Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006833.1 Hibiscus syriacus cultivar Beakdansim tig00017369_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: 54024
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2556 original size:33 final size:32
Alignment explanation
Indices: 2510--2574 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
2500 GTTAGTCATG
* *
2510 TAAGGAAAATGTCTCAATTGAGACAAATTTTT
1 TAAGGAAAATGTCTCAAGTGAGACAAAGTTTT
*
2542 TAAGTGAAAATGTCTCAAGTGAGATAAAGTTTT
1 TAAG-GAAAATGTCTCAAGTGAGACAAAGTTTT
2575 ATTTAGAGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 4 0.14
33 25 0.86
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.34
Consensus pattern (32 bp):
TAAGGAAAATGTCTCAAGTGAGACAAAGTTTT
Found at i:2708 original size:71 final size:71
Alignment explanation
Indices: 2547--3134 Score: 586
Period size: 71 Copynumber: 8.5 Consensus size: 71
2537 TTTTTTAAGT
* * * * * * *
2547 GAAAATGTCTCAAGTGAGAT-AAAGTTTTATTT-AGAGAGAAATTGTCTTGAGTGTGATGAAAAT
1 GAAAATATCTCAAGTGAGATGAAA-TTTTGTTTCA-AGAGAAACTGTCTCGAGTGAGACGAAAAA
2610 TTTCCAAGG
64 TTT-CAAGG
* * * *
2619 GAAAATATCTCATGTGAGATGAAATTTTGTTTCAAGAGAAATTGTTTCGAGTGAGACAAAAAATT
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTTCAAGAGAAACTGTCTCGAGTGAGACGAAAAATT
2684 TCAAGG
66 TCAAGG
* * * *
2690 GAAAATATCTCAAGTGAGACGAAGTTTTATTTCAAGAGAAAACTGTCTCGA--GAGACG--AATT
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTTCAAGAG-AAACTGTCTCGAGTGAGACGAAAAAT
2751 TTCAAGG
65 TTCAAGG
* * * * * *
2758 GAAAATATTTCAACTAAGA--AAATTTTGTTTCGAGAGAAACTGTCTTGAGTGAGAC-AAAATTT
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTTCAAGAGAAACTGTCTCGAGTGAGACGAAAAATT
2820 TCAAGG
66 TCAAGG
* * * * *
2826 GAAAATATCTCAAGTGAGATGAAA-TTTGTTACGAGAGAAACTGTCTCGACTAAGATGAAAAATT
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTTCAAGAGAAACTGTCTCGAGTGAGACGAAAAATT
2890 TCACA-G
66 TCA-AGG
* ** * * *
2896 GAAAATACCTCAAGTGAGATGAAATTTTGTTTTGAGAGAAACTATCTTGAGTGAGATGAAAAATT
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTTCAAGAGAAACTGTCTCGAGTGAGACGAAAAATT
2961 TCACA-G
66 TCA-AGG
* * ** *
2967 GAAAGTATCTCAAGTGAGATGAAAATTTGTTTTTAGAGAAACTGTCTCGAGTGAGA-TAAAAA-T
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTTCAAGAGAAACTGTCTCGAGTGAGACGAAAAATT
*
3030 T-AAAG
66 TCAAGG
* *
3035 GAAAATATCTCAAGTGAGATG-AATTTTATTT-AGAGAGAAAC--TCTCGAGTGAGAC-AGAAAT
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTTCA-AGAGAAACTGTCTCGAGTGAGACGA-AAAA
*
3095 TTTTAAGG
64 TTTCAAGG
*
3103 GAAAATATCTCAAGTGAGATGATATTTTGTTT
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTT
3135 GTGAGGAAAA
Statistics
Matches: 442, Mismatches: 55, Indels: 41
0.82 0.10 0.08
Matches are distributed among these distances:
65 24 0.05
66 17 0.04
67 24 0.05
68 99 0.22
69 37 0.08
70 46 0.10
71 130 0.29
72 61 0.14
73 4 0.01
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (71 bp):
GAAAATATCTCAAGTGAGATGAAATTTTGTTTCAAGAGAAACTGTCTCGAGTGAGACGAAAAATT
TCAAGG
Found at i:2725 original size:37 final size:36
Alignment explanation
Indices: 2514--3223 Score: 121
Period size: 34 Copynumber: 20.3 Consensus size: 36
2504 GTCATGTAAG
* * * *
2514 GAAAATGTCTCAATTGAGAC-AAATTT-TTT-AAGT
1 GAAAATATCTCAAGTGAGACGAATTTTATTTCAAGA
* **
2547 GAAAATGTCTCAAGTGAGATAAAGTTTTATTT-AGAGA
1 GAAAATATCTCAAGTGAGACGAA-TTTTATTTCA-AGA
* * ** * * ** * *
2584 GAAATTGTCTTGAGTGTGATGAAAATT-TTCCAAGG
1 GAAAATATCTCAAGTGAGACGAATTTTATTTCAAGA
* * *
2619 GAAAATATCTCATGTGAGATGAAATTTTGTTTCAAGA
1 GAAAATATCTCAAGTGAGACG-AATTTTATTTCAAGA
* * * * *** *
2656 GAAATTGTTTCGAGTGAGAC-AA-AAAATTTCAAGG
1 GAAAATATCTCAAGTGAGACGAATTTTATTTCAAGA
2690 GAAAATATCTCAAGTGAGACGAAGTTTTATTTCAAGA
1 GAAAATATCTCAAGTGAGACGAA-TTTTATTTCAAGA
* * *
2727 GAAAACTGTCTC--GAGAGACGAA---T-TTTCAAGG
1 GAAAA-TATCTCAAGTGAGACGAATTTTATTTCAAGA
* * * * * *
2758 GAAAATATTTCAACTAAGA-AAATTTTGTTTCGAGA
1 GAAAATATCTCAAGTGAGACGAATTTTATTTCAAGA
* * ** ** *
2793 GAAACTGTCTTGAGTGAGAC-AA-AAT-TTTCAAGG
1 GAAAATATCTCAAGTGAGACGAATTTTATTTCAAGA
* * * * *
2826 GAAAATATCTCAAGTGAGATGAAATTTGTTACGAGA
1 GAAAATATCTCAAGTGAGACGAATTTTATTTCAAGA
* * * * * * **
2862 GAAACTGTCTCGACTAAGATGAA--AAATTTCACAG-
1 GAAAATATCTCAAGTGAGACGAATTTTATTTCA-AGA
* * * **
2896 GAAAATACCTCAAGTGAGATGAAATTTTGTTTTGAGA
1 GAAAATATCTCAAGTGAGACG-AATTTTATTTCAAGA
* ** * **
2933 GAAACTATCTTGAGTGAGATGAA--AAATTTCACAG-
1 GAAAATATCTCAAGTGAGACGAATTTTATTTCA-AGA
* * * * **
2967 GAAAGTATCTCAAGTGAGATGAAAATTTGTTTTTAGA
1 GAAAATATCTCAAGTGAGACG-AATTTTATTTCAAGA
* * * * * * *
3004 GAAACTGTCTCGAGTGAGA-TAA---AAATTAAAG-
1 GAAAATATCTCAAGTGAGACGAATTTTATTTCAAGA
*
3035 GAAAATATCTCAAGTGAGATGAATTTTATTT--AGA
1 GAAAATATCTCAAGTGAGACGAATTTTATTTCAAGA
* * * *
3069 GAGAAA-CTCTCGAGTGAGACAGAA-ATT-TTT-AAGG
1 GA-AAATATCTCAAGTGAGAC-GAATTTTATTTCAAGA
* * **
3103 GAAAATATCTCAAGTGAGATGATATTTTGTTT-GTGA
1 GAAAATATCTCAAGTGAGACGA-ATTTTATTTCAAGA
** * *
3139 GGAAAATTATCTCAAGTGAGATAAAAAATTTGTTTCAAGA
1 -GAAAA-TATCTCAAGTGAG--ACGAATTTTATTTCAAGA
* *
3179 -AAAACTGTCTCGAGTGAGACGAATTTT-TTT-AAG-
1 GAAAA-TATCTCAAGTGAGACGAATTTTATTTCAAGA
3212 GAAAACTATCTC
1 GAAAA-TATCTC
3224 TAGTAAGATA
Statistics
Matches: 477, Mismatches: 151, Indels: 97
0.66 0.21 0.13
Matches are distributed among these distances:
30 4 0.01
31 30 0.06
32 10 0.02
33 49 0.10
34 112 0.23
35 71 0.15
36 59 0.12
37 97 0.20
38 33 0.07
39 8 0.02
40 4 0.01
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (36 bp):
GAAAATATCTCAAGTGAGACGAATTTTATTTCAAGA
Found at i:2919 original size:34 final size:34
Alignment explanation
Indices: 2825--3057 Score: 132
Period size: 37 Copynumber: 6.7 Consensus size: 34
2815 AATTTTCAAG
* *
2825 GGAAAATATCTCAAGTGAGATG-AAATTTGTTACGA
1 GGAAAATATCTCAAGTGAGATGAAAAATT-TCAC-A
* * * * *
2860 GAGAAACTGTCTCGACTAAGATGAAAAATTTCACA
1 G-GAAAATATCTCAAGTGAGATGAAAAATTTCACA
* ** ***
2895 GGAAAATACCTCAAGTGAGATGAAATTTTGTTTTGA
1 GGAAAATATCTCAAGTGAGATGAAA-AAT-TTCACA
* **
2931 GAGAAACTATCTTGAGTGAGATGAAAAATTTCACA
1 G-GAAAATATCTCAAGTGAGATGAAAAATTTCACA
* * ***
2966 GGAAAGTATCTCAAGTGAGATGAAAATTTGTTTTTA
1 GGAAAATATCTCAAGTGAGATGAAAA-AT-TTCACA
* * * *
3002 GAGAAACTGTCTCGAGTGAGAT-AAAAA-TT-AAA
1 G-GAAAATATCTCAAGTGAGATGAAAAATTTCACA
3034 GGAAAATATCTCAAGTGAGATGAA
1 GGAAAATATCTCAAGTGAGATGAA
3058 TTTTATTTAG
Statistics
Matches: 146, Mismatches: 43, Indels: 21
0.70 0.20 0.10
Matches are distributed among these distances:
31 17 0.12
32 4 0.03
33 2 0.01
34 40 0.27
35 9 0.06
36 32 0.22
37 42 0.29
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.27
Consensus pattern (34 bp):
GGAAAATATCTCAAGTGAGATGAAAAATTTCACA
Found at i:3040 original size:277 final size:277
Alignment explanation
Indices: 2528--3129 Score: 691
Period size: 277 Copynumber: 2.2 Consensus size: 277
2518 ATGTCTCAAT
* * * * *
2528 TGAGACAAATTTTTTAAGTGAAAATGTCTCAAGTGAGAT-AAAGTTTTATTTAGAGAGAAATTGT
1 TGAGACAAAATTTTTAAGGGAAAATATCTCAAGTGAGATGAAA--TTTAGTTAGAGAGAAACTGT
* * ** * * *
2592 CTTGAGTGTGATGAAAATTTTCCAAGGGAAAATATCTCATGTGAGATGAAATTTTGTTTCAAGAG
64 CTCGACTAAGATGAAAAATTTCCAAGGGAAAATACCTCAAGTGAGATGAAATTTTGTTTCAAGAG
* * **
2657 AAATTGTTTCGAGTGAGACAAAAAATTTCAAGGGAAAATATCTCAAGTGAGACGAAGTTTTATTT
129 AAACTATTTCGAGTGAGACAAAAAATTTCAAGGGAAAATATCTCAAGTGAGACGAAAATTTATTT
* ** * * *
2722 CAAGAGAAAACTGTCTCGAGAGACGAATTTTCAAGGGAAAATATTTCAACTAAGA-AAATTTTGT
194 CAAGAGAAAACTGTCTCGAGAGACAAAAATTCAAAGGAAAATATCTCAACTAAGATAAATTTTAT
* *
2786 TTCGAGAGAAACTGTCTTGAG
259 TTAGAGAGAAAC--TCTCGAG
*
2807 TGAGACAAAATTTTCAAGGGAAAATATCTCAAGTGAGATGAAATTT-GTTACGAGAGAAACTGTC
1 TGAGACAAAATTTTTAAGGGAAAATATCTCAAGTGAGATGAAATTTAGTTA-GAGAGAAACTGTC
**
2871 TCGACTAAGATGAAAAATTT-CACA-GGAAAATACCTCAAGTGAGATGAAATTTTGTTTTGAGAG
65 TCGACTAAGATGAAAAATTTCCA-AGGGAAAATACCTCAAGTGAGATGAAATTTTGTTTCAAGAG
** * * *
2934 AAACTATCTT-GAGTGAGATGAAAAATTTCACA-GGAAAGTATCTCAAGTGAGATGAAAATTTGT
129 AAACTAT-TTCGAGTGAGACAAAAAATTTCA-AGGGAAAATATCTCAAGTGAGACGAAAATTTAT
** * * * *
2997 TTTTAGAG-AAACTGTCTCGAGTGAGATAAAAATT-AAAGGAAAATATCTCAAGTGAGATGAATT
192 TTCAAGAGAAAACTGTCTCGA--GAGACAAAAATTCAAAGGAAAATATCTCAACTAAGATAAATT
3060 TTATTTAGAGAGAAACTCTCGAG
255 TTATTTAGAGAGAAACTCTCGAG
*
3083 TGAGACAGAAATTTTTAAGGGAAAATATCTCAAGTGAGATGATATTT
1 TGAGACA-AAATTTTTAAGGGAAAATATCTCAAGTGAGATGAAATTT
3130 TGTTTGTGAG
Statistics
Matches: 274, Mismatches: 40, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
276 25 0.09
277 151 0.55
278 60 0.22
279 35 0.13
280 3 0.01
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.30
Consensus pattern (277 bp):
TGAGACAAAATTTTTAAGGGAAAATATCTCAAGTGAGATGAAATTTAGTTAGAGAGAAACTGTCT
CGACTAAGATGAAAAATTTCCAAGGGAAAATACCTCAAGTGAGATGAAATTTTGTTTCAAGAGAA
ACTATTTCGAGTGAGACAAAAAATTTCAAGGGAAAATATCTCAAGTGAGACGAAAATTTATTTCA
AGAGAAAACTGTCTCGAGAGACAAAAATTCAAAGGAAAATATCTCAACTAAGATAAATTTTATTT
AGAGAGAAACTCTCGAG
Found at i:11880 original size:21 final size:21
Alignment explanation
Indices: 11856--11906 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
11846 CCTTCATTAT
11856 CACCACCATGATCATCATAAC
1 CACCACCATGATCATCATAAC
11877 CACCACCATGATCATCATAAC
1 CACCACCATGATCATCATAAC
11898 CACCACCAT
1 CACCACCAT
11907 CATTGTCGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.37, C:0.41, G:0.04, T:0.18
Consensus pattern (21 bp):
CACCACCATGATCATCATAAC
Found at i:18145 original size:23 final size:23
Alignment explanation
Indices: 18103--18206 Score: 117
Period size: 23 Copynumber: 4.7 Consensus size: 23
18093 TTGGTGCAGA
*
18103 GGGAATCGA-TACCCCCTTGAAT
1 GGGAATCGATTACCCCTTTGAAT
*
18125 GGGAACCGATTACCCCTTTGAAT
1 GGGAATCGATTACCCCTTTGAAT
* * *
18148 GGGAAACGATTCCCCCTTTGAAG
1 GGGAATCGATTACCCCTTTGAAT
* *
18171 GGGAATCGATTACCCCCTT--AG
1 GGGAATCGATTACCCCTTTGAAT
18192 GGGAATCGA-TACCCC
1 GGGAATCGATTACCCC
18207 CACGGGTTCT
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.08
21 11 0.15
22 8 0.11
23 48 0.66
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.22
Consensus pattern (23 bp):
GGGAATCGATTACCCCTTTGAAT
Found at i:21463 original size:22 final size:22
Alignment explanation
Indices: 21438--21484 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
21428 GATATGAAAA
21438 AATTTCAA-TTTAAAATTAA-ATT
1 AATTT-AATTTTAAAA-TAATATT
21460 AATTTAATTTTAAAATAATATT
1 AATTTAATTTTAAAATAATATT
21482 AAT
1 AAT
21485 AGTAATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
AATTTAATTTTAAAATAATATT
Found at i:21493 original size:22 final size:21
Alignment explanation
Indices: 21444--21503 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 21
21434 AAAAAATTTC
*
21444 AATTTAAAATTAAATTAATTT
1 AATTTAAAATTAAATTAATGT
21465 AATTTTAAAA-TAATATTAATAGT
1 AA-TTTAAAATTAA-ATTAAT-GT
21488 AATTTAATTAATTAAA
1 AATTTAA--AATTAAA
21504 ATTTAAGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
21 5 0.16
22 18 0.56
23 3 0.09
24 3 0.09
25 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
AATTTAAAATTAAATTAATGT
Found at i:21700 original size:16 final size:16
Alignment explanation
Indices: 21679--21713 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
21669 AAAAATTTTC
*
21679 AATTTAAATTTAAATT
1 AATTTAAATTTAAAAT
*
21695 AATTTAATTTTAAAAT
1 AATTTAAATTTAAAAT
21711 AAT
1 AAT
21714 GTCAATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTTAAATTTAAAAT
Found at i:21833 original size:235 final size:226
Alignment explanation
Indices: 21422--22089 Score: 1087
Period size: 235 Copynumber: 2.9 Consensus size: 226
21412 AATTACGTCA
* * *
21422 ATTTTAGATATGAAAAAATTTCAATTTAAAATTAAATTAATTTAATTTTAAAATAATATTAATAG
1 ATTTTAGATATG-AAAAATTTCAATTTAAATTTAAATTAATTTAATTTTAAAATAATGTTAATAA
*
21487 TAATTTAATTAATTAAAATTTAAGTAACTAACTTTAAACATAACTATTACGATATTAGTAATGAT
65 TAATTTAATTAATTCAAATTTAAGTAACTAACTTTAAACATAACTATTACGATATTAGTAATGAT
* *
21552 ATATATTTATAATCCAGTTTTAAAAATTAAATTAGAACAATTCATCTATGTAATTTTATATTTTA
130 ATATATTTATAATCCAGTTTTAAGAATTAAATTAGAACAATTCATCTATGTAATTTTATATTTCA
21617 GATAATTTAAAGTTTATTGCGACTTTGCGGTGTTGCATAT
195 GATAATTTAAAGTTTATTGCG-----GCGGTG-TG--TAT
*
21657 ATTTTAGATATGAAAAATTTTCAATTTAAATTTAAATTAATTTAATTTTAAAATAATGTCAATAA
1 ATTTTAGATATGAAAAA-TTTCAATTTAAATTTAAATTAATTTAATTTTAAAATAATGTTAATAA
*
21722 TAATTTAATTAATTCAAATTTAAGTAAGTAACTTTAAACATAACTATTACGATATTAGTAATGAT
65 TAATTTAATTAATTCAAATTTAAGTAACTAACTTTAAACATAACTATTACGATATTAGTAATGAT
21787 ATATATTTATAATCCAGTTTTAAGAATTAAATTAGAACAATTCATCTATGTAATTTTATATTTCA
130 ATATATTTATAATCCAGTTTTAAGAATTAAATTAGAACAATTCATCTATGTAATTTTATATTTCA
* *
21852 GATAATTTAAAGTTTGTTGCGGCGTTGTGTAT
195 GATAATTTAAAGTTTATTGCGGCGGTGTGTAT
21884 ATTTTAGATATG--AAATTT---TTT-AATTTAAATTAATTTAATTTTAAAATAATGTTAATAAA
1 ATTTTAGATATGAAAAATTTCAATTTAAATTTAAATTAATTTAATTTTAAAATAATGTTAAT-AA
21943 TAATTTAATTAATTCAAATTTAAGTAACTAACTTTAAACATAACTATTACGATATTAGTAATGAT
65 TAATTTAATTAATTCAAATTTAAGTAACTAACTTTAAACATAACTATTACGATATTAGTAATGAT
*
22008 ATATATTTATAATCCAGTTTTAAGAATTAAATTAGAACAATTCATATATGTAATTTTATATTTCA
130 ATATATTTATAATCCAGTTTTAAGAATTAAATTAGAACAATTCATCTATGTAATTTTATATTTCA
*
22073 AATAATTTAAAGTTTAT
195 GATAATTTAAAGTTTAT
22090 AACGCAATAT
Statistics
Matches: 416, Mismatches: 15, Indels: 18
0.93 0.03 0.04
Matches are distributed among these distances:
220 34 0.08
221 148 0.36
224 3 0.01
225 3 0.01
227 15 0.04
229 2 0.00
230 5 0.01
234 5 0.01
235 201 0.48
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.44
Consensus pattern (226 bp):
ATTTTAGATATGAAAAATTTCAATTTAAATTTAAATTAATTTAATTTTAAAATAATGTTAATAAT
AATTTAATTAATTCAAATTTAAGTAACTAACTTTAAACATAACTATTACGATATTAGTAATGATA
TATATTTATAATCCAGTTTTAAGAATTAAATTAGAACAATTCATCTATGTAATTTTATATTTCAG
ATAATTTAAAGTTTATTGCGGCGGTGTGTAT
Found at i:21928 original size:16 final size:16
Alignment explanation
Indices: 21902--21939 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
21892 TATGAAATTT
*
21902 TTTAA-TTTAAATTAA
1 TTTAATTTTAAAATAA
21917 TTTAATTTTAAAATAA
1 TTTAATTTTAAAATAA
21933 TGTTAAT
1 T-TTAAT
21940 AAATAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 5 0.25
16 10 0.50
17 5 0.25
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAATTTTAAAATAA
Found at i:34369 original size:21 final size:21
Alignment explanation
Indices: 34293--34363 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
34283 TTTTGGTGCA
* *
34293 GAGGGAATCGATCCCCCCCAT
1 GAGGGAACCGATTCCCCCCAT
**
34314 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCAT
34335 GAAGGGGAACCGATTCCCCCCAT
1 G-A-GGGAACCGATTCCCCCCAT
34358 -AGGGAA
1 GAGGGAA
34364 ATCGATACCC
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
20 5 0.12
21 19 0.45
22 1 0.02
23 17 0.40
ACGTcount: A:0.25, C:0.32, G:0.27, T:0.15
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCAT
Found at i:34764 original size:23 final size:23
Alignment explanation
Indices: 34738--34781 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
34728 AAAACACAAG
34738 AATTTTACAAAAAAAAATTTTAA
1 AATTTTACAAAAAAAAATTTTAA
** *
34761 AATTTTTGAAATAAAAATTTT
1 AATTTTACAAAAAAAAATTTT
34782 TTTGTTGACT
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:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
AATTTTACAAAAAAAAATTTTAA
Found at i:34845 original size:2 final size:2
Alignment explanation
Indices: 34838--34872 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
34828 TTATGAAAAC
34838 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
34873 TGTTTCTCAA
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:38451 original size:81 final size:82
Alignment explanation
Indices: 38347--38731 Score: 321
Period size: 81 Copynumber: 4.7 Consensus size: 82
38337 TTCAGAAAAT
* * ** * * * *
38347 AAACGTCACTATTTATCTTGCTATCGCGGCCTTTTTTACATAAACACCACTAAAGTATGCGTTTT
1 AAACGCCACTATATATCAGGCTATAGCGGCCTTTTTTACATAAACGCCACTAAAGTACGCATTTT
* * * * *
38412 CAGTGGCGTTTCCCCAA
66 TAGCGGTGTTTTCACAA
* * * * * *
38429 AAACG-CACTATATATCAGGCTATCA-CGACATTTTTAACATAAACGCCGCTAAAGCACGCGTTC
1 AAACGCCACTATATATCAGGCTAT-AGCGGCCTTTTTTACATAAACGCCACTAAAGTACGCATT-
* * *
38492 TTTAGTGGTATTTACACAA
64 TTTAGCGGTGTTTTCACAA
* * ** * *
38511 AAACACCACTATATATCTGGCTATAATGG-CTTTTTGACATAAACACCACTAAAGTACGCATTTT
1 AAACGCCACTATATATCAGGCTATAGCGGCCTTTTTTACATAAACGCCACTAAAGTACGCATTTT
*
38575 TAGCGGTGTTTTCACAT
66 TAGCGGTGTTTTCACAA
* * * ** * **
38592 AAACGCCACTATATATCCGGCTATAGCAGCGTCGTTTACATAAACGTCACTAAAGTGTGCA-TTT
1 AAACGCCACTATATATCAGGCTATAGCGGCCTTTTTTACATAAACGCCACTAAAGTACGCATTTT
* *
38656 TAGCGGAGTTTTCACAT
66 TAGCGGTGTTTTCACAA
* * **
38673 AAACGCCACTATACATCTA-TCTATAGCGGTGTTTTTTACATAAACGCCACTAAAGTACG
1 AAACGCCACTATATATC-AGGCTATAGCGGCCTTTTTTACATAAACGCCACTAAAGTACG
38732 TGTTTCTAGC
Statistics
Matches: 243, Mismatches: 54, Indels: 13
0.78 0.17 0.04
Matches are distributed among these distances:
81 151 0.62
82 74 0.30
83 18 0.07
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (82 bp):
AAACGCCACTATATATCAGGCTATAGCGGCCTTTTTTACATAAACGCCACTAAAGTACGCATTTT
TAGCGGTGTTTTCACAA
Found at i:39488 original size:2 final size:2
Alignment explanation
Indices: 39481--39517 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
39471 TACAAATTAC
39481 AT AT AT AT AT 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 AT AT AT AT AT A
39518 GCTTTAACAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48303 original size:102 final size:102
Alignment explanation
Indices: 48137--48332 Score: 295
Period size: 102 Copynumber: 1.9 Consensus size: 102
48127 AATATAATTA
* * *
48137 TATATACAATAAAGCTGAGCTATTCTATAAAGCAATTGGTTAAAAGCCCTGACTTTATGGATAGA
1 TATATACAATAAAGCTGAGCTATTCTATAAAGAAACTAGTTAAAAGCCCTGACTTTATGGATAGA
*
48202 TTCCTTCA-CTAGCCAAACAAAGGCAAATAATATATG
66 TTCCTTCAGCTAGCCAAACAAAGGAAAATAATATATG
* * * * *
48238 TATATACAATAAAGTTGAGTTATTTTTCTAAAGAAACTAGTTAAGAGCCCTGACTTTATGGATAG
1 TATATACAATAAAGCTGAGCTA-TTCTATAAAGAAACTAGTTAAAAGCCCTGACTTTATGGATAG
48303 ATTCCTTCAGCTAGCCAAACAAAGGAAAAT
65 ATTCCTTCAGCTAGCCAAACAAAGGAAAAT
48333 TAAATTAAAT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
101 20 0.24
102 45 0.54
103 19 0.23
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (102 bp):
TATATACAATAAAGCTGAGCTATTCTATAAAGAAACTAGTTAAAAGCCCTGACTTTATGGATAGA
TTCCTTCAGCTAGCCAAACAAAGGAAAATAATATATG
Found at i:49113 original size:17 final size:16
Alignment explanation
Indices: 49091--49136 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
49081 TCACAAGATG
*
49091 AAGACTCAACAAGGATA
1 AAGACTCAACAAGG-CA
49108 AAGACTCAACAAAGGCA
1 AAGACTCAAC-AAGGCA
49125 AAGACTCAACAA
1 AAGACTCAACAA
49137 CGAGAATGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 2 0.07
17 21 0.78
18 4 0.15
ACGTcount: A:0.54, C:0.22, G:0.15, T:0.09
Consensus pattern (16 bp):
AAGACTCAACAAGGCA
Found at i:50092 original size:15 final size:15
Alignment explanation
Indices: 50072--50105 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
50062 TGCTTCCGAA
**
50072 ATTTAAAATTTATTT
1 ATTTAAAAAATATTT
50087 ATTTAAAAAATATTT
1 ATTTAAAAAATATTT
50102 ATTT
1 ATTT
50106 TCTATTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTAAAAAATATTT
Found at i:51722 original size:14 final size:14
Alignment explanation
Indices: 51683--51723 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
51673 AATATTTTAA
51683 AATA-ATTAA-AAT
1 AATATATTAATAAT
*
51695 AATATAATTTATAAT
1 AATAT-ATTAATAAT
51710 AATATATTAATAAT
1 AATATATTAATAAT
51724 TATTTATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 4 0.17
14 12 0.50
15 8 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATATATTAATAAT
Found at i:51764 original size:30 final size:29
Alignment explanation
Indices: 51737--51809 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 29
51727 TTATTATATT
51737 TTAAAAAGTTAAATTAACATATTTTATAATA
1 TTAAAAA-TTAAA-TAACATATTTTATAATA
* *
51768 TTAATAATTAAATAATATATTTTAATAATA
1 TTAAAAATTAAATAACATATTTT-ATAATA
*
51798 -TAAAAATAAAAT
1 TTAAAAATTAAAT
51810 TATTAAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 20 0.54
30 11 0.30
31 6 0.16
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (29 bp):
TTAAAAATTAAATAACATATTTTATAATA
Found at i:53782 original size:16 final size:16
Alignment explanation
Indices: 53761--53791 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
53751 CGGATAAATT
53761 TTATTAATTTAGAGAG
1 TTATTAATTTAGAGAG
53777 TTATTAATTTAGAGA
1 TTATTAATTTAGAGA
53792 TAAAATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (16 bp):
TTATTAATTTAGAGAG
Done.