Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006203.1 Hibiscus syriacus cultivar Beakdansim tig00014769_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: 75658
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:111 original size:3 final size:3
Alignment explanation
Indices: 54--100 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
44 CATTCCATTT
54 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
101 AAATATTATT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1455 original size:11 final size:11
Alignment explanation
Indices: 1404--1490 Score: 59
Period size: 11 Copynumber: 7.5 Consensus size: 11
1394 TTAATTTCTT
*
1404 TTATTTTGATCA
1 TTATTTT-ATTA
*
1416 TTATTTAATTA
1 TTATTTTATTA
**
1427 CAATTTTATT-
1 TTATTTTATTA
*
1437 TTGTTTTTATTA
1 TT-ATTTTATTA
1449 TTATTTTTGATATA
1 TTA-TTTT-AT-TA
*
1463 TTATTTTCATGA
1 TTATTTT-ATTA
1475 TTATTTTATTA
1 TTATTTTATTA
1486 TTATT
1 TTATT
1491 ATCTTAAGTC
Statistics
Matches: 58, Mismatches: 12, Indels: 11
0.72 0.15 0.14
Matches are distributed among these distances:
11 25 0.43
12 20 0.34
13 8 0.14
14 5 0.09
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:4927 original size:16 final size:16
Alignment explanation
Indices: 4908--4938 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4898 AATTTACATT
*
4908 TACATTTTTGCATTTA
1 TACATTTATGCATTTA
4924 TACATTTATGCATTT
1 TACATTTATGCATTT
4939 TGTATTTTGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.13, G:0.06, T:0.55
Consensus pattern (16 bp):
TACATTTATGCATTTA
Found at i:4927 original size:22 final size:21
Alignment explanation
Indices: 4900--4960 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 21
4890 TTTTAAATAA
4900 TTTACATTTACATTTTTGCAT
1 TTTACATTTACATTTTTGCAT
*
4921 TTATACATTTATGCA-TTTTGTAT
1 TT-TACATTTA--CATTTTTGCAT
*
4944 TTTGCATTTACATTTTT
1 TTTACATTTACATTTTT
4961 TAAAGTATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
20 2 0.06
21 6 0.18
22 15 0.44
23 9 0.26
24 2 0.06
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.59
Consensus pattern (21 bp):
TTTACATTTACATTTTTGCAT
Found at i:11827 original size:22 final size:22
Alignment explanation
Indices: 11802--11878 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
11792 ATCTACACTT
11802 TTCAAAGATGATAGACTCTTTC
1 TTCAAAGATGATAGACTCTTTC
* * *
11824 TTCAAAGATGATAGCCTATCTC
1 TTCAAAGATGATAGACTCTTTC
* *
11846 TTTAAAGATGATAGATTCTCTT-
1 TTCAAAGATGATAGACTCT-TTC
11868 TTCAAAGATGA
1 TTCAAAGATGA
11879 AAGCTTTATT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 44 0.98
23 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGATAGACTCTTTC
Found at i:12642 original size:46 final size:46
Alignment explanation
Indices: 12543--13450 Score: 1455
Period size: 46 Copynumber: 20.0 Consensus size: 46
12533 CTATTTCCCA
*
12543 CATCTGTAAGCCCTTTAGTGCTTGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
12588 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
* *
12634 CATCTGTAAGCCCTTTAGTGCTTGATGTTTT-TAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
* *
12679 CATCTGTAAGCCCTTCAGTGCTTGATATTTTCAAAAACCTTCGGTT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
*
12725 CATCTGTAAGCCCTTCAGTGCTTGAAGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
*
12771 CATCTGTAAGTCCTTCA--GCTTGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
12814 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
12860 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
*
12906 CATCTGTAAGCCCTTCAGTGCTTGAAGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
* *
12952 CATCTGTAAGTCATTCA--GCTTGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
*
12995 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
13041 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
*
13087 CATCTGTAAGACCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
* * *
13132 CATATATAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
* *
13177 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACGTTCGAGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
13223 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
* * * *
13269 CATCTGTAAGCCCTTAAATGCTTGATGTTTTC-AAAACTTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
* * *
13314 CATCTGTAAGTCCTTTAGTGCTTGATGTTTTCAAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
* *
13360 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTAGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
* *
13405 CATCAT-TATGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGG
1 CATC-TGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAA-CCTTCGGG
13451 AGCTTTTTGG
Statistics
Matches: 803, Mismatches: 47, Indels: 24
0.92 0.05 0.03
Matches are distributed among these distances:
43 57 0.07
44 24 0.03
45 264 0.33
46 451 0.56
47 7 0.01
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (46 bp):
CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
Found at i:12698 original size:91 final size:92
Alignment explanation
Indices: 12543--13450 Score: 1455
Period size: 91 Copynumber: 10.0 Consensus size: 92
12533 CTATTTCCCA
*
12543 CATCTGTAAGCCCTTTAGTGCTTGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
12607 GCTTGATGTTTTCAAAAACCTTCGGGT
66 GCTTGATGTTTTCAAAAACCTTCGGGT
* *
12634 CATCTGTAAGCCCTTTAGTGCTTGATGTTTT-TAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
* *
12698 GCTTGATATTTTCAAAAACCTTCGGTT
66 GCTTGATGTTTTCAAAAACCTTCGGGT
* *
12725 CATCTGTAAGCCCTTCAGTGCTTGAAGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCA--
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
12788 GCTTGATGTTTTC-AAAACCTTCGGGT
66 GCTTGATGTTTTCAAAAACCTTCGGGT
12814 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
12879 GCTTGATGTTTTCAAAAACCTTCGGGT
66 GCTTGATGTTTTCAAAAACCTTCGGGT
* * *
12906 CATCTGTAAGCCCTTCAGTGCTTGAAGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCATTCA--
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
12969 GCTTGATGTTTTC-AAAACCTTCGGGT
66 GCTTGATGTTTTCAAAAACCTTCGGGT
*
12995 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTTGGGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
13060 GCTTGATGTTTTCAAAAACCTTCGGGT
66 GCTTGATGTTTTCAAAAACCTTCGGGT
* * *
13087 CATCTGTAAGACCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGTCATATATAAGCCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
*
13151 GCTTGATGTTTTC-AAAACCTTTGGGT
66 GCTTGATGTTTTCAAAAACCTTCGGGT
* *
13177 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACGTTCGAGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
13242 GCTTGATGTTTTCAAAAACCTTCGGGT
66 GCTTGATGTTTTCAAAAACCTTCGGGT
* * * * * *
13269 CATCTGTAAGCCCTTAAATGCTTGATGTTTTC-AAAACTTTTGGGTCATCTGTAAGTCCTTTAGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
*
13333 GCTTGATGTTTTCAAAAACCTTTGGGT
66 GCTTGATGTTTTCAAAAACCTTCGGGT
* * *
13360 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTAGGGTCATCAT-TATGCCCTTCAG
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATC-TGTAAGCCCTTCAG
*
13423 TGCATGATGTTTTCAAAAAGCCTTCGGG
65 TGCTTGATGTTTTCAAAAA-CCTTCGGG
13451 AGCTTTTTGG
Statistics
Matches: 759, Mismatches: 46, Indels: 23
0.92 0.06 0.03
Matches are distributed among these distances:
89 145 0.19
90 68 0.09
91 350 0.46
92 196 0.26
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (92 bp):
CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
GCTTGATGTTTTCAAAAACCTTCGGGT
Found at i:12872 original size:181 final size:181
Alignment explanation
Indices: 12543--13450 Score: 1457
Period size: 181 Copynumber: 5.0 Consensus size: 181
12533 CTATTTCCCA
* *
12543 CATCTGTAAGCCCTTTAGTGCTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAG-G
* *
12608 CTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTTAGTGCTTGATGTTTT-TAAAACC
65 CTTGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACC
* *
12672 TTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATATTTTCAAAAACCTTCGGTT
129 TTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
*
12725 CATCTGTAAGCCCTTCAGTGCTTGAAGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCA-G
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGTCCTTCAGG
12789 CTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCT
65 CTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCT
12854 TCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
130 TCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
* *
12906 CATCTGTAAGCCCTTCAGTGCTTGAAGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCATTCA-G
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGTCCTTCAGG
12970 CTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCT
65 CTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCT
*
13035 TTGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
130 TCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
* * * *
13087 CATCTGTAAGACCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTCATATATAAGCCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAG-G
* *
13152 CTTGATGTTTTCAAAACCTTTGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACGT
65 CTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCT
*
13217 TCGAGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
130 TCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
* * * * *
13269 CATCTGTAAGCCCTTAAATGCTTGATGTTTTCAAAACTTTTGGGTCATCTGTAAGTCCTTTAGTG
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAG-G
* *
13334 CTTGATGTTTTCAAAAACCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACC
65 CTTGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACC
* * *
13398 TTAGGGTCATCAT-TATGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGG
129 TTCGGGTCATC-TGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAA-CCTTCGGG
13451 AGCTTTTTGG
Statistics
Matches: 685, Mismatches: 34, Indels: 13
0.94 0.05 0.02
Matches are distributed among these distances:
180 69 0.10
181 279 0.41
182 255 0.37
183 82 0.12
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (181 bp):
CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGGC
TTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTT
CGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
Found at i:13723 original size:3 final size:3
Alignment explanation
Indices: 13675--13710 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
13665 TTTCATTCCG
13675 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
13711 AAAAATATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:15114 original size:12 final size:13
Alignment explanation
Indices: 15065--15118 Score: 56
Period size: 14 Copynumber: 4.0 Consensus size: 13
15055 TTTTATTTTG
15065 TTTTTATTATTAT
1 TTTTTATTATTAT
*
15078 TTTTGATATATTAT
1 TTTTTAT-TATTAT
*
15092 TTTCATGATTATT-T
1 TTT--TTATTATTAT
15106 TTTTTATTATTAT
1 TTTTTATTATTAT
15119 CTTAAGTCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
12 7 0.20
13 7 0.20
14 13 0.37
15 4 0.11
16 4 0.11
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (13 bp):
TTTTTATTATTAT
Found at i:15456 original size:2 final size:2
Alignment explanation
Indices: 15444--15488 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
15434 ATATCTTATT
* *
15444 TA TA AA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T- TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15484 TA TA T
1 TA TA T
15489 TTTTTCTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:17273 original size:12 final size:12
Alignment explanation
Indices: 17256--17308 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
17246 ACTATAGCAT
17256 TGTTCATGGTAC
1 TGTTCATGGTAC
*
17268 TGTTCATGATAC
1 TGTTCATGGTAC
*
17280 TGTTTAT--TAC
1 TGTTCATGGTAC
**
17290 TGTTCACAGTAC
1 TGTTCATGGTAC
17302 TGTTCAT
1 TGTTCAT
17309 ACCGTATAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
10 8 0.24
12 26 0.76
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.45
Consensus pattern (12 bp):
TGTTCATGGTAC
Found at i:18390 original size:6 final size:6
Alignment explanation
Indices: 18362--18426 Score: 51
Period size: 6 Copynumber: 10.2 Consensus size: 6
18352 TAATTAAAAT
* *
18362 AATAAA AACAACA AATAAAA AATAAA AATAGTAA AA-AAC AATATAA AATAAA
1 AATAAA AATAA-A AAT-AAA AATAAA AATA--AA AATAAA AATA-AA AATAAA
*
18414 GATAAA AATAAA A
1 AATAAA AATAAA A
18427 TATGAGGACC
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
5 3 0.06
6 25 0.53
7 13 0.28
8 6 0.13
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (6 bp):
AATAAA
Found at i:18404 original size:26 final size:29
Alignment explanation
Indices: 18357--18418 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 29
18347 AAACATAATT
18357 AAAATAATAAAAACAACAAATAAAAAATA
1 AAAATAATAAAAACAACAAATAAAAAATA
* *
18386 AAAATAGT-AAAA-AAC-AATATAAAATA
1 AAAATAATAAAAACAACAAATAAAAAATA
*
18412 AAGATAA
1 AAAATAA
18419 AAATAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 15 0.52
27 3 0.10
28 4 0.14
29 7 0.24
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (29 bp):
AAAATAATAAAAACAACAAATAAAAAATA
Found at i:25651 original size:55 final size:55
Alignment explanation
Indices: 25592--25795 Score: 218
Period size: 55 Copynumber: 3.7 Consensus size: 55
25582 TCTTCAAGTG
* * * * *
25592 ACGGGTCTGCTCCCTATTCTTTCAGGAAGTATA-AGACTTGAATAATCTTCATA-AA
1 ACGGGTCCGCTCTCTATTCCTTCAGGAAGTATAGA-ACTCGAACAATCTTCA-ACAA
*
25647 ACGGGTCCGCTCTCTATTCCTTCAGAAAGTATAGAACTCGAACAATCTTCAACAA
1 ACGGGTCCGCTCTCTATTCCTTCAGGAAGTATAGAACTCGAACAATCTTCAACAA
* *
25702 ACGGGTCCGATCTCTATTCCTTCA-GAGAGTATAGAACTCGAACAATCTTCAACGA
1 ACGGGTCCGCTCTCTATTCCTTCAGGA-AGTATAGAACTCGAACAATCTTCAACAA
*** * * *
25757 ATTTGTCCGCTCCCTATTCCCTCA-GAGAGTATAGGACTC
1 ACGGGTCCGCTCTCTATTCCTTCAGGA-AGTATAGAACTC
25796 AATCTTCAAC
Statistics
Matches: 130, Mismatches: 16, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
54 2 0.02
55 127 0.98
56 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.28
Consensus pattern (55 bp):
ACGGGTCCGCTCTCTATTCCTTCAGGAAGTATAGAACTCGAACAATCTTCAACAA
Found at i:27045 original size:27 final size:23
Alignment explanation
Indices: 26994--27059 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 23
26984 CCCCATTTTA
26994 TTTCTTTTTCTTTTTTCATCATTT
1 TTTC-TTTTCTTTTTTCATCATTT
*
27018 TTTCTTTTCTTTTTTCGTTCTCATTT
1 TTTCTTTTCTTTTTTC---ATCATTT
27044 TTTCTGTTTCTTTTTT
1 TTTCT-TTTCTTTTTT
27060 TATTTTTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
23 12 0.32
24 4 0.11
26 11 0.30
27 10 0.27
ACGTcount: A:0.05, C:0.17, G:0.03, T:0.76
Consensus pattern (23 bp):
TTTCTTTTCTTTTTTCATCATTT
Found at i:27054 original size:16 final size:15
Alignment explanation
Indices: 27007--27054 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 15
26997 CTTTTTCTTT
27007 TTTCATCATTTTTTC-
1 TTTC-TCATTTTTTCG
27022 TTT-TC-TTTTTTCG
1 TTTCTCATTTTTTCG
27035 -TTCTCATTTTTTCTG
1 TTTCTCATTTTTTC-G
27050 TTTCT
1 TTTCT
27055 TTTTTTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
12 9 0.32
13 4 0.14
14 7 0.25
15 4 0.14
16 4 0.14
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (15 bp):
TTTCTCATTTTTTCG
Found at i:27059 original size:29 final size:28
Alignment explanation
Indices: 26994--27060 Score: 84
Period size: 26 Copynumber: 2.4 Consensus size: 28
26984 CCCCATTTTA
*
26994 TTTCTTTTTCTTTTTTCATCATTTTTTCT
1 TTTCTTTTT-TTTGTTCATCATTTTTTCT
*
27023 TTTC-TTTTTTCGTTC-TCATTTTTTCT
1 TTTCTTTTTTTTGTTCATCATTTTTTCT
27049 GTTTCTTTTTTT
1 -TTTCTTTTTTT
27061 ATTTTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 11 0.32
27 9 0.26
28 10 0.29
29 4 0.12
ACGTcount: A:0.04, C:0.16, G:0.03, T:0.76
Consensus pattern (28 bp):
TTTCTTTTTTTTGTTCATCATTTTTTCT
Found at i:27067 original size:36 final size:37
Alignment explanation
Indices: 27022--27105 Score: 91
Period size: 38 Copynumber: 2.3 Consensus size: 37
27012 TCATTTTTTC
* * *
27022 TTTTCTTTTTTCGTTC-TCATTTT-TTCTGTTTCTTT
1 TTTTATTTTTTTGTTCATCATTTTATTCTGTTTATTT
* * *
27057 TTTTATTTTTTTTTTCATCATTTTCATTTTTTTTATTT
1 TTTTATTTTTTTGTTCATCATTTT-ATTCTGTTTATTT
27095 TTTTATTTTTT
1 TTTTATTTTTT
27106 CTTCTTTTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
35 13 0.32
36 7 0.17
38 20 0.50
ACGTcount: A:0.08, C:0.11, G:0.02, T:0.79
Consensus pattern (37 bp):
TTTTATTTTTTTGTTCATCATTTTATTCTGTTTATTT
Found at i:27068 original size:9 final size:9
Alignment explanation
Indices: 27054--27138 Score: 54
Period size: 9 Copynumber: 9.6 Consensus size: 9
27044 TTTCTGTTTC
27054 TTTTTTTAT
1 TTTTTTTAT
27063 TTTTTTT-T
1 TTTTTTTAT
*
27071 TCATCATTTTCAT
1 T--T--TTTTTAT
27084 TTTTTTTA-
1 TTTTTTTAT
27092 TTTTTTTA-
1 TTTTTTTAT
*
27100 -TTTTTTCT
1 TTTTTTTAT
*
27108 TCTTTTTAT
1 TTTTTTTAT
*
27117 TTTTTCT-T
1 TTTTTTTAT
*
27125 TTTTTTCAT
1 TTTTTTTAT
27134 TTTTT
1 TTTTT
27139 ATTTCTTTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
7 6 0.10
8 16 0.27
9 29 0.49
10 1 0.02
11 1 0.02
12 4 0.07
13 2 0.03
ACGTcount: A:0.09, C:0.08, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:27088 original size:17 final size:17
Alignment explanation
Indices: 27066--27138 Score: 69
Period size: 16 Copynumber: 4.4 Consensus size: 17
27056 TTTTTATTTT
*
27066 TTTTTTCATCATTTTCA
1 TTTTTTCATCTTTTTCA
* *
27083 TTTTTTTTAT-TTTTTTA
1 -TTTTTTCATCTTTTTCA
*
27100 TTTTTTCTTCTTTTT-A
1 TTTTTTCATCTTTTTCA
* *
27116 TTTTTTCTTTTTTTTCA
1 TTTTTTCATCTTTTTCA
27133 TTTTTT
1 TTTTTT
27139 ATTTCTTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
16 22 0.47
17 17 0.36
18 8 0.17
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTTCATCTTTTTCA
Found at i:27096 original size:16 final size:17
Alignment explanation
Indices: 27077--27138 Score: 74
Period size: 17 Copynumber: 3.7 Consensus size: 17
27067 TTTTTCATCA
27077 TTTTCATTTTTT-TTATT
1 TTTTCATTTTTTCTTA-T
* *
27094 TTTTTATTTTTTCTTCT
1 TTTTCATTTTTTCTTAT
*
27111 TTTT-ATTTTTTCTTTT
1 TTTTCATTTTTTCTTAT
27127 TTTTCATTTTTT
1 TTTTCATTTTTT
27139 ATTTCTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
16 15 0.38
17 23 0.57
18 2 0.05
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTCATTTTTTCTTAT
Found at i:27139 original size:24 final size:23
Alignment explanation
Indices: 27077--27142 Score: 57
Period size: 24 Copynumber: 2.8 Consensus size: 23
27067 TTTTTCATCA
27077 TTTTCATT-TTTTTTATTTTTTTATT
1 TTTTC-TTCTTTTTTA--TTTTTATT
27102 TTTTCTTC-TTTTTATTTTT-TCT
1 TTTTCTTCTTTTTTATTTTTAT-T
*
27124 TTTTTTTCATTTTTTATTT
1 TTTTCTTC-TTTTTTATTT
27143 CTTTTTCAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
21 1 0.03
22 13 0.36
24 17 0.47
25 5 0.14
ACGTcount: A:0.09, C:0.08, G:0.00, T:0.83
Consensus pattern (23 bp):
TTTTCTTCTTTTTTATTTTTATT
Found at i:27145 original size:34 final size:36
Alignment explanation
Indices: 26989--27148 Score: 107
Period size: 34 Copynumber: 4.4 Consensus size: 36
26979 TGAACCCCCA
* * *
26989 TTTTATTTCTTTTTCTTTTTTCATCATTTTTTC-TT
1 TTTTATTTCTTTTTATTTTTTCTTTATTTTTTCATT
* * * * *
27024 TTCTTTTTTCGTTCTCATTTTTTCTGTTTCTTTTTTTATT
1 TT-TTATTTC-TTTTTATTTTTTC--TTTATTTTTTCATT
* *
27064 TTTTTTTTCATCATTTTCA-TTTTT-TTTATTTTTTTATT
1 TTTTATTTC-T--TTTT-ATTTTTTCTTTATTTTTTCATT
*
27102 TTTT-CTTCTTTTTATTTTTTC-TT-TTTTTTCATT
1 TTTTATTTCTTTTTATTTTTTCTTTATTTTTTCATT
27135 TTTTATTTCTTTTT
1 TTTTATTTCTTTTT
27149 CAAGCGAAAT
Statistics
Matches: 99, Mismatches: 15, Indels: 23
0.72 0.11 0.17
Matches are distributed among these distances:
33 14 0.14
34 19 0.19
35 2 0.02
36 7 0.07
37 13 0.13
38 17 0.17
39 15 0.15
40 4 0.04
41 7 0.07
42 1 0.01
ACGTcount: A:0.08, C:0.12, G:0.01, T:0.79
Consensus pattern (36 bp):
TTTTATTTCTTTTTATTTTTTCTTTATTTTTTCATT
Found at i:27148 original size:59 final size:58
Alignment explanation
Indices: 26998--27148 Score: 141
Period size: 59 Copynumber: 2.6 Consensus size: 58
26988 ATTTTATTTC
* *
26998 TTTTTCTTTTTTCATCATTTTTTCTTTTCTTTTTTCGTTCTCATTTTTTCTGTTTCTTTT
1 TTTTTCTTTTTT-TTCATTTTTT-ATTTCTTTTTTCGTTCTCATTTTTTCTGTTTCTTTT
* * * *
27058 TTTATT-TTTTTTTTCATCATTTTCATTT-TTTTTAT-TTTTTTATTTTTTCT-TCTT-TTTAT
1 TTT-TTCTTTTTTTTCAT--TTTTTATTTCTTTTT-TCGTTCTCATTTTTTCTGT-TTCTTT-T
27117 TTTTTCTTTTTTTTCATTTTTTATTTCTTTTT
1 TTTTTCTTTTTTTTCATTTTTTATTTCTTTTT
27149 CAAGCGAAAT
Statistics
Matches: 76, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
57 8 0.11
58 11 0.14
59 38 0.50
60 13 0.17
61 6 0.08
ACGTcount: A:0.08, C:0.12, G:0.01, T:0.79
Consensus pattern (58 bp):
TTTTTCTTTTTTTTCATTTTTTATTTCTTTTTTCGTTCTCATTTTTTCTGTTTCTTTT
Found at i:36856 original size:45 final size:45
Alignment explanation
Indices: 36785--36913 Score: 177
Period size: 45 Copynumber: 2.8 Consensus size: 45
36775 TGTTATTCAC
* *
36785 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTGGTCG
1 AAAAATAAA-CCTAACCACATGATATCTAATTCGCATGCTTGGTCG
* * * *
36831 AAAAATAAACCTAACCTCATTATATCTAATTCACATGCTTGTTCG
1 AAAAATAAACCTAACCACATGATATCTAATTCGCATGCTTGGTCG
* *
36876 AAAAATAAACCTAACCACATGATATCTAGTTCGTATGC
1 AAAAATAAACCTAACCACATGATATCTAATTCGCATGC
36914 ATTTATTTGA
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
45 65 0.89
46 8 0.11
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.29
Consensus pattern (45 bp):
AAAAATAAACCTAACCACATGATATCTAATTCGCATGCTTGGTCG
Found at i:39603 original size:2 final size:2
Alignment explanation
Indices: 39596--39626 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39586 TATATTACCC
39596 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39627 AGTAATTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42706 original size:40 final size:40
Alignment explanation
Indices: 42651--42734 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
42641 AGAACGTTAA
42651 ATTATTATAATAATAGATAAAACCTTGACACTGAAAGAAG
1 ATTATTATAATAATAGATAAAACCTTGACACTGAAAGAAG
42691 ATTATTATAATAATAGATAAAACCTTGACACTGAAAGAAG
1 ATTATTATAATAATAGATAAAACCTTGACACTGAAAGAAG
42731 ATTA
1 ATTA
42735 GGGAAGTATC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.29
Consensus pattern (40 bp):
ATTATTATAATAATAGATAAAACCTTGACACTGAAAGAAG
Found at i:48273 original size:19 final size:20
Alignment explanation
Indices: 48246--48290 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
48236 ATTAGCAACA
* *
48246 TAAT-AAAAATGATTCTATT
1 TAATAAAAAATGATCCTATC
*
48265 TAATTAAAAATGATCCTATC
1 TAATAAAAAATGATCCTATC
48285 TAATAA
1 TAATAA
48291 CTAATAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (20 bp):
TAATAAAAAATGATCCTATC
Found at i:48274 original size:20 final size:20
Alignment explanation
Indices: 48249--48288 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
48239 AGCAACATAA
* *
48249 TAAAAATGATTCTATTTAAT
1 TAAAAATGATCCTATCTAAT
48269 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
48289 AACTAATAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:48331 original size:20 final size:21
Alignment explanation
Indices: 48302--48341 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
48292 TAATAGAATA
*
48302 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
48323 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
48342 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:48380 original size:20 final size:20
Alignment explanation
Indices: 48355--48393 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
48345 TAATAGAATA
*
48355 AAAACTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
48375 AAAACTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
48394 ATTTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:48384 original size:52 final size:52
Alignment explanation
Indices: 48247--48394 Score: 262
Period size: 52 Copynumber: 2.8 Consensus size: 52
48237 TTAGCAACAT
*
48247 AATAAAAA-TGATTCTATTTAATTAAAAATGATCCTATCTAATAACTAATAG
1 AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
48298 AATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
1 AAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
*
48351 AATAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
48395 TTTAATTTAG
Statistics
Matches: 93, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
51 3 0.03
52 45 0.48
53 45 0.48
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.34
Consensus pattern (52 bp):
AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
Found at i:52990 original size:19 final size:20
Alignment explanation
Indices: 52963--53007 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
52953 ATTAGCAACA
* *
52963 TAAT-AAAAATGATTCTATT
1 TAATAAAAAATGATCCTATC
*
52982 TAATTAAAAATGATCCTATC
1 TAATAAAAAATGATCCTATC
53002 TAATAA
1 TAATAA
53008 CTAATAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (20 bp):
TAATAAAAAATGATCCTATC
Found at i:52991 original size:20 final size:20
Alignment explanation
Indices: 52966--53005 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
52956 AGCAACATAA
* *
52966 TAAAAATGATTCTATTTAAT
1 TAAAAATGATCCTATCTAAT
52986 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
53006 AACTAATAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:53048 original size:20 final size:21
Alignment explanation
Indices: 53019--53058 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
53009 TAATAGAATA
*
53019 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
53040 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
53059 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:53097 original size:20 final size:20
Alignment explanation
Indices: 53072--53110 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
53062 TAATAGAATA
*
53072 AAAACTGATTCTATCTAATT
1 AAAACTGATCCTATCTAATT
53092 AAAACTGATCCTATCTAAT
1 AAAACTGATCCTATCTAAT
53111 ATTTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAACTGATCCTATCTAATT
Found at i:53101 original size:52 final size:52
Alignment explanation
Indices: 52964--53111 Score: 262
Period size: 52 Copynumber: 2.8 Consensus size: 52
52954 TTAGCAACAT
*
52964 AATAAAAA-TGATTCTATTTAATTAAAAATGATCCTATCTAATAACTAATAG
1 AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
53015 AATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
1 AAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
*
53068 AATAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATA
1 AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
53112 TTTAATTTAG
Statistics
Matches: 93, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
51 3 0.03
52 45 0.48
53 45 0.48
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.34
Consensus pattern (52 bp):
AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
Found at i:55318 original size:13 final size:13
Alignment explanation
Indices: 55283--55321 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
55273 CATCATCCGG
55283 TCTTTAATTTTTT
1 TCTTTAATTTTTT
* *
55296 TCCTT-CTTTTTT
1 TCTTTAATTTTTT
55308 TCTTTAATTTTTT
1 TCTTTAATTTTTT
55321 T
1 T
55322 AGCTTTTTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (13 bp):
TCTTTAATTTTTT
Found at i:56726 original size:38 final size:35
Alignment explanation
Indices: 56642--56726 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 35
56632 AATTTTGTAA
* *
56642 AAAAATATATATAAATATTATGAATTTAAATTTTT
1 AAAAATATATATAAATATTATGAACTTAAATTTAT
* * *
56677 AAAGAAAATATATAAATATTTTCTAACTTATAATATTAT
1 AAA-AATATATATAAATATTAT-GAACTTA-AAT-TTAT
56716 AAAAATATATA
1 AAAAATATATA
56727 ATAAGGACAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
35 3 0.08
36 16 0.40
37 5 0.12
38 10 0.25
39 6 0.15
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (35 bp):
AAAAATATATATAAATATTATGAACTTAAATTTAT
Found at i:56869 original size:18 final size:19
Alignment explanation
Indices: 56846--56888 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
56836 CAGTAATCCT
*
56846 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGATAATCTTAC
*
56864 ATTCCCACTGATAATCTTAT
1 ATT-CCACTGATAATCTTAC
56884 ATTCC
1 ATTCC
56889 GTGAACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.19
20 14 0.67
ACGTcount: A:0.26, C:0.28, G:0.07, T:0.40
Consensus pattern (19 bp):
ATTCCACTGATAATCTTAC
Found at i:62272 original size:28 final size:28
Alignment explanation
Indices: 62205--62399 Score: 210
Period size: 28 Copynumber: 6.8 Consensus size: 28
62195 CCCGTTGAAC
*
62205 TGGTGATATTTTAGTAATTATTTTTTAAAA
1 TGGTGATATTTTTGTAATTA--TTTTAAAA
* *
62235 TGGTGATATTTTGGTAATTATTTTCAAA
1 TGGTGATATTTTTGTAATTATTTTAAAA
* * **
62263 TTGTGTTATTTTCATAATTATTTTAAAA
1 TGGTGATATTTTTGTAATTATTTTAAAA
62291 TGGTGATATTTTTGTAATTATTTTAAAA
1 TGGTGATATTTTTGTAATTATTTTAAAA
* *
62319 AGATGATATTTTTGTAATTATTTTTAAAAA
1 TGGTGATATTTTTGTAATTA-TTTT-AAAA
* * * * *
62349 AGGTGACAGTTTCGTAATTATTTAAAAA
1 TGGTGATATTTTTGTAATTATTTTAAAA
* *
62377 GGGTGATATTTTTGTAAATATTT
1 TGGTGATATTTTTGTAATTATTT
62400 CTTCAAAGGG
Statistics
Matches: 140, Mismatches: 23, Indels: 6
0.83 0.14 0.04
Matches are distributed among these distances:
28 94 0.67
29 7 0.05
30 39 0.28
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.50
Consensus pattern (28 bp):
TGGTGATATTTTTGTAATTATTTTAAAA
Found at i:62367 original size:86 final size:84
Alignment explanation
Indices: 62205--62399 Score: 228
Period size: 86 Copynumber: 2.3 Consensus size: 84
62195 CCCGTTGAAC
* * * * ** **
62205 TGGTGATATTTTAGTAATTATTTTTTAAAATGGTGATATTTTGGTAATTATTTTCAAATTGTGTT
1 TGGTGATATTTTTGTAATTA--TTTTAAAAAGATGATATTTTGGTAATTATTTTAAAAAGGTGAC
* *
62270 ATTTTCATAATTATTTTAAAA
64 AGTTTCATAATTATTTAAAAA
*
62291 TGGTGATATTTTTGTAATTATTTTAAAAAGATGATATTTTTGTAATTATTTTTAAAAAAGGTGAC
1 TGGTGATATTTTTGTAATTATTTTAAAAAGATGATATTTTGGTAATTA-TTTT-AAAAAGGTGAC
*
62356 AGTTTCGTAATTATTTAAAAA
64 AGTTTCATAATTATTTAAAAA
* *
62377 GGGTGATATTTTTGTAAATATTT
1 TGGTGATATTTTTGTAATTATTT
62400 CTTCAAAGGG
Statistics
Matches: 93, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
84 25 0.27
85 4 0.04
86 64 0.69
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.50
Consensus pattern (84 bp):
TGGTGATATTTTTGTAATTATTTTAAAAAGATGATATTTTGGTAATTATTTTAAAAAGGTGACAG
TTTCATAATTATTTAAAAA
Found at i:62384 original size:58 final size:56
Alignment explanation
Indices: 62206--62414 Score: 213
Period size: 58 Copynumber: 3.6 Consensus size: 56
62196 CCGTTGAACT
* * * *
62206 GGTGATATTTTAGTAATTATTTTTTAAAATGGTGATATTTTGGTAATTATTTTCAAAT
1 GGTGATATTTTTGTAATTA-TTTTTAAAATGGTGATATTTTCGTAATTA-TTTAAAAA
* * ** *
62264 TGTGTTATTTTCATAATTA-TTTTAAAATGGTGATATTTTTGTAATTATTTTAAAAA
1 GGTGATATTTTTGTAATTATTTTTAAAATGGTGATATTTTCGTAATTA-TTTAAAAA
* * * *
62320 GATGATATTTTTGTAATTATTTTTAAAAAAGGTGACAGTTTCGTAATTATTTAAAAA
1 GGTGATATTTTTGTAATTATTTTT-AAAATGGTGATATTTTCGTAATTATTTAAAAA
* * *
62377 GGGTGATATTTTTGTAAATATTTCTTCAAAGGGTGATA
1 -GGTGATATTTTTGTAATTATTT-TTAAAATGGTGATA
62415 ATTGTGTAAA
Statistics
Matches: 126, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
56 48 0.38
57 12 0.10
58 64 0.51
59 2 0.02
ACGTcount: A:0.33, C:0.03, G:0.15, T:0.48
Consensus pattern (56 bp):
GGTGATATTTTTGTAATTATTTTTAAAATGGTGATATTTTCGTAATTATTTAAAAA
Found at i:62786 original size:21 final size:20
Alignment explanation
Indices: 62753--62791 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
62743 AAAGGCTTAA
*
62753 TATTTTAATATTTTGGTTATT
1 TATTTTAAGA-TTTGGTTATT
*
62774 TATTTTTAGATTTGGTTA
1 TATTTTAAGATTTGGTTA
62792 AGGAATTGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.64
Consensus pattern (20 bp):
TATTTTAAGATTTGGTTATT
Found at i:63564 original size:117 final size:116
Alignment explanation
Indices: 63353--63687 Score: 451
Period size: 117 Copynumber: 2.9 Consensus size: 116
63343 GAAAATATTT
*
63353 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTATTGG-AGTGCATGTGGGTGTATGGTTCTG
1 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTATTGGTA-TGCAGGT-GGTGTATGGTTCTG
*
63417 GGGAACCTACACATTTTAGTAATCGGAGTGATTGGATGGAGAATTTATTACCA
64 GGGAACCTACACATTTTAGTAATCGGAGTGATTGGATGGAGAAGTTATTACCA
63470 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTATTGGTATGCAGGTGAGTGTATGGTTCTGG
1 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTATTGGTATGCAGGTG-GTGTATGGTTCTGG
* * * *
63535 GGAACCTGCACATTTTAGTAATCGAAGTGATTGGATGGGGAAGTTATTACCG
65 GGAACCTACACATTTTAGTAATCGGAGTGATTGGATGGAGAAGTTATTACCA
* ** * * * * * *
63587 TAGGCTCCTCGGCTTTGTGCTTA-GGTAAGTCCTTACTGGTGTGCAGGTGG-GTGTGGTTCTGGA
1 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTATTGGTATGCAGGTGGTGTATGGTTCTGGG
* * * *
63650 GAACATACAAATTCTAGTAATCGGAGTGATTAGATGGA
66 GAACCTACACATTTTAGTAATCGGAGTGATTGGATGGA
63688 AATAGTGTTC
Statistics
Matches: 194, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
114 42 0.22
115 1 0.01
116 25 0.13
117 125 0.64
118 1 0.01
ACGTcount: A:0.21, C:0.15, G:0.31, T:0.33
Consensus pattern (116 bp):
CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTATTGGTATGCAGGTGGTGTATGGTTCTGGG
GAACCTACACATTTTAGTAATCGGAGTGATTGGATGGAGAAGTTATTACCA
Found at i:70502 original size:32 final size:32
Alignment explanation
Indices: 70466--70544 Score: 104
Period size: 32 Copynumber: 2.5 Consensus size: 32
70456 ATAATCCAAT
*
70466 GTGATGACGTGGTATATCTCACATCACCTAAG
1 GTGATGACGTGATATATCTCACATCACCTAAG
* * * * *
70498 GTGATGTCGTAATATATGTCGCATCACCTAAT
1 GTGATGACGTGATATATCTCACATCACCTAAG
70530 GTGATGACGTGATAT
1 GTGATGACGTGATAT
70545 GTATCACGTC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.32
Consensus pattern (32 bp):
GTGATGACGTGATATATCTCACATCACCTAAG
Found at i:73682 original size:112 final size:112
Alignment explanation
Indices: 73258--73711 Score: 595
Period size: 112 Copynumber: 4.1 Consensus size: 112
73248 TTGTCGGTTT
* * * *
73258 GTGTCGATATTTTATAAAAATATATTGATCCATAA-TA-ATAA-A-GTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
73319 -GTCTATAAATGATAAACCAGGTAAAACGCTA-CGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * * **
73364 -TATCGATACTTTATAAAAATGTATCGATCTATAAC-ATATAACAGGTAAAAAAATAACAAAATT
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
73427 AGTTTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
** * *
73474 GTGTCGATACTTTAT-AAAATGTATCGATCCACCATATTAATAACAGGT-AAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAAT-ATAACAGGTAAAAAAATGACAAAAC
**
73537 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACTAGATATATTGAAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
73585 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * * * *
73650 GGTCTATAAATAACAAAACAGATAAAGTGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
73697 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
73712 TATAAGTATC
Statistics
Matches: 300, Mismatches: 37, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
105 30 0.10
106 4 0.01
107 1 0.00
108 16 0.05
109 27 0.09
110 30 0.10
111 93 0.31
112 99 0.33
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.27
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:73723 original size:223 final size:218
Alignment explanation
Indices: 73258--73711 Score: 628
Period size: 223 Copynumber: 2.1 Consensus size: 218
73248 TTGTCGGTTT
* * *
73258 GTGTCGATATTTTATAAAAATATATTGAT---CCATAATAATAAAGTAAAAAAATGACAAAACCG
1 GTGTCGATACTTTAT-AAAATGTATCGATCCACCATAATAATAAAGTAAAAAAATGACAAAACCG
* * *
73320 TCTATAAATGATAAACCAGGTAAAACGCTACGGATATATTGAAATATCGATACTTTATAAAAATG
65 TCTATAAATGACAAAACAGGTAAAACGCTACAGATATATTGAAATATCGATACTTTATAAAAATG
* ** * * *
73385 TATCGATCTATAACATATAACAGGTAAAAAAATAACAAAATTAGTTTATAAATGACAAAACAGGT
130 TATCGATCCATAACATATAACAGGTAAAAAAATAACAAAACCAGTCTATAAATAACAAAACAGAT
73450 AAAGCGCTACCGGATATATTGAAA
195 AAAGCGCTACCGGATATATTGAAA
*
73474 GTGTCGATACTTTATAAAATGTATCGATCCACCATATTAATAACAGGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAATGTATCGATCCACCATAATAATAA-A-GTAAAAAAATGACAAAACC
* *
73538 GGTCTATAAATGACAAAACAGGTAAAGCGCTACTAGATATATTGAAAGTGTCGATACTTTATAAA
64 -GTCTATAAATGACAAAACAGGTAAAACGCTAC-AGATATATTGAAA-TATCGATACTTTATAAA
* * *
73603 AATGTATCGATCCATAACAATATAACATGTAAAAAAATGACAAAACCGGTCTATAAATAACAAAA
126 AATGTATCGATCCATAAC-ATATAACAGGTAAAAAAATAACAAAACCAGTCTATAAATAACAAAA
* * *
73668 CAGATAAAGTGCTACCGGATATGTTGATA
190 CAGATAAAGCGCTACCGGATATATTGAAA
73697 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
73712 TATAAGTATC
Statistics
Matches: 208, Mismatches: 21, Indels: 11
0.87 0.09 0.05
Matches are distributed among these distances:
215 11 0.05
216 14 0.07
218 11 0.05
219 17 0.08
220 31 0.15
221 12 0.06
222 33 0.16
223 79 0.38
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.27
Consensus pattern (218 bp):
GTGTCGATACTTTATAAAATGTATCGATCCACCATAATAATAAAGTAAAAAAATGACAAAACCGT
CTATAAATGACAAAACAGGTAAAACGCTACAGATATATTGAAATATCGATACTTTATAAAAATGT
ATCGATCCATAACATATAACAGGTAAAAAAATAACAAAACCAGTCTATAAATAACAAAACAGATA
AAGCGCTACCGGATATATTGAAA
Found at i:74031 original size:182 final size:182
Alignment explanation
Indices: 73582--74036 Score: 727
Period size: 180 Copynumber: 2.5 Consensus size: 182
73572 AGATATATTG
* *
73582 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAAAATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
** * * * *
73647 ACCGGTCTATAAATAACAAAACAGATAAAGTGCTACCGGATATGTTGATAGTGTCGATACTTTAT
66 ACCGGTCTCGAAATGACAAAACCGGTAAAGTGCTACCGGATATGTTGAAAGTGTCGATACTTTAT
** * * * *
73712 TATAAGTATCGACACTTTTGGAATTTAAAATAGAAGAAGTTGTAGCACTAAT
131 TATAAACATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCACCAAT
73764 -AAGTGTCGATACTTTAT-AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
73827 ACCGGTCTCGAAATGACAAAACCGGTAAAG-GACTACCGGATATGTTGAAAGTGTCGATACTTTA
66 ACCGGTCTCGAAATGACAAAACCGGTAAAGTG-CTACCGGATATGTTGAAAGTGTCGATACTTTA
*
73891 TTATAAACATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
130 TTATAAACATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCACCAAT
*
73944 AAAGTATCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
*
74009 ATCGGTCTCGAAATGACAAAACCGGTAA
66 ACCGGTCTCGAAATGACAAAACCGGTAA
74037 TAAAAAAGTG
Statistics
Matches: 253, Mismatches: 17, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
179 1 0.00
180 146 0.58
181 33 0.13
182 73 0.29
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ACCGGTCTCGAAATGACAAAACCGGTAAAGTGCTACCGGATATGTTGAAAGTGTCGATACTTTAT
TATAAACATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCACCAAT
Done.