Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001591.1 Hibiscus syriacus cultivar Beakdansim tig00003171_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: 45880
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2383 original size:14 final size:14
Alignment explanation
Indices: 2354--2407 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
2344 CGTTCGTGAA
2354 CGTTCGGTTA--TT
1 CGTTCGGTTATGTT
2366 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
2380 CG-T---TTATGTT
1 CGTTCGGTTATGTT
2390 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
2404 CGTT
1 CGTT
2408 TATGTTCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
10 9 0.25
11 1 0.03
12 10 0.28
13 1 0.03
14 15 0.42
ACGTcount: A:0.07, C:0.15, G:0.26, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:2386 original size:10 final size:10
Alignment explanation
Indices: 2367--2414 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
2357 TCGGTTATTC
*
2367 GTTCGGTTAT
1 GTTCGTTTAT
2377 GTTCGTTTAT
1 GTTCGTTTAT
2387 GTTCGTTCGGTTAT
1 GTTCG-T---TTAT
2401 GTTCGTTTAT
1 GTTCGTTTAT
2411 GTTC
1 GTTC
2415 ATTCATTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.08, C:0.12, G:0.25, T:0.54
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:2396 original size:24 final size:24
Alignment explanation
Indices: 2364--2414 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
2354 CGTTCGGTTA
2364 TTCGTTCGGTTATGTTCGTTTATG
1 TTCGTTCGGTTATGTTCGTTTATG
2388 TTCGTTCGGTTATGTTCGTTTATG
1 TTCGTTCGGTTATGTTCGTTTATG
2412 TTC
1 TTC
2415 ATTCATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.08, C:0.14, G:0.24, T:0.55
Consensus pattern (24 bp):
TTCGTTCGGTTATGTTCGTTTATG
Found at i:2424 original size:24 final size:24
Alignment explanation
Indices: 2372--2427 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
2362 TATTCGTTCG
* *
2372 GTTATGTTCGTTTATGTTCGTTCG
1 GTTATGTTCGTTTATGTTCATTCA
2396 GTTATGTTCGTTTATGTTCATTCA
1 GTTATGTTCGTTTATGTTCATTCA
*
2420 TTTATGTT
1 GTTATGTT
2428 TAACCCATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.12, C:0.11, G:0.20, T:0.57
Consensus pattern (24 bp):
GTTATGTTCGTTTATGTTCATTCA
Found at i:3433 original size:10 final size:10
Alignment explanation
Indices: 3418--3518 Score: 85
Period size: 10 Copynumber: 10.7 Consensus size: 10
3408 GGGTCTCTAA
3418 CGTTTATGTT
1 CGTTTATGTT
3428 CGTTTATGTT
1 CGTTTATGTT
3438 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* *
3449 ATGTTCATGTT
1 -CGTTTATGTT
3460 CGTTTATGTT
1 CGTTTATGTT
3470 CG----TGTT
1 CGTTTATGTT
*
3476 CGTTTGTGTT
1 CGTTTATGTT
3486 CGTTTATGTT
1 CGTTTATGTT
3496 C----ATGTT
1 CGTTTATGTT
3502 CGTTTATGTT
1 CGTTTATGTT
3512 CGTTTAT
1 CGTTTAT
3519 TTATTAAATG
Statistics
Matches: 74, Mismatches: 5, Indels: 24
0.72 0.05 0.23
Matches are distributed among these distances:
6 12 0.16
10 51 0.69
11 7 0.09
12 4 0.05
ACGTcount: A:0.10, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:3449 original size:16 final size:16
Alignment explanation
Indices: 3424--3514 Score: 113
Period size: 16 Copynumber: 6.1 Consensus size: 16
3414 CTAACGTTTA
3424 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
3440 TGTTCATTTATGTTCA
1 TGTTCGTTTATGTTCG
3456 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
3472 TGTTCG----T-TT-G
1 TGTTCGTTTATGTTCG
*
3482 TGTTCGTTTATGTTCA
1 TGTTCGTTTATGTTCG
3498 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
3514 T
1 T
3515 TTATTTATTA
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
10 7 0.11
11 2 0.03
12 1 0.02
14 1 0.02
15 2 0.03
16 50 0.79
ACGTcount: A:0.09, C:0.12, G:0.22, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:3469 original size:26 final size:26
Alignment explanation
Indices: 3418--3518 Score: 112
Period size: 26 Copynumber: 3.7 Consensus size: 26
3408 GGGTCTCTAA
*
3418 CGTTTATGTTCGTTTATGTTCGTGTT
1 CGTTTATGTTCGTTTATGTTCATGTT
* *
3444 CATTTATGTTCATGTTCGTTTATGTTCGTGTT
1 C------GTTTATGTTCGTTTATGTTCATGTT
*
3476 CGTTTGTGTTCGTTTATGTTCATGTT
1 CGTTTATGTTCGTTTATGTTCATGTT
3502 CGTTTATGTTCGTTTAT
1 CGTTTATGTTCGTTTAT
3519 TTATTAAATG
Statistics
Matches: 64, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
26 39 0.61
32 25 0.39
ACGTcount: A:0.10, C:0.12, G:0.21, T:0.57
Consensus pattern (26 bp):
CGTTTATGTTCGTTTATGTTCATGTT
Found at i:3485 original size:42 final size:42
Alignment explanation
Indices: 3418--3517 Score: 157
Period size: 42 Copynumber: 2.4 Consensus size: 42
3408 GGGTCTCTAA
*
3418 CGTTTATGTTCGTTTATGTTCGTGTTCATTTATGTTCATGTT
1 CGTTTATGTTCGTTTACGTTCGTGTTCATTTATGTTCATGTT
* *
3460 CGTTTATGTTCGTGTT-CGTTTGTGTTCGTTTATGTTCATGTT
1 CGTTTATGTTCGT-TTACGTTCGTGTTCATTTATGTTCATGTT
3502 CGTTTATGTTCGTTTA
1 CGTTTATGTTCGTTTA
3518 TTTATTAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
41 2 0.04
42 49 0.92
43 2 0.04
ACGTcount: A:0.10, C:0.12, G:0.21, T:0.57
Consensus pattern (42 bp):
CGTTTATGTTCGTTTACGTTCGTGTTCATTTATGTTCATGTT
Found at i:3605 original size:16 final size:16
Alignment explanation
Indices: 3584--3616 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3574 AAAAAAATTT
3584 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
3600 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
3616 T
1 T
3617 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:10940 original size:21 final size:22
Alignment explanation
Indices: 10898--10940 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
10888 AAAATAAAAT
*
10898 AATAAAACAAAGATGAAATGAA
1 AATAAAACAAACATGAAATGAA
*
10920 AATAAAA-AAACATGGAATGAA
1 AATAAAACAAACATGAAATGAA
10941 CTAAAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.67, C:0.05, G:0.14, T:0.14
Consensus pattern (22 bp):
AATAAAACAAACATGAAATGAA
Found at i:10946 original size:25 final size:24
Alignment explanation
Indices: 10889--10960 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 24
10879 ATAAAGGAAA
*
10889 AAATAAAATAATAAAACAAAGATG
1 AAATAAAATAAAAAAACAAAGATG
**
10913 AAATGAAAATAAAAAAACATGGAATG
1 AAAT-AAAATAAAAAAACAAAG-ATG
*
10939 AACTAAAATTAAAAAAAACAAA
1 AAATAAAA-T-AAAAAAACAAA
10961 AACAAAACAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
24 4 0.11
25 18 0.47
26 7 0.18
27 9 0.24
ACGTcount: A:0.71, C:0.06, G:0.08, T:0.15
Consensus pattern (24 bp):
AAATAAAATAAAAAAACAAAGATG
Found at i:19702 original size:29 final size:29
Alignment explanation
Indices: 19667--19724 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
19657 AACATTTCTG
*
19667 AAACTTGC-ATTTAGGTCCCCCAACATTTA
1 AAACTTGCAATATA-GTCCCCCAACATTTA
19696 AAACTTGCAATATAGTCCCCCAACATTTA
1 AAACTTGCAATATAGTCCCCCAACATTTA
19725 TTCCGTTTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.34, C:0.28, G:0.09, T:0.29
Consensus pattern (29 bp):
AAACTTGCAATATAGTCCCCCAACATTTA
Found at i:19923 original size:35 final size:35
Alignment explanation
Indices: 19850--19935 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 35
19840 AAAACAGTCA
* * * *
19850 TCAATTTCATTTTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
19885 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
19920 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
19936 ATACTTCAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.41, C:0.20, G:0.01, T:0.38
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:19929 original size:21 final size:21
Alignment explanation
Indices: 19904--19946 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
19894 TTCTAAACCC
19904 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
19925 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
19946 T
1 T
19947 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:20101 original size:16 final size:18
Alignment explanation
Indices: 20069--20102 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
20059 TATTAATATA
20069 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
20087 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
20103 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:22498 original size:34 final size:34
Alignment explanation
Indices: 22433--22757 Score: 302
Period size: 34 Copynumber: 9.6 Consensus size: 34
22423 ATTTTTTTGT
*
22433 GTTTTTAAAAATCAGTTTTAAAATATATATATATATATA
1 GTTTTT-AAAA-CA-TTTTGAAA-AT-TATATATATATA
22472 GTTTTTAAAACATTTTGAAAATTATATAATATATA
1 GTTTTTAAAACATTTTGAAAATTATAT-ATATATA
* *
22507 G-TTTT-AAATA-TTTGAATA-TATATATATATA
1 GTTTTTAAAACATTTTGAAAATTATATATATATA
* * * * * * *
22537 --ATATCATATATATAT-ATATATATATATATATATA
1 GTTTTTAAAACAT-TTTGA-AAAT-TATATATATATA
*
22571 G-TTTTAAAACATTTTAAAAACTTATA-ATATATA
1 GTTTTTAAAACATTTTGAAAA-TTATATATATATA
*
22604 GTTTTT-AAACATTTT-AAAACT-TATATATATA
1 GTTTTTAAAACATTTTGAAAATTATATATATATA
22635 GTTTTTAAAACATTTTGAAAA-TATATAATATATA
1 GTTTTTAAAACATTTTGAAAATTATAT-ATATATA
22669 GTTTTTAAAACATTTTGAAAATTATATATATATA
1 GTTTTTAAAACATTTTGAAAATTATATATATATA
22703 G-TTTT-AAACATTTTGAAAAACTTATATAATATATA
1 GTTTTTAAAACATTTTG-AAAA-TTATAT-ATATATA
*
22738 GTTTTTAAAAAATTTTGAAA
1 GTTTTTAAAACATTTTGAAA
22758 CATAAATATA
Statistics
Matches: 248, Mismatches: 16, Indels: 47
0.80 0.05 0.15
Matches are distributed among these distances:
29 2 0.01
30 13 0.05
31 20 0.08
32 36 0.15
33 36 0.15
34 75 0.30
35 31 0.12
36 14 0.06
37 11 0.04
38 4 0.02
39 6 0.02
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (34 bp):
GTTTTTAAAACATTTTGAAAATTATATATATATA
Found at i:22529 original size:2 final size:2
Alignment explanation
Indices: 22522--22570 Score: 82
Period size: 2 Copynumber: 24.5 Consensus size: 2
22512 AAATATTTGA
22522 AT AT AT AT AT AT AT A- AT AT CAT 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
22564 AT AT AT A
1 AT AT AT A
22571 GTTTTAAAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 42 0.93
3 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:22792 original size:69 final size:68
Alignment explanation
Indices: 22458--22767 Score: 265
Period size: 65 Copynumber: 4.6 Consensus size: 68
22448 TTTTAAAATA
* * *
22458 TATATATATATATAGTTTTTAAAACATTTTGAAAATTATATAATATATAGTTTTAAATA-TTTGA
1 TATATA-ATATATAGTTTTTAAAAAATTTTGAAAATTAAAT-ATATATAGTTTTAAACATTTTGA
*
22522 ATA--
64 AAACT
* * * * * * * *
22525 TATAT-ATATATA--ATATCATATATATAT-ATATATATATATATATATAGTTTTAAAACATTTT
1 TATATAATATATAGTTTTTAAAAAAT-TTTGA-AAAT-TAAATATATATAGTTTT-AAACATTTT
*
22586 AAAAAC-
62 GAAAACT
*
22592 T-TATAATATATAGTTTTT-AAACATTTT-AAAACTT--ATATATATAGTTTTTAAAACATTTTG
1 TATATAATATATAGTTTTTAAAAAATTTTGAAAA-TTAAATATATATAG-TTTT-AAACATTTTG
22652 AAAA--
63 AAAACT
* *
22656 TATATAATATATAGTTTTTAAAACATTTTGAAAATTATATATATATAGTTTTAAACATTTTGAAA
1 TATATAATATATAGTTTTTAAAAAATTTTGAAAATTAAATATATATAGTTTTAAACATTTTG-AA
22721 AACT
65 AACT
22725 TATATAATATATAGTTTTTAAAAAATTTTGAAACA-TAAATATA
1 TATATAATATATAGTTTTTAAAAAATTTTGAAA-ATTAAATATA
22768 ATTTTTTTAT
Statistics
Matches: 204, Mismatches: 19, Indels: 38
0.78 0.07 0.15
Matches are distributed among these distances:
63 7 0.03
64 28 0.14
65 51 0.25
66 33 0.16
67 29 0.14
68 14 0.07
69 41 0.20
70 1 0.00
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (68 bp):
TATATAATATATAGTTTTTAAAAAATTTTGAAAATTAAATATATATAGTTTTAAACATTTTGAAA
ACT
Found at i:22806 original size:69 final size:69
Alignment explanation
Indices: 22562--22767 Score: 263
Period size: 69 Copynumber: 3.1 Consensus size: 69
22552 ATATATATAT
*
22562 ATATATATAGTTTTAAAACATTTT-AAAAAC-T-TATAATATATAGTTTTT-AAACATTTT-AAA
1 ATATATATAGTTTT-AAACATTTTGAAAAACTTATATAATATATAGTTTTTAAAAAATTTTGAAA
22622 ACTT--
65 A-TTAA
*
22626 ATATATATAGTTTTTAAAACATTTTG-AAAA--TATATAATATATAGTTTTTAAAACATTTTGAA
1 ATATATATAG-TTTT-AAACATTTTGAAAAACTTATATAATATATAGTTTTTAAAAAATTTTGAA
*
22688 AATTAT
64 AATTAA
22694 ATATATATAGTTTTAAACATTTTGAAAAACTTATATAATATATAGTTTTTAAAAAATTTTGAAAC
1 ATATATATAGTTTTAAACATTTTGAAAAACTTATATAATATATAGTTTTTAAAAAATTTTGAAA-
22759 A-TAA
65 ATTAA
22763 ATATA
1 ATATA
22768 ATTTTTTTAT
Statistics
Matches: 129, Mismatches: 2, Indels: 17
0.87 0.01 0.11
Matches are distributed among these distances:
64 11 0.09
65 35 0.27
66 21 0.16
67 12 0.09
68 10 0.08
69 39 0.30
70 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (69 bp):
ATATATATAGTTTTAAACATTTTGAAAAACTTATATAATATATAGTTTTTAAAAAATTTTGAAAA
TTAA
Found at i:22841 original size:9 final size:9
Alignment explanation
Indices: 22827--22874 Score: 62
Period size: 9 Copynumber: 5.4 Consensus size: 9
22817 ATATATTTCC
22827 TTTTTTATT
1 TTTTTTATT
22836 TTTTTTATT
1 TTTTTTATT
* *
22845 TTATTTCTT
1 TTTTTTATT
*
22854 TTTTTT-TA
1 TTTTTTATT
22862 TTTTTTATT
1 TTTTTTATT
22871 TTTT
1 TTTT
22875 CTGTTTTTAG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
8 7 0.21
9 26 0.79
ACGTcount: A:0.10, C:0.02, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTATT
Found at i:22848 original size:14 final size:13
Alignment explanation
Indices: 22827--22874 Score: 69
Period size: 14 Copynumber: 3.5 Consensus size: 13
22817 ATATATTTCC
22827 TTTTTTATTTTTT
1 TTTTTTATTTTTT
22840 TTATTTTATTTCTTT
1 TT-TTTTATTT-TTT
22855 TTTTTTATTTTTT
1 TTTTTTATTTTTT
22868 ATTTTTT
1 -TTTTTT
22875 CTGTTTTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.16
14 22 0.69
15 5 0.16
ACGTcount: A:0.10, C:0.02, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTT
Found at i:22856 original size:26 final size:26
Alignment explanation
Indices: 22820--22872 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
22810 TATTAGTATA
22820 TATTTCCTTTTTTATT-TTTTTTATTT
1 TATTTCCTTTTTT-TTATTTTTTATTT
*
22846 TATTTCTTTTTTTTTATTTTTTATTT
1 TATTTCCTTTTTTTTATTTTTTATTT
22872 T
1 T
22873 TTCTGTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (26 bp):
TATTTCCTTTTTTTTATTTTTTATTT
Found at i:24818 original size:14 final size:16
Alignment explanation
Indices: 24799--24844 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
24789 TTTGTAAATA
24799 ATAATATTA-ATA-AT
1 ATAATATTATATATAT
24813 ATAATATTATTATATAT
1 ATAATATTA-TATATAT
*
24830 ATAATAGTATATATA
1 ATAATATTATATATA
24845 AAATTGTCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 9 0.32
16 9 0.32
17 10 0.36
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
ATAATATTATATATAT
Found at i:25613 original size:20 final size:19
Alignment explanation
Indices: 25585--25658 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 19
25575 AAAACATCCT
*
25585 ACCCTGAGGCTTTACAGATG
1 ACCC-GAGGCTTTACAAATG
* * *
25605 ACCCAGAGGTTTTAAAAATT
1 ACCC-GAGGCTTTACAAATG
*
25625 ACCCGAAGGATTTACAAATG
1 ACCCG-AGGCTTTACAAATG
25645 ACCCGGAGGCTTTA
1 ACCC-GAGGCTTTA
25659 ATTTTCTAGA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 41 0.95
21 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (19 bp):
ACCCGAGGCTTTACAAATG
Found at i:25721 original size:139 final size:140
Alignment explanation
Indices: 25486--25779 Score: 491
Period size: 139 Copynumber: 2.1 Consensus size: 140
25476 CTTACAGATG
* *
25486 ACCCGAAGGATTTAAAAATTAACTGGAGGCTTTAATTTTCTAGAACATTAAATGAGAAACTTTGA
1 ACCCGAAGGATTTAAAAATGAACCGGAGGCTTTAATTTTCTAGAACATTAAATGAGAAACTTTGA
*
25551 AAATTGCTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGCTTTACAGATGACCCAGAGG-T
66 AAATTGCTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGCTTTACAAATGACCCAGAGGTT
25615 TTTAAAAATT
131 TTTAAAAATT
* * *
25625 ACCCGAAGGATTTACAAATGACCCGGAGGCTTTAATTTTCTAGAACATTAAATGAGAAGCTTTGA
1 ACCCGAAGGATTTAAAAATGAACCGGAGGCTTTAATTTTCTAGAACATTAAATGAGAAACTTTGA
* *
25690 AAATTGCTTTCTCATTTTTATGCGAAAACATCCTACCCTGAGGCTTTACAAATGACCCCGAGGTT
66 AAATTGCTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGCTTTACAAATGACCCAGAGGTT
*
25755 TTTACAAATT
131 TTTAAAAATT
*
25765 ATCCGAAGGATTTAA
1 ACCCGAAGGATTTAA
25780 TTTTCTAGAA
Statistics
Matches: 143, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
139 120 0.84
140 23 0.16
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (140 bp):
ACCCGAAGGATTTAAAAATGAACCGGAGGCTTTAATTTTCTAGAACATTAAATGAGAAACTTTGA
AAATTGCTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGCTTTACAAATGACCCAGAGGTT
TTTAAAAATT
Found at i:25752 original size:20 final size:21
Alignment explanation
Indices: 25724--25763 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
25714 AAAACATCCT
*
25724 ACCCTGAGG-CTTTACAAATG
1 ACCCCGAGGTCTTTACAAATG
*
25744 ACCCCGAGGTTTTTACAAAT
1 ACCCCGAGGTCTTTACAAAT
25764 TATCCGAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (21 bp):
ACCCCGAGGTCTTTACAAATG
Found at i:25825 original size:259 final size:249
Alignment explanation
Indices: 25366--26002 Score: 841
Period size: 259 Copynumber: 2.6 Consensus size: 249
25356 CTTACAGATG
*
25366 ACCCGAAGGATTTAAAAATTACCCGGAGGCTTTAATTTTCTAGAACATTAAATGAGAAACTTTGA
1 ACCCGAAGGATTTACAAA-TACCCGGAGGCTTTAATTTTCTAGAACATTAAATGAGAAACTTTGA
* * * *
25431 AAATCGCTTTTTTCATTTTCATGTGAAAACATCATACCCTGAGGTCTTACAGATGA-CCCGAAGG
65 AAATTGC-TTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGT-TTACAGATGACCCCG-AGG
* * * * * *
25495 ATTTAAAAATTAACTGGAGGCTTTAATTTTCTAGAACATTAAATGAGAAACTTTGAAAATTGCTT
127 ATTTACAAATTAACCGAAGGATTTAATTTTCTAGAACATTAAAAGAGAAACTTTGAAAATCGCTT
25560 TCTCATTTTCATGCGAAAACATCCTACCCTGAGGCTTTACAGATGACCCAGAGGTTTTAAAAATT
192 TCTCATTTTCATGCGAAAACATCCTACCCTGAGGCTTTACAGATGACCCAGAGG--TT-----TT
*
25625 ACCCGAAGGATTTACAAATGACCCGGAGGCTTTAATTTTCTAGAACATTAAATGAGAAGCTTTGA
1 ACCCGAAGGATTTACAAAT-ACCCGGAGGCTTTAATTTTCTAGAACATTAAATGAGAAACTTTGA
* * *
25690 AAATTGCTTTCTCATTTTTATGCGAAAACATCCTACCCTGAGGCTTTACAAATGACCCCGAGGTT
65 AAATTGCTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGG-TTTACAGATGACCCCGAGG-A
*
25755 TTTACAAATTATCCGAAGGATTTAATTTTCTAGAACATTAAAAGAGAAACTTTGAAAATCGCTTT
128 TTTACAAATTAACCGAAGGATTTAATTTTCTAGAACATTAAAAGAGAAACTTTGAAAATCGCTTT
* * *
25820 CTCATTTTCATGCGAAAACATCCTACCTTGAGGTTTTATAGATGACCCAGAGGTTTT
193 CTCATTTTCATGCGAAAACATCCTACCCTGAGGCTTTACAGATGACCCAGAGGTTTT
* *
25877 A--C-AA--A--T-C----ACCCGGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTTAAA
1 ACCCGAAGGATTTACAAATACCCGGAGGCTTTAATTTTCTAGAACATTAAATGAGAAACTTTGAA
* *
25930 AATTGCTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGATTTACAGATAACCCGGAGGATT
66 AATTGCTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGG-TTTACAGATGACCCCGAGGATT
25995 TACAAATT
130 TACAAATT
26003 TGTGGAAATA
Statistics
Matches: 346, Mismatches: 28, Indels: 29
0.86 0.07 0.07
Matches are distributed among these distances:
238 10 0.03
239 100 0.29
244 1 0.00
245 1 0.00
247 1 0.00
249 2 0.01
250 1 0.00
252 3 0.01
257 2 0.01
258 45 0.13
259 180 0.52
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (249 bp):
ACCCGAAGGATTTACAAATACCCGGAGGCTTTAATTTTCTAGAACATTAAATGAGAAACTTTGAA
AATTGCTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGTTTACAGATGACCCCGAGGATTT
ACAAATTAACCGAAGGATTTAATTTTCTAGAACATTAAAAGAGAAACTTTGAAAATCGCTTTCTC
ATTTTCATGCGAAAACATCCTACCCTGAGGCTTTACAGATGACCCAGAGGTTTT
Found at i:25839 original size:120 final size:119
Alignment explanation
Indices: 25635--26002 Score: 556
Period size: 119 Copynumber: 3.1 Consensus size: 119
25625 ACCCGAAGGA
* * *
25635 TTTACAAATGACCCGGAGGCTTTAATTTTCTAGAACATTAAATGAGAAGCTTTGAAAATTGCTTT
1 TTTACAAATTACCCGGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTTGAAAATTGCTTT
* * * *
25700 CTCATTTTTATGCGAAAACATCCTACCCTGAGGCTTTACAAATGACCCCGAGGTT
66 CTCATTTTCATGCGAAAACATCCTACCCTGAGGATTTACAGATGACCCAGAGG-T
* * * *
25755 TTTACAAATTATCCGAAGGATTTAATTTTCTAGAACATTAAAAGAGAAACTTTGAAAATCGCTTT
1 TTTACAAATTACCCGGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTTGAAAATTGCTTT
* * *
25820 CTCATTTTCATGCGAAAACATCCTACCTTGAGGTTTTATAGATGACCCAGAGGT
66 CTCATTTTCATGCGAAAACATCCTACCCTGAGGATTTACAGATGACCCAGAGGT
* *
25874 TTTACAAATCACCCGGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTTAAAAATTGCTTT
1 TTTACAAATTACCCGGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTTGAAAATTGCTTT
* * *
25939 CTCATTTTCATGCGAAAACATCCTACCCTGAGGATTTACAGATAACCCGGAGGA
66 CTCATTTTCATGCGAAAACATCCTACCCTGAGGATTTACAGATGACCCAGAGGT
25993 TTTACAAATT
1 TTTACAAATT
26003 TGTGGAAATA
Statistics
Matches: 222, Mismatches: 26, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
119 117 0.53
120 105 0.47
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (119 bp):
TTTACAAATTACCCGGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTTGAAAATTGCTTT
CTCATTTTCATGCGAAAACATCCTACCCTGAGGATTTACAGATGACCCAGAGGT
Found at i:25887 original size:20 final size:20
Alignment explanation
Indices: 25849--25897 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
25839 ATCCTACCTT
* * *
25849 GAGGTTTTATAGATGACCCA
1 GAGGTTTTACAAATCACCCA
*
25869 GAGGTTTTACAAATCACCCG
1 GAGGTTTTACAAATCACCCA
*
25889 GAGGATTTA
1 GAGGTTTTA
25898 ATTTTCTAGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (20 bp):
GAGGTTTTACAAATCACCCA
Found at i:26613 original size:20 final size:21
Alignment explanation
Indices: 26576--26619 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
26566 AAAGCTTTCG
26576 TCTTTGAAAAGTGAATCTATCA
1 TCTTTGAAAAG-GAATCTATCA
26598 TCTTTGAAAA-GAATCTATCA
1 TCTTTGAAAAGGAATCTATCA
26618 TC
1 TC
26620 CTTGCAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 12 0.55
22 10 0.45
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (21 bp):
TCTTTGAAAAGGAATCTATCA
Found at i:26799 original size:57 final size:56
Alignment explanation
Indices: 26712--26820 Score: 182
Period size: 57 Copynumber: 1.9 Consensus size: 56
26702 GAAACACATC
*
26712 ATAAGAAGGATTTATCCTAATTTCTTTCATGTCTCCACATCTAATCAGATCTCTTT
1 ATAAGAAGGATTTATCCTAATTTATTTCATGTCTCCACATCTAATCAGATCTCTTT
**
26768 ATAAGAAGGATTTTATCCTAATTTATTTCATGTCTTTACATCTAATCAGATCT
1 ATAAGAAGGA-TTTATCCTAATTTATTTCATGTCTCCACATCTAATCAGATCT
26821 TGAATAAGGT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
56 10 0.20
57 39 0.80
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.42
Consensus pattern (56 bp):
ATAAGAAGGATTTATCCTAATTTATTTCATGTCTCCACATCTAATCAGATCTCTTT
Found at i:34414 original size:14 final size:16
Alignment explanation
Indices: 34395--34431 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
34385 TTTGTAAATA
34395 ATAATATTA-ATA-AT
1 ATAATATTATATATAT
34409 ATAATATTATTATATAT
1 ATAATATTA-TATATAT
34426 ATAATA
1 ATAATA
34432 GCATATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.45
16 3 0.15
17 8 0.40
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATATTATATATAT
Found at i:34414 original size:17 final size:17
Alignment explanation
Indices: 34392--34431 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
34382 GGCTTTGTAA
34392 ATAATAATATTA-ATAAT
1 ATAATAATATTATAT-AT
*
34409 ATAATATTATTATATAT
1 ATAATAATATTATATAT
34426 ATAATA
1 ATAATA
34432 GCATATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 19 0.90
18 2 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATAATAATATTATATAT
Found at i:36795 original size:59 final size:59
Alignment explanation
Indices: 36708--36837 Score: 136
Period size: 59 Copynumber: 2.2 Consensus size: 59
36698 ATTTTAGGGT
* *
36708 AAAGTATACATATGATCTCTAGACTATAAAACGTT-ATTTTATTGAGTCAATCGATTATTA
1 AAAGT-TACAAATGATCACTAGACTATAAAACGTTGA-TTTATTGAGTCAATCGATTATTA
* * ** * ** *
36768 AAAGTTACAAATGATCACTTGATTATAAAGTGTTGATTTGTTGAGTCCCTCGATTTTTA
1 AAAGTTACAAATGATCACTAGACTATAAAACGTTGATTTATTGAGTCAATCGATTATTA
*
36827 AAAATTACAAA
1 AAAGTTACAAA
36838 ATGGTCTCTC
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
59 52 0.90
60 6 0.10
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.38
Consensus pattern (59 bp):
AAAGTTACAAATGATCACTAGACTATAAAACGTTGATTTATTGAGTCAATCGATTATTA
Found at i:38457 original size:31 final size:31
Alignment explanation
Indices: 38422--38489 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
38412 TCATATGATC
*
38422 ATAAAATAAATATTATATTTATTAAA-TACTT
1 ATAAAATAAATATTAAATTTATTAAACTA-TT
** *
38453 ATAAAATATTTTTTAAATTTATTAAACTATT
1 ATAAAATAAATATTAAATTTATTAAACTATT
38484 ATAAAA
1 ATAAAA
38490 CATGTCATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 30 0.94
32 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (31 bp):
ATAAAATAAATATTAAATTTATTAAACTATT
Found at i:43786 original size:31 final size:31
Alignment explanation
Indices: 43751--43811 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
43741 TATTGGGATG
43751 TTACAAAAT-GATCCTTATA-CTTATCAAATTA
1 TTACAAAATAG-TCCTT-TACCTTATCAAATTA
43782 TTACAAAATAGTCCTTTACCTTATCAAATT
1 TTACAAAATAGTCCTTTACCTTATCAAATT
43812 TTATTGTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 2 0.07
31 25 0.89
32 1 0.04
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.39
Consensus pattern (31 bp):
TTACAAAATAGTCCTTTACCTTATCAAATTA
Found at i:44664 original size:2 final size:2
Alignment explanation
Indices: 44657--44694 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
44647 ATTAGGGTTC
44657 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
44695 GGAAGAGACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.