Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004413.1 Hibiscus syriacus cultivar Beakdansim tig00009677_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: 60799
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:1493 original size:9 final size:9
Alignment explanation
Indices: 1465--1497 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1455 ATGTTATTCT
1465 TTAATTAAA
1 TTAATTAAA
*
1474 TT-ATAAAA
1 TTAATTAAA
1482 TTAATTAAA
1 TTAATTAAA
1491 TTAATTA
1 TTAATTA
1498 GTATAAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TTAATTAAA
Found at i:3187 original size:3 final size:3
Alignment explanation
Indices: 3175--3251 Score: 106
Period size: 3 Copynumber: 26.7 Consensus size: 3
3165 TTTGTAATGT
* **
3175 TAA T-A TAA TAA TAA TAA T-A TGA TAA TAA TAA TTG TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3220 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3252 TATTATTGGA
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
2 6 0.09
3 60 0.91
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:11520 original size:21 final size:21
Alignment explanation
Indices: 11496--11605 Score: 80
Period size: 21 Copynumber: 5.3 Consensus size: 21
11486 TTTCGCAATA
11496 CGATAGTTGAAAATCGCGTTG
1 CGATAGTTGAAAATCGCGTTG
* ** ** *
11517 CGAT-TTTTCATTTTGCGTTG
1 CGATAGTTGAAAATCGCGTTG
11537 CGATAGTTGAAAATCGCGTTG
1 CGATAGTTGAAAATCGCGTTG
* * * ** **
11558 AGCT-TTTCCATTTCGCGTTG
1 CGATAGTTGAAAATCGCGTTG
*
11578 CGATAGTTGAAAATTGCGTTG
1 CGATAGTTGAAAATCGCGTTG
11599 CGATAGT
1 CGATAGT
11606 CTACAGTTGT
Statistics
Matches: 60, Mismatches: 27, Indels: 4
0.66 0.30 0.04
Matches are distributed among these distances:
20 27 0.45
21 33 0.55
ACGTcount: A:0.22, C:0.15, G:0.25, T:0.37
Consensus pattern (21 bp):
CGATAGTTGAAAATCGCGTTG
Found at i:11541 original size:41 final size:41
Alignment explanation
Indices: 11496--11602 Score: 169
Period size: 41 Copynumber: 2.6 Consensus size: 41
11486 TTTCGCAATA
* *
11496 CGATAGTTGAAAATCGCGTTGCGATTTTTCATTTTGCGTTG
1 CGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTG
* *
11537 CGATAGTTGAAAATCGCGTTGAGCTTTTCCATTTCGCGTTG
1 CGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTG
*
11578 CGATAGTTGAAAATTGCGTTGCGAT
1 CGATAGTTGAAAATCGCGTTGCGAT
11603 AGTCTACAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.37
Consensus pattern (41 bp):
CGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTG
Found at i:12387 original size:19 final size:19
Alignment explanation
Indices: 12363--12431 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
12353 CAACGAATTT
12363 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
* * **
12382 TCGCAACGACAACTGTAGACTA
1 TCGCAACG--AA-TTTGGAAAA
12404 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
12423 TCGCAACGA
1 TCGCAACGA
12432 CAACTGTAGA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 22 0.56
20 2 0.05
21 2 0.05
22 13 0.33
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:12408 original size:41 final size:41
Alignment explanation
Indices: 12363--12452 Score: 180
Period size: 41 Copynumber: 2.2 Consensus size: 41
12353 CAACGAATTT
12363 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
12404 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
12445 TCGCAACG
1 TCGCAACG
12453 CGAAATGCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (41 bp):
TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
Found at i:12409 original size:22 final size:22
Alignment explanation
Indices: 12381--12452 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
12371 AATTTGGAAA
12381 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
12403 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
12422 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
12444 ATCGCAACG
1 ATCGCAACG
12453 CGAAATGCAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 13 0.33
20 2 0.05
21 2 0.05
22 22 0.56
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:13686 original size:16 final size:17
Alignment explanation
Indices: 13659--13691 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
13649 AATATTAATA
*
13659 TTAATATTTTATTTATT
1 TTAATATTTTATATATT
13676 TTAAT-TTTTATATATT
1 TTAATATTTTATATATT
13692 CAAATTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTAATATTTTATATATT
Found at i:20399 original size:22 final size:23
Alignment explanation
Indices: 20368--20413 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
20358 ACTGTTGTCG
20368 ATTTTGTTTTCAAAT-TACAAAT
1 ATTTTGTTTTCAAATATACAAAT
* *
20390 ATTTTTTTTTCAAATATATAAAT
1 ATTTTGTTTTCAAATATACAAAT
20413 A
1 A
20414 ATACTTTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (23 bp):
ATTTTGTTTTCAAATATACAAAT
Found at i:21888 original size:20 final size:20
Alignment explanation
Indices: 21840--21916 Score: 109
Period size: 20 Copynumber: 3.8 Consensus size: 20
21830 GTACCTAGGG
* **
21840 GAGTATCGATACCATAGGTGG
1 GAGTATCGATACTATA-GTAA
21861 GTAGTATCGATACTATAGTAA
1 G-AGTATCGATACTATAGTAA
21882 GAGTATCGATACTATAGTAA
1 GAGTATCGATACTATAGTAA
21902 GAGTATCGATACTAT
1 GAGTATCGATACTAT
21917 TAAGCTAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
20 34 0.65
21 4 0.08
22 14 0.27
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (20 bp):
GAGTATCGATACTATAGTAA
Found at i:23465 original size:20 final size:20
Alignment explanation
Indices: 23440--23478 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
23430 GTGTCTAGTT
*
23440 ATATGTTATGGTATGTGTAG
1 ATATGTTATGGTATATGTAG
*
23460 ATATGTTATTGTATATGTA
1 ATATGTTATGGTATATGTA
23479 TTTCATGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.49
Consensus pattern (20 bp):
ATATGTTATGGTATATGTAG
Found at i:24042 original size:37 final size:37
Alignment explanation
Indices: 24001--24075 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
23991 GATTAAATTA
24001 GTATATAAATGAAATAATAGAAGTGACATATGTTTAT
1 GTATATAAATGAAATAATAGAAGTGACATATGTTTAT
24038 GTATATAAATGAAATAATAGAAGTGACATATGTTTAT
1 GTATATAAATGAAATAATAGAAGTGACATATGTTTAT
24075 G
1 G
24076 AGTATGGCAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.45, C:0.03, G:0.17, T:0.35
Consensus pattern (37 bp):
GTATATAAATGAAATAATAGAAGTGACATATGTTTAT
Found at i:24796 original size:23 final size:23
Alignment explanation
Indices: 24732--24796 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
24722 CTTATATGGT
24732 ACTTCGGTGCATTTCTACGCGGC
1 ACTTCGGTGCATTTCTACGCGGC
* * *
24755 ACTACGGTGCAATTCTACGTGGC
1 ACTTCGGTGCATTTCTACGCGGC
* *
24778 ACTTCAGTGCATTTATACG
1 ACTTCGGTGCATTTCTACG
24797 AGTTATGGTG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (23 bp):
ACTTCGGTGCATTTCTACGCGGC
Found at i:26028 original size:21 final size:21
Alignment explanation
Indices: 25953--26030 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
25943 CCTTCGGGAT
* *
25953 ATATATGTAATCCTTTGGAAC
1 ATATATGTAGTCCTTTAGAAC
* *
25974 ATATATGTAGTTC-TTCGAAAC
1 ATATATGTAGTCCTTTAG-AAC
* * * *
25995 ACATATTTTGTCCTTTAGAAT
1 ATATATGTAGTCCTTTAGAAC
26016 ATATATGTAGTCCTT
1 ATATATGTAGTCCTT
26031 AAGGAGTGGT
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
20 3 0.07
21 37 0.86
22 3 0.07
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (21 bp):
ATATATGTAGTCCTTTAGAAC
Found at i:26087 original size:21 final size:21
Alignment explanation
Indices: 26061--26101 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
26051 ATATGAGTTA
* *
26061 TATGTGGTCCTTCGGGACATC
1 TATGTGGTCCATCAGGACATC
26082 TATGTGGTCCATCAGGACAT
1 TATGTGGTCCATCAGGACAT
26102 TTCTACGCGG
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:0.20, C:0.22, G:0.27, T:0.32
Consensus pattern (21 bp):
TATGTGGTCCATCAGGACATC
Found at i:28941 original size:16 final size:17
Alignment explanation
Indices: 28920--28953 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28910 ATACACTAAA
*
28920 TCGG-TTTCGGTTTTTT
1 TCGGTTTTCAGTTTTTT
28936 TCGGTTTTCAGTTTTTT
1 TCGGTTTTCAGTTTTTT
28953 T
1 T
28954 GATCGGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.03, C:0.12, G:0.21, T:0.65
Consensus pattern (17 bp):
TCGGTTTTCAGTTTTTT
Found at i:32058 original size:24 final size:24
Alignment explanation
Indices: 32031--32082 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
32021 CGTTCATTTA
* *
32031 CGTTCGTGAACGTTCGGTTATGTT
1 CGTTCATGAACGTTCGATTATGTT
* **
32055 CGTTTATGTTCGTTCGATTATGTT
1 CGTTCATGAACGTTCGATTATGTT
32079 CGTT
1 CGTT
32083 TATGTTCATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.15, G:0.25, T:0.48
Consensus pattern (24 bp):
CGTTCATGAACGTTCGATTATGTT
Found at i:32069 original size:14 final size:14
Alignment explanation
Indices: 32052--32082 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
32042 GTTCGGTTAT
*
32052 GTTCGTTTATGTTC
1 GTTCGATTATGTTC
32066 GTTCGATTATGTTC
1 GTTCGATTATGTTC
32080 GTT
1 GTT
32083 TATGTTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.13, G:0.23, T:0.55
Consensus pattern (14 bp):
GTTCGATTATGTTC
Found at i:32083 original size:24 final size:24
Alignment explanation
Indices: 32041--32102 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
32031 CGTTCGTGAA
*
32041 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGATTATGTTCGTTTATGTT
32065 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGATTATGTTCGTTTATGTT
*
32089 CATTC-ATTTATGTT
1 CGTTCGA-TTATGTT
32103 TAACACAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 1 0.03
24 34 0.97
ACGTcount: A:0.13, C:0.13, G:0.19, T:0.55
Consensus pattern (24 bp):
CGTTCGATTATGTTCGTTTATGTT
Found at i:32840 original size:10 final size:10
Alignment explanation
Indices: 32825--32915 Score: 56
Period size: 10 Copynumber: 9.7 Consensus size: 10
32815 GGGTCTCCAA
32825 CGTTTATGTT
1 CGTTTATGTT
32835 CGTTTATGTT
1 CGTTTATGTT
32845 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
32856 ATGTTCGTGTT
1 -CGTTTATGTT
32867 CGTTTATGTT
1 CGTTTATGTT
32877 CG----TGTT
1 CGTTTATGTT
32883 CGTTTATGTT
1 CGTTTATGTT
32893 CG----TGTT
1 CGTTTATGTT
*
32899 CATTTATGTT
1 CGTTTATGTT
32909 CGTTTAT
1 CGTTTAT
32916 TTATTAAATA
Statistics
Matches: 61, Mismatches: 8, Indels: 24
0.66 0.09 0.26
Matches are distributed among these distances:
6 11 0.18
10 39 0.64
11 7 0.11
12 4 0.07
ACGTcount: A:0.10, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:32856 original size:16 final size:16
Alignment explanation
Indices: 32831--32919 Score: 137
Period size: 16 Copynumber: 5.7 Consensus size: 16
32821 CCAACGTTTA
*
32831 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
32847 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
32863 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
*
32879 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
32895 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
32911 T-TT-ATTTAT
1 TGTTCATTTAT
32920 TAAATAAACG
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
14 6 0.09
15 2 0.03
16 62 0.89
ACGTcount: A:0.10, C:0.11, G:0.20, T:0.58
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:35509 original size:21 final size:21
Alignment explanation
Indices: 35485--35525 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
35475 CAGGAACACT
35485 CACAGTAGTAGTAGCAGCAGC
1 CACAGTAGTAGTAGCAGCAGC
* *
35506 CACAGTCGTCGTAGCAGCAG
1 CACAGTAGTAGTAGCAGCAG
35526 TCGCAGGCAC
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:0.29, C:0.27, G:0.29, T:0.15
Consensus pattern (21 bp):
CACAGTAGTAGTAGCAGCAGC
Found at i:39122 original size:73 final size:73
Alignment explanation
Indices: 39003--39145 Score: 277
Period size: 73 Copynumber: 2.0 Consensus size: 73
38993 GTGATTGGGA
39003 AATCATTCCAAGAGGCAACATGCATGCTTTCACTAGAGGCTATGATTATGGGATTGGATACCTCC
1 AATCATTCCAAGAGGCAACATGCATGCTTTCACTAGAGGCTATGATTATGGGATTGGATACCTCC
39068 AAGGTCCC
66 AAGGTCCC
*
39076 AATCATTCCAAGAGGCAACATGCATGGTTTCACTAGAGGCTATGATTATGGGATTGGATACCTCC
1 AATCATTCCAAGAGGCAACATGCATGCTTTCACTAGAGGCTATGATTATGGGATTGGATACCTCC
39141 AAGGT
66 AAGGT
39146 TACCATCATA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (73 bp):
AATCATTCCAAGAGGCAACATGCATGCTTTCACTAGAGGCTATGATTATGGGATTGGATACCTCC
AAGGTCCC
Found at i:46730 original size:60 final size:60
Alignment explanation
Indices: 46582--46741 Score: 187
Period size: 60 Copynumber: 2.7 Consensus size: 60
46572 CTCTTATGTC
* * * * * * *
46582 AAATTAGTCCTTAAACTTTTAAACGTTTTAACTTCATCCTCAAAATATGAATCACATTTT
1 AAATTAGTCCTTAAACTTTTAGACATTTCAATTTTATCCCCAAAATATGAATCACATTGT
* * *
46642 AAATTAGTCTTTAAACTTTT-GAACATTTCAATTTTATCCCCAAACTATGAATCTCATTGT
1 AAATTAGTCCTTAAACTTTTAG-ACATTTCAATTTTATCCCCAAAATATGAATCACATTGT
* * *
46702 AAATTAGTCCCTAAACTTTTAGATATTTCTATTTTATCCC
1 AAATTAGTCCTTAAACTTTTAGACATTTCAATTTTATCCC
46742 TAAATTCATC
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
60 83 0.99
61 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.42
Consensus pattern (60 bp):
AAATTAGTCCTTAAACTTTTAGACATTTCAATTTTATCCCCAAAATATGAATCACATTGT
Found at i:46979 original size:60 final size:60
Alignment explanation
Indices: 46908--47035 Score: 150
Period size: 60 Copynumber: 2.1 Consensus size: 60
46898 AAAGCATGGG
* *
46908 ACTAATTTAGAATGA-AGATCACAGCTCGAGGACGAAAATGAAATGTTCAAAAGTTTAAGA
1 ACTAATTTAGAATGATAG-TCACAGCTCAAGGACGAAAATGAAATGTTCAAAAATTTAAGA
* * * * * * * *
46968 ACTAATTTAGAATGATAGTCATAGTTTAAGGATGAAATTGAAATGTTTAAAAATTTAGGT
1 ACTAATTTAGAATGATAGTCACAGCTCAAGGACGAAAATGAAATGTTCAAAAATTTAAGA
47028 ACTAATTT
1 ACTAATTT
47036 GAAATGAGGG
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 55 0.96
61 2 0.04
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (60 bp):
ACTAATTTAGAATGATAGTCACAGCTCAAGGACGAAAATGAAATGTTCAAAAATTTAAGA
Found at i:47042 original size:60 final size:60
Alignment explanation
Indices: 46908--47051 Score: 148
Period size: 60 Copynumber: 2.4 Consensus size: 60
46898 AAAGCATGGG
* * ** *
46908 ACTAATTTAGAATGA-AGATCACAGCTCGAGGACGAAAATGAAATGTTCAAAAGTTTAAGA
1 ACTAATTTAGAATGAGAG-TCATAGTTTAAGGACGAAAATGAAATGTTCAAAAATTTAAGA
* * * * * *
46968 ACTAATTTAGAATGATAGTCATAGTTTAAGGATGAAATTGAAATGTTTAAAAATTTAGGT
1 ACTAATTTAGAATGAGAGTCATAGTTTAAGGACGAAAATGAAATGTTCAAAAATTTAAGA
*
47028 ACTAATTT-GAAATGAGGGTCATAG
1 ACTAATTTAG-AATGAGAGTCATAG
47052 ATTGGGTATG
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
59 1 0.01
60 67 0.96
61 2 0.03
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.30
Consensus pattern (60 bp):
ACTAATTTAGAATGAGAGTCATAGTTTAAGGACGAAAATGAAATGTTCAAAAATTTAAGA
Found at i:49136 original size:60 final size:60
Alignment explanation
Indices: 49058--49202 Score: 152
Period size: 60 Copynumber: 2.4 Consensus size: 60
49048 TAGAAGATCT
* * **
49058 AAAGTTTAGGGACCAATTTAAAATGAGATTCATAGTTTGGA-GATGAAATTCG-AATGTTCA
1 AAAGTTTAAGGACTAATTTAAAATGAGAGCCATA-TTTGGACGATGAAATT-GAAATGTTCA
* * * *
49118 GAAGTTTAAGGACTAATTTATAATGAGAGCCATATTTTGACGATGAAATTGAAATGTTTA
1 AAAGTTTAAGGACTAATTTAAAATGAGAGCCATATTTGGACGATGAAATTGAAATGTTCA
* * *
49178 AAAG-TTAAAGAATAATTTTAAATGA
1 AAAGTTTAAGGACTAATTTAAAATGA
49203 AAGTCATAAT
Statistics
Matches: 70, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
59 23 0.33
60 47 0.67
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.33
Consensus pattern (60 bp):
AAAGTTTAAGGACTAATTTAAAATGAGAGCCATATTTGGACGATGAAATTGAAATGTTCA
Found at i:52606 original size:2 final size:2
Alignment explanation
Indices: 52599--52630 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
52589 CGACCCTTCA
52599 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
52631 TGTGTTTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60602 original size:72 final size:67
Alignment explanation
Indices: 60448--60671 Score: 215
Period size: 72 Copynumber: 3.2 Consensus size: 67
60438 TGAAAATACG
* * * *
60448 TATATAATATATAATTTCTAAAAACATTTTA-AAAATGTATATAATATGGTTTTTAAAACA-CTT
1 TATATAATATATAGTTT-TTAAAA-ATTTTAGAAAATATA-AT-ATAT-GTTTTTAAAACATTTT
60511 G-AAAC-
61 GAAAACT
60516 TATATAATATATAGTTTTTAAAATATTTTAGGAAAATATAATATATAGTTTTTAAAATCATTTTG
1 TATATAATATATAGTTTTTAAAA-ATTTTA-GAAAATATAATATAT-GTTTTTAAAA-CATTTT-
60581 GAAAACT
61 GAAAACT
*
60588 TATATAATATATAGTTTTTAAAAATTTTTTGAAATTTATATAATATAT-TTTTTAAAAACATTTT
1 TATATAATATATAGTTTTTAAAAA-TTTTAGAAA---ATATAATATATGTTTTT-AAAACA-TTT
60652 TGAAAACT
60 TGAAAACT
*
60660 TATAAAATATAT
1 TATATAATATAT
60672 TTTGAAAACA
Statistics
Matches: 135, Mismatches: 8, Indels: 22
0.82 0.05 0.13
Matches are distributed among these distances:
67 25 0.19
68 20 0.15
69 9 0.07
70 1 0.01
71 9 0.07
72 52 0.39
73 8 0.06
74 11 0.08
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.45
Consensus pattern (67 bp):
TATATAATATATAGTTTTTAAAAATTTTAGAAAATATAATATATGTTTTTAAAACATTTTGAAAA
CT
Found at i:60615 original size:36 final size:36
Alignment explanation
Indices: 60448--60685 Score: 200
Period size: 34 Copynumber: 6.8 Consensus size: 36
60438 TGAAAATACG
* * * *
60448 TATATAATATATAATTTCTAAAAACATTTT-AAAAAT
1 TATATAATATATAGTTT-TTAAAACATTTTGGAAACT
* *
60484 GTATAT-A-ATATGGTTTTTAAAACA-CTT-GAAAC-
1 -TATATAATATATAGTTTTTAAAACATTTTGGAAACT
*
60516 TATATAATATATAGTTTTTAAAATATTTTAGGAAA--
1 TATATAATATATAGTTTTTAAAACATTTT-GGAAACT
60551 -ATATAATATATAGTTTTTAAAATCATTTTGGAAAACT
1 TATATAATATATAGTTTTTAAAA-CATTTTGG-AAACT
* *
60588 TATATAATATATAGTTTTTAAAA-ATTTTTTGAAATT
1 TATATAATATATAGTTTTTAAAACA-TTTTGGAAACT
*
60624 TATATAATATAT--TTTTTAAAAACATTTTTGAAAACT
1 TATATAATATATAGTTTTT-AAAACA-TTTTGGAAACT
*
60660 TATA-AA-ATATA-TTTTGAAAACATTTT
1 TATATAATATATAGTTTTTAAAACATTTT
60686 TTGAAAATCA
Statistics
Matches: 171, Mismatches: 16, Indels: 32
0.78 0.07 0.15
Matches are distributed among these distances:
31 5 0.03
32 1 0.01
33 24 0.14
34 48 0.28
35 25 0.15
36 36 0.21
37 10 0.06
38 22 0.13
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAACATTTTGGAAACT
Found at i:60724 original size:32 final size:32
Alignment explanation
Indices: 60595--60763 Score: 148
Period size: 32 Copynumber: 5.2 Consensus size: 32
60585 ACTTATATAA
* *
60595 TATATAG-TTTTT-AAAAA-TTTTTTGAAATT
1 TATATAGTTTTTTAAAAAACATTTTTGAAAAT
* *
60624 TATATAATATATTTTTTAAAAACATTTTTGAAAACT
1 TATAT-A-GT-TTTTTAAAAAACATTTTTGAAAA-T
* * *
60660 TATAAAATATATTTT-GAAAACATTTTTTGAAAAT
1 TATATAGT-T-TTTTAAAAAACA-TTTTTGAAAAT
* **
60694 CATATAGTTTTTTAAAAAGTATTTTTGAAAAT
1 TATATAGTTTTTTAAAAAACATTTTTGAAAAT
*
60726 TATATAGTTTTTTAAAAAACATTTTTTAAAAT
1 TATATAGTTTTTTAAAAAACATTTTTGAAAAT
60758 TATATA
1 TATATA
60764 TAATATGAAG
Statistics
Matches: 115, Mismatches: 15, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
29 5 0.04
30 1 0.01
32 49 0.43
33 10 0.09
34 21 0.18
35 24 0.21
36 5 0.04
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (32 bp):
TATATAGTTTTTTAAAAAACATTTTTGAAAAT
Done.