Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005846.1 Hibiscus syriacus cultivar Beakdansim tig00013718_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: 70816
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:3443 original size:23 final size:24
Alignment explanation
Indices: 3408--3452 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
3398 TGCAAGCTAT
*
3408 AAATGTACAACT-ATTGTTGAAAG
1 AAATGTACAACTAATGGTTGAAAG
3431 AAATG-ACACACTAATGGTTGAA
1 AAATGTACA-ACTAATGGTTGAA
3453 TAAAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 3 0.16
23 8 0.42
24 8 0.42
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.27
Consensus pattern (24 bp):
AAATGTACAACTAATGGTTGAAAG
Found at i:7104 original size:40 final size:40
Alignment explanation
Indices: 7049--7210 Score: 279
Period size: 40 Copynumber: 4.0 Consensus size: 40
7039 TGCAGGTTTA
* * *
7049 TAATACACTTTGGTGTTTATGTTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
7089 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
7129 TAATACACTTCGGTGTATATGGTGGACACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
7169 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
7209 TA
1 TA
7211 GCACGACGGT
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 117 1.00
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:7358 original size:44 final size:44
Alignment explanation
Indices: 7287--7393 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
7277 TGGTATATGG
*
7287 TTATGGA-ATAATGGTAAGTGTAATGGTAAAATAAGCTTACGAGC
1 TTATGGATA-AATGGTAAGTATAATGGTAAAATAAGCTTACGAGC
* * *
7331 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTATGATC
1 TTATGGATAAATGGTAAGTATAATGGTAAAATAAGCTTACGAGC
7375 TTATGGTATTAAATGGTAA
1 TTATGG-A-TAAATGGTAA
7394 AATATTGCAC
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
44 44 0.79
45 2 0.04
46 10 0.18
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.35
Consensus pattern (44 bp):
TTATGGATAAATGGTAAGTATAATGGTAAAATAAGCTTACGAGC
Found at i:9151 original size:22 final size:22
Alignment explanation
Indices: 9079--9156 Score: 83
Period size: 22 Copynumber: 3.6 Consensus size: 22
9069 ATCGAAAGGG
* *
9079 AGTATCAATACCATAGTGTAGT
1 AGTATCGATACCATAGTGTAGA
*
9101 AGTATCGATA-C-T-GAG-AGAA
1 AGTATCGATACCATAGTGTAG-A
9120 AGATATCGATACCATAGTGTAGA
1 AG-TATCGATACCATAGTGTAGA
9143 AGTATCGATACCAT
1 AGTATCGATACCAT
9157 GATAAGGGTA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
18 2 0.04
19 4 0.09
20 9 0.20
21 2 0.04
22 22 0.48
23 5 0.11
24 2 0.04
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (22 bp):
AGTATCGATACCATAGTGTAGA
Found at i:9169 original size:42 final size:42
Alignment explanation
Indices: 9080--9173 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
9070 TCGAAAGGGA
* * *
9080 GTATCAATACCATAGTGTAGTAGTATCGATACTGAGAGAAAG
1 GTATCGATACCATAGTGTAGAAGTATCGATACTCAGAGAAAG
* * *
9122 ATATCGATACCATAGTGTAGAAGTATCGATAC-CATGATAAGG
1 GTATCGATACCATAGTGTAGAAGTATCGATACTCA-GAGAAAG
9164 GTATCGATAC
1 GTATCGATAC
9174 TATTGTGTCT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 1 0.02
42 43 0.98
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (42 bp):
GTATCGATACCATAGTGTAGAAGTATCGATACTCAGAGAAAG
Found at i:9629 original size:46 final size:46
Alignment explanation
Indices: 9576--9785 Score: 334
Period size: 46 Copynumber: 4.6 Consensus size: 46
9566 TAAAAAAAAT
* *
9576 CCATAAATGAAATGCATGAAA-TAGTGCATTAAGGCATGAAAAGATG
1 CCATAAATGAAATGCATGAAAGGA-TGCATTAAGGCATGAAAGGATG
9622 CCATAAATG-AATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
*
9667 CCATAAATGAAATGCATGAAAGGATACATTAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
9713 CCATAAATGAAATGCATTAAATGATGCATTAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
9759 CCATATATGAAATGAATGAAAGGATGC
1 CCATAAATGAAATGCATGAAAGGATGC
9786 CATAAATCAA
Statistics
Matches: 152, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
45 41 0.27
46 111 0.73
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.21
Consensus pattern (46 bp):
CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
Found at i:9659 original size:20 final size:20
Alignment explanation
Indices: 9600--9759 Score: 104
Period size: 20 Copynumber: 7.2 Consensus size: 20
9590 CATGAAATAG
*
9600 TGCATTAAGGCATGAAAAGA
1 TGCATTAAGGCATGAAAGGA
*
9620 TGCCATAAATGAATGCATGAAAGGA
1 TG-CAT---T-AAGGCATGAAAGGA
9645 TGCATTAAGGCATGAAAGGA
1 TGCATTAAGGCATGAAAGGA
*
9665 TGCCATAAATGAAATGCATGAAAGGA
1 TG-CAT---T--AAGGCATGAAAGGA
*
9691 TACATTAAGGCATGAAAGGA
1 TGCATTAAGGCATGAAAGGA
* * *
9711 TGCCATAAATGAAATGCATTAAATGA
1 TG-CAT---T--AAGGCATGAAAGGA
9737 TGCATTAAGGCATGAAAGGA
1 TGCATTAAGGCATGAAAGGA
9757 TGC
1 TGC
9760 CATATATGAA
Statistics
Matches: 110, Mismatches: 13, Indels: 34
0.70 0.08 0.22
Matches are distributed among these distances:
20 45 0.41
21 10 0.09
22 2 0.02
24 6 0.05
25 20 0.18
26 27 0.25
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.21
Consensus pattern (20 bp):
TGCATTAAGGCATGAAAGGA
Found at i:9684 original size:26 final size:25
Alignment explanation
Indices: 9609--9811 Score: 157
Period size: 26 Copynumber: 8.6 Consensus size: 25
9599 GTGCATTAAG
*
9609 GCATGAAAAGATGCCATAAATGAAT
1 GCATGAAAGGATGCCATAAATGAAT
*
9634 GCATGAAAGGATG-CAT---T-AAG
1 GCATGAAAGGATGCCATAAATGAAT
9654 GCATGAAAGGATGCCATAAATGAAAT
1 GCATGAAAGGATGCCATAAATG-AAT
* *
9680 GCATGAAAGGAT-ACAT---T-AAG
1 GCATGAAAGGATGCCATAAATGAAT
9700 GCATGAAAGGATGCCATAAATGAAAT
1 GCATGAAAGGATGCCATAAATG-AAT
* * *
9726 GCATTAAATGATG-CAT---T-AAG
1 GCATGAAAGGATGCCATAAATGAAT
*
9746 GCATGAAAGGATGCCATATATGAAAT
1 GCATGAAAGGATGCCATAAATG-AAT
* *
9772 GAATGAAAGGATGCCATAAATCAAAT
1 GCATGAAAGGATGCCATAAAT-GAAT
* *
9798 ACATGATAGGATGC
1 GCATGAAAGGATGC
9812 ATTAAGGCAT
Statistics
Matches: 140, Mismatches: 19, Indels: 37
0.71 0.10 0.19
Matches are distributed among these distances:
20 42 0.30
21 10 0.07
22 2 0.01
24 6 0.04
25 18 0.13
26 62 0.44
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.21
Consensus pattern (25 bp):
GCATGAAAGGATGCCATAAATGAAT
Found at i:9870 original size:118 final size:117
Alignment explanation
Indices: 9656--9871 Score: 265
Period size: 118 Copynumber: 1.8 Consensus size: 117
9646 GCATTAAGGC
* *
9656 ATGAAAGGATGCCATAAATGAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAAT
1 ATGAAAGGATGCCATAAATCAAATACATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAAT
** * * * *
9721 GAAATGCATTAAATGATGCATTAAGGCATGAAAGGATGCCATATATGAAATGA
66 GAAATGCAACAAATAATACAATAA-GAATGAAAGGATGCCATATATGAAATGA
* * * *
9774 ATGAAAGGATGCCATAAATCAAATACATGATAGGATGCATTAAGGCATGAAAGGATGCGATGAAT
1 ATGAAAGGATGCCATAAATCAAATACATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAAT
*
9839 GAAAT-TAACAAATAATTACTAAATAA-AATGAAA
66 GAAATGCAACAAATAA-TAC--AATAAGAATGAAA
9872 AACAATATAC
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
117 6 0.07
118 72 0.88
120 4 0.05
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.22
Consensus pattern (117 bp):
ATGAAAGGATGCCATAAATCAAATACATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAAT
GAAATGCAACAAATAATACAATAAGAATGAAAGGATGCCATATATGAAATGA
Found at i:10855 original size:16 final size:16
Alignment explanation
Indices: 10834--10870 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
10824 AATCTCAAAA
10834 GAGCTGAAGAGATTTG
1 GAGCTGAAGAGATTTG
*
10850 GAGCTGAAGAGCTTTG
1 GAGCTGAAGAGATTTG
10866 GAGCT
1 GAGCT
10871 CCAGAGTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.27, C:0.11, G:0.38, T:0.24
Consensus pattern (16 bp):
GAGCTGAAGAGATTTG
Found at i:10876 original size:16 final size:16
Alignment explanation
Indices: 10834--10876 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
10824 AATCTCAAAA
*
10834 GAGCTGAAGAGATTTG
1 GAGCTCAAGAGATTTG
* *
10850 GAGCTGAAGAGCTTTG
1 GAGCTCAAGAGATTTG
*
10866 GAGCTCCAGAG
1 GAGCTCAAGAG
10877 TTCTGGGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.28, C:0.14, G:0.37, T:0.21
Consensus pattern (16 bp):
GAGCTCAAGAGATTTG
Found at i:15818 original size:20 final size:20
Alignment explanation
Indices: 15793--15836 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
15783 GCAATGGTAT
15793 CGATACTAATAGAACAATAC
1 CGATACTAATAGAACAATAC
*
15813 CGATACTAATAGAACAATAT
1 CGATACTAATAGAACAATAC
15833 CGAT
1 CGAT
15837 GTAAGTGGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.48, C:0.18, G:0.11, T:0.23
Consensus pattern (20 bp):
CGATACTAATAGAACAATAC
Found at i:16460 original size:12 final size:12
Alignment explanation
Indices: 16443--16610 Score: 85
Period size: 12 Copynumber: 14.5 Consensus size: 12
16433 CATGAATGAA
16443 ATGCATGAAAGG
1 ATGCATGAAAGG
*
16455 ATGCAT-TAA-G
1 ATGCATGAAAGG
16465 --GCATGAAAGG
1 ATGCATGAAAGG
* * **
16475 ATTCCATAAATAAA
1 A-TGCATGAA-AGG
16489 ATGCATGAAAGG
1 ATGCATGAAAGG
*
16501 ATGCAT-TAA-G
1 ATGCATGAAAGG
16511 --GCATGAAAGG
1 ATGCATGAAAGG
*
16521 ATGTCAT-AAATGA
1 ATG-CATGAAA-GG
16534 AGTGCATGAAAGG
1 A-TGCATGAAAGG
*
16547 ATGCAT-TAA-G
1 ATGCATGAAAGG
16557 -T-CATGAAAGG
1 ATGCATGAAAGG
*
16567 ATGCAAT-AAATGAA
1 ATGC-ATGAAA-G-G
16581 ATGCATGAAAGG
1 ATGCATGAAAGG
16593 ATGCATGAAAGG
1 ATGCATGAAAGG
16605 ATGCAT
1 ATGCAT
16611 TAAGGCATGA
Statistics
Matches: 116, Mismatches: 18, Indels: 44
0.65 0.10 0.25
Matches are distributed among these distances:
8 11 0.09
9 7 0.06
10 6 0.05
11 7 0.06
12 44 0.38
13 27 0.23
14 14 0.12
ACGTcount: A:0.43, C:0.10, G:0.26, T:0.21
Consensus pattern (12 bp):
ATGCATGAAAGG
Found at i:16496 original size:26 final size:25
Alignment explanation
Indices: 16465--16594 Score: 84
Period size: 26 Copynumber: 5.5 Consensus size: 25
16455 ATGCATTAAG
16465 GCATGAAAGGATTCCATAAATAAAAT
1 GCATGAAAGGATTCCATAAAT-AAAT
* *
16491 GCATGAAAGGA-TGCAT---T-AAG
1 GCATGAAAGGATTCCATAAATAAAT
*
16511 GCATGAAAGGATGT-CATAAATGAAGT
1 GCATGAAAGGAT-TCCATAAAT-AAAT
* *
16537 GCATGAAAGGA-TGCAT---TAAGT
1 GCATGAAAGGATTCCATAAATAAAT
* *
16558 -CATGAAAGGATGCAATAAATGAAAT
1 GCATGAAAGGATTCCATAAAT-AAAT
16583 GCATGAAAGGAT
1 GCATGAAAGGAT
16595 GCATGAAAGG
Statistics
Matches: 82, Mismatches: 8, Indels: 28
0.69 0.07 0.24
Matches are distributed among these distances:
20 23 0.28
21 9 0.11
22 3 0.04
24 3 0.04
25 10 0.12
26 34 0.41
ACGTcount: A:0.45, C:0.09, G:0.25, T:0.22
Consensus pattern (25 bp):
GCATGAAAGGATTCCATAAATAAAT
Found at i:16498 original size:46 final size:46
Alignment explanation
Indices: 16431--16778 Score: 401
Period size: 46 Copynumber: 7.3 Consensus size: 46
16421 CTAAAACAAA
*
16431 TCCATGAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
1 TCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
*
16477 TCCATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
1 TCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
* *
16523 GT-CATAAATGAAGTGCATGAAAGGATGCATTAAGTCATGAAAGGAT
1 -TCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
** *
16569 GCAATAAATGAAATGCATGAAAGGATGCATGAAAGGATGCATTAAGGCATGAAAAGAT
1 ----TCCAT--AA---ATG-AA--ATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
* * *
16627 GCCATAAATGAAATGTATGAAAGGATGCATTAAGGCATGAAAAGAT
1 TCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
** *
16673 AGCATAAATGAAATGCATGAAAGGATGCATTAAGGAATGAAAGGAT
1 TCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
* * * *
16719 GCCATAAATGAAATGCATTAAAGGGTGCATTAAGGCATGAAAAGAT
1 TCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
* *
16765 GCCATGAATGAAAT
1 TCCATAAATGAAAT
16779 TAACAAATAA
Statistics
Matches: 263, Mismatches: 26, Indels: 26
0.83 0.08 0.08
Matches are distributed among these distances:
46 212 0.81
47 1 0.00
48 2 0.01
49 4 0.02
50 2 0.01
52 4 0.02
54 2 0.01
55 3 0.01
56 2 0.01
58 31 0.12
ACGTcount: A:0.45, C:0.09, G:0.25, T:0.21
Consensus pattern (46 bp):
TCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
Found at i:16653 original size:26 final size:25
Alignment explanation
Indices: 16593--16748 Score: 99
Period size: 20 Copynumber: 6.7 Consensus size: 25
16583 GCATGAAAGG
16593 ATGCATGAAAGGATGCAT---T--A
1 ATGCATGAAAGGATGCATAAATGAA
* *
16613 AGGCATGAAAAGATGCCATAAATGAA
1 ATGCATGAAAGGATG-CATAAATGAA
*
16639 ATGTATGAAAGGATGCAT---T--A
1 ATGCATGAAAGGATGCATAAATGAA
* *
16659 AGGCATGAAAAGATAGCATAAATGAA
1 ATGCATGAAAGGAT-GCATAAATGAA
16685 ATGCATGAAAGGATGCAT---T--A
1 ATGCATGAAAGGATGCATAAATGAA
* *
16705 AGGAATGAAAGGATGCCATAAATGAA
1 ATGCATGAAAGGATG-CATAAATGAA
* *
16731 ATGCATTAAAGGGTGCAT
1 ATGCATGAAAGGATGCAT
16749 TAAGGCATGA
Statistics
Matches: 102, Mismatches: 16, Indels: 31
0.68 0.11 0.21
Matches are distributed among these distances:
20 39 0.38
21 10 0.10
22 2 0.02
24 3 0.03
25 10 0.10
26 38 0.37
ACGTcount: A:0.45, C:0.09, G:0.25, T:0.21
Consensus pattern (25 bp):
ATGCATGAAAGGATGCATAAATGAA
Found at i:16677 original size:21 final size:20
Alignment explanation
Indices: 16445--16766 Score: 92
Period size: 20 Copynumber: 14.7 Consensus size: 20
16435 TGAATGAAAT
*
16445 GCATGAAAGGATGCATTAAG
1 GCATGAAAAGATGCATTAAG
* * *
16465 GCATGAAAGGATTCCATAAATAAAAT
1 GCATGAAAAGA-TGCAT---T--AAG
*
16491 GCATGAAAGGATGCATTAAG
1 GCATGAAAAGATGCATTAAG
*
16511 GCATGAAAGGATGTCATAAATGAAG
1 GCATGAAAAGATG-CAT---T-AAG
*
16536 TGCATGAAAGGATGCATTAAG
1 -GCATGAAAAGATGCATTAAG
* * *
16557 TCATGAAAGGATGCAATAA-
1 GCATGAAAAGATGCATTAAG
* * *** *
16576 --ATGAAATGCATGAAAGGAT
1 GCATGAAAAG-ATGCATTAAG
*
16595 GCATGAAAGGATGCATTAAG
1 GCATGAAAAGATGCATTAAG
*
16615 GCATGAAAAGATGCCATAAATGAAAT
1 GCATGAAAAGATG-CAT---T--AAG
* *
16641 GTATGAAAGGATGCATTAAG
1 GCATGAAAAGATGCATTAAG
*
16661 GCATGAAAAGATAGCATAAATGAAAT
1 GCATGAAAAGAT-GCAT---T--AAG
*
16687 GCATGAAAGGATGCATTAAG
1 GCATGAAAAGATGCATTAAG
* * *
16707 GAATGAAAGGATGCCATAAATGAAAT
1 GCATGAAAAGATG-CAT---T--AAG
* * *
16733 GCATTAAAGGGTGCATTAAG
1 GCATGAAAAGATGCATTAAG
16753 GCATGAAAAGATGC
1 GCATGAAAAGATGC
16767 CATGAATGAA
Statistics
Matches: 233, Mismatches: 35, Indels: 68
0.69 0.10 0.20
Matches are distributed among these distances:
17 7 0.03
18 6 0.03
20 99 0.42
21 27 0.12
22 5 0.02
24 5 0.02
25 20 0.09
26 64 0.27
ACGTcount: A:0.44, C:0.09, G:0.25, T:0.21
Consensus pattern (20 bp):
GCATGAAAAGATGCATTAAG
Found at i:16714 original size:150 final size:150
Alignment explanation
Indices: 16443--16748 Score: 497
Period size: 150 Copynumber: 2.0 Consensus size: 150
16433 CATGAATGAA
* *
16443 ATGCATGAAAGGATGCATTAAGGCATGAAAGGATTCCATAAATAAAATGCATGAAAGGATGCATT
1 ATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCATAAATAAAATGCATGAAAGGATGCATT
* * **
16508 AAGGCATGAAAGGATGTCATAAATGAAGTGCATGAAAGGATGCATTAAGTCATGAAAGGATGCAA
66 AAGGCATGAAAAGATGTCATAAATGAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGCAA
16573 TAAATGAAATGCATGAAAGG
131 TAAATGAAATGCATGAAAGG
* *
16593 ATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCATAAATGAAATGTATGAAAGGATGCATT
1 ATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCATAAATAAAATGCATGAAAGGATGCATT
*
16658 AAGGCATGAAAAGATAG-CATAAATGAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGCC
66 AAGGCATGAAAAGAT-GTCATAAATGAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGCA
*
16722 ATAAATGAAATGCATTAAAGG
130 ATAAATGAAATGCATGAAAGG
*
16743 GTGCAT
1 ATGCAT
16749 TAAGGCATGA
Statistics
Matches: 144, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
150 143 0.99
151 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.25, T:0.21
Consensus pattern (150 bp):
ATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCATAAATAAAATGCATGAAAGGATGCATT
AAGGCATGAAAAGATGTCATAAATGAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGCAA
TAAATGAAATGCATGAAAGG
Found at i:19309 original size:19 final size:19
Alignment explanation
Indices: 19285--19323 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
19275 TAGCTCAGGC
19285 TTAGACTAAGAATGAAGAG
1 TTAGACTAAGAATGAAGAG
19304 TTAGACTAAGAATGAAGAG
1 TTAGACTAAGAATGAAGAG
19323 T
1 T
19324 ATAGTTCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.05, G:0.26, T:0.23
Consensus pattern (19 bp):
TTAGACTAAGAATGAAGAG
Found at i:23346 original size:42 final size:42
Alignment explanation
Indices: 23272--23373 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
23262 AGATATGATG
* * *
23272 AATGTTGGGGCACTTTTGAAAGCCCGTATCATCCAGAAGTAATA
1 AATGTT-GGGCA-TTTTGAAAGCCCATATCATCAAGAAATAATA
* * *
23316 AATGTTGGGCATTTTGAAGGCCTATGTCATCAAGAAATAATA
1 AATGTTGGGCATTTTGAAAGCCCATATCATCAAGAAATAATA
23358 AATGTTGGGACATTTT
1 AATGTTGGG-CATTTT
23374 TTTGAGGCCC
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
42 34 0.67
43 11 0.22
44 6 0.12
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (42 bp):
AATGTTGGGCATTTTGAAAGCCCATATCATCAAGAAATAATA
Found at i:24545 original size:36 final size:37
Alignment explanation
Indices: 24486--24556 Score: 117
Period size: 36 Copynumber: 1.9 Consensus size: 37
24476 TTATTAAGAG
*
24486 AAGTCTATCTTTGTTATTCTTGACTTTCTCATGAAAA
1 AAGTCAATCTTTGTTATTCTTGACTTTCTCATGAAAA
*
24523 AAGTCAATCTTT-TTATTCTTGACTTTCTCGTGAA
1 AAGTCAATCTTTGTTATTCTTGACTTTCTCATGAA
24557 GAGAAGTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 21 0.66
37 11 0.34
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.46
Consensus pattern (37 bp):
AAGTCAATCTTTGTTATTCTTGACTTTCTCATGAAAA
Found at i:24569 original size:37 final size:38
Alignment explanation
Indices: 24481--24569 Score: 128
Period size: 37 Copynumber: 2.4 Consensus size: 38
24471 CTTCCTTATT
*
24481 AAGAGAAGTCTATCTTTGTTATTCTTGACTTTCTCATG
1 AAGAGAAGTCAATCTTTGTTATTCTTGACTTTCTCATG
* *
24519 AA-AAAAGTCAATCTTT-TTATTCTTGACTTTCTCGTG
1 AAGAGAAGTCAATCTTTGTTATTCTTGACTTTCTCATG
*
24555 AAGAGAAGTGAATCT
1 AAGAGAAGTCAATCT
24570 CTCAATATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
36 21 0.47
37 22 0.49
38 2 0.04
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (38 bp):
AAGAGAAGTCAATCTTTGTTATTCTTGACTTTCTCATG
Found at i:24668 original size:45 final size:43
Alignment explanation
Indices: 24538--24685 Score: 127
Period size: 45 Copynumber: 3.3 Consensus size: 43
24528 AATCTTTTTA
* * * * *
24538 TTCTTGACTTTCTCGTGAAGAGAAGTGAATCTCTCAATATTATCC
1 TTCTTGACTTTCTCGCGAAGAGAA-T-AATCTTTCAGTGTTGTCC
* * * * *
24583 TTCTTGAATTTCTCACGAATATGAGATAATATTTTAGTGTTGTCC
1 TTCTTGACTTTCTCGCGAAGA-GA-ATAATCTTTCAGTGTTGTCC
*
24628 TTCTTGACTTTCTCGCGAAGAGAATTCAATCTTTCGGTGTTGT-C
1 TTCTTGACTTTCTCGCGAAGAGAA-T-AATCTTTCAGTGTTGTCC
24672 TTCATTGACTTTCT
1 TTC-TTGACTTTCT
24686 TGTAAAGAGG
Statistics
Matches: 82, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
43 1 0.01
44 7 0.09
45 70 0.85
46 3 0.04
47 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.43
Consensus pattern (43 bp):
TTCTTGACTTTCTCGCGAAGAGAATAATCTTTCAGTGTTGTCC
Found at i:24754 original size:45 final size:45
Alignment explanation
Indices: 24690--24847 Score: 151
Period size: 45 Copynumber: 3.5 Consensus size: 45
24680 CTTTCTTGTA
* ** * *
24690 AAGAGGAGTTAATAGTTTAGTATTGTTCGTTTTGACTATCTCATG
1 AAGAGGAGTCAATCTTTTAGTATTGTTCTTTTTGACTATCTCACG
* *
24735 AAGAGGAGTCAATCTTTTAGTGTT-TTCCTTTTTTAC-ATTCTCACG
1 AAGAGGAGTCAATCTTTTAGTATTGTT-CTTTTTGACTA-TCTCACG
* * * * *
24780 AAGAGAAGTCGATCTTTTGGTGTTGTTCTTTTTGACTTTCTCACG
1 AAGAGGAGTCAATCTTTTAGTATTGTTCTTTTTGACTATCTCACG
*
24825 GAGAGGAGTCAA-CTTTTCAGTAT
1 AAGAGGAGTCAATCTTTT-AGTAT
24848 CATCATTCCT
Statistics
Matches: 91, Mismatches: 17, Indels: 10
0.77 0.14 0.08
Matches are distributed among these distances:
44 8 0.09
45 81 0.89
46 2 0.02
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.42
Consensus pattern (45 bp):
AAGAGGAGTCAATCTTTTAGTATTGTTCTTTTTGACTATCTCACG
Found at i:25628 original size:134 final size:134
Alignment explanation
Indices: 25429--25746 Score: 467
Period size: 134 Copynumber: 2.4 Consensus size: 134
25419 GCATACAGTG
* * *
25429 TTCTGATTCAATCTTCCCTAAAGAGCAGTGAAGTGGATCAAAATTTTCTCGAGTCTGATCTCCCC
1 TTCTGATTCAATCTTCCCTGAAGAGAAGTGAAGTGGATCAAAGTTTTCTCGAGTCTGATCTCCCC
* * *
25494 TAAAGAGTAGTGGAGAATATTCTTCTTCTTTCAGAGTTGGTCTTCCTAAAGAGCAATGAAGCAAA
66 TAAAGAGTAGTGGAGAAGATTCTTCTTCTTTCAAAGTTGGTATTCCTAAAGAGCAATGAAGCAAA
25559 TCGA
131 TCGA
* * * * *
25563 TTCTGATTCAATATTTCCTGAAGAGAAGTGAAGTCGACCAAAGTTTTGTCGAGTCTGATCTCCCC
1 TTCTGATTCAATCTTCCCTGAAGAGAAGTGAAGTGGATCAAAGTTTTCTCGAGTCTGATCTCCCC
* * * * *
25628 TAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAAATTTGGTATTCCTGAAGAGGAGTGAAGCAAA
66 TAAAGAGTAGTGGAGAAGATTCTTCTTCTTTCAAAGTTGGTATTCCTAAAGAGCAATGAAGCAAA
25693 TCGA
131 TCGA
*
25697 TTCTGAATCAATCTTCCCTGAAGA-ATAGTGAAGTGGATCAAAGTTTTCTC
1 TTCTGATTCAATCTTCCCTGAAGAGA-AGTGAAGTGGATCAAAGTTTTCTC
25747 AAGTTATTTG
Statistics
Matches: 161, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
133 1 0.01
134 160 0.99
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (134 bp):
TTCTGATTCAATCTTCCCTGAAGAGAAGTGAAGTGGATCAAAGTTTTCTCGAGTCTGATCTCCCC
TAAAGAGTAGTGGAGAAGATTCTTCTTCTTTCAAAGTTGGTATTCCTAAAGAGCAATGAAGCAAA
TCGA
Found at i:35074 original size:14 final size:14
Alignment explanation
Indices: 35055--35120 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 14
35045 AAGTTAATAG
35055 GTTGACTCGGACGA
1 GTTGACTCGGACGA
* ** *
35069 GTTGACACATATGA
1 GTTGACTCGGACGA
* ** *
35083 GTTAACTTTGACCA
1 GTTGACTCGGACGA
*
35097 GTTGACTTGGACGA
1 GTTGACTCGGACGA
35111 GTTGACTCGG
1 GTTGACTCGG
35121 TTTAGACTGG
Statistics
Matches: 37, Mismatches: 15, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (14 bp):
GTTGACTCGGACGA
Found at i:45836 original size:54 final size:54
Alignment explanation
Indices: 45749--46252 Score: 349
Period size: 54 Copynumber: 9.4 Consensus size: 54
45739 CAATTATGAG
* * * * * *
45749 CTCTACACTTCCATAACCAAGGAACGCTAGAGCTTGCTCGATCTTAAAAATTTT
1 CTCTACTCCTCCATAACAAAGAAACGCTAGAGCTTACTTGATCTTAAAAATTTT
* * **
45803 CTCTACTCCTCCAAAACAAAGAAACGCTGGAGCTTAC-ACAGTCTT-AAAATTTT
1 CTCTACTCCTCCATAACAAAGAAACGCTAGAGCTTACTTGA-TCTTAAAAATTTT
* **
45856 GCTCTACACCTCCATAACAAAGAAACAATAGAGCTTA--TGTAGTCTTAAAAATTTT
1 -CTCTACTCCTCCATAACAAAGAAACGCTAGAGCTTACTTG-A-TCTTAAAAATTTT
* * * * *
45911 CTCTACTCCTCAATAAGAAAGGAATGCTTGAGCTTA-TAT-AGTCTT-AAAATTTT
1 CTCTACTCCTCCATAACAAAGAAACGCTAGAGCTTACT-TGA-TCTTAAAAATTTT
* *
45964 CTCTACTCCTCCATAGA-AAATG-AACGCTAGAGCTTTCTTGTTCTT-AAAATTTT
1 CTCTACTCCTCCATA-ACAAA-GAAACGCTAGAGCTTACTTGATCTTAAAAATTTT
* ** * * * *
46017 GATCTA---CTCCATAGTAAAGGAATC-CTAGAGCTTACTGGGTCTTAAATATTTT
1 -CTCTACTCCTCCATAACAAA-GAAACGCTAGAGCTTACTTGATCTTAAAAATTTT
* * * * *
46069 CTCTACTCCTCCATAACAAAGGAATGCTAGAG-TGTGC-TAAGTCTTAAAAAAATTT
1 CTCTACTCCTCCATAACAAAGAAACGCTAGAGCT-TACTTGA-TCTT-AAAAATTTT
* * *
46124 CTCTACTCCTTCATAACAAAGAAACGCTAGAGCATACTTGATCTTTAAAATTTGT
1 CTCTACTCCTCCATAACAAAGAAACGCTAGAGCTTACTTGATCTTAAAAATTT-T
* * * * * * * * *
46179 -TATACTCATCCATAAGAAAGGAATGCTAGAGCGTGCTTGGTCTTAAAAATTTG
1 CTCTACTCCTCCATAACAAAGAAACGCTAGAGCTTACTTGATCTTAAAAATTTT
* *
46232 ATGTACTCCTCCATAACAAAG
1 CTCTACTCCTCCATAACAAAG
46253 TGTCACAATG
Statistics
Matches: 354, Mismatches: 71, Indels: 50
0.75 0.15 0.11
Matches are distributed among these distances:
51 31 0.09
52 9 0.03
53 61 0.17
54 199 0.56
55 51 0.14
56 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.31
Consensus pattern (54 bp):
CTCTACTCCTCCATAACAAAGAAACGCTAGAGCTTACTTGATCTTAAAAATTTT
Found at i:46048 original size:51 final size:51
Alignment explanation
Indices: 45972--46077 Score: 126
Period size: 51 Copynumber: 2.1 Consensus size: 51
45962 TTCTCTACTC
* * * *
45972 CTCCATAGAAAATGAACGCTAGAGCTTTCTTGTTCTTAAA-ATTTTGATCTA
1 CTCCATAGAAAAGGAACGCTAGAGCTTACTGGGTCTTAAATATTTT-ATCTA
* *
46023 CTCCATAGTAAAGGAATC-CTAGAGCTTACTGGGTCTTAAATATTTTCTCTA
1 CTCCATAGAAAAGGAA-CGCTAGAGCTTACTGGGTCTTAAATATTTTATCTA
46074 CTCC
1 CTCC
46078 TCCATAACAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
51 41 0.87
52 6 0.13
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (51 bp):
CTCCATAGAAAAGGAACGCTAGAGCTTACTGGGTCTTAAATATTTTATCTA
Found at i:46874 original size:23 final size:24
Alignment explanation
Indices: 46829--46874 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
46819 CCCTTTCGGG
46829 TTTTCACTTTCGTTTCTTCTTCTA
1 TTTTCACTTTCGTTTCTTCTTCTA
* *
46853 TTTTCTCTTT-GTTTCTTTTTCT
1 TTTTCACTTTCGTTTCTTCTTCT
46875 TTTCATTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.04, C:0.22, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTTCACTTTCGTTTCTTCTTCTA
Found at i:46948 original size:23 final size:21
Alignment explanation
Indices: 46899--46947 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
46889 CCTTCTTTCC
* *
46899 TTTCTT-TTTTTTTTTACTTT
1 TTTCTTCTTTTCTTTCACTTT
46919 TTTCTTCTTTTCTTTCAC-TT
1 TTTCTTCTTTTCTTTCACTTT
46939 TTTCTTCTT
1 TTTCTTCTT
46948 CATCAGCAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTCTTCTTTTCTTTCACTTT
Found at i:47666 original size:25 final size:24
Alignment explanation
Indices: 47616--47666 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
47606 TTGAAGCCCA
* *
47616 TTTTCATTTTCCTTTCTTTTTCTT
1 TTTTCATTTTCCTTTCTATCTCTT
47640 TTTTCTATTTTCCTTT-TATCTCTT
1 TTTTC-ATTTTCCTTTCTATCTCTT
47664 TTT
1 TTT
47667 ATTTTTCCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTCATTTTCCTTTCTATCTCTT
Found at i:47669 original size:21 final size:21
Alignment explanation
Indices: 47631--47698 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 21
47621 ATTTTCCTTT
*
47631 CTTTTTCTTTTTTCTATTTTC
1 CTTTTTCTCTTTTCTATTTTC
47652 CTTTTATCTCTTTT-TATTTTTCC
1 CTTTT-TCTCTTTTCTA-TTTT-C
* *
47675 CTTTTTC-CTTTCCT-TTTTT
1 CTTTTTCTCTTTTCTATTTTC
47694 CTTTT
1 CTTTT
47699 CTTTTCTGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
19 5 0.12
20 4 0.10
21 11 0.28
22 14 0.35
23 6 0.15
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (21 bp):
CTTTTTCTCTTTTCTATTTTC
Found at i:47671 original size:15 final size:14
Alignment explanation
Indices: 47630--47698 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
47620 CATTTTCCTT
47630 TCTTTTTCTTTTT-
1 TCTTTTTCTTTTTC
47643 TCTATTTTCCTTTTATC
1 TCT-TTTT-CTTTT-TC
*
47660 TCTTTTTATTTTTC
1 TCTTTTTCTTTTTC
* * *
47674 CCTTTTTCCTTTCC
1 TCTTTTTCTTTTTC
47688 T-TTTTTCTTTT
1 TCTTTTTCTTTT
47699 CTTTTCTGGA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
13 12 0.27
14 16 0.36
15 9 0.20
16 5 0.11
17 3 0.07
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (14 bp):
TCTTTTTCTTTTTC
Found at i:54791 original size:16 final size:16
Alignment explanation
Indices: 54770--54803 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
54760 AAAAGTTTTA
54770 ATAAATG-AATATAAAT
1 ATAAATGTAA-ATAAAT
54786 ATAAATGTAAATAAAT
1 ATAAATGTAAATAAAT
54802 AT
1 AT
54804 TAACACAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (16 bp):
ATAAATGTAAATAAAT
Found at i:59376 original size:26 final size:23
Alignment explanation
Indices: 59332--59383 Score: 59
Period size: 26 Copynumber: 2.1 Consensus size: 23
59322 CTATCATGCA
*
59332 ATTATTATTTATAACATGCTATT
1 ATTATTATTTATAACATGCAATT
*
59355 ATTATTATTATCTAACATATGCAATT
1 ATTATTATT-TATAAC--ATGCAATT
59381 ATT
1 ATT
59384 TAATACCTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 9 0.38
24 5 0.21
26 10 0.42
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.50
Consensus pattern (23 bp):
ATTATTATTTATAACATGCAATT
Found at i:59675 original size:51 final size:52
Alignment explanation
Indices: 59599--59738 Score: 174
Period size: 54 Copynumber: 2.7 Consensus size: 52
59589 AAACGAACAC
* * * *
59599 TAGAGCTTACTCGATCTTAAAAATTTGCTCTA-CTCCATAAAAAAGGAATTA
1 TAGAGCTTATTCGGTCTTAGAAATTTGCTCTACCTCCATAAAAAAGGAATGA
* *
59650 TAGAGCTTATTCGGTCTTAGAAATTTTCTCTACTCCTCCATAAAAAAGGAATGC
1 TAGAGCTTATTCGGTCTTAGAAATTTGCTCTA--CCTCCATAAAAAAGGAATGA
* * *
59704 TAGAGCATGTTCGGTCTTAGAAATTTGCTTTACCT
1 TAGAGCTTATTCGGTCTTAGAAATTTGCTCTACCT
59739 ATCGTTAGTA
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
51 28 0.37
52 3 0.04
54 45 0.59
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (52 bp):
TAGAGCTTATTCGGTCTTAGAAATTTGCTCTACCTCCATAAAAAAGGAATGA
Found at i:69611 original size:22 final size:21
Alignment explanation
Indices: 69586--69626 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
69576 ATATCCGATT
69586 TGATTTTTTTGAAAGTTTTGTA
1 TGATTTTTTT-AAAGTTTTGTA
*
69608 TGATTTTTTTAAATTTTTG
1 TGATTTTTTTAAAGTTTTG
69627 ATACTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.22, C:0.00, G:0.15, T:0.63
Consensus pattern (21 bp):
TGATTTTTTTAAAGTTTTGTA
Done.