Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008280.1 Hibiscus syriacus cultivar Beakdansim tig00110940_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: 3557051
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 17
Found at i:2064649 original size:14 final size:14
Alignment explanation
Indices: 2064630--2064687 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2064620 ATGCGAAATG
2064630 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2064644 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
2064660 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2064676 AAAATCGCAACG
1 AAAATCGCAACG
2064688 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2064672 original size:32 final size:33
Alignment explanation
Indices: 2064614--2064692 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
2064604 GGAAATGGCT
2064614 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2064647 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
2064679 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
2064693 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 29 0.64
33 16 0.36
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2064726 original size:19 final size:18
Alignment explanation
Indices: 2064702--2064750 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
2064692 ACACAAATCG
2064702 CATTGCGATTTTCATTTCA
1 CATTGCGATTTT-ATTTCA
* * *
2064721 CGTTGCGATTTTGTTTCG
1 CATTGCGATTTTATTTCA
2064739 CATTGCGATTTT
1 CATTGCGATTTT
2064751 GTCGTTGCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.14, C:0.18, G:0.18, T:0.49
Consensus pattern (18 bp):
CATTGCGATTTTATTTCA
Found at i:2064760 original size:14 final size:15
Alignment explanation
Indices: 2064721--2064764 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 15
2064711 TTTCATTTCA
2064721 CGTTGCGATTTTGTTT
1 CGTTGCGATTTTG-TT
2064737 CGCATTGCGATTTTG-T
1 CG--TTGCGATTTTGTT
2064753 CGTTGCGATTTT
1 CGTTGCGATTTT
2064765 CATTTCGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 10 0.38
16 5 0.19
18 11 0.42
ACGTcount: A:0.09, C:0.16, G:0.25, T:0.50
Consensus pattern (15 bp):
CGTTGCGATTTTGTT
Found at i:2064779 original size:19 final size:18
Alignment explanation
Indices: 2064699--2064780 Score: 82
Period size: 19 Copynumber: 4.7 Consensus size: 18
2064689 GAAACACAAA
2064699 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTT-ATT
* * *
2064718 TCACGTTGCGATTTTGTT
1 TCGCATTGCGATTTTATT
*
2064736 TCGCATTGCGA-TTT-TG
1 TCGCATTGCGATTTTATT
2064752 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTT-ATT
2064769 TCGCATTGCGAT
1 TCGCATTGCGAT
2064781 AGCCATTTCC
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
14 6 0.12
15 3 0.06
16 4 0.08
17 7 0.14
18 11 0.22
19 20 0.39
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.46
Consensus pattern (18 bp):
TCGCATTGCGATTTTATT
Found at i:2064799 original size:20 final size:19
Alignment explanation
Indices: 2064765--2064819 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
2064755 TTGCGATTTT
*
2064765 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
2064784 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
2064804 CATTTTCGGGTTGCGA
1 CA-TTTCGCGTTGCGA
2064820 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.25, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:2065327 original size:18 final size:18
Alignment explanation
Indices: 2065301--2065345 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2065291 GTCGATCAGA
*
2065301 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
2065319 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
2065337 TGATGGCTC
1 TGATGGCTC
2065346 CCGAAGTGGA
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:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:2067202 original size:20 final size:20
Alignment explanation
Indices: 2067177--2067228 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2067167 ATTATGTATT
*
2067177 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAATCAGA
*
2067197 ATCGCGTTGCGAAAATCAGT
1 ATCGCGTTGCGAAAATCAGA
*
2067217 ATCTCGTTGCGA
1 ATCGCGTTGCGA
2067229 TTTTGTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAATCAGA
Found at i:2067248 original size:61 final size:61
Alignment explanation
Indices: 2067156--2067293 Score: 177
Period size: 61 Copynumber: 2.3 Consensus size: 61
2067146 CGCTTTGAAA
* * * * *
2067156 ATCGCATTGTGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAATCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAATCAGT
* * * * * *
2067217 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAATCAGT
2067278 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
2067294 CCCAATTCGC
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.36
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAATCAGT
Found at i:2067262 original size:20 final size:20
Alignment explanation
Indices: 2067237--2067290 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
2067227 GATTTTGTAT
2067237 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
2067257 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
2067277 TATCGCATTGCGAT
1 TATCGCATTGCGAT
2067291 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:2067309 original size:61 final size:61
Alignment explanation
Indices: 2067176--2067311 Score: 148
Period size: 61 Copynumber: 2.2 Consensus size: 61
2067166 GATTATGTAT
* * * * * ** *
2067176 TATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAATCAGTATCTCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAATCAGTATCGCATTGCGATTTTCCAA
* * * *
2067237 TATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAATCAGTATCGCATTGCGATTTT-CCAA
2067299 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
2067312 TTACTTATTC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
TATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAATCAGTATCGCATTGCGATTTTCCAA
Found at i:2068787 original size:15 final size:15
Alignment explanation
Indices: 2068762--2068862 Score: 98
Period size: 15 Copynumber: 6.9 Consensus size: 15
2068752 TGGTTTTCCA
2068762 GAAAATGAATTACTG
1 GAAAATGAATTACTG
**
2068777 GAATTTGAATTACTG
1 GAAAATGAATTACTG
*
2068792 GAAAATAAATTACTG
1 GAAAATGAATTACTG
**
2068807 GAATTTGAATT-CTG
1 GAAAATGAATTACTG
* *
2068821 AAAAATAAATTACTG
1 GAAAATGAATTACTG
** *
2068836 GAATTTAAATT-CTG
1 GAAAATGAATTACTG
2068850 GAAAATGAATTAC
1 GAAAATGAATTAC
2068863 ATTTCTGTAA
Statistics
Matches: 66, Mismatches: 18, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
14 21 0.32
15 45 0.68
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.33
Consensus pattern (15 bp):
GAAAATGAATTACTG
Found at i:2068835 original size:29 final size:29
Alignment explanation
Indices: 2068762--2068862 Score: 157
Period size: 29 Copynumber: 3.4 Consensus size: 29
2068752 TGGTTTTCCA
*
2068762 GAAAATGAATTACTGGAATTTGAATTACTG
1 GAAAATAAATTACTGGAATTTGAATT-CTG
2068792 GAAAATAAATTACTGGAATTTGAATTCTG
1 GAAAATAAATTACTGGAATTTGAATTCTG
* *
2068821 AAAAATAAATTACTGGAATTTAAATTCTG
1 GAAAATAAATTACTGGAATTTGAATTCTG
*
2068850 GAAAATGAATTAC
1 GAAAATAAATTAC
2068863 ATTTCTGTAA
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
29 41 0.62
30 25 0.38
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.33
Consensus pattern (29 bp):
GAAAATAAATTACTGGAATTTGAATTCTG
Found at i:2068868 original size:20 final size:20
Alignment explanation
Indices: 2068845--2068914 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
2068835 GGAATTTAAA
2068845 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
2068865 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
2068885 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
2068905 TTCTGGAAAA
1 TTCTGGAAAA
2068915 CATCTGGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:2069127 original size:32 final size:32
Alignment explanation
Indices: 2069080--2069151 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
2069070 CTTTACTAAA
* *
2069080 ATATTATTGAA-ATATAT-AAATAA-TATTAT
1 ATATTATTAAATATATATAAAAAAATTATTAT
2069109 -TCATTATTAAATATATATAAAAAAATTATTAT
1 AT-ATTATTAAATATATATAAAAAAATTATTAT
2069141 ATATTATTAAA
1 ATATTATTAAA
2069152 ATAAAAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
28 1 0.03
29 8 0.22
30 6 0.17
31 5 0.14
32 15 0.42
33 1 0.03
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (32 bp):
ATATTATTAAATATATATAAAAAAATTATTAT
Found at i:2069136 original size:29 final size:27
Alignment explanation
Indices: 2069081--2069146 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 27
2069071 TTTACTAAAA
* *
2069081 TATTATTGAAATATATAAATAATATTAT
1 TATTATT-AAATATATAAAAAAAATTAT
2069109 TCATTATTAAATATATATAAAAAAATTAT
1 T-ATTATTAAATATATA-AAAAAAATTAT
2069138 TATATATTA
1 TAT-TATTA
2069147 TTAAAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 12 0.36
29 21 0.64
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (27 bp):
TATTATTAAATATATAAAAAAAATTAT
Found at i:2069139 original size:22 final size:21
Alignment explanation
Indices: 2069111--2069152 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2069101 AATATTATTC
2069111 ATTATTAAATATATATAAAAAA
1 ATTATTAAATAT-TATAAAAAA
* *
2069133 ATTATTATATATTATTAAAA
1 ATTATTAAATATTATAAAAA
2069153 TAAAAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTATTAAATATTATAAAAAA
Found at i:2069208 original size:15 final size:16
Alignment explanation
Indices: 2069170--2069233 Score: 58
Period size: 19 Copynumber: 3.8 Consensus size: 16
2069160 ATAATATCTT
2069170 ATATTATTATAATATA
1 ATATTATTATAATATA
*
2069186 ATTGATTATT-TTATATA
1 A-T-ATTATTATAATATA
*
2069203 ATATTAAAAATATAATATA
1 ATATT---ATTATAATATA
2069222 ATATTATTATAA
1 ATATTATTATAA
2069234 ATATTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
15 3 0.08
16 8 0.21
17 8 0.21
18 8 0.21
19 11 0.29
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
ATATTATTATAATATA
Found at i:2069243 original size:10 final size:10
Alignment explanation
Indices: 2069202--2069247 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
2069192 TATTTTATAT
2069202 AATATTAA-A
1 AATATTAATA
2069211 AATA-TAATA
1 AATATTAATA
2069220 TAATATTATTATA
1 -AATATTA--ATA
2069233 AATATTAATA
1 AATATTAATA
2069243 AATAT
1 AATAT
2069248 ATTTTAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
8 3 0.09
9 5 0.16
10 12 0.38
11 2 0.06
12 7 0.22
13 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AATATTAATA
Found at i:2069250 original size:21 final size:22
Alignment explanation
Indices: 2069203--2069259 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
2069193 ATTTTATATA
*
2069203 ATATTAAAAATA-TAATATAAT
1 ATATTATAAATATTAATATAAT
2069224 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
2069246 ATATTTTAAATATT
1 ATATTATAAATATT
2069260 TTAATAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 13 0.41
22 14 0.44
23 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:2069258 original size:52 final size:51
Alignment explanation
Indices: 2069139--2069259 Score: 124
Period size: 54 Copynumber: 2.3 Consensus size: 51
2069129 AAAAATTATT
* **
2069139 ATATATTATTAAA-A-TAAAAATATAATATCTTATATTATTATAATATAATTG
1 ATATATT-TTAAATATTAAAAATATAATA-CTAATATTATTATAATATAATAA
2069190 AT-TATTTTATATAATATTAAAAATATAATA-TAATATTATTATAAATATTAATAA
1 ATATA-TTT-TA-AATATTAAAAATATAATACTAATATTATTAT-AATA-TAATAA
2069244 ATATATTTTAAATATT
1 ATATATTTTAAATATT
2069260 TTAATAATTA
Statistics
Matches: 59, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 19 0.32
53 7 0.12
54 22 0.37
55 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (51 bp):
ATATATTTTAAATATTAAAAATATAATACTAATATTATTATAATATAATAA
Found at i:2069264 original size:23 final size:21
Alignment explanation
Indices: 2069210--2069259 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
2069200 ATAATATTAA
*
2069210 AAATA-TAATATAATATTATTAT
1 AAATATTAATA-AATA-TATTTT
2069232 AAATATTAATAAATATATTTT
1 AAATATTAATAAATATATTTT
2069253 AAATATT
1 AAATATT
2069260 TTAATAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 12 0.46
22 9 0.35
23 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATATTAATAAATATATTTT
Found at i:2069509 original size:42 final size:42
Alignment explanation
Indices: 2069450--2069569 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
2069440 ATGAATTACA
*
2069450 TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAACGGT
1 TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAACAGT
*
2069492 TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAACAGT
2069534 TTCCGAAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGAAAAACGAATTACGTGAAACAAACACGGGAA
2069570 TTCGGGGAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.15
Consensus pattern (42 bp):
TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAACAGT
Found at i:2070506 original size:54 final size:53
Alignment explanation
Indices: 2070276--2070502 Score: 287
Period size: 54 Copynumber: 4.2 Consensus size: 53
2070266 AACTGGAGGC
* *
2070276 GCAGGAGTTGGGGCCTTATACGGGGGTGTTGGAG-CTTTGGTTGGGGGTGCTGGT
1 GCAGGAGTTGGGG-CTTATATGGCGGTGTTGGAGCCTTT-GTTGGGGGTGCTGGT
** * *
2070330 GCAGGAGTTGGGGACTTATATGATGGGGTTGGAGCATTTGTTGGGGGTGCTGGT
1 GCAGGAGTTGGGG-CTTATATGGCGGTGTTGGAGCCTTTGTTGGGGGTGCTGGT
*
2070384 GCAGGAGTTGGGGGCTCATATGGGCGG-GTTGGAGCCTTTGTTGGGGGTGCTGGT
1 GCAGGAGTT-GGGGCTTATAT-GGCGGTGTTGGAGCCTTTGTTGGGGGTGCTGGT
* * *
2070438 GCTGTAGTTGGAGGCTTATATGGCGGTGTTGGAGCCTTTGTTGCGGGTGCTGGT
1 GCAGGAGTTGG-GGCTTATATGGCGGTGTTGGAGCCTTTGTTGGGGGTGCTGGT
*
2070492 GCTGGAGTTGG
1 GCAGGAGTTGG
2070503 AGGCATGACT
Statistics
Matches: 153, Mismatches: 15, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
53 7 0.05
54 136 0.89
55 10 0.07
ACGTcount: A:0.11, C:0.11, G:0.48, T:0.31
Consensus pattern (53 bp):
GCAGGAGTTGGGGCTTATATGGCGGTGTTGGAGCCTTTGTTGGGGGTGCTGGT
Found at i:2072040 original size:21 final size:21
Alignment explanation
Indices: 2072006--2072165 Score: 166
Period size: 21 Copynumber: 7.6 Consensus size: 21
2071996 GATTTACATA
* *
2072006 TTCGCATTGTGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
2072027 TTCGCGCTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
2072048 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
2072069 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
2072092 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
2072111 TTCGCGTTGCGATTTATTACAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
2072134 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
2072153 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
2072166 TTATTCTAAA
Statistics
Matches: 114, Mismatches: 17, Indels: 16
0.78 0.12 0.11
Matches are distributed among these distances:
19 16 0.14
21 82 0.72
23 16 0.14
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.33
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:2072062 original size:42 final size:41
Alignment explanation
Indices: 2072016--2072193 Score: 241
Period size: 42 Copynumber: 4.2 Consensus size: 41
2072006 TTCGCATTGT
* * *
2072016 GATAGTCCAAGTTCGCGCTGCGA-TAGTCCAAGTTCGCGTTGC
1 GATAGTCCAAGTTCGCGTTGCGATTATTCCAAATT--CGTTGC
*
2072058 GATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
1 GATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAATTCGTTGC
*
2072100 GATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGC
1 GATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAATTCGTTGC
* *
2072142 GATAGTCGAAGTTCGCGTTGCGATTTATTCTAAATTCGTTGC
1 GATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAATTCGTTGC
2072184 GATAGTCCAA
1 GATAGTCCAA
2072194 AATCACCACG
Statistics
Matches: 124, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
42 115 0.93
44 9 0.07
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.33
Consensus pattern (41 bp):
GATAGTCCAAGTTCGCGTTGCGATTATTCCAAATTCGTTGC
Found at i:2072114 original size:84 final size:83
Alignment explanation
Indices: 2072016--2072193 Score: 277
Period size: 84 Copynumber: 2.1 Consensus size: 83
2072006 TTCGCATTGT
* *
2072016 GATAGTCCAAGTTCGCGCTGCGA-TAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCG
1 GATAGTCCAAGTTCGCGCTGCGATTAGTACAAATT--CGTTGCGATAGTCGAAGTTCGCGTTGCG
2072080 ATTTATTCCAAATTCGTTGC
64 ATTTATTCCAAATTCGTTGC
* *
2072100 GATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGA
1 GATAGTCCAAGTTCGCGCTGCGA-TTAGTACAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGA
*
2072165 TTTATTCTAAATTCGTTGC
65 TTTATTCCAAATTCGTTGC
2072184 GATAGTCCAA
1 GATAGTCCAA
2072194 AATCACCACG
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
84 79 0.91
86 8 0.09
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.33
Consensus pattern (83 bp):
GATAGTCCAAGTTCGCGCTGCGATTAGTACAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGAT
TTATTCCAAATTCGTTGC
Found at i:2072181 original size:21 final size:21
Alignment explanation
Indices: 2072073--2072186 Score: 101
Period size: 21 Copynumber: 5.4 Consensus size: 21
2072063 TCGAAGTTCG
2072073 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATT
* *
2072094 CGTTGCGA--TAGTCCAAGTT
1 CGTTGCGATTTATTCCAAATT
*
2072113 CGCGTTGCGATTTATTACAAATT
1 --CGTTGCGATTTATTCCAAATT
* * *
2072136 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATT
*
2072155 CGCGTTGCGATTTATTCTAAATT
1 --CGTTGCGATTTATTCCAAATT
2072178 CGTTGCGAT
1 CGTTGCGAT
2072187 AGTCCAAAAT
Statistics
Matches: 73, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
19 16 0.22
21 41 0.56
23 16 0.22
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAATT
Found at i:2072844 original size:6 final size:6
Alignment explanation
Indices: 2072835--2072871 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
2072825 GCCGTCCGTC
2072835 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
2072872 AATACGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:2073022 original size:21 final size:21
Alignment explanation
Indices: 2072992--2073031 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2072982 GAACTTGGAC
2072992 GTCGAAGTTCGCGTTGCGATA
1 GTCGAAGTTCGCGTTGCGATA
*
2073013 GTCGATGTTCGCGTTGCGA
1 GTCGAAGTTCGCGTTGCGA
2073032 ATCTGGAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.20, G:0.35, T:0.30
Consensus pattern (21 bp):
GTCGAAGTTCGCGTTGCGATA
Found at i:2076821 original size:20 final size:20
Alignment explanation
Indices: 2076798--2076847 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
2076788 ACAGATTCAA
*
2076798 AAATTGCAACGCGAATAGGT
1 AAATCGCAACGCGAATAGGT
*
2076818 AAATCGCAACGCGAATATGT
1 AAATCGCAACGCGAATAGGT
2076838 AAATCGCAAC
1 AAATCGCAAC
2076848 ACAGAAGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGAATAGGT
Found at i:2077054 original size:20 final size:20
Alignment explanation
Indices: 2077029--2077074 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
2077019 AGAATTCGCA
2077029 TTGCGATTTACATATTATCG
1 TTGCGATTTACATATTATCG
*
2077049 TTGCGATTTACATATTCTCG
1 TTGCGATTTACATATTATCG
2077069 TTGCGA
1 TTGCGA
2077075 ATTTGGGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.43
Consensus pattern (20 bp):
TTGCGATTTACATATTATCG
Found at i:2077345 original size:21 final size:21
Alignment explanation
Indices: 2077269--2077345 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
2077259 ATAATTAGCG
*
2077269 TTTGCGAAATTCGTGTTGCGAA
1 TTTG-GAAATTCGCGTTGCGAA
2077291 TTTGGAGAATTCGCGTTGC-AA
1 TTTGGA-AATTCGCGTTGCGAA
****
2077312 TTTACCTATTCGCGTTGCGAA
1 TTTGGAAATTCGCGTTGCGAA
*
2077333 TTTGGAAAATCGC
1 TTTGGAAATTCGC
2077346 AACGCAATTC
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
20 11 0.26
21 17 0.40
22 15 0.35
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (21 bp):
TTTGGAAATTCGCGTTGCGAA
Found at i:2077471 original size:20 final size:20
Alignment explanation
Indices: 2077442--2077484 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2077432 ATCGCAACAC
* *
2077442 ATTTCGTTTTTGCAACGCGA
1 ATTTCATTTTCGCAACGCGA
*
2077462 ATTTCATTTTCGCAACGCTA
1 ATTTCATTTTCGCAACGCGA
2077482 ATT
1 ATT
2077485 ACCTATATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (20 bp):
ATTTCATTTTCGCAACGCGA
Found at i:2077582 original size:20 final size:20
Alignment explanation
Indices: 2077534--2077582 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
2077524 AATTTGGAGA
*
2077534 ATTCGTGTTGCGATTTACAT
1 ATTCGCGTTGCGATTTACAT
** *
2077554 ATTATCGTTGCGATTTACCT
1 ATTCGCGTTGCGATTTACAT
2077574 ATTCGCGTT
1 ATTCGCGTT
2077583 ACGAATTTGG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACAT
Found at i:2077657 original size:234 final size:236
Alignment explanation
Indices: 2077107--2077657 Score: 560
Period size: 237 Copynumber: 2.3 Consensus size: 236
2077097 TTTTGTTTTT
* * * * *
2077107 GCAACGCGATTCTCCAAAATCGCAACGAGAATTTCATTTTCGCAACGCTAACTACCTATATCGGT
1 GCAACGCAATTCTCCAAAATCGCAACGCGAATTTCATTTTCGCAACGCTAATTACCGATATAGGT
**** ** ** * *** *
2077172 AATTGGTGTTGCGAATTT-G-ATTTCGCATTGTGA-ATTTGGAAAATCGCAACGCGAATTTCATT
66 AATTAACATTGCGAATTTGGAAAATCGCA---ACACATTTCG-TTTTTGCAACGCGAATTTCATT
* * * * * *
2077234 TTCGCAACGTTAATTACCTATGTCGATAATTAGCGTTTGCGAAATTCGTGTTGCGAATTTGGAGA
127 TTCGCAACGCTAATTACCTATATCGATAATTAGCGATTACGAAATTCGAGTTACGAATTTGGAGA
* * **
2077299 ATTCGCGTTGCAATTTACCTATTCGCGTTGCGAATTTGGAAAATC
192 ATTCGCGTTGCAATTTACATATTAGCGTTGCGAATTTACAAAATC
* * * * *
2077344 GCAACGCAATTCTCCAAAATCTCAACGCGAATTTCATTTTTGCAACGCTAATTACCTATGTCGGT
1 GCAACGCAATTCTCCAAAATCGCAACGCGAATTTCATTTTCGCAACGCTAATTACCGATATAGGT
** *
2077409 AATTGGCGTTGCGAATTTGGAAAATCGCAACACATTTCGTTTTTGCAACGCGAATTTCATTTTCG
66 AATTAACATTGCGAATTTGGAAAATCGCAACACATTTCGTTTTTGCAACGCGAATTTCATTTTCG
*
2077474 CAACGCTAATTACCTATATC-AGTAATTGGC-ATTACGAAATTCGAGTTACGAATTTGGAGAATT
131 CAACGCTAATTACCTATATCGA-TAATTAGCGATTACGAAATTCGAGTTACGAATTTGGAGAATT
* * * ** *
2077537 CGTGTTGCGATTTACATATTATCGTTGCG-ATTTACCTATTC
195 CGCGTTGCAATTTACATATTAGCGTTGCGAATTTACAAAATC
* ** *
2077578 GCGTTACG-AATT-TGGAAAATCGCAACGCGAATTTCGTTTTCGCAACGCTAATTACCGATATAG
1 GC--AACGCAATTCTCCAAAATCGCAACGCGAATTTCATTTTCGCAACGCTAATTACCGATATAG
2077641 GTAATTAACATTGCGAA
64 GTAATTAACATTGCGAA
2077658 ATTCGAGTTG
Statistics
Matches: 263, Mismatches: 45, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
234 66 0.25
235 58 0.22
236 51 0.19
237 81 0.31
238 1 0.00
239 6 0.02
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (236 bp):
GCAACGCAATTCTCCAAAATCGCAACGCGAATTTCATTTTCGCAACGCTAATTACCGATATAGGT
AATTAACATTGCGAATTTGGAAAATCGCAACACATTTCGTTTTTGCAACGCGAATTTCATTTTCG
CAACGCTAATTACCTATATCGATAATTAGCGATTACGAAATTCGAGTTACGAATTTGGAGAATTC
GCGTTGCAATTTACATATTAGCGTTGCGAATTTACAAAATC
Found at i:2077717 original size:146 final size:146
Alignment explanation
Indices: 2077453--2077769 Score: 528
Period size: 146 Copynumber: 2.2 Consensus size: 146
2077443 TTTCGTTTTT
* * **
2077453 GCAACGCGAATTTCATTTTCGCAACGCTAATTACCTATATCAGTAATTGGCATTACGAAATTCGA
1 GCAACGCGAATTTCGTTTTCGCAACGCTAATTACCGATATCAGTAATTAACATTACGAAATTCGA
2077518 GTTACGAATTTGGAGAATTCGTGTTGCGATTTACATATTATCGTTGCGATTTACCTATTCGCGTT
66 GTTACGAATTTGGAGAATTCGTGTTGCGATTTACATATTATCGTTGCGATTTACCTATTCGCGTT
2077583 ACGAATTTGGAAAATC
131 ACGAATTTGGAAAATC
*
2077599 GCAACGCGAATTTCGTTTTCGCAACGCTAATTACCGATAT-AGGTAATTAACATTGCGAAATTCG
1 GCAACGCGAATTTCGTTTTCGCAACGCTAATTACCGATATCA-GTAATTAACATTACGAAATTCG
* *
2077663 AGTTGCGAATTTGGAGAATTCGTGTTGCGATTTACATATTATTGTTGCGATTTACCTATTCGCGT
65 AGTTACGAATTTGGAGAATTCGTGTTGCGATTTACATATTATCGTTGCGATTTACCTATTCGCGT
*
2077728 TGCGAATTTGGAAAATC
130 TACGAATTTGGAAAATC
* *
2077745 GCAACTCGAATATCGTTTTCGCAAC
1 GCAACGCGAATTTCGTTTTCGCAAC
2077770 ACAATTCTCC
Statistics
Matches: 160, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
145 1 0.01
146 159 0.99
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (146 bp):
GCAACGCGAATTTCGTTTTCGCAACGCTAATTACCGATATCAGTAATTAACATTACGAAATTCGA
GTTACGAATTTGGAGAATTCGTGTTGCGATTTACATATTATCGTTGCGATTTACCTATTCGCGTT
ACGAATTTGGAAAATC
Found at i:2077729 original size:20 final size:20
Alignment explanation
Indices: 2077680--2077732 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2077670 AATTTGGAGA
2077680 ATTCGTGTTGCGATTTACAT
1 ATTCGTGTTGCGATTTACAT
** *
2077700 ATTATTGTTGCGATTTACCT
1 ATTCGTGTTGCGATTTACAT
*
2077720 ATTCGCGTTGCGA
1 ATTCGTGTTGCGA
2077733 ATTTGGAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (20 bp):
ATTCGTGTTGCGATTTACAT
Found at i:2077872 original size:20 final size:20
Alignment explanation
Indices: 2077841--2077912 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
2077831 GGAGAATTTA
*
2077841 CGTTGTGATTTACATATTAT
1 CGTTGCGATTTACATATTAT
* * **
2077861 CATTGCGATTTACCTATTCG
1 CGTTGCGATTTACATATTAT
*
2077881 CGTTGCGAATTACATATTAT
1 CGTTGCGATTTACATATTAT
*
2077901 CGTTGCAATTTA
1 CGTTGCGATTTA
2077913 ACTATTCGCG
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTACATATTAT
Found at i:2077894 original size:40 final size:40
Alignment explanation
Indices: 2077841--2077931 Score: 128
Period size: 40 Copynumber: 2.3 Consensus size: 40
2077831 GGAGAATTTA
* * * *
2077841 CGTTGTGATTTACATATTATCATTGCGATTTACCTATTCG
1 CGTTGAGAATTACATATTATCATTGCAATTTAACTATTCG
* *
2077881 CGTTGCGAATTACATATTATCGTTGCAATTTAACTATTCG
1 CGTTGAGAATTACATATTATCATTGCAATTTAACTATTCG
2077921 CGTTGAGAATT
1 CGTTGAGAATT
2077932 TAACTTTCGC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.42
Consensus pattern (40 bp):
CGTTGAGAATTACATATTATCATTGCAATTTAACTATTCG
Found at i:2077950 original size:40 final size:39
Alignment explanation
Indices: 2077901--2077992 Score: 112
Period size: 40 Copynumber: 2.3 Consensus size: 39
2077891 TACATATTAT
*
2077901 CGTTGCAATTTAACTATTCGCGTTGAGAATTTAACTTTCG
1 CGTTACAATTTAACT-TTCGCGTTGAGAATTTAACTTTCG
* * * *
2077941 CGTTACAATTTTGACTTTGGCGTTGCGAATTTGACTTTCG
1 CGTTACAA-TTTAACTTTCGCGTTGAGAATTTAACTTTCG
2077981 CGTTACGAATTT
1 CGTTAC-AATTT
2077993 GTTGGTCATT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
40 37 0.82
41 8 0.18
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (39 bp):
CGTTACAATTTAACTTTCGCGTTGAGAATTTAACTTTCG
Found at i:2077989 original size:20 final size:20
Alignment explanation
Indices: 2077907--2077993 Score: 97
Period size: 20 Copynumber: 4.3 Consensus size: 20
2077897 TTATCGTTGC
*
2077907 AATTTAACTATTCGCGTTGA-G
1 AATTTGACT-TTCGCGTT-ACG
*
2077928 AATTTAACTTTCGCGTTAC-
1 AATTTGACTTTCGCGTTACG
* *
2077947 AATTTTGACTTTGGCGTTGCG
1 AA-TTTGACTTTCGCGTTACG
2077968 AATTTGACTTTCGCGTTACG
1 AATTTGACTTTCGCGTTACG
2077988 AATTTG
1 AATTTG
2077994 TTGGTCATTT
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.05
20 44 0.76
21 11 0.19
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (20 bp):
AATTTGACTTTCGCGTTACG
Found at i:2080181 original size:26 final size:25
Alignment explanation
Indices: 2080152--2080203 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
2080142 TTACTCGTTC
* *
2080152 AACTTTCGTTTTCATTTAATAAAAAA
1 AACTTTCATTTTCATCT-ATAAAAAA
2080178 AACTTTCATTTTCATCTATAAAAAA
1 AACTTTCATTTTCATCTATAAAAAA
2080203 A
1 A
2080204 TACATCCGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.44, C:0.13, G:0.02, T:0.40
Consensus pattern (25 bp):
AACTTTCATTTTCATCTATAAAAAA
Found at i:2080731 original size:12 final size:12
Alignment explanation
Indices: 2080716--2080772 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
2080706 TGTCCGAGTT
2080716 TTAAATATTATA
1 TTAAATATTATA
2080728 TTAAA-ATTATTA
1 TTAAATATTA-TA
*
2080740 TTATATATT-TA
1 TTAAATATTATA
*
2080751 TT-ATTATTAATA
1 TTAAATATT-ATA
2080763 TT-AATATTAT
1 TTAAATATTAT
2080773 TTATGTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
10 4 0.11
11 10 0.27
12 20 0.54
13 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TTAAATATTATA
Found at i:2080743 original size:17 final size:17
Alignment explanation
Indices: 2080721--2080773 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
2080711 GAGTTTTAAA
*
2080721 TATTATATTAAAATTAT
1 TATTATATTAATATTAT
*
2080738 TATTATA-TATTTATTAT
1 TATTATATTA-ATATTAT
2080755 TATTAATATTAATATTAT
1 TATT-ATATTAATATTAT
2080773 T
1 T
2080774 TATGTTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 2 0.07
17 16 0.53
18 10 0.33
19 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTATATTAATATTAT
Found at i:2083442 original size:15 final size:15
Alignment explanation
Indices: 2083422--2083459 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2083412 TTGCTTCTGA
2083422 TTATTTTATCTTTTT
1 TTATTTTATCTTTTT
* *
2083437 TTATTTCATGTTTTT
1 TTATTTTATCTTTTT
2083452 TTATTTTA
1 TTATTTTA
2083460 ATATTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (15 bp):
TTATTTTATCTTTTT
Found at i:2091991 original size:105 final size:104
Alignment explanation
Indices: 2091776--2092081 Score: 295
Period size: 105 Copynumber: 3.0 Consensus size: 104
2091766 GGTTGTATCA
* * * * **
2091776 CTTTCTTCCATGCAAAACCCACATCCCATTTTCAGGTAATCGTTAG-CGAGTCCGCCTTCAGAAA
1 CTTTCTTCCATGCAAAATCCACCTCCCATTTTCATGTAATCGTTAGTCG-GTTCGGTTTCAGAAA
* * * *
2091840 TGGGATCACCA-GCTTGACTTGTATCAGGTTGATCAATGTT
65 AGGGATCAACATG-TTGGCTTGCATCAGGTTGATCAATGTT
*
2091880 CTTTTCTTCCATGCAGAATCCACCTCCCATTTTCATGTAATCGTTAGTCGGTTCGGTTTCAGAAA
1 C-TTTCTTCCATGCAAAATCCACCTCCCATTTTCATGTAATCGTTAGTCGGTTCGGTTTCAGAAA
* * *
2091945 AGGGATCAACATGTTGGCTTGCCTCGGGTTTATC-ATCGTCT
65 AGGGATCAACATGTTGGCTTGCATCAGGTTGATCAAT-GT-T
* * * *
2091986 CTTTCTT-CAGTGCAAAATCCGCCTCCCATTTTC-TGGTAATCATTAGTTGGTTCAGTTTCAG--
1 CTTTCTTCCA-TGCAAAATCCACCTCCCATTTTCAT-GTAATCGTTAGTCGGTTCGGTTTCAGAA
* * * *
2092047 -AGGGATCAACATCTTGGTTTTCACCAGGTTGATCA
64 AAGGGATCAACATGTTGGCTTGCATCAGGTTGATCA
2092082 GTTCCCCTCT
Statistics
Matches: 168, Mismatches: 26, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
102 27 0.16
104 6 0.04
105 130 0.77
106 5 0.03
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (104 bp):
CTTTCTTCCATGCAAAATCCACCTCCCATTTTCATGTAATCGTTAGTCGGTTCGGTTTCAGAAAA
GGGATCAACATGTTGGCTTGCATCAGGTTGATCAATGTT
Found at i:2112069 original size:18 final size:18
Alignment explanation
Indices: 2111986--2112069 Score: 73
Period size: 17 Copynumber: 4.7 Consensus size: 18
2111976 ATATACGTTA
* *
2111986 GATAACTGTAAAACATAT
1 GATAACTGTAAATCATCT
*
2112004 GATAATTGTAAA-CATCT
1 GATAACTGTAAATCATCT
* *
2112021 AATAATTGTAAAT-ATCT
1 GATAACTGTAAATCATCT
* * *
2112038 TACAACTGAAAAATCATCT
1 GATAACTG-TAAATCATCT
2112057 GATAACTGTAAAT
1 GATAACTGTAAAT
2112070 ATTTAGAATA
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
17 24 0.45
18 19 0.36
19 10 0.19
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (18 bp):
GATAACTGTAAATCATCT
Found at i:2114119 original size:37 final size:36
Alignment explanation
Indices: 2114050--2114121 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
2114040 TAAATCATTC
*
2114050 TAATAATCTTTCATTAATTTTCCAACATCAAAAACA
1 TAATAATCTTTCATTAATTTTCAAACATCAAAAACA
2114086 TAATAATCTTTCATTAATTTTTCAAAC-TCCAAAAAC
1 TAATAATCTTTCATTAA-TTTTCAAACAT-CAAAAAC
2114122 CCTACATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 18 0.55
37 15 0.45
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.38
Consensus pattern (36 bp):
TAATAATCTTTCATTAATTTTCAAACATCAAAAACA
Found at i:2116573 original size:21 final size:20
Alignment explanation
Indices: 2116549--2116587 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2116539 CTCACATTTT
*
2116549 AAAAGAGGAAAAGCAAAAAAA
1 AAAAAAGGAAAAG-AAAAAAA
2116570 AAAAAAGGAAAAGAAAAA
1 AAAAAAGGAAAAGAAAAA
2116588 GAAGTGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAAAAGGAAAAGAAAAAAA
Found at i:2122286 original size:27 final size:29
Alignment explanation
Indices: 2122248--2122307 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
2122238 TCCCTAGAAA
* *
2122248 TATATTTTTAG-A-TCAAGTATCCAACAT
1 TATAATTTTAGAATTCAAATATCCAACAT
2122275 TATAATTTTAGAATTCAAATATCCAACAT
1 TATAATTTTAGAATTCAAATATCCAACAT
2122304 TATA
1 TATA
2122308 TAATACCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 10 0.34
28 1 0.03
29 18 0.62
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.40
Consensus pattern (29 bp):
TATAATTTTAGAATTCAAATATCCAACAT
Found at i:2129981 original size:17 final size:17
Alignment explanation
Indices: 2129952--2130018 Score: 109
Period size: 17 Copynumber: 4.0 Consensus size: 17
2129942 TGCAAAACAA
* *
2129952 TTAATTAAATAAAATA-
1 TTAAATAAATTAAATAC
2129968 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
2129985 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
2130002 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
2130019 AAAATATTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
16 14 0.29
17 34 0.71
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAATAAATTAAATAC
Found at i:2137690 original size:17 final size:17
Alignment explanation
Indices: 2137661--2137693 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2137651 ACGAGTCATG
2137661 TTTATATTTTTAAAATT
1 TTTATATTTTTAAAATT
2137678 TTTAT-TTTCTTAAAAT
1 TTTATATTT-TTAAAAT
2137694 ATTAAGCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTATATTTTTAAAATT
Found at i:2138050 original size:14 final size:14
Alignment explanation
Indices: 2138031--2138057 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2138021 AAACACTTAT
2138031 TTTTATATTAAATC
1 TTTTATATTAAATC
2138045 TTTTATATTAAAT
1 TTTTATATTAAAT
2138058 TGAAAATATT
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:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTTATATTAAATC
Found at i:2138992 original size:23 final size:24
Alignment explanation
Indices: 2138962--2139026 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 24
2138952 AATAGTATCA
2138962 TATATTATTAT-AATATA-ATTGAG
1 TATATTATTATAAATATATATT-AG
* *
2138985 TATATTATTGTAAATATATTATTAT
1 TATATTATTATAAATATA-TATTAG
*
2139010 TATATTATTAAAAATAT
1 TATATTATTATAAATAT
2139027 TAATAAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
23 10 0.29
24 6 0.17
25 16 0.46
26 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.51
Consensus pattern (24 bp):
TATATTATTATAAATATATATTAG
Found at i:2139027 original size:23 final size:24
Alignment explanation
Indices: 2138962--2139028 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 24
2138952 AATAGTATCA
* *
2138962 TATATTATT-ATAATATAATTGAG
1 TATATTATTAAAAATATTATTGAG
* *
2138985 TATATTATTGTAAATATATTATT-AT
1 TATATTA-T-TAAAAATATTATTGAG
2139010 TATATTATTAAAAATATTA
1 TATATTATTAAAAATATTA
2139029 ATAAATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
23 17 0.47
24 2 0.06
25 9 0.25
26 8 0.22
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (24 bp):
TATATTATTAAAAATATTATTGAG
Found at i:2139043 original size:23 final size:23
Alignment explanation
Indices: 2139010--2139065 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
2139000 ATATTATTAT
2139010 TATATTATTAAAAATATTAATAAA
1 TATATT-TTAAAAATATTAATAAA
* * *
2139034 TATATTTTAAATATGTTAATAAT
1 TATATTTTAAAAATATTAATAAA
2139057 TAATATTTT
1 T-ATATTTT
2139066 TATGAAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATAAA
Found at i:2139046 original size:11 final size:12
Alignment explanation
Indices: 2138941--2139047 Score: 78
Period size: 12 Copynumber: 8.9 Consensus size: 12
2138931 AATATAAATT
2138941 TTATTAAATATA
1 TTATTAAATATA
* * *
2138953 ATAGTATCATATA
1 TTATTA-AATATA
2138966 TTATTATAATATA
1 TTATTA-AATATA
* *
2138979 --ATTGAGTATA
1 TTATTAAATATA
2138989 TTATTGTAAATATA
1 TTA-T-TAAATATA
*
2139003 TTATT-ATTATA
1 TTATTAAATATA
*
2139014 TTATTAAAAATA
1 TTATTAAATATA
*
2139026 TTAATAAATATA
1 TTATTAAATATA
2139038 TT-TTAAATAT
1 TTATTAAATAT
2139048 GTTAATAATT
Statistics
Matches: 73, Mismatches: 16, Indels: 13
0.72 0.16 0.13
Matches are distributed among these distances:
10 5 0.07
11 20 0.27
12 22 0.30
13 17 0.23
14 9 0.12
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.49
Consensus pattern (12 bp):
TTATTAAATATA
Found at i:2143341 original size:21 final size:21
Alignment explanation
Indices: 2143317--2143356 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2143307 TTTAACTATA
*
2143317 TATTTTAG-AGATTATTAATTG
1 TATTATAGTAGATT-TTAATTG
2143338 TATTATAGTAGATTTTAAT
1 TATTATAGTAGATTTTAAT
2143357 CTAAATGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (21 bp):
TATTATAGTAGATTTTAATTG
Found at i:2144144 original size:55 final size:55
Alignment explanation
Indices: 2144076--2144195 Score: 161
Period size: 55 Copynumber: 2.2 Consensus size: 55
2144066 CAAATTAATG
* * * *
2144076 AGTTTAGGCTTGAGTACTGTAATGGGTCTTTATGATGGTTGAGAATTAATACAGT
1 AGTTTACGTTTGAGTACTGTAATAGGTATTTATGATGGTTGAGAATTAATACAGT
* * *
2144131 AGTTTACGTTTGAGTACTGTATTAGGTATTTATGTTGGTTGGGAATTAATACAGT
1 AGTTTACGTTTGAGTACTGTAATAGGTATTTATGATGGTTGAGAATTAATACAGT
*
2144186 A-TTTATGTTT
1 AGTTTACGTTT
2144196 AGGTGAATTT
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
54 8 0.14
55 49 0.86
ACGTcount: A:0.26, C:0.06, G:0.25, T:0.43
Consensus pattern (55 bp):
AGTTTACGTTTGAGTACTGTAATAGGTATTTATGATGGTTGAGAATTAATACAGT
Found at i:2145096 original size:24 final size:23
Alignment explanation
Indices: 2145058--2145132 Score: 63
Period size: 24 Copynumber: 3.4 Consensus size: 23
2145048 AAAGAAGAAA
**
2145058 TAAAAATAAAGAAAAAAATAAAAT
1 TAAAAATAATTAAAAAAAT-AAAT
2145082 TAAAAATAATT---AAAAT-AAT
1 TAAAAATAATTAAAAAAATAAAT
2145101 T-AAAATAATTAAAAATAA-ATAAT
1 TAAAAATAATTAAAAA-AATA-AAT
2145124 TAAAAATAA
1 TAAAAATAA
2145133 AGAAAAATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
18 9 0.21
19 4 0.10
21 7 0.17
22 2 0.05
23 4 0.10
24 16 0.38
ACGTcount: A:0.73, C:0.00, G:0.01, T:0.25
Consensus pattern (23 bp):
TAAAAATAATTAAAAAAATAAAT
Found at i:2145098 original size:9 final size:9
Alignment explanation
Indices: 2145079--2145114 Score: 63
Period size: 9 Copynumber: 3.9 Consensus size: 9
2145069 AAAAAAATAA
2145079 AATTAAAAAT
1 AATT-AAAAT
2145089 AATTAAAAT
1 AATTAAAAT
2145098 AATTAAAAT
1 AATTAAAAT
2145107 AATTAAAA
1 AATTAAAA
2145115 ATAAATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 22 0.85
10 4 0.15
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AATTAAAAT
Found at i:2149972 original size:20 final size:20
Alignment explanation
Indices: 2149937--2149987 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2149927 TAAATAACTA
*
2149937 TATATAA-ATGAATATATAAT
1 TATATAACATAAATATAT-AT
2149957 T-TATAACATAAATATATAT
1 TATATAACATAAATATATAT
*
2149976 TATATAATATAA
1 TATATAACATAA
2149988 TAACGTTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 8 0.30
20 19 0.70
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (20 bp):
TATATAACATAAATATATAT
Found at i:2149978 original size:18 final size:17
Alignment explanation
Indices: 2149925--2149989 Score: 51
Period size: 18 Copynumber: 3.5 Consensus size: 17
2149915 AAAAAGTGTT
2149925 AATAAATA-ACTATATATA
1 AATAAATATA-TAT-TATA
*
2149943 AATGAATATATAATTTATA
1 AATAAATATAT-A-TTATA
2149962 ACATAAATATATATTATA
1 A-ATAAATATATATTATA
2149980 TAATATAATA
1 -AATA-AATA
2149990 ACGTTTGAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
18 16 0.41
19 13 0.33
20 10 0.26
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (17 bp):
AATAAATATATATTATA
Found at i:2150334 original size:30 final size:30
Alignment explanation
Indices: 2150300--2150361 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
2150290 AACACATTTC
**
2150300 CATATAATTCACAT-ATCACATATTTCATGT
1 CATATAA-TCACATGATCACATAGCTCATGT
* *
2150330 CATATTATCATATGATCACATAGCTCATGT
1 CATATAATCACATGATCACATAGCTCATGT
2150360 CA
1 CA
2150362 CTTAATCTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 5 0.19
30 22 0.81
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.37
Consensus pattern (30 bp):
CATATAATCACATGATCACATAGCTCATGT
Found at i:2150933 original size:20 final size:21
Alignment explanation
Indices: 2150908--2150962 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
2150898 CGATGTTGTC
2150908 TGGTATCGATACCCT-TAAC-A
1 TGGTATCGATACCCTAT-ACTA
*
2150928 TGGTATCGATACTACTATACTA
1 TGGTATCGATAC-CCTATACTA
2150950 TGGTATCGATACC
1 TGGTATCGATACC
2150963 TCCTCATTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 12 0.40
21 4 0.13
22 14 0.47
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (21 bp):
TGGTATCGATACCCTATACTA
Found at i:2152375 original size:21 final size:21
Alignment explanation
Indices: 2152349--2152393 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2152339 GATTTCTGGG
* *
2152349 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2152370 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2152391 CAA
1 CAA
2152394 ACGACAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2152997 original size:18 final size:18
Alignment explanation
Indices: 2152974--2153008 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2152964 CTAGGAGATT
2152974 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
2152992 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
2153009 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:2153094 original size:21 final size:22
Alignment explanation
Indices: 2153065--2153108 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2153055 GTTGTATGAT
2153065 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
2153086 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
2153108 A
1 A
2153109 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:2154165 original size:149 final size:147
Alignment explanation
Indices: 2153985--2154286 Score: 568
Period size: 149 Copynumber: 2.0 Consensus size: 147
2153975 GAGTCGAGGG
2153985 TCTACGCGGTTCTTCGAGATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACATAC
1 TCTACGCGGTTCTTCGAGATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACATAC
* *
2154050 TTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTATA
66 TTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTATA
2154115 TGGCACTACGGTGCAAT
131 TGGCACTACGGTGCAAT
2154132 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGAG--ATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
2154197 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
64 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
2154262 TATGGCACTACGGTGCAAT
129 TATGGCACTACGGTGCAAT
2154281 TCTACG
1 TCTACG
2154287 GGGCACTTCG
Statistics
Matches: 151, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
147 18 0.12
149 133 0.88
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (147 bp):
TCTACGCGGTTCTTCGAGATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTATA
TGGCACTACGGTGCAAT
Found at i:2154309 original size:23 final size:23
Alignment explanation
Indices: 2154265--2154309 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2154255 ATCATTATAT
*
2154265 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
2154288 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
2154310 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:2157466 original size:21 final size:21
Alignment explanation
Indices: 2157440--2157484 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2157430 GATTTCTGGG
* *
2157440 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2157461 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2157482 CAA
1 CAA
2157485 ACGACAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2158088 original size:18 final size:18
Alignment explanation
Indices: 2158065--2158099 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2158055 CTAGGAGATT
2158065 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
2158083 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
2158100 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:2158185 original size:21 final size:22
Alignment explanation
Indices: 2158156--2158199 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2158146 GTTGTATGAT
2158156 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
2158177 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
2158199 A
1 A
2158200 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:2159267 original size:149 final size:149
Alignment explanation
Indices: 2159082--2159385 Score: 554
Period size: 149 Copynumber: 2.0 Consensus size: 149
2159072 GAGTCGAGGG
*
2159082 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTATTTGGAACATGTGTGAAGTCTAGAAAGACACAT
* * *
2159147 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGATTTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
2159212 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* *
2159231 TTTACGCGGTTCTTCGAGACATATGTATATTATTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTATTTGGAACATGTGTGAAGTCTAGAAAGACACAT
2159296 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
2159361 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
2159380 TCTACG
1 TCTACG
2159386 GGGCACTTCG
Statistics
Matches: 148, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
149 148 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGAGACATATGTATATTATTTGGAACATGTGTGAAGTCTAGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:2159408 original size:23 final size:23
Alignment explanation
Indices: 2159364--2159408 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2159354 ATCATTATAT
*
2159364 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
2159387 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
2159409 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:2160975 original size:11 final size:11
Alignment explanation
Indices: 2160959--2160991 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
2160949 TTTATCATTT
2160959 TAAAACACACA
1 TAAAACACACA
*
2160970 TAAAACACACT
1 TAAAACACACA
2160981 TAAAACACACA
1 TAAAACACACA
2160992 CTTCTCCCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.61, C:0.27, G:0.00, T:0.12
Consensus pattern (11 bp):
TAAAACACACA
Found at i:2172451 original size:5 final size:6
Alignment explanation
Indices: 2172436--2172467 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
2172426 AAAATTTACC
2172436 AAAAAT AAAAAT AAAAAT AAAAAT -AAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAA
2172468 TTCATTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:2175453 original size:55 final size:55
Alignment explanation
Indices: 2175381--2175489 Score: 146
Period size: 55 Copynumber: 2.0 Consensus size: 55
2175371 AAAATTAATG
*
2175381 AGTTTAGGTTTCAGTACTGTAGTGGGTAGGTAGGTTGGTTGAGAATTAATACAGT
1 AGTTTAGGTTTCAGTACTGTAGTGGGTAGGTAGGTTGGTAGAGAATTAATACAGT
* * * ** * *
2175436 AGTTTAGGTTTGAGTACTGTATTTGGTATTTATGTTGGTAGGGAATTAATACAG
1 AGTTTAGGTTTCAGTACTGTAGTGGGTAGGTAGGTTGGTAGAGAATTAATACAG
2175490 AATTTATGTT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.26, C:0.05, G:0.30, T:0.39
Consensus pattern (55 bp):
AGTTTAGGTTTCAGTACTGTAGTGGGTAGGTAGGTTGGTAGAGAATTAATACAGT
Found at i:2176476 original size:23 final size:23
Alignment explanation
Indices: 2176446--2176500 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
2176436 TTTTAATTTC
2176446 CCATCATCTTGTAAATATGTCGA
1 CCATCATCTTGTAAATATGTCGA
2176469 CCATCATCTTGTAAATATGTCGA
1 CCATCATCTTGTAAATATGTCGA
2176492 CCATCATCT
1 CCATCATCT
2176501 CTTGCAACAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (23 bp):
CCATCATCTTGTAAATATGTCGA
Found at i:2181771 original size:31 final size:31
Alignment explanation
Indices: 2181736--2181799 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
2181726 TTTTCAGACA
2181736 TGATTTAACAGGAAAGAAACATCAATTAAAC
1 TGATTTAACAGGAAAGAAACATCAATTAAAC
*
2181767 TGATTTAACAGGAATGAAACATCAATTAAAC
1 TGATTTAACAGGAAAGAAACATCAATTAAAC
2181798 TG
1 TG
2181800 TCCTGTGACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.25
Consensus pattern (31 bp):
TGATTTAACAGGAAAGAAACATCAATTAAAC
Found at i:2182335 original size:23 final size:23
Alignment explanation
Indices: 2182305--2182350 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
2182295 TTACAAGCAG
*
2182305 CTTATCAAATTTTGAAAGTAAGT
1 CTTATCAAATTTAGAAAGTAAGT
2182328 CTTATCAAATTTAGAAAGTAAGT
1 CTTATCAAATTTAGAAAGTAAGT
2182351 TCCGATTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (23 bp):
CTTATCAAATTTAGAAAGTAAGT
Found at i:2190413 original size:255 final size:253
Alignment explanation
Indices: 2189831--2190569 Score: 1218
Period size: 253 Copynumber: 2.9 Consensus size: 253
2189821 TTCAGATCGG
* *
2189831 GTCGGTTTTTTTAAGTGTAATACTTGGGTCGAGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGA
1 GTCGGTTTTTTTAAGTGTGATA-TTGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGA
2189896 CCCGACCCGAAAAAATATATAATTTTACCTTATATTTTAGGAATAATTACAATAATACCCCTCTA
65 CCCGACCCG-AAAAATATATAATTTTACCTTATATTTTAGGAATAATTACAATAATACCCCTCTA
*
2189961 TATATAATTTTTTTCAATTAAGTCACTATTTTTATTGAAT---AAT-TTTTTTTATTATTTCAGG
129 TATATAA-TTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAATATTTTTTTATTATTTCGGG
* * * *
2190022 TCGGGTTTTTAATTCATATATTCAGGTCAGGTCGGGTGAAACTTTATTTTGGTCGGGTCGG
193 TCGGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGA
*
2190083 GTCGGGTTTTTTTAAGTGTGATATTTGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCTG
1 GTC-GGTTTTTTTAAGTGTGATA-TTGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCG
2190148 ACCCGACCCGAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCT
64 ACCCGACCCGAAAAATATATAATTTTACCTTATAT-TTTAGGAATAATTACAATAATACCCCTCT
* *
2190213 CTATATATATTTTTTCAATTAAGTCACTGTTTTTATTGAATAAAAATATTTTTTTATTATTTCGG
128 ATATATA-ATTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAATATTTTTTTATTATTTCGG
*
2190278 GTCAGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGA
192 GTCGGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGA
2190340 GTCGG-TTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGA
1 GTCGGTTTTTTTAAGTGTGATATT-GGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGA
*
2190404 CCCGACCCGAAAAATATATAATTTTACCTTATATTTTGGGAATAATTACAATAATACCCCTCTAT
65 CCCGACCCGAAAAATATATAATTTTACCTTATATTTTAGGAATAATTACAATAATACCCCTCTAT
2190469 ATATAATTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAATATTTTTTTATTATTTCGGTTC
130 ATATAATTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAATATTTTTTTATTA--T---TTC
2190534 GGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTC
190 GGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTC
2190570 TCGGATGGAG
Statistics
Matches: 457, Mismatches: 17, Indels: 20
0.93 0.03 0.04
Matches are distributed among these distances:
252 28 0.06
253 183 0.40
254 37 0.08
255 90 0.20
256 5 0.01
257 76 0.17
258 38 0.08
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (253 bp):
GTCGGTTTTTTTAAGTGTGATATTGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGAC
CCGACCCGAAAAATATATAATTTTACCTTATATTTTAGGAATAATTACAATAATACCCCTCTATA
TATAATTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAATATTTTTTTATTATTTCGGGTCG
GGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGA
Found at i:2206479 original size:14 final size:15
Alignment explanation
Indices: 2206460--2206490 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2206450 AACTTTACAC
2206460 TAATTAAAAAA-ACT
1 TAATTAAAAAAGACT
2206474 TAATTAAAAAAGACT
1 TAATTAAAAAAGACT
2206489 TA
1 TA
2206491 CGTCTCAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.29
Consensus pattern (15 bp):
TAATTAAAAAAGACT
Found at i:2207126 original size:2 final size:2
Alignment explanation
Indices: 2207119--2207151 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2207109 GTAGCTATTA
2207119 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2207152 CGGATAAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2207176 original size:8 final size:8
Alignment explanation
Indices: 2207160--2207193 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
2207150 TACGGATAAG
2207160 TAATTAAA
1 TAATTAAA
*
2207168 TAGTTAAA
1 TAATTAAA
2207176 TAATTAAA
1 TAATTAAA
2207184 TAATTAAA
1 TAATTAAA
2207192 TA
1 TA
2207194 TATAAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (8 bp):
TAATTAAA
Found at i:2217265 original size:8 final size:8
Alignment explanation
Indices: 2217252--2217277 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2217242 AGATTCTCCC
2217252 ATATGTAT
1 ATATGTAT
2217260 ATATGTAT
1 ATATGTAT
2217268 ATATGTAT
1 ATATGTAT
2217276 AT
1 AT
2217278 CTTCTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (8 bp):
ATATGTAT
Found at i:2220797 original size:16 final size:16
Alignment explanation
Indices: 2220778--2220820 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
2220768 AAAATGAGTG
2220778 AAAATGAAAAAATAAA
1 AAAATGAAAAAATAAA
*
2220794 AAAAT-AAAAAA-ATA
1 AAAATGAAAAAATAAA
2220808 AAAATGAAAAAAT
1 AAAATGAAAAAAT
2220821 GGAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 7 0.29
15 12 0.50
16 5 0.21
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (16 bp):
AAAATGAAAAAATAAA
Found at i:2220818 original size:8 final size:8
Alignment explanation
Indices: 2220778--2220828 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
2220768 AAAATGAGTG
2220778 AAAATGAA
1 AAAATGAA
*
2220786 AAAATAAA
1 AAAATGAA
*
2220794 AAAATAAA
1 AAAATGAA
2220802 AAAAT--A
1 AAAATGAA
2220808 AAAATGAA
1 AAAATGAA
2220816 AAAATGGAA
1 AAAAT-GAA
2220825 AAAA
1 AAAA
2220829 AAAGAAGGGT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
6 6 0.15
8 26 0.67
9 7 0.18
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (8 bp):
AAAATGAA
Found at i:2220827 original size:16 final size:14
Alignment explanation
Indices: 2220778--2220820 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
2220768 AAAATGAGTG
2220778 AAAATGAAAAAATAAA
1 AAAATGAAAAAAT--A
*
2220794 AAAATAAAAAAATA
1 AAAATGAAAAAATA
2220808 AAAATGAAAAAAT
1 AAAATGAAAAAAT
2220821 GGAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.52
16 12 0.48
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (14 bp):
AAAATGAAAAAATA
Found at i:2221827 original size:55 final size:55
Alignment explanation
Indices: 2221759--2222245 Score: 875
Period size: 55 Copynumber: 8.9 Consensus size: 55
2221749 GGTTTCCCAA
*
2221759 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGATG
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
2221814 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* *
2221869 CGATCATTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGATG
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
*
2221924 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACA
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
2221979 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* * *
2222034 CGATCATTGAAAATTGTTCGAGTCTTATACTCTTTGAAGAAATAGGGGGCAGACG
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* *
2222089 CGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACA
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
2222144 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
* *
2222199 CGATCATTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAAGAGGG
1 CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGG
2222246 AGCGAACCCG
Statistics
Matches: 413, Mismatches: 19, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 413 1.00
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (55 bp):
CGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACG
Found at i:2222578 original size:2 final size:2
Alignment explanation
Indices: 2222571--2222601 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2222561 GTAGCTATTA
2222571 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2222602 CGGATAAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2222626 original size:8 final size:8
Alignment explanation
Indices: 2222610--2222643 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
2222600 TACGGATAAG
2222610 TAATTAAA
1 TAATTAAA
*
2222618 TAGTTAAA
1 TAATTAAA
2222626 TAATTAAA
1 TAATTAAA
2222634 TAATTAAA
1 TAATTAAA
2222642 TA
1 TA
2222644 TATAAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (8 bp):
TAATTAAA
Found at i:2224567 original size:13 final size:13
Alignment explanation
Indices: 2224549--2224573 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2224539 TATATAGTTT
2224549 TTTTTATTTATTC
1 TTTTTATTTATTC
2224562 TTTTTATTTATT
1 TTTTTATTTATT
2224574 TCACGTTGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTATTTATTC
Found at i:2231353 original size:20 final size:20
Alignment explanation
Indices: 2231286--2231352 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
2231276 AATCTGTAAA
2231286 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
2231306 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* *
2231326 TCACAACGCTAAAA-TCAAAT
1 TCGCAACAC-AAAAGTCAAAT
2231346 TCGCAAC
1 TCGCAAC
2231353 GTAAACTCCA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 39 0.91
21 4 0.09
ACGTcount: A:0.48, C:0.27, G:0.09, T:0.16
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:2231407 original size:21 final size:20
Alignment explanation
Indices: 2231370--2231454 Score: 125
Period size: 20 Copynumber: 4.2 Consensus size: 20
2231360 CCAATTTCGT
*
2231370 AACGTGAATAGAAAAATCGC
1 AACGTGAATAGTAAAATCGC
2231390 AACGTGAATAGTAAAAATCGC
1 AACGTGAATAGT-AAAATCGC
**
2231411 AACGTGAATAGTAAAATTAC
1 AACGTGAATAGTAAAATCGC
*
2231431 AACGTGAATAGTAAAATCGT
1 AACGTGAATAGTAAAATCGC
2231451 AACG
1 AACG
2231455 AATCTATATG
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 38 0.66
21 20 0.34
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.20
Consensus pattern (20 bp):
AACGTGAATAGTAAAATCGC
Found at i:2231419 original size:41 final size:40
Alignment explanation
Indices: 2231370--2231454 Score: 125
Period size: 41 Copynumber: 2.1 Consensus size: 40
2231360 CCAATTTCGT
*
2231370 AACGTGAATAGAAAAATCGCAACGTGAATAGTAAAAATCGC
1 AACGTGAATAGAAAAATCACAACGTGAATAGT-AAAATCGC
* * *
2231411 AACGTGAATAGTAAAATTACAACGTGAATAGTAAAATCGT
1 AACGTGAATAGAAAAATCACAACGTGAATAGTAAAATCGC
2231451 AACG
1 AACG
2231455 AATCTATATG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 11 0.28
41 29 0.73
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.20
Consensus pattern (40 bp):
AACGTGAATAGAAAAATCACAACGTGAATAGTAAAATCGC
Found at i:2231859 original size:19 final size:20
Alignment explanation
Indices: 2231804--2231894 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
2231794 CAACGCGATT
*
2231804 TTGCGATTTT-CTAAATTCGCG
1 TTGCGATTTTACT--ATTCACG
*
2231825 TTGCGATTTTATTATTCACG
1 TTGCGATTTTACTATTCACG
*
2231845 TTGTG-TTTTACTATTCACG
1 TTGCGATTTTACTATTCACG
2231864 TTGCGATTTTTACTATTCACG
1 TTGCGA-TTTTACTATTCACG
*
2231885 CTGCGATTTT
1 TTGCGATTTT
2231895 GGAAACTGAG
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
19 17 0.28
20 14 0.23
21 29 0.48
22 1 0.02
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (20 bp):
TTGCGATTTTACTATTCACG
Found at i:2232781 original size:61 final size:59
Alignment explanation
Indices: 2232712--2232897 Score: 178
Period size: 60 Copynumber: 3.1 Consensus size: 59
2232702 AGTATAGTTC
2232712 GGGATGAAATTGGAATGTTCAAAAAGTATGGGGACTAATTTAGAATGAAGGTCATAGTTTG
1 GGGATGAAATTGGAATGTTC-AAAAGT-TGGGGACTAATTTAGAATGAAGGTCATAGTTTG
* * * * *
2232773 GGGATGAAATTGAAATGTTCAAAAGCTTGAGTACTAATTTGGAATGATA-GTCATAGTTTA
1 GGGATGAAATTGGAATGTTCAAAAG-TTGGGGACTAATTTAGAATGA-AGGTCATAGTTTG
* * * * * * * *
2232833 GGGATTAAATTAGAATATTTAAAAGTTTAGAGACTAATTTAAAAT-AAGGGTCATACTTTG
1 GGGATGAAATTGGAATGTTCAAAAG-TTGGGGACTAATTTAGAATGAA-GGTCATAGTTTG
*
2232893 AGGAT
1 GGGAT
2232898 ACATTATGCA
Statistics
Matches: 101, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
58 1 0.01
59 1 0.01
60 78 0.77
61 21 0.21
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.32
Consensus pattern (59 bp):
GGGATGAAATTGGAATGTTCAAAAGTTGGGGACTAATTTAGAATGAAGGTCATAGTTTG
Found at i:2237710 original size:29 final size:29
Alignment explanation
Indices: 2237677--2237755 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
2237667 CGGTGATCGG
* *
2237677 TATATTTATTGATCTAACACTGGTTAGAT
1 TATATTTATTGATCTAACACCGATTAGAT
*
2237706 TATATTTTTTGATCTAACACCGATTAGAT
1 TATATTTATTGATCTAACACCGATTAGAT
***
2237735 TATATTTCCCGATCTAACACC
1 TATATTTATTGATCTAACACC
2237756 TGTAGCAGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.42
Consensus pattern (29 bp):
TATATTTATTGATCTAACACCGATTAGAT
Found at i:2238156 original size:17 final size:18
Alignment explanation
Indices: 2238119--2238159 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2238109 ATATTATGTA
*
2238119 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
2238137 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
2238154 TTTACT
1 TTTACT
2238160 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:2242266 original size:48 final size:48
Alignment explanation
Indices: 2242210--2242318 Score: 141
Period size: 48 Copynumber: 2.3 Consensus size: 48
2242200 AAATATTTTA
2242210 TCTGATTTCTGA-CTTGAATTCTGTTCTCATAAAT-TACCTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGTTCTCATAAATGT-CCTGAATTCTGT
* * * *
2242258 TCTGATTTCTGATCTGGATTCTGTTCTGATATATGTTCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGTTCTCATAAATGTCCTGAATTCTGT
*
2242306 TTTGATTTCTGAT
1 TCTGATTTCTGAT
2242319 ATCTTCGTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
48 52 0.96
49 2 0.04
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.50
Consensus pattern (48 bp):
TCTGATTTCTGATCTGAATTCTGTTCTCATAAATGTCCTGAATTCTGT
Found at i:2242267 original size:12 final size:12
Alignment explanation
Indices: 2242247--2242316 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
2242237 CATAAATTAC
*
2242247 CTGAATTCTGTT
1 CTGATTTCTGTT
*
2242259 CTGATTTCTGAT
1 CTGATTTCTGTT
2242271 CTGGA-TTCTGTT
1 CT-GATTTCTGTT
* *
2242283 CTGATATATGTT
1 CTGATTTCTGTT
*
2242295 CTGAATTCTGTT
1 CTGATTTCTGTT
*
2242307 TTGATTTCTG
1 CTGATTTCTG
2242317 ATATCTTCGT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.91
13 2 0.04
ACGTcount: A:0.16, C:0.14, G:0.19, T:0.51
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:2242278 original size:24 final size:24
Alignment explanation
Indices: 2242210--2242318 Score: 103
Period size: 24 Copynumber: 4.5 Consensus size: 24
2242200 AAATATTTTA
2242210 TCTGATTTCTGA-CTTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGT
* *** * *
2242234 TCTCATAAATTACCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
2242258 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* * *
2242282 TCTGATATATGTTCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
2242306 TTTGATTTCTGAT
1 TCTGATTTCTGAT
2242319 ATCTTCGTTT
Statistics
Matches: 64, Mismatches: 20, Indels: 2
0.74 0.23 0.02
Matches are distributed among these distances:
24 63 0.98
25 1 0.02
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.50
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:2253638 original size:18 final size:18
Alignment explanation
Indices: 2253615--2253660 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
2253605 TTTGATACCC
* *
2253615 TGACAAATGTATAAAAAT
1 TGACAAAAGCATAAAAAT
2253633 TGACAAAAGCATAAAAAT
1 TGACAAAAGCATAAAAAT
2253651 TGACAAAAGC
1 TGACAAAAGC
2253661 TTCATTCCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.57, C:0.11, G:0.13, T:0.20
Consensus pattern (18 bp):
TGACAAAAGCATAAAAAT
Found at i:2255211 original size:216 final size:216
Alignment explanation
Indices: 2254837--2255272 Score: 863
Period size: 216 Copynumber: 2.0 Consensus size: 216
2254827 GCAGGGAAAG
2254837 TTGGGACATATCAGCTCATCACTAGCTTTGGCAGTGAAGTCATGGTGGAAACCTTCGTTCACTTT
1 TTGGGACATATCAGCTCATCACTAGCTTTGGCAGTGAAGTCATGGTGGAAACCTTCGTTCACTTT
2254902 CAGTGTTTCCGGTATGCCTTTTTATTTGCCAGAACTCGATATTTATTACCACTATGGGTAATAAC
66 CAGTGTTTCCGGTATGCCTTTTTATTTGCCAGAACTCGATATTTATTACCACTATGGGTAATAAC
2254967 GGTTTGGTTTATATCAATTTGAAAAATATTAAAAACCAAACTAATTAGCAAAGGTAATCGAACCG
131 GGTTTGGTTTATATCAATTTGAAAAATATTAAAAACCAAACTAATTAGCAAAGGTAATCGAACCG
2255032 ATCCAAACCAAATCCATCTGC
196 ATCCAAACCAAATCCATCTGC
*
2255053 TTGGGACATCTCAGCTCATCACTAGCTTTGGCAGTGAAGTCATGGTGGAAACCTTCGTTCACTTT
1 TTGGGACATATCAGCTCATCACTAGCTTTGGCAGTGAAGTCATGGTGGAAACCTTCGTTCACTTT
2255118 CAGTGTTTCCGGTATGCCTTTTTATTTGCCAGAACTCGATATTTATTACCACTATGGGTAATAAC
66 CAGTGTTTCCGGTATGCCTTTTTATTTGCCAGAACTCGATATTTATTACCACTATGGGTAATAAC
2255183 GGTTTGGTTTATATCAATTTGAAAAATATTAAAAACCAAACTAATTAGCAAAGGTAATCGAACCG
131 GGTTTGGTTTATATCAATTTGAAAAATATTAAAAACCAAACTAATTAGCAAAGGTAATCGAACCG
2255248 ATCCAAACCAAATCCATCTGC
196 ATCCAAACCAAATCCATCTGC
2255269 TTGG
1 TTGG
2255273 TTCATCGTTT
Statistics
Matches: 219, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
216 219 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (216 bp):
TTGGGACATATCAGCTCATCACTAGCTTTGGCAGTGAAGTCATGGTGGAAACCTTCGTTCACTTT
CAGTGTTTCCGGTATGCCTTTTTATTTGCCAGAACTCGATATTTATTACCACTATGGGTAATAAC
GGTTTGGTTTATATCAATTTGAAAAATATTAAAAACCAAACTAATTAGCAAAGGTAATCGAACCG
ATCCAAACCAAATCCATCTGC
Found at i:2264708 original size:15 final size:16
Alignment explanation
Indices: 2264676--2264710 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
2264666 TTATAATCAA
2264676 AAGATGAAGAAGTTAT
1 AAGATGAAGAAGTTAT
2264692 AAGATGAAGAA-TTAT
1 AAGATGAAGAAGTTAT
2264707 AAGA
1 AAGA
2264711 GATTTAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (16 bp):
AAGATGAAGAAGTTAT
Found at i:2265703 original size:15 final size:15
Alignment explanation
Indices: 2265685--2265718 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
2265675 GAGGGTATTA
2265685 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
2265700 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
2265715 TAGT
1 TAGT
2265719 GGTCCTACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.15, C:0.24, G:0.32, T:0.29
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:2265834 original size:13 final size:13
Alignment explanation
Indices: 2265816--2265841 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2265806 TGACAGCATT
2265816 GGTGCACAACCTC
1 GGTGCACAACCTC
2265829 GGTGCACAACCTC
1 GGTGCACAACCTC
2265842 AATGTACTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.38, G:0.23, T:0.15
Consensus pattern (13 bp):
GGTGCACAACCTC
Found at i:2272550 original size:15 final size:15
Alignment explanation
Indices: 2272532--2272562 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2272522 CGAAGGTATT
2272532 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
2272547 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
2272562 G
1 G
2272563 AATACTGAAC
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:0.13, C:0.26, G:0.35, T:0.26
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:2296028 original size:257 final size:255
Alignment explanation
Indices: 2295531--2296071 Score: 811
Period size: 257 Copynumber: 2.1 Consensus size: 255
2295521 TTTTATTATT
2295531 TCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTCAGGTGAAACTTTATTTTGGTCGGGTCG
1 TCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTCAGGTGAAACTTTATTTTGGTCGGGTCG
* * *
2295596 ATTTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCG
66 AGTTTTTTAAGTGGGATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAAAACCCGACCCG
* * *
2295661 AAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTCTATATATA
131 AAAAAATATATAATTTTACCTTATATATTTAAGAATAATTACAATAATACCCCTCTATATATATA
* *
2295726 TTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAATATTTTTTTATTATTTTGGGTCGGG
196 TTTTTTCAATTAAATCAATATTTTTATTGAAT--AAATATTTTTTTATTATTTTGGGTCGGG
* * *
2295788 TCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGTTCGGGTCG
1 TCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTCAGGTGAAACTTTATTTTGGTCGGGTCG
* * *
2295853 GGTTTTTTAAGTGGGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGT-AAAAAAACCGGACCGA
66 AGTTTTTTAAGTGGGATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAAAACCCGACC--
2295917 CTTGAAAAAAATATATAATTTTACCTTATATATTTAAGAATAATTACAATAATACCCCTCTATAT
129 C--G-AAAAAATATATAATTTTACCTTATATATTTAAGAATAATTACAATAATACCCCTCTATAT
* * * * *
2295982 ATA-ATTTTTTTCAATTAAATTAATGTTTTTATTGAAT-AAT-TTTTTTTATTATTTTGTGTTGT
191 ATATA-TTTTTTCAATTAAATCAATATTTTTATTGAATAAATATTTTTTTATTATTTTGGGTCGG
2296044 G
255 G
2296045 TCGGGTCGGGTTTCTAATTCATATATT
1 TCGGGTCGGGTTTCTAATTCATATATT
2296072 GAATAAAAAT
Statistics
Matches: 258, Mismatches: 20, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
256 12 0.05
257 152 0.59
258 4 0.02
260 2 0.01
261 88 0.34
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (255 bp):
TCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTCAGGTGAAACTTTATTTTGGTCGGGTCG
AGTTTTTTAAGTGGGATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAAAACCCGACCCG
AAAAAATATATAATTTTACCTTATATATTTAAGAATAATTACAATAATACCCCTCTATATATATA
TTTTTTCAATTAAATCAATATTTTTATTGAATAAATATTTTTTTATTATTTTGGGTCGGG
Found at i:2298235 original size:35 final size:35
Alignment explanation
Indices: 2298121--2298257 Score: 163
Period size: 36 Copynumber: 3.9 Consensus size: 35
2298111 TTTAGATCCG
* *
2298121 TAAGTAATTACCAGTTCGATCAGTCTGAA--TATA
1 TAAGGAATTACCAGTTCGATCGGTCTGAACCTATA
* * * *
2298154 TAAGGAATTATCAGTTTGATCGATCTGAACCTACCA
1 TAAGGAATTACCAGTTCGATCGGTCTGAACCTA-TA
*
2298190 TAAGGAATTACAAGTTCGATCGGTCTGAACCTATA
1 TAAGGAATTACCAGTTCGATCGGTCTGAACCTATA
*
2298225 TAAGGAATTACCAGTTTGATCGAGT-TGAACCTA
1 TAAGGAATTACCAGTTCGATCG-GTCTGAACCTA
2298258 CAAAGATTTC
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
33 24 0.28
35 31 0.36
36 32 0.37
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (35 bp):
TAAGGAATTACCAGTTCGATCGGTCTGAACCTATA
Found at i:2298243 original size:71 final size:69
Alignment explanation
Indices: 2298121--2298258 Score: 206
Period size: 71 Copynumber: 2.0 Consensus size: 69
2298111 TTTAGATCCG
* * *
2298121 TAAGTAATTACCAGTTCGATCAGTCTGAATATATAAGGAATTATCAGTTTGATCGA-TCTGAACC
1 TAAGGAATTACAAGTTCGATCAGTCTGAATATATAAGGAATTACCAGTTTGATCGAGT-TGAACC
2298185 TACCA
65 TACCA
*
2298190 TAAGGAATTACAAGTTCGATCGGTCTGAACCTATATAAGGAATTACCAGTTTGATCGAGTTGAAC
1 TAAGGAATTACAAGTTCGATCAGTCTGAA--TATATAAGGAATTACCAGTTTGATCGAGTTGAAC
2298255 CTAC
64 CTAC
2298259 AAAGATTTCA
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
69 26 0.42
71 35 0.56
72 1 0.02
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (69 bp):
TAAGGAATTACAAGTTCGATCAGTCTGAATATATAAGGAATTACCAGTTTGATCGAGTTGAACCT
ACCA
Found at i:2298770 original size:35 final size:35
Alignment explanation
Indices: 2298730--2298800 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
2298720 AAATATGACA
*
2298730 TGAGTGATTCCATTATTCAGGAAATCAGAGACATT
1 TGAGTGATTCCATTATTCAGGAAATCAAAGACATT
2298765 TGAGTGATTCCATTATTCAGGAAATCAAAGACATT
1 TGAGTGATTCCATTATTCAGGAAATCAAAGACATT
2298800 T
1 T
2298801 CAGATATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.32
Consensus pattern (35 bp):
TGAGTGATTCCATTATTCAGGAAATCAAAGACATT
Found at i:2301225 original size:29 final size:30
Alignment explanation
Indices: 2301155--2301214 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
2301145 CAATTTAAAG
2301155 CAAAATGGTTTTTGGAATTGAATTGAATTTA
1 CAAAAT-GTTTTTGGAATTGAATTGAATTTA
* *
2301186 CAAAATATTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGAATTGAATTGAATTTA
2301215 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 11 0.41
30 10 0.37
31 6 0.22
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGAATTGAATTGAATTTA
Found at i:2301320 original size:21 final size:19
Alignment explanation
Indices: 2301294--2301388 Score: 91
Period size: 21 Copynumber: 4.6 Consensus size: 19
2301284 AGGGTGTCAA
*
2301294 AGTGCATCCATGTACCCATGC
1 AGTGCATCCATGCA-CC-TGC
*
2301315 AGTGCATCCATACATCCCTGC
1 AGTGCATCCATGCA--CCTGC
2301336 AGTGCATCCATGCACCTGCAC
1 AGTGCATCCATGCACCTG--C
*
2301357 TAGTGCATCGATGCACCATGC
1 -AGTGCATCCATGCACC-TGC
2301378 AGTGCATCCAT
1 AGTGCATCCAT
2301389 ACACTCAAAC
Statistics
Matches: 64, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
19 4 0.06
20 10 0.16
21 30 0.47
22 18 0.28
23 2 0.03
ACGTcount: A:0.24, C:0.34, G:0.19, T:0.23
Consensus pattern (19 bp):
AGTGCATCCATGCACCTGC
Found at i:2301364 original size:22 final size:23
Alignment explanation
Indices: 2301336--2301378 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
2301326 ACATCCCTGC
2301336 AGTGCATCCATGCACC-TGCACT
1 AGTGCATCCATGCACCATGCACT
*
2301358 AGTGCATCGATGCACCATGCA
1 AGTGCATCCATGCACCATGCA
2301379 GTGCATCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.26, C:0.33, G:0.21, T:0.21
Consensus pattern (23 bp):
AGTGCATCCATGCACCATGCACT
Found at i:2301478 original size:20 final size:20
Alignment explanation
Indices: 2301413--2301486 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
2301403 AATGCAATTA
* **
2301413 GTGCATTGATGCATCCTTCT
1 GTGCATCGATGCATCCTGAT
** *
2301433 GTGCATCGATGCATCAAGGTT
1 GTGCATCGATGCATC-CTGAT
2301454 GTGCATCGATGCATCCTGAT
1 GTGCATCGATGCATCCTGAT
*
2301474 GTGCATCCATGCA
1 GTGCATCGATGCA
2301487 CGAAGGCTGC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.31
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGAT
Found at i:2301627 original size:21 final size:21
Alignment explanation
Indices: 2301598--2301637 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2301588 TTTTGAGTAG
2301598 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCC-AACGGCTCC
*
2301620 AAAA-CATCCTCAACGGCT
1 AAAATCATCCCCAACGGCT
2301638 ATATACAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 6 0.35
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:2304764 original size:29 final size:31
Alignment explanation
Indices: 2304711--2304770 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
2304701 CAAATTAAGG
2304711 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
2304742 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
2304771 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Done.