Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1906
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: 31835
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:44 original size:32 final size:31
Alignment explanation
Indices: 2--68 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 31
1 G
* *
2 AAATGGGTTGCCACCGACTTGTGTCGGCTTTC
1 AAATGAGTTGCCACCAACTTGTGT-GGCTTTC
*
34 AAATGAGTTGCCACCAACTTGTGTGGCTTTG
1 AAATGAGTTGCCACCAACTTGTGTGGCTTTC
65 AAAT
1 AAAT
69 AATGCCACTG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 10 0.31
32 22 0.69
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.31
Consensus pattern (31 bp):
AAATGAGTTGCCACCAACTTGTGTGGCTTTC
Found at i:82 original size:29 final size:28
Alignment explanation
Indices: 50--198 Score: 92
Period size: 29 Copynumber: 5.4 Consensus size: 28
40 GTTGCCACCA
*
50 ACTTGTGTGGCTTTGAAATAATGCCACTG
1 ACTTGTG-GGCTTTGAAAGAATGCCACTG
* ** **
79 ACTTATGGGCTTAAAAAGGGGTGCCACTG
1 ACTTGTGGGCTTTGAAA-GAATGCCACTG
* ** *
108 ACTTATGGGCTTTGAAAGGGTGCCATTG
1 ACTTGTGGGCTTTGAAAGAATGCCACTG
*
136 ACTTGTGGGC-TT-AAAAAATGCCAC-G
1 ACTTGTGGGCTTTGAAAGAATGCCACTG
* * * *
161 AAGTTATGGACTTTGGATAG--TGCCACTG
1 -ACTTGTGGGCTTT-GAAAGAATGCCACTG
189 ACTTGTGGGC
1 ACTTGTGGGC
199 GTAAAAAGGA
Statistics
Matches: 92, Mismatches: 22, Indels: 14
0.72 0.17 0.11
Matches are distributed among these distances:
25 1 0.01
26 15 0.16
27 17 0.18
28 28 0.30
29 31 0.34
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.30
Consensus pattern (28 bp):
ACTTGTGGGCTTTGAAAGAATGCCACTG
Found at i:137 original size:28 final size:29
Alignment explanation
Indices: 71--152 Score: 121
Period size: 28 Copynumber: 2.9 Consensus size: 29
61 TTTGAAATAA
71 TGCCACTGACTTATGGGCTTAAAAAGGGG
1 TGCCACTGACTTATGGGCTTAAAAAGGGG
**
100 TGCCACTGACTTATGGGCTTTGAAA-GGG
1 TGCCACTGACTTATGGGCTTAAAAAGGGG
* *
128 TGCCATTGACTTGTGGGCTTAAAAA
1 TGCCACTGACTTATGGGCTTAAAAA
153 ATGCCACGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 24 0.51
29 23 0.49
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (29 bp):
TGCCACTGACTTATGGGCTTAAAAAGGGG
Found at i:240 original size:27 final size:27
Alignment explanation
Indices: 202--473 Score: 352
Period size: 27 Copynumber: 10.0 Consensus size: 27
192 TGTGGGCGTA
*
202 AAAAGGATGCCACGAAGTTGTGGACTT
1 AAAAGGATGCCACGGAGTTGTGGACTT
229 AAAAGGATGCCACGGAGTTGTGG-CTT
1 AAAAGGATGCCACGGAGTTGTGGACTT
* *
255 AAAAGGAACGCCACAGAGTTGTGGACTT
1 AAAAGG-ATGCCACGGAGTTGTGGACTT
* *
283 GAAACGGGTGCCACGGAGTTGTGGACTT
1 -AAAAGGATGCCACGGAGTTGTGGACTT
* * *
311 TAAAGGGTGCCACGGAGTTGTGGATTT
1 AAAAGGATGCCACGGAGTTGTGGACTT
*
338 AAAAAGATGCCACGGAGTTGTGGACTT
1 AAAAGGATGCCACGGAGTTGTGGACTT
*
365 AAAAAGATGCCACGGAGTTGTGGACTTT
1 AAAAGGATGCCACGGAGTTGTGGAC-TT
* * *
393 AAAA-GAGTGCCACGAAGTTTTAGACTTT
1 AAAAGGA-TGCCACGGAGTTGTGGAC-TT
*
421 AAAA-GATGCCACGGAGTTGTGGACAT
1 AAAAGGATGCCACGGAGTTGTGGACTT
447 AAAAGGATGCCACGGAGTTGTGGACTT
1 AAAAGGATGCCACGGAGTTGTGGACTT
474 TGAAAAGAAA
Statistics
Matches: 217, Mismatches: 22, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
26 14 0.06
27 147 0.68
28 51 0.24
29 5 0.02
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (27 bp):
AAAAGGATGCCACGGAGTTGTGGACTT
Found at i:316 original size:109 final size:109
Alignment explanation
Indices: 203--473 Score: 391
Period size: 109 Copynumber: 2.5 Consensus size: 109
193 GTGGGCGTAA
* *
203 AAAGGATGCCACGAAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGG-CTTAAAAGGAACGCC
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAAG-ACGCC
* * * *
267 ACAGAGTTGTGGACTTGAAACGGGTGCCACGGAGTTGTGGACTTT
65 ACAGAGTTGTGGACTTGAAAAGAGTGCCACGAAGTTGTAGACTTT
* * * *
312 AAAGGGTGCCACGGAGTTGTGGATTTAAAAAGATGCCACGGAGTTGTGGACTTAAAAAGATGCCA
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAAGACGCCA
* * *
377 CGGAGTTGTGGACTTTAAAAGAGTGCCACGAAGTTTTAGACTTT
66 CAGAGTTGTGGACTTGAAAAGAGTGCCACGAAGTTGTAGACTTT
* *
421 AAAAGATGCCACGGAGTTGTGGACATAAAAGGATGCCACGGAGTTGTGGACTT
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTT
474 TGAAAAGAAA
Statistics
Matches: 143, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
109 135 0.94
110 8 0.06
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.23
Consensus pattern (109 bp):
AAAGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAAGACGCCA
CAGAGTTGTGGACTTGAAAAGAGTGCCACGAAGTTGTAGACTTT
Found at i:474 original size:82 final size:81
Alignment explanation
Indices: 202--481 Score: 354
Period size: 82 Copynumber: 3.4 Consensus size: 81
192 TGTGGGCGTA
* * *
202 AAAAGGATGCCACGAAGTTGTGGAC-TTAAAAG-GATGCCACGGAGTTGTGGC-TTAAAAGGAAC
1 AAAAGGATGCCACGGAGTTGTGGACTTTAAAAGAG-TGCCACGGAGTTGTGACTTTAAAA-G-AT
*
264 GCCACAGAGTTGTGGACTT
63 GCCACGGAGTTGTGGACTT
* * *
283 GAAACGGGTGCCACGGAGTTGTGGACTTT-AAAGGGTGCCACGGAGTTGTGGA-TTTAAAAAGAT
1 -AAAAGGATGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGT-GACTTT-AAAAGAT
346 GCCACGGAGTTGTGGACTT
63 GCCACGGAGTTGTGGACTT
* * *
365 AAAAAGATGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGAAGTTTTAGACTTTAAAAGATGC
1 AAAAGGATGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGT-GACTTTAAAAGATGC
*
430 CACGGAGTTGTGGACAT
65 CACGGAGTTGTGGACTT
447 AAAAGGATGCCACGGAGTTGTGGACTTTGAAAAGA
1 AAAAGGATGCCACGGAGTTGTGGACTTT-AAAAGA
482 AATGCCACTG
Statistics
Matches: 175, Mismatches: 15, Indels: 15
0.85 0.07 0.07
Matches are distributed among these distances:
81 25 0.14
82 130 0.74
83 16 0.09
84 4 0.02
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (81 bp):
AAAAGGATGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGACTTTAAAAGATGCC
ACGGAGTTGTGGACTT
Found at i:1781 original size:22 final size:22
Alignment explanation
Indices: 1756--1827 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
1746 TTGTTGTTCC
1756 TTTTTTATTTTGCTTTTGCACT
1 TTTTTTATTTTGCTTTTGCACT
* *
1778 TTTTTTGTTTTTCTTTT-CA-T
1 TTTTTTATTTTGCTTTTGCACT
*
1798 ATTTTGTACTTTTGCTTTTG-ACAT
1 -TTTTTTA-TTTTGCTTTTGCAC-T
1822 TTTTTT
1 TTTTTT
1828 GTCATTATGA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
20 1 0.03
21 7 0.18
22 25 0.64
23 5 0.13
24 1 0.03
ACGTcount: A:0.10, C:0.11, G:0.08, T:0.71
Consensus pattern (22 bp):
TTTTTTATTTTGCTTTTGCACT
Found at i:1782 original size:44 final size:45
Alignment explanation
Indices: 1733--1828 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 45
1723 ATTCATGTCT
* *
1733 TTTTTTTGGATTTTTGTTGTTCCT-TTTT-TA-TTTTGCTTTTG-CA
1 TTTTTTTGG-TTTTTCTT-TTCATATTTTGTACTTTTGCTTTTGACA
1776 CTTTTTTT-GTTTTTCTTTTCATATTTTGTACTTTTGCTTTTGACA
1 -TTTTTTTGGTTTTTCTTTTCATATTTTGTACTTTTGCTTTTGACA
1821 TTTTTTTG
1 TTTTTTTG
1829 TCATTATGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
41 4 0.09
42 11 0.24
43 3 0.07
44 25 0.56
45 2 0.04
ACGTcount: A:0.08, C:0.10, G:0.11, T:0.70
Consensus pattern (45 bp):
TTTTTTTGGTTTTTCTTTTCATATTTTGTACTTTTGCTTTTGACA
Found at i:1816 original size:36 final size:35
Alignment explanation
Indices: 1743--1816 Score: 80
Period size: 36 Copynumber: 2.1 Consensus size: 35
1733 TTTTTTTGGA
*
1743 TTTTTGTTGTTCCTTTTTTATTTTGCTTTTGCACTT
1 TTTTTGTTGTTCCTTTTATATTTTGCTTTTG-ACTT
*
1779 TTTTTGTT-TTTCTTTTCATATTTTGTACTTTTG-CTT
1 TTTTTGTTGTTCCTTTT-ATATTTTG--CTTTTGACTT
1815 TT
1 TT
1817 GACATTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
35 7 0.21
36 20 0.61
38 6 0.18
ACGTcount: A:0.07, C:0.12, G:0.09, T:0.72
Consensus pattern (35 bp):
TTTTTGTTGTTCCTTTTATATTTTGCTTTTGACTT
Found at i:6778 original size:96 final size:96
Alignment explanation
Indices: 6522--6767 Score: 341
Period size: 97 Copynumber: 2.5 Consensus size: 96
6512 TTTTTGATTG
* * * *
6522 AAAAACGGGGTTGAAGTATCCCCTCGGAGGAATGGGGTTGGAATGTCCCCGATGATGACAATTTA
1 AAAAGCGGGGTTGGAGTATCCCCTCAGAGGAAT-GGGTTGGAGTGTCCCCGATGATGACAATTTA
*
6587 AGTAAGAATAAAATTTAAACTTTGATGCCTTT
65 ACTAAGAATAAAATTTAAACTTTGATGCCTTT
* * *
6619 AAAAGCGGGGTTGGAGTATCCCCTCAGAGGAATGGAGTTGAAGTGTCCCCGATGGTGGCAATTTA
1 AAAAGCGGGGTTGGAGTATCCCCTCAGAGGAATGG-GTTGGAGTGTCCCCGATGATGACAATTTA
* *
6684 ACTAAGAATAAGATTTAAACTTTGATG-TTTT
65 ACTAAGAATAAAATTTAAACTTTGATGCCTTT
* * *
6715 AAAAGCGGGGTTGGAGTATCCCATTAGAGGAATAGGGTTGGAGTATCCCCGAT
1 AAAAGCGGGGTTGGAGTATCCCCTCAGAGGAAT-GGGTTGGAGTGTCCCCGAT
6768 AAATAAAATT
Statistics
Matches: 133, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
96 51 0.38
97 82 0.62
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (96 bp):
AAAAGCGGGGTTGGAGTATCCCCTCAGAGGAATGGGTTGGAGTGTCCCCGATGATGACAATTTAA
CTAAGAATAAAATTTAAACTTTGATGCCTTT
Found at i:10033 original size:14 final size:14
Alignment explanation
Indices: 10011--10042 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
10001 TATGTCAAAA
*
10011 TATCTTTCCAAGGG
1 TATCCTTCCAAGGG
10025 TATCCTTCCAAGGG
1 TATCCTTCCAAGGG
10039 TATC
1 TATC
10043 TTATTTGCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (14 bp):
TATCCTTCCAAGGG
Found at i:13154 original size:109 final size:108
Alignment explanation
Indices: 12949--13162 Score: 401
Period size: 109 Copynumber: 2.0 Consensus size: 108
12939 CATGGTTTTT
12949 CAATCTAATCAGTTAATAGAACCATAAAATTTGACTCTTTTAATCTTATTATTCTAGCTCAAAGC
1 CAATCTAATCAGTTAATAGAACCATAAAATTTGACTCTTTTAATCTTATTATTCTAGCTCAAAGC
*
13014 ATAAGTACGATGGTGGATCTCTAAGGGAATAAAGCCAATCATG
66 ATAAGTACAATGGTGGATCTCTAAGGGAATAAAGCCAATCATG
13057 CAATCTAATCAGTTCAATAGAACCATAAAATTTGACTCTTTTAATCTTATTATTCTAGCTCAAAG
1 CAATCTAATCAGTT-AATAGAACCATAAAATTTGACTCTTTTAATCTTATTATTCTAGCTCAAAG
*
13122 CATAAGTATAATGGTGGATCTCTAAGGGAATAAAGCCAATC
65 CATAAGTACAATGGTGGATCTCTAAGGGAATAAAGCCAATC
13163 TTTTTCTTTA
Statistics
Matches: 103, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
108 14 0.14
109 89 0.86
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (108 bp):
CAATCTAATCAGTTAATAGAACCATAAAATTTGACTCTTTTAATCTTATTATTCTAGCTCAAAGC
ATAAGTACAATGGTGGATCTCTAAGGGAATAAAGCCAATCATG
Found at i:13714 original size:119 final size:118
Alignment explanation
Indices: 13515--13738 Score: 306
Period size: 119 Copynumber: 1.9 Consensus size: 118
13505 TTATATCCTT
* * * ** * *
13515 CTAAACATGAGCTTAAATTATTTCAAAAAAAAAATGATGATGCTCTTAAGCACATGCTCAAACTA
1 CTAAACATAAGCTTAAACTATTTCAAAAAAAAAATAATGACACTCCTAAACACATGCTCAAACTA
*
13580 CTATATCACTCCTAAACACGAGCTTAAACTATTTCTAAAATATGATTAAGCTC
66 CTATATCACTCCTAAACACGAGCTTAAACTATTTCAAAAATATGATTAAGCTC
*
13633 CTAAACATAAGCTTAAACTGTTTCAAAAAACAAAATAATGACACTCCTAAACACGA-GCTCAAAC
1 CTAAACATAAGCTTAAACTATTTCAAAAAA-AAAATAATGACACTCCTAAACAC-ATGCTCAAAC
** * *
13697 TACTATATTGCTTCTAAACATGAGCTTAAACTATTTCAAAAA
64 TACTATATCACTCCTAAACACGAGCTTAAACTATTTCAAAAA
13739 AACAAAATAA
Statistics
Matches: 91, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
118 27 0.30
119 63 0.69
120 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.28
Consensus pattern (118 bp):
CTAAACATAAGCTTAAACTATTTCAAAAAAAAAATAATGACACTCCTAAACACATGCTCAAACTA
CTATATCACTCCTAAACACGAGCTTAAACTATTTCAAAAATATGATTAAGCTC
Found at i:13738 original size:77 final size:78
Alignment explanation
Indices: 13629--13806 Score: 250
Period size: 78 Copynumber: 2.3 Consensus size: 78
13619 ATATGATTAA
* *
13629 GCTCCTAAACATAAGCTTAAACTGTTTC-AAAAAACAAAATAATGACACTCCTAAACACGAGCTC
1 GCTCCTAAACATGAGCTTAAACTATTTCAAAAAAACAAAATAATGACACTCCTAAACACGAGCTC
13693 AAACTACTATATT
66 AAACTACTATATT
* * ** *
13706 GCTTCTAAACATGAGCTTAAACTATTTCAAAAAAACAAAATAATTATGCTCCTAAACACGAGCTT
1 GCTCCTAAACATGAGCTTAAACTATTTCAAAAAAACAAAATAATGACACTCCTAAACACGAGCTC
**
13771 AAACTGTTATATT
66 AAACTACTATATT
* *
13784 GCTCCTAAGCATGAGCTCAAACT
1 GCTCCTAAACATGAGCTTAAACT
13807 GTTCCTCCAA
Statistics
Matches: 88, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
77 25 0.28
78 63 0.72
ACGTcount: A:0.42, C:0.22, G:0.10, T:0.27
Consensus pattern (78 bp):
GCTCCTAAACATGAGCTTAAACTATTTCAAAAAAACAAAATAATGACACTCCTAAACACGAGCTC
AAACTACTATATT
Found at i:13895 original size:77 final size:76
Alignment explanation
Indices: 13753--13898 Score: 179
Period size: 77 Copynumber: 1.9 Consensus size: 76
13743 AAATAATTAT
** * * * *
13753 GCTCCTAAACACGAGCTTAAACTGTTATATTGCTCCTAAGCATGAGCTCAAACTGTTCCTCCAAA
1 GCTCCTAAACAAAAGCTTAAACTATTATATTACTCCTAAGCACGAGCTCAAAC-GTACCTCCAAA
13818 AAAAAAGTTGTC
65 AAAAAAGTTGTC
*
13830 GCTCCTAAACAAAAGCTTAAACTATTATGA-TACTCCTAAGCACGAGCTTAAAC-TACCTACTCA
1 GCTCCTAAACAAAAGCTTAAACTATTAT-ATTACTCCTAAGCACGAGCTCAAACGTACCT-C-CA
13893 AAAAAA
63 AAAAAA
13899 TGATATTGAT
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
75 4 0.07
76 1 0.02
77 53 0.90
78 1 0.02
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (76 bp):
GCTCCTAAACAAAAGCTTAAACTATTATATTACTCCTAAGCACGAGCTCAAACGTACCTCCAAAA
AAAAAGTTGTC
Found at i:14629 original size:46 final size:46
Alignment explanation
Indices: 14527--14673 Score: 135
Period size: 46 Copynumber: 3.3 Consensus size: 46
14517 CATTTTTGTT
* * * * *
14527 TCTAATTAAATTATATTAATTAAGACATAAATAAAATAA-TTTATC
1 TCTAATTAAATTAAATTAATCAAAAGATAAATAAAAGAATTTTATC
* *
14572 TCTAATTAAATT-AA-T--T-AAAAGATGAATCAAAGAATTTTATC
1 TCTAATTAAATTAAATTAATCAAAAGATAAATAAAAGAATTTTATC
* * ** *
14613 TCTGATTCAATTAAATTAATCAAGGGATAAATAAAAGAGTTTTATC
1 TCTAATTAAATTAAATTAATCAAAAGATAAATAAAAGAATTTTATC
*
14659 TTTAATTAAATTAAA
1 TCTAATTAAATTAAA
14674 AATTAATTTA
Statistics
Matches: 80, Mismatches: 16, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
40 13 0.16
41 17 0.21
42 2 0.03
43 2 0.03
44 1 0.01
45 13 0.16
46 32 0.40
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (46 bp):
TCTAATTAAATTAAATTAATCAAAAGATAAATAAAAGAATTTTATC
Found at i:15107 original size:35 final size:35
Alignment explanation
Indices: 15068--15155 Score: 117
Period size: 35 Copynumber: 2.5 Consensus size: 35
15058 AGGCTTTGTT
*
15068 TTTCAAGATCAAGTTTGAA-GACCCTTGAAGCAAGA
1 TTTCAAGATCAAGTTT-AATGACCCTTAAAGCAAGA
*
15103 TTTCAAGATGAAGTTTAATGACCCTTAAAGCAAGA
1 TTTCAAGATCAAGTTTAATGACCCTTAAAGCAAGA
*
15138 -TTCATGATCAAGTCTTAA
1 TTTCAAGATCAAGT-TTAA
15156 AGCCTTGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
34 13 0.28
35 34 0.72
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.30
Consensus pattern (35 bp):
TTTCAAGATCAAGTTTAATGACCCTTAAAGCAAGA
Found at i:15258 original size:35 final size:35
Alignment explanation
Indices: 15212--15281 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
15202 GACCTATTGA
*
15212 TTCAAGATCAAGTCTCAAAAACCCTTGAAGCAAAT
1 TTCAAGATCAAGTCTCAAAAACCCTTGAAACAAAT
* *
15247 TTCAAGATCAAGTTTCCAAAACCCTTGAAACAAAT
1 TTCAAGATCAAGTCTCAAAAACCCTTGAAACAAAT
15282 CTAAGTTAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.43, C:0.23, G:0.10, T:0.24
Consensus pattern (35 bp):
TTCAAGATCAAGTCTCAAAAACCCTTGAAACAAAT
Found at i:18852 original size:156 final size:155
Alignment explanation
Indices: 18476--18964 Score: 480
Period size: 155 Copynumber: 3.2 Consensus size: 155
18466 TATTTTTTCT
* * * * * *
18476 ATCATTTTAGAGTCCTTTAGGGTTACCAAGATACTTTCACGTTGAAGGTATACTC-TAATGGCAT
1 ATCATTTTTGAGTCCTTTAGGGTTACCGAGATACTTTCAAGTCGAAGGTATACTCTTAAGGGTAT
* * *
18540 TTTGGTAATTTTTTAGAACT-GAGTTCGATATAGTCA-TCAGGGTGTTTTTATGT-TAAAAGTGT
66 TTTGGTAATTTATTAGAACTAGAGTTCGATATAGTCACT-A-GATGCTTTTAT-TCTAAAAGTGT
* * *
18602 GCATTAAGGATCGGTTCA--TTATTTATT
128 GCATTTAGGATAGGTTCACCTT-TTTATG
* * * * * *
18629 ATTATTTTTTAGTCTTTTAGGGTTACTGGGATACTTTCATA-TCGAAGATATAC-CTTAAGGGCT
1 ATCATTTTTGAGTCCTTTAGGGTTACCGAGATACTTTCA-AGTCGAAGGTATACTCTTAAGGG-T
** * *
18692 -TTTTGGTAATATTCCTAGAACTAGAGTTCGATATAGTCACTAGTATGCTTTTATTCCAAAGGTG
64 ATTTTGGTAAT-TTATTAGAACTAGAGTTCGATATAGTCACTAG-ATGCTTTTATTCTAAAAGTG
*
18756 TGCATTTAGGATATGTTCACCTTTTTATG
127 TGCATTTAGGATAGGTTCACCTTTTTATG
* * * * *
18785 ATCATTTTTTAGTCCTTTAGGGTCACCGAGATGCTTTCAAGACGAAGGTA-GCTCTTAAGGGTAT
1 ATCATTTTTGAGTCCTTTAGGGTTACCGAGATACTTTCAAGTCGAAGGTATACTCTTAAGGGTAT
* * * **
18849 TTTGGTAATTTTATTAGAACTA-AG-TCTAATGTAGTCATCGAGATGCTTTTACGCTAAAAGTGT
66 TTTGGTAA-TTTATTAGAACTAGAGTTC-GATATAGTCA-CTAGATGCTTTTATTCTAAAAGTGT
*
18912 GCATTTAGGATAGGTTCACCTTTCTATG
128 GCATTTAGGATAGGTTCACCTTTTTATG
*
18940 ATCATTTTTGAGTCCTTTAAGGTTA
1 ATCATTTTTGAGTCCTTTAGGGTTA
18965 TCAAAATACT
Statistics
Matches: 275, Mismatches: 45, Indels: 30
0.79 0.13 0.09
Matches are distributed among these distances:
152 1 0.00
153 57 0.21
154 13 0.05
155 125 0.45
156 76 0.28
157 3 0.01
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (155 bp):
ATCATTTTTGAGTCCTTTAGGGTTACCGAGATACTTTCAAGTCGAAGGTATACTCTTAAGGGTAT
TTTGGTAATTTATTAGAACTAGAGTTCGATATAGTCACTAGATGCTTTTATTCTAAAAGTGTGCA
TTTAGGATAGGTTCACCTTTTTATG
Found at i:22129 original size:3 final size:3
Alignment explanation
Indices: 22121--22151 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
22111 TCAACTATCA
*
22121 ATG ATG ATG AAG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
22152 AGTTGACTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (3 bp):
ATG
Found at i:22705 original size:20 final size:20
Alignment explanation
Indices: 22668--22705 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
22658 AAGTCTTAAC
*
22668 TAAGGAAAACAATGAATTAG
1 TAAGGAAAACAATAAATTAG
22688 TAAGGAAAAACAA-AAATT
1 TAAGG-AAAACAATAAATT
22706 TTCATGAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.61, C:0.05, G:0.16, T:0.18
Consensus pattern (20 bp):
TAAGGAAAACAATAAATTAG
Found at i:31356 original size:17 final size:17
Alignment explanation
Indices: 31336--31369 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
31326 CGTCCTTCAT
*
31336 AAAAAAA-ATAAAAACA
1 AAAAAAACAAAAAAACA
31352 AAAAAAACAAAAAAACA
1 AAAAAAACAAAAAAACA
31369 A
1 A
31370 CAAACAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.88, C:0.09, G:0.00, T:0.03
Consensus pattern (17 bp):
AAAAAAACAAAAAAACA
Found at i:31374 original size:24 final size:23
Alignment explanation
Indices: 31337--31381 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
31327 GTCCTTCATA
*
31337 AAAAAAATAAAAACAAAAAAAAC
1 AAAAAAACAAAAACAAAAAAAAC
*
31360 AAAAAAACAACAAACAAGAAAA
1 AAAAAAACAA-AAACAAAAAAA
31382 GGGGGAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.84, C:0.11, G:0.02, T:0.02
Consensus pattern (23 bp):
AAAAAAACAAAAACAAAAAAAAC
Done.