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 69 of 208
Found at i:20070365 original size:29 final size:30
Alignment explanation
Indices: 20070303--20070365 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
20070293 TAAATTTCAT
* *
20070303 TTTTTTAAGAAAATTTTAAAATTTTTTATT
1 TTTTTTAAGAAAATTTTAAAATTTTTAATA
*
20070333 TTTTTTAA-ATAATTTTAAAATTTTTAATA
1 TTTTTTAAGAAAATTTTAAAATTTTTAATA
20070362 TTTT
1 TTTT
20070366 CAACAATTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 22 0.73
30 8 0.27
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (30 bp):
TTTTTTAAGAAAATTTTAAAATTTTTAATA
Found at i:20071055 original size:124 final size:124
Alignment explanation
Indices: 20070835--20071114 Score: 361
Period size: 124 Copynumber: 2.3 Consensus size: 124
20070825 TCTTTTGGGC
*
20070835 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
1 GCGATTTGACACTATTTCCTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
* * * * **
20070900 AAATCGCATCCACGAGGGCGCGATTTTACAATTTCTTC-TAATATAGCATCCTGGTATCA
66 AAATCGCATCCACGAGGCCACGATTTCACAATTTCTTCTTAA-ATAGCATCCTAGTAGAA
* *
20070959 GCGATTTTATACTATTTCCTCAGAAAACGTCAAAAAAAATTATTT-CTCACATGACC-ACTGTAG
1 GCGATTTGACACTATTTCCTCAG-AAACGTCAAAAAAAATTATTTCCT-ACATGACCAACTGTAG
** *
20071022 CGAAATCGTGTCCACGAGGCCACTATTTCACAATTTCTTCTTAAATAGCATCCTAGTAGAA
64 CGAAATCGCATCCACGAGGCCACGATTTCACAATTTCTTCTTAAATAGCATCCTAGTAGAA
** *
20071083 GCGATTTCCCACTATTTAAC-CAGAAACGTCAA
1 GCGATTTGACACTATTT-CCTCAGAAACGTCAA
20071115 CTCGAAAAAA
Statistics
Matches: 136, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
123 9 0.07
124 94 0.69
125 33 0.24
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.29
Consensus pattern (124 bp):
GCGATTTGACACTATTTCCTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
AAATCGCATCCACGAGGCCACGATTTCACAATTTCTTCTTAAATAGCATCCTAGTAGAA
Found at i:20071572 original size:26 final size:26
Alignment explanation
Indices: 20071538--20071598 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
20071528 CCTTAAATAT
* *
20071538 AATTAAAATAT-ATTAAATTATTTAAC
1 AATTTAAATATGATAAAATT-TTTAAC
*
20071564 AATTTAAATATGATAAAATTTTTAAT
1 AATTTAAATATGATAAAATTTTTAAC
20071590 AATGTTAAA
1 AAT-TTAAA
20071599 AAAATCAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 18 0.60
27 12 0.40
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (26 bp):
AATTTAAATATGATAAAATTTTTAAC
Found at i:20072321 original size:2 final size:2
Alignment explanation
Indices: 20072314--20072367 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
20072304 TTAGATGTTG
20072314 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20072356 AT AT AT AT AT AT
1 AT AT AT AT AT AT
20072368 CCTCTAATTC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20074042 original size:23 final size:22
Alignment explanation
Indices: 20073971--20074056 Score: 97
Period size: 21 Copynumber: 4.0 Consensus size: 22
20073961 CCTGATCAGT
20073971 ATACGACACAT-AAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
** *
20073992 A-ACGACACACGAGGTGCCT-A
1 ATACGACACATAAAGTGCCTGA
*
20074012 ATACGACACATAAAGTGTCTGA
1 ATACGACACATAAAGTGCCTGA
*
20074034 GATACGACACATAAAGTGTCTGA
1 -ATACGACACATAAAGTGCCTGA
20074057 TCGGCAAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.18
21 22 0.40
22 1 0.02
23 22 0.40
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (22 bp):
ATACGACACATAAAGTGCCTGA
Found at i:20075009 original size:18 final size:17
Alignment explanation
Indices: 20074977--20075030 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
20074967 TCTTCCCCTG
*
20074977 TTTTCGTCTCTTTC-TC
1 TTTTCTTCTCTTTCTTC
20074993 TGTTTCTTCTCTGTTCTTC
1 T-TTTCTTCTCT-TTCTTC
20075012 TTTTCTT-TCTTT-TTC
1 TTTTCTTCTCTTTCTTC
20075027 TTTT
1 TTTT
20075031 TTTTTTGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
15 7 0.21
16 3 0.09
17 12 0.35
18 9 0.26
19 3 0.09
ACGTcount: A:0.00, C:0.24, G:0.06, T:0.70
Consensus pattern (17 bp):
TTTTCTTCTCTTTCTTC
Found at i:20075019 original size:30 final size:29
Alignment explanation
Indices: 20074948--20075028 Score: 85
Period size: 30 Copynumber: 2.8 Consensus size: 29
20074938 ATTTTCCCTC
*
20074948 TTTCTTTTCTTTCCCTTTTTCTTCCCCTGT
1 TTTCTTTTCTTTCTC-TTTTCTTCCCCTGT
* * *
20074978 TTTCGTCTCTTTCTCTGTTTCTT-CTCTGT
1 TTTCTTTTCTTTCTCT-TTTCTTCCCCTGT
20075007 TCTTCTTTTCTTTCT-TTTTCTT
1 T-TTCTTTTCTTTCTCTTTTCTT
20075029 TTTTTTTTGT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
28 6 0.14
29 8 0.19
30 29 0.67
ACGTcount: A:0.00, C:0.28, G:0.05, T:0.67
Consensus pattern (29 bp):
TTTCTTTTCTTTCTCTTTTCTTCCCCTGT
Found at i:20075283 original size:30 final size:27
Alignment explanation
Indices: 20075243--20075307 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 27
20075233 TTTCCTATAA
*
20075243 TATATTATTTTAATCTTAATTAATATAATT
1 TATAATATTTTAAT-TTAA-TAATAT-ATT
*
20075273 TATAATATTTTAATTTAATAATATTTT
1 TATAATATTTTAATTTAATAATATATT
20075300 TATAATAT
1 TATAATAT
20075308 AAATCAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 10 0.30
28 6 0.18
29 4 0.12
30 13 0.39
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (27 bp):
TATAATATTTTAATTTAATAATATATT
Found at i:20075290 original size:25 final size:26
Alignment explanation
Indices: 20075258--20075307 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
20075248 TATTTTAATC
20075258 TTAATTAAT-ATA-ATTTATAATATT
1 TTAATTAATAATATATTTATAATATT
*
20075282 TTAATTTAATAATATTTTTATAATAT
1 TTAA-TTAATAATATATTTATAATAT
20075308 AAATCAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 5 0.23
26 3 0.14
27 10 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
TTAATTAATAATATATTTATAATATT
Found at i:20075293 original size:16 final size:16
Alignment explanation
Indices: 20075248--20075299 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
20075238 TATAATATAT
20075248 TATTTTAATCTTAATTAA
1 TATTTTAAT-TTAA-TAA
20075266 TA---TAATTT-ATAA
1 TATTTTAATTTAATAA
20075278 TATTTTAATTTAATAA
1 TATTTTAATTTAATAA
20075294 TATTTT
1 TATTTT
20075300 TATAATATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
12 5 0.17
13 1 0.03
14 2 0.07
15 10 0.33
16 10 0.33
18 2 0.07
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTTTAATTTAATAA
Found at i:20077587 original size:21 final size:20
Alignment explanation
Indices: 20077554--20077592 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
20077544 ATTTTCACGA
20077554 TTTTAAATATAAAATATTTG
1 TTTTAAATATAAAATATTTG
*
20077574 TTTTATATCATAAAATATT
1 TTTTAAAT-ATAAAATATT
20077593 AAAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (20 bp):
TTTTAAATATAAAATATTTG
Found at i:20080301 original size:14 final size:15
Alignment explanation
Indices: 20080279--20080317 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
20080269 CCGTATATAT
*
20080279 TAATCTTTTAA-AAA
1 TAATTTTTTAATAAA
20080293 TAATTTTTTAATAAA
1 TAATTTTTTAATAAA
*
20080308 TTATTTTTTA
1 TAATTTTTTA
20080318 CAATTGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (15 bp):
TAATTTTTTAATAAA
Found at i:20081208 original size:6 final size:6
Alignment explanation
Indices: 20081142--20081205 Score: 110
Period size: 6 Copynumber: 10.7 Consensus size: 6
20081132 TAAAGGGATT
20081142 TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA
1 TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA
* *
20081190 TATATA TATATA TATA
1 TATAAA TATAAA TATA
20081206 TATTTCTTTT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
TATAAA
Found at i:20081740 original size:21 final size:21
Alignment explanation
Indices: 20081706--20081753 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
20081696 AAAAAATAGA
20081706 AAAAAATAAGAAAAATAATGT
1 AAAAAATAAGAAAAATAATGT
*
20081727 AAAAAA-AAGTAAAAGTAA--T
1 AAAAAATAAG-AAAAATAATGT
20081746 AAAAAATA
1 AAAAAATA
20081754 TTTTTTAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 7 0.29
20 4 0.17
21 13 0.54
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (21 bp):
AAAAAATAAGAAAAATAATGT
Found at i:20089955 original size:21 final size:21
Alignment explanation
Indices: 20089929--20089968 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20089919 TATAGATACA
20089929 ATTTTTAATTTTTGTTTAGTT
1 ATTTTTAATTTTTGTTTAGTT
* *
20089950 ATTTTTATTTTTTTTTTAG
1 ATTTTTAATTTTTGTTTAG
20089969 GTCATGTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.75
Consensus pattern (21 bp):
ATTTTTAATTTTTGTTTAGTT
Found at i:20097382 original size:58 final size:60
Alignment explanation
Indices: 20097313--20097431 Score: 224
Period size: 58 Copynumber: 2.0 Consensus size: 60
20097303 AGCTTGTGTG
20097313 AGCAGACCCATTTCACAGCTCGTGTGAGCAATGATGTAAAGG-AAAAG-AATGAAAGGTT
1 AGCAGACCCATTTCACAGCTCGTGTGAGCAATGATGTAAAGGAAAAAGAAATGAAAGGTT
20097371 AGCAGACCCATTTCACAGCTCGTGTGAGCAATGATGTAAAGGAAAAAGAAATGAAAGGTT
1 AGCAGACCCATTTCACAGCTCGTGTGAGCAATGATGTAAAGGAAAAAGAAATGAAAGGTT
20097431 A
1 A
20097432 TATGTTTAGC
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
58 42 0.71
59 5 0.08
60 12 0.20
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.20
Consensus pattern (60 bp):
AGCAGACCCATTTCACAGCTCGTGTGAGCAATGATGTAAAGGAAAAAGAAATGAAAGGTT
Found at i:20104917 original size:18 final size:18
Alignment explanation
Indices: 20104888--20104931 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
20104878 TGAGTCATGG
* *
20104888 AAGGAAGATGAAA-ATGA
1 AAGGAGGATGAAACATCA
20104905 AAGCGAGGATGAAACATCA
1 AAG-GAGGATGAAACATCA
20104924 AAGGAGGA
1 AAGGAGGA
20104932 AGACGAGGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 3 0.13
18 14 0.61
19 6 0.26
ACGTcount: A:0.52, C:0.07, G:0.32, T:0.09
Consensus pattern (18 bp):
AAGGAGGATGAAACATCA
Found at i:20105027 original size:25 final size:25
Alignment explanation
Indices: 20104981--20105028 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
20104971 ATTTCTTATC
* *
20104981 TTTAGTTTTTATTTCTTTTTAGATG
1 TTTAGTTTCTATTTCTTGTTAGATG
20105006 TTTA-TTTCTATTTCTTAGTTAGA
1 TTTAGTTTCTATTTCTT-GTTAGA
20105029 ATTTTGCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.19, C:0.06, G:0.10, T:0.65
Consensus pattern (25 bp):
TTTAGTTTCTATTTCTTGTTAGATG
Found at i:20113221 original size:46 final size:45
Alignment explanation
Indices: 20113111--20113240 Score: 145
Period size: 44 Copynumber: 2.9 Consensus size: 45
20113101 GTGTGCCATG
* * * * *
20113111 GTGTCTTTTAATCATGGTCTTATTTATTCTCTTCTTGATGGCATA
1 GTGTCTTTTAACCATGGTCTTATTCATTTTCTTCGTGATGGAATA
* *
20113156 GTGT-TTTTAACCATGGTCTTATTCATTTTCTATCGTGTTGTAATA
1 GTGTCTTTTAACCATGGTCTTATTCATTTTCT-TCGTGATGGAATA
* * **
20113201 GTGTCTTTCAACCATGGTCTTTTTCATTTGATTCGTGATG
1 GTGTCTTTTAACCATGGTCTTATTCATTTTCTTCGTGATG
20113241 CCATAACATC
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
44 24 0.34
45 24 0.34
46 23 0.32
ACGTcount: A:0.18, C:0.15, G:0.17, T:0.50
Consensus pattern (45 bp):
GTGTCTTTTAACCATGGTCTTATTCATTTTCTTCGTGATGGAATA
Found at i:20113263 original size:45 final size:45
Alignment explanation
Indices: 20113233--20113397 Score: 251
Period size: 45 Copynumber: 3.7 Consensus size: 45
20113223 TTCATTTGAT
* *
20113233 TCGTGATGCCATAACATCTTTCAGTTATGGTTTTACTCGATAGAA
1 TCGTGATGCCATAACATCTTTCAGTCATGGTCTTACTCGATAGAA
* *
20113278 TCGTGATGCCATAACGTCTTTTAGTCATGGTCTTACTCGATAGAA
1 TCGTGATGCCATAACATCTTTCAGTCATGGTCTTACTCGATAGAA
* *
20113323 TCGTAATGCCATAACATCTTTCAGTCATGATCTTACTCGATAGAA
1 TCGTGATGCCATAACATCTTTCAGTCATGGTCTTACTCGATAGAA
* *
20113368 TCGTGATGCCATAACGTCTTTCGGT-ATGGT
1 TCGTGATGCCATAACATCTTTCAGTCATGGT
20113398 GCCATAGTGT
Statistics
Matches: 108, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
44 4 0.04
45 104 0.96
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (45 bp):
TCGTGATGCCATAACATCTTTCAGTCATGGTCTTACTCGATAGAA
Found at i:20113297 original size:90 final size:90
Alignment explanation
Indices: 20113203--20113389 Score: 259
Period size: 90 Copynumber: 2.1 Consensus size: 90
20113193 TTGTAATAGT
** * * * * * *
20113203 GTCTTTCAACCATGGTCTTTTTC-ATTTGATTCGTGATGCCATAACATCTTTCAGTTATGGTTTT
1 GTCTTTCAACCATGGTCTTACTCGA-TAGAATCGTAATGCCATAACATCTTTCAGTCATGATCTT
20113267 ACTCGATAGAATCGTGATGCCATAAC
65 ACTCGATAGAATCGTGATGCCATAAC
* **
20113293 GTCTTTTAGTCATGGTCTTACTCGATAGAATCGTAATGCCATAACATCTTTCAGTCATGATCTTA
1 GTCTTTCAACCATGGTCTTACTCGATAGAATCGTAATGCCATAACATCTTTCAGTCATGATCTTA
20113358 CTCGATAGAATCGTGATGCCATAAC
66 CTCGATAGAATCGTGATGCCATAAC
20113383 GTCTTTC
1 GTCTTTC
20113390 GGTATGGTGC
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
90 83 0.99
91 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (90 bp):
GTCTTTCAACCATGGTCTTACTCGATAGAATCGTAATGCCATAACATCTTTCAGTCATGATCTTA
CTCGATAGAATCGTGATGCCATAAC
Found at i:20114906 original size:16 final size:16
Alignment explanation
Indices: 20114885--20114915 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20114875 CACGGCAGAA
*
20114885 ACCTATAGAGGTATGC
1 ACCTATAGAAGTATGC
20114901 ACCTATAGAAGTATG
1 ACCTATAGAAGTATG
20114916 TATCATGTTG
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:0.16, G:0.23, T:0.26
Consensus pattern (16 bp):
ACCTATAGAAGTATGC
Found at i:20132633 original size:16 final size:18
Alignment explanation
Indices: 20132612--20132644 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
20132602 TGCAAAGCAA
20132612 TTTTCTT-T-TAAAAAAG
1 TTTTCTTATATAAAAAAG
20132628 TTTTCTTATATAAAAAA
1 TTTTCTTATATAAAAAA
20132645 TGGGTAGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (18 bp):
TTTTCTTATATAAAAAAG
Found at i:20133112 original size:22 final size:22
Alignment explanation
Indices: 20133087--20133142 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
20133077 CAAGGGAGCC
20133087 TTGTCTCGAGACA-ATCAAAAAA
1 TTGTCTCGAGACATAT-AAAAAA
* **
20133109 TTGTCTCAAGACATATAGCAAA
1 TTGTCTCGAGACATATAAAAAA
20133131 TTGTCTCGAGAC
1 TTGTCTCGAGAC
20133143 CAAGTCATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 27 0.93
23 2 0.07
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.27
Consensus pattern (22 bp):
TTGTCTCGAGACATATAAAAAA
Found at i:20138461 original size:15 final size:15
Alignment explanation
Indices: 20138441--20138486 Score: 92
Period size: 15 Copynumber: 3.1 Consensus size: 15
20138431 ATGGGAGATT
20138441 AACAAGTGGATGGGG
1 AACAAGTGGATGGGG
20138456 AACAAGTGGATGGGG
1 AACAAGTGGATGGGG
20138471 AACAAGTGGATGGGG
1 AACAAGTGGATGGGG
20138486 A
1 A
20138487 CATGGTTAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.35, C:0.07, G:0.46, T:0.13
Consensus pattern (15 bp):
AACAAGTGGATGGGG
Found at i:20143356 original size:31 final size:29
Alignment explanation
Indices: 20143318--20143379 Score: 97
Period size: 31 Copynumber: 2.1 Consensus size: 29
20143308 TATTTTTAAA
20143318 ATTTTTAAAAATTCAAAAATATTATAAAAAT
1 ATTTTTAAAAATT-AAAAATATTA-AAAAAT
*
20143349 ATTTTTAAAAATTAAAATTATTAAAAAAT
1 ATTTTTAAAAATTAAAAATATTAAAAAAT
20143378 AT
1 AT
20143380 AAAAAAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 8 0.27
30 9 0.30
31 13 0.43
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (29 bp):
ATTTTTAAAAATTAAAAATATTAAAAAAT
Found at i:20143384 original size:19 final size:19
Alignment explanation
Indices: 20143340--20143410 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 19
20143330 TCAAAAATAT
* *
20143340 TATAAAAATATTTTTAAAAA
1 TATAAAAAT-TATTAAAAAA
20143360 T-T-AAAATTATTAAAAAA
1 TATAAAAATTATTAAAAAA
* *
20143377 TATAAAAA-AATT-AAAAT
1 TATAAAAATTATTAAAAAA
*
20143394 TTTAAAAATTAATTAAA
1 TATAAAAATT-ATTAAA
20143411 TGTTGATATA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
17 20 0.50
18 9 0.22
19 8 0.20
20 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TATAAAAATTATTAAAAAA
Found at i:20143470 original size:11 final size:11
Alignment explanation
Indices: 20143454--20143487 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
20143444 ATGCAAGTTC
20143454 AAAAACAAAAA
1 AAAAACAAAAA
20143465 AAAAACAAAAA
1 AAAAACAAAAA
20143476 AATAAA-AAAAA
1 AA-AAACAAAAA
20143487 A
1 A
20143488 TTAATGAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 19 0.86
12 3 0.14
ACGTcount: A:0.91, C:0.06, G:0.00, T:0.03
Consensus pattern (11 bp):
AAAAACAAAAA
Found at i:20144476 original size:18 final size:18
Alignment explanation
Indices: 20144450--20144566 Score: 85
Period size: 18 Copynumber: 6.3 Consensus size: 18
20144440 TAAAATTCAA
20144450 TAAAATTTATAAAAATAT
1 TAAAATTTATAAAAATAT
*
20144468 TAAATTTTAATAAAACAT-T
1 TAAAATTT-ATAAAA-ATAT
*
20144487 TAAAATTTATTAAAAATAGA
1 TAAAATTTA-TAAAAATA-T
* * **
20144507 AAAAAATTATAAAAATCG
1 TAAAATTTATAAAAATAT
**
20144525 TAAAAAATATAAAAAT-T
1 TAAAATTTATAAAAATAT
*
20144542 GTAAAATTTAGAAAAATCAT
1 -TAAAATTTATAAAAAT-AT
20144562 TAAAA
1 TAAAA
20144567 AATATAAAAT
Statistics
Matches: 78, Mismatches: 13, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
18 37 0.47
19 31 0.40
20 10 0.13
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (18 bp):
TAAAATTTATAAAAATAT
Found at i:20144480 original size:19 final size:19
Alignment explanation
Indices: 20144450--20144504 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
20144440 TAAAATTCAA
20144450 TAAAATTT-ATAAAAATAT
1 TAAAATTTAATAAAAATAT
*
20144468 TAAATTTTAATAAAACAT-T
1 TAAAATTTAATAAAA-ATAT
*
20144487 TAAAATTTATTAAAAATA
1 TAAAATTTAATAAAAATA
20144505 GAAAAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 9 0.29
19 20 0.65
20 2 0.06
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAAATTTAATAAAAATAT
Found at i:20144519 original size:19 final size:18
Alignment explanation
Indices: 20144497--20144540 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
20144487 TAAAATTTAT
20144497 TAAAAATAGAAAAAAATTA
1 TAAAAATAGAAAAAAA-TA
* *
20144516 TAAAAATCGTAAAAAATA
1 TAAAAATAGAAAAAAATA
20144534 TAAAAAT
1 TAAAAAT
20144541 TGTAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (18 bp):
TAAAAATAGAAAAAAATA
Found at i:20154288 original size:1 final size:1
Alignment explanation
Indices: 20154282--20154306 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
20154272 TGTCCCACGC
20154282 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
20154307 CTTGTCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:20155193 original size:28 final size:28
Alignment explanation
Indices: 20155153--20155217 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
20155143 TATTCACATG
*
20155153 TTTATTTATTTTAAATTAAT-TATATAAT
1 TTTATTTATTTT-AATTAATGTAAATAAT
20155181 TTTATTT-TATTTAATTAATGTAAATAAT
1 TTTATTTAT-TTTAATTAATGTAAATAAT
*
20155209 AATTATTTA
1 -TTTATTTA
20155218 AAATACATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
27 8 0.26
28 17 0.55
29 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
TTTATTTATTTTAATTAATGTAAATAAT
Found at i:20155582 original size:9 final size:10
Alignment explanation
Indices: 20155540--20155584 Score: 51
Period size: 9 Copynumber: 4.8 Consensus size: 10
20155530 TATTCTAATC
20155540 TATT-TTTTA
1 TATTATTTTA
*
20155549 TATT-TATTA
1 TATTATTTTA
*
20155558 CATTATTTTA
1 TATTATTTTA
20155568 TATTATTTT-
1 TATTATTTTA
20155577 TATTATTT
1 TATTATTT
20155585 ATTAATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
9 19 0.61
10 12 0.39
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (10 bp):
TATTATTTTA
Found at i:20161048 original size:30 final size:30
Alignment explanation
Indices: 20160993--20161054 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
20160983 CACTAAGCAA
20160993 GTTTCATATACATGTATCATCCATTT-CAT
1 GTTTCATATACATGTATCATCCATTTCCAT
20161022 GTTTCAATATATCATGTAAT-AT-CATTTCCAT
1 GTTTC-ATATA-CATGT-ATCATCCATTTCCAT
20161053 GT
1 GT
20161055 ATCTCATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
29 5 0.17
30 10 0.34
31 12 0.41
32 2 0.07
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (30 bp):
GTTTCATATACATGTATCATCCATTTCCAT
Found at i:20161231 original size:25 final size:25
Alignment explanation
Indices: 20161203--20161267 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
20161193 TCCTATTCAT
* *
20161203 GTATGCTCATACGAGCTATGAATCG
1 GTATGCTCATACGAGCTATAAATCA
*
20161228 GTATACTC-TCACGAGCTATAAATCA
1 GTATGCTCAT-ACGAGCTATAAATCA
*
20161253 GTACGCTCATACGAG
1 GTATGCTCATACGAG
20161268 TTGAGAATCG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
24 1 0.03
25 31 0.94
26 1 0.03
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (25 bp):
GTATGCTCATACGAGCTATAAATCA
Found at i:20161285 original size:25 final size:25
Alignment explanation
Indices: 20161257--20161325 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 25
20161247 AAATCAGTAC
*
20161257 GCTCATACGAGTTGAGAATCGATAA
1 GCTCATACGAGCTGAGAATCGATAA
* * *
20161282 GCTC-TCACGAGCTG-CAATTGGTAA
1 GCTCAT-ACGAGCTGAGAATCGATAA
*
20161306 GCTCATACAAGCTGAGAATC
1 GCTCATACGAGCTGAGAATC
20161326 AGTAATCCCT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
24 19 0.56
25 15 0.44
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (25 bp):
GCTCATACGAGCTGAGAATCGATAA
Found at i:20169642 original size:18 final size:16
Alignment explanation
Indices: 20169610--20169643 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
20169600 ATCATCTCCC
20169610 GAATAAAATAAAGAAA
1 GAATAAAATAAAGAAA
20169626 GAATAAGAATCAAAGAAA
1 GAATAA-AAT-AAAGAAA
20169644 AGGCAGCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.71, C:0.03, G:0.15, T:0.12
Consensus pattern (16 bp):
GAATAAAATAAAGAAA
Found at i:20187698 original size:15 final size:15
Alignment explanation
Indices: 20187678--20187706 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20187668 GTCACATCCC
20187678 AGAAATTGGGTTAGA
1 AGAAATTGGGTTAGA
20187693 AGAAATTGGGTTAG
1 AGAAATTGGGTTAG
20187707 TGAACTAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (15 bp):
AGAAATTGGGTTAGA
Found at i:20192395 original size:19 final size:19
Alignment explanation
Indices: 20192363--20192401 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
20192353 CTTGTCGCCC
**
20192363 CATCTTTCCCTTTTTATCT
1 CATCTTTCAATTTTTATCT
*
20192382 CATCTTTCAATTTTTCTCT
1 CATCTTTCAATTTTTATCT
20192401 C
1 C
20192402 TATTTTCTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.13, C:0.31, G:0.00, T:0.56
Consensus pattern (19 bp):
CATCTTTCAATTTTTATCT
Found at i:20195739 original size:44 final size:43
Alignment explanation
Indices: 20195600--20195732 Score: 128
Period size: 42 Copynumber: 3.1 Consensus size: 43
20195590 GTCTTTAGTT
* * * *
20195600 TAGCGGCGCTTTTTCTACAAACGCCACTAATGAACATGGTCTA
1 TAGCAGCGCTTTTTCTACAAACGCCACTAAAGAACATGTTTTA
* ** *
20195643 TAGCAGCGCTTTTT-TACAAATGCTGCTAAGGAACAT-TATCTT-
1 TAGCAGCGCTTTTTCTACAAACGCCACTAAAGAACATGT-T-TTA
* *
20195685 TAGCAGCGTTTTTTTCTACAAACGCCACTAAAGATCATGTTTTA
1 TAGCAGCG-CTTTTTCTACAAACGCCACTAAAGAACATGTTTTA
20195729 TAGC
1 TAGC
20195733 GGCGTTTATA
Statistics
Matches: 71, Mismatches: 13, Indels: 11
0.75 0.14 0.12
Matches are distributed among these distances:
42 27 0.38
43 21 0.30
44 22 0.31
45 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.33
Consensus pattern (43 bp):
TAGCAGCGCTTTTTCTACAAACGCCACTAAAGAACATGTTTTA
Found at i:20203587 original size:25 final size:25
Alignment explanation
Indices: 20203553--20203618 Score: 96
Period size: 25 Copynumber: 2.6 Consensus size: 25
20203543 AAAAACTTAC
* *
20203553 ACGGCGATGCAGTAGAGGACTATTG
1 ACGGCGATGCAGCAGAGGACTATCG
*
20203578 ACGGCGATGCAGCAGAGGACTGTCG
1 ACGGCGATGCAGCAGAGGACTATCG
*
20203603 ACGGCGATGTAGCAGA
1 ACGGCGATGCAGCAGA
20203619 CGTTGGGGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.27, C:0.20, G:0.38, T:0.15
Consensus pattern (25 bp):
ACGGCGATGCAGCAGAGGACTATCG
Found at i:20203719 original size:20 final size:21
Alignment explanation
Indices: 20203672--20203720 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
20203662 GGAAAAGATG
20203672 TTGGGGAAAAAAGTAAGGGAAT
1 TTGGGG-AAAAAGTAAGGGAAT
* * *
20203694 TGGGGGAAAAA-TTAGGGATT
1 TTGGGGAAAAAGTAAGGGAAT
20203714 TTGGGGA
1 TTGGGGA
20203721 GAGGAACTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 13 0.57
21 5 0.22
22 5 0.22
ACGTcount: A:0.37, C:0.00, G:0.41, T:0.22
Consensus pattern (21 bp):
TTGGGGAAAAAGTAAGGGAAT
Found at i:20206372 original size:17 final size:18
Alignment explanation
Indices: 20206350--20206389 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
20206340 CTTAAAAATT
*
20206350 AAAAATT-AAAAAGTAAA
1 AAAAATTCAAAAACTAAA
20206367 AAAAATTCAAAAACTAAA
1 AAAAATTCAAAAACTAAA
20206385 AAAAA
1 AAAAA
20206390 AATTCAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.15
Consensus pattern (18 bp):
AAAAATTCAAAAACTAAA
Found at i:20206391 original size:24 final size:24
Alignment explanation
Indices: 20206343--20206391 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
20206333 AGTGATTCTT
* *
20206343 AAAAATTAAAAATTAAAAAGTAAA
1 AAAAATTAAAAACTAAAAAGAAAA
20206367 AAAAATTCAAAAACTAAAAA-AAAA
1 AAAAATT-AAAAACTAAAAAGAAAA
20206391 A
1 A
20206392 TTCAAAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (24 bp):
AAAAATTAAAAACTAAAAAGAAAA
Found at i:20206739 original size:81 final size:81
Alignment explanation
Indices: 20206654--20206830 Score: 196
Period size: 81 Copynumber: 2.2 Consensus size: 81
20206644 CGTTTATGAC
* * * *
20206654 AAAAACGCTGCAAAAGGTCAAGCATTAGCGGCG-TTTCTAAAACAAACGTCGCTATAGGTTGAGC
1 AAAAACGCTGCAAAAGATCAAGCATTAGCAGCGCTTT-TAAAA-AAACGCCGCTATAGATTGAGC
*
20206718 ATTAGCATCGCTTTTT-G
64 ATTAGCAGCGCTTTTTCG
* * * * * *
20206735 AAAAACGCCGCTATAGATCGAGCATTAGCAGCGCTTTTCAAAAAATGCCGCTATAGATTGAGCAT
1 AAAAACGCTGCAAAAGATCAAGCATTAGCAGCGCTTTTAAAAAAACGCCGCTATAGATTGAGCAT
*
20206800 TAGCGGCGCTTTTTCG
66 TAGCAGCGCTTTTTCG
* *
20206816 GAAAACACTGCAAAA
1 AAAAACGCTGCAAAA
20206831 AAGTTGAGCA
Statistics
Matches: 77, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
80 32 0.42
81 42 0.55
82 3 0.04
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (81 bp):
AAAAACGCTGCAAAAGATCAAGCATTAGCAGCGCTTTTAAAAAAACGCCGCTATAGATTGAGCAT
TAGCAGCGCTTTTTCG
Found at i:20206747 original size:40 final size:40
Alignment explanation
Indices: 20206674--20206813 Score: 165
Period size: 40 Copynumber: 3.5 Consensus size: 40
20206664 CAAAAGGTCA
* * * *
20206674 AGCATTAGCGGCG-TTTCTAAAACAAACGTCGCTATAGGTTG
1 AGCATTAGCAGCGCTTT-TTAAA-AAACGCCGCTATAGATTG
* * *
20206715 AGCATTAGCATCGCTTTTTGAAAAACGCCGCTATAGATCG
1 AGCATTAGCAGCGCTTTTTAAAAAACGCCGCTATAGATTG
* *
20206755 AGCATTAGCAGCGCTTTTCAAAAAATGCCGCTATAGATTG
1 AGCATTAGCAGCGCTTTTTAAAAAACGCCGCTATAGATTG
*
20206795 AGCATTAGCGGCGCTTTTT
1 AGCATTAGCAGCGCTTTTT
20206814 CGGAAAACAC
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
40 67 0.80
41 14 0.17
42 3 0.04
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (40 bp):
AGCATTAGCAGCGCTTTTTAAAAAACGCCGCTATAGATTG
Found at i:20207333 original size:156 final size:155
Alignment explanation
Indices: 20206848--20207335 Score: 536
Period size: 156 Copynumber: 3.1 Consensus size: 155
20206838 GCAAAACAAG
* * * * *
20206848 TGAGCTTTAGTGGCATTAGCGGCACTTTTT-AAAAATCGCCGCAATAGATCGAGCATTAGCGGCG
1 TGAGCTTTAGTGGCATTAGCAGCGCTTTTTAAAAAAT-GCTGAAATAGATCGAGAATTAGCGGCG
* * * * * *
20206912 ATAT-TAGAAAAACGCCACTATAGATCGAGCATTAGCGGTACTTTTTGGAAAATACCGCAAAAAA
65 CT-TGTAGAAAAACGCCACTATAGATCGAGCATTAGCGGCATTTTTTGAAAAATGCCACAAAAAA
*
20206976 GTTGAGCAAAATGACATCGTTTGTTGT
129 GTTGAGCAAAACGACATCGTTTGTTGT
* * * *
20207003 TGAGCTTTAGTGGCATTGGCAGCGCTTTTTAAAAAATGCTGCAATAAATCGAGAATTAGCGGCAC
1 TGAGCTTTAGTGGCATTAGCAGCGCTTTTTAAAAAATGCTGAAATAGATCGAGAATTAGCGGCGC
* * *
20207068 TTTGTCGAAAAACGCCTCTATAGATCGAGCATTAGCGGCATTTTTCGAAAAAATGCCACAAAAAA
66 -TTGTAGAAAAACGCCACTATAGATCGAGCATTAGCGGCATTTTTTG-AAAAATGCCACAAAAAA
*
20207133 GTTGAGCAAAACGACGTCGTTTGTTGT
129 GTTGAGCAAAACGACATCGTTTGTTGT
* ** *
20207160 TGAGCTTTAGTGGCATTAGCTTTGCTTTTTTTTAAAAACAT-C-GAAATAGATTGAGAATTAGCG
1 TGAGCTTTAGTGGCATTAGC--AGC-GCTTTTTAAAAA-ATGCTGAAATAGATCGAGAATTAGCG
* * * * * * * * *
20207223 GCGCTTGTTGAAAAATGCCGCTATAGATCGAGCATTAGTGGCGTTTTTTGTAAAACGCAATAAAA
62 GCGCTTGTAGAAAAACGCCACTATAGATCGAGCATTAGCGGCATTTTTTGAAAAATGCCACAAAA
* * *
20207288 AAGTTAAG-AAAACGACCTCGTTTGTTCT
127 AAGTTGAGCAAAACGACATCGTTTGTTGT
*
20207316 CGAGCTTTAGTGGCATTAGC
1 TGAGCTTTAGTGGCATTAGC
20207336 GGCATTTTTA
Statistics
Matches: 285, Mismatches: 40, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
155 51 0.18
156 82 0.29
157 76 0.27
158 40 0.14
159 23 0.08
160 11 0.04
161 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (155 bp):
TGAGCTTTAGTGGCATTAGCAGCGCTTTTTAAAAAATGCTGAAATAGATCGAGAATTAGCGGCGC
TTGTAGAAAAACGCCACTATAGATCGAGCATTAGCGGCATTTTTTGAAAAATGCCACAAAAAAGT
TGAGCAAAACGACATCGTTTGTTGT
Found at i:20207454 original size:29 final size:29
Alignment explanation
Indices: 20207386--20207455 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
20207376 TAGGGTTTAG
*
20207386 GGTTTATTA-TTTAAGGTTTAATGTTTAT
1 GGTTTATTATTTTAAGGTTTAATGTTAAT
**
20207414 GGTTTAGGATTTTAAGGTTT-ATGATATAAT
1 GGTTTATTATTTTAAGGTTTAATG-T-TAAT
20207444 -GTTTATTATTTT
1 GGTTTATTATTTT
20207456 GGGATTAGAG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
28 10 0.29
29 21 0.62
30 3 0.09
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.56
Consensus pattern (29 bp):
GGTTTATTATTTTAAGGTTTAATGTTAAT
Found at i:20207477 original size:14 final size:14
Alignment explanation
Indices: 20207460--20207504 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
20207450 TATTTTGGGA
20207460 TTAGAGTTT-TGAGT
1 TTAGAGTTTATG-GT
*
20207474 TTAGGGTTTATGGT
1 TTAGAGTTTATGGT
20207488 TTAGAGTTTATGGT
1 TTAGAGTTTATGGT
20207502 TTA
1 TTA
20207505 TGGTTTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 26 0.93
15 2 0.07
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (14 bp):
TTAGAGTTTATGGT
Found at i:20207482 original size:7 final size:7
Alignment explanation
Indices: 20207472--20207510 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
20207462 AGAGTTTTGA
*
20207472 GTTTAGG
1 GTTTATG
20207479 GTTTATG
1 GTTTATG
20207486 GTTTA-G
1 GTTTATG
20207492 AGTTTATG
1 -GTTTATG
20207500 GTTTATG
1 GTTTATG
20207507 GTTT
1 GTTT
20207511 TATAGTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
6 1 0.03
7 27 0.93
8 1 0.03
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (7 bp):
GTTTATG
Found at i:20207836 original size:7 final size:7
Alignment explanation
Indices: 20207701--20207885 Score: 106
Period size: 7 Copynumber: 26.4 Consensus size: 7
20207691 TATATTTTGA
*
20207701 GGTTTAA
1 GGTTTAG
20207708 GGTTTAG
1 GGTTTAG
*
20207715 GGTTTAT
1 GGTTTAG
*
20207722 GATTTAG
1 GGTTTAG
* *
20207729 TGTTAAG
1 GGTTTAG
*
20207736 AGTTTAG
1 GGTTTAG
* *
20207743 TGTTTAC
1 GGTTTAG
*
20207750 GATTTAG
1 GGTTTAG
*
20207757 GGTGTA-
1 GGTTTAG
*
20207763 GGTTTAT
1 GGTTTAG
20207770 GGTTTAG
1 GGTTTAG
*
20207777 TGTTTAG
1 GGTTTAG
* *
20207784 GATTTAT
1 GGTTTAG
20207791 GGTTTAG
1 GGTTTAG
*
20207798 TGG-TTAT
1 -GGTTTAG
20207805 GGTTTAG
1 GGTTTAG
*
20207812 GGGTTAGG
1 GGTTTA-G
*
20207820 GGCTTAG
1 GGTTTAG
20207827 GGTTTAG
1 GGTTTAG
*
20207834 GGTTTAA
1 GGTTTAG
* *
20207841 AGTTTAT
1 GGTTTAG
*
20207848 GATTTAGG
1 GGTTTA-G
*
20207856 GGCTTAG
1 GGTTTAG
20207863 GGTTTA-
1 GGTTTAG
*
20207869 TGTTTAG
1 GGTTTAG
*
20207876 TGTTTAG
1 GGTTTAG
20207883 GGT
1 GGT
20207886 CTGATTTTAA
Statistics
Matches: 132, Mismatches: 40, Indels: 12
0.72 0.22 0.07
Matches are distributed among these distances:
6 12 0.09
7 108 0.82
8 12 0.09
ACGTcount: A:0.19, C:0.02, G:0.34, T:0.45
Consensus pattern (7 bp):
GGTTTAG
Found at i:20207855 original size:28 final size:27
Alignment explanation
Indices: 20207823--20207885 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 27
20207813 GGTTAGGGGC
20207823 TTAGGGTTTAGGGTTTAAAGTTTA-TGAT
1 TTAGGGTTTAGGGTTT-AAGTTTAGTG-T
* *
20207851 TTAGGGGCTTAGGGTTTATGTTTAGTGT
1 TTA-GGGTTTAGGGTTTAAGTTTAGTGT
20207879 TTAGGGT
1 TTAGGGT
20207886 CTGATTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 3 0.10
28 13 0.43
29 14 0.47
ACGTcount: A:0.19, C:0.02, G:0.33, T:0.46
Consensus pattern (27 bp):
TTAGGGTTTAGGGTTTAAGTTTAGTGT
Found at i:20216536 original size:30 final size:31
Alignment explanation
Indices: 20216476--20216544 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 31
20216466 GTCCTTATAC
* *
20216476 TTTAATTTGATTAATTTTAATCTTTGTATTT
1 TTTAATTAGATTAATTTTAATCCTTGTATTT
*
20216507 TTTAATTAG-TTAATTTTAGTCCCTT-TATTT
1 TTTAATTAGATTAATTTTAAT-CCTTGTATTT
20216537 TTCTAATT
1 TT-TAATT
20216545 TTGAAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 17 0.52
31 16 0.48
ACGTcount: A:0.25, C:0.07, G:0.06, T:0.62
Consensus pattern (31 bp):
TTTAATTAGATTAATTTTAATCCTTGTATTT
Found at i:20226042 original size:53 final size:53
Alignment explanation
Indices: 20225958--20226169 Score: 239
Period size: 53 Copynumber: 4.0 Consensus size: 53
20225948 CAATTGCATT
* * * * * *
20225958 GAAGACCATATCATGTAAGATCGTAATTGGTGGGTTATGACACCATAAGAAAA
1 GAAGACCATATCATGTAAGACCGTAACTGGTAGGTTATGACATCATATGGAAA
**
20226011 GAAGACCATATCATGTAAGATTGTAACTGGT-GGATTATGACATCATATGGAAA
1 GAAGACCATATCATGTAAGACCGTAACTGGTAGG-TTATGACATCATATGGAAA
** * *
20226064 GAAGACCATATTGTGTTAGACCATAACTGGTAGGTTATTG-CATCATATGGAAA
1 GAAGACCATATCATGTAAGACCGTAACTGGTAGGTTA-TGACATCATATGGAAA
* * * * *
20226117 GAATACCATATCGTGTAAGACCGTAACTGATAGGTTATGGCATTATATGGAAA
1 GAAGACCATATCATGTAAGACCGTAACTGGTAGGTTATGACATCATATGGAAA
20226170 ATTTAAGGAA
Statistics
Matches: 138, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
52 4 0.03
53 130 0.94
54 4 0.03
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.28
Consensus pattern (53 bp):
GAAGACCATATCATGTAAGACCGTAACTGGTAGGTTATGACATCATATGGAAA
Found at i:20228952 original size:15 final size:15
Alignment explanation
Indices: 20228934--20228963 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
20228924 ATCTTGTGGC
20228934 AAAAAGAAGAAGAAA
1 AAAAAGAAGAAGAAA
20228949 AAAAAGAAGAAGAAA
1 AAAAAGAAGAAGAAA
20228964 GATATGGTAA
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:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAAGAAGAAGAAA
Found at i:20239207 original size:18 final size:18
Alignment explanation
Indices: 20239186--20239252 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 18
20239176 GTTTGTCAAT
*
20239186 TTAATACAGTTCGCCATA
1 TTAATACAATTCGCCATA
* * *
20239204 TTAATACAAATCACCAAA
1 TTAATACAATTCGCCATA
* * *
20239222 TTAACACAGTTTGCCATA
1 TTAATACAATTCGCCATA
*
20239240 ATAATACAATTCG
1 TTAATACAATTCG
20239253 TCAAGTTAAC
Statistics
Matches: 35, Mismatches: 14, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (18 bp):
TTAATACAATTCGCCATA
Found at i:20239262 original size:36 final size:36
Alignment explanation
Indices: 20239180--20239269 Score: 99
Period size: 36 Copynumber: 2.5 Consensus size: 36
20239170 TAGATAGTTT
* * *
20239180 GTCAATTTAATACAGTTCGCCATATTAATACAAATC
1 GTCAAATTAACACAGTTCGCCATAATAATACAAATC
** * *
20239216 ACCAAATTAACACAGTTTGCCATAATAATACAATTC
1 GTCAAATTAACACAGTTCGCCATAATAATACAAATC
* *
20239252 GTCAAGTTAACATAGTTC
1 GTCAAATTAACACAGTTC
20239270 ACAATATAAC
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (36 bp):
GTCAAATTAACACAGTTCGCCATAATAATACAAATC
Found at i:20243970 original size:25 final size:25
Alignment explanation
Indices: 20243937--20243984 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
20243927 CGAATCAATG
20243937 AAAAGGTTGAAAAGGATGTTATCTA
1 AAAAGGTTGAAAAGGATGTTATCTA
20243962 AAAAGGTTGAAAAGGATGTTATC
1 AAAAGGTTGAAAAGGATGTTATC
20243985 CAGAAGGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.04, G:0.25, T:0.27
Consensus pattern (25 bp):
AAAAGGTTGAAAAGGATGTTATCTA
Found at i:20245860 original size:85 final size:85
Alignment explanation
Indices: 20245717--20245910 Score: 307
Period size: 85 Copynumber: 2.3 Consensus size: 85
20245707 CTAAAAACAT
* * *
20245717 TGTGGTTTATTCATGAACCAAGTGGCAGTTTGTTTAATCTGCAAATATGTTGTGCACCCACAACA
1 TGTGGTTTAATCATGAACCAAGTGGCAGTTTGTGTAATCTGCAAATATGTTGTGCACCCAAAACA
*
20245782 AGTGGCAGTAACTGCAAGTA
66 AGTGGCAGTAACTGCAAATA
* *
20245802 TGTGGTTTAATCATGAACCAAGTGGGAGTTTGTGTAATCTGCAAATATGTTGTGCACCCAAAATA
1 TGTGGTTTAATCATGAACCAAGTGGCAGTTTGTGTAATCTGCAAATATGTTGTGCACCCAAAACA
*
20245867 AGTTGCAGTAACTGCAAATA
66 AGTGGCAGTAACTGCAAATA
* *
20245887 TGTGGTTCAATCACGAACCAAGTG
1 TGTGGTTTAATCATGAACCAAGTG
20245911 ACTGCTTTTT
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 100 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (85 bp):
TGTGGTTTAATCATGAACCAAGTGGCAGTTTGTGTAATCTGCAAATATGTTGTGCACCCAAAACA
AGTGGCAGTAACTGCAAATA
Found at i:20248899 original size:9 final size:9
Alignment explanation
Indices: 20248868--20248900 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
20248858 TTTTTTCTTC
*
20248868 TATTTTTCT
1 TATTTCTCT
20248877 TATTT-TCT
1 TATTTCTCT
20248885 TATTTCTCT
1 TATTTCTCT
20248894 TATTTCT
1 TATTTCT
20248901 GCCGATTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (9 bp):
TATTTCTCT
Found at i:20257489 original size:607 final size:608
Alignment explanation
Indices: 20256336--20257549 Score: 2196
Period size: 607 Copynumber: 2.0 Consensus size: 608
20256326 GGATCCATTG
* *
20256336 ACCAAGTCCGCTCAATTTATTCTTGTTCAGATGGACTACTCTCTGCAAAAGTTAGTAAAGCTCTA
1 ACCAAGTCCGCTCAATTTATTCCTGTTCAGATGGACTACTCTATGCAAAAGTTAGTAAAGCTCTA
* *
20256401 CATTTCTGAGATTGTAAGACTGTATGGGGTTCTAATTTCAATAATCTCTGATATGGATCCTCTCT
66 CATTTCTGAGATTGTAAGACTGCATGGGGTTCCAATTTCAATAATCTCTGATATGGATCCTCTCT
* * * *
20256466 TCACTTCACGGTTCTAGAAGAAACTTTACAAGGCTCTGGGTTCGAGATTGGACTTCAGTATTGCG
131 TCACTTCACGGTTCTAGAAGAAACTTCACAAGGCTCTGGGTTCAAGATTAGACTTCAGTACTGCG
* * *
20256531 TTCCATCCTTAGACCGATGGTCAATTTGAGAGGGTGATTCATATACTAGAGGATATGATTTGGAG
196 TTCCATACTCAGACAGATGGTCAATTTGAGAGGGTGATTCATATACTAGAGGATATGATTTGGAG
20256596 CTATGTGATTTATTTCTGCGGTAGTTGGGAGGATTTTTTACCGTTAGTTGAGTTCACCTACAATA
261 CTATGTGATTTATTTCTGCGGTAGTTGGGAGGATTTTTTACCGTTAGTTGAGTTCACCTACAATA
* *
20256661 ACAGTTTCCAATCTAGCATCTAGATGGCACCTTACGAGGCTCTATATGGTCGTAAGTGGCATACT
326 ACAGTTTCCAATCTAGCATCTAGATGGCACCTTACGAGACTCTATATGGTCATAAGTGGCATACT
* * *
20256726 CTGTTATATTAGACTGAGTTGGGTGAGCGACGGGTTTTAGGTCCTGAGTTGGTTTTCGAGACTGA
391 CTGTTATATTAGACTGAGTTGGGTGAGCGACGAGTTTTAGGTCCTAAGTTGGTTTCCGAGACTGA
20256791 AGATAATGTTAGACTAATTTGGGATCGTCTGAAGGCATCTTCTGATAGATAGAAGTCTTATGCAA
456 AGATAATGTTAGACTAATTTGGGATCGTCTGAAGGCATCTTCTGATAGATAGAAGTCTTATGCAA
*
20256856 ATCTGAAAATCAGATATATCAAGTACTCTATGGGGGACTTTGTATTTCTTAAGGTATCTCCGTGG
521 ATCTGAAAATCAGAGATATCAAGTACTCTATGGGGGACTTTGTATTTCTTAAGGTATCTCCGTGG
20256921 AAAAAGGTTCTACGGTTCGGTTA
586 AAAAAGGTTCTACGGTTCGGTTA
*
20256944 ACCAAGTCCGCTCATTTTATTCCTGTTCAGATGGACTACTCTATGCAAAAGTTAGTAAAGCTCTA
1 ACCAAGTCCGCTCAATTTATTCCTGTTCAGATGGACTACTCTATGCAAAAGTTAGTAAAGCTCTA
20257009 CATTTCTGAGATTGTAAGACTGCATGGGGTTCCAATTTCAATAATCTCTGATATGGATCCTCTCT
66 CATTTCTGAGATTGTAAGACTGCATGGGGTTCCAATTTCAATAATCTCTGATATGGATCCTCTCT
*
20257074 TCACTTCACGGTTCTAGAAGAAACTTCACAAGGCTCTGGTTTCAAGATTAGACTTCAG-ACTGCG
131 TCACTTCACGGTTCTAGAAGAAACTTCACAAGGCTCTGGGTTCAAGATTAGACTTCAGTACTGCG
*
20257138 TTCCATACTCAGACAGATGGTCAATTTGAGAGGGTGGTTCATATACTAGAGGATATGATTTGGAG
196 TTCCATACTCAGACAGATGGTCAATTTGAGAGGGTGATTCATATACTAGAGGATATGATTTGGAG
*
20257203 CTATGTGATTTATTTCTGCGGTAGTTGGGAGGATTTTTTACCGTTAGTTGAGTTCGCCTACAATA
261 CTATGTGATTTATTTCTGCGGTAGTTGGGAGGATTTTTTACCGTTAGTTGAGTTCACCTACAATA
* *
20257268 ACAGTTTCCAATCTAGCATCTAGATGGCACCTTACGAGACTCTATTTGGTCATAAGTGTCATACT
326 ACAGTTTCCAATCTAGCATCTAGATGGCACCTTACGAGACTCTATATGGTCATAAGTGGCATACT
*
20257333 CTGTTATATTAGACTGAGTTGGGTGAGCGACGAGTTTTGGGTCCTAAGTTGGTTTCCGAGACTGA
391 CTGTTATATTAGACTGAGTTGGGTGAGCGACGAGTTTTAGGTCCTAAGTTGGTTTCCGAGACTGA
*
20257398 AGATAATGTTAGACTAATTTGGGATCGTCTGAAGGCGTCTTCTGATAGATAGAAGTCTTATGCAA
456 AGATAATGTTAGACTAATTTGGGATCGTCTGAAGGCATCTTCTGATAGATAGAAGTCTTATGCAA
20257463 ATCTGAAAATCAGAGATATCAAGTACTCTATGGGGGACTTTGTATTTCTTAAGGTATCTCCGTGG
521 ATCTGAAAATCAGAGATATCAAGTACTCTATGGGGGACTTTGTATTTCTTAAGGTATCTCCGTGG
20257528 AAAAAGGTTCTACGGTTCGGTT
586 AAAAAGGTTCTACGGTTCGGTT
20257550 GTAAGGACAA
Statistics
Matches: 581, Mismatches: 25, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
607 402 0.69
608 179 0.31
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (608 bp):
ACCAAGTCCGCTCAATTTATTCCTGTTCAGATGGACTACTCTATGCAAAAGTTAGTAAAGCTCTA
CATTTCTGAGATTGTAAGACTGCATGGGGTTCCAATTTCAATAATCTCTGATATGGATCCTCTCT
TCACTTCACGGTTCTAGAAGAAACTTCACAAGGCTCTGGGTTCAAGATTAGACTTCAGTACTGCG
TTCCATACTCAGACAGATGGTCAATTTGAGAGGGTGATTCATATACTAGAGGATATGATTTGGAG
CTATGTGATTTATTTCTGCGGTAGTTGGGAGGATTTTTTACCGTTAGTTGAGTTCACCTACAATA
ACAGTTTCCAATCTAGCATCTAGATGGCACCTTACGAGACTCTATATGGTCATAAGTGGCATACT
CTGTTATATTAGACTGAGTTGGGTGAGCGACGAGTTTTAGGTCCTAAGTTGGTTTCCGAGACTGA
AGATAATGTTAGACTAATTTGGGATCGTCTGAAGGCATCTTCTGATAGATAGAAGTCTTATGCAA
ATCTGAAAATCAGAGATATCAAGTACTCTATGGGGGACTTTGTATTTCTTAAGGTATCTCCGTGG
AAAAAGGTTCTACGGTTCGGTTA
Found at i:20258561 original size:32 final size:33
Alignment explanation
Indices: 20258520--20258596 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 33
20258510 CAGGTTGGGC
*
20258520 GTGTTGGCCACAC-AGGCAAAGCCGTTCTAGG-A
1 GTGTGGGCCACACAAGG-AAAGCCGTTCTAGGCA
* *
20258552 GTGTGGGCCACACAAGGAAGGCCGTTCTGGGCA
1 GTGTGGGCCACACAAGGAAAGCCGTTCTAGGCA
20258585 -TGTGGGCTCACA
1 GTGTGGGC-CACA
20258597 TGAACATGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
32 31 0.79
33 8 0.21
ACGTcount: A:0.22, C:0.25, G:0.35, T:0.18
Consensus pattern (33 bp):
GTGTGGGCCACACAAGGAAAGCCGTTCTAGGCA
Found at i:20263243 original size:27 final size:27
Alignment explanation
Indices: 20263212--20263270 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
20263202 TCATTGACTG
*
20263212 TCTTTGTAATTTGTTCATTTAATCTCA
1 TCTTTGTAATTTCTTCATTTAATCTCA
* **
20263239 TCTTTTTTGTTTCTTCATTTAATCTCA
1 TCTTTGTAATTTCTTCATTTAATCTCA
20263266 TCTTT
1 TCTTT
20263271 TTTTATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.17, C:0.17, G:0.05, T:0.61
Consensus pattern (27 bp):
TCTTTGTAATTTCTTCATTTAATCTCA
Found at i:20264406 original size:85 final size:85
Alignment explanation
Indices: 20264289--20264444 Score: 258
Period size: 85 Copynumber: 1.8 Consensus size: 85
20264279 TGGCAGTTTG
* * * *
20264289 TTTAATTTGCAAATATGTTGTGCACCTACAACAAGTGGCAATAACTGCAAGTATGTGGTTCGATC
1 TTTAATCTGCAAATATGTTGTACACCCACAACAAGTGGCAATAACTGCAAATATGTGGTTCGATC
20264354 ACGAACTAAATGGTAGTGTA
66 ACGAACTAAATGGTAGTGTA
* *
20264374 TTTAATCTGTAAATATGTTGTACACCCACAACAAGTGGCAATAACTGCAAATATGTGGTTCGATT
1 TTTAATCTGCAAATATGTTGTACACCCACAACAAGTGGCAATAACTGCAAATATGTGGTTCGATC
20264439 ACGAAC
66 ACGAAC
20264445 CAAGAGGCAG
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 65 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (85 bp):
TTTAATCTGCAAATATGTTGTACACCCACAACAAGTGGCAATAACTGCAAATATGTGGTTCGATC
ACGAACTAAATGGTAGTGTA
Found at i:20266641 original size:44 final size:42
Alignment explanation
Indices: 20266591--20266706 Score: 110
Period size: 43 Copynumber: 2.7 Consensus size: 42
20266581 ATGAGTATTT
*
20266591 GTGTAAGAACACATCTGGGACATTGGCATCGA-TTTGAGGTTTAC
1 GTGTAAGAACACGTCTGGGACATTGGCATCGAGTTTGA---TTAC
* * *
20266635 GTGTAAGATC-CTGTCTGGGACAGTGACATCGATGTTTGATTAC
1 GTGTAAGAACAC-GTCTGGGACATTGGCATCGA-GTTTGATTAC
* * *
20266678 ATGTAAGACCACGTCTGGGACGTTGGCAT
1 GTGTAAGAACACGTCTGGGACATTGGCAT
20266707 TGTACGAGCC
Statistics
Matches: 59, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
43 27 0.46
44 27 0.46
46 5 0.08
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.29
Consensus pattern (42 bp):
GTGTAAGAACACGTCTGGGACATTGGCATCGAGTTTGATTAC
Found at i:20267410 original size:23 final size:23
Alignment explanation
Indices: 20267367--20267412 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
20267357 GTTAATTATA
* *
20267367 GACTTATAGATTGACGTATAATT
1 GACTTATAAATAGACGTATAATT
20267390 GACTTATAAATAGA-GTGATAATT
1 GACTTATAAATAGACGT-ATAATT
20267413 AGTAAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (23 bp):
GACTTATAAATAGACGTATAATT
Found at i:20279718 original size:20 final size:20
Alignment explanation
Indices: 20279674--20279751 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
20279664 TCAATACCAA
* * *
20279674 GATAAAGGTTTCAATACTAT
1 GATAAAAGTATCAATACTTT
* * *
20279694 AATAAAAATATCGATACTTT
1 GATAAAAGTATCAATACTTT
* *
20279714 GATAAATGTGTCAATACTTT
1 GATAAAAGTATCAATACTTT
*
20279734 GAGAAAAGTATCAATACT
1 GATAAAAGTATCAATACT
20279752 ATAAGCAATG
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (20 bp):
GATAAAAGTATCAATACTTT
Found at i:20279751 original size:40 final size:40
Alignment explanation
Indices: 20279674--20279751 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
20279664 TCAATACCAA
* * *
20279674 GATAAAGGTTTCAATACTATAATAAAAATATCGATACTTT
1 GATAAAGGTGTCAATACTATAAGAAAAATATCAATACTTT
* * * *
20279714 GATAAATGTGTCAATACTTTGAGAAAAGTATCAATACT
1 GATAAAGGTGTCAATACTATAAGAAAAATATCAATACT
20279752 ATAAGCAATG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (40 bp):
GATAAAGGTGTCAATACTATAAGAAAAATATCAATACTTT
Found at i:20279764 original size:20 final size:20
Alignment explanation
Indices: 20279684--20279764 Score: 54
Period size: 20 Copynumber: 4.0 Consensus size: 20
20279674 GATAAAGGTT
* **
20279684 TCAATACTATAATAAAAATA
1 TCAATACTATAAGAAATGTA
* * * * *
20279704 TCGATACTTTGATAAATGTG
1 TCAATACTATAAGAAATGTA
* * *
20279724 TCAATACTTTGAGAAAAGTA
1 TCAATACTATAAGAAATGTA
*
20279744 TCAATACTATAAGCAATGTA
1 TCAATACTATAAGAAATGTA
20279764 T
1 T
20279765 GATCGAAATA
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (20 bp):
TCAATACTATAAGAAATGTA
Found at i:20279801 original size:27 final size:27
Alignment explanation
Indices: 20279770--20279954 Score: 234
Period size: 27 Copynumber: 7.0 Consensus size: 27
20279760 TGTATGATCG
20279770 AAATACCCTCATAGGGTAAAATGACCA
1 AAATACCCTCATAGGGTAAAATGACCA
* * * *
20279797 AAATACCCTTATAAGGTAAAATCACCG
1 AAATACCCTCATAGGGTAAAATGACCA
* *
20279824 AAATACCCCCATAGGGAAAAATGACCA
1 AAATACCCTCATAGGGTAAAATGACCA
* *
20279851 AAATACCC-CTATAGGGTAAAATGATCG
1 AAATACCCTC-ATAGGGTAAAATGACCA
*
20279878 AAATACCCTCATAGGGTAAAATGATCA
1 AAATACCCTCATAGGGTAAAATGACCA
*
20279905 AAATACCCTCATAGGGT--AA-GACCG
1 AAATACCCTCATAGGGTAAAATGACCA
*
20279929 AAATACCCCCATAGGGTAAAATGACC
1 AAATACCCTCATAGGGTAAAATGACC
20279955 GTTATACCCC
Statistics
Matches: 136, Mismatches: 17, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
24 19 0.14
25 2 0.01
26 3 0.02
27 111 0.82
28 1 0.01
ACGTcount: A:0.43, C:0.23, G:0.16, T:0.18
Consensus pattern (27 bp):
AAATACCCTCATAGGGTAAAATGACCA
Found at i:20279827 original size:54 final size:54
Alignment explanation
Indices: 20279763--20279954 Score: 273
Period size: 54 Copynumber: 3.6 Consensus size: 54
20279753 TAAGCAATGT
* * *
20279763 ATGATCGAAATACCCTCATAGGGTAAAATGACCAAAATACCCTTATAAGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCTTATAGGGTAAA
* * *
20279817 ATCACCGAAATACCCCCATAGGGAAAAATGACCAAAATACCCCTATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCTTATAGGGTAAA
* * * *
20279871 ATGATCGAAATACCCTCATAGGGTAAAATGATCAAAATACCCTCATAGGGT--A
1 ATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCTTATAGGGTAAA
20279923 A-GACCGAAATACCCCCATAGGGTAAAATGACC
1 ATGACCGAAATACCCCCATAGGGTAAAATGACC
20279955 GTTATACCCC
Statistics
Matches: 122, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
51 28 0.23
52 2 0.02
54 92 0.75
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.19
Consensus pattern (54 bp):
ATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCTTATAGGGTAAA
Found at i:20284509 original size:31 final size:31
Alignment explanation
Indices: 20284413--20284510 Score: 99
Period size: 31 Copynumber: 3.2 Consensus size: 31
20284403 CTATCCCAGC
* * *
20284413 GGACTCTCTATTTTA-TATTTACTCTCTCGAT
1 GGACTATCTA-TTTAGTGTTTACTATCTCGAT
* * * *
20284444 GGAATATCTATTTCGTGTTCACTATCTTGAT
1 GGACTATCTATTTAGTGTTTACTATCTCGAT
* *
20284475 GGACTATCTATTTAGTGTTTACTGTCTCGGT
1 GGACTATCTATTTAGTGTTTACTATCTCGAT
20284506 GGACT
1 GGACT
20284511 TCATTGCTAT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
30 3 0.06
31 50 0.94
ACGTcount: A:0.19, C:0.18, G:0.17, T:0.45
Consensus pattern (31 bp):
GGACTATCTATTTAGTGTTTACTATCTCGAT
Found at i:20302647 original size:16 final size:17
Alignment explanation
Indices: 20302616--20302649 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
20302606 AAAATTGGGG
20302616 TGAGAAAATAATTTAAT
1 TGAGAAAATAATTTAAT
*
20302633 TGAGAAATTAA-TTAAT
1 TGAGAAAATAATTTAAT
20302649 T
1 T
20302650 AATATTTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (17 bp):
TGAGAAAATAATTTAAT
Found at i:20303805 original size:19 final size:20
Alignment explanation
Indices: 20303762--20303828 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
20303752 TACAAAATAA
20303762 TCAAAATAATTTTCAAAAAT
1 TCAAAATAATTTTCAAAAAT
**
20303782 TCAAAATAATTTT-AAATTT
1 TCAAAATAATTTTCAAAAAT
*
20303801 TCAAAAT-ATTTATAAAAAAT
1 TCAAAATAATTT-TCAAAAAT
*
20303821 TTAAAATA
1 TCAAAATA
20303829 TTGTGTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
18 4 0.10
19 12 0.31
20 23 0.59
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (20 bp):
TCAAAATAATTTTCAAAAAT
Found at i:20312394 original size:3 final size:3
Alignment explanation
Indices: 20312388--20312444 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
20312378 AGGACTTTTA
20312388 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20312436 TAT TAT TAT
1 TAT TAT TAT
20312445 CATCATCATC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:20327239 original size:61 final size:56
Alignment explanation
Indices: 20327155--20327280 Score: 171
Period size: 61 Copynumber: 2.2 Consensus size: 56
20327145 TGCTATTATT
*
20327155 ATTAAATTTTAAAAAATTATTATTAAATATAATTTAATAAAAATAAAAATAAATAATTTA
1 ATTATATTTTAAAAAATTATTATTAAATATAATTTAAT-AAAAT---AATAAATAATTTA
* *
20327215 ATTATATTTTAACATAATTATTATTAAATATAATTTAATAAAATAATATATAATTTA
1 ATTATATTTTAA-AAAATTATTATTAAATATAATTTAATAAAATAATAAATAATTTA
*
20327272 ATCATATTT
1 ATTATATTT
20327281 CAATCTATTT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
57 20 0.33
60 16 0.26
61 25 0.41
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (56 bp):
ATTATATTTTAAAAAATTATTATTAAATATAATTTAATAAAATAATAAATAATTTA
Found at i:20328676 original size:98 final size:98
Alignment explanation
Indices: 20328507--20328701 Score: 345
Period size: 98 Copynumber: 2.0 Consensus size: 98
20328497 ATACAATAAA
* *
20328507 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACGCCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
20328572 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
* *
20328605 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
20328670 CCTTTAGAATCTCAAACTCGGAATATTTCCTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTT
20328702 CATGATTTTT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
Found at i:20328986 original size:3 final size:3
Alignment explanation
Indices: 20328978--20329014 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
20328968 TACAAATGCT
20328978 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
20329015 ATACATCATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:20330196 original size:19 final size:19
Alignment explanation
Indices: 20330169--20330279 Score: 168
Period size: 19 Copynumber: 5.8 Consensus size: 19
20330159 AATCATATCT
20330169 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* ** *
20330188 TCAAAGATTATACATCATA
1 TCTAAGATTGCATATCATA
20330207 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
20330226 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
20330245 TCTACGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
20330264 TATAAGATTGCATATC
1 TCTAAGATTGCATATC
20330280 CTCAAAAATT
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 81 1.00
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:20330992 original size:22 final size:20
Alignment explanation
Indices: 20330958--20330997 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
20330948 TAAATTTTAA
20330958 TTTTAATTATTTCAAAATTG
1 TTTTAATTATTTCAAAATTG
*
20330978 TTTTACATATATTTCTAAAT
1 TTTTA-AT-TATTTCAAAAT
20330998 ATAATAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 2 0.12
22 10 0.59
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTTAATTATTTCAAAATTG
Found at i:20331173 original size:45 final size:45
Alignment explanation
Indices: 20331111--20331198 Score: 176
Period size: 45 Copynumber: 2.0 Consensus size: 45
20331101 GAGAAAATCA
20331111 AGTAGTAGGAAAAGGGAACGAAGCGATAGCTTTTTTTATTTACGT
1 AGTAGTAGGAAAAGGGAACGAAGCGATAGCTTTTTTTATTTACGT
20331156 AGTAGTAGGAAAAGGGAACGAAGCGATAGCTTTTTTTATTTAC
1 AGTAGTAGGAAAAGGGAACGAAGCGATAGCTTTTTTTATTTAC
20331199 ATTTATTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.34, C:0.09, G:0.26, T:0.31
Consensus pattern (45 bp):
AGTAGTAGGAAAAGGGAACGAAGCGATAGCTTTTTTTATTTACGT
Found at i:20332199 original size:18 final size:18
Alignment explanation
Indices: 20332176--20332210 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
20332166 AACATGATTT
20332176 AAATAA-ATAATCAAATAG
1 AAATAAGAT-ATCAAATAG
20332194 AAATAAGATATCAAATA
1 AAATAAGATATCAAATA
20332211 CAATCAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.23
Consensus pattern (18 bp):
AAATAAGATATCAAATAG
Found at i:20339496 original size:12 final size:12
Alignment explanation
Indices: 20339481--20339524 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
20339471 AAACCGAGCC
20339481 ATAAATATTTTT
1 ATAAATATTTTT
20339493 ATAAATA--TTT
1 ATAAATATTTTT
20339503 ATAAATATTTTT
1 ATAAATATTTTT
20339515 ATAAATATTT
1 ATAAATATTT
20339525 ACGGAGTGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.33
12 20 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATAAATATTTTT
Found at i:20339505 original size:10 final size:10
Alignment explanation
Indices: 20339490--20339525 Score: 54
Period size: 10 Copynumber: 3.4 Consensus size: 10
20339480 CATAAATATT
20339490 TTTATAAATA
1 TTTATAAATA
20339500 TTTATAAATA
1 TTTATAAATA
20339510 TTTTTATAAATA
1 --TTTATAAATA
20339522 TTTA
1 TTTA
20339526 CGGAGTGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 14 0.58
12 10 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTATAAATA
Found at i:20339508 original size:22 final size:22
Alignment explanation
Indices: 20339481--20339525 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
20339471 AAACCGAGCC
20339481 ATAAATATTTTTATAAATATTT
1 ATAAATATTTTTATAAATATTT
20339503 ATAAATATTTTTATAAATATTT
1 ATAAATATTTTTATAAATATTT
20339525 A
1 A
20339526 CGGAGTGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATAAATATTTTTATAAATATTT
Found at i:20340922 original size:24 final size:24
Alignment explanation
Indices: 20340895--20340960 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
20340885 CTTGCTTGAA
* *
20340895 CTTCCCGATATTGGCTCATATGAG
1 CTTCCCGTTATTGGCTCATAGGAG
* * *
20340919 CTTCCCGTTAATGGCTTATCGGAG
1 CTTCCCGTTATTGGCTCATAGGAG
20340943 CTTCCCGTTATATGGCTC
1 CTTCCCGTTAT-TGGCTC
20340961 GAAAAAGCTT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
24 29 0.85
25 5 0.15
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (24 bp):
CTTCCCGTTATTGGCTCATAGGAG
Found at i:20353096 original size:8 final size:8
Alignment explanation
Indices: 20353083--20353114 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
20353073 AAAAGCTCTA
20353083 TCATCATC
1 TCATCATC
20353091 TCATCATC
1 TCATCATC
20353099 TCATCATC
1 TCATCATC
20353107 TCATCATC
1 TCATCATC
20353115 ACAAATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.25, C:0.38, G:0.00, T:0.38
Consensus pattern (8 bp):
TCATCATC
Found at i:20354124 original size:12 final size:12
Alignment explanation
Indices: 20354107--20354160 Score: 71
Period size: 11 Copynumber: 4.8 Consensus size: 12
20354097 AACTAATCCT
20354107 CTCTCAAATTTC
1 CTCTCAAATTTC
20354119 CTCTC-AATTTC
1 CTCTCAAATTTC
20354130 CTCTCAAA-TTC
1 CTCTCAAATTTC
20354141 CT-TCAAAATTT-
1 CTCTC-AAATTTC
20354152 CTCTCAAAT
1 CTCTCAAAT
20354161 CCATATTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
10 2 0.05
11 25 0.66
12 11 0.29
ACGTcount: A:0.28, C:0.31, G:0.00, T:0.41
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:20357745 original size:124 final size:124
Alignment explanation
Indices: 20357581--20357930 Score: 610
Period size: 124 Copynumber: 2.8 Consensus size: 124
20357571 CCCAAACATG
* *
20357581 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCTTGC
1 CTACTGTAGCAAAAGCGTGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
20357646 TAGAAGCGATTTTATACTATTTGCTTAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
* * * *
20357705 CTACTATAGCAAAAGCGTGTCCACGAAGGTGCGATTTCACAAATTCTTCTCAAATAGCATCCAGC
1 CTACTGTAGCAAAAGCGTGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
20357770 TAGAAGCGATTTTATACTATTTCCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
*
20357829 CTACTGTAGCAAAAGCGTGTCCACTAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGTGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
20357894 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
20357931 CTCGAAATTA
Statistics
Matches: 211, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
124 211 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGTGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
Found at i:20358638 original size:33 final size:30
Alignment explanation
Indices: 20358588--20358651 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 30
20358578 GCTTGACACA
*
20358588 TTGGCAGCACCAGTAAATTTATAATAAAGAAGT
1 TTGGCAACACCAGTAAATTT-TAA-AAA-AAGT
20358621 TTGGCAACACC-GATAAATTTTAAAAAAAGT
1 TTGGCAACACCAG-TAAATTTTAAAAAAAGT
20358651 T
1 T
20358652 CATTGATACC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 5 0.17
31 3 0.10
32 4 0.14
33 17 0.59
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (30 bp):
TTGGCAACACCAGTAAATTTTAAAAAAAGT
Found at i:20358966 original size:5 final size:5
Alignment explanation
Indices: 20358956--20358981 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
20358946 GTGAAAGTGA
20358956 ATTTT ATTTT ATTTT ATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT A
20358982 GCTTCCGGAT
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:20359725 original size:25 final size:25
Alignment explanation
Indices: 20359691--20359742 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
20359681 ATATGTAGTG
20359691 ATTACTCCTTACAAGCTGAGAATGC
1 ATTACTCCTTACAAGCTGAGAATGC
20359716 ATTACTCCTTACAAGCTGAGAATGC
1 ATTACTCCTTACAAGCTGAGAATGC
20359741 AT
1 AT
20359743 AATATAACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (25 bp):
ATTACTCCTTACAAGCTGAGAATGC
Found at i:20363189 original size:6 final size:6
Alignment explanation
Indices: 20363178--20363218 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
20363168 AACGCATATA
*
20363178 AGAAGG AGAAGG AGAAGG AGAAGA AGAAGG AGAAGG AGAAG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAG
20363219 CCATTTGTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (6 bp):
AGAAGG
Found at i:20370261 original size:17 final size:17
Alignment explanation
Indices: 20370214--20370273 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
20370204 TAAACATTTT
* *
20370214 TTTCTTTTTCCTCTTCC
1 TTTCCTTTTCCTTTTCC
*
20370231 CTTCTCTTTT-CTTTTCC
1 TTTC-CTTTTCCTTTTCC
*
20370248 TTTCCTTTTCCTTTTCT
1 TTTCCTTTTCCTTTTCC
*
20370265 TTTGCTTTT
1 TTTCCTTTT
20370274 GTTTTTTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
16 5 0.14
17 26 0.74
18 4 0.11
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (17 bp):
TTTCCTTTTCCTTTTCC
Found at i:20370273 original size:11 final size:11
Alignment explanation
Indices: 20370213--20370278 Score: 60
Period size: 11 Copynumber: 5.8 Consensus size: 11
20370203 TTAAACATTT
20370213 TTTTCTTTTTCC
1 TTTTC-TTTTCC
* **
20370225 TCTTCCCTTCTC
1 TTTTCTTTTC-C
20370237 TTTTCTTTTCC
1 TTTTCTTTTCC
*
20370248 TTTCCTTTTCC
1 TTTTCTTTTCC
*
20370259 TTTTCTTTTGC
1 TTTTCTTTTCC
*
20370270 TTTTGTTTT
1 TTTTCTTTT
20370279 TTTATATATC
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
11 31 0.72
12 12 0.28
ACGTcount: A:0.00, C:0.27, G:0.03, T:0.70
Consensus pattern (11 bp):
TTTTCTTTTCC
Found at i:20374151 original size:20 final size:20
Alignment explanation
Indices: 20374114--20374151 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20374104 TGTTATTTAT
*
20374114 TTAATAAAAAAAATAAAAGG
1 TTAATAAAAAAAAGAAAAGG
*
20374134 TTAATAAAATAAAGAAAA
1 TTAATAAAAAAAAGAAAA
20374152 CAAAATGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (20 bp):
TTAATAAAAAAAAGAAAAGG
Found at i:20376013 original size:21 final size:21
Alignment explanation
Indices: 20375997--20376042 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
20375987 ATTGTTTCTT
20375997 TTGTTCTCGTTCTTGTTGTTC
1 TTGTTCTCGTTCTTGTTGTTC
* *
20376018 TTGTTCTTGTTCTTGTTGTTG
1 TTGTTCTCGTTCTTGTTGTTC
20376039 TTGT
1 TTGT
20376043 GTCTGTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.00, C:0.13, G:0.22, T:0.65
Consensus pattern (21 bp):
TTGTTCTCGTTCTTGTTGTTC
Found at i:20376036 original size:15 final size:15
Alignment explanation
Indices: 20375992--20376042 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
20375982 TTTTGATTGT
*
20375992 TTCTT-TTGTTCTCG
1 TTCTTGTTGTTCTTG
20376006 TTCTTGTTGTTCTTG
1 TTCTTGTTGTTCTTG
* *
20376021 TTCTTGTTCTTGTTG
1 TTCTTGTTGTTCTTG
*
20376036 TTGTTGT
1 TTCTTGT
20376043 GTCTGTTTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 5 0.16
15 27 0.84
ACGTcount: A:0.00, C:0.14, G:0.20, T:0.67
Consensus pattern (15 bp):
TTCTTGTTGTTCTTG
Found at i:20376049 original size:21 final size:20
Alignment explanation
Indices: 20375997--20376049 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
20375987 ATTGTTTCTT
20375997 TTGTTCTCGTTCTTGTTGTTC
1 TTGTTCT-GTTCTTGTTGTTC
*
20376018 TTGTTCTTGTTCTTGTTGTTG
1 TTGTTC-TGTTCTTGTTGTTC
20376039 TTGTGTCTGTT
1 TTGT-TCTGTT
20376050 TGTTTGTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 26 0.90
22 3 0.10
ACGTcount: A:0.00, C:0.13, G:0.23, T:0.64
Consensus pattern (20 bp):
TTGTTCTGTTCTTGTTGTTC
Found at i:20376543 original size:31 final size:32
Alignment explanation
Indices: 20376484--20376548 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
20376474 GGCAAATTAC
20376484 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
20376516 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
20376547 AA
1 AA
20376549 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:20384441 original size:6 final size:5
Alignment explanation
Indices: 20384408--20384440 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
20384398 CAAAAAACAC
20384408 TTTCTT TTTCT TTTCT TTTCT TTT-T TTTCT TTT
1 TTTC-T TTTCT TTTCT TTTCT TTTCT TTTCT TTT
20384441 TTGGGTGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.15
5 18 0.69
6 4 0.15
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTCT
Found at i:20384543 original size:21 final size:21
Alignment explanation
Indices: 20384503--20384543 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20384493 ATAAAGTAGA
*
20384503 TTATATATTATTTTTATAGTG
1 TTATATATTATATTTATAGTG
20384524 TTATATATTATGATTT-TAGT
1 TTATATATTAT-ATTTATAGT
20384544 ATATTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (21 bp):
TTATATATTATATTTATAGTG
Found at i:20384586 original size:17 final size:18
Alignment explanation
Indices: 20384561--20384606 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
20384551 TATAAGAATA
*
20384561 ATTATATTA-AGAATTTT
1 ATTAAATTATAGAATTTT
* *
20384578 ATTAAATTATATATTTTT
1 ATTAAATTATAGAATTTT
20384596 ATTAAATTATA
1 ATTAAATTATA
20384607 TTTAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTAAATTATAGAATTTT
Found at i:20384836 original size:44 final size:45
Alignment explanation
Indices: 20384766--20384858 Score: 154
Period size: 44 Copynumber: 2.1 Consensus size: 45
20384756 ATTACATCAT
20384766 CATTCCATTCAACCAAACACAAGAAT-ACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATAACTATTACAGTTCTATTC
*
20384810 CATTCCATTCAACCAAACA-ATTGAATAACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACA-AGAATAACTATTACAGTTCTATTC
20384855 CATT
1 CATT
20384859 ACAGCTCTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.50
45 22 0.48
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (45 bp):
CATTCCATTCAACCAAACACAAGAATAACTATTACAGTTCTATTC
Found at i:20384861 original size:16 final size:16
Alignment explanation
Indices: 20384840--20384894 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
20384830 TTGAATAACT
*
20384840 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
*
20384856 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
*
20384872 ATTACAACTCTATTCC
1 ATTACAGCTCTATTCC
20384888 ATTACAG
1 ATTACAG
20384895 TGAACCAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:20385991 original size:35 final size:35
Alignment explanation
Indices: 20385951--20386020 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
20385941 GGTGTATGCT
20385951 TTTAAATGACCAAAATTGGTAT-G-TGTTAATGTATC
1 TTTAAATGACCAAAA-TGGTATGGTTGTT-ATGTATC
*
20385986 TTTAAATGGCCAAAATGGTATGGTTGTTATGTATC
1 TTTAAATGACCAAAATGGTATGGTTGTTATGTATC
20386021 AATTATGTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 6 0.19
35 22 0.69
36 4 0.12
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (35 bp):
TTTAAATGACCAAAATGGTATGGTTGTTATGTATC
Found at i:20387123 original size:20 final size:21
Alignment explanation
Indices: 20387081--20387126 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
20387071 TAGGGCGACT
* * *
20387081 AAGGCTGAATAATAATGACTA
1 AAGGTTGAATAATAATAAATA
20387102 AAGGTTGAA-AATAATAAATA
1 AAGGTTGAATAATAATAAATA
20387122 AAGGT
1 AAGGT
20387127 GATATTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.52, C:0.04, G:0.20, T:0.24
Consensus pattern (21 bp):
AAGGTTGAATAATAATAAATA
Found at i:20388136 original size:84 final size:84
Alignment explanation
Indices: 20387995--20388162 Score: 327
Period size: 84 Copynumber: 2.0 Consensus size: 84
20387985 TAGCTAAGTT
20387995 CTTAACTTGGGATGAACCGAAACTCTCAAAAACAAAATCTTATTCCACAATTATTGTTGTTGTGG
1 CTTAACTTGGGATGAACCGAAACTCTCAAAAACAAAATCTTATTCCACAATTATTGTTGTTGTGG
20388060 ATGCATGCAAGCATAATGA
66 ATGCATGCAAGCATAATGA
*
20388079 CTTAACTTGGGATGAACCGAAACTCTCAAAAACAAAATCTTATTCCACAATTGTTGTTGTTGTGG
1 CTTAACTTGGGATGAACCGAAACTCTCAAAAACAAAATCTTATTCCACAATTATTGTTGTTGTGG
20388144 ATGCATGCAAGCATAATGA
66 ATGCATGCAAGCATAATGA
20388163 TTTTGTATGC
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (84 bp):
CTTAACTTGGGATGAACCGAAACTCTCAAAAACAAAATCTTATTCCACAATTATTGTTGTTGTGG
ATGCATGCAAGCATAATGA
Found at i:20391704 original size:40 final size:40
Alignment explanation
Indices: 20391660--20391876 Score: 235
Period size: 40 Copynumber: 5.5 Consensus size: 40
20391650 TATAAACAGG
20391660 GGCACGTAAGTGCATTCAGGGGTACCGAAGTACAAATAGA
1 GGCACGTAAGTGCATTCAGGGGTACCGAAGTACAAATAGA
* *
20391700 GGCACGTATGTGCAATT-A-GGGTACCGAAGTACAAACAGA
1 GGCACGTAAGTGC-ATTCAGGGGTACCGAAGTACAAATAGA
* ** * * *
20391739 GGAACGTGTGTGCAATCAGGGGTACCAAAGTACAAATAGG
1 GGCACGTAAGTGCATTCAGGGGTACCGAAGTACAAATAGA
* *
20391779 GGCACGTAAGTGCATTCAGGGGTACCAAAGTACGAATAGA
1 GGCACGTAAGTGCATTCAGGGGTACCGAAGTACAAATAGA
* * * *
20391819 GGCACATAAGTGCAATT-AAGGGTACTGAAGTACAAACAG-
1 GGCACGTAAGTGC-ATTCAGGGGTACCGAAGTACAAATAGA
* *
20391858 GGACACATAAATGCATTCA
1 GG-CACGTAAGTGCATTCA
20391877 TCAATAGTTA
Statistics
Matches: 150, Mismatches: 21, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.01
39 37 0.25
40 105 0.70
41 6 0.04
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.18
Consensus pattern (40 bp):
GGCACGTAAGTGCATTCAGGGGTACCGAAGTACAAATAGA
Found at i:20391772 original size:79 final size:80
Alignment explanation
Indices: 20391641--20391820 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 80
20391631 TTGATTCAGT
* * * * ** * *
20391641 GTACCAGAGTATAAACAGGGGCACGTAAGTGCATTCAGGGGTACCGAAGTACAAATAGAGGCACG
1 GTACCAAAGTACAAACAGAGGAACGTGTGTGCAATCAGGGGTACCAAAGTACAAATAGAGGCACG
*
20391706 TATGTGCAATT-A-GG
66 TAAGTGC-ATTCAGGG
* *
20391720 GTACCGAAGTACAAACAGAGGAACGTGTGTGCAATCAGGGGTACCAAAGTACAAATAGGGGCACG
1 GTACCAAAGTACAAACAGAGGAACGTGTGTGCAATCAGGGGTACCAAAGTACAAATAGAGGCACG
20391785 TAAGTGCATTCAGGG
66 TAAGTGCATTCAGGG
* *
20391800 GTACCAAAGTACGAATAGAGG
1 GTACCAAAGTACAAACAGAGG
20391821 CACATAAGTG
Statistics
Matches: 85, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
78 3 0.04
79 62 0.73
80 20 0.24
ACGTcount: A:0.36, C:0.17, G:0.31, T:0.17
Consensus pattern (80 bp):
GTACCAAAGTACAAACAGAGGAACGTGTGTGCAATCAGGGGTACCAAAGTACAAATAGAGGCACG
TAAGTGCATTCAGGG
Found at i:20391809 original size:20 final size:20
Alignment explanation
Indices: 20391748--20391809 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
20391738 AGGAACGTGT
20391748 GTGCAATCAGGGGTACCAAA
1 GTGCAATCAGGGGTACCAAA
* * **
20391768 GTACAAAT-AGGGGCACGTAA
1 GTGC-AATCAGGGGTACCAAA
*
20391788 GTGCATTCAGGGGTACCAAA
1 GTGCAATCAGGGGTACCAAA
20391808 GT
1 GT
20391810 ACGAATAGAG
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
19 2 0.06
20 26 0.84
21 3 0.10
ACGTcount: A:0.34, C:0.18, G:0.31, T:0.18
Consensus pattern (20 bp):
GTGCAATCAGGGGTACCAAA
Found at i:20392718 original size:14 final size:11
Alignment explanation
Indices: 20392682--20392709 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
20392672 CATTTTAACC
20392682 TTAAAAATTCA
1 TTAAAAATTCA
20392693 TTAAAAATTCA
1 TTAAAAATTCA
20392704 TTAAAA
1 TTAAAA
20392710 CCTATTCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (11 bp):
TTAAAAATTCA
Found at i:20403564 original size:39 final size:39
Alignment explanation
Indices: 20403524--20403663 Score: 181
Period size: 39 Copynumber: 3.5 Consensus size: 39
20403514 ATTCACTTTT
* * *
20403524 AAGCATATATCACATTACACATATAATCACATAACATTT
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* * * **
20403563 AATCATATACCACAATACTCATATAATTACATAATGTTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
20403602 AAGCATATATCACAATACTCATATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
*
20403641 AAGCTTATATATCGCAATACTCA
1 AAGC--ATATATCACAATACTCA
20403664 AAAACATGTT
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
39 69 0.81
41 16 0.19
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.31
Consensus pattern (39 bp):
AAGCATATATCACAATACTCATATAATCACATAACATTC
Found at i:20403565 original size:15 final size:17
Alignment explanation
Indices: 20403527--20403567 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
20403517 CACTTTTAAG
20403527 CATAT-ATCACATTACA
1 CATATAATCACATTACA
20403543 CATATAATCACA-TA-A
1 CATATAATCACATTACA
*
20403558 CATTTAATCA
1 CATATAATCA
20403568 TATACCACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 10 0.43
16 7 0.30
17 6 0.26
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (17 bp):
CATATAATCACATTACA
Found at i:20403727 original size:14 final size:15
Alignment explanation
Indices: 20403696--20403728 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
20403686 ACATAATGGT
*
20403696 CACATGTCATATAAA
1 CACATATCATATAAA
20403711 CACATATCATA-AAA
1 CACATATCATATAAA
20403725 CACA
1 CACA
20403729 CATATATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.52, C:0.24, G:0.03, T:0.21
Consensus pattern (15 bp):
CACATATCATATAAA
Found at i:20406173 original size:19 final size:19
Alignment explanation
Indices: 20406122--20406173 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
20406112 CTGGCACGTA
* *
20406122 AAGTGCATACTGGAACACG
1 AAGTGCATATTGGCACACG
* *
20406141 GAGTGCATCTTGGCACACG
1 AAGTGCATATTGGCACACG
20406160 AAGTGCATATTGGC
1 AAGTGCATATTGGC
20406174 GCATATGCAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (19 bp):
AAGTGCATATTGGCACACG
Found at i:20415671 original size:31 final size:31
Alignment explanation
Indices: 20415633--20415696 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
20415623 TGATCATCTG
*
20415633 AGGGTGGTCTTACAGATACTTCGTGAAAAGT
1 AGGGTGGTCCTACAGATACTTCGTGAAAAGT
20415664 AGGGTGGTCCTACAGATACTTCGTGAAAAGT
1 AGGGTGGTCCTACAGATACTTCGTGAAAAGT
20415695 AG
1 AG
20415697 TTTTTCGTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.27
Consensus pattern (31 bp):
AGGGTGGTCCTACAGATACTTCGTGAAAAGT
Found at i:20420014 original size:30 final size:30
Alignment explanation
Indices: 20419958--20420017 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
20419948 TGGGAAGATG
* *
20419958 TAAAAGTTTTGGGGGAAAAGTAAAAATATT
1 TAAAAGTTTAGGGGAAAAAGTAAAAATATT
*
20419988 TAAAAGTTTAGGGTAAAAATGT-AAAATATT
1 TAAAAGTTTAGGGGAAAAA-GTAAAAATATT
20420018 ATAGTTTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (30 bp):
TAAAAGTTTAGGGGAAAAAGTAAAAATATT
Found at i:20428941 original size:16 final size:16
Alignment explanation
Indices: 20428920--20428952 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
20428910 CTCGATGGAG
20428920 TTATTTTGACTATATC
1 TTATTTTGACTATATC
20428936 TTATTTTGACTATATC
1 TTATTTTGACTATATC
20428952 T
1 T
20428953 CAATTAGCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.06, T:0.58
Consensus pattern (16 bp):
TTATTTTGACTATATC
Done.