Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004740.1 Hibiscus syriacus cultivar Beakdansim tig00010700_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: 84353
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2033 original size:31 final size:31
Alignment explanation
Indices: 1998--2069 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
1988 GGATTACTGG
* *
1998 TGTCATTGTTTGGCATTGTTCCTATCATCAT
1 TGTCATTGTTTGGCATTCTTCCGATCATCAT
* *
2029 TGTCACTGTTTGGCATTCTTCCGATCGTCAT
1 TGTCATTGTTTGGCATTCTTCCGATCATCAT
* *
2060 TCTTATTGTT
1 TGTCATTGTT
2070 CATCTTCTTC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.49
Consensus pattern (31 bp):
TGTCATTGTTTGGCATTCTTCCGATCATCAT
Found at i:3114 original size:44 final size:44
Alignment explanation
Indices: 3065--3154 Score: 137
Period size: 44 Copynumber: 2.0 Consensus size: 44
3055 TCATATAGGT
3065 TACGACTTTCAAAACATCAACAAATTTCT-GATCATCTAAATTCG
1 TACGACTTTCAAAACATCAACAAATTT-TGGATCATCTAAATTCG
***
3109 TACGACTTTCAAAACATCGTGAAATTTTGGATCATCTAAATTCG
1 TACGACTTTCAAAACATCAACAAATTTTGGATCATCTAAATTCG
3153 TA
1 TA
3155 TAACAAAAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
43 1 0.02
44 41 0.98
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (44 bp):
TACGACTTTCAAAACATCAACAAATTTTGGATCATCTAAATTCG
Found at i:11124 original size:30 final size:30
Alignment explanation
Indices: 11059--11123 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
11049 TAAATTGAAC
* * * *
11059 TTTTCAAAAATTTTAATTTATACTTCTAAA
1 TTTTTAAAAATTTTAATTGATACCTCCAAA
*
11089 TTTTTAAAAATTTTAAATTGATCCCTCCAAA
1 TTTTTAAAAATTTT-AATTGATACCTCCAAA
11120 TTTT
1 TTTT
11124 ATCACTAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 13 0.45
31 16 0.55
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.49
Consensus pattern (30 bp):
TTTTTAAAAATTTTAATTGATACCTCCAAA
Found at i:13086 original size:21 final size:21
Alignment explanation
Indices: 13057--13101 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
13047 ATTCTGACTA
13057 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
13078 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
13099 TCG
1 TCG
13102 TAATGCGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:13108 original size:21 final size:21
Alignment explanation
Indices: 13057--13109 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
13047 ATTCTGACTA
*
13057 TCGCATTGCGATTTTCCAAAT
1 TCGCAATGCGATTTTCCAAAT
** *
13078 TCGCGTTGCGATTTTCCTAAT
1 TCGCAATGCGATTTTCCAAAT
*
13099 TCGTAATGCGA
1 TCGCAATGCGA
13110 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAAAT
Found at i:13162 original size:20 final size:20
Alignment explanation
Indices: 13137--13181 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
13127 CGAATTTGGA
* *
13137 AAATCACAATGTGATTACGT
1 AAATCACAAAGTGAATACGT
13157 AAATCACAAAGTGAATACGT
1 AAATCACAAAGTGAATACGT
13177 AAATC
1 AAATC
13182 GAAATGCGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (20 bp):
AAATCACAAAGTGAATACGT
Found at i:13192 original size:20 final size:20
Alignment explanation
Indices: 13103--13212 Score: 62
Period size: 20 Copynumber: 5.5 Consensus size: 20
13093 CCTAATTCGT
* *
13103 AATGCGAATACGTAAATTGC
1 AATGCGAATACGTAAATCGA
* ** *
13123 AACGCGAATTTGGAAAATC-A
1 AATGCGAA-TACGTAAATCGA
* *
13143 CAATGTGATTACGTAAATC-A
1 -AATGCGAATACGTAAATCGA
* *
13163 CAAAGTGAATACGTAAATCGA
1 -AATGCGAATACGTAAATCGA
* *
13184 AATGCGAATATGTAAATCGC
1 AATGCGAATACGTAAATCGA
*
13204 AACGCGAAT
1 AATGCGAAT
13213 CTGACTATCG
Statistics
Matches: 68, Mismatches: 19, Indels: 6
0.73 0.20 0.06
Matches are distributed among these distances:
20 56 0.82
21 12 0.18
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (20 bp):
AATGCGAATACGTAAATCGA
Found at i:13433 original size:22 final size:22
Alignment explanation
Indices: 13408--13473 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
13398 GGCGACATCC
13408 GTCCTCATCTCCGACGAAATCA
1 GTCCTCATCTCCGACGAAATCA
* *
13430 GTCCCCATCTCCGACGATATCA
1 GTCCTCATCTCCGACGAAATCA
* *
13452 GT-CTCCATCTTCGGCGAAATCA
1 GTCCT-CATCTCCGACGAAATCA
13474 TTCACGATCA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
21 1 0.03
22 36 0.97
ACGTcount: A:0.24, C:0.36, G:0.15, T:0.24
Consensus pattern (22 bp):
GTCCTCATCTCCGACGAAATCA
Found at i:13837 original size:20 final size:20
Alignment explanation
Indices: 13812--13864 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
13802 CGATTTTCAT
13812 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
**
13832 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCAAA
*
13852 TTCGTGTTGCGAT
1 TTCGCGTTGCGAT
13865 TTTAAGTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:15727 original size:20 final size:20
Alignment explanation
Indices: 15702--15880 Score: 170
Period size: 20 Copynumber: 9.6 Consensus size: 20
15692 ATAATAGTTT
15702 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
15722 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
15742 ACTATCGCAA--CGAGAA--
1 ACTATCGCAATGCGAAAATG
15758 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
** *
15775 AAAATCACAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
15791 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
15809 ACTATCGCAATGAGAAAATG
1 ACTATCGCAATGCGAAAATG
15829 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
15849 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
15869 ACTATCGCAATG
1 ACTATCGCAATG
15881 AAAGAATCGC
Statistics
Matches: 134, Mismatches: 10, Indels: 30
0.77 0.06 0.17
Matches are distributed among these distances:
14 13 0.10
15 2 0.01
16 7 0.05
17 5 0.04
18 8 0.06
19 6 0.04
20 93 0.69
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:15979 original size:20 final size:20
Alignment explanation
Indices: 15923--16011 Score: 106
Period size: 20 Copynumber: 4.5 Consensus size: 20
15913 GCGATTCTCT
* **
15923 CGTTGCGATAGTCAAATTCG
1 CGTTACGATAGTCATTTTCG
*
15943 CATTACGATAGTCATTTTCG
1 CGTTACGATAGTCATTTTCG
*
15963 CGTTACGATAGTTATTTTCG
1 CGTTACGATAGTCATTTTCG
* *
15983 CGTTGCGATAGTCATTTTTG
1 CGTTACGATAGTCATTTTCG
*
16003 CGTTGCGAT
1 CGTTACGAT
16012 TTTAAGTTTC
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
CGTTACGATAGTCATTTTCG
Found at i:16534 original size:18 final size:19
Alignment explanation
Indices: 16495--16536 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
16485 CTCACCTGTC
16495 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
16516 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
16534 ATC
1 ATC
16537 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:17994 original size:14 final size:14
Alignment explanation
Indices: 17975--18010 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
17965 ATTGTTTAAT
17975 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
17989 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
18003 TGATTTGT
1 TGATTTGT
18011 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:18204 original size:34 final size:33
Alignment explanation
Indices: 18116--18211 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
18106 AAAACAGACT
* **
18116 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
18150 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
18183 ATCGTAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
18212 CGAAACTAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:18291 original size:20 final size:19
Alignment explanation
Indices: 18253--18345 Score: 107
Period size: 20 Copynumber: 4.8 Consensus size: 19
18243 TGCGATTTTT
*
18253 ATTTCGCATTGCG-TAGTC
1 ATTTCGCGTTGCGATAGTC
*
18271 ATTTCCGCGTTGCAATAGTC
1 ATTT-CGCGTTGCGATAGTC
*
18291 AATTCGCGTTGCGATAGTC
1 ATTTCGCGTTGCGATAGTC
* *
18310 ATTTATGTGTTGCGATAGTC
1 ATTT-CGCGTTGCGATAGTC
18330 ATATTCGCGTTGCGAT
1 AT-TTCGCGTTGCGAT
18346 TTCCGCATTG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
18 4 0.06
19 24 0.39
20 32 0.52
21 2 0.03
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (19 bp):
ATTTCGCGTTGCGATAGTC
Found at i:18322 original size:39 final size:40
Alignment explanation
Indices: 18255--18345 Score: 123
Period size: 39 Copynumber: 2.3 Consensus size: 40
18245 CGATTTTTAT
* *
18255 TTCGCATTGCG-TAGTCATTTCCGCGTTGCAATAGTCA-A
1 TTCGCGTTGCGATAGTCATTTACGCGTTGCAATAGTCATA
* * *
18293 TTCGCGTTGCGATAGTCATTTATGTGTTGCGATAGTCATA
1 TTCGCGTTGCGATAGTCATTTACGCGTTGCAATAGTCATA
18333 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
18346 TTCCGCATTG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 10 0.22
39 22 0.48
40 14 0.30
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (40 bp):
TTCGCGTTGCGATAGTCATTTACGCGTTGCAATAGTCATA
Found at i:20811 original size:24 final size:24
Alignment explanation
Indices: 20777--20830 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
20767 CTGAAAAATC
20777 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
20801 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
20825 ATCAAA
1 ATCAAA
20831 TTTCAAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:21698 original size:20 final size:20
Alignment explanation
Indices: 21673--21719 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
21663 AAATTCAGTA
*
21673 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
21693 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
21713 TTGCGAT
1 TTGCGAT
21720 TTACGTATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:21729 original size:20 final size:20
Alignment explanation
Indices: 21706--21799 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
21696 CGATAGTCAG
*
21706 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
21726 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
21746 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
21767 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
21787 ATTCGCAATGCGA
1 ATTCGCATTGCGA
21800 ATTAGGAAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 47 0.75
21 16 0.25
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.36
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:21839 original size:61 final size:60
Alignment explanation
Indices: 21694--21840 Score: 161
Period size: 61 Copynumber: 2.4 Consensus size: 60
21684 AGAATCTCGT
* * * * *
21694 TGCGATAGTCAGATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCAT
1 TGCGATAGTCAGAATCGCGTTGCGATTTACGTATTCGCAATGCGAATTACGAAATCGCAA
** * * *
21754 TGCGATTTTCCA-AATTCGCATTGCGATTTACGTATTCGCAATGCGAATTAGGAAAATTGCAA
1 TGCGATAGT-CAGAA-TCGCGTTGCGATTTACGTATTCGCAATGCGAATTACG-AAATCGCAA
*
21816 TGCTATAGTCAGAATCGCGTTGCGA
1 TGCGATAGTCAGAATCGCGTTGCGA
21841 ATCTGGAAAC
Statistics
Matches: 69, Mismatches: 14, Indels: 7
0.77 0.16 0.08
Matches are distributed among these distances:
60 8 0.12
61 47 0.68
62 14 0.20
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (60 bp):
TGCGATAGTCAGAATCGCGTTGCGATTTACGTATTCGCAATGCGAATTACGAAATCGCAA
Found at i:28271 original size:36 final size:36
Alignment explanation
Indices: 28221--28297 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 36
28211 CTCCTCTTCC
28221 GTCAATCCCAAATGCTTCTGCTCCATCTCCTTCTCT
1 GTCAATCCCAAATGCTTCTGCTCCATCTCCTTCTCT
* * *
28257 GTCAGTCCCGAATGCTTCTGCTCCGTCTCCTTCTCT
1 GTCAATCCCAAATGCTTCTGCTCCATCTCCTTCTCT
28293 GTCAA
1 GTCAA
28298 CCCCGCATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.14, C:0.38, G:0.13, T:0.35
Consensus pattern (36 bp):
GTCAATCCCAAATGCTTCTGCTCCATCTCCTTCTCT
Found at i:37741 original size:34 final size:37
Alignment explanation
Indices: 37694--37795 Score: 158
Period size: 34 Copynumber: 2.8 Consensus size: 37
37684 TTTCGTCCTA
*
37694 CTAGGATTTAAACTCCTAAAAATAGGATAGA-A-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
37729 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
37764 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
37796 GTTCTACTAA
Statistics
Matches: 61, Mismatches: 1, Indels: 7
0.88 0.01 0.10
Matches are distributed among these distances:
33 1 0.02
34 28 0.46
35 3 0.05
37 28 0.46
38 1 0.02
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
Found at i:37819 original size:37 final size:37
Alignment explanation
Indices: 37691--37821 Score: 162
Period size: 37 Copynumber: 3.6 Consensus size: 37
37681 ATTTTTCGTC
*
37691 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
37728 -T--TAGGATTCAAACTCCTAAAAATAGGATA-ACATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGA-ATT
* * *
37762 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
37799 CTACTAAGATTTAAATTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
37822 GATATGATCC
Statistics
Matches: 82, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
33 1 0.01
34 30 0.37
35 1 0.01
36 1 0.01
37 48 0.59
38 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:38224 original size:2 final size:2
Alignment explanation
Indices: 38217--38261 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
38207 TTCATGTTAT
38217 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38259 TA T
1 TA T
38262 TTCTTTAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38446 original size:2 final size:2
Alignment explanation
Indices: 38441--38469 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38431 CTTATAACTT
38441 TA TA 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 TA TA T
38470 TATTTTCGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38754 original size:9 final size:9
Alignment explanation
Indices: 38733--38766 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
38723 ATTTTTTTCC
38733 TTTATCTTA-
1 TTTAT-TTAT
38742 TTTATTTAT
1 TTTATTTAT
38751 TTTATTTAT
1 TTTATTTAT
38760 TTTATTT
1 TTTATTT
38767 TTCCCTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 3 0.12
9 21 0.88
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:38755 original size:13 final size:14
Alignment explanation
Indices: 38733--38767 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
38723 ATTTTTTTCC
*
38733 TTTATCTTATTTA-
1 TTTATTTTATTTAT
38746 TTTATTTTATTTAT
1 TTTATTTTATTTAT
38760 TTTATTTT
1 TTTATTTT
38768 TCCCTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTATTTAT
Found at i:41761 original size:22 final size:21
Alignment explanation
Indices: 41750--41798 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
41740 GAAAAGAAGG
41750 AAAAAAGGAAAAAACAAGAAC
1 AAAAAAGGAAAAAACAAGAAC
* * *
41771 AAAAAA-GAAAGAACAAAAAT
1 AAAAAAGGAAAAAACAAGAAC
41791 AAAAAAGG
1 AAAAAAGG
41799 GAACAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.78, C:0.06, G:0.14, T:0.02
Consensus pattern (21 bp):
AAAAAAGGAAAAAACAAGAAC
Found at i:42476 original size:22 final size:22
Alignment explanation
Indices: 42402--42478 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
42392 GCTACCCCAT
*
42402 CAAACCGTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
* *
42424 CAAACCTATGAGCATCAAATGA
1 CAAACCTTTGAGCATCAAATGC
42446 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
42468 CAAACCTTTGA
1 CAAACCTTTGA
42479 CCAAACATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.39, C:0.26, G:0.14, T:0.21
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:43228 original size:105 final size:105
Alignment explanation
Indices: 43046--44631 Score: 2366
Period size: 105 Copynumber: 15.3 Consensus size: 105
43036 TTTAGAGTCA
* *
43046 AATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
43111 GACCGCTGCTTGTCAACAACAACTTTTCAATCTCAGAGCC
66 GACCGCTGCTTGTCAACAACAACTTTTCAATCTCAGAGCC
43151 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
43216 GACCGCTGCTTGTCAACAA-AA--TTTC-AT-TCAGAGCC
66 GACCGCTGCTTGTCAACAACAACTTTTCAATCTCAGAGCC
* * *
43251 AATTTCAATTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
43316 GACCGCTGATTGTCAACAACAACTTTCCAATCTCAGAGCC
66 GACCGCTGCTTGTCAACAACAACTTTTCAATCTCAGAGCC
*
43356 AATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
43421 GACCGCTGCTTGTCAACAA-AA--TTTC-AT-TCAGAGCC
66 GACCGCTGCTTGTCAACAACAACTTTTCAATCTCAGAGCC
* *
43456 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* ** *
43521 GACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCC
66 GACCGCTGCTTGTCAACAACAACTTTTCAATCTCAGAGCC
** * *
43561 AATTTCAACTTCACAACGAAATATATTGGACTCCAGACAATGCAAGTTCAACTTCACAACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
43626 GACGGCTGGTTGTCAACAAACAACTTCTT-AATTTCAGAGCC
66 GACCGCTGCTTGTCAAC-AACAACTT-TTCAATCTCAGAGCC
*
43667 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
43732 GACCGCTGGTTGTCAATAAACAA-TTTTCCCAATTTCAGAGCC
66 GACCGCTGCTTGTCAA-CAACAACTTTT--CAATCTCAGAGCC
*
43774 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* **
43839 GACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCC
66 GACCGCTGCTTGTCAACAACAACTTTTCAATCTCAGAGCC
*
43879 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
43944 GACCACTGCTTGTCAACAACAACTTTTCAATCTCAGAGCC
66 GACCGCTGCTTGTCAACAACAACTTTTCAATCTCAGAGCC
43984 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
44049 GACCGCTGCTTGTCAACAA-AA--TTTC-AT-TCAGAGCC
66 GACCGCTGCTTGTCAACAACAACTTTTCAATCTCAGAGCC
* * *
44084 AATTTCAACTTCACAGCGAAGGATATTAGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
44149 GACCGCTGATTGTCAACAACAACTTTCCAATCTCAGAGCC
66 GACCGCTGCTTGTCAACAACAACTTTTCAATCTCAGAGCC
*
44189 AATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
44254 GACCGCTGCTTGTCAACAA-AA--TTTC-AT-TCAGAGCC
66 GACCGCTGCTTGTCAACAACAACTTTTCAATCTCAGAGCC
* * *
44289 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCATGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* ** *
44354 GACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCC
66 GACCGCTGCTTGTCAACAACAACTTTTCAATCTCAGAGCC
*
44394 AATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
**
44459 GACCGCTGCTTGTCAACAA-AA--TTTC-AT-TCAGATTC
66 GACCGCTGCTTGTCAACAACAACTTTTCAATCTCAGAGCC
* * *
44494 AATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * * * **
44559 GACGGCTGGTTGTCAACAA-ATAATTTCCCGGT-TCCAGAGCC
66 GACCGCTGCTTGTCAACAACA-ACTTT-TCAATCT-CAGAGCC
* * *
44600 AATTTCAACTTCACGACGGAGAATATTGGACT
1 AATTTCAACTTCACAACGAAGGATATTGGACT
44632 TGGAACAATG
Statistics
Matches: 1355, Mismatches: 93, Indels: 65
0.90 0.06 0.04
Matches are distributed among these distances:
100 435 0.32
101 19 0.01
102 16 0.01
103 12 0.01
104 21 0.02
105 622 0.46
106 137 0.10
107 93 0.07
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGCTTGTCAACAACAACTTTTCAATCTCAGAGCC
Found at i:43414 original size:205 final size:205
Alignment explanation
Indices: 43046--44631 Score: 2546
Period size: 205 Copynumber: 7.7 Consensus size: 205
43036 TTTAGAGTCA
*
43046 AATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGG
* *
43111 GACCGCTGCTTGTCAACAACAACTTTTCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATA
66 GACCGCTGATTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATA
43176 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTC
131 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTC
43241 ATTCAGAGCC
196 ATTCAGAGCC
* *
43251 AATTTCAATTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGG
*
43316 GACCGCTGATTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAATGATA
66 GACCGCTGATTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATA
43381 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTC
131 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTC
43446 ATTCAGAGCC
196 ATTCAGAGCC
*
43456 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGG
* * * **
43521 GACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCAATTTCAACTTCACAACGAAATATA
66 GACCGCTGATTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATA
* * * *
43586 TTGGACTCCAGACAATGCAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACT
131 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AA-AA--
*
43651 TCTTAATTTCAGAGCC
192 T-TTCA-TTCAGAGCC
* *
43667 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGG
* * * * *
43732 GACCGCTGGTTGTCAATAAACAATTTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGA
66 GACCGCTGATTGTCAA-CAACAACTTT-CCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGA
*
43797 TATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAAC
129 TATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-
*
43862 TTCCCAATCTCAGAGCC
192 TT-TC-AT-TCAGAGCC
43879 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGG
* * *
43944 GACCACTGCTTGTCAACAACAACTTTTCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATA
66 GACCGCTGATTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATA
44009 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTC
131 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTC
44074 ATTCAGAGCC
196 ATTCAGAGCC
* *
44084 AATTTCAACTTCACAGCGAAGGATATTAGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGG
*
44149 GACCGCTGATTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAATGATA
66 GACCGCTGATTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATA
44214 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTC
131 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTC
44279 ATTCAGAGCC
196 ATTCAGAGCC
* *
44289 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCATGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGG
* * * *
44354 GACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCAATTTCAACTTCACAACGAAAGATA
66 GACCGCTGATTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATA
44419 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTC
131 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTC
**
44484 ATTCAGATTC
196 ATTCAGAGCC
* ** *
44494 AATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGG
* * * ** * * *
44559 GACGGCTGGTTGTCAACAA-ATAATTTCCCGGT-TCCAGAGCCAATTTCAACTTCACGACGGAGA
66 GACCGCTGATTGTCAACAACA-ACTTT-CCAATCT-CAGAGCCAATTTCAACTTCACAACGAAGG
44622 ATATTGGACT
128 ATATTGGACT
44632 TGGAACAATG
Statistics
Matches: 1290, Mismatches: 77, Indels: 27
0.93 0.06 0.02
Matches are distributed among these distances:
204 1 0.00
205 859 0.67
206 42 0.03
207 3 0.00
208 2 0.00
209 3 0.00
210 98 0.08
211 96 0.07
212 98 0.08
213 88 0.07
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (205 bp):
AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGG
GACCGCTGATTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATA
TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTC
ATTCAGAGCC
Found at i:45223 original size:34 final size:37
Alignment explanation
Indices: 45179--45280 Score: 167
Period size: 34 Copynumber: 2.8 Consensus size: 37
45169 TTTCGTCCTA
45179 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
45214 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
45249 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
45281 GTTCTACTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
33 1 0.02
34 29 0.47
35 3 0.05
37 28 0.45
38 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
Found at i:45304 original size:37 final size:37
Alignment explanation
Indices: 45176--45306 Score: 171
Period size: 37 Copynumber: 3.6 Consensus size: 37
45166 ATTTTTCGTC
45176 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
45213 -T--TAGGATTCAAACTCCTAAAAATAGGATA-ACATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGA-ATT
* * *
45247 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
45284 CTACTAAGATTTAAATTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
45307 GATATGATCC
Statistics
Matches: 83, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
33 1 0.01
34 31 0.37
35 1 0.01
36 1 0.01
37 48 0.58
38 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:45697 original size:17 final size:18
Alignment explanation
Indices: 45671--45710 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
45661 ATTATATAGA
45671 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
45687 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
45705 TATTAT
1 TATTAT
45711 ATATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:45847 original size:17 final size:17
Alignment explanation
Indices: 45825--45859 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
45815 ATGGTTTATT
*
45825 TATATATCTATTATTAA
1 TATATATATATTATTAA
*
45842 TATATATATATTCTTAA
1 TATATATATATTATTAA
45859 T
1 T
45860 TATTTTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATATATATTATTAA
Found at i:45914 original size:2 final size:2
Alignment explanation
Indices: 45909--45933 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45899 CTTATAACTT
45909 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
45934 TTTCGTTTTT
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:46211 original size:9 final size:9
Alignment explanation
Indices: 46190--46223 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
46180 ATTTTTTTCC
46190 TTTATCTTA-
1 TTTAT-TTAT
46199 TTTATTTAT
1 TTTATTTAT
46208 TTTATTTAT
1 TTTATTTAT
46217 TTTATTT
1 TTTATTT
46224 TTCCCTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 3 0.12
9 21 0.88
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:46212 original size:13 final size:14
Alignment explanation
Indices: 46190--46224 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
46180 ATTTTTTTCC
*
46190 TTTATCTTATTTA-
1 TTTATTTTATTTAT
46203 TTTATTTTATTTAT
1 TTTATTTTATTTAT
46217 TTTATTTT
1 TTTATTTT
46225 TCCCTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTATTTAT
Found at i:49532 original size:21 final size:20
Alignment explanation
Indices: 49505--49602 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
49495 AATCAGTGTC
49505 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
49526 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
49546 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
49566 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
49587 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
49603 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 31 0.51
21 30 0.49
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:49555 original size:41 final size:41
Alignment explanation
Indices: 49446--49602 Score: 126
Period size: 41 Copynumber: 3.9 Consensus size: 41
49436 AAATGACCAA
* **
49446 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
49485 CAGAATCGCAAATC-AGTGTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
49526 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
49567 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
49603 ACACATAAAT
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 17 0.20
41 53 0.61
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:49612 original size:20 final size:20
Alignment explanation
Indices: 49569--49639 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
49559 CGATTTTCCA
* *
49569 AAATCGCAACGCGAATATGA-
1 AAATCGCAACGCGAACA-CAT
49589 AAATCGCAACGCGAACACAT
1 AAATCGCAACGCGAACACAT
* * *
49609 AAATCGCAATGCGTATC-CGT
1 AAATCGCAACGCG-AACACAT
49629 AAATCGCAACG
1 AAATCGCAACG
49640 TGTATCCGTA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
19 1 0.02
20 40 0.93
21 2 0.05
ACGTcount: A:0.41, C:0.25, G:0.18, T:0.15
Consensus pattern (20 bp):
AAATCGCAACGCGAACACAT
Found at i:49633 original size:40 final size:40
Alignment explanation
Indices: 49569--49798 Score: 223
Period size: 40 Copynumber: 5.8 Consensus size: 40
49559 CGATTTTCCA
* ** * *
49569 AAATCGCAACGCGAATATGAAAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAAC-CGT
* * *
49609 AAATCGCAATGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAACCGT
* * * *
49649 AAATCGCAACGTGTTTCCGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAACCGT
*
49689 AAATCGCAACGCGTATCCGTAAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAA-CCGT
* * * *
49729 AAATCGCAACGAGAATCTGTAAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAA-CCGT
* * * *
49769 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGCGTATCCGTAAATCGCAAC
49799 ACTGAAATTT
Statistics
Matches: 166, Mismatches: 22, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
39 2 0.01
40 162 0.98
41 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGTAACCGT
Found at i:49644 original size:20 final size:20
Alignment explanation
Indices: 49608--49798 Score: 215
Period size: 20 Copynumber: 9.6 Consensus size: 20
49598 CGCGAACACA
* *
49608 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGTGTATCCG
49628 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGTGTATCCG
*
49648 TAAATCGCAACGTGTTTCCG
1 TAAATCGCAACGTGTATCCG
* *
49668 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGTGTATCCG
*
49688 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGTGTATCCG
*
49708 TAAATCGCAACGAT-AATCCG
1 TAAATCGCAACG-TGTATCCG
* * *
49728 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGTGTATCCG
*
49748 TAAATCGCAACGAT-AATCCG
1 TAAATCGCAACG-TGTATCCG
* * *
49768 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGTGTATCCG
*
49788 TAAATCACAAC
1 TAAATCGCAAC
49799 ACTGAAATTT
Statistics
Matches: 151, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
20 151 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
TAAATCGCAACGTGTATCCG
Found at i:50520 original size:24 final size:24
Alignment explanation
Indices: 50481--50527 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
50471 AAATTTGGTC
50481 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
50505 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
50528 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:50719 original size:12 final size:12
Alignment explanation
Indices: 50702--50726 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
50692 ATATAATCCT
50702 GAAGAAGAAAAA
1 GAAGAAGAAAAA
50714 GAAGAAGAAAAA
1 GAAGAAGAAAAA
50726 G
1 G
50727 TCCCGAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:53031 original size:19 final size:19
Alignment explanation
Indices: 53009--53320 Score: 386
Period size: 19 Copynumber: 17.7 Consensus size: 19
52999 CGGAAATTAC
*
53009 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
53028 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
53042 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
53062 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
53076 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
53095 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
53114 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
53128 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
53147 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
53166 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
53185 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
53204 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
53223 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
53242 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
53256 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
53275 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
53289 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
53308 AATCGCATTGCGA
1 AATCGCAATGCGA
53321 TTTTCATTTC
Statistics
Matches: 258, Mismatches: 9, Indels: 52
0.81 0.03 0.16
Matches are distributed among these distances:
14 50 0.19
15 3 0.01
16 13 0.05
17 12 0.05
18 4 0.02
19 163 0.63
20 13 0.05
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:53096 original size:33 final size:34
Alignment explanation
Indices: 53009--53314 Score: 335
Period size: 33 Copynumber: 8.8 Consensus size: 34
52999 CGGAAATTAC
* *
53009 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
53042 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
53076 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
53114 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
53147 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
53185 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
53223 AATCGCAATGCGAAATGAAAATCGCAACGA--AA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
53255 GAATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 -AATCGCAATGCGAAATGAAAATCGCAACGATGAA
53289 AATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
53315 TTGCGATTTT
Statistics
Matches: 252, Mismatches: 7, Indels: 28
0.88 0.02 0.10
Matches are distributed among these distances:
32 2 0.01
33 111 0.44
34 32 0.13
35 5 0.02
36 4 0.02
37 2 0.01
38 96 0.38
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:53124 original size:52 final size:52
Alignment explanation
Indices: 53037--53320 Score: 407
Period size: 52 Copynumber: 5.3 Consensus size: 52
53027 AAATCCCAAC
53037 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
53090 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
53142 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
53199 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
53254 A-G--AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
53303 ATGAAAATCGCATTGCGA
1 ATGAAAATCGCAATGCGA
53321 TTTTCATTTC
Statistics
Matches: 218, Mismatches: 3, Indels: 21
0.90 0.01 0.09
Matches are distributed among these distances:
47 10 0.05
48 1 0.00
49 5 0.02
50 3 0.01
52 107 0.49
53 16 0.07
54 3 0.01
55 5 0.02
56 1 0.00
57 67 0.31
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:53261 original size:14 final size:14
Alignment explanation
Indices: 53242--53296 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
53232 GCGAAATGAA
53242 AATCGCAACGAAAG
1 AATCGCAACGAAAG
53256 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
53273 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
53289 AATCGCAA
1 AATCGCAA
53297 TGCGAAATGA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 5 0.14
19 8 0.23
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:53387 original size:19 final size:19
Alignment explanation
Indices: 53310--53379 Score: 131
Period size: 19 Copynumber: 3.6 Consensus size: 19
53300 GAAATGAAAA
53310 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
53329 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT
53349 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
53368 TCGCATTGCGAT
1 TCGCATTGCGAT
53380 AGTCATTTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
19 31 0.62
20 19 0.38
ACGTcount: A:0.16, C:0.23, G:0.17, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:53505 original size:14 final size:14
Alignment explanation
Indices: 53486--53522 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
53476 CATCAATTAC
53486 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
53500 ACAAATCATCTTTT
1 ACAAATCAACTTTT
53514 ACAAATCAA
1 ACAAATCAA
53523 TTAAATAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:55510 original size:14 final size:14
Alignment explanation
Indices: 55491--55547 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
55481 GCGAAATGAA
*
55491 AATCGCAACGACAG
1 AATCGCAACGAAAG
55505 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
55522 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
55538 AATCGCAACG
1 AATCGCAACG
55548 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:55518 original size:33 final size:33
Alignment explanation
Indices: 55472--55564 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
55462 GCGAAACCAA
*
55472 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
55505 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
55538 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
55565 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:55529 original size:19 final size:19
Alignment explanation
Indices: 55435--55569 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
55425 TAGTTTACTT
* *
55435 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
55455 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
55474 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
55493 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
55507 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
55526 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
55540 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
55559 TCGCAATGCGA
1 TCGCAACGCGA
55570 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:55587 original size:19 final size:19
Alignment explanation
Indices: 55565--55677 Score: 120
Period size: 19 Copynumber: 6.5 Consensus size: 19
55555 AAAATCGCAA
55565 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
55584 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
55598 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
55617 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
55631 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
55650 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
55669 TGCGATTTT
1 TGCGATTTT
55678 AACTTTCGTG
Statistics
Matches: 77, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
14 22 0.29
15 1 0.01
16 2 0.03
17 2 0.03
18 2 0.03
19 48 0.62
ACGTcount: A:0.07, C:0.18, G:0.28, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:55607 original size:33 final size:33
Alignment explanation
Indices: 55565--55656 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
55555 AAAATCGCAA
55565 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
55598 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
55631 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
55657 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:55690 original size:20 final size:18
Alignment explanation
Indices: 55595--55693 Score: 80
Period size: 19 Copynumber: 5.4 Consensus size: 18
55585 GCGATCTTGT
*
55595 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTT-ATTTCG
* *
55614 CGTTGCGA--TTCTGT--
1 CGTTGCGATTTTATTTCG
55628 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTT-ATTTCG
*
55647 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTT-ATTTCG
55666 CGTTGCGATTTTAACTTTCG
1 CGTTGCGATTTT-A-TTTCG
*
55686 TGTTGCGA
1 CGTTGCGA
55694 AAGTAAACTA
Statistics
Matches: 65, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
14 8 0.12
16 4 0.06
17 4 0.06
19 37 0.57
20 12 0.18
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.45
Consensus pattern (18 bp):
CGTTGCGATTTTATTTCG
Found at i:55857 original size:93 final size:93
Alignment explanation
Indices: 55741--56023 Score: 541
Period size: 93 Copynumber: 3.1 Consensus size: 93
55731 ATGGATTGCA
*
55741 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAAAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
55805 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
55833 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
55898 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
55926 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
55991 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
56019 TTACT
1 TTACT
56024 AAGCAATCTA
Statistics
Matches: 188, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
92 4 0.02
93 184 0.98
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:57768 original size:19 final size:19
Alignment explanation
Indices: 57744--57827 Score: 97
Period size: 19 Copynumber: 4.7 Consensus size: 19
57734 GCAACGAGAG
*
57744 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
57763 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
57782 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
57796 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATGAA
*
57815 AATCGCAATGCGA
1 AATCGCAACGCGA
57828 TTTTGGTTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 39 0.71
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:57784 original size:52 final size:52
Alignment explanation
Indices: 57722--57827 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
57712 TCTTTTGGTT
* *
57722 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGACAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATAAAAATCGCAACGC
*
57774 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATAAAAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATAAAAATCGCAACGC
57826 GA
1 GA
57828 TTTTGGTTTC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (52 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATAAAAATCGCAACGC
Found at i:57858 original size:14 final size:14
Alignment explanation
Indices: 57839--57895 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
57829 TTTGGTTTCG
57839 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
57853 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
57872 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
57886 CGTTGCGATT
1 CGTTGCGATT
57896 GTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:57877 original size:19 final size:19
Alignment explanation
Indices: 57853--57941 Score: 80
Period size: 19 Copynumber: 4.9 Consensus size: 19
57843 GCGATTCTCT
57853 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
57872 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
57886 CGTTGCGATTGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*** *
57905 CGTTGCGACAGTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
57925 CGTTGCGATTTTCATTT
1 CGTTGCGATTTTCATTT
57942 ATCTCGTTGC
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 3 0.05
19 25 0.45
20 15 0.27
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:57933 original size:39 final size:33
Alignment explanation
Indices: 57823--57941 Score: 157
Period size: 33 Copynumber: 3.4 Consensus size: 33
57813 AAAATCGCAA
**
57823 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
57856 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
57889 TGCGATTGTCATTTCGCGTTGCGACAGTCATTCTCTCGT
1 TGCGATTTTCATTTCGCGTT--G-C-G--ATTCTCTCGT
57928 TGCGATTTTCATTT
1 TGCGATTTTCATTT
57942 ATCTCGTTGC
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
33 50 0.66
35 1 0.01
36 1 0.01
37 1 0.01
39 23 0.30
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:58075 original size:33 final size:33
Alignment explanation
Indices: 58033--58103 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
58023 AATACTAACT
58033 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
58066 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
58099 TGAAA
1 TGAAA
58104 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:58337 original size:22 final size:22
Alignment explanation
Indices: 58285--58339 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
58275 TGGTTGTGAG
**
58285 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
58307 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
58329 GGATTTCTTCG
1 GGATTTCTTCG
58340 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:58511 original size:20 final size:20
Alignment explanation
Indices: 58486--58679 Score: 203
Period size: 20 Copynumber: 9.7 Consensus size: 20
58476 CTTTAAATAT
58486 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
58506 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
58528 -TCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGGATA
*
58547 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
58567 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
58587 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
58607 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
58627 CGCATTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
58647 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
58667 CGCGTTGCGATTT
1 CGCGTTGCGATTT
58680 TGGAAAATCG
Statistics
Matches: 143, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:58673 original size:60 final size:60
Alignment explanation
Indices: 58486--58679 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
58476 CTTTAAATAT
* ** *
58486 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTACAGATA
* *** * *
58547 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
* * * * *
58607 CACGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
58667 CGCGTTGCGATTT
1 CGCGTTGCGATTT
58680 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
Found at i:60352 original size:16 final size:15
Alignment explanation
Indices: 60331--60360 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
60321 AAACTATTAC
60331 TTATATTTTGTTTTAT
1 TTATATTTT-TTTTAT
60347 TTATATTTTTTTTA
1 TTATATTTTTTTTA
60361 AATCATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (15 bp):
TTATATTTTTTTTAT
Found at i:60702 original size:2 final size:2
Alignment explanation
Indices: 60691--60720 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
60681 ATAAATAACA
60691 AT AT -T 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
60721 ATTTCATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62429 original size:96 final size:91
Alignment explanation
Indices: 62308--62540 Score: 236
Period size: 96 Copynumber: 2.5 Consensus size: 91
62298 TTGGGTTGGG
* *
62308 TTGGGTATAGCTG-TGGAATATGTGTATGTATGGATATTACAGTGCTTGGCAG-CTATAGTTTTT
1 TTGGGTATAGTTGTTGG-ATA-GTGTATGTATGGATATTACAATGC-T--C-GTCTATAGTTTTT
* * * *
62371 GGATACGTTTATGTTTTTTCGTTATTGATATGC
60 GGATACGTGTATG-CTTTTCGGTATTGATATGA
* * * *
62404 TTGGGTATAGTTGTTGGATACGTGTATGTCTAGATATTACAATGCTCGTTTGTAGTTTTTGGATA
1 TTGGGTATAGTTGTTGGATA-GTGTATGTATGGATATTACAATGCTCGTCTATAGTTTTTGGATA
62469 CGTGTATGCTTTTCGGTATTGATATGA
65 CGTGTATGCTTTTCGGTATTGATATGA
* * * * **
62496 TCGTGTATAGTTGTTGCATAGTGTATGTTTGGATATGGCAATGCT
1 TTGGGTATAGTTGTTGGATAGTGTATGTATGGATATTACAATGCT
62541 TCGTGTGTAG
Statistics
Matches: 117, Mismatches: 18, Indels: 9
0.81 0.12 0.06
Matches are distributed among these distances:
91 21 0.18
92 34 0.29
93 22 0.19
95 1 0.01
96 36 0.31
97 3 0.03
ACGTcount: A:0.21, C:0.09, G:0.27, T:0.44
Consensus pattern (91 bp):
TTGGGTATAGTTGTTGGATAGTGTATGTATGGATATTACAATGCTCGTCTATAGTTTTTGGATAC
GTGTATGCTTTTCGGTATTGATATGA
Found at i:62504 original size:92 final size:93
Alignment explanation
Indices: 62363--62551 Score: 247
Period size: 92 Copynumber: 2.0 Consensus size: 93
62353 TTGGCAGCTA
* * * * * *
62363 TAGTTTTTGGATACGTTTATGTTTTTTCGTTATTGATATGCTTGGGTATAGTTGTTGGATACGTG
1 TAGTTTTTGGATACGTGTATGTCTTTTCGGTATTGATATGATCGGGTATAGTTGTTGCATA-GTG
* *
62428 TATGTCTAGATATTACAATGC-TCGTTTG
65 TATGTCTAGATATGACAATGCTTCGTGTG
*
62456 TAGTTTTTGGATACGTGTATG-CTTTTCGGTATTGATATGATCGTGTATAGTTGTTGCATAGTGT
1 TAGTTTTTGGATACGTGTATGTCTTTTCGGTATTGATATGATCGGGTATAGTTGTTGCATAGTGT
* * *
62520 ATGTTTGGATATGGCAATGCTTCGTGTG
66 ATGTCTAGATATGACAATGCTTCGTGTG
62548 TAGT
1 TAGT
62552 AGTAATATGG
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
91 20 0.24
92 43 0.52
93 20 0.24
ACGTcount: A:0.19, C:0.08, G:0.26, T:0.47
Consensus pattern (93 bp):
TAGTTTTTGGATACGTGTATGTCTTTTCGGTATTGATATGATCGGGTATAGTTGTTGCATAGTGT
ATGTCTAGATATGACAATGCTTCGTGTG
Found at i:62591 original size:22 final size:22
Alignment explanation
Indices: 62566--62657 Score: 78
Period size: 22 Copynumber: 4.1 Consensus size: 22
62556 ATATGGTGCT
62566 TGTTTTGATGTTGCTATGCTCG
1 TGTTTTGATGTTGCTATGCTCG
* * *
62588 TGTTTGGATATTGCAATGCTTCG
1 TGTTTTGATGTTGCTATGC-TCG
* * * * * *
62611 TCTGTTGTTGTAG-TATGGTGCT
1 TGTTTTGATGTTGCTATGCT-CG
62633 TGTTTTGATGTTGCTATGCTCG
1 TGTTTTGATGTTGCTATGCTCG
62655 TGT
1 TGT
62658 ATAGTTGTCG
Statistics
Matches: 49, Mismatches: 18, Indels: 6
0.67 0.25 0.08
Matches are distributed among these distances:
21 1 0.02
22 33 0.67
23 15 0.31
ACGTcount: A:0.11, C:0.12, G:0.28, T:0.49
Consensus pattern (22 bp):
TGTTTTGATGTTGCTATGCTCG
Found at i:62593 original size:67 final size:67
Alignment explanation
Indices: 62521--62657 Score: 229
Period size: 67 Copynumber: 2.0 Consensus size: 67
62511 GCATAGTGTA
*
62521 TGTTTGGATATGGCAATGCTTCGTGTGTAGTAGTAATATGGTGCTTGTTTTGATGTTGCTATGCT
1 TGTTTGGATATGGCAATGCTTCGTCTGTAGTAGTAATATGGTGCTTGTTTTGATGTTGCTATGCT
62586 CG
66 CG
* * * *
62588 TGTTTGGATATTGCAATGCTTCGTCTGTTGTTGTAGTATGGTGCTTGTTTTGATGTTGCTATGCT
1 TGTTTGGATATGGCAATGCTTCGTCTGTAGTAGTAATATGGTGCTTGTTTTGATGTTGCTATGCT
62653 CG
66 CG
62655 TGT
1 TGT
62658 ATAGTTGTCG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.14, C:0.11, G:0.29, T:0.46
Consensus pattern (67 bp):
TGTTTGGATATGGCAATGCTTCGTCTGTAGTAGTAATATGGTGCTTGTTTTGATGTTGCTATGCT
CG
Found at i:75513 original size:15 final size:16
Alignment explanation
Indices: 75493--75530 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
75483 TTTTCTTCAT
*
75493 AATGATT-AAACGCGG
1 AATGATTCAAACGCCG
*
75508 AATGATTCAAATGCCG
1 AATGATTCAAACGCCG
75524 AATGATT
1 AATGATT
75531 TAGAGTCTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (16 bp):
AATGATTCAAACGCCG
Found at i:75716 original size:22 final size:22
Alignment explanation
Indices: 75688--75778 Score: 148
Period size: 22 Copynumber: 4.2 Consensus size: 22
75678 CGCTGAATGT
75688 TGAACGGTTCAGTATTCAGCGC
1 TGAACGGTTCAGTATTCAGCGC
* *
75710 TGAACGGTTCAATATTCAGCGT
1 TGAACGGTTCAGTATTCAGCGC
75732 TGAACGGTTCAGTATTCAGCGC
1 TGAACGGTTCAGTATTCAGCGC
*
75754 TGAAC-GTTCAGTATTCAGCGT
1 TGAACGGTTCAGTATTCAGCGC
75775 TGAA
1 TGAA
75779 TGATTCCATT
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
21 19 0.30
22 45 0.70
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (22 bp):
TGAACGGTTCAGTATTCAGCGC
Found at i:75735 original size:44 final size:43
Alignment explanation
Indices: 75686--75778 Score: 168
Period size: 44 Copynumber: 2.1 Consensus size: 43
75676 CACGCTGAAT
75686 GTTGAACGGTTCAGTATTCAGCGCTGAACGGTTCAATATTCAGC
1 GTTGAACGGTTCAGTATTCAGCGCTGAAC-GTTCAATATTCAGC
*
75730 GTTGAACGGTTCAGTATTCAGCGCTGAACGTTCAGTATTCAGC
1 GTTGAACGGTTCAGTATTCAGCGCTGAACGTTCAATATTCAGC
75773 GTTGAA
1 GTTGAA
75779 TGATTCCATT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 19 0.40
44 29 0.60
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (43 bp):
GTTGAACGGTTCAGTATTCAGCGCTGAACGTTCAATATTCAGC
Found at i:78457 original size:20 final size:20
Alignment explanation
Indices: 78432--78469 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
78422 TTTGATTCAC
*
78432 GGAATATAAGATTATCAGTA
1 GGAATAAAAGATTATCAGTA
78452 GGAATAAAAGATTATCAG
1 GGAATAAAAGATTATCAG
78470 GAAATAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.05, G:0.21, T:0.26
Consensus pattern (20 bp):
GGAATAAAAGATTATCAGTA
Found at i:78475 original size:18 final size:19
Alignment explanation
Indices: 78434--78476 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
78424 TGATTCACGG
* *
78434 AATATAAGATTATCAGTAGG
1 AATAAAAGATTATCAG-AGA
78454 AATAAAAGATTATCAG-GA
1 AATAAAAGATTATCAGAGA
78472 AATAA
1 AATAA
78477 GATTACTGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
20 15 0.71
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.26
Consensus pattern (19 bp):
AATAAAAGATTATCAGAGA
Found at i:79500 original size:28 final size:29
Alignment explanation
Indices: 79452--79506 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
79442 TTATCTTTTT
79452 AATTTTGTAAAAAAAATTATATAAATTTA
1 AATTTTGTAAAAAAAATTATATAAATTTA
* *
79481 AATTTTTTAAAGAAAA-TATATAAATT
1 AATTTTGTAAAAAAAATTATATAAATT
79507 AATTATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (29 bp):
AATTTTGTAAAAAAAATTATATAAATTTA
Found at i:83276 original size:32 final size:34
Alignment explanation
Indices: 83230--83312 Score: 98
Period size: 32 Copynumber: 2.5 Consensus size: 34
83220 TTAGTATTTT
* *
83230 TTTAAATAGTTATTATATTTTATATT-AAT-ATA
1 TTTATATAATTATTATATTTTATATTAAATAATA
* * *
83262 TTTATGTAATTATTATTTTTTTTATTAAAATAATA
1 TTTATATAATTATTATATTTTATATT-AAATAATA
83297 TTTATATAATTATTAT
1 TTTATATAATTATTAT
83313 TTATTTAGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
32 21 0.50
34 3 0.07
35 18 0.43
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (34 bp):
TTTATATAATTATTATATTTTATATTAAATAATA
Found at i:83278 original size:35 final size:35
Alignment explanation
Indices: 83239--83318 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
83229 TTTTAAATAG
*
83239 TTATTATATTTTATATT-AAT-ATATTTATGTAATTA
1 TTATT-TATTTT-TATTAAATAATATTTATATAATTA
83274 TTATTT-TTTTTATTAAAATAATATTTATATAATTA
1 TTATTTATTTTTATT-AAATAATATTTATATAATTA
83309 TTATTTATTT
1 TTATTTATTT
83319 AGAATTATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
32 4 0.10
33 4 0.10
34 4 0.10
35 25 0.62
36 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (35 bp):
TTATTTATTTTTATTAAATAATATTTATATAATTA
Done.