Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 6 of 193
Found at i:2079971 original size:37 final size:35
Alignment explanation
Indices: 2079894--2079974 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 35
2079884 TAAAATTATT
*
2079894 ATTTTAAATTTTTTTTTAAATTTTAATTTTTTTTAAA
1 ATTTT-AATTTTTTTTTAAATTTTAAATTTTTTT-AA
*
2079931 ATTTTAATTTTTTTTATATATTTTTAGAATTTTTTT-A
1 ATTTTAATTTTTTTT-TA-AATTTTA-AATTTTTTTAA
2079968 ATTTTAA
1 ATTTTAA
2079975 AAAATATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
36 10 0.26
37 15 0.38
38 6 0.15
39 8 0.21
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (35 bp):
ATTTTAATTTTTTTTTAAATTTTAAATTTTTTTAA
Found at i:2080021 original size:19 final size:20
Alignment explanation
Indices: 2079962--2080034 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 20
2079952 TTTTAGAATT
*
2079962 TTTTTAATTTTAAAAAATATAAA
1 TTTTGAATTTTAAAAAA-AT--A
2079985 TTTTGTAATTTTAAAAAAATA
1 TTTTG-AATTTTAAAAAAATA
* *
2080006 TTTTGAATTTT-GAAAATTA
1 TTTTGAATTTTAAAAAAATA
2080025 TTTT-AATTTT
1 TTTTGAATTTT
2080035 TTTTTGTAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
18 6 0.13
19 10 0.22
20 6 0.13
21 6 0.13
23 6 0.13
24 12 0.26
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (20 bp):
TTTTGAATTTTAAAAAAATA
Found at i:2080035 original size:19 final size:19
Alignment explanation
Indices: 2079984--2080034 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
2079974 AAAAATATAA
*
2079984 ATTTTGTAATTTTAAAAAAAT
1 ATTTTG-AATTTT-GAAAAAT
*
2080005 ATTTTGAATTTTGAAAATT
1 ATTTTGAATTTTGAAAAAT
2080024 ATTTT-AATTTT
1 ATTTTGAATTTT
2080035 TTTTTGTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 6 0.21
21 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (19 bp):
ATTTTGAATTTTGAAAAAT
Found at i:2085695 original size:2 final size:2
Alignment explanation
Indices: 2085688--2085730 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2085678 CAATATTAAT
2085688 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2085730 A
1 A
2085731 TGTATAGGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2091826 original size:18 final size:19
Alignment explanation
Indices: 2091803--2091843 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
2091793 TAAAAAGATA
* *
2091803 AATTTTATAAATT-TTTTT
1 AATTTTAAAAATTATTTTG
2091821 AATTTTAAAAATTATTTTG
1 AATTTTAAAAATTATTTTG
2091840 AATT
1 AATT
2091844 ATTTTGTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
AATTTTAAAAATTATTTTG
Found at i:2099908 original size:31 final size:32
Alignment explanation
Indices: 2099858--2099922 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 32
2099848 TTAAAATTTC
2099858 AAAAAGTAAAGAGACTAAAACTGAT-AAATTA
1 AAAAAGTAAAGAGACTAAAACTGATCAAATTA
* * * * *
2099889 AAAAAGTATAGGGATTAAAATTGATCAAGTTA
1 AAAAAGTAAAGAGACTAAAACTGATCAAATTA
2099921 AA
1 AA
2099923 GTACAGGGAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 21 0.75
32 7 0.25
ACGTcount: A:0.57, C:0.05, G:0.15, T:0.23
Consensus pattern (32 bp):
AAAAAGTAAAGAGACTAAAACTGATCAAATTA
Found at i:2103663 original size:28 final size:28
Alignment explanation
Indices: 2103587--2103655 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
2103577 AAATTTTAAT
*
2103587 ATTTTACAGTTAAAAACTCAATTAATATA
1 ATTTTA-AGTTAAAAACTCAATTAAAATA
** **
2103616 ATAATACTTTAAAAACTCAATTAAAATA
1 ATTTTAAGTTAAAAACTCAATTAAAATA
2103644 ATTTTAAGTTAA
1 ATTTTAAGTTAA
2103656 GAATTCAAGA
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
28 27 0.87
29 4 0.13
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.38
Consensus pattern (28 bp):
ATTTTAAGTTAAAAACTCAATTAAAATA
Found at i:2104202 original size:27 final size:26
Alignment explanation
Indices: 2104153--2104213 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 26
2104143 AAAATTTTAC
* * *
2104153 TATATTATTATTTGAAAATATAAAAA
1 TATATTATAATTTAAAAAAATAAAAA
2104179 TATATATATAATTTAAAAAAATAAAAA
1 TATAT-TATAATTTAAAAAAATAAAAA
2104206 -A-ATTATAA
1 TATATTATAA
2104214 AGAATTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 5 0.16
25 2 0.06
26 6 0.19
27 18 0.58
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (26 bp):
TATATTATAATTTAAAAAAATAAAAA
Found at i:2104212 original size:28 final size:29
Alignment explanation
Indices: 2104167--2104221 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
2104157 TTATTATTTG
* * *
2104167 AAAATATAAAAATATATATATAATTTAAA
1 AAAATAAAAAAATATATAAAGAATTTAAA
2104196 AAAATAAAAAAAT-TATAAAGAATTTA
1 AAAATAAAAAAATATATAAAGAATTTA
2104222 TACTTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (29 bp):
AAAATAAAAAAATATATAAAGAATTTAAA
Found at i:2105355 original size:29 final size:28
Alignment explanation
Indices: 2105320--2105374 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
2105310 TTTAAAATTT
2105320 TAAAAGTAAAAAAATTAAATTTCTAAAAA
1 TAAAAGTAAAAAAATTAAA-TTCTAAAAA
* * *
2105349 TAAAAGTACAGAGATTAAATTCTAAA
1 TAAAAGTAAAAAAATTAAATTCTAAA
2105375 TTTCAAAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.27
Consensus pattern (28 bp):
TAAAAGTAAAAAAATTAAATTCTAAAAA
Found at i:2105382 original size:29 final size:28
Alignment explanation
Indices: 2105318--2105396 Score: 70
Period size: 29 Copynumber: 2.7 Consensus size: 28
2105308 ATTTTAAAAT
* * *
2105318 TTTAAAAGTAAAAAAATTAAATTTCTAAA
1 TTTAAAAGTACAGAGATTAAA-TTCTAAA
**
2105347 AATAAAAGTACAGAGATTAAATTCTAAA
1 TTTAAAAGTACAGAGATTAAATTCTAAA
2105375 TTTCAAAAAGTACATG-GATTAA
1 TTT--AAAAGTACA-GAGATTAA
2105397 TGAGATATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
28 8 0.20
29 16 0.40
30 15 0.38
31 1 0.03
ACGTcount: A:0.54, C:0.06, G:0.09, T:0.30
Consensus pattern (28 bp):
TTTAAAAGTACAGAGATTAAATTCTAAA
Found at i:2108720 original size:13 final size:14
Alignment explanation
Indices: 2108697--2108730 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
2108687 CAATCGATTC
2108697 TCGATCTAATTAAT
1 TCGATCTAATTAAT
2108711 TCGA-CTAATTAAT
1 TCGATCTAATTAAT
*
2108724 TTGATCT
1 TCGATCT
2108731 TATTCCAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (14 bp):
TCGATCTAATTAAT
Found at i:2113568 original size:6 final size:6
Alignment explanation
Indices: 2113546--2113625 Score: 139
Period size: 6 Copynumber: 13.8 Consensus size: 6
2113536 GCGTTCTCTT
2113546 TCCTTC TCCTT- T-C-TC TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC
1 TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC
2113591 TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TCCTT
1 TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC TCCTT
2113626 TTCTTTCCGC
Statistics
Matches: 71, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
3 1 0.01
4 2 0.03
5 2 0.03
6 66 0.93
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (6 bp):
TCCTTC
Found at i:2124388 original size:21 final size:21
Alignment explanation
Indices: 2124364--2124405 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2124354 CTCATATCCA
2124364 TAACAACAAATT-GTCATCAAT
1 TAACAACAAATTAGTC-TCAAT
* *
2124385 TAACTACATATTAGTCTCAAT
1 TAACAACAAATTAGTCTCAAT
2124406 GCATTATTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (21 bp):
TAACAACAAATTAGTCTCAAT
Found at i:2128910 original size:31 final size:30
Alignment explanation
Indices: 2128875--2129070 Score: 124
Period size: 31 Copynumber: 6.5 Consensus size: 30
2128865 TAAAAAAAGA
*
2128875 TTAGGTACCAAATTAGGAAAAAGAGTCAAGT
1 TTAGGTACCAAATTAGGAAAAA-AATCAAGT
**
2128906 TTAGGTACCAAATT--GAACCCCAAA--AAGT
1 TTAGGTACCAAATTAGGAA--AAAAATCAAGT
* *
2128934 TTAAGTACCAACTTTA--AAAAAAATGTCAAGT
1 TTAGGTACCAA-ATTAGGAAAAAAA--TCAAGT
2128965 TTAGGTACCAAATTAGGAAAAAAATGTCAAGT
1 TTAGGTACCAAATTAGGAAAAAAA--TCAAGT
2128997 TT-GAGTACCAAATT-GGACCAAAAAA--AAGT
1 TTAG-GTACCAAATTAGGA--AAAAAATCAAGT
* * * *
2129026 TTACGTACCAAATTAGGAAAAAGTATTAAAT
1 TTAGGTACCAAATTAGGAAAAA-AATCAAGT
*
2129057 TCAGGTACCAAATT
1 TTAGGTACCAAATT
2129071 TTATATTAAG
Statistics
Matches: 133, Mismatches: 14, Indels: 36
0.73 0.08 0.20
Matches are distributed among these distances:
27 3 0.02
28 18 0.14
29 24 0.18
30 7 0.05
31 48 0.36
32 27 0.20
33 6 0.05
ACGTcount: A:0.46, C:0.13, G:0.16, T:0.25
Consensus pattern (30 bp):
TTAGGTACCAAATTAGGAAAAAAATCAAGT
Found at i:2129020 original size:33 final size:32
Alignment explanation
Indices: 2128875--2129047 Score: 133
Period size: 31 Copynumber: 5.7 Consensus size: 32
2128865 TAAAAAAAGA
*
2128875 TTAGGTACCAAATTAGGAAAAAGA-GTCAAGT
1 TTAGGTACCAAATTAGGAAAAAAATGTCAAGT
**
2128906 TTAGGTACCAAATT--GAACCCCAAA----AAGT
1 TTAGGTACCAAATTAGGAA--AAAAATGTCAAGT
* *
2128934 TTAAGTACCAACTTTA--AAAAAAATGTCAAGT
1 TTAGGTACCAA-ATTAGGAAAAAAATGTCAAGT
2128965 TTAGGTACCAAATTAGGAAAAAAATGTCAAGT
1 TTAGGTACCAAATTAGGAAAAAAATGTCAAGT
2128997 TT-GAGTACCAAATT-GGACCAAAAAA----AAGT
1 TTAG-GTACCAAATTAGGA--AAAAAATGTCAAGT
*
2129026 TTACGTACCAAATTAGGAAAAA
1 TTAGGTACCAAATTAGGAAAAA
2129048 GTATTAAATT
Statistics
Matches: 117, Mismatches: 10, Indels: 33
0.73 0.06 0.21
Matches are distributed among these distances:
27 3 0.03
28 18 0.15
29 23 0.20
30 6 0.05
31 34 0.29
32 27 0.23
33 6 0.05
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (32 bp):
TTAGGTACCAAATTAGGAAAAAAATGTCAAGT
Found at i:2129066 original size:92 final size:90
Alignment explanation
Indices: 2128877--2129070 Score: 230
Period size: 92 Copynumber: 2.1 Consensus size: 90
2128867 AAAAAAGATT
* **
2128877 AGGTACCAAATTAGGAAAAAGAGTCAAGTTTAGGTACCAAATTGAACCCCAAAAAGTTTAAGTAC
1 AGGTACCAAATTAGGAAAAAAAGTCAAGTTTAGGTACCAAATTGAACCAAAAAAAGTTTAAGTAC
* * * *
2128942 CAACTTTAAAAAAAATGTCAAGTTT
66 CAACATTAAAAAAAATATCAAATTC
* *
2128967 AGGTACCAAATTAGGAAAAAAATGTCAAGTTT-GAGTACCAAATTGGACCAAAAAAAAGTTTACG
1 AGGTACCAAATTAGGAAAAAAA-GTCAAGTTTAG-GTACCAAATTGAACC-AAAAAAAGTTTAAG
* * *
2129031 TACCAA-ATTAGGAAAAAGTATTAAATTC
63 TACCAACATTA-AAAAAAATATCAAATTC
2129059 AGGTACCAAATT
1 AGGTACCAAATT
2129071 TTATATTAAG
Statistics
Matches: 88, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
90 22 0.25
91 26 0.30
92 40 0.45
ACGTcount: A:0.46, C:0.13, G:0.16, T:0.24
Consensus pattern (90 bp):
AGGTACCAAATTAGGAAAAAAAGTCAAGTTTAGGTACCAAATTGAACCAAAAAAAGTTTAAGTAC
CAACATTAAAAAAAATATCAAATTC
Found at i:2131750 original size:29 final size:28
Alignment explanation
Indices: 2131718--2131894 Score: 157
Period size: 29 Copynumber: 6.1 Consensus size: 28
2131708 AAAAATAGGG
*
2131718 TTTTGGAAAGTTTGAGGGTAAAATGATAA
1 TTTTGGAAAGTTCGAGGGTAAAATG-TAA
* *
2131747 TTTTGGTGAAG-TCGA-GGTCAAAAATGGAA
1 TTTTGG-AAAGTTCGAGGGT--AAAATGTAA
2131776 TTTTGGAAAGTTCG-GGGTAAAATGGTAA
1 TTTTGGAAAGTTCGAGGGTAAAAT-GTAA
* *
2131804 TTTTTGGTAAA-ATCG-GGGTTAAAATGGAA
1 -TTTTGG-AAAGTTCGAGGG-TAAAATGTAA
*
2131833 TTTTGGAAAATTCGAGGGTAAAAATGTAA
1 TTTTGGAAAGTTCGAGGGT-AAAATGTAA
* *
2131862 TTTTTGAAAGTTTCGAGGTTAAAATGTAA
1 TTTTGGAAAG-TTCGAGGGTAAAATGTAA
2131891 TTTT
1 TTTT
2131895 CTAAAGTTTT
Statistics
Matches: 123, Mismatches: 12, Indels: 26
0.76 0.07 0.16
Matches are distributed among these distances:
27 8 0.07
28 19 0.15
29 70 0.57
30 26 0.21
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (28 bp):
TTTTGGAAAGTTCGAGGGTAAAATGTAA
Found at i:2131850 original size:115 final size:116
Alignment explanation
Indices: 2131611--2131865 Score: 286
Period size: 116 Copynumber: 2.2 Consensus size: 116
2131601 ATTTTGACTC
* * * * * *
2131611 TCGAGGGGCAAAAATGTAATTTTGG-GAAAAATCAAGGTTAAAAATGGGATTTTAGAAGGTTCGG
1 TCGA-GGGTAAAAATGTAATTTTGGTG--AAGTCGAGGTCAAAAATGGAATTTTAGAAAGTTCGG
* * * *
2131675 GGGTAAAATGGTAATTTTAATGAAATTGAGGTTAAAAATAGGGTTTTGGAAAGT
63 GGGTAAAATGGTAATTTTAATAAAATCGAGGTTAAAAATAGGATTTTGGAAAAT
* *
2131729 TTGAGGGT-AAAATGATAATTTTGGTGAAGTCGAGGTCAAAAATGGAATTTTGGAAAGTTC-GGG
1 TCGAGGGTAAAAATG-TAATTTTGGTGAAGTCGAGGTCAAAAATGGAATTTTAGAAAGTTCGGGG
** *
2131792 GTAAAATGGTAATTTTTGGTAAAATCGGGGTT-AAAAT-GGAATTTTGGAAAAT
65 GTAAAATGGTAA-TTTTAATAAAATCGAGGTTAAAAATAGG-ATTTTGGAAAAT
2131844 TCGAGGGTAAAAATGTAATTTT
1 TCGAGGGTAAAAATGTAATTTT
2131866 TGAAAGTTTC
Statistics
Matches: 116, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
114 2 0.02
115 44 0.38
116 54 0.47
117 12 0.10
118 4 0.03
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.31
Consensus pattern (116 bp):
TCGAGGGTAAAAATGTAATTTTGGTGAAGTCGAGGTCAAAAATGGAATTTTAGAAAGTTCGGGGG
TAAAATGGTAATTTTAATAAAATCGAGGTTAAAAATAGGATTTTGGAAAAT
Found at i:2131866 original size:58 final size:58
Alignment explanation
Indices: 2131621--2131867 Score: 252
Period size: 58 Copynumber: 4.3 Consensus size: 58
2131611 TCGAGGGGCA
* * * * * * *
2131621 AAAATGTAATTTTGGGAAAAATCAAGGTTAAAAATGGGATTTTAGAAGGTTCGGGGGT
1 AAAATGTAATTTTTGGTAAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
** * * * *
2131679 AAAATGGTAA-TTTTAATGAAATTGAGGTTAAAAATAGG-GTTTTGGAAAGTTTGAGGGT
1 AAAAT-GTAATTTTTGGTAAAATCGAGGTTAAAAAT-GGAATTTTGGAAAGTTCGAGGGT
* * *
2131737 AAAATGATAA-TTTTGGTGAAGTCGAGGTCAAAAATGGAATTTTGGAAAGTTCG-GGGT
1 AAAATG-TAATTTTTGGTAAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
* *
2131794 AAAATGGTAATTTTTGGTAAAATCGGGGTT-AAAATGGAATTTTGGAAAATTCGAGGGT
1 AAAAT-GTAATTTTTGGTAAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
2131852 AAAAATGTAATTTTTG
1 -AAAATGTAATTTTTG
2131868 AAAGTTTCGA
Statistics
Matches: 157, Mismatches: 24, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
57 37 0.24
58 109 0.69
59 11 0.07
ACGTcount: A:0.37, C:0.03, G:0.28, T:0.32
Consensus pattern (58 bp):
AAAATGTAATTTTTGGTAAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
Found at i:2131882 original size:58 final size:57
Alignment explanation
Indices: 2131645--2131894 Score: 226
Period size: 58 Copynumber: 4.3 Consensus size: 57
2131635 GGAAAAATCA
* * * *
2131645 AGGTTAAAAATGGGATTTTAGAAGGTTCGGGGGTAAAATGGTAATTTTAATGAAATT-G
1 AGGTT-AAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTT-ATGAAATTCG
* * * * *
2131703 AGGTTAAAAATAGG-GTTTTGGAAAGTTTGAGGGTAAAATGATAATTTTGGTG-AAGTCG
1 AGGTT-AAAAT-GGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTT-ATGAAATTCG
* *
2131761 AGGTCAAAAATGGAATTTTGGAAAGTTCG-GGGTAAAATGGTAATTTT-TGGTAAAATCG
1 AGGT-TAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTAT-G-AAATTCG
* *
2131819 GGGTTAAAATGGAATTTTGGAAAATTCGAGGGTAAAAAT-GTAATTTT-TGAAAGTTTCG
1 AGGTTAAAATGGAATTTTGGAAAGTTCGAGGGT-AAAATGGTAATTTTATGAAA--TTCG
*
2131877 AGGTTAAAATGTAATTTT
1 AGGTTAAAATGGAATTTT
2131895 CTAAAGTTTT
Statistics
Matches: 161, Mismatches: 20, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
55 1 0.01
56 4 0.02
57 45 0.28
58 104 0.65
59 7 0.04
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.34
Consensus pattern (57 bp):
AGGTTAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTATGAAATTCG
Found at i:2131900 original size:29 final size:29
Alignment explanation
Indices: 2131819--2131925 Score: 94
Period size: 29 Copynumber: 3.7 Consensus size: 29
2131809 GGTAAAATCG
* * *
2131819 GGGTTAAAATGGAATTTTGGAAA-ATTCGA
1 GGGTTAAAATGTAATTTT-TAAAGTTTCGA
*
2131848 GGGTAAAAATGTAATTTTTGAAAGTTTCGA
1 GGGTTAAAATGTAATTTTT-AAAGTTTCGA
*
2131878 -GGTTAAAATGTAATTTTCTAAAGTTTTG-
1 GGGTTAAAATGTAATTTT-TAAAGTTTCGA
* *
2131906 GGGTCAAAAATGTGATTTTT
1 GGGT-TAAAATGTAATTTTT
2131926 GGATAGTTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
29 47 0.72
30 18 0.28
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.38
Consensus pattern (29 bp):
GGGTTAAAATGTAATTTTTAAAGTTTCGA
Found at i:2131901 original size:115 final size:115
Alignment explanation
Indices: 2131645--2131902 Score: 267
Period size: 115 Copynumber: 2.2 Consensus size: 115
2131635 GGAAAAATCA
* * * * * *
2131645 AGGTTAAAAATGGGATTTTAGAAGGTTCGGGGGTAAAATGGTAATTTTAATGAAATTGAGGTTAA
1 AGGTCAAAAATGGAATTTTCGAAAGTTCGGGGGTAAAATGGTAATTTTAATAAAATCGAGGTTAA
* * *
2131710 AAATAGGGTTTTGGAAAGTTTGAGGGTAAAATGATAATTTTGGTGAAGTCG
66 AAATAGGATTTTGGAAAATTCGAGGGTAAAATGATAATTTT-GTGAAGTCG
* ** *
2131761 AGGTCAAAAATGGAATTTTGGAAAGTTC-GGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTT-
1 AGGTCAAAAATGGAATTTTCGAAAGTTCGGGGGTAAAATGGTAA-TTTTAATAAAATCGAGGTTA
2131824 AAAAT-GGAATTTTGGAAAATTCGAGGGTAAAAATG-TAATTTT-TGAAAGTTTCG
65 AAAATAGG-ATTTTGGAAAATTCGAGGGT-AAAATGATAATTTTGTG-AAG--TCG
* * *
2131877 AGGT-TAAAATGTAATTTTCTAAAGTT
1 AGGTCAAAAATGGAATTTTCGAAAGTT
2131903 TTGGGGTCAA
Statistics
Matches: 120, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
113 2 0.02
114 5 0.04
115 62 0.52
116 51 0.43
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (115 bp):
AGGTCAAAAATGGAATTTTCGAAAGTTCGGGGGTAAAATGGTAATTTTAATAAAATCGAGGTTAA
AAATAGGATTTTGGAAAATTCGAGGGTAAAATGATAATTTTGTGAAGTCG
Found at i:2133434 original size:26 final size:25
Alignment explanation
Indices: 2133403--2133482 Score: 72
Period size: 26 Copynumber: 3.1 Consensus size: 25
2133393 CTTTTTCAGA
2133403 AAAGGGTTTGTATTTAGATTTCAAG
1 AAAGGGTTTGTATTTAGATTTCAAG
** *
2133428 AACAGGGTTCATATATTGGATTTTCAA-
1 AA-AGGGTTTGTAT-TTAGA-TTTCAAG
* *
2133455 AGATGGGTCTGTATTTAGATTTCAAG
1 A-AAGGGTTTGTATTTAGATTTCAAG
2133481 AA
1 AA
2133483 TCGGGTGTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
25 9 0.21
26 14 0.33
27 12 0.29
28 7 0.17
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.38
Consensus pattern (25 bp):
AAAGGGTTTGTATTTAGATTTCAAG
Found at i:2133488 original size:26 final size:25
Alignment explanation
Indices: 2133410--2133493 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 25
2133400 AGAAAAGGGT
2133410 TTGTATTTAGATTTCAAGAA-CAGGG
1 TTGTATTTAGATTTCAAGAATC-GGG
* *
2133435 TTCATATATTGGATTTTCAA-AGAT-GGG
1 TT-GTAT-TTAGA-TTTCAAGA-ATCGGG
2133462 TCTGTATTTAGATTTCAAGAATCGGG
1 T-TGTATTTAGATTTCAAGAATCGGG
2133488 TGTGTA
1 T-TGTA
2133494 ACCCTTTGTA
Statistics
Matches: 46, Mismatches: 5, Indels: 15
0.70 0.08 0.23
Matches are distributed among these distances:
25 10 0.22
26 16 0.35
27 12 0.26
28 8 0.17
ACGTcount: A:0.29, C:0.08, G:0.24, T:0.39
Consensus pattern (25 bp):
TTGTATTTAGATTTCAAGAATCGGG
Found at i:2133783 original size:13 final size:13
Alignment explanation
Indices: 2133765--2133803 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2133755 TTGTAATTGG
2133765 GCCTTTTATTTGA
1 GCCTTTTATTTGA
* *
2133778 GCCTTTGTAATTGG
1 GCCTTT-TATTTGA
2133792 GCCTTTTATTTG
1 GCCTTTTATTTG
2133804 GACATTTGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.13, C:0.15, G:0.21, T:0.51
Consensus pattern (13 bp):
GCCTTTTATTTGA
Found at i:2133784 original size:27 final size:28
Alignment explanation
Indices: 2133745--2133811 Score: 102
Period size: 27 Copynumber: 2.5 Consensus size: 28
2133735 CTAAATTTGG
*
2133745 TTTGGGCCATTTGTAATTGGGCCTTTTA
1 TTTGAGCCATTTGTAATTGGGCCTTTTA
2133773 TTTGAGCC-TTTGTAATTGGGCCTTTTA
1 TTTGAGCCATTTGTAATTGGGCCTTTTA
*
2133800 TTTG-GACATTTG
1 TTTGAGCCATTTG
2133812 GGTTTTTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 2 0.06
27 27 0.75
28 7 0.19
ACGTcount: A:0.15, C:0.13, G:0.24, T:0.48
Consensus pattern (28 bp):
TTTGAGCCATTTGTAATTGGGCCTTTTA
Found at i:2133797 original size:14 final size:14
Alignment explanation
Indices: 2133746--2133797 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
2133736 TAAATTTGGT
2133746 TTGGGCCATTTGTAA
1 TTGGGCC-TTTGTAA
*
2133761 TTGGGCCTTT-TAT
1 TTGGGCCTTTGTAA
*
2133774 TTGAGCCTTTGTAA
1 TTGGGCCTTTGTAA
2133788 TTGGGCCTTT
1 TTGGGCCTTT
2133798 TATTTGGACA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 11 0.34
14 14 0.44
15 7 0.22
ACGTcount: A:0.13, C:0.15, G:0.25, T:0.46
Consensus pattern (14 bp):
TTGGGCCTTTGTAA
Found at i:2133890 original size:18 final size:17
Alignment explanation
Indices: 2133819--2133898 Score: 72
Period size: 17 Copynumber: 4.5 Consensus size: 17
2133809 TTGGGTTTTT
* *
2133819 AATTTAAATTTTAATTA
1 AATTTAAATTTAAAATA
2133836 AATTTAAATTTATTTCAAAT-
1 AATTTAAATTTA----AAATA
*
2133856 ATTTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
*
2133873 AATTTATATTTAATAATA
1 AATTTAAATTTAA-AATA
2133891 AATTTAAA
1 AATTTAAA
2133899 CCTATTTAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
16 4 0.08
17 22 0.43
18 11 0.22
20 11 0.22
21 3 0.06
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:2134382 original size:27 final size:30
Alignment explanation
Indices: 2134342--2134410 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
2134332 TAAAATAAAA
*
2134342 TAAAAAATT-TAAA-AACATGATT-TTAAT
1 TAAAAAATTGAAAATAACATGATTATTAAT
* *
2134369 TAAAAACTTGAAAATAACATGTTTATTAAT
1 TAAAAAATTGAAAATAACATGATTATTAAT
2134399 TAAAAATATTGA
1 TAAAAA-ATTGA
2134411 TTAAATTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
27 8 0.24
28 3 0.09
29 8 0.24
30 11 0.32
31 4 0.12
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (30 bp):
TAAAAAATTGAAAATAACATGATTATTAAT
Found at i:2142149 original size:139 final size:139
Alignment explanation
Indices: 2141890--2142163 Score: 426
Period size: 139 Copynumber: 2.0 Consensus size: 139
2141880 GTCCTATAAA
* *
2141890 GGAAATGCCTCCTATGACTAAGAAGGGAAAGAAAACTAAATCTGTGAAGAAGGCTCGGAAAGTGA
1 GGAAATGCCTCCTATGACTAAGAAGGGAAAGAAAACTAAATCTGGGAAGAAGGCTCAGAAAGTGA
* * * *
2141955 TAAAGAGTATGTATCCTCTAGTCAAACGCACGAAGAAATTGAAATCTACGTCCTCTTAGCAGAGT
66 TAAAGAATATGTATCCTCTAGTCAAACGAACGAAGAAATTGAAATCCACGCCCTCTTAGCAGAGT
2142020 CTGCTCAAG
131 CTGCTCAAG
**
2142029 GGAAATGCCTCCTATGTA-TAAGCTGGTG-AAGAAAACTAAATCTGGGAAGAAGGCTCAGAAAGT
1 GGAAATGCCTCCTATG-ACTAAGAAGG-GAAAGAAAACTAAATCTGGGAAGAAGGCTCAGAAAGT
* *
2142092 GATAAAGAATGTGTATCCTCTAGTCAAACGAACGAAGAAATTGAAATCCATGCCCTCTTAGCAGA
64 GATAAAGAATATGTATCCTCTAGTCAAACGAACGAAGAAATTGAAATCCACGCCCTCTTAGCAGA
2142157 GTCTGCT
129 GTCTGCT
2142164 TTGTGAGTTT
Statistics
Matches: 123, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
139 121 0.98
140 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (139 bp):
GGAAATGCCTCCTATGACTAAGAAGGGAAAGAAAACTAAATCTGGGAAGAAGGCTCAGAAAGTGA
TAAAGAATATGTATCCTCTAGTCAAACGAACGAAGAAATTGAAATCCACGCCCTCTTAGCAGAGT
CTGCTCAAG
Found at i:2149002 original size:2 final size:2
Alignment explanation
Indices: 2148995--2149032 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2148985 AACATTCCTT
2148995 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2149033 TGTATGTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2151235 original size:29 final size:29
Alignment explanation
Indices: 2151202--2151257 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
2151192 ATGGTATCTA
2151202 GATCAAATTAGTCCCTTA-ATTATTAAATT
1 GATCAAATTAGT-CCTTATATTATTAAATT
* *
2151231 GATCAAGTTAGTCTTTATATTATTAAA
1 GATCAAATTAGTCCTTATATTATTAAA
2151258 AGAATCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.43
Consensus pattern (29 bp):
GATCAAATTAGTCCTTATATTATTAAATT
Found at i:2152688 original size:16 final size:16
Alignment explanation
Indices: 2152667--2152718 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2152657 AAATAATTTC
*
2152667 AAATGACTCATACTCA
1 AAATGACTCAAACTCA
* *
2152683 AAATGATTCAAACTTA
1 AAATGACTCAAACTCA
*
2152699 AAAT-AGCTTAAACTCA
1 AAATGA-CTCAAACTCA
2152715 AAAT
1 AAAT
2152719 ATCTCGAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
15 1 0.03
16 28 0.97
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.27
Consensus pattern (16 bp):
AAATGACTCAAACTCA
Found at i:2154548 original size:2 final size:2
Alignment explanation
Indices: 2154541--2154566 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2154531 CTCATTGCCG
2154541 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
2154567 CCACCCTTCA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2155231 original size:30 final size:30
Alignment explanation
Indices: 2155166--2155233 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
2155156 TACAATATTC
* * *
2155166 ATTTTTCTTTAAATTTTTTATTGTTTTGAAT
1 ATTTTT-TTGAAATTTATTATTATTTTGAAT
*
2155197 ATTTTTTTGAAATTTATTATGTATTTTTAA-
1 ATTTTTTTGAAATTTATTAT-TATTTTGAAT
2155227 ATTTTTT
1 ATTTTTT
2155234 GTAATCAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 19 0.59
31 13 0.41
ACGTcount: A:0.25, C:0.01, G:0.06, T:0.68
Consensus pattern (30 bp):
ATTTTTTTGAAATTTATTATTATTTTGAAT
Found at i:2158592 original size:111 final size:113
Alignment explanation
Indices: 2158396--2158618 Score: 324
Period size: 111 Copynumber: 2.0 Consensus size: 113
2158386 TATTCTGTTA
* * *
2158396 AATTAGGGTTACATGTGACTGTGGATTCGGGGGAATTTTTTTAATTTCTGCTGGGTTTAAGCTTT
1 AATTAGGGTTACAGGTGACTGTCGATTCGGGGGAATTTTTTTAATTTCTGCTAGGTTTAAGCTTT
* * * *
2158461 CTAAGTCTCTTTATTTTCAATTCCAGTGGTATAATATTTCTAGGGTTG
66 CTAAGACTCCTTATTTTCAATTCCACTGGTATAATAGTTCTAGGGTTG
* * * *
2158509 AATTAGGGTTACAGGTGACTGTCGATT-TGGGGAA-TTTTTTAATTTCTGTTAGGTTTAGGGTTT
1 AATTAGGGTTACAGGTGACTGTCGATTCGGGGGAATTTTTTTAATTTCTGCTAGGTTTAAGCTTT
*
2158572 CTAAGACTCCTTGTTTTCAATTCCACTGGTATAATAGTTCTAGGGTT
66 CTAAGACTCCTTATTTTCAATTCCACTGGTATAATAGTTCTAGGGTT
2158619 TTCGAGCTGT
Statistics
Matches: 98, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
111 67 0.68
112 6 0.06
113 25 0.26
ACGTcount: A:0.22, C:0.12, G:0.23, T:0.43
Consensus pattern (113 bp):
AATTAGGGTTACAGGTGACTGTCGATTCGGGGGAATTTTTTTAATTTCTGCTAGGTTTAAGCTTT
CTAAGACTCCTTATTTTCAATTCCACTGGTATAATAGTTCTAGGGTTG
Found at i:2163887 original size:161 final size:161
Alignment explanation
Indices: 2163613--2164148 Score: 652
Period size: 161 Copynumber: 3.3 Consensus size: 161
2163603 AAGCCTTAGA
* * * * * * *
2163613 ATATGTTTCATCATGTTGTTCTTTGGCTTGCTGCTCTAGTGATCCTCATATAATATTTTACCTTA
1 ATATGTTTCATCATATTGTT-TATGACTTGCTGCTCTAGTGAACCTCATATAATTTTTTATCATA
* * * *** * *
2163678 GCCATGATTGTAAATCATAATTCTTCATCT-AAGTAAACCCAGTGAAGCTTTTTCTTTATCGTCT
65 GCCATGATTGTTAATCAT-ACTCTTCAT-TAAAGTATACCTTTTGAAGCTTTTTCTTTATTGACT
*
2163742 CCTTTCAAAGCTTTTCTTTATTGCCTTAGAATTT
128 CCTTTCGAAGCTTTTCTTTATTGCCTTAGAATTT
* * * *
2163776 TTATGTTT-TTCATGTTGTTTATGACTTGCAGCTCTAGTGAACCTCATATAATTTTTTATCATAG
1 ATATGTTTCATCATATTGTTTATGACTTGCTGCTCTAGTGAACCTCATATAATTTTTTATCATAG
* * *
2163840 CCTTGATTGTTAATCATACTCCTTCATTAAAGTATACTTTTTGAAGCTTTTTCTTTATTGCCTCC
66 CCATGATTGTTAATCATACT-CTTCATTAAAGTATACCTTTTGAAGCTTTTTCTTTATTGACTCC
*
2163905 TTTTGAAGCTTTTCTTTATTGCCTTAGAATTT
130 TTTCGAAGCTTTTCTTTATTGCCTTAGAATTT
* * * * *
2163937 CTATG-TTCTATCATATTG-TT-TGATTTGCTGGTCTAGTGTACCTCATGTAATTTTTTTATCAT
1 ATATGTTTC-ATCATATTGTTTATGACTTGCTGCTCTAGTGAACCTCATATAA-TTTTTTATCAT
* *
2163999 AGCCAGGATTGTTAATCATACTCTGTCATCAAAGTATACCTTTTGAAGCTTTTTCTTTATTGACT
64 AGCCATGATTGTTAATCATACTCT-TCATTAAAGTATACCTTTTGAAGCTTTTTCTTTATTGACT
*
2164064 CCTTTCGAAGCTTTTCTTTATTACCTTAGAATTT
128 CCTTTCGAAGCTTTTCTTTATTGCCTTAGAATTT
* *
2164098 ATAT-TTTCTATCATATTGTTTATGACTTGCTGGTCTAGTGAACCGCATATA
1 ATATGTTTC-ATCATATTGTTTATGACTTGCTGCTCTAGTGAACCTCATATA
2164149 TATATTTATC
Statistics
Matches: 323, Mismatches: 41, Indels: 18
0.85 0.11 0.05
Matches are distributed among these distances:
160 32 0.10
161 240 0.74
162 19 0.06
163 32 0.10
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.47
Consensus pattern (161 bp):
ATATGTTTCATCATATTGTTTATGACTTGCTGCTCTAGTGAACCTCATATAATTTTTTATCATAG
CCATGATTGTTAATCATACTCTTCATTAAAGTATACCTTTTGAAGCTTTTTCTTTATTGACTCCT
TTCGAAGCTTTTCTTTATTGCCTTAGAATTT
Found at i:2163924 original size:26 final size:27
Alignment explanation
Indices: 2163878--2163928 Score: 95
Period size: 26 Copynumber: 1.9 Consensus size: 27
2163868 AAAGTATACT
2163878 TTTTGAAGCTTTTTCTTTATTGCCTCC
1 TTTTGAAGCTTTTTCTTTATTGCCTCC
2163905 TTTTGAAGC-TTTTCTTTATTGCCT
1 TTTTGAAGCTTTTTCTTTATTGCCT
2163929 TAGAATTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.12, C:0.20, G:0.12, T:0.57
Consensus pattern (27 bp):
TTTTGAAGCTTTTTCTTTATTGCCTCC
Found at i:2165668 original size:68 final size:69
Alignment explanation
Indices: 2165558--2165696 Score: 262
Period size: 68 Copynumber: 2.0 Consensus size: 69
2165548 TTTAGTTGTG
2165558 CAAAAAAGTTTAAAAAAAAAAAAAAAACACACTTTAGGTCATTCTTTGTTGTTTTAGTTGTGCAA
1 CAAAAAAGTTTAAAAAAAAAAAAAAAACACACTTTAGGTCATTCTTTGTTGTTTTAGTTGTGCAA
2165623 TGCA
66 TGCA
*
2165627 CAAAAAAG-TTCAAAAAAAAAAAAAAACACACTTTAGGTCATTCTTTGTTGTTTTAGTTGTGCAA
1 CAAAAAAGTTTAAAAAAAAAAAAAAAACACACTTTAGGTCATTCTTTGTTGTTTTAGTTGTGCAA
2165691 TGCA
66 TGCA
2165695 CA
1 CA
2165697 GATATGTCTA
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
68 61 0.88
69 8 0.12
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (69 bp):
CAAAAAAGTTTAAAAAAAAAAAAAAAACACACTTTAGGTCATTCTTTGTTGTTTTAGTTGTGCAA
TGCA
Found at i:2168478 original size:2 final size:2
Alignment explanation
Indices: 2168471--2168501 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2168461 GGATACATAT
2168471 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2168502 CAGCTAAAAT
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2171249 original size:2 final size:2
Alignment explanation
Indices: 2171242--2171280 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2171232 TTGAGTGCTT
2171242 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2171281 TGTTTTCATG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2172462 original size:32 final size:31
Alignment explanation
Indices: 2172406--2172466 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
2172396 AATATAAAAT
* *
2172406 AAATTATAAATGATTTTCACATTTTCAATAAA
1 AAATTAAAAATGATTTTAACATTTT-AATAAA
*
2172438 AAATTAAAAATGATTTTAATATTTTAATA
1 AAATTAAAAATGATTTTAACATTTTAATA
2172467 TTTAAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 4 0.15
32 22 0.85
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (31 bp):
AAATTAAAAATGATTTTAACATTTTAATAAA
Found at i:2173083 original size:2 final size:2
Alignment explanation
Indices: 2173076--2173103 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2173066 GAAAATTTAC
2173076 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
2173104 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2174774 original size:19 final size:17
Alignment explanation
Indices: 2174750--2174784 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
2174740 CGGATAATTC
2174750 TAAATATTATATAAAAAAA
1 TAAATA-TA-ATAAAAAAA
2174769 TAAATATAATAAAAAA
1 TAAATATAATAAAAAA
2174785 CTTATAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAATATAATAAAAAAA
Found at i:2180950 original size:38 final size:38
Alignment explanation
Indices: 2180903--2180975 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
2180893 TCATAATTAG
2180903 TTATGACTTTGTCTGCAACTATATATATATATATATAA
1 TTATGACTTTGTCTGCAACTATATATATATATATATAA
2180941 TTATGACTTTGTCTGCAACTATATATATATATATA
1 TTATGACTTTGTCTGCAACTATATATATATATATA
2180976 GGTTAAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (38 bp):
TTATGACTTTGTCTGCAACTATATATATATATATATAA
Found at i:2188932 original size:18 final size:18
Alignment explanation
Indices: 2188909--2188944 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2188899 AAAGGTCAAT
*
2188909 TTTTAATATTGGAAATGA
1 TTTTAATATTAGAAATGA
2188927 TTTTAATATTAGAAATGA
1 TTTTAATATTAGAAATGA
2188945 ATGAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (18 bp):
TTTTAATATTAGAAATGA
Found at i:2189628 original size:182 final size:183
Alignment explanation
Indices: 2189321--2189682 Score: 674
Period size: 182 Copynumber: 2.0 Consensus size: 183
2189311 GCACCTGACA
2189321 TTACTATTCGTACATGTTCCCCCTTTTCACATTCCAATCGGTGGTGTTTCCTTTTAGGTTTTGTT
1 TTACTATTCGTACATGTTCCCCCTTTTCACATTCCAATCGGTGGTGTTTCCTTTTAGGTTTTGTT
2189386 GAAAAAAGAAAACTTGAAAAAAGGACATGGTTTTTGTATGGTAAACAAGTTTCCATTCTTTTAAA
66 GAAAAAAGAAAACTTGAAAAAAGGACATGGTTTTTGTATGGTAAACAAGTTTCCATTCTTTTAAA
*
2189451 TCCACCTCAGTTTGATAGTTA-GGTGTTTATCG-TCCCAGGTGCAGTCTGGATT
131 TCCACCTCAGTTTGATAGTTAGGGTGTTCATCGCT-CCAGGTGCAGTCTGGATT
2189503 TTACTATTCGTACATGTTCCCCCTTTTCACATTCCAATCGGTGGTGTTTCCTTTTAGGTTTTGTT
1 TTACTATTCGTACATGTTCCCCCTTTTCACATTCCAATCGGTGGTGTTTCCTTTTAGGTTTTGTT
*
2189568 GAAAAAAGAAAACTTGAAAAAAGGACATGGTTTTTGTATGGTAAACAAGTTTTCATTCTTTTAAA
66 GAAAAAAGAAAACTTGAAAAAAGGACATGGTTTTTGTATGGTAAACAAGTTTCCATTCTTTTAAA
*
2189633 TCCACCTCAGTTTGATAGTTAGGGTGTTCATCGCTCCAGGTGTAGTCTGG
131 TCCACCTCAGTTTGATAGTTAGGGTGTTCATCGCTCCAGGTGCAGTCTGG
2189683 GTTCGAGTCA
Statistics
Matches: 175, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
182 150 0.86
183 24 0.14
184 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.38
Consensus pattern (183 bp):
TTACTATTCGTACATGTTCCCCCTTTTCACATTCCAATCGGTGGTGTTTCCTTTTAGGTTTTGTT
GAAAAAAGAAAACTTGAAAAAAGGACATGGTTTTTGTATGGTAAACAAGTTTCCATTCTTTTAAA
TCCACCTCAGTTTGATAGTTAGGGTGTTCATCGCTCCAGGTGCAGTCTGGATT
Found at i:2189865 original size:14 final size:14
Alignment explanation
Indices: 2189846--2189873 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2189836 TTTTCATGTA
2189846 AAATGGAAAGATAC
1 AAATGGAAAGATAC
2189860 AAATGGAAAGATAC
1 AAATGGAAAGATAC
2189874 CTTAGTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
AAATGGAAAGATAC
Found at i:2193634 original size:91 final size:91
Alignment explanation
Indices: 2193429--2193636 Score: 215
Period size: 91 Copynumber: 2.3 Consensus size: 91
2193419 TTTGTCAAGT
* * * * * * *
2193429 TTAGGGACTAATTTGAAACAAGAAAAAGTCAAGCATCAATGTGGAGACAATTGCCTAATTCAAGC
1 TTAGGGATTAACTCGAAACAAAAAAAAGTCAAGCACCAATATGGAGACAATTACCTAATTCAAGC
* *
2193494 CCTTGAGTATAGGAAGAATTATCAAG
66 CCTTAAGTATAGGAAGAATTATCAAA
* * * * *
2193520 TTAGGTATTAACTTGGAACAAAAAAAAGTCAAGCCCCAATATGGAGACAATTACCTAATTCACGC
1 TTAGGGATTAACTCGAAACAAAAAAAAGTCAAGCACCAATATGGAGACAATTACCTAATTCAAGC
* * *
2193585 TC-TAATGTA-A-GAATAATTGTCAAA
66 CCTTAA-GTATAGGAAGAATTATCAAA
*
2193609 TTCAGGGATTTACTCGAAACAAAAAAAA
1 TT-AGGGATTAACTCGAAACAAAAAAAA
2193637 TTAAGCTCTG
Statistics
Matches: 96, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
89 13 0.14
90 24 0.25
91 59 0.61
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (91 bp):
TTAGGGATTAACTCGAAACAAAAAAAAGTCAAGCACCAATATGGAGACAATTACCTAATTCAAGC
CCTTAAGTATAGGAAGAATTATCAAA
Found at i:2197968 original size:26 final size:22
Alignment explanation
Indices: 2197934--2197987 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 22
2197924 AAAACTTTCA
2197934 ATAAATA--AAAATATATATAAT
1 ATAAATATTAAAATA-ATATAAT
2197955 CATTAAATATTAAAATAATATAAT
1 -A-TAAATATTAAAATAATATAAT
2197979 ATAAATATT
1 ATAAATATT
2197988 TTTTAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 9 0.31
23 7 0.24
24 7 0.24
25 6 0.21
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
ATAAATATTAAAATAATATAAT
Found at i:2199434 original size:18 final size:19
Alignment explanation
Indices: 2199393--2199428 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2199383 TATTGTTTGG
2199393 ATATTGTATAATTCTTGTT
1 ATATTGTATAATTCTTGTT
2199412 ATATTGT-TAATT-TTGTT
1 ATATTGTATAATTCTTGTT
2199429 GCTATTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 5 0.29
19 7 0.41
ACGTcount: A:0.25, C:0.03, G:0.11, T:0.61
Consensus pattern (19 bp):
ATATTGTATAATTCTTGTT
Found at i:2205724 original size:195 final size:194
Alignment explanation
Indices: 2205318--2205765 Score: 420
Period size: 195 Copynumber: 2.3 Consensus size: 194
2205308 ATGGGATAGT
* * * * *
2205318 TGAGGTATCGCATACGTT-CGAGTCCTCGACAACTTGTGCGAGCAGCATCGTGAGTCAAGAAATG
1 TGAGGTACCGCATACATTGCGAGTCCTCGACAACTCGTGTGAGCAGCATCGTGACTC-------G
** * * *
2205382 AGAAAAGAAATATGGATTCTAAATGGAATACAGGCCCCCTACGATGGCTGAGATTTATGCATAAG
59 AG-AAAGTGATATGGATCCTAAATGGAATACAGG-CCCCTACGATGGCTGAGATCTATACATAAG
* * * * *
2205447 TGCATATTCTCGACAGCTCGTGTGAGTAGCATCGTTAGGGAACAATTATATGCATAGATACCATA
122 TGCATATTATCGACAGCTCGTGTGAGCAGCATCATTAGGGAACAATTATATGCACAGACACCATA
* *
2205512 TCGATGGC
187 CCGATGAC
* ** *
2205520 TGAGGTACCGTATATGTTGCGAGTCCTCGACATCTCGTGTGAGCAGCATCGTGACTCGAGAAAGT
1 TGAGGTACCGCATACATTGCGAGTCCTCGACAACTCGTGTGAGCAGCATCGTGACTCGAGAAAGT
* * *
2205585 GATATGGATCCTAAATGGATTACAGG-CCCTACGATGGCTGAGA-CTATAC-TTATTGCATATTA
66 GATATGGATCCTAAATGGAATACAGGCCCCTACGATGGCTGAGATCTATACATAAGTGCATATTA
* * * * *
2205647 TCGACAGCTCGTGTGAGCAGTATCATTAGGGAATAGTT-TATAGAACAGACAGGCACCGTACCGA
131 TCGACAGCTCGTGTGAGCAGCATCATTAGGGAACAATTATAT-G--C--ACAGACACCATACCGA
*
2205711 TGAT
191 TGAC
* * * * *
2205715 TGGGGTACCGCATACATTGTGAGTCCTCGATAACTTGTGTGAGTAGCATCG
1 TGAGGTACCGCATACATTGCGAGTCCTCGACAACTCGTGTGAGCAGCATCG
2205766 AGTACTGGTA
Statistics
Matches: 203, Mismatches: 37, Indels: 19
0.78 0.14 0.07
Matches are distributed among these distances:
190 3 0.01
191 44 0.22
192 4 0.02
193 18 0.09
195 82 0.40
196 3 0.01
202 15 0.07
203 34 0.17
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (194 bp):
TGAGGTACCGCATACATTGCGAGTCCTCGACAACTCGTGTGAGCAGCATCGTGACTCGAGAAAGT
GATATGGATCCTAAATGGAATACAGGCCCCTACGATGGCTGAGATCTATACATAAGTGCATATTA
TCGACAGCTCGTGTGAGCAGCATCATTAGGGAACAATTATATGCACAGACACCATACCGATGAC
Found at i:2206543 original size:21 final size:21
Alignment explanation
Indices: 2206517--2206568 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2206507 GGAGTTTTTA
2206517 GTATCGGTAGAAG-CATGACAT
1 GTATCGGTAGAAGTCAT-ACAT
* *
2206538 GTATCGGTCGAAGTCATACTT
1 GTATCGGTAGAAGTCATACAT
2206559 GTATCGGTAG
1 GTATCGGTAG
2206569 TATTATTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (21 bp):
GTATCGGTAGAAGTCATACAT
Found at i:2220899 original size:31 final size:31
Alignment explanation
Indices: 2220855--2220933 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
2220845 AAGTTATGAA
2220855 TTTAG-TCTT-TATATTTT-AATCTGATCAAT
1 TTTAGTTCTTGTATATTTTGAATCTG-TCAAT
* *
2220884 TTTAGTTCTTGTATATTTTGATTTTGTCAAT
1 TTTAGTTCTTGTATATTTTGAATCTGTCAAT
* *
2220915 TTAAGTTCTTGTATTTTTT
1 TTTAGTTCTTGTATATTTT
2220934 TTAAAATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 5 0.12
30 4 0.09
31 30 0.70
32 4 0.09
ACGTcount: A:0.22, C:0.08, G:0.10, T:0.61
Consensus pattern (31 bp):
TTTAGTTCTTGTATATTTTGAATCTGTCAAT
Found at i:2222070 original size:30 final size:29
Alignment explanation
Indices: 2222013--2222071 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
2222003 TATGCTTTAA
*
2222013 TGTGCAATTGTATACATGAACTTTGATTT
1 TGTGCAATTGTATACATAAACTTTGATTT
* *
2222042 TGTGCAATTTTATACATAAAATTTTGATTT
1 TGTGCAATTGTATACAT-AAACTTTGATTT
2222072 AATCCAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (29 bp):
TGTGCAATTGTATACATAAACTTTGATTT
Found at i:2224015 original size:7 final size:7
Alignment explanation
Indices: 2224003--2224028 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2223993 TTCATTTAAC
2224003 TATTTAT
1 TATTTAT
2224010 TATTTAT
1 TATTTAT
2224017 TATTTAT
1 TATTTAT
2224024 TATTT
1 TATTT
2224029 TTAATTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TATTTAT
Found at i:2224393 original size:2 final size:2
Alignment explanation
Indices: 2224386--2224429 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2224376 TTTAATATTA
*
2224386 AT AT AT AT AT AT AC 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
2224428 AT
1 AT
2224430 TATCATTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2229122 original size:42 final size:41
Alignment explanation
Indices: 2229050--2229128 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 41
2229040 AATTTAATAT
* *
2229050 TTAATATTTTTTTATTTATTAAAAATTTATATATTATCATC
1 TTAACATTTTTTTAATTATTAAAAATTTATATATTATCATC
*
2229091 TTAACATTTTTTTACATTA-TAATAATATTATATATTAT
1 TTAACATTTTTTTA-ATTATTAAAAAT-TTATATATTAT
2229129 TATAAATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 19 0.58
42 14 0.42
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (41 bp):
TTAACATTTTTTTAATTATTAAAAATTTATATATTATCATC
Found at i:2229517 original size:2 final size:2
Alignment explanation
Indices: 2229510--2229539 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2229500 TTGCAATTTA
2229510 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
2229540 TGTTTAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2232468 original size:31 final size:29
Alignment explanation
Indices: 2232407--2232499 Score: 98
Period size: 29 Copynumber: 3.1 Consensus size: 29
2232397 CATAAGGATT
*
2232407 AAACATTTCAAAATGGTCATATAAAGGCC
1 AAACATTTCAAAATGGTCAAATAAAGGCC
* *
2232436 AAACATTTACAAAAGTGTTCAAATGAAGGCC
1 AAACATTT-CAAAA-TGGTCAAATAAAGGCC
* * *
2232467 AAACCTTTCAAAATGATCAGAT-AAGAGCC
1 AAACATTTCAAAATGGTCAAATAAAG-GCC
2232496 AAAC
1 AAAC
2232500 CTTTTTGAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
28 3 0.05
29 22 0.40
30 10 0.18
31 20 0.36
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.22
Consensus pattern (29 bp):
AAACATTTCAAAATGGTCAAATAAAGGCC
Found at i:2238122 original size:4 final size:4
Alignment explanation
Indices: 2238113--2238140 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2238103 CTTGAAATTG
2238113 ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA
2238141 TAGAGACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:2239678 original size:25 final size:25
Alignment explanation
Indices: 2239650--2239702 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
2239640 ATGTCCTTTT
2239650 TTTTTTAAATTGGTACCTAAATTAA
1 TTTTTTAAATTGGTACCTAAATTAA
* **
2239675 TTTTTTTAATTGGTACCTTTATTAA
1 TTTTTTAAATTGGTACCTAAATTAA
2239700 TTT
1 TTT
2239703 AATCTTTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.57
Consensus pattern (25 bp):
TTTTTTAAATTGGTACCTAAATTAA
Found at i:2260824 original size:89 final size:90
Alignment explanation
Indices: 2260668--2260839 Score: 238
Period size: 89 Copynumber: 1.9 Consensus size: 90
2260658 AAATCTAACT
* * * *
2260668 TTATAACCATCTTTGAATGCTTGCAGACAGATTATACAAGCTTTGAAATAGCTTAGCATCTAGGG
1 TTATAACCATCTTTGAATGCTTACACACAGATTATACAAGCTTTGAAATAGCCTAGCATCTAAGG
* *
2260733 AGCATATTGGTGTGGTGCCAGAGTC
66 AGCATATTGCTATGGTGCCAGAGTC
* ** * *
2260758 TTATAATCATCTTTGTGTGCTTACACATAGA-TATACAATCTTTGAAATAGCCTAGCATCTAAGG
1 TTATAACCATCTTTGAATGCTTACACACAGATTATACAAGCTTTGAAATAGCCTAGCATCTAAGG
2260822 AGCATATTGCTATGGTGC
66 AGCATATTGCTATGGTGC
2260840 TAAGGTTAGT
Statistics
Matches: 71, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
89 46 0.65
90 25 0.35
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (90 bp):
TTATAACCATCTTTGAATGCTTACACACAGATTATACAAGCTTTGAAATAGCCTAGCATCTAAGG
AGCATATTGCTATGGTGCCAGAGTC
Found at i:2262212 original size:21 final size:21
Alignment explanation
Indices: 2262188--2262257 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 21
2262178 TTGAAAATTC
2262188 TAGTTAAGCTCTCTCAATATT
1 TAGTTAAGCTCTCTCAATATT
* * * *
2262209 TAGTAGTAAGATCTGTGAAAATT
1 TAGT--TAAGCTCTCTCAATATT
2262232 CTAGTTAAGCTCTCTCAATATT
1 -TAGTTAAGCTCTCTCAATATT
2262254 TAGT
1 TAGT
2262258 AGTAAGATCT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
21 8 0.21
22 13 0.34
23 13 0.34
24 4 0.11
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (21 bp):
TAGTTAAGCTCTCTCAATATT
Found at i:2262218 original size:23 final size:23
Alignment explanation
Indices: 2262192--2262273 Score: 87
Period size: 23 Copynumber: 3.6 Consensus size: 23
2262182 AAATTCTAGT
*
2262192 TAAGCTCTCTCAATATTTAGTAG
1 TAAGATCTCTCAATATTTAGTAG
* * *
2262215 TAAGATCTGTGAAAATTCTAGT--
1 TAAGATCTCTCAATATT-TAGTAG
*
2262237 TAAGCTCTCTCAATATTTAGTAG
1 TAAGATCTCTCAATATTTAGTAG
*
2262260 TAAGATCTGTCAAT
1 TAAGATCTCTCAAT
2262274 GAAGAGTAGT
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
21 4 0.09
22 13 0.28
23 25 0.54
24 4 0.09
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (23 bp):
TAAGATCTCTCAATATTTAGTAG
Found at i:2262230 original size:45 final size:45
Alignment explanation
Indices: 2262179--2262269 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
2262169 TTTAAATTTT
2262179 TGAAAATTCTAGTTAAGCTCTCTCAATATTTAGTAGTAAGATCTG
1 TGAAAATTCTAGTTAAGCTCTCTCAATATTTAGTAGTAAGATCTG
2262224 TGAAAATTCTAGTTAAGCTCTCTCAATATTTAGTAGTAAGATCTG
1 TGAAAATTCTAGTTAAGCTCTCTCAATATTTAGTAGTAAGATCTG
2262269 T
1 T
2262270 CAATGAAGAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (45 bp):
TGAAAATTCTAGTTAAGCTCTCTCAATATTTAGTAGTAAGATCTG
Found at i:2263516 original size:29 final size:29
Alignment explanation
Indices: 2263474--2263529 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
2263464 TATATCTTCA
2263474 ATTACATGTAATACTATGACACAAATAGT
1 ATTACATGTAATACTATGACACAAATAGT
*
2263503 ATTATATGTAATACTATGACACAAATA
1 ATTACATGTAATACTATGACACAAATA
2263530 TAATGCCAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.32
Consensus pattern (29 bp):
ATTACATGTAATACTATGACACAAATAGT
Found at i:2266850 original size:7 final size:7
Alignment explanation
Indices: 2266850--2266875 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2266840 AAAATATAAA
2266850 AAATATT
1 AAATATT
2266857 AAATATT
1 AAATATT
2266864 AAATATT
1 AAATATT
2266871 AAATA
1 AAATA
2266876 AAAATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AAATATT
Found at i:2271650 original size:21 final size:21
Alignment explanation
Indices: 2271626--2271665 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2271616 TAAAACGACG
2271626 TAGTTTTGACTTTTAACTTAA
1 TAGTTTTGACTTTTAACTTAA
*
2271647 TAGTTTTTACTTTTAACTT
1 TAGTTTTGACTTTTAACTT
2271666 TAGAAAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.10, G:0.07, T:0.57
Consensus pattern (21 bp):
TAGTTTTGACTTTTAACTTAA
Found at i:2272875 original size:636 final size:636
Alignment explanation
Indices: 2271647--2273022 Score: 2439
Period size: 636 Copynumber: 2.2 Consensus size: 636
2271637 TTTAACTTAA
* *
2271647 TAGTTTTTACTTTTAACTTTAGAAAATGTAAACATTTATGAAAACGATGTAGTTTTACCTTTTTT
1 TAGTTTTGACTTTTAACTTTAGAAAAGGTAAACATTTATGAAAACGATGTAGTTTTACCTTTTTT
2271712 TATTCAGATTTTCGAATAACTCAAATTGTGTAATTCATAAATGTCA-TATACCTACAAGGGCGAA
66 TATTCAGATTTTCGAATAACTCAAATTGTGTAATTCATAAATGTCATTATACCTACAAGGGCGAA
2271776 GTTAGAAAATTTTTTAAAGGGGTCGAAGTTAAATTGTAATTGTTACGATAGTAAAAGTGAAATTC
131 GTTAGAAAATTTTTTAAAGGGGTCGAAGTTAAATTGTAATTGTTACGATAGTAAAAGTGAAATTC
2271841 TTAAAAGAATAAATTAAAATTTTATCATTTCAAGGGAGATGCAATTTTACTTTTACTAATTTAAA
196 TTAAAAGAATAAATTAAAATTTTATCATTTCAAGGGAGATGCAATTTTACTTTTACTAATTTAAA
*
2271906 ATTTTAAAAAAATTTAAGGGTTTAAATGGAAATTTTTCCATTTTAGGGGGCTAGGACCACTGCCA
261 ATTTTAAAAAAATTTAAGGGTTTAAATGAAAATTTTTCCATTTTAGGGGGCTAGGACCACTGCCA
* * **
2271971 ACCCCCTGGCTAGGGGTGAGCTTCGATCAAGTTGAGTTTAATCGAGTCAAAAAATTTCGAGTTAG
326 ACCCCCTAGCTAGGGGTGAGATTCGATCAAGTTGAGTCGAATCGAGTCAAAAAATTTCGAGTTAG
* *
2272036 TAGAGTTGACGAATCTTATTTTAGCAATCGAATTCAATTTGAATTTTTTTCGAATTGAATCGAAT
391 TAGAGTTGACGAATCTTATTTTAGCAATCGAATTCAATTTGAATTTTTTTTGAATTAAATCGAAT
*
2272101 CGAGTCAAAAAAAATTCGAGTCAAATCGAGTTGAGTTAACGAATCTTATTATTTATACGCAACAT
456 CGAGTC-AAAAAAATTCGAGTCAAATCGAGTTGAGTTAACGAATCTTATTATTTATACGCAATAT
2272166 TGCGTTTGCATGGACCGATTGTTTAACTAGTAGACGAAGTACAAGATTATTTAACTTCATAAACA
520 TGCGTTTGCATGGACCGATTGTTTAACTAGTAGACGAAGTACAAGATTATTTAACTTCATAAACA
* * *
2272231 ATATAATGATTTTGTCTTTTGACTTAATGAGTAAACACTTATTAAAACAACG
585 ATATAATGATTTTGTCTTTTAACTTAATGAGTAAACATTTATTAAAACGACG
2272283 TAGTTTTGACTTTTAACTTTAGAAAAGGTAAACATTTATGAAAACGATGTAGTTTTACCTTTTTT
1 TAGTTTTGACTTTTAACTTTAGAAAAGGTAAACATTTATGAAAACGATGTAGTTTTACCTTTTTT
*
2272348 TATTCAGATTTTCGAATAACTCAAATTGTGTAATTCATAAATGTCATTATTCCTACAAGGGCGAA
66 TATTCAGATTTTCGAATAACTCAAATTGTGTAATTCATAAATGTCATTATACCTACAAGGGCGAA
*
2272413 GCTAGAAAATTTTTTAAAGGGGTCGAAGTTAAATTGTAATTGTTACGATAGTAAAAGTGAAATTC
131 GTTAGAAAATTTTTTAAAGGGGTCGAAGTTAAATTGTAATTGTTACGATAGTAAAAGTGAAATTC
*
2272478 TTAAAAGAATAAATTAAAATTTTATCATTTCAAGGGAGATGCAATTTTATTTTTACTAATTTAAA
196 TTAAAAGAATAAATTAAAATTTTATCATTTCAAGGGAGATGCAATTTTACTTTTACTAATTTAAA
*
2272543 ATTTTAAAAAAATTTAAGGGTTTAAATGAAAATTTTTTCATTTTAGGGGGCTAGGACCACTGCCA
261 ATTTTAAAAAAATTTAAGGGTTTAAATGAAAATTTTTCCATTTTAGGGGGCTAGGACCACTGCCA
* * *
2272608 ACCCCCTAGCTAGGGGTGAGATTCGATCAAATTGAGTCGAATCAAGTCAAAAAATTTCGAGTTGG
326 ACCCCCTAGCTAGGGGTGAGATTCGATCAAGTTGAGTCGAATCGAGTCAAAAAATTTCGAGTTAG
*
2272673 TAGAGTTGATGAATCTTATTTTAGCAATCGAATTCAATTTGAATTTTTTTTGAATTAAATCGAAT
391 TAGAGTTGACGAATCTTATTTTAGCAATCGAATTCAATTTGAATTTTTTTTGAATTAAATCGAAT
*
2272738 TGAGTCAAAAAAATTCGAGTCAAATCGAGTTGAGTTAACGAATCTTATTATTTATACGCAATATT
456 CGAGTCAAAAAAATTCGAGTCAAATCGAGTTGAGTTAACGAATCTTATTATTTATACGCAATATT
* *
2272803 GCGTTTGCATGGACCGATAGTTCAACTAGTAGACGAAGTACAAGATTATTTAACTTCATAAACAA
521 GCGTTTGCATGGACCGATTGTTTAACTAGTAGACGAAGTACAAGATTATTTAACTTCATAAACAA
* *
2272868 CATAATGATTTTATCTTTTAACTTAATGAGTAAACATTTATTAAAACGACG
586 TATAATGATTTTGTCTTTTAACTTAATGAGTAAACATTTATTAAAACGACG
* * * * *
2272919 TAGTTTTAACTTTTAACTTTAAAAAAGGTAAATATTTATGAAAACGATATAGTTTTACCTTTTCT
1 TAGTTTTGACTTTTAACTTTAGAAAAGGTAAACATTTATGAAAACGATGTAGTTTTACCTTTTTT
* *
2272984 TATTCGGATTTTCGGATAACTCAAATTGTGTAATTCATA
66 TATTCAGATTTTCGAATAACTCAAATTGTGTAATTCATA
2273023 TTCGAGTTAA
Statistics
Matches: 706, Mismatches: 33, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
636 373 0.53
637 333 0.47
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (636 bp):
TAGTTTTGACTTTTAACTTTAGAAAAGGTAAACATTTATGAAAACGATGTAGTTTTACCTTTTTT
TATTCAGATTTTCGAATAACTCAAATTGTGTAATTCATAAATGTCATTATACCTACAAGGGCGAA
GTTAGAAAATTTTTTAAAGGGGTCGAAGTTAAATTGTAATTGTTACGATAGTAAAAGTGAAATTC
TTAAAAGAATAAATTAAAATTTTATCATTTCAAGGGAGATGCAATTTTACTTTTACTAATTTAAA
ATTTTAAAAAAATTTAAGGGTTTAAATGAAAATTTTTCCATTTTAGGGGGCTAGGACCACTGCCA
ACCCCCTAGCTAGGGGTGAGATTCGATCAAGTTGAGTCGAATCGAGTCAAAAAATTTCGAGTTAG
TAGAGTTGACGAATCTTATTTTAGCAATCGAATTCAATTTGAATTTTTTTTGAATTAAATCGAAT
CGAGTCAAAAAAATTCGAGTCAAATCGAGTTGAGTTAACGAATCTTATTATTTATACGCAATATT
GCGTTTGCATGGACCGATTGTTTAACTAGTAGACGAAGTACAAGATTATTTAACTTCATAAACAA
TATAATGATTTTGTCTTTTAACTTAATGAGTAAACATTTATTAAAACGACG
Found at i:2273999 original size:2 final size:2
Alignment explanation
Indices: 2273992--2274020 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2273982 TAGGAAACAT
2273992 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2274021 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2276419 original size:18 final size:18
Alignment explanation
Indices: 2276398--2276435 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2276388 TAAATTTTCG
*
2276398 AATTCAAATAACTCGAAT
1 AATTCAAATAAATCGAAT
*
2276416 AATTCGAATAAATCGAAT
1 AATTCAAATAAATCGAAT
2276434 AA
1 AA
2276436 AATTATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.13, G:0.08, T:0.26
Consensus pattern (18 bp):
AATTCAAATAAATCGAAT
Found at i:2281043 original size:20 final size:19
Alignment explanation
Indices: 2280997--2281044 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
2280987 TTTTAGGAAG
* *
2280997 TAAAATGTAATTTTATAAT
1 TAAAATTTAAATTTATAAT
*
2281016 TACTAATTTAAATTTATAATT
1 TA-AAATTTAAATTTATAA-T
2281037 TAAAATTT
1 TAAAATTT
2281045 TATAAATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
TAAAATTTAAATTTATAAT
Found at i:2283335 original size:18 final size:18
Alignment explanation
Indices: 2283308--2283350 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
2283298 TGCCACATTA
* *
2283308 ATAAATAATTTTAAAATT
1 ATAAAAAATTCTAAAATT
*
2283326 ATAAAAAATTCTAAATTT
1 ATAAAAAATTCTAAAATT
*
2283344 TTAAAAA
1 ATAAAAA
2283351 GGAAGTTCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAAAAAATTCTAAAATT
Found at i:2286068 original size:17 final size:19
Alignment explanation
Indices: 2286036--2286070 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
2286026 ATATTAATAT
2286036 TTTAAAATTCAAAAATTAA
1 TTTAAAATTCAAAAATTAA
2286055 TTTAAAA-T-AAAAATTA
1 TTTAAAATTCAAAAATTA
2286071 TAATTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
TTTAAAATTCAAAAATTAA
Found at i:2288084 original size:39 final size:38
Alignment explanation
Indices: 2287992--2288080 Score: 117
Period size: 39 Copynumber: 2.3 Consensus size: 38
2287982 CACTCAATGG
*
2287992 ACACTTTTTGAAGAGTCACAACCCTTTCATATTGGACGA
1 ACACCTTTTGAAGAGTCACAACCCTTTCATATTGGAC-A
* *
2288031 ACACCTTTTGAAGAGTCATAACTCTTTTCATATTGGAC-
1 ACACCTTTTGAAGAGTCACAAC-CCTTTCATATTGGACA
*
2288069 ATACCTTTTGAA
1 ACACCTTTTGAA
2288081 AGAGACTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
38 11 0.24
39 20 0.44
40 14 0.31
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.35
Consensus pattern (38 bp):
ACACCTTTTGAAGAGTCACAACCCTTTCATATTGGACA
Found at i:2292944 original size:39 final size:40
Alignment explanation
Indices: 2292890--2292966 Score: 147
Period size: 39 Copynumber: 1.9 Consensus size: 40
2292880 GCACTCAATT
2292890 GACACCTTTTGAAGAGTCACAACCC-TTTCATATTGGATA
1 GACACCTTTTGAAGAGTCACAACCCTTTTCATATTGGATA
2292929 GACACCTTTTGAAGAGTCACAACCCTTTTCATATTGGA
1 GACACCTTTTGAAGAGTCACAACCCTTTTCATATTGGA
2292967 CATACCTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
39 25 0.68
40 12 0.32
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (40 bp):
GACACCTTTTGAAGAGTCACAACCCTTTTCATATTGGATA
Found at i:2292983 original size:39 final size:38
Alignment explanation
Indices: 2292891--2292976 Score: 129
Period size: 39 Copynumber: 2.2 Consensus size: 38
2292881 CACTCAATTG
*
2292891 ACACCTTTTGAAGAGTCACAACCCTTTCATATTGGATAG
1 ACACCTTTTGAAGAGTCACAACCCTTTCATATTGGA-AC
2292930 ACACCTTTTGAAGAGTCACAACCCTTTTCATATTGG-AC
1 ACACCTTTTGAAGAGTCACAACCC-TTTCATATTGGAAC
*
2292968 ATACCTTTT
1 ACACCTTTT
2292977 AAAAGAGACT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
38 9 0.20
39 24 0.55
40 11 0.25
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (38 bp):
ACACCTTTTGAAGAGTCACAACCCTTTCATATTGGAAC
Found at i:2302158 original size:30 final size:29
Alignment explanation
Indices: 2302097--2302161 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
2302087 AAGTTGTGGA
* *
2302097 TTTAATTTTTGTACTTTAATTTGGCTAAT
1 TTTAGTTTTTGTACTTTAATTTAGCTAAT
*
2302126 TTTAGTTTTTGTACTCTTCAA-TTAGTTAAT
1 TTTAGTTTTTGTACT-TT-AATTTAGCTAAT
2302156 TTTAGT
1 TTTAGT
2302162 CCCTACACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 14 0.45
30 15 0.48
31 2 0.06
ACGTcount: A:0.23, C:0.08, G:0.11, T:0.58
Consensus pattern (29 bp):
TTTAGTTTTTGTACTTTAATTTAGCTAAT
Found at i:2303424 original size:20 final size:20
Alignment explanation
Indices: 2303401--2303438 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2303391 ACGCACATAC
2303401 GTGTGTATGTATGTATGTGT
1 GTGTGTATGTATGTATGTGT
*
2303421 GTGTGTGTGTATGTATGT
1 GTGTGTATGTATGTATGT
2303439 ATGGTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.00, G:0.37, T:0.50
Consensus pattern (20 bp):
GTGTGTATGTATGTATGTGT
Found at i:2311700 original size:2 final size:2
Alignment explanation
Indices: 2311695--2311719 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2311685 ATATATATAT
2311695 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
2311720 CATAAGTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2316259 original size:31 final size:32
Alignment explanation
Indices: 2316221--2316291 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 32
2316211 TTGGGTTAGG
*
2316221 ACTAAAATTTCA-AAATTTGAAAAGTATAAGA
1 ACTAAAATTTCACAAATTCGAAAAGTATAAGA
* * * *
2316252 ACTAAAA-TTGACCAATTCGAAAAGTGTAGGA
1 ACTAAAATTTCACAAATTCGAAAAGTATAAGA
2316283 ACTAAAATT
1 ACTAAAATT
2316292 GATCAATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
30 3 0.09
31 29 0.88
32 1 0.03
ACGTcount: A:0.51, C:0.10, G:0.13, T:0.27
Consensus pattern (32 bp):
ACTAAAATTTCACAAATTCGAAAAGTATAAGA
Found at i:2316292 original size:31 final size:31
Alignment explanation
Indices: 2316234--2316299 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
2316224 AAAATTTCAA
*
2316234 AATTTGAAAAGTATAAGAACTAAAATTGACC
1 AATTCGAAAAGTATAAGAACTAAAATTGACC
* * *
2316265 AATTCGAAAAGTGTAGGAACTAAAATTGATC
1 AATTCGAAAAGTATAAGAACTAAAATTGACC
2316296 AATT
1 AATT
2316300 TAAAGTACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.48, C:0.09, G:0.15, T:0.27
Consensus pattern (31 bp):
AATTCGAAAAGTATAAGAACTAAAATTGACC
Found at i:2317262 original size:18 final size:20
Alignment explanation
Indices: 2317241--2317279 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
2317231 TAAATCATTT
2317241 TCAAGTATA-AAA-TACTCA
1 TCAAGTATATAAATTACTCA
*
2317259 TCAATTATATAAATTACTCA
1 TCAAGTATATAAATTACTCA
2317279 T
1 T
2317280 TAATAAACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 3 0.17
20 7 0.39
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.36
Consensus pattern (20 bp):
TCAAGTATATAAATTACTCA
Found at i:2320168 original size:3 final size:3
Alignment explanation
Indices: 2320154--2320186 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
2320144 ATATGACTGT
*
2320154 TGC TGT TGC TGC TGC TGC TGC TGC TGC TGC TGC
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
2320187 CTCCTTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.30, G:0.33, T:0.36
Consensus pattern (3 bp):
TGC
Found at i:2327939 original size:16 final size:16
Alignment explanation
Indices: 2327918--2327959 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
2327908 AGTATAATGA
2327918 TCAAGATGTTCATCGC
1 TCAAGATGTTCATCGC
2327934 TCAAGATGTTCATCGC
1 TCAAGATGTTCATCGC
*
2327950 TCTAGATGTT
1 TCAAGATGTT
2327960 ATTTGGATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (16 bp):
TCAAGATGTTCATCGC
Found at i:2335314 original size:26 final size:26
Alignment explanation
Indices: 2335280--2335330 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
2335270 AAAATTATAC
2335280 TTTAACTCTT-AAAAATAAAAAAATG
1 TTTAACTCTTCAAAAATAAAAAAATG
*
2335305 TTTAATCTCTTCAAAAATAATAAAAT
1 TTTAA-CTCTTCAAAAATAAAAAAAT
2335331 TATAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.22
26 5 0.22
27 13 0.57
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.35
Consensus pattern (26 bp):
TTTAACTCTTCAAAAATAAAAAAATG
Found at i:2337095 original size:21 final size:21
Alignment explanation
Indices: 2337057--2337108 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
2337047 GCATCAATAA
2337057 TTTTATGTATTTTCTTATATG
1 TTTTATGTATTTTCTTATATG
*
2337078 TTTT-TGTATTCTTGTTATA--
1 TTTTATGTATT-TTCTTATATG
2337097 -TTTATGTATTTT
1 TTTTATGTATTTT
2337109 TCATGTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 6 0.21
20 6 0.21
21 11 0.39
ACGTcount: A:0.17, C:0.04, G:0.10, T:0.69
Consensus pattern (21 bp):
TTTTATGTATTTTCTTATATG
Found at i:2337106 original size:19 final size:19
Alignment explanation
Indices: 2337058--2337108 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
2337048 CATCAATAAT
2337058 TTTATGTATTTTCTTATATG
1 TTTATGTATTTTCTTATA-G
* *
2337078 TTTTTGTATTCTTGTTATA-
1 TTTATGTATT-TTCTTATAG
2337097 TTTATGTATTTT
1 TTTATGTATTTT
2337109 TCATGTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 2 0.07
19 9 0.33
20 9 0.33
21 7 0.26
ACGTcount: A:0.18, C:0.04, G:0.10, T:0.69
Consensus pattern (19 bp):
TTTATGTATTTTCTTATAG
Found at i:2340650 original size:2 final size:2
Alignment explanation
Indices: 2340643--2340667 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2340633 TCTTGACCTA
2340643 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 A
2340668 GTTAGCCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2343370 original size:12 final size:14
Alignment explanation
Indices: 2343342--2343392 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 14
2343332 AAAATTATCC
2343342 AAAATAATAATATT
1 AAAATAATAATATT
2343356 AAAATAA-AA-ATT
1 AAAATAATAATATT
2343368 AAAA-AAT-AT-TT
1 AAAATAATAATATT
2343379 -AAA-AATAATATT
1 AAAATAATAATATT
2343391 AA
1 AA
2343393 TTTTTATCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
10 6 0.19
11 7 0.22
12 9 0.28
13 3 0.09
14 7 0.22
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAATAATAATATT
Found at i:2344919 original size:16 final size:17
Alignment explanation
Indices: 2344889--2344922 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2344879 AGCATCATTC
*
2344889 TTTTATAATTTATAAAA
1 TTTTATAATTAATAAAA
2344906 TTTTA-AATTAATAAAA
1 TTTTATAATTAATAAAA
2344922 T
1 T
2344923 AAAATTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTATAATTAATAAAA
Found at i:2346707 original size:12 final size:12
Alignment explanation
Indices: 2346690--2346714 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2346680 TTATATTATT
2346690 TTACCATTTCAA
1 TTACCATTTCAA
2346702 TTACCATTTCAA
1 TTACCATTTCAA
2346714 T
1 T
2346715 CATATCACGA
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:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (12 bp):
TTACCATTTCAA
Found at i:2347778 original size:2 final size:2
Alignment explanation
Indices: 2347771--2347805 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2347761 TGATTTATGA
2347771 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 A
2347806 AATACATAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2351792 original size:29 final size:28
Alignment explanation
Indices: 2351725--2351779 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
2351715 CTCAAGTTGG
*
2351725 TAAAAAAAAATTTGGGACCTTTAAAAAC
1 TAAAAAAAAATTTGGGACCCTTAAAAAC
*
2351753 TAAAAGAAAAATTTGGGGCCCTTAAAA
1 TAAAA-AAAAATTTGGGACCCTTAAAA
2351780 GTTGATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.51, C:0.11, G:0.15, T:0.24
Consensus pattern (28 bp):
TAAAAAAAAATTTGGGACCCTTAAAAAC
Found at i:2351795 original size:30 final size:30
Alignment explanation
Indices: 2351718--2351796 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 30
2351708 TTTAAGTCTC
* *
2351718 AAGTTGGTAAAAAAAAATTTGGGACCTTTAA
1 AAGTTGAT-AAAAAAAATTTGGGACCCTTAA
** *
2351749 AAACT-A-AAAGAAAAATTTGGGGCCCTTAA
1 AAGTTGATAAA-AAAAATTTGGGACCCTTAA
2351778 AAGTTGATAAAAAAAATTT
1 AAGTTGATAAAAAAAATTT
2351797 TTACCTGTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
28 3 0.08
29 20 0.53
30 9 0.24
31 6 0.16
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.27
Consensus pattern (30 bp):
AAGTTGATAAAAAAAATTTGGGACCCTTAA
Found at i:2354260 original size:23 final size:23
Alignment explanation
Indices: 2354234--2354306 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
2354224 TAAACATAAA
2354234 TATTTTTTTTTGTAAAATTCTGT
1 TATTTTTTTTTGTAAAATTCTGT
* ** ***
2354257 TATTATTTAATGATAAACA-T-AAA
1 TATTTTTTTTTG-TAAA-ATTCTGT
2354280 TATTTTTTTTTGTAAAATTCTGT
1 TATTTTTTTTTGTAAAATTCTGT
2354303 TATT
1 TATT
2354307 ATTTAATGAT
Statistics
Matches: 34, Mismatches: 12, Indels: 8
0.63 0.22 0.15
Matches are distributed among these distances:
21 1 0.03
22 5 0.15
23 22 0.65
24 5 0.15
25 1 0.03
ACGTcount: A:0.32, C:0.04, G:0.07, T:0.58
Consensus pattern (23 bp):
TATTTTTTTTTGTAAAATTCTGT
Found at i:2354273 original size:46 final size:46
Alignment explanation
Indices: 2354223--2354318 Score: 192
Period size: 46 Copynumber: 2.1 Consensus size: 46
2354213 AAATATTAAC
2354223 ATAAACATAAATATTTTTTTTTGTAAAATTCTGTTATTATTTAATG
1 ATAAACATAAATATTTTTTTTTGTAAAATTCTGTTATTATTTAATG
2354269 ATAAACATAAATATTTTTTTTTGTAAAATTCTGTTATTATTTAATG
1 ATAAACATAAATATTTTTTTTTGTAAAATTCTGTTATTATTTAATG
2354315 ATAA
1 ATAA
2354319 TTTATATTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (46 bp):
ATAAACATAAATATTTTTTTTTGTAAAATTCTGTTATTATTTAATG
Found at i:2354387 original size:23 final size:21
Alignment explanation
Indices: 2354343--2354388 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
2354333 ATTTTGTGGA
*
2354343 TTAAATTTAAACATTGAATTT
1 TTAAATTTAAACATTCAATTT
*
2354364 TTAAATTGTGAAACATTCATTTT
1 TTAAATT-T-AAACATTCAATTT
2354387 TT
1 TT
2354389 TTTGGTAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 1 0.05
23 13 0.62
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (21 bp):
TTAAATTTAAACATTCAATTT
Found at i:2355422 original size:44 final size:44
Alignment explanation
Indices: 2355373--2355462 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
2355363 CTAACCCATA
2355373 AATTGAGAATTATTGTTTAATATATAAGGCGCTTAGGATACTCG
1 AATTGAGAATTATTGTTTAATATATAAGGCGCTTAGGATACTCG
2355417 AATTGAGAATTATTGTTTAATATATAAGGCGCTTAGGATACTCG
1 AATTGAGAATTATTGTTTAATATATAAGGCGCTTAGGATACTCG
2355461 AA
1 AA
2355463 CCCACATCAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.36
Consensus pattern (44 bp):
AATTGAGAATTATTGTTTAATATATAAGGCGCTTAGGATACTCG
Found at i:2359200 original size:164 final size:164
Alignment explanation
Indices: 2358898--2359213 Score: 393
Period size: 164 Copynumber: 1.9 Consensus size: 164
2358888 TAACTTCGCC
* * * * * * *
2358898 ACAATGAATAGAATAAGTGATCTTAGTCTTGTACTAAGTGTGATCGTATCTCTTTTTTTCTGTAC
1 ACAATGAATAGAATAAGTGACCTCAGTCTTGTACTAAGTATGACCATATCTCTCTTTCTCTGTAC
* * ** * * *
2358963 TTAAGAAAATTTCATGATGTTAAAGGTCTTCAAAAGAGTCTTTATTGAAGAACAATTTGTTTACA
66 TTAAGAAAATTTCATCACGTTAAAGGTCTTCAAAAGACCCCTTATTGAAGAACAACTTGCTTACA
*
2359028 ATAATTTGCACTAAAATAAGTTCCTCACAATGAT
131 ACAATTTGCACTAAAATAAGTTCCTCACAATGAT
* * *
2359062 ACAATGAATAGAATAAGTGCCCTCAGTCTTGTACTAAGTATGGCCATATCTCTCTTTCTCTTTAC
1 ACAATGAATAGAATAAGTGACCTCAGTCTTGTACTAAGTATGACCATATCTCTCTTTCTCTGTAC
* ***
2359127 TTAAGGAAAATTT-ATCACGTTAAAGGTCTTTAAAAGACCCCTTATCT-TTTAACAACTTGCTTA
66 TTAA-GAAAATTTCATCACGTTAAAGGTCTTCAAAAGACCCCTTAT-TGAAGAACAACTTGCTTA
*
2359190 CAACAATTTGCATTAAAATAAGTT
129 CAACAATTTGCACTAAAATAAGTT
2359214 TCTCGCCGTG
Statistics
Matches: 127, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
164 118 0.93
165 9 0.07
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (164 bp):
ACAATGAATAGAATAAGTGACCTCAGTCTTGTACTAAGTATGACCATATCTCTCTTTCTCTGTAC
TTAAGAAAATTTCATCACGTTAAAGGTCTTCAAAAGACCCCTTATTGAAGAACAACTTGCTTACA
ACAATTTGCACTAAAATAAGTTCCTCACAATGAT
Found at i:2361751 original size:28 final size:26
Alignment explanation
Indices: 2361686--2361755 Score: 72
Period size: 28 Copynumber: 2.7 Consensus size: 26
2361676 TTAAATTTTT
*
2361686 TTGAAAATATTTATAT-TTTTTAATA
1 TTGAAAATTTTTATATATTTTTAATA
* *
2361711 TTTAATAA-TTTTATATATTTTCTATTTA
1 TTGAA-AATTTTTATATATTTT-TA-ATA
2361739 TTGAAAATTTTTATATA
1 TTGAAAATTTTTATATA
2361756 GTAATCTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
25 11 0.31
26 6 0.17
27 4 0.11
28 15 0.42
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (26 bp):
TTGAAAATTTTTATATATTTTTAATA
Found at i:2364273 original size:28 final size:27
Alignment explanation
Indices: 2364215--2364269 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
2364205 ATTTCACGTT
*
2364215 ATAATATTATTATAGTATTTAATTATA
1 ATAATATTATTATAGTATTTAATCATA
2364242 ATAATTATTATTAT--TATATTAATCATA
1 ATAA-TATTATTATAGTAT-TTAATCATA
2364269 A
1 A
2364270 ATAAATATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 3 0.12
27 13 0.52
28 9 0.36
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
ATAATATTATTATAGTATTTAATCATA
Found at i:2381763 original size:24 final size:26
Alignment explanation
Indices: 2381735--2381796 Score: 65
Period size: 30 Copynumber: 2.3 Consensus size: 26
2381725 ACAATAACAA
2381735 AATTT-TATTATT-AGTCATATTTTT
1 AATTTATATTATTAAGTCATATTTTT
2381759 AATTTTTATATTATTAACAGTCATATTTTT
1 AA--TTTATATTATT-A-AGTCATATTTTT
*
2381789 AATGTATA
1 AATTTATA
2381797 CATCATAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
24 2 0.06
26 3 0.10
27 7 0.23
28 5 0.16
30 14 0.45
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (26 bp):
AATTTATATTATTAAGTCATATTTTT
Found at i:2385799 original size:22 final size:20
Alignment explanation
Indices: 2385752--2385805 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 20
2385742 ATTGCATTTT
* *
2385752 GGTGCCTCTGTTTGCACTTC
1 GGTGCCTCTATTTGCACTAC
*
2385772 GATGCCTCTATATGTGCACTAC
1 GGTGCCTCTAT-T-TGCACTAC
2385794 GGTGCCTCTATT
1 GGTGCCTCTATT
2385806 ATCATTTTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 9 0.32
21 2 0.07
22 17 0.61
ACGTcount: A:0.13, C:0.28, G:0.22, T:0.37
Consensus pattern (20 bp):
GGTGCCTCTATTTGCACTAC
Found at i:2397255 original size:5 final size:5
Alignment explanation
Indices: 2397247--2397272 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2397237 GGCACAGTGA
2397247 CAGAC CAGAC CAGAC CAGAC CAGAC C
1 CAGAC CAGAC CAGAC CAGAC CAGAC C
2397273 GGCAGAAGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.42, G:0.19, T:0.00
Consensus pattern (5 bp):
CAGAC
Found at i:2420995 original size:17 final size:18
Alignment explanation
Indices: 2420973--2421008 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2420963 TAAATGAGTT
2420973 AATTAAGAT-TAAATTGG
1 AATTAAGATATAAATTGG
*
2420990 AATTAAGGTATAAATTGG
1 AATTAAGATATAAATTGG
2421008 A
1 A
2421009 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.33
Consensus pattern (18 bp):
AATTAAGATATAAATTGG
Found at i:2421441 original size:37 final size:38
Alignment explanation
Indices: 2421341--2421443 Score: 91
Period size: 37 Copynumber: 2.7 Consensus size: 38
2421331 GACCTCGAGT
* **
2421341 CGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGATT
1 CGATGAGACACTGGGTGTC---ACTTTACTTCGGATAGAGC
** * ** *
2421382 CGATGAGGTACTGAGTACCACTTTACTTCGGCTAG-GC
1 CGATGAGACACTGGGTGTCACTTTACTTCGGATAGAGC
2421419 CGATGAGACACTGGGTGTCACTTTA
1 CGATGAGACACTGGGTGTCACTTTA
2421444 TTGCTTCGAA
Statistics
Matches: 48, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
37 20 0.42
38 14 0.29
41 14 0.29
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.31
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCACTTTACTTCGGATAGAGC
Found at i:2424183 original size:14 final size:14
Alignment explanation
Indices: 2424164--2424190 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2424154 GGAAAAGGCT
2424164 GAAAAGCTTTTACG
1 GAAAAGCTTTTACG
2424178 GAAAAGCTTTTAC
1 GAAAAGCTTTTAC
2424191 AAGTAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (14 bp):
GAAAAGCTTTTACG
Found at i:2424707 original size:12 final size:12
Alignment explanation
Indices: 2424690--2424715 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2424680 ATAGTCCACA
2424690 TATTTTTTCCTT
1 TATTTTTTCCTT
2424702 TATTTTTTCCTT
1 TATTTTTTCCTT
2424714 TA
1 TA
2424716 AGAAGAAATT
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:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (12 bp):
TATTTTTTCCTT
Found at i:2430052 original size:42 final size:42
Alignment explanation
Indices: 2429993--2430099 Score: 198
Period size: 42 Copynumber: 2.5 Consensus size: 42
2429983 AGTAAAATAG
2429993 TAAATAAAA-ACACATGATAATTTTTTAAGGATACTTGTGAAA
1 TAAA-AAAATACACATGATAATTTTTTAAGGATACTTGTGAAA
2430035 TAAAAAAATACACATGATAATTTTTTAAGGATACTTGTGAAA
1 TAAAAAAATACACATGATAATTTTTTAAGGATACTTGTGAAA
2430077 TAAAAAAATACACATGATAATTT
1 TAAAAAAATACACATGATAATTT
2430100 AATGCATAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
41 4 0.06
42 60 0.94
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (42 bp):
TAAAAAAATACACATGATAATTTTTTAAGGATACTTGTGAAA
Found at i:2430879 original size:16 final size:16
Alignment explanation
Indices: 2430858--2430888 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2430848 ATTTTTTGTA
*
2430858 TAAATAATACAATTTT
1 TAAATAATAAAATTTT
2430874 TAAATAATAAAATTT
1 TAAATAATAAAATTT
2430889 CTAACTGCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATAATAAAATTTT
Found at i:2433960 original size:52 final size:52
Alignment explanation
Indices: 2433886--2433992 Score: 205
Period size: 52 Copynumber: 2.1 Consensus size: 52
2433876 AAAAAAAAGT
2433886 GTTGGGTTTGGATTTTTGAAACATTGGGCCTTAAAATTAGTTATTTACAAAA
1 GTTGGGTTTGGATTTTTGAAACATTGGGCCTTAAAATTAGTTATTTACAAAA
*
2433938 GTTGGGTTTGGATTTTTGAAACATTGGGCCTTAAAATTAGTTATTTACATAA
1 GTTGGGTTTGGATTTTTGAAACATTGGGCCTTAAAATTAGTTATTTACAAAA
2433990 GTT
1 GTT
2433993 AAAAGATCTA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.42
Consensus pattern (52 bp):
GTTGGGTTTGGATTTTTGAAACATTGGGCCTTAAAATTAGTTATTTACAAAA
Found at i:2437541 original size:31 final size:30
Alignment explanation
Indices: 2437485--2437542 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
2437475 AACAAAAATT
* *
2437485 AACAATAAAACAAGAGTTATACAATATCCA
1 AACAATAAAACAAGAATAATACAATATCCA
2437515 AACAATAACAACAA-AATAATATCAATAT
1 AACAATAA-AACAAGAATAATA-CAATAT
2437543 AATAGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.60, C:0.16, G:0.03, T:0.21
Consensus pattern (30 bp):
AACAATAAAACAAGAATAATACAATATCCA
Found at i:2451045 original size:33 final size:34
Alignment explanation
Indices: 2450991--2451054 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 34
2450981 TATAATTTTT
*
2450991 AAAAAATTAAATTATTTTTTTA-TATTTTAAGGG
1 AAAAAATTAAATTATTTTTTTACTAATTTAAGGG
2451024 AAAAAA-TATAATT-TTATTTTTACTAATTTAA
1 AAAAAATTA-AATTATT-TTTTTACTAATTTAA
2451055 AATTTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
32 4 0.15
33 16 0.59
34 7 0.26
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (34 bp):
AAAAAATTAAATTATTTTTTTACTAATTTAAGGG
Found at i:2465856 original size:4 final size:4
Alignment explanation
Indices: 2465847--2465893 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
2465837 GAAATAGATA
2465847 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
2465894 ATGGGCAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:2466378 original size:16 final size:16
Alignment explanation
Indices: 2466343--2466386 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
2466333 CTGACATGGC
* *
2466343 GCTGACGTGGA-GCTT
1 GCTGACGTGGACACAT
2466358 GCTGACGTGGACACAT
1 GCTGACGTGGACACAT
2466374 GCTGACGTGGACA
1 GCTGACGTGGACA
2466387 TGTGATGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.20, C:0.23, G:0.36, T:0.20
Consensus pattern (16 bp):
GCTGACGTGGACACAT
Found at i:2467048 original size:22 final size:22
Alignment explanation
Indices: 2467023--2467064 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2467013 TGTCACTGTT
2467023 TTGCTACTATTTTATTGTTATC
1 TTGCTACTATTTTATTGTTATC
*
2467045 TTGCTACTTTTTTATTGTTA
1 TTGCTACTATTTTATTGTTA
2467065 ATATTTGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.62
Consensus pattern (22 bp):
TTGCTACTATTTTATTGTTATC
Found at i:2473933 original size:23 final size:23
Alignment explanation
Indices: 2473898--2473956 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
2473888 ATTGGTGAGA
* *
2473898 GCATTCTGTCACTTTGATGCAAT
1 GCATTTTGACACTTTGATGCAAT
*
2473921 GCATTTTGACACTTTGGTGCAAT
1 GCATTTTGACACTTTGATGCAAT
*
2473944 TCATTTTGACACT
1 GCATTTTGACACT
2473957 ACTATTCATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (23 bp):
GCATTTTGACACTTTGATGCAAT
Done.