Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004934.1 Hibiscus syriacus cultivar Beakdansim tig00011100_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: 62537
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:12248 original size:87 final size:90
Alignment explanation
Indices: 12084--12295 Score: 295
Period size: 89 Copynumber: 2.4 Consensus size: 90
12074 GTCATCCCCA
* *
12084 GACCAGACCTCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTA
1 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTA
* **
12149 GGAACCGTGTTATCA-CCTTTAGAT
66 GGAACCGAGTTATCACCCTAAAGAT
* * *
12173 GGCCAGATCTCTTCATCACGTAAGAGCCGTGTCAACC-T-GATAACCAGTCGTCCTCATTACGTA
1 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTA
12236 GGAACCGAGTTATCATCCCTAAAGAT
66 GGAACCGAGTTATCA-CCCTAAAGAT
* * *
12262 GACCAGATTTCCTCATCACGTAGGAGCCGTGTCA
1 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCA
12296 CCCTTAGACG
Statistics
Matches: 109, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
87 37 0.34
88 1 0.01
89 71 0.65
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (90 bp):
GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTA
GGAACCGAGTTATCACCCTAAAGAT
Found at i:12506 original size:3 final size:3
Alignment explanation
Indices: 12495--12555 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
12485 TTTTTTTCCG
** *
12495 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12540 TTA TTA TTTA TTA TTA
1 TTA TTA -TTA TTA TTA
12556 CAATTTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12698 original size:25 final size:25
Alignment explanation
Indices: 12670--12739 Score: 131
Period size: 25 Copynumber: 2.8 Consensus size: 25
12660 AACCTAGCAG
*
12670 ATTAGGGTTTCAAACCCTAAATCAA
1 ATTAGGGTTTCAAACCCTAAAACAA
12695 ATTAGGGTTTCAAACCCTAAAACAA
1 ATTAGGGTTTCAAACCCTAAAACAA
12720 ATTAGGGTTTCAAACCCTAA
1 ATTAGGGTTTCAAACCCTAA
12740 TCCCCTACTC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (25 bp):
ATTAGGGTTTCAAACCCTAAAACAA
Found at i:16723 original size:35 final size:31
Alignment explanation
Indices: 16660--16724 Score: 85
Period size: 35 Copynumber: 2.0 Consensus size: 31
16650 ATTTTAATTA
*
16660 ATATTAAATTTTACATAATTTATCTAAATAT
1 ATATTAAATTTTACATAATTTAACTAAATAT
16691 ATATTAAAATTTTACATCAACATTTAACTAAATA
1 ATATT-AAATTTTACAT--A-ATTTAACTAAATA
16725 AACATATGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 5 0.17
32 11 0.38
34 1 0.03
35 12 0.41
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (31 bp):
ATATTAAATTTTACATAATTTAACTAAATAT
Found at i:16831 original size:22 final size:24
Alignment explanation
Indices: 16804--16849 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
16794 TATTTTTAAT
*
16804 TTATTA-ATTATAAAAT-ATATTA
1 TTATTAGATTAAAAAATCATATTA
16826 TTATTAGTATTAAAAAATCATATT
1 TTATTAG-ATTAAAAAATCATATT
16850 TTTACTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
24 9 0.45
25 5 0.25
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (24 bp):
TTATTAGATTAAAAAATCATATTA
Found at i:20558 original size:36 final size:35
Alignment explanation
Indices: 20477--20615 Score: 188
Period size: 36 Copynumber: 3.9 Consensus size: 35
20467 GATGAACAAC
* *
20477 TGAATCGAAAGTGCTGACGCTTCCTTCCGTTCACT
1 TGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACT
* * * *
20512 TGAATTGAAAGTGCCGGTGCTTCCTTTCGTTCTTCT
1 TGAATCGAAAGTGCCGATGCTTCCTTCCGTTC-ACT
20548 TGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACTT
1 TGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAC-T
* *
20584 TGAATCGAAAGTGCTGATGCTTCCTTTCGTTC
1 TGAATCGAAAGTGCCGATGCTTCCTTCCGTTC
20616 TTCTTATTCA
Statistics
Matches: 90, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
35 28 0.31
36 62 0.69
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (35 bp):
TGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACT
Found at i:20618 original size:72 final size:71
Alignment explanation
Indices: 20477--20620 Score: 234
Period size: 72 Copynumber: 2.0 Consensus size: 71
20467 GATGAACAAC
* * *
20477 TGAATCGAAAGTGCTGACGCTTCCTTCCGTTCACTTGAATTGAAAGTGCCGGTGCTTCCTTTCGT
1 TGAATCGAAAGTGCCGACGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTCCTTTCGT
20542 TCTTCT
66 TCTTCT
* *
20548 TGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGCTGATGCTTCCTTTCG
1 TGAATCGAAAGTGCCGACGCTTCCTTCCGTTCAC-TTGAATCGAAAGTGCCGATGCTTCCTTTCG
20613 TTCTTCT
65 TTCTTCT
20620 T
1 T
20621 ATTCACCTTC
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
71 32 0.48
72 35 0.52
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.38
Consensus pattern (71 bp):
TGAATCGAAAGTGCCGACGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTCCTTTCGT
TCTTCT
Found at i:23534 original size:21 final size:20
Alignment explanation
Indices: 23510--23553 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
23500 CCTCCAATTA
* *
23510 ATTATAATTTCAAAACTATTT
1 ATTATAA-TTCAAAAATAGTT
*
23531 ATTATTATTCAAAAATAGTT
1 ATTATAATTCAAAAATAGTT
23551 ATT
1 ATT
23554 TCATATTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (20 bp):
ATTATAATTCAAAAATAGTT
Found at i:24223 original size:13 final size:12
Alignment explanation
Indices: 24205--24234 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
24195 AATTTTTTAA
24205 AAATAAAATTTT
1 AAATAAAATTTT
24217 CAAATAAAATTTT
1 -AAATAAAATTTT
24230 AAATA
1 AAATA
24235 TAATATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (12 bp):
AAATAAAATTTT
Found at i:31412 original size:10 final size:10
Alignment explanation
Indices: 31397--31423 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
31387 AATTAATGTT
31397 AAATAAAACA
1 AAATAAAACA
31407 AAATAAAACA
1 AAATAAAACA
31417 AAATAAA
1 AAATAAA
31424 GAAAGGTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.81, C:0.07, G:0.00, T:0.11
Consensus pattern (10 bp):
AAATAAAACA
Found at i:32573 original size:3 final size:3
Alignment explanation
Indices: 32565--32629 Score: 52
Period size: 3 Copynumber: 22.7 Consensus size: 3
32555 TAAATAAATA
*
32565 AAT AAT AAT AAT AAT -AT AA- CAT AAT -AT AAT AA- ATAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
32606 AAT AAAT AAT -AT AATT AAT AAT AA
1 AAT -AAT AAT AAT AA-T AAT AAT AA
32630 AAACTATATA
Statistics
Matches: 51, Mismatches: 2, Indels: 18
0.72 0.03 0.25
Matches are distributed among these distances:
2 10 0.20
3 34 0.67
4 7 0.14
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:32588 original size:10 final size:10
Alignment explanation
Indices: 32542--32609 Score: 54
Period size: 9 Copynumber: 6.9 Consensus size: 10
32532 ACCTATTAAA
32542 AAAATAA-AT
1 AAAATAATAT
*
32551 TAAATAA-AT
1 AAAATAATAT
32560 -AAATAAATAAT
1 AAAAT-AAT-AT
32571 AATAATAATAT
1 AA-AATAATAT
*
32582 AACATAATAT
1 AAAATAATAT
*
32592 AATA-AATAT
1 AAAATAATAT
32601 AAAATAATA
1 AAAATAATA
32610 AATAATATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
8 4 0.08
9 18 0.37
10 14 0.29
11 6 0.12
12 4 0.08
13 3 0.06
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.29
Consensus pattern (10 bp):
AAAATAATAT
Found at i:32590 original size:19 final size:17
Alignment explanation
Indices: 32553--32625 Score: 80
Period size: 19 Copynumber: 4.2 Consensus size: 17
32543 AAATAAATTA
32553 AATA-AATAA-ATAAAT
1 AATATAATAATATAAAT
32568 AATAATAATAATATAACAT
1 AAT-ATAATAATATAA-AT
32587 AATATAATAAATATAAAAT
1 AATATAAT-AATAT-AAAT
*
32606 AATA-AATAATATAATT
1 AATATAATAATATAAAT
32622 AATA
1 AATA
32626 ATAAAAACTA
Statistics
Matches: 51, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
15 3 0.06
16 8 0.16
17 10 0.20
18 12 0.24
19 16 0.31
20 2 0.04
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (17 bp):
AATATAATAATATAAAT
Found at i:32624 original size:4 final size:5
Alignment explanation
Indices: 32553--32625 Score: 57
Period size: 5 Copynumber: 14.8 Consensus size: 5
32543 AAATAAATTA
*
32553 AATA- AATA- AATA- AATAAT AATAAT AATAT AACAT AATAT AATA- AATAT
1 AATAT AATAT AATAT AAT-AT AAT-AT AATAT AATAT AATAT AATAT AATAT
*
32601 AAAAT AATAAAT AATAT AAT-T AATA
1 AATAT AAT--AT AATAT AATAT AATA
32626 ATAAAAACTA
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
4 19 0.32
5 26 0.44
6 9 0.15
7 5 0.08
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (5 bp):
AATAT
Found at i:32625 original size:35 final size:35
Alignment explanation
Indices: 32544--32630 Score: 101
Period size: 35 Copynumber: 2.5 Consensus size: 35
32534 CTATTAAAAA
32544 AATA-AATTAA-ATAAATAAATAAATAATAATAAT
1 AATATAATTAATATAAATAAATAAATAATAATAAT
*
32577 AATATAACATAATAT-AATAAATATAA-AATAATAAAT
1 AATATAA-TTAATATAAATAAATA-AATAATAAT-AAT
32613 AATATAATTAATAATAAA
1 AATATAATTAAT-ATAAA
32631 AACTATATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
33 4 0.09
34 2 0.04
35 21 0.47
36 16 0.36
37 2 0.04
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (35 bp):
AATATAATTAATATAAATAAATAAATAATAATAAT
Found at i:32637 original size:19 final size:18
Alignment explanation
Indices: 32538--32637 Score: 84
Period size: 17 Copynumber: 5.6 Consensus size: 18
32528 TTGGACCTAT
* *
32538 TAAAAAAATAAATTA-AA
1 TAAAAATATAAATAATAA
32555 TAAATAA-ATAAATAATAA
1 TAAA-AATATAAATAATAA
*
32573 TAATAATATAACATAAT-A
1 TAAAAATATAA-ATAATAA
32591 TAATAAATAT-AA-AATAA
1 TAA-AAATATAAATAATAA
*
32608 TAAATAATATAATTAATAA
1 TAAA-AATATAAATAATAA
32627 TAAAAACTATA
1 TAAAAA-TATA
32638 TAACATATAT
Statistics
Matches: 69, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
16 4 0.06
17 23 0.33
18 19 0.28
19 23 0.33
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAAATATAAATAATAA
Found at i:32640 original size:26 final size:26
Alignment explanation
Indices: 32542--32631 Score: 83
Period size: 26 Copynumber: 3.2 Consensus size: 26
32532 ACCTATTAAA
32542 AAAATAAATTAAATAA-ATAAATAAATAAT
1 AAAAT-AA-TAAATAATAT-AATAAAT-AT
32571 AATAATAATATAACATAATATAATAAATAT
1 AA-AAT-A-ATAA-ATAATATAATAAATAT
*
32601 AAAATAATAAATAATATAATTAATAAT
1 AAAATAATAAATAATATAATAAAT-AT
32628 AAAA
1 AAAA
32632 ACTATATAAC
Statistics
Matches: 55, Mismatches: 1, Indels: 12
0.81 0.01 0.18
Matches are distributed among these distances:
26 13 0.24
27 10 0.18
28 1 0.02
29 5 0.09
30 12 0.22
31 12 0.22
32 2 0.04
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (26 bp):
AAAATAATAAATAATATAATAAATAT
Found at i:32683 original size:22 final size:22
Alignment explanation
Indices: 32643--32692 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
32633 CTATATAACA
*
32643 TATATATTATATTTCCAAAAAC
1 TATATAATATATTTCCAAAAAC
* * *
32665 TATATAATATGTTTTCAAAAAT
1 TATATAATATATTTCCAAAAAC
32687 TATATA
1 TATATA
32693 TATTACATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (22 bp):
TATATAATATATTTCCAAAAAC
Found at i:32774 original size:23 final size:24
Alignment explanation
Indices: 32730--32774 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
32720 TAAAAAAATC
*
32730 ATATATATATATGGTTTCAAAACT
1 ATATATATATAAGGTTTCAAAACT
* *
32754 ATAT-TATATAAGTTTTTAAAA
1 ATATATATATAAGGTTTCAAAA
32775 TTTGTTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (24 bp):
ATATATATATAAGGTTTCAAAACT
Found at i:32878 original size:33 final size:33
Alignment explanation
Indices: 32744--33008 Score: 224
Period size: 33 Copynumber: 7.5 Consensus size: 33
32734 ATATATATGG
* * *
32744 TTTCAAAACTATATTATATAAGTTTTTAAAATTTGTT
1 TTTCAAAACTATATTATA-CA-TTTTCAAAA-ATG-T
* *
32781 TTTTAAAACTATATATTATACGTTTTCAAAAATGT
1 TTTCAAAAC--TATATTATACATTTTCAAAAATGT
* *
32816 GGTTTCAAAAACCATATATCATACGTTTTCAAAAATGT
1 --TTTC-AAAA-C-TATATTATACATTTTCAAAAATGT
*
32854 TTTCAAAACTATATTATACATTTTCAAAAATAT
1 TTTCAAAACTATATTATACATTTTCAAAAATGT
* * *
32887 TTTTAAAATCATATTTTATACGTTTTCAAAAATGT
1 TTTCAAAA-C-TATATTATACATTTTCAAAAATGT
* *
32922 TTTCAAAACCATATTATATATTTTCAAAAATGT
1 TTTCAAAACTATATTATACATTTTCAAAAATGT
* * * *
32955 TTTCAAAACCATATTATATATGTTTTCAAAAGTAT
1 TTTCAAAACTATATTATACA--TTTTCAAAAATGT
*
32990 GTTCAAAAACTATATTATA
1 TTTC-AAAACTATATTATA
33009 TGATTATATA
Statistics
Matches: 194, Mismatches: 23, Indels: 23
0.81 0.10 0.10
Matches are distributed among these distances:
33 68 0.35
34 3 0.02
35 47 0.24
36 19 0.10
37 19 0.10
38 28 0.14
39 10 0.05
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (33 bp):
TTTCAAAACTATATTATACATTTTCAAAAATGT
Found at i:32913 original size:35 final size:35
Alignment explanation
Indices: 32744--33008 Score: 249
Period size: 35 Copynumber: 7.6 Consensus size: 35
32734 ATATATATGG
* * * *
32744 TTTCAAAACTATAT-TATATAAGTTTTTAAAATTTGTT
1 TTTCAAAACCATATAT-TATACGTTTTCAAAA-ATG-T
* *
32781 TTTTAAAACTATATATTATACGTTTTCAAAAATGT
1 TTTCAAAACCATATATTATACGTTTTCAAAAATGT
*
32816 GGTTTCAAAAACCATATATCATACGTTTTCAAAAATGT
1 --TTTC-AAAACCATATATTATACGTTTTCAAAAATGT
* *
32854 TTTCAAAA-C-TATATTATACATTTTCAAAAATAT
1 TTTCAAAACCATATATTATACGTTTTCAAAAATGT
* * *
32887 TTTTAAAATCATATTTTATACGTTTTCAAAAATGT
1 TTTCAAAACCATATATTATACGTTTTCAAAAATGT
32922 TTTCAAAACCATAT-TATATA--TTTTCAAAAATGT
1 TTTCAAAACCATATAT-TATACGTTTTCAAAAATGT
* * *
32955 TTTCAAAACCATAT-TATATATGTTTTCAAAAGTAT
1 TTTCAAAACCATATAT-TATACGTTTTCAAAAATGT
* *
32990 GTTCAAAAAC-TATATTATA
1 TTTCAAAACCATATATTATA
33009 TGATTATATA
Statistics
Matches: 198, Mismatches: 20, Indels: 23
0.82 0.08 0.10
Matches are distributed among these distances:
33 61 0.31
34 10 0.05
35 62 0.31
36 6 0.03
37 29 0.15
38 30 0.15
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (35 bp):
TTTCAAAACCATATATTATACGTTTTCAAAAATGT
Found at i:32919 original size:68 final size:68
Alignment explanation
Indices: 32792--33008 Score: 272
Period size: 68 Copynumber: 3.1 Consensus size: 68
32782 TTTAAAACTA
* * *
32792 TATATTATACGTTTTCAAAAATGTGGTTTCAAAAACCATATATCATACGTTTTCAAAAATGTTTT
1 TATATTATACATTTTCAAAAATGT--TTT-AAAAACCATATTTTATACGTTTTCAAAAATGTTTT
32857 CAAAAC
63 CAAAAC
* * *
32863 TATATTATACATTTTCAAAAATATTTTTAAAATCATATTTTATACGTTTTCAAAAATGTTTTCAA
1 TATATTATACATTTTCAAAAATGTTTTAAAAACCATATTTTATACGTTTTCAAAAATGTTTTCAA
32928 AAC
66 AAC
* * * * * * * *
32931 CATATTATATATTTTCAAAAATGTTTTCAAAACCATATTATATATGTTTTCAAAAGTATGTTCAA
1 TATATTATACATTTTCAAAAATGTTTTAAAAACCATATTTTATACGTTTTCAAAAATGTTTTC-A
32996 AAAC
65 AAAC
33000 TATATTATA
1 TATATTATA
33009 TGATTATATA
Statistics
Matches: 128, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
68 90 0.70
69 16 0.12
71 22 0.17
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.42
Consensus pattern (68 bp):
TATATTATACATTTTCAAAAATGTTTTAAAAACCATATTTTATACGTTTTCAAAAATGTTTTCAA
AAC
Found at i:34342 original size:28 final size:28
Alignment explanation
Indices: 34310--34364 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
34300 TACTAAACGC
34310 TTAGTTTACCCAGGAAAGAATTGATAAT
1 TTAGTTTACCCAGGAAAGAATTGATAAT
34338 TTAGTTTACCCAGGAAAGAATTGATAA
1 TTAGTTTACCCAGGAAAGAATTGATAA
34365 AGAAATCCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (28 bp):
TTAGTTTACCCAGGAAAGAATTGATAAT
Found at i:51541 original size:60 final size:59
Alignment explanation
Indices: 51475--51676 Score: 233
Period size: 60 Copynumber: 3.4 Consensus size: 59
51465 GTTATTTAAT
* * ** * *
51475 TATTAAAAGTTATAAAATAATTTTTTAATTATAAGGAGTTATTTTATTGAGTCTCTCGAC
1 TATTAAAAGTTACAAAATGATCATTCAATTAT-AGGAGTTACTTTATTGAGTCTCTCGAC
* * * *
51535 TATTAAAAGTTACAAAATGATCATTCAATTATAGAGAATTACTTTATTGAGTTTATCGAT
1 TATTAAAAGTTACAAAATGATCATTCAATTATAG-GAGTTACTTTATTGAGTCTCTCGAC
* * * * * *
51595 TATTAAAAGTTACAAAATGATCCTACAACTATAGGACGTTGCTTTATTAAGTCTCTCAAC
1 TATTAAAAGTTACAAAATGATCATTCAATTATAGGA-GTTACTTTATTGAGTCTCTCGAC
51655 TATTAAAAGTTACAAAATGATC
1 TATTAAAAGTTACAAAATGATC
51677 CTCTGACTAT
Statistics
Matches: 120, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
59 4 0.03
60 116 0.97
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (59 bp):
TATTAAAAGTTACAAAATGATCATTCAATTATAGGAGTTACTTTATTGAGTCTCTCGAC
Found at i:51677 original size:60 final size:60
Alignment explanation
Indices: 51517--51850 Score: 325
Period size: 60 Copynumber: 5.6 Consensus size: 60
51507 AAGGAGTTAT
* * * * ** *
51517 TTTATTGAGTCTCTCGACTATTAAAAGTTACAAAATGATCATTCAATTATAGAGAATTAC
1 TTTATTAAGTCTCTCGACTATTAAAAGTTACAAAATGATCCTTCAACTATAGGGCGTTGC
* * * * * *
51577 TTTATTGAGTTTATCGATTATTAAAAGTTACAAAATGATCCTACAACTATAGGACGTTGC
1 TTTATTAAGTCTCTCGACTATTAAAAGTTACAAAATGATCCTTCAACTATAGGGCGTTGC
* * ** *
51637 TTTATTAAGTCTCTCAACTATTAAAAGTTACAAAATGATCC-TCTGACTATAGGGTATTGT
1 TTTATTAAGTCTCTCGACTATTAAAAGTTACAAAATGATCCTTC-AACTATAGGGCGTTGC
* * * * **
51697 TTTGTTAAGTCAT-TTGACTATTAAACGTTGCAAAATGATCCTTTGACTATAGGGCGTTGC
1 TTTATTAAGTC-TCTCGACTATTAAAAGTTACAAAATGATCCTTCAACTATAGGGCGTTGC
* ** * * *
51757 TTTGTTAAGT-TCTCTGACTATTAAAAGTTGTAAAATAATCTTTCAACTATAGGGTGTTGC
1 TTTATTAAGTCTCTC-GACTATTAAAAGTTACAAAATGATCCTTCAACTATAGGGCGTTGC
*
51817 TTTATTAAGTC-CATCGATTATTAAAAGTTACAAA
1 TTTATTAAGTCTC-TCGACTATTAAAAGTTACAAA
51851 TATTCACTTG
Statistics
Matches: 224, Mismatches: 43, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
58 1 0.00
59 2 0.01
60 217 0.97
61 4 0.02
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (60 bp):
TTTATTAAGTCTCTCGACTATTAAAAGTTACAAAATGATCCTTCAACTATAGGGCGTTGC
Found at i:51688 original size:120 final size:120
Alignment explanation
Indices: 51517--51850 Score: 370
Period size: 120 Copynumber: 2.8 Consensus size: 120
51507 AAGGAGTTAT
* * * * * *
51517 TTTATTGAGTCTCTCGACTATTAAAAGTTACAAAATGATCATTCAATTATAGAGAATTACTTTAT
1 TTTATTAAGTCTCTCGACTATTAAAAGTTACAAAATGATCCTTCAACTATAGGGTATTGCTTTAT
*
51582 TGAGTTTATCGATTATTAAAAGTTACAAAATGATCCTACAACTATAGGACGTTGC
66 TAAGTTTATCGATTATTAAAAGTTACAAAATGATCCTACAACTATAGGACGTTGC
* * * *
51637 TTTATTAAGTCTCTCAACTATTAAAAGTTACAAAATGATCC-TCTGACTATAGGGTATTGTTTTG
1 TTTATTAAGTCTCTCGACTATTAAAAGTTACAAAATGATCCTTC-AACTATAGGGTATTGCTTTA
* * * *** *
51701 TTAAGTCATT-T-GACTATTAAACGTTGCAAAATGATCCTTTGACTATAGGGCGTTGC
65 TTAAGT--TTATCGATTATTAAAAGTTACAAAATGATCCTACAACTATAGGACGTTGC
* ** * * *
51757 TTTGTTAAGT-TCTCTGACTATTAAAAGTTGTAAAATAATCTTTCAACTATAGGGTGTTGCTTTA
1 TTTATTAAGTCTCTC-GACTATTAAAAGTTACAAAATGATCCTTCAACTATAGGGTATTGCTTTA
**
51821 TTAAGTCCATCGATTATTAAAAGTTACAAA
65 TTAAGTTTATCGATTATTAAAAGTTACAAA
51851 TATTCACTTG
Statistics
Matches: 174, Mismatches: 33, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
119 7 0.04
120 162 0.93
121 3 0.02
122 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (120 bp):
TTTATTAAGTCTCTCGACTATTAAAAGTTACAAAATGATCCTTCAACTATAGGGTATTGCTTTAT
TAAGTTTATCGATTATTAAAAGTTACAAAATGATCCTACAACTATAGGACGTTGC
Found at i:54491 original size:24 final size:22
Alignment explanation
Indices: 54443--54500 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
54433 TTTAGAATAA
*
54443 AAAACCATGTTTACTAGAACAG
1 AAAACTATGTTTACTAGAACAG
* * *
54465 AAAAACTTTGTTTACTAGAGTCGG
1 -AAAACTATGTTTACTAGA-ACAG
54489 AAAACTATGTTT
1 AAAACTATGTTT
54501 CTACATGGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
23 27 0.93
24 2 0.07
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.31
Consensus pattern (22 bp):
AAAACTATGTTTACTAGAACAG
Found at i:58563 original size:23 final size:23
Alignment explanation
Indices: 58529--58606 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 23
58519 TTTTAGAATA
* * *
58529 AAAAACTGTATTTATCAGAACCG
1 AAAAACTCTATTTACCAGAGCCG
58552 AAAAACTCTATTTACCAGAGCC-
1 AAAAACTCTATTTACCAGAGCCG
* *
58574 AGAAAGCTCAATTTACCAGAGCCG
1 A-AAAACTCTATTTACCAGAGCCG
*
58598 GAAAACTCT
1 AAAAACTCT
58607 GTTTCTACAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
22 1 0.02
23 44 0.98
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.22
Consensus pattern (23 bp):
AAAAACTCTATTTACCAGAGCCG
Found at i:58991 original size:12 final size:11
Alignment explanation
Indices: 58951--58996 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 11
58941 ATAATTTGTG
58951 ATATATTTTTA
1 ATATATTTTTA
*
58962 ATAGTGTTTTT-
1 ATA-TATTTTTA
58973 A-ATATTTTTA
1 ATATATTTTTA
58983 ATATAATTTTTA
1 ATAT-ATTTTTA
58995 AT
1 AT
58997 TTGGGGATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
9 6 0.21
10 2 0.07
11 6 0.21
12 15 0.52
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (11 bp):
ATATATTTTTA
Found at i:58992 original size:21 final size:21
Alignment explanation
Indices: 58953--58996 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
58943 AATTTGTGAT
*
58953 ATATTTTTAATAGTGTTTTTA
1 ATATTTTTAATAGTATTTTTA
58974 ATATTTTTAATA-TAATTTTTA
1 ATATTTTTAATAGT-ATTTTTA
58995 AT
1 AT
58997 TTGGGGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (21 bp):
ATATTTTTAATAGTATTTTTA
Found at i:62229 original size:60 final size:59
Alignment explanation
Indices: 62106--62233 Score: 161
Period size: 60 Copynumber: 2.2 Consensus size: 59
62096 TAAATATTTT
* * * * *
62106 AATTTCATCCCTAAATTATGACTCTCATCTAAATTAGTACTTAAACTTTTGATCATTCT
1 AATTTCATCCCTAAACTATGACCCTCATCTAAATTAGTACTCAAACGTTTGATCATTCC
*
62165 AATTTCATCCCTAAACTATGACCCTCTTTCTAAATTAGT-CTCCAAACGTTTGAAT-ATTCC
1 AATTTCATCCCTAAACTATGACCCTC-ATCTAAATTAGTACT-CAAACGTTTG-ATCATTCC
62225 AATTTCATC
1 AATTTCATC
62234 TCCAAATTCA
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
59 26 0.43
60 32 0.53
61 2 0.03
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.40
Consensus pattern (59 bp):
AATTTCATCCCTAAACTATGACCCTCATCTAAATTAGTACTCAAACGTTTGATCATTCC
Found at i:62435 original size:60 final size:60
Alignment explanation
Indices: 62361--62505 Score: 193
Period size: 60 Copynumber: 2.4 Consensus size: 60
62351 ATAATTTAGA
* * * *
62361 ATGAAATTGGAATGTTCAAAAGTTTGGGGAATAATTTAGAATGAA-GGTCATAGTTTAGGG
1 ATGAAATTAGAATGTTCAAAAGTTTGAGGAATAATTTAGAAT-AATAGTCATAGTTTAAGG
* * *
62421 ATGAAATTAAAATGTTCAAAAGTTTGAGGACTAGTTTAGAATAATAGTCATAGTTTAAGG
1 ATGAAATTAGAATGTTCAAAAGTTTGAGGAATAATTTAGAATAATAGTCATAGTTTAAGG
* *
62481 ATGAAATTAGAATATTTAAAAGTTT
1 ATGAAATTAGAATGTTCAAAAGTTT
62506 AGAAACCAAT
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
59 2 0.03
60 72 0.97
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (60 bp):
ATGAAATTAGAATGTTCAAAAGTTTGAGGAATAATTTAGAATAATAGTCATAGTTTAAGG
Found at i:62532 original size:60 final size:60
Alignment explanation
Indices: 62361--62532 Score: 145
Period size: 60 Copynumber: 2.9 Consensus size: 60
62351 ATAATTTAGA
** * * * *
62361 ATGAAATTGGAATGTTCAAAAGTTTGGGGAA-TAATTTAGAATGAAGG-TCATAGTTTAGGG
1 ATGAAATTAAAATATTCAAAAGTTT-GAGAACCAATTTAGAATG-AGGATCATAGTTTAAGG
* * * * **
62421 ATGAAATTAAAATGTTCAAAAGTTTGAGGACTAGTTTAGAAT-AATAGTCATAGTTTAAGG
1 ATGAAATTAAAATATTCAAAAGTTTGAGAACCAATTTAGAATGAGGA-TCATAGTTTAAGG
* * *
62481 ATGAAATTAGAATATTTAAAAGTTT-AGAAACCAATTTAAAATGAGGATCATA
1 ATGAAATTAAAATATTCAAAAGTTTGAG-AACCAATTTAGAATGAGGATCATA
62533 CTTTG
Statistics
Matches: 90, Mismatches: 17, Indels: 10
0.77 0.15 0.09
Matches are distributed among these distances:
58 1 0.01
59 5 0.06
60 82 0.91
61 2 0.02
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (60 bp):
ATGAAATTAAAATATTCAAAAGTTTGAGAACCAATTTAGAATGAGGATCATAGTTTAAGG
Done.