Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006112.1 Hibiscus syriacus cultivar Beakdansim tig00014487_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: 63382
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1902 original size:2 final size:2
Alignment explanation
Indices: 1897--1926 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1887 ATTTAAAAAT
1897 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1927 AAGAAAACAC
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):
TA
Found at i:2316 original size:20 final size:20
Alignment explanation
Indices: 2277--2316 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2267 GAATGTTTTT
* *
2277 TTTCAAAAAATTTGGGTTTA
1 TTTCAAAAAATTTCGCTTTA
*
2297 TTTCAAAAAATTTCTCTTTA
1 TTTCAAAAAATTTCGCTTTA
2317 AAATTATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.47
Consensus pattern (20 bp):
TTTCAAAAAATTTCGCTTTA
Found at i:10250 original size:2 final size:2
Alignment explanation
Indices: 10243--10289 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
10233 TTCACAAAGG
10243 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
10285 GA GA G
1 GA GA G
10290 CTAAAACCTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:11086 original size:118 final size:118
Alignment explanation
Indices: 10878--11115 Score: 406
Period size: 118 Copynumber: 2.0 Consensus size: 118
10868 TATTTTACCT
*
10878 ACTACAAATTAAATATTTTCCTTAAGTATAGCTTATCTTTTTTAATATTCTGAATCAAAAAGAAA
1 ACTACAAATTAAATATTTTCCTTAAGTATAGCTTATCTTTTTTAATAGTCTGAATCAAAAAGAAA
*
10943 ATTATGTGATTTCCTTTTAATTTAAATATTAAATATAGTATGACTTGCAATTC
66 ATTATGCGATTTCCTTTTAATTTAAATATTAAATATAGTATGACTTGCAATTC
* * *
10996 ACTACGAATTAAATATTTTCCTTAAGTGA-AGTTTATCTTTTTTAATAGTCTGAATTAAAAAGAA
1 ACTACAAATTAAATATTTTCCTTAAGT-ATAGCTTATCTTTTTTAATAGTCTGAATCAAAAAGAA
*
11060 AATTATGCGATTTCCTTTTAATTTAAATATTAAATATAGTATGACTTGTAATTC
65 AATTATGCGATTTCCTTTTAATTTAAATATTAAATATAGTATGACTTGCAATTC
11114 AC
1 AC
11116 GAATGTATTC
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
118 112 0.99
119 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.43
Consensus pattern (118 bp):
ACTACAAATTAAATATTTTCCTTAAGTATAGCTTATCTTTTTTAATAGTCTGAATCAAAAAGAAA
ATTATGCGATTTCCTTTTAATTTAAATATTAAATATAGTATGACTTGCAATTC
Found at i:13625 original size:31 final size:32
Alignment explanation
Indices: 13568--13633 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
13558 TGACTACATT
13568 TTAAATAAATAAAAAATAAAAGTGATAATATC
1 TTAAATAAATAAAAAATAAAAGTGATAATATC
* * *
13600 TTAATTAAATAAAAATTAAGA-TGATAATATC
1 TTAAATAAATAAAAAATAAAAGTGATAATATC
13631 TTA
1 TTA
13634 TATATTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 13 0.42
32 18 0.58
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (32 bp):
TTAAATAAATAAAAAATAAAAGTGATAATATC
Found at i:24497 original size:20 final size:20
Alignment explanation
Indices: 24472--24820 Score: 452
Period size: 20 Copynumber: 17.4 Consensus size: 20
24462 GATTTTCCAT
* ** *
24472 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
24492 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
24512 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
24532 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
24552 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
24572 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
24592 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
24612 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
24632 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
24652 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
24672 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
24692 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
24712 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
24732 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
24752 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
24772 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
24792 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
24812 AATCACAAC
1 AATCGCAAC
24821 ACTGAAATTT
Statistics
Matches: 291, Mismatches: 32, Indels: 12
0.87 0.10 0.04
Matches are distributed among these distances:
19 2 0.01
20 287 0.99
21 2 0.01
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:25541 original size:24 final size:24
Alignment explanation
Indices: 25502--25548 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
25492 AAATTTGGTC
25502 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
25526 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
25549 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:25740 original size:12 final size:12
Alignment explanation
Indices: 25723--25747 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25713 ATATAATCCT
25723 GAAGAAGAAAAA
1 GAAGAAGAAAAA
25735 GAAGAAGAAAAA
1 GAAGAAGAAAAA
25747 G
1 G
25748 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:28052 original size:19 final size:19
Alignment explanation
Indices: 28030--28335 Score: 367
Period size: 19 Copynumber: 17.4 Consensus size: 19
28020 CGGAAAATAC
*
28030 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
28049 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
28063 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
28083 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
28097 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
28116 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
28135 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
28149 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
28168 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
28187 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
28201 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
28220 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
28239 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
28258 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
28276 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
28290 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
28309 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
28328 AATCGCAA
1 AATCGCAA
28336 CGAGATAATC
Statistics
Matches: 251, Mismatches: 10, Indels: 52
0.80 0.03 0.17
Matches are distributed among these distances:
14 48 0.19
15 3 0.01
16 20 0.08
17 9 0.04
18 12 0.05
19 146 0.58
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:28117 original size:33 final size:33
Alignment explanation
Indices: 28030--28357 Score: 264
Period size: 33 Copynumber: 9.5 Consensus size: 33
28020 CGGAAAATAC
* *
28030 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
28063 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
28097 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
28135 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
* *
28168 AATCGCAATGCGAAATGAAAATCGCAACGACAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
*
28201 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
28239 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAGA--A
28276 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
28309 AATCGCAATGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
28342 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
28358 TATAAACGCA
Statistics
Matches: 253, Mismatches: 15, Indels: 54
0.79 0.05 0.17
Matches are distributed among these distances:
32 12 0.05
33 109 0.43
34 34 0.13
35 19 0.08
36 8 0.03
37 12 0.05
38 59 0.23
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:28145 original size:52 final size:52
Alignment explanation
Indices: 28058--28335 Score: 379
Period size: 52 Copynumber: 5.2 Consensus size: 52
28048 AAATCCCAAC
28058 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
28111 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
28163 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
28215 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
28272 ATG-AAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
28323 ATGAAAATCGCAA
1 ATGAAAATCGCAA
28336 CGAGATAATC
Statistics
Matches: 214, Mismatches: 5, Indels: 13
0.92 0.02 0.06
Matches are distributed among these distances:
51 36 0.17
52 127 0.59
53 17 0.08
54 7 0.03
56 10 0.05
57 17 0.08
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:28181 original size:71 final size:70
Alignment explanation
Indices: 28097--28335 Score: 369
Period size: 71 Copynumber: 3.4 Consensus size: 70
28087 GCAACGAGAG
*
28097 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATG-AAATCGCAACGAAAGAATCGCAATGCGA
28162 AATGAA
65 AATGAA
* *
28168 AATCGCAATGCGAAATGAAAATCGCAA--CGACA-G-AATCGCAATGCGAAATTAAAATCGCAAT
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAA--CG-AA--AGAATCGCAAT
28229 GCGAAATGAA
61 GCGAAATGAA
28239 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAAAGAATCGCAATGCGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAAAGAATCGCAATGCGAA
28304 ATGAA
66 ATGAA
28309 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
28336 CGAGATAATC
Statistics
Matches: 154, Mismatches: 5, Indels: 19
0.87 0.03 0.11
Matches are distributed among these distances:
66 8 0.05
68 3 0.02
69 5 0.03
70 47 0.31
71 74 0.48
72 2 0.01
73 6 0.04
74 1 0.01
75 8 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (70 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAAAGAATCGCAATGCGAA
ATGAA
Found at i:28473 original size:19 final size:19
Alignment explanation
Indices: 28364--28465 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
28354 AAATTATAAA
28364 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
28383 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
28403 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
28419 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
28436 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
28455 CGCATTGCGAT
1 CGCATTGCGAT
28466 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:28590 original size:14 final size:14
Alignment explanation
Indices: 28571--28607 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
28561 CATCAATTAC
28571 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
28585 ACAAATCATCTTTT
1 ACAAATCAACTTTT
28599 ACAAATCAA
1 ACAAATCAA
28608 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:30605 original size:14 final size:14
Alignment explanation
Indices: 30586--30642 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
30576 GCGAAATGAA
*
30586 AATCGCAACGACAG
1 AATCGCAACGAAAG
30600 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
30617 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
30633 AATCGCAACG
1 AATCGCAACG
30643 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:30613 original size:33 final size:33
Alignment explanation
Indices: 30567--30657 Score: 164
Period size: 33 Copynumber: 2.8 Consensus size: 33
30557 GCGAAACCAA
*
30567 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
30600 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
30633 AATCGCAACGCGAAATGAAAATCGC
1 AATCGCAACGCGAAATGAAAATCGC
30658 GATGCGATTT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:30664 original size:19 final size:19
Alignment explanation
Indices: 30530--30657 Score: 123
Period size: 19 Copynumber: 7.2 Consensus size: 19
30520 TAGTTTACTT
* *
30530 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
30550 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
30569 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
30588 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
30602 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
30621 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
30635 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
30654 TCGC
1 TCGC
30658 GATGCGATTT
Statistics
Matches: 91, Mismatches: 7, Indels: 21
0.76 0.06 0.18
Matches are distributed among these distances:
14 16 0.18
16 11 0.12
17 11 0.12
19 41 0.45
20 12 0.13
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:30676 original size:19 final size:19
Alignment explanation
Indices: 30654--30788 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
30644 GAAATGAAAA
*
30654 TCGCGATGCGATTTTGGTT
1 TCGCGTTGCGATTTTGGTT
*
30673 TCGCGTTGCGATCTT-G--
1 TCGCGTTGCGATTTTGGTT
30689 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTGGTT
*
30706 TCGCGTTGCGATTCT-G--
1 TCGCGTTGCGATTTTGGTT
**
30722 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTGGTT
30739 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTGGTT
*
30758 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTT-GGTT
*
30778 TCGTGTTGCGA
1 TCGCGTTGCGA
30789 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.23
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 53 0.56
20 13 0.14
ACGTcount: A:0.09, C:0.18, G:0.29, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTGGTT
Found at i:30702 original size:33 final size:33
Alignment explanation
Indices: 30660--30751 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
30650 AAAATCGCGA
30660 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
30693 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
30726 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
30752 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:30991 original size:93 final size:93
Alignment explanation
Indices: 30832--31304 Score: 921
Period size: 93 Copynumber: 5.1 Consensus size: 93
30822 TTGAATGGAT
30832 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
30897 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
30925 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
30990 AGTTTAGCAGAATTGGCAGCAACCGGAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
31018 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
31083 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
31111 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
31175 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
31203 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
31268 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
31296 AAATTTACT
1 AAATTTACT
31305 AAGCAATCTA
Statistics
Matches: 376, Mismatches: 3, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
92 92 0.24
93 284 0.76
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:31277 original size:185 final size:186
Alignment explanation
Indices: 30832--31304 Score: 921
Period size: 185 Copynumber: 2.5 Consensus size: 186
30822 TTGAATGGAT
30832 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
30897 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
30962 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGGAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
31018 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
31083 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
31148 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
31203 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
31268 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
31305 AAGCAATCTA
Statistics
Matches: 285, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
185 153 0.54
186 132 0.46
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:33029 original size:14 final size:14
Alignment explanation
Indices: 33010--33099 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
33000 TTGAAATGAA
33010 AATCGCAACGAGAG
1 AATCGCAACGAGAG
33024 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
33041 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
33057 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
33076 AATCGCAACGAGAG
1 AATCGCAACGAGAG
33090 AATCGCAACG
1 AATCGCAACG
33100 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:33047 original size:33 final size:33
Alignment explanation
Indices: 33002--33116 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
32992 TCTTTTGGTT
33002 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
33035 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
33068 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
33101 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
33117 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:33048 original size:19 final size:18
Alignment explanation
Indices: 33009--33121 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
32999 GTTGAAATGA
33009 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
33024 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
33041 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
33057 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
33074 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
33090 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
33107 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
33122 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:33150 original size:19 final size:19
Alignment explanation
Indices: 33117--33161 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
33107 AAAATCGCAA
**
33117 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
33136 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
33155 TGCGATT
1 TGCGATT
33162 CTCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.47
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:33336 original size:33 final size:33
Alignment explanation
Indices: 33294--33364 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
33284 AATACTAACT
*
33294 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
33327 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
33360 TGAAA
1 TGAAA
33365 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:33598 original size:22 final size:22
Alignment explanation
Indices: 33546--33600 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
33536 TGGTTGTGAG
**
33546 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
33568 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
33590 GGATTTCTTCG
1 GGATTTCTTCG
33601 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:33771 original size:20 final size:20
Alignment explanation
Indices: 33746--33939 Score: 203
Period size: 20 Copynumber: 9.6 Consensus size: 20
33736 CTTTAAATAT
33746 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
33766 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
33788 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
33807 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
33827 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
33847 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
33867 CACGTTACGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
33887 CGCGTTGCGATTTTATGTG-TT
1 CGCGTTGCGA-TTTACG-GATA
* ** *
33908 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
33928 CGCGTTGCGATT
1 CGCGTTGCGATT
33940 ATGGAAAATC
Statistics
Matches: 144, Mismatches: 24, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.01
20 109 0.76
21 30 0.21
22 3 0.02
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:34020 original size:20 final size:20
Alignment explanation
Indices: 33995--34046 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
33985 AAGAATCGCG
*
33995 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
34015 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
34035 TTGCGATTCTGG
1 TTGCGATTCTGG
34047 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:34745 original size:34 final size:34
Alignment explanation
Indices: 34702--34767 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
34692 TGGGTTTAAA
34702 ACATATGATTAGTTGG-GATGATAATTTTGTAACT
1 ACATATGATTAGTTGGAG-TGATAATTTTGTAACT
* *
34736 ACATATGATTAGTTTGAGTGATCATTTTGTAA
1 ACATATGATTAGTTGGAGTGATAATTTTGTAA
34768 TTTTTTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 28 0.97
35 1 0.03
ACGTcount: A:0.32, C:0.06, G:0.20, T:0.42
Consensus pattern (34 bp):
ACATATGATTAGTTGGAGTGATAATTTTGTAACT
Found at i:38773 original size:30 final size:30
Alignment explanation
Indices: 38739--38795 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
38729 CTATGGTTGT
38739 TATTAATC-AACGTTGAATCACCCTACTAGC
1 TATTAA-CGAACGTTGAATCACCCTACTAGC
* *
38769 TATTAACGAACGTTGAATTACTCTACT
1 TATTAACGAACGTTGAATCACCCTACT
38796 GTAGTTGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (30 bp):
TATTAACGAACGTTGAATCACCCTACTAGC
Found at i:40361 original size:23 final size:23
Alignment explanation
Indices: 40331--40378 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
40321 TATTCATGAA
40331 AAGAAAAGAGACGAAAGAGATCG
1 AAGAAAAGAGACGAAAGAGATCG
40354 AAGAAAAGAGACGAAAGAGATCG
1 AAGAAAAGAGACGAAAGAGATCG
40377 AA
1 AA
40379 CGCTTGTGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.58, C:0.08, G:0.29, T:0.04
Consensus pattern (23 bp):
AAGAAAAGAGACGAAAGAGATCG
Found at i:43271 original size:13 final size:13
Alignment explanation
Indices: 43248--43278 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
43238 AATCTACAAC
43248 TAAAA-AATAAAA
1 TAAAATAATAAAA
43260 TAAAATAATAAAA
1 TAAAATAATAAAA
43273 TAAAAT
1 TAAAAT
43279 TCTAGCTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAAATAATAAAA
Found at i:44975 original size:19 final size:20
Alignment explanation
Indices: 44950--45039 Score: 103
Period size: 19 Copynumber: 4.3 Consensus size: 20
44940 CTTATTTTGG
44950 ATTTTTCACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
44970 -TTTTTCACTATCGCAACAAC
1 ATTTTTCACTATCGCAAC-AC
*
44990 ACGTTTTTCAAACTCTCGCAACAC
1 A--TTTTTC--ACTATCGCAACAC
*
45014 A-TTTTAACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
45033 ATTTTTC
1 ATTTTTC
45040 GAAATCGCGT
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
19 30 0.51
20 6 0.10
21 4 0.07
23 6 0.10
24 3 0.05
25 10 0.17
ACGTcount: A:0.30, C:0.29, G:0.06, T:0.36
Consensus pattern (20 bp):
ATTTTTCACTATCGCAACAC
Found at i:45090 original size:21 final size:21
Alignment explanation
Indices: 45042--45102 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
45032 CATTTTTCGA
*
45042 AATCGCGTTGCGAATCT-TAC
1 AATCGCGTTGCGAATCTGGAC
*
45062 AATCGCGTTGCGAATCTGGAT
1 AATCGCGTTGCGAATCTGGAC
* *
45083 ATTCGCGTTGCGAATTTGGA
1 AATCGCGTTGCGAATCTGGA
45103 AACGGGGTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (21 bp):
AATCGCGTTGCGAATCTGGAC
Found at i:48568 original size:17 final size:17
Alignment explanation
Indices: 48546--48579 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
48536 AAGAGAAAGC
*
48546 AGTAAAACGTTTATTGA
1 AGTAAAACATTTATTGA
48563 AGTAAAACATTTATTGA
1 AGTAAAACATTTATTGA
48580 TACTCTGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (17 bp):
AGTAAAACATTTATTGA
Found at i:48813 original size:36 final size:36
Alignment explanation
Indices: 48757--48900 Score: 146
Period size: 36 Copynumber: 3.8 Consensus size: 36
48747 AGATGAACAA
*
48757 TTGAGTCGAAAGTGCTGATGCTTCCTTCCGTTCACT
1 TTGAATCGAAAGTGCTGATGCTTCCTTCCGTTCACT
*
48793 TTGAATCGAAAGTG-TCGATGCTTTCGATGCTTCCTTTCATTCTT
1 TTGAATCGAAAGTGCT-GATGC-TTC----CTTCCGTTCA--C-T
* *
48837 CTTGAACCGAAAGTGCCGATGCTTCCTTCCGTTCACT
1 -TTGAATCGAAAGTGCTGATGCTTCCTTCCGTTCACT
*
48874 TTGAATCGAAAGTGCTTATGCTTCCTT
1 TTGAATCGAAAGTGCTGATGCTTCCTT
48901 TCGTACTTCT
Statistics
Matches: 89, Mismatches: 8, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
35 1 0.01
36 42 0.47
37 4 0.04
38 1 0.01
40 9 0.10
41 9 0.10
43 1 0.01
44 4 0.04
45 18 0.20
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (36 bp):
TTGAATCGAAAGTGCTGATGCTTCCTTCCGTTCACT
Found at i:50106 original size:17 final size:17
Alignment explanation
Indices: 50084--50117 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
50074 AAGAGAAAGC
*
50084 AGTAAAACGTTTATTGA
1 AGTAAAACATTTATTGA
50101 AGTAAAACATTTATTGA
1 AGTAAAACATTTATTGA
50118 TACTCTGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (17 bp):
AGTAAAACATTTATTGA
Found at i:52527 original size:27 final size:27
Alignment explanation
Indices: 52471--52525 Score: 94
Period size: 26 Copynumber: 2.1 Consensus size: 27
52461 ATCGATCCAT
*
52471 AACAATATAACAAGTAAAAAAATGACA
1 AACAATATAACAAGGAAAAAAATGACA
52498 AACAATATAAC-AGGAAAAAAATGACA
1 AACAATATAACAAGGAAAAAAATGACA
52524 AA
1 AA
52526 ACCGGTCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.67, C:0.11, G:0.09, T:0.13
Consensus pattern (27 bp):
AACAATATAACAAGGAAAAAAATGACA
Found at i:52625 original size:137 final size:138
Alignment explanation
Indices: 52374--52636 Score: 438
Period size: 137 Copynumber: 1.9 Consensus size: 138
52364 ATAACATGTA
* *
52374 AAAAAAATGACAAAACCGGTCTATAAATGACAAAACATGTAAAGCGCTACCGGATATATTGAAAG
1 AAAAAAATGACAAAACCGGTCAATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAG
*
52439 TATCAATACTTTATAAAAATATATCGATCCATAACAATATAACAAGTAAAAAAATGACAAACAAT
66 TATCAATAATTTATAAAAATATATCGATCCATAACAATATAACAAGTAAAAAAATGACAAACAAT
52504 ATAACAGG
131 ATAACAGG
*
52512 AAAAAAATGACAAAACCGGTCAATAAATGACAAAACAGGTTAAGCGCTA-CGGATATATTGAAAG
1 AAAAAAATGACAAAACCGGTCAATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAG
* * * * *
52576 TGTCGATAATTTATAAAAATGTATCGATCTATAACAATATAACATGTAAAAAAATGACAAA
66 TATCAATAATTTATAAAAATATATCGATCCATAACAATATAACAAGTAAAAAAATGACAAA
52637 ACCGGTATAT
Statistics
Matches: 116, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
137 70 0.60
138 46 0.40
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.22
Consensus pattern (138 bp):
AAAAAAATGACAAAACCGGTCAATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAG
TATCAATAATTTATAAAAATATATCGATCCATAACAATATAACAAGTAAAAAAATGACAAACAAT
ATAACAGG
Found at i:52635 original size:111 final size:112
Alignment explanation
Indices: 52498--52755 Score: 432
Period size: 112 Copynumber: 2.3 Consensus size: 112
52488 AAAAATGACA
* * *
52498 AACAATATAACA-GGAAAAAAATGACAAAACCGGTCA-ATAAATGACAAAACAGGTTAAGCGCTA
1 AACAATATAACATGTAAAAAAATGACAAAACCGGT-ATATAAATGAAAAAACAGGTAAAGCGCTA
*
52561 -CGGATATATTGAAAGTGTCGATAATTTATAAAAATGTATCGATCTAT
65 CCGGATATATTGAAAGTGTCGATAATTTATAAAAATGTATCGATCCAT
52608 AACAATATAACATGTAAAAAAATGACAAAACCGGTATATAAATGAAAAAACAGGTAAAGCGCTAC
1 AACAATATAACATGTAAAAAAATGACAAAACCGGTATATAAATGAAAAAACAGGTAAAGCGCTAC
*
52673 CGGATATATTGAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
66 CGGATATATTGAAAGTGTCGATAATTTATAAAAATGTATCGATCCAT
*
52720 AACAATATAACATGTAAAAAAATGACAAAACAGGTA
1 AACAATATAACATGTAAAAAAATGACAAAACCGGTA
52756 AAACACTACC
Statistics
Matches: 139, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
110 13 0.09
111 46 0.33
112 80 0.58
ACGTcount: A:0.49, C:0.13, G:0.15, T:0.23
Consensus pattern (112 bp):
AACAATATAACATGTAAAAAAATGACAAAACCGGTATATAAATGAAAAAACAGGTAAAGCGCTAC
CGGATATATTGAAAGTGTCGATAATTTATAAAAATGTATCGATCCAT
Found at i:53046 original size:182 final size:181
Alignment explanation
Indices: 52768--53118 Score: 578
Period size: 182 Copynumber: 1.9 Consensus size: 181
52758 ACACTACCGT
* * *
52768 ATATGTTGATAGTGTCGATACTTTATTATAAATATCGACACTTTTGGAATTTAAAAGAGAATAAA
1 ATATGTTGAAAGTGTCGATACTTTATTATAAATATCGACACTTTTGGAATTTAAAAGAAAAGAAA
* * *
52833 TTATAGCGCTAATAAAGTGTCGATACTTTATAAGAATGTATCGATCCATAACAATATAACAGGTA
66 TTATAGCGCTAATAAAGTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGATA
52898 AAAATATGAAAAAATCGGTCTCGAAATGACAAAATCGGTAAAGAGCTACCAA
131 AAAATATGAAAAAATCGG-CTCGAAATGACAAAATCGGTAAAGAGCTACCAA
* * *
52950 ATATGTTGAAAGTGTCGATATTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAG
1 ATATGTTGAAAGTGTCGATACTTTATTATAAATATCGACACTTTTGGAATTTAAAAGAAAAGAAA
53015 TTATAGCG-TCAATAAAGTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGAT
66 TTATAGCGCT-AATAAAGTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGAT
* *
53079 AAAAATATGATAAAATCGGCTCGAAATGATAAAATCGGTA
130 AAAAATATGAAAAAATCGGCTCGAAATGACAAAATCGGTA
53119 GTAAAAAAGT
Statistics
Matches: 157, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
181 21 0.13
182 136 0.87
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (181 bp):
ATATGTTGAAAGTGTCGATACTTTATTATAAATATCGACACTTTTGGAATTTAAAAGAAAAGAAA
TTATAGCGCTAATAAAGTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGATA
AAAATATGAAAAAATCGGCTCGAAATGACAAAATCGGTAAAGAGCTACCAA
Found at i:56133 original size:24 final size:23
Alignment explanation
Indices: 56099--56143 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
56089 TAATAATACC
*
56099 AAAAATAAAAATTAAATTATTCA
1 AAAAATAAAAAATAAATTATTCA
*
56122 AAAAATTAAAAAATATATTATT
1 AAAAA-TAAAAAATAAATTATT
56144 ACTTTTTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAAATAAAAAATAAATTATTCA
Found at i:56620 original size:2 final size:2
Alignment explanation
Indices: 56613--56640 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
56603 AAACAAAATA
56613 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
56641 TAGTAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56693 original size:25 final size:26
Alignment explanation
Indices: 56665--56714 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
56655 TTATTTTTGG
* *
56665 TATTTTATATTT-ATATTTTTTTATA
1 TATTTTAAATTTAATATATTTTTATA
56690 TATTTTAAATTTAATATATTTTTAT
1 TATTTTAAATTTAATATATTTTTAT
56715 TTAAAAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (26 bp):
TATTTTAAATTTAATATATTTTTATA
Found at i:57781 original size:17 final size:17
Alignment explanation
Indices: 57759--57792 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
57749 AATATACTTT
57759 TTTATTATATTTTATGA
1 TTTATTATATTTTATGA
57776 TTTATTATATTTTATGA
1 TTTATTATATTTTATGA
57793 CATATGAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTATTATATTTTATGA
Found at i:59952 original size:13 final size:13
Alignment explanation
Indices: 59934--59960 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
59924 ATGATCGTTT
59934 TATAATATTGAAA
1 TATAATATTGAAA
59947 TATAATATTGAAA
1 TATAATATTGAAA
59960 T
1 T
59961 TTGAATCGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (13 bp):
TATAATATTGAAA
Found at i:60246 original size:6 final size:5
Alignment explanation
Indices: 60228--60270 Score: 50
Period size: 6 Copynumber: 7.8 Consensus size: 5
60218 TTAAAAATTT
60228 GAGTC GAGATC GAGCTC GAGTC GAGTTC GAGCTC GAGTC GAGT
1 GAGTC GAG-TC GAG-TC GAGTC GAG-TC GAG-TC GAGTC GAGT
60271 TCATTCGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 14 0.41
6 20 0.59
ACGTcount: A:0.21, C:0.21, G:0.37, T:0.21
Consensus pattern (5 bp):
GAGTC
Found at i:60270 original size:17 final size:17
Alignment explanation
Indices: 60228--60272 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
60218 TTAAAAATTT
*
60228 GAGTCGAGATCGAGCTC
1 GAGTCGAGTTCGAGCTC
60245 GAGTCGAGTTCGAGCTC
1 GAGTCGAGTTCGAGCTC
60262 GAGTCGAGTTC
1 GAGTCGAGTTC
60273 ATTCGATTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.20, C:0.22, G:0.36, T:0.22
Consensus pattern (17 bp):
GAGTCGAGTTCGAGCTC
Found at i:61096 original size:160 final size:162
Alignment explanation
Indices: 60815--61135 Score: 420
Period size: 159 Copynumber: 2.0 Consensus size: 162
60805 TGTTATATAT
* * * *
60815 ACACATATATTATCCACCAAAATCTAATTATCTTTTTGGGTAAATTAGACATTTAATATCTAAAC
1 ACACATATATTATCCACCAAAATCTAATTACCTTTTTGGGTAAACTAGACATTTAACACCTAAAC
** * *
60880 TATCAATTTTGATATATTTTAGTATTTAAATTTTTAAATTTTTAAAATTATACCTAACGTTTA-T
66 TATCAATTTTGATATATTTTAGTACCTAAATCTTCAAATTTTTAAAATTATACCTAACGTTTAGT
60944 TTTT-TTTCATTTTAGTATCACACTCTTAAAC
131 TTTTGTTTCATTTTAGTATCACACTCTTAAAC
60975 ACACATATATTATCCACCAAAATCTAATT-CCTTTTTGGGTAAACTATG-CATTTAACACCTAAA
1 ACACATATATTATCCACCAAAATCTAATTACCTTTTTGGGTAAACTA-GACATTTAACACCTAAA
* * ** * *
61038 CTATTAATTTTGAT-TCTTTTTTTTACCTAAA-CTTCAATTTTTTTAAAAATTATACCTAACTTT
65 CTATCAATTTTGATAT-ATTTTAGTACCTAAATCTTCAA-ATTTTT-AAAATTATACCTAACGTT
* *
61101 TAGTTTTTGTTTCATTTTAGTATCCCACTGTTAAA
127 TAGTTTTTGTTTCATTTTAGTATCACACTCTTAAA
61136 AACTTAACAT
Statistics
Matches: 139, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
158 5 0.04
159 56 0.40
160 49 0.35
161 5 0.04
162 24 0.17
ACGTcount: A:0.34, C:0.15, G:0.05, T:0.46
Consensus pattern (162 bp):
ACACATATATTATCCACCAAAATCTAATTACCTTTTTGGGTAAACTAGACATTTAACACCTAAAC
TATCAATTTTGATATATTTTAGTACCTAAATCTTCAAATTTTTAAAATTATACCTAACGTTTAGT
TTTTGTTTCATTTTAGTATCACACTCTTAAAC
Found at i:62052 original size:61 final size:61
Alignment explanation
Indices: 61987--62101 Score: 149
Period size: 61 Copynumber: 1.9 Consensus size: 61
61977 TCGGGTGACT
* *
61987 ATTTTGTAACTTTTAACAGTCAAGAGACTCAACAAAGTAACAAACTATAGTCGAAGGAAAA
1 ATTTTGTAACATTTAACAGTCAAGAGACTCAACAAAATAACAAACTATAGTCGAAGGAAAA
* * * * * **
62048 ATTTTGTAACATTTAAGAGTCGAGGGACTTAATAAAATAACACCCTATAGTCGA
1 ATTTTGTAACATTTAACAGTCAAGAGACTCAACAAAATAACAAACTATAGTCGA
62102 TGAATCATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 45 1.00
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.27
Consensus pattern (61 bp):
ATTTTGTAACATTTAACAGTCAAGAGACTCAACAAAATAACAAACTATAGTCGAAGGAAAA
Done.