Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003810.1 Hibiscus syriacus cultivar Beakdansim tig00008167_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: 41154
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:7372 original size:34 final size:33
Alignment explanation
Indices: 7287--7385 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
7277 AATTGGAAAG
7287 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
* *
7320 TTTGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
*
7353 TTGGAAAATTCATCTTTGGTAGGTGGCCAACTT
1 TTGGAAAATTCATC-TTGGTTGGTGGCCAACTT
7386 TGTATATGGG
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
33 43 0.72
34 17 0.28
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (33 bp):
TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
Found at i:12124 original size:34 final size:33
Alignment explanation
Indices: 12036--12131 Score: 142
Period size: 33 Copynumber: 2.9 Consensus size: 33
12026 TGACAAGTTG
12036 GAAAATTCATCTTGGTTGGTGGCCAACTTATTT
1 GAAAATTCATCTTGGTTGGTGGCCAACTTATTT
12069 G-AAATGTCATCTTGGTTGGTGGCCAACTTA-TT
1 GAAAAT-TCATCTTGGTTGGTGGCCAACTTATTT
*
12101 GAAAAATTCATCTTTGGTAGGTGGCCAACTT
1 G-AAAATTCATC-TTGGTTGGTGGCCAACTT
12132 TGCACATGGT
Statistics
Matches: 58, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
32 7 0.12
33 30 0.52
34 21 0.36
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (33 bp):
GAAAATTCATCTTGGTTGGTGGCCAACTTATTT
Found at i:18776 original size:25 final size:25
Alignment explanation
Indices: 18739--18790 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
18729 ATTTCCAGCT
*
18739 TTGATTTCCAGCCTCCAA-ATTTGAC
1 TTGATTTACAGCC-CCAACATTTGAC
* *
18764 TTGATTTATAGCCCCAACTTTTGAC
1 TTGATTTACAGCCCCAACATTTGAC
18789 TT
1 TT
18791 CCAACACCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (25 bp):
TTGATTTACAGCCCCAACATTTGAC
Found at i:29815 original size:22 final size:22
Alignment explanation
Indices: 29785--29835 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
29775 CATGGGCCTA
* *
29785 ATGGGCCTAGTTGTAAGACCTT
1 ATGGACCTAGTTGTAAGACATT
*
29807 ATGGACCTATTTGTAAGACATT
1 ATGGACCTAGTTGTAAGACATT
29829 ATGGACC
1 ATGGACC
29836 CTAAGGTACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (22 bp):
ATGGACCTAGTTGTAAGACATT
Found at i:31609 original size:3 final size:3
Alignment explanation
Indices: 31601--31627 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
31591 ATTAATGGCA
31601 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
31628 CACTACATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:32551 original size:14 final size:15
Alignment explanation
Indices: 32530--32621 Score: 68
Period size: 14 Copynumber: 6.3 Consensus size: 15
32520 ATGATAATTA
32530 ATATACTTTATATTT
1 ATATACTTTATATTT
32545 A-ATAC-TTATATTT
1 ATATACTTTATATTT
*
32558 ATATACTTTAATACTT
1 ATATACTTT-ATATTT
*** *
32574 ATAT-CCAAACACTTT
1 ATATACTTTATA-TTT
*
32589 AT-TACTTTACA-TT
1 ATATACTTTATATTT
*
32602 ATATACTTTATATAT
1 ATATACTTTATATTT
32617 ATATA
1 ATATA
32622 TAGATTATAT
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
13 13 0.22
14 19 0.32
15 18 0.31
16 9 0.15
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATACTTTATATTT
Found at i:32587 original size:22 final size:22
Alignment explanation
Indices: 32542--32595 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
32532 ATACTTTATA
** * *
32542 TTTAATACTTATATTTATATAC
1 TTTAATACTTATATCCAAACAC
32564 TTTAATACTTATATCCAAACAC
1 TTTAATACTTATATCCAAACAC
*
32586 TTTATTACTT
1 TTTAATACTT
32596 TACATTATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTAATACTTATATCCAAACAC
Found at i:32754 original size:25 final size:24
Alignment explanation
Indices: 32707--32752 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
32697 TGATGAGGGA
32707 TGAAATTGAATTAATTATAAAATT
1 TGAAATTGAATTAATTATAAAATT
*
32731 TGAAGTTGATATTAA-TATAAAA
1 TGAAATTGA-ATTAATTATAAAA
32753 ATGGACGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (24 bp):
TGAAATTGAATTAATTATAAAATT
Found at i:33108 original size:24 final size:26
Alignment explanation
Indices: 33062--33120 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 26
33052 TTATAATATA
* *
33062 TATATATATATATATATGTATG-TATG
1 TATA-ATATGTATATATGAATGTTATG
33088 TATAATATGTATA-ATGAATGTTATG
1 TATAATATGTATATATGAATGTTATG
33113 -ATAATATG
1 TATAATATG
33121 ATGCATGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 14 0.47
25 12 0.40
26 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.46
Consensus pattern (26 bp):
TATAATATGTATATATGAATGTTATG
Found at i:33137 original size:20 final size:21
Alignment explanation
Indices: 33066--33135 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 21
33056 AATATATATA
*
33066 TATATATATATATGTATGTATG
1 TATATATATATATG-ATGAATG
* *
33088 TATA-ATATGTATAATGAATG
1 TATATATATATATGATGAATG
*
33108 T-TATGATA-ATATGATGCATG
1 TATAT-ATATATATGATGAATG
33128 TATATATA
1 TATATATA
33136 ATGTACATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 2 0.05
20 20 0.51
21 13 0.33
22 4 0.10
ACGTcount: A:0.40, C:0.01, G:0.14, T:0.44
Consensus pattern (21 bp):
TATATATATATATGATGAATG
Found at i:33177 original size:14 final size:14
Alignment explanation
Indices: 33155--33199 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
33145 ATACTTTATG
*
33155 TATATATATATACA
1 TATACATATATACA
33169 TATAC--ATATACA
1 TATACATATATACA
*
33181 TATACATATATACT
1 TATACATATATACA
33195 TATAC
1 TATAC
33200 TTTATAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 12 0.44
14 15 0.56
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (14 bp):
TATACATATATACA
Found at i:33201 original size:6 final size:6
Alignment explanation
Indices: 33156--33190 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
33146 TACTTTATGT
*
33156 ATATAT ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
33191 TACTTATACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37
Consensus pattern (6 bp):
ATATAC
Found at i:33661 original size:2 final size:2
Alignment explanation
Indices: 33650--34430 Score: 148
Period size: 2 Copynumber: 395.0 Consensus size: 2
33640 TTAAAACAAT
33650 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TGA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
* * * * * *
33690 TG T- TA TA -A TA -A TA TGA TG CA TG TA TA TA TA -A TG TA -A AA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
33728 TA TA -A GTA TA TA TA TA AA GTG TA AA CTA TA AA GTA TA TA TA CTT
1 TA TA TA -TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA TA -TA
* * *
33772 TA AA GTA TA AA GTG 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
*
33816 TA TA TA TA TA TA CTA TA AA GTA TA -A GTA TA T- TA TA -A GTA TA
1 TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA
* * * * * *
33857 TA TA TA AA T- TA TA AA GTA TA TA TA CTT TT TA CTA -A AA CTT TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA TA -TA TA
* *
33899 TA TA TA T- TA TA AA CT- TA TA TA TA TA AA GTA TA -A T- TA TA -A
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * *
33938 GGA CA AA AA TA TA TA -A GTA TA TA -A TA T- TA -A GTA TA TA -A
1 -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA
* * * *
33976 GTA TA TA -A GTA TA TA TA CA TA TA AA GTA -A AA GTA TA TA CA TA
1 -TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA
* * * *
34018 AA CTA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA AA GT- TC TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * *
34061 GTA TA AA T- TA TA TA TA CA TA TA TA -A TA -A TA TA AA CTA TA -A
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * *
34101 GTA T- TA TA TA TA TA -A AA GTA TA -A T- TA TA AA GA T- TA AA GTA
1 -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA
* *
34141 TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTC TA T- TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * * * *
34182 TT TA TA TA TA TA CTT TA T- TC TT TA TA -A T- TA TA CTC TA TT TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
*
34223 TA TG TA TA -A TA TA CT- TA TA CTA TA TA T- TA T- 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
* * *
34263 TA CTT TA TA GTA TA TA TA TA TA TA CTT TA TA T- TC T- TA TA TA
1 TA -TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * *
34304 CT- TG TA TA TT TA TA CT- TA TA TA TT TA TA T- TA TA CT- TA GA
1 -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA
* *
34343 TA CTT TA TA T- TA TA TGA T- TA TA TA CT- TA TC T- TA TA -A T-
1 TA -TA TA TA TA TA TA T-A TA TA TA TA -TA TA TA TA TA TA TA TA
* * *
34380 TA TA CTA TA TA TA TA TA TA TA TT TA TA CTT TA TA T- TA TA TA TG
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
34423 TA TA TA TA
1 TA TA TA TA
34431 CTTTATACTA
Statistics
Matches: 568, Mismatches: 104, Indels: 214
0.64 0.12 0.24
Matches are distributed among these distances:
1 58 0.10
2 458 0.81
3 52 0.09
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:34330 original size:144 final size:143
Alignment explanation
Indices: 34164--34437 Score: 344
Period size: 142 Copynumber: 1.9 Consensus size: 143
34154 TATATATATA
* * * *
34164 TATATATATACTCTATTCTTTATATATATACTT-TATTCTTTATAATTATACTCTATT-TATA-T
1 TATATATATACTCTATTATTTATAT-TATACTTAGATACTTTAT-ATTATA-T-GATTATATACT
*
34226 GTATAATATACTTATACTATATAT-TATTATATATATATACTTTATAGTATATA-TATATATACT
62 -TATAATATAATTATACTATATATATA-TATATATATATACTTTATAGTATATAGTATATATACT
34289 TTATATTCTTATATACTTG
125 TTATATTCTTATATACTTG
*
34308 TATATTTATACT-TATATATTTATATTATACTTAGATACTTTATATTATATGATTATATACTTAT
1 TATATATATACTCTAT-TATTTATATTATACTTAGATACTTTATATTATATGATTATATACTTAT
** * *
34372 CTTATAATTATACTATATATATATATATATTTATACTTTATATTATATATGTATATATACTTTAT
65 AATATAATTATACTATATATATATATATATATATACTTTATAGTATATA-GTATATATACTTTAT
34437 A
129 A
34438 CTAAAACTTT
Statistics
Matches: 113, Mismatches: 10, Indels: 14
0.82 0.07 0.10
Matches are distributed among these distances:
141 3 0.03
142 49 0.43
143 19 0.17
144 42 0.37
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.54
Consensus pattern (143 bp):
TATATATATACTCTATTATTTATATTATACTTAGATACTTTATATTATATGATTATATACTTATA
ATATAATTATACTATATATATATATATATATATACTTTATAGTATATAGTATATATACTTTATAT
TCTTATATACTTG
Found at i:34346 original size:41 final size:40
Alignment explanation
Indices: 34143--34418 Score: 173
Period size: 41 Copynumber: 6.8 Consensus size: 40
34133 TTAAAGTATA
*
34143 TTATA-TATATATATATATATATATATATATACTCTAT-T-CT
1 TTATATTATATAT-TATATATTTATAT-TATACT-TATATACT
* *
34183 TTATA-TATATACTT-TATTCTTTATAATTATACTCTATTTA-T
1 TTATATTATATA-TTATA-TATTTAT-ATTATACT-TATATACT
* * * *
34224 ATGTATAATATACTTATACTATATATTATTATA-TATATATACT
1 TTATATTATATA-TTATA-TATTTA-TATTATACT-TATATACT
*
34267 TTATAGTATATATATATATACTTTATA-T-T-CTTATATACT
1 TTATATTATATAT-TATATA-TTTATATTATACTTATATACT
*
34306 TGTATATT-TATACTTATATATTTATATTATACTTAGATACT
1 T-TATATTATATA-TTATATATTTATATTATACTTATATACT
* * *
34347 TTATATTATATGATTATATACTTATCTTATAATTATACTA-T
1 TTATATTATAT-ATTATATATTTATATTATACTTATA-TACT
*
34388 ATATATATATATATT-TATACTTTATATTATA
1 TTATAT-TATATATTATATA-TTTATATTATA
34419 TATGTATATA
Statistics
Matches: 190, Mismatches: 24, Indels: 43
0.74 0.09 0.17
Matches are distributed among these distances:
38 6 0.03
39 22 0.12
40 46 0.24
41 60 0.32
42 27 0.14
43 28 0.15
44 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (40 bp):
TTATATTATATATTATATATTTATATTATACTTATATACT
Found at i:34451 original size:30 final size:30
Alignment explanation
Indices: 34385--34463 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
34375 ATAATTATAC
* *
34385 TATATATATATATATATTTATACTTTATAT
1 TATATATATATATATATTTATACTTAAAAT
*
34415 TATATATGTATATATACTTTATAC-TAAAACTT
1 TATATATATATATATA-TTTATACTTAAAA--T
*
34447 TATATACATATATATAT
1 TATATATATATATATAT
34464 ACATACTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
30 18 0.44
31 8 0.20
32 15 0.37
ACGTcount: A:0.42, C:0.06, G:0.01, T:0.51
Consensus pattern (30 bp):
TATATATATATATATATTTATACTTAAAAT
Found at i:34470 original size:38 final size:36
Alignment explanation
Indices: 34406--34476 Score: 97
Period size: 38 Copynumber: 1.9 Consensus size: 36
34396 ATATATTTAT
* * *
34406 ACTTTATATTATATATGTATATATACTTTATACTAAA
1 ACTTTATATCATATATATATACATACTTT-TACTAAA
34443 ACTTTATATACATATATATATACATACTTTTACT
1 ACTTTATAT-CATATATATATACATACTTTTACT
34477 TTATAGTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
37 13 0.43
38 17 0.57
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.48
Consensus pattern (36 bp):
ACTTTATATCATATATATATACATACTTTTACTAAA
Found at i:34514 original size:15 final size:14
Alignment explanation
Indices: 34494--34536 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
34484 TTACACACAC
34494 ACATATATATTGTAT
1 ACATATATATT-TAT
34509 ACATATATATTTAT
1 ACATATATATTTAT
* *
34523 A-TTATATACTTAT
1 ACATATATATTTAT
34536 A
1 A
34537 TACTTTTGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 11 0.42
14 4 0.15
15 11 0.42
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (14 bp):
ACATATATATTTAT
Found at i:34523 original size:21 final size:21
Alignment explanation
Indices: 34499--34538 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
34489 CACACACATA
*
34499 TATATTGTATACATATATATT
1 TATATTATATACATATATATT
*
34520 TATATTATATACTTATATA
1 TATATTATATACATATATA
34539 CTTTTGTCTC
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:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (21 bp):
TATATTATATACATATATATT
Found at i:34629 original size:19 final size:18
Alignment explanation
Indices: 34607--34654 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
34597 TATATATATT
* *
34607 TATAGTTTATATATACTCA
1 TATAATTTATATAAACT-A
* *
34626 TATACTTTATTTAAACTA
1 TATAATTTATATAAACTA
34644 TATAATTTATA
1 TATAATTTATA
34655 ATTATACATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (18 bp):
TATAATTTATATAAACTA
Found at i:34784 original size:21 final size:20
Alignment explanation
Indices: 34730--34820 Score: 73
Period size: 21 Copynumber: 4.7 Consensus size: 20
34720 CTATATAATT
34730 TATATAGTTTAATAGTTCATA
1 TATATAGTTT-ATAGTTCATA
* * *
34751 TATAAAGTCTATAGTTCATGG
1 TATATAGTTTATAGTTCAT-A
** *
34772 TATATAGTTTATACATAATA
1 TATATAGTTTATAGTTCATA
*
34792 TATATA-TATATA--T-ATA
1 TATATAGTTTATAGTTCATA
34808 TATATAGTTTATA
1 TATATAGTTTATA
34821 ATAATATAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
16 9 0.16
17 6 0.11
19 5 0.09
20 15 0.26
21 22 0.39
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (20 bp):
TATATAGTTTATAGTTCATA
Found at i:34794 original size:2 final size:2
Alignment explanation
Indices: 34789--34950 Score: 96
Period size: 2 Copynumber: 83.5 Consensus size: 2
34779 TTTATACATA
* *
34789 AT AT AT AT AT AT AT AT AT AT AT AT AGT TT AT A- AT A- AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* *
34830 AT AT AA ACT AT AT AGT TT AT AT A- AT AT A- AT AT A- AT AT A- AT
1 AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
34870 AT A- AT AT A- AT AT A- AT AT A- AT AT AT ACT TT AT AT AT ACT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT
* * *
34910 AT AT A- AT TT AT AT GT AGT TT AT AT AT AGT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT A
34951 ATTGTTTAAA
Statistics
Matches: 123, Mismatches: 18, Indels: 38
0.69 0.10 0.21
Matches are distributed among these distances:
1 12 0.10
2 103 0.84
3 8 0.07
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:34858 original size:5 final size:5
Alignment explanation
Indices: 34848--34892 Score: 90
Period size: 5 Copynumber: 9.0 Consensus size: 5
34838 TATATAGTTT
34848 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
34893 TACTTTATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:34904 original size:11 final size:11
Alignment explanation
Indices: 34888--34946 Score: 68
Period size: 11 Copynumber: 5.5 Consensus size: 11
34878 ATATAATATA
34888 ATATATACTTT
1 ATATATACTTT
34899 ATATATACTTT
1 ATATATACTTT
34910 ATATA-A-TTT
1 ATATATACTTT
* *
34919 ATATGTAGTTT
1 ATATATACTTT
* *
34930 ATATATAGTAT
1 ATATATACTTT
34941 ATATAT
1 ATATAT
34947 TATAATTGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
9 7 0.16
10 2 0.05
11 34 0.79
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (11 bp):
ATATATACTTT
Found at i:36594 original size:80 final size:80
Alignment explanation
Indices: 36469--36761 Score: 416
Period size: 80 Copynumber: 3.7 Consensus size: 80
36459 CAATAAAAAG
* * * * *
36469 GGGAGCCAATCTAAGGATATACCTT-GGATCTACCCAAGGACATCCTTAGATCCGTAGGGTTACC
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA-GATATCCTTAGGTCCGTAGGGTTACC
* * *
36533 TTAAGCACACAACTAA
65 TTATGCACACAGCAAA
*
36549 GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
36614 TATGCACACAGCAAA
66 TATGCACACAGCAAA
* *
36629 GGGAACCAACCTAAGGATATACCTTGGTACCTACCC-A-ATATCCTTAGGTCCGTAAGGTTACCT
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
36692 TATGCAC-CAGCAAA
66 TATGCACACAGCAAA
* *
36706 GGGAACCAACCTAAGGATATGCCTTGGGGCCT-CCCTAAGATATCCTTAGGTCCGTA
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCC-AAGATATCCTTAGGTCCGTA
36762 ATGACTTACA
Statistics
Matches: 194, Mismatches: 15, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
76 3 0.02
77 36 0.19
78 33 0.17
79 18 0.09
80 94 0.48
81 10 0.05
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (80 bp):
GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
TATGCACACAGCAAA
Done.