Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000351.1 Hibiscus syriacus cultivar Beakdansim tig00000645_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: 102759
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:27120 original size:2 final size:2
Alignment explanation
Indices: 27113--27149 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
27103 TAATAATTTA
27113 AT AT AT AT ACT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
27150 TGGGGAGTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28612 original size:23 final size:23
Alignment explanation
Indices: 28586--28630 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
28576 CACCACAGCT
*
28586 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
28609 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
28631 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:28868 original size:149 final size:149
Alignment explanation
Indices: 28609--28912 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
28599 CGAAGTGCCC
*
28609 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
28674 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
28739 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
28758 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
28823 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
28888 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
28907 CGTAGA
1 CGTAGA
28913 CCCTCGACTC
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:29452 original size:2 final size:2
Alignment explanation
Indices: 29445--29510 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
29435 CTTCTCTTAG
29445 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29487 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
29511 TCACATGTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29857 original size:18 final size:18
Alignment explanation
Indices: 29836--29870 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
29826 TCCCATCTAG
29836 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
29854 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
29871 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:35220 original size:2 final size:2
Alignment explanation
Indices: 35213--35239 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35203 ATAATAAATA
35213 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
35240 ATAGAATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36616 original size:16 final size:16
Alignment explanation
Indices: 36595--36625 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
36585 TACAAAATCT
36595 AATAATCCATAATATA
1 AATAATCCATAATATA
*
36611 AATAATCCATTATAT
1 AATAATCCATAATAT
36626 TACATTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (16 bp):
AATAATCCATAATATA
Found at i:36638 original size:2 final size:2
Alignment explanation
Indices: 36631--36684 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
36621 TATATTACAT
* * *
36631 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG CA 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
36673 TA TA TA TA TA TA
1 TA TA TA TA TA TA
36685 AACTAACCGG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:37335 original size:16 final size:16
Alignment explanation
Indices: 37314--37358 Score: 67
Period size: 14 Copynumber: 2.9 Consensus size: 16
37304 CCTTAAACTT
*
37314 TCTTAATAATCGAATA
1 TCTTAATAATTGAATA
37330 TCTT-A-AATTGAATA
1 TCTTAATAATTGAATA
37344 TCTTAATAATTGAAT
1 TCTTAATAATTGAAT
37359 TAAATAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 12 0.46
15 2 0.08
16 12 0.46
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (16 bp):
TCTTAATAATTGAATA
Found at i:48939 original size:3 final size:3
Alignment explanation
Indices: 48931--48955 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
48921 GAATTGGGTT
48931 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
48956 ATAGAGCGTT
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:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:49942 original size:14 final size:14
Alignment explanation
Indices: 49923--49949 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
49913 GAGTTTCCAT
49923 AAAATGCCTTTGGG
1 AAAATGCCTTTGGG
49937 AAAATGCCTTTGG
1 AAAATGCCTTTGG
49950 TCATCGTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (14 bp):
AAAATGCCTTTGGG
Found at i:59510 original size:42 final size:43
Alignment explanation
Indices: 59447--59535 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 43
59437 TATTTTCAAT
* * * * *
59447 TTTGTTTTTGATATGTTAGTTTGATTTATTTGTGGATTGTTA-
1 TTTGGTTTTAATATGTTAGTTTGATATATCTATGGATTGTTAC
*
59489 TTTGGTTTTAATATGTTAGTTTGGTATATCTATGGATTGTTAC
1 TTTGGTTTTAATATGTTAGTTTGATATATCTATGGATTGTTAC
59532 TTTG
1 TTTG
59536 AAATTTAGAC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 36 0.90
43 4 0.10
ACGTcount: A:0.18, C:0.02, G:0.21, T:0.58
Consensus pattern (43 bp):
TTTGGTTTTAATATGTTAGTTTGATATATCTATGGATTGTTAC
Found at i:62539 original size:30 final size:30
Alignment explanation
Indices: 62503--62566 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
62493 GAAGGACCTG
* *
62503 TCCAGAGGTTACAAAGAACCTCGGTAACTA
1 TCCAGAGGTCACAAAGAACCTCGGCAACTA
* *
62533 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCACAAAGAACCTCGGCAACTA
62563 TCCA
1 TCCA
62567 TATGTTCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCTCGGCAACTA
Found at i:63334 original size:64 final size:64
Alignment explanation
Indices: 63246--63516 Score: 236
Period size: 64 Copynumber: 4.2 Consensus size: 64
63236 CAATGAAGGT
* * * *
63246 ATGCATCGATGCACTA-CTTGTGCATCGGTGCATAAAATGCATTTGATGTT-TCCTTATTAATGA
1 ATGCATCGATGCACTACCTTATGCATCGATGCAT-AAATGCATTCGATGTTATCATT-TTAATGA
63309 G
64 G
* * * *
63310 ATGCATCGATGCA-TACCTTATGCATCGATGCACTAATTGCATTTGATGTTCT-ATTATTAATGG
1 ATGCATCGATGCACTACCTTATGCATCGATGCA-TAAATGCATTCGATGTTATCATT-TTAATGA
63373 G
64 G
* * * * *
63374 ATGCATTGATGCACT-CCTTATGCATCGATGCATTGATTGCATTCGATGTTATTATTTTAA-AAG
1 ATGCATCGATGCACTACCTTATGCATCGATGCA-TAAATGCATTCGATGTTATCATTTTAATGA-
63437 G
64 G
* * * * *
63438 ATGCATCGATGCATTAGC-TATGCATCGATGCATCAAAGGCATTCGATGTTCTTC-TTTTAAAG-
1 ATGCATCGATGCACTACCTTATGCATCGATGCAT-AAATGCATTCGATGTT-ATCATTTTAATGA
63500 G
64 G
63501 AATGCATCGATGCACT
1 -ATGCATCGATGCACT
63517 TATGAATGTG
Statistics
Matches: 174, Mismatches: 22, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
63 4 0.02
64 162 0.93
65 8 0.05
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.36
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTTATGCATCGATGCATAAATGCATTCGATGTTATCATTTTAATGAG
Found at i:64185 original size:23 final size:23
Alignment explanation
Indices: 64155--64210 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
64145 CAACTTTTAG
64155 GAATTATTTCCAAATAAATCATT
1 GAATTATTTCCAAATAAATCATT
64178 GAATTATTTCCAAATAAATCATT
1 GAATTATTTCCAAATAAATCATT
64201 GAATTATTTC
1 GAATTATTTC
64211 ATTCTTCTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.41
Consensus pattern (23 bp):
GAATTATTTCCAAATAAATCATT
Found at i:65303 original size:2 final size:2
Alignment explanation
Indices: 65288--65325 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
65278 GTCTACAAAA
65288 AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
65326 ATTATTTCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65359 original size:25 final size:25
Alignment explanation
Indices: 65319--65369 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
65309 TATATATATA
*
65319 TATTATAATTATTTCTATTATTTAT
1 TATTATAATTATTTCTATTACTTAT
*
65344 TATTATTAATTA-TTCTGTTACTTAT
1 TATTA-TAATTATTTCTATTACTTAT
65369 T
1 T
65370 TTGCAGGCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (25 bp):
TATTATAATTATTTCTATTACTTAT
Found at i:65938 original size:20 final size:22
Alignment explanation
Indices: 65894--65936 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
65884 GAAAAAACAC
65894 AGAG-AAAATAACTAAAGAAAAA
1 AGAGAAAAATAAC-AAAGAAAAA
65916 AGAGAAAAATAAC-AAGAAAAA
1 AGAGAAAAATAACAAAGAAAAA
65937 GAAAAAGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.40
22 4 0.20
23 8 0.40
ACGTcount: A:0.74, C:0.05, G:0.14, T:0.07
Consensus pattern (22 bp):
AGAGAAAAATAACAAAGAAAAA
Found at i:74922 original size:15 final size:16
Alignment explanation
Indices: 74899--74941 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
74889 CAATACTCAT
*
74899 TATTTTTATTTTATTT
1 TATTTTTATTTTATTG
*
74915 TA-TTTTATTATATTG
1 TATTTTTATTTTATTG
74930 TATTTTTATTTT
1 TATTTTTATTTT
74942 TTTAATAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (16 bp):
TATTTTTATTTTATTG
Found at i:74958 original size:5 final size:5
Alignment explanation
Indices: 74902--74941 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
74892 TACTCATTAT
* *
74902 TTTTA TTTTA TTTTA TTTTA TTATA TTGTA TTTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTT
74942 TTTAATAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:80569 original size:31 final size:32
Alignment explanation
Indices: 80527--80602 Score: 88
Period size: 31 Copynumber: 2.4 Consensus size: 32
80517 TAATTTAAAA
80527 TTTA-AAAAAAATTATA-GGTAT-AATTAAAATT
1 TTTATAAAAAAATTA-AGGGT-TCAATTAAAATT
* *
80558 TTT-TAAAAAAATTAAGGGTTCAATTCACATT
1 TTTATAAAAAAATTAAGGGTTCAATTAAAATT
80589 TTTATAAAAAAATT
1 TTTATAAAAAAATT
80603 GGGGTCTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
30 2 0.05
31 27 0.69
32 10 0.26
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (32 bp):
TTTATAAAAAAATTAAGGGTTCAATTAAAATT
Found at i:81405 original size:40 final size:40
Alignment explanation
Indices: 81257--81470 Score: 405
Period size: 40 Copynumber: 5.4 Consensus size: 40
81247 ATGCTTATCA
81257 ATGCATTAATTAGATACAGCATATGTATCTTGAATCCTTG
1 ATGCATTAATTAGATACAGCATATGTATCTTGAATCCTTG
81297 ATGCATTAATTAGA-ACAGCATATGTATCTTGAATCCTTG
1 ATGCATTAATTAGATACAGCATATGTATCTTGAATCCTTG
81336 ATGCATTAATTAGA-ACAGCATATGTATCTTGAATCCTTG
1 ATGCATTAATTAGATACAGCATATGTATCTTGAATCCTTG
81375 ATGCATTAATTAGATACAGCATATGTATCTTGAATCCTTG
1 ATGCATTAATTAGATACAGCATATGTATCTTGAATCCTTG
81415 ATGCATTAATTAGATACAGCATATGTATCTTGAATCCTTG
1 ATGCATTAATTAGATACAGCATATGTATCTTGAATCCTTG
*
81455 GTGCATTAATTAGATA
1 ATGCATTAATTAGATA
81471 TCTTCCACTA
Statistics
Matches: 172, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
39 78 0.45
40 94 0.55
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.37
Consensus pattern (40 bp):
ATGCATTAATTAGATACAGCATATGTATCTTGAATCCTTG
Found at i:82232 original size:42 final size:42
Alignment explanation
Indices: 82185--82269 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
82175 AACAAGTGAA
* * *
82185 AGTTTAAGTACATAATTAATTAGTCATTTAGCCTCAGAATTT
1 AGTTTAAGTACATAACTAATTAGACATTTAGCCTAAGAATTT
*
82227 AGTTTAAGTGCATAACTAATTAGACATTTAGCCTAAGAATTT
1 AGTTTAAGTACATAACTAATTAGACATTTAGCCTAAGAATTT
82269 A
1 A
82270 TACGTACTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.38
Consensus pattern (42 bp):
AGTTTAAGTACATAACTAATTAGACATTTAGCCTAAGAATTT
Found at i:83928 original size:28 final size:28
Alignment explanation
Indices: 83888--83944 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
83878 TGAGATCTAA
83888 AGTAGGTAATGGATTGAAACCATAAACT
1 AGTAGGTAATGGATTGAAACCATAAACT
* *
83916 AGTAGTTAGTGGATTGAAACCATAAACT
1 AGTAGGTAATGGATTGAAACCATAAACT
83944 A
1 A
83945 TTTCAAATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (28 bp):
AGTAGGTAATGGATTGAAACCATAAACT
Found at i:84562 original size:18 final size:17
Alignment explanation
Indices: 84534--84567 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
84524 GAGAGTAACC
84534 AGAAAAAAAAGAAAAAT
1 AGAAAAAAAAGAAAAAT
84551 AGAAAGAAAAAGAAAAA
1 AGAAA-AAAAAGAAAAA
84568 GAAGAGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (17 bp):
AGAAAAAAAAGAAAAAT
Found at i:85190 original size:2 final size:2
Alignment explanation
Indices: 85183--85213 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
85173 ATGTGCTACT
85183 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
85214 CAAGTGCTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:89872 original size:20 final size:19
Alignment explanation
Indices: 89816--89976 Score: 124
Period size: 20 Copynumber: 7.9 Consensus size: 19
89806 TTAAACAGGA
89816 GGAATCGGTACCCCCTGGGGGG
1 GGAATCGGTA-CCCCT--GGGG
* * *
89838 GGAATTTGTTCCCCCTGAGGG
1 GGAA-TCGGTACCCCTG-GGG
89859 GGAATCGGTACCCCCTGGGG
1 GGAATCGGTA-CCCCTGGGG
* * *
89879 GGAATCTGTTTCCCTTGGGG
1 GGAATC-GGTACCCCTGGGG
* *
89899 GGAATCTGTACCCCTGGAG
1 GGAATCGGTACCCCTGGGG
* *
89918 GGAATCTGTTCCCCCTGGGG
1 GGAATC-GGTACCCCTGGGG
*
89938 GAGAATCTGTACCCCTGGGG
1 G-GAATCGGTACCCCTGGGG
*
89958 GGAATCTGTACCCCCTGGG
1 GGAATCGGTA-CCCCTGGG
89977 CAATCTGATT
Statistics
Matches: 111, Mismatches: 21, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
19 23 0.21
20 56 0.50
21 20 0.18
22 9 0.08
23 3 0.03
ACGTcount: A:0.15, C:0.27, G:0.36, T:0.22
Consensus pattern (19 bp):
GGAATCGGTACCCCTGGGG
Found at i:89893 original size:19 final size:19
Alignment explanation
Indices: 89834--89976 Score: 151
Period size: 20 Copynumber: 7.2 Consensus size: 19
89824 TACCCCCTGG
*
89834 GGGGGGAATTTGTTCCCCCT
1 GGGGGGAATCTGTT-CCCCT
* *
89854 GAGGGGGAATCGGTACCCCCT
1 G-GGGGGAATCTGT-TCCCCT
*
89875 GGGGGGAATCTGTTTCCCTT
1 GGGGGGAATCTG-TTCCCCT
*
89895 GGGGGGAATCTGTACCCCT
1 GGGGGGAATCTGTTCCCCT
*
89914 GGAGGGAATCTGTTCCCCCT
1 GGGGGGAATCTGTT-CCCCT
*
89934 GGGGGAGAATCTGTACCCCT
1 GGGGG-GAATCTGTTCCCCT
*
89954 GGGGGGAATCTGTACCCCCT
1 GGGGGGAATCTGT-TCCCCT
89974 GGG
1 GGG
89977 CAATCTGATT
Statistics
Matches: 104, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
19 25 0.24
20 54 0.52
21 25 0.24
ACGTcount: A:0.15, C:0.26, G:0.36, T:0.23
Consensus pattern (19 bp):
GGGGGGAATCTGTTCCCCT
Found at i:89900 original size:40 final size:39
Alignment explanation
Indices: 89816--89976 Score: 205
Period size: 40 Copynumber: 4.0 Consensus size: 39
89806 TTAAACAGGA
*
89816 GGAATCGGTACCCCCTGGGGGGGGAATTTGTTCCCCCTGAGGG
1 GGAATCGGTA-CCCCT--GGGGGGAATCTGTTCCCCCTG-GGG
* *
89859 GGAATCGGTACCCCCTGGGGGGAATCTGTTTCCCTTGGGG
1 GGAATCGGTA-CCCCTGGGGGGAATCTGTTCCCCCTGGGG
* *
89899 GGAATCTGTACCCCTGGAGGGAATCTGTTCCCCCTGGGG
1 GGAATCGGTACCCCTGGGGGGAATCTGTTCCCCCTGGGG
* *
89938 GAGAATCTGTACCCCTGGGGGGAATCTGTACCCCCTGGG
1 G-GAATCGGTACCCCTGGGGGGAATCTGTTCCCCCTGGG
89977 CAATCTGATT
Statistics
Matches: 108, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
39 27 0.25
40 47 0.44
41 18 0.17
43 16 0.15
ACGTcount: A:0.15, C:0.27, G:0.36, T:0.22
Consensus pattern (39 bp):
GGAATCGGTACCCCTGGGGGGAATCTGTTCCCCCTGGGG
Found at i:90326 original size:24 final size:24
Alignment explanation
Indices: 90297--90362 Score: 132
Period size: 24 Copynumber: 2.8 Consensus size: 24
90287 CCCCCTTACT
90297 TTAACACTTCTCCCCTTTAACACC
1 TTAACACTTCTCCCCTTTAACACC
90321 TTAACACTTCTCCCCTTTAACACC
1 TTAACACTTCTCCCCTTTAACACC
90345 TTAACACTTCTCCCCTTT
1 TTAACACTTCTCCCCTTT
90363 TTTGTTAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.23, C:0.41, G:0.00, T:0.36
Consensus pattern (24 bp):
TTAACACTTCTCCCCTTTAACACC
Found at i:92758 original size:20 final size:20
Alignment explanation
Indices: 92733--92799 Score: 82
Period size: 20 Copynumber: 3.3 Consensus size: 20
92723 ATACCTCCTG
92733 GGGGGGAATTTGTTCCCTTT
1 GGGGGGAATTTGTTCCCTTT
*
92753 GGGGGGAATCTAT-TTCCCTTG
1 GGGGGGAAT-T-TGTTCCCTTT
* *
92774 GGGGGGAATCTGTTCCCCTT
1 GGGGGGAATTTGTTCCCTTT
92794 GGGGGG
1 GGGGGG
92800 GAATCTGTAC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 1 0.03
20 21 0.52
21 17 0.43
22 1 0.03
ACGTcount: A:0.10, C:0.18, G:0.40, T:0.31
Consensus pattern (20 bp):
GGGGGGAATTTGTTCCCTTT
Found at i:92804 original size:21 final size:21
Alignment explanation
Indices: 92731--92812 Score: 112
Period size: 21 Copynumber: 4.0 Consensus size: 21
92721 CGATACCTCC
*
92731 TGGGGGGGAATTTGTT-CCCT
1 TGGGGGGGAATCTGTTCCCCT
* * *
92751 TTGGGGGGAATCTATTTCCCT
1 TGGGGGGGAATCTGTTCCCCT
92772 TGGGGGGGAATCTGTTCCCCT
1 TGGGGGGGAATCTGTTCCCCT
*
92793 TGGGGGGGAATCTGTACCCC
1 TGGGGGGGAATCTGTTCCCC
92813 CTGGACAATC
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
20 13 0.24
21 41 0.76
ACGTcount: A:0.12, C:0.21, G:0.37, T:0.30
Consensus pattern (21 bp):
TGGGGGGGAATCTGTTCCCCT
Found at i:94648 original size:31 final size:31
Alignment explanation
Indices: 94611--94738 Score: 100
Period size: 31 Copynumber: 4.1 Consensus size: 31
94601 GAACCTCGAC
*
94611 AACTGTCCAT-TGGTTCCGAAGAACCCAGGTA
1 AACTGTCCATAT-GTTCCGAAGAACACAGGTA
** *
94642 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACACAGGTA
* * *
94673 TACTGTCCATATG-TCTCGAA-ATACATAGATA
1 AACTGTCCATATGTTC-CGAAGA-ACACAGGTA
* * * *
94704 ATTCTGTCCATATATTCCGTAGAACATAGGTA
1 A-ACTGTCCATATGTTCCGAAGAACACAGGTA
94736 AAC
1 AAC
94739 CCTCGACTCT
Statistics
Matches: 77, Mismatches: 14, Indels: 12
0.75 0.14 0.12
Matches are distributed among these distances:
30 3 0.04
31 48 0.62
32 23 0.30
33 3 0.04
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACACAGGTA
Found at i:94731 original size:32 final size:30
Alignment explanation
Indices: 94643--94732 Score: 83
Period size: 32 Copynumber: 2.9 Consensus size: 30
94633 ACCCAGGTAA
* *
94643 ACTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATAT-TTCCGTAGAACATAGATAT
* *
94674 ACTGTCCATATGTCTCG-AAATACATAGATAAT
1 ACTGTCCATATTTC-CGTAGA-ACATAGAT-AT
*
94706 TCTGTCCATATATTCCGTAGAACATAG
1 ACTGTCCATAT-TTCCGTAGAACATAG
94733 GTAAACCCTC
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
30 4 0.09
31 19 0.40
32 20 0.43
33 4 0.09
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.33
Consensus pattern (30 bp):
ACTGTCCATATTTCCGTAGAACATAGATAT
Found at i:99688 original size:64 final size:64
Alignment explanation
Indices: 99616--99757 Score: 186
Period size: 64 Copynumber: 2.2 Consensus size: 64
99606 ACCCTTGACG
* *
99616 GGTGCATCGATGCACT-ATCTATGCATCGATGCA-TAAATCT-CATTCGATGTTTGTAT-TTTAA
1 GGTGCATCGATGCACTCCTC-ATGCATCGATGCACT-AAT-TACATTCGATGTTTATATATTTAA
99677 GCA
63 G-A
*
99680 GGTGCATCGATGCACTCCTCATGCATCGATGCACTAATTACATTCGATGTTTATTTATTTAAGA
1 GGTGCATCGATGCACTCCTCATGCATCGATGCACTAATTACATTCGATGTTTATATATTTAAGA
99744 -GTGCATCGATGCAC
1 GGTGCATCGATGCAC
99758 AACCCAAAAA
Statistics
Matches: 71, Mismatches: 3, Indels: 9
0.86 0.04 0.11
Matches are distributed among these distances:
63 15 0.21
64 47 0.66
65 9 0.13
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (64 bp):
GGTGCATCGATGCACTCCTCATGCATCGATGCACTAATTACATTCGATGTTTATATATTTAAGA
Found at i:100487 original size:31 final size:32
Alignment explanation
Indices: 100449--100536 Score: 124
Period size: 31 Copynumber: 2.8 Consensus size: 32
100439 GAGTTGAGGG
* * *
100449 TTACCTATGTCTTTCGAGACATATGAATA-GT
1 TTACCTATGTCATTCGGGACATATGAATAGGA
* *
100480 TTACCTATGTCCTTCGGGACATATGGATAGGA
1 TTACCTATGTCATTCGGGACATATGAATAGGA
100512 TTACCTATGTCATTCGGGACATATG
1 TTACCTATGTCATTCGGGACATATG
100537 GACAATTACC
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
31 26 0.51
32 25 0.49
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (32 bp):
TTACCTATGTCATTCGGGACATATGAATAGGA
Found at i:100521 original size:32 final size:31
Alignment explanation
Indices: 100449--100549 Score: 132
Period size: 32 Copynumber: 3.3 Consensus size: 31
100439 GAGTTGAGGG
* * * *
100449 TTACCTATGTCTTTCGAGACATATGAATAGT
1 TTACCTATGTCATTCGGGACATATGGATAGA
*
100480 TTACCTATGTCCTTCGGGACATATGGATAGGA
1 TTACCTATGTCATTCGGGACATATGGATA-GA
*
100512 TTACCTATGTCATTCGGGACATATGGACA-A
1 TTACCTATGTCATTCGGGACATATGGATAGA
100542 TTACCTAT
1 TTACCTAT
100550 TTTCTTCGGA
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
30 9 0.14
31 26 0.41
32 28 0.44
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (31 bp):
TTACCTATGTCATTCGGGACATATGGATAGA
Found at i:100566 original size:21 final size:21
Alignment explanation
Indices: 100536--100580 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
100526 CGGGACATAT
* *
100536 GGACAATTACCTATTTTCTTC
1 GGACAATTACCTATGTTATTC
*
100557 GGACAGTTACCTATGTTATTC
1 GGACAATTACCTATGTTATTC
100578 GGA
1 GGA
100581 ACATATGGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (21 bp):
GGACAATTACCTATGTTATTC
Done.