Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 91 of 133
Found at i:17935137 original size:33 final size:33
Alignment explanation
Indices: 17935095--17935948 Score: 347
Period size: 33 Copynumber: 26.4 Consensus size: 33
17935085 TTATCCAAGT
* *
17935095 TTTAAGCCTAGTTTAGTTGACACCTAATGAAAA
1 TTTAAGCCTAGTTTAGCTGGCACCTAATGAAAA
* * *
17935128 TTTAAGCCTAGTCTAGCTAGCACCCAATGAAAA
1 TTTAAGCCTAGTTTAGCTGGCACCTAATGAAAA
* *
17935161 TTTAAGCCCAGTATAGCTGGCA-CTCAATCG-AAA
1 TTTAAGCCTAGTTTAGCTGGCACCT-AAT-GAAAA
* * * * * * **
17935194 TATGAGCCTAATTTAGTTAGCATC-AATGAAGT
1 TTTAAGCCTAGTTTAGCTGGCACCTAATGAAAA
* *
17935226 TTTAAGCCTAGTTTATCTAGCACC-AATGAAAA
1 TTTAAGCCTAGTTTAGCTGGCACCTAATGAAAA
* * * *
17935258 TTTAAGCCTAGCATTA-TTGCCACTCT-GTGAAAA
1 TTTAAGCCTAG-TTTAGCTGGCAC-CTAATGAAAA
* **
17935291 TTTAAGCCTAGTATAGCTGGCACCT-A-G--GT
1 TTTAAGCCTAGTTTAGCTGGCACCTAATGAAAA
* * * *
17935320 TTTAAGCCCACTTTAGCTGGCA-CTTATG---T
1 TTTAAGCCTAGTTTAGCTGGCACCTAATGAAAA
* * * *
17935349 TTTAAGCCCACTTTAGCTGGCACCCAATGAAGA
1 TTTAAGCCTAGTTTAGCTGGCACCTAATGAAAA
* * *
17935382 TTTAACCCTAGCTTAGCTAGCATCC-AATG-AAA
1 TTTAAGCCTAGTTTAGCTGGCA-CCTAATGAAAA
* * * * **
17935414 TTTAAGCCTAGATTATCAGACA-CTCAATGAAGT
1 TTTAAGCCTAGTTTAGCTGGCACCT-AATGAAAA
* **
17935447 TTTAAGCCTAGTTTAGTTGGCACCTAATGAAGT
1 TTTAAGCCTAGTTTAGCTGGCACCTAATGAAAA
* * **
17935480 TTTAAACCCAGTTTAGCTGGCA-CTCAATGAAGT
1 TTTAAGCCTAGTTTAGCTGGCACCT-AATGAAAA
* * * * *
17935513 TTTAAACCCAATTTAGCTGGCA-CTGATCAACAAA
1 TTTAAGCCTAGTTTAGCTGGCACCTAAT-GA-AAA
* ** * *
17935547 GTTTTAAGCCCAACTTAGCTGACACCCAATG-AAA
1 --TTTAAGCCTAGTTTAGCTGGCACCTAATGAAAA
* * *
17935581 TTTAAGCCCA-TTTGAACTGAC-CTCTAATGAAAA
1 TTTAAGCCTAGTTT-AGCTGGCAC-CTAATGAAAA
* * * *
17935614 TTTAAGCCTAATATAGTTGGCACC-AAT-AAAGT
1 TTTAAGCCTAGTTTAGCTGGCACCTAATGAAA-A
* ** *
17935646 TTTAAGCCCAGTTTATTTGGCATC-AATGAAAA
1 TTTAAGCCTAGTTTAGCTGGCACCTAATGAAAA
* ** * * * *
17935678 TTTAAGCCAAACTTAGTTGGCACCCAGTGAAAT
1 TTTAAGCCTAGTTTAGCTGGCACCTAATGAAAA
**
17935711 TTTAAGCCTAGTTTAGCTGGCACCT-A-G--GT
1 TTTAAGCCTAGTTTAGCTGGCACCTAATGAAAA
* * * * * *
17935740 TTTAAGCCAAGCTTAACTAGCACCCAATAAAAA
1 TTTAAGCCTAGTTTAGCTGGCACCTAATGAAAA
* ** * *
17935773 TTTAAACCTAGCATAGTTGGCACTTAATG-AAA
1 TTTAAGCCTAGTTTAGCTGGCACCTAATGAAAA
* * * * * *
17935805 TTTATA-CCAAGATTATCTAGCACTTAATGAAAT
1 TTTA-AGCCTAGTTTAGCTGGCACCTAATGAAAA
* *
17935838 TTTAAG-CTCAATTTAGCTGGCACCAAATG-AAA
1 TTTAAGCCT-AGTTTAGCTGGCACCTAATGAAAA
* * * *
17935870 TTTAAGCCTAGTTTCGTTGACATCC-AATTAAAA
1 TTTAAGCCTAGTTTAGCTGGCA-CCTAATGAAAA
* * * *
17935903 TTTAAGCCTAGTATAGTTGGTACC-AATAAAAA
1 TTTAAGCCTAGTTTAGCTGGCACCTAATGAAAA
* *
17935935 TTTAAACTTAGTTT
1 TTTAAGCCTAGTTT
17935949 TGGTTGGCAT
Statistics
Matches: 626, Mismatches: 151, Indels: 89
0.72 0.17 0.10
Matches are distributed among these distances:
28 2 0.00
29 64 0.10
30 7 0.01
31 9 0.01
32 205 0.33
33 304 0.49
34 13 0.02
36 19 0.03
37 3 0.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.31
Consensus pattern (33 bp):
TTTAAGCCTAGTTTAGCTGGCACCTAATGAAAA
Found at i:17935336 original size:29 final size:29
Alignment explanation
Indices: 17935304--17935372 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 29
17935294 AAGCCTAGTA
17935304 TAGCTGGCACCTAGGTTTTAAGCCCACTT
1 TAGCTGGCACCTAGGTTTTAAGCCCACTT
* *
17935333 TAGCTGGCACTTATGTTTTAAGCCCACTT
1 TAGCTGGCACCTAGGTTTTAAGCCCACTT
17935362 TAGCTGGCACC
1 TAGCTGGCACC
17935373 CAATGAAGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.32
Consensus pattern (29 bp):
TAGCTGGCACCTAGGTTTTAAGCCCACTT
Found at i:17935415 original size:156 final size:161
Alignment explanation
Indices: 17935095--17935913 Score: 408
Period size: 159 Copynumber: 5.1 Consensus size: 161
17935085 TTATCCAAGT
* * * * *
17935095 TTTAAGCCTAGTTTAGT-TGACAC-CTAATGAAAATTTAAGCCTAGTCTAGCTAGCACCCAATGA
1 TTTAAGCCTAGATTA-TCAGACACTC-AATGAAAATTTAAGCCTAGTATAGCTGGCACCTAATG-
** * * * * * * * * * * *
17935158 AAATTTAAGCCCAGTATAGCTGGCACTCAATCGAA-ATATGAGCCTAATTTAGTTAGCA-TCAAT
63 AGTTTTAAACCCACTTTAGCTGGCACT--AT-GAAGTTTTAAACCCAATTTAGCTGGCACCCAAT
* * * *
17935221 GAAGTTTTAAGCCTAGTTTATCTAGCACCAATGAAAA
125 GAAGATTTAACCCTAGCTTAGCTAGCACCAATGAAAA
* * **
17935258 TTTAAGCCTAGCATTAT-TGCCACTCTGTGAAAATTTAAGCCTAGTATAGCTGGCACCT-A-G-G
1 TTTAAGCCTAG-ATTATCAGACACTCAATGAAAATTTAAGCCTAGTATAGCTGGCACCTAATGAG
* * * *
17935319 TTTTAAGCCCACTTTAGCTGGCACT-T-ATGTTTTAAGCCCACTTTAGCTGGCACCCAATGAAGA
65 TTTTAAACCCACTTTAGCTGGCACTATGAAGTTTTAAACCCAATTTAGCTGGCACCCAATGAAGA
17935382 TTTAACCCTAGCTTAGCTAGCATCCAATG-AAA
130 TTTAACCCTAGCTTAGCTAGCA-CCAATGAAAA
** * *
17935414 TTTAAGCCTAGATTATCAGACACTCAATGAAGTTTTAAGCCTAGTTTAGTTGGCACCTAATGAAG
1 TTTAAGCCTAGATTATCAGACACTCAATGAAAATTTAAGCCTAGTATAGCTGGCACCTAATG-AG
* * *
17935479 TTTTAAACCCAGTTTAGCTGGCACTCAATGAAGTTTTAAACCCAATTTAGCTGGCACTGATCAAC
65 TTTTAAACCCACTTTAGCTGGCACT--ATGAAGTTTTAAACCCAATTTAGCTGGCAC---CCAAT
* * *
17935544 AAAGTTTTAAGCCC-AACTTAGCT-GACACCCAATG-AAA
125 GAAGATTTAA-CCCTAGCTTAGCTAG-CA-CCAATGAAAA
* * * * * * *
17935581 TTTAAGCCCA-TTTGAACTGAC-CTCTAATGAAAATTTAAGCCTAATATAGTTGGCACC-AATAA
1 TTTAAGCCTAGATT-ATCAGACACTC-AATGAAAATTTAAGCCTAGTATAGCTGGCACCTAAT-G
* * ** * ** * * * * *
17935643 AGTTTTAAGCCCAGTTTATTTGGCATCAATGAAAATTTAAGCCAAACTTAGTTGGCACCCAGTGA
63 AGTTTTAAACCCACTTTAGCTGGCA-CTATGAAGTTTTAAACCCAATTTAGCTGGCACCCAATGA
* * * ***
17935708 A-ATTTTAAGCCTAGTTTAGCTGGCACC--T-AGGT
127 AGA-TTTAACCCTAGCTTAGCTAGCACCAATGAAAA
* * * * * * * * * *
17935740 TTTAAGCCAAGCTTAACTAG-CACCCAATAAAAATTTAAACCTAGCATAGTTGGCACTTAATGAA
1 TTTAAGCCTAGATTATC-AGACACTCAATGAAAATTTAAGCCTAGTATAGCTGGCACCTAATGAG
* * * ** * * * * * *
17935804 ATTTATACCAAGATTATCTAGCACTTAATGAAATTTTAAGCTCAATTTAGCTGGCACCAAATGAA
65 TTTTAAACCCACTTTAGCTGGCAC-T-ATGAAGTTTTAAACCCAATTTAGCTGGCACCCAATGAA
* * * * *
17935869 -ATTTAAGCCTAGTTTCG-TTGACATCCAATTAAAA
128 GATTTAACCCTAGCTTAGCTAG-CA-CCAATGAAAA
17935903 TTTAAGCCTAG
1 TTTAAGCCTAG
17935914 TATAGTTGGT
Statistics
Matches: 513, Mismatches: 105, Indels: 76
0.74 0.15 0.11
Matches are distributed among these distances:
154 1 0.00
155 21 0.04
156 75 0.15
157 7 0.01
158 4 0.01
159 97 0.19
160 66 0.13
161 5 0.01
162 20 0.04
163 58 0.11
164 28 0.05
165 24 0.05
166 31 0.06
167 73 0.14
168 3 0.01
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (161 bp):
TTTAAGCCTAGATTATCAGACACTCAATGAAAATTTAAGCCTAGTATAGCTGGCACCTAATGAGT
TTTAAACCCACTTTAGCTGGCACTATGAAGTTTTAAACCCAATTTAGCTGGCACCCAATGAAGAT
TTAACCCTAGCTTAGCTAGCACCAATGAAAA
Found at i:17935476 original size:65 final size:65
Alignment explanation
Indices: 17935095--17935880 Score: 277
Period size: 65 Copynumber: 12.2 Consensus size: 65
17935085 TTATCCAAGT
* * * ** * * *
17935095 TTTAAGCCTAGTTTAGT-TGACACCTAATGAAAATTTAAGCCTAGTCTAGCTAGCACCCAATGAA
1 TTTAAGCCTAGATTA-TCTGGCACCCAATGAAGTTTTAAGCCTAGTTTAGCTGGCACCTAATG-A
17935159 AA
64 AA
* * * * * * * * * *
17935161 TTTAAGCCCAG-TATAGCTGGCACTCAATCGAA-ATATGAGCCTAATTTAGTTAGCATC-AATGA
1 TTTAAGCCTAGAT-TATCTGGCACCCAAT-GAAGTTTTAAGCCTAGTTTAGCTGGCACCTAATGA
*
17935223 AGT
64 A-A
* * ** * * * *
17935226 TTTAAGCCTAGTTTATCTAGCA-CCAATGAAAATTTAAGCCTAGCATTA-TTGCCACTCT-GTGA
1 TTTAAGCCTAGATTATCTGGCACCCAATGAAGTTTTAAGCCTAG-TTTAGCTGGCAC-CTAATG-
17935288 AAA
63 AAA
* * * * *
17935291 TTTAAGCCTAG-TATAGCTGGCA-CC--T-AGGTTTTAAGCCCACTTTAGCTGGCA-CTTATG--
1 TTTAAGCCTAGAT-TATCTGGCACCCAATGAAGTTTTAAGCCTAGTTTAGCTGGCACCTAATGAA
*
17935348 T
65 A
* ** * * * * *
17935349 TTTAAGCCCACTTTAGCTGGCACCCAATGAAGATTTAACCCTAGCTTAGCTAGCATCC-AATGAA
1 TTTAAGCCTAGATTATCTGGCACCCAATGAAGTTTTAAGCCTAGTTTAGCTGGCA-CCTAATGAA
17935413 A
65 A
* * * *
17935414 TTTAAGCCTAGATTATCAGACACTCAATGAAGTTTTAAGCCTAGTTTAGTTGGCACCTAATGAAG
1 TTTAAGCCTAGATTATCTGGCACCCAATGAAGTTTTAAGCCTAGTTTAGCTGGCACCTAATGAA-
*
17935479 T
65 A
* * * * * * * * **
17935480 TTTAAACCCAGTTTAGCTGGCACTCAATGAAGTTTTAAACCCAATTTAGCTGGCA-CTGATCAAC
1 TTTAAGCCTAGATTATCTGGCACCCAATGAAGTTTTAAGCCTAGTTTAGCTGGCACCT-A--ATG
17935544 AAA
63 AAA
* * * * * * *
17935547 GTTTTAAGCCCA-ACTTAGCTGACACCCAATGAA-ATTTAAGCCCA-TTTGAACTGAC-CTCTAA
1 --TTTAAGCCTAGA-TTATCTGGCACCCAATGAAGTTTTAAGCCTAGTTT-AGCTGGCAC-CTAA
17935608 TGAAAA
61 TG-AAA
* * ** *
17935614 TTTAAGCCTA-ATATAGT-TGGCA-CCAATAAAGTTTTAAGCCCAGTTTATTTGGCATC-AATGA
1 TTTAAGCCTAGAT-TA-TCTGGCACCCAATGAAGTTTTAAGCCTAGTTTAGCTGGCACCTAATG-
17935675 AAA
63 AAA
* * *
17935678 TTTAAGCC-AAACTTAGT-TGGCACCCAGTGAAATTTTAAGCCTAGTTTAGCTGGCACCT-A-G-
1 TTTAAGCCTAGA-TTA-TCTGGCACCCAATGAAGTTTTAAGCCTAGTTTAGCTGGCACCTAATGA
**
17935738 GT
64 AA
* * * * * ** * ** * *
17935740 TTTAAGCCAAGCTTAACTAGCACCCAATAAAAATTTAAACCTAGCATAGTTGGCACTTAATGAAA
1 TTTAAGCCTAGATTATCTGGCACCCAATGAAGTTTTAAGCCTAGTTTAGCTGGCACCTAATGAAA
* * ** * * *
17935805 TTTATA-CCAAGATTATCTAGCACTTAATGAAATTTTAAG-CTCAATTTAGCTGGCACCAAATGA
1 TTTA-AGCCTAGATTATCTGGCACCCAATGAAGTTTTAAGCCT-AGTTTAGCTGGCACCTAATGA
17935868 AA
64 AA
17935870 TTTAAGCCTAG
1 TTTAAGCCTAG
17935881 TTTCGTTGAC
Statistics
Matches: 539, Mismatches: 130, Indels: 103
0.70 0.17 0.13
Matches are distributed among these distances:
58 18 0.03
59 3 0.01
60 2 0.00
61 6 0.01
62 76 0.14
63 10 0.02
64 62 0.12
65 214 0.40
66 93 0.17
67 9 0.02
68 18 0.03
69 28 0.05
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (65 bp):
TTTAAGCCTAGATTATCTGGCACCCAATGAAGTTTTAAGCCTAGTTTAGCTGGCACCTAATGAAA
Found at i:17935794 original size:62 final size:62
Alignment explanation
Indices: 17935678--17935795 Score: 137
Period size: 62 Copynumber: 1.9 Consensus size: 62
17935668 TCAATGAAAA
** * * * * * **
17935678 TTTAAGCCAAACTTAGTTGGCACCCAGTGAAATTTTAAGCCTAGTTTAGCTGGCACCTAGGT
1 TTTAAGCCAAACTTAACTAGCACCCAATAAAAATTTAAACCTAGCATAGCTGGCACCTAGGT
* *
17935740 TTTAAGCCAAGCTTAACTAGCACCCAATAAAAATTTAAACCTAGCATAGTTGGCAC
1 TTTAAGCCAAACTTAACTAGCACCCAATAAAAATTTAAACCTAGCATAGCTGGCAC
17935796 TTAATGAAAT
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
62 45 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (62 bp):
TTTAAGCCAAACTTAACTAGCACCCAATAAAAATTTAAACCTAGCATAGCTGGCACCTAGGT
Found at i:17936069 original size:26 final size:26
Alignment explanation
Indices: 17936033--17936088 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
17936023 AATCCTGGTC
17936033 ATCTTTATCATTTGACTCGTAGTTTA
1 ATCTTTATCATTTGACTCGTAGTTTA
*
17936059 ATCTTTATCATTTGGCTCGTAGTTTA
1 ATCTTTATCATTTGACTCGTAGTTTA
17936085 ATCT
1 ATCT
17936089 CGATCACTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.50
Consensus pattern (26 bp):
ATCTTTATCATTTGACTCGTAGTTTA
Found at i:17936094 original size:26 final size:26
Alignment explanation
Indices: 17936039--17936103 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
17936029 GGTCATCTTT
**
17936039 ATCATTTGACTCGTAGTTTAATCTTT
1 ATCATTTGACTCGTAGTTTAATCTCG
*
17936065 ATCATTTGGCTCGTAGTTTAATCTCG
1 ATCATTTGACTCGTAGTTTAATCTCG
* *
17936091 ATCACTTCACTCG
1 ATCATTTGACTCG
17936104 ACTTACGATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.43
Consensus pattern (26 bp):
ATCATTTGACTCGTAGTTTAATCTCG
Found at i:17936175 original size:7 final size:7
Alignment explanation
Indices: 17936163--17936213 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
17936153 CCCAATCATC
17936163 ATAAAAA
1 ATAAAAA
17936170 ATAAAAA
1 ATAAAAA
17936177 ATAAAAA
1 ATAAAAA
* *
17936184 A-GAGAA
1 ATAAAAA
**
17936190 ATAAATG
1 ATAAAAA
17936197 A-AAAAA
1 ATAAAAA
17936203 ATAAAAA
1 ATAAAAA
17936210 ATAA
1 ATAA
17936214 TAATCTTCAA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
6 8 0.24
7 26 0.76
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (7 bp):
ATAAAAA
Found at i:17936310 original size:36 final size:36
Alignment explanation
Indices: 17936259--17936349 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 36
17936249 CAATAAACAG
* *
17936259 AAAAAATAAAT-AATAAAATATAA-AAATCATTAAAT
1 AAAAAATAAATAAATAAAATATAATAAATAAAT-AAT
17936294 AAAAAATAAATAAATAAAATATAATAAATAAATAAT
1 AAAAAATAAATAAATAAAATATAATAAATAAATAAT
* *
17936330 ATAAATATAAAAAAATAAAA
1 A-AAAAATAAATAAATAAAA
17936350 ACAAATAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
35 11 0.22
36 16 0.33
37 22 0.45
ACGTcount: A:0.75, C:0.01, G:0.00, T:0.24
Consensus pattern (36 bp):
AAAAAATAAATAAATAAAATATAATAAATAAATAAT
Found at i:17936317 original size:22 final size:22
Alignment explanation
Indices: 17936264--17936348 Score: 86
Period size: 22 Copynumber: 3.8 Consensus size: 22
17936254 AACAGAAAAA
*
17936264 ATAAATAATAAAATATAAA-AAT
1 ATAAAT-ATAAAAAATAAATAAT
*
17936286 CATTAA-ATAAAAAATAAATAA-
1 -ATAAATATAAAAAATAAATAAT
*
17936307 ATAAAATATAATAAATAAATAAT
1 AT-AAATATAAAAAATAAATAAT
17936330 ATAAATATAAAAAAATAAA
1 ATAAATAT-AAAAAATAAA
17936349 AACAAATAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
20 2 0.04
21 13 0.25
22 22 0.42
23 15 0.29
ACGTcount: A:0.73, C:0.01, G:0.00, T:0.26
Consensus pattern (22 bp):
ATAAATATAAAAAATAAATAAT
Found at i:17936355 original size:10 final size:9
Alignment explanation
Indices: 17936290--17936360 Score: 52
Period size: 10 Copynumber: 7.0 Consensus size: 9
17936280 AAAAATCATT
17936290 AAATAAAAAA
1 AAAT-AAAAA
17936300 TAAATAAATAA
1 -AAATAAA-AA
17936311 AATATAATAAA
1 AA-ATAA-AAA
* *
17936322 TAAATAATAT
1 -AAATAAAAA
17936332 AAATATAAAA
1 AAATA-AAAA
17936342 AAATAAAAA
1 AAATAAAAA
17936351 CAAATAAAAA
1 -AAATAAAAA
17936361 TGTTATACAA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
9 9 0.18
10 22 0.44
11 16 0.32
12 3 0.06
ACGTcount: A:0.77, C:0.01, G:0.00, T:0.21
Consensus pattern (9 bp):
AAATAAAAA
Found at i:17936359 original size:18 final size:17
Alignment explanation
Indices: 17936294--17936360 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 17
17936284 ATCATTAAAT
*
17936294 AAAAAATAAATAAATAA
1 AAAAAATAAAAAAATAA
* *
17936311 AATATAATAAATAAATAA
1 AA-AAAATAAAAAAATAA
*
17936329 TATAAATATAAAAAAATAA
1 -A-AAAAATAAAAAAATAA
17936348 AAACAAATAAAAA
1 AAA-AAATAAAAA
17936361 TGTTATACAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
17 4 0.10
18 23 0.56
19 13 0.32
20 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAAATAAAAAAATAA
Found at i:17936443 original size:10 final size:10
Alignment explanation
Indices: 17936400--17936441 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
17936390 AATAAAATAT
17936400 AAATATATAAA
1 AAATAT-TAAA
17936411 AAATAATTAAA
1 AAAT-ATTAAA
17936422 AAATATT-AA
1 AAATATTAAA
*
17936431 AGATATTAAA
1 AAATATTAAA
17936441 A
1 A
17936442 GACATATATC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
9 8 0.29
10 6 0.21
11 12 0.43
12 2 0.07
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (10 bp):
AAATATTAAA
Found at i:17938173 original size:15 final size:16
Alignment explanation
Indices: 17938153--17938222 Score: 65
Period size: 16 Copynumber: 4.4 Consensus size: 16
17938143 GAAATTATTA
17938153 AATAAAA-ATTAAAAT
1 AATAAAATATTAAAAT
*
17938168 AATAAAAGATT-AAAT
1 AATAAAATATTAAAAT
**
17938183 AATAATAATATTTTAAT
1 AATAA-AATATTAAAAT
*
17938200 AAAAAAATATATAAAAT
1 AATAAAATAT-TAAAAT
17938217 -ATAAAA
1 AATAAAA
17938223 ATTCATTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
15 16 0.36
16 18 0.40
17 11 0.24
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (16 bp):
AATAAAATATTAAAAT
Found at i:17938457 original size:38 final size:38
Alignment explanation
Indices: 17938343--17938475 Score: 133
Period size: 39 Copynumber: 3.4 Consensus size: 38
17938333 AGCGAAATCT
* * *
17938343 TAAATGAAACCCTAAACCTTAGGTAAACCCAAAAACCC
1 TAAATGAAACCCTAAATCATAGGTAAACCCTAAAACCC
** * * * **
17938381 TAACCGAAACCCTAAAATCGTAGGTGAATCCTTGAACCC
1 TAAATGAAACCCT-AAATCATAGGTAAACCCTAAAACCC
17938420 TAAATGAAACCCTAAATCATAAGG-AAACCCTAAAACCC
1 TAAATGAAACCCTAAATCAT-AGGTAAACCCTAAAACCC
*
17938458 TAAGGTGAAACCCTAAAT
1 TAA-ATGAAACCCTAAAT
17938476 TCATTCCAAA
Statistics
Matches: 75, Mismatches: 17, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
38 30 0.40
39 45 0.60
ACGTcount: A:0.44, C:0.26, G:0.11, T:0.18
Consensus pattern (38 bp):
TAAATGAAACCCTAAATCATAGGTAAACCCTAAAACCC
Found at i:17940469 original size:21 final size:21
Alignment explanation
Indices: 17940426--17940469 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
17940416 ATGTTTTAAC
* *
17940426 CCTCTTTTTTTTTACTAGAAG
1 CCTCTTTTTTTTTACAACAAG
* *
17940447 CCTCTTTTTTTTTTCAACTAG
1 CCTCTTTTTTTTTACAACAAG
17940468 CC
1 CC
17940470 CTTCTCTCCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.25, G:0.07, T:0.52
Consensus pattern (21 bp):
CCTCTTTTTTTTTACAACAAG
Found at i:17942416 original size:13 final size:13
Alignment explanation
Indices: 17942400--17942451 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
17942390 TAGGAAAATT
17942400 ATTAAATAAAAAA
1 ATTAAATAAAAAA
*
17942413 ATTAAATAATAATA
1 ATTAAATAA-AAAA
*
17942427 ATTTAATAAAAAA
1 ATTAAATAAAAAA
* *
17942440 AGTATATAAAAA
1 ATTAAATAAAAA
17942452 TATAAAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
13 21 0.66
14 11 0.34
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (13 bp):
ATTAAATAAAAAA
Found at i:17942577 original size:25 final size:24
Alignment explanation
Indices: 17942549--17942596 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
17942539 TAAAGTTTTG
17942549 AAATCTTAAAACAAAACCCTAAACA
1 AAATCTT-AAACAAAACCCTAAACA
**
17942574 AAATCTTAAATGAAACCCTAAAC
1 AAATCTTAAACAAAACCCTAAAC
17942597 CTTAGTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.56, C:0.23, G:0.02, T:0.19
Consensus pattern (24 bp):
AAATCTTAAACAAAACCCTAAACA
Found at i:17942614 original size:37 final size:38
Alignment explanation
Indices: 17942573--17942671 Score: 128
Period size: 39 Copynumber: 2.6 Consensus size: 38
17942563 AACCCTAAAC
*
17942573 AAAATCTTAAATGAAACCCTAAACCTTA-GTAAATCCT
1 AAAATCTTAAATGAAACCCTAAACCCTAGGTAAATCCT
*
17942610 AAAATCTTAAATGAAACCCTAAAACCCTAGGTGAATCCT
1 AAAATCTTAAATGAAACCCT-AAACCCTAGGTAAATCCT
* * * *
17942649 TAAACCCTAAATAAAACCCTAAA
1 AAAATCTTAAATGAAACCCTAAA
17942672 TAAAACCCTA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
37 20 0.37
38 10 0.19
39 24 0.44
ACGTcount: A:0.47, C:0.23, G:0.06, T:0.23
Consensus pattern (38 bp):
AAAATCTTAAATGAAACCCTAAACCCTAGGTAAATCCT
Found at i:17942644 original size:20 final size:20
Alignment explanation
Indices: 17942580--17942671 Score: 66
Period size: 20 Copynumber: 4.8 Consensus size: 20
17942570 AACAAAATCT
17942580 TAAATGAAACCCT-AAA-CC
1 TAAATGAAACCCTAAAACCC
* * * * *
17942598 TTAGT-AAATCCTAAAATCT
1 TAAATGAAACCCTAAAACCC
17942617 TAAATGAAACCCTAAAACCC
1 TAAATGAAACCCTAAAACCC
** * *
17942637 TAGGTG-AATCCTTAAACCC
1 TAAATGAAACCCTAAAACCC
*
17942656 TAAATAAAACCCTAAA
1 TAAATGAAACCCTAAA
17942672 TAAAACCCTA
Statistics
Matches: 52, Mismatches: 18, Indels: 6
0.68 0.24 0.08
Matches are distributed among these distances:
17 6 0.12
18 6 0.12
19 18 0.35
20 22 0.42
ACGTcount: A:0.47, C:0.24, G:0.07, T:0.23
Consensus pattern (20 bp):
TAAATGAAACCCTAAAACCC
Found at i:17942667 original size:12 final size:12
Alignment explanation
Indices: 17942650--17942683 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
17942640 GTGAATCCTT
17942650 AAACCCTAAATA
1 AAACCCTAAATA
17942662 AAACCCTAAATA
1 AAACCCTAAATA
17942674 AAACCCTAAA
1 AAACCCTAAA
17942684 CCATAAGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.59, C:0.26, G:0.00, T:0.15
Consensus pattern (12 bp):
AAACCCTAAATA
Found at i:17942671 original size:19 final size:19
Alignment explanation
Indices: 17942662--17942722 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
17942652 ACCCTAAATA
17942662 AAACCCTAAATAAAACCCT
1 AAACCCTAAATAAAACCCT
* ** *
17942681 AAACCAT-AAGCAAACCTCG
1 AAACCCTAAATAAAACC-CT
*
17942700 AAACCCTAACATGAAACCCT
1 AAACCCTAA-ATAAAACCCT
17942720 AAA
1 AAA
17942723 TTCATTCAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
18 7 0.23
19 13 0.42
20 5 0.16
21 6 0.19
ACGTcount: A:0.51, C:0.31, G:0.05, T:0.13
Consensus pattern (19 bp):
AAACCCTAAATAAAACCCT
Found at i:17942740 original size:18 final size:18
Alignment explanation
Indices: 17942713--17942747 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17942703 CCCTAACATG
*
17942713 AAACCCTAAATTCATTCA
1 AAACCCTAAAATCATTCA
*
17942731 AAACCTTAAAATCATTC
1 AAACCCTAAAATCATTC
17942748 CAAGATTCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.29
Consensus pattern (18 bp):
AAACCCTAAAATCATTCA
Found at i:17942926 original size:22 final size:22
Alignment explanation
Indices: 17942883--17942926 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
17942873 TTTGTTTTGT
*
17942883 TAAAATAACAAATATATAAATA
1 TAAAATAACAAAGATATAAATA
*
17942905 TAAAATAATAAAGA-ATAGAATA
1 TAAAATAACAAAGATATA-AATA
17942927 AGATTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (22 bp):
TAAAATAACAAAGATATAAATA
Found at i:17943428 original size:23 final size:23
Alignment explanation
Indices: 17943398--17943443 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
17943388 ATATTATTAA
17943398 ATAAAGATTTTTTAAAATTAATT
1 ATAAAGATTTTTTAAAATTAATT
17943421 ATAAAGATTTTTTAAAATTAATT
1 ATAAAGATTTTTTAAAATTAATT
17943444 TTCTTTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (23 bp):
ATAAAGATTTTTTAAAATTAATT
Found at i:17944410 original size:9 final size:9
Alignment explanation
Indices: 17944363--17944410 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
17944353 ATTTTTTTTC
17944363 AAAATTATAT
1 AAAATT-TAT
*
17944373 ACAAATTTTT
1 A-AAATTTAT
17944383 AAAATTTAT
1 AAAATTTAT
* *
17944392 AACATATAT
1 AAAATTTAT
17944401 AAAATTTAT
1 AAAATTTAT
17944410 A
1 A
17944411 TATATTGACT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
9 22 0.71
10 4 0.13
11 5 0.16
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (9 bp):
AAAATTTAT
Found at i:17948130 original size:13 final size:14
Alignment explanation
Indices: 17948112--17948140 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17948102 TAGAATTATA
17948112 TTATTT-CAAATTT
1 TTATTTACAAATTT
17948125 TTATTTACAAATTT
1 TTATTTACAAATTT
17948139 TT
1 TT
17948141 TACATATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATTTACAAATTT
Found at i:17949679 original size:16 final size:15
Alignment explanation
Indices: 17949658--17949691 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
17949648 CCTTACTATT
*
17949658 TTTCACTTTTTTTCTC
1 TTTCACTATTTTTC-C
17949674 TTTCACTATTTTTCC
1 TTTCACTATTTTTCC
17949689 TTT
1 TTT
17949692 TCTTTTACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTCACTATTTTTCC
Found at i:17949717 original size:20 final size:20
Alignment explanation
Indices: 17949664--17949716 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
17949654 TATTTTTCAC
*
17949664 TTTTTTTCTCTTTCACTATTT
1 TTTTTTTCT-TTTTACTATTT
*
17949685 TTCCTTTTC-TTTTAC-ATTT
1 TT-TTTTTCTTTTTACTATTT
17949704 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
17949717 TTTTTTCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 5 0.19
19 10 0.37
20 5 0.19
21 2 0.07
22 5 0.19
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTTTTCTTTTTACTATTT
Found at i:17949721 original size:12 final size:12
Alignment explanation
Indices: 17949682--17949727 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
17949672 TCTTTCACTA
* *
17949682 TTTTTCCTTTTC
1 TTTTTCTTTTTT
* *
17949694 TTTTACATTTTT
1 TTTTTCTTTTTT
17949706 TTTTTCTTTTTT
1 TTTTTCTTTTTT
17949718 TTTTTCTTTT
1 TTTTTCTTTT
17949728 GTTGAAAAGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:17952900 original size:12 final size:12
Alignment explanation
Indices: 17952883--17952926 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
17952873 ATTTCAAAAG
17952883 ATTTTTTTCTTT
1 ATTTTTTTCTTT
*
17952895 ATTTTTTTGTTT
1 ATTTTTTTCTTT
*
17952907 CTTTTATTTCTTT
1 ATTTT-TTTCTTT
17952920 ATTTTTT
1 ATTTTTT
17952927 AAAAAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.09, C:0.07, G:0.02, T:0.82
Consensus pattern (12 bp):
ATTTTTTTCTTT
Found at i:17953047 original size:24 final size:24
Alignment explanation
Indices: 17953008--17953083 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
17952998 TAAAAGTTAG
* *
17953008 TAAAATAAATAC-AAAAATTGAATA
1 TAAAAT-AATACAAAAAATTCAAAA
17953032 TAAAATAATACAAAAATATTTCAAAA
1 TAAAATAATACAAAAA-A-TTCAAAA
*
17953058 TAAAA-AATA-AAAAAAAT-AAAA
1 TAAAATAATACAAAAAATTCAAAA
17953079 TAAAA
1 TAAAA
17953084 AAAGAAAATG
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
21 9 0.20
22 1 0.02
23 6 0.13
24 15 0.33
25 5 0.11
26 10 0.22
ACGTcount: A:0.72, C:0.04, G:0.01, T:0.22
Consensus pattern (24 bp):
TAAAATAATACAAAAAATTCAAAA
Found at i:17953066 original size:7 final size:7
Alignment explanation
Indices: 17953054--17953105 Score: 54
Period size: 7 Copynumber: 7.4 Consensus size: 7
17953044 AAAATATTTC
17953054 AAAATAA
1 AAAATAA
17953061 AAAATAA
1 AAAATAA
17953068 AAAA-AA
1 AAAATAA
17953074 TAAAATAA
1 -AAAATAA
*
17953082 AAAA-AG
1 AAAATAA
17953088 AAAATGAA
1 AAAAT-AA
*
17953096 AAAAGAA
1 AAAATAA
17953103 AAA
1 AAA
17953106 CCTGCGATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
6 7 0.18
7 24 0.63
8 7 0.18
ACGTcount: A:0.85, C:0.00, G:0.06, T:0.10
Consensus pattern (7 bp):
AAAATAA
Found at i:17953083 original size:13 final size:13
Alignment explanation
Indices: 17953061--17953104 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
17953051 TTCAAAATAA
*
17953061 AAAATAAAAAAAAT
1 AAAAT-AAAAAAAG
17953075 AAAATAAAAAAAG
1 AAAATAAAAAAAG
*
17953088 AAAATGAAAAAAG
1 AAAATAAAAAAAG
17953101 AAAA
1 AAAA
17953105 ACCTGCGATC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
13 23 0.82
14 5 0.18
ACGTcount: A:0.84, C:0.00, G:0.07, T:0.09
Consensus pattern (13 bp):
AAAATAAAAAAAG
Found at i:17953575 original size:23 final size:23
Alignment explanation
Indices: 17953532--17953575 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
17953522 CAAACCGTTC
* *
17953532 CCAAAACCACTAATTCTAAACTT
1 CCAAAACCACAAATTCAAAACTT
17953555 CCAAAACCA-AAATCTCAAAAC
1 CCAAAACCACAAAT-TCAAAAC
17953576 CTGACCACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (23 bp):
CCAAAACCACAAATTCAAAACTT
Found at i:17953906 original size:3 final size:3
Alignment explanation
Indices: 17953889--17954078 Score: 112
Period size: 3 Copynumber: 68.0 Consensus size: 3
17953879 AAGAAAAATG
* *
17953889 ATA A-A ATA A-A ATA ATA ATA ATT ATT AT- ATA ATA AT- ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
17953932 A-A AGCT- ATA AT- ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA A-G
1 ATA A--TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
17953975 ATA CT- ATA AT- ATA AT- ATA ATA AT- ACA ATA ATA ACA ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
17954018 AT- ATA ATA TATT TTA AT- ATA ATA CGATA ATA AT- ATA AT- ATG ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA --ATA ATA ATA ATA ATA ATA ATA
17954062 ATA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA
17954079 TACCATACTA
Statistics
Matches: 147, Mismatches: 16, Indels: 48
0.70 0.08 0.23
Matches are distributed among these distances:
2 34 0.23
3 107 0.73
4 3 0.02
5 3 0.02
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:17953929 original size:5 final size:5
Alignment explanation
Indices: 17953889--17954080 Score: 105
Period size: 5 Copynumber: 37.6 Consensus size: 5
17953879 AAGAAAAATG
* * * *
17953889 ATAAA ATAAA ATAAT AATAAT -TATT AT-AT AATAAT ATAAT ATAA- A-AGCT
1 ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATA-AT
* *
17953938 ATAAT ATAAT AGT-A- ATAAT AATAAT AATAAT AATAAG ATACT ATAAT
1 ATAAT ATAAT A-TAAT ATAAT -ATAAT -ATAAT -ATAAT ATAAT ATAAT
*
17953985 ATAAT ATAAT AATACA- ATAAT A-ACA- ATAAT ATAAT ATAAT ATATT
1 ATAAT ATAAT -ATA-AT ATAAT ATA-AT ATAAT ATAAT ATAAT ATAAT
* ** *
17954030 TTAAT ATAAT ACGAT AATAAT ATAAT ATGAT AATAAT AATAAT ATAAT
1 ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT -ATAAT -ATAAT ATAAT
17954078 ATA
1 ATA
17954081 CCATACTATA
Statistics
Matches: 149, Mismatches: 19, Indels: 38
0.72 0.09 0.18
Matches are distributed among these distances:
3 2 0.01
4 11 0.07
5 94 0.63
6 41 0.28
7 1 0.01
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (5 bp):
ATAAT
Found at i:17953955 original size:9 final size:9
Alignment explanation
Indices: 17953938--17954078 Score: 99
Period size: 8 Copynumber: 16.7 Consensus size: 9
17953928 TATAAAAGCT
17953938 ATAAT-ATA
1 ATAATAATA
*
17953946 ATAGTAATA
1 ATAATAATA
17953955 ATAATAATA
1 ATAATAATA
17953964 ATAATAATA
1 ATAATAATA
* *
17953973 A-GATACT-
1 ATAATAATA
17953980 ATAAT-ATA
1 ATAATAATA
17953988 AT-ATAATA
1 ATAATAATA
*
17953996 AT-ACAATA
1 ATAATAATA
*
17954004 ATAACAATA
1 ATAATAATA
17954013 AT-ATAAT-
1 ATAATAATA
*
17954020 ATAATATATT
1 ATAATA-ATA
*
17954030 TTAAT-ATA
1 ATAATAATA
17954038 ATACGATAATA
1 ATA--ATAATA
17954049 AT-ATAAT-
1 ATAATAATA
*
17954056 ATGATAATA
1 ATAATAATA
17954065 ATAATAAT-
1 ATAATAATA
17954073 ATAATA
1 ATAATA
17954079 TACCATACTA
Statistics
Matches: 108, Mismatches: 12, Indels: 26
0.74 0.08 0.18
Matches are distributed among these distances:
7 8 0.07
8 51 0.47
9 38 0.35
10 6 0.06
11 5 0.05
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (9 bp):
ATAATAATA
Found at i:17954404 original size:55 final size:55
Alignment explanation
Indices: 17954315--17954436 Score: 156
Period size: 55 Copynumber: 2.2 Consensus size: 55
17954305 GACTAAGCCG
* * * * *
17954315 CAAGTCTGAAAAATGATTTGGACTGAGCCGAGATCGAACAACCGAGATTAAACTA
1 CAAGTTTGAAAAATGATATGGACTAAGCCAAGATCGAACAACCGAGATTAAACCA
* * * *
17954370 CAAGTTTGGAAAATGATATGGACTAAGCCAAGATCGAGCGACCGATATTAAACCA
1 CAAGTTTGAAAAATGATATGGACTAAGCCAAGATCGAACAACCGAGATTAAACCA
17954425 CAAGTTT-AAAAA
1 CAAGTTTGAAAAA
17954437 GTTGACTTGG
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
54 4 0.07
55 53 0.93
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.20
Consensus pattern (55 bp):
CAAGTTTGAAAAATGATATGGACTAAGCCAAGATCGAACAACCGAGATTAAACCA
Found at i:17954998 original size:16 final size:16
Alignment explanation
Indices: 17954965--17954998 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17954955 GTGTTTGCCC
* *
17954965 TTTTTTTTGTTTTTTT
1 TTTTTTTTGTTGTATT
17954981 TTTTTTTTGTTGTATT
1 TTTTTTTTGTTGTATT
17954997 TT
1 TT
17954999 CTCAGGCTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.00, G:0.09, T:0.88
Consensus pattern (16 bp):
TTTTTTTTGTTGTATT
Found at i:17958195 original size:72 final size:72
Alignment explanation
Indices: 17958073--17958219 Score: 249
Period size: 72 Copynumber: 2.0 Consensus size: 72
17958063 ATGTCTATGG
*
17958073 AACCCTCAGATTGTGCATGAATATGAATGCAAAAACAAAATGCATGAATGCAATAAGGAGAATTT
1 AACCCTCAGATTGTGCATGAAAATGAATGCAAAAACAAAATGCATGAATGCAATAAGGAGAATTT
*
17958138 ATCACAT
66 ACCACAT
* * *
17958145 AACCCTCAGATTGTGCATGAAAATGAATGTAAAAACAAAATGTATTAATGCAATAAGGAGAATTT
1 AACCCTCAGATTGTGCATGAAAATGAATGCAAAAACAAAATGCATGAATGCAATAAGGAGAATTT
17958210 ACCACAT
66 ACCACAT
17958217 AAC
1 AAC
17958220 AATTGTTATC
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.24
Consensus pattern (72 bp):
AACCCTCAGATTGTGCATGAAAATGAATGCAAAAACAAAATGCATGAATGCAATAAGGAGAATTT
ACCACAT
Found at i:17963196 original size:13 final size:14
Alignment explanation
Indices: 17963178--17963206 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17963168 TAGAATTATA
17963178 TTATTT-CAAATTT
1 TTATTTACAAATTT
17963191 TTATTTACAAATTT
1 TTATTTACAAATTT
17963205 TT
1 TT
17963207 TACATATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATTTACAAATTT
Found at i:17964762 original size:17 final size:18
Alignment explanation
Indices: 17964740--17964778 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
17964730 TACCTTACTA
17964740 TTTTTC-ACTTTTTTTTC
1 TTTTTCTACTTTTTTTTC
**
17964757 TTTTTCTTTTTTTTTTTC
1 TTTTTCTACTTTTTTTTC
17964775 TTTT
1 TTTT
17964779 GTTGAAAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTTCTACTTTTTTTTC
Found at i:17968025 original size:11 final size:10
Alignment explanation
Indices: 17968003--17968120 Score: 57
Period size: 10 Copynumber: 11.2 Consensus size: 10
17967993 CAAATTGCTT
17968003 AATAAAAATA
1 AATAAAAATA
17968013 AATAAATAATAA
1 AATAAA-AAT-A
17968025 AAGTTAGTAAAATA
1 AA--TA--AAAATA
*
17968039 AATAAAAAATTG
1 AAT-AAAAA-TA
17968051 AATATAAAATA
1 AATA-AAAATA
17968062 ATATAAAAATA
1 A-ATAAAAATA
** *
17968073 TTTCAAAAT-
1 AATAAAAATA
17968082 -AT-AAAATA
1 AATAAAAATA
17968090 AATAAAAATA
1 AATAAAAATA
*
17968100 AA-ATCAAA-A
1 AATA-AAAATA
17968109 AATAAAAATA
1 AATAAAAATA
17968119 AA
1 AA
17968121 ATGAAAAAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 32
0.68 0.06 0.26
Matches are distributed among these distances:
7 5 0.06
8 1 0.01
9 9 0.11
10 27 0.32
11 16 0.19
12 15 0.18
13 1 0.01
14 5 0.06
15 3 0.04
16 2 0.02
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.25
Consensus pattern (10 bp):
AATAAAAATA
Found at i:17968062 original size:23 final size:26
Alignment explanation
Indices: 17968032--17968099 Score: 88
Period size: 28 Copynumber: 2.7 Consensus size: 26
17968022 TAAAAGTTAG
*
17968032 TAAAATAAATAAAAA-A-TT-GAATA
1 TAAAATAAATAAAAATATTTAAAATA
17968055 TAAAATAATATAAAAATATTTCAAAATA
1 TAAAATAA-ATAAAAATATTT-AAAATA
17968083 TAAAATAAATAAAAATA
1 TAAAATAAATAAAAATA
17968100 AAATCAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
23 8 0.21
24 7 0.18
25 1 0.03
26 2 0.05
27 9 0.23
28 12 0.31
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (26 bp):
TAAAATAAATAAAAATATTTAAAATA
Found at i:17968106 original size:28 final size:27
Alignment explanation
Indices: 17968051--17968120 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 27
17968041 TAAAAAATTG
**
17968051 AATATAAAATAATATAAAAATATTTCAA
1 AATATAAAATAA-ATAAAAATAAATCAA
17968079 AATATAAAATAAATAAAAATAAAATCAA
1 AATATAAAATAAATAAAAAT-AAATCAA
*
17968107 AAAATAAAAATAAA
1 AATAT-AAAATAAA
17968121 ATGAAAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.22
28 21 0.57
29 8 0.22
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (27 bp):
AATATAAAATAAATAAAAATAAATCAA
Found at i:17968135 original size:19 final size:19
Alignment explanation
Indices: 17968089--17968129 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
17968079 AATATAAAAT
17968089 AAATAAAAATAAAATCAAA
1 AAATAAAAATAAAATCAAA
*
17968108 AAATAAAAATAAAATGAAA
1 AAATAAAAATAAAATCAAA
17968127 AAA
1 AAA
17968130 AGAAAACCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.15
Consensus pattern (19 bp):
AAATAAAAATAAAATCAAA
Found at i:17968351 original size:21 final size:20
Alignment explanation
Indices: 17968314--17968355 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
17968304 CCTCTCTAAA
17968314 AAAACTAAGAATGTTCAATCG
1 AAAACTAAGAATGTTC-ATCG
*
17968335 AAAACTGAA-AATTTTCATCG
1 AAAACT-AAGAATGTTCATCG
17968355 A
1 A
17968356 TTTTTGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 12 0.63
22 2 0.11
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (20 bp):
AAAACTAAGAATGTTCATCG
Found at i:17968934 original size:8 final size:8
Alignment explanation
Indices: 17968923--17969080 Score: 50
Period size: 8 Copynumber: 19.1 Consensus size: 8
17968913 AAAATGATAA
17968923 AATAAAAT
1 AATAAAAT
17968931 AATAATAAT
1 AATAA-AAT
* * *
17968940 TATTATAT
1 AATAAAAT
*
17968948 AATAATAT
1 AATAAAAT
*
17968956 AATATAAT
1 AATAAAAT
***
17968964 AATGCTAT
1 AATAAAAT
*
17968972 AATATAAT
1 AATAAAAT
*
17968980 AGTAATAAT
1 AATAA-AAT
17968989 AATAATAA-
1 AATAA-AAT
* **
17968997 GATACTAT
1 AATAAAAT
*
17969005 AATATAAT
1 AATAAAAT
*
17969013 AATATAAT
1 AATAAAAT
17969021 AATAACAAT
1 AATAA-AAT
*
17969030 AATATAGTAT
1 AATA-A-AAT
*
17969040 AATATAAT
1 AATAAAAT
*
17969048 -ATAATAT
1 AATAAAAT
* *
17969055 GATAATAT
1 AATAAAAT
17969063 AATAATAAT
1 AATAA-AAT
*
17969072 AATATAAT
1 AATAAAAT
17969080 A
1 A
17969081 TACCATACTA
Statistics
Matches: 111, Mismatches: 32, Indels: 14
0.71 0.20 0.09
Matches are distributed among these distances:
7 6 0.05
8 69 0.62
9 29 0.26
10 7 0.06
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (8 bp):
AATAAAAT
Found at i:17968936 original size:3 final size:3
Alignment explanation
Indices: 17968919--17969080 Score: 108
Period size: 3 Copynumber: 60.0 Consensus size: 3
17968909 AAGAAAAATG
* *
17968919 ATA A-A ATA A-A ATA ATA ATA ATT ATT AT- ATA ATA AT- ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
17968962 ATA ATG CT- ATA AT- ATA ATA GTA ATA ATA ATA ATA A-G ATA CT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
17969006 AT- ATA ATA AT- ATA ATA ATA ACA ATA AT- ATA GT- ATA AT- ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
17969048 ATA AT- ATG ATA AT- ATA ATA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17969081 TACCATACTA
Statistics
Matches: 126, Mismatches: 15, Indels: 36
0.71 0.08 0.20
Matches are distributed among these distances:
2 32 0.25
3 94 0.75
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:17968959 original size:5 final size:5
Alignment explanation
Indices: 17968919--17969082 Score: 104
Period size: 5 Copynumber: 31.6 Consensus size: 5
17968909 AAGAAAAATG
* * * **
17968919 ATAAA ATAAA ATAAT AATAAT -TATT AT-AT AATAAT ATAAT ATAAT AATGCT
1 ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT -ATAAT
* *
17968970 ATAAT ATAAT AGTAAT AATAAT AATAAG ATACT ATAAT AT-A- ATAAT
1 ATAAT ATAAT A-TAAT -ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT
* * *
17969016 ATAAT AATAACA ATAAT ATAGT ATAAT ATAAT ATAAT ATGAT A-ATAT
1 ATAAT -ATAA-T ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT
17969063 AATAAT AATAAT ATAAT ATA
1 -ATAAT -ATAAT ATAAT ATA
17969083 CCATACTATA
Statistics
Matches: 128, Mismatches: 17, Indels: 28
0.74 0.10 0.16
Matches are distributed among these distances:
3 2 0.02
4 6 0.05
5 78 0.61
6 40 0.31
7 2 0.02
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (5 bp):
ATAAT
Found at i:17969413 original size:55 final size:54
Alignment explanation
Indices: 17969320--17969445 Score: 162
Period size: 55 Copynumber: 2.3 Consensus size: 54
17969310 CATAAGTCTG
* *
17969320 AAAAATGATTTGGACTGAGCCAAGATCGAACAACCGAGATTAAACTACAAGTTT
1 AAAAATGATTTGGACTAAGCCAAGATCGAACAACCGAGATTAAACCACAAGTTT
* *** *
17969374 GGAAAATGATTTGGACTAAGCCAAGATCGAGTGATCGAGATTAAACCACAAGTTT
1 -AAAAATGATTTGGACTAAGCCAAGATCGAACAACCGAGATTAAACCACAAGTTT
17969429 AAAAAGTTGATTTGGAC
1 AAAAA--TGATTTGGAC
17969446 CAAGTCGAGG
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
54 4 0.07
55 47 0.77
56 10 0.16
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.24
Consensus pattern (54 bp):
AAAAATGATTTGGACTAAGCCAAGATCGAACAACCGAGATTAAACCACAAGTTT
Found at i:17969646 original size:55 final size:55
Alignment explanation
Indices: 17969521--17969652 Score: 142
Period size: 55 Copynumber: 2.4 Consensus size: 55
17969511 GAGATTAAAT
* * * *
17969521 GACCAGGATTGAATCGCAAGTCTAGAAAATGATCTGTATTGAGCCAATATCAAGC
1 GACCAGGATTGAACCACAAGTCTAGAAAATGATCTGTATTAAGCCAAGATCAAGC
* * * * *
17969576 GACCGGGGTTAAACCACAAGTCT-GAAAAGTGATCTAG-ATTAAGCCAAGATCGAGT
1 GACCAGGATTGAACCACAAGTCTAGAAAA-TGATCT-GTATTAAGCCAAGATCAAGC
*
17969631 GATCAGGATTGAACCACAAGTC
1 GACCAGGATTGAACCACAAGTC
17969653 AAAAAAACTA
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
54 5 0.08
55 56 0.90
56 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.21
Consensus pattern (55 bp):
GACCAGGATTGAACCACAAGTCTAGAAAATGATCTGTATTAAGCCAAGATCAAGC
Found at i:17973183 original size:70 final size:72
Alignment explanation
Indices: 17973066--17973210 Score: 249
Period size: 70 Copynumber: 2.0 Consensus size: 72
17973056 ATGTCTATGG
*
17973066 AACCCTCAGATTGTGCATGAACATGAATGCAAAAACAAAATGCATGAATGCAATAAGGAGAATTT
1 AACCCTCAGATTGTGCATGAAAATGAATGCAAAAACAAAATGCATGAATGCAATAAGGAGAATTT
17973131 ACCACAT
66 ACCACAT
* *
17973138 AACCCTCAGA-T-TGCATGAAAATGAATGTAAAAACAAAATGTATGAATGCAATAAGGAGAATTT
1 AACCCTCAGATTGTGCATGAAAATGAATGCAAAAACAAAATGCATGAATGCAATAAGGAGAATTT
17973201 ACCACAT
66 ACCACAT
17973208 AAC
1 AAC
17973211 AATTGTTATC
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
70 59 0.84
71 1 0.01
72 10 0.14
ACGTcount: A:0.46, C:0.17, G:0.16, T:0.21
Consensus pattern (72 bp):
AACCCTCAGATTGTGCATGAAAATGAATGCAAAAACAAAATGCATGAATGCAATAAGGAGAATTT
ACCACAT
Found at i:17975340 original size:22 final size:23
Alignment explanation
Indices: 17975311--17975369 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
17975301 TGCTCAGTAA
17975311 AAAT-AAATAAATAATAAAAGT-
1 AAATAAAATAAATAATAAAAGTG
* *
17975332 CAATAAAATAAAT-ATAAAATTG
1 AAATAAAATAAATAATAAAAGTG
17975354 AAATAAAATAATATAA
1 AAATAAAATAA-ATAA
17975370 AAATTTTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 10 0.32
22 18 0.58
23 2 0.06
24 1 0.03
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.25
Consensus pattern (23 bp):
AAATAAAATAAATAATAAAAGTG
Found at i:17975374 original size:22 final size:22
Alignment explanation
Indices: 17975311--17975371 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
17975301 TGCTCAGTAA
*
17975311 AAAT-AAATAAATAATAAAAGT-
1 AAATAAAATAAAT-ATAAAATTG
*
17975332 CAATAAAATAAATATAAAATTG
1 AAATAAAATAAATATAAAATTG
17975354 AAATAAAAT-AATATAAAA
1 AAATAAAATAAATATAAAA
17975372 ATTTTTCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 19 0.54
22 16 0.46
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (22 bp):
AAATAAAATAAATATAAAATTG
Found at i:17976241 original size:3 final size:3
Alignment explanation
Indices: 17976222--17976404 Score: 111
Period size: 3 Copynumber: 66.3 Consensus size: 3
17976212 AGAAAGGAAA
*
17976222 AAT AAT GAT AA- AAT AAT AAT AAT AAT -AT AAT -AT ATAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
* *
17976264 AAT -AT AAT AAT AAT AAT AA- GAT ACT -AT AAT -AT AAT -AT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
17976307 -AT AAT AAT AAC AAT AAT AAT -AT AAT -AT ATAC AAT -AT GAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT
*
17976348 AAT -AT AAT -AT GAT ACGAT AAT AA- AAT AAT -AT GAA- AAT -AT AAT
1 AAT AAT AAT AAT AAT A--AT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
17976390 AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT A
17976405 TACCACACTA
Statistics
Matches: 143, Mismatches: 11, Indels: 52
0.69 0.05 0.25
Matches are distributed among these distances:
2 40 0.28
3 94 0.66
4 6 0.04
5 3 0.02
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:17976241 original size:14 final size:14
Alignment explanation
Indices: 17976222--17976404 Score: 138
Period size: 14 Copynumber: 13.3 Consensus size: 14
17976212 AGAAAGGAAA
* *
17976222 AATAATGATAAAAT
1 AATAATAATAATAT
17976236 AATAATAATAATAT
1 AATAATAATAATAT
17976250 AAT-ATATATAATAT
1 AATAATA-ATAATAT
17976264 AAT-ATAAT-A-AT
1 AATAATAATAATAT
*
17976275 AATAATAA-GATACT
1 AATAATAATAATA-T
17976289 -ATAAT-ATAATAT
1 AATAATAATAATAT
17976301 AATAAT-ATAATAAT
1 AATAATAATAAT-AT
*
17976315 AACAATAATAATAT
1 AATAATAATAATAT
*
17976329 AAT-ATATACAATAT
1 AATAATA-ATAATAT
17976343 GATATAAT-ATAATAT
1 -A-ATAATAATAATAT
* *
17976358 GATACGATAATAAAAT
1 AATA--ATAATAATAT
17976374 AAT-ATGAA-AATAT
1 AATAAT-AATAATAT
17976387 AATAATAATAATAT
1 AATAATAATAATAT
17976401 AATA
1 AATA
17976405 TACCACACTA
Statistics
Matches: 139, Mismatches: 11, Indels: 38
0.74 0.06 0.20
Matches are distributed among these distances:
11 5 0.04
12 8 0.06
13 41 0.29
14 59 0.42
15 14 0.10
16 10 0.07
17 2 0.01
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (14 bp):
AATAATAATAATAT
Found at i:17976251 original size:8 final size:8
Alignment explanation
Indices: 17976223--17976404 Score: 117
Period size: 8 Copynumber: 21.8 Consensus size: 8
17976213 GAAAGGAAAA
*
17976223 ATAATGAT
1 ATAATAAT
*
17976231 AAAATAAT
1 ATAATAAT
17976239 AATAATAAT
1 -ATAATAAT
17976248 ATAATATAT
1 ATAATA-AT
17976257 ATAATATAAT
1 AT-A-ATAAT
17976267 ATAATAAT
1 ATAATAAT
*
17976275 AATAATAAG
1 -ATAATAAT
*
17976284 ATACT-AT
1 ATAATAAT
17976291 A-ATATAAT
1 ATA-ATAAT
17976299 ATAATAAT
1 ATAATAAT
17976307 ATAATAAT
1 ATAATAAT
*
17976315 AACAATAAT
1 -ATAATAAT
17976324 A-ATATAAT
1 ATA-ATAAT
*
17976332 ATATACAAT
1 ATA-ATAAT
17976341 ATGATATAAT
1 AT-A-ATAAT
17976351 ATAAT-AT
1 ATAATAAT
17976358 GATACGATAAT
1 -ATA--ATAAT
*
17976369 AAAATAAT
1 ATAATAAT
17976377 ATGAA-AAT
1 AT-AATAAT
17976385 ATAAT-A-
1 ATAATAAT
17976391 ATAATAAT
1 ATAATAAT
17976399 ATAATA
1 ATAATA
17976405 TACCACACTA
Statistics
Matches: 142, Mismatches: 12, Indels: 40
0.73 0.06 0.21
Matches are distributed among these distances:
6 6 0.04
7 10 0.07
8 66 0.46
9 38 0.27
10 17 0.12
11 5 0.04
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.34
Consensus pattern (8 bp):
ATAATAAT
Found at i:17976333 original size:5 final size:5
Alignment explanation
Indices: 17976237--17976406 Score: 123
Period size: 5 Copynumber: 32.6 Consensus size: 5
17976227 TGATAAAATA
*
17976237 ATAAT AATAAT ATAAT AT-AT ATAAT ATAAT ATAAT AATAAT AATAAG
1 ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT -ATAAT
* *
17976284 ATACT ATAAT ATAAT ATAAT A-ATAT AATAAT AACAAT AATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATA-AT -ATAAT -ATAAT -ATAAT ATAAT
* * * ** * *
17976332 AT-AT ACAAT ATGAT ATAAT ATAAT ATGAT ACGAT AATAAA ATAAT ATGAAA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT AT-AAT
17976383 AT-AT AATAAT AATAAT ATAAT ATA
1 ATAAT -ATAAT -ATAAT ATAAT ATA
17976407 CCACACTATT
Statistics
Matches: 136, Mismatches: 18, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
4 9 0.07
5 84 0.62
6 42 0.31
7 1 0.01
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (5 bp):
ATAAT
Found at i:17976333 original size:65 final size:66
Alignment explanation
Indices: 17976223--17976406 Score: 172
Period size: 70 Copynumber: 2.6 Consensus size: 66
17976213 GAAAGGAAAA
* * *
17976223 ATAATGATAA-AATAATAATAATAATATAATATATATAATATAATATAATAATAATAATAAGATA
1 ATAAT-ATAATAAT-ATAATAATAAAATAATA-ATATAATAT-ATACAAT-ATGAT-ATAAGATA
*
17976287 CTATAAT
60 ATATAAT
*
17976294 ATAATATAATAATATAATAATAACAATAATAATATAATATATACAATATGATATAATATAATATG
1 ATAATATAATAATATAATAATAA-AATAATAATATAATATATACAATATGATATAAGATAATAT-
*
17976359 ATACG
64 A-A-T
* *
17976364 ATAATAAAATAATATGAAAATATAATAATAATAATATAATATA
1 ATAATATAATAATAT-AATA-ATAA-AATAATAATATAATATA
17976407 CCACACTATT
Statistics
Matches: 97, Mismatches: 9, Indels: 13
0.82 0.08 0.11
Matches are distributed among these distances:
67 10 0.10
68 5 0.05
69 7 0.07
70 37 0.38
71 17 0.18
72 21 0.22
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.34
Consensus pattern (66 bp):
ATAATATAATAATATAATAATAAAATAATAATATAATATATACAATATGATATAAGATAATATAA
T
Found at i:17978072 original size:29 final size:31
Alignment explanation
Indices: 17978028--17978088 Score: 83
Period size: 29 Copynumber: 2.0 Consensus size: 31
17978018 AACCTTACTT
*
17978028 ATCTTTAAAATCATGCAA-TAAACTTAAATTA
1 ATCTTTAAAATCATGCAATTAAAC-CAAATTA
17978059 ATCTTT-AAA-CATGCAATTAAACCAAATTA
1 ATCTTTAAAATCATGCAATTAAACCAAATTA
17978088 A
1 A
17978089 ATCAAAATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 14 0.50
30 8 0.29
31 6 0.21
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.33
Consensus pattern (31 bp):
ATCTTTAAAATCATGCAATTAAACCAAATTA
Found at i:17980706 original size:29 final size:28
Alignment explanation
Indices: 17980652--17980706 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
17980642 TGAATCTCTT
**
17980652 TTTTTTAATTTTCTTTTGAAGGGAAATA
1 TTTTTTAATTTTCTTTTGAAAAGAAATA
17980680 TTTTTTAATCTTT-TTTTGAAAAAGAAA
1 TTTTTTAAT-TTTCTTTTG-AAAAGAAA
17980707 ATAATTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.53
Consensus pattern (28 bp):
TTTTTTAATTTTCTTTTGAAAAGAAATA
Found at i:17981992 original size:17 final size:17
Alignment explanation
Indices: 17981957--17982000 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
17981947 TCGATTTAAA
*
17981957 GTTTAGGGTTTTAGGTTG
1 GTTTAGGG-TTTAGATTG
17981975 G-TTAGGGTTTAGAATTG
1 GTTTAGGGTTTAG-ATTG
17981992 GTTTAGGGT
1 GTTTAGGGT
17982001 CATGGTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 5 0.22
17 10 0.43
18 8 0.35
ACGTcount: A:0.16, C:0.00, G:0.39, T:0.45
Consensus pattern (17 bp):
GTTTAGGGTTTAGATTG
Found at i:17982108 original size:13 final size:14
Alignment explanation
Indices: 17982027--17982282 Score: 106
Period size: 13 Copynumber: 19.4 Consensus size: 14
17982017 GCTTTAGTAT
*
17982027 AGGTTTAGAGTTT-
1 AGGTTTAGGGTTTA
*
17982040 TGGTTTAGGGTTTA
1 AGGTTTAGGGTTTA
*
17982054 AGGTTTAGGATTTA
1 AGGTTTAGGGTTTA
*
17982068 GGGTTTTAAGGGTTTA
1 AGG-TTT-AGGGTTTA
* *
17982084 AGG-TAAGAGTTT-
1 AGGTTTAGGGTTTA
*
17982096 TGGTTTAGGGTTT-
1 AGGTTTAGGGTTTA
* *
17982109 GGGATTTAGGATTTA
1 AGG-TTTAGGGTTTA
17982124 A---TTA-GG-TT-
1 AGGTTTAGGGTTTA
17982132 AGGTTT--GGTTTA
1 AGGTTTAGGGTTTA
*
17982144 AGTGTTTGGGGTTT-
1 AG-GTTTAGGGTTTA
*
17982158 AGGTTT--GATTTA
1 AGGTTTAGGGTTTA
*
17982170 AGGTTTTA-GATTT-
1 AGG-TTTAGGGTTTA
* *
17982183 TGGTTTAGAGTTTA
1 AGGTTTAGGGTTTA
*
17982197 GGGTTTAGGGTTT-
1 AGGTTTAGGGTTTA
* *
17982210 TGGCTTAGGGTTT-
1 AGGTTTAGGGTTTA
* *
17982223 TGGTTTAAGGTTTA
1 AGGTTTAGGGTTTA
* *
17982237 GGGTTTAGAGTTT-
1 AGGTTTAGGGTTTA
17982250 -GGTTTTAGGGTTT-
1 AGG-TTTAGGGTTTA
17982263 AGGTTTAGGGTTTA
1 AGGTTTAGGGTTTA
*
17982277 GGGTTT
1 AGGTTT
17982283 GCATGTAAAA
Statistics
Matches: 189, Mismatches: 31, Indels: 45
0.71 0.12 0.17
Matches are distributed among these distances:
8 1 0.01
9 2 0.01
10 3 0.02
11 11 0.06
12 13 0.07
13 83 0.44
14 59 0.31
15 8 0.04
16 9 0.05
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.47
Consensus pattern (14 bp):
AGGTTTAGGGTTTA
Found at i:17982219 original size:20 final size:20
Alignment explanation
Indices: 17982180--17982282 Score: 102
Period size: 20 Copynumber: 5.2 Consensus size: 20
17982170 AGGTTTTAGA
*
17982180 TTTTGGTTTAGAGTTTAGGG
1 TTTTGGTTTAGGGTTTAGGG
* * *
17982200 TTTAGGGTTT-TGGCTTAGGG
1 TTT-TGGTTTAGGGTTTAGGG
*
17982220 TTTTGGTTTAAGGTTTAGGG
1 TTTTGGTTTAGGGTTTAGGG
* *
17982240 TTTAGAGTTT-GGTTTTAGGG
1 TTTTG-GTTTAGGGTTTAGGG
*
17982260 TTTAGGTTTAGGGTTTAGGG
1 TTTTGGTTTAGGGTTTAGGG
17982280 TTT
1 TTT
17982283 GCATGTAAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
19 9 0.13
20 50 0.74
21 9 0.13
ACGTcount: A:0.14, C:0.01, G:0.36, T:0.50
Consensus pattern (20 bp):
TTTTGGTTTAGGGTTTAGGG
Found at i:17982226 original size:40 final size:40
Alignment explanation
Indices: 17982180--17982282 Score: 138
Period size: 40 Copynumber: 2.6 Consensus size: 40
17982170 AGGTTTTAGA
*
17982180 TTTTGGTTTAGAGTTTAGGGTTTAGGGTTTTGG-CTTAGGG
1 TTTTGGTTTAGAGTTTAGGGTTTAGAG-TTTGGTCTTAGGG
*
17982220 TTTTGGTTTA-AGGTTTAGGGTTTAGAGTTTGGTTTTAGGG
1 TTTTGGTTTAGA-GTTTAGGGTTTAGAGTTTGGTCTTAGGG
* *
17982260 TTTAGGTTTAGGGTTTAGGGTTT
1 TTTTGGTTTAGAGTTTAGGGTTT
17982283 GCATGTAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
39 6 0.11
40 50 0.89
ACGTcount: A:0.14, C:0.01, G:0.36, T:0.50
Consensus pattern (40 bp):
TTTTGGTTTAGAGTTTAGGGTTTAGAGTTTGGTCTTAGGG
Found at i:17982279 original size:7 final size:7
Alignment explanation
Indices: 17982028--17982282 Score: 112
Period size: 7 Copynumber: 37.7 Consensus size: 7
17982018 CTTTAGTATA
17982028 GGTTTAG
1 GGTTTAG
* *
17982035 AGTTT-T
1 GGTTTAG
17982041 GGTTTAG
1 GGTTTAG
*
17982048 GGTTTAA
1 GGTTTAG
17982055 GGTTTAG
1 GGTTTAG
*
17982062 GATTTAG
1 GGTTTAG
17982069 GGTTTTAAG
1 GG-TTT-AG
*
17982078 GGTTTAA
1 GGTTTAG
*
17982085 GG-TAAG
1 GGTTTAG
* *
17982091 AGTTT-T
1 GGTTTAG
17982097 GGTTTAG
1 GGTTTAG
17982104 GGTTT-G
1 GGTTTAG
17982110 GGATTTAG
1 GG-TTTAG
* *
17982118 GATTTAATTA
1 GGTTT-A--G
17982128 GG-TTA-
1 GGTTTAG
17982133 GGTTT--
1 GGTTTAG
17982138 GGTTTAAG
1 GGTTT-AG
* *
17982146 TGTTTGG
1 GGTTTAG
17982153 GGTTTA-
1 GGTTTAG
17982159 GGTTT--
1 GGTTTAG
*
17982164 GATTTAAG
1 GGTTT-AG
*
17982172 GTTTTA-
1 GGTTTAG
* *
17982178 GATTT-T
1 GGTTTAG
17982184 GGTTTAG
1 GGTTTAG
*
17982191 AGTTTAG
1 GGTTTAG
17982198 GGTTTAG
1 GGTTTAG
*
17982205 GGTTT-T
1 GGTTTAG
*
17982211 GGCTTAG
1 GGTTTAG
*
17982218 GGTTT-T
1 GGTTTAG
*
17982224 GGTTTAA
1 GGTTTAG
17982231 GGTTTAG
1 GGTTTAG
17982238 GGTTTAG
1 GGTTTAG
*
17982245 AGTTT-G
1 GGTTTAG
*
17982251 GTTTTAG
1 GGTTTAG
17982258 GGTTTA-
1 GGTTTAG
17982264 GGTTTAG
1 GGTTTAG
17982271 GGTTTAG
1 GGTTTAG
17982278 GGTTT
1 GGTTT
17982283 GCATGTAAAA
Statistics
Matches: 184, Mismatches: 41, Indels: 46
0.68 0.15 0.17
Matches are distributed among these distances:
5 11 0.06
6 48 0.26
7 100 0.54
8 18 0.10
9 6 0.03
10 1 0.01
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (7 bp):
GGTTTAG
Found at i:17983945 original size:30 final size:32
Alignment explanation
Indices: 17983909--17983975 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 32
17983899 CATTTTTACT
*
17983909 AATTTTTTATTA-TTTTTATTTTT-TATTAAA
1 AATTTTTTACTATTTTTTATTTTTATATTAAA
*
17983939 AA-TTTTTACTATTTTTTATTTTTAATTTTAAA
1 AATTTTTTACTATTTTTTATTTTT-ATATTAAA
17983971 AATTT
1 AATTT
17983976 ATCAAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 8 0.26
30 13 0.42
32 8 0.26
33 2 0.06
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.67
Consensus pattern (32 bp):
AATTTTTTACTATTTTTTATTTTTATATTAAA
Found at i:17984123 original size:18 final size:19
Alignment explanation
Indices: 17984102--17984141 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
17984092 TTTAACTATA
*
17984102 TATTTTATTT-TTTATTTT
1 TATTTTATTTATTTATTAT
17984120 TA-TTTATTTATTTATTAT
1 TATTTTATTTATTTATTAT
17984138 TATT
1 TATT
17984142 ATAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 7 0.37
18 11 0.58
19 1 0.05
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (19 bp):
TATTTTATTTATTTATTAT
Found at i:17984217 original size:21 final size:21
Alignment explanation
Indices: 17984193--17984244 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
17984183 TAGCATCCAT
17984193 AAATATTAATAACACA-ATTTA
1 AAATATTAATAACA-ATATTTA
* *
17984214 AAATAATAATAATAATATTTA
1 AAATATTAATAACAATATTTA
*
17984235 AAAAATTAAT
1 AAATATTAAT
17984245 TCAAAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATATTAATAACAATATTTA
Found at i:17985036 original size:44 final size:44
Alignment explanation
Indices: 17984982--17985092 Score: 168
Period size: 44 Copynumber: 2.5 Consensus size: 44
17984972 ATAGGCTCCC
* * *
17984982 CTAAGCAGAGGCTTAACAACTTTTTAAAATTTTAAAAAGCTCCT
1 CTAAACAGAGGCTTAACAACTTTTTAAAAATTTAAAAAGCCCCT
* * *
17985026 CTAAATAGAGGCTCAACAACTTTTTAAAAATTTAAAAGGCCCCT
1 CTAAACAGAGGCTTAACAACTTTTTAAAAATTTAAAAAGCCCCT
17985070 CTAAACAGAGGCTTAACAACTTT
1 CTAAACAGAGGCTTAACAACTTT
17985093 AAAATGCTCC
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 59 1.00
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.29
Consensus pattern (44 bp):
CTAAACAGAGGCTTAACAACTTTTTAAAAATTTAAAAAGCCCCT
Found at i:17985125 original size:34 final size:34
Alignment explanation
Indices: 17985056--17985126 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
17985046 TTTTTAAAAA
* *
17985056 TTTAAAAGGCCCCTCTAAACAGAGGCTTAACAAC
1 TTTAAAAGGCCCCTCTAAAAAGAGGCTCAACAAC
* * * *
17985090 TTTAAAATGCTCCTCTAAAAAGAGGCTCCATAAC
1 TTTAAAAGGCCCCTCTAAAAAGAGGCTCAACAAC
17985124 TTT
1 TTT
17985127 TTGTCAATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.27
Consensus pattern (34 bp):
TTTAAAAGGCCCCTCTAAAAAGAGGCTCAACAAC
Found at i:17985243 original size:48 final size:49
Alignment explanation
Indices: 17985176--17985573 Score: 283
Period size: 49 Copynumber: 7.9 Consensus size: 49
17985166 CTTGATAATG
*
17985176 AAAGCTCCTCTATA-CAAAGGCTTAACAACTTT-AAAATTTCATCTTGGA
1 AAAGCTCCTCTA-AGCAAAGGCTTAACAACTTTAAAAATTTCATCTTGAA
* **
17985224 AAAGCTCCTCTAAGTAAAGG-TTCAACAACTTTCATTGACTTTAAAAATTTCATCTCAAA
1 AAAGCTCCTCTAAGCAAAGGCTT----AA----CA---ACTTTAAAAATTTCATCTTGAA
* * * *
17985283 AAAGCTCCTTTAAGTAGAGGCTTAACAACTTTAAAAAATTT-ATCATGCAA
1 AAAGCTCCTCTAAGCAAAGGCTTAACAACTTT-AAAAATTTCATCTTG-AA
* ** * * ** *
17985333 AAGGCTTTTCTAAGTAAAGGCTCAATGACTTTAAAAATTTTATCTTG-A
1 AAAGCTCCTCTAAGCAAAGGCTTAACAACTTTAAAAATTTCATCTTGAA
* * *
17985381 AAAGTTTCCTCTAAGCAGAGG-TTCAACAACTTTAAAAATTTCAT-TTTAA
1 AAAG-CTCCTCTAAGCAAAGGCTT-AACAACTTTAAAAATTTCATCTTGAA
* * * *
17985430 AAAACTCCTCTAAGTAGAGGCTTAACAACTTTAAAAAATTCATCTTGAA
1 AAAGCTCCTCTAAGCAAAGGCTTAACAACTTTAAAAATTTCATCTTGAA
* * * *
17985479 AAAGGCTCATCTAAGCAAA-ACTCAACAACTTTAAAAATTTCATC-TCAA
1 AAA-GCTCCTCTAAGCAAAGGCTTAACAACTTTAAAAATTTCATCTTGAA
* * * * *
17985527 AAAGTTCCTCTAAACAGAGGCTTAACAACTTAAAAAAAATTCATCTT
1 AAAGCTCCTCTAAGCAAAGGCTTAACAACTT-TAAAAATTTCATCTT
17985574 TTCTCAAAAT
Statistics
Matches: 274, Mismatches: 50, Indels: 50
0.73 0.13 0.13
Matches are distributed among these distances:
47 14 0.05
48 73 0.27
49 90 0.33
50 51 0.19
51 2 0.01
52 2 0.01
55 2 0.01
56 2 0.01
58 5 0.02
59 31 0.11
60 2 0.01
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (49 bp):
AAAGCTCCTCTAAGCAAAGGCTTAACAACTTTAAAAATTTCATCTTGAA
Found at i:17985297 original size:59 final size:58
Alignment explanation
Indices: 17985203--17985314 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 58
17985193 AGGCTTAACA
***
17985203 ACTTTAAAATTTCATCTTGGAAAAGCTCCTCTAAGTAAAGG-TTCAACAACTTTCATTG
1 ACTTTAAAATTTCATCTCAAAAAAGCTCCTCTAAGTAAAGGCTT-AACAACTTTCATTG
* *
17985261 ACTTTAAAAATTTCATCTCAAAAAAGCTCCTTTAAGTAGAGGCTTAACAACTTT
1 ACTTT-AAAATTTCATCTCAAAAAAGCTCCTCTAAGTAAAGGCTTAACAACTTT
17985315 AAAAAATTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
58 5 0.11
59 40 0.85
60 2 0.04
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.34
Consensus pattern (58 bp):
ACTTTAAAATTTCATCTCAAAAAAGCTCCTCTAAGTAAAGGCTTAACAACTTTCATTG
Found at i:17985475 original size:97 final size:97
Alignment explanation
Indices: 17985306--17985573 Score: 270
Period size: 97 Copynumber: 2.7 Consensus size: 97
17985296 GTAGAGGCTT
** ** * * **
17985306 AACAACTTTAAAAAATTT-ATCATGCAAAAGGCTTTTCTAAGTAAAGGCTCAATGACTTTAAAAA
1 AACAACTTT-AAAAATTTCATC-T-CAAAAAACTCCTCTAAGTAGAGGCTTAACAACTTTAAAAA
* * ** * ***
17985370 TTTTATCTTG-AAAAGTTTCCTCTAAGCAGAGGTTC
63 ATTCATCTTGAAAAAGGCTCATCTAAGCA-AAACTC
* *
17985405 AACAACTTTAAAAATTTCATTTTAAAAAACTCCTCTAAGTAGAGGCTTAACAACTTTAAAAAATT
1 AACAACTTTAAAAATTTCATCTCAAAAAACTCCTCTAAGTAGAGGCTTAACAACTTTAAAAAATT
17985470 CATCTTGAAAAAGGCTCATCTAAGCAAAACTC
66 CATCTTGAAAAAGGCTCATCTAAGCAAAACTC
** ** *
17985502 AACAACTTTAAAAATTTCATCTCAAAAAGTTCCTCTAAACAGAGGCTTAACAACTTAAAAAAAAT
1 AACAACTTTAAAAATTTCATCTCAAAAAACTCCTCTAAGTAGAGGCTTAACAACTT-TAAAAAAT
17985567 TCATCTT
65 TCATCTT
17985574 TTCTCAAAAT
Statistics
Matches: 141, Mismatches: 25, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
97 92 0.65
98 38 0.27
99 11 0.08
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.31
Consensus pattern (97 bp):
AACAACTTTAAAAATTTCATCTCAAAAAACTCCTCTAAGTAGAGGCTTAACAACTTTAAAAAATT
CATCTTGAAAAAGGCTCATCTAAGCAAAACTC
Found at i:17985565 original size:147 final size:148
Alignment explanation
Indices: 17985261--17985572 Score: 407
Period size: 147 Copynumber: 2.1 Consensus size: 148
17985251 ACTTTCATTG
* * *
17985261 ACTTTAAAAATTTCATCTCAAAAAAGCTCCTTTAAGTAGAGGCTTAACAACTTTAAAAAATTTAT
1 ACTTAAAAAATTTCATCTCAAAAAAGCTCCTCTAAGTAGAGGCTTAACAACTTTAAAAAATTCAT
* ** * * ** * **
17985326 CATGCAAAAGGCTTTTCTAAGTAAAGGCTCAATGACTTTAAAAATTTTATCTTGAAAAGTTTCCT
66 CATGAAAAAGGCTCATCTAAGCAAAGACTCAACAACTTTAAAAATTTCATCTCAAAAAGTTTCCT
*
17985391 CTAAGCAGAGGTTCAACA
131 CTAAACAGAGGTTCAACA
* * *
17985409 ACTTTAAAAATTTCATTTTAAAAAA-CTCCTCTAAGTAGAGGCTTAACAACTTTAAAAAATTCAT
1 ACTTAAAAAATTTCATCTCAAAAAAGCTCCTCTAAGTAGAGGCTTAACAACTTTAAAAAATTCAT
*
17985473 CTTGAAAAAGGCTCATCTAAGCAAA-ACTCAACAACTTTAAAAATTTCATCTCAAAAAG-TTCCT
66 CATGAAAAAGGCTCATCTAAGCAAAGACTCAACAACTTTAAAAATTTCATCTCAAAAAGTTTCCT
17985536 CTAAACAGAGGCTT-AACA
131 CTAAACAGAGG-TTCAACA
*
17985554 ACTTAAAAAAAATTCATCT
1 ACTT-AAAAAATTTCATCT
17985573 TTTCTCAAAA
Statistics
Matches: 143, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
145 23 0.16
146 40 0.28
147 57 0.40
148 23 0.16
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.31
Consensus pattern (148 bp):
ACTTAAAAAATTTCATCTCAAAAAAGCTCCTCTAAGTAGAGGCTTAACAACTTTAAAAAATTCAT
CATGAAAAAGGCTCATCTAAGCAAAGACTCAACAACTTTAAAAATTTCATCTCAAAAAGTTTCCT
CTAAACAGAGGTTCAACA
Found at i:17986425 original size:17 final size:18
Alignment explanation
Indices: 17986392--17986426 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17986382 CTAAGATATA
*
17986392 TCTTTTTTTTTCTTTTTC
1 TCTTTTTTTTTCGTTTTC
17986410 TCTTTTTTTTT-GTTTTC
1 TCTTTTTTTTTCGTTTTC
17986427 AAGTAAAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (18 bp):
TCTTTTTTTTTCGTTTTC
Found at i:17996273 original size:146 final size:144
Alignment explanation
Indices: 17996008--17996274 Score: 358
Period size: 146 Copynumber: 1.8 Consensus size: 144
17995998 CATAGTGCCC
* * *
17996008 CAAAAAGGTAAAATTACCAAAATATCCTTATAGATGTAATTTCATAATTTGACCTTTTCCAGCTT
1 CAAAAAGGTAAAATTACCAAAATATCCTTATAGAGGTAATTTCATAATTTGACCTTTTCCAACTG
17996073 GAATTTTTTTGAAACTTCTCAAATCTTAATTTTATAATATTTCATAAATTTTGGTGCATTTAAAA
66 GAATTTTTTTGAAACTTCTCAAATCTTAATTTTATAATATTTCATAAATTTTGGTGCATTTAAAA
17996138 TCACGATGGTACCT
131 TCACGATGGTACCT
* * * * **
17996152 CAAAAAGGATGAAATTACCAAAATATCCTTATTAG-GGTATTTTCATAATTTTACTTTTTTGAAC
1 CAAAAAGG-TAAAATTACCAAAATATCCTTA-TAGAGGTAATTTCATAATTTGACCTTTTCCAAC
* * * * *
17996216 TCGGATTTTTTTTTAAAC-TCTTCAAATTTTAATTTTATAATATTTCATGATTTTTGGTG
64 T-GGAATTTTTTTGAAACTTC-TCAAATCTTAATTTTATAATATTTCATAAATTTTGGTG
17996275 AGTTCAAAGC
Statistics
Matches: 105, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
144 8 0.08
145 46 0.44
146 51 0.49
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (144 bp):
CAAAAAGGTAAAATTACCAAAATATCCTTATAGAGGTAATTTCATAATTTGACCTTTTCCAACTG
GAATTTTTTTGAAACTTCTCAAATCTTAATTTTATAATATTTCATAAATTTTGGTGCATTTAAAA
TCACGATGGTACCT
Found at i:17996303 original size:145 final size:143
Alignment explanation
Indices: 17995999--17996347 Score: 362
Period size: 145 Copynumber: 2.4 Consensus size: 143
17995989 TCAAATTTTC
* * * * *
17995999 ATAGTGCCCCAAAAAGGTAAAATTACCAAAATATCCTTATAGATGTAATTTCATAATTTGACCTT
1 ATAGTACCTCAAAAAGGTGAAATTACCAAAATATCCTTATAG-GGTATTTTCATAATTTGACCTT
* *
17996064 TTCCAGCTTGAATTTTTTTGAAACTTCTCAAATCTTAATTTTATAATATTTCATAAATTTTGGTG
65 TTCCAACTGGAATTTTTTTGAAACTTCTCAAATCTTAATTTTATAATATTTCATAAATTTTGGTG
* * *
17996129 CATTTAAAATCACG
130 CATTCAAAACCACA
* * *
17996143 ATGGTACCTCAAAAAGGATGAAATTACCAAAATATCCTTATTAGGGTATTTTCATAATTTTACTT
1 ATAGTACCTCAAAAAGG-TGAAATTACCAAAATATCCTTA-TAGGGTATTTTCATAATTTGACCT
** * * * * *
17996208 TTTTGAACTCGGATTTTTTTTTAAAC-TCTTCAAATTTTAATTTTATAATATTTCATGATTTTTG
64 TTTCCAACT-GGAATTTTTTTGAAACTTC-TCAAATCTTAATTTTATAATATTTCATAAATTTTG
*
17996272 GTG-AGTTCAAAGCCACA
127 GTGCA-TTCAAAACCACA
** * * ** *
17996289 ATAGTA-CTTGAAAAGCGTGATATTACCGAAATGCCCTTATAGGGTATTTTCGTAATTTG
1 ATAGTACCTCAAAAAG-GTGAAATTACCAAAATATCCTTATAGGGTATTTTCATAATTTG
17996348 GCTTTATCGA
Statistics
Matches: 169, Mismatches: 30, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
144 32 0.19
145 72 0.43
146 65 0.38
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (143 bp):
ATAGTACCTCAAAAAGGTGAAATTACCAAAATATCCTTATAGGGTATTTTCATAATTTGACCTTT
TCCAACTGGAATTTTTTTGAAACTTCTCAAATCTTAATTTTATAATATTTCATAAATTTTGGTGC
ATTCAAAACCACA
Found at i:17999751 original size:12 final size:12
Alignment explanation
Indices: 17999734--17999758 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17999724 TTCAAAATAA
17999734 ATATATATACAT
1 ATATATATACAT
17999746 ATATATATACAT
1 ATATATATACAT
17999758 A
1 A
17999759 AGTTAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATATATACAT
Found at i:17999836 original size:17 final size:17
Alignment explanation
Indices: 17999814--17999848 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
17999804 TTTGTGCTTA
17999814 TGATTTATTTATGATAT
1 TGATTTATTTATGATAT
17999831 TGATTTATTTATGATAT
1 TGATTTATTTATGATAT
17999848 T
1 T
17999849 TTGATTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.60
Consensus pattern (17 bp):
TGATTTATTTATGATAT
Found at i:18002095 original size:21 final size:20
Alignment explanation
Indices: 18002049--18002095 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
18002039 CAAATGTCAC
*
18002049 AAAAAAAAAAAGAGATAGAG
1 AAAAAAAAAAAGAGATAAAG
18002069 ACAAAAAAAAAAGA-ATGAAAAG
1 A-AAAAAAAAAAGAGAT--AAAG
18002091 AAAAA
1 AAAAA
18002096 TGGTTATGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 3 0.13
21 16 0.70
22 4 0.17
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.04
Consensus pattern (20 bp):
AAAAAAAAAAAGAGATAAAG
Found at i:18005063 original size:143 final size:143
Alignment explanation
Indices: 18004820--18005173 Score: 354
Period size: 143 Copynumber: 2.5 Consensus size: 143
18004810 TTCAATGTGC
* * * *
18004820 CAAAAAGTCATCAAATAATATGAAAACATTATCTGAAAGTTTTCGTGAAAAAATCAACCTCAAGA
1 CAAAAA-TCATAAAATAATATCAAAACATAATCT-AAAGTTTTCGTG-AAAAACCAACCTCAAGA
* * ** * *
18004885 AAGTTAAATTATGAAAATAATCCTAAAGAGAATTTTAATAATTTCACACCTTTTGAGATATGAT-
63 AAGTCAAATGACAAAAATAATCCTAAAGAGAATTTTAATAATTTCAAACCTTTCGAGATATGATC
** *
18004949 ATAGGTTTTTAATGTAT
128 A-AGGCCTTTAATATAT
* * * *
18004966 CAAAAATCATAAAATAATTTCAAAACATAATCTAAAGTGTTTCATGAAAAACCAACCTC-TGAAG
1 CAAAAATCATAAAATAATATCAAAACATAATCTAAAGT-TTTCGTGAAAAACCAACCTCAAGAAA
* * * * * * * *
18005030 GTCAAATGACAAAAATATTCCTATAGGGCATTTTAATAATTTTAAAGCTTTCGAGGTGTGATCAA
65 GTCAAATGACAAAAATAATCCTAAAGAGAATTTTAATAATTTCAAACCTTTCGAGATATGATCAA
18005095 GGCCTTTAATATAT
130 GGCCTTTAATATAT
* ** * * *
18005109 CAAAAATCATAAAATGATATCAAATTATAATCTAGAGCATTTCGTAAAAAACCAACCTCAA-AAA
1 CAAAAATCATAAAATAATATCAAAACATAATCTAAAG-TTTTCGTGAAAAACCAACCTCAAGAAA
18005173 G
65 G
18005174 GTAAAATTAT
Statistics
Matches: 169, Mismatches: 35, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
143 116 0.69
144 18 0.11
145 29 0.17
146 6 0.04
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (143 bp):
CAAAAATCATAAAATAATATCAAAACATAATCTAAAGTTTTCGTGAAAAACCAACCTCAAGAAAG
TCAAATGACAAAAATAATCCTAAAGAGAATTTTAATAATTTCAAACCTTTCGAGATATGATCAAG
GCCTTTAATATAT
Found at i:18005539 original size:20 final size:20
Alignment explanation
Indices: 18005494--18005540 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
18005484 ATTTTGATCG
18005494 AGTTTGATCAAATTTGACAA
1 AGTTTGATCAAATTTGACAA
* * *
18005514 AATTTGATTAAATTTGACCA
1 AGTTTGATCAAATTTGACAA
18005534 AGTTTGA
1 AGTTTGA
18005541 CCCTAAGGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (20 bp):
AGTTTGATCAAATTTGACAA
Found at i:18006385 original size:21 final size:21
Alignment explanation
Indices: 18006337--18006376 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
18006327 TGATTCAATT
*
18006337 TTATATTCTAATTTATTTTAG
1 TTATATTATAATTTATTTTAG
18006358 TTATATTATAATTT-TTTTA
1 TTATATTATAATTTATTTTA
18006377 TTGATTATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (21 bp):
TTATATTATAATTTATTTTAG
Found at i:18007351 original size:23 final size:22
Alignment explanation
Indices: 18007332--18007379 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 22
18007322 ACTTTTTTAG
18007332 TTTAGGATTTATTATATTTTCTA
1 TTTA-GATTTATTATATTTTCTA
*
18007355 TTTAGCTTTATTATATTTTCTA
1 TTTAGATTTATTATATTTTCTA
18007377 TTT
1 TTT
18007380 GACTTTAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (22 bp):
TTTAGATTTATTATATTTTCTA
Found at i:18007790 original size:20 final size:19
Alignment explanation
Indices: 18007734--18007790 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
18007724 TTTATTTTGC
18007734 ATATATATTTTTTATCTTTA
1 ATAT-TATTTTTTATCTTTA
* * *
18007754 ATATCA-TTATTATTCTTTT
1 ATATTATTTTTTA-TCTTTA
18007773 ATAATTATTTTTTATCTT
1 AT-ATTATTTTTTATCTT
18007791 ATCTAATTGC
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
18 5 0.17
19 8 0.28
20 11 0.38
21 5 0.17
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (19 bp):
ATATTATTTTTTATCTTTA
Found at i:18008932 original size:17 final size:17
Alignment explanation
Indices: 18008910--18008943 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
18008900 ATTCTTTTCC
*
18008910 TTTCATTTTTTTTATTT
1 TTTCATTTTTTTAATTT
18008927 TTTCATTTTTTTAATTT
1 TTTCATTTTTTTAATTT
18008944 CGAATTAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTCATTTTTTTAATTT
Found at i:18011394 original size:10 final size:10
Alignment explanation
Indices: 18011379--18011406 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
18011369 AAAAACTCTA
18011379 ATATATATTT
1 ATATATATTT
18011389 ATATATATTT
1 ATATATATTT
18011399 ATATATAT
1 ATATATAT
18011407 ACAAGAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
ATATATATTT
Found at i:18017347 original size:21 final size:21
Alignment explanation
Indices: 18017306--18017347 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
18017296 ATTTTAAATT
*
18017306 TGATAAGAGAATGAAAGAAAA
1 TGATAAGAGAATGAAAAAAAA
*
18017327 TGATATAGA-AATTAAAAAAAA
1 TGATA-AGAGAATGAAAAAAAA
18017348 AAAAAAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.64, C:0.00, G:0.17, T:0.19
Consensus pattern (21 bp):
TGATAAGAGAATGAAAAAAAA
Found at i:18018662 original size:2 final size:2
Alignment explanation
Indices: 18018655--18018693 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
18018645 ATGTTTGTTT
18018655 TA 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 TA T
18018694 TACATCGGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18021933 original size:17 final size:18
Alignment explanation
Indices: 18021894--18021936 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
18021884 TTTTTCTCCT
**
18021894 TTTTTAATATTTAATAATT
1 TTTTTAATATTT-ATAACC
18021913 TTTTTAATATTT-TAACC
1 TTTTTAATATTTATAACC
18021930 TTTTTAA
1 TTTTTAA
18021937 ATGTGGAGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 10 0.45
19 12 0.55
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTAATATTTATAACC
Found at i:18023452 original size:18 final size:17
Alignment explanation
Indices: 18023414--18023446 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
18023404 TTTCCATTTG
18023414 TTTA-TTTTCTATTTTT
1 TTTAGTTTTCTATTTTT
18023430 TTTAGTTTT-TATTTTT
1 TTTAGTTTTCTATTTTT
18023446 T
1 T
18023447 AATTAGATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTAGTTTTCTATTTTT
Found at i:18023934 original size:5 final size:6
Alignment explanation
Indices: 18023917--18023947 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
18023907 TCTCTTTGTA
*
18023917 TATTTT TATTTT TATTTT TATTTT TCTTTT T
1 TATTTT TATTTT TATTTT TATTTT TATTTT T
18023948 TATTCTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:18024374 original size:8 final size:8
Alignment explanation
Indices: 18024357--18024399 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
18024347 CTCTATCAGC
*
18024357 TTTTCTTT
1 TTTTCATT
18024365 TTTTCATT
1 TTTTCATT
18024373 TTTTCA-T
1 TTTTCATT
*
18024380 TTTTAATT
1 TTTTCATT
*
18024388 TTTTAATT
1 TTTTCATT
18024396 TTTT
1 TTTT
18024400 GTTTTTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
7 6 0.19
8 26 0.81
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTCATT
Found at i:18024406 original size:15 final size:15
Alignment explanation
Indices: 18024364--18024398 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
18024354 AGCTTTTCTT
* *
18024364 TTTTTCATTTTTTCA
1 TTTTTAATTTTTTAA
18024379 TTTTTAATTTTTTAA
1 TTTTTAATTTTTTAA
18024394 TTTTT
1 TTTTT
18024399 TGTTTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTAATTTTTTAA
Found at i:18033626 original size:3 final size:3
Alignment explanation
Indices: 18033620--18033645 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
18033610 TCTTCTTCCA
18033620 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
18033646 ACACCCAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:18035704 original size:14 final size:15
Alignment explanation
Indices: 18035685--18035717 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
18035675 AAAAAATATG
18035685 ATAAAATAAGA-TAA
1 ATAAAATAAGATTAA
*
18035699 ATAAAATTAGATTAA
1 ATAAAATAAGATTAA
18035714 ATAA
1 ATAA
18035718 TATCATCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (15 bp):
ATAAAATAAGATTAA
Found at i:18036929 original size:32 final size:30
Alignment explanation
Indices: 18036839--18036950 Score: 100
Period size: 32 Copynumber: 3.5 Consensus size: 30
18036829 TAATAAATCT
* *
18036839 ATTTTTGAAACTGATCTAAAAATTTTTATATA
1 ATTTTT-AAA-TGATATAAAAATTTTTATTTA
* *
18036871 ATATTTTAACATGATAT-AGAGTTTTTATTTA
1 AT-TTTTAA-ATGATATAAAAATTTTTATTTA
*
18036902 ATTTCTTAAATCGATATAAAAATTTTTACTTA
1 ATTT-TTAAAT-GATATAAAAATTTTTATTTA
18036934 ATTTTTTAAAATGATAT
1 A-TTTTT-AAATGATAT
18036951 GTAATTTTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
30 4 0.06
31 22 0.33
32 28 0.42
33 12 0.18
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.49
Consensus pattern (30 bp):
ATTTTTAAATGATATAAAAATTTTTATTTA
Found at i:18037690 original size:19 final size:21
Alignment explanation
Indices: 18037668--18037707 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
18037658 TCTAAAATGA
18037668 ATTATAAAT-AA-TAATTTTT
1 ATTATAAATAAATTAATTTTT
*
18037687 ATTATAATTAAATTAATTTTT
1 ATTATAAATAAATTAATTTTT
18037708 TAGTTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 2 0.11
21 8 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTATAAATAAATTAATTTTT
Found at i:18044893 original size:16 final size:18
Alignment explanation
Indices: 18044872--18044905 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
18044862 TACGAATTTC
18044872 TTTGG-ATTTT-TTTTTT
1 TTTGGAATTTTGTTTTTT
18044888 TTTGGAATTTTGTTTTTT
1 TTTGGAATTTTGTTTTTT
18044906 GATTAGGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 5 0.31
18 6 0.38
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (18 bp):
TTTGGAATTTTGTTTTTT
Found at i:18044903 original size:17 final size:16
Alignment explanation
Indices: 18044872--18044905 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
18044862 TACGAATTTC
*
18044872 TTTGGATTTTTTTTTT
1 TTTGGATTTTGTTTTT
18044888 TTTGGAATTTTGTTTTT
1 TTTGG-ATTTTGTTTTT
18044905 T
1 T
18044906 GATTAGGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (16 bp):
TTTGGATTTTGTTTTT
Found at i:18047009 original size:12 final size:12
Alignment explanation
Indices: 18046992--18047041 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
18046982 TTTTTTAATA
18046992 TAAATATAAAAT
1 TAAATATAAAAT
*
18047004 TAAATA-AATAT
1 TAAATATAAAAT
*
18047015 CTAAATAT-ATA-
1 -TAAATATAAAAT
18047026 TAAATATAAAAT
1 TAAATATAAAAT
18047038 TAAA
1 TAAA
18047042 AAAATAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
10 7 0.22
11 6 0.19
12 19 0.59
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (12 bp):
TAAATATAAAAT
Found at i:18047057 original size:34 final size:33
Alignment explanation
Indices: 18046963--18047059 Score: 113
Period size: 34 Copynumber: 2.8 Consensus size: 33
18046953 TGACCCAATC
* * *
18046963 TAAAATTAATAAAATATTATTTTTTAATATAAATA
1 TAAAATTAAAAAAATATTA-TATAT-ATATAAATA
* *
18046998 TAAAATTAAATAAATATCTAAATATATATAAATA
1 TAAAATTAAAAAAATAT-TATATATATATAAATA
18047032 TAAAATTAAAAAAATAATTATATATATA
1 TAAAATTAAAAAAAT-ATTATATATATA
18047060 CTGGATTGGA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
34 32 0.60
35 19 0.36
36 2 0.04
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
TAAAATTAAAAAAATATTATATATATATAAATA
Found at i:18048263 original size:14 final size:13
Alignment explanation
Indices: 18048239--18048273 Score: 61
Period size: 14 Copynumber: 2.6 Consensus size: 13
18048229 GTTTGATGGA
18048239 TAAAAAAATTTTC
1 TAAAAAAATTTTC
18048252 TAAAAGAAATTTTC
1 TAAAA-AAATTTTC
18048266 TAAAAAAA
1 TAAAAAAA
18048274 AAAAAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (13 bp):
TAAAAAAATTTTC
Found at i:18050000 original size:3 final size:3
Alignment explanation
Indices: 18049974--18050054 Score: 64
Period size: 3 Copynumber: 28.3 Consensus size: 3
18049964 TTTTTTGTTA
* * *
18049974 TAT TA- TAT TA- TAT TA- TAG TAT TAT TAT CA- TAT TAT TAT TAG TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
18050017 TAT TGT CTAG TAT TAT TAT TAT TAT TAT TAT TGT TAT T
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
18050055 GTATTTTATT
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
2 9 0.15
3 52 0.84
4 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:18051017 original size:7 final size:7
Alignment explanation
Indices: 18051002--18051035 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
18050992 AAAATGATGA
18051002 AAAAAAT
1 AAAAAAT
*
18051009 AAAAGAT
1 AAAAAAT
18051016 -AAAAAT
1 AAAAAAT
18051022 AAAAAAT
1 AAAAAAT
18051029 AAAAAAT
1 AAAAAAT
18051036 CTTTTTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (7 bp):
AAAAAAT
Found at i:18051019 original size:13 final size:13
Alignment explanation
Indices: 18051003--18051033 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
18050993 AAATGATGAA
*
18051003 AAAAATAAAAGAT
1 AAAAATAAAAAAT
18051016 AAAAATAAAAAAT
1 AAAAATAAAAAAT
18051029 AAAAA
1 AAAAA
18051034 ATCTTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:18055077 original size:10 final size:9
Alignment explanation
Indices: 18055064--18055122 Score: 55
Period size: 9 Copynumber: 5.9 Consensus size: 9
18055054 AAAAAGCAAA
18055064 TAAAAAAGAT
1 TAAAAAA-AT
*
18055074 TAAAAAAAA
1 TAAAAAAAT
18055083 TAAAAAAATT
1 TAAAAAAA-T
18055093 GTAAAAAAAAT
1 -T-AAAAAAAT
18055104 TAAAAAAAT
1 TAAAAAAAT
18055113 ATGAAAAAAA
1 -T-AAAAAAA
18055123 GCAAGAAGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
9 17 0.40
10 9 0.21
11 9 0.21
12 7 0.17
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (9 bp):
TAAAAAAAT
Found at i:18055079 original size:11 final size:10
Alignment explanation
Indices: 18055064--18055122 Score: 66
Period size: 11 Copynumber: 5.8 Consensus size: 10
18055054 AAAAAGCAAA
*
18055064 TAAAAAAGAT
1 TAAAAAAAAT
18055074 TAAAAAAAA-
1 TAAAAAAAAT
*
18055083 TAAAAAAATT
1 TAAAAAAAAT
18055093 GTAAAAAAAAT
1 -TAAAAAAAAT
18055104 TAAAAAAATAT
1 TAAAAAAA-AT
*
18055115 GAAAAAAA
1 TAAAAAAA
18055123 GCAAGAAGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
9 8 0.19
10 16 0.38
11 18 0.43
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (10 bp):
TAAAAAAAAT
Found at i:18055085 original size:19 final size:20
Alignment explanation
Indices: 18055061--18055122 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
18055051 TACAAAAAGC
18055061 AAATAAAAAAGA-T-TAAAAA
1 AAATAAAAAA-ATTGTAAAAA
18055080 AAATAAAAAAATTGTAAAAA
1 AAATAAAAAAATTGTAAAAA
18055100 AAATTAAAAAAATATG-AAAAA
1 AAA-TAAAAAAAT-TGTAAAAA
18055121 AA
1 AA
18055123 GCAAGAAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
18 1 0.03
19 11 0.28
20 9 0.23
21 16 0.41
22 2 0.05
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (20 bp):
AAATAAAAAAATTGTAAAAA
Found at i:18055140 original size:21 final size:22
Alignment explanation
Indices: 18055116--18055159 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
18055106 AAAAAATATG
*
18055116 AAAAAAAGCAAGAAGAAA-AGA
1 AAAAAAAGCAAAAAGAAAGAGA
*
18055137 AAAAAAAGGAAAAAGAAAGAGA
1 AAAAAAAGCAAAAAGAAAGAGA
18055159 A
1 A
18055160 TAAGAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.00
Consensus pattern (22 bp):
AAAAAAAGCAAAAAGAAAGAGA
Found at i:18055140 original size:30 final size:29
Alignment explanation
Indices: 18055106--18055170 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 29
18055096 AAAAAAATTA
*
18055106 AAAAAATATGAAAAAAAGCAAGAAGAA-AAG
1 AAAAAA-ATGAAAAAAAGAAAG-AGAATAAG
* *
18055136 AAAAAAAAG-GAAAAAGAAAGAGAATAAG
1 AAAAAAATGAAAAAAAGAAAGAGAATAAG
18055164 AAAAAAA
1 AAAAAAA
18055171 ATGATGACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 4 0.13
28 19 0.61
29 2 0.06
30 6 0.19
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.05
Consensus pattern (29 bp):
AAAAAAATGAAAAAAAGAAAGAGAATAAG
Found at i:18055150 original size:28 final size:28
Alignment explanation
Indices: 18055118--18055171 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
18055108 AAAATATGAA
*
18055118 AAAAAGCAAGAAGAA-AAGAAAAAAAAGG
1 AAAAAGAAAG-AGAATAAGAAAAAAAAGG
18055146 AAAAAGAAAGAGAATAAGAAAAAAAA
1 AAAAAGAAAGAGAATAAGAAAAAAAA
18055172 TGATGACTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.78, C:0.02, G:0.19, T:0.02
Consensus pattern (28 bp):
AAAAAGAAAGAGAATAAGAAAAAAAAGG
Found at i:18056281 original size:77 final size:79
Alignment explanation
Indices: 18056105--18056295 Score: 221
Period size: 77 Copynumber: 2.5 Consensus size: 79
18056095 TATTTTTTTG
* * * *
18056105 ACCTTTGCAAAACTTGAAATC-TTACGAATCTTTTTTTTTTTATGAATTTAAAAGTCCTTGCATC
1 ACCTTTACAAAACTTGAAATCTTTACGAATCTTTTTTTTTTTATAAATTCAAAAGTCCTTACATC
18056169 TTTGCGAATCTAAA
66 TTTGCGAATCTAAA
* * * *
18056183 ACCTTTATAAAA-TTTAGAATCTTTA-GAATC-TTTTTTTTTTATAAATTCGAAAGTCCTTATAT
1 ACCTTTACAAAACTTGA-AATCTTTACGAATCTTTTTTTTTTTATAAATTCAAAAGTCCTTACAT
* *
18056245 CTTTGCGAATTTAGA
65 CTTTGCGAATCTAAA
* * *
18056260 ACCTTTACGAAACTTGAAATC-TTGCCAATCTTTTTT
1 ACCTTTACAAAACTTGAAATCTTTACGAATCTTTTTT
18056296 CGCTGCGAAT
Statistics
Matches: 93, Mismatches: 15, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
76 2 0.02
77 61 0.66
78 27 0.29
79 3 0.03
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (79 bp):
ACCTTTACAAAACTTGAAATCTTTACGAATCTTTTTTTTTTTATAAATTCAAAAGTCCTTACATC
TTTGCGAATCTAAA
Found at i:18056359 original size:86 final size:86
Alignment explanation
Indices: 18056243--18056495 Score: 294
Period size: 86 Copynumber: 2.9 Consensus size: 86
18056233 AAGTCCTTAT
* * * *
18056243 ATCTTTGCGAATTTAGAACCTTTACGAAACTTGAAATCTTGCCAATCTTT-TTTCGCTGCGAATC
1 ATCTTTGCGAATCTAGAACCTTTGCGAAACTTGAAATCTTGCAAATCTTTCTTTC-TTGCGAATC
*
18056307 TGAAAATCCTTGCAATCCTAAA
65 TGAAAATCCTTGCAAACCTAAA
* * * *** * * *
18056329 ATCTTTACGAATCTAGAACCATTGCGAAACTTGAAACCTTATGAATATTTCTTTCTTGTGAATAT
1 ATCTTTGCGAATCTAGAACCTTTGCGAAACTTGAAATCTTGCAAATCTTTCTTTCTTGCGAATCT
* * *
18056394 GAAAGTCCTTGCAAACCTGAG
66 GAAAATCCTTGCAAACCTAAA
* * *
18056415 ATCTTTGTGAATCTAGAACCTTTGCAAAACTTGAAATCTTGCAAATCTTTCATTCTTGCGAATCT
1 ATCTTTGCGAATCTAGAACCTTTGCGAAACTTGAAATCTTGCAAATCTTTCTTTCTTGCGAATCT
18056480 GAAAA-CCTTTGCAAAC
66 GAAAATCC-TTGCAAAC
18056496 TTTGAATCTT
Statistics
Matches: 136, Mismatches: 29, Indels: 4
0.80 0.17 0.02
Matches are distributed among these distances:
85 2 0.01
86 130 0.96
87 4 0.03
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (86 bp):
ATCTTTGCGAATCTAGAACCTTTGCGAAACTTGAAATCTTGCAAATCTTTCTTTCTTGCGAATCT
GAAAATCCTTGCAAACCTAAA
Found at i:18056855 original size:115 final size:113
Alignment explanation
Indices: 18056703--18056916 Score: 248
Period size: 115 Copynumber: 1.9 Consensus size: 113
18056693 ATCGTTACGG
** * * ** *
18056703 TCATTCATCTTCGACCTTAACTCGATTTTGATTACTTTTAGACTCGTGGTATCATCCCAGTCATC
1 TCATTCATCTTCGACCTTAACTCGATCATGATCACTTTCAGACTCACGGCATCATCCCAGTCATC
*
18056768 CGATCTTGGCTCAAGCCAAAATTATTTTTCAACCCACGACATCATCCTGA
66 CGATCTTGGCTCAAGCC-AAATCATTTTT-AACCCACGACATCATCCTGA
* * * * * * *
18056818 TCATTCATCTTCGACCTTGACTTGGTCATGGTCACTTTCAGACTTACGGCATCATCTCAGTTATC
1 TCATTCATCTTCGACCTTAACTCGATCATGATCACTTTCAGACTCACGGCATCATCCCAGTCATC
* * *
18056883 CGATCTTGGTTCAGGTCAAATCATTTTTAACCCA
66 CGATCTTGGCTCAAGCCAAATCATTTTTAACCCA
18056917 TAATATTATC
Statistics
Matches: 81, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
113 6 0.07
114 10 0.12
115 65 0.80
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.36
Consensus pattern (113 bp):
TCATTCATCTTCGACCTTAACTCGATCATGATCACTTTCAGACTCACGGCATCATCCCAGTCATC
CGATCTTGGCTCAAGCCAAATCATTTTTAACCCACGACATCATCCTGA
Found at i:18057292 original size:29 final size:30
Alignment explanation
Indices: 18057243--18057317 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 30
18057233 TGGTCATTTA
*
18057243 ATCTCGACTTAGTCTAGATCA-TT-TTTTG
1 ATCTCGACTTAGTCCAGATCACTTGTTTTG
* * *
18057271 ATTTACGGCTTAGTCCCGATCACTTGTTTTG
1 ATCT-CGACTTAGTCCAGATCACTTGTTTTG
18057302 ATCTCGACTTAGTCCA
1 ATCTCGACTTAGTCCA
18057318 AATTATTTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
28 3 0.08
29 14 0.38
30 12 0.32
31 8 0.22
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (30 bp):
ATCTCGACTTAGTCCAGATCACTTGTTTTG
Found at i:18057315 original size:30 final size:28
Alignment explanation
Indices: 18057243--18057326 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 28
18057233 TGGTCATTTA
*
18057243 ATCTCGACTTAGTCTAGATCATTTTTTG
1 ATCTCGACTTAGTCCAGATCATTTTTTG
* * *
18057271 ATTTACGGCTTAGTCCCGATCACTTGTTTTG
1 ATCT-CGACTTAGTCCAGATCA-TT-TTTTG
* *
18057302 ATCTCGACTTAGTCCAAATTATTTT
1 ATCTCGACTTAGTCCAGATCATTTT
18057327 AATTTTTGAC
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
28 5 0.11
29 16 0.36
30 15 0.34
31 8 0.18
ACGTcount: A:0.21, C:0.20, G:0.14, T:0.44
Consensus pattern (28 bp):
ATCTCGACTTAGTCCAGATCATTTTTTG
Done.