Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 41 of 97
Found at i:16826908 original size:26 final size:26
Alignment explanation
Indices: 16826838--16827173 Score: 205
Period size: 26 Copynumber: 14.1 Consensus size: 26
16826828 TTTGTGGTTG
16826838 GTTTTTGATAAGGCATTGCGTGACT-
1 GTTTTTGATAAGGCATTGCGTGACTA
** *
16826863 GACTTTG----GACATTGCGTGACTA
1 GTTTTTGATAAGGCATTGCGTGACTA
* *
16826885 GTTTTTGATAAGTCATTGCGTGACCA
1 GTTTTTGATAAGGCATTGCGTGACTA
*
16826911 GTTTCTGATAAGGCATTGCGTGACTA
1 GTTTTTGATAAGGCATTGCGTGACTA
*
16826937 G---TTGAT-AGGTATTGCGTGACT-
1 GTTTTTGATAAGGCATTGCGTGACTA
** * *
16826958 GACTTTG----GGTATTACGTGACTA
1 GTTTTTGATAAGGCATTGCGTGACTA
*
16826980 GTTTTTGATAAGACATTGCGTGACTA
1 GTTTTTGATAAGGCATTGCGTGACTA
* *
16827006 GTTTCTAATAAGGCATTGCGTGACT-
1 GTTTTTGATAAGGCATTGCGTGACTA
* *
16827031 -TACTTTG-GAA---ATTGCGTGACT-
1 GT-TTTTGATAAGGCATTGCGTGACTA
** *
16827052 GACTTTG-GAA---ATTGCGTGACTA
1 GTTTTTGATAAGGCATTGCGTGACTA
*
16827074 GTTTTTGATAAGGCATTGTGTGACTA
1 GTTTTTGATAAGGCATTGCGTGACTA
* *
16827100 GTTTCTGATAAGGCATTGTGTGACTA
1 GTTTTTGATAAGGCATTGCGTGACTA
*
16827126 G---TTGAT-AGACATTGCGTGACT-
1 GTTTTTGATAAGGCATTGCGTGACTA
* * *
16827147 -TGTTAG-TAAAGCATTGCGTGACTA
1 GTTTTTGATAAGGCATTGCGTGACTA
16827171 GTT
1 GTT
16827174 AGTAAAGAAT
Statistics
Matches: 247, Mismatches: 38, Indels: 52
0.73 0.11 0.15
Matches are distributed among these distances:
21 57 0.23
22 43 0.17
23 25 0.10
24 6 0.02
25 8 0.03
26 108 0.44
ACGTcount: A:0.24, C:0.13, G:0.26, T:0.37
Consensus pattern (26 bp):
GTTTTTGATAAGGCATTGCGTGACTA
Found at i:16827017 original size:95 final size:95
Alignment explanation
Indices: 16826842--16827146 Score: 436
Period size: 95 Copynumber: 3.2 Consensus size: 95
16826832 TGGTTGGTTT
* *
16826842 TTGATAAGGCATTGCGTGACTGACTTTGGACATTGCGTGACTAGTTTTTGATAAGTCATTGCGTG
1 TTGAT-AGGCATTGCGTGACTGACTTTGGAAATTGCGTGACTAGTTTTTGATAAGACATTGCGTG
*
16826907 ACCAGTTTCTGATAAGGCATTGCGTGACTAG
65 ACTAGTTTCTGATAAGGCATTGCGTGACTAG
* ** *
16826938 TTGATAGGTATTGCGTGACTGACTTTGGGTATTACGTGACTAGTTTTTGATAAGACATTGCGTGA
1 TTGATAGGCATTGCGTGACTGACTTTGGAAATTGCGTGACTAGTTTTTGATAAGACATTGCGTGA
* *
16827003 CTAGTTTCTAATAAGGCATTGCGTGACTTAC
66 CTAGTTTCTGATAAGGCATTGCGTGAC-TAG
* * *
16827034 TT--T-GGAAATTGCGTGACTGACTTTGGAAATTGCGTGACTAGTTTTTGATAAGGCATTGTGTG
1 TTGATAGG-CATTGCGTGACTGACTTTGGAAATTGCGTGACTAGTTTTTGATAAGACATTGCGTG
*
16827096 ACTAGTTTCTGATAAGGCATTGTGTGACTAG
65 ACTAGTTTCTGATAAGGCATTGCGTGACTAG
*
16827127 TTGATAGACATTGCGTGACT
1 TTGATAGGCATTGCGTGACT
16827147 TGTTAGTAAA
Statistics
Matches: 185, Mismatches: 19, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
93 6 0.03
94 77 0.42
95 92 0.50
96 10 0.05
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (95 bp):
TTGATAGGCATTGCGTGACTGACTTTGGAAATTGCGTGACTAGTTTTTGATAAGACATTGCGTGA
CTAGTTTCTGATAAGGCATTGCGTGACTAG
Found at i:16827046 original size:21 final size:21
Alignment explanation
Indices: 16827020--16827072 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
16827010 CTAATAAGGC
*
16827020 ATTGCGTGACTTACTTTGGAA
1 ATTGCGTGACTGACTTTGGAA
16827041 ATTGCGTGACTGACTTTGGAA
1 ATTGCGTGACTGACTTTGGAA
16827062 ATTGCGTGACT
1 ATTGCGTGACT
16827073 AGTTTTTGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (21 bp):
ATTGCGTGACTGACTTTGGAA
Found at i:16828775 original size:15 final size:16
Alignment explanation
Indices: 16828754--16828798 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
16828744 GTTATCTTTC
16828754 CTGCAATCACATTACT
1 CTGCAATCACATTACT
*
16828770 -TGCAATCATATTA-T
1 CTGCAATCACATTACT
16828784 CTGCAATCACATTAC
1 CTGCAATCACATTAC
16828799 ATTGTAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 1 0.04
15 24 0.96
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (16 bp):
CTGCAATCACATTACT
Found at i:16830139 original size:2 final size:2
Alignment explanation
Indices: 16830132--16830188 Score: 62
Period size: 2 Copynumber: 29.0 Consensus size: 2
16830122 AATTTATCTA
* * * * *
16830132 AT AT AT AT GT GT AT AT AT AC A- AT AT AT GT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16830173 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
16830189 TTATTTAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (2 bp):
AT
Found at i:16839526 original size:3 final size:3
Alignment explanation
Indices: 16839518--16839542 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
16839508 AAATAGGTGA
16839518 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
16839543 TTGGAAGGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:16843093 original size:21 final size:21
Alignment explanation
Indices: 16843067--16843106 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
16843057 CAGAAATGAA
*
16843067 AAGTATAGATACTTATGTCTT
1 AAGTATAGATACCTATGTCTT
*
16843088 AAGTATCGATACCTATGTC
1 AAGTATAGATACCTATGTC
16843107 ACGTTTTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (21 bp):
AAGTATAGATACCTATGTCTT
Found at i:16856699 original size:13 final size:13
Alignment explanation
Indices: 16856681--16856706 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16856671 TTCCAGAAAA
16856681 TTTATAAAATCAT
1 TTTATAAAATCAT
16856694 TTTATAAAATCAT
1 TTTATAAAATCAT
16856707 AATTTCTCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:16857225 original size:10 final size:10
Alignment explanation
Indices: 16857212--16857246 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
16857202 TTTTCTAGGC
16857212 TCATAATTCA
1 TCATAATTCA
16857222 TCATAATTCA
1 TCATAATTCA
*
16857232 TCATAATTCC
1 TCATAATTCA
16857242 TCATA
1 TCATA
16857247 TAAACATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (10 bp):
TCATAATTCA
Found at i:16858897 original size:58 final size:58
Alignment explanation
Indices: 16858793--16858905 Score: 181
Period size: 58 Copynumber: 1.9 Consensus size: 58
16858783 CATAATCATC
* *
16858793 CAAAATAGTTTGCATGTGATAGATTTGTTTTATGCAATTTAATAAATGCTATGCAAAG
1 CAAAATAGTATGCATGTGATAGATTTATTTTATGCAATTTAATAAATGCTATGCAAAG
* * *
16858851 CAAAGTAGTATGCGTGTGATAGATTTATTTTATGCAATTTAATAAATGTTATGCA
1 CAAAATAGTATGCATGTGATAGATTTATTTTATGCAATTTAATAAATGCTATGCA
16858906 TGCAAAGATT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (58 bp):
CAAAATAGTATGCATGTGATAGATTTATTTTATGCAATTTAATAAATGCTATGCAAAG
Found at i:16864273 original size:20 final size:20
Alignment explanation
Indices: 16864248--16864302 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 20
16864238 TAAATGTATT
*
16864248 TAGAGGTTTTAGAATGTACC
1 TAGAGGTTTTAAAATGTACC
16864268 -ATGAGGTTTTTAAAATGTACC
1 TA-GAGG-TTTTAAAATGTACC
16864289 TAGAGGTTTTAAAA
1 TAGAGGTTTTAAAA
16864303 ATGGTTGCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 1 0.03
20 12 0.39
21 17 0.55
22 1 0.03
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.36
Consensus pattern (20 bp):
TAGAGGTTTTAAAATGTACC
Found at i:16864284 original size:21 final size:21
Alignment explanation
Indices: 16864239--16864305 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
16864229 AATGTTTTCT
**
16864239 AAATGTATTTAGAGG-TTTTA
1 AAATGTACCTAGAGGTTTTTA
*
16864259 GAATGTACC-ATGAGGTTTTTA
1 AAATGTACCTA-GAGGTTTTTA
*
16864280 AAATGTACCTAGAGGTTTTAA
1 AAATGTACCTAGAGGTTTTTA
16864301 AAATG
1 AAATG
16864306 GTTGCCTAGC
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 10 0.26
21 27 0.69
22 1 0.03
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.37
Consensus pattern (21 bp):
AAATGTACCTAGAGGTTTTTA
Found at i:16865005 original size:25 final size:24
Alignment explanation
Indices: 16864959--16865006 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
16864949 ATTTCTCCGC
*
16864959 TTTCTCTTTTTTTGTTAGTTTTGT
1 TTTCTCTTTTTTTGTCAGTTTTGT
16864983 TTTCATCTTTTTTTGTGCA-TTTTG
1 TTTC-TCTTTTTTTGT-CAGTTTTG
16865007 ATGATTTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 16 0.76
26 1 0.05
ACGTcount: A:0.06, C:0.10, G:0.12, T:0.71
Consensus pattern (24 bp):
TTTCTCTTTTTTTGTCAGTTTTGT
Found at i:16870171 original size:17 final size:18
Alignment explanation
Indices: 16870149--16870183 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
16870139 AGTAGTTGAC
16870149 ACAATA-ATTAATATCAA
1 ACAATATATTAATATCAA
*
16870166 ACAATATATTTATATCAA
1 ACAATATATTAATATCAA
16870184 TAGGAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.34
Consensus pattern (18 bp):
ACAATATATTAATATCAA
Found at i:16871252 original size:2 final size:2
Alignment explanation
Indices: 16871209--16871240 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16871199 GTGAATACCT
16871209 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16871241 ACTTGAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16872388 original size:23 final size:23
Alignment explanation
Indices: 16872358--16872404 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
16872348 TGTGGAAGTG
16872358 TCCACTCAAGTGCCACACAGACT
1 TCCACTCAAGTGCCACACAGACT
16872381 TCCACTCAAGTGCCACACAGACT
1 TCCACTCAAGTGCCACACAGACT
16872404 T
1 T
16872405 TCGCATACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.38, G:0.13, T:0.19
Consensus pattern (23 bp):
TCCACTCAAGTGCCACACAGACT
Found at i:16873772 original size:36 final size:36
Alignment explanation
Indices: 16873655--16873786 Score: 129
Period size: 36 Copynumber: 3.6 Consensus size: 36
16873645 ACTAAGGAAT
*
16873655 CTTGCTTTTTAACATGATCAAGCGATAACCCTTACA
1 CTTGCTTTTTAACAGGATCAAGCGATAACCCTTACA
* * * ** **
16873691 ATTAGCTTTCTCATGGGATCAAGCGATAACCCTTATG
1 CTT-GCTTTTTAACAGGATCAAGCGATAACCCTTACA
*** * *
16873728 CGAACTTTTTAACGGGATCAAGCGATAACCCTTGCA
1 CTTGCTTTTTAACAGGATCAAGCGATAACCCTTACA
*
16873764 CTTGCTTTTTAACAGAATCAAGC
1 CTTGCTTTTTAACAGGATCAAGC
16873787 AATATTTAAT
Statistics
Matches: 72, Mismatches: 23, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
36 46 0.64
37 26 0.36
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (36 bp):
CTTGCTTTTTAACAGGATCAAGCGATAACCCTTACA
Found at i:16875347 original size:71 final size:72
Alignment explanation
Indices: 16875260--16875454 Score: 220
Period size: 72 Copynumber: 2.7 Consensus size: 72
16875250 AGCTTCACAG
* **
16875260 AAAGATTTTGATTGATTAACTTAAGGTTTAATCGATTAAAGAAACATTGGAAAGG-ACACTGAGA
1 AAAGATTTTAATTGATTAACAAAAGGTTTAATCGATTAAAGAAACATTGGAAAGGCACACTGAGA
* *
16875324 TAAATAGA
66 CAAACA-A
* * *
16875332 AAAG-TTTTAATTGATTAACAAAAGATTTTAATTGATTGAAAG-AACATTAG-AAGGCACACTGA
1 AAAGATTTTAATTGATTAACAAAAG-GTTTAATCGATT-AAAGAAACATTGGAAAGGCACACTGA
16875394 GACAAACAA
64 GACAAACAA
** *
16875403 AAAGATTTTAACAGATTAACACAAGGTTTAATCGATTAAA-ACAACATTGGAA
1 AAAGATTTTAATTGATTAACAAAAGGTTTAATCGATTAAAGA-AACATTGGAA
16875455 GAGATAATAC
Statistics
Matches: 102, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
70 3 0.03
71 43 0.42
72 52 0.51
73 4 0.04
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (72 bp):
AAAGATTTTAATTGATTAACAAAAGGTTTAATCGATTAAAGAAACATTGGAAAGGCACACTGAGA
CAAACAA
Found at i:16912983 original size:167 final size:167
Alignment explanation
Indices: 16912707--16913040 Score: 564
Period size: 167 Copynumber: 2.0 Consensus size: 167
16912697 GTTCATGCTA
16912707 TGAAATACCCTATACTTTGATATGGTGATAAATAAAGTTGATACAAGAGCCTTGCGAGGTTTCGA
1 TGAAATACCCTATACTTTGATATGGTGATAAATAAAGTTGATACAAGAGCCTTGCGAGGTTTCGA
*
16912772 TCGACATTCGGGGTGAAGAATGTTTGTCGAGGCCTCGCGGCGGTTGTCACTGGCCCGATAGGG-A
66 TCGACATTCGGGGTGAAAAATGTTTGTCGAGGCCTCGCGGCGGTTGTCACTGGCCCGAT-GGGAA
* *
16912836 G-TTCTGGGTCATGACAATTTAGATTGATATCAGAGCAT
130 GTTTC-AGGTCATGACAATTTAGATTGATATCAAAGCAT
16912874 TGAAATACCCTATACTTTGATATGGTGATAAATAAAGTTGATACAAGAGCCTTGCGAGGTTTCGA
1 TGAAATACCCTATACTTTGATATGGTGATAAATAAAGTTGATACAAGAGCCTTGCGAGGTTTCGA
* * *
16912939 TCGATATTCGGGGTGAAAAATGTTTGTCGAGGCCTTGCGGCGGTTGTCACTGGCCCTATGGGAAG
66 TCGACATTCGGGGTGAAAAATGTTTGTCGAGGCCTCGCGGCGGTTGTCACTGGCCCGATGGGAAG
* *
16913004 TTTCAGGTCGTGACAATTTAGATTGGTATCAAAGCAT
131 TTTCAGGTCATGACAATTTAGATTGATATCAAAGCAT
16913041 GGTTTAAAGA
Statistics
Matches: 157, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
166 3 0.02
167 151 0.96
168 3 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.30
Consensus pattern (167 bp):
TGAAATACCCTATACTTTGATATGGTGATAAATAAAGTTGATACAAGAGCCTTGCGAGGTTTCGA
TCGACATTCGGGGTGAAAAATGTTTGTCGAGGCCTCGCGGCGGTTGTCACTGGCCCGATGGGAAG
TTTCAGGTCATGACAATTTAGATTGATATCAAAGCAT
Found at i:16913082 original size:15 final size:15
Alignment explanation
Indices: 16913059--16913099 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
16913049 GATCAAAGAT
16913059 TTTGG-TTTTAAAGC
1 TTTGGATTTTAAAGC
*
16913073 TTTGGATTTTAAAGT
1 TTTGGATTTTAAAGC
*
16913088 TTTTGATTTTAA
1 TTTGGATTTTAA
16913100 GGTTGTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 5 0.21
15 19 0.79
ACGTcount: A:0.24, C:0.02, G:0.17, T:0.56
Consensus pattern (15 bp):
TTTGGATTTTAAAGC
Found at i:16919381 original size:19 final size:19
Alignment explanation
Indices: 16919338--16919381 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
16919328 AAAATTTTAA
** *
16919338 AATAAAATAATATTTTATT
1 AATAAAATAATATTAAAAT
16919357 AATAAAATAATATTAAAAT
1 AATAAAATAATATTAAAAT
*
16919376 ATTAAA
1 AATAAA
16919382 TATTTTATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATAAAATAATATTAAAAT
Found at i:16919816 original size:15 final size:15
Alignment explanation
Indices: 16919796--16919824 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16919786 AAAAATTCAT
16919796 TATTACATGCAAAAC
1 TATTACATGCAAAAC
16919811 TATTACATGCAAAA
1 TATTACATGCAAAA
16919825 AAGGAGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.28
Consensus pattern (15 bp):
TATTACATGCAAAAC
Found at i:16920096 original size:17 final size:17
Alignment explanation
Indices: 16920072--16920119 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
16920062 TATTTAATTT
16920072 TTAG-TTATTTTTATAA
1 TTAGTTTATTTTTATAA
*
16920088 TTAGTTTATTTTT-TAG
1 TTAGTTTATTTTTATAA
* *
16920104 TTAATTTAATTTTATA
1 TTAGTTTATTTTTATA
16920120 TTTTTTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 17 0.63
17 10 0.37
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TTAGTTTATTTTTATAA
Found at i:16920127 original size:20 final size:19
Alignment explanation
Indices: 16920104--16920141 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
16920094 TATTTTTTAG
16920104 TTAATTTAATTTTATATTTT
1 TTAATTTAATTTT-TATTTT
16920124 TTAATTTAATTTTTATTT
1 TTAATTTAATTTTTATTT
16920142 ATTAGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTAATTTAATTTTTATTTT
Found at i:16926741 original size:17 final size:19
Alignment explanation
Indices: 16926700--16926741 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
16926690 ATATATATAT
16926700 ATGAATATATGTTGTGCACTG
1 ATGAATATATGTTGTG--CTG
16926721 ATGAATA-ATGTTGTG-TG
1 ATGAATATATGTTGTGCTG
16926738 ATGA
1 ATGA
16926742 TGTTGAAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.29
20 8 0.38
21 7 0.33
ACGTcount: A:0.31, C:0.05, G:0.26, T:0.38
Consensus pattern (19 bp):
ATGAATATATGTTGTGCTG
Found at i:16926779 original size:2 final size:2
Alignment explanation
Indices: 16926772--16926823 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
16926762 GAGTGAACNG
16926772 AT AT AT 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 AT AT AT
* *
16926814 GT AA AT AT AT
1 AT AT AT AT AT
16926824 GTTGTGCATT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16926892 original size:37 final size:37
Alignment explanation
Indices: 16926850--16926968 Score: 204
Period size: 37 Copynumber: 3.2 Consensus size: 37
16926840 TAATGTTGTG
*
16926850 TGATGATGTTGAAGTGTGCTAGTAGGGAGTGCACACA
1 TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
*
16926887 TGATGATGTT-AGAGTGTTCGAGTAGGGAGTGCACACA
1 TGATGATGTTGA-AGTGTGCGAGTAGGGAGTGCACACA
16926924 TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
1 TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
16926961 TGATGATG
1 TGATGATG
16926969 ATATTGCATT
Statistics
Matches: 77, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
36 1 0.01
37 75 0.97
38 1 0.01
ACGTcount: A:0.27, C:0.10, G:0.36, T:0.27
Consensus pattern (37 bp):
TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
Found at i:16931521 original size:15 final size:15
Alignment explanation
Indices: 16931483--16931523 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
16931473 AACCTCATGC
16931483 AAAAGGTTTTACATTA
1 AAAAGGTTTTACA-TA
16931499 AAAA-GTTTTACA-A
1 AAAAGGTTTTACATA
16931512 AAAAGGGTTTTA
1 AAAA-GGTTTTA
16931524 GTATGCTACC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 5 0.22
15 14 0.61
16 4 0.17
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.34
Consensus pattern (15 bp):
AAAAGGTTTTACATA
Found at i:16936796 original size:19 final size:20
Alignment explanation
Indices: 16936768--16936813 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
16936758 TATTGTAAGA
*
16936768 TATGTCTTGCATG-TTTATT
1 TATGTTTTGCATGTTTTATT
16936787 TATGTTTTGCATGTTTTATT
1 TATGTTTTGCATGTTTTATT
16936807 TATGTTT
1 TATGTTT
16936814 CAAAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.15, C:0.07, G:0.15, T:0.63
Consensus pattern (20 bp):
TATGTTTTGCATGTTTTATT
Found at i:16942004 original size:27 final size:28
Alignment explanation
Indices: 16941974--16942027 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
16941964 ATGTCCTGGT
*
16941974 GGTGG-AAAATTACAATTTTGCCCCTAG
1 GGTGGCAAAATTACAATTTTACCCCTAG
*
16942001 GGTGGCAAAATTACCATTTTACCCCTA
1 GGTGGCAAAATTACAATTTTACCCCTA
16942028 TACTCCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (28 bp):
GGTGGCAAAATTACAATTTTACCCCTAG
Found at i:16956550 original size:26 final size:27
Alignment explanation
Indices: 16956521--16956571 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
16956511 TGGGACAAAA
*
16956521 AATG-GGGTAGGGGATTTGGATTCGGG
1 AATGAGGGTAGGGGATTTGAATTCGGG
16956547 AATGAGGGTAGGGGATTTGAATTCG
1 AATGAGGGTAGGGGATTTGAATTCG
16956572 ACTCAAGGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.24, C:0.04, G:0.45, T:0.27
Consensus pattern (27 bp):
AATGAGGGTAGGGGATTTGAATTCGGG
Found at i:16965156 original size:35 final size:36
Alignment explanation
Indices: 16965108--16965196 Score: 94
Period size: 35 Copynumber: 2.5 Consensus size: 36
16965098 ACTCCAGTCG
* *
16965108 ATGATATGATTCTCCT-CTCGTTGCTTCGACACGTGC
1 ATGATCTGATTCTCCTCCT-GCTGCTTCGACACGTGC
* *
16965144 ATGATCTG-TTCT-CTGCCTGCTGCTTCGGCATGTGC
1 ATGATCTGATTCTCCT-CCTGCTGCTTCGACACGTGC
*
16965179 ATGATCTGTTTCTCCTCC
1 ATGATCTGATTCTCCTCC
16965197 AACAGCTTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
34 2 0.04
35 26 0.58
36 15 0.33
37 2 0.04
ACGTcount: A:0.12, C:0.29, G:0.20, T:0.38
Consensus pattern (36 bp):
ATGATCTGATTCTCCTCCTGCTGCTTCGACACGTGC
Found at i:16966998 original size:19 final size:19
Alignment explanation
Indices: 16966971--16967014 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
16966961 GTCCTTGAGT
*
16966971 AAAAGAAAAGAACATAAAG
1 AAAAGAAAAAAACATAAAG
* * *
16966990 AAAATAAAAAAACTTAATG
1 AAAAGAAAAAAACATAAAG
16967009 AAAAGA
1 AAAAGA
16967015 CTTTTCAAGA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.73, C:0.05, G:0.11, T:0.11
Consensus pattern (19 bp):
AAAAGAAAAAAACATAAAG
Found at i:16968400 original size:27 final size:27
Alignment explanation
Indices: 16968344--16968405 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
16968334 GTTTTACTGC
* *
16968344 AAAAATAAAATAAATAAAGATTAAAGT
1 AAAAATAAAATAAATAAAGATCAAAAT
16968371 AAAAATATAAATAAATAAA-A-CAAATAT
1 AAAAATA-AAATAAATAAAGATCAAA-AT
16968398 AAAAATAA
1 AAAAATAA
16968406 TTGAAATGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 4 0.13
27 16 0.52
28 11 0.35
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.21
Consensus pattern (27 bp):
AAAAATAAAATAAATAAAGATCAAAAT
Found at i:16977408 original size:12 final size:12
Alignment explanation
Indices: 16977361--16977409 Score: 57
Period size: 11 Copynumber: 4.2 Consensus size: 12
16977351 AGTGCAATGC
16977361 TCTTTTTCTT-T
1 TCTTTTTCTTCT
* *
16977372 TCCTTTGCTTC-
1 TCTTTTTCTTCT
16977383 TCTTTTGTCTTCT
1 TCTTTT-TCTTCT
16977396 TCTTTTTCTTCT
1 TCTTTTTCTTCT
16977408 TC
1 TC
16977410 CTTGAGCTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
11 13 0.42
12 12 0.39
13 6 0.19
ACGTcount: A:0.00, C:0.27, G:0.04, T:0.69
Consensus pattern (12 bp):
TCTTTTTCTTCT
Found at i:16983993 original size:35 final size:36
Alignment explanation
Indices: 16983951--16984021 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
16983941 TAGAGCTTAT
* * *
16983951 GCTTGATCTTG-TAAAAGGCATGTTGTGAAGGTTAC
1 GCTTGATCCTGTTAAAAGGCATGTTGTAAAAGTTAC
16983986 GCTTGATCCTGTTAAAAGGCATGTTGTAAAAGTTAC
1 GCTTGATCCTGTTAAAAGGCATGTTGTAAAAGTTAC
16984022 ATCCGATCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 10 0.31
36 22 0.69
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (36 bp):
GCTTGATCCTGTTAAAAGGCATGTTGTAAAAGTTAC
Found at i:16985511 original size:34 final size:33
Alignment explanation
Indices: 16985463--16985569 Score: 128
Period size: 32 Copynumber: 3.2 Consensus size: 33
16985453 TGAAAGTACT
* *
16985463 TTTTCAAAGCTCAAGTATAACCT-TCACAATGCC
1 TTTTCAAAGATCAAGTACAACCTCT-ACAATGCC
*
16985496 TTTTCAAATGATCAAGTAGAACCTCTACAATGCC
1 TTTTCAAA-GATCAAGTACAACCTCTACAATGCC
* * *
16985530 -TTTCAAGGAGCAAGCACAACCTCTACAATGCC
1 TTTTCAAAGATCAAGTACAACCTCTACAATGCC
16985562 TTTTCAAA
1 TTTTCAAA
16985570 CAACAAACAC
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 22 0.34
33 20 0.31
34 21 0.33
35 1 0.02
ACGTcount: A:0.35, C:0.26, G:0.11, T:0.28
Consensus pattern (33 bp):
TTTTCAAAGATCAAGTACAACCTCTACAATGCC
Found at i:16985581 original size:33 final size:33
Alignment explanation
Indices: 16985488--16985584 Score: 115
Period size: 33 Copynumber: 2.9 Consensus size: 33
16985478 TATAACCTTC
* * *
16985488 ACAATGCCTTTTCAAATGATCAAGTAGAACCTCT
1 ACAATGCCTTTTCAAA-GAACAAGCACAACCTCT
* *
16985522 ACAATGCC-TTTCAAGGAGCAAGCACAACCTCT
1 ACAATGCCTTTTCAAAGAACAAGCACAACCTCT
* *
16985554 ACAATGCCTTTTCAAACAACAAACACAACCT
1 ACAATGCCTTTTCAAAGAACAAGCACAACCT
16985585 TTATAATCTT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
32 22 0.41
33 24 0.44
34 8 0.15
ACGTcount: A:0.38, C:0.29, G:0.10, T:0.23
Consensus pattern (33 bp):
ACAATGCCTTTTCAAAGAACAAGCACAACCTCT
Found at i:16986691 original size:17 final size:18
Alignment explanation
Indices: 16986666--16986699 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16986656 TATTTTTGTC
16986666 ATTTCAAAATT-ATAATT
1 ATTTCAAAATTAATAATT
*
16986683 ATTTTAAAATTAATAAT
1 ATTTCAAAATTAATAAT
16986700 AAAAAACTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTCAAAATTAATAATT
Found at i:16988845 original size:2 final size:2
Alignment explanation
Indices: 16988829--16988957 Score: 98
Period size: 2 Copynumber: 68.0 Consensus size: 2
16988819 TAGGGTTATG
16988829 AT AT AT AGT AT -T AT AT A- AT AT AT AGT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
** ** ** *
16988871 AT AT AT -T AT -T AT AT -T AT NN NN NG GT -T AT GAT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
16988910 AT AT AT AT -T AT AT AT A- AT AT AT A- 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 AT AT AT
16988949 A- AT AT AT AT
1 AT AT AT AT AT
16988958 TCAAAAACGT
Statistics
Matches: 109, Mismatches: 5, Indels: 26
0.78 0.04 0.19
Matches are distributed among these distances:
1 10 0.09
2 93 0.85
3 6 0.06
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:16988845 original size:10 final size:9
Alignment explanation
Indices: 16988830--16988957 Score: 72
Period size: 9 Copynumber: 13.8 Consensus size: 9
16988820 AGGGTTATGA
16988830 TATATAGTAT
1 TATATA-TAT
16988840 TATATA-A-
1 TATATATAT
16988847 TATATAGTAT
1 TATATA-TAT
16988857 ATATATATAT
1 -TATATATAT
16988867 ATATATATAT
1 -TATATATAT
16988877 TAT-TATAT
1 TATATATAT
*
16988885 TATNNNNNGGT-TAT
1 TAT------ATATAT
*
16988899 GATATATAT
1 TATATATAT
16988908 ATATATATAT
1 -TATATATAT
16988918 TATATATA-
1 TATATATAT
*
16988926 -ATATATAA
1 TATATATAT
16988934 TATATATA-
1 TATATATAT
*
16988942 TATATATAA
1 TATATATAT
16988951 TATATAT
1 TATATAT
16988958 TCAAAAACGT
Statistics
Matches: 99, Mismatches: 3, Indels: 33
0.73 0.02 0.24
Matches are distributed among these distances:
7 13 0.13
8 18 0.18
9 29 0.29
10 27 0.27
11 6 0.06
14 5 0.05
15 1 0.01
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.48
Consensus pattern (9 bp):
TATATATAT
Found at i:16988955 original size:71 final size:66
Alignment explanation
Indices: 16988822--16988955 Score: 157
Period size: 71 Copynumber: 2.0 Consensus size: 66
16988812 TTTACCTTAG
* *
16988822 GGTTATGATATATAGTATTATATAATATATAGTATATATATATATATATATATATTATTATATTA
1 GGTTATGATATATAGTATTATATAATATATAATATATATATATATATATATATATTAATATATTA
16988887 T
66 T
16988888 NNNNNGGTTATGATATATA-TATATATATATTATATATAATATATA-ATATATATATATATA-TA
1 -----GGTTATGATATATAGTAT-TATATA--ATATATAATATATATATATATATATATATATTA
16988950 ATATAT
58 ATATAT
16988956 ATTCAAAAAC
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
70 3 0.05
71 27 0.47
72 15 0.26
73 13 0.22
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.47
Consensus pattern (66 bp):
GGTTATGATATATAGTATTATATAATATATAATATATATATATATATATATATATTAATATATTA
T
Found at i:17006560 original size:74 final size:71
Alignment explanation
Indices: 17006482--17006618 Score: 177
Period size: 71 Copynumber: 1.9 Consensus size: 71
17006472 ATTACATGAG
* * * * *
17006482 GCTCTAACTGATTA-AAAGTTCTCTGTCTTTAGACTTCTCTTCTTCAACAGACTTCCTCTAATTG
1 GCTCTAACTGATTACAAACTT-TCTGT-TTT-CACTTCTCTACAT-AACAGACTACCTCTAATTG
17006546 GTTATGGCAA
62 GTTATGGCAA
*
17006556 GCTCTAACTGATTACAAACTTTCTGTTTTCACTTCTCTACATAACAGTCTACCTCTAATTGGT
1 GCTCTAACTGATTACAAACTTTCTGTTTTCACTTCTCTACATAACAGACTACCTCTAATTGGT
17006619 CAACATTTCC
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
71 19 0.34
72 10 0.18
73 3 0.05
74 19 0.34
75 5 0.09
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (71 bp):
GCTCTAACTGATTACAAACTTTCTGTTTTCACTTCTCTACATAACAGACTACCTCTAATTGGTTA
TGGCAA
Found at i:17014103 original size:18 final size:18
Alignment explanation
Indices: 17014080--17014114 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17014070 AAAAGAAGTT
*
17014080 GAAATTGTTGTTGAAAAA
1 GAAATTGTGGTTGAAAAA
17014098 GAAATTGTGGTTGAAAA
1 GAAATTGTGGTTGAAAA
17014115 TTCTGGTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.26, T:0.31
Consensus pattern (18 bp):
GAAATTGTGGTTGAAAAA
Found at i:17017982 original size:43 final size:43
Alignment explanation
Indices: 17017919--17018030 Score: 179
Period size: 43 Copynumber: 2.6 Consensus size: 43
17017909 TATTGACTCG
*
17017919 GCTATGTGCGAGTAGGGAGTGCGCATAAGCCGAGGATGACCCA
1 GCTATGTGCGAGTAGGGAGTGCGCATAACCCGAGGATGACCCA
* *
17017962 GTTATGTGCGAGTAGGGAGTGCGCATAACCCGATGATGACCCA
1 GCTATGTGCGAGTAGGGAGTGCGCATAACCCGAGGATGACCCA
* *
17018005 GCCATCTGCGAGTAGGGAGTGCGCAT
1 GCTATGTGCGAGTAGGGAGTGCGCAT
17018031 GAGCTGGTGA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 63 1.00
ACGTcount: A:0.24, C:0.21, G:0.36, T:0.19
Consensus pattern (43 bp):
GCTATGTGCGAGTAGGGAGTGCGCATAACCCGAGGATGACCCA
Found at i:17018042 original size:43 final size:43
Alignment explanation
Indices: 17017925--17018043 Score: 159
Period size: 43 Copynumber: 2.8 Consensus size: 43
17017915 CTCGGCTATG
** *
17017925 TGCGAGTAGGGAGTGCGCATAAGCCGAG-GATGACCCAGTTATG
1 TGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCAGCCATC
* *
17017968 TGCGAGTAGGGAGTGCGCATAACCCGATGATGACCCAGCCATC
1 TGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCCATC
* *
17018011 TGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 TGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
17018044 TGATGATGGG
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.24, C:0.20, G:0.37, T:0.18
Consensus pattern (43 bp):
TGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCCATC
Found at i:17018088 original size:23 final size:23
Alignment explanation
Indices: 17018040--17018088 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
17018030 TGAGCTGGTG
* *
17018040 ATGATGATGATGGGATGGTGTGT
1 ATGATGATGATGGGATGATGTAT
*
17018063 ATGATGGTGATGGGTAT-ATGTAT
1 ATGATGATGATGGG-ATGATGTAT
17018086 ATG
1 ATG
17018089 TATACATACG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.24, C:0.00, G:0.39, T:0.37
Consensus pattern (23 bp):
ATGATGATGATGGGATGATGTAT
Found at i:17021587 original size:14 final size:14
Alignment explanation
Indices: 17021568--17021611 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
17021558 TTTTTCTAAA
17021568 AATTTTTAATATTT
1 AATTTTTAATATTT
17021582 AATTTTTAA-A---
1 AATTTTTAATATTT
*
17021592 AATTATTAATATTT
1 AATTTTTAATATTT
17021606 AATTTT
1 AATTTT
17021612 GACTACGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
10 8 0.33
11 1 0.04
13 1 0.04
14 14 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
AATTTTTAATATTT
Found at i:17021595 original size:24 final size:25
Alignment explanation
Indices: 17021559--17021611 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 25
17021549 CTTTTTATAT
*
17021559 TTTTCTAAAAATTTTTAATATTTAA
1 TTTTCTAAAAATTATTAATATTTAA
17021584 TTTT-TAAAAATTATTAATATTTAA
1 TTTTCTAAAAATTATTAATATTTAA
17021608 TTTT
1 TTTT
17021612 GACTACGTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTTCTAAAAATTATTAATATTTAA
Found at i:17021769 original size:20 final size:20
Alignment explanation
Indices: 17021744--17021782 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17021734 TCAAAGAATG
17021744 TATTTATTTAATAATTTATT
1 TATTTATTTAATAATTTATT
* *
17021764 TATTTATTTTATAGTTTAT
1 TATTTATTTAATAATTTAT
17021783 AGGTTATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (20 bp):
TATTTATTTAATAATTTATT
Found at i:17026684 original size:22 final size:22
Alignment explanation
Indices: 17026659--17026739 Score: 65
Period size: 22 Copynumber: 3.7 Consensus size: 22
17026649 AGAAAGAAAT
* * *
17026659 GTTTTTAGGCATTGCGTTAGTA
1 GTTTGTAGGCATTGCGTCACTA
* *** * *
17026681 GTTTGTAGGTATTGCAAGATTG
1 GTTTGTAGGCATTGCGTCACTA
17026703 GTATT-TAGGCATTGCGTCACTA
1 GT-TTGTAGGCATTGCGTCACTA
17026725 GTTTGTAGGCATTGC
1 GTTTGTAGGCATTGC
17026740 CAGACTGGTA
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
21 2 0.05
22 40 0.91
23 2 0.05
ACGTcount: A:0.20, C:0.11, G:0.28, T:0.41
Consensus pattern (22 bp):
GTTTGTAGGCATTGCGTCACTA
Found at i:17026712 original size:44 final size:44
Alignment explanation
Indices: 17026662--17026758 Score: 149
Period size: 44 Copynumber: 2.2 Consensus size: 44
17026652 AAGAAATGTT
* * * *
17026662 TTTAGGCATTGCGTTAGTAGTTTGTAGGTATTGCAAGATTGGTA
1 TTTAGGCATTGCGTCACTAGTTTGTAGGCATTGCAAGACTGGTA
*
17026706 TTTAGGCATTGCGTCACTAGTTTGTAGGCATTGCCAGACTGGTA
1 TTTAGGCATTGCGTCACTAGTTTGTAGGCATTGCAAGACTGGTA
17026750 TTTAGGCAT
1 TTTAGGCAT
17026759 CGCATGACTT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (44 bp):
TTTAGGCATTGCGTCACTAGTTTGTAGGCATTGCAAGACTGGTA
Found at i:17026755 original size:22 final size:22
Alignment explanation
Indices: 17026686--17026767 Score: 67
Period size: 22 Copynumber: 3.7 Consensus size: 22
17026676 TAGTAGTTTG
* *
17026686 TAGGTATTGCAAGATTGGTATT
1 TAGGCATTGCAAGACTGGTATT
*** *
17026708 TAGGCATTGCGTCACTAGT-TT
1 TAGGCATTGCAAGACTGGTATT
*
17026729 GTAGGCATTGCCAGACTGGTATT
1 -TAGGCATTGCAAGACTGGTATT
* *
17026752 TAGGCATCGCATGACT
1 TAGGCATTGCAAGACT
17026768 TAAGTATTGC
Statistics
Matches: 45, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
21 2 0.04
22 41 0.91
23 2 0.04
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (22 bp):
TAGGCATTGCAAGACTGGTATT
Found at i:17026812 original size:22 final size:22
Alignment explanation
Indices: 17026787--17026849 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
17026777 CAAGATTGGC
* *
17026787 TTTTAGGTATTGCGTGACTAGT
1 TTTTAGGCATTACGTGACTAGT
* *
17026809 TTTTAGGCATTACGTGATTGGT
1 TTTTAGGCATTACGTGACTAGT
17026831 TTTTAGGCATTACGTGACT
1 TTTTAGGCATTACGTGACT
17026850 GGATTGTAGG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.19, C:0.11, G:0.25, T:0.44
Consensus pattern (22 bp):
TTTTAGGCATTACGTGACTAGT
Found at i:17026836 original size:82 final size:82
Alignment explanation
Indices: 17026689--17026840 Score: 216
Period size: 82 Copynumber: 1.9 Consensus size: 82
17026679 TAGTTTGTAG
*
17026689 GTATTGCAAGATTGGTATTTAGGCATTGCGTCACTAGTTTGTAGGCATTGCCAGACTGGTATTTA
1 GTATTGCAAGATTGGTATTTAGGCATTGCGTCACTAGTTTGTAGGCATTACCAGACTGGTATTTA
17026754 GGCATCGCATGACTTAA
66 GGCATCGCATGACTTAA
* * * ** * *
17026771 GTATTGCAAGATTGGCT-TTTAGGTATTGCGTGACTAGTTTTTAGGCATTACGTGATTGGTTTTT
1 GTATTGCAAGATTGG-TATTTAGGCATTGCGTCACTAGTTTGTAGGCATTACCAGACTGGTATTT
17026835 AGGCAT
65 AGGCAT
17026841 TACGTGACTG
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
82 60 0.98
83 1 0.02
ACGTcount: A:0.22, C:0.13, G:0.26, T:0.38
Consensus pattern (82 bp):
GTATTGCAAGATTGGTATTTAGGCATTGCGTCACTAGTTTGTAGGCATTACCAGACTGGTATTTA
GGCATCGCATGACTTAA
Found at i:17026859 original size:22 final size:22
Alignment explanation
Indices: 17026812--17026859 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
17026802 GACTAGTTTT
* * *
17026812 TAGGCATTACGTGATTGGTTTT
1 TAGGCATTACGTGACTGGATTG
17026834 TAGGCATTACGTGACTGGATTG
1 TAGGCATTACGTGACTGGATTG
17026856 TAGG
1 TAGG
17026860 GATTTGTGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.21, C:0.10, G:0.31, T:0.38
Consensus pattern (22 bp):
TAGGCATTACGTGACTGGATTG
Found at i:17028169 original size:20 final size:18
Alignment explanation
Indices: 17028122--17028175 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 18
17028112 AAAAACTAAT
17028122 AAATAATAACT-AAATTA
1 AAATAATAACTAAAATTA
*
17028139 ACATGAATAACATAAAATTA
1 AAAT-AATAAC-TAAAATTA
17028159 AAATAACTAACTTAAAA
1 AAATAA-TAAC-TAAAA
17028176 GTAACCTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 3 0.10
18 6 0.20
19 3 0.10
20 18 0.60
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (18 bp):
AAATAATAACTAAAATTA
Found at i:17030032 original size:22 final size:22
Alignment explanation
Indices: 17029988--17030068 Score: 81
Period size: 22 Copynumber: 3.7 Consensus size: 22
17029978 ATCAACAACA
* * * *
17029988 GGATTGCGTGAATGATTTTTAG
1 GGATTGCGTGACTAAGTTGTAG
* *
17030010 GCATTGTGTGACTAAGTTGTAG
1 GGATTGCGTGACTAAGTTGTAG
* *
17030032 GGATTGCATGACTAGGTTGTAG
1 GGATTGCGTGACTAAGTTGTAG
*
17030054 GGATTGCGGGACTAA
1 GGATTGCGTGACTAA
17030069 TTTGATGGCG
Statistics
Matches: 46, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.23, C:0.09, G:0.35, T:0.33
Consensus pattern (22 bp):
GGATTGCGTGACTAAGTTGTAG
Found at i:17030088 original size:22 final size:23
Alignment explanation
Indices: 17030063--17030124 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
17030053 GGGATTGCGG
*
17030063 GACTAATTTGAT-GGCGCAAAAT
1 GACTAATTTGATAGGCACAAAAT
* * * *
17030085 GACTAGTTTGTTAGGCACTACAT
1 GACTAATTTGATAGGCACAAAAT
*
17030108 GACTAATTTGTTAGGCA
1 GACTAATTTGATAGGCA
17030125 TTATGTTACA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.30
23 23 0.70
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.32
Consensus pattern (23 bp):
GACTAATTTGATAGGCACAAAAT
Found at i:17032167 original size:19 final size:19
Alignment explanation
Indices: 17032140--17032180 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
17032130 GCTCAAATTA
17032140 TCAACTGGCCGAGGGTTTC
1 TCAACTGGCCGAGGGTTTC
* *
17032159 TCAATTGGCTGAGGGTTTC
1 TCAACTGGCCGAGGGTTTC
17032178 TCA
1 TCA
17032181 CTAAAACCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.22, G:0.29, T:0.32
Consensus pattern (19 bp):
TCAACTGGCCGAGGGTTTC
Found at i:17033322 original size:20 final size:20
Alignment explanation
Indices: 17033283--17033324 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
17033273 GGAAGAAGAA
* *
17033283 GAAGAAGCTACTGTAGAAAT
1 GAAGAAGCTACTGGAAAAAT
17033303 GAAGAAGCTACTGGAAAAAT
1 GAAGAAGCTACTGGAAAAAT
17033323 GA
1 GA
17033325 TATTTATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.48, C:0.10, G:0.26, T:0.17
Consensus pattern (20 bp):
GAAGAAGCTACTGGAAAAAT
Found at i:17039391 original size:71 final size:70
Alignment explanation
Indices: 17039316--17039562 Score: 207
Period size: 71 Copynumber: 3.5 Consensus size: 70
17039306 TGTTGGCCAA
*
17039316 GTATCGATACCTTTCCTTGAGGTCA-CAATACTTTTAACATAAAATGCCTCTT-GGAGCATTCTA
1 GTATCGATACCTTT-CTTGAGGT-ATCAATACTTTTAACATAGAATGCCTCTTCGGA-CATTCTA
17039379 TTAGCTAG
63 TTAGCTAG
* ** * * *
17039387 GTATCAATACCATTTCTAAAGGTATCGATACTTTCAACATAGAGTGCCTCTTCGGACATTCTATT
1 GTATCGATACC-TTTCTTGAGGTATCAATACTTTTAACATAGAATGCCTCTTCGGACATTCTATT
* *
17039452 GGCTAT
65 AGCTAG
* * * * *
17039458 GTATAGATACTTTTCTTGGAGGTATTAATACCTTTT-ACATAGAATGCCTTTTAAGG-CATTCTA
1 GTATCGATACCTTTCTT-GAGGTATCAATA-CTTTTAACATAGAATGCCTCTT-CGGACATTCTA
*
17039521 CTT-GCTAA
63 -TTAGCTAG
* ** *
17039529 GTATTGATACTCTTTCAAGAGGTATCGATACTTT
1 GTATCGATAC-CTTTCTTGAGGTATCAATACTTT
17039563 CATTCATCTT
Statistics
Matches: 141, Mismatches: 27, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
70 10 0.07
71 113 0.80
72 18 0.13
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.38
Consensus pattern (70 bp):
GTATCGATACCTTTCTTGAGGTATCAATACTTTTAACATAGAATGCCTCTTCGGACATTCTATTA
GCTAG
Found at i:17039887 original size:56 final size:54
Alignment explanation
Indices: 17039826--17039949 Score: 140
Period size: 56 Copynumber: 2.2 Consensus size: 54
17039816 ACATTTTTAA
* *
17039826 CTCACTACCTAGGCAATATCAAGGGGATTCAACCTAAAAAATAGTTGAATTTTTG
1 CTCACTACCTAGGCAATATCAAAGGGATTCAACC-AAAAAATAGTAGAATTTTTG
* * ** * *
17039881 CCTCACTACCTAAGCGATATCAAAGTTATTCAACCAAGACATAGTAGAATTTTTG
1 -CTCACTACCTAGGCAATATCAAAGGGATTCAACCAAAAAATAGTAGAATTTTTG
*
17039936 CTCTACTATCTAGG
1 CTC-ACTACCTAGG
17039950 TAACATTAAG
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
54 3 0.05
55 25 0.44
56 29 0.51
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.30
Consensus pattern (54 bp):
CTCACTACCTAGGCAATATCAAAGGGATTCAACCAAAAAATAGTAGAATTTTTG
Found at i:17044064 original size:59 final size:60
Alignment explanation
Indices: 17043989--17044106 Score: 193
Period size: 59 Copynumber: 2.0 Consensus size: 60
17043979 TATAACATAC
*
17043989 AGTTATCACACCCCTAAACTTAAGATTTTGCTAGTCCTCAAGC-AAAACATAAAAGAAAG
1 AGTTACCACACCCCTAAACTTAAGATTTTGCTAGTCCTCAAGCAAAAACATAAAAGAAAG
* **
17044048 AGTTACCACACTCCTAAACTTAAGATTTTGCTAGTCCTTGAGCAAAAACATAAAAGAAA
1 AGTTACCACACCCCTAAACTTAAGATTTTGCTAGTCCTCAAGCAAAAACATAAAAGAAA
17044107 ACTAAACAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
59 39 0.72
60 15 0.28
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (60 bp):
AGTTACCACACCCCTAAACTTAAGATTTTGCTAGTCCTCAAGCAAAAACATAAAAGAAAG
Found at i:17044168 original size:17 final size:18
Alignment explanation
Indices: 17044136--17044170 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
17044126 TGTAAATGAT
*
17044136 GAAAACAATTTAAATAAA
1 GAAAACAATCTAAATAAA
17044154 GAAAACAA-CTAAATAAA
1 GAAAACAATCTAAATAAA
17044171 AAGAGATGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.17
Consensus pattern (18 bp):
GAAAACAATCTAAATAAA
Found at i:17046687 original size:21 final size:22
Alignment explanation
Indices: 17046653--17046694 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
17046643 TACTCTACCA
*
17046653 CAATCATCTCAATTATTAATTT
1 CAATCATCCCAATTATTAATTT
*
17046675 CAATC-TCCCAATTTTTAATT
1 CAATCATCCCAATTATTAATT
17046695 AATTGCAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.45
Consensus pattern (22 bp):
CAATCATCCCAATTATTAATTT
Found at i:17050059 original size:23 final size:23
Alignment explanation
Indices: 17050033--17050089 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
17050023 ATACCAACAT
*
17050033 TTAACCACTTTATAATCTTATTC
1 TTAACCACTTTATAATCTCATTC
17050056 TTAACCACTTTATAATCTCATTC
1 TTAACCACTTTATAATCTCATTC
17050079 TTAACCACTTT
1 TTAACCACTTT
17050090 TTTCATGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.30, C:0.25, G:0.00, T:0.46
Consensus pattern (23 bp):
TTAACCACTTTATAATCTCATTC
Found at i:17053140 original size:9 final size:9
Alignment explanation
Indices: 17053126--17053171 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
17053116 AGTTAGGTGG
17053126 AATTTTTTA
1 AATTTTTTA
17053135 AA--TTTTA
1 AATTTTTTA
17053142 GAATTTTTTA
1 -AATTTTTTA
*
17053152 AATTTTATA
1 AATTTTTTA
*
17053161 ATTTTTTTA
1 AATTTTTTA
17053170 AA
1 AA
17053172 AAATATGACA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
7 5 0.17
8 2 0.07
9 18 0.60
10 5 0.17
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (9 bp):
AATTTTTTA
Found at i:17053145 original size:17 final size:17
Alignment explanation
Indices: 17053125--17053167 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
17053115 TAGTTAGGTG
17053125 GAATTTTTTAAATTTTA
1 GAATTTTTTAAATTTTA
17053142 GAATTTTTTAAATTTTA
1 GAATTTTTTAAATTTTA
*
17053159 TAATTTTTT
1 GAATTTTTT
17053168 TAAAAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (17 bp):
GAATTTTTTAAATTTTA
Found at i:17061373 original size:43 final size:42
Alignment explanation
Indices: 17061293--17061375 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
17061283 CAAAAAACGA
**
17061293 AATTACAAGTCACCATATGAAAAAAGTTAAGGCCACAATGTC
1 AATTACAAGTCACCATATGAAAAAAGTTAAAACCACAATGTC
*
17061335 AATTACAAGTCGCCATATGAAAAAAGTTAAAAACCACAATG
1 AATTACAAGTCACCATATGAAAAAAGTT-AAAACCACAATG
17061376 GGCTGGTGAC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
42 27 0.73
43 10 0.27
ACGTcount: A:0.48, C:0.18, G:0.13, T:0.20
Consensus pattern (42 bp):
AATTACAAGTCACCATATGAAAAAAGTTAAAACCACAATGTC
Found at i:17065959 original size:38 final size:40
Alignment explanation
Indices: 17065832--17065974 Score: 200
Period size: 40 Copynumber: 3.6 Consensus size: 40
17065822 ACCCGGCTCA
*
17065832 TGTGCATCCCCCCACATCGTGCACATAGCCGGCGCCATTG
1 TGTGCATCCCCCCACATCGTGCACATAGCCGGAGCCATTG
*
17065872 TGTGCATCCCCCCACATCGTGCACATAGCCGGAGCCATCG
1 TGTGCATCCCCCCACATCGTGCACATAGCCGGAGCCATTG
* * * * *
17065912 TGTGTATCCCCCCACATCGTGTACA-A-TCAGTGCCATTG
1 TGTGCATCCCCCCACATCGTGCACATAGCCGGAGCCATTG
*
17065950 TGTACATCCCCCCACATCGTGCACA
1 TGTGCATCCCCCCACATCGTGCACA
17065975 CGGGCACTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
38 30 0.33
39 1 0.01
40 61 0.66
ACGTcount: A:0.20, C:0.38, G:0.20, T:0.22
Consensus pattern (40 bp):
TGTGCATCCCCCCACATCGTGCACATAGCCGGAGCCATTG
Found at i:17066099 original size:2 final size:2
Alignment explanation
Indices: 17066092--17066135 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
17066082 CATGCACAAC
17066092 AT AT AT 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 AT AT AT
17066134 AT
1 AT
17066136 CATCATAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17072428 original size:21 final size:20
Alignment explanation
Indices: 17072399--17072457 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
17072389 TTTATGACTA
*
17072399 GATGCTATGTTATGTAGATAT
1 GATGATATGTTATGT-GATAT
* *
17072420 GATGTTATGTGTTATGTGCTAT
1 GATG--ATATGTTATGTGATAT
17072442 GAATGATATGTTATGT
1 G-ATGATATGTTATGT
17072458 TTGATGATGC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
21 14 0.45
22 5 0.16
23 12 0.39
ACGTcount: A:0.25, C:0.03, G:0.25, T:0.46
Consensus pattern (20 bp):
GATGATATGTTATGTGATAT
Found at i:17072451 original size:23 final size:23
Alignment explanation
Indices: 17072406--17072452 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
17072396 CTAGATGCTA
*
17072406 TGTTATGTAGATATGATGTTATG
1 TGTTATGTAGATATGATGATATG
*
17072429 TGTTATGT-GCTATGAATGATATG
1 TGTTATGTAGATATG-ATGATATG
17072452 T
1 T
17072453 TATGTTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.26, C:0.02, G:0.26, T:0.47
Consensus pattern (23 bp):
TGTTATGTAGATATGATGATATG
Found at i:17072746 original size:41 final size:41
Alignment explanation
Indices: 17072701--17072806 Score: 158
Period size: 41 Copynumber: 2.6 Consensus size: 41
17072691 TGTATGTAAC
* *
17072701 GTTTATGTATGTTACGGTGGGTAAAACCCAATTATTTTAAG
1 GTTTATGTATGTTATGATGGGTAAAACCCAATTATTTTAAG
* * * *
17072742 GTTTATGTATGCTATGATGGATAAGACCCAATTGTTTTAAG
1 GTTTATGTATGTTATGATGGGTAAAACCCAATTATTTTAAG
17072783 GTTTATGTATGTTATGATGGGTAA
1 GTTTATGTATGTTATGATGGGTAA
17072807 GGTCAAATCC
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.41
Consensus pattern (41 bp):
GTTTATGTATGTTATGATGGGTAAAACCCAATTATTTTAAG
Found at i:17076137 original size:2 final size:2
Alignment explanation
Indices: 17076132--17076158 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17076122 GTGTGTGTAT
17076132 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
17076159 TGTTAGCTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17077363 original size:34 final size:34
Alignment explanation
Indices: 17077282--17077350 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 34
17077272 AAAGGCATTA
* *
17077282 TAAAGCTTGTGCTTGCTCTTTTGAGAAAATATTG
1 TAAAGGTTGTGCTTGCTCCTTTGAGAAAATATTG
17077316 TAAAGGTTGTGCTTGCTCCTTTGA-AAAAGTATTG
1 TAAAGGTTGTGCTTGCTCCTTTGAGAAAA-TATTG
17077350 T
1 T
17077351 GTGGGTTGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 4 0.12
34 28 0.88
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.41
Consensus pattern (34 bp):
TAAAGGTTGTGCTTGCTCCTTTGAGAAAATATTG
Found at i:17077727 original size:16 final size:16
Alignment explanation
Indices: 17077688--17077727 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
17077678 AAACTTGTGG
17077688 CAACTTGATTTGTATT
1 CAACTTGATTTGTATT
17077704 CAAACTTGATTTGT-TT
1 C-AACTTGATTTGTATT
17077720 ACAACTTG
1 -CAACTTG
17077728 CTTATTCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (16 bp):
CAACTTGATTTGTATT
Found at i:17078011 original size:2 final size:2
Alignment explanation
Indices: 17078004--17078031 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17077994 ACCAACATTT
17078004 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
17078032 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:17079686 original size:71 final size:71
Alignment explanation
Indices: 17079611--17079780 Score: 191
Period size: 71 Copynumber: 2.4 Consensus size: 71
17079601 TTGATTAAAC
* * * * * * *
17079611 CTTGTGTTAAACGATTAGAATCTTTCTGTTTGTCTCAATGAGC-CTTCTAGTGTCATTTTAATCA
1 CTTGTGTTAAACAATTAAAATCTTTCTCTCTGTCTCAATG-GCTCTTCCAATGTCACTTTAATCA
17079675 ATTAATT
65 ATTAATT
* * * *
17079682 CTTGTGTTAATCAATTAAAATCTTTCTCTCTGTCTCAATGTCTCTTCCAATGTTACTTTAATCGA
1 CTTGTGTTAAACAATTAAAATCTTTCTCTCTGTCTCAATGGCTCTTCCAATGTCACTTTAATCAA
*
17079747 TTATTT
66 TTAATT
* *
17079753 CTTGTGTTAATCAATTAAAGTC-TTCTCT
1 CTTGTGTTAAACAATTAAAATCTTTCTCT
17079781 AAAGTTTCGA
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
70 7 0.08
71 78 0.92
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.46
Consensus pattern (71 bp):
CTTGTGTTAAACAATTAAAATCTTTCTCTCTGTCTCAATGGCTCTTCCAATGTCACTTTAATCAA
TTAATT
Found at i:17084455 original size:22 final size:23
Alignment explanation
Indices: 17084411--17084465 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
17084401 ATAAATATTT
*
17084411 CTAATTTTTTTAAAAAAATAAAAA
1 CTAA-TTTTTTAAAAAAACAAAAA
* **
17084435 -TACTTTTTTAAACTAACAAAAA
1 CTAATTTTTTAAAAAAACAAAAA
17084457 CTAATTTTT
1 CTAATTTTT
17084466 AATCTTTGTC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (23 bp):
CTAATTTTTTAAAAAAACAAAAA
Found at i:17085516 original size:27 final size:28
Alignment explanation
Indices: 17085478--17085539 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 28
17085468 AATCTCTAAT
*
17085478 TATAAATTATTAACATTT-TAAATAAAC
1 TATAAATTATTAACATTTAAAAATAAAC
*
17085505 TATAAATTATTAATATTTAAAAAATAAAC
1 TATAAATTATTAACATTT-AAAAATAAAC
17085534 TA-AAAT
1 TATAAAT
17085540 AAACAATCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 17 0.55
28 4 0.13
29 10 0.32
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (28 bp):
TATAAATTATTAACATTTAAAAATAAAC
Found at i:17091491 original size:39 final size:39
Alignment explanation
Indices: 17091441--17091523 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
17091431 CTCTTTTCTC
**
17091441 ATATATCCATAAGCTTATGGCTGCATTAGCCAGGTCTTT
1 ATATATCCATAAGCTTATGGAAGCATTAGCCAGGTCTTT
* *
17091480 ATATATTCATAAGCTTCTGGAAGCATTAGCCAGGTCTTT
1 ATATATCCATAAGCTTATGGAAGCATTAGCCAGGTCTTT
17091519 ATATA
1 ATATA
17091524 CTTTTACGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (39 bp):
ATATATCCATAAGCTTATGGAAGCATTAGCCAGGTCTTT
Found at i:17093458 original size:24 final size:25
Alignment explanation
Indices: 17093401--17093463 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
17093391 GTAATCATTT
17093401 AATATATTTATAT-TATTATATAAA
1 AATATATTTATATATATTATATAAA
*
17093425 AATTATATTTATATATATTATA-ATTA
1 AA-TATATTTATATATATTATATA-AA
17093451 AATA-ATTTATATA
1 AATATATTTATATA
17093464 CAAATCAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
24 11 0.31
25 14 0.40
26 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
AATATATTTATATATATTATATAAA
Found at i:17095446 original size:29 final size:30
Alignment explanation
Indices: 17095389--17095446 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
17095379 ATAAAACAAA
*
17095389 ATTAAAATTTTTTAAAAACTTAAATTAAAT
1 ATTAAAATTTCTTAAAAACTTAAATTAAAT
*
17095419 ATTAAAAGTTTCTTAATAA-TT-AATTAAA
1 ATTAAAA-TTTCTTAAAAACTTAAATTAAA
17095447 CAAAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.28
30 9 0.36
31 9 0.36
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (30 bp):
ATTAAAATTTCTTAAAAACTTAAATTAAAT
Found at i:17096384 original size:22 final size:22
Alignment explanation
Indices: 17096356--17096401 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
17096346 GTTGATAGAT
17096356 TAGCAGCTGTATAAAAGGAAAC
1 TAGCAGCTGTATAAAAGGAAAC
17096378 TAGCAGCTGTATAAAAGGAAAC
1 TAGCAGCTGTATAAAAGGAAAC
17096400 TA
1 TA
17096402 TCTATGATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.13, G:0.22, T:0.20
Consensus pattern (22 bp):
TAGCAGCTGTATAAAAGGAAAC
Found at i:17097287 original size:20 final size:21
Alignment explanation
Indices: 17097252--17097295 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
17097242 CTGCTTCTTT
17097252 TAATATATTCTTATTAATTAA
1 TAATATATTCTTATTAATTAA
17097273 TAATATATT-TTATTAATTAA
1 TAATATATTCTTATTAATTAA
17097293 TAA
1 TAA
17097296 GAAAGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TAATATATTCTTATTAATTAA
Found at i:17097308 original size:6 final size:6
Alignment explanation
Indices: 17097297--17097321 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
17097287 AATTAATAAG
17097297 AAAGAA AAAGAA AAAGAA AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA A
17097322 TGGTTTGGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:17108238 original size:2 final size:2
Alignment explanation
Indices: 17108231--17108256 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17108221 TCTCTTGCTA
17108231 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
17108257 CCTGTGCCCA
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:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:17119842 original size:34 final size:34
Alignment explanation
Indices: 17119804--17119876 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
17119794 AAGTTAGTGT
*
17119804 GGGTTGTGCTTG-CTTCCCTTAAAAGGCATTGTAA
1 GGGTTGTGCTTGACTT-CCGTAAAAGGCATTGTAA
* *
17119838 GGGTTGTGCTTGAGTTCGGTAAAAGGCATTGTAA
1 GGGTTGTGCTTGACTTCCGTAAAAGGCATTGTAA
*
17119872 AGGTT
1 GGGTT
17119877 TTCATTTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 32 0.94
35 2 0.06
ACGTcount: A:0.22, C:0.12, G:0.32, T:0.34
Consensus pattern (34 bp):
GGGTTGTGCTTGACTTCCGTAAAAGGCATTGTAA
Found at i:17122732 original size:2 final size:2
Alignment explanation
Indices: 17122725--17122758 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17122715 TTTAACTTAA
17122725 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
17122759 GTAAATATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17123093 original size:3 final size:3
Alignment explanation
Indices: 17123079--17123137 Score: 82
Period size: 3 Copynumber: 19.3 Consensus size: 3
17123069 AATAAATGCC
* *
17123079 ATG ATT ATG ATG ATG ATG ATG ATG GTG ATG ATG ATG ATG ATG ATG CATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG -ATG
*
17123128 ATT ATG ATG A
1 ATG ATG ATG A
17123138 ATTAAAAGAG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.32, C:0.02, G:0.31, T:0.36
Consensus pattern (3 bp):
ATG
Found at i:17130500 original size:37 final size:37
Alignment explanation
Indices: 17130346--17130490 Score: 231
Period size: 37 Copynumber: 4.0 Consensus size: 37
17130336 CTCAATGCAA
*
17130346 TATCATCATCATGTGTGCACTCCCTACTTGCACACTC
1 TATCATCATCATGTGTGCACTCCCTACTCGCACACTC
*
17130383 TATCATCATCA--TGTGCACTCCTTACTCGCACACTC
1 TATCATCATCATGTGTGCACTCCCTACTCGCACACTC
17130418 TATCATCATCATGTGTGCACTCCCTACTCGCACACTC
1 TATCATCATCATGTGTGCACTCCCTACTCGCACACTC
* * *
17130455 TATCATCATTATGTGTGGACTCCCTACTCTCACACT
1 TATCATCATCATGTGTGCACTCCCTACTCGCACACT
17130491 TCAACATCAT
Statistics
Matches: 100, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
35 33 0.33
37 67 0.67
ACGTcount: A:0.22, C:0.35, G:0.10, T:0.32
Consensus pattern (37 bp):
TATCATCATCATGTGTGCACTCCCTACTCGCACACTC
Found at i:17137422 original size:72 final size:72
Alignment explanation
Indices: 17137303--17137494 Score: 262
Period size: 72 Copynumber: 2.6 Consensus size: 72
17137293 CTCAATGCAA
*
17137303 TATCATCATCATGTGTGCACTCCCTACTTGCACACTTCAACATCATCATGTGTGCACTCCTTACT
1 TATCATCATCA--TGTGCACTCCCTACTTGCACACTTCAACATCATCATGTGTGCACTCCCTACT
17137368 CGCACACTC
64 CGCACACTC
*
17137377 TATCATCATCATGTGCACTCCCTA-TTCGCACAC-TCTATCATCATCATGTGTGCACTCCCTACT
1 TATCATCATCATGTGCACTCCCTACTT-GCACACTTC-AACATCATCATGTGTGCACTCCCTACT
17137440 CGCACACTC
64 CGCACACTC
* ** *
17137449 TATTATCATCATGTGTGGGCTCCCTACTCGCACACTTCAACATCAT
1 TATCATCATCA--TGTGCACTCCCTACTTGCACACTTCAACATCAT
17137495 GACACAACAT
Statistics
Matches: 105, Mismatches: 7, Indels: 12
0.85 0.06 0.10
Matches are distributed among these distances:
71 4 0.04
72 63 0.60
74 35 0.33
75 3 0.03
ACGTcount: A:0.23, C:0.35, G:0.11, T:0.31
Consensus pattern (72 bp):
TATCATCATCATGTGCACTCCCTACTTGCACACTTCAACATCATCATGTGTGCACTCCCTACTCG
CACACTC
Found at i:17137494 original size:37 final size:37
Alignment explanation
Indices: 17137303--17137484 Score: 271
Period size: 37 Copynumber: 5.0 Consensus size: 37
17137293 CTCAATGCAA
*
17137303 TATCATCATCATGTGTGCACTCCCTACTTGCACACT-
1 TATCATCATCATGTGTGCACTCCCTACTCGCACACTC
* *
17137339 TCAACATCATCATGTGTGCACTCCTTACTCGCACACTC
1 T-ATCATCATCATGTGTGCACTCCCTACTCGCACACTC
*
17137377 TATCATCATCA--TGTGCACTCCCTATTCGCACACTC
1 TATCATCATCATGTGTGCACTCCCTACTCGCACACTC
17137412 TATCATCATCATGTGTGCACTCCCTACTCGCACACTC
1 TATCATCATCATGTGTGCACTCCCTACTCGCACACTC
* **
17137449 TATTATCATCATGTGTGGGCTCCCTACTCGCACACT
1 TATCATCATCATGTGTGCACTCCCTACTCGCACACT
17137485 TCAACATCAT
Statistics
Matches: 132, Mismatches: 10, Indels: 7
0.89 0.07 0.05
Matches are distributed among these distances:
35 33 0.25
36 1 0.01
37 97 0.73
38 1 0.01
ACGTcount: A:0.22, C:0.35, G:0.12, T:0.31
Consensus pattern (37 bp):
TATCATCATCATGTGTGCACTCCCTACTCGCACACTC
Found at i:17146891 original size:19 final size:19
Alignment explanation
Indices: 17146867--17146917 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
17146857 AGCTATAAAT
*
17146867 TTCTTCTCCTTCCAGCAGC
1 TTCTTCTACTTCCAGCAGC
* *
17146886 TTCTTCAATTTCCAGCAGC
1 TTCTTCTACTTCCAGCAGC
*
17146905 TTCTTCTTCTTCC
1 TTCTTCTACTTCC
17146918 TCCTTCCATC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.12, C:0.37, G:0.08, T:0.43
Consensus pattern (19 bp):
TTCTTCTACTTCCAGCAGC
Found at i:17147635 original size:42 final size:42
Alignment explanation
Indices: 17147570--17147651 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
17147560 AATGATATTT
* *
17147570 ACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGCCATTGCTG
1 ACCCGGCTATGTGAGAATAGGAGTGCGCATAAGCCATTGCTG
* *
17147612 ACCCGGCTATGTGAGAATGGGAGTGCGCATAAGCCGTTGC
1 ACCCGGCTATGTGAGAATAGGAGTGCGCATAAGCCATTGC
17147652 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.22, C:0.23, G:0.34, T:0.21
Consensus pattern (42 bp):
ACCCGGCTATGTGAGAATAGGAGTGCGCATAAGCCATTGCTG
Found at i:17147943 original size:21 final size:22
Alignment explanation
Indices: 17147897--17147943 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
17147887 GGTGCCCTGC
17147897 TTCTTGCTGCAACGAGAAAGCA
1 TTCTTGCTGCAACGAGAAAGCA
**
17147919 TTCTTGCTGCAGTGAGAAA-CA
1 TTCTTGCTGCAACGAGAAAGCA
17147940 TTCT
1 TTCT
17147944 GTTTTGGCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (22 bp):
TTCTTGCTGCAACGAGAAAGCA
Found at i:17148396 original size:14 final size:14
Alignment explanation
Indices: 17148377--17148409 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
17148367 CATTAATCAA
17148377 GGTTTGAAATGAGG
1 GGTTTGAAATGAGG
17148391 GGTTTGAAATGAGG
1 GGTTTGAAATGAGG
17148405 GGTTT
1 GGTTT
17148410 TTAGTAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.42, T:0.33
Consensus pattern (14 bp):
GGTTTGAAATGAGG
Found at i:17150507 original size:42 final size:42
Alignment explanation
Indices: 17150438--17150601 Score: 202
Period size: 42 Copynumber: 3.9 Consensus size: 42
17150428 CACTCTCCCA
* * * * * *
17150438 CATCATCAGCTCATGTGCATTCCCCACTAGCACATGGTTGGGT
1 CATCATCGGCTTATGTGCACT-CCCACTCGCACATAGCTGGGT
*
17150481 CATCATCGGCTTATGTGCACTCCCACTCGCACATAGCTAGGT
1 CATCATCGGCTTATGTGCACTCCCACTCGCACATAGCTGGGT
* * * *
17150523 CATCATCGACTTATGCGCACTCCTACTCGCACGTAGCTGGGT
1 CATCATCGGCTTATGTGCACTCCCACTCGCACATAGCTGGGT
* *
17150565 CATCATCGGCTTATGTACACTCCTACTCGCACATAGC
1 CATCATCGGCTTATGTGCACTCCCACTCGCACATAGC
17150602 CAAGGCCACA
Statistics
Matches: 105, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 87 0.83
43 18 0.17
ACGTcount: A:0.21, C:0.33, G:0.19, T:0.27
Consensus pattern (42 bp):
CATCATCGGCTTATGTGCACTCCCACTCGCACATAGCTGGGT
Found at i:17163678 original size:38 final size:40
Alignment explanation
Indices: 17163636--17163738 Score: 133
Period size: 38 Copynumber: 2.6 Consensus size: 40
17163626 ATAGTGCCCG
17163636 TGTGCACGATGTGGGGGGATGTACACGAT-G-G-CA-CTGA
1 TGTGCACGATGTGGGGGGATGTACACGATGGTGCCACCT-A
* *
17163673 TTGTGCACGATGTGGGGGGATGCACATGATGGTGCCACCTA
1 -TGTGCACGATGTGGGGGGATGTACACGATGGTGCCACCTA
*
17163714 TATGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
17163739 TGAGCCAGGT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
38 27 0.47
39 1 0.02
40 24 0.42
41 3 0.05
42 2 0.04
ACGTcount: A:0.21, C:0.17, G:0.39, T:0.23
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACACGATGGTGCCACCTA
Found at i:17163731 original size:40 final size:38
Alignment explanation
Indices: 17163638--17163741 Score: 131
Period size: 40 Copynumber: 2.7 Consensus size: 38
17163628 AGTGCCCGTG
* *
17163638 TGCACGATGTGGGGGGATGTACACGATGGCACTGATTG
1 TGCACGATGTGGGGGGATGTACATGATGGCACTGATTA
*
17163676 TGCACGATGTGGGGGGATGCACATGATGGTGCCACCT-A-TA
1 TGCACGATGTGGGGGGATGTACATGAT-G-G-CA-CTGATTA
17163716 TGCACGATGTGGGGGGATGTACATGA
1 TGCACGATGTGGGGGGATGTACATGA
17163742 GCCAGGTGTG
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
38 25 0.43
39 1 0.02
40 27 0.47
41 3 0.05
42 2 0.03
ACGTcount: A:0.22, C:0.16, G:0.38, T:0.23
Consensus pattern (38 bp):
TGCACGATGTGGGGGGATGTACATGATGGCACTGATTA
Found at i:17164145 original size:39 final size:39
Alignment explanation
Indices: 17164102--17164176 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
17164092 CAAAAAACTC
*
17164102 TCTGTTTCATTAGCGA-AATTTCGTTGCAGCGAGAAACCT
1 TCTGTTTC-TGAGCGACAATTTCGTTGCAGCGAGAAACCT
* **
17164141 TCTGTTTCTGGGTTACAATTTCGTTGCAGCGAGAAA
1 TCTGTTTCTGAGCGACAATTTCGTTGCAGCGAGAAA
17164177 GAATCTCGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 3 0.10
39 28 0.90
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.35
Consensus pattern (39 bp):
TCTGTTTCTGAGCGACAATTTCGTTGCAGCGAGAAACCT
Found at i:17166401 original size:33 final size:34
Alignment explanation
Indices: 17166358--17166437 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
17166348 TTTTCAACAG
17166358 CTAAGGCTGCTCATATTGACTTC-C-AAATCAGCAA
1 CTAA-GCTGCTCATATT-ACTTCTCAAAATCAGCAA
* *
17166392 CTAAGCTGCTC-TATTTCTTCTCAAAAATCAGCAG
1 CTAAGCTGCTCATATTACTTCTC-AAAATCAGCAA
17166426 CTAAGCTGCTCA
1 CTAAGCTGCTCA
17166438 ATTTTCTCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
31 4 0.10
32 5 0.12
33 7 0.17
34 24 0.60
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.29
Consensus pattern (34 bp):
CTAAGCTGCTCATATTACTTCTCAAAATCAGCAA
Found at i:17166453 original size:35 final size:34
Alignment explanation
Indices: 17166382--17166461 Score: 117
Period size: 34 Copynumber: 2.3 Consensus size: 34
17166372 ATTGACTTCC
* *
17166382 AAATCAGCAACTAAGCTGCTCTATTTCTTCTCAA
1 AAATCAGCAGCTAAGCTGCTCAATTTCTTCTCAA
17166416 AAATCAGCAGCTAAGCTGCTCAATTT-TCTCTCAAA
1 AAATCAGCAGCTAAGCTGCTCAATTTCT-TCTC-AA
17166451 AAATCAGCAGC
1 AAATCAGCAGC
17166462 CAAAACAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
33 1 0.02
34 28 0.67
35 13 0.31
ACGTcount: A:0.35, C:0.26, G:0.11, T:0.28
Consensus pattern (34 bp):
AAATCAGCAGCTAAGCTGCTCAATTTCTTCTCAA
Found at i:17166587 original size:34 final size:36
Alignment explanation
Indices: 17166502--17166588 Score: 106
Period size: 34 Copynumber: 2.5 Consensus size: 36
17166492 CACCTTACAA
* *
17166502 CCTTCAAAATCAGCTGCAAAAATCTGCACTTCTCAG
1 CCTTCAAAATCAGCAGCAAAAATCTACACTTCTCAG
* * *
17166538 CCTCCAAAACCAGCAGC-AAAA-CTACACTTTTCAG
1 CCTTCAAAATCAGCAGCAAAAATCTACACTTCTCAG
*
17166572 CCTTCAAAATTAGCAGC
1 CCTTCAAAATCAGCAGC
17166589 TAAAGCTGCT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
34 25 0.58
35 4 0.09
36 14 0.33
ACGTcount: A:0.36, C:0.32, G:0.10, T:0.22
Consensus pattern (36 bp):
CCTTCAAAATCAGCAGCAAAAATCTACACTTCTCAG
Found at i:17174711 original size:18 final size:17
Alignment explanation
Indices: 17174688--17174721 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17174678 ACAATGATTA
*
17174688 CTTTTTCTGTTTTTTTAC
1 CTTTTT-TGCTTTTTTAC
17174706 CTTTTTTGCTTTTTTA
1 CTTTTTTGCTTTTTTA
17174722 TGTTGTCAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.74
Consensus pattern (17 bp):
CTTTTTTGCTTTTTTAC
Found at i:17175194 original size:17 final size:17
Alignment explanation
Indices: 17175172--17175224 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
17175162 AAGTAAAATA
17175172 AGCACACATTAAGGGGG
1 AGCACACATTAAGGGGG
* *
17175189 AGCACATACTAAGGGGG
1 AGCACACATTAAGGGGG
*
17175206 AGCACTCACTT-AGGGGG
1 AGCACACA-TTAAGGGGG
17175223 AG
1 AG
17175225 AAATCCTCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 29 0.97
18 1 0.03
ACGTcount: A:0.32, C:0.19, G:0.36, T:0.13
Consensus pattern (17 bp):
AGCACACATTAAGGGGG
Found at i:17177505 original size:15 final size:15
Alignment explanation
Indices: 17177485--17177523 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
17177475 AAAGAAGTAA
*
17177485 GAAAAGAAAAGAAAT
1 GAAAAGAAAAGAAAG
*
17177500 GAAAAG-AAAGGAAG
1 GAAAAGAAAAGAAAG
17177514 GAAAAGAAAA
1 GAAAAGAAAA
17177524 TGGAAAAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.03
Consensus pattern (15 bp):
GAAAAGAAAAGAAAG
Found at i:17195776 original size:2 final size:2
Alignment explanation
Indices: 17195730--17195768 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
17195720 ACATATTTAC
*
17195730 AT AT GT AT AT AT 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 AT AT AT AT AT AT A
17195769 CGTATATACC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17195838 original size:20 final size:20
Alignment explanation
Indices: 17195781--17195843 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
17195771 TATATACCCA
*
17195781 TCATCATCATC-TCACCAAC
1 TCATCATCATCATCACCAGC
*
17195800 CCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
17195820 TCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
17195840 TCAT
1 TCAT
17195844 GCGCACTCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.30, C:0.41, G:0.03, T:0.25
Consensus pattern (20 bp):
TCATCATCATCATCACCAGC
Found at i:17195890 original size:43 final size:43
Alignment explanation
Indices: 17195842--17195960 Score: 168
Period size: 43 Copynumber: 2.8 Consensus size: 43
17195832 TCACCAGCTC
** * *
17195842 ATGCGCACTCCCTACTCGCACATGGCTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATC-CTCGGCTT
17195885 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
* *
17195928 ATGCGCACTCCCTACTCGCACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCA
17195961 ACATAATTAC
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.19, C:0.38, G:0.21, T:0.22
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
Found at i:17199838 original size:19 final size:19
Alignment explanation
Indices: 17199814--17199882 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
17199804 TAGTCGGCAC
*
17199814 CATCGTGTGCATCCCCCCA
1 CATCGTGTACATCCCCCCA
****
17199833 CATCGTGTACAATCAGTGC-
1 CATCGTGTAC-ATCCCCCCA
17199852 CATCGTGTACATCCCCCCA
1 CATCGTGTACATCCCCCCA
*
17199871 CATCGTGCACAT
1 CATCGTGTACAT
17199883 GGACACTATC
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
18 4 0.11
19 30 0.79
20 4 0.11
ACGTcount: A:0.22, C:0.39, G:0.16, T:0.23
Consensus pattern (19 bp):
CATCGTGTACATCCCCCCA
Found at i:17199865 original size:38 final size:40
Alignment explanation
Indices: 17199779--17199882 Score: 140
Period size: 38 Copynumber: 2.6 Consensus size: 40
17199769 ACTCGGCTCA
* *
17199779 TGTACATCCCCCCACATAGTGCACATAGTCGGCACCATCG
1 TGTACATCCCCCCACATCGTGCACATAGTCAGCACCATCG
* * **
17199819 TGTGCATCCCCCCACATCGTGTACA-A-TCAGTGCCATCG
1 TGTACATCCCCCCACATCGTGCACATAGTCAGCACCATCG
17199857 TGTACATCCCCCCACATCGTGCACAT
1 TGTACATCCCCCCACATCGTGCACAT
17199883 GGACACTATC
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
38 32 0.58
39 1 0.02
40 22 0.40
ACGTcount: A:0.23, C:0.38, G:0.16, T:0.22
Consensus pattern (40 bp):
TGTACATCCCCCCACATCGTGCACATAGTCAGCACCATCG
Found at i:17207032 original size:43 final size:43
Alignment explanation
Indices: 17206970--17207090 Score: 172
Period size: 43 Copynumber: 2.8 Consensus size: 43
17206960 GACTCGGCTT
* **
17206970 TGTGCGAGTAGGGAATGCGCATAAGCCGAG-GATGACCCAATTA
1 TGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCAACCA
* *
17207013 TGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGCCA
1 TGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAACCA
*
17207056 TGTGCGAGTAGGGAGTGCGCATAAGCTGGTGATGA
1 TGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
17207091 TGATGATGGG
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 69 0.99
ACGTcount: A:0.26, C:0.19, G:0.36, T:0.19
Consensus pattern (43 bp):
TGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAACCA
Found at i:17215562 original size:15 final size:15
Alignment explanation
Indices: 17215542--17215579 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
17215532 GGAGAAAAAA
17215542 ATGAAAGATTAGCAG
1 ATGAAAGATTAGCAG
*
17215557 ATGAAAGATTAGTAG
1 ATGAAAGATTAGCAG
*
17215572 AAGAAAGA
1 ATGAAAGA
17215580 GATGAAGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.53, C:0.03, G:0.26, T:0.18
Consensus pattern (15 bp):
ATGAAAGATTAGCAG
Found at i:17219016 original size:58 final size:58
Alignment explanation
Indices: 17218837--17219018 Score: 265
Period size: 58 Copynumber: 3.1 Consensus size: 58
17218827 TGGCCAAACT
* * **
17218837 CATTTCATTCACCCATCTTGGGTGGACATATGCCCTTCAATTACACATATGGCCTACC
1 CATTACATTCACCCATCTTGGGTGGACATATGCCCTTCAATCATGCATATGGCCTACC
* * * * *
17218895 CAATACATTCTCCCATATTGGCTGGACATATGCCCTCCAATCATGCATATGGCCTACC
1 CATTACATTCACCCATCTTGGGTGGACATATGCCCTTCAATCATGCATATGGCCTACC
*
17218953 CATTACATTCACCCATCTTGGGTGGACATATGCCCTTCAATCATGCGTATGGCCTACC
1 CATTACATTCACCCATCTTGGGTGGACATATGCCCTTCAATCATGCATATGGCCTACC
*
17219011 TATTACAT
1 CATTACAT
17219019 GTGTCATACA
Statistics
Matches: 108, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
58 108 1.00
ACGTcount: A:0.25, C:0.31, G:0.14, T:0.30
Consensus pattern (58 bp):
CATTACATTCACCCATCTTGGGTGGACATATGCCCTTCAATCATGCATATGGCCTACC
Found at i:17219463 original size:2 final size:2
Alignment explanation
Indices: 17219458--17219482 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17219448 CACATATGTC
17219458 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
17219483 TTCCCTAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17224460 original size:27 final size:27
Alignment explanation
Indices: 17224422--17224488 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
17224412 ACCAAATTAT
*
17224422 ATGTTCAAAAAAATATTGTTACATGCC
1 ATGTTCAAAAAAATATTGTTACACGCC
* * *
17224449 ATGTTTAAAAAAATGTTGTTACACGTC
1 ATGTTCAAAAAAATATTGTTACACGCC
17224476 ATGTTCAAAAAAA
1 ATGTTCAAAAAAA
17224489 AAAATTATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (27 bp):
ATGTTCAAAAAAATATTGTTACACGCC
Found at i:17224636 original size:28 final size:28
Alignment explanation
Indices: 17224570--17224639 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
17224560 AGAGATCAAG
* * * *
17224570 TTACACGCCATGTTGAAAAACAAATTTG
1 TTACACACCATGTTGAAAAAAAAAGTTA
**
17224598 TTACATGCCATGTTGAAAAAAAAAGTTA
1 TTACACACCATGTTGAAAAAAAAAGTTA
*
17224626 TTATACACCATGTT
1 TTACACACCATGTT
17224640 TAAGGTGTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (28 bp):
TTACACACCATGTTGAAAAAAAAAGTTA
Done.