Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002222.1 Hibiscus syriacus cultivar Beakdansim tig00004520_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: 93303
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:22 original size:2 final size:2
Alignment explanation
Indices: 15--233 Score: 190
Period size: 2 Copynumber: 109.0 Consensus size: 2
5 TGATAAAAGC
* ** * * *
15 TA TA TA TA TA TA TA GTA AA CG TG TA TA CA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
58 TA TA CA TA TA TA TA TA TA TA CA TA CA TG TA TA -A TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
99 TA CA TA CA TA TA TA TA TA TA GTA TA TA TA T- TA TCA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA T-A TA TA TA TA
* * * * *
142 TA CA TA CA TA TA TA CA TA CA TA TA TA TG TA 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
* * * *
184 TA TA TA TA TA TA TA TG TA TA TC TA TG TC TA 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
226 TA TA TA TA
1 TA TA TA TA
234 GAGAGAGAGA
Statistics
Matches: 170, Mismatches: 42, Indels: 10
0.77 0.19 0.05
Matches are distributed among these distances:
1 2 0.01
2 162 0.95
3 6 0.04
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (2 bp):
TA
Found at i:3060 original size:21 final size:21
Alignment explanation
Indices: 3034--3076 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3024 TCAATGTATT
3034 ACTATGTAGATTTAGAACGTA
1 ACTATGTAGATTTAGAACGTA
3055 ACTATGTAGATTTAGAACGTA
1 ACTATGTAGATTTAGAACGTA
3076 A
1 A
3077 TCTCGTTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.33
Consensus pattern (21 bp):
ACTATGTAGATTTAGAACGTA
Found at i:5323 original size:59 final size:59
Alignment explanation
Indices: 5224--5340 Score: 157
Period size: 59 Copynumber: 2.0 Consensus size: 59
5214 TATTTGACAT
* *
5224 GATGCCTTCAAGTTCCAAGGGAGGCATTCAACTGCGAGCTTCTTCGACCTCAATGTCGA
1 GATGCCTTCAAGTTCCAAGGGAAGCATTCAACTGCGAGCTTCTTCGACCTAAATGTCGA
* * *
5283 GATGCCTTCAAGTT-CAAGGGAAAGCATTTAACTATC-AGCTTGTTCGACCTAAATGTCG
1 GATGCCTTCAAGTTCCAAGGG-AAGCATTCAACT-GCGAGCTTCTTCGACCTAAATGTCG
5341 GCATCATGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
58 6 0.12
59 44 0.86
60 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.27
Consensus pattern (59 bp):
GATGCCTTCAAGTTCCAAGGGAAGCATTCAACTGCGAGCTTCTTCGACCTAAATGTCGA
Found at i:7861 original size:3 final size:3
Alignment explanation
Indices: 7853--7877 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
7843 CTCCATACTC
7853 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
7878 TAGGAGCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:9822 original size:19 final size:22
Alignment explanation
Indices: 9770--9822 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 22
9760 TCTTAAATTA
9770 ATAAATAACATACATATTAAAAT
1 ATAAATAA-ATACATATTAAAAT
9793 ATAAACT-AATAC-TA-TAAAAT
1 ATAAA-TAAATACATATTAAAAT
9813 -TAAATAAATA
1 ATAAATAAATA
9823 AAACATTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
18 1 0.04
19 8 0.29
20 6 0.21
21 2 0.07
22 4 0.14
23 6 0.21
24 1 0.04
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (22 bp):
ATAAATAAATACATATTAAAAT
Found at i:20765 original size:45 final size:42
Alignment explanation
Indices: 20702--21001 Score: 220
Period size: 42 Copynumber: 7.0 Consensus size: 42
20692 TGGCTCAATT
* *
20702 AGTTAGAAATTGAGATTAAAAAAACTTAAGGGCCTCAATTATAA
1 AGTTAAAAAGTGAGATT-AAAAAA-TTAAGGGCCTCAATTATAA
** *
20746 AGTTAAGAAAGTGAGATTAAAAAATTGTGGGTCTCAATTATAA
1 AGTTAA-AAAGTGAGATTAAAAAATTAAGGGCCTCAATTATAA
* ** *
20789 AGGTAAAAAGTGAGATTGAAAAAAACTTAAAAGCCTCGATTATAA
1 AGTTAAAAAGTGAGATT--AAAAAA-TTAAGGGCCTCAATTATAA
* *
20834 AGTT-AAAAGTGAGATTATAAAATTAAGGTCCTCAATTATAA
1 AGTTAAAAAGTGAGATTAAAAAATTAAGGGCCTCAATTATAA
* ***
20875 AGGTAAAAAG-G-GATTGAAAAAAGTTACA-GATTTCAATTATAA
1 AGTTAAAAAGTGAGATT-AAAAAA-TTA-AGGGCCTCAATTATAA
* * * * *
20917 AGAT-AAAAGTTAGATTGAATAATATT-ACGACCTCAATTATAA
1 AGTTAAAAAGTGAGATT-AA-AAAATTAAGGGCCTCAATTATAA
* * * *
20959 AGGTGAAAA-TAAGATTTAAAAAATTAAGGACCT-AATTATAA
1 AGTTAAAAAGTGAGA-TTAAAAAATTAAGGGCCTCAATTATAA
21000 AG
1 AG
21002 ATGAAAAATG
Statistics
Matches: 209, Mismatches: 32, Indels: 33
0.76 0.12 0.12
Matches are distributed among these distances:
40 4 0.02
41 45 0.22
42 65 0.31
43 37 0.18
44 32 0.15
45 26 0.12
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.28
Consensus pattern (42 bp):
AGTTAAAAAGTGAGATTAAAAAATTAAGGGCCTCAATTATAA
Found at i:20831 original size:88 final size:86
Alignment explanation
Indices: 20712--20981 Score: 268
Period size: 86 Copynumber: 3.2 Consensus size: 86
20702 AGTTAGAAAT
** **
20712 TGAGATT-AAAAAAACTTAAGGGCCTCAATTATAAAGTTAAGAAAGTGAGATTAAAAAATTGTGG
1 TGAGATTGAAAAAAACTTAAAAGCCTCAATTATAAAGTT-A-AAAGTGAGATTAAAAAATT-AAG
20776 GT-CTCAATTATAAAGGTAAAAAG
63 GTCCTCAATTATAAAGGTAAAAAG
* *
20799 TGAGATTGAAAAAAACTTAAAAGCCTCGATTATAAAGTTAAAAGTGAGATTATAAAATTAAGGTC
1 TGAGATTGAAAAAAACTTAAAAGCCTCAATTATAAAGTTAAAAGTGAGATTAAAAAATTAAGGTC
20864 CTCAATTATAAAGGTAAAAAG
66 CTCAATTATAAAGGTAAAAAG
* * ** * * * *
20885 -G-GATTG-AAAAAAGTT-ACAGATTTCAATTATAAAGATAAAAGTTAGATTGAATAATATT-AC
1 TGAGATTGAAAAAAACTTAAAAG-CCTCAATTATAAAGTTAAAAGTGAGATT-AA-AAAATTAAG
* *
20945 GACCTCAATTATAAAGGTGAAAA-
63 GTCCTCAATTATAAAGGTAAAAAG
* *
20968 TAAGATTTAAAAAA
1 TGAGATTGAAAAAA
20982 TTAAGGACCT
Statistics
Matches: 155, Mismatches: 20, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
82 3 0.02
83 31 0.20
84 28 0.18
85 13 0.08
86 44 0.28
87 8 0.05
88 28 0.18
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.27
Consensus pattern (86 bp):
TGAGATTGAAAAAAACTTAAAAGCCTCAATTATAAAGTTAAAAGTGAGATTAAAAAATTAAGGTC
CTCAATTATAAAGGTAAAAAG
Found at i:20996 original size:83 final size:82
Alignment explanation
Indices: 20714--21008 Score: 238
Period size: 83 Copynumber: 3.5 Consensus size: 82
20704 TTAGAAATTG
* * * *** **
20714 AGATTAAAAAAACTTAAGGGCCTCAATTATAAAGTTAAGAAAGTGAGATTAAAAAATTGTGGGTC
1 AGATTAAAAAAACTTAA-GACCTCAATTATAAAGAT-A-AAAGTGAGATTATAAAATTAACGACC
*
20779 TCAATTATAAAGGTAAAAAGTG
63 TCAATTATAAAGGT-AAAA-TA
* * * * *
20801 AGATTGAAAAAAACTTAAAAGCCTCGATTATAAAGTTAAAAGTGAGATTATAAAATTAAGGTCCT
1 AGATT-AAAAAAACTTAAGA-CCTCAATTATAAAGATAAAAGTGAGATTATAAAATTAACGACCT
20866 CAATTATAAAGGTAAAA-A
64 CAATTATAAAGGTAAAATA
* * * ** * *
20884 GGGATTGAAAAAAGTTACAGATTTCAATTATAAAGATAAAAGTTAGATTGAATAATATT-ACGAC
1 -AGATTAAAAAAACTTA-AGACCTCAATTATAAAGATAAAAGTGAGATT--ATAAAATTAACGAC
20948 CTCAATTATAAAGGTGAAAATA
62 CTCAATTATAAAGGT-AAAATA
*
20970 AGATTTAAAAAA-TTAAGGACCT-AATTATAAAGATGAAAA
1 AGATTAAAAAAACTTAA-GACCTCAATTATAAAGAT-AAAA
21009 ATGGGGGCCC
Statistics
Matches: 173, Mismatches: 25, Indels: 23
0.78 0.11 0.10
Matches are distributed among these distances:
83 45 0.26
84 34 0.20
85 25 0.14
86 36 0.21
87 6 0.03
88 27 0.16
ACGTcount: A:0.49, C:0.07, G:0.16, T:0.27
Consensus pattern (82 bp):
AGATTAAAAAAACTTAAGACCTCAATTATAAAGATAAAAGTGAGATTATAAAATTAACGACCTCA
ATTATAAAGGTAAAATA
Found at i:21517 original size:4 final size:4
Alignment explanation
Indices: 21508--21532 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
21498 TTATTTTTAG
21508 TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT T
21533 CATATTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:21755 original size:24 final size:24
Alignment explanation
Indices: 21709--21755 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
21699 GACGGAGAGC
* * *
21709 ATAAATGAACATGACATATAATTT
1 ATAAATAAACATGACAAACAATTT
21733 ATAAATAAACATGACAAACAATT
1 ATAAATAAACATGACAAACAATT
21756 AACTCATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.55, C:0.11, G:0.06, T:0.28
Consensus pattern (24 bp):
ATAAATAAACATGACAAACAATTT
Found at i:34477 original size:521 final size:521
Alignment explanation
Indices: 33496--34554 Score: 2010
Period size: 521 Copynumber: 2.0 Consensus size: 521
33486 GTCCTCTTAA
33496 AAGTTTGATAGATTTTTTATCTTAAAATATTAATTAATTATAGGATAATTTCTTAAAAAACAACC
1 AAGTTTGATAGATTTTTTATCTTAAAATATTAATTAATTATAGGATAATTTCTTAAAAAACAACC
*
33561 TAACTATGGCGTTTGTGTAAACATGATCACTATTTTTAAATTTGGGTTAATATAACCACTTAACT
66 TAACTATGGCGTTTGTGTAAACATGATCACTATTTTTAAATTTGAGTTAATATAACCACTTAACT
*
33626 ATTTAATTGGTTTTAATATATCTACTCGTCGTTAACATTTAACAAGAGTACTTACATGACAGTTA
131 ATTTAATTGGTTTCAATATATCTACTCGTCGTTAACATTTAACAAGAGTACTTACATGACAGTTA
*
33691 ATAAAATTAGTATAATTACATATTTGATCTTCAATACTTGTAAATTCTATCAATTTGATCATAAT
196 ACAAAATTAGTATAATTACATATTTGATCTTCAATACTTGTAAATTCTATCAATTTGATCATAAT
33756 TTTAATTTAATTTAATTCAATAAATTTAATCATCTAATCGGATAATGACACATGTCACCATTAGA
261 TTTAATTTAATTTAATTCAATAAATTTAATCATCTAATCGGATAATGACACATGTCACCATTAGA
33821 TTAAATGATATTTTCTATAATTTAAATTTATTTAATTATTTATCTTCCAACAAAATAATAACATA
326 TTAAATGATATTTTCTATAATTTAAATTTATTTAATTATTTATCTTCCAACAAAATAATAACATA
33886 TGTCACTATCTGATTAAAGAAAAATATTACTAAGAAAGACACAATAATAATGTTAGGGGGATTTT
391 TGTCACTATCTGATTAAAGAAAAATATTACTAAGAAAGACACAATAATAATGTTAGGGGGATTTT
33951 TGAACGTAGAACTTAGGGAATCAAGCACGCACACATTGACATTGAGTCAACCTCCATGTTTGGGT
456 TGAACGTAGAACTTAGGGAATCAAGCACGCACACATTGACATTGAGTCAACCTCCATGTTTGGGT
34016 T
521 T
**
34017 AAGTTTGATAGATTTTTTATCTTAAAATATTAATTAATTATAGGATAATTTCTTAAACGACAACC
1 AAGTTTGATAGATTTTTTATCTTAAAATATTAATTAATTATAGGATAATTTCTTAAAAAACAACC
*
34082 TAACTATGGCGTTTGTGTAAACATGATCACTATTTTTAAATTTGAGTTAATATAACCACTTAATT
66 TAACTATGGCGTTTGTGTAAACATGATCACTATTTTTAAATTTGAGTTAATATAACCACTTAACT
* *
34147 ATTTAATTGGTTTCAATATATCTACTCGTCGTTAACATTTAACGAGAGTGCTTACATGACAGTTA
131 ATTTAATTGGTTTCAATATATCTACTCGTCGTTAACATTTAACAAGAGTACTTACATGACAGTTA
34212 ACAAAATTAGTATAATTACATATTTGATCTTCAATACTTGTAAATTCTATCAATTTGATCATAAT
196 ACAAAATTAGTATAATTACATATTTGATCTTCAATACTTGTAAATTCTATCAATTTGATCATAAT
*
34277 TTTAATTTAATTTAATTCAATAAATTTAATCATCTAATCGGATAATGACATATGTCACCATTAGA
261 TTTAATTTAATTTAATTCAATAAATTTAATCATCTAATCGGATAATGACACATGTCACCATTAGA
34342 TTAAATGATATTTTCTATAATTTAAATTTATTTAATTATTTATCTTCCAACAAAATAATAACATA
326 TTAAATGATATTTTCTATAATTTAAATTTATTTAATTATTTATCTTCCAACAAAATAATAACATA
34407 TGTCACTATCTGATTAAAGAAAAATATTACTAAGAAAGACACAATAATAATGTTAGGGGGATTTT
391 TGTCACTATCTGATTAAAGAAAAATATTACTAAGAAAGACACAATAATAATGTTAGGGGGATTTT
34472 TGAACGTAGAACTTAGGGAATCAAGCACGCACACATTGACATTGAGTCAACCTCCATGTTTGGGT
456 TGAACGTAGAACTTAGGGAATCAAGCACGCACACATTGACATTGAGTCAACCTCCATGTTTGGGT
34537 T
521 T
* *
34538 ATGTTTTATAGCATTTT
1 AAGTTTGATAG-ATTTT
34555 CTAGTGTTTG
Statistics
Matches: 526, Mismatches: 11, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
521 521 0.99
522 5 0.01
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (521 bp):
AAGTTTGATAGATTTTTTATCTTAAAATATTAATTAATTATAGGATAATTTCTTAAAAAACAACC
TAACTATGGCGTTTGTGTAAACATGATCACTATTTTTAAATTTGAGTTAATATAACCACTTAACT
ATTTAATTGGTTTCAATATATCTACTCGTCGTTAACATTTAACAAGAGTACTTACATGACAGTTA
ACAAAATTAGTATAATTACATATTTGATCTTCAATACTTGTAAATTCTATCAATTTGATCATAAT
TTTAATTTAATTTAATTCAATAAATTTAATCATCTAATCGGATAATGACACATGTCACCATTAGA
TTAAATGATATTTTCTATAATTTAAATTTATTTAATTATTTATCTTCCAACAAAATAATAACATA
TGTCACTATCTGATTAAAGAAAAATATTACTAAGAAAGACACAATAATAATGTTAGGGGGATTTT
TGAACGTAGAACTTAGGGAATCAAGCACGCACACATTGACATTGAGTCAACCTCCATGTTTGGGT
T
Found at i:39505 original size:62 final size:58
Alignment explanation
Indices: 39399--39535 Score: 193
Period size: 62 Copynumber: 2.3 Consensus size: 58
39389 TATTTCTTTA
* ** *
39399 AATCAATCACTCATCCCTTATCTTGATATATATATAAATAAATCACTCCCATGTATTC
1 AATCAATCACTTATCTTTTATCTTGATATATATATAAACAAATCACTCCCATGTATTC
*
39457 AATCAATCACTTATCTTTTATCTTGAAATATATATATAAAAACAAATCACTCCCTTGTATTC
1 AATCAATCACTTATCTTTTATCTTG--ATATATATAT--AAACAAATCACTCCCATGTATTC
39519 AATCAATCACTTATCTT
1 AATCAATCACTTATCTT
39536 AGCTTTATAA
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
58 22 0.31
60 10 0.14
62 38 0.54
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.38
Consensus pattern (58 bp):
AATCAATCACTTATCTTTTATCTTGATATATATATAAACAAATCACTCCCATGTATTC
Found at i:42161 original size:37 final size:37
Alignment explanation
Indices: 42111--42182 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
42101 ACTTTAACCA
* *
42111 AGTAGAGAGAAATGCCATCGTCATGTCTTGTAAGTCG
1 AGTAGAGAGAAATGCCATCATCATGTCTTATAAGTCG
* *
42148 AGTAGATAGAAATGTCATCATCATGTCTTATAAGT
1 AGTAGAGAGAAATGCCATCATCATGTCTTATAAGT
42183 TATAGAAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (37 bp):
AGTAGAGAGAAATGCCATCATCATGTCTTATAAGTCG
Found at i:44669 original size:23 final size:22
Alignment explanation
Indices: 44634--44678 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
44624 AGTCATTTTA
*
44634 TTTATTTTATTATTTAATTAAAT
1 TTTATTTTATTATATAA-TAAAT
44657 TTTA-TTTATTTATATAATAAAT
1 TTTATTTTA-TTATATAATAAAT
44679 ATTAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTATTTTATTATATAATAAAT
Found at i:45222 original size:6 final size:6
Alignment explanation
Indices: 45211--45236 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
45201 CGCGCCACTC
45211 CCGACG CCGACG CCGACG CCGACG CC
1 CCGACG CCGACG CCGACG CCGACG CC
45237 CCAACCGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.54, G:0.31, T:0.00
Consensus pattern (6 bp):
CCGACG
Found at i:49014 original size:41 final size:41
Alignment explanation
Indices: 48969--49107 Score: 208
Period size: 41 Copynumber: 3.4 Consensus size: 41
48959 ATTCGCGTTG
48969 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
***
49010 CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
49051 CATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
*
49092 CATTTCGTGTTGCGAT
1 CATTTCGCGTTGCGAT
49108 TTTCCATTTC
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
41 87 0.99
42 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:49105 original size:102 final size:102
Alignment explanation
Indices: 48994--49209 Score: 353
Period size: 102 Copynumber: 2.1 Consensus size: 102
48984 TAGTTGAAAA
48994 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTCCATTTCGC
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTCCATTTCGC
* *
49059 GTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTCCATT
66 GTTGCGATAGT-TGAAAATCGCGTTGCGATTTTCCATT
* ***
49096 TCGTGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGC
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTCCATTTCGC
*
49161 GTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCGTT
66 GTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
49198 TCGCGTTGCGAT
1 TCGCGTTGCGAT
49210 AGTCTACAGT
Statistics
Matches: 105, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
101 1 0.01
102 104 0.99
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.38
Consensus pattern (102 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTCCATTTCGC
GTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
Found at i:49107 original size:61 final size:61
Alignment explanation
Indices: 49042--49168 Score: 211
Period size: 61 Copynumber: 2.1 Consensus size: 61
49032 AAATCGCAAC
* * *
49042 GCGATTTTCCATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTCCATTTCGTGTT
1 GCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTCCATTTCGCGTT
49103 GCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTT
1 GCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTT
49164 GCGAT
1 GCGAT
49169 AGTTGAAAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
60 1 0.02
61 61 0.98
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (61 bp):
GCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTT
Found at i:49145 original size:41 final size:41
Alignment explanation
Indices: 49100--49212 Score: 217
Period size: 41 Copynumber: 2.8 Consensus size: 41
49090 TCCATTTCGT
49100 GTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGC
1 GTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGC
49141 GTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGC
1 GTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGC
*
49182 GTTGCGATTTTCCGTTTCGCGTTGCGATAGT
1 GTTGCGATTTTCCATTTCGCGTTGCGATAGT
49213 CTACAGTTGT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (41 bp):
GTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGC
Found at i:49200 original size:143 final size:144
Alignment explanation
Indices: 48969--49237 Score: 486
Period size: 143 Copynumber: 1.9 Consensus size: 144
48959 ATTCGCGTTG
48969 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
49034 ATCGCAACGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCG-CGTTGCGATTTTCCATTTC
66 ATCGCAACGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGTCGTTGCGATTTTCCATTTC
49098 GTGTTGCGATTTTC
131 GTGTTGCGATTTTC
49112 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
*** * *
49177 ATCGCGTTGCGATTTTCCGTTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCA
66 ATCGCAACGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGTCGTTGCGATTTTCCA
49238 AATTCGTTGC
Statistics
Matches: 120, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
143 105 0.88
144 15 0.12
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (144 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
ATCGCAACGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGTCGTTGCGATTTTCCATTTC
GTGTTGCGATTTTC
Found at i:49246 original size:82 final size:81
Alignment explanation
Indices: 49100--49253 Score: 213
Period size: 82 Copynumber: 1.9 Consensus size: 81
49090 TCCATTTCGT
*
49100 GTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTG
1 GTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTC-CGTTG
49165 CGATAGTTGAAAATCGC
65 CGATAGTTGAAAATCGC
* * * *
49182 GTTGCGATTTTCCGTTTCGCGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCAAATT-CGT
1 GTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-AATTCCGT
49245 TGCGATAGT
63 TGCGATAGT
49254 CTTAAAAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
82 46 0.72
83 15 0.23
84 3 0.05
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (81 bp):
GTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTCCGTTGC
GATAGTTGAAAATCGC
Found at i:49507 original size:3 final size:3
Alignment explanation
Indices: 49499--49547 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
49489 TCGAATTTAG
49499 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
49547 A
1 A
49548 CAGTTTAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:50923 original size:3 final size:3
Alignment explanation
Indices: 50912--50958 Score: 85
Period size: 3 Copynumber: 15.3 Consensus size: 3
50902 TGATGTTACT
50912 TAA TCAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
50958 T
1 T
50959 TTATGATTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:52128 original size:15 final size:15
Alignment explanation
Indices: 52108--52147 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
52098 ATTGGGAGAA
52108 TATTTTATTTAAAAG
1 TATTTTATTTAAAAG
52123 TATTTTATTTAAAAG
1 TATTTTATTTAAAAG
52138 TATTTTATTT
1 TATTTTATTT
52148 TTATTTTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (15 bp):
TATTTTATTTAAAAG
Found at i:52172 original size:26 final size:26
Alignment explanation
Indices: 52123--52174 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
52113 TATTTAAAAG
* *
52123 TATTTTATTTAAAAGTATTTTATTTT
1 TATTTTATTTAAAAATATTATATTTT
52149 TATTTTCATTTAAAAATA-TATATTTT
1 TATTTT-ATTTAAAAATATTATATTTT
52175 ATGTTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (26 bp):
TATTTTATTTAAAAATATTATATTTT
Found at i:52688 original size:42 final size:42
Alignment explanation
Indices: 52582--52814 Score: 163
Period size: 42 Copynumber: 5.7 Consensus size: 42
52572 ATTTATTAAA
* * * **
52582 AAAAAAGCCACTAAAGTGCATGATTATTGCGATGTTTA-TA-
1 AAAAACGCCACTAAAGTGCATGACTATTGTGACATTTACTAC
* ** * * * *
52622 AAAAACGTCGTTCATGTGCATGACTATTGTGGCATTTACTGC
1 AAAAACGCCACTAAAGTGCATGACTATTGTGACATTTACTAC
* * * *
52664 AACAACGCCACTAAAGTGTATGACTATTATGACATTTATTAC
1 AAAAACGCCACTAAAGTGCATGACTATTGTGACATTTACTAC
* * * *
52706 AAAAATGCCACTAAAGTGCATGACTATTGCGTCGTTTA-TA-
1 AAAAACGCCACTAAAGTGCATGACTATTGTGACATTTACTAC
** * * * *
52746 AAAAAAACC-CTAAAGTGCATGAGTATTGCG-CGTTTATTAC
1 AAAAACGCCACTAAAGTGCATGACTATTGTGACATTTACTAC
* * *
52786 AAAAAAGCCACTAAAGTGAATGATTATTG
1 AAAAACGCCACTAAAGTGCATGACTATTG
52815 CGGTGTTTAT
Statistics
Matches: 152, Mismatches: 36, Indels: 9
0.77 0.18 0.05
Matches are distributed among these distances:
38 6 0.04
39 22 0.14
40 42 0.28
41 20 0.13
42 62 0.41
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (42 bp):
AAAAACGCCACTAAAGTGCATGACTATTGTGACATTTACTAC
Found at i:52796 original size:80 final size:81
Alignment explanation
Indices: 52698--52856 Score: 232
Period size: 80 Copynumber: 2.0 Consensus size: 81
52688 TATTATGACA
* *
52698 TTTATTACAAAAATGCCACTAAAGTGCATGACTATTGC-GTCGTTTATAAAAAA-AACCCTAAAG
1 TTTATTACAAAAAAGCCACTAAAGTGAATGACTATTGCGGT-GTTTATAAAAAATAACCCTAAAG
52761 TGCATGAGTATTGCGCG
65 TGCATGAGTATTGCGCG
* * *
52778 TTTATTACAAAAAAGCCACTAAAGTGAATGATTATTGCGGTGTTTATAAAAAATGACGCTAAAGT
1 TTTATTACAAAAAAGCCACTAAAGTGAATGACTATTGCGGTGTTTATAAAAAATAACCCTAAAGT
* *
52843 TCATGATTATTGCG
66 GCATGAGTATTGCG
52857 ATGTTTTTGT
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
80 47 0.67
81 23 0.33
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (81 bp):
TTTATTACAAAAAAGCCACTAAAGTGAATGACTATTGCGGTGTTTATAAAAAATAACCCTAAAGT
GCATGAGTATTGCGCG
Found at i:52824 original size:42 final size:40
Alignment explanation
Indices: 52581--52862 Score: 192
Period size: 40 Copynumber: 7.0 Consensus size: 40
52571 CATTTATTAA
* *
52581 AAAAAAAGCCACTAAAGTGCATGATTATTGCGATGTTTAT
1 AAAAAAAGCCACTAAAGTGCATGACTATTGCGGTGTTTAT
* * ** * * * **
52621 AAAAAACGTCGTTCATGTGCATGACTATTGTGGCATTTACT
1 AAAAAAAGCCACTAAAGTGCATGACTATTGCGGTGTTTA-T
* * * * ** ***
52662 GCAACAACGCCACTAAAGTGTATGACTATTATGACATTTATT
1 -AAAAAAAGCCACTAAAGTGCATGACTATTGCGGTGTTTA-T
*
52704 ACAAAAATGCCACTAAAGTGCATGACTATTGC-GTCGTTTAT
1 A-AAAAAAGCCACTAAAGTGCATGACTATTGCGGT-GTTTAT
* * *
52745 AAAAAAAACC-CTAAAGTGCATGAGTATTGC-GCGTTTATT
1 AAAAAAAGCCACTAAAGTGCATGACTATTGCGGTGTTTA-T
* *
52784 ACAAAAAAGCCACTAAAGTGAATGATTATTGCGGTGTTTAT
1 A-AAAAAAGCCACTAAAGTGCATGACTATTGCGGTGTTTAT
* * * * * *
52825 AAAAAATGACGCTAAAGTTCATGATTATTGCGATGTTT
1 AAAAAAAGCCACTAAAGTGCATGACTATTGCGGTGTTT
52863 TTGTAGTAAA
Statistics
Matches: 189, Mismatches: 45, Indels: 16
0.76 0.18 0.06
Matches are distributed among these distances:
38 5 0.03
39 22 0.12
40 74 0.39
41 23 0.12
42 65 0.34
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (40 bp):
AAAAAAAGCCACTAAAGTGCATGACTATTGCGGTGTTTAT
Found at i:55768 original size:5 final size:5
Alignment explanation
Indices: 55758--55811 Score: 56
Period size: 5 Copynumber: 10.8 Consensus size: 5
55748 TTTATAAAAG
* * * *
55758 TTTTC TTTTC TTTTC TTTTA TTCTC TTTTC TTTTC ACTTTC -TTTA TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TTTTC TTTTC
55808 TTTT
1 TTTT
55812 AAGTTTTCTT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
4 3 0.08
5 33 0.82
6 4 0.10
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:55786 original size:25 final size:25
Alignment explanation
Indices: 55758--55811 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
55748 TTTATAAAAG
*
55758 TTTTCTTTTC-TTTTCTTTTATTCTC
1 TTTTCTTTTCACTTTC-TTTATTCTC
*
55783 TTTTCTTTTCACTTTCTTTATTTTC
1 TTTTCTTTTCACTTTCTTTATTCTC
55808 TTTT
1 TTTT
55812 AAGTTTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 22 0.85
26 4 0.15
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.76
Consensus pattern (25 bp):
TTTTCTTTTCACTTTCTTTATTCTC
Found at i:57647 original size:163 final size:163
Alignment explanation
Indices: 57371--57752 Score: 629
Period size: 163 Copynumber: 2.3 Consensus size: 163
57361 AAAACATATT
* * *
57371 TTTATTCAAAAACCATATTAATCCCTCCAACCAAACACTCCGTAATGTGTAGGTTCCCCAGAACC
1 TTTA-TCAAAAATCATATTATTCCCTCCAACC-AACACTCCATAATGTGTAGGTTCCCCAGAACC
* * * *
57436 ATACACCTACCTACACACTAAGTAAGGACTTACCCTGAGCCCAAAGCAGAGGAGCCTGCAGTAAC
64 ATACACCCACCTACACACCAAGTAAGGACTTACCCTGAGCACAAAGCAGAAGAGCCTGCAGTAAC
* *
57501 GATAACTTCTTCCAACAACACCCTCTCATAAAACA
129 GATAACTTCCTCCAACAACACCCTCCCATAAAACA
*
57536 TTTATCAAAAATCATATTATTCCCTCCAACCAACACTCCATAATGTGTAGGTTCCCTAGAACCAT
1 TTTATCAAAAATCATATTATTCCCTCCAACCAACACTCCATAATGTGTAGGTTCCCCAGAACCAT
*
57601 ACACCCACCTACACACCAAGTAAGGACTTACCCTGAGCACAAAGCAGAAGAGCCTGCAGTAACGG
66 ACACCCACCTACACACCAAGTAAGGACTTACCCTGAGCACAAAGCAGAAGAGCCTGCAGTAACGA
*
57666 TAACTTCCTCCAACAACACCTTCCCATAAAACA
131 TAACTTCCTCCAACAACACCCTCCCATAAAACA
*
57699 TTTATCAAAAATCATATTATTCCATCCAACCAACACTCCATAATGTGTAGGTTC
1 TTTATCAAAAATCATATTATTCCCTCCAACCAACACTCCATAATGTGTAGGTTC
57753 TTAGGTTCCA
Statistics
Matches: 204, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
163 175 0.86
164 25 0.12
165 4 0.02
ACGTcount: A:0.36, C:0.31, G:0.11, T:0.23
Consensus pattern (163 bp):
TTTATCAAAAATCATATTATTCCCTCCAACCAACACTCCATAATGTGTAGGTTCCCCAGAACCAT
ACACCCACCTACACACCAAGTAAGGACTTACCCTGAGCACAAAGCAGAAGAGCCTGCAGTAACGA
TAACTTCCTCCAACAACACCCTCCCATAAAACA
Found at i:60440 original size:32 final size:32
Alignment explanation
Indices: 60392--60452 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
60382 TAATGCCCGA
* *
60392 TCAACGTCGGTTAAAGTTCTGGTCAACTGTGG
1 TCAACGCCGGTCAAAGTTCTGGTCAACTGTGG
60424 TCAACGCCGGTCAAAGTTCTGGTCAACTG
1 TCAACGCCGGTCAAAGTTCTGGTCAACTG
60453 AGTTTAACGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (32 bp):
TCAACGCCGGTCAAAGTTCTGGTCAACTGTGG
Found at i:60462 original size:32 final size:32
Alignment explanation
Indices: 60392--60469 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
60382 TAATGCCCGA
* * *
60392 TCAACGTCGGTTAAAGTTCTGGTCAACTGTGG
1 TCAACGCCGGTCAAAGTTCTGGTCAACTGAGG
*
60424 TCAACGCCGGTCAAAGTTCTGGTCAACTGAGT
1 TCAACGCCGGTCAAAGTTCTGGTCAACTGAGG
* *
60456 TTAACGCAGGTCAA
1 TCAACGCCGGTCAA
60470 CGGTAACGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.27
Consensus pattern (32 bp):
TCAACGCCGGTCAAAGTTCTGGTCAACTGAGG
Found at i:60482 original size:16 final size:16
Alignment explanation
Indices: 60457--60489 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
60447 CAACTGAGTT
60457 TAACGCAGGTCAACGG
1 TAACGCAGGTCAACGG
*
60473 TAACGTAGGTCAACGG
1 TAACGCAGGTCAACGG
60489 T
1 T
60490 CAACAGTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.21, G:0.30, T:0.18
Consensus pattern (16 bp):
TAACGCAGGTCAACGG
Found at i:63719 original size:2 final size:2
Alignment explanation
Indices: 63712--63746 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
63702 CTTTTTAAAT
63712 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 T
63747 CTACATTGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:64477 original size:3 final size:3
Alignment explanation
Indices: 64469--64532 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
64459 ATCAATTCGA
64469 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
64517 ATT ATT TTT ATT ATT A
1 ATT ATT ATT ATT ATT A
64533 CAGTTTAAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:67138 original size:31 final size:31
Alignment explanation
Indices: 67086--67146 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
67076 ATTTAAAAGA
* *
67086 ATTTTATTTTTATTTTCATTTAAAAATATGT
1 ATTTTATGTTAATTTTCATTTAAAAATATGT
*
67117 ATTTTATGTTAATATTT-ATTTAAAAGTATG
1 ATTTTATGTTAAT-TTTCATTTAAAAATATG
67147 ACTAAATTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 23 0.88
32 3 0.12
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (31 bp):
ATTTTATGTTAATTTTCATTTAAAAATATGT
Found at i:67145 original size:27 final size:27
Alignment explanation
Indices: 67068--67145 Score: 68
Period size: 31 Copynumber: 2.7 Consensus size: 27
67058 AAGTTGGGAG
* *
67068 AATACTTTATTTAAAAGAATTTTATTTT
1 AATA-TTTATTTAAAAGTATTTTATGTT
*
67096 TAT-TTTCATTTAAAAATATGTATTTTATGTT
1 AATATTT-ATTT--AAA-A-GTATTTTATGTT
67127 AATATTTATTTAAAAGTAT
1 AATATTTATTTAAAAGTAT
67146 GACTAAATTG
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
26 3 0.08
27 8 0.20
28 3 0.08
29 6 0.15
30 1 0.03
31 16 0.40
32 3 0.08
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (27 bp):
AATATTTATTTAAAAGTATTTTATGTT
Found at i:68430 original size:131 final size:131
Alignment explanation
Indices: 68196--68431 Score: 301
Period size: 131 Copynumber: 1.8 Consensus size: 131
68186 TAATTTCAAG
* * ** * * *
68196 AGTGAAAACGATAATATCAAATTATTTACAATCGAGAATAAATGACATTTCGTGCACTAAAACAA
1 AGTGAAAACGATAATAGCAAATGAAATACAATCGAGAATAAATGACATCTCATACACTAAAACAA
* * * *
68261 TCATTTATTACCCCAATTGAAATAAAGAGATATTACTATTTCATCTTAAAATTCAATATCGATTC
66 TCATTTATCACCCCAATCGAAACAAAAAGATATTACTATTTCATCTTAAAATTCAATATCGATTC
68326 A
131 A
* * * * *
68327 AGTGAAAACGATAATAGCTAATGAAATCCAATCGAGAATAAATGACCTCTCATACATTAAAGCAA
1 AGTGAAAACGATAATAGCAAATGAAATACAATCGAGAATAAATGACATCTCATACACTAAAACAA
* **
68392 TCATTTATCACTCGGATCGAAACAAAAAGATATTACTATT
66 TCATTTATCACCCCAATCGAAACAAAAAGATATTACTATT
68432 CTTAGTGTCG
Statistics
Matches: 86, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
131 86 1.00
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (131 bp):
AGTGAAAACGATAATAGCAAATGAAATACAATCGAGAATAAATGACATCTCATACACTAAAACAA
TCATTTATCACCCCAATCGAAACAAAAAGATATTACTATTTCATCTTAAAATTCAATATCGATTC
A
Found at i:70485 original size:3 final size:3
Alignment explanation
Indices: 70477--70516 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
70467 TAAAATTAGT
70477 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
70517 GATGATGATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:70521 original size:3 final size:3
Alignment explanation
Indices: 70515--70543 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
70505 AATAATAATA
70515 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
70544 AATAGGACGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:72169 original size:35 final size:35
Alignment explanation
Indices: 72125--72192 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
72115 TTGGTCACAT
*
72125 TTGAATGATGTTATTGTTGAAGATGGTCGAAACTC
1 TTGAATGATGTTATTGTTGAAGATGGTCAAAACTC
* *
72160 TTGACTGATGTTGTTGTTGAAGATGGTCAAAAC
1 TTGAATGATGTTATTGTTGAAGATGGTCAAAAC
72193 CCTTATGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.28, C:0.09, G:0.26, T:0.37
Consensus pattern (35 bp):
TTGAATGATGTTATTGTTGAAGATGGTCAAAACTC
Found at i:72219 original size:47 final size:48
Alignment explanation
Indices: 72162--72278 Score: 148
Period size: 47 Copynumber: 2.5 Consensus size: 48
72152 CGAAACTCTT
* * **
72162 GACTGATGTTGTTGTTGAAGATGGTCAAAAC-CCTTATGA-TTTTTAAA
1 GACTGATGTTGTTGTTGAAGATGATCAAAACTCC-GATGACTTTCCAAA
* * *
72209 GATTGATGTTGTTGTTGAAGATGATCGAAACTCCGATGACTTTCCCAA
1 GACTGATGTTGTTGTTGAAGATGATCAAAACTCCGATGACTTTCCAAA
72257 GACTGATGTTGTTGTTGAAGAT
1 GACTGATGTTGTTGTTGAAGAT
72279 TATCGGAACT
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
47 32 0.53
48 28 0.47
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (48 bp):
GACTGATGTTGTTGTTGAAGATGATCAAAACTCCGATGACTTTCCAAA
Found at i:75694 original size:64 final size:63
Alignment explanation
Indices: 75645--75768 Score: 198
Period size: 64 Copynumber: 2.0 Consensus size: 63
75635 TGCACTAAGG
*
75645 GTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AACAAGCCTGAGTGCATCGATGCATGGTC
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AAACCTGAGTGCATCGATGCATGG--
75708 T
63 T
75709 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCTGAGTGCATCGATGCAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCTGAGTGCATCGATGCAT
75769 AAAATGCATT
Statistics
Matches: 57, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
64 29 0.51
65 26 0.46
66 2 0.04
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCTGAGTGCATCGATGCATGGT
Found at i:78503 original size:21 final size:23
Alignment explanation
Indices: 78439--78503 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
78429 ATGCACTGCT
78439 GAGTGCATCGATGCATATTCATG
1 GAGTGCATCGATGCATATTCATG
* *
78462 GAGTGCATCGGTGCATCTTCAT-
1 GAGTGCATCGATGCATATTCATG
* *
78484 GA-TGTATCGATGCAAATTCA
1 GAGTGCATCGATGCATATTCA
78504 AAGGATGCAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.39
22 2 0.06
23 20 0.56
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (23 bp):
GAGTGCATCGATGCATATTCATG
Found at i:86100 original size:19 final size:19
Alignment explanation
Indices: 86073--86124 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
86063 ACAAGCCTGA
*
86073 GTGCATCGATGCATGGTCT
1 GTGCATCGATGCATGGTAT
*
86092 GTGCCTCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
86111 GTGCATCGATGCAT
1 GTGCATCGATGCAT
86125 AAAATGCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.17, C:0.21, G:0.31, T:0.31
Consensus pattern (19 bp):
GTGCATCGATGCATGGTAT
Found at i:86214 original size:20 final size:20
Alignment explanation
Indices: 86189--86226 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
86179 TTCGAAATGG
86189 TGAGTGCATCGATGCATCAA
1 TGAGTGCATCGATGCATCAA
*
86209 TGAGTGCATCGGTGCATC
1 TGAGTGCATCGATGCATC
86227 CCTTTACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAGTGCATCGATGCATCAA
Found at i:87078 original size:2 final size:2
Alignment explanation
Indices: 87071--87105 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
87061 ATATCATAAA
87071 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
87106 TATATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:87322 original size:31 final size:31
Alignment explanation
Indices: 87284--87348 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
87274 GAACCTCAGC
87284 AACTGTCCATAGGTCTCGAAGAACCCAGGTA
1 AACTGTCCATAGGTCTCGAAGAACCCAGGTA
*
87315 AACTGTCCATAGGTCTCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCTCGAAGAACCCAGGTA
87346 AAC
1 AAC
87349 CCTCGACTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.20
Consensus pattern (31 bp):
AACTGTCCATAGGTCTCGAAGAACCCAGGTA
Found at i:88134 original size:20 final size:23
Alignment explanation
Indices: 88109--88162 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 23
88099 CCTTGAAGTT
88109 CATCGATGCATTC-T-ACA-GTG
1 CATCGATGCATTCTTAACATGTG
*
88129 CATCGATGTATTCTTTAACATGTG
1 CATCGATGCATTC-TTAACATGTG
88153 CATCGATGCA
1 CATCGATGCA
88163 CTACCCATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 12 0.43
22 1 0.04
23 3 0.11
24 12 0.43
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (23 bp):
CATCGATGCATTCTTAACATGTG
Found at i:88300 original size:62 final size:64
Alignment explanation
Indices: 88150--88308 Score: 189
Period size: 64 Copynumber: 2.5 Consensus size: 64
88140 TCTTTAACAT
* * *
88150 GTGCATCGATGCACTACCCATGCATCGATACACCAATCACCTTCGATGTTTTCAATTTAAGGGG
1 GTGCATCGATGCACTTCCTATGCATCGATACACCAATCACATTCGATGTTTTCAATTTAAGGGG
* * ** ** *
88214 GTGCATCGATGCAC-TCCTAATGCATCGATGCACTAATTGCATTCGATGTTTT-TTTTTAA-TGG
1 GTGCATCGATGCACTTCCT-ATGCATCGATACACCAATCACATTCGATGTTTTCAATTTAAGGGG
*
88276 GTGCATCGATGCACTTCCTGTGCATCGATACAC
1 GTGCATCGATGCACTTCCTATGCATCGATACAC
88309 ACTGAATAAT
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
62 28 0.35
63 11 0.14
64 42 0.52
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCACTTCCTATGCATCGATACACCAATCACATTCGATGTTTTCAATTTAAGGGG
Found at i:91530 original size:29 final size:28
Alignment explanation
Indices: 91493--91575 Score: 71
Period size: 31 Copynumber: 2.8 Consensus size: 28
91483 GAAGGACCTA
*
91493 TCCAGAGGTCATAAAGAACCTCA-AAACTG
1 TCCATAGGTCAT-AAGAACCT-AGAAACTG
*
91522 TCCATAGGTCCCTAAGAACCTAGGTAAACTG
1 TCCATAGGT-CATAAGAACCTA-G-AAACTG
91553 TCCATAGGTC-TCGAAGAACCTAG
1 TCCATAGGTCAT--AAGAACCTAG
91576 GTAAACCCTC
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
28 1 0.02
29 17 0.37
30 4 0.09
31 24 0.52
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.20
Consensus pattern (28 bp):
TCCATAGGTCATAAGAACCTAGAAACTG
Found at i:91554 original size:31 final size:31
Alignment explanation
Indices: 91516--91581 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
91506 AAGAACCTCA
*
91516 AAACTGTCCATAGGTCCCTAAGAACCTAGGT
1 AAACTGTCCATAGGTCCCGAAGAACCTAGGT
*
91547 AAACTGTCCATAGGTCTCGAAGAACCTAGGT
1 AAACTGTCCATAGGTCCCGAAGAACCTAGGT
91578 AAAC
1 AAAC
91582 CCTCGACTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (31 bp):
AAACTGTCCATAGGTCCCGAAGAACCTAGGT
Found at i:92403 original size:20 final size:22
Alignment explanation
Indices: 92378--92435 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
92368 TTTTCCTTGA
92378 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
92398 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
92421 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
92436 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:92540 original size:61 final size:64
Alignment explanation
Indices: 92423--92580 Score: 189
Period size: 61 Copynumber: 2.5 Consensus size: 64
92413 TCTTTAACAT
* *
92423 GTGCATCGATGCACTACCCATGCATCGATACACCAATCACCTTCGATGTTTTCATTTT-AAGGGG
1 GTGCATCGATGCACTACCAATGCATCGATACACCAATCACCTTCGATGTTTCCATTTTGAA-GGG
* * * *
92487 GTGCATCGATGCACT-CTAATGCATCGATGCA-CAATTA-CTTCGATGTTTCCATTTTGAATGG
1 GTGCATCGATGCACTACCAATGCATCGATACACCAATCACCTTCGATGTTTCCATTTTGAAGGG
* * **
92548 GTACATCGATGCACTTCCTGTGCATCGATACAC
1 GTGCATCGATGCACTACCAATGCATCGATACAC
92581 ACTGAATAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
61 33 0.41
62 19 0.24
63 13 0.16
64 15 0.19
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCACTACCAATGCATCGATACACCAATCACCTTCGATGTTTCCATTTTGAAGGG
Done.