Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004732.1 Hibiscus syriacus cultivar Beakdansim tig00010683_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: 94914
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:3740 original size:44 final size:44
Alignment explanation
Indices: 3650--3773 Score: 115
Period size: 44 Copynumber: 2.8 Consensus size: 44
3640 TTGTTCACCC
* * * * * * *
3650 TTTTGCTCGATTCTATCACAGAAGGAGATAGATCAGTGTCGACA
1 TTTTGTTCAATTCCATCACAGAAGGAGGTAGACCAATATCGACA
* *
3694 TTTTGTTCAATTCCATCACAGAAGGAGGTAGACCAATATTGTCA
1 TTTTGTTCAATTCCATCACAGAAGGAGGTAGACCAATATCGACA
* * *
3738 TTTT-TGCTAGATTTCATCACAGAAGGAGGTGGACCA
1 TTTTGTTC-A-ATTCCATCACAGAAGGAGGTAGACCA
3774 GCATGATCAA
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
43 2 0.03
44 40 0.61
45 24 0.36
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (44 bp):
TTTTGTTCAATTCCATCACAGAAGGAGGTAGACCAATATCGACA
Found at i:4278 original size:20 final size:20
Alignment explanation
Indices: 4253--4319 Score: 134
Period size: 20 Copynumber: 3.4 Consensus size: 20
4243 ATTCATTTTA
4253 TTAGCTCATATGCATTCATT
1 TTAGCTCATATGCATTCATT
4273 TTAGCTCATATGCATTCATT
1 TTAGCTCATATGCATTCATT
4293 TTAGCTCATATGCATTCATT
1 TTAGCTCATATGCATTCATT
4313 TTAGCTC
1 TTAGCTC
4320 TTAGGCTTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (20 bp):
TTAGCTCATATGCATTCATT
Found at i:5743 original size:22 final size:24
Alignment explanation
Indices: 5716--5766 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
5706 AAATCCAGCA
5716 AAGAAATCG-AAGCACTC-AAAAG
1 AAGAAATCGAAAGCACTCAAAAAG
* *
5738 AAGAAATTGAAATCACTCAAAAAG
1 AAGAAATCGAAAGCACTCAAAAAG
5762 AAGAA
1 AAGAA
5767 GAAAAAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.32
23 7 0.28
24 10 0.40
ACGTcount: A:0.59, C:0.14, G:0.16, T:0.12
Consensus pattern (24 bp):
AAGAAATCGAAAGCACTCAAAAAG
Found at i:12101 original size:2 final size:2
Alignment explanation
Indices: 12094--12125 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12084 TAAGCAATTC
12094 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12126 GCTTTCAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12579 original size:48 final size:48
Alignment explanation
Indices: 12469--12579 Score: 150
Period size: 48 Copynumber: 2.3 Consensus size: 48
12459 CATACAAATG
* * **
12469 TCAAACTCGTGCTCAATATCATATAATAGCACCACTGTCACACAGATG
1 TCAAACTCGTGCTCAATATCATACAATAGCACCACCGTCACACAGACA
* * *
12517 CCAAACTCATGCTCAATATCATACAATAGCACCACCGTCACACATACA
1 TCAAACTCGTGCTCAATATCATACAATAGCACCACCGTCACACAGACA
*
12565 TCAAACTCGCGCTCA
1 TCAAACTCGTGCTCA
12580 CAATAATGTC
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.36, C:0.32, G:0.10, T:0.22
Consensus pattern (48 bp):
TCAAACTCGTGCTCAATATCATACAATAGCACCACCGTCACACAGACA
Found at i:14879 original size:30 final size:31
Alignment explanation
Indices: 14805--14879 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 31
14795 TTAAATATCA
14805 AATTACTAATTTACCCTTGAAATTTTCATAT
1 AATTACTAATTTACCCTTGAAATTTTCATAT
* *
14836 ATTTAC-CATTTACCCTTG-AA-TTTCATGAT
1 AATTACTAATTTACCCTTGAAATTTTCAT-AT
*
14865 AATTACTAAATTACC
1 AATTACTAATTTACC
14880 ATGCTTTCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
28 6 0.16
29 9 0.24
30 17 0.46
31 5 0.14
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.43
Consensus pattern (31 bp):
AATTACTAATTTACCCTTGAAATTTTCATAT
Found at i:19921 original size:18 final size:18
Alignment explanation
Indices: 19898--19949 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
19888 TATGTTCTAT
*
19898 GTGGTCCTTCGAGAGATA
1 GTGGTCCTTCGAGACATA
* *
19916 GTGGTCATTCGGGACATA
1 GTGGTCCTTCGAGACATA
*
19934 GTGGTCCTACGAGACA
1 GTGGTCCTTCGAGACA
19950 AATTCTACAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (18 bp):
GTGGTCCTTCGAGACATA
Found at i:25245 original size:18 final size:17
Alignment explanation
Indices: 25218--25310 Score: 62
Period size: 18 Copynumber: 5.1 Consensus size: 17
25208 TACTCTTTGA
25218 AATTTAATTTTTATATT
1 AATTTAATTTTTATATT
*
25235 AATTATAATTTGTATATTATA
1 AATT-TAATTT-T-TA-TATT
*
25256 AATTTAGTTTTTATGA-T
1 AATTTAATTTTTAT-ATT
*
25273 AATTCCAATTCTTTATATT
1 AATT-TAATT-TTTATATT
* *
25292 ATTTATAATTCTTATATT
1 AATT-TAATTTTTATATT
25310 A
1 A
25311 TAAATTTTAT
Statistics
Matches: 59, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
17 9 0.15
18 21 0.36
19 15 0.25
20 7 0.12
21 7 0.12
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.57
Consensus pattern (17 bp):
AATTTAATTTTTATATT
Found at i:25324 original size:13 final size:14
Alignment explanation
Indices: 25290--25326 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
25280 ATTCTTTATA
25290 TTATTTAT-AATTC
1 TTATTTATAAATTC
25303 TTATATTATAAATT-
1 TTAT-TTATAAATTC
25317 TTATTTATAA
1 TTATTTATAA
25327 TCACTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 8 0.36
15 4 0.18
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTTATAAATTC
Found at i:25934 original size:23 final size:23
Alignment explanation
Indices: 25904--25959 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
25894 GCAGCAACCG
*
25904 GCAAGCATCACTATACCAATTCA
1 GCAAGCATCACTACACCAATTCA
* * *
25927 GCAAGCATCATTGCATCAATTCA
1 GCAAGCATCACTACACCAATTCA
*
25950 GCCAGCATCA
1 GCAAGCATCA
25960 TGTATTAAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.36, C:0.30, G:0.12, T:0.21
Consensus pattern (23 bp):
GCAAGCATCACTACACCAATTCA
Found at i:27862 original size:6 final size:6
Alignment explanation
Indices: 27842--27986 Score: 94
Period size: 6 Copynumber: 24.3 Consensus size: 6
27832 CATATTCGGA
* * * ** *
27842 TTTGGG TTCGGG TTTGGG TTTGAG TTTGGA TTCAGG TTTGGA TTTGGG
1 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG
* * ** * * * * *
27890 TTTGGG TTTGGA TTTGGC TTCAGG TTTGGA TAT-GG ATTGGG TTCGAG
1 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG
* * * * * *
27937 TTTGGG TTTGGG ATCGGG TTCGGG TTTGGG TTTTGG TTAGGG TTTAGG
1 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG
27985 TT
1 TT
27987 AGGGGTTAGA
Statistics
Matches: 100, Mismatches: 38, Indels: 2
0.71 0.27 0.01
Matches are distributed among these distances:
5 2 0.02
6 98 0.98
ACGTcount: A:0.09, C:0.05, G:0.41, T:0.45
Consensus pattern (6 bp):
TTTGGG
Found at i:28662 original size:61 final size:61
Alignment explanation
Indices: 28586--28722 Score: 211
Period size: 61 Copynumber: 2.2 Consensus size: 61
28576 TCCTAGTTTT
* *
28586 AAATTTGTTCAATTTAGTCCAAATTTAATGATGCAATATATTAATTTAAGCTTAATATTTC
1 AAATTTGTTCAATTTAGTCCAAATTTAATGATACAATATATTAATTTAAGCTTAATATTTA
* * * * *
28647 AAATTTCTTCAATTTAGTTCAAATTTAATGTTACAATTTATTAATTTAAGCTTCATATTTA
1 AAATTTGTTCAATTTAGTCCAAATTTAATGATACAATATATTAATTTAAGCTTAATATTTA
28708 AAATTTGTTCAATTT
1 AAATTTGTTCAATTT
28723 GATCCTTATA
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 68 1.00
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.47
Consensus pattern (61 bp):
AAATTTGTTCAATTTAGTCCAAATTTAATGATACAATATATTAATTTAAGCTTAATATTTA
Found at i:28782 original size:26 final size:27
Alignment explanation
Indices: 28750--28831 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 27
28740 CAATTCTTTT
28750 AATTAATATATATGTTTATAT-TAAT-A
1 AATTAATATATA-GTTTATATATAATGA
28776 AATTAATATATAAGTTATATATACTAATGA
1 AATTAATATAT-AGTT-TATATA-TAATGA
28806 ACTATATAATATATAGTTTATATATA
1 A--AT-TAATATATAGTTTATATATA
28832 CTAATGAACT
Statistics
Matches: 48, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
26 14 0.29
27 6 0.12
29 4 0.08
30 4 0.08
31 6 0.12
32 6 0.12
33 8 0.17
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (27 bp):
AATTAATATATAGTTTATATATAATGA
Found at i:28813 original size:17 final size:17
Alignment explanation
Indices: 28791--28848 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
28781 ATATATAAGT
28791 TATATATACTAATGAAC
1 TATATATACTAATGAAC
**
28808 TATATA-A-TATAT-AGTT
1 TATATATACTA-ATGA-AC
28824 TATATATACTAATGAAC
1 TATATATACTAATGAAC
28841 TATATATA
1 TATATATA
28849 ATGTATAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 3 0.09
16 9 0.28
17 17 0.53
18 3 0.09
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (17 bp):
TATATATACTAATGAAC
Found at i:28831 original size:18 final size:18
Alignment explanation
Indices: 28808--28952 Score: 113
Period size: 18 Copynumber: 8.3 Consensus size: 18
28798 ACTAATGAAC
*
28808 TATATAATATATAGTTTA
1 TATATACTATATAGTTTA
**
28826 TATATACTA-AT-GAACTA
1 TATATACTATATAG-TTTA
* *
28843 TATATAATGTATAGTTTA
1 TATATACTATATAGTTTA
* * *
28861 TACATACCATATAATTTA
1 TATATACTATATAGTTTA
*
28879 TATATATTATATAGTTTA
1 TATATACTATATAGTTTA
**
28897 TATATACTA-ATA-ACTA
1 TATATACTATATAGTTTA
*
28913 TATA-A-TATATAGTTTG
1 TATATACTATATAGTTTA
* *
28929 TATATACCATATACTTTA
1 TATATACTATATAGTTTA
28947 TATATA
1 TATATA
28953 TAGTTTTTAT
Statistics
Matches: 95, Mismatches: 25, Indels: 14
0.71 0.19 0.10
Matches are distributed among these distances:
14 2 0.02
15 4 0.04
16 12 0.13
17 15 0.16
18 61 0.64
19 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.46
Consensus pattern (18 bp):
TATATACTATATAGTTTA
Found at i:28947 original size:68 final size:70
Alignment explanation
Indices: 28808--28953 Score: 224
Period size: 68 Copynumber: 2.1 Consensus size: 70
28798 ACTAATGAAC
* *
28808 TATATAATATATAGTTTATATATACTAATGAACTATATATAATGTATAGTTTATACATACCATAT
1 TATATATTATATAGTTTATATATACTAATGAAC-ATATATAATATATAGTTTATACATACCATAT
28873 AATTTA
65 AATTTA
* *
28879 TATATATTATATAGTTTATATATACTAAT-AAC-TATATAATATATAGTTTGTATATACCATATA
1 TATATATTATATAGTTTATATATACTAATGAACATATATAATATATAGTTTATACATACCATATA
*
28942 CTTTA
66 ATTTA
28947 TATATAT
1 TATATAT
28954 AGTTTTTATA
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
68 39 0.56
70 3 0.04
71 28 0.40
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (70 bp):
TATATATTATATAGTTTATATATACTAATGAACATATATAATATATAGTTTATACATACCATATA
ATTTA
Found at i:28968 original size:13 final size:13
Alignment explanation
Indices: 28937--28975 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
28927 TGTATATACC
*
28937 ATATACTTTATAT
1 ATATAGTTTATAT
*
28950 ATATAGTTTTTAT
1 ATATAGTTTATAT
*
28963 ATATAGTTCATAT
1 ATATAGTTTATAT
28976 GTAAACTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (13 bp):
ATATAGTTTATAT
Found at i:29060 original size:17 final size:17
Alignment explanation
Indices: 29038--29077 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
29028 GTTTATTAAT
29038 TAATATATTCA-AC-TA
1 TAATATATTCATACATA
29053 T-ATAATATTCATACATA
1 TAAT-ATATTCATACATA
29070 TAATATAT
1 TAATATAT
29078 ACTTTGAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
14 2 0.10
15 8 0.38
16 2 0.10
17 7 0.33
18 2 0.10
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATATATTCATACATA
Found at i:29062 original size:15 final size:15
Alignment explanation
Indices: 29042--29075 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
29032 ATTAATTAAT
29042 ATATTCA-ACTATATA
1 ATATTCATAC-ATATA
29057 ATATTCATACATATA
1 ATATTCATACATATA
29072 ATAT
1 ATAT
29076 ATACTTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 16 0.89
16 2 0.11
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (15 bp):
ATATTCATACATATA
Found at i:29120 original size:27 final size:27
Alignment explanation
Indices: 29090--29161 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
29080 TTTGAATTTA
* *
29090 TATAGTATAAATTATATAAATATAAAT
1 TATAGTATAAAGTATATAAATATAAAC
* * *
29117 TATATTATATAGTATATAAATATCAAC
1 TATAGTATAAAGTATATAAATATAAAC
* *
29144 TATAGTATATAGTTTATA
1 TATAGTATAAAGTATATA
29162 TGGTTTTTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (27 bp):
TATAGTATAAAGTATATAAATATAAAC
Found at i:29229 original size:22 final size:24
Alignment explanation
Indices: 29190--29234 Score: 67
Period size: 22 Copynumber: 1.9 Consensus size: 24
29180 CATTTGTAAA
29190 TTATACTATATAGTATATATAGTTT
1 TTATACTATATAG-ATATATAGTTT
29215 TTATA-TATATA-ATATATAGT
1 TTATACTATATAGATATATAGT
29235 ATATAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 9 0.45
24 6 0.30
25 5 0.25
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (24 bp):
TTATACTATATAGATATATAGTTT
Found at i:29244 original size:22 final size:22
Alignment explanation
Indices: 29204--29245 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
29194 ACTATATAGT
* * *
29204 ATATATAGTTTTTATATATATA
1 ATATATAGTATATAAATATATA
29226 ATATATAGTATATAAATATA
1 ATATATAGTATATAAATATA
29246 AACCATGGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (22 bp):
ATATATAGTATATAAATATATA
Found at i:29277 original size:18 final size:18
Alignment explanation
Indices: 29256--29290 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29246 AACCATGGTT
*
29256 TATATATATAGTATATAC
1 TATATAAATAGTATATAC
*
29274 TATATAAATAGTTTATA
1 TATATAAATAGTATATA
29291 TAGTTCACTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (18 bp):
TATATAAATAGTATATAC
Found at i:29288 original size:31 final size:32
Alignment explanation
Indices: 29226--29292 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
29216 TATATATATA
*
29226 ATATATAGTATATAAATATAAACCATGGTTTAT
1 ATATATAGTATATAAATATAAA-CATAGTTTAT
*
29259 ATATATAGTATAT-ACTATATAA-ATAGTTTAT
1 ATATATAGTATATAAATATA-AACATAGTTTAT
29290 ATA
1 ATA
29293 GTTCACTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 11 0.35
32 5 0.16
33 15 0.48
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.42
Consensus pattern (32 bp):
ATATATAGTATATAAATATAAACATAGTTTAT
Found at i:29321 original size:24 final size:24
Alignment explanation
Indices: 29274--29336 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
29264 TAGTATATAC
* *
29274 TATATAAA-TAGTTTATATAGTTCA
1 TATATAAACTA-TATATATAATTCA
29298 CTA-ATAAACTATATATATAATTCA
1 -TATATAAACTATATATATAATTCA
*
29322 TATGTAAACTATATA
1 TATATAAACTATATA
29337 GTTTATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 2 0.06
24 27 0.82
25 4 0.12
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (24 bp):
TATATAAACTATATATATAATTCA
Found at i:29351 original size:15 final size:15
Alignment explanation
Indices: 29331--29362 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
29321 ATATGTAAAC
*
29331 TATATAGTTTATATA
1 TATATAGTTCATATA
29346 TATATAGTTCATATA
1 TATATAGTTCATATA
29361 TA
1 TA
29363 AACTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (15 bp):
TATATAGTTCATATA
Found at i:29385 original size:24 final size:24
Alignment explanation
Indices: 29358--29411 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
29348 TATAGTTCAT
29358 ATATAAACTATAATTCATATGTAA
1 ATATAAACTATAATTCATATGTAA
* * * *
29382 ATATCAATTATAGTTTATATGTAA
1 ATATAAACTATAATTCATATGTAA
29406 ACTATA
1 A-TATA
29412 GTTGGTATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (24 bp):
ATATAAACTATAATTCATATGTAA
Found at i:29390 original size:18 final size:18
Alignment explanation
Indices: 29313--29382 Score: 65
Period size: 18 Copynumber: 3.9 Consensus size: 18
29303 AAACTATATA
*
29313 TATAATTCATATGTAAAC
1 TATAATTCATATATAAAC
*
29331 TATATAGTT--TATATATA-
1 TATA-A-TTCATATATAAAC
*
29348 TATAGTTCATATATAAAC
1 TATAATTCATATATAAAC
*
29366 TATAATTCATATGTAAA
1 TATAATTCATATATAAA
29383 TATCAATTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
15 2 0.05
17 11 0.27
18 25 0.61
19 1 0.02
20 2 0.05
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (18 bp):
TATAATTCATATATAAAC
Found at i:29413 original size:18 final size:19
Alignment explanation
Indices: 29390--29473 Score: 73
Period size: 20 Copynumber: 4.3 Consensus size: 19
29380 AAATATCAAT
*
29390 TATAGTTTATATGTAAAC-
1 TATAGTTTATATATAAACA
**
29408 TATAGTTGGTATATAAACTA
1 TATAGTTTATATATAAAC-A
*
29428 TATAGTTTATATATATAATA
1 TATAGTTTATATATA-AACA
*
29448 TATAGTATATAAATATAAA-A
1 TATAGT-T-TATATATAAACA
29468 TATAGT
1 TATAGT
29474 ATGTTGTATA
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
18 15 0.28
20 27 0.50
21 5 0.09
22 7 0.13
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (19 bp):
TATAGTTTATATATAAACA
Found at i:29431 original size:20 final size:20
Alignment explanation
Indices: 29408--29602 Score: 78
Period size: 20 Copynumber: 9.2 Consensus size: 20
29398 ATATGTAAAC
*
29408 TATAGTTGGTATATA-AACTA
1 TATAGTTGATATATATAA-TA
*
29428 TATAGTTTATATATATAATA
1 TATAGTTGATATATATAATA
*
29448 TATAGTAT-ATAAATATAAAATA
1 TATAGT-TGAT--ATATATAATA
29470 TAGTATGTTGTATATAAATATAA-A
1 TA-TA-GTTG-ATAT--ATATAATA
* *
29494 CTATAGTTTATATATATAGTA
1 -TATAGTTGATATATATAATA
* * *
29515 TATA-CT-ATATAAATAGTTTA
1 TATAGTTGATATATATA--ATA
* *
29535 TATAGTTCACTAATAAACTATATA
1 TATAGTTGA-T-ATATA-TA-ATA
* *
29559 TATAGTTCATATGTA-AACTA
1 TATAGTTGATATATATAA-TA
*
29579 TATAGTTTATATATATAATA
1 TATAGTTGATATATATAATA
29599 TATA
1 TATA
29603 CTATATAAAT
Statistics
Matches: 139, Mismatches: 15, Indels: 42
0.71 0.08 0.21
Matches are distributed among these distances:
18 8 0.06
19 2 0.01
20 60 0.43
21 7 0.05
22 19 0.14
23 10 0.07
24 22 0.16
25 11 0.08
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (20 bp):
TATAGTTGATATATATAATA
Found at i:29448 original size:7 final size:7
Alignment explanation
Indices: 29438--29526 Score: 51
Period size: 7 Copynumber: 13.1 Consensus size: 7
29428 TATAGTTTAT
29438 ATATATA
1 ATATATA
29445 ATATATA
1 ATATATA
*
29452 GTATATA
1 ATATATA
29459 A-ATATA
1 ATATATA
*
29465 AAATATA
1 ATATATA
* * *
29472 GTATGTT
1 ATATATA
*
29479 GTATATA
1 ATATATA
29486 A-ATATA
1 ATATATA
29492 A-ACTATA
1 ATA-TATA
* *
29499 GTTTAT-
1 ATATATA
29505 ATATATA
1 ATATATA
*
29512 GTATATA
1 ATATATA
*
29519 CTATATA
1 ATATATA
29526 A
1 A
29527 ATAGTTTATA
Statistics
Matches: 62, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
6 17 0.27
7 45 0.73
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (7 bp):
ATATATA
Found at i:29470 original size:27 final size:27
Alignment explanation
Indices: 29440--29511 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
29430 TAGTTTATAT
*
29440 ATATAATATATAGTATATAAATATAAA
1 ATATAGTATATAGTATATAAATATAAA
* *
29467 ATATAGTATGTTGTATATAAATATAAA
1 ATATAGTATATAGTATATAAATATAAA
* *
29494 CTATAGTTTATA-TATATA
1 ATATAGTATATAGTATATA
29512 GTATATACTA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 6 0.16
27 32 0.84
ACGTcount: A:0.50, C:0.01, G:0.07, T:0.42
Consensus pattern (27 bp):
ATATAGTATATAGTATATAAATATAAA
Found at i:29523 original size:18 final size:18
Alignment explanation
Indices: 29502--29536 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29492 AACTATAGTT
*
29502 TATATATATAGTATATAC
1 TATATAAATAGTATATAC
*
29520 TATATAAATAGTTTATA
1 TATATAAATAGTATATA
29537 TAGTTCACTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (18 bp):
TATATAAATAGTATATAC
Found at i:29601 original size:84 final size:84
Alignment explanation
Indices: 29253--29671 Score: 385
Period size: 84 Copynumber: 5.1 Consensus size: 84
29243 ATAAACCATG
* *
29253 GTTTATATATATAGTATATACTATATAAATAGTTTATATAGTTCACTAATAAACTATATATATAA
1 GTTTATATATATAATATATACTATATAAATAGTTTATATAGTTCACTAATAAACTATATATATAG
29318 TTCATATGTAAACTATATA
66 TTCATATGTAAACTATATA
* *
29337 GTTTATATATAT-ATAGT-T-C-ATATATAA-A--CTATA-A-TTCA-TATGTAAA-TATCA-AT
1 GTTTATATATATAATA-TATACTATATA-AATAGTTTATATAGTTCACTA-ATAAACTAT-ATA-
*
29390 TATAGTTTATATGTAAAC--TATA
61 TATAGTTCATATGTAAACTATATA
** * * * * *
29412 GTTGGTATATA-AACTATATAGTTTATATATA-TAATATATAGTAT-A-TAAATATAA-AATATA
1 GTTTATATATATAA-TATATACTATATAAATAGT-TTATATAGT-TCACT-AATA-AACTATATA
* * *
29472 GTAT-GTT-GTATATAAATATAAACTATA
61 -TATAGTTCATATGTAAA-CT--A-TATA
*
29499 GTTTATATATATAGTATATACTATATAAATAGTTTATATAGTTCACTAATAAACTATATATATAG
1 GTTTATATATATAATATATACTATATAAATAGTTTATATAGTTCACTAATAAACTATATATATAG
29564 TTCATATGTAAACTATATA
66 TTCATATGTAAACTATATA
29583 GTTTATATATATAATATATACTATATAAATAGTTTATATAGTTCACTAATAAACTATATATATAG
1 GTTTATATATATAATATATACTATATAAATAGTTTATATAGTTCACTAATAAACTATATATATAG
* *
29648 GTCATATGTAGACTATATA
66 TTCATATGTAAACTATATA
*
29667 ATTTA
1 GTTTA
29672 CATAGTTTAT
Statistics
Matches: 271, Mismatches: 32, Indels: 64
0.74 0.09 0.17
Matches are distributed among these distances:
75 15 0.06
76 9 0.03
77 26 0.10
78 6 0.02
79 4 0.01
80 4 0.01
81 14 0.05
82 12 0.04
83 13 0.05
84 102 0.38
85 1 0.00
86 6 0.02
87 49 0.18
88 10 0.04
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (84 bp):
GTTTATATATATAATATATACTATATAAATAGTTTATATAGTTCACTAATAAACTATATATATAG
TTCATATGTAAACTATATA
Found at i:29609 original size:20 final size:20
Alignment explanation
Indices: 29417--29526 Score: 84
Period size: 20 Copynumber: 5.5 Consensus size: 20
29407 CTATAGTTGG
*
29417 TATATA-AACTATATAGTTTA
1 TATATATAA-TATATAGTATA
29437 TATATATAATATATAGTATA
1 TATATATAATATATAGTATA
* * *
29457 TAAATATAAAATATAGTATGT
1 TATATATAATATATAGTAT-A
* *
29478 TGTATATAA-ATATA-AACTA
1 TATATATAATATATAGTA-TA
*
29497 TAGTTTAT-ATATATAGTATA
1 TA-TATATAATATATAGTATA
29517 TACTATATAA
1 TA-TATATAA
29527 ATAGTTTATA
Statistics
Matches: 70, Mismatches: 13, Indels: 13
0.73 0.14 0.14
Matches are distributed among these distances:
19 3 0.04
20 56 0.80
21 11 0.16
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (20 bp):
TATATATAATATATAGTATA
Found at i:29685 original size:64 final size:64
Alignment explanation
Indices: 29617--29750 Score: 153
Period size: 64 Copynumber: 2.1 Consensus size: 64
29607 ATAAATAGTT
* *
29617 TATATAGTTCACTAATAAACTATATATATAGGTCATATGTAGACTATATAATT-TACATAGTTTA
1 TATATAGTTCA-T-ATAAACTATACATATAGGTCATATGTAAACTATAT-ATTATACATAGTTTA
29681 TA
63 TA
* *** * * *
29683 TATATAGTTTATATATTTTATACATATAGTTCATATGTAAACTATATATTATATATAGTTTACA
1 TATATAGTTCATATAAACTATACATATAGGTCATATGTAAACTATATATTATACATAGTTTATA
29747 TATA
1 TATA
29751 GTATATATTG
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
63 3 0.05
64 44 0.76
65 1 0.02
66 10 0.17
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (64 bp):
TATATAGTTCATATAAACTATACATATAGGTCATATGTAAACTATATATTATACATAGTTTATA
Found at i:29686 original size:22 final size:22
Alignment explanation
Indices: 29661--29710 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
29651 ATATGTAGAC
29661 TATATAATTTACATAGTTTATA
1 TATATAATTTACATAGTTTATA
* * *
29683 TATATAGTTTATATATTTTATA
1 TATATAATTTACATAGTTTATA
*
29705 CATATA
1 TATATA
29711 GTTCATATGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (22 bp):
TATATAATTTACATAGTTTATA
Found at i:29687 original size:246 final size:245
Alignment explanation
Indices: 29233--29688 Score: 633
Period size: 246 Copynumber: 1.9 Consensus size: 245
29223 ATAATATATA
*
29233 GTATATAAATATAAACCATGGTTTATATATATAGTATATACTATATAAATAGTTTATATAGTTCA
1 GTATATAAATATAAACCATAGTTTATATATATAGTATATACTATATAAATAGTTTATATAGTTCA
29298 CTAATAAACTATATATATAATTCATATGTAAACTATATAGTTTATATATATATAGTTCATATATA
66 CTAATAAACTATATATATAATTCATATGTAAACTATATAGTTTATATATATATAGTTCATATATA
* * * * * *
29363 AACTATAATTCATATGTAAATATCAATTATAGTTTATATGTAAACTATAGTTGGTATATAAACTA
131 AACTAT-ATTCATATGTAAATATAAACTATAGTATATAGGTAAACTATAGTAGCTATATAAACTA
*
29428 TATAGTTTATATATATAATATATAGTATATAAATATAAAATATAGTATGTT
195 CATAGTTTATATATATAATATATAGTATATAAATATAAAATATAGTATGTT
*
29479 GTATATAAATATAAACTATAGTTTATATATATAGTATATACTATATAAATAGTTTATATAGTTCA
1 GTATATAAATATAAACCATAGTTTATATATATAGTATATACTATATAAATAGTTTATATAGTTCA
*
29544 CTAATAAACTATATATATAGTTCATATGTAAACTATATAGTTTATATATATAATA-TAT-ACTAT
66 CTAATAAACTATATATATAATTCATATGTAAACTATATAGTTTATATATAT-ATAGT-TCA-TAT
* * *
29607 ATAAA-TAGT-TT-ATATAGTTCACTAATAAACTATA-TATATAGGT-CA-TAT-GTAGACTATA
128 ATAAACTA-TATTCATAT-G-TAAAT-ATAAACTATAGTATATAGGTAAACTATAGTAG-CTATA
**
29665 TAATTTACATAGTTTATATATATA
188 TAAACTACATAGTTTATATATATA
29689 GTTTATATAT
Statistics
Matches: 187, Mismatches: 15, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
243 3 0.02
244 32 0.17
245 4 0.02
246 127 0.68
247 21 0.11
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.42
Consensus pattern (245 bp):
GTATATAAATATAAACCATAGTTTATATATATAGTATATACTATATAAATAGTTTATATAGTTCA
CTAATAAACTATATATATAATTCATATGTAAACTATATAGTTTATATATATATAGTTCATATATA
AACTATATTCATATGTAAATATAAACTATAGTATATAGGTAAACTATAGTAGCTATATAAACTAC
ATAGTTTATATATATAATATATAGTATATAAATATAAAATATAGTATGTT
Found at i:29691 original size:13 final size:13
Alignment explanation
Indices: 29673--29698 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29663 TATAATTTAC
29673 ATAGTTTATATAT
1 ATAGTTTATATAT
29686 ATAGTTTATATAT
1 ATAGTTTATATAT
29699 TTTATACATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
ATAGTTTATATAT
Found at i:29711 original size:22 final size:22
Alignment explanation
Indices: 29662--29781 Score: 85
Period size: 20 Copynumber: 5.7 Consensus size: 22
29652 TATGTAGACT
* * *
29662 ATATAATTTACATAGTTTATAT
1 ATATAGTTTATATAGTTTATAC
*
29684 ATATAGTTTATATATTTTATAC
1 ATATAGTTTATATAGTTTATAC
* *
29706 ATATAGTTCATAT-G--TAAAC
1 ATATAGTTTATATAGTTTATAC
29725 TATATA-TTATATATAG-TT-TAC
1 -ATATAGTT-TATATAGTTTATAC
* *
29746 ATATAGTATATATTGTTTAT--
1 ATATAGTTTATATAGTTTATAC
*
29766 ATATAGTTTAAATAGT
1 ATATAGTTTATATAGT
29782 ATTGTCTATA
Statistics
Matches: 77, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
19 6 0.08
20 33 0.43
21 6 0.08
22 32 0.42
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.49
Consensus pattern (22 bp):
ATATAGTTTATATAGTTTATAC
Found at i:29749 original size:31 final size:31
Alignment explanation
Indices: 29706--29782 Score: 76
Period size: 31 Copynumber: 2.6 Consensus size: 31
29696 TATTTTATAC
29706 ATATAG-TT-CATAT-GTAAACTATAT-ATTAT
1 ATATAGTTTACATATAGTAAA-TAT-TGATTAT
* *
29735 ATATAGTTTACATATAGTATATATTGTTTAT
1 ATATAGTTTACATATAGTAAATATTGATTAT
29766 ATATAGTTTA-A-ATAGTA
1 ATATAGTTTACATATAGTA
29783 TTGTCTATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
29 12 0.29
30 4 0.10
31 22 0.52
32 4 0.10
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (31 bp):
ATATAGTTTACATATAGTAAATATTGATTAT
Found at i:29868 original size:2 final size:2
Alignment explanation
Indices: 29855--30237 Score: 96
Period size: 2 Copynumber: 192.0 Consensus size: 2
29845 ACCTTAAACC
* *
29855 AT AT AT ACT AT AT AT AT AT AA ACT AT AT AGT TT AT AT -T A- AT
1 AT AT AT A-T AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT
* * * *
29896 AA ACT AT AT A- AT TT AT AC A- AT AT AT AT -T AT TT AT A- AT -T
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
29934 AT AC AT A- AT AT AT AG AT AT AA AT -T GT AT AGT TT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* * *
29974 AT -T CAT AT AT A- AT TT AT AT AT AA ACT AT AT A- AT TT AT AT -T
1 AT AT -AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * * *
30014 A- AT AA ACT AT GT AGT TT AT AT AT AGT TT A- AT AGT -T CAT AT AT
1 AT AT AT A-T AT AT A-T AT AT AT AT A-T AT AT AT A-T AT -AT AT AT
* * * *
30056 AC ACT AT AT AGT AT -T AT AGT TT AT AC AT AGT AT AT AT AGT TT AT
1 AT A-T AT AT A-T AT AT AT A-T AT AT AT AT A-T AT AT AT A-T AT AT
* *
30100 AC AT A- AT AT AT AT A- AT AT AT AGT TT AT AT AT AGT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT
* * *
30141 A- AT AT AA AT AT AA AT -T AT AT AGT TT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
* * * *
30181 AT ACT TT AT AT AT AA ACT AT AT AT AT AA ACT AT AT AGT TT AT AT
1 AT A-T AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT A-T AT AT AT
30225 -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
30238 TATTTTTTTC
Statistics
Matches: 272, Mismatches: 60, Indels: 98
0.63 0.14 0.23
Matches are distributed among these distances:
1 25 0.09
2 219 0.81
3 28 0.10
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:29882 original size:24 final size:22
Alignment explanation
Indices: 29849--29905 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
29839 CCCTAAACCT
*
29849 TAAACCATATA-TACTATATATATA
1 TAAACTATATAGT-CTATAT-TA-A
*
29873 TAAACTATATAGTTTATATTAA
1 TAAACTATATAGTCTATATTAA
29895 TAAACTATATA
1 TAAACTATATA
29906 ATTTATACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 12 0.40
23 2 0.07
24 15 0.50
25 1 0.03
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAACTATATAGTCTATATTAA
Found at i:29991 original size:9 final size:10
Alignment explanation
Indices: 29915--30205 Score: 56
Period size: 11 Copynumber: 27.7 Consensus size: 10
29905 AATTTATACA
29915 ATATAT-ATT
1 ATATATAATT
*
29924 ATTTATAATT
1 ATATATAATT
*
29934 ATACATAATAT
1 ATATATAAT-T
29945 ATAGATATAAATT
1 AT--ATAT-AATT
*
29958 GTATAGT--TT
1 ATATA-TAATT
29967 ATATATAATT
1 ATATATAATT
29977 CATATATAATTT
1 -ATATATAA-TT
29989 ATATATAA--
1 ATATATAATT
29997 ACTATATAATT
1 A-TATATAATT
*
30008 -TATATTAATAA
1 ATATA-TAAT-T
* *
30019 ACTATGTAGTTT
1 A-TATATA-ATT
*
30031 ATATATAGTT
1 ATATATAATT
*
30041 -TA-ATAGTT
1 ATATATAATT
*
30049 CATATATACACT
1 -ATATATA-ATT
30061 ATATAGT-ATT
1 ATATA-TAATT
30071 ATAGTTTATACATAGT
1 ATA---TATA-AT--T
*
30087 ATATATAGTTT
1 ATATATA-ATT
*
30098 ATACATAA-T
1 ATATATAATT
30107 ATATATAA-T
1 ATATATAATT
30116 ATATAGT--TT
1 ATATA-TAATT
*
30125 ATATAT-AGT
1 ATATATAATT
30134 ATATAATAATAT
1 ATAT-ATAAT-T
*
30146 AAATATAAATT
1 ATATAT-AATT
30157 ATATAGT--TT
1 ATATA-TAATT
*
30166 ATATATATAAT
1 ATATATA-ATT
*
30177 ATATATACTTT
1 ATATATA-ATT
*
30188 ATATATAAACT
1 ATATAT-AATT
30199 ATATATA
1 ATATATA
30206 TAAACTATAT
Statistics
Matches: 210, Mismatches: 30, Indels: 83
0.65 0.09 0.26
Matches are distributed among these distances:
8 10 0.05
9 56 0.27
10 29 0.14
11 72 0.34
12 18 0.09
13 16 0.08
14 5 0.02
16 4 0.02
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (10 bp):
ATATATAATT
Found at i:29994 original size:13 final size:11
Alignment explanation
Indices: 29959--30205 Score: 63
Period size: 11 Copynumber: 22.4 Consensus size: 11
29949 ATATAAATTG
*
29959 TATAGTTTATA
1 TATAATTTATA
*
29970 TATAATTCATA
1 TATAATTTATA
29981 TATAATTTATA
1 TATAATTTATA
29992 TATAA---ACTA
1 TATAATTTA-TA
30001 TATAATTTATA
1 TATAATTTATA
**
30012 T-TAATAAACTA
1 TATAATTTA-TA
* *
30023 TGTAGTTTATA
1 TATAATTTATA
*
30034 TAT-AGTT-TA
1 TATAATTTATA
* *
30043 -ATAGTTCATA
1 TATAATTTATA
*
30053 TATACA-CTATA
1 TATA-ATTTATA
*
30064 TAGT-ATTATAGTT
1 TA-TAATT-TA-TA
*
30077 TATACATAGTATA
1 TATA-AT-TTATA
*
30090 TATAGTTTATA
1 TATAATTTATA
*
30101 CATAATATATATAA
1 TATAAT-T-TAT-A
30115 TATATAGTTTATA
1 TATA-A-TTTATA
* *
30128 TATAGTATATA
1 TATAATTTATA
* *
30139 -ATAATATAAA
1 TATAATTTATA
*
30149 TATAAATTATA
1 TATAATTTATA
30160 TAGT--TTATATA
1 TA-TAATT-TATA
30171 TATAA--TATA
1 TATAATTTATA
*
30180 TATACTTTATA
1 TATAATTTATA
**
30191 TATAAACTATA
1 TATAATTTATA
30202 TATA
1 TATA
30206 TAAACTATAT
Statistics
Matches: 169, Mismatches: 38, Indels: 58
0.64 0.14 0.22
Matches are distributed among these distances:
8 3 0.02
9 18 0.11
10 20 0.12
11 86 0.51
12 12 0.07
13 16 0.09
14 11 0.07
15 2 0.01
16 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (11 bp):
TATAATTTATA
Found at i:30117 original size:27 final size:28
Alignment explanation
Indices: 30087--30146 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 28
30077 TATACATAGT
30087 ATATATAGTTTATACATAATATAT-ATA
1 ATATATAGTTTATACATAATATATAATA
* *
30114 ATATATAGTTTATATATAGTATATAATA
1 ATATATAGTTTATACATAATATATAATA
30142 ATATA
1 ATATA
30147 AATATAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 22 0.73
28 8 0.27
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (28 bp):
ATATATAGTTTATACATAATATATAATA
Found at i:30119 original size:11 final size:11
Alignment explanation
Indices: 30105--30237 Score: 72
Period size: 11 Copynumber: 12.5 Consensus size: 11
30095 TTTATACATA
30105 ATATAT-ATA-
1 ATATATAATAT
* *
30114 ATATATAGTTT
1 ATATATAATAT
*
30125 ATATATAGTAT
1 ATATATAATAT
30136 ATA-ATAATAT
1 ATATATAATAT
*
30146 AAATATAA-AT
1 ATATATAATAT
*
30156 -TATATAGTTTAT
1 ATATATA--ATAT
30168 ATATATAATAT
1 ATATATAATAT
*
30179 ATATACT-TTAT
1 ATATA-TAATAT
30190 ATATA-AACTAT
1 ATATATAA-TAT
30201 ATATATAA-ACT
1 ATATATAATA-T
*
30212 ATATAGT-TTAT
1 ATATA-TAATAT
30223 AT-TAT-ATAT
1 ATATATAATAT
30232 ATATAT
1 ATATAT
30238 TATTTTTTTC
Statistics
Matches: 97, Mismatches: 12, Indels: 29
0.70 0.09 0.21
Matches are distributed among these distances:
9 17 0.18
10 17 0.18
11 50 0.52
12 7 0.07
13 6 0.06
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (11 bp):
ATATATAATAT
Found at i:30206 original size:13 final size:13
Alignment explanation
Indices: 30175--30216 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
30165 TATATATATA
* *
30175 ATATATATACTTT
1 ATATATAAACTAT
30188 ATATATAAACTAT
1 ATATATAAACTAT
30201 ATATATAAACTAT
1 ATATATAAACTAT
30214 ATA
1 ATA
30217 GTTTATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATATAAACTAT
Found at i:30232 original size:9 final size:9
Alignment explanation
Indices: 29915--30240 Score: 68
Period size: 9 Copynumber: 36.2 Consensus size: 9
29905 AATTTATACA
29915 ATATATATT
1 ATATATATT
*
29924 ATTTATAATT
1 ATATAT-ATT
*
29934 ATACATA--
1 ATATATATT
*
29941 ATATATA-G
1 ATATATATT
*
29949 ATATAAATT
1 ATATATATT
*
29958 GTATAGT-TT
1 ATATA-TATT
29967 ATATATAATT
1 ATATAT-ATT
29977 CATATATAATT
1 -ATATAT-ATT
29988 -TATATA-T
1 ATATATATT
* *
29995 AAACTATATA
1 ATA-TATATT
*
30005 ATTTATATT
1 ATATATATT
* *
30014 A-ATAAACT
1 ATATATATT
*
30022 ATGTAGT-TT
1 ATATA-TATT
30031 ATATATAGTT
1 ATATATA-TT
30041 -TA-ATAGTT
1 ATATATA-TT
*
30049 CATATATA-C
1 -ATATATATT
*
30058 ACTATATAGT
1 A-TATATATT
30068 AT-TATAGTTT
1 ATATATA--TT
* *
30078 ATACATAGT
1 ATATATATT
30087 ATATATAGTT
1 ATATATA-TT
* *
30097 -TATACATA
1 ATATATATT
*
30105 ATATATATA
1 ATATATATT
30114 ATATATAGTT
1 ATATATA-TT
30124 -TATATA-T
1 ATATATATT
*
30131 AGTATATAAT
1 A-TATATATT
*
30141 A-ATATA-A
1 ATATATATT
*
30148 ATATAAATT
1 ATATATATT
30157 ATATAGT-TT
1 ATATA-TATT
30166 ATATATATAAT
1 ATATATAT--T
30177 ATATATACTT
1 ATATATA-TT
30187 -TATATA-T
1 ATATATATT
*
30194 AAACTATA-T
1 ATA-TATATT
* *
30203 ATATAAACT
1 ATATATATT
30212 ATATAGT-TT
1 ATATA-TATT
30221 ATAT-TATAT
1 ATATATAT-T
30230 ATATATATT
1 ATATATATT
30239 AT
1 AT
30241 TTTTTTCAAA
Statistics
Matches: 234, Mismatches: 41, Indels: 84
0.65 0.11 0.23
Matches are distributed among these distances:
7 11 0.05
8 42 0.18
9 130 0.56
10 26 0.11
11 24 0.10
12 1 0.00
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.47
Consensus pattern (9 bp):
ATATATATT
Found at i:30718 original size:217 final size:217
Alignment explanation
Indices: 30363--30833 Score: 793
Period size: 217 Copynumber: 2.2 Consensus size: 217
30353 TTTTAAAAAA
* * * *
30363 AATTT-TAATTTAATATTTGTTCAATTTAGTCCTTAAAATTATATTTGCATATGAAATTGGCCCA
1 AATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAAATTATATGTGCATATAAAATTGGCACA
30427 TACTTATTACTTATTTATATTTTTTTAATTGACCCATAACTTTTTAAATGGGTATAATTTAGTAC
66 TACTTATTACTTATTTATATTTTTTTAATTGACCCATAACTTTTTAAATGGGTATAATTTAGTAC
*
30492 TTTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTG
131 TTTTTTGTATTAATCTAAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTG
30557 TTGTTTAATTTATATAAATTTT
196 TTGTTTAATTTATATAAATTTT
* * *
30579 TATTTGTAATTTCACATTTGTTCAATTTAGTCCTTAAAATTATATGTGCATCTAAAATTGGCACA
1 AATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAAATTATATGTGCATATAAAATTGGCACA
* *
30644 TACTTATTACTTATTTATA-TTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTAT
66 TACTTATTACTTATTTATATTTTTTTAATTGACCCATAACTTTTTAAATGGGTATAATTTAGTAC
*
30708 TTTCTTTGTATTAATCTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGT
131 TTT-TTTGTATTAATCTAAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGT
*
30773 GTTGTTTAATTTATTTAAATTTT
195 GTTGTTTAATTTATATAAATTTT
* *
30796 AATTTGTAATTTCATATTTGCTCAATTTAGTTCTTAAA
1 AATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAA
30834 TTTGTATTTT
Statistics
Matches: 237, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
216 50 0.21
217 187 0.79
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.49
Consensus pattern (217 bp):
AATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAAATTATATGTGCATATAAAATTGGCACA
TACTTATTACTTATTTATATTTTTTTAATTGACCCATAACTTTTTAAATGGGTATAATTTAGTAC
TTTTTTGTATTAATCTAAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTG
TTGTTTAATTTATATAAATTTT
Found at i:35316 original size:18 final size:18
Alignment explanation
Indices: 35293--35365 Score: 92
Period size: 18 Copynumber: 3.9 Consensus size: 18
35283 AGGGATTATC
*
35293 AGTGGTTCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
35311 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
*
35330 CAGTGGTCCTTCGAGACAT
1 -AGTGGTCCTTCGGGACAT
35349 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
35366 AATATTCAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 31 0.65
19 4 0.08
20 13 0.27
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:35342 original size:38 final size:38
Alignment explanation
Indices: 35290--35366 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
35280 TCAAGGGATT
* * *
35290 ATCAGTGGTTCTTCGGGACATAGTGGTTCTTCGGAACA
1 ATCAGTGGTCCTTCGAGACATAGTGGTCCTTCGGAACA
*
35328 ATCAGTGGTCCTTCGAGACATAGTGGTCCTTCGGGACA
1 ATCAGTGGTCCTTCGAGACATAGTGGTCCTTCGGAACA
35366 A
1 A
35367 ATATTCAGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (38 bp):
ATCAGTGGTCCTTCGAGACATAGTGGTCCTTCGGAACA
Found at i:35740 original size:4 final size:4
Alignment explanation
Indices: 35731--35778 Score: 96
Period size: 4 Copynumber: 12.0 Consensus size: 4
35721 TGATAATGAC
35731 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
35779 GTGTGTGTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:35783 original size:2 final size:2
Alignment explanation
Indices: 35776--35836 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
35766 TATGTATGTA
*
35776 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
35818 TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG T
35837 ATACATGCAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.02, C:0.00, G:0.48, T:0.51
Consensus pattern (2 bp):
TG
Found at i:36921 original size:44 final size:45
Alignment explanation
Indices: 36801--36926 Score: 191
Period size: 47 Copynumber: 2.8 Consensus size: 45
36791 TATAAAATCC
36801 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
36846 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
36893 CTTGCCA-TTATTCCAAAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
36927 GTATGCTTAC
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
44 24 0.32
45 10 0.13
46 2 0.03
47 39 0.52
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:37126 original size:59 final size:59
Alignment explanation
Indices: 37034--37162 Score: 168
Period size: 59 Copynumber: 2.2 Consensus size: 59
37024 CGTAGTGCTA
* * * **
37034 TCCCGAATATGACATATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
* * ** *
37093 TCCCGAATATTACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
37152 TCCCGAATATG
1 TCCCGAATATG
37163 CAGCCTGCTG
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
Found at i:42149 original size:19 final size:19
Alignment explanation
Indices: 42125--42176 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
42115 AAATGCAATT
42125 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
42144 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
*
42163 AGTGCATCAATGCA
1 AGTGCATCGATGCA
42177 CCCCCTTAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:43627 original size:18 final size:18
Alignment explanation
Indices: 43604--43666 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
43594 AGGGATTATC
43604 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* * * *
43622 AGTGGTTCTTCAGAATAAT
1 AGTGGTCCTTCGGGA-CAT
* *
43641 CAGTGGTCATTCGAGACAT
1 -AGTGGTCCTTCGGGACAT
43660 AGTGGTC
1 AGTGGTC
43667 ATTCAGGAAA
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
18 19 0.58
19 4 0.12
20 10 0.30
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:44057 original size:4 final size:4
Alignment explanation
Indices: 44043--44888 Score: 1605
Period size: 4 Copynumber: 212.2 Consensus size: 4
44033 TGATAATGAC
44043 ATGT AATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT -ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
44092 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
44140 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG-
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
44187 -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
44234 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
44282 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
44330 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
44378 GTAGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 AT-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
44427 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
44475 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
44523 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
44571 ATGT ATGT ATGT ATGT ATTGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT A-TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
44620 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
44668 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
44716 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
44764 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
44812 ATGT ATGT ATGT A--T ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
44858 ATGT ATGT ATGT ATGT AT-T GTGT A-GT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
44889 ATGAATAAGG
Statistics
Matches: 829, Mismatches: 4, Indels: 17
0.98 0.00 0.02
Matches are distributed among these distances:
2 4 0.00
3 5 0.01
4 809 0.98
5 11 0.01
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:49763 original size:23 final size:25
Alignment explanation
Indices: 49726--49773 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
49716 AAATATATTA
* *
49726 ATTTATATATATTTATAAATAAAAT
1 ATTTATATATATTTAGAAAAAAAAT
49751 ATTTAT-T-TATTTAGAAAAAAAAT
1 ATTTATATATATTTAGAAAAAAAAT
49774 GGTTGTCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.67
24 1 0.05
25 6 0.29
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
ATTTATATATATTTAGAAAAAAAAT
Found at i:50140 original size:21 final size:20
Alignment explanation
Indices: 50100--50145 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
50090 ATTAAATAAG
50100 ATTT-TAATAAATATTATTT
1 ATTTATAATAAATATTATTT
*
50119 ATTTATAATATATATATATTT
1 ATTTATAATAAATAT-TATTT
50140 ATTTAT
1 ATTTAT
50146 GGCTAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 4 0.17
20 9 0.38
21 11 0.46
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTATAATAAATATTATTT
Found at i:50369 original size:144 final size:153
Alignment explanation
Indices: 50208--50505 Score: 524
Period size: 144 Copynumber: 2.0 Consensus size: 153
50198 TAACTAAACA
50208 ATGAATAAAATTAAAACTATATATTTAAAATAAATAAAAC-T-T-AAAAAA-AAAT-AAATTGAA
1 ATGAATAAAATTAAAACTATATATTTAAAATAAATAAAACTTGTAAAAAAATAAATAAAATTGAA
50268 GTTAGTGACT-AATTATAACCTAATAGAATT-ATACCTAATTCATAATTAATTATTT-AAATTTG
66 GTTAGTGACTAAATTATAACCTAATAGAATTAATACCTAATTCATAATTAATTATTTAAAATTTG
50330 AGTGACTAAACATGC-TTTCTCT
131 AGTGACTAAACATGCATTTCTCT
50352 ATGAATAAAATTAAAACTATATATTTAAAATAAATAAAACTTGTAAAAAAATAAATAAAATTGAA
1 ATGAATAAAATTAAAACTATATATTTAAAATAAATAAAACTTGTAAAAAAATAAATAAAATTGAA
50417 GTTAGTGACTAAATTATAACCTAATAGAATTAAATACCTAATTCATAATTAATTATTTAAAATTT
66 GTTAGTGACTAAATTATAACCTAATAGAATT-AATACCTAATTCATAATTAATTATTTAAAATTT
50482 GAGTGACTAAACATGCATTTCTCT
130 GAGTGACTAAACATGCATTTCTCT
50506 TATTTATTAA
Statistics
Matches: 144, Mismatches: 0, Indels: 10
0.94 0.00 0.06
Matches are distributed among these distances:
144 40 0.28
145 1 0.01
146 1 0.01
147 6 0.04
148 4 0.03
149 18 0.12
150 20 0.14
152 25 0.17
153 22 0.15
154 7 0.05
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (153 bp):
ATGAATAAAATTAAAACTATATATTTAAAATAAATAAAACTTGTAAAAAAATAAATAAAATTGAA
GTTAGTGACTAAATTATAACCTAATAGAATTAATACCTAATTCATAATTAATTATTTAAAATTTG
AGTGACTAAACATGCATTTCTCT
Found at i:51828 original size:3 final size:3
Alignment explanation
Indices: 51820--51879 Score: 68
Period size: 3 Copynumber: 19.7 Consensus size: 3
51810 ATATTTATTA
*
51820 AAT AAT AAT AAT -AT ATAT AAT ATAT AAT ATT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
**
51866 TTT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
51880 ATTAAGTAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 40 0.83
4 6 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:51992 original size:21 final size:21
Alignment explanation
Indices: 51966--52008 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
51956 CGAAAAACAA
51966 TAATTTTTCATTTGACTTCTT
1 TAATTTTTCATTTGACTTCTT
51987 TAATTTTTCATTTGACTTCTT
1 TAATTTTTCATTTGACTTCTT
52008 T
1 T
52009 GAGTAAGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.14, G:0.05, T:0.63
Consensus pattern (21 bp):
TAATTTTTCATTTGACTTCTT
Found at i:52494 original size:19 final size:21
Alignment explanation
Indices: 52456--52503 Score: 82
Period size: 20 Copynumber: 2.4 Consensus size: 21
52446 AGATGACCCT
52456 AAGGCTTTGAAAACCATCAAA
1 AAGGCTTTGAAAACCATCAAA
52477 AA-GCTTTGAAAA-CATCAAA
1 AAGGCTTTGAAAACCATCAAA
52496 AAGGCTTT
1 AAGGCTTT
52504 TTGGAAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.35
20 15 0.58
21 2 0.08
ACGTcount: A:0.46, C:0.17, G:0.15, T:0.23
Consensus pattern (21 bp):
AAGGCTTTGAAAACCATCAAA
Found at i:53398 original size:76 final size:76
Alignment explanation
Indices: 52071--53367 Score: 2079
Period size: 76 Copynumber: 17.1 Consensus size: 76
52061 ATGCGAAGGG
52071 CTTACAGATGACCCTAAGGCTTTG-AAACATCAAAAAAGCTCCCGAAGGCTTTTT-GAAACA-CA
1 CTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAAGCTCCCGAAGGCTTTTTGGAAACATCA
*
52133 TTGCA-TGCAGGA
65 -TGCACTGTAGGA
* *
52145 CTTACATATGACCC-ACGGCTTTG-AAACA-CAAAAAAGCTCCCGAAGGCTTTTTGG-AACATCA
1 CTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAAGCTCCCGAAGGCTTTTTGGAAACATCA
52206 TGCACTGTA-GA
65 TGCACTGTAGGA
*
52217 CTTACAGATGACCCTAAGGCTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
1 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
*
52282 GCACTGAAGGA
66 GCACTGTAGGA
* *
52293 CTTAACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTGAAAGCTTTTTGG-AA-A-CA
1 CTT-ACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCA
*
52355 T-CACTGAAGGA
65 TGCACTGTAGGA
52366 CTTACAGATGA-CCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
1 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
52430 GCACTGTAGGA
66 GCACTGTAGGA
**
52441 CTTACAGATGACCCTAAGGCTTTGAAAACCATCAAAAAGCTTTGAAAACATCAAAAAGGCTTTTT
1 CTTACAGATGACCCTAAGGCTTTGAAAA-CATCAAAAAGC--T-----C--C-CGAAGGCTTTTT
*
52506 GG-AA-ATCATGCACTGTAAGA
55 GGAAACATCATGCACTGTAGGA
*
52526 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCAT
1 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
52591 GCACTGTAGGA
66 GCACTGTAGGA
* *
52602 CTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTAGAAACATCAT
1 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
**
52667 GCACTAAAGGA
66 GCACTGTAGGA
*
52678 CTTACAAATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
1 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
*
52743 GCACTGAAGGA
66 GCACTGTAGGA
*
52754 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCAT
1 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
52819 GCACTGTAGGA
66 GCACTGTAGGA
*
52830 CTTACAGATTACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
1 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
52895 GCACTGTAGGA
66 GCACTGTAGGA
*
52906 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGATTTTTGGAAACATCAT
1 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
52971 GCACTGTAGGA
66 GCACTGTAGGA
*
52982 CTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
1 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
* *
53047 GCACTGCAAGA
66 GCACTGTAGGA
53058 CTTACAGAT-ATCCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCA
1 CTTACAGATGA-CCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCA
*
53122 TGCTCTGTAGGA
65 TGCACTGTAGGA
*
53134 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCAT
1 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
53199 GCACTGTAGGA
66 GCACTGTAGGA
* *
53210 CTTACAGATGACCATAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCGTTTTGGAAACATCAT
1 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
53275 GCACTGTAGGA
66 GCACTGTAGGA
53286 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
1 CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
53351 GCACTGTAGGA
66 GCACTGTAGGA
53362 CTTACA
1 CTTACA
53368 CATGTGGGAA
Statistics
Matches: 1145, Mismatches: 49, Indels: 56
0.92 0.04 0.04
Matches are distributed among these distances:
71 42 0.04
72 57 0.05
73 41 0.04
74 60 0.05
75 41 0.04
76 769 0.67
77 63 0.06
79 1 0.00
82 1 0.00
84 12 0.01
85 43 0.04
86 3 0.00
87 12 0.01
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.24
Consensus pattern (76 bp):
CTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
GCACTGTAGGA
Found at i:53648 original size:166 final size:168
Alignment explanation
Indices: 53374--53702 Score: 538
Period size: 166 Copynumber: 2.0 Consensus size: 168
53364 TACACATGTG
53374 GGAAATAGTTTACTAAGTAAAAAAACCAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTC
1 GGAAATAGTTTACTAAGTAAAAAAACCAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTC
**
53439 TAGAAAAGATTGAATGAGAAACTATGGAAATCGTTTTCTC-ATTA-TTTTTCAAAATAACATGTT
66 TAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCTATTATTTTTTCAAAATAACATGTT
* *
53502 GATTGGGTAACATGCCCCAATCTTAAGATAAGGCTGTT
131 GATTGGGTAACATGACCCAATCTCAAGATAAGGCTGTT
*
53540 GGAAATAGTTTACTAAGTAAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTT
1 GGAAATAGTTTACTAAGT-AAAAAAACCAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTT
* **
53605 -TAGAAAAGATAAAATGAGAAACTATGGAAATTGTTTTCTCATTATTATTTTTTTGAAATAACAT
65 CTAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTC--TATTATTTTTTCAAAATAACAT
53669 GTTGATTGGGTAACATGACCCAATCTCAAGATAA
128 GTTGATTGGGTAACATGACCCAATCTCAAGATAA
53703 TGTTCATTCT
Statistics
Matches: 150, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
166 55 0.37
167 45 0.30
169 4 0.03
170 46 0.31
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Consensus pattern (168 bp):
GGAAATAGTTTACTAAGTAAAAAAACCAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTC
TAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCTATTATTTTTTCAAAATAACATGTT
GATTGGGTAACATGACCCAATCTCAAGATAAGGCTGTT
Found at i:54244 original size:22 final size:22
Alignment explanation
Indices: 54216--54270 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
54206 CATAAAGCTT
*
54216 TCATCTTTGAAAATAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
54238 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
54260 TCATCTTTGAA
1 TCATCTTTGAA
54271 GAGTGTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:56943 original size:114 final size:114
Alignment explanation
Indices: 56743--56962 Score: 332
Period size: 114 Copynumber: 1.9 Consensus size: 114
56733 GATCATGCAG
* * * *
56743 TTCATCATTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCATTCAAATCCAATGATTGGTTCTGGGATTCATACCAAACCAGATCAGATAACTCAAAGA
** *
56808 ACACTTTTAGAATATGCTATTGGGTCTCCTTATTTCTACTATGAACAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAACAAA
* * * * *
56857 TTCATCTTTCAAATCTAATGATTGGTTTTTGGATTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCATTCAAATCCAATGATTGGTTCTGGGATTCATACCAAACCAGATCAGATAACTCAAAGA
56922 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
56963 CGAGAACGTG
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
114 94 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (114 bp):
TTCATCATTCAAATCCAATGATTGGTTCTGGGATTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAACAAA
Found at i:58633 original size:32 final size:32
Alignment explanation
Indices: 58592--58656 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 32
58582 GAAGAAATGA
58592 TTGTTATGCTCATCT-TGTAGAGATAATTCTCG
1 TTGTTATGCTCATCTGT-TAGAGATAATTCTCG
*
58624 TTGTTATGCTCATCTGTTAGAGATACTTCTCG
1 TTGTTATGCTCATCTGTTAGAGATAATTCTCG
58656 T
1 T
58657 GTCTTACTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 30 0.97
33 1 0.03
ACGTcount: A:0.20, C:0.17, G:0.18, T:0.45
Consensus pattern (32 bp):
TTGTTATGCTCATCTGTTAGAGATAATTCTCG
Found at i:59272 original size:8 final size:8
Alignment explanation
Indices: 59259--59337 Score: 68
Period size: 8 Copynumber: 9.4 Consensus size: 8
59249 CTTGATTCAA
59259 TTTTTTTC
1 TTTTTTTC
59267 TTTTTTTCC
1 TTTTTTT-C
*
59276 TTTTTGTTG
1 TTTTT-TTC
*
59285 TTTTTTTA
1 TTTTTTTC
*
59293 TTTCTTTCC
1 TTT-TTTTC
59302 TTTTTTTTC
1 -TTTTTTTC
*
59311 TTTTTTCC
1 TTTTTTTC
*
59319 TCTTTTTC
1 TTTTTTTC
*
59327 TTTTTTCC
1 TTTTTTTC
59335 TTT
1 TTT
59338 CTTTGCTGGA
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
8 34 0.60
9 18 0.32
10 5 0.09
ACGTcount: A:0.01, C:0.16, G:0.03, T:0.80
Consensus pattern (8 bp):
TTTTTTTC
Found at i:59273 original size:9 final size:9
Alignment explanation
Indices: 59259--59316 Score: 55
Period size: 9 Copynumber: 6.6 Consensus size: 9
59249 CTTGATTCAA
59259 TTTTTTTCT
1 TTTTTTTCT
*
59268 TTTTTTCCT
1 TTTTTTTCT
* *
59277 TTTTGTT-G
1 TTTTTTTCT
*
59285 TTTTTTTAT
1 TTTTTTTCT
* *
59294 TTCTTTCCT
1 TTTTTTTCT
59303 TTTTTTTCT
1 TTTTTTTCT
59312 TTTTT
1 TTTTT
59317 CCTCTTTTTC
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
8 6 0.16
9 31 0.84
ACGTcount: A:0.02, C:0.12, G:0.03, T:0.83
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:59300 original size:26 final size:26
Alignment explanation
Indices: 59259--59316 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
59249 CTTGATTCAA
* * *
59259 TTTTTTTCTTTTTTTCCTTTTTGTTG
1 TTTTTTTATTTCTTTCCTTTTTGTTC
*
59285 TTTTTTTATTTCTTTCCTTTTTTTTC
1 TTTTTTTATTTCTTTCCTTTTTGTTC
59311 TTTTTT
1 TTTTTT
59317 CCTCTTTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.02, C:0.12, G:0.03, T:0.83
Consensus pattern (26 bp):
TTTTTTTATTTCTTTCCTTTTTGTTC
Found at i:59326 original size:26 final size:24
Alignment explanation
Indices: 59260--59332 Score: 69
Period size: 26 Copynumber: 2.9 Consensus size: 24
59250 TTGATTCAAT
59260 TTTTTTCTTTTTTTCCTTTTTGTTGT-
1 TTTTTTC-TTTTTTCCTTTTT-TT-TC
*
59286 TTTTTTATTTCTTTCCTTTTTTTTC
1 TTTTTTCTTT-TTTCCTTTTTTTTC
59311 TTTTTTCCTCTTTTT-CTTTTTT
1 TTTTTT-CT-TTTTTCCTTTTTT
59333 CCTTTCTTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
24 1 0.02
25 18 0.44
26 20 0.49
27 2 0.05
ACGTcount: A:0.01, C:0.15, G:0.03, T:0.81
Consensus pattern (24 bp):
TTTTTTCTTTTTTCCTTTTTTTTC
Found at i:59351 original size:27 final size:26
Alignment explanation
Indices: 59321--59374 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 26
59311 TTTTTTCCTC
59321 TTTTTCTTTTTTCCTTTCTTTGCTGGA
1 TTTTTCTTTTTT-CTTTCTTTGCTGGA
59348 TTTTTCTTTTTTCTTTCTTTGCTGGA
1 TTTTTCTTTTTTCTTTCTTTGCTGGA
59374 T
1 T
59375 GAGTATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.04, C:0.17, G:0.11, T:0.69
Consensus pattern (26 bp):
TTTTTCTTTTTTCTTTCTTTGCTGGA
Found at i:59352 original size:43 final size:43
Alignment explanation
Indices: 59261--59360 Score: 112
Period size: 43 Copynumber: 2.3 Consensus size: 43
59251 TGATTCAATT
* * * **
59261 TTTTTCTTTTTTTCCTTTTTGTTGTTTTTTTATTTCTTTCCTTT
1 TTTTTC-TTTTTTCCTCTTTGTTCTTTTTTCATTTCTTTCCTGA
* *
59305 TTTTTCTTTTTTCCTCTTT-TTCTTTTTTCCTTTCTTTGCTGGA
1 TTTTTCTTTTTTCCTCTTTGTTCTTTTTTCATTTCTTTCCT-GA
59348 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
59361 TTTCTTTGCT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 17 0.35
43 25 0.52
44 6 0.12
ACGTcount: A:0.02, C:0.17, G:0.05, T:0.76
Consensus pattern (43 bp):
TTTTTCTTTTTTCCTCTTTGTTCTTTTTTCATTTCTTTCCTGA
Found at i:64318 original size:25 final size:26
Alignment explanation
Indices: 64290--64342 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
64280 TTAATACCTG
*
64290 AATAAAATAAAAATAAT-ATTAATAA
1 AATAAAATAAAAATAATAAGTAATAA
*
64315 AATAATATAAAAATAATAAGTAATAA
1 AATAAAATAAAAATAATAAGTAATAA
64341 AA
1 AA
64343 AATTTGAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (26 bp):
AATAAAATAAAAATAATAAGTAATAA
Found at i:64327 original size:11 final size:11
Alignment explanation
Indices: 64290--64332 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
64280 TTAATACCTG
*
64290 AATAAAATAAA
1 AATAATATAAA
64301 AATAATATTAATAA
1 AATAATA-T-A-AA
64315 AATAATATAAA
1 AATAATATAAA
64326 AATAATA
1 AATAATA
64333 AGTAATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 15 0.54
12 2 0.07
13 2 0.07
14 9 0.32
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAATATAAA
Found at i:64973 original size:20 final size:19
Alignment explanation
Indices: 64934--64975 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
64924 TTTCTTCGAT
64934 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
64953 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
64973 ATT
1 ATT
64976 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:65061 original size:120 final size:117
Alignment explanation
Indices: 64843--65067 Score: 265
Period size: 120 Copynumber: 1.9 Consensus size: 117
64833 AAAATATATT
* * * *
64843 AATTTATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAAAAAAAGACTTCTAGGT
1 AATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAAAAAAAGACATCCAGGT
* *
64908 GCCTTAAGACAGCTCTTTTCTTCGATATTAAAAAATAAATAAATAATTAAAAC
66 GCCTTAAGACAGCTCATTTCTTCAATATT-AAAAATAAATAAATAATTAAAAC
** **
64961 AATTAATATATAATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCA
1 AATTAATATAT-ATTTAT-AAATAAAATATTTATTTATTTAAAAATATCA-AAAAAAGACATCCA
* ** *
65026 GTTGTTTTAAGACTGC-CATTTCTT-AATATTGAAAAATAAATA
63 GGTGCCTTAAGACAGCTCATTTCTTCAATATT-AAAAATAAATA
65068 TTAAAACATG
Statistics
Matches: 89, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
118 10 0.11
119 22 0.25
120 35 0.39
121 22 0.25
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (117 bp):
AATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAAAAAAAGACATCCAGGT
GCCTTAAGACAGCTCATTTCTTCAATATTAAAAATAAATAAATAATTAAAAC
Found at i:66691 original size:3 final size:3
Alignment explanation
Indices: 66683--66739 Score: 71
Period size: 3 Copynumber: 18.7 Consensus size: 3
66673 ATATTTATTA
**
66683 AAT AAT AAT AAT -AT ATAT AAT ATAT AAT AAT AAT AAT AAT AAT TTT
1 AAT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
66729 AAT AAT AAT AA
1 AAT AAT AAT AA
66740 ATTAAGTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 2 0.04
3 39 0.83
4 6 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:73272 original size:264 final size:262
Alignment explanation
Indices: 72630--73414 Score: 1107
Period size: 264 Copynumber: 3.0 Consensus size: 262
72620 CTCTTCAGTA
* * * *
72630 GAAGCCAAATCGTCAAAGCA-A-GAGATCGAAGATAGA-GCCAAAATGCTGAAGGAGGTGAAAGC
1 GAAGCCAAATCATCAAAGAAGAGGAGATCGAAGATA-ATGACAAAATGCCGAAGGAGGTGAAAGC
* * *
72692 AGGCCAGGAGTTCATGATAGCTAATGCATCAGAAAGGGACAATTCTCCAGCTGAAGTCAAATCCA
65 AGGCCAGGAGTTCATGATAGCTAATGCATCAGAAAGGGAGAATTCTCCAGCTGAAGTAAAATCTA
* *
72757 CAAAAGAGTCTGAAGAGCAAGAGAGGAGGAATCTGGATGCAAGTGATGGTTTCAATAATCTGCAG
130 CAAAAGAGTCTGAAGAACAAGAGAGGAGGAATCTGGATGCAAGTGATGGCTTCAA-AATCTGCAG
* * *
72822 TCTGCAAAACAAGCAATGGTTGTGGTCTCAAATTCATTATCCGAGGAAGAGGA--CTGTGGTTAA
194 TCTGCAAAACAAGCAATGGTTGTGGTCTCAGATTCATTATCCAAAGAAGAGGACTCTGTGGTTAA
*
72885 AGTG
259 AGCG
* * * *
72889 GAAGCCAAATCATCAAAAGAAGAGGAGATTGAAGATATTGACAAAACGCCAAAGGAGGTGAAAGC
1 GAAGCCAAATCATC-AAAGAAGAGGAGATCGAAGATAATGACAAAATGCCGAAGGAGGTGAAAGC
* * * *
72954 AGGCCAGGAGTCCATGATAGCTAATGTATCAGAAAGGGATG-CTTCTCCAGCTGAAGTTAAATCT
65 AGGCCAGGAGTTCATGATAGCTAATGCATCAGAAAGGGA-GAATTCTCCAGCTGAAGTAAAATCT
*
73018 GCAAAAGAGTCTGAAGAACAAGAGAGGAGGAATCTGGATGCAAGTGATGGCTTCAAAAGTCTGCA
129 ACAAAAGAGTCTGAAGAACAAGAGAGGAGGAATCTGGATGCAAGTGATGGCTTCAAAA-TCTGCA
* *
73083 GTCTGCAAAACAAGC-ATGGATTGTGATCTCGGATTCATTATCCAAAGAAGAGGACTCTGTGGTT
193 GTCTGCAAAACAAGCAATGG-TTGTGGTCTCAGATTCATTATCCAAAGAAGAGGACTCTGTGGTT
73147 AAAGCG
257 AAAGCG
*
73153 GAAGCCAAATCATCAAAGGAAGAGGAGATCGAAGATAATGACAAAATGCCGAAGGAGGCGAAAGC
1 GAAGCCAAATCATCAAA-GAAGAGGAGATCGAAGATAATGACAAAATGCCGAAGGAGGTGAAAGC
* * *
73218 AGGCCAGGAGTTTATGATATCTAATGCACCAGAAAGGGAGAATTCTCCAGCTGAAGTAAAATCTA
65 AGGCCAGGAGTTCATGATAGCTAATGCATCAGAAAGGGAGAATTCTCCAGCTGAAGTAAAATCTA
* * * *
73283 CACAAGAGTCTGAAGAACAGGAGCGGAGGAATCTGGATGCAAGTGATGGCTGCAAAAATCTGCAG
130 CAAAAGAGTCTGAAGAACAAGAGAGGAGGAATCTGGATGCAAGTGATGGCTTC-AAAATCTGCAG
* ** * * *
73348 CCCACAAAACAAGCAATGGTTGTGGTCTCAGATTCATTATCAAAAGAAGAGAACTCTGTGATTAA
194 TCTGCAAAACAAGCAATGGTTGTGGTCTCAGATTCATTATCCAAAGAAGAGGACTCTGTGGTTAA
73413 AG
259 AG
73415 TAGCACTGCC
Statistics
Matches: 465, Mismatches: 48, Indels: 21
0.87 0.09 0.04
Matches are distributed among these distances:
259 13 0.03
260 5 0.01
261 7 0.02
262 194 0.42
263 4 0.01
264 234 0.50
265 8 0.02
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.19
Consensus pattern (262 bp):
GAAGCCAAATCATCAAAGAAGAGGAGATCGAAGATAATGACAAAATGCCGAAGGAGGTGAAAGCA
GGCCAGGAGTTCATGATAGCTAATGCATCAGAAAGGGAGAATTCTCCAGCTGAAGTAAAATCTAC
AAAAGAGTCTGAAGAACAAGAGAGGAGGAATCTGGATGCAAGTGATGGCTTCAAAATCTGCAGTC
TGCAAAACAAGCAATGGTTGTGGTCTCAGATTCATTATCCAAAGAAGAGGACTCTGTGGTTAAAG
CG
Found at i:75470 original size:78 final size:78
Alignment explanation
Indices: 75313--75476 Score: 186
Period size: 78 Copynumber: 2.1 Consensus size: 78
75303 AGTGCTGCCA
*
75313 TCTTTTCTTGCAATGCCTGTGCAAGGGCATCTGAGACATCACCTTTAGTCTCAACAGTATTTAAA
1 TCTTTTCTTGCAATGCCTGTGCAAGGGCATCTGAGACATAACCTTTAGTCTCAACAGTATTTAAA
* **
75378 TCCAGCATGCCCC
66 TACAGCAAACCCC
* * * * * *
75391 TCTTTTCTTGCAATGCCTTTGCAAGGGCTTCTGAGGCATTAAGC-TTAGTCTCAGCAGTATTTGA
1 TCTTTTCTTGCAATGCCTGTGCAAGGGCATCTGAGACA-TAACCTTTAGTCTCAACAGTATTTAA
* *
75455 ATAGAGTAAATCCCTC
65 ATACAGCAAA-CCC-C
75471 TCTTTT
1 TCTTTT
75477 ACCTCATCCT
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
78 58 0.82
79 6 0.08
80 7 0.10
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (78 bp):
TCTTTTCTTGCAATGCCTGTGCAAGGGCATCTGAGACATAACCTTTAGTCTCAACAGTATTTAAA
TACAGCAAACCCC
Found at i:81203 original size:14 final size:15
Alignment explanation
Indices: 81184--81223 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
81174 GTGTTCTTTT
81184 TTTATTATTA-TTAC-
1 TTTATT-TTATTTACA
81198 TTTATTTTATTTACA
1 TTTATTTTATTTACA
81213 TTTA-TTTATTT
1 TTTATTTTATTT
81224 GATTTAAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.12
14 17 0.71
15 4 0.17
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTATTTTATTTACA
Found at i:83461 original size:29 final size:29
Alignment explanation
Indices: 83429--83516 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 29
83419 ATTTGGTCTT
83429 TAAATTTATGTTTTGTTATTTTAGTCCTA
1 TAAATTTATGTTTTGTTATTTTAGTCCTA
* * *
83458 TAAATTTATGTTTGTATTATTTTGGTCCTT
1 TAAATTTATGTTT-TGTTATTTTAGTCCTA
* * *
83488 TAAAGCTTCTGTTATTGTTGTTTTAGTCC
1 TAAA-TTTATGTT-TTGTTATTTTAGTCC
83517 CTTAAAGTCA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 13 0.27
30 17 0.35
31 17 0.35
32 1 0.02
ACGTcount: A:0.20, C:0.09, G:0.14, T:0.57
Consensus pattern (29 bp):
TAAATTTATGTTTTGTTATTTTAGTCCTA
Found at i:85442 original size:32 final size:32
Alignment explanation
Indices: 85392--85452 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
85382 TTTCACCTGT
*
85392 ACTAACTAATTTGTTTTCTTTTGTTTGTGCAC
1 ACTAACTAATTTGTTTTCTTTTGATTGTGCAC
*
85424 ACTAACTTATTT-TATTTCTTTTGATTGTG
1 ACTAACTAATTTGT-TTTCTTTTGATTGTG
85453 TCATTTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 1 0.04
32 25 0.96
ACGTcount: A:0.20, C:0.13, G:0.11, T:0.56
Consensus pattern (32 bp):
ACTAACTAATTTGTTTTCTTTTGATTGTGCAC
Found at i:87472 original size:27 final size:27
Alignment explanation
Indices: 87442--87505 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
87432 GGATCAATAT
87442 TTTTGCATATGCATTTTCATATTT-GCA
1 TTTTGCATATGCA-TTTCATATTTAGCA
* *
87469 TTTTGCATCTGCATTTCATTTTTAAGCA
1 TTTTGCATATGCATTTCATATTT-AGCA
87497 TTTT-CATAT
1 TTTTGCATAT
87506 AAAAAATAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 9 0.28
27 16 0.50
28 7 0.22
ACGTcount: A:0.22, C:0.16, G:0.09, T:0.53
Consensus pattern (27 bp):
TTTTGCATATGCATTTCATATTTAGCA
Found at i:87483 original size:13 final size:13
Alignment explanation
Indices: 87442--87484 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
87432 GGATCAATAT
87442 TTTTGCATATGCA
1 TTTTGCATATGCA
87455 TTTT-CATATTTGCA
1 TTTTGCATA--TGCA
*
87469 TTTTGCATCTGCA
1 TTTTGCATATGCA
87482 TTT
1 TTT
87485 CATTTTTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 4 0.15
13 11 0.42
14 8 0.31
15 3 0.12
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (13 bp):
TTTTGCATATGCA
Found at i:92390 original size:88 final size:86
Alignment explanation
Indices: 92242--92412 Score: 279
Period size: 88 Copynumber: 2.0 Consensus size: 86
92232 TAATCAGATC
* * *
92242 TCCTCATTATGTAGGAGTGTGTCAACTTAGATAACCAGCCGTCCCCATCAGAGTGGAACCGTGTT
1 TCCTCATTATGTAGGAGTGTGTCAAATTAGATAACCAGCCATCCCCATCAGAGTGGAACCGTATT
*
92307 ATCACCTTTAGATGACCAAATT
66 ACCACC-TTAGATGACCAAATT
92329 TCCTCATTATGTAGGAGTTGTGTCAAATTAGATAACCAGCCATCCCCATCAGAGTGGAACCGTAT
1 TCCTCATTATGTAGGAG-TGTGTCAAATTAGATAACCAGCCATCCCCATCAGAGTGGAACCGTAT
*
92394 TACCACCTTAGATGGCCAA
65 TACCACCTTAGATGACCAA
92413 GACTCATGAA
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
87 28 0.36
88 50 0.64
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (86 bp):
TCCTCATTATGTAGGAGTGTGTCAAATTAGATAACCAGCCATCCCCATCAGAGTGGAACCGTATT
ACCACCTTAGATGACCAAATT
Found at i:92505 original size:43 final size:45
Alignment explanation
Indices: 92444--92655 Score: 140
Period size: 43 Copynumber: 4.8 Consensus size: 45
92434 TGTCATCACC
*
92444 TGACCA-AATCTCCTCATCACGTAGGAGCCGTGTCA-ACCCTT-GA
1 TGACCAGAA-CTCTTCATCACGTAGGAGCCGTGTCATACCCTTAGA
* * * *
92487 TAACCAGAACTCTTCATCACGTATGAGCAGTGTTATCACCCTTCCTAAAGA
1 TGACCAGAACTCTTCATCACGTAGGAGCCGTGTCAT-ACCC-T--T--AGA
* * *
92538 TGGCCAAGAACTCTTCATCACGT-GTGAGCAGTGTCATTCCC-----
1 TGACC-AGAACTCTTCATCACGTAG-GAGCCGTGTCATACCCTTAGA
* * * *
92579 TGACTAGATCTCCTCATCACGTAGGAGCCTTGTC--ACCCTTAGA
1 TGACCAGAACTCTTCATCACGTAGGAGCCGTGTCATACCCTTAGA
* *
92622 TGACCAGAACTCTTCATCACGTATGAGTCGTGTC
1 TGACCAGAACTCTTCATCACGTAGGAGCCGTGTC
92656 GTCTCCCCAC
Statistics
Matches: 129, Mismatches: 23, Indels: 34
0.69 0.12 0.18
Matches are distributed among these distances:
38 3 0.02
40 23 0.18
41 4 0.03
43 55 0.43
44 2 0.02
45 4 0.03
46 1 0.01
48 1 0.01
51 8 0.06
52 28 0.22
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27
Consensus pattern (45 bp):
TGACCAGAACTCTTCATCACGTAGGAGCCGTGTCATACCCTTAGA
Found at i:94285 original size:28 final size:30
Alignment explanation
Indices: 94221--94285 Score: 82
Period size: 28 Copynumber: 2.2 Consensus size: 30
94211 ATGATTTGGT
*
94221 CTTTAAATTTATGTTTTGTTATTTTTAGTC
1 CTTTAAATTCATGTTTTGTTATTTTTAGTC
*
94251 CTATAAATTCATG-TTTG-TATTATTT-GTC
1 CTTTAAATTCATGTTTTGTTATT-TTTAGTC
94279 CTTTAAA
1 CTTTAAA
94286 GCTTCTGTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 13 0.42
29 7 0.23
30 11 0.35
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.57
Consensus pattern (30 bp):
CTTTAAATTCATGTTTTGTTATTTTTAGTC
Done.