Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006973.1 Hibiscus syriacus cultivar Beakdansim tig00017959_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: 138769
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2198 original size:12 final size:12
Alignment explanation
Indices: 2181--2206 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2171 TGAATTAGTG
2181 ATGTTAATTTCA
1 ATGTTAATTTCA
2193 ATGTTAATTTCA
1 ATGTTAATTTCA
2205 AT
1 AT
2207 TATCATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.50
Consensus pattern (12 bp):
ATGTTAATTTCA
Found at i:5303 original size:27 final size:26
Alignment explanation
Indices: 5264--5386 Score: 77
Period size: 29 Copynumber: 4.4 Consensus size: 26
5254 ATTAACAATA
*
5264 TTTTATATCTTAAATATATATTTTATT
1 TTTTAT-TATTAAATATATATTTTATT
*
5291 TTTTACTTATTAAATATATTTCATTTT-TA
1 TTTTA-TTATTAAATATA--T-ATTTTATT
* *
5320 TTTTAATATAAAAATATATATTTTATAT
1 TTTTATTAT-TAAATATATATTTTAT-T
* * *
5348 TTATAATCACTTAAATATATCTTTTATT
1 TT-TTATTA-TTAAATATATATTTTATT
*
5376 TTATTTTTATT
1 TT-TTATTATT
5387 TATTAAATAT
Statistics
Matches: 74, Mismatches: 13, Indels: 18
0.70 0.12 0.17
Matches are distributed among these distances:
26 5 0.07
27 19 0.26
28 13 0.18
29 31 0.42
30 6 0.08
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (26 bp):
TTTTATTATTAAATATATATTTTATT
Found at i:16471 original size:57 final size:58
Alignment explanation
Indices: 16394--16556 Score: 204
Period size: 57 Copynumber: 2.8 Consensus size: 58
16384 AATTGTTGTT
* * * * *
16394 AGGTGATATTCTGGGAAATATTTCGATAAAGGTGACATTTTTGGAATTATTTTGTAAA
1 AGGTGACATTCTGGGAAATATTTCAAAAAAGGTGACATTTTGGGAATTATTTTATAAA
* * *
16452 A-GTGACATTATGGGAAATATTTCAAAAAAGGTAACATATTGGGAATTATTTTATAAA
1 AGGTGACATTCTGGGAAATATTTCAAAAAAGGTGACATTTTGGGAATTATTTTATAAA
* * *
16509 AGGTGACACTCTGGGAATTATATT-AAAAAAAGTGACATTTTGGGAATT
1 AGGTGACATTCTGGGAAATAT-TTCAAAAAAGGTGACATTTTGGGAATT
16557 TTCAAATGTT
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
57 49 0.55
58 38 0.43
59 2 0.02
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (58 bp):
AGGTGACATTCTGGGAAATATTTCAAAAAAGGTGACATTTTGGGAATTATTTTATAAA
Found at i:16526 original size:29 final size:29
Alignment explanation
Indices: 16394--16556 Score: 150
Period size: 29 Copynumber: 5.7 Consensus size: 29
16384 AATTGTTGTT
* * * *
16394 AGGTGATATTCTGGGAAATATTTCGAT-AA
1 AGGTGACATTTTGGGAATTATTT-TATAAA
* *
16423 AGGTGACATTTTTGGAATTATTTTGTAAA
1 AGGTGACATTTTGGGAATTATTTTATAAA
* * * *
16452 A-GTGACATTATGGGAAATATTTCAAAAA
1 AGGTGACATTTTGGGAATTATTTTATAAA
* *
16480 AGGTAACATATTGGGAATTATTTTATAAA
1 AGGTGACATTTTGGGAATTATTTTATAAA
* * * *
16509 AGGTGACACTCTGGGAATTATATTAAAAA
1 AGGTGACATTTTGGGAATTATTTTATAAA
*
16538 AAGTGACATTTTGGGAATT
1 AGGTGACATTTTGGGAATT
16557 TTCAAATGTT
Statistics
Matches: 105, Mismatches: 27, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
28 23 0.22
29 82 0.78
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (29 bp):
AGGTGACATTTTGGGAATTATTTTATAAA
Found at i:23022 original size:29 final size:28
Alignment explanation
Indices: 22990--23112 Score: 138
Period size: 29 Copynumber: 4.3 Consensus size: 28
22980 AATTGTTGTT
*
22990 AGGTGATATTTTGGGAAATATTTCGATAA
1 AGGTGACATTTTGGGAAATATTTCG-TAA
* *
23019 AGGTGACATTTTGGGAATTATTTTGTAA
1 AGGTGACATTTTGGGAAATATTTCGTAA
* * *
23047 AGGTGACATTATAGGAAATATTTCGAAAA
1 AGGTGACATTTTGGGAAATATTTCG-TAA
* * *
23076 AGGTAACATATTGGGAATTATTTCGTAAA
1 AGGTGACATTTTGGGAAATATTTCGT-AA
23105 AGGTGACA
1 AGGTGACA
23113 CTCAAGGAAT
Statistics
Matches: 77, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
28 24 0.31
29 53 0.69
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.34
Consensus pattern (28 bp):
AGGTGACATTTTGGGAAATATTTCGTAA
Found at i:23064 original size:57 final size:58
Alignment explanation
Indices: 23003--23151 Score: 196
Period size: 57 Copynumber: 2.6 Consensus size: 58
22993 TGATATTTTG
* * *
23003 GGAAATATTTCGATAAAGGTGACATTTTGGGAATTATTTTGT-AAAGGTGACA-TTATA
1 GGAAATATTTCGAAAAAGGTGACATTTTGGGAATTATTTCGTAAAAGGTGACACTCA-A
* *
23060 GGAAATATTTCGAAAAAGGTAACATATTGGGAATTATTTCGTAAAAGGTGACACTCAA
1 GGAAATATTTCGAAAAAGGTGACATTTTGGGAATTATTTCGTAAAAGGTGACACTCAA
* * *
23118 GGAATTATTT-TAAAAAAGTGACATTTTGGGAATT
1 GGAAATATTTCGAAAAAGGTGACATTTTGGGAATT
23152 TTCAAATGTT
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
57 58 0.73
58 20 0.25
59 2 0.03
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (58 bp):
GGAAATATTTCGAAAAAGGTGACATTTTGGGAATTATTTCGTAAAAGGTGACACTCAA
Found at i:23121 original size:29 final size:28
Alignment explanation
Indices: 23003--23127 Score: 103
Period size: 29 Copynumber: 4.4 Consensus size: 28
22993 TGATATTTTG
* * *
23003 GGAAATATTTCG-ATAAAGGTGACATTTTG
1 GGAATTATTTCGTA-AAAGGTGACA-TATA
*
23032 GGAATTATTTTGT-AAAGGTGACATTATA
1 GGAATTATTTCGTAAAAGGTGACA-TATA
* * * *
23060 GGAAATATTTCGAAAAAGGTAACATATTG
1 GGAATTATTTCGTAAAAGGTGACATA-TA
23089 GGAATTATTTCGTAAAAGGTGACACTCA-A
1 GGAATTATTTCGTAAAAGGTGACA-T-ATA
23118 GGAATTATTT
1 GGAATTATTT
23128 TAAAAAAGTG
Statistics
Matches: 78, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
28 25 0.32
29 51 0.65
30 1 0.01
31 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.34
Consensus pattern (28 bp):
GGAATTATTTCGTAAAAGGTGACATATA
Found at i:27189 original size:2 final size:2
Alignment explanation
Indices: 27184--27210 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
27174 TTCGTGTGTG
27184 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
27211 GCGTGTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29146 original size:34 final size:34
Alignment explanation
Indices: 29103--29175 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
29093 GGATACCTTG
29103 AATTTAGGTGGATTCTTGTTCACAATTATAATGA
1 AATTTAGGTGGATTCTTGTTCACAATTATAATGA
29137 AATTTAGGTGGATTCTTGTTCACAATTATAATGA
1 AATTTAGGTGGATTCTTGTTCACAATTATAATGA
29171 AATTT
1 AATTT
29176 TTATTCAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.42
Consensus pattern (34 bp):
AATTTAGGTGGATTCTTGTTCACAATTATAATGA
Found at i:35793 original size:20 final size:20
Alignment explanation
Indices: 35765--35807 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
35755 ATATAAAACA
35765 TTAT-TTTTTATTAAATATTT
1 TTATATTTTTATTAAAT-TTT
*
35785 TTATATTTTTATTTAATTTT
1 TTATATTTTTATTAAATTTT
35805 TTA
1 TTA
35808 AATAATTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTATATTTTTATTAAATTTT
Found at i:36000 original size:88 final size:86
Alignment explanation
Indices: 35859--36117 Score: 378
Period size: 88 Copynumber: 3.0 Consensus size: 86
35849 GGTTCGATCG
*
35859 GTTGAACCAGTGAACCGATAACATGACCGGTTCGCTAACTGGTCCGGTTCTGAAAACATGCATTC
1 GTTGAACCAGTGAACCGATAACATGACCAGTTCGCTAACT-GTCCGGTTCTGAAAACATGCATTC
35924 AACGCCACATACTTTTTCGACC
65 AACGCCACATACTTTTTCGACC
* *
35946 AGTTGAACCAGTGAATCGATAACATGACCAGTTCGCTAACTAGTCCGGTTCTGAAAACATACATT
1 -GTTGAACCAGTGAACCGATAACATGACCAGTTCGCTAACT-GTCCGGTTCTGAAAACATGCATT
*
36011 CAATGCCACATA-TTTTTCCGACC
64 CAACGCCACATACTTTTT-CGACC
* * *
36034 GATTGAACCAATAAACCGATAACATG-CCTAATTCGCTAACTGATCCGGTTCTGAAAACATGCAT
1 G-TTGAACCAGTGAACCGATAACATGACC-AGTTCGCTAACTG-TCCGGTTCTGAAAACATGCAT
36098 TCAACGCCACATACTTTTTC
63 TCAACGCCACATACTTTTTC
36118 CCAGTCAAAA
Statistics
Matches: 155, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
87 9 0.06
88 141 0.91
89 5 0.03
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (86 bp):
GTTGAACCAGTGAACCGATAACATGACCAGTTCGCTAACTGTCCGGTTCTGAAAACATGCATTCA
ACGCCACATACTTTTTCGACC
Found at i:36877 original size:18 final size:19
Alignment explanation
Indices: 36842--36878 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
36832 TACGGAATGT
36842 AAGATTACCAGTGAGAATAA
1 AAGATTACCAG-GAGAATAA
36862 AAGATTACCA-GAGAATA
1 AAGATTACCAGGAGAATA
36879 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGAGAATAA
Found at i:38417 original size:14 final size:14
Alignment explanation
Indices: 38400--38438 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
38390 CATAAAATAT
*
38400 AATTCATTTTTCAA
1 AATTCATTTTCCAA
* *
38414 AATTCATTGTCCGA
1 AATTCATTTTCCAA
38428 AATTCATTTTC
1 AATTCATTTTC
38439 AATGAATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.18, G:0.05, T:0.46
Consensus pattern (14 bp):
AATTCATTTTCCAA
Found at i:38720 original size:323 final size:318
Alignment explanation
Indices: 38135--38767 Score: 1158
Period size: 323 Copynumber: 2.0 Consensus size: 318
38125 ACGCCACTTG
38135 TTTTTGAGAGGGAGAAGAGATATAAAAATTGACAAAATAATAAAATCTTAACTCAAAAATTGAAA
1 TTTTTGAGAGGGAGAAGAGATATAAAAATTGACAAAATAATAAAATCTTAACTCAAAAATTGAAA
* *
38200 AAAACTAAAAATATATACATTTTTACAAAAATAACTTTAAAAAAAGTAAATAACAATAAATATAT
66 AAAACTAAAAATATATACATTTTAACAAAAATAACTTTAAAAAAAGTAAATAACAAGAAATATAT
38265 AAAAATAAATACATTTAAAAAAAAATAGATCTTGTAAATTATTTTAAAAAAATTAATTAAACAGT
131 AAAAATAAATACATTTAAAAAAAAATAGATCTTGTAAATTATTTTAAAAAAATTAATTAAACAGT
38330 GTAAAACATTTTACAATACAACATTCAAATAATGTAAAATATTTTCTGAAAAATAATTTACATAA
196 GTAAAACATTTTACAATACAACATTCAAATAATGTAAAATATTTTCTGAAAAATAATTTACATAA
38395 AATATAATTCATTTTTCAAAATTCATTGTCCGAAATTCATTTTCAATGAATATATACA
261 AATATAATTCATTTTTCAAAATTCATTGTCCGAAATTCATTTTCAATGAATATATACA
38453 TTTTTGAGAGGGAGAAGAGATATAAAAATTGACAAAATAATAAAATCTTAACTCAAAAATTGAAA
1 TTTTTGAGAGGGAGAAGAGATATAAAAATTGACAAAATAATAAAATCTTAACTCAAAAATTGAAA
*
38518 AAAATTAAAAATATATACATTTTAACAAAAAAATAACTTTTAAAAAAAGTAAATAACAAGAAATA
66 AAAACTAAAAATATATACATTTTAAC--AAAAATAAC-TTTAAAAAAAGTAAATAACAAGAAATA
**
38583 TATAAAAATAAATACATTTTTCAAAAAAATAGATCTTGTAAATTATTTTAAAAAAAATTAATTAA
128 TATAAAAATAAATACA-TTTAAAAAAAAATAGATCTTGTAAATTATTTT-AAAAAAATTAATTAA
*
38648 ACAGTGTAAAACATTTTACAATACAACATTCAAATAATGTAAAATATTTTCTGAAAAATGATTTA
191 ACAGTGTAAAACATTTTACAATACAACATTCAAATAATGTAAAATATTTTCTGAAAAATAATTTA
*
38713 CATAAAATGTAATTCATTTTTCAAAATTCATTGTCCGAAATTCATTTTCAATGAA
256 CATAAAATATAATTCATTTTTCAAAATTCATTGTCCGAAATTCATTTTCAATGAA
38768 ACAAACAGAC
Statistics
Matches: 303, Mismatches: 7, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
318 89 0.29
320 9 0.03
321 42 0.14
322 30 0.10
323 133 0.44
ACGTcount: A:0.52, C:0.08, G:0.07, T:0.32
Consensus pattern (318 bp):
TTTTTGAGAGGGAGAAGAGATATAAAAATTGACAAAATAATAAAATCTTAACTCAAAAATTGAAA
AAAACTAAAAATATATACATTTTAACAAAAATAACTTTAAAAAAAGTAAATAACAAGAAATATAT
AAAAATAAATACATTTAAAAAAAAATAGATCTTGTAAATTATTTTAAAAAAATTAATTAAACAGT
GTAAAACATTTTACAATACAACATTCAAATAATGTAAAATATTTTCTGAAAAATAATTTACATAA
AATATAATTCATTTTTCAAAATTCATTGTCCGAAATTCATTTTCAATGAATATATACA
Found at i:38740 original size:14 final size:14
Alignment explanation
Indices: 38723--38761 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
38713 CATAAAATGT
*
38723 AATTCATTTTTCAA
1 AATTCATTTTCCAA
* *
38737 AATTCATTGTCCGA
1 AATTCATTTTCCAA
38751 AATTCATTTTC
1 AATTCATTTTC
38762 AATGAAACAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.18, G:0.05, T:0.46
Consensus pattern (14 bp):
AATTCATTTTCCAA
Found at i:53178 original size:35 final size:36
Alignment explanation
Indices: 53132--53202 Score: 135
Period size: 35 Copynumber: 2.0 Consensus size: 36
53122 TCACTTATTC
53132 ACTTGGGTAAAATAAGAATAAAATTAAAAAA-AATA
1 ACTTGGGTAAAATAAGAATAAAATTAAAAAATAATA
53167 ACTTGGGTAAAATAAGAATAAAATTAAAAAATAATA
1 ACTTGGGTAAAATAAGAATAAAATTAAAAAATAATA
53203 TAAAAAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 31 0.89
36 4 0.11
ACGTcount: A:0.62, C:0.03, G:0.11, T:0.24
Consensus pattern (36 bp):
ACTTGGGTAAAATAAGAATAAAATTAAAAAATAATA
Found at i:53194 original size:17 final size:17
Alignment explanation
Indices: 53139--53195 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
53129 TTCACTTGGG
53139 TAAAATAAGAATAAAAT
1 TAAAATAAGAATAAAAT
**
53156 TAAAA-AA-AATAACTT
1 TAAAATAAGAATAAAAT
53171 GGGTAAAATAAGAATAAAAT
1 ---TAAAATAAGAATAAAAT
53191 TAAAA
1 TAAAA
53196 AATAATATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
15 6 0.19
16 2 0.06
17 10 0.32
18 5 0.16
19 2 0.06
20 6 0.19
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.23
Consensus pattern (17 bp):
TAAAATAAGAATAAAAT
Found at i:69592 original size:22 final size:22
Alignment explanation
Indices: 69567--69629 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 22
69557 GCAACGCGAT
69567 TTTGAAAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGAGAG
*
69589 TTTGAAAAACGTGTTGTTGCGATAG
1 TTTGAAAAA--TG-TGTTGCGAGAG
69614 --TGAAAAA-GTGTTGCGA
1 TTTGAAAAATGTGTTGCGA
69630 TAGTGAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
19 8 0.22
20 1 0.03
22 9 0.24
23 7 0.19
24 2 0.05
25 10 0.27
ACGTcount: A:0.32, C:0.06, G:0.30, T:0.32
Consensus pattern (22 bp):
TTTGAAAAATGTGTTGCGAGAG
Found at i:69627 original size:19 final size:19
Alignment explanation
Indices: 69603--69639 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
69593 AAAAACGTGT
69603 TGTTGCGATAGTGAAAAAG
1 TGTTGCGATAGTGAAAAAG
69622 TGTTGCGATAGTGAAAAA
1 TGTTGCGATAGTGAAAAA
69640 TCCAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (19 bp):
TGTTGCGATAGTGAAAAAG
Found at i:70088 original size:40 final size:40
Alignment explanation
Indices: 70033--70120 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 40
70023 TCATTGCGAT
70033 TTTGGAAAATCGCAACGCGAACTTAGACTACCGCAACGAA
1 TTTGGAAAATCGCAACGCGAACTTAGACTACCGCAACGAA
* * * * *
70073 TTTGGAAAATTGCAACGCGAACTTGGATTATCGTAACGAA
1 TTTGGAAAATCGCAACGCGAACTTAGACTACCGCAACGAA
70113 TTTGGAAA
1 TTTGGAAA
70121 GAGATAATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (40 bp):
TTTGGAAAATCGCAACGCGAACTTAGACTACCGCAACGAA
Found at i:70098 original size:21 final size:21
Alignment explanation
Indices: 70034--70099 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
70024 CATTGCGATT
70034 TTGGAAAATCGCAACGCGAAC
1 TTGGAAAATCGCAACGCGAAC
* ** * *
70055 TTAGACTACCGCAA--CGAAT
1 TTGGAAAATCGCAACGCGAAC
*
70074 TTGGAAAATTGCAACGCGAAC
1 TTGGAAAATCGCAACGCGAAC
70095 TTGGA
1 TTGGA
70100 TTATCGTAAC
Statistics
Matches: 32, Mismatches: 11, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
19 13 0.41
21 19 0.59
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (21 bp):
TTGGAAAATCGCAACGCGAAC
Found at i:70337 original size:21 final size:21
Alignment explanation
Indices: 70286--70338 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
70276 ATTATGACTA
*
70286 TCGCAATGCGATTTTATAATT
1 TCGCAATGCGATTTTACAATT
** *
70307 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-ACAATT
70328 TCGCAATGCGA
1 TCGCAATGCGA
70339 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTACAATT
Found at i:70353 original size:20 final size:21
Alignment explanation
Indices: 70328--70379 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
70318 TTTTCCCAAT
*
70328 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
70348 TCGCAATACGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
70369 TCGCAATGCGA
1 TCGCAATGCGA
70380 TACTAACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:70393 original size:20 final size:20
Alignment explanation
Indices: 70368--70445 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
70358 AATTTGGAAA
* * *
70368 ATCGCAATGCGATACTAACT
1 ATCGCAACGCGATTCTGACT
70388 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
70408 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
70428 TTCGCAACGAGATTCTGA
1 ATCGCAACGCGATTCTGA
70446 AAATCACAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:70674 original size:20 final size:20
Alignment explanation
Indices: 70652--70829 Score: 329
Period size: 20 Copynumber: 8.9 Consensus size: 20
70642 ATTCATTTGA
* *
70652 CTATCGCAACGTGAAAATGA
1 CTATCGCAACGCGAAAATGG
70672 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
70692 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
70712 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
70732 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
70752 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
70772 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
70792 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
70812 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
70830 TGCGATTTTC
Statistics
Matches: 155, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 155 1.00
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:70859 original size:20 final size:20
Alignment explanation
Indices: 70834--70911 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
70824 GAAAATTGCG
* *
70834 ATTTTCTCGTTGCGATATCC
1 ATTTTCGCGTTGCGATAGCC
70854 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
70874 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGCC
* *
70894 AGTTTCGTGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
70912 TCTGTTTTGC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.15, C:0.21, G:0.24, T:0.40
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:72517 original size:40 final size:42
Alignment explanation
Indices: 72464--72553 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
72454 CCTGTTCAAC
72464 GATGACAGAGGCCTCTTGAACG-GTGG-GGGGACTCTTGAGG
1 GATGACAGAGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* * *
72504 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGAGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
72546 GATGACAG
1 GATGACAG
72554 GTGAGTCGGG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 20 0.45
41 3 0.07
42 21 0.48
ACGTcount: A:0.22, C:0.16, G:0.41, T:0.21
Consensus pattern (42 bp):
GATGACAGAGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:72519 original size:21 final size:21
Alignment explanation
Indices: 72490--72550 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
72480 TGAACGGTGG
*
72490 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
72511 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
72532 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
72551 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:72917 original size:20 final size:20
Alignment explanation
Indices: 72892--72930 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
72882 GAAGAATAGT
*
72892 TTACTTTTGCAACACGAAAC
1 TTACTTTCGCAACACGAAAC
*
72912 TTACTTTCGCAACGCGAAA
1 TTACTTTCGCAACACGAAA
72931 ATGACTATCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAC
Found at i:72982 original size:14 final size:14
Alignment explanation
Indices: 72960--73018 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
72950 TTGTGTTTCG
* *
72960 CGTTACGATTTTGT
1 CGTTGCGATTTTTT
72974 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TTT
72991 CGCATTGCGATTTTTT
1 CG--TTGCGATTTTTT
73007 CGTTGCGATTTT
1 CGTTGCGATTTT
73019 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 17 0.45
15 3 0.08
16 5 0.13
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.12, C:0.17, G:0.20, T:0.51
Consensus pattern (14 bp):
CGTTGCGATTTTTT
Found at i:72992 original size:33 final size:33
Alignment explanation
Indices: 72955--73034 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
72945 GCGATTTGTG
*
72955 TTTCGCGTTACGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTACGATTTTGTCGTTGCGATTTTCA
* *
72988 TTTCGCATTGCGATTTTTTCGTTGCGATTTTCA
1 TTTCGCATTACGATTTTGTCGTTGCGATTTTCA
*
73021 TTTCGCATTGCGAT
1 TTTCGCATTACGAT
73035 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.12, C:0.19, G:0.20, T:0.49
Consensus pattern (33 bp):
TTTCGCATTACGATTTTGTCGTTGCGATTTTCA
Found at i:73000 original size:19 final size:19
Alignment explanation
Indices: 72976--73034 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 19
72966 GATTTTGTCG
72976 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
72995 TTGCGA-TTT--TTTCG--
1 TTGCGATTTTCATTTCGCA
73009 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
73028 TTGCGAT
1 TTGCGAT
73035 AGCCATTTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 6 0.17
15 3 0.09
16 5 0.14
17 5 0.14
18 3 0.09
19 13 0.37
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:73041 original size:19 final size:20
Alignment explanation
Indices: 73019--73062 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
73009 TTGCGATTTT
73019 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
* *
73038 CATTTCCGCATTGTGATAGT
1 CATTTCCGCATTGCGATAGC
73058 CATTT
1 CATTT
73063 TCGTGTTGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:73624 original size:18 final size:18
Alignment explanation
Indices: 73577--73624 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
73567 CGGGTCGATC
*
73577 AGGTGATGTCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
73595 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
73613 AGGTGATGGCTC
1 AGGTGATGGCTC
73625 CCGAAGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.15, C:0.12, G:0.44, T:0.29
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:74993 original size:20 final size:20
Alignment explanation
Indices: 74946--75003 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
74936 ATAGTTTCTA
* *
74946 AAAATGAAAATCGCAACACG
1 AAAATGACAATCGCAACGCG
74966 AAAATGACAATCGCAACGCG
1 AAAATGACAATCGCAACGCG
** *
74986 AATTTGACTATCGCAACG
1 AAAATGACAATCGCAACG
75004 AGAGAATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.45, C:0.22, G:0.17, T:0.16
Consensus pattern (20 bp):
AAAATGACAATCGCAACGCG
Found at i:75611 original size:20 final size:20
Alignment explanation
Indices: 75497--75610 Score: 149
Period size: 20 Copynumber: 5.7 Consensus size: 20
75487 GATTATGTAT
*
75497 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
75517 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
75537 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
75557 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
75578 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
75598 TATCGCGTTGCGA
1 TATCGCGTTGCGA
75611 TTTTCCAAAT
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
19 3 0.04
20 64 0.77
21 14 0.17
22 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:75614 original size:41 final size:41
Alignment explanation
Indices: 75477--75612 Score: 195
Period size: 41 Copynumber: 3.3 Consensus size: 41
75467 CGCTTTGAAA
* *
75477 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* *
75518 ATCGCGTTGCGA--AAGTAAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* *
75558 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
75599 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
75613 TTCCAAATTC
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
39 3 0.04
40 33 0.39
41 46 0.55
42 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (41 bp):
ATCGCGTTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:75630 original size:41 final size:41
Alignment explanation
Indices: 75504--75651 Score: 140
Period size: 41 Copynumber: 3.6 Consensus size: 41
75494 TATTATCTCG
* *** * * *
75504 TTGCGAAAGTCAGTATCGCGTTGCGAAAGT-AAGTATCGCG
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTCAAATATCACA
* ** * * *
75544 TTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATTATCGCG
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTCAAATATCACA
75585 TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAAT-TCACA
1 TTGCGATAGTCAGTATCGCGTTGCGATTTT-CAAATATCACA
75626 TTGCGATAGTCA-TAATCGCGTTGCGA
1 TTGCGATAGTCAGT-ATCGCGTTGCGA
75652 ATCTGGAAAC
Statistics
Matches: 94, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
40 28 0.30
41 64 0.68
42 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.32
Consensus pattern (41 bp):
TTGCGATAGTCAGTATCGCGTTGCGATTTTCAAATATCACA
Found at i:75832 original size:21 final size:21
Alignment explanation
Indices: 75806--76018 Score: 204
Period size: 21 Copynumber: 10.4 Consensus size: 21
75796 CATTTGGAAA
*
75806 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
*
75827 ATCGCAACGTGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* **
75848 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTGGACT
*
75867 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
* * **
75888 ATCACAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTGGACT
* *
75907 ATCGCAACACGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
* *
75928 ATCGCAATGTGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* **
75949 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTGGACT
*
75968 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
**
75989 ATCGCAACATGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
76010 ATCGCAACG
1 ATCGCAACG
76019 AATTTGGACT
Statistics
Matches: 150, Mismatches: 36, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
19 44 0.29
21 106 0.71
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:75919 original size:61 final size:61
Alignment explanation
Indices: 75802--76026 Score: 265
Period size: 61 Copynumber: 3.7 Consensus size: 61
75792 TTCTCATTTG
* ** * *
75802 GAAAATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGC-A-ACGAATTTG
1 GAAAATCGCAACGCGAACTTCGACTATCGCAAC--GAATTTGGAAAATCGCAACACGAACTTC
*
75863 GAAAATCGCAACGCGAACTTCGACTATCACAACGAATTTGGAAAATCGCAACACGAACTTC
1 GAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACACGAACTTC
** * * * *
75924 GACTATCGCAATGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
1 GAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACACGAACTTC
** ** *
75985 GACTATCGCAACATGAACTTGGACTATCGCAACGAATTTGGA
1 GAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGA
76027 CTAACGTAAA
Statistics
Matches: 147, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
59 13 0.09
60 1 0.01
61 133 0.90
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (61 bp):
GAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACACGAACTTC
Found at i:75972 original size:101 final size:101
Alignment explanation
Indices: 75797--75996 Score: 373
Period size: 101 Copynumber: 2.0 Consensus size: 101
75787 TTATTTTCTC
*
75797 ATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACGAATTT
1 ATTTGGAAAATCGCAACACGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACGAATTT
75862 GGAAAATCGCAACGCGAACTTCGACTATCACAACGA
66 GGAAAATCGCAACGCGAACTTCGACTATCACAACGA
*
75898 ATTTGGAAAATCGCAACACGAACTTCGACTATCGCAATGTGAACTTGGACTATCGCAACGAATTT
1 ATTTGGAAAATCGCAACACGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACGAATTT
*
75963 GGAAAATCGCAACGCGAACTTCGACTATCGCAAC
66 GGAAAATCGCAACGCGAACTTCGACTATCACAAC
75997 ATGAACTTGG
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 96 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.21
Consensus pattern (101 bp):
ATTTGGAAAATCGCAACACGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACGAATTT
GGAAAATCGCAACGCGAACTTCGACTATCACAACGA
Found at i:76020 original size:101 final size:99
Alignment explanation
Indices: 75799--76029 Score: 345
Period size: 101 Copynumber: 2.3 Consensus size: 99
75789 ATTTTCTCAT
75799 TTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTGG
1 TTGGAAAATCGCAA--CGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTGG
*
75864 AAAATCGCAACGCGAACTTCGACTATCACAACGAAT
64 AAAATCGCAACGCGAACTTCGACTATCACAACGAAC
*
75900 TTGGAAAATCGCAACACGAACTTCGACTATCGCAATGTGAACTTGGACTATCGCAACGAATTTGG
1 TTGGAAAATCGC-A-ACGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTGG
*
75965 AAAATCGCAACGCGAACTTCGACTATCGCAACATGAAC
64 AAAATCGCAACGCGAACTTCGACTATCACAAC--GAAC
** * *
76003 TTGGACTATCGCAACGAATTTGGACTA
1 TTGGAAAATCGCAACGAACTTCGACTA
76030 ACGTAAATTT
Statistics
Matches: 119, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
101 103 0.87
102 2 0.02
103 14 0.12
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (99 bp):
TTGGAAAATCGCAACGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAA
AATCGCAACGCGAACTTCGACTATCACAACGAAC
Found at i:76029 original size:40 final size:40
Alignment explanation
Indices: 75823--76029 Score: 202
Period size: 40 Copynumber: 5.1 Consensus size: 40
75813 CGCGAACTTC
**
75823 GACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTG
1 GACTATCGCAACACGAACTTGGACTATCGCAACGAATTTG
** * * *
75863 GAAAATCGCAACGCGAACTTCGACTATCACAACGAATTTG
1 GACTATCGCAACACGAACTTGGACTATCGCAACGAATTTG
** * * *
75903 GAAAATCGCAACACGAACTTCGACTATCGCAATGTGAACTTG
1 GACTATCGCAACACGAACTTGGACTATCGCAA--CGAATTTG
* ** * *
75945 GACTATCGC-A-ACGAATTTGGAAAATCGCAACGCGAACTTC
1 GACTATCGCAACACGAACTTGGACTATCGCAA--CGAATTTG
*
75985 GACTATCGCAACATGAACTTGGACTATCGCAACGAATTTG
1 GACTATCGCAACACGAACTTGGACTATCGCAACGAATTTG
76025 GACTA
1 GACTA
76030 ACGTAAATTT
Statistics
Matches: 139, Mismatches: 24, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
40 108 0.78
41 2 0.01
42 29 0.21
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (40 bp):
GACTATCGCAACACGAACTTGGACTATCGCAACGAATTTG
Found at i:76536 original size:20 final size:19
Alignment explanation
Indices: 76511--76578 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
76501 AGCTAAAATA
76511 TCGAAACTTTAGGAAAAGTT
1 TCGAAACTTT-GGAAAAGTT
*
76531 TCGAAACTTTGAGATAA-TT
1 TCGAAACTTTG-GAAAAGTT
* *
76550 TTGAAACTCTT-GAAAAGTA
1 TCGAAACT-TTGGAAAAGTT
76569 TCGAAACTTT
1 TCGAAACTTT
76579 TTGGAAATTG
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
18 6 0.15
19 18 0.45
20 16 0.40
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (19 bp):
TCGAAACTTTGGAAAAGTT
Found at i:83131 original size:18 final size:18
Alignment explanation
Indices: 83086--83143 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
83076 TGGGTTTAGG
* *
83086 TTTTCAAAAATTTGATGTTA
1 TTTTAAAAAATTT-AT-TTT
*
83106 TTTCAAAAAATTTATTTT
1 TTTTAAAAAATTTATTTT
* *
83124 TTTTAAAATATATATTTT
1 TTTTAAAAAATTTATTTT
83142 TT
1 TT
83144 AATTCTTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 19 0.59
19 2 0.06
20 11 0.34
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.57
Consensus pattern (18 bp):
TTTTAAAAAATTTATTTT
Found at i:83141 original size:16 final size:16
Alignment explanation
Indices: 83112--83145 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
83102 GTTATTTCAA
* *
83112 AAAATTTATTTTTTTT
1 AAAATATATATTTTTT
83128 AAAATATATATTTTTT
1 AAAATATATATTTTTT
83144 AA
1 AA
83146 TTCTTTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AAAATATATATTTTTT
Found at i:83722 original size:21 final size:22
Alignment explanation
Indices: 83698--83744 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
83688 GGTAAAAAAA
*
83698 TTTACATAAAACATT-ATTTTT
1 TTTACATAAAACATTAATATTT
*
83719 TTTACCTAAAACATTAATATTT
1 TTTACATAAAACATTAATATTT
83741 TTTA
1 TTTA
83745 ACATTTCCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTACATAAAACATTAATATTT
Found at i:86601 original size:23 final size:23
Alignment explanation
Indices: 86575--86619 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
86565 CACCACAGCT
*
86575 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
86598 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
86620 ATATAATAAT
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:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:87331 original size:21 final size:21
Alignment explanation
Indices: 87307--87349 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
87297 TTCATATTCG
* *
87307 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
87328 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
87349 T
1 T
87350 AGCCCCGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:94141 original size:21 final size:21
Alignment explanation
Indices: 94117--94159 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
94107 TTCATATTCG
* *
94117 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
94138 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
94159 T
1 T
94160 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:99468 original size:13 final size:13
Alignment explanation
Indices: 99450--99498 Score: 55
Period size: 12 Copynumber: 3.7 Consensus size: 13
99440 TATTGATTAT
99450 AAAATTATATATA
1 AAAATTATATATA
*
99463 AAAATTAT-TATT
1 AAAATTATATATA
*
99475 AAAATTATACTTTTA
1 AAAATTATA--TATA
99490 AAAATTATA
1 AAAATTATA
99499 AAAAATTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 11 0.37
13 8 0.27
15 11 0.37
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (13 bp):
AAAATTATATATA
Found at i:99475 original size:27 final size:27
Alignment explanation
Indices: 99439--99497 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 27
99429 ATAAAGCGTC
99439 TTATTGATTATAAAATTATA-TATAAAAA
1 TTATTGA-T-TAAAATTATACTATAAAAA
*
99467 TTATT-ATTAAAATTATACTTTTAAAAA
1 TTATTGATTAAAATTATAC-TATAAAAA
99494 TTAT
1 TTAT
99498 AAAAAATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 10 0.36
26 1 0.04
27 12 0.43
28 5 0.18
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (27 bp):
TTATTGATTAAAATTATACTATAAAAA
Found at i:101767 original size:22 final size:22
Alignment explanation
Indices: 101740--101786 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
101730 ATTTTTAATA
101740 AAAAATATATAGGAAA-AATTTT
1 AAAAATATATA-GAAATAATTTT
*
101762 AAAAATATATATAAATAATTTT
1 AAAAATATATAGAAATAATTTT
101784 AAA
1 AAA
101787 TTTTCAAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (22 bp):
AAAAATATATAGAAATAATTTT
Found at i:104060 original size:79 final size:79
Alignment explanation
Indices: 103969--104127 Score: 309
Period size: 79 Copynumber: 2.0 Consensus size: 79
103959 GGTATTTGTT
*
103969 TTATTTATATATTGCAATAGACTTCAAGATGACCAACGTACTTGTGGAGTATGACGATATAATAC
1 TTATTTATATATTGCAATAGACTCCAAGATGACCAACGTACTTGTGGAGTATGACGATATAATAC
104034 TTAGGTTTTCTAGG
66 TTAGGTTTTCTAGG
104048 TTATTTATATATTGCAATAGACTCCAAGATGACCAACGTACTTGTGGAGTATGACGATATAATAC
1 TTATTTATATATTGCAATAGACTCCAAGATGACCAACGTACTTGTGGAGTATGACGATATAATAC
104113 TTAGGTTTTCTAGG
66 TTAGGTTTTCTAGG
104127 T
1 T
104128 GTTTCCAGAA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.36
Consensus pattern (79 bp):
TTATTTATATATTGCAATAGACTCCAAGATGACCAACGTACTTGTGGAGTATGACGATATAATAC
TTAGGTTTTCTAGG
Found at i:109180 original size:29 final size:28
Alignment explanation
Indices: 109147--109226 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 28
109137 TTGACTAGTA
*
109147 ACTAAAATATAAGTTTTGAAAGTTTAATG
1 ACTAAAATATAA-TTTTGAAAGTTTAAGG
* *
109176 ACTAAAGTATAAACTTTGAAAAGTTTAAGG
1 ACTAAAATAT-AATTTTG-AAAGTTTAAGG
*
109206 ACTAAAAATGTAATTTTGAAA
1 ACT-AAAATATAATTTTGAAA
109227 AGTTATATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
29 16 0.38
30 21 0.50
31 5 0.12
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.34
Consensus pattern (28 bp):
ACTAAAATATAATTTTGAAAGTTTAAGG
Found at i:122144 original size:18 final size:18
Alignment explanation
Indices: 122121--122157 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
122111 GTTCTTAAGG
* *
122121 AGTAGTCCTTCGGGACAT
1 AGTAGTCCTACGAGACAT
122139 AGTAGTCCTACGAGACAT
1 AGTAGTCCTACGAGACAT
122157 A
1 A
122158 TACAGTGGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (18 bp):
AGTAGTCCTACGAGACAT
Found at i:122959 original size:23 final size:23
Alignment explanation
Indices: 122930--122985 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
122920 CAGCTCGTAT
* *
122930 AAATGCATCGAAGTGCCACGTAG
1 AAATGCATCGAAGTACCACATAG
* *
122953 AATTGCACCGAAGTACCACATAG
1 AAATGCATCGAAGTACCACATAG
122976 AAATGCATCG
1 AAATGCATCG
122986 TAGTTTCATA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (23 bp):
AAATGCATCGAAGTACCACATAG
Found at i:128933 original size:18 final size:18
Alignment explanation
Indices: 128912--128946 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
128902 CCAGTAATTT
* *
128912 TATTCCCGCCGGTAATCC
1 TATTCCCACCGATAATCC
128930 TATTCCCACCGATAATC
1 TATTCCCACCGATAATC
128947 TTACATTTCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.37, G:0.11, T:0.29
Consensus pattern (18 bp):
TATTCCCACCGATAATCC
Found at i:130337 original size:14 final size:13
Alignment explanation
Indices: 130315--130360 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
130305 CCTCGCAAAG
*
130315 CTCGCTCGGATAGC
1 CTCGGTCGGAT-GC
130329 CTCGGTCGGATGCC
1 CTCGGTCGGATG-C
130343 CTCGGTCGGATGGC
1 CTCGGTCGGAT-GC
130357 CTCG
1 CTCG
130361 AATGCCCAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 1 0.03
14 27 0.93
15 1 0.03
ACGTcount: A:0.09, C:0.35, G:0.35, T:0.22
Consensus pattern (13 bp):
CTCGGTCGGATGC
Done.