Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001884.1 Hibiscus syriacus cultivar Beakdansim tig00003825_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: 109377
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:951 original size:2 final size:2
Alignment explanation
Indices: 944--986 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
934 TTATGCTTGA
944 AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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 AT AT
985 AT
1 AT
987 CATCTTCTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3126 original size:20 final size:21
Alignment explanation
Indices: 3084--3126 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
3074 GTTAATAATA
* **
3084 TTAACATTTATATATTATTTT
1 TTAAAATTTATATATTAGATT
3105 TTAAAATTTA-ATATTAGATT
1 TTAAAATTTATATATTAGATT
3125 TT
1 TT
3127 TCATGTACTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTAAAATTTATATATTAGATT
Found at i:3126 original size:21 final size:21
Alignment explanation
Indices: 3084--3127 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3074 GTTAATAATA
* *
3084 TTAACATTTATATATTATTTT
1 TTAAAATTTATATATTAATTT
3105 TTAAAATTTA-ATATTAGATTT
1 TTAAAATTTATATATTA-ATTT
3126 TT
1 TT
3128 CATGTACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTAAAATTTATATATTAATTT
Found at i:13795 original size:14 final size:14
Alignment explanation
Indices: 13772--13809 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
13762 TTCAAGATCG
*
13772 ATTGACTCAACACA
1 ATTGATTCAACACA
13786 ATTGATTCAACACA
1 ATTGATTCAACACA
13800 ATTGATTCAA
1 ATTGATTCAA
13810 ATTCTTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (14 bp):
ATTGATTCAACACA
Found at i:20309 original size:21 final size:20
Alignment explanation
Indices: 20223--20380 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
20213 AAATGACCAA
**
20223 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
20242 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
20262 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
20282 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
20303 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
20324 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
20344 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
20365 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
20381 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:20373 original size:20 final size:20
Alignment explanation
Indices: 20348--20540 Score: 246
Period size: 20 Copynumber: 9.6 Consensus size: 20
20338 GATTTTCCAG
* ** *
20348 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
20368 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
20388 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
20408 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
20428 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
20448 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
20468 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
20488 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
20509 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
20529 AATCGCAACGCG
1 AATCGCAACGCG
20541 GTTTTTAAAG
Statistics
Matches: 151, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 131 0.87
21 19 0.13
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:20948 original size:33 final size:33
Alignment explanation
Indices: 20909--20979 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
20899 TTCACTTAGA
20909 TTTCATTTCGCGTTG-TGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTGCT-ATTCTCTCGTTGCGAT
20942 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
20975 TTTCA
1 TTTCA
20980 AGTTAGTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 36 0.97
34 1 0.03
ACGTcount: A:0.10, C:0.23, G:0.18, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
Found at i:21085 original size:21 final size:21
Alignment explanation
Indices: 21059--21135 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
21049 TGCAGAAGAG
21059 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
* **
21080 TCGCAACGCGA-AAATGACTA
1 TCGCAACGAGAGAAATGAAAA
21100 TCTGCAACGAGAGAAATGAAAA
1 TC-GCAACGAGAGAAATGAAAA
21122 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
21136 TCGCAACGCG
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 9 0.19
21 30 0.62
22 9 0.19
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:21139 original size:14 final size:14
Alignment explanation
Indices: 21120--21176 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
21110 GAGAAATGAA
21120 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
21134 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
21153 AATCGCAACGAGAG
1 AATCGCAACGAGAG
21167 AATCGCAACG
1 AATCGCAACG
21177 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:21150 original size:33 final size:33
Alignment explanation
Indices: 21112--21192 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
21102 TGCAACGAGA
21112 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
21145 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
21178 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
21193 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:21229 original size:14 final size:14
Alignment explanation
Indices: 21210--21266 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
21200 TTTCATTTCG
21210 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
21224 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
21243 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
21257 CGTTGCGATT
1 CGTTGCGATT
21267 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:21235 original size:33 final size:33
Alignment explanation
Indices: 21193--21315 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
21183 CAAAATCGCA
21193 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
21226 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
21259 TTGCGATTTTCATTTCTCTCGTTGCGATAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTTGC----G--ATTCTCTCG
21300 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
21316 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 8 0.10
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:21277 original size:21 final size:21
Alignment explanation
Indices: 21251--21315 Score: 105
Period size: 21 Copynumber: 3.1 Consensus size: 21
21241 CGCGTTGCGA
21251 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
21272 TTCTCTCGTTGCGATAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
21292 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
21313 TTC
1 TTC
21316 AACCAAAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 18 0.46
21 21 0.54
ACGTcount: A:0.11, C:0.25, G:0.15, T:0.49
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:23323 original size:33 final size:33
Alignment explanation
Indices: 23275--23369 Score: 154
Period size: 33 Copynumber: 2.9 Consensus size: 33
23265 AACGCGAAAC
**
23275 CAAAATCGCAACGCGAAATGAAAATCGCAACGA
1 CAAAATCGCAACGCGAAACCAAAATCGCAACGA
* *
23308 CAGAATCGCATCGCGAAACCAAAATCGCAACGA
1 CAAAATCGCAACGCGAAACCAAAATCGCAACGA
23341 CAAAATCGCAACGCGAAACCAAAATCGCA
1 CAAAATCGCAACGCGAAACCAAAATCGCA
23370 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.08
Consensus pattern (33 bp):
CAAAATCGCAACGCGAAACCAAAATCGCAACGA
Found at i:23344 original size:14 final size:14
Alignment explanation
Indices: 23327--23353 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
23317 ATCGCGAAAC
23327 CAAAATCGCAACGA
1 CAAAATCGCAACGA
23341 CAAAATCGCAACG
1 CAAAATCGCAACG
23354 CGAAACCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.30, G:0.15, T:0.07
Consensus pattern (14 bp):
CAAAATCGCAACGA
Found at i:23367 original size:52 final size:52
Alignment explanation
Indices: 23241--23375 Score: 141
Period size: 52 Copynumber: 2.6 Consensus size: 52
23231 TAGTTTACTT
** * *
23241 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCATCGCGAAACCAAAATCGCAACGCAAAA
* * *
23293 T-G-AAAATCGCAACGACAGAATCGCATCGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACA-CGAAAC-ACAAAATCGCATCGCGAAACCAAAATCGCAACG-CAAAA
* *
23346 TCGCAACGCGAAAC-CAAAATCGCATTGCGA
1 TCGCAACACGAAACACAAAATCGCATCGCGA
23376 TTTTCATTTC
Statistics
Matches: 66, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
50 3 0.05
51 6 0.09
52 44 0.67
53 5 0.08
54 6 0.09
55 2 0.03
ACGTcount: A:0.44, C:0.28, G:0.17, T:0.10
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCATCGCGAAACCAAAATCGCAACGCAAAA
Found at i:23375 original size:19 final size:19
Alignment explanation
Indices: 23241--23369 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
23231 TAGTTTACTT
* *
23241 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
23261 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
23280 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
23299 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
*
23313 TCGCATCGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
23332 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAACCAAAA
23346 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
23365 TCGCA
1 TCGCA
23370 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:23387 original size:19 final size:19
Alignment explanation
Indices: 23365--23521 Score: 154
Period size: 19 Copynumber: 8.8 Consensus size: 19
23355 GAAACCAAAA
*
23365 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
23384 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
23398 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
23417 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
23433 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
23450 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
23469 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
23488 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
23507 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
23522 AAGTTTCGTG
Statistics
Matches: 113, Mismatches: 15, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
14 17 0.15
16 8 0.07
17 8 0.07
19 80 0.71
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:23406 original size:14 final size:14
Alignment explanation
Indices: 23387--23443 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
23377 TTTCATTTCG
23387 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
23401 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
23418 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
23434 CGTTGCGATT
1 CGTTGCGATT
23444 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:23412 original size:33 final size:33
Alignment explanation
Indices: 23370--23462 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
23360 CAAAATCGCA
23370 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
23403 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
23436 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
23463 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:0.22, G:0.22, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:23495 original size:38 final size:38
Alignment explanation
Indices: 23365--23521 Score: 163
Period size: 33 Copynumber: 4.4 Consensus size: 38
23355 GAAACCAAAA
*
23365 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
23400 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* **
23433 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
** *
23469 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
23507 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
23522 AAGTTTCGTG
Statistics
Matches: 104, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 52 0.50
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.42
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
Found at i:25479 original size:14 final size:14
Alignment explanation
Indices: 25460--25495 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
25450 ATTGTTTAAT
25460 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
25474 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
25488 TGATTTGT
1 TGATTTGT
25496 TTAATTGATG
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:25619 original size:20 final size:19
Alignment explanation
Indices: 25602--25700 Score: 136
Period size: 19 Copynumber: 5.4 Consensus size: 19
25592 AAAAATGACT
25602 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
25622 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
25641 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
25655 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
25674 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
25694 ATCGCAA
1 ATCGCAA
25701 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 29 0.41
20 26 0.37
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:25732 original size:53 final size:53
Alignment explanation
Indices: 25602--25719 Score: 220
Period size: 53 Copynumber: 2.2 Consensus size: 53
25592 AAAAATGACT
25602 ATCGCAATGCGGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
25655 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
25708 ATCGCAATGCGA
1 ATCGCAATGCGA
25720 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
52 19 0.30
53 45 0.70
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:25772 original size:14 final size:14
Alignment explanation
Indices: 25753--25788 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
25743 CATTTCCGCA
25753 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
25767 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
25781 TTGCGATT
1 TTGCGATT
25789 TTCATTTCGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.08, C:0.25, G:0.22, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:25835 original size:53 final size:52
Alignment explanation
Indices: 25733--25946 Score: 250
Period size: 53 Copynumber: 4.2 Consensus size: 52
25723 TCATTTCGCA
*
25733 TTGCGATTTTCATTTCCGCATTGCGA--TTC-TCTCG--TTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
25781 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
* *
25834 TTGCGATTTTCATTTTGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG
*
25890 CATTGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
25939 TTGCGATT
1 TTGCGATT
25947 GTAATTTCCG
Statistics
Matches: 149, Mismatches: 5, Indels: 25
0.83 0.03 0.14
Matches are distributed among these distances:
47 18 0.12
48 15 0.10
49 5 0.03
50 4 0.03
51 5 0.03
52 10 0.07
53 71 0.48
54 3 0.02
55 3 0.02
56 3 0.02
58 12 0.08
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:25898 original size:72 final size:72
Alignment explanation
Indices: 25715--25932 Score: 340
Period size: 72 Copynumber: 3.1 Consensus size: 72
25705 AGAATCGCAA
25715 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGA--TTC--
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
* *
25776 TCT-CGT
66 TTTGCAT
25782 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
25847 TTTGCAT
66 TTTGCAT
* *
25854 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCA
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGTTGCGATTTTCA
*
25918 TTTCGCAT
65 TTTTGCAT
25926 TGCGATT
1 TGCGATT
25933 CTCTCGTTGC
Statistics
Matches: 140, Mismatches: 5, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
67 58 0.41
69 3 0.02
71 2 0.01
72 76 0.54
73 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (72 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTTGCAT
Found at i:28247 original size:12 final size:12
Alignment explanation
Indices: 28230--28254 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28220 TCTTCGGGGA
28230 CTTTTTCTTCTT
1 CTTTTTCTTCTT
28242 CTTTTTCTTCTT
1 CTTTTTCTTCTT
28254 C
1 C
28255 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:29196 original size:20 final size:20
Alignment explanation
Indices: 29168--29396 Score: 239
Period size: 20 Copynumber: 11.4 Consensus size: 20
29158 AAATTTCAGT
* * * *
29168 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
29188 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
29208 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
29228 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
*
29248 GTTGTGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
29268 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
29288 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
29308 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
29328 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
29348 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
29368 GTTGCGATTTTCTTATTCGC
1 GTTGCGATTTACGGATACGC
29388 GTTGCGATT
1 GTTGCGATT
29397 CTGGAAAATC
Statistics
Matches: 181, Mismatches: 22, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
19 3 0.02
20 175 0.97
21 3 0.02
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:34588 original size:24 final size:23
Alignment explanation
Indices: 34535--34596 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
34525 TTAATATTTC
* *
34535 TATTATAACTTTTTTTTGAATTA
1 TATTAAAACTTTTATTTGAATTA
*
34558 TAATAAAACTTTTATTT-AATCGTA
1 TATTAAAACTTTTATTTGAAT--TA
*
34582 TATTAAAACTATTAT
1 TATTAAAACTTTTAT
34597 ACGTTATACA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
22 3 0.09
23 14 0.44
24 15 0.47
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (23 bp):
TATTAAAACTTTTATTTGAATTA
Found at i:35799 original size:2 final size:2
Alignment explanation
Indices: 35792--35880 Score: 57
Period size: 2 Copynumber: 48.0 Consensus size: 2
35782 TTGGTATGAG
* * * *
35792 TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- 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
* * * *
35832 TA TA TA TA TA T- TA -A TT TA AA T- TA AA TT TA T- TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35869 TA TA TA TA TA TA
1 TA TA TA TA TA TA
35881 ATAATTATTT
Statistics
Matches: 64, Mismatches: 16, Indels: 14
0.68 0.17 0.15
Matches are distributed among these distances:
1 7 0.11
2 57 0.89
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:39970 original size:21 final size:21
Alignment explanation
Indices: 39936--39976 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
39926 GGTAGAATCC
*
39936 AATATTAACATTTTTTGTAGA
1 AATATTAACATTTTATGTAGA
**
39957 AATATTAATGTTTTATGTAG
1 AATATTAACATTTTATGTAG
39977 CGTTTTACCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (21 bp):
AATATTAACATTTTATGTAGA
Found at i:63594 original size:41 final size:41
Alignment explanation
Indices: 63537--63618 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
63527 AAACTTGAAG
63537 TTAGTACATTTTTGTATTTACTGGTTTGATAAGGAAGGTCA
1 TTAGTACATTTTTGTATTTACTGGTTTGATAAGGAAGGTCA
63578 TTAGTACATTTTTGTATTTACTGGTTTGATAAGGAAGGTCA
1 TTAGTACATTTTTGTATTTACTGGTTTGATAAGGAAGGTCA
63619 CCTGCTCACC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.27, C:0.07, G:0.22, T:0.44
Consensus pattern (41 bp):
TTAGTACATTTTTGTATTTACTGGTTTGATAAGGAAGGTCA
Found at i:66754 original size:21 final size:20
Alignment explanation
Indices: 66728--66826 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
66718 AATCAGTTTC
66728 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
66749 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
66770 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
66790 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
66811 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
66827 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 16 0.26
21 45 0.74
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:66858 original size:20 final size:20
Alignment explanation
Indices: 66793--67062 Score: 242
Period size: 20 Copynumber: 13.5 Consensus size: 20
66783 CGATTTTCCA
* ** *
66793 AAATCGCAACGCGAATATGA
1 AAATCGCAACGTGAATCCGT
* *
66813 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGTGAATC-CGT
*
66833 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGTGAATCCGT
* *
66853 ATATCGCAACGTGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
66873 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * * *
66893 ATATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
66913 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
66933 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
66953 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
66973 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
66993 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
67013 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
67033 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
*
67053 AAATCACAAC
1 AAATCGCAAC
67063 ACTGAAATTT
Statistics
Matches: 215, Mismatches: 27, Indels: 16
0.83 0.10 0.06
Matches are distributed among these distances:
20 214 1.00
21 1 0.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (20 bp):
AAATCGCAACGTGAATCCGT
Found at i:67981 original size:12 final size:12
Alignment explanation
Indices: 67964--67988 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
67954 ATATAATCCT
67964 GAAGAAGAAAAA
1 GAAGAAGAAAAA
67976 GAAGAAGAAAAA
1 GAAGAAGAAAAA
67988 G
1 G
67989 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:70328 original size:33 final size:33
Alignment explanation
Indices: 70291--70361 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
70281 AGAATCGCAA
*
70291 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
1 TGCGAAATGAAAATCGCATTACGATTCTCTCGT
** ** **
70324 TGCGATTTTCATTTCGCATTACGATTCTCTCGT
1 TGCGAAATGAAAATCGCATTACGATTCTCTCGT
70357 TGCGA
1 TGCGA
70362 TTTTCATTTC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.37
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTACGATTCTCTCGT
Found at i:70362 original size:33 final size:33
Alignment explanation
Indices: 70304--70382 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
70294 GAAATGAAAA
70304 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
70337 TCGCATTACGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
70370 TCGCATTGCGATT
1 TCGCATTGCGATT
70383 TTCATTTCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (33 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:70380 original size:19 final size:19
Alignment explanation
Indices: 70323--70400 Score: 103
Period size: 19 Copynumber: 4.4 Consensus size: 19
70313 GATTCTCTCG
70323 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
70342 TTACGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
70356 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
70375 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
70394 TTGCGAT
1 TTGCGAT
70401 AGTCAATTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
14 5 0.10
16 7 0.14
17 7 0.14
19 31 0.62
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:70534 original size:13 final size:14
Alignment explanation
Indices: 70507--70542 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
70497 CATCAATTAC
70507 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
70521 ACAAATCATC-TTT
1 ACAAATCAACTTTT
70534 ACAAATCAA
1 ACAAATCAA
70543 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:72542 original size:14 final size:14
Alignment explanation
Indices: 72523--72579 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
72513 GCGAAATGAA
*
72523 AATCGCAACGACAG
1 AATCGCAACGAAAG
72537 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
72554 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
72570 AATCGCAACG
1 AATCGCAACG
72580 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:72550 original size:33 final size:33
Alignment explanation
Indices: 72504--72596 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
72494 GCGAAACCAA
*
72504 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
72537 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
72570 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
72597 TGCGATTTTG
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:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:72561 original size:19 final size:19
Alignment explanation
Indices: 72467--72601 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
72457 TAGTTTACTT
* *
72467 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
72487 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
72506 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
72525 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
72539 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
72558 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
72572 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
72591 TCGCAATGCGA
1 TCGCAACGCGA
72602 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:72619 original size:19 final size:19
Alignment explanation
Indices: 72597--72725 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
72587 AAAATCGCAA
72597 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
72616 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
72630 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
72649 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
72663 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
72682 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
72701 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
72721 TGCGA
1 TGCGA
72726 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:72639 original size:33 final size:33
Alignment explanation
Indices: 72597--72688 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
72587 AAAATCGCAA
72597 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
72630 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
72663 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
72689 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:72928 original size:93 final size:93
Alignment explanation
Indices: 72769--73335 Score: 1098
Period size: 93 Copynumber: 6.1 Consensus size: 93
72759 TTGAATGGAT
72769 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
72834 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
* *
72862 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACGGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
72927 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
72955 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
73020 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
73048 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
73113 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
73141 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
73206 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
73234 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
73299 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
73327 AAATTTACT
1 AAATTTACT
73336 AAGCAATCTA
Statistics
Matches: 467, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 467 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:75061 original size:14 final size:14
Alignment explanation
Indices: 75042--75131 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
75032 TTGAAATGAA
75042 AATCGCAACGAGAG
1 AATCGCAACGAGAG
75056 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
75073 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
75089 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
75108 AATCGCAACGAGAG
1 AATCGCAACGAGAG
75122 AATCGCAACG
1 AATCGCAACG
75132 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:75079 original size:33 final size:33
Alignment explanation
Indices: 75034--75148 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
75024 TCTTTTGGTT
75034 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
75067 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
75100 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
75133 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
75149 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:75080 original size:19 final size:18
Alignment explanation
Indices: 75041--75153 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
75031 GTTGAAATGA
75041 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
75056 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
75073 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
75089 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
75106 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
75122 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
75139 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
75154 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:75184 original size:14 final size:14
Alignment explanation
Indices: 75165--75221 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
75155 TTTGGTTTCG
75165 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
75179 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
75198 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
75212 CGTTGCGATT
1 CGTTGCGATT
75222 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:75197 original size:33 final size:33
Alignment explanation
Indices: 75149--75229 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
75139 AAAATCGCAA
**
75149 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
75182 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
75215 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
75230 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:75232 original size:21 final size:21
Alignment explanation
Indices: 75206--75281 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
75196 CGCGTTGCGA
75206 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
75227 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
75247 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
75268 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
75282 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:75262 original size:41 final size:41
Alignment explanation
Indices: 75205--75282 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
75195 TCGCGTTGCG
*
75205 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
75246 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
75283 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:75408 original size:33 final size:33
Alignment explanation
Indices: 75361--75431 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
75351 AATACTAACT
* *
75361 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
75394 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
75427 TGAAA
1 TGAAA
75432 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:75665 original size:22 final size:22
Alignment explanation
Indices: 75613--75667 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
75603 TGGTTGTGAG
**
75613 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
75635 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
75657 GGATTTCTTCG
1 GGATTTCTTCG
75668 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:75838 original size:20 final size:20
Alignment explanation
Indices: 75813--76006 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
75803 CTTTAAATAT
75813 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
75833 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
75855 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
75874 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
75894 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
75914 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
75934 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
75954 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
75974 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
75994 CGCGTTGCGATTT
1 CGCGTTGCGATTT
76007 TCCAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:76000 original size:60 final size:60
Alignment explanation
Indices: 75813--76006 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
75803 CTTTAAATAT
**
75813 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
75874 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
75934 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
75994 CGCGTTGCGATTT
1 CGCGTTGCGATTT
76007 TCCAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:92662 original size:17 final size:18
Alignment explanation
Indices: 92619--92659 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
92609 GAATTATATT
92619 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
92636 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
92654 ATTAAA
1 AGTAAA
92660 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:98538 original size:24 final size:23
Alignment explanation
Indices: 98511--98566 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 23
98501 CAAATAAGAT
*
98511 ATCAGAACAGAATCCAGATCATAA
1 ATCAGAACAAAATCCAGATCA-AA
* * *
98535 ATCAGAACAAAATTCATATCAGA
1 ATCAGAACAAAATCCAGATCAAA
98558 ATCAGAACA
1 ATCAGAACA
98567 TAATTCAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 10 0.36
24 18 0.64
ACGTcount: A:0.52, C:0.20, G:0.11, T:0.18
Consensus pattern (23 bp):
ATCAGAACAAAATCCAGATCAAA
Found at i:98584 original size:47 final size:48
Alignment explanation
Indices: 98492--98587 Score: 113
Period size: 47 Copynumber: 2.0 Consensus size: 48
98482 CAGAAAATAA
* * *
98492 AACAGAATTCAAATAAGATATCAGAACAGAATCCAGATCATAAATCAG
1 AACAAAATTCAAATAAGATATCAGAACAGAATCCAAATCAGAAATCAG
* * * * *
98540 AACAAAATTCATATCAGA-ATCAGAACATAATTCAAATCGGAAATCAG
1 AACAAAATTCAAATAAGATATCAGAACAGAATCCAAATCAGAAATCAG
98587 A
1 A
98588 TAAAACAATC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
47 25 0.62
48 15 0.38
ACGTcount: A:0.52, C:0.17, G:0.11, T:0.20
Consensus pattern (48 bp):
AACAAAATTCAAATAAGATATCAGAACAGAATCCAAATCAGAAATCAG
Found at i:106083 original size:51 final size:51
Alignment explanation
Indices: 106023--106119 Score: 158
Period size: 51 Copynumber: 1.9 Consensus size: 51
106013 ATTTAACCTT
*
106023 TGAATATGACACATTACGAATAGGGAATAATTTAGAAAAATGTTAAATGAA
1 TGAATATGACACATTACGAATAGGGAATAATTTAGAAAAAGGTTAAATGAA
* **
106074 TGAATATGACACGTTGTGAATAGGGAATAATTTAGAAAAAGGTTAA
1 TGAATATGACACATTACGAATAGGGAATAATTTAGAAAAAGGTTAA
106120 GGGAGAGAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.46, C:0.05, G:0.21, T:0.28
Consensus pattern (51 bp):
TGAATATGACACATTACGAATAGGGAATAATTTAGAAAAAGGTTAAATGAA
Found at i:106406 original size:24 final size:24
Alignment explanation
Indices: 106371--106424 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
106361 AGAGAAAGAG
106371 AAGAGA-TCGAGAGAGGGAACGGGA
1 AAGAGAGT-GAGAGAGGGAACGGGA
* * *
106395 TAGAGAGTGAGATATGGAACGGGA
1 AAGAGAGTGAGAGAGGGAACGGGA
106419 AAGAGA
1 AAGAGA
106425 AAGAGATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.43, C:0.06, G:0.43, T:0.09
Consensus pattern (24 bp):
AAGAGAGTGAGAGAGGGAACGGGA
Found at i:106430 original size:24 final size:24
Alignment explanation
Indices: 106386--106431 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
106376 ATCGAGAGAG
* **
106386 GGAACGGGATAGAGAGTGAGATAT
1 GGAACGGGAAAGAGAAAGAGATAT
106410 GGAACGGGAAAGAGAAAGAGAT
1 GGAACGGGAAAGAGAAAGAGAT
106432 CGCTTGAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.43, C:0.04, G:0.41, T:0.11
Consensus pattern (24 bp):
GGAACGGGAAAGAGAAAGAGATAT
Found at i:106882 original size:12 final size:12
Alignment explanation
Indices: 106865--106896 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
106855 CTTTCTTCGA
106865 AACGCCTCGCCT
1 AACGCCTCGCCT
106877 AACGCCTCGCCT
1 AACGCCTCGCCT
106889 AACGCCTC
1 AACGCCTC
106897 AGGCGCGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.19, C:0.50, G:0.16, T:0.16
Consensus pattern (12 bp):
AACGCCTCGCCT
Done.