Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006950.1 Hibiscus syriacus cultivar Beakdansim tig00017862_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: 114309
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:10462 original size:41 final size:42
Alignment explanation
Indices: 10404--10487 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
10394 TTTTGTGATA
*
10404 AACTTTTATATTTAGGA-TTTTAGTTAGATTATTTTATTATT
1 AACTTTTATATTCAGGATTTTTAGTTAGATTATTTTATTATT
* *
10445 AACTTTTTTATTCAGGATTTTTAGTTTGATTATTTTATTATT
1 AACTTTTATATTCAGGATTTTTAGTTAGATTATTTTATTATT
10487 A
1 A
10488 TTTTATTAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 15 0.38
42 24 0.62
ACGTcount: A:0.27, C:0.04, G:0.10, T:0.60
Consensus pattern (42 bp):
AACTTTTATATTCAGGATTTTTAGTTAGATTATTTTATTATT
Found at i:16927 original size:620 final size:612
Alignment explanation
Indices: 15684--16881 Score: 1561
Period size: 620 Copynumber: 1.9 Consensus size: 612
15674 GTACCCCGTT
* *
15684 AAAAACTTAACATTAAGTTTTGAATTTTTTTTAAAAGTTTAGGTATTAAAACGGGCAAAAACTTA
1 AAAAACTTAACATTAAGTTTTG-ATTTTTTTTAAAAGTTTACGTATTAAAACGGGCAAAAACTGA
* *
15749 TAGTTTAGGTACTAAACACATTAAGTTTTTAACTGTGGGTACTAAAATGAAACAAAAATTAAATG
65 TAGTTTAGGTACTAAACACATTAAGTTTTTAACTGTGGGTACTAAAATGAAACAAAAAATAAACG
* *
15814 TTATGTGTGATTTTCAAAAAATTGAAAGTTTAAGCATTAAAATAGACCAAAACTGATAGGTTAGG
130 TTATGTATGATTTTCAAAAAATTAAAAGTTTAAGCATTAAAATAGACCAAAACTGATAGGTTAGG
* * *
15879 TACTAAATTTGTAGTTTACCCTAGTTTTTAATGCATTATTGTTGCTTAAGCCCACACTAATAATT
195 TACTAAAATTATAGTTTACCCTAGTTTTTAATGCATTATTGTTGCTCAAGCCCACACTAATAATT
15944 GACTAAAGACCTTTTAAGAATAATCATATTATTTAGATTTTATTAAAATGTAAGTAATTTATATA
260 GACTAAAGACCTTTTAAGAATAATCATATTATTTAGATTTTATTAAAATGTAAGTAATTTATATA
16009 TTCAAAAAAGTAATTGAAATAAAAATGACAGTATCTTATATTAATAAATAAGATAAAATATATCA
325 TTCAAAAAAGTAATTGAAATAAAAATGACAGTATCTTATATTAATAAATAAGATAAAATATAT-A
* * ** *
16074 ATGAGTGTTAGTACAAGTGGTTGTGATTCATGAATTTGAGCTTGTAAAACTAAGTTTGAATCCTA
389 ATGAGTGTTAGTACAAGTGGTTGAGATTCAAGAATTTGAGCTTGTAAAACTAAGTTCAAATACTA
* * * * *
16139 CCACCGTCACTCTTGGTGGGCAATCTGTAAATTCTTATATAAATCGCAATTGGGTCTTAGGTATG
454 CCACCGTCACTCTTGATGGGCAATCTATAAATTCTTACATAAATCGCAATTAGGTCTTAGATATG
* ** * * * ******* *
16204 CCTTGGCCCTTTATTGGGGGAGCCATTCTTGACCTAAATTTAATTTTTTTTCCAAATCATACTTA
519 CCTTGACCCTGAACTGGGGAAACCATTCTTGACCTAAATTTAATTACCAAAACAAATAATACTTA
* * * * **
16269 ATGTTTTGTTTTTGTTTCGTTTTTACCCCGTT
584 ATGTTTTATTTTTGATTAGTCTTTA---CGAC
* * *
16301 AAAAACTTATCGTTAAGTTTTG-TTTTTTTTAAAAAAAAGTTTACGTATTAAAACGGGCCAAAAC
1 AAAAACTTAACATTAAGTTTTGATTTTTTTT----AAAAGTTTACGTATTAAAACGGGCAAAAAC
* ** *
16365 TGATAGTTTAGGTACTAAATATGTTCAGTTTTTAACTGTGGGTTACTAAAATGAAACAAAAAATA
62 TGATAGTTTAGGTACTAAACACATTAAGTTTTTAACTGTGGG-TACTAAAATGAAACAAAAAATA
* * * ** *
16430 AACGTTATGTATGATTTTGAAAAAATTAAAAG-TTAAGATATTAAAATATACCAAAGTTGATAGT
126 AACGTTATGTATGATTTTCAAAAAATTAAAAGTTTAAG-CATTAAAATAGACCAAAACTGATAGG
16494 TTAGGTACTAAAATTATAGTTTACCCTAGTTTTTTAATGCATTATTGTTGCTCAAGCCCACACTA
190 TTAGGTACTAAAATTATAGTTTACCCTAG-TTTTTAATGCATTATTGTTGCTCAAGCCCACACTA
* * *
16559 ATAATTGACTAAAGATCTTTTAAGAATAATCGTATTATTCTTATGATTTTATTAAAATGTATGTA
254 ATAATTGACTAAAGACCTTTTAAGAATAATCATATTA-T-TTA-GATTTTATTAAAATGTAAGTA
* *
16624 ATTTATATATTCAAAAAAAGTAATTGGAAA-AAAAGTGACAGTATCTTATATTAGTAAATAAGAT
316 ATTTATATATTC-AAAAAAGTAATT-GAAATAAAAATGACAGTATCTTATATTAATAAATAAGAT
* * **
16688 -AAA-ATAT-AT-AGTGTTAGTACAAGTGGTTGAGTTTCAAGATTTTGAGCTTGTAAGGCTAAGT
379 AAAATATATAATGAGTGTTAGTACAAGTGGTTGAGATTCAAGAATTTGAGCTTGTAAAACTAAGT
* * *
16749 TCAAATACTACCACTGTCACTCTTGATGGGCAATCTATAAATTCTTCCATAAATTGCAATTAGGT
444 TCAAATACTACCACCGTCACTCTTGATGGGCAATCTATAAATTCTTACATAAATCGCAATTAGGT
* *
16814 CTTAGATATGTCC-TGATCCTGAACT-GGGAAACCATTCTTGACCTAAATTT-ATGTACCAAAAT
509 CTTAGATATG-CCTTGACCCTGAACTGGGGAAACCATTCTTGACCTAAATTTAAT-TACCAAAAC
16876 AAATAA
572 AAATAA
16882 AATATGTCAT
Statistics
Matches: 507, Mismatches: 60, Indels: 26
0.85 0.10 0.04
Matches are distributed among these distances:
615 8 0.02
617 20 0.04
618 2 0.00
619 99 0.20
620 214 0.42
621 73 0.14
622 1 0.00
623 7 0.01
624 35 0.07
625 44 0.09
626 4 0.01
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (612 bp):
AAAAACTTAACATTAAGTTTTGATTTTTTTTAAAAGTTTACGTATTAAAACGGGCAAAAACTGAT
AGTTTAGGTACTAAACACATTAAGTTTTTAACTGTGGGTACTAAAATGAAACAAAAAATAAACGT
TATGTATGATTTTCAAAAAATTAAAAGTTTAAGCATTAAAATAGACCAAAACTGATAGGTTAGGT
ACTAAAATTATAGTTTACCCTAGTTTTTAATGCATTATTGTTGCTCAAGCCCACACTAATAATTG
ACTAAAGACCTTTTAAGAATAATCATATTATTTAGATTTTATTAAAATGTAAGTAATTTATATAT
TCAAAAAAGTAATTGAAATAAAAATGACAGTATCTTATATTAATAAATAAGATAAAATATATAAT
GAGTGTTAGTACAAGTGGTTGAGATTCAAGAATTTGAGCTTGTAAAACTAAGTTCAAATACTACC
ACCGTCACTCTTGATGGGCAATCTATAAATTCTTACATAAATCGCAATTAGGTCTTAGATATGCC
TTGACCCTGAACTGGGGAAACCATTCTTGACCTAAATTTAATTACCAAAACAAATAATACTTAAT
GTTTTATTTTTGATTAGTCTTTACGAC
Found at i:19486 original size:11 final size:11
Alignment explanation
Indices: 19472--19538 Score: 82
Period size: 11 Copynumber: 6.2 Consensus size: 11
19462 TTAGAGTGCA
19472 ATTAGTTTGTT
1 ATTAGTTTGTT
19483 ATTAGTTTGTT
1 ATTAGTTTGTT
*
19494 A-TGGTTTGTT
1 ATTAGTTTGTT
* **
19504 ATTAGCTTAAT
1 ATTAGTTTGTT
*
19515 ACTAGTTTGTT
1 ATTAGTTTGTT
19526 ATTAGTTTGTT
1 ATTAGTTTGTT
19537 AT
1 AT
19539 GGTGTGTTGG
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
10 9 0.20
11 36 0.80
ACGTcount: A:0.21, C:0.03, G:0.18, T:0.58
Consensus pattern (11 bp):
ATTAGTTTGTT
Found at i:19501 original size:21 final size:21
Alignment explanation
Indices: 19476--19546 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
19466 AGTGCAATTA
19476 GTTTGTTATTAGTTTGTTATG
1 GTTTGTTATTAGTTTGTTATG
* ** *
19497 GTTTGTTATTAGCTTAATACTA
1 GTTTGTTATTAGTTTGTTA-TG
19519 GTTTGTTATTAGTTTGTTATG
1 GTTTGTTATTAGTTTGTTATG
*
19540 GTGTGTT
1 GTTTGTT
19547 GGTTAATTCG
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 23 0.57
22 17 0.43
ACGTcount: A:0.17, C:0.03, G:0.23, T:0.58
Consensus pattern (21 bp):
GTTTGTTATTAGTTTGTTATG
Found at i:22946 original size:16 final size:16
Alignment explanation
Indices: 22927--22960 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
22917 ATTATAAGAG
22927 TTTGACTCAAATTCAA
1 TTTGACTCAAATTCAA
* *
22943 TTTGACTTAAATTGAA
1 TTTGACTCAAATTCAA
22959 TT
1 TT
22961 GAGAAATCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (16 bp):
TTTGACTCAAATTCAA
Found at i:31212 original size:44 final size:44
Alignment explanation
Indices: 31152--31235 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
31142 GTGATAAACC
*
31152 TTTTATATTTAGGATTTTTAGTTTGATTATTTTATTATTAACTT
1 TTTTATATTCAGGATTTTTAGTTTGATTATTTTATTATTAACTT
*
31196 TTTTTTATTCAGGATTTTTAGTTTGATTATTTTATTATTA
1 TTTTATATTCAGGATTTTTAGTTTGATTATTTTATTATTA
31236 TTTTATTAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.64
Consensus pattern (44 bp):
TTTTATATTCAGGATTTTTAGTTTGATTATTTTATTATTAACTT
Found at i:39933 original size:11 final size:11
Alignment explanation
Indices: 39919--39985 Score: 82
Period size: 11 Copynumber: 6.2 Consensus size: 11
39909 TTAGAGTGCA
39919 ATTAGTTTGTT
1 ATTAGTTTGTT
39930 ATTAGTTTGTT
1 ATTAGTTTGTT
*
39941 A-TGGTTTGTT
1 ATTAGTTTGTT
* **
39951 ATTAGCTTAAT
1 ATTAGTTTGTT
*
39962 ACTAGTTTGTT
1 ATTAGTTTGTT
39973 ATTAGTTTGTT
1 ATTAGTTTGTT
39984 AT
1 AT
39986 GGTGTGTTGG
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
10 9 0.20
11 36 0.80
ACGTcount: A:0.21, C:0.03, G:0.18, T:0.58
Consensus pattern (11 bp):
ATTAGTTTGTT
Found at i:39948 original size:21 final size:21
Alignment explanation
Indices: 39923--39993 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
39913 AGTGCAATTA
39923 GTTTGTTATTAGTTTGTTATG
1 GTTTGTTATTAGTTTGTTATG
* ** *
39944 GTTTGTTATTAGCTTAATACTA
1 GTTTGTTATTAGTTTGTTA-TG
39966 GTTTGTTATTAGTTTGTTATG
1 GTTTGTTATTAGTTTGTTATG
*
39987 GTGTGTT
1 GTTTGTT
39994 GGTTAATTCG
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 23 0.57
22 17 0.43
ACGTcount: A:0.17, C:0.03, G:0.23, T:0.58
Consensus pattern (21 bp):
GTTTGTTATTAGTTTGTTATG
Found at i:43378 original size:16 final size:16
Alignment explanation
Indices: 43359--43392 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
43349 ATTATAAGAG
43359 TTTGACTCAAATTCAA
1 TTTGACTCAAATTCAA
* *
43375 TTTGACTTAAATTGAA
1 TTTGACTCAAATTCAA
43391 TT
1 TT
43393 GAGAAATCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (16 bp):
TTTGACTCAAATTCAA
Found at i:44170 original size:2 final size:2
Alignment explanation
Indices: 44165--44190 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44155 AGAAAAAATG
44165 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
44191 CTTATATGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45395 original size:17 final size:17
Alignment explanation
Indices: 45358--45408 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
45348 TAAAAATACC
*
45358 AAAATAAAATTGGAATA
1 AAAATAAAATTGAAATA
45375 AAAATAAAATT-AAATAA
1 AAAATAAAATTGAAAT-A
45392 AAAATTAAATATTGAAA
1 AAAA-TAAA-ATTGAAA
45409 AACGAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 3 0.10
17 16 0.55
18 4 0.14
19 3 0.10
20 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (17 bp):
AAAATAAAATTGAAATA
Found at i:47149 original size:21 final size:22
Alignment explanation
Indices: 47108--47157 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
47098 GAAACTATCC
*
47108 CAAGAGAGACACAACTTTGTTT
1 CAAGAGAGACACAAATTTGTTT
*
47130 CAAGAGTGACA-AAATTTGTTT
1 CAAGAGAGACACAAATTTGTTT
47151 CAAGAGA
1 CAAGAGA
47158 AACTGGCTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (22 bp):
CAAGAGAGACACAAATTTGTTT
Found at i:47276 original size:36 final size:36
Alignment explanation
Indices: 47224--47339 Score: 187
Period size: 36 Copynumber: 3.2 Consensus size: 36
47214 ATTCAAAGAT
47224 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
47260 TTTGATTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
47296 TTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
47332 CTTTGTTT
1 -TTTGTTT
47340 TGAGTAAATT
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
36 67 0.91
37 7 0.09
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:48848 original size:95 final size:95
Alignment explanation
Indices: 48653--48913 Score: 328
Period size: 95 Copynumber: 2.7 Consensus size: 95
48643 GGCTAGCTAA
* * * * * * *
48653 ATCCGTAAAGCCGGGGCATTTAACCAATTGTTCTAGAGGGACAGCTTAATATCATTGTATAG-AT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAAC-TCA-AGC-TT-TATTGTAT
** *
48717 ATTATAATTGCCTTTATCAGGCTAGCTGAATTTT
62 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
* *
48751 ATCCATAAAGCCTGGCCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
*
48816 TAATCACCTTTATCAGGTTAGCTGAATATT
66 TAATCACCTTTATCAGGCTAGCTGAATATT
* * *
48846 ATCTATAAAGCCGGGGCGTTTAACCAATTTCTTTAGAGGGACAACTCAAGCTTTATTGTATA-TA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
48910 TAAT
66 TAAT
48914 ATTATAATGT
Statistics
Matches: 144, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
94 10 0.07
95 91 0.63
96 2 0.01
97 2 0.01
98 39 0.27
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (95 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
TAATCACCTTTATCAGGCTAGCTGAATATT
Found at i:53081 original size:3 final size:3
Alignment explanation
Indices: 53016--53061 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
53006 ATATGAGATA
53016 AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
53062 AGAGAGATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:53136 original size:16 final size:17
Alignment explanation
Indices: 53104--53140 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
53094 AAAACAAACC
*
53104 AAAATAAAATTGGAATA
1 AAAATAAAATTGAAATA
53121 AAAATAAAA-TGAAATA
1 AAAATAAAATTGAAATA
53137 AAAA
1 AAAA
53141 ATTAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (17 bp):
AAAATAAAATTGAAATA
Found at i:55078 original size:7 final size:7
Alignment explanation
Indices: 55063--55103 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
55053 TAATTAACCC
55063 GTAAAAG
1 GTAAAAG
*
55070 GTGAAAG
1 GTAAAAG
55077 GTAAAAG
1 GTAAAAG
55084 GTAAAAG
1 GTAAAAG
55091 GTAAAAG
1 GTAAAAG
55098 GTAAAA
1 GTAAAA
55104 AGATTTCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.56, C:0.00, G:0.29, T:0.15
Consensus pattern (7 bp):
GTAAAAG
Found at i:57039 original size:18 final size:18
Alignment explanation
Indices: 57006--57040 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
56996 AAATATCTTC
57006 TAATTGAATAAAAATTAT
1 TAATTGAATAAAAATTAT
57024 TAATT-AATAAATAATTA
1 TAATTGAATAAA-AATTA
57041 ATACTTATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
TAATTGAATAAAAATTAT
Found at i:58422 original size:66 final size:63
Alignment explanation
Indices: 58315--58437 Score: 158
Period size: 66 Copynumber: 1.9 Consensus size: 63
58305 TTTATTGAAG
* *
58315 GTGCATCGATGCACATGGAGTGTATCGATGCACTCATTTAAAATAAATGAACATCGAATGCCATT
1 GTGCATCGATGCACAAGGAGTGCATCGATGCACTCA-TTAAAATAAA--AACATCGAATGCCATT
58380 A
63 A
* *
58381 GTGCATCGATGCATAAGGAGTGCATCGATGCACCTGC-TTAAAATACAAACATCGAAT
1 GTGCATCGATGCACAAGGAGTGCATCGATGCA-CT-CATTAAAATAAAAACATCGAAT
58438 AGGATTTATG
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
64 10 0.20
66 38 0.75
67 2 0.04
68 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (63 bp):
GTGCATCGATGCACAAGGAGTGCATCGATGCACTCATTAAAATAAAAACATCGAATGCCATTA
Found at i:59213 original size:24 final size:24
Alignment explanation
Indices: 59181--59231 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
59171 TTACGAATGC
59181 TCTGATCGATTTTGTATTTCGTGA
1 TCTGATCGATTTTGTATTTCGTGA
59205 TCTGATCGATTTTGTATTTCGTGA
1 TCTGATCGATTTTGTATTTCGTGA
59229 TCT
1 TCT
59232 ATTTTATGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.51
Consensus pattern (24 bp):
TCTGATCGATTTTGTATTTCGTGA
Found at i:64148 original size:22 final size:22
Alignment explanation
Indices: 64123--64218 Score: 119
Period size: 22 Copynumber: 4.5 Consensus size: 22
64113 GGGTATATTA
*
64123 GTCCTTCGGGACGTATTCAGTG
1 GTCCTTCGGGACGTATCCAGTG
* *
64145 GTCCTTCGAGATGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
*
64167 GTCCTTCGGGATGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
*
64189 GTCTTTCGGGAC--AT--AGTG
1 GTCCTTCGGGACGTATCCAGTG
64207 GTCCTTCGGGAC
1 GTCCTTCGGGAC
64219 AAATACTGAA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.22
20 2 0.03
22 50 0.75
ACGTcount: A:0.15, C:0.23, G:0.31, T:0.31
Consensus pattern (22 bp):
GTCCTTCGGGACGTATCCAGTG
Found at i:64208 original size:18 final size:18
Alignment explanation
Indices: 64185--64219 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
64175 GGATGTATCC
*
64185 AGTGGTCTTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
64203 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
64220 AATACTGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:66039 original size:17 final size:17
Alignment explanation
Indices: 65994--66056 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 17
65984 TGCATGAAAC
* *
65994 AATTAA-GAATTAATTT
1 AATTAATGAACTAGTTT
* *
66010 AATAAACGAACTAGTTT
1 AATTAATGAACTAGTTT
*
66027 GATTAATGAACTAGTTT
1 AATTAATGAACTAGTTT
66044 AATTAATGAACTA
1 AATTAATGAACTA
66057 CTTCCTTAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
16 5 0.13
17 34 0.87
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (17 bp):
AATTAATGAACTAGTTT
Found at i:80833 original size:45 final size:45
Alignment explanation
Indices: 80769--80885 Score: 234
Period size: 45 Copynumber: 2.6 Consensus size: 45
80759 AAAATAATAC
80769 GGTAACCATTAGCAGAAGTTGATGGATTTGTGTATGTTCCAGTTT
1 GGTAACCATTAGCAGAAGTTGATGGATTTGTGTATGTTCCAGTTT
80814 GGTAACCATTAGCAGAAGTTGATGGATTTGTGTATGTTCCAGTTT
1 GGTAACCATTAGCAGAAGTTGATGGATTTGTGTATGTTCCAGTTT
80859 GGTAACCATTAGCAGAAGTTGATGGAT
1 GGTAACCATTAGCAGAAGTTGATGGAT
80886 ACATATAACT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 72 1.00
ACGTcount: A:0.26, C:0.11, G:0.27, T:0.35
Consensus pattern (45 bp):
GGTAACCATTAGCAGAAGTTGATGGATTTGTGTATGTTCCAGTTT
Found at i:86664 original size:14 final size:14
Alignment explanation
Indices: 86636--86672 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
86626 GTTTTTTTTT
86636 GTTTGTGTT-GTTC
1 GTTTGTGTTCGTTC
*
86649 GTTTATGTTCGTTC
1 GTTTGTGTTCGTTC
86663 GTTTGTGTTC
1 GTTTGTGTTC
86673 ATTTATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.03, C:0.11, G:0.27, T:0.59
Consensus pattern (14 bp):
GTTTGTGTTCGTTC
Found at i:87697 original size:31 final size:31
Alignment explanation
Indices: 87661--87721 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
87651 CAACTTTTTC
* * *
87661 TCTTATTTTATATATGTTGAATTCAACTTAT
1 TCTTATTTGATATATGTCGAAATCAACTTAT
87692 TCTTATTTGATATATGTCGAAATCAACTTA
1 TCTTATTTGATATATGTCGAAATCAACTTA
87722 AATAAGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.49
Consensus pattern (31 bp):
TCTTATTTGATATATGTCGAAATCAACTTAT
Found at i:89202 original size:80 final size:82
Alignment explanation
Indices: 89093--89261 Score: 315
Period size: 82 Copynumber: 2.1 Consensus size: 82
89083 TTATATATGC
89093 TTAATATGTTGAAGTTAAGCGAAGTGATGACACTAAAAATTCAAC-ATATAGTTGTCTCAATTTG
1 TTAATATGTTGAAGTTAAGCGAAGTGATGACACTAAAAATTCAACAATATAGTTGTCTCAATTTG
89157 TAAGCTGCCTTATCCAT
66 TAAGCTGCCTTATCCAT
89174 TTAATATGTTGAAG-TAAGCGAAGTGATGACACTAAAAATTCAACATATATAGTTGTCTCAATTT
1 TTAATATGTTGAAGTTAAGCGAAGTGATGACACTAAAAATTCAACA-ATATAGTTGTCTCAATTT
89238 GTAAGCTGCCTTATCCAT
65 GTAAGCTGCCTTATCCAT
89256 TTAATA
1 TTAATA
89262 AACAAAGGCG
Statistics
Matches: 86, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
80 30 0.35
81 14 0.16
82 42 0.49
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (82 bp):
TTAATATGTTGAAGTTAAGCGAAGTGATGACACTAAAAATTCAACAATATAGTTGTCTCAATTTG
TAAGCTGCCTTATCCAT
Found at i:89496 original size:25 final size:25
Alignment explanation
Indices: 89450--89497 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
89440 TTCTCCCCCG
*
89450 TAAATTTTATAAATCCTTTCTTTCT
1 TAAATTTTATAAATCCTATCTTTCT
*
89475 TAAAGTTTTGTAAAT-CTATCTTT
1 TAAA-TTTTATAAATCCTATCTTT
89498 TAACATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.54
Consensus pattern (25 bp):
TAAATTTTATAAATCCTATCTTTCT
Found at i:99843 original size:29 final size:29
Alignment explanation
Indices: 99764--99826 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
99754 AATTGCAATC
99764 AAATAAAACATAACATTAAATAGAAATAG
1 AAATAAAACATAACATTAAATAGAAATAG
99793 AAATAAAACATAACATTAAATAGAAATAG
1 AAATAAAACATAACATTAAATAGAAATAG
99822 AAATA
1 AAATA
99827 TGAAAATAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.21
Consensus pattern (29 bp):
AAATAAAACATAACATTAAATAGAAATAG
Found at i:105133 original size:2 final size:2
Alignment explanation
Indices: 105086--105119 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
105076 TTTATATTTA
105086 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
105120 TAATTGAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:105326 original size:3 final size:3
Alignment explanation
Indices: 105318--105357 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
105308 ATATTTATAA
*
105318 TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT T-T TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
105358 CAAGACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:105506 original size:21 final size:21
Alignment explanation
Indices: 105482--105538 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
105472 CCATCTAACC
*
105482 CAGAAGTCCAACAAGTTGAAT
1 CAGAAGCCCAACAAGTTGAAT
105503 CAGAAGCCCAACAAGTTGAA-
1 CAGAAGCCCAACAAGTTGAAT
*
105523 CTGGAAGCCCAACAAG
1 C-AGAAGCCCAACAAG
105539 CTGGCACAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 1 0.03
21 32 0.97
ACGTcount: A:0.42, C:0.25, G:0.21, T:0.12
Consensus pattern (21 bp):
CAGAAGCCCAACAAGTTGAAT
Found at i:114086 original size:41 final size:43
Alignment explanation
Indices: 114014--114096 Score: 98
Period size: 41 Copynumber: 2.0 Consensus size: 43
114004 TTACGACTTG
* *
114014 GAATGTTGAGGGTATTTTTGAAGGCCCATTTCAACCAGAAATA
1 GAATGTTGAGGGCATTTTTGAAGGCCCATTTCAACCAAAAATA
*** *
114057 GAATGTTGA-GGCA-TTTTGAAGGTTTATTTCAGCCAAAAAT
1 GAATGTTGAGGGCATTTTTGAAGGCCCATTTCAACCAAAAAT
114097 GATCCATGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
41 22 0.65
42 3 0.09
43 9 0.26
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (43 bp):
GAATGTTGAGGGCATTTTTGAAGGCCCATTTCAACCAAAAATA
Found at i:114228 original size:39 final size:37
Alignment explanation
Indices: 114102--114222 Score: 145
Period size: 37 Copynumber: 3.2 Consensus size: 37
114092 AAAATGATCC
*
114102 ATGTGGGGCATCTTGAAGGCTCACATCAGTATGAAAA
1 ATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAA
114139 ATGTGGGGCATCTTGAAGGCTCACATCAGCATG-AAA
1 ATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAA
** * * * * *
114175 ATGTTGGGATATTTTGAAGGTTCATATCAACAAGAAATA
1 ATG-TGGGGCATCTTGAAGGCTCACATCAGCATGAAA-A
114214 ATGTGGGGC
1 ATGTGGGGC
114223 CATTTTTTAA
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
36 6 0.08
37 55 0.77
38 6 0.08
39 4 0.06
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.26
Consensus pattern (37 bp):
ATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAA
Done.