Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001170.1 Hibiscus syriacus cultivar Beakdansim tig00002333_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: 63420
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1669 original size:12 final size:12
Alignment explanation
Indices: 1654--1687 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1644 TACATATACT
1654 ATCATTATCAAC
1 ATCATTATCAAC
**
1666 ATCAACATCAAC
1 ATCATTATCAAC
1678 ATCATTATCA
1 ATCATTATCA
1688 TTATCATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.29
Consensus pattern (12 bp):
ATCATTATCAAC
Found at i:1940 original size:22 final size:22
Alignment explanation
Indices: 1912--2017 Score: 185
Period size: 22 Copynumber: 4.8 Consensus size: 22
1902 GGCATGTGAA
*
1912 ATTTGTCCCGAAGGACCTATGT
1 ATTTGTCCCGAAGGACCTATGC
*
1934 ATTTGTCCTGAAGGACCTATGC
1 ATTTGTCCCGAAGGACCTATGC
1956 ATTTGTCCCGAAGGACCTATGC
1 ATTTGTCCCGAAGGACCTATGC
*
1978 ATTTGTCCTGAAGGACCTATGC
1 ATTTGTCCCGAAGGACCTATGC
2000 ATTTGTCCCGAAGGACCT
1 ATTTGTCCCGAAGGACCT
2018 CTGTATACTG
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 79 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCTATGC
Found at i:1962 original size:44 final size:44
Alignment explanation
Indices: 1912--2023 Score: 206
Period size: 44 Copynumber: 2.5 Consensus size: 44
1902 GGCATGTGAA
1912 ATTTGTCCCGAAGGACCTATGTATTTGTCCTGAAGGACCTATGC
1 ATTTGTCCCGAAGGACCTATGTATTTGTCCTGAAGGACCTATGC
*
1956 ATTTGTCCCGAAGGACCTATGCATTTGTCCTGAAGGACCTATGC
1 ATTTGTCCCGAAGGACCTATGTATTTGTCCTGAAGGACCTATGC
*
2000 ATTTGTCCCGAAGGACCTCTGTAT
1 ATTTGTCCCGAAGGACCTATGTAT
2024 ACTGTATATG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 65 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.31
Consensus pattern (44 bp):
ATTTGTCCCGAAGGACCTATGTATTTGTCCTGAAGGACCTATGC
Found at i:5589 original size:44 final size:44
Alignment explanation
Indices: 5498--5589 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
5488 TTTATTTCAA
* *
5498 TTTAGTTATTTATTTTTTCCTTTTTAATTTTAGCATTTTTTTAT
1 TTTAGTTATTCATTTTTTCCTTTTTAATTTTAGCATATTTTTAT
**
5542 TTTAGTTATTCATTTTTGT-CTCTTTTAATTTTAGTGTATTTTT-T
1 TTTAGTTATTCATTTTT-TCCT-TTTTAATTTTAGCATATTTTTAT
5586 TTTA
1 TTTA
5590 TTTTTCTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
44 23 0.55
45 19 0.45
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.70
Consensus pattern (44 bp):
TTTAGTTATTCATTTTTTCCTTTTTAATTTTAGCATATTTTTAT
Found at i:5592 original size:20 final size:19
Alignment explanation
Indices: 5564--5611 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
5554 TTTTTGTCTC
* *
5564 TTTTAATTTTAGTGTATTTT
1 TTTTTATTTTACT-TATTTT
*
5584 TTTTTATTTTTCTTATTTT
1 TTTTTATTTTACTTATTTT
5603 TATTTTATT
1 T-TTTTATT
5612 ACCTTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.77
Consensus pattern (19 bp):
TTTTTATTTTACTTATTTT
Found at i:5602 original size:45 final size:46
Alignment explanation
Indices: 5498--5603 Score: 109
Period size: 45 Copynumber: 2.4 Consensus size: 46
5488 TTTATTTCAA
*
5498 TTTAGTTA-T-TTATTTTTTCCTTTTTAATTTTAGCATTTTTTTAT
1 TTTAGTTATTCTTATTTTTTCCTTTTTAATTTTAGCATATTTTTAT
**
5542 TTTAGTTATTC--ATTTTTGT-CTCTTTTAATTTTAGTGTATTTTT-T
1 TTTAGTTATTCTTATTTTT-TCCT-TTTTAATTTTAGCATATTTTTAT
*
5586 TTTA-TTTTTCTTATTTTT
1 TTTAGTTATTCTTATTTTT
5604 ATTTTATTAC
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
43 5 0.10
44 21 0.40
45 26 0.50
ACGTcount: A:0.16, C:0.07, G:0.06, T:0.72
Consensus pattern (46 bp):
TTTAGTTATTCTTATTTTTTCCTTTTTAATTTTAGCATATTTTTAT
Found at i:8683 original size:27 final size:27
Alignment explanation
Indices: 8652--8711 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
8642 GAACAAAAAA
* *
8652 AGAAAA-AAAGAAGAGAGAAAATCAAAG
1 AGAAAATAAAAAAGAGA-AAAAACAAAG
8679 AGAAAATAAAAAAGAGAAAAAACAAAG
1 AGAAAATAAAAAAGAGAAAAAACAAAG
8706 -GAAAAT
1 AGAAAAT
8712 TGAAGAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 6 0.20
27 15 0.50
28 9 0.30
ACGTcount: A:0.73, C:0.03, G:0.18, T:0.05
Consensus pattern (27 bp):
AGAAAATAAAAAAGAGAAAAAACAAAG
Found at i:8684 original size:26 final size:25
Alignment explanation
Indices: 8650--8698 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
8640 AAGAACAAAA
*
8650 AAAGAAAAA-AAGAAGAGAGAAAATC
1 AAAGAAAAATAA-AAAAGAGAAAATC
8675 AAAGAGAAAATAAAAAAGAGAAAA
1 AAAGA-AAAATAAAAAAGAGAAAA
8699 AACAAAGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 5 0.24
26 14 0.67
27 2 0.10
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (25 bp):
AAAGAAAAATAAAAAAGAGAAAATC
Found at i:8709 original size:26 final size:26
Alignment explanation
Indices: 8641--8711 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 26
8631 GATTCAATCA
*
8641 AGAACAAAA-AAA-GAAAA-AAAGAAG
1 AGAA-AAAACAAAGGAAAATAAAAAAG
*
8665 AGAGAAAATCAAAGAGAAAATAAAAAAG
1 AGA-AAAAACAAAG-GAAAATAAAAAAG
8693 AGAAAAAACAAAGGAAAAT
1 AGAAAAAACAAAGGAAAAT
8712 TGAAGAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 6 0.15
25 4 0.10
26 6 0.15
27 14 0.36
28 9 0.23
ACGTcount: A:0.75, C:0.04, G:0.17, T:0.04
Consensus pattern (26 bp):
AGAAAAAACAAAGGAAAATAAAAAAG
Found at i:9866 original size:32 final size:31
Alignment explanation
Indices: 9830--9944 Score: 122
Period size: 31 Copynumber: 3.6 Consensus size: 31
9820 GGAACAATGA
* *
9830 GGGCATCTTTGAAGATTCAGCATCAAATACTG
1 GGGCATCTTTG-AGATTCAACATCAAATATTG
* * *
9862 GGGCATTTTTTGAGATTTAACATCAAATGTTG
1 GGGCA-TCTTTGAGATTCAACATCAAATATTG
* * *
9894 GGGCATTTTTTAGATTCAACATCGAATATTG
1 GGGCATCTTTGAGATTCAACATCAAATATTG
*
9925 GGGCATCTTTGGGAATTCAA
1 GGGCATCTTTGAG-ATTCAA
9945 TATCCTAATT
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
31 32 0.46
32 32 0.46
33 5 0.07
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.35
Consensus pattern (31 bp):
GGGCATCTTTGAGATTCAACATCAAATATTG
Found at i:9909 original size:31 final size:32
Alignment explanation
Indices: 9837--9930 Score: 127
Period size: 32 Copynumber: 2.9 Consensus size: 32
9827 TGAGGGCATC
* *
9837 TTTGAAGATTCAGCATCAAATACTGGGGCATTT
1 TTTG-AGATTCAACATCAAATATTGGGGCATTT
* *
9870 TTTGAGATTTAACATCAAATGTTGGGGCATTT
1 TTTGAGATTCAACATCAAATATTGGGGCATTT
*
9902 TTT-AGATTCAACATCGAATATTGGGGCAT
1 TTTGAGATTCAACATCAAATATTGGGGCAT
9931 CTTTGGGAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
31 23 0.43
32 27 0.50
33 4 0.07
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (32 bp):
TTTGAGATTCAACATCAAATATTGGGGCATTT
Found at i:12584 original size:21 final size:21
Alignment explanation
Indices: 12555--12626 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 21
12545 ATCAATTTTA
*
12555 ATTTATTTCAATTTAGTTATTC
1 ATTT-TTTCATTTTAGTTATTC
* *
12577 ATTTTTTCCTTTTTAATT-TTAGC
1 ATTTTTT-CATTTTAGTTATT--C
*
12600 ATTTTTTTATTTTAGTTATTC
1 ATTTTTTCATTTTAGTTATTC
12621 ATTTTT
1 ATTTTT
12627 GTCTCTTTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
21 12 0.30
22 18 0.45
23 10 0.25
ACGTcount: A:0.21, C:0.08, G:0.04, T:0.67
Consensus pattern (21 bp):
ATTTTTTCATTTTAGTTATTC
Found at i:12616 original size:44 final size:46
Alignment explanation
Indices: 12566--12657 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 46
12556 TTTATTTCAA
12566 TTTAGTTATTCATTTTT-TC-CTTTTTAATTTTAGCAT-TTTTTTAT
1 TTTAGTTATTCATTTTTGTCTC-TTTTAATTTTAGCATATTTTTTAT
**
12610 TTTAGTTATTCATTTTTGTCTCTTTTAATTTTAGTGTATTTTTTAT
1 TTTAGTTATTCATTTTTGTCTCTTTTAATTTTAGCATATTTTTTAT
12656 TT
1 TT
12658 ATTTTTCTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
44 17 0.40
45 15 0.35
46 11 0.26
ACGTcount: A:0.17, C:0.08, G:0.07, T:0.68
Consensus pattern (46 bp):
TTTAGTTATTCATTTTTGTCTCTTTTAATTTTAGCATATTTTTTAT
Found at i:15091 original size:3 final size:3
Alignment explanation
Indices: 15068--15120 Score: 85
Period size: 3 Copynumber: 18.7 Consensus size: 3
15058 TTTTGGGTTT
15068 TTA TT- TTA TT- TTA TT- 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 TTA TTA
15113 TTA TTA TT
1 TTA TTA TT
15121 TTTGCAGTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 6 0.13
3 41 0.87
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:20404 original size:19 final size:20
Alignment explanation
Indices: 20362--20401 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
20352 TGATCAGGTC
20362 TCTTTCTATGCACCTTTTTT
1 TCTTTCTATGCACCTTTTTT
*
20382 TCTTTCTATGTACCTTTTTT
1 TCTTTCTATGCACCTTTTTT
20402 CTTCCTGCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.23, G:0.05, T:0.62
Consensus pattern (20 bp):
TCTTTCTATGCACCTTTTTT
Found at i:20494 original size:2 final size:2
Alignment explanation
Indices: 20487--20534 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
20477 TTCGTAAGTC
* *
20487 AT AT AT AT AT AT AT AT CT AT AT CT 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
20529 AT AT AT
1 AT AT AT
20535 CAGACTTGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26181 original size:105 final size:107
Alignment explanation
Indices: 25993--26199 Score: 285
Period size: 105 Copynumber: 2.0 Consensus size: 107
25983 TTCAAATGAC
* * *
25993 GGGTCCGCTCCCTCTTGTTCAGGGATTAAGGAACTCGAACAATCTTTTAAAAACGGGTTCGCTCC
1 GGGTCCGCTCCCTCTTGATCAGGGAGTAAGGAACTCGAACAATCTTCTAAAAACGGGTTCGCTCC
*
26058 CTATTGCTTCAGGGAGTAGAACTCGAATAATCTTCTGCTTAT
66 CTATTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCTTAT
* ****
26100 GGGTTCGCTCCCTCTTGCATCAGGGAGT-A-GAACTCGAACAATCTTCTGCCTACGGGTT-GCTC
1 GGGTCCGCTCCCTCTTG-ATCAGGGAGTAAGGAACTCGAACAATCTTCTAAAAACGGGTTCGCTC
* *
26162 CCTCTTGCTTCAGGGAGTAGAACTCGAGCAATCTTCTG
65 CCTATTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
26200 GTGTGATTCT
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
105 39 0.44
106 24 0.27
107 17 0.19
108 8 0.09
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (107 bp):
GGGTCCGCTCCCTCTTGATCAGGGAGTAAGGAACTCGAACAATCTTCTAAAAACGGGTTCGCTCC
CTATTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCTTAT
Found at i:26184 original size:52 final size:53
Alignment explanation
Indices: 25991--26199 Score: 269
Period size: 53 Copynumber: 3.9 Consensus size: 53
25981 TCTTCAAATG
* * * ** *
25991 ACGGGTCCGCTCCCTCTTG-TTCAGGGATTAAGGAACTCGAACAATCTTTTAAAA
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGT-A-GAACTCGAACAATCTTCTGCAT
* * *
26045 ACGGGTTCGCTCCCTATTGCTTCAGGGAGTAGAACTCGAATAATCTTCTGCTT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCAT
* * *
26098 ATGGGTTCGCTCCCTCTTGCATCAGGGAGTAGAACTCGAACAATCTTCTGCCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCAT
*
26151 ACGGGTT-GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAGCAATCTTCTG
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
26200 GTGTGATTCT
Statistics
Matches: 137, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
52 40 0.29
53 70 0.51
54 18 0.13
55 9 0.07
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (53 bp):
ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCAT
Found at i:35500 original size:27 final size:27
Alignment explanation
Indices: 35463--35515 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
35453 AAATCAGAAA
*
35463 TAAATCGGTGACCTAAACATAAAATAC
1 TAAATCAGTGACCTAAACATAAAATAC
*
35490 TAAATCAGTGACCTAAATATAAAATA
1 TAAATCAGTGACCTAAACATAAAATA
35516 TGTATAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.51, C:0.15, G:0.09, T:0.25
Consensus pattern (27 bp):
TAAATCAGTGACCTAAACATAAAATAC
Found at i:43300 original size:64 final size:63
Alignment explanation
Indices: 43184--43324 Score: 142
Period size: 64 Copynumber: 2.2 Consensus size: 63
43174 CACATTGAAT
* *
43184 GTGCGTCGATGCACTCTTTAAAGAAGAAACAACGAATGCAATTGGTGCATCGATGCATAAAGA
1 GTGCATCGATGCACTCTTTAAAGAAGAAACAACGAAGGCAATTGGTGCATCGATGCATAAAGA
* * * * * * * **
43247 GTGCATCGATGCATTCTTTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATCGATGTAT-GGGT
1 GTGCATCGATGCACTC-TTTAAAGAAG-AAACAACGAAGGCAATTGGTGCATCGATGCATAAAG-
43310 A
63 A
43311 GTGCATCGATGCAC
1 GTGCATCGATGCAC
43325 ATGTTAAAGA
Statistics
Matches: 63, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
63 17 0.27
64 46 0.73
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.28
Consensus pattern (63 bp):
GTGCATCGATGCACTCTTTAAAGAAGAAACAACGAAGGCAATTGGTGCATCGATGCATAAAGA
Found at i:43367 original size:20 final size:22
Alignment explanation
Indices: 43312--43369 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 22
43302 GTATGGGTAG
43312 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
*
43336 TACATC-AGTGCACTG-T-AGAA
1 TGCATCGA-TGCACTGTTAAGAA
43356 TGCATCGATGCACT
1 TGCATCGATGCACT
43370 TCAAGGGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
20 15 0.50
21 1 0.03
22 1 0.03
23 3 0.10
24 10 0.33
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:44915 original size:19 final size:19
Alignment explanation
Indices: 44891--44930 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
44881 AATAAGTTAT
44891 ATGTTATAAAAGTTTTTAA
1 ATGTTATAAAAGTTTTTAA
44910 ATGTTATAAAAGTTTTTAA
1 ATGTTATAAAAGTTTTTAA
44929 AT
1 AT
44931 TACTCACTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (19 bp):
ATGTTATAAAAGTTTTTAA
Found at i:47456 original size:64 final size:63
Alignment explanation
Indices: 47361--47501 Score: 178
Period size: 64 Copynumber: 2.2 Consensus size: 63
47351 CACATTGAAT
* *
47361 GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAATTGGTGCATCGATGCATAAGG-A
1 GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATGCAT-AGGTA
* * * * *
47424 GTGCATCGATGCATCCCTTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGGGTA
1 GTGCATCGATGCA-CCCTTTAAAGAAG-AAACATCGAAGGCAATTGGTGCATCGATGCATAGGTA
47488 GTGCATCGATGCAC
1 GTGCATCGATGCAC
47502 ATGTTAAAGA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
63 18 0.26
64 50 0.74
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATGCATAGGTA
Found at i:47516 original size:24 final size:20
Alignment explanation
Indices: 47489--47546 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
47479 GCATGGGTAG
47489 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
47513 TGCATAGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
47533 TGCATCGATGCACT
1 TGCATCGATGCACT
47547 TCAAGGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 2 0.06
24 12 0.38
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:60893 original size:19 final size:19
Alignment explanation
Indices: 60868--60942 Score: 55
Period size: 19 Copynumber: 3.9 Consensus size: 19
60858 TGAAAAAAAC
60868 CTATGAATATGAAATTAAG
1 CTATGAATATGAAATTAAG
* * *
60887 CTGTGAATCT-AAAATAAG
1 CTATGAATATGAAATTAAG
* * *
60905 TTATAAATATGGAAA-TAGG
1 CTATGAATAT-GAAATTAAG
*
60924 CTTTGAATATGAGAATTAA
1 CTATGAATATGA-AATTAA
60943 TTATGAAATG
Statistics
Matches: 40, Mismatches: 12, Indels: 7
0.68 0.20 0.12
Matches are distributed among these distances:
18 15 0.38
19 20 0.50
20 5 0.12
ACGTcount: A:0.45, C:0.05, G:0.17, T:0.32
Consensus pattern (19 bp):
CTATGAATATGAAATTAAG
Found at i:60987 original size:13 final size:13
Alignment explanation
Indices: 60966--61035 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
60956 AAGTACTTGT
*
60966 TATGGAAATGAAA
1 TATGAAAATGAAA
60979 TATGAAAATG-AA
1 TATGAAAATGAAA
*
60991 TCT-ATAAATG-AA
1 TATGA-AAATGAAA
*
61003 TATGAAAGTGAAA
1 TATGAAAATGAAA
* *
61016 GATGAGAATGAAA
1 TATGAAAATGAAA
61029 TATGAAA
1 TATGAAA
61036 GTTCTGAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
11 1 0.02
12 17 0.38
13 27 0.60
ACGTcount: A:0.54, C:0.01, G:0.20, T:0.24
Consensus pattern (13 bp):
TATGAAAATGAAA
Done.