Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004453.1 Hibiscus syriacus cultivar Beakdansim tig00009794_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: 92960
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1550 original size:30 final size:30
Alignment explanation
Indices: 1516--1587 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
1506 CGATGGTTCA
1516 AGCTCCACCGCCACCAGTAGTAGCTATAAC
1 AGCTCCACCGCCACCAGTAGTAGCTATAAC
* * *
1546 AGCTCCACCGCCACCGGTGGTAGCTATACC
1 AGCTCCACCGCCACCAGTAGTAGCTATAAC
1576 AGCTCCACCGCC
1 AGCTCCACCGCC
1588 GTCACCATCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.24, C:0.42, G:0.19, T:0.15
Consensus pattern (30 bp):
AGCTCCACCGCCACCAGTAGTAGCTATAAC
Found at i:1977 original size:27 final size:27
Alignment explanation
Indices: 1947--2002 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
1937 AATCTTTTTG
* *
1947 AATTATTGTAATTTTT-AACAATTATAA
1 AATTATTAT-ATTTTTCAACAATTAAAA
*
1974 AATTATTATTTTTTTCAACAATTAAAA
1 AATTATTATATTTTTCAACAATTAAAA
2001 AA
1 AA
2003 ATGTCATCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (27 bp):
AATTATTATATTTTTCAACAATTAAAA
Found at i:2306 original size:23 final size:22
Alignment explanation
Indices: 2279--2333 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 22
2269 ATAATTTTAT
*
2279 CTTTATGACACGTTTTTCTCTAC
1 CTTTATGACAC-TTTCTCTCTAC
*
2302 CTTTATGATATACTTTCTCTCTAC
1 CTTTATG--ACACTTTCTCTCTAC
2326 CTTTATGA
1 CTTTATGA
2334 TATGATTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 1 0.04
23 7 0.25
24 17 0.61
25 3 0.11
ACGTcount: A:0.20, C:0.24, G:0.07, T:0.49
Consensus pattern (22 bp):
CTTTATGACACTTTCTCTCTAC
Found at i:2326 original size:24 final size:24
Alignment explanation
Indices: 2295--2347 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2285 GACACGTTTT
2295 TCTCTACCTTTATGATAT-ACTTTC
1 TCTCTACCTTTATGATATGA-TTTC
2319 TCTCTACCTTTATGATATGATTTC
1 TCTCTACCTTTATGATATGATTTC
2343 TCTCT
1 TCTCT
2348 CTTTTGGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 27 0.96
25 1 0.04
ACGTcount: A:0.19, C:0.25, G:0.06, T:0.51
Consensus pattern (24 bp):
TCTCTACCTTTATGATATGATTTC
Found at i:2902 original size:23 final size:22
Alignment explanation
Indices: 2863--2910 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
2853 ATTTAAAAAT
*
2863 AAAAATATGAAATTTATATTTTA
1 AAAAATATGAAATTTAT-TTGTA
*
2886 AAAAATTATTAAA-TTATTTGTA
1 AAAAA-TATGAAATTTATTTGTA
2908 AAA
1 AAA
2911 TTATAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 7 0.32
23 9 0.41
24 6 0.27
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
AAAAATATGAAATTTATTTGTA
Found at i:4613 original size:40 final size:39
Alignment explanation
Indices: 4535--4613 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 39
4525 TACCGGAAAC
*
4535 ATTATTATTTCTACCATTTTGTTATTATTGGGCGCTTTA
1 ATTATTATTTCTACCATTTTGTTATTATTGGGCACTTTA
* *
4574 ATTATTTTTTCTACTGC-TTTTGTTATTATTGGTCACTTTA
1 ATTATTATTTCTAC--CATTTTGTTATTATTGGGCACTTTA
4614 CCATAAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
39 13 0.37
40 21 0.60
41 1 0.03
ACGTcount: A:0.19, C:0.13, G:0.11, T:0.57
Consensus pattern (39 bp):
ATTATTATTTCTACCATTTTGTTATTATTGGGCACTTTA
Found at i:5194 original size:41 final size:41
Alignment explanation
Indices: 5149--5241 Score: 100
Period size: 41 Copynumber: 2.3 Consensus size: 41
5139 ATTTGAAAAA
*
5149 TCGCAATGCGATACTGAC-TA-TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGAT--TGACGTATTCGCAATGCAATTTTCATAAT
* * ** *
5190 TCGCATTGCGATTTACGTATTCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTGACGTATTCGCAATGCAATTTTCATAAT
5231 TCGCAATGCGA
1 TCGCAATGCGA
5242 ATTAGGAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
39 3 0.07
40 2 0.05
41 38 0.88
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (41 bp):
TCGCAATGCGATTGACGTATTCGCAATGCAATTTTCATAAT
Found at i:5203 original size:21 final size:21
Alignment explanation
Indices: 5066--5241 Score: 76
Period size: 21 Copynumber: 8.5 Consensus size: 21
5056 ATTATGACTA
*
5066 TCGCAATGCGATTTTCCA-ATT
1 TCGCAATGCGATTTT-CATAAT
** **
5087 TCGCGTTGCGATTTTCCCAAT
1 TCGCAATGCGATTTTCATAAT
* * * *
5108 TCGCAATGTGA--ATAAGTAAA
1 TCGCAATGCGATTTTCA-TAAT
* * * *
5128 TCGCAATGCGAATTTGAAAAA
1 TCGCAATGCGATTTTCATAAT
** *
5149 TCGCAATGCGATACTGACT-A-
1 TCGCAATGCGATTTTCA-TAAT
* *
5169 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
5190 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
5210 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
5231 TCGCAATGCGA
1 TCGCAATGCGA
5242 ATTAGGAAAA
Statistics
Matches: 113, Mismatches: 34, Indels: 16
0.69 0.21 0.10
Matches are distributed among these distances:
19 2 0.02
20 43 0.38
21 66 0.58
22 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:5891 original size:14 final size:14
Alignment explanation
Indices: 5872--5960 Score: 70
Period size: 14 Copynumber: 5.6 Consensus size: 14
5862 TTTCATTTCG
5872 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
5886 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
5905 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
5919 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
5938 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
5952 CGTTGCGAT
1 CGTTGCGAT
5961 AGTCATTTCC
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
14 30 0.49
16 5 0.08
17 5 0.08
19 21 0.34
ACGTcount: A:0.10, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:5897 original size:33 final size:33
Alignment explanation
Indices: 5855--5984 Score: 215
Period size: 33 Copynumber: 3.9 Consensus size: 33
5845 CAAAATCGCA
**
5855 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
**
5888 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
5921 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
5954 TTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 TTGCGATAGTCATTT-CGCGTTGCGATTCTC
5985 ATTATCTCGT
Statistics
Matches: 94, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
33 79 0.84
34 15 0.16
ACGTcount: A:0.11, C:0.25, G:0.22, T:0.42
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
Found at i:8161 original size:21 final size:21
Alignment explanation
Indices: 8137--8203 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
8127 TCATTCCTCG
8137 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
8158 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
8179 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
8200 AGAG
1 AGAG
8204 CTCGATTCAC
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:8162 original size:42 final size:42
Alignment explanation
Indices: 8110--8203 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
8100 CCACTCCTAT
* *
8110 CGTTGAAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCAC
* * *
8152 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
*
8194 CATTCAAGAG
1 CGTTCAAGAG
8204 CTCGATTCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
41 4 0.09
42 38 0.86
43 2 0.05
ACGTcount: A:0.22, C:0.35, G:0.21, T:0.21
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
Found at i:9573 original size:13 final size:14
Alignment explanation
Indices: 9557--9591 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
9547 ATTGTTTAAT
9557 TGATTTGT-AAAGG
1 TGATTTGTAAAAGG
*
9570 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
9584 TGATTTGT
1 TGATTTGT
9592 TTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:9758 original size:19 final size:19
Alignment explanation
Indices: 9697--9749 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
9687 AAAAAGTACT
*
9697 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
9716 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
9735 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
9750 TAAATTCGCG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:9808 original size:33 final size:32
Alignment explanation
Indices: 9758--9883 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
9748 ATTAAATTCG
9758 CGTTGCGA-TTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
*
9790 CGTTGCGATTTTCATTTCGCATTGCGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
9823 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
9856 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
9884 AGTAATTTCG
Statistics
Matches: 87, Mismatches: 2, Indels: 9
0.89 0.02 0.09
Matches are distributed among these distances:
31 3 0.03
32 8 0.09
33 73 0.84
35 3 0.03
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:9816 original size:19 final size:19
Alignment explanation
Indices: 9754--9902 Score: 96
Period size: 19 Copynumber: 8.7 Consensus size: 19
9744 CGAAATTAAA
*
9754 TTCGCGTTGCGA-TTTCAT
1 TTCGCATTGCGATTTTCAT
*
9772 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
9788 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
9805 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
*
9819 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
9838 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
9854 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
** *
9871 TTCGCATTGCGATAGTAAT
1 TTCGCATTGCGATTTTCAT
*
9890 TTCGCGTTGCGAT
1 TTCGCATTGCGAT
9903 AGACATTAAG
Statistics
Matches: 101, Mismatches: 15, Indels: 29
0.70 0.10 0.20
Matches are distributed among these distances:
14 24 0.24
16 13 0.13
17 13 0.13
18 11 0.11
19 40 0.40
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:9849 original size:66 final size:65
Alignment explanation
Indices: 9751--9882 Score: 246
Period size: 66 Copynumber: 2.0 Consensus size: 65
9741 ACGCGAAATT
9751 AAATTCGCGTTGCGATTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
1 AAATTCGCGTTGCGATTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
*
9816 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGA-TTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
9881 G
65 G
9882 A
1 A
9883 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
65 15 0.23
66 50 0.77
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (65 bp):
AAATTCGCGTTGCGATTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
Found at i:12259 original size:24 final size:24
Alignment explanation
Indices: 12225--12278 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
12215 CTGAAACATC
*
12225 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
12249 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
12273 ATCAAA
1 ATCAAA
12279 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:13090 original size:20 final size:21
Alignment explanation
Indices: 13065--13114 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
13055 TTCCTAATTT
*
13065 GCAATGCGAA-TAAGTAAATC
1 GCAATGCGAATTAAGAAAATC
**
13085 GCAATGCGAATTTGGAAAATC
1 GCAATGCGAATTAAGAAAATC
13106 GCAATGCGA
1 GCAATGCGA
13115 TACTGACTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (21 bp):
GCAATGCGAATTAAGAAAATC
Found at i:13188 original size:20 final size:20
Alignment explanation
Indices: 13099--13190 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
13089 TGCGAATTTG
* *
13099 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
13119 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
13139 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
13160 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
13180 GAAAATCGCAA
1 GAAAATCGCAA
13191 TCATCTTCAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:13445 original size:20 final size:20
Alignment explanation
Indices: 13388--13437 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
13378 ATTCATTTGA
13388 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
13408 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
13428 CTATCGCAAC
1 CTATCGCAAC
13438 TAGAAAATCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.28, G:0.22, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:13505 original size:19 final size:19
Alignment explanation
Indices: 13464--13531 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
13454 GAAATGAAAA
13464 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
13480 TCG--TTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
13497 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
13516 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
13532 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.22
16 3 0.07
17 3 0.07
19 29 0.64
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:15592 original size:20 final size:20
Alignment explanation
Indices: 15569--15622 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
15559 GAAACTTAAA
15569 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
* *
15589 ATCGCAACGC-AGAAATGGCT
1 ATCGCAATGCGA-AAATGACT
15609 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
15623 TGCAAATCGC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:15752 original size:20 final size:20
Alignment explanation
Indices: 15724--15764 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
15714 TCGCATTACA
15724 ATAGCCATTTCCGCGTTGCG
1 ATAGCCATTTCCGCGTTGCG
* * *
15744 ATAGTCATTTTCGTGTTGCG
1 ATAGCCATTTCCGCGTTGCG
15764 A
1 A
15765 AAGTAAACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (20 bp):
ATAGCCATTTCCGCGTTGCG
Found at i:16272 original size:18 final size:18
Alignment explanation
Indices: 16246--16285 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
16236 GTCGATCAGA
* *
16246 TGATGGCTCTGGGTGAGG
1 TGATAGCTCTGGGCGAGG
16264 TGATAGCTCTGGGCGAGG
1 TGATAGCTCTGGGCGAGG
16282 TGAT
1 TGAT
16286 GGCTACCGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.12, G:0.45, T:0.28
Consensus pattern (18 bp):
TGATAGCTCTGGGCGAGG
Found at i:17634 original size:20 final size:20
Alignment explanation
Indices: 17609--17646 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17599 AATAGTTTCT
17609 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
17629 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
17647 GCAAAACTAA
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:17923 original size:22 final size:22
Alignment explanation
Indices: 17896--17939 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
17886 GATGGAGATA
17896 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
17918 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
17940 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:18178 original size:20 final size:20
Alignment explanation
Indices: 18128--18179 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
18118 ATTATGTATT
**
18128 ATCGCGTTGTAAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
*
18148 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
18168 ATCTCGTTGCGA
1 ATCGCGTTGCGA
18180 TTTTGTATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:18213 original size:20 final size:20
Alignment explanation
Indices: 18188--18241 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
18178 GATTTTGTAT
18188 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
18208 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
18228 TATCGCATTGCGAT
1 TATCGCATTGCGAT
18242 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:18213 original size:61 final size:61
Alignment explanation
Indices: 18107--18244 Score: 177
Period size: 61 Copynumber: 2.3 Consensus size: 61
18097 CGCTTTGAAA
* * * * *
18107 ATCGCATTGCGATTATGTATTATCGCGTTGTAAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCAAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * * *
18168 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCAAAAGTAAGAATCGCATTGCGAAAGTCAGT
18229 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
18245 CCCAATTCGC
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.36
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCAAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:18260 original size:61 final size:61
Alignment explanation
Indices: 18148--18262 Score: 142
Period size: 61 Copynumber: 1.9 Consensus size: 61
18138 AAAAGTCAGA
* * * ** *
18148 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCATTGCGATAGTAAGT
* *
18209 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAATATCGCATTGCGAT
18263 TTACTTATTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
61 43 0.96
62 2 0.04
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCATTGCGATAGTAAGT
Found at i:18352 original size:21 final size:21
Alignment explanation
Indices: 18312--18352 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
18302 ACTGTAGACC
** *
18312 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGAAATGCAATT
18333 ATCGCAACGCGAAATGCAAT
1 ATCGCAACGCGAAATGCAAT
18353 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAATT
Found at i:18646 original size:2 final size:2
Alignment explanation
Indices: 18641--18681 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
18631 CTCTTCCTCT
18641 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18682 CGAATAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18723 original size:12 final size:12
Alignment explanation
Indices: 18706--18750 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
18696 ATGACCTAAA
18706 AATAATTTATAG
1 AATAATTTATAG
* *
18718 AATAATTGTTTAAA
1 AATAATT-TAT-AG
18732 AATAATTTATAG
1 AATAATTTATAG
18744 AATAATT
1 AATAATT
18751 GTTTAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 15 0.56
13 4 0.15
14 8 0.30
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (12 bp):
AATAATTTATAG
Found at i:18731 original size:26 final size:26
Alignment explanation
Indices: 18702--18756 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
18692 AAATATGACC
18702 TAAAAATAATTTATAGAATAATTGTT
1 TAAAAATAATTTATAGAATAATTGTT
18728 TAAAAATAATTTATAGAATAATTGTT
1 TAAAAATAATTTATAGAATAATTGTT
18754 TAA
1 TAA
18757 TTTTTTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (26 bp):
TAAAAATAATTTATAGAATAATTGTT
Found at i:18906 original size:13 final size:13
Alignment explanation
Indices: 18888--18915 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
18878 TTTTATAGGA
18888 TAAAATTTAAATT
1 TAAAATTTAAATT
18901 TAAAATTTAAATT
1 TAAAATTTAAATT
18914 TA
1 TA
18916 GTTAAATATA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAAAATTTAAATT
Found at i:24087 original size:14 final size:14
Alignment explanation
Indices: 24068--24097 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
24058 ATGCTTTGTG
24068 GATGTAATCTGCTC
1 GATGTAATCTGCTC
24082 GATGTAATCTGCTC
1 GATGTAATCTGCTC
24096 GA
1 GA
24098 ATTTGAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (14 bp):
GATGTAATCTGCTC
Found at i:28248 original size:3 final size:3
Alignment explanation
Indices: 28222--28268 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
28212 GTCTACCTCA
* * * *
28222 TTC TTC TTA TTG TTT TTC TT- TTC TTC TTC TTC TTC TTC TTG TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
28269 CTTTACCATC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.02, C:0.23, G:0.04, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:29844 original size:20 final size:20
Alignment explanation
Indices: 29821--29885 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
29811 ACGTGAACAA
29821 TATCGGTATTGTTCATGCAG
1 TATCGGTATTGTTCATGCAG
* * * *
29841 TATCGATACTG-T-AAGAACAA
1 TATCGGTATTGTTCATG--CAG
*
29861 TATCAGTATTGTTCATGCAG
1 TATCGGTATTGTTCATGCAG
29881 TATCG
1 TATCG
29886 ATACTGTAAG
Statistics
Matches: 31, Mismatches: 10, Indels: 8
0.63 0.20 0.16
Matches are distributed among these distances:
18 2 0.06
19 1 0.03
20 25 0.81
21 1 0.03
22 2 0.06
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.35
Consensus pattern (20 bp):
TATCGGTATTGTTCATGCAG
Found at i:29845 original size:40 final size:39
Alignment explanation
Indices: 29815--29904 Score: 135
Period size: 40 Copynumber: 2.3 Consensus size: 39
29805 GGTACCACGT
* *
29815 GAACAATATCGGTATTGTTCATGCAGTATCGATACTGTAA
1 GAACAATATCAGTATTGTTCATGCAGTATCGATACCGT-A
*
29855 GAACAATATCAGTATTGTTCATGCAGTATCGATACTGTAA
1 GAACAATATCAGTATTGTTCATGCAGTATCGATACCGT-A
29895 GAACAATATC
1 GAACAATATC
29905 GGTACTTCTC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.31
Consensus pattern (39 bp):
GAACAATATCAGTATTGTTCATGCAGTATCGATACCGTA
Found at i:29910 original size:20 final size:20
Alignment explanation
Indices: 29841--29910 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
29831 GTTCATGCAG
29841 TATCGATACTGTAAGAACAA
1 TATCGATACTGTAAGAACAA
* * *
29861 TATC-AGTATTGTTCATG--CAG
1 TATCGA-TACTG-T-AAGAACAA
29881 TATCGATACTGTAAGAACAA
1 TATCGATACTGTAAGAACAA
*
29901 TATCGGTACT
1 TATCGATACT
29911 TCTCACCCAG
Statistics
Matches: 37, Mismatches: 7, Indels: 12
0.66 0.12 0.21
Matches are distributed among these distances:
18 2 0.05
19 2 0.05
20 29 0.78
21 2 0.05
22 2 0.05
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (20 bp):
TATCGATACTGTAAGAACAA
Found at i:32349 original size:23 final size:24
Alignment explanation
Indices: 32306--32350 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
32296 TACTAAGGGG
*
32306 GTATCGATACCTCAATTGAGGGAT
1 GTATCGATACCTCAATAGAGGGAT
*
32330 GTATCGATACC-CTATAGAGGG
1 GTATCGATACCTCAATAGAGGG
32351 TACCGATACC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (24 bp):
GTATCGATACCTCAATAGAGGGAT
Found at i:32924 original size:18 final size:18
Alignment explanation
Indices: 32901--32935 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
32891 ATGGATTATC
*
32901 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
32919 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGGGACA
32936 AATATTCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:37070 original size:65 final size:63
Alignment explanation
Indices: 36995--37154 Score: 191
Period size: 65 Copynumber: 2.5 Consensus size: 63
36985 GAATAAATTG
* * *
36995 AACATCGAATGCATTATATGCATCGATGCACATA-CCATGCATAGATGCACTCAGG-TTTTTATG
1 AACATTGAATGCATT-TATGCATCGATGCACA-AGACATGCATAGATGCACTCAGGCTATTT-TG
37058 AA
63 -A
*
37060 AACATTGAATGCATTTGATGCATCGATGCACAAGACATGCATCGATGCACTCAGGCTATTTTGA
1 AACATTGAATGCATTT-ATGCATCGATGCACAAGACATGCATAGATGCACTCAGGCTATTTTGA
*
37124 AACATCT-AATGCACTTCATGCATCGATGCAC
1 AACAT-TGAATGCA-TTTATGCATCGATGCAC
37155 TAAGGGTCCA
Statistics
Matches: 85, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
64 28 0.33
65 53 0.62
66 4 0.05
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (63 bp):
AACATTGAATGCATTTATGCATCGATGCACAAGACATGCATAGATGCACTCAGGCTATTTTGA
Found at i:39104 original size:20 final size:21
Alignment explanation
Indices: 39079--39117 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
39069 GAGAAATTGT
39079 TTTTAAAA-TAAAAAATGATA
1 TTTTAAAATTAAAAAATGATA
39099 TTTTAAAATTAAAAAATGA
1 TTTTAAAATTAAAAAATGA
39118 AAATAACCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (21 bp):
TTTTAAAATTAAAAAATGATA
Found at i:40946 original size:12 final size:12
Alignment explanation
Indices: 40929--40953 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40919 GAACCATCAT
40929 CAAAAGATGAAA
1 CAAAAGATGAAA
40941 CAAAAGATGAAA
1 CAAAAGATGAAA
40953 C
1 C
40954 TCATGATCCT
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:0.64, C:0.12, G:0.16, T:0.08
Consensus pattern (12 bp):
CAAAAGATGAAA
Found at i:42975 original size:21 final size:23
Alignment explanation
Indices: 42927--43001 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 23
42917 ACACTGATCA
* *
42927 GTGCATCGATACATCCCTTTGAAT
1 GTGCATCGATACA-CCCTATGAAG
42951 GTGCATCGATACA-CC-ATGAAG
1 GTGCATCGATACACCCTATGAAG
* *
42972 GTGCA-CTGATGCACTCCT-TGAAT
1 GTGCATC-GATACAC-CCTATGAAG
42995 GTGCATC
1 GTGCATC
43002 AATGCACAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
20 1 0.02
21 14 0.33
22 2 0.05
23 11 0.26
24 14 0.33
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.28
Consensus pattern (23 bp):
GTGCATCGATACACCCTATGAAG
Found at i:45888 original size:64 final size:64
Alignment explanation
Indices: 45746--45888 Score: 166
Period size: 65 Copynumber: 2.2 Consensus size: 64
45736 AGTGCATTAT
* * * * * *
45746 ATGCATCGATGCATATACCATGCATCGTTGCACTCAGGTTTTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACATAACATGCATCGATGCACTCAGGTTTTTAT-AAAACATCGAATACACTTC
*
45811 AAGCATCGATGCACA-AGACATGCATCGATGCACTCAGGCTATTTT-T-AAACATCGAATACACT
1 ATGCATCGATGCACATA-ACATGCATCGATGCACTCAGG-T-TTTTATAAAACATCGAATACACT
45873 TC
63 TC
45875 ATGCATCGATGCAC
1 ATGCATCGATGCAC
45889 TCTTAGTGCA
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
64 29 0.43
65 32 0.48
66 2 0.03
67 4 0.06
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.28
Consensus pattern (64 bp):
ATGCATCGATGCACATAACATGCATCGATGCACTCAGGTTTTTATAAAACATCGAATACACTTC
Found at i:57273 original size:7 final size:7
Alignment explanation
Indices: 57256--57324 Score: 129
Period size: 7 Copynumber: 9.7 Consensus size: 7
57246 AACAATCACC
57256 TCTCTCCT
1 TCTC-CCT
57264 TCTCCCT
1 TCTCCCT
57271 TCTCCCT
1 TCTCCCT
57278 TCTCCCT
1 TCTCCCT
57285 TCTCCCT
1 TCTCCCT
57292 TCTCCCT
1 TCTCCCT
57299 TCTCCCT
1 TCTCCCT
57306 TCTCCCT
1 TCTCCCT
57313 TCTCCCT
1 TCTCCCT
57320 TCTCC
1 TCTCC
57325 TACCTATCAT
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
7 57 0.93
8 4 0.07
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (7 bp):
TCTCCCT
Found at i:61932 original size:57 final size:57
Alignment explanation
Indices: 61852--62077 Score: 319
Period size: 57 Copynumber: 4.0 Consensus size: 57
61842 TTGTAGATGA
* * * *
61852 AGCCCGATCTTCCGGATCTTGCAAGCATAACCGTTTAGGCAATCTGCTAGACTCACC
1 AGCCTGATCTTCCGGATCATGCAAGCGTAACTGTTTAGGCAATCTGCTAGACTCACC
* *
61909 AGGCTGATCTTCCAGATCATGCAAGCGTAACTGTTTAGGCAATCTGCTAGACTCACC
1 AGCCTGATCTTCCGGATCATGCAAGCGTAACTGTTTAGGCAATCTGCTAGACTCACC
** *
61966 AGCCCAATCTTCCGGAT-ATTGCAAGCGTAACTGTTTAGGCAATCTGCTAGACTCGCC
1 AGCCTGATCTTCCGGATCA-TGCAAGCGTAACTGTTTAGGCAATCTGCTAGACTCACC
* * * *
62023 AGCCTGATCTTCCTGCTCTTGCAAGCGTAACTGTTTAGGAAATCTGCTAGACTCA
1 AGCCTGATCTTCCGGATCATGCAAGCGTAACTGTTTAGGCAATCTGCTAGACTCA
62078 TCATGCTCCA
Statistics
Matches: 149, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
56 1 0.01
57 148 0.99
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (57 bp):
AGCCTGATCTTCCGGATCATGCAAGCGTAACTGTTTAGGCAATCTGCTAGACTCACC
Found at i:62052 original size:114 final size:114
Alignment explanation
Indices: 61852--62077 Score: 362
Period size: 114 Copynumber: 2.0 Consensus size: 114
61842 TTGTAGATGA
* * *
61852 AGCCCGATCTTCCGGATCTTGCAAGCATAACCGTTTAGGCAATCTGCTAGACTCACCAGGCTGAT
1 AGCCCAATCTTCCGGATATTGCAAGCATAACCGTTTAGGCAATCTGCTAGACTCACCAGCCTGAT
*
61917 CTTCCAGATCATGCAAGCGTAACTGTTTAGGCAATCTGCTAGACTCACC
66 CTTCCAGATCATGCAAGCGTAACTGTTTAGGAAATCTGCTAGACTCACC
* * *
61966 AGCCCAATCTTCCGGATATTGCAAGCGTAACTGTTTAGGCAATCTGCTAGACTCGCCAGCCTGAT
1 AGCCCAATCTTCCGGATATTGCAAGCATAACCGTTTAGGCAATCTGCTAGACTCACCAGCCTGAT
* * *
62031 CTTCCTGCTCTTGCAAGCGTAACTGTTTAGGAAATCTGCTAGACTCA
66 CTTCCAGATCATGCAAGCGTAACTGTTTAGGAAATCTGCTAGACTCA
62078 TCATGCTCCA
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 102 1.00
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (114 bp):
AGCCCAATCTTCCGGATATTGCAAGCATAACCGTTTAGGCAATCTGCTAGACTCACCAGCCTGAT
CTTCCAGATCATGCAAGCGTAACTGTTTAGGAAATCTGCTAGACTCACC
Found at i:67664 original size:15 final size:14
Alignment explanation
Indices: 67637--67670 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
67627 AGATGTAATT
67637 TATTTTACGAAAAA
1 TATTTTACGAAAAA
*
67651 TATTTTTCGAAAAA
1 TATTTTACGAAAAA
*
67665 TGTTTT
1 TATTTT
67671 CAATGAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (14 bp):
TATTTTACGAAAAA
Found at i:72643 original size:21 final size:22
Alignment explanation
Indices: 72611--72665 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
72601 TCATCAACTA
*
72611 ATATATAT-TTTAATA-TACTTT
1 ATAT-TATGTTTAATATTACGTT
*
72632 ATATTATGTTTAATATTTCGTT
1 ATATTATGTTTAATATTACGTT
72654 AT-TTATGTTTAA
1 ATATTATGTTTAA
72666 CAAGTAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 3 0.10
21 21 0.70
22 6 0.20
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.58
Consensus pattern (22 bp):
ATATTATGTTTAATATTACGTT
Found at i:81994 original size:19 final size:19
Alignment explanation
Indices: 81972--82051 Score: 92
Period size: 19 Copynumber: 4.1 Consensus size: 19
81962 GTAAAAAAAG
*
81972 ATAAAACAAACAATAAA-AA
1 ATAAAATAAA-AATAAACAA
81991 ATAAAATAAGATAATAAACAA
1 ATAAAATAA-A-AATAAACAA
82012 ATAAAATAAAAATAAACAA
1 ATAAAATAAAAATAAACAA
*
82031 ATAAACA-AGAAATAAACAA
1 ATAAA-ATAAAAATAAACAA
82050 AT
1 AT
82052 TAGAAAAATC
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
19 35 0.64
20 9 0.16
21 11 0.20
ACGTcount: A:0.75, C:0.07, G:0.03, T:0.15
Consensus pattern (19 bp):
ATAAAATAAAAATAAACAA
Found at i:82023 original size:32 final size:29
Alignment explanation
Indices: 81963--82027 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 29
81953 AAATAGGAAG
*
81963 TAAAAAAAGATAAAACAAACAATAAAAAA
1 TAAAAAAAGATAAAACAAACAAAAAAAAA
* *
81992 TAAAATAAGATAATAAACAAATAAAATAAAAA
1 TAAAAAAAGAT-A-AAACAAACAAAA-AAAAA
82024 TAAA
1 TAAA
82028 CAAATAAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 10 0.33
30 1 0.03
31 10 0.33
32 9 0.30
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (29 bp):
TAAAAAAAGATAAAACAAACAAAAAAAAA
Found at i:82133 original size:19 final size:20
Alignment explanation
Indices: 82088--82135 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
82078 TGAAAATACA
*
82088 AATACAAATATTAAGTAAAAT
1 AATA-AAATAGTAAGTAAAAT
*
82109 AA-AAAATAGTAA-TAACAT
1 AATAAAATAGTAAGTAAAAT
82127 AATAAAATA
1 AATAAAATA
82136 TGAAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 7 0.29
19 14 0.58
20 1 0.04
21 2 0.08
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (20 bp):
AATAAAATAGTAAGTAAAAT
Found at i:82358 original size:2 final size:2
Alignment explanation
Indices: 82346--82375 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
82336 GTTTAATAAA
*
82346 AT AT GT 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
82376 TAGTTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82489 original size:15 final size:16
Alignment explanation
Indices: 82469--82505 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
82459 AATAATAAAT
82469 AAAGAAAAAG-AATAA
1 AAAGAAAAAGAAATAA
*
82484 AAAG-AAAAGAAATTA
1 AAAGAAAAAGAAATAA
82499 AAAGAAA
1 AAAGAAA
82506 TTAAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 5 0.26
15 12 0.63
16 2 0.11
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (16 bp):
AAAGAAAAAGAAATAA
Found at i:82501 original size:10 final size:10
Alignment explanation
Indices: 82488--82515 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
82478 GAATAAAAAG
82488 AAAAGAAATT
1 AAAAGAAATT
82498 AAAAGAAATT
1 AAAAGAAATT
82508 AAAAGAAA
1 AAAAGAAA
82516 GAAAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (10 bp):
AAAAGAAATT
Found at i:82501 original size:24 final size:24
Alignment explanation
Indices: 82474--82519 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
82464 TAAATAAAGA
82474 AAAAG-AATAAAAAGAAAAGAAATT
1 AAAAGAAATAAAAAG-AAAGAAATT
*
82498 AAAAGAAATTAAAAGAAAGAAA
1 AAAAGAAATAAAAAGAAAGAAA
82520 ATATAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (24 bp):
AAAAGAAATAAAAAGAAAGAAATT
Found at i:82501 original size:25 final size:27
Alignment explanation
Indices: 82473--82528 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 27
82463 ATAAATAAAG
82473 AAAAAG-AATAAAAAGAAA-AGAAAT-T
1 AAAAAGAAATAAAAAGAAAGA-AAATAT
*
82498 -AAAAGAAATTAAAAGAAAGAAAATAT
1 AAAAAGAAATAAAAAGAAAGAAAATAT
82524 AAAAA
1 AAAAA
82529 ACGTATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 5 0.19
25 15 0.58
26 2 0.08
27 4 0.15
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.12
Consensus pattern (27 bp):
AAAAAGAAATAAAAAGAAAGAAAATAT
Found at i:82582 original size:18 final size:18
Alignment explanation
Indices: 82561--82627 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 18
82551 ATAGATAAGT
82561 AAAAAAATAGTAATAATA
1 AAAAAAATAGTAATAATA
* *
82579 AAAATAATAAG-GATAATA
1 AAAAAAAT-AGTAATAATA
* * *
82597 TAAAGAATAATAATAA-A
1 AAAAAAATAGTAATAATA
82614 AATAAAAATAGTAA
1 AA-AAAAATAGTAA
82628 AAGAGTATAA
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
17 3 0.08
18 32 0.86
19 2 0.05
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (18 bp):
AAAAAAATAGTAATAATA
Found at i:82588 original size:12 final size:12
Alignment explanation
Indices: 82563--82712 Score: 63
Period size: 14 Copynumber: 11.4 Consensus size: 12
82553 AGATAAGTAA
*
82563 AAAAATAGTAAT
1 AAAAATAATAAT
82575 AATAAA-AATAAT
1 AA-AAATAATAAT
**
82587 AAGGATAAT-AT
1 AAAAATAATAAT
82598 AAAGAATAATAAT
1 AAA-AATAATAAT
*
82611 AAAAATAAAAAT
1 AAAAATAATAAT
* *
82623 AGTAAAAGAGT-AT
1 A--AAAATAATAAT
*
82636 AAAAAGAAATAAGT
1 AAAAA-TAATAA-T
82650 AAATATATATATACAT
1 AAA-A-ATA-ATA-AT
82666 ATAATAATAATAAT
1 A-AA-AATAATAAT
*
82680 AATATATATATAAT
1 AA-AAATA-ATAAT
82694 AAAACATAATATAT
1 AAAA-ATAATA-AT
82708 AAAAA
1 AAAAA
82713 AGTTTTAAAA
Statistics
Matches: 106, Mismatches: 14, Indels: 35
0.68 0.09 0.23
Matches are distributed among these distances:
11 9 0.08
12 28 0.26
13 21 0.20
14 29 0.27
15 5 0.05
16 9 0.08
17 5 0.05
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.27
Consensus pattern (12 bp):
AAAAATAATAAT
Found at i:82684 original size:23 final size:23
Alignment explanation
Indices: 82656--82708 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
82646 AAGTAAATAT
*
82656 ATATATACATATAATAATA-ATA
1 ATATATACATATAATAAAACATA
*
82678 ATAATATATATATAATAAAACATA
1 AT-ATATACATATAATAAAACATA
82702 ATATATA
1 ATATATA
82709 AAAAAGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 2 0.07
23 20 0.74
24 5 0.19
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (23 bp):
ATATATACATATAATAAAACATA
Found at i:82702 original size:21 final size:19
Alignment explanation
Indices: 82664--82709 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 19
82654 ATATATATAC
*
82664 ATATAATAATAATAATAAT
1 ATATAATAATAAAAATAAT
82683 ATATATATAATAAAACATAAT
1 ATATA-ATAATAAAA-ATAAT
82704 ATATAA
1 ATATAA
82710 AAAAGTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 5 0.21
20 9 0.38
21 10 0.42
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
ATATAATAATAAAAATAAT
Found at i:84857 original size:106 final size:106
Alignment explanation
Indices: 84671--84867 Score: 299
Period size: 106 Copynumber: 1.9 Consensus size: 106
84661 AATTTAACAA
* * * *
84671 TCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCTTTCACTGTGAA
1 TCAGCCGCCCCTTCCTCGTGAAGTTGAGCTTGTGCTATCTTGGGTCCAATATCCTTCACTGTGAA
84736 GTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGACAG
66 GTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGACAG
*
84777 TCAGCCGCCCCTTCACT-GTGAAGTTGAGCTTGTGCTATCTTGGGTCCAATATCCTTC-GTCGTG
1 TCAGCCGCCCCTTC-CTCGTGAAGTTGAGCTTGTGCTATCTTGGGTCCAATATCCTTCACT-GTG
* *
84840 AAGTTGAATTTGGCTCTGAAATTGGGAA
64 AAGTTGAAATTGACTCTGAAATTGGGAA
84868 GCCCCTTCGT
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
105 1 0.01
106 80 0.98
107 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.35
Consensus pattern (106 bp):
TCAGCCGCCCCTTCCTCGTGAAGTTGAGCTTGTGCTATCTTGGGTCCAATATCCTTCACTGTGAA
GTTGAAATTGACTCTGAAATTGGGAAATTATTTGTTGACAG
Found at i:84889 original size:191 final size:191
Alignment explanation
Indices: 84523--84890 Score: 456
Period size: 190 Copynumber: 1.9 Consensus size: 191
84513 ATTGTTCCGA
* *
84523 GTCCAATATCCTCCATCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAAATTATTTGTTGACAGT
1 GTCCAATATCCTCCATCGTGAAGTTGAAATTGACTCTGAAACTGGGAAAATTATTTGTTGACAGT
* * * ** *
84588 CAGTCGTCCCTTCGCTGTGAAGTTGAACTTGTGCTATCTCGAGTTTAATGTCCTTCGCTGTGAAG
66 CAGCCGCCCCTTCACTGTGAAGTTGAACTTGTGCTATCTCGAGTCCAATATCCTTCGCTGTGAAG
* **
84653 TTAAGATGAATTTAACAATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGG
131 TTAAGATGAATTGAACAATCAGAAGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGG
* * *
84714 GTCCAATATCTTTCA-CTGTGAAGTTGAAATTGACTCTGAAATTGGG-AAATTATTTGTTGACAG
1 GTCCAATATCCTCCATC-GTGAAGTTGAAATTGACTCTGAAACTGGGAAAATTATTTGTTGACAG
* * *
84777 TCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTATCTTGGGTCCAATATCCTTCG-TCGTGA
65 TCAGCCGCCCCTTCACTGTGAAGTTGAACTTGTGCTATCTCGAGTCCAATATCCTTCGCT-GTGA
** ** * **
84841 AGTTGAATTTGGCTCTGAA-ATTGGGAAGCCCCTTCGTCGTGAAGTTGAGC
129 AGTT-AAGATGAAT-TGAACAATCAGAAGCCCCTTCGTCGTGAAGTTGAGC
84891 CCTGAATGGC
Statistics
Matches: 149, Mismatches: 24, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
189 1 0.01
190 75 0.50
191 70 0.47
192 3 0.02
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (191 bp):
GTCCAATATCCTCCATCGTGAAGTTGAAATTGACTCTGAAACTGGGAAAATTATTTGTTGACAGT
CAGCCGCCCCTTCACTGTGAAGTTGAACTTGTGCTATCTCGAGTCCAATATCCTTCGCTGTGAAG
TTAAGATGAATTGAACAATCAGAAGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGG
Found at i:85958 original size:14 final size:12
Alignment explanation
Indices: 85928--85983 Score: 76
Period size: 12 Copynumber: 4.4 Consensus size: 12
85918 ACCCACCTTA
*
85928 TTTTTCTTTTCTT
1 TTTTTCTCTT-TT
85941 TTTTTCTCTTGTT
1 TTTTTCTCTT-TT
85954 CTTTTTCTCTTTT
1 -TTTTTCTCTTTT
85967 TTTTTCTCTTTT
1 TTTTTCTCTTTT
85979 TTTTT
1 TTTTT
85984 TCAATTTAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
12 17 0.43
13 13 0.32
14 10 0.25
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (12 bp):
TTTTTCTCTTTT
Found at i:85984 original size:13 final size:13
Alignment explanation
Indices: 85928--85985 Score: 75
Period size: 13 Copynumber: 4.5 Consensus size: 13
85918 ACCCACCTTA
85928 TTTTTCT-TTTCTT
1 TTTTTCTCTTT-TT
*
85941 TTTTTCTCTTGTTC
1 TTTTTCTCTT-TTT
85955 TTTTTCTC-TTTT
1 TTTTTCTCTTTTT
85967 TTTTTCTCTTTTT
1 TTTTTCTCTTTTT
85980 TTTTTC
1 TTTTTC
85986 AATTTAGGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
12 10 0.25
13 18 0.45
14 11 0.28
15 1 0.03
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (13 bp):
TTTTTCTCTTTTT
Found at i:85984 original size:14 final size:14
Alignment explanation
Indices: 85928--85984 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
85918 ACCCACCTTA
*
85928 TTTTTCT-TTTCTT
1 TTTTTCTCTTTTTT
* *
85941 TTTTTCTCTTGTTC
1 TTTTTCTCTTTTTT
85955 TTTTTCTC--TTTT
1 TTTTTCTCTTTTTT
85967 TTTTTCTCTTTTTT
1 TTTTTCTCTTTTTT
85981 TTTT
1 TTTT
85985 CAATTTAGGG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
12 10 0.28
13 7 0.19
14 19 0.53
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (14 bp):
TTTTTCTCTTTTTT
Found at i:86059 original size:16 final size:15
Alignment explanation
Indices: 86022--86060 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
86012 ACCATAAACG
*
86022 TTTTTCTCCTTTTTT
1 TTTTTTTCCTTTTTT
86037 TTCTTTTTCCTTTTTT
1 TT-TTTTTCCTTTTTT
*
86053 CTTTTTTC
1 TTTTTTTC
86061 AACTTAGGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTTTCCTTTTTT
Done.