Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001212.1 Hibiscus syriacus cultivar Beakdansim tig00002394_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: 57107
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:7485 original size:6 final size:6
Alignment explanation
Indices: 7469--7508 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
7459 TTAAAAAGTA
7469 ATTTAAT ATTTAT ATTTAT ATTTAT ATTT-T ATTTAT ATTT
1 ATTT-AT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTT
7509 TTTAAAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 5 0.16
6 23 0.72
7 4 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
ATTTAT
Found at i:17439 original size:18 final size:18
Alignment explanation
Indices: 17416--17456 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
17406 GTAACTTATG
17416 TTGTGTTGTGTCTTTGAA
1 TTGTGTTGTGTCTTTGAA
17434 TTGTGTTGTGTCTTTGAA
1 TTGTGTTGTGTCTTTGAA
17452 TTGTG
1 TTGTG
17457 CCTCAAGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.10, C:0.05, G:0.29, T:0.56
Consensus pattern (18 bp):
TTGTGTTGTGTCTTTGAA
Found at i:20976 original size:14 final size:15
Alignment explanation
Indices: 20943--21005 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 15
20933 AAAGACTAAA
20943 AATTAATAATAATAT
1 AATTAATAATAATAT
20958 AATTAA-AATAAT-T
1 AATTAATAATAATAT
*
20971 ACATTAATTAA-AAAAT
1 A-ATTAA-TAATAATAT
20987 AGA-TAATAATAATAAT
1 A-ATTAATAATAAT-AT
21003 AAT
1 AAT
21006 ACTAACAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 13
0.70 0.06 0.24
Matches are distributed among these distances:
13 2 0.05
14 14 0.37
15 14 0.37
16 8 0.21
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (15 bp):
AATTAATAATAATAT
Found at i:22299 original size:44 final size:44
Alignment explanation
Indices: 22249--22344 Score: 149
Period size: 44 Copynumber: 2.2 Consensus size: 44
22239 TCATGTTCGA
* *
22249 TATTGATACTACTATACATAGTGGTATCGATACTCAC-TGGACAG
1 TATTGATACTACTATACAAAGTAGTATCGATACTC-CTTGGACAG
22293 TATTGATACTACTATACAAAGTAGTATCGATACTCCTTGGACAG
1 TATTGATACTACTATACAAAGTAGTATCGATACTCCTTGGACAG
*
22337 TATCGATA
1 TATTGATA
22345 TCGTTGAGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
43 1 0.02
44 47 0.98
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (44 bp):
TATTGATACTACTATACAAAGTAGTATCGATACTCCTTGGACAG
Found at i:24970 original size:21 final size:22
Alignment explanation
Indices: 24953--24995 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
24943 CTAAAATTAT
24953 AATATCAAATAAAAAAATAAATG
1 AATAT-AAATAAAAAAATAAATG
*
24976 CATATAAATAAAAAAATAAA
1 AATATAAATAAAAAAATAAA
24996 GGATAAATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.21
Consensus pattern (22 bp):
AATATAAATAAAAAAATAAATG
Found at i:25599 original size:112 final size:113
Alignment explanation
Indices: 25466--25698 Score: 308
Period size: 113 Copynumber: 2.1 Consensus size: 113
25456 TAAAGGTAGT
** * * * *
25466 TATTTTTTATTTTTGCCAGAATGATTATTTTATCATAAATTAAATTGGTA-ATTTTAATTAAAGT
1 TATTTTTTATTTCCGACAGAATGATTATTCTATCACAAATTAAATCGGTATATTTTAATTAAAGT
****** *
25530 TGATTTTTTTTTTCGACAGAATCATTGT-CCAGTCATAAATTAAATTGA
66 TGAACAAAATTTCCGACAGAATCATTGTCCCA-TCATAAATTAAATTGA
25578 TATTTTTTATTTCCGACAGAATGATTATTCTATCACAAATTAAATCGGTATATTTTAATTAAAGT
1 TATTTTTTATTTCCGACAGAATGATTATTCTATCACAAATTAAATCGGTATATTTTAATTAAAGT
* *
25643 TGAACAAAATTTCCGACGGAATCATTGTCCCATTATAAATTAAATTGA
66 TGAACAAAATTTCCGACAGAATCATTGTCCCATCATAAATTAAATTGA
25691 TATTTTTT
1 TATTTTTT
25699 TATTGAAATG
Statistics
Matches: 104, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
112 44 0.42
113 57 0.55
114 3 0.03
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.45
Consensus pattern (113 bp):
TATTTTTTATTTCCGACAGAATGATTATTCTATCACAAATTAAATCGGTATATTTTAATTAAAGT
TGAACAAAATTTCCGACAGAATCATTGTCCCATCATAAATTAAATTGA
Found at i:25618 original size:48 final size:45
Alignment explanation
Indices: 25521--25622 Score: 116
Period size: 48 Copynumber: 2.2 Consensus size: 45
25511 TGGTAATTTT
*
25521 AATTAAAGTTGATTTTTTTTTTCGACAGAATCATTGTCCAGTCATA
1 AATTAAA-TTGATTTTTTTTTTCGACAGAATCATTGTCCAGTCACA
* * *
25567 AATTAAATTGATATTTTTTATTTCCGACAGAATGATTATTCTA-TCACA
1 AATTAAATTGAT-TTTTTT-TTT-CGACAGAATCATT-GTCCAGTCACA
25615 AATTAAAT
1 AATTAAAT
25623 CGGTATATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
45 5 0.10
46 13 0.27
47 3 0.06
48 24 0.50
49 3 0.06
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (45 bp):
AATTAAATTGATTTTTTTTTTCGACAGAATCATTGTCCAGTCACA
Found at i:26187 original size:35 final size:35
Alignment explanation
Indices: 26141--26242 Score: 186
Period size: 35 Copynumber: 2.9 Consensus size: 35
26131 TAAAATCTAA
26141 GTCCATTCACCAAGTGACATAACTTATTATAATAG
1 GTCCATTCACCAAGTGACATAACTTATTATAATAG
26176 GTCCATTCACCAAGTGACATAACTTATTATAATAG
1 GTCCATTCACCAAGTGACATAACTTATTATAATAG
* *
26211 GTCCATTCACCAAGTGACATGATTTATTATAA
1 GTCCATTCACCAAGTGACATAACTTATTATAA
26243 GTAGCACAAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (35 bp):
GTCCATTCACCAAGTGACATAACTTATTATAATAG
Found at i:28832 original size:25 final size:26
Alignment explanation
Indices: 28777--28832 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
28767 CGAAAATATT
*
28777 ATATATATAATAAAAAATATAAAATA
1 ATATATATAATAAAAAATATAAAAAA
* **
28803 TTATATAT-ATAATTAATATAAAAAA
1 ATATATATAATAAAAAATATAAAAAA
28828 ATATA
1 ATATA
28833 AAATATATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
ATATATATAATAAAAAATATAAAAAA
Found at i:29447 original size:21 final size:21
Alignment explanation
Indices: 29423--29468 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
29413 TACAAGTTAT
* *
29423 AAATAGGTCACT-TATTATTA
1 AAATAAGTCACTCTATCATTA
29443 CAAATAAGTCACTCTATCATTA
1 -AAATAAGTCACTCTATCATTA
29465 AAAT
1 AAAT
29469 TGAAAAGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (21 bp):
AAATAAGTCACTCTATCATTA
Found at i:30208 original size:2 final size:2
Alignment explanation
Indices: 30201--30230 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
30191 GAAAAGTAAA
30201 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
30231 CAATGGAAAT
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:30970 original size:25 final size:24
Alignment explanation
Indices: 30942--31004 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
30932 TTATTTGAAC
*
30942 TTAAAATATAAAATACAAATAACTA
1 TTAAAATATAAAATAC-AATAAATA
* **
30967 TTAAGATATTCAATACAATAAATA
1 TTAAAATATAAAATACAATAAATA
30991 TATACAAATATAAA
1 T-TA-AAATATAAA
31005 TTATTAAAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
24 8 0.28
25 15 0.52
26 6 0.21
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (24 bp):
TTAAAATATAAAATACAATAAATA
Found at i:31772 original size:35 final size:34
Alignment explanation
Indices: 31696--31818 Score: 126
Period size: 34 Copynumber: 3.6 Consensus size: 34
31686 TTGTGCATAC
*
31696 TCTAAATGCGACACATGACATTGTTGTAT--ATTA
1 TCTAAATGCGACACATGACATTCTT-TATGCATTA
* * **
31729 TATGAATGCGACACATGACACACTTCTATGCATTA
1 TCTAAATGCGACACATGACATTCTT-TATGCATTA
*
31764 TCTAAATGCGACACATGGCATTCTGTT-TGCATTA
1 TCTAAATGCGACACATGACATTCT-TTATGCATTA
* *
31798 TCTAAATGTGACACATTACAT
1 TCTAAATGCGACACATGACAT
31819 ACTGCTAGCA
Statistics
Matches: 73, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
33 23 0.32
34 25 0.34
35 24 0.33
36 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (34 bp):
TCTAAATGCGACACATGACATTCTTTATGCATTA
Found at i:32835 original size:20 final size:20
Alignment explanation
Indices: 32810--32862 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
32800 CAAAATGGGT
*
32810 AGTATCAATACCCTAAATGA
1 AGTATCAATACCCTAAATAA
32830 AGTATCAATACCCTAAATAA
1 AGTATCAATACCCTAAATAA
*
32850 AGCATCAATACCC
1 AGTATCAATACCC
32863 CTAGTCAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.45, C:0.25, G:0.08, T:0.23
Consensus pattern (20 bp):
AGTATCAATACCCTAAATAA
Found at i:34267 original size:45 final size:45
Alignment explanation
Indices: 34203--34310 Score: 157
Period size: 45 Copynumber: 2.4 Consensus size: 45
34193 CGGTGCACTA
*
34203 AGAGTGCATCGATGCATGAAATGCATTTGATGTTTT-A-AAATAGCC
1 AGAGTGCATCGATGCATGAAATGCATTCGATGTTTTCATAAA-A-CC
*
34248 AGAGTGCATCGATGCATGAAATGCATTCGATGTTTTCATAAAACT
1 AGAGTGCATCGATGCATGAAATGCATTCGATGTTTTCATAAAACC
34293 ATGAGTGCATCGATGCAT
1 A-GAGTGCATCGATGCAT
34311 AGTATGTGCA
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
45 37 0.64
46 18 0.31
47 3 0.05
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (45 bp):
AGAGTGCATCGATGCATGAAATGCATTCGATGTTTTCATAAAACC
Found at i:34847 original size:2 final size:2
Alignment explanation
Indices: 34840--34890 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
34830 TAGCTAATTG
34840 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
34882 AT AT AT AT A
1 AT AT AT AT A
34891 GCTTAAGCTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35359 original size:9 final size:9
Alignment explanation
Indices: 35345--35370 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
35335 CGACTCTAAG
35345 AAAGATCGA
1 AAAGATCGA
35354 AAAGATCGA
1 AAAGATCGA
35363 AAAGATCG
1 AAAGATCG
35371 GGAGTGTGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.54, C:0.12, G:0.23, T:0.12
Consensus pattern (9 bp):
AAAGATCGA
Found at i:37259 original size:28 final size:30
Alignment explanation
Indices: 37222--37303 Score: 105
Period size: 35 Copynumber: 2.6 Consensus size: 30
37212 CCCGAACCCG
37222 AAAATATTATATATATA-AT-AAAAAATAT
1 AAAATATTATATATATATATAAAAAAATAT
37250 AAAATATTATATATATAATTAATATAAAAAAATAT
1 AAAATA-T-TATATAT-A-T-ATATAAAAAAATAT
37285 AAAATATTATATATATATA
1 AAAATATTATATATATATA
37304 ATCGTGGCAG
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
28 6 0.13
29 1 0.02
30 10 0.21
31 2 0.04
32 2 0.04
33 8 0.17
34 3 0.06
35 15 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (30 bp):
AAAATATTATATATATATATAAAAAAATAT
Found at i:37285 original size:25 final size:26
Alignment explanation
Indices: 37230--37285 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
37220 CGAAAATATT
*
37230 ATATATATAATAAAAAATATAAAATA
1 ATATATATAATAAAAAATATAAAAAA
* **
37256 TTATATAT-ATAATTAATATAAAAAA
1 ATATATATAATAAAAAATATAAAAAA
37281 ATATA
1 ATATA
37286 AAATATTATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
ATATATATAATAAAAAATATAAAAAA
Found at i:37903 original size:21 final size:21
Alignment explanation
Indices: 37879--37924 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
37869 TACAAGTTAT
*
37879 AAATAAGTCACT-TATTATTA
1 AAATAAGTCACTCTATCATTA
37899 CAAATAAGTCACTCTATCATTA
1 -AAATAAGTCACTCTATCATTA
37921 AAAT
1 AAAT
37925 TGAAAAGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (21 bp):
AAATAAGTCACTCTATCATTA
Found at i:39404 original size:25 final size:24
Alignment explanation
Indices: 39376--39438 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
39366 TTATTTAAAC
*
39376 TTAAAATATAAAATACAAATAACTA
1 TTAAAATATAAAATAC-AATAAATA
* **
39401 TTAAGATATTCAATACAATAAATA
1 TTAAAATATAAAATACAATAAATA
39425 TATACAAATATAAA
1 T-TA-AAATATAAA
39439 TTATTAAAGA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
24 8 0.28
25 15 0.52
26 6 0.21
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (24 bp):
TTAAAATATAAAATACAATAAATA
Found at i:40206 original size:35 final size:34
Alignment explanation
Indices: 40130--40252 Score: 126
Period size: 34 Copynumber: 3.6 Consensus size: 34
40120 TTGTGCATAC
*
40130 TCTAAATGCGACACATGACATTGTTGTAT--ATTA
1 TCTAAATGCGACACATGACATTCTT-TATGCATTA
* * **
40163 TATGAATGCGACACATGACACACTTCTATGCATTA
1 TCTAAATGCGACACATGACATTCTT-TATGCATTA
*
40198 TCTAAATGCGACACATGGCATTCTGTT-TGCATTA
1 TCTAAATGCGACACATGACATTCT-TTATGCATTA
* *
40232 TCTAAATGTGACACATTACAT
1 TCTAAATGCGACACATGACAT
40253 ACTGCTAGCA
Statistics
Matches: 73, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
33 23 0.32
34 25 0.34
35 24 0.33
36 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (34 bp):
TCTAAATGCGACACATGACATTCTTTATGCATTA
Found at i:45423 original size:23 final size:22
Alignment explanation
Indices: 45393--45474 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 22
45383 GCATGACCTT
45393 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * * *
45415 AGTGCATCGGTACACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
* *
45437 GTGTATCGATGCATATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
45460 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
45475 TGTTAAGTGT
Statistics
Matches: 44, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
21 13 0.30
22 2 0.05
23 18 0.41
24 11 0.25
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:51271 original size:19 final size:19
Alignment explanation
Indices: 51222--51271 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
51212 GGACCCTTAT
**
51222 TGCATCGATATACTAAGAG
1 TGCATCGATGCACTAAGAG
*
51241 TGCATCGGTGCACTAAGAG
1 TGCATCGATGCACTAAGAG
51260 TGCATCGATGCA
1 TGCATCGATGCA
51272 TGAAATGCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (19 bp):
TGCATCGATGCACTAAGAG
Found at i:51341 original size:63 final size:61
Alignment explanation
Indices: 51261--51463 Score: 212
Period size: 63 Copynumber: 3.2 Consensus size: 61
51251 CACTAAGAGT
*
51261 GCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGCCATAGTGCATCGATGCATGGCTGG
1 GCATCGATGCATGAAATGCATTCGATG-TTCAAAATA-CCATAGTGCATCGATGCATGGATGG
* * *
51324 GCATCGATGCATTAAATGCATTCGATGTTCATAAA-ACTC-TGAGTGCATCGATGCATAGTATGT
1 GCATCGATGCATGAAATGCATTCGATGTTCA-AAATAC-CAT-AGTGCATCGATGCAT-GGATGG
* * * * *
51387 GCATCAATGCATGGAATGCATTCGATGTTCAATTTATTCCATGGTGCATCGATGCATGGATTGG
1 GCATCGATGCATGAAATGCATTCGATGTTCAA--AATACCATAGTGCATCGATGCATGGA-TGG
*
51451 TGCATCGGTGCAT
1 -GCATCGATGCAT
51464 CACTTTGAAA
Statistics
Matches: 116, Mismatches: 14, Indels: 18
0.78 0.09 0.12
Matches are distributed among these distances:
61 2 0.02
62 22 0.19
63 62 0.53
64 18 0.16
65 12 0.10
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (61 bp):
GCATCGATGCATGAAATGCATTCGATGTTCAAAATACCATAGTGCATCGATGCATGGATGG
Found at i:53370 original size:18 final size:18
Alignment explanation
Indices: 53323--53370 Score: 64
Period size: 16 Copynumber: 2.8 Consensus size: 18
53313 ATTTATTTTA
*
53323 ATTATTTATTATATAAAT
1 ATTATTTATTTTATAAAT
*
53341 ATTATTTA--TTATAATT
1 ATTATTTATTTTATAAAT
53357 ATTATTTATTTTAT
1 ATTATTTATTTTAT
53371 TATAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 14 0.54
18 12 0.46
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTATTTATTTTATAAAT
Found at i:53572 original size:13 final size:13
Alignment explanation
Indices: 53554--53586 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
53544 AACAATTAAA
53554 TTTTAAACAACAC
1 TTTTAAACAACAC
*
53567 TTTTAAACAATAC
1 TTTTAAACAACAC
53580 TTTTAAA
1 TTTTAAA
53587 AATTCGTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.39
Consensus pattern (13 bp):
TTTTAAACAACAC
Found at i:54545 original size:2 final size:2
Alignment explanation
Indices: 54538--54572 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
54528 AACACCTATC
54538 AT AT AT AT AT AT AT -T 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
54573 CTCACACCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Done.