Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005301.1 Hibiscus syriacus cultivar Beakdansim tig00011998_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: 65477
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4447 original size:15 final size:16
Alignment explanation
Indices: 4422--4454 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4412 ATATGAGAAA
4422 AATTCAATTTAAATTT
1 AATTCAATTTAAATTT
*
4438 AATT-AATTTAATTTT
1 AATTCAATTTAAATTT
4453 AA
1 AA
4455 ATAACGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTCAATTTAAATTT
Found at i:4629 original size:22 final size:22
Alignment explanation
Indices: 4597--4671 Score: 123
Period size: 22 Copynumber: 3.4 Consensus size: 22
4587 TATTTCAAAT
* *
4597 AATTTAAAGTTTGTTGTGGCTC
1 AATTTATAGTTTGTTGCGGCTC
4619 AATTTATAGTTTGTTGCGGCTC
1 AATTTATAGTTTGTTGCGGCTC
*
4641 AATTTATAGTTTGTTGCAGCTC
1 AATTTATAGTTTGTTGCGGCTC
4663 AATTTATAG
1 AATTTATAG
4672 CGTGTTGCAG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.45
Consensus pattern (22 bp):
AATTTATAGTTTGTTGCGGCTC
Found at i:4677 original size:22 final size:22
Alignment explanation
Indices: 4597--4681 Score: 116
Period size: 22 Copynumber: 3.9 Consensus size: 22
4587 TATTTCAAAT
* **
4597 AATTTAAAGTTTGTTGTGGCTC
1 AATTTATAGTTTGTTGCAGCTC
*
4619 AATTTATAGTTTGTTGCGGCTC
1 AATTTATAGTTTGTTGCAGCTC
4641 AATTTATAGTTTGTTGCAGCTC
1 AATTTATAGTTTGTTGCAGCTC
**
4663 AATTTATAGCGTGTTGCAG
1 AATTTATAGTTTGTTGCAG
4682 TGTTACGTAA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.44
Consensus pattern (22 bp):
AATTTATAGTTTGTTGCAGCTC
Found at i:5900 original size:19 final size:19
Alignment explanation
Indices: 5876--5915 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
5866 AGTTTAGGGT
*
5876 TTAGAGTTTGGGGTTTAAG
1 TTAGAGTTTAGGGTTTAAG
*
5895 TTAGAGTTTATGGTTTAAG
1 TTAGAGTTTAGGGTTTAAG
5914 TT
1 TT
5916 TTAAGGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (19 bp):
TTAGAGTTTAGGGTTTAAG
Found at i:5924 original size:33 final size:33
Alignment explanation
Indices: 5852--5927 Score: 82
Period size: 33 Copynumber: 2.2 Consensus size: 33
5842 TTTAAGTTAG
**
5852 GGTTTAAGTGTTAAAGTTTAGGGTTTAGAGTTTGG
1 GGTTTAA--GTTAAAGTTTAGGGTTTAGAGTTTAA
* *
5887 GGTTTAAGTTAGAGTTTATGGTTTA-AGTTTTAA
1 GGTTTAAGTTAAAGTTTAGGGTTTAGAG-TTTAA
5920 GGTTTAAG
1 GGTTTAAG
5928 CATTAGGATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
32 2 0.06
33 27 0.75
35 7 0.19
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (33 bp):
GGTTTAAGTTAAAGTTTAGGGTTTAGAGTTTAA
Found at i:10977 original size:35 final size:35
Alignment explanation
Indices: 10919--11007 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
10909 TTGCACTGTA
* * * *
10919 TTTTCTGCACTGTTCGAAGCAAATCTACACTGCAT
1 TTTTCTGCACTGTTTGAACCAAATATACACTACAT
* * * *
10954 TTTTCTGCATTGTTTTAACCAAATATGCACTATAT
1 TTTTCTGCACTGTTTGAACCAAATATACACTACAT
10989 TTTTCTGCACTGTTTGAAC
1 TTTTCTGCACTGTTTGAAC
11008 AATGAAAATT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (35 bp):
TTTTCTGCACTGTTTGAACCAAATATACACTACAT
Found at i:16950 original size:21 final size:20
Alignment explanation
Indices: 16926--16979 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
16916 ATATTTAAAA
16926 ATAATAATAAATTTAATATGT
1 ATAA-AATAAATTTAATATGT
* *
16947 ATAAAAGTAAATATAATATTT
1 ATAAAA-TAAATTTAATATGT
*
16968 TTAAAATAAATT
1 ATAAAATAAATT
16980 CAAAAATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (20 bp):
ATAAAATAAATTTAATATGT
Found at i:17135 original size:26 final size:27
Alignment explanation
Indices: 17106--17167 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 27
17096 ATCATTAAAT
*
17106 AAAATTAAAATTATTAATTATAT-TAA
1 AAAATTAAAATTAATAATTATATATAA
* *
17132 AAAATT-AATTTAATGATTATATATAA
1 AAAATTAAAATTAATAATTATATATAA
*
17158 AAAATAAAAA
1 AAAATTAAAA
17168 AATAATATAG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 13 0.45
26 14 0.48
27 2 0.07
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (27 bp):
AAAATTAAAATTAATAATTATATATAA
Found at i:17176 original size:24 final size:24
Alignment explanation
Indices: 17149--17194 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
17139 ATTTAATGAT
*
17149 TATATATAAAAAATAAAAAAATAA
1 TATAGATAAAAAATAAAAAAATAA
* * *
17173 TATAGCTTAAAAATATAAAAAT
1 TATAGATAAAAAATAAAAAAAT
17195 CTTAAATTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (24 bp):
TATAGATAAAAAATAAAAAAATAA
Found at i:18669 original size:38 final size:35
Alignment explanation
Indices: 18624--18850 Score: 162
Period size: 38 Copynumber: 6.2 Consensus size: 35
18614 TTTTGGAAAT
18624 ATTTTTGAAAACATGTAATATATAGTTTTTAGAAAACG
1 ATTTTTGAAAACA-GT-ATATATAGTTTTTA-AAAACG
* * *
18662 GTTTTTGAAAGCATATAATATATAGTTTTTAAAAATCG
1 ATTTTTGAAAACA-GT-ATATATAGTTTTTAAAAA-CG
* * *
18700 ATTTTTGAATATA-TATATAGTATGGTTTTAAAATACG
1 ATTTTTGAAAACAGTATATA-TA-GTTTTTAAAA-ACG
*
18737 -TTTTTGAAAA-AGTATAGTATAGTTTTTTTAAAAAATG
1 ATTTTTGAAAACAGTATA-TATAG--TTTTT-AAAAACG
* *
18774 GTTTTTGAAAAC-GTATATAATA-TAGTTTTGAAAAC-
1 ATTTTTGAAAACAGTATAT-ATAGT--TTTTAAAAACG
*
18809 ATATTTTGAAAACA-TATATATAGTTTTTTAAAACG
1 AT-TTTTGAAAACAGTATATATAGTTTTTAAAAACG
18844 ATTTTTG
1 ATTTTTG
18851 GAACTATATA
Statistics
Matches: 156, Mismatches: 15, Indels: 40
0.74 0.07 0.19
Matches are distributed among these distances:
34 14 0.09
35 14 0.09
36 38 0.24
37 28 0.18
38 62 0.40
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.44
Consensus pattern (35 bp):
ATTTTTGAAAACAGTATATATAGTTTTTAAAAACG
Found at i:18744 original size:74 final size:71
Alignment explanation
Indices: 18643--18867 Score: 192
Period size: 74 Copynumber: 3.1 Consensus size: 71
18633 AACATGTAAT
18643 ATATAGTTTTTAGAAAACGGTTTTTGAAAGCATATAATATATAGTTTTTAAAAATCGATTTTTGA
1 ATATAG-TTTTA-AAAAC-GTTTTTGAAA--ATATAATATATAGTTTTTAAAAATCGATTTTTGA
18708 ATATATATATA
61 ATATATATATA
* * *
18719 GTATGGTTTTAAAATACGTTTTTGAAAA-AGT-ATAGTATAGTTTTTTTAAAAAAT-GGTTTTTG
1 ATATAGTTTTAAAA-ACGTTTTTGAAAATA-TAATA-TATAG--TTTTT-AAAAATCGATTTTTG
* **
18781 AAAACGTATATA
60 AATATATATATA
* * * * *
18793 ATATAGTTTTGAAAACATATTTTGAAAACAT-ATATATAGTTTTTTAAAA-CGATTTTTGGAA-C
1 ATATAGTTTTAAAAACGT-TTTTGAAAATATAATATATAGTTTTTAAAAATCGATTTTT-GAATA
18855 TATATATA
64 TATATATA
18863 ATATA
1 ATATA
18868 TAATTTCTGA
Statistics
Matches: 124, Mismatches: 15, Indels: 26
0.75 0.09 0.16
Matches are distributed among these distances:
70 21 0.17
71 12 0.10
72 7 0.06
73 8 0.06
74 58 0.47
75 14 0.11
76 4 0.03
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.43
Consensus pattern (71 bp):
ATATAGTTTTAAAAACGTTTTTGAAAATATAATATATAGTTTTTAAAAATCGATTTTTGAATATA
TATATA
Found at i:18817 original size:13 final size:13
Alignment explanation
Indices: 18799--18825 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
18789 TATAATATAG
18799 TTTTGAAAACATA
1 TTTTGAAAACATA
18812 TTTTGAAAACATA
1 TTTTGAAAACATA
18825 T
1 T
18826 ATATAGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
TTTTGAAAACATA
Found at i:18826 original size:112 final size:111
Alignment explanation
Indices: 18625--18832 Score: 248
Period size: 112 Copynumber: 1.9 Consensus size: 111
18615 TTTGGAAATA
* *
18625 TTTTTGAAAACATGTAATATATAGTTTTTAGAAAACGGTTTTTGAAAGCATATAATATATAGTTT
1 TTTTTGAAAACATGTAATATATAGTTTTTAAAAAACGGTTTTTGAAAACATATAATATATAGTTT
* *
18690 TTAAAAATCGATTTTTGAATATATATATAGTATGGTTTTAAAATACG
66 TGAAAAATC-ATTTTTGAACATATATATAGTATGGTTTTAAAATACG
* *
18737 TTTTTGAAAA-A-GT-ATAGTATAGTTTTTTTAAAAAATGGTTTTTGAAAACGTAT-ATAATATA
1 TTTTTGAAAACATGTAATA-TATAG--TTTTTAAAAAACGGTTTTTGAAAACATATAAT-ATATA
18798 GTTTTG-AAAA-CATATTTTGAAAACATATATATAGT
62 GTTTTGAAAAATCAT-TTTTG--AACATATATATAGT
18833 TTTTTAAAAC
Statistics
Matches: 83, Mismatches: 6, Indels: 14
0.81 0.06 0.14
Matches are distributed among these distances:
109 5 0.06
110 13 0.16
111 7 0.08
112 58 0.70
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.43
Consensus pattern (111 bp):
TTTTTGAAAACATGTAATATATAGTTTTTAAAAAACGGTTTTTGAAAACATATAATATATAGTTT
TGAAAAATCATTTTTGAACATATATATAGTATGGTTTTAAAATACG
Found at i:18945 original size:16 final size:16
Alignment explanation
Indices: 18897--18956 Score: 52
Period size: 16 Copynumber: 3.7 Consensus size: 16
18887 TTTTTTGAAA
* *
18897 ATATTATATATATTTT
1 ATATTATTTATATTAT
*
18913 ACA-TAGTTTATTATTAT
1 ATATTA-TTTA-TATTAT
18930 ATATTATTTATATTAT
1 ATATTATTTATATTAT
18946 -TATTTATTTAT
1 ATA-TTATTTAT
18957 TTTTATTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
15 4 0.11
16 19 0.53
17 11 0.31
18 2 0.06
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (16 bp):
ATATTATTTATATTAT
Found at i:18945 original size:19 final size:20
Alignment explanation
Indices: 18921--18963 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
18911 TTACATAGTT
18921 TATTATTATATA-TTATTTA
1 TATTATTATATATTTATTTA
* *
18940 TATTATTATTTATTTATTTT
1 TATTATTATATATTTATTTA
18960 TATT
1 TATT
18964 TAAAAAATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TATTATTATATATTTATTTA
Found at i:25130 original size:18 final size:18
Alignment explanation
Indices: 25107--25160 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
25097 AATGGTAGTA
25107 GTATCGATACTAGTAAGG
1 GTATCGATACTAGTAAGG
*
25125 GTATCGACACCAATAGTAA-G
1 GTATCGATA-C--TAGTAAGG
25145 GTATCGATACTA-TAAG
1 GTATCGATACTAGTAAG
25161 TAAAGATGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
16 3 0.10
17 2 0.07
18 8 0.27
19 2 0.07
20 9 0.30
21 6 0.20
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (18 bp):
GTATCGATACTAGTAAGG
Found at i:25232 original size:22 final size:22
Alignment explanation
Indices: 25207--25248 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
25197 TACTGAAGTG
*
25207 GGTATCGGTACCATAGAAGAGA
1 GGTATCAGTACCATAGAAGAGA
25229 GGTATCAGTACCATAGAAGA
1 GGTATCAGTACCATAGAAGA
25249 AAAATATCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.14, G:0.29, T:0.19
Consensus pattern (22 bp):
GGTATCAGTACCATAGAAGAGA
Found at i:25256 original size:22 final size:22
Alignment explanation
Indices: 25209--25261 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
25199 CTGAAGTGGG
* **
25209 TATCGGTACCATAGAAGAGAGG
1 TATCGGTACCATAGAAGAAAAA
*
25231 TATCAGTACCATAGAAGAAAAA
1 TATCGGTACCATAGAAGAAAAA
25253 TATCGGTAC
1 TATCGGTAC
25262 TGTGGGTAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.21
Consensus pattern (22 bp):
TATCGGTACCATAGAAGAAAAA
Found at i:25915 original size:23 final size:23
Alignment explanation
Indices: 25885--25958 Score: 112
Period size: 23 Copynumber: 3.2 Consensus size: 23
25875 TATGTTTGGG
25885 ACAAAACTAAGTGGTCATTCGGA
1 ACAAAACTAAGTGGTCATTCGGA
*
25908 ACAAAACTAAGTGGTCATTTGGA
1 ACAAAACTAAGTGGTCATTCGGA
* * *
25931 ACAAAACTATGTGGTCCTTCGGG
1 ACAAAACTAAGTGGTCATTCGGA
25954 ACAAA
1 ACAAA
25959 TATGTGGTAC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.23
Consensus pattern (23 bp):
ACAAAACTAAGTGGTCATTCGGA
Found at i:25964 original size:21 final size:22
Alignment explanation
Indices: 25938--25986 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
25928 GGAACAAAAC
*
25938 TATGTGGTCCTTCGG-GACAAA-
1 TATGTGGTACTTCGGTG-CAAAT
25959 TATGTGGTACTTCGGTGCAAAT
1 TATGTGGTACTTCGGTGCAAAT
25981 TATGTG
1 TATGTG
25987 AGCTGTGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.22, C:0.14, G:0.29, T:0.35
Consensus pattern (22 bp):
TATGTGGTACTTCGGTGCAAAT
Found at i:41314 original size:37 final size:37
Alignment explanation
Indices: 41287--41384 Score: 117
Period size: 37 Copynumber: 2.6 Consensus size: 37
41277 TTGGAAATAT
* *
41287 TTTTGAAAACATGTAATATATAGTTTTTAGAAAACGG
1 TTTTGAAAACATATAATATATAGTTTTTAGAAAACAG
*
41324 TTTTGAAAGCATATAATATATAGTTTTTA-AAAATCAG
1 TTTTGAAAACATATAATATATAGTTTTTAGAAAA-CAG
* *
41361 TTTTTGAATATATATATATATATA
1 -TTTTGAAAACATATA-ATATATA
41385 TATATATATA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
36 4 0.08
37 29 0.56
38 12 0.23
39 7 0.13
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (37 bp):
TTTTGAAAACATATAATATATAGTTTTTAGAAAACAG
Found at i:41375 original size:2 final size:2
Alignment explanation
Indices: 41368--41412 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
41358 CAGTTTTTGA
41368 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
41410 AT A
1 AT A
41413 GTATGGCTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41460 original size:36 final size:37
Alignment explanation
Indices: 41420--41540 Score: 131
Period size: 36 Copynumber: 3.2 Consensus size: 37
41410 ATAGTATGGC
*
41420 TTTGAAAATATGTTTTTGAAAAAGTTA-ATATATAGT
1 TTTGAAAAAATGTTTTTGAAAAAGTTATATATATAGT
* *
41456 TTTGAAAACACGTTTTTGAAAAACGTATAATATATATAGT
1 TTTGAAAAAATGTTTTTGAAAAA-GT-T-ATATATATAGT
**
41496 TTT-AAAAAATAGTTTTTGAAAGCG-TATATAATATAGT
1 TTTGAAAAAAT-GTTTTTGAAAAAGTTATAT-ATATAGT
41533 TTTGAAAA
1 TTTGAAAA
41541 CGTATTTTGA
Statistics
Matches: 72, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
36 25 0.35
37 13 0.18
38 5 0.07
39 7 0.10
40 22 0.31
ACGTcount: A:0.43, C:0.03, G:0.13, T:0.40
Consensus pattern (37 bp):
TTTGAAAAAATGTTTTTGAAAAAGTTATATATATAGT
Found at i:41595 original size:36 final size:34
Alignment explanation
Indices: 41485--41600 Score: 94
Period size: 37 Copynumber: 3.3 Consensus size: 34
41475 AAAACGTATA
*
41485 ATATATATAGTTTTAAAAAATAGTTTTTGAAAGCGTAT
1 ATATATATAGTTTTAAAAAAGA-TTTTTGAAA---TAT
* * *
41523 ATA-ATATAGTTTTGAAAACG-TATTTTGAAA-AC
1 ATATATATAGTTTTAAAAAAGAT-TTTTGAAATAT
*
41555 ATATATATAGTTTTTTAAAAAGATTTTTGGAAATAT
1 ATATATATAG-TTTTAAAAAAGATTTTT-GAAATAT
41591 ATATAATATA
1 ATAT-ATATA
41601 TAATTTTTGA
Statistics
Matches: 64, Mismatches: 7, Indels: 15
0.74 0.08 0.17
Matches are distributed among these distances:
32 4 0.06
33 6 0.09
34 13 0.20
35 6 0.09
36 13 0.20
37 19 0.30
38 3 0.05
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.42
Consensus pattern (34 bp):
ATATATATAGTTTTAAAAAAGATTTTTGAAATAT
Found at i:41623 original size:17 final size:17
Alignment explanation
Indices: 41598--41630 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41588 TATATATAAT
41598 ATATAATTTTTGAAAAC
1 ATATAATTTTTGAAAAC
*
41615 ATATTATTTTTGAAAA
1 ATATAATTTTTGAAAA
41631 TATAATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (17 bp):
ATATAATTTTTGAAAAC
Found at i:41691 original size:24 final size:24
Alignment explanation
Indices: 41664--41722 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
41654 TTATTATAAA
41664 TTATTTATATTATTACTTA-TTATT
1 TTATTTATATTATTACTTATTTA-T
*
41688 TTATTTATATTATTATTTATTTAT
1 TTATTTATATTATTACTTATTTAT
*
41712 TTATTTTTATT
1 TTATTTATATT
41723 TACAAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 29 0.91
25 3 0.09
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (24 bp):
TTATTTATATTATTACTTATTTAT
Found at i:41700 original size:14 final size:15
Alignment explanation
Indices: 41681--41724 Score: 65
Period size: 14 Copynumber: 3.0 Consensus size: 15
41671 TATTATTACT
41681 TATTA-TTTTATTTA
1 TATTATTTTTATTTA
41695 TATTATTATTTATTTA
1 TATTATT-TTTATTTA
41711 T-TTATTTTTATTTA
1 TATTATTTTTATTTA
41725 CAAAAATAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 13 0.46
15 6 0.21
16 9 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TATTATTTTTATTTA
Found at i:41715 original size:12 final size:12
Alignment explanation
Indices: 41651--41722 Score: 71
Period size: 12 Copynumber: 6.2 Consensus size: 12
41641 GTTATATAGT
41651 TTATTA-TTATA
1 TTATTATTTATA
*
41662 -AATTATTTATA
1 TTATTATTTATA
*
41673 TTATTACTTATTA
1 TTATTATTTA-TA
41686 TT-TTATTTATA
1 TTATTATTTATA
41697 TTATTATTTAT-
1 TTATTATTTATA
*
41708 TTATTTATTTTTA
1 TTA-TTATTTATA
41721 TT
1 TT
41723 TACAAAAATA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
10 4 0.08
11 12 0.24
12 28 0.56
13 6 0.12
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATTATTTATA
Found at i:41724 original size:4 final size:4
Alignment explanation
Indices: 41664--41717 Score: 51
Period size: 4 Copynumber: 13.5 Consensus size: 4
41654 TTATTATAAA
*
41664 TTAT TTAT ATTA- TTAC TTA- TTATT TTAT TTAT ATTA- TTAT TTAT TTAT
1 TTAT TTAT -TTAT TTAT TTAT TTA-T TTAT TTAT -TTAT TTAT TTAT TTAT
41712 TTAT TT
1 TTAT TT
41718 TTATTTACAA
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
3 9 0.20
4 26 0.59
5 9 0.20
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (4 bp):
TTAT
Found at i:42884 original size:14 final size:14
Alignment explanation
Indices: 42848--42890 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
42838 TTAACGATTG
42848 TTTTCTTTTAATTT
1 TTTTCTTTTAATTT
* *
42862 ATATCTTTTAATTT
1 TTTTCTTTTAATTT
*
42876 TTTTATTTT-ATTT
1 TTTTCTTTTAATTT
42889 TT
1 TT
42891 ATTTAACATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 6 0.25
14 18 0.75
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTCTTTTAATTT
Found at i:43973 original size:54 final size:54
Alignment explanation
Indices: 43908--44358 Score: 496
Period size: 54 Copynumber: 8.4 Consensus size: 54
43898 TTCATTGACA
* ** * * *
43908 TGCACACATAGTGCCTATACGGTCATTCATAAAAATATTATGAATTATGT-GGT
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTATGTGGGT
* ** * *
43961 T-CACATATATAGTGTATATACGATCT-TTCATCAACCTATGATGAATT-TCGTGGGT
1 TGCACA-CT-TAGTGCCTATACGGT-TGTTCATCAACATATGATGAATTAT-GTGGGT
* * ***
44016 TACACACTTAGTGCCTATATGGTTGTTCATCAACATATGATGAATTCCATGGGT
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTATGTGGGT
* * ***
44070 TGCACACTTAGTGCCTATACGGTTGTTTATCAATATATGATGAATTCCATGGGT
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTATGTGGGT
* * * * * *
44124 TGCACACTTAGTGCTTATATGGTTGATCATTAATATATGATGAATTTTGTGGGT
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTATGTGGGT
* *
44178 TGCACACTTGGTGCCTATACGGTTGTTCATCAATATATGATGAATTATGTGGGT
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTATGTGGGT
* *
44232 TGCACACTTAGTGCCTATACGGTTGTTCATTAACATATGATGAATTTTGTGGGT
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTATGTGGGT
** * * * *
44286 TGCACACTTAGTGCCTATACATTTGTTCATTAACATATGATCAATTTTGTGGGA
1 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTATGTGGGT
*
44340 TGCACATTTAGTGCCTATA
1 TGCACACTTAGTGCCTATA
44359 AGGAAATTCA
Statistics
Matches: 345, Mismatches: 45, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
52 4 0.01
53 3 0.01
54 329 0.95
55 5 0.01
56 4 0.01
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.38
Consensus pattern (54 bp):
TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTATGTGGGT
Found at i:51107 original size:54 final size:54
Alignment explanation
Indices: 51036--51377 Score: 383
Period size: 54 Copynumber: 6.4 Consensus size: 54
51026 CGTTGAGATT
* * ** * *
51036 CACACGTAGTACCTATACGATCATTCATAAACATATTATGAATTATGT-GGTT-
1 CACACTTAGTGCCTATACGATTGTTCATCAACATATGATGAATTATGTGGGTTG
* * * * *
51088 CACACATATAGTGCCTATACGGTCGTTCATCAACCTATGATGAATAATGTGGATTG
1 CACAC-T-TAGTGCCTATACGATTGTTCATCAACATATGATGAATTATGTGGGTTG
*
51144 CACACTTAGTGCCTATACTG-TTGTTCATCAATATATGATGAATTATGTGGGTT-
1 CACACTTAGTGCCTATAC-GATTGTTCATCAACATATGATGAATTATGTGGGTTG
* * * ** *
51197 -ACACTTAGTGCCTATACGGTTGTTCATCAACATATAATAAATTCCGTTGGTTG
1 CACACTTAGTGCCTATACGATTGTTCATCAACATATGATGAATTATGTGGGTTG
* * *
51250 CACACTTAGTGCCTATATGGTTGTTCATCAACATATGATGAATTTTGTGGGTTG
1 CACACTTAGTGCCTATACGATTGTTCATCAACATATGATGAATTATGTGGGTTG
* *
51304 CACACTTAGTGCCCATAC-AGTTGTTCATCAATATATGATGAATT-TCGTGGGTTG
1 CACACTTAGTGCCTATACGA-TTGTTCATCAACATATGATGAATTAT-GTGGGTTG
51358 CACACTTAGTGCCTATACGA
1 CACACTTAGTGCCTATACGA
51378 AAATTCATAA
Statistics
Matches: 248, Mismatches: 31, Indels: 19
0.83 0.10 0.06
Matches are distributed among these distances:
51 1 0.00
52 49 0.20
53 1 0.00
54 186 0.75
55 6 0.02
56 5 0.02
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (54 bp):
CACACTTAGTGCCTATACGATTGTTCATCAACATATGATGAATTATGTGGGTTG
Found at i:51311 original size:160 final size:162
Alignment explanation
Indices: 51034--51376 Score: 462
Period size: 160 Copynumber: 2.1 Consensus size: 162
51024 TTCGTTGAGA
* * * ** * * * **
51034 TTCACACGTAGTACCTATACGATCATTCATAAACATATTATGAATTATG-TGGTTCACACATATA
1 TTCACACTTAGTGCCTATACGGTTGTTCATCAACATATAATAAATTCCGTTGGTTCACACATATA
* * *
51098 GTGCCTATACGGTCGTTCATCAACCTATGATGAATAATGTGGATTGCACACTTAGTGCCTATACT
66 GTGCCTATACGGTCGTTCATCAACATATGATGAATAATGTGGATTGCACACTTAGTGCCCATACA
51163 GTTGTTCATCAATATATGATGAATTAT-GTGGG
131 GTTGTTCATCAATATATGATGAATT-TCGTGGG
51195 TT-ACACTTAGTGCCTATACGGTTGTTCATCAACATATAATAAATTCCGTTGGTTGCACAC-T-T
1 TTCACACTTAGTGCCTATACGGTTGTTCATCAACATATAATAAATTCCGTTGGTT-CACACATAT
* * ** *
51257 AGTGCCTATATGGTTGTTCATCAACATATGATGAATTTTGTGGGTTGCACACTTAGTGCCCATAC
65 AGTGCCTATACGGTCGTTCATCAACATATGATGAATAATGTGGATTGCACACTTAGTGCCCATAC
51322 AGTTGTTCATCAATATATGATGAATTTCGTGGG
130 AGTTGTTCATCAATATATGATGAATTTCGTGGG
51355 TTGCACACTTAGTGCCTATACG
1 TT-CACACTTAGTGCCTATACG
51377 AAAATTCATA
Statistics
Matches: 159, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
159 1 0.01
160 127 0.80
161 8 0.05
162 23 0.14
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (162 bp):
TTCACACTTAGTGCCTATACGGTTGTTCATCAACATATAATAAATTCCGTTGGTTCACACATATA
GTGCCTATACGGTCGTTCATCAACATATGATGAATAATGTGGATTGCACACTTAGTGCCCATACA
GTTGTTCATCAATATATGATGAATTTCGTGGG
Found at i:51945 original size:95 final size:93
Alignment explanation
Indices: 51756--51936 Score: 215
Period size: 95 Copynumber: 1.9 Consensus size: 93
51746 TACCCCCTTT
** * * *
51756 CAGTATCAATACCATTTTGACATTCTGGAATCCATGGTATTAATACCTTCCTCTTAGTATCGACA
1 CAGTATCAATACCATTTTGACATTCTAAAATCAATGGTATCAATACCTTCCTCATAGTATCGACA
* * *
51821 CTCATATACTATAGTATCGATACTCCATCA
66 CCCACATAC--TAGTATCGATACTACATCA
* * *
51851 CAGTATCAATACCATTTCTG-CATTCTAAAATCAATGGTATCGATATCTTCCTCATAGTATCGAT
1 CAGTATCAATACCATTT-TGACATTCTAAAATCAATGGTATCAATACCTTCCTCATAGTATCGAC
51915 ACCCACAT-C-AGTATCGATACTA
65 ACCCACATACTAGTATCGATACTA
51937 ATTACATCAG
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
91 12 0.16
94 1 0.01
95 59 0.80
96 2 0.03
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.34
Consensus pattern (93 bp):
CAGTATCAATACCATTTTGACATTCTAAAATCAATGGTATCAATACCTTCCTCATAGTATCGACA
CCCACATACTAGTATCGATACTACATCA
Found at i:60684 original size:29 final size:30
Alignment explanation
Indices: 60639--60706 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
60629 CACCAAAATT
* **
60639 ACCAAAATAT-AATTTTTTAAAGTTTAGTGG
1 ACCAAAGTATAAATTTTGAAAAGTTTAG-GG
60669 -CCAAAGTATAAATTTTGGAAAAGTTTAGGG
1 ACCAAAGTATAAATTTT-GAAAAGTTTAGGG
60699 ACCAAAGT
1 ACCAAAGT
60707 GGTAATTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
29 8 0.25
30 8 0.25
31 16 0.50
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (30 bp):
ACCAAAGTATAAATTTTGAAAAGTTTAGGG
Done.