Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006267.1 Hibiscus syriacus cultivar Beakdansim tig00014946_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: 75045
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:587 original size:22 final size:22
Alignment explanation
Indices: 562--604 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
552 AAATCCAGCA
562 AAGAAAATCAAAGCACTCAAAG
1 AAGAAAATCAAAGCACTCAAAG
* *
584 AAGAAATTGAAAGCACTCAAA
1 AAGAAAATCAAAGCACTCAAA
605 AATGAAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.16, G:0.14, T:0.12
Consensus pattern (22 bp):
AAGAAAATCAAAGCACTCAAAG
Found at i:621 original size:16 final size:16
Alignment explanation
Indices: 609--640 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
599 CTCAAAAATG
609 AAGAAAAATAAAAGAA
1 AAGAAAAATAAAAGAA
625 AAGAAAAAT-AAAGAA
1 AAGAAAAATAAAAGAA
640 A
1 A
641 GTTGAAGCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.06
Consensus pattern (16 bp):
AAGAAAAATAAAAGAA
Found at i:8605 original size:21 final size:20
Alignment explanation
Indices: 8579--8617 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
8569 ATAAATGTAA
8579 AAACATGGAAAATAGAAATAT
1 AAACATGGAAAATA-AAATAT
8600 AAACATGGAAAATAAAAT
1 AAACATGGAAAATAAAAT
8618 GCAAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.64, C:0.05, G:0.13, T:0.18
Consensus pattern (20 bp):
AAACATGGAAAATAAAATAT
Found at i:10896 original size:3 final size:3
Alignment explanation
Indices: 10888--10919 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
10878 AAGTTAGTAA
10888 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
10920 CGATGAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12136 original size:5 final size:5
Alignment explanation
Indices: 12122--12269 Score: 94
Period size: 5 Copynumber: 30.0 Consensus size: 5
12112 TAACATAAGG
* *
12122 TAAAG TAAAA TAAAA -AAAA CAAAA T-AAA TAAAA T-AAA T-AAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
* * * * * * *
12168 CAAAG TAAAA TAAAA TAGAAA TAAAG TAAGA CAAAA TTAAA TAAAA TTAAA
1 TAAAA TAAAA TAAAA TA-AAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
* * *
12219 TAAAA -AACA -AAAA CAAGAA -AACA TAAAAA TGAAAA TAAAA TAAATA
1 TAAAA TAAAA TAAAA TAA-AA TAAAA T-AAAA T-AAAA TAAAA TAAA-A
12265 TAAAA
1 TAAAA
12270 ACAAAAATAA
Statistics
Matches: 113, Mismatches: 21, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
4 23 0.20
5 69 0.61
6 21 0.19
ACGTcount: A:0.74, C:0.04, G:0.05, T:0.17
Consensus pattern (5 bp):
TAAAA
Found at i:12157 original size:23 final size:24
Alignment explanation
Indices: 12122--12182 Score: 81
Period size: 22 Copynumber: 2.6 Consensus size: 24
12112 TAACATAAGG
12122 TAAAGTAAAATAAAAAAAACAAAA
1 TAAAGTAAAATAAAAAAAACAAAA
* *
12146 TAAA-TAAAAT-AAATAAATAAAA
1 TAAAGTAAAATAAAAAAAACAAAA
*
12168 CAAAGTAAAATAAAA
1 TAAAGTAAAATAAAA
12183 TAGAAATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 13 0.41
23 12 0.38
24 7 0.22
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.16
Consensus pattern (24 bp):
TAAAGTAAAATAAAAAAAACAAAA
Found at i:12167 original size:31 final size:31
Alignment explanation
Indices: 12129--12275 Score: 88
Period size: 31 Copynumber: 4.5 Consensus size: 31
12119 AGGTAAAGTA
12129 AAATAAAAAAAACAAAATAAATAAAATAAAT
1 AAATAAAAAAAACAAAATAAATAAAATAAAT
**
12160 AAATAAAACAAAGTAAAATAAAATAGAAATAAAGT
1 AAATAAAA-AAAACAAAAT-AAATA-AAATAAA-T
* * *
12195 AAGACAAAATTAAATAAAATTAAATAAAA-AACA-
1 AA-ATAAAA-AAAACAAAA-TAAATAAAATAA-AT
* *
12228 AAA-ACAAGAAAACATAA-AAATGAAAATAAAAT
1 AAATA-AAAAAAACAAAATAAAT-AAAAT-AAAT
*
12260 AAAT-ATAAAAACAAAA
1 AAATAAAAAAAACAAAA
12276 ATAACTTATA
Statistics
Matches: 90, Mismatches: 13, Indels: 26
0.70 0.10 0.20
Matches are distributed among these distances:
29 4 0.04
30 4 0.04
31 25 0.28
32 16 0.18
33 7 0.08
34 9 0.10
35 7 0.08
36 17 0.19
37 1 0.01
ACGTcount: A:0.76, C:0.05, G:0.04, T:0.16
Consensus pattern (31 bp):
AAATAAAAAAAACAAAATAAATAAAATAAAT
Found at i:12267 original size:23 final size:23
Alignment explanation
Indices: 12206--12316 Score: 86
Period size: 23 Copynumber: 4.8 Consensus size: 23
12196 AGACAAAATT
12206 AAATAAAATTAAATA-AAAAACAA
1 AAATAAAA-TAAATATAAAAACAA
* * * **
12229 AAACAAGA-AAACATAAAAATGA
1 AAATAAAATAAATATAAAAACAA
12251 AAATAAAATAAATATAAAAACAA
1 AAATAAAATAAATATAAAAACAA
* *
12274 AAATAACTTATATATATAGAAAA-AA
1 AAATAA--AATAAATATA-AAAACAA
12299 TAAATAAAATAAA-ATAAA
1 -AAATAAAATAAATATAAA
12317 TAATAATAGG
Statistics
Matches: 68, Mismatches: 14, Indels: 13
0.72 0.15 0.14
Matches are distributed among these distances:
21 4 0.06
22 14 0.21
23 26 0.38
24 4 0.06
25 10 0.15
26 10 0.15
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.19
Consensus pattern (23 bp):
AAATAAAATAAATATAAAAACAA
Found at i:12450 original size:17 final size:17
Alignment explanation
Indices: 12428--12463 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12418 TAATAAGAAC
12428 AAAAAAAAAAAAATAAT
1 AAAAAAAAAAAAATAAT
* *
12445 AAAAAAGAAAAGATAAT
1 AAAAAAAAAAAAATAAT
12462 AA
1 AA
12464 TATAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (17 bp):
AAAAAAAAAAAAATAAT
Found at i:12455 original size:20 final size:20
Alignment explanation
Indices: 12428--12472 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
12418 TAATAAGAAC
12428 AAAAAAAAAAAAATAATA-A
1 AAAAAAAAAAAAATAATATA
* *
12447 AAAAGAAAAGATAATAATATA
1 AAAA-AAAAAAAAATAATATA
12468 AAAAA
1 AAAAA
12473 TATATGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 4 0.18
20 13 0.59
21 5 0.23
ACGTcount: A:0.82, C:0.00, G:0.04, T:0.13
Consensus pattern (20 bp):
AAAAAAAAAAAAATAATATA
Found at i:12455 original size:23 final size:22
Alignment explanation
Indices: 12416--12472 Score: 53
Period size: 23 Copynumber: 2.5 Consensus size: 22
12406 ACATAATAAT
*
12416 AATAATAAGAACAAAAAAAAAAA
1 AATAATAA-AAAAAAAAAAAAAA
* * *
12439 AATAATAAAAAAGAAAAGATAAT
1 AATAATAAAAAA-AAAAAAAAAA
12462 AAT-ATAAAAAA
1 AATAATAAAAAA
12473 TATATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 11 0.38
23 18 0.62
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (22 bp):
AATAATAAAAAAAAAAAAAAAA
Found at i:14234 original size:29 final size:31
Alignment explanation
Indices: 14192--14263 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
14182 GTGATAGGCA
*
14192 TCTTCTTGAAAGAC-C-ATGTTGTTTGGTCG
1 TCTTCTTGAAAGACTCTATGTCGTTTGGTCG
14221 TCTTCTTGAAAGACTCTATGTCGTTTGGTCG
1 TCTTCTTGAAAGACTCTATGTCGTTTGGTCG
14252 T-TTGCTTGAAAG
1 TCTT-CTTGAAAG
14264 GTGTCATGTC
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
29 14 0.36
30 3 0.08
31 22 0.56
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.42
Consensus pattern (31 bp):
TCTTCTTGAAAGACTCTATGTCGTTTGGTCG
Found at i:18599 original size:31 final size:31
Alignment explanation
Indices: 18532--18591 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
18522 CAATTTAAGG
*
18532 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
18563 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
18592 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:18683 original size:19 final size:19
Alignment explanation
Indices: 18656--18722 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
18646 AATGTTTTTA
*
18656 TGAATAGTAATTTCCTATT
1 TGAACAGTAATTTCCTATT
* *
18675 TGAACAGTAAATTACTATT
1 TGAACAGTAATTTCCTATT
* * *
18694 TGAATAGT-ATATCACTGTT
1 TGAACAGTAATTTC-CTATT
18713 TGAACAGTAA
1 TGAACAGTAA
18723 CTCGAGGCTC
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
18 2 0.05
19 34 0.92
20 1 0.03
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.39
Consensus pattern (19 bp):
TGAACAGTAATTTCCTATT
Found at i:18854 original size:21 final size:21
Alignment explanation
Indices: 18828--18869 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
18818 ATTTGAATAT
*
18828 TATGAAGAGGTATCGATTCCC
1 TATGAAGAGGTACCGATTCCC
*
18849 TATGAAGGGGTACCGATTCCC
1 TATGAAGAGGTACCGATTCCC
18870 CCCATTCTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (21 bp):
TATGAAGAGGTACCGATTCCC
Found at i:18931 original size:21 final size:21
Alignment explanation
Indices: 18898--18937 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
18888 TTTTTGCATA
*
18898 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
18920 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
18938 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:22082 original size:31 final size:31
Alignment explanation
Indices: 22015--22074 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
22005 CAATTTAAGG
*
22015 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
22046 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
22075 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:22166 original size:19 final size:19
Alignment explanation
Indices: 22139--22205 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
22129 AATGTTTTTA
*
22139 TGAATAGTAATTTCCTATT
1 TGAACAGTAATTTCCTATT
* *
22158 TGAACAGTAAATTACTATT
1 TGAACAGTAATTTCCTATT
* * *
22177 TGAATAGT-ATATCACTGTT
1 TGAACAGTAATTTC-CTATT
22196 TGAACAGTAA
1 TGAACAGTAA
22206 CTCGAGGCTC
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
18 2 0.05
19 34 0.92
20 1 0.03
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.39
Consensus pattern (19 bp):
TGAACAGTAATTTCCTATT
Found at i:22265 original size:21 final size:21
Alignment explanation
Indices: 22236--22275 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
22226 ATATGTAAAA
22236 GGGGAACCGATTCCCCCCAAG
1 GGGGAACCGATTCCCCCCAAG
*
22257 GGGGTACCGATTCCCCCCA
1 GGGGAACCGATTCCCCCCA
22276 TTCTGGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.40, G:0.28, T:0.12
Consensus pattern (21 bp):
GGGGAACCGATTCCCCCCAAG
Found at i:22333 original size:21 final size:21
Alignment explanation
Indices: 22300--22339 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
22290 TTTTTGCATA
*
22300 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
22322 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
22340 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:22594 original size:34 final size:32
Alignment explanation
Indices: 22555--22624 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
22545 TTTTGTAAAG
*
22555 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
22589 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
22621 GGGA
1 GGGA
22625 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:27651 original size:32 final size:32
Alignment explanation
Indices: 27614--27739 Score: 137
Period size: 32 Copynumber: 3.9 Consensus size: 32
27604 ATATTCTTGA
* *
27614 TGTGCATTATTTGAATGCAAAACTAACTCTGT
1 TGTGCATTATCTGAATGCAATACTAACTCTGT
* * **
27646 TGTGCATTATCTGAATACAATACGAACTCTAA
1 TGTGCATTATCTGAATGCAATACTAACTCTGT
* * * *
27678 TGTGCATTA-CATGCATGCAGTATTGACTCTGT
1 TGTGCATTATC-TGAATGCAATACTAACTCTGT
*
27710 TGTGCATTATCTGAATGCAATACTGACTCT
1 TGTGCATTATCTGAATGCAATACTAACTCT
27740 ACTGAGTATT
Statistics
Matches: 75, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
31 1 0.01
32 73 0.97
33 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTGCATTATCTGAATGCAATACTAACTCTGT
Found at i:27696 original size:64 final size:64
Alignment explanation
Indices: 27613--27740 Score: 168
Period size: 64 Copynumber: 2.0 Consensus size: 64
27603 AATATTCTTG
**
27613 ATGTGCATTATTTGAATGCAAAACTAACTCTGTTGTGCATTATCTGAATACAATAC-GAACTCTA
1 ATGTGCATTACATGAATGCAAAACTAACTCTGTTGTGCATTATCTGAATACAATACTG-ACTCTA
* ** * * *
27677 ATGTGCATTACATGCATGCAGTATTGACTCTGTTGTGCATTATCTGAATGCAATACTGACTCTA
1 ATGTGCATTACATGAATGCAAAACTAACTCTGTTGTGCATTATCTGAATACAATACTGACTCTA
27741 CTGAGTATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
64 54 0.98
65 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.35
Consensus pattern (64 bp):
ATGTGCATTACATGAATGCAAAACTAACTCTGTTGTGCATTATCTGAATACAATACTGACTCTA
Found at i:31236 original size:46 final size:45
Alignment explanation
Indices: 31057--31278 Score: 324
Period size: 44 Copynumber: 4.9 Consensus size: 45
31047 GTAAGCATGC
**
31057 AAATAAGCTTACGAGCTTATGGAAT-AATGACAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * * *
31101 AAATAAGATTACGATCTTATGGAAT-AATGGCAAATATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
31145 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
31190 AAATAAGCTTACGAGCTTATGGGATTAAATAGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAGTATATTGGTA
31236 AAATAAGCTTACGAGCTTATGTG-ATAAAATGGTAAGTATATTG
1 AAATAAGCTTACGAGCTTATG-GAAT-AAATGGTAAGTATATTG
31279 ATAAGAAATT
Statistics
Matches: 162, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
44 63 0.39
45 39 0.24
46 60 0.37
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:31897 original size:11 final size:11
Alignment explanation
Indices: 31881--31905 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31871 CATTTTAGGA
31881 AAATCAATTTT
1 AAATCAATTTT
31892 AAATCAATTTT
1 AAATCAATTTT
31903 AAA
1 AAA
31906 ATAGAAATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (11 bp):
AAATCAATTTT
Found at i:37679 original size:21 final size:19
Alignment explanation
Indices: 37619--37692 Score: 105
Period size: 19 Copynumber: 3.8 Consensus size: 19
37609 TATTGTTCAT
37619 AGTTTTGAAACTTTGTAAG
1 AGTTTTGAAACTTTGTAAG
37638 AGTTTTGAAACTTTGTAAG
1 AGTTTTGAAACTTTGTAAG
37657 AGTTTTGAAACCTCTAT-TAAG
1 AGTTTTGAAA-CT-T-TGTAAG
*
37678 AGTTTCGAAACTTTG
1 AGTTTTGAAACTTTG
37693 CACCCAAAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 8
0.85 0.02 0.14
Matches are distributed among these distances:
18 1 0.02
19 30 0.60
20 4 0.08
21 14 0.28
22 1 0.02
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (19 bp):
AGTTTTGAAACTTTGTAAG
Found at i:40960 original size:45 final size:45
Alignment explanation
Indices: 40909--41130 Score: 225
Period size: 45 Copynumber: 4.9 Consensus size: 45
40899 ATGAATAAAA
* *
40909 GAAAATGCATAACTTTGCATTATCGACATAAAAGGTGCCATTAAT
1 GAAAATGCATAACTGTGCATTATCGACATAAAAGGTGCCACTAAT
* * *
40954 GAAAATGCATAA-TGGTGCATTATCAACATAAAAGGCGACACTAAT
1 GAAAATGCATAACT-GTGCATTATCGACATAAAAGGTGCCACTAAT
* * * * * *
40999 GAATATGCATAACGGTGCATTTTTGGCATAAAAGGTGCCAGTAAT
1 GAAAATGCATAACTGTGCATTATCGACATAAAAGGTGCCACTAAT
* * * *
41044 GAAAATACATAA-TGGTGTATTATC-AGTATAAAAGGTGCTACTAAT
1 GAAAATGCATAACT-GTGCATTATCGA-CATAAAAGGTGCCACTAAT
* * * *
41089 GAAAATGCATAACGGTGCATCATTGGCATAAAAGGTGCCACT
1 GAAAATGCATAACTGTGCATTATCGACATAAAAGGTGCCACT
41131 CATGGTATTA
Statistics
Matches: 139, Mismatches: 32, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
44 1 0.01
45 138 0.99
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (45 bp):
GAAAATGCATAACTGTGCATTATCGACATAAAAGGTGCCACTAAT
Found at i:41033 original size:90 final size:90
Alignment explanation
Indices: 40909--41128 Score: 298
Period size: 90 Copynumber: 2.4 Consensus size: 90
40899 ATGAATAAAA
** * * * * *
40909 GAAAATGCATAACTTTGCATTATCGACATAAAAGGTGCCATTAATGAAAATGCATAATGGTGCAT
1 GAAAATGCATAACGGTGCATCATTGGCATAAAAGGTGCCAGTAATGAAAATACATAATGGTGCAT
40974 TATCAACATAAAAGGCGAC-ACTAAT
66 TATCAACATAAAAGGCG-CTACTAAT
* ** *
40999 GAATATGCATAACGGTGCATTTTTGGCATAAAAGGTGCCAGTAATGAAAATACATAATGGTGTAT
1 GAAAATGCATAACGGTGCATCATTGGCATAAAAGGTGCCAGTAATGAAAATACATAATGGTGCAT
** *
41064 TATCAGTATAAAAGGTGCTACTAAT
66 TATCAACATAAAAGGCGCTACTAAT
41089 GAAAATGCATAACGGTGCATCATTGGCATAAAAGGTGCCA
1 GAAAATGCATAACGGTGCATCATTGGCATAAAAGGTGCCA
41129 CTCATGGTAT
Statistics
Matches: 114, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
89 1 0.01
90 113 0.99
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (90 bp):
GAAAATGCATAACGGTGCATCATTGGCATAAAAGGTGCCAGTAATGAAAATACATAATGGTGCAT
TATCAACATAAAAGGCGCTACTAAT
Found at i:47439 original size:179 final size:178
Alignment explanation
Indices: 47128--47505 Score: 435
Period size: 179 Copynumber: 2.1 Consensus size: 178
47118 TTATTTGTAA
* *
47128 TTATATATTTTAATTATAGTTACAAAATGTATAGTCACAAATGATTATCTCCAATTTTTGGTAAA
1 TTATATATTTTAATTATAGTGACAAAATATATAGTCACAAATGATTATCTCCAATTTTTGGTAAA
* * * *
47193 AAAACAAAATCATATAGTGACATGTTTTGTAACTATAAGCTATAATTATTGTTACAAAAAAATTG
66 AAAACAAAATCATATAATGACATATTTTGTAACTATAAGCTATAATAATTATTACAAAAAAATTG
47258 TCACAACAAATAATGAGATTCAAGTTTTTAGTAAAAAACAATGTTTGTCG
131 TCACAA-AAA-AATGAGATTCAAGTTTTTAGTAAAAAACAATGTTTGTCG
* * * *
47308 TTATATGTTTTAATTATAGTGACAAAATATATTGTCACAAAT-ATTTCTCTCCATATTTTT-GTG
1 TTATATATTTTAATTATAGTGACAAAATATATAGTCACAAATGA-TTATCTCCA-ATTTTTGGTA
** * * *
47371 CCAAAA-AAAGTCATATAATGACCA-ATTTTGTAACTATAAG-TGTTAATAATTATTACAAAAAC
64 AAAAAACAAAATCATATAATGA-CATATTTTGTAACTATAAGCT-ATAATAATTATTACAAAAAA
* * * * ** * *
47433 ATTGTCACAAAAAAATGATATTCACGTTTTT-GTGACAAATTATATTTGTAG
127 ATTGTCACAAAAAAATGAGATTCAAGTTTTTAGTAAAAAACAATGTTTGTCG
* *
47484 TTATAAATTTTAACTATAGTGA
1 TTATATATTTTAATTATAGTGA
47506 TAGTATATAT
Statistics
Matches: 168, Mismatches: 26, Indels: 12
0.82 0.13 0.06
Matches are distributed among these distances:
176 33 0.20
177 16 0.10
178 4 0.02
179 55 0.33
180 54 0.32
181 6 0.04
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (178 bp):
TTATATATTTTAATTATAGTGACAAAATATATAGTCACAAATGATTATCTCCAATTTTTGGTAAA
AAAACAAAATCATATAATGACATATTTTGTAACTATAAGCTATAATAATTATTACAAAAAAATTG
TCACAAAAAAATGAGATTCAAGTTTTTAGTAAAAAACAATGTTTGTCG
Found at i:48065 original size:419 final size:412
Alignment explanation
Indices: 47329--48117 Score: 1062
Period size: 419 Copynumber: 1.9 Consensus size: 412
47319 AATTATAGTG
* * *
47329 ACAAAATATATTGTCACAAATATTTCTCTCCATATTTTTGTGCCAAAAAAAGTCATATAATGACC
1 ACAAAATATATTGCCACAAATATTTCTCTCCATATTTTTGTACCAAAAAAAGTCATATAATGAAC
*
47394 AATTTTGTAACTATAAGTGTTAATAATTATTACAAAAACATTGTCACAAAAAAATGATATTCACG
66 AATTTTGTAACTATAAGTGTTAATAATTATTACAAAAACATTGTCACAAAAAAATGATATTCACA
* *
47459 TTTTTGTGACAAATTATATTTGTAGTTATAAATTTTAACTATAGTGATAGTATATATTTAATTTT
131 TTTTTGTGACAAATTATACTTGTAGTTATAAATTTTAACTATAGTGATAG-ACATA-TTAATTTT
* *
47524 CATAACTATTTTTCTCCACTTTTTTGTTTCAAAAGTTATATTGAAAATTTTTATAATTACAATTT
194 CATAAATATTTTTCTCCACTTTTTTGTTTCAAAAGTTATATTGAAAAGTTTTATAATTACAATTT
* *
47589 ATAGTTATTGTTATAGAAACAATTATCACATCAAATAATAAAATTCAAGTTTTTTGTAATAAATT
259 ATAGTTATTGTTATAGAAAAAATTATCACATCAAATAATAAAATTAAAGTTTTTTGTAATAAATT
*
47654 ATTTTTGTACTTATATATTTTAATTATTATGAAAAATTATACTATCAGAACCATTTCTCCCTATT
324 ATTTTTGTACTTATATATTTTAATCATTATGAAAAATTATACTATCAGAACCATTTCTCCCTATT
47719 TTTTGTCAAAAATGTTATATATTA
389 TTTTGTCAAAAATGTTATATATTA
* * *
47743 ACAAAATATATTGCCATAAATATTT-TCCTCCATATTTTTTTTACACCAAAAAAA-TCATATAGT
1 ACAAAATATATTGCCACAAATATTTCT-CTCCATA-TTTTTGT--ACCAAAAAAAGTCATATAAT
** *
47806 -AACAATTTTTGTAACTATAAGTGTTTGTAATTATTACAAAAAACTTTGACTCA-AAAAATAATG
62 GAACAA-TTTTGTAACTATAAGTGTTAATAATTATTAC-AAAAACATTG--TCACAAAAA-AATG
* * * * *
47869 GTATTTACATTTTTGTTAGAAATTATACTTGTAGTTATAAATTTTAATTATAGTGATA-ACATA-
122 ATATTCACATTTTTGTGACAAATTATACTTGTAGTTATAAATTTTAACTATAGTGATAGACATAT
47932 T-ATTGTT-ATAAATATTTTTCTCCACTTTTTTTTTTTTTGTTTCAAAAAGTTATATT-AATAAG
187 TAATT-TTCATAAATATTTTTCTCCAC-------TTTTTTGTTTC-AAAAGTTATATTGAA-AAG
* * *
47994 TTTTGTAATTATAATTTATAGTTATTGTTATAGAAAAAATT-T-ACATCAGATAATAAAATTAAA
242 TTTTATAATTACAATTTATAGTTATTGTTATAGAAAAAATTATCACATCAAATAATAAAATTAAA
* *
48057 G-TTTTTGTAATCAATTATTTTTGTAGTTATATATTTTAATCATTATGAAAAATTATACTAT
307 GTTTTTTGTAATAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAAATTATACTAT
48118 AAAAAATTTT
Statistics
Matches: 329, Mismatches: 27, Indels: 33
0.85 0.07 0.08
Matches are distributed among these distances:
413 1 0.00
414 50 0.15
415 13 0.04
416 37 0.11
417 22 0.07
418 5 0.02
419 115 0.35
420 20 0.06
421 14 0.04
422 52 0.16
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.44
Consensus pattern (412 bp):
ACAAAATATATTGCCACAAATATTTCTCTCCATATTTTTGTACCAAAAAAAGTCATATAATGAAC
AATTTTGTAACTATAAGTGTTAATAATTATTACAAAAACATTGTCACAAAAAAATGATATTCACA
TTTTTGTGACAAATTATACTTGTAGTTATAAATTTTAACTATAGTGATAGACATATTAATTTTCA
TAAATATTTTTCTCCACTTTTTTGTTTCAAAAGTTATATTGAAAAGTTTTATAATTACAATTTAT
AGTTATTGTTATAGAAAAAATTATCACATCAAATAATAAAATTAAAGTTTTTTGTAATAAATTAT
TTTTGTACTTATATATTTTAATCATTATGAAAAATTATACTATCAGAACCATTTCTCCCTATTTT
TTGTCAAAAATGTTATATATTA
Found at i:53176 original size:2 final size:2
Alignment explanation
Indices: 53166--53346 Score: 60
Period size: 2 Copynumber: 92.5 Consensus size: 2
53156 TATATGGTGT
* * * *
53166 TA TA T- TA TA TA GTA CA TA TA TT TA TA GTG TT TA TA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * * * *
53209 TA TA TA TA T- TG TG TA TT TA TA TA TA T- TA TA AA GTA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * *
53250 T- TA TT TA TA TA T- TA TA TGG TA TT TT TA T- TA TA TA -A TA T-
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
* * *
53288 TA TA GTG TA GTA TT TA TA GTA TA TA -A TA TA TA CA TA TA TA T-
1 TA TA -TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* *
53329 TA TT TA TA -A TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA T
53347 TTTATAATAT
Statistics
Matches: 131, Mismatches: 30, Indels: 36
0.66 0.15 0.18
Matches are distributed among these distances:
1 11 0.08
2 110 0.84
3 10 0.08
ACGTcount: A:0.39, C:0.01, G:0.07, T:0.54
Consensus pattern (2 bp):
TA
Found at i:53227 original size:29 final size:30
Alignment explanation
Indices: 53165--53266 Score: 90
Period size: 29 Copynumber: 3.5 Consensus size: 30
53155 ATATATGGTG
* *
53165 TTATAT-TATATAGTACA-TATATTTATAGTGT
1 TTATATATATATA-TAAAGTATA-TT-TAGTAT
*
53196 TTATATATATATATATA-TATATTGT-GTAT
1 TTATATATATATATAAAGTATATT-TAGTAT
*
53225 TTATATATAT-TATAAAGTATATTTATTAT
1 TTATATATATATATAAAGTATATTTAGTAT
53254 TTATATAT-TATAT
1 TTATATATATATAT
53267 GGTATTTTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
28 7 0.11
29 33 0.53
30 3 0.05
31 13 0.21
32 6 0.10
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (30 bp):
TTATATATATATATAAAGTATATTTAGTAT
Found at i:53238 original size:7 final size:7
Alignment explanation
Indices: 53196--53429 Score: 59
Period size: 7 Copynumber: 31.9 Consensus size: 7
53186 TTTATAGTGT
53196 TTATATA
1 TTATATA
53203 -TATATA
1 TTATATA
53209 TATATATA
1 T-TATATA
* *
53217 TTGTGTATT
1 -T-TATATA
53226 TATATATA
1 T-TATATA
*
53234 TTATAAA
1 TTATATA
*
53241 GTATAT-
1 TTATATA
53247 TTAT-TA
1 TTATATA
53253 TTTATATA
1 -TTATATA
53261 TTATATGGTA
1 TTATA---TA
*
53271 TT-TTTA
1 TTATATA
53277 TTATATA
1 TTATATA
*
53284 ATATTATA
1 TTA-TATA
* *
53292 GTGTAGTA
1 TTATA-TA
53300 TT-TATA
1 TTATATA
*
53306 GTATATA
1 TTATATA
*
53313 ATATATA
1 TTATATA
*
53320 CATATATA
1 -TTATATA
*
53328 TTATTTA
1 TTATATA
*
53335 TAATAT-
1 TTATATA
*
53341 TTATATT
1 TTATATA
53348 TTATAATA
1 TTAT-ATA
*
53356 TGTA-GTA
1 T-TATATA
* *
53363 GTATGTA
1 TTATATA
*
53370 TTAAATA
1 TTATATA
*
53377 TTATAGA
1 TTATATA
*
53384 CATATACTA
1 -TTATA-TA
53393 TTTATATA
1 -TTATATA
53401 TTATATA
1 TTATATA
*
53408 GTCTTTATA
1 -T-TATATA
*
53417 TTATATT
1 TTATATA
53424 TTATAT
1 TTATAT
53430 TTTTAGTATC
Statistics
Matches: 167, Mismatches: 38, Indels: 44
0.67 0.15 0.18
Matches are distributed among these distances:
5 1 0.01
6 23 0.14
7 81 0.49
8 40 0.24
9 18 0.11
10 4 0.02
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.53
Consensus pattern (7 bp):
TTATATA
Found at i:53258 original size:27 final size:27
Alignment explanation
Indices: 53196--53341 Score: 94
Period size: 27 Copynumber: 5.5 Consensus size: 27
53186 TTTATAGTGT
*
53196 TTATATATATA-TATATA-TATATTGTGTA
1 TTATATATATATTATAAAGTATA-T-T-TA
53224 TT-TATATATATTATAAAGTATATTTA
1 TTATATATATATTATAAAGTATATTTA
* ** *
53250 TTATTTATATATTATATGGTATTTTTA
1 TTATATATATATTATAAAGTATATTTA
**
53277 TTATATA-ATATTATAGTGTAGTATTTA
1 TTATATATATATTATAAAGTA-TATTTA
*
53304 -TAGTATATA-ATATATACA-TATATATTA
1 TTA-TATATATAT-TATAAAGTATAT-TTA
53331 TT-TATA-ATATT
1 TTATATATATATT
53342 TATATTTTAT
Statistics
Matches: 97, Mismatches: 11, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
25 2 0.02
26 26 0.27
27 51 0.53
28 14 0.14
29 4 0.04
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (27 bp):
TTATATATATATTATAAAGTATATTTA
Found at i:53405 original size:69 final size:69
Alignment explanation
Indices: 53251--53422 Score: 156
Period size: 69 Copynumber: 2.4 Consensus size: 69
53241 GTATATTTAT
* * * * *
53251 TATTTATATATTATATGGTATTTTTATTATATAATATTATAGTGTAGTATTTATAGTATATAATA
1 TATTTATATATTATA-GATATTTATATTATATAATATTATAGTATAGTATTAATAGTATATAACA
53316 TATAC
65 TATAC
* *
53321 -ATATATATTATTTATA-ATATTTATATTTTATAATATGTAGTAGTAT-GTATTAA-A-TATTAT
1 TATTTATA-TA-TTATAGATATTTATATTATATAATAT-TA-TAGTATAGTATTAATAGTA-TAT
53381 AGACATATAC
61 A-ACATATAC
* *
53391 TATTTATATATTATATAGTCTTTATATTATAT
1 TATTTATATATTATAGA-TATTTATATTATAT
53423 TTTATATTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 17
0.75 0.09 0.15
Matches are distributed among these distances:
68 2 0.02
69 33 0.40
70 20 0.24
71 28 0.34
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.52
Consensus pattern (69 bp):
TATTTATATATTATAGATATTTATATTATATAATATTATAGTATAGTATTAATAGTATATAACAT
ATAC
Found at i:54772 original size:263 final size:263
Alignment explanation
Indices: 54300--54826 Score: 844
Period size: 263 Copynumber: 2.0 Consensus size: 263
54290 ATGTTGAATG
* *
54300 AATCAAGTGGTCTCCGTGATAAAGGAATGATTATCGTTCTTTGAGACTTGGGTTCGAATACCGAA
1 AATCAAGTGGTCTCCGTGATAAAGGAATCATTATCGTTCTTTGAGACTTGGGTTCGAACACCGAA
* * * * * *
54365 AATGTTAGGGGTGTAAGCGTTTAATGTTAAGAGTTTGAGAGTAATCTTAAAATAAATACTACCTT
66 AACGTCAGGGATATAAGCGTTCAATGTTAAGAGTTTGAGAGTAATCTTAAAACAAATACTACCTT
* *
54430 ATACTTATCTCATATTAATTAAAAAAAATAAAGAGACATCGTTGAAAAAGTAAAAAAGTGAAACC
131 ATACTTACCTCATATTAATTAAAAAAAATAAAGAGACATCGTCGAAAAAGTAAAAAAGTGAAACC
* *
54495 TTGCATGGTAGATCTAAGTCATTGGGGTTGGTTCTTGGATATATATAACACCCTTAATTTGTATT
196 TTGCATGCTAGATCTAAGTCATTGGGGTTGGTTCTTGGATATATATAACACCCTTAACTTGTATT
54560 CGT
261 CGT
*
54563 AATCAAGTGGTCTCCGTGATAAAGGAATCATTATCGTT-TCTTGAGACTTGGGTTCGAGCACCGA
1 AATCAAGTGGTCTCCGTGATAAAGGAATCATTATCGTTCT-TTGAGACTTGGGTTCGAACACCGA
* * * *
54627 GAACGTCAGGGATATAAGCGTTCAATGTTAAGAGTTTGAGAGTAATCTTAGAACAAATATTATCT
65 AAACGTCAGGGATATAAGCGTTCAATGTTAAGAGTTTGAGAGTAATCTTAAAACAAATACTACCT
54692 TATACTTACCTCATATTAATTAAAAAAAATAAAGA-A-ATCCTGTCGAAAAAGTAAAAAAGTGAA
130 TATACTTACCTCATATTAATTAAAAAAAATAAAGAGACAT-C-GTCGAAAAAGTAAAAAAGTGAA
*
54755 ACTTTGCATGCTAGATCTAAGTCATTGGGGTTGGTTCTTGGATATATATAACACCCTTAACTTGT
193 ACCTTGCATGCTAGATCTAAGTCATTGGGGTTGGTTCTTGGATATATATAACACCCTTAACTTGT
54820 ATTCGT
258 ATTCGT
54826 A
1 A
54827 CCCGAATACA
Statistics
Matches: 243, Mismatches: 18, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
261 2 0.01
262 3 0.01
263 238 0.98
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32
Consensus pattern (263 bp):
AATCAAGTGGTCTCCGTGATAAAGGAATCATTATCGTTCTTTGAGACTTGGGTTCGAACACCGAA
AACGTCAGGGATATAAGCGTTCAATGTTAAGAGTTTGAGAGTAATCTTAAAACAAATACTACCTT
ATACTTACCTCATATTAATTAAAAAAAATAAAGAGACATCGTCGAAAAAGTAAAAAAGTGAAACC
TTGCATGCTAGATCTAAGTCATTGGGGTTGGTTCTTGGATATATATAACACCCTTAACTTGTATT
CGT
Found at i:55524 original size:14 final size:14
Alignment explanation
Indices: 55501--55533 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
55491 TTTAACCTAT
*
55501 TTAAATCATATTTA
1 TTAAAACATATTTA
55515 TTAAAACATATTTA
1 TTAAAACATATTTA
55529 TTAAA
1 TTAAA
55534 TCACATAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (14 bp):
TTAAAACATATTTA
Found at i:56067 original size:56 final size:59
Alignment explanation
Indices: 56005--56361 Score: 215
Period size: 65 Copynumber: 5.7 Consensus size: 59
55995 CAGTACAGTA
56005 TTCAATTATCACTCCACCTCATGCATCACAAAGGTACATGAGTGA-T-T-TGTACA-TT
1 TTCAATTATCACTCCACCTCATGCATCACAAAGGTACATGAGTGAGTATCTGTACACTT
* *
56060 GTTCAATTATCACTCCACCTCATGC-TCTGCACAGGTACATGAGCCATATGAGTAATCTGTACAG
1 -TTCAATTATCACTCCACCTCATGCATC-ACAAAGGTACATGAG-----TGAGT-ATCTGTACA-
56124 CTT
57 CTT
* * * *
56127 TT-AATTATCACTCCACCTCATGCATCACAAAGGTACATGAGTCATATGAATGATATGTATAGTG
1 TTCAATTATCACTCCACCTCATGCATCACAAAGGTACATGAG-----TGAGT-ATCTGTACACT-
56191 T
59 T
* * * * * * *
56192 TT-AATTATCTCTCCACCTCATGCACCACTAAGGTACATGAGTCATATGAGTGATTTGTATAGTG
1 TTCAATTATCACTCCACCTCATGCATCACAAAGGTACATGAG-----TGAGT-ATCTGTACACTT
* * * * * * *
56256 TTCAATTATCACTCCACCTCATGCACCATAATGATACATGAGTCATATGAGTAATCCGTACAGTA
1 TTCAATTATCACTCCACCTCATGCATCACAAAGGTACATGAG-----TGAGT-ATCTGTACACTT
* *
56321 TTCAATTATCACTCCACCTCATGCACCACAAAGGTGCATGA
1 TTCAATTATCACTCCACCTCATGCATCACAAAGGTACATGA
56362 ATCATATGAG
Statistics
Matches: 256, Mismatches: 30, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
55 2 0.01
56 37 0.14
61 3 0.01
62 1 0.00
64 4 0.02
65 203 0.79
66 4 0.02
67 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (59 bp):
TTCAATTATCACTCCACCTCATGCATCACAAAGGTACATGAGTGAGTATCTGTACACTT
Found at i:56273 original size:195 final size:195
Alignment explanation
Indices: 56040--56470 Score: 564
Period size: 195 Copynumber: 2.2 Consensus size: 195
56030 TCACAAAGGT
* * * * *
56040 ACATGAGTGATTTGTACATTGTTCAATTATCACTCCACCTCATGCTCTGCA-CA-GGTACATGAG
1 ACATGAGTGATTTGTATAGTGTTCAATTATCACTCCACCTCATGCAC--CATAATGATACATGAG
* * *
56103 CCATATGAGTAATCTGTACAGCT-TTTAATTATCACTCCACCTCATGCATCACAAAGGTACATGA
64 CCATATGAGTAATCCGTACAG-TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGA
* * * * * * * *
56167 GTCATATGAATGATAT-GTATAGTGTTTAATTATCTCTCCACCTCATGCACCACTAAGGTACATG
128 ATCATATGAATGAT-TCGTATAGTATTCAACTATCACTCCACCTAATGCACCACAAAGGTACATA
56231 AGTC
192 AGTC
* *
56235 ATATGAGTGATTTGTATAGTGTTCAATTATCACTCCACCTCATGCACCATAATGATACATGAGTC
1 ACATGAGTGATTTGTATAGTGTTCAATTATCACTCCACCTCATGCACCATAATGATACATGAGCC
*
56300 ATATGAGTAATCCGTACAGTATTCAATTATCACTCCACCTCATGCACCACAAAGGTGCATGAATC
66 ATATGAGTAATCCGTACAGTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAATC
*
56365 ATATGAGTGATTCGTATAGTATTCAACTATCACTCCACCTAATGCACCACAAAGGTACATAAGTC
131 ATATGAATGATTCGTATAGTATTCAACTATCACTCCACCTAATGCACCACAAAGGTACATAAGTC
* * * ** *
56430 ACATGAGTGATTTATATTGTATTCAACAATCACTACACCTC
1 ACATGAGTGATTTGTATAGTGTTCAATTATCACTCCACCTC
56471 GTACATCATT
Statistics
Matches: 205, Mismatches: 27, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
193 2 0.01
194 3 0.01
195 200 0.98
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (195 bp):
ACATGAGTGATTTGTATAGTGTTCAATTATCACTCCACCTCATGCACCATAATGATACATGAGCC
ATATGAGTAATCCGTACAGTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAATC
ATATGAATGATTCGTATAGTATTCAACTATCACTCCACCTAATGCACCACAAAGGTACATAAGTC
Found at i:56438 original size:65 final size:65
Alignment explanation
Indices: 56042--56470 Score: 468
Period size: 65 Copynumber: 6.6 Consensus size: 65
56032 ACAAAGGTAC
* * * * * ** * *
56042 ATGAGTGATTTGTACATTGTTCAATTATCACTCCACCTCATGCTCTGCACAGGTACATGAGCCAT
1 ATGAGTGATTCGTATAGTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCAT
* * * *
56107 ATGAGT-AATCTGTACAGCT-TTTAATTATCACTCCACCTCATGCATCACAAAGGTACATGAGTC
1 ATGAGTGATTC-GTATAG-TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTC
56170 AT
64 AT
* * * * *
56172 ATGAATGATAT-GTATAGTGTTTAATTATCTCTCCACCTCATGCACCACTAAGGTACATGAGTCA
1 ATGAGTGAT-TCGTATAGTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCA
56236 T
65 T
* * * * *
56237 ATGAGTGATTTGTATAGTGTTCAATTATCACTCCACCTCATGCACCATAATGATACATGAGTCAT
1 ATGAGTGATTCGTATAGTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCAT
* * * * *
56302 ATGAGTAATCCGTACAGTATTCAATTATCACTCCACCTCATGCACCACAAAGGTGCATGAATCAT
1 ATGAGTGATTCGTATAGTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCAT
* * * *
56367 ATGAGTGATTCGTATAGTATTCAACTATCACTCCACCTAATGCACCACAAAGGTACATAAGTCAC
1 ATGAGTGATTCGTATAGTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCAT
** * ** *
56432 ATGAGTGATTTATATTGTATTCAACAATCACTACACCTC
1 ATGAGTGATTCGTATAGTATTCAATTATCACTCCACCTC
56471 GTACATCATT
Statistics
Matches: 310, Mismatches: 48, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
64 4 0.01
65 303 0.98
66 2 0.01
67 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (65 bp):
ATGAGTGATTCGTATAGTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCAT
Found at i:56591 original size:189 final size:189
Alignment explanation
Indices: 56366--56746 Score: 681
Period size: 189 Copynumber: 2.0 Consensus size: 189
56356 GCATGAATCA
56366 TATGAGTGATTCGTATAGTATTCAACTATCACTCCACCTAATGCACCACAAAGGTACATAAGTCA
1 TATGAGTGATTCGTATAGTATTCAACTATCACTCCACCTAATGCACCACAAAGGTACATAAGTCA
* * *
56431 CATGAGTGATTTATATTGTATTCAACAATCACTACACCTCGTACATCATTGACTCTCATGGCTTA
66 CATGAATGATTTATATTGTATTCAACAATCACTACACCTCATACATCATTGACTCTCACGGCTTA
56496 TATATTGCCCTTTTATTTAAATTTATATTATTTTTAATATAAAACATTTATAGAATAAT
131 TATATTGCCCTTTTATTTAAATTTATATTATTTTTAATATAAAACATTTATAGAATAAT
* *
56555 TATGAGTGATTCGTATAGTATTCAACTATCACTCCACCTAATGCAGCACAAAGGTACATGAGTCA
1 TATGAGTGATTCGTATAGTATTCAACTATCACTCCACCTAATGCACCACAAAGGTACATAAGTCA
* * * *
56620 CATGAATGATTTGTATTGTATTCAGCAATCACTACACCTCATACATCATTGTCTCTCACGTCTTA
66 CATGAATGATTTATATTGTATTCAACAATCACTACACCTCATACATCATTGACTCTCACGGCTTA
56685 TATATTGCCCTTTTATTTAAATTTATATTATTTTTAATATAAAACATTTATAGAATAAT
131 TATATTGCCCTTTTATTTAAATTTATATTATTTTTAATATAAAACATTTATAGAATAAT
56744 TAT
1 TAT
56747 CAACTTCATA
Statistics
Matches: 183, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
189 183 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (189 bp):
TATGAGTGATTCGTATAGTATTCAACTATCACTCCACCTAATGCACCACAAAGGTACATAAGTCA
CATGAATGATTTATATTGTATTCAACAATCACTACACCTCATACATCATTGACTCTCACGGCTTA
TATATTGCCCTTTTATTTAAATTTATATTATTTTTAATATAAAACATTTATAGAATAAT
Found at i:56826 original size:15 final size:17
Alignment explanation
Indices: 56784--56818 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
56774 ATATTTTAAT
*
56784 TAACTTAATAACTCATG
1 TAACTTTATAACTCATG
56801 TAACTTTATAACTCATG
1 TAACTTTATAACTCATG
56818 T
1 T
56819 TCTTATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (17 bp):
TAACTTTATAACTCATG
Found at i:59956 original size:21 final size:24
Alignment explanation
Indices: 59926--59974 Score: 68
Period size: 21 Copynumber: 2.2 Consensus size: 24
59916 TTTCAATGCA
59926 ATTTGATCC-TTG-ATTTA-TTTT
1 ATTTGATCCTTTGAATTTATTTTT
*
59947 ATTTGTTCCTTTGAATTTATTTTT
1 ATTTGATCCTTTGAATTTATTTTT
59971 ATTT
1 ATTT
59975 AAATTGGTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 8 0.33
22 3 0.12
23 5 0.21
24 8 0.33
ACGTcount: A:0.18, C:0.08, G:0.08, T:0.65
Consensus pattern (24 bp):
ATTTGATCCTTTGAATTTATTTTT
Found at i:63985 original size:23 final size:23
Alignment explanation
Indices: 63959--64002 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
63949 ATCTTATATG
63959 GCACTACGATGCAATTCTACGCT
1 GCACTACGATGCAATTCTACGCT
** *
63982 GCACTTTGGTGCAATTCTACG
1 GCACTACGATGCAATTCTACG
64003 TGGCACCTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (23 bp):
GCACTACGATGCAATTCTACGCT
Found at i:64016 original size:23 final size:23
Alignment explanation
Indices: 63968--64017 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
63958 GGCACTACGA
* **
63968 TGCAATTCTACGCTGCACTTTGG
1 TGCAATTCTACGCTGCACCTCAG
63991 TGCAATTCTACG-TGGCACCTCAG
1 TGCAATTCTACGCT-GCACCTCAG
64014 TGCA
1 TGCA
64018 TTTATACGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.30
Consensus pattern (23 bp):
TGCAATTCTACGCTGCACCTCAG
Found at i:67255 original size:13 final size:13
Alignment explanation
Indices: 67219--67271 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
67209 TCATAAATCG
*
67219 ATGACGTGCATTT
1 ATGACGCGCATTT
* *
67232 ATGGCACGCATTT
1 ATGACGCGCATTT
*
67245 ATGACGTGCATTT
1 ATGACGCGCATTT
*
67258 ATGATGCGCATTT
1 ATGACGCGCATTT
67271 A
1 A
67272 CGACTTACAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.36
Consensus pattern (13 bp):
ATGACGCGCATTT
Found at i:67267 original size:26 final size:26
Alignment explanation
Indices: 67219--67271 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
67209 TCATAAATCG
*
67219 ATGACGTGCATTTATGGCACGCATTT
1 ATGACGTGCATTTATGACACGCATTT
**
67245 ATGACGTGCATTTATGATGCGCATTT
1 ATGACGTGCATTTATGACACGCATTT
67271 A
1 A
67272 CGACTTACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.36
Consensus pattern (26 bp):
ATGACGTGCATTTATGACACGCATTT
Done.