Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003669.1 Hibiscus syriacus cultivar Beakdansim tig00007842_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: 103964
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4679 original size:11 final size:11
Alignment explanation
Indices: 4660--4695 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
4650 AGGCAACACA
*
4660 TTTCGTTTTAT
1 TTTCATTTTAT
*
4671 TTTCATTTTAA
1 TTTCATTTTAT
4682 TTTCATTTTAT
1 TTTCATTTTAT
4693 TTT
1 TTT
4696 TAGAAAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.17, C:0.08, G:0.03, T:0.72
Consensus pattern (11 bp):
TTTCATTTTAT
Found at i:4742 original size:19 final size:20
Alignment explanation
Indices: 4705--4748 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
4695 TTAGAAAAAC
*
4705 TTTATTTCATTTTAATTTAT
1 TTTATTCCATTTTAATTTAT
*
4725 TTTATTCCA-TTTATTTTAT
1 TTTATTCCATTTTAATTTAT
4744 TTTAT
1 TTTAT
4749 CATATGCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTATTCCATTTTAATTTAT
Found at i:8784 original size:14 final size:14
Alignment explanation
Indices: 8749--8803 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
8739 GACCCAGTCA
*
8749 CCGAGTCAACTCGAT
1 CCGAGTCAAC-CCAT
* *
8764 CCAAGTCTACCCAT
1 CCGAGTCAACCCAT
**
8778 CCGAGTCAACCGGT
1 CCGAGTCAACCCAT
8792 CCGAGTCAACCC
1 CCGAGTCAACCC
8804 TCTTGACTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
14 24 0.75
15 8 0.25
ACGTcount: A:0.25, C:0.40, G:0.18, T:0.16
Consensus pattern (14 bp):
CCGAGTCAACCCAT
Found at i:13618 original size:29 final size:29
Alignment explanation
Indices: 13571--13639 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 29
13561 AACAACCATT
* * *
13571 TTACGAAAATAGCATCATTTTTAAAACAA
1 TTACCAAAATAGCACCATTTTCAAAACAA
* *
13600 TTACCAAAATATCACCATTTTCAAAATAA
1 TTACCAAAATAGCACCATTTTCAAAACAA
*
13629 TTACTAAAATA
1 TTACCAAAATA
13640 ACATTTTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.49, C:0.16, G:0.03, T:0.32
Consensus pattern (29 bp):
TTACCAAAATAGCACCATTTTCAAAACAA
Found at i:13705 original size:29 final size:29
Alignment explanation
Indices: 13679--13747 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
13669 TTAAATTATG
*
13679 AAAATAGCACCTTTTTCAAAATAATTACC
1 AAAATAGCACCCTTTTCAAAATAATTACC
* *
13708 AGAATAGCACCCTTTTCCAAATAATTACC
1 AAAATAGCACCCTTTTCAAAATAATTACC
* *
13737 AGAATAACACC
1 AAAATAGCACC
13748 TGGTCAACGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.43, C:0.25, G:0.06, T:0.26
Consensus pattern (29 bp):
AAAATAGCACCCTTTTCAAAATAATTACC
Found at i:15605 original size:24 final size:24
Alignment explanation
Indices: 15578--15634 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
15568 TGGCTTAGCG
*
15578 AACAGTCCACCAATAAGTCCACTA
1 AACAGACCACCAATAAGTCCACTA
*
15602 AACAGACCACCAATTAGTCCACTA
1 AACAGACCACCAATAAGTCCACTA
*
15626 AACATACCA
1 AACAGACCA
15635 AACACTAGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.44, C:0.33, G:0.07, T:0.16
Consensus pattern (24 bp):
AACAGACCACCAATAAGTCCACTA
Found at i:15643 original size:24 final size:24
Alignment explanation
Indices: 15593--15645 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
15583 TCCACCAATA
* *
15593 AGTCCACTAAACAGACCACCAATT
1 AGTCCACTAAACAGACCAACAACT
*
15617 AGTCCACTAAACATACCAA-ACACT
1 AGTCCACTAAACAGACCAACA-ACT
15641 AGTCC
1 AGTCC
15646 TACAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.42, C:0.34, G:0.08, T:0.17
Consensus pattern (24 bp):
AGTCCACTAAACAGACCAACAACT
Found at i:17500 original size:21 final size:22
Alignment explanation
Indices: 17455--17500 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
17445 TTTCTACATT
** *
17455 TTTCAGAAAAATGATTGATCCC
1 TTTCAGAAAAATGATCCATCAC
17477 TTTCA-AAAAATGATCCATCAC
1 TTTCAGAAAAATGATCCATCAC
17498 TTT
1 TTT
17501 TGAAAAGGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.35
Consensus pattern (22 bp):
TTTCAGAAAAATGATCCATCAC
Found at i:31098 original size:71 final size:75
Alignment explanation
Indices: 31016--31200 Score: 224
Period size: 71 Copynumber: 2.5 Consensus size: 75
31006 AAGCTAAAAC
*
31016 ATCT-TAAATCCTAATTAAAATACTTAAAACTATTTAAACCAAAATACCT-AA-AAA-ATAATAT
1 ATCTATAAATCCTAATTAAAATAC-TAAAACTATTTAAACCAAAATACCTAAACAAAGATAAAAT
*
31077 -TATAAATAAT
65 ATAGAAATAAT
* *
31087 AT-TATAAATCCTAATTAAAATACTAAAACCTTTTTAAACTAAAATACCTAAAACAAAGATAAAA
1 ATCTATAAATCCTAATTAAAATACTAAAA-CTATTTAAACCAAAATACCT-AAACAAAGATAAAA
31151 TATAGAAATAAT
64 TATAGAAATAAT
*
31163 ATCCTA-AAAT-TTAATTAAAATACTAAAACATATTTAAA
1 AT-CTATAAATCCTAATTAAAATACTAAAAC-TATTTAAA
31201 ATAAAATTCA
Statistics
Matches: 98, Mismatches: 6, Indels: 15
0.82 0.05 0.13
Matches are distributed among these distances:
70 6 0.06
71 39 0.40
73 2 0.02
74 3 0.03
75 7 0.07
76 35 0.36
77 4 0.04
78 2 0.02
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.31
Consensus pattern (75 bp):
ATCTATAAATCCTAATTAAAATACTAAAACTATTTAAACCAAAATACCTAAACAAAGATAAAATA
TAGAAATAAT
Found at i:31101 original size:15 final size:12
Alignment explanation
Indices: 31068--31095 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
31058 AATACCTAAA
31068 AAATAATATTAT
1 AAATAATATTAT
31080 AAATAATATTAT
1 AAATAATATTAT
31092 AAAT
1 AAAT
31096 CCTAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AAATAATATTAT
Found at i:31184 original size:76 final size:71
Alignment explanation
Indices: 31020--31207 Score: 220
Period size: 76 Copynumber: 2.6 Consensus size: 71
31010 TAAAACATCT
* * *
31020 TAAATCCTAATTAAAATACTTAAAA-CTATTTAAACCAAAATACCTAAAAAATAATATTATAAAT
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAAAATAAAATTAGAAAT
31084 AATATTA
65 AATATTA
*
31091 TAAATCCTAATTAAAATACTAAAACCTTTTTAAACTAAAATACCTAAAACAAAGATAAAATATAG
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCT--AA-AAA-ATAAAAT-TAG
31156 AAATAATATCCTA
61 AAATAATAT--TA
* * *
31169 -AAAT-TTAATTAAAATACTAAAACATATTTAAAATAAAAT
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAAT
31208 TCAAATATAA
Statistics
Matches: 101, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
70 5 0.05
71 37 0.37
73 2 0.02
74 3 0.03
75 6 0.06
76 42 0.42
77 4 0.04
78 2 0.02
ACGTcount: A:0.57, C:0.11, G:0.01, T:0.31
Consensus pattern (71 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAAATAAAATTAGAAATA
ATATTA
Found at i:32877 original size:5 final size:5
Alignment explanation
Indices: 32867--32954 Score: 52
Period size: 5 Copynumber: 17.0 Consensus size: 5
32857 AAAAAATAAT
* * ***
32867 TAAAA TAAAA T-AAA TAGAA TGAAAA TAAAG TTTTA TAAAAA TAAAA TAAAAA
1 TAAAA TAAAA TAAAA TAAAA T-AAAA TAAAA TAAAA T-AAAA TAAAA T-AAAA
* * * *
32919 TAAAA TGAAA TAGAAC GAAAA TAAAA TGAAA TAAAA
1 TAAAA TAAAA TA-AAA TAAAA TAAAA TAAAA TAAAA
32955 AATAGAACGA
Statistics
Matches: 60, Mismatches: 18, Indels: 10
0.68 0.20 0.11
Matches are distributed among these distances:
4 4 0.07
5 42 0.70
6 14 0.23
ACGTcount: A:0.69, C:0.01, G:0.08, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:32929 original size:21 final size:21
Alignment explanation
Indices: 32905--32954 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
32895 AGTTTTATAA
*
32905 AAATAAAATAAAAATAAAATG
1 AAATAAAACAAAAATAAAATG
* *
32926 AAATAGAACGAAAATAAAATG
1 AAATAAAACAAAAATAAAATG
32947 AAATAAAA
1 AAATAAAA
32955 AATAGAACGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.16
Consensus pattern (21 bp):
AAATAAAACAAAAATAAAATG
Found at i:38229 original size:24 final size:24
Alignment explanation
Indices: 38199--38244 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
38189 CTTCGTCCAT
38199 TTTTAT-ATTAATATCAACTTCACA
1 TTTTATAATTAAT-TCAACTTCACA
*
38223 TTTTATAATTAATTCAATTTCA
1 TTTTATAATTAATTCAACTTCA
38245 TCCCTCATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTTATAATTAATTCAACTTCACA
Found at i:38281 original size:554 final size:557
Alignment explanation
Indices: 37214--38312 Score: 1608
Period size: 554 Copynumber: 2.0 Consensus size: 557
37204 GATGGTCATA
* *
37214 AACTATAAAGTATAAGTATATATGTATATTTATATATATATACATAAAGTATAATGTACATTATA
1 AACTATAAAGTATAAGTATATATGCATATTTATATATATATACATAAAGTATAATGTACATTAGA
*
37279 TATACATGCATCATATTATCAAAACATTCATTATACATATTATACATATATATATATTATAATTG
66 TATACATGCATCATATTATCAAAACATTC--TAT--ATA-TATACATAAATATATATTATAATTG
* * * *
37344 TTTCAATTTTTTCTTAACTTTTGAAATTAATGCAATTTAGTTAATTTTACACATTTTCTTCACAT
126 TTTCAATTTTTTCTCAACTTTTAAAATTAATGCAATTCAGTTAATTTTACACATTTTCCTCACAT
* *
37409 TTTACAATTATTTCGATTTAATCCATTTGTGTTGTTTAATTTATTTAAAATTTTATTTTTAATTT
191 TTTACAATTATTTCGATTTAATCCATTTATGTTGTTTAATTTATTTAAAATTTTATTTGTAATTT
* * * *
37474 CATATTTGTTCAATTTATTCCTTCAAATTATATTTGTATCCAAAATTGACCCATGCTTATTTATA
256 CATATTAGTTCAATTTAGTCCTTCAAAGTATATTTGTATCCAAAATTGACCCATACTTATTTATA
* *
37539 TTTTTGTAATTTACTTTAAAAAAAACCCTATAAAATATGAATCACATAATAAATTTCTTTTCAAA
321 TTTTTGTAATTTACTTT---AAAAACCCTATAAAATATAAATCACATAATAAATTTATTTTCAAA
* * * * * **
37604 TTATGTTCATCGACTTTTTAAGTGTATGCAATTTATTCCATTTTTATATTAATATCTGCTTCACA
383 TTATGTTCACCAACTTTTTAAATGTATGCAACTTAGTCCATTTTTATATTAATATCAACTTCACA
37669 TTTTATAATTAATTCAATTTCATCCCTCATCAATGTGTGTTGCTTAATTTATTCAATTTTTTATT
448 TTTTATAATTAATTCAATTTCATCCCTCATCAATGTGTGTTGCTTAATTTATTCAATTTTTTATT
37734 TCCAATTTCATGTTTGCTCAATTTGGTACTTTATATACATATATG
513 TCCAATTTCATGTTTGCTCAATTTGGTACTTTATATACATATATG
* *
37779 AACTATAAAGTATAAGTATATATGCATATGTGTATATCTATATATATAAAGTATAATGTACATTA
1 AACTATAAAGTATAAGTATATATGCATAT-T-TATATATATATACATAAAGTATAATGTACATTA
*
37844 GATATACATGCATCATATTATCATAACATTC-AT-TA-A-ACATAAATATATATTATAATT-TTT
64 GATATACATGCATCATATTATCAAAACATTCTATATATATACATAAATATATATTATAATTGTTT
** **
37904 TTA-TTTTTCTCCAACTTTTAAAATTAATGCAATTCAGTTCTTTTTACA-ATTTTCCTCACATTT
129 CAATTTTTTCT-CAACTTTTAAAATTAATGCAATTCAGTTAATTTTACACATTTTCCTCACATTT
* * * * *
37967 TACACTTTTTTTTTTGATTTGATCCTTTTATGTTGTTT-ATTGTATTT-AAATTTTAATTTGTAA
193 TACA---ATTATTTCGATTTAATCCATTTATGTTGTTTAATT-TATTTAAAATTTT-ATTTGTAA
**
38030 TTTCATATTAGTTCAATTTAGTCCTTCAAAGTATATTTGTATCTGAAATTGACCCATACTTATTT
253 TTTCATATTAGTTCAATTTAGTCCTTCAAAGTATATTTGTATCCAAAATTGACCCATACTTATTT
*
38095 ATATTTTTGTAATTTAC-TT-AAAACCCTATAAAATGTAAATCACATAATAAATTTATTTTCAAA
318 ATATTTTTGTAATTTACTTTAAAAACCCTATAAAATATAAATCACATAATAAATTTATTTTCAAA
*
38158 TTATGTTCACCAACTTTTTAAATGTATGCAACTTCGTCCATTTTTATATTAATATCAACTTCACA
383 TTATGTTCACCAACTTTTTAAATGTATGCAACTTAGTCCATTTTTATATTAATATCAACTTCACA
*
38223 TTTTATAATTAATTCAATTTCATCCCTCATCAATGTGTGTTGTTTAATTTATTCAATTTTTTATT
448 TTTTATAATTAATTCAATTTCATCCCTCATCAATGTGTGTTGCTTAATTTATTCAATTTTTTATT
* *
38288 TTCAATTTCATGTTTGTTCAATTTG
513 TCCAATTTCATGTTTGCTCAATTTG
38313 TATACATATA
Statistics
Matches: 485, Mismatches: 41, Indels: 27
0.88 0.07 0.05
Matches are distributed among these distances:
554 185 0.38
556 25 0.05
557 36 0.07
558 32 0.07
559 114 0.24
561 2 0.00
564 2 0.00
565 28 0.06
566 1 0.00
567 60 0.12
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.48
Consensus pattern (557 bp):
AACTATAAAGTATAAGTATATATGCATATTTATATATATATACATAAAGTATAATGTACATTAGA
TATACATGCATCATATTATCAAAACATTCTATATATATACATAAATATATATTATAATTGTTTCA
ATTTTTTCTCAACTTTTAAAATTAATGCAATTCAGTTAATTTTACACATTTTCCTCACATTTTAC
AATTATTTCGATTTAATCCATTTATGTTGTTTAATTTATTTAAAATTTTATTTGTAATTTCATAT
TAGTTCAATTTAGTCCTTCAAAGTATATTTGTATCCAAAATTGACCCATACTTATTTATATTTTT
GTAATTTACTTTAAAAACCCTATAAAATATAAATCACATAATAAATTTATTTTCAAATTATGTTC
ACCAACTTTTTAAATGTATGCAACTTAGTCCATTTTTATATTAATATCAACTTCACATTTTATAA
TTAATTCAATTTCATCCCTCATCAATGTGTGTTGCTTAATTTATTCAATTTTTTATTTCCAATTT
CATGTTTGCTCAATTTGGTACTTTATATACATATATG
Found at i:38415 original size:13 final size:15
Alignment explanation
Indices: 38334--38425 Score: 68
Period size: 14 Copynumber: 6.3 Consensus size: 15
38324 AATCTCTCTC
*
38334 TATATATATATAAAG
1 TATATAAATATAAAG
*
38349 TATAT-AATGTAAAG
1 TATATAAATATAAAG
* **
38363 TA-ATAAAGTGT-TTG
1 TATATAAA-TATAAAG
* *
38377 GATATAAGTATTAAAG
1 TATATAAATA-TAAAG
38393 TATATAAATAT-AAG
1 TATATAAATATAAAG
38407 TAT-TAAATATAAAG
1 TATATAAATATAAAG
38421 TATAT
1 TATAT
38426 TAATTATCAT
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
13 9 0.15
14 26 0.44
15 15 0.25
16 9 0.15
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (15 bp):
TATATAAATATAAAG
Found at i:38492 original size:17 final size:18
Alignment explanation
Indices: 38425--38482 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
38415 ATAAAGTATA
*
38425 TTAATTATCATGATTAAT
1 TTAATTATCATAATTAAT
* *
38443 AATTAAGTAT-ATTTATTAAT
1 --TTAATTATCA-TAATTAAT
38463 TTAATTATCATAATTAAT
1 TTAATTATCATAATTAAT
38481 TT
1 TT
38483 TTTATTATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 16 0.50
19 2 0.06
20 14 0.44
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (18 bp):
TTAATTATCATAATTAAT
Found at i:39352 original size:3 final size:3
Alignment explanation
Indices: 39344--39373 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
39334 CAATGTAGTG
39344 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
39374 TGCCATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:41169 original size:22 final size:22
Alignment explanation
Indices: 41143--41193 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
41133 AGTACCTTAG
41143 GGTCCATAAGGTCTTACAAATA
1 GGTCCATAAGGTCTTACAAATA
*
41165 GGTCCATAAGGTCTTACAACTA
1 GGTCCATAAGGTCTTACAAATA
*
41187 GGCCCAT
1 GGTCCAT
41194 TAGGCCCATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (22 bp):
GGTCCATAAGGTCTTACAAATA
Found at i:43244 original size:17 final size:17
Alignment explanation
Indices: 43222--43254 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
43212 GTCTTACCTT
*
43222 TACCATATCCATTTCTA
1 TACCATAACCATTTCTA
43239 TACCATAACCATTTCT
1 TACCATAACCATTTCT
43255 TTTAGCCGAC
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:0.30, C:0.30, G:0.00, T:0.39
Consensus pattern (17 bp):
TACCATAACCATTTCTA
Found at i:46422 original size:11 final size:11
Alignment explanation
Indices: 46403--46436 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
46393 GACCCACCCT
*
46403 AGCACATGCTC
1 AGCACATGCCC
*
46414 AGTACATGCCC
1 AGCACATGCCC
46425 AGCACATGCCC
1 AGCACATGCCC
46436 A
1 A
46437 AGGCTTGGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.29, C:0.38, G:0.18, T:0.15
Consensus pattern (11 bp):
AGCACATGCCC
Found at i:49705 original size:16 final size:17
Alignment explanation
Indices: 49678--49720 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
49668 TAATTGTTTA
49678 TTATTAATTATTATTGTTGT
1 TTATT-ATTATTATTG-T-T
*
49698 TTATTATTGTTATTGTT
1 TTATTATTATTATTGTT
49715 TTATTA
1 TTATTA
49721 ATAATATCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 7 0.32
18 1 0.05
19 9 0.41
20 5 0.23
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.67
Consensus pattern (17 bp):
TTATTATTATTATTGTT
Found at i:50803 original size:10 final size:10
Alignment explanation
Indices: 50788--50814 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
50778 AAATGTCAGT
50788 TGTTCGAACA
1 TGTTCGAACA
50798 TGTTCGAACA
1 TGTTCGAACA
50808 TGTTCGA
1 TGTTCGA
50815 GAACACTGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (10 bp):
TGTTCGAACA
Found at i:52998 original size:16 final size:17
Alignment explanation
Indices: 52977--53010 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
52967 ACTATTCATA
*
52977 TGAATAGTG-AATTTTG
1 TGAATACTGAAATTTTG
52993 TGAATACTGAAATTTTG
1 TGAATACTGAAATTTTG
53010 T
1 T
53011 CGGCGATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.44
Consensus pattern (17 bp):
TGAATACTGAAATTTTG
Found at i:58747 original size:34 final size:34
Alignment explanation
Indices: 58704--58798 Score: 140
Period size: 33 Copynumber: 2.8 Consensus size: 34
58694 ACCATGTGCA
* *
58704 AAGTTGGCCACCTACCAAAGATGAATTTTTC-AAT
1 AAGTTGGCCACCAACC-AAGATGAATTTTTCAAAC
*
58738 AAGTTGGCCACCAACCAAGATGAA-ATTTCAAAC
1 AAGTTGGCCACCAACCAAGATGAATTTTTCAAAC
58771 AAGTTGGCCACCAACCAAGATGAATTTT
1 AAGTTGGCCACCAACCAAGATGAATTTT
58799 CCAACTTATC
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
32 4 0.07
33 34 0.62
34 17 0.31
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (34 bp):
AAGTTGGCCACCAACCAAGATGAATTTTTCAAAC
Found at i:63529 original size:15 final size:14
Alignment explanation
Indices: 63509--63543 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
63499 TTTAGCAGAC
*
63509 TTTATTTCATTTTAA
1 TTTATTTCATTCT-A
63524 TTTATTTCATTCTA
1 TTTATTTCATTCTA
63538 TTTATT
1 TTTATT
63544 CTATCTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTATTTCATTCTA
Found at i:76612 original size:12 final size:12
Alignment explanation
Indices: 76595--76625 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
76585 GGATTAGTGG
76595 GCATGACTTTGT
1 GCATGACTTTGT
76607 GCATGACTTTGT
1 GCATGACTTTGT
76619 GCATGAC
1 GCATGAC
76626 GTATCTGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.35
Consensus pattern (12 bp):
GCATGACTTTGT
Found at i:81106 original size:46 final size:46
Alignment explanation
Indices: 81047--81212 Score: 242
Period size: 46 Copynumber: 3.6 Consensus size: 46
81037 TATGGTCTCT
* * * *
81047 TTTCATGCATTAATACATCCGTTCATGCATTTTAATCATGGCATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCC
* * *
81093 TTTCATCCCTTAATGCATCCTTTCACGCATTTTAATTATGGAATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCC
* * *
81139 TTTCATGCCTTGATGCATCCTTTCATGCATTTTAGTTATGACATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCC
81185 TTTCATGCCTTAATGCATCCTTTCATGC
1 TTTCATGCCTTAATGCATCCTTTCATGC
81213 CTTAATGCAT
Statistics
Matches: 106, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 106 1.00
ACGTcount: A:0.22, C:0.25, G:0.11, T:0.42
Consensus pattern (46 bp):
TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCC
Found at i:81249 original size:46 final size:46
Alignment explanation
Indices: 81199--81657 Score: 695
Period size: 46 Copynumber: 10.0 Consensus size: 46
81189 ATGCCTTAAT
* ** *
81199 GCATCCTTTCATGCCTTAATGCATCTTTTCATGCAAATTAATTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
*
81245 GCATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
* *
81291 ACATCCTTTCATGCCTTAATTCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
81337 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
*
81383 GCATCCTTTCATGCCTTAATGCAT-CTGTTCATGCATTTTAATTATG
1 GCATCCTTTCATGCCTTAATGCATCCT-TTCATGCATTTTAGTTATG
* *
81429 GCATCCTTTCATACCTTAATGCATCATTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
* * * *
81475 GCATCCTTTAATGCCATAATGCATCCGTTCATGCATTTTATTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
* *
81521 GCATCATTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
* * * *
81567 GCATCCTTTCTTGCATTAATGCATCCATTCATGCATTTTAATTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
* *
81613 GCATCCTTTTCATGCCTTAATCCATCCTTTCATTCATTTTAGTTA
1 GCATCC-TTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTA
81658 CGGATTCTGT
Statistics
Matches: 375, Mismatches: 35, Indels: 5
0.90 0.08 0.01
Matches are distributed among these distances:
45 2 0.01
46 340 0.91
47 33 0.09
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.43
Consensus pattern (46 bp):
GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
Found at i:81298 original size:158 final size:158
Alignment explanation
Indices: 81047--81373 Score: 512
Period size: 158 Copynumber: 2.1 Consensus size: 158
81037 TATGGTCTCT
**
81047 TTTCATGCATTAATACATCCGTTCATGCATTTTAATCATGGCATCCTTTCATCCCTTAATGCATC
1 TTTCATGCATTAATACATCCGTTCATGCAAATTAATCATGGCATCCTTTCATCCCTTAATGCATC
* *
81112 CTTTCACGCATTTTAATTATGGAATCCTTTCATGCCTTGATGCATCCTTTCATGCATTTTAGTTA
66 CATTCACGCATTTTAATTATGGAATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTA
81177 TGACATCCTTTCATGCCTTAATGCATCC
131 TGACATCCTTTCATGCCTTAATGCATCC
* * ** * *
81205 TTTCATGCCTTAATGCATCTTTTCATGCAAATTAATTATGGCATCCTTTCATGCCTTAATGCATC
1 TTTCATGCATTAATACATCCGTTCATGCAAATTAATCATGGCATCCTTTCATCCCTTAATGCATC
* * *
81270 CATTCATGCATTTTAGTTAT-GACATCCTTTCATGCCTTAATTCATCCTTTCATGCATTTTAGTT
66 CATTCACGCATTTTAATTATGGA-ATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTT
*
81334 ATGGCATCCTTTCATGCCTTAATGCATCC
130 ATGACATCCTTTCATGCCTTAATGCATCC
81363 TTTCATGCATT
1 TTTCATGCATT
81374 TTAGTTATGG
Statistics
Matches: 153, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
157 2 0.01
158 151 0.99
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.42
Consensus pattern (158 bp):
TTTCATGCATTAATACATCCGTTCATGCAAATTAATCATGGCATCCTTTCATCCCTTAATGCATC
CATTCACGCATTTTAATTATGGAATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTA
TGACATCCTTTCATGCCTTAATGCATCC
Found at i:88463 original size:46 final size:46
Alignment explanation
Indices: 88413--89004 Score: 733
Period size: 46 Copynumber: 12.9 Consensus size: 46
88403 TTATGTATAT
* * *
88413 TTTCATGCATTAATACATCCGTTCATGCATTTTAATCATGGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
* * * *
88459 TTTCATTCCTTAATGTATCC-TCTCATGTATTTTAATTATGGAATCC
1 TTTCATGCCTTAATGCATCCGT-TCATGCATTTTAATTATGGCATCC
* * * * *
88505 TTTAATGCCTTAATGCTTCCTTTCATGCATTTTAGTTATGGCGTCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
*
88551 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
* * *
88597 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGTCATCT
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
* * * * * *
88643 TTTCATGCCTTAATTCATTCTTTCAAGCATTTTAGTTATGACATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
* * *
88689 TTTCATGCCTTAATGCATCCGTTCTTGCATTTTAAGTATGGCATCT
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
* * * *
88735 TTTCATGACTTAATGCATCCTTTCATGCATTTTAGTTATGGTATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
*
88781 TTTCATGCCTTAATGCATCC-TTATATGCATTTTAATTATGGCATCC
1 TTTCATGCCTTAATGCATCCGTT-CATGCATTTTAATTATGGCATCC
* ** * * *
88827 TTTCATGCCTTATTG-AGTATGTTCATGCA-TTTAGTTATAGCATCT
1 TTTCATGCCTTAATGCA-TCCGTTCATGCATTTTAATTATGGCATCC
* *
88872 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATAGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
* *
88918 TTTAATGCCTTAATGCATCCGTTCATGCATTTTAATTTTGGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
* ** *
88964 TTTCATGCATTAATGCATCTTTTCATGCATTTTAGTTATGG
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGG
89005 ATTCGGTTTA
Statistics
Matches: 469, Mismatches: 70, Indels: 14
0.85 0.13 0.03
Matches are distributed among these distances:
45 41 0.09
46 425 0.91
47 3 0.01
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.45
Consensus pattern (46 bp):
TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
Found at i:88992 original size:20 final size:20
Alignment explanation
Indices: 88501--88994 Score: 141
Period size: 20 Copynumber: 21.8 Consensus size: 20
88491 TAATTATGGA
* *
88501 ATCCTTTAATGCCTTAATGC
1 ATCCTTTCATGCATTAATGC
*
88521 TTCCTTTCATGCATTTTAGTTATGGC
1 ATCCTTTCATGCA--TTA---AT-GC
* *
88547 GTCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCATTAATGC
88567 ATCCTTTCATGCATTTTAATTATGGC
1 ATCCTTTCATGCA--TT-A--AT-GC
*
88593 ATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCATTAATGC
*
88613 ATCCGTTCATGCATTTTAGTTATGTC
1 ATCCTTTCATGCA--TTA---ATG-C
* * *
88639 ATCTTTTCATGCCTTAATTC
1 ATCCTTTCATGCATTAATGC
* *
88659 ATTCTTTCAAGCATTTTAGTTATGAC
1 ATCCTTTCATGCA--TTA---ATG-C
*
88685 ATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCATTAATGC
* *
88705 ATCCGTTCTTGCATTTTAAGTATGGC
1 ATCCTTTCATGCA--TT-A--AT-GC
*
88731 ATCTTTTCATG-ACTTAATGC
1 ATCCTTTCATGCA-TTAATGC
*
88751 ATCCTTTCATGCATTTTAGTTATGGT
1 ATCCTTTCATGCA--TTA---AT-GC
*
88777 ATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCATTAATGC
88797 ATCCTTAT-ATGCATTTTAATTATGGC
1 ATCCTT-TCATGCA--TT-A--AT-GC
* *
88823 ATCCTTTCATGCCTTATTG-
1 ATCCTTTCATGCATTAATGC
*
88842 AGT-ATGTTCATGCATTTAGTTATAGC
1 A-TCCT-TTCATGCA-TTA---AT-GC
* *
88868 ATCTTTTCATGCCTTAATGC
1 ATCCTTTCATGCATTAATGC
*
88888 ATCCGTTCATGCATTTTAGTTATAGC
1 ATCCTTTCATGCA--TTA---AT-GC
* *
88914 ATCCTTTAATGCCTTAATGC
1 ATCCTTTCATGCATTAATGC
*
88934 ATCCGTTCATGCATTTTAATTTTGGC
1 ATCCTTTCATGCA--TTAA---T-GC
88960 ATCCTTTCATGCATTAATGC
1 ATCCTTTCATGCATTAATGC
*
88980 ATCTTTTCATGCATT
1 ATCCTTTCATGCATT
88995 TTAGTTATGG
Statistics
Matches: 356, Mismatches: 53, Indels: 130
0.66 0.10 0.24
Matches are distributed among these distances:
19 2 0.01
20 129 0.36
21 24 0.07
22 25 0.07
23 6 0.02
24 29 0.08
25 29 0.08
26 112 0.31
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (20 bp):
ATCCTTTCATGCATTAATGC
Found at i:93939 original size:180 final size:181
Alignment explanation
Indices: 93629--93991 Score: 584
Period size: 180 Copynumber: 2.0 Consensus size: 181
93619 AATGTAAAAT
* *
93629 CATCCCACAAAGAAAATCGTATCATAAAAACCTTTTCAATAAAAATATAATTTAAAAATTGGATA
1 CATCCAACAAAGAAAATCATATCATAAAAACCTTTTCAATAAAAATATAATTTAAAAATTGGATA
*
93694 GATTGGAGACCAAAATAATTTTATAAAGGGATAATGAAAATATACATAATTATACAAAAGTAATT
66 GATTGGAGACCAAAATAATTTTATAAAAGGATAATGAAAATATACATAATTATACAAAAGTAATT
* * ** * *
93759 ATGTATTTATTTCTTAATTATCAAAATAGTGTTAGATGTATATATTTTCAC
131 ATATACTTATTTCTTAATTATCAAAATAGTGGAAGATATATATATTTGCAC
* * * *
93810 CATCCAACAAAGATAATTATATCATAAAAACCTTTTCAATAAAAGTATACTTTAAAAATTGGATA
1 CATCCAACAAAGAAAATCATATCATAAAAACCTTTTCAATAAAAATATAATTTAAAAATTGGATA
* *
93875 GATT-GAGACCAAAATAATTTTATAAAAGGATAATGAAAATATACATAATTATGCAAATGTAATT
66 GATTGGAGACCAAAATAATTTTATAAAAGGATAATGAAAATATACATAATTATACAAAAGTAATT
93939 ATATACTTATTTCTTAATTATCAAAATAGTGGAAGATATATATATTTGCAC
131 ATATACTTATTTCTTAATTATCAAAATAGTGGAAGATATATATATTTGCAC
93990 CA
1 CA
93992 GTGTAAATCT
Statistics
Matches: 167, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
180 104 0.62
181 63 0.38
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (181 bp):
CATCCAACAAAGAAAATCATATCATAAAAACCTTTTCAATAAAAATATAATTTAAAAATTGGATA
GATTGGAGACCAAAATAATTTTATAAAAGGATAATGAAAATATACATAATTATACAAAAGTAATT
ATATACTTATTTCTTAATTATCAAAATAGTGGAAGATATATATATTTGCAC
Found at i:95708 original size:21 final size:22
Alignment explanation
Indices: 95682--95723 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
95672 GTTTTTAATA
*
95682 AAAGTT-TTTCTTTTCTTTTTC
1 AAAGTTCTTTCTTTTATTTTTC
*
95703 AAAGTTCTTTGTTTTATTTTT
1 AAAGTTCTTTCTTTTATTTTT
95724 TTTATTTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.67
Consensus pattern (22 bp):
AAAGTTCTTTCTTTTATTTTTC
Found at i:103510 original size:26 final size:26
Alignment explanation
Indices: 103474--103527 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
103464 AATCTTCTCT
103474 TTTTTTGACTAATGCCATTCGGTGCA
1 TTTTTTGACTAATGCCATTCGGTGCA
*
103500 TTTTTTGACTAATGTCATTCGGTGCA
1 TTTTTTGACTAATGCCATTCGGTGCA
103526 TT
1 TT
103528 AATGCACCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.46
Consensus pattern (26 bp):
TTTTTTGACTAATGCCATTCGGTGCA
Done.