Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004308.1 Hibiscus syriacus cultivar Beakdansim tig00009446_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: 56126
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1619 original size:92 final size:92
Alignment explanation
Indices: 1462--1657 Score: 322
Period size: 92 Copynumber: 2.1 Consensus size: 92
1452 CAATGAAACT
1462 GGTTTTGTCATATTTTTACATGTTATATTGTTATGTATCGATACATTTTTATAAAGTATTAATAC
1 GGTTTTGTCATATTTTTACATGTTATATTGTTATGTATCGATACATTTTTATAAAGTATTAATAC
*
1527 TTTTAACATATCCGATAGCTCTTTACC
66 TTTTAACATATCCGATAACTCTTTACC
* * *
1554 GGTTTTTTCATATTTTTACCTGTTATATTGTTATGTATCGATATATTTTTATAAAGTA-TAGATA
1 GGTTTTGTCATATTTTTACATGTTATATTGTTATGTATCGATACATTTTTATAAAGTATTA-ATA
*
1618 CTTTTAACATATCCGGTAACTCTTTACC
65 CTTTTAACATATCCGATAACTCTTTACC
*
1646 AGTTTTGTCATA
1 GGTTTTGTCATA
1658 ATGAAACTGG
Statistics
Matches: 96, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
91 2 0.02
92 94 0.98
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.48
Consensus pattern (92 bp):
GGTTTTGTCATATTTTTACATGTTATATTGTTATGTATCGATACATTTTTATAAAGTATTAATAC
TTTTAACATATCCGATAACTCTTTACC
Found at i:1734 original size:204 final size:204
Alignment explanation
Indices: 1402--1769 Score: 578
Period size: 204 Copynumber: 1.8 Consensus size: 204
1392 ACATATACAA
* * *
1402 AAAGTATCAATACTTTTAACATATTCGGTAGCTCTTTACCGGTTTTATCACAATGAAACTGGTTT
1 AAAGTATCAATACTTTTAACATATCCGGTAACTCTTTACCAGTTTTATCACAATGAAACTGGTTT
* * *
1467 TGTCATATTTTTACATGTTATATTGTTATGTATCGATACATTTTTATAAAGTATTAATACTTTTA
66 TGTCAGATTTTTACATGTTATATTGTTATGTATCGATACATTTTTATAAAATATCAATACTTTTA
* *
1532 ACATATCCGATAGCTCTTTACCGGTTTTTTCATATTTTTACCTGTTATATTGTTATGTATCGATA
131 ACATATCCGATAGCTCTTTACCGGTATTGTCATATTTTTACCTGTTATATTGTTATGTATCGATA
1597 TATTTTTAT
196 TATTTTTAT
* *
1606 AAAGTAT-AGATACTTTTAACATATCCGGTAACTCTTTACCAGTTTTGTCATAATGAAACTGGTT
1 AAAGTATCA-ATACTTTTAACATATCCGGTAACTCTTTACCAGTTTTATCACAATGAAACTGGTT
* * *
1670 TTGTCAGGTTTTTATC-TGTTATATTTTTATGTATCGATACATTTTTATAAAATATCGATACTTT
65 TTGTCAGATTTTTA-CATGTTATATTGTTATGTATCGATACATTTTTATAAAATATCAATACTTT
*
1734 TAACATATCCGGTAGCTCTTTACCGGTATTGTCATA
129 TAACATATCCGATAGCTCTTTACCGGTATTGTCATA
1770 ATGAAACTGG
Statistics
Matches: 148, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
203 1 0.01
204 146 0.99
205 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (204 bp):
AAAGTATCAATACTTTTAACATATCCGGTAACTCTTTACCAGTTTTATCACAATGAAACTGGTTT
TGTCAGATTTTTACATGTTATATTGTTATGTATCGATACATTTTTATAAAATATCAATACTTTTA
ACATATCCGATAGCTCTTTACCGGTATTGTCATATTTTTACCTGTTATATTGTTATGTATCGATA
TATTTTTAT
Found at i:1753 original size:112 final size:111
Alignment explanation
Indices: 1554--1837 Score: 424
Period size: 112 Copynumber: 2.5 Consensus size: 111
1544 GCTCTTTACC
* * * *
1554 GGTTTTTTCATATTTTTACCTGTTATATTGTTATGTATCGATATATTTTTATAAAGTATAGATAC
1 GGTTTTGTCAGATTTTTA-CTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCGATAC
*
1619 TTTTAACATATCCGGTAACTCTTTACCAGTTTTGTCATAATGAAACT
65 TTTTAACATATCCGGTAACTCTTTACCAGTATTGTCATAATGAAACT
* * *
1666 GGTTTTGTCAGGTTTTTATCTGTTATATTTTTATGTATCGATACATTTTTATAAAATATCGATAC
1 GGTTTTGTCAGATTTTTA-CTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCGATAC
* *
1731 TTTTAACATATCCGGTAGCTCTTTACCGGTATTGTCATAATGAAACT
65 TTTTAACATATCCGGTAACTCTTTACCAGTATTGTCATAATGAAACT
* **
1778 GGTTTTGTCATATTTTTACTTGTTATATTGTTATGTATTAATACATTTTTATAAAGTATC
1 GGTTTTGTCAGATTTTTAC-TGTTATATTGTTATGTATCGATACATTTTTATAAAGTATC
1838 AATAGTTTAT
Statistics
Matches: 154, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
111 1 0.01
112 153 0.99
ACGTcount: A:0.27, C:0.12, G:0.13, T:0.48
Consensus pattern (111 bp):
GGTTTTGTCAGATTTTTACTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCGATACT
TTTAACATATCCGGTAACTCTTTACCAGTATTGTCATAATGAAACT
Found at i:2108 original size:75 final size:74
Alignment explanation
Indices: 1928--2184 Score: 358
Period size: 74 Copynumber: 3.5 Consensus size: 74
1918 AACATATCCG
*
1928 GTAGGTAGTTTAATGTAATAGGTAGCGCCTA-TTTTTTTACCGTTTACATTATTAGCAACCTTAA
1 GTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTAA
*
1992 AAAAAAACTA
66 AAAAAATC-A
*
2002 GTAGGTATTTTAATGTGATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGCAACCTTA
1 GTAGGTATTTTAATGTAATAGGTAGCGCCTATTTT-TTTTACCGTTTACATTATTAGCAACCTTA
2067 AAAAAAATCA
65 AAAAAAATCA
* * * * * *
2077 GTAGGTATTTTAACGTAATAGGCAGCGCCTATTATTTTTACCATTTACATTTTTAGTAACCTT-A
1 GTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTAA
2141 AAAAAATC-
66 AAAAAATCA
* * *
2149 GATAGATATTTTAATGTAATAGGTAACACCTATTTT
1 G-TAGGTATTTTAATGTAATAGGTAGCGCCTATTTT
2185 ATATTTCCTG
Statistics
Matches: 164, Mismatches: 16, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
72 1 0.01
73 37 0.23
74 54 0.33
75 35 0.21
76 37 0.23
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (74 bp):
GTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTAA
AAAAAATCA
Found at i:3784 original size:16 final size:16
Alignment explanation
Indices: 3740--3795 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
3730 CTGTAATGTT
*
3740 TCTGAGGGAATTGAAA
1 TCTGAAGGAATTGAAA
3756 TCTATGAAGGAATTGAAA
1 TC--TGAAGGAATTGAAA
*
3774 TCTGTAGGAATTGAAA
1 TCTGAAGGAATTGAAA
3790 TCTGAA
1 TCTGAA
3796 ACCTATTTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 20 0.57
18 15 0.43
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.29
Consensus pattern (16 bp):
TCTGAAGGAATTGAAA
Found at i:4441 original size:28 final size:28
Alignment explanation
Indices: 4374--4473 Score: 137
Period size: 28 Copynumber: 3.4 Consensus size: 28
4364 CCTAAACCCG
4374 AACCCGACCCGAATATCACACTTAAAAAA
1 AACCCGACCCGAATATCACACTT-AAAAA
4403 CCATACCCGACCCGAATATCACACTTAAAAA
1 --A-ACCCGACCCGAATATCACACTTAAAAA
* *
4434 AGCCCGACCCGAATATCAAACTTAAAAA
1 AACCCGACCCGAATATCACACTTAAAAA
*
4462 AACCTGACCCGA
1 AACCCGACCCGA
4474 TCCTGATTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
28 35 0.55
29 1 0.02
31 6 0.09
32 22 0.34
ACGTcount: A:0.44, C:0.33, G:0.09, T:0.14
Consensus pattern (28 bp):
AACCCGACCCGAATATCACACTTAAAAA
Found at i:8826 original size:14 final size:16
Alignment explanation
Indices: 8803--8842 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
8793 AAATGTGTAC
*
8803 AAAATTAAATAAC-AT
1 AAAATAAAATAACAAT
8818 -AAATAAAAT-ACAAT
1 AAAATAAAATAACAAT
8832 AAAATAAAATA
1 AAAATAAAATA
8843 TTAATATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
13 2 0.10
14 10 0.48
15 9 0.43
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATAAAATAACAAT
Found at i:9504 original size:3 final size:3
Alignment explanation
Indices: 9496--9530 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
9486 ATAAATGTTG
9496 TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT T
9531 TTAGATCCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:17665 original size:14 final size:15
Alignment explanation
Indices: 17640--17678 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
17630 TAGACGGGCA
*
17640 GATGTGGGGCAGGTG
1 GATGTGGGGCAGGCG
17655 GATGT-GGGCAGGCG
1 GATGTGGGGCAGGCG
*
17669 GATGCGGGGC
1 GATGTGGGGC
17679 GGGTAAGGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.13, C:0.13, G:0.59, T:0.15
Consensus pattern (15 bp):
GATGTGGGGCAGGCG
Found at i:23694 original size:54 final size:51
Alignment explanation
Indices: 23633--23736 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 51
23623 GCTCATCAGC
23633 TTATTTTTACCAAAATACTTACCATTTAAATTCCATAAGCTCATAAGCTTATTA
1 TTATTTTTACCAAAATACTTACCA-TT--ATTCCATAAGCTCATAAGCTTATTA
** * ** *
23687 TTATTTTTTTCAATATACTTGTCATTATTCCGTAAGCTCATAAGCTTATT
1 TTATTTTTACCAAAATACTTACCATTATTCCATAAGCTCATAAGCTTATT
23737 TGCACGGTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
51 23 0.52
53 2 0.05
54 19 0.43
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.45
Consensus pattern (51 bp):
TTATTTTTACCAAAATACTTACCATTATTCCATAAGCTCATAAGCTTATTA
Found at i:23897 original size:40 final size:40
Alignment explanation
Indices: 23842--23963 Score: 244
Period size: 40 Copynumber: 3.0 Consensus size: 40
23832 ACCATAGTGC
23842 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
23882 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
23922 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
23962 TA
1 TA
23964 TAAACCTGCA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:31232 original size:51 final size:51
Alignment explanation
Indices: 31169--31282 Score: 192
Period size: 51 Copynumber: 2.2 Consensus size: 51
31159 AACGATACTA
* *
31169 TCAATAAAATAAATAAATAATCGAAGAAAAAATAGATTTCAATCTCGACCC
1 TCAATAACATAAATAAATAATCAAAGAAAAAATAGATTTCAATCTCGACCC
* *
31220 TCAATAACATAAATAAATAATTAAAGAAAAAATAGATTTCAATCTTGACCC
1 TCAATAACATAAATAAATAATCAAAGAAAAAATAGATTTCAATCTCGACCC
31271 TCAATAACATAA
1 TCAATAACATAA
31283 TATGTAACTC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.54, C:0.15, G:0.06, T:0.25
Consensus pattern (51 bp):
TCAATAACATAAATAAATAATCAAAGAAAAAATAGATTTCAATCTCGACCC
Found at i:36237 original size:2 final size:2
Alignment explanation
Indices: 36230--36275 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
36220 ACATGGTATG
36230 AT AT AT AT AT 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
36272 AT AT
1 AT AT
36276 GATTTTTGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42148 original size:25 final size:25
Alignment explanation
Indices: 42114--42163 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
42104 GTTAAAGTAA
42114 AAATTATACCCTTTTACTAACGTAC
1 AAATTATACCCTTTTACTAACGTAC
42139 AAATTATACCCTTTTACTAACGTAC
1 AAATTATACCCTTTTACTAACGTAC
42164 CACATCATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (25 bp):
AAATTATACCCTTTTACTAACGTAC
Found at i:43818 original size:2 final size:2
Alignment explanation
Indices: 43811--43835 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43801 GTTCAAACAT
43811 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 T
43836 GCATATTATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44841 original size:2 final size:2
Alignment explanation
Indices: 44836--45004 Score: 94
Period size: 2 Copynumber: 87.0 Consensus size: 2
44826 ACACAACATA
*
44836 AT AT AT AGT AT CT AT AT -T AT AT -T AT AT AT AT AT AGT AT -T AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * *
44877 AT AG A- AT AT AT AT A- AT AT GGT AT AGT AT TT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT A-T AT AT AT AT AT AT AT AT
* *
44918 AT AT A- AT AT AT AGT AT AT AGT AT TT AT AT A- AT AT AT TT AT AGT
1 AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T
* * *
44961 AT AT AT -T TT AT AGT AT -T TT AT AT TT AT AT AT A- AT AT -T A-
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44999 AT AT AT
1 AT AT AT
45005 TATGTTATTA
Statistics
Matches: 131, Mismatches: 15, Indels: 42
0.70 0.08 0.22
Matches are distributed among these distances:
1 13 0.10
2 103 0.79
3 15 0.11
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.51
Consensus pattern (2 bp):
AT
Found at i:44922 original size:36 final size:37
Alignment explanation
Indices: 44882--45002 Score: 105
Period size: 36 Copynumber: 3.4 Consensus size: 37
44872 ATTATATAGA
*
44882 ATATATA-TAATATGGTATAGTATTTATATATATTAT
1 ATATATAGTAATATGATATAGTATTTATATATATTAT
44918 ATATA-A-T-ATATAGTATATAGTATTTATATA-A-TAT
1 ATATATAGTAATAT-G-ATATAGTATTTATATATATTAT
* **
44952 ATTTATAGTATATATTTTATAGTATTT-TATAT-TTAT
1 ATATATAGTA-ATATGATATAGTATTTATATATATTAT
*
44988 ATATAATATTAATAT
1 ATAT-ATAGTAATAT
45003 ATTATGTTAT
Statistics
Matches: 70, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
34 11 0.16
35 9 0.13
36 41 0.59
37 5 0.07
38 4 0.06
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (37 bp):
ATATATAGTAATATGATATAGTATTTATATATATTAT
Found at i:46605 original size:14 final size:14
Alignment explanation
Indices: 46586--46678 Score: 70
Period size: 14 Copynumber: 6.7 Consensus size: 14
46576 GCACAGTGTA
46586 ATATAATATTTTAT
1 ATATAATATTTTAT
*
46600 ATATAATATATTAT
1 ATATAATATTTTAT
* *
46614 GTATAGTA--TT-T
1 ATATAATATTTTAT
46625 ATATAATATATTTAT
1 ATATAATAT-TTTAT
46640 AGTAT-ATATTTTAT
1 A-TATAATATTTTAT
*
46654 A-ATATTTATATTTAT
1 ATATA-ATAT-TTTAT
*
46669 ATATATTATT
1 ATATAATATT
46679 AATATATTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
11 7 0.11
12 4 0.06
14 31 0.48
15 16 0.25
16 6 0.09
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (14 bp):
ATATAATATTTTAT
Found at i:46609 original size:9 final size:8
Alignment explanation
Indices: 46597--46743 Score: 75
Period size: 7 Copynumber: 19.1 Consensus size: 8
46587 TATAATATTT
46597 TATATATA
1 TATATATA
46605 -ATATAT-
1 TATATATA
*
46611 TATGTATA
1 TATATATA
*
46619 GTATTTATA
1 -TATATATA
46628 TA-ATATA
1 TATATATA
*
46635 TTTATAGTA
1 TATATA-TA
*
46644 TATAT-TT
1 TATATATA
46651 TATA-ATA
1 TATATATA
* *
46658 TTTATATT
1 TATATATA
46666 TATATATA
1 TATATATA
46674 T-TAT-TA
1 TATATATA
46680 -ATATAT-
1 TATATATA
46686 TATATATA
1 TATATATA
46694 TA-ATATA
1 TATATATA
*
46701 TAGTATTTA
1 TA-TATATA
*
46710 TAGTTTATA
1 TA-TATATA
*
46719 TGTAGTATA
1 TATA-TATA
46728 TATAGTAT-
1 TATA-TATA
46736 TAT-TATA
1 TATATATA
46743 T
1 T
46744 TATTTTTGGT
Statistics
Matches: 107, Mismatches: 17, Indels: 31
0.69 0.11 0.20
Matches are distributed among these distances:
6 8 0.07
7 43 0.40
8 20 0.19
9 36 0.34
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (8 bp):
TATATATA
Found at i:46632 original size:25 final size:24
Alignment explanation
Indices: 46599--46748 Score: 112
Period size: 25 Copynumber: 6.0 Consensus size: 24
46589 TAATATTTTA
46599 TATATAATATATTATGTATAGTATT
1 TATATAATATATTATGTATA-TATT
46624 TATATAATATATTTATAGTATATATT
1 TATATAATATA-TTAT-GTATATATT
* *
46650 T-TATAATATTTATATTTATATATAT
1 TATATAATATAT-TATGTATATAT-T
* *
46675 TAT-TAATATATTATATATATA-A
1 TATATAATATATTATGTATATATT
* * *
46697 TATATAGTAT-TTATAGTTTATATG
1 TATATAATATATTAT-GTATATATT
46721 TAGTATATATAGTATTAT-TATATTATT
1 TA-TATA-ATA-TATTATGTATA-TATT
46748 T
1 T
46749 TTGGTTTTAT
Statistics
Matches: 100, Mismatches: 12, Indels: 24
0.74 0.09 0.18
Matches are distributed among these distances:
22 7 0.07
23 10 0.10
24 19 0.19
25 35 0.35
26 15 0.15
27 10 0.10
28 4 0.04
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (24 bp):
TATATAATATATTATGTATATATT
Found at i:46670 original size:42 final size:42
Alignment explanation
Indices: 46597--46711 Score: 121
Period size: 42 Copynumber: 2.7 Consensus size: 42
46587 TATAATATTT
* * *
46597 TATA-TATAATATATTATGTATAGTATTTATATA-ATATATTTA
1 TATATTAT-ATATATAATATATAGTATTTATATATAT-TATTAA
* *
46639 TAGTA-TATATTTTATAATATTTA-TATTTATATATATTATTAA
1 TA-TATTATA-TATATAATATATAGTATTTATATATATTATTAA
46681 TATATTATATATATAATATATAGTATTTATA
1 TATATTATATATATAATATATAGTATTTATA
46712 GTTTATATGT
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
41 13 0.21
42 32 0.52
43 16 0.26
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (42 bp):
TATATTATATATATAATATATAGTATTTATATATATTATTAA
Found at i:46717 original size:29 final size:29
Alignment explanation
Indices: 46586--46746 Score: 124
Period size: 29 Copynumber: 5.7 Consensus size: 29
46576 GCACAGTGTA
* *
46586 ATATAATATTT-TATA-TATAATATATTAT
1 ATATAGTATTTATATATTAT-ATATATAAT
* * * *
46614 GTATAGTATTTATATAATATATTTATAGT
1 ATATAGTATTTATATATTATATATATAAT
*
46643 ATATA-T-TTTATAATATT-TATAT-TTAT
1 ATATAGTATTTAT-ATATTATATATATAAT
* *
46669 ATATATTATTAATATATTATATATATAAT
1 ATATAGTATTTATATATTATATATATAAT
*
46698 ATATAGTATTTATAGT-TTATATGTAGT-AT
1 ATATAGTATTTATA-TATTATATATA-TAAT
46727 ATATAGTA-TTATTATATTAT
1 ATATAGTATTTA-TATATTAT
46747 TTTTGGTTTT
Statistics
Matches: 107, Mismatches: 15, Indels: 21
0.75 0.10 0.15
Matches are distributed among these distances:
26 7 0.07
27 15 0.14
28 27 0.25
29 53 0.50
30 5 0.05
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (29 bp):
ATATAGTATTTATATATTATATATATAAT
Found at i:46717 original size:64 final size:64
Alignment explanation
Indices: 46587--46718 Score: 157
Period size: 64 Copynumber: 2.1 Consensus size: 64
46577 CACAGTGTAA
* *
46587 TATAATATTTTATATATAATATATTATGTATAGTATTTATATAATATATTTATAGTATATATTT
1 TATAATATTTTATATATAATATATTATGTATAGTATTTATATAATATATATATAGTATATAGTT
*
46651 TATAATA-TTTATATTTATATATATTAT-TA-A-TATATTATAT-ATATAATATATAGTATTTAT
1 TATAATATTTTATATATA-ATATATTATGTATAGTAT-TTATATAATAT-ATATATAGTA--TAT
46711 AGTT
61 AGTT
46715 TATA
1 TATA
46719 TGTAGTATAT
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
61 7 0.12
62 16 0.27
63 11 0.18
64 26 0.43
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (64 bp):
TATAATATTTTATATATAATATATTATGTATAGTATTTATATAATATATATATAGTATATAGTT
Found at i:46718 original size:16 final size:14
Alignment explanation
Indices: 46620--46711 Score: 66
Period size: 13 Copynumber: 6.6 Consensus size: 14
46610 TTATGTATAG
*
46620 TATTTATATA-ATA
1 TATTTATATATTTA
*
46633 TATTTATAGTATATA
1 TATTTATA-TATTTA
46648 T-TTTATAATATTTA
1 TATTTAT-ATATTTA
*
46662 TATTTATATATAT-
1 TATTTATATATTTA
*
46675 TATTAATATA-TTA
1 TATTTATATATTTA
* *
46688 TATATATAATATATA
1 TATTTAT-ATATTTA
46703 GTATTTATA
1 -TATTTATA
46712 GTTTATATGT
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
12 1 0.02
13 22 0.35
14 21 0.33
15 13 0.21
16 6 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.55
Consensus pattern (14 bp):
TATTTATATATTTA
Found at i:46732 original size:20 final size:21
Alignment explanation
Indices: 46605--46735 Score: 57
Period size: 20 Copynumber: 6.4 Consensus size: 21
46595 TTTATATATA
* *
46605 ATATATTATGTATAGTATTTAT
1 ATATAGTATATATAGTA-TTAT
*
46627 ATAATA-TATTTATAGTATATATT
1 AT-ATAGTATATATAGTAT-TA-T
* * *
46650 TTATAATATTTATA-T-TTAT
1 ATATAGTATATATAGTATTAT
*
46669 ATATATTAT-TAATA-TATTAT
1 ATATAGTATAT-ATAGTATTAT
46689 ATATA-TAATATATAGTA-T-T
1 ATATAGT-ATATATAGTATTAT
* *
46708 -TATAGTTTATAT-GTAGTAT
1 ATATAGTATATATAGTATTAT
46727 ATATAGTAT
1 ATATAGTAT
46736 TATTATATTA
Statistics
Matches: 90, Mismatches: 6, Indels: 28
0.73 0.05 0.23
Matches are distributed among these distances:
17 3 0.03
18 11 0.12
19 16 0.18
20 24 0.27
21 5 0.06
22 18 0.20
23 13 0.14
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (21 bp):
ATATAGTATATATAGTATTAT
Found at i:47189 original size:38 final size:38
Alignment explanation
Indices: 47137--47212 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
47127 GAATACTAAC
47137 GCCAGATTTCTTGGTCGCGTTTTTGGCAAGAAAAACTT
1 GCCAGATTTCTTGGTCGCGTTTTTGGCAAGAAAAACTT
* *
47175 GCCAGATTTTTTGGTCGTGTTTTTGGCAAGAAAAACTT
1 GCCAGATTTCTTGGTCGCGTTTTTGGCAAGAAAAACTT
47213 TGAATTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.37
Consensus pattern (38 bp):
GCCAGATTTCTTGGTCGCGTTTTTGGCAAGAAAAACTT
Done.