Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002760.1 Hibiscus syriacus cultivar Beakdansim tig00005690_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: 84990
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:3349 original size:28 final size:28
Alignment explanation
Indices: 3306--3370 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
3296 AACCAAAGTA
*
3306 AGCATCATGGTGTAGCTCGGGTTCACTT
1 AGCATCATGGTGTAGCTCGGGGTCACTT
*
3334 AGTATCATGGTGTAGCTCGGGGTCACTT
1 AGCATCATGGTGTAGCTCGGGGTCACTT
3362 AGCATCATG
1 AGCATCATG
3371 AAACTCACAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (28 bp):
AGCATCATGGTGTAGCTCGGGGTCACTT
Found at i:11747 original size:20 final size:20
Alignment explanation
Indices: 11724--11761 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
11714 ACCGATATTG
11724 ACCCCTGAGTATCGATACTA
1 ACCCCTGAGTATCGATACTA
11744 ACCCCTGAGTATCGATAC
1 ACCCCTGAGTATCGATAC
11762 CCATATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.24
Consensus pattern (20 bp):
ACCCCTGAGTATCGATACTA
Found at i:15756 original size:22 final size:23
Alignment explanation
Indices: 15723--15778 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
15713 CTGTATGAAT
15723 AGTATC-AGTACCATAAG-GAAGG
1 AGTATCGA-TACCATAAGTGAAGG
*
15745 AGTATCGATACC-TATGTGAAGG
1 AGTATCGATACCATAAGTGAAGG
15767 -GTATCGATACCA
1 AGTATCGATACCA
15779 AGAAACATCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 14 0.47
22 15 0.50
23 1 0.03
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (23 bp):
AGTATCGATACCATAAGTGAAGG
Found at i:30014 original size:8 final size:8
Alignment explanation
Indices: 30003--30029 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
29993 TTTTTTTTGC
30003 TTTTTTAT
1 TTTTTTAT
30011 TTTTTTAT
1 TTTTTTAT
30019 TTTTTTAT
1 TTTTTTAT
30027 TTT
1 TTT
30030 CGAATTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTAT
Found at i:30015 original size:16 final size:16
Alignment explanation
Indices: 29994--30029 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
29984 AAAACACATT
*
29994 TTTTTTTGCTTTTTTA
1 TTTTTTTACTTTTTTA
*
30010 TTTTTTTATTTTTTTA
1 TTTTTTTACTTTTTTA
30026 TTTT
1 TTTT
30030 CGAATTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.08, C:0.03, G:0.03, T:0.86
Consensus pattern (16 bp):
TTTTTTTACTTTTTTA
Found at i:34624 original size:224 final size:223
Alignment explanation
Indices: 34187--34630 Score: 852
Period size: 224 Copynumber: 2.0 Consensus size: 223
34177 AGGAGATATG
*
34187 AACAAAATTTTTCCAAGACGAAAATGATAACAAAGAGTTCTTTTTCAGTAGTCAAATAATTTTGT
1 AACAAAATTTTTCCAAGACAAAAATGATAACAAAGAGTTCTTTTTCAGTAGTCAAATAATTTTGT
34252 TTTGGACACATAGGATATCACGTGGGGTTCTTTGTCGATTTTTTTCCAAGTACAGCTCTCACACT
66 TTTGGACACATAGGATATCACGTGGGGTTCTTTGTCGATTTTTTTCCAAGTACAGCTCTCACACT
34317 TCAATCTTTTGCATCGCACATTATTTCGAAAGGATAATCCCAATTGGGTGGTTGAATGATGGTTG
131 TCAATCTTTTGCATCGCACATTATTTCGAAAGGATAATCCCAATTGGGTGGTTGAATGATGGTTG
34382 CTGAAACAAGCTTTTCCTTTAAAATGAT
196 CTGAAACAAGCTTTTCCTTTAAAATGAT
34410 AACAAAATTTTTCCAAGACAAAAATGATAACAAAGAGTTCTTTTTCAGTAGTCAAATAATTTTGT
1 AACAAAATTTTTCCAAGACAAAAATGATAACAAAGAGTTCTTTTTCAGTAGTCAAATAATTTTGT
34475 TTTGGACACATAGGATATCACGTGGGGTTCTTTGTCGATTTTTTTTCCAAGTACAGCTCTCACAC
66 TTTGGACACATAGGATATCACGTGGGGTTCTTTGTCGA-TTTTTTTCCAAGTACAGCTCTCACAC
* *
34540 TTCAATCTTTTGCATCTCACATTATTTTGAAAGGATAATCCCAATTGGGTGGTTGAATGATGGTT
130 TTCAATCTTTTGCATCGCACATTATTTCGAAAGGATAATCCCAATTGGGTGGTTGAATGATGGTT
34605 GCTGAAACAAGCTTTTCCTTTAAAAT
195 GCTGAAACAAGCTTTTCCTTTAAAAT
34631 ATCAAAAGAA
Statistics
Matches: 217, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
223 102 0.47
224 115 0.53
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (223 bp):
AACAAAATTTTTCCAAGACAAAAATGATAACAAAGAGTTCTTTTTCAGTAGTCAAATAATTTTGT
TTTGGACACATAGGATATCACGTGGGGTTCTTTGTCGATTTTTTTCCAAGTACAGCTCTCACACT
TCAATCTTTTGCATCGCACATTATTTCGAAAGGATAATCCCAATTGGGTGGTTGAATGATGGTTG
CTGAAACAAGCTTTTCCTTTAAAATGAT
Found at i:42503 original size:18 final size:17
Alignment explanation
Indices: 42482--42524 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
42472 ATATATACAT
42482 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
42500 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
42517 ATAA-AATA
1 ATAATAATA
42525 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:42981 original size:34 final size:33
Alignment explanation
Indices: 42885--43005 Score: 121
Period size: 33 Copynumber: 3.7 Consensus size: 33
42875 CTTGTGGATC
* *
42885 CTATCTTTAGGAGTTTAAATCATAAAATTCTAT
1 CTATCTTTAGGAGTTTGAATCCTAAAATTCTAT
42918 CCTA--TTT-----TTTGAATCCTAGCAAAATTCTAT
1 -CTATCTTTAGGAGTTTGAATCCT---AAAATTCTAT
42948 CATATCTTTAGGAGTTTGAATCCTAAAATTCTAT
1 C-TATCTTTAGGAGTTTGAATCCTAAAATTCTAT
*
42982 CTATTTTTAGGAGTTTGAATCCTA
1 CTATCTTTAGGAGTTTGAATCCTA
43006 GTAGGACGAA
Statistics
Matches: 73, Mismatches: 3, Indels: 23
0.74 0.03 0.23
Matches are distributed among these distances:
27 8 0.11
29 1 0.01
30 12 0.16
32 6 0.08
33 22 0.30
34 14 0.19
37 10 0.14
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (33 bp):
CTATCTTTAGGAGTTTGAATCCTAAAATTCTAT
Found at i:43659 original size:100 final size:100
Alignment explanation
Indices: 43467--44096 Score: 359
Period size: 109 Copynumber: 5.9 Consensus size: 100
43457 AATATTGTTC
* * *
43467 CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACCAGGAAATTGTTGGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAA-C--GAAA-TCTT-GTTGACA
* * * * *
43532 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
60 ATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
43573 CGAGTCTAATATCCTTCGCTGTGAAGTTCAAATTGACTCTGAACGAAATCTTGTTGACAATCAGC
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAACGAAATCTTGTTGACAATCAGC
43638 CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * ** *
43673 CGAGTCCAATATCCTTCACTGTGAAGTTGGAATTGGCTATGAAATTTAAAAAATGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTG--A---ACGAAAT-CTTGTTGACA
* * *
43738 ACCAGCTGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
60 ATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * ** * *
43779 CGAGTGGCACGATATCCTCCG-TCGTGGAGTTGAAA-TCGCGGATGAAACTGAAAAGTTGTTCAT
1 CGAGT--C-CAATATCCTTCGCT-GTGAAGTTGAAATTGGC-TCTG-AAC-G-AAA--TCTT-GT
* * * *
43842 TGACAACCAGTCGTCCCTTCGTTGTGAAGTTGGACTTGTGTTTTCT
55 TGACAATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * * * * * *
43888 CGGGTAGCACGATATCCTCCG-TCGTGGAGTTGAAATCGGTTCTGGAATTGGGAAGTTGTTCATT
1 CGAGT--C-CAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCT-GAA---CGAA-ATCTT-GTT
*
43952 GACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
56 GACAATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * ** * * *
43997 CGGGTAGCACGATATCCTTCG-TCGTGGAGTTGAAATCGATTCCGAAATTGGGAAATTGTTGTTG
1 CGAGT--C-CAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTG-AA---CGAAA-TCTTGTTG
* * *
44061 GCAACCAGACGTCCCTTCGTTGTGAAGTTGAACTTG
57 ACAATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
44097 ACTCTAGCTA
Statistics
Matches: 442, Mismatches: 58, Indels: 46
0.81 0.11 0.08
Matches are distributed among these distances:
100 78 0.18
101 3 0.01
102 5 0.01
104 1 0.00
105 9 0.02
106 87 0.20
107 3 0.01
108 47 0.11
109 204 0.46
110 4 0.01
111 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.32
Consensus pattern (100 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAACGAAATCTTGTTGACAATCAGC
CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:43771 original size:106 final size:108
Alignment explanation
Indices: 43534--44096 Score: 463
Period size: 109 Copynumber: 5.3 Consensus size: 108
43524 GGTTGACAGT
* * * * * *
43534 CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGT-C-TAATATCCTTCG-CTGTG
1 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCACAATATCCTCCGTC-GTG
* * * * * * *
43596 AAGTTCAAATTGACTCTG-AA-CG---AAATCTT-GTTGACAAT
65 AAGTTGAAATTGGCTATGAAATTGAAAAAATGTTCATTGACAAC
43634 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-C-CAATATCCTTCAC-T-GT
1 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCACAATATCC-TC-CGTCGT
* * **
43695 GAAGTTGGAATTGGCTATGAAATTTAAAAAATGTTTGTTGACAAC
64 GAAGTTGAAATTGGCTATGAAATTGAAAAAATGTTCATTGACAAC
* * *
43740 CAGCTGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCACGATATCCTCCGTCGTG
1 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCACAATATCCTCCGTCGTG
* * * * **
43805 GAGTTGAAA-TCGCGGATGAAACTGAAAAGTTGTTCATTGACAAC
65 AAGTTGAAATTGGC-TATGAAATTGAAAAAATGTTCATTGACAAC
* * * * *
43849 CAGTCGTCCCTTCGTTGTGAAGTTGGACTTGTGTTTTCTCGGGTAGCACGATATCCTCCGTCGTG
1 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCACAATATCCTCCGTCGTG
* * * * * ** **
43914 GAGTTGAAATCGGTTCTGGAATTGGGAAGTTGTTCATTGACAAC
65 AAGTTGAAATTGGCTATGAAATTGAAAAAATGTTCATTGACAAC
* * *
43958 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGCACGATATCCTTCGTCGTG
1 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCACAATATCCTCCGTCGTG
* * ** ** ** * * *
44023 GAGTTGAAATCGATTCCGAAATTGGGAAATTGTT-GTTGGCAAC
65 AAGTTGAAATTGGCTATGAAATTGAAAAAATGTTCATTGACAAC
*
44066 CAGACGTCCCTTCGTTGTGAAGTTGAACTTG
1 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
44097 ACTCTAGCTA
Statistics
Matches: 393, Mismatches: 54, Indels: 24
0.83 0.11 0.05
Matches are distributed among these distances:
100 65 0.17
101 3 0.01
102 1 0.00
105 6 0.02
106 50 0.13
107 1 0.00
108 44 0.11
109 222 0.56
110 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (108 bp):
CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCACAATATCCTCCGTCGTGA
AGTTGAAATTGGCTATGAAATTGAAAAAATGTTCATTGACAAC
Found at i:43858 original size:109 final size:109
Alignment explanation
Indices: 43626--44096 Score: 544
Period size: 109 Copynumber: 4.4 Consensus size: 109
43616 CGAAATCTTG
* *
43626 TTGACAATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT--C-CAATATCCT
1 TTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTAGCACGATATCC-
* * * * ** **
43688 TCAC-T-GTGAAGTTGGAATTGGCTATGAAATTTAAAAAATGTTTG
65 TC-CGTCGTGGAGTTGAAATCGGCTATGAAATTGAAAAGTTGTTCA
* * *
43732 TTGACAACCAGCTGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCACGATATCCT
1 TTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTAGCACGATATCCT
* *
43797 CCGTCGTGGAGTTGAAATC-GCGGATGAAACTGAAAAGTTGTTCA
66 CCGTCGTGGAGTTGAAATCGGC-TATGAAATTGAAAAGTTGTTCA
* * * *
43841 TTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGGACTTGTGTTTTCTCGGGTAGCACGATATCCT
1 TTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTAGCACGATATCCT
* * * **
43906 CCGTCGTGGAGTTGAAATCGGTTCTGGAATTGGGAAGTTGTTCA
66 CCGTCGTGGAGTTGAAATCGGCTATGAAATTGAAAAGTTGTTCA
*
43950 TTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGCACGATATCCT
1 TTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTAGCACGATATCCT
* ** ** * *
44015 TCGTCGTGGAGTTGAAATCGATTCCGAAATTGGGAAA-TTGTT-G
66 CCGTCGTGGAGTTGAAATCGGCTATGAAATT-GAAAAGTTGTTCA
* *
44058 TTGGCAACCAGACGTCCCTTCGTTGTGAAGTTGAACTTG
1 TTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
44097 ACTCTAGCTA
Statistics
Matches: 318, Mismatches: 39, Indels: 14
0.86 0.11 0.04
Matches are distributed among these distances:
106 49 0.15
107 1 0.00
108 43 0.14
109 220 0.69
110 5 0.02
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (109 bp):
TTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTAGCACGATATCCT
CCGTCGTGGAGTTGAAATCGGCTATGAAATTGAAAAGTTGTTCA
Found at i:44750 original size:67 final size:67
Alignment explanation
Indices: 44677--44835 Score: 223
Period size: 67 Copynumber: 2.4 Consensus size: 67
44667 GAAACGAAAT
* *
44677 TTTGTTTTAAGGGAGATA-AAT-TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCATGGGAGAC
1 TTTGTTTCAAGGGA-A-ACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGAC
*
44740 AAAG
64 AAAA
* *
44744 TTTGTTTCGAGGGAAACAATCTCAAAGGTTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAA
1 TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAA
44809 AA
66 AA
**
44811 TTTGTTTCAAGGGAAATTATCTCAA
1 TTTGTTTCAAGGGAAACAATCTCAA
44836 GAGAGACGAA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 77 0.94
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (67 bp):
TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAA
AA
Found at i:44834 original size:36 final size:36
Alignment explanation
Indices: 44710--45186 Score: 219
Period size: 36 Copynumber: 13.9 Consensus size: 36
44700 AAAGATTTTG
* * * *
44710 TGTTTCAAGAGAAACTGTCTCATGGGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* ** **
44746 TGTTTCGAGGGAAACAATCTCAA-AG-G----TTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* *
44776 GTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * * *
44813 TGTTTCAAGGGAAATTATCTCAAGAGAGACGAAATC
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * *
44849 CATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT
* *
44877 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
* *
44915 TGTTTCGAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * * *
44951 CATTTCAAGGGAAA-TGTTTCCA-A-TG-----TTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * * *
44979 ATGTTTCAAGAGAAACTATCTCAATG-GAGACGGAATTT
1 -TGTTTCAAGGGAAACTGTCTCAA-GAGAGAC-AAAATT
* *
45017 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * *
45053 CATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT
* * *
45081 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
*
45119 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*
45155 TGTTTTAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
45187 TGGTGAGCAC
Statistics
Matches: 321, Mismatches: 77, Indels: 86
0.66 0.16 0.18
Matches are distributed among these distances:
28 4 0.01
29 39 0.12
30 13 0.04
31 19 0.06
32 4 0.01
33 4 0.01
34 4 0.01
35 10 0.03
36 128 0.40
37 89 0.28
38 7 0.02
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:44929 original size:37 final size:37
Alignment explanation
Indices: 44878--45186 Score: 205
Period size: 37 Copynumber: 8.9 Consensus size: 37
44868 TCAATGTTTA
* *
44878 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
44915 TGTTTCGAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * **
44951 CATTTCAAGGGAAA-TGTTTC--------CAATGTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * **
44979 ATGTTTCAAGAGAAACTATCTCAATG-GAGACGGAATTT
1 -TGTTTCAAGGGAAACTGTCTCAA-GAGAGACAAAATTT
* *
45017 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-CT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * *
45053 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* * *
45081 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
45119 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
45155 TGTTTTAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
45187 TGGTGAGCAC
Statistics
Matches: 205, Mismatches: 41, Indels: 52
0.69 0.14 0.17
Matches are distributed among these distances:
27 3 0.01
28 3 0.01
29 25 0.12
30 7 0.03
32 1 0.00
33 1 0.00
34 1 0.00
35 6 0.03
36 64 0.31
37 87 0.42
38 7 0.03
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.28
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:45167 original size:204 final size:205
Alignment explanation
Indices: 44710--45169 Score: 674
Period size: 204 Copynumber: 2.2 Consensus size: 205
44700 AAAGATTTTG
* * * *
44710 TGTTTCAAGAGAAACTGTCTCATGGGAGACAAAGTTTGTTTCGAGGGAAACAATCTCAAAGGTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTTTGTTTCAAGGGAAACAATCTCAAAGGTTT
* * *
44775 TGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATTATCTCAAGAGA
66 TATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGA
*
44840 GACGAAATCCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGA
131 GACAAAATCCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGA
*
44905 GACAAAATTT
196 GAAAAAATTT
* * * ** ** * * *
44915 TGTTTCGAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA-TGTTTCCAATG-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTTTGTTTCAAGGGAAACAATCTCAAAGGTTT
* * *
44978 TATGTTTCAAGAGAAACTATCTCAATGGAGACGGAATTTTGTTTCAAGGGAAACTATCTCAAGAG
66 TATGTTTCAAGAGAAACTATCTCAAGGGAGAC-AAAATTTGTTTCAAGGGAAACTATCTCAAGAG
45043 AGACAAAA-CTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGG
130 AGACAAAATC-CATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGG
45107 GAGAAAAAATTT
194 GAGAAAAAATTT
*
45119 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTTTGTTTTAAGGGAAAC
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTTTGTTTCAAGGGAAAC
45170 TGTCTCAAGA
Statistics
Matches: 224, Mismatches: 28, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
203 32 0.14
204 151 0.67
205 41 0.18
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (205 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTTTGTTTCAAGGGAAACAATCTCAAAGGTTT
TATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGA
GACAAAATCCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGA
GAAAAAATTT
Found at i:45168 original size:102 final size:102
Alignment explanation
Indices: 44777--45151 Score: 635
Period size: 102 Copynumber: 3.7 Consensus size: 102
44767 AAAGGTTTTG
*
44777 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAATTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* *
44841 ACGAAATCCATTTCAAGGGAAATGTTTTCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
44878 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCGAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
44943 ACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* * **
44980 TGTTTCAAGAGAAACTATCTCAATGGAGACGGAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
45045 ACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
45082 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
45147 ACAAA
66 ACAAA
45152 GTTTGTTTTA
Statistics
Matches: 255, Mismatches: 18, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
101 34 0.13
102 221 0.87
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (102 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:46072 original size:22 final size:22
Alignment explanation
Indices: 46047--46095 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
46037 TTGTGTTTGG
* *
46047 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
46069 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
46091 TCAAA
1 TCAAA
46096 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:46102 original size:22 final size:22
Alignment explanation
Indices: 46059--46102 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
46049 AAAGGTTTGG
* * *
46059 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
46081 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
46103 TGGGGTAGCT
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:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:46766 original size:8 final size:8
Alignment explanation
Indices: 46755--46823 Score: 70
Period size: 8 Copynumber: 8.8 Consensus size: 8
46745 TTTTTGCTCT
46755 TTTTTTTC
1 TTTTTTTC
*
46763 TTTTGTTC
1 TTTTTTTC
*
46771 -TTGTTTC
1 TTTTTTTC
*
46778 TCTTTTTC
1 TTTTTTTC
46786 TTTGTTTT-
1 TTT-TTTTC
*
46794 TTTTTTGC
1 TTTTTTTC
46802 TTTTTTTC
1 TTTTTTTC
*
46810 TTCTTTTC
1 TTTTTTTC
46818 TTTTTT
1 TTTTTT
46824 GTTCTTGATT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
7 8 0.17
8 36 0.75
9 4 0.08
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (8 bp):
TTTTTTTC
Found at i:46767 original size:24 final size:24
Alignment explanation
Indices: 46732--46829 Score: 92
Period size: 24 Copynumber: 4.0 Consensus size: 24
46722 TTTTTGTCCC
*
46732 TTTTTCTTTTTGATTTTTGCTCTTT
1 TTTTTC-TTTTGTTTTTTGCTCTTT
*
46757 TTTTTCTTTTGTTCTTGTTTCTCTTT
1 TTTTTCTTTTGTT-TT-TTGCTCTTT
*
46783 TTCTTTGTTTT-TTTTTTGCT-TTT
1 TT-TTTCTTTTGTTTTTTGCTCTTT
* *
46806 TTTCTTCTTTTCTTTTTTGTTCTT
1 TTT-TTCTTTTGTTTTTTGCTCTT
46830 GATTGGATCT
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
22 1 0.02
23 11 0.18
24 18 0.30
25 12 0.20
26 12 0.20
27 7 0.11
ACGTcount: A:0.01, C:0.13, G:0.07, T:0.79
Consensus pattern (24 bp):
TTTTTCTTTTGTTTTTTGCTCTTT
Found at i:46788 original size:32 final size:31
Alignment explanation
Indices: 46752--46829 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 31
46742 TGATTTTTGC
46752 TCTTTTTTTTCTTTTG-TTCTTGTTTC-TCTTTT
1 TCTTTTTTTTCTTTTGCTT-TT-TTTCTTC-TTT
*
46784 TCTTTGTTTTTTTTTTGCTTTTTTTCTTCTTT
1 TCTTT-TTTTTCTTTTGCTTTTTTTCTTCTTT
46816 TCTTTTTTGTTCTT
1 TCTTTTTT-TTCTT
46830 GATTGGATCT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
31 3 0.08
32 21 0.52
33 14 0.35
34 2 0.05
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.79
Consensus pattern (31 bp):
TCTTTTTTTTCTTTTGCTTTTTTTCTTCTTT
Found at i:46821 original size:16 final size:15
Alignment explanation
Indices: 46755--46823 Score: 70
Period size: 15 Copynumber: 4.4 Consensus size: 15
46745 TTTTTGCTCT
46755 TTTTTTTCTTTTGTTC
1 TTTTTTTCTTTT-TTC
*
46771 -TTGTTTCTCTTTTTC
1 TTTTTTTCT-TTTTTC
46786 TTTGTTTT-TTTTTTGC
1 TTT-TTTTCTTTTTT-C
46802 TTTTTTTCTTCTTTTC
1 TTTTTTTCTT-TTTTC
46818 TTTTTT
1 TTTTTT
46824 GTTCTTGATT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
15 19 0.42
16 19 0.42
17 7 0.16
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (15 bp):
TTTTTTTCTTTTTTC
Found at i:47952 original size:8 final size:8
Alignment explanation
Indices: 47936--47974 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
47926 AATGTAGATG
47936 AAAATGCA
1 AAAATGCA
*
47944 AAAAGGCA
1 AAAATGCA
47952 AAAATGC-
1 AAAATGCA
47959 AAAATGCA
1 AAAATGCA
*
47967 AGAATGCA
1 AAAATGCA
47975 TGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:47962 original size:15 final size:15
Alignment explanation
Indices: 47936--47974 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
47926 AATGTAGATG
47936 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
47952 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
47967 AGAATGCA
1 AAAATGCA
47975 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:51045 original size:16 final size:18
Alignment explanation
Indices: 51013--51051 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
51003 ATATACATAT
51013 ATAATAATAACATGAATA
1 ATAATAATAACATGAATA
51031 ATAA-AATAA-ATGAATA
1 ATAATAATAACATGAATA
51047 A-AATA
1 ATAATA
51052 TCCATATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 2 0.10
16 9 0.45
17 5 0.25
18 4 0.20
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.26
Consensus pattern (18 bp):
ATAATAATAACATGAATA
Found at i:51506 original size:34 final size:34
Alignment explanation
Indices: 51463--51531 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
51453 GAATCCTAGC
51463 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
* *
51497 AAAATTCTATCCTATTTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
51531 A
1 A
51532 GTAGGACGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
Found at i:53931 original size:13 final size:13
Alignment explanation
Indices: 53913--53946 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
53903 ATAGATTTAG
*
53913 CTGAACCTTTACT
1 CTGAACCGTTACT
53926 CTGAACCGTTACT
1 CTGAACCGTTACT
53939 CTGAACCG
1 CTGAACCG
53947 GTCTACTCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (13 bp):
CTGAACCGTTACT
Found at i:56644 original size:26 final size:26
Alignment explanation
Indices: 56588--56655 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 26
56578 TAAATCTCAG
*
56588 ATGACACGCAATTGTGTGTCACAAATCT
1 ATGACACGC-ATT-TATGTCACAAATCT
* *
56616 ATGACACGCATTTATGTCACATATTT
1 ATGACACGCATTTATGTCACAAATCT
56642 ATGACA--CATTTATG
1 ATGACACGCATTTATG
56656 ACGCTCATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 8 0.22
26 17 0.46
27 3 0.08
28 9 0.24
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (26 bp):
ATGACACGCATTTATGTCACAAATCT
Found at i:56842 original size:2 final size:2
Alignment explanation
Indices: 56835--56869 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
56825 GTTCGTAAAT
56835 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
56870 TGTAGATTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:64127 original size:22 final size:24
Alignment explanation
Indices: 64096--64144 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
64086 CCATTTCATT
64096 ATCAACACCATC-ATCTT-CATCC
1 ATCAACACCATCAATCTTGCATCC
* *
64118 ATCAAGACCATCAATTTTGCATCC
1 ATCAACACCATCAATCTTGCATCC
64142 ATC
1 ATC
64145 TATATACTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 11 0.48
23 4 0.17
24 8 0.35
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.29
Consensus pattern (24 bp):
ATCAACACCATCAATCTTGCATCC
Found at i:65062 original size:24 final size:24
Alignment explanation
Indices: 65029--65074 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
65019 AGAATTACCA
* *
65029 CTCTTTGCTCTTCAATAGTCACAC
1 CTCTTGGCTCTTCAAAAGTCACAC
*
65053 CTCTTGGCTCTTGAAAAGTCAC
1 CTCTTGGCTCTTCAAAAGTCAC
65075 TTCCTTTAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.22, C:0.30, G:0.13, T:0.35
Consensus pattern (24 bp):
CTCTTGGCTCTTCAAAAGTCACAC
Found at i:65840 original size:22 final size:21
Alignment explanation
Indices: 65815--65855 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
65805 GTTGCGGAAT
65815 TGATGGTCTTGATGAATGAAGA
1 TGATGGTCTTGATG-ATGAAGA
*
65837 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
65856 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.29, C:0.02, G:0.34, T:0.34
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:65863 original size:26 final size:25
Alignment explanation
Indices: 65824--65873 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
65814 TTGATGGTCT
65824 TGATGAATGAAGATGATGGTGTTGA
1 TGATGAATGAAGATGATGGTGTTGA
* * *
65849 TGATGAAATGGAGATGGTGTTGTTG
1 TGATG-AATGAAGATGATGGTGTTG
65874 TTGTATCTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.28, C:0.00, G:0.38, T:0.34
Consensus pattern (25 bp):
TGATGAATGAAGATGATGGTGTTGA
Found at i:70650 original size:13 final size:13
Alignment explanation
Indices: 70632--70662 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
70622 TCTTTTTGAA
*
70632 TTTCTTTTCTTTT
1 TTTCTTTTCTTCT
70645 TTTCTTTTCTTCT
1 TTTCTTTTCTTCT
70658 TTTCT
1 TTTCT
70663 GAATTTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTCTTTTCTTCT
Found at i:70667 original size:34 final size:32
Alignment explanation
Indices: 70618--70691 Score: 98
Period size: 34 Copynumber: 2.3 Consensus size: 32
70608 CTTGGCTTGC
*
70618 TTTCTCTTTTTGAATTTCTT-TTCTTTTTTTCT
1 TTTCTCTTTTTGAATTT-TTCTTCTTTTTGTCT
70650 TTTCTTCTTTTCTGAATTTTTCTTCTTTTTGTCT
1 TTTC-TCTTTT-TGAATTTTTCTTCTTTTTGTCT
70684 TTT-TCTTT
1 TTTCTCTTT
70692 CATTTTGCAC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
32 9 0.24
33 8 0.21
34 21 0.55
ACGTcount: A:0.05, C:0.16, G:0.04, T:0.74
Consensus pattern (32 bp):
TTTCTCTTTTTGAATTTTTCTTCTTTTTGTCT
Found at i:70987 original size:21 final size:21
Alignment explanation
Indices: 70948--70989 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
70938 AAGGAAGATT
*
70948 AATGAAATGATAAATATAAAG
1 AATGAAATGATAAAAATAAAG
70969 AATGAAATGA-AATAAATAAAG
1 AATGAAATGATAA-AAATAAAG
70990 GATAGAGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.21
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAAG
Found at i:71036 original size:22 final size:21
Alignment explanation
Indices: 71010--71050 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
71000 GTTATGGAAT
71010 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
71032 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
71051 ATAGAGATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.34
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:72616 original size:21 final size:21
Alignment explanation
Indices: 72577--72616 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
72567 ACGGAAGACT
*
72577 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
72598 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
72617 AGGATAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:72664 original size:19 final size:18
Alignment explanation
Indices: 72640--72676 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
72630 CTGCGGAATT
72640 GATGGTCTTGATGGATGAA
1 GATGGTCTTGAT-GATGAA
*
72659 GATGGTGTTGATGATGAA
1 GATGGTCTTGATGATGAA
72677 ATAGAGATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.27, C:0.03, G:0.38, T:0.32
Consensus pattern (18 bp):
GATGGTCTTGATGATGAA
Found at i:77167 original size:22 final size:21
Alignment explanation
Indices: 77141--77181 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
77131 GCTGCGGAAT
77141 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
77163 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
77182 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.34
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Done.