Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007519.1 Hibiscus syriacus cultivar Beakdansim tig00020947_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: 87730
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:955 original size:51 final size:51
Alignment explanation
Indices: 838--938 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
828 TCACATGATG
* ** *
838 GTGGCAGGAGTAGCTGGTGCTTCACGTGGGTGATGTAGCTGCAGTATGGTA
1 GTGGCAGGAGTAGTTGGTGCTTCACGTGGGTGATGTAGCTGCAACAGGGTA
*
889 GTGGCAGGAGTAGTTGGTGCTTCACGTGGGTGATGTAGCTGCAACCGGGT
1 GTGGCAGGAGTAGTTGGTGCTTCACGTGGGTGATGTAGCTGCAACAGGGT
939 CTGGGTCGGG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.17, C:0.15, G:0.42, T:0.27
Consensus pattern (51 bp):
GTGGCAGGAGTAGTTGGTGCTTCACGTGGGTGATGTAGCTGCAACAGGGTA
Found at i:1145 original size:3 final size:3
Alignment explanation
Indices: 1137--1185 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
1127 AACAAAACAA
*
1137 AAT AAT AAT AAT AAT AAT AAT AAAT AAT GAT AAT AAT AA- AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT
1181 AAT AA
1 AAT AA
1186 AAATGGGTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1183 original size:22 final size:22
Alignment explanation
Indices: 1130--1185 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
1120 TCCTACAAAC
*
1130 AAAACAAAATAATAATAATAAT
1 AAAATAAAATAATAATAATAAT
*
1152 AATAAT-AAATAATGATAATAAT
1 AA-AATAAAATAATAATAATAAT
1174 AAAATAAAATAA
1 AAAATAAAATAA
1186 AAATGGGTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 3 0.10
22 25 0.83
23 2 0.07
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (22 bp):
AAAATAAAATAATAATAATAAT
Found at i:4823 original size:21 final size:21
Alignment explanation
Indices: 4797--4859 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
4787 TGAGGGTTCC
*
4797 ATGTGGTCTTTCGGGATAAAT
1 ATGTGGTCTTTCGGGACAAAT
*
4818 ATGTGGTTTTTCGGGACAAAT
1 ATGTGGTCTTTCGGGACAAAT
*
4839 ATGTGGTCCTTCGGGACAAAT
1 ATGTGGTCTTTCGGGACAAAT
4860 TCTATGTTCC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.24, C:0.13, G:0.29, T:0.35
Consensus pattern (21 bp):
ATGTGGTCTTTCGGGACAAAT
Found at i:10110 original size:27 final size:28
Alignment explanation
Indices: 10055--10111 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
10045 GTTCCCCAAC
10055 TCTGAATGTTCCTATTAAACTGAAATCT
1 TCTGAATGTTCCTATTAAACTGAAATCT
* *
10083 TCTGAATGTTCCTA-TGAACTGGAATCT
1 TCTGAATGTTCCTATTAAACTGAAATCT
10110 TC
1 TC
10112 ATGTCTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 13 0.48
28 14 0.52
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (28 bp):
TCTGAATGTTCCTATTAAACTGAAATCT
Found at i:11936 original size:21 final size:21
Alignment explanation
Indices: 11907--11980 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
11897 GCGCTGCATT
11907 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
11928 TCGCATTGCGAT-TTTCTATT
1 TCGCGTTGCGATAGTTGAAAA
11948 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
11969 TCGCGTTACGAT
1 TCGCGTTGCGAT
11981 TTTCCTTTTC
Statistics
Matches: 39, Mismatches: 13, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 14 0.36
21 25 0.64
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:11949 original size:41 final size:41
Alignment explanation
Indices: 11903--12103 Score: 266
Period size: 41 Copynumber: 4.9 Consensus size: 41
11893 ATTCGCGCTG
*
11903 CATTTCGCGTTGCGATAGTTGAAAATCGCATTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
11944 TATTTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* * *
11985 CTTTTCGCGTTGCGATAGTCT-ACAGT-GTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTC
* *
12026 CATTTCGCGTTGCGATAGTCT-ACAGT-GTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTC
12067 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
12104 AGTGTACAGT
Statistics
Matches: 145, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
40 2 0.01
41 141 0.97
42 2 0.01
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:11956 original size:20 final size:20
Alignment explanation
Indices: 11928--12082 Score: 82
Period size: 20 Copynumber: 7.6 Consensus size: 20
11918 TAGTTGAAAA
*
11928 TCGCATTGCGATTTTCTATT
1 TCGCGTTGCGATTTTCTATT
* ** **
11948 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCTATT
*
11969 TCGCGTTACGATTTTCCT-TT
1 TCGCGTTGCGATTTT-CTATT
** **
11989 TCGCGTTGCGATAGTCTACAG
1 TCGCGTTGCGATTTTCTA-TT
*
12010 T-GTCGTTGCGATTTTCCATT
1 TCG-CGTTGCGATTTTCTATT
** **
12030 TCGCGTTGCGATAGTCTACAG
1 TCGCGTTGCGATTTTCTA-TT
*
12051 T-GTCGTTGCGATTTTCCATT
1 TCG-CGTTGCGATTTTCTATT
12071 TCGCGTTGCGAT
1 TCGCGTTGCGAT
12083 AGTTGAAAAT
Statistics
Matches: 94, Mismatches: 32, Indels: 18
0.65 0.22 0.12
Matches are distributed among these distances:
19 2 0.02
20 50 0.53
21 42 0.45
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCTATT
Found at i:12016 original size:21 final size:21
Alignment explanation
Indices: 11992--12125 Score: 77
Period size: 21 Copynumber: 6.5 Consensus size: 21
11982 TTCCTTTTCG
11992 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * *
12013 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
12031 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
* * *
12054 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
* *
12072 CGCGTTGCGATAGT-TGAAAATCG-
1 --CGTTGCGATAGTCT-ACAGT-GT
*
12095 CGTTGCGATAGTGTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
12116 CGTTGCGATA
1 CGTTGCGATA
12126 ATTTTCTCTA
Statistics
Matches: 85, Mismatches: 14, Indels: 28
0.67 0.11 0.22
Matches are distributed among these distances:
18 4 0.05
19 8 0.09
20 19 0.22
21 44 0.52
22 7 0.08
23 3 0.04
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:12187 original size:6 final size:6
Alignment explanation
Indices: 12176--12238 Score: 126
Period size: 6 Copynumber: 10.5 Consensus size: 6
12166 GACACGTATT
12176 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
12224 ACCACG ACCACG ACC
1 ACCACG ACCACG ACC
12239 CGAGACGAGA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:12745 original size:6 final size:6
Alignment explanation
Indices: 12734--12826 Score: 186
Period size: 6 Copynumber: 15.5 Consensus size: 6
12724 TCTCGTCTCG
12734 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
12782 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
12827 AATACGTGTC
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 87 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:14076 original size:6 final size:6
Alignment explanation
Indices: 14065--14116 Score: 104
Period size: 6 Copynumber: 8.7 Consensus size: 6
14055 TAACCATGGG
14065 GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT
1 GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT
14113 GTTT
1 GTTT
14117 CGTACATGGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (6 bp):
GTTTTT
Found at i:15691 original size:118 final size:120
Alignment explanation
Indices: 15548--15791 Score: 429
Period size: 118 Copynumber: 2.0 Consensus size: 120
15538 AGATGCAGAC
* *
15548 ATAAAAGACAAAAAAAGTACTACTTTTGTCTCATAAAATTTGTCTCTTACTAATTTTTTATGATC
1 ATAAAAGACAAAAAAAGTACTACTTTTGTCTCATAAAATTTGTCACTTACTAATTTTTTATGATA
*
15613 ATTTTTATTTTTATTTATTATTATTTAAAAATCATTTTTGAT-AAAAATATATAA
66 ATTTTTATTTTTATTTATTATTATTTAAAAATCATTTTTGATAAAAAAAATATAA
15667 ATAAAAGAC-AAAAAAGTACTACTTTTGTCTCATAAAATTTGTCACTTACTAATTTTTTATGATA
1 ATAAAAGACAAAAAAAGTACTACTTTTGTCTCATAAAATTTGTCACTTACTAATTTTTTATGATA
* *
15731 ATTTTTATTTTTATTTATTATTATTTAAAAATCCTTTTTGATAAAAAAAATATAT
66 ATTTTTATTTTTATTTATTATTATTTAAAAATCATTTTTGATAAAAAAAATATAA
15786 ATAAAA
1 ATAAAA
15792 ATATTTAAAA
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
118 94 0.79
119 25 0.21
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (120 bp):
ATAAAAGACAAAAAAAGTACTACTTTTGTCTCATAAAATTTGTCACTTACTAATTTTTTATGATA
ATTTTTATTTTTATTTATTATTATTTAAAAATCATTTTTGATAAAAAAAATATAA
Found at i:18721 original size:17 final size:17
Alignment explanation
Indices: 18701--18734 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
18691 TCTTGACATT
18701 TAAGAAATAGGACTGTA
1 TAAGAAATAGGACTGTA
18718 TAAGAAATAGGACTGTA
1 TAAGAAATAGGACTGTA
18735 GTAATTGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.24, T:0.24
Consensus pattern (17 bp):
TAAGAAATAGGACTGTA
Found at i:22418 original size:16 final size:16
Alignment explanation
Indices: 22393--22447 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
22383 TAATAAGTTG
22393 TTAT-AAAAATTAAAAT
1 TTATAAAAAATT-AAAT
22409 TT-TAAAAAATTAAAT
1 TTATAAAAAATTAAAT
*
22424 TTATAAAAGA--AAA-
1 TTATAAAAAATTAAAT
22437 TTATAAAAAAT
1 TTATAAAAAAT
22448 CTGGTAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
13 9 0.26
14 3 0.09
15 7 0.21
16 15 0.44
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
TTATAAAAAATTAAAT
Found at i:22446 original size:15 final size:15
Alignment explanation
Indices: 22393--22447 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
22383 TAATAAGTTG
*
22393 TTATAAAAATTAAAA
1 TTATAAAAAATAAAA
* *
22408 TTTTAAAAAATTAAA
1 TTATAAAAAATAAAA
* *
22423 TT-TATAAAAGAAAA
1 TTATAAAAAATAAAA
22437 TTATAAAAAAT
1 TTATAAAAAAT
22448 CTGGTAATTT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
14 11 0.35
15 20 0.65
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
TTATAAAAAATAAAA
Found at i:27696 original size:35 final size:31
Alignment explanation
Indices: 27619--27699 Score: 81
Period size: 35 Copynumber: 2.5 Consensus size: 31
27609 TATATATATA
* *
27619 TATTTTTTTCATTTTAGTTTATCTTATTTTT
1 TATTTTTTTTATTTTAGTTTATCTCATTTTT
***
27650 TATTCGATTTATTTAATAGTTTTATCATCATTTTT
1 TATTTTTTTTATTT--TAG-TTTATC-TCATTTTT
27685 TATTTTTTTTATTTT
1 TATTTTTTTTATTTT
27700 TTTTTAATTA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
31 10 0.26
33 4 0.11
34 6 0.16
35 18 0.47
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.70
Consensus pattern (31 bp):
TATTTTTTTTATTTTAGTTTATCTCATTTTT
Found at i:27717 original size:4 final size:4
Alignment explanation
Indices: 27679--27763 Score: 52
Period size: 4 Copynumber: 21.0 Consensus size: 4
27669 TTTTATCATC
* * * *
27679 ATTT -TTT ATTTT TTTT ATTT -TTT -TTT AATTA ATTT ATTT ATTC CTTT
1 ATTT ATTT A-TTT ATTT ATTT ATTT ATTT -ATTT ATTT ATTT ATTT ATTT
*
27726 CATTT GATTT ATTT A-GT ATTTT ATTT ATTT ATTT ATTT
1 -ATTT -ATTT ATTT ATTT A-TTT ATTT ATTT ATTT ATTT
27764 CTTCTAACAT
Statistics
Matches: 63, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
3 11 0.17
4 38 0.60
5 14 0.22
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:39420 original size:65 final size:65
Alignment explanation
Indices: 39270--39580 Score: 507
Period size: 65 Copynumber: 4.8 Consensus size: 65
39260 GTGCCACTCA
*
39270 AGACAACACAAGTTCAACTTCACGACGAAGGGGCCGCTGGTTGTCAAC-AAAATTTCCCAGTATC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTATC
* *
39334 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCTCAGTGTC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTATC
* * * *
39399 AGACAACACAAGTTCAACTTCACGACGAAGGGGCCGCTGGTTGTCGACGAAAATTTCTCAGTATC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTATC
* *
39464 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTTA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTATC
* * *
39529 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCACTGGCTGTCAACAAAA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAA
39581 GACTTCCCCA
Statistics
Matches: 230, Mismatches: 16, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
64 47 0.20
65 183 0.80
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (65 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTATC
Found at i:39611 original size:194 final size:193
Alignment explanation
Indices: 39270--39623 Score: 534
Period size: 194 Copynumber: 1.8 Consensus size: 193
39260 GTGCCACTCA
* *
39270 AGACAACACAAGTTCAACTTCACGACGAAGGGGCCGCTGGTTGTCAACAAAATTTCCCAGTATCA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAATTTCCCAGTATAA
* * * * *
39335 GACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCTCAGTGTCA
66 GACAACACAAGTTCAACTTCACAACGAAGGGGCCACTGGCTGTCAACAAAAATTCCCCAATGTCA
39400 GACAACACAAGTTCAACTTCAC-GACGAAGGGGCCGCTGGTTGTCGACGAAAATTTCTCAGTATC
131 GA-AACACAAGTTCAACTTCACAG-CGAAGGGGCCGCTGGTTGTCGACGAAAATTTCTCAGTATC
*
39464 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTTA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAAC-AAAATTTCCCAGTATA
* *
39529 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCACTGGCTGTCAACAAAAGACTTCCCCAATT
65 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCACTGGCTGTCAACAAAA-A-TTCCCCAATG
* *
39594 TCAG-AGC-CAATTTCAACTTCACAGCGAAGG
128 TCAGAAACACAAGTTCAACTTCACAGCGAAGG
39624 ATATTGGACT
Statistics
Matches: 144, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
194 67 0.47
195 66 0.46
196 1 0.01
197 10 0.07
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (193 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAATTTCCCAGTATAA
GACAACACAAGTTCAACTTCACAACGAAGGGGCCACTGGCTGTCAACAAAAATTCCCCAATGTCA
GAAACACAAGTTCAACTTCACAGCGAAGGGGCCGCTGGTTGTCGACGAAAATTTCTCAGTATC
Found at i:41955 original size:4 final size:4
Alignment explanation
Indices: 41937--42019 Score: 62
Period size: 4 Copynumber: 20.0 Consensus size: 4
41927 TTTTATCATC
* * * *
41937 ATTT -TTT ATTTT ATTT ATTT TTTT AATTA ATTT ATTT ATTC CTTT CATTT
1 ATTT ATTT A-TTT ATTT ATTT ATTT -ATTT ATTT ATTT ATTT ATTT -ATTT
*
41987 GATTT ATTT A-GT ATTTT ATTT ATTT ATTT ATTT
1 -ATTT ATTT ATTT A-TTT ATTT ATTT ATTT ATTT
42020 TTTCTAACAT
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
3 5 0.08
4 42 0.68
5 15 0.24
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:41960 original size:17 final size:17
Alignment explanation
Indices: 41938--42020 Score: 67
Period size: 17 Copynumber: 4.6 Consensus size: 17
41928 TTTATCATCA
41938 TTTTTTATTTTATTTAT
1 TTTTTTATTTTATTTAT
* *
41955 TTTTTTAATTAATTTAT
1 TTTTTTATTTTATTTAT
* ** *
41972 TTATTCCTTTCATTTGAT
1 TTTTTTATTTTATTT-AT
41990 TTATTTAGTATTTTATTTAT
1 TT-TTT--TATTTTATTTAT
*
42010 TTATTTATTTT
1 TTTTTTATTTT
42021 TTCTAACATT
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
17 31 0.62
18 4 0.08
19 4 0.08
20 4 0.08
21 7 0.14
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (17 bp):
TTTTTTATTTTATTTAT
Found at i:50493 original size:14 final size:14
Alignment explanation
Indices: 50471--50553 Score: 121
Period size: 14 Copynumber: 5.9 Consensus size: 14
50461 TCGGTAATAT
*
50471 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
50485 GTTCATTTATGTTC
1 GTTCATTTATGTTC
**
50499 GTTTGTTTATGTTC
1 GTTCATTTATGTTC
50513 GTTCATTTATGTTC
1 GTTCATTTATGTTC
**
50527 GTTTGTTTATGTTC
1 GTTCATTTATGTTC
50541 GTTCATTTATGTT
1 GTTCATTTATGTT
50554 TAACACAATC
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 60 1.00
ACGTcount: A:0.11, C:0.11, G:0.18, T:0.60
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:50507 original size:28 final size:28
Alignment explanation
Indices: 50475--50553 Score: 158
Period size: 28 Copynumber: 2.8 Consensus size: 28
50465 TAATATGTTC
50475 GTTTATGTTCGTTCATTTATGTTCGTTT
1 GTTTATGTTCGTTCATTTATGTTCGTTT
50503 GTTTATGTTCGTTCATTTATGTTCGTTT
1 GTTTATGTTCGTTCATTTATGTTCGTTT
50531 GTTTATGTTCGTTCATTTATGTT
1 GTTTATGTTCGTTCATTTATGTT
50554 TAACACAATC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.11, C:0.10, G:0.18, T:0.61
Consensus pattern (28 bp):
GTTTATGTTCGTTCATTTATGTTCGTTT
Found at i:50747 original size:20 final size:20
Alignment explanation
Indices: 50710--50747 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
50700 AGGAAAGAAA
* *
50710 TTCATTTATGTTCGTTTACG
1 TTCATTTATGATCATTTACG
50730 TTCATTTATGATCATTTA
1 TTCATTTATGATCATTTA
50748 TTGTGTTCGT
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:0.13, G:0.11, T:0.55
Consensus pattern (20 bp):
TTCATTTATGATCATTTACG
Found at i:50748 original size:10 final size:10
Alignment explanation
Indices: 50710--50748 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
50700 AGGAAAGAAA
50710 TTCATTTATG
1 TTCATTTATG
* *
50720 TTCGTTTACG
1 TTCATTTATG
50730 TTCATTTATG
1 TTCATTTATG
*
50740 ATCATTTAT
1 TTCATTTAT
50749 TGTGTTCGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.21, C:0.13, G:0.10, T:0.56
Consensus pattern (10 bp):
TTCATTTATG
Found at i:53883 original size:10 final size:10
Alignment explanation
Indices: 53868--53959 Score: 50
Period size: 10 Copynumber: 9.2 Consensus size: 10
53858 AATACAAATG
53868 AACGAACATA
1 AACGAACATA
53878 AACGAACAAAATA
1 AACGAAC---ATA
*
53891 AACGAACGTA
1 AACGAACATA
*
53901 AACGAACAAA
1 AACGAACATA
*
53911 AAC-AA-ACA
1 AACGAACATA
* *
53919 AACG-TCAATG
1 AACGAAC-ATA
53929 AAC--ACAATA
1 AACGAAC-ATA
*
53938 AATGAACATA
1 AACGAACATA
53948 AACGAACATA
1 AACGAACATA
53958 AA
1 AA
53960 TGAAAATATA
Statistics
Matches: 63, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
8 5 0.08
9 8 0.13
10 38 0.60
11 2 0.03
13 10 0.16
ACGTcount: A:0.62, C:0.18, G:0.10, T:0.10
Consensus pattern (10 bp):
AACGAACATA
Found at i:53894 original size:23 final size:23
Alignment explanation
Indices: 53851--53960 Score: 103
Period size: 23 Copynumber: 4.7 Consensus size: 23
53841 CATTTAAATG
* *
53851 ATAAACGAATACAAATGAACGAAC
1 ATAAACGAACA-AAATAAACGAAC
53875 ATAAACGAACAAAATAAACGAAC
1 ATAAACGAACAAAATAAACGAAC
* * *
53898 GTAAACGAACAAAAACAAACAAAC
1 ATAAACGAAC-AAAATAAACGAAC
* * * * *
53922 GTCAATGAACACAATAAATGAAC
1 ATAAACGAACAAAATAAACGAAC
53945 ATAAACGAACATAAAT
1 ATAAACGAACA-AAAT
53961 GAAAATATAT
Statistics
Matches: 69, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
23 37 0.54
24 32 0.46
ACGTcount: A:0.61, C:0.17, G:0.10, T:0.12
Consensus pattern (23 bp):
ATAAACGAACAAAATAAACGAAC
Found at i:54161 original size:14 final size:14
Alignment explanation
Indices: 54144--54176 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
54134 AAATAAACAC
54144 ACATAAACGAACGA
1 ACATAAACGAACGA
*
54158 ACATAAATGAACGA
1 ACATAAACGAACGA
54172 ACATA
1 ACATA
54177 TTACTGAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.58, C:0.18, G:0.12, T:0.12
Consensus pattern (14 bp):
ACATAAACGAACGA
Found at i:55515 original size:20 final size:22
Alignment explanation
Indices: 55473--55517 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
55463 ATTAAAGAAA
*
55473 TGACACCACTTTCAAAAATAAT
1 TGACACCACTTTCAAAAAAAAT
55495 TGACACC-CTTT-AAAAAAAAT
1 TGACACCACTTTCAAAAAAAAT
55515 TGA
1 TGA
55518 TCCCACATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.50
21 4 0.18
22 7 0.32
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.27
Consensus pattern (22 bp):
TGACACCACTTTCAAAAAAAAT
Found at i:58228 original size:22 final size:23
Alignment explanation
Indices: 58198--58247 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
58188 CGATACCGGT
*
58198 AGGG-AGTATCGGTACCATAG-A
1 AGGGTAGTATCGATACCATAGTA
*
58219 AGGGTAGTATCGATACCATGGTA
1 AGGGTAGTATCGATACCATAGTA
58242 AGGGTA
1 AGGGTA
58248 TCGATACCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 4 0.16
22 14 0.56
23 7 0.28
ACGTcount: A:0.32, C:0.12, G:0.34, T:0.22
Consensus pattern (23 bp):
AGGGTAGTATCGATACCATAGTA
Found at i:58280 original size:95 final size:97
Alignment explanation
Indices: 58120--58312 Score: 243
Period size: 95 Copynumber: 2.0 Consensus size: 97
58110 TATCGATACC
* * **
58120 GAAGAGGTGGTATCGATACCATGATGAAGGGTATCGATACTTAGAAACATCGAATTTAATTTTGG
1 GAAGAGGTAGTATCGATACCATGATGAAGGGTATCGATACTCAGAAACATCGAACCTAATTTTGG
*
58185 TATCGATA-CCGGTAGGGAGTATCGGTACCATA
66 TATCGATATCC-GAAGGGAGTATCGGTACCATA
* *
58217 GAAG-GGTAGTATCGATACCATGGT-AAGGGTATCGATAC-CAGGCAACATCGAACCT-ATTATT
1 GAAGAGGTAGTATCGATACCATGATGAAGGGTATCGATACTCA-GAAACATCGAACCTAATT-TT
* *
58278 GGTATCGATATCCGAAGGGGGTATCGTTACCATA
64 GGTATCGATATCCGAAGGGAGTATCGGTACCATA
58312 G
1 G
58313 TATAGAAGTA
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
94 4 0.05
95 56 0.67
96 20 0.24
97 4 0.05
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (97 bp):
GAAGAGGTAGTATCGATACCATGATGAAGGGTATCGATACTCAGAAACATCGAACCTAATTTTGG
TATCGATATCCGAAGGGAGTATCGGTACCATA
Found at i:58764 original size:55 final size:55
Alignment explanation
Indices: 58678--59067 Score: 496
Period size: 55 Copynumber: 7.1 Consensus size: 55
58668 ATGTGTACTG
* *
58678 AGGCACTTCGTGTGCATAATCATGGAATTCATCCTGAGTGGATGAATCACCGTAC
1 AGGCACTTTGTGTGCATAATCACGGAATTCATCCTGAGTGGATGAATCACCGTAC
* *
58733 ATGCACTTTGTGTGCATAATCACGGAATTCATCCTGAGTGGATGAATCACCATAC
1 AGGCACTTTGTGTGCATAATCACGGAATTCATCCTGAGTGGATGAATCACCGTAC
* * * *
58788 ATGCACTTTGTGTGAATAAACACGGAATTCATCATGAGTGGAT-AATCACCGTAC
1 AGGCACTTTGTGTGCATAATCACGGAATTCATCCTGAGTGGATGAATCACCGTAC
* *
58842 AGGCACTTCGTGTGCATAATCACAGAATTCATCCTGAGTGGATGAATCACCGTAC
1 AGGCACTTTGTGTGCATAATCACGGAATTCATCCTGAGTGGATGAATCACCGTAC
* * * * *
58897 ATGAACTTTGTGTGCACAATCATGGAATTCATCCTGAGTGGATGAATCATCGTAC
1 AGGCACTTTGTGTGCATAATCACGGAATTCATCCTGAGTGGATGAATCACCGTAC
* * * * *
58952 AGGCACTTCGTGTGCATATTCACGAAATTCATCTTGGGTGGATGAATCACCGTAC
1 AGGCACTTTGTGTGCATAATCACGGAATTCATCCTGAGTGGATGAATCACCGTAC
* ** ** * * ** *
59007 AGGCACTATGTGTGCA-ACCCACATAATTCATCATGAGTTGATGAATTTCCGTAT
1 AGGCACTTTGTGTGCATAATCACGGAATTCATCCTGAGTGGATGAATCACCGTAC
59061 AGGCACT
1 AGGCACT
59068 AAATGTATAT
Statistics
Matches: 291, Mismatches: 43, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
54 82 0.28
55 209 0.72
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (55 bp):
AGGCACTTTGTGTGCATAATCACGGAATTCATCCTGAGTGGATGAATCACCGTAC
Found at i:58782 original size:27 final size:27
Alignment explanation
Indices: 58695--58782 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 27
58685 TCGTGTGCAT
*
58695 AATCATGGAATTCATCCTGAGTGGATG
1 AATCACGGAATTCATCCTGAGTGGATG
* * * * *
58722 AATCACCGTACATGCA-CTTTGTGTGCAT-
1 AATCA-CGGA-ATTCATC-CTGAGTGGATG
58750 AATCACGGAATTCATCCTGAGTGGATG
1 AATCACGGAATTCATCCTGAGTGGATG
58777 AATCAC
1 AATCAC
58783 CATACATGCA
Statistics
Matches: 45, Mismatches: 11, Indels: 10
0.68 0.17 0.15
Matches are distributed among these distances:
26 11 0.24
27 15 0.33
28 8 0.18
29 11 0.24
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (27 bp):
AATCACGGAATTCATCCTGAGTGGATG
Found at i:58983 original size:164 final size:165
Alignment explanation
Indices: 58678--59052 Score: 540
Period size: 164 Copynumber: 2.3 Consensus size: 165
58668 ATGTGTACTG
** *
58678 AGGCACTTCGTGTGCATAATCATGGAATTCATCCTGAGTGGATGAATCACCGTACATGCACTTTG
1 AGGCACTTCGTGTGCATAATCACAGAATTCATCCTGAGTGGATGAATCACCGTACATGAACTTTG
* * *
58743 TGTGCATAATCACGGAATTCATCCTGAGTGGATGAATCACCATACATGCACTTTGTGTGAATAAA
66 TGTGCACAATCACGGAATTCATCCTGAGTGGATGAATCACCATACAGGCACTTCGTGTGAATAAA
*
58808 CACGGAATTCATCATGAGTGGAT-AATCACCGTAC
131 CACGAAATTCATCATGAGTGGATGAATCACCGTAC
58842 AGGCACTTCGTGTGCATAATCACAGAATTCATCCTGAGTGGATGAATCACCGTACATGAACTTTG
1 AGGCACTTCGTGTGCATAATCACAGAATTCATCCTGAGTGGATGAATCACCGTACATGAACTTTG
* * * * **
58907 TGTGCACAATCATGGAATTCATCCTGAGTGGATGAATCATCGTACAGGCACTTCGTGTGCATATT
66 TGTGCACAATCACGGAATTCATCCTGAGTGGATGAATCACCATACAGGCACTTCGTGTGAATAAA
* *
58972 CACGAAATTCATCTTGGGTGGATGAATCACCGTAC
131 CACGAAATTCATCATGAGTGGATGAATCACCGTAC
** * * *
59007 AGGCACTAT-GTGTGCA-ACCCACATAATTCATCATGAGTTGATGAAT
1 AGGCACT-TCGTGTGCATAATCACAGAATTCATCCTGAGTGGATGAAT
59053 TTCCGTATAG
Statistics
Matches: 189, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
164 163 0.86
165 25 0.13
166 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (165 bp):
AGGCACTTCGTGTGCATAATCACAGAATTCATCCTGAGTGGATGAATCACCGTACATGAACTTTG
TGTGCACAATCACGGAATTCATCCTGAGTGGATGAATCACCATACAGGCACTTCGTGTGAATAAA
CACGAAATTCATCATGAGTGGATGAATCACCGTAC
Found at i:61223 original size:21 final size:20
Alignment explanation
Indices: 61178--61231 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
61168 GATTCAATCA
61178 GTATCGATACCGAAGAGGTG
1 GTATCGATACCGAAGAGGTG
*
61198 GTATCGATACCATGATGAGG-G
1 GTATCGATACC--GAAGAGGTG
61219 GTATCGATACCGA
1 GTATCGATACCGA
61232 GAAACATCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 2 0.06
20 11 0.35
21 12 0.39
22 6 0.19
ACGTcount: A:0.30, C:0.17, G:0.31, T:0.22
Consensus pattern (20 bp):
GTATCGATACCGAAGAGGTG
Found at i:61297 original size:22 final size:23
Alignment explanation
Indices: 61271--61315 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
61261 ACCGGTAGGG
61271 GTATCAATACCATAG-AAGGGTA
1 GTATCAATACCATAGTAAGGGTA
* *
61293 GTATCGATACCATGGTAAGGGTA
1 GTATCAATACCATAGTAAGGGTA
61316 TCGATACTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.24
Consensus pattern (23 bp):
GTATCAATACCATAGTAAGGGTA
Found at i:61332 original size:94 final size:97
Alignment explanation
Indices: 61189--61380 Score: 221
Period size: 94 Copynumber: 2.0 Consensus size: 97
61179 TATCGATACC
* * * **
61189 GAAGAGGTGGTATCGATACCATGATGAGGGGTATCGATACCGAGAAACATCAAATTTAATTTTGG
1 GAAGAGGTAGTATCGATACCATGATGAAGGGTATCGATACAGAGAAACATCAAACCTAATTTTGG
* * * *
61254 TCTCGATACCGGTA-GGGGTATCAATACCATA
66 TATCAATACCCGAAGGGGGTATCAATACCATA
* * * *
61285 GAAG-GGTAGTATCGATACCATGGT-AAGGGTATCGATACTAG-GCAACATCGAACCTATTTTTG
1 GAAGAGGTAGTATCGATACCATGATGAAGGGTATCGATAC-AGAGAAACATCAAACCTAATTTTG
*
61347 GTATCAATACCCGAAGGGGGTATCGATACCATA
65 GTATCAATACCCGAAGGGGGTATCAATACCATA
61380 G
1 G
61381 TATAGAAGTA
Statistics
Matches: 80, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
94 40 0.50
95 36 0.45
96 4 0.05
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.26
Consensus pattern (97 bp):
GAAGAGGTAGTATCGATACCATGATGAAGGGTATCGATACAGAGAAACATCAAACCTAATTTTGG
TATCAATACCCGAAGGGGGTATCAATACCATA
Found at i:61391 original size:95 final size:95
Alignment explanation
Indices: 61198--61393 Score: 207
Period size: 95 Copynumber: 2.1 Consensus size: 95
61188 CGAAGAGGTG
* * ** * *
61198 GTATCGATACCATGATGAGGGGTATCGATACCGAGAAACATCAAATTTAATTTTGGTCTCGATAC
1 GTATCGATACCATGATGAAGGGTATCGATACAGAGAAACATCAAACCTAATTTTGGTATCAATAC
* * * *
61263 CGGTAGGGGTATCAATACCATAGAAGGGTA
66 CCGAAGGGGTATCAATACCATAGAAGAGAA
* * * *
61293 GTATCGATACCATGGT-AAGGGTATCGATACTAG-GCAACATCGAACCTATTTTTGGTATCAATA
1 GTATCGATACCATGATGAAGGGTATCGATAC-AGAGAAACATCAAACCTAATTTTGGTATCAATA
* * *
61356 CCCGAAGGGGGTATCGATACCATAGTATAGAA
65 CCCGAA-GGGGTATCAATACCATAGAAGAGAA
61388 GTATCG
1 GTATCG
61394 GTACTGGTAG
Statistics
Matches: 82, Mismatches: 17, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
94 40 0.49
95 42 0.51
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (95 bp):
GTATCGATACCATGATGAAGGGTATCGATACAGAGAAACATCAAACCTAATTTTGGTATCAATAC
CCGAAGGGGTATCAATACCATAGAAGAGAA
Found at i:63041 original size:33 final size:33
Alignment explanation
Indices: 62997--63072 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 33
62987 ATACTTTTTA
62997 TATTTTATTCTT-TGTTTTTAATGTT-TTT-TTATT
1 TATTTTATTCTTCT-TTTTT--TGTTGTTTGTTATT
*
63030 TATTTTTTTCTTCTTTTTTTGTTGTTTGTTATT
1 TATTTTATTCTTCTTTTTTTGTTGTTTGTTATT
63063 TATTATTATT
1 TATT-TTATT
63073 ATTATATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
31 4 0.11
32 3 0.08
33 25 0.68
34 5 0.14
ACGTcount: A:0.13, C:0.04, G:0.07, T:0.76
Consensus pattern (33 bp):
TATTTTATTCTTCTTTTTTTGTTGTTTGTTATT
Found at i:63085 original size:19 final size:19
Alignment explanation
Indices: 63061--63153 Score: 86
Period size: 19 Copynumber: 4.9 Consensus size: 19
63051 TTGTTTGTTA
63061 TTTATTATTATTATTATAT
1 TTTATTATTATTATTATAT
*
63080 TTTATTTTTATTATTATAT
1 TTTATTATTATTATTATAT
* * *
63099 TTCT-CTATTATCATTATAAC
1 TT-TATTATTATTATTAT-AT
63119 TTTATTATTAACTTA-TATAT
1 TTTATTATT-A-TTATTATAT
63139 TTTATT-TTATT-TTAT
1 TTTATTATTATTATTAT
63154 TTCTATTTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
17 5 0.08
18 1 0.02
19 33 0.55
20 15 0.25
21 4 0.07
22 2 0.03
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTATTATTATTATTATAT
Found at i:63162 original size:21 final size:20
Alignment explanation
Indices: 63136--63190 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
63126 TTAACTTATA
*
63136 TATTTTATTTTATTT-TATTT
1 TATTTTATTTT-TTTCCATTT
63156 CTATTTTCATTTTTTTCCATTT
1 -TATTTT-ATTTTTTTCCATTT
63178 TATTTTTATTTTT
1 TA-TTTTATTTTT
63191 GTTGTATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.76
Consensus pattern (20 bp):
TATTTTATTTTTTTCCATTT
Found at i:63167 original size:6 final size:5
Alignment explanation
Indices: 63136--63189 Score: 56
Period size: 5 Copynumber: 10.2 Consensus size: 5
63126 TTAACTTATA
*
63136 TATTT TATTT TATTT TATTT CTATTT TCATTT T-TTT CCATTT TATTTT
1 TATTT TATTT TATTT TATTT -TATTT T-ATTT TATTT -TATTT TA-TTT
63184 TATTT T
1 TATTT T
63190 TGTTGTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
4 3 0.07
5 21 0.50
6 18 0.43
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (5 bp):
TATTT
Found at i:63280 original size:26 final size:28
Alignment explanation
Indices: 63230--63286 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 28
63220 TTAGGTTTTA
* * *
63230 TTTTATCTTTTTTGTTTATTTGTATTTC
1 TTTTATCTTCTTTATTTATTTGTATCTC
63258 TTTTAT-TTCTTTATTT-TTTGTATCTC
1 TTTTATCTTCTTTATTTATTTGTATCTC
63284 TTT
1 TTT
63287 CTTCTTATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 12 0.46
27 8 0.31
28 6 0.23
ACGTcount: A:0.11, C:0.09, G:0.05, T:0.75
Consensus pattern (28 bp):
TTTTATCTTCTTTATTTATTTGTATCTC
Found at i:65569 original size:64 final size:65
Alignment explanation
Indices: 65443--65600 Score: 187
Period size: 64 Copynumber: 2.4 Consensus size: 65
65433 TTAAGTGTGT
* * * *
65443 ATCGATGCACAGGAAGTACATCGATGCA-CCCATTAAAAAATGGAAACATCGAATGCAATTAGTG
1 ATCGATGCATAGGAAGTGCATCGATGCACCCCATT-AAAAATGAAAACATCGAAGGCAATTAGTG
65507 C
65 C
* **
65508 ATCGATGCATAAGG-AGTGCATCGATGCACCCCCTT-AAAATGAAAACATCGAAGGTGATTAGTG
1 ATCGATGCAT-AGGAAGTGCATCGATGCACCCCATTAAAAATGAAAACATCGAAGGCAATTAGTG
*
65571 T
65 C
* *
65572 ATCGATGCATGGGTAGTGCATCGATGCAC
1 ATCGATGCATAGGAAGTGCATCGATGCAC
65601 ATCTTAAAGA
Statistics
Matches: 81, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
63 2 0.02
64 49 0.60
65 22 0.27
66 8 0.10
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (65 bp):
ATCGATGCATAGGAAGTGCATCGATGCACCCCATTAAAAATGAAAACATCGAAGGCAATTAGTGC
Found at i:65633 original size:20 final size:20
Alignment explanation
Indices: 65608--65645 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
65598 CACATCTTAA
65608 AGAATGTATCGATGCACTGT
1 AGAATGTATCGATGCACTGT
65628 AGAATGTATCGATGCACT
1 AGAATGTATCGATGCACT
65646 TCAAGGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (20 bp):
AGAATGTATCGATGCACTGT
Found at i:66333 original size:18 final size:18
Alignment explanation
Indices: 66310--66361 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
66300 GGATCTACAC
66310 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
* *
66328 GGTCCTTTGGGATATAGT
1 GGTCCTTCGGGACATAGT
66346 GGTCCTTCGGGACATA
1 GGTCCTTCGGGACATA
66362 TGTGTTGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.31
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:73478 original size:13 final size:14
Alignment explanation
Indices: 73462--73495 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
73452 TGAAAATAAG
73462 AGAAAAAA-ACAAA
1 AGAAAAAAGACAAA
*
73475 AGAAAAAAGAGAAA
1 AGAAAAAAGACAAA
73489 AGAAAAA
1 AGAAAAA
73496 TAAGGTGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (14 bp):
AGAAAAAAGACAAA
Found at i:74117 original size:14 final size:14
Alignment explanation
Indices: 74098--74124 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
74088 AATCAGAACT
74098 TCAAGATTCCAGAA
1 TCAAGATTCCAGAA
74112 TCAAGATTCCAGA
1 TCAAGATTCCAGA
74125 CAGGCAACCG
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:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (14 bp):
TCAAGATTCCAGAA
Found at i:74540 original size:43 final size:43
Alignment explanation
Indices: 74430--74549 Score: 150
Period size: 43 Copynumber: 2.8 Consensus size: 43
74420 ACGAATGGGC
* *
74430 CATCCACGATTTCAACTCCACGACAGAGGATATCATACCTACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCATACCCACA
* ** * *
74473 AATCCAATATTTCAACTCCACGACGGAGGATATTATGCCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCATACCCACA
* * *
74516 CATCCACGATTTCAACTTCACGACGAAAGATATC
1 CATCCACGATTTCAACTCCACGACGGAGGATATC
74550 GTGCCAACTC
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 63 1.00
ACGTcount: A:0.35, C:0.30, G:0.12, T:0.23
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCATACCCACA
Found at i:76840 original size:6 final size:5
Alignment explanation
Indices: 76809--76847 Score: 51
Period size: 5 Copynumber: 7.2 Consensus size: 5
76799 TTAACTTATA
76809 TATTT TATTT TATTT TATTT CTATTT TCATTT TCATTT T
1 TATTT TATTT TATTT TATTT -TATTT T-ATTT T-ATTT T
76848 TCTATTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 16 0.50
6 16 0.50
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (5 bp):
TATTT
Found at i:76864 original size:9 final size:8
Alignment explanation
Indices: 76826--76920 Score: 51
Period size: 9 Copynumber: 12.1 Consensus size: 8
76816 TTTTATTTTA
76826 TTTCTA-T
1 TTTCTATT
76833 TTTC-A-T
1 TTTCTATT
76839 TTTC-ATT
1 TTTCTATT
76846 TTTCTATT
1 TTTCTATT
76854 TTTCTA-T
1 TTTCTATT
76861 TTT-TATT
1 TTTCTATT
*
76868 TCTTTTATT
1 T-TTCTATT
*
76877 TTCTTTATT
1 TT-TCTATT
*
76886 TTCTGTATT
1 TT-TCTATT
*
76895 TTTTTCATAT
1 TTTCT-AT-T
76905 TTT-TATT
1 TTTCTATT
*
76912 TTTATATT
1 TTTCTATT
76920 T
1 T
76921 ATTTTCTTTA
Statistics
Matches: 77, Mismatches: 2, Indels: 17
0.80 0.02 0.18
Matches are distributed among these distances:
6 9 0.12
7 19 0.25
8 21 0.27
9 24 0.31
10 4 0.05
ACGTcount: A:0.15, C:0.09, G:0.01, T:0.75
Consensus pattern (8 bp):
TTTCTATT
Found at i:76944 original size:47 final size:43
Alignment explanation
Indices: 76852--76945 Score: 100
Period size: 47 Copynumber: 2.1 Consensus size: 43
76842 CATTTTTCTA
* * **
76852 TTTTTCTATTTTTATTTCTTTTATTTTCTTTATTTTCTGTATT
1 TTTTTCTATTTTTATTTATTTTATTTTCTTTATCTTCCCTATT
76895 TTTTTCATATTTTTATTTTTATATTTATTTTCTTTATCTTCACCT-TT
1 TTTTTC-TATTTTTA--TTTAT-TTTATTTTCTTTATCTTC-CCTATT
76942 TTTT
1 TTTT
76946 ATATTTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
43 6 0.14
44 8 0.19
46 4 0.10
47 23 0.55
48 1 0.02
ACGTcount: A:0.14, C:0.11, G:0.01, T:0.74
Consensus pattern (43 bp):
TTTTTCTATTTTTATTTATTTTATTTTCTTTATCTTCCCTATT
Found at i:76968 original size:22 final size:21
Alignment explanation
Indices: 76943--76990 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
76933 TTCACCTTTT
76943 TTTATATTTA-TTTTGTTTCTTA
1 TTTATATTTATTTTTG-TTC-TA
*
76965 TTTATTTTTATTTTTGTTCTA
1 TTTATATTTATTTTTGTTCTA
76986 TTTAT
1 TTTAT
76991 TTAGCATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 7 0.29
22 12 0.50
23 5 0.21
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.75
Consensus pattern (21 bp):
TTTATATTTATTTTTGTTCTA
Found at i:77048 original size:17 final size:17
Alignment explanation
Indices: 77020--77071 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
77010 TAGGTTTTAT
77020 TTTATTTTTATTTTTTG
1 TTTATTTTTATTTTTTG
*
77037 TTTATTTTTA-TTTCT-
1 TTTATTTTTATTTTTTG
77052 TTTATTTCCTTATTTTTTG
1 TTTATTT--TTATTTTTTG
77071 T
1 T
77072 ATCTCTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 7 0.24
16 4 0.14
17 13 0.45
18 4 0.14
19 1 0.03
ACGTcount: A:0.12, C:0.06, G:0.04, T:0.79
Consensus pattern (17 bp):
TTTATTTTTATTTTTTG
Found at i:77568 original size:55 final size:55
Alignment explanation
Indices: 77478--77703 Score: 294
Period size: 55 Copynumber: 4.1 Consensus size: 55
77468 GGTTCCGACA
* * * *
77478 TGTGCATAAACACAGAATTCATCCTGAGTGCATGAATCACCGTACATGCACTTTG
1 TGTGCATAATCACAGAATTCATCCTGAGTGGATGAATCACCGTACAGGCACTTCG
* * *
77533 TGTGCATAATCACAGAATTCATCCTGAGTAGATGAATCACCGTACATGCACTTCA
1 TGTGCATAATCACAGAATTCATCCTGAGTGGATGAATCACCGTACAGGCACTTCG
* *
77588 TGTGCATAATCAC-GTAATTTATCTTGAGTGGATGAATCACCGTACAGGCACTTCG
1 TGTGCATAATCACAG-AATTCATCCTGAGTGGATGAATCACCGTACAGGCACTTCG
* * * * *
77643 TGTGCATATTCACGGAATTCAACATGGGTGGATGAATCACCGTACAGGCACTAT-G
1 TGTGCATAATCACAGAATTCATCCTGAGTGGATGAATCACCGTACAGGCACT-TCG
77698 TGTGCA
1 TGTGCA
77704 ACCCATGGAA
Statistics
Matches: 153, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
54 1 0.01
55 150 0.98
56 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.28
Consensus pattern (55 bp):
TGTGCATAATCACAGAATTCATCCTGAGTGGATGAATCACCGTACAGGCACTTCG
Found at i:77740 original size:54 final size:56
Alignment explanation
Indices: 77478--77749 Score: 221
Period size: 55 Copynumber: 4.9 Consensus size: 56
77468 GGTTCCGACA
** * * * * * *
77478 TGTGCATAAACACAGAATTCATCCTGAGTGCATGAATCACCGTACATGCACT-TTG
1 TGTGCATACCCACGGAATTCAACATGAGTGGATGAATCACCGTACAGGCACTATCG
** * * * * * *
77533 TGTGCATAATCACAGAATTCATCCTGAGTAGATGAATCACCGTACATGCACT-TCA
1 TGTGCATACCCACGGAATTCAACATGAGTGGATGAATCACCGTACAGGCACTATCG
** * * * *
77588 TGTGCATAATCACGTAATTTATCTTGAGTGGATGAATCACCGTACAGGCACT-TCG
1 TGTGCATACCCACGGAATTCAACATGAGTGGATGAATCACCGTACAGGCACTATCG
** *
77643 TGTGCATATTCACGGAATTCAACATGGGTGGATGAATCACCGTACAGGCACTAT-G
1 TGTGCATACCCACGGAATTCAACATGAGTGGATGAATCACCGTACAGGCACTATCG
* ** * ** *
77698 TGTGCA-ACCCATGGAATTCATGATGAGTTGATGAATTTCCGTATAGGCACTA
1 TGTGCATACCCACGGAATTCAACATGAGTGGATGAATCACCGTACAGGCACTA
77750 AATGTGTATT
Statistics
Matches: 188, Mismatches: 28, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
54 36 0.19
55 151 0.80
56 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (56 bp):
TGTGCATACCCACGGAATTCAACATGAGTGGATGAATCACCGTACAGGCACTATCG
Found at i:79352 original size:24 final size:24
Alignment explanation
Indices: 79299--79355 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
79289 AGTTTTCATA
*
79299 ATATTAGTATGGTTTTAATATGCT
1 ATATTAATATGGTTTTAATATGCT
* *
79323 AGTATTAATAT-GTTTTACTATGTT
1 A-TATTAATATGGTTTTAATATGCT
79347 GATATTAAT
1 -ATATTAAT
79356 TTTTTTCTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 19 0.68
25 9 0.32
ACGTcount: A:0.32, C:0.04, G:0.14, T:0.51
Consensus pattern (24 bp):
ATATTAATATGGTTTTAATATGCT
Done.