Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006640.1 Hibiscus syriacus cultivar Beakdansim tig00016353_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: 182799
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 2 of 2
Found at i:126360 original size:64 final size:66
Alignment explanation
Indices: 126275--126419 Score: 181
Period size: 64 Copynumber: 2.2 Consensus size: 66
126265 GCACTAAGAA
* * *
126275 TGCATCGATTCATCAAGTGCATTCGATG-TTTCA-AAATAGCCAGAGTGCATCGATGCATGG-CT
1 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-AGCCACAGTGCATCGATGCATGGACT
126337 GG
65 GG
* * * *
126339 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCATTGCATCGATGCATGGATTG
1 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCACAGTGCATCGATGCATGGACTG
126404 G
66 G
126405 TGCATC-AGTGCATCA
1 TGCATCGA-TGCATCA
126420 CTTTGATAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
64 26 0.37
65 25 0.36
66 19 0.27
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (66 bp):
TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCACAGTGCATCGATGCATGGACTG
G
Found at i:127243 original size:33 final size:34
Alignment explanation
Indices: 127206--127288 Score: 86
Period size: 33 Copynumber: 2.5 Consensus size: 34
127196 CAATTAATAA
* * *
127206 AATAAAATAAAATAATTAAACCAATAA-ATA-AAT
1 AATAAAATAAAATAAGTAAA-AAACAACATAGAAT
127239 AATAATAA-AAAAT-AGTAAAAAACAACATAGAAT
1 AATAA-AATAAAATAAGTAAAAAACAACATAGAAT
127272 AA-AAAATAAAATAAGTA
1 AATAAAATAAAATAAGTA
127289 CAAGGACCTA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
31 6 0.14
32 15 0.36
33 19 0.45
34 2 0.05
ACGTcount: A:0.71, C:0.05, G:0.04, T:0.20
Consensus pattern (34 bp):
AATAAAATAAAATAAGTAAAAAACAACATAGAAT
Found at i:129366 original size:7 final size:7
Alignment explanation
Indices: 129354--129379 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
129344 GGTTCCTATG
129354 TATCATA
1 TATCATA
129361 TATCATA
1 TATCATA
129368 TATCATA
1 TATCATA
129375 TATCA
1 TATCA
129380 AAACATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (7 bp):
TATCATA
Found at i:135438 original size:23 final size:23
Alignment explanation
Indices: 135412--135455 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
135402 CACCACAGCT
*
135412 CGTATAATTGCACCGAAGTGCTG
1 CGTAGAATTGCACCGAAGTGCTG
*
135435 CGTAGAATTGCACCGTAGTGC
1 CGTAGAATTGCACCGAAGTGC
135456 CATATAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCTG
Found at i:135677 original size:149 final size:149
Alignment explanation
Indices: 135434--135738 Score: 488
Period size: 149 Copynumber: 2.0 Consensus size: 149
135424 CCGAAGTGCT
*
135434 GCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGATCACATAGAATTCCTTAAGAA
1 GCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAA
** *
135499 TCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCACAA-AATA
66 TCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATATTCCA-AAGAATA
*
135563 TATATATATCTCAAAGAACC
130 TATATATATCCCAAAGAACC
*
135583 GCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAA
1 GCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAA
* *
135648 TCATATACATATGCTAGGGATTATA-TATGTGTCTCACCAGACTTCACACATATTCCAAAGAATA
66 TCATATACATATGCTAGGGATCA-AGTATGTGTCTCACAAGACTTCACACATATTCCAAAGAATA
* *
135712 TATATATATCCCGAAGGACC
130 TATATATATCCCAAAGAACC
135732 GCGTAGA
1 GCGTAGA
135739 CCCTCGACTC
Statistics
Matches: 144, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
148 2 0.01
149 141 0.98
150 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (149 bp):
GCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAA
TCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATATTCCAAAGAATAT
ATATATATCCCAAAGAACC
Found at i:136358 original size:5 final size:5
Alignment explanation
Indices: 136348--136372 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
136338 ATTCATATAA
136348 TTCAT TTCAT TTCAT TTCAT TTCAT
1 TTCAT TTCAT TTCAT TTCAT TTCAT
136373 ATCTATCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (5 bp):
TTCAT
Found at i:136654 original size:18 final size:18
Alignment explanation
Indices: 136631--136665 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
136621 TCCCATCTAG
136631 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
136649 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
136666 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:138591 original size:54 final size:54
Alignment explanation
Indices: 138527--138652 Score: 157
Period size: 54 Copynumber: 2.3 Consensus size: 54
138517 GATACTATTC
* *
138527 TTCAAGGGTATCAATACC-TCATCATGGTACCAATACCGAA-ATAACATTCGATGT
1 TTCAAGGGTATCGATACCTTC-TCAAGGTACCAATACC-AATATAACATTCGATGT
* * **
138581 TTCAAGGGTATCGATACCTTCTCAAGGTACCGATACCAATTTCGCATTCGATGT
1 TTCAAGGGTATCGATACCTTCTCAAGGTACCAATACCAATATAACATTCGATGT
*
138635 TTTAAGGGTATCGATACC
1 TTCAAGGGTATCGATACC
138653 ATCCATTAGG
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
53 2 0.03
54 59 0.94
55 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (54 bp):
TTCAAGGGTATCGATACCTTCTCAAGGTACCAATACCAATATAACATTCGATGT
Found at i:138666 original size:20 final size:20
Alignment explanation
Indices: 138641--138694 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
138631 ATGTTTTAAG
138641 GGTATCGATACCATCCATTA-
1 GGTATCGATACCA-CCATTAC
138661 GGTATCGATACCACCATTAC
1 GGTATCGATACCACCATTAC
*
138681 AGTATCGATACCAC
1 GGTATCGATACCAC
138695 TATCAACAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 6 0.19
20 26 0.81
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (20 bp):
GGTATCGATACCACCATTAC
Found at i:138709 original size:22 final size:20
Alignment explanation
Indices: 138642--138713 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
138632 TGTTTTAAGG
* *
138642 GTATCGATACCATCCATTA-G
1 GTATCGATACCA-CCATAACA
*
138662 GTATCGATACCACCATTACA
1 GTATCGATACCACCATAACA
*
138682 GTATCGATACCACTATCAACAA
1 GTATCGATACCACCAT-AAC-A
138704 GTATCGATAC
1 GTATCGATAC
138714 AAACCTTGCA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
19 6 0.13
20 27 0.59
21 2 0.04
22 11 0.24
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.26
Consensus pattern (20 bp):
GTATCGATACCACCATAACA
Found at i:149681 original size:21 final size:22
Alignment explanation
Indices: 149634--149686 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
149624 TTTTGTGCAC
* *
149634 AGTGTATCGATACACCCTTACT
1 AGTGTATCGATACACCATGACT
*
149656 A-TGTATCGATACACTATGA-T
1 AGTGTATCGATACACCATGACT
*
149676 AGTGTACCGAT
1 AGTGTATCGAT
149687 GCATTCCTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 2 0.08
21 23 0.88
22 1 0.04
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (22 bp):
AGTGTATCGATACACCATGACT
Found at i:149896 original size:24 final size:24
Alignment explanation
Indices: 149853--149902 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
149843 TCAAATCAAC
*
149853 ATTTTCAATTCAGAATCTGCT-CG
1 ATTTTCAATTCAGAACCTGCTACG
149876 ATTTTCAAATTCTA-AACCTGCTACG
1 ATTTTC-AATTC-AGAACCTGCTACG
149901 AT
1 AT
149903 CAACAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 6 0.26
24 12 0.52
25 5 0.22
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (24 bp):
ATTTTCAATTCAGAACCTGCTACG
Found at i:151342 original size:19 final size:21
Alignment explanation
Indices: 151313--151351 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
151303 ATATATATAT
151313 TTGGTTTTGATT-GTTTGAAC
1 TTGGTTTTGATTAGTTTGAAC
151333 TTGG-TTTGATTAGTTTGAA
1 TTGGTTTTGATTAGTTTGAA
151352 TTTAATGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.18, C:0.03, G:0.26, T:0.54
Consensus pattern (21 bp):
TTGGTTTTGATTAGTTTGAAC
Found at i:153948 original size:21 final size:23
Alignment explanation
Indices: 153923--153982 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
153913 GTAATTTGCA
153923 CTGAAGTGCCACATA-ATTGT-C
1 CTGAAGTGCCACATAGATTGTAC
*
153944 CTGAAG-GACCACATAGTTTTGTAC
1 CTGAAGTG-CCACATAG-ATTGTAC
153968 C-GAAGTGCCACATAG
1 CTGAAGTGCCACATAG
153983 GTTTGCACCG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 1 0.03
21 13 0.39
23 16 0.48
24 3 0.09
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (23 bp):
CTGAAGTGCCACATAGATTGTAC
Found at i:153972 original size:23 final size:23
Alignment explanation
Indices: 153946--154001 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
153936 TAATTGTCCT
* *
153946 GAAGGACCACATAGTTTTGTACC
1 GAAGGACCACATAGGTTTGCACC
153969 GAAGTG-CCACATAGGTTTGCACC
1 GAAG-GACCACATAGGTTTGCACC
*
153992 GAAGTACCAC
1 GAAGGACCAC
154002 GTAATTGTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 27 0.96
24 1 0.04
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.21
Consensus pattern (23 bp):
GAAGGACCACATAGGTTTGCACC
Found at i:154675 original size:20 final size:20
Alignment explanation
Indices: 154650--154702 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
154640 ATGTTTTAAG
154650 GGTATCGATACCATCCATCA
1 GGTATCGATACCATCCATCA
154670 GGTATCGATACCATCCATCA
1 GGTATCGATACCATCCATCA
*
154690 GGTATCAATACCA
1 GGTATCGATACCA
154703 CCTTTACAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (20 bp):
GGTATCGATACCATCCATCA
Found at i:155608 original size:23 final size:22
Alignment explanation
Indices: 155566--155613 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
155556 TCCCAAATGA
* *
155566 CCATATAGTTTGCATTGAAGTG
1 CCATATAGGTTGCATCGAAGTG
155588 CCATATAGGGTTGCATCGAAGTG
1 CCATATA-GGTTGCATCGAAGTG
155611 CCA
1 CCA
155614 CATATTTGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (22 bp):
CCATATAGGTTGCATCGAAGTG
Found at i:155819 original size:21 final size:21
Alignment explanation
Indices: 155793--155842 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
155783 ATAGAGTTTA
*
155793 TTCACATTCACTGGTTCAAAG
1 TTCACATTCACTGATTCAAAG
* *
155814 TTCACATTCACTTATTCAAGG
1 TTCACATTCACTGATTCAAAG
155835 TTCACATT
1 TTCACATT
155843 TCCATAACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (21 bp):
TTCACATTCACTGATTCAAAG
Found at i:156953 original size:4 final size:4
Alignment explanation
Indices: 156938--156975 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
156928 ACACAGTAAG
*
156938 AAGA ATGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
156976 ACTTGTAGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (4 bp):
AAGA
Found at i:163056 original size:22 final size:20
Alignment explanation
Indices: 163006--163059 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
162996 CATACTTGGA
163006 GGTATCGATACCACCCTAAG
1 GGTATCGATACCACCCTAAG
* * *
163026 GGTACCGATACCACCTTTACGG
1 GGTATCGATACCACC-CTA-AG
163048 GGTATCGATACC
1 GGTATCGATACC
163060 TCTGCATGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 14 0.50
21 2 0.07
22 12 0.43
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.22
Consensus pattern (20 bp):
GGTATCGATACCACCCTAAG
Found at i:163175 original size:21 final size:21
Alignment explanation
Indices: 163149--163208 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
163139 ATTCGATGTT
*
163149 TTAAGGGTATAGATACCAT-CC
1 TTAA-GGTATCGATACCATCCC
*
163170 TTAAGGTACCGATACCCATCCC
1 TTAAGGTATCGATA-CCATCCC
163192 TTAAGGTATCGATACCA
1 TTAAGGTATCGATACCA
163209 CTCTCAACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.24
21 11 0.32
22 15 0.44
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.27
Consensus pattern (21 bp):
TTAAGGTATCGATACCATCCC
Found at i:169657 original size:2 final size:2
Alignment explanation
Indices: 169650--169679 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
169640 TGTGAGAAAA
169650 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
169680 GGTGTCATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:177230 original size:18 final size:18
Alignment explanation
Indices: 177207--177278 Score: 60
Period size: 18 Copynumber: 3.8 Consensus size: 18
177197 GAAACAATTA
177207 ATATATATATATACACTT
1 ATATATATATATACACTT
*
177225 ATATATATTATGTACA-TAT
1 ATATATA-TATATACACT-T
177244 ATTATAAGTATAATATAC-CTT
1 A-TAT-A-TAT-ATATACACTT
177265 ATA-ATATATATACA
1 ATATATATATATACA
177279 TATATATTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 17
0.70 0.03 0.27
Matches are distributed among these distances:
16 6 0.14
17 3 0.07
18 9 0.20
19 9 0.20
20 5 0.11
21 4 0.09
22 8 0.18
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (18 bp):
ATATATATATATACACTT
Found at i:177696 original size:113 final size:113
Alignment explanation
Indices: 177498--177704 Score: 362
Period size: 113 Copynumber: 1.8 Consensus size: 113
177488 GTGTGCCTGG
*
177498 TCGTGATTCTAGTAAGAACTTCGCAGTGCTTTGATTGAAGATTGAAAATGCACAAACAACGTTAC
1 TCGTGATTCTAGTAAGAACTTCGCAGTGCTTTGATTGAAGACTGAAAATGCACAAACAACGTTAC
*
177563 AAGAATGGAAATATGTATATATAAATATGATCTCGATTATGTGTTCGA
66 AAGAATGGAAACATGTATATATAAATATGATCTCGATTATGTGTTCGA
* *
177611 TCGTGATTCTAGTAAGAACTTCGCATTGCTTTGATTGAAGGCTGAAAATGCACAAACAACGTTAC
1 TCGTGATTCTAGTAAGAACTTCGCAGTGCTTTGATTGAAGACTGAAAATGCACAAACAACGTTAC
177676 AAGAA-GAGAAACATGTATATATAAATATG
66 AAGAATG-GAAACATGTATATATAAATATG
177705 TATATGAAAG
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
112 1 0.01
113 88 0.99
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (113 bp):
TCGTGATTCTAGTAAGAACTTCGCAGTGCTTTGATTGAAGACTGAAAATGCACAAACAACGTTAC
AAGAATGGAAACATGTATATATAAATATGATCTCGATTATGTGTTCGA
Found at i:178667 original size:17 final size:17
Alignment explanation
Indices: 178647--178688 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
178637 ACAACTTCCC
178647 TAAATGAAATACATGCT
1 TAAATGAAATACATGCT
* *
178664 TAAATGCAATGCATGCT
1 TAAATGAAATACATGCT
*
178681 TTAATGAA
1 TAAATGAA
178689 CAATATACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (17 bp):
TAAATGAAATACATGCT
Found at i:179361 original size:24 final size:24
Alignment explanation
Indices: 179305--179348 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
179295 TGTTTCTTTT
179305 TATAAAACATTGTAATTAAACTAA
1 TATAAAACATTGTAATTAAACTAA
179329 TATAAAACA-TGT-ATTAAACT
1 TATAAAACATTGTAATTAAACT
179349 TAATTACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 3 0.15
24 9 0.45
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.34
Consensus pattern (24 bp):
TATAAAACATTGTAATTAAACTAA
Found at i:179856 original size:53 final size:53
Alignment explanation
Indices: 179723--180131 Score: 438
Period size: 53 Copynumber: 7.7 Consensus size: 53
179713 CCCAATACCA
* * * * * *
179723 ATACAGAAATTTATACATTTAGTATGAATTTCCT-AGTTTTGCACATATAGTGCCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAG-TTT--ACATAAAGTGCCC
* * * *
179778 ATACAGAAATTCAT-C-CTTAATATGAATTTCTTCAGTTTACATAAAATGCCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACATAAAGTGCCC
* *
179829 ATACGGAAATTCATCCATTTAGTATGAACTTCTTAAGTTTATACATAAAGTGCCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAG-TT-TACATAAAGTGCCC
* *
179884 ATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTACACATAAAGTG-CC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTT-TACATAAAGTGCCC
* *
179937 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGGCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTT--ACATAAAGTGCCC
* * *
179992 ATACGAAAATTCAT-C-CTTAGTATGAATTTCTTAAGTTTACACATATAGTGTCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTT--ACATAAAGTGCCC
** * * * *
180045 ATACAAAAATTCAT-CACTTAGTATGAATTTATTAAGTTTACACATA-TACCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACATAAAGTGCCC
*
180096 ATACGGAAATTCATCCACTTAGTATGAATTTATTAA
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAA
180132 ATTTTTGCAC
Statistics
Matches: 316, Mismatches: 28, Indels: 23
0.86 0.08 0.06
Matches are distributed among these distances:
51 39 0.12
52 28 0.09
53 124 0.39
54 50 0.16
55 75 0.24
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (53 bp):
ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACATAAAGTGCCC
Found at i:179962 original size:108 final size:107
Alignment explanation
Indices: 179723--180131 Score: 501
Period size: 108 Copynumber: 3.8 Consensus size: 107
179713 CCCAATACCA
* * * * * *
179723 ATACAGAAATTTATACATTTAGTATGAATTTCCT-AGTTTTGCACATATAGTGCCCATAC-AGAA
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAG-TTTACACATATAGTGCCCATACGA-AA
* * * *
179786 ATTCATCCTTAATATGAATTTCTTCAGTT-TACATAAAATGCCC
64 ATTCATCCTTAGTATGAATTTCTTAAGTTACACATAAAGTGCCC
* * * *
179829 ATACGGAAATTCATCCATTTAGTATGAACTTCTTAAGTTTATACATAAAGTGCCCATACGAAAAT
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCCATACGAAAAT
179894 TCATCCACTTAGTATGAATTTCTTAAGTTACACATAAAGTG-CC
66 TCAT-C-CTTAGTATGAATTTCTTAAGTTACACATAAAGTGCCC
*
179937 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGGCCATACGAAAAT
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCCATACGAAAAT
* *
180002 TCATCCTTAGTATGAATTTCTTAAGTTTACACATATAGTGTCC
66 TCATCCTTAGTATGAATTTCTTAAG-TTACACATAAAGTGCCC
** * *
180045 ATACAAAAATTCAT-CACTTAGTATGAATTTATTAAGTTTACACATATA---CCCATACGGAAAT
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCCATACGAAAAT
*
180106 TCATCCACTTAGTATGAATTTATTAA
66 TCAT-C-CTTAGTATGAATTTCTTAA
180132 ATTTTTGCAC
Statistics
Matches: 270, Mismatches: 24, Indels: 18
0.87 0.08 0.06
Matches are distributed among these distances:
104 15 0.06
105 1 0.00
106 94 0.35
107 51 0.19
108 100 0.37
109 9 0.03
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (107 bp):
ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCCATACGAAAAT
TCATCCTTAGTATGAATTTCTTAAGTTACACATAAAGTGCCC
Found at i:179966 original size:161 final size:160
Alignment explanation
Indices: 179723--180131 Score: 517
Period size: 161 Copynumber: 2.6 Consensus size: 160
179713 CCCAATACCA
* * * * * *
179723 ATACAGAAATTTATACATTTAGTATGAATTTCCT-AGTTTTGCACATATAGTGCCCATACAGAAA
1 ATACAAAAATTCAT-CACTTAGTATGAATTTCTTAAG-TTTACACATATAGTG-CCATACGGAAA
* * *
179787 TTCAT-C-CTTAATATGAATTTCTTCAGTTT-ACATAAAATGCCCATACGGAAATTCATCCATTT
63 TTCATCCACTTAGTATGAATTTCTTAAGTTTAACATAAAATGCCCATACGAAAATTCATCC--TT
*
179849 AGTATGAACTTCTTAAGTTTATACATAAAGTGCCC
126 AGTATGAACTTCTTAAGTTTACACATAAAGTGCCC
* *
179884 ATACGAAAATTCATCCACTTAGTATGAATTTCTTAAG-TTACACATAAAGTGCCATACGGAAATT
1 ATACAAAAATTCAT-CACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCATACGGAAATT
* * *
179948 CATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGGCCATACGAAAATTCATCCTTAGT
65 CATCCACTTAGTATGAATTTCTTAAGTTTA-ACATAAAATGCCCATACGAAAATTCATCCTTAGT
* * *
180013 ATGAATTTCTTAAGTTTACACATATAGTGTCC
129 ATGAACTTCTTAAGTTTACACATAAAGTGCCC
* *
180045 ATACAAAAATTCATCACTTAGTATGAATTTATTAAGTTTACACATATA--CCCATACGGAAATTC
1 ATACAAAAATTCATCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCATACGGAAATTC
*
180108 ATCCACTTAGTATGAATTTATTAA
66 ATCCACTTAGTATGAATTTCTTAA
180132 ATTTTTGCAC
Statistics
Matches: 218, Mismatches: 24, Indels: 14
0.85 0.09 0.05
Matches are distributed among these distances:
159 52 0.24
160 34 0.16
161 105 0.48
162 2 0.01
163 25 0.11
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (160 bp):
ATACAAAAATTCATCACTTAGTATGAATTTCTTAAGTTTACACATATAGTGCCATACGGAAATTC
ATCCACTTAGTATGAATTTCTTAAGTTTAACATAAAATGCCCATACGAAAATTCATCCTTAGTAT
GAACTTCTTAAGTTTACACATAAAGTGCCC
Found at i:180566 original size:22 final size:19
Alignment explanation
Indices: 180527--180595 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 19
180517 TATCGATATC
*
180527 ATCGATACCCCTACTATGGT
1 ATCGATA-CTCTACTATGGT
180547 ATCGATACTACTATACTAT-GT
1 ATCGATACT-C--TACTATGGT
*
180568 AACTGATACTCTACTATGGT
1 ATC-GATACTCTACTATGGT
*
180588 ATCAATAC
1 ATCGATAC
180596 CATTTTTGCA
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
19 11 0.28
20 12 0.30
21 5 0.12
22 12 0.30
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (19 bp):
ATCGATACTCTACTATGGT
Found at i:180595 original size:19 final size:20
Alignment explanation
Indices: 180537--180595 Score: 52
Period size: 19 Copynumber: 3.0 Consensus size: 20
180527 ATCGATACCC
180537 CTACTATGGTATCGATACTACT
1 CTACTATGGTATCGA-A-TACT
* *
180559 ATACTAT-GTAACTG-ATACT
1 CTACTATGGTATC-GAATACT
180578 CTACTATGGTATC-AATAC
1 CTACTATGGTATCGAATAC
180596 CATTTTTGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 9
0.70 0.09 0.21
Matches are distributed among these distances:
19 14 0.47
20 5 0.17
21 4 0.13
22 7 0.23
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (20 bp):
CTACTATGGTATCGAATACT
Done.