Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000401.1 Hibiscus syriacus cultivar Beakdansim tig00000737_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: 58594
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:7452 original size:21 final size:21
Alignment explanation
Indices: 7428--7469 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
7418 GGCAGATTGT
*
7428 CCAGAGGGAACCGATTCCCCC
1 CCAGAGGGAACCGATTACCCC
* *
7449 CCAGGGGGTACCGATTACCCC
1 CCAGAGGGAACCGATTACCCC
7470 TGAATGGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.40, G:0.26, T:0.12
Consensus pattern (21 bp):
CCAGAGGGAACCGATTACCCC
Found at i:8200 original size:19 final size:19
Alignment explanation
Indices: 8176--8218 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
8166 TTTAATTACT
8176 AATTCACCCCCTCTTGGCC
1 AATTCACCCCCTCTTGGCC
8195 AATTCACCCCCTCTTGGCC
1 AATTCACCCCCTCTTGGCC
8214 AATTC
1 AATTC
8219 CATCGATCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.19, C:0.44, G:0.09, T:0.28
Consensus pattern (19 bp):
AATTCACCCCCTCTTGGCC
Found at i:9777 original size:5 final size:5
Alignment explanation
Indices: 9762--9828 Score: 73
Period size: 5 Copynumber: 12.6 Consensus size: 5
9752 TGCTTGAAGT
*
9762 AAAGAA AAAGA AAAGA AAAGAA AAAGA ACAGA AAAGAA AAAGAA AAAGA
1 AAAG-A AAAGA AAAGA AAAG-A AAAGA AAAGA AAAG-A AAAG-A AAAGA
9811 AAAGA AAA-A AGAAGA AAA
1 AAAGA AAAGA A-AAGA AAA
9829 AAGGAAAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
4 2 0.04
5 31 0.56
6 22 0.40
ACGTcount: A:0.81, C:0.01, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:9778 original size:11 final size:11
Alignment explanation
Indices: 9762--9829 Score: 79
Period size: 11 Copynumber: 6.3 Consensus size: 11
9752 TGCTTGAAGT
9762 AAAGAAAA-AGA
1 AAAGAAAAGA-A
9773 AAAGAAAAGAA
1 AAAGAAAAGAA
*
9784 AAAGAACAG-A
1 AAAGAAAAGAA
9794 AAAGAAAAAGAA
1 AAAG-AAAAGAA
9806 AAAGAAAAGAA
1 AAAGAAAAGAA
*
9817 AAA-AGAAGAA
1 AAAGAAAAGAA
9827 AAA
1 AAA
9830 AGGAAAAAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
10 14 0.27
11 31 0.61
12 6 0.12
ACGTcount: A:0.81, C:0.01, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:9783 original size:16 final size:16
Alignment explanation
Indices: 9762--9857 Score: 106
Period size: 16 Copynumber: 5.8 Consensus size: 16
9752 TGCTTGAAGT
9762 AAAGAAAAAGAAAAGA
1 AAAGAAAAAGAAAAGA
*
9778 AAAGAAAAAGAACAGA
1 AAAGAAAAAGAAAAGA
9794 AAAGAAAAAGAAAAAGA
1 AAAGAAAAAG-AAAAGA
9811 AAAGAAAAAAGAAGAA-A
1 AAAG-AAAAAGAA-AAGA
*
9828 AAAGGAAAAAAGGAAA-A
1 AAA-G-AAAAAGAAAAGA
9845 AAAGAATAAAGAA
1 AAAGAA-AAAGAA
9858 TAAAGAAAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
15 2 0.03
16 31 0.44
17 21 0.30
18 17 0.24
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.01
Consensus pattern (16 bp):
AAAGAAAAAGAAAAGA
Found at i:9829 original size:27 final size:26
Alignment explanation
Indices: 9766--9866 Score: 93
Period size: 27 Copynumber: 3.8 Consensus size: 26
9756 TGAAGTAAAG
9766 AAAAAG-AAAAG-AAAAGAAAAAGAACA
1 AAAAAGAAAAAGAAAAAG-AAAAGAA-A
*
9792 GAAAAGAAAAAGAAAAAGAAAAGAAA
1 AAAAAGAAAAAGAAAAAGAAAAGAAA
** *
9818 AAAGAAGAAAAA-AGGAA-AAAAGGAA
1 AAA-AAGAAAAAGAAAAAGAAAAGAAA
9843 AAAAAGAATAAAGAATAAAGAAAA
1 AAAAAGAA-AAAGAA-AAAGAAAA
9867 AATATATAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
24 5 0.08
25 13 0.21
26 12 0.20
27 22 0.36
28 9 0.15
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.02
Consensus pattern (26 bp):
AAAAAGAAAAAGAAAAAGAAAAGAAA
Found at i:9830 original size:11 final size:11
Alignment explanation
Indices: 9763--9830 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 11
9753 GCTTGAAGTA
9763 AAGAAAAAGAA-
1 AAGAAAAA-AAG
9774 AAGAAAAGAAA-
1 AAGAAAA-AAAG
9785 AAGAACAGAAAAG
1 AAGAA-A-AAAAG
*
9798 AAAAAGAAAAAG
1 AAGAA-AAAAAG
*
9810 AAAAGAAAAAAG
1 AAGA-AAAAAAG
9822 AAGAAAAAA
1 AAGAAAAAA
9831 GGAAAAAAGG
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
11 19 0.39
12 23 0.47
13 7 0.14
ACGTcount: A:0.81, C:0.01, G:0.18, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAG
Found at i:9835 original size:8 final size:7
Alignment explanation
Indices: 9762--9868 Score: 69
Period size: 7 Copynumber: 14.4 Consensus size: 7
9752 TGCTTGAAGT
9762 AAAG-AA
1 AAAGAAA
9768 AAAGAAA
1 AAAGAAA
*
9775 AGAAAAGAA
1 A-AAGA-AA
9784 AAAGAACA
1 AAAGAA-A
9792 GAAA-AGAA
1 -AAAGA-AA
9800 AAAG-AA
1 AAAGAAA
9806 AAAGAAA
1 AAAGAAA
9813 AGAA-AAA
1 A-AAGAAA
9820 AGAAGAAA
1 A-AAGAAA
9828 AAAGGAAA
1 AAA-GAAA
9836 AAAGGAAAA
1 AAA-G-AAA
*
9845 AAAGAAT
1 AAAGAAA
*
9852 AAAGAAT
1 AAAGAAA
9859 AAAGAAA
1 AAAGAAA
9866 AAA
1 AAA
9869 TATATAAAGC
Statistics
Matches: 85, Mismatches: 4, Indels: 23
0.76 0.04 0.21
Matches are distributed among these distances:
6 10 0.12
7 37 0.44
8 25 0.29
9 13 0.15
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.02
Consensus pattern (7 bp):
AAAGAAA
Found at i:11146 original size:42 final size:42
Alignment explanation
Indices: 11087--11482 Score: 287
Period size: 42 Copynumber: 9.0 Consensus size: 42
11077 TCTCTCTTTT
* *
11087 CCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGT-TTGC
1 CCAAGATCTGATATTCCCTGAGTGACAGTGGAACAAGTCTT-C
* * * *
11129 CCAAGATCTGATATTCCCTGAGTGACAGTAGAATAAATCACTCC
1 CCAAGATCTGATATTCCCTGAGTGACAGTGGAACAAGT--CTTC
* * *
11173 CTTTCAATATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTTC
1 C---CAAGATCTGATATTCCCTGAGTGACAGTGGAACAAGTCTTC
* * * *
11218 CCCAGATCTGATATTCCTTGAGTGACAGTGGAATAGATCCTCTTTC
1 CCAAGATCTGATATTCCCTGAGTGACAGTGGAACA-A--GTC-TTC
* * * * *
11264 TCAATATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGC
1 CCAAGATCTGATATTCCCTGAGTGACAGTGGAACAAGTCTTC
* * *
11306 ACGAGATCTGATATTTCCTGAGTGACAGTGGAAC-AGATCACTCTC
1 CCAAGATCTGATATTCCCTGAGTGACAGTGGAACAAG-T--CT-TC
* * * *
11351 TTTCAAGATTTGATATTCCCTGAGTGACAGAGGAACAAGTCTGC
1 --CCAAGATCTGATATTCCCTGAGTGACAGTGGAACAAGTCTTC
* *
11395 CCCAGATCTGATATTCTCTGAGTGACAGTGGAATAGATCCATATGT-TTC
1 CCAAGATCTGATATTCCCTGAGTGACAGTGG---A-A--CA-A-GTCTTC
* *
11444 CC-AGATCTGATATTCCCTGAGTGATAGAGGAACAAGTCT
1 CCAAGATCTGATATTCCCTGAGTGACAGTGGAACAAGTCT
11483 ACCCTGATTC
Statistics
Matches: 277, Mismatches: 51, Indels: 53
0.73 0.13 0.14
Matches are distributed among these distances:
40 2 0.01
41 4 0.01
42 120 0.43
43 3 0.01
44 6 0.02
45 13 0.05
46 32 0.12
47 61 0.22
48 29 0.10
49 5 0.02
50 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.29
Consensus pattern (42 bp):
CCAAGATCTGATATTCCCTGAGTGACAGTGGAACAAGTCTTC
Found at i:11197 original size:89 final size:89
Alignment explanation
Indices: 11092--11482 Score: 527
Period size: 89 Copynumber: 4.4 Consensus size: 89
11082 CTTTTCCAAG
* *
11092 ATTTGATATTCCCTGAGTGACAGCGGAACAAGTTTGCCCAAGATCTGATATTCCCTGAGTGACAG
1 ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCAGATCTGATATTCCCTGAGTGACAG
* *
11157 TAGAATAAATCACTCCCTTTCAAT
66 TGGAATAGATCACTCCCTTTCAAT
* *
11181 ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTTCCCCAGATCTGATATTCCTTGAGTGACAG
1 ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCAGATCTGATATTCCCTGAGTGACAG
*
11246 TGGAATAGATC-CT-CTTTCTCAAT
66 TGGAATAGATCACTCCCTT-TCAAT
* * *
11269 ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCACGAGATCTGATATTTCCTGAGTGACAG
1 ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCAGATCTGATATTCCCTGAGTGACAG
* * *
11334 TGGAACAGATCACTCTCTTTCAAG
66 TGGAATAGATCACTCCCTTTCAAT
* *
11358 ATTTGATATTCCCTGAGTGACAGAGGAACAAGTCTGCCCCAGATCTGATATTCTCTGAGTGACAG
1 ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCAGATCTGATATTCCCTGAGTGACAG
*** * *
11423 TGGAATAGATC-CATATGTTTCCCAG
66 TGGAATAGATCAC-TCCCTTT-CAAT
* * *
11448 ATCTGATATTCCCTGAGTGATAGAGGAACAAGTCT
1 ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCT
11483 ACCCTGATTC
Statistics
Matches: 270, Mismatches: 27, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
87 3 0.01
88 78 0.29
89 151 0.56
90 38 0.14
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29
Consensus pattern (89 bp):
ATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCAGATCTGATATTCCCTGAGTGACAG
TGGAATAGATCACTCCCTTTCAAT
Found at i:11388 original size:177 final size:178
Alignment explanation
Indices: 11084--11482 Score: 590
Period size: 177 Copynumber: 2.2 Consensus size: 178
11074 ATATCTCTCT
* *
11084 TTTC-CAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTTTGCCCAAGATCTGATATTCCCT
1 TTTCTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCACAAGATCTGATATTCCCT
* * *
11148 GAGTGACAGTAGAATAAATCACTCCCTTTCAATATTTGATATTCCCTGAGTGACAGCGGAACAAG
66 GAGTGACAGTAGAACAAATCACTCCCTTTCAAGATTTGATATTCCCTGAGTGACAGAGGAACAAG
* *
11213 TCTTCCCCAGATCTGATATTC-CTTGAGTGACAGTGGAATAGATCC-TC
131 TCTGCCCCAGATCTGATATTCTC-TGAGTGACAGTGGAATAGATCCATA
* * *
11260 TTTCTCAATATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCACGAGATCTGATATTTCCT
1 TTTCTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCACAAGATCTGATATTCCCT
* * *
11325 GAGTGACAGTGGAACAGATCACTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGAGGAACAAG
66 GAGTGACAGTAGAACAAATCACTCCCTTTCAAGATTTGATATTCCCTGAGTGACAGAGGAACAAG
11390 TCTGCCCCAGATCTGATATTCTCTGAGTGACAGTGGAATAGATCCATA
131 TCTGCCCCAGATCTGATATTCTCTGAGTGACAGTGGAATAGATCCATA
* * * *
11438 TGTT-TCCCAGATCTGATATTCCCTGAGTGATAGAGGAACAAGTCT
1 T-TTCT-CAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCT
11483 ACCCTGATTC
Statistics
Matches: 200, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
176 4 0.02
177 156 0.78
178 4 0.02
179 36 0.18
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.30
Consensus pattern (178 bp):
TTTCTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCACAAGATCTGATATTCCCT
GAGTGACAGTAGAACAAATCACTCCCTTTCAAGATTTGATATTCCCTGAGTGACAGAGGAACAAG
TCTGCCCCAGATCTGATATTCTCTGAGTGACAGTGGAATAGATCCATA
Found at i:11590 original size:111 final size:111
Alignment explanation
Indices: 11451--11700 Score: 376
Period size: 111 Copynumber: 2.3 Consensus size: 111
11441 TTCCCAGATC
* * *
11451 TGATATTCCCTGAGTGATAGA-GGAACAAGTCTACCCTGATTCAATTGATCAACACCCCCAGATC
1 TGATATTCCCTGAGTGACA-ACGGAACAAGTCTACCCCGATTCAATGGATCAACACCCCCAGATC
*
11515 TGATATCCCCTTAGAAGAAGCGGAACATATCACCCTCTTCCAATATT
65 TGATATCCCCTTAGAAGAAGCAGAACATATCACCCTCTTCCAATATT
* *
11562 TGATATTCCCTGAGTGACAACGTAACAAGTCTACCCCGATTCAATGGATCAACTCCCCCAGATCT
1 TGATATTCCCTGAGTGACAACGGAACAAGTCTACCCCGATTCAATGGATCAACACCCCCAGATCT
* * * * *
11627 TATATTCCCTTAGAAGAATCAGAACATATCACTCTCTTTCAATATT
66 GATATCCCCTTAGAAGAAGCAGAACATATCACCCTCTTCCAATATT
*
11673 TGATATTCCCTGAGTGACAGCGGAACAA
1 TGATATTCCCTGAGTGACAACGGAACAA
11701 TTTTTCCCCA
Statistics
Matches: 125, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
110 1 0.01
111 124 0.99
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (111 bp):
TGATATTCCCTGAGTGACAACGGAACAAGTCTACCCCGATTCAATGGATCAACACCCCCAGATCT
GATATCCCCTTAGAAGAAGCAGAACATATCACCCTCTTCCAATATT
Found at i:11895 original size:3 final size:3
Alignment explanation
Indices: 11887--11971 Score: 122
Period size: 3 Copynumber: 28.7 Consensus size: 3
11877 ATATTACCAC
11887 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
11935 TAT TAT T-T TAT TAT TAACT T-T T-T TGT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT T-A-T TAT TAT TAT TAT TAT TAT TA
11972 CAAGATCCAA
Statistics
Matches: 77, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
2 6 0.08
3 68 0.88
4 1 0.01
5 2 0.03
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:14807 original size:19 final size:19
Alignment explanation
Indices: 14783--14819 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
14773 GATCGCAATT
14783 TCTCAATGGTTAAAGTACA
1 TCTCAATGGTTAAAGTACA
14802 TCTCAATGGTTAAAGTAC
1 TCTCAATGGTTAAAGTAC
14820 TTATTGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (19 bp):
TCTCAATGGTTAAAGTACA
Found at i:19010 original size:17 final size:18
Alignment explanation
Indices: 18988--19029 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
18978 CTTTAGATTA
*
18988 TTTATTTAATTATTTTC-
1 TTTATTTAATTATTATCT
*
19005 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
19023 TTTATTT
1 TTTATTT
19030 TAAAAATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:22120 original size:64 final size:65
Alignment explanation
Indices: 22032--22187 Score: 208
Period size: 65 Copynumber: 2.4 Consensus size: 65
22022 ATAAGACTTA
* * * * *
22032 GTGCATTGGTACACTAATTACATTCGATGTTTC-AAAGAGCCAGGAGTGCATCGATGCATGG-TC
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCT-
22095 T
65 T
* **
22096 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCATGGCTT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCTT
*
22161 GTGCATCGATACACAAAATGCATTCGA
1 GTGCATCGGTACACAAAATGCATTCGA
22188 AATGAGTATG
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 29 0.36
65 51 0.63
66 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (65 bp):
GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCTT
Found at i:28378 original size:79 final size:79
Alignment explanation
Indices: 28247--28406 Score: 320
Period size: 79 Copynumber: 2.0 Consensus size: 79
28237 TGTTCATCAT
28247 AAAACCTTTTTAACATACATGAGATTAAAACAATAATGTATAATCATTTAAAACCAAAAACTCAT
1 AAAACCTTTTTAACATACATGAGATTAAAACAATAATGTATAATCATTTAAAACCAAAAACTCAT
28312 GCATGTATAGACTA
66 GCATGTATAGACTA
28326 AAAACCTTTTTAACATACATGAGATTAAAACAATAATGTATAATCATTTAAAACCAAAAACTCAT
1 AAAACCTTTTTAACATACATGAGATTAAAACAATAATGTATAATCATTTAAAACCAAAAACTCAT
28391 GCATGTATAGACTA
66 GCATGTATAGACTA
28405 AA
1 AA
28407 TGAGCAACCA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.29
Consensus pattern (79 bp):
AAAACCTTTTTAACATACATGAGATTAAAACAATAATGTATAATCATTTAAAACCAAAAACTCAT
GCATGTATAGACTA
Found at i:28990 original size:117 final size:117
Alignment explanation
Indices: 28770--28991 Score: 277
Period size: 117 Copynumber: 1.9 Consensus size: 117
28760 CTTTCAAGTC
* * *
28770 GAAATTTTATTTTTCAATACTTTTAAATTTCATTTTTGAAAACTCTAAATCCTTCTTCAATATTT
1 GAAAATTTATTTTTCAATACTTTTAAATTTCATTTTTGAAAACTCTAAATCCTTCTTCAACATCT
* * *
28835 CTTTTTTATTTTCAAAATCCATTTTAGTTTCTAGAAGAAGTTTGTTTAATTT
66 CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
* * ** * *
28887 GAAAATTTATTTTTCAA-AGTTTTCAGATTTCATTTTTGAAAGTTCTAACTCCTTTTTCAACATC
1 GAAAATTTATTTTTCAATACTTTT-AAATTTCATTTTTGAAAACTCTAAATCCTTCTTCAACATC
* * *
28951 TCATTTTGATTTTCCAAGTCTATTTTAGCTTTC-AAAAGAAG
65 TCATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAAG
28992 ATAATTTTTA
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
116 5 0.06
117 79 0.90
118 4 0.05
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.49
Consensus pattern (117 bp):
GAAAATTTATTTTTCAATACTTTTAAATTTCATTTTTGAAAACTCTAAATCCTTCTTCAACATCT
CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
Found at i:29487 original size:64 final size:66
Alignment explanation
Indices: 29417--29569 Score: 181
Period size: 65 Copynumber: 2.4 Consensus size: 66
29407 ACTAGGGGTC
* *
29417 CATCGGTACACT-AATTACATTCGATGTTTC-AAAGAGCCAAGAGTGCATCGATGCATGG-TCTG
1 CATCGGTACACTAAAATACATTCGATGTTTCAAAAGAGCCAAGAGTACATCGATGCATGGCT-TG
29479 TG
65 TG
* * ** *
29481 CATCGGTACA-TAAAATGCATTCGATGTTTCAAAATATTCAAGAGTACATTGATGCATGGCTTGT
1 CATCGGTACACTAAAATACATTCGATGTTTCAAAAGAGCCAAGAGTACATCGATGCATGGCTTGT
29545 G
66 G
* *
29546 CATCAGTACAC-AAAATGCATTCGA
1 CATCGGTACACTAAAATACATTCGA
29570 AATGGGCGTG
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
63 1 0.01
64 26 0.34
65 49 0.64
66 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (66 bp):
CATCGGTACACTAAAATACATTCGATGTTTCAAAAGAGCCAAGAGTACATCGATGCATGGCTTGT
G
Found at i:29555 original size:65 final size:64
Alignment explanation
Indices: 29434--29569 Score: 184
Period size: 65 Copynumber: 2.1 Consensus size: 64
29424 ACACTAATTA
* * *
29434 CATTCGATGTTTCAAAGAGCCAAGAGTGCATCGATGCATGGTCTGTGCATCGGTACATAAAATG
1 CATTCGATGTTTCAAAGAGCCAAGAGTACATCGATGCATGGTCTGTGCATCAGTACACAAAATG
* ** *
29498 CATTCGATGTTTCAAAATATTCAAGAGTACATTGATGCATGG-CTTGTGCATCAGTACACAAAAT
1 CATTCGATGTTTC-AAAGAGCCAAGAGTACATCGATGCATGGTC-TGTGCATCAGTACACAAAAT
29562 G
64 G
29563 CATTCGA
1 CATTCGA
29570 AATGGGCGTG
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
64 14 0.22
65 49 0.78
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (64 bp):
CATTCGATGTTTCAAAGAGCCAAGAGTACATCGATGCATGGTCTGTGCATCAGTACACAAAATG
Found at i:33543 original size:42 final size:42
Alignment explanation
Indices: 33495--33716 Score: 128
Period size: 42 Copynumber: 5.2 Consensus size: 42
33485 CAGACCTGAT
*
33495 AAGGGGAACCACATGAGGAATATACCACTTGGCTTTCCTGTG
1 AAGGGGAACCACATGAGGAATATACCACTTGGCTTTCCCGTG
** * * ** * * * *
33537 AAGGGGAGTCATC-CGAAGACCATATCACTT-GATTCAGACCCGCG
1 AAGGGGAACCA-CATGAGGAATATACCACTTGGCTT---TCCCGTG
* *
33581 AAGGGGAACCACTTGAGGAATATACCACTTTGCTTTCCCGTG
1 AAGGGGAACCACATGAGGAATATACCACTTGGCTTTCCCGTG
** * * ** * *
33623 AAGGGGAGTCATATAAAAAATAT-CTCACTTGG-TTCAACCCCGCG
1 AAGGGGAACCACATGAGGAATATAC-CACTTGGCTT---TCCCGTG
* * *
33667 AAGGGGAACCACCTGAGGAATATACCACTTAGCTTTCCCATG
1 AAGGGGAACCACATGAGGAATATACCACTTGGCTTTCCCGTG
33709 AAGGGGAA
1 AAGGGGAA
33717 TCATTTAAAG
Statistics
Matches: 126, Mismatches: 42, Indels: 24
0.66 0.22 0.12
Matches are distributed among these distances:
41 6 0.05
42 60 0.48
43 2 0.02
44 52 0.41
45 6 0.05
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.22
Consensus pattern (42 bp):
AAGGGGAACCACATGAGGAATATACCACTTGGCTTTCCCGTG
Found at i:33573 original size:86 final size:86
Alignment explanation
Indices: 33423--33720 Score: 368
Period size: 86 Copynumber: 3.5 Consensus size: 86
33413 TTCTCACAAA
* *
33423 GAGGAATATACCAATTGGCTTTCCCGTG-AGGAGGAGTCATCCAAAGATCC-TTTCACTTGGTTC
1 GAGGAATATACCACTTGGCTTTCCCGTGAAGG-GGAGTCATCCAAAGA-CCATATCACTTGGTTC
* **
33486 AGACCTGATAAGGGGAACCACAT
64 AGACCCGCGAAGGGGAACCACAT
* * *
33509 GAGGAATATACCACTTGGCTTTCCTGTGAAGGGGAGTCATCCGAAGACCATATCACTTGATTCAG
1 GAGGAATATACCACTTGGCTTTCCCGTGAAGGGGAGTCATCCAAAGACCATATCACTTGGTTCAG
*
33574 ACCCGCGAAGGGGAACCACTT
66 ACCCGCGAAGGGGAACCACAT
* ** * ** *
33595 GAGGAATATACCACTTTGCTTTCCCGTGAAGGGGAGTCATATAAAAAATATCTCACTTGGTTCA-
1 GAGGAATATACCACTTGGCTTTCCCGTGAAGGGGAGTCATCCAAAGACCATATCACTTGGTTCAG
*
33659 ACCCCGCGAAGGGGAACCACCT
66 A-CCCGCGAAGGGGAACCACAT
* * *
33681 GAGGAATATACCACTTAGCTTTCCCATGAAGGGGAATCAT
1 GAGGAATATACCACTTGGCTTTCCCGTGAAGGGGAGTCAT
33721 TTAAAGAATT
Statistics
Matches: 186, Mismatches: 23, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
85 3 0.02
86 180 0.97
87 3 0.02
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.23
Consensus pattern (86 bp):
GAGGAATATACCACTTGGCTTTCCCGTGAAGGGGAGTCATCCAAAGACCATATCACTTGGTTCAG
ACCCGCGAAGGGGAACCACAT
Found at i:33610 original size:44 final size:43
Alignment explanation
Indices: 33562--33696 Score: 107
Period size: 44 Copynumber: 3.1 Consensus size: 43
33552 AAGACCATAT
33562 CACTTGATTCAGACCCGCGAAGGGGAACCACTTGAGGAATATAC
1 CACTTGATTCA-ACCCGCGAAGGGGAACCACTTGAGGAATATAC
* * * ** * **
33606 CACTTTGCTT--TCCCGTGAAGGGGAGTCA-TATAAAAAATAT-C
1 CAC-TTGATTCAACCCGCGAAGGGGAACCACT-TGAGGAATATAC
* *
33647 TCACTTGGTTCAACCCCGCGAAGGGGAACCACCTGAGGAATATAC
1 -CACTTGATTCAA-CCCGCGAAGGGGAACCACTTGAGGAATATAC
33692 CACTT
1 CACTT
33697 AGCTTTCCCA
Statistics
Matches: 66, Mismatches: 17, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
41 7 0.11
42 24 0.36
44 29 0.44
45 6 0.09
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.22
Consensus pattern (43 bp):
CACTTGATTCAACCCGCGAAGGGGAACCACTTGAGGAATATAC
Found at i:34521 original size:18 final size:18
Alignment explanation
Indices: 34498--34541 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
34488 TCTTTAGATT
*
34498 TTTTATTTAATTATTTTC
1 TTTTATTTAATTATTATC
*
34516 TTTTATTTAATTCTTATC
1 TTTTATTTAATTATTATC
34534 TTTTATTT
1 TTTTATTT
34542 TAAAAATAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTATTTAATTATTATC
Found at i:34655 original size:6 final size:6
Alignment explanation
Indices: 34646--34688 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
34636 TTTTCACACT
34646 TTTTTA -TTTTA -TTTTA -TTTTA TTTTTA TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
34689 CTCTTTTAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 15 0.42
6 21 0.58
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:34657 original size:5 final size:5
Alignment explanation
Indices: 34610--34688 Score: 61
Period size: 5 Copynumber: 14.8 Consensus size: 5
34600 ATATTTCCCT
* * **
34610 TTTTA TTATA TTTTG TTTTA TCTTTA TTTTCA CACTT- TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA T-TTTA TTTT-A -TTTTA TTTTA TTTTA
34657 TTTTA TTTTA TTTTTA TTTTTA TTTTTA TTTT
1 TTTTA TTTTA -TTTTA -TTTTA -TTTTA TTTT
34689 CTCTTTTAAC
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
4 2 0.03
5 34 0.56
6 23 0.38
7 2 0.03
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:34696 original size:18 final size:17
Alignment explanation
Indices: 34625--34688 Score: 53
Period size: 18 Copynumber: 3.8 Consensus size: 17
34615 TTATATTTTG
*
34625 TTTTATCTTTATTTTCAC
1 TTTTAT-TTTATTTTTAC
**
34643 ACTT-TTTTA-TTTTA-
1 TTTTATTTTATTTTTAC
*
34657 TTTTATTTTATTTTTAT
1 TTTTATTTTATTTTTAC
34674 TTTTATTTTTATTTT
1 TTTTA-TTTTATTTT
34689 CTCTTTTAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
14 2 0.05
15 9 0.24
16 9 0.24
17 6 0.16
18 11 0.30
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTATTTTATTTTTAC
Found at i:35829 original size:41 final size:40
Alignment explanation
Indices: 35770--35856 Score: 95
Period size: 41 Copynumber: 2.2 Consensus size: 40
35760 GGAAAAATTG
* *
35770 ATTTTTTGAAAATTTAGAAGAGAAAAGAGAGAAAATTTGAT
1 ATTTTTTGAAAATGTAGAAAAGAAAAGAG-GAAAATTTGAT
** ** *
35811 ATTTTTTGGGAATGTAGAAAAGGGAAGAGGAAAATTTTAT
1 ATTTTTTGAAAATGTAGAAAAGAAAAGAGGAAAATTTGAT
35851 -TTTTTT
1 ATTTTTT
35857 ACAAAGGTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
39 6 0.15
40 10 0.26
41 23 0.59
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (40 bp):
ATTTTTTGAAAATGTAGAAAAGAAAAGAGGAAAATTTGAT
Found at i:37040 original size:20 final size:21
Alignment explanation
Indices: 36979--37029 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
36969 TTTGAATGAG
* *
36979 GGTACCAAAACTGATAGTTTA
1 GGTACTAAAACTGATAATTTA
37000 GGTACTAAAACTGATAATTTA
1 GGTACTAAAACTGATAATTTA
*
37021 TGTACTAAA
1 GGTACTAAA
37030 CATGTAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (21 bp):
GGTACTAAAACTGATAATTTA
Found at i:40381 original size:12 final size:12
Alignment explanation
Indices: 40364--40388 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40354 AATATAACAA
40364 AAATTAATTTTT
1 AAATTAATTTTT
40376 AAATTAATTTTT
1 AAATTAATTTTT
40388 A
1 A
40389 TTTAGGTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AAATTAATTTTT
Done.