Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004403.1 Hibiscus syriacus cultivar Beakdansim tig00009651_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: 76300
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:785 original size:165 final size:165
Alignment explanation
Indices: 113--903 Score: 1146
Period size: 164 Copynumber: 4.8 Consensus size: 165
103 CATTAACTGA
* *
113 AAGATGAGTTTGCTCATAGCAT-TTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
*
177 ATCAATCATTGAATTTGGAAGATGAATTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
66 ACCAATCATTGAATTTGGAAGATGAATTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
*
242 TGATCTGGTTG-GACAGAATCAATCATTGAATTTGG
131 TGATCTGGTTGAG-CAGAACCAATCATTGAATTTGG
* * * **
277 AAGATGAGTTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTTAGCAG
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAG
*
342 AACCAATCATTGAATTTGGAAGATAAATGTGCTAATAGCATCTTCT-G--GTGTTCTTTGAGTTA
65 AACCAATCATTGAATTTGGAAGATGAAT-TGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
* *
404 TCTGACCTGGTTTAGCAGAACCAATCATTGAA-TTGG
129 TCTGATCTGGTTGAGCAGAACCAATCATTGAATTTGG
* *
440 AAGATGAATTTGCTAATAGCATCTTCTGGAA--GTTCTTTGAG-TATCTGACCTGGTT-TAGCAG
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAG
* *
501 AA-CAATCATTGAATTGGGAAGATGAATTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
65 AACCAATCATTGAATTTGGAAGATGAATTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
* * *
565 CTGACCTGGTTTAGCAGAACCAATCATTGAATTTAG
130 CTGATCTGGTTGAGCAGAACCAATCATTGAATTTGG
*
601 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
* *
666 ACCAATCATTGAATTTAGAAGATGAATTGTTAATAGC-TCTTCTGGAAGTGTTCTTTGAGTTATC
66 ACCAATCATTGAATTTGGAAGATGAATTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
*
730 TGATCTGGTTG-GACAGAATCAATCATTGAATTTTGG
131 TGATCTGGTTGAG-CAGAACCAATCATTGAA-TTTGG
*
766 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAA
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
* * * *
830 AACCAATCATTGAATTTAGAAG-TG-ATTGTTCATAGCATCTTCTGGAAGTATTCTTTGAGTTAT
65 AACCAATCATTGAATTTGGAAGATGAATTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
*
893 TTGATCTGGTT
130 CTGATCTGGTT
904 TGGTAGGAAC
Statistics
Matches: 580, Mismatches: 30, Indels: 34
0.90 0.05 0.05
Matches are distributed among these distances:
157 16 0.03
158 24 0.04
159 8 0.01
160 61 0.11
161 43 0.07
163 55 0.09
164 171 0.29
165 151 0.26
166 34 0.06
167 17 0.03
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.37
Consensus pattern (165 bp):
AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
ACCAATCATTGAATTTGGAAGATGAATTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGGTTGAGCAGAACCAATCATTGAATTTGG
Found at i:2162 original size:74 final size:74
Alignment explanation
Indices: 2010--2171 Score: 193
Period size: 74 Copynumber: 2.2 Consensus size: 74
2000 AGAAGCAAAT
* * * *
2010 TGGGGCATGCTAAAAACCCTTTTCAAACAGAATCAGAAATGTTGAAATATTCTGAATATTTATCA
1 TGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACATTTATCA
2075 GCAAAATGC
66 GCAAAATGC
* * ** *
2084 TGGGGCATGCTGAAAACCCATTTCAATCAGAATCAGAACTGTTGATGCATTTTGAACACTTGTAT
1 TGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACA-TT-TAT
* *
2149 TAGC-CAATG-
64 CAGCAAAATGC
2158 TGGGGCATGCTGAA
1 TGGGGCATGCTGAA
2172 GGCCTATATC
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
74 63 0.84
75 6 0.08
76 6 0.08
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.28
Consensus pattern (74 bp):
TGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACATTTATCA
GCAAAATGC
Found at i:3477 original size:21 final size:22
Alignment explanation
Indices: 3452--3505 Score: 92
Period size: 21 Copynumber: 2.5 Consensus size: 22
3442 ATCTACACTC
*
3452 TTCAAAGATGATAGATTCTC-T
1 TTCAAAGATGACAGATTCTCTT
3473 TTCAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
3495 TTCAAAGATGA
1 TTCAAAGATGA
3506 AAACTTTATG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 19 0.61
22 12 0.39
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:4503 original size:113 final size:112
Alignment explanation
Indices: 3971--5548 Score: 1987
Period size: 113 Copynumber: 14.2 Consensus size: 112
3961 CATTTGAAGA
** * * * ** *
3971 AGAAGAACTTGTTCAA-CTTTTGCTTAAATTCATCACCGGTGGATCAGCAGTGT-C-GTTAGAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTGATGGATCAACA-TTTCCAGAGAAAGT
*
4033 TCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAATTCATAAT-
65 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * * * * *** *
4079 -GAAGAATTTGTTCAACCTTTTCCCTGAATTCATTACTTGAT-GATTATTTTTTCCAGAGGAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCA-TTGATGGATCAACATTTCCAGAGAAAGT
*
4142 TCATAAT--GAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATG
65 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* ** *
4187 AGAAGAACTTGTTAAACC-TTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCA-TTGATGGATCAACATTTCCAGAGAAAGT
*
4251 TCAT-ATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATG
65 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * * * *
4297 AGAAGAAC-TGTTTAACCTTTTGCTTGAATTCATCACTTGATGGATTATCATTGCCAGAG-AAGG
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCA-TTGATGGATCAACATTTCCAGAGAAAGT
*
4360 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
65 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * *
4408 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATT-GATGGATCAACATTTCCAGAGAAAGT
4473 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
65 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * *
4521 A-AAGAACTTGTTCAA-CTTGTTGCTTAAATTCATCATTTGATGGATCAGC-TTTTCAGAAAAAG
1 AGAAGAACTTGTTCAACCTT-TTGCTTAAATTCATCA-TTGATGGATCAACATTTCCAGAGAAAG
* *
4583 TTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAG-TAATAATG
64 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* ** *
4630 AGAAGAACTTGTTTAACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCA-TTGATGGATCAACATTTCCAGAGAAAGT
*
4695 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
65 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * * * * *
4743 AGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACTTGATGGATTATCATTGCCAGAGAAGGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCA-TTGATGGATCAACATTTCCAGAGAAAGT
*
4808 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
65 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * * *
4856 AGAAGAATTTGTTCAAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCTTTTCCAGAGAAAG
1 AGAAGAACTTGTTC-AACCTTTTGCTTAAATTCATCATT-GATGGATCAACATTTCCAGAGAAAG
4921 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
64 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* ** *
4970 AGAAGAACTTGTTCAA-CTTTTGCTTAAATTTCATCATTTGATGGAT-TATTTTTGCCAGA-TAA
1 AGAAGAACTTGTTCAACCTTTTGCTTAAA-TTCATCA-TTGATGGATCAACATTT-CCAGAGAAA
5032 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA-TTCATAAT-
63 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * * *
5080 -GAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCATTCATTGCCAGA-TAAG
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCA-TTGATGGATCA-ACATTTCCAGAGAAAG
5143 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-AGAAGTTCATAATG
64 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * *
5191 AGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGAGAAGGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCA-TTGATGGATCAACATTTCCAGAGAAAGT
*
5256 TCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGTTCATAATG
65 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * *
5304 AGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGAGAAAGT
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCA-TTGATGGATCAACATTTCCAGAGAAAGT
5369 TCATGAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
65 TCAT-AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * * ** *
5418 AGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACTTGATGGAT-TATTTTTGCCAGAGAAGG
1 AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCA-TTGATGGATCAACATTT-CCAGAGAAAG
5482 TTCATAATGAGAAGAACTCATCTGAAGAA-G--GAAGAAGTTCATAATG
64 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
*
5528 AGAAGAGCTTGTTCAACCTTT
1 AGAAGAACTTGTTCAACCTTT
5549 GTTTGATACT
Statistics
Matches: 1321, Mismatches: 112, Indels: 72
0.88 0.07 0.05
Matches are distributed among these distances:
107 51 0.04
108 41 0.03
109 109 0.08
110 250 0.19
111 129 0.10
112 230 0.17
113 311 0.24
114 200 0.15
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (112 bp):
AGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTGATGGATCAACATTTCCAGAGAAAGTT
CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
Found at i:5177 original size:561 final size:558
Alignment explanation
Indices: 3972--5549 Score: 2214
Period size: 561 Copynumber: 2.8 Consensus size: 558
3962 ATTTGAAGAA
** * * *
3972 GAAGAACTTGTTCAAC-TTTTGCTTAAATTCATCA-CCGGTGGATCAGCAGTGTC-GTTAGAGTT
1 GAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATCAGCATTGTCAGATA-AGTT
* *
4034 CATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAAT--GAAGAATTTGTTCAACCT
65 CATAATGAGAAGAACTCATCTGAAGAGGAAGAAG-AAGTCATAATGAGAAGAACTTGTTCAACCT
* * *** * *
4097 TTT-CCCTGAATTCATTACTTGAT-GATTATTTTTTCCAGAGGAAGTTCATAAT--GAAGAACTT
129 TTTGCTC-GAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTC
* * *
4158 ATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTAAACC-TTTGCTCGAATTCATC
193 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTGAATTCATC
* *
4221 ACTTGATGGATTAACATTTCCAGAGAAAGTTCAT-ATGAGAAGAACTTATCTGAAG-AGGAAGAA
258 ACTTGATGGATTAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
* * *
4284 GAAGTTCATAATGAGAAGAA-CTGTTTAACCTTTTGCTTGAATTCATCACTTGATGGATTATCAT
323 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATTA-CTT
* * *
4348 TGCCAGAG-AAGGTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAA
387 TTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
*
4412 GAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCAT
452 GAACTTGTTCAA-CTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCAT
4477 AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
516 AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* * *
4520 GAAAGAACTTGTTCAACTTGTTGCTTAAATTCATCATTTGATGGATCAGC-TTTTCAGAAAAAGT
1 G-AAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATCAGCATTGTCAG-ATAAGT
* * *
4584 TCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTAATAATGAGAAGAACTTGTTTAACCT
64 TCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTCATAATGAGAAGAACTTGTTCAACCT
4649 TTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCA
129 TTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCA
* *
4714 TCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCA
194 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTGAATTCATCA
* *
4779 CTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
259 CTTGATGGATTAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
* ** * *
4844 AAATTCATAATGAGAAGAATTTGTTCAAACCTTTTGCTCAAATCCATCA-TTCGATGGATCAGCT
324 AAGTTCATAATGAGAAGAATTTGTTC-AACCTTTTGCTTGAATTCATCACTT-GATGGATTA-CT
4908 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
386 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * * ** *
4973 AGAACTTGTTCAACTTTTGCTTAAATTTCATCATTTGATGGATTA-TTTTTGCCAGA-TAAGTTC
451 AGAACTTGTTCAACTTTTGCTCAAA-TCCATCATTCGATGGATCAGCATTT-CCAGAGAAAGTTC
5036 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA-TTCATAAT
514 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* * *
5080 GAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCATTCATTGCCAGATAAGTT
1 GAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATCA-GCATTGTCAGATAAGTT
*
5145 CATAATGAGAAGAACTCATCTGAAGAAGGAAG-AGAAGTTCATAATGAGAAGAACTTGTTCAACT
65 CATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAG-TCATAATGAGAAGAACTTGTTCAACC
* ** * * * *
5209 TTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTC
128 TTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTC
* * *
5274 ATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATC
193 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTGAATTCATC
* *
5339 ATTTGATGGATCAACATTGCCAGAGAAAGTTCATGAATGAGAAGAACTCATCTGAAGAAGGAAGA
258 ACTTGATGGATTAACATTGCCAGAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAGAAGGAAGA
* *
5404 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACTTGATGGATTATTT
322 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATTACTT
*
5469 TTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAA-G--GAAGAAGTTCATAATGAGA
387 TT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* *
5531 AGAGCTTGTTCAACCTTTG
451 AGAACTTGTTCAACTTTTG
5550 TTTGATACTA
Statistics
Matches: 917, Mismatches: 85, Indels: 46
0.88 0.08 0.04
Matches are distributed among these distances:
548 1 0.00
549 15 0.02
550 28 0.03
551 48 0.05
552 35 0.04
553 27 0.03
555 16 0.02
556 36 0.04
557 45 0.05
558 56 0.06
559 71 0.08
560 56 0.06
561 338 0.37
562 145 0.16
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (558 bp):
GAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATCAGCATTGTCAGATAAGTTC
ATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTCATAATGAGAAGAACTTGTTCAACCTTT
TGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATC
TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTGAATTCATCACT
TGATGGATTAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
GTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATTACTTTTCC
AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
TTGTTCAACTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGA
GAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
Found at i:5873 original size:3 final size:3
Alignment explanation
Indices: 5860--5911 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
5850 TTTTTATCCA
*
5860 TAT TA- TAT TAT TAT TA- TAT TATT TAT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
5904 TAT TAT TA
1 TAT TAT TA
5912 AATAATAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
2 4 0.09
3 37 0.84
4 3 0.07
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:6382 original size:21 final size:22
Alignment explanation
Indices: 6357--6402 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
6347 AGAACGAGAC
*
6357 AGAGACA-A-AAAAAAAGAATAG
1 AGAGACATAGAAAAAAA-AACAG
6378 AGAGACATAGAAAAAAAAACAG
1 AGAGACATAGAAAAAAAAACAG
6400 AGA
1 AGA
6403 AAATACAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 8 0.36
23 7 0.32
ACGTcount: A:0.70, C:0.07, G:0.20, T:0.04
Consensus pattern (22 bp):
AGAGACATAGAAAAAAAAACAG
Found at i:7217 original size:19 final size:18
Alignment explanation
Indices: 7189--7235 Score: 78
Period size: 19 Copynumber: 2.6 Consensus size: 18
7179 AGATTTTTGA
7189 TTTATT-TTTTCATTTAT
1 TTTATTGTTTTCATTTAT
7206 TTTATATGTTTTCATTTAT
1 TTTAT-TGTTTTCATTTAT
7225 TTTATTGTTTT
1 TTTATTGTTTT
7236 TAAATATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.18
18 7 0.25
19 16 0.57
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.74
Consensus pattern (18 bp):
TTTATTGTTTTCATTTAT
Found at i:7302 original size:13 final size:12
Alignment explanation
Indices: 7275--7299 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7265 TTTTATTATA
7275 TATTAAATATTT
1 TATTAAATATTT
7287 TATTAAATATTT
1 TATTAAATATTT
7299 T
1 T
7300 TATAATATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTAAATATTT
Found at i:7993 original size:44 final size:44
Alignment explanation
Indices: 7930--8017 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
7920 GTTAAATGTT
* *
7930 TACCGGTACTTGGGTAAGTAAAACTAATAAAAGTAAACATAGAG
1 TACCGGTACTAGGGTAAGTAAAACGAATAAAAGTAAACATAGAG
7974 TACCGGTACTAGGGTAAGTAAAACGAATAAAAGTAAACATAGAG
1 TACCGGTACTAGGGTAAGTAAAACGAATAAAAGTAAACATAGAG
8018 ATTAAGTTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.47, C:0.11, G:0.22, T:0.20
Consensus pattern (44 bp):
TACCGGTACTAGGGTAAGTAAAACGAATAAAAGTAAACATAGAG
Found at i:12559 original size:23 final size:23
Alignment explanation
Indices: 12533--12576 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
12523 ATATTGTGAC
12533 ACGCTTTTCTATGCTCTTGTGCT
1 ACGCTTTTCTATGCTCTTGTGCT
*
12556 ACGCTTTTTTATGCTCTTGTG
1 ACGCTTTTCTATGCTCTTGTG
12577 ACACATTCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.09, C:0.23, G:0.18, T:0.50
Consensus pattern (23 bp):
ACGCTTTTCTATGCTCTTGTGCT
Found at i:16003 original size:21 final size:22
Alignment explanation
Indices: 15979--16021 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
15969 TAGTTTATTT
15979 TAAAC-TTTGTTTCAATTATCG
1 TAAACTTTTGTTTCAATTATCG
*
16000 TAAACTTTTTTTTCAATTATCG
1 TAAACTTTTGTTTCAATTATCG
16022 AACTTGGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.51
Consensus pattern (22 bp):
TAAACTTTTGTTTCAATTATCG
Found at i:16058 original size:33 final size:33
Alignment explanation
Indices: 16010--16082 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
16000 TAAACTTTTT
*
16010 TTTCAA-TTATCGAACTTGGAAGTTTTTAAGTA
1 TTTCAATTTATCGAACTTGGAAGTATTTAAGTA
*
16042 TTTGAATTTATCGAACTTGGAAGTATTTAAGTA
1 TTTCAATTTATCGAACTTGGAAGTATTTAAGTA
16075 TTTCAATT
1 TTTCAATT
16083 ACCGTAAACT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
32 5 0.14
33 32 0.86
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (33 bp):
TTTCAATTTATCGAACTTGGAAGTATTTAAGTA
Found at i:16691 original size:21 final size:22
Alignment explanation
Indices: 16611--16689 Score: 133
Period size: 22 Copynumber: 3.6 Consensus size: 22
16601 TATGAAAAAA
16611 CCGGATCGA-TTTTTATCCGAT
1 CCGGATCGATTTTTTATCCGAT
16632 CCGGATCGATTTTTTATCCGAT
1 CCGGATCGATTTTTTATCCGAT
*
16654 CCGGATCGATTTTTTATTCGAT
1 CCGGATCGATTTTTTATCCGAT
*
16676 CCGAATCGATTTTT
1 CCGGATCGATTTTT
16690 ATCTGACTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
21 9 0.16
22 46 0.84
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.42
Consensus pattern (22 bp):
CCGGATCGATTTTTTATCCGAT
Found at i:18496 original size:41 final size:43
Alignment explanation
Indices: 18430--18518 Score: 112
Period size: 41 Copynumber: 2.1 Consensus size: 43
18420 AATTTACAAT
* *
18430 AAAATAATAAAAAAAATTATTGAATACAAA-ATTAATTAA-ACA
1 AAAATAATAAAAAAAATTATTGAATA-AAATATAAATTAATAAA
**
18472 AAAATAAT-AAAAATCTTATTGAATAAAATATAAATTAATAAA
1 AAAATAATAAAAAAAATTATTGAATAAAATATAAATTAATAAA
18514 AAAAT
1 AAAAT
18519 GGTAAAGACA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 3 0.07
41 23 0.56
42 15 0.37
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.28
Consensus pattern (43 bp):
AAAATAATAAAAAAAATTATTGAATAAAATATAAATTAATAAA
Found at i:22035 original size:21 final size:20
Alignment explanation
Indices: 22009--22059 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
21999 TCTATTTTAT
22009 AATTCGAGTTG-GTTTAAAAA
1 AATTCGAGTTGAGTTT-AAAA
* *
22029 AATTTCGAGTCGAGTTTATAA
1 AA-TTCGAGTTGAGTTTAAAA
22050 AATTCGAGTT
1 AATTCGAGTT
22060 TATTTTTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 9 0.35
21 13 0.50
22 4 0.15
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (20 bp):
AATTCGAGTTGAGTTTAAAA
Found at i:23543 original size:31 final size:30
Alignment explanation
Indices: 23489--23555 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
23479 ATCGTTTTAT
*
23489 TCATTAA-ATTTTTAAAAATTATAAAATAA
1 TCATTAATTTTTTTAAAAATTATAAAATAA
* * *
23518 TTATTAATTTTTTTGAATAATTATAAAATGA
1 TCATTAATTTTTTT-AAAAATTATAAAATAA
23549 TCATTAA
1 TCATTAA
23556 ATTTATCAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 6 0.19
30 5 0.16
31 20 0.65
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (30 bp):
TCATTAATTTTTTTAAAAATTATAAAATAA
Found at i:23918 original size:23 final size:23
Alignment explanation
Indices: 23874--23918 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
23864 TATTAGGTAA
**
23874 CGCTTATATAATGTAATAGATAG
1 CGCTTATATAATAAAATAGATAG
*
23897 CGCTTATATAATAAAATGGATA
1 CGCTTATATAATAAAATAGATA
23919 TTTAACGGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (23 bp):
CGCTTATATAATAAAATAGATAG
Found at i:23976 original size:87 final size:87
Alignment explanation
Indices: 23830--24079 Score: 448
Period size: 87 Copynumber: 2.9 Consensus size: 87
23820 TATGTTATAT
*
23830 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
23895 AGCGCTTATATAATAAAAT-GG
66 AGCGCTTATATAATAAAATAGG
*
23916 ATATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACACTTATATAATGTAATAGA
1 -TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGA
23981 TAGCGCTTATATAATAAAATAGG
65 TAGCGCTTATATAATAAAATAGG
* *
24004 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
24069 AGCGCTTATAT
66 AGCGCTTATAT
24080 TGACCTATTT
Statistics
Matches: 157, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
87 155 0.99
88 2 0.01
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (87 bp):
TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AGCGCTTATATAATAAAATAGG
Found at i:28105 original size:120 final size:120
Alignment explanation
Indices: 27892--28138 Score: 431
Period size: 120 Copynumber: 2.1 Consensus size: 120
27882 TTTTTCTTCC
*
27892 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGAAATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGAAATAGGTTGTAGACCTATTCGCT
*
27957 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
66 AATAAAACCGGTATACTTATACCGGTTATAATACAAAATTATCTAGTACATTATA
*
28012 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGAAATAGGTTGTAGACCTATTCGCT
* * * *
28077 CATAAAACCGGTATATTTATACCGGTTATAATATAAAATTATCTATTACATTATA
66 AATAAAACCGGTATACTTATACCGGTTATAATACAAAATTATCTAGTACATTATA
28132 ATTCTGG
1 ATTCTGG
28139 GTTCCGGTGT
Statistics
Matches: 120, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 120 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.32
Consensus pattern (120 bp):
ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGAAATAGGTTGTAGACCTATTCGCT
AATAAAACCGGTATACTTATACCGGTTATAATACAAAATTATCTAGTACATTATA
Found at i:28267 original size:303 final size:303
Alignment explanation
Indices: 27425--28321 Score: 1634
Period size: 302 Copynumber: 3.0 Consensus size: 303
27415 TTAAAATTAG
* *
27425 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGATATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
27490 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
* *
27555 TACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTAGACATAAAGTACCGACACAATATT
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
* *
27620 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACTGGTATACTTATACCGGTTATA
196 AAAAAGTGTCGAAATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
27685 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
261 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
27728 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA-TT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
*
27792 ATATCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
*
27857 CACTTTTAGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
27922 AAAAAGTGTCGAAATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
196 AAAAAGTGTCGAAATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
27987 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
261 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
28030 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
* * *
28095 ATACCGGTTATAATATAAAATTATCTATTACATTATAATTCTGGGTTCCGGTGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
*
28160 CACTTTTTGACAAGGCATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
* * * *
28225 AAAAAGGGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTATA
196 AAAAAGTGTCGAAATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
*
28290 TTACAAAATTATCTATTACATTATAATTCTGG
261 TTACAAAATTATCTAGTACATTATAATTCTGG
28322 GTTCCGATGT
Statistics
Matches: 574, Mismatches: 19, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
302 296 0.52
303 278 0.48
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Consensus pattern (303 bp):
CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
AAAAAGTGTCGAAATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
Found at i:28510 original size:182 final size:183
Alignment explanation
Indices: 28012--28597 Score: 1002
Period size: 183 Copynumber: 3.2 Consensus size: 183
28002 GTACATTATA
*
28012 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
* *
28077 CATAAAACCGGTATATTTATACCGGTTATAATATAAAATTATCTATTACATTATAATTCTGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
* *
28142 CCGGTGTGTAAATGTCGACACTTTTTGACAAGGCATCGACACATTTTTCTTCC
131 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
*
28195 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGGGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
28260 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
28325 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
131 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
*
28378 ATTATGGACATAAAGTACCGACACAATATT-AAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
* *
28442 CATAAAACCGGTATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
* * *
28507 CCGATGTTTTTTCAA--TCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCC
131 CCGATG---TGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
28561 ATTCTGGACATAAAGTACCGACACAATA-T-AAAAGTGT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGT
28598 GAAAACTTTG
Statistics
Matches: 386, Mismatches: 14, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
182 111 0.29
183 271 0.70
185 4 0.01
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Consensus pattern (183 bp):
ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
Found at i:28907 original size:33 final size:33
Alignment explanation
Indices: 28870--28938 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
28860 CATCTTAATA
*
28870 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
28903 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
28936 TCA
1 TCA
28939 TCTATTTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:28994 original size:21 final size:21
Alignment explanation
Indices: 28972--29054 Score: 130
Period size: 21 Copynumber: 4.0 Consensus size: 21
28962 CTTATGCCTC
* * *
28972 TCAAGTGTATCTTCGACTCTC
1 TCAAGTTTCTCTTCGACTCTA
28993 TCAAGTTTCTCTTCGACTCTA
1 TCAAGTTTCTCTTCGACTCTA
*
29014 TCAAGTTTCTTTTCGACTCTA
1 TCAAGTTTCTCTTCGACTCTA
29035 TCAAGTTTCTCTTCGACTCT
1 TCAAGTTTCTCTTCGACTCT
29055 TGATTGTCTT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.18, C:0.28, G:0.11, T:0.43
Consensus pattern (21 bp):
TCAAGTTTCTCTTCGACTCTA
Found at i:31330 original size:20 final size:19
Alignment explanation
Indices: 31275--31321 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
31265 TCCGGTATCG
31275 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
31294 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
31315 TTTTACC
1 TTTTACC
31322 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:31502 original size:20 final size:19
Alignment explanation
Indices: 31456--31502 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
31446 TCCGGTAACG
*
31456 TTTTACCGGTTTTATCATT
1 TTTTACCGATTTTATCATT
*
31475 TTGATACCGATTTTATCATAT
1 TT-TTACCGATTTTATCAT-T
31496 TTTTACC
1 TTTTACC
31503 TGGTATATCG
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:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (19 bp):
TTTTACCGATTTTATCATT
Found at i:31546 original size:181 final size:182
Alignment explanation
Indices: 31242--31714 Score: 732
Period size: 181 Copynumber: 2.6 Consensus size: 182
31232 CGTACTTACG
* *
31242 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGATTT
* * *
31307 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
*
31372 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
31423 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGATTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGATTT
* *
31488 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
31553 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * * * * **
31605 AAAGTACCGACACTTTAAATGTATCTGGTAGCGCTTTACCGATTTTATCATTTCAATACCGATTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGATTT
* * *
31670 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
31715 AATTTGGATC
Statistics
Matches: 267, Mismatches: 24, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
181 169 0.63
182 98 0.37
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGATTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:41542 original size:164 final size:165
Alignment explanation
Indices: 41159--41675 Score: 867
Period size: 164 Copynumber: 3.1 Consensus size: 165
41149 TATGAATTAG
41159 AAACCCGACCCGACACGAAATAATAAAAAAATTATTTTTATTCAATAAAAACATTGACTTAATTG
1 AAACCCGACCCGACACGAAATAATAAAAAAATTATTTTTATTCAATAAAAACATTGACTTAATTG
41224 AAAAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATAT
66 -AAAAAAA-T-TATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATAT
**
41289 ATTTTTTTCGGGTCGGGTAGAGTTTTTTCACCCTAAACCC
128 A--TTTTTCGGGTCGGGTCCAGTTTTTTCACCCTAAACCC
* * * *
41329 -GACTCGACCCGACATGAAATAATAAAAAAGTTATTTTTATTCAATAAAAACATTGACTTAATTG
1 AAACCCGACCCGACACGAAATAATAAAAAAATTATTTTTATTCAATAAAAACATTGACTTAATTG
*
41393 AAAAAAATTATATAGAGGGGTATTATTGTAATTATTCATAAATATATAAGGTAAAATTATATATT
66 AAAAAAATTATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATT
*
41458 TTTCGGGTCGGGTCCA-ATTTTTCACCCTAAACCC
131 TTTCGGGTCGGGTCCAGTTTTTTCACCCTAAACCC
41492 AAACCCGACCCGACACGAAATAATAAAAAAATTATTTTTATTCAATAAAAACATTGACTTAATTG
1 AAACCCGACCCGACACGAAATAATAAAAAAATTATTTTTATTCAATAAAAACATTGACTTAATTG
* *
41557 AAAAAACTTATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATTTT
66 AAAAAAATTATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATT
41622 TTTCGGGTCGGGTCCAGTTTTTTCACCCTAAACCC
131 TTTCGGGTCGGGTCCAGTTTTTTCACCCTAAACCC
* *
41657 GAACCCGACCCGACCCGAA
1 AAACCCGACCCGACACGAA
41676 TATCACACTT
Statistics
Matches: 327, Mismatches: 18, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
163 17 0.05
164 154 0.47
165 34 0.10
166 54 0.17
167 1 0.00
168 7 0.02
169 60 0.18
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (165 bp):
AAACCCGACCCGACACGAAATAATAAAAAAATTATTTTTATTCAATAAAAACATTGACTTAATTG
AAAAAAATTATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATT
TTTCGGGTCGGGTCCAGTTTTTTCACCCTAAACCC
Found at i:41709 original size:38 final size:37
Alignment explanation
Indices: 41651--41739 Score: 142
Period size: 38 Copynumber: 2.4 Consensus size: 37
41641 TTTTCACCCT
41651 AAACCCGAACCCGACCCGACCCGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCCGACCCGAATATCACACTT-AAA
* *
41690 AAACCCGATCCGACTCGACCCGAATATCACACTTAAA
1 AAACCCGACCCGACCCGACCCGAATATCACACTTAAA
41727 AAACCCGACCCGA
1 AAACCCGACCCGA
41740 ACAAATAAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
37 15 0.32
38 25 0.53
39 7 0.15
ACGTcount: A:0.39, C:0.38, G:0.11, T:0.11
Consensus pattern (37 bp):
AAACCCGACCCGACCCGACCCGAATATCACACTTAAA
Found at i:43631 original size:18 final size:19
Alignment explanation
Indices: 43596--43631 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
43586 CGACCCGGCC
43596 CAAAATAATATATTTATTA
1 CAAAATAATATATTTATTA
*
43615 CAAAATATTAT-TTTATT
1 CAAAATAATATATTTATT
43632 CAATAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (19 bp):
CAAAATAATATATTTATTA
Found at i:50003 original size:23 final size:23
Alignment explanation
Indices: 49971--50014 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
49961 CGATACCCCC
49971 TTGAAGGGGAACCGATTCCCCAT
1 TTGAAGGGGAACCGATTCCCCAT
*
49994 TTGAATGGGAACCGATTCCCC
1 TTGAAGGGGAACCGATTCCCC
50015 CTAGGGGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (23 bp):
TTGAAGGGGAACCGATTCCCCAT
Found at i:50040 original size:18 final size:19
Alignment explanation
Indices: 49998--50040 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
49988 CCCCATTTGA
*
49998 ATGGGAACCGATTCCCCCT
1 ATGGGAACCGATACCCCCT
* *
50017 AGGGGAATCGATACCCCC-
1 ATGGGAACCGATACCCCCT
50035 ATGGGA
1 ATGGGA
50041 TTCTGGTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.26, C:0.30, G:0.28, T:0.16
Consensus pattern (19 bp):
ATGGGAACCGATACCCCCT
Found at i:55609 original size:24 final size:22
Alignment explanation
Indices: 55582--55629 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
55572 AATAAATTTT
55582 AATAT-AAATATTCAAATATTAAAA
1 AATATAAAATA-T-AAA-ATTAAAA
55606 AATATAAAATATAAAATTAAAA
1 AATATAAAATATAAAATTAAAA
55628 AA
1 AA
55630 AAATACATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 9 0.39
23 3 0.13
24 6 0.26
25 5 0.22
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (22 bp):
AATATAAAATATAAAATTAAAA
Found at i:55870 original size:25 final size:25
Alignment explanation
Indices: 55814--55870 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 25
55804 GTAATCTTAA
55814 TGGATTAATCAAGAATTACAAATTT
1 TGGATTAATCAAGAATTACAAATTT
** * * * *
55839 TAAATTAATTAAGACTTATAATTTT
1 TGGATTAATCAAGAATTACAAATTT
55864 TGGATTA
1 TGGATTA
55871 GTCGAAACTT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (25 bp):
TGGATTAATCAAGAATTACAAATTT
Found at i:56012 original size:25 final size:25
Alignment explanation
Indices: 55977--56030 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
55967 AAATCACATA
55977 AAGTTTCGACTAATCTAAAATTTGT
1 AAGTTTCGACTAATCTAAAATTTGT
* * *
56002 AAGTTTTGACTAATTTAAATTTTGT
1 AAGTTTCGACTAATCTAAAATTTGT
56027 AAGT
1 AAGT
56031 CTCAATTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.44
Consensus pattern (25 bp):
AAGTTTCGACTAATCTAAAATTTGT
Found at i:57418 original size:30 final size:31
Alignment explanation
Indices: 57362--57419 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
57352 AACTAAATAG
57362 GGACCAAAAGGCTAATTTTCCAAAAGTTTAT
1 GGACCAAAAGGCTAATTTTCCAAAAGTTTAT
57393 GGACCAAAAGTG-TAATTTT-CAAAAGTT
1 GGACCAAAAG-GCTAATTTTCCAAAAGTT
57420 AGGTGTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 8 0.31
31 17 0.65
32 1 0.04
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (31 bp):
GGACCAAAAGGCTAATTTTCCAAAAGTTTAT
Found at i:60343 original size:19 final size:19
Alignment explanation
Indices: 60319--60363 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
60309 TATGCATTAG
60319 GCTATGAACT-TGAAAATAA
1 GCTATGAA-TATGAAAATAA
*
60338 GCTATGAATATGAAATTAA
1 GCTATGAATATGAAAATAA
*
60357 GTTATGA
1 GCTATGA
60364 GTCCAGAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 1 0.04
19 22 0.96
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.31
Consensus pattern (19 bp):
GCTATGAATATGAAAATAA
Found at i:60450 original size:19 final size:19
Alignment explanation
Indices: 60426--60462 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
60416 AATTATGAAA
60426 ATAAAATGTGAAAG-TAAAT
1 ATAAAA-GTGAAAGATAAAT
60445 ATAAAAGTGAAAGATAAA
1 ATAAAAGTGAAAGATAAA
60463 AATGAGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.62, C:0.00, G:0.16, T:0.22
Consensus pattern (19 bp):
ATAAAAGTGAAAGATAAAT
Found at i:60527 original size:18 final size:18
Alignment explanation
Indices: 60504--60569 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 18
60494 AATGAAAAGA
60504 ATATGATATGACTATTAT
1 ATATGATATGACTATTAT
**
60522 ATATGATATTGTTTATTAT
1 ATATGATA-TGACTATTAT
* *
60541 GGCTTTGATATGACTATTAT
1 --ATATGATATGACTATTAT
*
60561 GTATGATAT
1 ATATGATAT
60570 TATTTATCAA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
18 15 0.41
19 8 0.22
20 8 0.22
21 6 0.16
ACGTcount: A:0.32, C:0.05, G:0.15, T:0.48
Consensus pattern (18 bp):
ATATGATATGACTATTAT
Found at i:60587 original size:39 final size:39
Alignment explanation
Indices: 60507--60589 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
60497 GAAAAGAATA
* * * *
60507 TGATATGACTATTATATATGATATTGTTTATTATGGCTT
1 TGATATGACTATTATATATGATATTATTTATCAAGACTT
* *
60546 TGATATGACTATTATGTATGATATTATTTATCAAGATTT
1 TGATATGACTATTATATATGATATTATTTATCAAGACTT
60585 TGATA
1 TGATA
60590 AAATCATGAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.49
Consensus pattern (39 bp):
TGATATGACTATTATATATGATATTATTTATCAAGACTT
Found at i:62076 original size:17 final size:17
Alignment explanation
Indices: 62044--62081 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
62034 ACAGTCTTTT
62044 AAAAATAATTTTAAGA-
1 AAAAATAATTTTAAGAC
*
62060 AAAAATCATTTTAAAGAC
1 AAAAATAATTTT-AAGAC
62078 AAAA
1 AAAA
62082 GTTGGTCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.58
17 4 0.21
18 4 0.21
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (17 bp):
AAAAATAATTTTAAGAC
Found at i:64575 original size:3 final size:3
Alignment explanation
Indices: 64567--64645 Score: 104
Period size: 3 Copynumber: 26.0 Consensus size: 3
64557 CCTACAAATG
* * * *
64567 TAA TAA TAA TAA TAT TAA TAA TAG TAA TAG TAA TAA TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
64615 TAA TAG TAA TAA TAA TAA TAA TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
64646 ACTCGGACTA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
3 62 0.95
4 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:65021 original size:117 final size:118
Alignment explanation
Indices: 64881--65207 Score: 469
Period size: 117 Copynumber: 2.8 Consensus size: 118
64871 AATACTGATG
*
64881 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTTGGATGAGTTCTTCTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTA
* ** *
64946 TGAACTCTCCACTGTAAATGTTGATCCACCTCCTTCTGTGATGGAATCG-AAT
66 TGAACTCTCCACTGAAAATGTTGATCCACCTCCTTCTACGATGGAATCGAAAC
* * * * * *
64998 CAAGGTTTAACAAGTTCTTCTCATTATGAAATTATCCTCCCTCATTGGACGAGTTCTTCTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTA
* * * ** *
65063 TGAACTCTCCATTGAAAATGTTGAGT-CATCTCCTTCTACGGTGGGCTTGAAAC
66 TGAACTCTCCACTGAAAATGTTGA-TCCACCTCCTTCTACGATGGAATCGAAAC
65116 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTA
*
65181 TGAACTCTCCACTGGAAATGTTGATCC
66 TGAACTCTCCACTGAAAATGTTGATCC
65208 CTCAAGCGAG
Statistics
Matches: 182, Mismatches: 25, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
117 97 0.53
118 85 0.47
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.37
Consensus pattern (118 bp):
CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTA
TGAACTCTCCACTGAAAATGTTGATCCACCTCCTTCTACGATGGAATCGAAAC
Found at i:65714 original size:15 final size:15
Alignment explanation
Indices: 65694--65733 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
65684 AAATGAAAAT
65694 TGTCTCAAGCGAGAC
1 TGTCTCAAGCGAGAC
* *
65709 TGTCTCAAGGGAGAT
1 TGTCTCAAGCGAGAC
65724 TGTCTCAAGC
1 TGTCTCAAGC
65734 AAGAAGAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (15 bp):
TGTCTCAAGCGAGAC
Found at i:65845 original size:74 final size:73
Alignment explanation
Indices: 65724--65885 Score: 225
Period size: 74 Copynumber: 2.2 Consensus size: 73
65714 CAAGGGAGAT
* * * *
65724 TGTCTCAAGCAAGAAGAAGTAGGTTTTAAGAAAAACCATCTCAAGGGAGACAAAACTTTGTTTCA
1 TGTCTCAAGCGAGACGAAGTAGATTTTAAGAAAAACCATCTCAAGGGAGACAAAAATTTGTTTCA
65789 AGAGAAAAA
66 AGAG-AAAA
* * * *
65798 TGTCTCAAGCGAGACGAAGTTGATTTTAAGAAAAACTATTTTAAGGGAGACAAAAATTTGTTTCA
1 TGTCTCAAGCGAGACGAAGTAGATTTTAAGAAAAACCATCTCAAGGGAGACAAAAATTTGTTTCA
*
65863 AGAGAAAC
66 AGAGAAAA
*
65871 TGTCTCAAGGGAGAC
1 TGTCTCAAGCGAGAC
65886 AAAATTCGTT
Statistics
Matches: 78, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
73 17 0.22
74 61 0.78
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.24
Consensus pattern (73 bp):
TGTCTCAAGCGAGACGAAGTAGATTTTAAGAAAAACCATCTCAAGGGAGACAAAAATTTGTTTCA
AGAGAAAA
Found at i:65871 original size:37 final size:36
Alignment explanation
Indices: 65746--66128 Score: 275
Period size: 36 Copynumber: 10.9 Consensus size: 36
65736 GAAGAAGTAG
* * *
65746 GTTTTAAGAAAAACCATCTCAAGGGAGACAAAACTTT
1 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAA-TTT
* * * * *
65783 GTTTCAAGAGAAAAATGTCTCAAGCGAGAC-GAAGTT
1 GTTTCAAGAG-AAACTATCTCAAGGGAGACAAAATTT
* * * *
65819 GATTTTAAGAAAAACTATTTTAAGGGAGACAAAAATTT
1 G-TTTCAAGAGAAACTATCTCAAGGGAGAC-AAAATTT
* *
65857 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTC
1 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
* **
65893 GTTTCAAGGGAAAC-ATTCTC-----A-A-AATTTTGT
1 GTTTCAAGAGAAACTA-TCTCAAGGGAGACAAAATT-T
65923 GTTTCAAGAGAAACTATCTCAA-GGAGACAAAATTT
1 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
* * * *
65958 GTTTCAAGGGAAAATGTCTCAAGAGAGACAAAATTT
1 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
* * *
65994 GTTTCAAGGGAAACGT-TTTCAA---AG-----TTTAT
1 GTTTCAAGAGAAAC-TATCTCAAGGGAGACAAAATT-T
* *
66023 GTTTCAAAAGAAACTGTCTCAAGGGAGACAAAATTTT
1 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAA-TTT
*
66060 GTTTAAAGAGAAACTATCTCAAGGGAGAC-AAATTT
1 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
* * *
66095 GTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 GTTTCAAGAGAAACTATCTCAAGGGAGACAAAAT
66129 CTCCTATTTC
Statistics
Matches: 270, Mismatches: 49, Indels: 55
0.72 0.13 0.15
Matches are distributed among these distances:
28 3 0.01
29 22 0.08
30 18 0.07
31 2 0.01
32 2 0.01
33 2 0.01
34 1 0.00
35 49 0.18
36 81 0.30
37 68 0.25
38 22 0.08
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (36 bp):
GTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
Found at i:65969 original size:65 final size:66
Alignment explanation
Indices: 65856--65979 Score: 207
Period size: 65 Copynumber: 1.9 Consensus size: 66
65846 GACAAAAATT
*
65856 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAACAT-TCTCAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTCGTTTCAAGGGAAA-ATGTCTCAAAATTT
65920 TG
65 TG
*
65922 TGTTTCAAGAGAAACTATCTCAA-GGAGACAAAATTTGTTTCAAGGGAAAATGTCTCAA
1 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTCGTTTCAAGGGAAAATGTCTCAA
65980 GAGAGACAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
64 2 0.04
65 31 0.56
66 22 0.40
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTCGTTTCAAGGGAAAATGTCTCAAAATTTT
G
Found at i:65978 original size:35 final size:35
Alignment explanation
Indices: 65922--66128 Score: 189
Period size: 35 Copynumber: 6.0 Consensus size: 35
65912 CAAAATTTTG
65922 TGTTTCAAGAGAAACTATCTCAAGGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGGAGACAAAATT
* * *
65957 TGTTTCAAGGGAAAATGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAG-GAGACAAAATT
* * *
65993 TGTTTCAAGGGAAACGT-TTTCAA--AG-----TTT
1 TGTTTCAAGAGAAAC-TATCTCAAGGAGACAAAATT
* *
66021 ATGTTTCAAAAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGAGAAACTATCTCAA-GGAGACAAAA-TT
*
66059 TGTTTAAAGAGAAACTATCTCAAGGGAGAC-AAATT
1 TGTTTCAAGAGAAACTATCTCAA-GGAGACAAAATT
* *
66094 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 TGTTTCAAGAGAAACTATCTCAAG-GAGACAAAAT
66129 CTCCTATTTC
Statistics
Matches: 141, Mismatches: 16, Indels: 29
0.76 0.09 0.16
Matches are distributed among these distances:
28 3 0.02
29 18 0.13
32 2 0.01
33 2 0.01
34 1 0.01
35 48 0.34
36 37 0.26
37 28 0.20
38 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.28
Consensus pattern (35 bp):
TGTTTCAAGAGAAACTATCTCAAGGAGACAAAATT
Found at i:66050 original size:101 final size:102
Alignment explanation
Indices: 65830--66116 Score: 393
Period size: 101 Copynumber: 2.8 Consensus size: 102
65820 ATTTTAAGAA
* * *
65830 AAACTATTTTAAGGGAGACAAAAATTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCGT
1 AAACTATCTCAAGGGAGAC-AAAATTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGT
* * *
65895 TTCAAGGGAAACATTCTCAAAATTTTGTGTTTCAAGAG
65 TTCAAGGGAAACATTCTCAAAAGTTTATGTTTCAAAAG
* * *
65933 AAACTATCTCAA-GGAGACAAAATTTGTTTCAAGGGAAAATGTCTCAAGAGAGACAAAATTTGTT
1 AAACTATCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTT
* *
65997 TCAAGGGAAACGTTTTC-AAAGTTTATGTTTCAAAAG
66 TCAAGGGAAACATTCTCAAAAGTTTATGTTTCAAAAG
* * *
66033 AAACTGTCTCAAGGGAGACAAAATTTTGTTTAAAGAGAAACTATCTCAAGGGAGAC-AAATTTGT
1 AAACTATCTCAAGGGAGACAAAA-TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGT
66097 TTCAAGGGAAAC-TATCTCAA
65 TTCAAGGGAAACAT-TCTCAA
66117 GCGAGATAAA
Statistics
Matches: 162, Mismatches: 18, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
100 28 0.17
101 90 0.56
102 34 0.21
103 10 0.06
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (102 bp):
AAACTATCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTT
TCAAGGGAAACATTCTCAAAAGTTTATGTTTCAAAAG
Found at i:66163 original size:40 final size:40
Alignment explanation
Indices: 66119--66518 Score: 665
Period size: 40 Copynumber: 10.0 Consensus size: 40
66109 TATCTCAAGC
* * * *
66119 GAGATAAAATCTCCTATTTCGAGGAAAACCAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
66159 GAGATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
66199 GAGATAAAATCTTCTGTTTCAAGGAAAATCAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
66239 GAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGACT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
66279 GAGATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* * *
66319 GAGATAAAATCTTTTGTTTCAAGGAAAAGCAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
66359 GAAATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
66399 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
66439 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
66479 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
66519 AAAATGAAAT
Statistics
Matches: 337, Mismatches: 23, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 337 1.00
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (40 bp):
GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
Found at i:66539 original size:40 final size:40
Alignment explanation
Indices: 66119--66563 Score: 510
Period size: 40 Copynumber: 11.2 Consensus size: 40
66109 TATCTCAAGC
* * * *
66119 GAGATAAAATCTCCTATTTCGAGGAAAACCAATCTTGAGT
1 GAGATAAAATCTCTTCTTTCAAGGAAAAACAATCTTGAGT
* *
66159 GAGATAAAATCT-TATGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTCT-TCTTTCAAGGAAAAACAATCTTGAGT
* *
66199 GAGATAAAATCT-TCTGTTTCAAGGAAAATCAATCTTGAGT
1 GAGATAAAATCTCT-TCTTTCAAGGAAAAACAATCTTGAGT
* * *
66239 GAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGACT
1 GAGATAAAATCTCTTCTTTCAAGGAAAAACAATCTTGAGT
*
66279 GAGATAAAATCT-TATGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTCT-TCTTTCAAGGAAAAACAATCTTGAGT
* * * *
66319 GAGATAAAATCTTTTGTTTCAAGGAAAAGCAATCTTGAAT
1 GAGATAAAATCTCTTCTTTCAAGGAAAAACAATCTTGAGT
* *
66359 GAAATAAAATCT-TATGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTCT-TCTTTCAAGGAAAAACAATCTTGAGT
*
66399 GAGATAAAATCT-TCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTCT-TCTTTCAAGGAAAAACAATCTTGAGT
*
66439 GAGATAAAATCT-TCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTCT-TCTTTCAAGGAAAAACAATCTTGAGT
*
66479 GAGATAAAATCT-TCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTCT-TCTTTCAAGGAAAAACAATCTTGAGT
* * * * * * **
66519 AAAATGAAATGTCTTCTTTCAA-GTAAAACAGTCTCAAGT
1 GAGATAAAATCTCTTCTTTCAAGGAAAAACAATCTTGAGT
66558 GAGATA
1 GAGATA
66564 GAGTCTGTTT
Statistics
Matches: 369, Mismatches: 30, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
39 18 0.05
40 348 0.94
41 3 0.01
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (40 bp):
GAGATAAAATCTCTTCTTTCAAGGAAAAACAATCTTGAGT
Found at i:66539 original size:80 final size:79
Alignment explanation
Indices: 66135--66563 Score: 562
Period size: 80 Copynumber: 5.4 Consensus size: 79
66125 AAATCTCCTA
* * *
66135 TTTCGAGGAAAACCAATCTTGAGTGAGATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAATG
1 TTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAATG
66200 AGATAAA-ATCTTC
66 AGATAAATATCTTC
* * *
66213 TGTTTCAAGGAAAATCAATCTTGAGTGAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGAC
1 --TTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAA
*
66278 TGAGATAAA-ATCTTATG
64 TGAGATAAATATC-T-TC
* *
66295 TTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTTTGTTTCAAGGAAAAGCAATCTTGAATG
1 TTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAATG
* *
66360 AAATAAA-ATCTTATG
66 AGATAAATATC-T-TC
*
66375 TTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTG
1 TTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAATG
66440 AGATAAA-ATCTTC
66 AGATAAATATCTTC
*
66453 TGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAG
1 --TTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAA
* * *
66518 TAAAATGAAATGTCTTC
64 TGAGAT-AAATATCTTC
* * **
66535 TTTCAA-GTAAAACAGTCTCAAGTGAGATA
1 TTTCAAGGAAAAACAATCTTGAGTGAGATA
66564 GAGTCTGTTT
Statistics
Matches: 322, Mismatches: 21, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
78 1 0.00
79 20 0.06
80 291 0.90
81 4 0.01
82 6 0.02
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.31
Consensus pattern (79 bp):
TTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAATG
AGATAAATATCTTC
Done.