Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002281.1 Hibiscus syriacus cultivar Beakdansim tig00004642_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: 99687
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:10408 original size:15 final size:15
Alignment explanation
Indices: 10388--10426 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
10378 GGCTAGATCG
10388 AATTAAAGAATTGCA
1 AATTAAAGAATTGCA
* *
10403 AATTAAATAATTTCA
1 AATTAAAGAATTGCA
*
10418 AACTAAAGA
1 AATTAAAGA
10427 TGGAAAGTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (15 bp):
AATTAAAGAATTGCA
Found at i:12711 original size:64 final size:64
Alignment explanation
Indices: 12643--12792 Score: 182
Period size: 64 Copynumber: 2.3 Consensus size: 64
12633 TTGAAGGTGT
*
12643 ATCGATGCACAAGTAGTGCATCGATGTACTCTT-TTAA-AATATAAACATCGAATGCA-ATTAGT
1 ATCGATGCACAAGTAGTGCATCGATGCA-TCTTATTAATAATA-AAACATCGAATGCATATTA-T
12705 GC
63 GC
* * * *
12707 ATCGATGCATAAGGCA-TGCATCGATGCATTTTATTAATAATAAAACATCGAATGCATTTTATGC
1 ATCGATGCACAA-GTAGTGCATCGATGCATCTTATTAATAATAAAACATCGAATGCATATTATGC
*
12771 ACCGATGCACAAGTAGTGCATC
1 ATCGATGCACAAGTAGTGCATC
12793 AATACATGCC
Statistics
Matches: 73, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
63 5 0.07
64 59 0.81
65 9 0.12
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29
Consensus pattern (64 bp):
ATCGATGCACAAGTAGTGCATCGATGCATCTTATTAATAATAAAACATCGAATGCATATTATGC
Found at i:13344 original size:15 final size:15
Alignment explanation
Indices: 13326--13359 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
13316 GAGGGTATAA
13326 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
13341 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
13356 TAGT
1 TAGT
13360 GGTCCTACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.21, G:0.32, T:0.32
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:17336 original size:15 final size:15
Alignment explanation
Indices: 17316--17354 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
17306 GGCTAGATCG
17316 AATTAAAGAATTACA
1 AATTAAAGAATTACA
*
17331 AATTAAAGAATTGCA
1 AATTAAAGAATTACA
*
17346 AACTAAAGA
1 AATTAAAGA
17355 TGGAAAGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.23
Consensus pattern (15 bp):
AATTAAAGAATTACA
Found at i:19635 original size:64 final size:64
Alignment explanation
Indices: 19553--19706 Score: 170
Period size: 64 Copynumber: 2.4 Consensus size: 64
19543 GAAGGTGTAT
* * * *
19553 CGATGCACAGGTAGTGCATCGATGCACTCTTTTAA-AATATAAACATCGAATGCA-ATTAGTGCA
1 CGATGCACAAGCAGTGCATCGATGCACTCTATTAATAATA-AAACATCGAATACATATTA-TGCA
*
19616 T
64 C
* * * *
19617 CGATGCATAAGGCA-TGCATCGATGTATTCTATTAATAATAAAACATCGAATACATTTTATGCAC
1 CGATGCACAA-GCAGTGCATCGATGCACTCTATTAATAATAAAACATCGAATACATATTATGCAC
*
19681 CGATGCACAAGTAGTGCATCGATGCA
1 CGATGCACAAGCAGTGCATCGATGCA
19707 TACCTTCATT
Statistics
Matches: 74, Mismatches: 12, Indels: 8
0.79 0.13 0.09
Matches are distributed among these distances:
63 2 0.03
64 63 0.85
65 9 0.12
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (64 bp):
CGATGCACAAGCAGTGCATCGATGCACTCTATTAATAATAAAACATCGAATACATATTATGCAC
Found at i:20297 original size:15 final size:15
Alignment explanation
Indices: 20233--20291 Score: 109
Period size: 15 Copynumber: 3.9 Consensus size: 15
20223 CGAGGGTATA
20233 ATAGTCCTTCGGGAC
1 ATAGTCCTTCGGGAC
20248 ATAGTCCTTCGGGAC
1 ATAGTCCTTCGGGAC
*
20263 ATATTCCTTCGGGAC
1 ATAGTCCTTCGGGAC
20278 ATAGTCCTTCGGGA
1 ATAGTCCTTCGGGA
20292 TGTAGTGATC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.29
Consensus pattern (15 bp):
ATAGTCCTTCGGGAC
Found at i:25679 original size:2 final size:2
Alignment explanation
Indices: 25672--25696 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25662 TTTATTAATT
25672 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
25697 TTACTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25714 original size:8 final size:8
Alignment explanation
Indices: 25703--25807 Score: 74
Period size: 8 Copynumber: 13.0 Consensus size: 8
25693 ATATTTACTA
25703 TTTTTTA-
1 TTTTTTAT
25710 TTTTTTA-
1 TTTTTTAT
*
25717 TTTATTAT
1 TTTTTTAT
* * *
25725 ATATATAT
1 TTTTTTAT
*
25733 ATTTTTACT
1 TTTTTTA-T
25742 TTTTATTA-
1 TTTT-TTAT
25750 TTTTTTAT
1 TTTTTTAT
25758 TTGTTTTAT
1 TT-TTTTAT
* *
25767 TTATATAT
1 TTTTTTAT
25775 TTTTTCT-T
1 TTTTT-TAT
25783 TTTCTTTAT
1 TTT-TTTAT
25792 TTTTTTAT
1 TTTTTTAT
25800 TTTTTTAT
1 TTTTTTAT
25808 ATTTATTTTA
Statistics
Matches: 78, Mismatches: 12, Indels: 15
0.74 0.11 0.14
Matches are distributed among these distances:
7 16 0.21
8 40 0.51
9 19 0.24
10 3 0.04
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.77
Consensus pattern (8 bp):
TTTTTTAT
Found at i:25722 original size:4 final size:4
Alignment explanation
Indices: 25701--25902 Score: 52
Period size: 4 Copynumber: 51.2 Consensus size: 4
25691 ATATATTTAC
* * *
25701 TATT T-TT TATT T-TT TATT TA-T TATA TATA TATAT T-TT TACT T-TT
1 TATT TATT TATT TATT TATT TATT TATT TATT TAT-T TATT TATT TATT
* * * * *
25745 TA-T TATT T-TT TATT TGTTT TATT TATA TATT TTTT CTTTT TCTT TATT
1 TATT TATT TATT TATT T-ATT TATT TATT TATT TATT -TATT TATT TATT
* * * * * *
25793 TTTT TATT T-TT T-TA TATT TATTT TACT TA-C TATT T-TA TATT TGCTT
1 TATT TATT TATT TATT TATT TA-TT TATT TATT TATT TATT TATT T-ATT
* * * * *
25839 TCTT TATCT TATC T-TT TATT TAATT TGTT T-TT TCTT CATTT TAATTT
1 TATT TAT-T TATT TATT TATT T-ATT TATT TATT TATT TA-TT T-A-TT
25886 TATT TATT TATT TATT T
1 TATT TATT TATT TATT T
25903 CTTACATTTT
Statistics
Matches: 149, Mismatches: 28, Indels: 42
0.68 0.13 0.19
Matches are distributed among these distances:
3 33 0.22
4 85 0.57
5 26 0.17
6 5 0.03
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:25740 original size:40 final size:39
Alignment explanation
Indices: 25682--25834 Score: 157
Period size: 40 Copynumber: 3.8 Consensus size: 39
25672 TATATATATA
*
25682 TATATATATATATATTTACTATTTTTTATTTTTTATTTAT
1 TATATATATATATTTTTACTATTTTTTATTTTTTATTT-T
25722 TATATATATATATTTTTACT-TTTTATTATTTTTTATTTGT
1 TATATATATATATTTTTACTATTTT-TTATTTTTTATTT-T
* * * *
25762 TTTATTTATATATTTTTTCTTTTTCTTTATTTTTTTATTTT
1 TATATATATATATTTTTACTATTT-TTTA-TTTTTTATTTT
* * *
25803 TTTATATTTAT-TTTACTTACTATTTTATATTT
1 TATATATATATATTT--TTACTATTTTTTATTT
25835 GCTTTCTTTA
Statistics
Matches: 97, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
39 4 0.04
40 56 0.58
41 19 0.20
42 18 0.19
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.72
Consensus pattern (39 bp):
TATATATATATATTTTTACTATTTTTTATTTTTTATTTT
Found at i:25790 original size:25 final size:23
Alignment explanation
Indices: 25743--25859 Score: 72
Period size: 23 Copynumber: 4.7 Consensus size: 23
25733 ATTTTTACTT
25743 TTTATTATTTTTTATTTGTTTTA
1 TTTATTATTTTTTATTTGTTTTA
* *
25766 TTTATATATTTTTTCTTTTTCTTTA
1 TTTAT-TATTTTTTATTTGT-TTTA
* *
25791 TTTTTTTATTTTTTTATATTTATTTTA
1 -TTTATTA--TTTTT-TATTTGTTTTA
* * * * *
25818 CTTACTATTTTATATTTGCTTTC
1 TTTATTATTTTTTATTTGTTTTA
*
25841 TTTATCTTATCTTTTATTT
1 TTTA--TTATTTTTTATTT
25860 AATTTGTTTT
Statistics
Matches: 70, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
23 16 0.23
24 16 0.23
25 16 0.23
26 8 0.11
27 9 0.13
28 5 0.07
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.74
Consensus pattern (23 bp):
TTTATTATTTTTTATTTGTTTTA
Found at i:25797 original size:18 final size:18
Alignment explanation
Indices: 25703--25817 Score: 79
Period size: 20 Copynumber: 5.9 Consensus size: 18
25693 ATATTTACTA
*
25703 TTTTTTATTTTTTATTTAT
1 TTTTTTATATTTT-TTTAT
* * *
25722 TATATATATATATTTTTACT
1 T-TTTTTATATTTTTTTA-T
* *
25742 TTTTATTATTTTTTATTTGT
1 TTTT-TTATATTTT-TTTAT
*
25762 TTTATTTATATATTTTTTCT
1 TTT-TTTATAT-TTTTTTAT
25782 TTTTCTT-TATTTTTTTAT
1 TTTT-TTATATTTTTTTAT
25800 TTTTTTATATTTATTTTA
1 TTTTTTATATTT-TTTTA
25818 CTTACTATTT
Statistics
Matches: 75, Mismatches: 12, Indels: 18
0.71 0.11 0.17
Matches are distributed among these distances:
17 2 0.03
18 16 0.21
19 16 0.21
20 34 0.45
21 7 0.09
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.77
Consensus pattern (18 bp):
TTTTTTATATTTTTTTAT
Found at i:25890 original size:31 final size:32
Alignment explanation
Indices: 25852--25912 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
25842 TTATCTTATC
*
25852 TTTTATTTAATTTGTTT-TTTCTT-CATTTTAA
1 TTTTATTT-ATTTATTTATTTCTTACATTTTAA
25883 TTTTATTTATTTATTTATTTCTTACATTTT
1 TTTTATTTATTTATTTATTTCTTACATTTT
25913 TTATATAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 7 0.26
31 14 0.52
32 6 0.22
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.72
Consensus pattern (32 bp):
TTTTATTTATTTATTTATTTCTTACATTTTAA
Found at i:30756 original size:33 final size:33
Alignment explanation
Indices: 30714--30778 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
30704 TTTTTCAAAA
30714 GAAAAAGCTTCAAATTTAAGATTATAATTTGGT
1 GAAAAAGCTTCAAATTTAAGATTATAATTTGGT
*
30747 GAAAAAGCTTCAATTTTAAGATTATAATTTGG
1 GAAAAAGCTTCAAATTTAAGATTATAATTTGG
30779 AGTTGCTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.37
Consensus pattern (33 bp):
GAAAAAGCTTCAAATTTAAGATTATAATTTGGT
Found at i:37169 original size:18 final size:19
Alignment explanation
Indices: 37146--37181 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
37136 ACAATATATT
37146 TAAAAACA-ATAAAATAAA
1 TAAAAACATATAAAATAAA
37164 TAAAAACATATAAAATAA
1 TAAAAACATATAAAATAA
37182 CTGACTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (19 bp):
TAAAAACATATAAAATAAA
Found at i:38441 original size:3 final size:3
Alignment explanation
Indices: 38424--38493 Score: 124
Period size: 3 Copynumber: 23.7 Consensus size: 3
38414 CTTGTAATTT
*
38424 TAA TAA T-A TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
38471 TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
38494 TGAGTAAAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 62 0.97
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:39003 original size:117 final size:116
Alignment explanation
Indices: 38722--39152 Score: 564
Period size: 117 Copynumber: 3.7 Consensus size: 116
38712 TAGAATTATG
* * * *
38722 CAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCATATGAGGAGTTCTTC
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTC
* * * *
38787 TCATTATGAACTTTCTCTGG-AA-GAAATAATCCATCCAGTGATGAATTCAGA-
66 TCATTATGAACTTTC-CTGGCAATG--ATGATCCATCAAATGATGAATTCAAAC
* * * *
38838 TAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTC
*
38903 TCATTATGAACTCTTCCTGGCAATGCTGATCCATCAAATGATGAATTCAAAC
66 TCATTATGAACT-TTCCTGGCAATGATGATCCATCAAATGATGAATTCAAAC
* * * *
38955 CAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTTTTCCTTCTTCAGATGATGAGTTCTTA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTC
* *
39020 TCATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
66 TCATTATGAACT-TTCCTGGCAATGATGATCCATCAAATGATGAATTCAAAC
* * ***
39072 CAAAAAATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTTTTCAT-ATGAGTTCTT
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTC-TTCAGATGATGAGTTCTT
39136 CTCATTATGAACTTTCC
65 CTCATTATGAACTTTCC
39153 GCTGGGGATG
Statistics
Matches: 280, Mismatches: 30, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
116 98 0.35
117 177 0.63
118 5 0.02
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (116 bp):
CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTC
TCATTATGAACTTTCCTGGCAATGATGATCCATCAAATGATGAATTCAAAC
Found at i:39068 original size:233 final size:232
Alignment explanation
Indices: 38722--39152 Score: 593
Period size: 233 Copynumber: 1.8 Consensus size: 232
38712 TAGAATTATG
* *
38722 CAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCATATGAGGAGTTCTTC
1 CAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGGAGTTCTTA
* * * * * **
38787 TCATTATGAACTTTCTCTGGAAGAAATAATCCATCCAGTGATGAATTCAGA-TAAAAGGTTGAAC
66 TCATTATGAACTTACTCTGGAAG-AATAATCCATCAAATGATGAATTCAAACCAAAAAATTGAAC
*
38851 AAATTCTTCTCATTATGAACTTCTTCTTCCTTC-TTCAGATGACGAGTTCTTCTCATTATGAACT
130 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTTCACAT-ACGAGTTCTTCTCATTATGAACT
38915 CTTCCTGGCAATGCTGATCCATCAAATGATGAATTCAAAC
194 -TTCCTGGCAATGCTGATCCATCAAATGATGAATTCAAAC
* *
38955 CAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTT-TTTCCTTCTTCAGATGATGAGTTCTT
1 CAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTT-CTTCTTCAGATGAGGAGTTCTT
* *
39019 ATCATTATGAACTCTAC-CTGGCAATG-TTGATCCATCAAATGATGAATTCAAACCAAAAAATTG
65 ATCATTATGAACT-TACTCTGG-AA-GAATAATCCATCAAATGATGAATTCAAACCAAAAAATTG
* * ** *
39082 AACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTTTTCATATGAGTTCTTCTCATTATGAA
127 AACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTTCACATACGAGTTCTTCTCATTATGAA
39147 CTTTCC
192 CTTTCC
39153 GCTGGGGATG
Statistics
Matches: 173, Mismatches: 19, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
232 3 0.02
233 98 0.57
234 67 0.39
235 5 0.03
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (232 bp):
CAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGGAGTTCTTA
TCATTATGAACTTACTCTGGAAGAATAATCCATCAAATGATGAATTCAAACCAAAAAATTGAACA
AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTTCACATACGAGTTCTTCTCATTATGAACTTT
CCTGGCAATGCTGATCCATCAAATGATGAATTCAAAC
Found at i:39235 original size:95 final size:93
Alignment explanation
Indices: 39129--39304 Score: 253
Period size: 94 Copynumber: 1.9 Consensus size: 93
39119 TTTTCATATG
** * * * *
39129 AGTTCTTCTCATTATGAACTTTCCGCTGGGGATGATGCTCCATCAAGTAATGGATTCATGTAAAA
1 AGTTCTTCTCATTATGAACTTT-CGCTGGAAAAGATGATCCATCAAATAATGGATTCAAGTAAAA
39194 GGTTTGAACAAATTCTTCCTTCTTTAGATT
65 GG-TTGAACAAATTCTTCCTTCTTTAGATT
* * *
39224 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAAGTAAAAG
1 AGTTCTTCTCATTATGAACTTTCGCTGGAAAAGATGATCCATCAAATAATGGATTCAAGTAAAAG
39289 GTTGAACAAATTCTTC
66 GTTGAACAAATTCTTC
39305 TCATTATGAA
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
93 15 0.21
94 35 0.49
95 22 0.31
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.36
Consensus pattern (93 bp):
AGTTCTTCTCATTATGAACTTTCGCTGGAAAAGATGATCCATCAAATAATGGATTCAAGTAAAAG
GTTGAACAAATTCTTCCTTCTTTAGATT
Found at i:39326 original size:113 final size:112
Alignment explanation
Indices: 39206--39494 Score: 515
Period size: 113 Copynumber: 2.6 Consensus size: 112
39196 TTTGAACAAA
* *
39206 TTCTTCCTTCTTTAGATTAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAAT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAA-CTGATCCATCAAAT
39271 GATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
65 GATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
39319 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAACTGATCCATCAAAT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG-AAAACTGATCCATCAAAT
*
39384 GATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
65 GATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
*
39432 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAGAAATGATCCATCAA
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA-AACTGATCCATCAA
39495 GTGGATTCGA
Statistics
Matches: 170, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
112 2 0.01
113 164 0.96
114 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.38
Consensus pattern (112 bp):
TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAACTGATCCATCAAATG
ATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
Found at i:40535 original size:82 final size:82
Alignment explanation
Indices: 40237--40785 Score: 892
Period size: 82 Copynumber: 6.7 Consensus size: 82
40227 CCTACTGAAT
** *
40237 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCGAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAACTCAA
40302 TGATTGGTTCTG-CCAAAC
66 TGATT-GTTCTGTCC-AAC
* * *
40320 TAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCTAAACTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCTAAACTCA
40384 ATGATTGGTTCTG-CCAAAC
65 ATGATT-GTTCTGTCC-AAC
* ** *
40403 CAGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCGAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAACTCAA
40468 TGATTGTTCTGTCCAAC
66 TGATTGTTCTGTCCAAC
*
40485 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATCTTCTAAACTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCTAAACTCA
40549 ATGATTGTTCTGTCCAAC
65 ATGATTGTTCTGTCCAAC
*
40567 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATCTTCTAAACTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCTAAACTCA
40631 ATGATTGTTCTGTCCAAC
65 ATGATTGTTCTGTCCAAC
40649 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAACTCAA
40714 TGATTGTTCTGTCCAAC
66 TGATTGTTCTGTCCAAC
40731 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTT
40786 TCATTTAATT
Statistics
Matches: 442, Mismatches: 19, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
81 2 0.00
82 300 0.68
83 138 0.31
84 2 0.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (82 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAACTCAA
TGATTGTTCTGTCCAAC
Found at i:41588 original size:16 final size:18
Alignment explanation
Indices: 41548--41593 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
41538 ATCATAGAAG
*
41548 AATAAATTGAATTTCCCAA
1 AATAAATTGAATCTCCC-A
41567 AATAAATTGAATCT-CC-
1 AATAAATTGAATCTCCCA
41583 AATAAATTGAA
1 AATAAATTGAA
41594 CTTGAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 11 0.42
18 2 0.08
19 13 0.50
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (18 bp):
AATAAATTGAATCTCCCA
Found at i:41963 original size:9 final size:8
Alignment explanation
Indices: 41920--42016 Score: 70
Period size: 9 Copynumber: 11.2 Consensus size: 8
41910 CTTGACCCCC
41920 TTTCTTTT
1 TTTCTTTT
41928 TCCTTCTTTT
1 T--TTCTTTT
*
41938 TTCCTCTTT
1 TTTCT-TTT
41947 TTTCTTTT
1 TTTCTTTT
*
41955 TTCTATTTT
1 TT-TCTTTT
*
41964 TCTTCTATTC
1 T-TTCT-TTT
41974 TTTCTTTT
1 TTTCTTTT
* *
41982 TCTATTTT
1 TTTCTTTT
41990 CTTTCTTTT
1 -TTTCTTTT
41999 CTTTC-TTT
1 -TTTCTTTT
42007 TTTCTTTT
1 TTTCTTTT
42015 TT
1 TT
42017 CTTCAAGCAT
Statistics
Matches: 71, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
7 4 0.06
8 25 0.35
9 30 0.42
10 12 0.17
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTCTTTT
Found at i:41964 original size:17 final size:17
Alignment explanation
Indices: 41920--42016 Score: 74
Period size: 17 Copynumber: 5.6 Consensus size: 17
41910 CTTGACCCCC
**
41920 TTTCTTTTTCCTTCTTT
1 TTTCTTTTTTATTCTTT
*
41937 TTTCCTCTTTT-TTCTTT
1 TTT-CTTTTTTATTCTTT
*
41954 TTTCTATTTTTCTTCTATT
1 TTTCT-TTTTTATTCT-TT
*
41973 CTTTCTTTTTCTATT-TTC
1 -TTTCTTTTT-TATTCTTT
*
41991 TTTCTTTTCT-TTCTTT
1 TTTCTTTTTTATTCTTT
42007 TTTCTTTTTT
1 TTTCTTTTTT
42017 CTTCAAGCAT
Statistics
Matches: 65, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
15 2 0.03
16 14 0.22
17 24 0.37
18 10 0.15
19 7 0.11
20 8 0.12
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTCTTTTTTATTCTTT
Found at i:41990 original size:33 final size:33
Alignment explanation
Indices: 41945--42015 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
41935 TTTTTCCTCT
*
41945 TTTTTCTTTTTTCTAT-TTTTC-TTCTATTCTTTC
1 TTTTTCTATTTTCTATCTTTTCTTTCT-TT-TTTC
*
41978 TTTTTCTATTTTCTTTCTTTTCTTTCTTTTTTC
1 TTTTTCTATTTTCTATCTTTTCTTTCTTTTTTC
42011 TTTTT
1 TTTTT
42016 TCTTCAAGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 23 0.68
34 7 0.21
35 4 0.12
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (33 bp):
TTTTTCTATTTTCTATCTTTTCTTTCTTTTTTC
Found at i:42017 original size:27 final size:27
Alignment explanation
Indices: 41919--42019 Score: 111
Period size: 27 Copynumber: 3.8 Consensus size: 27
41909 CCTTGACCCC
* *
41919 CTTTCTTTTTCCTTCTTTT-TTCCTCTTT
1 CTTTCTTTTTTCTT-TTTTCTTTCT-TTT
*
41947 -TTTCTTTTTTCTATTTTTC-TTCTATT
1 CTTTCTTTTTTCT-TTTTTCTTTCTTTT
*
41973 CTTTC-TTTTTCTATTTTCTTTCTTTT
1 CTTTCTTTTTTCTTTTTTCTTTCTTTT
41999 CTTTCTTTTTTCTTTTTTCTT
1 CTTTCTTTTTTCTTTTTTCTT
42020 CAAGCATAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
25 5 0.08
26 20 0.32
27 36 0.58
28 1 0.02
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (27 bp):
CTTTCTTTTTTCTTTTTTCTTTCTTTT
Found at i:53467 original size:18 final size:19
Alignment explanation
Indices: 53444--53479 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
53434 ACAATATATT
53444 TAAAAACA-ATAAAATAAA
1 TAAAAACATATAAAATAAA
53462 TAAAAACATATAAAATAA
1 TAAAAACATATAAAATAA
53480 CTGACTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (19 bp):
TAAAAACATATAAAATAAA
Found at i:54253 original size:15 final size:14
Alignment explanation
Indices: 54230--54270 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
54220 GACAGTAAGC
*
54230 TTCTCTTCTTTCTTT
1 TTCTTTTCTTTC-TT
54245 TTCTTTTCTTTCTT
1 TTCTTTTCTTTCTT
54259 TTCTGTTTCTTT
1 TTCT-TTTCTTT
54271 GTATCTCTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.25
15 18 0.75
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (14 bp):
TTCTTTTCTTTCTT
Found at i:54742 original size:3 final size:3
Alignment explanation
Indices: 54726--54782 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
54716 TGTAATTTTA
*
54726 AAT AAT -AT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
54773 AAT AAT AAT A
1 AAT AAT AAT A
54783 TGAGTAAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:55568 original size:31 final size:31
Alignment explanation
Indices: 55506--55577 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 31
55496 AGTCTTTCTA
* * * *
55506 TTTTGTTAATTAAATCATTTAAATATGTAAG
1 TTTTGTCAATCAAATCACTCAAATATGTAAG
* *
55537 TTTTGTCAATCAAATCACTCAACTATTTAAG
1 TTTTGTCAATCAAATCACTCAAATATGTAAG
* *
55568 TATTGACAAT
1 TTTTGTCAAT
55578 TAAACCACAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (31 bp):
TTTTGTCAATCAAATCACTCAAATATGTAAG
Found at i:57601 original size:3 final size:3
Alignment explanation
Indices: 57593--57884 Score: 494
Period size: 3 Copynumber: 97.3 Consensus size: 3
57583 TGACCTATGT
57593 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
57641 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
57689 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG ACG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
57737 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * * * * *
57785 ACG AAG ACG ACG AAG ACG ACG AAG AAG AAG AAG AAG AAG AAG AAG ACG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * *
57833 ACG AAG ACG AAG ACG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
57881 AAG A
1 AAG A
57885 CATGTATTTT
Statistics
Matches: 275, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 275 1.00
ACGTcount: A:0.63, C:0.03, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:59213 original size:2 final size:2
Alignment explanation
Indices: 59206--59240 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
59196 TATTAACATC
*
59206 AG AG AG AG AG AG AC AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
59241 ATACCATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:59852 original size:20 final size:20
Alignment explanation
Indices: 59804--59852 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
59794 TAAGTAATTG
*
59804 TTTTTATTGAATAAAAATAT
1 TTTTTATTTAATAAAAATAT
59824 TTTTTATTTAATAAAAATAT
1 TTTTTATTTAATAAAAATAT
59844 TTTTTATTT
1 TTTTTATTT
59853 CAGGTCGGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTTATTTAATAAAAATAT
Found at i:64505 original size:24 final size:24
Alignment explanation
Indices: 64475--64530 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
64465 TAGAAATTCG
64475 ATTGAAGCATAAAATTTGAACTCA
1 ATTGAAGCATAAAATTTGAACTCA
* * *
64499 ATTGAAGCCTAAAGTTTGAGCTCA
1 ATTGAAGCATAAAATTTGAACTCA
64523 ATTGAAGC
1 ATTGAAGC
64531 GAAAGAATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (24 bp):
ATTGAAGCATAAAATTTGAACTCA
Found at i:70049 original size:14 final size:14
Alignment explanation
Indices: 70030--70059 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
70020 AGCTATGGTT
70030 GATAGGACCGTAGG
1 GATAGGACCGTAGG
*
70044 GATAGGACTGTAGG
1 GATAGGACCGTAGG
70058 GA
1 GA
70060 CAGACGTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.10, G:0.43, T:0.17
Consensus pattern (14 bp):
GATAGGACCGTAGG
Found at i:72257 original size:205 final size:205
Alignment explanation
Indices: 71905--72317 Score: 826
Period size: 205 Copynumber: 2.0 Consensus size: 205
71895 TTGACTTTTT
71905 TAATTTTAGAAAAATATTAATTTATTCATTTTTACATTCTTTAAATATAATTGAAACTTTCTGAC
1 TAATTTTAGAAAAATATTAATTTATTCATTTTTACATTCTTTAAATATAATTGAAACTTTCTGAC
71970 GCTCAAAATCCGATCAAAATATACCAACACCACTTGGTTAAGTGGGATGAACATTAGATCTCTTA
66 GCTCAAAATCCGATCAAAATATACCAACACCACTTGGTTAAGTGGGATGAACATTAGATCTCTTA
72035 AACAAGGTTAGAGGTGCAAATCCTAGTGATTGAGAAGTGAGCAAACTGAGTTGGGAGTCGCCCTT
131 AACAAGGTTAGAGGTGCAAATCCTAGTGATTGAGAAGTGAGCAAACTGAGTTGGGAGTCGCCCTT
72100 ACCTCTATTG
196 ACCTCTATTG
72110 TAATTTTAGAAAAATATTAATTTATTCATTTTTACATTCTTTAAATATAATTGAAACTTTCTGAC
1 TAATTTTAGAAAAATATTAATTTATTCATTTTTACATTCTTTAAATATAATTGAAACTTTCTGAC
72175 GCTCAAAATCCGATCAAAATATACCAACACCACTTGGTTAAGTGGGATGAACATTAGATCTCTTA
66 GCTCAAAATCCGATCAAAATATACCAACACCACTTGGTTAAGTGGGATGAACATTAGATCTCTTA
72240 AACAAGGTTAGAGGTGCAAATCCTAGTGATTGAGAAGTGAGCAAACTGAGTTGGGAGTCGCCCTT
131 AACAAGGTTAGAGGTGCAAATCCTAGTGATTGAGAAGTGAGCAAACTGAGTTGGGAGTCGCCCTT
72305 ACCTCTATTG
196 ACCTCTATTG
72315 TAA
1 TAA
72318 CCCCTTACCT
Statistics
Matches: 208, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
205 208 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (205 bp):
TAATTTTAGAAAAATATTAATTTATTCATTTTTACATTCTTTAAATATAATTGAAACTTTCTGAC
GCTCAAAATCCGATCAAAATATACCAACACCACTTGGTTAAGTGGGATGAACATTAGATCTCTTA
AACAAGGTTAGAGGTGCAAATCCTAGTGATTGAGAAGTGAGCAAACTGAGTTGGGAGTCGCCCTT
ACCTCTATTG
Found at i:72324 original size:19 final size:19
Alignment explanation
Indices: 72300--72337 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
72290 TTGGGAGTCG
72300 CCCTTACCTCTATTGTAAC
1 CCCTTACCTCTATTGTAAC
72319 CCCTTACCTCTATTGTAAC
1 CCCTTACCTCTATTGTAAC
72338 ATCCTCAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.37, G:0.05, T:0.37
Consensus pattern (19 bp):
CCCTTACCTCTATTGTAAC
Found at i:73116 original size:20 final size:20
Alignment explanation
Indices: 73091--73144 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
73081 CAATTTTGAA
73091 GGTGCATCGATGCATTAAGG
1 GGTGCATCGATGCATTAAGG
73111 GGTGCATCGATGCATTAAGG
1 GGTGCATCGATGCATTAAGG
73131 GGTGCATCGATGCA
1 GGTGCATCGATGCA
73145 CGGAAATTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.24, C:0.17, G:0.35, T:0.24
Consensus pattern (20 bp):
GGTGCATCGATGCATTAAGG
Found at i:74028 original size:30 final size:29
Alignment explanation
Indices: 73965--74028 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 29
73955 GAAATGACAT
** * *
73965 ATGTTACATGATATAAACCTATGTGATAT
1 ATGTTACATGATATAAACCTATGACACAG
73994 ATGTTACATGATATGAAACCTATGACACAG
1 ATGTTACATGATAT-AAACCTATGACACAG
74024 ATGTT
1 ATGTT
74029 TACACATGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 14 0.47
30 16 0.53
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (29 bp):
ATGTTACATGATATAAACCTATGACACAG
Found at i:79609 original size:27 final size:27
Alignment explanation
Indices: 79546--79609 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
79536 TTATTTTTAT
*
79546 ATATTTAAATTAAAAAAATAAATTCAA
1 ATATCTAAATTAAAAAAATAAATTCAA
*
79573 ATATCT-AATTAAATAAAA-AAATTACAG
1 ATATCTAAATTAAA-AAAATAAATT-CAA
79600 ATA-CTAAATT
1 ATATCTAAATT
79610 TAACTACAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 14 0.44
27 18 0.56
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (27 bp):
ATATCTAAATTAAAAAAATAAATTCAA
Found at i:89660 original size:31 final size:31
Alignment explanation
Indices: 89601--89662 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
89591 TAGAAAATGA
* *
89601 TACGTGACGTTATTGATCCATCCGATTTAAG
1 TACGTAACGTTATTGATCCATCCAATTTAAG
* *
89632 TACGTAACGTTATTGATCTATCTAATTTAAG
1 TACGTAACGTTATTGATCCATCCAATTTAAG
89663 ATCATCCGCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (31 bp):
TACGTAACGTTATTGATCCATCCAATTTAAG
Found at i:90977 original size:24 final size:23
Alignment explanation
Indices: 90929--90976 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
90919 CATATTTTTT
90929 AATTTTTCAAAAGTAAAAAATAA
1 AATTTTTCAAAAGTAAAAAATAA
90952 AATTTATTCAAAAGT-AAAAATAA
1 AATTT-TTCAAAAGTAAAAAATAA
90975 AA
1 AA
90977 AATATTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.29
Consensus pattern (23 bp):
AATTTTTCAAAAGTAAAAAATAA
Found at i:90982 original size:23 final size:24
Alignment explanation
Indices: 90934--90982 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
90924 TTTTTAATTT
**
90934 TTCAAAAGTAAAAAATAAAATTTA
1 TTCAAAAGTAAAAAATAAAAAATA
90958 TTCAAAAGT-AAAAATAAAAAATA
1 TTCAAAAGTAAAAAATAAAAAATA
90981 TT
1 TT
90983 TTCTAGAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (24 bp):
TTCAAAAGTAAAAAATAAAAAATA
Done.