Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001988.1 Hibiscus syriacus cultivar Beakdansim tig00004059_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: 81214
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6170 original size:16 final size:16
Alignment explanation
Indices: 6140--6185 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
6130 TTTTAGTAAT
6140 TTATTTAATTATTTTAA
1 TTATTTAA-TATTTTAA
*
6157 TTATTTAATATTTTAT
1 TTATTTAATATTTTAA
*
6173 TTAATTAAT-TTTT
1 TTATTTAATATTTT
6186 TTTACAGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 8 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTTAATATTTTAA
Found at i:10202 original size:51 final size:50
Alignment explanation
Indices: 10140--10262 Score: 138
Period size: 51 Copynumber: 2.4 Consensus size: 50
10130 CAGTAAAGCG
* * * ** *
10140 CGCCCCTTGCACTGCGTTATACGATGATTTGGCGTCACGTGGGGTATAACA
1 CGCCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGT-GGGTATAACA
* *
10191 CGCCCCCTGCACCGCGCTATACGGTGAGCTGGCGCCACGTGGGTATAGCA
1 CGCCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGTATAACA
* * *
10241 CGACCCCTGTAGCGCGCTATAC
1 CGCCCCCTGCACCGCGCTATAC
10263 CTGTATATCT
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
50 28 0.46
51 33 0.54
ACGTcount: A:0.18, C:0.33, G:0.28, T:0.21
Consensus pattern (50 bp):
CGCCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGTATAACA
Found at i:10406 original size:20 final size:19
Alignment explanation
Indices: 10375--10413 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
10365 TTATCACACC
*
10375 AAATTTTCTCAAATTCTCT
1 AAATTTTCTCAAATACTCT
10394 AAATTTCTCTCAAATACTCT
1 AAATTT-TCTCAAATACTCT
10414 CTTTTTAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATTTTCTCAAATACTCT
Found at i:12176 original size:18 final size:18
Alignment explanation
Indices: 12153--12191 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
12143 CCAGCAGCCA
12153 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
12171 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
12189 CCG
1 CCG
12192 ACATCGCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.21
Consensus pattern (18 bp):
CCGCAGCCATATATGATG
Found at i:12756 original size:25 final size:25
Alignment explanation
Indices: 12692--12758 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 25
12682 TTGTATTTAC
**
12692 TTTATTTTGTTAAATTGTAATTTTTAT
1 TTTATTTTGTT-AATT-TAATACTTAT
*
12719 TATTA-TTT-CTAATTTAATACTTAT
1 T-TTATTTTGTTAATTTAATACTTAT
12743 TTTATTTTGTTAATTT
1 TTTATTTTGTTAATTT
12759 TGTTGGACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
23 3 0.09
24 12 0.36
25 10 0.30
26 1 0.03
27 4 0.12
28 3 0.09
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.66
Consensus pattern (25 bp):
TTTATTTTGTTAATTTAATACTTAT
Found at i:16409 original size:51 final size:50
Alignment explanation
Indices: 16289--16412 Score: 160
Period size: 50 Copynumber: 2.5 Consensus size: 50
16279 TTATATAAAA
*
16289 CGCAGTACCTGATCCGCGCTATATAAAATTATGGCAGAGTAAAGGTATGT
1 CGCAGTACCTGATCCGCGCTATATAAAATTATGGCAGAGTAAAAGTATGT
* * * * *
16339 CGCGGTACTTGTTCCGCGCTATATAAAATTATGTCGGGAGTAAAAGTATAGT
1 CGCAGTACCTGATCCGCGCTATATAAAATTATGGC-AGAGTAAAAGTAT-GT
*
16391 -GCAGTACCTAATCCGCGCTATA
1 CGCAGTACCTGATCCGCGCTATA
16413 CCCTTATGTG
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
50 31 0.50
51 29 0.47
52 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.27
Consensus pattern (50 bp):
CGCAGTACCTGATCCGCGCTATATAAAATTATGGCAGAGTAAAAGTATGT
Found at i:16500 original size:50 final size:50
Alignment explanation
Indices: 16425--16550 Score: 146
Period size: 50 Copynumber: 2.5 Consensus size: 50
16415 CTTATGTGGT
* * * **
16425 GTATAGTGCGCTTCAGGGGTCGCGCTATACCC-ACGTGGCGCCAGCTCACC
1 GTATAGCGCGGTTCAGGGG-CGCGCTATACCCTACGTGACGCCAAATCACC
* *
16475 GTATAGCGCGGTTCAAGGGGCGCGCTATACCCTACGTGACGTCAAATCATC
1 GTATAGCGCGGTTC-AGGGGCGCGCTATACCCTACGTGACGCCAAATCACC
* *
16526 GTATAGCGCGGTGCAGGGGCACGCT
1 GTATAGCGCGGTTCAGGGGCGCGCT
16551 TTACTGCTAA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
50 34 0.52
51 31 0.48
ACGTcount: A:0.19, C:0.29, G:0.32, T:0.20
Consensus pattern (50 bp):
GTATAGCGCGGTTCAGGGGCGCGCTATACCCTACGTGACGCCAAATCACC
Found at i:23132 original size:2 final size:2
Alignment explanation
Indices: 23125--23160 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
23115 TGTTAAAATG
23125 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23161 GGGTTAGGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28869 original size:32 final size:29
Alignment explanation
Indices: 28829--28935 Score: 82
Period size: 24 Copynumber: 3.7 Consensus size: 29
28819 TTTTTAAAAT
28829 TTATAAAATGATCATTTTATTTTATTGAATTA
1 TTATAAAATGATCATTTTATTTTATT-AA--A
28861 TTATAAAATAATGATTC-TTTTATTTTATTAAA
1 TTAT--AA-AATGA-TCATTTTATTTTATTAAA
*
28893 TAATAAAATG---A--TTATTTTATTAAA
1 TTATAAAATGATCATTTTATTTTATTAAA
* *
28917 TAATAAAATGATTATTTTA
1 TTATAAAATGATCATTTTA
28936 AAATTTTTAA
Statistics
Matches: 64, Mismatches: 1, Indels: 23
0.73 0.01 0.26
Matches are distributed among these distances:
24 23 0.36
27 1 0.02
29 7 0.11
30 2 0.03
32 8 0.12
34 4 0.06
35 17 0.27
36 2 0.03
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (29 bp):
TTATAAAATGATCATTTTATTTTATTAAA
Found at i:28907 original size:24 final size:24
Alignment explanation
Indices: 28880--28935 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
28870 AATGATTCTT
28880 TTATTTTATTAAATAATAAAATGA
1 TTATTTTATTAAATAATAAAATGA
28904 TTATTTTATTAAATAATAAAATGA
1 TTATTTTATTAAATAATAAAATGA
28928 TTATTTTA
1 TTATTTTA
28936 AAATTTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (24 bp):
TTATTTTATTAAATAATAAAATGA
Found at i:29795 original size:5 final size:5
Alignment explanation
Indices: 29785--29818 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
29775 GAGTTGAAGA
*
29785 CAAAC CAAAC CAAAC CAAAC CAAAC CAGAC CAAA
1 CAAAC CAAAC CAAAC CAAAC CAAAC CAAAC CAAA
29819 GGCAGTTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.38, G:0.03, T:0.00
Consensus pattern (5 bp):
CAAAC
Found at i:30628 original size:2 final size:2
Alignment explanation
Indices: 30621--30658 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
30611 TAATTTATGG
30621 TA 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
30659 CTAAATCCAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31548 original size:16 final size:17
Alignment explanation
Indices: 31527--31562 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
31517 CGAACAAACG
31527 AAACAATATATA-AAAA
1 AAACAATATATACAAAA
*
31543 AAACAATGTATACAAAA
1 AAACAATATATACAAAA
31560 AAA
1 AAA
31563 AATGAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.72, C:0.08, G:0.03, T:0.17
Consensus pattern (17 bp):
AAACAATATATACAAAA
Found at i:31668 original size:19 final size:19
Alignment explanation
Indices: 31638--31693 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
31628 AAAAGAAGAA
*
31638 AATATAATAAAATATAAAT
1 AATAAAATAAAATATAAAT
* * *
31657 GGATAAAA-AAAATACACAT
1 -AATAAAATAAAATATAAAT
31676 AATAAAATAAAATATAAA
1 AATAAAATAAAATATAAA
31694 GCAATGAGAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
18 6 0.21
19 17 0.61
20 5 0.18
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATATAAAT
Found at i:31928 original size:25 final size:24
Alignment explanation
Indices: 31890--31955 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 24
31880 CGTATATAAT
* *
31890 AATAAAAAATAATATGATAGCATA
1 AATAAAAAATAATATAATAGCAAA
*
31914 AATAAATAAATAATATAATAGTAAA
1 AATAAA-AAATAATATAATAGCAAA
31939 AAGTAAAAAATAA-ATAA
1 AA-TAAAAAATAATATAA
31956 AAAAAAATGG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 10 0.27
25 23 0.62
26 4 0.11
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.24
Consensus pattern (24 bp):
AATAAAAAATAATATAATAGCAAA
Found at i:32655 original size:20 final size:20
Alignment explanation
Indices: 32630--32668 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
32620 CCGCCTCGCC
*
32630 GCCGCCGTTGAACGGCGACG
1 GCCGCCGTTCAACGGCGACG
*
32650 GCCGCCGTTCATCGGCGAC
1 GCCGCCGTTCAACGGCGAC
32669 AAAACCCGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.38, G:0.36, T:0.13
Consensus pattern (20 bp):
GCCGCCGTTCAACGGCGACG
Found at i:34170 original size:211 final size:211
Alignment explanation
Indices: 33878--34336 Score: 787
Period size: 211 Copynumber: 2.2 Consensus size: 211
33868 TGTTCCGAGG
*
33878 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTTGGAAATTGTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTTGGAAATTGTTTGTTGACAACCAG
33943 CGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTG
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTG
* * * *
34008 AAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCTTCGTGAAGTTGAA
131 AAATTGGCTCTGAAATTGAGAA-ATATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
*
34073 CTTGCGTTGTCTGGAGT
195 CTTACGTTGTCTGGAGT
* *
34090 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA-TTGAGAAA-TGTTTGTTGACAAGCA
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTTG-GAAATTGTTTGTTGACAACCA
* *
34153 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
65 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTT
*
34218 GAAATTGGCTCTGACATTGAGAAATATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
130 GAAATTGGCTCTGAAATTGAGAAATATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
34283 CTTACGTTGTCTGGAGT
195 CTTACGTTGTCTGGAGT
34300 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
34337 GTAAAACCTG
Statistics
Matches: 234, Mismatches: 12, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
210 91 0.39
211 102 0.44
212 41 0.18
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (211 bp):
CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTTGGAAATTGTTTGTTGACAACCAG
CGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTG
AAATTGGCTCTGAAATTGAGAAATATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
TTACGTTGTCTGGAGT
Found at i:34189 original size:105 final size:105
Alignment explanation
Indices: 33878--34336 Score: 785
Period size: 105 Copynumber: 4.4 Consensus size: 105
33868 TGTTCCGAGG
*
33878 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTTG-GAAATTGTTTGTTGACAACCA
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA-TTGAGAAA-TGTTTGTTGACAACCA
* *
33942 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTCGAGT
64 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
33984 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAACCAG
*
34049 CGGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
65 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
34090 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAGCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
34155 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
34195 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGACATTGAGAAATATTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
*
34260 GGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
34300 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
34337 GTAAAACCTG
Statistics
Matches: 336, Mismatches: 15, Indels: 5
0.94 0.04 0.01
Matches are distributed among these distances:
105 196 0.58
106 140 0.42
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (105 bp):
CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
Found at i:35141 original size:51 final size:51
Alignment explanation
Indices: 35079--35175 Score: 140
Period size: 51 Copynumber: 1.9 Consensus size: 51
35069 CTTTTTCCTC
* * * *
35079 TTTTTCTTTTTTCGATTTAGGGCGCCCTTTCGGGTTTTCACCCTAAACGTT
1 TTTTTCTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAACGTT
* *
35130 TTTTTTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCATCCTAA
1 TTTTTCTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAA
35176 GCGAAGTATT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.13, C:0.24, G:0.15, T:0.47
Consensus pattern (51 bp):
TTTTTCTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAACGTT
Found at i:45548 original size:15 final size:16
Alignment explanation
Indices: 45528--45561 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
45518 CGAACAAACG
45528 AAACAATATATA-AAA
1 AAACAATATATACAAA
*
45543 AAACAATGTATACAAA
1 AAACAATATATACAAA
45559 AAA
1 AAA
45562 AAAATGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.71, C:0.09, G:0.03, T:0.18
Consensus pattern (16 bp):
AAACAATATATACAAA
Found at i:45559 original size:17 final size:17
Alignment explanation
Indices: 45534--45567 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
45524 AACGAAACAA
* *
45534 TATATAAAAAAACAATG
1 TATACAAAAAAAAAATG
45551 TATACAAAAAAAAAATG
1 TATACAAAAAAAAAATG
45568 AAATATGACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.21
Consensus pattern (17 bp):
TATACAAAAAAAAAATG
Found at i:45945 original size:26 final size:25
Alignment explanation
Indices: 45898--45970 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 25
45888 CGTATATAAT
*
45898 AATAAAAAAT-ATAATATGATAGCATA
1 AATAAAAAATAATAATA--ATAGCAAA
*
45924 AATAAATAAATAATAATAATAGTAAA
1 AATAAA-AAATAATAATAATAGCAAA
45950 AAGTAAAAAATAAATAA-AATA
1 AA-TAAAAAAT-AATAATAATA
45971 AAAATGGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 22 0.54
27 13 0.32
28 6 0.15
ACGTcount: A:0.68, C:0.01, G:0.05, T:0.25
Consensus pattern (25 bp):
AATAAAAAATAATAATAATAGCAAA
Found at i:46673 original size:20 final size:20
Alignment explanation
Indices: 46648--46686 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
46638 CCGCCTCGCC
*
46648 GCCGCCGTTGAACGGCGACG
1 GCCGCCGTTCAACGGCGACG
*
46668 GCCGCCGTTCATCGGCGAC
1 GCCGCCGTTCAACGGCGAC
46687 AAAACCCGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.38, G:0.36, T:0.13
Consensus pattern (20 bp):
GCCGCCGTTCAACGGCGACG
Found at i:48635 original size:13 final size:13
Alignment explanation
Indices: 48617--48643 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
48607 GAACGAAAAA
48617 GGAAACATTGAAT
1 GGAAACATTGAAT
48630 GGAAACATTGAAT
1 GGAAACATTGAAT
48643 G
1 G
48644 TGCGATAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.26, T:0.22
Consensus pattern (13 bp):
GGAAACATTGAAT
Found at i:48943 original size:13 final size:13
Alignment explanation
Indices: 48925--48951 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
48915 GAATGAAAAA
48925 GGAAACATTGAAT
1 GGAAACATTGAAT
48938 GGAAACATTGAAT
1 GGAAACATTGAAT
48951 G
1 G
48952 TGCGATAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.26, T:0.22
Consensus pattern (13 bp):
GGAAACATTGAAT
Found at i:49022 original size:308 final size:308
Alignment explanation
Indices: 48464--49081 Score: 1218
Period size: 308 Copynumber: 2.0 Consensus size: 308
48454 AAATGATCAT
48464 TTCAATAAACGTTGGGAGCTAATTTATATATTTTAATTGATAAAATAAGCCGCCAAAATGGAATT
1 TTCAATAAACGTTGGGAGCTAATTTATATATTTTAATTGATAAAATAAGCCGCCAAAATGGAATT
48529 TAGTAAATGTTTTGAAAAATAAAATGATATCGAAACCCTACGTGAATATCATAATTCTCTGAATT
66 TAGTAAATGTTTTGAAAAATAAAATGATATCGAAACCCTACGTGAATATCATAATTCTCTGAATT
48594 AAGTTGGGGGTTGGAACGAAAAAGGAAACATTGAATGGAAACATTGAATGTGCGATAGTTACAAT
131 AAGTTGGGGGTTGGAACGAAAAAGGAAACATTGAATGGAAACATTGAATGTGCGATAGTTACAAT
48659 TGCCAAAAATAGTTAGATATGCAATTAATAAAATTGAAGCTTATATGATGAAATAAATATCAAGT
196 TGCCAAAAATAGTTAGATATGCAATTAATAAAATTGAAGCTTATATGATGAAATAAATATCAAGT
48724 GGGAGTACCAATAGGGGTTGGTTTAAGTAGTAAGCAGTTTGATTCCGC
261 GGGAGTACCAATAGGGGTTGGTTTAAGTAGTAAGCAGTTTGATTCCGC
48772 TTCAATAAACGTTGGGAGCTAATTTATATATTTTAATTGATAAAATAAGCCGCCAAAATGGAATT
1 TTCAATAAACGTTGGGAGCTAATTTATATATTTTAATTGATAAAATAAGCCGCCAAAATGGAATT
*
48837 TAGTAAATGTTTTGAAAAATAAAATGATATCGAAACCCTACTTGAATATCATAATTCTCTGAATT
66 TAGTAAATGTTTTGAAAAATAAAATGATATCGAAACCCTACGTGAATATCATAATTCTCTGAATT
*
48902 AAGTTGGGGGTTGGAATGAAAAAGGAAACATTGAATGGAAACATTGAATGTGCGATAGTTACAAT
131 AAGTTGGGGGTTGGAACGAAAAAGGAAACATTGAATGGAAACATTGAATGTGCGATAGTTACAAT
48967 TGCCAAAAATAGTTAGATATGCAATTAATAAAATTGAAGCTTATATGATGAAATAAATATCAAGT
196 TGCCAAAAATAGTTAGATATGCAATTAATAAAATTGAAGCTTATATGATGAAATAAATATCAAGT
49032 GGGAGTACCAATAGGGGTTGGTTTAAGTAGTAAGCAGTTTGATTCCGC
261 GGGAGTACCAATAGGGGTTGGTTTAAGTAGTAAGCAGTTTGATTCCGC
49080 TT
1 TT
49082 AAGCAATATC
Statistics
Matches: 308, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
308 308 1.00
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (308 bp):
TTCAATAAACGTTGGGAGCTAATTTATATATTTTAATTGATAAAATAAGCCGCCAAAATGGAATT
TAGTAAATGTTTTGAAAAATAAAATGATATCGAAACCCTACGTGAATATCATAATTCTCTGAATT
AAGTTGGGGGTTGGAACGAAAAAGGAAACATTGAATGGAAACATTGAATGTGCGATAGTTACAAT
TGCCAAAAATAGTTAGATATGCAATTAATAAAATTGAAGCTTATATGATGAAATAAATATCAAGT
GGGAGTACCAATAGGGGTTGGTTTAAGTAGTAAGCAGTTTGATTCCGC
Found at i:49192 original size:13 final size:13
Alignment explanation
Indices: 49174--49200 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
49164 AAACGAAAAA
49174 GGAAACATTGAAT
1 GGAAACATTGAAT
49187 GGAAACATTGAAT
1 GGAAACATTGAAT
49200 G
1 G
49201 TGCGATAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.26, T:0.22
Consensus pattern (13 bp):
GGAAACATTGAAT
Found at i:49336 original size:249 final size:249
Alignment explanation
Indices: 48898--49639 Score: 1330
Period size: 249 Copynumber: 3.0 Consensus size: 249
48888 TAATTCTCTG
*
48898 AATTAAGTTGGGGGTTGGAATGAAAAAGGAAACATTGAATGGAAACATTGAATGTGCGATAGTTA
1 AATTAAGTTGGGGGTTGGAACGAAAAAGGAAACATTGAATGGAAACATTGAATGTGCGATAGTTA
48963 CAATTGCCAAAAATAGTTAGATATGCAATTAATAAAATTGAAGCTTATATGATGAAATAAATATC
66 CAATTGCCAAAAATAGTTAGATATGCAATTAATAAAATTGAAGCTTATATGATGAAATAAATATC
49028 AAGTGGGAGTACCAATAGGGGTTGGTTTAAGTAGTAAGCAGTTTGATTCCGCTTAAGCAATATCT
131 AAGTGGGAGTACCAATAGGGGTTGGTTTAAGTAGTAAGCAGTTTGATTCCGCTTAAGCAATATCT
*
49093 CAAATTTAAGTTCTTGTGTATGCAAAAAATCCATGCTAGGGGACTCATCACCAA
196 CAAATTTAAGTTATTGTGTATGCAAAAAATCCATGCTAGGGGACTCATCACCAA
*
49147 AATTAAGTTGGGGGTTGAAACGAAAAAGGAAACATTGAATGGAAACATTGAATGTGCGATAGTTA
1 AATTAAGTTGGGGGTTGGAACGAAAAAGGAAACATTGAATGGAAACATTGAATGTGCGATAGTTA
49212 CAATTGCCAAAAATAGTTAGATATGCAATTAATAAAATTGAAGCTTATATGATGAAATAAATATC
66 CAATTGCCAAAAATAGTTAGATATGCAATTAATAAAATTGAAGCTTATATGATGAAATAAATATC
* *
49277 AAGTGGGAGTATCAATAGGGGTTGGTTTAAGTAGTAAGCAGTTTGATTCCACTTAAGCAATATCT
131 AAGTGGGAGTACCAATAGGGGTTGGTTTAAGTAGTAAGCAGTTTGATTCCGCTTAAGCAATATCT
*
49342 CAAATTTAAGTTATTGTGTATGCAAAAAATCCATACTAGGGGACTCATCACCAA
196 CAAATTTAAGTTATTGTGTATGCAAAAAATCCATGCTAGGGGACTCATCACCAA
49396 AATTAAGTTGGGGGTTGGAACGAAAAAGGAAACA-T---T-G--A-A-TG--TGT--GATAGTTA
1 AATTAAGTTGGGGGTTGGAACGAAAAAGGAAACATTGAATGGAAACATTGAATGTGCGATAGTTA
49448 CAATTGCCAAAAATAGTTAGATATGCAATTAATAAAATTGAAGCTTATATGATGAAATAAATATC
66 CAATTGCCAAAAATAGTTAGATATGCAATTAATAAAATTGAAGCTTATATGATGAAATAAATATC
49513 AAGTGGGAGTACCAATAGGGGTTGGTTTAAGTAGTAAGCAGTTTGATTCCGCTTAAGCAATATCT
131 AAGTGGGAGTACCAATAGGGGTTGGTTTAAGTAGTAAGCAGTTTGATTCCGCTTAAGCAATATCT
*
49578 CAAATTTAAGTTTTTGTGTATGCAAAAAATCCATGCTAGGGGACTCATCACCAA
196 CAAATTTAAGTTATTGTGTATGCAAAAAATCCATGCTAGGGGACTCATCACCAA
49632 AATTAAGT
1 AATTAAGT
49640 GTGCGACGCG
Statistics
Matches: 482, Mismatches: 11, Indels: 13
0.95 0.02 0.03
Matches are distributed among these distances:
236 196 0.41
238 3 0.01
240 2 0.00
241 1 0.00
242 1 0.00
244 1 0.00
245 1 0.00
248 1 0.00
249 276 0.57
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (249 bp):
AATTAAGTTGGGGGTTGGAACGAAAAAGGAAACATTGAATGGAAACATTGAATGTGCGATAGTTA
CAATTGCCAAAAATAGTTAGATATGCAATTAATAAAATTGAAGCTTATATGATGAAATAAATATC
AAGTGGGAGTACCAATAGGGGTTGGTTTAAGTAGTAAGCAGTTTGATTCCGCTTAAGCAATATCT
CAAATTTAAGTTATTGTGTATGCAAAAAATCCATGCTAGGGGACTCATCACCAA
Found at i:50161 original size:22 final size:22
Alignment explanation
Indices: 50136--50179 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
50126 AAAACAAGAA
*
50136 AAATAATAATATATATACATTC
1 AAATAACAATATATATACATTC
* *
50158 AAATACCAATATATATATATTC
1 AAATAACAATATATATACATTC
50180 GATCATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATAACAATATATATACATTC
Found at i:54322 original size:4 final size:4
Alignment explanation
Indices: 54295--54339 Score: 63
Period size: 4 Copynumber: 11.2 Consensus size: 4
54285 CAATGACCAT
* * *
54295 CATA CGTA CCTA CATA CCTA CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C
54340 CCCTCTCTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.42, C:0.31, G:0.02, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:55188 original size:12 final size:12
Alignment explanation
Indices: 55173--55201 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
55163 GAAACCCGAG
55173 GAGAAGAAAGAA
1 GAGAAGAAAGAA
55185 GAGAAGAAAGAA
1 GAGAAGAAAGAA
55197 GAGAA
1 GAGAA
55202 AAAACCACCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (12 bp):
GAGAAGAAAGAA
Found at i:62569 original size:155 final size:155
Alignment explanation
Indices: 62287--62597 Score: 595
Period size: 155 Copynumber: 2.0 Consensus size: 155
62277 AGATTATATT
62287 ATAGAAGGAAATGTTGCATACTGCCTTTTAATAGAGGACGGTGAGCCATCAACATACCAGGAGGC
1 ATAGAAGGAAATGTTGCATACTGCCTTTTAATAGAGGACGGTGAGCCATCAACATACCAGGAGGC
* *
62352 AATAAACAGTTCATGTGTTTCACTGTGGATGATGGTGATGCAAGAAGAAATTGAAGCCCTTCATA
66 AATAAACAGTTCATATGTTTCACTGTGGATGATGGTGATGCAAGAAGAAATTCAAGCCCTTCATA
62417 AAAATAATACATGAGACCTTGTGCC
131 AAAATAATACATGAGACCTTGTGCC
62442 ATAGAAGGAAATGTTGCATACTGCCTTTTAATAGAGGACGGTGAGCCATCAACATACCAGGAGGC
1 ATAGAAGGAAATGTTGCATACTGCCTTTTAATAGAGGACGGTGAGCCATCAACATACCAGGAGGC
62507 AATAAACAGTTCATATGTTTCACTGTGGATGATGGTGATGCAAGAAGAAATTCAAGCCCTTCATA
66 AATAAACAGTTCATATGTTTCACTGTGGATGATGGTGATGCAAGAAGAAATTCAAGCCCTTCATA
*
62572 AAAATAATACATGGGACCTTGTGCC
131 AAAATAATACATGAGACCTTGTGCC
62597 A
1 A
62598 CTACCACAAG
Statistics
Matches: 153, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
155 153 1.00
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (155 bp):
ATAGAAGGAAATGTTGCATACTGCCTTTTAATAGAGGACGGTGAGCCATCAACATACCAGGAGGC
AATAAACAGTTCATATGTTTCACTGTGGATGATGGTGATGCAAGAAGAAATTCAAGCCCTTCATA
AAAATAATACATGAGACCTTGTGCC
Found at i:66354 original size:83 final size:83
Alignment explanation
Indices: 66238--66397 Score: 302
Period size: 83 Copynumber: 1.9 Consensus size: 83
66228 ATTTAAAATT
66238 AATTTAGAGTAAAGTTTGAATATTTATTTTTATATTAAACCTAAAAATTAATAATTCATATAAAA
1 AATTTAGAGTAAAGTTTGAATATTTATTTTTATATTAAACCTAAAAATTAATAATTCATATAAAA
66303 TGAATTATAAAAATTTTA
66 TGAATTATAAAAATTTTA
* *
66321 AATTTAGAGTATAGTTTGAATATTTATTTTTATATTAAATCTAAAAATTAATAATTCATATAAAA
1 AATTTAGAGTAAAGTTTGAATATTTATTTTTATATTAAACCTAAAAATTAATAATTCATATAAAA
66386 TGAATTATAAAA
66 TGAATTATAAAA
66398 CATTGTTTAT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 75 1.00
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (83 bp):
AATTTAGAGTAAAGTTTGAATATTTATTTTTATATTAAACCTAAAAATTAATAATTCATATAAAA
TGAATTATAAAAATTTTA
Found at i:67614 original size:20 final size:20
Alignment explanation
Indices: 67569--67614 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
67559 CTCAAATTAT
67569 ATCTCA-AACCCTAAACCTC
1 ATCTCACAACCCTAAACCTC
* *
67588 ATATCACAACCC-AATCCTC
1 ATCTCACAACCCTAAACCTC
67607 ACTCTCAC
1 A-TCTCAC
67615 TTAGAGTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.35, C:0.43, G:0.00, T:0.22
Consensus pattern (20 bp):
ATCTCACAACCCTAAACCTC
Found at i:67889 original size:2 final size:2
Alignment explanation
Indices: 67884--67910 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
67874 TGAGTAATTT
67884 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 T
67911 TGAATAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:69035 original size:33 final size:33
Alignment explanation
Indices: 68998--69062 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
68988 GGTTTTTTGG
68998 ACTCAAGGTATCTGAAAAACTCAGAATTCTTGT
1 ACTCAAGGTATCTGAAAAACTCAGAATTCTTGT
*
69031 ACTCAAGGTATCTGAAAATCTCAGAATTCTTG
1 ACTCAAGGTATCTGAAAAACTCAGAATTCTTG
69063 GAGCTGTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.31
Consensus pattern (33 bp):
ACTCAAGGTATCTGAAAAACTCAGAATTCTTGT
Found at i:69813 original size:36 final size:36
Alignment explanation
Indices: 69763--69838 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
69753 TTATAGCAAA
*
69763 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
69799 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
69835 AAAA
1 AAAA
69839 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:74299 original size:15 final size:15
Alignment explanation
Indices: 74281--74310 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
74271 CCACGGTGCT
74281 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
74296 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
74311 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:74789 original size:34 final size:36
Alignment explanation
Indices: 74731--74804 Score: 125
Period size: 35 Copynumber: 2.1 Consensus size: 36
74721 TATAGCAAAA
*
74731 AAAAATCGTCTTTATTCGAATTTTGCC-AAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
74766 AAAAATCGTATTTA-TCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
74801 AAAA
1 AAAA
74805 TCCCGAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
34 12 0.32
35 25 0.68
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:80501 original size:2 final size:2
Alignment explanation
Indices: 80494--80521 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
80484 CTTTTAATAA
80494 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
80522 TATTCTTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:80609 original size:35 final size:32
Alignment explanation
Indices: 80569--80657 Score: 99
Period size: 32 Copynumber: 2.7 Consensus size: 32
80559 TTTTAAATCT
80569 TAAAAATAAAATATTCTTAAATATATATTTAAAAA
1 TAAAAATAAAATATTCTTAAATAT-TA--TAAAAA
* *
80604 TAAAAATAAAATATATTTTAAA-ATTATAATAA
1 TAAAAATAAAATAT-TCTTAAATATTATAAAAA
* *
80636 TAATAATAAAACATTCTTAAAT
1 TAAAAATAAAATATTCTTAAAT
80658 TAAGTTAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
31 6 0.13
32 17 0.36
34 2 0.04
35 16 0.34
36 6 0.13
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (32 bp):
TAAAAATAAAATATTCTTAAATATTATAAAAA
Done.