Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009624.1 Hibiscus syriacus cultivar Beakdansim tig00117016_pilon, 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: 8249038
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 38
Found at i:2944256 original size:21 final size:21
Alignment explanation
Indices: 2944232--2944293 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
2944222 CTTGACCCCC
2944232 TTTTTTTTTCTTTTTCTTTTT
1 TTTTTTTTTCTTTTTCTTTTT
*
2944253 TTTTTCTTTCTTTTT-TTCTTT
1 TTTTTTTTTCTTTTTCTT-TTT
*
2944274 CTTTTTTTTC-TTTTCTTTTT
1 TTTTTTTTTCTTTTTCTTTTT
2944294 CTTCTCTTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 9 0.25
21 27 0.75
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (21 bp):
TTTTTTTTTCTTTTTCTTTTT
Found at i:2944257 original size:12 final size:12
Alignment explanation
Indices: 2944235--2944298 Score: 76
Period size: 12 Copynumber: 5.1 Consensus size: 12
2944225 GACCCCCTTT
2944235 TTTTTTCTTTTTC
1 TTTTTT-TTTTTC
2944248 -TTTTTTTTTTC
1 TTTTTTTTTTTC
*
2944259 TTTCTTTTTTTC
1 TTTTTTTTTTTC
2944271 TTTCTTTTTTTTC
1 TTT-TTTTTTTTC
2944284 TTTTCTTTTTCTTC
1 TTTT-TTTTT-TTC
2944298 T
1 T
2944299 CTTCAAGCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
11 6 0.13
12 19 0.42
13 16 0.36
14 4 0.09
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:2951504 original size:15 final size:15
Alignment explanation
Indices: 2951481--2951512 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2951471 TGAAATGAAT
2951481 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
2951496 AATGCATGTATGCAA
1 AATGAATGTATGCAA
2951511 AA
1 AA
2951513 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:2953076 original size:155 final size:158
Alignment explanation
Indices: 2952790--2953099 Score: 581
Period size: 155 Copynumber: 2.0 Consensus size: 158
2952780 CTTCCATAGA
2952790 GATATCCTCATTTTGATCTGGTAGAGGAATATTTTCATTTTTCCTGACAGATCTCCATTCCTCAT
1 GATATCCTCATTTTGATCTGGTAGAGGAATATTTTCATTTTTCCTGACAGATCTCCATTCCTCAT
2952855 AATCAGGAGTTAGCATTTCCTTTGCTGCTTTAGCTCGGATACAAAAAGTTGTTTTCCAAGCTGTA
66 AATC--GAGTTAGCATTTCCTTTGCTGCTTTAGCTCGGATACAAAAAGTTGTTTTCCAAGCTGTA
2952920 ACGGCTTCCATGATATTT-TTTTATTTGCT
129 ACGGCTTCCATGATATTTCTTTTATTTGCT
2952949 GATATCCTCATTTTGATCTGGTAGAGGAATA-TTTCATTTTTCCTGACAGATCTCCATTCCTCAT
1 GATATCCTCATTTTGATCTGGTAGAGGAATATTTTCATTTTTCCTGACAGATCTCCATTCCTCAT
2953013 AATC-AGTTAGCATTTCCTTTGCTGCTTTAGCTCGGATACAAAAAGTTGTTTTCCAAGCTGTAAC
66 AATCGAGTTAGCATTTCCTTTGCTGCTTTAGCTCGGATACAAAAAGTTGTTTTCCAAGCTGTAAC
2953077 GGCTTCCATGATATTTCTTTTAT
131 GGCTTCCATGATATTTCTTTTAT
2953100 AATTTTGCTG
Statistics
Matches: 150, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
155 76 0.51
156 6 0.04
158 37 0.25
159 31 0.21
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.41
Consensus pattern (158 bp):
GATATCCTCATTTTGATCTGGTAGAGGAATATTTTCATTTTTCCTGACAGATCTCCATTCCTCAT
AATCGAGTTAGCATTTCCTTTGCTGCTTTAGCTCGGATACAAAAAGTTGTTTTCCAAGCTGTAAC
GGCTTCCATGATATTTCTTTTATTTGCT
Found at i:2954979 original size:18 final size:20
Alignment explanation
Indices: 2954934--2954980 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
2954924 TGAAATATTA
2954934 ATAAGAAAATATATAAATACT
1 ATAA-AAAATATATAAATACT
*
2954955 AT-GAAAATA-ATAAATA-T
1 ATAAAAAATATATAAATACT
2954972 ATAAAAAAT
1 ATAAAAAAT
2954981 TTGAAAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 3 0.13
18 12 0.52
19 6 0.26
21 2 0.09
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (20 bp):
ATAAAAAATATATAAATACT
Found at i:2956917 original size:2 final size:2
Alignment explanation
Indices: 2956912--2956936 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2956902 ATTATTTATG
2956912 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2956937 TTAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2956946 original size:3 final size:3
Alignment explanation
Indices: 2956938--2957061 Score: 140
Period size: 3 Copynumber: 41.0 Consensus size: 3
2956928 TATATATATT
* * *
2956938 TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAT TTA TAA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
2956984 TTA TAA TAA TAA TAA TAA TAA TTA TTA TTA TTA TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
2957032 TAA TAA TAA TTA TAG TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2957062 ATAAATCAAA
Statistics
Matches: 106, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
3 103 0.97
4 3 0.03
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:2957289 original size:25 final size:25
Alignment explanation
Indices: 2957261--2957310 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
2957251 CATGATTTTC
*
2957261 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
2957286 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
2957311 TAATTGGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:2957448 original size:21 final size:20
Alignment explanation
Indices: 2957416--2957508 Score: 141
Period size: 20 Copynumber: 4.6 Consensus size: 20
2957406 TTCACAACTT
*
2957416 GAAAGTAAAATTCGCAACGC
1 GAAAGTCAAATTCGCAACGC
*
2957436 TAATAGTCAAATTCGCAACGC
1 GAA-AGTCAAATTCGCAACGC
*
2957457 GAAAGTCAAATTCACAACGC
1 GAAAGTCAAATTCGCAACGC
2957477 GAAAGTCAAATTCGCAACGC
1 GAAAGTCAAATTCGCAACGC
*
2957497 GAAAGCCAAATT
1 GAAAGTCAAATT
2957509 TGCGTTGCGA
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 48 0.73
21 18 0.27
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (20 bp):
GAAAGTCAAATTCGCAACGC
Found at i:2957545 original size:13 final size:13
Alignment explanation
Indices: 2957507--2957550 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
2957497 GAAAGCCAAA
2957507 TTTGCGTTGCGAT
1 TTTGCGTTGCGAT
2957520 TTT-CGGTTTGCGAT
1 TTTGC-G-TTGCGAT
2957534 TTTGCGTTGCGAT
1 TTTGCGTTGCGAT
2957547 TTTG
1 TTTG
2957551 ACTTTCGCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 15 0.54
14 11 0.39
15 1 0.04
ACGTcount: A:0.07, C:0.14, G:0.30, T:0.50
Consensus pattern (13 bp):
TTTGCGTTGCGAT
Found at i:2957864 original size:6 final size:6
Alignment explanation
Indices: 2957855--2957889 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
2957845 TTGTGATTAG
**
2957855 GATTTT GATTTT GATTGC GATTTT GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTT
2957890 CCTTTTGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.17, C:0.03, G:0.20, T:0.60
Consensus pattern (6 bp):
GATTTT
Found at i:2960185 original size:24 final size:24
Alignment explanation
Indices: 2960134--2960188 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
2960124 AAAATCCGAG
**
2960134 TATTGACCAAGATCAAAGTCTGGG
1 TATTGACCAAGATCAAAGTCTGAA
* * *
2960158 TATTGATCAAGATCAAATTTTGAA
1 TATTGACCAAGATCAAAGTCTGAA
2960182 TATTGAC
1 TATTGAC
2960189 TAGTACTCAC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (24 bp):
TATTGACCAAGATCAAAGTCTGAA
Found at i:2960965 original size:14 final size:15
Alignment explanation
Indices: 2960929--2960966 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2960919 GAAATCATTG
2960929 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
2960944 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
2960959 AAAAATTA
1 AAAAATTA
2960967 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:2961185 original size:19 final size:19
Alignment explanation
Indices: 2961125--2961233 Score: 148
Period size: 19 Copynumber: 5.7 Consensus size: 19
2961115 ACTAAAACCT
* *
2961125 GTTGCGAAATT-AAATTCGT
1 GTTGCGAATTTGAAATTC-A
* *
2961144 GTTGCGAATTCGAAAATCTA
1 GTTGCGAATTTGAAATTC-A
*
2961164 GTTGTGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
2961183 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
2961202 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
2961221 GTTGCGAATTTGA
1 GTTGCGAATTTGA
2961234 CTTATGTGTT
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
19 60 0.75
20 20 0.25
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:2961206 original size:58 final size:57
Alignment explanation
Indices: 2961125--2961233 Score: 148
Period size: 58 Copynumber: 1.9 Consensus size: 57
2961115 ACTAAAACCT
* *
2961125 GTTGCGAAATTAAATTCGTGTTGCGAATTCGAAAATCTAGTTGTGAATTTGAAATTCA
1 GTTGCGAAATTAAATTCGAGTTGCGAATTCGAAAATC-AGTTGCGAATTTGAAATTCA
* * *
2961183 GTTGCGAATTTGAAATTC-AGTTGCGAATTTGAAATTCAGTTGCGAATTTGA
1 GTTGCGAAATT-AAATTCGAGTTGCGAATTCGAAAATCAGTTGCGAATTTGA
2961234 CTTATGTGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
57 13 0.29
58 26 0.58
59 6 0.13
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (57 bp):
GTTGCGAAATTAAATTCGAGTTGCGAATTCGAAAATCAGTTGCGAATTTGAAATTCA
Found at i:2961246 original size:20 final size:20
Alignment explanation
Indices: 2961221--2961307 Score: 74
Period size: 20 Copynumber: 4.3 Consensus size: 20
2961211 TTGAAATTCA
2961221 GTTGCGAATTTGACTTATGT
1 GTTGCGAATTTGACTTATGT
**
2961241 GTTGCG-ATTT-ACAAAT-T
1 GTTGCGAATTTGACTTATGT
*
2961258 CGCATTGCGAATTTGAC-TATCGC
1 -G--TTGCGAATTTGACTTAT-GT
*
2961281 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTATGT
2961301 GTTGCGA
1 GTTGCGA
2961308 TTTACAAATT
Statistics
Matches: 53, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
17 1 0.02
18 5 0.09
19 4 0.08
20 32 0.60
21 8 0.15
22 3 0.06
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (20 bp):
GTTGCGAATTTGACTTATGT
Found at i:2961324 original size:20 final size:20
Alignment explanation
Indices: 2961241--2961347 Score: 80
Period size: 20 Copynumber: 5.3 Consensus size: 20
2961231 TGACTTATGT
2961241 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
* *
2961261 ATTGCGAATTTGAC-TA-TCGC
1 GTTGCG-ATTT-ACAAATTCGC
*
2961281 GTTGCGAATTTGAC---TTCTGT
1 GTTGCG-ATTT-ACAAATTC-GC
2961301 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
* * *
2961321 GTTGCGATTTACAGATCCGT
1 GTTGCGATTTACAAATTCGC
2961341 GTTGCGA
1 GTTGCGA
2961348 AATTGGAGTT
Statistics
Matches: 72, Mismatches: 8, Indels: 14
0.77 0.09 0.15
Matches are distributed among these distances:
18 2 0.03
19 6 0.08
20 54 0.75
21 8 0.11
22 2 0.03
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:2961345 original size:60 final size:59
Alignment explanation
Indices: 2961221--2961367 Score: 190
Period size: 60 Copynumber: 2.4 Consensus size: 59
2961211 TTGAAATTCA
*
2961221 GTTGCGAATTTGACTTATGTGTTGCGATTTACAAATTCGCATTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTT-TGTGTTGCGATTTACAAATTCGCATTGCGAATTTGACGATCGC
* *
2961281 GTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCG-ATTT-ACAGATCCGT
1 GTTGCGAATTTGACTT-TGTGTTGCGATTTACAAATTCGCATTGCGAATTTGAC-GAT-CGC
* *
2961341 GTTGCGAAATTGGAGTTTGTGTTGCGA
1 GTTGCG-AATTTGACTTTGTGTTGCGA
2961368 ATTTGTTGGT
Statistics
Matches: 78, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
58 2 0.03
59 6 0.08
60 62 0.79
61 8 0.10
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.38
Consensus pattern (59 bp):
GTTGCGAATTTGACTTTGTGTTGCGATTTACAAATTCGCATTGCGAATTTGACGATCGC
Found at i:2961699 original size:17 final size:19
Alignment explanation
Indices: 2961665--2961701 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
2961655 TTAATTAAGA
2961665 TTTACATATTTATTAAAAT
1 TTTACATATTTATTAAAAT
2961684 TTTA-ATATTT-TTAAAAT
1 TTTACATATTTATTAAAAT
2961701 T
1 T
2961702 AAATAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 6 0.33
19 4 0.22
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTACATATTTATTAAAAT
Found at i:2961710 original size:17 final size:17
Alignment explanation
Indices: 2961659--2961712 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
2961649 TTGTTTTTAA
* *
2961659 TTAAGATTTACATATTT
1 TTAAAATTTAAATATTT
*
2961676 ATTAAAATTTTAATATTT
1 -TTAAAATTTAAATATTT
2961694 TTAAAA-TTAAATAATTT
1 TTAAAATTTAAAT-ATTT
2961711 TT
1 TT
2961713 TATATTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 5 0.16
17 12 0.39
18 14 0.45
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
TTAAAATTTAAATATTT
Found at i:2964075 original size:17 final size:17
Alignment explanation
Indices: 2964053--2964116 Score: 103
Period size: 17 Copynumber: 3.8 Consensus size: 17
2964043 CTGATCGAAT
*
2964053 GAACTCGACTCTAGCTC
1 GAACTCGACTCGAGCTC
2964070 GAACTCGACTCGAGCTC
1 GAACTCGACTCGAGCTC
2964087 GAACTCGACTCGAGCTC
1 GAACTCGACTCGAGCTC
2964104 -AAGCTCGACTCGA
1 GAA-CTCGACTCGA
2964117 ATTCTTAACG
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
16 2 0.04
17 43 0.96
ACGTcount: A:0.25, C:0.34, G:0.22, T:0.19
Consensus pattern (17 bp):
GAACTCGACTCGAGCTC
Found at i:2964081 original size:11 final size:11
Alignment explanation
Indices: 2964067--2964117 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
2964057 TCGACTCTAG
2964067 CTCGAACTCGA
1 CTCGAACTCGA
*
2964078 CTCGAGCTCGAA
1 CTCGAACTCG-A
2964090 CTCG-ACTCGA
1 CTCGAACTCGA
2964100 GCTC-AAGCTCGA
1 -CTCGAA-CTCGA
2964112 CTCGAA
1 CTCGAA
2964118 TTCTTAACGA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
10 1 0.03
11 20 0.61
12 12 0.36
ACGTcount: A:0.25, C:0.35, G:0.22, T:0.18
Consensus pattern (11 bp):
CTCGAACTCGA
Found at i:2965105 original size:63 final size:60
Alignment explanation
Indices: 2965032--2965151 Score: 152
Period size: 60 Copynumber: 1.9 Consensus size: 60
2965022 ATGTATTTGC
* * *
2965032 TATCTTTTTAACTTTGAAT-ATTAAAGATAATTATATACTTTTGTATATTTTAAATTAAAATAA
1 TATCTATTTAACTTTGAATGA-TAAAG-GAATT-TAT-CTTTTGAATATTTTAAATTAAAATAA
* *
2965095 TATCTATTTAAGTTTGAATGATAAAGGAGTTTATCTTTTGAATATTTTAAATTAAAA
1 TATCTATTTAACTTTGAATGATAAAGGAATTTATCTTTTGAATATTTTAAATTAAAA
2965152 GATATTATCA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
60 22 0.43
61 3 0.06
62 3 0.06
63 22 0.43
64 1 0.02
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.47
Consensus pattern (60 bp):
TATCTATTTAACTTTGAATGATAAAGGAATTTATCTTTTGAATATTTTAAATTAAAATAA
Found at i:2968200 original size:20 final size:20
Alignment explanation
Indices: 2968171--2968220 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
2968161 GCTTAAAATG
* *
2968171 GTATCAATACCCAGGGGTCA
1 GTATCGATACCCAGAGGTCA
* *
2968191 GTATCGATACCTAGAGGTTA
1 GTATCGATACCCAGAGGTCA
*
2968211 GTACCGATAC
1 GTATCGATAC
2968221 TGAAGGCTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (20 bp):
GTATCGATACCCAGAGGTCA
Found at i:2972689 original size:15 final size:15
Alignment explanation
Indices: 2972671--2972701 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2972661 ATGACCATTC
2972671 AAATAAATGTTAGGG
1 AAATAAATGTTAGGG
2972686 AAATAAATGTTAGGG
1 AAATAAATGTTAGGG
2972701 A
1 A
2972702 CTAATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (15 bp):
AAATAAATGTTAGGG
Found at i:2972975 original size:2 final size:2
Alignment explanation
Indices: 2972970--2973017 Score: 87
Period size: 2 Copynumber: 23.5 Consensus size: 2
2972960 TTCATATGTA
2972970 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
2973012 CAT AT A
1 -AT AT A
2973018 GAATTGAGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 43 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2979244 original size:2 final size:2
Alignment explanation
Indices: 2979237--2979280 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2979227 AGTACTTGTT
2979237 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2979279 TA
1 TA
2979281 CTTCATTACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2981403 original size:25 final size:26
Alignment explanation
Indices: 2981352--2981414 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
2981342 TTTTATAAAA
*
2981352 AAATTAAAATATATTAAATTATAAGAT
1 AAATAAAAATATATTAAA-TATAAGAT
* *
2981379 AGATAAAAATATATTAAA-ATTAGAT
1 AAATAAAAATATATTAAATATAAGAT
*
2981404 AAATAATAATA
1 AAATAAAAATA
2981415 CTAATTTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 15 0.48
27 16 0.52
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (26 bp):
AAATAAAAATATATTAAATATAAGAT
Found at i:2981464 original size:19 final size:19
Alignment explanation
Indices: 2981422--2981465 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2981412 ATACTAATTT
2981422 TTTTTTGTCATTTTTCGGA
1 TTTTTTGTCATTTTTCGGA
* *
2981441 GTTTTTGT-ATTTTTTCTGA
1 TTTTTTGTCA-TTTTTCGGA
2981460 TTTTTT
1 TTTTTT
2981466 TATATTTGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.09, C:0.07, G:0.14, T:0.70
Consensus pattern (19 bp):
TTTTTTGTCATTTTTCGGA
Found at i:2984543 original size:89 final size:89
Alignment explanation
Indices: 2984433--2984671 Score: 304
Period size: 89 Copynumber: 2.7 Consensus size: 89
2984423 AATCCAAGTC
** *
2984433 TTTTAATTATTGGGTTGCCAAAAGTAAAATCAAAGGATTAGTTCCTTTTGATTATTGTGTTACCA
1 TTTTAATTATTAAGTTGCCAAAA-TAAAATCAAAGGATTAGTTCCTTTTGATTATTGGGTTACCA
2984498 AAA-CAAAATCAAAGGATTAGTTCT-
65 AAATCAAAATCAAAGGATTAGTT-TA
* * * * *
2984522 TTTTAATTATTAAGTTGCCAAAATTAAATCAAATGATTAGTTCCTTTTGATGATTGGGTTGCGAA
1 TTTTAATTATTAAGTTGCCAAAATAAAATCAAAGGATTAGTTCCTTTTGATTATTGGGTTACCAA
*
2984587 AATTAAAATCAAAGGATTAGTTTA
66 AATCAAAATCAAAGGATTAGTTTA
** * *
2984611 TTTCGATTATTGAA-TTGCGAAAATTAAAATCAAAGGATTAGTTCCTTGTGATTATTGGGTT
1 TTTTAATTATT-AAGTTGCCAAAA-TAAAATCAAAGGATTAGTTCCTTTTGATTATTGGGTT
2984672 GGTAAAATTA
Statistics
Matches: 130, Mismatches: 16, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
88 39 0.30
89 56 0.43
90 35 0.27
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (89 bp):
TTTTAATTATTAAGTTGCCAAAATAAAATCAAAGGATTAGTTCCTTTTGATTATTGGGTTACCAA
AATCAAAATCAAAGGATTAGTTTA
Found at i:2984679 original size:45 final size:45
Alignment explanation
Indices: 2984432--2984683 Score: 301
Period size: 45 Copynumber: 5.6 Consensus size: 45
2984422 TAATCCAAGT
* *
2984432 CTTTTAATTATTGGGTTGCCAAAAGTAAAATCAAAGGATTAGTTC
1 CTTTTGATTATTGGGTTGCCAAAATTAAAATCAAAGGATTAGTTC
* * *
2984477 CTTTTGATTATTGTGTTACCAAAA-CAAAATCAAAGGATTAGTTC
1 CTTTTGATTATTGGGTTGCCAAAATTAAAATCAAAGGATTAGTTC
* * ** *
2984521 TTTTTAATTATTAAGTTGCCAAAATT-AAATCAAATGATTAGTTC
1 CTTTTGATTATTGGGTTGCCAAAATTAAAATCAAAGGATTAGTTC
* * *
2984565 CTTTTGATGATTGGGTTGCGAAAATTAAAATCAAAGGATTAGTTT
1 CTTTTGATTATTGGGTTGCCAAAATTAAAATCAAAGGATTAGTTC
* * ** *
2984610 ATTTCGATTATTGAATTGCGAAAATTAAAATCAAAGGATTAGTTC
1 CTTTTGATTATTGGGTTGCCAAAATTAAAATCAAAGGATTAGTTC
* **
2984655 CTTGTGATTATTGGGTTGGTAAAATTAAA
1 CTTTTGATTATTGGGTTGCCAAAATTAAA
2984684 GAATTAATTC
Statistics
Matches: 173, Mismatches: 32, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
44 75 0.43
45 98 0.57
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (45 bp):
CTTTTGATTATTGGGTTGCCAAAATTAAAATCAAAGGATTAGTTC
Found at i:2984859 original size:61 final size:58
Alignment explanation
Indices: 2984787--2984942 Score: 163
Period size: 58 Copynumber: 2.7 Consensus size: 58
2984777 ACAGAATATA
* ** *
2984787 AAGG-AAATAAATCACTGGATTTATTTCATCATT-AGAATCTTGTGTTGATTCTAGCTTTGT
1 AAGGAAAATAAATCACTGAATTTATTTC--C-TTGAGAATCTTG-AATGATTCTAACTTTGT
***
2984847 AAGGAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTTGT
1 AAGGAAAATAAATCACTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTTGT
*** *
2984905 AAGGAAAATAAATTGTTGAATTTATTTCTTTGAGAATC
1 AAGGAAAATAAATCACTGAATTTATTTCCTTGAGAATC
2984943 ATTCAAATAA
Statistics
Matches: 86, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
58 53 0.62
59 10 0.12
60 4 0.05
61 19 0.22
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (58 bp):
AAGGAAAATAAATCACTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTTGT
Found at i:2984907 original size:58 final size:58
Alignment explanation
Indices: 2984832--2984942 Score: 204
Period size: 58 Copynumber: 1.9 Consensus size: 58
2984822 AATCTTGTGT
*
2984832 TGATTCTAGCTTTGTAAGGAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTTGAA
1 TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTTGAA
*
2984890 TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTTCTTTGAGAATC
1 TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTTCCTTGAGAATC
2984943 ATTCAAATAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.42
Consensus pattern (58 bp):
TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTTGAA
Found at i:2985022 original size:58 final size:57
Alignment explanation
Indices: 2984947--2985100 Score: 202
Period size: 58 Copynumber: 2.7 Consensus size: 57
2984937 AGAATCATTC
* *
2984947 AAATAAATTGTTGAATTTATTTCCATGAGAATCTTGAATGATTCTATATT-TTAAGAAG
1 AAATAAATTGTTAAATTTATTT-CTTGAGAATCTTGAATGATTCTATATTGTTAA-AAG
* * * *
2985005 AAATAAATTATTAAATTTATTTTCTTGAGAATCTTAAATGATTCTATTTTGTTAAAGG
1 AAATAAATTGTTAAATTTA-TTTCTTGAGAATCTTGAATGATTCTATATTGTTAAAAG
* *
2985063 AAATAAATTGTTAAATCTATTTCTTGAAAATCTTGAAT
1 AAATAAATTGTTAAATTTATTTCTTGAGAATCTTGAAT
2985101 AAAGAAATAA
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
57 17 0.20
58 60 0.71
59 7 0.08
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (57 bp):
AAATAAATTGTTAAATTTATTTCTTGAGAATCTTGAATGATTCTATATTGTTAAAAG
Found at i:2985022 original size:95 final size:95
Alignment explanation
Indices: 2984852--2985037 Score: 288
Period size: 95 Copynumber: 2.0 Consensus size: 95
2984842 TTTGTAAGGA
* *
2984852 AAATAAATTGTTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTTGTAAGGAAAATAAA
1 AAATAAATTGTTGAATTTATTTCCATGAGAATCTTGAATGATTCTAACTTTGTAAGAAAAATAAA
* *
2984917 TTGTTGAATTTA-TTTCTTTGAGAATCATTC
66 TTATTAAATTTATTTTC-TTGAGAATCATTC
2984947 AAATAAATTGTTGAATTTATTTCCATGAGAATCTTGAATGATTCTATA-TTT-TAAGAAGAAATA
1 AAATAAATTGTTGAATTTATTTCCATGAGAATCTTGAATGATTCTA-ACTTTGTAAGAA-AAATA
2985010 AATTATTAAATTTATTTTCTTGAGAATC
64 AATTATTAAATTTATTTTCTTGAGAATC
2985038 TTAAATGATT
Statistics
Matches: 84, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
94 5 0.06
95 74 0.88
96 5 0.06
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (95 bp):
AAATAAATTGTTGAATTTATTTCCATGAGAATCTTGAATGATTCTAACTTTGTAAGAAAAATAAA
TTATTAAATTTATTTTCTTGAGAATCATTC
Found at i:2985108 original size:42 final size:44
Alignment explanation
Indices: 2985057--2985145 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 44
2985047 TCTATTTTGT
2985057 TAAAGGAAATAAATTGTTAAATCTA-TTTCTTGAAAATCTTGAA
1 TAAAGGAAATAAATTGTTAAATCTATTTTCTTGAAAATCTTGAA
* * ** *
2985100 TAAA-GAAATAAATTGTTGAATTTATTTTCTTGTGAATCTTTAA
1 TAAAGGAAATAAATTGTTAAATCTATTTTCTTGAAAATCTTGAA
2985143 TAA
1 TAA
2985146 TTCTATCTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 18 0.45
43 22 0.55
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.42
Consensus pattern (44 bp):
TAAAGGAAATAAATTGTTAAATCTATTTTCTTGAAAATCTTGAA
Found at i:2985122 original size:100 final size:96
Alignment explanation
Indices: 2985002--2985625 Score: 269
Period size: 97 Copynumber: 6.5 Consensus size: 96
2984992 ATATTTTAAG
* * * *
2985002 AAGAAATAAATTATTAAATTTATTTTCTTGAGAATCTTAAATGATTCTATTTTGTTAAAGGAAAT
1 AAGAAATAAATTGTTGAATTTATTTTCTTGAGAATCTTAAATGATTCTATCTT-TAAAAGGAAAT
* *
2985067 AAATTGTTAAATCTATTTCTTGAAAATCTTG-AATA
65 AAATCGATAAATCTA-TT-TT-AAAATCTTGTAA-A
* * * * *
2985102 AAGAAATAAATTGTTGAATTTATTTTCTTGTGAATCTTTAATAATTCTATCTTTAAAATGAATTA
1 AAGAAATAAATTGTTGAATTTATTTTCTTGAGAATCTTAAATGATTCTATCTTTAAAAGGAAATA
* * ** *
2985167 AATCGATGAATTTATTTTCCAATTTTGTAAA
66 AATCGATAAATCTATTTTAAAATCTTGTAAA
* * * * * *
2985198 AGGAAATAAATTGTTGAATTTATTTTCTTAAGAATCTTATATGATTCTGATATGTAAAAAGAAAA
1 AAGAAATAAATTGTTGAATTTATTTTCTTGAGAATCTTAAATGATTCT-ATCT-TTAAAAGGAAA
* ** *** *
2985263 AAAATTTAT-AAT-TAGTTTTCCTATTTTGTAAA
64 TAAATCGATAAATCTA-TTTTAAAATCTTGTAAA
* * * * * * *** * * * * ** *
2985295 ATGAAATAGATCGTTGGATTTAGTTTCCT-ATTTTGTAAAAGGAAATAAATC---AAAA-CAAAT
1 AAGAAATAAATTGTTGAATTTATTTTCTTGAGAATCTTAAATG-ATTCTATCTTTAAAAGGAAAT
* ** * **** *
2985355 ---T-GTTGGATTTATTTTCCTTTTTTGTAAA
65 AAATCGATAAATCTATTTTAAAATCTTGTAAA
* * * * * *
2985383 AGGAAATAAATTGTTTAATTTATTTT-TCTGAGAATCTTAAACGATTATGGT-TTGTAAAATGAA
1 AAGAAATAAATTGTTGAATTTATTTTCT-TGAGAATCTTAAATGATTCT-ATCTT-TAAAAGGAA
** * *** *
2985446 ATAAATC-ATTGGATTTATTTTCCTATTTTGTAAA
63 ATAAATCGA-TAAATCTATTTTAAAATCTTGTAAA
* * *
2985480 AGGAAATAAATTGTTGAATTTAATTTCTTGAGAATCTTAAATGATTCTGGT-TTGTAAAAGGAAA
1 AAGAAATAAATTGTTGAATTTATTTTCTTGAGAATCTTAAATGATTCT-ATCTT-TAAAAGGAAA
* * *** *
2985544 TAAATC-ATTAGATTTATTTTCCTAT-TTTTAAA
64 TAAATCGA-TAAATCTATTTTAAAATCTTGTAAA
*
2985576 AAGAAATAAATTGTTGAATCTATTTT-TCTGAGAATCTTAAATGATTCTAT
1 AAGAAATAAATTGTTGAATTTATTTTCT-TGAGAATCTTAAATGATTCTAT
2985626 TTTGTAAGGG
Statistics
Matches: 418, Mismatches: 84, Indels: 49
0.76 0.15 0.09
Matches are distributed among these distances:
87 1 0.00
88 43 0.10
89 10 0.02
91 3 0.01
92 8 0.02
93 4 0.01
95 2 0.00
96 109 0.26
97 156 0.37
98 16 0.04
99 19 0.05
100 47 0.11
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (96 bp):
AAGAAATAAATTGTTGAATTTATTTTCTTGAGAATCTTAAATGATTCTATCTTTAAAAGGAAATA
AATCGATAAATCTATTTTAAAATCTTGTAAA
Found at i:2985641 original size:96 final size:97
Alignment explanation
Indices: 2985357--2985674 Score: 453
Period size: 97 Copynumber: 3.3 Consensus size: 97
2985347 AAACAAATTG
* *
2985357 TTGGATTTATTTTCCTTTTTTGTAAAAGGAAATAAATTGTTTAATTTATTTTTCTGAGAATCTTA
1 TTGGATTTATTTTCCTATTTTGTAAAAGGAAATAAATTGTTGAATTTATTTTTCTGAGAATCTTA
* * *
2985422 AACGATTATGGTTTGTAAAATGAAATAAATCA
66 AATGATTCTGGTTTGTAAAAGGAAATAAATCA
*
2985454 TTGGATTTATTTTCCTATTTTGTAAAAGGAAATAAATTGTTGAATTTA-ATTTCTTGAGAATCTT
1 TTGGATTTATTTTCCTATTTTGTAAAAGGAAATAAATTGTTGAATTTATTTTTC-TGAGAATCTT
2985518 AAATGATTCTGGTTTGTAAAAGGAAATAAATCA
65 AAATGATTCTGGTTTGTAAAAGGAAATAAATCA
* * *
2985551 TTAGATTTATTTTCCTATTTT-TAAAAAGAAATAAATTGTTGAATCTATTTTTCTGAGAATCTTA
1 TTGGATTTATTTTCCTATTTTGTAAAAGGAAATAAATTGTTGAATTTATTTTTCTGAGAATCTTA
** *
2985615 AATGATTCTATTTTGT-AAGGGAAAATAAATCA
66 AATGATTCTGGTTTGTAAAAGG-AAATAAATCA
* **
2985647 TTGGGTTTATTTTTATATTTTTGTAAAA
1 TTGGATTTATTTTCCTA-TTTTGTAAAA
2985675 TAAAATATAT
Statistics
Matches: 199, Mismatches: 17, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
95 4 0.02
96 76 0.38
97 114 0.57
98 5 0.03
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.45
Consensus pattern (97 bp):
TTGGATTTATTTTCCTATTTTGTAAAAGGAAATAAATTGTTGAATTTATTTTTCTGAGAATCTTA
AATGATTCTGGTTTGTAAAAGGAAATAAATCA
Found at i:2985680 original size:40 final size:39
Alignment explanation
Indices: 2985623--2985722 Score: 101
Period size: 40 Copynumber: 2.5 Consensus size: 39
2985613 TAAATGATTC
** * * *
2985623 TATTTTGTAAGGGAAAATAAATCATTGGGTTTATTTTTA
1 TATTTTGTAAAAGAAAATAAATCATTAGATTTATTTTCA
* * * *
2985662 TATTTTTGTAAAATAAAATATATCGTTAGATTTATTTTCC
1 TA-TTTTGTAAAAGAAAATAAATCATTAGATTTATTTTCA
*
2985702 TATTTTGTAAAAGGAAATAAA
1 TATTTTGTAAAAGAAAATAAA
2985723 CTGTTGGATC
Statistics
Matches: 48, Mismatches: 12, Indels: 2
0.77 0.19 0.03
Matches are distributed among these distances:
39 18 0.38
40 30 0.62
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45
Consensus pattern (39 bp):
TATTTTGTAAAAGAAAATAAATCATTAGATTTATTTTCA
Found at i:2988374 original size:11 final size:12
Alignment explanation
Indices: 2988344--2988397 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
2988334 ATTATTTAAA
2988344 CGGGTATTGGGC
1 CGGGTATTGGGC
*
2988356 CGGGTATTGGGT
1 CGGGTATTGGGC
2988368 C-GGTATTGGGC
1 CGGGTATTGGGC
* *
2988379 CGGGAATCGGGC
1 CGGGTATTGGGC
2988391 CGGGTAT
1 CGGGTAT
2988398 ATATATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
11 10 0.28
12 26 0.72
ACGTcount: A:0.11, C:0.17, G:0.48, T:0.24
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:2988455 original size:24 final size:25
Alignment explanation
Indices: 2988395--2988455 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
2988385 TCGGGCCGGG
2988395 TATATA-TATA-TATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
*
2988418 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
2988442 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
2988456 ATATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 8 0.25
24 20 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:2990051 original size:5 final size:5
Alignment explanation
Indices: 2990041--2990070 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
2990031 ATTATTATTA
*
2990041 TTTTC TTTTC TTTTA TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
2990071 GAATTTGATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:2990056 original size:15 final size:15
Alignment explanation
Indices: 2990038--2990069 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2990028 ATTATTATTA
2990038 TTATTTTCTTTTCTT
1 TTATTTTCTTTTCTT
2990053 TTATTTTCTTTTCTT
1 TTATTTTCTTTTCTT
2990068 TT
1 TT
2990070 CGAATTTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.81
Consensus pattern (15 bp):
TTATTTTCTTTTCTT
Found at i:2990907 original size:20 final size:21
Alignment explanation
Indices: 2990882--2990933 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2990872 TTTTCCCAAT
*
2990882 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
2990902 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2990923 TCGCAATGCGA
1 TCGCAATGCGA
2990934 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2990947 original size:20 final size:20
Alignment explanation
Indices: 2990922--2991056 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
2990912 AATTGGGAAA
2990922 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
2990942 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
2990962 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
2990983 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
2991003 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
2991023 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
2991043 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
2991057 TTTCAAAGCG
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 4 0.04
20 66 0.69
21 24 0.25
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:2990966 original size:61 final size:61
Alignment explanation
Indices: 2990919--2991050 Score: 183
Period size: 61 Copynumber: 2.2 Consensus size: 61
2990909 GCGAATTGGG
* * * * *
2990919 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
2990980 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
2991041 ATAATCGCAA
1 AAAATCGCAA
2991051 TGCGATTTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:2991252 original size:22 final size:22
Alignment explanation
Indices: 2991224--2991267 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2991214 CACTCTCTCA
2991224 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
2991246 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
2991268 TATCTCCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:2991574 original size:20 final size:20
Alignment explanation
Indices: 2991551--2991589 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2991541 TCAAATTTGC
2991551 GTTGCGATAGTCATTTTCAT
1 GTTGCGATAGTCATTTTCAT
**
2991571 GTTGCGATTTTCATTTTCA
1 GTTGCGATAGTCATTTTCA
2991590 GAAACTATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.15, G:0.18, T:0.49
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCAT
Found at i:2991779 original size:25 final size:24
Alignment explanation
Indices: 2991725--2991779 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
2991715 TGTTTATTAT
* *
2991725 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
2991749 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
2991775 TGTTT
1 TGTTT
2991780 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:2992929 original size:18 final size:18
Alignment explanation
Indices: 2992908--2992952 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2992898 TCCACTTCGG
*
2992908 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
2992926 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
2992944 GAGCCATCA
1 GAGCCATCA
2992953 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2993489 original size:19 final size:20
Alignment explanation
Indices: 2993435--2993501 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
2993425 TAGTTTACTT
* *
2993435 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
2993455 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
2993475 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
2993494 TCGCAACG
1 TCGCAACG
2993502 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:2993509 original size:14 final size:14
Alignment explanation
Indices: 2993490--2993546 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2993480 ATGCGAAATG
2993490 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2993504 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
2993523 AAAATCGCAACGAC
1 AAAATCGCAACGAC
2993537 AAAATCGCAA
1 AAAATCGCAA
2993547 AGCGAAATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.51, C:0.23, G:0.16, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2993516 original size:33 final size:33
Alignment explanation
Indices: 2993474--2993565 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
2993464 GGAAATGGCT
2993474 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2993507 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
2993540 ATCGCAAAGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
2993566 TGCGATTTGT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2993528 original size:19 final size:19
Alignment explanation
Indices: 2993474--2993570 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
2993464 GGAAATGGCT
2993474 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2993493 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
2993507 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2993526 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
2993540 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2993559 ATCGCAATGCGA
1 ATCGCAATGCGA
2993571 TTTGTGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2993642 original size:50 final size:51
Alignment explanation
Indices: 2993577--2993673 Score: 160
Period size: 50 Copynumber: 1.9 Consensus size: 51
2993567 GCGATTTGTG
* * *
2993577 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCATTTCGCGTTGCGATTTCA
1 TTTCGCATTACGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGATTTCA
2993627 TTTCGCATTACGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TTTCGCATTACGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGAT
2993674 AGCCATTTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
50 25 0.58
51 18 0.42
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (51 bp):
TTTCGCATTACGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGATTTCA
Found at i:2993692 original size:20 final size:20
Alignment explanation
Indices: 2993658--2993713 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
2993648 TTGCGATTTT
*
2993658 CATTTC-GCATTGCGATAGC
1 CATTTCTGCGTTGCGATAGC
*
2993677 CATTTCTGCGTTGCGATAGT
1 CATTTCTGCGTTGCGATAGC
2993697 CATTT-TCGCGTTGCGAT
1 CATTTCT-GCGTTGCGAT
2993714 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 7 0.21
20 26 0.79
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (20 bp):
CATTTCTGCGTTGCGATAGC
Found at i:2995603 original size:14 final size:14
Alignment explanation
Indices: 2995584--2995619 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2995574 ATTGTTTAAT
2995584 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2995598 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2995612 TGATTTGT
1 TGATTTGT
2995620 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2995743 original size:14 final size:14
Alignment explanation
Indices: 2995726--2995779 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
2995716 AAAAGAGACT
2995726 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
2995740 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
2995759 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
*
2995773 ATTGCAA
1 ATCGCAA
2995780 TGCGATTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 17 0.50
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.32
ACGTcount: A:0.48, C:0.19, G:0.20, T:0.13
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:2995772 original size:19 final size:19
Alignment explanation
Indices: 2995736--2995772 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2995726 ATCGCAACGA
* *
2995736 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAACGAGAAAT
2995755 GAAAATCGCAACGAGAAA
1 GAAAATCGCAACGAGAAA
2995773 ATTGCAATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.16, G:0.22, T:0.11
Consensus pattern (19 bp):
GAAAATCGCAACGAGAAAT
Found at i:2995828 original size:20 final size:20
Alignment explanation
Indices: 2995811--2995898 Score: 97
Period size: 20 Copynumber: 4.4 Consensus size: 20
2995801 TGATTTTCTA
2995811 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
*** *
2995831 GTTGCGATTTTTCA-TTTCGA
1 GTTGCGA-TAGCCATTTTCGC
* * *
2995851 ATTGCGATAGCTAGTTTCGC
1 GTTGCGATAGCCATTTTCGC
2995871 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
2995891 GTTGCGAT
1 GTTGCGAT
2995899 TTCCCCGTTG
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
19 2 0.04
20 48 0.91
21 3 0.06
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:2996137 original size:20 final size:20
Alignment explanation
Indices: 2996112--2996161 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
2996102 TTGAAGATGA
2996112 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
2996132 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
2996152 TTGCGATTTT
1 TTGCGATTTT
2996162 GTATTATCTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:2996218 original size:21 final size:20
Alignment explanation
Indices: 2996192--2996239 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2996182 TCAGTATCGT
*
2996192 ATTGCGATTTTCCAAATTCGC
1 ATTGCGA-TTTACAAATTCGC
**
2996213 ATTGCGATTTACTTATTCGC
1 ATTGCGATTTACAAATTCGC
2996233 ATTGCGA
1 ATTGCGA
2996240 ATTAGGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.40
Consensus pattern (20 bp):
ATTGCGATTTACAAATTCGC
Found at i:2997039 original size:24 final size:24
Alignment explanation
Indices: 2997012--2997065 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2997002 GTATTCGAAA
*
2997012 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
2997036 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
2997060 TTTGAT
1 TTTGAT
2997066 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:2997257 original size:12 final size:12
Alignment explanation
Indices: 2997240--2997276 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
2997230 ATATAATCCT
2997240 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2997252 GAAGAAGAAAAA
1 GAAGAAGAAAAA
*
2997264 GAAGAATAAAAA
1 GAAGAAGAAAAA
2997276 G
1 G
2997277 TCCCCGAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2999590 original size:19 final size:19
Alignment explanation
Indices: 2999568--2999698 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
2999558 GGAAATTACT
2999568 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2999587 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2999601 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
2999620 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
2999634 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
2999653 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
2999667 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2999686 ATCGCAACGCGAA
1 ATCGCAATGCGAA
2999699 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2999610 original size:33 final size:33
Alignment explanation
Indices: 2999568--2999694 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
2999558 GGAAATTACT
2999568 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
2999601 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
2999633 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
2999667 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
2999695 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2999675 original size:66 final size:66
Alignment explanation
Indices: 2999569--2999701 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
2999559 GAAATTACTA
*
2999569 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
2999634 T
66 T
*
2999635 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
2999700 T
66 T
2999701 T
1 T
2999702 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:2999745 original size:33 final size:33
Alignment explanation
Indices: 2999694--2999772 Score: 131
Period size: 33 Copynumber: 2.4 Consensus size: 33
2999684 AAATCGCAAC
* *
2999694 GCGAATTTAATTTCGCGTTACGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTACGATTCTCTCGTT
*
2999727 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTACGATTCTCTCGTT
2999760 GCGATTTTCATTT
1 GCGATTTTCATTT
2999773 TGCATTGCGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTACGATTCTCTCGTT
Found at i:2999747 original size:19 final size:19
Alignment explanation
Indices: 2999723--2999783 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
2999713 ACGATTCTCT
2999723 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
2999742 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
2999756 CGTTGCGATTTTCATTTTG
1 CGTTGCGATTTTCATTTCG
*
2999775 CATTGCGAT
1 CGTTGCGAT
2999784 AGTACTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 10 0.30
16 3 0.09
17 3 0.09
19 17 0.52
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:2999761 original size:14 final size:14
Alignment explanation
Indices: 2999709--2999765 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2999699 TTTAATTTCG
*
2999709 CGTTACGATTCTCT
1 CGTTGCGATTCTCT
*
2999723 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2999742 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2999756 CGTTGCGATT
1 CGTTGCGATT
2999766 TTCATTTTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2999781 original size:33 final size:33
Alignment explanation
Indices: 2999694--2999783 Score: 126
Period size: 33 Copynumber: 2.7 Consensus size: 33
2999684 AAATCGCAAC
* * * *
2999694 GCGAATTTAATTTCGCGTTACGATTCTCTCGTT
1 GCGATTTTCATTTCGCATTGCGATTCTCTCGTT
*
2999727 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCATTGCGATTCTCTCGTT
*
2999760 GCGATTTTCATTTTGCATTGCGAT
1 GCGATTTTCATTTCGCATTGCGAT
2999784 AGTACTTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.44
Consensus pattern (33 bp):
GCGATTTTCATTTCGCATTGCGATTCTCTCGTT
Found at i:2999909 original size:14 final size:14
Alignment explanation
Indices: 2999890--2999926 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2999880 CATCAATTAA
2999890 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2999904 ACAAATCACCTTTT
1 ACAAATCAACTTTT
2999918 ACAAATCAA
1 ACAAATCAA
2999927 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3001368 original size:42 final size:42
Alignment explanation
Indices: 3001322--3001401 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
3001312 CGATGACAGT
* *
3001322 GGCCTCTTGAACGGTAGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
3001364 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
3001402 CAGGCGAGTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:3001797 original size:91 final size:90
Alignment explanation
Indices: 3001623--3001807 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
3001613 ATTTCAAACT
*
3001623 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
3001688 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
3001716 TTCAACCAAAAGACAAAACAAAAAGACAAATGCTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
3001780 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
3001807 T
1 T
3001808 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 42 0.48
93 19 0.22
95 26 0.30
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:3003539 original size:20 final size:19
Alignment explanation
Indices: 3003494--3003639 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
3003484 TCTTTTGGTT
*
3003494 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
3003513 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
3003533 GGAAATGACTATCACAA--C
1 -GAAATGAAAATCGCAACGC
*
3003551 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
3003567 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
3003584 --AA-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
3003600 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
3003619 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
3003638 GA
1 GA
3003640 TTTTGGTTTC
Statistics
Matches: 101, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
14 17 0.17
15 3 0.03
16 3 0.03
17 2 0.02
18 4 0.04
19 44 0.44
20 26 0.26
21 2 0.02
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:3003613 original size:33 final size:33
Alignment explanation
Indices: 3003519--3003616 Score: 151
Period size: 33 Copynumber: 2.9 Consensus size: 33
3003509 ACGAGATAAT
* *
3003519 GAGAATCGCAACGCGGAAATGACTATCACAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACAA
3003553 GAGAATCGCAACGCGAAATGACTATCGCAACAA
1 GAGAATCGCAACGCGAAATGACTATCGCAACAA
**
3003586 GAGAATCGCAACGCGAAATGAAAATCGCAAC
1 GAGAATCGCAACGCGAAATGACTATCGCAAC
3003617 GCGAAATGAA
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 46 0.77
34 14 0.23
ACGTcount: A:0.43, C:0.23, G:0.22, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACAA
Found at i:3003668 original size:19 final size:18
Alignment explanation
Indices: 3003635--3003701 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 18
3003625 AAAATCGCAA
* *
3003635 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-ATTTCACGT
3003654 TGCGATTTTAATTTCACGT
1 TGCGATTTT-ATTTCACGT
*
3003673 TGCGATAGTTATTTCCACGT
1 TGCGAT-TTTATTT-CACGT
3003693 TGCGATTTT
1 TGCGATTTT
3003702 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 28 0.68
20 13 0.32
ACGTcount: A:0.15, C:0.16, G:0.22, T:0.46
Consensus pattern (18 bp):
TGCGATTTTATTTCACGT
Found at i:3004244 original size:20 final size:20
Alignment explanation
Indices: 3004219--3004271 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
3004209 GAGCTATGTA
3004219 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
3004239 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
3004259 TATCTCGTTGCGA
1 AATCGCGTTGCGA
3004272 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:3004305 original size:20 final size:20
Alignment explanation
Indices: 3004280--3004333 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
3004270 GATTTTGTAT
3004280 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
3004300 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
3004320 TATCGCATTGCGAT
1 TATCGCATTGCGAT
3004334 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:3004318 original size:61 final size:61
Alignment explanation
Indices: 3004220--3004336 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
3004210 AGCTATGTAA
* * * * *
3004220 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
3004281 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
3004337 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:3004352 original size:61 final size:61
Alignment explanation
Indices: 3004220--3004354 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
3004210 AGCTATGTAA
* * * * * ** *
3004220 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
3004281 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
3004343 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
3004355 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:3004444 original size:21 final size:21
Alignment explanation
Indices: 3004404--3004444 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3004394 ACTGTAGACC
** *
3004404 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
3004425 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
3004445 GCGAATTTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:3007395 original size:14 final size:14
Alignment explanation
Indices: 3007376--3007402 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3007366 CTTGTTTGAA
3007376 TTTGTTTTTCTTTC
1 TTTGTTTTTCTTTC
3007390 TTTGTTTTTCTTT
1 TTTGTTTTTCTTT
3007403 TAAAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.11, G:0.07, T:0.81
Consensus pattern (14 bp):
TTTGTTTTTCTTTC
Found at i:3009574 original size:16 final size:16
Alignment explanation
Indices: 3009549--3009594 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
3009539 TTTCAGATTC
3009549 AGATTCCAATTCCTTT
1 AGATTCCAATTCCTTT
* *
3009565 AGATTTCAATTCCTTCAC
1 AGATTCCAATTCCTT--T
3009583 AGATTCCAATTC
1 AGATTCCAATTC
3009595 TCTCATAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
18 11 0.44
ACGTcount: A:0.28, C:0.26, G:0.07, T:0.39
Consensus pattern (16 bp):
AGATTCCAATTCCTTT
Found at i:3009701 original size:72 final size:72
Alignment explanation
Indices: 3009615--3009759 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
3009605 ATTCCCGCGA
3009615 ACCAAACGCCACCTTAATGTATTTCATGTTGTTCAAATTCAGTTGTTTGAAAAGGAGAAATTATT
1 ACCAAACGCCACCTTAATGTATTTCATGTTGTTCAAATTCAGTTGTTTGAAAAGGAGAAATTATT
3009680 AATTTAC
66 AATTTAC
3009687 ACCAAACGCCACCTTAATGTATTTCATGTTGTTCAAATTCAGTTGTTTGAAAAGGAGAAATTATT
1 ACCAAACGCCACCTTAATGTATTTCATGTTGTTCAAATTCAGTTGTTTGAAAAGGAGAAATTATT
3009752 AATTTAC
66 AATTTAC
3009759 A
1 A
3009760 TGAACCCTTT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (72 bp):
ACCAAACGCCACCTTAATGTATTTCATGTTGTTCAAATTCAGTTGTTTGAAAAGGAGAAATTATT
AATTTAC
Found at i:3010457 original size:109 final size:111
Alignment explanation
Indices: 3010266--3010483 Score: 280
Period size: 109 Copynumber: 2.0 Consensus size: 111
3010256 CTTAAGATGA
* *
3010266 ATTATAATGGTGAACCAAAGAAATAACATAGCAAAAACATGGAGATTTAATGCTTAAGATTGGGT
1 ATTATAATGGTGAACCAAAGAAAGAACATAGCAAAAACATGGAGATTTAATGCTTAAGATTGGGG
* *
3010331 AATAAAAAGATGAGATAAAGAAGAAG-TTATGATTTT-TAATTTAG
66 AAGAAAAAGATGAGATAAAGAAGAAGATGATGATTTTGTAATTTAG
* ** ** *
3010375 ATTATAATGGTGGATTAAAGAAAGAGTATAGC-AAAACATGGAGATTTGATGCTTTAAGATTGGG
1 ATTATAATGGTGAACCAAAGAAAGAACATAGCAAAAACATGGAGATTTAATGC-TTAAGATTGGG
* * * *
3010439 GAAGGAGAGGATGAGATAAAGAAGAAGATGGTGATTTTGTAATTT
65 GAAGAAAAAGATGAGATAAAGAAGAAGATGATGATTTTGTAATTT
3010484 TAATTTTTAA
Statistics
Matches: 92, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
108 19 0.21
109 59 0.64
110 8 0.09
111 6 0.07
ACGTcount: A:0.43, C:0.04, G:0.24, T:0.28
Consensus pattern (111 bp):
ATTATAATGGTGAACCAAAGAAAGAACATAGCAAAAACATGGAGATTTAATGCTTAAGATTGGGG
AAGAAAAAGATGAGATAAAGAAGAAGATGATGATTTTGTAATTTAG
Found at i:3017914 original size:23 final size:23
Alignment explanation
Indices: 3017888--3017987 Score: 98
Period size: 23 Copynumber: 4.3 Consensus size: 23
3017878 TTCTACGCGA
3017888 TCCTTCGGGACAATTCTATGTGG
1 TCCTTCGGGACAATTCTATGTGG
* * * *
3017911 TCCTTCGAGACATTTCTACGCGG
1 TCCTTCGGGACAATTCTATGTGG
* *
3017934 TCCTTCGAGA-TATATCTATGTGG
1 TCCTTCGGGACAAT-TCTATGTGG
3017957 TCCTTCGGGAC-ATTCCTATGTGG
1 TCCTTCGGGACAATT-CTATGTGG
3017980 -CACTTCGG
1 TC-CTTCGG
3017988 TGCATATTCT
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
22 3 0.05
23 61 0.95
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.34
Consensus pattern (23 bp):
TCCTTCGGGACAATTCTATGTGG
Found at i:3017938 original size:46 final size:46
Alignment explanation
Indices: 3017878--3017970 Score: 134
Period size: 46 Copynumber: 2.0 Consensus size: 46
3017868 GAGTCGAGGG
*
3017878 TTCTACGCGATCCTTCGGGACAAT-TCTATGTGGTCCTTCGAGACAT
1 TTCTACGCGATCCTTCGAGA-AATATCTATGTGGTCCTTCGAGACAT
* * *
3017924 TTCTACGCGGTCCTTCGAGATATATCTATGTGGTCCTTCGGGACAT
1 TTCTACGCGATCCTTCGAGAAATATCTATGTGGTCCTTCGAGACAT
3017970 T
1 T
3017971 CCTATGTGGC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 2 0.05
46 40 0.95
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (46 bp):
TTCTACGCGATCCTTCGAGAAATATCTATGTGGTCCTTCGAGACAT
Found at i:3020333 original size:19 final size:20
Alignment explanation
Indices: 3020309--3020350 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3020299 TTCGATTAAA
*
3020309 TTAAATTACA-TTAAAAATT
1 TTAAATTAAATTTAAAAATT
*
3020328 TTAAATTAAATTTATAAATT
1 TTAAATTAAATTTAAAAATT
3020348 TTA
1 TTA
3020351 TTGTTAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TTAAATTAAATTTAAAAATT
Found at i:3022017 original size:31 final size:31
Alignment explanation
Indices: 3021967--3022052 Score: 91
Period size: 31 Copynumber: 2.8 Consensus size: 31
3021957 GATGGTGTAT
* * *
3021967 TACATGTTACATATTTAAAGTGATGACATGA
1 TACATGTCACATGTCTAAAGTGATGACATGA
** * **
3021998 TATGTGTCATATGTCTAAAGTGATGATGTGA
1 TACATGTCACATGTCTAAAGTGATGACATGA
*
3022029 TACATGTCACATGTCCAAAGTGAT
1 TACATGTCACATGTCTAAAGTGAT
3022053 TATATGACAT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.35
Consensus pattern (31 bp):
TACATGTCACATGTCTAAAGTGATGACATGA
Found at i:3025108 original size:21 final size:20
Alignment explanation
Indices: 3025061--3025115 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
3025051 GATTCTTGAC
3025061 AATCGCAATGCGATAGTACA
1 AATCGCAATGCGATAGTACA
* * *
3025081 AATTCGCATTGCGATATTCCA
1 AA-TCGCAATGCGATAGTACA
*
3025102 GAATCGCAACGCGA
1 -AATCGCAATGCGA
3025116 ACACATAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (20 bp):
AATCGCAATGCGATAGTACA
Found at i:3025128 original size:20 final size:20
Alignment explanation
Indices: 3025103--3025275 Score: 127
Period size: 20 Copynumber: 8.6 Consensus size: 20
3025093 GATATTCCAG
3025103 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTAAC-CATA
* *
3025123 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTAACCATA
* * *
3025143 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTAACCATA
* * *
3025163 AATCACAACGCGTATCCGTA
1 AATCGCAACGCGTAACCATA
* * *
3025183 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTAACCATA
* * *
3025203 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTAACCATA
* *
3025223 AATCGCAACGAC--AATACGTAA
1 AATCGCAACG-CGTAA-CCAT-A
* *
3025244 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTAACCATA
3025264 AATCGCAACGCG
1 AATCGCAACGCG
3025276 ATTTTTAAAG
Statistics
Matches: 133, Mismatches: 14, Indels: 12
0.84 0.09 0.08
Matches are distributed among these distances:
19 1 0.01
20 114 0.86
21 17 0.13
22 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTAACCATA
Found at i:3025150 original size:40 final size:39
Alignment explanation
Indices: 3025103--3025276 Score: 215
Period size: 40 Copynumber: 4.3 Consensus size: 39
3025093 GATATTCCAG
*
3025103 AATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAAC-CGTAAATCGCAACGCGTATCCGTA
* * *
3025143 AATCGCAACGTGTATCCGTAAATCACAACGCGTATCCGTA
1 AATCGCAACGCG-AACCGTAAATCGCAACGCGTATCCGTA
* * *
3025183 AATCGCAATGCGTATCCGTATATCGCAACGCGTATCCGTA
1 AATCGCAACGCG-AACCGTAAATCGCAACGCGTATCCGTA
*
3025223 AATCGCAACGAC-AATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACG-CGAA-CCGT-AAATCGCAACGCGTATCCGTA
3025264 AATCGCAACGCGA
1 AATCGCAACGCGA
3025277 TTTTTAAAGC
Statistics
Matches: 117, Mismatches: 12, Indels: 9
0.85 0.09 0.07
Matches are distributed among these distances:
39 1 0.01
40 82 0.70
41 34 0.29
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.19
Consensus pattern (39 bp):
AATCGCAACGCGAACCGTAAATCGCAACGCGTATCCGTA
Found at i:3025185 original size:60 final size:60
Alignment explanation
Indices: 3025121--3025275 Score: 231
Period size: 60 Copynumber: 2.6 Consensus size: 60
3025111 CGCGAACACA
* * *
3025121 TAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTAAATCACAACG-CGTATCCG
1 TAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCACAACGAC-AATACG
* * *
3025181 TAAATCGCAATGCGTATCCGTATATCGCAACGCGTATCCGTAAATCGCAACGACAATACG
1 TAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCACAACGACAATACG
3025241 TAAAATCGCAACGCGTATCCGTAAATCGCAACGCG
1 T-AAATCGCAACGCGTATCCGTAAATCGCAACGCG
3025276 ATTTTTAAAG
Statistics
Matches: 85, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
60 53 0.62
61 32 0.38
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.21
Consensus pattern (60 bp):
TAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCACAACGACAATACG
Found at i:3025694 original size:33 final size:33
Alignment explanation
Indices: 3025655--3025725 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
3025645 TTCACTTAGA
3025655 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
3025688 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
3025721 TTTCA
1 TTTCA
3025726 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:3025831 original size:21 final size:20
Alignment explanation
Indices: 3025805--3025878 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 20
3025795 TGCAGAAGAG
3025805 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
3025826 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
3025846 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
3025868 TCGCAACGAGA
1 TCGCAACGAGA
3025879 GAATCACAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 10 0.22
21 25 0.56
22 10 0.22
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:3025896 original size:33 final size:33
Alignment explanation
Indices: 3025859--3025938 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
3025849 GCAACGAGAA
3025859 AAATGAAAATCGCAACGAGAGAATCACAACGCG
1 AAATGAAAATCGCAACGAGAGAATCACAACGCG
*
3025892 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCACAACGCG
**
3025925 AAACCAAAATCGCA
1 AAATGAAAATCGCA
3025939 TTGCGATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.49, C:0.23, G:0.20, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCACAACGCG
Found at i:3025918 original size:14 final size:14
Alignment explanation
Indices: 3025866--3025922 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
3025856 GAAAAATGAA
3025866 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
3025880 AATCACAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3025899 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3025913 AATCGCAACG
1 AATCGCAACG
3025923 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3025956 original size:19 final size:19
Alignment explanation
Indices: 3025934--3026061 Score: 78
Period size: 19 Copynumber: 7.1 Consensus size: 19
3025924 GAAACCAAAA
*
3025934 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3025953 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
3025967 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
3025986 TCACGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
3026000 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
3026020 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
3026040 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
3026060 TC
1 TC
3026062 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3025975 original size:14 final size:14
Alignment explanation
Indices: 3025956--3026012 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3025946 TTTCATTTCG
3025956 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3025970 CGTTGCGATTTTCATTTCA
1 CGTTGCGA--TTC---TCT
3025989 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3026003 CGTTGCGATT
1 CGTTGCGATT
3026013 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3025981 original size:33 final size:33
Alignment explanation
Indices: 3025939--3026062 Score: 158
Period size: 33 Copynumber: 3.5 Consensus size: 33
3025929 CAAAATCGCA
*
3025939 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
3025972 TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
*
3026005 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCACGTT--G-C-G--ATTCTCTCG
3026046 TTGCGATTTTCATTTCA
1 TTGCGATTTTCATTTCA
3026063 ACCAAAAGAA
Statistics
Matches: 80, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
33 44 0.55
34 2 0.03
35 6 0.08
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.03
41 21 0.26
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
Found at i:3026023 original size:21 final size:21
Alignment explanation
Indices: 3025997--3026061 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
3025987 CACGTTGCGA
3025997 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
3026018 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
3026038 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
3026059 TTC
1 TTC
3026062 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:3027902 original size:93 final size:93
Alignment explanation
Indices: 3027743--3028058 Score: 614
Period size: 93 Copynumber: 3.4 Consensus size: 93
3027733 TAGATTGCTT
*
3027743 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3027808 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3027836 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3027901 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
3027929 AGTAAATTTGTTTGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3027994 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3028022 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
3028059 AATACCCTGA
Statistics
Matches: 220, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 220 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:3028211 original size:33 final size:33
Alignment explanation
Indices: 3028172--3028279 Score: 171
Period size: 33 Copynumber: 3.3 Consensus size: 33
3028162 CACAAAACTT
* **
3028172 AAAATCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGACAGAATCGCAACGCGAAACC
*
3028205 AAAATCGCAACGACAGAATCGTAACGCGAAACC
1 AAAATCGCAACGACAGAATCGCAACGCGAAACC
*
3028238 AAAATCGCAACGACAAAATCGCAACGCGAAACC
1 AAAATCGCAACGACAGAATCGCAACGCGAAACC
3028271 AAAATCGCA
1 AAAATCGCA
3028280 TTGCGATTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 69 1.00
ACGTcount: A:0.47, C:0.26, G:0.19, T:0.08
Consensus pattern (33 bp):
AAAATCGCAACGACAGAATCGCAACGCGAAACC
Found at i:3028249 original size:19 final size:18
Alignment explanation
Indices: 3028188--3028279 Score: 74
Period size: 19 Copynumber: 5.4 Consensus size: 18
3028178 GCAACGAGAG
*
3028188 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-CAA
*
3028207 AATCGCAA--CG--ACAG
1 AATCGCAACGCGAAACAA
*
3028221 AATCGTAACGCGAAACCAA
1 AATCGCAACGCGAAA-CAA
3028240 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAACAA
3028254 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-CAA
3028273 AATCGCA
1 AATCGCA
3028280 TTGCGATTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 19 0.33
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 27 0.47
ACGTcount: A:0.47, C:0.27, G:0.17, T:0.09
Consensus pattern (18 bp):
AATCGCAACGCGAAACAA
Found at i:3028256 original size:14 final size:14
Alignment explanation
Indices: 3028205--3028263 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
3028195 ACGCGAAATG
3028205 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
3028219 AGAATCGTAACGCGAAACC
1 AAAATCGCAA--CG--A-C
3028238 AAAATCGCAACGAC
1 AAAATCGCAACGAC
3028252 AAAATCGCAACG
1 AAAATCGCAACG
3028264 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 21 0.58
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.25
ACGTcount: A:0.47, C:0.27, G:0.17, T:0.08
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3028297 original size:19 final size:19
Alignment explanation
Indices: 3028275--3028428 Score: 130
Period size: 19 Copynumber: 8.6 Consensus size: 19
3028265 GAAACCAAAA
*
3028275 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3028294 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
3028308 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
3028327 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
*
3028343 T--CATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
3028360 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
3028379 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
3028398 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
3028418 TCGTGTTGCGA
1 TCGCGTTGCGA
3028429 AAGTAAACTA
Statistics
Matches: 107, Mismatches: 17, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
14 18 0.17
16 8 0.07
17 8 0.07
19 61 0.57
20 12 0.11
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3028322 original size:33 final size:33
Alignment explanation
Indices: 3028280--3028410 Score: 172
Period size: 33 Copynumber: 3.8 Consensus size: 33
3028270 CAAAATCGCA
3028280 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* * *
3028313 TTGCGATTTTCATTTCGCATTGCGATTCTGTCA
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
3028346 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGA---T--TCTCTCG
*
3028384 TTGCGATTCTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
3028411 TTAAGTTTCG
Statistics
Matches: 85, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
33 55 0.65
35 1 0.01
36 1 0.01
38 28 0.33
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:3030373 original size:14 final size:14
Alignment explanation
Indices: 3030354--3030389 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3030344 ATTGTTTAAT
3030354 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
3030368 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
3030382 TGATTTGT
1 TGATTTGT
3030390 GTAATTGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3030553 original size:20 final size:19
Alignment explanation
Indices: 3030496--3030575 Score: 98
Period size: 20 Copynumber: 4.4 Consensus size: 19
3030486 AAAAATGACT
3030496 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3030515 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3030529 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
3030549 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
3030569 ATCGCAA
1 ATCGCAA
3030576 CGAGAGAATC
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 1 0.02
17 3 0.06
19 8 0.15
20 30 0.57
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3030653 original size:53 final size:53
Alignment explanation
Indices: 3030590--3030826 Score: 315
Period size: 53 Copynumber: 4.5 Consensus size: 53
3030580 AGAATCACAA
3030590 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
3030643 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
* * * * *
3030695 TGCGATTTTCATTTCCGCATTGCGATTCTCTC-GTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATTTTCATTT-CGCATTGCGATT-T-TCATTTCCGCA-TTGCGATTCTCTCGT
* *
3030748 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCAATTTTCAT-GT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGT
*
3030801 TGGGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
3030827 CTCTCGTTGC
Statistics
Matches: 164, Mismatches: 10, Indels: 20
0.85 0.05 0.10
Matches are distributed among these distances:
50 2 0.01
51 8 0.05
52 49 0.30
53 91 0.55
54 7 0.04
55 7 0.04
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (53 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
Found at i:3030715 original size:86 final size:86
Alignment explanation
Indices: 3030608--3030773 Score: 332
Period size: 86 Copynumber: 1.9 Consensus size: 86
3030598 TCATTTCGCA
3030608 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
3030673 TTTCGCATTGCGATTCTCTCG
66 TTTCGCATTGCGATTCTCTCG
3030694 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
3030759 TTTCGCATTGCGATT
66 TTTCGCATTGCGATT
3030774 TTCATTTCCG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 80 1.00
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.46
Consensus pattern (86 bp):
TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
TTTCGCATTGCGATTCTCTCG
Found at i:3030848 original size:33 final size:33
Alignment explanation
Indices: 3030661--3030840 Score: 245
Period size: 34 Copynumber: 5.2 Consensus size: 33
3030651 TCATTTCGCA
3030661 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
3030694 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
*
3030728 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* *
3030764 CATTGCGATTTTCATTTCCGCATTGCAATTTTCAT-G
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
3030800 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
3030833 TTGCGATT
1 TTGCGATT
3030841 GTAATTTCCG
Statistics
Matches: 130, Mismatches: 8, Indels: 18
0.83 0.05 0.12
Matches are distributed among these distances:
32 1 0.01
33 46 0.35
34 47 0.36
35 3 0.02
36 6 0.05
37 3 0.02
38 15 0.12
39 9 0.07
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:3030855 original size:53 final size:52
Alignment explanation
Indices: 3030590--3030859 Score: 241
Period size: 53 Copynumber: 5.1 Consensus size: 52
3030580 AGAATCACAA
* * *
3030590 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGA-TTCTC-TCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTC-GTTGCGCATTGCAATTTC-CGT-GT
* * *
3030643 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTCTC-TCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCGTTGCGCATTGCAATTTC-CGT-GT
* **
3030695 TGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATTT-CGCAT
1 TGCGATTTTCATTT-CGCATTGCGATT-T-TCGTTGCGCA-TTGCAATTTCCGTGT
* * * *
3030748 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCAATTTTCATGT
1 TGCGATTTTCATTTCGCATTGCGATTTTC-GTTGCGCATTGCAATTTCCGTGT
* *
3030801 TGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG-ATTGTAATTTCCGTGT
1 TGCGATTTTCATTTCGCATTGCGATT-T-TCGTTGCGCATTGCAATTTCCGTGT
3030854 TGCGAT
1 TGCGAT
3030860 AGTCAAATGC
Statistics
Matches: 185, Mismatches: 20, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
50 2 0.01
51 8 0.04
52 52 0.28
53 102 0.55
54 8 0.04
55 13 0.07
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCGTTGCGCATTGCAATTTCCGTGT
Found at i:3033141 original size:12 final size:12
Alignment explanation
Indices: 3033124--3033148 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3033114 TCTTCGGGGA
3033124 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3033136 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3033148 C
1 C
3033149 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3033357 original size:24 final size:24
Alignment explanation
Indices: 3033323--3033369 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3033313 CTGAAACATC
3033323 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
3033347 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
3033370 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:3034090 original size:20 final size:20
Alignment explanation
Indices: 3034062--3034290 Score: 208
Period size: 20 Copynumber: 11.4 Consensus size: 20
3034052 AAATTTCAGT
* * *
3034062 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
3034082 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
3034102 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
3034122 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
3034142 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
3034162 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * * *
3034182 ATTGCGATTTACAGATACGA
1 GTTGCGATTTACGGATTCGC
* * * *
3034202 GTTTCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
3034222 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
3034242 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
3034262 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
3034282 GTTGCGATT
1 GTTGCGATT
3034291 CTTGAAAATC
Statistics
Matches: 175, Mismatches: 32, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
20 174 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:3034343 original size:21 final size:20
Alignment explanation
Indices: 3034258--3034355 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
3034248 ATTTATGTGT
* *
3034258 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
3034278 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
3034299 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
3034320 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
3034341 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
3034356 GGAAACTGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:3034351 original size:42 final size:43
Alignment explanation
Indices: 3034258--3034356 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
3034248 ATTTATGTGT
* *
3034258 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
3034299 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
3034341 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
3034357 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:3036361 original size:6 final size:7
Alignment explanation
Indices: 3036342--3036372 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
3036332 TTGAATTGCG
3036342 AAAATTT
1 AAAATTT
3036349 AAAATTT
1 AAAATTT
3036356 -AAATTT
1 AAAATTT
3036362 AAAATTT
1 AAAATTT
3036369 AAAA
1 AAAA
3036373 CCCAATTCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AAAATTT
Done.