Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 61 of 208
Found at i:17543428 original size:19 final size:19
Alignment explanation
Indices: 17543406--17543451 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
17543396 TTTGCTATAA
17543406 AATAAAGAGAAATGGAGAG
1 AATAAAGAGAAATGGAGAG
17543425 AATAAAGAGAAATGGAGAG
1 AATAAAGAGAAATGGAGAG
17543444 AATAAAGA
1 AATAAAGA
17543452 ACAAAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.61, C:0.00, G:0.28, T:0.11
Consensus pattern (19 bp):
AATAAAGAGAAATGGAGAG
Found at i:17554556 original size:20 final size:21
Alignment explanation
Indices: 17554518--17554558 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17554508 TGAGAATGTT
*
17554518 GATGCAACTTTTTCAAAAATC
1 GATGCAACTTTTACAAAAATC
*
17554539 GATGCAAGTTTTACAAAAAT
1 GATGCAACTTTTACAAAAAT
17554559 TTCCTACTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (21 bp):
GATGCAACTTTTACAAAAATC
Found at i:17554705 original size:24 final size:24
Alignment explanation
Indices: 17554668--17554803 Score: 114
Period size: 24 Copynumber: 5.7 Consensus size: 24
17554658 AGCTGCACGG
* *
17554668 TGTGGTCAAACCACTCATTTA-CGT
1 TGTGGACAAGCCACTCA-TTAGCGT
* * * *
17554692 TGTGGCCAAGCCACTCAATATCAT
1 TGTGGACAAGCCACTCATTAGCGT
* ** *
17554716 TCTGGTTAAGCCACTCATTAGTGT
1 TGTGGACAAGCCACTCATTAGCGT
17554740 TGTGGACAAGCCACTCA-TAGCGT
1 TGTGGACAAGCCACTCATTAGCGT
* * * *
17554763 TGTGGACATGCCACTCAATATCAT
1 TGTGGACAAGCCACTCATTAGCGT
*
17554787 TGTGGACAAGTCACTCA
1 TGTGGACAAGCCACTCA
17554804 ATTTTGGAGT
Statistics
Matches: 90, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
23 23 0.26
24 67 0.74
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (24 bp):
TGTGGACAAGCCACTCATTAGCGT
Found at i:17554804 original size:24 final size:24
Alignment explanation
Indices: 17554691--17554805 Score: 117
Period size: 24 Copynumber: 4.8 Consensus size: 24
17554681 CTCATTTACG
*
17554691 TTGTGGCCAAGCCACTCAATATCA
1 TTGTGGACAAGCCACTCAATATCA
* ** * *
17554715 TTCTGGTTAAGCCACTCATTAGT-G
1 TTGTGGACAAGCCACTCAATA-TCA
* *
17554739 TTGTGGACAAGCCACTC-ATAGCG
1 TTGTGGACAAGCCACTCAATATCA
*
17554762 TTGTGGACATGCCACTCAATATCA
1 TTGTGGACAAGCCACTCAATATCA
*
17554786 TTGTGGACAAGTCACTCAAT
1 TTGTGGACAAGCCACTCAAT
17554806 TTTGGAGTAA
Statistics
Matches: 73, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
23 19 0.26
24 53 0.73
25 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (24 bp):
TTGTGGACAAGCCACTCAATATCA
Found at i:17554955 original size:42 final size:42
Alignment explanation
Indices: 17554890--17555002 Score: 163
Period size: 42 Copynumber: 2.7 Consensus size: 42
17554880 GGTATTTATC
*
17554890 AGTCGACATGCTTAACATGCAAATCAAATCTAAGATCAACAT
1 AGTCGGCATGCTTAACATGCAAATCAAATCTAAGATCAACAT
* * * * * *
17554932 ATTTGGCATGCTTAACATGCAAATCAAATCTCAGTTTATCAT
1 AGTCGGCATGCTTAACATGCAAATCAAATCTAAGATCAACAT
17554974 AGTCGGCATGCTTAACATGCAAATCAAAT
1 AGTCGGCATGCTTAACATGCAAATCAAAT
17555003 ATTAGTTAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.28
Consensus pattern (42 bp):
AGTCGGCATGCTTAACATGCAAATCAAATCTAAGATCAACAT
Found at i:17556617 original size:28 final size:28
Alignment explanation
Indices: 17556576--17556640 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
17556566 TGTTTGAAAA
17556576 CACTTATTTTATAGTAAAAGCACTTAAT
1 CACTTATTTTATAGTAAAAGCACTTAAT
*
17556604 TACTTATTTTATAGTAAAAGCACTTAAT
1 CACTTATTTTATAGTAAAAGCACTTAAT
17556632 CACTTATTT
1 CACTTATTT
17556641 GATCATTCGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (28 bp):
CACTTATTTTATAGTAAAAGCACTTAAT
Found at i:17564897 original size:140 final size:138
Alignment explanation
Indices: 17564645--17565053 Score: 452
Period size: 140 Copynumber: 3.0 Consensus size: 138
17564635 TATAACTAAA
* * *
17564645 GTCGGCATAGTGTTGTACAAAGCCGACTCTTATTTTA-GTGTTGCCTTAGGCATGCGTATCCCAA
1 GTCGGCATAGTGTTGGACAAAGCCGACTCTTATTTAACGTGTTGCCTTAGGCATGCATATCCCAA
* * * * *
17564709 CCCTTATATAAATAGTTGGCCAAAGCGTATATCCACAAGTTTATCCCAAAACTTAGGAAAGCGTC
66 CCCTTATACAAATAGTTGGCCAAAGCGTATGTCCGCAAGTCTATCCCAACACTTAGGAAAG-GTC
17564774 AGTCCAAAAGT
130 -GT-CAAAAGT
* * * *
17564785 GTCGGCAGAGTGTTGGACAAAGTCGACTCTTA-TTCACGTGTTGCCTTAGGCATGCATATCCCTA
1 GTCGGCATAGTGTTGGACAAAGCCGACTCTTATTTAACGTGTTGCCTTAGGCATGCATATCCCAA
* *
17564849 CCCTTATACAAATAGTTGGACAAAGCGTATGTCGGCAAGTCTATCCCAACACTT-----A-G--G
66 CCCTTATACAAATAGTTGGCCAAAGCGTATGTCCGCAAGTCTATCCCAACACTTAGGAAAGGTCG
17564906 ---AAAGT
131 TCAAAAGT
* * * *
17564911 GTCGACATAGTGTTGGACGAAGCCGACTCTTATTTGAAC--GTTGCCTTAGGCATGCATATCTCG
1 GTCGGCATAGTGTTGGACAAAGCCGACTCTTATTT-AACGTGTTGCCTTAGGCATGCATATCCCA
* * * *
17564974 ACCCATATACAAAGAGTTAGCCAAAGCGTATGTCTGCAAGTCTATCCCAACACTTAGGAAAGTGT
65 ACCCTTATACAAATAGTTGGCCAAAGCGTATGTCCGCAAGTCTATCCCAACACTTAGGAAAG-GT
17565039 CGATCAAAAAGT
129 CG-TC-AAAAGT
17565051 GTC
1 GTC
17565054 ATCTTAGGAT
Statistics
Matches: 227, Mismatches: 25, Indels: 34
0.79 0.09 0.12
Matches are distributed among these distances:
126 105 0.46
127 2 0.01
128 2 0.01
130 1 0.00
131 1 0.00
133 2 0.01
135 2 0.01
139 3 0.01
140 109 0.48
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.27
Consensus pattern (138 bp):
GTCGGCATAGTGTTGGACAAAGCCGACTCTTATTTAACGTGTTGCCTTAGGCATGCATATCCCAA
CCCTTATACAAATAGTTGGCCAAAGCGTATGTCCGCAAGTCTATCCCAACACTTAGGAAAGGTCG
TCAAAAGT
Found at i:17565005 original size:126 final size:125
Alignment explanation
Indices: 17564780--17565041 Score: 382
Period size: 126 Copynumber: 2.1 Consensus size: 125
17564770 CGTCAGTCCA
* * *
17564780 AAAGTGTCGGCAGAGTGTTGGACAAAGTCGACTCTTATTCACGTGTTGCCTTAGGCATGCATATC
1 AAAGTGTCGACAGAGTGTTGGACAAAGCCGACTCTTATTAACG-GTTGCCTTAGGCATGCATATC
* * * *
17564845 CCTACCCTTATACAAATAGTTGGACAAAGCGTATGTCGGCAAGTCTATCCCAACACTTAGG
65 CCGACCCATATACAAAGAGTTAGACAAAGCGTATGTCGGCAAGTCTATCCCAACACTTAGG
* *
17564906 AAAGTGTCGACATAGTGTTGGACGAAGCCGACTCTTATTTGAAC-GTTGCCTTAGGCATGCATAT
1 AAAGTGTCGACAGAGTGTTGGACAAAGCCGACTCTTA-TT-AACGGTTGCCTTAGGCATGCATAT
* * *
17564970 CTCGACCCATATACAAAGAGTTAGCCAAAGCGTATGTCTGCAAGTCTATCCCAACACTTAGG
64 CCCGACCCATATACAAAGAGTTAGACAAAGCGTATGTCGGCAAGTCTATCCCAACACTTAGG
17565032 AAAGTGTCGA
1 AAAGTGTCGA
17565042 TCAAAAAGTG
Statistics
Matches: 122, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
126 118 0.97
127 2 0.02
128 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (125 bp):
AAAGTGTCGACAGAGTGTTGGACAAAGCCGACTCTTATTAACGGTTGCCTTAGGCATGCATATCC
CGACCCATATACAAAGAGTTAGACAAAGCGTATGTCGGCAAGTCTATCCCAACACTTAGG
Found at i:17566710 original size:43 final size:43
Alignment explanation
Indices: 17566649--17566736 Score: 160
Period size: 43 Copynumber: 2.0 Consensus size: 43
17566639 ATGTGAGATA
17566649 GAGATAAGAATTATTTAGGAATTGAATTCTATTGCAAAATATG
1 GAGATAAGAATTATTTAGGAATTGAATTCTATTGCAAAATATG
17566692 GAGATAATG-ATTATTTAGGAATTGAATTCTATTGCAAAATATG
1 GAGATAA-GAATTATTTAGGAATTGAATTCTATTGCAAAATATG
17566735 GA
1 GA
17566737 ATGATTGAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
43 43 0.98
44 1 0.02
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.35
Consensus pattern (43 bp):
GAGATAAGAATTATTTAGGAATTGAATTCTATTGCAAAATATG
Found at i:17577654 original size:15 final size:15
Alignment explanation
Indices: 17577634--17577669 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
17577624 ATGACTTTCT
17577634 GGGGTTGTCAAACCC
1 GGGGTTGTCAAACCC
17577649 GGGGTTGTCAAACCC
1 GGGGTTGTCAAACCC
*
17577664 AGGGTT
1 GGGGTT
17577670 TGTTTCATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.19, C:0.22, G:0.36, T:0.22
Consensus pattern (15 bp):
GGGGTTGTCAAACCC
Found at i:17578441 original size:19 final size:20
Alignment explanation
Indices: 17578417--17578455 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
17578407 GTTAGTGAAC
17578417 AAATATAAATAT-AAATAAA
1 AAATATAAATATAAAATAAA
**
17578436 AAATATTTATATAAAATAAA
1 AAATATAAATATAAAATAAA
17578456 TTACATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATATAAATATAAAATAAA
Found at i:17578454 original size:20 final size:20
Alignment explanation
Indices: 17578425--17578469 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
17578415 ACAAATATAA
17578425 ATATAAATAAA-AAATATTT
1 ATATAAATAAATAAATATTT
*
17578444 ATATAAAATAAATTACATATTT
1 ATAT-AAATAAA-TAAATATTT
17578466 ATAT
1 ATAT
17578470 TTAAAATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 4 0.18
20 7 0.32
22 11 0.50
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATAAATAAATAAATATTT
Found at i:17588031 original size:77 final size:77
Alignment explanation
Indices: 17587945--17588527 Score: 482
Period size: 77 Copynumber: 7.3 Consensus size: 77
17587935 GTTGAATAGT
* * *
17587945 AGGATTAAATCCTGAAACATAATTATTTAATTAAATCTTATTTGGAAACAAAATCAAAATAAAAT
1 AGGAATAAATCCTGAAACAGAATTATTTAATTAAATCTTGTTTGGAAACAAAATCAAAATAAAAT
* *
17588010 TTGTTAAATGGC
66 CTGTTAAACGGC
* *
17588022 AGGAATAAATCCCT-AAACAAAATTATTTGATTAAATCTTGTTTGGAAACAAAATCAAAATAAAA
1 AGGAATAAAT-CCTGAAACAGAATTATTTAATTAAATCTTGTTTGGAAACAAAATCAAAATAAAA
17588086 TCTGTTAAACGGC
65 TCTGTTAAACGGC
* * *
17588099 GGGAATAAAT-TTGAAAACAGAATTATTTGATTAAATCTTGTTTGGAAACAAAATCAAAATAAAA
1 AGGAATAAATCCTG-AAACAGAATTATTTAATTAAATCTTGTTTGGAAACAAAATCAAAATAAAA
17588163 TCTGTT-AA--GC
65 TCTGTTAAACGGC
* * * *
17588173 AATGGAATAAATCCCGAAATAGAATTATTCAATTAAATCTTCTCATTTGGAAACAAAATCAAAAT
1 -A-GGAATAAATCCTGAAACAGAATTATTTAATTAAATC-T-T-GTTTGGAAACAAAATC--AA-
17588238 CGAATAAAATCTGTTAAACGG-
58 --AATAAAATCTGTTAAACGGC
* * * * *
17588259 AGGAAATAAATCTTGAAATAGAATTATTTGATTAAATCTTGTTTGGGAACAAAATCAAGATAAAA
1 AGG-AATAAATCCTGAAACAGAATTATTTAATTAAATCTTGTTTGGAAACAAAATCAAAATAAAA
* *
17588324 TCTGTTAAGCGTC
65 TCTGTTAAACGGC
* * * * * *
17588337 A-AAATAAATCCCGAAAAAAAAATTATTTAATTAAATCTTCTCATTTGGAAACAAAAACAAAATC
1 AGGAATAAATCCTG-AAACAGAATTATTTAATTAAATC-T-T-GTTTGGAAACAAAATC--AA--
** *
17588401 GAATAAAATCTACTAAATGGC
58 -AATAAAATCTGTTAAACGGC
* * * * *
17588422 GGGAATAAATCCAGAAACA-AATTATATTCAATTTTAATCCTCGTTTGGAAAGAAAATCAAAATG
1 AGGAATAAATCCTGAAACAGAATTAT-TT-AA-TTAAAT-CTTGTTTGGAAACAAAATC--AA--
*
17588486 GAATAAAATCTGTTAAACGGT
58 -AATAAAATCTGTTAAACGGC
*
17588507 GGGAATAAATCACTG-AACAGA
1 AGGAATAAATC-CTGAAACAGA
17588528 TTTTATTCAA
Statistics
Matches: 416, Mismatches: 55, Indels: 61
0.78 0.10 0.11
Matches are distributed among these distances:
74 2 0.00
75 1 0.00
76 40 0.10
77 169 0.41
78 6 0.01
79 16 0.04
80 15 0.04
81 2 0.00
82 16 0.04
83 1 0.00
84 22 0.05
85 103 0.25
86 15 0.04
87 7 0.02
88 1 0.00
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (77 bp):
AGGAATAAATCCTGAAACAGAATTATTTAATTAAATCTTGTTTGGAAACAAAATCAAAATAAAAT
CTGTTAAACGGC
Found at i:17588291 original size:161 final size:160
Alignment explanation
Indices: 17587950--17588484 Score: 606
Period size: 161 Copynumber: 3.3 Consensus size: 160
17587940 ATAGTAGGAT
* * * * *
17587950 TAAATCCTGAAACATAATTATTTAATTAAATCTTATTTGGAAACAAAATCAAAATAAAATTTGTT
1 TAAATCTTGAAACAGAATTATTTGATTAAATCTTGTTTGGAAACAAAATCAAAATAAAATCTGTT
* * * *
17588015 AAATGGCA-GGAATAAATCCCTAAACAAAATTATTTGATTAAATC-T-T-GTTTGGAAACAAAAT
66 -AA--GCATGGAATAAATCCCGAAAAAAAATTATTTAATTAAATCTTCTCATTTGGAAACAAAAT
* *
17588076 C--AA---AATAAAATCTGTTAAACGGCGGGAA
128 CAAAATCGAATAAAATCTGTTAAACGGAGGAAA
17588104 TAAAT-TTGAAAACAGAATTATTTGATTAAATCTTGTTTGGAAACAAAATCAAAATAAAATCTGT
1 TAAATCTTG-AAACAGAATTATTTGATTAAATCTTGTTTGGAAACAAAATCAAAATAAAATCTGT
* * *
17588168 TAAGCAATGGAATAAATCCCGAAATAGAATTATTCAATTAAATCTTCTCATTTGGAAACAAAATC
65 TAAGC-ATGGAATAAATCCCGAAAAAAAATTATTTAATTAAATCTTCTCATTTGGAAACAAAATC
17588233 AAAATCGAATAAAATCTGTTAAACGGAGGAAA
129 AAAATCGAATAAAATCTGTTAAACGGAGGAAA
* * *
17588265 TAAATCTTGAAATAGAATTATTTGATTAAATCTTGTTTGGGAACAAAATCAAGATAAAATCTGTT
1 TAAATCTTGAAACAGAATTATTTGATTAAATCTTGTTTGGAAACAAAATCAAAATAAAATCTGTT
* ** *
17588330 AAGCGTCAAAATAAATCCCGAAAAAAAAATTATTTAATTAAATCTTCTCATTTGGAAACAAAAAC
66 AAGCAT-GGAATAAATCCCG-AAAAAAAATTATTTAATTAAATCTTCTCATTTGGAAACAAAATC
** * * *
17588395 AAAATCGAATAAAATCTACTAAATGGCGGGAA
129 AAAATCGAATAAAATCTGTTAAACGGAGGAAA
** * * * *
17588427 TAAATCCAGAAACA-AATTATATTCAATTTTAATCCTCGTTTGGAAAGAAAATCAAAAT
1 TAAATCTTGAAACAGAATTAT-TT-GA-TTAAAT-CTTGTTTGGAAACAAAATCAAAAT
17588485 GGAATAAAAT
Statistics
Matches: 326, Mismatches: 37, Indels: 25
0.84 0.10 0.06
Matches are distributed among these distances:
151 2 0.01
152 1 0.00
153 35 0.11
154 58 0.18
155 1 0.00
156 15 0.05
158 2 0.01
160 1 0.00
161 102 0.31
162 83 0.25
163 1 0.00
164 5 0.02
165 20 0.06
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.30
Consensus pattern (160 bp):
TAAATCTTGAAACAGAATTATTTGATTAAATCTTGTTTGGAAACAAAATCAAAATAAAATCTGTT
AAGCATGGAATAAATCCCGAAAAAAAATTATTTAATTAAATCTTCTCATTTGGAAACAAAATCAA
AATCGAATAAAATCTGTTAAACGGAGGAAA
Found at i:17588363 original size:238 final size:238
Alignment explanation
Indices: 17587950--17588517 Score: 590
Period size: 238 Copynumber: 2.4 Consensus size: 238
17587940 ATAGTAGGAT
* *
17587950 TAAATCCTGAAACATAATTATTTAATTAAATCT-T-ATTTGGAAACAAAATC--AA--AATAAAA
1 TAAATCCAGAAACA-AATTATTCAATTAAATCTCTCATTTGGAAACAAAATCAAAATGAATAAAA
* *
17588009 TTTGTTAAATGGCAGGAATAAATCCCTAAACAAAATTATTTGATTAAATCTTGTTTGGAAACAAA
65 TCTGTTAAACGG-AGGAATAAAT-CCTAAACAAAATTATTTGATTAAATCTTGTTTGGAAACAAA
** ** * * *
17588074 ATCAAAATAAAATCTGTTAAACGGCGGGAATAAATTTGAAAACAGAATTATTTGATTAAATC-T-
128 ATCAAAATAAAATCTGTTAAACGGCGAAAATAAATCCGAAAAAAAAATTATTTAATTAAATCTTC
* * * * *
17588137 T-GTTTGGAAACAAAATC-AA-AATAAAATCT-GTTAA-GCAATGGAA
193 TCATTTGGAAACAAAAACAAACAATAAAATCTACTAAAGGC--GGGAA
* *
17588180 TAAATCCCGAAATAGAATTATTCAATTAAATCTTCTCATTTGGAAACAAAATCAAAATCGAATAA
1 TAAATCCAGAAACA-AATTATTCAATTAAATC-TCTCATTTGGAAACAAAATCAAAAT-GAATAA
* * * *
17588245 AATCTGTTAAACGGAGGAAATAAATCTTGAAATAGAATTATTTGATTAAATCTTGTTTGGGAACA
63 AATCTGTTAAACGGAGG-AATAAATCCT-AAACAAAATTATTTGATTAAATCTTGTTTGGAAACA
* * *
17588310 AAATCAAGATAAAATCTGTTAAGCGTC-AAAATAAATCCCGAAAAAAAAATTATTTAATTAAATC
126 AAATCAAAATAAAATCTGTTAAACGGCGAAAATAAAT-CCGAAAAAAAAATTATTTAATTAAATC
17588374 TTCTCATTTGGAAACAAAAACAAAATCGAATAAAATCTACTAAATGGCGGGAA
190 TTCTCATTTGGAAACAAAAAC-AAA-C-AATAAAATCTACTAAA-GGCGGGAA
* * *
17588427 TAAATCCAGAAACAAATTATATTCAATTTTAATC-CTCGTTTGGAAAGAAAATCAAAATGGAATA
1 TAAATCCAGAAACAAA-T-TATTCAA-TTAAATCTCTCATTTGGAAACAAAATCAAAAT-GAATA
*
17588491 AAATCTGTTAAACGGTGGGAATAAATC
62 AAATCTGTTAAACGG-AGGAATAAATC
17588518 ACTGAACAGA
Statistics
Matches: 280, Mismatches: 32, Indels: 35
0.81 0.09 0.10
Matches are distributed among these distances:
230 28 0.10
231 1 0.00
232 1 0.00
233 16 0.06
235 2 0.01
237 12 0.04
238 103 0.37
239 1 0.00
240 1 0.00
241 14 0.05
243 2 0.01
246 12 0.04
247 70 0.25
248 9 0.03
249 8 0.03
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.29
Consensus pattern (238 bp):
TAAATCCAGAAACAAATTATTCAATTAAATCTCTCATTTGGAAACAAAATCAAAATGAATAAAAT
CTGTTAAACGGAGGAATAAATCCTAAACAAAATTATTTGATTAAATCTTGTTTGGAAACAAAATC
AAAATAAAATCTGTTAAACGGCGAAAATAAATCCGAAAAAAAAATTATTTAATTAAATCTTCTCA
TTTGGAAACAAAAACAAACAATAAAATCTACTAAAGGCGGGAA
Found at i:17588429 original size:86 final size:86
Alignment explanation
Indices: 17588339--17588517 Score: 204
Period size: 85 Copynumber: 2.1 Consensus size: 86
17588329 TAAGCGTCAA
17588339 AATAAATCCCGAAAAAAAAATTAT-TT-AA-TTAAATCTTCTCATTTGGAAACAAAAACAAAATC
1 AATAAATCCC-AAAAAAAAATTATATTCAATTTAAATC--CTCATTTGGAAACAAAAACAAAATC
*
17588401 GAATAAAATCTACTAAATGGCGGG
63 GAATAAAATCTACTAAACGGCGGG
* * * * * * *
17588425 AATAAAT-CCAGAAACAAATTATATTCAATTTTAATCCTCGTTTGGAAAGAAAATCAAAATGGAA
1 AATAAATCCCAAAAAAAAATTATATTCAATTTAAATCCTCATTTGGAAACAAAAACAAAATCGAA
** *
17588489 TAAAATCTGTTAAACGGTGGG
66 TAAAATCTACTAAACGGCGGG
17588510 AATAAATC
1 AATAAATC
17588518 ACTGAACAGA
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
84 11 0.14
85 52 0.67
86 9 0.12
87 6 0.08
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (86 bp):
AATAAATCCCAAAAAAAAATTATATTCAATTTAAATCCTCATTTGGAAACAAAAACAAAATCGAA
TAAAATCTACTAAACGGCGGG
Found at i:17588535 original size:85 final size:85
Alignment explanation
Indices: 17588380--17588540 Score: 216
Period size: 85 Copynumber: 1.9 Consensus size: 85
17588370 AATCTTCTCA
*
17588380 TTTGGAAACAAAAACAAAATCGAATAAAATCTACTAAATGGCGGGAATAAATCCAGAAACAAATT
1 TTTGGAAACAAAAACAAAATCGAATAAAATCTACTAAACGGCGGGAATAAATCCAGAAACAAATT
17588445 ATATTCAATTTTAATCCTCG
66 ATATTCAATTTTAATCCTCG
* * * ** * * *
17588465 TTTGGAAAGAAAATCAAAATGGAATAAAATCTGTTAAACGGTGGGAATAAATCACTG-AACAGAT
1 TTTGGAAACAAAAACAAAATCGAATAAAATCTACTAAACGGCGGGAATAAATC-CAGAAACAAAT
*
17588529 TTTATTCAATTT
65 TATATTCAATTT
17588541 AATTCTCATT
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
85 63 0.97
86 2 0.03
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.28
Consensus pattern (85 bp):
TTTGGAAACAAAAACAAAATCGAATAAAATCTACTAAACGGCGGGAATAAATCCAGAAACAAATT
ATATTCAATTTTAATCCTCG
Found at i:17588689 original size:16 final size:17
Alignment explanation
Indices: 17588668--17588711 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
17588658 GTTAGTGAAC
17588668 AAATATAAATATAAA-T
1 AAATATAAATATAAATT
**
17588684 AAATATTTATATAAATT
1 AAATATAAATATAAATT
17588701 AAAT-TAAATAT
1 AAATATAAATAT
17588712 TTATATTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATATAAATATAAATT
Found at i:17588697 original size:22 final size:22
Alignment explanation
Indices: 17588670--17588717 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
17588660 TAGTGAACAA
17588670 ATATAAATATAAA-TAAATATTT
1 ATATAAAT-TAAATTAAATATTT
17588692 ATATAAATTAAATTAAATATTT
1 ATATAAATTAAATTAAATATTT
17588714 ATAT
1 ATAT
17588718 TTAAAATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATATAAATTAAATTAAATATTT
Found at i:17591060 original size:18 final size:17
Alignment explanation
Indices: 17591037--17591072 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17591027 CATGTTGTAT
17591037 GCCCATATGGGCCCACAC
1 GCCCATAT-GGCCCACAC
*
17591055 GCCCATGTGGCCCACAC
1 GCCCATATGGCCCACAC
17591072 G
1 G
17591073 ACCTACAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.19, C:0.44, G:0.25, T:0.11
Consensus pattern (17 bp):
GCCCATATGGCCCACAC
Found at i:17598841 original size:25 final size:24
Alignment explanation
Indices: 17598813--17598881 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 24
17598803 TATTTTTGTA
17598813 ATATTTTTAAAATTTTTAGA-TACAT
1 ATATTTTTAAAATTTTTA-ATTAC-T
* * *
17598838 ATATTCTTATAATTTTTAATTTCT
1 ATATTTTTAAAATTTTTAATTACT
17598862 ATATTTTATATAAATTTTTA
1 ATATTTT-TA-AAATTTTTA
17598882 TATATTTTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
24 8 0.22
25 20 0.56
26 8 0.22
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58
Consensus pattern (24 bp):
ATATTTTTAAAATTTTTAATTACT
Found at i:17603058 original size:45 final size:45
Alignment explanation
Indices: 17602991--17603114 Score: 131
Period size: 45 Copynumber: 2.7 Consensus size: 45
17602981 GCAAAATTTT
* *
17602991 TTGTGTATCCACAACTAAAGGCATATTCCATCTACAAGTTATCTA
1 TTGTGTATCCACAGCCAAAGGCATATTCCATCTACAAGTTATCTA
* * *** *
17603036 TTGTGTATCCACAGCCAGAGGCAGATTCCATCTGTTAGTTATTTA
1 TTGTGTATCCACAGCCAAAGGCATATTCCATCTACAAGTTATCTA
* * * *
17603081 CTATGAAATCCACAGCCAAAGGCATATTTCATCT
1 TTGTG-TATCCACAGCCAAAGGCATATTCCATCT
17603115 GCTAGACTAT
Statistics
Matches: 64, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
45 40 0.62
46 24 0.38
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.32
Consensus pattern (45 bp):
TTGTGTATCCACAGCCAAAGGCATATTCCATCTACAAGTTATCTA
Found at i:17615568 original size:12 final size:12
Alignment explanation
Indices: 17615553--17615585 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
17615543 TATCGTGTCG
17615553 ATAGTCGTGGCA
1 ATAGTCGTGGCA
17615565 ATAGTCGTGGCA
1 ATAGTCGTGGCA
17615577 ATAGTCGTG
1 ATAGTCGTG
17615586 CCCACGACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.27
Consensus pattern (12 bp):
ATAGTCGTGGCA
Found at i:17615708 original size:17 final size:17
Alignment explanation
Indices: 17615682--17615723 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
17615672 ATAAATAATT
17615682 AATT-AATTAAATTGGA
1 AATTAAATTAAATTGGA
17615698 AATTAAATTAAATTGGA
1 AATTAAATTAAATTGGA
17615715 AATTAAATT
1 AATTAAATT
17615724 CGAATTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (17 bp):
AATTAAATTAAATTGGA
Found at i:17617291 original size:22 final size:22
Alignment explanation
Indices: 17617259--17617310 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
17617249 ATAAATAAAT
17617259 AATTAAA--AAATTAGAAATTA
1 AATTAAATTAAATTAGAAATTA
*
17617279 AATTAAATTAAATTGGAAATTA
1 AATTAAATTAAATTAGAAATTA
17617301 AATTCAAATT
1 AATT-AAATT
17617311 TTGTAATCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 7 0.25
22 16 0.57
23 5 0.18
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.35
Consensus pattern (22 bp):
AATTAAATTAAATTAGAAATTA
Found at i:17643027 original size:2 final size:2
Alignment explanation
Indices: 17643020--17643056 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
17643010 GGAATTGGAT
17643020 TA TA TA TA TA 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 TA TA TA TA TA T
17643057 GATAGTTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17643240 original size:25 final size:23
Alignment explanation
Indices: 17643191--17643240 Score: 55
Period size: 25 Copynumber: 2.1 Consensus size: 23
17643181 TATTATAAAT
* *
17643191 TAAAAAAATAACTATTTATTTTA
1 TAAAAAAATAACTATTAATTATA
*
17643214 TAAAAAAATTTAACTGTTAATTATA
1 TAAAAAAA--TAACTATTAATTATA
17643239 TA
1 TA
17643241 TTAATATAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 8 0.36
25 14 0.64
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (23 bp):
TAAAAAAATAACTATTAATTATA
Found at i:17644277 original size:17 final size:16
Alignment explanation
Indices: 17644220--17644315 Score: 54
Period size: 16 Copynumber: 5.9 Consensus size: 16
17644210 TGAATTTTGG
17644220 AATTTTTATATTTTTAA
1 AATTTTT-TATTTTTAA
**
17644237 AATATTTTTAAATTTAA
1 AAT-TTTTTATTTTTAA
**
17644254 TTTTTTTTTATTTTTAA
1 -AATTTTTTATTTTTAA
*
17644271 AGA-TTTTTATTTTAAA
1 A-ATTTTTTATTTTTAA
* * *
17644287 AAATTATAATTTTT--
1 AATTTTTTATTTTTAA
17644301 AATTTTTTAATTTTT
1 AATTTTTT-ATTTTT
17644316 TTGTTTAAAA
Statistics
Matches: 59, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
14 5 0.08
15 7 0.12
16 21 0.36
17 21 0.36
18 5 0.08
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (16 bp):
AATTTTTTATTTTTAA
Found at i:17670660 original size:38 final size:38
Alignment explanation
Indices: 17670618--17670695 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
17670608 CTGCGATAAT
17670618 GTGATGATTCCTGACAATTAAAAATGTGTTTTTGTATA
1 GTGATGATTCCTGACAATTAAAAATGTGTTTTTGTATA
* *
17670656 GTGATGATTCTTGACAATTAGAAATGTGTTTTTGTATA
1 GTGATGATTCCTGACAATTAAAAATGTGTTTTTGTATA
17670694 GT
1 GT
17670696 AAATGGATCC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44
Consensus pattern (38 bp):
GTGATGATTCCTGACAATTAAAAATGTGTTTTTGTATA
Found at i:17671331 original size:30 final size:31
Alignment explanation
Indices: 17671292--17671350 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
17671282 AGTGATAGAG
* *
17671292 ACAGAATATGAGC-GGGGATTTGTGAGACTCA
1 ACAGAATATG-CCTGGGAATTTGTGAGACTCA
17671323 ACAG-ATATGCCTGGGAATTTGTGAGACT
1 ACAGAATATGCCTGGGAATTTGTGAGACT
17671351 GAAGCTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 1 0.04
30 20 0.80
31 4 0.16
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.25
Consensus pattern (31 bp):
ACAGAATATGCCTGGGAATTTGTGAGACTCA
Found at i:17677236 original size:74 final size:76
Alignment explanation
Indices: 17677107--17677253 Score: 228
Period size: 74 Copynumber: 2.0 Consensus size: 76
17677097 ATGGAAATTA
* *
17677107 ATATTCTTTTGGAAAAAAATATAATTCATTTTTCTAACTTTACATTTTCCTTCTCTATTAATAAT
1 ATATTCTTTTGGAAAAAAATATAATTCATTTTTCTAACTTTACATTTGCCTTCTCTATTAATAAG
17677172 GGAATAATCCT
66 GGAATAATCCT
* *
17677183 ATATTCTTTTGG-AAAGAATATAATTTC-TTTTT-TAACTTTCCATTTGCCTTCTCTATTAATAA
1 ATATTCTTTTGGAAAAAAATATAA-TTCATTTTTCTAACTTTACATTTGCCTTCTCTATTAATAA
17677245 GGGAATAAT
65 GGGAATAAT
17677254 ATTGGTTTTT
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
74 36 0.55
75 15 0.23
76 15 0.23
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.46
Consensus pattern (76 bp):
ATATTCTTTTGGAAAAAAATATAATTCATTTTTCTAACTTTACATTTGCCTTCTCTATTAATAAG
GGAATAATCCT
Found at i:17678884 original size:18 final size:18
Alignment explanation
Indices: 17678863--17678968 Score: 76
Period size: 18 Copynumber: 6.0 Consensus size: 18
17678853 TTACAACAAA
*
17678863 GGTTCGCATAACATCATG
1 GGTTCGCATAACAACATG
* * * *
17678881 GGTTCG-ATTATAGCATA
1 GGTTCGCATAACAACATG
* *
17678898 GGTTCACATAACAACATA
1 GGTTCGCATAACAACATG
*
17678916 AGTTCGCATATAGC-ACA--
1 GGTTCGCATA-A-CAACATG
* *
17678933 GGTCCACATAACAACATG
1 GGTTCGCATAACAACATG
17678951 GGTTCGCATAACAACATG
1 GGTTCGCATAACAACATG
17678969 ATTTCACACA
Statistics
Matches: 67, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
15 1 0.01
16 4 0.06
17 19 0.28
18 38 0.57
19 4 0.06
20 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.25
Consensus pattern (18 bp):
GGTTCGCATAACAACATG
Found at i:17678901 original size:35 final size:35
Alignment explanation
Indices: 17678862--17678960 Score: 128
Period size: 35 Copynumber: 2.8 Consensus size: 35
17678852 ATTACAACAA
* * *
17678862 AGGTTCGCATAACATCATGGGTTCG-ATTATAGCAT
1 AGGTTCACATAACAACATGGGTTCGCA-TATAGCAC
**
17678897 AGGTTCACATAACAACATAAGTTCGCATATAGCAC
1 AGGTTCACATAACAACATGGGTTCGCATATAGCAC
*
17678932 AGGTCCACATAACAACATGGGTTCGCATA
1 AGGTTCACATAACAACATGGGTTCGCATA
17678961 ACAACATGAT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
35 54 0.98
36 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.25
Consensus pattern (35 bp):
AGGTTCACATAACAACATGGGTTCGCATATAGCAC
Found at i:17689800 original size:16 final size:16
Alignment explanation
Indices: 17689779--17689814 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
17689769 TGGTTCGCTA
* *
17689779 TAATGGAATAGAGGTG
1 TAATGGAATAAAGCTG
17689795 TAATGGAATAAAGCTG
1 TAATGGAATAAAGCTG
17689811 TAAT
1 TAAT
17689815 AGTAATTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.28, T:0.28
Consensus pattern (16 bp):
TAATGGAATAAAGCTG
Found at i:17689860 original size:45 final size:44
Alignment explanation
Indices: 17689796--17689888 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 44
17689786 ATAGAGGTGT
17689796 AATGGAATAAAGCTGTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAAAGCTGTAATAGT-ATTC-ATGTGTTTGGTTGAATGG
*
17689841 AATGGAATAGAA-CTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATA-AAGCTGTAATAGTATTCATGTGTTTGGTTGAATGG
17689885 AATG
1 AATG
17689889 ATGTTGTAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
43 1 0.02
44 23 0.51
45 19 0.42
46 2 0.04
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (44 bp):
AATGGAATAAAGCTGTAATAGTATTCATGTGTTTGGTTGAATGG
Found at i:17691132 original size:16 final size:16
Alignment explanation
Indices: 17691093--17691126 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
17691083 AATAAATTGG
17691093 AATATTAAAAATAAAA
1 AATATTAAAAATAAAA
17691109 AATATTAAAAATAAAA
1 AATATTAAAAATAAAA
17691125 AA
1 AA
17691127 ATTTAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AATATTAAAAATAAAA
Found at i:17702442 original size:22 final size:21
Alignment explanation
Indices: 17702417--17702460 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
17702407 TGATAAACTT
17702417 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
17702439 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
17702460 T
1 T
17702461 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:17708202 original size:18 final size:17
Alignment explanation
Indices: 17708176--17708209 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17708166 AAGAAAAAGA
17708176 ATATAAGTTTGGTAATTG
1 ATATAAG-TTGGTAATTG
*
17708194 ATATTAGTTGGTAATT
1 ATATAAGTTGGTAATT
17708210 CATTTAACTT
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:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (17 bp):
ATATAAGTTGGTAATTG
Found at i:17712090 original size:27 final size:27
Alignment explanation
Indices: 17712059--17712113 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
17712049 AATAAGACAT
17712059 ACTATACCTTTGATAATAATTCAAATC
1 ACTATACCTTTGATAATAATTCAAATC
17712086 ACTATACCTTTGATAATAATTCAAATC
1 ACTATACCTTTGATAATAATTCAAATC
17712113 A
1 A
17712114 TACTTACCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.36
Consensus pattern (27 bp):
ACTATACCTTTGATAATAATTCAAATC
Found at i:17714370 original size:11 final size:11
Alignment explanation
Indices: 17714356--17714418 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
17714346 AATTCGAGGC
17714356 TAATTTAAAAA
1 TAATTTAAAAA
17714367 TAATTTAAAAA
1 TAATTTAAAAA
*
17714378 TCCA-TTAAAAA
1 T-AATTTAAAAA
**
17714389 T-ATGGAAAAA
1 TAATTTAAAAA
17714399 TAAATTT-AAAA
1 T-AATTTAAAAA
17714410 T-ATTTAAAA
1 TAATTTAAAA
17714419 TTACCCTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
9 5 0.12
10 9 0.21
11 25 0.60
12 3 0.07
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (11 bp):
TAATTTAAAAA
Found at i:17714418 original size:21 final size:21
Alignment explanation
Indices: 17714357--17714418 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
17714347 ATTCGAGGCT
*
17714357 AATTTAAAAATAATTTAAAAATC
1 AATTT-AAAAT-ATTTAAAAATA
* * **
17714380 CATTAAAAATATGGAAAAATA
1 AATTTAAAATATTTAAAAATA
17714401 AATTTAAAATATTTAAAA
1 AATTTAAAATATTTAAAA
17714419 TTACCCTAAA
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
21 22 0.73
22 5 0.17
23 3 0.10
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (21 bp):
AATTTAAAATATTTAAAAATA
Found at i:17718963 original size:160 final size:160
Alignment explanation
Indices: 17718699--17719009 Score: 525
Period size: 160 Copynumber: 1.9 Consensus size: 160
17718689 CTGTTTTCCA
17718699 TACTTGAAGCCTTTTATGGCCTAAACACACTGCTATTGATGGTAAACAATTTTCAGATTGCATCT
1 TACTTGAAGCCTTTTATGGCCTAAACACACTGCTATTGATGGTAAACAATTTTCAGATTGCATCT
* *
17718764 GTATGGAAAAGTTGTTGGTACCATACGATATGTTTGTCTTACCAGACTAGATATTTCTTACAGTG
66 GTATGGAAAAGTGGTTGGTACCATACGATATGTTTGTCTTACCAAACTAGATATTTCTTACAGTG
17718829 AACAAAGTAAGTCAATACATGCTATTCACT
131 AACAAAGTAAGTCAATACATGCTATTCACT
* ** * *
17718859 TACTTGAGGCCTTTTATGGCCTAAACTTTA-TGCTATTGATGGTCAACCATTTTCAGATTGCATC
1 TACTTGAAGCCTTTTATGGCCTAAAC-ACACTGCTATTGATGGTAAACAATTTTCAGATTGCATC
* *
17718923 TGTCTGGAAAAGTGGTTGGTACCCTACGATATGTTTGTCTTACCAAACTAGATATTTCTTACAGT
65 TGTATGGAAAAGTGGTTGGTACCATACGATATGTTTGTCTTACCAAACTAGATATTTCTTACAGT
17718988 GAACAAAGTAAGTCAATACATG
130 GAACAAAGTAAGTCAATACATG
17719010 AATATTCCTT
Statistics
Matches: 141, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
160 140 0.99
161 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (160 bp):
TACTTGAAGCCTTTTATGGCCTAAACACACTGCTATTGATGGTAAACAATTTTCAGATTGCATCT
GTATGGAAAAGTGGTTGGTACCATACGATATGTTTGTCTTACCAAACTAGATATTTCTTACAGTG
AACAAAGTAAGTCAATACATGCTATTCACT
Found at i:17719211 original size:12 final size:12
Alignment explanation
Indices: 17719194--17719219 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17719184 TCTATCTTGA
17719194 TGATAATCCTAT
1 TGATAATCCTAT
17719206 TGATAATCCTAT
1 TGATAATCCTAT
17719218 TG
1 TG
17719220 GGTGGTGTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (12 bp):
TGATAATCCTAT
Found at i:17720202 original size:21 final size:21
Alignment explanation
Indices: 17720178--17720219 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
17720168 TATTTAATGG
17720178 TTATATTTAA-ATATTTAAAAT
1 TTATATTTAATATA-TTAAAAT
*
17720199 TTATATTTCATATATTAAAAT
1 TTATATTTAATATATTAAAAT
17720220 ATTAACAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATATTTAATATATTAAAAT
Found at i:17720432 original size:13 final size:13
Alignment explanation
Indices: 17720394--17720433 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
17720384 TTTAAACTAA
*
17720394 ACTTTTCAAAAGC
1 ACTTTTCAAAAGT
17720407 ACTTCTT-AAAAGT
1 ACTT-TTCAAAAGT
17720420 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
17720433 A
1 A
17720434 ATGAAGAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 2 0.08
13 20 0.83
14 2 0.08
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.35
Consensus pattern (13 bp):
ACTTTTCAAAAGT
Found at i:17737501 original size:15 final size:16
Alignment explanation
Indices: 17737481--17737511 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
17737471 TATTATTTAT
17737481 TTATTTAATTA-CTAA
1 TTATTTAATTATCTAA
17737496 TTATTTAATTATCTAA
1 TTATTTAATTATCTAA
17737512 CCTAATTGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATTTAATTATCTAA
Found at i:17741819 original size:14 final size:14
Alignment explanation
Indices: 17741800--17741827 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17741790 CCAATTTATT
17741800 AATGAATTATTAAA
1 AATGAATTATTAAA
17741814 AATGAATTATTAAA
1 AATGAATTATTAAA
17741828 TATAAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AATGAATTATTAAA
Found at i:17757226 original size:33 final size:33
Alignment explanation
Indices: 17757189--17757256 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 33
17757179 GGCAAAAAGA
*
17757189 AAAAAAGGAAACAAG-AATAAA-ATAAAATAGAAT
1 AAAAAAGAAAACAAGAAATAAATA-AAAATA-AAT
**
17757222 AAAAACTAAAACAAGAAATAAATAAAAATAAAT
1 AAAAAAGAAAACAAGAAATAAATAAAAATAAAT
17757255 AA
1 AA
17757257 GAAGAAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
33 17 0.57
34 12 0.40
35 1 0.03
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.13
Consensus pattern (33 bp):
AAAAAAGAAAACAAGAAATAAATAAAAATAAAT
Found at i:17757252 original size:10 final size:10
Alignment explanation
Indices: 17757208--17757268 Score: 52
Period size: 10 Copynumber: 5.8 Consensus size: 10
17757198 AACAAGAATA
17757208 AAAT-AAAAT
1 AAATAAAAAT
17757217 AGAATAAAAACT
1 A-AATAAAAA-T
*
17757229 AAAACAAGAAAT
1 -AAATAA-AAAT
17757241 AAATAAAAAT
1 AAATAAAAAT
* *
17757251 AAATAAGAAG
1 AAATAAAAAT
17757261 AAATAAAA
1 AAATAAAA
17757269 TTATTAACAT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
9 1 0.02
10 22 0.52
11 9 0.21
12 6 0.14
13 4 0.10
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:17757261 original size:24 final size:23
Alignment explanation
Indices: 17757213--17757267 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
17757203 GAATAAAATA
17757213 AAATAGAATAAAAACTAAAACAAG
1 AAATA-AATAAAAACTAAAACAAG
*
17757237 AAATAAATAAAAA-TAAATAAGAAG
1 AAATAAATAAAAACT-AA-AACAAG
17757261 AAATAAA
1 AAATAAA
17757268 ATTATTAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 1 0.04
23 10 0.36
24 17 0.61
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.15
Consensus pattern (23 bp):
AAATAAATAAAAACTAAAACAAG
Found at i:17758455 original size:21 final size:21
Alignment explanation
Indices: 17758425--17758542 Score: 85
Period size: 21 Copynumber: 5.5 Consensus size: 21
17758415 TGCTAGTACA
* *
17758425 GTGTAAATAAACCACTCATTG
1 GTGTAGATAAACCACTCAATG
* *
17758446 GTGTAGATAAAAACTACTACACT-
1 GTGTAGAT--AAACCACT-CAATG
* * *
17758469 ATGTGGATAAACCACTCAACG
1 GTGTAGATAAACCACTCAATG
* **
17758490 ATGTAGATAAACTGCTCAAATG
1 GTGTAGATAAACCACTC-AATG
*
17758512 GTGTGGATAAACCACTCAATG
1 GTGTAGATAAACCACTCAATG
*
17758533 GTGCAGATAA
1 GTGTAGATAA
17758543 TTTGTTCACA
Statistics
Matches: 74, Mismatches: 18, Indels: 10
0.73 0.18 0.10
Matches are distributed among these distances:
20 2 0.03
21 40 0.54
22 16 0.22
23 13 0.18
24 3 0.04
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.25
Consensus pattern (21 bp):
GTGTAGATAAACCACTCAATG
Found at i:17771433 original size:19 final size:19
Alignment explanation
Indices: 17771411--17771454 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
17771401 AAAAATATTA
* *
17771411 AAAATTAATAAAATTCTAT
1 AAAATTAAAAAAAATCTAT
* *
17771430 AAAAATAAAAAAAATCTTT
1 AAAATTAAAAAAAATCTAT
17771449 AAAATT
1 AAAATT
17771455 TATTAGAAAG
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:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAATTAAAAAAAATCTAT
Found at i:17772148 original size:11 final size:12
Alignment explanation
Indices: 17772120--17772147 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
17772110 TTGTTTATAA
17772120 TTTTTAACAATT
1 TTTTTAACAATT
17772132 TTTTTAACAATT
1 TTTTTAACAATT
17772144 TTTT
1 TTTT
17772148 ATGTTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTTTAACAATT
Found at i:17773959 original size:8 final size:8
Alignment explanation
Indices: 17773946--17773979 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
17773936 ATATGGATGC
17773946 TTGTGAAA
1 TTGTGAAA
17773954 TTGTGAAA
1 TTGTGAAA
17773962 TTGTGAAA
1 TTGTGAAA
17773970 TTGTGAAA
1 TTGTGAAA
17773978 TT
1 TT
17773980 AAGAACATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.24, T:0.41
Consensus pattern (8 bp):
TTGTGAAA
Found at i:17784781 original size:39 final size:39
Alignment explanation
Indices: 17784738--17784839 Score: 134
Period size: 39 Copynumber: 2.6 Consensus size: 39
17784728 CACAGCCTTG
* *
17784738 CCCAACACCTACATCCCCGTGTGGGCCAACAC-GACCTGA
1 CCCAACACCTACATGCTCGTGTGGGCCAACACGGA-CTGA
* * *
17784777 CCCAACACCAACATGCTTGTGTGGGCCCACACGGACTGA
1 CCCAACACCTACATGCTCGTGTGGGCCAACACGGACTGA
*
17784816 CCCAACACTTACATGCTCGTGTGG
1 CCCAACACCTACATGCTCGTGTGG
17784840 TATGTCCGTG
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
39 52 0.96
40 2 0.04
ACGTcount: A:0.25, C:0.38, G:0.21, T:0.17
Consensus pattern (39 bp):
CCCAACACCTACATGCTCGTGTGGGCCAACACGGACTGA
Found at i:17792075 original size:15 final size:15
Alignment explanation
Indices: 17792055--17792084 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17792045 TTCGTCGCGC
17792055 CCACGAATACCACGA
1 CCACGAATACCACGA
*
17792070 CCACGAATTCCACGA
1 CCACGAATACCACGA
17792085 GCGCTCATTG
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:0.37, C:0.40, G:0.13, T:0.10
Consensus pattern (15 bp):
CCACGAATACCACGA
Found at i:17794013 original size:17 final size:17
Alignment explanation
Indices: 17793991--17794035 Score: 90
Period size: 17 Copynumber: 2.6 Consensus size: 17
17793981 AAAGAATGTG
17793991 AATTTGGAAAAAGGCAA
1 AATTTGGAAAAAGGCAA
17794008 AATTTGGAAAAAGGCAA
1 AATTTGGAAAAAGGCAA
17794025 AATTTGGAAAA
1 AATTTGGAAAA
17794036 GAAAAGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.20
Consensus pattern (17 bp):
AATTTGGAAAAAGGCAA
Found at i:17795285 original size:16 final size:16
Alignment explanation
Indices: 17795264--17795294 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17795254 ATATGTACGC
*
17795264 TTGTGAAATTGTGAAG
1 TTGTGAAATTATGAAG
17795280 TTGTGAAATTATGAA
1 TTGTGAAATTATGAA
17795295 CATACATGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.39
Consensus pattern (16 bp):
TTGTGAAATTATGAAG
Found at i:17798417 original size:22 final size:22
Alignment explanation
Indices: 17798392--17798436 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
17798382 AGATACAAAA
17798392 GTAGAAAATATCAGATATAGAT
1 GTAGAAAATATCAGATATAGAT
* * *
17798414 GTAGGACATATTAGATATAGAT
1 GTAGAAAATATCAGATATAGAT
17798436 G
1 G
17798437 CAAACTCCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.04, G:0.22, T:0.29
Consensus pattern (22 bp):
GTAGAAAATATCAGATATAGAT
Found at i:17801569 original size:22 final size:22
Alignment explanation
Indices: 17801544--17801588 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
17801534 ATACAGAAAT
*
17801544 AGAAAATATCATATACAAATGC
1 AGAAAATATCAAATACAAATGC
* *
17801566 AGAACATATCAAATACAGATGC
1 AGAAAATATCAAATACAAATGC
17801588 A
1 A
17801589 AATTCCTACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.16, G:0.11, T:0.20
Consensus pattern (22 bp):
AGAAAATATCAAATACAAATGC
Found at i:17802317 original size:63 final size:62
Alignment explanation
Indices: 17802201--17802323 Score: 149
Period size: 63 Copynumber: 2.0 Consensus size: 62
17802191 TCCTAGGCCT
* * * *
17802201 GTGTGACCTTAAATCCAAACAATGAGTTACACGGCCTCGGCACATGCCCGTGTCTCTAGCTC
1 GTGTGACCTTAAATCCAAACAATAAGTTACACAGCCTCGGCACACGCCCGTGTCCCTAGCTC
* * * *
17802263 GTGTGACCTTAAATCCAAAACAGTAAGTTATACAG-CTTGGACGCACGCCCGTGTCCCTAGC
1 GTGTGACCTTAAATCC-AAACAATAAGTTACACAGCCTCGG-CACACGCCCGTGTCCCTAGC
17802324 CCGTATGCCT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
62 20 0.39
63 31 0.61
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (62 bp):
GTGTGACCTTAAATCCAAACAATAAGTTACACAGCCTCGGCACACGCCCGTGTCCCTAGCTC
Found at i:17802911 original size:17 final size:17
Alignment explanation
Indices: 17802841--17802913 Score: 51
Period size: 17 Copynumber: 4.1 Consensus size: 17
17802831 ATAAAAAATG
*
17802841 AAAGAAGAAA-TAAGAAA
1 AAAGAAGAAAGGAA-AAA
* *
17802858 TAAGAAGAAAAGGAAAACG
1 AAAGAAG-AAAGGAAAA-A
*
17802877 AAA-AATAAAGGAAGAAAA
1 AAAGAAGAAAGG-A-AAAA
17802895 AAAGAAGAAAGGAAAAA
1 AAAGAAGAAAGGAAAAA
17802912 AA
1 AA
17802914 CATTAAATAA
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
17 17 0.40
18 12 0.28
19 14 0.33
ACGTcount: A:0.74, C:0.01, G:0.21, T:0.04
Consensus pattern (17 bp):
AAAGAAGAAAGGAAAAA
Found at i:17806806 original size:16 final size:17
Alignment explanation
Indices: 17806785--17806816 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
17806775 AAATATGCAA
17806785 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
17806801 TCACATAACTTCATAT
1 TCACATAACTTCATAT
17806817 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:17807044 original size:43 final size:43
Alignment explanation
Indices: 17806977--17807147 Score: 145
Period size: 43 Copynumber: 4.0 Consensus size: 43
17806967 GACTCGTACA
* * * * *
17806977 ATGCCAAC-GTCCCAGACGTTGTCTTACATGTAATCACATATTG
1 ATGCC-ACTGTCCCAGACATGGTCTTACATGAAAACACATATCG
* * * *
17807020 ATGCCACTGTCCCAGACAAGGTCTTACA-CAAATCAAATA-CG
1 ATGCCACTGTCCCAGACATGGTCTTACATGAAAACACATATCG
* * * * *
17807061 ATGCTAATGTCCTAGACATGGTCTTACACGTAAACACA-AGTCG
1 ATGCCACTGTCCCAGACATGGTCTTACATGAAAACACATA-TCG
*
17807104 ATGCCAAC-ATCCCAGACATGGTCTTACATGAAAACACATATCG
1 ATGCC-ACTGTCCCAGACATGGTCTTACATGAAAACACATATCG
17807147 A
1 A
17807148 AATCCTATGT
Statistics
Matches: 101, Mismatches: 21, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
41 26 0.26
42 15 0.15
43 58 0.57
44 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACATGGTCTTACATGAAAACACATATCG
Found at i:17812831 original size:7 final size:7
Alignment explanation
Indices: 17812819--17812844 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
17812809 TAAAAGAATT
17812819 GTCCAAA
1 GTCCAAA
17812826 GTCCAAA
1 GTCCAAA
17812833 GTCCAAA
1 GTCCAAA
17812840 GTCCA
1 GTCCA
17812845 CAAACAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.31, G:0.15, T:0.15
Consensus pattern (7 bp):
GTCCAAA
Found at i:17813262 original size:47 final size:47
Alignment explanation
Indices: 17813208--17813358 Score: 207
Period size: 47 Copynumber: 3.2 Consensus size: 47
17813198 GTCACAGTAA
*
17813208 TGCAGATAAACTT-CCAGTTAATAATATTGTGGACAAGCCACCACTTT
1 TGCAGATAAA-TTGCCACTTAATAATATTGTGGACAAGCCACCACTTT
* * *
17813255 TGCAGAT-AATTCGCCACTTAATAAAATTATAGACAAGCCACCACTTT
1 TGCAGATAAATT-GCCACTTAATAATATTGTGGACAAGCCACCACTTT
* * *
17813302 TGTAGATAAATTGCCACTTTATAATATTGTGGACAAGCCACCATTTT
1 TGCAGATAAATTGCCACTTAATAATATTGTGGACAAGCCACCACTTT
17813349 TGCAGATAAA
1 TGCAGATAAA
17813359 CTATCACTTT
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
45 2 0.02
46 2 0.02
47 82 0.91
48 4 0.04
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (47 bp):
TGCAGATAAATTGCCACTTAATAATATTGTGGACAAGCCACCACTTT
Found at i:17813439 original size:20 final size:20
Alignment explanation
Indices: 17813414--17813452 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17813404 TATGGCCACT
*
17813414 AAAATCACTTTTTAACTTTA
1 AAAATCAATTTTTAACTTTA
*
17813434 AAAATCAATTTTTCACTTT
1 AAAATCAATTTTTAACTTT
17813453 GGCATGTGAG
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:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (20 bp):
AAAATCAATTTTTAACTTTA
Found at i:17817543 original size:3 final size:3
Alignment explanation
Indices: 17817535--17817575 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
17817525 GTTTGATATA
17817535 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
17817576 TTTGGTTGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:17827019 original size:19 final size:19
Alignment explanation
Indices: 17826995--17827037 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
17826985 GTGGGGTGGG
*
17826995 AATATACTT-TTTTAATATT
1 AATATAATTATTTTAA-ATT
*
17827014 AATATAATTATTTTTAATT
1 AATATAATTATTTTAAATT
17827033 AATAT
1 AATAT
17827038 TAATATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
AATATAATTATTTTAAATT
Found at i:17827044 original size:31 final size:33
Alignment explanation
Indices: 17827006--17827067 Score: 101
Period size: 31 Copynumber: 1.9 Consensus size: 33
17826996 ATATACTTTT
17827006 TTAATATTAATATAA-TTATT-TTTAATTAATA
1 TTAATATTAATATAATTTATTATTTAATTAATA
*
17827037 TTAATATTAATATAATTTTTTATTTAATTAA
1 TTAATATTAATATAATTTATTATTTAATTAA
17827068 ATTTTAATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 15 0.54
32 4 0.14
33 9 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
TTAATATTAATATAATTTATTATTTAATTAATA
Found at i:17827074 original size:28 final size:31
Alignment explanation
Indices: 17827008--17827075 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
17826998 ATACTTTTTT
*
17827008 AATATTAATATAATTATTTTTAATTAATATT
1 AATATTAATATAATTATTTTTAATTAATATA
*
17827039 AATATTAATATAA-T-TTTTTATTTAAT-TA
1 AATATTAATATAATTATTTTTAATTAATATA
*
17827067 AATTTTAAT
1 AATATTAAT
17827076 GAAATGATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 9 0.26
29 11 0.32
30 1 0.03
31 13 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
AATATTAATATAATTATTTTTAATTAATATA
Found at i:17827293 original size:16 final size:15
Alignment explanation
Indices: 17827272--17827303 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
17827262 TTTAGGATAA
17827272 TAATTTAGAGTTAATT
1 TAATTTAGA-TTAATT
17827288 TAATTTAGATTAATT
1 TAATTTAGATTAATT
17827303 T
1 T
17827304 TTACTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (15 bp):
TAATTTAGATTAATT
Found at i:17827502 original size:14 final size:15
Alignment explanation
Indices: 17827474--17827549 Score: 70
Period size: 14 Copynumber: 5.0 Consensus size: 15
17827464 GTTTGGCAGT
17827474 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
17827488 AAAATGATTTT-TGG
1 AAAATGATTTTCTGG
17827502 AAAATGATTTATATTTCTGG
1 AAAATG----AT-TTTCTGG
*
17827522 AAAATGATTTACT-G
1 AAAATGATTTTCTGG
17827536 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
17827550 TATTTGGATG
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
13 6 0.12
14 21 0.40
15 9 0.17
16 2 0.04
18 2 0.04
19 3 0.06
20 9 0.17
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:17827522 original size:20 final size:20
Alignment explanation
Indices: 17827494--17827532 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
17827484 CTGGAAAATG
*
17827494 ATTTTTGGAAAATGATTTAT
1 ATTTCTGGAAAATGATTTAT
17827514 ATTTCTGGAAAATGATTTA
1 ATTTCTGGAAAATGATTTA
17827533 CTGAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.46
Consensus pattern (20 bp):
ATTTCTGGAAAATGATTTAT
Found at i:17827539 original size:34 final size:33
Alignment explanation
Indices: 17827481--17827544 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
17827471 AGTAAAATAT
*
17827481 TTTCTGGAAAATGATTTTTGGAAAATGATTTATA
1 TTTCTGGAAAATGATTTCTGGAAAAT-ATTTATA
17827515 TTTCTGGAAAATGATTTACT-GAAAATATTT
1 TTTCTGGAAAATGATTT-CTGGAAAATATTT
17827545 TCTGGTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 4 0.14
34 23 0.82
35 1 0.04
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.44
Consensus pattern (33 bp):
TTTCTGGAAAATGATTTCTGGAAAATATTTATA
Found at i:17827610 original size:32 final size:32
Alignment explanation
Indices: 17827525--17827611 Score: 106
Period size: 33 Copynumber: 2.7 Consensus size: 32
17827515 TTTCTGGAAA
17827525 ATGATTTACTGAAAATATTTTCTGGTATTTGG
1 ATGATTTACTGAAAATATTTTCTGGTATTTGG
* * *
17827557 ATGAATTT-GTGTAAAATATTTTCTGTTGTTTGG
1 ATG-ATTTACTG-AAAATATTTTCTGGTATTTGG
17827590 CA-GATTTACTGAAAATATTTTC
1 -ATGATTTACTGAAAATATTTTC
17827612 CGAAAAAGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
32 20 0.43
33 26 0.55
34 1 0.02
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.47
Consensus pattern (32 bp):
ATGATTTACTGAAAATATTTTCTGGTATTTGG
Found at i:17830139 original size:13 final size:13
Alignment explanation
Indices: 17830121--17830146 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17830111 CCATTATTCA
17830121 TATATCTCTCACT
1 TATATCTCTCACT
17830134 TATATCTCTCACT
1 TATATCTCTCACT
17830147 CCTAACCTGA
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:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (13 bp):
TATATCTCTCACT
Found at i:17831000 original size:22 final size:22
Alignment explanation
Indices: 17830953--17831007 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
17830943 GAATTCTTTT
*
17830953 TAAATTTATTATAATTTAATTG
1 TAAATTTATTATAATTTAATTC
*
17830975 TAAATTTATTCTAATTTACA-TC
1 TAAATTTATTATAATTTA-ATTC
*
17830997 TAAATATATTA
1 TAAATTTATTA
17831008 AATGTATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (22 bp):
TAAATTTATTATAATTTAATTC
Found at i:17834819 original size:69 final size:69
Alignment explanation
Indices: 17834741--17835035 Score: 413
Period size: 69 Copynumber: 4.3 Consensus size: 69
17834731 ATTTCATCCT
*
17834741 TTTATATTTGTTTTATCTATTTATTTATTTATTATTCTTTTACTTTTTAAATACCTAAACTTAAT
1 TTTATATTTGTTTTATCTATTTATTTATTTATTATTCTTTTACTTTTTAAATACCTAAATTTAAT
*
17834806 ATGA
66 ATTA
17834810 TTTATATTTGTTTTATCTATTTATTTATTTATTATTCTTTTACTTTTTAAATACCTAAATTTAAT
1 TTTATATTTGTTTTATCTATTTATTTATTTATTATTCTTTTACTTTTTAAATACCTAAATTTAAT
17834875 ATTA
66 ATTA
* * * *
17834879 TTTATATTTGTTATATCTATTTATTTATTTTTTCATATTATTTTACTTTTTAAATACTTAAATTT
1 TTTATATTTGTTTTATCTATTTATTTA-TTTAT--TATTCTTTTACTTTTTAAATACCTAAATTT
17834944 -A-A-TA
63 AATATTA
* * * *
17834948 -TTATATTTATTTTATCAATTTATTTATTTATTATTCTTTTACTTCTTAAATACTTAAATTTAAT
1 TTTATATTTGTTTTATCTATTTATTTATTTATTATTCTTTTACTTTTTAAATACCTAAATTTAAT
17835012 ATTA
66 ATTA
* *
17835016 TGTATA--TATTTTATCTATTT
1 TTTATATTTGTTTTATCTATTT
17835036 TTACTTTTTA
Statistics
Matches: 205, Mismatches: 14, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
65 28 0.14
66 1 0.00
67 18 0.09
68 25 0.12
69 99 0.48
70 5 0.02
71 1 0.00
72 28 0.14
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (69 bp):
TTTATATTTGTTTTATCTATTTATTTATTTATTATTCTTTTACTTTTTAAATACCTAAATTTAAT
ATTA
Found at i:17834959 original size:59 final size:63
Alignment explanation
Indices: 17834889--17835016 Score: 167
Period size: 65 Copynumber: 2.1 Consensus size: 63
17834879 TTTATATTTG
*
17834889 TTATATCTA-TT-T-ATTTATTT-TTTCA-TATTATTTTACTTTTTAAATACTTAAATTTAATA
1 TTATATCTATTTATAATTTATTTATTT-ATTATTATTTTACTTCTTAAATACTTAAATTTAATA
* *
17834948 TTATATTTATTTTATCAATTTATTTATTTATTATTCTTTTACTTCTTAAATACTTAAATTTAATA
1 TTATATCTA-TTTAT-AATTTATTTATTTATTATTATTTTACTTCTTAAATACTTAAATTTAATA
17835013 TTAT
1 TTAT
17835017 GTATATATTT
Statistics
Matches: 59, Mismatches: 3, Indels: 8
0.84 0.04 0.11
Matches are distributed among these distances:
59 8 0.14
61 2 0.03
62 1 0.02
64 9 0.15
65 39 0.66
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (63 bp):
TTATATCTATTTATAATTTATTTATTTATTATTATTTTACTTCTTAAATACTTAAATTTAATA
Found at i:17834985 original size:137 final size:137
Alignment explanation
Indices: 17834741--17835035 Score: 420
Period size: 137 Copynumber: 2.2 Consensus size: 137
17834731 ATTTCATCCT
*
17834741 TTTATATTTGTTTTATCTATTTATTTATTTATTATTCTTTTACTTTTTAAATACCTAAACTTAAT
1 TTTATATTTG-TTTATCTATTTATTTATTTATTATTATTTTACTTTTTAAATACCTAAACTTAAT
* * *
17834806 ATGATTTATATTTGTTTTATCTATTTATTTATTTATTATTCTTTTACTTTTTAAATACCTAAATT
65 ATGATTTATATTTATTTTATCAATTTATTTATTTATTATTCTTTTACTTCTTAAATACCTAAATT
17834871 TAATATTA
130 TAATATTA
* *
17834879 TTTATATTTGTTATATCTATTTATTTATTTTTTCATATTATTTTACTTTTTAAATACTTAAA-TT
1 TTTATATTTGTT-TATCTATTTATTTA-TTTAT--TATTATTTTACTTTTTAAATACCTAAACTT
* *
17834943 TA-AT-A-TTATATTTATTTTATCAATTTATTTATTTATTATTCTTTTACTTCTTAAATACTTAA
62 AATATGATTTATATTTATTTTATCAATTTATTTATTTATTATTCTTTTACTTCTTAAATACCTAA
17835005 ATTTAATATTA
127 ATTTAATATTA
* *
17835016 TGTATATAT-TTTATCTATTT
1 TTTATATTTGTTTATCTATTT
17835036 TTACTTTTTA
Statistics
Matches: 143, Mismatches: 10, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
135 9 0.06
136 2 0.01
137 73 0.51
138 25 0.17
139 6 0.04
140 3 0.02
141 25 0.17
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (137 bp):
TTTATATTTGTTTATCTATTTATTTATTTATTATTATTTTACTTTTTAAATACCTAAACTTAATA
TGATTTATATTTATTTTATCAATTTATTTATTTATTATTCTTTTACTTCTTAAATACCTAAATTT
AATATTA
Found at i:17838711 original size:19 final size:20
Alignment explanation
Indices: 17838672--17838711 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
17838662 CAATGTCGTA
*
17838672 TATGTAAAATGTATCCGTTT
1 TATGTAAAAAGTATCCGTTT
*
17838692 TATGTAAAAAG-ATTCGTTT
1 TATGTAAAAAGTATCCGTTT
17838711 T
1 T
17838712 CTAGTAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (20 bp):
TATGTAAAAAGTATCCGTTT
Found at i:17846434 original size:20 final size:19
Alignment explanation
Indices: 17846401--17846474 Score: 53
Period size: 20 Copynumber: 3.8 Consensus size: 19
17846391 ATTCCAAAAA
**
17846401 TAATATTATTTTAATAGATT
1 TAATATTAAATTAATA-ATT
17846421 TAATATTAAATT-A-AATT
1 TAATATTAAATTAATAATT
*
17846438 TAATAATTATATTAATAAATT
1 TAAT-ATTAAATTAAT-AATT
** *
17846459 TTTTATTAATTTAATA
1 TAATATTAAATTAATA
17846475 TTAAAGTGAT
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
17 7 0.16
18 8 0.19
19 3 0.07
20 19 0.44
21 6 0.14
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (19 bp):
TAATATTAAATTAATAATT
Found at i:17846438 original size:17 final size:18
Alignment explanation
Indices: 17846418--17846452 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17846408 ATTTTAATAG
17846418 ATTTAAT-ATTAAATTAA
1 ATTTAATAATTAAATTAA
*
17846435 ATTTAATAATTATATTAA
1 ATTTAATAATTAAATTAA
17846453 TAAATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTAATAATTAAATTAA
Found at i:17846439 original size:26 final size:23
Alignment explanation
Indices: 17846405--17846479 Score: 69
Period size: 26 Copynumber: 3.0 Consensus size: 23
17846395 CAAAAATAAT
17846405 ATTATTTTAATAGATTTAATATTAA
1 ATTA-TTTAATA-ATTTAATATTAA
* *
17846430 ATTAAATTTAATAATTATATTAATAA
1 ATT--ATTTAATAATT-TAATATTAA
* *
17846456 ATTTTTTATTAATTTAATATTAA
1 ATTATTTAATAATTTAATATTAA
17846479 A
1 A
17846480 GTGATTATCT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
23 8 0.20
24 9 0.22
25 6 0.15
26 17 0.41
27 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (23 bp):
ATTATTTAATAATTTAATATTAA
Found at i:17848085 original size:15 final size:15
Alignment explanation
Indices: 17848067--17848106 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
17848057 TTAATTTTCA
17848067 TTTTAATTATTTATT
1 TTTTAATTATTTATT
*
17848082 TTTTAAATATTTATT
1 TTTTAATTATTTATT
17848097 TTTT-ATTATT
1 TTTTAATTATT
17848107 GAATTTCTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTAATTATTTATT
Found at i:17849259 original size:3 final size:3
Alignment explanation
Indices: 17849251--17849312 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
17849241 GGATGTTAAC
*
17849251 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT AAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
17849299 GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GA
17849313 GCACCCTCTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:17853577 original size:5 final size:5
Alignment explanation
Indices: 17853569--17853594 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
17853559 GAGACGAAAT
17853569 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
17853595 ATATTTATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:17854108 original size:20 final size:20
Alignment explanation
Indices: 17854074--17854123 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
17854064 AGGTAAAGGT
17854074 GAAAAGTAAAAG-TTTAGGAG
1 GAAAA-TAAAAGTTTTAGGAG
* *
17854094 GAAAATAAAAGGTTTTGGGGG
1 GAAAATAAAA-GTTTTAGGAG
17854115 GAAAATAAA
1 GAAAATAAA
17854124 TGGGGGAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 5 0.19
20 6 0.23
21 15 0.58
ACGTcount: A:0.50, C:0.00, G:0.30, T:0.20
Consensus pattern (20 bp):
GAAAATAAAAGTTTTAGGAG
Found at i:17855427 original size:15 final size:16
Alignment explanation
Indices: 17855399--17855428 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17855389 GAAAAAAAAT
17855399 TTAAATTCTATTTTCC
1 TTAAATTCTATTTTCC
17855415 TTAAATT-TATTTTC
1 TTAAATTCTATTTTC
17855429 TGTTGTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.13, G:0.00, T:0.60
Consensus pattern (16 bp):
TTAAATTCTATTTTCC
Found at i:17856151 original size:21 final size:21
Alignment explanation
Indices: 17856125--17856165 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
17856115 CTAAAAGGGT
17856125 TCAGTTGGACAACTATTTTCC
1 TCAGTTGGACAACTATTTTCC
17856146 TCAGTTGGACAACTATTTTC
1 TCAGTTGGACAACTATTTTC
17856166 TATCCATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (21 bp):
TCAGTTGGACAACTATTTTCC
Found at i:17861399 original size:29 final size:30
Alignment explanation
Indices: 17861378--17861440 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
17861368 TCATGTGTAC
17861378 AATTACAC-CAAATCAAAATTCATGTATCA
1 AATTACACACAAATCAAAATTCATGTATCA
* *
17861407 AATTACACATTAAATCAAAATTCATATAT-A
1 AATTACACA-CAAATCAAAATTCATGTATCA
17861437 AATT
1 AATT
17861441 TAATATTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 8 0.27
30 5 0.17
31 17 0.57
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.32
Consensus pattern (30 bp):
AATTACACACAAATCAAAATTCATGTATCA
Found at i:17864089 original size:2 final size:2
Alignment explanation
Indices: 17864082--17864119 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
17864072 AACAAAAACC
17864082 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
17864120 ATGAAAAACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17870399 original size:22 final size:22
Alignment explanation
Indices: 17870365--17870633 Score: 322
Period size: 22 Copynumber: 12.2 Consensus size: 22
17870355 AAGTAAAAAT
17870365 TGTTGATTAAATGTTGTCCAAA
1 TGTTGATTAAATGTTGTCCAAA
* * * *
17870387 TATGGATTGAATGTTGTCCAAT
1 TGTTGATTAAATGTTGTCCAAA
17870409 TGTTGATTAAATGTTGTCCAAA
1 TGTTGATTAAATGTTGTCCAAA
* *
17870431 TGTTGATTTAATGTTGTCCAAT
1 TGTTGATTAAATGTTGTCCAAA
17870453 TGTTGATTAAATGTTGTCCAAA
1 TGTTGATTAAATGTTGTCCAAA
* * * *
17870475 TATTGATTGAATGATGTCCAAT
1 TGTTGATTAAATGTTGTCCAAA
**
17870497 TGTTGATTAAATACTGTCCAAA
1 TGTTGATTAAATGTTGTCCAAA
* * *
17870519 TGTTGATTTAATGCTGTCCAAT
1 TGTTGATTAAATGTTGTCCAAA
*
17870541 TGTTGATTAAATGTTGTCTAAA
1 TGTTGATTAAATGTTGTCCAAA
*** * *
17870563 TGTTGATTGGTTGATGTCCAAT
1 TGTTGATTAAATGTTGTCCAAA
17870585 TGTTGATTAAATGTTGTCCAAA
1 TGTTGATTAAATGTTGTCCAAA
* **
17870607 TGTTAATTAAATGTTGTCTGAA
1 TGTTGATTAAATGTTGTCCAAA
17870629 TGTTG
1 TGTTG
17870634 GATAATTGTT
Statistics
Matches: 204, Mismatches: 43, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 204 1.00
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.43
Consensus pattern (22 bp):
TGTTGATTAAATGTTGTCCAAA
Found at i:17870633 original size:44 final size:44
Alignment explanation
Indices: 17870362--17870624 Score: 391
Period size: 44 Copynumber: 6.0 Consensus size: 44
17870352 TTGAAGTAAA
* *
17870362 AATTGTTGATTAAATGTTGTCCAAATATGGATTGAATGTTGTCC
1 AATTGTTGATTAAATGTTGTCCAAATGTTGATTGAATGTTGTCC
*
17870406 AATTGTTGATTAAATGTTGTCCAAATGTTGATTTAATGTTGTCC
1 AATTGTTGATTAAATGTTGTCCAAATGTTGATTGAATGTTGTCC
* *
17870450 AATTGTTGATTAAATGTTGTCCAAATATTGATTGAATGATGTCC
1 AATTGTTGATTAAATGTTGTCCAAATGTTGATTGAATGTTGTCC
** * *
17870494 AATTGTTGATTAAATACTGTCCAAATGTTGATTTAATGCTGTCC
1 AATTGTTGATTAAATGTTGTCCAAATGTTGATTGAATGTTGTCC
* ** *
17870538 AATTGTTGATTAAATGTTGTCTAAATGTTGATTGGTTGATGTCC
1 AATTGTTGATTAAATGTTGTCCAAATGTTGATTGAATGTTGTCC
* *
17870582 AATTGTTGATTAAATGTTGTCCAAATGTTAATTAAATGTTGTC
1 AATTGTTGATTAAATGTTGTCCAAATGTTGATTGAATGTTGTC
17870625 TGAATGTTGG
Statistics
Matches: 195, Mismatches: 24, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 195 1.00
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.43
Consensus pattern (44 bp):
AATTGTTGATTAAATGTTGTCCAAATGTTGATTGAATGTTGTCC
Found at i:17872599 original size:160 final size:161
Alignment explanation
Indices: 17872417--17872737 Score: 536
Period size: 160 Copynumber: 2.0 Consensus size: 161
17872407 TTTTAATATA
* *
17872417 CACGGTCATCCATAAGAATTTCCAATGATGAGTTAAGAATTTCAGATAATTATAAAAATCAAGAA
1 CACGGTCATCCATAAGAATTTCCAACGATGAGTTAAGAATTTCACATAATTATAAAAATCAAGAA
* *
17872482 GTTTAATAGTGTTATGTAAAAATTCATC-GTTAAAGGTCAAGATAAAAACTTTTGTTGCAAGAGA
66 GTTTAATAGTATTATGTAAAAATTCATCAGTTAAAGGTCAAGATAAAAAATTTTGTTGCAAGAGA
* ** *
17872546 AAATATTTAAAATGGTTTAAGAAAACTTATT
131 AAATATGTAAAATACTTTAAAAAAACTTATT
17872577 CACGGTCATCCATAAGAATTTCCAACGATGAGTTAAGAATTTCACATAATTATAAAAATCAAGAA
1 CACGGTCATCCATAAGAATTTCCAACGATGAGTTAAGAATTTCACATAATTATAAAAATCAAGAA
** *
17872642 GTTTAATCTTATTATGTAAAAATTCATCATTTAAAGGTCAAGATAAAAAATTTTGTTGCAAGAGA
66 GTTTAATAGTATTATGTAAAAATTCATCAGTTAAAGGTCAAGATAAAAAATTTTGTTGCAAGAGA
17872707 AAATATGTAAAATACTTTAAAAAAACTTATT
131 AAATATGTAAAATACTTTAAAAAAACTTATT
17872738 TAATGCAAAA
Statistics
Matches: 149, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
160 88 0.59
161 61 0.41
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.32
Consensus pattern (161 bp):
CACGGTCATCCATAAGAATTTCCAACGATGAGTTAAGAATTTCACATAATTATAAAAATCAAGAA
GTTTAATAGTATTATGTAAAAATTCATCAGTTAAAGGTCAAGATAAAAAATTTTGTTGCAAGAGA
AAATATGTAAAATACTTTAAAAAAACTTATT
Found at i:17873109 original size:8 final size:7
Alignment explanation
Indices: 17873087--17873118 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
17873077 AGAAACACCA
17873087 CTAAACC
1 CTAAACC
17873094 CTAAACC
1 CTAAACC
17873101 CTAAAACC
1 CT-AAACC
17873109 CTAAACC
1 CTAAACC
17873116 CTA
1 CTA
17873119 GGGTAAGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.16
Consensus pattern (7 bp):
CTAAACC
Found at i:17873109 original size:15 final size:15
Alignment explanation
Indices: 17873089--17873118 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
17873079 AAACACCACT
17873089 AAACCCTAAACCCTA
1 AAACCCTAAACCCTA
17873104 AAACCCTAAACCCTA
1 AAACCCTAAACCCTA
17873119 GGGTAAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.40, G:0.00, T:0.13
Consensus pattern (15 bp):
AAACCCTAAACCCTA
Found at i:17874727 original size:13 final size:14
Alignment explanation
Indices: 17874686--17874727 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
17874676 AATCCAAGTC
* *
17874686 AAATAAAACAATTA
1 AAATAAAATAACTA
17874700 AAAT-AAATAACTA
1 AAATAAAATAACTA
17874713 AAATAAAATAA-TA
1 AAATAAAATAACTA
17874726 AA
1 AA
17874728 TCAAATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAAATAACTA
Found at i:17876928 original size:62 final size:59
Alignment explanation
Indices: 17876824--17877024 Score: 156
Period size: 62 Copynumber: 3.2 Consensus size: 59
17876814 ATCACTTTAA
* * * *
17876824 TATTAAATTAATATAATACTTTTCAAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAATTAATAGAATACTTTTCAAGATAAACATTAAATTAAATTAAATATTAAATCT
17876883 TATTAAATTAATAGAATA-TTAATCTACAAGATAAACATTAAATTAAATTAAATATTAAGATAAT
1 TATTAAATTAATAGAATACTT--T-T-CAAGATAAACATTAAATTAAATTAAATATT---A-AAT
17876947 CACTTT
58 --C--T
* * * ** *
17876953 AATATTAAATTAATAAAATAATATT-AAGATAATTATTAAATTAAATTTAATATTAAATC-
1 --TATTAAATTAATAGAATACTTTTCAAGATAAACATTAAATTAAATTAAATATTAAATCT
*
17877012 TATTAAAATAATA
1 TATTAAATTAATA
17877025 TTATATTTGG
Statistics
Matches: 117, Mismatches: 10, Indels: 32
0.74 0.06 0.20
Matches are distributed among these distances:
57 12 0.10
58 2 0.02
59 17 0.15
60 1 0.01
61 1 0.01
62 28 0.24
64 3 0.03
65 2 0.02
66 3 0.03
68 27 0.23
70 2 0.02
71 1 0.01
72 17 0.15
73 1 0.01
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.40
Consensus pattern (59 bp):
TATTAAATTAATAGAATACTTTTCAAGATAAACATTAAATTAAATTAAATATTAAATCT
Found at i:17876965 original size:37 final size:35
Alignment explanation
Indices: 17876919--17877027 Score: 105
Period size: 37 Copynumber: 3.0 Consensus size: 35
17876909 CAAGATAAAC
17876919 ATTAAATTAA-ATTAAATATTAAGATAATCACTTTAA
1 ATTAAATTAATATTAAATATTAAGATAATCA--TTAA
** *
17876955 TATTAAATTAATAAAATAATATTAAGATAATTATTAA
1 -ATTAAATTAATATTA-AATATTAAGATAATCATTAA
*
17876992 ATTAAATTTAATATTAAATCTATTAAAATAAT-ATTA
1 ATTAAA-TTAATATTAAA--TATTAAGATAATCATTA
17877028 TATTTGGAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
36 8 0.13
37 25 0.41
38 13 0.21
39 15 0.25
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (35 bp):
ATTAAATTAATATTAAATATTAAGATAATCATTAA
Found at i:17876986 original size:23 final size:25
Alignment explanation
Indices: 17876924--17877027 Score: 83
Period size: 23 Copynumber: 4.2 Consensus size: 25
17876914 TAAACATTAA
*
17876924 ATTAA-ATTAAA-TATTAAGATAAT
1 ATTAAGATTAAATTATTAAAATAAT
* *
17876947 CACTTTAATATTAAATTAATAAAATAAT
1 -A--TTAAGATTAAATTATTAAAATAAT
*
17876975 ATTAAGA-T-AATTATTAAATTAA-
1 ATTAAGATTAAATTATTAAAATAAT
*
17876997 ATTTAATATTAAATCTATTAAAATAAT
1 A-TTAAGATTAAAT-TATTAAAATAAT
17877024 ATTA
1 ATTA
17877028 TATTTGGAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
22 1 0.02
23 17 0.27
24 3 0.05
25 8 0.12
26 17 0.27
27 8 0.12
28 10 0.16
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (25 bp):
ATTAAGATTAAATTATTAAAATAAT
Found at i:17878512 original size:14 final size:14
Alignment explanation
Indices: 17878495--17878525 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
17878485 AATATTTGCT
*
17878495 TATCACAATTTCGC
1 TATCACAATTTCAC
17878509 TATCACAATTTCAC
1 TATCACAATTTCAC
17878523 TAT
1 TAT
17878526 GCATGCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.39
Consensus pattern (14 bp):
TATCACAATTTCAC
Found at i:17879109 original size:22 final size:22
Alignment explanation
Indices: 17879084--17879128 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
17879074 AATAAAGAAA
*
17879084 TATAATTCTATAAGGATTTTAC
1 TATAATTCTATAAGAATTTTAC
*
17879106 TATAATTCTATGAGAATTTTAC
1 TATAATTCTATAAGAATTTTAC
17879128 T
1 T
17879129 TTTATTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.47
Consensus pattern (22 bp):
TATAATTCTATAAGAATTTTAC
Found at i:17883746 original size:5 final size:5
Alignment explanation
Indices: 17883736--17883925 Score: 308
Period size: 5 Copynumber: 38.0 Consensus size: 5
17883726 AAATGTTATA
17883736 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* * * * * *
17883786 ATAAT ATAAT ATAAT ATAAT ACAAT ACAAT ACAAT ACAAT ACAAT ACAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* *
17883836 ACAAT ACAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
17883886 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
17883926 GTGATAATGA
Statistics
Matches: 183, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
5 183 1.00
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (5 bp):
ATAAT
Found at i:17890806 original size:175 final size:175
Alignment explanation
Indices: 17890515--17890864 Score: 673
Period size: 175 Copynumber: 2.0 Consensus size: 175
17890505 CCTCTTCCAT
17890515 AATCCAGCGGTGGTCTCCTCACTCATCACATCCTGCAAAATTTTGTTAGACAAATGCAGATGTAA
1 AATCCAGCGGTGGTCTCCTCACTCATCACATCCTGCAAAATTTTGTTAGACAAATGCAGATGTAA
*
17890580 CTATGTTAATGCCTTTCGATCCTTGCGCTTCTTCTCTTCCTCTGTCAATGTTGAAGGCATCTTAT
66 CTATGTTAACGCCTTTCGATCCTTGCGCTTCTTCTCTTCCTCTGTCAATGTTGAAGGCATCTTAT
17890645 CTACCCCTAACATGGCTTCCTCTAAGTCCATCTGTGCAAGAACTA
131 CTACCCCTAACATGGCTTCCTCTAAGTCCATCTGTGCAAGAACTA
17890690 AATCCAGCGGTGGTCTCCTCACTCATCACATCCTGCAAAATTTTGTTAGACAAATGCAGATGTAA
1 AATCCAGCGGTGGTCTCCTCACTCATCACATCCTGCAAAATTTTGTTAGACAAATGCAGATGTAA
*
17890755 CTGTGTTAACGCCTTTCGATCCTTGCGCTTCTTCTCTTCCTCTGTCAATGTTGAAGGCATCTTAT
66 CTATGTTAACGCCTTTCGATCCTTGCGCTTCTTCTCTTCCTCTGTCAATGTTGAAGGCATCTTAT
*
17890820 CTACCCCTAACATGGCTTCCTCTAAGTCCATCTGTGTAAGAACTA
131 CTACCCCTAACATGGCTTCCTCTAAGTCCATCTGTGCAAGAACTA
17890865 CATGCATCTT
Statistics
Matches: 172, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
175 172 1.00
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (175 bp):
AATCCAGCGGTGGTCTCCTCACTCATCACATCCTGCAAAATTTTGTTAGACAAATGCAGATGTAA
CTATGTTAACGCCTTTCGATCCTTGCGCTTCTTCTCTTCCTCTGTCAATGTTGAAGGCATCTTAT
CTACCCCTAACATGGCTTCCTCTAAGTCCATCTGTGCAAGAACTA
Found at i:17892954 original size:44 final size:44
Alignment explanation
Indices: 17892904--17892992 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
17892894 ACTTTTGAAC
17892904 AGACACAATGATACTTCATGAATTATGATGATATCAATAAAATG
1 AGACACAATGATACTTCATGAATTATGATGATATCAATAAAATG
17892948 AGACACAATGATACTTCATGAATTATGATGATATCAATAAAATG
1 AGACACAATGATACTTCATGAATTATGATGATATCAATAAAATG
17892992 A
1 A
17892993 TTATATAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.29
Consensus pattern (44 bp):
AGACACAATGATACTTCATGAATTATGATGATATCAATAAAATG
Found at i:17895319 original size:15 final size:15
Alignment explanation
Indices: 17895301--17895331 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17895291 GAAGAAGAGG
*
17895301 AGAAGGAGGAGAAAA
1 AGAAGGAGAAGAAAA
17895316 AGAAGGAGAAGAAAA
1 AGAAGGAGAAGAAAA
17895331 A
1 A
17895332 AAATAGAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
AGAAGGAGAAGAAAA
Found at i:17896408 original size:21 final size:21
Alignment explanation
Indices: 17896383--17896436 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
17896373 ATCTTTTTGG
*
17896383 TGAGTTGGGGCAGATTGTTGA-
1 TGAGTTGGGGCAGATTG-TAAC
* *
17896404 TGAGTTTGGGCAGTTTGTAAC
1 TGAGTTGGGGCAGATTGTAAC
17896425 TGAGTTGGGGCA
1 TGAGTTGGGGCA
17896437 ACCACTTGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.19, C:0.07, G:0.41, T:0.33
Consensus pattern (21 bp):
TGAGTTGGGGCAGATTGTAAC
Found at i:17897240 original size:77 final size:77
Alignment explanation
Indices: 17897128--17897302 Score: 251
Period size: 77 Copynumber: 2.3 Consensus size: 77
17897118 AAAAAACAAT
* * * * *
17897128 CACTGCATGCATATTAAAAAATAGTCAATAGCATGTGACCATCCCCACCAAAAATCATACACAGA
1 CACTACATGCATATTAAAAAATAGTCAACAACATGTGACCAGCCCCACCAAAAATCATACACAAA
* * *
17897193 TAGATTAGAAAA
66 CAAATTAAAAAA
* *
17897205 CACTACATGCATATTAAAAAATAGTCAACAACATGTGACTAGCCCCACCAACAATCATACACAAA
1 CACTACATGCATATTAAAAAATAGTCAACAACATGTGACCAGCCCCACCAAAAATCATACACAAA
17897270 CAAATTAAAAAA
66 CAAATTAAAAAA
*
17897282 CACTACATGCATGTTAAAAAA
1 CACTACATGCATATTAAAAAA
17897303 CACTCACTAA
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
77 87 1.00
ACGTcount: A:0.48, C:0.23, G:0.09, T:0.20
Consensus pattern (77 bp):
CACTACATGCATATTAAAAAATAGTCAACAACATGTGACCAGCCCCACCAAAAATCATACACAAA
CAAATTAAAAAA
Found at i:17901687 original size:26 final size:26
Alignment explanation
Indices: 17901657--17901709 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
17901647 CCATAAAGGT
17901657 AGACAAAAACCAAACCATTTAATACA
1 AGACAAAAACCAAACCATTTAATACA
*
17901683 AGACAATAACCAAACCATTTAATACA
1 AGACAAAAACCAAACCATTTAATACA
17901709 A
1 A
17901710 CATAGGCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.57, C:0.23, G:0.04, T:0.17
Consensus pattern (26 bp):
AGACAAAAACCAAACCATTTAATACA
Found at i:17901991 original size:48 final size:48
Alignment explanation
Indices: 17901922--17902055 Score: 207
Period size: 48 Copynumber: 2.8 Consensus size: 48
17901912 TAGGATACAA
17901922 ACAATGGAAGATACAAACAATAAACATCAGTTTGATAATGTCATTCAT
1 ACAATGGAAGATACAAACAATAAACATCAGTTTGATAATGTCATTCAT
** *
17901970 ACAATGGTTGATACAAACAATAAACATCAGTTTCATAATGTCATTCAT
1 ACAATGGAAGATACAAACAATAAACATCAGTTTGATAATGTCATTCAT
*
17902018 ACAAT-GACAGATACAAAACAATAAACACCAGTTTGATA
1 ACAATGGA-AGATAC-AAACAATAAACATCAGTTTGATA
17902056 CAAACAATAA
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
47 1 0.01
48 55 0.71
49 21 0.27
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.26
Consensus pattern (48 bp):
ACAATGGAAGATACAAACAATAAACATCAGTTTGATAATGTCATTCAT
Found at i:17902198 original size:35 final size:34
Alignment explanation
Indices: 17902149--17902215 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
17902139 CATTAATAAA
* *
17902149 AAAATAAAACCAAAATTAAAATAACCCTAAATCC
1 AAAATAAAACCAAAATCAAAATAACCCAAAATCC
* *
17902183 AAAATCAAAATCAAAATCGAAATAACCCAAAAT
1 AAAAT-AAAACCAAAATCAAAATAACCCAAAAT
17902216 AACCCTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 5 0.18
35 23 0.82
ACGTcount: A:0.63, C:0.19, G:0.01, T:0.16
Consensus pattern (34 bp):
AAAATAAAACCAAAATCAAAATAACCCAAAATCC
Found at i:17902451 original size:44 final size:41
Alignment explanation
Indices: 17902374--17902480 Score: 130
Period size: 44 Copynumber: 2.6 Consensus size: 41
17902364 GAAAAAGATC
* *
17902374 AATCGATTTCTAACCCTATACC-A-TGTTAATCGATTATTG
1 AATCGATTTCTAACCCTAAACCAACTGTTAATCGATTACTG
*
17902413 AATCGATATTCTAACCCTAAACCAACTTTGTTAATCGATTCCTG
1 AATCGAT-TTCTAACCCTAAACCAAC--TGTTAATCGATTACTG
*
17902457 AATCAATTTCTAACCC-AAACCAAC
1 AATCGATTTCTAACCCTAAACCAAC
17902481 CCAAATCACA
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
39 7 0.12
40 14 0.24
41 1 0.02
42 8 0.14
43 9 0.15
44 20 0.34
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33
Consensus pattern (41 bp):
AATCGATTTCTAACCCTAAACCAACTGTTAATCGATTACTG
Found at i:17903575 original size:10 final size:10
Alignment explanation
Indices: 17903553--17903603 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
17903543 ATATTTTTAA
17903553 TTATAAT-TT
1 TTATAATATT
*
17903562 TTATGATATT
1 TTATAATATT
17903572 TTATAATATT
1 TTATAATATT
*
17903582 TGA-AATATTT
1 TTATAATA-TT
17903592 TTATAA-ATT
1 TTATAATATT
17903601 TTA
1 TTA
17903604 ATTAGATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 15 0.43
10 18 0.51
11 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (10 bp):
TTATAATATT
Found at i:17903590 original size:43 final size:43
Alignment explanation
Indices: 17903543--17903647 Score: 114
Period size: 43 Copynumber: 2.5 Consensus size: 43
17903533 ATTATTTTTT
17903543 ATATTTTTAATTATAATTTTTA-T-GA-TATTTTATAATATTTGAA
1 ATATTTTT-ATTATAATTTTTATTAGATTATTTTA-AA-ATTTGAA
* *
17903586 ATATTTTTA-TA-AATTTTAATTAGATTATTTTAAAATTTTAA
1 ATATTTTTATTATAATTTTTATTAGATTATTTTAAAATTTGAA
17903627 ATATATTTTATT-TAATTTTTA
1 ATAT-TTTTATTATAATTTTTA
17903648 AAAAATAATA
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
40 7 0.13
41 13 0.25
42 10 0.19
43 23 0.43
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (43 bp):
ATATTTTTATTATAATTTTTATTAGATTATTTTAAAATTTGAA
Found at i:17903635 original size:19 final size:20
Alignment explanation
Indices: 17903567--17903637 Score: 74
Period size: 19 Copynumber: 3.5 Consensus size: 20
17903557 AATTTTTATG
*
17903567 ATATTTTATAATATTTGAAAT
1 ATATTTTATAA-ATTTTAAAT
*
17903588 AT-TTTTATAAATTTTAATTAG
1 ATATTTTATAAATTTTAA--AT
17903609 ATTATTTTA-AAATTTTAAAT
1 A-TATTTTATAAATTTTAAAT
17903629 ATATTTTAT
1 ATATTTTAT
17903638 TTAATTTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
19 13 0.31
20 10 0.24
21 4 0.10
22 10 0.24
23 5 0.12
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
ATATTTTATAAATTTTAAAT
Found at i:17907532 original size:28 final size:26
Alignment explanation
Indices: 17907476--17907532 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 26
17907466 TTTATATAAG
* *
17907476 TTTTTATAATTAAAACTATAATATAA
1 TTTTTATAATTAAAACTATAAAAAAA
17907502 TTTTTATAATT-AAACTTGTATAAAAAAA
1 TTTTTATAATTAAAAC---TATAAAAAAA
17907530 TTT
1 TTT
17907533 CTTAAAGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 4 0.15
26 11 0.42
28 11 0.42
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (26 bp):
TTTTTATAATTAAAACTATAAAAAAA
Found at i:17909516 original size:18 final size:16
Alignment explanation
Indices: 17909482--17909517 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
17909472 CAATATAATA
17909482 TATTTTTAATAACTTT
1 TATTTTTAATAACTTT
17909498 TATTTTATAATATACTTT
1 TATTTT-TAATA-ACTTT
17909516 TA
1 TA
17909518 AAAGCCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTTTAATAACTTT
Found at i:17913012 original size:275 final size:275
Alignment explanation
Indices: 17912521--17913070 Score: 1046
Period size: 275 Copynumber: 2.0 Consensus size: 275
17912511 AATCAACCTA
*
17912521 ACACGAATTAAATTCAAGCTAAATTGATTAAATTAATCATTCCAACAACATAAATATTCATAGAT
1 ACACGAATTAAATTCAAGCTAAATTGATTAAATTAACCATTCCAACAACATAAATATTCATAGAT
**
17912586 ATGTTCATTATAACAACAACAAAAATTAAAAAGATAGGGAATAAGAATCAAATCCAGTGTTTTTC
66 ATGTTCAGCATAACAACAACAAAAATTAAAAAGATAGGGAATAAGAATCAAATCCAGTGTTTTTC
*
17912651 CGTGGCTTGACTAGTTGCTCTGTTCTTCCTTCTCTGTTGTCCTCGTCGACAAAGGCTGCTAACAC
131 CGTGGCTTGACTAGTTGCTCTGTTCTTCCTTCTCCGTTGTCCTCGTCGACAAAGGCTGCTAACAC
*
17912716 TTAATTGTTTCTCCAAATAGATGATGAATTCCCCTTTCCCAATAGGAGAAATTGGCAAGACAGCA
196 TTAATTGTTTCTCCAAATAGATGATGAATTCCCCTTTCCCAATAGGAGAAATTGACAAGACAGCA
17912781 AGAGAATTTTGGAAT
261 AGAGAATTTTGGAAT
*
17912796 ACACGAATTAAATTCAAGCTAAATTGATTAAATTAACCATTCCAATAACATAAATATTCATAGAT
1 ACACGAATTAAATTCAAGCTAAATTGATTAAATTAACCATTCCAACAACATAAATATTCATAGAT
17912861 ATGTTCAGCATAACAACAACAAAAATTAAAAAGATAGGGAATAAGAATCAAATCCAGTGTTTTTC
66 ATGTTCAGCATAACAACAACAAAAATTAAAAAGATAGGGAATAAGAATCAAATCCAGTGTTTTTC
17912926 CGTGGCTTGACTAGTTGCTCTGTTCTTCCTTCTCCGTTGTCCTCGTCGACAAAGGCTGCTAACAC
131 CGTGGCTTGACTAGTTGCTCTGTTCTTCCTTCTCCGTTGTCCTCGTCGACAAAGGCTGCTAACAC
17912991 TTAATTGTTTCTCCAAATAGATGATGAATTCCCCTTTCCCAATAGGAGAAATTGACAAGACAGCA
196 TTAATTGTTTCTCCAAATAGATGATGAATTCCCCTTTCCCAATAGGAGAAATTGACAAGACAGCA
17913056 AGAGAATTTTGGAAT
261 AGAGAATTTTGGAAT
17913071 GGAAAAGAAT
Statistics
Matches: 269, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
275 269 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (275 bp):
ACACGAATTAAATTCAAGCTAAATTGATTAAATTAACCATTCCAACAACATAAATATTCATAGAT
ATGTTCAGCATAACAACAACAAAAATTAAAAAGATAGGGAATAAGAATCAAATCCAGTGTTTTTC
CGTGGCTTGACTAGTTGCTCTGTTCTTCCTTCTCCGTTGTCCTCGTCGACAAAGGCTGCTAACAC
TTAATTGTTTCTCCAAATAGATGATGAATTCCCCTTTCCCAATAGGAGAAATTGACAAGACAGCA
AGAGAATTTTGGAAT
Done.