Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001537.1 Hibiscus syriacus cultivar Beakdansim tig00003019_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: 107001
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:408 original size:56 final size:57
Alignment explanation
Indices: 346--875 Score: 577
Period size: 56 Copynumber: 9.5 Consensus size: 57
336 GTGTGAAAAA
* * * *
346 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTTGTATGCCAAAAAGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * * *
403 T-AGAAATCATACTAAGTGTATGAATTTTAGATAGGGCATTTTGTATGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * * **
459 TAAGAAATCATATTAAGTGTATGAATTTCAGATA-GGTGTTTTGTAATCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * *
515 TAAGAAATCATACTAAGTGTAT---TTTCAGATAAGGTGTTTTGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * * *
569 TAAGAACTCAAAACTAAGTGTAT-AATTTCATAT-GTGG-ATTTCGTACGCTAAAATGT
1 TAAGAAATC-ATACTAAGTGTATGAATTTCAGATAG-GGCGTTTCGTACGCTAAAATGT
* * * * *
625 TAAGAAATTATACTAAGTGTATGAATTTCAGATAGAGTGTTTCATATGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
682 TAAG-AATCATACTAAGTGTATGAATTTCAGATAGGGTGTTTCGTACGCTAAAATTT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * * *
738 TAAAAAATCATACCAAGTGTATGAATTT-ATATAGGGCGTTTCGTACGCTAAAATGA
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* ** ** *
794 TAAGGAAATCAT-CTAAGTGTATGAATTTCCAGATGGGGCACTTCGTGTGCTAACATG-
1 TAA-GAAATCATACTAAGTGTATGAATTT-CAGATAGGGCGTTTCGTACGCTAAAATGT
851 -AAGAAATTCATA--AAGTGTATGAATT
1 TAAGAAA-TCATACTAAGTGTATGAATT
876 CTGTATTGGA
Statistics
Matches: 411, Mismatches: 47, Indels: 32
0.84 0.10 0.07
Matches are distributed among these distances:
53 9 0.02
54 28 0.07
55 41 0.10
56 223 0.54
57 90 0.22
58 20 0.05
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.35
Consensus pattern (57 bp):
TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
Found at i:724 original size:113 final size:114
Alignment explanation
Indices: 346--827 Score: 565
Period size: 113 Copynumber: 4.3 Consensus size: 114
336 GTGTGAAAAA
* * * * *
346 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTTGTATGCCAAAAAGTT-AGAAAT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGTGTTTCGTACGCTAAAATGTTAAGAAAT
* * * * *
410 CATACTAAGTGTATGAATTTTAGATAGGGCATTTTGTATGCTAAAATGT
66 CATACTAAGTGTATGAATTTCAGATAGAGCGTTTCGTACGCTAAAATGT
* * **
459 TAAGAAATCATATTAAGTGTATGAATTTCAGATA-GGTGTTTTGTAATCTAAAATGTTAAGAAAT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGTGTTTCGTACGCTAAAATGTTAAGAAAT
* *
523 CATACTAAGTGTAT---TTTCAGATA-AGGTGTTTTGTACGCTAAAATGT
66 CATACTAAGTGTATGAATTTCAGATAGA-GCGTTTCGTACGCTAAAATGT
* * * *
569 TAAGAACTCAAAACTAAGTGTAT-AATTTCATAT-GTGG-ATTTCGTACGCTAAAATGTTAAGAA
1 TAAGAAATC-ATACTAAGTGTATGAATTTCAGATAG-GGTGTTTCGTACGCTAAAATGTTAAGAA
* * * *
631 ATTATACTAAGTGTATGAATTTCAGATAGAGTGTTTCATATGCTAAAATGT
64 ATCATACTAAGTGTATGAATTTCAGATAGAGCGTTTCGTACGCTAAAATGT
* *
682 TAAG-AATCATACTAAGTGTATGAATTTCAGATAGGGTGTTTCGTACGCTAAAATTTTAAAAAAT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGTGTTTCGTACGCTAAAATGTTAAGAAAT
* * * *
746 CATACCAAGTGTATGAATTT-ATATAGGGCGTTTCGTACGCTAAAATGA
66 CATACTAAGTGTATGAATTTCAGATAGAGCGTTTCGTACGCTAAAATGT
794 TAAGGAAATCAT-CTAAGTGTATGAATTTCCAGAT
1 TAA-GAAATCATACTAAGTGTATGAATTT-CAGAT
828 GGGGCACTTC
Statistics
Matches: 317, Mismatches: 37, Indels: 29
0.83 0.10 0.08
Matches are distributed among these distances:
110 79 0.25
111 25 0.08
112 57 0.18
113 144 0.45
114 12 0.04
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (114 bp):
TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGTGTTTCGTACGCTAAAATGTTAAGAAAT
CATACTAAGTGTATGAATTTCAGATAGAGCGTTTCGTACGCTAAAATGT
Found at i:1369 original size:81 final size:81
Alignment explanation
Indices: 1231--1381 Score: 212
Period size: 81 Copynumber: 1.9 Consensus size: 81
1221 GGCCTAGTTG
* **
1231 TGCAATTGACAGAAAAGTGTCAACTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAG
1 TGCAATTGACAGAAAAGTGTCAACTATGCCAGTTAGATAAACGGTTAAACACCGTTGAGTAAAAG
1296 AATAATGGTCTAACTA
66 AATAATGGTCTAACTA
* * * * * **
1312 TGCAATTGGCAGAAATGTGTCAATTATGCCAGTTAGATAAAGGGTTAAACACTGTTGAGTAGGAG
1 TGCAATTGACAGAAAAGTGTCAACTATGCCAGTTAGATAAACGGTTAAACACCGTTGAGTAAAAG
1377 AATAA
66 AATAA
1382 AGGTATTTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 60 1.00
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (81 bp):
TGCAATTGACAGAAAAGTGTCAACTATGCCAGTTAGATAAACGGTTAAACACCGTTGAGTAAAAG
AATAATGGTCTAACTA
Found at i:1441 original size:2 final size:2
Alignment explanation
Indices: 1434--1490 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
1424 TGAAGGGATA
1434 AT AT AT AT AT 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 AT AT AT AT AT
*
1476 AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT A
1491 ACCACACATA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3174 original size:3 final size:3
Alignment explanation
Indices: 3166--3205 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
3156 CAAAATGTAT
3166 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3206 TTTTTTATAG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:7023 original size:22 final size:22
Alignment explanation
Indices: 6995--7043 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
6985 AACATCGGCA
6995 GCGGCGGTTAGAAGCTGA-GGCG
1 GCGGCGGTTAGAAGCT-ATGGCG
*
7017 GCGGCGGTTGGAAGCTATGGCG
1 GCGGCGGTTAGAAGCTATGGCG
7039 GCGGC
1 GCGGC
7044 AACTGGGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.14, C:0.20, G:0.51, T:0.14
Consensus pattern (22 bp):
GCGGCGGTTAGAAGCTATGGCG
Found at i:7184 original size:13 final size:14
Alignment explanation
Indices: 7160--7196 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
7150 TTATTATTTA
7160 ATAATAATAATAAT
1 ATAATAATAATAAT
7174 ATAAT-ATAATAAT
1 ATAATAATAATAAT
*
7187 ATACTAATAA
1 ATAATAATAA
7197 AAATGATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:7628 original size:31 final size:33
Alignment explanation
Indices: 7593--7676 Score: 77
Period size: 31 Copynumber: 2.6 Consensus size: 33
7583 CTCTTCAGAT
*
7593 AAGTTCTTCTCATTATGAACTCTACA-TGGAA-
1 AAGTTCTTCTCATTATGAACTCTAAAGTGGAAC
** * * *
7624 AAGTTGATC-CATTGATCAA-GCTAAAGTTGAAC
1 AAGTTCTTCTCATT-ATGAACTCTAAAGTGGAAC
7656 AAGTTCTTCTCATTATGAACT
1 AAGTTCTTCTCATTATGAACT
7677 TCTTCTTCTT
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
30 8 0.21
31 15 0.39
32 11 0.29
33 4 0.11
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (33 bp):
AAGTTCTTCTCATTATGAACTCTAAAGTGGAAC
Found at i:7781 original size:112 final size:112
Alignment explanation
Indices: 7649--8194 Score: 805
Period size: 112 Copynumber: 4.9 Consensus size: 112
7639 TCAAGCTAAA
7649 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAA
**
7714 CTCTACCTAGCAATACTGATCCATCGAGTGATGAATTCGAGCAAAAG
66 CTCTACCTAGCAATGTTGATCCATCGAGTGATGAATTCGAGCAAAAG
*
7761 GTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGA
* * * *
7826 ACTCT--TTCGCTAATGCTGATCCATTGAGTGATGAATTCGAGCAAAAG
65 ACTCTACCTAGC-AATGTTGATCCATCGAGTGATGAATTCGAGCAAAAG
* * *
7873 GTTGAACAAGTTCTTCTCATTATAAACTTTTTCTTCGTTCTTCAGATGAGTTCTTCTCGTTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGAGTTCTTCTCATTATGA
* *
7938 ACTCTTCC-GGCAATGTTGATCCATCGAGTGATGAATTCGAGCAAAAG
65 ACTCTACCTAGCAATGTTGATCCATCGAGTGATGAATTCGAGCAAAAG
* *
7985 GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGA
* *
8050 ACTCTTCC-GGCAATGTTGATCCATCGAGTGATGAATTCGAGCAAAAG
65 ACTCTACCTAGCAATGTTGATCCATCGAGTGATGAATTCGAGCAAAAG
* * * *
8097 GTTGAACAAGTTCTTCTCATTAAGAACTTCTTTTTCCTCTTCATATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
8162 CTCTATCTGAG-AATATTGATCCATCGAATGATG
66 CTCTACCT-AGCAATGTTGATCCATCGAGTGATG
8195 GATCTGAATC
Statistics
Matches: 397, Mismatches: 29, Indels: 16
0.90 0.07 0.04
Matches are distributed among these distances:
111 36 0.09
112 323 0.81
113 38 0.10
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (112 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTCTACCTAGCAATGTTGATCCATCGAGTGATGAATTCGAGCAAAAG
Found at i:7966 original size:224 final size:222
Alignment explanation
Indices: 7540--8194 Score: 888
Period size: 224 Copynumber: 3.0 Consensus size: 222
7530 ATAGTGTCAT
* * *
7540 GCAAAAGGTTGAACAAGCTCTTCTTATTATGAATTTCTTCTTCC-TCTTCAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
7604 ATTATGAACTC-TACATGGAAAAGTTGATCC---A-T--TG-A-TCAAGCTAAA-GTTGAACAAG
66 ATTATGAACTCTTACA--GCAATGTTGATCCATGAGTGATGAATTCGAGCAAAAGGTTGAACAAG
* * *
7659 TTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTAG
129 TTCTTCTCATTATAAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCC-GG
*
7724 CAATACTGATCCATCGAGTGATGAATTCGA
193 CAATATTGATCCATCGAGTGATGAATTCGA
* *
7754 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
7819 ATTATGAACTCTTTC-GCTAATGCTGATCCATTGAGTGATGAATTCGAGCAAAAGGTTGAACAAG
66 ATTATGAACTCTTACAGC-AATGTTGATCCA-TGAGTGATGAATTCGAGCAAAAGGTTGAACAAG
* *
7883 TTCTTCTCATTATAAACTTTTTCTTCGTTCTTCAGATGAGTTCTTCTCGTTATGAACTCTTCCGG
129 TTCTTCTCATTATAAACTTCTTCTTC-TTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCCGG
*
7948 CAATGTTGATCCATCGAGTGATGAATTCGA
193 CAATATTGATCCATCGAGTGATGAATTCGA
*
7978 GCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
8043 ATTATGAACTCTTCCGGCAATGTTGATCCATCGAGTGATGAATTCGAGCAAAAGGTTGAACAAGT
66 ATTATGAACTCTTACAGCAATGTTGATCCAT-GAGTGATGAATTCGAGCAAAAGGTTGAACAAGT
* * * *
8108 TCTTCTCATTA-AGAACTTCTTTTTCCTCTTCATATGAGTTCTTCTCATTATGAACTCTATCTGA
130 TCTTCTCATTATA-AACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT-TCCG-
*
8172 G-AATATTGATCCATCGAATGATG
192 GCAATATTGATCCATCGAGTGATG
8195 GATCTGAATC
Statistics
Matches: 391, Mismatches: 31, Indels: 28
0.87 0.07 0.06
Matches are distributed among these distances:
213 1 0.00
214 49 0.13
215 30 0.08
216 2 0.01
218 1 0.00
219 1 0.00
221 2 0.01
222 1 0.00
223 40 0.10
224 227 0.58
225 37 0.09
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (222 bp):
GCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCTTACAGCAATGTTGATCCATGAGTGATGAATTCGAGCAAAAGGTTGAACAAGTT
CTTCTCATTATAAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCCGGCAA
TATTGATCCATCGAGTGATGAATTCGA
Found at i:8096 original size:336 final size:333
Alignment explanation
Indices: 7416--8165 Score: 932
Period size: 336 Copynumber: 2.2 Consensus size: 333
7406 GATGTAATCT
* * * *
7416 AGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-CTTTTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCT
* * * * * *** *
7480 CATTATGAACTCCTTCTGGAAATGTTGATGTTGATCTATCTTCTTCTATGATAGTGTCATGCAAA
66 CATTATGAACT-CTTCT----ACGCTAATGCTGATCCATCTGAGTCGATGATAGTGTCATGCAAA
* *
7545 AGGTTGAACAAGCTCTTCTTATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATG
126 AGGTTGAACAAGCTCTTCTCATTATAAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATG
* *
7610 AACTCTACATGGAAAAGTTGATCCATTGATCAAGCTAAAGTTGAACAAGTTCTTCTCATTATGAA
191 AACTCTACACGGAAAAGTTGATCCATTGATCAAGCAAAAGTTGAACAAGTTCTTCTCATTATGAA
*
7675 CTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTAGCAATACTGATCCATCG
256 CTTCTTCTTCTTCTTCAGATGAGTTATTCTCATTATGAACTCTACCTAGCAATACTGATCCATCG
7740 AGTGATGAATTCG
321 AGTGATGAATTCG
7753 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCT
7818 CATTATGAACTCTT-T-CGCTAATGCTGATCCAT-TGAGT-GATGA-A-T-TCGA-GCAAAAGGT
66 CATTATGAACTCTTCTACGCTAATGCTGATCCATCTGAGTCGATGATAGTGTC-ATGCAAAAGGT
* * * *
7875 TGAACAAGTTCTTCTCATTATAAACTTT-TTCTTCGTTCTTCAGATGAGTTCTTCTCGTTATGAA
130 TGAACAAGCTCTTCTCATTATAAA-TTTCTTCTTC-CTCTTCAGATAAGTTCTTCTCATTATGAA
* * * * *
7939 CTCTTC-CGGCAATGTTGATCCATCGAGTGATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTT
193 CTCTACACGGAAAAGTTGAT-C--C-A-T--TG-A-TCAAGCAAAA-GTTGAACAAGTTCTTCTC
* * **
8003 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTCTTCC-GGCAATGTT
248 ATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTATTCTCATTATGAACTCTACCTAGCAATACT
8067 GATCCATCGAGTGATGAATTCG
312 GATCCATCGAGTGATGAATTCG
* * *
8089 AGCAAAAGGTTGAACAAGTTCTTCTCATTAAGAACTTCTTTTTCC-TCTTCATATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCT
8153 CATTATGAACTCT
66 CATTATGAACTCT
8166 ATCTGAGAAT
Statistics
Matches: 364, Mismatches: 34, Indels: 32
0.85 0.08 0.07
Matches are distributed among these distances:
326 48 0.13
327 37 0.10
328 1 0.00
329 5 0.01
330 3 0.01
331 13 0.04
333 2 0.01
334 1 0.00
335 39 0.11
336 106 0.29
337 78 0.21
338 31 0.09
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.39
Consensus pattern (333 bp):
AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCT
CATTATGAACTCTTCTACGCTAATGCTGATCCATCTGAGTCGATGATAGTGTCATGCAAAAGGTT
GAACAAGCTCTTCTCATTATAAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTC
TACACGGAAAAGTTGATCCATTGATCAAGCAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCT
TCTTCTTCTTCAGATGAGTTATTCTCATTATGAACTCTACCTAGCAATACTGATCCATCGAGTGA
TGAATTCG
Found at i:8577 original size:22 final size:22
Alignment explanation
Indices: 8546--8671 Score: 148
Period size: 22 Copynumber: 5.7 Consensus size: 22
8536 TCCAATAAAA
* *
8546 CTATCATCTTTAAAGAGAGAAC
1 CTATCATCTTTGAAGAGAGAAG
* *
8568 CTGTCATCTTTGAAGA-ATGTAG
1 CTATCATCTTTGAAGAGA-GAAG
* *
8590 TTATCATCTTTGAAGAGAGAAT
1 CTATCATCTTTGAAGAGAGAAG
*
8612 CTATCATCTTTGAAGA-ATGTAG
1 CTATCATCTTTGAAGAGA-GAAG
*
8634 CTATCATCTTTGAAGAGAGAAT
1 CTATCATCTTTGAAGAGAGAAG
8656 CTATCATCTTTGAAGA
1 CTATCATCTTTGAAGA
8672 ATGTAGATGT
Statistics
Matches: 87, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
21 2 0.02
22 83 0.95
23 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (22 bp):
CTATCATCTTTGAAGAGAGAAG
Found at i:8610 original size:44 final size:44
Alignment explanation
Indices: 8546--8677 Score: 228
Period size: 44 Copynumber: 3.0 Consensus size: 44
8536 TCCAATAAAA
* * *
8546 CTATCATCTTTAAAGAGAGAACCTGTCATCTTTGAAGAATGTAG
1 CTATCATCTTTGAAGAGAGAATCTATCATCTTTGAAGAATGTAG
*
8590 TTATCATCTTTGAAGAGAGAATCTATCATCTTTGAAGAATGTAG
1 CTATCATCTTTGAAGAGAGAATCTATCATCTTTGAAGAATGTAG
8634 CTATCATCTTTGAAGAGAGAATCTATCATCTTTGAAGAATGTAG
1 CTATCATCTTTGAAGAGAGAATCTATCATCTTTGAAGAATGTAG
8678 ATGTAGATAT
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 83 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (44 bp):
CTATCATCTTTGAAGAGAGAATCTATCATCTTTGAAGAATGTAG
Found at i:9144 original size:44 final size:42
Alignment explanation
Indices: 9081--9166 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 42
9071 GTGGTTTTTA
* * * *
9081 CCCAGATGTTCGTAAAGCATTTTACAACGCATTCATCCTTTCTT
1 CCCAGATATTCGTAAAGCA-TTGACAA-ACATTCATCATTTCTT
9125 CCCAGATATTCGTAAAGCATTGACAAACATTCATCATTTCTT
1 CCCAGATATTCGTAAAGCATTGACAAACATTCATCATTTCTT
9167 GTATTTTCTG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 14 0.37
43 6 0.16
44 18 0.47
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (42 bp):
CCCAGATATTCGTAAAGCATTGACAAACATTCATCATTTCTT
Found at i:10155 original size:75 final size:75
Alignment explanation
Indices: 10039--10183 Score: 218
Period size: 75 Copynumber: 1.9 Consensus size: 75
10029 TGCCCCAACG
* * * *
10039 TTTATTGATACGAATGTTCAAAATGCGTCAACATTCCTGATTCTGATTGAAATGAGCTTTTAACA
1 TTTACTGATACAAATGTTCAAAATGAGTCAACATTCCTGATTCTGATTGAAATGAGCTTTCAACA
10104 TGCCCCAGTA
66 TGCCCCAGTA
* * * *
10114 TTTACTGATACAAATGTTCAAAATGAGTCAATATTCTTGATTCTGATTGAAATGGGCTTTCAGCA
1 TTTACTGATACAAATGTTCAAAATGAGTCAACATTCCTGATTCTGATTGAAATGAGCTTTCAACA
10179 TGCCC
66 TGCCC
10184 TAGCATTTGC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 62 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (75 bp):
TTTACTGATACAAATGTTCAAAATGAGTCAACATTCCTGATTCTGATTGAAATGAGCTTTCAACA
TGCCCCAGTA
Found at i:19023 original size:18 final size:18
Alignment explanation
Indices: 19002--19039 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
18992 TATCGAAAAA
*
19002 TAAATAAATA-ATAATATT
1 TAAACAAATATAT-ATATT
19020 TAAACAAATATATATATT
1 TAAACAAATATATATATT
19038 TA
1 TA
19040 TATATGACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAACAAATATATATATT
Found at i:20437 original size:3 final size:3
Alignment explanation
Indices: 20431--20497 Score: 75
Period size: 3 Copynumber: 23.0 Consensus size: 3
20421 ATTTATTATT
* *
20431 TAA TAA TAA TAA T-A TAA -CA TAA TAA TAA TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
20477 TAA AAA TAA TAC TAC TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
20498 AAATTTAGTG
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
2 3 0.06
3 51 0.94
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:24603 original size:20 final size:20
Alignment explanation
Indices: 24578--24624 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
24568 ATAAATTGGT
*
24578 GTTGATGGTTTGAGGTATAG
1 GTTGATGGTTTGAAGTATAG
24598 GTTGATGGTTTGAAGTATAG
1 GTTGATGGTTTGAAGTATAG
24618 GTTGATG
1 GTTGATG
24625 ATATATCCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.40
Consensus pattern (20 bp):
GTTGATGGTTTGAAGTATAG
Found at i:28130 original size:15 final size:15
Alignment explanation
Indices: 28104--28143 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
28094 CTGCACTTGC
28104 AGAAGAAAAAGAAAGGA
1 AGAAG-AAAAGAAA-GA
28121 A-AAGAAAAGAAAGA
1 AGAAGAAAAGAAAGA
28135 AGAAGAAAA
1 AGAAGAAAA
28144 ATGAAGGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 3 0.14
15 15 0.68
16 3 0.14
17 1 0.05
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (15 bp):
AGAAGAAAAGAAAGA
Found at i:29786 original size:36 final size:36
Alignment explanation
Indices: 29735--30009 Score: 186
Period size: 36 Copynumber: 7.6 Consensus size: 36
29725 GTCTCTTTTA
* * * *
29735 AGAAACCAACATAGTCTTTCTTGATACCATTTACCT
1 AGAAACCAACCTAGTCTTCCTTAAGACCATTTACCT
*
29771 AGAAACCAACCTAGTCTTCCTTAAGACCATTTCCCT
1 AGAAACCAACCTAGTCTTCCTTAAGACCATTTACCT
* ****
29807 AGAAACCAACCTAGTCTTCTTTAAGGTTGTTT-CCAT
1 AGAAACCAACCTAGTCTTCCTTAAGACCATTTACC-T
* * * * * *
29843 AGAAACCAACCTTGTCTTACTTAACG-TCGTTTTCAT
1 AGAAACCAACCTAGTCTTCCTTAA-GACCATTTACCT
29879 AGAAACCAACCTAGTCTTCCTTAAGGA--AGTTT-CCGT
1 AGAAACCAACCTAGTCTTCCTTAA-GACCA-TTTACC-T
* * * * *
29915 ATAATCCAACCTAGTCTTCTTTAAGATCGTTT-CACT
1 AGAAACCAACCTAGTCTTCCTTAAGACCATTTAC-CT
* * * ***
29951 AGAAACCAAACTAGACTTTCTTAAGATTGTTT-CCTT
1 AGAAACCAACCTAGTCTTCCTTAAGACCATTTACC-T
*
29987 AGAAACCAACTTAGTCTTCCTTA
1 AGAAACCAACCTAGTCTTCCTTA
30010 GTATCGTCTC
Statistics
Matches: 194, Mismatches: 35, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
35 6 0.03
36 185 0.95
37 3 0.02
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (36 bp):
AGAAACCAACCTAGTCTTCCTTAAGACCATTTACCT
Found at i:29852 original size:72 final size:72
Alignment explanation
Indices: 29770--30056 Score: 292
Period size: 72 Copynumber: 3.9 Consensus size: 72
29760 ACCATTTACC
* *
29770 TAGAAACCAACCTAGTCTTCCTTAAGACCATTTCCCTAGAAACCAACCTAGTCTTCTTTAAGGTT
1 TAGAAACCAACCTAGTCTTCCTTAAGATCGTTTCCCTAGAAACCAACCTAGTCTTCTTTAAGGTT
29835 GTTTCCA
66 GTTTCCA
* * * * * *
29842 TAGAAACCAACCTTGTCTTACTTAACG-TCGTTTTCATAGAAACCAACCTAGTCTTCCTTAAGGA
1 TAGAAACCAACCTAGTCTTCCTTAA-GATCGTTTCCCTAGAAACCAACCTAGTCTTCTTTAAGGT
* *
29906 AGTTTCCG
65 TGTTTCCA
* * * * * * *
29914 TATAATCCAACCTAGTCTTCTTTAAGATCGTTTCACTAGAAACCAAACTAGACTT-TCTTAAGAT
1 TAGAAACCAACCTAGTCTTCCTTAAGATCGTTTCCCTAGAAACCAACCTAGTCTTCT-TTAAGGT
*
29978 TGTTTCCT
65 TGTTTCCA
* * * * *
29986 TAGAAACCAACTTAGTCTTCCTT-AGTATCGTCTCCCTAAGAATCCTTAACCTCGTGTTCTTTAA
1 TAGAAACCAACCTAGTCTTCCTTAAG-ATCGTTTCCCT-AGAAACC--AACCTAGTCTTCTTTAA
30050 GGTTGTT
62 GGTTGTT
30057 CCTCAAGAAA
Statistics
Matches: 170, Mismatches: 37, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
71 3 0.02
72 142 0.84
73 7 0.04
75 17 0.10
76 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (72 bp):
TAGAAACCAACCTAGTCTTCCTTAAGATCGTTTCCCTAGAAACCAACCTAGTCTTCTTTAAGGTT
GTTTCCA
Found at i:29924 original size:108 final size:107
Alignment explanation
Indices: 29770--30009 Score: 297
Period size: 108 Copynumber: 2.2 Consensus size: 107
29760 ACCATTTACC
* *
29770 TAGAAACCAACCTAGTCTTCCTTAAGACCATTTCCCTAGAAACCAACCTAGTCTTCTTTAAGGTT
1 TAGAAACCAACCTAGTCTTCCTTAAGA-CATTTCCCTAGAAACCAACCTAGTCTTCTTTAAGATC
* * * *
29835 GTTTC-CATAGAAACCAACCTTGTCTTACTTAACG-TCGTTTTCA
65 GTTTCAC-TAGAAACCAAACTAGACTTACTTAA-GATCGTTTCCA
* * *
29878 TAGAAACCAACCTAGTCTTCCTTAAGGA-AGTTTCCGTATAATCCAACCTAGTCTTCTTTAAGAT
1 TAGAAACCAACCTAGTCTTCCTTAA-GACA-TTTCCCTAGAAACCAACCTAGTCTTCTTTAAGAT
* * *
29942 CGTTTCACTAGAAACCAAACTAGACTTTCTTAAGATTGTTTCCT
64 CGTTTCACTAGAAACCAAACTAGACTTACTTAAGATCGTTTCCA
*
29986 TAGAAACCAACTTAGTCTTCCTTA
1 TAGAAACCAACCTAGTCTTCCTTA
30010 GTATCGTCTC
Statistics
Matches: 115, Mismatches: 13, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
107 2 0.02
108 110 0.96
109 3 0.03
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (107 bp):
TAGAAACCAACCTAGTCTTCCTTAAGACATTTCCCTAGAAACCAACCTAGTCTTCTTTAAGATCG
TTTCACTAGAAACCAAACTAGACTTACTTAAGATCGTTTCCA
Found at i:30457 original size:71 final size:71
Alignment explanation
Indices: 30295--30466 Score: 175
Period size: 71 Copynumber: 2.4 Consensus size: 71
30285 TGGAGGAAAT
* * * ** * *
30295 CAAACGCAACCCCAATCCTCAATCATAGAGGACACCCCATTAGTAGGTGAACCCTTAATCATGAA
1 CAAACACAACCCCAATCCTCAATCATAGAGAAAACCCCATTAGTAGGCAAACCCTCAACCATGAA
*
30360 GAAAGT
66 GAAAGA
* * * * *
30366 CAAACACAACTCCAAGCCTCAGTCATTGAGAAAACCCCATTAGTAGGCAAACCCTCAGCCAT-AG
1 CAAACACAACCCCAATCCTCAATCATAGAGAAAACCCCATTAGTAGGCAAACCCTCAACCATGA-
*
30430 AGGAAGA
65 AGAAAGA
* * *
30437 CAAATATAACCCCAATCCTCAATAATAGAG
1 CAAACACAACCCCAATCCTCAATCATAGAG
30467 GACATCCCGC
Statistics
Matches: 79, Mismatches: 21, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
70 1 0.01
71 78 0.99
ACGTcount: A:0.40, C:0.28, G:0.15, T:0.17
Consensus pattern (71 bp):
CAAACACAACCCCAATCCTCAATCATAGAGAAAACCCCATTAGTAGGCAAACCCTCAACCATGAA
GAAAGA
Found at i:38875 original size:20 final size:22
Alignment explanation
Indices: 38820--38876 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 22
38810 TTGGGGGTCA
*
38820 AGAATTAGGGATTACGAGTAAGG
1 AGAATTAGGGATT-TGAGTAAGG
38843 -GAATT-GGGAATTTG-G-AAGG
1 AGAATTAGGG-ATTTGAGTAAGG
38862 AGAATTAGGGATTTG
1 AGAATTAGGGATTTG
38877 TAATTATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
19 4 0.13
20 11 0.37
21 7 0.23
22 8 0.27
ACGTcount: A:0.35, C:0.02, G:0.37, T:0.26
Consensus pattern (22 bp):
AGAATTAGGGATTTGAGTAAGG
Found at i:44281 original size:17 final size:18
Alignment explanation
Indices: 44259--44297 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
44249 AATAACCTAA
44259 AATACCC-TAAGCTCTAG
1 AATACCCTTAAGCTCTAG
*
44276 AATACCCTTTAAGCTCTTG
1 AATACCC-TTAAGCTCTAG
44295 AAT
1 AAT
44298 GAATAAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
19 12 0.63
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31
Consensus pattern (18 bp):
AATACCCTTAAGCTCTAG
Found at i:45325 original size:32 final size:32
Alignment explanation
Indices: 45284--45405 Score: 109
Period size: 32 Copynumber: 3.8 Consensus size: 32
45274 CCTATGGTGA
* * *
45284 CCTTGGGTAGGGTCTGAGGCCCCAAGGCATTT
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGCACTT
* * *
45316 CCTTGGGTAGACTCTAAGGCCCCGAGGTACTT
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGCACTT
* * * * * *
45348 CATTGGGTAGGCTCTTAGTCCCTAAGGTACTA
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGCACTT
* * *
45380 CCTCGTGTAGGCTCTCAGGCCCCAAG
1 CCTTGGGTAGGCTCTAAGGCCCCAAG
45406 ATATTCCCTT
Statistics
Matches: 71, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 71 1.00
ACGTcount: A:0.18, C:0.28, G:0.29, T:0.25
Consensus pattern (32 bp):
CCTTGGGTAGGCTCTAAGGCCCCAAGGCACTT
Found at i:50401 original size:12 final size:12
Alignment explanation
Indices: 50376--50468 Score: 82
Period size: 12 Copynumber: 7.8 Consensus size: 12
50366 ACGGGGATAT
* *
50376 CAGAAATCAAAA
1 CAGAATTCAGAA
50388 CAGAATTCAGAA
1 CAGAATTCAGAA
50400 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
50412 CAGAATCCAGAT
1 CAGAATTCAGAA
*
50424 CAGAAATCAGAA
1 CAGAATTCAGAA
**
50436 CAGAATTCAGGT
1 CAGAATTCAGAA
*
50448 CA-TATATCAGAA
1 CAGAAT-TCAGAA
50460 CAGAATTCA
1 CAGAATTCA
50469 AGTCGGAAAT
Statistics
Matches: 63, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
11 4 0.06
12 55 0.87
13 4 0.06
ACGTcount: A:0.49, C:0.18, G:0.15, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:50403 original size:24 final size:24
Alignment explanation
Indices: 50374--50482 Score: 130
Period size: 24 Copynumber: 4.5 Consensus size: 24
50364 AAACGGGGAT
*
50374 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
50398 AACAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
50422 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
50446 GTCATATATCAGAACAGAATTCA-
1 ATCAGAAATCAGAACAGAATTCAG
*
50469 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
50483 TAAAATATTT
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
24 70 1.00
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:50445 original size:48 final size:47
Alignment explanation
Indices: 50374--50482 Score: 146
Period size: 48 Copynumber: 2.3 Consensus size: 47
50364 AAACGGGGAT
*
50374 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
** * *
50421 GATCAGAAATCAGAACAGAATTCAGGTCATATATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
*
50469 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
50483 TAAAATATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
47 1 0.02
48 53 0.98
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
Found at i:53007 original size:18 final size:18
Alignment explanation
Indices: 52988--53053 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 18
52978 GTCAACGGTC
*
52988 AACGGGTCGGGTCGGGTC
1 AACGGGTCGGGTCGGGTA
53006 AACGGGT----T-GGGTA
1 AACGGGTCGGGTCGGGTA
* *
53019 AACAGGTCGGGTCGAGTA
1 AACGGGTCGGGTCGGGTA
53037 AACGGGTCGGGTCGGGT
1 AACGGGTCGGGTCGGGT
53054 TGTGACCGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
17 1 0.03
18 26 0.68
ACGTcount: A:0.18, C:0.17, G:0.47, T:0.18
Consensus pattern (18 bp):
AACGGGTCGGGTCGGGTA
Found at i:55124 original size:12 final size:12
Alignment explanation
Indices: 55099--55167 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
55089 ACGGAGATAT
* *
55099 CAGAAATCAAAA
1 CAGAATTCAGAA
55111 CAGAATTCAGAA
1 CAGAATTCAGAA
*
55123 CAG-ATATCATAA
1 CAGAAT-TCAGAA
* *
55135 CAGAATCCAGAT
1 CAGAATTCAGAA
55147 CAGAAATT-AGAA
1 CAG-AATTCAGAA
55159 CAGAATTCA
1 CAGAATTCA
55168 CGTCATATAT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
11 6 0.13
12 34 0.76
13 5 0.11
ACGTcount: A:0.52, C:0.17, G:0.13, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:55203 original size:24 final size:24
Alignment explanation
Indices: 55098--55205 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
55088 AACGGAGATA
*
55098 TCAGAAATCAAAACAGAATTC-AG
1 TCAGAAATCAGAACAGAATTCAAG
* * * *
55121 AACAGATATCATAACAGAA-TCCAG
1 -TCAGAAATCAGAACAGAATTCAAG
* *
55145 ATCAGAAATTAGAACAGAATTCACG
1 -TCAGAAATCAGAACAGAATTCAAG
* * *
55170 TCATATATCAGAATAGAATTCAAG
1 TCAGAAATCAGAACAGAATTCAAG
*
55194 TCGGAAATCAGA
1 TCAGAAATCAGA
55206 TAAAATATTT
Statistics
Matches: 65, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
23 2 0.03
24 60 0.92
25 3 0.05
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.20
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAATTCAAG
Found at i:57724 original size:13 final size:13
Alignment explanation
Indices: 57706--57748 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
57696 AGTGGTCAAC
57706 GGTCAACGGGTCG
1 GGTCAACGGGTCG
57719 GGTCAACGGGTCG
1 GGTCAACGGGTCG
* *
57732 GGTAAACAGGTCG
1 GGTCAACGGGTCG
57745 GGTC
1 GGTC
57749 GAGTAAACGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.19, C:0.21, G:0.44, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:57746 original size:18 final size:18
Alignment explanation
Indices: 57725--57770 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
57715 GTCGGGTCAA
57725 CGGGTCGGGTAAACAGGT
1 CGGGTCGGGTAAACAGGT
* *
57743 CGGGTCGAGTAAACGGGT
1 CGGGTCGGGTAAACAGGT
57761 CGGGTCGGGT
1 CGGGTCGGGT
57771 TGTGACCGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.17, C:0.17, G:0.48, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTAAACAGGT
Found at i:57797 original size:11 final size:11
Alignment explanation
Indices: 57781--57808 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
57771 TGTGACCGGT
57781 CAAAACAGTTC
1 CAAAACAGTTC
57792 CAAAACAGTTC
1 CAAAACAGTTC
57803 CAAAAC
1 CAAAAC
57809 CGATCAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.29, G:0.07, T:0.14
Consensus pattern (11 bp):
CAAAACAGTTC
Found at i:58646 original size:36 final size:35
Alignment explanation
Indices: 58568--58653 Score: 91
Period size: 36 Copynumber: 2.4 Consensus size: 35
58558 GTCGTTTCCC
* **
58568 TAGAAACCAACCTAGTCTTCCTAAGGCAGTTTCCT
1 TAGAAACCAACCTAGTCTTCCTAAGACAGTTTCAA
* ** *
58603 TATAAACCAACCTAGTCTTATTTAAGACCGTTTCAA
1 TAGAAACCAACCTAGTCTT-CCTAAGACAGTTTCAA
*
58639 TAGAAACCAATCTAG
1 TAGAAACCAACCTAG
58654 ACATTCTCAA
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
35 18 0.44
36 23 0.56
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (35 bp):
TAGAAACCAACCTAGTCTTCCTAAGACAGTTTCAA
Found at i:63362 original size:14 final size:14
Alignment explanation
Indices: 63341--63378 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
63331 TTTAACGTTC
63341 AAATATTCTTCACA
1 AAATATTCTTCACA
*
63355 ATATATTCTTCACA
1 AAATATTCTTCACA
63369 AAATATTCTT
1 AAATATTCTT
63379 ATTTTTAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATATTCTTCACA
Found at i:66856 original size:13 final size:13
Alignment explanation
Indices: 66838--66866 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
66828 AAATCTTATA
66838 TTTTTAATATATT
1 TTTTTAATATATT
66851 TTTTTAATATATT
1 TTTTTAATATATT
66864 TTT
1 TTT
66867 GAGGAAAACT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTAATATATT
Found at i:78384 original size:23 final size:23
Alignment explanation
Indices: 78358--78406 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
78348 ATAAAGAACC
78358 AAAATAAA-CTTAAATATACCATT
1 AAAATAAAGCTTAAATAT-CCATT
*
78381 AAAATAAAGTTTAAATATCCATT
1 AAAATAAAGCTTAAATATCCATT
78404 AAA
1 AAA
78407 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (23 bp):
AAAATAAAGCTTAAATATCCATT
Found at i:81409 original size:27 final size:27
Alignment explanation
Indices: 81371--81429 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
81361 GTCAGGTTCA
* *
81371 GGTCGGGTAGAGGGTGTATATTTTTCG
1 GGTCGGGTAGAGGATGTATAATTTTCG
81398 GGTCGGGTAGAGGATGTATAATTTTCG
1 GGTCGGGTAGAGGATGTATAATTTTCG
81425 GGTCG
1 GGTCG
81430 AGTTAGGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.17, C:0.08, G:0.41, T:0.34
Consensus pattern (27 bp):
GGTCGGGTAGAGGATGTATAATTTTCG
Found at i:84571 original size:19 final size:19
Alignment explanation
Indices: 84547--84585 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
84537 CTTACATGAC
84547 ACATTTAATCAAAAAATTA
1 ACATTTAATCAAAAAATTA
** *
84566 ACATTTTTTTAAAAAATTA
1 ACATTTAATCAAAAAATTA
84585 A
1 A
84586 TCTTAAATGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (19 bp):
ACATTTAATCAAAAAATTA
Found at i:88287 original size:74 final size:74
Alignment explanation
Indices: 88149--88313 Score: 197
Period size: 74 Copynumber: 2.2 Consensus size: 74
88139 TTAAATAGGG
* * ** * *
88149 AGGTACCGATACCCCTATGATAATTTTGGCTCTGAGAAAAACAGAATGTCAAATGGGCACCGATA
1 AGGTACCGATACCCCTATGACAAATTTGGCTCCAAGAAAAACAGAATGCCAAATAGGCACCGATA
88214 -CCCCTCAT
66 CCCCCTCAT
* * ** * *
88222 AGGGTACCAATACCCCTATGCCAAATTTGGCTCCAAGAAAAACAGAATGCCTTATAGGTATCGAT
1 A-GGTACCGATACCCCTATGACAAATTTGGCTCCAAGAAAAACAGAATGCCAAATAGGCACCGAT
*
88287 ACCCCCTTAT
65 ACCCCCTCAT
88297 AGGTACCGATACCCCTA
1 AGGTACCGATACCCCTA
88314 GTCATTTAAC
Statistics
Matches: 76, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
73 1 0.01
74 67 0.88
75 8 0.11
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.23
Consensus pattern (74 bp):
AGGTACCGATACCCCTATGACAAATTTGGCTCCAAGAAAAACAGAATGCCAAATAGGCACCGATA
CCCCCTCAT
Found at i:88296 original size:20 final size:20
Alignment explanation
Indices: 88271--88311 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
88261 AAACAGAATG
*
88271 CCTTATAGGTATCGATACCC
1 CCTTATAGGTACCGATACCC
88291 CCTTATAGGTACCGATACCC
1 CCTTATAGGTACCGATACCC
88311 C
1 C
88312 TAGTCATTTA
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:0.24, C:0.34, G:0.15, T:0.27
Consensus pattern (20 bp):
CCTTATAGGTACCGATACCC
Found at i:96394 original size:13 final size:14
Alignment explanation
Indices: 96364--96396 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
96354 GGGGAGTAGT
96364 TTTTCAAAAATTGA
1 TTTTCAAAAATTGA
96378 -TTTCAAAAA-TGA
1 TTTTCAAAAATTGA
96390 TTTTCAA
1 TTTTCAA
96397 TAAGAAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.17
13 15 0.83
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42
Consensus pattern (14 bp):
TTTTCAAAAATTGA
Found at i:96839 original size:54 final size:54
Alignment explanation
Indices: 96718--96837 Score: 172
Period size: 54 Copynumber: 2.2 Consensus size: 54
96708 CTCATAGGGT
* * *
96718 GTACCAATACCCTTATGACAATTTTGGCTCTGAGAAAAATAGAATGCCAAATGG
1 GTACCGATACCCCTATGACAATTTTGGCTCTGAGAAAAACAGAATGCCAAATGG
* *
96772 GTACCGATACCCCTATGCCAATTTTGGCTAC-GAGAAAAACAGAATGCCCAATGG
1 GTACCGATACCCCTATGACAATTTTGGCT-CTGAGAAAAACAGAATGCCAAATGG
96826 GT-CCGATACCCC
1 GTACCGATACCCC
96838 CTTAGAGGTA
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
53 10 0.17
54 49 0.82
55 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (54 bp):
GTACCGATACCCCTATGACAATTTTGGCTCTGAGAAAAACAGAATGCCAAATGG
Found at i:98590 original size:18 final size:19
Alignment explanation
Indices: 98559--98605 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
98549 TTTTGGGGAT
* *
98559 TTTTCAAGATTTTTA-AGA
1 TTTTCAAAAATTTTAGAGA
* *
98577 TTTTCAAAAATTTTAGGGG
1 TTTTCAAAAATTTTAGAGA
98596 TTTTCAAAAA
1 TTTTCAAAAA
98606 ATAATTTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.45
Consensus pattern (19 bp):
TTTTCAAAAATTTTAGAGA
Found at i:102118 original size:22 final size:22
Alignment explanation
Indices: 102047--102124 Score: 74
Period size: 22 Copynumber: 3.6 Consensus size: 22
102037 ACCAAAAGGG
* * *
102047 AGTATCGGTACCATAGTGTAGT
1 AGTATCGATACCATAGTATAGA
*
102069 AGTATCGATA-C-T-G-AGAGAA
1 AGTATCGATACCATAGTATAG-A
102088 AGGTATCGATACCATAGTATAGA
1 A-GTATCGATACCATAGTATAGA
102111 AGTATCGATACCAT
1 AGTATCGATACCAT
102125 GGTAGGGGTA
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
18 2 0.04
19 2 0.04
20 10 0.22
21 2 0.04
22 23 0.51
23 3 0.07
24 3 0.07
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (22 bp):
AGTATCGATACCATAGTATAGA
Found at i:102137 original size:20 final size:20
Alignment explanation
Indices: 102088--102146 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
102078 ACTGAGAGAA
*
102088 AGGTATCGATACCATAGTATAG
1 AGGTATCGATACCAT-G-GTAG
*
102110 AAGTATCGATACCATGGTAG
1 AGGTATCGATACCATGGTAG
* *
102130 GGGTATCGATACTATGG
1 AGGTATCGATACCATGG
102147 AGTCTAGAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 17 0.53
21 1 0.03
22 14 0.44
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (20 bp):
AGGTATCGATACCATGGTAG
Found at i:102566 original size:54 final size:54
Alignment explanation
Indices: 102480--102906 Score: 584
Period size: 54 Copynumber: 7.9 Consensus size: 54
102470 GCACTCTGTG
* * * *
102480 CGGAATTCATCATGATTTGATGAACAACCGTACATGCACTATGTGTTCAATTCA
1 CGGAATTCATCATGAGTTGATGAACAACCGTACAAGCACTATGTGTGCAATCCA
* * * *
102534 TGGAATTCATCATGAGTTTATGAACAATCGTACATGCACTATGTGTGCAATCCA
1 CGGAATTCATCATGAGTTGATGAACAACCGTACAAGCACTATGTGTGCAATCCA
* * * *
102588 CGGAATTCATCATGAGTTGATGAACAACCGTACAGGCACTATGTATGTAATTCA
1 CGGAATTCATCATGAGTTGATGAACAACCGTACAAGCACTATGTGTGCAATCCA
*
102642 CGGAATTCATCATGAGTTGATGAACAACTGTACAAGCACTATGTGTGCAATCCA
1 CGGAATTCATCATGAGTTGATGAACAACCGTACAAGCACTATGTGTGCAATCCA
* **
102696 CGGAATTCATCATGAGTTGATGAACAATCGTACAAGCACTATGTGTATAATCCA
1 CGGAATTCATCATGAGTTGATGAACAACCGTACAAGCACTATGTGTGCAATCCA
* * * * *
102750 AGGAATTTATCATGAGTTGATGAACAACCGTACATGCACTATATGTGCAATCTA
1 CGGAATTCATCATGAGTTGATGAACAACCGTACAAGCACTATGTGTGCAATCCA
* * * *
102804 TGGAATTCATCATGAGTTGATGAACAACTGTAAAAGCACTATGTGTGCAACCCA
1 CGGAATTCATCATGAGTTGATGAACAACCGTACAAGCACTATGTGTGCAATCCA
* * * * *
102858 CGAAATTCATCATGAGTTGATGAACTACCGTATAGGCACTACGTGTGCA
1 CGGAATTCATCATGAGTTGATGAACAACCGTACAAGCACTATGTGTGCA
102907 TCTTAATAAA
Statistics
Matches: 328, Mismatches: 45, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 328 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (54 bp):
CGGAATTCATCATGAGTTGATGAACAACCGTACAAGCACTATGTGTGCAATCCA
Found at i:106225 original size:28 final size:29
Alignment explanation
Indices: 106174--106234 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
106164 CAATTCTTAT
* *
106174 TTTGAATGATTTGTTTAAGTGATT-GTTC
1 TTTGAATGATTTGTTAAACTGATTCGTTC
*
106202 TTTGAAT-ATTTGTTAAACTAGATTCGTTT
1 TTTGAATGATTTGTTAAACT-GATTCGTTC
106231 TTTG
1 TTTG
106235 TATTATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 10 0.36
28 11 0.39
29 7 0.25
ACGTcount: A:0.23, C:0.05, G:0.18, T:0.54
Consensus pattern (29 bp):
TTTGAATGATTTGTTAAACTGATTCGTTC
Done.