Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003131.1 Hibiscus syriacus cultivar Beakdansim tig00006567_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: 85766
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:148 original size:19 final size:19
Alignment explanation
Indices: 108--187 Score: 71
Period size: 19 Copynumber: 4.4 Consensus size: 19
98 TAGTTTACTT
* *
108 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
128 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
147 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
**
161 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
180 TCGCAACG
1 TCGCAACG
188 ACAAGATCGC
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
14 8 0.16
16 5 0.10
17 4 0.08
19 21 0.42
20 12 0.24
ACGTcount: A:0.45, C:0.28, G:0.17, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:168 original size:33 final size:32
Alignment explanation
Indices: 125--216 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
115 ACGAAACTTA
**
125 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
157 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
190 AAGATCGC-ACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
217 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
32 21 0.38
33 35 0.62
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:234 original size:19 final size:19
Alignment explanation
Indices: 212--345 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
202 GAAACCAAAA
*
212 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
231 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
247 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
264 TCGCATTGCGA---TC-TG
1 TCGCGTTGCGATTTTCATT
279 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
296 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
315 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
335 TCGTGTTGCGA
1 TCGCGTTGCGA
346 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
13 7 0.08
14 8 0.09
15 2 0.02
16 10 0.11
17 8 0.09
19 46 0.49
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:288 original size:32 final size:32
Alignment explanation
Indices: 217--307 Score: 155
Period size: 32 Copynumber: 2.8 Consensus size: 32
207 CAAAATCGCA
*
217 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGA-TCTGTCG
*
250 TTGCGATTTTCATTTCGCATTGCGATCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATCTGTCG
282 TTGCGATTTTCATTTCGCGTTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
308 TTTGGTTTCG
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.46
Consensus pattern (32 bp):
TTGCGATTTTCATTTCGCGTTGCGATCTGTCG
Found at i:2265 original size:14 final size:14
Alignment explanation
Indices: 2246--2281 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2236 ATTGTTTAAT
2246 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2260 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2274 TGATTTGT
1 TGATTTGT
2282 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:2474 original size:20 final size:19
Alignment explanation
Indices: 2388--2488 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
2378 AAAAATGACT
2388 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
2406 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2425 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2439 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2458 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2478 ATCGCAATGCG
1 ATCGCAATGCG
2489 TTTATAATTT
Statistics
Matches: 74, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 17 0.23
19 23 0.31
20 19 0.26
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2541 original size:19 final size:19
Alignment explanation
Indices: 2517--2771 Score: 289
Period size: 19 Copynumber: 14.4 Consensus size: 19
2507 GATTATCTCG
2517 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2536 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2555 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
2569 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2588 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2607 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2626 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2645 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
*
2659 TTGCGATTTTCATTTTGCA
1 TTGCGATTTTCATTTCGCA
* *
2678 TTGCGTTTTTCATTTTGCA
1 TTGCGATTTTCATTTCGCA
*
2697 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2711 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2731 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
2745 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
2764 TTGCGATT
1 TTGCGATT
2772 GTATTTTCCG
Statistics
Matches: 203, Mismatches: 12, Indels: 42
0.79 0.05 0.16
Matches are distributed among these distances:
14 29 0.14
16 23 0.11
17 19 0.09
18 3 0.01
19 117 0.58
20 12 0.06
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2557 original size:52 final size:52
Alignment explanation
Indices: 2495--2652 Score: 244
Period size: 52 Copynumber: 2.9 Consensus size: 52
2485 TGCGTTTATA
*
2495 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
2547 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
2599 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGATT
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATT
2653 CTGTCGTTGC
Statistics
Matches: 97, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
52 64 0.66
54 2 0.02
55 5 0.05
57 26 0.27
ACGTcount: A:0.16, C:0.20, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:2622 original size:90 final size:90
Alignment explanation
Indices: 2495--2771 Score: 362
Period size: 90 Copynumber: 3.2 Consensus size: 90
2485 TGCGTTTATA
*
2495 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
2555 TTGCGATTCTTTCGTTGCGATTTTC
66 TTGCGATTCTTTCGTTGCGATTTTC
*
2580 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCA
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
*
2645 TTGCGATTCTGTCGTTGCGATTTTC
66 TTGCGATTCTTTCGTTGCGATTTTC
* * * *
2670 ATTTTGCATTGCGTTTTTCATTTTGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCCGC
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGC
*
2730 ATTGCGA-T-TTTCATGTTGGGATTTTC
65 ATTGCGATTCTTTC--GTTGCGATTTTC
*
2756 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
2772 GTATTTTCCG
Statistics
Matches: 171, Mismatches: 13, Indels: 15
0.86 0.07 0.08
Matches are distributed among these distances:
84 3 0.02
85 29 0.17
86 34 0.20
87 6 0.04
88 8 0.05
90 91 0.53
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.48
Consensus pattern (90 bp):
ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
TTGCGATTCTTTCGTTGCGATTTTC
Found at i:2649 original size:142 final size:139
Alignment explanation
Indices: 2479--2771 Score: 439
Period size: 142 Copynumber: 2.1 Consensus size: 139
2469 GAAATGAAAA
*
2479 TCGCAATGCG-TTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGAT
*
2543 TTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCGCA
66 TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCA--T-G--
2607 TTGCGATTTTCATT
126 TTGCGATTTTCATT
* * * *
2621 TCGCATTGCGATTT-TAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTTGCATTGCGTT
1 TCGCATTGCGATTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGAT
* *
2685 TTTCATTTTGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGG
66 TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGCG
2750 ATTTTCATT
131 ATTTTCATT
*
2759 TCGCGTTGCGATT
1 TCGCATTGCGATT
2772 GTATTTTCCG
Statistics
Matches: 140, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
138 25 0.18
140 1 0.01
141 1 0.01
142 94 0.67
143 19 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (139 bp):
TCGCATTGCGATTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGAT
TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGCG
ATTTTCATT
Found at i:2663 original size:52 final size:55
Alignment explanation
Indices: 2517--2743 Score: 278
Period size: 52 Copynumber: 4.2 Consensus size: 55
2507 GATTATCTCG
2517 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCA
2569 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCA
* * *
2626 TTGCGATTTTAATTTCGCATTGCGA-TTC-TGTCG-TTGCGATTTTCATTTTGCA
1 TTGCGATTTTCATTTCGCATTGCGATTTCATTTCGATTGCGATTTTCATTTCGCA
* * *
2678 TTGCGTTTTTCATTTTGCATTGCGA-TTC-TCTCG-TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTTCATTTCGATTGCGATTTTCATTT-CGCA
2731 TTGCGATTTTCAT
1 TTGCGATTTTCAT
2744 GTTGGGATTT
Statistics
Matches: 160, Mismatches: 9, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
52 106 0.66
53 15 0.09
54 7 0.04
55 8 0.05
57 24 0.15
ACGTcount: A:0.14, C:0.20, G:0.17, T:0.48
Consensus pattern (55 bp):
TTGCGATTTTCATTTCGCATTGCGATTTCATTTCGATTGCGATTTTCATTTCGCA
Found at i:5064 original size:12 final size:12
Alignment explanation
Indices: 5047--5071 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5037 TCTTCGGGGA
5047 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5059 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5071 C
1 C
5072 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:5280 original size:24 final size:24
Alignment explanation
Indices: 5246--5292 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5236 CTGAAACATC
5246 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
5270 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
5293 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:6002 original size:20 final size:20
Alignment explanation
Indices: 5974--6342 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
5964 AAATTTCAGT
* * * *
5974 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
5994 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
6014 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
6034 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
6054 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
6074 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
6094 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
6114 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
6134 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
6154 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
6174 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
6194 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
6214 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
6234 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
6254 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
6274 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
6294 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
6314 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
6334 GTTGCGATT
1 GTTGCGATT
6343 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:6973 original size:29 final size:26
Alignment explanation
Indices: 6932--6999 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 26
6922 AATAATTTAC
* *
6932 AAAAAATAGTAAAAGATCAAATATATA
1 AAAAAAAATTAAAAGATCAAAT-TATA
*
6959 AAATATAAAATT-AAAGATTAAATTATA
1 AAA-A-AAAATTAAAAGATCAAATTATA
6986 AAAAAAAATTAAAA
1 AAAAAAAATTAAAA
7000 TTACATAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
25 6 0.17
26 4 0.11
27 10 0.29
28 11 0.31
29 4 0.11
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.25
Consensus pattern (26 bp):
AAAAAAAATTAAAAGATCAAATTATA
Found at i:6981 original size:28 final size:25
Alignment explanation
Indices: 6943--7002 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 25
6933 AAAAATAGTA
*
6943 AAAGATCAAATATATAAAATATAAAATT
1 AAAGATTAAAT-TATAAAA-A-AAAATT
6971 AAAGATTAAATTATAAAAAAAAATT
1 AAAGATTAAATTATAAAAAAAAATT
6996 AAA-ATTA
1 AAAGATTA
7003 CATAAATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 4 0.13
25 9 0.29
26 1 0.03
27 7 0.23
28 10 0.32
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (25 bp):
AAAGATTAAATTATAAAAAAAAATT
Found at i:7172 original size:19 final size:19
Alignment explanation
Indices: 7147--7188 Score: 77
Period size: 18 Copynumber: 2.3 Consensus size: 19
7137 AAATCGAGTT
7147 ATTTTTTTAATTGAAAT-A
1 ATTTTTTTAATTGAAATAA
7165 ATTTTTTTAATTGAAATAA
1 ATTTTTTTAATTGAAATAA
7184 ATTTT
1 ATTTT
7189 ACACACTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
ATTTTTTTAATTGAAATAA
Found at i:7792 original size:27 final size:28
Alignment explanation
Indices: 7740--7792 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
7730 AAATAATGAA
*
7740 AATTATATAATATATTAAATATAATAAT
1 AATTATATAATATATTAAATACAATAAT
*
7768 AATTA-ATAATAT-TATAATTACAATA
1 AATTATATAATATAT-TAAATACAATA
7793 TATTTTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 1 0.05
27 16 0.73
28 5 0.23
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
AATTATATAATATATTAAATACAATAAT
Found at i:9187 original size:18 final size:17
Alignment explanation
Indices: 9157--9190 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
9147 TAATATAATG
*
9157 TTTTATTTTTTTATTTA
1 TTTTATTTGTTTATTTA
9174 TTTTGATTTGTTTATTT
1 TTTT-ATTTGTTTATTT
9191 GTAAGTTGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (17 bp):
TTTTATTTGTTTATTTA
Found at i:10776 original size:12 final size:12
Alignment explanation
Indices: 10761--10798 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
10751 ATTTCAAAAT
10761 TTATAAAATATA
1 TTATAAAATATA
10773 TTATAATAAT-TA
1 TTATAA-AATATA
10785 TTTATAAAATATA
1 -TTATAAAATATA
10798 T
1 T
10799 ATTTTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TTATAAAATATA
Found at i:10813 original size:16 final size:15
Alignment explanation
Indices: 10793--10887 Score: 55
Period size: 16 Copynumber: 6.7 Consensus size: 15
10783 TATTTATAAA
10793 ATATATATTTTAATT
1 ATATATATTTTAATT
*
10808 ACTATAT-TTATTTATT
1 A-TATATATT-TTAATT
10824 AT-TATATTTTAATT
1 ATATATATTTTAATT
*
10838 AT-T-TA--TTATTT
1 ATATATATTTTAATT
10849 AT-TATA-TTTAA-T
1 ATATATATTTTAATT
*
10861 ATTTAATATTATTAATT
1 ATAT-ATATT-TTAATT
*
10878 ATATTTATTT
1 ATATATATTT
10888 GTTATTAATT
Statistics
Matches: 64, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
11 8 0.12
12 5 0.08
13 6 0.09
14 14 0.22
15 8 0.12
16 19 0.30
17 4 0.06
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (15 bp):
ATATATATTTTAATT
Found at i:10815 original size:14 final size:14
Alignment explanation
Indices: 10796--10838 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
10786 TTATAAAATA
10796 TATATTTTAATTAC
1 TATATTTTAATTAC
* *
10810 TATATTTATTTATTAT
1 TATA-TT-TTAATTAC
10826 TATATTTTAATTA
1 TATATTTTAATTA
10839 TTTATTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 10 0.42
15 4 0.17
16 10 0.42
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
TATATTTTAATTAC
Found at i:10832 original size:30 final size:30
Alignment explanation
Indices: 10796--10903 Score: 103
Period size: 32 Copynumber: 3.4 Consensus size: 30
10786 TTATAAAATA
*
10796 TATATTTTAATTACTATATTTATTTATTAT
1 TATATTTTAATTATTATATTTATTTATTAT
10826 TATATTTTAATTATTTATTATTTATTATATT-T
1 TATATTTTAATTA-TTA-TATTTATT-TATTAT
* *
10858 AATATTTAATATTATTAATTATATTTATTTGTTAT
1 TATATTT--TA--ATT-ATTATATTTATTTATTAT
10893 TA-ATTTTAATT
1 TATATTTTAATT
10904 TAAAAAATTA
Statistics
Matches: 65, Mismatches: 4, Indels: 18
0.75 0.05 0.21
Matches are distributed among these distances:
30 16 0.25
31 2 0.03
32 17 0.26
33 4 0.06
34 9 0.14
35 10 0.15
36 6 0.09
37 1 0.02
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (30 bp):
TATATTTTAATTATTATATTTATTTATTAT
Found at i:10840 original size:25 final size:24
Alignment explanation
Indices: 10811--10902 Score: 92
Period size: 25 Copynumber: 4.1 Consensus size: 24
10801 TTTAATTACT
10811 ATATTTATTTATTATTATATTTTA
1 ATATTTATTTATTATTATATTTTA
10835 ATTATTTA-TTATTTATTATA-TTTA
1 A-TATTTATTTA-TTATTATATTTTA
*
10859 ATATTTA-ATATTATTA-A--TT-
1 ATATTTATTTATTATTATATTTTA
*
10878 ATATTTATTTGTTATTA-ATTTTA
1 ATATTTATTTATTATTATATTTTA
10901 AT
1 AT
10903 TTAAAAAATT
Statistics
Matches: 59, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
19 7 0.12
20 10 0.17
21 1 0.02
22 8 0.14
23 10 0.17
24 9 0.15
25 14 0.24
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (24 bp):
ATATTTATTTATTATTATATTTTA
Found at i:10845 original size:7 final size:7
Alignment explanation
Indices: 10815--10886 Score: 60
Period size: 7 Copynumber: 10.3 Consensus size: 7
10805 ATTACTATAT
10815 TTATTTA
1 TTATTTA
10822 TTATTATA
1 TTATT-TA
*
10830 TT-TTAA
1 TTATTTA
10836 TTATTTA
1 TTATTTA
10843 TTATTTA
1 TTATTTA
10850 TTATATTTA
1 -T-TATTTA
*
10859 ATATTTA
1 TTATTTA
*
10866 ATA-TTA
1 TTATTTA
*
10872 TTAATTA
1 TTATTTA
10879 -TATTTA
1 TTATTTA
10885 TT
1 TT
10887 TGTTATTAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
6 13 0.24
7 30 0.56
8 5 0.09
9 6 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (7 bp):
TTATTTA
Found at i:10894 original size:16 final size:16
Alignment explanation
Indices: 10805--10898 Score: 70
Period size: 16 Copynumber: 5.8 Consensus size: 16
10795 ATATATTTTA
*
10805 ATTACTATATTTATTT
1 ATTATTATATTTATTT
*
10821 ATTATTATA-TT-TTA
1 ATTATTATATTTATTT
10835 ATTATTTATTATTTATTAT
1 ATTA-TTA-TATTTATT-T
*
10854 ATT-TAATATTTAATATT
1 ATTATTATATTT-AT-TT
10871 ATTAATTATATTTATTT
1 ATT-ATTATATTTATTT
*
10888 GTTATTA-ATTT
1 ATTATTATATTT
10899 TAATTTAAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 19
0.72 0.07 0.22
Matches are distributed among these distances:
14 6 0.10
15 9 0.14
16 19 0.30
17 14 0.22
18 5 0.08
19 10 0.16
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (16 bp):
ATTATTATATTTATTT
Found at i:14011 original size:23 final size:21
Alignment explanation
Indices: 13985--14038 Score: 54
Period size: 25 Copynumber: 2.4 Consensus size: 21
13975 ATGTCACGAC
13985 ATTATTTTAAATATATGACATA
1 ATTATTTTAAATATAT-ACATA
*
14007 TATTATTATTTATATATATACATA
1 -ATTA-T-TTTAAATATATACATA
*
14031 ATAATTTT
1 ATTATTTT
14039 TTTAGAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 3 0.11
22 1 0.04
23 7 0.26
24 6 0.22
25 10 0.37
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (21 bp):
ATTATTTTAAATATATACATA
Found at i:14412 original size:19 final size:19
Alignment explanation
Indices: 14388--14431 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
14378 ACGCGATTTT
*
14388 GCGACGTTAATATTTTCTC
1 GCGACGTTAATAGTTTCTC
14407 GCGACGTTAATAGTTTCTC
1 GCGACGTTAATAGTTTCTC
*
14426 ACGACG
1 GCGACG
14432 CTCGAATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (19 bp):
GCGACGTTAATAGTTTCTC
Found at i:15105 original size:26 final size:26
Alignment explanation
Indices: 15044--15104 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
15034 GAATAAATGA
*
15044 AATATTAAAATTAATATTTTAATCCT
1 AATATTAAAACTAATATTTTAATCCT
*
15070 AATATTAAAACTAATTTTTTAA-CCT
1 AATATTAAAACTAATATTTTAATCCT
15095 AA-ATGTAAAA
1 AATAT-TAAAA
15105 ATGTAAAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 2 0.06
25 10 0.31
26 20 0.62
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (26 bp):
AATATTAAAACTAATATTTTAATCCT
Found at i:15827 original size:35 final size:35
Alignment explanation
Indices: 15788--15863 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
15778 AAAGCAGTCC
* *
15788 TCAATTTCATGCTAAACCCTAATTTCCAAAGTAAT
1 TCAATTTCATGCTAAACCCTAAATTCCAAAATAAT
*
15823 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATGCTAAACCCTAAATTCCAAAATAAT
15858 TCAATT
1 TCAATT
15864 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (35 bp):
TCAATTTCATGCTAAACCCTAAATTCCAAAATAAT
Found at i:16438 original size:131 final size:130
Alignment explanation
Indices: 16260--16508 Score: 399
Period size: 131 Copynumber: 1.9 Consensus size: 130
16250 TATTTATATA
* ** *
16260 ATCAATTTGGTCCTAAATAAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATAAAATAAAATTTAATAAATTAATCATTTAACCAGGACCTGACATGTG
* *
16325 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
*
16390 ATCAATTTGGTCCTAAATTAAATAAAAATTTAATAAATTAATCATTTAACCAGGACCTGACATGT
1 ATCAATTTGGTCCTAAATAAAAT-AAAATTTAATAAATTAATCATTTAACCAGGACCTGACATGT
* * *
16455 GTTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
65 GTTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
16509 GAAGAAAATT
Statistics
Matches: 108, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
130 22 0.20
131 86 0.80
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATAAAATAAAATTTAATAAATTAATCATTTAACCAGGACCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:16539 original size:131 final size:130
Alignment explanation
Indices: 16285--16539 Score: 289
Period size: 131 Copynumber: 1.9 Consensus size: 130
16275 AATAAAATAG
** * * *
16285 AATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCATGACACGTGTC
1 AATTTAATAAATTAATCATTTAACCAGGACCTGACATGTGTTAACACATGATCATGACACATGTC
*** * * **** *
16350 ATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCTAAATTAAATAA
66 ATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CAAAATTAAATAA
16415 A
130 A
* * *
16416 AATTTAATAAATTAATCATTTAACCAGGACCTGACATGTGTTAACACATGATCATGATATATGTT
1 AATTTAATAAATTAATCATTTAACCAGGACCTGACATGTGTTAACACATGATCATGACACATGTC
*
16481 ATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT-AAAATT
66 ATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGTCAAAATT
16540 TGGGTCTTGG
Statistics
Matches: 102, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
131 89 0.87
133 8 0.08
134 5 0.05
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (130 bp):
AATTTAATAAATTAATCATTTAACCAGGACCTGACATGTGTTAACACATGATCATGACACATGTC
ATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCAAAATTAAATAAA
Found at i:16999 original size:16 final size:18
Alignment explanation
Indices: 16978--17011 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
16968 ATTTCTTATT
16978 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
16994 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
17012 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:18208 original size:20 final size:20
Alignment explanation
Indices: 18179--18232 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
18169 TTTAATTCAC
*
18179 GGAATATAAGATTATCAATA
1 GGAATGTAAGATTATCAATA
* *
18199 GGAATGTAAGATTATTAGTA
1 GGAATGTAAGATTATCAATA
18219 GGAATGTAAGATTA
1 GGAATGTAAGATTA
18233 CTAGATAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.44, C:0.02, G:0.22, T:0.31
Consensus pattern (20 bp):
GGAATGTAAGATTATCAATA
Found at i:19525 original size:26 final size:25
Alignment explanation
Indices: 19490--19542 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 25
19480 AAACGCACCC
*
19490 TTAGGTTAAAAGATTAGTTTTAATA
1 TTAGGTTAAAAGATTAATTTTAATA
*
19515 TTAGGATTAAAATATTAATTTTAATA
1 TTAGG-TTAAAAGATTAATTTTAATA
19541 TT
1 TT
19543 TTATTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (25 bp):
TTAGGTTAAAAGATTAATTTTAATA
Found at i:19803 original size:2 final size:2
Alignment explanation
Indices: 19796--19820 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19786 AAATATTTAA
19796 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 A
19821 AACTAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26764 original size:23 final size:23
Alignment explanation
Indices: 26731--26792 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
26721 TAGATTTAAC
* *
26731 TCGATTGAAGCTTGAACTCGAGT
1 TCGATTTAAGCTTGAACTCAAGT
* *
26754 TTGATTTAAGCTTAAACTCAAGT
1 TCGATTTAAGCTTGAACTCAAGT
*
26777 TCGA-TTAAGCTCGAAC
1 TCGATTTAAGCTTGAAC
26793 ATGAACATTA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 10 0.31
23 22 0.69
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (23 bp):
TCGATTTAAGCTTGAACTCAAGT
Found at i:30518 original size:60 final size:61
Alignment explanation
Indices: 30445--30570 Score: 188
Period size: 60 Copynumber: 2.1 Consensus size: 61
30435 ATGATCTCCT
*
30445 GACTATAAGGTGTTGCTTTGTTAAGTCC-TCCGACTATTAAAAGTTACAAAATAGTC-CTCA
1 GACTATAAGGTGTTACTTTGTTAAGTCCAT-CGACTATTAAAAGTTACAAAATAGTCACTCA
*
30505 GACTAT-AGAGTGTTACTTTGTTGAGTCCATCGACTATTAAAAGTTACAAAATAGTCACTCA
1 GACTATAAG-GTGTTACTTTGTTAAGTCCATCGACTATTAAAAGTTACAAAATAGTCACTCA
30566 -ACTAT
1 GACTAT
30571 TCATATGTCG
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
59 2 0.03
60 54 0.89
61 5 0.08
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (61 bp):
GACTATAAGGTGTTACTTTGTTAAGTCCATCGACTATTAAAAGTTACAAAATAGTCACTCA
Found at i:36429 original size:2 final size:2
Alignment explanation
Indices: 36422--36453 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
36412 ATAATTCTTT
36422 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
36454 ACAATTCTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45263 original size:2 final size:2
Alignment explanation
Indices: 45256--45293 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
45246 TCAAAGAATA
45256 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45294 TAGTACTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45838 original size:2 final size:2
Alignment explanation
Indices: 45831--45859 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
45821 TGTCCAACAT
45831 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 T
45860 TAATAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46974 original size:3 final size:3
Alignment explanation
Indices: 46968--47024 Score: 71
Period size: 3 Copynumber: 18.3 Consensus size: 3
46958 TTTTTTTTAT
*
46968 TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TT- TTGT TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT-A TTA TTA TTA
47014 TTA TTAA TTA T
1 TTA TT-A TTA T
47025 GTTACATATA
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
2 2 0.04
3 39 0.80
4 8 0.16
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:46980 original size:13 final size:13
Alignment explanation
Indices: 46964--47024 Score: 74
Period size: 13 Copynumber: 4.8 Consensus size: 13
46954 GGTCTTTTTT
46964 TTATTTATTATTA
1 TTATTTATTATTA
46977 TTA-TTATTATTTA
1 TTATTTATTA-TTA
46990 TTA-TTATTATT-
1 TTATTTATTATTA
*
47001 TTGTTTATTATTA
1 TTATTTATTATTA
*
47014 TTATTAATTAT
1 TTATTTATTAT
47025 GTTACATATA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
11 2 0.05
12 16 0.38
13 24 0.57
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (13 bp):
TTATTTATTATTA
Found at i:48142 original size:19 final size:19
Alignment explanation
Indices: 48096--48142 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
48086 CATTAATTTG
*
48096 TATATTATGTTTGCTGATAT
1 TATATT-TGGTTGCTGATAT
48116 TATAATTTGGTTG-TGATATT
1 TAT-ATTTGGTTGCTGATA-T
48136 TATATTT
1 TATATTT
48143 ATTTCGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 9 0.38
20 12 0.50
21 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (19 bp):
TATATTTGGTTGCTGATAT
Found at i:52797 original size:16 final size:15
Alignment explanation
Indices: 52775--52838 Score: 65
Period size: 16 Copynumber: 4.0 Consensus size: 15
52765 AGATCCAATT
52775 AAAACAAAGAAAAAG
1 AAAACAAAGAAAAAG
*
52790 AGAAACAAAGAAAAAA
1 A-AAACAAAGAAAAAG
* *
52806 ACAAAGCAAAAAAAAAC
1 A-AAA-CAAAGAAAAAG
52823 AACAACAAAGAAAAAG
1 AA-AACAAAGAAAAAG
52839 CAAAGAACAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
15 1 0.03
16 27 0.68
17 12 0.30
ACGTcount: A:0.78, C:0.11, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAACAAAGAAAAAG
Found at i:53897 original size:4 final size:4
Alignment explanation
Indices: 53880--53944 Score: 64
Period size: 4 Copynumber: 16.2 Consensus size: 4
53870 AATCAAGAAA
*
53880 ACAT ACAT -CAAT ACAT ACAT ACAT ACAA ACAT ACAT -CA- ACCCAT ACAT
1 ACAT ACAT AC-AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A--CAT ACAT
*
53928 ACAT ACAT ATAT ACAT A
1 ACAT ACAT ACAT ACAT A
53945 ACACATGAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
3 3 0.06
4 44 0.86
5 3 0.06
6 1 0.02
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:53918 original size:28 final size:28
Alignment explanation
Indices: 53878--53950 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
53868 CAAATCAAGA
*
53878 AAACATACATCAATACATACATACATAC
1 AAACATACATCAACACATACATACATAC
*
53906 AAACATACATCAACCCATACATACATAC
1 AAACATACATCAACACATACATACATAC
* *
53934 ATATATACAT-AACACAT
1 AAACATACATCAACACAT
53951 GAAATTTGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 6 0.15
28 34 0.85
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (28 bp):
AAACATACATCAACACATACATACATAC
Found at i:54555 original size:102 final size:101
Alignment explanation
Indices: 54378--54679 Score: 376
Period size: 102 Copynumber: 2.9 Consensus size: 101
54368 ATTTGAGAAA
*
54378 TTTAAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGATATACAAATTTCGAATTTGCTTC
1 TTTAAAACAAATT-CGTCTCGCTTGAGACATTTTTCCTTTGA-ATACAAATTTAGAATTTGCTTC
*
54443 ACTTGAAACAAATTAATCTCACTTGAGATTGTTGTTTC
64 ACTTAAAACAAATTAATCTCACTTGAGATTGTTGTTTC
* * *
54481 -TTAAAACAAACTTCATCTCGCTTTAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGCTTC
1 TTTAAAACAAA-TTCGTCTCGCTTGAGACATTTTTCCTTTGA-ATACAAATTTAGAATTTGCTTC
*
54545 ACTTAAAACAATATTAATCTCAATTGAGATTGTTGTTTC
64 ACTTAAAACAA-ATTAATCTCACTTGAGATTGTTGTTTC
* * * *
54584 TTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTCAT-AATACAAATTTAAAAGTTG-TT
1 TTT-AAAACAAA-TTCGTCTCGCTTGAGACATTTTTCCT-TTGAATACAAATTTAGAATTTGCTT
* * *
54647 GTATTTAAAACAAAATTAATATCACTTGAGATT
63 -CACTTAAAAC-AAATTAATCTCACTTGAGATT
54680 TTCAAAGATG
Statistics
Matches: 174, Mismatches: 18, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
102 67 0.39
103 30 0.17
104 42 0.24
105 34 0.20
106 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.40
Consensus pattern (101 bp):
TTTAAAACAAATTCGTCTCGCTTGAGACATTTTTCCTTTGAATACAAATTTAGAATTTGCTTCAC
TTAAAACAAATTAATCTCACTTGAGATTGTTGTTTC
Found at i:54919 original size:26 final size:27
Alignment explanation
Indices: 54883--54934 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
54873 TTTCAAATAA
*
54883 AAATCTTTGAGT-TATTTTTTTTGAAC
1 AAATCTTTGAGTCTATTTCTTTTGAAC
54909 AAATCTTTGAGTCTATTTCTTTTGAA
1 AAATCTTTGAGTCTATTTCTTTTGAA
54935 ACAAGTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.52
Consensus pattern (27 bp):
AAATCTTTGAGTCTATTTCTTTTGAAC
Found at i:55013 original size:28 final size:28
Alignment explanation
Indices: 54967--55025 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
54957 CAATTTCGTG
*
54967 AAAAATCTTGAGTCGTTTCTTTTGAAAC
1 AAAAATCTTGAGTCGTTTCTTTGGAAAC
54995 AAAAATCTTTGAGTC-TTTCTTTGGAAAC
1 AAAAATC-TTGAGTCGTTTCTTTGGAAAC
55023 AAA
1 AAA
55026 TTTTTGTCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 22 0.76
29 7 0.24
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
Consensus pattern (28 bp):
AAAAATCTTGAGTCGTTTCTTTGGAAAC
Found at i:55024 original size:114 final size:119
Alignment explanation
Indices: 54807--55031 Score: 266
Period size: 114 Copynumber: 1.9 Consensus size: 119
54797 AATTTTTGAA
* * * * *
54807 TCTTTTAAAACGATTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATCTTTGAGTTTGTTC
1 TCTTTTAAAACAAGTTTTGTCTCTCTTGAGACAGATTCTCGTGAAACAAATCTTTGAGTGTGTTC
* * *
54872 CTTTCAAATAAAAATCTTTGAGTTATTTTTTTTGAACAAATCTTTGAGTCTATT
66 CTTTCAAACAAAAATCTTTGAGTTATTTCTTTGGAACAAATCTTTGAGTCTATT
*
54926 TCTTTTGAAACAAGTTTTGTCTCTCTTGAGACA-ATT-TCGTG-AA-AAATC-TTGAGTCGT-TT
1 TCTTTTAAAACAAGTTTTGTCTCTCTTGAGACAGATTCTCGTGAAACAAATCTTTGAGT-GTGTT
* * * *
54985 CTTTTGAAACAAAAATCTTTGAG-TCTTTCTTTGGAAACAAATTTTTG
65 CCTTTCAAACAAAAATCTTTGAGTTATTTCTTTGG-AACAAATCTTTG
55032 TCTCTCTTGA
Statistics
Matches: 91, Mismatches: 13, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
113 8 0.09
114 39 0.43
115 6 0.07
116 2 0.02
117 4 0.04
118 2 0.02
119 30 0.33
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.45
Consensus pattern (119 bp):
TCTTTTAAAACAAGTTTTGTCTCTCTTGAGACAGATTCTCGTGAAACAAATCTTTGAGTGTGTTC
CTTTCAAACAAAAATCTTTGAGTTATTTCTTTGGAACAAATCTTTGAGTCTATT
Found at i:55103 original size:65 final size:65
Alignment explanation
Indices: 54982--55104 Score: 162
Period size: 65 Copynumber: 1.9 Consensus size: 65
54972 TCTTGAGTCG
*
54982 TTTCTTTTGAAACAAAAATCTTTGAGTCTTTCTTTGGAAACAAATTTTTGTCTCTCTTGAGACAA
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTTTCTTTGAAAACAAATTTTTGTCTCTCTTGAGACAA
* **
55047 TTTCTTTTGAGA-AAAAATCTTTGAGTCTGTTTCTCTT-AAAATGAA-TTTTGTCTCTCTT
1 TTTCTTTTGAAACAAAAATCTTTGAGTC--TTTCT-TTGAAAACAAATTTTTGTCTCTCTT
55105 AAAACAAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
64 15 0.29
65 24 0.47
66 10 0.20
67 2 0.04
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (65 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTCTTTCTTTGAAAACAAATTTTTGTCTCTCTTGAGACAA
Found at i:55159 original size:28 final size:30
Alignment explanation
Indices: 55097--55170 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 30
55087 ATGAATTTTG
* *
55097 TCTC-TCTTAAAACAAATTTTTGAGTCTGT
1 TCTCTTCTTAAAACAAATATTTGAGTCTAT
* *
55126 TCTCTTCTTAACA-AAATATTTGAGTTTAT
1 TCTCTTCTTAAAACAAATATTTGAGTCTAT
*
55155 T-TCTT-TAAAAACAAAT
1 TCTCTTCTTAAAACAAAT
55171 TGTGTCCTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
27 4 0.11
28 8 0.22
29 18 0.49
30 7 0.19
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.45
Consensus pattern (30 bp):
TCTCTTCTTAAAACAAATATTTGAGTCTAT
Found at i:55363 original size:66 final size:64
Alignment explanation
Indices: 55257--55378 Score: 183
Period size: 66 Copynumber: 1.9 Consensus size: 64
55247 GATGTAATCC
*
55257 ATCTTTGAGTATATTTCTTTGGAAACAAATTTTTGTCTCTCTTGAGACAATTTCTTTTGAGAAAA
1 ATCTTTGAGTATATTTCTTTGGAAACAAAATTTTGTCTCTC--GAGACAATTTCTTTTGAGAAAA
55322 A
64 A
* *
55323 ATCTTTGAGTTTGTTTCCTTT-GAAACAAAATTTTGTCTCTCGAGACAATTTCTTTT
1 ATCTTTGAGTATATTT-CTTTGGAAACAAAATTTTGTCTCTCGAGACAATTTCTTTT
55379 AAAACTACCC
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
64 15 0.29
66 33 0.63
67 4 0.08
ACGTcount: A:0.27, C:0.14, G:0.13, T:0.46
Consensus pattern (64 bp):
ATCTTTGAGTATATTTCTTTGGAAACAAAATTTTGTCTCTCGAGACAATTTCTTTTGAGAAAAA
Found at i:55503 original size:31 final size:31
Alignment explanation
Indices: 55437--55511 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
55427 CCTTGAGGCA
* *
55437 GTTTCTCTAGAAATACAAAATCTTTGAGTTT
1 GTTTCTCTTGAAATACAAAATCTTTGAGTTC
*
55468 GTTTCTCTTGAAATA-AAACCATTTTTGAG-TC
1 GTTTCTCTTGAAATACAAA--ATCTTTGAGTTC
*
55499 GTTTCACTTGAAA
1 GTTTCTCTTGAAA
55512 CATTTTCTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 3 0.08
31 27 0.71
32 8 0.21
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (31 bp):
GTTTCTCTTGAAATACAAAATCTTTGAGTTC
Found at i:55523 original size:15 final size:15
Alignment explanation
Indices: 55500--55543 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
55490 TTTTGAGTCG
*
55500 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
55515 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
*
55530 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
55544 AGATCATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:55653 original size:28 final size:29
Alignment explanation
Indices: 55596--55653 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
55586 CCTTAAAACA
* *
55596 ATTTCTTTTGAAGAAAAATCTTTGAGTCT
1 ATTTCTTTGGAAGAAAAATCTTTGACTCT
*
55625 ATTTCTTTGGAA-ACAAAAT-TTTGTCTCT
1 ATTTCTTTGGAAGA-AAAATCTTTGACTCT
55653 A
1 A
55654 AGATACAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (29 bp):
ATTTCTTTGGAAGAAAAATCTTTGACTCT
Found at i:55918 original size:66 final size:63
Alignment explanation
Indices: 55844--56021 Score: 180
Period size: 66 Copynumber: 2.7 Consensus size: 63
55834 CAAAACAAAT
*
55844 ATCTTTGAGATCGTTTCCCTTGAAATGAATTTTGTCTCATTTGAGACAATTTCCCATGAAACAT-
1 ATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTC-TTTGAGACAA-TTCCC-TGAAA-ATG
*
55908 CG
62 CC
* * * * **
55910 ATCTTTGAGAACGTTTCCCTTAAAAACAAATTTTGTCTCGCTTGAGACAATTCCCTTTAAATGCC
1 ATCTTTGAGATCGTTTCCCTT-GAAACGAATTTTGTCTC-TTTGAGACAATTCCCTGAAAATGCC
* * *
55975 ATCTTTG-GGTTGTTTCCTTTGAAACGAATTTTGTCTCTTTCGAGACA
1 ATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTTT-GAGACA
56022 GTTGCTTTTG
Statistics
Matches: 93, Mismatches: 16, Indels: 9
0.79 0.14 0.08
Matches are distributed among these distances:
62 2 0.02
63 21 0.23
64 11 0.12
65 11 0.12
66 25 0.27
67 23 0.25
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (63 bp):
ATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTTTGAGACAATTCCCTGAAAATGCC
Found at i:56515 original size:130 final size:134
Alignment explanation
Indices: 56235--56517 Score: 396
Period size: 134 Copynumber: 2.1 Consensus size: 134
56225 CATAGGAACC
* * *
56235 GTGTCATCCCCTGACCAGATCTCCTCATCATGTAGGAGCCATGTCAACCATAGATAACCAGCCGT
1 GTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCATGTCAACCATAGATAACCAACCGT
* * *
56300 CCTCATCACATAGGAACCGTGTTATCGCCCTACCTAAAGATGGCCAGAACTCTTCATCACGTATG
66 CATCATCACATAGGAACCGTGTTATCACCCTACCTAAAGATGACCAGAACTCTTCATCACGTATG
56365 AGCA
131 AGCA
* * * *
56369 GTGCCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCGTGTCATCC-TAGATAATCAACCGT
1 GTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCATGTCAACCATAGATAACCAACCGT
* * *
56433 CATCATCACGTAGGAATCGTGTT-TCACTCCT-CCTAAAG-TGACCAGAA-TCTTCATCATGTAT
66 CATCATCACATAGGAACCGTGTTATCAC-CCTACCTAAAGATGACCAGAACTCTTCATCACGTAT
56494 GAGCA
130 GAGCA
*
56499 GTGTCATCCCTTGACCAGA
1 GTGTCATCCCCTGACCAGA
56518 TTTTTCATCA
Statistics
Matches: 133, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
130 35 0.26
131 8 0.06
132 10 0.08
133 36 0.27
134 44 0.33
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (134 bp):
GTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCATGTCAACCATAGATAACCAACCGT
CATCATCACATAGGAACCGTGTTATCACCCTACCTAAAGATGACCAGAACTCTTCATCACGTATG
AGCA
Found at i:56745 original size:3 final size:3
Alignment explanation
Indices: 56739--56792 Score: 56
Period size: 3 Copynumber: 17.3 Consensus size: 3
56729 CTTTTTTTAT
* *
56739 TTA TTA TTA TTA GTA TTTA TTA TTA TTA TT- TTGT TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
56785 TTAA TTA T
1 TT-A TTA T
56793 GTTACATATA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
2 2 0.05
3 35 0.80
4 7 0.16
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:71903 original size:2 final size:2
Alignment explanation
Indices: 71896--71931 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
71886 GATAAGAGGG
71896 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
71932 AATAGGTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:72492 original size:5 final size:5
Alignment explanation
Indices: 72482--72513 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
72472 ATCTTAAATT
72482 TTATA TTATA TTATA TTATA TTA-A TT-TA TTAT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTAT
72514 TATTTTGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 6 0.24
5 19 0.76
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:72738 original size:60 final size:60
Alignment explanation
Indices: 72667--72781 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
72657 ACGAGAGAAA
* * * * *
72667 AAAAATAATGATGACGAGTTTATGTAGAT-CAATAAAGGTGATAATGGCTAAGGTTGAGGT
1 AAAAATAATGATAACAAGTTTATGTAG-TCCAATAAAGATGATAACGCCTAAGGTTGAGGT
* * *
72727 AAAAATGATGATAATAAGTTTATGTAGTCCAATAAAGATGGTAACGCCTAAGGTT
1 AAAAATAATGATAACAAGTTTATGTAGTCCAATAAAGATGATAACGCCTAAGGTT
72782 TAAAGATAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 1 0.02
60 45 0.98
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.29
Consensus pattern (60 bp):
AAAAATAATGATAACAAGTTTATGTAGTCCAATAAAGATGATAACGCCTAAGGTTGAGGT
Found at i:73159 original size:2 final size:2
Alignment explanation
Indices: 73152--73177 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
73142 CAGTATTTTA
73152 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
73178 GTATTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73262 original size:19 final size:19
Alignment explanation
Indices: 73227--73265 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
73217 AAACTTTTAT
*
73227 TTTTTATATAATAAAATTA
1 TTTTTATAAAATAAAATTA
73246 TTTTTATAAAA-ATAAATTA
1 TTTTTATAAAATA-AAATTA
73265 T
1 T
73266 ATTTGTGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 17 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTTTATAAAATAAAATTA
Found at i:84103 original size:17 final size:18
Alignment explanation
Indices: 84065--84103 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
84055 TTTCAATAAG
84065 AAATATATAGAAAAAATA
1 AAATATATAGAAAAAATA
* *
84083 AAATATAT-GATAAAATT
1 AAATATATAGAAAAAATA
84100 AAAT
1 AAAT
84104 TTCCAGGGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (18 bp):
AAATATATAGAAAAAATA
Done.