAAAT
* * *
19671 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACCTTGTTTCAAGGGAAATTATCTCAAGAGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAGAGA
19736 GACAAAAT
66 GACAAAAT
* * *
19744 TTGTTTCAAGGGAAACTGTCTCAAGAGAAACAAAA-TTTGTTTCAAGAGAAAC
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAAC
19796 AAAATTTGTT
Statistics
Matches: 223, Mismatches: 28, Indels: 25
0.81 0.10 0.09
Matches are distributed among these distances:
64 2 0.01
65 47 0.21
66 2 0.01
67 1 0.00
68 2 0.01
70 2 0.01
71 1 0.00
72 16 0.07
73 148 0.66
74 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (73 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAGAGA
GACAAAAT
Found at i:19676 original size:138 final size:137
Alignment explanation
Indices: 19490--19838 Score: 407
Period size: 138 Copynumber: 2.6 Consensus size: 137
19480 TCAAGAGAGA
* * * *
19490 CAAA-ATTTTGTTTCAAGGGAAACTATCTCGAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCT
1 CAAAGATTTTATTTCAAGGGAAACTGTCTCAAGAGAGAAAAAATTTGTTTCAAGAGAAACTGTCT
* *
19554 CAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGAA
66 CAAGAGAGACAAAACTT-GTTCCAAAAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGAA
19619 AACATAT-T
130 AAC-TATCT
*
19627 CAAAGATTTTATTTCAAGGGAAACTGTCTCAAGAGAGAAAAAATTTGTTTCAAGGGAAACTGTCT
1 CAAAGATTTTATTTCAAGGGAAACTGTCTCAAGAGAGAAAAAATTTGTTTCAAGAGAAACTGTCT
* ** * *
19692 CAAGAGAGACAAAACCTTGTTTCAAGGGAAATTATCTCAAGAGAGACAAAATTTGTTTCAAGGGA
66 CAAGAGAGACAAAA-CTTGTTCCAAAAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGAA
*
19757 AACTGTCT
130 AACTATCT
* ** *
19765 CAAGAGA----A--ACAA---AATTTGTTTCAAGAGA-AACAAAATTTGTTTCAAGAGAAACTGT
1 CAA-AGATTTTATTTCAAGGGAAACTGTCTCAAGAGAGAA-AAAATTTGTTTCAAGAGAAACTGT
*
19820 CTCTAGAGAGACAAAACTT
64 CTCAAGAGAGACAAAACTT
19839 TGTTTCGAGT
Statistics
Matches: 188, Mismatches: 19, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
129 5 0.03
130 51 0.27
133 3 0.02
135 1 0.01
137 6 0.03
138 116 0.62
139 6 0.03
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.26
Consensus pattern (137 bp):
CAAAGATTTTATTTCAAGGGAAACTGTCTCAAGAGAGAAAAAATTTGTTTCAAGAGAAACTGTCT
CAAGAGAGACAAAACTTGTTCCAAAAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGAAA
ACTATCT
Found at i:19753 original size:21 final size:21
Alignment explanation
Indices: 19728--19816 Score: 109
Period size: 21 Copynumber: 4.5 Consensus size: 21
19718 GGAAATTATC
*
19728 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAAACAAAATTTGTT
* *
19749 TCAAGGGAAAC------TGTC
1 TCAAGAGAAACAAAATTTGTT
19764 TCAAGAGAAACAAAATTTGTT
1 TCAAGAGAAACAAAATTTGTT
19785 TCAAGAGAAACAAAATTTGTT
1 TCAAGAGAAACAAAATTTGTT
19806 TCAAGAGAAAC
1 TCAAGAGAAAC
19817 TGTCTCTAGA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
15 13 0.23
21 44 0.77
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (21 bp):
TCAAGAGAAACAAAATTTGTT
Found at i:19792 original size:57 final size:58
Alignment explanation
Indices: 19728--19844 Score: 191
Period size: 57 Copynumber: 2.0 Consensus size: 58
19718 GGAAATTATC
* *
19728 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAAACAAAA-TTTGTT
1 TCAAGAGAAACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAAACAAAACTTTGTT
* *
19785 TCAAGAGAAACAAAATTTGTTTCAAGAGAAACTGTCTCTAGAGAGACAAAACTTTGTT
1 TCAAGAGAAACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAAACAAAACTTTGTT
19843 TC
1 TC
19845 GAGTAAATTA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
57 47 0.85
58 8 0.15
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (58 bp):
TCAAGAGAAACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAAACAAAACTTTGTT
Found at i:21303 original size:95 final size:95
Alignment explanation
Indices: 21108--21362 Score: 329
Period size: 95 Copynumber: 2.7 Consensus size: 95
21098 GGCTAGCTGG
* ** * *
21108 ATCCATAAAGCCGGGGCTTTTAACCAATTACTCCAGAGGGACAACTCAA----TATCGTTGTATT
1 ATCCATAAAGCCGGGGCATTTAACCAATTACTTAAGAGGGACAACTCAAGCTTTATAG-TATATT
21169 ATAATCACCTTTATCAGGCTAGCTGAATATT
65 ATAATCACCTTTATCAGGCTAGCTGAATATT
* * * *
21200 ATCCATAAAGCGGGGGCGTTTAACCAATTTCTTAAGAGGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCCGGGGCATTTAACCAATTACTTAAGAGGGACAACTCAAGCTTTATAGTATATTA
* *
21265 TAATCACCTTTATCAGGCTAGTTGAATCTT
66 TAATCACCTTTATCAGGCTAGCTGAATATT
* * * *
21295 ATCTATAAAGCCGGGGCATTTAACCAATTGCTTTAGAGGGACAGCTCAAGCTTTATAGTATATAT
1 ATCCATAAAGCCGGGGCATTTAACCAATTACTTAAGAGGGACAACTCAAGCTTTATAGTATAT-T
21360 ATA
65 ATA
21363 TATATAATTA
Statistics
Matches: 142, Mismatches: 16, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
92 44 0.31
95 90 0.63
96 8 0.06
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (95 bp):
ATCCATAAAGCCGGGGCATTTAACCAATTACTTAAGAGGGACAACTCAAGCTTTATAGTATATTA
TAATCACCTTTATCAGGCTAGCTGAATATT
Found at i:24756 original size:2 final size:2
Alignment explanation
Indices: 24749--24784 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
24739 CTACCATGCA
24749 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24785 TATGAAACAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24863 original size:2 final size:2
Alignment explanation
Indices: 24856--24882 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24846 CTGCAAAATA
24856 AT 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 AT A
24883 AGAGAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25113 original size:20 final size:20
Alignment explanation
Indices: 25088--25164 Score: 120
Period size: 20 Copynumber: 3.9 Consensus size: 20
25078 GCTACTTTCC
25088 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
25108 TAAATCGCAATGC-AGATACG
1 TAAATCGCAATGCGA-ATACG
*
25128 TAAATCGCAATGCGAATATG
1 TAAATCGCAATGCGAATACG
*
25148 TAAATCGCAACGCGAAT
1 TAAATCGCAATGCGAAT
25165 CTGACTATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 1 0.02
20 51 0.96
21 1 0.02
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (20 bp):
TAAATCGCAATGCGAATACG
Found at i:25386 original size:22 final size:22
Alignment explanation
Indices: 25361--25426 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
25351 GGCGACATCC
25361 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
25383 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
25405 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
25427 TTCACGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:25822 original size:20 final size:20
Alignment explanation
Indices: 25749--25839 Score: 94
Period size: 20 Copynumber: 4.6 Consensus size: 20
25739 GCGATTCTGT
25749 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
** **
25768 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTTTCATTTTCG
**
25788 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
* *
25808 TGTTGCGATTTTCATTTTCA
1 CGTTGCGATTTTCATTTTCG
*
25828 TGTTGCGATTTT
1 CGTTGCGATTTT
25840 AAGTTTCAGA
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
19 12 0.19
20 50 0.81
ACGTcount: A:0.15, C:0.18, G:0.22, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:25846 original size:20 final size:20
Alignment explanation
Indices: 25803--25847 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
25793 CGATAGTCAT
* * *
25803 TTTCGTGTTGCGATTTTCAT
1 TTTCATGTTGCGATTTTAAG
25823 TTTCATGTTGCGATTTTAAG
1 TTTCATGTTGCGATTTTAAG
25843 TTTCA
1 TTTCA
25848 GAAACTATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.13, G:0.18, T:0.53
Consensus pattern (20 bp):
TTTCATGTTGCGATTTTAAG
Found at i:27865 original size:20 final size:20
Alignment explanation
Indices: 27728--27877 Score: 73
Period size: 20 Copynumber: 8.3 Consensus size: 20
27718 AAAATAGTTT
*
27728 ACTATAGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* * *
27748 ACTATCACAACGCAAAAATG
1 ACTATCGCAATGCGAAAATG
*
27768 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
27784 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
27801 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
* *
27817 A--ATTGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
27835 ACTAT---AATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
27852 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
27872 ACTATC
1 ACTATC
27878 TCAACGAAAG
Statistics
Matches: 101, Mismatches: 12, Indels: 34
0.69 0.08 0.23
Matches are distributed among these distances:
14 13 0.13
16 10 0.10
17 24 0.24
18 4 0.04
19 7 0.07
20 43 0.43
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:28020 original size:20 final size:20
Alignment explanation
Indices: 27926--28031 Score: 131
Period size: 20 Copynumber: 5.3 Consensus size: 20
27916 GCGATTCTCT
* **
27926 CATTGTGATAGTCAAATTCG
1 CATTGCGATAGTCATTTTCG
**
27946 CATTGCGATAGTCAAATTCG
1 CATTGCGATAGTCATTTTCG
27966 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
27986 CGTTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
* *
28006 CGTTGTGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
28026 CTTTGC
1 CATTGC
28032 CATTTTAAGT
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 79 1.00
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.39
Consensus pattern (20 bp):
CATTGCGATAGTCATTTTCG
Found at i:28556 original size:18 final size:19
Alignment explanation
Indices: 28517--28558 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
28507 CTCACTTGTC
28517 ATCGTTCAAGAGGTCTCCCCT
1 ATCGTTCAAGAGG--TCCCCT
28538 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGTCCCCT
28556 ATC
1 ATC
28559 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.33, G:0.19, T:0.26
Consensus pattern (19 bp):
ATCGTTCAAGAGGTCCCCT
Found at i:28619 original size:42 final size:42
Alignment explanation
Indices: 28513--28619 Score: 119
Period size: 42 Copynumber: 2.5 Consensus size: 42
28503 CCAACTCACT
* * * *
28513 TGTCATCGTTCAAGAGGTCTCC-CCTATCGTTCAAGAGGCCCC
1 TGTCATCGCTCAAGAGGTC-CCTCCCACCGTTCAAGAGGCCAC
* *
28555 TATCATCCCTCAAGA-GTCCCCTCCCACCGTTCAAGAGGCCAC
1 TGTCATCGCTCAAGAGGT-CCCTCCCACCGTTCAAGAGGCCAC
*
28597 TGTCATCGCTGAAGAGGTCCCTC
1 TGTCATCGCTCAAGAGGTCCCTC
28620 TCAACATTCT
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
41 4 0.08
42 47 0.89
43 2 0.04
ACGTcount: A:0.21, C:0.36, G:0.20, T:0.23
Consensus pattern (42 bp):
TGTCATCGCTCAAGAGGTCCCTCCCACCGTTCAAGAGGCCAC
Found at i:30023 original size:14 final size:14
Alignment explanation
Indices: 30004--30039 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
29994 ATTGTTTAAT
30004 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
30018 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
30032 TGATTTGT
1 TGATTTGT
30040 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:30184 original size:14 final size:14
Alignment explanation
Indices: 30165--30218 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
30155 GGAAATGACT
30165 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
30179 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
30198 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
30212 ATCGCAA
1 ATCGCAA
30219 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:30188 original size:34 final size:34
Alignment explanation
Indices: 30145--30240 Score: 158
Period size: 33 Copynumber: 2.9 Consensus size: 34
30135 AAAACAGACT
**
30145 ATCGCAATGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
30179 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
30212 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCGGAAATGAAAATCGCAACG
30241 CGAAACTAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 31 0.53
34 27 0.47
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.14
Consensus pattern (34 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:30236 original size:20 final size:19
Alignment explanation
Indices: 30178--30245 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 19
30168 GCAACGAGAG
30178 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
30197 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
30211 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
30231 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
30246 CTAAATTCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
19 12 0.30
20 13 0.32
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:30280 original size:20 final size:19
Alignment explanation
Indices: 30251--30317 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
30241 CGAAACTAAA
*
30251 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCA-T
30271 TTCGCATTGCGA--TT-AT
1 TTCGCATTGCGATTTTCAT
*
30287 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
30304 TTCGCATTGCGATT
1 TTCGCATTGCGATT
30318 CTCTCGTTGC
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
14 6 0.15
16 6 0.15
17 6 0.15
18 2 0.05
19 8 0.21
20 11 0.28
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.46
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:30298 original size:34 final size:34
Alignment explanation
Indices: 30255--30350 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 34
30245 ACTAAATTCG
30255 CGTTGCGATTTTCATTTTCGCATTGCGATTATCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCT
*
30289 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCT
** * *
30322 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
30351 AGTCAATTCC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTATCT
Found at i:30347 original size:20 final size:20
Alignment explanation
Indices: 30322--30410 Score: 144
Period size: 20 Copynumber: 4.5 Consensus size: 20
30312 GCGATTCTCT
30322 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
30342 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
30362 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
30382 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
30402 CGTTGCGAT
1 CGTTGCGAT
30411 TTCCGCGTTG
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
20 62 0.97
21 2 0.03
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:32870 original size:24 final size:24
Alignment explanation
Indices: 32843--32896 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
32833 TTGAAAAATC
32843 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
32867 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
32891 ATCAAA
1 ATCAAA
32897 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:32910 original size:24 final size:24
Alignment explanation
Indices: 32843--32910 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
32833 TTGAAAAATC
* * *
32843 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
32867 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
32891 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
32911 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:33762 original size:20 final size:20
Alignment explanation
Indices: 33737--33820 Score: 141
Period size: 20 Copynumber: 4.2 Consensus size: 20
33727 AAATTCAGTA
33737 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
*
33757 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
33777 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
33797 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
33817 TTGC
1 TTGC
33821 AATTTACATA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:33833 original size:20 final size:20
Alignment explanation
Indices: 33810--33922 Score: 163
Period size: 20 Copynumber: 5.7 Consensus size: 20
33800 CGATAGTCAG
* * *
33810 ATTCGCGTTGCAATTTACAT
1 ATTCGCATTGCGATTTACGT
*
33830 ATTCGCATTGCGATTTATGT
1 ATTCGCATTGCGATTTACGT
*
33850 ATTCGTATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
33870 ATTCGCATTACGATTTACGT
1 ATTCGCATTGCGATTTACGT
33890 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
33910 ATTTGCATTGCGA
1 ATTCGCATTGCGA
33923 ATTAGGAAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 83 1.00
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.42
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:33945 original size:21 final size:21
Alignment explanation
Indices: 33919--33964 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
33909 TATTTGCATT
33919 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
*
33940 GCGAATTTGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
33961 GCGA
1 GCGA
33965 TAGTCAGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.15
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:39617 original size:75 final size:75
Alignment explanation
Indices: 39524--39694 Score: 211
Period size: 76 Copynumber: 2.3 Consensus size: 75
39514 GATTAAACTC
* *
39524 AAGTTTTAGAATAATATTTTAAACATTATAT-TTTATCTTT-GTATTTTAGTTTATATAGGTTTT
1 AAGTTTTAGAATATTATTTT-AACATTATATCTTTAT-TTTAGTATTTTAGTTTAAATAGGTTTT
39587 AGTATTTTAATT
64 AGTATTTTAATT
* * * * * *
39599 AAGTTTTAGGATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATATGTTTTA
1 AAGTTTTAGAATATTATTTTAACATTATATCTTTATTTTA-GTATTTTAGTTTAAATAGGTTTTA
39664 GTATTTTAATT
65 GTATTTTAATT
* *
39675 AGGATTTAGAATATTATTTT
1 AAGTTTTAGAATATTATTTT
39695 TTAGGTATTT
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
74 10 0.12
75 22 0.27
76 50 0.61
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (75 bp):
AAGTTTTAGAATATTATTTTAACATTATATCTTTATTTTAGTATTTTAGTTTAAATAGGTTTTAG
TATTTTAATT
Found at i:40371 original size:18 final size:19
Alignment explanation
Indices: 40332--40375 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
40322 CTTTAATTTA
* *
40332 TTTATTTAATTATTTTTCT
1 TTTATTTAATTACTTATCT
40351 TTTATTTAATT-CTTATCT
1 TTTATTTAATTACTTATCT
40369 TTTATTT
1 TTTATTT
40376 TAAAAATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTATTTAATTACTTATCT
Found at i:40473 original size:18 final size:18
Alignment explanation
Indices: 40428--40479 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
40418 TTACTATTAA
* *
40428 TATTTATTATTTTATTAT
1 TATTTATTTTTTTATAAT
* *
40446 TTTTTCTTTTTTTATAAT
1 TATTTATTTTTTTATAAT
*
40464 TATTTATTTTATTATA
1 TATTTATTTTTTTATA
40480 CCTTTTCAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (18 bp):
TATTTATTTTTTTATAAT
Found at i:45911 original size:15 final size:15
Alignment explanation
Indices: 45891--45923 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
45881 TTCGTAAAAA
45891 GGTGGAATAAGGGAC
1 GGTGGAATAAGGGAC
45906 GGTGGAATAAGGGAC
1 GGTGGAATAAGGGAC
45921 GGT
1 GGT
45924 AGATATGCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.30, C:0.06, G:0.48, T:0.15
Consensus pattern (15 bp):
GGTGGAATAAGGGAC
Found at i:52480 original size:21 final size:20
Alignment explanation
Indices: 52394--52551 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
52384 AAATGACCAA
**
52394 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
52413 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
52433 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
52453 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
52474 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
52495 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
52515 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
52536 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
52552 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:52544 original size:20 final size:20
Alignment explanation
Indices: 52519--52712 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
52509 GATTTTCAAT
* *
52519 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
52539 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
52559 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
52579 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
52599 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
52619 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
52639 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
52659 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
52680 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
52700 AATCGCAACGCGA
1 AATCGCAACGCGA
52713 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:52564 original size:40 final size:39
Alignment explanation
Indices: 52519--52712 Score: 199
Period size: 40 Copynumber: 4.8 Consensus size: 39
52509 GATTTTCAAT
* ** *
52519 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CATA
* * *
52559 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
** * * *
52599 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
* ** *
52639 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT-A
52680 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
52713 TATTTAAAGC
Statistics
Matches: 128, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.73
41 33 0.26
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (39 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCATA
Found at i:52602 original size:60 final size:60
Alignment explanation
Indices: 52519--52711 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
52509 GATTTTCAAT
* ** * *
52519 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
52579 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
52639 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
52700 AATCGCAACGCG
1 AATCGCAACGCG
52712 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:53129 original size:33 final size:33
Alignment explanation
Indices: 53090--53160 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
53080 TTCACTTAGA
*
53090 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
53123 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
53156 TTTCA
1 TTTCA
53161 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:53300 original size:14 final size:14
Alignment explanation
Indices: 53281--53335 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
53271 AGAATGACTG
53281 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
53295 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
53314 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
53328 TCGCAACG
1 TCGCAACG
53336 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:53318 original size:33 final size:33
Alignment explanation
Indices: 53281--53351 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
53271 AGAATGACTG
**
53281 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
53314 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
53347 TCGCA
1 TCGCA
53352 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:53369 original size:19 final size:19
Alignment explanation
Indices: 53347--53444 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
53337 GAAACCAAAA
*
53347 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
53366 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
53380 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
53399 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
53413 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
53432 TCGCGTTGCGATT
1 TCGCGTTGCGATT
53445 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:53388 original size:14 final size:14
Alignment explanation
Indices: 53369--53458 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
53359 TTTCATTTCG
53369 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
53383 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
53402 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
53416 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
53433 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
53449 CGTTGCGATT
1 CGTTGCGATT
53459 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:53394 original size:33 final size:33
Alignment explanation
Indices: 53352--53466 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
53342 CAAAATCGCA
53352 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
53385 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
53418 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
53451 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
53467 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:55356 original size:92 final size:93
Alignment explanation
Indices: 55154--55527 Score: 697
Period size: 92 Copynumber: 4.1 Consensus size: 93
55144 TAGATTGCTT
*
55154 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
55219 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
55247 AGTAAATTTGTTC-GTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
55310 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
55338 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
55402 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
55430 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCT-AACTGTGTATTC-TTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
55493 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
55520 AGTAAATT
1 AGTAAATT
55528 ATCCATTCAA
Statistics
Matches: 278, Mismatches: 1, Indels: 7
0.97 0.00 0.02
Matches are distributed among these distances:
90 34 0.12
91 74 0.27
92 158 0.57
93 12 0.04
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:55608 original size:19 final size:18
Alignment explanation
Indices: 55586--55697 Score: 105
Period size: 19 Copynumber: 6.5 Consensus size: 18
55576 CACGAAACTT
55586 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAA-C
*
55605 AAAATCGCAACGCGAAAT
1 AAAATCGCAACGCGAAAC
*
55623 GAAATCGCAA--CG--AC
1 AAAATCGCAACGCGAAAC
*
55637 AGAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAA-C
55656 AAAATCGCAA--CG--AC
1 AAAATCGCAACGCGAAAC
*
55670 AAGATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAA-C
55689 AAAATCGCA
1 AAAATCGCA
55698 TTGCGATTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
14 19 0.25
15 1 0.01
16 6 0.08
17 2 0.03
18 11 0.15
19 36 0.48
ACGTcount: A:0.46, C:0.29, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAATCGCAACGCGAAAC
Found at i:55666 original size:33 final size:32
Alignment explanation
Indices: 55606--55697 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
55596 CGCGAAACCA
**
55606 AAATCGCAACGCGAAA-TGAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
55637 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
55670 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
55698 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
31 1 0.02
32 16 0.29
33 39 0.70
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:55715 original size:19 final size:19
Alignment explanation
Indices: 55693--55827 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
55683 GAAACCAAAA
*
55693 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
55712 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
55728 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
55745 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
55761 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
55778 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
55797 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
55817 TCGTGTTGCGA
1 TCGCGTTGCGA
55828 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:55734 original size:14 final size:14
Alignment explanation
Indices: 55715--55771 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
55705 TTTCATTTCG
55715 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
55729 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
55746 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
55762 CGTTGCGATT
1 CGTTGCGATT
55772 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:55740 original size:33 final size:33
Alignment explanation
Indices: 55698--55790 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
55688 CAAAATCGCA
*
55698 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
55731 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
55764 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
55791 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Done.