Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 9 of 250
Found at i:2599539 original size:151 final size:146
Alignment explanation
Indices: 2599232--2599682 Score: 458
Period size: 151 Copynumber: 3.0 Consensus size: 146
2599222 ATTTTCATTA
* *
2599232 TATATGTATATGTATATATATTTGTATATAGTATTATTTTTATTA-TTTATTTTAATATTTTTAT
1 TATA-GTATATGTATATATATTTATAT-TAGTATTATTTTTATTACTTTATTTTAATATTTATAT
2599296 TATATTTGCTTTTTTTTGTATTTCAATATTATTACTATTATTATTATTATTATTATTATTATTA-
64 TATA-----TTTTTTTTGTATTTCAATATTATTACTATTATTATTATTATTATTA-TA-TATTAG
* * *
2599360 TTATATATTAGTGTATATTTTTAT-TG
122 TTATATTTTA-T-TATATATGTATATG
2599386 TATAGGTATATGTATATATATTTATATCTAGTATTACTTTTTATTACTTTATTTTAATATTTATA
1 TATA-GTATATGTATATATATTTATAT-TAGTATTA-TTTTTATTACTTTATTTTAATATTTATA
* * * *
2599451 TTATATATATTTTGTATTCCAATATTATTACCATTATTATTATTATTATTATATATTAGTCTATA
63 TTATATTTTTTTTGTATTTCAATATTATTACTATTATTATTATTATTATTATATATTAGT-TATA
2599516 TTTTCATTATATATGTATATG
127 TTTT-ATTATATATGTATATG
*
2599537 TATA-TATA--TAT-T-TA--TATA-TAGTATTATTTTTAATTACTTTATTTCAATATTTTTATT
1 TATAGTATATGTATATATATTTATATTAGTATTATTTTT-ATTACTTTATTTTAATA--TTTA--
* * *
2599594 GTATTATATTTGCTTTTTGTATTTCAATATTATTGCTATTATTATTATTGTTATTA-CTATTAGT
61 -TATTATATTT--TTTTTGTATTTCAATATTATTACTATTATTATTATTATTATTATATATTAGT
*
2599658 GTATATTTTTATTATATATGCATAT
123 -TATA-TTTTATTATATATGTATAT
2599683 ATATTTATAT
Statistics
Matches: 261, Mismatches: 21, Indels: 37
0.82 0.07 0.12
Matches are distributed among these distances:
140 5 0.02
141 24 0.09
143 8 0.03
145 2 0.01
146 10 0.04
147 28 0.11
148 42 0.16
149 9 0.03
150 12 0.05
151 56 0.21
152 1 0.00
154 33 0.13
155 9 0.03
156 22 0.08
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (146 bp):
TATAGTATATGTATATATATTTATATTAGTATTATTTTTATTACTTTATTTTAATATTTATATTA
TATTTTTTTTGTATTTCAATATTATTACTATTATTATTATTATTATTATATATTAGTTATATTTT
ATTATATATGTATATG
Found at i:2599794 original size:139 final size:140
Alignment explanation
Indices: 2599197--2599794 Score: 576
Period size: 139 Copynumber: 4.1 Consensus size: 140
2599187 TATTTTCATC
*
2599197 TTATTATTATTATATATTAGTGTATATTTTCATTATATATGTATATGTATATATATTTGTATATA
1 TTATTATTATTAT-TATTAGTGTATA-TTT--TTATATA-GTATATGTATATATATTTATATATA
*
2599262 GTATTATTTTTATTA-TTTATTTTAATATT-TT-TATTATATTTGCTTTTTTTTGTATTTCAATA
61 GTATTATTTTAATTACTTTATTTTAATATTATTATATTATATTTGC---TTTTTGTATTTCAATA
*
2599324 TTATTACTATTATTATTATTATTATTA
123 TTATTGC---------TATTATTATTA
*
2599351 TTATTATTATTATATATTAGTGTATATTTTTATTGTATAGGTATATGTATATATATTTATATCTA
1 TTATTATTATTAT-TATTAGTGTATATTTTTA---TATA-GTATATGTATATATATTTATATATA
* * * *
2599416 GTATTACTTTTTATTACTTTATTTTAATA-T-TTATATTATATAT--ATTTTGTATTCCAATATT
61 GTATTA-TTTTAATTACTTTATTTTAATATTATTATATTATATTTGCTTTTTGTATTTCAATATT
* *
2599477 ATTACCATTATTATTA
125 ATTGCTATTATTATTA
*
2599493 TTATTATTA-TA-TATTAGTCTATATTTTCATTATATATGTATATGTATATATATATTTATATAT
1 TTATTATTATTATTATTAGTGTATA-TTT--TTATATA-GTATATG--TATATATATTTATATAT
* *
2599556 AGTATTATTTTTAATTACTTTATTTCAATATTTTTATTGTATTATATTTGCTTTTTGTATTTCAA
60 AGTATTA-TTTTAATTACTTTATTTTAATA---TTATTATATTATATTTGCTTTTTGTATTTCAA
2599621 TATTATTGC---TATTATTA
121 TATTATTGCTATTATTATTA
* * * * *
2599638 TTATTGTTATTACTATTAGTGTATATTTTTAT-TA-TATATGCATATATATTTATATATAGCACT
1 TTATTATTATTATTATTAGTGTATATTTTTATATAGTATATGTATATATATTTATATATAGTATT
* * *
2599701 ATTTTCAATTACTTTATTTTAACATTATTATATTCTATTTGCTTTTTGTATTTCATTATTATTGC
66 ATTTT-AATTACTTTATTTTAATATTATTATATTATATTTGCTTTTTGTATTTCAATATTATTGC
*
2599766 TAGTATTATTA
130 TATTATTATTA
* *
2599777 TCATTATCATTATTATTA
1 TTATTATTATTATTATTA
2599795 ACATATATAT
Statistics
Matches: 388, Mismatches: 32, Indels: 63
0.80 0.07 0.13
Matches are distributed among these distances:
136 38 0.10
138 4 0.01
139 81 0.21
140 3 0.01
141 51 0.13
142 22 0.06
143 2 0.01
144 4 0.01
145 17 0.04
146 16 0.04
147 11 0.03
148 20 0.05
151 24 0.06
153 3 0.01
154 59 0.15
155 12 0.03
156 21 0.05
ACGTcount: A:0.30, C:0.05, G:0.06, T:0.59
Consensus pattern (140 bp):
TTATTATTATTATTATTAGTGTATATTTTTATATAGTATATGTATATATATTTATATATAGTATT
ATTTTAATTACTTTATTTTAATATTATTATATTATATTTGCTTTTTGTATTTCAATATTATTGCT
ATTATTATTA
Found at i:2600838 original size:13 final size:11
Alignment explanation
Indices: 2600792--2600850 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
2600782 TTGTTTACTG
*
2600792 TTTTGCCATTA
1 TTTTGCTATTA
* *
2600803 TTTTTCCATT-
1 TTTTGCTATTA
2600813 TTTTGCTATTA
1 TTTTGCTATTA
2600824 TTTTGCTATTA
1 TTTTGCTATTA
* * *
2600835 TATTACTACTA
1 TTTTGCTATTA
2600846 TTTTG
1 TTTTG
2600851 TTGCTATTGT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
10 8 0.21
11 31 0.79
ACGTcount: A:0.19, C:0.14, G:0.07, T:0.61
Consensus pattern (11 bp):
TTTTGCTATTA
Found at i:2614230 original size:14 final size:14
Alignment explanation
Indices: 2614210--2614242 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2614200 AAACATGCAT
2614210 AAATATT-TTTAAA
1 AAATATTATTTAAA
2614223 ATAATATTATTTAAA
1 A-AATATTATTTAAA
2614238 AAATA
1 AAATA
2614243 AAAATTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.06
14 10 0.56
15 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATATTATTTAAA
Found at i:2615291 original size:5 final size:5
Alignment explanation
Indices: 2615281--2615306 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2615271 GTTTTTTTTG
2615281 TTATT TTATT TTATT TTATT TTATT T
1 TTATT TTATT TTATT TTATT TTATT T
2615307 AGAACCTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:2616019 original size:19 final size:20
Alignment explanation
Indices: 2615997--2616034 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2615987 TTATCGTTAT
*
2615997 TATTATTAGTA-TATTTTTA
1 TATTATTAGAATTATTTTTA
2616016 TATTATTAGAATTATTTTT
1 TATTATTAGAATTATTTTT
2616035 TAGTTTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (20 bp):
TATTATTAGAATTATTTTTA
Found at i:2616172 original size:24 final size:24
Alignment explanation
Indices: 2616127--2616181 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
2616117 ATATATGTAT
* *
2616127 ACATATTTAAATACTATATTATAC
1 ACATATTTAAATACCACATTATAC
* * *
2616151 ACATATTTTAATACCACGTTATAT
1 ACATATTTAAATACCACATTATAC
2616175 ACATATT
1 ACATATT
2616182 ATTATTATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.02, T:0.42
Consensus pattern (24 bp):
ACATATTTAAATACCACATTATAC
Found at i:2616242 original size:21 final size:21
Alignment explanation
Indices: 2616210--2616293 Score: 77
Period size: 21 Copynumber: 4.0 Consensus size: 21
2616200 TTACCCTTAT
2616210 TATATTTGTTATTA-ATATTAG
1 TATATTT-TTATTACATATTAG
2616231 TATATGTTTTATTACATATGTA-
1 TATAT-TTTTATTACATAT-TAG
*
2616253 TATATTTTTAATACATA-TATG
1 TATATTTTTATTACATATTA-G
*
2616274 TATATATTTATGTA-ATATTA
1 TATATTTTTAT-TACATATTA
2616294 TTAATAATTG
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
19 2 0.04
21 34 0.64
22 15 0.28
23 2 0.04
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (21 bp):
TATATTTTTATTACATATTAG
Found at i:2616255 original size:20 final size:21
Alignment explanation
Indices: 2616230--2616279 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
2616220 ATTAATATTA
*
2616230 GTATAT-GTTTTATTACATAT
1 GTATATAGTTTTAATACATAT
*
2616250 GTATATATTTTTAATACATATAT
1 GTATATAGTTTTAATAC--ATAT
2616273 GTATATA
1 GTATATA
2616280 TTTATGTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.24
21 8 0.32
23 11 0.44
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.52
Consensus pattern (21 bp):
GTATATAGTTTTAATACATAT
Found at i:2616660 original size:20 final size:20
Alignment explanation
Indices: 2616635--2616686 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2616625 TTTAATATTG
*
2616635 TATTTTTATTATTATGTATA
1 TATTTTTATTATTACGTATA
* *
2616655 TATTTTTAATACTACGTATA
1 TATTTTTATTATTACGTATA
2616675 TATTTTT-TTATT
1 TATTTTTATTATT
2616687 TCTATTATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (20 bp):
TATTTTTATTATTACGTATA
Found at i:2616803 original size:61 final size:65
Alignment explanation
Indices: 2616647--2616804 Score: 157
Period size: 61 Copynumber: 2.4 Consensus size: 65
2616637 TTTTTATTAT
** * *
2616647 TATGTATATATTTTTAATACTACGTATATATTTTTTTATTTCTATTATTACGATATATTTTAATA
1 TATGTATATATTTTTAAT-CTA-GTAT-TATTAGTTTATTTATATTATTAC-ATATATTTCAATA
*
2616712 CATA
62 AATA
* *
2616716 TATGTATATATTTATATATC--GTTATTATTAGTTT-TTTATATTATTAC-TGT-TTTCAATAAA
1 TATGTATATATTTTTA-ATCTAG-TATTATTAGTTTATTTATATTATTACATATATTTCAATAAA
2616776 TA
64 TA
2616778 T-TGTATATATTTTTAATCTAGTATTAT
1 TATGTATATATTTTTAATCTAGTATTAT
2616805 ATGTTACATA
Statistics
Matches: 77, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
60 3 0.04
61 19 0.25
62 12 0.16
63 2 0.03
65 12 0.16
66 8 0.10
67 3 0.04
69 16 0.21
70 2 0.03
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (65 bp):
TATGTATATATTTTTAATCTAGTATTATTAGTTTATTTATATTATTACATATATTTCAATAAATA
Found at i:2616886 original size:3 final size:3
Alignment explanation
Indices: 2616878--2616944 Score: 77
Period size: 3 Copynumber: 23.0 Consensus size: 3
2616868 ATACCATATG
* * *
2616878 TAT TAT TAT CAT T-T TA- TAC TAT TAT TAT T-T ACAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
2616921 TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
2616945 CGTTTTCGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
2 5 0.09
3 49 0.89
4 1 0.02
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:2618724 original size:2 final size:2
Alignment explanation
Indices: 2618717--2618743 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2618707 GAGATTAATA
2618717 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 A
2618744 AAATTAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2622675 original size:19 final size:19
Alignment explanation
Indices: 2622638--2622695 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
2622628 TTTTTTTAAA
*
2622638 ATAAAAATTTTAGAATTTTT
1 ATAAATATTTTA-AATTTTT
2622658 ATAAATATTTTAAA-TTTT
1 ATAAATATTTTAAATTTTT
*
2622676 AAAAATTATTTTCAAATTTT
1 ATAAA-TATTTT-AAATTTT
2622696 GAAAATTACT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 8 0.24
19 8 0.24
20 14 0.42
21 3 0.09
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
ATAAATATTTTAAATTTTT
Found at i:2622694 original size:20 final size:19
Alignment explanation
Indices: 2622644--2622703 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
2622634 TAAAATAAAA
*
2622644 ATTTTAGAATTTTTATAAA-T
1 ATTTTA-AA-TTTTAAAAATT
2622664 ATTTTAAATTTTAAAAATT
1 ATTTTAAATTTTAAAAATT
*
2622683 ATTTTCAAATTTTGAAAATT
1 ATTTT-AAATTTTAAAAATT
2622703 A
1 A
2622704 CTTTGATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.22
19 8 0.22
20 20 0.56
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (19 bp):
ATTTTAAATTTTAAAAATT
Found at i:2623251 original size:3 final size:3
Alignment explanation
Indices: 2623243--2623274 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2623233 CCATAATCAA
2623243 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
2623275 ATATTGTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:2626866 original size:23 final size:23
Alignment explanation
Indices: 2626802--2626866 Score: 55
Period size: 23 Copynumber: 2.9 Consensus size: 23
2626792 ATAATTAATA
* *
2626802 ATAAATATTATGTGA-TTTTATT
1 ATAAATATTATTTAATTTTTATT
* *
2626824 A-AAATTAGTA-TAAATATTTTATT
1 ATAAA-TATTATTTAAT-TTTTATT
2626847 ATAAATATTATTTAATTTTT
1 ATAAATATTATTTAATTTTT
2626867 GAATAAAGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 9
0.68 0.13 0.19
Matches are distributed among these distances:
21 4 0.12
22 5 0.16
23 16 0.50
24 7 0.22
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.54
Consensus pattern (23 bp):
ATAAATATTATTTAATTTTTATT
Found at i:2627545 original size:24 final size:24
Alignment explanation
Indices: 2627494--2627565 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 24
2627484 AAAACTGTTA
* * * * *
2627494 TTTTTTTATTGTTTTCTTGCTCTC
1 TTTTTTTAATGTTTTGTTGTTATT
2627518 TTTTTTTAATGTTTTGTTGTTATT
1 TTTTTTTAATGTTTTGTTGTTATT
* * * *
2627542 TTTTTTCACTATTATGTTGTTATT
1 TTTTTTTAATGTTTTGTTGTTATT
2627566 GTATAACTCT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.11, C:0.08, G:0.10, T:0.71
Consensus pattern (24 bp):
TTTTTTTAATGTTTTGTTGTTATT
Found at i:2639614 original size:58 final size:58
Alignment explanation
Indices: 2639551--2639690 Score: 140
Period size: 64 Copynumber: 2.3 Consensus size: 58
2639541 GGGGTTAAAT
*
2639551 ATTTTTTTTCCCAAGTTAAACTCTGAACTTGGCAATTGTTC-CACATTGTGG-CTTGAAC
1 ATTTTTTTT-CCAAGTTAAACCCTGAACTTGGCAATTGTTCTCACATTG-GGACTTGAAC
**
2639609 ATTTTTTTCTTTTTGTCCAAGTTAGGCCCTGAACTTGGCAATTGTTCTCACATTGGGACTTGAAC
1 A-----TT-TTTTT-TCCAAGTTAAACCCTGAACTTGGCAATTGTTCTCACATTGGGACTTGAAC
* *
2639674 CTTTTTTGTCCAAGTTA
1 ATTTTTTTTCCAAGTTA
2639691 GTTTTTGGAA
Statistics
Matches: 68, Mismatches: 5, Indels: 18
0.75 0.05 0.20
Matches are distributed among these distances:
58 10 0.15
59 4 0.06
60 2 0.03
63 2 0.03
64 35 0.51
65 15 0.22
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.42
Consensus pattern (58 bp):
ATTTTTTTTCCAAGTTAAACCCTGAACTTGGCAATTGTTCTCACATTGGGACTTGAAC
Found at i:2644651 original size:25 final size:26
Alignment explanation
Indices: 2644614--2644665 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
2644604 TCAAACATGC
2644614 ATTTAGGTCAATTTAACCCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
* * *
2644640 ATTTCGGT-AATTTATCTCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
2644665 A
1 A
2644666 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.38
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACCCTAGGGGT
Found at i:2646183 original size:26 final size:26
Alignment explanation
Indices: 2646147--2646229 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
2646137 CATGAAATTC
2646147 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
2646173 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
2646199 TTATCATGGAACATTTACCTAA-CTA
1 TTATCATGAAACATTTACCTAACCCA
2646224 TTATCA
1 TTATCA
2646230 ATTTGTATCA
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
25 8 0.15
26 47 0.85
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:2650448 original size:25 final size:26
Alignment explanation
Indices: 2650411--2650462 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
2650401 TCAAACATGC
2650411 ATTTAGGTCAATTTAACCCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
* * *
2650437 ATTTCGGT-AATTTATCTCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
2650462 A
1 A
2650463 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.38
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACCCTAGGGGT
Found at i:2651971 original size:26 final size:26
Alignment explanation
Indices: 2651935--2652018 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
2651925 CATGAAATTT
2651935 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
2651961 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
2651987 TTATCATGGATCATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
2652013 TTATCA
1 TTATCA
2652019 ATTTGTATCA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:2655303 original size:14 final size:14
Alignment explanation
Indices: 2655284--2655322 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2655274 TTGTTTCACT
2655284 GAAAATGACTTTC-A
1 GAAAATGA-TTTCTA
2655298 GAAAATGATTTCTA
1 GAAAATGATTTCTA
*
2655312 GAAAATAATTT
1 GAAAATGATTT
2655323 ACTTTTTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (14 bp):
GAAAATGATTTCTA
Found at i:2657197 original size:11 final size:11
Alignment explanation
Indices: 2657117--2657200 Score: 66
Period size: 11 Copynumber: 7.3 Consensus size: 11
2657107 TTTTCACATA
2657117 TATTATATATT
1 TATTATATATT
2657128 TATTA-ATTATT
1 TATTATA-TATT
2657139 TATATATATATT
1 TAT-TATATATT
2657151 GT-TT-TATATGT
1 -TATTATATAT-T
*
2657162 TATTTTATATT
1 TATTATATATT
2657173 ATATCTATTATATT
1 -TAT-TA-TATATT
*
2657187 TCTTATATATT
1 TATTATATATT
2657198 TAT
1 TAT
2657201 ATTACATTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
10 7 0.12
11 25 0.42
12 17 0.28
13 5 0.08
14 6 0.10
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (11 bp):
TATTATATATT
Found at i:2657282 original size:20 final size:20
Alignment explanation
Indices: 2657249--2657287 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2657239 TGTATCGCCA
* *
2657249 ATTATATTTTTTATGATTAC
1 ATTATATATATTATGATTAC
*
2657269 ATTATATATATTATTATTA
1 ATTATATATATTATGATTA
2657288 TTATTAAATC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (20 bp):
ATTATATATATTATGATTAC
Found at i:2657301 original size:26 final size:24
Alignment explanation
Indices: 2657251--2657301 Score: 57
Period size: 26 Copynumber: 2.0 Consensus size: 24
2657241 TATCGCCAAT
* *
2657251 TATATTTTTTATGATTACATTATA
1 TATATTTTTTATGATTAAATCATA
*
2657275 TATATTATTATTATTATTAAATCATA
1 TATATT-TT-TTATGATTAAATCATA
2657301 T
1 T
2657302 TTTTAACACA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 6 0.27
25 2 0.09
26 14 0.64
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (24 bp):
TATATTTTTTATGATTAAATCATA
Found at i:2658637 original size:19 final size:19
Alignment explanation
Indices: 2658601--2658639 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2658591 TATTATTAAT
**
2658601 ATATTTATAATTGTAATAA
1 ATATTTATAATTAAAATAA
*
2658620 ATATTTATTATTAAAATAA
1 ATATTTATAATTAAAATAA
2658639 A
1 A
2658640 ATTGAAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:2658665 original size:37 final size:37
Alignment explanation
Indices: 2658624--2658701 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 37
2658614 TAATAAATAT
2658624 TTATTATTAA-AATAAAATTGA-AATATTAAATAATTTA
1 TTATT-TTAATAATAAAATTGAGAATATT-AATAATTTA
* * * *
2658661 TTATTTTAATAATTATATTTAGTATATTAATAATTTA
1 TTATTTTAATAATAAAATTGAGAATATTAATAATTTA
2658698 TTAT
1 TTAT
2658702 ATGACTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
36 4 0.11
37 26 0.74
38 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (37 bp):
TTATTTTAATAATAAAATTGAGAATATTAATAATTTA
Found at i:2658680 original size:21 final size:20
Alignment explanation
Indices: 2658646--2658699 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
2658636 TAAAATTGAA
2658646 ATATTAAATAATTTA-TTA-T
1 ATATT-AATAATTTATTTAGT
2658665 -T-TTAATAATTATATTTAGT
1 ATATTAATAATT-TATTTAGT
2658684 ATATTAATAATTTATT
1 ATATTAATAATTTATT
2658700 ATATGACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
16 7 0.23
17 4 0.13
18 4 0.13
19 1 0.03
20 5 0.17
21 9 0.30
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
ATATTAATAATTTATTTAGT
Found at i:2661716 original size:24 final size:24
Alignment explanation
Indices: 2661587--2661746 Score: 110
Period size: 24 Copynumber: 6.7 Consensus size: 24
2661577 CAACCGATTT
* * *
2661587 CGCACACATAGTGCTAAAT-AAATT
1 CGCACACATAGTGC-CATTCAAATC
* *
2661611 CGCACACATAGTGCCATGCTACA-C
1 CGCACACATAGTGCCATTC-AAATC
* *
2661635 CGCACACATAGTGCC-TTGAAGATT
1 CGCACACATAGTGCCATTCAA-ATC
* * ** * * *
2661659 CACTCATGTATTGACATCCAAATC
1 CGCACACATAGTGCCATTCAAATC
* *
2661683 AGCACACATAGTGCCATTCAATTC
1 CGCACACATAGTGCCATTCAAATC
*
2661707 CGCACACATAGAGCCATTCAAATC
1 CGCACACATAGTGCCATTCAAATC
*
2661731 CGCACACTTAGTGCCA
1 CGCACACATAGTGCCA
2661747 ATGTAAACCC
Statistics
Matches: 99, Mismatches: 32, Indels: 10
0.70 0.23 0.07
Matches are distributed among these distances:
22 1 0.01
23 3 0.03
24 90 0.91
25 5 0.05
ACGTcount: A:0.33, C:0.30, G:0.14, T:0.23
Consensus pattern (24 bp):
CGCACACATAGTGCCATTCAAATC
Found at i:2663118 original size:26 final size:26
Alignment explanation
Indices: 2663081--2663164 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
2663071 TGATACAAAT
* *
2663081 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
2663107 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
2663133 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
2663159 TGATAA
1 TGATAA
2663165 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:2664677 original size:25 final size:26
Alignment explanation
Indices: 2664649--2664700 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
2664639 TTTACAGTTT
2664649 TACCCCTAGAGATAAATT-ACCGAAA
1 TACCCCTAGAGATAAATTGACCGAAA
* * *
2664674 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGAGATAAATTGACCGAAA
2664700 T
1 T
2664701 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (26 bp):
TACCCCTAGAGATAAATTGACCGAAA
Found at i:2674923 original size:18 final size:18
Alignment explanation
Indices: 2674886--2674942 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
2674876 ATTATTCACC
* *
2674886 ATTATTTATTATTGTAATT
1 ATTAGTTATTATT-TTATT
2674905 ATT-GTTATTATTATTATT
1 ATTAGTTATTATT-TTATT
2674923 ATTAGTT-TATATTTTATT
1 ATTAGTTAT-TATTTTATT
2674941 AT
1 AT
2674943 GTATATATCT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 23 0.70
19 10 0.30
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (18 bp):
ATTAGTTATTATTTTATT
Found at i:2687183 original size:41 final size:43
Alignment explanation
Indices: 2687138--2687254 Score: 116
Period size: 44 Copynumber: 2.8 Consensus size: 43
2687128 ATGCTTGAAG
*
2687138 AAAAAGAAAATTAAGATGAAAACCCGAAAGGGCATCTT-A-AA
1 AAAAAGAAGATTAAGATGAAAACCCGAAAGGGCATCTTGATAA
* * * *
2687179 AAAAAG-GGATCAAGGTGAAAACCCAAAAAGGGCATCTTGATTAA
1 AAAAAGAAGATTAAGATGAAAACCC-GAAAGGGCATCTTGA-TAA
* * *
2687223 CACAA-AAGATTAGGATGAAAACCCGAAAGGGC
1 AAAAAGAAGATTAAGATGAAAACCCGAAAGGGC
2687255 GTTCTAATGA
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
40 14 0.24
41 18 0.31
42 1 0.02
43 7 0.12
44 19 0.32
ACGTcount: A:0.50, C:0.15, G:0.21, T:0.14
Consensus pattern (43 bp):
AAAAAGAAGATTAAGATGAAAACCCGAAAGGGCATCTTGATAA
Found at i:2688189 original size:73 final size:74
Alignment explanation
Indices: 2688032--2688182 Score: 209
Period size: 73 Copynumber: 2.1 Consensus size: 74
2688022 TGATATTTTT
* * * *
2688032 ATTTCTG--TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTTAGCCTCAAGAGACGTTGAG
1 ATTTCTGCTTTTTAAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAG
*
2688095 GTATTTTCA
66 GTATCTTCA
** *
2688104 ATTTCTGCTTTTTAAAAATT-AACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 ATTTCTGCTTTTTAAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAG
2688168 GTATCTTCA
66 GTATCTTCA
2688177 ATTTCT
1 ATTTCT
2688183 TTTTTTTCAA
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
72 7 0.10
73 52 0.75
74 10 0.14
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (74 bp):
ATTTCTGCTTTTTAAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAG
GTATCTTCA
Found at i:2688278 original size:90 final size:87
Alignment explanation
Indices: 2688117--2688349 Score: 279
Period size: 90 Copynumber: 2.6 Consensus size: 87
2688107 TCTGCTTTTT
* * **
2688117 AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATCTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCCGAGGTATCTTCAAAATC
2688182 TTTTTTTTCAATTTATATTTTTCAA
66 -TTTTTTT-AATTTATATTTTTC-A
* * * * *
2688207 AAAAATCAACTCATATTGCGAGGGGTGAGTTGAACCTCGGGGCACAGGCCGAGGTATTTTCAAAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGG-ACACGCCGAGGTATCTTCAAAA
* * *
2688272 TC-TTTTTTAATTTCTGTTTTTCT
64 TCTTTTTTTAATTTATATTTTTCA
* * *
2688295 AAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCCGAGGTAT
2688350 TTTTAATTCC
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
86 11 0.09
87 2 0.02
88 35 0.29
89 12 0.10
90 41 0.34
91 2 0.02
92 19 0.16
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (87 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCCGAGGTATCTTCAAAATC
TTTTTTTAATTTATATTTTTCA
Found at i:2688366 original size:88 final size:86
Alignment explanation
Indices: 2688098--2688358 Score: 292
Period size: 88 Copynumber: 3.0 Consensus size: 86
2688088 CGTTGAGGTA
* * *
2688098 TTTTCAATTTCTGCTTTT-TAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
1 TTTTTAATTTCTGTTTTTCTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
* *
2688162 GCTGAGGTATCTTCAATTTCTTT
66 GCTGAGGTAT-TTTAAATTC-TT
* * * * * *
2688185 TTTTTCAATTTATATTTTTCAAAAAAATCAACTCATATTGCGAGGGGTGAGTTGAACCTCGGGGC
1 TTTTT-AATTTCTGTTTTTC-TAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGG-
* * *
2688250 ACAGGCCGAGGTATTTTCAAAATC-T
62 ACACGCTGAGGTATTTT-AAATTCTT
* *
2688275 TTTTTAATTTCTGTTTTTCTAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCAC
1 TTTTTAATTTCTGTTTTTCTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
*
2688340 GCTGAGGTATTTTTAATTC
66 GCTGAGGTATTTTAAATTC
2688359 CTGTTTTTCA
Statistics
Matches: 142, Mismatches: 26, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
85 4 0.03
86 14 0.10
87 6 0.04
88 45 0.32
89 12 0.08
90 41 0.29
91 4 0.03
92 16 0.11
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (86 bp):
TTTTTAATTTCTGTTTTTCTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
GCTGAGGTATTTTAAATTCTT
Found at i:2688395 original size:73 final size:73
Alignment explanation
Indices: 2688275--2688520 Score: 341
Period size: 73 Copynumber: 3.3 Consensus size: 73
2688265 TTCAAAATCT
* *
2688275 TTTTTAATTTCTGTTTTTCTAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCAC
1 TTTTCAATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCAC
2688340 GCTGAGGTA
65 GCTGAGGTA
* * * *
2688349 TTTTTAATTCCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCCCAGGTCACA
1 TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACG
2688414 CTGAAGG-A
66 CTG-AGGTA
* *
2688422 TTTTCAATTTCTGTTTATTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGC
1 TTTTCAATTTCTGTTT-TT--CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTC
*
2688487 ACGCTGAAGTA
63 ACGCTGAGGTA
*
2688498 TTTTCAATTTCTGATTTTGCAAA
1 TTTTCAATTTCTG-TTTTTCAAA
2688521 TTCTGTTTTC
Statistics
Matches: 153, Mismatches: 13, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
73 61 0.40
74 26 0.17
75 2 0.01
76 61 0.40
77 3 0.02
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (73 bp):
TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACG
CTGAGGTA
Found at i:2688476 original size:76 final size:73
Alignment explanation
Indices: 2688275--2688515 Score: 331
Period size: 76 Copynumber: 3.2 Consensus size: 73
2688265 TTCAAAATCT
* * *
2688275 TTTTTAATTTCTGTTTTTCTAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCAC
1 TTTTCAATTTCTGTTTTT-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCAC
2688340 GCTG-AGGTA
65 GCTGAAGG-A
* * * * *
2688349 TTTTTAATTCCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCCCAGGTCACA
1 TTTTCAATTTCTGTTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACG
2688414 CTGAAGGA
66 CTGAAGGA
*
2688422 TTTTCAATTTCTGTTTATTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGC
1 TTTTCAATTTCTGTTT-TT--AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTC
*
2688487 ACGCTGAAGTA
63 ACGCTGAAGGA
*
2688498 TTTTCAATTTCTGATTTT
1 TTTTCAATTTCTGTTTTT
2688516 GCAAATTCTG
Statistics
Matches: 150, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
73 61 0.41
74 22 0.15
75 2 0.01
76 65 0.43
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (73 bp):
TTTTCAATTTCTGTTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACG
CTGAAGGA
Found at i:2688619 original size:88 final size:88
Alignment explanation
Indices: 2688443--2688657 Score: 278
Period size: 88 Copynumber: 2.4 Consensus size: 88
2688433 TGTTTATTAA
* **
2688443 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAAGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAAGTACTTTCAAAAT
**
2688508 CTGATTTTGCAAATTCTGTTTTC
66 CTGATTTTGCAAATTAAGTTTTC
*
2688531 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGTCACATGAC-GAGGTACTTTCA
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGG-CAC--G-CTGAAGTACTTTCA
2688594 AAATCT-ACTTTT-CAAATTAAG-TTTC
62 AAATCTGA-TTTTGCAAATTAAGTTTTC
*
2688619 AAAAAGACCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 AAAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
2688658 TGGCCCACGT
Statistics
Matches: 114, Mismatches: 7, Indels: 11
0.86 0.05 0.08
Matches are distributed among these distances:
87 3 0.03
88 51 0.45
89 40 0.35
90 19 0.17
91 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Consensus pattern (88 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAAGTACTTTCAAAAT
CTGATTTTGCAAATTAAGTTTTC
Found at i:2688682 original size:89 final size:86
Alignment explanation
Indices: 2688443--2688683 Score: 236
Period size: 88 Copynumber: 2.7 Consensus size: 86
2688433 TGTTTATTAA
* * * **
2688443 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAAGTATTTTCAATTT
1 AAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGGCCACG-TGGAGTATTTTCAAAAT
**
2688508 CTGATTTTGCAAATTCTGTTTTC
64 CTGATTTTGCAAATTAAGTTTTC
* * * * *
2688531 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGACGAGGTACTTTCAAA
1 AAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGGCCACGTG--GA-GTATTTTCAAA
2688596 ATCT-ACTTTT-CAAATTAAG-TTTC
62 ATCTGA-TTTTGCAAATTAAGTTTTC
*
2688619 AAAAAGACCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCCCACGTGTTGAGCTATTTTCAA
1 AAAAA-ACCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGG-CCACGTG--GAG-TATTTTCAA
2688684 TTTCTGTTTT
Statistics
Matches: 130, Mismatches: 16, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
87 2 0.02
88 56 0.43
89 56 0.43
90 16 0.12
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (86 bp):
AAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGCCACGTGGAGTATTTTCAAAATCT
GATTTTGCAAATTAAGTTTTC
Found at i:2696363 original size:26 final size:26
Alignment explanation
Indices: 2696334--2696386 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
2696324 TCAAACATGC
2696334 ATTTAAGTCAATTTAAC-CCTAGGGGT
1 ATTTAAGT-AATTTAACTCCTAGGGGT
** *
2696360 ATTTCGGTAATTTATCTCCTAGGGGT
1 ATTTAAGTAATTTAACTCCTAGGGGT
2696386 A
1 A
2696387 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (26 bp):
ATTTAAGTAATTTAACTCCTAGGGGT
Found at i:2697904 original size:26 final size:25
Alignment explanation
Indices: 2697866--2697949 Score: 132
Period size: 26 Copynumber: 3.2 Consensus size: 25
2697856 CATGAAATTC
*
2697866 TTATCATGAAACATTTACCTAACCCA
1 TTATCATG-AACATTTACCTAACCTA
2697892 TTATCATCGAACATTTACCTAACCTA
1 TTATCAT-GAACATTTACCTAACCTA
2697918 TTATCATGGAACATTTACCTAACCTA
1 TTATCAT-GAACATTTACCTAACCTA
2697944 TTATCA
1 TTATCA
2697950 ATTTGTATCA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
26 54 0.98
27 1 0.02
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (25 bp):
TTATCATGAACATTTACCTAACCTA
Found at i:2699148 original size:12 final size:12
Alignment explanation
Indices: 2699131--2699155 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2699121 AGTGTCGAAT
2699131 CGGTAACAGTAA
1 CGGTAACAGTAA
2699143 CGGTAACAGTAA
1 CGGTAACAGTAA
2699155 C
1 C
2699156 AGTAGTCGGC
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:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:2700235 original size:5 final size:5
Alignment explanation
Indices: 2700225--2700325 Score: 174
Period size: 5 Copynumber: 21.0 Consensus size: 5
2700215 TGTCTCTTTT
2700225 ATATA ATATA ATATA ATATA ATATA ATAT- ATAT- ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
2700273 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATAT- A-ATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
2700321 ATATA
1 ATATA
2700326 CTTAATTATT
Statistics
Matches: 93, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
3 2 0.02
4 10 0.11
5 81 0.87
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:2701482 original size:26 final size:26
Alignment explanation
Indices: 2701446--2701527 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
2701436 TGATACAAAT
*
2701446 TGATAATGGGTTAGGTAAATATTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
2701472 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
2701498 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
2701524 TGAT
1 TGAT
2701528 GGGAATTTCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:2706479 original size:27 final size:26
Alignment explanation
Indices: 2706449--2706510 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
2706439 AGATAATTAA
2706449 AATAAAATCTTAA-ATTTGAATAATCCT
1 AATAAAATCTTAATA-TT-AATAATCCT
* *
2706476 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCTTAATATTAATAATCCT
2706503 AATAAAAT
1 AATAAAAT
2706511 AAAATAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 2 0.07
27 18 0.60
28 9 0.30
29 1 0.03
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (26 bp):
AATAAAATCTTAATATTAATAATCCT
Found at i:2707097 original size:14 final size:13
Alignment explanation
Indices: 2707078--2707120 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 13
2707068 TTAGTAGTAC
2707078 TTTTTTTTCTTCTT
1 TTTTTTTTCTT-TT
2707092 TTTTTTTTCTTTT
1 TTTTTTTTCTTTT
2707105 TTTTTCTTT-TTTT
1 TTTTT-TTTCTTTT
2707118 TTT
1 TTT
2707121 GATTTTTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 14 0.50
14 14 0.50
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (13 bp):
TTTTTTTTCTTTT
Found at i:2707104 original size:9 final size:10
Alignment explanation
Indices: 2707079--2707119 Score: 64
Period size: 10 Copynumber: 3.9 Consensus size: 10
2707069 TAGTAGTACT
2707079 TTTTTTTCTTC
1 TTTTTTT-TTC
2707090 TTTTTTTTTTC
1 -TTTTTTTTTC
2707101 TTTTTTTTTC
1 TTTTTTTTTC
2707111 TTTTTTTTT
1 TTTTTTTTT
2707120 TGATTTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 19 0.66
11 3 0.10
12 7 0.24
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:2707120 original size:11 final size:11
Alignment explanation
Indices: 2707077--2707120 Score: 72
Period size: 11 Copynumber: 4.0 Consensus size: 11
2707067 TTTAGTAGTA
2707077 CTTTTTTTTCTT
1 CTTTTTTTT-TT
2707089 CTTTTTTTTTT
1 CTTTTTTTTTT
2707100 C-TTTTTTTTT
1 CTTTTTTTTTT
2707110 CTTTTTTTTTT
1 CTTTTTTTTTT
2707121 GATTTTTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.32
11 12 0.39
12 9 0.29
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:2707126 original size:21 final size:22
Alignment explanation
Indices: 2707080--2707128 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
2707070 AGTAGTACTT
2707080 TTTTTTCTTCTTTTTTTTTTC-
1 TTTTTTCTTCTTTTTTTTTTCA
* *
2707101 TTTTTTTTTCTTTTTTTTTTGA
1 TTTTTTCTTCTTTTTTTTTTCA
2707123 TTTTTT
1 TTTTTT
2707129 GATTTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.02, C:0.08, G:0.02, T:0.88
Consensus pattern (22 bp):
TTTTTTCTTCTTTTTTTTTTCA
Found at i:2707137 original size:1 final size:1
Alignment explanation
Indices: 2707078--2707120 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
2707068 TTAGTAGTAC
* * * *
2707078 TTTTTTTTCTTCTTTTTTTTTTCTTTTTTTTTCTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2707121 GATTTTTTGA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:2707137 original size:11 final size:11
Alignment explanation
Indices: 2707079--2707128 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
2707069 TAGTAGTACT
*
2707079 TTTTTTTCTTCT
1 TTTTTTT-TTCA
2707091 TTTTTTTTTC-
1 TTTTTTTTTCA
*
2707101 TTTTTTTTTCT
1 TTTTTTTTTCA
*
2707112 TTTTTTTTTGA
1 TTTTTTTTTCA
2707123 TTTTTT
1 TTTTTT
2707129 GATTTTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
10 10 0.29
11 18 0.51
12 7 0.20
ACGTcount: A:0.02, C:0.08, G:0.02, T:0.88
Consensus pattern (11 bp):
TTTTTTTTTCA
Found at i:2707445 original size:118 final size:119
Alignment explanation
Indices: 2707281--2707494 Score: 349
Period size: 118 Copynumber: 1.8 Consensus size: 119
2707271 TTTTACCCAA
*
2707281 CACGTCACACAACTTTTTTGACACGAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTCA
1 CACGTCACACAACTCTTTTGACACGAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTCA
* *
2707346 GTCAGTCACGATTTGAGCCATACTCATAACCTCGGCTAGCGGAGTTTTACTTGT
66 GTCAGTCACGATCTAAGCCATACTCATAACCTCGGCTAGCGGAGTTTTACTTGT
* * *
2707400 CACGTCACATAAC-CTTTTGACGCGAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTTA
1 CACGTCACACAACTCTTTTGACACGAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTCA
**
2707464 GTCAGTCACGATCTAAGCTGTACTCATAACC
66 GTCAGTCACGATCTAAGCCATACTCATAACC
2707495 ATGGAAAACT
Statistics
Matches: 87, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
118 75 0.86
119 12 0.14
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (119 bp):
CACGTCACACAACTCTTTTGACACGAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTCA
GTCAGTCACGATCTAAGCCATACTCATAACCTCGGCTAGCGGAGTTTTACTTGT
Found at i:2708449 original size:6 final size:6
Alignment explanation
Indices: 2708438--2708487 Score: 57
Period size: 6 Copynumber: 7.8 Consensus size: 6
2708428 ATTTATTAAT
2708438 ATAAAA AT-AAA ATAAAA ATAAAA ATAAAA TAGTAAAAA ATAAAGA ATAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA -A-T-AAAA ATAAA-A ATAAA
2708488 TAAAAAAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
5 5 0.13
6 20 0.51
7 8 0.21
8 2 0.05
9 4 0.10
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:2708454 original size:11 final size:12
Alignment explanation
Indices: 2708438--2708487 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 12
2708428 ATTTATTAAT
2708438 ATAAAAAT-AAA
1 ATAAAAATAAAA
2708449 ATAAAAATAAAA
1 ATAAAAATAAAA
2708461 ATAAAATAGTAAAAA
1 ATAAAA-A-T-AAAA
2708476 ATAAAGAATAAA
1 ATAAA-AATAAA
2708488 TAAAAAAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
11 8 0.24
12 9 0.26
13 4 0.12
14 2 0.06
15 10 0.29
16 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (12 bp):
ATAAAAATAAAA
Found at i:2714947 original size:27 final size:26
Alignment explanation
Indices: 2714917--2714978 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
2714907 AGATAATTAA
2714917 AATAAAATCCTAA-ATGTGAATAATCCT
1 AATAAAATCCTAATAT-T-AATAATCCT
* * *
2714944 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCCTAATATTAATAATCCT
2714971 AATAAAAT
1 AATAAAAT
2714979 AAAATAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.07
27 18 0.62
28 7 0.24
29 2 0.07
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.37
Consensus pattern (26 bp):
AATAAAATCCTAATATTAATAATCCT
Found at i:2715416 original size:47 final size:48
Alignment explanation
Indices: 2715362--2715492 Score: 176
Period size: 47 Copynumber: 2.8 Consensus size: 48
2715352 CACAATCGAT
* *
2715362 AAGTACCTATACCATGACCCATAGCCAAATCAAGGTAACTTATCCCAG
1 AAGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCATCCCAG
* ** *
2715410 -AGTACCTATACCATGGCTCATAGCCAAATCAAGGTAACTCATTTCTG
1 AAGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCATCCCAG
* *
2715457 AAATACCTATACCATGGCCCGTAGCCAAAT-AAGGTA
1 AAGTACCTATACCATGGCCCATAGCCAAATCAAGGTA
2715493 TCACTCGCAT
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
47 47 0.64
48 26 0.36
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.23
Consensus pattern (48 bp):
AAGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCATCCCAG
Found at i:2716555 original size:40 final size:40
Alignment explanation
Indices: 2716493--2716568 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
2716483 GCTATACTAG
* *
2716493 CATTAGTGGCGTTTGTTGT-AAAACGCCGCAATATATCTGT
1 CATTAGCGGCGTTTGTAGTAAAAACGCCGCAA-ATATCTGT
2716533 CATTAGCGGCGTTT-TAGCTAAAAACGCCGCAAATAT
1 CATTAGCGGCGTTTGTAG-TAAAAACGCCGCAAATAT
2716569 GTTTAAGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
39 2 0.06
40 18 0.56
41 12 0.38
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (40 bp):
CATTAGCGGCGTTTGTAGTAAAAACGCCGCAAATATCTGT
Found at i:2717207 original size:21 final size:21
Alignment explanation
Indices: 2717183--2717259 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
2717173 TATGGTTTAA
2717183 GGGTT-GGGGTTTAAGGGTTAT
1 GGGTTAGGGG-TTAAGGGTTAT
*
2717204 GGGTTAGGGGTTAGGGGTTAT
1 GGGTTAGGGGTTAAGGGTTAT
* ** * *
2717225 GGATTAATGGTTTAGGTGTTAA
1 GGGTTAGGGGTTAAGG-GTTAT
*
2717247 GGCTTAGGGGTTA
1 GGGTTAGGGGTTA
2717260 TTGTTTTATG
Statistics
Matches: 43, Mismatches: 11, Indels: 3
0.75 0.19 0.05
Matches are distributed among these distances:
21 26 0.60
22 17 0.40
ACGTcount: A:0.18, C:0.01, G:0.44, T:0.36
Consensus pattern (21 bp):
GGGTTAGGGGTTAAGGGTTAT
Found at i:2717214 original size:14 final size:14
Alignment explanation
Indices: 2717197--2717260 Score: 56
Period size: 14 Copynumber: 4.5 Consensus size: 14
2717187 TGGGGTTTAA
2717197 GGGTTATGGGTTAG
1 GGGTTATGGGTTAG
* *
2717211 GGGTTAGGGGTTAT
1 GGGTTATGGGTTAG
* *
2717225 GGATTAATGGTTTAG
1 GGGTT-ATGGGTTAG
* * *
2717240 GTGTTAAGGCTTAG
1 GGGTTATGGGTTAG
2717254 GGGTTAT
1 GGGTTAT
2717261 TGTTTTATGG
Statistics
Matches: 37, Mismatches: 12, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
14 28 0.76
15 9 0.24
ACGTcount: A:0.19, C:0.02, G:0.42, T:0.38
Consensus pattern (14 bp):
GGGTTATGGGTTAG
Found at i:2717267 original size:29 final size:29
Alignment explanation
Indices: 2717235--2717294 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
2717225 GGATTAATGG
* *
2717235 TTTA-GGTGTTAAGGCTTAGGGGTTATTGT
1 TTTATGGT-TTAAGGCTTAGGGGATATAGT
* *
2717264 TTTATGGTTTAGGGTTTAGGGGATATAGT
1 TTTATGGTTTAAGGCTTAGGGGATATAGT
2717293 TT
1 TT
2717295 AGGGTACTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 23 0.88
30 3 0.12
ACGTcount: A:0.18, C:0.02, G:0.33, T:0.47
Consensus pattern (29 bp):
TTTATGGTTTAAGGCTTAGGGGATATAGT
Found at i:2717464 original size:29 final size:29
Alignment explanation
Indices: 2717417--2717495 Score: 97
Period size: 29 Copynumber: 2.8 Consensus size: 29
2717407 AATTCATACA
* * *
2717417 TTTTGT-GTTTAAGGCTTAGGGGTTATTG
1 TTTTGTGGTTTAAGGTTTAGGGGATATAG
*
2717445 TTTTGTGGTTTATGGTTTAGGGGATATAG
1 TTTTGTGGTTTAAGGTTTAGGGGATATAG
**
2717474 TTTAATGGTTTAAGGTTTAGGG
1 TTTTGTGGTTTAAGGTTTAGGG
2717496 TTTTGATTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 6 0.14
29 37 0.86
ACGTcount: A:0.18, C:0.01, G:0.33, T:0.48
Consensus pattern (29 bp):
TTTTGTGGTTTAAGGTTTAGGGGATATAG
Found at i:2719694 original size:25 final size:25
Alignment explanation
Indices: 2719661--2719732 Score: 90
Period size: 25 Copynumber: 2.9 Consensus size: 25
2719651 TAGTCCTCCG
* *
2719661 CATCGTCGTCGGCAGCCCTCTGCTA
1 CATCTTCGTCGGCATCCCTCTGCTA
* *
2719686 CATTTTCGTCAGCATCCCTCTGCTA
1 CATCTTCGTCGGCATCCCTCTGCTA
* *
2719711 CATCTCCGTCGACATCCCTCTG
1 CATCTTCGTCGGCATCCCTCTG
2719733 TTGCTTCTCT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.14, C:0.40, G:0.17, T:0.29
Consensus pattern (25 bp):
CATCTTCGTCGGCATCCCTCTGCTA
Found at i:2720434 original size:23 final size:23
Alignment explanation
Indices: 2720404--2720448 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2720394 AAGTATTTTC
* *
2720404 TTAAGAAATTTTATTTGATAATG
1 TTAAGAAAATTCATTTGATAATG
2720427 TTAAGAAAATTCATTTGATAAT
1 TTAAGAAAATTCATTTGATAAT
2720449 AATAATAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.44
Consensus pattern (23 bp):
TTAAGAAAATTCATTTGATAATG
Found at i:2721165 original size:9 final size:9
Alignment explanation
Indices: 2721153--2721415 Score: 205
Period size: 9 Copynumber: 29.6 Consensus size: 9
2721143 CATATCATAT
2721153 CATAACTTA
1 CATAACTTA
*
2721162 CATAATTTA
1 CATAACTTA
2721171 CATAACTTA
1 CATAACTTA
*
2721180 TATAACTTA
1 CATAACTTA
* *
2721189 GATAA-ATA
1 CATAACTTA
*
2721197 TATAACTTA
1 CATAACTTA
2721206 CATAACTTA
1 CATAACTTA
*
2721215 CATAA-ATA
1 CATAACTTA
* * *
2721223 TATATCATA
1 CATAACTTA
2721232 TCATAACTTA
1 -CATAACTTA
2721242 CATAACTTA
1 CATAACTTA
*
2721251 TATAACTTA
1 CATAACTTA
* *
2721260 GATAA-ATA
1 CATAACTTA
*
2721268 TATAACTTA
1 CATAACTTA
2721277 CATAACTTA
1 CATAACTTA
2721286 CATAAC-TA
1 CATAACTTA
* * *
2721294 TATATCATA
1 CATAACTTA
*
2721303 TCATAGCTTA
1 -CATAACTTA
2721313 CATAACTTA
1 CATAACTTA
*
2721322 TATAACTTA
1 CATAACTTA
* *
2721331 GATAA-ATA
1 CATAACTTA
*
2721339 TATAACTTA
1 CATAACTTA
2721348 CATAACTTA
1 CATAACTTA
*
2721357 CATAA-ATA
1 CATAACTTA
* * *
2721365 TATATCATA
1 CATAACTTA
*
2721374 TCATATCTTA
1 -CATAACTTA
2721384 CATAACTTA
1 CATAACTTA
*
2721393 CAAAACTTA
1 CATAACTTA
*
2721402 CTTAACTTA
1 CATAACTTA
2721411 CATAA
1 CATAA
2721416 TACATAAATA
Statistics
Matches: 203, Mismatches: 42, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
8 34 0.17
9 150 0.74
10 19 0.09
ACGTcount: A:0.46, C:0.16, G:0.02, T:0.37
Consensus pattern (9 bp):
CATAACTTA
Found at i:2721269 original size:71 final size:71
Alignment explanation
Indices: 2721162--2721401 Score: 426
Period size: 71 Copynumber: 3.4 Consensus size: 71
2721152 TCATAACTTA
*
2721162 CATAATTTACATAACTTATATAACTTAGATAAATATATAACTTACATAACTTACATAAATATATA
1 CATAACTTACATAACTTATATAACTTAGATAAATATATAACTTACATAACTTACATAAATATATA
2721227 TCATAT
66 TCATAT
*
2721233 CATAACTTACATAACTTATATAACTTAGATAAATATATAACTTACATAACTTACATAACTATATA
1 CATAACTTACATAACTTATATAACTTAGATAAATATATAACTTACATAACTTACATAAATATATA
2721298 TCATAT
66 TCATAT
*
2721304 CATAGCTTACATAACTTATATAACTTAGATAAATATATAACTTACATAACTTACATAAATATATA
1 CATAACTTACATAACTTATATAACTTAGATAAATATATAACTTACATAACTTACATAAATATATA
2721369 TCATAT
66 TCATAT
* * *
2721375 CATATCTTACATAACTTACAAAACTTA
1 CATAACTTACATAACTTATATAACTTA
2721402 CTTAACTTAC
Statistics
Matches: 162, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 162 1.00
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.37
Consensus pattern (71 bp):
CATAACTTACATAACTTATATAACTTAGATAAATATATAACTTACATAACTTACATAAATATATA
TCATAT
Found at i:2721272 original size:26 final size:26
Alignment explanation
Indices: 2721243--2721335 Score: 96
Period size: 26 Copynumber: 3.5 Consensus size: 26
2721233 CATAACTTAC
*
2721243 ATAACTTATATAACTTAGATAAATAT
1 ATAACTTATATAACTTACATAAATAT
* *
2721269 ATAACTTACATAACTTACATAACTAT
1 ATAACTTATATAACTTACATAAATAT
* * * *
2721295 ATATCATATCATAGCTTACATAACTTAT
1 ATAACTTAT-ATAACTTACATAA-ATAT
*
2721323 ATAACTTAGATAA
1 ATAACTTATATAA
2721336 ATATATAACT
Statistics
Matches: 53, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
26 29 0.55
27 15 0.28
28 9 0.17
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (26 bp):
ATAACTTATATAACTTACATAAATAT
Found at i:2721343 original size:26 final size:26
Alignment explanation
Indices: 2721314--2721415 Score: 105
Period size: 26 Copynumber: 3.8 Consensus size: 26
2721304 CATAGCTTAC
* *
2721314 ATAACTTATATAACTTAGATAAATAT
1 ATAACTTACATAACTTACATAAATAT
2721340 ATAACTTACATAACTTACATAAATAT
1 ATAACTTACATAACTTACATAAATAT
* * * * *
2721366 ATATCATATCATATCTTACATAACTTAC
1 ATAACTTA-CATAACTTACATAA-ATAT
* *
2721394 AAAACTTACTTAACTTACATAA
1 ATAACTTACATAACTTACATAA
2721416 TACATAAATA
Statistics
Matches: 62, Mismatches: 12, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
26 30 0.48
27 25 0.40
28 7 0.11
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.36
Consensus pattern (26 bp):
ATAACTTACATAACTTACATAAATAT
Found at i:2724470 original size:26 final size:26
Alignment explanation
Indices: 2724432--2724489 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
2724422 CATGAAATTC
2724432 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
2724458 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
2724484 TTATCA
1 TTATCA
2724490 ATTTGTATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:2731739 original size:131 final size:130
Alignment explanation
Indices: 2731490--2731821 Score: 447
Period size: 131 Copynumber: 2.6 Consensus size: 130
2731480 TAATTATTCA
* * * * * *
2731490 TTTAAAAATT-TTCAAAACGAAGGCAATATTCGAGGTTTGGGAATTTGGGGAATCGTGCCCAATC
1 TTTAAAAATTCTTTAAAACGAAGGCAATGTTCGATGTTTGGAAATTCGGGGAATCGTGCCCTATC
*
2731554 GTGCTGGGTTGCAATTTCCCGTTTCTTCAAAATAATCGAATATTCCTTTGGAATTTCAATCATGT
66 GTGCTGGGTTGCAATTTCCCGTTTCTTCAAAATAATCGAATATTCCTTTAGAATTTCAATCATGT
* * *
2731619 CTTTAAAAATTCTTTAAAACGAAGGCAACGTTCGATGTTTGGCAATTCGGGGAATTGTGCCCTAT
1 -TTTAAAAATTCTTTAAAACGAAGGCAATGTTCGATGTTTGGAAATTCGGGGAATCGTGCCCTAT
* * *
2731684 CGTGCTGGGTTGCAATTTCCCGTTTGTTCAAAATAATTGAATATTCCTTTAGAATTTCACTCATG
65 CGTGCTGGGTTGCAATTTCCCGTTTCTTCAAAATAATCGAATATTCCTTTAGAATTTCAATCATG
2731749 T
130 T
* * * * * *
2731750 TTTCAAGATTC--TAAAGCG-AGGCAATGTTCAATGTTTGGAAATTCGAGGAATCGTGCCCTACC
1 TTTAAAAATTCTTTAAAACGAAGGCAATGTTCGATGTTTGGAAATTCGGGGAATCGTGCCCTATC
*
2731812 GTGCTAGGTT
66 GTGCTGGGTT
2731822 TCGATTTTTT
Statistics
Matches: 179, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
127 47 0.26
128 6 0.03
130 19 0.11
131 107 0.60
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (130 bp):
TTTAAAAATTCTTTAAAACGAAGGCAATGTTCGATGTTTGGAAATTCGGGGAATCGTGCCCTATC
GTGCTGGGTTGCAATTTCCCGTTTCTTCAAAATAATCGAATATTCCTTTAGAATTTCAATCATGT
Found at i:2732677 original size:13 final size:14
Alignment explanation
Indices: 2732661--2732692 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
2732651 TTATTATAAA
2732661 TAATTATAAT-GTT
1 TAATTATAATGGTT
2732674 TAATTATAATGGTT
1 TAATTATAATGGTT
2732688 TAATT
1 TAATT
2732693 CGCCGTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (14 bp):
TAATTATAATGGTT
Found at i:2733385 original size:33 final size:33
Alignment explanation
Indices: 2733337--2733415 Score: 99
Period size: 31 Copynumber: 2.5 Consensus size: 33
2733327 TCATTTAATG
* *
2733337 TTTTTTGTTGCATTTTTTATGCTATATTTGCTA
1 TTTTTGGTTGGATTTTTTATGCTATATTTGCTA
* *
2733370 TTTTTGGTTGGA--TTTTATGTTATATTTGCTG
1 TTTTTGGTTGGATTTTTTATGCTATATTTGCTA
*
2733401 TTTTTGGTTCGATTT
1 TTTTTGGTTGGATTT
2733416 AATGCAAGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
31 28 0.72
33 11 0.28
ACGTcount: A:0.13, C:0.06, G:0.18, T:0.63
Consensus pattern (33 bp):
TTTTTGGTTGGATTTTTTATGCTATATTTGCTA
Found at i:2733394 original size:31 final size:31
Alignment explanation
Indices: 2733351--2733420 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
2733341 TTGTTGCATT
*
2733351 TTTTATGCTATATTTGCTATTTTTGGTTGGA
1 TTTTATGCTATATTTGCTATTTTTGGTTCGA
* *
2733382 TTTTATGTTATATTTGCTGTTTTTGGTTCGA
1 TTTTATGCTATATTTGCTATTTTTGGTTCGA
*
2733413 TTTAATGC
1 TTTTATGC
2733421 AAGAAGGGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.16, C:0.07, G:0.19, T:0.59
Consensus pattern (31 bp):
TTTTATGCTATATTTGCTATTTTTGGTTCGA
Found at i:2735682 original size:28 final size:28
Alignment explanation
Indices: 2735650--2735706 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
2735640 CTGCTTTCTT
* *
2735650 TTGTTCTGCT-TTTTTTTTTTTTTGAAAA
1 TTGTTCT-CTATTTTTTTTTATTTAAAAA
2735678 TTGTTCTCTACTTTTTTTTTATTTAAAAA
1 TTGTTCTCTA-TTTTTTTTTATTTAAAAA
2735707 GAATCGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.08
28 7 0.28
29 16 0.64
ACGTcount: A:0.19, C:0.09, G:0.07, T:0.65
Consensus pattern (28 bp):
TTGTTCTCTATTTTTTTTTATTTAAAAA
Found at i:2742327 original size:29 final size:29
Alignment explanation
Indices: 2742266--2742331 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
2742256 ATGTGGCCTC
* *
2742266 TGTTATATGTGAGCCCTAGTTGCAAAATC
1 TGTTATATGTGAGCCCTAGTGGCAAAATA
* * **
2742295 TGTTATATGTGAGCCTTTGTGGCTGAATA
1 TGTTATATGTGAGCCCTAGTGGCAAAATA
2742324 TGTTATAT
1 TGTTATAT
2742332 ACGGAAGCCC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.24, C:0.12, G:0.23, T:0.41
Consensus pattern (29 bp):
TGTTATATGTGAGCCCTAGTGGCAAAATA
Found at i:2744841 original size:24 final size:24
Alignment explanation
Indices: 2744796--2744841 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
2744786 TAATATTTAG
** *
2744796 TATTTATTAGCATAGTATATTTGA
1 TATTTATTAGCATAAAACATTTGA
*
2744820 TATTTATTAGTATAAAACATTT
1 TATTTATTAGCATAAAACATTT
2744842 TTTTATTTCT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (24 bp):
TATTTATTAGCATAAAACATTTGA
Found at i:2748235 original size:39 final size:39
Alignment explanation
Indices: 2748181--2748255 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
2748171 TGTATAAGTC
*
2748181 AATAGCGACACGACTTGATATTATGTACACAGTTGATTT
1 AATAGCAACACGACTTGATATTATGTACACAGTTGATTT
*
2748220 AATAGCAACACGACTTGATATTATGTACGCAGTTGA
1 AATAGCAACACGACTTGATATTATGTACACAGTTGA
2748256 CTTGTTAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.31
Consensus pattern (39 bp):
AATAGCAACACGACTTGATATTATGTACACAGTTGATTT
Found at i:2748908 original size:18 final size:18
Alignment explanation
Indices: 2748885--2748930 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
2748875 CAAACACACT
2748885 TGGCGAACTCTCCAAGAA
1 TGGCGAACTCTCCAAGAA
* * *
2748903 TGGCGAACTCTTCGAGAG
1 TGGCGAACTCTCCAAGAA
2748921 TGGCGAACTC
1 TGGCGAACTC
2748931 ACAGCACATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (18 bp):
TGGCGAACTCTCCAAGAA
Found at i:2750741 original size:21 final size:20
Alignment explanation
Indices: 2750715--2750759 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
2750705 TTGCACATTT
2750715 TTTTTAATTCAATTCAATTCA
1 TTTTTAATTCAATTCAATT-A
* *
2750736 TTTTTAATTTAATTTAATTA
1 TTTTTAATTCAATTCAATTA
2750756 TTTT
1 TTTT
2750760 AAAAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTAATTCAATTCAATTA
Found at i:2751068 original size:3 final size:3
Alignment explanation
Indices: 2751062--2751116 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
2751052 GTTACCATCA
*
2751062 AAG AAG -AG AAG -AG CAG AACG ACAG A-G AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AA-G A-AG AAG AAG AAG AAG AAG AAG AAG
*
2751106 AAA AAG AAG AA
1 AAG AAG AAG AA
2751117 ATGGATGCAT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
2 6 0.14
3 33 0.75
4 4 0.09
5 1 0.02
ACGTcount: A:0.64, C:0.05, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2751606 original size:14 final size:15
Alignment explanation
Indices: 2751588--2751631 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
2751578 ATTAATTTAG
2751588 AAAATTCAATTAATT
1 AAAATTCAATTAATT
* *
2751603 -AAATTTATTTAATT
1 AAAATTCAATTAATT
*
2751617 AAAAATCAATTAATT
1 AAAATTCAATTAATT
2751632 TACTTGGTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAATTCAATTAATT
Found at i:2752224 original size:30 final size:29
Alignment explanation
Indices: 2752161--2752225 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
2752151 ATAGTAAAAT
* * *
2752161 AGTCACTAAACTTTGAAAAGTTACAACTT
1 AGTCACTAAACTTTGAAAAATAACAACTC
2752190 AGTCACTAAACTTTAGAAAAATAACAAAC-C
1 AGTCACTAAACTTT-GAAAAATAAC-AACTC
2752220 AGTCAC
1 AGTCAC
2752226 CAATAACCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 14 0.45
30 14 0.45
31 3 0.10
ACGTcount: A:0.46, C:0.20, G:0.09, T:0.25
Consensus pattern (29 bp):
AGTCACTAAACTTTGAAAAATAACAACTC
Found at i:2753043 original size:31 final size:29
Alignment explanation
Indices: 2753000--2753097 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 29
2752990 ATGTTAATAG
*
2753000 GTGACTGATTTGTCACTTTTTGATAACA-TTA
1 GTGACTGTTTTGTCA-TTTTTG-TAA-AGTTA
*
2753031 GTGACTGTTTTGTTATTTTTGTAAAGTTTA
1 GTGACTGTTTTGTCATTTTTGTAAAG-TTA
* * **
2753061 GTGACTATTTTGTTATTTTAATCAAAGTTGA
1 GTGACTGTTTTGTCATTTTTGT-AAAGTT-A
2753092 GTGACT
1 GTGACT
2753098 ATTGGTGTAC
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
28 1 0.02
29 3 0.05
30 30 0.52
31 24 0.41
ACGTcount: A:0.24, C:0.08, G:0.18, T:0.49
Consensus pattern (29 bp):
GTGACTGTTTTGTCATTTTTGTAAAGTTA
Found at i:2753062 original size:30 final size:31
Alignment explanation
Indices: 2753028--2753100 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 31
2753018 TTTGATAACA
* **
2753028 TTAGTGACTGTTTTGTTATTTTTGT-AAAGT
1 TTAGTGACTATTTTGTTATTTTAATCAAAGT
2753058 TTAGTGACTATTTTGTTATTTTAATCAAAGT
1 TTAGTGACTATTTTGTTATTTTAATCAAAGT
*
2753089 TGAGTGACTATT
1 TTAGTGACTATT
2753101 GGTGTACTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
30 22 0.58
31 16 0.42
ACGTcount: A:0.25, C:0.05, G:0.18, T:0.52
Consensus pattern (31 bp):
TTAGTGACTATTTTGTTATTTTAATCAAAGT
Found at i:2755818 original size:27 final size:27
Alignment explanation
Indices: 2755780--2755834 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
2755770 ATATATTTTT
*
2755780 TACCCCCATTTTCATCTAGTTTGACTA
1 TACCCCCATTTTCATCTAGTTTAACTA
2755807 TACCCCCATTTTCATCTAGTTTAACTA
1 TACCCCCATTTTCATCTAGTTTAACTA
2755834 T
1 T
2755835 CTTTAAACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.29, G:0.05, T:0.42
Consensus pattern (27 bp):
TACCCCCATTTTCATCTAGTTTAACTA
Found at i:2759102 original size:10 final size:10
Alignment explanation
Indices: 2759087--2759114 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
2759077 ATATTACATG
2759087 TTTACTTTGT
1 TTTACTTTGT
2759097 TTTACTTTGT
1 TTTACTTTGT
2759107 TTTACTTT
1 TTTACTTT
2759115 TTCCCCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.07, T:0.71
Consensus pattern (10 bp):
TTTACTTTGT
Found at i:2764115 original size:15 final size:15
Alignment explanation
Indices: 2764095--2764124 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2764085 TTCCTTATTA
*
2764095 TGTCTTTTATATTTT
1 TGTCTTTCATATTTT
2764110 TGTCTTTCATATTTT
1 TGTCTTTCATATTTT
2764125 GCATGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.07, T:0.70
Consensus pattern (15 bp):
TGTCTTTCATATTTT
Found at i:2765759 original size:29 final size:29
Alignment explanation
Indices: 2765724--2765783 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
2765714 TTTAATATAT
2765724 TTAATATTAAATTTAATTTAATACTTATC
1 TTAATATTAAATTTAATTTAATACTTATC
* **
2765753 TTAATATTGAATTTAATTTAATGTTTATC
1 TTAATATTAAATTTAATTTAATACTTATC
2765782 TT
1 TT
2765784 GTAGATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (29 bp):
TTAATATTAAATTTAATTTAATACTTATC
Found at i:2767404 original size:30 final size:30
Alignment explanation
Indices: 2767352--2767409 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
2767342 CACGGCCAGG
* * *
2767352 ACACACGGGCGTGTGCTCTACCCGTGTGTC
1 ACACACAGGCGTGTGATCTACCCATGTGTC
2767382 ACACACAGGCGTGTGGAT-TACCCATGTG
1 ACACACAGGCGTGT-GATCTACCCATGTG
2767410 GAATTGCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.19, C:0.29, G:0.29, T:0.22
Consensus pattern (30 bp):
ACACACAGGCGTGTGATCTACCCATGTGTC
Found at i:2772510 original size:26 final size:26
Alignment explanation
Indices: 2772480--2772561 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
2772470 TGAAATTCCC
2772480 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
2772506 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
2772532 ATCATGGAACGTTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
2772558 ATCA
1 ATCA
2772562 ATTTGTATCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.35, C:0.27, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:2774252 original size:46 final size:46
Alignment explanation
Indices: 2774202--2774369 Score: 200
Period size: 46 Copynumber: 3.6 Consensus size: 46
2774192 TGGTTGAGCA
2774202 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
2774248 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
2774293 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
2774341 CCCGAGCTCATTGAGTTGAGTCCGAGTTC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
2774370 GCTTTGGGCG
Statistics
Matches: 103, Mismatches: 10, Indels: 18
0.79 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 55 0.53
47 29 0.28
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:2774358 original size:93 final size:93
Alignment explanation
Indices: 2774199--2774370 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
2774189 GGATGGTTGA
* * *
2774199 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
2774264 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
2774292 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
2774357 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
2774371 CTTTGGGCGG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:2780788 original size:46 final size:46
Alignment explanation
Indices: 2780738--2780913 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
2780728 TGGTTGAGCA
2780738 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
2780784 TCCGAACTCGCTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
2780829 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
2780877 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
2780914 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.57
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:2780894 original size:93 final size:93
Alignment explanation
Indices: 2780735--2780906 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
2780725 GGATGGTTGA
* *
2780735 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGCTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGCTGAGT
2780800 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
2780828 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGCTGAGT
2780893 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
2780907 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGCTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:2785319 original size:118 final size:118
Alignment explanation
Indices: 2785108--2785338 Score: 372
Period size: 118 Copynumber: 2.0 Consensus size: 118
2785098 AGTTTTCCAT
* * *
2785108 GGTTATGAGTACAGCTTAGATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGATGCTTGGGTTGTCATT
2785173 CTACTTCGCGTCAAAAGGTTGTGCGACGTGACAAGTAAAACTCCGCTAGCCGA
66 CTACTTCGCGTCAAAAGGTTGTGCGACGTGACAAGTAAAACTCCGCTAGCCGA
**
2785226 GGTTATGAGTATGGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGATGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGATGCTTGGGTTGTCATT
* ****
2785291 CTACTTCGCGTCAAAAGGTTGTGTGACGTGTTGGGTAAAACTCCGCTA
66 CTACTTCGCGTCAAAAGGTTGTGCGACGTGACAAGTAAAACTCCGCTA
2785339 ACCGGAAATA
Statistics
Matches: 103, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
118 103 1.00
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (118 bp):
GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGATGCTTGGGTTGTCATT
CTACTTCGCGTCAAAAGGTTGTGCGACGTGACAAGTAAAACTCCGCTAGCCGA
Found at i:2785486 original size:9 final size:9
Alignment explanation
Indices: 2785474--2785502 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
2785464 AAAAAAATCA
2785474 AAAAAAAAG
1 AAAAAAAAG
2785483 AAAAAAAAG
1 AAAAAAAAG
2785492 AAAAAAAAG
1 AAAAAAAAG
2785501 AA
1 AA
2785503 GAAGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:2790735 original size:6 final size:6
Alignment explanation
Indices: 2790724--2790749 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2790714 TAAAAAATAA
2790724 TATATG TATATG TATATG TATATG TA
1 TATATG TATATG TATATG TATATG TA
2790750 AATAGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:2795598 original size:514 final size:514
Alignment explanation
Indices: 2794631--2795658 Score: 2056
Period size: 514 Copynumber: 2.0 Consensus size: 514
2794621 GTACAGATGA
2794631 TCCGCCGGTCATCATTGCAAGTGAACATCTTCGATCCTTGTCAGTTTCTCGTCCCGAGAACATCG
1 TCCGCCGGTCATCATTGCAAGTGAACATCTTCGATCCTTGTCAGTTTCTCGTCCCGAGAACATCG
2794696 ATTCCGATCTTTTGGCATACCTAATCTCGACCTGTGTTCATATATCTGAGTTGAGTTTAACTGGT
66 ATTCCGATCTTTTGGCATACCTAATCTCGACCTGTGTTCATATATCTGAGTTGAGTTTAACTGGT
2794761 TCCATAGGTAAGTTCTTACCAGCATGCCAATCTCCGTACCAAATCACTTTCATGTCGTTGAGTGA
131 TCCATAGGTAAGTTCTTACCAGCATGCCAATCTCCGTACCAAATCACTTTCATGTCGTTGAGTGA
2794826 GACCGAGCTTAGTACAGATCCAATGCCAACTCTAGGGAAACTACCCAACTTAAAGATTCTCGAAC
196 GACCGAGCTTAGTACAGATCCAATGCCAACTCTAGGGAAACTACCCAACTTAAAGATTCTCGAAC
2794891 TGAAAAAGGCATTCATTGGAGAGGAACTTCACTGTTCTACAGAAGGTTTTCCTGAACTAAACTCC
261 TGAAAAAGGCATTCATTGGAGAGGAACTTCACTGTTCTACAGAAGGTTTTCCTGAACTAAACTCC
2794956 CTGAAACTTAGTTCCATTTCTACGGTAAAGCACTGGATCGTTGATAAATCTAGCATGCCTAAACT
326 CTGAAACTTAGTTCCATTTCTACGGTAAAGCACTGGATCGTTGATAAATCTAGCATGCCTAAACT
2795021 TCGTCATTTGGAGATCATCGATTGCAAAAGCTTAGAGATGTTACCAGTTGGATTGATGTTCATTA
391 TCGTCATTTGGAGATCATCGATTGCAAAAGCTTAGAGATGTTACCAGTTGGATTGATGTTCATTA
2795086 CAACACTTGAAGAACTCAAGATTGAACTAATGCCAAAAGCTTTCAAGGATAGATTGTGT
456 CAACACTTGAAGAACTCAAGATTGAACTAATGCCAAAAGCTTTCAAGGATAGATTGTGT
2795145 TCCGCCGGTCATCATTGCAAGTGAACATCTTCGATCCTTGTCAGTTTCTCGTCCCGAGAACATCG
1 TCCGCCGGTCATCATTGCAAGTGAACATCTTCGATCCTTGTCAGTTTCTCGTCCCGAGAACATCG
2795210 ATTCCGATCTTTTGGCATACCTAATCTCGACCTGTGTTCATATATCTGAGTTGAGTTTAACTGGT
66 ATTCCGATCTTTTGGCATACCTAATCTCGACCTGTGTTCATATATCTGAGTTGAGTTTAACTGGT
2795275 TCCATAGGTAAGTTCTTACCAGCATGCCAATCTCCGTACCAAATCACTTTCATGTCGTTGAGTGA
131 TCCATAGGTAAGTTCTTACCAGCATGCCAATCTCCGTACCAAATCACTTTCATGTCGTTGAGTGA
2795340 GACCGAGCTTAGTACAGATCCAATGCCAACTCTAGGGAAACTACCCAACTTAAAGATTCTCGAAC
196 GACCGAGCTTAGTACAGATCCAATGCCAACTCTAGGGAAACTACCCAACTTAAAGATTCTCGAAC
2795405 TGAAAAAGGCATTCATTGGAGAGGAACTTCACTGTTCTACAGAAGGTTTTCCTGAACTAAACTCC
261 TGAAAAAGGCATTCATTGGAGAGGAACTTCACTGTTCTACAGAAGGTTTTCCTGAACTAAACTCC
2795470 CTGAAACTTAGTTCCATTTCTACGGTAAAGCACTGGATCGTTGATAAATCTAGCATGCCTAAACT
326 CTGAAACTTAGTTCCATTTCTACGGTAAAGCACTGGATCGTTGATAAATCTAGCATGCCTAAACT
2795535 TCGTCATTTGGAGATCATCGATTGCAAAAGCTTAGAGATGTTACCAGTTGGATTGATGTTCATTA
391 TCGTCATTTGGAGATCATCGATTGCAAAAGCTTAGAGATGTTACCAGTTGGATTGATGTTCATTA
2795600 CAACACTTGAAGAACTCAAGATTGAACTAATGCCAAAAGCTTTCAAGGATAGATTGTGT
456 CAACACTTGAAGAACTCAAGATTGAACTAATGCCAAAAGCTTTCAAGGATAGATTGTGT
2795659 GAAGGAGACC
Statistics
Matches: 514, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
514 514 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (514 bp):
TCCGCCGGTCATCATTGCAAGTGAACATCTTCGATCCTTGTCAGTTTCTCGTCCCGAGAACATCG
ATTCCGATCTTTTGGCATACCTAATCTCGACCTGTGTTCATATATCTGAGTTGAGTTTAACTGGT
TCCATAGGTAAGTTCTTACCAGCATGCCAATCTCCGTACCAAATCACTTTCATGTCGTTGAGTGA
GACCGAGCTTAGTACAGATCCAATGCCAACTCTAGGGAAACTACCCAACTTAAAGATTCTCGAAC
TGAAAAAGGCATTCATTGGAGAGGAACTTCACTGTTCTACAGAAGGTTTTCCTGAACTAAACTCC
CTGAAACTTAGTTCCATTTCTACGGTAAAGCACTGGATCGTTGATAAATCTAGCATGCCTAAACT
TCGTCATTTGGAGATCATCGATTGCAAAAGCTTAGAGATGTTACCAGTTGGATTGATGTTCATTA
CAACACTTGAAGAACTCAAGATTGAACTAATGCCAAAAGCTTTCAAGGATAGATTGTGT
Found at i:2798531 original size:21 final size:22
Alignment explanation
Indices: 2798507--2798560 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
2798497 ACATACACGT
2798507 TTTAAAAACTATCGATACTCA-
1 TTTAAAAACTATCGATACTCAG
* *
2798528 TTTAGGAAA-TATTGATACTCAG
1 TTTA-AAAACTATCGATACTCAG
2798550 TTTTAAAAACT
1 -TTTAAAAACT
2798561 CATGCAGCGT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
21 15 0.58
22 6 0.23
23 5 0.19
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (22 bp):
TTTAAAAACTATCGATACTCAG
Found at i:2799193 original size:37 final size:37
Alignment explanation
Indices: 2799152--2799227 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
2799142 ACTTGCACAC
2799152 TTGATTTTAAAATTTTTATCCCAAATCAATTTTCAAT
1 TTGATTTTAAAATTTTTATCCCAAATCAATTTTCAAT
2799189 TTGATTTTAAAATTTTTATCCCAAATCAATTTTCAAT
1 TTGATTTTAAAATTTTTATCCCAAATCAATTTTCAAT
2799226 TT
1 TT
2799228 CTTGAAATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.34, C:0.13, G:0.03, T:0.50
Consensus pattern (37 bp):
TTGATTTTAAAATTTTTATCCCAAATCAATTTTCAAT
Found at i:2800354 original size:20 final size:21
Alignment explanation
Indices: 2800329--2800371 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2800319 CATGGGTAAA
2800329 CCACACGCCCGTCTGTCA-GG
1 CCACACGCCCGTCTGTCATGG
* *
2800349 CCACACGCCTGTGTGTCATGG
1 CCACACGCCCGTCTGTCATGG
2800370 CC
1 CC
2800372 GTGTCGATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.14, C:0.42, G:0.26, T:0.19
Consensus pattern (21 bp):
CCACACGCCCGTCTGTCATGG
Found at i:2801458 original size:22 final size:22
Alignment explanation
Indices: 2801427--2801493 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
2801417 TGCACAAACG
* *
2801427 ACAGAAAGCACTAAAGTGCTAT
1 ACAGAGAGCACTAAAGTGCTAA
2801449 ACAGAGAGCA--AAGATGTGCTAA
1 ACAGAGAGCACTAA-A-GTGCTAA
*
2801471 ACAGAGAGCACTTAACGTGCTAA
1 ACAGAGAGCAC-TAAAGTGCTAA
2801494 TAATAGAACG
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 2 0.05
21 1 0.03
22 25 0.68
23 7 0.19
25 2 0.05
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.16
Consensus pattern (22 bp):
ACAGAGAGCACTAAAGTGCTAA
Found at i:2802664 original size:7 final size:7
Alignment explanation
Indices: 2802654--2802742 Score: 64
Period size: 7 Copynumber: 13.3 Consensus size: 7
2802644 TACTTATGTT
2802654 TTATATA
1 TTATATA
2802661 -T-TATA
1 TTATATA
2802666 TTATATA
1 TTATATA
*
2802673 TAATATA
1 TTATATA
*
2802680 ATA-ATA
1 TTATATA
*
2802686 TGATATA
1 TTATATA
2802693 TTATATA
1 TTATATA
2802700 TTA-ATA
1 TTATATA
*
2802706 CTTAAATA
1 -TTATATA
2802714 TTA-A-A
1 TTATATA
2802719 TTAATATA
1 TT-ATATA
*
2802727 ATATATA
1 TTATATA
*
2802734 ATATATA
1 TTATATA
2802741 TT
1 TT
2802743 TTTATATTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
5 7 0.11
6 11 0.17
7 43 0.65
8 5 0.08
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (7 bp):
TTATATA
Found at i:2802691 original size:20 final size:20
Alignment explanation
Indices: 2802663--2802705 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2802653 TTTATATATT
*
2802663 ATATTATATATAATATAATA
1 ATATGATATATAATATAATA
* *
2802683 ATATGATATATTATATATTA
1 ATATGATATATAATATAATA
2802703 ATA
1 ATA
2802706 CTTAAATATT
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:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
ATATGATATATAATATAATA
Found at i:2804745 original size:21 final size:19
Alignment explanation
Indices: 2804719--2804763 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
2804709 AAAAAGTATT
2804719 GATACCCATATGATTTTTATC
1 GATACCCAT-T-ATTTTTATC
*
2804740 GATA-CCATTCTTTTTATC
1 GATACCCATTATTTTTATC
2804758 GATACC
1 GATACC
2804764 AAAGTTGCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 12 0.55
19 2 0.09
20 4 0.18
21 4 0.18
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (19 bp):
GATACCCATTATTTTTATC
Found at i:2807604 original size:16 final size:16
Alignment explanation
Indices: 2807583--2807614 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2807573 AAATTCATCC
2807583 GATTACTTGATGGATG
1 GATTACTTGATGGATG
2807599 GATTACTTGATGGATG
1 GATTACTTGATGGATG
2807615 TACAGATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.31, T:0.38
Consensus pattern (16 bp):
GATTACTTGATGGATG
Found at i:2814656 original size:23 final size:25
Alignment explanation
Indices: 2814629--2814678 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
2814619 AAGCTAAGGA
*
2814629 TAATA-TTTATATTATTAAA-ATAT
1 TAATATTTTATACTATTAAATATAT
*
2814652 TAATATTTTGTACTATTAAATATAT
1 TAATATTTTATACTATTAAATATAT
2814677 TA
1 TA
2814679 TAATTATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 5 0.22
24 12 0.52
25 6 0.26
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTTTATACTATTAAATATAT
Found at i:2816992 original size:21 final size:23
Alignment explanation
Indices: 2816968--2817022 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
2816958 GAAGTAAATT
*
2816968 AGATTTTT-TTTAA-TGGTTATA
1 AGATTTTTGTTTAATTGATTATA
2816989 AGATTTTTTTGTTTAATTGATTATA
1 AGA--TTTTTGTTTAATTGATTATA
2817014 AGATTTTTG
1 AGATTTTTG
2817023 AAATATAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 3 0.10
23 11 0.38
24 5 0.17
25 10 0.34
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (23 bp):
AGATTTTTGTTTAATTGATTATA
Found at i:2816998 original size:24 final size:25
Alignment explanation
Indices: 2816971--2817021 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
2816961 GTAAATTAGA
*
2816971 TTTTT-TTTAA-TGGTTATAAGATT
1 TTTTTGTTTAATTGATTATAAGATT
2816994 TTTTTGTTTAATTGATTATAAGATT
1 TTTTTGTTTAATTGATTATAAGATT
2817019 TTT
1 TTT
2817022 GAAATATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 5 0.20
24 5 0.20
25 15 0.60
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.63
Consensus pattern (25 bp):
TTTTTGTTTAATTGATTATAAGATT
Found at i:2822113 original size:13 final size:13
Alignment explanation
Indices: 2822097--2822122 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2822087 AGTATATTAT
2822097 TTTATTAATTTAA
1 TTTATTAATTTAA
2822110 TTTATTAATTTAA
1 TTTATTAATTTAA
2822123 GAGTAGAGAA
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTATTAATTTAA
Found at i:2837589 original size:25 final size:25
Alignment explanation
Indices: 2837540--2837598 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
2837530 GAGCAGAATT
* *
2837540 GAACAAAACATAGTAGAATAGAACA
1 GAACAGAACATAGTAGAAGAGAACA
*
2837565 TAACAGAACATAGTAGAACGA-AACA
1 GAACAGAACATAGTAGAA-GAGAACA
*
2837590 GAGCAGAAC
1 GAACAGAAC
2837599 TGAACAGAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 27 0.96
26 1 0.04
ACGTcount: A:0.56, C:0.15, G:0.19, T:0.10
Consensus pattern (25 bp):
GAACAGAACATAGTAGAAGAGAACA
Found at i:2841124 original size:15 final size:15
Alignment explanation
Indices: 2841104--2841133 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2841094 TTCCAATTCT
*
2841104 TTCTTTTTCTATTGA
1 TTCTTTTTCGATTGA
2841119 TTCTTTTTCGATTGA
1 TTCTTTTTCGATTGA
2841134 GATGTATGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.13, G:0.10, T:0.63
Consensus pattern (15 bp):
TTCTTTTTCGATTGA
Found at i:2850679 original size:3 final size:3
Alignment explanation
Indices: 2850671--2850791 Score: 68
Period size: 3 Copynumber: 40.7 Consensus size: 3
2850661 AATATGATAG
* * * * * * * * *
2850671 TAA TAA TAA CAA T-A TAG TAA TAG TAG TAG TAA TAG TAA TAG TGA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * **
2850718 TAA TAA AAA TAA TAG TAA TAA -AGA TAG TTC TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
*
2850763 TAA TAA TAA TAA TTAA -AA TAA TCA TAA TA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TA
2850792 TAAAATTTGA
Statistics
Matches: 88, Mismatches: 25, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
2 5 0.06
3 79 0.90
4 4 0.05
ACGTcount: A:0.56, C:0.02, G:0.09, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:2850687 original size:17 final size:16
Alignment explanation
Indices: 2850649--2850692 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
2850639 ATAAAAATAG
* *
2850649 TATAGTAATGATAATA
1 TATAGTAATAATAAAA
2850665 TGATAGTAATAATAACAA
1 T-ATAGTAATAATAA-AA
2850683 TATAGTAATA
1 TATAGTAATA
2850693 GTAGTAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 1 0.04
17 21 0.88
18 2 0.08
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.34
Consensus pattern (16 bp):
TATAGTAATAATAAAA
Found at i:2850737 original size:6 final size:6
Alignment explanation
Indices: 2850644--2850722 Score: 67
Period size: 6 Copynumber: 13.7 Consensus size: 6
2850634 AATAGATAAA
* * * *
2850644 AATAGT -ATAGT AAT-GAT AATA-T GATAGT AATAAT AACAAT -ATAGT
1 AATAGT AATAGT AATAG-T AATAGT AATAGT AATAGT AATAGT AATAGT
* *
2850689 AATAGT AGTAGT AATAGT AATAGT GATAGT AATA
1 AATAGT AATAGT AATAGT AATAGT AATAGT AATA
2850723 AAAATAATAG
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
5 13 0.22
6 45 0.78
ACGTcount: A:0.49, C:0.01, G:0.16, T:0.33
Consensus pattern (6 bp):
AATAGT
Found at i:2850994 original size:3 final size:3
Alignment explanation
Indices: 2850988--2851094 Score: 58
Period size: 3 Copynumber: 35.0 Consensus size: 3
2850978 ATGGTAAAAC
** **
2850988 ATA ATA ATA ATA AT- ATGA ATA ATA ATA ACG ATA ATAA ATA ATA GCA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA AT-A ATA ATA ATA
* * * * * *
2851034 AGA ATA ATA ATA GTA ATG ATA ATA GA-A GACA ATA ATA GTA CT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA -ATA ATA ATA ATA ATA ATA
2851079 ATAA ATA ATA ATA ATA
1 AT-A ATA ATA ATA ATA
2851095 GATTAAATTA
Statistics
Matches: 80, Mismatches: 17, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
2 3 0.04
3 67 0.84
4 10 0.12
ACGTcount: A:0.60, C:0.04, G:0.08, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:2851050 original size:28 final size:27
Alignment explanation
Indices: 2850992--2851095 Score: 78
Period size: 28 Copynumber: 4.0 Consensus size: 27
2850982 TAAAACATAA
* *
2850992 TAAT-AATAATATGAATAATAATAA-CG
1 TAATAAATAATA-GAAGAATAATAATAG
2851018 ATAATAAATAATAGCAAGAATAATAATAG
1 -TAATAAATAATAG-AAGAATAATAATAG
* *
2851047 TAAT-GATAATAGAAG-ACAATAATAG
1 TAATAAATAATAGAAGAATAATAATAG
* *
2851072 TACT--ATAATA-AATAATAATAATAG
1 TAATAAATAATAGAAGAATAATAATAG
2851096 ATTAAATTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
23 2 0.03
24 15 0.23
25 12 0.18
26 3 0.05
27 12 0.18
28 21 0.32
29 1 0.02
ACGTcount: A:0.59, C:0.04, G:0.10, T:0.28
Consensus pattern (27 bp):
TAATAAATAATAGAAGAATAATAATAG
Found at i:2858274 original size:30 final size:30
Alignment explanation
Indices: 2858175--2858370 Score: 114
Period size: 30 Copynumber: 6.7 Consensus size: 30
2858165 GTTTTGTTAT
* * *
2858175 TTATATATAATAAATATG-G-GTTTTGGTG
1 TTATATATAATATATATGCGTGTATGGGTG
* *
2858203 TTATATATATAATATTTATGAGTG---GGGT-
1 -T-TATATATAATATATATGCGTGTATGGGTG
2858231 TTATA-ATATATATATATGCGTGTATGGGTG
1 TTATATATA-ATATATATGCGTGTATGGGTG
* *
2858261 TTATATATAATATATATTTGGGTGCATGGGTG
1 TTATATATAATATATA--TGCGTGTATGGGTG
* *
2858293 TTATATGTATAATATATCTGCGTGGT-T--CTG
1 TTATA--TATAATATATATGCGT-GTATGGGTG
* *
2858323 CTATATATAATATATA----TGTATGGGTT
1 TTATATATAATATATATGCGTGTATGGGTG
2858349 TTATTATATAATATATATGCGT
1 TTA-TATATAATATATATGCGT
2858371 TTATCTAATA
Statistics
Matches: 129, Mismatches: 16, Indels: 42
0.69 0.09 0.22
Matches are distributed among these distances:
23 2 0.02
24 2 0.02
25 3 0.02
26 18 0.14
27 14 0.11
28 10 0.08
29 8 0.06
30 33 0.26
31 5 0.04
32 23 0.18
33 1 0.01
34 10 0.08
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.46
Consensus pattern (30 bp):
TTATATATAATATATATGCGTGTATGGGTG
Done.