Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007276.1 Hibiscus syriacus cultivar Beakdansim tig00019290_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: 59488
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:1546 original size:20 final size:20
Alignment explanation
Indices: 1523--1561 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1513 TCTGGTTCGT
* *
1523 TTGAGGGGGTATCGGTTCCC
1 TTGAAGGGGTATCGATTCCC
*
1543 TTGAATGGGTATCGATTCC
1 TTGAAGGGGTATCGATTCC
1562 ATAGTCCAGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.15, C:0.18, G:0.33, T:0.33
Consensus pattern (20 bp):
TTGAAGGGGTATCGATTCCC
Found at i:19859 original size:28 final size:28
Alignment explanation
Indices: 19827--19880 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
19817 ATCATAAAAC
*
19827 ATAATATTA-TTATTTTTAAAATATTAAA
1 ATAAT-TTATTTATTATTAAAATATTAAA
19855 ATAATTTATTTATTATTAAAATATTA
1 ATAATTTATTTATTATTAAAATATTA
19881 TTTTTATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 3 0.12
28 21 0.88
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
ATAATTTATTTATTATTAAAATATTAAA
Found at i:19886 original size:20 final size:20
Alignment explanation
Indices: 19834--19887 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
19824 AACATAATAT
*
19834 TATTATTTTTAAAATATTAAAA
1 TATTATTTTT--ATTATTAAAA
*
19856 TAATT-TATTTATTATTAAAA
1 T-ATTATTTTTATTATTAAAA
19876 TATTATTTTTAT
1 TATTATTTTTAT
19888 AATTTTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.11
20 16 0.59
22 5 0.19
23 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTATTTTTATTATTAAAA
Found at i:19894 original size:50 final size:52
Alignment explanation
Indices: 19769--19894 Score: 120
Period size: 50 Copynumber: 2.5 Consensus size: 52
19759 GATGAATTTT
*
19769 TTAAAA-ATTATTTATTATAAATATT-AAATACAATAAATAATATTATTTATCA
1 TTAAAATATTATTT-TTAT-AATTTTAAAATACAATAAATAATATTATTTATCA
* * * ** *
19821 TAAAACATAATATTATTAT--TTTTAAAATATTA-AAATAAT-TTATTTATTA
1 TTAAA-ATATTATTTTTATAATTTTAAAATACAATAAATAATATTATTTATCA
19870 TTAAAATATTATTTTTATAATTTTA
1 TTAAAATATTATTTTTATAATTTTA
19895 TTAATAAAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
48 11 0.19
49 13 0.22
50 15 0.25
51 6 0.10
52 4 0.07
53 5 0.08
54 5 0.08
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (52 bp):
TTAAAATATTATTTTTATAATTTTAAAATACAATAAATAATATTATTTATCA
Found at i:19952 original size:31 final size:29
Alignment explanation
Indices: 19844--19952 Score: 75
Period size: 28 Copynumber: 3.7 Consensus size: 29
19834 TATTATTTTT
*
19844 AAAATATTAAAATAATT-TA-TTTATT-ATT
1 AAAATATT--AATAATTATATTTTATTAATA
**
19872 AAAATATT-ATTTTTATAATTTTATTAATA
1 AAAATATTAATAATTAT-ATTTTATTAATA
*
19901 AAAATATTAATATTGGTATATTTTATTGAAATA
1 AAAATATTAATAAT--TATATTTTATT--AATA
19934 AAAATATT-ATAAATTATAT
1 AAAATATTAAT-AATTATAT
19953 AAATTATTTA
Statistics
Matches: 66, Mismatches: 5, Indels: 17
0.75 0.06 0.19
Matches are distributed among these distances:
25 4 0.06
26 1 0.02
27 1 0.02
28 14 0.21
29 10 0.15
30 4 0.06
31 13 0.20
32 5 0.08
33 14 0.21
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (29 bp):
AAAATATTAATAATTATATTTTATTAATA
Found at i:19960 original size:33 final size:33
Alignment explanation
Indices: 19897--19960 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
19887 TAATTTTATT
* * **
19897 AATAAAAATATTAATATTGGTATATTTTATTGA
1 AATAAAAATATTAAAATTGATATAAATTATTGA
19930 AATAAAAATATTATAAATT-ATATAAATTATT
1 AATAAAAATATTA-AAATTGATATAAATTATT
19961 TATTAAAGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
33 22 0.85
34 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.44
Consensus pattern (33 bp):
AATAAAAATATTAAAATTGATATAAATTATTGA
Found at i:20036 original size:11 final size:11
Alignment explanation
Indices: 19992--20038 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
19982 TTATATTTTA
19992 AAAATATTAATT
1 AAAATATT-ATT
*
20004 AATATATT-TT
1 AAAATATTATT
20014 AAATATATTTATT
1 AAA-ATA-TTATT
20027 AAAATATTATT
1 AAAATATTATT
20038 A
1 A
20039 GATTATTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
10 4 0.13
11 9 0.30
12 12 0.40
13 5 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
AAAATATTATT
Found at i:20045 original size:23 final size:23
Alignment explanation
Indices: 19984--20052 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
19974 GTGTTATATT
* * *
19984 ATATTTTAAAAATATTAATTAAT
1 ATATTTTAAATATATTTATTAAA
20007 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAATATATTTATTAAA
*
20030 ATATTATTAGAT-TATTATATTAA
1 ATATT-TTAAATATATT-TATTAA
20053 TATTAAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 29 0.73
24 11 0.28
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTTATTAAA
Found at i:20056 original size:34 final size:34
Alignment explanation
Indices: 19977--20102 Score: 88
Period size: 34 Copynumber: 3.7 Consensus size: 34
19967 AGTAATAGTG
19977 TTATATT-ATATTTTAAAAATATTAATTAATATA
1 TTATATTAATATTTTAAAAATATTAATTAATATA
*
20010 TT-T-TAAATATATTTATTAAAATATT-ATTAGAT-TA
1 TTATATTAATAT-TTTA--AAAATATTAATTA-ATATA
* *
20044 TTATATTAATA--TTAAATATA-TAAATAATATTA
1 TTATATTAATATTTTAAAAATATTAATTAATA-TA
* *
20076 TTCATTATTAATAATTTAATAATATTA
1 TT-A-TATTAATATTTTAAAAATATTA
20103 TTTATATGAA
Statistics
Matches: 72, Mismatches: 6, Indels: 26
0.69 0.06 0.25
Matches are distributed among these distances:
30 3 0.04
31 9 0.12
32 9 0.12
33 10 0.14
34 16 0.22
35 11 0.15
36 12 0.17
37 2 0.03
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.51
Consensus pattern (34 bp):
TTATATTAATATTTTAAAAATATTAATTAATATA
Found at i:20073 original size:54 final size:53
Alignment explanation
Indices: 20015--20325 Score: 143
Period size: 54 Copynumber: 5.8 Consensus size: 53
20005 ATATATTTTA
*
20015 AATATATTTATTAAAATATTATTAGATTATTATATTAATATTAAATATATAAAT
1 AATATATTTATTAAAATATTATTAAATTATT-TATTAATATTAAATATATAAAT
* * * * * *
20069 AATATTATTCATTATTAATA--ATTTAATAATATTATTTATATGAAAT-TAATAAAT
1 AATA-TATTTATTA-AAATATTATTAAATTAT-TTATTAATATTAAATAT-ATAAAT
* * *
20123 AATATGAAATTTATTAATAAT-TTATTATA-TA-TTATTAA-AATAAAAATATAATAT
1 AATAT---ATTTATTAA-AATATTATTAAATTATTTATTAATATTAAATATATAA-AT
** * * * *
20177 CTTATA-TTATTATAATATAATT-GATTATTTTATTATAATATTAAAAATAT-AAT
1 AATATATTTATTAAAATATTATTAAATTA-TTTA-T-TAATATTAAATATATAAAT
* * * * *
20230 ATTATA-TTATTAGAAATATTAATAAATATATTT-TAAATATT--TTA-ATAATT
1 AATATATTTATTA-AAATATTATTAAAT-TATTTATTAATATTAAATATATAAAT
*
20280 AATAT-TTTGATTAAAATGA-TATTAAAATATTTTATTAATATTAAAT
1 AATATATTT-ATTAAAAT-ATTATTAAATTA-TTTATTAATATTAAAT
20326 TCATAAAATA
Statistics
Matches: 191, Mismatches: 36, Indels: 61
0.66 0.12 0.21
Matches are distributed among these distances:
49 8 0.04
50 34 0.18
51 13 0.07
52 9 0.05
53 26 0.14
54 56 0.29
55 24 0.13
56 17 0.09
57 4 0.02
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (53 bp):
AATATATTTATTAAAATATTATTAAATTATTTATTAATATTAAATATATAAAT
Found at i:20090 original size:19 final size:19
Alignment explanation
Indices: 20022--20102 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 19
20012 TTAAATATAT
20022 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
20041 TTATTATATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
20060 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
*
20080 TTATTAATAAT-TTAATAA
1 TTATTAATAATATTATTAA
20098 -TATTA
1 TTATTA
20103 TTTATATGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
17 5 0.10
18 13 0.25
19 18 0.35
20 8 0.16
22 7 0.14
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:20123 original size:27 final size:26
Alignment explanation
Indices: 20056--20127 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 26
20046 ATATTAATAT
20056 TAAATATATAAATAATATTATTCATTA
1 TAAATA-ATAAATAATATTATTCATTA
* * *
20083 TTAATAATTTAATAATATTATTTA-TA
1 TAAATAA-TAAATAATATTATTCATTA
20109 TGAAATTAATAAATAATAT
1 T-AAA-TAATAAATAATAT
20128 GAAATTTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
26 4 0.11
27 30 0.81
28 3 0.08
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (26 bp):
TAAATAATAAATAATATTATTCATTA
Found at i:20129 original size:18 final size:18
Alignment explanation
Indices: 20106--20143 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
20096 AATATTATTT
20106 ATATGAAATTAATAAATA
1 ATATGAAATTAATAAATA
* *
20124 ATATGAAATTTATTAATA
1 ATATGAAATTAATAAATA
20142 AT
1 AT
20144 TTATTATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (18 bp):
ATATGAAATTAATAAATA
Found at i:20235 original size:22 final size:23
Alignment explanation
Indices: 20207--20253 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
20197 TTGATTATTT
20207 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
20229 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
20252 TA
1 TA
20254 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:20258 original size:22 final size:22
Alignment explanation
Indices: 20215--20258 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
20205 TTTATTATAA
*
20215 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
20237 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
20259 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:22420 original size:18 final size:19
Alignment explanation
Indices: 22399--22434 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
22389 GATGAAATAT
22399 AAATGGCGTTG-TCGTGGC
1 AAATGGCGTTGTTCGTGGC
*
22417 AAATGGTGTTGTTCGTGG
1 AAATGGCGTTGTTCGTGG
22435 TAAGTGTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.17, C:0.11, G:0.39, T:0.33
Consensus pattern (19 bp):
AAATGGCGTTGTTCGTGGC
Found at i:24277 original size:18 final size:18
Alignment explanation
Indices: 24254--24288 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24244 TCGCGTAGAA
24254 ATGTCCCGAAGGACCACT
1 ATGTCCCGAAGGACCACT
* *
24272 ATGTCCTGAAGGGCCAC
1 ATGTCCCGAAGGACCAC
24289 ATATCACATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.31, G:0.26, T:0.17
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACT
Found at i:27447 original size:29 final size:29
Alignment explanation
Indices: 27412--27469 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
27402 TTGTTTAATC
*
27412 GGTTTCTAATTTGTATCTTTTATTTATTT
1 GGTTTCTAATTTGTATCTTGTATTTATTT
*
27441 GGTTTCTAATTTGTATGTTGTATTTATTT
1 GGTTTCTAATTTGTATCTTGTATTTATTT
27470 CAGTCTATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.17, C:0.05, G:0.14, T:0.64
Consensus pattern (29 bp):
GGTTTCTAATTTGTATCTTGTATTTATTT
Found at i:28660 original size:20 final size:20
Alignment explanation
Indices: 28635--28672 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28625 CTATATGAGT
28635 TTGTTTTATTTATCTTTTGA
1 TTGTTTTATTTATCTTTTGA
*
28655 TTGTTTTATTTATGTTTT
1 TTGTTTTATTTATCTTTT
28673 AAATGTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.03, G:0.11, T:0.74
Consensus pattern (20 bp):
TTGTTTTATTTATCTTTTGA
Found at i:30492 original size:20 final size:20
Alignment explanation
Indices: 30467--30521 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
30457 CGAAATTTCC
30467 ATGCATCGATGCACCCCTTA
1 ATGCATCGATGCACCCCTTA
*
30487 ATGCATCGATGCATCCCTTA
1 ATGCATCGATGCACCCCTTA
*
30507 ATGCATCGACGCACC
1 ATGCATCGATGCACC
30522 TTCAAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.35, G:0.16, T:0.24
Consensus pattern (20 bp):
ATGCATCGATGCACCCCTTA
Found at i:34230 original size:46 final size:46
Alignment explanation
Indices: 34178--34271 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
34168 AGTAGGACAA
34178 AAACTTAATTCGACACTGATTCATGTTCATATCTCTATACTAATAT
1 AAACTTAATTCGACACTGATTCATGTTCATATCTCTATACTAATAT
34224 AAACTTAATTCGACACTGATTCATGTTCATATCTCTATACTAATAT
1 AAACTTAATTCGACACTGATTCATGTTCATATCTCTATACTAATAT
34270 AA
1 AA
34272 GCTTGTCCCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.38
Consensus pattern (46 bp):
AAACTTAATTCGACACTGATTCATGTTCATATCTCTATACTAATAT
Found at i:40236 original size:44 final size:43
Alignment explanation
Indices: 40141--40247 Score: 128
Period size: 43 Copynumber: 2.5 Consensus size: 43
40131 TGAATTTTGT
* **
40141 ATTGAATGAGCTCTGAAAAAGCCAACCGGTGCATTATTGTTGC
1 ATTGAATGAGCTCTGAAAAAGCCAAACGGTGCATTATTACTGC
* *
40184 ATTGAATGAGCTCTGAAAAAGCTGAAATGGTGCATTATTACTGC
1 ATTGAATGAGCTCTGAAAAAGC-CAAACGGTGCATTATTACTGC
*
40228 AATT-AATGACCTCT-AAAAAG
1 -ATTGAATGAGCTCTGAAAAAG
40248 TAGCTGAAAC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
43 28 0.50
44 25 0.45
45 3 0.05
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.28
Consensus pattern (43 bp):
ATTGAATGAGCTCTGAAAAAGCCAAACGGTGCATTATTACTGC
Found at i:40809 original size:272 final size:276
Alignment explanation
Indices: 40181--40842 Score: 884
Period size: 277 Copynumber: 2.4 Consensus size: 276
40171 GCATTATTGT
*
40181 TGCATTGAATGAGCTCTGAAAAAGCTGAAATGGTGCATTATT-ACTGCAATTAATGACCTCTAAA
1 TGCATTGAATGAGCTCTGAAAAAGCTGAAATGGTGCATTATTGA-TGCAATGAATGACCTCTAAA
* * * * *
40245 AAGTAGCTGAAACGATGCATTGATTGAGCACCGAAAAGTAGGTGAAACATTGAAAAATCTGGCCT
65 AAGTAGCTGAAATGGTGCATTGATTGAGCACCGAAAAGTAGATGAATCAGTGAAAAATCTGGCCT
* * *
40310 AGTTAAAATACACGATTTTTTTATAATTTGAAGTGATAATTCAACACTGAAAAGGTTTCTGCTTT
130 AGTTAAAATACACGA-TTTTTAATAATTTGAAGTAATAATTCAACACTGAAAAGGTTTCTGATTT
* * * * * *
40375 GAGTTGGTATATCACTGAAAATTTACAGAATATGATAATGCACCACTATTTTCACCCATTTTTTT
194 GAGTTGATATATCACTAAAAAATTACAGAAGATGATAATGCACCACTATTTTCACCCAGTTTTCT
* * *
40440 GAATAGTTATTTGAATTC
259 GAATAATTATTTAAATTA
* * * * *
40458 TACATTGAATGAACTATGAAAAAGTTGAAATTGTGCATTATTGATGCAATGAATGACCTCTAAAA
1 TGCATTGAATGAGCTCTGAAAAAGCTGAAATGGTGCATTATTGATGCAATGAATGACCTCTAAAA
* * * * * * *
40523 AATAGCTAAAATGGTGCATCGATTGAGCAGCGAAAAGTAGATGAATCAGTGAAACATTTGGCCTT
66 AGTAGCTGAAATGGTGCATTGATTGAGCACCGAAAAGTAGATGAATCAGTGAAAAATCTGGCCTA
* *
40588 GTTAAAATACAC-A-TTTTAATGATTTGAAGTAATAATTCAACACTGAAAA-GTTTTTGATTTGA
131 GTTAAAATACACGATTTTTAATAATTTGAAGTAATAATTCAACACTGAAAAGGTTTCTGATTTGA
* *
40650 GTTGATATATGACTAAAAAATTGCAGAAGATGATAATGCACCACTATTTTCACCC-GTTTTCTGA
196 GTTGATATATCACTAAAAAATTACAGAAGATGATAATGCACCACTATTTTCACCCAGTTTTCTGA
*
40714 ATAATTGTTTAAATTA
261 ATAATTATTTAAATTA
* * * * * *
40730 TGCATTGAATGAGCTCTGAAAAAACTGAAATGGTGCATAAATGTTGCAATGAATGAACTCTGAAA
1 TGCATTGAATGAGCTCTGAAAAAGCTGAAATGGTGCATTATTGATGCAATGAATGACCTCTAAAA
* *
40795 AGTAGCTGAAATGGTGCATTGATTGAGAACCGAAAAGTAGTTGAATCA
66 AGTAGCTGAAATGGTGCATTGATTGAGCACCGAAAAGTAGATGAATCA
40843 TGGAATACTG
Statistics
Matches: 332, Mismatches: 52, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
272 115 0.35
273 60 0.18
274 33 0.10
276 1 0.00
277 122 0.37
278 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (276 bp):
TGCATTGAATGAGCTCTGAAAAAGCTGAAATGGTGCATTATTGATGCAATGAATGACCTCTAAAA
AGTAGCTGAAATGGTGCATTGATTGAGCACCGAAAAGTAGATGAATCAGTGAAAAATCTGGCCTA
GTTAAAATACACGATTTTTAATAATTTGAAGTAATAATTCAACACTGAAAAGGTTTCTGATTTGA
GTTGATATATCACTAAAAAATTACAGAAGATGATAATGCACCACTATTTTCACCCAGTTTTCTGA
ATAATTATTTAAATTA
Found at i:41935 original size:64 final size:63
Alignment explanation
Indices: 41864--42073 Score: 219
Period size: 65 Copynumber: 3.3 Consensus size: 63
41854 TGCACTAAGA
* * *
41864 GTGCATCGATGCATCAAGTGCATTCAATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGG-TG
** *
41928 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATATCCAGAGTGCATCGATGCATGGT-
*
41992 T
63 G
* ** *
41993 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT-ATCCA-GAGTGCATCGATGCATGG--
42056 TG
62 TG
*
42058 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
42074 CTCTGAAAAT
Statistics
Matches: 121, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 46 0.38
65 66 0.55
66 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.30
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGTG
Found at i:43030 original size:18 final size:18
Alignment explanation
Indices: 43007--43044 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
42997 TAGGAGGAGG
43007 AGGAGCACGAGAAGAGCT
1 AGGAGCACGAGAAGAGCT
* *
43025 AGGAGCTCGTGAAGAGCT
1 AGGAGCACGAGAAGAGCT
43043 AG
1 AG
43045 CTCCCGGGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.39, T:0.11
Consensus pattern (18 bp):
AGGAGCACGAGAAGAGCT
Found at i:43870 original size:21 final size:21
Alignment explanation
Indices: 43844--43898 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
43834 CTAATAGGCC
43844 ATTAGGAGGTTGAGGAATGAG
1 ATTAGGAGGTTGAGGAATGAG
*
43865 ATTAGGAGGTTGAGGAATGGG
1 ATTAGGAGGTTGAGGAATGAG
43886 ATTAGGAGGTTGA
1 ATTAGGAGGTTGA
43899 TTTGAACGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.31, C:0.00, G:0.44, T:0.25
Consensus pattern (21 bp):
ATTAGGAGGTTGAGGAATGAG
Found at i:44648 original size:23 final size:23
Alignment explanation
Indices: 44618--44698 Score: 96
Period size: 23 Copynumber: 3.7 Consensus size: 23
44608 TGCATGGCCT
44618 TGTGCATCGATGCACATTCAAGG
1 TGTGCATCGATGCACATTCAAGG
* * * *
44641 TGTGCATCGGTGCACCTTTATGG
1 TGTGCATCGATGCACATTCAAGG
44664 TGT--ATCGATGCACATTCAAGG
1 TGTGCATCGATGCACATTCAAGG
*
44685 -ATGCATCGATGCAC
1 TGTGCATCGATGCAC
44699 TGTTAGGTGT
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.02
21 14 0.30
22 10 0.21
23 22 0.47
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.28
Consensus pattern (23 bp):
TGTGCATCGATGCACATTCAAGG
Found at i:44673 original size:44 final size:42
Alignment explanation
Indices: 44623--44717 Score: 138
Period size: 44 Copynumber: 2.2 Consensus size: 42
44613 GGCCTTGTGC
* *
44623 ATCGATGCACATTCAAGGTGTGCATCGGTGCACCT-TTATGGTGT
1 ATCGATGCACATTCAAGG-ATGCATCGATGCA-CTGTTA-GGTGT
44667 ATCGATGCACATTCAAGGATGCATCGATGCACTGTTAGGTGT
1 ATCGATGCACATTCAAGGATGCATCGATGCACTGTTAGGTGT
44709 ATCGATGCA
1 ATCGATGCA
44718 TGAATCACAA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
42 16 0.33
43 14 0.29
44 18 0.38
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.29
Consensus pattern (42 bp):
ATCGATGCACATTCAAGGATGCATCGATGCACTGTTAGGTGT
Found at i:44714 original size:20 final size:21
Alignment explanation
Indices: 44623--44717 Score: 86
Period size: 21 Copynumber: 4.4 Consensus size: 21
44613 GGCCTTGTGC
44623 ATCGATGCACATTCAAGGTGT
1 ATCGATGCACATTCAAGGTGT
* * * *
44644 GCATCGGTGCACCTTTATGGTGT
1 --ATCGATGCACATTCAAGGTGT
*
44667 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACATTCAAGG-TGT
*
44689 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
44709 ATCGATGCA
1 ATCGATGCA
44718 TGAATCACAA
Statistics
Matches: 59, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
20 11 0.19
21 18 0.31
22 13 0.22
23 17 0.29
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.29
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:50428 original size:21 final size:21
Alignment explanation
Indices: 50402--50441 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
50392 CAGAACCCCA
*
50402 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
50423 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
50442 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:50471 original size:21 final size:23
Alignment explanation
Indices: 50423--50473 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
50413 ATTCCCCTGT
50423 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
*
50446 AGGGGGAATCGGTT-CCC-TCAA
1 GGGGGGAATCGGTTCCCCTTCAA
50467 GGGGGGA
1 GGGGGGA
50474 TTGATTCCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 10 0.38
22 3 0.12
23 13 0.50
ACGTcount: A:0.20, C:0.22, G:0.41, T:0.18
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:57557 original size:23 final size:23
Alignment explanation
Indices: 57531--57608 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
57521 CACCACAACT
57531 CATATAATTACACCGAAGTGCCA
1 CATATAATTACACCGAAGTGCCA
* * * *
57554 CATATAATTGCACTGGAGTGCCG
1 CATATAATTACACCGAAGTGCCA
* *
57577 CATAGAATTACACCGTAGTGCCA
1 CATATAATTACACCGAAGTGCCA
*
57600 TATAATAAT
1 CAT-ATAAT
57609 GTCCATAAGG
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 39 0.91
24 4 0.09
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.26
Consensus pattern (23 bp):
CATATAATTACACCGAAGTGCCA
Found at i:57786 original size:103 final size:103
Alignment explanation
Indices: 57615--57832 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
57605 TAATGTCCAT
* * *
57615 AAGGATCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
57680 GACTTCACACATGTTCCAAAGAATACATATATGTCTCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
57718 AATGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
57783 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
57821 AAGGACCACATA
1 AAGGACCACATA
57833 GACCCTCGAC
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:58578 original size:2 final size:2
Alignment explanation
Indices: 58571--58611 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
58561 ACTGATAAAC
58571 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT A
58612 CTTCTATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58756 original size:20 final size:20
Alignment explanation
Indices: 58731--58771 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
58721 TCTCATTTCA
58731 TTCTATAATTCAATATTATT
1 TTCTATAATTCAATATTATT
58751 TTCTATAATTCAATATTATT
1 TTCTATAATTCAATATTATT
58771 T
1 T
58772 AGTTTCTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.56
Consensus pattern (20 bp):
TTCTATAATTCAATATTATT
Done.