Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004164.1 Hibiscus syriacus cultivar Beakdansim tig00009105_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: 140292
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:11986 original size:13 final size:12
Alignment explanation
Indices: 11968--12015 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
11958 AAACAAGAAT
11968 AAAATAAAAAAA
1 AAAATAAAAAAA
*
11980 GAAAATAAAATAA
1 -AAAATAAAAAAA
* *
11993 AAAAGAAAAATA
1 AAAATAAAAAAA
12005 AAAATAAAAAA
1 AAAATAAAAAA
12016 TAGAAAGAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.85, C:0.00, G:0.04, T:0.10
Consensus pattern (12 bp):
AAAATAAAAAAA
Found at i:11988 original size:18 final size:18
Alignment explanation
Indices: 11965--12021 Score: 80
Period size: 18 Copynumber: 3.1 Consensus size: 18
11955 CCTAAACAAG
11965 AATAAAATAAAAAAAGAA
1 AATAAAATAAAAAAAGAA
11983 AATAAAAT-AAAAAAGAAA
1 AATAAAATAAAAAAAG-AA
12001 AATAAAAATAAAAAATAGAA
1 AAT-AAAATAAAAAA-AGAA
12021 A
1 A
12022 GAAAAGGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
17 7 0.20
18 13 0.37
19 5 0.14
20 8 0.23
21 2 0.06
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.12
Consensus pattern (18 bp):
AATAAAATAAAAAAAGAA
Found at i:12026 original size:18 final size:17
Alignment explanation
Indices: 11968--12026 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 17
11958 AAACAAGAAT
11968 AAAATAAAAAAAGAAAA
1 AAAATAAAAAAAGAAAA
*
11985 TAAAATAAAAAAGAAAAATA
1 -AAAATAAAAAA-AGAAA-A
12005 AAAATAAAAAATAGAAAGA
1 AAAATAAAAAA-AGAAA-A
12024 AAA
1 AAA
12027 GGAGAGGTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 11 0.31
19 23 0.66
20 1 0.03
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (17 bp):
AAAATAAAAAAAGAAAA
Found at i:12724 original size:33 final size:33
Alignment explanation
Indices: 12682--12755 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
12672 ACACACACCC
*
12682 ATGCATACTCATGCATTCATTTAATAGGATCAA
1 ATGCATACTCATGCATTCATTTAATAGGAGCAA
*
12715 ATGCATACTCATGCATTCATTTAATAGGAGCAT
1 ATGCATACTCATGCATTCATTTAATAGGAGCAA
12748 ATGCATAC
1 ATGCATAC
12756 ATCAAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (33 bp):
ATGCATACTCATGCATTCATTTAATAGGAGCAA
Found at i:12963 original size:44 final size:44
Alignment explanation
Indices: 12900--13095 Score: 135
Period size: 44 Copynumber: 4.4 Consensus size: 44
12890 AACTTTCAGC
*
12900 TCGATTCTATCACAGAAGGAGGTAGATCAACACTAACATCTCAT
1 TCGATTCCATCACAGAAGGAGGTAGATCAACACTAACATCTCAT
* * **** * *
12944 TCGATTCCATCACAGAAGGAGGTGGATCAACATTTTTTTGTTCGT
1 TCGATTCCATCACAGAAGGAGGTAGATCAACACTAACAT-CTCAT
* * * * * * * * *
12989 TCAAATCCATCGCAGAAGGAGTTAGATCAGC-GTCAAC-TTTTAGC
1 TCGATTCCATCACAGAAGGAGGTAGATCAACACT-AACATCTCA-T
* * * * *
13033 TCGATTCTATCACAGAATGAGGTAGATCAGCACCAACATCTCGT
1 TCGATTCCATCACAGAAGGAGGTAGATCAACACTAACATCTCAT
*
13077 TCGATTCCATCACATAAGG
1 TCGATTCCATCACAGAAGG
13096 GGGTGAATCG
Statistics
Matches: 110, Mismatches: 37, Indels: 10
0.70 0.24 0.06
Matches are distributed among these distances:
43 2 0.02
44 78 0.71
45 30 0.27
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (44 bp):
TCGATTCCATCACAGAAGGAGGTAGATCAACACTAACATCTCAT
Found at i:13126 original size:133 final size:133
Alignment explanation
Indices: 12888--14079 Score: 1633
Period size: 133 Copynumber: 9.0 Consensus size: 133
12878 AAGAACTTGT
* * ** *
12888 TCAACTTTCAGCTCGATTCTATCACAGAAGGAGGTAGATCAACACTAACATCTCATTCGATTCCA
1 TCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCCA
* * *
12953 TCACAGAAGGAGGTGGATCAACATTTTT-TTGTTCGTTCAAATCCATCGCAGAAGGAGTTAGATC
66 TCACAGAAGGAGGTGGATCGACATTTTTATT-TTCGCTCAAATCCATCGCAGAAGGAGTTGGATC
13017 AGCG
130 AGCG
* *
13021 TCAACTTTTAGCTCGATTCTATCACAGAATGAGGTAGATCAGCACCAACATCTCGTTCGATTCCA
1 TCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCCA
* * * * * * *
13086 TCACATAAGGGGGTGAATCGACATTTTTATTTTCACTCAAATTCATCGCAGAAGGAATTAGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
*
13151 ACG
131 GCG
* * *
13154 TCAACTTTTAGCTCGATTCTATCACATAAGAAGGTAGATCAGCACCGACATCTCGTTCGATTCTA
1 TCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCCA
** * * * **
13219 TCACAGAAAAAGGTGGATCGACCTTTTTATTTTCACTTAAATCCATCATAGAAGGAGTTGGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
*
13284 ACG
131 GCG
* * *
13287 TCAACTTTCAGCTTGATTCTGTCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCCA
1 TCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCCA
* * * *
13352 TCACAGAAGGAGGTAGATCGACCTTTTTATTTTCGTTCAAATCCATCGCAGAAGGAGTTCGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
13417 GCG
131 GCG
* * *
13420 TCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCTGCACCAACATCTCGTTCGATTCTA
1 TCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCCA
* *
13485 TCACAGAAGGAGGAGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAATGAGTTGGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
13550 GCG
131 GCG
* * *
13553 TCAACTTTTAGCTCAATTCTATCACAGAAGAAAGTAGATCAGCACCGACATCTCGTTCGATTCCA
1 TCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCCA
* * **
13618 TCACAGAAGGAGGTGGATCGACCTCTTTATTTTTTCTCAAATCCATCGCAGAAGGAGTTGGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
13683 GCG
131 GCG
* * * *
13686 TCAACTTTCAGCTTGATTCTATCACAGAAGGAGGTAGATAAGCACCAACATCTCGTTCGATTCCA
1 TCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCCA
* *
13751 TCATAGAAGGAGGTGGATCGACATTTTTTATTTTCGCTCAAATCCATTGCAGAAGGAGTTGGATC
66 TCACAGAAGGAGGTGGATCGACA-TTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATC
13816 AGCG
130 AGCG
* * *
13820 TCAACTTTTAGCTCGATTCTATAATAGAAAGGAGGTAGATCATCACCGACATCTCGTTCGATTCC
1 TCAACTTTTAGCTCGATTCTATCACAG-AAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCC
* *
13885 ATCACAGAATGAGGTGGATCGACATTTTTATTTTCACTCAAATCCATCGCAGAAGGAGTTGGATC
65 ATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATC
13950 AGCG
130 AGCG
* * * ** * * *
13954 TCAACTTTCAACTTGATTCTATCGTAGAATGAGGTAGATCAGCACCGATATCTCGTTAGATTCCA
1 TCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCCA
* * ** * *
14019 TCATAAAAAAAGAG-GGATCGACA---TT-TTTTCGCTCAAATCCATAC-CAGAAAGAGTTAGAT
66 TCACAGAAGGAG-GTGGATCGACATTTTTATTTTCGCTCAAATCCAT-CGCAGAAGGAGTTGGAT
14078 CA
129 CA
14080 TCATCATCAA
Statistics
Matches: 943, Mismatches: 111, Indels: 14
0.88 0.10 0.01
Matches are distributed among these distances:
129 31 0.03
130 3 0.00
133 721 0.76
134 132 0.14
135 56 0.06
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (133 bp):
TCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCCA
TCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
GCG
Found at i:13349 original size:44 final size:44
Alignment explanation
Indices: 13301--13769 Score: 200
Period size: 44 Copynumber: 10.6 Consensus size: 44
13291 CTTTCAGCTT
* *
13301 GATTCTGTCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTC
1 GATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTC
* *** *
13345 GATTCCATCACAGAAGGAGGTAGATC-G-ACCTTTTTATTTTCGTTC
1 GATTCTATCACAGAAGGAGGTAGATCAGCACC--AACA-TCTCGTTC
* * * * * * ** * * * *
13390 AAATCCATCGCAGAAGGAGTTCGATCAGCGTCAACTTTTAGCTC
1 GATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTC
*
13434 GATTCTATCACAGAAGGAGGTAGATCTGCACCAACATCTCGTTC
1 GATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTC
***** * *
13478 GATTCTATCACAGAAGGAGG-AGGATC-GACATTTTTATTTTCGCTC
1 GATTCTATCACAGAAGGAGGTA-GATCAG-CACCAACA-TCTCGTTC
* * * * * * * ** * * * *
13523 AAATCCATCGCAGAATGAGTTGGATCAGCGTCAACTTTTAGCTC
1 GATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTC
* * * *
13567 AATTCTATCACAGAAGAAAGTAGATCAGCACCGACATCTCGTTC
1 GATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTC
* * * * **
13611 GATTCCATCACAGAAGGAGGTGGATC-G-ACC-TCTTTATTTTTTCTC
1 GATTCTATCACAGAAGGAGGTAGATCAGCACCAAC---ATCTCGT-TC
* * * * * * ** *
13656 AAATCCATCGCAGAAGGAGTTGGATCAGCGTCAAC-TTTCAGCTT-
1 GATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTC-G-TTC
*
13700 GATTCTATCACAGAAGGAGGTAGATAAGCACCAACATCTCGTTC
1 GATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTC
* * *
13744 GATTCCATCATAGAAGGAGGTGGATC
1 GATTCTATCACAGAAGGAGGTAGATC
13770 GACATTTTTT
Statistics
Matches: 304, Mismatches: 100, Indels: 42
0.68 0.22 0.09
Matches are distributed among these distances:
41 1 0.00
42 6 0.02
43 6 0.02
44 202 0.66
45 82 0.27
46 4 0.01
47 2 0.01
48 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.27
Consensus pattern (44 bp):
GATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTC
Found at i:19640 original size:20 final size:20
Alignment explanation
Indices: 19589--19640 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
19579 ATAGTTGTAG
**
19589 GGGTATTGATACCTTAGGTA
1 GGGTATTGATACAGTAGGTA
**
19609 GGGTATCAATACAGTAGAG-A
1 GGGTATTGATACAGTAG-GTA
19629 GGGTATTGATAC
1 GGGTATTGATAC
19641 TATAAGGCCA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.29
Consensus pattern (20 bp):
GGGTATTGATACAGTAGGTA
Found at i:26082 original size:20 final size:19
Alignment explanation
Indices: 26040--26092 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
26030 ATAGTTGTAG
26040 GGGTATCGATACCTTAGGTA
1 GGGTATCGATA-CTTAGGTA
26060 GGGTATCGATACTTCAGAG-A
1 GGGTATCGATACTT-AG-GTA
*
26080 GGGTATTGATACT
1 GGGTATCGATACT
26093 GTAAGGCCAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 3 0.10
20 26 0.87
21 1 0.03
ACGTcount: A:0.26, C:0.13, G:0.30, T:0.30
Consensus pattern (19 bp):
GGGTATCGATACTTAGGTA
Found at i:29112 original size:114 final size:114
Alignment explanation
Indices: 28994--29229 Score: 418
Period size: 114 Copynumber: 2.1 Consensus size: 114
28984 TGATCTTGCA
28994 TAGTATCTGGGCAATTTAATACTATTTCATAACATAATCTAAAACTGCCTAATTTAAAACTTAAC
1 TAGTATCTGGGCAATTTAATACTATTTCATAACATAATCTAAAACTGCCTAATTTAAAACTTAAC
*
29059 TGATTAATCTTTATAATACAATATTTTACTGCCGTCATGTATAACCATT
66 TGATTAATCTTTATAATACAATATTTTACTACCGTCATGTATAACCATT
* * *
29108 TAGTATATGGGCAATTTAATACTATTTCATATCATAATCTAATACTGCCTAATTTAAAACTTAAC
1 TAGTATCTGGGCAATTTAATACTATTTCATAACATAATCTAAAACTGCCTAATTTAAAACTTAAC
* *
29173 TGCTTAATCTTTATAATATAATATTTTACTACCGTCATGTATAACCATT
66 TGATTAATCTTTATAATACAATATTTTACTACCGTCATGTATAACCATT
29222 TAGTATCT
1 TAGTATCT
29230 TATCATATTT
Statistics
Matches: 115, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 115 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (114 bp):
TAGTATCTGGGCAATTTAATACTATTTCATAACATAATCTAAAACTGCCTAATTTAAAACTTAAC
TGATTAATCTTTATAATACAATATTTTACTACCGTCATGTATAACCATT
Found at i:30168 original size:65 final size:65
Alignment explanation
Indices: 30092--30351 Score: 414
Period size: 65 Copynumber: 4.0 Consensus size: 65
30082 GATCTTTGTA
*
30092 GTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATAAGTGATCTGTACT
1 GTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTACT
* * * *
30157 GTATAT-AATTATCACTCCACTTCATGCACCACAAAGGTGCATGAGTCATATGAGTGATCTATAT
1 GTAT-TCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTAC
30221 T
65 T
* * * *
30222 GTATTCAATTATCACTCCACCTTATGCACCAGAAAGGTACATGAGTCATATGAGTGATATGAACT
1 GTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTACT
*
30287 ATATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTACT
1 GTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTACT
30352 TGTTCACTCT
Statistics
Matches: 175, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
64 1 0.01
65 173 0.99
66 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (65 bp):
GTATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTACT
Found at i:33102 original size:29 final size:28
Alignment explanation
Indices: 33026--33109 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 28
33016 AATAAAAATA
* * *
33026 TAAATTTTGAAAATTTACATTGTTAGTTCC
1 TAAATTTT-AAAATTTATACT-TTAGTCCC
* *
33056 TATACTTTTACAACTTTATACTTTAGTCCC
1 TA-AATTTTA-AAATTTATACTTTAGTCCC
33086 TAAATTTTCAAAATTTATACTTTA
1 TAAATTTT-AAAATTTATACTTTA
33110 ATCACTAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
29 18 0.41
30 13 0.30
31 13 0.30
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (28 bp):
TAAATTTTAAAATTTATACTTTAGTCCC
Found at i:35529 original size:35 final size:36
Alignment explanation
Indices: 35478--35551 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 36
35468 TGAAGTTATT
** *
35478 CATGAGGTATCAATACC-TGGAGGGTAGTATCGATAC
1 CATGAGGTATCAATACCATAAAGAG-AGTATCGATAC
*
35514 CATG-GGTATCGATACCATAAAGAGAGTATCGATAC
1 CATGAGGTATCAATACCATAAAGAGAGTATCGATAC
35549 CAT
1 CAT
35552 TTTTGAAGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
35 25 0.76
36 8 0.24
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (36 bp):
CATGAGGTATCAATACCATAAAGAGAGTATCGATAC
Found at i:37057 original size:12 final size:12
Alignment explanation
Indices: 37027--37060 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
37017 TATTTTCCAC
37027 TTTCATATTCAT
1 TTTCATATTCAT
**
37039 TCACATATTCAT
1 TTTCATATTCAT
37051 TTTCATATTC
1 TTTCATATTC
37061 CATGTCCATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (12 bp):
TTTCATATTCAT
Found at i:37180 original size:19 final size:19
Alignment explanation
Indices: 37087--37187 Score: 96
Period size: 19 Copynumber: 5.3 Consensus size: 19
37077 ACTTTCACAT
* *
37087 TTCATAATTTATTTTCTGAA
1 TTCATAACTTATTTTC-AAA
* * *
37107 -TCAGAACTTATTTCCAGA
1 TTCATAACTTATTTTCAAA
*
37125 TTCATAACTTATTTTCAGA
1 TTCATAACTTATTTTCAAA
* ** *
37144 CTCATAGTTTACTTTCAAA
1 TTCATAACTTATTTTCAAA
37163 TTCATAACTTATTTTCAAA
1 TTCATAACTTATTTTCAAA
37182 TTCATA
1 TTCATA
37188 GCCCAATGCA
Statistics
Matches: 64, Mismatches: 16, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
18 1 0.02
19 63 0.98
ACGTcount: A:0.33, C:0.17, G:0.05, T:0.46
Consensus pattern (19 bp):
TTCATAACTTATTTTCAAA
Found at i:41513 original size:16 final size:17
Alignment explanation
Indices: 41492--41525 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
41482 TTTTTATTTC
*
41492 ATATAAAGATA-ATTAA
1 ATATAAAAATATATTAA
41508 ATATAAAAATATATTAA
1 ATATAAAAATATATTAA
41525 A
1 A
41526 ATTGAAGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
ATATAAAAATATATTAA
Found at i:41889 original size:99 final size:97
Alignment explanation
Indices: 41761--41971 Score: 305
Period size: 99 Copynumber: 2.2 Consensus size: 97
41751 GAAAAGAAAT
* * *
41761 AAAGGTAATATCTATCCCTTAATAGTAATCTATATTGTCCATCAAAAACTTATATTTTTAATAAT
1 AAAGTTAATATCTATCCCTAAATAATAATCTATATTGTCCATCAAAAACTT-TATTTTTAATAAT
41826 ATGAAATTATATTTATTTGAAAAAGGAGAAAAAG
65 ATGAAATTATATTTATTT-AAAAAGGAGAAAAAG
* ** * *
41860 AAAGTTGATATCTATCCCTAAATAATAATCTATATTGTCCATCAAATTCTTTATTTTTAGTGATA
1 AAAGTTAATATCTATCCCTAAATAATAATCTATATTGTCCATCAAAAACTTTATTTTTAATAATA
** *
41925 TTTAGTTATATTTATTTAAAAAGGAGAAAAAG
66 TGAAATTATATTTATTTAAAAAGGAGAAAAAG
41957 AAAGTTAATATCTAT
1 AAAGTTAATATCTAT
41972 ATATTAACAA
Statistics
Matches: 100, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
97 29 0.29
98 26 0.26
99 45 0.45
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (97 bp):
AAAGTTAATATCTATCCCTAAATAATAATCTATATTGTCCATCAAAAACTTTATTTTTAATAATA
TGAAATTATATTTATTTAAAAAGGAGAAAAAG
Found at i:43163 original size:36 final size:37
Alignment explanation
Indices: 43078--43170 Score: 143
Period size: 38 Copynumber: 2.5 Consensus size: 37
43068 TTTTCACCCT
43078 AAACCCGAACCCGACCCGACCCGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCCGACCCGAATATCACACTT-AAA
*
43117 AAACCCGACCCGACTCGACCCGAATATCACACTT-AA
1 AAACCCGACCCGACCCGACCCGAATATCACACTTAAA
*
43153 AAACCTGACCCGACCCGA
1 AAACCCGACCCGACCCGA
43171 ACAAAATAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
36 18 0.35
38 26 0.51
39 7 0.14
ACGTcount: A:0.38, C:0.40, G:0.12, T:0.11
Consensus pattern (37 bp):
AAACCCGACCCGACCCGACCCGAATATCACACTTAAA
Found at i:45781 original size:32 final size:33
Alignment explanation
Indices: 45744--45806 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
45734 TTAAATTTTA
45744 TACAAATGT-AAAAATATATAACTAAAAATATC
1 TACAAATGTAAAAAATATATAACTAAAAATATC
45776 TACAAATGTAAAAAATATATAACTAAAAATA
1 TACAAATGTAAAAAATATATAACTAAAAATA
45807 ACTTACTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 9 0.30
33 21 0.70
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.27
Consensus pattern (33 bp):
TACAAATGTAAAAAATATATAACTAAAAATATC
Found at i:50822 original size:12 final size:13
Alignment explanation
Indices: 50803--50840 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
50793 ATGGTGAGAC
50803 ATATAAAAATAAA
1 ATATAAAAATAAA
*
50816 A-ATAAAAACAAA
1 ATATAAAAATAAA
*
50828 ATATAAATATAAA
1 ATATAAAAATAAA
50841 TATTTTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (13 bp):
ATATAAAAATAAA
Found at i:53236 original size:18 final size:19
Alignment explanation
Indices: 53198--53239 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
53188 GAAATGAAAG
*
53198 TTTTCAAAGTTTAGGTGTT
1 TTTTCAAAATTTAGGTGTT
*
53217 TTTTCAAAATTTATGT-TT
1 TTTTCAAAATTTAGGTGTT
53235 TTTTC
1 TTTTC
53240 TTTTTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.21, C:0.07, G:0.12, T:0.60
Consensus pattern (19 bp):
TTTTCAAAATTTAGGTGTT
Found at i:55499 original size:33 final size:33
Alignment explanation
Indices: 55462--55528 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
55452 AGTTTACGGT
*
55462 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAATTCGATA
55495 AATTCAAATACTTAAAAACTTCCAAATTCGATA
1 AATTCAAATACTTAAAAACTTCCAAATTCGATA
55528 A
1 A
55529 TTGAAACAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.48, C:0.18, G:0.04, T:0.30
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAATTCGATA
Found at i:55547 original size:21 final size:21
Alignment explanation
Indices: 55523--55564 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
55513 CTTCCAAATT
55523 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
55544 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
55565 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:57929 original size:14 final size:13
Alignment explanation
Indices: 57902--57926 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57892 TTTTTTCCCA
57902 AACCGGTTAAAAT
1 AACCGGTTAAAAT
57915 AACCGGTTAAAA
1 AACCGGTTAAAA
57927 ATATCCGATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (13 bp):
AACCGGTTAAAAT
Found at i:61468 original size:28 final size:28
Alignment explanation
Indices: 61432--61489 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
61422 GTTGCATTCA
*
61432 CATTCTGCATTTGTATCTTTGCATGTTG
1 CATTCTGCATCTGTATCTTTGCATGTTG
* *
61460 CATTTTGCATCTGTATCTTTGCATTTTG
1 CATTCTGCATCTGTATCTTTGCATGTTG
61488 CA
1 CA
61490 CTGGCATTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.50
Consensus pattern (28 bp):
CATTCTGCATCTGTATCTTTGCATGTTG
Found at i:61480 original size:14 final size:14
Alignment explanation
Indices: 61437--61485 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
61427 ATTCACATTC
61437 TGCATTTGTATCTT
1 TGCATTTGTATCTT
*
61451 TGCATGTTGCAT-TT
1 TGCAT-TTGTATCTT
*
61465 TGCATCTGTATCTT
1 TGCATTTGTATCTT
61479 TGCATTT
1 TGCATTT
61486 TGCACTGGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 4 0.14
14 20 0.69
15 5 0.17
ACGTcount: A:0.14, C:0.16, G:0.16, T:0.53
Consensus pattern (14 bp):
TGCATTTGTATCTT
Found at i:61501 original size:12 final size:14
Alignment explanation
Indices: 61437--61511 Score: 57
Period size: 14 Copynumber: 5.4 Consensus size: 14
61427 ATTCACATTC
* *
61437 TGCATTTGTATCTT
1 TGCATTTGCATCTG
*
61451 TGCATGTTGCAT-TT
1 TGCAT-TTGCATCTG
* * *
61465 TGCATCTGTATCTT
1 TGCATTTGCATCTG
61479 TGCATTTTGCA-CTG
1 TGCA-TTTGCATCTG
61493 -GCATTTGCATCTG
1 TGCATTTGCATCTG
61506 TGCATT
1 TGCATT
61512 CATTTTTTCT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
12 6 0.12
13 10 0.20
14 25 0.50
15 9 0.18
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.48
Consensus pattern (14 bp):
TGCATTTGCATCTG
Found at i:62097 original size:11 final size:11
Alignment explanation
Indices: 62078--62107 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
62068 AATTAAGTTT
*
62078 TAATCTTAAAA
1 TAATTTTAAAA
62089 TAATTTTAAAA
1 TAATTTTAAAA
62100 TAATTTTA
1 TAATTTTA
62108 CAAAGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (11 bp):
TAATTTTAAAA
Found at i:67485 original size:21 final size:22
Alignment explanation
Indices: 67438--67499 Score: 81
Period size: 21 Copynumber: 2.8 Consensus size: 22
67428 ACCCTCATGA
*
67438 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCTT-AAG
67461 GGGAACCGATTCCCCCCTT-AG
1 GGGAACCGATTCCCCCCTTAAG
* *
67482 GGGAATCGATACCCCCCT
1 GGGAACCGATTCCCCCCT
67500 GGGGTTCTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 18 0.50
23 18 0.50
ACGTcount: A:0.21, C:0.35, G:0.24, T:0.19
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCTTAAG
Found at i:72135 original size:14 final size:14
Alignment explanation
Indices: 72116--72144 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
72106 AACCGTGAGC
72116 CCTGCACTACATTA
1 CCTGCACTACATTA
72130 CCTGCACTACATTA
1 CCTGCACTACATTA
72144 C
1 C
72145 GTGCCTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.38, G:0.07, T:0.28
Consensus pattern (14 bp):
CCTGCACTACATTA
Found at i:74053 original size:57 final size:57
Alignment explanation
Indices: 73908--74089 Score: 251
Period size: 55 Copynumber: 3.2 Consensus size: 57
73898 ATATGATGTT
** * *
73908 TTCAAATGAATTTGAAAAGAATCTAAGCATGATTTTCAGGGGTTTCTTGATGATT--
1 TTCAAATGAATTTTTAAAGAAGCTAAGCATGATTTTTAGGGGTTTCTTGATGATTAC
* * *
73963 TTCGAATGAACTTTTAAAGAAGCTAAGCTTGATTTTTAGGGGTTTCTTGATGATTAC
1 TTCAAATGAATTTTTAAAGAAGCTAAGCATGATTTTTAGGGGTTTCTTGATGATTAC
* *
74020 TTCAAATGAATTTTTAAAGAAGCTAAACATGATTTTTAGGGGTTTTTTTGATGATTAC
1 TTCAAATGAATTTTTAAAGAAGCTAAGCATGATTTTTAGGGG-TTTCTTGATGATTAC
*
74078 ATCAAATGAATT
1 TTCAAATGAATT
74090 GGAGTTATTC
Statistics
Matches: 111, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
55 48 0.43
57 38 0.34
58 25 0.23
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (57 bp):
TTCAAATGAATTTTTAAAGAAGCTAAGCATGATTTTTAGGGGTTTCTTGATGATTAC
Found at i:75962 original size:21 final size:21
Alignment explanation
Indices: 75938--76026 Score: 119
Period size: 21 Copynumber: 4.3 Consensus size: 21
75928 TTTTCCCAAT
75938 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
* **
75959 TCGCAATGCG-ATACT-GACTA
1 TCGCAATGCGAAT-TTGGAAAA
*
75979 TCGCAAAGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
76000 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
76021 TCGCAA
1 TCGCAA
76027 CGCGGTACTG
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
20 15 0.26
21 42 0.74
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:76044 original size:41 final size:41
Alignment explanation
Indices: 76017--76154 Score: 127
Period size: 41 Copynumber: 3.4 Consensus size: 41
76007 GCGAATTTGG
*
76017 AAAATCGCAACGCGGTACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAATGCGATAATAC
* * * *
76058 AAAATCGCAACGCGATACTGACTTTCGCAACT-CGGTACT-T
1 AAAATCGCAACGCGATACTGACTATCGCAA-TGCGATAATAC
** * * * * *
76098 AATTTCGCAACTCAATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAATGCGATAATAC
* *
76139 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
76155 TTTCAAAGCT
Statistics
Matches: 74, Mismatches: 20, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
40 30 0.41
41 43 0.58
42 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAATGCGATAATAC
Found at i:76062 original size:62 final size:62
Alignment explanation
Indices: 75938--76072 Score: 191
Period size: 62 Copynumber: 2.2 Consensus size: 62
75928 TTTTCCCAAT
* * **
75938 TCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAAAGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAATCGCAACGCGATACTGACTATCGCAAAGCGAATATACAAAA
* *
76000 TCGCAATGCGAATTTGGAAAATCGCAACGCGGTACTGACTATCGCAATGCG-ATAATACAAAA
1 TCGCAATGCGAATTTGGAAAATCGCAACGCGATACTGACTATCGCAAAGCGAAT-ATACAAAA
*
76062 TCGCAACGCGA
1 TCGCAATGCGA
76073 TACTGACTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
61 2 0.03
62 63 0.97
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (62 bp):
TCGCAATGCGAATTTGGAAAATCGCAACGCGATACTGACTATCGCAAAGCGAATATACAAAA
Found at i:76088 original size:20 final size:20
Alignment explanation
Indices: 76021--76134 Score: 86
Period size: 20 Copynumber: 5.7 Consensus size: 20
76011 ATTTGGAAAA
* *
76021 TCGCAACGCGGTACTGACTA
1 TCGCAACGCGATACTGACTT
* * **
76041 TCGCAATGCGATAAT-ACAAAA
1 TCGCAACGCGATACTGAC--TT
76062 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
* * * *
76082 TCGCAACTCGGTACTTAATT
1 TCGCAACGCGATACTGACTT
* *
76102 TCGCAACTCAATACTGACTT
1 TCGCAACGCGATACTGACTT
*
76122 TCGCAACGAGATA
1 TCGCAACGCGATA
76135 ATACATAATC
Statistics
Matches: 72, Mismatches: 19, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
19 2 0.03
20 54 0.75
21 14 0.19
22 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:76349 original size:22 final size:22
Alignment explanation
Indices: 76321--76364 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
76311 CACTCTCTCA
76321 CCCATCTCCGATGAAATCCGTC
1 CCCATCTCCGATGAAATCCGTC
76343 CCCATCTCCGATGAAATCCGTC
1 CCCATCTCCGATGAAATCCGTC
76365 TATCTCCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.41, G:0.14, T:0.23
Consensus pattern (22 bp):
CCCATCTCCGATGAAATCCGTC
Found at i:76666 original size:20 final size:20
Alignment explanation
Indices: 76643--76685 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
76633 GATAGTCAAA
76643 TTCGCGTTGCGATTTTCTTT
1 TTCGCGTTGCGATTTTCTTT
*
76663 TTCGTGTTGCGATTTTCTTT
1 TTCGCGTTGCGATTTTCTTT
76683 TTC
1 TTC
76686 AGAAATTATT
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:0.05, C:0.19, G:0.19, T:0.58
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCTTT
Found at i:76876 original size:25 final size:24
Alignment explanation
Indices: 76822--76876 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
76812 TGTTTATTAT
* *
76822 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
76846 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
76872 TGTTT
1 TGTTT
76877 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:78594 original size:20 final size:20
Alignment explanation
Indices: 78569--78614 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
78559 TAGTTTACTT
78569 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
** * *
78589 TCGCAATGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
78609 TCGCAA
1 TCGCAA
78615 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:78623 original size:19 final size:20
Alignment explanation
Indices: 78580--78624 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
78570 CGCAACACGA
78580 AAATGACTATCGCAATGCGG
1 AAATGACTATCGCAATGCGG
*
78600 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAATGCGG
78619 AAATGA
1 AAATGA
78625 AAATCGCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (20 bp):
AAATGACTATCGCAATGCGG
Found at i:78630 original size:19 final size:19
Alignment explanation
Indices: 78588--78704 Score: 92
Period size: 19 Copynumber: 6.6 Consensus size: 19
78578 GAAAATGACT
***
78588 ATCGCAATGCGGAAATGGCT
1 ATCGCAATGC-GAAATGAAA
78608 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
78627 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
78641 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
78660 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
* *
78674 ATCGCAACGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
78693 ATCGCAATGCGA
1 ATCGCAATGCGA
78705 TTTGTGTTTC
Statistics
Matches: 77, Mismatches: 10, Indels: 21
0.71 0.09 0.19
Matches are distributed among these distances:
14 20 0.26
15 2 0.03
16 3 0.04
17 4 0.05
18 2 0.03
19 36 0.47
20 10 0.13
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:78650 original size:33 final size:33
Alignment explanation
Indices: 78608--78699 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
78598 GGAAATGGCT
78608 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
78641 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
78674 ATCGCAACGCAAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
78700 TGCGATTTGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:78688 original size:13 final size:14
Alignment explanation
Indices: 78624--78688 Score: 69
Period size: 14 Copynumber: 4.4 Consensus size: 14
78614 ATGCGAAATG
78624 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
78638 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
78657 AAAATCGCAACGAC
1 AAAATCGCAACGAC
78671 AAAATCGCAACG-C
1 AAAATCGCAACGAC
78684 AAAAT
1 AAAAT
78689 GAAAATCGCA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
13 6 0.14
14 22 0.50
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 10 0.23
ACGTcount: A:0.51, C:0.23, G:0.15, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:78776 original size:20 final size:20
Alignment explanation
Indices: 78751--78796 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
78741 TCAATTCGCA
78751 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
*
78771 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
78791 TTGCGA
1 TTGCGA
78797 AAGTAAGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.15, C:0.26, G:0.26, T:0.33
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:79248 original size:39 final size:42
Alignment explanation
Indices: 79160--79248 Score: 121
Period size: 39 Copynumber: 2.2 Consensus size: 42
79150 CCCGACTCAC
* * *
79160 CTGTCATTCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
*
79202 CTATCATCCCTCAAGAGT-CCC-CC-ACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
79241 CTGTCATC
1 CTGTCATC
79249 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
39 21 0.50
40 2 0.05
41 3 0.07
42 16 0.38
ACGTcount: A:0.22, C:0.39, G:0.16, T:0.22
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:80692 original size:14 final size:14
Alignment explanation
Indices: 80658--80696 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
80648 TTGATTGTTT
80658 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
80672 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
80686 TGTTGATTTGT
1 AATTGATTTGT
80697 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:80842 original size:14 final size:14
Alignment explanation
Indices: 80823--80876 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
80813 GAAACTGACT
80823 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
80837 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
80856 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
80870 ATCGCAA
1 ATCGCAA
80877 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:80988 original size:20 final size:20
Alignment explanation
Indices: 80909--80988 Score: 90
Period size: 20 Copynumber: 4.0 Consensus size: 20
80899 GATTTTCTAG
*
80909 TTGCGATAGCCATTTTTCGCG
1 TTGCGATAGCCA-TTTTCGCA
*** *
80930 TTGCGATTTTTCA-TTTCGAA
1 TTGCGA-TAGCCATTTTCGCA
80950 TTGCGATAGCCATTTTCGCA
1 TTGCGATAGCCATTTTCGCA
80970 TTGCGATAGCCATTTTCGC
1 TTGCGATAGCCATTTTCGC
80989 GTTGTGATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
19 3 0.06
20 36 0.75
21 6 0.12
22 3 0.06
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.40
Consensus pattern (20 bp):
TTGCGATAGCCATTTTCGCA
Found at i:81235 original size:20 final size:20
Alignment explanation
Indices: 81210--81259 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
81200 TTGAAGATGA
81210 TTGCGATTTTCAAAATCTCG
1 TTGCGATTTTCAAAATCTCG
*** *
81230 TTGCGAAAGTCAAGATCTCG
1 TTGCGATTTTCAAAATCTCG
81250 TTGCGATTTT
1 TTGCGATTTT
81260 GTATTATCTC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (20 bp):
TTGCGATTTTCAAAATCTCG
Found at i:81330 original size:20 final size:21
Alignment explanation
Indices: 81286--81337 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
81276 ATAGTCAGTA
*
81286 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
81307 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
81327 TCGCATTGCGA
1 TCGCATTGCGA
81338 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:81553 original size:12 final size:12
Alignment explanation
Indices: 81534--81575 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
81524 CTCTCCGGCG
81534 ACATCCGTTCCT
1 ACATCCGTTCCT
*
81546 ATATCCGTTCCT
1 ACATCCGTTCCT
81558 ACATCC-TT-CT
1 ACATCCGTTCCT
*
81568 CCATCCGT
1 ACATCCGT
81576 CAACAGGTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
10 7 0.27
11 3 0.12
12 16 0.62
ACGTcount: A:0.17, C:0.40, G:0.07, T:0.36
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:82173 original size:24 final size:24
Alignment explanation
Indices: 82116--82175 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
82106 TAGTCAGTAT
*
82116 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATATTGGTCAATAC
* * *
82140 CCGGACTTTGATATTGGTCAATAC
1 TCGAAATTTGATATTGGTCAATAC
*
82164 TCGAATTTTGAT
1 TCGAAATTTGAT
82176 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATATTGGTCAATAC
Found at i:82367 original size:12 final size:12
Alignment explanation
Indices: 82350--82384 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
82340 ATATAATCCT
82350 GAAGAAGAAAAA
1 GAAGAAGAAAAA
82362 GAAGAAGAAAAA
1 GAAGAAGAAAAA
82374 GAAGAAGAAAA
1 GAAGAAGAAAA
82385 GTCCCTGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:84700 original size:19 final size:19
Alignment explanation
Indices: 84678--84742 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
84668 GAAAATTACT
84678 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
84697 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
84711 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
84730 ATCGCAACGCGAA
1 ATCGCAATGCGAA
84743 TTTCGCATTG
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:84701 original size:39 final size:36
Alignment explanation
Indices: 84658--84742 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 36
84648 CTTAATGTCT
*
84658 ATCGCAACGCGAAAATTACTATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAAA-GA--ATCGCAATGCGAAATGAAA
*
84697 ATCGCAA--CG-AGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAAAGAATCGCAATGCGAAATGAAA
84730 ATCGCAACGCGAA
1 ATCGCAACGCGAA
84743 TTTCGCATTG
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
33 26 0.63
35 3 0.07
36 3 0.07
37 2 0.05
39 7 0.17
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.14
Consensus pattern (36 bp):
ATCGCAACGCGAAAAGAATCGCAATGCGAAATGAAA
Found at i:84882 original size:14 final size:14
Alignment explanation
Indices: 84863--84899 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
84853 CATCAATTAA
84863 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
84877 ACAAATCACCTTTT
1 ACAAATCAACTTTT
84891 ACAAATCAA
1 ACAAATCAA
84900 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:86317 original size:21 final size:21
Alignment explanation
Indices: 86251--86317 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
86241 GTGAATCGGG
*
86251 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
86271 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
86293 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
86314 CTCT
1 CTCT
86318 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:86770 original size:91 final size:92
Alignment explanation
Indices: 86591--86774 Score: 293
Period size: 91 Copynumber: 2.0 Consensus size: 92
86581 ATTTAAAACT
86591 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACATTTAGCA
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACATTTAGCA
*
86656 GAATTGGCAGCAATCGAATAAATTTAC
66 GAATTGGCAGCAACCGAATAAATTTAC
* *
86683 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAA-ACA-GTTTAG
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACATTTAG
*
86745 CAGTATTGGCAGCAACCGAATAAATTTAC
64 CAGAATTGGCAGCAACCGAATAAATTTAC
86774 T
1 T
86775 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
91 33 0.38
92 22 0.26
93 4 0.05
94 27 0.31
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (92 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACATTTAGCA
GAATTGGCAGCAACCGAATAAATTTAC
Found at i:88489 original size:20 final size:19
Alignment explanation
Indices: 88458--88598 Score: 113
Period size: 19 Copynumber: 7.8 Consensus size: 19
88448 GTCTTTGGTT
88458 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
88477 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
88498 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
88517 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
88531 GAAATGACTATCGCAACGC
1 GAAATGAAAATCGCAACGA
88550 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
88569 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
88583 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
88599 TGCGATTTTG
Statistics
Matches: 98, Mismatches: 12, Indels: 24
0.73 0.09 0.18
Matches are distributed among these distances:
14 21 0.21
16 4 0.04
17 4 0.04
19 38 0.39
20 29 0.30
21 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:88502 original size:40 final size:37
Alignment explanation
Indices: 88458--88603 Score: 130
Period size: 33 Copynumber: 4.1 Consensus size: 37
88448 GTCTTTGGTT
**
88458 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGACTATCGCAACG-GA-AATGAGAATCGCAACGC
88497 GGAAATGACTATCGCAAC-G--A-GAGAATCGCAACGC
1 -GAAATGACTATCGCAACGGAAATGAGAATCGCAACGC
*
88531 GAAATGACTATCGCAACGCGAAATGAAAATCGCAA--C
1 GAAATGACTATCGCAACG-GAAATGAGAATCGCAACGC
* * *
88567 GAGA-GA--ATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGACTATCGCAACG-GAAATGAGAATCGCAACGC
88602 GA
1 GA
88604 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 4, Indels: 19
0.81 0.03 0.16
Matches are distributed among these distances:
33 43 0.45
34 14 0.15
35 7 0.07
36 4 0.04
37 1 0.01
38 11 0.12
40 15 0.16
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (37 bp):
GAAATGACTATCGCAACGGAAATGAGAATCGCAACGC
Found at i:88567 original size:52 final size:52
Alignment explanation
Indices: 88466--88603 Score: 195
Period size: 52 Copynumber: 2.6 Consensus size: 52
88456 TTGAAATGAA
* * **
88466 AATCGCAACGAGATAATGAGAATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGA-AATGAAAATCGCAACGC-GAAATGAAAATCGCAACGAGAG
**
88520 AATCGCAACGCGAAATGACTATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
*
88572 AATCGCAACGCGAAATGAAAATCGCAATGCGA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGA
88604 TTTTGGTTTC
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
52 49 0.64
53 15 0.20
54 12 0.16
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (52 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:88632 original size:19 final size:19
Alignment explanation
Indices: 88599--88643 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
88589 AAAATCGCAA
*
88599 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
88618 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
88637 TGCGATT
1 TGCGATT
88644 CTCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:89239 original size:20 final size:20
Alignment explanation
Indices: 89198--89306 Score: 121
Period size: 20 Copynumber: 5.4 Consensus size: 20
89188 GCTATGTAAA
* *
89198 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
89218 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* * *
89238 TCGCATTACGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
* *
89259 TCGCATTGCGATTTACTTAA
1 TCGCATTGCGATTTACGTAT
*
89279 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
89299 TCGCATTG
1 TCGCATTG
89307 AGAATTATTA
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
19 3 0.04
20 54 0.73
21 17 0.23
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:89263 original size:41 final size:40
Alignment explanation
Indices: 89216--89306 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 40
89206 CGATAGTAAG
* *
89216 ATTCGCATTGCGATTTACGTATTCGCATTACGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCGCATTACGATTTACCT
* * * *
89256 AATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCATTACGATTTACCT
89297 ATTCGCATTG
1 ATTCGCATTG
89307 AGAATTATTA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 10 0.23
41 34 0.77
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.41
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTACGATTTACCT
Found at i:89474 original size:21 final size:22
Alignment explanation
Indices: 89424--89474 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
89414 TTACTTATTT
89424 GCATTGCG-AATTGGGAAAATC
1 GCATTGCGAAATTGGGAAAATC
* **
89445 GTAACGCGAAATT-GGAAAATC
1 GCATTGCGAAATTGGGAAAATC
89466 GCATTGCGA
1 GCATTGCGA
89475 TAGTCATAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (22 bp):
GCATTGCGAAATTGGGAAAATC
Found at i:93569 original size:20 final size:20
Alignment explanation
Indices: 93544--93583 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
93534 ATTGCTACCT
93544 TCTCATAAAAGTATCAATAC
1 TCTCATAAAAGTATCAATAC
*
93564 TCTCATAAGAGTATCAATAC
1 TCTCATAAAAGTATCAATAC
93584 AGTAGGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.30
Consensus pattern (20 bp):
TCTCATAAAAGTATCAATAC
Found at i:100541 original size:30 final size:30
Alignment explanation
Indices: 100500--100561 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
100490 AGGGATGGAA
*
100500 AAAAACCGTTTATGCCAAACGGGGACGGGG
1 AAAAACCGTTTATGCCAAACGCGGACGGGG
* **
100530 AAAAACTGTTTATGTTAAACGCGGACGGGG
1 AAAAACCGTTTATGCCAAACGCGGACGGGG
100560 AA
1 AA
100562 GAGTTTAGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.18
Consensus pattern (30 bp):
AAAAACCGTTTATGCCAAACGCGGACGGGG
Found at i:100645 original size:2 final size:2
Alignment explanation
Indices: 100638--100737 Score: 57
Period size: 2 Copynumber: 52.0 Consensus size: 2
100628 TTATTATTAT
*
100638 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA CTA T- TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * * * * *
100679 AA TT TA -A TT TA AA TT TA AA TA TA TA TA TA -A TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
100719 TT TA -A TT TA AA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
100738 CCCGGCCCGA
Statistics
Matches: 70, Mismatches: 22, Indels: 12
0.67 0.21 0.12
Matches are distributed among these distances:
1 5 0.07
2 63 0.90
3 2 0.03
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:100718 original size:15 final size:15
Alignment explanation
Indices: 100637--100737 Score: 56
Period size: 15 Copynumber: 6.9 Consensus size: 15
100627 ATTATTATTA
100637 TTATATATATATATAT
1 TTATATATATATA-AT
*
100653 ATATATATATATACAT
1 TTATATATATATA-AT
*
100669 ACTAT-TA-ATA-AAT
1 -TTATATATATATAAT
100682 TTA-AT-T-TA-AAT
1 TTATATATATATAAT
100693 TTAAATATATATATAAT
1 TT--ATATATATATAAT
*
100710 ATT-TATATATTTAAT
1 -TTATATATATATAAT
*
100725 TTAAATATATATA
1 TTATATATATATA
100738 CCCGGCCCGA
Statistics
Matches: 67, Mismatches: 7, Indels: 23
0.69 0.07 0.24
Matches are distributed among these distances:
11 7 0.10
12 3 0.04
13 3 0.04
14 5 0.07
15 23 0.34
16 18 0.27
17 6 0.09
18 2 0.03
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATATATATATAAT
Found at i:107949 original size:182 final size:182
Alignment explanation
Indices: 107642--107973 Score: 513
Period size: 182 Copynumber: 1.8 Consensus size: 182
107632 TCATGCCCCT
* *
107642 TATTTCAGTTGTATTGATAGACTGAAATCTTTGATAAATTAAACGCGTTGACTTATTGTGATTTA
1 TATTTCAATTGTATTGATAGACTGAAATCTTTGATAAATTAAACGCATTGACTTATTGTGATTTA
* * * * * * * *
107707 TCTTGAACGTTAAGTTGTTGTGTATGATTTATCCCGATTGATTTAGATGAAAAATCTTAAAGATT
66 CCATGAACGTCAAGTTATCGTGTATGATTTACCCCGATTGATTTAGATGAAAAATCTTAAAAATC
107772 TGATTCAAGAGTTTGAAGATCGAAATTCTTTGATCATATCCATTTTTTTTAC
131 TGATTCAAGAGTTTGAAGATCGAAATTCTTTGATCATATCCATTTTTTTTAC
* * * *
107824 TATTTCAATTGTATTGATCGATTGAAATCTTTGATAAATTAGACGCATT-AGTTTATTGTGATTT
1 TATTTCAATTGTATTGATAGACTGAAATCTTTGATAAATTAAACGCATTGA-CTTATTGTGATTT
*
107888 ACCATGAACGTCAAGTTATCGTGTATGATTTACCCCGATTGATTTAGATGAAGAATCTTAAAAAT
65 ACCATGAACGTCAAGTTATCGTGTATGATTTACCCCGATTGATTTAGATGAAAAATCTTAAAAAT
107953 CTGATTCAAGAGTTTGAAGAT
130 CTGATTCAAGAGTTTGAAGAT
107974 TCAAAGTACA
Statistics
Matches: 134, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
181 1 0.01
182 133 0.99
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (182 bp):
TATTTCAATTGTATTGATAGACTGAAATCTTTGATAAATTAAACGCATTGACTTATTGTGATTTA
CCATGAACGTCAAGTTATCGTGTATGATTTACCCCGATTGATTTAGATGAAAAATCTTAAAAATC
TGATTCAAGAGTTTGAAGATCGAAATTCTTTGATCATATCCATTTTTTTTAC
Found at i:118761 original size:23 final size:23
Alignment explanation
Indices: 118715--118768 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
118705 TGCTCGTTAA
* * * *
118715 GCTCATTGCTCGTTAAGTTTGAT
1 GCTCGTTGCTCATTAAGCTCGAT
118738 GCTCGTTGCTCATTAAGCTCGAT
1 GCTCGTTGCTCATTAAGCTCGAT
*
118761 GTTCGTTG
1 GCTCGTTG
118769 TTCGCCTCGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (23 bp):
GCTCGTTGCTCATTAAGCTCGAT
Found at i:118789 original size:35 final size:35
Alignment explanation
Indices: 118700--118827 Score: 125
Period size: 35 Copynumber: 3.5 Consensus size: 35
118690 GATTGCTTAA
* *
118700 CTCGTTGCTCGTTAAGCTC-ATTGCTCGTTAAGTTTGATG
1 CTCGTTGCTCGTTAAGCTCGA-TGCTCGTT--GCTTG--C
* *
118739 CTCGTTGCTCATTAAGCTCGATGTTCGTTG-TTCGC
1 CTCGTTGCTCGTTAAGCTCGATGCTCGTTGCTT-GC
*
118774 CTCGTTGCTCGTTAAGCTCGATGCTCGTTGCTTGT
1 CTCGTTGCTCGTTAAGCTCGATGCTCGTTGCTTGC
* *
118809 CTCATTGCTTGTTAAGCTC
1 CTCGTTGCTCGTTAAGCTC
118828 ACTAAAATTT
Statistics
Matches: 78, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
35 46 0.59
36 4 0.05
37 2 0.03
39 25 0.32
40 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.23, T:0.41
Consensus pattern (35 bp):
CTCGTTGCTCGTTAAGCTCGATGCTCGTTGCTTGC
Found at i:124111 original size:23 final size:24
Alignment explanation
Indices: 124074--124119 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
124064 TTCGATATTG
124074 AAAAAATATTAAAATAATTTATTTT
1 AAAAAATATTAAAATAA-TTATTTT
*
124099 AAAAAATA-T-AAATTATTATTT
1 AAAAAATATTAAAATAATTATTT
124120 ATCATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
23 5 0.25
24 1 0.05
25 8 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAAAATATTAAAATAATTATTTT
Found at i:125594 original size:3 final size:3
Alignment explanation
Indices: 125586--125661 Score: 136
Period size: 3 Copynumber: 25.7 Consensus size: 3
125576 AATATATATT
125586 TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
125633 TAC TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
125662 TGGATAAAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 68 0.97
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:126165 original size:113 final size:114
Alignment explanation
Indices: 125914--126801 Score: 1436
Period size: 113 Copynumber: 7.8 Consensus size: 114
125904 TTTTGATGAG
*
125914 TTCTTCTCATTATGAACTT-TCTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
1 TTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
*** * * * * *
125978 AAAAAAAAAATAACCCATCAAGTAATAGATTTGAG-CAAAAAGGTTGAACAAA
65 -GGCAAAAGATAATCCATCAAGTGAT-GAATTCAGAC-AAAAGGTTGAACAAA
126030 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
126095 GCAAAA-ATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
66 GCAAAAGATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
126143 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
126208 GCAAAA-ATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
66 GCAAAAGATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
126256 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
126321 GCAAAA-ATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
66 GCAAAAGATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
126369 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * *
126433 G-AAAAGCTAATCAATCAATTTGATGAATTCAAATAAAAGGTTGAACAAA
66 GCAAAAGATAATCCATCAA-GTGATGAATTCAGACAAAAGGTTGAACAAA
*
126482 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
126547 GCAAAAGCTAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
66 GCAAAAGATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
126596 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * *
126660 G-AAAAGCTAATCAATCAATTTGATGAATTCAAATAAAAGGTTGAACAAA
66 GCAAAAGATAATCCATCAA-GTGATGAATTCAGACAAAAGGTTGAACAAA
*
126709 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
126774 G-AAAAGATAATCCATCAAATGATAAATT
66 GCAAAAGATAATCCATCAAGTGATGAATT
126802 TGAATCTTTG
Statistics
Matches: 736, Mismatches: 28, Indels: 19
0.94 0.04 0.02
Matches are distributed among these distances:
111 4 0.01
112 34 0.05
113 486 0.66
114 130 0.18
115 20 0.03
116 61 0.08
117 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (114 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GCAAAAGATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
Found at i:127733 original size:84 final size:84
Alignment explanation
Indices: 127530--127936 Score: 678
Period size: 84 Copynumber: 4.9 Consensus size: 84
127520 CCTACTGAAT
* *
127530 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCTAAACTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCA
*
127594 ATGATT-GTTCTGTGC-AAC
66 ATGATTGGTTCTG-CCAAAC
127612 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCA
* *
127677 ATGATTGATTATGTCC-AAC
66 ATGATTGGTTCTG-CCAAAC
*
127696 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTTCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCA
*
127761 ATGATTGGTTCTGCCAAAT
66 ATGATTGGTTCTGCCAAAC
*
127780 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTTCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCA
*
127845 ATGATTGGTTCTGCCAAAT
66 ATGATTGGTTCTGCCAAAC
*
127864 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCTAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCA
127929 ATGATTGG
66 ATGATTGG
127937 ACTAAGATAT
Statistics
Matches: 311, Mismatches: 11, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
82 42 0.14
83 28 0.09
84 241 0.77
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (84 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCA
ATGATTGGTTCTGCCAAAC
Found at i:129038 original size:12 final size:12
Alignment explanation
Indices: 129015--129102 Score: 94
Period size: 12 Copynumber: 7.2 Consensus size: 12
129005 CCTTGACCCC
129015 CTTTTC-TTTTT
1 CTTTTCTTTTTT
*
129026 CTTCTCTTTTTT
1 CTTTTCTTTTTT
129038 CATTTTCTATTTTT
1 C-TTTTCT-TTTTT
129052 -TTTTCTTTTCTT
1 CTTTTCTTTT-TT
129064 -TTTTCTTTTCTTT
1 CTTTTC-TTT-TTT
129077 CTTTTC-TTTTT
1 CTTTTCTTTTTT
129088 CTTTTCTTTTTT
1 CTTTTCTTTTTT
129100 CTT
1 CTT
129103 CAAGCATAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 15
0.80 0.02 0.18
Matches are distributed among these distances:
11 17 0.25
12 29 0.43
13 10 0.15
14 11 0.16
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (12 bp):
CTTTTCTTTTTT
Found at i:129049 original size:7 final size:6
Alignment explanation
Indices: 129016--129098 Score: 66
Period size: 6 Copynumber: 13.7 Consensus size: 6
129006 CTTGACCCCC
* *
129016 TTTTCT TTTTC- TTCTCTT TTTTCA TTTTCT ATTTT-T TTTTC- TTTTCTT
1 TTTTCT TTTTCT TTTTC-T TTTTCT TTTTCT -TTTTCT TTTTCT TTTTC-T
*
129064 TTTTCT TTTCTTT CTTTTCT TTTTC- TTTTCT TTTT
1 TTTTCT TTT-TCT -TTTTCT TTTTCT TTTTCT TTTT
129099 TCTTCAAGCA
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
5 18 0.29
6 24 0.39
7 17 0.27
8 3 0.05
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:129060 original size:5 final size:5
Alignment explanation
Indices: 129015--129097 Score: 64
Period size: 5 Copynumber: 16.0 Consensus size: 5
129005 CCTTGACCCC
* * *
129015 CTTTT CTTTT -TCTT CTCTT -TTTT CATTTT CTATTTT TTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT C-TTTT C--TTTT CTTTT CTTTT
129061 CTTTTTT CTTTT C-TTT CTTTT CTTTTT CTTTT CTTTT
1 C--TTTT CTTTT CTTTT CTTTT C-TTTT CTTTT CTTTT
129098 TTCTTCAAGC
Statistics
Matches: 66, Mismatches: 4, Indels: 16
0.77 0.05 0.19
Matches are distributed among these distances:
4 10 0.15
5 36 0.55
6 10 0.15
7 10 0.15
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:129092 original size:32 final size:30
Alignment explanation
Indices: 129015--129102 Score: 124
Period size: 32 Copynumber: 2.9 Consensus size: 30
129005 CCTTGACCCC
*
129015 CTTTTCTTTTTCTTCTCTTTTTTCATTTTCT
1 CTTTTCTTTTTCTTTTCTTTTTTC-TTTTCT
*
129046 ATTTT-TTTTTCTTTTCTTTTTTCTTTTCTTT
1 CTTTTCTTTTTCTTTTCTTTTTTCTTTTC--T
129077 CTTTTCTTTTTCTTTTCTTTTTTCTT
1 CTTTTCTTTTTCTTTTCTTTTTTCTT
129103 CAAGCATAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
29 5 0.10
30 17 0.33
31 9 0.18
32 20 0.39
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (30 bp):
CTTTTCTTTTTCTTTTCTTTTTTCTTTTCT
Found at i:139679 original size:13 final size:15
Alignment explanation
Indices: 139657--139693 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
139647 TTTGACAGAA
139657 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
139669 AAATAAAATACTTGC
1 AAATAAAATACTTGC
139684 AAATAAAATA
1 AAATAAAATA
139694 AAACATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Done.