Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005155.1 Hibiscus syriacus cultivar Beakdansim tig00011624_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: 97605
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:7955 original size:21 final size:21
Alignment explanation
Indices: 7931--7972 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
7921 AGTTTATTTT
7931 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
7952 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
7973 AACTTGTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:10697 original size:79 final size:78
Alignment explanation
Indices: 10564--10720 Score: 271
Period size: 79 Copynumber: 2.0 Consensus size: 78
10554 CATTTGAAAT
* *
10564 CGTTAAGATTTAAACATTTAATATTACTTTAAGGAGAAATTCAGAGATGGAATACTTATATTCAT
1 CGTTAAGATTCAAACATTTAATATTACTTTAAGGAGAAATTCAGAGATGAAATAC-T-TATTCAT
10629 T-GTACCAAGTGGCG
64 TCGTACCAAGTGGCG
10643 CGTTAAGATTCAAACATTTAATATTACTTTAAGGAGAAATTCAGAGATGAAATACTTATTCATTC
1 CGTTAAGATTCAAACATTTAATATTACTTTAAGGAGAAATTCAGAGATGAAATACTTATTCATTC
10708 GTACCAAGTGGCG
66 GTACCAAGTGGCG
10721 GAATGGTCCC
Statistics
Matches: 75, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
77 8 0.11
78 14 0.19
79 53 0.71
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (78 bp):
CGTTAAGATTCAAACATTTAATATTACTTTAAGGAGAAATTCAGAGATGAAATACTTATTCATTC
GTACCAAGTGGCG
Found at i:10876 original size:31 final size:31
Alignment explanation
Indices: 10835--10898 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
10825 AATTTGTATG
*
10835 TTCTTAATTAAATCCTCCCATAATTTAAAAAA
1 TTCTTAATTAAAT-CTCCCAAAATTTAAAAAA
* * *
10867 TTCTT-ATTAAGTCTCTCAAAATTTCAAAAA
1 TTCTTAATTAAATCTCCCAAAATTTAAAAAA
10897 TT
1 TT
10899 TTAGTTAGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 17 0.61
31 6 0.21
32 5 0.18
ACGTcount: A:0.41, C:0.17, G:0.02, T:0.41
Consensus pattern (31 bp):
TTCTTAATTAAATCTCCCAAAATTTAAAAAA
Found at i:15599 original size:28 final size:29
Alignment explanation
Indices: 15568--15647 Score: 87
Period size: 28 Copynumber: 2.8 Consensus size: 29
15558 TAAAAACACT
15568 TGGAAAACAACAAAGCAATAAAGTTT-CA
1 TGGAAAACAACAAAGCAATAAAGTTTCCA
*
15596 TGGAGAAA-AACAAAGCAATACA-TTTCCA
1 TGGA-AAACAACAAAGCAATAAAGTTTCCA
* *
15624 TAGG-AAACAATAAAGTAATAAAGT
1 T-GGAAAACAACAAAGCAATAAAGT
15648 CCTATGAGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
27 6 0.14
28 31 0.72
29 6 0.14
ACGTcount: A:0.54, C:0.12, G:0.15, T:0.19
Consensus pattern (29 bp):
TGGAAAACAACAAAGCAATAAAGTTTCCA
Found at i:17475 original size:21 final size:20
Alignment explanation
Indices: 17438--17476 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
17428 AGAAGGTGCA
* *
17438 AGAACCTAAGTAGCAAAACC
1 AGAACCTAAGGAACAAAACC
17458 AGAAGCCTAAGGAACAAAA
1 AGAA-CCTAAGGAACAAAA
17477 ATGGCAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.54, C:0.21, G:0.18, T:0.08
Consensus pattern (20 bp):
AGAACCTAAGGAACAAAACC
Found at i:19069 original size:3 final size:3
Alignment explanation
Indices: 19043--19189 Score: 185
Period size: 3 Copynumber: 49.0 Consensus size: 3
19033 ATGTGTAGTG
* * * *
19043 TAA TAT TAA TAA AAA TAG TAA TAA TAA TAA TAA TTAA TAA -ACA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TA-A TAA
*
19089 TAA TAA TAA TAA TAA TAC TAA TAA -AA TAA TAA TAA T-A TATA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A T-AA
19134 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19181 TAA TAA TAA
1 TAA TAA TAA
19190 ATTAAAAAAA
Statistics
Matches: 127, Mismatches: 9, Indels: 16
0.84 0.06 0.11
Matches are distributed among these distances:
2 7 0.06
3 111 0.87
4 8 0.06
5 1 0.01
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:19567 original size:39 final size:39
Alignment explanation
Indices: 19519--19593 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
19509 TGGTTATCTA
*
19519 GGGGTGACACGGCTCATACGCGATGAAGAGATCTGGTCG
1 GGGGAGACACGGCTCATACGCGATGAAGAGATCTGGTCG
* *
19558 GGGGAGACACGGCTCATACGTGATGAAGAGTTCTGG
1 GGGGAGACACGGCTCATACGCGATGAAGAGATCTGG
19594 CCATCTTTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.24, C:0.19, G:0.39, T:0.19
Consensus pattern (39 bp):
GGGGAGACACGGCTCATACGCGATGAAGAGATCTGGTCG
Found at i:19625 original size:132 final size:132
Alignment explanation
Indices: 19383--19737 Score: 473
Period size: 132 Copynumber: 2.7 Consensus size: 132
19373 GTTCGGGTCG
* * * **
19383 TCTAAGGGTGACACGGTTCCTACGTGATGAGGAAATCTGGTCGAGGGATGACATTGCTCATACGT
1 TCTAAGGGTGACACGGCT-CTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACGT
* * *
19448 GATGAAGAGTTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTATGTGATGAGG-CGGCTGG
65 GATGAAGAGTTTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACGTGATGAGGACGGCTGG
19512 TTA
130 TTA
* * *
19515 TCTAGGGGTGACACGGCTCATACGCGATGAAGAGATCTGGTCGGGGGA-GACACGGCTCATACGT
1 TCTAAGGGTGACACGGCTC-TACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACGT
**
19579 GATGAAGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACGTGATGAGGACGTTTG
65 GATGAAGAGTT-TGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACGTGATGAGGACGGCTG
19644 GTTA
129 GTTA
* * * * **
19648 TCTATGGTTGACACGGCTTCTACGTGATGAGGAGATCTGGTCAGGAGATGACACGAATC-TACGT
1 TCTAAGGGTGACACGGC-TCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACGT
19712 GATGAAGAGTTTTGGCCATCTTTAGG
65 GATGAAGAG-TTTGGCCATCTTTAGG
19738 GATAATGATT
Statistics
Matches: 196, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
131 26 0.13
132 83 0.42
133 75 0.38
134 12 0.06
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.26
Consensus pattern (132 bp):
TCTAAGGGTGACACGGCTCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCATACGTG
ATGAAGAGTTTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACGTGATGAGGACGGCTGGT
TA
Found at i:20063 original size:29 final size:30
Alignment explanation
Indices: 20014--20242 Score: 132
Period size: 29 Copynumber: 7.9 Consensus size: 30
20004 GACAAACTTT
*
20014 GTTTCAAAAGAAACAAACTCAAATATTTTG
1 GTTTCAAAAGAAACAAACTCAAAGATTTTG
**
20044 GTTTCAAAAGAAA-TGACTCAAAGATTTT-
1 GTTTCAAAAGAAACAAACTCAAAGATTTTG
* * * *
20072 -TTCCACGAAATTATCTTAAGAGAA-ACAAA-ATTTTG
1 GTTTCA--AAA-GA----AACA-AACTCAAAGATTTTG
* *
20107 G-TTCAAAAGAAACAGACTCAAAGA-ATT-
1 GTTTCAAAAGAAACAAACTCAAAGATTTTG
*
20134 -TTTCAAAAGAAAC-AACTCAAAGATTTTT
1 GTTTCAAAAGAAACAAACTCAAAGATTTTG
*
20162 ATTTCAAAAGAAAC-AACTCACAA-ATTTT-
1 GTTTCAAAAGAAACAAACTCA-AAGATTTTG
*
20190 ATTTCAAAAGAAAC-AACTC--AGACTTTT-
1 GTTTCAAAAGAAACAAACTCAAAGA-TTTTG
*
20217 GTTTCAAGAGAAACAAACTCAAAGAT
1 GTTTCAAAAGAAACAAACTCAAAGAT
20243 AGGTTTCGTT
Statistics
Matches: 158, Mismatches: 18, Indels: 47
0.71 0.08 0.21
Matches are distributed among these distances:
25 1 0.01
26 10 0.06
27 35 0.22
28 33 0.21
29 41 0.26
30 19 0.12
32 1 0.01
33 3 0.02
34 7 0.04
35 7 0.04
36 1 0.01
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.28
Consensus pattern (30 bp):
GTTTCAAAAGAAACAAACTCAAAGATTTTG
Found at i:20112 original size:92 final size:88
Alignment explanation
Indices: 19992--20161 Score: 223
Period size: 92 Copynumber: 1.9 Consensus size: 88
19982 TAAGAAAAAC
* * * *
19992 TATCTCAAGAGAGACAAACTTTGTTTCAAAAGAAACAAACTCAAATATTTTGGTTTCAAAAGAAA
1 TATCTCAAGAGAAACAAACTTTGGTTCAAAAGAAACAAACTCAAAGA-ATT--TTTCAAAAGAAA
**
20057 TGACTCAAAGATTTTTTCCACGAAAT
63 CAACTCAAAGATTTTTTCCACGAAAT
* * *
20083 TATCTTAAGAGAAACAAAATTTTGGTTCAAAAGAAACAGACTCAAAGAATTTTTCAAAAGAAACA
1 TATCTCAAGAGAAAC-AAACTTTGGTTCAAAAGAAACAAACTCAAAGAATTTTTCAAAAGAAACA
20148 ACTCAAAGATTTTT
65 ACTCAAAGATTTTT
20162 ATTTCAAAAG
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
89 26 0.38
91 15 0.22
92 28 0.41
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (88 bp):
TATCTCAAGAGAAACAAACTTTGGTTCAAAAGAAACAAACTCAAAGAATTTTTCAAAAGAAACAA
CTCAAAGATTTTTTCCACGAAAT
Found at i:20138 original size:27 final size:28
Alignment explanation
Indices: 20108--20242 Score: 163
Period size: 28 Copynumber: 4.8 Consensus size: 28
20098 AAAATTTTGG
*
20108 TTCAAAAGAAACAGACTCAAAGA-ATT-T
1 TTCAAAAGAAACA-ACTCAAAGATTTTAT
20135 TTCAAAAGAAACAACTCAAAGATTTTTAT
1 TTCAAAAGAAACAACTCAAAGA-TTTTAT
20164 TTCAAAAGAAACAACTCACAA-ATTTTAT
1 TTCAAAAGAAACAACTCA-AAGATTTTAT
*
20192 TTCAAAAGAAACAACTC--AGACTTTTGT
1 TTCAAAAGAAACAACTCAAAGA-TTTTAT
*
20219 TTCAAGAGAAACAAACTCAAAGAT
1 TTCAAAAGAAAC-AACTCAAAGAT
20243 AGGTTTCGTT
Statistics
Matches: 96, Mismatches: 3, Indels: 16
0.83 0.03 0.14
Matches are distributed among these distances:
25 1 0.01
26 10 0.10
27 29 0.30
28 30 0.31
29 21 0.22
30 5 0.05
ACGTcount: A:0.49, C:0.16, G:0.09, T:0.26
Consensus pattern (28 bp):
TTCAAAAGAAACAACTCAAAGATTTTAT
Found at i:20578 original size:29 final size:30
Alignment explanation
Indices: 20528--20584 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
20518 CTCAAGGTGT
* *
20528 GTGTTTCAAGAGAAACTAACTCAAAGATAG
1 GTGTTTCAAAAGAAACGAACTCAAAGATAG
*
20558 GTGTTTCAAAAGAAA-GGACTCAAAGAT
1 GTGTTTCAAAAGAAACGAACTCAAAGAT
20585 TTTTCATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (30 bp):
GTGTTTCAAAAGAAACGAACTCAAAGATAG
Found at i:20944 original size:35 final size:35
Alignment explanation
Indices: 20878--21000 Score: 149
Period size: 35 Copynumber: 3.5 Consensus size: 35
20868 ATAATTTGGA
*
20878 AAATTGTCTCAAGTAAGACAAAATTTG-TTTAGAG
1 AAATTGTCTCAAGTGAGACAAAATTTGTTTTAGAG
* *
20912 AAATTGTCTCAAATGAGACAAAAATTGTTTTAGAG
1 AAATTGTCTCAAGTGAGACAAAATTTGTTTTAGAG
* * * *
20947 AAATTCTCTCAAGCGAGACAAAGTTTGTTTTTGAG
1 AAATTGTCTCAAGTGAGACAAAATTTGTTTTAGAG
**
20982 AAAACGATCTCAAGTGAGA
1 AAATTG-TCTCAAGTGAGA
21001 TCAACTTTGT
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
34 24 0.32
35 39 0.53
36 11 0.15
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (35 bp):
AAATTGTCTCAAGTGAGACAAAATTTGTTTTAGAG
Found at i:21178 original size:101 final size:104
Alignment explanation
Indices: 20967--21188 Score: 239
Period size: 101 Copynumber: 2.2 Consensus size: 104
20957 AAGCGAGACA
* * *
20967 AAGTTTGTTTT-TGAG-AA-AACGATCTCAAGTGAGATCAACTTTGTTTAATGTGAACAAATTCA
1 AAGTTTGTTTTAAGAGAAATAACAATCTCAAGAGAGATCAACTTTGTTTAATGTGAACAAATTCA
* *
21029 AAATTTGTATTCTCAAAGGAAAAATGTCTCAACAACACG
66 AAATTTGTATTATCAAAGGAAAAATATCTCAACAACACG
* * *
21068 AATTTTGTTTTGAA-AGAAATAACAATCTCAAGAGAGATTAATTTTGTTTCAA-GTG-A-AAATT
1 AAGTTTGTTTT-AAGAGAAATAACAATCTCAAGAGAGATCAACTTTGTTT-AATGTGAACAAATT
* * *
21129 CGAAATTTGTA-TATCAAAGGAAAAA-ATCTCAAGTAAGGA-G
64 CAAAATTTGTATTATCAAAGGAAAAATATCTCAA-CAA-CACG
21169 AAGTTTGTTTTAAGAGAAAT
1 AAGTTTGTTTTAAGAGAAAT
21189 TGCCTTAAAT
Statistics
Matches: 101, Mismatches: 12, Indels: 16
0.78 0.09 0.12
Matches are distributed among these distances:
100 8 0.08
101 42 0.42
102 18 0.18
103 3 0.03
104 28 0.28
105 2 0.02
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.32
Consensus pattern (104 bp):
AAGTTTGTTTTAAGAGAAATAACAATCTCAAGAGAGATCAACTTTGTTTAATGTGAACAAATTCA
AAATTTGTATTATCAAAGGAAAAATATCTCAACAACACG
Found at i:22945 original size:15 final size:16
Alignment explanation
Indices: 22900--22969 Score: 58
Period size: 15 Copynumber: 4.5 Consensus size: 16
22890 TTCTCTTTGT
* *
22900 TTCTTTCCTTTACTTC
1 TTCTTTGCTTTATTTC
*
22916 TT-TTTGCTTTGTTTC
1 TTCTTTGCTTTATTTC
22931 TTCTTTGC-TTATTTC
1 TTCTTTGCTTTATTTC
*
22946 -TCTTTGTTTTGATTTGC
1 TTCTTTGCTTT-ATTT-C
22963 -TCTTTGC
1 TTCTTTGC
22970 ACTTTGTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
14 6 0.14
15 20 0.45
16 11 0.25
17 7 0.16
ACGTcount: A:0.04, C:0.20, G:0.10, T:0.66
Consensus pattern (16 bp):
TTCTTTGCTTTATTTC
Found at i:23375 original size:23 final size:23
Alignment explanation
Indices: 23349--23412 Score: 103
Period size: 22 Copynumber: 2.8 Consensus size: 23
23339 GAAAATTGAT
*
23349 TCGAGATGCCCCACATTGTCTTC
1 TCGAGATGCCCCATATTGTCTTC
*
23372 TCGAGATG-CCCATGTTGTCTTC
1 TCGAGATGCCCCATATTGTCTTC
23394 TCGAGATGCCCCATATTGT
1 TCGAGATGCCCCATATTGT
23413 GACTTCTTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 20 0.54
23 17 0.46
ACGTcount: A:0.17, C:0.30, G:0.20, T:0.33
Consensus pattern (23 bp):
TCGAGATGCCCCATATTGTCTTC
Found at i:28385 original size:3 final size:3
Alignment explanation
Indices: 28364--28458 Score: 129
Period size: 3 Copynumber: 32.0 Consensus size: 3
28354 ATATGTAGTG
* * *
28364 TAA TAT TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
28412 CAA -AA TAA TAA TAA TAA TAA CAT TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
28459 ATAAGATTAA
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
2 2 0.03
3 78 0.98
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:28472 original size:15 final size:16
Alignment explanation
Indices: 28368--28476 Score: 73
Period size: 15 Copynumber: 6.9 Consensus size: 16
28358 GTAGTGTAAT
*
28368 ATTAATAA-AAATAAT
1 ATTAATAATAAATAAC
* *
28383 AATAATAATAATAATAAA
1 ATTAATAAT-A-AATAAC
* * *
28401 AATAATAATAACAAAAT
1 ATTAATAATAA-ATAAC
*
28418 AATAATAAT-AATAAC
1 ATTAATAATAAATAAC
*
28433 ATTAATAAT-AATAAT
1 ATTAATAATAAATAAC
* *
28448 AATAATAATAAATAAG
1 ATTAATAATAAATAAC
28464 ATTAA-AATAAATA
1 ATTAATAATAAATA
28477 GAAAGAGGAC
Statistics
Matches: 78, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
15 39 0.50
16 11 0.14
17 14 0.18
18 14 0.18
ACGTcount: A:0.68, C:0.02, G:0.01, T:0.29
Consensus pattern (16 bp):
ATTAATAATAAATAAC
Found at i:28685 original size:11 final size:11
Alignment explanation
Indices: 28643--28686 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
28633 CACGGTAAAA
28643 AGAAGAAGAAG
1 AGAAGAAGAAG
28654 AG-A-AAGAAG
1 AGAAGAAGAAG
*
28663 AGAAGAAAAAG
1 AGAAGAAGAAG
*
28674 AGAAGATGAAG
1 AGAAGAAGAAG
28685 AG
1 AG
28687 CTAGCTTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
9 8 0.29
10 2 0.07
11 18 0.64
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (11 bp):
AGAAGAAGAAG
Found at i:33769 original size:23 final size:23
Alignment explanation
Indices: 33734--33795 Score: 65
Period size: 25 Copynumber: 2.7 Consensus size: 23
33724 TGCCATAACC
33734 ATATT-TTTTAAAAACAATTA-A
1 ATATTATTTTAAAAACAATTAGA
*
33755 ATATTATTTTAAAAAATAATTATGA
1 ATATTATTTT-AAAAACAATTA-GA
*
33780 ATTTTATTTTGAAAAA
1 ATATTATTTT-AAAAA
33796 TTGATGATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 5 0.15
22 4 0.12
23 10 0.29
25 15 0.44
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (23 bp):
ATATTATTTTAAAAACAATTAGA
Found at i:36084 original size:12 final size:11
Alignment explanation
Indices: 36067--36114 Score: 69
Period size: 12 Copynumber: 4.1 Consensus size: 11
36057 ATTTGTAAAC
36067 AAAATAATTAAT
1 AAAATAA-TAAT
36079 AAAATAATAAT
1 AAAATAATAAT
36090 AATAATAATAATT
1 AA-AATAATAA-T
36103 AAAATAATAAT
1 AAAATAATAAT
36114 A
1 A
36115 TTTTTTTGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
11 8 0.24
12 23 0.68
13 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:36089 original size:3 final size:3
Alignment explanation
Indices: 36069--36114 Score: 60
Period size: 3 Copynumber: 15.3 Consensus size: 3
36059 TTGTAAACAA
36069 AAT AATT AAT AA- AAT AAT AAT AAT AAT AAT AATT AA- AAT AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
36114 A
1 A
36115 TTTTTTTGAC
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 4 0.10
3 29 0.74
4 6 0.15
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:36098 original size:24 final size:24
Alignment explanation
Indices: 36069--36114 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
36059 TTGTAAACAA
36069 AATAATTAA-TAAAATAATAATAAT
1 AATAA-TAATTAAAATAATAATAAT
36093 AATAATAATTAAAATAATAATA
1 AATAATAATTAAAATAATAATA
36115 TTTTTTTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
AATAATAATTAAAATAATAATAAT
Found at i:36450 original size:43 final size:43
Alignment explanation
Indices: 36401--36633 Score: 165
Period size: 43 Copynumber: 5.4 Consensus size: 43
36391 ATAACACGGT
*
36401 TCCTACGCGATGAGGACGGCTAGTTATCTAGGGGTGACACTGC
1 TCCTACGTGATGAGGACGGCTAGTTATCTAGGGGTGACACTGC
* ** *
36444 TCCTACGTGATGAGGA-GGTCT-GGTCGCT--GGATGACA-TGGC
1 TCCTACGTGATGAGGACGG-CTAGTTATCTAGGGGTGACACT-GC
* * * * * *
36484 TCCTACGTGATGAGGACTG-TAGATCATCTTTAGAGATGATAACACGGT
1 TCCTACGTGATGAGGACGGCTAG-TTATC--TAG-G--GGTGACACTGC
* * * *
36532 TCCTACGTGATGAGGACGGCTGGTTATATAGGGGTGACACGGT
1 TCCTACGTGATGAGGACGGCTAGTTATCTAGGGGTGACACTGC
* * *
36575 TCCTACGTGATGAGGACAGCTGGTTATATAGGGGTGACA-TAGC
1 TCCTACGTGATGAGGACGGCTAGTTATCTAGGGGTGACACT-GC
*
36618 TCCTACATGATGAGGA
1 TCCTACGTGATGAGGA
36634 GGTCTGGTCG
Statistics
Matches: 152, Mismatches: 23, Indels: 30
0.74 0.11 0.15
Matches are distributed among these distances:
39 2 0.01
40 26 0.17
41 2 0.01
42 6 0.04
43 81 0.53
45 1 0.01
46 4 0.03
48 28 0.18
49 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (43 bp):
TCCTACGTGATGAGGACGGCTAGTTATCTAGGGGTGACACTGC
Found at i:36584 original size:131 final size:133
Alignment explanation
Indices: 36298--36590 Score: 405
Period size: 134 Copynumber: 2.2 Consensus size: 133
36288 GGTCTTCTAA
* *
36298 GGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGTAGATGACACAGTTCCTACGCGATGA
1 GGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGCTAGATGACACAGCTCCTACGCGATGA
*
36363 GGACGATATGCCATCTTTAGGGAGGGTGATAACACGGTTCCTACGCGATGAGGACGGCTAGTTAT
66 GGACGATATGCCATCTTTA-GGAGGATGATAACACGGTTCCTACGCGATGAGGACGGCTAGTTAT
*
36428 CTAG
130 ATAG
* * * ** *
36432 GGGTGACACTGCTCCTACGTGATGAGGAGGTCTGGTCGCTGGATGACATGGCTCCTACGTGATGA
1 GGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGCTAGATGACACAGCTCCTACGCGATGA
* * *
36497 GGACTG-TA-GATCATCTTTA-GA-GATGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTA
66 GGAC-GATATG-CCATCTTTAGGAGGATGATAACACGGTTCCTACGCGATGAGGACGGCTAGTTA
36558 TATAG
129 TATAG
*
36563 GGGTGACACGGTTCCTACGTGATGAGGA
1 GGGTGACACGGCTCCTACGTGATGAGGA
36591 CAGCTGGTTA
Statistics
Matches: 142, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
131 67 0.47
132 2 0.01
133 1 0.01
134 71 0.50
135 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (133 bp):
GGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGCTAGATGACACAGCTCCTACGCGATGA
GGACGATATGCCATCTTTAGGAGGATGATAACACGGTTCCTACGCGATGAGGACGGCTAGTTATA
TAG
Found at i:36598 original size:131 final size:132
Alignment explanation
Indices: 36298--36598 Score: 385
Period size: 131 Copynumber: 2.3 Consensus size: 132
36288 GGTCTTCTAA
* * *
36298 GGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGTAGATGACACAGTTCCTACGCGATGA
1 GGGTGACACGGCTCCTACGTGATGAGGA-AGCTGGTCGCTAGATGACACAGCTCCTACGCGATGA
*
36363 GGACGATATGCCATCTTTAGGGAGGGTGATAACACGGTTCCTACGCGATGAGGACGGCTAGTTAT
65 GGACGATATGCCATCTTTA-GGAGGATGATAACACGGTTCCTACGCGATGAGGACGGCTAGTTAT
*
36428 CTAG
129 ATAG
* * * ** *
36432 GGGTGACACTGCTCCTACGTGATGAGGAGGTCTGGTCGCTGGATGACATGGCTCCTACGTGATGA
1 GGGTGACACGGCTCCTACGTGATGAGGAAG-CTGGTCGCTAGATGACACAGCTCCTACGCGATGA
* * *
36497 GGACTG-TA-GATCATCTTTA-GA-GATGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTA
65 GGAC-GATATG-CCATCTTTAGGAGGATGATAACACGGTTCCTACGCGATGAGGACGGCTAGTTA
36558 TATAG
128 TATAG
*
36563 GGGTGACACGGTTCCTACGTGATGAGGACAGCTGGT
1 GGGTGACACGGCTCCTACGTGATGAGGA-AGCTGGT
36599 TATATAGGGG
Statistics
Matches: 146, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
131 72 0.49
132 3 0.02
133 1 0.01
134 69 0.47
135 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (132 bp):
GGGTGACACGGCTCCTACGTGATGAGGAAGCTGGTCGCTAGATGACACAGCTCCTACGCGATGAG
GACGATATGCCATCTTTAGGAGGATGATAACACGGTTCCTACGCGATGAGGACGGCTAGTTATAT
AG
Found at i:37106 original size:36 final size:36
Alignment explanation
Indices: 37048--37130 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 36
37038 AGTGAGACGG
* *
37048 AATTTGTTTTGAGAGAAATTGTCTTAAGCGAGACAA
1 AATTTGTTTTGAGAGAAATTGTCTCAAGCAAGACAA
* * *
37084 AATTTGTTTTTATA-AAACTTGTCTCAAGCAAGAGAA
1 AATTTGTTTTGAGAGAAA-TTGTCTCAAGCAAGACAA
37120 AATTTTGTTTT
1 AA-TTTGTTTT
37131 AAGAAAAACA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
35 3 0.08
36 29 0.73
37 8 0.20
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (36 bp):
AATTTGTTTTGAGAGAAATTGTCTCAAGCAAGACAA
Found at i:37483 original size:16 final size:16
Alignment explanation
Indices: 37452--37485 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
37442 TTCATGTTTC
*
37452 ATGTATGTATGCATTG
1 ATGTATGTATACATTG
*
37468 ATGTATGTATATATTG
1 ATGTATGTATACATTG
37484 AT
1 AT
37486 ATGTGAGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (16 bp):
ATGTATGTATACATTG
Found at i:39941 original size:23 final size:22
Alignment explanation
Indices: 39915--39978 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
39905 CAGCTCATAT
39915 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* *
39938 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
39961 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
39979 TATAAAAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:40119 original size:103 final size:103
Alignment explanation
Indices: 39994--40211 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
39984 AAATGTCCAT
**
39994 AAGGACCACATATCATTCCTTAAGAACCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAACCATATACATATAACAAGGATCAAGTATGTGTCTCACCA
*
40059 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
*
40097 AAGGACCACATATCATTCCTTAAGAATCATATACATATAACAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAACCATATACATATAACAAGGATCAAGTATGTGTCTCACCA
40162 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
40200 AAGGACCACATA
1 AAGGACCACATA
40212 GACCCTCTAC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAACCATATACATATAACAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATATCCCG
Found at i:40715 original size:20 final size:20
Alignment explanation
Indices: 40690--40730 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
40680 TTTTTCATTA
*
40690 TGGGGGAATCGGTTCCCCTC
1 TGGGGGAATCGATTCCCCTC
*
40710 TGGGGGTATCGATTCCCCTC
1 TGGGGGAATCGATTCCCCTC
40730 T
1 T
40731 AGCGTTCTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.29, G:0.32, T:0.29
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCTC
Found at i:46880 original size:23 final size:22
Alignment explanation
Indices: 46854--46917 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
46844 CAGCTCATAT
46854 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* *
46877 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
46900 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
46918 TATAAAAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:47058 original size:103 final size:102
Alignment explanation
Indices: 46933--47149 Score: 380
Period size: 103 Copynumber: 2.1 Consensus size: 102
46923 AAATGTCCAT
** *
46933 AAGGACCACATATCATTCCTTAAGAACCATATACATATGCCAAGGATCAAGTATGTGTCTTACCA
1 AAGGACCACATATCATTCCTTAAGAACCATATACATATAACAAGGATCAAGTATGTGTCTCACCA
*
46998 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GAC-TCACACATGTTCCAAAGAATACATATATATCCCG
*
47036 AAGGACCACATATCATTCCTTAAGAATCATATACATATAACAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAACCATATACATATAACAAGGATCAAGTATGTGTCTCACCA
47101 GACTCACACATGTTCCAAAGAATACATATATATCCCG
66 GACTCACACATGTTCCAAAGAATACATATATATCCCG
47138 AAGGACCACATA
1 AAGGACCACATA
47150 GACCCTCTAC
Statistics
Matches: 109, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
102 45 0.41
103 64 0.59
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (102 bp):
AAGGACCACATATCATTCCTTAAGAACCATATACATATAACAAGGATCAAGTATGTGTCTCACCA
GACTCACACATGTTCCAAAGAATACATATATATCCCG
Found at i:48183 original size:3 final size:3
Alignment explanation
Indices: 48175--48201 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
48165 TCACGGTTGG
48175 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
48202 GAAATGTCTG
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:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:48592 original size:23 final size:23
Alignment explanation
Indices: 48562--48608 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
48552 TCAATGTCAA
48562 TACTGTTAGTGCTTCTTATATGG
1 TACTGTTAGTGCTTCTTATATGG
*
48585 TACTGTTAGTGCTTCTTTTATGG
1 TACTGTTAGTGCTTCTTATATGG
48608 T
1 T
48609 CATTCTTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (23 bp):
TACTGTTAGTGCTTCTTATATGG
Found at i:53236 original size:11 final size:13
Alignment explanation
Indices: 53204--53233 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
53194 TGGCCAAAGA
53204 TGAAAAGGTATGT
1 TGAAAAGGTATGT
53217 TGAAAAGGTATG-
1 TGAAAAGGTATGT
53229 TGAAA
1 TGAAA
53234 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:58299 original size:23 final size:23
Alignment explanation
Indices: 58269--58327 Score: 104
Period size: 22 Copynumber: 2.7 Consensus size: 23
58259 ATAACCATTT
58269 TTTTAAAAACAATT-AAATATTA
1 TTTTAAAAACAATTAAAATATTA
58291 TTTTAAAAACAATTAAAATATTA
1 TTTTAAAAACAATTAAAATATTA
58314 TTTTAAAAA-AATTA
1 TTTTAAAAACAATTA
58328 TGACTTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
22 19 0.53
23 17 0.47
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (23 bp):
TTTTAAAAACAATTAAAATATTA
Found at i:58345 original size:22 final size:24
Alignment explanation
Indices: 58311--58358 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
58301 AATTAAAATA
58311 TTATTTTAAAAAAATT-ATGACTT
1 TTATTTTAAAAAAATTGATGACTT
* *
58334 TTATTTT-GAAAAATTGATGATTT
1 TTATTTTAAAAAAATTGATGACTT
58357 TT
1 TT
58359 TAATTGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (24 bp):
TTATTTTAAAAAAATTGATGACTT
Found at i:58358 original size:23 final size:23
Alignment explanation
Indices: 58288--58346 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
58278 CAATTAAATA
* * *
58288 TTATTTTAAAAACAATTA-AAATA
1 TTATTTTAAAAA-AATTATGACTT
58311 TTATTTTAAAAAAATTATGACTT
1 TTATTTTAAAAAAATTATGACTT
*
58334 TTATTTTGAAAAA
1 TTATTTTAAAAAA
58347 TTGATGATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 5 0.16
23 26 0.84
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (23 bp):
TTATTTTAAAAAAATTATGACTT
Found at i:59721 original size:2 final size:2
Alignment explanation
Indices: 59709--59754 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
59699 CGTTTCTATT
59709 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59750 TA TA T
1 TA TA T
59755 GAAAAACATA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60174 original size:18 final size:17
Alignment explanation
Indices: 60147--60180 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
60137 GATTCGTGGT
60147 TTTCCTTTTTTTTCTTC
1 TTTCCTTTTTTTTCTTC
60164 TTTCTCTTTTTTTTCTT
1 TTTC-CTTTTTTTTCTT
60181 TTCAAGCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTCCTTTTTTTTCTTC
Found at i:61218 original size:21 final size:21
Alignment explanation
Indices: 61194--61254 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
61184 AATAACCATC
61194 GAATTCGCAACACAGAATTTG
1 GAATTCGCAACACAGAATTTG
* *
61215 GAATTCGCAACATAGAA-TTC
1 GAATTCGCAACACAGAATTTG
* *
61235 GAATTCACAACTC-GAATTTG
1 GAATTCGCAACACAGAATTTG
61255 ACAATTTCGC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 3 0.09
20 14 0.42
21 16 0.48
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (21 bp):
GAATTCGCAACACAGAATTTG
Found at i:61274 original size:41 final size:41
Alignment explanation
Indices: 61192--61274 Score: 98
Period size: 41 Copynumber: 2.0 Consensus size: 41
61182 AAAATAACCA
* *
61192 TCGAATTCGCAACACAGAATTTGGAATTCGCAACATAGAAT
1 TCGAATTCACAACACAGAATTTGCAATTCGCAACATAGAAT
* *
61233 TCGAATTCACAACTC-GAATTTGACAATTTCGCAATAT-GAAT
1 TCGAATTCACAACACAGAATTTG-CAA-TTCGCAACATAGAAT
61274 T
1 T
61275 TCTTTTTCGC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
40 7 0.19
41 20 0.56
42 9 0.25
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.29
Consensus pattern (41 bp):
TCGAATTCACAACACAGAATTTGCAATTCGCAACATAGAAT
Found at i:62202 original size:12 final size:12
Alignment explanation
Indices: 62181--62214 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
62171 ACTAAATTTC
*
62181 CAATACCAAACA
1 CAATATCAAACA
62193 CAATATCAAACA
1 CAATATCAAACA
*
62205 CAATCTCAAA
1 CAATATCAAA
62215 ATCCATAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:62410 original size:24 final size:24
Alignment explanation
Indices: 62340--62417 Score: 120
Period size: 24 Copynumber: 3.2 Consensus size: 24
62330 GTATTCGAAA
*
62340 TTTGATCTTGGTCAATACCCAGAC
1 TTTGATCTTGGTCAATACCCGGAC
*
62364 TTTGAGCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
62388 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
62412 TTTGAT
1 TTTGAT
62418 GATGTTTCAG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.37
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:63242 original size:20 final size:20
Alignment explanation
Indices: 63217--63339 Score: 131
Period size: 20 Copynumber: 6.2 Consensus size: 20
63207 TTTATTTCAA
*
63217 GAAAATCAAATTCGCAACAC
1 GAAAATCAAATTCGCAACTC
* *
63237 GAAAATCGAATTCGCAATTC
1 GAAAATCAAATTCGCAACTC
* *
63257 GAAAATGAAATTCGCAACTT
1 GAAAATCAAATTCGCAACTC
*
63277 GAAAA-CAAAAATCGCAACTC
1 GAAAATC-AAATTCGCAACTC
*
63297 GAAAATGAAATTCGCAACTC
1 GAAAATCAAATTCGCAACTC
** **
63317 GAATTTTGAATTCGCAACTC
1 GAAAATCAAATTCGCAACTC
63337 GAA
1 GAA
63340 TTTCATTTTC
Statistics
Matches: 85, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
20 85 1.00
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.21
Consensus pattern (20 bp):
GAAAATCAAATTCGCAACTC
Found at i:63261 original size:40 final size:40
Alignment explanation
Indices: 63217--63339 Score: 149
Period size: 40 Copynumber: 3.1 Consensus size: 40
63207 TTTATTTCAA
* * *
63217 GAAAATCAAATTCGCAACACGAAAATCGAATTCGCAATTC
1 GAAAATGAAATTCGCAACTCGAAAATCGAATTCGCAACTC
* * *
63257 GAAAATGAAATTCGCAACTTGAAAA-CAAAAATCGCAACTC
1 GAAAATGAAATTCGCAACTCGAAAATC-GAATTCGCAACTC
** *
63297 GAAAATGAAATTCGCAACTCGAATTTTGAATTCGCAACTC
1 GAAAATGAAATTCGCAACTCGAAAATCGAATTCGCAACTC
63337 GAA
1 GAA
63340 TTTCATTTTC
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
39 1 0.01
40 68 0.99
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.21
Consensus pattern (40 bp):
GAAAATGAAATTCGCAACTCGAAAATCGAATTCGCAACTC
Found at i:63364 original size:40 final size:40
Alignment explanation
Indices: 63320--63398 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
63310 GCAACTCGAA
63320 TTTTGAATTCGCAACT-CGAATTTCATTTTCGAGTTGCGAT
1 TTTTGAATTCG-AACTGCGAATTTCATTTTCGAGTTGCGAT
** **
63360 TTTTGTTTTCGAGTTGCGAATTTCATTTTCGAGTTGCGA
1 TTTTGAATTCGAACTGCGAATTTCATTTTCGAGTTGCGA
63399 ATTTCATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 2 0.06
40 32 0.94
ACGTcount: A:0.19, C:0.15, G:0.20, T:0.46
Consensus pattern (40 bp):
TTTTGAATTCGAACTGCGAATTTCATTTTCGAGTTGCGAT
Found at i:63409 original size:40 final size:40
Alignment explanation
Indices: 63336--63423 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 40
63326 ATTCGCAACT
* ** *
63336 CGAATTTCATTTTCGAGTTGCGATTTTTGTTTTCGAGTTG
1 CGAATTTCATTTTCGAGTTGCGAATTTCATTTTCGAGTTA
63376 CGAATTTCATTTTCGAGTTGCGAATTTCATTTTCGAGTTA
1 CGAATTTCATTTTCGAGTTGCGAATTTCATTTTCGAGTTA
*
63416 CGATTTTC
1 CGAATTTC
63424 GTGTTGCGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.18, C:0.15, G:0.19, T:0.48
Consensus pattern (40 bp):
CGAATTTCATTTTCGAGTTGCGAATTTCATTTTCGAGTTA
Found at i:63423 original size:20 final size:20
Alignment explanation
Indices: 63336--63414 Score: 131
Period size: 20 Copynumber: 4.0 Consensus size: 20
63326 ATTCGCAACT
63336 CGAATTTCATTTTCGAGTTG
1 CGAATTTCATTTTCGAGTTG
* **
63356 CGATTTTTGTTTTCGAGTTG
1 CGAATTTCATTTTCGAGTTG
63376 CGAATTTCATTTTCGAGTTG
1 CGAATTTCATTTTCGAGTTG
63396 CGAATTTCATTTTCGAGTT
1 CGAATTTCATTTTCGAGTT
63415 ACGATTTTCG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.18, C:0.14, G:0.20, T:0.48
Consensus pattern (20 bp):
CGAATTTCATTTTCGAGTTG
Found at i:64095 original size:40 final size:40
Alignment explanation
Indices: 64051--64134 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
64041 TTGTGAAATT
** ** *
64051 GAAACTTGCTTTGAGAA-TTAGAAAATCTTGTTGCGAAAAG
1 GAAACTTGAGTTGAGAATTTA-AAAATCGAGTTGCGAAAAA
*
64091 GAAACTTGAGTTGTGAATTTAAAAATCGAGTTGCGAAAAA
1 GAAACTTGAGTTGAGAATTTAAAAATCGAGTTGCGAAAAA
64131 GAAA
1 GAAA
64135 TTCGTGTTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
40 34 0.92
41 3 0.08
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (40 bp):
GAAACTTGAGTTGAGAATTTAAAAATCGAGTTGCGAAAAA
Found at i:64144 original size:40 final size:40
Alignment explanation
Indices: 64080--64167 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
64070 AGAAAATCTT
* *
64080 GTTGCGAAAAGGAAACTTGAGTTGTGAATTTAAAAATCGA
1 GTTGCGAAAAAGAAACTTGAGTTGTGAATTCAAAAATCGA
* * * *
64120 GTTGCGAAAAAGAAA-TTCGTGTTGTGAATTCCAAATTTGA
1 GTTGCGAAAAAGAAACTT-GAGTTGTGAATTCAAAAATCGA
64160 GTTGCGAA
1 GTTGCGAA
64168 TTTGGAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 2 0.05
40 39 0.95
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.30
Consensus pattern (40 bp):
GTTGCGAAAAAGAAACTTGAGTTGTGAATTCAAAAATCGA
Found at i:64183 original size:20 final size:20
Alignment explanation
Indices: 64160--64211 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
64150 CCAAATTTGA
64160 GTTGCGAATTTGGAAATT-GT
1 GTTGCGAATTTGG-AATTAGT
* **
64180 GTTGCGAAATTGGCTTTAGT
1 GTTGCGAATTTGGAATTAGT
64200 GTTGCGAATTTG
1 GTTGCGAATTTG
64212 TTGGTTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.21, C:0.08, G:0.31, T:0.40
Consensus pattern (20 bp):
GTTGCGAATTTGGAATTAGT
Found at i:65388 original size:24 final size:24
Alignment explanation
Indices: 65361--65414 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
65351 TTAAGTCACT
*
65361 TTATTTTATCAA-CAAAAAATAACC
1 TTATTATATCAATC-AAAAATAACC
* *
65385 TTATTATATCAATCATAAATAATC
1 TTATTATATCAATCAAAAATAACC
65409 TTATTA
1 TTATTA
65415 AAATGATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (24 bp):
TTATTATATCAATCAAAAATAACC
Found at i:65819 original size:29 final size:29
Alignment explanation
Indices: 65744--65826 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 29
65734 ACCCCAATAC
* *
65744 AGGTCGTCATGCACTCCCAGCGACCTACA
1 AGGTCGCCAAGCACTCCCAGCGACCTACA
* ***
65773 AGGTCGCCATGCACTCCCAGCGACCTTGT
1 AGGTCGCCAAGCACTCCCAGCGACCTACA
* * *
65802 AGGTTGCCAAGCAGTCCCGGCGACC
1 AGGTCGCCAAGCACTCCCAGCGACC
65827 AAGCTGGTGA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.20, C:0.37, G:0.25, T:0.17
Consensus pattern (29 bp):
AGGTCGCCAAGCACTCCCAGCGACCTACA
Found at i:66085 original size:29 final size:28
Alignment explanation
Indices: 66037--66117 Score: 99
Period size: 29 Copynumber: 2.8 Consensus size: 28
66027 AACCAAGCTT
* * *
66037 GGTCGCCGGGACTGCTTGGCGACTTACAA
1 GGTCGCTGGGAGTGCATGGCGACTT-CAA
**
66066 GGTCGCTGGGAGTGCATGGCGACCTTGTA
1 GGTCGCTGGGAGTGCATGGCGA-CTTCAA
66095 GGTCGCTGGGAGTGCATGGCGAC
1 GGTCGCTGGGAGTGCATGGCGAC
66118 CTGTGTTGGG
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
28 1 0.02
29 42 0.91
30 3 0.07
ACGTcount: A:0.15, C:0.23, G:0.41, T:0.21
Consensus pattern (28 bp):
GGTCGCTGGGAGTGCATGGCGACTTCAA
Found at i:66143 original size:32 final size:32
Alignment explanation
Indices: 66066--66160 Score: 135
Period size: 32 Copynumber: 3.1 Consensus size: 32
66056 CGACTTACAA
*
66066 GGTCGCTGGGAGTGCATGGCGACCT-TG-T-A
1 GGTCGCTGGGAGTGCATGGCGACCTGTGTTGG
66095 GGTCGCTGGGAGTGCATGGCGACCTGTGTTGG
1 GGTCGCTGGGAGTGCATGGCGACCTGTGTTGG
*
66127 GGT-GTTGGGGAGTGCATGGCGACCTGTGTTGG
1 GGTCGCT-GGGAGTGCATGGCGACCTGTGTTGG
66159 GG
1 GG
66161 ACGTGCATGG
Statistics
Matches: 60, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
29 25 0.42
30 2 0.03
31 3 0.05
32 30 0.50
ACGTcount: A:0.11, C:0.17, G:0.47, T:0.25
Consensus pattern (32 bp):
GGTCGCTGGGAGTGCATGGCGACCTGTGTTGG
Found at i:70334 original size:16 final size:17
Alignment explanation
Indices: 70309--70342 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
70299 CTGAGGTATC
70309 ACATTGACTTTT-CAAA
1 ACATTGACTTTTACAAA
*
70325 ACATTTACTTTTACAAA
1 ACATTGACTTTTACAAA
70342 A
1 A
70343 GAATGAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (17 bp):
ACATTGACTTTTACAAA
Found at i:72360 original size:2 final size:2
Alignment explanation
Indices: 72355--72388 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
72345 CTAGTGTTTG
72355 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
72389 TAACCAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:89202 original size:3 final size:3
Alignment explanation
Indices: 89194--89238 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
89184 TGTAATTAGA
* *
89194 AAT AAT AATT ATT AAT AAT AAT ATT AAT AATT AAT AAT AAT AAT A
1 AAT AAT AA-T AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT A
89239 TATATTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
3 31 0.86
4 5 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:89216 original size:19 final size:19
Alignment explanation
Indices: 89194--89238 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
89184 TGTAATTAGA
*
89194 AATAATAATTATTAATAAT
1 AATAATAATAATTAATAAT
*
89213 AATATTAATAATTAATAAT
1 AATAATAATAATTAATAAT
89232 AATAATA
1 AATAATA
89239 TATATTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AATAATAATAATTAATAAT
Found at i:89224 original size:22 final size:22
Alignment explanation
Indices: 89196--89239 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
89186 TAATTAGAAA
*
89196 TAATAATTATTAATAATAATAT
1 TAATAATTAATAATAATAATAT
89218 TAATAATTAATAATAATAATAT
1 TAATAATTAATAATAATAATAT
89240 ATATTTTTTA
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAATAATTAATAATAATAATAT
Found at i:89780 original size:131 final size:131
Alignment explanation
Indices: 89430--89788 Score: 414
Period size: 131 Copynumber: 2.7 Consensus size: 131
89420 GTTTTGGTCG
* * *
89430 TCTAAGGGTGACATGGCTCCTACGTGATGAGGAGATCTGGTTGGTGGATGAAACGGTTCCTACAT
1 TCTAAGGGTGACATGGCTCCTACATGATGAGGAGATCTGGTCGGTGGATGAAACGGTTCCTACGT
* * *
89495 GATGAGGACGACTGGCCATCTTTAGAAATGG-TGATAACACGATTCCTACGCGATGAGGATGGCT
66 GATGAGGACGATTGGCCATCTTTAG----GGATGATAACACGATTCCTACGCGATGAGGACGACT
89559 GGTTA
127 GGTTA
* * * *
89564 TATAGGGGTGACATGGCTCGTACATGATGAGGAGATCTGGTCGGTGGATGAAACGGTTCCTCCGT
1 TCTAAGGGTGACATGGCTCCTACATGATGAGGAGATCTGGTCGGTGGATGAAACGGTTCCTACGT
* ** * * ** * *
89629 GATGAGGACGGTAAGCCATCTTTAGGGATGATAATACGGTTCCTGTGTGATGAGGACGACTTGTT
66 GATGAGGACGATTGGCCATCTTTAGGGATGATAACACGATTCCTACGCGATGAGGACGACTGGTT
89694 A
131 A
* * * * * * *
89695 TCTAAGGGTGACAGGGCTCCTACTTGATGAGGAGGTCTGCTCGGTGGATGACACGATTCCTATGT
1 TCTAAGGGTGACATGGCTCCTACATGATGAGGAGATCTGGTCGGTGGATGAAACGGTTCCTACGT
* * *
89760 GATGAGGACAATTGGTCATCTTTAAGGAT
66 GATGAGGACGATTGGCCATCTTTAGGGAT
89789 TTGTTTCAAG
Statistics
Matches: 188, Mismatches: 36, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
130 2 0.01
131 107 0.57
134 79 0.42
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.27
Consensus pattern (131 bp):
TCTAAGGGTGACATGGCTCCTACATGATGAGGAGATCTGGTCGGTGGATGAAACGGTTCCTACGT
GATGAGGACGATTGGCCATCTTTAGGGATGATAACACGATTCCTACGCGATGAGGACGACTGGTT
A
Found at i:90097 original size:102 final size:98
Alignment explanation
Indices: 89868--90098 Score: 228
Period size: 102 Copynumber: 2.3 Consensus size: 98
89858 GTTTCAAGGG
* * ** * * *
89868 AAACACTCTCAAGAGAGACAAAAATTGTTTCAAGAGAAACAATTTCAAAGTTTGTCTTAAGGAAG
1 AAACAATCTCAAGAGAGAC-AAAATTGTTTAAAGAGAAACAAACTCAAAATTTGTCTAAAGGAAA
* * * *
89933 ACTGTCTCAAGTGAGACATAGTTTGTTTTGAGAA
65 AATGTCTCAAGAGAGACAAAATTTGTTTTGAGAA
* * *
89967 AAACAATCTCAAGTGAGATCAACATTGTTTAAAGTGAAACAAACTCAAAATTTGTATCTCAAAGG
1 AAACAATCTCAAGAGAGA-CAAAATTGTTTAAAGAGAAACAAACTCAAAATTTG--TCT-AAAGG
* *
90032 AAAAATGTCTCAAGAGATACAAAATTTGTTTTGAGAG
62 AAAAATGTCTCAAGAGAGACAAAATTTGTTTTGAGAA
*** *
90069 AAATTGTCTCAAGCGAGACAAAATTTGTTT
1 AAACAATCTCAAGAGAGACAAAA-TTGTTT
90099 CTAGATAAAA
Statistics
Matches: 106, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
99 44 0.42
100 1 0.01
101 7 0.07
102 54 0.51
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (98 bp):
AAACAATCTCAAGAGAGACAAAATTGTTTAAAGAGAAACAAACTCAAAATTTGTCTAAAGGAAAA
ATGTCTCAAGAGAGACAAAATTTGTTTTGAGAA
Found at i:90118 original size:37 final size:35
Alignment explanation
Indices: 90031--90136 Score: 133
Period size: 37 Copynumber: 3.0 Consensus size: 35
90021 TATCTCAAAG
* *
90031 GAAAAA-TGTCTCAAGAGATACAAAATTTGTTTTGA
1 GAAAAATTGTCTCAAGCGAGACAAAATTTGTTTT-A
*
90066 GAGAAATTGTCTCAAGCGAGACAAAATTTGTTTCTA
1 GAAAAATTGTCTCAAGCGAGACAAAATTTGTTT-TA
* *
90102 GATAAAATTGTCTCAAGCGAGATAAATTTTGTTTT
1 GA-AAAATTGTCTCAAGCGAGACAAAATTTGTTTT
90137 TAAGAAAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
35 5 0.08
36 28 0.45
37 29 0.47
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (35 bp):
GAAAAATTGTCTCAAGCGAGACAAAATTTGTTTTA
Found at i:90145 original size:36 final size:36
Alignment explanation
Indices: 90031--90148 Score: 139
Period size: 36 Copynumber: 3.2 Consensus size: 36
90021 TATCTCAAAG
* * * *
90031 GAAAAATGTCTCAAGAGATACAAAATTTG-TTTTGA
1 GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTTAA
*
90066 GAGAAATTGTCTCAAGCGAGACAAAATTTGTTTCTAGA
1 GA-AAATTGTCTCAAGCGAGACAAAATTTGTTTTTA-A
* * *
90104 TAAAATTGTCTCAAGCGAGATAAATTTTGTTTTTAA
1 GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTTAA
90140 GAAAATTGT
1 GAAAATTGT
90149 ATCTAGTAAG
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
35 2 0.03
36 33 0.47
37 33 0.47
38 2 0.03
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (36 bp):
GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTTAA
Found at i:91830 original size:21 final size:21
Alignment explanation
Indices: 91805--91845 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
91795 CTCGTACAGG
91805 GGGTATCAGTACCCCTTCATA
1 GGGTATCAGTACCCCTTCATA
* *
91826 GGGTATCGGTACTCCTTCAT
1 GGGTATCAGTACCCCTTCAT
91846 TAAATTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.32
Consensus pattern (21 bp):
GGGTATCAGTACCCCTTCATA
Found at i:92230 original size:20 final size:21
Alignment explanation
Indices: 92205--92248 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
92195 ATTTTTAATG
*
92205 AAAAA-GATACCAATTGTTAA
1 AAAAAGGATACAAATTGTTAA
*
92225 AAAAAGGATATAAATTGTTAA
1 AAAAAGGATACAAATTGTTAA
92246 AAA
1 AAA
92249 GATACATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.59, C:0.05, G:0.11, T:0.25
Consensus pattern (21 bp):
AAAAAGGATACAAATTGTTAA
Found at i:92234 original size:21 final size:20
Alignment explanation
Indices: 92205--92262 Score: 66
Period size: 18 Copynumber: 3.0 Consensus size: 20
92195 ATTTTTAATG
*
92205 AAAAAGATACCAATTGTTAA
1 AAAAAGATACAAATTGTTAA
*
92225 AAAAAGGATATAAATTGTT--
1 AAAAA-GATACAAATTGTTAA
*
92244 AAAAAGATACATATTGTTA
1 AAAAAGATACAAATTGTTA
92263 CCAATTGTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 11 0.34
19 5 0.16
20 5 0.16
21 11 0.34
ACGTcount: A:0.53, C:0.05, G:0.12, T:0.29
Consensus pattern (20 bp):
AAAAAGATACAAATTGTTAA
Found at i:93416 original size:19 final size:20
Alignment explanation
Indices: 93373--93420 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
93363 TCTAAATCCT
*
93373 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
93393 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
93412 TTTTCAAAA
1 TTTTCAAAA
93421 GAAATTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:95110 original size:15 final size:15
Alignment explanation
Indices: 95060--95117 Score: 52
Period size: 17 Copynumber: 4.0 Consensus size: 15
95050 TGCTTCTTGT
95060 CTTCTTTTCTCTTTG
1 CTTCTTTTCTCTTTG
*
95075 CGTTTTTTTTCTCTTT-
1 C--TTCTTTTCTCTTTG
*
95091 -AT-TTTT-TCTTTG
1 CTTCTTTTCTCTTTG
95103 CTTCTTTTCTCTTTG
1 CTTCTTTTCTCTTTG
95118 TTTTGATTGG
Statistics
Matches: 34, Mismatches: 3, Indels: 12
0.69 0.06 0.24
Matches are distributed among these distances:
11 5 0.15
12 4 0.12
13 2 0.06
14 4 0.12
15 7 0.21
17 12 0.35
ACGTcount: A:0.02, C:0.21, G:0.07, T:0.71
Consensus pattern (15 bp):
CTTCTTTTCTCTTTG
Done.