Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007117.1 Hibiscus syriacus cultivar Beakdansim tig00018602_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: 63761
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:44 original size:2 final size:2
Alignment explanation
Indices: 39--64 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29 TTAAAAAAAG
39 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
65 ATAATAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:122 original size:21 final size:21
Alignment explanation
Indices: 98--147 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
88 ACCAAATGAA
98 TATAAATAAATAAAATATA-TG
1 TATAAAT-AATAAAATATAGTG
*
119 TATATAATAATAATATATAGTG
1 TATA-AATAATAAAATATAGTG
*
141 TAAAAAT
1 TATAAAT
148 CAATTGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (21 bp):
TATAAATAATAAAATATAGTG
Found at i:637 original size:37 final size:37
Alignment explanation
Indices: 596--700 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
586 GTGCTTGTGG
* * *
596 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * *
633 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
670 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
701 GACGAAAATA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:1747 original size:106 final size:106
Alignment explanation
Indices: 1435--3124 Score: 2484
Period size: 106 Copynumber: 16.0 Consensus size: 106
1425 TTCTAAGACT
* * ** *
1435 AATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACAGGGAAATTGTTTGTTGACAACCAGC
1 AATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGC
* * * * *
1499 CGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTTGAGTCC
65 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* * * *
1541 AATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAATCAGCC
1 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCG
* * * *
1600 ATCCCTTCTTCGTGAAGTTGAGCTTGTGTTGTCTTGG-GTCC
66 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TGGAGTCC
* * *
1641 AAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCG
1 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCG
*
1706 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCC
66 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* * * * *
1747 AATATCCTACGTTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCG
1 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCG
* * * *
1812 ATCCCTTCGTCGTGAAGTTGAAATTGTGTTGTCTTGAGTCC
66 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* * *
1853 AATATCTTTCGCTGTGAAGTTGAAATTGGCTCTG-AATATGAGAAGTTTTTTTGTTGACAACCAG
1 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAAT-TGGGAAG-TTGTTTGTTGACAACCAG
*
1917 CGGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
64 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* *
1960 AAAATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCG
1 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCG
* *
2025 GTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTTGAGTCC
66 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
*
2066 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCG
1 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCG
* *
2131 GTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTGTAGTCC
66 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* *
2172 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCG
1 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCG
*
2237 GTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
66 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* * *
2278 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTATTGACAAACAGCG
1 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCG
* *
2343 GTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTTGAGTCC
66 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* * * *
2384 AATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTTTTTATTGACAACCAGCG
1 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCG
*
2449 GTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
66 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* * * *
2490 AATATCCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCA
1 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCG
*
2555 GTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCC
66 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
*
2596 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCG
1 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCG
*
2661 GTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTGGAGTCC
66 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* * *
2702 AATATCCTTCGTTGTGAAATTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCG
1 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCG
*
2767 GTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
66 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* * * *
2808 AATATCCTTCGTTGTAAAATTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCG
1 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCG
*
2873 GTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
66 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* * *
2914 AATATCCTTCGCTGTGATGTTGAAATTGGCTCT-AAACTTTGGGAAATTGTTTATTGACAACCAG
1 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA--TTGGGAAGTTGTTTGTTGACAACCAG
*
2978 CGGTCCCTTCGTCGTGAAGTTGAATTTGCGTTGTCTGGAGTCC
64 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* * * * *
3021 AATATCCTTTGTTGTGAAATTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAACCCA-C
1 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA-CCAGC
* * * *
3085 GGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTTGAGT
65 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
3125 GGCACGATAT
Statistics
Matches: 1440, Mismatches: 128, Indels: 32
0.90 0.08 0.02
Matches are distributed among these distances:
100 80 0.06
101 5 0.00
102 4 0.00
104 3 0.00
105 11 0.01
106 1142 0.79
107 189 0.13
108 6 0.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCG
GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
Found at i:3522 original size:30 final size:32
Alignment explanation
Indices: 3486--3547 Score: 92
Period size: 30 Copynumber: 2.0 Consensus size: 32
3476 TTTGCATTAG
3486 GATGTTGAATC-CAAAAATGCCCC-AATATTT
1 GATGTTGAATCTCAAAAATGCCCCAAATATTT
*
3516 GATGTTGAATCTTCAAAGATGCCCCAAATATT
1 GATGTTGAATC-TCAAAAATGCCCCAAATATT
3548 CCTCATTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 11 0.39
32 11 0.39
33 6 0.21
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (32 bp):
GATGTTGAATCTCAAAAATGCCCCAAATATTT
Found at i:3727 original size:24 final size:24
Alignment explanation
Indices: 3699--3754 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
3689 AATATCAATA
3699 AAGAGTTTCGAAAGATGTTTAATC
1 AAGAGTTTCGAAAGATGTTTAATC
* *
3723 AAGAGTTTTGAAAGATGTTTAATT
1 AAGAGTTTCGAAAGATGTTTAATC
*
3747 AAAAGTTT
1 AAGAGTTT
3755 TGGAAATATC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.38
Consensus pattern (24 bp):
AAGAGTTTCGAAAGATGTTTAATC
Found at i:3971 original size:22 final size:22
Alignment explanation
Indices: 3953--4022 Score: 113
Period size: 22 Copynumber: 3.2 Consensus size: 22
3943 TGGTCAAATA
3953 TTTGGCATTTGATGCTCAAAGG
1 TTTGGCATTTGATGCTCAAAGG
*
3975 TTTGGCATTTGATGCTCATAGG
1 TTTGGCATTTGATGCTCAAAGG
* *
3997 TTTGGCATTTGATGTTCAATGG
1 TTTGGCATTTGATGCTCAAAGG
4019 TTTG
1 TTTG
4023 ATGGGGTAGC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.19, C:0.11, G:0.27, T:0.43
Consensus pattern (22 bp):
TTTGGCATTTGATGCTCAAAGG
Found at i:4644 original size:7 final size:7
Alignment explanation
Indices: 4628--4707 Score: 67
Period size: 7 Copynumber: 11.6 Consensus size: 7
4618 TTTTTGTCCC
4628 TTTTTC-
1 TTTTTCT
*
4634 TTTTTAT
1 TTTTTCT
4641 TTTTT-T
1 TTTTTCT
*
4647 TCTTTCT
1 TTTTTCT
4654 TTTTTCT
1 TTTTTCT
*
4661 TTTGT-T
1 TTTTTCT
*
4667 TTCTTCT
1 TTTTTCT
*
4674 TTTTAGCT
1 TTTT-TCT
4682 TCTTTTCT
1 T-TTTTCT
*
4690 TTTTTGT
1 TTTTTCT
4697 TTTTTCT
1 TTTTTCT
4704 TTTT
1 TTTT
4708 GTTCCTGATT
Statistics
Matches: 58, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
6 14 0.24
7 35 0.60
8 6 0.10
9 3 0.05
ACGTcount: A:0.03, C:0.12, G:0.04, T:0.81
Consensus pattern (7 bp):
TTTTTCT
Found at i:4654 original size:19 final size:20
Alignment explanation
Indices: 4630--4678 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
4620 TTTGTCCCTT
4630 TTTCTTTTTATTTT-TTTTC
1 TTTCTTTTTATTTTGTTTTC
*
4649 TTTCTTTTTTCTTTTGTTTTC
1 TTTC-TTTTTATTTTGTTTTC
4670 -TTCTTTTTA
1 TTTCTTTTTA
4679 GCTTCTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 9 0.35
20 12 0.46
21 5 0.19
ACGTcount: A:0.04, C:0.12, G:0.02, T:0.82
Consensus pattern (20 bp):
TTTCTTTTTATTTTGTTTTC
Found at i:4656 original size:11 final size:11
Alignment explanation
Indices: 4642--4705 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
4632 TCTTTTTATT
4642 TTTTTTCTTTC
1 TTTTTTCTTTC
4653 TTTTTTCTTT-
1 TTTTTTCTTTC
*
4663 TGTTTTC-TTC
1 TTTTTTCTTTC
*
4673 TTTTTAGC-TTC
1 TTTTT-TCTTTC
* *
4684 TTTTCTTTTTTG
1 TTTT-TTCTTTC
4696 TTTTTTCTTT
1 TTTTTTCTTT
4706 TTGTTCCTGA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
9 2 0.05
10 10 0.24
11 23 0.55
12 7 0.17
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.80
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:4677 original size:31 final size:30
Alignment explanation
Indices: 4650--4707 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
4640 TTTTTTTTCT
4650 TTCTTTT-TTCTTTTGTTTTCTTCTTTTTAGC
1 TTCTTTTCTT-TTTTGTTTT-TTCTTTTTAGC
4681 TTCTTTTCTTTTTTGTTTTTTCTTTTT
1 TTCTTTTCTTTTTTGTTTTTTCTTTTT
4708 GTTCCTGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 8 0.31
31 16 0.62
32 2 0.08
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.79
Consensus pattern (30 bp):
TTCTTTTCTTTTTTGTTTTTTCTTTTTAGC
Found at i:4691 original size:16 final size:14
Alignment explanation
Indices: 4628--4707 Score: 71
Period size: 13 Copynumber: 5.8 Consensus size: 14
4618 TTTTTGTCCC
4628 TTTTTCTTTTTA-T
1 TTTTTCTTTTTAGT
*
4641 TTTTT-TTCTTT-CT
1 TTTTTCTT-TTTAGT
4654 TTTTTC-TTTT-GT
1 TTTTTCTTTTTAGT
4666 TTTCTTCTTTTTAGCT
1 TTT-TTCTTTTTAG-T
*
4682 TCTTTTCTTTTTTGT
1 T-TTTTCTTTTTAGT
4697 TTTTTCTTTTT
1 TTTTTCTTTTT
4708 GTTCCTGATT
Statistics
Matches: 57, Mismatches: 2, Indels: 15
0.77 0.03 0.20
Matches are distributed among these distances:
12 9 0.16
13 18 0.32
14 14 0.25
15 3 0.05
16 11 0.19
17 2 0.04
ACGTcount: A:0.03, C:0.12, G:0.04, T:0.81
Consensus pattern (14 bp):
TTTTTCTTTTTAGT
Found at i:4703 original size:19 final size:19
Alignment explanation
Indices: 4629--4706 Score: 58
Period size: 19 Copynumber: 4.2 Consensus size: 19
4619 TTTTGTCCCT
*
4629 TTTTCTTTTTATTTTTTTTC
1 TTTTCTTTTT-TGTTTTTTC
*
4649 -TTTCTTTTTTCTTTTGTT-
1 TTTTCTTTTTTGTTTT-TTC
* *
4667 TTCTTCTTTTTAG---CTTC
1 TT-TTCTTTTTTGTTTTTTC
4684 TTTTCTTTTTTGTTTTTTC
1 TTTTCTTTTTTGTTTTTTC
4703 TTTT
1 TTTT
4707 TGTTCCTGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 15
0.68 0.09 0.23
Matches are distributed among these distances:
16 11 0.24
17 2 0.04
18 5 0.11
19 19 0.42
20 8 0.18
ACGTcount: A:0.03, C:0.13, G:0.04, T:0.81
Consensus pattern (19 bp):
TTTTCTTTTTTGTTTTTTC
Found at i:9224 original size:2 final size:2
Alignment explanation
Indices: 9217--9248 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9207 AATAAATGAA
9217 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
9249 GAGTAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10132 original size:37 final size:36
Alignment explanation
Indices: 10091--10187 Score: 113
Period size: 37 Copynumber: 2.6 Consensus size: 36
10081 GGATCATATC
*
10091 TTTAGGAGTTTAAATCATAGTAGAACTCTATCCTATT
1 TTTAGGAGTTTAAATC-TAGTAGAACTCTATCCTATA
* * * *
10128 TTTAGGAGTTTGAATTCTAGCAAAATTCTATCCTATA
1 TTTAGGAGTTT-AAATCTAGTAGAACTCTATCCTATA
*
10165 TTTAGGAGTTTGAATCCTAGTAG
1 TTTAGGAGTTTAAAT-CTAGTAG
10188 GATAAAAAGG
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
36 2 0.04
37 43 0.88
38 4 0.08
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.40
Consensus pattern (36 bp):
TTTAGGAGTTTAAATCTAGTAGAACTCTATCCTATA
Found at i:12393 original size:102 final size:102
Alignment explanation
Indices: 12212--12409 Score: 344
Period size: 102 Copynumber: 1.9 Consensus size: 102
12202 CCTCAGACTC
* *
12212 AGAAAGACCAACCTAAAGGACTCAAAAGTGAAAAAATGAAGGAATTTGCCATAGATCCTCATTTT
1 AGAAAGACCAACCTAAAGGACTCAAAAGTCAAAAAATGAAAGAATTTGCCATAGATCCTCATTTT
12277 CCCTCTAGATTCGCTAAGTCCAAGAAAGAAGCATAAG
66 CCCTCTAGATTCGCTAAGTCCAAGAAAGAAGCATAAG
* *
12314 AGAATGACCAACCTAAAGGACTCAAAAG-CAAAAAACTGAAAGAATTTGCCATAGATCCTCCTTT
1 AGAAAGACCAACCTAAAGGACTCAAAAGTCAAAAAA-TGAAAGAATTTGCCATAGATCCTCATTT
12378 TCCCTCTAGATTCGCTAAGTCCAAGAAAGAAG
65 TCCCTCTAGATTCGCTAAGTCCAAGAAAGAAG
12410 AAGAAGATAA
Statistics
Matches: 91, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
101 6 0.07
102 85 0.93
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.21
Consensus pattern (102 bp):
AGAAAGACCAACCTAAAGGACTCAAAAGTCAAAAAATGAAAGAATTTGCCATAGATCCTCATTTT
CCCTCTAGATTCGCTAAGTCCAAGAAAGAAGCATAAG
Found at i:14872 original size:9 final size:9
Alignment explanation
Indices: 14846--14879 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
14836 TCATTTGAAG
*
14846 AAAAAACAA
1 AAAAAAGAA
14855 AACAAAAGAA
1 AA-AAAAGAA
14865 AAAAAAGAA
1 AAAAAAGAA
14874 AAAAAA
1 AAAAAA
14880 TCGTGCAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:30613 original size:21 final size:21
Alignment explanation
Indices: 30561--30629 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 21
30551 TTTAGTAAAA
* *
30561 TATTATTTAAAGTGTT-ATTT
1 TATTATTTAAAATATTAATTT
* *
30581 T-TTACTGAAAATATTAATTT
1 TATTATTTAAAATATTAATTT
*
30601 TATTATTTAAAATAATTATTTT
1 TATTATTTAAAAT-ATTAATTT
*
30623 TAATATT
1 TATTATT
30630 AATATTTTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 10 0.26
20 6 0.16
21 9 0.24
22 13 0.34
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (21 bp):
TATTATTTAAAATATTAATTT
Found at i:33466 original size:34 final size:35
Alignment explanation
Indices: 33410--33483 Score: 123
Period size: 34 Copynumber: 2.1 Consensus size: 35
33400 AAAATACTTT
*
33410 AATTTAGGGCTTAGAATGTAATTGAAGTATTTTGG
1 AATTTAGGGCTTAAAATGTAATTGAAGTATTTTGG
*
33445 AATTTAGGG-TTAAAATGTAATTGATGTATTTTGG
1 AATTTAGGGCTTAAAATGTAATTGAAGTATTTTGG
33479 AATTT
1 AATTT
33484 TGAACATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
34 28 0.76
35 9 0.24
ACGTcount: A:0.32, C:0.01, G:0.23, T:0.43
Consensus pattern (35 bp):
AATTTAGGGCTTAAAATGTAATTGAAGTATTTTGG
Found at i:36583 original size:13 final size:14
Alignment explanation
Indices: 36546--36588 Score: 52
Period size: 13 Copynumber: 3.0 Consensus size: 14
36536 ATTTTATTTT
36546 TTTTAGAAAAAATCA
1 TTTTA-AAAAAATCA
*
36561 TTTTTTAAAAAATCA
1 -TTTTAAAAAAATCA
36576 -TTTAAAAAAATCA
1 TTTTAAAAAAATCA
36589 ACTCTTTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 12 0.48
15 9 0.36
16 4 0.16
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.37
Consensus pattern (14 bp):
TTTTAAAAAAATCA
Found at i:41491 original size:16 final size:16
Alignment explanation
Indices: 41472--41505 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
41462 CAATATACGA
41472 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
41488 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
41504 AT
1 AT
41506 TTAGATGTAT
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:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:42110 original size:21 final size:23
Alignment explanation
Indices: 42065--42111 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
42055 GTGTCACCAA
42065 TAACATATATCATGATCATGTGT
1 TAACATATATCATGATCATGTGT
* *
42088 TAACATATGTCA-GATCTTG-GT
1 TAACATATATCATGATCATGTGT
42109 TAA
1 TAA
42112 ATGATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (23 bp):
TAACATATATCATGATCATGTGT
Found at i:42242 original size:130 final size:130
Alignment explanation
Indices: 42038--42285 Score: 397
Period size: 130 Copynumber: 1.9 Consensus size: 130
42028 AATTTTCTTC
* * *
42038 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACATATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
* ** *
42103 CTTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
42168 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCATAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
42233 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
42286 TATATAAATA
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 107 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:42743 original size:35 final size:35
Alignment explanation
Indices: 42682--42757 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
42672 AATTGAATTG
* * *
42682 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTAGAAATTAGGGTTTAGAATGA
*
42717 AATTGAATTACTTTAGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTAGAAATTAGGGTTTAGAATGA
42752 AATTGA
1 AATTGA
42758 GGATTGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTAGAAATTAGGGTTTAGAATGA
Found at i:55035 original size:44 final size:44
Alignment explanation
Indices: 54981--55198 Score: 355
Period size: 44 Copynumber: 5.0 Consensus size: 44
54971 CCATGAGTGG
54981 CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
1 CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
* *
55025 CACATTTCTGCCAATAATGCACCGTTATGCATTTTTATTTATGA
1 CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
* * * *
55069 CACCTTTCTTCCAATAATGCACTGTTATGCATTTTTATTTATGT
1 CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
*
55113 CACCTTTTTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
1 CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
* *
55157 CACCTTTCTACCAATAATGTACCGTTATGCATTTTCATTTAT
1 CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTAT
55199 TTCGGTAACA
Statistics
Matches: 160, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 160 1.00
ACGTcount: A:0.25, C:0.22, G:0.10, T:0.42
Consensus pattern (44 bp):
CACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGA
Found at i:57299 original size:17 final size:16
Alignment explanation
Indices: 57279--57326 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
57269 TTTTTAAAAA
*
57279 TTTTAAATTTTAAT-T
1 TTTTTAATTTTAATAT
*
57294 TTTTTTATTTTAATAT
1 TTTTTAATTTTAATAT
57310 TTTTTATATTTT-ATAT
1 TTTTTA-ATTTTAATAT
57326 T
1 T
57327 AATTATCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 12 0.43
16 11 0.39
17 5 0.18
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTAATTTTAATAT
Found at i:57303 original size:15 final size:17
Alignment explanation
Indices: 57279--57326 Score: 66
Period size: 16 Copynumber: 3.0 Consensus size: 17
57269 TTTTTAAAAA
*
57279 TTTTAAATTTTAAT-TT
1 TTTTATATTTTAATATT
57295 TTTT-TATTTTAATATT
1 TTTTATATTTTAATATT
57311 TTTTATATTTT-ATATT
1 TTTTATATTTTAATATT
57327 AATTATCTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 8 0.28
16 15 0.52
17 6 0.21
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATATTTTAATATT
Found at i:58597 original size:18 final size:16
Alignment explanation
Indices: 58574--58617 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
58564 CCGATCAGCT
*
58574 GTTGACAGTTGACCGACC
1 GTTGACA-TTG-CCCACC
58592 GTTGACCATTGCCCACC
1 GTTGA-CATTGCCCACC
58609 GTTGACATT
1 GTTGACATT
58618 TTTTGAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 4 0.17
17 10 0.42
18 8 0.33
19 2 0.08
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (16 bp):
GTTGACATTGCCCACC
Found at i:59017 original size:27 final size:27
Alignment explanation
Indices: 58965--59017 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 27
58955 TTACCATATA
**
58965 TTTTGATATGATCTCTGGTTACTGTAT
1 TTTTGATATGATCTCTGAATACTGTAT
*
58992 TTTTGAATCTGATCTCTGAATA-TGTA
1 TTTTG-ATATGATCTCTGAATACTGTA
59018 ATATTTTCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.23, C:0.11, G:0.17, T:0.49
Consensus pattern (27 bp):
TTTTGATATGATCTCTGAATACTGTAT
Found at i:61427 original size:23 final size:24
Alignment explanation
Indices: 61401--61448 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
61391 CTTAAAAAAT
*
61401 TTAAT-TTTTTTTTTATATTTTTA
1 TTAATATTTGTTTTTATATTTTTA
*
61424 TTAATAATTTGTTTTTATTTTTTTA
1 TTAAT-ATTTGTTTTTATATTTTTA
61449 AAATTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
25 16 0.76
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (24 bp):
TTAATATTTGTTTTTATATTTTTA
Found at i:62357 original size:2 final size:2
Alignment explanation
Indices: 62350--62383 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
62340 TAGCTTAATA
62350 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
62384 GTGATATACT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.