Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008949.1 Hibiscus syriacus cultivar Beakdansim tig00112275_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: 81017
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:145 original size:39 final size:38
Alignment explanation
Indices: 102--250 Score: 176
Period size: 39 Copynumber: 3.8 Consensus size: 38
92 CGCGAACACA
102 TAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCG
1 TAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT-CG
** * *
141 TAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCG
1 TAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCG
* *
179 TATATCGCAACGCGTATCCGTAAATCGCAACGAT-AATACA
1 TA-ATCGCAACGCGTATCCGTAAATCGCAACG-TGTAT-CG
219 TAAAATCGCAACGCGTATCCGT-AATCGCAACG
1 T--AATCGCAACGCGTATCCGTAAATCGCAACG
251 CGATATTTAA
Statistics
Matches: 95, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
38 4 0.04
39 60 0.63
40 12 0.13
41 18 0.19
42 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (38 bp):
TAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCG
Found at i:147 original size:19 final size:20
Alignment explanation
Indices: 64--252 Score: 183
Period size: 20 Copynumber: 9.6 Consensus size: 20
54 CATTTTCCAT
* ** *
64 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
84 AATCGCAACGCG-AACACAT-
1 AATCGCAACGCGTATC-CGTA
103 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
123 AATCGCAACGTGTATCCGT-
1 AATCGCAACGCGTATCCGTA
**
142 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
162 AATCGCAATGCGTAT-CGTA
1 AATCGCAACGCGTATCCGTA
*
181 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
201 AATCGCAACG-ATAATACATAA
1 AATCGCAACGCGT-ATCCGT-A
222 AATCGCAACGCGTATCCGT-
1 AATCGCAACGCGTATCCGTA
241 AATCGCAACGCG
1 AATCGCAACGCG
253 ATATTTAAAG
Statistics
Matches: 139, Mismatches: 22, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
19 60 0.43
20 63 0.45
21 15 0.11
22 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:165 original size:78 final size:78
Alignment explanation
Indices: 61--253 Score: 212
Period size: 78 Copynumber: 2.5 Consensus size: 78
51 TTCCATTTTC
* * *
61 CATAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA-ATCGCAACGCGTATCCGTAAA
1 CATAATCGCAACGCGTATACGTAAATCGCAACGCGAA-ACATATATCGCAACGCGTATCCGTAAA
* *
125 TCGCAACG-TGTATC
65 TCGCAACGAT-AATA
* ** * * * *
139 CGTAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCGTATATCGCAACGCGTATCCGTAAAT
1 CATAATCGCAACGCGTATACGTAAATCGCAACGCGAAACATATATCGCAACGCGTATCCGTAAAT
204 CGCAACGATAATA
66 CGCAACGATAATA
*
217 CATAAAATCGCAACGCGTATCCGT-AATCGCAACGCGA
1 CAT--AATCGCAACGCGTATACGTAAATCGCAACGCGA
254 TATTTAAAGC
Statistics
Matches: 95, Mismatches: 16, Indels: 7
0.81 0.14 0.06
Matches are distributed among these distances:
77 3 0.03
78 63 0.66
79 12 0.13
80 17 0.18
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (78 bp):
CATAATCGCAACGCGTATACGTAAATCGCAACGCGAAACATATATCGCAACGCGTATCCGTAAAT
CGCAACGATAATA
Found at i:669 original size:32 final size:33
Alignment explanation
Indices: 631--700 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
621 TTCACTTAGA
*
631 TTTCATTTCGCGTT-CGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTGCGATTCTCTCGTTGCGAT
*
663 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTGCGATTCTCTCGTTGCGAT
696 TTTCA
1 TTTCA
701 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 14 0.40
33 21 0.60
ACGTcount: A:0.10, C:0.23, G:0.19, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTGCGATTCTCTCGTTGCGAT
Found at i:837 original size:14 final size:14
Alignment explanation
Indices: 818--872 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
808 GAGATGACTG
818 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
832 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
851 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
865 TCGCAACG
1 TCGCAACG
873 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:839 original size:33 final size:33
Alignment explanation
Indices: 797--888 Score: 112
Period size: 33 Copynumber: 2.8 Consensus size: 33
787 GATAAATGAA
* ***
797 AATCGCAACGAGAGATGACTGTCGCAACGAGAG
1 AATCGCAACGAGAAATGAAAATCGCAACGAGAG
*
830 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGAGAAATGAAAATCGCAACGAGAG
* **
863 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGAGAAATGAAAATCGCA
889 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.42, C:0.24, G:0.24, T:0.10
Consensus pattern (33 bp):
AATCGCAACGAGAAATGAAAATCGCAACGAGAG
Found at i:906 original size:19 final size:19
Alignment explanation
Indices: 884--981 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
874 GAAACCAAAA
*
884 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
903 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
*
919 T--CGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
936 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
950 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
969 TCGCGTTGCGATT
1 TCGCGTTGCGATT
982 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 18 0.30
16 6 0.10
17 7 0.11
19 30 0.49
ACGTcount: A:0.10, C:0.22, G:0.23, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:931 original size:33 final size:33
Alignment explanation
Indices: 889--1003 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
879 CAAAATCGCA
*
889 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
922 TTGCGATTTTTATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
955 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
988 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1004 AACCAAAAGA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 75 1.00
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:958 original size:14 final size:14
Alignment explanation
Indices: 939--995 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 14
929 TTTTATTTCG
939 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
953 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
970 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
986 CGTTGCGATT
1 CGTTGCGATT
996 TTCATTTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 18 0.47
15 1 0.03
16 5 0.13
17 5 0.13
18 1 0.03
19 8 0.21
ACGTcount: A:0.09, C:0.26, G:0.25, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2845 original size:92 final size:92
Alignment explanation
Indices: 2684--3148 Score: 852
Period size: 92 Copynumber: 5.1 Consensus size: 92
2674 TAGATTGCTT
*
2684 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2749 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
*
2776 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2840 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
2868 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2933 TTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
2959 AGTAAA-TTGTTCGG-TGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3021 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
3048 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTA-TCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3112 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
3140 AGTAAATTT
1 AGTAAATTT
3149 ATCCATTCAA
Statistics
Matches: 363, Mismatches: 3, Indels: 14
0.96 0.01 0.04
Matches are distributed among these distances:
88 18 0.05
89 62 0.17
90 35 0.10
91 46 0.13
92 200 0.55
93 2 0.01
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (92 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:3119 original size:180 final size:183
Alignment explanation
Indices: 2684--3147 Score: 864
Period size: 180 Copynumber: 2.5 Consensus size: 183
2674 TAGATTGCTT
*
2684 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2749 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAA-TTGTTCGGTTGCTGCCAATTCTGCTAAACTG
2814 TATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 TATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
2868 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2933 TTGTCTTTGTTTTGTC-TTTGGTTGAAAGTAAATTGTTCGG-TGCTGCCAATTCTGCTAAACTGT
66 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
*
2996 GTATTCTTTAACACTGTGAAATATA-TTGTCTTTGTTTTGTCTTTTGGTTGAA
131 ATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
3048 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTA-TCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3112 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATT
66 -TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATT
3148 TATCCATTCA
Statistics
Matches: 276, Mismatches: 2, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
179 22 0.08
180 85 0.31
181 65 0.24
182 8 0.03
183 16 0.06
184 80 0.29
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.45
Consensus pattern (183 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
ATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:3232 original size:19 final size:19
Alignment explanation
Indices: 3192--3319 Score: 107
Period size: 19 Copynumber: 7.3 Consensus size: 19
3182 TAGTTTACTT
* *
3192 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
3212 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
3231 TCGCAACGCGAAA-TGAAA
1 TCGCAACGCGAAACCAAAA
*
3249 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
3263 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
3282 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
*
3296 TTGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
3315 TCGCA
1 TCGCA
3320 TTGCGATTTT
Statistics
Matches: 86, Mismatches: 12, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
14 18 0.21
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.13
19 35 0.41
20 13 0.15
ACGTcount: A:0.45, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:3288 original size:33 final size:32
Alignment explanation
Indices: 3228--3319 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 32
3218 CGCGAAACCA
**
3228 AAATCGCAACGCGAAA-TGAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
3259 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
*
3292 AAGATTGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
3320 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
31 1 0.02
32 16 0.29
33 38 0.69
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:3337 original size:19 final size:19
Alignment explanation
Indices: 3315--3449 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
3305 GAAACCAAAA
*
3315 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3334 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
3350 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
3367 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
3383 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
3400 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
3419 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
3439 TCGTGTTGCGA
1 TCGCGTTGCGA
3450 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3356 original size:14 final size:14
Alignment explanation
Indices: 3337--3393 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3327 TTTCATTTCG
3337 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
3351 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
3368 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
3384 CGTTGCGATT
1 CGTTGCGATT
3394 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:3362 original size:33 final size:33
Alignment explanation
Indices: 3320--3412 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
3310 CAAAATCGCA
*
3320 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
3353 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
3386 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
3413 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:5343 original size:14 final size:14
Alignment explanation
Indices: 5324--5359 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
5314 ATTGTTTAAT
5324 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
5338 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
5352 TGATTTGT
1 TGATTTGT
5360 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:5481 original size:19 final size:18
Alignment explanation
Indices: 5465--5564 Score: 136
Period size: 19 Copynumber: 5.6 Consensus size: 18
5455 AAAAATGACT
5465 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
5484 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
*
5502 ATCGCAA--CGAGA-G-A
1 ATCGCAATGCGAAATGAA
5516 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
5535 ATCGCAATGCGGAAATGAA
1 ATCGCAATGC-GAAATGAA
5554 ATCGCAATGCG
1 ATCGCAATGCG
5565 TTTATAATTT
Statistics
Matches: 73, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
14 8 0.11
15 1 0.01
16 8 0.11
17 1 0.01
18 10 0.14
19 39 0.53
20 6 0.08
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.15
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:5611 original size:52 final size:52
Alignment explanation
Indices: 5571--5836 Score: 444
Period size: 52 Copynumber: 5.0 Consensus size: 52
5561 TGCGTTTATA
* *
5571 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
5623 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
5675 ATTTCGCATTGCGATTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTA
1 ATTTCGCATTGCGA-TTC-TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
5731 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCA-TTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
5782 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
5835 AT
1 AT
5837 GTTGGGATTT
Statistics
Matches: 203, Mismatches: 5, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
51 49 0.24
52 78 0.38
53 20 0.10
54 10 0.05
55 3 0.01
56 43 0.21
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:5613 original size:33 final size:35
Alignment explanation
Indices: 5571--5864 Score: 246
Period size: 33 Copynumber: 8.5 Consensus size: 35
5561 TGCGTTTATA
5571 ATTTCGCATTGCGATT-ATCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTCATCTCGATTGCGATTTTC
*
5604 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TTCATCTCG-ATTGCGATTTTC
*
5640 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTCATCTCG-ATTGCGATTTTC
*
5675 ATTTCGCATTGCGATTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTCATCTCG-ATTGCGATTTTC
* *
5712 ATTTCGCATTGCGATTTTAATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TTCATCTCG-ATTGCGATTTTC
5748 -TTTCG--TTGCGATTTTCAT-TCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTCATCTCG-ATTGCGATTTTC
5782 ATTTCGCATTGCGATTC-TCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTCATCTCGATTGCGATTTTC
* *
5815 ATTTCCGCATTGCGATT-TTCAT-G-TTGGGATTTTC
1 ATTT-CGCATTGCGATTCATC-TCGATTGCGATTTTC
*
5849 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
5865 GTATTTTCCG
Statistics
Matches: 236, Mismatches: 5, Indels: 40
0.84 0.02 0.14
Matches are distributed among these distances:
32 11 0.05
33 77 0.33
34 33 0.14
35 27 0.11
36 16 0.07
37 43 0.18
38 29 0.12
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (35 bp):
ATTTCGCATTGCGATTCATCTCGATTGCGATTTTC
Found at i:5617 original size:19 final size:19
Alignment explanation
Indices: 5593--5864 Score: 345
Period size: 19 Copynumber: 15.4 Consensus size: 19
5583 GATTATCTCG
5593 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5612 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5631 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
5645 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5664 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5683 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5701 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5720 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
5739 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
5753 TTGCGATTTTCA-TTCGCA
1 TTGCGATTTTCATTTCGCA
5771 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5790 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
5804 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
5824 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
5838 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
5857 TTGCGATT
1 TTGCGATT
5865 GTATTTTCCG
Statistics
Matches: 224, Mismatches: 6, Indels: 46
0.81 0.02 0.17
Matches are distributed among these distances:
14 29 0.13
16 29 0.13
17 16 0.07
18 33 0.15
19 105 0.47
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:5707 original size:89 final size:91
Alignment explanation
Indices: 5571--5797 Score: 309
Period size: 89 Copynumber: 2.6 Consensus size: 91
5561 TGCGTTTATA
*
5571 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
*
5631 TTGCGA-TT-CTTTCG-TTGCGATTTTC
66 TTGCGATTTAATTTCGATTGCGA--TTC
5656 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTTCATTTCGCATTGCGATTTTCATTTCGCA
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
5720 TTGCGATTTTAATTTCGCATTGCGATTC
66 TTGCGA-TTTAATTTCG-ATTGCGATTC
5748 -TTTCG--TTGCGATTTTCA-TTCGCATTGCGATTTTCATTTCGCATTGCGATT
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
5798 CTCTCGTTGC
Statistics
Matches: 129, Mismatches: 2, Indels: 18
0.87 0.01 0.12
Matches are distributed among these distances:
85 14 0.11
87 2 0.02
88 17 0.13
89 69 0.53
90 6 0.05
91 7 0.05
92 8 0.06
94 6 0.05
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (91 bp):
ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
TTGCGATTTAATTTCGATTGCGATTC
Found at i:5757 original size:70 final size:74
Alignment explanation
Indices: 5571--5864 Score: 296
Period size: 70 Copynumber: 4.2 Consensus size: 74
5561 TGCGTTTATA
*
5571 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 ATTTCGCATTGCGATTTTAATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCA
5631 TTGCGA--TTC
64 TTGCGATTTTC
*
5640 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTTCATTTCGCA
1 ATTTCGCATTGCGATTTTAATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCA
5701 TTGCGATTTTC
64 TTGCGATTTTC
5712 ATTTCGCATTGCGATTTTAATTTCGCATTGCGA-TTC-TTTCG-TTGCGATTTTCA-TTCGCATT
1 ATTTCGCATTGCGATTTTAATTTCGCATTGCGATTTCATTTCGATTGCGATTTTCATTTCGCATT
5773 GCGATTTTC
66 GCGATTTTC
* *
5782 ATTTCGCATTGCGA--TT-CTCTCG--TTGCGATTTTCATTTCCGCATTGCGATTTTCA--T-G-
1 ATTTCGCATTGCGATTTTAATTTCGCATTGCGA-TTTCATTT-CG-ATTGCGATTTTCATTTCGC
*
5838 -TTGGGATTTTC
63 ATTGCGATTTTC
*
5849 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
5865 GTATTTTCCG
Statistics
Matches: 200, Mismatches: 6, Indels: 38
0.82 0.02 0.16
Matches are distributed among these distances:
65 6 0.03
66 6 0.03
67 30 0.15
68 12 0.06
69 8 0.04
70 56 0.28
71 42 0.21
72 8 0.04
73 8 0.04
75 24 0.12
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (74 bp):
ATTTCGCATTGCGATTTTAATTTCGCATTGCGATTTCATTTCGATTGCGATTTTCATTTCGCATT
GCGATTTTC
Found at i:5874 original size:53 final size:53
Alignment explanation
Indices: 5571--5870 Score: 337
Period size: 52 Copynumber: 5.7 Consensus size: 53
5561 TGCGTTTATA
* * *
5571 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCGCGTTGCGATTGTCATTTCCGCATTGCGATTTTC
** *
5623 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCGCGTTGCGATTGTCATTTCCGCATTGCGATTTTC
* * *
5675 ATTTCGCATTGCGATTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTTTA
1 ATTTCGCATTGCGA-TTC---TCGCGTTGCGATTGTCATTTCCGCATTGCGATTTTC
** *
5731 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCA-TT-CGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCGCGTTGCGATTGTCATTTCCGCATTGCGATTTTC
* *
5782 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCGCGTTGCGATTGTCATTTCCGCATTGCGATTTTC
* * *
5835 ATGTTGGGATTTTC-ATT-TCGCGTTGCGATTGT-ATTT
1 AT-TTCGCA-TTGCGATTCTCGCGTTGCGATTGTCATTT
5871 TCCGTGTTGC
Statistics
Matches: 224, Mismatches: 16, Indels: 16
0.88 0.06 0.06
Matches are distributed among these distances:
51 49 0.22
52 84 0.38
53 33 0.15
54 7 0.03
55 6 0.03
56 45 0.20
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (53 bp):
ATTTCGCATTGCGATTCTCGCGTTGCGATTGTCATTTCCGCATTGCGATTTTC
Found at i:8360 original size:24 final size:24
Alignment explanation
Indices: 8326--8372 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
8316 CTGAAACATC
8326 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
8350 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
8373 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:9080 original size:20 final size:20
Alignment explanation
Indices: 9052--9420 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
9042 AAATTTAAGT
* * * *
9052 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
9072 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
9092 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
9112 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
9132 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
9152 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
9172 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
9192 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
9212 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
9232 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
9252 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
9272 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
9292 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
9312 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
9332 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
9352 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
9372 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
9392 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
9412 GTTGCGATT
1 GTTGCGATT
9421 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 30, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
19 6 0.02
20 297 0.96
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:13340 original size:120 final size:113
Alignment explanation
Indices: 13090--13584 Score: 550
Period size: 113 Copynumber: 4.3 Consensus size: 113
13080 GTTGAACAAA
* * * * *
13090 TTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAAT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGTTGATCTATCCAGT
** * * *
13154 GATGAATTTGAACAAAAGGTTAAACAAGTTCTTCCCATTATGAACTTC
66 GATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
*
13202 TTCTTCCTTTTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGTGATGATCTATCTT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGT--TGATCTATC--
* **
13267 TTTCTGTGATAGAA-TCATGCAAAAGGTTGAACAAACTT-TTCTCATTATGAACTTC
62 ---CAGTGAT-GAATTCAAACAAAAGGTTGAACAAA-TTCTTCTCATTATGAACTTC
* * *
13322 TTCTCCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGTTTATCTATCGAGT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGTTGATCTATCCAGT
* *
13387 GATGAATTCAAATAAAAGGTTTGAACAAATTCTTCTCATTATGAATTTC
66 GATGAATTCAAACAAAAGG-TTGAACAAATTCTTCTCATTATGAACTTC
* * * * *
13436 TTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCTTC-C-GGAAATGTTGATCTATCGAA
1 TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACT-TTCTCTGGAAAAGTTGATCTATCCAG
* ** * * * *
13499 TGATGGATTTGAGCAAAAGGTTGAACAAGTTCTTATCATTATAAACTTC
65 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
* * *
13548 CTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAAC
1 TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAAC
13585 ACTACCTAGC
Statistics
Matches: 328, Mismatches: 41, Indels: 28
0.83 0.10 0.07
Matches are distributed among these distances:
112 67 0.20
113 91 0.28
114 61 0.19
115 11 0.03
118 8 0.02
120 85 0.26
121 5 0.02
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (113 bp):
TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGTTGATCTATCCAGT
GATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
Found at i:13615 original size:226 final size:230
Alignment explanation
Indices: 13091--13625 Score: 620
Period size: 226 Copynumber: 2.3 Consensus size: 230
13081 TTGAACAAAT
* *
13091 TCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAATGA
1 TCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGA
** * * * *
13156 TGAATTTGAACAAAAGGTTAAACAAGTTCTTCCCATTATGAACTTCTTCTTCCTTTTTCAGATGA
66 TGAATTCAAATAAAAGGTTAAACAAATTCTTCCCATTATGAACTTCTTCTTCCTTCTTCAAATGA
* *** **
13221 GTTCTTCTTATTATGAACTTTCTCTGGAAAAGTGATGATCTATCTTTTTCTGTGATAGAATCATG
131 GTTCTTCTCATTATGAACTTTCTCTGGAAAAGTGATGATCTATCGAATGATGTGAT--AATCATG
* * *
13286 CAAAAGGTTGAACAAACTTTTCTCATTATGAACTTCT
194 CAAAAGGTTGAACAAACTTTTATCATTATAAACTTCC
* * * *
13323 TCTCCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGTTTATCTATCGAGTG
1 TCT-TCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTG
* * *
13388 ATGAATTCAAATAAAAGGTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAAT
65 ATGAATTCAAATAAAAGG-TTAAACAAATTCTTCCCATTATGAACTTCTTCTTCCTTCTTCAAAT
* * *
13453 GAGTTCTTCTCATTATGAACTCTTC-C-GG-AAA-TGTTGATCTATCGAATGATG-GAT-TTGA-
129 GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGTGATGATCTATCGAATGATGTGATAATCAT
*
13511 GCAAAAGGTTGAAC-AAGTTCTTATCATTATAAACTTCC
193 GCAAAAGGTTGAACAAACTT-TTATCATTATAAACTTCC
* * * * * *
13549 TCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACACTAC-CTAGCAATGTTGATCCATTGAGT
1 TCTTC-TTCTTCAGATGAGTTCTTCTCATTATGAAC-TTTCTCTGGAAAAGTTGATCCATCGAGT
*
13613 GATGGATTCAAAT
64 GATGAATTCAAAT
13626 CTTGCTAAAA
Statistics
Matches: 258, Mismatches: 39, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
225 5 0.02
226 90 0.35
227 4 0.02
230 3 0.01
231 14 0.05
232 6 0.02
233 72 0.28
234 61 0.24
235 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.39
Consensus pattern (230 bp):
TCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGA
TGAATTCAAATAAAAGGTTAAACAAATTCTTCCCATTATGAACTTCTTCTTCCTTCTTCAAATGA
GTTCTTCTCATTATGAACTTTCTCTGGAAAAGTGATGATCTATCGAATGATGTGATAATCATGCA
AAAGGTTGAACAAACTTTTATCATTATAAACTTCC
Found at i:14792 original size:21 final size:21
Alignment explanation
Indices: 14763--14803 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
14753 TTTATGTGAA
14763 AAAAAAAATTGAATTTCAAAC
1 AAAAAAAATTGAATTTCAAAC
*
14784 AAAAGAAATTGAATTTCAAA
1 AAAAAAAATTGAATTTCAAA
14804 AAGATAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.24
Consensus pattern (21 bp):
AAAAAAAATTGAATTTCAAAC
Found at i:15185 original size:11 final size:10
Alignment explanation
Indices: 15167--15214 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
15157 TATATATAAA
15167 TTTTTTCATT
1 TTTTTTCATT
15177 TTCTTTTCATT
1 TT-TTTTCATT
15188 TTTTTT-ATT
1 TTTTTTCATT
* * *
15197 TTTTATAAAT
1 TTTTTTCATT
15207 TTTTTTCA
1 TTTTTTCA
15215 AGCATAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 8 0.25
10 14 0.44
11 10 0.31
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTTTCATT
Found at i:18361 original size:24 final size:23
Alignment explanation
Indices: 18334--18386 Score: 54
Period size: 24 Copynumber: 2.2 Consensus size: 23
18324 ATACTTGAAA
18334 AATAAAATAAAGCATTAAT-AAAAT
1 AATAAAATAAA-CATT-ATGAAAAT
* *
18358 AATATATATAAATATTATGAAAAT
1 AATA-AAATAAACATTATGAAAAT
18382 AATAA
1 AATAA
18387 GTATATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 3 0.12
24 16 0.64
25 6 0.24
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (23 bp):
AATAAAATAAACATTATGAAAAT
Found at i:18406 original size:28 final size:27
Alignment explanation
Indices: 18355--18408 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
18345 GCATTAATAA
*
18355 AATAATATATATAAATATTATGAAAAT
1 AATAATATATATAAAAATTATGAAAAT
*
18382 AATAAGTATATATAAAAATTTTGAAAA
1 AATAA-TATATATAAAAATTATGAAAA
18409 GAAAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (27 bp):
AATAATATATATAAAAATTATGAAAAT
Found at i:20522 original size:3 final size:3
Alignment explanation
Indices: 20514--20544 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
20504 AATTATTTAG
20514 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
20545 CAAATGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:23870 original size:43 final size:43
Alignment explanation
Indices: 23737--23872 Score: 113
Period size: 43 Copynumber: 3.2 Consensus size: 43
23727 CCCTTTCATC
*
23737 TACAAATAAAACTTATAAGTTTCAAGGATCAAATATATTATTA
1 TACAAATAAAACTTATAAGTTTCAAGGGTCAAATATATTATTA
*** * * *
23780 TACAAAT-TTTC-T-TAA-TTATC-A-CGTTAACATAATAATTATGATC
1 TACAAATAAAACTTATAAGTT-TCAAGGGTCAA-AT-AT-ATTAT--TA
23823 TACAAATAAAACTTATAAGTTTCAAGGGTCAAATATATTATTA
1 TACAAATAAAACTTATAAGTTTCAAGGGTCAAATATATTATTA
23866 TACAAAT
1 TACAAAT
23873 TTTTTTAGTT
Statistics
Matches: 68, Mismatches: 13, Indels: 24
0.65 0.12 0.23
Matches are distributed among these distances:
38 3 0.04
39 5 0.07
40 7 0.10
41 6 0.09
42 1 0.01
43 23 0.34
44 1 0.01
45 6 0.09
46 7 0.10
47 5 0.07
48 4 0.06
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (43 bp):
TACAAATAAAACTTATAAGTTTCAAGGGTCAAATATATTATTA
Found at i:36359 original size:14 final size:14
Alignment explanation
Indices: 36340--36373 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
36330 AGGTTTGTTG
36340 GTGTGTATATATGT
1 GTGTGTATATATGT
36354 GTGTGTATATATGT
1 GTGTGTATATATGT
36368 GTGTGT
1 GTGTGT
36374 GGGGGGGGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (14 bp):
GTGTGTATATATGT
Found at i:37541 original size:18 final size:18
Alignment explanation
Indices: 37518--37552 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
37508 CCATACTCTG
*
37518 TTTTGCAATGTGCACTTT
1 TTTTGCAATATGCACTTT
*
37536 TTTTGCTATATGCACTT
1 TTTTGCAATATGCACTT
37553 GCAATTCCTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.17, G:0.14, T:0.51
Consensus pattern (18 bp):
TTTTGCAATATGCACTTT
Found at i:43340 original size:23 final size:23
Alignment explanation
Indices: 43322--43381 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
43312 CTCGTATAAA
43322 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
43345 TACACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
43368 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
43382 ATATAATGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.25, C:0.32, G:0.25, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:44100 original size:67 final size:66
Alignment explanation
Indices: 43992--44142 Score: 221
Period size: 67 Copynumber: 2.3 Consensus size: 66
43982 TTTTTCTCAT
* * * *
43992 GGGGGAATCGGTTCCCCCCCTGGGGTATCGGTTCCCCTCTAGCATTCTGGAATTTTATATCCGTT
1 GGGGGTATCGGTT-CCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTT
44057 GA
65 GA
* *
44059 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGTATTCTGGAAATTCATATTCGTT
1 GGGGGTATCGGTTCCCCCCT-GGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTT
44124 GA
65 GA
*
44126 TGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
44143 TTGAATGGGT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
66 7 0.09
67 69 0.91
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.32
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTTG
A
Found at i:50218 original size:23 final size:23
Alignment explanation
Indices: 50200--50259 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
50190 CTCGTATAAA
50200 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
50223 TACACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
50246 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
50260 ATATAATGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.25, C:0.32, G:0.25, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:50974 original size:67 final size:66
Alignment explanation
Indices: 50866--51016 Score: 221
Period size: 67 Copynumber: 2.3 Consensus size: 66
50856 TTTTTCTCAT
* * * *
50866 GGGGGAATCGGTTCCCCCCCTGGGGTATCGGTTCCCCTCTAGCATTCTGGAATTTTATATCCGTT
1 GGGGGTATCGGTT-CCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTT
50931 GA
65 GA
* *
50933 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGTATTCTGGAAATTCATATTCGTT
1 GGGGGTATCGGTTCCCCCCT-GGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTT
50998 GA
65 GA
*
51000 TGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
51017 TTGAATGGGT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
66 7 0.09
67 69 0.91
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.32
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTTG
A
Found at i:51800 original size:23 final size:20
Alignment explanation
Indices: 51769--51825 Score: 51
Period size: 20 Copynumber: 2.7 Consensus size: 20
51759 CTATGAGATT
*
51769 TATCTCGAATGACCACTATGAAA
1 TATCCCGAATGACCAC--TG-AA
* * *
51792 TATCCCGAAGGATCACTGTA
1 TATCCCGAATGACCACTGAA
51812 TATCCCGAATGACC
1 TATCCCGAATGACC
51826 GCGTAGACCC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 13 0.46
21 2 0.07
23 13 0.46
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (20 bp):
TATCCCGAATGACCACTGAA
Found at i:65500 original size:2 final size:2
Alignment explanation
Indices: 65493--65531 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
65483 AATCCAGGAT
65493 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
65532 TTGTGTGTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:70883 original size:16 final size:16
Alignment explanation
Indices: 70862--70892 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
70852 GATCCAAAAA
70862 CAGCTCCAAACAGCAG
1 CAGCTCCAAACAGCAG
70878 CAGCTCCAAACAGCA
1 CAGCTCCAAACAGCA
70893 ACATGATCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.39, G:0.16, T:0.06
Consensus pattern (16 bp):
CAGCTCCAAACAGCAG
Found at i:74901 original size:16 final size:17
Alignment explanation
Indices: 74877--74909 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
74867 ATTCTTTAAA
*
74877 GTTTTGGAT-AAAATGG
1 GTTTCGGATCAAAATGG
74893 GTTTCGGATCAAAATGG
1 GTTTCGGATCAAAATGG
74910 TGTAGCTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.30, C:0.06, G:0.30, T:0.33
Consensus pattern (17 bp):
GTTTCGGATCAAAATGG
Done.