Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002802.1 Hibiscus syriacus cultivar Beakdansim tig00005767_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: 118359
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:14949 original size:15 final size:15
Alignment explanation
Indices: 14929--14960 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
14919 GATATCTGAA
14929 ACGATCTTTTATTAT
1 ACGATCTTTTATTAT
14944 ACGATCTTTTATTAT
1 ACGATCTTTTATTAT
14959 AC
1 AC
14961 AATCATTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50
Consensus pattern (15 bp):
ACGATCTTTTATTAT
Found at i:15257 original size:2 final size:2
Alignment explanation
Indices: 15250--15283 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
15240 TAAAAGTTAA
15250 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
15284 TATCAATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17587 original size:5 final size:5
Alignment explanation
Indices: 17577--17867 Score: 539
Period size: 5 Copynumber: 58.2 Consensus size: 5
17567 TGCTGAAATA
* * *
17577 TGTAT TGTAT TATAT TATAT TGTAT TGTAT TGTAT TGTAT TGTAA TGTAT
1 TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT
17627 TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT
1 TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT
17677 TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT
1 TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT
17727 TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT
1 TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT
17777 TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT
1 TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT
17827 TGTAT TGTAT TGTAT TGT-T CTGTAT TGTAT TGTAT TGTAT T
1 TGTAT TGTAT TGTAT TGTAT -TGTAT TGTAT TGTAT TGTAT T
17868 ATAATAATTG
Statistics
Matches: 280, Mismatches: 4, Indels: 4
0.97 0.01 0.01
Matches are distributed among these distances:
4 1 0.00
5 278 0.99
6 1 0.00
ACGTcount: A:0.21, C:0.00, G:0.19, T:0.60
Consensus pattern (5 bp):
TGTAT
Found at i:21153 original size:18 final size:19
Alignment explanation
Indices: 21109--21157 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
21099 GAAATTGATC
21109 AAAGAAAATAAGATTAAGA
1 AAAGAAAATAAGATTAAGA
* *
21128 TAATAAAATATA-A-TAAGA
1 AAAGAAAATA-AGATTAAGA
21146 AAAGAAAA-AAGA
1 AAAGAAAATAAGA
21158 AAAAAATAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
16 1 0.04
17 2 0.08
18 11 0.46
19 9 0.38
20 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.16
Consensus pattern (19 bp):
AAAGAAAATAAGATTAAGA
Found at i:31591 original size:17 final size:17
Alignment explanation
Indices: 31569--31603 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
31559 TTGTTTTGAC
31569 TCTTCCTGCTTTTACTG
1 TCTTCCTGCTTTTACTG
31586 TCTTCCTGCTTTTACTG
1 TCTTCCTGCTTTTACTG
31603 T
1 T
31604 GACCACGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.06, C:0.29, G:0.11, T:0.54
Consensus pattern (17 bp):
TCTTCCTGCTTTTACTG
Found at i:31884 original size:22 final size:23
Alignment explanation
Indices: 31872--31915 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
31862 TTGTTTTTAC
31872 TTTGTTTTTAAG-TATTTTAAGA
1 TTTGTTTTTAAGTTATTTTAAGA
31894 TTTGTTTTTAAG-TATTTTAAGA
1 TTTGTTTTTAAGTTATTTTAAGA
31916 GTTATCTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59
Consensus pattern (23 bp):
TTTGTTTTTAAGTTATTTTAAGA
Found at i:34158 original size:14 final size:14
Alignment explanation
Indices: 34139--34170 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
34129 AAGGTGCATA
34139 AAATACTAAAAATT
1 AAATACTAAAAATT
*
34153 AAATACTGAAAATT
1 AAATACTAAAAATT
34167 AAAT
1 AAAT
34171 GATTAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.28
Consensus pattern (14 bp):
AAATACTAAAAATT
Found at i:34178 original size:14 final size:15
Alignment explanation
Indices: 34147--34187 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
34137 TAAAATACTA
34147 AAAATTAAAT-ACTG
1 AAAATTAAATGACTG
*
34161 AAAATTAAATGA-TT
1 AAAATTAAATGACTG
34175 AAAATGTAAATGA
1 AAAAT-TAAATGA
34188 AAGAAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.59, C:0.02, G:0.10, T:0.29
Consensus pattern (15 bp):
AAAATTAAATGACTG
Found at i:35185 original size:15 final size:16
Alignment explanation
Indices: 35160--35190 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
35150 TTTGGGATTA
35160 TTTTTTACTATTTTAG
1 TTTTTTACTATTTTAG
35176 TTTTTT-CTATTTTAG
1 TTTTTTACTATTTTAG
35191 ATTGATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.71
Consensus pattern (16 bp):
TTTTTTACTATTTTAG
Found at i:36174 original size:21 final size:21
Alignment explanation
Indices: 36130--36174 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
36120 GATTTCTGGG
* * *
36130 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
36151 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
36172 CAA
1 CAA
36175 ACAAACCAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:41163 original size:21 final size:21
Alignment explanation
Indices: 41098--41157 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
41088 GATTTCTGAG
41098 CAAGGGGAATCGATACCCATT
1 CAAGGGGAATCGATACCCATT
41119 CAAGGGGAATCGATACCCATT
1 CAAGGGGAATCGATACCCATT
*
41140 CAAGGGGAACCGATACCC
1 CAAGGGGAATCGATACCC
41158 CCTCAAACGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.33, C:0.27, G:0.25, T:0.15
Consensus pattern (21 bp):
CAAGGGGAATCGATACCCATT
Found at i:42270 original size:13 final size:14
Alignment explanation
Indices: 42252--42280 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
42242 TGTCTATAAA
42252 AATATATAAG-AAC
1 AATATATAAGCAAC
42265 AATATATAAGCAAC
1 AATATATAAGCAAC
42279 AA
1 AA
42281 AATCGGAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.21
Consensus pattern (14 bp):
AATATATAAGCAAC
Found at i:42816 original size:23 final size:21
Alignment explanation
Indices: 42765--42816 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 21
42755 TTAGGGACAT
42765 TTTATATGGCACTTCGGTGCA
1 TTTATATGGCACTTCGGTGCA
* *
42786 ATTCTATGCTGCACTTCGGTGCA
1 TTTATATG--GCACTTCGGTGCA
42809 TTTATATG
1 TTTATATG
42817 AGCTGTGGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 6 0.24
23 19 0.76
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (21 bp):
TTTATATGGCACTTCGGTGCA
Found at i:43616 original size:22 final size:22
Alignment explanation
Indices: 43588--43631 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
43578 AAAATTGATG
43588 TAAATAA-AATTAATAATAAAAA
1 TAAATAATAA-TAATAATAAAAA
43610 TAAATAATAATAATAATAAAAA
1 TAAATAATAATAATAATAAAAA
43632 ACAATTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (22 bp):
TAAATAATAATAATAATAAAAA
Found at i:43617 original size:16 final size:16
Alignment explanation
Indices: 43598--43629 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
43588 TAAATAAAAT
43598 TAATAATAAAAATAAA
1 TAATAATAAAAATAAA
*
43614 TAATAATAATAATAAA
1 TAATAATAAAAATAAA
43630 AAACAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
TAATAATAAAAATAAA
Found at i:43962 original size:102 final size:102
Alignment explanation
Indices: 43842--44127 Score: 421
Period size: 102 Copynumber: 2.8 Consensus size: 102
43832 TTCTCAAGGG
* * *
43842 AAACTATCTCAAGCGAGACAAAATTTGTTTTAAGAACAATATTCTCAAGCGAGATGAAATTTTGT
1 AAACTATCTCAAGCGAGACAAAATTTGTTTTAAGAACAACAATCTCAAGTGAGATGAAATTTTGT
43907 TTTAAGAAAAACAATCTAAAAGTTTGAGTTTCATGAA
66 TTTAAGAAAAACAATCTAAAAGTTTGAGTTTCATGAA
* * * *
43944 AAATTGTCTCAAGGGAGACAAAATTTGTTTCAAGAACAACAATCTCAAGTGAGATGAAATTTTGT
1 AAACTATCTCAAGCGAGACAAAATTTGTTTTAAGAACAACAATCTCAAGTGAGATGAAATTTTGT
* * * *
44009 TTTACGCAAAACAATCTCAAAGTTTGAGTTTCATGAG
66 TTTAAGAAAAACAATCTAAAAGTTTGAGTTTCATGAA
* * * *
44046 AAACTATCTCAACCAAGACAAAATTTGTTTTAAGAACAACAATCTCAATTGAGATG-AATTTTTT
1 AAACTATCTCAAGCGAGACAAAATTTGTTTTAAGAACAACAATCTCAAGTGAGATGAAATTTTGT
44110 TTTGAAGAAAAACAATCT
66 TTT-AAGAAAAACAATCT
44128 TGAGTGAGAT
Statistics
Matches: 162, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
101 10 0.06
102 152 0.94
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (102 bp):
AAACTATCTCAAGCGAGACAAAATTTGTTTTAAGAACAACAATCTCAAGTGAGATGAAATTTTGT
TTTAAGAAAAACAATCTAAAAGTTTGAGTTTCATGAA
Found at i:43990 original size:36 final size:37
Alignment explanation
Indices: 43950--44028 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 37
43940 TGAAAAATTG
43950 TCTCAAGGGAGA-CAAAATTTGTTTCAAG-AACAACAA
1 TCTCAAGGGAGATCAAAATTTGTTTCAAGCAA-AACAA
* * * * *
43986 TCTCAAGTGAGATGAAATTTTGTTTTACGCAAAACAA
1 TCTCAAGGGAGATCAAAATTTGTTTCAAGCAAAACAA
44023 TCTCAA
1 TCTCAA
44029 AGTTTGAGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
36 11 0.31
37 23 0.64
38 2 0.06
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (37 bp):
TCTCAAGGGAGATCAAAATTTGTTTCAAGCAAAACAA
Found at i:44124 original size:37 final size:33
Alignment explanation
Indices: 44068--44163 Score: 111
Period size: 37 Copynumber: 2.8 Consensus size: 33
44058 CCAAGACAAA
* *
44068 ATTTGTTTTAAGAACAACAATCTCAATTGAGATG
1 ATTT-TTTTAAGAAAAACAATCTCAAGTGAGATG
**
44102 AATTTTTTTTTGAAGAAAAACAATCTTGAGTGAGATG
1 -A--TTTTTTT-AAGAAAAACAATCTCAAGTGAGATG
44139 ATTTTTTTAAGAAAAACAATCTCAA
1 ATTTTTTTAAGAAAAACAATCTCAA
44164 AGTTTGAGTT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
33 15 0.29
34 7 0.13
35 1 0.02
36 5 0.10
37 24 0.46
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (33 bp):
ATTTTTTTAAGAAAAACAATCTCAAGTGAGATG
Found at i:44227 original size:135 final size:138
Alignment explanation
Indices: 43975--44228 Score: 311
Period size: 135 Copynumber: 1.9 Consensus size: 138
43965 AATTTGTTTC
* * *
43975 AAGAACAACAATCTCAAGTGAGATGAAATTTTGTTTTACGCAAAACAATCTCAAAGTTTGAGTTT
1 AAGAAAAACAATCTCAAGTGAGATG-AATTTTGTTTTAAGAAAAACAATCTCAAAGTTTGAGTTT
* * * * *
44040 CATGAGAAACTATCTCAACCAAGACAAAATTTGTTTTAAGAACAACAATCTCAATTGAGATGAAT
65 CAAGAGAAACAACCTCAACCAAGACAAAATTTGTTCTAAGAAAAACAATCTCAATTGAGATGAAT
44105 TTTTTTTTG
130 TTTTTTTTG
**
44114 AAGAAAAACAATCTTGAGTGAGATG-A-TTT-TTTTAAGAAAAACAATCTCAAAGTTTGAGTTTC
1 AAGAAAAACAATCTCAAGTGAGATGAATTTTGTTTTAAGAAAAACAATCTCAAAGTTTGAGTTTC
* *** *
44176 GAAG-GAAACAACCTTAAGTGAGA-ATAAATTTGTTCTAAGAAAAACATTCTCAA
66 -AAGAGAAACAACCTCAACCAAGACA-AAATTTGTTCTAAGAAAAACAATCTCAA
44229 GATAGATAAA
Statistics
Matches: 98, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
134 1 0.01
135 69 0.70
136 5 0.05
137 1 0.01
139 22 0.22
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.31
Consensus pattern (138 bp):
AAGAAAAACAATCTCAAGTGAGATGAATTTTGTTTTAAGAAAAACAATCTCAAAGTTTGAGTTTC
AAGAGAAACAACCTCAACCAAGACAAAATTTGTTCTAAGAAAAACAATCTCAATTGAGATGAATT
TTTTTTTG
Found at i:44530 original size:38 final size:36
Alignment explanation
Indices: 44414--44579 Score: 106
Period size: 38 Copynumber: 4.6 Consensus size: 36
44404 AAGACAAAAA
44414 TTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTT
1 TTTCAAGGGAAAATATCTCAAGTGAGATG-AATTTTT
* * * * ****
44451 ATTTCAA-GGAAAACTGTCTCGAGTGGGA-CAAAAAAT
1 -TTTCAAGGGAAAA-TATCTCAAGTGAGATGAATTTTT
*
44487 TTTCAAGGGAAAATATATCAAGTGAGATGAATTTTTT
1 TTTCAAGGGAAAATATCTCAAGTGAGATGAA-TTTTT
* * * * **
44524 GTTTCAAGAGG-AACTGTCTCGAGCGAGATGAA-AATT
1 -TTTCAAG-GGAAAATATCTCAAGTGAGATGAATTTTT
*
44560 TTTCAAAGGAAAATATCTCA
1 TTTCAAGGGAAAATATCTCA
44580 TGGGAGATAA
Statistics
Matches: 93, Mismatches: 28, Indels: 17
0.67 0.20 0.12
Matches are distributed among these distances:
34 2 0.02
35 29 0.31
36 13 0.14
37 7 0.08
38 40 0.43
39 2 0.02
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (36 bp):
TTTCAAGGGAAAATATCTCAAGTGAGATGAATTTTT
Found at i:44587 original size:73 final size:73
Alignment explanation
Indices: 44405--44579 Score: 230
Period size: 73 Copynumber: 2.4 Consensus size: 73
44395 GTTTCGAGTA
44405 AGAC-AAAAA-TTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTTATTTCAAGGAAAACTGT
1 AGACAAAAAATTTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTTATTTCAAGGAAAACTGT
*
44468 CTCGAGTG
66 CTCGAGCG
* * * * *
44476 GGACAAAAAATTTTCAAGGGAAAATATATCAAGTGAGATGAATTTTTTGTTTCAA-GAGGAACTG
1 AGACAAAAAATTTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTTATTTCAAGGA-AAACTG
44540 TCTCGAGCG
65 TCTCGAGCG
** * *
44549 AGATGAAAATTTTTCAAAGGAAAATATCTCA
1 AGACAAAAAATTTTCAAGGGAAAATATCTCA
44580 TGGGAGATAA
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
71 3 0.03
72 7 0.08
73 79 0.89
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.29
Consensus pattern (73 bp):
AGACAAAAAATTTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTTATTTCAAGGAAAACTGT
CTCGAGCG
Found at i:44666 original size:20 final size:20
Alignment explanation
Indices: 44643--44682 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
44633 AAATATCTAA
44643 AGGGAGAAGGAATTTTGTTT
1 AGGGAGAAGGAATTTTGTTT
44663 AGGGAGAAGGAATTTTGTTT
1 AGGGAGAAGGAATTTTGTTT
44683 CGAGAGAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.35, T:0.35
Consensus pattern (20 bp):
AGGGAGAAGGAATTTTGTTT
Found at i:44689 original size:20 final size:20
Alignment explanation
Indices: 44646--44690 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
44636 TATCTAAAGG
*
44646 GAGAAGGAATTTTGTTTAGG
1 GAGAAGGAATTTTGTTTAGA
*
44666 GAGAAGGAATTTTGTTTCGA
1 GAGAAGGAATTTTGTTTAGA
44686 GAGAA
1 GAGAA
44691 ACTATATTGA
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:0.33, C:0.02, G:0.33, T:0.31
Consensus pattern (20 bp):
GAGAAGGAATTTTGTTTAGA
Found at i:44766 original size:18 final size:19
Alignment explanation
Indices: 44740--44779 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
44730 ATCTAAAGTG
* *
44740 AGATGAAATTT-TGTTTCA
1 AGATAAAATTTATGTTTAA
44758 AGATAAAATTTATGTTTAA
1 AGATAAAATTTATGTTTAA
44777 AGA
1 AGA
44780 GAAACAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.40
Consensus pattern (19 bp):
AGATAAAATTTATGTTTAA
Found at i:45454 original size:26 final size:24
Alignment explanation
Indices: 45402--45486 Score: 93
Period size: 26 Copynumber: 3.4 Consensus size: 24
45392 TTTTCAAAAG
*
45402 TTGAAAAA-GATTAATGAAGAAGTT
1 TTGAAAAATGATTAATAAAGAA-TT
*
45426 TTGAAAAATGATTCATAAAAGAATTT
1 TTGAAAAATGATTAAT-AAAGAA-TT
45452 TTGAAAAAT-ATTTAATGAAAGAATT
1 TTGAAAAATGA-TTAAT-AAAGAATT
45477 TTGAAAAATG
1 TTGAAAAATG
45487 TTGCCCCTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
24 8 0.15
25 18 0.35
26 26 0.50
ACGTcount: A:0.51, C:0.01, G:0.15, T:0.33
Consensus pattern (24 bp):
TTGAAAAATGATTAATAAAGAATT
Found at i:46062 original size:14 final size:15
Alignment explanation
Indices: 46043--46075 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
46033 TTTCTTTTAT
*
46043 TTTTATTTT-TTCTC
1 TTTTATTTTACTCTC
46057 TTTTATTTTACTCTC
1 TTTTATTTTACTCTC
46072 TTTT
1 TTTT
46076 CTTTCCCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTATTTTACTCTC
Found at i:46078 original size:20 final size:19
Alignment explanation
Indices: 46033--46079 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
46023 TTCTTTCTTC
*
46033 TTTCTTTTATTTTTATTTT
1 TTTCTTTTATTTTTATTCT
46052 TTCTCTTTTA-TTTTACTCTCT
1 TT-TCTTTTATTTTTA-T-TCT
46073 TTTCTTT
1 TTTCTTT
46080 CCCTTACCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 7 0.29
20 13 0.54
21 4 0.17
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTCTTTTATTTTTATTCT
Found at i:51129 original size:2 final size:2
Alignment explanation
Indices: 51122--51154 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
51112 TACTGTTGTT
51122 TA TA 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 TA TA T
51155 TTGTTTTGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:51651 original size:34 final size:34
Alignment explanation
Indices: 51608--51718 Score: 213
Period size: 34 Copynumber: 3.3 Consensus size: 34
51598 TTTTCTCCCT
51608 ATTCACCACAAATCAAATCCAAGGTGACGATTAG
1 ATTCACCACAAATCAAATCCAAGGTGACGATTAG
*
51642 ATTCACCACAAATCAAATCCAAGGTGAGGATTAG
1 ATTCACCACAAATCAAATCCAAGGTGACGATTAG
51676 ATTCACCACAAATCAAATCCAAGGTGACGATTAG
1 ATTCACCACAAATCAAATCCAAGGTGACGATTAG
51710 ATTCACCAC
1 ATTCACCAC
51719 TATATCCCCA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 75 1.00
ACGTcount: A:0.41, C:0.24, G:0.14, T:0.21
Consensus pattern (34 bp):
ATTCACCACAAATCAAATCCAAGGTGACGATTAG
Found at i:52803 original size:262 final size:260
Alignment explanation
Indices: 52298--52936 Score: 827
Period size: 262 Copynumber: 2.4 Consensus size: 260
52288 TAACCATAAC
* * * * *
52298 ATTCTTAGGCACAATTTATTTTATTAATAAAAATATTGACATTAAAAATCGTAACTTATTAT-TT
1 ATTC-TAGGCGCAATCTATTTTATTAATAAAAATATTAACATTACAAATC-T-ACATATT-TCTT
* * * * **
52362 ATTAAACCATGATATAATTGGACGCAACCGTATCTAATATGTATATTCATAAAATTTTAAGCTTT
62 -TTAAACCATGATATTATTGGGCGCAACCATATATAATATACATATTCATAAAATTTTAAGCTTT
* *
52427 TAACTTATTTTATTATCGTAGCAAACTCCAAGGCTCATCGACTTAAACTTTTATAATATTTTAGG
126 TAACTTATTTTATTATCGTAGCAAACTCCAAGACTCATCGACTTAAACTTTCATAATATTTTAGG
** * * *
52492 CGCAATTAATTTTATTATTAAAAAATAGTAAGATTTTAGATTGCAACATGCTTTCTTAGGGAGCC
191 CGCAACCAACTTTATTATTAAAAAATAGTAACATTCTAGATTGCAACATGCTTTCTTAGGGAGCC
52557 ATGAA
256 ATGAA
52562 ATTCTAGGCGCAATCTATTTTATTAATAAAAATATTAACATTACAAATGCTACATATTTCTTTTA
1 ATTCTAGGCGCAATCTATTTTATTAATAAAAATATTAACATTACAAAT-CTACATATTTCTTTTA
* * * * *
52627 GAACCATGTTATTATTGGGTGCAACTATATATATTATACATGTTCATAAAATTTTAAGCTTTTAA
65 -AACCATGATATTATTGGGCGCAACCATATATAATATACATATTCATAAAATTTTAAGCTTTTAA
* * *
52692 CTTATTTTATTATCGTGGGAAACTTCAAGACTCCATCGGA-TTAAACTTTCATAATATTTTAGGC
129 CTTATTTTATTATCGTAGCAAACTCCAAGACT-CATC-GACTTAAACTTTCATAATATTTTAGGC
52756 GCAACCAACTTTATTATT-AAAAATAGTAACATTCTAGATTGCAACATGCTTTCTTAGGGAGCCA
192 GCAACCAACTTTATTATTAAAAAATAGTAACATTCTAGATTGCAACATGCTTTCTTAGGGAGCCA
*
52820 TGAT
257 TGAA
*
52824 ATTTTAGGCGCAATCTATTTTATTAATAAAAATATTAACATTACAAATC-ACAATTTATTTCTTT
1 ATTCTAGGCGCAATCTATTTTATTAATAAAAATATTAACATTACAAATCTAC-A--TATTTCTTT
** * * * *
52888 TATAACCATGATATTATTGGGAACAACCGTATCTATTATATATATTCAT
63 TA-AACCATGATATTATTGGGCGCAACCATATATAATATACATATTCAT
52937 TCTTTTAAAA
Statistics
Matches: 330, Mismatches: 37, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
260 2 0.01
261 6 0.02
262 183 0.55
263 132 0.40
264 7 0.02
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (260 bp):
ATTCTAGGCGCAATCTATTTTATTAATAAAAATATTAACATTACAAATCTACATATTTCTTTTAA
ACCATGATATTATTGGGCGCAACCATATATAATATACATATTCATAAAATTTTAAGCTTTTAACT
TATTTTATTATCGTAGCAAACTCCAAGACTCATCGACTTAAACTTTCATAATATTTTAGGCGCAA
CCAACTTTATTATTAAAAAATAGTAACATTCTAGATTGCAACATGCTTTCTTAGGGAGCCATGAA
Found at i:60909 original size:12 final size:12
Alignment explanation
Indices: 60892--60923 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
60882 AACACATGTG
60892 AAATTAGATACA
1 AAATTAGATACA
60904 AAATTAGATACA
1 AAATTAGATACA
60916 AAATTAGA
1 AAATTAGA
60924 AACATAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.59, C:0.06, G:0.09, T:0.25
Consensus pattern (12 bp):
AAATTAGATACA
Found at i:62547 original size:5 final size:5
Alignment explanation
Indices: 62537--62719 Score: 366
Period size: 5 Copynumber: 36.6 Consensus size: 5
62527 ACAATGAACA
62537 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
62587 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
62637 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
62687 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
62720 TGTGTCTATT
Statistics
Matches: 178, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 178 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:67887 original size:54 final size:54
Alignment explanation
Indices: 67822--67928 Score: 142
Period size: 54 Copynumber: 2.0 Consensus size: 54
67812 TGTATTTTTG
** *
67822 GCACTAAATGTGCAACCCATGGTATTCATAATGTGTTTATGAATGACCATTTCA
1 GCACTAAATGTGCAACCCATGAAATTCATAATGAGTTTATGAATGACCATTTCA
* * * **
67876 GCACTATATGTGCAATCCATGAAATTCATAATGAGTTTTTGAATTTCCATTTC
1 GCACTAAATGTGCAACCCATGAAATTCATAATGAGTTTATGAATGACCATTTC
67929 GGCATTTTGG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (54 bp):
GCACTAAATGTGCAACCCATGAAATTCATAATGAGTTTATGAATGACCATTTCA
Found at i:74389 original size:21 final size:22
Alignment explanation
Indices: 74337--74389 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
74327 ATGTAAAGTT
74337 CATT-TAA-TTACATCAAAGAG
1 CATTCTAAGTTACATCAAAGAG
* **
74357 GATTCTTCGTTACATCAAAG-G
1 CATTCTAAGTTACATCAAAGAG
74378 CATTCTAAGTTA
1 CATTCTAAGTTA
74390 TGGCTTAATG
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
20 3 0.12
21 11 0.44
22 11 0.44
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (22 bp):
CATTCTAAGTTACATCAAAGAG
Found at i:78359 original size:21 final size:20
Alignment explanation
Indices: 78335--78386 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 20
78325 TGTGGTAAAT
*
78335 TACTAACTTTTATATTTCTTA
1 TACTAACTTTTATATAT-TTA
78356 TACTAA-TTTT-T-TATTTA
1 TACTAACTTTTATATATTTA
78373 TACTAACTTTTATA
1 TACTAACTTTTATA
78387 ATTAATGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
17 9 0.33
18 6 0.22
19 2 0.07
20 4 0.15
21 6 0.22
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.58
Consensus pattern (20 bp):
TACTAACTTTTATATATTTA
Found at i:79803 original size:2 final size:2
Alignment explanation
Indices: 79796--79850 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
79786 TTTTACCTAT
79796 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
79838 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
79851 GTGTGTGTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:80212 original size:13 final size:14
Alignment explanation
Indices: 80196--80224 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
80186 AAATAATTTT
80196 TTAATTTTAA-TAA
1 TTAATTTTAATTAA
80209 TTAATTTTAATTAA
1 TTAATTTTAATTAA
80223 TT
1 TT
80225 TAAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAATTTTAATTAA
Found at i:80471 original size:19 final size:20
Alignment explanation
Indices: 80422--80472 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
80412 TCAATCCCAA
*
80422 AAAGTTATATAATTTATATAT
1 AAAG-TATAAAATTTATATAT
*
80443 AAATTGATAAAATTTATATAT
1 AAAGT-ATAAAATTTATATAT
80464 -AAGTATAAA
1 AAAGTATAAA
80473 TATAATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 5 0.19
20 4 0.15
21 17 0.65
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (20 bp):
AAAGTATAAAATTTATATAT
Found at i:80479 original size:23 final size:21
Alignment explanation
Indices: 80428--80481 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
80418 CCAAAAAGTT
**
80428 ATATAATTTATATATAAATTG
1 ATATAATTTATATATAAATAA
*
80449 ATAAAATTTATATATAAGTATAA
1 ATATAATTTATATATAA--ATAA
80472 ATATAATTTA
1 ATATAATTTA
80482 AATGTTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 16 0.59
23 11 0.41
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (21 bp):
ATATAATTTATATATAAATAA
Found at i:80937 original size:14 final size:14
Alignment explanation
Indices: 80920--80984 Score: 59
Period size: 14 Copynumber: 4.8 Consensus size: 14
80910 TCATTTTCAT
80920 TTTATGGTTTAAGA
1 TTTATGGTTTAAGA
80934 TTTATGGTTT-AGA
1 TTTATGGTTTAAGA
80947 TTT-TGAGTTT-AGAA
1 TTTATG-GTTTAAG-A
80961 TTTA-GGTTTAA-A
1 TTTATGGTTTAAGA
*
80973 GTTTAGGGTTTA
1 -TTTATGGTTTA
80985 TGGATTTTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.07
13 20 0.44
14 22 0.49
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (14 bp):
TTTATGGTTTAAGA
Found at i:80949 original size:13 final size:13
Alignment explanation
Indices: 80920--80984 Score: 62
Period size: 13 Copynumber: 4.8 Consensus size: 13
80910 TCATTTTCAT
80920 TTTATGGTTTAAGA
1 TTTATGGTTT-AGA
80934 TTTATGGTTTAGA
1 TTTATGGTTTAGA
80947 TTT-TGAGTTTAGAA
1 TTTATG-GTTTAG-A
*
80961 TTTA-GGTTTAAA
1 TTTATGGTTTAGA
*
80973 GTTTAGGGTTTA
1 -TTTATGGTTTA
80985 TGGATTTTGA
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
12 3 0.07
13 21 0.47
14 21 0.47
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (13 bp):
TTTATGGTTTAGA
Found at i:81042 original size:14 final size:15
Alignment explanation
Indices: 81023--81055 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
81013 ATTTAGTTTC
81023 TAAATTCATT-AAAT
1 TAAATTCATTGAAAT
*
81037 TAAATTTATTGAAAT
1 TAAATTCATTGAAAT
81052 TAAA
1 TAAA
81056 AAAATGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (15 bp):
TAAATTCATTGAAAT
Found at i:83713 original size:59 final size:57
Alignment explanation
Indices: 83627--83772 Score: 154
Period size: 57 Copynumber: 2.5 Consensus size: 57
83617 TATCGAGATT
*
83627 TTCAAG-AAATAAATTTAACAATTTATTT-CTTTCTTACAAAATAGAATCATACTTAAT-
1 TTCAAGAAAATAAATTAAACAATTTATTTCCTTTCTTA-AAAATAG--TCATACTTAATC
* * * **
83684 TCTCAAGAAAATGAATTAAATAATTTATTTCCTTTTTTAAGTATAGTCATACTTAATC
1 T-TCAAGAAAATAAATTAAACAATTTATTTCCTTTCTTAAAAATAGTCATACTTAATC
* * *
83742 TTCAAGAAAATAAATTCATCGATTTATTTCC
1 TTCAAGAAAATAAATTAAACAATTTATTTCC
83773 CTTTACAAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
57 37 0.50
58 6 0.08
59 24 0.32
60 7 0.09
ACGTcount: A:0.40, C:0.13, G:0.05, T:0.41
Consensus pattern (57 bp):
TTCAAGAAAATAAATTAAACAATTTATTTCCTTTCTTAAAAATAGTCATACTTAATC
Found at i:83903 original size:97 final size:97
Alignment explanation
Indices: 83800--84001 Score: 277
Period size: 97 Copynumber: 2.1 Consensus size: 97
83790 TAAAAAACAT
*
83800 TTTATTTTCTTTTTCAAAATAGGAAAA-ATAATCCTAA-GATTTATTTCATTTTAAAAAATAGAA
1 TTTATTTTCTTTTACAAAATAGGAAAATA-AAT-CTAAGGATTTATTTCATTTTAAAAAATAGAA
* **
83863 TCA-TATAAGATT-ATTAGGAAAATAAATTTAACGA
64 TCATTA-AAGATTCA-TAAGAAAATAAATTTAAAAA
* * *
83897 TTTATTTTCTTTTACAAAATAGGAAAATAAATCTAAGGATTTATTTCCTTTTACAAGATAGAATC
1 TTTATTTTCTTTTACAAAATAGGAAAATAAATCTAAGGATTTATTTCATTTTAAAAAATAGAATC
83962 ATTAAAGATTCATAAGAAAATAAATTTAAAAA
66 ATTAAAGATTCATAAGAAAATAAATTTAAAAA
83994 TTTATTTT
1 TTTATTTT
84002 TTTAATTCAA
Statistics
Matches: 94, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
96 4 0.04
97 86 0.91
98 4 0.04
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.40
Consensus pattern (97 bp):
TTTATTTTCTTTTACAAAATAGGAAAATAAATCTAAGGATTTATTTCATTTTAAAAAATAGAATC
ATTAAAGATTCATAAGAAAATAAATTTAAAAA
Found at i:83920 original size:39 final size:39
Alignment explanation
Indices: 83877--83957 Score: 126
Period size: 39 Copynumber: 2.1 Consensus size: 39
83867 ATAAGATTAT
* *
83877 TAGGAAAATAAATTTAACGATTTATTTTCTTTTACAAAA
1 TAGGAAAATAAATCTAACGATTTATTTCCTTTTACAAAA
* *
83916 TAGGAAAATAAATCTAAGGATTTATTTCCTTTTACAAGA
1 TAGGAAAATAAATCTAACGATTTATTTCCTTTTACAAAA
83955 TAG
1 TAG
83958 AATCATTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (39 bp):
TAGGAAAATAAATCTAACGATTTATTTCCTTTTACAAAA
Found at i:84084 original size:102 final size:102
Alignment explanation
Indices: 83919--84103 Score: 232
Period size: 102 Copynumber: 1.8 Consensus size: 102
83909 TACAAAATAG
* * * *
83919 GAAAATAAATCTAAGGATTTATTTCCTTTTACAAGATAGAATCATTAAAGATTCATAAGAAAATA
1 GAAAATAAATCTAAGAATTTATTTCCTTTTAAAAGATAAAATCATCAAAGATTCATAAGAAAATA
83984 AATTTA-AAAATTTATTTTTTTAATTCAAGATTCCTAA
66 AA-TTAGAAAATTTATTTTTTTAATTCAAGATTCCTAA
* * * * *
84021 GAAAATAAATTTAATAATTTATTTCTTTTTAAAAGATAAAATCATCCACGATCCTCA-AA-AAAA
1 GAAAATAAATCTAAGAATTTATTTCCTTTTAAAAGATAAAATCATCAAAGAT--TCATAAGAAAA
*
84084 TAAATTAGATAATTTATTTT
64 TAAATTAGAAAATTTATTTT
84104 CCTTACGAAG
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
101 3 0.04
102 62 0.89
103 2 0.03
104 3 0.04
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.38
Consensus pattern (102 bp):
GAAAATAAATCTAAGAATTTATTTCCTTTTAAAAGATAAAATCATCAAAGATTCATAAGAAAATA
AATTAGAAAATTTATTTTTTTAATTCAAGATTCCTAA
Found at i:84307 original size:174 final size:174
Alignment explanation
Indices: 84081--84409 Score: 409
Period size: 174 Copynumber: 1.9 Consensus size: 174
84071 ATCCTCAAAA
* * *
84081 AAATAAATTAGATAATTTATTTTCCTTACGAAGTTAGAATCATTCAAGATTCTCAAGAAAATAAA
1 AAATAAATTAGACAATTTATTTTCCTTACAAAGTTAGAATCATTCAAGATTCTCAAGAAAAGAAA
* *
84146 GTT-AACT-ATTTATTTTCATTACAAAGTTAGAATCA-TTTAAGATTCTCAAGGAAATAAATTTA
66 -TTCAA-TGATTTATTTTCATTACAAAGTTAGAAT-ATTTTAAGATTCTCAAGAAAATAAATTCA
** *
84208 ACT-ATTTATTTTTCTTAGAAAGTTAGAACCATTCAAAATTCACAATG
128 A-TAATTTATTTCCCTTACAAAGTTAGAACCATTCAAAATTCACAATG
* * * * * *
84255 AAATAAATTCA-ACAATTTATTTT-CTTAATAAAGTTATAATCGTTCTAGATTCTCGAGGAAAGA
1 AAATAAATT-AGACAATTTATTTTCCTT-ACAAAGTTAGAATCATTCAAGATTCTCAAGAAAAGA
* * *
84318 AATTCAATGATTTATTTTCCTTACAAATTTAGAATATTTTAAGATTTTCAAGAAAATAAATTCAA
64 AATTCAATGATTTATTTTCATTACAAAGTTAGAATATTTTAAGATTCTCAAGAAAATAAATTCAA
84383 TAATTTATTTCCCTTACAAAGTTAGAA
129 TAATTTATTTCCCTTACAAAGTTAGAA
84410 TATACACAAG
Statistics
Matches: 132, Mismatches: 17, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
173 8 0.06
174 123 0.93
175 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (174 bp):
AAATAAATTAGACAATTTATTTTCCTTACAAAGTTAGAATCATTCAAGATTCTCAAGAAAAGAAA
TTCAATGATTTATTTTCATTACAAAGTTAGAATATTTTAAGATTCTCAAGAAAATAAATTCAATA
ATTTATTTCCCTTACAAAGTTAGAACCATTCAAAATTCACAATG
Found at i:84412 original size:58 final size:58
Alignment explanation
Indices: 84010--84410 Score: 354
Period size: 58 Copynumber: 6.9 Consensus size: 58
84000 TTTTTAATTC
* ** * * **
84010 AAGATTC-CTAAGAAAATAAATTTAATAATTTATTTCTTTTTA-AAAGATAAAATCATCC
1 AAGATTCTC-AAGAAAATAAATTCAATAATTTATTT-TCCTTACAAAGTTAGAATCATTT
* * * * *
84068 ACGATCCTCAAAAAAATAAATT-AGATAATTTATTTTCCTTACGAAGTTAGAATCATTC
1 AAGATTCTCAAGAAAATAAATTCA-ATAATTTATTTTCCTTACAAAGTTAGAATCATTT
*
84126 AAGATTCTCAAGAAAATAAAGTT-AACT-ATTTATTTTCATTACAAAGTTAGAATCATTT
1 AAGATTCTCAAGAAAATAAA-TTCAA-TAATTTATTTTCCTTACAAAGTTAGAATCATTT
* * * * * *
84184 AAGATTCTCAAGGAAATAAATTTAACT-ATTTATTTTTCTTAGAAAGTTAGAACCATTC
1 AAGATTCTCAAGAAAATAAATTCAA-TAATTTATTTTCCTTACAAAGTTAGAATCATTT
* * * * * *
84242 AAAATTCACAATG-AAATAAATTCAACAATTTATTTT-CTTAATAAAGTTATAATCGTTCT
1 AAGATTCTCAA-GAAAATAAATTCAATAATTTATTTTCCTT-ACAAAGTTAGAATCATT-T
* * * * *
84301 -AGATTCTCGAGGAAAGAAATTCAATGATTTATTTTCCTTACAAATTTAGAAT-ATTTT
1 AAGATTCTCAAGAAAATAAATTCAATAATTTATTTTCCTTACAAAGTTAGAATCA-TTT
* *
84358 AAGATTTTCAAGAAAATAAATTCAATAATTTATTTCCCTTACAAAGTTAGAAT
1 AAGATTCTCAAGAAAATAAATTCAATAATTTATTTTCCTTACAAAGTTAGAAT
84411 ATACACAAGA
Statistics
Matches: 282, Mismatches: 47, Indels: 28
0.79 0.13 0.08
Matches are distributed among these distances:
57 12 0.04
58 261 0.93
59 9 0.03
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (58 bp):
AAGATTCTCAAGAAAATAAATTCAATAATTTATTTTCCTTACAAAGTTAGAATCATTT
Found at i:84627 original size:32 final size:33
Alignment explanation
Indices: 84591--84652 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
84581 TTTAGCAACC
*
84591 CAATAATC-AAAAGGATTTAATCATTTGATACA
1 CAATAATCAAAAAGGAATTAATCATTTGATACA
84623 CAATAATCAAAAAGGAATTAATCATTTGAT
1 CAATAATCAAAAAGGAATTAATCATTTGAT
84653 TTTACTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 8 0.29
33 20 0.71
ACGTcount: A:0.48, C:0.11, G:0.10, T:0.31
Consensus pattern (33 bp):
CAATAATCAAAAAGGAATTAATCATTTGATACA
Found at i:93528 original size:20 final size:18
Alignment explanation
Indices: 93505--93541 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
93495 AAAATAGATA
93505 TTAAATTAATAAATTATAAT
1 TTAAATTAA-AAA-TATAAT
93525 TTAAATTAAAAATATAA
1 TTAAATTAAAAATATAA
93542 AATAAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 3 0.18
20 9 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TTAAATTAAAAATATAAT
Found at i:94754 original size:14 final size:14
Alignment explanation
Indices: 94732--94857 Score: 83
Period size: 14 Copynumber: 9.7 Consensus size: 14
94722 CATTTAAATG
94732 ATAAACGAACACAA
1 ATAAACGAACACAA
*
94746 ATGAACG-A-AC--
1 ATAAACGAACACAA
* *
94756 ATAAACGAACAGAT
1 ATAAACGAACACAA
* *
94770 GTAAACGAACA-TA
1 ATAAACGAACACAA
94783 ATAAACGAACACAA
1 ATAAACGAACACAA
*
94797 ATGAACG-A-AC--
1 ATAAACGAACACAA
* *
94807 ATAAACGAACAGAT
1 ATAAACGAACACAA
* *
94821 GTAAACGAACA-TA
1 ATAAACGAACACAA
94834 ATAAACGAACACAA
1 ATAAACGAACACAA
*
94848 ATGAACGAAC
1 ATAAACGAAC
94858 GTAAACAAAG
Statistics
Matches: 85, Mismatches: 17, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
10 12 0.14
11 2 0.02
12 6 0.07
13 22 0.26
14 43 0.51
ACGTcount: A:0.57, C:0.18, G:0.13, T:0.11
Consensus pattern (14 bp):
ATAAACGAACACAA
Found at i:94764 original size:24 final size:24
Alignment explanation
Indices: 94732--94863 Score: 129
Period size: 24 Copynumber: 5.2 Consensus size: 24
94722 CATTTAAATG
94732 ATAAACGAACACAAATGAACGAAC
1 ATAAACGAACACAAATGAACGAAC
* ** *
94756 ATAAACGAACAGATGTAAACGAAC
1 ATAAACGAACACAAATGAACGAAC
94780 ATAATAAACGAACACAAATGAACGAAC
1 ---ATAAACGAACACAAATGAACGAAC
* ** *
94807 ATAAACGAACAGATGTAAACGAAC
1 ATAAACGAACACAAATGAACGAAC
94831 ATAATAAACGAACACAAATGAACGAAC
1 ---ATAAACGAACACAAATGAACGAAC
*
94858 GTAAAC
1 ATAAAC
94864 AAAGACAATA
Statistics
Matches: 85, Mismatches: 17, Indels: 12
0.75 0.15 0.11
Matches are distributed among these distances:
24 45 0.53
27 40 0.47
ACGTcount: A:0.57, C:0.18, G:0.14, T:0.11
Consensus pattern (24 bp):
ATAAACGAACACAAATGAACGAAC
Found at i:94793 original size:27 final size:27
Alignment explanation
Indices: 94756--94844 Score: 121
Period size: 27 Copynumber: 3.4 Consensus size: 27
94746 ATGAACGAAC
94756 ATAAACGAACAGATGTAAACGAACATA
1 ATAAACGAACAGATGTAAACGAACATA
* ** *
94783 ATAAACGAACACAAATGAACGAAC---
1 ATAAACGAACAGATGTAAACGAACATA
94807 ATAAACGAACAGATGTAAACGAACATA
1 ATAAACGAACAGATGTAAACGAACATA
94834 ATAAACGAACA
1 ATAAACGAACA
94845 CAAATGAACG
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
24 20 0.39
27 31 0.61
ACGTcount: A:0.57, C:0.17, G:0.13, T:0.12
Consensus pattern (27 bp):
ATAAACGAACAGATGTAAACGAACATA
Found at i:94808 original size:51 final size:51
Alignment explanation
Indices: 94732--94863 Score: 255
Period size: 51 Copynumber: 2.6 Consensus size: 51
94722 CATTTAAATG
94732 ATAAACGAACACAAATGAACGAACATAAACGAACAGATGTAAACGAACATA
1 ATAAACGAACACAAATGAACGAACATAAACGAACAGATGTAAACGAACATA
94783 ATAAACGAACACAAATGAACGAACATAAACGAACAGATGTAAACGAACATA
1 ATAAACGAACACAAATGAACGAACATAAACGAACAGATGTAAACGAACATA
*
94834 ATAAACGAACACAAATGAACGAACGTAAAC
1 ATAAACGAACACAAATGAACGAACATAAAC
94864 AAAGACAATA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
51 80 1.00
ACGTcount: A:0.57, C:0.18, G:0.14, T:0.11
Consensus pattern (51 bp):
ATAAACGAACACAAATGAACGAACATAAACGAACAGATGTAAACGAACATA
Found at i:94812 original size:37 final size:37
Alignment explanation
Indices: 94771--94853 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 37
94761 CGAACAGATG
* *
94771 TAAACGAACATA-ATAAACGAACACAAATGAACGAACA
1 TAAACGAACAGATATAAACGAACA-AAATAAACGAACA
* *
94808 TAAACGAACAGATGTAAACGAACATAATAAACGAACA
1 TAAACGAACAGATATAAACGAACAAAATAAACGAACA
* *
94845 CAAATGAAC
1 TAAACGAAC
94854 GAACGTAAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 29 0.74
38 10 0.26
ACGTcount: A:0.58, C:0.18, G:0.12, T:0.12
Consensus pattern (37 bp):
TAAACGAACAGATATAAACGAACAAAATAAACGAACA
Found at i:94862 original size:37 final size:38
Alignment explanation
Indices: 94784--94891 Score: 103
Period size: 37 Copynumber: 2.9 Consensus size: 38
94774 ACGAACATAA
* * *
94784 TAAACGAACACAAATGAACGAACATAAACGAAC-AGATG
1 TAAACGAACA-AAATAAACGAACATAAATGAACGAGACG
* *
94822 TAAACGAACATAATAAACGAACACAAATGAACGA-ACG
1 TAAACGAACAAAATAAACGAACATAAATGAACGAGACG
* * * * *
94859 TAAACAAAGACAATAAATGGACATAAATGAACG
1 TAAACGAACAAAATAAACGAACATAAATGAACG
94892 TAAACGAACA
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
37 47 0.81
38 11 0.19
ACGTcount: A:0.56, C:0.17, G:0.15, T:0.12
Consensus pattern (38 bp):
TAAACGAACAAAATAAACGAACATAAATGAACGAGACG
Found at i:94886 original size:10 final size:10
Alignment explanation
Indices: 94871--94909 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
94861 AACAAAGACA
*
94871 ATAAATGGAC
1 ATAAATGAAC
94881 ATAAATGAAC
1 ATAAATGAAC
* *
94891 GTAAACGAAC
1 ATAAATGAAC
94901 ATAAATGAA
1 ATAAATGAA
94910 AATAGATTTT
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:0.56, C:0.10, G:0.15, T:0.18
Consensus pattern (10 bp):
ATAAATGAAC
Found at i:95190 original size:40 final size:40
Alignment explanation
Indices: 95141--95220 Score: 108
Period size: 40 Copynumber: 1.9 Consensus size: 40
95131 AACAAGCCTT
*
95141 TTGTTCATGTTTGTTCATTTAAT-TAAACGAACACAAAATA
1 TTGTTCATGTTCGTTCATTTAATATAAACGAACA-AAAATA
*
95181 TTGTTCATGTTCGTTCGTTTAATAAATAAACGAACAAAAA
1 TTGTTCATGTTCGTTCATTTAAT--ATAAACGAACAAAAA
95221 CGAACTTCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 21 0.60
42 4 0.11
43 10 0.29
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (40 bp):
TTGTTCATGTTCGTTCATTTAATATAAACGAACAAAAATA
Done.