Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007281.1 Hibiscus syriacus cultivar Beakdansim tig00019320_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: 67912
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:10686 original size:137 final size:137
Alignment explanation
Indices: 10512--10793 Score: 521
Period size: 137 Copynumber: 2.1 Consensus size: 137
10502 TTTAATGAGG
*
10512 CATCCTATTCCTATAAAAAAAAAATAGAAAACCTGTAATCGTATGACCTTTACAAACCCATTATT
1 CATCCTATTCCTAT-AAAAAAAAATAGAAAACCTGTAATCATATGACCTTTACAAACCCATTATT
*
10577 GCACATTCTGAATTTTGTAAAGAACAGCTCACTTGCCCAAAAATAAAACTTATATGAAACAACAA
65 GCACATTCTGAATTTTGAAAAGAACAGCTCACTTGCCCAAAAA-AAAACTTATATGAAACAACAA
10642 TTGTAATGT
129 TTGTAATGT
10651 CATCCTATTCCTAT-AAAAAAAATAGAAAACCTGTAATCATATGACCTTTACAAACCCATTATTG
1 CATCCTATTCCTATAAAAAAAAATAGAAAACCTGTAATCATATGACCTTTACAAACCCATTATTG
10715 CACATTCTGAATTTTGAAAAGAACAGCTCACTTGCCCAAAAAAAAACTTATATGAAACAACAATT
66 CACATTCTGAATTTTGAAAAGAACAGCTCACTTGCCCAAAAAAAAACTTATATGAAACAACAATT
10780 GTAATGT
131 GTAATGT
10787 CATCCTA
1 CATCCTA
10794 GTACTACATG
Statistics
Matches: 141, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
136 37 0.26
137 90 0.64
139 14 0.10
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (137 bp):
CATCCTATTCCTATAAAAAAAAATAGAAAACCTGTAATCATATGACCTTTACAAACCCATTATTG
CACATTCTGAATTTTGAAAAGAACAGCTCACTTGCCCAAAAAAAAACTTATATGAAACAACAATT
GTAATGT
Found at i:13044 original size:22 final size:22
Alignment explanation
Indices: 13017--13079 Score: 117
Period size: 22 Copynumber: 2.9 Consensus size: 22
13007 AACACTTGAA
13017 CTCGATTGAAACACAAACTTAG
1 CTCGATTGAAACACAAACTTAG
13039 CTCGATTGAAACACAAACTTAG
1 CTCGATTGAAACACAAACTTAG
*
13061 CTCGATTGAAACTCAAACT
1 CTCGATTGAAACACAAACT
13080 CAATCTCGGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.24
Consensus pattern (22 bp):
CTCGATTGAAACACAAACTTAG
Found at i:15053 original size:46 final size:46
Alignment explanation
Indices: 14986--15075 Score: 171
Period size: 46 Copynumber: 2.0 Consensus size: 46
14976 ATTACTTTTT
*
14986 AAAGTTTTAGGCTTCAGCATTACGTATGGAGAAATAGATACAAGTA
1 AAAGTTTTAGGCTTCAGCATTACGTATGAAGAAATAGATACAAGTA
15032 AAAGTTTTAGGCTTCAGCATTACGTATGAAGAAATAGATACAAG
1 AAAGTTTTAGGCTTCAGCATTACGTATGAAGAAATAGATACAAG
15076 ATTTATGTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (46 bp):
AAAGTTTTAGGCTTCAGCATTACGTATGAAGAAATAGATACAAGTA
Found at i:18140 original size:12 final size:13
Alignment explanation
Indices: 18114--18142 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
18104 TTAATTTTTG
18114 ATTTTTTAAATAA
1 ATTTTTTAAATAA
18127 ATTTTTTAAA-AA
1 ATTTTTTAAATAA
18139 ATTT
1 ATTT
18143 AAGCATGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTTTTTAAATAA
Found at i:22952 original size:19 final size:17
Alignment explanation
Indices: 22928--22967 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 17
22918 TTATTTAATG
22928 ATATAATTTTATAAATATA
1 ATATAA-TTTATAAA-ATA
22947 ATATAATTTATAAAATA
1 ATATAATTTATAAAATA
22964 ATAT
1 ATAT
22968 TTATAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 7 0.33
18 8 0.38
19 6 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATAATTTATAAAATA
Found at i:28540 original size:23 final size:23
Alignment explanation
Indices: 28505--28552 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
28495 ATCAAGTACA
* *
28505 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAACGCTTAT
* *
28528 ATAATGTAATAGGTAACGTTTAT
1 ATAATATAATAGGTAACGCTTAT
28551 AT
1 AT
28553 TGACTTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.40
Consensus pattern (23 bp):
ATAATATAATAGGTAACGCTTAT
Found at i:29517 original size:182 final size:182
Alignment explanation
Indices: 29198--29647 Score: 659
Period size: 182 Copynumber: 2.5 Consensus size: 182
29188 TTACTATCGA
* *
29198 TTTTGTCATTTCAAGATCAATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCAAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
* *
29263 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTATTTTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTAGCGCTATAACTTATTCTCTTTTAAATTCCAAAAGTGTCGA
* * ** ** *
29328 AACTTATAATAAAATATCGACACTTTTAACATATCCGGTAGCTCTTTACCGG
131 AACTTATAATAAAATATCGACACTATCAACATATCCAATAGCGATTTACAGG
* * * *
29380 TTTTATCATTTCGAGACCGATTTTGTCATATTTTTATCTGTTATATTGTTATAGATCGATACATT
1 TTTTGTCATTTCAAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
* * *
29445 TTTATAAAGTATCGATATTTTATTAGCGCTATAATTTATTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTAGCGCTATAACTTATTCTCTTTTAAATTCCAAAAGTGTCGA
* * * *
29510 TACTTATAATAAAGTATCGACACTATCAACATATCTAATAGCGATTTACATG
131 AACTTATAATAAAATATCGACACTATCAACATATCCAATAGCGATTTACAGG
* *
29562 TTTTGTCATTT-ATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACAT
1 TTTTGTCATTTCA-AGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAT
*
29626 TTTTATTAAGTATCGACACTTT
65 TTTTATAAAGTATCGACACTTT
29648 CAATATATTA
Statistics
Matches: 236, Mismatches: 31, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
182 236 1.00
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.44
Consensus pattern (182 bp):
TTTTGTCATTTCAAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
TTTATAAAGTATCGACACTTTATTAGCGCTATAACTTATTCTCTTTTAAATTCCAAAAGTGTCGA
AACTTATAATAAAATATCGACACTATCAACATATCCAATAGCGATTTACAGG
Found at i:29718 original size:112 final size:112
Alignment explanation
Indices: 29518--30093 Score: 911
Period size: 112 Copynumber: 5.1 Consensus size: 112
29508 GATACTTATA
* * ** * *
29518 ATAAAGTATCGACACTATCAACATATCTAATAGCGATTTACATGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
29583 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACATGTTATATTGTTATGGATCGATACATTTTT
* *
29630 ATTAAGTATCGACACTTTCAATATAT-TAGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGA
1 ATAAAGTATCGACACTTTCAATATATCT-GGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGG
29694 TTTTGTCATTTTTTTACATGTTATATTGTTATGGATCGATACATTTTT
65 TTTTGTCATTTTTTTACATGTTATATTGTTATGGATCGATACATTTTT
29742 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
29807 TTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCA-TTTTTTTACATGTTATATTGTTATGGATCGATACATTTTT
* * *
29855 ATAAAGTATGGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
29920 TGTGTCATTTTTTTACATGTTATATTGTTATGGATCAATATATTTTT
66 TTTGTCATTTTTTTACATGTTATATTGTTATGGATCGATACATTTTT
* * * *
29967 ATAAAGTATCGATATTTTTAATATATCTGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* ** *
30032 TTTGTCATTTTTTTACATATTATATTGTTATGGATTAATATATTTTT
66 TTTGTCATTTTTTTACATGTTATATTGTTATGGATCGATACATTTTT
30079 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
30094 AACCCGACAA
Statistics
Matches: 430, Mismatches: 31, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
111 1 0.00
112 321 0.75
113 108 0.25
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.47
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACATGTTATATTGTTATGGATCGATACATTTTT
Found at i:29908 original size:225 final size:224
Alignment explanation
Indices: 29518--30093 Score: 927
Period size: 225 Copynumber: 2.6 Consensus size: 224
29508 GATACTTATA
* * ** *
29518 ATAAAGTATCGACACTATCAACATATCTAATAGCGATTTACATGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGATTTACCTGTTTTGTCATTTATAGACCGGT
*
29583 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATTAAGTATCGACACTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
* *
29648 CAATATATTAGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGATTTTGTCATTTTTTTACAT
131 CAATATATCAGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGATTGTGTCATTTTTTTACAT
*
29713 GTTATATTGTTATGGATCGATACATTTTT
196 GTTATATTGTTATGGATCAATACATTTTT
*
29742 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGATTTACCTGTTTTGTCATTTATAGACCGGT
*
29807 TTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATGGACACTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTT
* * *
29872 TCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGTTGTGTCATTTTTTTACA
130 TCAATATATCAGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGATTGTGTCATTTTTTTACA
*
29937 TGTTATATTGTTATGGATCAATATATTTTT
195 TGTTATATTGTTATGGATCAATACATTTTT
* * * *
29967 ATAAAGTATCGATATTTTTAATATATCTGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGATTTACCTGTTTTGTCATTTATAGACCGGT
* * ** *
30032 TTTGTCATTTTTTTACATATTATATTGTTATGGATTAATATATTTTTATAAAGTATCGACAC
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
30094 AACCCGACAA
Statistics
Matches: 326, Mismatches: 25, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
224 115 0.35
225 211 0.65
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.47
Consensus pattern (224 bp):
ATAAAGTATCGACACTTTCAATATATCTGGTAGCGATTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
CAATATATCAGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGATTGTGTCATTTTTTTACAT
GTTATATTGTTATGGATCAATACATTTTT
Found at i:32974 original size:57 final size:58
Alignment explanation
Indices: 32894--33005 Score: 156
Period size: 57 Copynumber: 1.9 Consensus size: 58
32884 ACAAATGATC
** *
32894 CCCTTGACTATAGGACATCTC-TT-TTGAATTTCTGAATATTAAAAGTTACAAAATAGT
1 CCCTTGACTATAGGACATCTCTTTGTTGAATCCCGGAATATT-AAAGTTACAAAATAGT
* *
32951 CCCTTGACTATAGGGCATTTCTTTGTTGAATCCCGGAATATTAAAGTTACAAAAT
1 CCCTTGACTATAGGACATCTCTTTGTTGAATCCCGGAATATTAAAGTTACAAAAT
33006 GGTTCCTCGA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
57 19 0.40
58 15 0.31
59 14 0.29
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (58 bp):
CCCTTGACTATAGGACATCTCTTTGTTGAATCCCGGAATATTAAAGTTACAAAATAGT
Found at i:34938 original size:2 final size:2
Alignment explanation
Indices: 34931--34981 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
34921 GGGATGGGTC
*
34931 AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34973 AT AT AT AT A
1 AT AT AT AT A
34982 GTACAGCAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:37806 original size:27 final size:28
Alignment explanation
Indices: 37776--37833 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
37766 ATCTATTAAC
* **
37776 CTTTTGA-CTTTGATCATTGACAATTGA
1 CTTTTGATCGTTGATCATCAACAATTGA
*
37803 C-TTTGATCGTTGATCATCAACAGTTGA
1 CTTTTGATCGTTGATCATCAACAATTGA
37830 CTTT
1 CTTT
37834 GACCATTAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
26 5 0.20
27 18 0.72
28 2 0.08
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.43
Consensus pattern (28 bp):
CTTTTGATCGTTGATCATCAACAATTGA
Found at i:38220 original size:8 final size:8
Alignment explanation
Indices: 38207--38244 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
38197 GGTATATATG
38207 GTATGTGT
1 GTATGTGT
*
38215 GTATGTAT
1 GTATGTGT
38223 GTATGTGT
1 GTATGTGT
*
38231 ATATGT-T
1 GTATGTGT
38238 GTATGTG
1 GTATGTG
38245 AGCATGAGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
7 6 0.24
8 19 0.76
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (8 bp):
GTATGTGT
Found at i:38227 original size:31 final size:30
Alignment explanation
Indices: 38181--38244 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
38171 AATTATTTAG
38181 GTGTGTTATATGTATGGGTATATATGGTAT
1 GTGTGTTATATGTATGGGTATATATGGTAT
* * * *
38211 GTGTGTATGTATGTATGTGTATATGTTGTAT
1 GTGTGT-TATATGTATGGGTATATATGGTAT
38242 GTG
1 GTG
38245 AGCATGAGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 6 0.21
31 23 0.79
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.48
Consensus pattern (30 bp):
GTGTGTTATATGTATGGGTATATATGGTAT
Found at i:40403 original size:3 final size:3
Alignment explanation
Indices: 40395--40453 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
40385 TTATCCATTA
40395 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
40443 ATT ATT ATT AT
1 ATT ATT ATT AT
40454 AGTTAGAGTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:49134 original size:19 final size:18
Alignment explanation
Indices: 49098--49140 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
49088 ACCCGTTAAT
49098 TTTGACTTGCTCGTTGAC
1 TTTGACTTGCTCGTTGAC
49116 TTTGACTATGACT-GTTGAC
1 TTTGACT-TG-CTCGTTGAC
49135 TTTGAC
1 TTTGAC
49141 CAAAAAGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.30
19 14 0.61
20 2 0.09
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.44
Consensus pattern (18 bp):
TTTGACTTGCTCGTTGAC
Found at i:52612 original size:9 final size:8
Alignment explanation
Indices: 52590--52716 Score: 75
Period size: 9 Copynumber: 15.4 Consensus size: 8
52580 CGAACTCAAA
*
52590 AATATTAT
1 AATATAAT
52598 ATATATAATT
1 A-ATATAA-T
*
52608 AATATAAAA
1 AATAT-AAT
52617 AATATAA-
1 AATATAAT
*
52624 AATATTAT
1 AATATAAT
52632 ATATATAATT
1 A-ATATAA-T
*
52642 AATATAAA
1 AATATAAT
52650 AATATAA-
1 AATATAAT
*
52657 AATATTAT
1 AATATAAT
52665 -ATATAATT
1 AATATAA-T
*
52673 AATATAAA
1 AATATAAT
52681 AATATAA-
1 AATATAAT
*
52688 AATATTAT
1 AATATAAT
52696 -ATATATAT
1 AATATA-AT
52704 ATATATATAT
1 A-ATATA-AT
52714 AAT
1 AAT
52717 CGGGGCGGGG
Statistics
Matches: 96, Mismatches: 10, Indels: 25
0.73 0.08 0.19
Matches are distributed among these distances:
7 27 0.28
8 21 0.22
9 33 0.34
10 15 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
AATATAAT
Found at i:52628 original size:25 final size:26
Alignment explanation
Indices: 52600--52692 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 26
52590 AATATTATAT
52600 ATATAAT-TAATATAAAAAATAT-AAA
1 ATATAATAT-ATATAAAAAATATAAAA
* **
52625 ATATTATATATATAATTAATATAAAA
1 ATATAATATATATAAAAAATATAAAA
*
52651 ATATAAAATATTATATATAATTAATATAAAA
1 ATAT--AATA-TATATA-AA-AAATATAAAA
*
52682 ATATAAAATAT
1 ATATAATATAT
52693 TATATATATA
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
25 17 0.31
26 8 0.15
28 6 0.11
29 9 0.16
30 1 0.02
31 14 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
ATATAATATATATAAAAAATATAAAA
Found at i:52669 original size:31 final size:33
Alignment explanation
Indices: 52588--52702 Score: 207
Period size: 31 Copynumber: 3.5 Consensus size: 33
52578 CCCGAACTCA
52588 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATAT-AAAAATAT
52622 AAAATATTATATATATAATTAATATAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAATAT
52655 AAAATA-T-TATATATAATTAATATAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAATAT
52686 AAAATATTATATATATA
1 AAAATATTATATATATA
52703 TATATATATA
Statistics
Matches: 79, Mismatches: 0, Indels: 5
0.94 0.00 0.06
Matches are distributed among these distances:
31 30 0.38
32 2 0.03
33 22 0.28
34 25 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (33 bp):
AAAATATTATATATATAATTAATATAAAAATAT
Found at i:58157 original size:17 final size:17
Alignment explanation
Indices: 58135--58170 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
58125 TTTATCGAAT
58135 TATGTAGAGGTTTATTA
1 TATGTAGAGGTTTATTA
58152 TATGTAGAGGTTTATTA
1 TATGTAGAGGTTTATTA
58169 TA
1 TA
58171 GGATGATCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (17 bp):
TATGTAGAGGTTTATTA
Found at i:59040 original size:60 final size:60
Alignment explanation
Indices: 58947--59070 Score: 248
Period size: 60 Copynumber: 2.1 Consensus size: 60
58937 GGTGTTAGTT
58947 ACAATGTCGGTAGAAAGACACGCAGATTATATGACGTCTTTAAGAAGATGTCTGGAAGAC
1 ACAATGTCGGTAGAAAGACACGCAGATTATATGACGTCTTTAAGAAGATGTCTGGAAGAC
59007 ACAATGTCGGTAGAAAGACACGCAGATTATATGACGTCTTTAAGAAGATGTCTGGAAGAC
1 ACAATGTCGGTAGAAAGACACGCAGATTATATGACGTCTTTAAGAAGATGTCTGGAAGAC
59067 ACAA
1 ACAA
59071 CGTCTTCTCC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (60 bp):
ACAATGTCGGTAGAAAGACACGCAGATTATATGACGTCTTTAAGAAGATGTCTGGAAGAC
Found at i:59444 original size:43 final size:43
Alignment explanation
Indices: 59379--59742 Score: 261
Period size: 43 Copynumber: 8.6 Consensus size: 43
59369 TTTTTTATTC
* * * *
59379 TCACTTTATACATTTACAATTGAGACTCATAAGTTTTTCAATA
1 TCACTTTTTACTTTTATAATTGAGACTCATAATTTTTTCAATA
* * * *
59422 TCACTTTCTACTTTTATGATTGA-AGCTCCTAATTTTTT-TAT-
1 TCACTTTTTACTTTTATAATTGAGA-CTCATAATTTTTTCAATA
*
59463 TCACTTTTTA-TCTTTATAATTGAGAC-CCTAATTTTTTCAAT-
1 TCACTTTTTACT-TTTATAATTGAGACTCATAATTTTTTCAATA
* * * *
59504 CCAACTTTTTATTTTTATAATTGATG-CCCATAATTTTTTCAATC
1 TC-ACTTTTTACTTTTATAATTGA-GACTCATAATTTTTTCAATA
* *
59548 TCACATTTTAGC-TTTATAATTGAAGTCTC-TAATTTTTT-AATA
1 TCACTTTTTA-CTTTTATAATTG-AGACTCATAATTTTTTCAATA
* * ** *
59590 TCACTTTTTACCTTTATAAATGAGGTTCTTAATTCTTTT-AATA
1 TCACTTTTTACTTTTATAATTGAGACTCATAATT-TTTTCAATA
* * * *
59633 TCATTTTTTA-TCTTTATAATTGAGGCCCCA-AATTTTTTCAATC
1 TCACTTTTTACT-TTTATAATTGA-GACTCATAATTTTTTCAATA
* * * ** * *
59676 TCACTTTCTACCTTTACAAATAAAGCCTC-TAATTTTTTTAATA
1 TCACTTTTTACTTTTA-TAATTGAGACTCATAATTTTTTCAATA
59719 TCACTTTTTACTTTTATAATTGAG
1 TCACTTTTTACTTTTATAATTGAG
59743 GCTTTCAATC
Statistics
Matches: 257, Mismatches: 43, Indels: 43
0.75 0.13 0.13
Matches are distributed among these distances:
40 12 0.05
41 28 0.11
42 59 0.23
43 148 0.58
44 10 0.04
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.49
Consensus pattern (43 bp):
TCACTTTTTACTTTTATAATTGAGACTCATAATTTTTTCAATA
Found at i:59672 original size:128 final size:126
Alignment explanation
Indices: 59318--59743 Score: 386
Period size: 128 Copynumber: 3.3 Consensus size: 126
59308 GGGTGCACGT
* * * * * *
59318 CTCTAATTTTTATAATCTCA-TTATTTACCTTCATAATTGA-GACCTTTAGTTTTTTTTATTCTC
1 CTCTAATTTTT-TAATATCACTT-TTTACCTTTATAATTGAGGACC-CTA-ATTTTTTCAATC-C
* * * * * * *
59381 -ACTTTATA-CATTTACAATTGAGACTCATAAGTTTTTCAATATCACTTTCTACTTTTATGATTG
61 AACTTTTTATC-TTTATAATTGAGGCCCATAATTTTTTCAATCTCACTTTCTAC-TTTATAATTG
59444 AAG
124 AAG
* *
59447 CTCCTAATTTTTTTAT-TCACTTTTTATCTTTATAATTGA-GACCCTAATTTTTTCAATCCAACT
1 CT-CTAATTTTTTAATATCACTTTTTACCTTTATAATTGAGGACCCTAATTTTTTCAATCCAACT
* *
59510 TTTTATTTTTATAATTGATGCCCATAATTTTTTCAATCTCACATTT-TAGCTTTATAATTGAAG
65 TTTTATCTTTATAATTGAGGCCCATAATTTTTTCAATCTCAC-TTTCTA-CTTTATAATTGAAG
* ** * *
59573 TCTCTAATTTTTTAATATCACTTTTTACCTTTATAAATGAGGTTCTTAATTCTTTT-AATATC-A
1 -CTCTAATTTTTTAATATCACTTTTTACCTTTATAATTGAGGACCCTAATT-TTTTCAAT-CCAA
* * * *
59636 TTTTTTATCTTTATAATTGAGGCCCCA-AATTTTTTCAATCTCACTTTCTACCTTTACAAATAAA
63 CTTTTTATCTTTATAATTGAGG-CCCATAATTTTTTCAATCTCACTTTCTA-CTTTATAATTGAA
59700 G
126 G
*
59701 CCTCTAATTTTTTTAATATCACTTTTTACTTTTATAATTGAGG
1 -CTCTAA-TTTTTTAATATCACTTTTTACCTTTATAATTGAGG
59744 CTTTCAATCT
Statistics
Matches: 250, Mismatches: 33, Indels: 28
0.80 0.11 0.09
Matches are distributed among these distances:
125 1 0.00
126 71 0.28
127 32 0.13
128 88 0.35
129 49 0.20
130 9 0.04
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50
Consensus pattern (126 bp):
CTCTAATTTTTTAATATCACTTTTTACCTTTATAATTGAGGACCCTAATTTTTTCAATCCAACTT
TTTATCTTTATAATTGAGGCCCATAATTTTTTCAATCTCACTTTCTACTTTATAATTGAAG
Found at i:59744 original size:86 final size:86
Alignment explanation
Indices: 59368--59742 Score: 304
Period size: 85 Copynumber: 4.4 Consensus size: 86
59358 GACCTTTAGT
* * * * * * *
59368 TTTTTTTATTCTCACTTTATACATTTACAATTGAGACTCATAAGTTTTTCAATATCACTTTCTAC
1 TTTTTTTAATATCACTTTTTACTTTTATAATTGAGACCCA-AATTTTTTCAATATCACTTTCTAC
* * * *
59433 TTTTATGATTGAAG-CTCCTAA
65 CTTTATAAATGAAGCCTCATAA
* * *
59454 TTTTTTT-AT-TCACTTTTTA-TCTTTATAATTGAGACCCTAATTTTTTCAAT-CCAACTTTTTA
1 TTTTTTTAATATCACTTTTTACT-TTTATAATTGAGACCCAAATTTTTTCAATATC-ACTTTCTA
** * *
59515 TTTTTATAATTGATGCC-CATAA
64 CCTTTATAAATGAAGCCTCATAA
* * * * * * *
59537 TTTTTTCAATCTCACATTTTAGC-TTTATAATTGAAGTCTCTAATTTTTT-AATATCACTTTTTA
1 TTTTTTTAATATCACTTTTTA-CTTTTATAATTG-AGACCCAAATTTTTTCAATATCACTTTCTA
** *
59600 CCTTTATAAATG-AGGTTCTTAA
64 CCTTTATAAATGAAGCCTCATAA
* * * *
59622 TTCTTTTAATATCATTTTTTA-TCTTTATAATTGAGGCCCCAAATTTTTTCAATCTCACTTTCTA
1 TTTTTTTAATATCACTTTTTACT-TTTATAATTGA-GACCCAAATTTTTTCAATATCACTTTCTA
* *
59686 CCTTTACAAATAAAGCCTC-TAA
64 CCTTTATAAATGAAGCCTCATAA
59708 TTTTTTTAATATCACTTTTTACTTTTATAATTGAG
1 TTTTTTTAATATCACTTTTTACTTTTATAATTGAG
59743 GCTTTCAATC
Statistics
Matches: 232, Mismatches: 41, Indels: 33
0.76 0.13 0.11
Matches are distributed among these distances:
82 1 0.00
83 40 0.17
84 28 0.12
85 82 0.35
86 76 0.33
87 5 0.02
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50
Consensus pattern (86 bp):
TTTTTTTAATATCACTTTTTACTTTTATAATTGAGACCCAAATTTTTTCAATATCACTTTCTACC
TTTATAAATGAAGCCTCATAA
Found at i:59810 original size:75 final size:77
Alignment explanation
Indices: 59668--59817 Score: 211
Period size: 75 Copynumber: 2.0 Consensus size: 77
59658 CCCCAAATTT
59668 TTTCAATCTCACTTTCTACCTTTACAAATAAAGCCTCTAATTTTTTTAATATCACTTTTTACTTT
1 TTTCAATCTCACTTTCTACCTTTACAAATAAAGCCTCTAATTTTTTTAATATCACTTTTTACTTT
59733 TATAATTGAGGC
66 TATAATTGAGGC
* * *
59745 TTTCAATCTCACCTTT-TACCTTTA-AATTGAAGTCC-CT-ATTTTTTTAATCTCACTTTTTA-T
1 TTTCAATCTCA-CTTTCTACCTTTACAAATAAAG-CCTCTAATTTTTTTAATATCACTTTTTACT
59805 ATTTATAATTGAG
64 -TTTATAATTGAG
59818 ACCCTTAATT
Statistics
Matches: 67, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
74 1 0.01
75 33 0.49
76 8 0.12
77 21 0.31
78 4 0.06
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.49
Consensus pattern (77 bp):
TTTCAATCTCACTTTCTACCTTTACAAATAAAGCCTCTAATTTTTTTAATATCACTTTTTACTTT
TATAATTGAGGC
Found at i:65618 original size:29 final size:28
Alignment explanation
Indices: 65562--65618 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
65552 ACTCGTACCT
*
65562 AAGGTTATTTTTTAGATTTGACTTAAAA
1 AAGGTTATTTTTTAGATTTAACTTAAAA
*
65590 AAGGTTATTTTTT-TATATTAACTTAAAA
1 AAGGTTATTTTTTAGAT-TTAACTTAAAA
65618 A
1 A
65619 TAATAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 2 0.08
28 24 0.92
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.47
Consensus pattern (28 bp):
AAGGTTATTTTTTAGATTTAACTTAAAA
Done.