Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000162.1 Hibiscus syriacus cultivar Beakdansim tig00000286_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: 128669
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:396 original size:85 final size:84
Alignment explanation
Indices: 247--417 Score: 238
Period size: 85 Copynumber: 2.0 Consensus size: 84
237 ATTACGGTTA
* * * *
247 ACGGTCAACTGTTTTACACAATTATCACCCTAACAGTAATTAATTACAAATTAGGCACCCTTTTA
1 ACGGTCAACTGTTTTACACAAATATCACCATAACAGTAATTAATTACAAATGAGGCACCATTTT-
312 AAAATATTTACAAAACTAGC
65 AAAATATTTACAAAACTAGC
* * *
332 ACGGTCAAC-GATTTTACATAAATATCACCATAACA-TAAATTAATTACATATGAGGCACTATTT
1 ACGGTCAACTG-TTTTACACAAATATCACCATAACAGT-AATTAATTACAAATGAGGCACCATTT
395 TAAAATATTTACAAAACTAGC
64 TAAAATATTTACAAAACTAGC
416 AC
1 AC
418 CCGATTCAAC
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
84 24 0.31
85 53 0.69
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.30
Consensus pattern (84 bp):
ACGGTCAACTGTTTTACACAAATATCACCATAACAGTAATTAATTACAAATGAGGCACCATTTTA
AAATATTTACAAAACTAGC
Found at i:2365 original size:20 final size:20
Alignment explanation
Indices: 2340--2380 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
2330 TTGCGGCATC
*
2340 TGTCGCAGTTGCCATTGTGG
1 TGTCGCAATTGCCATTGTGG
2360 TGTCGCAATTGCCATTGTGG
1 TGTCGCAATTGCCATTGTGG
2380 T
1 T
2381 ATCACTGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.12, C:0.20, G:0.32, T:0.37
Consensus pattern (20 bp):
TGTCGCAATTGCCATTGTGG
Found at i:2391 original size:20 final size:20
Alignment explanation
Indices: 2345--2391 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
2335 GCATCTGTCG
* *
2345 CAGTTGCCATTGTGGTGTCG
1 CAGTTGCCATTGTGGTATCA
*
2365 CAATTGCCATTGTGGTATCA
1 CAGTTGCCATTGTGGTATCA
*
2385 CTGTTGC
1 CAGTTGC
2392 AGATGTTACG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.15, C:0.21, G:0.28, T:0.36
Consensus pattern (20 bp):
CAGTTGCCATTGTGGTATCA
Found at i:3179 original size:3 final size:3
Alignment explanation
Indices: 3173--3255 Score: 69
Period size: 3 Copynumber: 28.0 Consensus size: 3
3163 CCATGATCAT
* * * * *
3173 CAC CAC CAC TAC CAC CAC CAT CAT CAC CAC CAC CAC CAC CAC CAT CAT
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
* * * * *
3221 CAT CAC CAC C-C CAC CAT CAT CAT CAT CAC CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
3256 ATGACATTGA
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
2 2 0.03
3 69 0.97
ACGTcount: A:0.33, C:0.55, G:0.00, T:0.12
Consensus pattern (3 bp):
CAC
Found at i:3195 original size:24 final size:23
Alignment explanation
Indices: 3158--3252 Score: 118
Period size: 24 Copynumber: 4.0 Consensus size: 23
3148 CCTTCATTAT
**
3158 CACCACCATGATCATCACCACCA
1 CACCACCACCATCATCACCACCA
3181 CTACCACCACCATCATCACCACCA
1 C-ACCACCACCATCATCACCACCA
*
3205 CCACCACCACCATCATCATCACCA
1 -CACCACCACCATCATCACCACCA
* * *
3229 CCCCACCATCATCATCATCACCA
1 CACCACCACCATCATCACCACCA
3252 C
1 C
3253 CACATGACAT
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
23 23 0.35
24 41 0.63
25 1 0.02
ACGTcount: A:0.33, C:0.53, G:0.01, T:0.14
Consensus pattern (23 bp):
CACCACCACCATCATCACCACCA
Found at i:8740 original size:201 final size:202
Alignment explanation
Indices: 8337--8746 Score: 619
Period size: 201 Copynumber: 2.0 Consensus size: 202
8327 GATGAAAAGT
* * * *
8337 TTACACTTTGAAACTAAAGTTTCTGTGCTTCCTCCCGTTGTCTTCTTTACTTCTTACTTTGGTTG
1 TTACACTTTGAAACTAAAGTTTCTATGCTTCCTACCATTGTCTTCTTTACTTCTTACTTTGATTG
* * *
8402 TGAATTTTTTTAATATTTTAATTGTGAAATTCATTTTTTTTTATTTATTTTTAACACTTCCAAAC
66 TGAATTTTTTTAATATTTTAATTGTGAAATTCATTTTTTTTCAATTATTTTTAACACTTCCAAAA
*
8467 AAATTCTCTACTATTTGCTTTAGTATTGTCTTACACACCTACATCATCTACTACATGCTTTACTA
131 AAATTCTCTACTATTTGCTTTAGTATTGTCTTACACACCTACATCATCTACTACATACTTTACTA
*
8532 TTTTTAC
196 CTTTTAC
* *
8539 TTACACTTTGAAACTAGAGTTTCTATGTTTCCTACCATT-TCCTTCTTTACTTCTTACTTTGATT
1 TTACACTTTGAAACTAAAGTTTCTATGCTTCCTACCATTGT-CTTCTTTACTTCTTACTTTGATT
* * * *
8603 GTGAATTTTTTTAATATTTTGATTTTTAAATTCA-TTTTTTTCAATTATTTTTAACACTTCTAAA
65 GTGAATTTTTTTAATATTTTAATTGTGAAATTCATTTTTTTTCAATTATTTTTAACACTTCCAAA
* * *
8667 AAAATTCTCTACTATTTGCTTTAGTACTT-TTTTACACACCTGCATCATTTACTACATACTTTAC
130 AAAATTCTCTACTATTTGCTTTAGTA-TTGTCTTACACACCTACATCATCTACTACATACTTTAC
8731 TACTTTTAC
194 TACTTTTAC
8740 TTACACT
1 TTACACT
8747 CTTCTTTTTT
Statistics
Matches: 188, Mismatches: 18, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
201 99 0.53
202 89 0.47
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.50
Consensus pattern (202 bp):
TTACACTTTGAAACTAAAGTTTCTATGCTTCCTACCATTGTCTTCTTTACTTCTTACTTTGATTG
TGAATTTTTTTAATATTTTAATTGTGAAATTCATTTTTTTTCAATTATTTTTAACACTTCCAAAA
AAATTCTCTACTATTTGCTTTAGTATTGTCTTACACACCTACATCATCTACTACATACTTTACTA
CTTTTAC
Found at i:8814 original size:17 final size:16
Alignment explanation
Indices: 8780--8845 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 16
8770 TCCAAGAATC
* *
8780 ATATTTTTTTATTTTTT
1 ATATATTTTT-TTATTT
8797 ATAATATTTTTTTATTT
1 AT-ATATTTTTTTATTT
* *
8814 ACATGTATTTTTTATTT
1 ATATAT-TTTTTTATTT
8831 -TATATTTTTTGTATT
1 ATATATTTTTT-TATT
8846 ATGAATAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
15 5 0.12
16 10 0.25
17 18 0.45
18 7 0.17
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.73
Consensus pattern (16 bp):
ATATATTTTTTTATTT
Found at i:9148 original size:45 final size:45
Alignment explanation
Indices: 9099--9196 Score: 160
Period size: 45 Copynumber: 2.2 Consensus size: 45
9089 GAAATGATTC
* * *
9099 AATTTAAAGTAAAATTGGTTTAATTTTAAAATAACGTGAATAAAT
1 AATTTAAAGGAAAATTAGTTTAATTTTAAAATAACATGAATAAAT
*
9144 AATTTAAAGGAAAATTAGTTTACTTTTAAAATAACATGAATAAAT
1 AATTTAAAGGAAAATTAGTTTAATTTTAAAATAACATGAATAAAT
9189 AATTTAAA
1 AATTTAAA
9197 TAATTCATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.37
Consensus pattern (45 bp):
AATTTAAAGGAAAATTAGTTTAATTTTAAAATAACATGAATAAAT
Found at i:10745 original size:17 final size:17
Alignment explanation
Indices: 10723--10758 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
10713 ACATCCATTT
10723 CTATATCCAACGACATC
1 CTATATCCAACGACATC
10740 CTATATCCAACGACATC
1 CTATATCCAACGACATC
10757 CT
1 CT
10759 TCCTCATCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.36, G:0.06, T:0.25
Consensus pattern (17 bp):
CTATATCCAACGACATC
Found at i:11465 original size:24 final size:24
Alignment explanation
Indices: 11407--11453 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
11397 AGTCAGAATT
* * *
11407 CGAAATTTAATCTTGGTCAATACC
1 CGAACTTTGATCTTGATCAATACC
11431 CGAACTTTGATCTTGATCAATAC
1 CGAACTTTGATCTTGATCAATAC
11454 TCGGATTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGATCAATACC
Found at i:12330 original size:21 final size:21
Alignment explanation
Indices: 12304--12344 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12294 TCGTGATACG
12304 AAAATGAAAATCGCAACACGA
1 AAAATGAAAATCGCAACACGA
**
12325 AAAATGACTATCGCAACACG
1 AAAATGAAAATCGCAACACG
12345 GATTTTACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.22, G:0.15, T:0.12
Consensus pattern (21 bp):
AAAATGAAAATCGCAACACGA
Found at i:12826 original size:22 final size:22
Alignment explanation
Indices: 12799--12856 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
12789 GATGGAGATA
12799 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
12821 GACGGATTTTGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
12843 GACGGATGTCGCCG
1 GACGGATTTCGCCG
12857 TAGAGAACGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.17, C:0.17, G:0.45, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:13085 original size:20 final size:20
Alignment explanation
Indices: 13016--13087 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
13006 ATTTTGTATT
* * *
13016 ATCGCGTTGTGATAGTCAGA
1 ATCGCGTTGCGATAGTTAAA
13036 ATCGCGTTGCGAT--TTACATA
1 ATCGCGTTGCGATAGTTA-A-A
* * *
13056 TTCACATTGCGATAGTTAAA
1 ATCGCGTTGCGATAGTTAAA
13076 ATCGCGTTGCGA
1 ATCGCGTTGCGA
13088 ATCTGGAAAC
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
18 2 0.05
20 33 0.85
21 1 0.03
22 3 0.08
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTTAAA
Found at i:13137 original size:19 final size:19
Alignment explanation
Indices: 13113--13149 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
13103 TGAGATACTG
*
13113 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
13132 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
13150 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:16028 original size:80 final size:81
Alignment explanation
Indices: 15885--16123 Score: 288
Period size: 80 Copynumber: 3.0 Consensus size: 81
15875 TACATCACTG
* * * *
15885 AAAAGTTGCTGAAGATGATAA-GATACCACTATTTCATCTGTTGTCTGAAATGTTGTTTAAATTA
1 AAAAGTTGCAGAAGATGATAATG-CACCACTATTTCACCTGTTTTCTGAAAT-TTGTTTAAATTA
15949 TGCATTGAATGACC-TAA
64 TGCATTGAATGACCTTAA
**
15966 AAAAG-TGCAGAAGATGATAATGCACCACTATTTCACCTGTTTTAAGAAACTTTGTTTAAATTAT
1 AAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCTGTTTTCTGAAA-TTTGTTTAAATTAT
* **
16030 GCATTGAATAACCTTTG
65 GCATTGAATGACCTTAA
* ** * *
16047 AAAAGTTGCAGAAGATGATAATGCA-TACTATTTCACCCATTTTCTGAAAAATTGCTTAAATTAT
1 AAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCTGTTTTCTG-AAATTTGTTTAAATTAT
16111 GCATTGAATGACC
65 GCATTGAATGACC
16124 AGTGAAAAGT
Statistics
Matches: 136, Mismatches: 17, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
80 61 0.45
81 53 0.39
82 22 0.16
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.34
Consensus pattern (81 bp):
AAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCTGTTTTCTGAAATTTGTTTAAATTATG
CATTGAATGACCTTAA
Found at i:16106 original size:81 final size:80
Alignment explanation
Indices: 15883--16147 Score: 284
Period size: 81 Copynumber: 3.3 Consensus size: 80
15873 AATACATCAC
* * * **
15883 TGAAAAGTTGCTGAAGATGATAA-G-ATACCACTATTTCATCTGTTGTCTGAAATGTTGTTTAAA
1 TGAAAAGTTGCAGAAGATGATAATGCAT---ACTATTTCACCTGTTTTCTGAAAAATTGTTTAAA
15946 TTATGCATTGAATGACCT
63 TTATGCATTGAATGACCT
** * ** **
15964 AAAAAAG-TGCAGAAGATGATAATGCACCACTATTTCACCTGTTTTAAGAAACTTTGTTTAAATT
1 TGAAAAGTTGCAGAAGATGATAATGCA-TACTATTTCACCTGTTTTCTGAAAAATTGTTTAAATT
*
16028 ATGCATTGAATAACCTT
65 ATGCATTGAATGACC-T
** *
16045 TGAAAAGTTGCAGAAGATGATAATGCATACTATTTCACCCATTTTCTGAAAAATTGCTTAAATTA
1 TGAAAAGTTGCAGAAGATGATAATGCATACTATTTCACCTGTTTTCTGAAAAATTGTTTAAATTA
*
16110 TGCATTGAATGACCAG
66 TGCATTGAATGACC-T
* *
16126 TGAAAAGTTGAACAAGATGATA
1 TGAAAAGTTGCAGAAGATGATA
16148 TTGGACCACC
Statistics
Matches: 153, Mismatches: 26, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
80 58 0.38
81 75 0.49
82 20 0.13
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (80 bp):
TGAAAAGTTGCAGAAGATGATAATGCATACTATTTCACCTGTTTTCTGAAAAATTGTTTAAATTA
TGCATTGAATGACCT
Found at i:19173 original size:40 final size:40
Alignment explanation
Indices: 19129--19267 Score: 104
Period size: 40 Copynumber: 3.2 Consensus size: 40
19119 ACTCTAGTTT
19129 ATTTAAGGAGAACATTATGTACATGAATTATATGATATTA
1 ATTTAAGGAGAACATTATGTACATGAATTATATGATATTA
* * *
19169 ATTTAAGGTTAGAGA-ATGTGTTTAAAATCTAGCATGAATT-TACT-CTAGTTT
1 ATTTAAGG--AGA-ACA-----TT---ATGTA-CATGAATTATA-TGATA-TTA
19220 ATTTAAGGAGAACATTATGTACATGAATTATATGATATTA
1 ATTTAAGGAGAACATTATGTACATGAATTATATGATATTA
19260 ATTTAAGG
1 ATTTAAGG
19268 TTAGAGAATG
Statistics
Matches: 76, Mismatches: 6, Indels: 34
0.66 0.05 0.29
Matches are distributed among these distances:
40 27 0.36
41 8 0.11
42 4 0.05
43 1 0.01
44 2 0.03
47 2 0.03
48 1 0.01
49 4 0.05
50 8 0.11
51 19 0.25
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.39
Consensus pattern (40 bp):
ATTTAAGGAGAACATTATGTACATGAATTATATGATATTA
Found at i:19251 original size:91 final size:91
Alignment explanation
Indices: 19096--19279 Score: 359
Period size: 91 Copynumber: 2.0 Consensus size: 91
19086 TGTGATTTCA
*
19096 TGTTTAAAATCTAGTATGAATTTACTCTAGTTTATTTAAGGAGAACATTATGTACATGAATTATA
1 TGTTTAAAATCTAGCATGAATTTACTCTAGTTTATTTAAGGAGAACATTATGTACATGAATTATA
19161 TGATATTAATTTAAGGTTAGAGAATG
66 TGATATTAATTTAAGGTTAGAGAATG
19187 TGTTTAAAATCTAGCATGAATTTACTCTAGTTTATTTAAGGAGAACATTATGTACATGAATTATA
1 TGTTTAAAATCTAGCATGAATTTACTCTAGTTTATTTAAGGAGAACATTATGTACATGAATTATA
19252 TGATATTAATTTAAGGTTAGAGAATG
66 TGATATTAATTTAAGGTTAGAGAATG
19278 TG
1 TG
19280 AGGGTAATTG
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 92 1.00
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.40
Consensus pattern (91 bp):
TGTTTAAAATCTAGCATGAATTTACTCTAGTTTATTTAAGGAGAACATTATGTACATGAATTATA
TGATATTAATTTAAGGTTAGAGAATG
Found at i:21005 original size:6 final size:7
Alignment explanation
Indices: 20986--21016 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
20976 TTTAACTGCG
20986 AAAATTT
1 AAAATTT
20993 AAAATTT
1 AAAATTT
21000 -AAATTT
1 AAAATTT
21006 AAAATTT
1 AAAATTT
21013 AAAA
1 AAAA
21017 AAACCGATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AAAATTT
Found at i:21005 original size:13 final size:13
Alignment explanation
Indices: 20987--21015 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
20977 TTAACTGCGA
20987 AAATTTAAAATTT
1 AAATTTAAAATTT
21000 AAATTTAAAATTT
1 AAATTTAAAATTT
21013 AAA
1 AAA
21016 AAAACCGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATTTAAAATTT
Found at i:21212 original size:16 final size:17
Alignment explanation
Indices: 21179--21223 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
21169 AATTTAGTAA
21179 AAAAATAATAAA-ATAAT
1 AAAAAT-ATAAATATAAT
21196 AAAAATATAAATA-AAT
1 AAAAATATAAATATAAT
21212 AAATAA-ATAAAT
1 AAA-AATATAAAT
21224 TAACCAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 17 0.65
17 9 0.35
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAATATAAATATAAT
Found at i:21216 original size:20 final size:19
Alignment explanation
Indices: 21176--21223 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
21166 TGAAATTTAG
21176 TAAAAAAATAATAAAATAA
1 TAAAAAAATAATAAAATAA
*
21195 TAAAAATATAA-ATAAATAAA
1 TAAAAAAATAATA-AAAT-AA
*
21215 TAAATAAAT
1 TAAAAAAAT
21224 TAACCAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 1 0.04
19 14 0.58
20 9 0.38
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (19 bp):
TAAAAAAATAATAAAATAA
Found at i:23650 original size:84 final size:84
Alignment explanation
Indices: 23145--24340 Score: 1284
Period size: 84 Copynumber: 14.5 Consensus size: 84
23135 TTTTCTCGAA
* * * * * * * * * *
23145 TGAGCTGAATGAAATCAAACTCGAATGT-ATTTGTTGACATATAGCCCTTCTTACCTTGAACTAT
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTAT
* * **
23209 ACTGTAAATTTGATAAGCCTT
66 GCTGCAAA--TGATGTGCCTT
* * * * *
23230 TGAGATGAATGTAATCGAACTCGAAGGTC-TTGGTTGACAGATAACCCTTCTCGCCTTGAGCTAT
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTAT
* * *
23294 GATGTAAATGGTGTGCCTT
66 GCTGCAAATGATGTGCCTT
* * * * * *
23313 TGAGTTGAGTGTAATTGAACTCGAAGGT-ATTTGTTGACAGATAGCCCTTCTTTCCTTGAGCTAT
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTAT
* **
23377 GCTGTAAATTTGATAAGCCTT
66 GCTGCAAA--TGATGTGCCTT
* * * * * * * *
23398 TGAGTTGAATGTGATCGAACTCAAAGGT-TTTGGTTGACAGATAACCCTTATTGCCTTAAGCTAT
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTAT
* * *
23462 GTTGTAAATGATGTACCTT
66 GCTGCAAATGATGTGCCTT
* * * * * * * *
23481 TGAGTTGAGTGTAATCGAACTCGAATGTC---T-TTGGTAGATAGCCCTTCTCGTCTTTAGTTAT
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTAT
*
23542 GCTGCAAATGATGTGACTT
66 GCTGCAAATGATGTGCCTT
* * * ** * *
23561 TGAGCTGAGTATAATCGAACTCGAAGGTCTTTTATTGGCAAATAACATTTATTTCCTTGAGCTAT
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTAT
*
23626 GTTGCAAATGATGTGCCTT
66 GCTGCAAATGATGTGCCTT
* *
23645 TGAGCTGAGTGTAATCGAACTCGAAGGTC---T-TTGGCAGATAACCTTTCTTGCCTTGAACTAT
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTAT
* *
23706 GTTGCAAATGATGTACCTT
66 GCTGCAAATGATGTGCCTT
* * *
23725 TGAGCTAAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCTTTCTTGCCTTGAGCTAT
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTAT
** *
23790 ATTGCAAATGATGTGTCTT
66 GCTGCAAATGATGTGCCTT
* * * *
23809 TGAGCTGAGTGTAATCGAACTCGAAGATC---T-TTGGCAGATAGCCTTTCTCGCCTTGAGCTAT
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTAT
* *
23870 GCTGAAAATG-T-TTCCTT
66 GCTGCAAATGATGTGCCTT
* *
23887 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTAT
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTAT
* * *
23952 GTTGAAAATGACGTGCCTT
66 GCTGCAAATGATGTGCCTT
* * * ** *
23971 TGAGCTGAGTGTAATCAAACTCGAAGG--TATT-TT-GCAGATATCTATTCTTGCCTTGAGTTAT
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTAT
* *
24032 ACTGCAAATGATGTGTCTT
66 GCTGCAAATGATGTGCCTT
* * * *
24051 TGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTTGCAGATAGCCCTTCTTGTCTTGAGCTAT
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTAT
*
24116 ACTGCAAATGATGTGCCTT
66 GCTGCAAATGATGTGCCTT
* * * *
24135 TGAGCTGAGTGGAATCGAACTCGAAGGTCTTTTGTTGGTAAATAACCCTTCTTGTCTTGAGCTAT
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTAT
*
24200 GTTGCAAATGATGTGCCTT
66 GCTGCAAATGATGTGCCTT
* * *
24219 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCATATATCCCTTCTTTCCTTGAGCTAT
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTAT
24284 GCTGCAAATGATGTGCCTT
66 GCTGCAAATGATGTGCCTT
*
24303 TGAGCTGAGTGTAATCGAACTCAAAGGTCTTTTGTTGG
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGG
24341 AGGTGCTTTT
Statistics
Matches: 950, Mismatches: 138, Indels: 47
0.84 0.12 0.04
Matches are distributed among these distances:
78 32 0.03
79 1 0.00
80 235 0.25
81 5 0.01
82 43 0.05
83 107 0.11
84 399 0.42
85 128 0.13
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (84 bp):
TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTAT
GCTGCAAATGATGTGCCTT
Found at i:23656 original size:164 final size:164
Alignment explanation
Indices: 23185--24334 Score: 1354
Period size: 164 Copynumber: 7.0 Consensus size: 164
23175 TTGTTGACAT
* * * * ** * *
23185 ATAGCCCTTCTTACCTTGAACTATACTGTAAATTTGATAAGCCTTTGAGATGAATGTAATCGAAC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAA--TGATGTGCCTTTGAGCTGAGTGTAATCGAAC
* * * * * * *
23250 TCGAAGGTC-TTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGATGTAAATGGTGTGCCTTT
64 TCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTT
* * *
23314 GAGTTGAGTGTAATTGAACTCGAAGGTATTTGTTGACAG
129 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTG--G-CAG
* * ** * * *
23353 ATAGCCCTTCTTTCCTTGAGCTATGCTGTAAATTTGATAAGCCTTTGAGTTGAATGTGATCGAAC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAA--TGATGTGCCTTTGAGCTGAGTGTAATCGAAC
* * * * * * * *
23418 TCAAAGGT-TTTGGTTGACAGATAACCCTTATTGCCTTAAGCTATGTTGTAAATGATGTACCTTT
64 TCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTT
* * *
23482 GAGTTGAGTGTAATCGAACTCGAATGTCTTTGGTAG
129 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAG
* * * * * *
23518 ATAGCCCTTCTCGTCTTTAGTTATGCTGCAAATGATGTGACTTTGAGCTGAGTATAATCGAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
* ** * *
23583 GAAGGTCTTTTATTGGCAAATAACATTTATTTCCTTGAGCTATGTTGCAAATGATGTGCCTTTGA
66 GAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGA
23648 GCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAG
131 GCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAG
* * * * * *
23682 ATAACCTTTCTTGCCTTGAACTATGTTGCAAATGATGTACCTTTGAGCTAAGTGTAATCGAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
* * *
23747 GAAGGTCTTTTGTTGGCAAATAACCTTTCTTGCCTTGAGCTATATTGCAAATGATGTGTCTTTGA
66 GAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGA
*
23812 GCTGAGTGTAATCGAACTCGAAGATCTTTGGCAG
131 GCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAG
* * * *
23846 ATAGCCTTTCTCGCCTTGAGCTATGCTGAAAATG-T-TTCCTTTGAGCTGAGTGTAATCGAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
* * *
23909 GAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGAAAATGACGTGCCTTTGA
66 GAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGA
* * *
23974 GCTGAGTGTAATCAAACTCGAAGGTATTTTGCAG
131 GCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAG
* ** * * * *
24008 ATATCTATTCTTGCCTTGAGTTATACTGCAAATGATGTGTCTTTGAGCTGAGTGTAATCAAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
* * * * **
24073 GAAGGTCTTTTGTTTGCAGATAGCCCTTCTTGTCTTGAGCTATACTGCAAATGATGTGCCTTTGA
66 GAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGA
* * *
24138 GCTGAGTGGAATCGAACTCGAAGGTCTTTTGTTGGTAA
131 GCTGAGTGTAATCGAACTCGAAGGTC---T-TTGGCAG
* * *
24176 ATAACCCTTCTTGTCTTGAGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
* * * *
24241 GAAGGTCTTTTGTTGGCATATATCCCTTCTTTCCTTGAGCTATGCTGCAAATGATGTGCCTTTGA
66 GAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGA
*
24306 GCTGAGTGTAATCGAACTCAAAGGTCTTT
131 GCTGAGTGTAATCGAACTCGAAGGTCTTT
24335 TGTTGGAGGT
Statistics
Matches: 855, Mismatches: 119, Indels: 20
0.86 0.12 0.02
Matches are distributed among these distances:
162 142 0.17
163 33 0.04
164 361 0.42
165 29 0.03
166 1 0.00
167 1 0.00
168 288 0.34
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (164 bp):
ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
GAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGA
GCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAG
Found at i:25337 original size:88 final size:88
Alignment explanation
Indices: 25186--25361 Score: 212
Period size: 88 Copynumber: 2.0 Consensus size: 88
25176 GTTTTGTAGA
* * * *
25186 TATTATAATCACCTTTATCAGTCTAGCTGAATATTATCTATAAAGCCAAGGCATTTAATCAATTG
1 TATTACAATCACCTTTATCAGTCTAGCTGAATAGTATCCATAAAGCCAAGGCATTTAACCAATTG
*
25251 -CTCTAGAGGGACAACTCGAGCTT
66 CCT-TAGAGGGACAACTCAAGCTT
* *** *
25274 TATTACAATCACCTTTATCAAG-CTAGCTGAATCGTATCCATAAAGCTGGGGCGTTTAACCAATT
1 TATTACAATCACCTTTATC-AGTCTAGCTGAATAGTATCCATAAAGCCAAGGCATTTAACCAATT
* *
25338 TCCTTAGAGGGACATCTCAAGCTT
65 GCCTTAGAGGGACAACTCAAGCTT
25362 GATTGTATAT
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
88 70 0.95
89 4 0.05
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (88 bp):
TATTACAATCACCTTTATCAGTCTAGCTGAATAGTATCCATAAAGCCAAGGCATTTAACCAATTG
CCTTAGAGGGACAACTCAAGCTT
Found at i:29043 original size:20 final size:19
Alignment explanation
Indices: 29020--29062 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
29010 TGAAATTTAG
29020 TAAAAAT-AATAATAAAATAA
1 TAAAAATGAA-AATAAAA-AA
29040 TAAAAATGAAAATAAAAAA
1 TAAAAATGAAAATAAAAAA
29059 TAAA
1 TAAA
29063 TAAATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.27
20 14 0.64
21 2 0.09
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (19 bp):
TAAAAATGAAAATAAAAAA
Found at i:30153 original size:21 final size:22
Alignment explanation
Indices: 30128--30171 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
30118 TACTTCACTA
30128 TTTTTA-TATACCAATTC-CTTC
1 TTTTTACTATA-CAATTCTCTTC
*
30149 TTTTTACTCTACAATTCTCTTC
1 TTTTTACTATACAATTCTCTTC
30171 T
1 T
30172 ACTTTATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.20, C:0.25, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTTACTATACAATTCTCTTC
Found at i:35753 original size:29 final size:29
Alignment explanation
Indices: 35718--35785 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
35708 TATGGTTAAA
**
35718 AATCAATGTGACCACCTAACT-TTTAATT
1 AATCAATCAGACCACCTAACTATTTAATT
35746 GAATCAATCAGACCACCTAACTATTTAATT
1 -AATCAATCAGACCACCTAACTATTTAATT
35776 AATTCAATCA
1 AA-TCAATCA
35786 AGCTACCGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
29 21 0.60
30 14 0.40
ACGTcount: A:0.40, C:0.22, G:0.06, T:0.32
Consensus pattern (29 bp):
AATCAATCAGACCACCTAACTATTTAATT
Found at i:36411 original size:29 final size:29
Alignment explanation
Indices: 36377--36441 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
36367 AAAAAATTTG
*
36377 ATTAATTCGGTTCGGTTAATAATTTTCAA
1 ATTAATTCGGTTCAGTTAATAATTTTCAA
36406 ATTAATTCGGTTCAGTTAATAATTTTCAA
1 ATTAATTCGGTTCAGTTAATAATTTTCAA
*
36435 ATAAATT
1 ATTAATT
36442 TTGGTTTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (29 bp):
ATTAATTCGGTTCAGTTAATAATTTTCAA
Found at i:36558 original size:29 final size:29
Alignment explanation
Indices: 36517--36580 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
36507 AAAAAAACGG
36517 TTAATTCACTTCGGTTAATAATTTTCAAA
1 TTAATTCACTTCGGTTAATAATTTTCAAA
**
36546 TTAATTCGGTTCGGTTAATAATTTTCAAA
1 TTAATTCACTTCGGTTAATAATTTTCAAA
*
36575 TAAATT
1 TTAATT
36581 TTGGTTCAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.45
Consensus pattern (29 bp):
TTAATTCACTTCGGTTAATAATTTTCAAA
Found at i:36686 original size:29 final size:29
Alignment explanation
Indices: 36654--36730 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
36644 AAAAAATCGG
*
36654 TTAATTTGGTTCGATTAATAATTTTCAAA
1 TTAATTTGGTTCGATTAATAATGTTCAAA
* * *
36683 TTAATTCGATTCGGTTAATAATGTTCAAA
1 TTAATTTGGTTCGATTAATAATGTTCAAA
*
36712 TAAATTTTGGTTCGATTAA
1 TTAA-TTTGGTTCGATTAA
36731 ACGAACCTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 28 0.72
30 11 0.28
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (29 bp):
TTAATTTGGTTCGATTAATAATGTTCAAA
Found at i:36730 original size:137 final size:139
Alignment explanation
Indices: 36378--36755 Score: 555
Period size: 139 Copynumber: 2.7 Consensus size: 139
36368 AAAAATTTGA
*
36378 TTAATTCGGTTCGGTTAATAATTTTCAAATTAATTCGGTTCAGTTAATAATTTTCAAATAAATTT
1 TTAATTCGGTTCGGTTAATAATTTTCAAATTAATTCGGTTCGGTTAATAATTTTCAAATAAATTT
* ** * *
36443 TGGTTTGATTAACTAAACCGAATTAA-TAGAATTTTTGCTTCGATTAATTCAATTAATAATTTAA
66 TGGTTCGATTAACCGAACCGAATTAACCA-AATTTTTTCTTCGATTAATTCAATTAATAATTTAA
36507 AAAAAAACGG
130 AAAAAAACGG
**
36517 TTAATTCACTTCGGTTAATAATTTTCAAATTAATTCGGTTCGGTTAATAATTTTCAAATAAATTT
1 TTAATTCGGTTCGGTTAATAATTTTCAAATTAATTCGGTTCGGTTAATAATTTTCAAATAAATTT
* * **
36582 TGGTTCAATTAACCGAACCGAACTAACCAAATTTTTTCTTCGATTAATTCGGTTAATAA-TT-AA
66 TGGTTCGATTAACCGAACCGAATTAACCAAATTTTTTCTTCGATTAATTCAATTAATAATTTAAA
*
36645 AAAAATCGG
131 AAAAAACGG
* * * *
36654 TTAATTTGGTTCGATTAATAATTTTCAAATTAATTCGATTCGGTTAATAATGTTCAAATAAATTT
1 TTAATTCGGTTCGGTTAATAATTTTCAAATTAATTCGGTTCGGTTAATAATTTTCAAATAAATTT
* *
36719 TGGTTCGATTAAACGAACCTAATTAACCAAATTTTTT
66 TGGTTCGATTAACCGAACCGAATTAACCAAATTTTTT
36756 TCTTTAACCG
Statistics
Matches: 215, Mismatches: 23, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
137 102 0.47
138 2 0.01
139 110 0.51
140 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (139 bp):
TTAATTCGGTTCGGTTAATAATTTTCAAATTAATTCGGTTCGGTTAATAATTTTCAAATAAATTT
TGGTTCGATTAACCGAACCGAATTAACCAAATTTTTTCTTCGATTAATTCAATTAATAATTTAAA
AAAAAACGG
Found at i:36777 original size:137 final size:137
Alignment explanation
Indices: 36378--36777 Score: 460
Period size: 137 Copynumber: 2.9 Consensus size: 137
36368 AAAAATTTGA
*
36378 TTAATTCGGTTCGGTTAATAATTTTCAAATTAATTCGGTTCAGTTAATAATTTTCAAATAAATTT
1 TTAATTCGGTTCGGTTAATAATTTTCAAATTAATTCGGTTCGGTTAATAATTTTCAAATAAATTT
* * * *
36443 TGGTTTGATT-AACTAAACCGAATTAA-TAGAATTTTTGCTTCGATTAA--TTCAAT-TAATAAT
66 TGGTTCGATTAAAC-GAACCGAATTAACCA-AATTTTT--TTC--TTAACGTT-AATCGAATAAT
36503 TTAAAAAAAAACGG
124 TTAAAAAAAAACGG
**
36517 TTAATTCACTTCGGTTAATAATTTTCAAATTAATTCGGTTCGGTTAATAATTTTCAAATAAATTT
1 TTAATTCGGTTCGGTTAATAATTTTCAAATTAATTCGGTTCGGTTAATAATTTTCAAATAAATTT
* * *
36582 TGGTTCAATTAACCGAACCGAACTAACCAAA-TTTTTTCTT--CGATTAATTCGGTTAATAA-TT
66 TGGTTCGATTAAACGAACCGAATTAACCAAATTTTTTTCTTAACG-TTAA-TC-G--AATAATTT
*
36643 -AAAAAAATCGG
126 AAAAAAAAACGG
* * * *
36654 TTAATTTGGTTCGATTAATAATTTTCAAATTAATTCGATTCGGTTAATAATGTTCAAATAAATTT
1 TTAATTCGGTTCGGTTAATAATTTTCAAATTAATTCGGTTCGGTTAATAATTTTCAAATAAATTT
*
36719 TGGTTCGATTAAACGAACCTAATTAACCAAATTTTTTTCTTTAACCGTTAATCGAATAA
66 TGGTTCGATTAAACGAACCGAATTAACCAAATTTTTTTC-TTAA-CGTTAATCGAATAA
36778 AAAATTATTT
Statistics
Matches: 225, Mismatches: 21, Indels: 32
0.81 0.08 0.12
Matches are distributed among these distances:
134 4 0.02
135 3 0.01
136 3 0.01
137 101 0.45
138 13 0.06
139 90 0.40
140 5 0.02
141 4 0.02
142 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (137 bp):
TTAATTCGGTTCGGTTAATAATTTTCAAATTAATTCGGTTCGGTTAATAATTTTCAAATAAATTT
TGGTTCGATTAAACGAACCGAATTAACCAAATTTTTTTCTTAACGTTAATCGAATAATTTAAAAA
AAAACGG
Found at i:38435 original size:17 final size:17
Alignment explanation
Indices: 38413--38447 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
38403 GACCTCAGTT
38413 GTGAAGCCTTTATTCAG
1 GTGAAGCCTTTATTCAG
38430 GTGAAGCCTTTATTCAG
1 GTGAAGCCTTTATTCAG
38447 G
1 G
38448 GGAAAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (17 bp):
GTGAAGCCTTTATTCAG
Found at i:40255 original size:14 final size:14
Alignment explanation
Indices: 40236--40265 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
40226 GATTGATCAA
40236 TTATGTAAGGTTAT
1 TTATGTAAGGTTAT
40250 TTATGTAAGGTTAT
1 TTATGTAAGGTTAT
40264 TT
1 TT
40266 GTTGCGGGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (14 bp):
TTATGTAAGGTTAT
Found at i:42848 original size:20 final size:20
Alignment explanation
Indices: 42813--42862 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
42803 TGGAAAATAT
42813 TAAAACATAA-TCCTAAAAA
1 TAAAACATAATTCCTAAAAA
*
42832 TAAAAGATAATTCCTAAAAA
1 TAAAACATAATTCCTAAAAA
*
42852 TAAAATATAAT
1 TAAAACATAAT
42863 CTTGATTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 9 0.32
20 19 0.68
ACGTcount: A:0.62, C:0.10, G:0.02, T:0.26
Consensus pattern (20 bp):
TAAAACATAATTCCTAAAAA
Found at i:46838 original size:14 final size:14
Alignment explanation
Indices: 46819--46850 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
46809 AATTGAATGT
46819 AAATCGAAAATCAA
1 AAATCGAAAATCAA
46833 AAATCGAAAATCAA
1 AAATCGAAAATCAA
46847 AAAT
1 AAAT
46851 TAAAGCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.66, C:0.12, G:0.06, T:0.16
Consensus pattern (14 bp):
AAATCGAAAATCAA
Found at i:48642 original size:21 final size:20
Alignment explanation
Indices: 48590--48666 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
48580 TTTCTGGATC
* *
48590 AAAGGATCGATCACTTAGAA
1 AAAGGATCGATCCCTTTGAA
* * * *
48610 AATGCATTGATCCCTTTGACC
1 AAAGGATCGATCCCTTTGA-A
*
48631 AAAGGATCGATCCCCTTGAA
1 AAAGGATCGATCCCTTTGAA
*
48651 AAATGATCGATCCCTT
1 AAAGGATCGATCCCTT
48667 GGATTTTAGT
Statistics
Matches: 43, Mismatches: 13, Indels: 2
0.74 0.22 0.03
Matches are distributed among these distances:
20 28 0.65
21 15 0.35
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (20 bp):
AAAGGATCGATCCCTTTGAA
Found at i:48652 original size:41 final size:41
Alignment explanation
Indices: 48589--48666 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 41
48579 TTTTCTGGAT
*
48589 CAAAGGATCGATCACTTAG-AAAATGCATTGATCCCTTTGAC
1 CAAAGGATCGATCACTTAGAAAAATG-ATCGATCCCTTTGAC
*
48630 CAAAGGATCGATCCCCTT-GAAAAATGATCGATCCCTT
1 CAAAGGATCGAT-CACTTAGAAAAATGATCGATCCCTT
48667 GGATTTTAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 23 0.70
42 10 0.30
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (41 bp):
CAAAGGATCGATCACTTAGAAAAATGATCGATCCCTTTGAC
Found at i:48725 original size:21 final size:21
Alignment explanation
Indices: 48683--48801 Score: 84
Period size: 21 Copynumber: 5.7 Consensus size: 21
48673 TAGTAGGTTT
* * *
48683 AGGATCAATCCCTTTACAAAA
1 AGGATCGATCCCTTCACTAAA
* *
48704 AGGATCGATCCCTTGAGTAAA
1 AGGATCGATCCCTTCACTAAA
* * *
48725 AGCATCGATTCCTTCACCAAA
1 AGGATCGATCCCTTCACTAAA
48746 AGGATC-AGT-CCTTCGA-TGAAA
1 AGGATCGA-TCCCTTC-ACT-AAA
* *
48767 AGGATTGATCCCTTC-CTTTAA
1 AGGATCGATCCCTTCAC-TAAA
48788 AGGATCGATCCCTT
1 AGGATCGATCCCTT
48802 TCTTACAACA
Statistics
Matches: 77, Mismatches: 14, Indels: 14
0.73 0.13 0.13
Matches are distributed among these distances:
20 6 0.08
21 64 0.83
22 7 0.09
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (21 bp):
AGGATCGATCCCTTCACTAAA
Found at i:50143 original size:12 final size:12
Alignment explanation
Indices: 50115--50154 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
50105 GAGGATGAGC
50115 AAGAAAG-AGAA
1 AAGAAAGAAGAA
*
50126 AAGAAAGAAGAG
1 AAGAAAGAAGAA
50138 AAGAAAGAA-AA
1 AAGAAAGAAGAA
50149 AA-AAAG
1 AAGAAAG
50155 CATGTTGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 4 0.15
11 10 0.38
12 12 0.46
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (12 bp):
AAGAAAGAAGAA
Found at i:66993 original size:56 final size:55
Alignment explanation
Indices: 66897--67027 Score: 165
Period size: 60 Copynumber: 2.3 Consensus size: 55
66887 CAATTCGTGT
* *
66897 GTATGTGTTTGTTCTTGTTTTTTTCTTTTCTTTTCTAAGTATACAGTTATTCGTAATTTC
1 GTATGTGTCTGTTCTTGTTTTTTTC---TCTTTTCTAAGTATACAGTTATTCGT--TTGC
* * *
66957 GTATGTGTCTGTTCTTGTTTTTTTC-CTTTTTTAAGTATGCAGTTATTTGTTTGC
1 GTATGTGTCTGTTCTTGTTTTTTTCTCTTTTCTAAGTATACAGTTATTCGTTTGC
67011 GTATGTGTCTGTTCTTG
1 GTATGTGTCTGTTCTTG
67028 ATAATCACAG
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
54 20 0.30
56 22 0.33
60 24 0.36
ACGTcount: A:0.12, C:0.11, G:0.18, T:0.59
Consensus pattern (55 bp):
GTATGTGTCTGTTCTTGTTTTTTTCTCTTTTCTAAGTATACAGTTATTCGTTTGC
Found at i:69375 original size:9 final size:9
Alignment explanation
Indices: 69361--69385 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
69351 ACACCTTGTA
69361 GATGAAGAT
1 GATGAAGAT
69370 GATGAAGAT
1 GATGAAGAT
69379 GATGAAG
1 GATGAAG
69386 TTGTTATGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.36, T:0.20
Consensus pattern (9 bp):
GATGAAGAT
Found at i:74733 original size:12 final size:12
Alignment explanation
Indices: 74711--74744 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
74701 CGTTAAGAAT
74711 TCAAG-TCGAGC
1 TCAAGCTCGAGC
*
74722 TCGAGCTCGAGC
1 TCAAGCTCGAGC
74734 TCAAGCTCGAG
1 TCAAGCTCGAG
74745 TCCATTCGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.24, C:0.29, G:0.29, T:0.18
Consensus pattern (12 bp):
TCAAGCTCGAGC
Found at i:89163 original size:29 final size:29
Alignment explanation
Indices: 89121--89224 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
89111 TCCATAGAGG
*
89121 ATCCCATGCAGAATCAGGATGGGGATACA
1 ATCCCATGCAGAATCAGGATGGGGATAAA
* * * *
89150 ATCCCATGAAGAATCATGATGGGGACATA
1 ATCCCATGCAGAATCAGGATGGGGATAAA
* * *
89179 ATCACATGCAGAATCAGGACGAGGATAAA
1 ATCCCATGCAGAATCAGGATGGGGATAAA
* *
89208 ATCTCATGCATAATCAG
1 ATCCCATGCAGAATCAG
89225 AACGATGAAA
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 62 1.00
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (29 bp):
ATCCCATGCAGAATCAGGATGGGGATAAA
Found at i:89229 original size:29 final size:29
Alignment explanation
Indices: 89176--89258 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
89166 TGATGGGGAC
* *
89176 ATAATCACATGCAGAATCAGGACGAGGATA
1 ATAATCTCATGCAGAATCAGAACGAGGA-A
* *
89206 A-AATCTCATGCATAATCAGAACGATGAA
1 ATAATCTCATGCAGAATCAGAACGAGGAA
89234 ATAAT-TCTATGCAGAATCAGAACGA
1 ATAATCTC-ATGCAGAATCAGAACGA
89259 CGATTATGCC
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
28 4 0.09
29 41 0.89
30 1 0.02
ACGTcount: A:0.45, C:0.17, G:0.18, T:0.20
Consensus pattern (29 bp):
ATAATCTCATGCAGAATCAGAACGAGGAA
Found at i:96693 original size:2 final size:2
Alignment explanation
Indices: 96648--96679 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
96638 ACTATAGATA
96648 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
96680 GAAAATAAAT
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:98739 original size:18 final size:19
Alignment explanation
Indices: 98699--98736 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
98689 TGGTTCACGA
98699 AATGTAAGATTACCAGTGGG
1 AATGTAAGATTACCAG-GGG
*
98719 AATGTAAGATTATCAGGG
1 AATGTAAGATTACCAGGG
98737 AATAGGATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.37, C:0.08, G:0.29, T:0.26
Consensus pattern (19 bp):
AATGTAAGATTACCAGGGG
Found at i:98964 original size:37 final size:39
Alignment explanation
Indices: 98886--98965 Score: 94
Period size: 38 Copynumber: 2.1 Consensus size: 39
98876 AACAAGTTGG
* * *
98886 AAAATATTTATATATTTTCTTTAAAAAATTTACATTCAT
1 AAAATATTTATATATTTTCTTTAAAAAATTGAAAATCAT
*
98925 AAAAT-TTATATATATTTT-TTTACAAAATTGAAAAT-AT
1 AAAATATT-TATATATTTTCTTTAAAAAATTGAAAATCAT
98962 AAAA
1 AAAA
98966 AAGTTTAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
37 6 0.17
38 15 0.42
39 15 0.42
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (39 bp):
AAAATATTTATATATTTTCTTTAAAAAATTGAAAATCAT
Found at i:104853 original size:15 final size:15
Alignment explanation
Indices: 104835--104866 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
104825 ATCAAAATAG
*
104835 TCATCATCATCTCCA
1 TCATCATCACCTCCA
104850 TCATCATCACCTCCA
1 TCATCATCACCTCCA
104865 TC
1 TC
104867 CCCACCTCCA
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:0.25, C:0.44, G:0.00, T:0.31
Consensus pattern (15 bp):
TCATCATCACCTCCA
Found at i:108551 original size:229 final size:226
Alignment explanation
Indices: 108119--108566 Score: 788
Period size: 229 Copynumber: 2.0 Consensus size: 226
108109 GTAAATTATC
* * *
108119 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
*
108184 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAATTTT
*
108249 GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGA
131 GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTGA
108314 AACATAAATTACATAACTTTCAAAAAAGTATA
196 AACATAAATTACATAACTTT-AAAAAAGTATA
*
108346 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
108411 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAAT-AAATT
* *
108476 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAATT
129 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATT
108541 GAAACATAAATTACATAACTTTAAAA
194 GAAACATAAATTACATAACTTTAAAA
108567 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
227 36 0.17
228 86 0.41
229 88 0.42
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (226 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAATTTT
GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTGA
AACATAAATTACATAACTTTAAAAAAGTATA
Found at i:108655 original size:20 final size:19
Alignment explanation
Indices: 108632--108678 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
108622 CGATATACCA
108632 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
108652 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
108672 GGTAAAA
1 GGTAAAA
108679 TTAAAAGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:108822 original size:20 final size:19
Alignment explanation
Indices: 108799--108845 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
108789 CGATATAACA
*
108799 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
108819 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
108839 GGTAAAA
1 GGTAAAA
108846 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:111188 original size:33 final size:33
Alignment explanation
Indices: 111146--111211 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
111136 AAATAGATGG
*
111146 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
111179 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
111212 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:113064 original size:19 final size:19
Alignment explanation
Indices: 113001--113063 Score: 110
Period size: 19 Copynumber: 3.4 Consensus size: 19
112991 AATGTCGAGT
*
113001 TAATTTTGTATAAGATTTA
1 TAATTTTGTATACGATTTA
113020 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
113039 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
113058 T-ATTTT
1 TAATTTT
113064 TTTATGTGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
18 5 0.12
19 38 0.88
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATACGATTTA
Found at i:113820 original size:196 final size:199
Alignment explanation
Indices: 113146--113963 Score: 1411
Period size: 200 Copynumber: 4.1 Consensus size: 199
113136 TTAAGGGTCA
* * ** *
113146 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
113210 ATAAAGTG-CGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
113274 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
113339 AATG
196 AATG
113343 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACAAGGTGCACC
*
113408 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
113473 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
113538 TAATG
195 TAATG
*** *
113543 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
113607 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
113671 T-ATATGTAATTTTTCAATCTAACCGGTAC-ATTATA-CGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
113733 AATG
196 AATG
113737 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACAAGGTGCACC
*
113802 CATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
* *
113866 GTAATATGTAA-TTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
113930 TAATG
195 TAATG
*
113935 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
113964 CTAATTTAAA
Statistics
Matches: 593, Mismatches: 20, Indels: 15
0.94 0.03 0.02
Matches are distributed among these distances:
194 67 0.11
195 18 0.03
196 122 0.21
197 104 0.18
198 90 0.15
199 31 0.05
200 161 0.27
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (199 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCA
ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATG
Found at i:115444 original size:18 final size:18
Alignment explanation
Indices: 115421--115482 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
115411 ATCGGTCGCA
* * *
115421 GAAGATGAAGCTGACGAT
1 GAAGATGACGATGATGAT
115439 GAAGATGACGATGATGAT
1 GAAGATGACGATGATGAT
*
115457 GATGATGACGATGATGAT
1 GAAGATGACGATGATGAT
115475 GAAGATGA
1 GAAGATGA
115483 TGATCCAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.39, C:0.06, G:0.34, T:0.21
Consensus pattern (18 bp):
GAAGATGACGATGATGAT
Found at i:115445 original size:6 final size:6
Alignment explanation
Indices: 115421--115482 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
115411 ATCGGTCGCA
* * * * * *
115421 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
*
115469 GATGAT GAAGAT GA
1 GAAGAT GAAGAT GA
115483 TGATCCAAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.39, C:0.06, G:0.34, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:115456 original size:3 final size:3
Alignment explanation
Indices: 115436--115486 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
115426 TGAAGCTGAC
* * * *
115436 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAT GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
115484 GAT
1 GAT
115487 CCAAACAAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.37, C:0.04, G:0.33, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:115483 original size:12 final size:12
Alignment explanation
Indices: 115424--115486 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
115414 GGTCGCAGAA
* *
115424 GATGAAGCTGAC
1 GATGAAGATGAT
*
115436 GATGAAGATGAC
1 GATGAAGATGAT
*
115448 GATGATGATGAT
1 GATGAAGATGAT
*
115460 GATGACGATGAT
1 GATGAAGATGAT
115472 GATGAAGATGAT
1 GATGAAGATGAT
115484 GAT
1 GAT
115487 CCAAACAAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.37, C:0.06, G:0.33, T:0.24
Consensus pattern (12 bp):
GATGAAGATGAT
Found at i:117446 original size:183 final size:184
Alignment explanation
Indices: 116845--117878 Score: 1824
Period size: 183 Copynumber: 5.7 Consensus size: 184
116835 CTTTCAACAT
**
116845 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
116910 GGTCTACAACCTACAACCTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTG
66 GG--T-----CTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTG
* *
116974 GAAGAAAAATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
124 GAAGAAAATTGTGTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
117035 A-T-T-ATGTAATAGATAATTTTGTAATATAACCGG--TAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
117095 GGTCTAC-ACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
117159 ATTGTGTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 ATTGTGTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
117213 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
117278 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
117343 ATTGTGTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 ATTGTGTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
117397 ATTATAATGTAATAGATAATTTTGTAATATAACC-GTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
117461 GGTCTACAACCTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
117525 ATTGTGTCGATATAATTT-AAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 ATTGTGTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
117578 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
117643 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* * *
117708 AATGTGTCGATACAATTT-AAAAAGTGTCGGCATTTTACACATCGGAACCCATA
131 ATTGTGTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* **
117761 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATAAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
117826 GGTCTACAACCTATATCG--ACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
117879 CCATTTAAAA
Statistics
Matches: 825, Mismatches: 10, Indels: 27
0.96 0.01 0.03
Matches are distributed among these distances:
177 14 0.02
178 99 0.12
179 1 0.00
180 1 0.00
181 134 0.16
182 112 0.14
183 259 0.31
184 145 0.18
185 29 0.04
187 28 0.03
188 1 0.00
189 1 0.00
190 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
ATTGTGTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:117613 original size:365 final size:366
Alignment explanation
Indices: 116845--117878 Score: 1834
Period size: 365 Copynumber: 2.8 Consensus size: 366
116835 CTTTCAACAT
**
116845 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
116910 GGTCTACAACCTACAACCTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTG
66 GG--T-----CTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTG
116974 GAAGAAAAATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAA-T-
124 GAAGAAAAATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTA
*
117037 T-ATGTAATAGATAATTTTGTAATATAACCG-GTAAATATACCGGTCTTATGCGCGAATAGGTCT
189 TAATGTAATAGATAATTTTGTAATATAACCGTATAAATATACCGGTCTTATGCGCGAATAGGTCT
117100 AC-ACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAATTGT
254 ACAACCTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAATTGT
117164 GTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
318 GTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
117213 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
117278 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* *
117343 ATTGTGTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTA
117408 ATAGATAATTTTGTAATATAACCGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACCT
196 ATAGATAATTTTGTAATATAACCGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACCT
117473 ATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAATTGTGTCGATAT
261 ATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAATTGTGTCGATAT
117538 AATTT-AAAAAGTGTCGACATTTTACACATCGGAACCCATA
326 AATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
117578 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
117643 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
117708 AATGTGTCGATACAATTT-AAAAAGTGTCGGCATTTTACACATCGGAACCCATAATTATAATGTA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTA
* **
117772 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATAAGCGAATAGGTCTACAACC
196 ATAGATAATTTTGTAATATAACC-GTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACC
*
117837 TATATCGAC-TTTTTAATATTGTGTCGGTACTTTATGTCCATA
260 TATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATA
117879 CCATTTAAAA
Statistics
Matches: 647, Mismatches: 12, Indels: 18
0.96 0.02 0.03
Matches are distributed among these distances:
361 19 0.03
362 95 0.15
363 1 0.00
364 101 0.16
365 257 0.40
366 95 0.15
367 14 0.02
368 65 0.10
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (366 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTA
ATAGATAATTTTGTAATATAACCGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACCT
ATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAATTGTGTCGATAT
AATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:120380 original size:23 final size:23
Alignment explanation
Indices: 120353--120410 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
120343 ATTACATAAG
120353 ATGTAATAGGTAGCCCTTATATA
1 ATGTAATAGGTAGCCCTTATATA
* **
120376 ATGTAATAGGTATCGTTTATATA
1 ATGTAATAGGTAGCCCTTATATA
120399 ATGTAATAGGTA
1 ATGTAATAGGTA
120411 ATGGTTATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.38
Consensus pattern (23 bp):
ATGTAATAGGTAGCCCTTATATA
Found at i:120418 original size:23 final size:23
Alignment explanation
Indices: 120353--120420 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
120343 ATTACATAAG
* **
120353 ATGTAATAGGTAGCCCTTATATA
1 ATGTAATAGGTATCGGTTATATA
*
120376 ATGTAATAGGTATCGTTTATATA
1 ATGTAATAGGTATCGGTTATATA
120399 ATGTAATAGGTAAT-GGTTATAT
1 ATGTAATAGGT-ATCGGTTATAT
120421 TGTAAGTGTC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 38 0.95
24 2 0.05
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (23 bp):
ATGTAATAGGTATCGGTTATATA
Found at i:120842 original size:21 final size:21
Alignment explanation
Indices: 120798--120849 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
120788 GTAGCCCTTA
*
120798 TATAATGTAATAGGTATCGTT
1 TATAATGTAATAGGTATCGGT
120819 TATAATGTAATAGGTAAT-GGT
1 TATAATGTAATAGGT-ATCGGT
*
120840 TATATTGTAA
1 TATAATGTAA
120850 AGTGTCTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.19, T:0.42
Consensus pattern (21 bp):
TATAATGTAATAGGTATCGGT
Found at i:120872 original size:20 final size:20
Alignment explanation
Indices: 120847--120885 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
120837 GGTTATATTG
* *
120847 TAAAGTGTCTATCCTTTTTA
1 TAAAGTGTCCATACTTTTTA
120867 TAAAGTGTCCATACTTTTT
1 TAAAGTGTCCATACTTTTT
120886 TCACTGTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (20 bp):
TAAAGTGTCCATACTTTTTA
Found at i:126475 original size:36 final size:35
Alignment explanation
Indices: 126405--126482 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 35
126395 TAAATGAACT
* *
126405 AACATAAACACCTTTAAAAATAATAAAGGAACACA
1 AACATAAACACCTTCAAAAATAATAAAAGAACACA
* *
126440 AATATAAATACCTTCAAAAATAAATAAACAG-ACACA
1 AACATAAACACCTTCAAAAAT-AATAAA-AGAACACA
126476 AACATAA
1 AACATAA
126483 TTTTATTCGT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
35 18 0.50
36 17 0.47
37 1 0.03
ACGTcount: A:0.62, C:0.17, G:0.04, T:0.18
Consensus pattern (35 bp):
AACATAAACACCTTCAAAAATAATAAAAGAACACA
Done.