Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000676.1 Hibiscus syriacus cultivar Beakdansim tig00001311_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: 83524
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Found at i:6460 original size:2 final size:2
Alignment explanation
Indices: 6455--6483 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6445 AGCAAGTGTG
6455 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
6484 TTCATATTAT
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:10747 original size:2 final size:2
Alignment explanation
Indices: 10734--10775 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
10724 AGATGTTCCG
*
10734 TA TA TG 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
10776 AACTATCCAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20896 original size:22 final size:22
Alignment explanation
Indices: 20855--20921 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
20845 CTCGTATAAA
20855 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
20878 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
20900 TGCACCTAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
20922 AATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:21252 original size:29 final size:29
Alignment explanation
Indices: 21216--21287 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
21206 TTTTCTGCAT
**
21216 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
21245 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
21274 ATTCATGTCATGTA
1 ATTCATGTCATGTA
21288 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:21575 original size:4 final size:4
Alignment explanation
Indices: 21557--21599 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
21547 TATAGCTTAG
* *
21557 TCTT GCTT TCTTT TCTT TCTT TCTT TCTT TCTT T-TT TTTT TCT
1 TCTT TCTT TC-TT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT
21600 CATGGGGGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
3 3 0.09
4 27 0.79
5 4 0.12
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (4 bp):
TCTT
Found at i:21586 original size:21 final size:19
Alignment explanation
Indices: 21557--21599 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
21547 TATAGCTTAG
21557 TCTTGCTTTCTTTTCTTTCTT
1 TCTTGCTTTCTTTT-TTT-TT
*
21578 TCTTTCTTTCTTTTTTTTT
1 TCTTGCTTTCTTTTTTTTT
21597 TCT
1 TCT
21600 CATGGGGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 3 0.14
21 13 0.62
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (19 bp):
TCTTGCTTTCTTTTTTTTT
Found at i:21628 original size:21 final size:21
Alignment explanation
Indices: 21602--21642 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
21592 TTTTTTCTCA
*
21602 TGGGGGAATCGGTTCCCCTCC
1 TGGGGGAATCGATTCCCCTCC
*
21623 TGGGGGTATCGATTCCCCTC
1 TGGGGGAATCGATTCCCCTC
21643 AAGCATTCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.32, G:0.32, T:0.27
Consensus pattern (21 bp):
TGGGGGAATCGATTCCCCTCC
Found at i:27779 original size:22 final size:22
Alignment explanation
Indices: 27738--27804 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
27728 CTCGTATAAA
27738 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
27761 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
27783 TGCACCTAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
27805 AATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:28135 original size:29 final size:29
Alignment explanation
Indices: 28099--28170 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
28089 TTTTCTGCAT
**
28099 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
28128 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
28157 ATTCATGTCATGTA
1 ATTCATGTCATGTA
28171 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:28456 original size:4 final size:4
Alignment explanation
Indices: 28438--28480 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
28428 TATAGCTTAG
* *
28438 TCTT GCTT TCTTT TCTT TCTT TCTT TCTT TCTT T-TT TTTT TCT
1 TCTT TCTT TC-TT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT
28481 CATGGGGGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
3 3 0.09
4 27 0.79
5 4 0.12
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (4 bp):
TCTT
Found at i:28467 original size:21 final size:19
Alignment explanation
Indices: 28438--28480 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
28428 TATAGCTTAG
28438 TCTTGCTTTCTTTTCTTTCTT
1 TCTTGCTTTCTTTT-TTT-TT
*
28459 TCTTTCTTTCTTTTTTTTT
1 TCTTGCTTTCTTTTTTTTT
28478 TCT
1 TCT
28481 CATGGGGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 3 0.14
21 13 0.62
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (19 bp):
TCTTGCTTTCTTTTTTTTT
Found at i:28509 original size:21 final size:21
Alignment explanation
Indices: 28483--28523 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28473 TTTTTTCTCA
*
28483 TGGGGGAATCGGTTCCCCTCC
1 TGGGGGAATCGATTCCCCTCC
*
28504 TGGGGGTATCGATTCCCCTC
1 TGGGGGAATCGATTCCCCTC
28524 AAGCATTCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.32, G:0.32, T:0.27
Consensus pattern (21 bp):
TGGGGGAATCGATTCCCCTCC
Found at i:29439 original size:21 final size:22
Alignment explanation
Indices: 29410--29453 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
29400 CTTGTATGAT
29410 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
29431 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
29453 A
1 A
29454 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:30410 original size:23 final size:23
Alignment explanation
Indices: 30366--30410 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
30356 ATCATTATAT
*
30366 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
30389 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
30411 AGCTGTGGTG
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:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:33702 original size:21 final size:21
Alignment explanation
Indices: 33673--33717 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
33663 GATTTCTGGG
* *
33673 CAAGAGGAATCGGTACCCATT
1 CAAGAGGAACCGATACCCATT
* *
33694 CAAGGGGAACCGATACCCCTT
1 CAAGAGGAACCGATACCCATT
33715 CAA
1 CAA
33718 ACGACAAAAT
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:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGAGGAACCGATACCCATT
Found at i:34321 original size:18 final size:18
Alignment explanation
Indices: 34298--34332 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
34288 CTAGGAGATT
34298 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
34316 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
34333 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:34667 original size:2 final size:2
Alignment explanation
Indices: 34660--34711 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
34650 GAACATGTGA
34660 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
34702 AT AT AT AT AT
1 AT AT AT AT AT
34712 GTCTAAGAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35423 original size:23 final size:23
Alignment explanation
Indices: 35378--35423 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
35368 TATCATTATA
*
35378 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTATACG
* *
35401 TGGCACTTCGGTGCATTTATACG
1 TGGCACTACGGTGCAATTATACG
35424 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:36422 original size:23 final size:23
Alignment explanation
Indices: 36388--36441 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
36378 CGACACGCGA
*
36388 TCCTTCGAGACAATTCTACGTGG
1 TCCTTCGGGACAATTCTACGTGG
*
36411 TCCTTCGGGACATTTCTACGTGG
1 TCCTTCGGGACAATTCTACGTGG
36434 -CACTTCGG
1 TC-CTTCGG
36442 TGCTTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 1 0.04
23 27 0.96
ACGTcount: A:0.17, C:0.28, G:0.24, T:0.31
Consensus pattern (23 bp):
TCCTTCGGGACAATTCTACGTGG
Found at i:36459 original size:24 final size:25
Alignment explanation
Indices: 36422--36468 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
36412 CCTTCGGGAC
*
36422 ATTTCTACGTGGCACTTCGGTGCTT
1 ATTTCTACGCGGCACTTCGGTGCTT
36447 ATTT-TACGCGGCACTTCGGTGC
1 ATTTCTACGCGGCACTTCGGTGC
36469 AATTATATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.13, C:0.26, G:0.26, T:0.36
Consensus pattern (25 bp):
ATTTCTACGCGGCACTTCGGTGCTT
Found at i:39067 original size:19 final size:19
Alignment explanation
Indices: 39043--39081 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
39033 AAGGGATACT
*
39043 ATTTTAATTACTGGTTTTC
1 ATTTTAATTACTGATTTTC
39062 ATTTTAATTACTGATTTTC
1 ATTTTAATTACTGATTTTC
39081 A
1 A
39082 CTCATTGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.10, G:0.08, T:0.56
Consensus pattern (19 bp):
ATTTTAATTACTGATTTTC
Found at i:39985 original size:15 final size:15
Alignment explanation
Indices: 39965--39994 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39955 CAAGTACAAG
39965 TACTTAACTGTCCAA
1 TACTTAACTGTCCAA
*
39980 TACTTAACTTTCCAA
1 TACTTAACTGTCCAA
39995 AAAAAAAAAA
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:0.33, C:0.27, G:0.03, T:0.37
Consensus pattern (15 bp):
TACTTAACTGTCCAA
Found at i:60248 original size:11 final size:11
Alignment explanation
Indices: 60232--60256 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
60222 GAACCTAGAG
60232 ATTCTTAATGT
1 ATTCTTAATGT
60243 ATTCTTAATGT
1 ATTCTTAATGT
60254 ATT
1 ATT
60257 GTTGTTTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (11 bp):
ATTCTTAATGT
Found at i:65003 original size:103 final size:103
Alignment explanation
Indices: 64824--65036 Score: 399
Period size: 103 Copynumber: 2.1 Consensus size: 103
64814 GGATCTACGC
64824 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
64889 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
64927 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
64992 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
65030 GGTCCTT
1 GGTCCTT
65037 ATGGATATTA
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:65088 original size:23 final size:23
Alignment explanation
Indices: 65053--65120 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
65043 ATTATTATAT
65053 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
65076 GGCACTCCAGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
65099 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
65121 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:67365 original size:19 final size:20
Alignment explanation
Indices: 67341--67391 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
67331 AATGACCAAT
67341 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* * *
67360 AAAATCGCAATGCGATTTAG
1 AAAATCGCAACGCGATATAC
67380 AAAATCGCAACG
1 AAAATCGCAACG
67392 TTAAAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:67403 original size:20 final size:20
Alignment explanation
Indices: 67380--67418 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
67370 TGCGATTTAG
*
67380 AAAATCGCAACGTTAAAAAT
1 AAAATCGCAACGGTAAAAAT
67400 AAAATCGCAACGGTAAAAA
1 AAAATCGCAACGGTAAAAA
67419 GAATAGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.15, G:0.13, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGGTAAAAAT
Found at i:67506 original size:6 final size:6
Alignment explanation
Indices: 67490--67587 Score: 189
Period size: 6 Copynumber: 16.5 Consensus size: 6
67480 TCTCGTCTCG
67490 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
67537 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
67585 GGT
1 GGT
67588 AATACGTGTC
Statistics
Matches: 92, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.05
6 87 0.95
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:67698 original size:20 final size:20
Alignment explanation
Indices: 67677--67867 Score: 229
Period size: 20 Copynumber: 9.4 Consensus size: 20
67667 CTTTTTAACG
* * *
67677 TTGCGATTTTCTAAATCGCG
1 TTGCGATTCTCTCAATCGCA
*
67697 TTGCAATTCTCTCAATCGCA
1 TTGCGATTCTCTCAATCGCA
* *
67717 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAATCGCA
*
67737 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAATCGCA
**
67757 TTGCGATTCTCTCGGTCGCA
1 TTGCGATTCTCTCAATCGCA
*
67777 TTGCGATTTTCTTCTAAATCGCA
1 TTGCGA--TTC-TCTCAATCGCA
67800 TTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTCAATCGCA
* *
67820 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAATCGCA
* *
67840 TTGTGATTCTATCAATCGCA
1 TTGCGATTCTCTCAATCGCA
67860 TTGCGATT
1 TTGCGATT
67868 TTCTTCTAAA
Statistics
Matches: 148, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
20 128 0.86
21 3 0.02
22 3 0.02
23 14 0.09
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTCTCAATCGCA
Found at i:67809 original size:83 final size:83
Alignment explanation
Indices: 67710--67881 Score: 263
Period size: 83 Copynumber: 2.1 Consensus size: 83
67700 CAATTCTCTC
* * * * **
67710 AATCGCATTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCGGTCG
1 AATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCG
67775 CATTGCGATTTTCTTCTA
66 CATTGCGATTTTCTTCTA
* * *
67793 AATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGTGATTCTATCAATCG
1 AATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCG
67858 CATTGCGATTTTCTTCTA
66 CATTGCGATTTTCTTCTA
67876 AATCGC
1 AATCGC
67882 GTTACGAACT
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
83 80 1.00
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.37
Consensus pattern (83 bp):
AATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCG
CATTGCGATTTTCTTCTA
Found at i:67931 original size:20 final size:20
Alignment explanation
Indices: 67902--67953 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
67892 TGGAAGCTCG
*
67902 CGTTGCGATTTTCTTTTGAT
1 CGTTGCGATTTTCTTTTGAA
* *
67922 CGTTGTGATTTTCTTTTTAA
1 CGTTGCGATTTTCTTTTGAA
67942 CGTTGCGATTTT
1 CGTTGCGATTTT
67954 GATATCGCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.12, C:0.13, G:0.19, T:0.56
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAA
Found at i:75922 original size:2 final size:2
Alignment explanation
Indices: 75915--75949 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
75905 TTTTGTTGGA
*
75915 TC TC TC TC TC TC GC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
75950 ATATATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.49, G:0.03, T:0.49
Consensus pattern (2 bp):
TC
Found at i:79123 original size:5 final size:5
Alignment explanation
Indices: 79106--79137 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
79096 GAAAGCTCCA
79106 TTCTT TCTCTT TTCTT TTCTT TTCTT TTCTT T
1 TTCTT T-TCTT TTCTT TTCTT TTCTT TTCTT T
79138 GATAATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TTCTT
Found at i:80096 original size:26 final size:25
Alignment explanation
Indices: 80067--80135 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 25
80057 TTTTATAATT
*
80067 AAATATATGTGATAAATATTTTTTGG
1 AAATA-ATGTAATAAATATTTTTTGG
* * *
80093 AAATACTGTAATAAATGTTTTTT-T
1 AAATAATGTAATAAATATTTTTTGG
* *
80117 AAATAATATAATAATTATT
1 AAATAATGTAATAAATATT
80136 AATTAATAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
24 15 0.43
25 15 0.43
26 5 0.14
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.46
Consensus pattern (25 bp):
AAATAATGTAATAAATATTTTTTGG
Found at i:80804 original size:45 final size:46
Alignment explanation
Indices: 80727--80816 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 46
80717 CTCGTTAAAT
* *
80727 TAATAAAATTACGTAGTTCCAGACTCCCAACATTATTAATTTCTAG
1 TAATAAAATTACATAGTCCCAGACTCCCAACATTATTAATTTCTAG
*
80773 TAATAAAATT-CATAGTCCCAGGCTCCCAACATTATTAATTTCTA
1 TAATAAAATTACATAGTCCCAGACTCCCAACATTATTAATTTCTA
80817 AAGATTTTAC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 31 0.76
46 10 0.24
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.34
Consensus pattern (46 bp):
TAATAAAATTACATAGTCCCAGACTCCCAACATTATTAATTTCTAG
Done.