Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005156.1 Hibiscus syriacus cultivar Beakdansim tig00011627_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: 77980
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:661 original size:29 final size:30
Alignment explanation
Indices: 629--686 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
619 TTTTTCACCC
**
629 AACTTT-CAATTTGATCAATTTGCTCACTG
1 AACTTTACAATTAAATCAATTTGCTCACTG
*
658 AACTTTACAATTAAATCATTTTGCTCACT
1 AACTTTACAATTAAATCAATTTGCTCACT
687 TACCGTTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (30 bp):
AACTTTACAATTAAATCAATTTGCTCACTG
Found at i:730 original size:3 final size:3
Alignment explanation
Indices: 724--765 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
714 TGTGATAGTT
724 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
766 AAATAATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1579 original size:15 final size:16
Alignment explanation
Indices: 1559--1589 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1549 ATTAAACATT
1559 AAATATAAT-TTTGAA
1 AAATATAATATTTGAA
1574 AAATATAATATTTGAA
1 AAATATAATATTTGAA
1590 TATCAAAATA
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:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (16 bp):
AAATATAATATTTGAA
Found at i:2081 original size:89 final size:87
Alignment explanation
Indices: 1932--2098 Score: 271
Period size: 89 Copynumber: 1.9 Consensus size: 87
1922 TTACAGATTA
** *
1932 AAAGTTATTACTATCAATTTTATATTAAATTTCTATAAATATGATGAGTTATTTGTAATAATATA
1 AAAGTTATTACTAAAAATTTTATATTAAATTTCTACAAATATGATGAGTTATTTGTAATAATATA
1997 ATCATAATTTTAGAACAAATTG
66 ATCATAATTTTAGAACAAATTG
*
2019 AAAGTTATTACTAAAAATTATTTATCTTAAATTTCTACAAATATGATGAGTTATTTGTAATAATA
1 AAAGTTATTACTAAAAA-T-TTTATATTAAATTTCTACAAATATGATGAGTTATTTGTAATAATA
*
2084 TAATTATAATTTTAG
64 TAATCATAATTTTAG
2099 TTCTTAAAAT
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
87 15 0.21
88 1 0.01
89 57 0.78
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (87 bp):
AAAGTTATTACTAAAAATTTTATATTAAATTTCTACAAATATGATGAGTTATTTGTAATAATATA
ATCATAATTTTAGAACAAATTG
Found at i:2808 original size:34 final size:35
Alignment explanation
Indices: 2764--2839 Score: 109
Period size: 34 Copynumber: 2.2 Consensus size: 35
2754 AACACATTCC
2764 TCAATTTCATTCTAAACCCAAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCAAAATTCCAAAATAAT
* * *
2799 TCAA-TTCATTTTAAACCCCAAATTCCAAAATACT
1 TCAATTTCATTCTAAACCCAAAATTCCAAAATAAT
*
2833 TTAATTT
1 TCAATTT
2840 AGGGTTTAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
34 30 0.83
35 6 0.17
ACGTcount: A:0.42, C:0.22, G:0.00, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCAAAATTCCAAAATAAT
Found at i:11290 original size:12 final size:12
Alignment explanation
Indices: 11273--11298 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11263 GGTAGGCAAT
11273 ATGTAAATTCCA
1 ATGTAAATTCCA
11285 ATGTAAATTCCA
1 ATGTAAATTCCA
11297 AT
1 AT
11299 TGAATCTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATGTAAATTCCA
Found at i:11354 original size:2 final size:2
Alignment explanation
Indices: 11347--11380 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
11337 CTAAACTTTA
11347 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
11381 TAAATGTTTT
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:13898 original size:100 final size:100
Alignment explanation
Indices: 13733--14189 Score: 693
Period size: 100 Copynumber: 4.6 Consensus size: 100
13723 GTTGAGATTT
* * *
13733 AAAGAGTCAATTCTTAATCAATAGGTAGAATTGTTTTCACATGGATTGTGTTTTCTTGCAAGCAC
1 AAAGATTCATTTCTTAATCAATGGGTAGAATTGTTTTCACATGGATTGTGTTTTCTTGCAAGCAC
13798 AATTCACATGGATTGTGAATGTATGGCTGAGATCG
66 AATTCACATGGATTGTGAATGTATGGCTGAGATCG
* * *
13833 AAAGATTCATTTCTTAATCAATGGGTAGAATTATTTTCACATAGATTGTGTTTTCTTACAAGCAC
1 AAAGATTCATTTCTTAATCAATGGGTAGAATTGTTTTCACATGGATTGTGTTTTCTTGCAAGCAC
13898 AATTCACATGGATTGTGAATGTATGGCTGAGATCG
66 AATTCACATGGATTGTGAATGTATGGCTGAGATCG
* *
13933 AAAGATTCCTTTCTTAATCAATGGGTAGAATTGTTTTCACATGGATTGTGTTTTCTTGCAAGAAC
1 AAAGATTCATTTCTTAATCAATGGGTAGAATTGTTTTCACATGGATTGTGTTTTCTTGCAAGCAC
* *
13998 AATTCTCATGGATTGTGAATGTATGGCTGAGATCA
66 AATTCACATGGATTGTGAATGTATGGCTGAGATCG
* * * * * *
14033 AAATATTCCTTTCTTTATCAATTGTTAGAATTGTTTTCACATGGATTGTGTTTTCTTGTAAGCAC
1 AAAGATTCATTTCTTAATCAATGGGTAGAATTGTTTTCACATGGATTGTGTTTTCTTGCAAGCAC
*
14098 AATTCACATGGATTATGAATGTATGGCTGAGATCG
66 AATTCACATGGATTGTGAATGTATGGCTGAGATCG
* * **
14133 AAAGATTCATTTCTTTATCAAT-GGTTGCAATTCAATTT-ACATGGATTGTGTTTTCTT
1 AAAGATTCATTTCTTAATCAATGGGTAG-AATT-GTTTTCACATGGATTGTGTTTTCTT
14190 AAAGTACATG
Statistics
Matches: 327, Mismatches: 28, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
99 3 0.01
100 321 0.98
101 3 0.01
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (100 bp):
AAAGATTCATTTCTTAATCAATGGGTAGAATTGTTTTCACATGGATTGTGTTTTCTTGCAAGCAC
AATTCACATGGATTGTGAATGTATGGCTGAGATCG
Found at i:16478 original size:18 final size:17
Alignment explanation
Indices: 16455--16515 Score: 88
Period size: 18 Copynumber: 3.5 Consensus size: 17
16445 CTTTGCACGA
16455 TTTTTTTCTTTTTCTTT
1 TTTTTTTCTTTTTCTTT
16472 TTCTTTTTCTTTTTCTTT
1 TT-TTTTTCTTTTTCTTT
16490 TTTTTTTCTTTTGT-TTT
1 TTTTTTTCTTTT-TCTTT
16507 GTTTTTTTC
1 -TTTTTTTC
16516 CAAATGAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.37
18 26 0.63
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.85
Consensus pattern (17 bp):
TTTTTTTCTTTTTCTTT
Found at i:16506 original size:12 final size:11
Alignment explanation
Indices: 16455--16506 Score: 77
Period size: 12 Copynumber: 4.5 Consensus size: 11
16445 CTTTGCACGA
16455 TTTTTTTCTTT
1 TTTTTTTCTTT
16466 TTCTTTTTCTTT
1 TT-TTTTTCTTT
16478 TTCTTTTTCTTT
1 TT-TTTTTCTTT
16490 TTTTTTTCTTT
1 TTTTTTTCTTT
*
16501 TGTTTT
1 TTTTTT
16507 GTTTTTTTCC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
11 16 0.41
12 23 0.59
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.87
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:16512 original size:6 final size:6
Alignment explanation
Indices: 16457--16501 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
16447 TTGCACGATT
16457 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT- TTTTTC TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTT
16502 GTTTTGTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTTC
Found at i:17689 original size:5 final size:5
Alignment explanation
Indices: 17675--17707 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
17665 AAAATCAAGG
17675 AAAA- AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
17708 AGAACGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:17724 original size:26 final size:25
Alignment explanation
Indices: 17689--17737 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
17679 AAAATAAAAT
17689 AAAATAAAA-TAAAATAAAAAGAACG
1 AAAATAAAATTAAAA-AAAAAGAACG
*
17714 AAAATAGAAATTGAAAAAAAAGAA
1 AAAATA-AAATTAAAAAAAAAGAA
17738 AAATCGGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 6 0.29
26 11 0.52
27 4 0.19
ACGTcount: A:0.76, C:0.02, G:0.10, T:0.12
Consensus pattern (25 bp):
AAAATAAAATTAAAAAAAAAGAACG
Found at i:23289 original size:13 final size:13
Alignment explanation
Indices: 23268--23297 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
23258 TCTTTTTATT
23268 TTTTATTAAAATA
1 TTTTATTAAAATA
*
23281 TTTTGTTAAAATA
1 TTTTATTAAAATA
23294 TTTT
1 TTTT
23298 TTATTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (13 bp):
TTTTATTAAAATA
Found at i:35077 original size:52 final size:52
Alignment explanation
Indices: 35014--35112 Score: 189
Period size: 52 Copynumber: 1.9 Consensus size: 52
35004 TTATTATAAT
*
35014 ACACATATATATTAGTTTTCTTTCCATAATAATAATAATAATAATAACTTAA
1 ACACACATATATTAGTTTTCTTTCCATAATAATAATAATAATAATAACTTAA
35066 ACACACATATATTAGTTTTCTTTCCATAATAATAATAATAATAATAA
1 ACACACATATATTAGTTTTCTTTCCATAATAATAATAATAATAATAA
35113 TAACTTACAC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.46, C:0.12, G:0.02, T:0.39
Consensus pattern (52 bp):
ACACACATATATTAGTTTTCTTTCCATAATAATAATAATAATAATAACTTAA
Found at i:35099 original size:3 final size:3
Alignment explanation
Indices: 35091--35115 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35081 TTTTCTTTCC
35091 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
35116 CTTACACATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:39821 original size:21 final size:21
Alignment explanation
Indices: 39795--39839 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
39785 GATTTCTGGG
* *
39795 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
39816 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
39837 CAA
1 CAA
39840 ATGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:40666 original size:31 final size:31
Alignment explanation
Indices: 40625--40747 Score: 185
Period size: 31 Copynumber: 4.0 Consensus size: 31
40615 GGGTCGAGGG
*
40625 TTACCAATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
40656 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
40687 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
40718 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
40748 GTCCTTCGGG
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
31 84 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:47228 original size:65 final size:66
Alignment explanation
Indices: 47106--47360 Score: 316
Period size: 66 Copynumber: 3.9 Consensus size: 66
47096 TTTTTTACAC
* * * *
47106 TCACTTCATTCATCTCCATCCACACATCCACAACAATTATCATCTCCGTCTCCTCCATCTCCACT
1 TCACTTCATCCATCTCCATCCACACATCCACAACAATTATCATCTCCATCTCTTCCATCTCCACA
47171 T
66 T
* * *
47172 TCACTTCATCCATCTCCATCCAGACA-CTACAACAGTTATCATCTCCATCTCTTCCATCTCCACA
1 TCACTTCATCCATCTCCATCCACACATCCACAACAATTATCATCTCCATCTCTTCCATCTCCACA
47236 T
66 T
* * *
47237 TCACTTCATCAATCCCCATCCACACATCCACAACAATTATCATCTCTATCTCTTCCATCTCCACA
1 TCACTTCATCCATCTCCATCCACACATCCACAACAATTATCATCTCCATCTCTTCCATCTCCACA
47302 T
66 T
* * ** * * * * *
47303 TCAGTTCCTCCAT-TACTGTCCACACAACCTCAACAATTATCATTTCCTTCTCCTCCAT
1 TCACTTCATCCATCT-CCATCCACACATCCACAACAATTATCATCTCCATCTCTTCCAT
47361 ATTCACCTCA
Statistics
Matches: 162, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
65 57 0.35
66 105 0.65
ACGTcount: A:0.26, C:0.40, G:0.02, T:0.32
Consensus pattern (66 bp):
TCACTTCATCCATCTCCATCCACACATCCACAACAATTATCATCTCCATCTCTTCCATCTCCACA
T
Found at i:48354 original size:15 final size:15
Alignment explanation
Indices: 48334--48369 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
48324 AGTTCATTTC
48334 ATATCTCCTTTTATA
1 ATATCTCCTTTTATA
48349 ATATCTCCTTTTATA
1 ATATCTCCTTTTATA
48364 ATATCT
1 ATATCT
48370 AAATATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.28, C:0.19, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATCTCCTTTTATA
Found at i:50206 original size:17 final size:17
Alignment explanation
Indices: 50184--50216 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
50174 ATTATTTTAA
50184 ATAAATATAGTATAAAG
1 ATAAATATAGTATAAAG
*
50201 ATAAATATATTATAAA
1 ATAAATATAGTATAAA
50217 AATTAGGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (17 bp):
ATAAATATAGTATAAAG
Found at i:50343 original size:32 final size:32
Alignment explanation
Indices: 50293--50368 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
50283 TTAAAACTTC
* *
50293 CAATACAGT-CCCCCAACATTTAGTCCGTTTG
1 CAATATAGTCCCCCCAACATTTAGTCCGTTTA
* *
50324 CAATATAGTCCCCCCAACATTTCGTCTGTTTA
1 CAATATAGTCCCCCCAACATTTAGTCCGTTTA
*
50356 CAATATGGTCCCC
1 CAATATAGTCCCC
50369 GACCGTTTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 8 0.21
32 31 0.79
ACGTcount: A:0.25, C:0.33, G:0.12, T:0.30
Consensus pattern (32 bp):
CAATATAGTCCCCCCAACATTTAGTCCGTTTA
Found at i:52338 original size:31 final size:31
Alignment explanation
Indices: 52303--52380 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
52293 TCAAATGGTC
*
52303 GGGGACCATATTGCAAAT-AGACTAAATGTTG
1 GGGGACCATATTGCAAATGA-ACTAAATATTG
*
52334 GGGGACCATTTTGCAAATGAACTAAATATTG
1 GGGGACCATATTGCAAATGAACTAAATATTG
**
52365 GGGGACTGTATTGCAA
1 GGGGACCATATTGCAA
52381 GTTTTAAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
31 40 0.98
32 1 0.02
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (31 bp):
GGGGACCATATTGCAAATGAACTAAATATTG
Found at i:56275 original size:70 final size:70
Alignment explanation
Indices: 56195--56339 Score: 272
Period size: 70 Copynumber: 2.1 Consensus size: 70
56185 TCAATATTTA
*
56195 AACAATTATAAAAAGCTAAAGTGAAATGGTCCATGCCTATGTAAGATAAATAGTTTACACATTTG
1 AACAATTATAAAAAGCTAAAGTGAAATGGTCCATGACTATGTAAGATAAATAGTTTACACATTTG
56260 GTTTG
66 GTTTG
*
56265 AACAATTATAAAAGGCTAAAGTGAAATGGTCCATGACTATGTAAGATAAATAGTTTACACATTTG
1 AACAATTATAAAAAGCTAAAGTGAAATGGTCCATGACTATGTAAGATAAATAGTTTACACATTTG
56330 GTTTG
66 GTTTG
56335 AACAA
1 AACAA
56340 ATAAAATAAA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 73 1.00
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.30
Consensus pattern (70 bp):
AACAATTATAAAAAGCTAAAGTGAAATGGTCCATGACTATGTAAGATAAATAGTTTACACATTTG
GTTTG
Found at i:58293 original size:6 final size:6
Alignment explanation
Indices: 58282--58314 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
58272 ATACGTACGT
*
58282 CCCAGG CCCAGG CCCAGG ACCAGG CCCAGG CCC
1 CCCAGG CCCAGG CCCAGG CCCAGG CCCAGG CCC
58315 GAGCGTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.18, C:0.52, G:0.30, T:0.00
Consensus pattern (6 bp):
CCCAGG
Found at i:58803 original size:15 final size:17
Alignment explanation
Indices: 58770--58806 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
58760 GGTTTTTTTA
*
58770 AATATAATTTTATACAT
1 AATAAAATTTTATACAT
58787 AATAAAATTTTA-A-AT
1 AATAAAATTTTATACAT
58802 AATAA
1 AATAA
58807 GAGTTAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 1 0.05
17 11 0.58
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
AATAAAATTTTATACAT
Found at i:60461 original size:23 final size:23
Alignment explanation
Indices: 60429--60496 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
60419 GTGTTCGTTT
*
60429 ATTTATTGTTCACGAACATGTTC
1 ATTTAATGTTCACGAACATGTTC
* * **
60452 ATTTAATGTTCGCAAATGTGTTC
1 ATTTAATGTTCACGAACATGTTC
*
60475 GTTTATATGTTCACGAACATGT
1 ATTTA-ATGTTCACGAACATGT
60497 CCGTTTAACG
Statistics
Matches: 34, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
23 22 0.65
24 12 0.35
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (23 bp):
ATTTAATGTTCACGAACATGTTC
Found at i:60521 original size:47 final size:47
Alignment explanation
Indices: 60420--60568 Score: 127
Period size: 47 Copynumber: 3.1 Consensus size: 47
60410 AAGGTGTTGG
* * *** *
60420 TGTTCGTTTATTTATTGTTCACGAACATGTTCATTTAATGTTCGCAAATG
1 TGTTCGTTTA--TA-TGTTCACGAACATGTTCGTTTAACGTTCGTTTATA
*
60470 TGTTCGTTTATATGTTCACGAACATGTCCGTTTAACGTTCGTTTATA
1 TGTTCGTTTATATGTTCACGAACATGTTCGTTTAACGTTCGTTTATA
**** * * ** *
60517 TGTTCACGAATTTATTCTTGAACATGTTCGTTTAGCGTTCGTTTATA
1 TGTTCGTTTATATGTTCACGAACATGTTCGTTTAACGTTCGTTTATA
60564 TGTTC
1 TGTTC
60569 ACGAATTTAT
Statistics
Matches: 82, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
47 70 0.85
48 2 0.02
50 10 0.12
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.46
Consensus pattern (47 bp):
TGTTCGTTTATATGTTCACGAACATGTTCGTTTAACGTTCGTTTATA
Found at i:60543 original size:24 final size:24
Alignment explanation
Indices: 60516--60592 Score: 65
Period size: 24 Copynumber: 3.2 Consensus size: 24
60506 GTTCGTTTAT
60516 ATGTTCACGAATTTATTCTTGAAC
1 ATGTTCACGAATTTATTCTTGAAC
* *
60540 ATGTT--CG--TTTAGCGTTCGTT-TAT
1 ATGTTCACGAATTTA---TTC-TTGAAC
60563 ATGTTCACGAATTTATTCTTGAAC
1 ATGTTCACGAATTTATTCTTGAAC
60587 ATGTTC
1 ATGTTC
60593 GTTTAACGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
20 4 0.10
22 2 0.05
23 11 0.28
24 17 0.43
25 2 0.05
27 4 0.10
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (24 bp):
ATGTTCACGAATTTATTCTTGAAC
Found at i:60569 original size:47 final size:47
Alignment explanation
Indices: 60489--60608 Score: 213
Period size: 47 Copynumber: 2.6 Consensus size: 47
60479 ATATGTTCAC
*
60489 GAACATGTCCGTTTAACGTTCGTTTATATGTTCACGAATTTATTCTT
1 GAACATGTTCGTTTAACGTTCGTTTATATGTTCACGAATTTATTCTT
*
60536 GAACATGTTCGTTTAGCGTTCGTTTATATGTTCACGAATTTATTCTT
1 GAACATGTTCGTTTAACGTTCGTTTATATGTTCACGAATTTATTCTT
*
60583 GAACATGTTCGTTTAACGTTCATTTA
1 GAACATGTTCGTTTAACGTTCGTTTA
60609 GTGTTTGTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 69 1.00
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (47 bp):
GAACATGTTCGTTTAACGTTCGTTTATATGTTCACGAATTTATTCTT
Found at i:66852 original size:44 final size:45
Alignment explanation
Indices: 66789--66883 Score: 165
Period size: 44 Copynumber: 2.1 Consensus size: 45
66779 TTTATTTCGT
*
66789 TTTTTAAATAAGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
1 TTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGGATTTA
*
66833 TTTTTGAATAAGCATGCGAATTAGATATCATGCGGTTAGGATTTA
1 TTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGGATTTA
66878 TTTTTG
1 TTTTTG
66884 TGAATAACAA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 38 0.79
45 10 0.21
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.40
Consensus pattern (45 bp):
TTTTTGAATAAGCATGCGAACTAGATATCATGCGGTTAGGATTTA
Found at i:72314 original size:25 final size:25
Alignment explanation
Indices: 72280--72334 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
72270 GACAGGAAGA
72280 TACC-AAGCCTCGATTGTCAGATTG
1 TACCAAAGCCTCGATTGTCAGATTG
72304 TACCAAAGCCTCGATTGTCAGATTG
1 TACCAAAGCCTCGATTGTCAGATTG
72329 TACCAA
1 TACCAA
72335 GATATGGCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 4 0.13
25 26 0.87
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (25 bp):
TACCAAAGCCTCGATTGTCAGATTG
Found at i:74927 original size:14 final size:14
Alignment explanation
Indices: 74908--74941 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
74898 TGTTGAACGC
74908 AAAGTAAAATGCTT
1 AAAGTAAAATGCTT
74922 AAAGTAAAATGCTT
1 AAAGTAAAATGCTT
74936 AAAGTA
1 AAAGTA
74942 TATGGAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.53, C:0.06, G:0.15, T:0.26
Consensus pattern (14 bp):
AAAGTAAAATGCTT
Found at i:76490 original size:28 final size:27
Alignment explanation
Indices: 76451--76540 Score: 96
Period size: 28 Copynumber: 3.3 Consensus size: 27
76441 ATTTCGCTTG
*
76451 AAGAAGAAATAAAAGAGAAAATGA-AAA
1 AAGAAAAAATAAAAGA-AAAATGAGAAA
*
76478 AATGAAAAAATAATA-AAAAATGAGAAGA
1 AA-GAAAAAATAAAAGAAAAATGAGAA-A
*
76506 AA-AAAAGAAGAAAAGAAAAATGAGAAA
1 AAGAAAA-AATAAAAGAAAAATGAGAAA
76533 AAGAAAAA
1 AAGAAAAA
76541 TGATGGAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
26 11 0.21
27 14 0.26
28 28 0.53
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.08
Consensus pattern (27 bp):
AAGAAAAAATAAAAGAAAAATGAGAAA
Found at i:76494 original size:31 final size:31
Alignment explanation
Indices: 76450--76540 Score: 80
Period size: 31 Copynumber: 2.9 Consensus size: 31
76440 TATTTCGCTT
* *
76450 GAAGAAGA-AATAAAAGAGAAAATGAAAAAAT
1 GAAGAAAAGAATAAAAGAGAAAA-GAAAAAAA
* * *
76481 GAA-AAAATAATAAAAAATGAGAAGAAAAAAA
1 GAAGAAAAGAATAAAAGA-GAAAAGAAAAAAA
*
76512 GAAGAAAAGAA-AAATGAGAAAAAGAAAAA
1 GAAGAAAAGAATAAAAGAG-AAAAGAAAAA
76541 TGATGGAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
30 4 0.08
31 34 0.71
32 10 0.21
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.08
Consensus pattern (31 bp):
GAAGAAAAGAATAAAAGAGAAAAGAAAAAAA
Found at i:76511 original size:14 final size:14
Alignment explanation
Indices: 76493--76543 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
76483 AAAAATAATA
76493 AAAAATGAGAAGAA-
1 AAAAATGAGAA-AAG
76507 AAAAA-GAAGAAAAG
1 AAAAATG-AGAAAAG
76521 AAAAATGAGAAAAAG
1 AAAAATGAG-AAAAG
76536 AAAAATGA
1 AAAAATGA
76544 TGGAAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
13 3 0.09
14 16 0.48
15 14 0.42
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.06
Consensus pattern (14 bp):
AAAAATGAGAAAAG
Found at i:76511 original size:16 final size:16
Alignment explanation
Indices: 76492--76570 Score: 55
Period size: 15 Copynumber: 5.1 Consensus size: 16
76482 AAAAAATAAT
76492 AAAAAATGAGAAG---
1 AAAAAATGAGAAGAAA
76505 AAAAAA--AGAAGAAA
1 AAAAAATGAGAAGAAA
76519 AGAAAAATGAGAA-AAA
1 A-AAAAATGAGAAGAAA
* *
76535 GAAAAATGATGGAAAAAA
1 AAAAAATGA--GAAGAAA
76553 AAGAAAATG-GAAGAAA
1 AA-AAAATGAGAAGAAA
76569 AA
1 AA
76571 TGAAAGAGAA
Statistics
Matches: 53, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
11 5 0.09
13 6 0.11
14 1 0.02
15 13 0.25
16 11 0.21
17 7 0.13
18 4 0.08
19 6 0.11
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.06
Consensus pattern (16 bp):
AAAAAATGAGAAGAAA
Found at i:76541 original size:15 final size:15
Alignment explanation
Indices: 76493--76543 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
76483 AAAAATAATA
*
76493 AAAAATGAGAAGAA-
1 AAAAATGAGAAAAAG
76507 AAAAA-GA-AGAAAAG
1 AAAAATGAGA-AAAAG
76521 AAAAATGAGAAAAAG
1 AAAAATGAGAAAAAG
76536 AAAAATGA
1 AAAAATGA
76544 TGGAAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
12 1 0.03
13 5 0.16
14 10 0.31
15 15 0.47
16 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.06
Consensus pattern (15 bp):
AAAAATGAGAAAAAG
Found at i:76554 original size:15 final size:15
Alignment explanation
Indices: 76493--76554 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
76483 AAAAATAATA
76493 AAAAATGA-GAAGAA-
1 AAAAATGAGGAA-AAG
*
76507 AAAAA-GAAGAAAAG
1 AAAAATGAGGAAAAG
*
76521 AAAAATGAGAAAAAG
1 AAAAATGAGGAAAAG
76536 AAAAATGATGGAAAA-
1 AAAAATGA-GGAAAAG
76551 AAAA
1 AAAA
76555 GAAAATGGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
13 4 0.10
14 13 0.32
15 19 0.46
16 5 0.12
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.06
Consensus pattern (15 bp):
AAAAATGAGGAAAAG
Found at i:76567 original size:30 final size:33
Alignment explanation
Indices: 76533--76592 Score: 90
Period size: 30 Copynumber: 1.9 Consensus size: 33
76523 AAATGAGAAA
*
76533 AAGAAAAATG-ATG-GAAAA-AAAAGAAAATGG
1 AAGAAAAATGAAAGAGAAAATAAAAGAAAATGG
76563 AAGAAAAATGAAAGAGAAAATAAAAGAAAA
1 AAGAAAAATGAAAGAGAAAATAAAAGAAAA
76593 AACAAAAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 10 0.38
31 2 0.08
32 5 0.19
33 9 0.35
ACGTcount: A:0.72, C:0.00, G:0.20, T:0.08
Consensus pattern (33 bp):
AAGAAAAATGAAAGAGAAAATAAAAGAAAATGG
Found at i:76570 original size:11 final size:11
Alignment explanation
Indices: 76532--76593 Score: 58
Period size: 11 Copynumber: 5.8 Consensus size: 11
76522 AAAATGAGAA
76532 AAAGAAAAATG
1 AAAGAAAAATG
**
76543 ATGGAAAAA--
1 AAAGAAAAATG
76552 AAAG-AAAATG
1 AAAGAAAAATG
*
76562 GAAGAAAAATG
1 AAAGAAAAATG
*
76573 AAAGAGAAAATA
1 AAAGA-AAAATG
76585 AAAGAAAAA
1 AAAGAAAAA
76594 ACAAAAGAGA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
8 4 0.10
9 2 0.05
10 3 0.08
11 21 0.52
12 10 0.25
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (11 bp):
AAAGAAAAATG
Found at i:76628 original size:73 final size:73
Alignment explanation
Indices: 76493--76628 Score: 161
Period size: 73 Copynumber: 1.9 Consensus size: 73
76483 AAAAATAATA
* * * * *
76493 AAAAATGAGAAGAAAAAAAGAAGAAAAGAAAAATGAGAAAAAGAAAAATGATGGAAAAAAAAGAA
1 AAAAATGAGAAGAAAAAAAAAAGAAAAGAAAAAAGAGAAAAAGAAAAATAAAGAAAAAAAAAGAA
76558 AATGGAAG
66 AATGGAAG
* *
76566 AAAAATGA-AAGAGAAAATAAAAGAAAA-AACAAAAGAG-AAATGAAAAATAAAGAAAAATAAAA
1 AAAAATGAGAAGA-AAAAAAAAAGAAAAGAA-AAAAGAGAAAAAGAAAAATAAAGAAAAA-AAAA
76628 G
63 G
76629 GGGGTTCAAG
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
72 22 0.42
73 31 0.58
ACGTcount: A:0.74, C:0.01, G:0.18, T:0.07
Consensus pattern (73 bp):
AAAAATGAGAAGAAAAAAAAAAGAAAAGAAAAAAGAGAAAAAGAAAAATAAAGAAAAAAAAAGAA
AATGGAAG
Done.