Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397275.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_34.0, 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: 2955990
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 53928 characters in sequence are not A, C, G, or T
File 7 of 8
Found at i:2310215 original size:128 final size:127
Alignment explanation
Indices: 2309841--2310292 Score: 478
Period size: 126 Copynumber: 3.6 Consensus size: 127
2309831 ACATAATATT
* * * * * * * *
2309841 GTTACACACAATGTTCAAAAAATAATATTGTTACACACTATGTTTAAAAAAATGTTGTTATACAT
1 GTTACACACCATGTTTAAAAAATAATGTTATTACACACCATGTTTAAAAAAATATTGTTACACGT
* * * * *
2309906 TATGTTTAAAGTTTTTAACTCCAAGAGTTTATGTTTTACTAAAATATAAAGATAGAGATTAA
66 CATGTTTAAAGTATTTAACTCAAAGAGTTTATGTTTTAGTAAAATATAAAGATAGAGATCAA
* * * * *
2309968 GTTACACACTATATTTAAAAAATAATGTTATTATA-AGCCATGTTCAAAAAAATGTTGTTCACAC
1 GTTACACACCATGTTTAAAAAATAATGTTATTACACA-CCATGTTTAAAAAAATATTGTT-ACAC
* * * * *
2310032 -T-ATGTTTAAGGTATTTAACTCTAAGAGTTTATGTCTTAGTAAAATATAAAGATAGAAACCAA
64 GTCATGTTTAAAGTATTTAACTCAAAGAGTTTATGTTTTAGTAAAATATAAAGATAGAGATCAA
* * * * *
2310094 GTTATATACCATGTTTAAAAAATAATGTTATTACACATCATGTTAAAAAATAAAATTGTTACACG
1 GTTACACACCATGTTTAAAAAATAATGTTATTACACACCATGTTTAAAAA-AATATTGTTACACG
* * * * * *
2310159 TCATGTTTAAAGCATTTAACTCAAAGAGTTTTTATTTTAGTGAAATACAAAAATAGAGATCAA
65 TCATGTTTAAAGTATTTAACTCAAAGAGTTTATGTTTTAGTAAAATATAAAGATAGAGATCAA
** * * ** * *
2310222 AATACACATCATGTTTAAAAAATAATGTTGTTACAGGCCATGTTTAAAAAAATATTTTTACATGT
1 GTTACACACCATGTTTAAAAAATAATGTTATTACACACCATGTTTAAAAAAATATTGTTACACGT
2310287 CATGTT
66 CATGTT
2310293 GCAAAATTAA
Statistics
Matches: 269, Mismatches: 50, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
126 99 0.37
127 77 0.29
128 93 0.35
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.36
Consensus pattern (127 bp):
GTTACACACCATGTTTAAAAAATAATGTTATTACACACCATGTTTAAAAAAATATTGTTACACGT
CATGTTTAAAGTATTTAACTCAAAGAGTTTATGTTTTAGTAAAATATAAAGATAGAGATCAA
Found at i:2310263 original size:29 final size:29
Alignment explanation
Indices: 2310231--2310326 Score: 108
Period size: 29 Copynumber: 3.4 Consensus size: 29
2310221 AAATACACAT
*
2310231 CATGTTTAAAAAATAATGTTGTTACAGGC
1 CATGTTTAAAAAATAATGTTGTTACATGC
*
2310260 CATGTTTAAAAAA-ATAT-TT-TTACATGT
1 CATGTTTAAAAAATA-ATGTTGTTACATGC
** * *
2310287 CATGTTGCAAAATTAAAGTTGTTACATGC
1 CATGTTTAAAAAATAATGTTGTTACATGC
2310316 CATGTTTAAAA
1 CATGTTTAAAA
2310327 TATTTAACTC
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
27 17 0.31
28 6 0.11
29 31 0.57
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (29 bp):
CATGTTTAAAAAATAATGTTGTTACATGC
Found at i:2328707 original size:23 final size:20
Alignment explanation
Indices: 2328670--2328711 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 20
2328660 TAAAACTGCT
2328670 CAAACAAAACAAACCAATTC
1 CAAACAAAACAAACCAATTC
2328690 CAAACAACAACACTAACCAATT
1 CAAACAA-AACA--AACCAATT
2328712 AGGATTGTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
23 8 0.42
ACGTcount: A:0.57, C:0.31, G:0.00, T:0.12
Consensus pattern (20 bp):
CAAACAAAACAAACCAATTC
Found at i:2329145 original size:2 final size:2
Alignment explanation
Indices: 2329138--2329163 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2329128 AAATAAATAA
2329138 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
2329164 GCAGCAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2337156 original size:10 final size:9
Alignment explanation
Indices: 2337118--2337152 Score: 54
Period size: 8 Copynumber: 3.9 Consensus size: 9
2337108 TGTCTGTTGA
2337118 AAATAAAAT
1 AAATAAAAT
2337127 AAAT-AAAT
1 AAATAAAAT
2337135 AAATAAAAAT
1 AAAT-AAAAT
2337145 AAATAAAA
1 AAATAAAA
2337153 ATAAGAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.33
9 8 0.33
10 8 0.33
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATAAAAT
Found at i:2337161 original size:18 final size:18
Alignment explanation
Indices: 2337118--2337151 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2337108 TGTCTGTTGA
2337118 AAAT-AAAATAAATAAAT
1 AAATAAAAATAAATAAAT
2337135 AAATAAAAATAAATAAA
1 AAATAAAAATAAATAAA
2337152 AATAAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (18 bp):
AAATAAAAATAAATAAAT
Found at i:2341734 original size:17 final size:17
Alignment explanation
Indices: 2341697--2341734 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2341687 ATAAATTTGT
*
2341697 AAATAAAAAACATAATG
1 AAATAAAAAACATAATA
2341714 AAATAAATAAACA-AATA
1 AAATAAA-AAACATAATA
2341731 AAAT
1 AAAT
2341735 TGACATGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (17 bp):
AAATAAAAAACATAATA
Found at i:2346649 original size:50 final size:48
Alignment explanation
Indices: 2346541--2346652 Score: 122
Period size: 49 Copynumber: 2.3 Consensus size: 48
2346531 AAATTTTTGA
* *
2346541 AAAAAAATCTCT--AAATTTTGAAAAACATAAAAATAAATTTTTTATTT
1 AAAAAAAT-TCTAGAAATTTTGAAAAACACAAAAATAAATTTTTCATTT
* * *
2346588 TAAGAAATTCTAGAAATTTTTGAAAAACACAAAAA-ATATTTTTCATTGCT
1 AAAAAAATTCTAGAAA-TTTTGAAAAACACAAAAATAAATTTTTCATT--T
2346638 AAAAAAATTCTAGAA
1 AAAAAAATTCTAGAA
2346653 TGATAGAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
46 3 0.06
47 6 0.11
48 13 0.25
49 17 0.32
50 14 0.26
ACGTcount: A:0.52, C:0.08, G:0.05, T:0.35
Consensus pattern (48 bp):
AAAAAAATTCTAGAAATTTTGAAAAACACAAAAATAAATTTTTCATTT
Found at i:2347863 original size:13 final size:13
Alignment explanation
Indices: 2347847--2347888 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2347837 CTTCTTTTTC
2347847 TTTCTATTTTATT
1 TTTCTATTTTATT
2347860 TTTC-ATTTTATTT
1 TTTCTATTTTA-TT
* *
2347873 TTTGTATTTTCTT
1 TTTCTATTTTATT
2347886 TTT
1 TTT
2347889 AGATTTTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 6 0.24
13 14 0.56
14 5 0.20
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTCTATTTTATT
Found at i:2347863 original size:17 final size:17
Alignment explanation
Indices: 2347841--2347873 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2347831 TTATTTCTTC
2347841 TTTTTC-TTTCTATTTTA
1 TTTTTCATTT-TATTTTA
2347858 TTTTTCATTTTATTTT
1 TTTTTCATTTTATTTT
2347874 TTGTATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTCATTTTATTTTA
Found at i:2347867 original size:12 final size:12
Alignment explanation
Indices: 2347829--2347874 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
2347819 TGCATTAAAG
2347829 TTTTATTTCTTC-
1 TTTTATTT-TTCA
*
2347841 TTTT-TCTTTCTA
1 TTTTATTTTTC-A
2347853 TTTTATTTTTCA
1 TTTTATTTTTCA
2347865 TTTTATTTTT
1 TTTTATTTTT
2347875 TGTATTTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
10 3 0.10
11 2 0.07
12 19 0.66
13 5 0.17
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTATTTTTCA
Found at i:2350563 original size:19 final size:19
Alignment explanation
Indices: 2350539--2350580 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2350529 AAGTTTTTTT
* *
2350539 AATTAGTATCTAGCTTTAA
1 AATTAGTACCAAGCTTTAA
*
2350558 AATTAGTACCAAGCTTTAG
1 AATTAGTACCAAGCTTTAA
2350577 AATT
1 AATT
2350581 GTCTTTTCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (19 bp):
AATTAGTACCAAGCTTTAA
Found at i:2351713 original size:29 final size:29
Alignment explanation
Indices: 2351679--2351739 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
2351669 TAGATATTCA
*
2351679 ATATATCTTGTTTAACCATTGTGGATATT
1 ATATATCTTGTTTAACCACTGTGGATATT
*
2351708 ATATATCTTGTTTAACTACTGTGGATATT
1 ATATATCTTGTTTAACCACTGTGGATATT
2351737 ATA
1 ATA
2351740 AATATTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.48
Consensus pattern (29 bp):
ATATATCTTGTTTAACCACTGTGGATATT
Found at i:2353901 original size:21 final size:21
Alignment explanation
Indices: 2353876--2353931 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
2353866 CAGAGAAGAC
*
2353876 TTAATCGACTAAGAAGTATGG
1 TTAATCAACTAAGAAGTATGG
*
2353897 TTAATCAACCAAGAAGTATGG
1 TTAATCAACTAAGAAGTATGG
2353918 TTAATCAACTAAGA
1 TTAATCAACTAAGA
2353932 GCACATTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (21 bp):
TTAATCAACTAAGAAGTATGG
Found at i:2354385 original size:35 final size:35
Alignment explanation
Indices: 2354341--2354465 Score: 132
Period size: 35 Copynumber: 3.7 Consensus size: 35
2354331 GTTAGTTTTG
*
2354341 GGTTTTGGTTGATCTTGTGAAAAACTATTGTTAAA
1 GGTTGTGGTTGATCTTGTGAAAAACTATTGTTAAA
* * *
2354376 GGTTGTGGTTTAGCCTT-TGAAAAACTATT-TT--G
1 GGTTGTGGTTGA-TCTTGTGAAAAACTATTGTTAAA
* * *
2354408 GGTTTTGGTCGATCTTGAGAAAAACTATTGTTAAA
1 GGTTGTGGTTGATCTTGTGAAAAACTATTGTTAAA
* *
2354443 GGTTGTGGCTGAGCTTGTGAAAA
1 GGTTGTGGTTGATCTTGTGAAAA
2354466 GCCATTGTAA
Statistics
Matches: 70, Mismatches: 15, Indels: 10
0.74 0.16 0.11
Matches are distributed among these distances:
31 3 0.04
32 20 0.29
33 2 0.03
34 2 0.03
35 40 0.57
36 3 0.04
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.39
Consensus pattern (35 bp):
GGTTGTGGTTGATCTTGTGAAAAACTATTGTTAAA
Found at i:2354435 original size:32 final size:32
Alignment explanation
Indices: 2354336--2354436 Score: 105
Period size: 32 Copynumber: 3.1 Consensus size: 32
2354326 GAAAAGTTAG
2354336 TTTTGGGTTTTGGTTGATCTTGTGAAAAACTA
1 TTTTGGGTTTTGGTTGATCTTGTGAAAAACTA
* * * *
2354368 TTGTTAAAGGTTGTGGTTTAGCCTT-TGAAAAACTA
1 TT-TT--GGGTTTTGGTTGA-TCTTGTGAAAAACTA
* *
2354403 TTTTGGGTTTTGGTCGATCTTGAGAAAAACTA
1 TTTTGGGTTTTGGTTGATCTTGTGAAAAACTA
2354435 TT
1 TT
2354437 GTTAAAGGTT
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
31 3 0.06
32 22 0.41
33 2 0.04
34 2 0.04
35 22 0.41
36 3 0.06
ACGTcount: A:0.25, C:0.08, G:0.24, T:0.44
Consensus pattern (32 bp):
TTTTGGGTTTTGGTTGATCTTGTGAAAAACTA
Found at i:2354464 original size:67 final size:67
Alignment explanation
Indices: 2354336--2354465 Score: 208
Period size: 67 Copynumber: 1.9 Consensus size: 67
2354326 GAAAAGTTAG
* * * *
2354336 TTTTGGGTTTTGGTTGATCTTGTGAAAAACTATTGTTAAAGGTTGTGGTTTAGCCTTTGAAAAAC
1 TTTTGGGTTTTGGTCGATCTTGAGAAAAACTATTGTTAAAGGTTGTGGCTGAGCCTTTGAAAAAC
2354401 TA
66 TA
2354403 TTTTGGGTTTTGGTCGATCTTGAGAAAAACTATTGTTAAAGGTTGTGGCTGAG-CTTGTGAAAA
1 TTTTGGGTTTTGGTCGATCTTGAGAAAAACTATTGTTAAAGGTTGTGGCTGAGCCTT-TGAAAA
2354466 GCCATTGTAA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
66 3 0.05
67 55 0.95
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (67 bp):
TTTTGGGTTTTGGTCGATCTTGAGAAAAACTATTGTTAAAGGTTGTGGCTGAGCCTTTGAAAAAC
TA
Found at i:2366918 original size:24 final size:24
Alignment explanation
Indices: 2366886--2366931 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
2366876 ACCGCACTGG
2366886 CCAATTAAAAAAGGAAAAAGGACA
1 CCAATTAAAAAAGGAAAAAGGACA
2366910 CCAATTAAAAAAGGAAAAAGGA
1 CCAATTAAAAAAGGAAAAAGGA
2366932 ATCCCGATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.63, C:0.11, G:0.17, T:0.09
Consensus pattern (24 bp):
CCAATTAAAAAAGGAAAAAGGACA
Found at i:2382252 original size:36 final size:36
Alignment explanation
Indices: 2382169--2382252 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 36
2382159 CAACAAGGTT
* * * **
2382169 AGGCATAACCTTTACAACATGCCTTTTAATAGGGTC
1 AGGCATAACCTTCACAACATGCCTTTTAACAAGACC
* * *
2382205 AGGCGTGACCTTCACAACATGCCTTTTCACAAGACC
1 AGGCATAACCTTCACAACATGCCTTTTAACAAGACC
2382241 AGGCATAACCTT
1 AGGCATAACCTT
2382253 AACCAAGACA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (36 bp):
AGGCATAACCTTCACAACATGCCTTTTAACAAGACC
Found at i:2391040 original size:28 final size:27
Alignment explanation
Indices: 2390980--2391045 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
2390970 TTTCCAAACA
* *
2390980 TCAAAGCATAAGCCAACTCATGGTAAAT
1 TCAAAGTAT-AGCCAACTCATGGCAAAT
* *
2391008 TCAAAGTATAGCCACCTTATGGCAAAT
1 TCAAAGTATAGCCAACTCATGGCAAAT
2391035 TCCAAAGTATA
1 T-CAAAGTATA
2391046 ACATTTATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 16 0.48
28 17 0.52
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (27 bp):
TCAAAGTATAGCCAACTCATGGCAAAT
Found at i:2403369 original size:36 final size:36
Alignment explanation
Indices: 2403324--2403397 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
2403314 AGAATATTAA
*
2403324 TTTAAAACCTAAGATTATGGTAAATTTCATCTGAAT
1 TTTAAAACCTAAGATTATGGGAAATTTCATCTGAAT
* *
2403360 TTTAAAACCTAGGATTATGGGAAATTTCATCTGGAT
1 TTTAAAACCTAAGATTATGGGAAATTTCATCTGAAT
2403396 TT
1 TT
2403398 AATTGTTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (36 bp):
TTTAAAACCTAAGATTATGGGAAATTTCATCTGAAT
Found at i:2405196 original size:27 final size:26
Alignment explanation
Indices: 2405159--2405215 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
2405149 ATTTTATTTT
*
2405159 ATTT-TTTAAATATGAATAATTTATA
1 ATTTATTTAAATATGAATAATTGATA
* * *
2405184 ATTTATTTAAAATCTTAATAATTGATC
1 ATTTATTT-AAATATGAATAATTGATA
2405211 ATTTA
1 ATTTA
2405216 AATATTAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 4 0.15
26 3 0.12
27 19 0.73
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (26 bp):
ATTTATTTAAATATGAATAATTGATA
Found at i:2405389 original size:26 final size:28
Alignment explanation
Indices: 2405360--2405412 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 28
2405350 TCCAAAAAAT
2405360 ATTAATATTTTATTTAT-AAT-TTAATC
1 ATTAATATTTTATTTATGAATATTAATC
2405386 ATTAATATTTTATTTATGAATATTAAT
1 ATTAATATTTTATTTATGAATATTAAT
2405413 ATGGGTAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 17 0.68
27 3 0.12
28 5 0.20
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (28 bp):
ATTAATATTTTATTTATGAATATTAATC
Found at i:2415095 original size:21 final size:21
Alignment explanation
Indices: 2415069--2415125 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
2415059 TCCTAGGTTT
2415069 CATGTATCGATACATAATGAA
1 CATGTATCGATACATAATGAA
2415090 CATGTATCGATACATAATGAA
1 CATGTATCGATACATAATGAA
*
2415111 CATGTATCGAAACAT
1 CATGTATCGATACAT
2415126 GTTCATAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (21 bp):
CATGTATCGATACATAATGAA
Found at i:2419390 original size:60 final size:60
Alignment explanation
Indices: 2419286--2419402 Score: 148
Period size: 60 Copynumber: 1.9 Consensus size: 60
2419276 ATATTTGACT
* *
2419286 GTAAAGGGGGACCTGAAGCCCTGATTCATATTAGGTGGCATGAGCAGTTCCCATGAGTGG
1 GTAAAGGGGGACCTGAAGCCCTAATTCATATTAGGCGGCATGAGCAGTTCCCATGAGTGG
* * * *
2419346 GTAAAGGGGGACTTGAAG-CCTCAATTTATA-TATGGCGGCGTGAGCAGTTCCCGTGAG
1 GTAAAGGGGGACCTGAAGCCCT-AATTCATATTA-GGCGGCATGAGCAGTTCCCATGAG
2419403 GAGGTGATGA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 5 0.10
60 44 0.90
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (60 bp):
GTAAAGGGGGACCTGAAGCCCTAATTCATATTAGGCGGCATGAGCAGTTCCCATGAGTGG
Found at i:2423116 original size:29 final size:29
Alignment explanation
Indices: 2423091--2423157 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 29
2423081 ACAAAAATGG
*
2423091 AAAAAAGAAAGAATAAGAGAAAAAAAAGAAA
1 AAAAAATAAA-AA-AAGAGAAAAAAAAGAAA
*
2423122 AAAAAATAAAAAAAGAGAAAAGAAAGAAA
1 AAAAAATAAAAAAAGAGAAAAAAAAGAAA
2423151 AAGAAAA
1 AA-AAAA
2423158 AAGAACAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 18 0.55
30 6 0.18
31 9 0.27
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (29 bp):
AAAAAATAAAAAAAGAGAAAAAAAAGAAA
Found at i:2423160 original size:17 final size:16
Alignment explanation
Indices: 2423092--2423162 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 16
2423082 CAAAAATGGA
*
2423092 AAAAAGAAAGAATAAGAG
1 AAAAA-AAAGAA-AAAAG
*
2423110 AAAAAAAAGAAAAAAAA
1 AAAAAAAAG-AAAAAAG
*
2423127 ATAAAAAAAGAGAAAAG
1 A-AAAAAAAGAAAAAAG
2423144 AAAGAAAAAGAAAAAAG
1 AAA-AAAAAGAAAAAAG
2423161 AA
1 AA
2423163 CAAACAAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
16 2 0.04
17 28 0.62
18 15 0.33
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAAAAAAGAAAAAAG
Found at i:2438427 original size:18 final size:17
Alignment explanation
Indices: 2438400--2438437 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
2438390 TGTAGGTGCT
2438400 TATGGAACTCCACTTGG
1 TATGGAACTCCACTTGG
2438417 TATGAGAACTCCACTTGG
1 TATG-GAACTCCACTTGG
2438435 TAT
1 TAT
2438438 TTCACTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (17 bp):
TATGGAACTCCACTTGG
Found at i:2440448 original size:76 final size:77
Alignment explanation
Indices: 2440310--2440472 Score: 247
Period size: 76 Copynumber: 2.1 Consensus size: 77
2440300 AATACCATCT
* *
2440310 ATTTTAATTTTGGGTGATCCATAAAAAGTAAGAAAGTGTTTCCTACTTTAAAAGCAATTCCTAAA
1 ATTTTAATTTTAGGTGATCCATAAAAAGTAAGAAAGTGTTTCCTACTTTAAAAGAAATTCCTAAA
2440375 ATTAAGGATAGA
66 ATTAAGGATAGA
* ** * *
2440387 ATTTTAATTTTAGGTGATTCATAAAAA-TACTAAATTGTTTCCTACTTTAAAATAAATTCCTAAA
1 ATTTTAATTTTAGGTGATCCATAAAAAGTAAGAAAGTGTTTCCTACTTTAAAAGAAATTCCTAAA
*
2440451 ATTAAGGATAGC
66 ATTAAGGATAGA
2440463 ATTTTAATTT
1 ATTTTAATTT
2440473 GGGAAATTGA
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
76 53 0.68
77 25 0.32
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.39
Consensus pattern (77 bp):
ATTTTAATTTTAGGTGATCCATAAAAAGTAAGAAAGTGTTTCCTACTTTAAAAGAAATTCCTAAA
ATTAAGGATAGA
Found at i:2443631 original size:5 final size:5
Alignment explanation
Indices: 2443621--2443656 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
2443611 NNNNNNGTTG
2443621 AAAAT AAAAT -AAAT -AAAT -AAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
2443657 ATAAGAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 12 0.40
5 18 0.60
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:2456081 original size:34 final size:34
Alignment explanation
Indices: 2456037--2456103 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
2456027 TTGGGGATGA
2456037 GAGATCTTGGGAA-GGATGATATGCTCCCATATTG
1 GAGATCTTGGGAATGG-TGATATGCTCCCATATTG
*
2456071 GAGATGTTGGGAATGGTGATATGCTCCCATATT
1 GAGATCTTGGGAATGGTGATATGCTCCCATATT
2456104 CAAGAATTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 29 0.94
35 2 0.06
ACGTcount: A:0.25, C:0.13, G:0.30, T:0.31
Consensus pattern (34 bp):
GAGATCTTGGGAATGGTGATATGCTCCCATATTG
Found at i:2461039 original size:12 final size:12
Alignment explanation
Indices: 2461018--2461063 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
2461008 TGAAAAGAAA
2461018 ATAAATAAAAAT
1 ATAAATAAAAAT
2461030 -TAATATAAAAAT
1 ATAA-ATAAAAAT
2461042 ATAAAT--AAAT
1 ATAAATAAAAAT
2461052 A-AAATAAAAAT
1 ATAAATAAAAAT
2461063 A
1 A
2461064 GCAAAAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
9 4 0.13
10 5 0.17
11 8 0.27
12 10 0.33
13 3 0.10
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
ATAAATAAAAAT
Found at i:2461047 original size:18 final size:16
Alignment explanation
Indices: 2461020--2461063 Score: 54
Period size: 15 Copynumber: 2.7 Consensus size: 16
2461010 AAAAGAAAAT
2461020 AAATAAAAATTAATATAA
1 AAATAAAAA-TAA-ATAA
*
2461038 AAATATAAATAAAT-A
1 AAATAAAAATAAATAA
2461053 AAATAAAAATA
1 AAATAAAAATA
2461064 GCAAAAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 11 0.46
16 2 0.08
17 3 0.12
18 8 0.33
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
AAATAAAAATAAATAA
Found at i:2468066 original size:94 final size:94
Alignment explanation
Indices: 2467990--2468163 Score: 231
Period size: 94 Copynumber: 1.8 Consensus size: 94
2467980 TTTTTTTTAC
* * * **
2467990 ATATATGCATATCTATATTTTATATAGCTAATTATTTCATAAAAAAAACTTTGCATTAACACATT
1 ATATATACATATATATATTTTATATAACTAACAATTTCATAAAAAAAACTTTGCATTAACACATT
*
2468055 TTATTTTTTTTTTATCGTGTTTCTCTTTT
66 TTATTTTTTTTTTATCGTCTTTCTCTTTT
* * * * * *
2468084 TTATATACCTATATATATTTTGTATAATTAACAATTTCATTAAAAAAGCTTTGCATTAACACATT
1 ATATATACATATATATATTTTATATAACTAACAATTTCATAAAAAAAACTTTGCATTAACACATT
2468149 TTATTTTATTTTTTA
66 TTATTTT-TTTTTTA
2468164 AAATTTTTAT
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
94 61 0.90
95 7 0.10
ACGTcount: A:0.33, C:0.11, G:0.05, T:0.51
Consensus pattern (94 bp):
ATATATACATATATATATTTTATATAACTAACAATTTCATAAAAAAAACTTTGCATTAACACATT
TTATTTTTTTTTTATCGTCTTTCTCTTTT
Found at i:2470343 original size:5 final size:5
Alignment explanation
Indices: 2470333--2470396 Score: 56
Period size: 5 Copynumber: 11.8 Consensus size: 5
2470323 AAGAATAATG
* *
2470333 TAAAA TAAAA TAGAAC TAAAA TAAATA AAAAA TAAGAA TAAAAA TAAAAA
1 TAAAA TAAAA TA-AAA TAAAA TAAA-A TAAAA TAA-AA T-AAAA T-AAAA
*
2470383 TAAAA TGAAA TAAA
1 TAAAA TAAAA TAAA
2470397 TATATTCGAG
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
5 27 0.55
6 20 0.41
7 2 0.04
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:2470374 original size:17 final size:16
Alignment explanation
Indices: 2470349--2470396 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 16
2470339 AAAATAGAAC
2470349 TAAAATAAATAAAAAA
1 TAAAATAAATAAAAAA
*
2470365 TAAGAATAAAAATAAAAA
1 TAA-AATAAATA-AAAAA
2470383 TAAAATGAAATAAA
1 TAAAAT-AAATAAA
2470397 TATATTCGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 3 0.11
17 12 0.44
18 12 0.44
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (16 bp):
TAAAATAAATAAAAAA
Found at i:2470378 original size:6 final size:6
Alignment explanation
Indices: 2470350--2470387 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
2470340 AAATAGAACT
* *
2470350 AAAATA AATA-A AAAATA AGAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA
2470388 TGAAATAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:2486685 original size:27 final size:27
Alignment explanation
Indices: 2486647--2486859 Score: 214
Period size: 27 Copynumber: 7.9 Consensus size: 27
2486637 AATACCATCC
*
2486647 AAAGTGGATGGATACATTTAATCACCG
1 AAAGTGGATGGATACATTTAACCACCG
*
2486674 AAAGTGGATGGATACATTTAACTACCG
1 AAAGTGGATGGATACATTTAACCACCG
*
2486701 AAAGTGGATTGATACATTTAACCACC-
1 AAAGTGGATGGATACATTTAACCACCG
* ** * *
2486727 AGAAGTGAATAAATACATTTAATC-CCA
1 A-AAGTGGATGGATACATTTAACCACCG
* * * **
2486754 AAAATGGATAGATACATTTAACTATTG
1 AAAGTGGATGGATACATTTAACCACCG
* *
2486781 AAAGTAGATGGATACATTTAACCACTG
1 AAAGTGGATGGATACATTTAACCACCG
** * * *
2486808 AAAGTTAATTGATACATTTAACCATCA
1 AAAGTGGATGGATACATTTAACCACCG
*
2486835 AAAGTAGATGGATACATTTAACCAC
1 AAAGTGGATGGATACATTTAACCAC
2486860 TAGAAGTGAA
Statistics
Matches: 152, Mismatches: 31, Indels: 6
0.80 0.16 0.03
Matches are distributed among these distances:
26 20 0.13
27 132 0.87
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.28
Consensus pattern (27 bp):
AAAGTGGATGGATACATTTAACCACCG
Found at i:2496918 original size:112 final size:112
Alignment explanation
Indices: 2496716--2496920 Score: 285
Period size: 112 Copynumber: 1.8 Consensus size: 112
2496706 GTATTGACGA
* *
2496716 ATTTTTAATGAAATTTTCCAATGGAAATGATTCTGTTAGAAATTCATAGGAAATAGTTTTGGTGC
1 ATTTTTAATGAAATTTTCCAATGGAAATCATTCTGTTAGAAATCCATAGGAAATAGTTTTGGTGC
2496781 AAAAAAAAAATTAATCCCACCAAATTTTCTAATGGAATTTTTGATGG
66 AAAAAAAAAATTAATCCCACCAAATTTTCTAATGGAATTTTTGATGG
* *
2496828 ATTTTTTATGAAAATTTT-CAATGG-AATCATTTCTGTTGGAAATCCATCA-GAAATAGTTTTGG
1 ATTTTTAATG-AAATTTTCCAATGGAAATCA-TTCTGTTAGAAATCCAT-AGGAAATAGTTTTGG
* *
2496890 TAG-AAAAAGAAAATTAAT-CCACCAAAATTTC
63 T-GCAAAAAAAAAATTAATCCCACCAAATTTTC
2496921 CAACCGAACT
Statistics
Matches: 83, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
111 16 0.19
112 58 0.70
113 9 0.11
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (112 bp):
ATTTTTAATGAAATTTTCCAATGGAAATCATTCTGTTAGAAATCCATAGGAAATAGTTTTGGTGC
AAAAAAAAAATTAATCCCACCAAATTTTCTAATGGAATTTTTGATGG
Found at i:2497706 original size:29 final size:29
Alignment explanation
Indices: 2497656--2497726 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
2497646 CTAGTTATTA
*
2497656 TGGATATTCAATATATCTTGTTTAGCTACTG
1 TGGATATT--ATACATCTTGTTTAGCTACTG
2497687 TGGATATTATACATCTTGTTTAGCTACTG
1 TGGATATTATACATCTTGTTTAGCTACTG
*
2497716 TGGATGTTATA
1 TGGATATTATA
2497727 AATATTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 30 0.79
31 8 0.21
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.45
Consensus pattern (29 bp):
TGGATATTATACATCTTGTTTAGCTACTG
Found at i:2500804 original size:34 final size:35
Alignment explanation
Indices: 2500751--2500827 Score: 102
Period size: 34 Copynumber: 2.2 Consensus size: 35
2500741 CTTTTTATAT
* * * *
2500751 ATTTTAATGATCATATTCATATCCGATGTGAGATA
1 ATTTTAGTGATCAAATTCATATCCAATATGAGATA
2500786 ATTTTAGT-ATCAAATTCATATCCAATATGAGATA
1 ATTTTAGTGATCAAATTCATATCCAATATGAGATA
*
2500820 GTTTTAGT
1 ATTTTAGT
2500828 TACTTTTTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 30 0.81
35 7 0.19
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (35 bp):
ATTTTAGTGATCAAATTCATATCCAATATGAGATA
Found at i:2501071 original size:15 final size:15
Alignment explanation
Indices: 2501041--2501107 Score: 80
Period size: 15 Copynumber: 4.4 Consensus size: 15
2501031 CGTTTGGTAC
*
2501041 ATTACAATGCAATGTG
1 ATTACAA-GTAATGTG
*
2501057 ATTACAGGTAATGTG
1 ATTACAAGTAATGTG
*
2501072 ATTGCAAGTAATGTG
1 ATTACAAGTAATGTG
* *
2501087 ATTGCAAGCAATGTG
1 ATTACAAGTAATGTG
2501102 ATTACA
1 ATTACA
2501108 GGGAAAATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
15 39 0.87
16 6 0.13
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.31
Consensus pattern (15 bp):
ATTACAAGTAATGTG
Found at i:2501318 original size:60 final size:59
Alignment explanation
Indices: 2501245--2501432 Score: 205
Period size: 56 Copynumber: 3.3 Consensus size: 59
2501235 CTAATTATTA
**
2501245 AAATATAAGTTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTCTT
1 AAATATATTTTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTT-TT
* *
2501305 AAATATATTTTTAATATCA--TATA--TTTTATT-TTTATTTATTATTATAATAT--TTTAT
1 AAATATATTTTTAATAT-ATTTATATTTTTTATTATTAATTT-TTA-TATAATATCATTTTT
* * *
2501360 -ATTTTATTTTTAATATATTTATA-TTTATATTATTAATTTTTATATAATATCATATTTT
1 AAATATATTTTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCAT-TTTT
2501418 AAATATATTTTTAAT
1 AAATATATTTTTAAT
2501433 GTCATATATT
Statistics
Matches: 106, Mismatches: 11, Indels: 23
0.76 0.08 0.16
Matches are distributed among these distances:
53 1 0.01
54 14 0.13
55 13 0.12
56 18 0.17
57 17 0.16
58 11 0.10
59 16 0.15
60 15 0.14
61 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.61
Consensus pattern (59 bp):
AAATATATTTTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTTT
Found at i:2501334 original size:21 final size:21
Alignment explanation
Indices: 2501310--2501451 Score: 58
Period size: 21 Copynumber: 6.4 Consensus size: 21
2501300 TTCTTAAATA
2501310 TATTTTTAATATCATATATTT
1 TATTTTTAATATCATATATTT
*
2501331 TATTTTTATTTATTATTATAATATTT
1 TATTTTTA---A-TATCAT-ATATTT
* * *
2501357 TATATTTTATTTTTA-ATATATT
1 TAT-TTTTAATATCATATAT-TT
* *
2501379 TATATTT-ATATTAT-TAATTT
1 TATTTTTAATATCATAT-ATTT
* * *
2501399 T-TATATAATATCATATTTTAAAT
1 TATTTTTAATATCATATATT---T
*
2501422 ATATTTTTAATGTCATATATTT
1 -TATTTTTAATATCATATATTT
2501444 TATTTTTA
1 TATTTTTA
2501452 TTTATTATTA
Statistics
Matches: 92, Mismatches: 13, Indels: 32
0.67 0.09 0.23
Matches are distributed among these distances:
19 4 0.04
20 16 0.17
21 26 0.28
22 6 0.07
23 5 0.05
24 2 0.02
25 19 0.21
26 9 0.10
27 5 0.05
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (21 bp):
TATTTTTAATATCATATATTT
Found at i:2501344 original size:15 final size:15
Alignment explanation
Indices: 2501323--2501482 Score: 92
Period size: 15 Copynumber: 9.9 Consensus size: 15
2501313 TTTTAATATC
2501323 ATATATTTTATTTTT
1 ATATATTTTATTTTT
*
2501338 ATTTATTATTATAATATTT
1 ATATATT-TTAT--T-TTT
2501357 -TATATTTTATTTTT
1 ATATATTTTATTTTT
*
2501371 A-ATATATTTATATTT
1 ATATAT-TTTATTTTT
*
2501386 ATAT-TATTAATTTTT
1 ATATAT-TTTATTTTT
* *
2501401 ATATAATATCATATTTTAA
1 ATAT-AT-T-TTATTTT-T
* * *
2501420 ATATATTTTTAATGTC
1 ATATA-TTTTATTTTT
2501436 ATATATTTTATTTTT
1 ATATATTTTATTTTT
*
2501451 ATTTATTATTATAATTTT
1 ATATATT-TTAT--TTTT
2501469 ATATATTTTATTTT
1 ATATATTTTATTTT
2501483 CATTTCTTTA
Statistics
Matches: 113, Mismatches: 17, Indels: 30
0.71 0.11 0.19
Matches are distributed among these distances:
14 7 0.06
15 45 0.40
16 15 0.13
17 15 0.13
18 23 0.20
19 8 0.07
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (15 bp):
ATATATTTTATTTTT
Found at i:2501365 original size:23 final size:23
Alignment explanation
Indices: 2501331--2501394 Score: 82
Period size: 22 Copynumber: 2.9 Consensus size: 23
2501321 TCATATATTT
2501331 TATTTT-TA-TTTATTATTATAA
1 TATTTTATATTTTATTATTATAA
2501352 TATTTTATATTTTATT-TT-TAA
1 TATTTTATATTTTATTATTATAA
2501373 TATATTTATATTTATATTATTA
1 TAT-TTTATATTT-TATTATTA
2501395 ATTTTTATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
21 12 0.32
22 13 0.35
23 10 0.27
24 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TATTTTATATTTTATTATTATAA
Found at i:2501405 original size:23 final size:24
Alignment explanation
Indices: 2501337--2501405 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 24
2501327 ATTTTATTTT
2501337 TATTTATTATTA-TAATATTTTATA
1 TATTTA-TATTATTAATATTTTATA
*
2501361 T-TTTAT-TT-TTAATATATT-TA
1 TATTTATATTATTAATATTTTATA
2501381 TATTTATATTATTAAT-TTTTATA
1 TATTTATATTATTAATATTTTATA
2501404 TA
1 TA
2501406 ATATCATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
20 3 0.08
21 15 0.39
22 6 0.16
23 13 0.34
24 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TATTTATATTATTAATATTTTATA
Found at i:2501453 original size:27 final size:26
Alignment explanation
Indices: 2501310--2501482 Score: 136
Period size: 27 Copynumber: 6.2 Consensus size: 26
2501300 TTCTTAAATA
2501310 TATTTTTAATATCATATATTTTATTTT
1 TATTTTTAATAT-ATATATTTTATTTT
*
2501337 TATTTATTATTATA-ATATTTTATATTT
1 TATTT-TTAATATATATATTTTAT-TTT
2501364 TATTTTTAATATATTTATATTTATATTATT
1 TATTTTTAATATA--TATATTT-TATT-TT
* ** *
2501394 AATTTTTATATAATATCATATTTTAAATA
1 TATTTTTA-AT-ATAT-ATATTTTATTTT
*
2501423 TATTTTTAATGTCATATATTTTATTTT
1 TATTTTTAATAT-ATATATTTTATTTT
*
2501450 TATTTATTATTATA-AT-TTTATATATTT
1 TATTT-TTAATATATATATTT-TAT-TTT
2501477 TATTTT
1 TATTTT
2501483 CATTTCTTTA
Statistics
Matches: 119, Mismatches: 13, Indels: 29
0.74 0.08 0.18
Matches are distributed among these distances:
25 3 0.03
26 22 0.18
27 38 0.32
28 15 0.13
29 15 0.13
30 15 0.13
31 8 0.07
32 3 0.03
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.65
Consensus pattern (26 bp):
TATTTTTAATATATATATTTTATTTT
Found at i:2501453 original size:113 final size:114
Alignment explanation
Indices: 2501254--2501482 Score: 401
Period size: 113 Copynumber: 2.0 Consensus size: 114
2501244 AAAATATAAG
*
2501254 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
1 TTTAATATATTTATATTTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
2501319 TATCATATATTTTATTTTTATTTATTATTATAATATTT-TATATTTTATT
66 TATCATATATTTTATTTTTATTTATTATTATAAT-TTTATATATTTTATT
2501368 TTTAATATATTTATA-TTTATATTATTAATTTTTATATAATATCATATT-TTAAATATATTTTTA
1 TTTAATATATTTATATTTTATATTATTAATTTTTATATAATATCAT-TTCTTAAATATATTTTTA
*
2501431 ATGTCATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATT
65 ATATCATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATT
2501481 TT
1 TT
2501483 CATTTCTTTA
Statistics
Matches: 111, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
112 3 0.03
113 91 0.82
114 17 0.15
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (114 bp):
TTTAATATATTTATATTTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
TATCATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATT
Found at i:2501473 original size:10 final size:9
Alignment explanation
Indices: 2501323--2501479 Score: 56
Period size: 9 Copynumber: 18.2 Consensus size: 9
2501313 TTTTAATATC
2501323 ATATA-TTT
1 ATATATTTT
2501331 -TAT-TTTT
1 ATATATTTT
*
2501338 ATTTATTATT
1 ATATATT-TT
2501348 ATA-ATATTT
1 ATATAT-TTT
2501357 -TATATTTT
1 ATATATTTT
*
2501365 AT-T-TTTA
1 ATATATTTT
2501372 ATATATTTAT
1 ATATATTT-T
* *
2501382 ATTTATATT
1 ATATATTTT
2501391 AT-TAATTTT
1 ATAT-ATTTT
**
2501400 -TATATAAT
1 ATATATTTT
2501408 ATCATATTTT
1 AT-ATATTTT
2501418 AAATATATTTT
1 --ATATATTTT
* *
2501429 -TA-ATGTC
1 ATATATTTT
2501436 ATATA-TTT
1 ATATATTTT
2501444 -TAT-TTTT
1 ATATATTTT
*
2501451 ATTTATTATT
1 ATATATT-TT
2501461 ATA-ATTTT
1 ATATATTTT
2501469 ATATATTTT
1 ATATATTTT
2501478 AT
1 AT
2501480 TTTCATTTCT
Statistics
Matches: 109, Mismatches: 17, Indels: 45
0.64 0.10 0.26
Matches are distributed among these distances:
7 20 0.18
8 26 0.24
9 34 0.31
10 20 0.18
11 7 0.06
12 2 0.02
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (9 bp):
ATATATTTT
Found at i:2501473 original size:33 final size:33
Alignment explanation
Indices: 2501436--2501521 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 33
2501426 TTTTAATGTC
*
2501436 ATATATTTTATTTTTATTTA-TTATTATAATTTT
1 ATATATTTTATTTTTATTTATTTAATAT-ATTTT
* *
2501469 ATATATTTTATTTTCATTTCTTTAATATATTTT
1 ATATATTTTATTTTTATTTATTTAATATATTTT
* *
2501502 TTATATTATATATTTTATTT
1 ATATATTTTAT-TTTTATTT
2501522 TAATTTGTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
33 32 0.71
34 13 0.29
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (33 bp):
ATATATTTTATTTTTATTTATTTAATATATTTT
Found at i:2501475 original size:60 final size:60
Alignment explanation
Indices: 2501303--2501478 Score: 192
Period size: 60 Copynumber: 3.0 Consensus size: 60
2501293 ATATCATTTC
2501303 TTAAATATATTTTTAATATCATATATTTTATTTTTATTTATTATTATAATATTT-TATA--
1 TTAAATATATTTTTAATATCATATATTTTATTTTTATTTATTATTATAAT-TTTATATATT
* * * * **
2501361 TT---T-TATTTTTAATAT-ATTTATATTTA-TATTATTAATTTTTAT-ATAATATCATATT
1 TTAAATATATTTTTAATATCATATAT-TTTATTTTTATTTATTATTATAATTTTAT-ATATT
*
2501416 TTAAATATATTTTTAATGTCATATATTTTATTTTTATTTATTATTATAATTTTATATATT
1 TTAAATATATTTTTAATATCATATATTTTATTTTTATTTATTATTATAATTTTATATATT
2501476 TTA
1 TTA
2501479 TTTTCATTTC
Statistics
Matches: 93, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
51 1 0.01
52 3 0.03
53 21 0.23
54 16 0.17
55 3 0.03
58 3 0.03
59 15 0.16
60 26 0.28
61 5 0.05
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.63
Consensus pattern (60 bp):
TTAAATATATTTTTAATATCATATATTTTATTTTTATTTATTATTATAATTTTATATATT
Found at i:2501545 original size:31 final size:30
Alignment explanation
Indices: 2501498--2501612 Score: 95
Period size: 31 Copynumber: 4.0 Consensus size: 30
2501488 CTTTAATATA
*
2501498 TTTTTTATAT-TA-TATATTTTATTTTAAT
1 TTTTTTATCTATATTATATTTTATTTTAAT
** *
2501526 TTGTTTTATCTATATTATA-TAAATATTAA-
1 TT-TTTTATCTATATTATATTTTATTTTAAT
2501555 TTTTTTA--TAT-TT-TATTTTATTTTAAT
1 TTTTTTATCTATATTATATTTTATTTTAAT
*
2501581 TTTTAT-TCTTATATTATATATTTATTTTAAT
1 TTTTTTATC-TATATTATAT-TTTATTTTAAT
2501612 T
1 T
2501613 ATAATATTAT
Statistics
Matches: 68, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
24 2 0.03
25 9 0.13
26 8 0.12
28 10 0.15
29 11 0.16
30 12 0.18
31 16 0.24
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.68
Consensus pattern (30 bp):
TTTTTTATCTATATTATATTTTATTTTAAT
Found at i:2501608 original size:50 final size:55
Alignment explanation
Indices: 2501491--2501608 Score: 151
Period size: 55 Copynumber: 2.2 Consensus size: 55
2501481 TTCATTTCTT
2501491 TAATA-TATTTTTTATATTATATATTTTATTTTAATTTGTTTTATCTATATTATA
1 TAATATTATTTTTTATATTATATATTTTATTTTAATTTGTTTTATCTATATTATA
*
2501545 TAAATATTAATTTTTTATATT-T-TATTTTATTTTAATTT-TTAT-TCTTATATTATA
1 T-AATATT-ATTTTTTATATTATATATTTTATTTTAATTTGTTTTATC-TATATTATA
2501599 T-AT-TTATTTT
1 TAATATTATTTT
2501609 AATTATAATA
Statistics
Matches: 59, Mismatches: 1, Indels: 12
0.82 0.01 0.17
Matches are distributed among these distances:
50 5 0.08
51 2 0.03
52 2 0.03
53 2 0.03
54 14 0.24
55 20 0.34
56 2 0.03
57 12 0.20
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.67
Consensus pattern (55 bp):
TAATATTATTTTTTATATTATATATTTTATTTTAATTTGTTTTATCTATATTATA
Found at i:2509346 original size:110 final size:110
Alignment explanation
Indices: 2509194--2509400 Score: 344
Period size: 110 Copynumber: 1.9 Consensus size: 110
2509184 TAAAATGGCA
* * *
2509194 TGTTTTTGTTAACATTTTTTATTGTTAACATGTATGGGAATTAGTCT-TGATTCTTACATTTTCA
1 TGTTTTTGTTAACATTTTTTATTGTAAACATGAATGGGAATTAGT-TGTAATTCTTACATTTTCA
*
2509258 TGATGATTTTGATAGTTTGTTTCAATTTCTTTTAGCATAGCTTCCT
65 TGATGATATTGATAGTTTGTTTCAATTTCTTTTAGCATAGCTTCCT
* *
2509304 TGTTTTTGTTAACATTTTTTATTGTAAACATGAATGGGAATTAGTTGTAATTCTTATATTTTGAT
1 TGTTTTTGTTAACATTTTTTATTGTAAACATGAATGGGAATTAGTTGTAATTCTTACATTTTCAT
2509369 GATGATATTGATAGTTTGTTTCAATTTCTTTT
66 GATGATATTGATAGTTTGTTTCAATTTCTTTT
2509401 TAGCTTATGT
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
109 1 0.01
110 89 0.99
ACGTcount: A:0.24, C:0.08, G:0.15, T:0.53
Consensus pattern (110 bp):
TGTTTTTGTTAACATTTTTTATTGTAAACATGAATGGGAATTAGTTGTAATTCTTACATTTTCAT
GATGATATTGATAGTTTGTTTCAATTTCTTTTAGCATAGCTTCCT
Found at i:2511494 original size:13 final size:13
Alignment explanation
Indices: 2511468--2511509 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
2511458 AGTTACAAAT
*
2511468 TTCCAATGAAAAA
1 TTCCAATGGAAAA
* *
2511481 TTCCATTGGTAAA
1 TTCCAATGGAAAA
2511494 TTCCAATGGAAAA
1 TTCCAATGGAAAA
2511507 TTC
1 TTC
2511510 GGTTAGAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (13 bp):
TTCCAATGGAAAA
Found at i:2513456 original size:19 final size:20
Alignment explanation
Indices: 2513419--2513457 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2513409 ATAGACATAA
2513419 TATTTAACAAAACTTTAAAT
1 TATTTAACAAAACTTTAAAT
2513439 TATTTAA-AAATA-TTTAAAT
1 TATTTAACAAA-ACTTTAAAT
2513458 ATGTTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
TATTTAACAAAACTTTAAAT
Found at i:2520151 original size:29 final size:28
Alignment explanation
Indices: 2520117--2520216 Score: 110
Period size: 29 Copynumber: 3.5 Consensus size: 28
2520107 CACGTGAAAG
* * *
2520117 GTACAAAAGAAGAAGCTGTACTTGAACAA
1 GTACAAAA-AAGAAGTTGTACATGAATAA
* * *
2520146 GTACAAGAAAGAAGTTGTACAAGAATAG
1 GTACAAAAAAGAAGTTGTACATGAATAA
*
2520174 GTACAAAAGAAGAAGTTATACATGAATAA
1 GTACAAAA-AAGAAGTTGTACATGAATAA
2520203 GTACAAGAAAAGAA
1 GTACAA-AAAAGAA
2520217 ACCATATGTG
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
28 22 0.37
29 35 0.59
30 2 0.03
ACGTcount: A:0.53, C:0.09, G:0.21, T:0.17
Consensus pattern (28 bp):
GTACAAAAAAGAAGTTGTACATGAATAA
Found at i:2521010 original size:17 final size:17
Alignment explanation
Indices: 2520978--2521019 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
2520968 ATAATCTATC
2520978 TAAATTAAT-ACTTGA-
1 TAAATTAATAACTTGAT
2520993 TAAATTAATAACCTTGAT
1 TAAATTAATAA-CTTGAT
2521011 TAAA-TAATA
1 TAAATTAATA
2521020 TTTTTGGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.38
16 1 0.04
17 10 0.42
18 4 0.17
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (17 bp):
TAAATTAATAACTTGAT
Found at i:2527685 original size:12 final size:12
Alignment explanation
Indices: 2527668--2527734 Score: 50
Period size: 12 Copynumber: 5.6 Consensus size: 12
2527658 TTTATATTTT
2527668 AAAATTTAATTA
1 AAAATTTAATTA
2527680 AAAATTTAATT-
1 AAAATTTAATTA
*
2527691 ATAATTT--TTAA
1 AAAATTTAATT-A
*
2527702 AAAATTAATATTTA
1 AAAATT--TAATTA
*
2527716 AAATTTTAATTA
1 AAAATTTAATTA
*
2527728 TAAATTT
1 AAAATTT
2527735 TTAATATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
9 2 0.05
11 11 0.26
12 21 0.49
13 1 0.02
14 6 0.14
15 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAAATTTAATTA
Found at i:2527724 original size:15 final size:15
Alignment explanation
Indices: 2527687--2527743 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
2527677 TTAAAAATTT
* *
2527687 AATTATAATTTTTAA
1 AATTTTAATATTTAA
**
2527702 AAAATTAATATTTAA
1 AATTTTAATATTTAA
*
2527717 AATTTTAAT-TATAA
1 AATTTTAATATTTAA
*
2527731 ATTTTTAATATTT
1 AATTTTAATATTT
2527744 TAATATTTAA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
14 12 0.38
15 20 0.62
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATTTTAATATTTAA
Found at i:2527724 original size:36 final size:37
Alignment explanation
Indices: 2527677--2527756 Score: 117
Period size: 37 Copynumber: 2.2 Consensus size: 37
2527667 TAAAATTTAA
2527677 TTAAAAATTTAATTAT-AATTTTTAAAAAATTAATAT
1 TTAAAAATTTAATTATAAATTTTTAAAAAATTAATAT
* * **
2527713 TTAAAATTTTAATTATAAATTTTTAATATTTTAATAT
1 TTAAAAATTTAATTATAAATTTTTAAAAAATTAATAT
2527750 TTAAAAA
1 TTAAAAA
2527757 AATAAAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
36 15 0.39
37 23 0.61
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (37 bp):
TTAAAAATTTAATTATAAATTTTTAAAAAATTAATAT
Found at i:2550972 original size:44 final size:43
Alignment explanation
Indices: 2550862--2550978 Score: 121
Period size: 44 Copynumber: 2.7 Consensus size: 43
2550852 TTTTATATAA
* * *
2550862 CTATATATATTTTGTATAACTAAACATTTTATTATTATTTTTAC
1 CTATGTATATTTT-TATAACTAAATATTTTATTATTATTTCTAC
* * *
2550906 CTATGTATATTTCATGTTACTAAATACTTTT-TTATTATTTCTAC
1 CTATGTATATTT-TTATAACTAAATA-TTTTATTATTATTTCTAC
2550950 CTATGTGA-AGTTTTTATAACTAAATATTT
1 CTATGT-ATA-TTTTTATAACTAAATATTT
2550979 ATTCTTCTCT
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
43 3 0.05
44 49 0.82
45 8 0.13
ACGTcount: A:0.32, C:0.10, G:0.05, T:0.53
Consensus pattern (43 bp):
CTATGTATATTTTTATAACTAAATATTTTATTATTATTTCTAC
Found at i:2554163 original size:25 final size:25
Alignment explanation
Indices: 2554129--2554183 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
2554119 GGTTTGTGAT
* *
2554129 ATATATGTGACAAGGCCATGAGTTG
1 ATATACGTGACAAGGCCACGAGTTG
*
2554154 ATATACGTGACTAGGCCACGAGTTG
1 ATATACGTGACAAGGCCACGAGTTG
2554179 ATATA
1 ATATA
2554184 TGTGGTTGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (25 bp):
ATATACGTGACAAGGCCACGAGTTG
Found at i:2555550 original size:19 final size:19
Alignment explanation
Indices: 2555526--2555572 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
2555516 GGGCTTTTTA
2555526 TTTTTTTGCT-ATTTTTGTG
1 TTTTTTT-CTCATTTTTGTG
2555545 TTTTTTTCTCATTTTTGTG
1 TTTTTTTCTCATTTTTGTG
*
2555564 GTTTTTTCT
1 TTTTTTTCT
2555573 TGATTATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 2 0.08
19 24 0.92
ACGTcount: A:0.04, C:0.09, G:0.13, T:0.74
Consensus pattern (19 bp):
TTTTTTTCTCATTTTTGTG
Found at i:2562595 original size:25 final size:25
Alignment explanation
Indices: 2562561--2562632 Score: 144
Period size: 25 Copynumber: 2.9 Consensus size: 25
2562551 AAGAATACTC
2562561 TGGAACAAAAACTACATAGGCACTT
1 TGGAACAAAAACTACATAGGCACTT
2562586 TGGAACAAAAACTACATAGGCACTT
1 TGGAACAAAAACTACATAGGCACTT
2562611 TGGAACAAAAACTACATAGGCA
1 TGGAACAAAAACTACATAGGCA
2562633 AGCCTCCACT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.46, C:0.19, G:0.17, T:0.18
Consensus pattern (25 bp):
TGGAACAAAAACTACATAGGCACTT
Found at i:2563869 original size:21 final size:22
Alignment explanation
Indices: 2563844--2563887 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
2563834 AAGTGATTAA
2563844 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
*
2563865 TTTAAGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
2563887 T
1 T
2563888 ACTTTAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:2567724 original size:20 final size:20
Alignment explanation
Indices: 2567699--2567739 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
2567689 ATAGATACAA
*
2567699 TGGTTTTAATTGATTGAAAC
1 TGGTTTTAATTGATTAAAAC
2567719 TGGTTTTAATTGATTAAAAC
1 TGGTTTTAATTGATTAAAAC
2567739 T
1 T
2567740 AATTTTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.17, T:0.46
Consensus pattern (20 bp):
TGGTTTTAATTGATTAAAAC
Found at i:2567745 original size:20 final size:20
Alignment explanation
Indices: 2567702--2567748 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2567692 GATACAATGG
* **
2567702 TTTTAATTGATTGAAACTGG
1 TTTTAATTGATTAAAACTAA
2567722 TTTTAATTGATTAAAACTAA
1 TTTTAATTGATTAAAACTAA
2567742 TTTTAAT
1 TTTTAAT
2567749 CGAAGAACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (20 bp):
TTTTAATTGATTAAAACTAA
Found at i:2577566 original size:11 final size:11
Alignment explanation
Indices: 2577550--2577574 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2577540 TCTCTATGTG
2577550 ATAAAATAATA
1 ATAAAATAATA
2577561 ATAAAATAATA
1 ATAAAATAATA
2577572 ATA
1 ATA
2577575 TTTTATTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAAAATAATA
Found at i:2577693 original size:19 final size:19
Alignment explanation
Indices: 2577669--2577707 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2577659 GCTAAAGGAA
2577669 AATTTTAAAATAAAATAAT
1 AATTTTAAAATAAAATAAT
**
2577688 AATTTTTGAATAAAATAAT
1 AATTTTAAAATAAAATAAT
2577707 A
1 A
2577708 TTAAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
AATTTTAAAATAAAATAAT
Found at i:2580127 original size:25 final size:25
Alignment explanation
Indices: 2580098--2580153 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
2580088 TGGTATGTGA
*
2580098 TTATACGTGGCAAGGCCACGAGTTG
1 TTATACGTGGCAAGGCCACAAGTTG
* *
2580123 TTATATGTGGCGAGGCCACAAGTTG
1 TTATACGTGGCAAGGCCACAAGTTG
*
2580148 ATATAC
1 TTATAC
2580154 AAGGTTATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (25 bp):
TTATACGTGGCAAGGCCACAAGTTG
Found at i:2596392 original size:16 final size:16
Alignment explanation
Indices: 2596373--2596403 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2596363 AGATATATAT
2596373 ATATATATACATGTTA
1 ATATATATACATGTTA
*
2596389 ATATATATATATGTT
1 ATATATATACATGTT
2596404 TGCTTTTGAA
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:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (16 bp):
ATATATATACATGTTA
Found at i:2601060 original size:11 final size:11
Alignment explanation
Indices: 2601044--2601069 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2601034 GATGCAAACG
2601044 TTGTGAAAGGC
1 TTGTGAAAGGC
2601055 TTGTGAAAGGC
1 TTGTGAAAGGC
2601066 TTGT
1 TTGT
2601070 TTCTTGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.08, G:0.35, T:0.35
Consensus pattern (11 bp):
TTGTGAAAGGC
Found at i:2608590 original size:23 final size:22
Alignment explanation
Indices: 2608547--2608603 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 22
2608537 CTAGGACGAA
*
2608547 TCCTCCTTTC-TCTTTTCTTCT
1 TCCTCCTTTCTTCCTTTCTTCT
2608568 TCCTCCTTTCTTCCTTTCTTTCT
1 TCCTCCTTTCTTCCTTTC-TTCT
* *
2608591 TTCTCTTTTCTTC
1 TCCTCCTTTCTTC
2608604 TTTTTTAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 10 0.32
22 6 0.19
23 15 0.48
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (22 bp):
TCCTCCTTTCTTCCTTTCTTCT
Found at i:2612894 original size:180 final size:180
Alignment explanation
Indices: 2612658--2613049 Score: 504
Period size: 180 Copynumber: 2.2 Consensus size: 180
2612648 AGTTACCTAT
*
2612658 CAGGATAAATTTTATTAGGAAGTAAATTCCTAAGTTTTAGTCACAAAGAATTTCAAAAGTACACA
1 CAGGATAAATTTTATTAGGAATTAAATTCCTAAGTTTTAGTCACAAAGAATTTCAAAAGTACACA
* * *
2612723 TAAATCT-ATTCTACTACCCGCAGATAAAAGG-CACAGTTTTTAAATTTTTTGAATGGCCAAATC
66 -AAAACTGATTCTACCACCCGCAGAT-AAAGGTCACAGTTTTGAAATTTTTTGAATGGCCAAATC
* * *
2612786 ACATCCTAAAATCCTGAAAATTTATTCTGGAATAGCTACATGGGATATCTAC
129 ACATCATAAAATCCTGAAAATTTATTCTGGAATAGCTACATGAGATATATAC
* * * *
2612838 CAGGATAAATTTTATTAGGATTTAAATTCCTAAGTTTTAGTCACAAA-AAGTTTCAAAATTTCTC
1 CAGGATAAATTTTATTAGGAATTAAATTCCTAAGTTTTAGTCACAAAGAA-TTTCAAAAGTACAC
* * ** *
2612902 AAAAACTGATTCTGCCACCTGCAGATAAAGGTCATGGTTTTGGAATTTTTTGAATGGCCAAATCA
65 AAAAACTGATTCTACCACCCGCAGATAAAGGTCACAGTTTTGAAATTTTTTGAATGGCCAAATCA
* * * ** * * *
2612967 CCTCATAAAATCCTGAAAATTTATTTTGTAATATTTCCATGAGTTATATAT
130 CATCATAAAATCCTGAAAATTTATTCTGGAATAGCTACATGAGATATATAC
*
2613018 CAGGAAAAATTTTATT-GGAATTAAATTCCTAA
1 CAGGATAAATTTTATTAGGAATTAAATTCCTAA
2613050 AGATACACCA
Statistics
Matches: 183, Mismatches: 26, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
179 27 0.15
180 156 0.85
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.34
Consensus pattern (180 bp):
CAGGATAAATTTTATTAGGAATTAAATTCCTAAGTTTTAGTCACAAAGAATTTCAAAAGTACACA
AAAACTGATTCTACCACCCGCAGATAAAGGTCACAGTTTTGAAATTTTTTGAATGGCCAAATCAC
ATCATAAAATCCTGAAAATTTATTCTGGAATAGCTACATGAGATATATAC
Found at i:2623540 original size:122 final size:122
Alignment explanation
Indices: 2623387--2623634 Score: 444
Period size: 122 Copynumber: 2.0 Consensus size: 122
2623377 ACTTTAAATC
*
2623387 AGACAATGGTTTAGGACAATGACAACAATGGCAACAATGCCATTAATCTGGTTCTAGAAGAAAAT
1 AGACAATGGTTTAGGACAATGACAACAATGGCAACAATGCCATTAATCTGGTTCCAGAAGAAAAT
*
2623452 AGAGCACTGTGAGATTATA-CTGTTCCTCTTTTGCAAGGTGTGCACCAAAGCATTAGA
66 AGAGCACTGCGAGATTA-AGCTGTTCCTCTTTTGCAAGGTGTGCACCAAAGCATTAGA
2623509 AGACAATGGTTTAGGACAATGACAACAATGGCAACAATGCCATTAATCTGGTTCCAGAAGAAAAT
1 AGACAATGGTTTAGGACAATGACAACAATGGCAACAATGCCATTAATCTGGTTCCAGAAGAAAAT
* *
2623574 AGAGCACTGCGAGATTAAGTTGTTCCTCTTTTGCAAGGTGTGCACTAAAGCATTAGA
66 AGAGCACTGCGAGATTAAGCTGTTCCTCTTTTGCAAGGTGTGCACCAAAGCATTAGA
2623631 AGAC
1 AGAC
2623635 CTTCCATCAA
Statistics
Matches: 121, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
121 1 0.01
122 120 0.99
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.25
Consensus pattern (122 bp):
AGACAATGGTTTAGGACAATGACAACAATGGCAACAATGCCATTAATCTGGTTCCAGAAGAAAAT
AGAGCACTGCGAGATTAAGCTGTTCCTCTTTTGCAAGGTGTGCACCAAAGCATTAGA
Found at i:2634195 original size:17 final size:18
Alignment explanation
Indices: 2634175--2634208 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2634165 TTTAATTAAG
2634175 TAATGGGC-CTAATATTA
1 TAATGGGCACTAATATTA
*
2634192 TAATGTGCACTAATATT
1 TAATGGGCACTAATATT
2634209 GAAGGCTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (18 bp):
TAATGGGCACTAATATTA
Found at i:2634925 original size:204 final size:204
Alignment explanation
Indices: 2634566--2634964 Score: 550
Period size: 204 Copynumber: 2.0 Consensus size: 204
2634556 GTGTTGGCGA
* *
2634566 GATTGCTTTGAGAAGTACCATTGTGATTACAAAATTACTTGGCAAGGTAAATTTCTAAATAATAA
1 GATTGCTTCGAGAAGTACCATTATGATTACAAAATTACTTGGCAAGGTAAATTTCTAAATAATAA
* * *
2634631 TTAATTTTGTGATTTGATGTGTTAATATCACTAAGGTGATCCATGGGTAAAGGCATGTCTTTGTT
66 TTAATTTTGTGATTTGATGAGTTAATATCACCAAGGTGATCCATGGGTAAAGGCATCTCTTTGTT
* * * *
2634696 GTTTAGTTCTATAGTTTTAATTTTCTTTCTACTACATATTTTGAGCATGCCATCCATAGCCAAAC
131 GTTTAGTTCTAAAGTTTTAATTTTCTTCCTACTACATATTTTAAGCATACCATCCATAGCCAAAC
2634761 CCATCACAG
196 CCATCACAG
* * ** *
2634770 GATTGCTTCGGGAAGTGCCATTATGATTAGGAAATTACTTGGCAAGGTAACTTTCTAAATAATAA
1 GATTGCTTCGAGAAGTACCATTATGATTACAAAATTACTTGGCAAGGTAAATTTCTAAATAATAA
* * * * **
2634835 TTAATTTTGTGCTTTTATGAGTTAAATATCACCAATGTGAT-CGTGGGTGGAGGCATCT-TTTGG
66 TTAATTTTGTGATTTGATGAGTT-AATATCACCAAGGTGATCCATGGGTAAAGGCATCTCTTT-G
* * * *
2634898 TTGTTTAGTTCTAAAGTTTTGATTTTCTTCCTCCTGCATATTTTAAGCATATCATCCATAGCCAA
129 TTGTTTAGTTCTAAAGTTTTAATTTTCTTCCTACTACATATTTTAAGCATACCATCCATAGCCAA
2634963 AC
194 AC
2634965 GCATTAGGAT
Statistics
Matches: 169, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
203 3 0.02
204 151 0.89
205 15 0.09
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.39
Consensus pattern (204 bp):
GATTGCTTCGAGAAGTACCATTATGATTACAAAATTACTTGGCAAGGTAAATTTCTAAATAATAA
TTAATTTTGTGATTTGATGAGTTAATATCACCAAGGTGATCCATGGGTAAAGGCATCTCTTTGTT
GTTTAGTTCTAAAGTTTTAATTTTCTTCCTACTACATATTTTAAGCATACCATCCATAGCCAAAC
CCATCACAG
Found at i:2655879 original size:8 final size:8
Alignment explanation
Indices: 2655850--2655904 Score: 60
Period size: 8 Copynumber: 7.0 Consensus size: 8
2655840 GAATCAGCTT
2655850 GGAAGAAAA
1 GGAAG-AAA
*
2655859 GGGAGAAA
1 GGAAGAAA
*
2655867 AGAAGAAA
1 GGAAGAAA
2655875 GGAAGAAA
1 GGAAGAAA
*
2655883 GAAAGAAA
1 GGAAGAAA
2655891 GG-AGAAA
1 GGAAGAAA
2655898 -GAAGAAA
1 GGAAGAAA
2655905 AAGACAAGNN
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
6 1 0.03
7 10 0.26
8 24 0.62
9 4 0.10
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (8 bp):
GGAAGAAA
Found at i:2655881 original size:16 final size:14
Alignment explanation
Indices: 2655860--2655904 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 14
2655850 GGAAGAAAAG
2655860 GGAGAAAAGAAGAAA
1 GGAG-AAAGAAGAAA
2655875 GGAAGAAAGAAAGAAA
1 GG-AGAAAG-AAGAAA
2655891 GGAGAAAGAAGAAA
1 GGAGAAAGAAGAAA
2655905 AAGACAAGNN
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 6 0.21
15 12 0.43
16 10 0.36
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (14 bp):
GGAGAAAGAAGAAA
Found at i:2655907 original size:16 final size:16
Alignment explanation
Indices: 2655851--2655907 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 16
2655841 AATCAGCTTG
*
2655851 GAAGAAAAGGGAG-AA
1 GAAGAAAAAGGAGAAA
2655866 -AAGAAGAAAGGAAGAAA
1 GAAGAA-AAAGG-AGAAA
*
2655883 GAA-AGAAAGGAGAAA
1 GAAGAAAAAGGAGAAA
2655898 GAAGAAAAAG
1 GAAGAAAAAG
2655908 ACAAGNNNNN
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
14 5 0.15
15 12 0.35
16 12 0.35
17 3 0.09
18 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (16 bp):
GAAGAAAAAGGAGAAA
Found at i:2656464 original size:21 final size:22
Alignment explanation
Indices: 2656435--2656478 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2656425 AAGTGATTAA
2656435 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* *
2656456 TTTAGGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
2656478 T
1 T
2656479 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:2664591 original size:21 final size:22
Alignment explanation
Indices: 2664562--2664605 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
2664552 AAGTGATTAA
2664562 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
*
2664583 TTTAGGTTATTTTATGTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
2664605 T
1 T
2664606 ACTTTAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:2667000 original size:3 final size:3
Alignment explanation
Indices: 2666992--2667016 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2666982 TCTTGAAATG
2666992 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
2667017 TAGTTTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2669458 original size:23 final size:25
Alignment explanation
Indices: 2669412--2669458 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
2669402 TAAATATATA
*
2669412 TTTAAATAACATTTTTTTTACTCTT
1 TTTAAATAACATTTCTTTTACTCTT
*
2669437 TTTAAAT-AC-TTTCTTTTCCTCT
1 TTTAAATAACATTTCTTTTACTCT
2669459 AGATACTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
24 2 0.10
25 7 0.35
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTAAATAACATTTCTTTTACTCTT
Found at i:2676308 original size:45 final size:45
Alignment explanation
Indices: 2676259--2676974 Score: 278
Period size: 45 Copynumber: 16.0 Consensus size: 45
2676249 GTCATATAGT
*
2676259 CTCATTTCAGATGAAGAGCTTTCATTCCTTTTAAAGTTACATAGC
1 CTCATTTCAGATGAAGAGCTTTCATTCCTTTTAAAGTTACGTAGC
* * * * * * *
2676304 CTCATTGT-AAATGAGGAGTTTTGACTCTTTTTAAAGTTATGTAGC
1 CTCATT-TCAGATGAAGAGCTTTCATTCCTTTTAAAGTTACGTAGC
* * * * * * *
2676349 CTCATTTCAAATGATAAACCTTT-ATTCTTTTTATAGTTAGGTACC
1 CTCATTTCAGATGA-AGAGCTTTCATTCCTTTTAAAGTTACGTAGC
* * * * *
2676394 CTC-GTTCTAGAT-AAGGAGCTTTTATTTCTTTTAAAGTTATGCAGC
1 CTCATTTC-AGATGAA-GAGCTTTCATTCCTTTTAAAGTTACGTAGC
* * * * *
2676439 CTCA-TTCTAGAT-AATGAGCGCTT-ATTCCATTTAAAGTTATGCAAC
1 CTCATTTC-AGATGAA-GAGC-TTTCATTCCTTTTAAAGTTACGTAGC
* * * * **
2676484 CTTAATCCCGATGAAGAGCTTTCATTCCTTTTAAAGTTACACAGC
1 CTCATTTCAGATGAAGAGCTTTCATTCCTTTTAAAGTTACGTAGC
* * * * *
2676529 CTCA-TTCTAAATGAGGAG-TTTCTACTCCTTTTAAAGTTATGTAAC
1 CTCATTTC-AGATGAAGAGCTTTC-ATTCCTTTTAAAGTTACGTAGC
* ** *
2676574 CTTAATTT-AGAT-AAGGATTTTTCATT-C-TTTAAAGTTATGTAGC
1 C-TCATTTCAGATGAA-GAGCTTTCATTCCTTTTAAAGTTACGTAGC
* * * * * *
2676617 CTCATTCCAAATGATAAACCTTT-ATTCCTTTTATAGTTAGGTAGC
1 CTCATTTCAGATGA-AGAGCTTTCATTCCTTTTAAAGTTACGTAGC
** * * * *
2676662 CTGGTTTTAGAT-AACGAGCATTT-ATTTCTTTTAAAGTTATGTAGT
1 CTCATTTCAGATGAA-GAGC-TTTCATTCCTTTTAAAGTTACGTAGC
* ** * *
2676707 CGCATCCCAGATGAGGAGCATTT-ATTCCATTTAAAGTTATC-TAGC
1 CTCATTTCAGATGAAGAGC-TTTCATTCCTTTTAAAGTTA-CGTAGC
* * *
2676752 CTCA-TTCTAAATGATCTGAGCTTTCATT-C---TAAAGTTACATAGC
1 CTCATTTC-AGATGA--AGAGCTTTCATTCCTTTTAAAGTTACGTAGC
* * * * * * *
2676795 CTCATTTTAGATGAGGAACCTTT-ACTCATTTTAAAGTTATGTAGT
1 CTCATTTCAGATGAAG-AGCTTTCATTCCTTTTAAAGTTACGTAGC
* * * * * *
2676840 CTTATTCCAAAT-AAGGAGTTTTCATTCCATTTAAAGTTACATAGC
1 CTCATTTCAGATGAA-GAGCTTTCATTCCTTTTAAAGTTACGTAGC
* * * * *
2676885 CTCATTCCAGATG-AGAAGCCTTTCATTCTTTTTAAAATTACATTGC
1 CTCATTTCAGATGAAG-AG-CTTTCATTCCTTTTAAAGTTACGTAGC
* ** * * *
2676931 CTCATTCCAGACAAAGAGCCTGCTATTCCTTTTAAGGTTACGTA
1 CTCATTTCAGATGAAGAGCTTTC-ATTCCTTTTAAAGTTACGTA
2676975 CCCTTGTTAG
Statistics
Matches: 499, Mismatches: 128, Indels: 87
0.70 0.18 0.12
Matches are distributed among these distances:
41 3 0.01
42 10 0.02
43 45 0.09
44 38 0.08
45 320 0.64
46 72 0.14
47 11 0.02
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (45 bp):
CTCATTTCAGATGAAGAGCTTTCATTCCTTTTAAAGTTACGTAGC
Found at i:2676411 original size:90 final size:89
Alignment explanation
Indices: 2676233--2676444 Score: 212
Period size: 90 Copynumber: 2.3 Consensus size: 89
2676223 AGAGGTTTTT
* * * * * *
2676233 TTTTATTCTTTTTAAAGTCATATAGTCTCATTTCAGATGAAGAGCTTTCATTCCTTTTAAAGTTA
1 TTTTA-TCTTTTTAAAGTTATGTAGCCTCATTTCAAATGAAAACCTTTCATTCCTTTTAAAGTTA
* * *
2676298 CATAGCCTCATTGTAAATGAGGAG-
65 CATACCCTCATTCTAAATAAGGAGC
* *
2676322 TTTTGACTCTTTTTAAAGTTATGTAGCCTCATTTCAAATGATAAACCTTT-ATTCTTTTTATAGT
1 TTTT-A-TCTTTTTAAAGTTATGTAGCCTCATTTCAAATGA-AAACCTTTCATTCCTTTTAAAGT
** * *
2676386 TAGGTACCCTCGTTCTAGATAAGGAGC
63 TACATACCCTCATTCTAAATAAGGAGC
* *
2676413 TTTTATTTCTTTTAAAGTTATGCAGCCTCATT
1 TTTTATCT-TTTTAAAGTTATGTAGCCTCATT
2676445 CTAGATAATG
Statistics
Matches: 101, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
89 6 0.06
90 85 0.84
91 10 0.10
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.44
Consensus pattern (89 bp):
TTTTATCTTTTTAAAGTTATGTAGCCTCATTTCAAATGAAAACCTTTCATTCCTTTTAAAGTTAC
ATACCCTCATTCTAAATAAGGAGC
Found at i:2676762 original size:21 final size:21
Alignment explanation
Indices: 2676734--2676800 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 21
2676724 GCATTTATTC
2676734 CATT-TAAAGTTATCTAGCCT
1 CATTCTAAAGTTATCTAGCCT
* *
2676754 CATTCTAAA-TGATCTGAGCTTT
1 CATTCTAAAGTTATCT-AGC-CT
2676776 CATTCTAAAGTTA-CATAGCCT
1 CATTCTAAAGTTATC-TAGCCT
2676797 CATT
1 CATT
2676801 TTAGATGAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
20 9 0.24
21 12 0.32
22 14 0.37
23 3 0.08
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (21 bp):
CATTCTAAAGTTATCTAGCCT
Found at i:2676951 original size:46 final size:46
Alignment explanation
Indices: 2676859--2676951 Score: 116
Period size: 46 Copynumber: 2.0 Consensus size: 46
2676849 AATAAGGAGT
* **
2676859 TTTCATTCCATTTAAAGTTACATAGCCTCATTCCAGATGAGAAGCC
1 TTTCATTCCATTTAAAATTACATAGCCTCATTCCAGAAAAGAAGCC
** *
2676905 TTTCATTCTTTTTAAAATTACATTGCCTCATTCCAGACAAAG-AGCC
1 TTTCATTCCATTTAAAATTACATAGCCTCATTCCAGA-AAAGAAGCC
2676951 T
1 T
2676952 GCTATTCCTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
46 38 0.95
47 2 0.05
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (46 bp):
TTTCATTCCATTTAAAATTACATAGCCTCATTCCAGAAAAGAAGCC
Found at i:2676964 original size:46 final size:46
Alignment explanation
Indices: 2676861--2676965 Score: 115
Period size: 46 Copynumber: 2.3 Consensus size: 46
2676851 TAAGGAGTTT
* * ** *
2676861 TCATTCCATTTAAAGTTACATAGCCTCATTCCAGATGAGAAGCCTT
1 TCATTCCTTTTAAAATTACATAGCCTCATTCCAGAAAAGAAGCCTC
* *
2676907 TCATTCTTTTTAAAATTACATTGCCTCATTCCAGACAAAG-AGCCTGC
1 TCATTCCTTTTAAAATTACATAGCCTCATTCCAGA-AAAGAAGCCT-C
2676954 T-ATTCCTTTTAA
1 TCATTCCTTTTAA
2676966 GGTTACGTAC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
46 46 0.94
47 3 0.06
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (46 bp):
TCATTCCTTTTAAAATTACATAGCCTCATTCCAGAAAAGAAGCCTC
Found at i:2678023 original size:26 final size:26
Alignment explanation
Indices: 2677991--2678042 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2677981 TTTTTAGCCA
2677991 TAGTCAACCCTTGAGTGAACTAGTTG
1 TAGTCAACCCTTGAGTGAACTAGTTG
2678017 TAGTCAACCCTTGAGTGAACTAGTTG
1 TAGTCAACCCTTGAGTGAACTAGTTG
2678043 AAAAATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (26 bp):
TAGTCAACCCTTGAGTGAACTAGTTG
Found at i:2678513 original size:20 final size:20
Alignment explanation
Indices: 2678488--2678537 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
2678478 GTTTTCTTTG
*
2678488 TTTATGTTTTTTCTTTTCAT
1 TTTATGTTTTTTCATTTCAT
*
2678508 TTTATGTTATTTCATTTCAT
1 TTTATGTTTTTTCATTTCAT
*
2678528 TTTAAGTTTT
1 TTTATGTTTT
2678538 GCTTTAGGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.16, C:0.08, G:0.06, T:0.70
Consensus pattern (20 bp):
TTTATGTTTTTTCATTTCAT
Found at i:2678663 original size:23 final size:23
Alignment explanation
Indices: 2678637--2678684 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
2678627 AGTTTTAGGT
2678637 GTAGTTCTAAGTTGTTTAAGTTG
1 GTAGTTCTAAGTTGTTTAAGTTG
2678660 GTAGTTCTAAGTTGTTTAAGTTG
1 GTAGTTCTAAGTTGTTTAAGTTG
2678683 GT
1 GT
2678685 TTTCTTTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.04, G:0.27, T:0.48
Consensus pattern (23 bp):
GTAGTTCTAAGTTGTTTAAGTTG
Found at i:2683312 original size:23 final size:23
Alignment explanation
Indices: 2683278--2683337 Score: 95
Period size: 23 Copynumber: 2.6 Consensus size: 23
2683268 ATTCAAATGT
2683278 AATTAGAA-TTTGGATAGATTAGG
1 AATT-GAATTTTGGATAGATTAGG
2683301 AATTGAATTTTGGATAGATTAGG
1 AATTGAATTTTGGATAGATTAGG
*
2683324 AATTAAATTTTGGA
1 AATTGAATTTTGGA
2683338 AAATTGACGA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 3 0.09
23 32 0.91
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (23 bp):
AATTGAATTTTGGATAGATTAGG
Found at i:2689662 original size:21 final size:21
Alignment explanation
Indices: 2689637--2689702 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
2689627 AACCTTCCCT
2689637 TTTCTTTTTTCTTCTTCC-TCC
1 TTTCTTTTTTC-TCTTCCTTCC
*
2689658 TTTCTCTCTTTCT-TTCCTTCC
1 TTTCT-TTTTTCTCTTCCTTCC
*
2689679 TTTCTTTCTTTCTCTTCTTTCC
1 TTTCTTT-TTTCTCTTCCTTCC
2689701 TT
1 TT
2689703 CTTCTCCTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 5 0.13
21 19 0.50
22 14 0.37
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTCTTTTTTCTCTTCCTTCC
Found at i:2689673 original size:4 final size:4
Alignment explanation
Indices: 2689637--2689705 Score: 54
Period size: 4 Copynumber: 17.5 Consensus size: 4
2689627 AACCTTCCCT
* * * *
2689637 TTTC TTT- TTTC -TTC -TTC CTCC TTTC TCTC TTTC TTTCC TTCC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC
*
2689683 TTTC TTTC TCTTC TTTC CTTC TT
1 TTTC TTTC T-TTC TTTC TTTC TT
2689706 CTCCTTTCTC
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
3 9 0.17
4 36 0.69
5 7 0.13
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (4 bp):
TTTC
Found at i:2689704 original size:13 final size:13
Alignment explanation
Indices: 2689662--2689725 Score: 58
Period size: 13 Copynumber: 4.7 Consensus size: 13
2689652 TCCTCCTTTC
2689662 TCTCTTTCTTTCCT
1 TCTC-TTCTTTCCT
*
2689676 TC-CTTTCTTTCTT
1 TCTC-TTCTTTCCT
2689689 TCTCTTCTTTCCT
1 TCTCTTCTTTCCT
*
2689702 TCTTCTCCTTTCTCT
1 TC-TCTTCTTTC-CT
*
2689717 TTTCTTCTT
1 TCTCTTCTT
2689726 GGTAGTGGAC
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
13 22 0.52
14 17 0.40
15 3 0.07
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (13 bp):
TCTCTTCTTTCCT
Found at i:2689704 original size:17 final size:17
Alignment explanation
Indices: 2689667--2689725 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 17
2689657 CTTTCTCTCT
*
2689667 TTCTTTCCTTCCTTTCT
1 TTCTTTCCTTCCTTTCC
2689684 TTCTTTCTCTT-CTTTCC
1 TTCTTTC-CTTCCTTTCC
*
2689701 TTCTTCTCCTTTCTCTTTTC
1 TTCTT-TCC-TTC-CTTTCC
2689721 TTCTT
1 TTCTT
2689726 GGTAGTGGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
17 18 0.51
18 7 0.20
20 10 0.29
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (17 bp):
TTCTTTCCTTCCTTTCC
Found at i:2690509 original size:18 final size:19
Alignment explanation
Indices: 2690462--2690509 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
2690452 TTAATATTTT
*
2690462 AATATTGTTTTATTAATAA
1 AATATTATTTTATTAATAA
* *
2690481 AATAATATTTTATT-CTAA
1 AATATTATTTTATTAATAA
*
2690499 AATATTCTTTT
1 AATATTATTTT
2690510 CGCTCACTAC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (19 bp):
AATATTATTTTATTAATAA
Found at i:2698158 original size:21 final size:23
Alignment explanation
Indices: 2698129--2698181 Score: 83
Period size: 21 Copynumber: 2.3 Consensus size: 23
2698119 CCTTTTCCTT
2698129 TTTCTTCTTCCTCCTTTC-TC-CC
1 TTTC-TCTTCCTCCTTTCTTCTCC
2698151 TTTCTCTTCCTCCTTTCTTCTCC
1 TTTCTCTTCCTCCTTTCTTCTCC
2698174 TTTCTCTT
1 TTTCTCTT
2698182 TTCTTCTTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 13 0.45
22 6 0.21
23 10 0.34
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTCTCTTCCTCCTTTCTTCTCC
Found at i:2698175 original size:10 final size:11
Alignment explanation
Indices: 2698133--2698178 Score: 53
Period size: 10 Copynumber: 4.4 Consensus size: 11
2698123 TTCCTTTTTC
2698133 TTCTTCCTCCT
1 TTCTTCCTCCT
*
2698144 TTC-TCC-CTT
1 TTCTTCCTCCT
2698153 TCTCTTCCTCCT
1 T-TCTTCCTCCT
2698165 TTCTT-CTCCT
1 TTCTTCCTCCT
2698175 TTCT
1 TTCT
2698179 CTTTTCTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
9 3 0.10
10 14 0.47
11 10 0.33
12 3 0.10
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (11 bp):
TTCTTCCTCCT
Found at i:2698953 original size:18 final size:19
Alignment explanation
Indices: 2698911--2698959 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
2698901 TTAATATTTT
*
2698911 AATATTATTTTATTAATAA
1 AATATTCTTTTATTAATAA
* *
2698930 ACTATTCTTTTATT-CTAA
1 AATATTCTTTTATTAATAA
2698948 AATATTCTTTTA
1 AATATTCTTTTA
2698960 ACTCACTACA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (19 bp):
AATATTCTTTTATTAATAA
Found at i:2701256 original size:21 final size:20
Alignment explanation
Indices: 2701227--2701274 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
2701217 ATAATCAATT
* *
2701227 GGATGAAATTTGAGACTAAAA
1 GGATAAAATTTGACA-TAAAA
2701248 GGATAAAA-TTGACATAAAA
1 GGATAAAATTTGACATAAAA
2701267 GG-TAAAAT
1 GGATAAAAT
2701275 GGTAAATTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 5 0.21
19 7 0.29
20 5 0.21
21 7 0.29
ACGTcount: A:0.52, C:0.04, G:0.21, T:0.23
Consensus pattern (20 bp):
GGATAAAATTTGACATAAAA
Found at i:2701648 original size:20 final size:21
Alignment explanation
Indices: 2701605--2701648 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2701595 GGTAACTAAG
*
2701605 TGTTGTCTTAGTTAAGAGAAA
1 TGTTGTCTTAATTAAGAGAAA
*
2701626 TGTTGTCTTAATTTAGA-AAA
1 TGTTGTCTTAATTAAGAGAAA
2701646 TGT
1 TGT
2701649 GCATATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (21 bp):
TGTTGTCTTAATTAAGAGAAA
Found at i:2703182 original size:35 final size:35
Alignment explanation
Indices: 2703157--2703489 Score: 270
Period size: 35 Copynumber: 9.4 Consensus size: 35
2703147 TTAATTGTTT
* *
2703157 AATTTAATCAATTAAACCCAATAACTTAGTTAAAC
1 AATTTAATCAATTAGACCCAATAACTTAATTAAAC
* *
2703192 AATTTAATCAATTAGACCCACTAACTTGATTAAAC
1 AATTTAATCAATTAGACCCAATAACTTAATTAAAC
* * * ****
2703227 AGATTTAATCAATTAGGCCAAATAAATTAATTGTTT
1 A-ATTTAATCAATTAGACCCAATAACTTAATTAAAC
* * *
2703263 ATTTTAATCAATGAGGCCCAATAACTTAATTAAAC
1 AATTTAATCAATTAGACCCAATAACTTAATTAAAC
* * **********
2703298 AATTTAATCAATTAGGCCTANNNNNNNNNNTAAAC
1 AATTTAATCAATTAGACCCAATAACTTAATTAAAC
* *
2703333 AAATTTAATCAATTAGGCCCAATAACTTAACTAAAC
1 -AATTTAATCAATTAGACCCAATAACTTAATTAAAC
* * *
2703369 AATTTAATCAATTAGGCCAAATAACTTGATTAAAC
1 AATTTAATCAATTAGACCCAATAACTTAATTAAAC
* ***
2703404 AATTTTAATCAATTAGGCCCAATAACTTAATTATTT
1 AA-TTTAATCAATTAGACCCAATAACTTAATTAAAC
* ** * *
2703440 AATTTAATTAATTAGACATAATGACTTAATTAAAT
1 AATTTAATCAATTAGACCCAATAACTTAATTAAAC
*
2703475 AATTTAATAAATTAG
1 AATTTAATCAATTAG
2703490 GTACAACTTA
Statistics
Matches: 234, Mismatches: 61, Indels: 6
0.78 0.20 0.02
Matches are distributed among these distances:
35 154 0.66
36 80 0.34
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.33
Consensus pattern (35 bp):
AATTTAATCAATTAGACCCAATAACTTAATTAAAC
Found at i:2703236 original size:71 final size:70
Alignment explanation
Indices: 2703157--2703490 Score: 310
Period size: 71 Copynumber: 4.7 Consensus size: 70
2703147 TTAATTGTTT
** * * * * *
2703157 AATTTAATCAATTAAACCCAATAACTTAGTTAAACAATTTAATCAATTAGACCCACTAACTTGAT
1 AATTTAATCAATTAGGCCAAATAACTTAATTAAACAATTTAATCAATTAGGCCCAATAACTTAAT
2703222 TAAAC
66 TAAAC
* **** * *
2703227 AGATTTAATCAATTAGGCCAAATAAATTAATTGTTTATTTTAATCAATGAGGCCCAATAACTTAA
1 A-ATTTAATCAATTAGGCCAAATAACTTAATTAAACAATTTAATCAATTAGGCCCAATAACTTAA
2703292 TTAAAC
65 TTAAAC
* **********
2703298 AATTTAATCAATTAGGCCTANNNNNNNNNNTAAACAAATTTAATCAATTAGGCCCAATAACTTAA
1 AATTTAATCAATTAGGCCAAATAACTTAATTAAAC-AATTTAATCAATTAGGCCCAATAACTTAA
*
2703363 CTAAAC
65 TTAAAC
*
2703369 AATTTAATCAATTAGGCCAAATAACTTGATTAAACAATTTTAATCAATTAGGCCCAATAACTTAA
1 AATTTAATCAATTAGGCCAAATAACTTAATTAAACAA-TTTAATCAATTAGGCCCAATAACTTAA
***
2703434 TTATTT
65 TTAAAC
* * * * *
2703440 AATTTAATTAATTA-GACATAATGACTTAATTAAATAATTTAATAAATTAGG
1 AATTTAATCAATTAGGCCA-AATAACTTAATTAAACAATTTAATCAATTAGG
2703491 TACAACTTAA
Statistics
Matches: 207, Mismatches: 53, Indels: 8
0.77 0.20 0.03
Matches are distributed among these distances:
70 38 0.18
71 169 0.82
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.33
Consensus pattern (70 bp):
AATTTAATCAATTAGGCCAAATAACTTAATTAAACAATTTAATCAATTAGGCCCAATAACTTAAT
TAAAC
Found at i:2703444 original size:106 final size:104
Alignment explanation
Indices: 2703138--2703490 Score: 294
Period size: 106 Copynumber: 3.3 Consensus size: 104
2703128 CTTTAGAAGC
* *** **
2703138 CCAATTAACTTAATTGTTTAATTTAATCAATTAAACCCAATAACTTAGTTAAACAATTTAATCAA
1 CCAAATAACTTAATTAAATAATTTAATCAATTAGGCCCAATAACTTA-TTAAACAATTTAATCAA
* * * *
2703203 TTAGACCCACTAACTTGATTAAACAGATTTAATCAATTAGG
65 TTAGGCCCAATAACTTAATTAAA-AAATTTAATCAATTAGG
* *** * *
2703244 CCAAATAAATTAATTGTTTATTTTAATCAATGAGGCCCAATAACTTAATTAAACAATTTAATCAA
1 CCAAATAACTTAATTAAATAATTTAATCAATTAGGCCCAATAACTT-ATTAAACAATTTAATCAA
* **********
2703309 TTAGGCCTANNNNNNNNNNTAAACAAATTTAATCAATTAGG
65 TTAGGCCCAATAACTTAATTAAA-AAATTTAATCAATTAGG
* * * *
2703350 CCCAATAACTTAACTAAACAATTTAATCAATTAGGCCAAATAACTTGATTAAACAATTTTAATCA
1 CCAAATAACTTAATTAAATAATTTAATCAATTAGGCCCAATAACTT-ATTAAACAA-TTTAATCA
*** *
2703415 ATTAGGCCCAATAACTTAATTATTTAATTTAATTAATTA-G
64 ATTAGGCCCAATAACTTAATTAAAAAATTTAATCAATTAGG
* * *
2703455 ACATAATGACTTAATTAAATAATTTAATAAATTAGG
1 CCA-AATAACTTAATTAAATAATTTAATCAATTAGG
2703491 TACAACTTAA
Statistics
Matches: 193, Mismatches: 51, Indels: 6
0.77 0.20 0.02
Matches are distributed among these distances:
105 2 0.01
106 171 0.89
107 20 0.10
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.34
Consensus pattern (104 bp):
CCAAATAACTTAATTAAATAATTTAATCAATTAGGCCCAATAACTTATTAAACAATTTAATCAAT
TAGGCCCAATAACTTAATTAAAAAATTTAATCAATTAGG
Found at i:2705398 original size:14 final size:14
Alignment explanation
Indices: 2705379--2705406 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2705369 TCAATATTCA
2705379 ACCTTTTGATCAAT
1 ACCTTTTGATCAAT
2705393 ACCTTTTGATCAAT
1 ACCTTTTGATCAAT
2705407 TGAATATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (14 bp):
ACCTTTTGATCAAT
Found at i:2710669 original size:35 final size:35
Alignment explanation
Indices: 2710618--2710839 Score: 196
Period size: 35 Copynumber: 6.3 Consensus size: 35
2710608 NNNNNNNNNN
* * ** *
2710618 TCAATTAGGTCAAATAACTTAATTGTTTAATTTAA
1 TCAATTAGGCCCAATAACTTAATTAATAAATTTAA
* *
2710653 TCAATGAGGCCCAATAACTAAATTAA-ACAATTTAA
1 TCAATTAGGCCCAATAACTTAATTAATA-AATTTAA
* * *
2710688 TCAATTGGGCCCAATAACTTGATTAAACAAATTTAA
1 TCAATTAGGCCCAATAACTTAATT-AATAAATTTAA
* * * *
2710724 TCAATTAGGCCTAATAGCTTGATTAAAGAAATTTAA
1 TCAATTAGGCCCAATAACTTAATT-AATAAATTTAA
* * ** *
2710760 TCAATTAAGCTCAATAACTTAATTTTTTAATTTAA
1 TCAATTAGGCCCAATAACTTAATTAATAAATTTAA
* *
2710795 TTAATTAGACCCAATAACTTAATTAA-ATAATTTAA
1 TCAATTAGGCCCAATAACTTAATTAATA-AATTTAA
*
2710830 TGAATTAGGC
1 TCAATTAGGC
2710840 ACAACTTGGT
Statistics
Matches: 150, Mismatches: 33, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
35 89 0.59
36 60 0.40
37 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.36
Consensus pattern (35 bp):
TCAATTAGGCCCAATAACTTAATTAATAAATTTAA
Found at i:2710728 original size:36 final size:36
Alignment explanation
Indices: 2710646--2710839 Score: 205
Period size: 35 Copynumber: 5.5 Consensus size: 36
2710636 TTAATTGTTT
* *
2710646 AATTTAATCAATGAGGCCCAATAACTAAATTAAAC-
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACA
* *
2710681 AATTTAATCAATTGGGCCCAATAACTTGATTAAACA
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACA
* * * *
2710717 AATTTAATCAATTAGGCCTAATAGCTTGATTAAAGA
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACA
* * ****
2710753 AATTTAATCAATTAAGCTCAATAACTTAATT-TTTT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACA
* * *
2710788 AATTTAATTAATTAGACCCAATAACTTAATTAAA-T
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACA
*
2710823 AATTTAATGAATTAGGC
1 AATTTAATCAATTAGGC
2710840 ACAACTTGGT
Statistics
Matches: 132, Mismatches: 25, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
35 74 0.56
36 58 0.44
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.35
Consensus pattern (36 bp):
AATTTAATCAATTAGGCCCAATAACTTAATTAAACA
Found at i:2732546 original size:21 final size:22
Alignment explanation
Indices: 2732511--2732554 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
2732501 CTCTTAAAGT
2732511 AATTTAAAATAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
*
2732533 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
2732554 A
1 A
2732555 TTGATCACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (22 bp):
AATTTAAAATAAAATAACTTAA
Found at i:2739528 original size:29 final size:28
Alignment explanation
Indices: 2739481--2739623 Score: 169
Period size: 29 Copynumber: 5.0 Consensus size: 28
2739471 TAGTAGCTTT
2739481 AACATGTTTGTCTTAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
2739509 AACATGTTTGGTCTTAATTTAGACAAGAA
1 AACATGTTT-GTCTTAATTTAGACAAGAA
*
2739538 AATATGTTTGTCTTAATTTAAGACAAGAAA
1 AACATGTTTGTCTTAATTT-AGACAAG-AA
* * * *
2739568 AATATTTTTTATCTTAATCTAGACAAGAA
1 AACA-TGTTTGTCTTAATTTAGACAAGAA
* * * *
2739597 AGCATATATGTCTCAATTTAGACAAGA
1 AACATGTTTGTCTTAATTTAGACAAGA
2739624 CAAAATAATT
Statistics
Matches: 100, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
28 37 0.37
29 38 0.38
30 13 0.13
31 12 0.12
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAGAA
Found at i:2739596 original size:59 final size:58
Alignment explanation
Indices: 2739481--2739640 Score: 189
Period size: 59 Copynumber: 2.8 Consensus size: 58
2739471 TAGTAGCTTT
* * * *
2739481 AACATGTTTGTCTTAATTTAGACAAG-AAAACATGTTTGGTCTTAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTGATCTTAATCTAGACAAGAA
* *
2739538 AATATGTTTGTCTTAATTTAAGACAAGAAAAATATTTTTTATCTTAATCTAGACAAGAA
1 AACATGTTTGTCTTAATTT-AGACAAGAAAAATATTTTTGATCTTAATCTAGACAAGAA
* * * * *
2739597 AGCATATATGTCTCAATTTAGACAAGACAAAATAATTTTG-TCTT
1 AACATGTTTGTCTTAATTTAGACAAGA-AAAATATTTTTGATCTT
2739641 GATTACAAAA
Statistics
Matches: 87, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
57 18 0.21
58 19 0.22
59 50 0.57
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (58 bp):
AACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTGATCTTAATCTAGACAAGAA
Found at i:2758411 original size:20 final size:20
Alignment explanation
Indices: 2758386--2758430 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2758376 CAATTAGTTT
2758386 ATTTTAAGTGAGTTATTTTA
1 ATTTTAAGTGAGTTATTTTA
* * *
2758406 ATTTTATGTTATTTATTTTA
1 ATTTTAAGTGAGTTATTTTA
2758426 ATTTT
1 ATTTT
2758431 CTTATTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (20 bp):
ATTTTAAGTGAGTTATTTTA
Found at i:2758440 original size:21 final size:20
Alignment explanation
Indices: 2758398--2758443 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
2758388 TTTAAGTGAG
*
2758398 TTATTTTAATTTTATGTTAT
1 TTATTTTAATTTTATATTAT
*
2758418 TTATTTTAATTTTCTTATTAT
1 TTATTTTAATTTT-ATATTAT
2758439 TTATT
1 TTATT
2758444 AGTTTTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (20 bp):
TTATTTTAATTTTATATTAT
Found at i:2761210 original size:16 final size:16
Alignment explanation
Indices: 2761174--2761209 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
2761164 TGAAACTAAA
2761174 ATTTTAGATTTTGATT
1 ATTTTAGATTTTGATT
2761190 ATTTTAGATTTTGATT
1 ATTTTAGATTTTGATT
2761206 -TTTT
1 ATTTT
2761210 TTATTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (16 bp):
ATTTTAGATTTTGATT
Found at i:2762148 original size:9 final size:10
Alignment explanation
Indices: 2762129--2762161 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
2762119 AAATTGAAGA
2762129 AAAACTAATT
1 AAAACTAATT
2762139 AAAA-TAATT
1 AAAACTAATT
*
2762148 AAAAGTAATT
1 AAAACTAATT
2762158 AAAA
1 AAAA
2762162 ATCAACACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (10 bp):
AAAACTAATT
Found at i:2764296 original size:68 final size:68
Alignment explanation
Indices: 2764108--2764299 Score: 174
Period size: 68 Copynumber: 2.8 Consensus size: 68
2764098 CATGTTTGGT
* * * * * *
2764108 ATGATGAATGCAATAACATTATGCATATGATATAATTTCCATATACCATATAAGATGATTAAGTA
1 ATGATGAATGCAATAAGATTATGTATATGATGTATTTTCCATATACCTTATGAGATGATTAAGTA
2764173 TGC
66 TGC
* * * * * * * * *
2764176 ATTAT-ATATACTATAAGATTGTGTATATGATGTATATGCCACATA-ATATATGAGATGATTGAG
1 ATGATGA-ATGCAATAAGATTATGTATATGATGTATTTTCCATATACCT-TATGAGATGATTAAG
2764239 -ATAGC
64 TAT-GC
* * *
2764244 ATGATGAATGCCATGAGATTATGTATATGATGTATTTTCAATATACCTTATGAGAT
1 ATGATGAATGCAATAAGATTATGTATATGATGTATTTTCCATATACCTTATGAGAT
2764300 AAGTAAGCTT
Statistics
Matches: 94, Mismatches: 25, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
67 3 0.03
68 89 0.95
69 2 0.02
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (68 bp):
ATGATGAATGCAATAAGATTATGTATATGATGTATTTTCCATATACCTTATGAGATGATTAAGTA
TGC
Found at i:2776275 original size:11 final size:11
Alignment explanation
Indices: 2776261--2776285 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2776251 TGATTGATGC
2776261 AATGGTTTACA
1 AATGGTTTACA
2776272 AATGGTTTACA
1 AATGGTTTACA
2776283 AAT
1 AAT
2776286 CTACTATGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (11 bp):
AATGGTTTACA
Done.