Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002517.1 Hibiscus syriacus cultivar Beakdansim tig00005120_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: 47277
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:10283 original size:22 final size:22
Alignment explanation
Indices: 10266--10310 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
10256 TCAGCATTAG
10266 TACTAAAATGCCTAAGCACTGA
1 TACTAAAATGCCTAAGCACTGA
*
10288 TACTAAAGTGCCTAAGCACTGA
1 TACTAAAATGCCTAAGCACTGA
10310 T
1 T
10311 TGGAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (22 bp):
TACTAAAATGCCTAAGCACTGA
Found at i:13388 original size:2 final size:2
Alignment explanation
Indices: 13381--13426 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
13371 TTGTGTTATT
*
13381 TA TA TA TA TA CA TA -A TA -A TA TA TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13420 TA TA TA T
1 TA TA TA T
13427 TAAATTATAG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 3 0.08
2 36 0.92
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:34312 original size:18 final size:18
Alignment explanation
Indices: 34289--34335 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
34279 AAATTATTAG
34289 TCTCACGCTTCAGACGAA
1 TCTCACGCTTCAGACGAA
34307 TCTCACGCTTCAGACGAA
1 TCTCACGCTTCAGACGAA
34325 TCTCACGCTTC
1 TCTCACGCTTC
34336 GGCCACAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.23, C:0.36, G:0.15, T:0.26
Consensus pattern (18 bp):
TCTCACGCTTCAGACGAA
Found at i:34801 original size:110 final size:110
Alignment explanation
Indices: 34619--34835 Score: 416
Period size: 110 Copynumber: 2.0 Consensus size: 110
34609 TTCCCGCCAG
*
34619 ACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATTCCTTGTAGCATGCAGAAGACGCCGAGA
1 ACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATTCCTTGTAGCATGCAGAAGACACCGAGA
34684 GATCCCACAGTCCAATTGCTTGAAGACGCCGAGCATTCCCATCAA
66 GATCCCACAGTCCAATTGCTTGAAGACGCCGAGCATTCCCATCAA
34729 ACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATTCCTTGTAGCATGCAGAAGACACCGAGA
1 ACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATTCCTTGTAGCATGCAGAAGACACCGAGA
*
34794 TATCCCACAGTCCAATTGCTTGAAGACGCCGAGCATTCCCAT
66 GATCCCACAGTCCAATTGCTTGAAGACGCCGAGCATTCCCAT
34836 AGTGTCATAA
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
110 105 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (110 bp):
ACGACAGGTGAAGACGCCGAGAGATCCACCTTGGCATTCCTTGTAGCATGCAGAAGACACCGAGA
GATCCCACAGTCCAATTGCTTGAAGACGCCGAGCATTCCCATCAA
Found at i:36017 original size:14 final size:13
Alignment explanation
Indices: 35989--36022 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
35979 ACAAAAGACG
*
35989 TAAAAAATAATAA
1 TAAAAAATAAAAA
36002 TAAAATAATAAAAA
1 TAAAA-AATAAAAA
36016 TAAAAAA
1 TAAAAAA
36023 ATGAATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
TAAAAAATAAAAA
Found at i:36023 original size:17 final size:18
Alignment explanation
Indices: 35997--36032 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
35987 CGTAAAAAAT
*
35997 AATAATAAAAT-AATAAA
1 AATAAAAAAATGAATAAA
36014 AATAAAAAAATGAATAAA
1 AATAAAAAAATGAATAAA
36032 A
1 A
36033 TGTTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (18 bp):
AATAAAAAAATGAATAAA
Found at i:36093 original size:10 final size:10
Alignment explanation
Indices: 36078--36120 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
36068 TTAATGGAGT
36078 AAAAAAATAA
1 AAAAAAATAA
36088 AAAAAAATAA
1 AAAAAAATAA
* *
36098 AAGAAATTAA
1 AAAAAAATAA
**
36108 AAATGAATAA
1 AAAAAAATAA
36118 AAA
1 AAA
36121 TAATGTGTAC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:36192 original size:32 final size:33
Alignment explanation
Indices: 36156--36236 Score: 78
Period size: 34 Copynumber: 2.5 Consensus size: 33
36146 TACTAAAACA
* *
36156 AATAAAAATAATAAATATATA-ATGCTAAGT-AG
1 AATAAAAATAATAAAGATATACATGAT-AGTAAG
* *
36188 AATAAATAAAAAATAAAGATATACATGATATTAAG
1 AAT-AA-AAATAATAAAGATATACATGATAGTAAG
36223 AA-AAAAATAATAAA
1 AATAAAAATAATAAA
36237 ATAAATAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
32 12 0.30
33 4 0.10
34 16 0.40
35 8 0.20
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.25
Consensus pattern (33 bp):
AATAAAAATAATAAAGATATACATGATAGTAAG
Found at i:36419 original size:25 final size:25
Alignment explanation
Indices: 36373--36421 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
36363 TTAATACATC
* *
36373 ATATATATATATATAATGATATAAG
1 ATATATATATATAAAATAATATAAG
36398 ATATATATA-ATGAAAATAATATAA
1 ATATATATATAT-AAAATAATATAA
36422 TATAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (25 bp):
ATATATATATATAAAATAATATAAG
Found at i:36424 original size:19 final size:19
Alignment explanation
Indices: 36377--36426 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
36367 TACATCATAT
*
36377 ATATATATATAATGATATA
1 ATATATATATAATGAAATA
*
36396 AGATATATATAATGAAAATA
1 ATATATATATAATG-AAATA
36416 ATATA-ATATAA
1 ATATATATATAA
36427 ATAAAAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (19 bp):
ATATATATATAATGAAATA
Found at i:37696 original size:83 final size:86
Alignment explanation
Indices: 37510--37696 Score: 224
Period size: 83 Copynumber: 2.2 Consensus size: 86
37500 ATAATTCCTG
* * * * * *
37510 TTGACATATAACCCTTCTTGCCTTGAGCTATGCTGTAAATTTGATTTACATCTGAGTTAAATGTA
1 TTGACAGATAACCCTTCTTGCCTTGAGATATGCTGCAAATTTGATGTACATCTGAGCTAAACGTA
37575 ATCGAACTCGAAGGTCTTTGA
66 ATCGAACTCGAAGGTCTTTGA
* * *
37596 -TGATAGATAACCCTTCTTGCCTTGAGATATGCTGCAAATTATG-TGT-C-T-TGGAGCTGAGCG
1 TTGACAGATAACCCTTCTTGCCTTGAGATATGCTGCAAATT-TGATGTACATCT-GAGCTAAACG
*
37656 TAGTCGAACTCGAAGGTCTTT-A
64 TAATCGAACTCGAAGGTCTTTGA
37678 TTGACAGATAACCCTTCTT
1 TTGACAGATAACCCTTCTT
37697 TGAGTTGGAT
Statistics
Matches: 87, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
82 2 0.02
83 44 0.51
84 1 0.01
85 38 0.44
86 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (86 bp):
TTGACAGATAACCCTTCTTGCCTTGAGATATGCTGCAAATTTGATGTACATCTGAGCTAAACGTA
ATCGAACTCGAAGGTCTTTGA
Found at i:38266 original size:106 final size:107
Alignment explanation
Indices: 37915--38272 Score: 414
Period size: 106 Copynumber: 3.4 Consensus size: 107
37905 AATTAGCTCT
* * * *
37915 GGAAATTGTTTGTTGACAGTCAGCCG-CCCCTTCACTGTGAAGTTGAGCTTGTGCTGTCTCGAGT
1 GGAAATTGTTTGTTGACAATCAGCCGTCCCATTCACTGTGAAGTTGAGCTTGTGTTGTCTTGAGT
* * *
37979 CTAATACCCTTCATTGTGAAGTTGAAATTGACTCTG-AA-T-
66 CCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTG
* *
38018 -GAAA-T-TTTGTTGACAATCAGTC-TCCCATTCA-TCGTGAAGTTGAGCTTGTGTTGTCTTGGG
1 GGAAATTGTTTGTTGACAATCAGCCGTCCCATTCACT-GTGAAGTTGAGCTTGTGTTGTCTTGAG
* * * *
38078 TCCAATATCCTTCGCTGGGAAGTTGAAATTCACCCTGAAATTG
65 TCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTG
* * * * * *
38121 GGAAGTTGTTTATTGATAGTCAGCCG-CCCATTCGCTGTGAAGTTGAGCTTGTGTTGTCTTAAGT
1 GGAAATTGTTTGTTGACAATCAGCCGTCCCATTCACTGTGAAGTTGAGCTTGTGTTGTCTTGAGT
*
38185 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTG
66 CCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTG
* * **
38227 GGAAATTGTTTGTTGACAACCAGTCGTCCC-TTCGTTGTGAAGTTGA
1 GGAAATTGTTTGTTGACAATCAGCCGTCCCATTCACTGTGAAGTTGA
38273 AATTGGTTCT
Statistics
Matches: 211, Mismatches: 33, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
99 1 0.00
100 76 0.36
101 3 0.01
102 5 0.02
104 3 0.01
105 1 0.00
106 118 0.56
107 4 0.02
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (107 bp):
GGAAATTGTTTGTTGACAATCAGCCGTCCCATTCACTGTGAAGTTGAGCTTGTGTTGTCTTGAGT
CCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTG
Found at i:38294 original size:63 final size:63
Alignment explanation
Indices: 38192--38336 Score: 247
Period size: 63 Copynumber: 2.3 Consensus size: 63
38182 AGTCCAATAT
* *
38192 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG-TCGTC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTGTTTATTGACAACCAGCT-GTC
*
38255 CCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTAGGAAATTGTTTATTGACAACCAGCTGTC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTGTTTATTGACAACCAGCTGTC
38318 CCTTCGTTGTGAAGTTGAA
1 CCTTCGTTGTGAAGTTGAA
38337 CTTGTGTTGT
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
63 77 0.99
64 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (63 bp):
CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTGTTTATTGACAACCAGCTGTC
Found at i:39117 original size:68 final size:65
Alignment explanation
Indices: 39037--39348 Score: 230
Period size: 65 Copynumber: 4.6 Consensus size: 65
39027 TGTCTCATGA
* * **
39037 AAACGGTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTTGAAGATTTTGTGTTTCAA
1 AAACTGTCTCAAGGGAGACAAAA-TTTGTTTTAAGGGAAATAAATTCAAAGA-TTT-TGTTTCAA
39102 GAG
63 GAG
* *
39105 AAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGG
1 AAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTTTCAAGAG
* * * * ** *
39170 AAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGAGAAAT-TGTCTCAAGAGAGAGACAAAACTT
1 AAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAAT-TC---A-A-AG-----ATTT
* * *
39234 AGTTCCAAAAG
55 TGTTTCAAGAG
** * *** * * * * *
39245 AAACTGTCTCAAGGGAGATGAAATTTGTTTCAAATAAAACATATTCAAATAATTTGTTTCAAGGG
1 AAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTTTCAAGAG
* *
39310 AAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
1 AAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA
39349 CTGTCTCAAG
Statistics
Matches: 195, Mismatches: 37, Indels: 27
0.75 0.14 0.10
Matches are distributed among these distances:
64 1 0.01
65 90 0.46
66 3 0.02
67 25 0.13
68 22 0.11
69 1 0.01
70 3 0.02
71 1 0.01
72 1 0.01
75 46 0.24
76 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.29
Consensus pattern (65 bp):
AAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTTTCAAGAG
Found at i:39194 original size:65 final size:67
Alignment explanation
Indices: 39013--39209 Score: 238
Period size: 65 Copynumber: 2.9 Consensus size: 67
39003 GGAAACGATC
* * * *
39013 TCAAAGATATTTGTTGTCTCATGA-AAACGGTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAA
1 TCAAAGAT-TTTG-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTTAAGGGAAA
39077 TAAAT
63 TAAAT
** *
39082 TTGAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAA
39147 AT
66 AT
* * * * *
39149 TCAAAGA-TTT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGAGAAAT
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAAT
39210 TGTCTCAAGA
Statistics
Matches: 112, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
65 45 0.40
66 3 0.03
67 33 0.29
68 25 0.22
69 6 0.05
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (67 bp):
TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAA
AT
Found at i:39214 original size:36 final size:36
Alignment explanation
Indices: 39157--39486 Score: 262
Period size: 36 Copynumber: 9.4 Consensus size: 36
39147 ATTCAAAGAT
*
39157 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
39193 TTTGTTTCAAGAGAAATTGTCTCAAGAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTC-A-AGAGAGACAAAA
* * ** * **
39231 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGATGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*** * *
39268 TTTGTTTCAAATAAAACATAT-TC-----A-A-ATAA
1 TTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAA
39297 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
39333 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * *
39369 TTTATTTCAAGGGAAA-TGCTTTC-A-A-TG-----T
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAA
* *
39397 TTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
1 TT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
39434 TTTCGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA
1 TTT-GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
39471 TTCGTTTCAAGGGAAA
1 TTTGTTTCAAGGGAAA
39487 TGTTTTCAAT
Statistics
Matches: 233, Mismatches: 37, Indels: 48
0.73 0.12 0.15
Matches are distributed among these distances:
28 4 0.02
29 33 0.14
30 4 0.02
31 1 0.00
32 1 0.00
33 1 0.00
34 2 0.01
35 4 0.02
36 106 0.45
37 46 0.20
38 12 0.05
39 19 0.08
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:39217 original size:15 final size:16
Alignment explanation
Indices: 39189--39221 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
39179 CAAGAGAGAC
*
39189 GAAATTTGTTTCAAGA
1 GAAATTTGTCTCAAGA
39205 GAAA-TTGTCTCAAGA
1 GAAATTTGTCTCAAGA
39220 GA
1 GA
39222 GAGACAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.30
Consensus pattern (16 bp):
GAAATTTGTCTCAAGA
Found at i:39256 original size:140 final size:140
Alignment explanation
Indices: 39103--39363 Score: 396
Period size: 140 Copynumber: 1.9 Consensus size: 140
39093 GTGTTTCAAG
* ** * * *
39103 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
* *
39168 GGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGAGAAATTGTCTCAAGAGAGAGACAAAACT
66 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGAGACAAAACT
39233 TAGTTCCAAA
131 TAGTTCCAAA
** * * *
39243 AGAAACTGTCTCAAGGGAGATGAAATTTGTTTCAAATAAAACATATTCAAATAATTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
*
39308 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
66 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
39364 CGAAATTTAT
Statistics
Matches: 107, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
140 107 1.00
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (140 bp):
AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGAGACAAAACT
TAGTTCCAAA
Found at i:39257 original size:39 final size:38
Alignment explanation
Indices: 39169--39262 Score: 111
Period size: 39 Copynumber: 2.5 Consensus size: 38
39159 TGTTTCAAGG
* * * *
39169 GAAACTGTCTC-A-AGAGAGACGAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGAGACAAAATTAGTTCCAAAA
*
39205 GAAATTGTCTCAAGAGAGAGACAAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGAGACAAAA-TTAGTTCCAAAA
*
39244 GAAACTGTCTCAAGGGAGA
1 GAAACTGTCTCAAGAGAGA
39263 TGAAATTTGT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
36 10 0.21
37 1 0.02
38 11 0.23
39 26 0.54
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.21
Consensus pattern (38 bp):
GAAACTGTCTCAAGAGAGAGACAAAATTAGTTCCAAAA
Found at i:39378 original size:101 final size:99
Alignment explanation
Indices: 39191--39562 Score: 397
Period size: 102 Copynumber: 3.7 Consensus size: 99
39181 AGAGAGACGA
* * * ** *
39191 AATT-TGTTTCAAGAGAAATTGTCTCAAGAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTC
1 AATTATGTTTCAAGAGAAACTGTCTC-A-AGAGAGACAAAA-TTTGTTTCAAGGGAAACTATCTC
* * **
39255 AAGGGAGATGAAATTTGTTTCAAATAAAACATATTCAAAT
63 AAGAGAGACGAAATTTGTTTCAAGGAAAAC-T-TTC-AAT
* *
39295 AATT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAG
1 AATTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAG
* *
39359 AGAGACGAAATTTATTTCAAGGGAAATGCTTTCAAT
66 AGAGACGAAATTTGTTTCAA-GGAAA-ACTTTCAAT
** *
39395 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAA
1 AATTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT-GTTTCAAGGGAAACTATCTCAA
* * **
39460 GAGAGACAAAATTCGTTTCAAGGGAAATGTTTTCAAT
65 GAGAGACGAAATTTGTTTCAA-GGAAA-ACTTTCAAT
** * *
39497 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAATATTTTGTTTCAAGGGAAACTATCTCAA
1 AATTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAA-AATTTGTTTCAAGGGAAACTATCTCAA
39562 G
65 G
39563 CAAGATAAAA
Statistics
Matches: 241, Mismatches: 22, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
100 5 0.02
101 77 0.32
102 130 0.54
103 6 0.02
104 23 0.10
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (99 bp):
AATTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAG
AGAGACGAAATTTGTTTCAAGGAAAACTTTCAAT
Found at i:39451 original size:37 final size:37
Alignment explanation
Indices: 39401--39562 Score: 139
Period size: 37 Copynumber: 4.6 Consensus size: 37
39391 CAATGTTTAT
*
39401 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTC
1 GTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTC
* *
39438 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TTC
1 GTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTC
* * *
39474 GTTTCAAGGGAAA-TGTTTTCAA---TG------TTTAT
1 GTTTCAAGGGAAACTG-TCTCAAGGGAGACAAAATTT-C
* * *
39503 GTTTCAAGAGAAACTGTCTCAAGGGAGACAATATTTT
1 GTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTC
*
39540 GTTTCAAGGGAAACTATCTCAAG
1 GTTTCAAGGGAAACTGTCTCAAG
39563 CAAGATAAAA
Statistics
Matches: 100, Mismatches: 12, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
28 2 0.02
29 17 0.17
30 2 0.02
32 1 0.01
33 1 0.01
35 1 0.01
36 21 0.21
37 52 0.52
38 3 0.03
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (37 bp):
GTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTC
Found at i:39481 original size:102 final size:101
Alignment explanation
Indices: 39299--39562 Score: 438
Period size: 102 Copynumber: 2.6 Consensus size: 101
39289 TCAAATAATT
* * *
39299 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGA
* *
39364 CGAAATTTATTTCAAGGGAAATGCTTTCAATGTTTA
66 CAAAATTCATTTCAAGGGAAATGCTTTCAATGTTTA
39400 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT-GTTTCAAGGGAAACTATCTCAAGAGAG
* *
39465 ACAAAATTCGTTTCAAGGGAAATGTTTTCAATGTTTA
65 ACAAAATTCATTTCAAGGGAAATGCTTTCAATGTTTA
*
39502 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAATATTTTGTTTCAAGGGAAACTATCTCAAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAA-AATTTGTTTCAAGGGAAACTATCTCAAG
39563 CAAGATAAAA
Statistics
Matches: 153, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
101 35 0.23
102 114 0.75
103 4 0.03
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.30
Consensus pattern (101 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGA
CAAAATTCATTTCAAGGGAAATGCTTTCAATGTTTA
Found at i:41274 original size:26 final size:25
Alignment explanation
Indices: 41232--41291 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
41222 TTTTTCTTCA
* *
41232 ATTTTC-CTTTGTTTTTTCTCTTTTT
1 ATTTTCTCTTTGCTTTTTCTC-TCTT
*
41257 ATTTTCTCTTTGCTTTTTTTCTCTT
1 ATTTTCTCTTTGCTTTTTCTCTCTT
41282 -TTTTCTCTTT
1 ATTTTCTCTTT
41292 TTGTTATGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.32
25 9 0.29
26 12 0.39
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.75
Consensus pattern (25 bp):
ATTTTCTCTTTGCTTTTTCTCTCTT
Found at i:41276 original size:15 final size:13
Alignment explanation
Indices: 41233--41285 Score: 63
Period size: 13 Copynumber: 4.0 Consensus size: 13
41223 TTTTCTTCAA
*
41233 TTTTC-CTTTGTT
1 TTTTCTCTTTTTT
*
41245 TTTTCTCTTTTTA
1 TTTTCTCTTTTTT
41258 TTTTCTCTTTGCTTT
1 TTTTCTCTTT--TTT
41273 TTTTCTCTTTTTT
1 TTTTCTCTTTTTT
41286 CTCTTTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 5 0.14
13 18 0.51
15 12 0.34
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.77
Consensus pattern (13 bp):
TTTTCTCTTTTTT
Found at i:41280 original size:28 final size:25
Alignment explanation
Indices: 41232--41284 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 25
41222 TTTTTCTTCA
41232 ATTTTCCTTTGTTTTTTCTCTTTTT
1 ATTTTCCTTTGTTTTTTCTCTTTTT
41257 ATTTTCTCTTTGCTTTTTTTCTCTTTTT
1 ATTTTC-CTTTG--TTTTTTCTCTTTTT
41285 TCTCTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
28 14 0.56
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.75
Consensus pattern (25 bp):
ATTTTCCTTTGTTTTTTCTCTTTTT
Found at i:44450 original size:11 final size:11
Alignment explanation
Indices: 44434--44458 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
44424 CAAAACACGT
44434 AAAAATAATAA
1 AAAAATAATAA
44445 AAAAATAATAA
1 AAAAATAATAA
44456 AAA
1 AAA
44459 TAAACAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAATAATAA
Found at i:46628 original size:18 final size:19
Alignment explanation
Indices: 46586--46628 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
46576 TTTATATAAT
46586 ATTTA-TAAATACATATTC
1 ATTTATTAAATACATATTC
* *
46604 ATATATTAAATA-ATTTTC
1 ATTTATTAAATACATATTC
46622 ATTTATT
1 ATTTATT
46629 CACTTTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTATTAAATACATATTC
Done.