Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000873.1 Hibiscus syriacus cultivar Beakdansim tig00001687_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: 169192
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:10678 original size:34 final size:34
Alignment explanation
Indices: 10627--10691 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
10617 GCATTCAAAT
10627 TGAAGTATTTTAAAATTTGAGGTTTACAATGTAA
1 TGAAGTATTTTAAAATTTGAGGTTTACAATGTAA
* * * *
10661 TGAATTATTTTAGAATTTGGGGTTTAGAATG
1 TGAAGTATTTTAAAATTTGAGGTTTACAATG
10692 AAATTGAGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.34, C:0.02, G:0.22, T:0.43
Consensus pattern (34 bp):
TGAAGTATTTTAAAATTTGAGGTTTACAATGTAA
Found at i:12122 original size:2 final size:2
Alignment explanation
Indices: 12115--12158 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
12105 CTAGAATTTC
12115 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12157 AT
1 AT
12159 TTGAACTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14459 original size:2 final size:2
Alignment explanation
Indices: 14448--14537 Score: 67
Period size: 2 Copynumber: 50.5 Consensus size: 2
14438 GAACCCGAAA
* *
14448 AT AT -T AT AT AT A- AT -T A- AT AT A- AA AT AT AT AA AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
14484 AT AT AT A- AT -T A- AT AT A- AA AT AT AT AA AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14521 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
14538 ATCGGGCGGG
Statistics
Matches: 71, Mismatches: 6, Indels: 22
0.72 0.06 0.22
Matches are distributed among these distances:
1 11 0.15
2 60 0.85
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:14537 original size:31 final size:31
Alignment explanation
Indices: 14446--14521 Score: 152
Period size: 31 Copynumber: 2.5 Consensus size: 31
14436 CCGAACCCGA
14446 AAATATTATATATAATTAATATAAAATATAT
1 AAATATTATATATAATTAATATAAAATATAT
14477 AAATATTATATATAATTAATATAAAATATAT
1 AAATATTATATATAATTAATATAAAATATAT
14508 AAATATTATATATA
1 AAATATTATATATA
14522 TATATATATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
AAATATTATATATAATTAATATAAAATATAT
Found at i:16352 original size:20 final size:20
Alignment explanation
Indices: 16316--16353 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
16306 ATCCTATTCT
**
16316 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
16336 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
16354 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:23359 original size:24 final size:23
Alignment explanation
Indices: 23332--23376 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
23322 AAAGTAAATA
23332 AATAAT-AAAAATATAGAATAAAAG
1 AATAATGAAAAA-ATA-AATAAAAG
23356 AATAATGAAAAAATAAATAAA
1 AATAATGAAAAAATAAATAAA
23377 GTATAAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 6 0.30
24 9 0.45
25 5 0.25
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (23 bp):
AATAATGAAAAAATAAATAAAAG
Found at i:23846 original size:13 final size:13
Alignment explanation
Indices: 23828--23852 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23818 TAGCATTGGG
23828 AAAAGAAAATAAT
1 AAAAGAAAATAAT
23841 AAAAGAAAATAA
1 AAAAGAAAATAA
23853 AGAAATAAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (13 bp):
AAAAGAAAATAAT
Found at i:34944 original size:12 final size:12
Alignment explanation
Indices: 34927--34951 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34917 CCCATGCATG
34927 CATACAGACATA
1 CATACAGACATA
34939 CATACAGACATA
1 CATACAGACATA
34951 C
1 C
34952 GTAAATGTGT
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:0.48, C:0.28, G:0.08, T:0.16
Consensus pattern (12 bp):
CATACAGACATA
Found at i:38004 original size:21 final size:21
Alignment explanation
Indices: 37978--38020 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
37968 AATTCGCAGC
37978 AGTTGGTGGTAGATAGGTTGA
1 AGTTGGTGGTAGATAGGTTGA
37999 AGTTGGTGGTAGATAGGTTGA
1 AGTTGGTGGTAGATAGGTTGA
38020 A
1 A
38021 TTTTCAGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.42, T:0.33
Consensus pattern (21 bp):
AGTTGGTGGTAGATAGGTTGA
Found at i:39487 original size:32 final size:32
Alignment explanation
Indices: 39450--39522 Score: 119
Period size: 32 Copynumber: 2.3 Consensus size: 32
39440 CATGTTCATT
39450 TAACGTTTACGAACATATCCATGTCATACGTG
1 TAACGTTTACGAACATATCCATGTCATACGTG
* * *
39482 TAACGTTTACGAACATGTTCGTGTCATACGTG
1 TAACGTTTACGAACATATCCATGTCATACGTG
39514 TAACGTTTA
1 TAACGTTTA
39523 ATGTTTACGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (32 bp):
TAACGTTTACGAACATATCCATGTCATACGTG
Found at i:40929 original size:7 final size:7
Alignment explanation
Indices: 40917--40943 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
40907 TTAATTTTAT
40917 AAAAAAG
1 AAAAAAG
40924 AAAAAAG
1 AAAAAAG
40931 AAAAAAG
1 AAAAAAG
40938 AAAAAA
1 AAAAAA
40944 AAGTGAACCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:42590 original size:21 final size:21
Alignment explanation
Indices: 42555--42595 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
42545 AAATTACGCA
*
42555 TTTAATACCTGAACTATCAAT
1 TTTAATACCTAAACTATCAAT
* *
42576 TTTAATATCTAAACTTTCAA
1 TTTAATACCTAAACTATCAA
42596 AAAAATTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.17, G:0.02, T:0.41
Consensus pattern (21 bp):
TTTAATACCTAAACTATCAAT
Found at i:44038 original size:31 final size:31
Alignment explanation
Indices: 44003--44068 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
43993 GTCTTTTCTT
44003 GGTGTCTAACGTTTTC-TCTGTTACCATTTTA
1 GGTGTCTAACGTTTTCTTC-GTTACCATTTTA
* *
44034 GGTGTCTAACTTTTTCTTCGTTATCATTTTA
1 GGTGTCTAACGTTTTCTTCGTTACCATTTTA
44065 GGTG
1 GGTG
44069 CACAGGCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 30 0.94
32 2 0.06
ACGTcount: A:0.15, C:0.17, G:0.18, T:0.50
Consensus pattern (31 bp):
GGTGTCTAACGTTTTCTTCGTTACCATTTTA
Found at i:63373 original size:60 final size:61
Alignment explanation
Indices: 63280--63455 Score: 177
Period size: 60 Copynumber: 3.0 Consensus size: 61
63270 TTTGGCGATA
* * * * *
63280 AAATTGAAAGATCTAAAAGTTTAGGGACCAATTTAGAATGAAATTCATAGTTTG-GGGATG
1 AAATTGAAATATTTAAAAGTTTAAGGACTAATTTAGAATGAAATTCATAGTTTGAAGGATG
* * *
63340 AAATT-AGAT-TGTTCAAAAGTTTAAGGACTAATTTACAAT-AAAATCATAG-TTGAAGGATG
1 AAATTGAAATAT-TT-AAAAGTTTAAGGACTAATTTAGAATGAAATTCATAGTTTGAAGGATG
* * *
63399 AAATTGAAATATTT-AAAGTTTAAGGACTAATTT-GAAATGAGATACATAGTTTAAAGG
1 AAATTGAAATATTTAAAAGTTTAAGGACTAATTTAG-AATGAAATTCATAGTTTGAAGG
63456 CATATAATGC
Statistics
Matches: 94, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
58 26 0.28
59 29 0.31
60 38 0.40
61 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.32
Consensus pattern (61 bp):
AAATTGAAATATTTAAAAGTTTAAGGACTAATTTAGAATGAAATTCATAGTTTGAAGGATG
Found at i:65802 original size:205 final size:208
Alignment explanation
Indices: 65433--65848 Score: 613
Period size: 205 Copynumber: 2.0 Consensus size: 208
65423 AATTACACTG
* *
65433 GATGTCACTGACCCATAATTTAAATTCTAAATTAGTCTTCAAACTTTAAAGCATTATAATAAAGT
1 GATGTCACTGACCCATAATTTAAATTCTAAATTAGTCTTCAAACTTCAAAACATTATAATAAAGT
* ** * *
65498 CCTCATATAATCAATTTCATATCACCAATCAGGTCTTTTTATCAAACTAATCATTAATTTTAGCC
66 CCTCATAGAATCAATTTCATATCACCAATCAGGTCTTTCCATCAAACTAATCATTAATTTAAACC
65563 TTAAATATCAAATCAGATCTCAACTAAAGCCTATTCGAAGAATATCGATAAGCTTT-CCCCC-TT
131 TTAAATATCAAATCAGATCTCAACTAAAGCCTATTCGAAGAATATCGATAAGCTTTCCCCCCTTT
*
65626 TTTAAACACGGTA
196 TTTAAACACGATA
* * * *
65639 GATGTCCCTGA-CCATGATTTAAATTCTAAATTAGTCTTCAAACTTCAAAACATTCTAATTAAGT
1 GATGTCACTGACCCATAATTTAAATTCTAAATTAGTCTTCAAACTTCAAAACATTATAATAAAGT
* * * * * * *
65703 CCTCGTAGAATCGATTTCCTATCACCAATCAGGTCTTTCCATCAAACTAGTCCTTGATTTAAACG
66 CCTCATAGAATCAATTTCATATCACCAATCAGGTCTTTCCATCAAACTAATCATTAATTTAAACC
* * *
65768 TTAAATGTCAAATCGGATCTCAACTAAAGCCTATTTGAAGAATATCGATAAGCTTTCCCCCCTTT
131 TTAAATATCAAATCAGATCTCAACTAAAGCCTATTCGAAGAATATCGATAAGCTTTCCCCCCTTT
65833 TTTAAACACGATA
196 TTTAAACACGATA
65846 GAT
1 GAT
65849 AAAAATATTG
Statistics
Matches: 186, Mismatches: 22, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
205 154 0.83
206 15 0.08
207 17 0.09
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.34
Consensus pattern (208 bp):
GATGTCACTGACCCATAATTTAAATTCTAAATTAGTCTTCAAACTTCAAAACATTATAATAAAGT
CCTCATAGAATCAATTTCATATCACCAATCAGGTCTTTCCATCAAACTAATCATTAATTTAAACC
TTAAATATCAAATCAGATCTCAACTAAAGCCTATTCGAAGAATATCGATAAGCTTTCCCCCCTTT
TTTAAACACGATA
Found at i:67216 original size:2 final size:2
Alignment explanation
Indices: 67209--67251 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
67199 ATAAAGCAAT
67209 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
67251 T
1 T
67252 TGGCAATGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:73157 original size:23 final size:23
Alignment explanation
Indices: 73113--73157 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
73103 GTGTTGCTCG
* *
73113 TTTATCTATGTCTTTGTGACACA
1 TTTATCTATGTCTTTATAACACA
*
73136 TTTATCTCTGTCTTTATAACAC
1 TTTATCTATGTCTTTATAACAC
73158 GTTTTTCGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.20, G:0.09, T:0.49
Consensus pattern (23 bp):
TTTATCTATGTCTTTATAACACA
Found at i:73620 original size:18 final size:17
Alignment explanation
Indices: 73592--73629 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
73582 AAAAATTATG
73592 ATTTTCGGTTTAGTTTA
1 ATTTTCGGTTTAGTTTA
73609 ATTTTACGGTTTAGTTTA
1 ATTTT-CGGTTTAGTTTA
73627 ATT
1 ATT
73630 CAAATCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.21, C:0.05, G:0.16, T:0.58
Consensus pattern (17 bp):
ATTTTCGGTTTAGTTTA
Found at i:79002 original size:20 final size:20
Alignment explanation
Indices: 78973--79014 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
78963 CGGTTCACCT
*
78973 CGATTTTACCGGTTTTCAGC
1 CGATTCTACCGGTTTTCAGC
*
78993 CGATTCTACCTGTTTTCAGC
1 CGATTCTACCGGTTTTCAGC
79013 CG
1 CG
79015 GTTCATTGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.29, G:0.19, T:0.38
Consensus pattern (20 bp):
CGATTCTACCGGTTTTCAGC
Found at i:79362 original size:2 final size:2
Alignment explanation
Indices: 79355--79385 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
79345 CGGATTGTCC
79355 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
79386 ATGCGGCCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:83613 original size:25 final size:24
Alignment explanation
Indices: 83556--83614 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
83546 TATTGAGATT
* *
83556 GAGGAGAAAAATATGTAGGAAAAGA
1 GAGGA-AAAAAGATATAGGAAAAGA
* *
83581 AAGAAAAAAAGATATAGGAAAATGA
1 GAGGAAAAAAGATATAGGAAAA-GA
83606 GAGGAAAAA
1 GAGGAAAAA
83615 TTAACTTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
24 15 0.56
25 12 0.44
ACGTcount: A:0.63, C:0.00, G:0.27, T:0.10
Consensus pattern (24 bp):
GAGGAAAAAAGATATAGGAAAAGA
Found at i:86920 original size:22 final size:21
Alignment explanation
Indices: 86888--86929 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
86878 GGGCGGTTCA
86888 ACTCAGCGAGTTAACTCAGTG
1 ACTCAGCGAGTTAACTCAGTG
*
86909 ACTCAGGCGAGTTGACTCAGT
1 ACTCA-GCGAGTTAACTCAGT
86930 TATTTAGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (21 bp):
ACTCAGCGAGTTAACTCAGTG
Found at i:89771 original size:44 final size:44
Alignment explanation
Indices: 89639--89773 Score: 234
Period size: 44 Copynumber: 3.1 Consensus size: 44
89629 TAAAAGCTAT
*
89639 GGTTTAAAAATTGATGAAACTTTGAATACTTCTCTACAGTAAAC
1 GGTTTAAAAATTGATGAAACTTTGAATGCTTCTCTACAGTAAAC
* * *
89683 AGTTTAAAAATTGATGAAATTTTGAATGCTTCTCTATAGTAAAC
1 GGTTTAAAAATTGATGAAACTTTGAATGCTTCTCTACAGTAAAC
89727 GGTTTAAAAATTGATGAAACTTTGAATGCTTCTCTACAGTAAAC
1 GGTTTAAAAATTGATGAAACTTTGAATGCTTCTCTACAGTAAAC
89771 GGT
1 GGT
89774 GGCATATTAG
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 84 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.36
Consensus pattern (44 bp):
GGTTTAAAAATTGATGAAACTTTGAATGCTTCTCTACAGTAAAC
Found at i:90392 original size:18 final size:18
Alignment explanation
Indices: 90371--90413 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
90361 CTTATGTCAA
90371 TGTCGGCTATTATTACAT
1 TGTCGGCTATTATTACAT
90389 TGTCGGCTATTATTACAT
1 TGTCGGCTATTATTACAT
90407 TGTCGGC
1 TGTCGGC
90414 ATTCCATTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.42
Consensus pattern (18 bp):
TGTCGGCTATTATTACAT
Found at i:92705 original size:36 final size:36
Alignment explanation
Indices: 92664--92739 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
92654 ATTTTCGGGA
*
92664 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
92700 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
92736 TTTT
1 TTTT
92740 TTAGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:93181 original size:15 final size:15
Alignment explanation
Indices: 93161--93190 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
93151 TATCACAATC
93161 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
93176 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
93191 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:97708 original size:36 final size:36
Alignment explanation
Indices: 97667--97742 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
97657 ATTTTCGGGA
*
97667 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
97703 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
97739 TTTT
1 TTTT
97743 TTAGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:105210 original size:35 final size:35
Alignment explanation
Indices: 105143--105212 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
105133 TGAAAAATAT
* *
105143 TTATTTATTTTCTTTAAAAATTAAATTCATAAAAA
1 TTATATATTTTCTTTAAAAATTAAAATCATAAAAA
105178 TTATATATTTT-TTTACAAAATTAAAAAT-ATAAAAA
1 TTATATATTTTCTTTA-AAAATT-AAAATCATAAAAA
105213 AGTTTAATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 4 0.13
35 23 0.74
36 4 0.13
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (35 bp):
TTATATATTTTCTTTAAAAATTAAAATCATAAAAA
Found at i:106052 original size:29 final size:30
Alignment explanation
Indices: 105996--106052 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
105986 AATCTATTAA
* **
105996 TTAAGTGATTCATTTTTAATTTTTTTAAAT
1 TTAAGTGATTCATTTATAATTTCATTAAAT
*
106026 TTAA-TGATTTATTTATAATTTCATTAA
1 TTAAGTGATTCATTTATAATTTCATTAA
106053 TAATTAAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 19 0.83
30 4 0.17
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.58
Consensus pattern (30 bp):
TTAAGTGATTCATTTATAATTTCATTAAAT
Found at i:106224 original size:40 final size:40
Alignment explanation
Indices: 106171--106280 Score: 193
Period size: 40 Copynumber: 2.8 Consensus size: 40
106161 ATACCTAAAG
* *
106171 TTTAATTTTTGTTTCATTTTAGTATCCCGTCGTTAAAAAC
1 TTTAGTTTTTGTTTCATTTTAGTATCCCGTCGTTAAAAAA
106211 TTTAGTTTTTGTTTCATTTTAGTATCCCGTCGTTAAAAAA
1 TTTAGTTTTTGTTTCATTTTAGTATCCCGTCGTTAAAAAA
*
106251 TTTAGTTTTTGTTTCATTTTAGTACCCCGT
1 TTTAGTTTTTGTTTCATTTTAGTATCCCGT
106281 GCAAAATTTA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.22, C:0.15, G:0.12, T:0.52
Consensus pattern (40 bp):
TTTAGTTTTTGTTTCATTTTAGTATCCCGTCGTTAAAAAA
Found at i:110209 original size:2 final size:2
Alignment explanation
Indices: 110204--110234 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
110194 AATGTGTGTG
110204 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
110235 GTTAGGGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:112038 original size:19 final size:19
Alignment explanation
Indices: 112014--112050 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
112004 TGATTATTTC
*
112014 AACTCGATTCGAATTGAAA
1 AACTCGACTCGAATTGAAA
112033 AACTCGACTCGAATTGAA
1 AACTCGACTCGAATTGAA
112051 TTCGAGTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (19 bp):
AACTCGACTCGAATTGAAA
Found at i:118778 original size:15 final size:15
Alignment explanation
Indices: 118760--118789 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
118750 AAGTATGCTA
*
118760 CTATCTGGTCTACTG
1 CTATCTAGTCTACTG
118775 CTATCTAGTCTACTG
1 CTATCTAGTCTACTG
118790 GTATGTTCTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.27, G:0.17, T:0.40
Consensus pattern (15 bp):
CTATCTAGTCTACTG
Found at i:121080 original size:3 final size:3
Alignment explanation
Indices: 121074--121112 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
121064 ATGAAAGGAG
121074 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
121113 TGGGTGAGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:133006 original size:30 final size:29
Alignment explanation
Indices: 132953--133021 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
132943 TTGACAATGA
* *
132953 AATGATTGAATTGAAGTAAATTAAAATTTT
1 AATGATTAAATTGAAGTAAATT-AAACTTT
**
132983 AATGATTAAATTGAAGTGTATTAAACTTT
1 AATGATTAAATTGAAGTAAATTAAACTTT
*
133012 AATTATTAAA
1 AATGATTAAA
133022 ATAAGAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 15 0.44
30 19 0.56
ACGTcount: A:0.46, C:0.01, G:0.12, T:0.41
Consensus pattern (29 bp):
AATGATTAAATTGAAGTAAATTAAACTTT
Found at i:138522 original size:24 final size:23
Alignment explanation
Indices: 138479--138523 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
138469 ACCAAATTAT
138479 ATCACATTAAAATATAGGGACTA
1 ATCACATTAAAATATAGGGACTA
138502 ATCA-ATTAAACATAGTAGGGAC
1 ATCACATTAAA-ATA-TAGGGAC
138524 GAAAACTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.30
23 7 0.35
24 7 0.35
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (23 bp):
ATCACATTAAAATATAGGGACTA
Found at i:140615 original size:204 final size:204
Alignment explanation
Indices: 140265--140672 Score: 816
Period size: 204 Copynumber: 2.0 Consensus size: 204
140255 GGTGTAATAC
140265 AATAATACAGGAGTCAGCAAGTGCTCGAGCAGCTGGCATAAAATTGGCTTGGCATGAAACCTCAA
1 AATAATACAGGAGTCAGCAAGTGCTCGAGCAGCTGGCATAAAATTGGCTTGGCATGAAACCTCAA
140330 TTAAATAAATTTAATGACAGGTTCCGTTAATCGAACACATTTCTTTGACTTCTGGTGTTCTATAT
66 TTAAATAAATTTAATGACAGGTTCCGTTAATCGAACACATTTCTTTGACTTCTGGTGTTCTATAT
140395 GATTCTGCCTTTTGGGCATCAATCCCAGTACATGCAACTAAATCAATTTAAATGCGAACCTACCT
131 GATTCTGCCTTTTGGGCATCAATCCCAGTACATGCAACTAAATCAATTTAAATGCGAACCTACCT
140460 GAGGCAAGG
196 GAGGCAAGG
140469 AATAATACAGGAGTCAGCAAGTGCTCGAGCAGCTGGCATAAAATTGGCTTGGCATGAAACCTCAA
1 AATAATACAGGAGTCAGCAAGTGCTCGAGCAGCTGGCATAAAATTGGCTTGGCATGAAACCTCAA
140534 TTAAATAAATTTAATGACAGGTTCCGTTAATCGAACACATTTCTTTGACTTCTGGTGTTCTATAT
66 TTAAATAAATTTAATGACAGGTTCCGTTAATCGAACACATTTCTTTGACTTCTGGTGTTCTATAT
140599 GATTCTGCCTTTTGGGCATCAATCCCAGTACATGCAACTAAATCAATTTAAATGCGAACCTACCT
131 GATTCTGCCTTTTGGGCATCAATCCCAGTACATGCAACTAAATCAATTTAAATGCGAACCTACCT
140664 GAGGCAAGG
196 GAGGCAAGG
140673 CATTAGTTGC
Statistics
Matches: 204, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
204 204 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (204 bp):
AATAATACAGGAGTCAGCAAGTGCTCGAGCAGCTGGCATAAAATTGGCTTGGCATGAAACCTCAA
TTAAATAAATTTAATGACAGGTTCCGTTAATCGAACACATTTCTTTGACTTCTGGTGTTCTATAT
GATTCTGCCTTTTGGGCATCAATCCCAGTACATGCAACTAAATCAATTTAAATGCGAACCTACCT
GAGGCAAGG
Found at i:146662 original size:2 final size:2
Alignment explanation
Indices: 146655--146680 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
146645 GTGCAAATCA
146655 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
146681 GTTCTGGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:152168 original size:23 final size:23
Alignment explanation
Indices: 152109--152215 Score: 101
Period size: 23 Copynumber: 4.7 Consensus size: 23
152099 TTGAATTAAT
*
152109 GTTAAATGAACATGTTCACGAAC
1 GTTAAACGAACATGTTCACGAAC
* * * *
152132 G-TAAATGAATATGTTGACGAAT
1 GTTAAACGAACATGTTCACGAAC
* * *
152154 GTTAAACGAACATGTTTATGAAA
1 GTTAAACGAACATGTTCACGAAC
*
152177 GTTAAACAAACATGTTCACGAAC
1 GTTAAACGAACATGTTCACGAAC
*
152200 GCTAAAC-ATACATGTT
1 GTTAAACGA-ACATGTT
152216 TGCAAATGCT
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (23 bp):
GTTAAACGAACATGTTCACGAAC
Found at i:154217 original size:20 final size:20
Alignment explanation
Indices: 154192--154234 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
154182 AACTCTCAAC
*
154192 CATTTGACATTTAATGATCA
1 CATTTGACATTGAATGATCA
*
154212 CATTTGACATTGAATGCTCA
1 CATTTGACATTGAATGATCA
154232 CAT
1 CAT
154235 CCCTGACATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (20 bp):
CATTTGACATTGAATGATCA
Found at i:161071 original size:374 final size:366
Alignment explanation
Indices: 160390--161131 Score: 1324
Period size: 374 Copynumber: 2.0 Consensus size: 366
160380 AATCTGGCCA
*
160390 AAAAGTTTCCCAGTTTTTGGATTTACATGCATGAACTTTGATCAAGTAATATATTACTGGTCATA
1 AAAAGTTTCCCAGTTTTTGGATTTACATGCATGAACTTTGATCAAGTAATATATAACTGGTCATA
160455 GTCTTTCTATACCAACTACCTCCACAAAGAAAACTTTTATTCAATGCATGAAACGGTCTAAACAT
66 GTCTTTCTATACCAACTACCTCCACAAAGAAAACTTTTATTCAATGCATGAAACGGTCTAAACAT
*
160520 GAAAAATATCATGGGATAATTGACTAACGTTATCGAAACTGAATTTTAATAAGTCCAATCAACTT
131 GAAAAATATCATGGGATAATTGACTAACGTTATCGAAACTGAATTTTAACAAGTCCAATCAACTT
* *
160585 CATTGACAGTTTCATGGTTGAGTTCTTTAATTAACAAAAAAATATCTGTTGACATTCCTGCCCTA
196 CATTGACAGTTTCATGGTTGAGTTCTTTAATTAAAAAAAAAAAATCTGTTGACATTCCTGCCCTA
160650 CTGCTAACATAAATTCAATGGTCCAACTTTCAACTGTCAACCAAATGCTAGCAAGTGTATAAATT
261 CTGCTAACATAAATTCAATGGTCCAACTTTCAACTGTCAACCAAATGCTAGCAAGTGTATAAATT
160715 CACAGCTATGAATTCTTTAGTTTTATCAATGGAAAATGAAT
326 CACAGCTATGAATTCTTTAGTTTTATCAATGGAAAATGAAT
160756 AAAAGTTTCCCAGTTTTTGGATTTACATGCATGAACTTTGATCAAGTAATATATAACTGGT-ATA
1 AAAAGTTTCCCAGTTTTTGGATTTACATGCATGAACTTTGATCAAGTAATATATAACTGGTCATA
160820 GTCTTTCTATACCAACTACCTCCACAAAGAAAACTTTTATTCAATGCATGAAACTTGAAACGGTC
66 GTCTTTCTATACCAACTACCTCCACAAAGAAAACTTTTATTCAATGC-----A--TGAAACGGTC
*
160885 TAAACATGAAAAATATCTTGGGATAATTGACTAACGTTATCGAAACTGAATTTTTAACAAGTCCA
124 TAAACATGAAAAATATCATGGGATAATTGACTAACGTTATCGAAACTGAA-TTTTAACAAGTCCA
160950 ATCAACTTCATTGACAGTTTCATGGTTGAGTTCTTTAATTAATAAAAAAAAAATCTGTTGACATT
188 ATCAACTTCATTGACAGTTTCATGGTTGAGTTCTTTAATTAA-AAAAAAAAAATCTGTTGACATT
* * *
161015 CCTGGCCTATTGCTAACATAAATTCAATGTTCCAACTTTCAACTGTCAACCAAATGCTAGCAAGT
252 CCTGCCCTACTGCTAACATAAATTCAATGGTCCAACTTTCAACTGTCAACCAAATGCTAGCAAGT
161080 GTATAAATTCACAGCTATGAATTCTTTAGTTTTATCAATGGAAAATGAAT
317 GTATAAATTCACAGCTATGAATTCTTTAGTTTTATCAATGGAAAATGAAT
161130 AA
1 AA
161132 TTTATTTTTG
Statistics
Matches: 359, Mismatches: 8, Indels: 10
0.95 0.02 0.03
Matches are distributed among these distances:
365 50 0.14
366 60 0.17
370 1 0.00
372 59 0.16
373 55 0.15
374 134 0.37
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.33
Consensus pattern (366 bp):
AAAAGTTTCCCAGTTTTTGGATTTACATGCATGAACTTTGATCAAGTAATATATAACTGGTCATA
GTCTTTCTATACCAACTACCTCCACAAAGAAAACTTTTATTCAATGCATGAAACGGTCTAAACAT
GAAAAATATCATGGGATAATTGACTAACGTTATCGAAACTGAATTTTAACAAGTCCAATCAACTT
CATTGACAGTTTCATGGTTGAGTTCTTTAATTAAAAAAAAAAAATCTGTTGACATTCCTGCCCTA
CTGCTAACATAAATTCAATGGTCCAACTTTCAACTGTCAACCAAATGCTAGCAAGTGTATAAATT
CACAGCTATGAATTCTTTAGTTTTATCAATGGAAAATGAAT
Found at i:161800 original size:59 final size:59
Alignment explanation
Indices: 161694--161807 Score: 133
Period size: 59 Copynumber: 1.9 Consensus size: 59
161684 CAAACTATAA
* * * *
161694 CTCTCATTCTAAATTGATCCTAAACTTTTTAACATTACAGGTTCATCCCTAAAATATGC
1 CTCTCATTCTAAATTGATCCCAAACTTTTTAACATTACAGATACATCCCCAAAATATGC
* * *
161753 CTCTCTTTCTAAATTGGTCCCAAACTTTTGT-ACATTCCA-ATAACATCCCCAAAAT
1 CTCTCATTCTAAATTGATCCCAAACTTTT-TAACATTACAGAT-ACATCCCCAAAAT
161808 CATTCAAAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
58 1 0.02
59 44 0.96
60 1 0.02
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (59 bp):
CTCTCATTCTAAATTGATCCCAAACTTTTTAACATTACAGATACATCCCCAAAATATGC
Found at i:162122 original size:32 final size:30
Alignment explanation
Indices: 162027--162123 Score: 97
Period size: 32 Copynumber: 3.2 Consensus size: 30
162017 AAAAGTTTAA
* *
162027 ATAAATTTAATGATCATTT-TAACAGTTCG
1 ATAAAATTAATGATCTTTTATAACAGTTCG
** * * *
162056 ATAAAATTGGTGATTATTTTATAATAGTTTG
1 ATAAAATTAATGA-TCTTTTATAACAGTTCG
162087 ATAAAATTCAATGATCGTTTTATAACAGTTCG
1 ATAAAATT-AATGATC-TTTTATAACAGTTCG
162119 ATAAA
1 ATAAA
162124 TTTACAATCA
Statistics
Matches: 52, Mismatches: 12, Indels: 5
0.75 0.17 0.07
Matches are distributed among these distances:
29 10 0.19
30 4 0.08
31 17 0.33
32 21 0.40
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.41
Consensus pattern (30 bp):
ATAAAATTAATGATCTTTTATAACAGTTCG
Done.