Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000944.1 Hibiscus syriacus cultivar Beakdansim tig00001884_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: 70745
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:15829 original size:63 final size:63
Alignment explanation
Indices: 15756--15874 Score: 168
Period size: 63 Copynumber: 1.9 Consensus size: 63
15746 TAATAATATC
* * * * *
15756 TTTTAATTTGACATATTC-AAAAGATATAATCACCTTTTACTATTCAAACTTAAATAGATACTA
1 TTTTAATTTGAAATATTCAAAAAGATACAATAACC-TTTAATATTCAAAATTAAATAGATACTA
*
15819 TTTTAATTTGAAATATTCAAAAAGATACAATAATCTTTAATATTCAAAATTAAATA
1 TTTTAATTTGAAATATTCAAAAAGATACAATAACCTTTAATATTCAAAATTAAATA
15875 AGTAACAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
63 36 0.73
64 13 0.27
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.39
Consensus pattern (63 bp):
TTTTAATTTGAAATATTCAAAAAGATACAATAACCTTTAATATTCAAAATTAAATAGATACTA
Found at i:19580 original size:29 final size:29
Alignment explanation
Indices: 19527--19611 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 29
19517 AACCCAACCC
**
19527 ATAGGTCGCCATGCACTCCCAGCGACCTC
1 ATAGGTCGCCATGCACTCCCAGCGACCAA
* ***
19556 CTAGGTCGCCATGCACTCTGGGCGACCAA
1 ATAGGTCGCCATGCACTCCCAGCGACCAA
* * *
19585 AGAGGTCGCCATGCACGCCCGGCGACC
1 ATAGGTCGCCATGCACTCCCAGCGACC
19612 TTGTCTCCTT
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.20, C:0.39, G:0.27, T:0.14
Consensus pattern (29 bp):
ATAGGTCGCCATGCACTCCCAGCGACCAA
Found at i:19820 original size:29 final size:29
Alignment explanation
Indices: 19759--19842 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 29
19749 TTAAAAGCTT
* * **
19759 GGTCACCGGGCGTGCATGGCGACCTCCTT
1 GGTCACCGGGAGTGCATGGCGACCTACGA
* *
19788 GGTCACCCGGAGTGCATGGCGACCTAGGA
1 GGTCACCGGGAGTGCATGGCGACCTACGA
* *
19817 GGTCGCTGGGAGTGCATGGCGACCTA
1 GGTCACCGGGAGTGCATGGCGACCTA
19843 TGGGTTGGGT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.15, C:0.29, G:0.38, T:0.18
Consensus pattern (29 bp):
GGTCACCGGGAGTGCATGGCGACCTACGA
Found at i:21119 original size:20 final size:20
Alignment explanation
Indices: 21096--21140 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
21086 TAGTTCCATT
21096 ACCTTCTATGA-AGTTTTAAA
1 ACCTTCT-TGAGAGTTTTAAA
* *
21116 ACCTTCTTTAGTGTTTTAAA
1 ACCTTCTTGAGAGTTTTAAA
21136 ACCTT
1 ACCTT
21141 TCACAATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (20 bp):
ACCTTCTTGAGAGTTTTAAA
Found at i:21201 original size:20 final size:20
Alignment explanation
Indices: 21178--21219 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
21168 ATCTAGGATG
21178 TTCCAAAATATTCTAAAACT
1 TTCCAAAATATTCTAAAACT
* * *
21198 TTCCATAATGTTCTAAACCT
1 TTCCAAAATATTCTAAAACT
21218 TT
1 TT
21220 TTATTGTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.21, G:0.02, T:0.40
Consensus pattern (20 bp):
TTCCAAAATATTCTAAAACT
Found at i:21501 original size:60 final size:60
Alignment explanation
Indices: 21380--21502 Score: 167
Period size: 60 Copynumber: 2.0 Consensus size: 60
21370 GTCTATCAAT
* * * *
21380 TATATAGTATTGTTTTATTAAGTCTATCGACTATTAAAAGTTATAAAATGATTATTGGAC
1 TATAGAGTATTGTTTTATTAAGTCCATCGACTATTAAAAGTTATAAAATGATCACTGGAC
* * *
21440 TATAGAGTATTGTTTTGTTGAGTCCATCGACTATTAAAAGTTATAAAATGGTCACCT-GAC
1 TATAGAGTATTGTTTTATTAAGTCCATCGACTATTAAAAGTTATAAAATGATCA-CTGGAC
21500 TAT
1 TAT
21503 TCATTGTGTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 54 0.98
61 1 0.02
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (60 bp):
TATAGAGTATTGTTTTATTAAGTCCATCGACTATTAAAAGTTATAAAATGATCACTGGAC
Found at i:25660 original size:31 final size:31
Alignment explanation
Indices: 25622--25684 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
25612 ACCGAAGGAC
* *
25622 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
25653 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
25684 C
1 C
25685 CCTCGACCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:27340 original size:18 final size:18
Alignment explanation
Indices: 27317--27369 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
27307 AGGACAAATC
*
27317 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
27335 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGGGACAT
* *
27353 AGTGGCCATTCGAGACA
1 AGTGGTCATTCGGGACA
27370 AATATAAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.25
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:28893 original size:18 final size:19
Alignment explanation
Indices: 28863--28906 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
28853 CGTAAAATCT
28863 TTCAATATAT-AAACA-AA
1 TTCAATATATAAAACATAA
*
28880 TTCAGATATCTAAAACATAA
1 TTCA-ATATATAAAACATAA
28900 TTCAATA
1 TTCAATA
28907 ATACACTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 8 0.35
20 6 0.26
ACGTcount: A:0.52, C:0.14, G:0.02, T:0.32
Consensus pattern (19 bp):
TTCAATATATAAAACATAA
Found at i:31873 original size:21 final size:20
Alignment explanation
Indices: 31788--31944 Score: 84
Period size: 21 Copynumber: 7.8 Consensus size: 20
31778 AATGACCAAT
** *
31788 AAAATCGCAACGCGA-AATA
1 AAAATCGCAACGCGATTTTC
***
31807 AAAATCGCAACGCGATCCCC
1 AAAATCGCAACGCGATTTTC
* ** *
31827 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGA-TTTTC
*
31847 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTC
* * *
31868 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGAT-TTTC
* **
31889 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-C
* * *
31910 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTC
31930 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
31945 ACACATAAAT
Statistics
Matches: 104, Mismatches: 28, Indels: 11
0.73 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTC
Found at i:31973 original size:20 final size:20
Alignment explanation
Indices: 31911--32155 Score: 246
Period size: 20 Copynumber: 12.2 Consensus size: 20
31901 CGATTTTCCA
* ** *
31911 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
31931 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
31951 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
31971 AAATCGCAACGTATATCCGT
1 AAATCGCAACGCGTATCCGT
**
31991 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
32011 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
32031 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
32051 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* *
32071 AAATCGCAACGAGAATCCGT
1 AAATCGCAACGCGTATCCGT
*
32091 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
*
32111 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
32131 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
32151 AAATC
1 AAATC
32156 CGGTAGGGCA
Statistics
Matches: 192, Mismatches: 27, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 188 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:31994 original size:40 final size:40
Alignment explanation
Indices: 31950--32155 Score: 276
Period size: 40 Copynumber: 5.2 Consensus size: 40
31940 CGCGAACACA
31950 TAAATCGCAACGCGTATCCGTAAATCGCAACG-TATATCCG
1 TAAATCGCAACGCGTATCCGTAAATCGCAACGATA-ATCCG
**
31990 TAAATCGCAACGCGTATGGGTAAATCGCAATGCG-T-ATCCG
1 TAAATCGCAACGCGTATCCGTAAATCGCAA--CGATAATCCG
*
32030 TATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCG
* *
32070 TAAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCG
* * *
32110 TAAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGT-ATCCGTAAATCGCAACGATAATCCG
32150 TAAATC
1 TAAATC
32156 CGGTAGGGCA
Statistics
Matches: 149, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
38 2 0.01
39 1 0.01
40 143 0.96
42 3 0.02
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.21
Consensus pattern (40 bp):
TAAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCG
Found at i:32906 original size:24 final size:24
Alignment explanation
Indices: 32867--32913 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
32857 AAATTTGGTC
32867 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
32891 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
32914 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:33102 original size:12 final size:12
Alignment explanation
Indices: 33085--33109 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33075 ATATAATCCT
33085 GAAGAAGAAAAA
1 GAAGAAGAAAAA
33097 GAAGAAGAAAAA
1 GAAGAAGAAAAA
33109 G
1 G
33110 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:35667 original size:20 final size:20
Alignment explanation
Indices: 35469--35696 Score: 248
Period size: 20 Copynumber: 11.4 Consensus size: 20
35459 AAAATCGCAA
*
35469 TGCGATTTACGGATTA-TCGT
1 TGCGATTTACGGA-TACGCGT
*
35489 TGCGATTTACGGATTA-TCGT
1 TGCGATTTACGGA-TACGCGT
* *
35509 TGCGATTTACGGATTCTCGT
1 TGCGATTTACGGATACGCGT
*
35529 TGCGATTTACGGATTA-TCGT
1 TGCGATTTACGGA-TACGCGT
35549 TGCGATTTACGGATACGCGT
1 TGCGATTTACGGATACGCGT
* *
35569 TGCGATATACGGATACGCAT
1 TGCGATTTACGGATACGCGT
**
35589 TGCGATTTACCCATACGCGT
1 TGCGATTTACGGATACGCGT
*
35609 TGCGATTTACGGATACACGT
1 TGCGATTTACGGATACGCGT
35629 TGCGATTTACGGATACGCGT
1 TGCGATTTACGGATACGCGT
* *
35649 TGCGATTTATGTG-TTCGCGT
1 TGCGATTTACG-GATACGCGT
* ** *
35669 TGCGATTTTCATATTCGCGT
1 TGCGATTTACGGATACGCGT
35689 TGCGATTT
1 TGCGATTT
35697 TTGGAAAATC
Statistics
Matches: 184, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
19 3 0.02
20 179 0.97
21 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
TGCGATTTACGGATACGCGT
Found at i:37352 original size:16 final size:17
Alignment explanation
Indices: 37322--37355 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
37312 TTTTTGAATT
*
37322 ATATAGATAAGATTTAG
1 ATATAGATAAAATTTAG
37339 ATATA-ATAAAATTTAG
1 ATATAGATAAAATTTAG
37355 A
1 A
37356 ATTCATCATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (17 bp):
ATATAGATAAAATTTAG
Found at i:38655 original size:20 final size:20
Alignment explanation
Indices: 38618--38656 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38608 ACAAAAACTG
* **
38618 ATAATTTATGCATTAATTAT
1 ATAATTTATCCAAAAATTAT
38638 ATAATTTATCCAAAAATTA
1 ATAATTTATCCAAAAATTA
38657 ATGATTTCAC
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:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (20 bp):
ATAATTTATCCAAAAATTAT
Found at i:45055 original size:2 final size:2
Alignment explanation
Indices: 45048--45120 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
45038 TAGCTATAAT
45048 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45090 TA TA TA 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 TA TA TA T
45121 GCATTGTGTG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:46351 original size:14 final size:14
Alignment explanation
Indices: 46289--46359 Score: 58
Period size: 14 Copynumber: 5.0 Consensus size: 14
46279 GAGCACACAC
*
46289 ATATATAATTATAA
1 ATATATAATTATAT
*
46303 AAATA-AATT-TA-
1 ATATATAATTATAT
*
46314 ATAAATAAATTATATCT
1 ATATAT-AATTATA--T
46331 CATATATAATTATAT
1 -ATATATAATTATAT
46346 ATATATAATTATAT
1 ATATATAATTATAT
46360 CTAATAAACT
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
11 3 0.07
12 2 0.04
13 8 0.17
14 20 0.43
15 1 0.02
17 7 0.15
18 5 0.11
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATATAATTATAT
Found at i:46411 original size:2 final size:2
Alignment explanation
Indices: 46404--46434 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
46394 TAGCTATAAT
46404 TA TA TA 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 TA TA TA T
46435 GCATTGTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47662 original size:14 final size:14
Alignment explanation
Indices: 47600--47670 Score: 58
Period size: 14 Copynumber: 5.0 Consensus size: 14
47590 GAGCACACAC
*
47600 ATATATAATTATAA
1 ATATATAATTATAT
*
47614 AAATA-AATT-TA-
1 ATATATAATTATAT
*
47625 ATAAATAAATTATATCT
1 ATATAT-AATTATA--T
47642 CATATATAATTATAT
1 -ATATATAATTATAT
47657 ATATATAATTATAT
1 ATATATAATTATAT
47671 CTAATAAACT
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
11 3 0.07
12 2 0.04
13 8 0.17
14 20 0.43
15 1 0.02
17 7 0.15
18 5 0.11
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATATAATTATAT
Found at i:51396 original size:60 final size:60
Alignment explanation
Indices: 51277--51446 Score: 141
Period size: 60 Copynumber: 2.8 Consensus size: 60
51267 GTTTGAAAAC
* * ** * **
51277 ATGACTTATATTTTAGATTGATCCTTAAACTTTTAAATGTTTCAATTTCATCCTTAAATT
1 ATGACTTATATTTTAAATTGATCCTCAAACTTTTAAACATTTCAATTTCACCCCCAAATT
*
51337 ATGA-TTATCATTTTAAATT-AGTCCTCAAACTTTTAAACATTTTAATTTCACCCCCAAATT
1 ATGACTTAT-ATTTTAAATTGA-TCCTCAAACTTTTAAACATTTCAATTTCACCCCCAAATT
* ** * * * *
51397 GTTCCTT-TATTTTCAATT-AGTCCCCAAAATTTTTAAACATTCCAATTTCA
1 ATGACTTATATTTTAAATTGA-TCCTC-AAACTTTTAAACATTTCAATTTCA
51447 TCCCAAACTA
Statistics
Matches: 90, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
59 20 0.22
60 68 0.76
61 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (60 bp):
ATGACTTATATTTTAAATTGATCCTCAAACTTTTAAACATTTCAATTTCACCCCCAAATT
Found at i:62983 original size:2 final size:2
Alignment explanation
Indices: 62976--63012 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
62966 TGAATATGTT
*
62976 TA TA TA TA TA TT TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
63013 GTTCACAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:62989 original size:12 final size:12
Alignment explanation
Indices: 62969--63011 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
62959 TTTTATTTGA
*
62969 ATATGTTTATAT
1 ATATATTTATAT
62981 ATATATTTATAT
1 ATATATTTATAT
*
62993 ATATATATATAT
1 ATATATTTATAT
63005 ATTATAT
1 A-TATAT
63012 AGTTCACAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
12 23 0.82
13 5 0.18
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (12 bp):
ATATATTTATAT
Found at i:63116 original size:36 final size:37
Alignment explanation
Indices: 63037--63302 Score: 294
Period size: 37 Copynumber: 7.2 Consensus size: 37
63027 TGAAAATACG
* *
63037 TATATAATATATATTTTTTAAAA-ACCTTTTGAAAA-T
1 TATATAATATATAATTTTTAAAACA-TTTTTGAAAACT
* ** *
63073 GAATATAATATATGGTTTTTAAAACACTTTTGAAAAC-
1 -TATATAATATATAATTTTTAAAACATTTTTGAAAACT
* * *
63110 TGTATAATATATAGTTTTTAAAACATTTTAAGAAAA--
1 TATATAATATATAATTTTTAAAACATTTT-TGAAAACT
*
63146 TATATAATATATGATTTTTAAAATCA-TTTTGAAAACT
1 TATATAATATATAATTTTTAAAA-CATTTTTGAAAACT
*
63183 TATATAATATATAATTTTTGAAAACATTTTTTTAAAACT
1 TATATAATATATAATTTTT-AAAACA-TTTTTGAAAACT
*
63222 TATATAATATATAGTTTTTGAAAACATTTTTGAAAACT
1 TATATAATATATAATTTTT-AAAACATTTTTGAAAACT
*
63260 TATATAATATATGATTTTTGAAAACATTTTTGAAAA-T
1 TATATAATATATAATTTTT-AAAACATTTTTGAAAACT
63297 TATATA
1 TATATA
63303 GTTTTTAAAA
Statistics
Matches: 202, Mismatches: 18, Indels: 18
0.85 0.08 0.08
Matches are distributed among these distances:
35 5 0.02
36 48 0.24
37 64 0.32
38 50 0.25
39 35 0.17
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (37 bp):
TATATAATATATAATTTTTAAAACATTTTTGAAAACT
Found at i:63122 original size:38 final size:35
Alignment explanation
Indices: 63043--63302 Score: 230
Period size: 38 Copynumber: 7.1 Consensus size: 35
63033 TACGTATATA
* *
63043 ATATATAT-TTTTTAAAA-ACCTTTTGAAAA-TGAAT
1 ATATATATGTTTTTAAAACA-TTTTTGAAAACT-TAT
*
63077 ATAATATATGGTTTTTAAAACACTTTTGAAAACTGTAT
1 AT-ATATAT-GTTTTTAAAACATTTTTGAAAACT-TAT
*
63115 A-ATATATAGTTTTTAAAACATTTTAAGAAAA--TAT
1 ATATATAT-GTTTTTAAAACATTTT-TGAAAACTTAT
63149 ATAATATATGATTTTTAAAATCA-TTTTGAAAACTTAT
1 AT-ATATATG-TTTTTAAAA-CATTTTTGAAAACTTAT
* *
63186 ATAATATATAATTTTTGAAAACATTTTTTTAAAACTTAT
1 AT-ATATAT-GTTTTT-AAAACA-TTTTTGAAAACTTAT
63225 ATAATATATAGTTTTTGAAAACATTTTTGAAAACTTAT
1 AT-ATATAT-GTTTTT-AAAACATTTTTGAAAACTTAT
63263 ATAATATATGATTTTTGAAAACATTTTTGAAAA-TTAT
1 AT-ATATATG-TTTTT-AAAACATTTTTGAAAACTTAT
63300 ATA
1 ATA
63303 GTTTTTAAAA
Statistics
Matches: 200, Mismatches: 9, Indels: 32
0.83 0.04 0.13
Matches are distributed among these distances:
34 6 0.03
35 12 0.06
36 40 0.20
37 52 0.26
38 55 0.28
39 35 0.17
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.45
Consensus pattern (35 bp):
ATATATATGTTTTTAAAACATTTTTGAAAACTTAT
Found at i:63253 original size:12 final size:12
Alignment explanation
Indices: 63236--63295 Score: 52
Period size: 12 Copynumber: 4.8 Consensus size: 12
63226 TAATATATAG
63236 TTTTTGAAAACA
1 TTTTTGAAAACA
63248 TTTTTGAAAAC-
1 TTTTTGAAAACA
* *
63259 TTATAT-AATATATGA
1 TT-TTTGAA-A-A-CA
63274 TTTTTGAAAACA
1 TTTTTGAAAACA
63286 TTTTTGAAAA
1 TTTTTGAAAA
63296 TTATATAGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
11 4 0.11
12 25 0.66
13 2 0.05
14 3 0.08
15 4 0.11
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:63333 original size:34 final size:34
Alignment explanation
Indices: 63286--63356 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
63276 TTTGAAAACA
*
63286 TTTTTGAAAATTATATAGTTTTTAAAAAAACTTT
1 TTTTTGAAAATTATATAGTTTTTAAAAAAACATT
* *
63320 TTTTTTAAGATTATATAGTTTTTAAAAAAACATT
1 TTTTTGAAAATTATATAGTTTTTAAAAAAACATT
63354 TTT
1 TTT
63357 GAAATTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (34 bp):
TTTTTGAAAATTATATAGTTTTTAAAAAAACATT
Found at i:63381 original size:44 final size:46
Alignment explanation
Indices: 63331--63419 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 46
63321 TTTTTAAGAT
* *
63331 TATATAG-TTTTTAAAAAAACATTTTTGAAATTTTATA-TATATAA
1 TATATAGTTTTTTAAAAAAACATTTTTAAAAATTTATATTATATAA
*
63375 TATATAGTTTTTTAAAAAAACCTTTTTAAAAATTTATATTATATA
1 TATATAGTTTTTTAAAAAAACATTTTTAAAAATTTATATTATATA
63420 GTTTTTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 7 0.17
45 27 0.68
46 6 0.15
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (46 bp):
TATATAGTTTTTTAAAAAAACATTTTTAAAAATTTATATTATATAA
Found at i:63445 original size:4 final size:4
Alignment explanation
Indices: 63436--63521 Score: 55
Period size: 4 Copynumber: 22.8 Consensus size: 4
63426 AAAAAATACT
*
63436 TTTA TTTA TTTA TTTA TTTA -TTA -TTA -TTA TTTA -TTC TTTA TCATT-
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T--TTA
*
63481 TTTA -TTA CTTA -TT- TTTA TTCTTA TTTA TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTTA -T-TTA TTTA TTTA TTTA TTTA TTT
63522 CTTTTCCAGG
Statistics
Matches: 69, Mismatches: 2, Indels: 22
0.74 0.02 0.24
Matches are distributed among these distances:
3 23 0.33
4 38 0.55
5 3 0.04
6 5 0.07
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:64127 original size:29 final size:29
Alignment explanation
Indices: 64095--64157 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
64085 AAAAACAAGA
64095 AAGCAAATATTCTACACAAGAAAACCCAC
1 AAGCAAATATTCTACACAAGAAAACCCAC
*
64124 AAGCAAATATTCTACATAAGAAAACCCAC
1 AAGCAAATATTCTACACAAGAAAACCCAC
*
64153 GAGCA
1 AAGCA
64158 CAAGACCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.51, C:0.25, G:0.10, T:0.14
Consensus pattern (29 bp):
AAGCAAATATTCTACACAAGAAAACCCAC
Found at i:64709 original size:5 final size:5
Alignment explanation
Indices: 64699--64737 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
64689 CATTTTTATA
*
64699 TATTT TATTT TATTT TATTT TACTTT T-TTT TGTTT TATT
1 TATTT TATTT TATTT TATTT TA-TTT TATTT TATTT TATT
64738 AATATTATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
4 4 0.13
5 23 0.74
6 4 0.13
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:64748 original size:2 final size:2
Alignment explanation
Indices: 64739--64767 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
64729 TGTTTTATTA
64739 AT AT -T 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
64768 TCGTTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:64830 original size:16 final size:16
Alignment explanation
Indices: 64810--64852 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
64800 ATCTACTTTA
64810 TTTTTTTTATTTT-AC
1 TTTTTTTTATTTTAAC
* *
64825 TATTTTTCATTTTAAC
1 TTTTTTTTATTTTAAC
*
64841 TTTTTATTATTT
1 TTTTTTTTATTT
64853 GTTTTTCTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTTTATTTTAAC
Found at i:64863 original size:35 final size:36
Alignment explanation
Indices: 64819--64896 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 36
64809 ATTTTTTTTA
* *
64819 TTTTACTATTTTTC-ATTTTAACTTTTTATTATTTG
1 TTTTTCTATTTTTCTATTTGAACTTTTTATTATTTG
***
64854 TTTTTCTATTTTTCTATTTGGTTTTTTTATTATTTG
1 TTTTTCTATTTTTCTATTTGAACTTTTTATTATTTG
64890 TTTTTCT
1 TTTTTCT
64897 TACATGTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 13 0.35
36 24 0.65
ACGTcount: A:0.14, C:0.08, G:0.05, T:0.73
Consensus pattern (36 bp):
TTTTTCTATTTTTCTATTTGAACTTTTTATTATTTG
Found at i:65052 original size:15 final size:14
Alignment explanation
Indices: 65034--65095 Score: 56
Period size: 15 Copynumber: 4.4 Consensus size: 14
65024 TTATTTTTCC
65034 TTTATTTTGTTTTT
1 TTTATTTTGTTTTT
65048 GTTTA--TTGCTTTTT
1 -TTTATTTTG-TTTTT
* *
65062 TTTATTTTGTATGT
1 TTTATTTTGTTTTT
*
65076 TTTATTTTTGTTTAT
1 TTTA-TTTTGTTTTT
65091 TTTAT
1 TTTAT
65096 CAGTCTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
13 7 0.18
14 13 0.33
15 19 0.49
ACGTcount: A:0.11, C:0.02, G:0.10, T:0.77
Consensus pattern (14 bp):
TTTATTTTGTTTTT
Found at i:65123 original size:19 final size:18
Alignment explanation
Indices: 65086--65147 Score: 65
Period size: 17 Copynumber: 3.4 Consensus size: 18
65076 TTTATTTTTG
*
65086 TTTATTTTATCA-GTCTA
1 TTTATTTTATCATTTCTA
*
65103 TTTATTTTGTTCATTTCTA
1 TTTATTTT-ATCATTTCTA
*
65122 TTTTATTTTATCATTT-TT
1 -TTTATTTTATCATTTCTA
65140 TTTATTTT
1 TTTATTTT
65148 TTTATGTTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
17 16 0.42
18 4 0.11
19 10 0.26
20 8 0.21
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTATTTTATCATTTCTA
Done.