Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000571.1 Hibiscus syriacus cultivar Beakdansim tig00001117_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: 128199
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:4926 original size:21 final size:21
Alignment explanation
Indices: 4884--4926 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4874 TTTTTGGGCT
* *
4884 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
4905 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
4926 A
1 A
4927 ACGAACCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:4999 original size:23 final size:22
Alignment explanation
Indices: 4955--4999 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
4945 AATCTCATAG
*
4955 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
4977 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
5000 AATTGTGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.29, C:0.33, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:6464 original size:103 final size:103
Alignment explanation
Indices: 6285--6497 Score: 372
Period size: 103 Copynumber: 2.1 Consensus size: 103
6275 GGGTCTACGC
* *
6285 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGAGACATATATGTATTCTTTGGAACATATGTGAAGTCTGGTGAGACACATACTTGAT
* * *
6350 CCTTGGCATATGTATATGATTTTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
6388 GGTCCTTCGAGACATATATGTATTCTTTGGAACATATGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGAGACATATATGTATTCTTTGGAACATATGTGAAGTCTGGTGAGACACATACTTGAT
*
6453 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
6491 GGTCCTT
1 GGTCCTT
6498 ATGGACATTA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
GGTCCTTCGAGACATATATGTATTCTTTGGAACATATGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:6553 original size:23 final size:23
Alignment explanation
Indices: 6527--6581 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
6517 ACTACGATGT
6527 AATTCTACGCGGCACTCCAGTGC
1 AATTCTACGCGGCACTCCAGTGC
* * * *
6550 AATTCTAAGTGGCAGTTCAGTGC
1 AATTCTACGCGGCACTCCAGTGC
*
6573 AATTATACG
1 AATTCTACG
6582 AGCTGTGGTG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (23 bp):
AATTCTACGCGGCACTCCAGTGC
Found at i:15216 original size:3 final size:3
Alignment explanation
Indices: 15208--15285 Score: 156
Period size: 3 Copynumber: 26.0 Consensus size: 3
15198 CAATTTTTTA
15208 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
15256 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
15286 ATGAATGAAG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:16093 original size:17 final size:17
Alignment explanation
Indices: 16071--16108 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
16061 ATCTCCACTA
16071 TTTGTATAGATGATTAT
1 TTTGTATAGATGATTAT
16088 TTTGTATAGATGATTAT
1 TTTGTATAGATGATTAT
16105 TTTG
1 TTTG
16109 AATTCTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.55
Consensus pattern (17 bp):
TTTGTATAGATGATTAT
Found at i:23431 original size:22 final size:21
Alignment explanation
Indices: 23403--23458 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
23393 CTCCTAAAAA
* *
23403 TATTAAAATTTTATTTATTTTT
1 TATTAAAATTTT-TCTATTTCT
23425 TATTAAAAATTATTTCTATTTCT
1 TATT-AAAATT-TTTCTATTTCT
23448 T-TTAAAATTTT
1 TATTAAAATTTT
23459 GTAAATCTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 2 0.07
21 6 0.20
22 6 0.20
23 14 0.47
24 2 0.07
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTAAAATTTTTCTATTTCT
Found at i:26930 original size:170 final size:170
Alignment explanation
Indices: 26648--26987 Score: 662
Period size: 170 Copynumber: 2.0 Consensus size: 170
26638 GAAACTTTTT
26648 TTCCTGGAAGATAGATGAGTTCAAATTCCCATCAAGAATCTAATGGAACAGTTTCACAGGAAAGT
1 TTCCTGGAAGATAGATGAGTTCAAATTCCCATCAAGAATCTAATGGAACAGTTTCACAGGAAAGT
26713 TTATGAATAGCTGCTGAGACACTAACTTATCCACCTGTATTTCTAATTGAAGTATGACATTGTGC
66 TTATGAATAGCTGCTGAGACACTAACTTATCCACCTGTATTTCTAATTGAAGTATGACATTGTGC
26778 AGACCTTCAAGTTGTTTGGCAAGTTCTAGGCAGAATACAA
131 AGACCTTCAAGTTGTTTGGCAAGTTCTAGGCAGAATACAA
26818 TTCCTGGAAGATAGATGAGTTCAAATTCCCATCAAGAATCTAATGGAACAGTTTCACAGGAAAGT
1 TTCCTGGAAGATAGATGAGTTCAAATTCCCATCAAGAATCTAATGGAACAGTTTCACAGGAAAGT
* *
26883 TTATGAATAGCTGCTGAGACACTAACTTATCCTCTTGTATTTCTAATTGAAGTATGACATTGTGC
66 TTATGAATAGCTGCTGAGACACTAACTTATCCACCTGTATTTCTAATTGAAGTATGACATTGTGC
26948 AGACCTTCAAGTTGTTTGGCAAGTTCTAGGCAGAATACAA
131 AGACCTTCAAGTTGTTTGGCAAGTTCTAGGCAGAATACAA
26988 ACTACTAAAT
Statistics
Matches: 168, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
170 168 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (170 bp):
TTCCTGGAAGATAGATGAGTTCAAATTCCCATCAAGAATCTAATGGAACAGTTTCACAGGAAAGT
TTATGAATAGCTGCTGAGACACTAACTTATCCACCTGTATTTCTAATTGAAGTATGACATTGTGC
AGACCTTCAAGTTGTTTGGCAAGTTCTAGGCAGAATACAA
Found at i:34438 original size:18 final size:18
Alignment explanation
Indices: 34411--34445 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
34401 CCATTATGAA
*
34411 ATGTCTCGAAGGACCACT
1 ATGTCCCGAAGGACCACT
34429 ATGTCCCGAAGGACCAC
1 ATGTCCCGAAGGACCAC
34446 GTAGAACCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACT
Found at i:34808 original size:19 final size:17
Alignment explanation
Indices: 34774--34824 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
34764 ACTCATTTAT
* *
34774 ATCATATATCATATACCA
1 ATCATATAACACATA-CA
34792 ATACATATAACACATACA
1 AT-CATATAACACATACA
34810 ATCATATCAACACAT
1 ATCATAT-AACACAT
34825 GCTTATATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 5 0.17
18 13 0.45
19 11 0.38
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (17 bp):
ATCATATAACACATACA
Found at i:38835 original size:19 final size:17
Alignment explanation
Indices: 38801--38851 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
38791 ACTCATTTAT
* *
38801 ATCATATATCATATACCA
1 ATCATATAACACATA-CA
38819 ATACATATAACACATACA
1 AT-CATATAACACATACA
38837 ATCATATCAACACAT
1 ATCATAT-AACACAT
38852 GCCTATATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 5 0.17
18 13 0.45
19 11 0.38
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (17 bp):
ATCATATAACACATACA
Found at i:40841 original size:20 final size:21
Alignment explanation
Indices: 40811--40851 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
40801 AGCCGTTGGG
40811 GCCTGATGGTATCGATACTAT
1 GCCTGATGGTATCGATACTAT
40832 GCCT-ATGGTATCGATACTAT
1 GCCTGATGGTATCGATACTAT
40852 TATGTTGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (21 bp):
GCCTGATGGTATCGATACTAT
Found at i:41649 original size:19 final size:21
Alignment explanation
Indices: 41609--41657 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
41599 AATAATTTTC
* *
41609 TTTTG-AAAGCAAAATTGGA-
1 TTTTGAAAAACAAAATTGAAT
41628 TTTTGAAAAACAAAA-TGAAT
1 TTTTGAAAAACAAAATTGAAT
41648 TTTTGAAAAA
1 TTTTGAAAAA
41658 TGAGTTAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.49, C:0.04, G:0.14, T:0.33
Consensus pattern (21 bp):
TTTTGAAAAACAAAATTGAAT
Found at i:44995 original size:18 final size:18
Alignment explanation
Indices: 44972--45033 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
44962 GATTAGTACC
44972 TAAACTATCAGTTTTGAG
1 TAAACTATCAGTTTTGAG
* *
44990 TAAACTA-C-GTTTTAATACC
1 TAAACTATCAGTTTT--GA-G
45009 TAAACTATCAGTTTTGAG
1 TAAACTATCAGTTTTGAG
45027 TAAACTA
1 TAAACTA
45034 AGTTTTAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
16 5 0.14
17 1 0.03
18 15 0.43
19 8 0.23
20 1 0.03
21 5 0.14
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (18 bp):
TAAACTATCAGTTTTGAG
Found at i:45014 original size:37 final size:37
Alignment explanation
Indices: 44952--45064 Score: 183
Period size: 37 Copynumber: 3.1 Consensus size: 37
44942 TAAAAATGGC
* *
44952 TAAACTACGTGATTAGTACCTAAACTATCAGTTTTGAG
1 TAAACTACGT-TTTAATACCTAAACTATCAGTTTTGAG
44990 TAAACTACGTTTTAATACCTAAACTATCAGTTTTGAG
1 TAAACTACGTTTTAATACCTAAACTATCAGTTTTGAG
*
45027 TAAACTAAGTTTTAATACCTAAACTATCAGTTTT-AG
1 TAAACTACGTTTTAATACCTAAACTATCAGTTTTGAG
45063 TA
1 TA
45065 CCTAAACTTT
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
36 4 0.06
37 58 0.81
38 10 0.14
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (37 bp):
TAAACTACGTTTTAATACCTAAACTATCAGTTTTGAG
Found at i:45081 original size:21 final size:21
Alignment explanation
Indices: 44968--45081 Score: 95
Period size: 21 Copynumber: 5.9 Consensus size: 21
44958 ACGTGATTAG
44968 TACCTAAACTATCAGTTTT--
1 TACCTAAACTATCAGTTTTAA
* *
44987 GA-GTAAACTA-C-GTTTTAA
1 TACCTAAACTATCAGTTTTAA
45005 TACCTAAACTATCAGTTTT--
1 TACCTAAACTATCAGTTTTAA
* *
45024 GA-GTAAACTA--AGTTTTAA
1 TACCTAAACTATCAGTTTTAA
*
45042 TACCTAAACTATCAGTTTTAG
1 TACCTAAACTATCAGTTTTAA
* *
45063 TACCTAAACTTTCATTTTT
1 TACCTAAACTATCAGTTTT
45082 TTCATAACCA
Statistics
Matches: 74, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
16 11 0.15
17 1 0.01
18 16 0.22
19 16 0.22
20 1 0.01
21 29 0.39
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (21 bp):
TACCTAAACTATCAGTTTTAA
Found at i:45634 original size:15 final size:15
Alignment explanation
Indices: 45596--45638 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
45586 CTTAATCTTA
45596 TTAAAATTATAATTT
1 TTAAAATTATAATTT
45611 TTAATAATTA-ACATTT
1 TTAA-AATTATA-ATTT
45627 TTAAAATTATAA
1 TTAAAATTATAA
45639 ATAATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
TTAAAATTATAATTT
Found at i:60911 original size:7 final size:7
Alignment explanation
Indices: 60901--60935 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
60891 TTTATTTTCT
60901 CTCTCAA
1 CTCTCAA
60908 CTCTCAA
1 CTCTCAA
60915 CTCTCACAA
1 CTCT--CAA
60924 CTCTCAA
1 CTCTCAA
60931 CTCTC
1 CTCTC
60936 TCAAATTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 19 0.73
9 7 0.27
ACGTcount: A:0.26, C:0.46, G:0.00, T:0.29
Consensus pattern (7 bp):
CTCTCAA
Found at i:60924 original size:16 final size:16
Alignment explanation
Indices: 60899--60935 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
60889 CTTTTATTTT
*
60899 CTCTCTCAACTCTCAA
1 CTCTCACAACTCTCAA
60915 CTCTCACAACTCTCAA
1 CTCTCACAACTCTCAA
60931 CTCTC
1 CTCTC
60936 TCAAATTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.24, C:0.46, G:0.00, T:0.30
Consensus pattern (16 bp):
CTCTCACAACTCTCAA
Found at i:76740 original size:55 final size:55
Alignment explanation
Indices: 76597--77518 Score: 1349
Period size: 55 Copynumber: 16.9 Consensus size: 55
76587 TGGTTTTACC
* * * * **
76597 CCCTATTGCTTCAGGGAGTA--AAACTCGAA-TATCTTCGTCAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
* * * * * * *
76649 CCCTATTT-TCCAGAGAGTATAAGACTCAAACGAT-TCTCGATAATCTTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCT-TCAACAATCGTGTCTGCT
* * *
76703 CCCTATTTTTTCAGAGAGTATGAGACTCGAACAAT-TCTCAATAATCGTGCCTGCT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCT-TCAACAATCGTGTCTGCT
* *
76758 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAACCGTGTCTGTT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
* * *
76813 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCTTGTATGTT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
* *
76868 CTCTATTTCTTCAGAGAGTATGAGACTCGAATAATCTTCAACAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
76923 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
* * *
76978 CCCTATTTTTTCAGAGAGTATGAGACTCGAACAATCTTCAAAAATCGTGCCTGCT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
* *
77033 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTATGTT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
* *
77088 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCTTGTCTGTT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
* * *
77143 CTCTATTTCTTCAGAGAGTATGAGACTCGAATAATCTTCAACAATCATGTCTGCT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
*
77198 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTTAACAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
77253 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
* *
77308 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
* * * * *
77363 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
* *
77416 CCCTATTTCTTCAGAGAGTAT-AGGACTCGAACAATCTTCAACAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATGA-GACTCGAACAATCTTCAACAATCGTGTCTGCT
* *
77471 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGT
1 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGT
77519 TGGGAAACCT
Statistics
Matches: 801, Mismatches: 59, Indels: 17
0.91 0.07 0.02
Matches are distributed among these distances:
51 9 0.01
52 8 0.01
53 56 0.07
54 27 0.03
55 699 0.87
56 2 0.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.32
Consensus pattern (55 bp):
CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
Found at i:78548 original size:21 final size:20
Alignment explanation
Indices: 78519--78557 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
78509 AACCCTCATC
*
78519 TTTTGTTTCTCTTTTTTTCTT
1 TTTTGTTTC-CATTTTTTCTT
*
78540 TTTTTTTTCCATTTTTTC
1 TTTTGTTTCCATTTTTTC
78558 ACTCATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (20 bp):
TTTTGTTTCCATTTTTTCTT
Found at i:78585 original size:12 final size:12
Alignment explanation
Indices: 78530--78586 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 12
78520 TTTGTTTCTC
78530 TTTTTTTCTT-T
1 TTTTTTTCTTAT
*
78541 TTTTTTTC-CAT
1 TTTTTTTCTTAT
** *
78552 TTTTTCACTCAT
1 TTTTTTTCTTAT
78564 TTTTTCTTCTTAT
1 TTTTT-TTCTTAT
78577 TTTTTTTCTT
1 TTTTTTTCTT
78587 CAAGCAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
11 15 0.41
12 13 0.35
13 9 0.24
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTTTCTTAT
Found at i:116198 original size:21 final size:21
Alignment explanation
Indices: 116159--116198 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
116149 ATATCACGTA
*
116159 TTAATAATAAATAATATTAAT
1 TTAATAATAAATAAAATTAAT
**
116180 TTAATAATATCTAAAATTA
1 TTAATAATAAATAAAATTA
116199 GTGACTAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAATAATAAATAAAATTAAT
Found at i:118167 original size:2 final size:2
Alignment explanation
Indices: 118162--118190 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
118152 TTTTTTTTAT
118162 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
118191 CCGTCTCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:118489 original size:16 final size:16
Alignment explanation
Indices: 118465--118495 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
118455 ACCGACTATA
118465 ATATAATGAATTATTT
1 ATATAATGAATTATTT
*
118481 ATATTATGAATTATT
1 ATATAATGAATTATT
118496 AGATTTTGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
ATATAATGAATTATTT
Found at i:118646 original size:15 final size:15
Alignment explanation
Indices: 118626--118676 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
118616 AAAAACCGGG
118626 TACCGGGTACCCGAT
1 TACCGGGTACCCGAT
* *
118641 TACCGGATACCCGTAA
1 TACCGGGTACCCG-AT
*
118657 AATCCGGGTACCCGAT
1 TA-CCGGGTACCCGAT
118673 TACC
1 TACC
118677 AAATACTCGT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 14 0.50
16 4 0.14
17 10 0.36
ACGTcount: A:0.25, C:0.33, G:0.22, T:0.20
Consensus pattern (15 bp):
TACCGGGTACCCGAT
Found at i:118688 original size:32 final size:32
Alignment explanation
Indices: 118628--118697 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
118618 AAACCGGGTA
**
118628 CCGGGTACCCGATTACCGGATACCCGTAAAAT
1 CCGGGTACCCGATTACCAAATACCCGTAAAAT
* *
118660 CCGGGTACCCGATTACCAAATACTCGTAACAT
1 CCGGGTACCCGATTACCAAATACCCGTAAAAT
*
118692 TCGGGT
1 CCGGGT
118698 CAAGACACGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.21
Consensus pattern (32 bp):
CCGGGTACCCGATTACCAAATACCCGTAAAAT
Found at i:122763 original size:18 final size:19
Alignment explanation
Indices: 122735--122773 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
122725 TTCTCTTATT
122735 TTTACTTTAATAGCTTTTA
1 TTTACTTTAATAGCTTTTA
* *
122754 TTTA-TTTAATCGTTTTTA
1 TTTACTTTAATAGCTTTTA
122772 TT
1 TT
122774 ACTATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.23, C:0.08, G:0.05, T:0.64
Consensus pattern (19 bp):
TTTACTTTAATAGCTTTTA
Done.