Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004755.1 Hibiscus syriacus cultivar Beakdansim tig00010732_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: 67773
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:19398 original size:2 final size:2
Alignment explanation
Indices: 19391--19469 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
19381 ATCTTAACCC
19391 AT AT AT 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 AT AT AT
19433 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19470 ATCTGATTAA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21107 original size:7 final size:7
Alignment explanation
Indices: 21095--21153 Score: 97
Period size: 7 Copynumber: 8.9 Consensus size: 7
21085 CGTCTCGTCT
21095 CGTGGTC
1 CGTGGTC
21102 CGTGGTC
1 CGTGGTC
21109 CGTGGTC
1 CGTGGTC
21116 CGTGGTC
1 CGTGGTC
21123 CGTGGT-
1 CGTGGTC
21129 CGTGGTC
1 CGTGGTC
21136 CGTGGT-
1 CGTGGTC
21142 CGTGGT-
1 CGTGGTC
21148 CGTGGT
1 CGTGGT
21154 AATACGTGTC
Statistics
Matches: 51, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
6 18 0.35
7 33 0.65
ACGTcount: A:0.00, C:0.24, G:0.46, T:0.31
Consensus pattern (7 bp):
CGTGGTC
Found at i:21263 original size:40 final size:39
Alignment explanation
Indices: 21214--21313 Score: 110
Period size: 41 Copynumber: 2.5 Consensus size: 39
21204 AAATCTTTTT
* * *
21214 TTTTTAACTATCACAACGAATTTAGAAAATCGCGTTGCAA
1 TTTTCAACTATCGCAACGAA-ATAGAAAATCGCGTTGCAA
* * *
21254 TTTTCAACTATCGCAACGTGAAATGGAAAGTCGCGTTGCGA
1 TTTTCAACTATCGCAAC--GAAATAGAAAATCGCGTTGCAA
*
21295 TTTTCAACTACCGCAACGA
1 TTTTCAACTATCGCAACGA
21314 CAACTGCAGA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
39 2 0.04
40 15 0.29
41 31 0.61
42 3 0.06
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (39 bp):
TTTTCAACTATCGCAACGAAATAGAAAATCGCGTTGCAA
Found at i:27675 original size:33 final size:31
Alignment explanation
Indices: 27634--27694 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 31
27624 AAATAAAATA
*
27634 TTAATA-TTTTTAAGTTTTAAATATTAATATTT
1 TTAATATTTTTTAA-ATTTAAATA-TAATATTT
27666 TTAATTATTTTTTAAATTTAAATATAATA
1 TTAA-TATTTTTTAAATTTAAATATAATA
27695 AATATCTGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
32 9 0.35
33 10 0.38
34 7 0.27
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (31 bp):
TTAATATTTTTTAAATTTAAATATAATATTT
Found at i:29124 original size:34 final size:32
Alignment explanation
Indices: 29071--29140 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
29061 CCTTACAAAC
*
29071 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
29103 TCCCTAGATTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
29137 TCCC
1 TCCC
29141 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:29446 original size:21 final size:21
Alignment explanation
Indices: 29420--29461 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
29410 CCCAGAATGG
*
29420 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
29441 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
29462 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:29591 original size:19 final size:19
Alignment explanation
Indices: 29567--29633 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
29557 GAGCCTCGGG
*
29567 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAACAGTAAT
*
29586 TTACTGTTCAAATAGTAAT
1 TTACTGTTCAAACAGTAAT
* *
29605 TTACTGTTCAAATAGTAAA
1 TTACTGTTCAAACAGTAAT
*
29624 TTACTATTCA
1 TTACTGTTCA
29634 TAAAAACATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.40
Consensus pattern (19 bp):
TTACTGTTCAAACAGTAAT
Found at i:29745 original size:30 final size:31
Alignment explanation
Indices: 29698--29788 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
29688 AAATTTTGAA
29698 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
29727 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
29758 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
29789 CCTTAAATTG
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 11 0.18
31 38 0.63
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:29856 original size:2 final size:2
Alignment explanation
Indices: 29849--29909 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
29839 ATTTATTGTT
29849 TA TA 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 TA TA
29891 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
29910 GTATGTATGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35250 original size:21 final size:21
Alignment explanation
Indices: 35133--35270 Score: 77
Period size: 21 Copynumber: 6.7 Consensus size: 21
35123 ACGCGAAATA
**
35133 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
35153 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
* *
35173 AAAATCGTAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* ** *
35194 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* **
35215 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
* * *
35236 AAAATCGCAACGCGAATAT-G
1 AAAATCGCAACGCGATTTTCC
35256 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
35271 ACACATAAAT
Statistics
Matches: 87, Mismatches: 27, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
19 1 0.01
20 38 0.44
21 46 0.53
22 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:35299 original size:20 final size:20
Alignment explanation
Indices: 35237--35390 Score: 159
Period size: 20 Copynumber: 7.7 Consensus size: 20
35227 CGATTTTCCA
* ** *
35237 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
35257 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
35277 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
35297 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
35317 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * * *
35337 AAATCGCAATG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
35357 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
35378 AAATCGCAACGCG
1 AAATCGCAACGCG
35391 ATATTTAAAG
Statistics
Matches: 110, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.02
20 91 0.83
21 16 0.15
22 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:35811 original size:33 final size:33
Alignment explanation
Indices: 35772--35842 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
35762 TTCACTTAGA
*
35772 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
35805 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
35838 TTTCA
1 TTTCA
35843 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:35948 original size:21 final size:20
Alignment explanation
Indices: 35922--36013 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
35912 TGCAGAAGAG
35922 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
35943 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
*
35963 TCGCAATGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
35984 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
36003 TCGCAACGAGA
1 TCGCAACGAGA
36014 GAATCGCAAC
Statistics
Matches: 57, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
19 18 0.32
20 15 0.26
21 24 0.42
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:35979 original size:41 final size:40
Alignment explanation
Indices: 35921--36016 Score: 129
Period size: 41 Copynumber: 2.4 Consensus size: 40
35911 TTGCAGAAGA
*
35921 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGA-AATGACT
* * **
35962 GTCGCAATGAGAGAAATGAAAATCGCAACGCGAAATGAAA
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAAATGACT
*
36002 ATCGCAACGAGAGAA
1 GTCGCAACGAGAGAA
36017 TCGCAACGCG
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 18 0.38
41 30 0.62
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (40 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAAATGACT
Found at i:35998 original size:19 final size:19
Alignment explanation
Indices: 35974--36010 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
35964 CGCAATGAGA
35974 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
35993 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
36011 AGAGAATCGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.19, G:0.22, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:36077 original size:14 final size:14
Alignment explanation
Indices: 36058--36114 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
36048 TTTTATTTCG
36058 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
36072 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
36091 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
36105 CGTTGCGATT
1 CGTTGCGATT
36115 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:36083 original size:33 final size:33
Alignment explanation
Indices: 36041--36133 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
36031 CAAAATCGCA
*
36041 TTGCGATTTTTATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
36074 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
36107 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
36134 TTCATTTCAA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:36096 original size:19 final size:19
Alignment explanation
Indices: 36036--36141 Score: 106
Period size: 19 Copynumber: 6.1 Consensus size: 19
36026 GAAACCAAAA
* *
36036 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
36055 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
36069 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
36088 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
36102 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
36121 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
36140 TC
1 TC
36142 AACCAAAAGA
Statistics
Matches: 71, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.28
16 6 0.08
17 5 0.07
19 40 0.56
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:38067 original size:185 final size:185
Alignment explanation
Indices: 37837--38488 Score: 1272
Period size: 185 Copynumber: 3.5 Consensus size: 185
37827 TAGATTGCTT
*
37837 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
37902 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
37967 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTGGTTGAA
38022 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
38087 TTTGTCTTTGTTTTGTC-TTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
38151 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTC-TTTGGTTGAA
38207 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
38272 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
38337 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTGGTTGAA
38392 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
38457 TTTGTCTTTGTTTTGTCTTTTGGTTG-AAGTAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAA
38489 TGCAATCCAT
Statistics
Matches: 464, Mismatches: 1, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
184 98 0.21
185 274 0.59
186 92 0.20
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (185 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTGGTTGAA
Found at i:38077 original size:92 final size:93
Alignment explanation
Indices: 37837--38488 Score: 1267
Period size: 92 Copynumber: 7.1 Consensus size: 93
37827 TAGATTGCTT
*
37837 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
37902 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
37930 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
37995 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
38022 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
38087 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
38114 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
38179 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
38207 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
38272 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
38300 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
38365 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
38392 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
38457 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
38484 AGTAA
1 AGTAA
38489 TGCAATCCAT
Statistics
Matches: 556, Mismatches: 1, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
92 282 0.51
93 274 0.49
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:38576 original size:19 final size:19
Alignment explanation
Indices: 38536--38664 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
38526 TAGTTTACTT
* *
38536 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
38556 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
38575 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
* *
38594 TTGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
38608 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
38627 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
38641 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
38660 TCGCA
1 TCGCA
38665 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 18 0.20
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 45 0.51
20 13 0.15
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:38615 original size:33 final size:32
Alignment explanation
Indices: 38572--38664 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
38562 CGCGAAACCA
** *
38572 AAATCGCAACGCGAAATGAAAATTGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
38604 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
38637 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
38665 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.04
33 54 0.96
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:38662 original size:52 final size:52
Alignment explanation
Indices: 38536--38664 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
38526 TAGTTTACTT
**
38536 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * * *
38588 T-G-AAAATTGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
38641 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
38665 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
50 3 0.05
51 5 0.08
52 42 0.70
53 3 0.05
54 5 0.08
55 2 0.03
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:38682 original size:19 final size:19
Alignment explanation
Indices: 38660--38778 Score: 123
Period size: 19 Copynumber: 6.8 Consensus size: 19
38650 GAAACCAAAA
*
38660 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
38679 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
38695 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
38712 TCGCGTTGC-A-ATTC-TG
1 TCGCGTTGCGATTTTCATT
38728 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
38745 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
38764 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
38779 AAGTTTCGTG
Statistics
Matches: 83, Mismatches: 7, Indels: 20
0.75 0.06 0.18
Matches are distributed among these distances:
14 14 0.17
15 1 0.01
16 11 0.13
17 11 0.13
18 1 0.01
19 45 0.54
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:38701 original size:14 final size:14
Alignment explanation
Indices: 38682--38738 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
38672 TTTCATTTCG
38682 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
38696 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
* *
38713 CGCGTTGCAATTCTGT
1 --CGTTGCGATTCTTT
38729 CGTTGCGATT
1 CGTTGCGATT
38739 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 17 0.49
16 5 0.14
17 6 0.17
19 7 0.20
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:38707 original size:33 final size:33
Alignment explanation
Indices: 38665--38757 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
38655 CAAAATCGCA
*
38665 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
38698 TTGCGATTTTCATTTCGCGTTGCAATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
38731 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
38758 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:40756 original size:14 final size:14
Alignment explanation
Indices: 40714--40750 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
40704 GATTGTTTAA
*
40714 TTGATTTGTAAAAG
1 TTGATTTGTAAAAT
*
40728 ATGATTTGTAAAAT
1 TTGATTTGTAAAAT
40742 TTGATTTGT
1 TTGATTTGT
40751 GTAATTGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAT
Found at i:40881 original size:19 final size:19
Alignment explanation
Indices: 40857--40934 Score: 96
Period size: 19 Copynumber: 4.4 Consensus size: 19
40847 AAAATTGACT
40857 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
40876 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
40894 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
40908 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
40928 ATCGCAA
1 ATCGCAA
40935 CGGGAGAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
13 1 0.02
14 9 0.18
16 3 0.06
17 1 0.02
18 9 0.18
19 17 0.34
20 10 0.20
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:40935 original size:34 final size:33
Alignment explanation
Indices: 40875--40952 Score: 131
Period size: 34 Copynumber: 2.4 Consensus size: 33
40865 GCGAAATGAA
40875 AATCGCAATGC-GAAATGAAATCGCAACGAGAG
1 AATCGCAATGCGGAAATGAAATCGCAACGAGAG
*
40907 AATCGCAATGCGGAAATGAAAATCGCAACGGGAG
1 AATCGCAATGCGGAAATG-AAATCGCAACGAGAG
40941 AATCGCAATGCG
1 AATCGCAATGCG
40953 ATTTTAATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
32 11 0.26
33 6 0.14
34 26 0.60
ACGTcount: A:0.41, C:0.19, G:0.27, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGGAAATGAAATCGCAACGAGAG
Found at i:40971 original size:19 final size:19
Alignment explanation
Indices: 40943--41111 Score: 172
Period size: 19 Copynumber: 9.7 Consensus size: 19
40933 AACGGGAGAA
* *
40943 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
40962 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
40978 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
40995 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
41014 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
41030 TCG--TTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
41046 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
41065 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
41083 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
41099 TCGCATTGCGATT
1 TCGCATTGCGATT
41112 CTCTCGTTGC
Statistics
Matches: 126, Mismatches: 8, Indels: 32
0.76 0.05 0.19
Matches are distributed among these distances:
14 23 0.18
15 3 0.02
16 17 0.13
17 10 0.08
18 7 0.06
19 50 0.40
20 16 0.13
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:41006 original size:52 final size:52
Alignment explanation
Indices: 40943--41111 Score: 270
Period size: 52 Copynumber: 3.2 Consensus size: 52
40933 AACGGGAGAA
* *
40943 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
40995 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
* *
41046 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATT
1 TCGCATTGCGATTTTCATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATT
41099 TCGCATTGCGATT
1 TCGCATTGCGATT
41112 CTCTCGTTGC
Statistics
Matches: 110, Mismatches: 4, Indels: 5
0.92 0.03 0.04
Matches are distributed among these distances:
51 27 0.25
52 62 0.56
53 21 0.19
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:41133 original size:33 final size:33
Alignment explanation
Indices: 40949--41125 Score: 164
Period size: 33 Copynumber: 5.2 Consensus size: 33
40939 AGAATCGCAA
*
40949 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
40982 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
41020 TGCGATTCTCTCGTTGCG-ATTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCATTGCGATTCTCTCGT
*
41052 TGCGATTTTCATTTCCGCATTGCGATTTTCAT-GT
1 TGCGATTTTCATTT-CGCATTGCGATTCTC-TCGT
*
41086 TGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
41119 TGCGATT
1 TGCGATT
41126 GTAATTTCCG
Statistics
Matches: 115, Mismatches: 16, Indels: 26
0.73 0.10 0.17
Matches are distributed among these distances:
30 4 0.03
31 3 0.03
32 13 0.11
33 48 0.42
34 18 0.16
35 3 0.03
36 6 0.05
38 9 0.08
39 5 0.04
40 6 0.05
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:43581 original size:24 final size:24
Alignment explanation
Indices: 43547--43593 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
43537 CTGAAACATC
43547 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
43571 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
43594 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:44302 original size:20 final size:20
Alignment explanation
Indices: 44274--44583 Score: 352
Period size: 20 Copynumber: 15.5 Consensus size: 20
44264 AAATTTCAGT
* *
44274 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
44294 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
44314 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
44334 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
44354 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
44374 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
44394 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
44414 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
44434 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
44454 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
44474 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
44494 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
44514 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* *
44534 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
44554 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
44574 GTTGCGATTT
1 GTTGCGATTT
44584 TGGAAAATCG
Statistics
Matches: 256, Mismatches: 32, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
20 255 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:44600 original size:21 final size:21
Alignment explanation
Indices: 44570--44652 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
44560 ATTTTCATAT
*
44570 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
44591 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
44612 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
44633 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
44653 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:44643 original size:42 final size:43
Alignment explanation
Indices: 44550--44648 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
44540 ATTTATGTGT
* *
44550 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
44591 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
44633 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
44649 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:50582 original size:24 final size:24
Alignment explanation
Indices: 50549--50595 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
50539 TTTATTAGTT
*
50549 TAATTTAATATATAAAATTATTAA
1 TAATTAAATATATAAAATTATTAA
* *
50573 TAATTAAATATGTAATATTATTA
1 TAATTAAATATATAAAATTATTA
50596 TATTATTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
TAATTAAATATATAAAATTATTAA
Found at i:58154 original size:30 final size:30
Alignment explanation
Indices: 58091--58147 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
58081 AGAATCGAAA
*
58091 GAACCGACTGAAAATCGAGAAAACCGGGGT
1 GAACCGACTGAAAACCGAGAAAACCGGGGT
*
58121 GAACCGGCTGAAAACCG-GCAAAACCGG
1 GAACCGACTGAAAACCGAG-AAAACCGG
58148 TTTGAACTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.39, C:0.25, G:0.30, T:0.07
Consensus pattern (30 bp):
GAACCGACTGAAAACCGAGAAAACCGGGGT
Found at i:58406 original size:24 final size:24
Alignment explanation
Indices: 58377--58435 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
58367 AATTAGAAGT
58377 TCAATTGAAGCCTAAAATTTGAGC
1 TCAATTGAAGCCTAAAATTTGAGC
58401 TCAATTGAAGCCTAAAATTTGAGC
1 TCAATTGAAGCCTAAAATTTGAGC
*
58425 TTAATTGAAGC
1 TCAATTGAAGC
58436 GAAAGAATAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (24 bp):
TCAATTGAAGCCTAAAATTTGAGC
Found at i:59733 original size:19 final size:19
Alignment explanation
Indices: 59711--59757 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
59701 TTGATAATGG
59711 ATACAAAAATATTAAATAA
1 ATACAAAAATATTAAATAA
59730 ATACAAAAATATTAAATAA
1 ATACAAAAATATTAAATAA
59749 A-A-AAAAATA
1 ATACAAAAATA
59758 AAAAAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 7 0.25
18 1 0.04
19 20 0.71
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.23
Consensus pattern (19 bp):
ATACAAAAATATTAAATAA
Found at i:59925 original size:16 final size:16
Alignment explanation
Indices: 59906--59942 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
59896 ACAAGTGACT
59906 GGTTAAAATTTAGACC
1 GGTTAAAATTTAGACC
*
59922 GGTTAAAATTTAGATC
1 GGTTAAAATTTAGACC
59938 GGTTA
1 GGTTA
59943 TGTTATAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (16 bp):
GGTTAAAATTTAGACC
Found at i:60058 original size:23 final size:23
Alignment explanation
Indices: 59991--60052 Score: 115
Period size: 23 Copynumber: 2.7 Consensus size: 23
59981 AGCATATTAG
*
59991 GTAGCGTTTATATAATGTAATAA
1 GTAGCGCTTATATAATGTAATAA
60014 GTAGCGCTTATATAATGTAATAA
1 GTAGCGCTTATATAATGTAATAA
60037 GTAGCGCTTATATAAT
1 GTAGCGCTTATATAAT
60053 AAAATAGGCA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (23 bp):
GTAGCGCTTATATAATGTAATAA
Found at i:60513 original size:200 final size:198
Alignment explanation
Indices: 60165--60812 Score: 867
Period size: 198 Copynumber: 3.3 Consensus size: 198
60155 ACAATAGCAT
* * *
60165 ATTATCGGTTTCGATGTTTTTGGGATCGATACAATTT--TAAACGTATCGACACTTTATGCGTGC
1 ATTATCGGTTTCAATGTTTTTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGCGTGC
* * * *
60228 ACCTCGTTGGGCATTCATTCTGAAAAAAGTATCGACACAAACTTAAAAAGTGTCGATATATTATG
65 ACCTCGTTTGGCATTCATTCTGACAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATG
* * * **
60293 TAGACCTATTTTCTCATAAAACCGGTATATTTCTACCGGGCACATTGTAAATTTACCTATTACAT
130 TTGACATATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACAT
*
60358 TGTA
195 TATA
* * *
60362 ATTATCGGTTTCAATGTTTTTGGGATTGGTACTTTTAATAAATGTATCGACACTTTATGAGTGCA
1 ATTATCGGTTTCAATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCA
* *
60427 CCTCGTTTGACATTCATTCTGGACAAAATGTATCGACACAAATTTAAAAAGTGTCGATACAATAT
66 CCTCGTTTGGCATTCATTCT-GACAAAA-GTATCGACACAAATTTAAAAAGTGTCGATACATTAT
* *
60492 GTTGACATATTCTCTCATAAAATCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACA
129 GTTGACATATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACA
60557 TTATA
194 TTATA
* *
60562 ATTAT--GTTTCGATGTTTTTGGGATCGATACTTTTAATAAATTTATCGACACTTTATGCGTGCA
1 ATTATCGGTTTCAATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCA
* ** *
60625 CCTCGTTTGGGGATTCATTCTAGACAATAAGTATCGACACAAATTCCACAAGTGTCGATACATTA
66 CCTCGTTT-GGCATTCATTCT-GACAA-AAGTATCGACACAAATTTAAAAAGTGTCGATACATTA
* * * * * *
60690 TGTTGACATGTTTTCTAAT-TAACAGGTATATTTATACTGGTTACATTGTTAATTTACCTATTAC
128 TGTTGACATATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTAC
60754 ATTATA
193 ATTATA
* * * *
60760 ATTATTGGTTTCAATATTTTTGGGGTCGATATTTTTAGA-AAATGTATCGACAC
1 ATTATCGGTTTCAATGTTTTTGGGATCGATACTTTTA-ATAAATGTATCGACAC
60813 ATACGTTTAC
Statistics
Matches: 397, Mismatches: 45, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
196 3 0.01
197 29 0.07
198 155 0.39
199 68 0.17
200 141 0.36
201 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (198 bp):
ATTATCGGTTTCAATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCA
CCTCGTTTGGCATTCATTCTGACAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGT
TGACATATTTTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATT
ATA
Found at i:61038 original size:91 final size:91
Alignment explanation
Indices: 60930--61203 Score: 430
Period size: 91 Copynumber: 3.0 Consensus size: 91
60920 TTATAAAAAT
60930 GTATCGATACTTTACAATATAACAGTTAAAAATATGGA-AAAATCAGTTTCATTATGACAAAACC
1 GTATCGATACTTTACAATATAACAGTTAAAAATAT-GACAAAATCAGTTTCATTATGACAAAACC
60994 GGTAAAGAGCTACCTGATATGTTGAAA
65 GGTAAAGAGCTACCTGATATGTTGAAA
* * *
61021 GTATCGATACTTAACAATATAACA-TGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACT
1 GTATCGATACTTTACAATATAACAGT-TAAAAATATGACAAAATCAGTTTCATTATGACAAAACC
61085 GGTAAAGAGCTACCTGATATGTTGAAA
65 GGTAAAGAGCTACCTGATATGTTGAAA
* * *
61112 ATATCGATACTTTACAATATAACAAG-TAAAAATATGACAAAATCAGTTTCATTATGATAAAAAC
1 GTATCGATACTTTACAATATAAC-AGTTAAAAATATGACAAAATCAGTTTCATTATGACAAAACC
*
61176 GGTAAAGAGCTACCTAATATGTT-AAA
65 GGTAAAGAGCTACCTGATATGTTGAAA
61202 GT
1 GT
61204 TATGTAATTT
Statistics
Matches: 168, Mismatches: 11, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
90 7 0.04
91 160 0.95
92 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.28
Consensus pattern (91 bp):
GTATCGATACTTTACAATATAACAGTTAAAAATATGACAAAATCAGTTTCATTATGACAAAACCG
GTAAAGAGCTACCTGATATGTTGAAA
Found at i:65544 original size:23 final size:22
Alignment explanation
Indices: 65501--65544 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
65491 ATTAATAATT
*
65501 TATTTAATTTAAAAAGTTTATA
1 TATTTAATTTAAAAAGATTATA
65523 TATTATAATATTAAAAA-ATTAT
1 TATT-TAAT-TTAAAAAGATTAT
65545 TTAAAGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 8 0.42
24 7 0.37
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TATTTAATTTAAAAAGATTATA
Done.