Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003390.1 Hibiscus syriacus cultivar Beakdansim tig00007135_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: 66302
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4321 original size:2 final size:2
Alignment explanation
Indices: 4314--4343 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4304 ATGTCATGGA
4314 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
4344 TATTTACAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20896 original size:20 final size:20
Alignment explanation
Indices: 20871--20909 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
20861 TAAATTAAAT
* *
20871 ATTAGATAGGATCCGTTTTA
1 ATTAGATAGAATCAGTTTTA
20891 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
20910 TATTCTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:20942 original size:32 final size:32
Alignment explanation
Indices: 20891--20995 Score: 95
Period size: 32 Copynumber: 3.6 Consensus size: 32
20881 ATCCGTTTTA
* *
20891 ATTAGATAGAATCAGTTTTTATTCTATTAGTT
1 ATTAGATAGGATCATTTTTTATTCTATTAGTT
20923 ATTAGATAGGATCATTTTTTA----ATTAG--
1 ATTAGATAGGATCATTTTTTATTCTATTAGTT
** *
20949 A-TAGA-ATCA--GTTTTTTATTCTATTAGTT
1 ATTAGATAGGATCATTTTTTATTCTATTAGTT
20977 ATTAGATAGGATCATTTTT
1 ATTAGATAGGATCATTTTT
20996 AATTAGATAG
Statistics
Matches: 55, Mismatches: 8, Indels: 20
0.66 0.10 0.24
Matches are distributed among these distances:
22 7 0.13
24 2 0.04
25 4 0.07
26 6 0.11
28 6 0.11
29 4 0.07
30 2 0.04
32 24 0.44
ACGTcount: A:0.31, C:0.06, G:0.13, T:0.50
Consensus pattern (32 bp):
ATTAGATAGGATCATTTTTTATTCTATTAGTT
Found at i:20949 original size:21 final size:22
Alignment explanation
Indices: 20923--20965 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
20913 TCTATTAGTT
*
20923 ATTAGATAGGATCA-TTTTTTA
1 ATTAGATAGAATCAGTTTTTTA
20944 ATTAGATAGAATCAGTTTTTTA
1 ATTAGATAGAATCAGTTTTTTA
20966 TTCTATTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.47
Consensus pattern (22 bp):
ATTAGATAGAATCAGTTTTTTA
Found at i:20952 original size:53 final size:52
Alignment explanation
Indices: 20870--21018 Score: 255
Period size: 53 Copynumber: 2.8 Consensus size: 52
20860 CTAAATTAAA
**
20870 TATTAGATAGGATCCGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
20922 TATTAGATAGGATCATTTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCA-TTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
20976 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTATT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATT
21019 ATGTTGCTAA
Statistics
Matches: 93, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
51 8 0.09
52 14 0.15
53 40 0.43
54 31 0.33
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.48
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:21019 original size:19 final size:19
Alignment explanation
Indices: 20975--21019 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
20965 ATTCTATTAG
*
20975 TTATTAGATAGGATCATTT
1 TTATTAGATAGAATCATTT
20994 TTAATTAGATAGAATCATTT
1 TT-ATTAGATAGAATCATTT
21014 TTATTA
1 TTATTA
21020 TGTTGCTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (19 bp):
TTATTAGATAGAATCATTT
Found at i:25609 original size:20 final size:20
Alignment explanation
Indices: 25584--25622 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
25574 TAAATTAAAT
*
25584 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
25604 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
25623 TATTCTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:25669 original size:20 final size:21
Alignment explanation
Indices: 25636--25675 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
25626 TCTATTAGTT
25636 ATTAGATATGATCA-TTTTTA
1 ATTAGATATGATCAGTTTTTA
25656 ATTAGATA-GAATCAGTTTTT
1 ATTAGATATG-ATCAGTTTTT
25676 TATTCTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.06
20 12 0.67
21 5 0.28
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.47
Consensus pattern (21 bp):
ATTAGATATGATCAGTTTTTA
Found at i:25702 original size:53 final size:53
Alignment explanation
Indices: 25583--25731 Score: 266
Period size: 53 Copynumber: 2.8 Consensus size: 53
25573 CTAAATTAAA
*
25583 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
*
25635 TATTAGATATGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
25688 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTTATT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATT
25732 ATGTTGCTAA
Statistics
Matches: 93, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
52 43 0.46
53 50 0.54
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (53 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
Found at i:25729 original size:21 final size:20
Alignment explanation
Indices: 25689--25732 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
25679 TCTATTAGTT
*
25689 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
*
25709 ATTAGATAGAATCATTTTTT
1 ATTAGATAGAATCATTTTTA
25729 ATTA
1 ATTA
25733 TGTTGCTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:28491 original size:29 final size:29
Alignment explanation
Indices: 28458--28517 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
28448 CATATATCTC
28458 TCTTTTTGTTCATATGTGATATACATATA
1 TCTTTTTGTTCATATGTGATATACATATA
28487 TCTTTTTGTTCATATGTGATATACATATA
1 TCTTTTTGTTCATATGTGATATACATATA
28516 TC
1 TC
28518 ATACAGAGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.52
Consensus pattern (29 bp):
TCTTTTTGTTCATATGTGATATACATATA
Found at i:30002 original size:21 final size:21
Alignment explanation
Indices: 29959--30002 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
29949 ATTTTATTAT
* *
29959 AATTTATTAAAATTATGATCA
1 AATTTATTAAAATTAGGACCA
29980 AATTTATTAAAATTAGGACCA
1 AATTTATTAAAATTAGGACCA
30001 AA
1 AA
30003 ATTCAGAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (21 bp):
AATTTATTAAAATTAGGACCA
Found at i:30600 original size:44 final size:41
Alignment explanation
Indices: 30523--30604 Score: 110
Period size: 44 Copynumber: 1.9 Consensus size: 41
30513 GCAACGCGAT
* * *
30523 TTTGAAAAATGTGTTGCGGTAGTTAAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGAGAG
30564 TTTGAAAAATGTGTTGTTGCGATAGTGAAAAAGTGTTGCGA
1 TTTGAAAAA--TG-TGTTGCGATAGTGAAAAAGTGTTGCGA
30605 TAGTGAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
41 9 0.26
43 2 0.06
44 24 0.69
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.34
Consensus pattern (41 bp):
TTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGAGAG
Found at i:30602 original size:19 final size:20
Alignment explanation
Indices: 30525--30615 Score: 96
Period size: 19 Copynumber: 4.4 Consensus size: 20
30515 AACGCGATTT
*
30525 TGAAAAATGTGTTGCGGTAG
1 TGAAAAATGTGTTGCGATAG
* *
30545 T-TAAAATGTGTTGCGAGAG
1 TGAAAAATGTGTTGCGATAG
30564 TTTGAAAAATGTGTTGTTGCGATAG
1 --TGAAAAA--TG-TGTTGCGATAG
30589 TGAAAAA-GTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
30608 TGAAAAAT
1 TGAAAAAT
30616 CCAAAATAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
19 33 0.56
20 2 0.03
21 1 0.02
22 4 0.07
23 7 0.12
24 2 0.03
25 10 0.17
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (20 bp):
TGAAAAATGTGTTGCGATAG
Found at i:31033 original size:23 final size:23
Alignment explanation
Indices: 30990--31040 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
30980 AAATCATATT
*
30990 AGATTATTATTGATAATAAAAGA
1 AGATTATTATTGATAAGAAAAGA
* *
31013 AGATTATT-TTTATTAAGAAAAGC
1 AGATTATTATTGA-TAAGAAAAGA
31036 AGATT
1 AGATT
31041 CCATATCACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.47, C:0.02, G:0.14, T:0.37
Consensus pattern (23 bp):
AGATTATTATTGATAAGAAAAGA
Found at i:36217 original size:55 final size:54
Alignment explanation
Indices: 36126--36287 Score: 207
Period size: 55 Copynumber: 3.0 Consensus size: 54
36116 TATTTATCGG
* * ** *
36126 ATGCTTTGCTACTTGTGTTTGATACGAATGTTCGACACCACCTCAAGTTCGAGGA
1 ATGCTTTGTTACTCGTGTTTGATACGTGTGTCCGACACCACC-CAAGTTCGAGGA
* * * *
36181 CTGCTTTGTTACTCGTGTTTGATATGTGTGTCCGACACCACGCCGAGTTTGAGGA
1 ATGCTTTGTTACTCGTGTTTGATACGTGTGTCCGACACCAC-CCAAGTTCGAGGA
* *
36236 ATGCTTTGTTACTCGTGTTTGATACGTGTGTCCGACACCACCCGAGCTCGAG
1 ATGCTTTGTTACTCGTGTTTGATACGTGTGTCCGACACCACCCAAGTTCGAG
36288 TACCGTGAGT
Statistics
Matches: 93, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
54 9 0.10
55 83 0.89
56 1 0.01
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.33
Consensus pattern (54 bp):
ATGCTTTGTTACTCGTGTTTGATACGTGTGTCCGACACCACCCAAGTTCGAGGA
Found at i:39151 original size:24 final size:24
Alignment explanation
Indices: 39119--39191 Score: 137
Period size: 24 Copynumber: 3.0 Consensus size: 24
39109 CTCTGAGATA
*
39119 CGACCCCTAAACCGCATCATGATG
1 CGACCCCTAAGCCGCATCATGATG
39143 CGACCCCTAAGCCGCATCATGATG
1 CGACCCCTAAGCCGCATCATGATG
39167 CGACCCCTAAGCCGCATCATGATG
1 CGACCCCTAAGCCGCATCATGATG
39191 C
1 C
39192 CTACCTTAGC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.26, C:0.38, G:0.19, T:0.16
Consensus pattern (24 bp):
CGACCCCTAAGCCGCATCATGATG
Found at i:39266 original size:32 final size:32
Alignment explanation
Indices: 39230--39341 Score: 107
Period size: 32 Copynumber: 3.5 Consensus size: 32
39220 TGAGTTAGTT
*
39230 TTGCATTCAGATAATGCACAATAAAATCAATA
1 TTGCATTCAGATAATGCACAATAGAATCAATA
* * * * *
39262 TTGCATTCAGATAATCCACAACAGAGTTAGTA
1 TTGCATTCAGATAATGCACAATAGAATCAATA
** * *
39294 TAACATTCAGATAATGCACAGTAGAACCAATA
1 TTGCATTCAGATAATGCACAATAGAATCAATA
* * *
39326 TCGCATTTAAATAATG
1 TTGCATTCAGATAATG
39342 TGTAGCATAT
Statistics
Matches: 61, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (32 bp):
TTGCATTCAGATAATGCACAATAGAATCAATA
Found at i:39340 original size:64 final size:64
Alignment explanation
Indices: 39214--39340 Score: 164
Period size: 64 Copynumber: 2.0 Consensus size: 64
39204 GTGTATGAGT
* * ** * * *
39214 CACAACTGAGTTAGTTTTGCATTCAGATAATGCACAATAAAATCAATATTGCATTCAGATAATC
1 CACAACAGAGTTAGTATAACATTCAGATAATGCACAATAAAACCAATATCGCATTCAAATAATC
* * *
39278 CACAACAGAGTTAGTATAACATTCAGATAATGCACAGTAGAACCAATATCGCATTTAAATAAT
1 CACAACAGAGTTAGTATAACATTCAGATAATGCACAATAAAACCAATATCGCATTCAAATAAT
39341 GTGTAGCATA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (64 bp):
CACAACAGAGTTAGTATAACATTCAGATAATGCACAATAAAACCAATATCGCATTCAAATAATC
Found at i:41124 original size:71 final size:71
Alignment explanation
Indices: 41035--41177 Score: 214
Period size: 71 Copynumber: 2.0 Consensus size: 71
41025 AGTATACTCA
* * *
41035 AAGATTTCCCGAGTTCTGTTACATATCTAGAGGATCATATATGAATATGTGTTAGACACAAATGC
1 AAGATTTCCCGAGATCTGTTACATATCTAGAGGATCATATACGAATAGGTGTTAGACACAAATGC
41100 CGGTAC
66 CGGTAC
* * * *
41106 AAGATTTCCCGAGATCTGTTACATATTTTGAGGATTATATACGAATAGGTGTTAGACATAAATGC
1 AAGATTTCCCGAGATCTGTTACATATCTAGAGGATCATATACGAATAGGTGTTAGACACAAATGC
*
41171 GGGTAC
66 CGGTAC
41177 A
1 A
41178 TTAGAAGAAG
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
71 64 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (71 bp):
AAGATTTCCCGAGATCTGTTACATATCTAGAGGATCATATACGAATAGGTGTTAGACACAAATGC
CGGTAC
Found at i:41734 original size:3 final size:3
Alignment explanation
Indices: 41726--41776 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
41716 TAAGAACAAA
* *
41726 AAG AAG AAG AAA AAG AAG AA- AGAG AAG AAG AAG AAG AAC AA- AATG
1 AAG AAG AAG AAG AAG AAG AAG A-AG AAG AAG AAG AAG AAG AAG AA-G
41771 AAG AAG
1 AAG AAG
41777 GTTGCCTTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
2 3 0.07
3 35 0.85
4 3 0.07
ACGTcount: A:0.69, C:0.02, G:0.27, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:41738 original size:12 final size:12
Alignment explanation
Indices: 41717--41763 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
41707 GAAACAGGAT
*
41717 AAGAACAAAAAG
1 AAGAAGAAAAAG
41729 AAGAAGAAAAAG
1 AAGAAGAAAAAG
41741 AAGAAAGAGAAGAAG
1 AAG-AAGA-AA-AAG
41756 AAGAAGAA
1 AAGAAGAA
41764 CAAAATGAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
12 14 0.45
13 5 0.16
14 6 0.19
15 6 0.19
ACGTcount: A:0.72, C:0.02, G:0.26, T:0.00
Consensus pattern (12 bp):
AAGAAGAAAAAG
Found at i:41742 original size:21 final size:21
Alignment explanation
Indices: 41717--41776 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
41707 GAAACAGGAT
41717 AAGAACAAAAAGAAGAAGAAA
1 AAGAACAAAAAGAAGAAGAAA
* * *
41738 AAGAAGAAAGAGAAGAAGAAG
1 AAGAACAAAAAGAAGAAGAAA
*
41759 AAGAACAAAATGAAGAAG
1 AAGAACAAAAAGAAGAAG
41777 GTTGCCTTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.70, C:0.03, G:0.25, T:0.02
Consensus pattern (21 bp):
AAGAACAAAAAGAAGAAGAAA
Found at i:58322 original size:19 final size:19
Alignment explanation
Indices: 58265--58324 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
58255 TGTTATTTTC
* *
58265 TTTTAATTAAATCTATTTTT
1 TTTTAA-TAAATATATTATT
*
58285 TTGTTAA-AAA-AGTAATATT
1 TT-TTAATAAATA-TATTATT
58304 TTTTAATAAATATATTATT
1 TTTTAATAAATATATTATT
58323 TT
1 TT
58325 GGGTCGGGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
18 4 0.12
19 21 0.66
20 3 0.09
21 4 0.12
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (19 bp):
TTTTAATAAATATATTATT
Found at i:59335 original size:18 final size:18
Alignment explanation
Indices: 59284--59335 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
59274 TTTCTTATAT
59284 TTTATCAAAACGATAAAA
1 TTTATCAAAACGATAAAA
* *
59302 TATT-TCCAAAA-AATAACA
1 T-TTAT-CAAAACGATAAAA
59320 TTTATCAAAACGATAA
1 TTTATCAAAACGATAA
59336 TGGTTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
17 7 0.26
18 13 0.48
19 7 0.26
ACGTcount: A:0.54, C:0.13, G:0.04, T:0.29
Consensus pattern (18 bp):
TTTATCAAAACGATAAAA
Found at i:60689 original size:25 final size:21
Alignment explanation
Indices: 60631--60689 Score: 50
Period size: 22 Copynumber: 2.6 Consensus size: 21
60621 CGGAAGAATG
60631 TAAAAAAAT-AAAAATACAAA
1 TAAAAAAATAAAAAATACAAA
60651 TAAAGAGAAA-AAAAAATAACATAGA
1 TAAA-A-AAATAAAAAAT-ACA-A-A
60676 TAAAATAAATAAAA
1 TAAAA-AAATAAAA
60690 CAAAGGAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
20 4 0.13
21 1 0.03
22 9 0.29
23 3 0.10
24 5 0.16
25 9 0.29
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.15
Consensus pattern (21 bp):
TAAAAAAATAAAAAATACAAA
Found at i:61021 original size:15 final size:15
Alignment explanation
Indices: 60982--61013 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
60972 ATATATATAT
*
60982 ATATATAATAAAATA
1 ATATAAAATAAAATA
60997 ATATAAAATAAAATA
1 ATATAAAATAAAATA
61012 AT
1 AT
61014 GAAAAATAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATATAAAATAAAATA
Found at i:63690 original size:31 final size:31
Alignment explanation
Indices: 63629--63690 Score: 72
Period size: 32 Copynumber: 2.0 Consensus size: 31
63619 TCACATTTAT
*
63629 ATAAAAGGAATAATCTTCTATCCAAAATTAAA
1 ATAAAAGGAATAATCTTCAAT-CAAAATTAAA
* *
63661 ATAAAGGGATTAATCTTCAAT-AAATATTAA
1 ATAAAAGGAATAATCTTCAATCAAA-ATTAA
63691 TTTAGAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 3 0.12
31 5 0.19
32 18 0.69
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.31
Consensus pattern (31 bp):
ATAAAAGGAATAATCTTCAATCAAAATTAAA
Found at i:65331 original size:2 final size:2
Alignment explanation
Indices: 65324--65383 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
65314 AAACTGAAGC
*
65324 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG A- AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
65365 AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
65384 ACCAGACCAA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.