Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009251.1 Hibiscus syriacus cultivar Beakdansim tig00112894_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: 52425
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:5948 original size:13 final size:13
Alignment explanation
Indices: 5930--5957 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5920 CAGCATCCCC
5930 ATACTCAAGCGAG
1 ATACTCAAGCGAG
5943 ATACTCAAGCGAG
1 ATACTCAAGCGAG
5956 AT
1 AT
5958 CCAAGCAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (13 bp):
ATACTCAAGCGAG
Found at i:7941 original size:18 final size:18
Alignment explanation
Indices: 7918--7967 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
7908 ATGCGCTTAT
7918 TTTTCAAAATCAAAACAG
1 TTTTCAAAATCAAAACAG
7936 TTTTCAAAATCAAAACAG
1 TTTTCAAAATCAAAACAG
7954 TTTTCAAAATCAAA
1 TTTTCAAAATCAAA
7968 GATTGACTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.50, C:0.16, G:0.04, T:0.30
Consensus pattern (18 bp):
TTTTCAAAATCAAAACAG
Found at i:10013 original size:21 final size:21
Alignment explanation
Indices: 9987--10026 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
9977 TCTAGATTGC
*
9987 ATGGCGACTTTTGGGGACTGT
1 ATGGCGACCTTTGGGGACTGT
10008 ATGGCGACCTTTGGGGACT
1 ATGGCGACCTTTGGGGACT
10027 ACATGACGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.17, G:0.38, T:0.30
Consensus pattern (21 bp):
ATGGCGACCTTTGGGGACTGT
Found at i:10036 original size:21 final size:21
Alignment explanation
Indices: 9986--10038 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
9976 TTCTAGATTG
* *
9986 CATGGCGACTTTTGGGGACTG
1 CATGGCGACCTTTGGGGACTA
*
10007 TATGGCGACCTTTGGGGACTA
1 CATGGCGACCTTTGGGGACTA
*
10028 CATGACGACCT
1 CATGGCGACCT
10039 GGTAGGTCGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.19, C:0.23, G:0.32, T:0.26
Consensus pattern (21 bp):
CATGGCGACCTTTGGGGACTA
Found at i:14124 original size:3 final size:3
Alignment explanation
Indices: 14116--14142 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
14106 AAAAATGTAA
14116 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
14143 GGGTTGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:18148 original size:2 final size:2
Alignment explanation
Indices: 18141--18187 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
18131 ACGTTTGCAA
18141 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
18183 AT AT A
1 AT AT A
18188 AGTTGTAAAG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18734 original size:12 final size:12
Alignment explanation
Indices: 18717--18741 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18707 CCTCAACGGC
18717 CCTACCTGCCTG
1 CCTACCTGCCTG
18729 CCTACCTGCCTG
1 CCTACCTGCCTG
18741 C
1 C
18742 TTTTCCACAC
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:0.08, C:0.52, G:0.16, T:0.24
Consensus pattern (12 bp):
CCTACCTGCCTG
Found at i:19825 original size:20 final size:20
Alignment explanation
Indices: 19789--19826 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
19779 ATCCTATTCC
**
19789 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
19809 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
19827 GTGAACTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:20483 original size:16 final size:17
Alignment explanation
Indices: 20462--20495 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
20452 TTACTATTCA
20462 CGTGAATAGT-AAATTT
1 CGTGAATAGTGAAATTT
20478 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
20495 C
1 C
20496 AGTCGGCGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:25026 original size:20 final size:20
Alignment explanation
Indices: 24990--25027 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
24980 ATCCTATTCC
**
24990 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
25010 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
25028 GTGAACTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:26461 original size:21 final size:21
Alignment explanation
Indices: 26437--26532 Score: 97
Period size: 20 Copynumber: 4.7 Consensus size: 21
26427 CGATTTTCCC
*
26437 AATTCGCAATGCGAATAAGTA
1 AATTCGCAATGCGAATAAGGA
* **
26458 AATT-GCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGGA
*
26478 AATTCGCAATGCGAATAAGTA
1 AATTCGCAATGCGAATAAGGA
* **
26499 AA-TCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGGA
*
26519 AAATCGCAATGCGA
1 AATTCGCAATGCGA
26533 TACTGACTAT
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
20 32 0.53
21 28 0.47
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.20
Consensus pattern (21 bp):
AATTCGCAATGCGAATAAGGA
Found at i:26482 original size:41 final size:41
Alignment explanation
Indices: 26437--26532 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
26427 CGATTTTCCC
*
26437 AATTCGCAATGCGAATAAGTAAATTGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
26478 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
26519 AAATCGCAATGCGA
1 AATTCGCAATGCGA
26533 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.20
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:26545 original size:41 final size:41
Alignment explanation
Indices: 26462--26594 Score: 117
Period size: 41 Copynumber: 3.2 Consensus size: 41
26452 TAAGTAAATT
* * *
26462 GCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-AATC
1 GCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACTATC
26503 GCAACGCGAATTGGGAAAATCGCAATGCGATACTGACTATC
1 GCAACGCGAATTGGGAAAATCGCAATGCGATACTGACTATC
* * *** * * * *
26544 GCAATGCGATAATAAAAAAATCGCAACGAGATACTTACTTTC
1 GCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACTATC
26586 GCAACGCGA
1 GCAACGCGA
26595 TACTGACTTT
Statistics
Matches: 76, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
40 4 0.05
41 40 0.53
42 32 0.42
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (41 bp):
GCAACGCGAATTGGGAAAATCGCAATGCGATACTGACTATC
Found at i:26546 original size:20 final size:20
Alignment explanation
Indices: 26521--26615 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
26511 AATTGGGAAA
*
26521 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
26541 ATCGCAATGCGATAATAAAAAA
1 ATCGCAACGCGATACT--GACT
* *
26563 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
26583 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
26603 TTCGCAACGCGAT
1 ATCGCAACGCGAT
26616 TTACTTAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
20 46 0.77
22 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:27173 original size:19 final size:19
Alignment explanation
Indices: 27135--27201 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
27125 TTCGAGAATG
*
27135 AAAATCGCAAAGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
27155 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
27174 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
27193 AAAATCGCA
1 AAAATCGCA
27202 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 30 0.75
20 10 0.25
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:27219 original size:19 final size:19
Alignment explanation
Indices: 27197--27380 Score: 172
Period size: 19 Copynumber: 10.1 Consensus size: 19
27187 GAAACCAAAA
*
27197 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
27216 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
27235 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
27254 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
27273 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
27287 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
27306 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
27320 TCTCATTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
27339 TCCGCGTTGCAATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
27359 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
27379 TC
1 TC
27381 AACCAAAAGA
Statistics
Matches: 135, Mismatches: 18, Indels: 24
0.76 0.10 0.14
Matches are distributed among these distances:
14 18 0.13
16 4 0.03
17 5 0.04
19 79 0.59
20 28 0.21
21 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:27305 original size:33 final size:33
Alignment explanation
Indices: 27268--27355 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
27258 GTTGCGATTT
*
27268 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
*
27301 TCATTTCGCGTTGCGATTCTCTCATTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
*
27334 TCATTTCCGCGTTGCAATTCTC
1 TCATTT-CGCGTTGCGATTCTC
27356 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 37 0.73
34 14 0.27
ACGTcount: A:0.14, C:0.27, G:0.20, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
Found at i:27357 original size:20 final size:20
Alignment explanation
Indices: 27334--27380 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
27324 ATTGCGATAG
27334 TCATTTCCGCGTTGCAATTC
1 TCATTTCCGCGTTGCAATTC
* * *
27354 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCAATTC
27374 TCATTTC
1 TCATTTC
27381 AACCAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.15, C:0.26, G:0.13, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCAATTC
Found at i:29418 original size:42 final size:42
Alignment explanation
Indices: 29358--29480 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
29348 GCCCGACTCG
* * *
29358 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
29400 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
29442 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
29481 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:29438 original size:21 final size:21
Alignment explanation
Indices: 29414--29480 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
29404 TCATTCCTCG
29414 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
29435 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
29456 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
29477 AGAG
1 AGAG
29481 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:30855 original size:14 final size:14
Alignment explanation
Indices: 30836--30871 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
30826 ATTGTTTAAT
30836 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
30850 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
30864 TGATTTGT
1 TGATTTGT
30872 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:31071 original size:19 final size:19
Alignment explanation
Indices: 31049--31166 Score: 67
Period size: 19 Copynumber: 6.7 Consensus size: 19
31039 CGAAATTAAA
31049 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
31068 TTCGCATTGCG--GTTC--
1 TTCGCGTTGCGATTTTCAT
* *
31083 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
31101 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
31116 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
31134 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
31153 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
31167 GGACATTAAG
Statistics
Matches: 71, Mismatches: 17, Indels: 21
0.65 0.16 0.19
Matches are distributed among these distances:
14 16 0.23
16 6 0.08
17 6 0.08
19 33 0.46
20 10 0.14
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:31095 original size:33 final size:33
Alignment explanation
Indices: 31053--31146 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
31043 ATTAAATTCG
*
31053 CGTTGCGATTTTCATTTCGCATTGCGGTTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
31086 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
31119 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
31147 AGTAATTTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:35540 original size:14 final size:14
Alignment explanation
Indices: 35521--35555 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
35511 TCAATTAAAT
35521 AAATCAACATTTAC
1 AAATCAACATTTAC
* *
35535 AAATCATCTTTTAC
1 AAATCAACATTTAC
35549 AAATCAA
1 AAATCAA
35556 TTAAACAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATCAACATTTAC
Found at i:35737 original size:589 final size:587
Alignment explanation
Indices: 34560--35956 Score: 2685
Period size: 589 Copynumber: 2.4 Consensus size: 587
34550 TTTAACAATT
*
34560 ATTATTGAATTCTAGGTACTTAACCAAATATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
34625 CTTGCATTATGTGTATTTTATGTGTGCACTTTT----TTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
34686 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
*
34751 AATGCGAAAATGGTTATCGCAACGAGAAAATCGCAATGCGAAACGAAAATCGCATTGCGATTTTC
196 AATGCGAAAATGGTTATCGCAACGAG-AAATCGCAAAGCGAAACGAAAATCGCATTGCGATTTTC
34816 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
260 TCGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAA
*
34881 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAACAATCAACATTTA
325 TCAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAAAAATCAACATTTA
34946 CAAATCATCTTTTACAAATCAATTAAACAATCAAAAATAATAATAATTCTTATTTCTTCATCAAT
390 CAAATCATCTTTTACAAATCAATTAAACAATCAAAAATAATAATAATTCTTATTTCTTCATCAAT
35011 TATTGAATCAATGAATCAACAACTTTGAGACCCCGTACATCCATTTCACACAGCTCACTTAAGGA
455 TATTGAATCAATGAATCAACAACTTTGAGACCCCGTACATCCATTTCACACAGCTCACTTAAGGA
35076 TTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAG
520 TTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAG
35141 CAA
585 CAA
35144 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
*
35209 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
35274 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
35339 AATGCGAAAATGGTTATCGCAACGAGAAATCGCAAAGCGAAACGAAAATCGCATTGCGATTTTCT
196 AATGCGAAAATGGTTATCGCAACGAGAAATCGCAAAGCGAAACGAAAATCGCATTGCGATTTTCT
35404 CGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAAT
261 CGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAAT
35469 CAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAATAAATCAACATTTA
326 CAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAA-AAATCAACATTTA
35534 CAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAATAATAATTCTTATTTCTTCATCAA
390 CAAATCATCTTTTACAAATCAATTAAACAATC-AAAAATAATAATAATTCTTATTTCTTCATCAA
*
35599 TTATTGAATCAATGAATCAACAACTTTGTGACCCCGTACATCCATTTCACACAGCTCACTTAAGG
454 TTATTGAATCAATGAATCAACAACTTTGAGACCCCGTACATCCATTTCACACAGCTCACTTAAGG
35664 ATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
519 ATTAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACA
35729 GCAA
584 GCAA
35733 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
1 ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
35798 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
66 CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
35863 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
131 GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
*
35928 AATGCGAAAATGGTTATCGCAACGCGAAA
196 AATGCGAAAATGGTTATCGCAACGAGAAA
35957 ATGGTTATCG
Statistics
Matches: 800, Mismatches: 7, Indels: 7
0.98 0.01 0.01
Matches are distributed among these distances:
584 97 0.12
587 154 0.19
588 162 0.20
589 387 0.48
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (587 bp):
ATTATTGAATTCTAGGTACTTAACCAAACATTTTCAAACCAAAAGGAGTATATATGTTAACAAAA
CTTGCATTATGTGTATTTTATGTGTGCACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTT
GAGTTTGAACATTGCTATGATCTGTTCAGTTGTCATCACTTATTAGACATTCATTTGACTATCGC
AATGCGAAAATGGTTATCGCAACGAGAAATCGCAAAGCGAAACGAAAATCGCATTGCGATTTTCT
CGTTGCGATAGCCATTTCGCGTTGCGATAGTCTGTTTTGCCTTCAACATAAAGCAGATTGAAAAT
CAACAAATCAACTATTACATTTCAACACAAATTATGTACACATCAATTAAAAAATCAACATTTAC
AAATCATCTTTTACAAATCAATTAAACAATCAAAAATAATAATAATTCTTATTTCTTCATCAATT
ATTGAATCAATGAATCAACAACTTTGAGACCCCGTACATCCATTTCACACAGCTCACTTAAGGAT
TAACCTGCAGAAACCAAACATTTGCTCAAACAAGACTTCCTACACATCTAAAACCTACAAACAGC
AA
Found at i:35947 original size:20 final size:20
Alignment explanation
Indices: 35922--35998 Score: 136
Period size: 20 Copynumber: 3.9 Consensus size: 20
35912 TTCATTTGAC
*
35922 TATCGCAATGCGAAAATGGT
1 TATCGCAACGCGAAAATGGT
35942 TATCGCAACGCGAAAATGGT
1 TATCGCAACGCGAAAATGGT
35962 TATCGCAACGCGAAAATGGT
1 TATCGCAACGCGAAAATGGT
*
35982 TATCGCAACGAGAAAAT
1 TATCGCAACGCGAAAAT
35999 CGCAATGCGA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (20 bp):
TATCGCAACGCGAAAATGGT
Found at i:36058 original size:19 final size:19
Alignment explanation
Indices: 36017--36084 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
36007 GAAATGAAAA
36017 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
36033 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
36050 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
36069 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
36085 GTTGCGATAG
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:36218 original size:14 final size:14
Alignment explanation
Indices: 36199--36235 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
36189 CATCAATTAA
36199 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
36213 ACAAATCATCTTTT
1 ACAAATCAACATTT
36227 ACAAATCAA
1 ACAAATCAA
36236 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:38133 original size:20 final size:19
Alignment explanation
Indices: 38098--38164 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
38088 GAAACTTAAA
38098 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
38117 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
38137 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
38156 ATCGCAACG
1 ATCGCAACG
38165 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:38206 original size:31 final size:32
Alignment explanation
Indices: 38137--38246 Score: 195
Period size: 31 Copynumber: 3.4 Consensus size: 32
38127 GGAAATGGCT
*
38137 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
38170 ATCGCAACGCGAAATGAAATCGCAACGAC-AA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
38201 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
38233 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
38247 CACAAATCGC
Statistics
Matches: 75, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
31 31 0.41
32 29 0.39
33 15 0.20
ACGTcount: A:0.46, C:0.25, G:0.19, T:0.10
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:38355 original size:20 final size:20
Alignment explanation
Indices: 38330--38375 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
38320 TTATTTCGCA
38330 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
38350 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
38370 TTGCGA
1 TTGCGA
38376 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:38874 original size:18 final size:18
Alignment explanation
Indices: 38848--38892 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
38838 GTCGATCAGA
*
38848 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
38866 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
38884 TGATGGCTC
1 TGATGGCTC
38893 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:40223 original size:20 final size:20
Alignment explanation
Indices: 40198--40235 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40188 AATAGTTTCT
40198 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
40218 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
40236 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:40521 original size:21 final size:21
Alignment explanation
Indices: 40497--40539 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
40487 GATTTAGATA
40497 GACGGATTTCGCCGGAGATGG
1 GACGGATTTCGCCGGAGATGG
*
40518 GACGGATTTCGTCGGAGATGG
1 GACGGATTTCGCCGGAGATGG
40539 G
1 G
40540 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.16, G:0.44, T:0.21
Consensus pattern (21 bp):
GACGGATTTCGCCGGAGATGG
Found at i:40749 original size:20 final size:20
Alignment explanation
Indices: 40724--40817 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
40714 GATTATGTAT
40724 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
40744 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
40764 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
40785 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
40805 TATCGCATTGCGA
1 TATCGCGTTGCGA
40818 TTTTCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:40789 original size:41 final size:41
Alignment explanation
Indices: 40744--40821 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
40734 CGAAAGTCAG
* * *
40744 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
40785 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
40822 CCAATTCGCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:40818 original size:20 final size:20
Alignment explanation
Indices: 40704--40818 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
40694 CGCTTTGAAA
*
40704 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
40725 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
40745 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
40765 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
40786 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
40806 ATCGCATTGCGAT
1 ATCGCATTGCGAT
40819 TTTCCAATTC
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:40830 original size:20 final size:20
Alignment explanation
Indices: 40807--40857 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
40797 ATAGTCAGTA
*
40807 TCGCATTGCGATTTTCCAAT
1 TCGCATTGCGATTTACCAAT
* **
40827 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
40847 TCGCATTGCGA
1 TCGCATTGCGA
40858 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:46003 original size:59 final size:59
Alignment explanation
Indices: 45893--46038 Score: 190
Period size: 59 Copynumber: 2.5 Consensus size: 59
45883 GGTAGATTTG
*
45893 GGATGAAATTTGAATATTCAAAAGTTT-AGGACCAATTTAGAAAGAGGGTCATAGTTT-A
1 GGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAGAAAGA-GGTCATAGTTTAA
* * *
45951 GGAATGAAATTAGAATGTTCAAAAGTTTAAGGACTAATTTAGAATTGA-GTCATAGTTTAA
1 GG-ATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAGAA-AGAGGTCATAGTTTAA
* *
46011 GGATGTAATTAGAATATTTAAAAGTTTA
1 GGATGAAATTAGAATATTCAAAAGTTTA
46039 GGAATCAATT
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
58 2 0.03
59 56 0.73
60 17 0.22
61 2 0.03
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.34
Consensus pattern (59 bp):
GGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAGAAAGAGGTCATAGTTTAA
Found at i:46023 original size:30 final size:29
Alignment explanation
Indices: 45939--46025 Score: 81
Period size: 30 Copynumber: 3.0 Consensus size: 29
45929 TTAGAAAGAG
*
45939 GGTCATAGTTT-AGGAATGAAATTAGAA-T
1 GGTCATAGTTTAAGG-ATGTAATTAGAATT
* * *
45967 GTTCAAAAGTTTAAGGA-CTAATTTAGAATT
1 GGTC-ATAGTTTAAGGATGTAA-TTAGAATT
45997 GAGTCATAGTTTAAGGATGTAATTAGAAT
1 G-GTCATAGTTTAAGGATGTAATTAGAAT
46026 ATTTAAAAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
28 5 0.11
29 13 0.28
30 23 0.50
31 5 0.11
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (29 bp):
GGTCATAGTTTAAGGATGTAATTAGAATT
Found at i:46049 original size:59 final size:58
Alignment explanation
Indices: 45893--46067 Score: 187
Period size: 59 Copynumber: 3.0 Consensus size: 58
45883 GGTAGATTTG
* *
45893 GGATGAAATTTGAATATTCAAAAGTTTAGG-ACCAATTTAGAAAGAGGGTCATAGTTTA
1 GGATGAAATTAGAATATTCAAAAGTTTAGGAATCAATTTAGAAAGA-GGTCATAGTTTA
* * *
45951 GGAATGAAATTAGAATGTTCAAAAGTTTAAGGACT-AATTTAGAATTGA-GTCATAGTTTAA
1 GG-ATGAAATTAGAATATTCAAAAGTTT-AGGAATCAATTTAGAA-AGAGGTCATAGTTT-A
* * * *
46011 GGATGTAATTAGAATATTTAAAAGTTTAGGAATCAATTTA-AAACAAGATCATAGTTT
1 GGATGAAATTAGAATATTCAAAAGTTTAGGAATCAATTTAGAAA-GAGGTCATAGTTT
46068 GGAGATATAG
Statistics
Matches: 97, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
58 10 0.10
59 70 0.72
60 15 0.15
61 2 0.02
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (58 bp):
GGATGAAATTAGAATATTCAAAAGTTTAGGAATCAATTTAGAAAGAGGTCATAGTTTA
Found at i:46242 original size:3 final size:3
Alignment explanation
Indices: 46236--46263 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
46226 CTAGATTTTT
46236 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
46264 CGGAACAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:47604 original size:18 final size:16
Alignment explanation
Indices: 47566--47605 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
47556 GGTTAAAAAG
*
47566 TATATTCATTCTATTT
1 TATATTCATTCTATAT
47582 TATATTCATTCTAATAAT
1 TATATTCATTCT-AT-AT
47600 TATATT
1 TATATT
47606 AAAAATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.57
17 2 0.10
18 7 0.33
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATTCATTCTATAT
Found at i:48771 original size:21 final size:21
Alignment explanation
Indices: 48745--48878 Score: 104
Period size: 21 Copynumber: 6.5 Consensus size: 21
48735 GTTTTCAGAT
*
48745 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
* *
48766 TCGCAATGCGAGCTTGGACTA
1 TCGCAATGCGAACTTCGACTA
48787 TCGCAATGCGAA-TAT-G--TAA
1 TCGCAATGCGAACT-TCGACT-A
* *
48806 ACGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
48827 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
*
48847 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
48868 TCGCAATGCGA
1 TCGCAATGCGA
48879 TTTCATATTC
Statistics
Matches: 93, Mismatches: 9, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
18 1 0.01
19 13 0.14
20 20 0.22
21 58 0.62
22 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:48811 original size:40 final size:41
Alignment explanation
Indices: 48765--48878 Score: 178
Period size: 40 Copynumber: 2.8 Consensus size: 41
48755 AACTTCGACT
*
48765 ATCGCAATGCGAGCTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
48806 A-CGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
* *
48846 ATCGCAATGCGATA-GTCGACTATCGCAATGCGA
1 ATCGCAATGCGA-ACTTGGACTATCGCAATGCGA
48879 TTTCATATTC
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
40 39 0.57
41 28 0.41
42 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (41 bp):
ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
Found at i:49668 original size:21 final size:20
Alignment explanation
Indices: 49623--49755 Score: 119
Period size: 21 Copynumber: 6.5 Consensus size: 20
49613 ATTTTGGACT
49623 ATCGCAACGAACTTGGAATA
1 ATCGCAACGAACTTGGAATA
* *
49643 ATCGCAACGAATTTAGAATAA
1 ATCGCAACGAACTTGGAAT-A
* *
49664 ATCGCAACGCAAACTTCGACT-
1 ATCGCAACG--AACTTGGAATA
*
49685 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAAT-A
* *
49706 ATCGCAACGCGAACTT-CACT-
1 ATCGCAA--CGAACTTGGAATA
49726 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAAT-A
49747 ATCGCAACG
1 ATCGCAACG
49756 CGAACTTGAC
Statistics
Matches: 90, Mismatches: 13, Indels: 19
0.74 0.11 0.16
Matches are distributed among these distances:
18 7 0.08
19 9 0.10
20 24 0.27
21 35 0.39
22 2 0.02
23 13 0.14
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.20
Consensus pattern (20 bp):
ATCGCAACGAACTTGGAATA
Found at i:49693 original size:42 final size:42
Alignment explanation
Indices: 49643--49773 Score: 221
Period size: 41 Copynumber: 3.2 Consensus size: 42
49633 ACTTGGAATA
* *
49643 ATCGCAACGAATTTAGAATAAATCGCAACGCAAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
49685 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC-ACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
*
49726 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTT-GACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
49767 ATCGCAA
1 ATCGCAA
49774 TGCGGATATG
Statistics
Matches: 85, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
41 49 0.58
42 36 0.42
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (42 bp):
ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
Found at i:50020 original size:15 final size:14
Alignment explanation
Indices: 50002--50031 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
49992 AACATATTAA
50002 ATATAACTAATAATT
1 ATATAACT-ATAATT
50017 ATATAACTATAATT
1 ATATAACTATAATT
50031 A
1 A
50032 AAAAATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATAACTATAATT
Found at i:50244 original size:24 final size:24
Alignment explanation
Indices: 50217--50278 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
50207 CTATTATTTC
* *
50217 ACTTCAATTAAGCTCGAATTTTAG
1 ACTTCAATCAAGCTCGAATTTCAG
50241 ACTTCAATCAAGCTCGAATTTCAG
1 ACTTCAATCAAGCTCGAATTTCAG
*
50265 ACTTCAATCGAGCT
1 ACTTCAATCAAGCT
50279 TCTAAATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (24 bp):
ACTTCAATCAAGCTCGAATTTCAG
Found at i:50745 original size:13 final size:13
Alignment explanation
Indices: 50727--50765 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
50717 TAAAATTAGT
50727 TAAAATTTTAAAA
1 TAAAATTTTAAAA
50740 TAAAATTATTTAAAA
1 TAAAA-T-TTTAAAA
*
50755 TAAAATATTAA
1 TAAAATTTTAA
50766 TTACATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 9 0.39
14 2 0.09
15 12 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATTTTAAAA
Done.