Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009615.1 Hibiscus syriacus cultivar Beakdansim tig00117001_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: 259590
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:2534 original size:11 final size:11
Alignment explanation
Indices: 2500--2894 Score: 99
Period size: 11 Copynumber: 36.5 Consensus size: 11
2490 ATAATATATA
* *
2500 TATATAAAAAG
1 TATATATAAAC
2511 TATATAT-AA-
1 TATATATAAAC
2520 TATATATAAAC
1 TATATATAAAC
2531 TATAGTATGTAAAC
1 TATA-TA--TAAAC
2545 TATATATTATAAAC
1 --TATA-TATAAAC
*
2559 TATATAGAAAC
1 TATATATAAAC
* *
2570 TATTTATGAAC
1 TATATATAAAC
*
2581 TATATATTATGTAAA
1 TATATA-TA---AAC
**
2596 T-TATATGTAC
1 TATATATAAAC
2606 TATATATAAAC
1 TATATATAAAC
2617 --TA-ATAAAC
1 TATATATAAAC
* *
2625 TATATGTAGTA-
1 TATATATA-AAC
* *
2636 TAAATATAAAG
1 TATATATAAAC
2647 TATATATAAA-
1 TATATATAAAC
* *
2657 TATGTATATAC
1 TATATATAAAC
**
2668 ATATAATATATAGTT
1 -TAT-ATATA-A-AC
*
2683 TATATTTATATAC
1 TATA--TATAAAC
2696 TATATATAAA-
1 TATATATAAAC
***
2706 T-TATATAGTG
1 TATATATAAAC
*
2716 TATATATGAAC
1 TATATATAAAC
2727 --TATATAAAC
1 TATATATAAAC
2736 TATATATAAAC
1 TATATATAAAC
** *
2747 TATATAGTTTAT
1 TATATA-TAAAC
*
2759 TA-ATATGAAC
1 TATATATAAAC
*
2769 TATATATATAC
1 TATATATAAAC
2780 --TATATAAAC
1 TATATATAAAC
**
2789 TATATAGTTTA-
1 TATATA-TAAAC
* *
2800 TATTTATATAC
1 TATATATAAAC
* *
2811 AATGTAT-AAC
1 TATATATAAAC
2821 T-TATAT--AC
1 TATATATAAAC
*
2829 TAT-TATATAC
1 TATATATAAAC
2839 TATATAT--A-
1 TATATATAAAC
*
2847 TATATA-AATC
1 TATATATAAAC
2857 -ATATAT--AC
1 TATATATAAAC
2865 TATATATAAAC
1 TATATATAAAC
2876 TATATATGTAAAC
1 TATATA--TAAAC
2889 TATATA
1 TATATA
2895 ATTTATATAA
Statistics
Matches: 280, Mismatches: 57, Indels: 92
0.65 0.13 0.21
Matches are distributed among these distances:
8 19 0.07
9 48 0.17
10 33 0.12
11 112 0.40
12 17 0.06
13 21 0.08
14 17 0.06
15 7 0.03
16 6 0.02
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (11 bp):
TATATATAAAC
Found at i:2545 original size:14 final size:14
Alignment explanation
Indices: 2519--2564 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
2509 AGTATATATA
2519 ATATA-TATAAACT
1 ATATATTATAAACT
*
2532 ATAGTA-TGTAAACT
1 ATA-TATTATAAACT
2546 ATATATTATAAACT
1 ATATATTATAAACT
2560 ATATA
1 ATATA
2565 GAAACTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 5 0.17
14 24 0.83
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (14 bp):
ATATATTATAAACT
Found at i:2654 original size:2 final size:2
Alignment explanation
Indices: 2647--3041 Score: 86
Period size: 2 Copynumber: 190.0 Consensus size: 2
2637 AAATATAAAG
* * * * *
2647 TA TA TA TA AA TA TG TA TA TA CA TA TA -A TA TA TA GTT TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* *
2689 TA TA TA CTA TA TA TA AA T- TA TA TA GTG TA TA TA TGA -A CTA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA T-A TA -TA TA
* * *
2731 TA AA CTA TA TA TA AA CTA TA TA GTT TA T- TA -A TA TGA -A CTA TA
1 TA TA -TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA T-A TA -TA TA
* * * * *
2773 TA TA TA CTA TA TA AA CTA TA TA GTT TA TA TT TA TA TA CA -A TG
1 TA TA TA -TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA
*
2815 TA TA -A CT- TA TA TA CTA T- TA TA TA CTA TA TA TA TA TA TA AA
1 TA TA TA -TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * * *
2855 TCA TA TA TA CTA TA TA TA AA CTA TA TA TG TA AA CTA TA TA -A TT
1 T-A TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA
* * * * *
2898 TA TA TA AA CTA TA TG TA -A TA TA CA CTA TA TA GTT TA CA TA TGA
1 TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA T-A
* * * *
2941 -A CCA TA TA TA -A TC TA TA TA TA CTA TA TA AA CTA TA -A AA TA
1 TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA
* * * *
2981 TG TG TA TA AA CTA TG TA TA CTA CTA TA TA TA T- TA TA TA TA TA
1 TA TA TA TA TA -TA TA TA TA -TA -TA TA TA TA TA TA TA TA TA TA
3023 CTA TA TA TA -A CTA TA TA TA
1 -TA TA TA TA TA -TA TA TA TA
3042 CTATGGTTTA
Statistics
Matches: 284, Mismatches: 61, Indels: 96
0.64 0.14 0.22
Matches are distributed among these distances:
1 17 0.06
2 225 0.79
3 42 0.15
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.43
Consensus pattern (2 bp):
TA
Found at i:2765 original size:42 final size:41
Alignment explanation
Indices: 2689--2968 Score: 178
Period size: 42 Copynumber: 6.6 Consensus size: 41
2679 AGTTTATATT
* *
2689 TATATACTATATATAAATTATATAGTGTA-TATATGAACTA
1 TATATACTATATATAAACTATATAGTTTATTATATGAACTA
*
2729 TATAAACTATATATAAACTATATAGTTTATTAATATGAACTA
1 TATATACTATATATAAACTATATAGTTTATT-ATATGAACTA
* *
2771 TATATA-TACTATATAAACTATATAGTTTATATTTAT-ATACAA
1 TATATACTA-TATATAAACTATATAGTTTAT-TATATGA-ACTA
* * * * *
2813 TGTATAACT-TATATACTATTATATACTATATATATATAT-AAATCA
1 TATAT-ACTATATATA-AACTATATAGT-T-TAT-TATATGAACT-A
** * *
2858 TATATACTATATATAAACTATATATGTAAACTATAT-AATTTA
1 TATATACTATATATAAACTATATA-GTTTATTATATGAA-CTA
* * *
2900 TATAAACTATATGTAATATACACTATATAGTTTA-CATATGAACCA
1 TATATACTATA--T-ATA-A-ACTATATAGTTTATTATATGAACTA
* * *
2945 TATATAATCTATATATACTATATA
1 TATATACTATATATAAACTATATA
2969 AACTATAAAA
Statistics
Matches: 189, Mismatches: 31, Indels: 40
0.73 0.12 0.15
Matches are distributed among these distances:
40 34 0.18
41 4 0.02
42 73 0.39
43 13 0.07
44 14 0.07
45 37 0.20
46 6 0.03
47 8 0.04
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (41 bp):
TATATACTATATATAAACTATATAGTTTATTATATGAACTA
Found at i:2887 original size:13 final size:13
Alignment explanation
Indices: 2865--2894 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2855 TCATATATAC
2865 TATATATAAACTA
1 TATATATAAACTA
*
2878 TATATGTAAACTA
1 TATATATAAACTA
2891 TATA
1 TATA
2895 ATTTATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:3193 original size:32 final size:31
Alignment explanation
Indices: 3152--3356 Score: 142
Period size: 30 Copynumber: 6.9 Consensus size: 31
3142 CACACACACA
*
3152 TATATATATATATATATATATA-TAATATAGTT
1 TATATATATATATATATATAAACT-ATATAG-T
3184 TATATATATATATATATATAAACTATATAGT
1 TATATATATATATATATATAAACTATATAGT
3215 TAT-TATATAT-T-TGA-ATAAACTATATAGT
1 TATATATATATATAT-ATATAAACTATATAGT
3243 T-TAT-TACTATATATGA-ATAAACTATATAGT
1 TATATATA-TATATAT-ATATAAACTATATAGT
*
3273 T-TAT-TACTATATATGA-ACAAA-TATATA-T
1 TATATATA-TATATAT-ATATAAACTATATAGT
* * *
3301 GA-ACTAAATAT-TATATATAAATTATATA-T
1 TATA-TATATATATATATATAAACTATATAGT
3330 TATATAGT-TCAT-TA-ATATAAACTATAT
1 TATATA-TAT-ATATATATATAAACTATAT
3357 TAATTTATTA
Statistics
Matches: 151, Mismatches: 8, Indels: 31
0.79 0.04 0.16
Matches are distributed among these distances:
27 4 0.03
28 29 0.19
29 36 0.24
30 50 0.33
31 4 0.03
32 27 0.18
33 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.45
Consensus pattern (31 bp):
TATATATATATATATATATAAACTATATAGT
Found at i:3221 original size:28 final size:29
Alignment explanation
Indices: 3176--3299 Score: 162
Period size: 30 Copynumber: 4.2 Consensus size: 29
3166 TATATATATA
*
3176 ATATAGTTTATATATATATATATATATAAACT
1 ATATAGTTTAT-TATATATAT-GA-ATAAACT
*
3208 ATATAG-TTATTATATATTTGAATAAACT
1 ATATAGTTTATTATATATATGAATAAACT
3236 ATATAGTTTATTACTATATATGAATAAACT
1 ATATAGTTTATTA-TATATATGAATAAACT
*
3266 ATATAGTTTATTACTATATATGAACAAA-T
1 ATATAGTTTATTA-TATATATGAATAAACT
3295 ATATA
1 ATATA
3300 TGAACTAAAT
Statistics
Matches: 86, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
28 13 0.15
29 13 0.15
30 50 0.58
31 4 0.05
32 6 0.07
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (29 bp):
ATATAGTTTATTATATATATGAATAAACT
Found at i:3240 original size:2 final size:2
Alignment explanation
Indices: 3151--3224 Score: 82
Period size: 2 Copynumber: 37.0 Consensus size: 2
3141 ACACACACAC
*
3151 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AGT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
*
3193 AT AT AT AT AT AA ACT AT AT AGT -T AT -T AT AT AT
1 AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT
3225 TTGAATAAAC
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
1 3 0.05
2 56 0.90
3 3 0.05
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3240 original size:17 final size:17
Alignment explanation
Indices: 3218--3270 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 17
3208 ATATAGTTAT
3218 TATATATTTGAATAAAC
1 TATATATTTGAATAAAC
*
3235 TATATAGTTT--AT-TAC
1 TATATA-TTTGAATAAAC
3250 TATATA--TGAATAAAC
1 TATATATTTGAATAAAC
3265 TATATA
1 TATATA
3271 GTTTATTACT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
12 1 0.03
14 2 0.07
15 16 0.53
16 2 0.07
17 6 0.20
18 3 0.10
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (17 bp):
TATATATTTGAATAAAC
Found at i:3251 original size:15 final size:15
Alignment explanation
Indices: 3233--3285 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
3223 ATTTGAATAA
3233 ACTATATAGTTTATT
1 ACTATATAGTTTATT
** *
3248 ACTATATA-TGAATAA
1 ACTATATAGTTTAT-T
3263 ACTATATAGTTTATT
1 ACTATATAGTTTATT
3278 ACTATATA
1 ACTATATA
3286 TGAACAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 3 0.10
15 24 0.80
16 3 0.10
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.45
Consensus pattern (15 bp):
ACTATATAGTTTATT
Found at i:3299 original size:14 final size:15
Alignment explanation
Indices: 3280--3316 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
3270 AGTTTATTAC
3280 TATATATGAAC-AAA
1 TATATATGAACTAAA
3294 TATATATGAACTAAA
1 TATATATGAACTAAA
3309 TATTATAT
1 TA-TATAT
3317 ATAAATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 11 0.52
15 5 0.24
16 5 0.24
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (15 bp):
TATATATGAACTAAA
Found at i:3317 original size:18 final size:18
Alignment explanation
Indices: 3294--3335 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3284 TATGAACAAA
*
3294 TATATATGAACTAAATAT
1 TATATATAAACTAAATAT
* *
3312 TATATATAAATTATATAT
1 TATATATAAACTAAATAT
3330 TATATA
1 TATATA
3336 GTTCATTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
TATATATAAACTAAATAT
Found at i:3321 original size:58 final size:57
Alignment explanation
Indices: 3191--3332 Score: 139
Period size: 58 Copynumber: 2.5 Consensus size: 57
3181 GTTTATATAT
* * ** *
3191 ATATATATATATAAACTATATAGTTATTATATATTTGAATAAACTATATAGTTTATTA
1 ATAT-TATATATAAACTATATAGTTATTATATATATGAACAAACTATATAGTGAATAA
*
3249 CTA-TATATGAATAAACTATATAGTTTATTACTATATATGAACAAA-TATATA-TGAACTAA
1 ATATTATAT--ATAAACTATATAG-TTATTA-TATATATGAACAAACTATATAGTGAA-TAA
*
3308 ATATTATATATAAATTATATA-TTAT
1 ATATTATATATAAACTATATAGTTAT
3333 ATAGTTCATT
Statistics
Matches: 70, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
56 9 0.13
58 28 0.40
59 16 0.23
60 17 0.24
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (57 bp):
ATATTATATATAAACTATATAGTTATTATATATATGAACAAACTATATAGTGAATAA
Found at i:3393 original size:23 final size:20
Alignment explanation
Indices: 3341--3394 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 20
3331 ATATAGTTCA
3341 TTAATATAAACTATATTAAT
1 TTAATATAAACTATATTAAT
*
3361 TTATTAATAAACTATATATTATAT
1 TTAAT-ATAAAC--TATATTA-AT
3385 TTAATATAAA
1 TTAATATAAA
3395 ACTTTATGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 4 0.14
21 6 0.21
23 12 0.43
24 6 0.21
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAATATAAACTATATTAAT
Found at i:3413 original size:2 final size:2
Alignment explanation
Indices: 3406--3442 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
3396 CTTTATGAAC
*
3406 TA TA TA TA TA TA T- TA TA TA TA AA T- TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3443 TTTAATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3419 original size:107 final size:104
Alignment explanation
Indices: 3308--3582 Score: 273
Period size: 107 Copynumber: 2.6 Consensus size: 104
3298 TATGAACTAA
3308 ATATTATATATAAATTATATATTATATAGTTCATTAATATAAAC-TATATTAATTTATT-A-ATA
1 ATATTATATATAAATTATATA-TATATA-TT--TTAATATAAACATATATTAATTTATTAATATA
3370 AACTATATATTA-T-ATTTAATATAAAACTTTATGAACTATA-TATAT
62 AACTATATA-TAGTCA-TTAATAT-AAAC--TATGAACTATATTATAT
* *
3415 ATATTATATATAAATTATATATATATATTTTAATATAAACAATGTATTAATTTCTTAATATAAAC
1 ATATTATATATAAATTATATATATATATTTTAATATAAAC-ATATATTAATTTATTAATATAAAC
*
3480 TATATATAGTCCATTAGTATAAACTATGAACTATATTATAT
65 TATATATAGT-CATTAATATAAACTATGAACTATATTATAT
* * *
3521 ATACTATGTATAAACTATATAGT-T-TA--TTAATATAAACTATATGAATTATAGTTTATTAATA
1 ATATTATATATAAATTATATA-TATATATTTTAATATAAAC-ATAT--ATTA-A-TTTATTAATA
3582 T
60 T
3583 TAAATTTCAT
Statistics
Matches: 146, Mismatches: 9, Indels: 26
0.81 0.05 0.14
Matches are distributed among these distances:
103 25 0.17
105 31 0.21
106 34 0.23
107 49 0.34
108 6 0.04
109 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (104 bp):
ATATTATATATAAATTATATATATATATTTTAATATAAACATATATTAATTTATTAATATAAACT
ATATATAGTCATTAATATAAACTATGAACTATATTATAT
Found at i:3424 original size:11 final size:11
Alignment explanation
Indices: 3408--3440 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
3398 TTATGAACTA
3408 TATATATATAT
1 TATATATATAT
*
3419 TATATATAAAT
1 TATATATATAT
3430 TATATATATAT
1 TATATATATAT
3441 ATTTTAATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TATATATATAT
Found at i:3424 original size:13 final size:13
Alignment explanation
Indices: 3406--3443 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
3396 CTTTATGAAC
3406 TATATATATATAT
1 TATATATATATAT
3419 TATATATA-A-AT
1 TATATATATATAT
3430 TATATATATATAT
1 TATATATATATAT
3443 T
1 T
3444 TTAATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 10 0.43
12 2 0.09
13 11 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATATATATATAT
Found at i:3512 original size:105 final size:106
Alignment explanation
Indices: 3308--3541 Score: 277
Period size: 107 Copynumber: 2.2 Consensus size: 106
3298 TATGAACTAA
3308 ATATTATATATAAATTATATATTATATAGTTCATTAATATAAACTATATTAATTTATTAATAAAC
1 ATATTATATATAAATTATATATTATATAGTT-ATTAATATAAACTATATTAATTTATTAATAAAC
3373 TATATATTATATTTAATATAAAACTTTATGAACTATA-TATAT
65 TATATATTATATTTAATATAAAAC-TTATGAACTATATTATAT
* *
3415 ATATTATATATAAATTATATA-TATATA-TT-TTAATATAAACAATGTATTAATTTCTTAATATA
1 ATATTATATATAAATTATATATTATATAGTTATTAATATAAAC--TATATTAATTTATT-A-ATA
*
3477 AACTATATA-TAGTCCA-TTAGTAT-AAAC-TATGAACTATATTATAT
62 AACTATATATTA-T--ATTTAATATAAAACTTATGAACTATATTATAT
* * *
3521 ATACTATGTATAAACTATATA
1 ATATTATATATAAATTATATA
3542 GTTTATTAAT
Statistics
Matches: 113, Mismatches: 6, Indels: 17
0.83 0.04 0.12
Matches are distributed among these distances:
103 11 0.10
105 25 0.22
106 32 0.28
107 38 0.34
108 6 0.05
109 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (106 bp):
ATATTATATATAAATTATATATTATATAGTTATTAATATAAACTATATTAATTTATTAATAAACT
ATATATTATATTTAATATAAAACTTATGAACTATATTATAT
Found at i:4095 original size:102 final size:101
Alignment explanation
Indices: 3903--4137 Score: 289
Period size: 102 Copynumber: 2.3 Consensus size: 101
3893 AAAATCATCA
* * *
3903 TTTGATCTTCACAAACACCAAAACTCAAACCTATCCTATTTTTTTCGATCAAACACCCCAAAATT
1 TTTGATCTTTACAAACACTAAAACCCAAACCTATCCTATTTTTTTCGATCAAACACCCCAAAATT
* * *
3968 AAACCCTTGTTTTTCTATGTTATCCCC-AACCTTATTC
66 AAACCATTATTTATCTATGTTATCCCCAAACC-T-TTC
4005 TTTGATCTTTACAAACACTAAAACCCAAACTCTATCCTA-TTTTTTCGATCAAACACCCC-AAAT
1 TTTGATCTTTACAAACACTAAAACCCAAAC-CTATCCTATTTTTTTCGATCAAACACCCCAAAAT
*
4068 TCAACCATTATTTAT-TAGTGTTCATCCCCAAACCTTTC
65 TAAACCATTATTTATCTA-TGTT-ATCCCCAAACCTTTC
* * * *
4106 TTTAACCCTTACAAACACCTAAAACCAAAACC
1 TTTGATCTTTACAAACA-CTAAAACCCAAACC
4138 CAACCCAACC
Statistics
Matches: 117, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
100 2 0.02
101 37 0.32
102 66 0.56
103 12 0.10
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (101 bp):
TTTGATCTTTACAAACACTAAAACCCAAACCTATCCTATTTTTTTCGATCAAACACCCCAAAATT
AAACCATTATTTATCTATGTTATCCCCAAACCTTTC
Found at i:4178 original size:106 final size:106
Alignment explanation
Indices: 4040--4246 Score: 251
Period size: 106 Copynumber: 2.0 Consensus size: 106
4030 CAAACTCTAT
* * * * * *
4040 CCTATTTTTTCGATCAAACACCCCAAATTCAAC-CATTATTTAT-TAGTGTTCATCCCCAAACCT
1 CCTATTTTTTCAATCAAACACCCCAAACTCAACAC-TTATTCATCCA-TATTCATCCCCAAACCC
*
4103 TTCTTTAACCCTTACAAACACCTAAAACCAAAACCCAACCCAA
64 TTCTTTAACCCTTACAAACACCCAAAACCAAAACCCAACCCAA
4146 CCTATTTTTTCAATC-AA-ACCCCAAACCCTCAACACTTATTCATCCATATTCATCCCCAAACCC
1 CCTATTTTTTCAATCAAACACCCCAAA--CTCAACACTTATTCATCCATATTCATCCCCAAACCC
* * * *
4209 TTGTTTGATCCTTACAAACACCCAAAAGCAAAACCCAA
64 TTCTTTAACCCTTACAAACACCCAAAACCAAAACCCAA
4247 ACTATTTTTA
Statistics
Matches: 86, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
104 8 0.09
105 2 0.02
106 74 0.86
107 2 0.02
ACGTcount: A:0.36, C:0.34, G:0.03, T:0.27
Consensus pattern (106 bp):
CCTATTTTTTCAATCAAACACCCCAAACTCAACACTTATTCATCCATATTCATCCCCAAACCCTT
CTTTAACCCTTACAAACACCCAAAACCAAAACCCAACCCAA
Found at i:4420 original size:53 final size:54
Alignment explanation
Indices: 4290--4466 Score: 189
Period size: 53 Copynumber: 3.3 Consensus size: 54
4280 TTCTAACTTT
* * * *
4290 TTCTCTAACCTTAAACCCTAACCAAA-CATTTTTTTATTCTTTT-TTATCTGTTCATC
1 TTCTCTAACCCTAAACCCTAACCAAAGC--CTATTCA-TCTTTTGTT-TCTGTTCATC
* * * * *
4346 TTCTTTAACCTTAAACCCTAACTAAAGCCTATTTATCTTTTGTTT-TGTTCATA
1 TTCTCTAACCCTAAACCCTAACCAAAGCCTATTCATCTTTTGTTTCTGTTCATC
** *
4399 TTCTCTAACCCTAAATTCTAACCAAAGCCTATTCATCTTTTGTTTCTATTCATC
1 TTCTCTAACCCTAAACCCTAACCAAAGCCTATTCATCTTTTGTTTCTGTTCATC
4453 TTCTCTAACCCTAA
1 TTCTCTAACCCTAA
4467 TCGATAATGT
Statistics
Matches: 105, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
53 46 0.44
54 27 0.26
55 7 0.07
56 24 0.23
57 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.03, T:0.45
Consensus pattern (54 bp):
TTCTCTAACCCTAAACCCTAACCAAAGCCTATTCATCTTTTGTTTCTGTTCATC
Found at i:7827 original size:30 final size:31
Alignment explanation
Indices: 7786--7843 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
7776 GTAACTTTTG
7786 TTTATTTATGTTTATTAAATTAAATTTTATA
1 TTTATTTATGTTTATTAAATTAAATTTTATA
*
7817 TTTA-TTATGTTTATTAAATTAATTTTT
1 TTTATTTATGTTTATTAAATTAAATTTT
7844 CGATAAGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (31 bp):
TTTATTTATGTTTATTAAATTAAATTTTATA
Found at i:8872 original size:16 final size:16
Alignment explanation
Indices: 8836--8891 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
8826 TTTCATCAAT
*
8836 GGTAATATAT-AATTCA
1 GGTAA-ATATCAAATCA
8852 GGTAAATATCAAATCA
1 GGTAAATATCAAATCA
* *
8868 TGTAAATATCATATCA
1 GGTAAATATCAAATCA
8884 GGTAAATA
1 GGTAAATA
8892 ACAAGTCGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 4 0.11
16 31 0.89
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.32
Consensus pattern (16 bp):
GGTAAATATCAAATCA
Found at i:9503 original size:27 final size:26
Alignment explanation
Indices: 9425--9506 Score: 146
Period size: 26 Copynumber: 3.1 Consensus size: 26
9415 GTGGTGGCCG
*
9425 GGTAAAACGGAGTGTTTGAGCTAGCT
1 GGTAAAACGGAGTGTTTGAGGTAGCT
9451 GGTAAAACGGAGTGTTTGAGGTAGCT
1 GGTAAAACGGAGTGTTTGAGGTAGCT
9477 GGTAAAACGGAGTGTTTTGAGGTAGCT
1 GGTAAAACGGAGTG-TTTGAGGTAGCT
9504 GGT
1 GGT
9507 TGAGCGAAGA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
26 39 0.72
27 15 0.28
ACGTcount: A:0.26, C:0.09, G:0.38, T:0.28
Consensus pattern (26 bp):
GGTAAAACGGAGTGTTTGAGGTAGCT
Found at i:19070 original size:19 final size:20
Alignment explanation
Indices: 19046--19104 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 20
19036 TTTGGTGCAG
*
19046 AGGGAATCGA-TCCCCCTTC
1 AGGGAACCGATTCCCCCTTC
*
19065 AGGGAACCGATTCCCCCTTTGA
1 AGGGAACCGATTCCCCC-TT-C
19087 AGGGGAACCGATTCCCCC
1 A-GGGAACCGATTCCCCC
19105 CCACAGGGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.26
20 6 0.18
21 2 0.06
22 1 0.03
23 16 0.47
ACGTcount: A:0.22, C:0.36, G:0.24, T:0.19
Consensus pattern (20 bp):
AGGGAACCGATTCCCCCTTC
Found at i:30185 original size:40 final size:40
Alignment explanation
Indices: 30073--30185 Score: 163
Period size: 41 Copynumber: 2.8 Consensus size: 40
30063 TTGGGTAAAC
*
30073 AGTACCGATATTGTTCTTACAGGATCGATACCTCCTGAAT
1 AGTACCGATATTGTTCTTACAGGATCGATACCGCCTGAAT
*
30113 TGTACACGATATTGTTCTTACAGGATCGATACCGCCTGAAT
1 AGTAC-CGATATTGTTCTTACAGGATCGATACCGCCTGAAT
* * * *
30154 AGTACCGATACTGTTCTTGCAGTATCAATACC
1 AGTACCGATATTGTTCTTACAGGATCGATACC
30186 AAAGGTAAGA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
40 27 0.42
41 38 0.58
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (40 bp):
AGTACCGATATTGTTCTTACAGGATCGATACCGCCTGAAT
Found at i:36054 original size:31 final size:31
Alignment explanation
Indices: 36019--36077 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
36009 ATAAAGGTGA
*
36019 AGTGACCA-TTTTGTTACAAATTGATAACTGT
1 AGTGA-CAGTTTTGTTACAAATCGATAACTGT
36050 AGTGACAGTTTTGTTACAAATCGATAAC
1 AGTGACAGTTTTGTTACAAATCGATAAC
36078 GTTAGTAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (31 bp):
AGTGACAGTTTTGTTACAAATCGATAACTGT
Found at i:37967 original size:92 final size:92
Alignment explanation
Indices: 37810--37982 Score: 285
Period size: 92 Copynumber: 1.9 Consensus size: 92
37800 ATTTTCTTGA
37810 GATAGATTTTCGGAGACTCCTTACGTGTTCAAGATCTTTTGGTCACCTGTCTCCTTAAATACAAC
1 GATAGATTTTCGGAGACTCCTTACGTGTTCAAGATCTTTTGGTCACCTGTCTCCTTAAATACAAC
37875 AACTCGATTCGAGATCGTTTGCATATT
66 AACTCGATTCGAGATCGTTTGCATATT
* * * * *
37902 GATAGATTTTTGGCGACTCCTTAGGTGTTCAAGATCTTTTGGTTATCTGTCTCC-TAAGATACAA
1 GATAGATTTTCGGAGACTCCTTACGTGTTCAAGATCTTTTGGTCACCTGTCTCCTTAA-ATACAA
37966 CAACTCGATTCGAGATC
65 CAACTCGATTCGAGATC
37983 ACAAACTATT
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
91 3 0.04
92 72 0.96
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (92 bp):
GATAGATTTTCGGAGACTCCTTACGTGTTCAAGATCTTTTGGTCACCTGTCTCCTTAAATACAAC
AACTCGATTCGAGATCGTTTGCATATT
Found at i:38187 original size:34 final size:34
Alignment explanation
Indices: 38142--38206 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
38132 AGTCAAACAT
*
38142 ATATTTTTTAATATTCAAAT-TTAAAAAGATAATA
1 ATATCTTTTAAT-TTCAAATATTAAAAAGATAATA
* *
38176 ATATCTTTTAATTTGAAATATTCAAAAGATA
1 ATATCTTTTAATTTCAAATATTAAAAAGATA
38207 TAAACAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 6 0.22
34 21 0.78
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (34 bp):
ATATCTTTTAATTTCAAATATTAAAAAGATAATA
Found at i:40257 original size:36 final size:36
Alignment explanation
Indices: 40215--40290 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
40205 TTATAGCTAA
*
40215 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
40251 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
40287 AAAA
1 AAAA
40291 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:44783 original size:15 final size:15
Alignment explanation
Indices: 44765--44794 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
44755 CCACGGTACT
44765 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
44780 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
44795 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:45258 original size:36 final size:36
Alignment explanation
Indices: 45216--45291 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
45206 TTATAGCTAA
*
45216 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
45252 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
45288 AAAA
1 AAAA
45292 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:50126 original size:19 final size:19
Alignment explanation
Indices: 50102--50146 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
50092 AGAGCAGCTG
50102 AAATGTTTGATGAAATGAC
1 AAATGTTTGATGAAATGAC
*
50121 AAATGTTTGATGAAGTGAC
1 AAATGTTTGATGAAATGAC
50140 AAATGTT
1 AAATGTT
50147 GTAACTGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.33
Consensus pattern (19 bp):
AAATGTTTGATGAAATGAC
Found at i:51281 original size:6 final size:6
Alignment explanation
Indices: 51272--51296 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
51262 ATATCTTAAC
51272 CATGGA CATGGA CATGGA CATGGA C
1 CATGGA CATGGA CATGGA CATGGA C
51297 TTGTGTGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.20, G:0.32, T:0.16
Consensus pattern (6 bp):
CATGGA
Found at i:52149 original size:10 final size:10
Alignment explanation
Indices: 52134--52159 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
52124 AATACACATT
52134 CATATATATA
1 CATATATATA
52144 CATATATATA
1 CATATATATA
52154 CATATA
1 CATATA
52160 AGAGGTAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (10 bp):
CATATATATA
Found at i:53927 original size:17 final size:17
Alignment explanation
Indices: 53900--53935 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
53890 AGTAATTGCG
53900 AAATTTTATTTTTT-AT
1 AAATTTTATTTTTTGAT
53916 AAATTATTATTTTTTGAT
1 AAATT-TTATTTTTTGAT
53934 AA
1 AA
53936 TTCTGATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 9 0.50
18 4 0.22
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
AAATTTTATTTTTTGAT
Found at i:59213 original size:30 final size:30
Alignment explanation
Indices: 59177--59273 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
59167 GTCATGAAAT
59177 TAGAATGTTTTAAAAGTTTGGGGACCAATA
1 TAGAATGTTTTAAAAGTTTGGGGACCAATA
* * * * * **
59207 TAGAATGAATGTCAAAGTTTGAGAATGAA-A
1 TAGAATG-TTTTAAAAGTTTGGGGACCAATA
* *
59237 TTGAACTGTTTAAAAAGTTTGGGGACCAATA
1 TAGAA-TGTTTTAAAAGTTTGGGGACCAATA
59268 TAGAAT
1 TAGAAT
59274 AAATGTCAAA
Statistics
Matches: 47, Mismatches: 17, Indels: 6
0.67 0.24 0.09
Matches are distributed among these distances:
30 26 0.55
31 21 0.45
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (30 bp):
TAGAATGTTTTAAAAGTTTGGGGACCAATA
Found at i:59226 original size:31 final size:31
Alignment explanation
Indices: 59189--59288 Score: 89
Period size: 31 Copynumber: 3.3 Consensus size: 31
59179 GAATGTTTTA
59189 AAAGTTTGGGGACCAATATAGAATGAATGTC
1 AAAGTTTGGGGACCAATATAGAATGAATGTC
* * ** * * *
59220 AAAGTTTGAGAATGAA-ATTGAACTG--TTTAA
1 AAAGTTTGGGGACCAATATAGAA-TGAATGT-C
*
59250 AAAGTTTGGGGACCAATATAGAATAAATGTC
1 AAAGTTTGGGGACCAATATAGAATGAATGTC
59281 AAAGTTTG
1 AAAGTTTG
59289 AGAATGAAAT
Statistics
Matches: 49, Mismatches: 15, Indels: 10
0.66 0.20 0.14
Matches are distributed among these distances:
29 2 0.04
30 18 0.37
31 27 0.55
32 2 0.04
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.29
Consensus pattern (31 bp):
AAAGTTTGGGGACCAATATAGAATGAATGTC
Found at i:59247 original size:61 final size:60
Alignment explanation
Indices: 59170--59316 Score: 242
Period size: 61 Copynumber: 2.4 Consensus size: 60
59160 GTATGCTGTC
*
59170 ATGAAATTAGAATGTTTTAAAAGTTTGGGGACCAATATAGAATGAATGTCAAAGTTTGAGA
1 ATGAAATT-GAATGTTTTAAAAGTTTGGGGACCAATATAGAATAAATGTCAAAGTTTGAGA
*
59231 ATGAAATTGAACTGTTTAAAAAGTTTGGGGACCAATATAGAATAAATGTCAAAGTTTGAGA
1 ATGAAATTGAA-TGTTTTAAAAGTTTGGGGACCAATATAGAATAAATGTCAAAGTTTGAGA
59292 ATGAAATTGAAATG-TTTAAAAGTTT
1 ATGAAATTG-AATGTTTTAAAAGTTT
59317 AAGGACTAAT
Statistics
Matches: 81, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
60 13 0.16
61 66 0.81
62 2 0.02
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (60 bp):
ATGAAATTGAATGTTTTAAAAGTTTGGGGACCAATATAGAATAAATGTCAAAGTTTGAGA
Found at i:62101 original size:17 final size:18
Alignment explanation
Indices: 62079--62125 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
62069 TTCTTTACCA
62079 TCCTCTTGTTTTCTTCT-
1 TCCTCTTGTTTTCTTCTC
*
62096 TCCTC-TATTTTCTTCTC
1 TCCTCTTGTTTTCTTCTC
62113 TCCT-TTGGTTTTC
1 TCCTCTT-GTTTTC
62126 AAAAAGTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 10 0.40
17 10 0.40
18 5 0.20
ACGTcount: A:0.02, C:0.30, G:0.06, T:0.62
Consensus pattern (18 bp):
TCCTCTTGTTTTCTTCTC
Found at i:66620 original size:17 final size:17
Alignment explanation
Indices: 66598--66640 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
66588 TGAGGGTAGC
*
66598 AGGTGAGGGGGAGGGAG
1 AGGTGAGAGGGAGGGAG
66615 AGGTGAGAGGGAGGGAG
1 AGGTGAGAGGGAGGGAG
66632 AGGTGAGAG
1 AGGTGAGAG
66641 AAAGGTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.65, T:0.07
Consensus pattern (17 bp):
AGGTGAGAGGGAGGGAG
Found at i:67810 original size:37 final size:37
Alignment explanation
Indices: 67734--67810 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
67724 TTTTTATATT
* *
67734 TTTAATTTTGTAAACAAAATTATATAAATGTTATGAA
1 TTTAATTTTGTAAACAAAATTATATAAATATTATCAA
* * *
67771 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAACAAAATTATATAAATATTAT-CAA
67808 TTT
1 TTT
67811 GTAATATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 12 0.35
37 22 0.65
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAACAAAATTATATAAATATTATCAA
Found at i:68980 original size:45 final size:44
Alignment explanation
Indices: 68917--69001 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 44
68907 GTTTGGTTCG
*
68917 CGAAAAAAATATTATCAA-GAGGATTAATATTTTCTGAAATGACA
1 CGAAAAAAATATTATCAAGGA-GAATAATATTTTCTGAAATGACA
68961 CGAAAAAGAATATTATCAAGGAGAATAATATTTTCTGAAAT
1 CGAAAAA-AATATTATCAAGGAGAATAATATTTTCTGAAAT
69002 TGTATTTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
44 7 0.18
45 29 0.76
46 2 0.05
ACGTcount: A:0.48, C:0.08, G:0.14, T:0.29
Consensus pattern (44 bp):
CGAAAAAAATATTATCAAGGAGAATAATATTTTCTGAAATGACA
Found at i:72762 original size:73 final size:72
Alignment explanation
Indices: 72632--72769 Score: 204
Period size: 73 Copynumber: 1.9 Consensus size: 72
72622 AGTTAATTAG
* * * *
72632 GAAATTAAAATATCGATAGTTATGCTTTAATGTTCAATACATTTAAATTTTAAAAAGTTTATGAA
1 GAAATTAAAATATCGATACTTATGCTTTAATGTTCAATAAATTTAAATTTGAAAAAGTATATGAA
72697 AGTAATC
66 AGTAATC
* * *
72704 GAAAGTTAAAATATTGATACTTATGCTTTAATGTTCAATAAATTTACATTTGACAAAGTATATGA
1 GAAA-TTAAAATATCGATACTTATGCTTTAATGTTCAATAAATTTAAATTTGAAAAAGTATATGA
72769 A
65 A
72770 TATAATACTG
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
72 4 0.07
73 54 0.93
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (72 bp):
GAAATTAAAATATCGATACTTATGCTTTAATGTTCAATAAATTTAAATTTGAAAAAGTATATGAA
AGTAATC
Found at i:78136 original size:24 final size:24
Alignment explanation
Indices: 78090--78136 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
78080 ACTCGATTTG
*
78090 AAAAAAATAAATGATTTATAAATT
1 AAAAAAATAAATGATTTAAAAATT
*
78114 AAAAAATTAAATCGA-TTAAAAAT
1 AAAAAAATAAAT-GATTTAAAAAT
78137 ATTATCTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (24 bp):
AAAAAAATAAATGATTTAAAAATT
Found at i:78662 original size:29 final size:29
Alignment explanation
Indices: 78629--78712 Score: 141
Period size: 29 Copynumber: 2.8 Consensus size: 29
78619 ATTACTGATA
78629 AAAATTATAATAAAATAAAATAAAATTTC
1 AAAATTATAATAAAATAAAATAAAATTTC
78658 AAAATTATAATAAAATAAAATAAAATTTC
1 AAAATTATAATAAAATAAAATAAAATTTC
*
78687 AAAATTATAAATAAAAATATAATAAA
1 AAAATTAT-AAT-AAAATAAAATAAA
78713 TAATCATAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
29 37 0.71
30 3 0.06
31 12 0.23
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (29 bp):
AAAATTATAATAAAATAAAATAAAATTTC
Found at i:78682 original size:21 final size:21
Alignment explanation
Indices: 78642--78712 Score: 65
Period size: 24 Copynumber: 3.3 Consensus size: 21
78632 ATTATAATAA
78642 AATAAAATAAAATTTCAAAATTAT
1 AATAAAATAAAA--T-AAAATTAT
78666 AATAAAATAAAATAAAATT-T
1 AATAAAATAAAATAAAATTAT
* * *
78686 CA-AAATTATAAATAAAAATAT
1 AATAAAATA-AAATAAAATTAT
78707 AATAAA
1 AATAAA
78713 TAATCATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
19 5 0.12
20 11 0.28
21 8 0.20
22 4 0.10
24 12 0.30
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (21 bp):
AATAAAATAAAATAAAATTAT
Found at i:79207 original size:24 final size:24
Alignment explanation
Indices: 79180--79226 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
79170 ATAATAAATA
79180 AATAAAT-ACTTAACAATTAATAAG
1 AATAAATCACTTAACAA-TAATAAG
* *
79204 AATAATTCACTTAATAATAATAA
1 AATAAATCACTTAACAATAATAA
79227 ATAAGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (24 bp):
AATAAATCACTTAACAATAATAAG
Found at i:85069 original size:15 final size:15
Alignment explanation
Indices: 85049--85081 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
85039 TTTAGCTGGA
85049 CGGGCGGATGTGGGG
1 CGGGCGGATGTGGGG
85064 CGGGCGGATGTGGGG
1 CGGGCGGATGTGGGG
85079 CGG
1 CGG
85082 ATGCGGGGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.15, G:0.67, T:0.12
Consensus pattern (15 bp):
CGGGCGGATGTGGGG
Found at i:87662 original size:11 final size:11
Alignment explanation
Indices: 87646--87707 Score: 56
Period size: 11 Copynumber: 5.4 Consensus size: 11
87636 AAAAATTTAG
87646 AGCTCAATTGA
1 AGCTCAATTGA
87657 AGCTCAAGACTTG-
1 AGCTC-A-A-TTGA
87670 AGCTCAATTGA
1 AGCTCAATTGA
87681 AGCTCAATTTTG-
1 AGCTCAA--TTGA
*
87693 AGCTCAATTCA
1 AGCTCAATTGA
87704 AGCT
1 AGCT
87708 AGACAAGTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
10 5 0.12
11 17 0.40
12 9 0.21
13 9 0.21
14 3 0.07
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (11 bp):
AGCTCAATTGA
Found at i:87672 original size:24 final size:23
Alignment explanation
Indices: 87645--87707 Score: 90
Period size: 24 Copynumber: 2.7 Consensus size: 23
87635 AAAAAATTTA
87645 GAGCTCAATTGAAGCTCAAGACTT
1 GAGCTCAATTGAAGCTCAA-ACTT
**
87669 GAGCTCAATTGAAGCTCAATTTT
1 GAGCTCAATTGAAGCTCAAACTT
*
87692 GAGCTCAATTCAAGCT
1 GAGCTCAATTGAAGCT
87708 AGACAAGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
23 17 0.47
24 19 0.53
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (23 bp):
GAGCTCAATTGAAGCTCAAACTT
Found at i:89325 original size:14 final size:14
Alignment explanation
Indices: 89302--89356 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
89292 ACATAATCAA
89302 ATTTAGGGTTTAAG
1 ATTTAGGGTTTAAG
*
89316 ATTTATGGTTTAAG
1 ATTTAGGGTTTAAG
* *
89330 ATTTAGAGTTTAGGG
1 ATTTAGGGTTTA-AG
*
89345 TTTTAGGGTTTA
1 ATTTAGGGTTTA
89357 TGGTTCATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
14 23 0.68
15 11 0.32
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.47
Consensus pattern (14 bp):
ATTTAGGGTTTAAG
Found at i:89782 original size:3 final size:3
Alignment explanation
Indices: 89774--89805 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
89764 ATCAACATTA
89774 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
89806 ACATCTCAAC
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:90923 original size:234 final size:233
Alignment explanation
Indices: 90506--90976 Score: 660
Period size: 234 Copynumber: 2.0 Consensus size: 233
90496 CTGAAATAAT
* * *
90506 AAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATTGGAAAAATATAGAGAGAGAGGTATT
1 AAAAAAATAATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAATATAGAGAGAGAGGTATT
* *
90571 ATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTTTGGGTCGGGTGGGGTCGGGT
66 ATTGTAATTATTCCTAAATATATAAGGTAAAATTATATA--TTATT--GT---GTAGGGTCGGGT
* * * **
90636 ATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAAAAAAAATCGACGCGGT
124 ATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTT-AAAAAAACCAACCCGAC
*
90701 CCGACCAAAATAAAGTTTCACCCGACCTGACCCAAATATATAAATTA
188 CCGACCAAAATAAAGTTTCACCCGACCCGACCCAAATA-ATAAATTA
* * * *
90748 AAAAAAATAATTTTTATTCAATAAAAATAGTGACTTAATTGAAAAAAATTATATATAGAGGGGTA
1 AAAAAAATAATTTTTATTCAATAAAAACAGTGACTTAATTG-AAAAAA-TATAGAGAGAGAGGTA
*
90813 TTATTGTAATTATTCTTAAATATATAAGGTAAAATTATATA-TATT-T-TAGGGTCGGGTATTTT
64 TTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTATTGTGTAGGGTCGGGTATTTT
*
90875 TCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTTAAAAAAACCAACCCGACCCGACC
129 TCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAAAAAAACCAACCCGACCCGACC
*
90940 AAAATAAAGTTTCACCCGACCCGACCGAAATAATAAA
194 AAAATAAAGTTTCACCCGACCCGACCCAAATAATAAA
90977 AAAATATTTT
Statistics
Matches: 209, Mismatches: 18, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
232 5 0.02
233 48 0.23
234 56 0.27
238 1 0.00
241 3 0.01
242 38 0.18
243 5 0.02
244 53 0.25
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.28
Consensus pattern (233 bp):
AAAAAAATAATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAATATAGAGAGAGAGGTATT
ATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTATTGTGTAGGGTCGGGTATTTTTC
ACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAAAAAAACCAACCCGACCCGACCAA
AATAAAGTTTCACCCGACCCGACCCAAATAATAAATTA
Found at i:92215 original size:20 final size:20
Alignment explanation
Indices: 92190--92234 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
92180 AAGTGTAAAA
*
92190 ATTATACTCAAAATTAACTT
1 ATTATACTCAAAAATAACTT
92210 ATTATACTCAAAAATAACTT
1 ATTATACTCAAAAATAACTT
*
92230 TTTAT
1 ATTAT
92235 TGTTTAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTATACTCAAAAATAACTT
Found at i:96826 original size:16 final size:16
Alignment explanation
Indices: 96805--96847 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
96795 TTTTAATGTA
*
96805 AGAGTTTCAAAGTTTT
1 AGAGTTTCAAAGTTTG
* *
96821 AGAGTTTTAGAGTTTG
1 AGAGTTTCAAAGTTTG
96837 AGA-TTTCAAAG
1 AGAGTTTCAAAG
96848 ATACATAGTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.40
Consensus pattern (16 bp):
AGAGTTTCAAAGTTTG
Found at i:97062 original size:83 final size:82
Alignment explanation
Indices: 96923--97360 Score: 447
Period size: 83 Copynumber: 5.3 Consensus size: 82
96913 GTGAAATGGC
** * *
96923 AGAGATTCTCTGAATAATAATGGAAAATGTTTCCCCTAGAACGTGCCTTTCATTTCGGATGGGAT
1 AGAGATTCTCTGAATAATAATGGAAAATACTTCCCCTGGAACATGCCTTTCATTTCGGATGGGAT
96988 GAAACACTATGACATGAT
66 G-AACACTATGACATGAT
* * **
97006 AGAGATTCTCTGAATAATAATGGAAAACACTTCCCCTGGAACATGCATTTTGTTTCGGATGGGAT
1 AGAGATTCTCTGAATAATAATGGAAAATACTTCCCCTGGAACATGCCTTTCATTTCGGATGGGAT
* **
97071 TAGACACTATGACATGGC
66 GA-ACACTATGACATGAT
* * * * * * **
97089 AGAGATTCTCTAAATAATAATGTAAAATATTTTCCTTGTAACACACCTTTCATTTCGGATGGGAT
1 AGAGATTCTCTGAATAATAATGGAAAATACTTCCCCTGGAACATGCCTTTCATTTCGGATGGGA-
*
97154 TGAACACTATGACATGAC
65 TGAACACTATGACATGAT
* * * **
97172 AAAGATTCT-TGAAT-ATAATGGAAAA-ACTTCCTCTGGAACATGCCTTTTATTTCGGATGATAT
1 AGAGATTCTCTGAATAATAATGGAAAATACTTCCCCTGGAACATGCCTTTCATTTCGGATGGGAT
* *
97234 GTAATACTACGACATTG-T
66 G-AACACTATGACA-TGAT
* * * * * *
97252 AGATATTCTCTTAATAATAATGGAAAATACTTCACCT-GAATC-CGCCTTTCATTTTGGATGAGA
1 AGAGATTCTCTGAATAATAATGGAAAATACTTCCCCTGGAA-CATGCCTTTCATTTCGGATG-GG
* *
97315 ATGAACATTATGACATGGT
64 ATGAACACTATGACATGAT
*
97334 AGAGATTATCTGAATAATAATGGAAAA
1 AGAGATTCTCTGAATAATAATGGAAAA
97361 CACTATGACA
Statistics
Matches: 288, Mismatches: 57, Indels: 21
0.79 0.16 0.06
Matches are distributed among these distances:
79 2 0.01
80 43 0.15
81 18 0.06
82 68 0.24
83 155 0.54
84 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (82 bp):
AGAGATTCTCTGAATAATAATGGAAAATACTTCCCCTGGAACATGCCTTTCATTTCGGATGGGAT
GAACACTATGACATGAT
Found at i:99845 original size:14 final size:13
Alignment explanation
Indices: 99818--99865 Score: 60
Period size: 14 Copynumber: 3.5 Consensus size: 13
99808 ATTTACAATT
*
99818 AAATAATCAAATA
1 AAATAATAAAATA
*
99831 AAGATACTAAAATA
1 AA-ATAATAAAATA
99845 AAATAATAATAATA
1 AAATAATAA-AATA
99859 AAATAAT
1 AAATAAT
99866 TAATTACTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
13 8 0.27
14 22 0.73
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (13 bp):
AAATAATAAAATA
Found at i:116509 original size:17 final size:17
Alignment explanation
Indices: 116487--116519 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
116477 TTAGTGTTCC
116487 TTCAATT-TGTGCTTGTT
1 TTCAATTGTGT-CTTGTT
116504 TTCAATTGTGTCTTGT
1 TTCAATTGTGTCTTGT
116520 AATTTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.58
Consensus pattern (17 bp):
TTCAATTGTGTCTTGTT
Found at i:116947 original size:7 final size:7
Alignment explanation
Indices: 116912--117013 Score: 71
Period size: 7 Copynumber: 14.6 Consensus size: 7
116902 ATGGGTAACT
116912 TAAACCC
1 TAAACCC
* *
116919 TAAATCT
1 TAAACCC
* *
116926 TAAATCA
1 TAAACCC
116933 TAAA-CC
1 TAAACCC
116939 TAAACCC
1 TAAACCC
**
116946 TAAATAC
1 TAAACCC
*
116953 TAAACCA
1 TAAACCC
*
116960 TAAAACCT
1 T-AAACCC
116968 TAAACCC
1 TAAACCC
**
116975 TAAATAC
1 TAAACCC
**
116982 TAAACTA
1 TAAACCC
116989 TAAACCC
1 TAAACCC
116996 TAAACCC
1 TAAACCC
*
117003 TAAACAC
1 TAAACCC
117010 TAAA
1 TAAA
117014 TCATAAACAC
Statistics
Matches: 74, Mismatches: 19, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
6 5 0.07
7 63 0.85
8 6 0.08
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAACCC
Found at i:117020 original size:14 final size:14
Alignment explanation
Indices: 116926--117025 Score: 87
Period size: 14 Copynumber: 7.1 Consensus size: 14
116916 CCCTAAATCT
*
116926 TAAATCATAAAC-C
1 TAAACCATAAACAC
* *
116939 TAAACCCTAAATAC
1 TAAACCATAAACAC
116953 TAAACCATAAA-ACC
1 TAAACCATAAACA-C
* *
116967 TTAAACCCTAAATAC
1 -TAAACCATAAACAC
* *
116982 TAAACTATAAACCC
1 TAAACCATAAACAC
*
116996 TAAACCCTAAACAC
1 TAAACCATAAACAC
*
117010 TAAATCATAAACAC
1 TAAACCATAAACAC
117024 TA
1 TA
117026 TCACATAATT
Statistics
Matches: 69, Mismatches: 14, Indels: 7
0.77 0.16 0.08
Matches are distributed among these distances:
13 10 0.14
14 47 0.68
15 11 0.16
16 1 0.01
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAACCATAAACAC
Found at i:117536 original size:12 final size:12
Alignment explanation
Indices: 117521--117545 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
117511 ATTATATCAA
117521 ATATTTATTTTT
1 ATATTTATTTTT
117533 ATATTTATTTTT
1 ATATTTATTTTT
117545 A
1 A
117546 ATAATTTGAA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
ATATTTATTTTT
Found at i:117657 original size:19 final size:20
Alignment explanation
Indices: 117616--117662 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
117606 ATGCATGATA
* *
117616 ATATTTATTTAGATATATTT
1 ATATTTATTTAGAAATATAT
117636 ATATTTATTTA-AAATATAT
1 ATATTTATTTAGAAATATAT
117655 ATATTTAT
1 ATATTTAT
117663 AAATTAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
ATATTTATTTAGAAATATAT
Found at i:118211 original size:17 final size:18
Alignment explanation
Indices: 118178--118211 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
118168 AGTTGATGTG
118178 ACAATTAAACTATTTGGT
1 ACAATTAAACTATTTGGT
*
118196 ACAATTACAC-ATTTGG
1 ACAATTAAACTATTTGG
118212 CCACAATCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
ACAATTAAACTATTTGGT
Found at i:118524 original size:16 final size:16
Alignment explanation
Indices: 118503--118535 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
118493 TAATAAATAA
118503 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
118519 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
118535 A
1 A
118536 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:118615 original size:10 final size:10
Alignment explanation
Indices: 118600--118642 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
118590 CATTTAATAA
118600 ATAAACGAAC
1 ATAAACGAAC
118610 ATAAACGAAC
1 ATAAACGAAC
118620 AT----GAAC
1 ATAAACGAAC
118626 ATAAACGAAC
1 ATAAACGAAC
118636 ATAAACG
1 ATAAACG
118643 TTGGAGACCC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
6 6 0.21
10 23 0.79
ACGTcount: A:0.58, C:0.19, G:0.12, T:0.12
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:118627 original size:16 final size:16
Alignment explanation
Indices: 118606--118637 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
118596 ATAAATAAAC
118606 GAACATAAACGAACAT
1 GAACATAAACGAACAT
118622 GAACATAAACGAACAT
1 GAACATAAACGAACAT
118638 AAACGTTGGA
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:0.56, C:0.19, G:0.12, T:0.12
Consensus pattern (16 bp):
GAACATAAACGAACAT
Found at i:122420 original size:16 final size:16
Alignment explanation
Indices: 122401--122432 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
122391 GTTTAGGGAC
122401 AAAAAATGTA-ATTTT
1 AAAAAATGTATATTTT
122416 AAAAAATGTATATTTT
1 AAAAAATGTATATTTT
122432 A
1 A
122433 GCCCGTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (16 bp):
AAAAAATGTATATTTT
Found at i:123374 original size:65 final size:64
Alignment explanation
Indices: 123257--123464 Score: 246
Period size: 65 Copynumber: 3.2 Consensus size: 64
123247 TTTCAAAGTG
* * *
123257 ATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGG-AATAAATTG-AACATCGAATGCAT
1 ATGCATCGATGCA-CAATCCATGCATCGATGCACTCA-GGCTAT-TA-TGAAACATCGAATGCAT
*
123319 TTT
62 TTC
123322 ATGCATCGATGCAC-ATACCATGCATCGATGCACTCAGGGCT-TTATGAAAACATCGAATGCATT
1 ATGCATCGATGCACAAT-CCATGCATCGATGCACTCA-GGCTATTATG-AAACATCGAATGCATT
*
123385 TG
63 TC
* * *
123387 ATGTATCGATGCACAATCCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCACTTC
1 ATGCATCGATGCACAATCCATGCATCGATGCACTCAGGCTATTATGAAACATCGAATGCATTTC
123451 ATGCATCGATGCAC
1 ATGCATCGATGCAC
123465 TCTTAGTGCA
Statistics
Matches: 126, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
63 4 0.03
64 51 0.40
65 69 0.55
66 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (64 bp):
ATGCATCGATGCACAATCCATGCATCGATGCACTCAGGCTATTATGAAACATCGAATGCATTTC
Found at i:123464 original size:17 final size:19
Alignment explanation
Indices: 123436--123484 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
123426 TATTTTGAAA
123436 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
123454 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
123473 CACCGATGCACT
1 CATCGATGCACT
123485 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:128148 original size:19 final size:19
Alignment explanation
Indices: 128095--128149 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
128085 AAATAAAGAA
*
128095 AAAATGAAATTAAAAT-TAT
1 AAAAT-AAACTAAAATATAT
*
128114 AAAATAAACCATAAATATAT
1 AAAATAAACTA-AAATATAT
*
128134 AAAATAAAGTAAAATA
1 AAAATAAACTAAAATA
128150 AAAGGAAGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 4 0.13
19 14 0.47
20 12 0.40
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (19 bp):
AAAATAAACTAAAATATAT
Found at i:128843 original size:16 final size:16
Alignment explanation
Indices: 128791--128834 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
128781 CAATGAACAC
*
128791 CGAGTTTAACGAGTAA
1 CGAGTTTAACGAGCAA
* *
128807 CGAGCTTAATGAGCAA
1 CGAGTTTAACGAGCAA
128823 CGAGTTTAACGA
1 CGAGTTTAACGA
128835 ACAAAGAGTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (16 bp):
CGAGTTTAACGAGCAA
Found at i:131049 original size:3 final size:3
Alignment explanation
Indices: 131041--131106 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
131031 ACCTAGTTTA
131041 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
131089 TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT
131107 GCATCACCTC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:132999 original size:31 final size:31
Alignment explanation
Indices: 132961--133054 Score: 145
Period size: 31 Copynumber: 3.0 Consensus size: 31
132951 CCCGAAGGAC
* * *
132961 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
132992 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
133023 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
133054 C
1 C
133055 CCTCGACCCT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 58 0.98
32 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:144723 original size:21 final size:21
Alignment explanation
Indices: 144684--144723 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
144674 AACTTTTCTA
* * *
144684 AAAAAATAATACAAGTTAAAG
1 AAAAAATAAAAAAAATTAAAG
144705 AAAAAATAAAAAAAATTAA
1 AAAAAATAAAAAAAATTAA
144724 GAACCGGGTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17
Consensus pattern (21 bp):
AAAAAATAAAAAAAATTAAAG
Found at i:144809 original size:25 final size:25
Alignment explanation
Indices: 144747--144817 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 25
144737 ATGACCCGAA
* *
144747 TTATATAATATAATTTTATATATAT
1 TTATAAAATATATTTTTATATATAT
* *
144772 TAACTTAAA-ATATTTTTATATCA-AT
1 TTA-TAAAATATATTTTTATAT-ATAT
*
144797 TTATAAAATATATTTTAATAT
1 TTATAAAATATATTTTTATAT
144818 TACCTTAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
24 4 0.11
25 28 0.78
26 4 0.11
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (25 bp):
TTATAAAATATATTTTTATATATAT
Found at i:144839 original size:27 final size:27
Alignment explanation
Indices: 144800--144863 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
144790 TATCAATTTA
144800 TAAAATATATTTTAATATTACCTTAATT
1 TAAAA-ATATTTTAATATTACCTTAATT
* * ** *
144828 TAAAAATATTTTATTTTTATTTTCATT
1 TAAAAATATTTTAATATTACCTTAATT
144855 TAAAAATAT
1 TAAAAATAT
144864 ACAGTTTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
27 26 0.84
28 5 0.16
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (27 bp):
TAAAAATATTTTAATATTACCTTAATT
Found at i:158573 original size:2 final size:2
Alignment explanation
Indices: 158568--158594 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
158558 CACAATTTCG
158568 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
158595 AGAAAATAGA
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:162058 original size:29 final size:31
Alignment explanation
Indices: 161995--162068 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
161985 TCAAAATACA
*
161995 TAAGATATGGTCACTTTCGTTTTTATTTAAT
1 TAAGATATGATCACTTTCGTTTTTATTTAAT
* *
162026 TAAGATATGATCACTTT-GTTTTTGTTT-TT
1 TAAGATATGATCACTTTCGTTTTTATTTAAT
*
162055 TAAGATGTGATCAC
1 TAAGATATGATCAC
162069 CATAGGTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 14 0.36
30 9 0.23
31 16 0.41
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (31 bp):
TAAGATATGATCACTTTCGTTTTTATTTAAT
Found at i:168247 original size:66 final size:66
Alignment explanation
Indices: 168144--168270 Score: 166
Period size: 66 Copynumber: 1.9 Consensus size: 66
168134 TCAAATATTT
* * * **
168144 TATAGTCATCATATCTGAACTCGAAATGTTTAGGAATTTATTTCAATAAGTGAAATATTTAGATT
1 TATAGACATCATATCTGAACTCGAAATGTTTAAGAATTTATTTCAACAAAAGAAATATTTAGATT
168209 C
66 C
* * *
168210 TATAGACATCATATTTGAATTCGAAAAT-TTTAAGAATTTATTTTAACAAAAGAAATATTTA
1 TATAGACATCATATCTGAACTCG-AAATGTTTAAGAATTTATTTCAACAAAAGAAATATTTA
168271 TTTCATGCCT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
66 48 0.92
67 4 0.08
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (66 bp):
TATAGACATCATATCTGAACTCGAAATGTTTAAGAATTTATTTCAACAAAAGAAATATTTAGATT
C
Found at i:171573 original size:63 final size:64
Alignment explanation
Indices: 171518--171812 Score: 346
Period size: 63 Copynumber: 4.6 Consensus size: 64
171508 CACTCCTGCA
** * *
171518 CCACCCAAGCCACCAGTTCATCCTCCAAAAAAGCCACCGACCACTAAACCACCCACTTACCT-G
1 CCACCCAAGCCACCAGTTCATCCTCCAACTAAGCCACCAACCACTAAACCACCGACTTACCTCG
* * * * *
171581 CCAGCCAAGCAACCAGTTCATCCTCCAACTAAGCCACCAACCATTAAACCACCGACATATC-CG
1 CCACCCAAGCCACCAGTTCATCCTCCAACTAAGCCACCAACCACTAAACCACCGACTTACCTCG
* * * * *
171644 CCACCCAAGCCACCAGTTCATCCTACAACTAAGCCACCAACTACCAAACCGCCGACCTACC-CG
1 CCACCCAAGCCACCAGTTCATCCTCCAACTAAGCCACCAACCACTAAACCACCGACTTACCTCG
* * ** * *
171707 CCACCTAAGTCACCAGTTCATCCTCCAACTAAGCCACCAAAAACCAAACCGCCGACTTACC-CG
1 CCACCCAAGCCACCAGTTCATCCTCCAACTAAGCCACCAACCACTAAACCACCGACTTACCTCG
*
171770 CCACCCAAGTCACCAGTTCATCCTCCAACAACTAAGCCACCAA
1 CCACCCAAGCCACCAGTTCATCCT-C--CAACTAAGCCACCAA
171813 GCAAGCCTCC
Statistics
Matches: 203, Mismatches: 25, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
63 187 0.92
64 1 0.00
66 15 0.07
ACGTcount: A:0.34, C:0.44, G:0.09, T:0.13
Consensus pattern (64 bp):
CCACCCAAGCCACCAGTTCATCCTCCAACTAAGCCACCAACCACTAAACCACCGACTTACCTCG
Found at i:171830 original size:12 final size:12
Alignment explanation
Indices: 171798--171835 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
171788 CATCCTCCAA
171798 CAACTAAGCCAC
1 CAACTAAGCCAC
*
171810 CAAGC-AAGCCTC
1 CAA-CTAAGCCAC
171822 CAACTAAGCCAC
1 CAACTAAGCCAC
171834 CA
1 CA
171836 TCTCCACCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 1 0.05
12 20 0.91
13 1 0.05
ACGTcount: A:0.39, C:0.42, G:0.11, T:0.08
Consensus pattern (12 bp):
CAACTAAGCCAC
Found at i:176271 original size:105 final size:105
Alignment explanation
Indices: 176131--176338 Score: 292
Period size: 105 Copynumber: 2.0 Consensus size: 105
176121 TAATATTGAT
* *
176131 TATCGAACATTTGATCACTAAAAATCACTTAGTGTGACAACATTGGTGGTCACAGAATATACTTT
1 TATCAAACATTTGATCACTAAAAATCACTTAGTGTGACAACATTGGTGGTCACAAAATATACTTT
* * * *
176196 TAGTGTCAAATAAATTTATCATAATTTCTATTGATAATAG
66 TAGTGTCAAAAAAATTCATCACAATTTATATTGATAATAG
* * * * **
176236 TATCAAACATTTGGTTACTGAAAAAT-ACTTAGTGTGATAATATTGGTGGTCACAAAATATTTTT
1 TATCAAACATTTGATCACT-AAAAATCACTTAGTGTGACAACATTGGTGGTCACAAAATATACTT
176300 TTAGTGTCAAAAAAATTCATCACAATTTATATTGATAAT
65 TTAGTGTCAAAAAAATTCATCACAATTTATATTGATAAT
176339 TGTGTCGAAT
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
105 84 0.93
106 6 0.07
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.38
Consensus pattern (105 bp):
TATCAAACATTTGATCACTAAAAATCACTTAGTGTGACAACATTGGTGGTCACAAAATATACTTT
TAGTGTCAAAAAAATTCATCACAATTTATATTGATAATAG
Found at i:176365 original size:105 final size:106
Alignment explanation
Indices: 176150--176365 Score: 263
Period size: 105 Copynumber: 2.0 Consensus size: 106
176140 TTTGATCACT
* * *
176150 AAAAATCACTTAGTGTGACAACATTGGTGGTCACAGAATATACTTTTAGTGTCAAATAAATTTAT
1 AAAAATCACTTAGTGTGACAACATTGGTGGTCACAAAATATACTTTTAGTGTCAAAAAAATTCAT
* * ** * **
176215 CATAATTTCTATTGATAATAGTATCAAACATTTGGTTACTG
66 CACAATTTATATTGATAATAGTATCAAACAGATGGTCACAA
* * **
176256 AAAAAT-ACTTAGTGTGATAATATTGGTGGTCACAAAATATTTTTTTAGTGTCAAAAAAATTCAT
1 AAAAATCACTTAGTGTGACAACATTGGTGGTCACAAAATATACTTTTAGTGTCAAAAAAATTCAT
* * * *
176320 CACAATTTATATTGATAATTGTGTCGAATAGATGGTCACAA
66 CACAATTTATATTGATAATAGTATCAAACAGATGGTCACAA
176361 AAAAA
1 AAAAA
176366 ATGATAAATT
Statistics
Matches: 92, Mismatches: 18, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
105 86 0.93
106 6 0.07
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (106 bp):
AAAAATCACTTAGTGTGACAACATTGGTGGTCACAAAATATACTTTTAGTGTCAAAAAAATTCAT
CACAATTTATATTGATAATAGTATCAAACAGATGGTCACAA
Found at i:178235 original size:43 final size:43
Alignment explanation
Indices: 178174--178260 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
178164 GAAAAAAAAT
178174 ACACGGTCAGACAATACAAAGAGACACTTTAAGTCGAGGTCTC
1 ACACGGTCAGACAATACAAAGAGACACTTTAAGTCGAGGTCTC
178217 ACACGGTCAGACAATACAAAGAGACACTTTAAGTCGAGGTCTC
1 ACACGGTCAGACAATACAAAGAGACACTTTAAGTCGAGGTCTC
178260 A
1 A
178261 TAAGACTTCG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (43 bp):
ACACGGTCAGACAATACAAAGAGACACTTTAAGTCGAGGTCTC
Found at i:190969 original size:20 final size:20
Alignment explanation
Indices: 190925--191184 Score: 149
Period size: 20 Copynumber: 12.8 Consensus size: 20
190915 AATGACCAAC
* *
190925 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
190944 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* **
190964 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTTAG
**
190984 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
**
191004 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
* ***
191025 AAGAATCGCAATGCGAGCCA-
1 AA-AATCGCAACGCGATTTAG
* *
191045 AAGAATCGCAATGCGATTCCA-
1 AA-AATCGCAACGCGATT-TAG
* * *
191066 AGAATCGCAATGCGATCTTCG
1 AAAATCGCAACGCGAT-TTAG
*
191087 AAGAATCGCAATGCGATTCTA-
1 AA-AATCGCAACGCGATT-TAG
* *
191108 AGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
191128 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-TAG
* *
191148 ATAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTTAG
191168 AAAATCGCAACGCGATT
1 AAAATCGCAACGCGATT
191185 CCAAGAATCG
Statistics
Matches: 195, Mismatches: 30, Indels: 31
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.01
19 19 0.10
20 134 0.69
21 13 0.07
22 28 0.14
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:191055 original size:62 final size:62
Alignment explanation
Indices: 190986--191162 Score: 161
Period size: 62 Copynumber: 2.9 Consensus size: 62
190976 TTGAAAAGAA
190986 AATCGCAACGGTCAAAAGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGAGCCAAAG
1 AATCGCAACGGTCAAAAGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGAGCCAAAG
* * * * ** *
191048 AATCGCAATGCGATTC-CAAG--AATCGCAATGCGATCTTCGAAGAATCGCAATGCGATTCTAAG
1 AATCGCAA--CG-GTCAAAAGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGAGCCAAAG
** * *
191110 AATCGCAAC-G-CGATTGAGAAAATCGCAACGCGA--TTCCAATAATCGCAACGCGA
1 AATCGCAACGGTC-A-AAAGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGA
191163 TTGAGAAAAT
Statistics
Matches: 93, Mismatches: 14, Indels: 18
0.74 0.11 0.14
Matches are distributed among these distances:
57 1 0.01
60 20 0.22
62 65 0.70
64 5 0.05
65 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17
Consensus pattern (62 bp):
AATCGCAACGGTCAAAAGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGAGCCAAAG
Found at i:191076 original size:40 final size:39
Alignment explanation
Indices: 191004--191232 Score: 223
Period size: 40 Copynumber: 5.8 Consensus size: 39
190994 CGGTCAAAAG
*
191004 AAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGAGCCA
1 AAAATCGCAACGCGA--TTCCAAGAATCGCAATGCGATCCA
*
191045 AAGAATCGCAATGCGATTCCAAGAATCGCAATGCGATCTTCGA
1 AA-AATCGCAACGCGATTCCAAGAATCGCAATGCGATC--C-A
* * * * **
191088 AGAATCGCAATGCGATTCTAAGAATCGCAACGCGATTGA
1 AAAATCGCAACGCGATTCCAAGAATCGCAATGCGATCCA
* * **
191127 GAAAATCGCAACGCGATTCCAATAATCGCAACGCGATTGA
1 -AAAATCGCAACGCGATTCCAAGAATCGCAATGCGATCCA
* *
191167 GAAAATCGCAACGCGATTCCAAGAATCGCAAT-TGA---G
1 -AAAATCGCAACGCGATTCCAAGAATCGCAATGCGATCCA
*
191203 AAAATCGCAATGCGATTCCAAGAATCGCAA
1 AAAATCGCAACGCGATTCCAAGAATCGCAA
191233 AACGGCAAAA
Statistics
Matches: 167, Mismatches: 16, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
35 29 0.17
39 3 0.02
40 86 0.51
41 2 0.01
42 45 0.27
43 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.18
Consensus pattern (39 bp):
AAAATCGCAACGCGATTCCAAGAATCGCAATGCGATCCA
Found at i:191230 original size:20 final size:20
Alignment explanation
Indices: 191006--191232 Score: 200
Period size: 20 Copynumber: 11.4 Consensus size: 20
190996 GTCAAAAGAA
*
191006 AATCGCAACGCGATCTTCCAAG
1 AATCGCAATGCGA--TTCCAAG
*
191028 AATCGCAATGCGA-GCCAAAG
1 AATCGCAATGCGATTCC-AAG
191048 AATCGCAATGCGATTCCAAG
1 AATCGCAATGCGATTCCAAG
*
191068 AATCGCAATGCGATCTTCGAAG
1 AATCGCAATGCGA--TTCCAAG
*
191090 AATCGCAATGCGATTCTAAG
1 AATCGCAATGCGATTCCAAG
* * *
191110 AATCGCAACGCGATT-GAGAA
1 AATCGCAATGCGATTCCA-AG
* *
191130 AATCGCAACGCGATTCCAAT
1 AATCGCAATGCGATTCCAAG
* * *
191150 AATCGCAACGCGATT-GAGAA
1 AATCGCAATGCGATTCCA-AG
*
191170 AATCGCAACGCGATTCCAAG
1 AATCGCAATGCGATTCCAAG
* *
191190 AATCGCAAT-TGA---GAA-
1 AATCGCAATGCGATTCCAAG
191205 AATCGCAATGCGATTCCAAG
1 AATCGCAATGCGATTCCAAG
191225 AATCGCAA
1 AATCGCAA
191233 AACGGCAAAA
Statistics
Matches: 173, Mismatches: 19, Indels: 28
0.79 0.09 0.13
Matches are distributed among these distances:
15 9 0.05
16 4 0.02
19 8 0.05
20 117 0.68
21 4 0.02
22 31 0.18
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (20 bp):
AATCGCAATGCGATTCCAAG
Found at i:191353 original size:6 final size:6
Alignment explanation
Indices: 191342--191387 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
191332 AGACACGTAT
191342 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
191388 CGAGACGAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:192153 original size:6 final size:6
Alignment explanation
Indices: 192142--192186 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
192132 TCTCGTCTCG
192142 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
192187 AATACGTGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:192322 original size:20 final size:20
Alignment explanation
Indices: 192297--192426 Score: 138
Period size: 20 Copynumber: 6.4 Consensus size: 20
192287 TTTTGCCGTT
192297 TTGCGATTCTTGGAATCGCG
1 TTGCGATTCTTGGAATCGCG
** *
192317 TTGCGATT-TTCTCAATCGCA
1 TTGCGATTCTT-GGAATCGCG
*
192337 TTGCGATTCCTGGAATCGCG
1 TTGCGATTCTTGGAATCGCG
**
192357 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-GGAATCGCG
* *
192377 TTGCGATTCTTTGAATCGCA
1 TTGCGATTCTTGGAATCGCG
192397 TTGCGATTCTTGGAAGATCGCG
1 TTGCGATTCTTGG-A-ATCGCG
192419 TTGCGATT
1 TTGCGATT
192427 TTCTTTTGAC
Statistics
Matches: 90, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
19 3 0.03
20 70 0.78
21 4 0.04
22 13 0.14
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.37
Consensus pattern (20 bp):
TTGCGATTCTTGGAATCGCG
Found at i:192344 original size:40 final size:40
Alignment explanation
Indices: 192297--192404 Score: 180
Period size: 40 Copynumber: 2.7 Consensus size: 40
192287 TTTTGCCGTT
192297 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCA
1 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCA
* *
192337 TTGCGATTCCTGGAATCGCGTTGCGATTTTCTCAATCGCG
1 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCA
* *
192377 TTGCGATTCTTTGAATCGCATTGCGATT
1 TTGCGATTCTTGGAATCGCGTTGCGATT
192405 CTTGGAAGAT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (40 bp):
TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCA
Found at i:192394 original size:60 final size:62
Alignment explanation
Indices: 192310--192430 Score: 194
Period size: 60 Copynumber: 2.0 Consensus size: 62
192300 CGATTCTTGG
192310 AATCGCGTTGCGATTTTCTCAATCGCATTGCGATTCCTGG-A-ATCGCGTTGCGATTTTCTC
1 AATCGCGTTGCGATTTTCTCAATCGCATTGCGATTCCTGGAAGATCGCGTTGCGATTTTCTC
* *
192370 AATCGCGTTGCGATTCTT-TGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTTTCT
1 AATCGCGTTGCGATT-TTCTCAATCGCATTGCGATTCCTGGAAGATCGCGTTGCGATTTTCT
192431 TTTGACCGTT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
60 35 0.62
61 3 0.05
62 18 0.32
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.37
Consensus pattern (62 bp):
AATCGCGTTGCGATTTTCTCAATCGCATTGCGATTCCTGGAAGATCGCGTTGCGATTTTCTC
Found at i:192442 original size:20 final size:20
Alignment explanation
Indices: 192417--192488 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
192407 TGGAAGATCG
* *
192417 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTCAA
192437 CGTTGCGATTTTCTTTTCAA
1 CGTTGCGATTTTCTTTTCAA
* **
192457 CATTGCGATTTTCTAAATC-A
1 CGTTGCGATTTTCT-TTTCAA
192477 CGTTGCGATTTT
1 CGTTGCGATTTT
192489 TGTTTCGCAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTCAA
Found at i:193720 original size:20 final size:20
Alignment explanation
Indices: 193695--193732 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
193685 CACATGTTAA
193695 AGAATGCATCGATACACTGT
1 AGAATGCATCGATACACTGT
* *
193715 AGAATGTATCGATGCACT
1 AGAATGCATCGATACACT
193733 TTAAGGGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATACACTGT
Found at i:195229 original size:23 final size:23
Alignment explanation
Indices: 195161--195221 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
195151 ACATTTTATA
195161 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
195184 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
195207 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
195222 TTTATACGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:196335 original size:53 final size:53
Alignment explanation
Indices: 196276--196386 Score: 129
Period size: 53 Copynumber: 2.1 Consensus size: 53
196266 TTTTAATCAA
* **
196276 AATATTA-ATTATTAA-AATAT-TTAAAATATATTTATTAATATTTATAATAATAT
1 AATATTATATTATTAATAATATACTAAAATA-ATCAATT-ATA-TTATAATAATAT
* *
196329 AATATTATATTTTTAATATTATACTAAAATAATCAATTATATTATAATAATAT
1 AATATTATATTATTAATAATATACTAAAATAATCAATTATATTATAATAATAT
196382 AATAT
1 AATAT
196387 AAGATATTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
53 24 0.48
54 10 0.20
55 9 0.18
56 7 0.14
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (53 bp):
AATATTATATTATTAATAATATACTAAAATAATCAATTATATTATAATAATAT
Found at i:196338 original size:22 final size:23
Alignment explanation
Indices: 196291--196351 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
196281 TAATTATTAA
* *
196291 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
196312 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
196335 -ATATTTTTAATATTATA
1 AATATTTATAATAATATA
196352 CTAAAATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.32
22 19 0.56
23 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:196359 original size:27 final size:32
Alignment explanation
Indices: 196302--196421 Score: 100
Period size: 30 Copynumber: 4.0 Consensus size: 32
196292 ATATTTAAAA
196302 TATATTTATTAATATTTATAATAATATAATAT
1 TATATTTATTAATATTTATAATAATATAATAT
* *
196334 TATATTT-TTAATA-TTATACTAAAATAATCAAT
1 TATATTTATTAATATTTATAATAATATAAT--AT
*
196366 TATA-TTA-TAATA-ATATAAT-ATA-AGATAT
1 TATATTTATTAATATTTATAATAATATA-ATAT
196394 TATATTT-TT-AT-TTTAATAAT-ATATAATA
1 TATATTTATTAATATTT-ATAATAATATAATA
196422 AATTATTAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 21
0.73 0.06 0.21
Matches are distributed among these distances:
28 9 0.12
29 15 0.21
30 18 0.25
31 18 0.25
32 13 0.18
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAATATAATAT
Found at i:196368 original size:32 final size:32
Alignment explanation
Indices: 196302--196400 Score: 93
Period size: 31 Copynumber: 3.2 Consensus size: 32
196292 ATATTTAAAA
*
196302 TATATTTATTAATATTTATAATAATATAATAT
1 TATATTTATTAATATTTATAATAAAATAATAT
*
196334 TATATTT-TTAATA-TTATACTAAAATAATCAAT
1 TATATTTATTAATATTTATAATAAAATAAT--AT
* * *
196366 TATA-TTA-TAATA-ATATAATATAA-GATAT
1 TATATTTATTAATATTTATAATAAAATAATAT
196394 TATATTT
1 TATATTT
196401 TTATTTTAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
28 6 0.11
29 2 0.04
30 15 0.26
31 21 0.37
32 13 0.23
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAAAATAATAT
Found at i:196565 original size:23 final size:23
Alignment explanation
Indices: 196539--196583 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
196529 AATAATATTT
196539 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* ** *
196562 TAATTACTATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
196584 ATACAATATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:196739 original size:14 final size:14
Alignment explanation
Indices: 196720--196775 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
196710 CCAGAAATGT
*
196720 AATTCATTTTTCAG
1 AATTCAATTTTCAG
** *
196734 AATTCAAAATCCAG
1 AATTCAATTTTCAG
*
196748 TAATTCATTTTTCAG
1 -AATTCAATTTTCAG
196763 AATTCAATTTTCA
1 AATTCAATTTTCA
196776 AAAAAATCAA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
14 22 0.69
15 10 0.31
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.43
Consensus pattern (14 bp):
AATTCAATTTTCAG
Found at i:200409 original size:18 final size:18
Alignment explanation
Indices: 200230--200402 Score: 249
Period size: 18 Copynumber: 9.5 Consensus size: 18
200220 TATAATGTGT
200230 TTTTTGGATTAGAAATAC
1 TTTTTGGATTAGAAATAC
** *
200248 TCCTTGGATTAGAAATAA
1 TTTTTGGATTAGAAATAC
200266 TTTTTGATGATTAGAAATAC
1 TTTTTG--GATTAGAAATAC
200286 TTTTTGGATTAGAAATAC
1 TTTTTGGATTAGAAATAC
*
200304 TCTTTGGATTAGAAATAC
1 TTTTTGGATTAGAAATAC
* *
200322 ATTTTGGATTGGAAATAC
1 TTTTTGGATTAGAAATAC
*
200340 TTTTTGTATTAGAAATA-
1 TTTTTGGATTAGAAATAC
200357 TTCTTTGGATTAGAAATAC
1 TT-TTTGGATTAGAAATAC
200376 TTTTTGGATTAGAAATAC
1 TTTTTGGATTAGAAATAC
200394 TTTTTGGAT
1 TTTTTGGAT
200403 CATAAATCAA
Statistics
Matches: 137, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
17 2 0.01
18 116 0.85
19 2 0.01
20 17 0.12
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (18 bp):
TTTTTGGATTAGAAATAC
Found at i:202115 original size:20 final size:20
Alignment explanation
Indices: 202074--202118 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
202064 TGGTACCATA
*
202074 TTTATTATATATTTATTATT
1 TTTATTATATATTAATTATT
* *
202094 TTTATTTTATATTAAAT-TT
1 TTTATTATATATTAATTATT
202113 TTTATT
1 TTTATT
202119 CATAATTCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTATTATATATTAATTATT
Found at i:202437 original size:16 final size:17
Alignment explanation
Indices: 202410--202445 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
202400 ATATATATAT
*
202410 ATATATATTTAAAAATA
1 ATATATATTTAAAAAAA
202427 ATATA-ATTTAAAAAAA
1 ATATATATTTAAAAAAA
202443 ATA
1 ATA
202446 AAAAAATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATATATATTTAAAAAAA
Found at i:202498 original size:14 final size:14
Alignment explanation
Indices: 202476--202511 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 14
202466 GTGACCCAAA
202476 TTATATATAATATTAT
1 TTATATA-AATATT-T
202492 TTATATAAATATTT
1 TTATATAAATATTT
202506 TTATAT
1 TTATAT
202512 TAACTTATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.35
15 6 0.30
16 7 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTATATAAATATTT
Found at i:202537 original size:25 final size:25
Alignment explanation
Indices: 202492--202568 Score: 104
Period size: 25 Copynumber: 3.1 Consensus size: 25
202482 ATAATATTAT
202492 TTATATAAATAT-TTTTA-TATTAAC
1 TTAT-TAAATATATTTTATTATTAAC
*
202516 TTATTGAATATATTTTATTATTAAC
1 TTATTAAATATATTTTATTATTAAC
* *
202541 ATATTAAATATATTTTATTGTTAAC
1 TTATTAAATATATTTTATTATTAAC
202566 TTA
1 TTA
202569 ATTTAAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 6 0.13
24 9 0.20
25 31 0.67
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.55
Consensus pattern (25 bp):
TTATTAAATATATTTTATTATTAAC
Found at i:202605 original size:25 final size:25
Alignment explanation
Indices: 202566--202623 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
202556 TATTGTTAAC
* **
202566 TTAATTTAAAAATATGTTTTTTATT
1 TTAATTTAAAAATATATAATTTATT
* *
202591 TTCATTTAAACATATATAATTTATT
1 TTAATTTAAAAATATATAATTTATT
202616 TTAATTTA
1 TTAATTTA
202624 TTAAAAATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (25 bp):
TTAATTTAAAAATATATAATTTATT
Found at i:210981 original size:111 final size:112
Alignment explanation
Indices: 210531--210992 Score: 705
Period size: 112 Copynumber: 4.1 Consensus size: 112
210521 TTGTCGGTTT
* *
210531 GTGTCGATACTTTATAAAAATATATTGATCTATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * * *
210596 GGTCTATAAATGAAAAAACAGGTAAAACGCTACCAGATATATTGGAA
66 GATCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
* * *
210643 GTGTCGATACTTTATAAAAATGTATCGATCTATAACAATATAACAGGTAAACAAATGGA-AAAAC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAAT-GACAAAAC
* * * *
210707 CGGTCTATAAATGACAAAACAGGTAAAGTGCTATCGGATATATTGAAA
65 CGATCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
* * *
210755 GAGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGATAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
210820 GATCTATAAATGACAAAACTA-GTAAAGCGCTACCGGATATATTGAAA
66 GATCTATAAATGACAAAAC-AGGTAAAGCGCTACCAGATATATTGAAA
210867 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
210931 GATCTATAAATGACAAAACAGGTAAAGCGCTACAAGATATGTTGATA
66 GATCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
210978 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
210993 TATAAGTATC
Statistics
Matches: 324, Mismatches: 22, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
110 1 0.00
111 73 0.23
112 247 0.76
113 3 0.01
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GATCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
Found at i:211232 original size:161 final size:163
Alignment explanation
Indices: 210940--211278 Score: 508
Period size: 161 Copynumber: 2.1 Consensus size: 163
210930 CGATCTATAA
* * *
210940 ATGACAAAACAGGTAAAGCGCTACAAGATATGTTGATAGTGTCGATACTTTATTATAAGTATCGA
1 ATGACAAAACCGGTAAAGAGCTACAAGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGA
*
211005 CACTTTTGGAATTTAAAAGAGAAGAAGTTATAACGCTAATAAAATGTCGATACTTTATACAAAAT
66 CACTTTTGGAATTTAAAAGAAAAGAAGTTATAACGCTAATAAAATGTCGATACTTTATACAAAAT
211070 GTATCGATCCATAACAATATAACAGGTAAAAAT
131 GTATCGATCCATAACAATATAACAGGTAAAAAT
*
211103 ATGACAAAACCGGTAAAGAGCTATC-GGATATGTTGAAAGT-T-GATACTTTATTATAAGTATCG
1 ATGACAAAACCGGTAAAGAGCTA-CAAGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCG
* * *
211165 ACATTTTTGGAATTTAAAAGAAAAAGAAGTTATAGCG-TCAATAAAGTGTCGATACTTTATA-AA
65 ACACTTTTGGAATTTAAAAG-AAAAGAAGTTATAACGCT-AATAAAATGTCGATACTTTATACAA
* * *
211228 AATGTATTGATCCATAATAATGTAACAGGTAAAAAT
128 AATGTATCGATCCATAACAATATAACAGGTAAAAAT
*
211264 ATGACAAAATCGGTA
1 ATGACAAAACCGGTA
211279 TCAAAAAAAT
Statistics
Matches: 161, Mismatches: 12, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
161 90 0.56
162 36 0.22
163 34 0.21
164 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (163 bp):
ATGACAAAACCGGTAAAGAGCTACAAGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGA
CACTTTTGGAATTTAAAAGAAAAGAAGTTATAACGCTAATAAAATGTCGATACTTTATACAAAAT
GTATCGATCCATAACAATATAACAGGTAAAAAT
Found at i:211739 original size:23 final size:23
Alignment explanation
Indices: 211710--211757 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
211700 AAATAGGTCA
*
211710 ATATAAATATTACCTATTACATT
1 ATATAAATATTACCTAATACATT
* *
211733 ATATAAATGTTACCTAATATATT
1 ATATAAATATTACCTAATACATT
211756 AT
1 AT
211758 TGTACTTAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (23 bp):
ATATAAATATTACCTAATACATT
Found at i:212105 original size:22 final size:23
Alignment explanation
Indices: 212061--212105 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
212051 ATTAATAATT
*
212061 AAAAATAAAAAGATATTCATTAA
1 AAAAATAAAAAGATAATCATTAA
* *
212084 AAAAATAAATATATAATC-TTAA
1 AAAAATAAAAAGATAATCATTAA
212106 TAATATATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAAATAAAAAGATAATCATTAA
Found at i:212194 original size:2 final size:2
Alignment explanation
Indices: 212187--212231 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
212177 TTTTAATCTT
212187 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
212229 TA T
1 TA T
212232 GCTCCGTACA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:212569 original size:24 final size:24
Alignment explanation
Indices: 212518--212574 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
212508 GAACGTTCGA
* *
212518 TTATGTTTATTTATGTTCGTTCCG
1 TTATGTTTATTTATGTTCATTCAG
* *
212542 TTATGTTTGTTTATGTTCATTCAT
1 TTATGTTTATTTATGTTCATTCAG
*
212566 TTATATTTA
1 TTATGTTTA
212575 ACCCAATCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.18, C:0.09, G:0.12, T:0.61
Consensus pattern (24 bp):
TTATGTTTATTTATGTTCATTCAG
Found at i:213505 original size:16 final size:16
Alignment explanation
Indices: 213484--213520 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
213474 GTCTCCAACG
213484 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
213500 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
213516 TTTAT
1 TTTAT
213521 TTATTAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.59
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:218772 original size:33 final size:33
Alignment explanation
Indices: 218731--218796 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
218721 GAGAATTGAG
218731 ATATATAATTGGCCTCGTGTCCTACCCTAGACT
1 ATATATAATTGGCCTCGTGTCCTACCCTAGACT
218764 ATATATAATTGGCCTCGTGTCCTACCCTAGACT
1 ATATATAATTGGCCTCGTGTCCTACCCTAGACT
218797 GCCCTAAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.33
Consensus pattern (33 bp):
ATATATAATTGGCCTCGTGTCCTACCCTAGACT
Found at i:219591 original size:37 final size:38
Alignment explanation
Indices: 219507--219593 Score: 151
Period size: 38 Copynumber: 2.3 Consensus size: 38
219497 CCTAAACCCG
219507 AACCCGACCCGACCTGACCCGAATATCACACTTAAAAA
1 AACCCGACCCGACCTGACCCGAATATCACACTTAAAAA
219545 AACCCGACCCGA-CTCGACCCGAATATCACACTT-AAAA
1 AACCCGACCCGACCT-GACCCGAATATCACACTTAAAAA
219582 AACCCGACCCGA
1 AACCCGACCCGA
219594 ACAAAACAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
37 18 0.38
38 30 0.62
ACGTcount: A:0.38, C:0.39, G:0.11, T:0.11
Consensus pattern (38 bp):
AACCCGACCCGACCTGACCCGAATATCACACTTAAAAA
Found at i:220007 original size:5 final size:5
Alignment explanation
Indices: 219997--220022 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
219987 ATAAAGTTTC
219997 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
220023 ATATATGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Done.