Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004475.1 Hibiscus syriacus cultivar Beakdansim tig00009864_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: 117769
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:3933 original size:18 final size:17
Alignment explanation
Indices: 3912--3955 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
3902 ACAACAAATG
3912 AAATAAAAACAATACTAA
1 AAATAAAAACAA-ACTAA
* * *
3930 AAATGAAAACAAAGTCA
1 AAATAAAAACAAACTAA
3947 AAATAAAAA
1 AAATAAAAA
3956 GGAATTAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.73, C:0.09, G:0.05, T:0.14
Consensus pattern (17 bp):
AAATAAAAACAAACTAA
Found at i:4160 original size:12 final size:12
Alignment explanation
Indices: 4143--4216 Score: 71
Period size: 12 Copynumber: 6.2 Consensus size: 12
4133 AAAATAATAG
*
4143 TAATAATGAAAA
1 TAATAATAAAAA
4155 TAATAATAAAAA
1 TAATAATAAAAA
*
4167 TAATAGT-AAAA
1 TAATAATAAAAA
* *
4178 GAGTAATAAAAA
1 TAATAATAAAAA
*
4190 TAA-AAGAAAACA
1 TAATAATAAAA-A
*
4202 TAAAAATAAAAA
1 TAATAATAAAAA
4214 TAA
1 TAA
4217 AGGGGAAAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
11 14 0.28
12 30 0.60
13 6 0.12
ACGTcount: A:0.72, C:0.01, G:0.07, T:0.20
Consensus pattern (12 bp):
TAATAATAAAAA
Found at i:4212 original size:35 final size:35
Alignment explanation
Indices: 4123--4212 Score: 83
Period size: 35 Copynumber: 2.5 Consensus size: 35
4113 AAAGATATAC
* * *
4123 GAAAAATAACAAAATAATAGTAATAATGAAAATAATAA
1 GAAAAAT-A-AAAATAAAAG-AGTAATAAAAATAATAA
* * *
4161 TAAAAATAATAGTAAAAGAGTAATAAAAATAA-AA
1 GAAAAATAAAAATAAAAGAGTAATAAAAATAATAA
4195 GAAAACATAAAAATAAAA
1 GAAAA-ATAAAAATAAAA
4213 ATAAAGGGGA
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
34 6 0.14
35 22 0.52
36 7 0.17
37 1 0.02
38 6 0.14
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.19
Consensus pattern (35 bp):
GAAAAATAAAAATAAAAGAGTAATAAAAATAATAA
Found at i:6358 original size:107 final size:106
Alignment explanation
Indices: 6114--6362 Score: 301
Period size: 107 Copynumber: 2.3 Consensus size: 106
6104 TTTTATTGTT
* * * *
6114 TCGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGAC
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTGGAAAATTGTTTGTTGAC
* *
6179 AGTCAGCCGCCCCTTCGGTGTGAAATCAAGCTTGTGCTGTC
66 AATCAGCCGCCCCTTCGGTATGAAATCAAGCTTGTGCTGTC
*
6220 TCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACT-GAAAAGTTGTTTG
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTC----TGAAACTGGAAAA-TTGTTTG
* ** *
6284 TTGACAATCAGCCGCCCCTT-GTTAT-AAAGTTGAG-TT-TGTTGTC
61 TTGACAATCAGCCGCCCCTTCGGTATGAAA-TCAAGCTTGTGCTGTC
*
6327 TTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
6363 GGAAGCCCCT
Statistics
Matches: 124, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
106 36 0.29
107 40 0.32
108 5 0.04
109 10 0.08
110 33 0.27
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (106 bp):
TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTGGAAAATTGTTTGTTGAC
AATCAGCCGCCCCTTCGGTATGAAATCAAGCTTGTGCTGTC
Found at i:6493 original size:66 final size:65
Alignment explanation
Indices: 6334--6494 Score: 173
Period size: 69 Copynumber: 2.4 Consensus size: 65
6324 GTCTTGAGTC
* *
6334 CAATATCCTTCG-CTGTGAAGTTGAAATTGGGAAGCCCCTTCGTCGTGAAGTTAAGCCTCAAATG
1 CAATATCCTTCGTC-GTGAAGTTGAAATCGGGAAGCCCCTTCATCGTGAAGTTAAGCCTCAAATG
6398 G
65 G
* * * * **
6399 CACGATATCCTCCGTCGTGGAGTTGAAATCGCGGATGGCCCCTTCATCGTGAAGTTGAGCCTTGA
1 CA--ATATCCTTCGTCGTGAAGTTGAAATCG-GGA-AGCCCCTTCATCGTGAAGTTAAGCCTCAA
* *
6464 CTTG
62 ATGG
6468 -AATATCCTTCGTCGTGAAGTTGAAATC
1 CAATATCCTTCGTCGTGAAGTTGAAATC
6495 CAAGTATTGT
Statistics
Matches: 79, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
65 2 0.03
66 24 0.30
67 22 0.28
68 5 0.06
69 26 0.33
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.29
Consensus pattern (65 bp):
CAATATCCTTCGTCGTGAAGTTGAAATCGGGAAGCCCCTTCATCGTGAAGTTAAGCCTCAAATGG
Found at i:19261 original size:24 final size:24
Alignment explanation
Indices: 19233--19295 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 24
19223 TAAAATTAAT
*
19233 AATATTATATATATATAATTATAC
1 AATATAATATATATATAATTATAC
* *
19257 AATATAATATGTA-AT-ATTATAT
1 AATATAATATATATATAATTATAC
19279 AATATAATA-ATAT-TAAT
1 AATATAATATATATATAAT
19296 AACAAAAGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 3 0.09
22 17 0.52
23 2 0.06
24 11 0.33
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
AATATAATATATATATAATTATAC
Found at i:19278 original size:17 final size:18
Alignment explanation
Indices: 19229--19297 Score: 79
Period size: 17 Copynumber: 3.9 Consensus size: 18
19219 TAAATAAAAT
19229 TAATAATATTATATATATA
1 TAATAATATTATATA-ATA
* **
19248 TAATTATACAATATAATA
1 TAATAATATTATATAATA
*
19266 T-GTAATATTATATAATA
1 TAATAATATTATATAATA
19283 TAATAATATTA-ATAA
1 TAATAATATTATATAA
19298 CAAAAGACGA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
17 17 0.41
18 12 0.29
19 12 0.29
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (18 bp):
TAATAATATTATATAATA
Found at i:19794 original size:63 final size:63
Alignment explanation
Indices: 19695--19821 Score: 227
Period size: 63 Copynumber: 2.0 Consensus size: 63
19685 TTTGTCTAAA
** *
19695 ATCTAAATGAGAGAAATTATGGGGTTCATGAAATTTGATTATTTAAATTAAAACACAAGTATG
1 ATCTAAATGAGAGAAATTATGGGGTTCATGAAATTTGACCATTTAAATTAAAACACAAATATG
19758 ATCTAAATGAGAGAAATTATGGGGTTCATGAAATTTGACCATTTAAATTAAAACACAAATATG
1 ATCTAAATGAGAGAAATTATGGGGTTCATGAAATTTGACCATTTAAATTAAAACACAAATATG
19821 A
1 A
19822 AGGTGGGTAG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (63 bp):
ATCTAAATGAGAGAAATTATGGGGTTCATGAAATTTGACCATTTAAATTAAAACACAAATATG
Found at i:21362 original size:23 final size:23
Alignment explanation
Indices: 21328--21383 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
21318 TTAAAATGTT
*
21328 TTTTGTCTCCTAAGACATAATAC
1 TTTTGTCCCCTAAGACATAATAC
21351 TTTTGTCCCCTAAGACATAATAC
1 TTTTGTCCCCTAAGACATAATAC
21374 TTTTGTCCCC
1 TTTTGTCCCC
21384 AATAAGGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.25, C:0.27, G:0.09, T:0.39
Consensus pattern (23 bp):
TTTTGTCCCCTAAGACATAATAC
Found at i:22678 original size:14 final size:13
Alignment explanation
Indices: 22638--22699 Score: 61
Period size: 14 Copynumber: 4.5 Consensus size: 13
22628 CAATCAGAAC
*
22638 AAAAAGAAAAAAAG
1 AAAAA-AAAAAGAG
*
22652 AAAAAACAAAGAG
1 AAAAAAAAAAGAG
22665 AAAATAAAAAAGAG
1 AAAA-AAAAAAGAG
*
22679 AAACAAAAAAAAAGG
1 AAA-AAAAAAAGA-G
22694 AAAAAA
1 AAAAAA
22700 TGAAGAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
13 10 0.24
14 26 0.63
15 5 0.12
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.02
Consensus pattern (13 bp):
AAAAAAAAAAGAG
Found at i:24649 original size:73 final size:73
Alignment explanation
Indices: 24566--24711 Score: 188
Period size: 72 Copynumber: 2.0 Consensus size: 73
24556 ACAATGGGTC
* * *
24566 ATCTCGCTTGAGACTAATTT-ACTCAAAACAAAGTTTTGTCTCTTTTGAGACAGTTTCTCTTGAA
1 ATCTCGCTTGAGAC-AATTTCACTCAAAACAAA-TTTTGTCTCTCTTGAGACAGATTCCCTTGAA
24630 AC-AAATCTT
64 ACAAAATCTT
* * * **
24639 ATCTCTCTTGAGACAGTTTCCCTGGAAACAAATTTTGTCTCTCTTGAGACAGATTCCCTTGAAAC
1 ATCTCGCTTGAGACAATTTCACTCAAAACAAATTTTGTCTCTCTTGAGACAGATTCCCTTGAAAC
24704 AAAATCTT
66 AAAATCTT
24712 TGAATATGTT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
72 34 0.54
73 29 0.46
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.36
Consensus pattern (73 bp):
ATCTCGCTTGAGACAATTTCACTCAAAACAAATTTTGTCTCTCTTGAGACAGATTCCCTTGAAAC
AAAATCTT
Found at i:24651 original size:36 final size:36
Alignment explanation
Indices: 24591--25094 Score: 357
Period size: 36 Copynumber: 14.1 Consensus size: 36
24581 AATTTACTCA
* *
24591 AAACAAAGTTTTGTCTCTTTTGAGACAGTTTCTCTTG
1 AAACAAA-TTTTATCTCTCTTGAGACAGTTTCTCTTG
* * *
24628 AAACAAATCTTATCTCTCTTGAGACAGTTTCCCTGG
1 AAACAAATTTTATCTCTCTTGAGACAGTTTCTCTTG
* * *
24664 AAACAAATTTTGTCTCTCTTGAGACAGATTCCCTTG
1 AAACAAATTTTATCTCTCTTGAGACAGTTTCTCTTG
* *
24700 AAACAAA----A--TCT-TTGA-ATATGTTT-TAGATT-
1 AAACAAATTTTATCTCTCTTGAGACA-GTTTCT--CTTG
* * * *
24729 AAAAAAATTTCATCTCCCTTGAGACAGTTTCTTTTG
1 AAACAAATTTTATCTCTCTTGAGACAGTTTCTCTTG
* * * *
24765 GAACTAATTTTAGTATCTCTTGAGACAATTTCTCTTG
1 AAACAAATTTTA-TCTCTCTTGAGACAGTTTCTCTTG
24802 AAACAAATTTTATCTTTATCTCTCTTGAGACAGTTTCTCTTG
1 AAAC-AA----AT-TTTATCTCTCTTGAGACAGTTTCTCTTG
* * * * *
24844 AAACAAATTTTGTCTCTCTTAAGATAATTTCCCTTG
1 AAACAAATTTTATCTCTCTTGAGACAGTTTCTCTTG
* * * *
24880 AAACAAATTTTCTCTCTCTTGAGATAATTTCCCTTG
1 AAACAAATTTTATCTCTCTTGAGACAGTTTCTCTTG
*
24916 AAA-AAA----A--TCT-TTGA-ATATGTTT-TCTTTG
1 AAACAAATTTTATCTCTCTTGAGACA-GTTTCTC-TTG
* * * *
24944 AAATAAATTTCATCTCCCTTGAGACAGGTTCT-TTCG
1 AAACAAATTTTATCTCTCTTGAGACAGTTTCTCTT-G
* * *
24980 GAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAAC-AAATTTTATCTCTCTTGAGACAGTTTCTCTTG
* * * *
25017 AAATAAATTTTGTATCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTATCTCTCTTGAGACAGTTTCTCTTG
*
25053 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAA-TTTTATCTCTCTTGAGACAGTTTCTCTTG
25090 AAACA
1 AAACA
25095 CAAAAAAAAA
Statistics
Matches: 373, Mismatches: 58, Indels: 72
0.74 0.12 0.14
Matches are distributed among these distances:
27 4 0.01
28 15 0.04
29 19 0.05
30 5 0.01
33 2 0.01
35 11 0.03
36 184 0.49
37 96 0.26
38 3 0.01
41 2 0.01
42 28 0.08
43 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (36 bp):
AAACAAATTTTATCTCTCTTGAGACAGTTTCTCTTG
Found at i:24862 original size:21 final size:20
Alignment explanation
Indices: 24837--24901 Score: 52
Period size: 21 Copynumber: 3.4 Consensus size: 20
24827 TGAGACAGTT
24837 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTT-TC
*
24858 TCTCTT-AAGA-TAA--TTTC
1 TCTCTTGAA-ACAAATTTTTC
24875 -C-CTTGAAACAAATTTTCTC
1 TCTCTTGAAACAAATTTT-TC
24894 TCTCTTGA
1 TCTCTTGA
24902 GATAATTTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 16
0.65 0.04 0.31
Matches are distributed among these distances:
15 4 0.12
16 5 0.15
17 2 0.06
18 4 0.12
19 2 0.06
20 5 0.15
21 12 0.35
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.43
Consensus pattern (20 bp):
TCTCTTGAAACAAATTTTTC
Found at i:24889 original size:78 final size:79
Alignment explanation
Indices: 24740--24890 Score: 223
Period size: 78 Copynumber: 1.9 Consensus size: 79
24730 AAAAAATTTC
* * * * *
24740 ATCTCCCTTGAGACAGTTTCTTTTGGAACTAATTTTAGTATCTCTTGAGACAATTTCTCTTGAAA
1 ATCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTTAGTATCTCTTAAGACAATTTCCCTTGAAA
24805 CAAATTTTATCTTT
66 CAAATTTTATCTTT
* * *
24819 ATCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTT-GTCTCTCTTAAGATAATTTCCCTTGAAA
1 ATCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTTAGTATCTCTTAAGACAATTTCCCTTGAAA
24883 CAAATTTT
66 CAAATTTT
24891 CTCTCTCTTG
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
78 32 0.50
79 32 0.50
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.43
Consensus pattern (79 bp):
ATCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTTAGTATCTCTTAAGACAATTTCCCTTGAAA
CAAATTTTATCTTT
Found at i:25027 original size:215 final size:212
Alignment explanation
Indices: 24591--25094 Score: 691
Period size: 216 Copynumber: 2.4 Consensus size: 212
24581 AATTTACTCA
* * *
24591 AAACAAAGTTTTG--TCTCTTTTGAGACAGTTTCTCTTGAAACAAATCTTATCTCTCTTGAGACA
1 AAACAAA-TTTTGTATCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
24654 GTTTCCCTGGAAACAAATTTTGTCTCTCTTGAGACAGATTCCCTTGAAACAAAATCTTTGAATAT
65 GTTTCCCTTGAAACAAATTTTCTCTCTCTTGAGACAGATTCCCTTGAAACAAAATCTTTGAATAT
* * *
24719 GTTTTAGATTAAAAAAATTTCATCTCCCTTGAGACAGTTTCTTTTGGAACTAATTTTAGTATCTC
130 GTTTTACATTAAAAAAATTTCATCTCCCTTGAGACAGGTTCTTTCGGAACTAATTTTAGTATCTC
24784 TTGAGACAATTTCTCTTG
195 TTGAGACAATTTCTCTTG
* *
24802 AAACAAATTTTATCTTTATCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTAAG
1 AAACAAA--TT-T-TGTATCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAG
* * *
24867 ATAATTTCCCTTGAAACAAATTTTCTCTCTCTTGAGATA-ATTTCCCTTGAAA-AAAATCTTTGA
62 ACAGTTTCCCTTGAAACAAATTTTCTCTCTCTTGAGACAGA-TTCCCTTGAAACAAAATCTTTGA
* *
24930 ATATGTTTT-CTTTGAAATAAATTTCATCTCCCTTGAGACAGGTTCTTTCGGAACTAAGTTTT-G
126 ATATGTTTTACATT-AAAAAAATTTCATCTCCCTTGAGACAGGTTCTTTCGGAACTAA-TTTTAG
* *
24993 TCTCTCTTGAGACAGTTTCTCTTG
189 TATCTCTTGAGACAATTTCTCTTG
* *
25017 AAATAAATTTTGTA--TCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
1 AAACAAATTTTGTATCTCTCTTGAGACAGTTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
*
25080 GTTTCTCTTGAAACA
65 GTTTCCCTTGAAACA
25095 CAAAAAAAAA
Statistics
Matches: 259, Mismatches: 25, Indels: 19
0.85 0.08 0.06
Matches are distributed among these distances:
209 28 0.11
210 30 0.12
211 10 0.04
212 3 0.01
213 3 0.01
214 3 0.01
215 90 0.35
216 92 0.36
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (212 bp):
AAACAAATTTTGTATCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
TTTCCCTTGAAACAAATTTTCTCTCTCTTGAGACAGATTCCCTTGAAACAAAATCTTTGAATATG
TTTTACATTAAAAAAATTTCATCTCCCTTGAGACAGGTTCTTTCGGAACTAATTTTAGTATCTCT
TGAGACAATTTCTCTTG
Found at i:25062 original size:73 final size:73
Alignment explanation
Indices: 24936--25092 Score: 219
Period size: 73 Copynumber: 2.2 Consensus size: 73
24926 TTGAATATGT
* * * *
24936 TTTCT-TTGAAATAAATTTCATCTCCCTTGAGACAGGTTCTTTCGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAATAAATTTCATATCCCTTGAGACAGGTTCCTTCGAAACAAAGTTTTGTCTCTCT
25000 TGAGACAG
66 TGAGACAG
** * *
25008 TTTCTCTTGAAATAAATTTTGTATCTCTTGAGACAGTTTCCCTT-GAAACAAAGTTTTGTCTCTC
1 TTTCTCTTGAAATAAATTTCATATCCCTTGAGACAGGTT-CCTTCGAAACAAAGTTTTGTCTCTC
25072 TTGAGACAG
65 TTGAGACAG
25081 TTTCTCTTGAAA
1 TTTCTCTTGAAA
25093 CACAAAAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
72 5 0.07
73 67 0.89
74 3 0.04
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.41
Consensus pattern (73 bp):
TTTCTCTTGAAATAAATTTCATATCCCTTGAGACAGGTTCCTTCGAAACAAAGTTTTGTCTCTCT
TGAGACAG
Found at i:25120 original size:73 final size:73
Alignment explanation
Indices: 24985--25126 Score: 162
Period size: 73 Copynumber: 1.9 Consensus size: 73
24975 TTTCGGAACT
* ****** * *
24985 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAATTTTGTATCTCTTGAGACAGTTTCCC
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAAAAAAACCTCTTGAGAAAGTTTCCC
25050 TTGAAACA
66 TTGAAACA
25058 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACAAAAAAAAACCT-TTGA-AAATGTTTC
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA-AAAAAAAAACCTCTTGAGAAA-GTTTC
*
25121 TCTTGA
64 CCTTGA
25127 GACACCAAAC
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
72 2 0.04
73 50 0.88
74 5 0.09
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.39
Consensus pattern (73 bp):
AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAAAAAAACCTCTTGAGAAAGTTTCCC
TTGAAACA
Found at i:25283 original size:84 final size:84
Alignment explanation
Indices: 25133--25317 Score: 253
Period size: 84 Copynumber: 2.2 Consensus size: 84
25123 TTGAGACACC
* * *
25133 AAACTTTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTGCAACATATCTTAAGGCAAGA
1 AAACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAACATAGCTTAAGGCAAGA
* * *
25198 AGGGTTATTTGTCAACCAA
66 AGGGCTATCTGCCAACCAA
* * * *
25217 AAACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGA
1 AAACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAACATAGCTTAAGGCAAGA
25282 AGGGCTATCTGCCAACCAA
66 AGGGCTATCTGCCAACCAA
* *
25301 AGACCTGACGAGTTCGA
1 AAACCT-TCGAGTTCGA
25318 TTTCATTCAG
Statistics
Matches: 88, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
84 79 0.90
85 9 0.10
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (84 bp):
AAACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAACATAGCTTAAGGCAAGA
AGGGCTATCTGCCAACCAA
Found at i:30445 original size:35 final size:35
Alignment explanation
Indices: 30406--30480 Score: 91
Period size: 35 Copynumber: 2.1 Consensus size: 35
30396 AAAATACTTC
*
30406 AATTTAGGGG-TTATAATGTAATT-AAAGTATTTTAG
1 AATTT-GGGGTTTAGAATGTAATTGAAA-TATTTTAG
* *
30441 AATTTGGGGTTTAGAATGTAATTGAAATGTTTTGG
1 AATTTGGGGTTTAGAATGTAATTGAAATATTTTAG
30476 AATTT
1 AATTT
30481 TGAACATGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 4 0.11
35 28 0.80
36 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (35 bp):
AATTTGGGGTTTAGAATGTAATTGAAATATTTTAG
Found at i:31708 original size:30 final size:33
Alignment explanation
Indices: 31650--31726 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 33
31640 GATCTTTGAT
31650 TTTATTAAAATAA-AATTATTATTATATTAATTA
1 TTTATTAAAATAAGAATTA-TATTATATTAATTA
*
31683 TTTATTAAAATAAGAA-TA-A-TATATTATTTA
1 TTTATTAAAATAAGAATTATATTATATTAATTA
* *
31713 CTAATTAAAATAAG
1 TTTATTAAAATAAG
31727 GGTACAATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
30 22 0.55
31 1 0.03
33 15 0.38
34 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (33 bp):
TTTATTAAAATAAGAATTATATTATATTAATTA
Found at i:32519 original size:2 final size:2
Alignment explanation
Indices: 32512--32537 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
32502 CATGTCATCA
32512 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
32538 CCACTAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:33727 original size:20 final size:20
Alignment explanation
Indices: 33633--34001 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
33623 GATTTTCCAT
* ** *
33633 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
33653 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
33673 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
33693 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
33713 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
33733 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
33753 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
33773 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
33793 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
33813 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
33833 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
33853 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
33873 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
33893 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
33913 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
33933 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
33953 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
33973 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
33993 AATCACAAC
1 AATCGCAAC
34002 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:34712 original size:24 final size:24
Alignment explanation
Indices: 34673--34719 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
34663 AAATTTGGTC
34673 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
34697 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
34720 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:34911 original size:12 final size:12
Alignment explanation
Indices: 34894--34918 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34884 ATATAATCCT
34894 GAAGAAGAAAAA
1 GAAGAAGAAAAA
34906 GAAGAAGAAAAA
1 GAAGAAGAAAAA
34918 G
1 G
34919 TCCCCGAAGA
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:37241 original size:19 final size:19
Alignment explanation
Indices: 37219--37543 Score: 396
Period size: 19 Copynumber: 18.4 Consensus size: 19
37209 CGGAAAATAC
*
37219 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
37238 AATCCCAA--C---ATG-A
1 AATCGCAATGCGAAATGAA
37251 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
37271 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
37285 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
37304 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
37323 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
37337 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
37356 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
37375 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
37389 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
37408 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
37427 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
37446 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
37465 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
37484 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
37498 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
37517 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
37536 AATCGCAA
1 AATCGCAA
37544 CGAGATAATC
Statistics
Matches: 267, Mismatches: 12, Indels: 54
0.80 0.04 0.16
Matches are distributed among these distances:
13 8 0.03
14 41 0.15
15 4 0.01
16 12 0.04
17 12 0.04
18 4 0.01
19 177 0.66
20 9 0.03
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:37270 original size:33 final size:33
Alignment explanation
Indices: 37219--37524 Score: 266
Period size: 33 Copynumber: 8.8 Consensus size: 33
37209 CGGAAAATAC
* *
37219 AATCGCAACGCGAAATGAAAATCCCAAC-ATGA
1 AATCGCAATGCGAAATGAAAATCGCAACAATGA
*
37251 AATCGCAATGCGGAAATGAAAATCGCAACGA-GA
1 AATCGCAATGC-GAAATGAAAATCGCAACAATGA
37284 GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAATGCGAAATGAAAATCGCAA--C--AATG-A
* * * *
37323 AATCGCAACGAGAGAATCG-CAAT-GCGA-AATGAA
1 AATCGCAATGCGA-AAT-GAAAATCGCAACAATG-A
*
37356 AATCGCAATGCGAAATGAAAATCGCAACGA-GA
1 AATCGCAATGCGAAATGAAAATCGCAACAATGA
*
37388 GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATTAA
1 -AATCGCAATGCGAAATGAAAATCGCAA--C--AA-TGA
*
37427 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C--AATG-A
*
37465 AATCGCAATGCGAAATGAAAATCGCAACGAAAG-
1 AATCGCAATGCGAAATGAAAATCGCAAC-AATGA
37498 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
37525 TGCGAAATGA
Statistics
Matches: 233, Mismatches: 19, Indels: 43
0.79 0.06 0.15
Matches are distributed among these distances:
31 1 0.00
32 17 0.07
33 109 0.47
34 13 0.06
35 5 0.02
36 1 0.00
37 3 0.01
38 75 0.32
39 8 0.03
40 1 0.00
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACAATGA
Found at i:37476 original size:161 final size:157
Alignment explanation
Indices: 37250--37565 Score: 544
Period size: 161 Copynumber: 2.0 Consensus size: 157
37240 TCCCAACATG
*
37250 AAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGC
1 AAATCGCAATGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAATGC
*
37315 GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCG
66 GAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCG
37380 CAACGAGAGAATCGCAATGCGAAATGA
131 CAACGAGAGAATCGCAATGCGAAATGA
*
37407 AAATCGCAATGC-GAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGC
1 AAATCGCAATGCGGAAATGAAAATCGC-A-ACG--A-GAAAATCGCAATGCGAAATGAAAATCGC
37471 AATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
61 AATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
37536 AATCGCAACGAGATAATCGCAATGCGAAAT
126 AATCGCAACGAGAGAATCGCAATGCGAAAT
37566 TATAAACGCA
Statistics
Matches: 150, Mismatches: 4, Indels: 6
0.94 0.03 0.04
Matches are distributed among these distances:
156 13 0.09
157 13 0.09
158 3 0.02
160 1 0.01
161 120 0.80
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (157 bp):
AAATCGCAATGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAATGC
GAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCG
CAACGAGAGAATCGCAATGCGAAATGA
Found at i:37581 original size:52 final size:52
Alignment explanation
Indices: 37250--37565 Score: 542
Period size: 52 Copynumber: 6.0 Consensus size: 52
37240 TCCCAACATG
37250 AAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
1 AAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
37303 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
37355 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
* *
37407 AAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAGAATCGCAATGCGAAATGA
*
37464 AAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
*
37516 AAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
37566 TATAAACGCA
Statistics
Matches: 251, Mismatches: 7, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
52 184 0.73
53 14 0.06
54 3 0.01
55 3 0.01
56 2 0.01
57 45 0.18
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
Found at i:37681 original size:19 final size:19
Alignment explanation
Indices: 37572--37673 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
37562 AAATTATAAA
37572 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
37591 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
37611 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
37627 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
37644 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
37663 CGCATTGCGAT
1 CGCATTGCGAT
37674 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:37799 original size:14 final size:14
Alignment explanation
Indices: 37780--37816 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
37770 CATCAATTAC
37780 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
37794 ACAAATCATCTTTT
1 ACAAATCAACTTTT
37808 ACAAATCAA
1 ACAAATCAA
37817 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:37828 original size:12 final size:12
Alignment explanation
Indices: 37811--37883 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
37801 ATCTTTTACA
37811 AATCAATTAAAC
1 AATCAATTAAAC
*
37823 AATCAA--AAATTG
1 AATCAATTAAA--C
**
37835 AATCAACTTTTAC
1 AATCAA-TTAAAC
37848 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
37861 AATCAA-AAAAC
1 AATCAATTAAAC
37872 AATCAATTAAAC
1 AATCAATTAAAC
37884 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:37845 original size:38 final size:38
Alignment explanation
Indices: 37797--37869 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
37787 AACTTTTACA
*
37797 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
37835 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
37870 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:39755 original size:14 final size:14
Alignment explanation
Indices: 39736--39791 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
39726 GCGAAATGAA
*
39736 AATCGCAACGACAG
1 AATCGCAACGAAAG
39750 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
39767 AAATCGCAACGAAAG
1 -AATCGCAACGAAAG
39782 AATCGCAACG
1 AATCGCAACG
39792 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 18 0.49
15 1 0.03
16 9 0.24
17 1 0.03
18 8 0.22
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:39776 original size:32 final size:33
Alignment explanation
Indices: 39717--39808 Score: 159
Period size: 32 Copynumber: 2.8 Consensus size: 33
39707 GCGAAACCAA
*
39717 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
39750 AATCGCAATGCGAAATG-AAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
39782 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
39809 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:39806 original size:19 final size:19
Alignment explanation
Indices: 39680--39813 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
39670 TAGTTTACTT
* *
39680 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
39700 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
39719 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
39738 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
39752 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
39770 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
39784 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
39803 TCGCAATGCGA
1 TCGCAACGCGA
39814 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 19
0.78 0.06 0.15
Matches are distributed among these distances:
14 16 0.16
15 1 0.01
16 15 0.15
17 6 0.06
18 8 0.08
19 39 0.40
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:39831 original size:19 final size:19
Alignment explanation
Indices: 39809--39937 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
39799 AAAATCGCAA
39809 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
39828 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
39842 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
39861 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
39875 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
39894 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
39913 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
39933 TGCGA
1 TGCGA
39938 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:39851 original size:33 final size:33
Alignment explanation
Indices: 39809--39900 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
39799 AAAATCGCAA
39809 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
39842 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
39875 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
39901 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:40140 original size:93 final size:93
Alignment explanation
Indices: 39981--40359 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
39971 TTGAATGGAT
39981 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
40046 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
40074 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
40139 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
40167 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TA-TTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
40230 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
40258 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
40323 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
40351 AAATTTACT
1 AAATTTACT
40360 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
91 89 0.31
92 4 0.01
93 191 0.67
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:40292 original size:184 final size:186
Alignment explanation
Indices: 39981--40359 Score: 744
Period size: 184 Copynumber: 2.0 Consensus size: 186
39971 TTGAATGGAT
39981 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
40046 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
40111 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
40167 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TA-TTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
40230 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
40295 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
40351 AAATTTACT
1 AAATTTACT
40360 AAGCAATCTA
Statistics
Matches: 193, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
184 152 0.79
185 2 0.01
186 39 0.20
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:42096 original size:33 final size:33
Alignment explanation
Indices: 42051--42164 Score: 185
Period size: 33 Copynumber: 3.5 Consensus size: 33
42041 TCTTTTGGTT
42051 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
42084 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
42117 GAAATGAAAATCGCAACGACAGAATCGTAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
42150 GAAATG-AAATCGCAA
1 GAAATGAAAATCGCAA
42165 TGCGATTTTG
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 9 0.12
33 66 0.88
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:42097 original size:19 final size:18
Alignment explanation
Indices: 42058--42169 Score: 77
Period size: 14 Copynumber: 6.8 Consensus size: 18
42048 GTTGAAATGA
42058 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
42073 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
42090 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
42106 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
42123 AAAATCGCAA--CGACA-G
1 -AAATCGCAACGCGAGATG
* *
42139 -AATCGTAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
42156 AAATCGCAATGCGA
1 AAATCGCAACGCGA
42170 TTTTGGTTTC
Statistics
Matches: 77, Mismatches: 6, Indels: 25
0.71 0.06 0.23
Matches are distributed among these distances:
14 23 0.30
16 15 0.19
17 12 0.16
18 11 0.14
19 16 0.21
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:42200 original size:14 final size:14
Alignment explanation
Indices: 42181--42234 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 14
42171 TTTGGTTTCG
42181 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
42195 CGTTGCGATTTCATTTCG
1 CGTTGCGA-TTC---TCT
42213 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
42227 CGTTGCGA
1 CGTTGCGA
42235 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 18 0.53
15 3 0.09
17 3 0.09
18 10 0.29
ACGTcount: A:0.09, C:0.26, G:0.24, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:42218 original size:18 final size:17
Alignment explanation
Indices: 42176--42222 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 17
42166 GCGATTTTGG
42176 TTTCGCGTTGCGA-TTC
1 TTTCGCGTTGCGATTTC
*
42192 --TCTCGTTGCGATTTC
1 TTTCGCGTTGCGATTTC
42207 ATTTCGCGTTGCGATT
1 -TTTCGCGTTGCGATT
42223 CTCTCGTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 10 0.40
15 3 0.12
18 12 0.48
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.45
Consensus pattern (17 bp):
TTTCGCGTTGCGATTTC
Found at i:42396 original size:33 final size:33
Alignment explanation
Indices: 42354--42424 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
42344 AATACTAACT
*
42354 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
42387 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
42420 TGAAA
1 TGAAA
42425 TCTAAGTGAA
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:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:42658 original size:22 final size:22
Alignment explanation
Indices: 42606--42660 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
42596 TGGTTGTGAG
**
42606 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
42628 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
42650 GGATTTCTTCG
1 GGATTTCTTCG
42661 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:42832 original size:20 final size:20
Alignment explanation
Indices: 42807--43000 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
42797 CTTTAAATAT
42807 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
42827 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
42849 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
42868 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
42888 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
42908 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
42928 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
42948 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
42968 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
42988 CGCGTTGCGATTT
1 CGCGTTGCGATTT
43001 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:42994 original size:60 final size:60
Alignment explanation
Indices: 42807--43000 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
42797 CTTTAAATAT
**
42807 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
42868 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
42928 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
42988 CGCGTTGCGATTT
1 CGCGTTGCGATTT
43001 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:43017 original size:21 final size:20
Alignment explanation
Indices: 42993--43069 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
42983 ATATTCGCGT
42993 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
43014 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
43034 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
43056 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
43070 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:43080 original size:20 final size:20
Alignment explanation
Indices: 43055--43106 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
43045 AAGAATCGCG
*
43055 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
43075 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
43095 TTGCGATTCTGG
1 TTGCGATTCTGG
43107 GGATCGCGTT
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:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:50146 original size:2 final size:2
Alignment explanation
Indices: 50139--50174 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
50129 TGAATGTCCA
50139 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50175 GGTAATTACA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50587 original size:3 final size:3
Alignment explanation
Indices: 50581--50640 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
50571 ACCCATTTTT
50581 TTA TTA TTGA -TA TTA TTA TTA TTA TT- TTA TTTA TTA TTA TTA TTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
**
50626 TTA AAA TTA TTA TTA
1 TTA TTA TTA TTA TTA
50641 CAAACATGCC
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 3 0.06
3 42 0.86
4 4 0.08
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:52400 original size:128 final size:127
Alignment explanation
Indices: 52173--52402 Score: 275
Period size: 128 Copynumber: 1.8 Consensus size: 127
52163 TATATTTATC
* * * *
52173 AATATTAAGAAAGGACAGTCTTAAAGCAACTGGATGTCCATTTTATGATATTTTTAAATAAAATA
1 AATATTAAGAAAGGACAGTCTTAAAGCAACTAGAAGCCCATTTTATGATATTTCTAAATAAAATA
* * * **
52238 AATAAATATTTTAATATATAAATCTGTTTTTATATTATTTTCTATTAAAATTTATTTTTTTT
66 AATAAATATTTTAATAAATAAATATATTAATATATTATTTTCTATTAAAATTTATTTTTTTT
* * * *
52300 AATATTAAGAAAGGAGCTGTCTTAAAGCACCTAGAAGCCCTTTTTCTGATATTTCTAAAT-AAAT
1 AATATTAAGAAAGGA-CAGTCTTAAAGCAACTAGAAGCCCATTTTATGATATTTCTAAATAAAAT
** *
52364 AAATATCT-TGTTTAATAAAATATATATATTAATATATTA
65 AAATAAATAT-TTTAAT-AAATAAATATATTAATATATTA
52403 CCTTAAAATT
Statistics
Matches: 84, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
126 1 0.01
127 31 0.37
128 52 0.62
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (127 bp):
AATATTAAGAAAGGACAGTCTTAAAGCAACTAGAAGCCCATTTTATGATATTTCTAAATAAAATA
AATAAATATTTTAATAAATAAATATATTAATATATTATTTTCTATTAAAATTTATTTTTTTT
Found at i:52839 original size:31 final size:31
Alignment explanation
Indices: 52800--52866 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
52790 ACATACATCA
* * **
52800 GGGG-CCATATTATAAACGGACTAAATGTTG
1 GGGGACCATAGTACAAACGGACTAAATACTG
*
52830 GGGGACCATAGTACAAATGGACTAAATACTG
1 GGGGACCATAGTACAAACGGACTAAATACTG
52861 GGGGAC
1 GGGGAC
52867 TGTATTGTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.34, C:0.15, G:0.30, T:0.21
Consensus pattern (31 bp):
GGGGACCATAGTACAAACGGACTAAATACTG
Found at i:53229 original size:36 final size:36
Alignment explanation
Indices: 53182--53321 Score: 226
Period size: 36 Copynumber: 3.9 Consensus size: 36
53172 TTAGTTGAGT
* ** * *
53182 ATATCAACTTTGACACATTCATTTATCAATGTTATC
1 ATATCAGCTTTGGTACATTCGTGTATCAATGTTATC
53218 ATATCAGCTTTGGTACATTCGTGTATCAATGTTATC
1 ATATCAGCTTTGGTACATTCGTGTATCAATGTTATC
*
53254 ATATCAGCTTTGGTACATTCGTGTACCAATGTTATC
1 ATATCAGCTTTGGTACATTCGTGTATCAATGTTATC
53290 ATATCAGCTTTGGTACATTCGTGTATCAATGT
1 ATATCAGCTTTGGTACATTCGTGTATCAATGT
53322 CCAGCACCGT
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 97 1.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (36 bp):
ATATCAGCTTTGGTACATTCGTGTATCAATGTTATC
Found at i:55527 original size:23 final size:22
Alignment explanation
Indices: 55497--55576 Score: 90
Period size: 23 Copynumber: 3.6 Consensus size: 22
55487 GAATGGCCTT
55497 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
55519 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
55541 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* *
55563 ATGCATTGATGCAC
1 GTGCATCGATGCAC
55577 TGTTAGGTGT
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
21 15 0.33
22 15 0.33
23 16 0.35
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:55553 original size:21 final size:20
Alignment explanation
Indices: 55497--55576 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 20
55487 GAATGGCCTT
55497 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTC-A-G
* *
55519 CGTGCATCGGTGCACCTTCATG
1 -GTGCATCGATGCACATTCA-G
*
55541 GTGTATCGATGCACATTCAAG
1 GTGCATCGATGCACATTC-AG
*
55562 GATGCATTGATGCAC
1 G-TGCATCGATGCAC
55577 TGTTAGGTGT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
21 17 0.36
22 14 0.30
23 16 0.34
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (20 bp):
GTGCATCGATGCACATTCAG
Found at i:66854 original size:19 final size:19
Alignment explanation
Indices: 66830--66881 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
66820 TTGGACCCTT
66830 AGTGCATCGGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
66849 AGTGCATCGGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
*
66868 AGTGCATCGATGCA
1 AGTGCATCGGTGCA
66882 TCAAGTGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.21
Consensus pattern (19 bp):
AGTGCATCGGTGCACTAAG
Found at i:67002 original size:65 final size:64
Alignment explanation
Indices: 66869--67031 Score: 172
Period size: 65 Copynumber: 2.5 Consensus size: 64
66859 TGCACTAAGA
* * * * * *
66869 GTGCATCGATGCATCAAGTGTATTCGATGTTTCAAAATAGCTAGAGTGCATCGATGCGTGGCTG
1 GTGCATCGATGCATCAAATGAATTCGATGTTTCAAAATACCTACAGTGCATCGATGCATAGCTG
* *
66933 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCT-CAGTGCATTGATGCATAG-
1 GTGCATCGATGCATCAAATGAATTCGATG-TTTCA-AAATA-CCTACAGTGCATCGATGCATAGC
*
66995 TAT
63 T-G
*
66998 GTGCATCGATGCATGAAATGAATTCGAT-TTTCAA
1 GTGCATCGATGCATCAAATGAATTCGATGTTTCAA
67032 TTTAATTCAT
Statistics
Matches: 85, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
62 1 0.01
63 5 0.06
64 28 0.33
65 46 0.54
66 5 0.06
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGAATTCGATGTTTCAAAATACCTACAGTGCATCGATGCATAGCTG
Found at i:67067 original size:65 final size:63
Alignment explanation
Indices: 66869--67070 Score: 171
Period size: 65 Copynumber: 3.1 Consensus size: 63
66859 TGCACTAAGA
* * * * * *
66869 GTGCATCGATGCATCAAGTGTATTCGA-TGTTTCA-AAATAGCTAGAGTGCATCGATGCGTGGCT
1 GTGCATCGATGCATCAAATGAATTCGAGT-TTTCATAAA-ATCT-CAGTGCATCGATGCATGGTT
66932 G
63 G
* * *
66933 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATTGATGCATAGTAT
1 GTGCATCGATGCATCAAATGAATTCGA-GTTTTCATAAAAT-CTCAGTGCATCGATGCATGGT-T
66998 -
63 G
* **
66998 GTGCATCGATGCATGAAATGAATTCGA-TTTTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGAATTCGAGTTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-T
67061 TG
62 TG
67063 GTGCATCG
1 GTGCATCG
67071 GGGCATCCAT
Statistics
Matches: 114, Mismatches: 14, Indels: 19
0.78 0.10 0.13
Matches are distributed among these distances:
62 3 0.03
63 5 0.04
64 45 0.39
65 54 0.47
66 7 0.06
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGAATTCGAGTTTTCATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:67896 original size:14 final size:15
Alignment explanation
Indices: 67871--67899 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
67861 TTATTTTTGA
67871 TGTTTCTGGATTGTT
1 TGTTTCTGGATTGTT
67886 TGTTT-TGGATTGTT
1 TGTTTCTGGATTGTT
67900 AAATGCTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.07, C:0.03, G:0.28, T:0.62
Consensus pattern (15 bp):
TGTTTCTGGATTGTT
Found at i:68681 original size:65 final size:64
Alignment explanation
Indices: 68559--68748 Score: 210
Period size: 65 Copynumber: 2.9 Consensus size: 64
68549 TATCAAAGTG
* *
68559 ATGCATCGATACACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGCAT
1 ATGCATCGATGCACCAA-CCATGCATCGATGCACTCAGGATATT---TTGAAACATCGAATGCAT
68621 TTC
62 TTC
* *
68624 ATGCATTGATGCA-CATACCATGCATCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATT
1 ATGCATCGATGCACCA-ACCATGCATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCATT
*
68687 TG
63 TC
* * *
68689 ATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCA
1 ATGCATCGATGCACCAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCA
68749 CCGATGCACT
Statistics
Matches: 107, Mismatches: 10, Indels: 17
0.80 0.07 0.13
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 32 0.30
65 67 0.63
66 5 0.05
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (64 bp):
ATGCATCGATGCACCAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATTTC
Found at i:69705 original size:20 final size:20
Alignment explanation
Indices: 69680--69730 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
69670 TTTGATGGTG
69680 CATCGATGCATTAAGGGGTC
1 CATCGATGCATTAAGGGGTC
*
69700 CATCGATGCATTAAGGGGTG
1 CATCGATGCATTAAGGGGTC
*
69720 CATCAATGCAT
1 CATCGATGCAT
69731 GAGAATTTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (20 bp):
CATCGATGCATTAAGGGGTC
Found at i:74016 original size:20 final size:20
Alignment explanation
Indices: 73991--74041 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
73981 TTTGAAGGTG
73991 CATCGATGCATTAAGGGGTA
1 CATCGATGCATTAAGGGGTA
74011 CATCGATGCATTAAGGGGTA
1 CATCGATGCATTAAGGGGTA
74031 CATCGATGCAT
1 CATCGATGCAT
74042 GAGAATTTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.25
Consensus pattern (20 bp):
CATCGATGCATTAAGGGGTA
Found at i:76004 original size:31 final size:31
Alignment explanation
Indices: 75951--76012 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
75941 AAGAGGATAG
*
75951 AAATTGGTGAGGCTTATTAAACAATTTAATT
1 AAATTGGGGAGGCTTATTAAACAATTTAATT
*
75982 AAATTGGGGAGG-TTTTTGAAACAATTTAATT
1 AAATTGGGGAGGCTTATT-AAACAATTTAATT
76013 TTAAATTTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.39
Consensus pattern (31 bp):
AAATTGGGGAGGCTTATTAAACAATTTAATT
Found at i:81273 original size:29 final size:29
Alignment explanation
Indices: 81231--81312 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
81221 AAACTAAATT
* * *
81231 GATGTAATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
81260 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
81289 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
81313 GTTAGGTGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 43 0.90
30 5 0.10
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:82613 original size:15 final size:15
Alignment explanation
Indices: 82590--82619 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
82580 ACGAGGCTGG
82590 AATTACAACAACAAC
1 AATTACAACAACAAC
*
82605 AATTCCAACAACAAC
1 AATTACAACAACAAC
82620 TATGAGAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.13
Consensus pattern (15 bp):
AATTACAACAACAAC
Found at i:86022 original size:29 final size:29
Alignment explanation
Indices: 85987--86068 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
85977 AAACTAAATT
* *
85987 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
86016 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
86045 GATATCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
86069 GTTAGGTGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 43 0.90
30 5 0.10
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:87314 original size:22 final size:21
Alignment explanation
Indices: 87289--87338 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
87279 AATTAAAACT
87289 TTAAATTAATAAA-TTATATCAA
1 TTAAATTAATAAATTTA-ATC-A
*
87311 TTAAATTATTAAATTTAATCA
1 TTAAATTAATAAATTTAATCA
87332 TTAAATT
1 TTAAATT
87339 TTAATGATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 8 0.31
22 15 0.58
23 3 0.12
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (21 bp):
TTAAATTAATAAATTTAATCA
Found at i:89403 original size:35 final size:35
Alignment explanation
Indices: 89355--89422 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
89345 TGAATAAGAA
* *
89355 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGT
1 GAACGGAAAGAAGCATCAGCACTTTCGATTCAAGT
89390 GAACGGAAAGAAGCATCAGCACTTTCGATTCAA
1 GAACGGAAAGAAGCATCAGCACTTTCGATTCAA
89423 TTGTTCATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (35 bp):
GAACGGAAAGAAGCATCAGCACTTTCGATTCAAGT
Found at i:91170 original size:25 final size:24
Alignment explanation
Indices: 91138--91197 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 24
91128 ATTTAAGGGG
91138 ATTT-TATTTTTTAAAATATATAAA
1 ATTTATATTTTTTAAAATAT-TAAA
* *
91162 ATTTATATTTTTTTAAATCTTAAA
1 ATTTATATTTTTTAAAATATTAAA
91186 ATTTAGTATTTT
1 ATTTA-TATTTT
91198 ATTTTCAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 13 0.41
25 19 0.59
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (24 bp):
ATTTATATTTTTTAAAATATTAAA
Found at i:98043 original size:32 final size:32
Alignment explanation
Indices: 97926--98044 Score: 132
Period size: 32 Copynumber: 3.7 Consensus size: 32
97916 ACCCAAACTG
* *
97926 AAAATCAACCGATCTTATATTGACTCGACCC-
1 AAAATCAACCGATCTGATATTGACCCGACCCA
* * * * * *
97957 AAAATCTAAACGATCTGTTGTTAACCCGATCTA
1 AAAATC-AACCGATCTGATATTGACCCGACCCA
*
97990 AAAATCAACTGATCTGATATTGACCCGACCCA
1 AAAATCAACCGATCTGATATTGACCCGACCCA
*
98022 AAAATCAACCGATCCGATATTGA
1 AAAATCAACCGATCTGATATTGA
98045 TCTAAATCGA
Statistics
Matches: 69, Mismatches: 17, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
31 6 0.09
32 57 0.83
33 6 0.09
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (32 bp):
AAAATCAACCGATCTGATATTGACCCGACCCA
Found at i:98205 original size:15 final size:15
Alignment explanation
Indices: 98182--98213 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
98172 TCTAGACTTG
98182 AAATAACCCGACCCA
1 AAATAACCCGACCCA
*
98197 AAATGACCCGACCCA
1 AAATAACCCGACCCA
98212 AA
1 AA
98214 CCCAATCCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.38, G:0.09, T:0.06
Consensus pattern (15 bp):
AAATAACCCGACCCA
Found at i:100983 original size:19 final size:19
Alignment explanation
Indices: 100959--101010 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
100949 ATTTTAAGGG
*
100959 ATGCATCAATGCACTCCTT
1 ATGCATCGATGCACTCCTT
100978 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
*
100997 ATGTATCGATGCAC
1 ATGCATCGATGCAC
101011 GAATTACATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (19 bp):
ATGCATCGATGCACTCCTT
Found at i:108543 original size:21 final size:21
Alignment explanation
Indices: 108517--108588 Score: 126
Period size: 21 Copynumber: 3.4 Consensus size: 21
108507 CCCTCTCCAA
*
108517 CAACTCTTCCATTTGTTGCTG
1 CAACTCTTCCATCTGTTGCTG
108538 CAACTCTTCCATCTGTTGCTG
1 CAACTCTTCCATCTGTTGCTG
*
108559 CAACTCTTCAATCTGTTGCTG
1 CAACTCTTCCATCTGTTGCTG
108580 CAACTCTTC
1 CAACTCTTC
108589 AGCCTCCTTG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.17, C:0.32, G:0.12, T:0.39
Consensus pattern (21 bp):
CAACTCTTCCATCTGTTGCTG
Found at i:111270 original size:20 final size:19
Alignment explanation
Indices: 111243--111280 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
111233 ATGAGTTAAA
111243 GTGATATAAGTTG-GTTTGG
1 GTGATAT-AGTTGAGTTTGG
111262 GTGAGTATAGTTGAGTTTG
1 GTGA-TATAGTTGAGTTTG
111281 ATGTACTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.21, C:0.00, G:0.37, T:0.42
Consensus pattern (19 bp):
GTGATATAGTTGAGTTTGG
Found at i:115842 original size:21 final size:22
Alignment explanation
Indices: 115788--115842 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
115778 ACCCCTAGGG
*
115788 GTATCGATACTCATTCAAAAGAT
1 GTATCGATACACATTC-AAAGAT
*
115811 GTATC-AGTACACATTC-AAGGT
1 GTATCGA-TACACATTCAAAGAT
115832 GTATCGATACA
1 GTATCGATACA
115843 TAGCAAGGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 13 0.46
22 2 0.07
23 13 0.46
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29
Consensus pattern (22 bp):
GTATCGATACACATTCAAAGAT
Done.