Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008707.1 Hibiscus syriacus cultivar Beakdansim tig00111749_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: 138913
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:17361 original size:11 final size:11
Alignment explanation
Indices: 17345--17372 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
17335 GAGTAAGAAT
17345 AATTATGGAAA
1 AATTATGGAAA
17356 AATTATGGAAA
1 AATTATGGAAA
17367 AATTAT
1 AATTAT
17373 ATATGGGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.32
Consensus pattern (11 bp):
AATTATGGAAA
Found at i:25875 original size:13 final size:13
Alignment explanation
Indices: 25828--25876 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
25818 GTTTTTATGC
*
25828 ATTTTAGTTCTTT
1 ATTTTAGATCTTT
* *
25841 ATTTTAGGTTTTT
1 ATTTTAGATCTTT
*
25854 AGTTTTAGATCATT
1 A-TTTTAGATCTTT
25868 ATTTTAGAT
1 ATTTTAGAT
25877 TCCTTTTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
13 20 0.67
14 10 0.33
ACGTcount: A:0.22, C:0.04, G:0.12, T:0.61
Consensus pattern (13 bp):
ATTTTAGATCTTT
Found at i:27957 original size:2 final size:2
Alignment explanation
Indices: 27952--27984 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
27942 TGTTATTAAA
27952 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 A
27985 CACGTCCACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34975 original size:21 final size:21
Alignment explanation
Indices: 34949--34993 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
34939 GATTTCTGGG
* *
34949 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
34970 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
34991 CAA
1 CAA
34994 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:35472 original size:2 final size:2
Alignment explanation
Indices: 35465--35503 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
35455 CATGAGTTAG
35465 AT 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 AT A
35504 GGAATTGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36314 original size:32 final size:32
Alignment explanation
Indices: 36276--36372 Score: 119
Period size: 32 Copynumber: 3.1 Consensus size: 32
36266 GAGTCGAGGG
*
36276 TTTACCTATGTTCTACGGAACATATGGACGGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
36308 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
36339 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
36371 TT
1 TT
36373 ACCGAGGATC
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
31 26 0.48
32 28 0.52
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:36348 original size:31 final size:31
Alignment explanation
Indices: 36275--36375 Score: 116
Period size: 31 Copynumber: 3.2 Consensus size: 31
36265 AGAGTCGAGG
*
36275 GTTTACCTATGTTCT-ACGGAACATATGGACG
1 GTTTACCTATGTTCTAAC-GAACATATGGACA
**
36306 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTAACGA-ACATATGGACA
* *
36338 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAACGAACATATGGACA
36369 GTTTACC
1 GTTTACC
36376 GAGGATCTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
31 32 0.54
32 27 0.46
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTAACGAACATATGGACA
Found at i:36407 original size:30 final size:30
Alignment explanation
Indices: 36363--36456 Score: 136
Period size: 30 Copynumber: 3.1 Consensus size: 30
36353 AAGGAACATA
36363 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
36394 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * *
36424 TGGATAGTTACCG-GGGTCTGTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
36453 TGGA
1 TGGA
36457 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
29 17 0.29
30 35 0.59
31 7 0.12
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:39882 original size:2 final size:2
Alignment explanation
Indices: 39875--39918 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
39865 CATGAGTTAG
39875 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
39917 AT
1 AT
39919 TGTATAACCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40730 original size:32 final size:32
Alignment explanation
Indices: 40689--40785 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
40679 GAGTCGAGGG
40689 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
40721 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
40752 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
40784 TT
1 TT
40786 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:40761 original size:31 final size:31
Alignment explanation
Indices: 40688--40788 Score: 125
Period size: 31 Copynumber: 3.2 Consensus size: 31
40678 AGAGTCGAGG
40688 GTTTACCTATGTTCT-ACGGAACATATGGACA
1 GTTTACCTATGTTCTAAC-GAACATATGGACA
**
40719 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTAACGA-ACATATGGACA
* *
40751 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAACGAACATATGGACA
40782 GTTTACC
1 GTTTACC
40789 GAGGATCTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
31 32 0.53
32 28 0.47
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTAACGAACATATGGACA
Found at i:40820 original size:30 final size:30
Alignment explanation
Indices: 40776--40869 Score: 127
Period size: 30 Copynumber: 3.1 Consensus size: 30
40766 AAGGAACATA
40776 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
40807 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * * *
40837 TGGATAGTTACTG-GGGTCTGTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
40866 TGGA
1 TGGA
40870 TAGGTCCTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 17 0.29
30 34 0.59
31 7 0.12
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:45300 original size:25 final size:23
Alignment explanation
Indices: 45249--45319 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 23
45239 TATATTTTTA
*
45249 ATTATATTTTTTTATTTAT-T-T
1 ATTATATTTTTTTTTTTATATAT
*
45270 ACTATATTTCTCTTTTTTTATATAT
1 ATTATATTT-T-TTTTTTTATATAT
* *
45295 ATTATATTATTTTTGTTATATAT
1 ATTATATTTTTTTTTTTATATAT
45318 AT
1 AT
45320 CTTATATCAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
21 8 0.20
22 1 0.02
23 22 0.54
24 2 0.05
25 8 0.20
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (23 bp):
ATTATATTTTTTTTTTTATATAT
Found at i:45711 original size:11 final size:11
Alignment explanation
Indices: 45695--45720 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
45685 TTTTGTTTAT
45695 TTTTATTATTA
1 TTTTATTATTA
45706 TTTTATTATTA
1 TTTTATTATTA
45717 TTTT
1 TTTT
45721 TTTACGTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:45712 original size:17 final size:19
Alignment explanation
Indices: 45676--45718 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
45666 TTTTTTAACA
*
45676 TTTTATTCATTTTGTTTAT
1 TTTTATTCATTATGTTTAT
45695 TTTTATT-ATTAT-TTTAT
1 TTTTATTCATTATGTTTAT
*
45712 TATTATT
1 TTTTATT
45719 TTTTTACGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 11 0.50
18 4 0.18
19 7 0.32
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTATTCATTATGTTTAT
Found at i:46825 original size:14 final size:14
Alignment explanation
Indices: 46806--46840 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
46796 GGGTAGGATC
46806 TTTTATTTTCATTA
1 TTTTATTTTCATTA
46820 TTTTATTTTCATTA
1 TTTTATTTTCATTA
46834 TTATTAT
1 TT-TTAT
46841 CATATGCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTATTTTCATTA
Found at i:48143 original size:14 final size:13
Alignment explanation
Indices: 48108--48162 Score: 67
Period size: 14 Copynumber: 4.0 Consensus size: 13
48098 ACAAAAAGAG
48108 AAAAAAGAGAAAA
1 AAAAAAGAGAAAA
48121 AAAGCAAAGAGAAAA
1 AAA--AAAGAGAAAA
48136 TAAAAAAGAGAAAA
1 -AAAAAAGAGAAAA
48150 AACAAAAG-GAAAA
1 AA-AAAAGAGAAAA
48163 TTGAAGAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
13 10 0.26
14 15 0.39
15 10 0.26
16 3 0.08
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.02
Consensus pattern (13 bp):
AAAAAAGAGAAAA
Found at i:48149 original size:27 final size:28
Alignment explanation
Indices: 48108--48163 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
48098 ACAAAAAGAG
48108 AAAAAAGAGAAAAAAAGC-AAAGAGAAAAT
1 AAAAAAGAGAAAAAAA-CAAAAG-GAAAAT
48137 AAAAAAGAG-AAAAAACAAAAGGAAAAT
1 AAAAAAGAGAAAAAAACAAAAGGAAAAT
48164 TGAAGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 7 0.27
28 10 0.38
29 9 0.35
ACGTcount: A:0.77, C:0.04, G:0.16, T:0.04
Consensus pattern (28 bp):
AAAAAAGAGAAAAAAACAAAAGGAAAAT
Found at i:49952 original size:36 final size:36
Alignment explanation
Indices: 49905--50131 Score: 218
Period size: 36 Copynumber: 6.4 Consensus size: 36
49895 ATTGAAAACA
* *
49905 TTTCCCTTGAAATAAATTTCGTCTCTCTTAAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
49941 TTTCCCTTGAAACAAATTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAA-TTTCGTCTCTCTTGAGACAG
* *
49978 TTTCCCTTGAAACAAA-----T-TAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA-G
*** * *
50007 TTTTATTTGAAACAAATTTCATCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
** * * *
50043 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
*
50080 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
50116 TTTCTCTTGAAACAAA
1 TTTCCCTTGAAACAAA
50132 AAATCTTCAA
Statistics
Matches: 158, Mismatches: 22, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.01
29 18 0.11
30 2 0.01
31 1 0.01
34 1 0.01
35 1 0.01
36 67 0.42
37 66 0.42
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:49976 original size:37 final size:37
Alignment explanation
Indices: 49905--50000 Score: 149
Period size: 37 Copynumber: 2.6 Consensus size: 37
49895 ATTGAAAACA
* *
49905 TTTCCCTTGAAATAAA-TTTCGTCTCTCTTAAGACAG
1 TTTCCCTTGAAACAAATTTTTGTCTCTCTTAAGACAG
*
49941 TTTCCCTTGAAACAAATTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTTGTCTCTCTTAAGACAG
49978 TTTCCCTTGAAACAAATTATTTG
1 TTTCCCTTGAAACAAATT-TTTG
50001 AATATGTTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 15 0.27
37 36 0.65
38 4 0.07
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.41
Consensus pattern (37 bp):
TTTCCCTTGAAACAAATTTTTGTCTCTCTTAAGACAG
Found at i:50017 original size:102 final size:101
Alignment explanation
Indices: 49818--50097 Score: 317
Period size: 102 Copynumber: 2.8 Consensus size: 101
49808 TAAAAAGAAT
* * * * *
49818 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
1 ATTTCATCTCCCTTAAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCT
* ** * *
49883 TGAAATATAAACATTGAAAACATTTCCCTTGAAATAA
66 TGAAACA-AATTATTGAAAACATTTCACTTGAAACAA
* * * *
49920 ATTTCGTCTCTCTTAAGACAGTTTCCCTTGAAACAAATTTTTGTCTCTCTTGAGACAGTTTCCCT
1 ATTTCATCTCCCTTAAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCT
* ** * *
49985 TGAAACAAATTATTTGAATATGTTTTATTTGAAACAA
66 TGAAACAAATTA-TTGAAAACATTTCACTTGAAACAA
* ** * * *
50022 ATTTCATCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCT
1 ATTTCATCTCCCTTAAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCT
50087 TGAAACAAATT
66 TGAAACAAATT
50098 TCGTCTCTCT
Statistics
Matches: 150, Mismatches: 27, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
101 3 0.02
102 147 0.98
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (101 bp):
ATTTCATCTCCCTTAAGACAGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCT
TGAAACAAATTATTGAAAACATTTCACTTGAAACAA
Found at i:51100 original size:110 final size:110
Alignment explanation
Indices: 50898--51104 Score: 315
Period size: 110 Copynumber: 1.9 Consensus size: 110
50888 GCTTCCCAGT
* * *
50898 TTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGATAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
* *
50963 CAACGAAAGGGCGACTGATTGTTAACAAACAACTTTTTAGTTTTA
66 CAACGAAAGGGCGACTGATGGTCAACAAACAACTTTTTAGTTTTA
* **
51008 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTTGAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
* * *
51073 CAACGAAGGGGCGGCTGGTGGTCAACAAACAA
66 CAACGAAAGGGCGACTGATGGTCAACAAACAA
51105 TTTCCCAGTT
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
110 86 1.00
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
CAACGAAAGGGCGACTGATGGTCAACAAACAACTTTTTAGTTTTA
Found at i:52510 original size:4 final size:4
Alignment explanation
Indices: 52491--52562 Score: 65
Period size: 4 Copynumber: 17.2 Consensus size: 4
52481 TATATATATA
* ** *
52491 TATT TAAT TATAT TATT TATT TATT TATT TATT ATATT CCTC T-TT TATT
1 TATT TATT TAT-T TATT TATT TATT TATT TATT -TATT TATT TATT TATT
52540 TATT TATT TATAT TATAT TATT T
1 TATT TATT TAT-T TAT-T TATT T
52563 TTATTATATA
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
3 2 0.04
4 38 0.67
5 17 0.30
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (4 bp):
TATT
Found at i:52564 original size:28 final size:28
Alignment explanation
Indices: 52491--52582 Score: 95
Period size: 28 Copynumber: 3.3 Consensus size: 28
52481 TATATATATA
52491 TATTTA-ATTATATTA--TTTATTTATT
1 TATTTATATTATATTATTTTTATTTATT
*
52516 TA-TT-TATTATATTCCTCTTTTATTTATT
1 TATTTATATTATATT-AT-TTTTATTTATT
*
52544 TATTTATATTATATTATTTTTATTATATA
1 TATTTATATTATATTATTTTTATT-TATT
52573 TATCTTATAT
1 TAT-TTATAT
52583 CATTATATAT
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
24 10 0.18
25 2 0.04
28 19 0.35
29 9 0.16
30 15 0.27
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.66
Consensus pattern (28 bp):
TATTTATATTATATTATTTTTATTTATT
Found at i:52565 original size:24 final size:25
Alignment explanation
Indices: 52492--52608 Score: 89
Period size: 25 Copynumber: 4.7 Consensus size: 25
52482 ATATATATAT
*
52492 ATTTAATTATATTAT-TTATTTATTT
1 ATTTATTTATATTATATTA-TTATTT
* *
52517 ATTTA-TTATATTCCTCTT-TTATTT
1 ATTTATTTATATT-ATATTATTATTT
52541 ATTTATTTATATTATATTATT-TTT
1 ATTTATTTATATTATATTATTATTT
* * * *
52565 ATTATATATATCTTATATCATTATAT
1 ATT-TATTTATATTATATTATTATTT
* *
52591 ATATATATATATATATAT
1 ATTTATTTATAT-TATAT
52609 ATATATATAT
Statistics
Matches: 76, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
24 27 0.36
25 38 0.50
26 11 0.14
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (25 bp):
ATTTATTTATATTATATTATTATTT
Found at i:52574 original size:2 final size:2
Alignment explanation
Indices: 52567--52631 Score: 98
Period size: 2 Copynumber: 33.0 Consensus size: 2
52557 TTATTTTTAT
*
52567 TA TA TA TA TC T- TA TA TCA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
52608 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
52632 GATGTATTAA
Statistics
Matches: 59, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
1 2 0.03
2 55 0.93
3 2 0.03
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:58825 original size:27 final size:27
Alignment explanation
Indices: 58786--58843 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
58776 AGATGAATGA
58786 AAATGAATGATTGAGATCAACATTAGT
1 AAATGAATGATTGAGATCAACATTAGT
*
58813 AAATGAATTATTGAGATCAACATTAGT
1 AAATGAATGATTGAGATCAACATTAGT
58840 AAAT
1 AAAT
58844 AAAGATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.31
Consensus pattern (27 bp):
AAATGAATGATTGAGATCAACATTAGT
Found at i:59588 original size:2 final size:2
Alignment explanation
Indices: 59583--59608 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
59573 GATGCAATCA
59583 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
59609 GAAAATTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:64592 original size:18 final size:18
Alignment explanation
Indices: 64553--64600 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
64543 ATTAACATGC
*
64553 TTATCATTACTTATTTTA
1 TTATCATTAATTATTTTA
*
64571 TTATCATTAATTCCTTTT-
1 TTATCATTAATT-ATTTTA
64589 TTATCATATAAT
1 TTATCAT-TAAT
64601 CATATACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATCATTAATTATTTTA
Found at i:67898 original size:15 final size:15
Alignment explanation
Indices: 67880--67913 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
67870 GTGAAATTCT
67880 AATTATTTAAATAAA
1 AATTATTTAAATAAA
*
67895 AATTATTTATATAAA
1 AATTATTTAAATAAA
67910 AATT
1 AATT
67914 CATACCATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTATTTAAATAAA
Found at i:71034 original size:18 final size:18
Alignment explanation
Indices: 71011--71045 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
71001 GCGTAGAATT
*
71011 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
71029 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
71046 TATAACACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.34, G:0.23, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:71934 original size:20 final size:20
Alignment explanation
Indices: 71909--71960 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
71899 ATAACTGGAG
71909 GTATCGATACACTCCTCAAT
1 GTATCGATACACTCCTCAAT
71929 GTATCGATACACTCCTCAAT
1 GTATCGATACACTCCTCAAT
*
71949 GTACCGATACAC
1 GTATCGATACAC
71961 AAATTGCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.31, C:0.31, G:0.12, T:0.27
Consensus pattern (20 bp):
GTATCGATACACTCCTCAAT
Found at i:72006 original size:54 final size:55
Alignment explanation
Indices: 71929--72070 Score: 187
Period size: 54 Copynumber: 2.6 Consensus size: 55
71919 ACTCCTCAAT
* * **
71929 GTATCGATACACTCCTCAATGTACCGATACACAAATTGCATTCGATG-TTTGAGG
1 GTATCGATAAACTCCTCAGTGTACCGATACACAAATAACATTCGATGTTTTGAGG
* * * *
71983 GTATCGATATACTACTCAGTGTACCGATACACAAATAACATTTGATGTTTTGAGT
1 GTATCGATAAACTCCTCAGTGTACCGATACACAAATAACATTCGATGTTTTGAGG
* *
72038 GTACCGATAAACTCCTTAGTGTACCGATACACA
1 GTATCGATAAACTCCTCAGTGTACCGATACACA
72071 CTCATACAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
54 41 0.54
55 35 0.46
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (55 bp):
GTATCGATAAACTCCTCAGTGTACCGATACACAAATAACATTCGATGTTTTGAGG
Found at i:75415 original size:20 final size:20
Alignment explanation
Indices: 75392--75437 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
75382 TGTAAAATAG
75392 TATATATTATAAAATGTATA
1 TATATATTATAAAATGTATA
* *
75412 TATAAATTTTATCAAATGTATA
1 TAT--ATATTATAAAATGTATA
75434 TATA
1 TATA
75438 AATTTGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 4 0.18
22 18 0.82
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (20 bp):
TATATATTATAAAATGTATA
Found at i:75428 original size:22 final size:22
Alignment explanation
Indices: 75398--75442 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
75388 ATAGTATATA
75398 TTATAAAATGTATATATAAATT
1 TTATAAAATGTATATATAAATT
*
75420 TTATCAAATGTATATATAAATT
1 TTATAAAATGTATATATAAATT
75442 T
1 T
75443 GAAAAAATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (22 bp):
TTATAAAATGTATATATAAATT
Found at i:75450 original size:22 final size:22
Alignment explanation
Indices: 75402--75450 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
75392 TATATATTAT
* *
75402 AAAATGTATATATAAATTTTAT
1 AAAATGTATATATAAATTTGAA
*
75424 CAAATGTATATATAAATTTGAA
1 AAAATGTATATATAAATTTGAA
75446 AAAAT
1 AAAAT
75451 AGCCTCAGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (22 bp):
AAAATGTATATATAAATTTGAA
Found at i:75660 original size:22 final size:22
Alignment explanation
Indices: 75603--75661 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
75593 ACGCGATTCT
75603 GACTATCGCATTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * *
75625 AAAT-TCGCGTTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
*
75646 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
75662 ATATGTAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:75733 original size:20 final size:20
Alignment explanation
Indices: 75646--75779 Score: 130
Period size: 20 Copynumber: 6.7 Consensus size: 20
75636 GCGATTTTCC
*
75646 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGATTAT
* *
75666 GTA-AATCGCAATGCGAGTAT
1 G-ACTATCGCAATGCGATTAT
* *
75686 GACTATCGCAACGCGAATAT
1 GACTATCGCAATGCGATTAT
*
75706 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGATTAT
* *
75726 GACTATCGCAATGTGATTCT
1 GACTATCGCAATGCGATTAT
*
75746 GACTATCGCAACT-CGATTCT
1 GACTATCGCAA-TGCGATTAT
*
75766 GACTGTCGCAATGC
1 GACTATCGCAATGC
75780 TGAATTTCAA
Statistics
Matches: 95, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
19 3 0.03
20 89 0.94
21 3 0.03
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.27
Consensus pattern (20 bp):
GACTATCGCAATGCGATTAT
Found at i:75756 original size:40 final size:40
Alignment explanation
Indices: 75646--75738 Score: 168
Period size: 40 Copynumber: 2.3 Consensus size: 40
75636 GCGATTTTCC
*
75646 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATTAT
*
75686 GACTATCGCAACGCGAATATGTAAATCGCAATGCGATTAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATTAT
75726 GACTATCGCAATG
1 GACTATCGCAATG
75739 TGATTCTGAC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (40 bp):
GACTATCGCAATGCGAATATGTAAATCGCAATGCGATTAT
Found at i:78934 original size:18 final size:18
Alignment explanation
Indices: 78911--78945 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
78901 AGCAAAAGGC
*
78911 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
78929 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
78946 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:79148 original size:20 final size:20
Alignment explanation
Indices: 79123--79362 Score: 157
Period size: 20 Copynumber: 12.7 Consensus size: 20
79113 CACATTCATT
79123 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
* ** *
79143 TGACTATCACAACATGAATT
1 TGACTATCGCAACGCGAATA
* * *
79163 TGAATATCACAACG-G--GA
1 TGACTATCGCAACGCGAATA
* * *
79180 T-A--ATCGCAATGCAAAAA
1 TGACTATCGCAACGCGAATA
*
79197 TGACTATCGCAA--CGAATT
1 TGACTATCGCAACGCGAATA
*
79215 TGACTATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* * *
79232 T-A--ATCGCAATGCAAAAA
1 TGACTATCGCAACGCGAATA
* *
79249 TGACTATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
79269 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
* *
79289 TGACTATCGCAACTCGAATT
1 TGACTATCGCAACGCGAATA
* *
79309 TGACTATCGCAACGCAAATT
1 TGACTATCGCAACGCGAATA
* * * *
79329 TGATTATCACAACGGGAATT
1 TGACTATCGCAACGCGAATA
79349 TGACTATCGCAACG
1 TGACTATCGCAACG
79363 AGAAAATCGC
Statistics
Matches: 173, Mismatches: 33, Indels: 28
0.74 0.14 0.12
Matches are distributed among these distances:
14 15 0.09
16 2 0.01
17 6 0.03
18 17 0.10
19 2 0.01
20 131 0.76
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.23
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATA
Found at i:79231 original size:52 final size:52
Alignment explanation
Indices: 79128--79282 Score: 202
Period size: 52 Copynumber: 2.9 Consensus size: 52
79118 TCATTTGACT
* * * * * *
79128 ATCGCAACGCGAATATGACTATCACAACATGAATTTGAATATCACAACGGGATA
1 ATCGCAATGCAAAAATGACTATCGCAAC--GAATTTGACTATCGCAACGGGATA
79182 ATCGCAATGCAAAAATGACTATCGCAACGAATTTGACTATCGCAACGGGATA
1 ATCGCAATGCAAAAATGACTATCGCAACGAATTTGACTATCGCAACGGGATA
**
79234 ATCGCAATGCAAAAATGACTATCGCAATGCGAAAATGACTATCGCAACG
1 ATCGCAATGCAAAAATGACTATCGCAA--CGAATTTGACTATCGCAACG
79283 CGAATATGAC
Statistics
Matches: 91, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
52 49 0.54
54 42 0.46
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (52 bp):
ATCGCAATGCAAAAATGACTATCGCAACGAATTTGACTATCGCAACGGGATA
Found at i:79537 original size:36 final size:34
Alignment explanation
Indices: 79497--79576 Score: 114
Period size: 30 Copynumber: 2.4 Consensus size: 34
79487 TCAACTTTTA
79497 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAACAA--ACAAATAAGAATTATTTACAC
79533 ATCAATT----AAACAAATAAGAATTATTTACAC
1 ATCAATTAAACAAACAAATAAGAATTATTTACAC
79563 ATCAATTAAACAAA
1 ATCAATTAAACAAA
79577 TCAACTTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
30 28 0.70
32 2 0.05
34 3 0.08
36 7 0.17
ACGTcount: A:0.55, C:0.15, G:0.04, T:0.26
Consensus pattern (34 bp):
ATCAATTAAACAAACAAATAAGAATTATTTACAC
Found at i:79546 original size:30 final size:30
Alignment explanation
Indices: 79512--79577 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
79502 TTAAACAAGC
79512 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
79542 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
79572 ACAAAT
1 ACAAAT
79578 CAACTTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.29
Consensus pattern (30 bp):
ACAAATAAGAATTATTTACACATCAATTAA
Found at i:81022 original size:21 final size:21
Alignment explanation
Indices: 80998--81042 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
80988 GAACGGTGGG
**
80998 AGGGGACTCTTGAGGGATGAT
1 AGGGGACTCTTGAAAGATGAT
*
81019 AGGGGCCTCTTGAAAGATGAT
1 AGGGGACTCTTGAAAGATGAT
81040 AGG
1 AGG
81043 TGAGTCGGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.11, G:0.40, T:0.22
Consensus pattern (21 bp):
AGGGGACTCTTGAAAGATGAT
Found at i:81666 original size:20 final size:20
Alignment explanation
Indices: 81638--81704 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
81628 CGATTCTCTT
81638 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
* **
81658 GTTGTGATAGTCATTTTCGC
1 GTTGCGATAGTCAAATTCGC
*
81678 GTTGCGATAGTC-ATTTCTGC
1 GTTGCGATAGTCAAATTC-GC
81698 GTTGCGA
1 GTTGCGA
81705 AAGTAAACTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
19 4 0.10
20 37 0.90
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
GTTGCGATAGTCAAATTCGC
Found at i:81871 original size:18 final size:18
Alignment explanation
Indices: 81848--81897 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
81838 TTTACTAAGC
81848 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
81866 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
81884 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
81898 TACGAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:83672 original size:20 final size:20
Alignment explanation
Indices: 83629--83696 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
83619 GAAACTTAAA
**
83629 ATCGCAACACGAAAATGAAA
1 ATCGCAACACGAAAATGACT
83649 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* * **
83669 ATCGTAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
83689 ATCGCAAC
1 ATCGCAAC
83697 GCAAAACTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.43, C:0.24, G:0.16, T:0.18
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:84126 original size:22 final size:22
Alignment explanation
Indices: 84095--84151 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
84085 GATGGAGATA
84095 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* **
84117 GACTGATTTCGTTGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
84139 GACGGATGTCGCC
1 GACGGATTTCGCC
84152 TTAGAGAGTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.18, C:0.18, G:0.42, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:84341 original size:20 final size:20
Alignment explanation
Indices: 84316--84530 Score: 139
Period size: 20 Copynumber: 10.7 Consensus size: 20
84306 GCGCTTTGAA
*
84316 AATCGCATTGCGACAGTCAG
1 AATCGCATTGCGATAGTCAG
*
84336 AATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* *
84356 AATTGCATTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAG
* * *
84376 AATCACATTGCGAT-TTACAT
1 AATCGCATTGCGATAGT-CAG
* * *
84396 ATTCGCGTTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAG
* * *
84416 AATCACATTGCGAT-TTACAT
1 AATCGCATTGCGATAGT-CAG
* * *
84436 ATTCGCGTTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAG
* * *
84456 ACTCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGT-CAG
* *
84476 ATTCGCATTGCGATAGTCGGAA
1 AATCGCATTGCGATAGTC--AG
* * *
84498 AATTGCAATGTGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
84518 AATCGCGTTGCGA
1 AATCGCATTGCGA
84531 ATCTGGAAAC
Statistics
Matches: 152, Mismatches: 35, Indels: 16
0.75 0.17 0.08
Matches are distributed among these distances:
19 3 0.02
20 131 0.86
21 3 0.02
22 15 0.10
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.31
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:84387 original size:40 final size:40
Alignment explanation
Indices: 84360--84493 Score: 232
Period size: 40 Copynumber: 3.4 Consensus size: 40
84350 AGTCAGAATT
84360 GCATTGCGATAGTCATAATCACATTGCGATTTACATATTC
1 GCATTGCGATAGTCATAATCACATTGCGATTTACATATTC
*
84400 GCGTTGCGATAGTCATAATCACATTGCGATTTACATATTC
1 GCATTGCGATAGTCATAATCACATTGCGATTTACATATTC
* * *
84440 GCGTTGCGATAGTCATACTCGCATTGCGATTTACATATTC
1 GCATTGCGATAGTCATAATCACATTGCGATTTACATATTC
84480 GCATTGCGATAGTC
1 GCATTGCGATAGTC
84494 GGAAAATTGC
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 90 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (40 bp):
GCATTGCGATAGTCATAATCACATTGCGATTTACATATTC
Found at i:84467 original size:60 final size:60
Alignment explanation
Indices: 84316--84530 Score: 166
Period size: 60 Copynumber: 3.5 Consensus size: 60
84306 GCGCTTTGAA
* * **
84316 AATCGCATTGCGACAGTCAGAATCGCGTTGCGATAGTCAGAATTGCATTGCGATAGTCAT
1 AATCGCATTGCGATAGTCATAATCGCGTTGCGATAGTCAGAATCACATTGCGATAGTCAT
* * * * *
84376 AATCACATTGCGAT-TTACATATTCGCGTTGCGATAGTCATAATCACATTGCGAT-TTACAT
1 AATCGCATTGCGATAGT-CATAATCGCGTTGCGATAGTCAGAATCACATTGCGATAGT-CAT
* * * * * * * * *
84436 ATTCGCGTTGCGATAGTCATACTCGCATTGCGAT-TTACATATTCGCATTGCGATAGTCGGAA
1 AATCGCATTGCGATAGTCATAATCGCGTTGCGATAGT-CAGAATCACATTGCGATAGTC--AT
* * * *
84498 AATTGCAATGTGATAGTCAGAATCGCGTTGCGA
1 AATCGCATTGCGATAGTCATAATCGCGTTGCGA
84531 ATCTGGAAAC
Statistics
Matches: 120, Mismatches: 28, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
59 3 0.03
60 89 0.74
61 2 0.02
62 26 0.22
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.31
Consensus pattern (60 bp):
AATCGCATTGCGATAGTCATAATCGCGTTGCGATAGTCAGAATCACATTGCGATAGTCAT
Found at i:88184 original size:21 final size:20
Alignment explanation
Indices: 88155--88209 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
88145 CGAGCCTTCG
88155 GTATAGATACCAATCCATCTA
1 GTATAGATACCAATCCATC-A
* * *
88176 GTATGGATATCAGTCCATCA
1 GTATAGATACCAATCCATCA
*
88196 GTATAGAGACCAAT
1 GTATAGATACCAAT
88210 TTACCGGTAT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (20 bp):
GTATAGATACCAATCCATCA
Found at i:90713 original size:16 final size:17
Alignment explanation
Indices: 90692--90738 Score: 71
Period size: 16 Copynumber: 2.9 Consensus size: 17
90682 TGCTTAACTC
90692 TTGCTCGTTAAGCTC-G
1 TTGCTCGTTAAGCTCTG
*
90708 TTGCTCATTAAG-TCTG
1 TTGCTCGTTAAGCTCTG
90724 TTGCTCGTTAAGCTC
1 TTGCTCGTTAAGCTC
90739 ACTGAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 2 0.07
16 23 0.85
17 2 0.07
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.40
Consensus pattern (17 bp):
TTGCTCGTTAAGCTCTG
Found at i:92059 original size:31 final size:31
Alignment explanation
Indices: 92024--92104 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
92014 AGGCTCGTGA
* * *
92024 GTTTTTGAGTCGATTCGAGTTTCATTTTAGG
1 GTTTTTGAGTCGAGTCGAGTTCCATTTTAAG
92055 GTTTTTGAGTCGAGTCGAGTTCCATTTTAAG
1 GTTTTTGAGTCGAGTCGAGTTCCATTTTAAG
*
92086 GTTTTCGAGTCGAGTCGAG
1 GTTTTTGAGTCGAGTCGAG
92105 CTCATCAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.17, C:0.12, G:0.28, T:0.42
Consensus pattern (31 bp):
GTTTTTGAGTCGAGTCGAGTTCCATTTTAAG
Found at i:93410 original size:3 final size:3
Alignment explanation
Indices: 93404--93442 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
93394 TTTTTTAAAC
93404 TAT TAT TATT TAT TAT TAT TAT GT-T TAT TAT TAT TAT TA
1 TAT TAT TA-T TAT TAT TAT TAT -TAT TAT TAT TAT TAT TA
93443 ATCATTTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.03
3 28 0.85
4 4 0.12
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:93430 original size:15 final size:14
Alignment explanation
Indices: 93404--93441 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
93394 TTTTTTAAAC
93404 TATTATTA-TTTAT
1 TATTATTATTTTAT
93417 TATTATTATGTTTAT
1 TATTATTAT-TTTAT
93432 TATTATTATT
1 TATTATTATT
93442 AATCATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.35
14 1 0.04
15 14 0.61
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (14 bp):
TATTATTATTTTAT
Found at i:94529 original size:2 final size:2
Alignment explanation
Indices: 94522--94552 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
94512 TGTATATTCG
94522 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 T
94553 GTACACATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:96293 original size:9 final size:9
Alignment explanation
Indices: 96279--96303 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
96269 TTTTGACTAA
96279 TTGTTTTGT
1 TTGTTTTGT
96288 TTGTTTTGT
1 TTGTTTTGT
96297 TTGTTTT
1 TTGTTTT
96304 TTTATTCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (9 bp):
TTGTTTTGT
Found at i:99018 original size:30 final size:30
Alignment explanation
Indices: 98961--99028 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
98951 ATGCATAAGT
* **
98961 AAATTCATCATTTATAATGCATCACCAATA
1 AAATGCATCATTTATAACACATCACCAATA
* *
98991 AAATGCATCATTTATAGCACATTACCAATA
1 AAATGCATCATTTATAACACATCACCAATA
*
99021 ATATGCAT
1 AAATGCAT
99029 TCGAATTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (30 bp):
AAATGCATCATTTATAACACATCACCAATA
Found at i:106149 original size:8 final size:8
Alignment explanation
Indices: 106138--106218 Score: 65
Period size: 8 Copynumber: 9.6 Consensus size: 8
106128 CTTAAAAAAG
106138 AAAAAGAA
1 AAAAAGAA
106146 AAAAAGGAA
1 AAAAA-GAA
*
106155 AAAAGGAA
1 AAAAAGAA
* *
106163 AATATGATGGA
1 AA-A--AAGAA
*
106174 AAAATGAA
1 AAAAAGAA
106182 AAAAAGAA
1 AAAAAGAA
106190 GAAAAAGAA
1 -AAAAAGAA
*
106199 AATAA-AA
1 AAAAAGAA
106206 AAAAAGAA
1 AAAAAGAA
106214 AAAAA
1 AAAAA
106219 TAAATAAAGG
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
7 6 0.10
8 32 0.53
9 16 0.27
10 1 0.02
11 5 0.08
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (8 bp):
AAAAAGAA
Found at i:106205 original size:22 final size:21
Alignment explanation
Indices: 106173--106226 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 21
106163 AATATGATGG
106173 AAAAATGAAAAAAAGAAGAAAAA
1 AAAAAT-AAAAAAA-AAGAAAAA
*
106196 GAAAATAAAAAAAAAGAAAAA
1 AAAAATAAAAAAAAAGAAAAA
106217 AATAAATAAA
1 AA-AAATAAA
106227 GGAGGGTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 9 0.32
22 14 0.50
23 5 0.18
ACGTcount: A:0.83, C:0.00, G:0.09, T:0.07
Consensus pattern (21 bp):
AAAAATAAAAAAAAAGAAAAA
Found at i:107217 original size:39 final size:40
Alignment explanation
Indices: 107163--107273 Score: 111
Period size: 39 Copynumber: 2.8 Consensus size: 40
107153 CATCAGCTGG
* * *
107163 CCAGAACTCTTCATCACGTATGAGCCATGTCATCCCC-G-A
1 CCAGATCTCCTCATCACGTAGGAGCCATGTCA-CCCCAGAA
* *
107202 CCAGATCTCCTCATCACGTAGGAGTCGTGTCACCCCAGATAA
1 CCAGATCTCCTCATCACGTAGGAGCCATGTCACCCCAG--AA
*
107244 CCAG-TCGTCCTCATCACGTAGGAACCATGT
1 CCAGATC-TCCTCATCACGTAGGAGCCATGT
107274 TATCACCCCA
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
38 4 0.07
39 28 0.47
41 2 0.03
42 25 0.42
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.23
Consensus pattern (40 bp):
CCAGATCTCCTCATCACGTAGGAGCCATGTCACCCCAGAA
Found at i:107260 original size:42 final size:45
Alignment explanation
Indices: 107201--107326 Score: 136
Period size: 47 Copynumber: 2.8 Consensus size: 45
107191 GTCATCCCCG
** *
107201 ACCAGATC-TCCTCATCACGTAGGAGTC-G-TGTCACCCC-AGATA
1 ACCAG-TCGTCCTCATCACGTAGGAACCAGTTATCACCCCAAGATA
107243 ACCAGTCGTCCTCATCACGTAGGAACCATGTTATCACCCCATAGATA
1 ACCAGTCGTCCTCATCACGTAGGAACCA-GTTATCACCCCA-AGATA
*
107290 ACCAG-CTGTCCTCATCACGTAGGAACCGTGTTATCAC
1 ACCAGTC-GTCCTCATCACGTAGGAACC-AGTTATCAC
107327 ATCTCCTAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 11
0.83 0.05 0.13
Matches are distributed among these distances:
41 2 0.03
42 22 0.31
44 1 0.01
45 8 0.11
46 1 0.01
47 38 0.53
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.23
Consensus pattern (45 bp):
ACCAGTCGTCCTCATCACGTAGGAACCAGTTATCACCCCAAGATA
Found at i:107301 original size:47 final size:45
Alignment explanation
Indices: 107231--107326 Score: 149
Period size: 47 Copynumber: 2.1 Consensus size: 45
107221 AGGAGTCGTG
107231 TCACCCCAGATAACCAGTCGTCCTCATCACGTAGGAACCATGTTA
1 TCACCCCAGATAACCAGTCGTCCTCATCACGTAGGAACCATGTTA
*
107276 TCACCCCATAGATAACCAG-CTGTCCTCATCACGTAGGAACCGTGTTA
1 TCACCCC--AGATAACCAGTC-GTCCTCATCACGTAGGAACCATGTTA
107323 TCAC
1 TCAC
107327 ATCTCCTAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
45 7 0.15
46 1 0.02
47 39 0.83
ACGTcount: A:0.28, C:0.33, G:0.16, T:0.23
Consensus pattern (45 bp):
TCACCCCAGATAACCAGTCGTCCTCATCACGTAGGAACCATGTTA
Found at i:107456 original size:43 final size:40
Alignment explanation
Indices: 107345--107461 Score: 103
Period size: 43 Copynumber: 2.9 Consensus size: 40
107335 AAGATGGCCA
*
107345 AGAACTCTTCATCACGTATGAGCAGTGTCATCCCCCGACC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCCACGACC
* * * * *
107385 AGATA-TCCTCATCATGTAGGATCCGTGTCA-CCCTTAGACGACC
1 AGA-ACTCTTCATCACGTATGAGCAGTGTCATCCC----ACGACC
* *
107428 CGAACTCTTCATCACGTATGAGCAGTGTCGTCCC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCC
107462 CAACAACCAA
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
39 3 0.05
40 23 0.40
41 1 0.02
42 1 0.02
43 26 0.46
44 3 0.05
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (40 bp):
AGAACTCTTCATCACGTATGAGCAGTGTCATCCCACGACC
Found at i:107623 original size:3 final size:3
Alignment explanation
Indices: 107617--107655 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
107607 TTTTTTAAAC
107617 TAT TAT TATT TAT TAT TAT TAT GT-T TAT TAT TAT TAT TA
1 TAT TAT TA-T TAT TAT TAT TAT -TAT TAT TAT TAT TAT TA
107656 ATCATTTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.03
3 28 0.85
4 4 0.12
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:107643 original size:15 final size:14
Alignment explanation
Indices: 107617--107654 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
107607 TTTTTTAAAC
107617 TATTATTA-TTTAT
1 TATTATTATTTTAT
107630 TATTATTATGTTTAT
1 TATTATTAT-TTTAT
107645 TATTATTATT
1 TATTATTATT
107655 AATCATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.35
14 1 0.04
15 14 0.61
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (14 bp):
TATTATTATTTTAT
Found at i:112129 original size:20 final size:20
Alignment explanation
Indices: 112106--112171 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
112096 TTTCTTTTCT
112106 GCAACGAGAATATGTAAATC
1 GCAACGAGAATATGTAAATC
* * * * *
112126 GCAACGTGATTTTCTGAATTC
1 GCAACGAGAATATGT-AAATC
* *
112147 GCAACGCGAAAATGTAAATC
1 GCAACGAGAATATGTAAATC
112167 GCAAC
1 GCAAC
112172 ACATAAGTCA
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
20 20 0.59
21 14 0.41
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (20 bp):
GCAACGAGAATATGTAAATC
Found at i:112363 original size:22 final size:22
Alignment explanation
Indices: 112338--112395 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
112328 TCACCCTCTA
*
112338 CGGCGACATCCATCCCCATCTC
1 CGGCGACATCCATCCCCATATC
*
112360 CGGCGACATCCGTCCCCATATC
1 CGGCGACATCCATCCCCATATC
*
112382 CGGCGACCTCCATC
1 CGGCGACATCCATC
112396 TATCTCCATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.17, C:0.48, G:0.17, T:0.17
Consensus pattern (22 bp):
CGGCGACATCCATCCCCATATC
Found at i:112790 original size:20 final size:19
Alignment explanation
Indices: 112749--112791 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
112739 AAATCGTAAC
*
112749 GCGATTTCATTTTCGCGTT
1 GCGATTTCATTTTCGCGCT
*
112768 GCGATTTTCATTTTCGTGCT
1 GCGA-TTTCATTTTCGCGCT
112788 GCGA
1 GCGA
112792 ATTTAAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.44
Consensus pattern (19 bp):
GCGATTTCATTTTCGCGCT
Found at i:113815 original size:42 final size:42
Alignment explanation
Indices: 113731--113827 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 42
113721 CCCCCTACTT
* * *
113731 CGAGAGCCATCACCTAATCGAGTCAATTCTACAGCTCAACAC
1 CGAGAGCCATCACCTAATCGAGCCAATTATACACCTCAACAC
* * * *
113773 CGAGAGCCATCACCTGATTGAGCCGATTATACACCTCCACAC
1 CGAGAGCCATCACCTAATCGAGCCAATTATACACCTCAACAC
113815 CGAGAGCCATCAC
1 CGAGAGCCATCAC
113828 ATATTCCATC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.31, C:0.35, G:0.16, T:0.18
Consensus pattern (42 bp):
CGAGAGCCATCACCTAATCGAGCCAATTATACACCTCAACAC
Found at i:114040 original size:21 final size:22
Alignment explanation
Indices: 114010--114126 Score: 68
Period size: 21 Copynumber: 5.5 Consensus size: 22
114000 TGGTGCATGG
*
114010 CGTGAGGAGGTACGGT-CTTTA
1 CGTGATGAGGTACGGTACTTTA
**
114031 CGTGATGAGGTA-GGTGTTTTA
1 CGTGATGAGGTACGGTACTTTA
* ** * *
114052 CGCGATGA-CAATGGTGCTTTA
1 CGTGATGAGGTACGGTACTTTA
*
114073 CGTGGTGAGGTATC--TACTTTA
1 CGTGATGAGGTA-CGGTACTTTA
* *
114094 CGTGGTGAGATATC--TACTTTA
1 CGTGATGAGGTA-CGGTACTTTA
114115 CGTGATGAGGTA
1 CGTGATGAGGTA
114127 GCCGCTCTAC
Statistics
Matches: 77, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
20 4 0.05
21 72 0.94
22 1 0.01
ACGTcount: A:0.21, C:0.13, G:0.32, T:0.33
Consensus pattern (22 bp):
CGTGATGAGGTACGGTACTTTA
Found at i:114444 original size:21 final size:21
Alignment explanation
Indices: 114418--114510 Score: 129
Period size: 21 Copynumber: 4.6 Consensus size: 21
114408 TTCACCTGTC
114418 ATCGTTCAAGAGGCCCCTCCT
1 ATCGTTCAAGAGGCCCCTCCT
*
114439 ATCGTTCAAAAGGCCCCTCCT
1 ATCGTTCAAGAGGCCCCTCCT
*
114460 ATCGTTCAAGA-GCCTCT-C-
1 ATCGTTCAAGAGGCCCCTCCT
*
114478 ATCGTTCAAGAGGCCCCTCCC
1 ATCGTTCAAGAGGCCCCTCCT
*
114499 ACCGTTCAAGAG
1 ATCGTTCAAGAG
114511 CCCGATTCGC
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
18 11 0.17
19 6 0.09
20 6 0.09
21 41 0.64
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCCT
Found at i:114492 original size:39 final size:41
Alignment explanation
Indices: 114417--114513 Score: 135
Period size: 39 Copynumber: 2.4 Consensus size: 41
114407 ATTCACCTGT
114417 CATCGTTCAAGAGGCCCCTCCTATCGTTCAAAAGGCCCCTCC
1 CATCGTTCAAGA-GCCCCTCCTATCGTTCAAAAGGCCCCTCC
* * *
114459 TATCGTTCAAGAGCCTCT-C-ATCGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGCCCCTCCTATCGTTCAAAAGGCCCCTCC
*
114498 CACCGTTCAAGAGCCC
1 CATCGTTCAAGAGCCC
114514 GATTCGCATG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
39 32 0.65
40 1 0.02
41 5 0.10
42 11 0.22
ACGTcount: A:0.22, C:0.39, G:0.18, T:0.22
Consensus pattern (41 bp):
CATCGTTCAAGAGCCCCTCCTATCGTTCAAAAGGCCCCTCC
Found at i:115933 original size:16 final size:15
Alignment explanation
Indices: 115903--115937 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
115893 TGTAAATAAG
*
115903 AATTGTTTTTTGTTT
1 AATTGTTTGTTGTTT
115918 AATTGATTTGTTGTTT
1 AATTG-TTTGTTGTTT
115934 AATT
1 AATT
115938 TCAATCTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.20, C:0.00, G:0.14, T:0.66
Consensus pattern (15 bp):
AATTGTTTGTTGTTT
Found at i:119513 original size:14 final size:16
Alignment explanation
Indices: 119478--119514 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
119468 GAAATCATTG
119478 AAAATTATATAGAAAT
1 AAAATTATATAGAAAT
*
119494 AAAATTATGTA-AAA-
1 AAAATTATATAGAAAT
119508 AAAATTA
1 AAAATTA
119515 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 3 0.15
16 10 0.50
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (16 bp):
AAAATTATATAGAAAT
Found at i:119696 original size:20 final size:20
Alignment explanation
Indices: 119671--119821 Score: 81
Period size: 20 Copynumber: 7.5 Consensus size: 20
119661 AATAAAAGTT
119671 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTCGAAAATCGA
** * * *
119691 GTTGCGAAAACTAAATTCGT
1 GTTGCGAATTCGAAAATCGA
* * **
119711 GTTGCGATTTAGAAAATCTT
1 GTTGCGAATTCGAAAATCGA
*** * * *
119731 GTTGCGAAAAGGAAACTTGT
1 GTTGCGAATTCGAAAATCGA
119751 GTTGCGAATTC-AGAAATCGA
1 GTTGCGAATTCGA-AAATCGA
* *
119771 GTTGCGAATTTGAAATTTC-A
1 GTTGCGAATTCGAAA-ATCGA
* * *
119791 TGTTGCGAATTTGGAAATCGC
1 -GTTGCGAATTCGAAAATCGA
119812 GTTGCGAATT
1 GTTGCGAATT
119822 TGTTGGTCAT
Statistics
Matches: 96, Mismatches: 30, Indels: 10
0.71 0.22 0.07
Matches are distributed among these distances:
19 1 0.01
20 78 0.81
21 17 0.18
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.32
Consensus pattern (20 bp):
GTTGCGAATTCGAAAATCGA
Found at i:119715 original size:40 final size:41
Alignment explanation
Indices: 119670--119819 Score: 137
Period size: 40 Copynumber: 3.7 Consensus size: 41
119660 AAATAAAAGT
119670 TGTTGCGAATTCGAAAATCGAGTTGCGAAAACTAAA-TTCG
1 TGTTGCGAATTCGAAAATCGAGTTGCGAAAACTAAACTTCG
* * ** **
119710 TGTTGCGATTTAGAAAATCTTGTTGCGAAAAGGAAACTT-G
1 TGTTGCGAATTCGAAAATCGAGTTGCGAAAACTAAACTTCG
** * *
119750 TGTTGCGAATTC-AGAAATCGAGTTGCG-AATTTGAAATTTCA
1 TGTTGCGAATTCGA-AAATCGAGTTGCGAAAACT-AAACTTCG
* * *
119791 TGTTGCGAATTTGGAAATCGCGTTGCGAA
1 TGTTGCGAATTCGAAAATCGAGTTGCGAA
119820 TTTGTTGGTC
Statistics
Matches: 86, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
39 3 0.03
40 57 0.66
41 25 0.29
42 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (41 bp):
TGTTGCGAATTCGAAAATCGAGTTGCGAAAACTAAACTTCG
Found at i:123360 original size:2 final size:2
Alignment explanation
Indices: 123353--123378 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
123343 TAAATTATTA
123353 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
123379 CTTCAACTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:129119 original size:6 final size:5
Alignment explanation
Indices: 129099--129135 Score: 56
Period size: 5 Copynumber: 7.0 Consensus size: 5
129089 TACAAATAAG
129099 ATCAA ATCAA ATCAGA ATCAGA ATCAA ATCAA ATCAA
1 ATCAA ATCAA ATCA-A ATCA-A ATCAA ATCAA ATCAA
129136 TGGATGCAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 20 0.65
6 11 0.35
ACGTcount: A:0.57, C:0.19, G:0.05, T:0.19
Consensus pattern (5 bp):
ATCAA
Found at i:131992 original size:55 final size:55
Alignment explanation
Indices: 131906--132011 Score: 185
Period size: 55 Copynumber: 1.9 Consensus size: 55
131896 TGAGGAGAAG
*
131906 AACAAGAACATGGGTGTTGATTTTTGAAACTAAAAAAGGGGAAAAGAAAGGAAAT
1 AACAAGAACATGGGTGTTGATTGTTGAAACTAAAAAAGGGGAAAAGAAAGGAAAT
* *
131961 AACAAGAACATGTGTGTTGATTGTTGGAACTAAAAAAGGGGAAAAGAAAGG
1 AACAAGAACATGGGTGTTGATTGTTGAAACTAAAAAAGGGGAAAAGAAAGG
132012 GAGAAAGGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.47, C:0.06, G:0.27, T:0.20
Consensus pattern (55 bp):
AACAAGAACATGGGTGTTGATTGTTGAAACTAAAAAAGGGGAAAAGAAAGGAAAT
Found at i:132672 original size:12 final size:12
Alignment explanation
Indices: 132655--132680 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
132645 CATTACAAAT
132655 TTAAAATATAAA
1 TTAAAATATAAA
132667 TTAAAATATAAA
1 TTAAAATATAAA
132679 TT
1 TT
132681 TACACAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TTAAAATATAAA
Found at i:137399 original size:34 final size:34
Alignment explanation
Indices: 137361--137458 Score: 187
Period size: 34 Copynumber: 2.9 Consensus size: 34
137351 TATATGTGTT
*
137361 CAAAATAGTACGAACTTAGAGTTATAAATAAAAC
1 CAAAATAGTACTAACTTAGAGTTATAAATAAAAC
137395 CAAAATAGTACTAACTTAGAGTTATAAATAAAAC
1 CAAAATAGTACTAACTTAGAGTTATAAATAAAAC
137429 CAAAATAGTACTAACTTAGAGTTATAAATA
1 CAAAATAGTACTAACTTAGAGTTATAAATA
137459 TGAAATACAA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.52, C:0.11, G:0.10, T:0.27
Consensus pattern (34 bp):
CAAAATAGTACTAACTTAGAGTTATAAATAAAAC
Found at i:137920 original size:2 final size:2
Alignment explanation
Indices: 137913--137954 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
137903 CTGGTTAGTT
137913 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
137953 TA
1 TA
137955 ATCCAATTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Done.