Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000139.1 Hibiscus syriacus cultivar Beakdansim tig00000254_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: 98541
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:426 original size:29 final size:29
Alignment explanation
Indices: 389--445 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
379 TGTTTAATAA
* * *
389 TTAAAAATTATTTTTTCTATTAGTAAAAG
1 TTAAAAATTATTTCTTCCATTAATAAAAG
*
418 TTAAGAATTATTTCTTCCATTAATAAAA
1 TTAAAAATTATTTCTTCCATTAATAAAA
446 ATTTAAAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (29 bp):
TTAAAAATTATTTCTTCCATTAATAAAAG
Found at i:1885 original size:32 final size:32
Alignment explanation
Indices: 1849--1924 Score: 93
Period size: 32 Copynumber: 2.3 Consensus size: 32
1839 TCGGGCCTGA
1849 TATATATATATTTAAA-TTAAATATATAA-ATAT
1 TATATATATATTTAAATTTAAAT-TA-AATATAT
* *
1881 TATATATATTTTTAAATTTAAATTAAATTTAT
1 TATATATATATTTAAATTTAAATTAAATATAT
1913 TAATATATATAT
1 T-ATATATATAT
1925 ATATAATAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
31 2 0.05
32 21 0.55
33 15 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
TATATATATATTTAAATTTAAATTAAATATAT
Found at i:2044 original size:35 final size:35
Alignment explanation
Indices: 1997--2071 Score: 134
Period size: 35 Copynumber: 2.1 Consensus size: 35
1987 CAAACTCGTC
1997 CCCGTCTCCGTTTAACATAAACGA-TTTTTCTTGT
1 CCCGTCTCCGTTTAACATAAACGATTTTTTCTTGT
2031 CTCCGTCTCCGTTTAACATAAACGATTTTTTCTTGT
1 C-CCGTCTCCGTTTAACATAAACGATTTTTTCTTGT
2067 CCCGT
1 CCCGT
2072 TTAATTCAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
34 1 0.03
35 27 0.69
36 11 0.28
ACGTcount: A:0.19, C:0.28, G:0.12, T:0.41
Consensus pattern (35 bp):
CCCGTCTCCGTTTAACATAAACGATTTTTTCTTGT
Found at i:2874 original size:200 final size:199
Alignment explanation
Indices: 2520--2933 Score: 747
Period size: 200 Copynumber: 2.1 Consensus size: 199
2510 TAAGACATAA
* *
2520 TTCCTCAATAATTTCACAACTTAAGTCCCTATCTTTTCCATATTTACAATTTGATCCTCAAACTT
1 TTCCTTAATAATTTCACAACTCAAGTCCCTATCTTTTCCATATTTACAATTTGATCCTCAAACTT
2585 TACCAACTTTCCAAACTAGTCAAATTTCACCTTCTAACATCAAAATTCAAATTTCAACATAATCA
66 TACCAACTTTCCAAACTAGTCAAATTTCACCTTCTAACATCAAAATTCAAATTTCAACATAATCA
* *
2650 TTCTAGCATAGTCCTTCAACTATTAATCGATTACACTTAAATCCTCATATTTCTCAAGGTATGCA
131 TTCTAGCATAGTCCTTCAACTATTAATCGATTACACTTAAATCCTCATATTTCTCAAAGTATAC-
2715 AAATT
195 AAATT
*
2720 TTCCTTAATAATTTCACAACTCAAGTCCCTATCTTTTTCATATTTACAATTTGATCCTCAAACTT
1 TTCCTTAATAATTTCACAACTCAAGTCCCTATCTTTTCCATATTTACAATTTGATCCTCAAACTT
*
2785 TACCAACTTTCCAAACTAGTCAAATTTCACCTTCTAACATCAAAATTCAAATTTCAACATTATCA
66 TACCAACTTTCCAAACTAGTCAAATTTCACCTTCTAACATCAAAATTCAAATTTCAACATAATCA
*
2850 TTCTAGCATAGTCCTTCGACTATTAATCGATTACACTTAAATCCTCATATTTCTCAAAGTATACA
131 TTCTAGCATAGTCCTTCAACTATTAATCGATTACACTTAAATCCTCATATTTCTCAAAGTATACA
2915 AATT
196 AATT
2919 TGTCCTTAATAATTT
1 T-TCCTTAATAATTT
2934 ATAAATTTCT
Statistics
Matches: 206, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
199 6 0.03
200 200 0.97
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (199 bp):
TTCCTTAATAATTTCACAACTCAAGTCCCTATCTTTTCCATATTTACAATTTGATCCTCAAACTT
TACCAACTTTCCAAACTAGTCAAATTTCACCTTCTAACATCAAAATTCAAATTTCAACATAATCA
TTCTAGCATAGTCCTTCAACTATTAATCGATTACACTTAAATCCTCATATTTCTCAAAGTATACA
AATT
Found at i:5443 original size:54 final size:54
Alignment explanation
Indices: 5296--5433 Score: 172
Period size: 54 Copynumber: 2.6 Consensus size: 54
5286 ATTAAAAACT
* *
5296 TTGATTCA-T-TAGACAAACAAATTAGTACAATAAATACTTGATAATATTAACC
1 TTGATTCATTATAGACAAATAAATTGGTACAATAAATACTTGATAATATTAACC
* ** * *
5348 TTGATTCATTATAGATAAATAAATTGACACAATAAATACTTGATAATGTTAATC
1 TTGATTCATTATAGACAAATAAATTGGTACAATAAATACTTGATAATATTAACC
* * *
5402 TTGGTTTATTGTAGACAAATAAATTGGTACAA
1 TTGATTCATTATAGACAAATAAATTGGTACAA
5434 CAGGTACTTG
Statistics
Matches: 71, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
52 8 0.11
53 1 0.01
54 62 0.87
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (54 bp):
TTGATTCATTATAGACAAATAAATTGGTACAATAAATACTTGATAATATTAACC
Found at i:6546 original size:18 final size:18
Alignment explanation
Indices: 6509--6542 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6499 CAAAGTTTTT
*
6509 TAAATAATATTAAAATTA
1 TAAATAATATGAAAATTA
6527 TAAATAATA-GAAAATT
1 TAAATAATATGAAAATT
6543 TATATTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
TAAATAATATGAAAATTA
Found at i:10112 original size:28 final size:28
Alignment explanation
Indices: 10083--10137 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
10073 TTATTTTTAC
10083 TTTAAAATA-AAATATTAAATCAAAATACT
1 TTTAAAA-AGAAATA-TAAATCAAAATACT
*
10112 TTTAAAAAGTAATATAAATCAAAATA
1 TTTAAAAAGAAATATAAATCAAAATA
10138 ATCTTTTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (28 bp):
TTTAAAAAGAAATATAAATCAAAATACT
Found at i:11764 original size:18 final size:18
Alignment explanation
Indices: 11743--11790 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
11733 AAATAAAATA
*
11743 ATAAGTAAAAATATATAT
1 ATAAGTAAAAATATATAC
*
11761 ATAA-TAAAAA-ATGTAC
1 ATAAGTAAAAATATATAC
11777 ATAAG-AAAAATATA
1 ATAAGTAAAAATATA
11791 ATAAAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 13 0.52
17 8 0.32
18 4 0.16
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (18 bp):
ATAAGTAAAAATATATAC
Found at i:11801 original size:16 final size:17
Alignment explanation
Indices: 11733--11801 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 17
11723 TTTAATAATC
*
11733 AAATAAAATAATAAGTAA
1 AAATATAATAATAA-TAA
11751 AAATAT-ATATATAATAA
1 AAATATAATA-ATAATAA
* *
11768 AAA-AT-GTACATAAGAA
1 AAATATAATA-ATAATAA
11784 AAATATAATAA-AATAA
1 AAATATAATAATAATAA
11800 AA
1 AA
11802 TACATGGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
16 19 0.45
17 12 0.29
18 11 0.26
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.25
Consensus pattern (17 bp):
AAATATAATAATAATAA
Found at i:11816 original size:27 final size:27
Alignment explanation
Indices: 11757--11817 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
11747 GTAAAAATAT
**
11757 ATATATAATAAAAAATGTACATAAGAA
1 ATATATAATAAAAAAAATACATAAGAA
* *
11784 AAATATAATAAAATAAAATACAT-GGAA
1 ATATATAATAAAA-AAAATACATAAGAA
11811 ATATATA
1 ATATATA
11818 TATAGCTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.64, C:0.03, G:0.07, T:0.26
Consensus pattern (27 bp):
ATATATAATAAAAAAAATACATAAGAA
Found at i:12056 original size:10 final size:10
Alignment explanation
Indices: 12043--12070 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
12033 ATAAAAATAA
12043 AAATAAAAAC
1 AAATAAAAAC
12053 AAATAAAAAC
1 AAATAAAAAC
12063 AAATAAAA
1 AAATAAAA
12071 TATAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.82, C:0.07, G:0.00, T:0.11
Consensus pattern (10 bp):
AAATAAAAAC
Found at i:14141 original size:110 final size:109
Alignment explanation
Indices: 13933--14191 Score: 321
Period size: 110 Copynumber: 2.4 Consensus size: 109
13923 TGTATTATTC
* * * * *
13933 CGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTG-GCT--ATGGAACTGGGAAATTGTTTGTTG
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGCTCTGAATGAAACTGGAAAATTGTTTGTTG
* * *
13995 ACAGTCAGCCGCCCCTTCGCTTTGAAGTTGAGCTTGTGTTGTCT
66 ACAATCAGCCACCCCTTCGCTTTGAAATTGAGCTTGTGTTGTCT
*
14039 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACT-GAAAAGTTGTTTTT
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG-CTCTGAATGAAACTGGAAAA-TTGTTTGT
*
14103 TGACAATCAGTCACCCCTTCG-TTGTGAAATTGAGCTTGTGTTGTCT
64 TGACAATCAGCCACCCCTTCGCTT-TGAAATTGAGCTTGTGTTGTCT
* * * *
14149 TGGGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT-GCTCTGAA
14192 ATTGGGAAGC
Statistics
Matches: 132, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
106 33 0.25
108 2 0.02
109 6 0.05
110 90 0.68
111 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (109 bp):
CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGCTCTGAATGAAACTGGAAAATTGTTTGTTG
ACAATCAGCCACCCCTTCGCTTTGAAATTGAGCTTGTGTTGTCT
Found at i:16078 original size:64 final size:63
Alignment explanation
Indices: 15968--16120 Score: 175
Period size: 64 Copynumber: 2.4 Consensus size: 63
15958 TTCAGTGTGT
* *
15968 ATCGATGCATAAGAAGTGCATCGATGCACCCATTAAAAAAGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAAGGAGTGCATCGATGCACCCATTAAAAAA-GAAACATCGAAGGCAATTAGTGC
* * ** * *
16032 ATCGATGCATAAGGAGTGCATCGATGCACCCCCTTAAAATCA-AAACATCGAAGGTGATTTGTGT
1 ATCGATGCATAAGGAGTGCATCGATGCA-CCCATTAAAA-AAGAAACATCGAAGGCAATTAGTGC
*
16096 ATCGATGCAT-GGGTAGTGCATCGAT
1 ATCGATGCATAAGG-AGTGCATCGAT
16121 ACACATGTTA
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
63 2 0.03
64 65 0.84
65 9 0.12
66 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.24
Consensus pattern (63 bp):
ATCGATGCATAAGGAGTGCATCGATGCACCCATTAAAAAAGAAACATCGAAGGCAATTAGTGC
Found at i:16875 original size:28 final size:29
Alignment explanation
Indices: 16834--16889 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
16824 ATAAGAAATA
* *
16834 ATATGTTATATGAATATGAG-AAAAAGGT
1 ATATGTGATATGAACATGAGTAAAAAGGT
* *
16862 ATATGTGATGTGAACATGTGTAAAAAGG
1 ATATGTGATATGAACATGAGTAAAAAGG
16890 ATGAATAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.43, C:0.02, G:0.25, T:0.30
Consensus pattern (29 bp):
ATATGTGATATGAACATGAGTAAAAAGGT
Found at i:21500 original size:18 final size:19
Alignment explanation
Indices: 21477--21529 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 19
21467 GAGGGTCTAC
21477 GTGGTCCTTCGGGATATA-
1 GTGGTCCTTCGGGATATAT
*
21495 GTGGTCATTCGGGACATATAT
1 GTGGTCCTTCGGG--ATATAT
*
21516 ATGGTCCTTCGGGA
1 GTGGTCCTTCGGGA
21530 CAAATTCTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 12 0.41
19 1 0.03
20 5 0.17
21 11 0.38
ACGTcount: A:0.19, C:0.17, G:0.32, T:0.32
Consensus pattern (19 bp):
GTGGTCCTTCGGGATATAT
Found at i:21526 original size:21 final size:20
Alignment explanation
Indices: 21478--21531 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
21468 AGGGTCTACG
*
21478 TGGTCCTTCGGG--ATATAG
1 TGGTCCTTCGGGACATATAA
*
21496 TGGTCATTCGGGACATATATA
1 TGGTCCTTCGGGACATATA-A
21517 TGGTCCTTCGGGACA
1 TGGTCCTTCGGGACA
21532 AATTCTACGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 11 0.37
20 5 0.17
21 14 0.47
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (20 bp):
TGGTCCTTCGGGACATATAA
Found at i:22606 original size:10 final size:10
Alignment explanation
Indices: 22591--22628 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
22581 ATTCTTTTAC
22591 TTTTTTTC-T
1 TTTTTTTCTT
22600 TTTTTTTCTT
1 TTTTTTTCTT
22610 TTTTTTTCTT
1 TTTTTTTCTT
22620 TTTTCTTTC
1 TTTT-TTTC
22629 GACTTAAGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 8 0.30
10 15 0.56
11 4 0.15
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:22614 original size:26 final size:26
Alignment explanation
Indices: 22567--22627 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
22557 ACTCTAAATG
**
22567 TTTTTCTCCTTTTTATTCTTTTACT-T
1 TTTTTCTTTTTTTTATTCTTTT-CTCT
* * *
22593 TTTTTCTTTTTTTTCTTTTTTTTTCT
1 TTTTTCTTTTTTTTATTCTTTTCTCT
22619 TTTTTCTTT
1 TTTTTCTTT
22628 CGACTTAAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 1 0.03
26 28 0.97
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (26 bp):
TTTTTCTTTTTTTTATTCTTTTCTCT
Found at i:22622 original size:17 final size:17
Alignment explanation
Indices: 22576--22627 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
22566 GTTTTTCTCC
* *
22576 TTTTTATTC-TTTTACT
1 TTTTTTTTCTTTTTTCT
22592 TTTTTTCTT-TTTTTTCT
1 TTTTTT-TTCTTTTTTCT
22609 TTTTTTTTCTTTTTTCT
1 TTTTTTTTCTTTTTTCT
22626 TT
1 TT
22628 CGACTTAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 7 0.23
17 24 0.77
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTTTCTTTTTTCT
Found at i:22623 original size:9 final size:9
Alignment explanation
Indices: 22591--22627 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
22581 ATTCTTTTAC
22591 TTTTTTTCT
1 TTTTTTTCT
22600 TTTTTTTCT
1 TTTTTTTCT
22609 TTTTTTT-T
1 TTTTTTTCT
*
22617 CTTTTTTCT
1 TTTTTTTCT
22626 TT
1 TT
22628 CGACTTAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:25635 original size:64 final size:64
Alignment explanation
Indices: 25582--25744 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 64
25572 CGGTGCACCA
* *
25582 AGTGTGCATTGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * **
25646 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * *
25711 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
25745 CAATTAATTC
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
64 38 0.45
65 46 0.55
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:25716 original size:19 final size:19
Alignment explanation
Indices: 25692--25742 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
25682 GAAAATATTC
25692 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
25711 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
25730 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
25743 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:25784 original size:65 final size:65
Alignment explanation
Indices: 25594--25793 Score: 207
Period size: 65 Copynumber: 3.1 Consensus size: 65
25584 TGTGCATTGA
* ** *
25594 TGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG-CTTG-TGCATC
1 TGCATGAAATGCATTCGATGTTT-CAAAATATTCAGAGTGCATCGATGCATGGAC-TGATGCATC
*
25656 GA
64 GG
* *
25658 TGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGA--GAGTGCATC
1 TGCATGAAATGCATTCGATG-TTTCAAAATATTCAGAGTGCATCGATGCATGGACTGA-TGCATC
25721 GG
64 GG
* * *
25723 TGCATGGAATGCATTCGATG-TTC-AATTAATTCATAGATGCATCGATGCATGGACTGATGCATC
1 TGCATGAAATGCATTCGATGTTTCAAAAT-ATTCAGAG-TGCATCGATGCATGGACTGATGCATC
25786 GG
64 GG
25788 TGCATG
1 TGCATG
25794 CCTTTGAATA
Statistics
Matches: 116, Mismatches: 11, Indels: 17
0.81 0.08 0.12
Matches are distributed among these distances:
62 3 0.03
63 10 0.09
64 43 0.37
65 58 0.50
66 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (65 bp):
TGCATGAAATGCATTCGATGTTTCAAAATATTCAGAGTGCATCGATGCATGGACTGATGCATCGG
Found at i:32232 original size:22 final size:21
Alignment explanation
Indices: 32190--32229 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
32180 GAGTTTGTTT
*
32190 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
32211 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
32230 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:34245 original size:65 final size:64
Alignment explanation
Indices: 34174--34337 Score: 204
Period size: 65 Copynumber: 2.5 Consensus size: 64
34164 CGGTGCACCA
*
34174 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAATAGCCTG-GTGCATCGATGCATG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG--AAAATAGCCAGAGTGCATCGATGCATG
34238 G
64 G
** * * **
34239 CTTGTGCATTGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * *
34304 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
34338 CAATTAATTC
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
64 10 0.12
65 69 0.83
66 4 0.05
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:34309 original size:19 final size:19
Alignment explanation
Indices: 34285--34335 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
34275 GAAAATATTC
34285 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
34304 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
34323 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
34336 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:34377 original size:65 final size:65
Alignment explanation
Indices: 34178--34386 Score: 198
Period size: 65 Copynumber: 3.2 Consensus size: 65
34168 GCACCAAGTG
* * ** *
34178 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAATAGCCTG-GTGCATCGATGCATGG-CT
1 TGCATCGGTGCATGAAATGCATTCGATGTTT--CAAAATATTCAGAGTGCATCGATGCATGGAC-
34241 TG-
63 TGA
* * * *
34243 TGCATTGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGA--G
1 TGCATCGGTGCATGAAATGCATTCGATG-TTTCAAAATATTCAGAGTGCATCGATGCATGGACTG
34306 A
65 A
* * *
34307 GTGCATCGGTGCATGGAATGCATTCGATG-TTC-AATTAATTCATAGATGCATCGATGCATGGAC
1 -TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAT-ATTCAGAG-TGCATCGATGCATGGAC
34370 TGA
63 TGA
34373 TGCATCGGTGCATG
1 TGCATCGGTGCATG
34387 CCTTTGAATA
Statistics
Matches: 122, Mismatches: 13, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
62 3 0.02
63 10 0.08
64 24 0.20
65 80 0.66
66 5 0.04
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (65 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAATATTCAGAGTGCATCGATGCATGGACTGA
Found at i:39465 original size:17 final size:19
Alignment explanation
Indices: 39432--39469 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
39422 ATACGAATGT
39432 AAAAACATAGAACATATAA
1 AAAAACATAGAACATATAA
39451 AAAAACAT-GAA-ATATAA
1 AAAAACATAGAACATATAA
39468 AA
1 AA
39470 TGCAAAGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 3 0.16
19 8 0.42
ACGTcount: A:0.71, C:0.08, G:0.05, T:0.16
Consensus pattern (19 bp):
AAAAACATAGAACATATAA
Found at i:42734 original size:7 final size:7
Alignment explanation
Indices: 42719--42846 Score: 55
Period size: 7 Copynumber: 17.0 Consensus size: 7
42709 CAATGCGATG
42719 TAAAAAA
1 TAAAAAA
*
42726 TAAATAA
1 TAAAAAA
42733 TAAAAAGA
1 TAAAAA-A
**
42741 -CCAAAA
1 TAAAAAA
42747 TAAAAAA
1 TAAAAAA
42754 TAAATAAA
1 TAAA-AAA
42762 TAAAGGAAA
1 TAAA--AAA
*
42771 TAAATATGCA
1 TAAA-A--AA
42781 TAAAAAA
1 TAAAAAA
**
42788 TAAAATG
1 TAAAAAA
42795 TAAAAGAA
1 TAAAA-AA
42803 -AAAAAGA
1 TAAAAA-A
42810 TAAATAAA
1 TAAA-AAA
42818 TAACTAAAA
1 TAA--AAAA
*
42827 T-AGAAA
1 TAAAAAA
*
42833 TAAATAA
1 TAAAAAA
42840 TAAAAAA
1 TAAAAAA
42847 ATGAAAGTAT
Statistics
Matches: 90, Mismatches: 18, Indels: 26
0.67 0.13 0.19
Matches are distributed among these distances:
6 6 0.07
7 47 0.52
8 17 0.19
9 14 0.16
10 6 0.07
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.18
Consensus pattern (7 bp):
TAAAAAA
Found at i:42826 original size:19 final size:18
Alignment explanation
Indices: 42804--42844 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
42794 GTAAAAGAAA
*
42804 AAAAGATAAATAAATAACT
1 AAAAGAGAAATAAATAA-T
*
42823 AAAATAGAAATAAATAAT
1 AAAAGAGAAATAAATAAT
42841 AAAA
1 AAAA
42845 AAATGAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (18 bp):
AAAAGAGAAATAAATAAT
Found at i:42953 original size:33 final size:35
Alignment explanation
Indices: 42880--42961 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 35
42870 AAAAAACAAA
*
42880 TAAATATATATATAATAATCAAATAAAATAATAAG
1 TAAAAATATATATAATAATCAAATAAAATAATAAG
*
42915 TAAAAATATATAT-ATAAT-AAA-AAATGTACATAAG
1 TAAAAATATATATAATAATCAAATAAA-ATA-ATAAG
42949 -AAAAATATA-ATAA
1 TAAAAATATATATAA
42962 AAAAATACAT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
32 5 0.12
33 15 0.36
34 10 0.24
35 12 0.29
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (35 bp):
TAAAAATATATATAATAATCAAATAAAATAATAAG
Found at i:42965 original size:13 final size:13
Alignment explanation
Indices: 42926--42968 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
42916 AAAAATATAT
42926 ATATAAT-AAAAA
1 ATATAATAAAAAA
*
42938 ATGTACATAAGAAAA
1 ATATA-ATAA-AAAA
42953 ATATAATAAAAAA
1 ATATAATAAAAAA
42966 ATA
1 ATA
42969 CATGGAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 4 0.15
13 9 0.35
14 5 0.19
15 8 0.31
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (13 bp):
ATATAATAAAAAA
Found at i:42979 original size:27 final size:28
Alignment explanation
Indices: 42924--42985 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 28
42914 GTAAAAATAT
*
42924 ATATATAATAAAAAATGTACATAAGAAA
1 ATATATAATAAAAAATATACATAAGAAA
42952 A-ATATAATAAAAAA-ATACATGGAA-AAA
1 ATATATAATAAAAAATATACAT--AAGAAA
42979 ATATATA
1 ATATATA
42986 TATAGCTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
26 5 0.17
27 17 0.57
28 8 0.27
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.24
Consensus pattern (28 bp):
ATATATAATAAAAAATATACATAAGAAA
Found at i:43178 original size:28 final size:27
Alignment explanation
Indices: 43116--43188 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 27
43106 ATATAATATT
43116 TAAAAATAATAAT-AAATATATATATAG
1 TAAAAATAA-AATAAAATATATATATAG
* *
43143 TAATAATAAAATGAAAATATGTATATA-
1 TAAAAATAAAAT-AAAATATATATATAG
*
43170 TACAAAATAAGATAAAATA
1 TA-AAAATAAAATAAAATA
43189 AAAATAATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
26 3 0.08
27 16 0.41
28 20 0.51
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.30
Consensus pattern (27 bp):
TAAAAATAAAATAAAATATATATATAG
Found at i:43185 original size:33 final size:31
Alignment explanation
Indices: 43148--43210 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 31
43138 TATAGTAATA
*
43148 ATAAAATGAAAAT-ATGTATATATACAAAATAAG
1 ATAAAATAAAAATAAT-TATA-ATA-AAAATAAG
43181 ATAAAATAAAAATAATTATAATAAAAATAA
1 ATAAAATAAAAATAATTATAATAAAAATAA
43211 ATAGAAACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 7 0.25
32 3 0.11
33 16 0.57
34 2 0.07
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.27
Consensus pattern (31 bp):
ATAAAATAAAAATAATTATAATAAAAATAAG
Found at i:44157 original size:4 final size:4
Alignment explanation
Indices: 44148--44184 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
44138 AATAAAACCC
44148 AAAT AAAT AAAT AAAT AAAT AAAT -AAT -AAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
44185 CATATATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 6 0.19
4 26 0.81
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:44212 original size:12 final size:12
Alignment explanation
Indices: 44195--44219 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44185 CATATATATT
44195 TATTATATAATA
1 TATTATATAATA
44207 TATTATATAATA
1 TATTATATAATA
44219 T
1 T
44220 TAATGTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TATTATATAATA
Found at i:45288 original size:12 final size:12
Alignment explanation
Indices: 45271--45295 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45261 TCTTTGGGGA
45271 CTTTTTCTTCTT
1 CTTTTTCTTCTT
45283 CTTTTTCTTCTT
1 CTTTTTCTTCTT
45295 C
1 C
45296 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:45504 original size:24 final size:24
Alignment explanation
Indices: 45470--45523 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
45460 CTGAAACATC
*
45470 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
45494 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
45518 ATCAAA
1 ATCAAA
45524 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:46381 original size:20 final size:20
Alignment explanation
Indices: 46347--46426 Score: 63
Period size: 20 Copynumber: 4.0 Consensus size: 20
46337 GAATTTGGAA
* *
46347 TATCGCAAAGCGATACTGAC
1 TATCGCAACGAGATACTGAC
*
46367 TATCGCAACGAGATAAT-AC
1 TATCGCAACGAGATACTGAC
* * *
46386 AAAATCGCAACGAGATTCTAAC
1 --TATCGCAACGAGATACTGAC
* *
46408 TTTCGCAACGAGATTCTGA
1 TATCGCAACGAGATACTGA
46427 AAATCGCAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
19 2 0.04
20 30 0.62
21 14 0.29
22 2 0.04
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.23
Consensus pattern (20 bp):
TATCGCAACGAGATACTGAC
Found at i:46433 original size:20 final size:19
Alignment explanation
Indices: 46368--46435 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 19
46358 GATACTGACT
46368 ATCGCAACGAGATAATAC-AAA
1 ATCGCAACGAGAT--T-CTAAA
*
46389 ATCGCAACGAGATTCTAACT
1 ATCGCAACGAGATTCTAA-A
*
46409 TTCGCAACGAGATTCTGAAA
1 ATCGCAACGAGATTCT-AAA
46429 ATCGCAA
1 ATCGCAA
46436 TCATCTTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 1 0.03
19 3 0.08
20 21 0.52
21 15 0.38
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.21
Consensus pattern (19 bp):
ATCGCAACGAGATTCTAAA
Found at i:46701 original size:20 final size:20
Alignment explanation
Indices: 46649--46695 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
46639 CAATGGGGAA
46649 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
46669 ATCGCAACGCGAATATGGCT
1 ATCGCAACGCGAAAATGGCT
46689 ATCGCAA
1 ATCGCAA
46696 TTCGAAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:46780 original size:33 final size:33
Alignment explanation
Indices: 46743--46839 Score: 122
Period size: 38 Copynumber: 2.8 Consensus size: 33
46733 GAAATGAAAA
*
46743 TCGCACTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
46776 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTC---TCG--TTGCGATTTTCATT
* *
46814 TCGCATTGCAATTTTCTCATTGCGAT
1 TCGCATTGCGATTTTCTCGTTGCGAT
46840 AGTCAGTTTC
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
33 22 0.39
35 2 0.04
36 3 0.05
38 29 0.52
ACGTcount: A:0.15, C:0.23, G:0.16, T:0.45
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
Found at i:46784 original size:19 final size:19
Alignment explanation
Indices: 46762--46829 Score: 127
Period size: 19 Copynumber: 3.6 Consensus size: 19
46752 GATTTTCTCG
46762 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
46781 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
46800 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
46819 TTGCAATTTTC
1 TTGCGATTTTC
46830 TCATTGCGAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.16, C:0.21, G:0.15, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:48460 original size:40 final size:42
Alignment explanation
Indices: 48416--48506 Score: 123
Period size: 40 Copynumber: 2.2 Consensus size: 42
48406 CCTCTTCAAC
*
48416 GATGACAGTGGCCTCTTGAACG-GTGG-GGGGACTCTTAAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTAAGG
* * *
48456 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTAAGG
*
48498 AATGACAGG
1 GATGACAGG
48507 TGAGTCGGGC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 20 0.47
41 3 0.07
42 20 0.47
ACGTcount: A:0.23, C:0.15, G:0.40, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTAAGG
Found at i:48868 original size:20 final size:20
Alignment explanation
Indices: 48843--48914 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
48833 GAAGAATAGT
*
48843 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
*
48863 TTACTTTCGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAA
* * * *
48883 TGACTATCGCAACGCGGAAA
1 TTACTTTCGCAACACGAAAA
* *
48903 TGACTATCGCAA
1 TTACTTTCGCAA
48915 TACGGAAATG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:48913 original size:40 final size:39
Alignment explanation
Indices: 48869--48955 Score: 102
Period size: 40 Copynumber: 2.2 Consensus size: 39
48859 AAACTTACTT
**
48869 TCGCAACGCGAAAATGACTATCGCAACGCGGAAATGACTA
1 TCGCAACGCGAAAATGACTATCGCAACGC-GAAATGAAAA
** * * *
48909 TCGCAATACGGAAATGGCTATCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAAATGACTATCGCAACGCGAAATGAAAA
48948 TCGCAACG
1 TCGCAACG
48956 ACAAAATCGC
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
39 14 0.37
40 24 0.63
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (39 bp):
TCGCAACGCGAAAATGACTATCGCAACGCGAAATGAAAA
Found at i:48920 original size:20 final size:20
Alignment explanation
Indices: 48869--48944 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 20
48859 AAACTTACTT
* *
48869 TCGCAACGCGAAAATGACTA
1 TCGCAATGCGGAAATGACTA
*
48889 TCGCAACGCGGAAATGACTA
1 TCGCAATGCGGAAATGACTA
* *
48909 TCGCAATACGGAAATGGCTA
1 TCGCAATGCGGAAATGACTA
48929 TCGCAATGC-GAAATGA
1 TCGCAATGCGGAAATGA
48945 AAATCGCAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
19 6 0.12
20 44 0.88
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (20 bp):
TCGCAATGCGGAAATGACTA
Found at i:49008 original size:19 final size:19
Alignment explanation
Indices: 48981--49096 Score: 126
Period size: 19 Copynumber: 6.6 Consensus size: 19
48971 GAAACACAAA
48981 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* * *
49000 TCACGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
49016 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
49033 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
49052 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
49068 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
49085 TCGCATTGCGAT
1 TCGCATTGCGAT
49097 AGCCATTTCC
Statistics
Matches: 80, Mismatches: 7, Indels: 20
0.75 0.07 0.19
Matches are distributed among these distances:
14 12 0.15
15 6 0.08
16 7 0.09
17 8 0.10
18 6 0.08
19 41 0.51
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:49104 original size:52 final size:52
Alignment explanation
Indices: 48981--49116 Score: 218
Period size: 52 Copynumber: 2.6 Consensus size: 52
48971 GAAACACAAA
*
48981 TCGCATTGCGATTTTCATTTCACGTTGCGATTTTGTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTGTCGTTGCGATTTTCATT
*
49033 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTGTCGTTGCGATTTTCATT
***
49085 TCGCATTGCGATAGCCATTTCCGCGTTGCGAT
1 TCGCATTGCGATTTTCATTT-CGCGTTGCGAT
49117 AGTCATTTTC
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
52 67 0.87
53 10 0.13
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTGTCGTTGCGATTTTCATT
Found at i:49115 original size:20 final size:19
Alignment explanation
Indices: 49081--49135 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
49071 TTGCGATTTT
*
49081 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
49100 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
49120 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
49136 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:49699 original size:18 final size:18
Alignment explanation
Indices: 49676--49723 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
49666 CGGGTCGATC
49676 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
49694 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
49712 AGGTGATGGCTC
1 AGGTGATGGCTC
49724 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:51065 original size:20 final size:20
Alignment explanation
Indices: 51040--51082 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
51030 AATAGTTTCT
51040 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
51060 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
51080 GAA
1 GAA
51083 TTTGACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:51388 original size:22 final size:22
Alignment explanation
Indices: 51361--51404 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
51351 GATGGAGATA
51361 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
51383 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
51405 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:51690 original size:41 final size:41
Alignment explanation
Indices: 51571--51705 Score: 155
Period size: 41 Copynumber: 3.3 Consensus size: 41
51561 CGCTTTGAAA
* * *
51571 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* * ** * * *
51612 ATTGAGTTGCGAAATT-AAGTATCGAGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
51652 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
51693 ACCGCGTTGCGAT
1 ATCGCGTTGCGAT
51706 AGTCAGTACC
Statistics
Matches: 74, Mismatches: 19, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
40 32 0.43
41 42 0.57
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:51722 original size:81 final size:81
Alignment explanation
Indices: 51571--51724 Score: 200
Period size: 81 Copynumber: 1.9 Consensus size: 81
51561 CGCTTTGAAA
* ** * *
51571 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGTATTGAGTTGCGAAATTAAGTATCG
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTACCGAGTTGCGAAAGTAAGTACCG
51636 AGTTGCGAAAGTCAGT
66 AGTTGCGAAAGTCAGT
* * * * * *
51652 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTACCGCGTTGCGATAGTCAGTACCG
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTACCGAGTTGCGAAAGTAAGTACCG
*
51717 CGTTGCGA
66 AGTTGCGA
51725 TTTTCCAAAT
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
81 61 1.00
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (81 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTACCGAGTTGCGAAAGTAAGTACCG
AGTTGCGAAAGTCAGT
Found at i:51725 original size:20 final size:20
Alignment explanation
Indices: 51591--51725 Score: 128
Period size: 20 Copynumber: 6.7 Consensus size: 20
51581 GATTATGTAT
* *
51591 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * * * *
51611 TATTGAGTTGCGAAATTAAG
1 TATCGCGTTGCGATAGTCAG
* *
51631 TATCGAGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
51651 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
51672 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
51692 TACCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
51712 TACCGCGTTGCGAT
1 TATCGCGTTGCGAT
51726 TTTCCAAATT
Statistics
Matches: 97, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
19 3 0.03
20 78 0.80
21 14 0.14
22 2 0.02
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:51800 original size:20 final size:21
Alignment explanation
Indices: 51719--51807 Score: 144
Period size: 21 Copynumber: 4.3 Consensus size: 21
51709 CAGTACCGCG
51719 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
51740 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
51761 TTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTCCAAATTCGCA
* **
51782 TTGCGA-TTTACTTATTCGCA
1 TTGCGATTTTCCAAATTCGCA
51802 TTGCGA
1 TTGCGA
51808 ATTGGGAAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
20 17 0.26
21 48 0.74
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGCA
Found at i:51822 original size:41 final size:42
Alignment explanation
Indices: 51719--51822 Score: 102
Period size: 41 Copynumber: 2.5 Consensus size: 42
51709 CAGTACCGCG
* * * *
51719 TTGCGATTTTCCAAATTCGCATTGCGATTTTCCAAATTCGCA
1 TTGCGAATTGCCAAAATCGCATTGCGATTTTACAAATTCGCA
* * * **
51761 TTGCGATTTTCCAAATTCGCATTGCGA-TTTACTTATTCGCA
1 TTGCGAATTGCCAAAATCGCATTGCGATTTTACAAATTCGCA
**
51802 TTGCGAATTGGGAAAATCGCA
1 TTGCGAATTGCCAAAATCGCA
51823 ACGCGAAATT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
41 27 0.50
42 27 0.50
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (42 bp):
TTGCGAATTGCCAAAATCGCATTGCGATTTTACAAATTCGCA
Found at i:51849 original size:21 final size:22
Alignment explanation
Indices: 51797--51849 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
51787 ATTTACTTAT
51797 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
51818 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
51839 TCGCATTGCGA
1 TCGCATTGCGA
51850 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:52188 original size:29 final size:29
Alignment explanation
Indices: 52151--52207 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
52141 ATTTTAACTT
* **
52151 TAAAATTTTTAAAAATAAATTTAAATTTA
1 TAAAATTTTAAAAAATAAAAATAAATTTA
52180 TAAAATTTTAAAAAATAAAAATAAATTT
1 TAAAATTTTAAAAAATAAAAATAAATTT
52208 TTAATAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
TAAAATTTTAAAAAATAAAAATAAATTTA
Found at i:53433 original size:17 final size:17
Alignment explanation
Indices: 53413--53445 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53403 ATATTTATTT
*
53413 ATATAAAATATAATATA
1 ATATAAAAAATAATATA
53430 ATATAAAAAATAATAT
1 ATATAAAAAATAATAT
53446 TATGGTAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATAAAAAATAATATA
Found at i:53491 original size:17 final size:16
Alignment explanation
Indices: 53457--53500 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
53447 ATGGTAGTAA
53457 AATACTA-TTTTAAAT
1 AATACTATTTTTAAAT
53472 AATTA-TATTTTTACAAT
1 AA-TACTATTTTTA-AAT
53489 AATACTATTTTT
1 AATACTATTTTT
53501 TCATCCCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.16
16 9 0.36
17 12 0.48
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (16 bp):
AATACTATTTTTAAAT
Found at i:53499 original size:16 final size:15
Alignment explanation
Indices: 53457--53499 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
53447 ATGGTAGTAA
53457 AATACTATTTTAAAT
1 AATACTATTTTAAAT
53472 AATTA-TATTTTTACAAT
1 AA-TACTA-TTTTA-AAT
53489 AATACTATTTT
1 AATACTATTTT
53500 TTCATCCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
15 4 0.17
16 13 0.54
17 7 0.29
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (15 bp):
AATACTATTTTAAAT
Found at i:53555 original size:16 final size:16
Alignment explanation
Indices: 53509--53575 Score: 66
Period size: 15 Copynumber: 4.2 Consensus size: 16
53499 TTTCATCCCA
53509 TAAAATTAT-AAATAT
1 TAAAATTATAAAATAT
**
53524 TAAAA-TATTGAATAT
1 TAAAATTATAAAATAT
53539 TAAAATTATAAAATAT
1 TAAAATTATAAAATAT
* *
53555 TTAAATTCTCAAAATTAT
1 TAAAATTAT-AAAA-TAT
53573 TAA
1 TAA
53576 TATTTTAGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
14 3 0.07
15 15 0.36
16 15 0.36
17 4 0.10
18 5 0.12
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.40
Consensus pattern (16 bp):
TAAAATTATAAAATAT
Found at i:54696 original size:21 final size:21
Alignment explanation
Indices: 54667--54719 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
54657 ATTCTGACTA
54667 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
54688 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
54709 TCGCAATGCGA
1 TCGCATTGCGA
54720 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:54734 original size:20 final size:20
Alignment explanation
Indices: 54709--54802 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
54699 TTTTCCTAAT
*
54709 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATAAGTAAA
* *
54729 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* *
54749 TCGCAATACGAATTAAGAAAA
1 TCGCAATGCGAA-TAAGTAAA
*
54770 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATAAGTAAA
*
54790 TCGCAATACGAAT
1 TCGCAATGCGAAT
54803 CTGACTATCG
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
20 44 0.71
21 18 0.29
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:54771 original size:41 final size:41
Alignment explanation
Indices: 54709--54802 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
54699 TTTTCCTAAT
* * * *
54709 TCGCAATGCGAA-TACGTAAATCGCAACGCGATTAAGTAAA
1 TCGCAATACGAATTAAGAAAATCGCAACGCGAATAAGTAAA
* *
54749 TCGCAATACGAATTAAGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATACGAATTAAGAAAATCGCAACGCGAATAAGTAAA
54790 TCGCAATACGAAT
1 TCGCAATACGAAT
54803 CTGACTATCG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 11 0.23
41 36 0.77
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.20
Consensus pattern (41 bp):
TCGCAATACGAATTAAGAAAATCGCAACGCGAATAAGTAAA
Found at i:54962 original size:20 final size:20
Alignment explanation
Indices: 54933--54976 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
54923 TCATAACCTC
* *
54933 AAACCTAAAATCGCAACTCG
1 AAACCAAAAATCGCAACGCG
54953 AAACCAAAAATCGCAACGCG
1 AAACCAAAAATCGCAACGCG
54973 AAAC
1 AAAC
54977 TATAATCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.30, G:0.11, T:0.09
Consensus pattern (20 bp):
AAACCAAAAATCGCAACGCG
Found at i:55073 original size:21 final size:20
Alignment explanation
Indices: 55019--55095 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
55009 GCAATTTTGT
*
55019 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCA
**
55038 CGTTGCGATAGTCATTTTTCA
1 CGTTGCGATTTTCA-TTTTCA
* *
55059 CGTTGCGATTTTCATTCTCT
1 CGTTGCGATTTTCATTTTCA
*
55079 CGTTGCGATTTTTATTT
1 CGTTGCGATTTTCATTT
55096 CAACCAAAAG
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
19 12 0.26
20 19 0.40
21 16 0.34
ACGTcount: A:0.13, C:0.19, G:0.18, T:0.49
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCA
Found at i:57039 original size:94 final size:92
Alignment explanation
Indices: 56791--57067 Score: 390
Period size: 94 Copynumber: 3.1 Consensus size: 92
56781 TAGATTGCTT
* * * *
56791 AGTAAATTTATTCGGCTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTC-GTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
56852 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
65 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
*
56881 AGTATATTTG---GTTGCTGCCAATTCTGCT-AACTGTGTATTCTTTAACACTGTGAAGTTAGTA
1 AGTAAATTTGTTCGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTA
56942 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * *
56970 AGTAAATTTGTTCGTTTGCTGCCAATTCTGTTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTGTTCG-TTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
57035 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
57063 AGTAA
1 AGTAA
57068 TGCAATCCAT
Statistics
Matches: 168, Mismatches: 9, Indels: 17
0.87 0.05 0.09
Matches are distributed among these distances:
85 3 0.02
86 16 0.10
87 3 0.02
88 22 0.13
89 36 0.21
90 8 0.05
92 1 0.01
93 22 0.13
94 57 0.34
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (92 bp):
AGTAAATTTGTTCGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:57186 original size:20 final size:19
Alignment explanation
Indices: 57156--57270 Score: 114
Period size: 20 Copynumber: 6.2 Consensus size: 19
57146 TCTTTTGGTT
*
57156 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
57175 GAGAATGCAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
*
57195 GAAACGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
57214 GAAATGAAAATCGCAA--T
1 GAAATGAAAATCGCAACGC
*
57231 G--A-CAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
57247 GAAACCAAAAATCGCAACGC
1 GAAA-TGAAAATCGCAACGC
57267 GAAA
1 GAAA
57271 CTATAATCGC
Statistics
Matches: 80, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 32 0.40
20 34 0.43
ACGTcount: A:0.49, C:0.23, G:0.20, T:0.09
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:57204 original size:39 final size:38
Alignment explanation
Indices: 57156--57280 Score: 116
Period size: 39 Copynumber: 3.4 Consensus size: 38
57146 TCTTTTGGTT
* *
57156 GAAATGAAAATCGCAACGAGAGAATGCAAATCGCAACGC
1 GAAACGAAAATCGCAACGAGA-AATGAAAATCGCAACGC
* *
57195 GAAACGAAAATCGCAACGCGAAATGAAAATCGCAA--T
1 GAAACGAAAATCGCAACGAGAAATGAAAATCGCAACGC
* **
57231 G--AC-AAAATCGCAACGCGAAACCAAAAATCGCAACGC
1 GAAACGAAAATCGCAACGAGAAA-TGAAAATCGCAACGC
* *
57267 GAAACTATAATCGC
1 GAAACGAAAATCGC
57281 GTTGCGATTT
Statistics
Matches: 72, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
33 17 0.24
34 12 0.17
36 2 0.03
38 15 0.21
39 26 0.36
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.10
Consensus pattern (38 bp):
GAAACGAAAATCGCAACGAGAAATGAAAATCGCAACGC
Found at i:57271 original size:20 final size:19
Alignment explanation
Indices: 57156--57271 Score: 116
Period size: 19 Copynumber: 6.3 Consensus size: 19
57146 TCTTTTGGTT
* *
57156 GAAATGAAAATCGCAACGA
1 GAAACGAAAATCGCAACGC
* *
57175 GAGAATGCAAATCGCAACGC
1 GA-AACGAAAATCGCAACGC
57195 GAAACGAAAATCGCAACGC
1 GAAACGAAAATCGCAACGC
* *
57214 GAAATGAAAATCGCAA--T
1 GAAACGAAAATCGCAACGC
57231 G--AC-AAAATCGCAACGC
1 GAAACGAAAATCGCAACGC
*
57247 GAAACCAAAAATCGCAACGC
1 GAAA-CGAAAATCGCAACGC
57267 GAAAC
1 GAAAC
57272 TATAATCGCG
Statistics
Matches: 82, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 34 0.41
20 34 0.41
ACGTcount: A:0.48, C:0.23, G:0.20, T:0.09
Consensus pattern (19 bp):
GAAACGAAAATCGCAACGC
Found at i:59231 original size:33 final size:33
Alignment explanation
Indices: 59186--59279 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 33
59176 AAAAATGACT
* * * *
59186 ATCGCAATGCGAAACGAAAATTACAACGAGAGA
1 ATCGCAACGCGAAACGAAAATCACAACGACAAA
* *
59219 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAACGAAAATCACAACGACAAA
* *
59252 ATCGCAACGCGAAACTAAAATCGCAACG
1 ATCGCAACGCGAAACGAAAATCACAACG
59280 CGAAACCGCT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAACGAAAATCACAACGACAAA
Found at i:59285 original size:19 final size:19
Alignment explanation
Indices: 59218--59285 Score: 85
Period size: 19 Copynumber: 3.8 Consensus size: 19
59208 ACAACGAGAG
59218 AATCGCAACGCGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
59237 AATCGCAA--CG--AC-AA
1 AATCGCAACGCGAAACTAA
59251 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
59270 AATCGCAACGCGAAAC
1 AATCGCAACGCGAAAC
59286 CGCTTTGCGA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
14 10 0.23
15 1 0.02
16 2 0.05
17 2 0.05
18 2 0.05
19 26 0.60
ACGTcount: A:0.47, C:0.26, G:0.18, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:59337 original size:33 final size:33
Alignment explanation
Indices: 59290--59395 Score: 167
Period size: 33 Copynumber: 3.2 Consensus size: 33
59280 CGAAACCGCT
* * *
59290 TTGCGATTCCCTCGTTGCGATTTTTATTTCTCA
1 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
*
59323 TTGCGATTCTCTCGTTGCAATTTTCATTTCGCA
1 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
*
59356 TTGCGATTCTTTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
59389 TTGCGAT
1 TTGCGAT
59396 AGTCATTTCC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 67 1.00
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.47
Consensus pattern (33 bp):
TTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:59394 original size:19 final size:19
Alignment explanation
Indices: 59304--59415 Score: 82
Period size: 19 Copynumber: 6.4 Consensus size: 19
59294 GATTCCCTCG
* *
59304 TTGCGATTTTTATTTCTCA
1 TTGCGATTTTCATTTCGCA
*
59323 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
59337 TTGCAATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
59356 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
59370 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
59389 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
59409 TTGCGAT
1 TTGCGAT
59416 AGACATTAAG
Statistics
Matches: 73, Mismatches: 9, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
14 11 0.15
16 14 0.19
17 14 0.19
19 24 0.33
20 10 0.14
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:59414 original size:20 final size:19
Alignment explanation
Indices: 59368--59422 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
59358 GCGATTCTTT
**
59368 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
59387 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
59407 CGTTGCGATAGACATT
1 CGTTGCGATAGTCATT
59423 AAGATGATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:61952 original size:24 final size:24
Alignment explanation
Indices: 61925--61978 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
61915 CTGAAAAATC
61925 ATCAAAATCCGAGTATTGAACAAG
1 ATCAAAATCCGAGTATTGAACAAG
* * *
61949 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGAACAAG
61973 ATCAAA
1 ATCAAA
61979 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGAACAAG
Found at i:62842 original size:20 final size:20
Alignment explanation
Indices: 62819--63282 Score: 446
Period size: 20 Copynumber: 23.0 Consensus size: 20
62809 AATTCAGTAT
62819 TGCGATTTAC-TAAATCGCAA
1 TGCGA-TTACGTAAATCGCAA
*
62839 TGCGATTACATAAATCG-AA
1 TGCGATTACGTAAATCGCAA
* *
62858 GTGCGAATTAGGAAAATCGCAA
1 -TGCG-ATTACGTAAATCGCAA
62880 TGCGATTACGTAAATCG-AA
1 TGCGATTACGTAAATCGCAA
* *
62899 GTGCGAATTAGGAAAATCGCAA
1 -TGCG-ATTACGTAAATCGCAA
62921 TGCGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
* *
62941 TGCGAATTAGGAAAATCGCAA
1 TGCG-ATTACGTAAATCGCAA
62962 TGCGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
* *
62982 TGCGAATTAGGAAAATCGCAA
1 TGCG-ATTACGTAAATCGCAA
63003 TGCGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
*
63023 TGCGAATACGT-AATCGCAA
1 TGCGATTACGTAAATCGCAA
63042 TGCGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
*
63062 TGCGAATACGT-AATCGCAA
1 TGCGATTACGTAAATCGCAA
63081 TGCGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
*
63101 TGCGAATACGT-AATCGCAA
1 TGCGATTACGTAAATCGCAA
*
63120 TGCGATTTACGT-AATCGCAT
1 TGCGA-TTACGTAAATCGCAA
* * * *
63140 TGCGATTTTCCTAATTCGCAT
1 TGCGA-TTACGTAAATCGCAA
* *
63161 TGCAATTTACGT-AATCGCAT
1 TGCGA-TTACGTAAATCGCAA
* * * *
63181 TGCGATTTTCCTAATTCGCAT
1 TGCGA-TTACGTAAATCGCAA
*
63202 TGCGATTTACGT-AATCGCAT
1 TGCGA-TTACGTAAATCGCAA
* *
63222 TGCGATTTACGT-ATTCGCAT
1 TGCGA-TTACGTAAATCGCAA
* *
63242 TGCGAATTACGT-ATTCGCAT
1 TGCG-ATTACGTAAATCGCAA
* *
63262 TGCGAATTAGGAAAATCGCAA
1 TGCG-ATTACGTAAATCGCAA
63283 CGTGAATTTG
Statistics
Matches: 385, Mismatches: 43, Indels: 31
0.84 0.09 0.07
Matches are distributed among these distances:
19 57 0.15
20 219 0.57
21 105 0.27
22 4 0.01
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (20 bp):
TGCGATTACGTAAATCGCAA
Found at i:62875 original size:41 final size:41
Alignment explanation
Indices: 62830--63282 Score: 473
Period size: 41 Copynumber: 11.2 Consensus size: 41
62820 GCGATTTACT
*
62830 AAATCGCAATGCGATTACATAAATCG-AAGTGCGAATTAGGA
1 AAATCGCAATGCGATTACGTAAATCGCAA-TGCGAATTAGGA
62871 AAATCGCAATGCGATTACGTAAATCG-AAGTGCGAATTAGGA
1 AAATCGCAATGCGATTACGTAAATCGCAA-TGCGAATTAGGA
62912 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
62953 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
*
62994 AAATCGCAATGCGATTACGTAAATCGCAATGCGAA-TACG-
1 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
* *
63033 TAATCGCAATGCGATTACGTAAATCGCAATGCGAA-TACG-
1 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
* *
63072 TAATCGCAATGCGATTACGTAAATCGCAATGCGAA-TACG-
1 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
* * * ****
63111 TAATCGCAATGCGATTTACGT-AATCGCATTGCGATTTTCCT
1 AAATCGCAATGCGA-TTACGTAAATCGCAATGCGAATTAGGA
* * * * * ****
63152 AATTCGCATTGCAATTTACGT-AATCGCATTGCGATTTTCCT
1 AAATCGCAATGCGA-TTACGTAAATCGCAATGCGAATTAGGA
* * * * *
63193 AATTCGCATTGCGATTTACGT-AATCGCATTGCGATTTACG-
1 AAATCGCAATGCGA-TTACGTAAATCGCAATGCGAATTAGGA
* * * * *
63233 TATTCGCATTGCGAATTACGT-ATTCGCATTGCGAATTAGGA
1 AAATCGCAATGCG-ATTACGTAAATCGCAATGCGAATTAGGA
63274 AAATCGCAA
1 AAATCGCAA
63283 CGTGAATTTG
Statistics
Matches: 385, Mismatches: 21, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
39 103 0.27
40 45 0.12
41 235 0.61
42 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (41 bp):
AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
Found at i:63289 original size:21 final size:21
Alignment explanation
Indices: 63265--63308 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
63255 TTCGCATTGC
63265 GAATTAGGAAAATCGCAACGT
1 GAATTAGGAAAATCGCAACGT
* * *
63286 GAATTTGGGAAATCGCAATGT
1 GAATTAGGAAAATCGCAACGT
63307 GA
1 GA
63309 TAGTCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.27, T:0.23
Consensus pattern (21 bp):
GAATTAGGAAAATCGCAACGT
Found at i:68907 original size:167 final size:167
Alignment explanation
Indices: 68631--68964 Score: 668
Period size: 167 Copynumber: 2.0 Consensus size: 167
68621 CAAAGGGTCT
68631 GAACTTTTTGCTGCAATACACCAATGAATTGCAGGAACCCGTTCTCCCGGGTGCTTTCTTCGGGC
1 GAACTTTTTGCTGCAATACACCAATGAATTGCAGGAACCCGTTCTCCCGGGTGCTTTCTTCGGGC
68696 TAAAGCTATAGGTCTGATGCCTATGATTGACCAGGTATGCATTAGCCACTGATTAAAAATTTAAA
66 TAAAGCTATAGGTCTGATGCCTATGATTGACCAGGTATGCATTAGCCACTGATTAAAAATTTAAA
68761 ACACTTGTACAATGTTTAAGACCAGATGAGAAAAATA
131 ACACTTGTACAATGTTTAAGACCAGATGAGAAAAATA
68798 GAACTTTTTGCTGCAATACACCAATGAATTGCAGGAACCCGTTCTCCCGGGTGCTTTCTTCGGGC
1 GAACTTTTTGCTGCAATACACCAATGAATTGCAGGAACCCGTTCTCCCGGGTGCTTTCTTCGGGC
68863 TAAAGCTATAGGTCTGATGCCTATGATTGACCAGGTATGCATTAGCCACTGATTAAAAATTTAAA
66 TAAAGCTATAGGTCTGATGCCTATGATTGACCAGGTATGCATTAGCCACTGATTAAAAATTTAAA
68928 ACACTTGTACAATGTTTAAGACCAGATGAGAAAAATA
131 ACACTTGTACAATGTTTAAGACCAGATGAGAAAAATA
68965 AAATCTGAAC
Statistics
Matches: 167, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
167 167 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (167 bp):
GAACTTTTTGCTGCAATACACCAATGAATTGCAGGAACCCGTTCTCCCGGGTGCTTTCTTCGGGC
TAAAGCTATAGGTCTGATGCCTATGATTGACCAGGTATGCATTAGCCACTGATTAAAAATTTAAA
ACACTTGTACAATGTTTAAGACCAGATGAGAAAAATA
Found at i:69133 original size:26 final size:26
Alignment explanation
Indices: 69097--69149 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
69087 AGATTCGCCG
*
69097 CTTCTTTGAAGACTGTAAGTTTAATC
1 CTTCTTTGAAGACTGCAAGTTTAATC
69123 CTTCTTTGAAGACTGCAAGTTTAATC
1 CTTCTTTGAAGACTGCAAGTTTAATC
69149 C
1 C
69150 ATGTGAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (26 bp):
CTTCTTTGAAGACTGCAAGTTTAATC
Found at i:70394 original size:16 final size:16
Alignment explanation
Indices: 70373--70410 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
70363 GAAGAATTTA
70373 TTTAATTTTAATTAAT
1 TTTAATTTTAATTAAT
*
70389 TTTAATTTTAATTATT
1 TTTAATTTTAATTAAT
70405 TTTAAT
1 TTTAAT
70411 ATATTAGGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTAATTTTAATTAAT
Found at i:70443 original size:17 final size:17
Alignment explanation
Indices: 70421--70471 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
70411 ATATTAGGTC
70421 AATAAATTAATAAATAT
1 AATAAATTAATAAATAT
*
70438 AATAAATCAATAACATA-
1 AATAAATTAATAA-ATAT
70455 AAT-AATT-A-AAATAT
1 AATAAATTAATAAATAT
70469 AAT
1 AAT
70472 GTTTTTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
13 3 0.10
14 5 0.17
15 1 0.03
16 3 0.10
17 15 0.50
18 3 0.10
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (17 bp):
AATAAATTAATAAATAT
Found at i:71789 original size:27 final size:26
Alignment explanation
Indices: 71759--71824 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 26
71749 TATTAACAAC
71759 TGAATTAGTTTAAGTTATAAGTAATTT
1 TGAATTAGTTTAAGTTATAAGTAA-TT
71786 TGAATTAGTTTAAGTTATAAGTAATT
1 TGAATTAGTTTAAGTTATAAGTAATT
71812 TGATATTA-TTTAA
1 TGA-ATTAGTTTAA
71825 ATAAGAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
26 10 0.26
27 28 0.74
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (26 bp):
TGAATTAGTTTAAGTTATAAGTAATT
Found at i:75287 original size:20 final size:20
Alignment explanation
Indices: 75258--75315 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
75248 GAACATCTTA
*
75258 GAACCAGTTTGAGTTAACTC
1 GAACCGGTTTGAGTTAACTC
*
75278 GAACCGGTTTGAGTCAACTC
1 GAACCGGTTTGAGTTAACTC
* * *
75298 GGACCGATATGAGTTAAC
1 GAACCGGTTTGAGTTAAC
75316 CCAAAACGGC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (20 bp):
GAACCGGTTTGAGTTAACTC
Found at i:81356 original size:20 final size:20
Alignment explanation
Indices: 81331--81442 Score: 118
Period size: 20 Copynumber: 5.5 Consensus size: 20
81321 TTTTCCCAAT
* * *
81331 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAGGGAAA
*
81351 TCGCAACGCGAATTGGGAAA
1 TCGCAACGCGAATAGGGAAA
* * *
81371 TTCGCAATGCGAATAAGTAAA
1 -TCGCAACGCGAATAGGGAAA
*
81392 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAATAGGG-AAA
81413 TCGCAACGCGAAT-GGGAAA
1 TCGCAACGCGAATAGGGAAA
*
81432 TCGCAATGCGA
1 TCGCAACGCGA
81443 TACTGACTAT
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
19 13 0.17
20 32 0.42
21 32 0.42
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (20 bp):
TCGCAACGCGAATAGGGAAA
Found at i:81373 original size:41 final size:41
Alignment explanation
Indices: 81328--81442 Score: 178
Period size: 41 Copynumber: 2.8 Consensus size: 41
81318 CGATTTTCCC
81328 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
81369 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
* * * * *
81410 AAATCGCAACGCGAAT-GGGAAATCGCAATGCGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGA
81443 TACTGACTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
40 14 0.20
41 55 0.80
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:81377 original size:21 final size:20
Alignment explanation
Indices: 81348--81442 Score: 120
Period size: 21 Copynumber: 4.7 Consensus size: 20
81338 GCGAATAAGT
81348 AAATCGCAACGCGAATTGGG
1 AAATCGCAACGCGAATTGGG
* ** *
81368 AAATTCGCAATGCGAATAAGT
1 AAA-TCGCAACGCGAATTGGG
81389 AAATCGCAACGCGAATTGGG
1 AAATCGCAACGCGAATTGGG
81409 AAAATCGCAACGCGAA-TGGG
1 -AAATCGCAACGCGAATTGGG
*
81429 AAATCGCAATGCGA
1 AAATCGCAACGCGA
81443 TACTGACTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
19 13 0.20
20 20 0.31
21 31 0.48
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.16
Consensus pattern (20 bp):
AAATCGCAACGCGAATTGGG
Found at i:81456 original size:20 final size:20
Alignment explanation
Indices: 81431--81545 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
81421 CGAATGGGAA
81431 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * **
81451 ATCGCAATGCGATAATAAAAA
1 ATCGCAATGCGATACT-GACT
* * *
81472 ATCGCAACGAGATACTTACT
1 ATCGCAATGCGATACTGACT
*
81492 TTCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * * *
81512 TTCGCAACGCGGTAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
81532 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
81546 TTTCAAAGCG
Statistics
Matches: 72, Mismatches: 20, Indels: 5
0.74 0.21 0.05
Matches are distributed among these distances:
19 2 0.03
20 46 0.64
21 24 0.33
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:81741 original size:22 final size:22
Alignment explanation
Indices: 81713--81756 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
81703 CACTCTCTCA
81713 CCCATCTCCAACGAAATCCGTC
1 CCCATCTCCAACGAAATCCGTC
**
81735 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCAACGAAATCCGTC
81757 TATCTAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCAACGAAATCCGTC
Found at i:82044 original size:20 final size:20
Alignment explanation
Indices: 82019--82056 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
82009 CGATTCTCTC
82019 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
82039 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
82057 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:83394 original size:18 final size:18
Alignment explanation
Indices: 83373--83417 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
83363 TCCACTTCGG
*
83373 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
83391 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
83409 GAGCCATCA
1 GAGCCATCA
83418 TGATCGACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:83913 original size:20 final size:20
Alignment explanation
Indices: 83888--83933 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
83878 TAGTTTACTT
83888 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
83908 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
83928 TCGCAA
1 TCGCAA
83934 TGCGAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:83949 original size:19 final size:19
Alignment explanation
Indices: 83927--83990 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
83917 GGAAATGGCT
83927 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATAAAA
*
83946 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATAAAA
* *
83960 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATAAAA
83979 ATCGCAATGCGA
1 ATCGCAATGCGA
83991 TTTGTGTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 10 0.27
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 21 0.57
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATAAAA
Found at i:84061 original size:20 final size:19
Alignment explanation
Indices: 84027--84081 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
84017 GTTGCGATTT
*
84027 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
84046 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
84066 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
84082 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:86107 original size:33 final size:33
Alignment explanation
Indices: 86062--86176 Score: 133
Period size: 33 Copynumber: 3.4 Consensus size: 33
86052 AAAACAGACT
* **
86062 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGGAAATCGCAACGAGAAA
*
86095 ATCGCAATGCGAAAT-GAAATCGCAATGCGAAATGATA
1 ATCGCAATGCGAAATGGAAATCGCAA--CG--A-GAAA
*
86132 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGGAAATCGCAACGAGAAA
86165 ATCGCAATGCGA
1 ATCGCAATGCGA
86177 TTTTCATTTC
Statistics
Matches: 70, Mismatches: 6, Indels: 12
0.80 0.07 0.14
Matches are distributed among these distances:
32 8 0.11
33 29 0.41
34 3 0.04
36 3 0.04
37 18 0.26
38 9 0.13
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGGAAATCGCAACGAGAAA
Found at i:86113 original size:19 final size:19
Alignment explanation
Indices: 86091--86176 Score: 121
Period size: 19 Copynumber: 4.8 Consensus size: 19
86081 ATCGCAACGA
86091 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
86110 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
86128 GATAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
86147 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
86161 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
86177 TTTTCATTTC
Statistics
Matches: 61, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
14 11 0.18
15 1 0.02
16 2 0.03
17 2 0.03
18 18 0.30
19 27 0.44
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:86252 original size:20 final size:20
Alignment explanation
Indices: 86195--86252 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
86185 TCGCATTGCG
* *
86195 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
86215 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
86235 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
86253 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:87337 original size:24 final size:24
Alignment explanation
Indices: 87310--87363 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
87300 GTATTCGAAA
* *
87310 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
87334 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
87358 TTTGAT
1 TTTGAT
87364 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:87555 original size:12 final size:12
Alignment explanation
Indices: 87538--87562 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
87528 ATATAATCCT
87538 GAAGAAGAAAAA
1 GAAGAAGAAAAA
87550 GAAGAAGAAAAA
1 GAAGAAGAAAAA
87562 G
1 G
87563 TCCCTGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:89969 original size:21 final size:21
Alignment explanation
Indices: 89903--89969 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
89893 GTGAATCGGG
*
89903 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
89923 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
89945 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
89966 CTCT
1 CTCT
89970 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:89988 original size:42 final size:41
Alignment explanation
Indices: 89903--90025 Score: 104
Period size: 42 Copynumber: 2.9 Consensus size: 41
89893 GTGAATCGGG
* * * * *
89903 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
89945 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * * *
89987 CTCTTCAACGATAGGAGTGGAATCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
90026 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.24, C:0.17, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:92051 original size:20 final size:18
Alignment explanation
Indices: 92019--92179 Score: 68
Period size: 20 Copynumber: 8.8 Consensus size: 18
92009 TCTTTTGGTT
92019 GAAATGAAATCGCAACGA
1 GAAATGAAATCGCAACGA
*
92037 GATAATGAGAATCGCAACGCG
1 GA-AATGA-AATCGCAACG-A
*
92058 GAAATGACTATCGCAACGA
1 GAAATGA-AATCGCAACGA
*
92077 G--A-G-AATCGCAACGC
1 GAAATGAAATCGCAACGA
* * *
92091 GAAATGACTATCGCGACCA
1 GAAATGA-AATCGCAACGA
* * *
92110 G--A--CAATCACAACGC
1 GAAATGAAATCGCAACGA
*
92124 GAAATGAAAATCGCAACCGC
1 GAAATG-AAATCGCAA-CGA
* *
92144 GAAATAAAAAATCGCAACGC
1 GAAAT--GAAATCGCAACGA
92164 GAAATGAAAATCGCAA
1 GAAATG-AAATCGCAA
92180 TGTGATTTTG
Statistics
Matches: 106, Mismatches: 20, Indels: 33
0.67 0.13 0.21
Matches are distributed among these distances:
14 17 0.16
16 3 0.03
17 3 0.03
18 2 0.02
19 30 0.28
20 40 0.38
21 11 0.10
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (18 bp):
GAAATGAAATCGCAACGA
Found at i:92100 original size:33 final size:33
Alignment explanation
Indices: 92043--92141 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
92033 ACGAGATAAT
*
92043 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
92077 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* * **
92110 GACAATCACAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
92142 GCGAAATAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 44 0.76
34 14 0.24
ACGTcount: A:0.40, C:0.26, G:0.22, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:92205 original size:19 final size:19
Alignment explanation
Indices: 92183--92224 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
92173 ATCGCAATGT
*
92183 GATTTTGGTTTCGCGTTGC
1 GATTTTGATTTCGCGTTGC
*
92202 GATTTTTATTTCGCGTTGC
1 GATTTTGATTTCGCGTTGC
92221 GATT
1 GATT
92225 ATCTCGTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.10, C:0.14, G:0.26, T:0.50
Consensus pattern (19 bp):
GATTTTGATTTCGCGTTGC
Found at i:92800 original size:20 final size:20
Alignment explanation
Indices: 92775--92826 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
92765 CGCTATGTAA
*
92775 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTAAGT
92795 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
*
92815 ATCTCGTTGCGA
1 ATCGCGTTGCGA
92827 TTTTTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTAAGT
Found at i:92861 original size:21 final size:20
Alignment explanation
Indices: 92837--92926 Score: 90
Period size: 21 Copynumber: 4.4 Consensus size: 20
92827 TTTTTTATTA
92837 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTT-CCAAT
* * **
92858 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCAAT
92878 TCGCATTGCGAATTTTCCAAT
1 TCGCATTGCG-ATTTTCCAAT
* * **
92899 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCAAT
92919 TCGCATTG
1 TCGCATTG
92927 TGAATTGGGA
Statistics
Matches: 55, Mismatches: 13, Indels: 3
0.77 0.18 0.04
Matches are distributed among these distances:
20 26 0.47
21 29 0.53
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATTTTCCAAT
Found at i:92881 original size:20 final size:20
Alignment explanation
Indices: 92856--92922 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
92846 GATTTTCCCA
92856 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
* * **
92876 ATTCGCATTGCGAATTTTCCA
1 ATTCGCGTTGCG-ATTTACTT
92897 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
92917 ATTCGC
1 ATTCGC
92923 ATTGTGAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACTT
Found at i:92882 original size:41 final size:41
Alignment explanation
Indices: 92819--92932 Score: 169
Period size: 41 Copynumber: 2.8 Consensus size: 41
92809 GTAAGTATCT
*
92819 CGTTGCGATTT-TTTATTATCGCATTGCG-ATTTTCCCAATTCG
1 CGTTGCGATTTACTTA-T-TCGCATTGCGAATTTT-CCAATTCG
92861 CGTTGCGATTTACTTATTCGCATTGCGAATTTTCCAATTCG
1 CGTTGCGATTTACTTATTCGCATTGCGAATTTTCCAATTCG
*
92902 CGTTGCGATTTACTTATTCGCATTGTGAATT
1 CGTTGCGATTTACTTATTCGCATTGCGAATT
92933 GGGAAAATCG
Statistics
Matches: 68, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
41 48 0.71
42 17 0.25
43 3 0.04
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.44
Consensus pattern (41 bp):
CGTTGCGATTTACTTATTCGCATTGCGAATTTTCCAATTCG
Done.