Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005824.1 Hibiscus syriacus cultivar Beakdansim tig00013646_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: 69911
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:77 original size:47 final size:47
Alignment explanation
Indices: 6--101 Score: 122
Period size: 47 Copynumber: 2.0 Consensus size: 47
1 CAAAA
* *
6 TATATATATCAATTGATACGTCGCTTCAAATTATTCAACAATATAATAT
1 TATATATATC-ATTGATACATCGCTTCAAATGATTCAACAATAT-ATAT
* * *
55 TATATATATC-TTGATGCATCGCTTCAAATGATTTAATAATATATAT
1 TATATATATCATTGATACATCGCTTCAAATGATTCAACAATATATAT
101 T
1 T
102 GTCACATTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
46 5 0.12
47 27 0.64
49 10 0.24
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (47 bp):
TATATATATCATTGATACATCGCTTCAAATGATTCAACAATATATAT
Found at i:1142 original size:2 final size:2
Alignment explanation
Indices: 1137--1186 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
1127 TATATTTAAT
* * *
1137 TC TC TC -C TC TC TC CC TC TC CC TC TC CC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1178 TC TC TC TC T
1 TC TC TC TC T
1187 TAAATTATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (2 bp):
TC
Found at i:2356 original size:156 final size:157
Alignment explanation
Indices: 2038--2377 Score: 492
Period size: 156 Copynumber: 2.2 Consensus size: 157
2028 TTCCTCCTCC
*
2038 ATTTTAAG-TCTATTTTTTACAAAATTTGAACCACATGCTCCTAAACCATAGTAGAATACATGTG
1 ATTTTAAGTTCT-TTTTTTACCAAATTTGAACCACATGCTCCTAAACCATAGTA-AATACATGTG
2102 TACTTTCAATTCATCTTTTTGATAACAAATTTTTTATTTTTCAATTTAGTCCTTCAATTATTCAT
64 TACTTTCAATTCATCTTTTTGATAACAAATTTTTTATTTTTCAATTTAGTCCTTCAATTATTCAT
* * *
2167 AGTCTCCTTATTTCTTCAATTCATCATTT
129 AATATCCTTATTCCTTCAATTCATCATTT
*
2196 -TTTTAAGTTCGTTTTTTTACCAAATTTGAGCCACATGCTCCTAAACCATAGT-AATACATGTGT
1 ATTTTAAGTTC-TTTTTTTACCAAATTTGAACCACATGCTCCTAAACCATAGTAAATACATGTGT
* * *
2259 ACTTTCAATTCCTCTTTTTGGTAACAAATTTTTTA-TTTTCAATTTAGTTCTTCAAATT-TTCAT
65 ACTTTCAATTCATCTTTTTGATAACAAATTTTTTATTTTTCAATTTAGTCCTTC-AATTATTCAT
** *
2322 AATATCCTTATTCCTTCAATTTGTGATTT
129 AATATCCTTATTCCTTCAATTCATCATTT
*
2351 ATTTTAAGTCCATTTTTTTACCAAATT
1 ATTTTAAGTTC-TTTTTTTACCAAATT
2378 GTTTATTTAG
Statistics
Matches: 165, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
155 45 0.27
156 72 0.44
157 7 0.04
158 40 0.24
159 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.47
Consensus pattern (157 bp):
ATTTTAAGTTCTTTTTTTACCAAATTTGAACCACATGCTCCTAAACCATAGTAAATACATGTGTA
CTTTCAATTCATCTTTTTGATAACAAATTTTTTATTTTTCAATTTAGTCCTTCAATTATTCATAA
TATCCTTATTCCTTCAATTCATCATTT
Found at i:5512 original size:29 final size:27
Alignment explanation
Indices: 5465--5528 Score: 83
Period size: 29 Copynumber: 2.3 Consensus size: 27
5455 TTCTAATATT
*
5465 TATTTGTTATTACAAGTCTAATTTTTCAG
1 TATTTTTTATTACAAGTCT-A-TTTTCAG
* *
5494 TATTTTTTATTAGAGGTCTATTTTCAG
1 TATTTTTTATTACAAGTCTATTTTCAG
5521 TATTTTTT
1 TATTTTTT
5529 TAATATTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 15 0.47
28 1 0.03
29 16 0.50
ACGTcount: A:0.23, C:0.08, G:0.11, T:0.58
Consensus pattern (27 bp):
TATTTTTTATTACAAGTCTATTTTCAG
Found at i:5583 original size:11 final size:11
Alignment explanation
Indices: 5553--5589 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5543 TTTGAGTTAA
*
5553 TTAAAATATGT
1 TTAAAATGTGT
5564 TT-AAA-GTGT
1 TTAAAATGTGT
5573 TTAAAATGTGT
1 TTAAAATGTGT
5584 TTAAAA
1 TTAAAA
5590 CTTTTTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
9 5 0.22
10 6 0.26
11 12 0.52
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (11 bp):
TTAAAATGTGT
Found at i:7965 original size:3 final size:3
Alignment explanation
Indices: 7959--7994 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
7949 AATGACTCGT
7959 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG TATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG -ATG AT
7995 CATAGCTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.36
Consensus pattern (3 bp):
ATG
Found at i:8274 original size:67 final size:68
Alignment explanation
Indices: 8190--8524 Score: 447
Period size: 67 Copynumber: 5.0 Consensus size: 68
8180 GTTAGGGTTT
**
8190 TTTAGGGTAAACTACCTA-TTCATCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
8254 TTA
66 TTA
* *
8257 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTAT-TTTTGGTCATTAGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
8321 TTA
66 TTA
* *
8324 TTTAGAGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTTACTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
8389 TTA
66 TTA
* * ** *
8392 TTTAGGGTAAACTACCTATTTGGTCACTAATAT-TTATCTAATATAAT-TCAT-AT-A-T--ATT
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAAT-TTATGTTTTGGTCACTCGATT
*
8450 TTTA
65 ATTA
* **
8454 TTTAGGGTAAACTACCTATTTGGTCACTTATCTATTATCTAATTTATGTTTTGAG-CACTTTATT
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTG-GTCACTCGATT
8518 ATTA
65 ATTA
8522 TTT
1 TTT
8525 TTTCAAAATT
Statistics
Matches: 235, Mismatches: 22, Indels: 21
0.85 0.08 0.08
Matches are distributed among these distances:
62 40 0.17
63 11 0.05
64 1 0.00
65 2 0.01
66 2 0.01
67 93 0.40
68 86 0.37
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (68 bp):
TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
TTA
Found at i:8293 original size:37 final size:36
Alignment explanation
Indices: 8238--8361 Score: 102
Period size: 37 Copynumber: 3.6 Consensus size: 36
8228 TAATTTATGT
*
8238 TTTGGTCACTCGAT-TATTATTTAGGGTAAACTACCTA
1 TTTGGTCACT-TATATATTATTTA-GGTAAACTACCTA
* ** *
8275 TTTGGTCACTTATATATTA--T--CTAATTTA--TT
1 TTTGGTCACTTATATATTATTTAGGTAAACTACCTA
*
8305 TTTGGTCA-TTAGATTATTATTTAGAGTAAACTACCTA
1 TTTGGTCACTTATA-TATTATTTAG-GTAAACTACCTA
8342 TTTGGTCACTTATATATTAT
1 TTTGGTCACTTATATATTAT
8362 CTAATTTATG
Statistics
Matches: 66, Mismatches: 11, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
29 4 0.06
30 14 0.21
32 6 0.09
35 6 0.09
36 2 0.03
37 30 0.45
38 4 0.06
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (36 bp):
TTTGGTCACTTATATATTATTTAGGTAAACTACCTA
Found at i:8309 original size:30 final size:30
Alignment explanation
Indices: 8275--8378 Score: 84
Period size: 30 Copynumber: 3.2 Consensus size: 30
8265 AAACTACCTA
8275 TTTGGTCACTTATATATTATCTAATTTATT
1 TTTGGTCACTTATATATTATCTAATTTATT
* * * *
8305 TTTGGTCA-TTAGATTATTATTTAGAGTAAACTACCTA
1 TTTGGTCACTTATA-TATTATCTA-A-T---TTA--TT
8342 TTTGGTCACTTATATATTATCTAATTTATGT
1 TTTGGTCACTTATATATTATCTAATTTAT-T
8373 TTTGGT
1 TTTGGT
8379 TACTCGATTA
Statistics
Matches: 56, Mismatches: 8, Indels: 19
0.67 0.10 0.23
Matches are distributed among these distances:
29 4 0.07
30 17 0.30
31 7 0.12
32 3 0.05
35 3 0.05
36 1 0.02
37 17 0.30
38 4 0.07
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.52
Consensus pattern (30 bp):
TTTGGTCACTTATATATTATCTAATTTATT
Found at i:8519 original size:130 final size:133
Alignment explanation
Indices: 8190--8524 Score: 484
Period size: 135 Copynumber: 2.5 Consensus size: 133
8180 GTTAGGGTTT
**
8190 TTTAGGGTAAACTACCTA-TTCATCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
* **
8254 TTATTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATTTTTGGTCATTAGAT
66 TTATTTAGGGTAAACTACCTATTTGGTCACTAATATATTATCTAA-TTATTAAT-GTCATTAGAT
8319 TATTA
129 TATTA
* *
8324 TTTAGAGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTTACTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
*
8389 TTATTTAGGGTAAACTACCTATTTGGTCACTAATAT-TTATCTAA-TA-TAAT-TCATATATATT
66 TTATTTAGGGTAAACTACCTATTTGGTCACTAATATATTATCTAATTATTAATGTCAT-TAGATT
*
8450 TTTA
130 ATTA
* **
8454 TTTAGGGTAAACTACCTATTTGGTCACTTATCTATTATCTAATTTATGTTTTGAG-CACTTTATT
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTG-GTCACTCGATT
8518 ATTATTT
65 ATTATTT
8525 TTTCAAAATT
Statistics
Matches: 184, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
129 4 0.02
130 72 0.39
131 3 0.02
132 2 0.01
134 25 0.14
135 78 0.42
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (133 bp):
TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
TTATTTAGGGTAAACTACCTATTTGGTCACTAATATATTATCTAATTATTAATGTCATTAGATTA
TTA
Found at i:8647 original size:32 final size:32
Alignment explanation
Indices: 8603--8666 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
8593 TGCTAACATG
8603 ACATTTTCTAATTATGTTTGGATGTTGGACTA
1 ACATTTTCTAATTATGTTTGGATGTTGGACTA
*
8635 ACATTTTTTAATTATGTTTGGATGTTGGACTA
1 ACATTTTCTAATTATGTTTGGATGTTGGACTA
8667 TGTAATTTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.48
Consensus pattern (32 bp):
ACATTTTCTAATTATGTTTGGATGTTGGACTA
Found at i:10032 original size:20 final size:20
Alignment explanation
Indices: 10007--10056 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
9997 TCCTATTCCA
*
10007 TGGTAATCTTTTATTCTCAC
1 TGGTAATCTTTTATTCCCAC
10027 TGGTAATCTTTTATTCCCAC
1 TGGTAATCTTTTATTCCCAC
*
10047 TAGTAATCTT
1 TGGTAATCTT
10057 ACATTCCGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.48
Consensus pattern (20 bp):
TGGTAATCTTTTATTCCCAC
Found at i:12912 original size:121 final size:121
Alignment explanation
Indices: 12707--13042 Score: 528
Period size: 121 Copynumber: 2.8 Consensus size: 121
12697 TTGGGCACAT
* * * * * * * *
12707 TATCCTTCTTTGTGAAGTTGAAACCGTGGGTGGCTCATTCGTCGTGAAGTTGAGCTTTGAGTTGG
1 TATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGA
*
12772 ATATCCTTCGTCTTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTGTGGGCATGA
66 ATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTGTGGGCATGA
*
12828 TATCCTTCGTCGTGAAGTTGAAATCATGGATGGCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGA
1 TATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGA
12893 ATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTGTGGGCATGA
66 ATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTGTGGGCATGA
* * *
12949 TATCCTTCGTCGTGAAGTTGAAATCGTGGATGGATCCTTCATTGTGAAGTTGAGTTTTGAATTGA
1 TATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGA
* * *
13014 ATATCATTCGTTGTGAAGTTAAAATCCAA
66 ATATCCTTCGTCGTGAAGTTGAAATCCAA
13043 TCTTGTGTAA
Statistics
Matches: 198, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
121 198 1.00
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.36
Consensus pattern (121 bp):
TATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTGAAGTTGAGCTTTGAATTGA
ATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTGTGGGCATGA
Found at i:13266 original size:34 final size:34
Alignment explanation
Indices: 13223--13301 Score: 158
Period size: 34 Copynumber: 2.3 Consensus size: 34
13213 GCTCATTCCC
13223 TGTGAAGTTGAGCTTCGAGTTAGATATCCTCCGT
1 TGTGAAGTTGAGCTTCGAGTTAGATATCCTCCGT
13257 TGTGAAGTTGAGCTTCGAGTTAGATATCCTCCGT
1 TGTGAAGTTGAGCTTCGAGTTAGATATCCTCCGT
13291 TGTGAAGTTGA
1 TGTGAAGTTGA
13302 AATCCAATCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (34 bp):
TGTGAAGTTGAGCTTCGAGTTAGATATCCTCCGT
Found at i:16952 original size:18 final size:18
Alignment explanation
Indices: 16925--16959 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16915 ATGTTTAACG
*
16925 AACACGTTTTTGTGAATC
1 AACACCTTTTTGTGAATC
*
16943 AACACCTTTTTTTGAAT
1 AACACCTTTTTGTGAAT
16960 GATGTAGTGC
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:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (18 bp):
AACACCTTTTTGTGAATC
Found at i:18404 original size:16 final size:16
Alignment explanation
Indices: 18385--18435 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
18375 ATAAGTATTT
18385 AAATTTATAAAGACCA
1 AAATTTATAAAGACCA
* * *
18401 AAATATAGAAAAACCA
1 AAATTTATAAAGACCA
* *
18417 AAATTT-TAAGGATCA
1 AAATTTATAAAGACCA
18432 AAAT
1 AAAT
18436 AGCAAAAATA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
15 9 0.33
16 18 0.67
ACGTcount: A:0.59, C:0.10, G:0.08, T:0.24
Consensus pattern (16 bp):
AAATTTATAAAGACCA
Found at i:24452 original size:2 final size:2
Alignment explanation
Indices: 24445--24481 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
24435 AACTATATTT
24445 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 T
24482 CAATTTCGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:26202 original size:31 final size:29
Alignment explanation
Indices: 26166--26238 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 29
26156 ATAGTAAAAC
* *
26166 TTGGTCAAAGTTAAAGTCAAAGTTAACGGGT
1 TTGGTCAAAGTT-AAGTCAAAGTCAAC-AGT
*
26197 TTGGTCAACAGTTAGGTCAAAGTCAACAGT
1 TTGGTCAA-AGTTAAGTCAAAGTCAACAGT
26227 TTGGGTCAAAGT
1 TT-GGTCAAAGT
26239 CAACAAGTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 7 0.19
31 26 0.70
32 4 0.11
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (29 bp):
TTGGTCAAAGTTAAGTCAAAGTCAACAGT
Found at i:26223 original size:18 final size:19
Alignment explanation
Indices: 26200--26243 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
26190 AACGGGTTTG
26200 GTCAACAG-TTAGGTCAAA
1 GTCAACAGTTTAGGTCAAA
*
26218 GTCAACAGTTTGGGTCAAA
1 GTCAACAGTTTAGGTCAAA
26237 GTCAACA
1 GTCAACA
26244 AGTCAGACTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (19 bp):
GTCAACAGTTTAGGTCAAA
Found at i:30628 original size:19 final size:18
Alignment explanation
Indices: 30579--30628 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
30569 CAACGGGTTT
*
30579 GTCAACAGTCAAGTCAAA
1 GTCAACAGTCAGGTCAAA
* *
30597 GTCAAAAGTTCAGGTTAAA
1 GTCAACAG-TCAGGTCAAA
30616 GTCAACACGTCAG
1 GTCAACA-GTCAG
30629 ATCGGTTCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 7 0.27
19 18 0.69
20 1 0.04
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (18 bp):
GTCAACAGTCAGGTCAAA
Found at i:32881 original size:19 final size:19
Alignment explanation
Indices: 32853--32891 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
32843 TGTCTCCCTC
*
32853 ATTTTCTATGGTTAATTAT
1 ATTTTCTATGATTAATTAT
*
32872 ATTTTTTATGATTAATTAT
1 ATTTTCTATGATTAATTAT
32891 A
1 A
32892 CTTTGCTCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.59
Consensus pattern (19 bp):
ATTTTCTATGATTAATTAT
Found at i:34544 original size:10 final size:10
Alignment explanation
Indices: 34515--34602 Score: 85
Period size: 10 Copynumber: 9.1 Consensus size: 10
34505 GCTGTTGGAA
34515 AACCGGTTTG
1 AACCGGTTTG
*
34525 -ACCAGTTTTG
1 AACC-GGTTTG
*
34535 AACCAGTTTG
1 AACCGGTTTG
34545 -ACCGGTTTG
1 AACCGGTTTG
34554 AACCGGTTTG
1 AACCGGTTTG
* *
34564 -ACCGGTCTA
1 AACCGGTTTG
34573 AACCGGTTTG
1 AACCGGTTTG
*
34583 -ACCGGTCTG
1 AACCGGTTTG
*
34592 AACCGGGTTG
1 AACCGGTTTG
34602 A
1 A
34603 CCCGACCCGA
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
9 26 0.42
10 33 0.53
11 3 0.05
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:34555 original size:19 final size:19
Alignment explanation
Indices: 34515--34604 Score: 117
Period size: 19 Copynumber: 4.7 Consensus size: 19
34505 GCTGTTGGAA
* *
34515 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
* *
34535 AACCAGTTTGACCGGTTTG
1 AACCGGTTTGACCGGTCTG
*
34554 AACCGGTTTGACCGGTCTA
1 AACCGGTTTGACCGGTCTG
34573 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
34592 AACCGGGTTGACC
1 AACCGGTTTGACC
34605 CGACCCGACT
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
19 51 0.81
20 12 0.19
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.28
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:34621 original size:17 final size:17
Alignment explanation
Indices: 34599--34655 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 17
34589 CTGAACCGGG
*
34599 TTGACCCGACCCGACTA
1 TTGACCCGACCCGACCA
*
34616 TTGACCCGACCCGACCG
1 TTGACCCGACCCGACCA
* *
34633 TTGACCTGACCCGACCG
1 TTGACCCGACCCGACCA
34650 TTGACC
1 TTGACC
34656 GTGACCGTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.19, C:0.42, G:0.21, T:0.18
Consensus pattern (17 bp):
TTGACCCGACCCGACCA
Found at i:34655 original size:7 final size:7
Alignment explanation
Indices: 34645--34681 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
34635 GACCTGACCC
34645 GACCGTT
1 GACCGTT
34652 GACCG-T
1 GACCGTT
34658 GACCGTT
1 GACCGTT
34665 GACCGTT
1 GACCGTT
34672 GACCGTT
1 GACCGTT
34679 GAC
1 GAC
34682 TTTCTTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:34663 original size:13 final size:14
Alignment explanation
Indices: 34645--34681 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
34635 GACCTGACCC
34645 GACCGTTGACCG-T
1 GACCGTTGACCGTT
34658 GACCGTTGACCGTT
1 GACCGTTGACCGTT
34672 GACCGTTGAC
1 GACCGTTGAC
34682 TTTCTTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (14 bp):
GACCGTTGACCGTT
Found at i:34670 original size:20 final size:18
Alignment explanation
Indices: 34623--34677 Score: 76
Period size: 17 Copynumber: 3.0 Consensus size: 18
34613 CTATTGACCC
34623 GACCCGACCGTTGACC-T
1 GACCCGACCGTTGACCGT
34640 GACCCGACCGTTGACCGT
1 GACCCGACCGTTGACCGT
*
34658 GACCGTTGACCGTTGACCGT
1 GACC--CGACCGTTGACCGT
34678 TGACTTTCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
17 16 0.47
18 5 0.15
20 13 0.38
ACGTcount: A:0.16, C:0.36, G:0.27, T:0.20
Consensus pattern (18 bp):
GACCCGACCGTTGACCGT
Found at i:41885 original size:10 final size:10
Alignment explanation
Indices: 41856--41924 Score: 54
Period size: 10 Copynumber: 7.1 Consensus size: 10
41846 GCTGTTGGAA
41856 AACCGGTTTG
1 AACCGGTTTG
*
41866 -ACCAGTTTTG
1 AACC-GGTTTG
*
41876 AACCAGTTTG
1 AACCGGTTTG
*
41886 -ACCGGTTCG
1 AACCGGTTTG
41895 AACCGGTTTG
1 AACCGGTTTG
* *
41905 -ACTGGTCTG
1 AACCGGTTTG
*
41914 AACCGGGTTG
1 AACCGGTTTG
41924 A
1 A
41925 CCCGACCCGA
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
9 17 0.39
10 24 0.55
11 3 0.07
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:41903 original size:19 final size:19
Alignment explanation
Indices: 41856--41926 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
41846 GCTGTTGGAA
* *
41856 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTTCG
*
41876 AACCAGTTTGACCGGTTCG
1 AACCGGTTTGACCGGTTCG
*
41895 AACCGGTTTGACTGG-TCTG
1 AACCGGTTTGACCGGTTC-G
*
41914 AACCGGGTTGACC
1 AACCGGTTTGACC
41927 CGACCCGACT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 2 0.05
19 29 0.67
20 12 0.28
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.28
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:41942 original size:17 final size:17
Alignment explanation
Indices: 41920--41977 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
41910 TCTGAACCGG
*
41920 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
41937 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
*
41954 GTTAACCCGACCCGACC
1 GTTGACCCGACCCGACC
41971 GTTGACC
1 GTTGACC
41978 GTTGATCGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.19, C:0.43, G:0.22, T:0.16
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:41979 original size:7 final size:7
Alignment explanation
Indices: 41967--42003 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
41957 AACCCGACCC
41967 GACCGTT
1 GACCGTT
41974 GACCGTT
1 GACCGTT
*
41981 GATCG-T
1 GACCGTT
41987 GACCGTT
1 GACCGTT
41994 GACCGTT
1 GACCGTT
42001 GAC
1 GAC
42004 TTTCTTTGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (7 bp):
GACCGTT
Found at i:46173 original size:21 final size:21
Alignment explanation
Indices: 46143--46247 Score: 92
Period size: 21 Copynumber: 5.1 Consensus size: 21
46133 GATTTACATA
* *
46143 TTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
46164 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
46185 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
46204 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
46227 TT--TGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
46246 TT
1 TT
46248 TGCAACGACT
Statistics
Matches: 67, Mismatches: 13, Indels: 10
0.74 0.14 0.11
Matches are distributed among these distances:
19 25 0.37
21 33 0.49
23 9 0.13
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:46192 original size:19 final size:19
Alignment explanation
Indices: 46168--46237 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
46158 TCGAAGTTCG
46168 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
** *
46187 CGTTGCGATAGTCCAAGTT
1 CGTTGCGATTTTCCAAATT
46206 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA-TT-TTCCAAATT
*
46229 TGTTGCGAT
1 CGTTGCGAT
46238 AGTCCAAGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
19 16 0.40
20 1 0.03
21 15 0.38
22 1 0.03
23 7 0.17
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:46197 original size:40 final size:42
Alignment explanation
Indices: 46149--46247 Score: 166
Period size: 42 Copynumber: 2.4 Consensus size: 42
46139 CATATTCGCA
*
46149 TTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
46189 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTTG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
46231 TTGCGATAGTCCAAGTT
1 TTGCGATAGTCCAAGTT
46248 TGCAACGACT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
40 26 0.47
41 2 0.04
42 27 0.49
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:47121 original size:21 final size:21
Alignment explanation
Indices: 47097--47322 Score: 216
Period size: 21 Copynumber: 10.8 Consensus size: 21
47087 CGTTGCGATT
47097 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
* *
47118 TTGGAATAAATCGCAACGCGAAG
1 TTGGACT--ATCGCAACGCGAAC
* *
47141 TTCGACTATCTCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
47160 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
47183 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
47202 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
47225 TTCGACTATCGCAA--CAAAC
1 TTGGACTATCGCAACGCGAAC
47244 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
47265 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
47284 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
47307 TTTGACTATCGCAACG
1 TTGGACTATCGCAACG
47323 AATTTAGAAA
Statistics
Matches: 166, Mismatches: 23, Indels: 32
0.75 0.10 0.14
Matches are distributed among these distances:
19 46 0.28
21 73 0.44
23 47 0.28
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:47297 original size:82 final size:83
Alignment explanation
Indices: 47097--47338 Score: 353
Period size: 82 Copynumber: 2.9 Consensus size: 83
47087 CGTTGCGATT
* * *
47097 TTGGACTATCGCAACGCGAACTTGGAATAAATCGCAACGCGAAGTTCGACTATCTCAACGAACTT
1 TTGGACTATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACAAACTT
47162 GGAATAAATCGCAACGCGAAC
64 GGAAT-AATCGCAACGCGAAC
*
47183 TTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACAAACTTGG
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACAAACTTGG
*
47248 ACT-ATCGCAACGCGAAC
66 AATAATCGCAACGCGAAC
* * * * *
47265 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTTGACTATCGCAACGAATTTAG
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACAAACTTGG
47330 AA-AATCGCA
66 AATAATCGCA
47339 TTGCGATAGT
Statistics
Matches: 143, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
82 80 0.56
84 50 0.35
86 13 0.09
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.21
Consensus pattern (83 bp):
TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACAAACTTGG
AATAATCGCAACGCGAAC
Found at i:47327 original size:42 final size:42
Alignment explanation
Indices: 47100--47324 Score: 355
Period size: 42 Copynumber: 5.4 Consensus size: 42
47090 TGCGATTTTG
*
47100 GACTATCGCAACGCGAACTTGGAATAAATCGCAACGCGAAGTTC
1 GACTATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTC
*
47144 GACTATCTCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
47186 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
47228 GACTATCGCAACAAACTTGGACT--ATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
47268 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTT
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
47310 GACTATCGCAACGAA
1 GACTATCGCAACGAA
47325 TTTAGAAAAT
Statistics
Matches: 169, Mismatches: 10, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
40 36 0.21
42 123 0.73
44 10 0.06
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:47336 original size:19 final size:18
Alignment explanation
Indices: 47272--47338 Score: 53
Period size: 21 Copynumber: 3.3 Consensus size: 18
47262 AACTTGGACT
47272 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTT-G-A-AA
**
47293 ATCGCAACGCGAACTTTGACT
1 ATCGCAA--CGAA-TTTGAAA
47314 ATCGCAACGAATTTAGAAA
1 ATCGCAACGAATTT-GAAA
47333 ATCGCA
1 ATCGCA
47339 TTGCGATAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
18 3 0.08
19 12 0.32
21 14 0.37
22 1 0.03
23 5 0.13
24 3 0.08
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (18 bp):
ATCGCAACGAATTTGAAA
Found at i:47367 original size:21 final size:21
Alignment explanation
Indices: 47334--47386 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
47324 ATTTAGAAAA
47334 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
* *
47355 TCGCGTTGTGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
47376 TCGCATTGCGA
1 TCGCATTGCGA
47387 ATCTGGAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:48155 original size:24 final size:24
Alignment explanation
Indices: 48118--48171 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
48108 AGTGAATCAA
*
48118 TTGACCCAACCTGACCCATTAACT
1 TTGACCCAAACTGACCCATTAACT
* *
48142 TTGACTCAAACTGACCCATTGACT
1 TTGACCCAAACTGACCCATTAACT
48166 TTGACC
1 TTGACC
48172 TGATCCGTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.28, C:0.33, G:0.11, T:0.28
Consensus pattern (24 bp):
TTGACCCAAACTGACCCATTAACT
Found at i:49237 original size:15 final size:16
Alignment explanation
Indices: 49219--49248 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
49209 AAAATGTTTA
49219 ATTTATTA-TTATTTT
1 ATTTATTACTTATTTT
49234 ATTTATTACTTATTT
1 ATTTATTACTTATTT
49249 AGGACTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTTATTACTTATTTT
Found at i:50403 original size:17 final size:17
Alignment explanation
Indices: 50381--50415 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
50371 TTCAACCTGG
50381 CAAAGCTCGTAGGGCGA
1 CAAAGCTCGTAGGGCGA
50398 CAAAGCTCGTAGGGCGA
1 CAAAGCTCGTAGGGCGA
50415 C
1 C
50416 TTCAGCAGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.34, T:0.11
Consensus pattern (17 bp):
CAAAGCTCGTAGGGCGA
Found at i:51872 original size:11 final size:13
Alignment explanation
Indices: 51852--51897 Score: 55
Period size: 14 Copynumber: 3.8 Consensus size: 13
51842 AGTTTAAACA
51852 CAAT-TCAAAAAT
1 CAATCTCAAAAAT
51864 -AA-CTCAAAAAT
1 CAATCTCAAAAAT
51875 CAATTCTCAAAAAT
1 CAA-TCTCAAAAAT
51889 CAAT-TCAAA
1 CAATCTCAAA
51898 GGAATTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
11 10 0.33
12 7 0.23
13 1 0.03
14 12 0.40
ACGTcount: A:0.57, C:0.20, G:0.00, T:0.24
Consensus pattern (13 bp):
CAATCTCAAAAAT
Found at i:51885 original size:14 final size:14
Alignment explanation
Indices: 51866--51894 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
51856 TCAAAAATAA
51866 CTCAAAAATCAATT
1 CTCAAAAATCAATT
51880 CTCAAAAATCAATT
1 CTCAAAAATCAATT
51894 C
1 C
51895 AAAGGAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (14 bp):
CTCAAAAATCAATT
Found at i:52913 original size:24 final size:24
Alignment explanation
Indices: 52881--52950 Score: 113
Period size: 24 Copynumber: 2.9 Consensus size: 24
52871 TATTCTTTCA
52881 CTTCAATCAAGCTCGAATTTTAGG
1 CTTCAATCAAGCTCGAATTTTAGG
52905 CTTCAATCAAGCTCGAATTTTAGG
1 CTTCAATCAAGCTCGAATTTTAGG
* *
52929 CTTCAATCGAGCTTCTAATTTT
1 CTTCAATCAAGC-TCGAATTTT
52951 TTTTGAGTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
24 35 0.81
25 8 0.19
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.37
Consensus pattern (24 bp):
CTTCAATCAAGCTCGAATTTTAGG
Found at i:53222 original size:17 final size:18
Alignment explanation
Indices: 53200--53233 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53190 TTAGCCGGTC
53200 CGGTTC-GAACGGTTCAG
1 CGGTTCTGAACGGTTCAG
*
53217 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
53234 CTAATAGCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAG
Found at i:54142 original size:45 final size:45
Alignment explanation
Indices: 54092--54238 Score: 167
Period size: 45 Copynumber: 3.3 Consensus size: 45
54082 TAATACAAGG
*
54092 ATTTTGCTTATTTGGTTGTC-AAAAGTAAAATCAAATGATTAGTTC
1 ATTTTGATTATTTGGTTG-CAAAAAGTAAAATCAAATGATTAGTTC
*
54137 ATTTTGATTA-TTGTGTTACAAAAAGTAAAATCAAATGATTAGTT-
1 ATTTTGATTATTTG-GTTGCAAAAAGTAAAATCAAATGATTAGTTC
* * * * *
54181 ACTTTCGATTATTAGATTGCGAAAATTAAAATCAAATGATTAGTTC
1 A-TTTTGATTATTTGGTTGCAAAAAGTAAAATCAAATGATTAGTTC
54227 -TTTGTGATTATT
1 ATTT-TGATTATT
54239 GGGTCGGTAA
Statistics
Matches: 87, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
44 8 0.09
45 77 0.89
46 2 0.02
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.42
Consensus pattern (45 bp):
ATTTTGATTATTTGGTTGCAAAAAGTAAAATCAAATGATTAGTTC
Found at i:54251 original size:45 final size:43
Alignment explanation
Indices: 54093--54256 Score: 157
Period size: 45 Copynumber: 3.7 Consensus size: 43
54083 AATACAAGGA
* * *
54093 TTTTGCTTATTTGGTTGTCAAAAGTAAAATCAAATGATTAGTTC
1 TTTTGATTATTGGGTTG-GAAAAGTAAAATCAAATGATTAGTTC
* **
54137 ATTTTGATTATTGTGTTACAAAAAGTAAAATCAAATGATTAGTTAC
1 -TTTTGATTATTGGGTT-GGAAAAGTAAAATCAAATGATTAGTT-C
* * * *
54183 TTTCGATTATTAGATTGCGAAAATTAAAATCAAATGATTAGTTC
1 TTTTGATTATTGGGTTG-GAAAAGTAAAATCAAATGATTAGTTC
* *
54227 TTTGTGATTATTGGGTCGGTAAAATTAAAA
1 TTT-TGATTATTGGGTTGG-AAAAGTAAAA
54257 GATCAATTTT
Statistics
Matches: 98, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
44 5 0.05
45 92 0.94
46 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (43 bp):
TTTTGATTATTGGGTTGGAAAAGTAAAATCAAATGATTAGTTC
Found at i:54494 original size:57 final size:56
Alignment explanation
Indices: 54410--54532 Score: 167
Period size: 56 Copynumber: 2.2 Consensus size: 56
54400 TTTTAAATGG
* * * *
54410 AAATTATTTCTTTGAGAATCTTGAATGATTCTAACTTTGTAAGGAGAATAAATTGTT
1 AAATTATTTCATTGAGAATCTTAAATGATT-TAACTTTGTAAGGAAAATAAATTGTC
*
54467 AAATGTATTTCATTGA-AATCTTAAATGATTTAATTTTGTAAGGAAAATAAATTGTC
1 AAAT-TATTTCATTGAGAATCTTAAATGATTTAACTTTGTAAGGAAAATAAATTGTC
54523 AAATTTATTT
1 AAA-TTATTT
54533 TCTTGATAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
56 31 0.53
57 18 0.31
58 10 0.17
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (56 bp):
AAATTATTTCATTGAGAATCTTAAATGATTTAACTTTGTAAGGAAAATAAATTGTC
Found at i:54788 original size:64 final size:64
Alignment explanation
Indices: 54687--54807 Score: 181
Period size: 64 Copynumber: 1.9 Consensus size: 64
54677 AATAAATTAT
* *
54687 GATTTATTTTCCTATTTTAGAAAAGGAAACAACTCGTTGAATTTAGTTTCCTGTTTTGTATAAG
1 GATTTATTTTCCTATTTTAGAAAAGGAAACAAATCGTTGAATTTAGTTTCCTCTTTTGTATAAG
* * *
54751 GATTTATTTTCCTATTTTATGAAAA-GAAATAAATCGTTGAGTTTATTTTCCTCTTTT
1 GATTTATTTTCCTATTTTA-GAAAAGGAAACAAATCGTTGAATTTAGTTTCCTCTTTT
54808 ACTAAAGGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
64 46 0.90
65 5 0.10
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (64 bp):
GATTTATTTTCCTATTTTAGAAAAGGAAACAAATCGTTGAATTTAGTTTCCTCTTTTGTATAAG
Found at i:54835 original size:39 final size:38
Alignment explanation
Indices: 54750--54839 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 38
54740 TTTTGTATAA
54750 GGATTTATTTTCCTATTTTATGAAAAGAAATAAATCGT
1 GGATTTATTTTCCTATTTTATGAAAAGAAATAAATCGT
* * * * *
54788 TGAGTTTATTTTCCTCTTTTACT-AAAGGAAATAAGTTGGT
1 GGA-TTTATTTTCCTATTTTA-TGAAAAGAAATAA-ATCGT
54828 GGATTTATTTTC
1 GGATTTATTTTC
54840 ATGTGAATCT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
38 2 0.05
39 35 0.81
40 6 0.14
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.46
Consensus pattern (38 bp):
GGATTTATTTTCCTATTTTATGAAAAGAAATAAATCGT
Found at i:54989 original size:97 final size:95
Alignment explanation
Indices: 54772--55036 Score: 280
Period size: 97 Copynumber: 2.7 Consensus size: 95
54762 CTATTTTATG
* * * * **
54772 AAAAGAAATAAATCGTTGAGTTTATTTTCCTCTTTTACTAAAGGAAATAAGTTGGTGGATTTATT
1 AAAAGAAATAAATCATTGA-TTTATTTTCCTATTTT-GTAAAGGAAATAAATTGGTAAATTTATT
* ** * *
54837 TTCATGTGAATCTTATATGATTTTGATTTATA
64 TTCCTAAGAATCTTATATGATTCTGATATATA
** *
54869 AAAAGAAATAAATCATAAAATTTATTTTCCTGTTTTGGTAAAGGAAATAAATTGGTAAATTTATT
1 AAAAGAAATAAATCAT-TGATTTATTTTCCTATTTT-GTAAAGGAAATAAATTGGTAAATTTATT
* *
54934 TTCCTAAGAATCTTGTATGATTCTGATATGTA
64 TTCCTAAGAATCTTATATGATTCTGATATATA
* * * *
54966 AAAAGAAATAAATCATTGGATTTATTTTTCTATTGTGTAAAAAGAAATAAA-TCGTAGAATTTAT
1 AAAAGAAATAAATCATT-GATTTATTTTCCTATTTTGT-AAAGGAAATAAATTGGTA-AATTTAT
55030 TTTCCTA
63 TTTCCTA
55037 TTTTGTATAA
Statistics
Matches: 141, Mismatches: 23, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
96 6 0.04
97 134 0.95
98 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.42
Consensus pattern (95 bp):
AAAAGAAATAAATCATTGATTTATTTTCCTATTTTGTAAAGGAAATAAATTGGTAAATTTATTTT
CCTAAGAATCTTATATGATTCTGATATATA
Found at i:55005 original size:39 final size:39
Alignment explanation
Indices: 54962--55075 Score: 156
Period size: 39 Copynumber: 2.9 Consensus size: 39
54952 GATTCTGATA
* * *
54962 TGTAAAAAGAAATAAATCATTGGATTTATTTTTCTATTG
1 TGTAAAAAGAAATAAATCGTTGAATTTATTTTCCTATTG
* *
55001 TGTAAAAAGAAATAAATCGTAGAATTTATTTTCCTATTT
1 TGTAAAAAGAAATAAATCGTTGAATTTATTTTCCTATTG
* * *
55040 TGTATAAGGAAATAAATCGTTAAATTTATTTTCCTA
1 TGTAAAAAGAAATAAATCGTTGAATTTATTTTCCTA
55076 AGAATCTTGT
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 66 1.00
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.42
Consensus pattern (39 bp):
TGTAAAAAGAAATAAATCGTTGAATTTATTTTCCTATTG
Found at i:55155 original size:136 final size:136
Alignment explanation
Indices: 54867--55168 Score: 453
Period size: 136 Copynumber: 2.2 Consensus size: 136
54857 TTTTGATTTA
* * * *
54867 TAAAAAGAAATAAATCATAAAATTTATTTTCCTGTTTTGGTAAAGGAAATAAATTGGTAAATTTA
1 TAAAAAGAAATAAATCGTAGAATTTATTTTCCTATTTTGGTAAAGGAAATAAATCGGTAAATTTA
* *
54932 TTTTCCTAAGAATCTTGTATGATTCTGATATGTAAAAAGAAATAAATCATTGGATTTATTTTTCT
66 TTTTCCTAAGAATCTTGTATGATTCTAATATGTAAAAAGAAATAAATCATTGGATTTATTTTCCT
*
54997 ATTGTG
131 ATTCTG
*
55003 TAAAAAGAAATAAATCGTAGAATTTATTTTCCTATTTT-GTATAAGGAAATAAATCGTTAAATTT
1 TAAAAAGAAATAAATCGTAGAATTTATTTTCCTATTTTGGTA-AAGGAAATAAATCGGTAAATTT
* **
55067 ATTTTCCTAAGAATCTTGTATGATTCTAATATGTAAAAGGAAATAAATTGTTGGATTTATTTTCC
65 ATTTTCCTAAGAATCTTGTATGATTCTAATATGTAAAAAGAAATAAATCATTGGATTTATTTTCC
55132 TATTCTG
130 TATTCTG
* * * *
55139 TAAAATGAAAAAAATCGTTGGATTTATTTT
1 TAAAAAGAAATAAATCGTAGAATTTATTTT
55169 TTTAGGAATC
Statistics
Matches: 150, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
135 3 0.02
136 147 0.98
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (136 bp):
TAAAAAGAAATAAATCGTAGAATTTATTTTCCTATTTTGGTAAAGGAAATAAATCGGTAAATTTA
TTTTCCTAAGAATCTTGTATGATTCTAATATGTAAAAAGAAATAAATCATTGGATTTATTTTCCT
ATTCTG
Found at i:55166 original size:233 final size:233
Alignment explanation
Indices: 54750--55227 Score: 530
Period size: 233 Copynumber: 2.1 Consensus size: 233
54740 TTTTGTATAA
* * * * *
54750 GGATTTATTTTCCTATTTTATGAAAAGAAATAAATCGTTGAGTTTATTTTCCTCTTTTACTAAAG
1 GGATTTATTTTCCTATTGTATAAAAAGAAATAAATCGTAGAATTTATTTTCCTATTTTACTAAAG
* * ** ** * * *
54815 GAAATAAGTTGGTGGATTTATTTTCATGTGAATCTTATATGATTTTGATTTATAAAAAGAAATAA
66 GAAATAAATCGGTAAATTTATTTTCATAAGAATCTTATATGATTCTAATATATAAAAAGAAATAA
* * * *
54880 ATCATAAAATTTATTTTCCTGTTTTGGTAAAGGAAATAAATTGGTAAATTTATTTTCCTAAGAAT
131 ATCATAAAATTTATTTTCCTATTCTGGTAAAGGAAAAAAATCGGTAAATTTATTTTCCTAAGAAT
*
54945 CTTGTATGATTC-TGATATGTAAAAAGAAATAAATCATT
196 CTTGTATGATTCTTG-TATATAAAAAGAAATAAATCATT
* * *
54983 GGATTTATTTTTCTATTGTGTAAAAAGAAATAAATCGTAGAATTTATTTTCCTATTTT-GTATAA
1 GGATTTATTTTCCTATTGTATAAAAAGAAATAAATCGTAGAATTTATTTTCCTATTTTACTA-AA
* * * * *
55047 GGAAATAAATCGTTAAATTTATTTTCCTAAGAATCTTGTATGATTCTAATATGTAAAAGGAAATA
65 GGAAATAAATCGGTAAATTTATTTTCATAAGAATCTTATATGATTCTAATATATAAAAAGAAATA
** *** * * ** ** *
55112 AATTGTTGGATTTATTTTCCTATTCT-GTAAAATGAAAAAAATCGTTGGATTTATTTTTTTAGGA
130 AATCATAAAATTTATTTTCCTATTCTGGT-AAAGGAAAAAAATCGGTAAATTTATTTTCCTAAGA
* * *
55176 ATCTTGTATGATTCTTGTTTATAAAAGGAAATAAATCGTT
194 ATCTTGTATGATTCTTGTATATAAAAAGAAATAAATCATT
55216 GGATTTATTTTC
1 GGATTTATTTTC
55228 ATGATTTGCA
Statistics
Matches: 199, Mismatches: 43, Indels: 6
0.80 0.17 0.02
Matches are distributed among these distances:
232 4 0.02
233 193 0.97
234 2 0.01
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (233 bp):
GGATTTATTTTCCTATTGTATAAAAAGAAATAAATCGTAGAATTTATTTTCCTATTTTACTAAAG
GAAATAAATCGGTAAATTTATTTTCATAAGAATCTTATATGATTCTAATATATAAAAAGAAATAA
ATCATAAAATTTATTTTCCTATTCTGGTAAAGGAAAAAAATCGGTAAATTTATTTTCCTAAGAAT
CTTGTATGATTCTTGTATATAAAAAGAAATAAATCATT
Found at i:55251 original size:97 final size:96
Alignment explanation
Indices: 55003--55259 Score: 302
Period size: 97 Copynumber: 2.6 Consensus size: 96
54993 TTCTATTGTG
* * * * * **
55003 TAAAAAGAAATAAATCGTAGAATTTATTTTCCTATTTTGTATAAGGAAATAAATCGTTAAATTTA
1 TAAAAGGAAATAAATCGTTGGATTTATTTTCCTA-TTTGTAAAAGAAAATAAATCGTTGGATTTA
*
55068 TTTTCCTAAGAATCTTGTATGATTCTAATATG
65 TTTTCCTAAGAATCTTGTATGATTCTAATATA
*
55100 TAAAAGGAAATAAATTGTTGGATTTATTTTCCTATTCTGTAAAATGAAAA-AAATCGTTGGATTT
1 TAAAAGGAAATAAATCGTTGGATTTATTTTCCTATT-TGTAAAA-GAAAATAAATCGTTGGATTT
** * ** *
55164 ATTTTTTTAGGAATCTTGTATGATTCTTGTTTA
64 ATTTTCCTAAGAATCTTGTATGATTCTAATATA
* *
55197 TAAAAGGAAATAAATCGTTGGATTTATTTTCATGATTTGCAAAAGAAAATAAATCAG-TGGATT
1 TAAAAGGAAATAAATCGTTGGATTTATTTTCCT-ATTTGTAAAAGAAAATAAATC-GTTGGATT
55260 GAATTTATTT
Statistics
Matches: 137, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
96 7 0.05
97 122 0.89
98 8 0.06
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (96 bp):
TAAAAGGAAATAAATCGTTGGATTTATTTTCCTATTTGTAAAAGAAAATAAATCGTTGGATTTAT
TTTCCTAAGAATCTTGTATGATTCTAATATA
Found at i:59298 original size:23 final size:22
Alignment explanation
Indices: 59270--59312 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
59260 AATATTCCTT
*
59270 TAATTTCATGTTAATTTTTTTAA
1 TAATTTCAT-ATAATTTTTTTAA
*
59293 TAATTTTATATAATTTTTTT
1 TAATTTCATATAATTTTTTT
59313 TAAAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
TAATTTCATATAATTTTTTTAA
Found at i:61207 original size:12 final size:12
Alignment explanation
Indices: 61180--61236 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
61170 ATTTTAAATC
**
61180 ATTTAAATTTAA
1 ATTTAAATTTGG
61192 ATTTAAATTTGG
1 ATTTAAATTTGG
**
61204 ATTTGGATTTGG
1 ATTTAAATTTGG
61216 ATTTTAAATTT-G
1 A-TTTAAATTTGG
61228 ATTTAAATT
1 ATTTAAATT
61237 AATTTTTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
11 8 0.21
12 23 0.61
13 7 0.18
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (12 bp):
ATTTAAATTTGG
Found at i:64474 original size:64 final size:64
Alignment explanation
Indices: 64406--64566 Score: 162
Period size: 64 Copynumber: 2.5 Consensus size: 64
64396 ATTGTTCAAG
* * * *
64406 GTGTATCGATGCACATGAAGTGTATCAATGCACTCCTTTAA-AATAGAAACATCGAATGCCATAA
1 GTGTATCGATGCACAAGAAGTGCATCAATGCACCCCCTTAAGAATA-AAACATCGAATGCCATAA
* * * * ** **
64470 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAGATTAAAACATCGAAGGTGATTT
1 GTGTATCGATGCACAAGAAGTGCATCAATGCACCCCCTTAAGAATAAAACATCGAATGCCATAA
* * * *
64534 GTGTACCGATGCACAGGTAGTGCATCGATGCAC
1 GTGTATCGATGCACAAGAAGTGCATCAATGCAC
64567 ACGTTATAGA
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
64 79 0.96
65 3 0.04
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.25
Consensus pattern (64 bp):
GTGTATCGATGCACAAGAAGTGCATCAATGCACCCCCTTAAGAATAAAACATCGAATGCCATAA
Found at i:67404 original size:64 final size:64
Alignment explanation
Indices: 67334--67494 Score: 198
Period size: 64 Copynumber: 2.5 Consensus size: 64
67324 ATTGTTCAAG
* * * *
67334 GTGTATCGATGCACATGAAGTGTATCGATGCACTCCT-TTAAAATAAAAACATCAAATGCCATAA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCAC-CCTCTTAAAATAAAAACATCAAAGGCCATAA
* * * ** **
67398 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCTCTTAAGATTAAAACATCGAAGGTGATTT
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCTCTTAAAATAAAAACATCAAAGGCCATAA
*
67462 GTGTATCGATGCACAGGTAGTGCATCGATGCAC
1 GTGTATCGATGCACAAGTAGTGCATCGATGCAC
67495 ACGTTATGGA
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
63 3 0.04
64 81 0.96
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (64 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACCCTCTTAAAATAAAAACATCAAAGGCCATAA
Done.