Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004754.1 Hibiscus syriacus cultivar Beakdansim tig00010729_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: 89412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:106 original size:12 final size:12
Alignment explanation
Indices: 79--132 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
69 TACGATTTAT
* *
79 AAAATTTTAGAT
1 AAAATTTTATAA
91 AAAATTTTATAAA
1 AAAATTTTAT-AA
104 AAAATTTT-TAA
1 AAAATTTTATAA
*
115 TAAAAATTTATAA
1 -AAAATTTTATAA
128 AAAAT
1 AAAAT
133 AAAAATATAC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
11 2 0.06
12 21 0.60
13 12 0.34
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (12 bp):
AAAATTTTATAA
Found at i:107 original size:25 final size:25
Alignment explanation
Indices: 79--131 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
69 TACGATTTAT
*
79 AAAA-TTTTAGATAAAATTTTATAAA
1 AAAATTTTTA-ATAAAAATTTATAAA
104 AAAATTTTTAATAAAAATTTATAAA
1 AAAATTTTTAATAAAAATTTATAAA
129 AAA
1 AAA
132 TAAAAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 21 0.81
26 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
AAAATTTTTAATAAAAATTTATAAA
Found at i:109 original size:13 final size:13
Alignment explanation
Indices: 91--131 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
81 AATTTTAGAT
91 AAAATTTTATAAA
1 AAAATTTTATAAA
104 AAAATTTT-TAATA
1 AAAATTTTATAA-A
117 AAAA-TTTATAAA
1 AAAATTTTATAAA
129 AAA
1 AAA
132 TAAAAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AAAATTTTATAAA
Found at i:1058 original size:31 final size:30
Alignment explanation
Indices: 1023--1111 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 30
1013 ATAATAATAA
1023 AGTTTGATAAGTATAAGGATCATTTTGTAAT
1 AGTTTGATAAGT-TAAGGATCATTTTGTAAT
* *
1054 AGTTTGATAAGTTTTAATGACCATTTTGTAAT
1 AGTTTGATAAG--TTAAGGATCATTTTGTAAT
* *
1086 AGTTTGGTAAGTTTAGTGATCATTTT
1 AGTTTGATAAGTTAAG-GATCATTTT
1112 ATAACTTTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 3 0.06
31 19 0.39
32 26 0.53
33 1 0.02
ACGTcount: A:0.30, C:0.04, G:0.19, T:0.46
Consensus pattern (30 bp):
AGTTTGATAAGTTAAGGATCATTTTGTAAT
Found at i:1084 original size:32 final size:32
Alignment explanation
Indices: 1023--1099 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 32
1013 ATAATAATAA
* *
1023 AGTTTGATAAG-TATAAGGATCATTTTGTAAT
1 AGTTTGATAAGTTTTAAGGACCATTTTGTAAT
*
1054 AGTTTGATAAGTTTTAATGACCATTTTGTAAT
1 AGTTTGATAAGTTTTAAGGACCATTTTGTAAT
*
1086 AGTTTGGTAAGTTT
1 AGTTTGATAAGTTT
1100 AGTGATCATT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
31 11 0.27
32 30 0.73
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.45
Consensus pattern (32 bp):
AGTTTGATAAGTTTTAAGGACCATTTTGTAAT
Found at i:6022 original size:2 final size:2
Alignment explanation
Indices: 6015--6039 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6005 ACTAAAAACA
6015 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6040 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6044 original size:2 final size:2
Alignment explanation
Indices: 6039--6065 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6029 ATATATATAT
6039 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
6066 ATCGATAAGA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:7389 original size:12 final size:12
Alignment explanation
Indices: 7371--7409 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
7361 GTGGGCTGTC
7371 AGATGAAGAAGA
1 AGATGAAGAAGA
*
7383 TGATGAAGAAGA
1 AGATGAAGAAGA
*
7395 AGAAGAAGAAGA
1 AGATGAAGAAGA
7407 AGA
1 AGA
7410 AGGTGATGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.33, T:0.08
Consensus pattern (12 bp):
AGATGAAGAAGA
Found at i:7393 original size:3 final size:3
Alignment explanation
Indices: 7375--7411 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
7365 GCTGTCAGAT
* *
7375 GAA GAA GAT GAT GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
7412 GTGATGATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.59, C:0.00, G:0.35, T:0.05
Consensus pattern (3 bp):
GAA
Found at i:13604 original size:18 final size:18
Alignment explanation
Indices: 13583--13621 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
13573 AAAATAAATA
13583 AATATTTATAATA-ATAAT
1 AATATTTA-AATATATAAT
13601 AATATTTAAATATATAAT
1 AATATTTAAATATATAAT
13619 AAT
1 AAT
13622 CATATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATATTTAAATATATAAT
Found at i:14979 original size:3 final size:3
Alignment explanation
Indices: 14971--15058 Score: 56
Period size: 3 Copynumber: 29.7 Consensus size: 3
14961 TTGTAATATG
* * *
14971 TAA TAA TAA TATT TAT TAA TAA -AA GT-A TAA TAA TAA TAG TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
* * * * * *
15016 TTA TAA TAA TTA TAA CAA TTA TAA TAA TTA TAA AAA TAA -AA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
15059 GGCAAAAATT
Statistics
Matches: 64, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
2 5 0.08
3 57 0.89
4 2 0.03
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:15023 original size:18 final size:17
Alignment explanation
Indices: 15000--15048 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 17
14990 TAAAAGTATA
*
15000 ATAATAATAGTAATAATT
1 ATAATAATA-TAACAATT
15018 ATAATAATTATAACAATT
1 ATAATAA-TATAACAATT
15036 ATAATAATTATAA
1 ATAATAA-TATAA
15049 AAATAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 27 0.93
19 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (17 bp):
ATAATAATATAACAATT
Found at i:15423 original size:58 final size:58
Alignment explanation
Indices: 15333--15443 Score: 179
Period size: 58 Copynumber: 1.9 Consensus size: 58
15323 ATGTTGATGT
* *
15333 TAATCTATCTCCTTCTATGATAGATTATACAAAAGGTTGAAC-AATCTCTTCTCGATAC
1 TAATCTATCTCCTTCTATGATAAATCATACAAAAGGTTGAACAAAT-TCTTCTCGATAC
*
15391 TAATCTATCTCCTTCTGTGATAAATCATACAAAAGGTTGAACAAATTCTTCTC
1 TAATCTATCTCCTTCTATGATAAATCATACAAAAGGTTGAACAAATTCTTCTC
15444 ATTATGAACT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
58 46 0.94
59 3 0.06
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (58 bp):
TAATCTATCTCCTTCTATGATAAATCATACAAAAGGTTGAACAAATTCTTCTCGATAC
Found at i:15634 original size:124 final size:124
Alignment explanation
Indices: 15393--15883 Score: 801
Period size: 124 Copynumber: 4.0 Consensus size: 124
15383 CTCGATACTA
* **
15393 ATCTATCTCCTTCTGTGATA-AATCATAC-AAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
1 ATCTATCTCCTTCTGTGATAGAGTCATACAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
* *
15456 TTCTT-CTTCTTTAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTG
66 TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAAC-TTCTCTGGAAAAGTTGATGTTG
* *
15515 ATATATCTCCTTCTGTGATAGAGTCATGC-AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
1 ATCTATCTCCTTCTGTGATAGAGTCATACAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
* *
15579 TTCTTCTTTCTTCAGATAAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGTTGATGTTG
66 TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAAC-TTCTCTGGAAAAGTTGATGTTG
*
15639 ATCTATCTCCTTCTGTGATAGAGTCATGCAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
1 ATCTATCTCCTTCTGTGATAGAGTCATACAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
* *
15704 TTCTTCCTTCTTCAGATGGGTTATTCTTATTATGAACTTCTCTGGAAAAGTTGATGTTG
66 TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAGTTGATGTTG
*
15763 ATCTATATCCTTCTGTGATAGAGTCATACAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
1 ATCTATCTCCTTCTGTGATAGAGTCATACAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
*
15828 TTCTTCCTTCTTCAGATGAGTTCTTCTTAATATGAACTTCTTCTGGAAAAGTTGAT
66 TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTC-TCTGGAAAAGTTGAT
15884 CCATCGAATG
Statistics
Matches: 346, Mismatches: 19, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
122 19 0.05
123 44 0.13
124 200 0.58
125 83 0.24
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.40
Consensus pattern (124 bp):
ATCTATCTCCTTCTGTGATAGAGTCATACAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAGTTGATGTTG
Found at i:15706 original size:248 final size:247
Alignment explanation
Indices: 15393--15883 Score: 799
Period size: 249 Copynumber: 2.0 Consensus size: 247
15383 CTCGATACTA
*
15393 ATCTATCTCCTTCTGTGATAAATCATACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTT
1 ATCTATCTCCTTCTGTGATAAATCATACAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTT
* * *
15458 CTT-CTTCTTTAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGATATATC
66 CTTCCTTCTTCAGATGAGTTATTCTCATTATGAAC-TTCTCTGGAAAAGTTGATGTTGATATATA
* *
15522 TCCTTCTGTGATAGAGTCATGC-AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCT
130 TCCTTCTGTGATAGAGTCATACAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC
*
15586 TTCTTCAGATAAGTTCTTCTTATTATGAACTT-TCTCTGGAAAAGTTGATGTTG
195 TTCTTCAGATAAGTTCTTCTTAATATGAACTTCT-TCTGGAAAAGTTGATGTTG
* * *
15639 ATCTATCTCCTTCTGTGATAGAGTCATGCAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
1 ATCTATCTCCTTCTGTGATA-AATCATAC-AAAAGGTTGAACAAACTCTTCTCATTATGAACTTC
* * *
15704 TTCTTCCTTCTTCAGATGGGTTATTCTTATTATGAACTTCTCTGGAAAAGTTGATGTTGATCTAT
64 TTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTTCTCTGGAAAAGTTGATGTTGATATAT
15769 ATCCTTCTGTGATAGAGTCATACAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTC
129 ATCCTTCTGTGATAGAGTCATACAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTC
*
15834 CTTCTTCAGATGAGTTCTTCTTAATATGAACTTCTTCTGGAAAAGTTGAT
194 CTTCTTCAGATAAGTTCTTCTTAATATGAACTTCTTCTGGAAAAGTTGAT
15884 CCATCGAATG
Statistics
Matches: 226, Mismatches: 14, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
246 20 0.09
247 6 0.03
248 86 0.38
249 113 0.50
250 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.40
Consensus pattern (247 bp):
ATCTATCTCCTTCTGTGATAAATCATACAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTT
CTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTTCTCTGGAAAAGTTGATGTTGATATATAT
CCTTCTGTGATAGAGTCATACAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCT
TCTTCAGATAAGTTCTTCTTAATATGAACTTCTTCTGGAAAAGTTGATGTTG
Found at i:15944 original size:112 final size:113
Alignment explanation
Indices: 15809--16015 Score: 312
Period size: 114 Copynumber: 1.8 Consensus size: 113
15799 TTGAACAAGC
* *
15809 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTTAATATGAACT-TCTTCT
1 TCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATAGAGTTCTTCTCAATATGAACTCT-TTCT
*
15872 GGAAA-AGTTGATCCATCGAATGATGAATTCAAACAAAAGGTTTGAAAAT
65 GGAAATA-TTGATCCATCAAATGATGAATTCAAACAAAAGGTTTGAAAAT
* *
15921 TCTTCTCATTATGAATTTATTCTTCCTTCTTCAGATGAGAGTTCTTCTCATTATGAACTCTTTCT
1 TCTTCTCATTATGAACTTATTCTTCCTTCTTCAGAT-AGAGTTCTTCTCAATATGAACTCTTTCT
*
15986 GGAAATATTGATCCATCAAATGATGGATTC
65 GGAAATATTGATCCATCAAATGATGAATTC
16016 GAATCTTTGC
Statistics
Matches: 85, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
112 34 0.40
114 49 0.58
115 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (113 bp):
TCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATAGAGTTCTTCTCAATATGAACTCTTTCTG
GAAATATTGATCCATCAAATGATGAATTCAAACAAAAGGTTTGAAAAT
Found at i:17195 original size:18 final size:18
Alignment explanation
Indices: 17172--17206 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17162 TATGTGAAAC
*
17172 AAATTGAATTTTAAAAAT
1 AAATTGAATTTCAAAAAT
17190 AAATTGAATTTCAAAAA
1 AAATTGAATTTCAAAAA
17207 GATAAACTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (18 bp):
AAATTGAATTTCAAAAAT
Found at i:17599 original size:27 final size:28
Alignment explanation
Indices: 17550--17623 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 28
17540 TCCTTTTATA
**
17550 TTTTTTTCTTTTTTCAACA-TTTTTCCC
1 TTTTTTTCTTTTTTCTTCATTTTTTCCC
** * *
17577 TTTTTTTCTTTTTTCTTTGTTTTTTTCT
1 TTTTTTTCTTTTTTCTTCATTTTTTCCC
*
17605 TTTTTTTCTTTCTTCTTCA
1 TTTTTTTCTTTTTTCTTCA
17624 AGCATAATAT
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
27 15 0.41
28 22 0.59
ACGTcount: A:0.05, C:0.18, G:0.01, T:0.76
Consensus pattern (28 bp):
TTTTTTTCTTTTTTCTTCATTTTTTCCC
Found at i:17602 original size:12 final size:12
Alignment explanation
Indices: 17585--17618 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
17575 CCTTTTTTTC
17585 TTTTTTCTTTGT
1 TTTTTTCTTTGT
*
17597 TTTTTTCTTTTT
1 TTTTTTCTTTGT
17609 TTTCTTTCTT
1 TTT-TTTCTT
17619 CTTCAAGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (12 bp):
TTTTTTCTTTGT
Found at i:28276 original size:27 final size:26
Alignment explanation
Indices: 28240--28302 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
28230 AAAGTGAAAC
*
28240 ATTATTAAAATAATATA-CATATAAAA
1 ATTATGAAAATAATA-AGCATATAAAA
*
28266 TATTATGAAAATAATAAGTATATAAAA
1 -ATTATGAAAATAATAAGCATATAAAA
*
28293 ATTTTGAAAA
1 ATTATGAAAA
28303 GAAAGAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 10 0.31
27 22 0.69
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.35
Consensus pattern (26 bp):
ATTATGAAAATAATAAGCATATAAAA
Found at i:28314 original size:27 final size:27
Alignment explanation
Indices: 28258--28314 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
28248 AATAATATAC
* *
28258 ATATAAAATATTATGAAAATAATAAGT
1 ATATAAAATATTATGAAAAAAAGAAGT
* *
28285 ATATAAAA-ATTTTGAAAAGAAAGAATT
1 ATATAAAATATTATGAAAA-AAAGAAGT
28312 ATA
1 ATA
28315 AATTAAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.32
Consensus pattern (27 bp):
ATATAAAATATTATGAAAAAAAGAAGT
Found at i:31173 original size:29 final size:30
Alignment explanation
Indices: 31122--31182 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
31112 AAATTTTGTC
* **
31122 TAGTGACTAAAGTGTAAGTTTTG-AAAGTT
1 TAGTGACTAAAGTATAAACTTTGAAAAGTT
*
31151 TAGTGGCTAAAGTATAAACTTTGAAAAGTT
1 TAGTGACTAAAGTATAAACTTTGAAAAGTT
31181 TA
1 TA
31183 TAGACCAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (30 bp):
TAGTGACTAAAGTATAAACTTTGAAAAGTT
Found at i:38235 original size:4 final size:4
Alignment explanation
Indices: 38211--38289 Score: 131
Period size: 4 Copynumber: 19.8 Consensus size: 4
38201 TTCTGGTATG
* * *
38211 ATAC ATGC ATAC ATAT GTAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
38259 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
38290 TCGGGATAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 69 1.00
ACGTcount: A:0.48, C:0.23, G:0.03, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:40185 original size:17 final size:17
Alignment explanation
Indices: 40157--40189 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40147 TATTAATGTA
40157 TGAATCATTTATATTTTT
1 TGAATCATTTAT-TTTTT
40175 TGAAT-ATTTATTTTT
1 TGAATCATTTATTTTT
40190 AATAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (17 bp):
TGAATCATTTATTTTTT
Found at i:40726 original size:21 final size:23
Alignment explanation
Indices: 40681--40727 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
40671 GTGTCACCAA
40681 TAACATATATCATGATCATGTGT
1 TAACATATATCATGATCATGTGT
* *
40704 TAACATATGTCA-GATCCTG-GT
1 TAACATATATCATGATCATGTGT
40725 TAA
1 TAA
40728 ATGATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (23 bp):
TAACATATATCATGATCATGTGT
Found at i:40858 original size:130 final size:130
Alignment explanation
Indices: 40654--40901 Score: 397
Period size: 130 Copynumber: 1.9 Consensus size: 130
40644 AATTTTCTTC
* * * *
40654 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACATATGTCAGAT
1 TAATTAGGTGGTGACATGCGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
40719 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
40784 TAATTAGGTGGTGACATGCGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGCGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
40849 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAATTTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
40902 TATATAAATA
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 107 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGCGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:41347 original size:35 final size:35
Alignment explanation
Indices: 41297--41369 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
41287 AATTGAATTT
* *
41297 AATTGAATTATTTTGGAATTTAGGGTTGAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTGAGAATGA
* *
41332 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTGAGAATGA
41367 AAT
1 AAT
41370 CGAGGATTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.01, G:0.25, T:0.38
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTGAGAATGA
Found at i:49064 original size:2 final size:2
Alignment explanation
Indices: 49057--49146 Score: 66
Period size: 2 Copynumber: 48.0 Consensus size: 2
49047 TTGGGCCGGG
* * *
49057 TA TA TA TA TT TA AA T- TA AA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
49098 TA TA TA TT TA -A TT TA AA T- TA AA TT TA T- TA -A TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49135 TA TA TA TA TA TA
1 TA TA TA TA TA TA
49147 ATTATTATTT
Statistics
Matches: 66, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
1 6 0.09
2 60 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:51764 original size:60 final size:60
Alignment explanation
Indices: 51662--51829 Score: 196
Period size: 60 Copynumber: 2.8 Consensus size: 60
51652 CATATAGTAT
* * * *
51662 AGGATGAAATTGACATGTTCAAAAAGTTTGAGAACTAATTTAGAATGA-ATGTCATAGTTTC
1 AGGATGAAATTGAAATGTTC-AAAAGATTGAGGACTAATTTAGAATGACA-GTCATAGTTTA
* * *
51723 AGGGTGGAATTGAAATGTTCAAAAGATTGAGGACTAGTTTAGAATGACAGTCATAGTTTA
1 AGGATGAAATTGAAATGTTCAAAAGATTGAGGACTAATTTAGAATGACAGTCATAGTTTA
* * * *
51783 AGGATGAAATTTAAATGTTTAAAA-ATTTATGGACTAATTTAAAATGA
1 AGGATGAAATTGAAATGTTCAAAAGATTGA-GGACTAATTTAGAATGA
51830 GAATCATAAT
Statistics
Matches: 91, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
59 4 0.04
60 69 0.76
61 18 0.20
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (60 bp):
AGGATGAAATTGAAATGTTCAAAAGATTGAGGACTAATTTAGAATGACAGTCATAGTTTA
Found at i:60765 original size:14 final size:13
Alignment explanation
Indices: 60743--60783 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
60733 AGTGGAAGCA
*
60743 TTATTTATTATTAT
1 TTATATATT-TTAT
60757 TTATATATTTCTAT
1 TTATATATTT-TAT
60771 TTATATATTTTAT
1 TTATATATTTTAT
60784 ATTTCTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 4 0.16
14 21 0.84
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATATATTTTAT
Found at i:60784 original size:21 final size:21
Alignment explanation
Indices: 60744--60803 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 21
60734 GTGGAAGCAT
60744 TATTTATTATTATTTATATATTTC
1 TATTTA-TA-TATTT-TATATTTC
60768 TATTTATATATTTTATATTTC
1 TATTTATATATTTTATATTTC
*
60789 TATTTCATTTATTTT
1 TATTT-ATATATTTT
60804 CATTTATTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
21 13 0.38
22 13 0.38
23 2 0.06
24 6 0.18
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTTATATATTTTATATTTC
Found at i:67509 original size:31 final size:31
Alignment explanation
Indices: 67474--67533 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
67464 TAGTTGTATG
67474 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATTTCAGTATTGTAAAACTAA
*
67505 AATTATTTAAATTTTAGTATTGTAAAACT
1 AATTATTTAAATTTCAGTATTGTAAAACT
67534 CTTTTAAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (31 bp):
AATTATTTAAATTTCAGTATTGTAAAACTAA
Found at i:82092 original size:2 final size:2
Alignment explanation
Indices: 82085--82111 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
82075 AATAAGGTAA
82085 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
82112 AGAGGATGCA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:83721 original size:21 final size:23
Alignment explanation
Indices: 83679--83731 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
83669 CATTTTAATC
83679 AAAATATTAATTATTAAATATTT
1 AAAATATTAATTATTAAATATTT
*
83702 AAAATA-TATTTATT-AATATTT
1 AAAATATTAATTATTAAATATTT
**
83723 TTAATATTA
1 AAAATATTA
83732 TAATAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 11 0.42
22 9 0.35
23 6 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AAAATATTAATTATTAAATATTT
Found at i:83763 original size:21 final size:21
Alignment explanation
Indices: 83733--83773 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
83723 TTAATATTAT
*
83733 AATAAAATAATAAATTATATA
1 AATAAAATAAGAAATTATATA
* *
83754 AATAATATAAGATATTATAT
1 AATAAAATAAGAAATTATAT
83774 TTTTATTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
AATAAAATAAGAAATTATATA
Found at i:83893 original size:27 final size:27
Alignment explanation
Indices: 83813--83898 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
83803 TAATAAATTT
*
83813 ATATTATTTAT-TAATTTAATAGAAATA
1 ATATTATTTATAT-ATTTAATATAAATA
* * *
83840 GTATTA-TTAAAT-TATTAATAATGAATA
1 ATATTATTTATATAT-TTAAT-ATAAATA
83867 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
83896 ATA
1 ATA
83899 ATCCAATAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
25 1 0.02
26 8 0.18
27 17 0.38
28 12 0.27
29 7 0.16
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:83938 original size:23 final size:23
Alignment explanation
Indices: 83912--83956 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
83902 CAATAATATT
83912 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
83935 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
83957 ATATACTATT
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:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:84018 original size:23 final size:24
Alignment explanation
Indices: 83980--84043 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 24
83970 TTAATAAATA
83980 ATTAATATAATT-T-ATAATATTTTT
1 ATTAATA-AATTATAATAATA-TTTT
*
84004 ATTTCAATAAA-TATATTAATATTTT
1 A-TT-AATAAATTATAATAATATTTT
84029 ATTAATAAATTATAA
1 ATTAATAAATTATAA
84044 AAGTAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
23 6 0.18
24 8 0.24
25 10 0.30
26 9 0.27
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTAATAAATTATAATAATATTTT
Done.