Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002422.1 Hibiscus syriacus cultivar Beakdansim tig00004957_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: 101664
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2156 original size:25 final size:25
Alignment explanation
Indices: 2128--2175 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
2118 CAAAATAAGA
2128 ATAATAAAGTTAAA-TAAAAAAATTT
1 ATAATAAA-TTAAATTAAAAAAATTT
**
2153 ATAATTTATTAAATTAAAAAAAT
1 ATAATAAATTAAATTAAAAAAAT
2176 AAATCAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
ATAATAAATTAAATTAAAAAAATTT
Found at i:5604 original size:51 final size:51
Alignment explanation
Indices: 5528--5936 Score: 554
Period size: 51 Copynumber: 8.0 Consensus size: 51
5518 GGCGCAGACA
** * *
5528 CAGCAAGGTGGAAAC-TCAGAGTCCCAAACATATACTCAACTACCTCAACAG
1 CAGCAAGGTGGAAACATTGGA-TCCCAAACATATACTCAGCTACCACAACAG
* * ***
5579 CAGCAAGGTGGAAACTTTGGATCCCAAACATATAGTCAGCTATGGCAACAG
1 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
* * * * *
5630 CAGCAAGGTGGAAACTTTGGATCCCAGACGTATAGTCAGCTACCGCAACAG
1 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
* *
5681 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTAATCTACCACAACAG
1 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
* *
5732 CAGCAAGGTGGAAACATT-GATACCCAAACATATACTCTGCTACCACATCAG
1 CAGCAAGGTGGAAACATTGGAT-CCCAAACATATACTCAGCTACCACAACAG
*
5783 CAGCAAGGTGGAAACAATGGATCCCAAACATATACTCAGCTACCACAACAG
1 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
* * *
5834 CAGCAAGGTGGAAACATT-GATTCCCAAACATTTACTCTGTTACCACAACAG
1 CAGCAAGGTGGAAACATTGGA-TCCCAAACATATACTCAGCTACCACAACAG
* *
5885 CAGCAAGGTGGAAACATTGGTTCCCAAACATATACTCAGCTACCACAGCAG
1 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
5936 C
1 C
5937 TCTTAATGTC
Statistics
Matches: 319, Mismatches: 34, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
50 5 0.02
51 307 0.96
52 7 0.02
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (51 bp):
CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
Found at i:20870 original size:12 final size:12
Alignment explanation
Indices: 20853--20877 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20843 ATATTTTTAA
20853 TAAAAAATTATT
1 TAAAAAATTATT
20865 TAAAAAATTATT
1 TAAAAAATTATT
20877 T
1 T
20878 TTTTTACCGA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAAAATTATT
Found at i:20975 original size:21 final size:20
Alignment explanation
Indices: 20951--21003 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
20941 TAAAAATATT
*
20951 TATTTTAAATAATTAAATTAA
1 TATTTTAAATAA-TAAAATAA
*
20972 TATTTCAAATAA-AAAATAA
1 TATTTTAAATAATAAAATAA
*
20991 CATTTTAAATAAT
1 TATTTTAAATAAT
21004 GTTCTATCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 16 0.59
21 11 0.41
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (20 bp):
TATTTTAAATAATAAAATAA
Found at i:21421 original size:59 final size:59
Alignment explanation
Indices: 21297--21444 Score: 167
Period size: 59 Copynumber: 2.5 Consensus size: 59
21287 AATTAATTCT
* * * * * *
21297 TAAACTTTTAAATATTTCAATTTCATCTTCAAACTATGATTCTCATTTTAAATTAGTCT
1 TAAACTTTTAAATATTTCAATTTCATCCTCAAACTATGAATCTCATTCTAAATAAATCC
*
21356 TCAAACTTTTAAA-ATTTTAA-TTCTATCC-CTAAACTATGAATCTCATTCTAAATAAATCCC
1 T-AAACTTTTAAATATTTCAATTTC-ATCCTC-AAACTATGAATCTCATTCTAAATAAAT-CC
*
21416 TAAACTTTTGAATATTTCAATTTCATCCT
1 TAAACTTTTAAATATTTCAATTTCATCCT
21445 AATATTCGTC
Statistics
Matches: 73, Mismatches: 9, Indels: 12
0.78 0.10 0.13
Matches are distributed among these distances:
58 4 0.05
59 43 0.59
60 23 0.32
61 3 0.04
ACGTcount: A:0.35, C:0.18, G:0.03, T:0.44
Consensus pattern (59 bp):
TAAACTTTTAAATATTTCAATTTCATCCTCAAACTATGAATCTCATTCTAAATAAATCC
Found at i:21676 original size:29 final size:29
Alignment explanation
Indices: 21637--21748 Score: 86
Period size: 29 Copynumber: 3.8 Consensus size: 29
21627 TGAATGTCAT
*
21637 AGTTTAGGAATACAATTAAAATATTCAAA
1 AGTTTAAGAATACAATTAAAATATTCAAA
* *
21666 AGTTTAAGAATTA-ATTTAAAATGATAATCATA
1 AGTTTAAGAA-TACAATTAAAAT-AT--TCAAA
* * *
21698 A-TTTGAGAATAAAATTAAAATATTTAAA
1 AGTTTAAGAATACAATTAAAATATTCAAA
* *
21726 AGTTCAAGGAT-CAATCTAAAATA
1 AGTTTAAGAATACAAT-TAAAATA
21749 AAGACCATAA
Statistics
Matches: 65, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
28 7 0.11
29 30 0.46
30 8 0.12
31 15 0.23
32 5 0.08
ACGTcount: A:0.52, C:0.05, G:0.10, T:0.33
Consensus pattern (29 bp):
AGTTTAAGAATACAATTAAAATATTCAAA
Found at i:21682 original size:60 final size:60
Alignment explanation
Indices: 21616--21747 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 60
21606 ATTTTTGGGG
* * * *
21616 TCAATTTAAAATGA-ATGTCATAGTTT-AGGAATACAATTAAAATATTCAAAAGTTTAAGAA
1 TCAATTTAAAATGATA-ATCATAATTTGA-GAATAAAATTAAAATATTCAAAAGTTCAAGAA
* * *
21676 TTAATTTAAAATGATAATCATAATTTGAGAATAAAATTAAAATATTTAAAAGTTCAAGGA
1 TCAATTTAAAATGATAATCATAATTTGAGAATAAAATTAAAATATTCAAAAGTTCAAGAA
*
21736 TCAATCTAAAAT
1 TCAATTTAAAAT
21748 AAAGACCATA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
60 59 0.97
61 2 0.03
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.34
Consensus pattern (60 bp):
TCAATTTAAAATGATAATCATAATTTGAGAATAAAATTAAAATATTCAAAAGTTCAAGAA
Found at i:21758 original size:60 final size:60
Alignment explanation
Indices: 21644--21759 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
21634 CATAGTTTAG
* * * * * *
21644 GAATACAATTAAAATATTCAAAAGTTTAAGAATTAATTTAAAATGATAATCATAATTTGA
1 GAATAAAATTAAAATATTCAAAAGTTCAAGAATCAATCTAAAATGAAAACCATAATTTGA
* *
21704 GAATAAAATTAAAATATTTAAAAGTTCAAGGATCAATCTAAAAT-AAAGACCATAAT
1 GAATAAAATTAAAATATTCAAAAGTTCAAGAATCAATCTAAAATGAAA-ACCATAAT
21760 GCAATAACAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 2 0.04
60 45 0.96
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.31
Consensus pattern (60 bp):
GAATAAAATTAAAATATTCAAAAGTTCAAGAATCAATCTAAAATGAAAACCATAATTTGA
Found at i:30655 original size:31 final size:31
Alignment explanation
Indices: 30594--30656 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
30584 GACTCTCAAC
* * **
30594 TTTAGATAAAATATTAATTTAATCTTTAAAT
1 TTTAAATAAAATATCAATTTAATCCGTAAAT
30625 TTTAAATAAAATATCAATTT-ATCACGTAAAT
1 TTTAAATAAAATATCAATTTAATC-CGTAAAT
30656 T
1 T
30657 CAATCAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 3 0.11
31 24 0.89
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.44
Consensus pattern (31 bp):
TTTAAATAAAATATCAATTTAATCCGTAAAT
Found at i:40526 original size:15 final size:15
Alignment explanation
Indices: 40506--40535 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40496 AACTTCATAC
40506 CATCTTCTAGACGCA
1 CATCTTCTAGACGCA
*
40521 CATCTTCTGGACGCA
1 CATCTTCTAGACGCA
40536 GACTATGACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.33, G:0.17, T:0.27
Consensus pattern (15 bp):
CATCTTCTAGACGCA
Found at i:48387 original size:20 final size:20
Alignment explanation
Indices: 48364--48415 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
48354 AACGCGATCC
48364 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
48384 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
48404 CCAAAATCGCAA
1 CCAGAATCGCAA
48416 CGCGATTCTT
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:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:48432 original size:21 final size:20
Alignment explanation
Indices: 48406--48503 Score: 65
Period size: 21 Copynumber: 4.8 Consensus size: 20
48396 ATCAGTTTCC
48406 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* * **
48427 AAAATCGCGATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
**
48446 ACAAATTCGCATTGCGATTTT-
1 A-AAA-TCGCAACGCGATTTTG
* *
48467 ACATAATCGCAACGCGAATATG
1 A-A-AATCGCAACGCGATTTTG
48489 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
48504 ACACATAAAT
Statistics
Matches: 61, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
19 1 0.02
20 17 0.28
21 40 0.66
22 3 0.05
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:48565 original size:20 final size:20
Alignment explanation
Indices: 48471--48819 Score: 418
Period size: 20 Copynumber: 17.4 Consensus size: 20
48461 GATTTTACAT
* ** *
48471 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
48491 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
48511 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
48531 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
48551 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
48571 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
48591 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
48611 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
48631 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
48651 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
48671 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
48691 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
48711 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
48731 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
48751 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
48771 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
48791 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
48811 AATCACAAC
1 AATCGCAAC
48820 ACTGAAATTT
Statistics
Matches: 285, Mismatches: 36, Indels: 16
0.85 0.11 0.05
Matches are distributed among these distances:
19 3 0.01
20 279 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:49544 original size:24 final size:24
Alignment explanation
Indices: 49500--49546 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
49490 AAATTTGGTC
*
49500 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCAGACTTTGATA
*
49524 TTGGTCAATA-CACAGATTTTGAT
1 TTGGTCAATATC-CAGACTTTGAT
49547 GATGTTTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCAGACTTTGATA
Found at i:49738 original size:12 final size:12
Alignment explanation
Indices: 49721--49745 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49711 ATATAATCCT
49721 GAAGAAGAAAAA
1 GAAGAAGAAAAA
49733 GAAGAAGAAAAA
1 GAAGAAGAAAAA
49745 G
1 G
49746 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:52037 original size:19 final size:19
Alignment explanation
Indices: 52015--52337 Score: 378
Period size: 19 Copynumber: 18.4 Consensus size: 19
52005 CGGAAAATAC
*
52015 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
52034 AATCCCAA--C---ATG-A
1 AATCGCAATGCGAAATGAA
52047 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
52067 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
52081 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
52100 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
52119 AATCGCAA--CG--A-G-A
1 AATCGCAATGCGAAATGAA
* *
52132 GATCGCAATGCGAAATAAA
1 AATCGCAATGCGAAATGAA
52151 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
52170 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
*
52188 AATCGCAA--CGACAT---
1 AATCGCAATGCGAAATGAA
*
52202 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
52221 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
52240 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
52259 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
52278 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
52292 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
52311 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
52330 AATCGCAA
1 AATCGCAA
52338 CGAGATAATC
Statistics
Matches: 265, Mismatches: 11, Indels: 56
0.80 0.03 0.17
Matches are distributed among these distances:
13 16 0.06
14 30 0.11
15 5 0.02
16 18 0.07
17 11 0.04
18 11 0.04
19 165 0.62
20 9 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:52169 original size:70 final size:71
Alignment explanation
Indices: 52081--52359 Score: 424
Period size: 70 Copynumber: 4.0 Consensus size: 71
52071 GCAACGAGAG
*
52081 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA-GATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGA
52145 AATAAA
66 AATAAA
*
52151 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATG-AAATCGCAACGACATAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGA
*
52215 AATTAA
66 AATAAA
* * *
52221 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCG-CAATGCG
**
52283 CAACGAAA
65 -AAATAAA
52291 GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCG
1 -AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCG
52356 AAAT
65 AAAT
52360 TATAAACGCA
Statistics
Matches: 186, Mismatches: 15, Indels: 14
0.87 0.07 0.07
Matches are distributed among these distances:
69 16 0.09
70 99 0.53
71 60 0.32
72 8 0.04
73 3 0.02
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGA
AATAAA
Found at i:52375 original size:52 final size:52
Alignment explanation
Indices: 52046--52359 Score: 438
Period size: 52 Copynumber: 6.0 Consensus size: 52
52036 TCCCAACATG
52046 AAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
1 AAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
*
52099 AAATCGCAATGCGAAATGAAAATCGCAACGAGAG-ATCGCAATGCGAAATAA
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
* * * * *
52150 AAATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAT-CGCAACGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
* *
52199 CATAATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGA
1 -A-AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGA
*
52258 AAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
*
52310 AAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
52360 TATAAACGCA
Statistics
Matches: 232, Mismatches: 18, Indels: 23
0.85 0.07 0.08
Matches are distributed among these distances:
49 5 0.02
50 5 0.02
51 75 0.32
52 89 0.38
53 14 0.06
55 2 0.01
56 2 0.01
57 29 0.12
58 5 0.02
59 6 0.03
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (52 bp):
AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
Found at i:52456 original size:19 final size:19
Alignment explanation
Indices: 52366--52448 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
52356 AAATTATAAA
52366 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
*
52385 CCGCATTGCGA--TTC-TCT
1 -CGCATTGCGATTTTCATTT
52402 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
52419 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
52438 CGCATTGCGAT
1 CGCATTGCGAT
52449 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 5 0.09
17 6 0.11
18 3 0.05
19 26 0.46
20 10 0.18
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:52580 original size:14 final size:14
Alignment explanation
Indices: 52551--52590 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
52541 TTCGCATCAA
52551 TTACACAATCAACTT
1 TTACA-AATCAACTT
*
52566 TTACAAATCATCTT
1 TTACAAATCAACTT
52580 TTACAAATCAA
1 TTACAAATCAA
52591 TTAAACAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (14 bp):
TTACAAATCAACTT
Found at i:54526 original size:20 final size:19
Alignment explanation
Indices: 54501--54546 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
54491 TAGTTTACTT
*
54501 TCGCAACACAAAACTTAAAA
1 TCGCAACACAAAAC-CAAAA
* *
54521 TCGCAACGCGAAACCAAAA
1 TCGCAACACAAAACCAAAA
54540 TCGCAAC
1 TCGCAAC
54547 GCGAATGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.48, C:0.30, G:0.11, T:0.11
Consensus pattern (19 bp):
TCGCAACACAAAACCAAAA
Found at i:54541 original size:19 final size:18
Alignment explanation
Indices: 54517--54634 Score: 99
Period size: 19 Copynumber: 6.8 Consensus size: 18
54507 CACAAAACTT
54517 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAA-C
**
54536 AAAATCGCAACGCGAATG
1 AAAATCGCAACGCGAAAC
54554 AAAATCGCAA--CG--AC
1 AAAATCGCAACGCGAAAC
*
54568 AGAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAA-C
54587 AAAATCGCAA--CG-AA-
1 AAAATCGCAACGCGAAAC
* *
54601 AGAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAA-C
*
54620 AAAATCGCAATGCGA
1 AAAATCGCAACGCGA
54635 TTTTGGTTTT
Statistics
Matches: 80, Mismatches: 9, Indels: 20
0.73 0.08 0.18
Matches are distributed among these distances:
14 18 0.22
16 8 0.10
17 4 0.05
18 11 0.14
19 39 0.49
ACGTcount: A:0.47, C:0.25, G:0.19, T:0.08
Consensus pattern (18 bp):
AAAATCGCAACGCGAAAC
Found at i:54575 original size:14 final size:14
Alignment explanation
Indices: 54556--54612 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
54546 CGCGAATGAA
54556 AATCGCAACGACAG
1 AATCGCAACGACAG
*
54570 AATCGCAACGCGAAACCAA
1 AATCGCAA--CG--A-CAG
*
54589 AATCGCAACGAAAG
1 AATCGCAACGACAG
54603 AATCGCAACG
1 AATCGCAACG
54613 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.28, G:0.19, T:0.07
Consensus pattern (14 bp):
AATCGCAACGACAG
Found at i:54596 original size:33 final size:33
Alignment explanation
Indices: 54538--54629 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
54528 GCGAAACCAA
*
54538 AATCGCAACGCG-AATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
**
54570 AATCGCAACGCGAAACCAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
54603 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
54630 TGCGATTTTG
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 12 0.22
33 42 0.78
ACGTcount: A:0.47, C:0.25, G:0.20, T:0.09
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:54666 original size:14 final size:13
Alignment explanation
Indices: 54647--54703 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 13
54637 TTGGTTTTCG
54647 CGTTGCGATCTTGT
1 CGTTGCGAT-TTGT
54661 CGTTGCGATTTTGTTT
1 CGTTGCGA-TTTG--T
54677 CGCGTTGCGATTCTGT
1 --CGTTGCGATT-TGT
54693 CGTTGCGATTT
1 CGTTGCGATTT
54704 TCATTTCGCG
Statistics
Matches: 37, Mismatches: 0, Indels: 13
0.74 0.00 0.26
Matches are distributed among these distances:
13 1 0.03
14 21 0.57
15 1 0.03
16 2 0.05
17 2 0.05
18 10 0.27
ACGTcount: A:0.07, C:0.19, G:0.28, T:0.46
Consensus pattern (13 bp):
CGTTGCGATTTGT
Found at i:54683 original size:32 final size:33
Alignment explanation
Indices: 54630--54721 Score: 134
Period size: 32 Copynumber: 2.8 Consensus size: 33
54620 AAAATCGCAA
*
54630 TGCGATTTTGGTTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTCG-TTTCGCGTTGCGATTC-TGTCGT
54664 TGCGATTTT-GTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTCGTTTCGCGTTGCGATTCTGTCGT
*
54696 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTCGTTTCGCGTTGCGATT
54722 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
32 28 0.51
33 18 0.33
34 9 0.16
ACGTcount: A:0.08, C:0.18, G:0.27, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCGTTTCGCGTTGCGATTCTGTCGT
Found at i:54750 original size:20 final size:19
Alignment explanation
Indices: 54661--54758 Score: 102
Period size: 19 Copynumber: 5.4 Consensus size: 19
54651 GCGATCTTGT
54661 CGTTGCGATTTT-GTTTCG
1 CGTTGCGATTTTAGTTTCG
*
54679 CGTTGCGATTCT-G--T--
1 CGTTGCGATTTTAGTTTCG
54693 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTT-AGTTTCG
*
54712 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAGTTTCG
54731 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT-AGTTTCG
*
54751 TGTTGCGA
1 CGTTGCGA
54759 AAGTAAACTA
Statistics
Matches: 67, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
14 11 0.16
16 1 0.01
17 1 0.01
18 12 0.18
19 29 0.43
20 13 0.19
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTAGTTTCG
Found at i:55122 original size:182 final size:185
Alignment explanation
Indices: 54802--55544 Score: 1403
Period size: 182 Copynumber: 4.0 Consensus size: 185
54792 TTGAATGGAT
54802 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
54867 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
54931 TACTATTTCACA-G-TAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
54984 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
55049 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
55114 TA-TATTTCACA-GTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
55167 AAATTTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
55231 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
55295 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAG-GTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
55351 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
55415 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
55480 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TACTATTTCACAG-GTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
55536 AAATTTACT
1 AAATTTACT
55545 AAGCAATCTA
Statistics
Matches: 553, Mismatches: 1, Indels: 11
0.98 0.00 0.02
Matches are distributed among these distances:
181 4 0.01
182 245 0.44
183 71 0.13
184 145 0.26
185 88 0.16
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:55297 original size:92 final size:93
Alignment explanation
Indices: 54802--55544 Score: 1407
Period size: 92 Copynumber: 8.1 Consensus size: 93
54792 TTGAATGGAT
54802 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
54867 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
54895 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACA--G-TAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
54956 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
54984 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
55049 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
55077 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACA--GTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
55139 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
55167 AAATTTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
55231 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
55259 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
55323 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
55351 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
55415 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
55443 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
55508 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
55536 AAATTTACT
1 AAATTTACT
55545 AAGCAATCTA
Statistics
Matches: 639, Mismatches: 1, Indels: 20
0.97 0.00 0.03
Matches are distributed among these distances:
89 85 0.13
90 93 0.15
92 277 0.43
93 184 0.29
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:57267 original size:14 final size:14
Alignment explanation
Indices: 57248--57337 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
57238 TTGAAATGAA
57248 AATCGCAACGAGAG
1 AATCGCAACGAGAG
57262 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
57279 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
57295 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
57314 AATCGCAACGAGAG
1 AATCGCAACGAGAG
57328 AATCGCAACG
1 AATCGCAACG
57338 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:57285 original size:33 final size:33
Alignment explanation
Indices: 57240--57354 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
57230 TCTTTTGGTT
57240 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
57273 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
57306 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
57339 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
57355 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:57286 original size:19 final size:18
Alignment explanation
Indices: 57247--57359 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
57237 GTTGAAATGA
57247 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
57262 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
57279 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
57295 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
57312 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
57328 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
57345 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
57360 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:57390 original size:14 final size:14
Alignment explanation
Indices: 57371--57425 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
57361 TTTGGTTTCG
57371 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
57385 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
57404 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
57418 CGTTGCGA
1 CGTTGCGA
57426 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:57403 original size:33 final size:33
Alignment explanation
Indices: 57355--57425 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
57345 AAAATCGCAA
**
57355 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
57388 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
57421 TGCGA
1 TGCGA
57426 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:57433 original size:33 final size:33
Alignment explanation
Indices: 57366--57447 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
57356 GCGATTTTGG
***
57366 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
57399 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
57432 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
57448 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:57452 original size:20 final size:20
Alignment explanation
Indices: 57378--57466 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
57368 TCGCGTTGCG
57378 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
57398 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
57411 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
57431 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
57451 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
57467 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:57588 original size:33 final size:33
Alignment explanation
Indices: 57546--57616 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
57536 AATACTAACT
*
57546 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
57579 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
57612 TGAAA
1 TGAAA
57617 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:57848 original size:22 final size:21
Alignment explanation
Indices: 57797--57850 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
57787 TGGTTGTGAG
**
57797 GGATTTCGCCGGAGATGGGAC
1 GGATTTCTTCGGAGATGGGAC
**
57818 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGAT-GGGAC
57840 GGATTTCTTCG
1 GGATTTCTTCG
57851 CCGTAGAGAG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.20, C:0.17, G:0.39, T:0.24
Consensus pattern (21 bp):
GGATTTCTTCGGAGATGGGAC
Found at i:58021 original size:20 final size:20
Alignment explanation
Indices: 57996--58188 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
57986 CTTTAAATAT
57996 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
58016 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
58038 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
58057 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
58077 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
58097 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
58117 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
58137 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
58157 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
58177 CGCGTTGCGATT
1 CGCGTTGCGATT
58189 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:58183 original size:60 final size:60
Alignment explanation
Indices: 57996--58188 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
57986 CTTTAAATAT
**
57996 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
58057 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
58117 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
58177 CGCGTTGCGATT
1 CGCGTTGCGATT
58189 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:58269 original size:20 final size:20
Alignment explanation
Indices: 58244--58295 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
58234 AAGAATCGCG
*
58244 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
58264 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
58284 TTGCGATTCTGG
1 TTGCGATTCTGG
58296 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:60257 original size:53 final size:53
Alignment explanation
Indices: 60200--60304 Score: 165
Period size: 53 Copynumber: 2.0 Consensus size: 53
60190 GGTGGTCCTC
* *
60200 CATTTCTGCACTTTTTTTATTCTTATTTGTACACTTATATTAAATTATGTCCA
1 CATTTCTGCACATTTTTTATGCTTATTTGTACACTTATATTAAATTATGTCCA
* * *
60253 CATTTCTGCTCATTTTTTATGCTTATTTGTACACTTTTATTAAATTCTGTCC
1 CATTTCTGCACATTTTTTATGCTTATTTGTACACTTATATTAAATTATGTCC
60305 GGATCCCATT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.22, C:0.18, G:0.07, T:0.53
Consensus pattern (53 bp):
CATTTCTGCACATTTTTTATGCTTATTTGTACACTTATATTAAATTATGTCCA
Found at i:61331 original size:27 final size:26
Alignment explanation
Indices: 61282--61332 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
61272 TTTTATCCCA
*
61282 TAAAATTTAATAAGTTATTTCCTACT
1 TAAAATTTAATAAGTTATCTCCTACT
* *
61308 TAAAATTTTATAAGGTTGTCTCCTA
1 TAAAATTTAATAA-GTTATCTCCTA
61333 ACATAAAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (26 bp):
TAAAATTTAATAAGTTATCTCCTACT
Found at i:63808 original size:16 final size:16
Alignment explanation
Indices: 63784--63825 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
63774 GATAAATGAA
63784 TTTAACAAGTAACGAG
1 TTTAACAAGTAACGAG
* *
63800 TTTACCAAGCAACGAG
1 TTTAACAAGTAACGAG
*
63816 CTTAACAAGT
1 TTTAACAAGT
63826 CGAGTCAAGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (16 bp):
TTTAACAAGTAACGAG
Found at i:66282 original size:60 final size:60
Alignment explanation
Indices: 66151--66289 Score: 145
Period size: 60 Copynumber: 2.3 Consensus size: 60
66141 CTAATATTTT
* ** * * * *
66151 GGTAAGAAATTGAAACGTTCAAAAGTTTAAGGACTAATTTAGAATAAGTGTCATAGTTTG
1 GGTATGAAATTGAAATATTTAAAAGTTTAAGGACTAATTCAAAATAAGGGTCATAGTTTG
* * * * * *
66211 GGTATGTAATTGGAATATTTAAAAGTTTGAGGATTAATTCAAAATGAGGGTCATAGTTTAT
1 GGTATGAAATTGAAATATTTAAAAGTTTAAGGACTAATTCAAAATAAGGGTCATAGTTT-G
66272 GG-ATGAAATTGAAATATT
1 GGTATGAAATTGAAATATT
66290 CAAATATTTA
Statistics
Matches: 63, Mismatches: 15, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
60 61 0.97
61 2 0.03
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (60 bp):
GGTATGAAATTGAAATATTTAAAAGTTTAAGGACTAATTCAAAATAAGGGTCATAGTTTG
Found at i:82062 original size:40 final size:40
Alignment explanation
Indices: 81973--82109 Score: 124
Period size: 40 Copynumber: 3.4 Consensus size: 40
81963 AAATGACCAA
* * *
81973 CAAATTCGCAACGCG-AACTCCAATTTCGCAAC-A-CAAGTT
1 CAAATTCGCAACGCGAAAGT-CAAATTCGCAACGATAAAG-T
*
82012 CCAAAATCGCAACGCGAAAGTCAAATTCGCAACGATAAAGT
1 -CAAATTCGCAACGCGAAAGTCAAATTCGCAACGATAAAGT
* *
82053 CAAATTCGCAACGTGAATAGTTAAA-TCGCAACGATAATATGT
1 CAAATTCGCAACGCGAA-AGTCAAATTCGCAACGATAA-A-GT
82095 -AAA-TCGCAACGCGAA
1 CAAATTCGCAACGCGAA
82110 TTTCATTTTC
Statistics
Matches: 83, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
40 63 0.76
41 15 0.18
42 5 0.06
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (40 bp):
CAAATTCGCAACGCGAAAGTCAAATTCGCAACGATAAAGT
Found at i:82091 original size:20 final size:19
Alignment explanation
Indices: 82015--82105 Score: 87
Period size: 20 Copynumber: 4.6 Consensus size: 19
82005 ACAAGTTCCA
**
82015 AAATCGCAACGCGAAAGTC
1 AAATCGCAACGATAAAGTC
82034 AAATTCGCAACGATAAAGTC
1 AAA-TCGCAACGATAAAGTC
*
82054 AAATTCGCAACG-TGAATAGTT
1 AAA-TCGCAACGAT-AA-AGTC
82075 AAATCGCAACGATAATATGT-
1 AAATCGCAACGATAA-A-GTC
82095 AAATCGCAACG
1 AAATCGCAACG
82106 CGAATTTCAT
Statistics
Matches: 64, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.06
20 51 0.80
21 9 0.14
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.20
Consensus pattern (19 bp):
AAATCGCAACGATAAAGTC
Found at i:82170 original size:16 final size:16
Alignment explanation
Indices: 82151--82183 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
82141 TAATTACCTA
*
82151 TATAGGTAATTAGCGT
1 TATAAGTAATTAGCGT
82167 TATAAGTAATTAGCGT
1 TATAAGTAATTAGCGT
82183 T
1 T
82184 GCGAATTACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.39
Consensus pattern (16 bp):
TATAAGTAATTAGCGT
Found at i:82301 original size:20 final size:21
Alignment explanation
Indices: 82276--82327 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
82266 ACGATTTTCT
82276 AAATTCGCAACGC-AAAAGTC
1 AAATTCGCAACGCGAAAAGTC
* *
82296 AAATTCGCAACGCGAATAGTT
1 AAATTCGCAACGCGAAAAGTC
82317 AAA-TCGCAACG
1 AAATTCGCAACG
82328 ATAATATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 21 0.72
21 8 0.28
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.17
Consensus pattern (21 bp):
AAATTCGCAACGCGAAAAGTC
Found at i:82333 original size:20 final size:20
Alignment explanation
Indices: 82300--82392 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
82290 AAAGTCAAAT
*
82300 TCGCAACGCGAATA-GTTAAA
1 TCGCAACGAGAATATG-TAAA
* *
82320 TCGCAACGATAATATGTAAT
1 TCGCAACGAGAATATGTAAA
* * * *
82340 TCTCAATGCGAATAGGTAAA
1 TCGCAACGAGAATATGTAAA
*
82360 TCGCAACGATAATATGTAAA
1 TCGCAACGAGAATATGTAAA
*
82380 TCGCAACGCGAAT
1 TCGCAACGAGAAT
82393 TCTCCAAATT
Statistics
Matches: 56, Mismatches: 16, Indels: 2
0.76 0.22 0.03
Matches are distributed among these distances:
20 55 0.98
21 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (20 bp):
TCGCAACGAGAATATGTAAA
Found at i:82341 original size:40 final size:40
Alignment explanation
Indices: 82297--82392 Score: 156
Period size: 40 Copynumber: 2.4 Consensus size: 40
82287 GCAAAAGTCA
*
82297 AATTCGCAACGCGAATAGTTAAATCGCAACGATAATATGT
1 AATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGT
* *
82337 AATTCTCAATGCGAATAGGTAAATCGCAACGATAATATGT
1 AATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGT
*
82377 AAATCGCAACGCGAAT
1 AATTCGCAACGCGAAT
82393 TCTCCAAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (40 bp):
AATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGT
Found at i:86446 original size:23 final size:23
Alignment explanation
Indices: 86420--86467 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
86410 TATTTGTTTG
86420 TTAAGAT-CATTTAATAAATTTAA
1 TTAAGATCCATTTAA-AAATTTAA
*
86443 TTAATATCCATTTAAAAATTTAA
1 TTAAGATCCATTTAAAAATTTAA
86466 TT
1 TT
86468 GAATCGACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (23 bp):
TTAAGATCCATTTAAAAATTTAA
Found at i:89236 original size:15 final size:15
Alignment explanation
Indices: 89216--89315 Score: 55
Period size: 15 Copynumber: 6.9 Consensus size: 15
89206 GAGCGGTGAA
89216 GAGGATGATGAAGAT
1 GAGGATGATGAAGAT
*
89231 GAGGATGATG-ACA-
1 GAGGATGATGAAGAT
*
89244 G-GGATGA-CAATGAT
1 GAGGATGATGAA-GAT
* * * *
89258 GATGATGACGAGGAG
1 GAGGATGATGAAGAT
* * *
89273 GAGGATGAAGTAGAG
1 GAGGATGATGAAGAT
* * *
89288 GAGAACGAAGAAGAT
1 GAGGATGATGAAGAT
89303 GAGGATGATGAAG
1 GAGGATGATGAAG
89316 TTCCTCAGCC
Statistics
Matches: 62, Mismatches: 18, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
12 7 0.11
13 2 0.03
14 3 0.05
15 49 0.79
16 1 0.02
ACGTcount: A:0.40, C:0.04, G:0.41, T:0.15
Consensus pattern (15 bp):
GAGGATGATGAAGAT
Found at i:98131 original size:37 final size:36
Alignment explanation
Indices: 98071--98144 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 36
98061 GTTGAAAAAT
*
98071 ATTTATAAATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATAAATTTTCTTTAAAAAAATTAAAAT-ATAAA
*
98108 ATTTATATAATTTT-TTTACAAAAATTAAAATATAAA
1 ATTTATA-AATTTTCTTTAAAAAAATTAAAATATAAA
98144 A
1 A
98145 AGGTTTGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 6 0.18
37 22 0.65
38 6 0.18
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (36 bp):
ATTTATAAATTTTCTTTAAAAAAATTAAAATATAAA
Found at i:100619 original size:22 final size:22
Alignment explanation
Indices: 100576--100620 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
100566 TAAATTATCA
*
100576 TTTTATTTTAATATTTATTTTT
1 TTTTATTTTAATATCTATTTTT
* *
100598 TTTTTTTTTAAT-TCTATGTTT
1 TTTTATTTTAATATCTATTTTT
100619 TT
1 TT
100621 ATCAAACAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTTATTTTAATATCTATTTTT
Done.