Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002206.1 Hibiscus syriacus cultivar Beakdansim tig00004497_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: 112810
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:341 original size:3 final size:3
Alignment explanation
Indices: 335--385 Score: 54
Period size: 3 Copynumber: 17.0 Consensus size: 3
325 TTTTTTTTTT
335 TTA TTA -TA TTA TTA TTA TTA TTA TTTA TTA TTTA TTAA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA TT-A TTA TTA TTA
381 -TA TTA
1 TTA TTA
386 CAGGCCCAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
2 6 0.14
3 27 0.64
4 9 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:384 original size:14 final size:13
Alignment explanation
Indices: 333--385 Score: 56
Period size: 13 Copynumber: 4.0 Consensus size: 13
323 GGTTTTTTTT
333 TTTTATTATATTA
1 TTTTATTATATTA
346 TTATTATTATTATT-
1 TT-TTATTA-TATTA
*
360 TATTATT-TATTAA
1 TTTTATTATATT-A
373 TTTTATTATATTA
1 TTTTATTATATTA
386 CAGGCCCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
11 4 0.12
13 14 0.42
14 11 0.33
15 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTATTATATTA
Found at i:13794 original size:114 final size:114
Alignment explanation
Indices: 13589--13925 Score: 593
Period size: 114 Copynumber: 3.0 Consensus size: 114
13579 TGCCACGTTA
* *
13589 TCATGGTAGAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
13654 TTTGGTATAAACCCCAAAACCAATTATTAGATTTGAAAGATGAATTTGC
66 TTTGGTATAAACCCCAAAACCAATTATTAGATTTGAAAGATGAATTTGC
13703 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
13768 TTTGGTATAAACCCCAAAACCAATTATTAGATTTGAAAGATGAATTTGC
66 TTTGGTATAAACCCCAAAACCAATTATTAGATTTGAAAGATGAATTTGC
13817 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
* ** * * * *
13882 TTCGGTAGGAACCACAGAACCAATCATTAGAATTGAAAGATGAA
66 TTTGGTATAAACCCCAAAACCAATTATTAGATTTGAAAGATGAA
13926 CTGCATGATT
Statistics
Matches: 214, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 214 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (114 bp):
TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
TTTGGTATAAACCCCAAAACCAATTATTAGATTTGAAAGATGAATTTGC
Found at i:14968 original size:112 final size:112
Alignment explanation
Indices: 14619--15301 Score: 734
Period size: 112 Copynumber: 6.0 Consensus size: 112
14609 TTAGCAAAGA
* * * * *
14619 TTTAAATCCATCATTCAATGGATCAACATTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCTG
1 TTTAAATTCATCATTCGATGGATCATCATTTCCAGAGAAAGTTCATAATGAAAAGAACTCATCTG
*
14683 AAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTG
66 AAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
* * * * * * ** * *
14730 CTTAAATTCATCACTCGGTGGATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTG
1 TTTAAATTCATCATTCGATGGATCATCATTTCCAGAGAAAGTTCATAATGAAAAGAACTCATCTG
*
14795 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTG
66 AAGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
* * *
14843 TTTGAATTCATCATTCGATGGATCATCATTTCAAGAGAAAGTTCATAATGAAAAGAACTTATCTG
1 TTTAAATTCATCATTCGATGGATCATCATTTCCAGAGAAAGTTCATAATGAAAAGAACTCATCTG
* * *
14908 AAGAAGAAGAAGAAGTTTATAATGAGAAGAGCTTATTCAACCTTTTG
66 AAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
* * * * *
14955 TTTAAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGATAAGAACTCATCT
1 TTTAAATTCATCATTCGATGGATCATCATTTCCAGAG-AAAGTTCATAATGAAAAGAACTCATCT
* * *
15019 --A-AAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTG
65 GAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
* *
15064 TTTGAATTCATCATTCGATGGATCATCAACTTTTCCAGAGAAAGTTCATAAT-AAGAAGAACTTA
1 TTTAAATTCATCATTCGATGGATCATC-A--TTTCCAGAGAAAGTTCATAATGAA-AAGAACTCA
*
15128 TCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTT-
62 TCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
* * * ** **
15178 TCATAACTTTATCACAGCAGGAGATATATCATCATCAACTTTTCCAGAGAAAGTTCATAAT-AAG
1 T-TTAAATTCATCA-TTC----G--AT-GGATCATC-A--TTTCCAGAGAAAGTTCATAATGAA-
* * * *
15242 AAGAACTTATCTGAAGAAGAAGAATAAGTTCATAATAAGAAGAGCTTGTTCAACCTTTTG
53 AAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
15302 CATAACTCTA
Statistics
Matches: 490, Mismatches: 61, Indels: 29
0.84 0.11 0.05
Matches are distributed among these distances:
109 62 0.13
110 2 0.00
111 29 0.06
112 153 0.31
113 100 0.20
114 2 0.00
115 47 0.10
116 1 0.00
120 1 0.00
122 2 0.00
123 91 0.19
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.30
Consensus pattern (112 bp):
TTTAAATTCATCATTCGATGGATCATCATTTCCAGAGAAAGTTCATAATGAAAAGAACTCATCTG
AAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
Found at i:15242 original size:123 final size:123
Alignment explanation
Indices: 15085--15420 Score: 520
Period size: 123 Copynumber: 2.8 Consensus size: 123
15075 CATTCGATGG
15085 ATCATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTTATCTGAAGAAGAAGAAGAAGTTC
1 ATCATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTTATCTGAAGAAGAAGAAGAAGTTC
*
15150 ATAATGAGAAGAGCTTGTTCAACCTTTTTCATAACTTTATCACAGCAGGAGATATATC
66 ATAATGAGAAGAGCTTGTTCAACCTTTTTCATAACTCTATCACAGCAGGAGATATATC
*
15208 ATCATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTTATCTGAAGAAGAAGAATAAGTTC
1 ATCATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTTATCTGAAGAAGAAGAAGAAGTTC
* *
15273 ATAATAAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGCAGGAGATATATC
66 ATAATGAGAAGAGCTTGTTCAACCTTTTTCATAACTCTATCACAGCAGGAGATATATC
* * * * *
15331 ATCATCAGCATTTCCAGA-AGGAGTTCATAATGAGAAGAACTCATCT---GAAGAAGAAGAAGTT
1 ATCATCAACTTTTCCAGAGA-AAGTTCATAATAAGAAGAACTTATCTGAAGAAGAAGAAGAAGTT
* **
15392 CATAAGGAGAAGAATTTGTTCAA-CTTTTT
65 CATAATGAGAAGAGCTTGTTCAACCTTTTT
15421 GCTAGATTAC
Statistics
Matches: 197, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
119 5 0.03
120 33 0.17
122 1 0.01
123 158 0.80
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (123 bp):
ATCATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTTATCTGAAGAAGAAGAAGAAGTTC
ATAATGAGAAGAGCTTGTTCAACCTTTTTCATAACTCTATCACAGCAGGAGATATATC
Found at i:15404 original size:17 final size:17
Alignment explanation
Indices: 15346--15405 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
15336 CAGCATTTCC
* *
15346 AGAAGGAGTTCATAATG
1 AGAAGAAGTTCATAAGG
* *
15363 AGAAGAA-CTCATCTGAAGA
1 AGAAGAAGTTCA--T-AAGG
15382 AGAAGAAGTTCATAAGG
1 AGAAGAAGTTCATAAGG
15399 AGAAGAA
1 AGAAGAA
15406 TTTGTTCAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 3 0.09
17 16 0.48
18 2 0.06
19 9 0.27
20 3 0.09
ACGTcount: A:0.48, C:0.08, G:0.27, T:0.17
Consensus pattern (17 bp):
AGAAGAAGTTCATAAGG
Found at i:15839 original size:14 final size:14
Alignment explanation
Indices: 15820--15848 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
15810 TGGATCTGAG
15820 AGATCCAACGGCCC
1 AGATCCAACGGCCC
15834 AGATCCAACGGCCC
1 AGATCCAACGGCCC
15848 A
1 A
15849 CACTCATCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.41, G:0.21, T:0.07
Consensus pattern (14 bp):
AGATCCAACGGCCC
Found at i:16518 original size:9 final size:9
Alignment explanation
Indices: 16504--16530 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
16494 GAGAGGAAGA
16504 AAATGAGAG
1 AAATGAGAG
16513 AAATGAGAG
1 AAATGAGAG
16522 AAATGAGAG
1 AAATGAGAG
16531 CTGGCCCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.33, T:0.11
Consensus pattern (9 bp):
AAATGAGAG
Found at i:20148 original size:18 final size:18
Alignment explanation
Indices: 20121--20320 Score: 107
Period size: 18 Copynumber: 11.1 Consensus size: 18
20111 AATAAATTAA
*
20121 TATATTGTTTATATATAC
1 TATATAGTTTATATATAC
20139 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
* *
20157 TA-AT-G--AACTATATAA
1 TATATAGTTTA-TATATAC
20172 TATATAGTTTGTATATACCATATAC
1 TATATAG--T-T-TAT---ATATAC
20197 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
* *
20215 TA-AT-G--AACTATATAA
1 TATATAGTTTA-TATATAC
20230 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
** *
20248 TA-AT-GAACTATATATAA
1 TATATAG-TTTATATATAC
* *
20265 TGTATAGTTTATAAATA-
1 TATATAGTTTATATATAC
* **
20282 TGATATAGTCTATATATGT
1 T-ATATAGTTTATATATAC
20301 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
20319 TA
1 TA
20321 ATAAACTATA
Statistics
Matches: 137, Mismatches: 23, Indels: 44
0.67 0.11 0.22
Matches are distributed among these distances:
14 2 0.01
15 16 0.12
16 7 0.05
17 18 0.13
18 72 0.53
19 3 0.02
21 3 0.02
22 2 0.01
23 2 0.01
25 12 0.09
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (18 bp):
TATATAGTTTATATATAC
Found at i:20176 original size:33 final size:33
Alignment explanation
Indices: 20132--20344 Score: 212
Period size: 33 Copynumber: 6.5 Consensus size: 33
20122 ATATTGTTTA
*
20132 TATATACTATATAGTTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
*
20165 TATATAATATATAGTTTGTATATAC-------C
1 TATATAATATATAGTTTATATATACTAATGAAC
*
20191 -ATATACTATATAGTTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
20223 TATATAATATATAGTTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
* * *
20256 TATATATAATGTATAGTTTATAAATA-TGATAT-AGTC
1 --TATATAATATATAGTTTATATATACT-A-ATGA-AC
* *
20292 TATATATGTTATATAGTTTATATATACTAATAAAC
1 TATATA--ATATATAGTTTATATATACTAATGAAC
*
20327 TATATAATGTATAGTTTA
1 TATATAATATATAGTTTA
20345 GGGTTTAGGG
Statistics
Matches: 149, Mismatches: 14, Indels: 34
0.76 0.07 0.17
Matches are distributed among these distances:
25 22 0.15
26 1 0.01
32 1 0.01
33 64 0.43
34 7 0.05
35 33 0.22
36 20 0.13
37 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (33 bp):
TATATAATATATAGTTTATATATACTAATGAAC
Found at i:20200 original size:25 final size:25
Alignment explanation
Indices: 20092--20214 Score: 83
Period size: 25 Copynumber: 4.8 Consensus size: 25
20082 TTCTTTCAAT
*
20092 TAATATATATGTTTATATTAATA-AAT-
1 TAATATATA-GTTTATA-T-ATACCATA
* *
20118 TAATATATTGTTTATATATACTATA
1 TAATATATAGTTTATATATACCATA
* * * *
20143 TAGTTTATA-TATACTA-ATGAACTATA
1 TAATATATAGTTTA-TATAT--ACCATA
*
20169 TAATATATAGTTTGTATATACCATA
1 TAATATATAGTTTATATATACCATA
*
20194 TACTATATAGTTTATATATAC
1 TAATATATAGTTTATATATAC
20215 TAATGAACTA
Statistics
Matches: 77, Mismatches: 13, Indels: 15
0.73 0.12 0.14
Matches are distributed among these distances:
23 3 0.04
24 8 0.10
25 39 0.51
26 23 0.30
27 4 0.05
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (25 bp):
TAATATATAGTTTATATATACCATA
Found at i:20207 original size:58 final size:58
Alignment explanation
Indices: 20133--20247 Score: 221
Period size: 58 Copynumber: 2.0 Consensus size: 58
20123 TATTGTTTAT
*
20133 ATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTGTATATACC
1 ATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACC
20191 ATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATAC
1 ATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATAC
20248 TAATGAACTA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (58 bp):
ATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACC
Found at i:20228 original size:17 final size:17
Alignment explanation
Indices: 20206--20263 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
20196 CTATATAGTT
20206 TATATATACTAATGAAC
1 TATATATACTAATGAAC
**
20223 TATATA-A-TATAT-AGTT
1 TATATATACTA-ATGA-AC
20239 TATATATACTAATGAAC
1 TATATATACTAATGAAC
20256 TATATATA
1 TATATATA
20264 ATGTATAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 3 0.09
16 9 0.28
17 17 0.53
18 3 0.09
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (17 bp):
TATATATACTAATGAAC
Found at i:20482 original size:33 final size:33
Alignment explanation
Indices: 20437--20569 Score: 140
Period size: 33 Copynumber: 4.3 Consensus size: 33
20427 GATATGAATA
20437 TAAACTAT--AGTATATATATATAGGTCATATG
1 TAAACTATAGAGTATATATATATAGGTCATATG
*
20468 TAAACTATAGAGTATATA-A-ATA--TCA-A-C
1 TAAACTATAGAGTATATATATATAGGTCATATG
* * *
20495 TATAGTATATA-TATATATATATAGGTCATATG
1 TAAACTATAGAGTATATATATATAGGTCATATG
* * *
20527 TAAACTATATAGTTTATATATATAGTTCATATG
1 TAAACTATAGAGTATATATATATAGGTCATATG
20560 TAAACTATAG
1 TAAACTATAG
20570 TTCAAATGTA
Statistics
Matches: 83, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
26 6 0.07
27 9 0.11
28 4 0.05
29 3 0.04
30 3 0.04
31 12 0.14
32 10 0.12
33 36 0.43
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.39
Consensus pattern (33 bp):
TAAACTATAGAGTATATATATATAGGTCATATG
Found at i:20484 original size:59 final size:59
Alignment explanation
Indices: 20421--20549 Score: 172
Period size: 59 Copynumber: 2.2 Consensus size: 59
20411 ATCTATATAA
* *
20421 TATATAGATATGAA-TATA-AACTATAGTATATATATATAGGTCATATGTAAACTATAGAG
1 TATATAAATATCAACTATAGAA-TATA-TATATATATATAGGTCATATGTAAACTATAGAG
* *
20480 TATATAAATATCAACTATAGTATATATATATATATATAGGTCATATGTAAACTATATAG
1 TATATAAATATCAACTATAGAATATATATATATATATAGGTCATATGTAAACTATAGAG
* *
20539 TTTATATATAT
1 TATATAAATAT
20550 AGTTCATATG
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
59 53 0.85
60 8 0.13
61 1 0.02
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (59 bp):
TATATAAATATCAACTATAGAATATATATATATATATAGGTCATATGTAAACTATAGAG
Found at i:20495 original size:22 final size:22
Alignment explanation
Indices: 20470--20512 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
20460 GTCATATGTA
20470 AACTATAG-AGTATATAAATATC
1 AACTATAGTA-TATATAAATATC
*
20492 AACTATAGTATATATATATAT
1 AACTATAGTATATATAAATAT
20513 ATATAGGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (22 bp):
AACTATAGTATATATAAATATC
Found at i:20570 original size:18 final size:18
Alignment explanation
Indices: 20547--20661 Score: 88
Period size: 18 Copynumber: 5.9 Consensus size: 18
20537 AGTTTATATA
20547 TATAGTTCATATGTAAAC
1 TATAGTTCATATGTAAAC
* *
20565 TATAGTTCAAATGTAAATATTAAT
1 TATAGTTCATATG----TA--AAC
*
20589 TATAGTTTATATGTAAAC
1 TATAGTTCATATGTAAAC
*
20607 TATAGTT-AGTATATAAAC
1 TATAGTTCA-TATGTAAAC
*
20625 TATATAGTTTATATGTAAAC
1 --TATAGTTCATATGTAAAC
*
20645 TATAGTTCATATATAAA
1 TATAGTTCATATGTAAA
20662 TATCAACCTT
Statistics
Matches: 78, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
17 1 0.01
18 44 0.56
20 17 0.22
21 1 0.01
22 2 0.03
24 13 0.17
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.42
Consensus pattern (18 bp):
TATAGTTCATATGTAAAC
Found at i:20650 original size:80 final size:75
Alignment explanation
Indices: 20522--20664 Score: 205
Period size: 80 Copynumber: 1.8 Consensus size: 75
20512 TATATAGGTC
* *
20522 ATATGTAAACTATATAGTTTATATATATAGTTCATATGTAAACTATAGTTCAAATGTAAATATTA
1 ATATGTAAACTATATAGTTTAAATATATAGTTCATATGTAAACTATAGTTCAAATATAAATATTA
20587 ATTATAGTTT
66 ATTATAGTTT
* *
20597 ATATGTAAACTATAGTTAGTATATAAACTATATAGTTTATATGTAAACTATAGTTCATATATAAA
1 ATATGTAAACTATA--TAGT-T-TAAA-TATATAGTTCATATGTAAACTATAGTTCAAATATAAA
20662 TAT
61 TAT
20665 CAACCTTAGT
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
75 14 0.24
77 4 0.07
78 1 0.02
79 3 0.05
80 37 0.63
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (75 bp):
ATATGTAAACTATATAGTTTAAATATATAGTTCATATGTAAACTATAGTTCAAATATAAATATTA
ATTATAGTTT
Found at i:20742 original size:33 final size:33
Alignment explanation
Indices: 20687--20771 Score: 113
Period size: 33 Copynumber: 2.7 Consensus size: 33
20677 ATACATATTT
* *
20687 ATATATATAGT-T-TATATGTAAACTATAGTTC
1 ATATATATAGTATATAAATATAAACTATAGTTC
*
20718 ATATATATAGTATATAAATATAAACTATAGTTT
1 ATATATATAGTATATAAATATAAACTATAGTTC
*
20751 ATATAAATAGTATA-AAATATA
1 ATATATATAGTATATAAATATA
20772 GTATATAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
31 11 0.23
32 8 0.17
33 29 0.60
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (33 bp):
ATATATATAGTATATAAATATAAACTATAGTTC
Found at i:20746 original size:20 final size:20
Alignment explanation
Indices: 20722--20795 Score: 85
Period size: 20 Copynumber: 3.5 Consensus size: 20
20712 TAGTTCATAT
20722 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
20742 CTATAGTTTATATAAATAGTATAAA
1 ATATAG--TATAT-AA-A-TATAAA
20767 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
20787 TTATAGTAT
1 ATATAGTAT
20796 GTAGTTTATA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
20 19 0.41
21 1 0.02
22 7 0.15
23 7 0.15
24 1 0.02
25 11 0.24
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (20 bp):
ATATAGTATATAAATATAAA
Found at i:20771 original size:25 final size:23
Alignment explanation
Indices: 20722--20782 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
20712 TAGTTCATAT
20722 ATATAGTATAT-AA-A-TATAAA
1 ATATAGTATATAAATAGTATAAA
*
20742 CTATAGTTTATATAAATAGTATAAA
1 ATATAG--TATATAAATAGTATAAA
20767 ATATAGTATATAAATA
1 ATATAGTATATAAATA
20783 TAAATTATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 5 0.15
22 5 0.15
23 12 0.35
24 1 0.03
25 11 0.32
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.38
Consensus pattern (23 bp):
ATATAGTATATAAATAGTATAAA
Found at i:20774 original size:12 final size:13
Alignment explanation
Indices: 20735--20784 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
20725 TAGTATATAA
20735 ATATAAACTATAGT
1 ATATAAA-TATAGT
*
20749 TTATATAA-ATAGT
1 ATATA-AATATAGT
20762 ATA-AAATATAGT
1 ATATAAATATAGT
20774 ATATAAATATA
1 ATATAAATATA
20785 AATTATAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 2 0.06
12 9 0.29
13 14 0.45
14 4 0.13
15 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (13 bp):
ATATAAATATAGT
Found at i:20801 original size:103 final size:99
Alignment explanation
Indices: 20578--20806 Score: 229
Period size: 103 Copynumber: 2.3 Consensus size: 99
20568 AGTTCAAATG
*
20578 TAAATA-TTA-AT-TATAGTTTATATGTAAACTATAGTTAGTATATAAACTATATAGTTTATATG
1 TAAATATTTATATATATAGTTTATATGTAAACTATAGTTAGTATATAAACTATATA---TATATA
**
20640 TAAACTATAGTTCATATATAAATATCAACCTTAGTATA
63 TAAACTATAGTT-ATATATAAATATCAAAATTAGTATA
* * *
20678 TACATATTTATATATATAGTTTATATGTAAACTATAGTTCA-TATATATAGTATATA-A-ATATA
1 TAAATATTTATATATATAGTTTATATGTAAACTATAGTT-AGTATATAAACTATATATATATATA
*
20740 AACTATAGTT-TATATAAATAGTATAAAATATAGTATA
65 AACTATAGTTATATATAAATA-T-CAAAAT-TAGTATA
*
20777 TAAATATAAATTATAGTATGTAGTTTATAT
1 TAAATAT---TTATA-TATATAGTTTATAT
20807 AAATATAAAT
Statistics
Matches: 109, Mismatches: 9, Indels: 19
0.80 0.07 0.14
Matches are distributed among these distances:
96 10 0.09
97 1 0.01
98 17 0.16
99 14 0.13
100 5 0.05
101 3 0.03
102 7 0.06
103 51 0.47
104 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.43
Consensus pattern (99 bp):
TAAATATTTATATATATAGTTTATATGTAAACTATAGTTAGTATATAAACTATATATATATATAA
ACTATAGTTATATATAAATATCAAAATTAGTATA
Found at i:20861 original size:22 final size:21
Alignment explanation
Indices: 20833--20897 Score: 71
Period size: 20 Copynumber: 3.1 Consensus size: 21
20823 TCCTAAACCC
20833 TAAACTATATAATATATATATA
1 TAAACTATATAATATATATA-A
*
20855 TAAACTATAGT-TTATAT-TAA
1 TAAACTATA-TAATATATATAA
* *
20875 TAAACTATATAATTTATACAA
1 TAAACTATATAATATATATAA
20896 TA
1 TA
20898 TATATTATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
19 1 0.03
20 14 0.39
21 6 0.17
22 14 0.39
23 1 0.03
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (21 bp):
TAAACTATATAATATATATAA
Found at i:20954 original size:20 final size:20
Alignment explanation
Indices: 20929--21031 Score: 75
Period size: 20 Copynumber: 5.0 Consensus size: 20
20919 TAATATATAA
*
20929 ATATAAATTGTATAGTTTAT
1 ATATAAATTATATAGTTTAT
* *
20949 ATATAATTCATATATAATTTAT
1 ATATAAAT--TATATAGTTTAT
* * *
20971 ATATAAACTATGTAGTTTCT
1 ATATAAATTATATAGTTTAT
* *
20991 ATAT-AGTTCA-ATAGTTCAT
1 ATATAAATT-ATATAGTTTAT
*
21010 ATATAAACTATATAGTATTAT
1 ATATAAATTATATAGT-TTAT
21031 A
1 A
21032 GTTTATGCAT
Statistics
Matches: 61, Mismatches: 16, Indels: 11
0.69 0.18 0.12
Matches are distributed among these distances:
19 13 0.21
20 28 0.46
21 4 0.07
22 16 0.26
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.46
Consensus pattern (20 bp):
ATATAAATTATATAGTTTAT
Found at i:20971 original size:9 final size:10
Alignment explanation
Indices: 20895--20976 Score: 53
Period size: 11 Copynumber: 7.8 Consensus size: 10
20885 AATTTATACA
20895 ATATAT-ATT
1 ATATATAATT
*
20904 ATTTATAATT
1 ATATATAATT
*
20914 ATACATAATAT
1 ATATATAAT-T
20925 ATAAATATAAATT
1 AT--ATAT-AATT
*
20938 GTATAGT--TT
1 ATATA-TAATT
20947 ATATATAATT
1 ATATATAATT
20957 CATATATAATTT
1 -ATATATAA-TT
20969 ATATATAA
1 ATATATAA
20977 ACTATGTAGT
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
8 1 0.02
9 11 0.19
10 12 0.21
11 22 0.39
12 3 0.05
13 5 0.09
14 3 0.05
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (10 bp):
ATATATAATT
Found at i:20974 original size:13 final size:11
Alignment explanation
Indices: 20939--20976 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
20929 ATATAAATTG
*
20939 TATAGTTTATA
1 TATAATTTATA
*
20950 TATAATTCATA
1 TATAATTTATA
20961 TATAATTTATA
1 TATAATTTATA
20972 TATAA
1 TATAA
20977 ACTATGTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (11 bp):
TATAATTTATA
Found at i:21063 original size:27 final size:28
Alignment explanation
Indices: 21018--21102 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 28
21008 ATATATAAAC
* * **
21018 TATATAGTATTATAGTTTATGCATGGTA
1 TATATAGTATTATACTTTATACATAATA
21046 TATATAGT-TTATACTTTATACATAATA
1 TATATAGTATTATACTTTATACATAATA
* *
21073 TATATA-TA-TATA-TATATATAT-ATA
1 TATATAGTATTATACTTTATACATAATA
21097 TATATA
1 TATATA
21103 AACTATATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
24 9 0.18
25 7 0.14
26 5 0.10
27 21 0.42
28 8 0.16
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (28 bp):
TATATAGTATTATACTTTATACATAATA
Found at i:21077 original size:2 final size:2
Alignment explanation
Indices: 21070--21167 Score: 112
Period size: 2 Copynumber: 49.0 Consensus size: 2
21060 TTTATACATA
*
21070 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA ACT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * *
21112 AT -T A- AG AT AT AT AT AT AT AT AT AT AT AA ACT AT AT AGT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT
21154 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
21168 TAGTTGTTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
1 3 0.04
2 77 0.93
3 3 0.04
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:21125 original size:36 final size:36
Alignment explanation
Indices: 21082--21167 Score: 145
Period size: 36 Copynumber: 2.4 Consensus size: 36
21072 ATATATATAT
21082 ATATATATATATATATATATAAACTATATAATTAAG
1 ATATATATATATATATATATAAACTATATAATTAAG
* * *
21118 ATATATATATATATATATATAAACTATATAGTTTAT
1 ATATATATATATATATATATAAACTATATAATTAAG
21154 ATATATATATATAT
1 ATATATATATATAT
21168 TAGTTGTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (36 bp):
ATATATATATATATATATATAAACTATATAATTAAG
Found at i:21164 original size:42 final size:42
Alignment explanation
Indices: 20838--21167 Score: 174
Period size: 39 Copynumber: 8.2 Consensus size: 42
20828 AACCCTAAAC
20838 TATATA-ATATATATATATAAAC--TATAGTTTATAT-TA-A
1 TATATATATATATATATATAAACTATATAGTTTATATATATA
* * *
20875 TAAACTATATA-ATTTATACAATA-TATATTA-TTTATA-AT-TA
1 TATA-TATATATATATATATAA-ACTATA-TAGTTTATATATATA
* * * *
20915 TACATA-ATATATAAATATAAATTGTATAGTTTATATATA-A
1 TATATATATATATATATATAAACTATATAGTTTATATATATA
* * *
20955 T-TCATATATAATTTATATATAAACTATGTAGTTTCTATATAGT-
1 TAT-ATATAT-ATATATATATAAACTATATAGTTTATATATA-TA
* * *
20998 TCA-ATA-GT-T-CATATATAAACTATATAGTATTATAGTTTATGCA
1 T-ATATATATATATATATATAAACTATATAGT-TTATA-TATAT--A
* * * * *
21041 TGGTATATATAGTTTATACTTTATAC-ATA-A-TATATATATATA
1 T-ATATATATA-TATATA-TATAAACTATATAGTTTATATATATA
*
21083 TATATATATATATATATATAAACTATATA----AT-TA-AGA
1 TATATATATATATATATATAAACTATATAGTTTATATATATA
21119 TATATATATATATATATATAAACTATATAGTTTATATATATA
1 TATATATATATATATATATAAACTATATAGTTTATATATATA
21161 TATATAT
1 TATATAT
21168 TAGTTGTTTT
Statistics
Matches: 220, Mismatches: 34, Indels: 73
0.67 0.10 0.22
Matches are distributed among these distances:
36 31 0.14
37 5 0.02
38 18 0.08
39 44 0.20
40 36 0.16
41 18 0.08
42 37 0.17
43 5 0.02
44 7 0.03
45 5 0.02
46 1 0.00
47 2 0.01
48 6 0.03
49 5 0.02
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.46
Consensus pattern (42 bp):
TATATATATATATATATATAAACTATATAGTTTATATATATA
Found at i:21973 original size:217 final size:210
Alignment explanation
Indices: 21190--22001 Score: 1138
Period size: 209 Copynumber: 3.8 Consensus size: 210
21180 TTTTTTCTCA
* * *
21190 ACTTATTACTTATTTCTATTTATT-AATTGGTCCATAACTTTTTAAATGAGTATAATTTAGT-AT
1 ACTTATTACTTATTTATATTT-TTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTAAT
* * * * *
21253 ATTTTTGTATTAATTTCAACCTCAAAATTTAAATTTATTTTGATTTGATCCCTTTTGTGTTATTT
65 -TTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTTGTGTGTTGTTT
* *
21318 AATATATTTAAATTTTTATTTGTAATTT-TTATTTTTTCAATTTAGTCCTCCAAATTTTATTTGC
129 AATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGC
** *
21382 ACCTGAAATTGACCCAT
194 ATATGAAATTGACCAAT
*
21399 ACTTATTACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTATTT
1 ACTTATTACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTAATT
* *
21464 TTTTGTATTAATTTCAACCTCA-AAGTTTAAAATTATTTTGATTTGATCCCTTTTGTGTTGTTTA
66 TTTTGTATTAATTTCAACCTCACAA-TTTAAAATTATTTCGATTTGATCCCTTGTGTGTTGTTTA
21528 ATATATTTAAATTTTTATTT-TAAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGC
130 ATATATTTAAATTTTTATTTGT-AATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGC
21592 ATATGAAATTGACCAAT
194 ATATGAAATTGACCAAT
** * *
21609 ACTTATTACTTATTTATATTTTTAAATT--AACACAACTTTTTAAATAGGTATAATTTAGTAA-T
1 ACTTATTACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTAATT
*
21671 TTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTT
66 TTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGAT-CC-C-T---TGTGTGTT
*
21736 GTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTAT
125 GTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTAT
* *
21801 TTGCATATGAAATTGATCTAT
190 TTGCATATGAAATTGACCAAT
* *
21822 ACTTATTACTTAATTCTAT-TTTTTTAATTGGCCCATAACTTTTTAAATGGGTAAAATTTAGTAA
1 ACTTATTACTT-ATT-TATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTAA
* *
21886 TTTTTTGTATTAATTTCAACCTCACAACTTAAAATTATTTCGAGTTGATCCCACATCAATGTGTG
64 TTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGAT-CC-C-T---TGTGTG
*
21951 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
123 TTGTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
22002 ATTCTTAAAT
Statistics
Matches: 553, Mismatches: 32, Indels: 28
0.90 0.05 0.05
Matches are distributed among these distances:
207 43 0.08
208 37 0.07
209 141 0.25
210 78 0.14
213 99 0.18
214 13 0.02
215 3 0.01
216 28 0.05
217 111 0.20
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (210 bp):
ACTTATTACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTAATT
TTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTTGTGTGTTGTTTAA
TATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCAT
ATGAAATTGACCAAT
Found at i:27348 original size:123 final size:124
Alignment explanation
Indices: 27116--27366 Score: 436
Period size: 123 Copynumber: 2.0 Consensus size: 124
27106 CAAAATCATC
* *
27116 ATTAAACTTAAGTTTTTGTTTCGTTTTGATCACCTAATTTGATTCATCTATTTTTTAACTTTTTA
1 ATTAAACTTAAGTTTTTATTTCGTTTTGATCACCTAATTTGATTCATCTATTTTCTAACTTTTTA
*
27181 ATATATAAGAATTCATTTATATAAGAGTAAAATTAATATATAAGAATTCATTTTATCTT
66 ATATATAAGAATTCATTTATATAAGAGTAAAAGTAATATATAAGAATTCATTTTATCTT
*
27240 ATTAAACTTAAGTTTTTATTTCGTTTTGATCACGTAATTTGATT-AGTCTATTTTCTAA-TTTTT
1 ATTAAACTTAAGTTTTTATTTCGTTTTGATCACCTAATTTGATTCA-TCTATTTTCTAACTTTTT
27303 AATATATAAGAATTCATTTATATAAGAGTAAAAGTAATATATAAGAATTCATTTTATCTT
65 AATATATAAGAATTCATTTATATAAGAGTAAAAGTAATATATAAGAATTCATTTTATCTT
27363 -TTAA
1 ATTAA
27367 CACATAAAAT
Statistics
Matches: 122, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
122 4 0.03
123 65 0.53
124 53 0.43
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.49
Consensus pattern (124 bp):
ATTAAACTTAAGTTTTTATTTCGTTTTGATCACCTAATTTGATTCATCTATTTTCTAACTTTTTA
ATATATAAGAATTCATTTATATAAGAGTAAAAGTAATATATAAGAATTCATTTTATCTT
Found at i:30500 original size:17 final size:17
Alignment explanation
Indices: 30478--30510 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
30468 GATTAAGCGT
30478 TGAATGATTCAATGGCC
1 TGAATGATTCAATGGCC
30495 TGAATGATTCAATGGC
1 TGAATGATTCAATGGC
30511 TCTGTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (17 bp):
TGAATGATTCAATGGCC
Found at i:31326 original size:15 final size:15
Alignment explanation
Indices: 31297--31334 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
31287 TGATATGGTA
*
31297 TTTATT-ATTATTAT
1 TTTATTAATTAATAT
31311 TTTATTAATTAATAT
1 TTTATTAATTAATAT
31326 TTTATTAAT
1 TTTATTAAT
31335 ATTATTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTATTAATTAATAT
Found at i:33915 original size:21 final size:21
Alignment explanation
Indices: 33876--33915 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
33866 ACGTGTAAAG
*
33876 ATTTAAGATTTATAGTTTAGA
1 ATTTAAGATTTATAATTTAGA
33897 ATTTAAGATTT-TAAATTTA
1 ATTTAAGATTTAT-AATTTA
33916 TGATTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (21 bp):
ATTTAAGATTTATAATTTAGA
Found at i:35048 original size:17 final size:16
Alignment explanation
Indices: 35025--35088 Score: 71
Period size: 17 Copynumber: 4.0 Consensus size: 16
35015 GAAAAAATAT
35025 AATA-TATAAA-TATA
1 AATATTATAAACTATA
35039 AATTATATATAAACTATA
1 AA-TAT-TATAAACTATA
*
35057 TATATTATAAACTATA
1 AATATTATAAACTATA
35073 TAATATTATAAA-TATA
1 -AATATTATAAACTATA
35089 TATGAATTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
14 2 0.05
15 2 0.05
16 15 0.35
17 19 0.44
18 5 0.12
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
AATATTATAAACTATA
Found at i:35050 original size:11 final size:11
Alignment explanation
Indices: 35034--35100 Score: 50
Period size: 11 Copynumber: 6.2 Consensus size: 11
35024 TAATATATAA
35034 ATATAAATTAT
1 ATATAAATTAT
*
35045 ATATAAACTAT
1 ATATAAATTAT
35056 ATAT--ATTAT
1 ATATAAATTAT
* * *
35065 AAACTATATAAT
1 ATA-TAAATTAT
35077 ATTATAAA-TAT
1 A-TATAAATTAT
*
35088 ATATGAATTAT
1 ATATAAATTAT
35099 AT
1 AT
35101 TTATGTGAAC
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
9 6 0.14
10 6 0.14
11 22 0.51
12 8 0.19
13 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (11 bp):
ATATAAATTAT
Found at i:35132 original size:17 final size:17
Alignment explanation
Indices: 35026--35133 Score: 62
Period size: 17 Copynumber: 6.2 Consensus size: 17
35016 AAAAAATATA
*
35026 ATATATAAATATAAATT
1 ATATATAAATATAAAAT
*
35043 ATATATAAACTAT-ATAT
1 ATATATAAA-TATAAAAT
*
35060 AT-TATAAACTATATAAT
1 ATATATAAA-TATAAAAT
35077 AT-TATAAATATATATGAAT
1 ATATATAAATATA-A--AAT
** * *
35096 -TATATTTATGTGAACTAT
1 ATATATAAATAT-AA-AAT
35114 ATATATAAATATAAAAT
1 ATATATAAATATAAAAT
35131 ATA
1 ATA
35134 AACTATATTA
Statistics
Matches: 69, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
16 14 0.20
17 28 0.41
18 8 0.12
19 18 0.26
20 1 0.01
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (17 bp):
ATATATAAATATAAAAT
Found at i:35150 original size:17 final size:16
Alignment explanation
Indices: 35130--35173 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
35120 AAATATAAAA
35130 TATAAACTATATTATAT
1 TATAAACTATATTA-AT
35147 TATAAACTATA-TAAT
1 TATAAACTATATTAAT
*
35162 TATAAGCTATAT
1 TATAAACTATAT
35174 ATAAAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 12 0.48
16 2 0.08
17 11 0.44
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (16 bp):
TATAAACTATATTAAT
Found at i:35269 original size:8 final size:9
Alignment explanation
Indices: 35256--35423 Score: 51
Period size: 9 Copynumber: 19.7 Consensus size: 9
35246 AGTTTATAAA
35256 ATATTAT-T
1 ATATTATAT
35264 ATATTA-AT
1 ATATTATAT
*
35272 ATAGTATAT
1 ATATTATAT
35281 ATA-TATAT
1 ATATTATAT
35289 ATA-TATAT
1 ATATTATAT
* *
35297 AAACTATAT
1 ATATTATAT
*
35306 AT-GTATA-
1 ATATTATAT
*
35313 A-ACTATAT
1 ATATTATAT
* *
35321 AAAATATAT
1 ATATTATAT
35330 AGT-TTATAT
1 A-TATTATAT
* * *
35339 GTTATAATTT
1 -ATATTATAT
35349 ATATTA-AT
1 ATATTATAT
*
35357 ATAGTATAT
1 ATATTATAT
35366 ATATGTATGCAT
1 ATAT-TAT--AT
*
35378 A-ACTA-AT
1 ATATTATAT
*
35385 ATAACTA-AT
1 AT-ATTATAT
*
35394 ATA-TAGA-
1 ATATTATAT
35401 ATA-TATAT
1 ATATTATAT
35409 ATATTATAT
1 ATATTATAT
35418 ATATTA
1 ATATTA
35424 AAGAAATACT
Statistics
Matches: 124, Mismatches: 18, Indels: 35
0.70 0.10 0.20
Matches are distributed among these distances:
7 16 0.13
8 43 0.35
9 52 0.42
10 9 0.07
11 1 0.01
12 3 0.02
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (9 bp):
ATATTATAT
Found at i:35283 original size:2 final size:2
Alignment explanation
Indices: 35270--35421 Score: 65
Period size: 2 Copynumber: 78.0 Consensus size: 2
35260 TATTATATTA
* * *
35270 AT AT AGT AT AT AT AT AT AT AT AT AT AT AA ACT AT AT AT GT AT AA
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * * *
35314 ACT AT AT A- AA AT AT AT AGT TT AT AT GT -T AT A- AT TT AT AT -T
1 A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* **
35354 A- AT AT AGT AT AT AT AT GT AT GC AT A- ACT A- AT AT A- ACT A-
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT
*
35392 AT AT AT AG A- AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35422 TAAAGAAATA
Statistics
Matches: 113, Mismatches: 19, Indels: 36
0.67 0.11 0.21
Matches are distributed among these distances:
1 11 0.10
2 93 0.82
3 9 0.08
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Found at i:35359 original size:68 final size:65
Alignment explanation
Indices: 35212--35366 Score: 150
Period size: 68 Copynumber: 2.3 Consensus size: 65
35202 TATAACTATG
* * * * * *
35212 TATATAAATATATGTATAAACTATAAAAGTATATAGTTTATAAAATATTATTATATTAATATAGT
1 TATATTAATATATATATAAACTATAAAAGTATAAACTATATAAAATATTATTATATT-ATATAAT
35277 A
65 A
* *
35278 TATATATATATATATATATAAACTATATATGTATAAACTATATAAAATATATAGTTTATATGT-T
1 TATAT-TA-ATATATATATAAACTATAAAAGTATAAACTATATAAAATAT-TA--TTATAT-TAT
*
35342 ATAATT
60 ATAATA
35348 TATATTAATATAGTATATA
1 TATATTAATATA-TATATA
35367 TATGTATGCA
Statistics
Matches: 73, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
66 5 0.07
67 1 0.01
68 40 0.55
69 10 0.14
70 10 0.14
71 6 0.08
72 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (65 bp):
TATATTAATATATATATAAACTATAAAAGTATAAACTATATAAAATATTATTATATTATATAATA
Found at i:35362 original size:85 final size:87
Alignment explanation
Indices: 35020--35369 Score: 265
Period size: 85 Copynumber: 4.2 Consensus size: 87
35010 AAATTGAAAA
* * * * * *
35020 AATATAATATATAAATATAAATTATATATAAACTATATATATTATAAACTATATAATAT-TATAA
1 AATATAGTATATATATATATACTATATATAAACTATATATAGTATAAACTATATAAAATATAT-A
* * * *
35084 ATATATATGA-ATTATATTTATGTG
65 GTTTATATGATA-TA-ATTTATATT
* * *
35108 AACTATA-TATATA-A-ATATA--AAATATAAACTATATTATATTATAAACTATAT-AATTATA-
1 AA-TATAGTATATATATATATACTATATATAAACTATA-TATAGTATAAACTATATAAAATATAT
* * *
35166 AG-CTATAT-ATA-AAATTATGTT
64 AGTTTATATGATATAATTTATATT
* * * * *
35187 TATGT-GAACTATATATATA-ACTATGTATATAA--ATATAT-GTATAAACTATA-AAAGTATAT
1 AATATAGTA-TATATATATATACTATATATA-AACTATATATAGTATAAACTATATAAAATATAT
** *
35246 AGTTTATAAAATATTA-TTATATT
64 AGTTTATATGATATAATTTATATT
35269 AATATAGTATATATATATATA-TATATATAAACTATATAT-GTATAAACTATATAAAATATATAG
1 AATATAGTATATATATATATACTATATATAAACTATATATAGTATAAACTATATAAAATATATAG
*
35332 TTTATATGTTATAATTTATATT
66 TTTATATGATATAATTTATATT
35354 AATATAGTATATATAT
1 AATATAGTATATATAT
35370 GTATGCATAA
Statistics
Matches: 212, Mismatches: 28, Indels: 47
0.74 0.10 0.16
Matches are distributed among these distances:
78 3 0.01
79 29 0.14
80 8 0.04
81 13 0.06
82 40 0.19
83 25 0.12
84 35 0.17
85 42 0.20
86 4 0.02
87 1 0.00
88 8 0.04
89 4 0.02
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (87 bp):
AATATAGTATATATATATATACTATATATAAACTATATATAGTATAAACTATATAAAATATATAG
TTTATATGATATAATTTATATT
Found at i:35818 original size:7 final size:7
Alignment explanation
Indices: 35808--35860 Score: 70
Period size: 7 Copynumber: 7.6 Consensus size: 7
35798 TAGTTTATAA
35808 AAACCCT
1 AAACCCT
35815 AAACCCT
1 AAACCCT
**
35822 AAACTTT
1 AAACCCT
**
35829 AAGTCCT
1 AAACCCT
35836 AAACCCT
1 AAACCCT
35843 AAACCCT
1 AAACCCT
35850 AAACCCT
1 AAACCCT
35857 AAAC
1 AAAC
35861 ATAAGCAATA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.43, C:0.36, G:0.02, T:0.19
Consensus pattern (7 bp):
AAACCCT
Found at i:35976 original size:18 final size:18
Alignment explanation
Indices: 35953--35987 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
35943 GTATCATGTA
35953 TGTATA-AACTATGTATAG
1 TGTATATAACTA-GTATAG
35971 TGTATATAACTAGTATA
1 TGTATATAACTAGTATA
35988 TATACAACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (18 bp):
TGTATATAACTAGTATAG
Found at i:36184 original size:15 final size:14
Alignment explanation
Indices: 36154--36402 Score: 73
Period size: 14 Copynumber: 17.4 Consensus size: 14
36144 GCTATATAGT
*
36154 TTATATTAATGTTAA
1 TTATATTAAT-ATAA
*
36169 TTATCTTAACTATAA
1 TTATATTAA-TATAA
36184 TTATATTAATATATA
1 TTATATTAATATA-A
*
36199 GTT-TATAAACTAT-A
1 -TTATATTAA-TATAA
36213 TTATATTAATATTAA
1 TTATATTAATA-TAA
36228 -T-T-TT-AT-TAA
1 TTATATTAATATAA
* *
36237 CTATAGTTTATA-AA
1 TTATA-TTAATATAA
* *
36251 CTATACTAA-ATAA
1 TTATATTAATATAA
* *
36264 TT-TATAACATATAG
1 TTATATTA-ATATAA
36278 TT-TATTAATATTAA
1 TTATATTAATA-TAA
*
36292 TGT-TA-TAGACTATATT
1 T-TATATTA-A-TATA-A
36308 TTATATTAATATTAA
1 TTATATTAATA-TAA
36323 TTATA--AATTATAAA
1 TTATATTAA-TAT-AA
36337 CTATATATTTAATATAA
1 -T-TATA-TTAATATAA
36354 TTTAATATTAATATTAA
1 -TT-ATATTAATA-TAA
*
36371 TTATAAT-ATATAA
1 TTATATTAATATAA
36384 TTATA-TAATATTAA
1 TTATATTAATA-TAA
36398 TTATA
1 TTATA
36403 AATAGTTAAT
Statistics
Matches: 182, Mismatches: 17, Indels: 71
0.67 0.06 0.26
Matches are distributed among these distances:
9 3 0.02
10 1 0.01
11 3 0.02
12 7 0.04
13 30 0.16
14 50 0.27
15 45 0.25
16 27 0.15
17 11 0.06
18 3 0.02
19 2 0.01
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (14 bp):
TTATATTAATATAA
Found at i:36223 original size:29 final size:29
Alignment explanation
Indices: 36154--36334 Score: 90
Period size: 29 Copynumber: 6.0 Consensus size: 29
36144 GCTATATAGT
* * *
36154 TTATATTAATGTTAA-TTATCTTAACTATAA
1 TTATATTAATATTAAGTT-TATAAACTAT-A
36184 TTATATTAATA-TATAGTTTATAAACTATA
1 TTATATTAATATTA-AGTTTATAAACTATA
* *
36213 TTATATTAATATTAATTTTATTAACTATA
1 TTATATTAATATTAAGTTTATAAACTATA
* *
36242 GTT-TATAAACTATACTAAATAATT-TATAACATATA
1 -TTATATTAA-TAT--TAAGT--TTATA-AAC-TATA
*
36277 GTT-TATTAATATTAA-TGTTATAGACTATA
1 -TTATATTAATATTAAGT-TTATAAACTATA
*
36306 TTTTATATTAATATTAA--TTATAAATTATA
1 --TTATATTAATATTAAGTTTATAAACTATA
36335 AACTATATAT
Statistics
Matches: 123, Mismatches: 14, Indels: 29
0.74 0.08 0.17
Matches are distributed among these distances:
29 46 0.37
30 32 0.26
31 17 0.14
32 7 0.06
33 1 0.01
34 8 0.07
35 12 0.10
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.49
Consensus pattern (29 bp):
TTATATTAATATTAAGTTTATAAACTATA
Found at i:36253 original size:43 final size:44
Alignment explanation
Indices: 36168--36255 Score: 126
Period size: 43 Copynumber: 2.0 Consensus size: 44
36158 ATTAATGTTA
*
36168 ATTATCTTAACTATAATTATATTAATATATAGTTTATAAACTAT
1 ATTATATTAACTATAATTATATTAATATATAGTTTATAAACTAT
* *
36212 ATTATATTAA-TATTAATTTTATTAA-CTATAGTTTATAAACTAT
1 ATTATATTAACTA-TAATTATATTAATATATAGTTTATAAACTAT
36255 A
1 A
36256 CTAAATAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
43 20 0.50
44 20 0.50
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (44 bp):
ATTATATTAACTATAATTATATTAATATATAGTTTATAAACTAT
Found at i:36291 original size:6 final size:6
Alignment explanation
Indices: 36280--36412 Score: 53
Period size: 6 Copynumber: 21.2 Consensus size: 6
36270 ACATATAGTT
* * * *
36280 TATTAA TATTAA TGTTATA GACTATA TTTTA- TATTAA TATTAA T-TATAA
1 TATTAA TATTAA TATTA-A TATTA-A TATTAA TATTAA TATTAA TAT-TAA
* *
36329 -ATTATA AACTATA TATTTAA TA-TAA T-TTAA TATTAA TATTAA T-TATAA
1 TATTA-A TATTA-A TA-TTAA TATTAA TATTAA TATTAA TATTAA TAT-TAA
*
36377 TATATAA TTATATAA TATTAA TTATAAA TAGTTAA T
1 TAT-TAA -TAT-TAA TATTAA -TATTAA TA-TTAA T
36413 TAATAAAAAT
Statistics
Matches: 100, Mismatches: 13, Indels: 27
0.71 0.09 0.19
Matches are distributed among these distances:
5 16 0.16
6 42 0.42
7 33 0.33
8 9 0.09
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (6 bp):
TATTAA
Found at i:36399 original size:27 final size:30
Alignment explanation
Indices: 36348--36403 Score: 91
Period size: 27 Copynumber: 2.0 Consensus size: 30
36338 TATATATTTA
36348 ATATAATTTAATATTAATATTAATTATAAT
1 ATATAATTTAATATTAATATTAATTATAAT
36378 ATATAA-TT-ATA-TAATATTAATTATAA
1 ATATAATTTAATATTAATATTAATTATAA
36404 ATAGTTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 15 0.58
28 3 0.12
29 2 0.08
30 6 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
ATATAATTTAATATTAATATTAATTATAAT
Found at i:36412 original size:41 final size:41
Alignment explanation
Indices: 36313--36419 Score: 112
Period size: 41 Copynumber: 2.6 Consensus size: 41
36303 ATATTTTATA
* * *
36313 TTAATATTAATTATAAATTATAAACTATATATTTAATATAAT
1 TTAATA-TAAATATTAATTATAAACTATATAATTAATATAAT
*
36355 TTAATATTAATATTAATTAT-AA-TATATAATT-ATATAAT
1 TTAATATAAATATTAATTATAAACTATATAATTAATATAAT
36393 ATTAATTATAAATAGTTAATTAATAAA
1 -TTAA-TATAAATA-TTAATT-ATAAA
36420 AATTATATAG
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
38 7 0.13
39 12 0.22
40 9 0.16
41 17 0.31
42 8 0.15
43 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (41 bp):
TTAATATAAATATTAATTATAAACTATATAATTAATATAAT
Found at i:40637 original size:29 final size:29
Alignment explanation
Indices: 40595--40671 Score: 100
Period size: 29 Copynumber: 2.7 Consensus size: 29
40585 CTTTTTTAAA
* * ***
40595 AATTACCAAAATAGCACCGATTTCGAATT
1 AATTCCCAGAATAGCACCGAACCCGAATT
*
40624 AATTCCCAGAATAGCACCAAACCCGAATT
1 AATTCCCAGAATAGCACCGAACCCGAATT
40653 AATTCCCAGAATAGCACCG
1 AATTCCCAGAATAGCACCG
40672 GTCAACGATC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.40, C:0.27, G:0.12, T:0.21
Consensus pattern (29 bp):
AATTCCCAGAATAGCACCGAACCCGAATT
Found at i:47708 original size:10 final size:12
Alignment explanation
Indices: 47691--47722 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
47681 CGTTTAATAG
47691 CTGGTCAAAG-T
1 CTGGTCAAAGTT
47702 C-GGTCAAAGTT
1 CTGGTCAAAGTT
47713 CTGGTCAAAG
1 CTGGTCAAAG
47723 GAGGTCAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 8 0.42
11 3 0.16
12 8 0.42
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (12 bp):
CTGGTCAAAGTT
Found at i:47885 original size:13 final size:13
Alignment explanation
Indices: 47869--47899 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
47859 GTTAATGGGT
*
47869 CGGGTTGGGTCAA
1 CGGGTCGGGTCAA
47882 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
47895 CGGGT
1 CGGGT
47900 AAACAGGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.19, G:0.48, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:53660 original size:20 final size:21
Alignment explanation
Indices: 53614--53674 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
53604 TTCCCCTGTG
53614 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
53637 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
53657 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
53675 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:62373 original size:21 final size:22
Alignment explanation
Indices: 62349--62393 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
62339 TACGGAAGTG
62349 CTGTA-CAGGGGAATCGGTTCC
1 CTGTAGCAGGGGAATCGGTTCC
62370 CTGTAGCAGGGGAATCGGTTCC
1 CTGTAGCAGGGGAATCGGTTCC
62392 CT
1 CT
62394 ATTTGTAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.18, C:0.24, G:0.33, T:0.24
Consensus pattern (22 bp):
CTGTAGCAGGGGAATCGGTTCC
Found at i:66859 original size:22 final size:22
Alignment explanation
Indices: 66833--66874 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
66823 AGAATACGCA
66833 GGGGGTA-CAGATTCCCCCCTGG
1 GGGGGTATC-GATTCCCCCCTGG
66855 GGGGGTATCGATTCCCCCCT
1 GGGGGTATCGATTCCCCCCT
66875 AAATGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.12, C:0.33, G:0.33, T:0.21
Consensus pattern (22 bp):
GGGGGTATCGATTCCCCCCTGG
Found at i:67746 original size:2 final size:2
Alignment explanation
Indices: 67733--67767 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
67723 AATACAATAC
*
67733 AT AT AT AC AT AT AT AT AT AT AT AT AT GAT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
67768 GTTTGTTACT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:69733 original size:14 final size:14
Alignment explanation
Indices: 69714--69760 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
69704 ATTTTTTCTT
69714 TATATAAATTAAAC
1 TATATAAATTAAAC
69728 TATAT-AATT----
1 TATATAAATTAAAC
69737 TATATAAATTAAAC
1 TATATAAATTAAAC
*
69751 TATATTAATT
1 TATATAAATT
69761 TTCTTTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:69738 original size:23 final size:24
Alignment explanation
Indices: 69712--69761 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
69702 TTATTTTTTC
69712 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
69735 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
69759 TTT
1 TTT
69762 TCTTTTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:73466 original size:63 final size:63
Alignment explanation
Indices: 73364--73489 Score: 234
Period size: 63 Copynumber: 2.0 Consensus size: 63
73354 AAAAGTGTTT
*
73364 GAATAATGCAATGAAAAAAAAAATTCTTCACATACTGCAGTCGCACAATTATTTGCTTAAGTA
1 GAATAATGCAATGAAAAAAAAAATTCTTCACATAATGCAGTCGCACAATTATTTGCTTAAGTA
*
73427 GAATAATGCAATGGAAAAAAAAATTCTTCACATAATGCAGTCGCACAATTATTTGCTTAAGTA
1 GAATAATGCAATGAAAAAAAAAATTCTTCACATAATGCAGTCGCACAATTATTTGCTTAAGTA
73490 TGGTGATTGC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (63 bp):
GAATAATGCAATGAAAAAAAAAATTCTTCACATAATGCAGTCGCACAATTATTTGCTTAAGTA
Found at i:76164 original size:24 final size:23
Alignment explanation
Indices: 76137--76182 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
76127 ATTTTTAATA
*
76137 TATATACTTTTTTAATAAAATTTT
1 TATATAATTTTTT-ATAAAATTTT
76161 TATATAATTTTTTATAAAATTT
1 TATATAATTTTTTATAAAATTT
76183 AAAAGATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TATATAATTTTTTATAAAATTTT
Found at i:79867 original size:24 final size:24
Alignment explanation
Indices: 79839--79918 Score: 74
Period size: 24 Copynumber: 3.3 Consensus size: 24
79829 GAAGTTCCAC
79839 ATTTTGGAGGTTGAAGTATACATA
1 ATTTTGGAGGTTGAAGTATACATA
* * * *
79863 ATTTTGGTTGAGTAGAAGT-TCCCA-C
1 ATTTTGG-AG-GTTGAAGTAT-ACATA
*
79888 ATTTTGGAGGTTGAAGTATATATA
1 ATTTTGGAGGTTGAAGTATACATA
79912 ATTTTGG
1 ATTTTGG
79919 TTGAAAAATA
Statistics
Matches: 42, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
23 8 0.19
24 16 0.38
25 9 0.21
26 9 0.21
ACGTcount: A:0.29, C:0.06, G:0.25, T:0.40
Consensus pattern (24 bp):
ATTTTGGAGGTTGAAGTATACATA
Found at i:79881 original size:48 final size:49
Alignment explanation
Indices: 79826--79922 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
79816 ATATCGCACG
79826 GTAGAAGTT-CCACATTTTGGAGGTTGAAGTATACATAATTTTGGTTGA
1 GTAGAAGTTCCCACATTTTGGAGGTTGAAGTATACATAATTTTGGTTGA
*
79874 GTAGAAGTTCCCACATTTTGGAGGTTGAAGTATATATAATTTTGGTTGA
1 GTAGAAGTTCCCACATTTTGGAGGTTGAAGTATACATAATTTTGGTTGA
79923 AAAATAAACA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 9 0.19
49 38 0.81
ACGTcount: A:0.29, C:0.08, G:0.25, T:0.38
Consensus pattern (49 bp):
GTAGAAGTTCCCACATTTTGGAGGTTGAAGTATACATAATTTTGGTTGA
Found at i:80682 original size:37 final size:37
Alignment explanation
Indices: 80606--80682 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
80596 TTTTTATATT
*
80606 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
80643 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
80680 TTT
1 TTT
80683 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:80864 original size:20 final size:20
Alignment explanation
Indices: 80828--80865 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
80818 ATCCTATTCC
**
80828 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
80848 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
80866 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:80957 original size:14 final size:14
Alignment explanation
Indices: 80938--80964 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
80928 AAAGGTAAGC
80938 TAATTTAAAATTAG
1 TAATTTAAAATTAG
80952 TAATTTAAAATTA
1 TAATTTAAAATTA
80965 CTATCCAGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (14 bp):
TAATTTAAAATTAG
Found at i:82920 original size:12 final size:13
Alignment explanation
Indices: 82897--82921 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
82887 ATTTTATAAC
82897 TTAAATTTTTTTT
1 TTAAATTTTTTTT
82910 TTAAATTTTTTT
1 TTAAATTTTTTT
82922 GAGTCAAGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTAAATTTTTTTT
Found at i:83345 original size:6 final size:6
Alignment explanation
Indices: 83334--83361 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
83324 TTAAAATTTT
83334 TAAAAA TAAAAA TAAAAA TAAAAA TAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAA
83362 TAATTATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:88814 original size:25 final size:25
Alignment explanation
Indices: 88762--88816 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
88752 CGAATACCTT
**
88762 AATAATTGTTTATATTTTTAATCTA
1 AATAATTGTTTATATTTTTAATAAA
*
88787 AATAATTGTTTTTAATTTTTAA-AAA
1 AATAATTGTTTAT-ATTTTTAATAAA
88812 AATAA
1 AATAA
88817 ATAAGTCCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 18 0.69
26 8 0.31
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (25 bp):
AATAATTGTTTATATTTTTAATAAA
Found at i:91451 original size:31 final size:31
Alignment explanation
Indices: 91415--91622 Score: 271
Period size: 31 Copynumber: 6.8 Consensus size: 31
91405 GTTGATAATG
91415 ATAATGCTCAATCAACTAGTATTGAATTTTA
1 ATAATGCTCAATCAACTAGTATTGAATTTTA
91446 ATAATGCTCAATCAACTAGTATTGAATTTTA
1 ATAATGCTCAATCAACTAGTATTGAATTTTA
* *
91477 ATAATGCTCAATCAACTAGTATTGAATATTG
1 ATAATGCTCAATCAACTAGTATTGAATTTTA
*
91508 ATAATGCTCAATTC-ACTAGTATTGAATGTTA
1 ATAATGCTCAA-TCAACTAGTATTGAATTTTA
* *
91539 ATAATGCTCAATTC-ACTAGTATT-AAATGTA
1 ATAATGCTCAA-TCAACTAGTATTGAATTTTA
* * * *
91569 ATAATGCTCAAACCACTAGTATT-AAATGTA
1 ATAATGCTCAATCAACTAGTATTGAATTTTA
* *
91599 ATAATGCTCAAACCACTAGTATTG
1 ATAATGCTCAATCAACTAGTATTG
91623 GAAATGACAA
Statistics
Matches: 166, Mismatches: 8, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
29 1 0.01
30 54 0.33
31 109 0.66
32 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (31 bp):
ATAATGCTCAATCAACTAGTATTGAATTTTA
Found at i:96694 original size:31 final size:30
Alignment explanation
Indices: 96658--96804 Score: 197
Period size: 31 Copynumber: 4.8 Consensus size: 30
96648 ATTGATAACG
96658 ATAATGCTCAATCAACTAGTATTGAATGTTA
1 ATAATGCTCAATC-ACTAGTATTGAATGTTA
* * *
96689 ATAATGCTCAATCAACTAGTATTGATTATTG
1 ATAATGCTCAATC-ACTAGTATTGAATGTTA
96720 ATAATGCTCAATTCACTAGTATTGAATGTTA
1 ATAATGCTCAA-TCACTAGTATTGAATGTTA
*
96751 ATAATGCTCAATTCACTAGTATTAAATG-TA
1 ATAATGCTCAA-TCACTAGTATTGAATGTTA
*
96781 ATAATGCTCAAACCACTAGTATTG
1 ATAATGCTC-AATCACTAGTATTG
96805 TAAATGACAA
Statistics
Matches: 105, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
30 21 0.20
31 82 0.78
32 2 0.02
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.36
Consensus pattern (30 bp):
ATAATGCTCAATCACTAGTATTGAATGTTA
Found at i:99715 original size:31 final size:31
Alignment explanation
Indices: 99680--99739 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
99670 GTTCCTTCTA
99680 TACCAGAGTTACAAGGAATCTTCACCATCTG
1 TACCAGAGTTACAAGGAATCTTCACCATCTG
99711 TACCAGAGTTACAAGGAATCTTCACCATC
1 TACCAGAGTTACAAGGAATCTTCACCATC
99740 CACACTGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (31 bp):
TACCAGAGTTACAAGGAATCTTCACCATCTG
Done.