Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002949.1 Hibiscus syriacus cultivar Beakdansim tig00006085_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: 96079
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:2884 original size:15 final size:14
Alignment explanation
Indices: 2862--2896 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
2852 GAAAAAGAGG
2862 AAGAAAAAGAAGAA
1 AAGAAAAAGAAGAA
*
2876 AAGAGAAAATAAGAA
1 AAGA-AAAAGAAGAA
2891 AAGAAA
1 AAGAAA
2897 GAAAAACGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (14 bp):
AAGAAAAAGAAGAA
Found at i:4734 original size:20 final size:21
Alignment explanation
Indices: 4709--4766 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 21
4699 ATTTTCAGCA
4709 TGGTTTCGAAACCCCT-TACC
1 TGGTTTCGAAACCCCTATACC
*
4729 TGGTTTTGAAACCCCCCTATACC
1 TGGTTTCGAAA--CCCCTATACC
* *
4752 TGATTTCAAAACCCC
1 TGGTTTCGAAACCCC
4767 CTGCCTAGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 10 0.32
21 4 0.13
22 5 0.16
23 12 0.39
ACGTcount: A:0.24, C:0.34, G:0.12, T:0.29
Consensus pattern (21 bp):
TGGTTTCGAAACCCCTATACC
Found at i:6709 original size:20 final size:20
Alignment explanation
Indices: 6684--6726 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
6674 ATTTTCTTTC
* *
6684 AAAAACAAAATTAGATTTTG
1 AAAAACAAAATGAAATTTTG
6704 AAAAACAAAATGAAATTTTG
1 AAAAACAAAATGAAATTTTG
6724 AAA
1 AAA
6727 CATAATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.60, C:0.05, G:0.09, T:0.26
Consensus pattern (20 bp):
AAAAACAAAATGAAATTTTG
Found at i:9163 original size:34 final size:34
Alignment explanation
Indices: 9124--9196 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
9114 TTATTTTAAC
9124 GATAAACTATATTATGAACATAGGATTCTATTTT
1 GATAAACTATATTATGAACATAGGATTCTATTTT
* * *
9158 GATAAATTATATTATTACCATAGGATTCTATTTT
1 GATAAACTATATTATGAACATAGGATTCTATTTT
9192 GATAA
1 GATAA
9197 TTATCTTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.42
Consensus pattern (34 bp):
GATAAACTATATTATGAACATAGGATTCTATTTT
Found at i:13100 original size:67 final size:67
Alignment explanation
Indices: 13029--13810 Score: 1046
Period size: 67 Copynumber: 11.8 Consensus size: 67
13019 AAATAGAAGA
* * *
13029 TTTGAGGCATAACTGTGCATTGATAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
1 TTTGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
13094 CC
66 CC
* * * * *
13096 TTTGAGGCCTAACTGTGCATTGATAGAAAGGTTTTAATTATGCCAGTTACATTAAAGGCTAAGTG
1 TTTGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
*
13161 TC
66 CC
* * * *
13163 TTTGAGGCCTAACTATGCATTGATAGAAAGGTGTCAATCATG-CA---AG-T--TA-GCTAAGTG
1 TTTGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
13220 CC
66 CC
*
13222 TTTGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTG
1 TTTGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
13287 CC
66 CC
* * * * *
13289 TTTGAGGCCTAACTATACATTAACAGAAATGTGTCAATTATGTCAGTTAGATGAAAGGCT-AGTG
1 TTTGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
13353 CC
66 CC
* * * * *
13355 TTTGAGGCCTAACTTTGCTTTGACAGAAATGTGTCAATTATGCCAATTAGATGAAATGCTAAGTG
1 TTTGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
13420 CC
66 CC
** * * *
13422 TTTGAGGCCTAACTGTGCATACACAGAAAGGTGGCAATTATTCCATTTAGATGAAAGGCTAAGTG
1 TTTGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
13487 CC
66 CC
* * * *
13489 TTTGAGTCATAACTATTCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
1 TTTGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
13554 CC
66 CC
* *
13556 TTTGAGGCCTAACTGTGCATTGACAGAAAGATGTCAATTATGTCAGTTAGATGAAAGGCTAAGTG
1 TTTGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
13621 CC
66 CC
* * *
13623 TTTGAGGCCTAATTGTGTATTGACAGAAAGATGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
1 TTTGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
13688 CC
66 CC
* * * * ***
13690 -TTGAGGCCTAACTGTGCATTGGCAGAAATGTGTCAATTATGCCTGTTAGATGACAGAAGAAGTG
1 TTTGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
13754 CC
66 CC
* * *
13756 TTTGAGGACTAACTGTGCATTGGCAGAAAGGTGCCAATTATGCCA-TCTAGATGAA
1 TTTGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGT-TAGATGAA
13811 CAGTTAAAGA
Statistics
Matches: 632, Mismatches: 72, Indels: 22
0.87 0.10 0.03
Matches are distributed among these distances:
59 49 0.08
60 3 0.00
62 1 0.00
63 3 0.00
64 1 0.00
66 119 0.19
67 456 0.72
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (67 bp):
TTTGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
CC
Found at i:13552 original size:267 final size:266
Alignment explanation
Indices: 13029--13810 Score: 1018
Period size: 267 Copynumber: 3.0 Consensus size: 266
13019 AAATAGAAGA
* * *
13029 TTTGAGGCATAACTGTGCATTGATAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
1 TTTGAGGCCTAACTGTGCATTGACAGAAATGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGTG
* * * * * * *
13094 CCTTTGAGGCCTAACTGTGCATTGATAGAAAGGTTTTAATTATGCCAGTTACATTAAAGGCTAAG
66 CCTTTGAGGCCTAACTTTGCTTTGACAGAAA-GTGTCAATTATGCCAGTTAGATGAAAGGCTAAG
* * * * * *
13159 TGTCTTTGAGGCCTAACTATGCATTGATAGAAAGGTGTCAATCA-TGCA---AG-T--TA-GCTA
130 TGCCTTTGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATTCCATTTAGATGAAAGGCTA
* *
13216 AGTGCCTTTGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGC
195 AGTGCCTTTGA-GCATAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGC
13281 TAAGTGCC
259 TAAGTGCC
* * *
13289 TTTGAGGCCTAACTATACATTAACAGAAATGTGTCAATTATGTCAGTTAGATGAAAGGCT-AGTG
1 TTTGAGGCCTAACTGTGCATTGACAGAAATGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGTG
* *
13353 CCTTTGAGGCCTAACTTTGCTTTGACAGAAATGTGTCAATTATGCCAATTAGATGAAATGCTAAG
66 CCTTTGAGGCCTAACTTTGCTTTGACAGAAA-GTGTCAATTATGCCAGTTAGATGAAAGGCTAAG
** *
13418 TGCCTTTGAGGCCTAACTGTGCATACACAGAAAGGTGGCAATTATTCCATTTAGATGAAAGGCTA
130 TGCCTTTGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATTCCATTTAGATGAAAGGCTA
* *
13483 AGTGCCTTTGAGTCATAACTATTCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGC
195 AGTGCCTTTGAG-CATAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGC
13548 TAAGTGCC
259 TAAGTGCC
13556 TTTGAGGCCTAACTGTGCATTGACAGAAA-GATGTCAATTATGTCAGTTAGATGAAAGGCTAAGT
1 TTTGAGGCCTAACTGTGCATTGACAGAAATG-TGTCAATTATGTCAGTTAGATGAAAGGCTAAGT
13620 GCCTTTGAGGCCTAA-TTGTG-TATTGACAGAAAGATGTCAATTATGCCAGTTAGATGAAAGGCT
65 GCCTTTGAGGCCTAACTT-TGCT-TTGACAGAAAG-TGTCAATTATGCCAGTTAGATGAAAGGCT
* * * *
13683 AAGTGCC-TTGAGGCCTAACTGTGCATTGGCAGAAATGTGTCAATTATGCC-TGTTAGATGACAG
127 AAGTGCCTTTGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATTCCAT-TTAGATGAAAG
*** * * *
13746 AAGAAGTGCCTTTGAGGACTAACTGTGCATTGGCAGAAAGGTGCCAATTATGCCA-TCTAGATGA
191 GCTAAGTGCCTTTGAGCA-TAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGT-TAGATGA
13810 A
254 A
13811 CAGTTAAAGA
Statistics
Matches: 456, Mismatches: 49, Indels: 27
0.86 0.09 0.05
Matches are distributed among these distances:
259 96 0.21
260 57 0.12
263 2 0.00
264 1 0.00
266 6 0.01
267 230 0.50
268 64 0.14
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (266 bp):
TTTGAGGCCTAACTGTGCATTGACAGAAATGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGTG
CCTTTGAGGCCTAACTTTGCTTTGACAGAAAGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
GCCTTTGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATTCCATTTAGATGAAAGGCTAA
GTGCCTTTGAGCATAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTA
AGTGCC
Found at i:13681 original size:334 final size:327
Alignment explanation
Indices: 13029--13810 Score: 1079
Period size: 334 Copynumber: 2.4 Consensus size: 327
13019 AAATAGAAGA
* * *
13029 TTTGAGGCATAACTGTGCATTGATAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
1 TTTGAGGCCTAACTGTGCATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAAGCTAAGTG
* *** * * *
13094 CCTTTGAGGCCTAACTGTGCATTGATAGAAAGGTTTTAATTATGCCAGTTACATTAAAGGCTAAG
66 CCTTTGAGGCCTAACTGTGCATTGACAGAAAGGTGCCAATTATGCCATTTAGATGAAAGGCTAAG
* * * *
13159 TGTCTTTGAGGCCTAACTATGCATTGATAGAAAGGTGTCAATCATGCAAGTTAGCTAAGTGCCTT
131 TGCCTTTGAGGCATAACTATGCATTGACAGAAAGGTGTCAATCATGCAAGTAAGCTAAGTGCCTT
*
13224 TGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCC
196 TGAGGCCTAACTGTGCATTGACAGAAAGATGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCC
*
13289 TTTGAGGCCTAACTATACATTAACAGAAATGTGTCAATTATGTCAGTTAGATGAAAGGCT-AGTG
261 TTTGAGGCCTAACTATACATTAACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
13353 CC
326 CC
* * * *
13355 TTTGAGGCCTAACTTTGCTTTGACAGAAATGTGTCAATTATGCCAATTAGATGAAATGCTAAGTG
1 TTTGAGGCCTAACTGTGCATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAAGCTAAGTG
** * *
13420 CCTTTGAGGCCTAACTGTGCATACACAGAAAGGTGGCAATTATTCCATTTAGATGAAAGGCTAAG
66 CCTTTGAGGCCTAACTGTGCATTGACAGAAAGGTGCCAATTATGCCATTTAGATGAAAGGCTAAG
* * *
13485 TGCCTTTGAGTCATAACTATTCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTA
131 TGCCTTTGAGGCATAACTATGCATTGACAGAAAGGTGTCAATCATG-CA---AG-T--AA-GCTA
* *
13550 AGTGCCTTTGAGGCCTAACTGTGCATTGACAGAAAGATGTCAATTATGTCAGTTAGATGAAAGGC
188 AGTGCCTTTGAGGCCTAACTGTGCATTGACAGAAAGATGTCAATCATGCCAGTTAGATGAAAGGC
* * ** *
13615 TAAGTGCCTTTGAGGCCTAATTGTGTATTGACAGAAA-GATGTCAATTATGCCAGTTAGATGAAA
253 TAAGTGCCTTTGAGGCCTAACTATACATTAACAGAAATG-TGTCAATTATGCCAGTTAGATGAAA
13679 GGCTAAGTGCC
317 GGCTAAGTGCC
* *
13690 -TTGAGGCCTAACTGTGCATTGGCAGAAATGTGTCAATTATGCCTGTTAGATGACAGAAG--AAG
1 TTTGAGGCCTAACTGTGCATTGACAGAAATGTGTCAATTATGCCAGTTAGATGA-A-AAGCTAAG
* * *
13752 TGCCTTTGAGGACTAACTGTGCATTGGCAGAAAGGTGCCAATTATGCCATCTAGATGAA
64 TGCCTTTGAGGCCTAACTGTGCATTGACAGAAAGGTGCCAATTATGCCATTTAGATGAA
13811 CAGTTAAAGA
Statistics
Matches: 399, Mismatches: 45, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
326 154 0.39
327 2 0.01
330 2 0.01
331 1 0.00
333 2 0.01
334 229 0.57
335 7 0.02
336 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (327 bp):
TTTGAGGCCTAACTGTGCATTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAAGCTAAGTG
CCTTTGAGGCCTAACTGTGCATTGACAGAAAGGTGCCAATTATGCCATTTAGATGAAAGGCTAAG
TGCCTTTGAGGCATAACTATGCATTGACAGAAAGGTGTCAATCATGCAAGTAAGCTAAGTGCCTT
TGAGGCCTAACTGTGCATTGACAGAAAGATGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCC
TTTGAGGCCTAACTATACATTAACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
CC
Found at i:13915 original size:81 final size:80
Alignment explanation
Indices: 13768--13923 Score: 235
Period size: 81 Copynumber: 1.9 Consensus size: 80
13758 TGAGGACTAA
*
13768 CTGTGCATTGGCAGAAAGGTGCCAATTATGCCATCTAGATGAACAGTTAAAGACCGTTGAGTAAA
1 CTGTGCATTGGCAGAAAGGTGCCAATTATGCCATCTAGATGAACAGTTAAAGACCATTGAGTAAA
13833 AGATAAATGGCCTAG
66 AGATAAATGGCCTAG
* * *
13848 CTGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGT-TAGATGAA-TGATTAAAGACCATTGAGT
1 CTGTGCA-TTGGCAGAAAGGTGCCAATTATGCCA-TCTAGATGAACAG-TTAAAGACCATTGAGT
13911 AAAAGATAAATGG
63 AAAAGATAAATGG
13924 GATTATAATG
Statistics
Matches: 69, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
80 8 0.12
81 60 0.87
82 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (80 bp):
CTGTGCATTGGCAGAAAGGTGCCAATTATGCCATCTAGATGAACAGTTAAAGACCATTGAGTAAA
AGATAAATGGCCTAG
Found at i:13936 original size:81 final size:80
Alignment explanation
Indices: 13761--13940 Score: 206
Period size: 81 Copynumber: 2.2 Consensus size: 80
13751 GTGCCTTTGA
* *
13761 GGACTAACTGTGCA-TTGGCAGAAAGGTGCCAATTATGCCATCTAGATGAACAGTTAAAGACCGT
1 GGACT-ACTATGCATTTGGCAGAAAGGTGCCAATTATGCCATCTAGATGAACAGTTAAAGACCAT
13825 TGAGTAAAAGATAAAT
65 TGAGTAAAAGATAAAT
* * * * *
13841 GGCCTAGCTGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGT-TAGATGAA-TGATTAAAGACC
1 GGACTA-CTATGCATTTGGCAGAAAGGTGCCAATTATGCCA-TCTAGATGAACAG-TTAAAGACC
13904 ATTGAGTAAAAGATAAAT
63 ATTGAGTAAAAGATAAAT
*
13922 GGGATTA-TAATGCATTTGG
1 -GGACTACT-ATGCATTTGG
13941 ATATAAACTG
Statistics
Matches: 86, Mismatches: 8, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
79 1 0.01
80 13 0.15
81 67 0.78
82 5 0.06
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (80 bp):
GGACTACTATGCATTTGGCAGAAAGGTGCCAATTATGCCATCTAGATGAACAGTTAAAGACCATT
GAGTAAAAGATAAAT
Found at i:14378 original size:55 final size:55
Alignment explanation
Indices: 14312--14420 Score: 209
Period size: 55 Copynumber: 2.0 Consensus size: 55
14302 CGTCCTTATG
*
14312 GATTTTTCAACTTTAAATCGTCATTCAGTATTCAGAAGATATTTATGCATAAAGT
1 GATTTTTCAACTTTAAATCGTCATTCAGTATTCAGAAGATATTTATACATAAAGT
14367 GATTTTTCAACTTTAAATCGTCATTCAGTATTCAGAAGATATTTATACATAAAG
1 GATTTTTCAACTTTAAATCGTCATTCAGTATTCAGAAGATATTTATACATAAAG
14421 AGTATTTGCA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (55 bp):
GATTTTTCAACTTTAAATCGTCATTCAGTATTCAGAAGATATTTATACATAAAGT
Found at i:26111 original size:11 final size:11
Alignment explanation
Indices: 26095--26124 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
26085 TAAAAAATGG
26095 TAAATAAACAA
1 TAAATAAACAA
26106 TAAATAAACAA
1 TAAATAAACAA
*
26117 AAAATAAA
1 TAAATAAA
26125 ATGAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.17
Consensus pattern (11 bp):
TAAATAAACAA
Found at i:26642 original size:23 final size:23
Alignment explanation
Indices: 26616--26664 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
26606 ATAAAGAACA
*
26616 AAAATAAA-CTTAAATATACCATT
1 AAAATAAAGCTTAAACAT-CCATT
*
26639 AAAATAAAGTTTAAACATCCATT
1 AAAATAAAGCTTAAACATCCATT
26662 AAA
1 AAA
26665 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAAGCTTAAACATCCATT
Found at i:28018 original size:2 final size:2
Alignment explanation
Indices: 28005--28047 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
27995 AAAATAGGAA
*
28005 AT AT AT AA 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 AT AT AT AT
28047 A
1 A
28048 ATAACACTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28498 original size:37 final size:37
Alignment explanation
Indices: 28457--28561 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
28447 GTGCTTGTGG
* * *
28457 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
28494 ATCCTATTTTTAGGAGTTTGAATCCTTGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
28531 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
28562 GACGAAAGGG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:29565 original size:106 final size:106
Alignment explanation
Indices: 29234--30703 Score: 2180
Period size: 106 Copynumber: 13.9 Consensus size: 106
29224 GCATTGTTCT
* * * * *
29234 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
** * * *
29299 CCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
29340 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * * * * *
29399 TCAGCCGCCCCTTTGTCGTGAAGTTGAGCTTGTGTTGCCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * * *
29441 G-GTTCAAGATCTTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
29505 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
29546 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTAACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
29611 CTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
29652 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGGTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
29717 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
29758 GAGTCCAATATCCTTCGGTGTGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
29823 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
29864 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTTTGAAATTGGGAAATTGTTTGTTAACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
29929 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
29970 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
30035 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
30076 GAGTCCAAAATCCTTCGTTCTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
30141 CCAACGGTCCCTTCGTTGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
30182 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTTTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
30247 CTAGCAGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
30288 GAGTCCAATATCCTTCGTTGTGAAGATGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
30353 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTATG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
30394 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
30459 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
30500 GAGTCCAAAATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
30565 CCAGCGGTCCCTTCATTGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
30606 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTAGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
30671 CCAGTGGTCCCTTCGTCGTGAAGTTGAAACTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTG-AACTTG
30704 ACTCTAAAAG
Statistics
Matches: 1237, Mismatches: 118, Indels: 17
0.90 0.09 0.01
Matches are distributed among these distances:
100 75 0.06
101 5 0.00
102 4 0.00
104 4 0.00
105 5 0.00
106 1139 0.92
107 5 0.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:31275 original size:22 final size:22
Alignment explanation
Indices: 31249--31301 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
31239 GTGTTTGGTC
31249 AAAGGTTTGGAATTTGATGCTA
1 AAAGGTTTGGAATTTGATGCTA
* *
31271 AAAGGTTTGGCATTTGATGCTC
1 AAAGGTTTGGAATTTGATGCTA
31293 AAAGGTTTG
1 AAAGGTTTG
31302 ATGGGGTAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.36
Consensus pattern (22 bp):
AAAGGTTTGGAATTTGATGCTA
Found at i:31932 original size:18 final size:17
Alignment explanation
Indices: 31911--31950 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
31901 TCCCTTTTTC
31911 TTTTTGATTTTTGTTCTTTT
1 TTTTTG-TTTTT-TTC-TTT
31931 TTTTTGTTTTTTTCTTT
1 TTTTTGTTTTTTTCTTT
31948 TTT
1 TTT
31951 GTTCTGATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.30
18 3 0.15
19 5 0.25
20 6 0.30
ACGTcount: A:0.03, C:0.05, G:0.07, T:0.85
Consensus pattern (17 bp):
TTTTTGTTTTTTTCTTT
Found at i:36704 original size:37 final size:36
Alignment explanation
Indices: 36663--36736 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
36653 GGATAAAGAT
*
36663 AAAAAGAAAATAG-ATAAATAAATGAGTAAAATATATA
1 AAAAAGAAAA-AGCATAAATAAATAAGTAAAATA-ATA
* * *
36700 AAAAAGTAAAAGCATATATATATAAGTAAAATAATA
1 AAAAAGAAAAAGCATAAATAAATAAGTAAAATAATA
36736 A
1 A
36737 TAATAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 6 0.19
37 26 0.81
ACGTcount: A:0.66, C:0.01, G:0.09, T:0.23
Consensus pattern (36 bp):
AAAAAGAAAAAGCATAAATAAATAAGTAAAATAATA
Found at i:36718 original size:20 final size:20
Alignment explanation
Indices: 36693--36730 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
36683 AATGAGTAAA
36693 ATATATAAAAAAGTAAAAGC
1 ATATATAAAAAAGTAAAAGC
* *
36713 ATATATATATAAGTAAAA
1 ATATATAAAAAAGTAAAA
36731 TAATAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (20 bp):
ATATATAAAAAAGTAAAAGC
Found at i:37265 original size:37 final size:37
Alignment explanation
Indices: 37224--37328 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
37214 GTGCTTTTGG
* *
37224 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
* * *
37261 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
*
37298 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAG
37329 GACGAAAAGG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
Found at i:40022 original size:20 final size:20
Alignment explanation
Indices: 39997--40041 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
39987 GAGAAAAAAT
*
39997 AAAAGTTAAAAATGAAATAG
1 AAAAGTTAAAAATGAAAGAG
**
40017 AAAAGTTAAGGATGAAAGAG
1 AAAAGTTAAAAATGAAAGAG
40037 AAAAG
1 AAAAG
40042 AAAAAGTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.22, T:0.16
Consensus pattern (20 bp):
AAAAGTTAAAAATGAAAGAG
Found at i:46856 original size:23 final size:23
Alignment explanation
Indices: 46830--46878 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
46820 ATAAAGAACC
*
46830 AAAATAAA-CTTAAATATACCATT
1 AAAATAAAGCTTAAACAT-CCATT
*
46853 AAAATAAAGTTTAAACATCCATT
1 AAAATAAAGCTTAAACATCCATT
46876 AAA
1 AAA
46879 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAAGCTTAAACATCCATT
Found at i:48026 original size:18 final size:18
Alignment explanation
Indices: 48003--48039 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
47993 GTAGAATATC
48003 TAAACAAGTCTTAATTAG
1 TAAACAAGTCTTAATTAG
48021 TAAACAAGTCTTAATTAG
1 TAAACAAGTCTTAATTAG
48039 T
1 T
48040 GTACACGGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (18 bp):
TAAACAAGTCTTAATTAG
Found at i:52206 original size:11 final size:11
Alignment explanation
Indices: 52190--52215 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
52180 GTAAACTGTA
52190 ATATTAGGCAT
1 ATATTAGGCAT
52201 ATATTAGGCAT
1 ATATTAGGCAT
52212 ATAT
1 ATAT
52216 AAGGAGAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (11 bp):
ATATTAGGCAT
Found at i:56254 original size:17 final size:17
Alignment explanation
Indices: 56232--56265 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
56222 TTCATCTATC
56232 TCATTTAGCTCCAACAA
1 TCATTTAGCTCCAACAA
*
56249 TCATTTATCTCCAACAA
1 TCATTTAGCTCCAACAA
56266 GTTGTGCATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.32
Consensus pattern (17 bp):
TCATTTAGCTCCAACAA
Found at i:64001 original size:32 final size:32
Alignment explanation
Indices: 63960--64022 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
63950 ATTCAAAGAC
*
63960 TATTGTCTAAAATAAGGAGAACCATGGAGGTT
1 TATTGTCTAAAACAAGGAGAACCATGGAGGTT
* * *
63992 TATTGTCTAAAACAAGGGGGACCGTGGAGGT
1 TATTGTCTAAAACAAGGAGAACCATGGAGGT
64023 CTCTATGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.25
Consensus pattern (32 bp):
TATTGTCTAAAACAAGGAGAACCATGGAGGTT
Found at i:79083 original size:48 final size:48
Alignment explanation
Indices: 78943--79089 Score: 231
Period size: 48 Copynumber: 3.1 Consensus size: 48
78933 ACATTGAATA
* * * * * *
78943 GAGACAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTAGAA
1 GAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAGATCTTGGAG
*
78991 AAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAGATCTTGGAG
1 GAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAGATCTTGGAG
79039 GAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAGATCTTGGAG
1 GAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAGATCTTGGAG
79087 GAG
1 GAG
79090 TTTGATCCAT
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 91 1.00
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (48 bp):
GAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAGATCTTGGAG
Found at i:79258 original size:114 final size:114
Alignment explanation
Indices: 78996--79310 Score: 479
Period size: 114 Copynumber: 2.8 Consensus size: 114
78986 TAGAAAAGAG
* * * **
78996 AGACATGTTCCGCTTACTCTGAAGGGAATATCAGATCTTGGAGGAGAGAGACATGTTCCGCTTAC
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTAC
* *
79061 TCTGAAGGGAATATCAGATCTTGGAGGAGTTTGATCCATTGAATCGAAGC
66 TCTGAAGGGAATATCAGATC-TGAAGGAGTTTAATCCATTGAATCGAAGC
*
79111 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGATAGACATGTTCCGCTTAC
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTAC
* **
79176 TCGGAAGGGAATATCAGATCTGAAGG-GTTTTAATCCATTGAATCGGGGC
66 TCTGAAGGGAATATCAGATCTGAAGGAG-TTTAATCCATTGAATCGAAGC
* *
79225 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCTTAC
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTAC
*
79290 TCTGAAGGGAATATCAAATCT
66 TCTGAAGGGAATATCAGATCT
79311 TGGGAAAGAG
Statistics
Matches: 183, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
113 1 0.01
114 104 0.57
115 78 0.43
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (114 bp):
AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTAC
TCTGAAGGGAATATCAGATCTGAAGGAGTTTAATCCATTGAATCGAAGC
Found at i:79282 original size:48 final size:48
Alignment explanation
Indices: 79225--79353 Score: 231
Period size: 48 Copynumber: 2.7 Consensus size: 48
79215 GAATCGGGGC
*
79225 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAG
1 AGACCTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAG
*
79273 AGACCTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAG
1 AGACCTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAG
*
79321 AGACCTGTTCCACTGACTCTGAAGGGAATATCA
1 AGACCTGTTCCACTTACTCTGAAGGGAATATCA
79354 GATATGAAGG
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 77 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (48 bp):
AGACCTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAG
Found at i:80374 original size:1 final size:1
Alignment explanation
Indices: 80370--80450 Score: 81
Period size: 1 Copynumber: 81.0 Consensus size: 1
80360 TTTTCATATA
* * * * * * *
80370 TTTTTTCTTTCTTTTTTTTTCTTCTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTATTTTTTTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
80435 TTCTTTCTTTTTTTTT
1 TTTTTTTTTTTTTTTT
80451 CAAGCAAAAT
Statistics
Matches: 62, Mismatches: 18, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
1 62 1.00
ACGTcount: A:0.01, C:0.10, G:0.00, T:0.89
Consensus pattern (1 bp):
T
Found at i:80386 original size:13 final size:12
Alignment explanation
Indices: 80370--80450 Score: 96
Period size: 12 Copynumber: 6.7 Consensus size: 12
80360 TTTTCATATA
*
80370 TTTTTTCTTTCT
1 TTTTTTTTTTCT
80382 TTTTTTTTCTTC-
1 TTTTTTTT-TTCT
80394 TTTTTTTTTTCT
1 TTTTTTTTTTCT
80406 TTTTTTTTTT-T
1 TTTTTTTTTTCT
80417 TTTTTTTATTT-T
1 TTTTTTT-TTTCT
80429 TTTCTTTTCTTTCT
1 TTT-TTTT-TTTCT
80443 TTTTTTTT
1 TTTTTTTT
80451 CAAGCAAAAT
Statistics
Matches: 62, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
11 11 0.18
12 33 0.53
13 14 0.23
14 4 0.06
ACGTcount: A:0.01, C:0.10, G:0.00, T:0.89
Consensus pattern (12 bp):
TTTTTTTTTTCT
Found at i:80401 original size:28 final size:29
Alignment explanation
Indices: 80370--80447 Score: 106
Period size: 28 Copynumber: 2.7 Consensus size: 29
80360 TTTTCATATA
80370 TTTTTTCTTTCTTTTTTTTTCTTCTTT-T
1 TTTTTTCTTTCTTTTTTTTTCTTCTTTAT
* *
80398 TTTTTTCTTT-TTTTTTTTTTTTTTTTAT
1 TTTTTTCTTTCTTTTTTTTTCTTCTTTAT
80426 TTTTTTCTTTTCTTTCTTTTTT
1 TTTTTTC-TTTCTTT-TTTTTT
80448 TTTCAAGCAA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
27 14 0.32
28 18 0.41
29 3 0.07
30 3 0.07
31 6 0.14
ACGTcount: A:0.01, C:0.10, G:0.00, T:0.88
Consensus pattern (29 bp):
TTTTTTCTTTCTTTTTTTTTCTTCTTTAT
Found at i:80448 original size:28 final size:27
Alignment explanation
Indices: 80352--80450 Score: 101
Period size: 28 Copynumber: 3.5 Consensus size: 27
80342 TTGAACCCTC
**
80352 CTTTTTGTTTTTCATATATTTTTTC-TTT
1 CTTTTT-TTTTTTTTAT-TTTTTTCTTTT
*
80380 CTTTTTTTTTCTTCTTTTTTTTTTCTTTTT
1 CTTTTTTTTT-TT-TTATTTTTTTC-TTTT
*
80410 TTTTTTTTTTTTTTATTTTTTTCTTTT
1 CTTTTTTTTTTTTTATTTTTTTCTTTT
*
80437 CTTTCTTTTTTTTT
1 CTTTTTTTTTTTTT
80451 CAAGCAAAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
27 20 0.33
28 24 0.40
29 4 0.07
30 12 0.20
ACGTcount: A:0.04, C:0.10, G:0.01, T:0.85
Consensus pattern (27 bp):
CTTTTTTTTTTTTTATTTTTTTCTTTT
Found at i:94730 original size:11 final size:11
Alignment explanation
Indices: 94710--94745 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
94700 ACACTTATAA
*
94710 TATATATAGTT
1 TATATGTAGTT
94721 TATATGTAGTT
1 TATATGTAGTT
*
94732 TACATGTAGTT
1 TATATGTAGTT
94743 TAT
1 TAT
94746 TAATAAACTA
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:0.31, C:0.03, G:0.14, T:0.53
Consensus pattern (11 bp):
TATATGTAGTT
Found at i:94770 original size:2 final size:2
Alignment explanation
Indices: 94763--94846 Score: 63
Period size: 2 Copynumber: 44.0 Consensus size: 2
94753 CTATGTAATT
* * *
94763 TA TA TA TA TA TA TA TA TA TA TA TA TA -A GA TT TA TG 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
* *
94804 GTT TA TA TA TA TA -A TA TA T- TA -A GTA CA TA TA TA 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
94843 TA TA
1 TA TA
94847 AATAGTTTAC
Statistics
Matches: 65, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
1 6 0.09
2 57 0.88
3 2 0.03
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:94808 original size:13 final size:13
Alignment explanation
Indices: 94767--94816 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
94757 GTAATTTATA
*
94767 TATATATATA-TA
1 TATATATATAGTT
94779 TATATATATAAGATT
1 TATATATAT-AG-TT
*
94794 TATGTATATAGTT
1 TATATATATAGTT
94807 TATATATATA
1 TATATATATA
94817 ATATATTAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
12 9 0.28
13 12 0.38
14 2 0.06
15 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (13 bp):
TATATATATAGTT
Found at i:94814 original size:11 final size:11
Alignment explanation
Indices: 94710--94814 Score: 51
Period size: 11 Copynumber: 9.7 Consensus size: 11
94700 ACACTTATAA
94710 TATATATAGTT
1 TATATATAGTT
*
94721 TATATGTAGTT
1 TATATATAGTT
* *
94732 TACATGTAGTT
1 TATATATAGTT
*
94743 TAT-TA-A-TA
1 TATATATAGTT
* * *
94751 AACTATGTAATT
1 TA-TATATAGTT
*
94763 TATATATA-TA
1 TATATATAGTT
*
94773 TATATATA-TA
1 TATATATAGTT
94783 TATATA-AGATT
1 TATATATAG-TT
94794 TATGTATATAGTT
1 TA--TATATAGTT
94807 TATATATA
1 TATATATA
94815 TAATATATTA
Statistics
Matches: 73, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
8 2 0.03
9 3 0.04
10 19 0.26
11 37 0.51
12 2 0.03
13 8 0.11
14 2 0.03
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.50
Consensus pattern (11 bp):
TATATATAGTT
Done.