Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005733.1 Hibiscus syriacus cultivar Beakdansim tig00013400_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: 92727
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:987 original size:14 final size:14
Alignment explanation
Indices: 968--1003 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
958 ATTGTTTAAT
968 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
982 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
996 TGATTTGT
1 TGATTTGT
1004 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1209 original size:19 final size:19
Alignment explanation
Indices: 1181--1278 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1171 GCGAAATTAA
*
1181 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
1200 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
1214 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
1233 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
1249 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
1266 TTCGCATTGCGAT
1 TTCGCATTGCGAT
1279 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 9, Indels: 20
0.67 0.10 0.22
Matches are distributed among these distances:
14 17 0.28
16 7 0.12
17 7 0.12
19 29 0.48
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:1226 original size:33 final size:33
Alignment explanation
Indices: 1179--1277 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
1169 ACGCGAAATT
1179 AATTCGCGTTGCGATTTTCATTTCGCATTGCGA
1 AATTCGCGTTGCGATTTTCATTTCGCATTGCGA
*
1212 AATTAGCGTTGCGATTTTCATTTCGCATTGCG-
1 AATTCGCGTTGCGATTTTCATTTCGCATTGCGA
* *
1244 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA
1 AAT-TCGCGTTGCGATTTTCATTTCGCATTGCGA
1278 TAGTAATTTC
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
32 2 0.03
33 58 0.97
ACGTcount: A:0.17, C:0.21, G:0.20, T:0.41
Consensus pattern (33 bp):
AATTCGCGTTGCGATTTTCATTTCGCATTGCGA
Found at i:3579 original size:12 final size:12
Alignment explanation
Indices: 3562--3586 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3552 TCTTCGGGGA
3562 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3574 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3586 C
1 C
3587 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3795 original size:24 final size:24
Alignment explanation
Indices: 3761--3814 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
3751 CTGAAACATC
* *
3761 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
3785 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
3809 ATCAAA
1 ATCAAA
3815 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:4894 original size:20 final size:20
Alignment explanation
Indices: 4869--4926 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
4859 ATTCATTTGA
4869 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
4889 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
4909 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
4927 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:4986 original size:19 final size:19
Alignment explanation
Indices: 4945--5136 Score: 287
Period size: 19 Copynumber: 10.6 Consensus size: 19
4935 GAAATGAAAA
4945 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
4961 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
4978 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
4997 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5016 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
5032 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
5049 TAGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5068 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5087 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
5106 TCGCATTGCGATTTCCATT
1 TCGCATTGCGATTTTCATT
*
5125 TCGCGTTGCGAT
1 TCGCATTGCGAT
5137 AGTCTGTTTT
Statistics
Matches: 162, Mismatches: 4, Indels: 17
0.89 0.02 0.09
Matches are distributed among these distances:
14 22 0.14
16 6 0.04
17 5 0.03
19 129 0.80
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:5042 original size:71 final size:71
Alignment explanation
Indices: 4945--5136 Score: 312
Period size: 71 Copynumber: 2.6 Consensus size: 71
4935 GAAATGAAAA
4945 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
5010 TTCATT
66 TTCATT
*
5016 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTAGCATTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
5081 TTCATT
66 TTCATT
* *
5087 TCGCATTGCGATTTTCATTTCGCATTGCGATTTCCATTTCGCGTTGCGAT
1 TCGCATTGCGATTTTC---TCG--TTGCGATTTTCATTTCGCATTGCGAT
5137 AGTCTGTTTT
Statistics
Matches: 112, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
71 86 0.77
74 3 0.03
76 23 0.21
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (71 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
TTCATT
Found at i:7162 original size:20 final size:19
Alignment explanation
Indices: 7127--7193 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
7117 GAAACTTAAA
7127 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
7146 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
7166 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
7185 ATCGCAACG
1 ATCGCAACG
7194 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:7201 original size:14 final size:14
Alignment explanation
Indices: 7182--7239 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
7172 ATGCGAAATG
7182 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
7196 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
7212 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
7228 AAAATCGCAACG
1 AAAATCGCAACG
7240 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:7224 original size:32 final size:33
Alignment explanation
Indices: 7166--7244 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
7156 GGAAATGGCT
*
7166 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
7199 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
7231 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
7245 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:7273 original size:19 final size:19
Alignment explanation
Indices: 7251--7332 Score: 95
Period size: 19 Copynumber: 4.6 Consensus size: 19
7241 GAAACACAAA
7251 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
7270 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
7286 TCG--TTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
* *
7302 TCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
7321 TCGCATTGCGAT
1 TCGCATTGCGAT
7333 AGCCATTTCC
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
14 9 0.17
16 7 0.13
18 9 0.17
19 28 0.53
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:7339 original size:19 final size:19
Alignment explanation
Indices: 7317--7362 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
7307 TTGCGATTTT
7317 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
* *
7336 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCATTGCGATAGC
7356 CATTTCG
1 CATTTCG
7363 TGTTGCGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.17, C:0.26, G:0.22, T:0.35
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:7369 original size:19 final size:19
Alignment explanation
Indices: 7287--7370 Score: 89
Period size: 19 Copynumber: 4.4 Consensus size: 19
7277 GCGATTTTGT
* *
7287 CGTTGCGAT-TTCATTTCT
1 CGTTGCGATAGTCATTTCG
**
7305 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
7324 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
7344 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
7363 TGTTGCGA
1 CGTTGCGA
7371 AAGTAAACTA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
18 9 0.16
19 30 0.54
20 17 0.30
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:8186 original size:20 final size:20
Alignment explanation
Indices: 8161--8198 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
8151 AATAGTTTCT
8161 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
8181 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
8199 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:8786 original size:20 final size:20
Alignment explanation
Indices: 8673--8786 Score: 90
Period size: 20 Copynumber: 5.7 Consensus size: 20
8663 CGCTTTGAAA
8673 ATCGCATTGCGATTATGTAA--
1 ATCGCATTGCGA-TA-GTAAGT
* * *
8693 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* *
8713 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * * *
8733 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
8754 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
8774 ATCGCATTGCGAT
1 ATCGCATTGCGAT
8787 TTTCCCAATT
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
18 3 0.04
19 4 0.05
20 56 0.73
21 12 0.16
22 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:8804 original size:21 final size:21
Alignment explanation
Indices: 8775--8867 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
8765 ATAGTAAGTA
8775 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
8796 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
8816 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
8837 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
8857 TCGCATTGCGA
1 TCGCATTGCGA
8868 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:8805 original size:41 final size:41
Alignment explanation
Indices: 8714--8848 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
8704 AAAGTCAGTA
* * * ** *
8714 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
8754 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
8796 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
8837 TCGCGTTGCGAT
1 TCGCGTTGCGAT
8849 TTACTTATTC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 4 0.05
41 75 0.93
42 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:8849 original size:41 final size:41
Alignment explanation
Indices: 8775--8867 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
8765 ATAGTAAGTA
8775 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
8816 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
8857 TCGCATTGCGA
1 TCGCATTGCGA
8868 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:10771 original size:21 final size:20
Alignment explanation
Indices: 10747--10802 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 20
10737 AAGATATGAA
10747 AAAAATATAAAAATATTATAG
1 AAAAATATAAAAATATT-TAG
** *
10768 AAAAGCATAAAAA-AGTTAG
1 AAAAATATAAAAATATTTAG
* *
10787 AAAATTGTAAAAATAT
1 AAAAATATAAAAATAT
10803 AAAATCTAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
19 13 0.48
20 3 0.11
21 11 0.41
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25
Consensus pattern (20 bp):
AAAAATATAAAAATATTTAG
Found at i:10822 original size:16 final size:17
Alignment explanation
Indices: 10777--10822 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
10767 GAAAAGCATA
*
10777 AAAAAGTTAGAAAATTGT
1 AAAAA-TTAGAAAATTCT
*
10795 AAAAA-TATAAAA-TCT
1 AAAAATTAGAAAATTCT
10810 AAAAATTAGAAAA
1 AAAAATTAGAAAA
10823 CAAAAATATC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 7 0.29
16 12 0.50
18 5 0.21
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.24
Consensus pattern (17 bp):
AAAAATTAGAAAATTCT
Found at i:11501 original size:24 final size:24
Alignment explanation
Indices: 11427--11505 Score: 95
Period size: 24 Copynumber: 3.3 Consensus size: 24
11417 CGTTCGGTAA
* *
11427 TATGATTGTTTATGTTCGTTCATT
1 TATGTTTGTTTATGTTCATTCATT
* * *
11451 TACGTTCGTTTATGTTCATTCGTT
1 TATGTTTGTTTATGTTCATTCATT
* *
11475 TATGTTTGTTTATGTACTTTCATT
1 TATGTTTGTTTATGTTCATTCATT
11499 TATGTTT
1 TATGTTT
11506 AGCCCAGTCT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.59
Consensus pattern (24 bp):
TATGTTTGTTTATGTTCATTCATT
Found at i:11695 original size:10 final size:10
Alignment explanation
Indices: 11677--11780 Score: 82
Period size: 10 Copynumber: 9.4 Consensus size: 10
11667 TCTATTTTCA
11677 TTTATGTTCG
1 TTTATGTTCG
* *
11687 TTTACGTTCA
1 TTTATGTTCG
*
11697 TTTATGTTCA
1 TTTATGTTCG
11707 TTTATTGTGTTCG
1 TTTA---TGTTCG
11720 TTTACGTTCGTTCG
1 TTTA---T-GTTCG
11734 TTTATGTTCG
1 TTTATGTTCG
*
11744 TTTACGTTCG
1 TTTATGTTCG
11754 TTTATTGTGTTCG
1 TTTA---TGTTCG
11767 TTTATGTTCG
1 TTTATGTTCG
11777 TTTA
1 TTTA
11781 CATCCGTTCG
Statistics
Matches: 78, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
10 49 0.63
11 1 0.01
13 19 0.24
14 9 0.12
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.58
Consensus pattern (10 bp):
TTTATGTTCG
Found at i:11698 original size:20 final size:20
Alignment explanation
Indices: 11673--11710 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
11663 AAAATCTATT
*
11673 TTCATTTATGTTCGTTTACG
1 TTCATTTATGTTCATTTACG
11693 TTCATTTATGTTCATTTA
1 TTCATTTATGTTCATTTA
11711 TTGTGTTCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (20 bp):
TTCATTTATGTTCATTTACG
Found at i:11723 original size:23 final size:23
Alignment explanation
Indices: 11692--11780 Score: 108
Period size: 23 Copynumber: 3.8 Consensus size: 23
11682 GTTCGTTTAC
* * *
11692 GTTCATTTATGTTCATTTATTGT
1 GTTCGTTTACGTTCGTTTATTGT
*
11715 GTTCGTTTACGTTCGTTCGT-TTAT
1 GTTCGTTTACGTTCGTT--TATTGT
11739 GTTCGTTTACGTTCGTTTATTGT
1 GTTCGTTTACGTTCGTTTATTGT
*
11762 GTTCGTTTATGTTCGTTTA
1 GTTCGTTTACGTTCGTTTA
11781 CATCCGTTCG
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.02
23 35 0.61
24 20 0.35
25 1 0.02
ACGTcount: A:0.11, C:0.12, G:0.19, T:0.57
Consensus pattern (23 bp):
GTTCGTTTACGTTCGTTTATTGT
Found at i:11734 original size:14 final size:14
Alignment explanation
Indices: 11715--11755 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
11705 CATTTATTGT
11715 GTTCGTTTACGTTC
1 GTTCGTTTACGTTC
11729 GTTCGTTTA---T-
1 GTTCGTTTACGTTC
11739 GTTCGTTTACGTTC
1 GTTCGTTTACGTTC
11753 GTT
1 GTT
11756 TATTGTGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
10 9 0.39
11 1 0.04
13 1 0.04
14 12 0.52
ACGTcount: A:0.07, C:0.17, G:0.22, T:0.54
Consensus pattern (14 bp):
GTTCGTTTACGTTC
Found at i:11758 original size:47 final size:47
Alignment explanation
Indices: 11682--11778 Score: 149
Period size: 47 Copynumber: 2.1 Consensus size: 47
11672 TTTCATTTAT
*
11682 GTTCGTTTACGTTCATTTATGTTCATTTATTGTGTTCGTTTACGTTC
1 GTTCGTTTACGTTCATTTACGTTCATTTATTGTGTTCGTTTACGTTC
* * * *
11729 GTTCGTTTATGTTCGTTTACGTTCGTTTATTGTGTTCGTTTATGTTC
1 GTTCGTTTACGTTCATTTACGTTCATTTATTGTGTTCGTTTACGTTC
11776 GTT
1 GTT
11779 TACATCCGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.10, C:0.13, G:0.20, T:0.57
Consensus pattern (47 bp):
GTTCGTTTACGTTCATTTACGTTCATTTATTGTGTTCGTTTACGTTC
Found at i:11771 original size:33 final size:35
Alignment explanation
Indices: 11715--11818 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 35
11705 CATTTATTGT
**
11715 GTTCGTTTACGTTCGTTCGTTTATGTTCGTTTA-C
1 GTTCGTTTATATTCGTTCGTTTATGTTCGTTTACC
11749 GTTCGTTTAT-TGT-GTTCGTTTATGTTCGTTTACATCC
1 GTTCGTTTATAT-TCGTTCGTTTATGTTCGTTT--A-CC
*
11786 GTTCGTTTATATTCGTTCATTTATGTTCGTTTA
1 GTTCGTTTATATTCGTTCGTTTATGTTCGTTTA
11819 TCATTTAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
33 19 0.31
34 10 0.16
35 1 0.02
36 1 0.02
37 12 0.20
38 18 0.30
ACGTcount: A:0.12, C:0.15, G:0.18, T:0.55
Consensus pattern (35 bp):
GTTCGTTTATATTCGTTCGTTTATGTTCGTTTACC
Found at i:11775 original size:57 final size:55
Alignment explanation
Indices: 11677--11802 Score: 155
Period size: 57 Copynumber: 2.2 Consensus size: 55
11667 TCTATTTTCA
* *
11677 TTTATGTTCGTTTACGTTCATTTATGTTCATTTATTGTGTTCGTTTACGTTCGTTCG
1 TTTATGTTCGTTTACGTTCATTTATGTTCATTTA-T-TGTTCGTTTACATCCGTTCG
* *
11734 TTTATGTTCGTTTACGTTCGTTTATTGTGTTCGTTTA-TGTTCGTTTACATCCGTTCG
1 TTTATGTTCGTTTACGTTCATTTA---TGTTCATTTATTGTTCGTTTACATCCGTTCG
*
11791 TTTATATTCGTT
1 TTTATGTTCGTT
11803 CATTTATGTT
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
57 52 0.85
60 9 0.15
ACGTcount: A:0.12, C:0.14, G:0.17, T:0.56
Consensus pattern (55 bp):
TTTATGTTCGTTTACGTTCATTTATGTTCATTTATTGTTCGTTTACATCCGTTCG
Found at i:11819 original size:24 final size:24
Alignment explanation
Indices: 11682--11819 Score: 109
Period size: 24 Copynumber: 5.8 Consensus size: 24
11672 TTTCATTTAT
* * *
11682 GTTCGTTTACGTTCATTTATGTTC
1 GTTCATTTATGTTCGTTTATGTTC
* * * *
11706 ATTTA-TTGTGTTCGTTTACGTTC
1 GTTCATTTATGTTCGTTTATGTTC
* *
11729 GTTCGTTTATGTTCGTTTACGTTC
1 GTTCATTTATGTTCGTTTATGTTC
* *
11753 GTTTA-TTGTGTTCGTTTATGTTC
1 GTTCATTTATGTTCGTTTATGTTC
* ** ** *
11776 GTTTACATCCGTTCGTTTATATTC
1 GTTCATTTATGTTCGTTTATGTTC
11800 GTTCATTTATGTTCGTTTAT
1 GTTCATTTATGTTCGTTTAT
11820 CATTTAAATG
Statistics
Matches: 88, Mismatches: 24, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
23 37 0.42
24 51 0.58
ACGTcount: A:0.12, C:0.14, G:0.17, T:0.56
Consensus pattern (24 bp):
GTTCATTTATGTTCGTTTATGTTC
Found at i:13419 original size:32 final size:33
Alignment explanation
Indices: 13383--13491 Score: 170
Period size: 33 Copynumber: 3.4 Consensus size: 33
13373 ACAAAGTTTA
*
13383 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTGAAATACTTAAAAACTTCCAAGTT
*
13415 CGATAAATTAAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTGAAATACTTAAAAACTTCCAAGTT
*
13448 CGATAAATTCAAATACTTAAAAACTT-CAAGTT
1 CGATAAATTGAAATACTTAAAAACTTCCAAGTT
13480 CGAT-AATTGAAA
1 CGATAAATTGAAA
13492 CAAAGTTTAC
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
31 7 0.10
32 14 0.19
33 51 0.71
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (33 bp):
CGATAAATTGAAATACTTAAAAACTTCCAAGTT
Found at i:13506 original size:21 final size:21
Alignment explanation
Indices: 13482--13521 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
13472 TTCAAGTTCG
*
13482 ATAATTGAAACAAAGTTTACA
1 ATAATTAAAACAAAGTTTACA
*
13503 ATAATTAAAATAAAGTTTA
1 ATAATTAAAACAAAGTTTA
13522 AAAATAAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (21 bp):
ATAATTAAAACAAAGTTTACA
Found at i:25117 original size:121 final size:121
Alignment explanation
Indices: 24903--25136 Score: 441
Period size: 121 Copynumber: 1.9 Consensus size: 121
24893 TACTACCACT
* * *
24903 GTTAGGCATTCAACCTAAATTAGTTGGCTAATGTATGATAGCTAGCTAATTAGGGTTTGTGGCAG
1 GTTAGGCATTCAACCTAAATCAGCTGGCTAATGAATGATAGCTAGCTAATTAGGGTTTGTGGCAG
24968 TTTTCTTATTTAAGTTTGGACAAAGTTTTGAAATATTGTGTGTGTGTGAGTGACAG
66 TTTTCTTATTTAAGTTTGGACAAAGTTTTGAAATATTGTGTGTGTGTGAGTGACAG
25024 GTTAGGCATTCAACCTAAATCAGCTGGCTAATGAATGATAGCTAGCTAATTAGGGTTTGTGGCAG
1 GTTAGGCATTCAACCTAAATCAGCTGGCTAATGAATGATAGCTAGCTAATTAGGGTTTGTGGCAG
25089 TTTTCTTATTTAAGTTTGGACAAAGTTTTGAAATATTGTGTGTGTGTG
66 TTTTCTTATTTAAGTTTGGACAAAGTTTTGAAATATTGTGTGTGTGTG
25137 TGTGTGTGTG
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
121 110 1.00
ACGTcount: A:0.26, C:0.10, G:0.25, T:0.38
Consensus pattern (121 bp):
GTTAGGCATTCAACCTAAATCAGCTGGCTAATGAATGATAGCTAGCTAATTAGGGTTTGTGGCAG
TTTTCTTATTTAAGTTTGGACAAAGTTTTGAAATATTGTGTGTGTGTGAGTGACAG
Found at i:30565 original size:23 final size:22
Alignment explanation
Indices: 30534--30586 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
30524 TCTTTTTTGT
* *
30534 ACGTATTTTTATATTTTTATGGC
1 ACGT-TTTTTATATTTCTATGAC
*
30557 ACGCTTTTTTATGTTTCTATGAC
1 ACG-TTTTTTATATTTCTATGAC
30580 ACGTTTT
1 ACGTTTT
30587 CGGTTGTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 21 0.81
24 1 0.04
ACGTcount: A:0.19, C:0.13, G:0.13, T:0.55
Consensus pattern (22 bp):
ACGTTTTTTATATTTCTATGAC
Found at i:31006 original size:2 final size:2
Alignment explanation
Indices: 30999--31049 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
30989 ATTAGAGGAT
30999 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31041 TA TA TA TA T
1 TA TA TA TA T
31050 TCTACCAACA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:32524 original size:20 final size:21
Alignment explanation
Indices: 32499--32550 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
32489 TGGAGCGTGG
32499 GGGGAATCGGTA-CCCCTTAT
1 GGGGAATCGGTACCCCCTTAT
32519 GGGGAATCGGTACCCCCTTAT
1 GGGGAATCGGTACCCCCTTAT
32540 GGGGAATCGGT
1 GGGGAATCGGT
32551 TCCCTAAGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 12 0.39
21 19 0.61
ACGTcount: A:0.19, C:0.23, G:0.35, T:0.23
Consensus pattern (21 bp):
GGGGAATCGGTACCCCCTTAT
Found at i:35318 original size:23 final size:22
Alignment explanation
Indices: 35290--35349 Score: 84
Period size: 23 Copynumber: 2.7 Consensus size: 22
35280 ATTCCCCTAA
35290 GGGGAATCGGTTCCCATTCAAAG
1 GGGGAATCGGTTCCCATTC-AAG
*
35313 GGGGAATCGGTTCCCCTTCAAG
1 GGGGAATCGGTTCCCATTCAAG
* *
35335 GGGGTATCGATTCCC
1 GGGGAATCGGTTCCC
35350 TCTACCCTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 16 0.47
23 18 0.53
ACGTcount: A:0.20, C:0.25, G:0.32, T:0.23
Consensus pattern (22 bp):
GGGGAATCGGTTCCCATTCAAG
Found at i:35335 original size:22 final size:22
Alignment explanation
Indices: 35269--35349 Score: 87
Period size: 22 Copynumber: 3.8 Consensus size: 22
35259 CCAGAACCCC
*
35269 AGGGGGTATCGATTCCCC-T-A
1 AGGGGGAATCGATTCCCCTTCA
* *
35289 A-GGGGAATCGGTTCCCATTCAA
1 AGGGGGAATCGATTCCCCTTC-A
*
35311 AGGGGGAATCGGTTCCCCTTCA
1 AGGGGGAATCGATTCCCCTTCA
*
35333 AGGGGGTATCGATTCCC
1 AGGGGGAATCGATTCCC
35350 TCTACCCTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
19 13 0.25
20 2 0.04
22 18 0.35
23 18 0.35
ACGTcount: A:0.21, C:0.25, G:0.31, T:0.23
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTTCA
Found at i:52489 original size:48 final size:49
Alignment explanation
Indices: 52398--52492 Score: 156
Period size: 49 Copynumber: 2.0 Consensus size: 49
52388 GCAGGATATG
* *
52398 AATTTAAAATTTATTTTTTTAAAGATATTTAAGAATATGGAAAAAAGGA
1 AATTTAAAATTCATTTTTTAAAAGATATTTAAGAATATGGAAAAAAGGA
*
52447 AATTTAAAATTCATTTTTTAAAAGATATTTAAGCATAT-GAAAAAAG
1 AATTTAAAATTCATTTTTTAAAAGATATTTAAGAATATGGAAAAAAG
52493 AGAGGAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
48 8 0.19
49 35 0.81
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (49 bp):
AATTTAAAATTCATTTTTTAAAAGATATTTAAGAATATGGAAAAAAGGA
Found at i:56201 original size:21 final size:22
Alignment explanation
Indices: 56151--56202 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
56141 GTCAATGGTT
* *
56151 CTATTTGGTCCTTCGGGGCAAA
1 CTATGTGGTCCTTCGGGACAAA
*
56173 CCTATGTGGTCTTTCGGGACAAA
1 -CTATGTGGTCCTTCGGGACAAA
56196 -TATGTGG
1 CTATGTGG
56203 CACTTCGCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 7 0.27
23 19 0.73
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (22 bp):
CTATGTGGTCCTTCGGGACAAA
Found at i:59603 original size:52 final size:52
Alignment explanation
Indices: 59541--59643 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
59531 AAATTGGACA
59541 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
*
59593 CATAGAAATAGGAGACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
59644 AATATTATAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (52 bp):
CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
Found at i:63361 original size:52 final size:52
Alignment explanation
Indices: 63283--63385 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
63273 TTATAATATT
63283 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
*
63335 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATG
63386 TGTCCAATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
Found at i:67959 original size:52 final size:52
Alignment explanation
Indices: 67881--67983 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
67871 TTATAATATT
67881 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
*
67933 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATG
67984 TGTCCAATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
Found at i:72589 original size:32 final size:32
Alignment explanation
Indices: 72543--72608 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
72533 TCATTACCTA
*
72543 TATCCTTTATTAATTTGATATTAATTTTAATT
1 TATCCTTTATTAATTTAATATTAATTTTAATT
* * * *
72575 TATCTTTTATTAATTTAATTTTTATTTTATTT
1 TATCCTTTATTAATTTAATATTAATTTTAATT
72607 TA
1 TA
72609 ATTTAATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.65
Consensus pattern (32 bp):
TATCCTTTATTAATTTAATATTAATTTTAATT
Found at i:74608 original size:14 final size:14
Alignment explanation
Indices: 74589--74618 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
74579 GGATCACCTT
74589 GACGGATCCCTCAA
1 GACGGATCCCTCAA
74603 GACGGATCCCTCAA
1 GACGGATCCCTCAA
74617 GA
1 GA
74619 TGGTCGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.33, G:0.23, T:0.13
Consensus pattern (14 bp):
GACGGATCCCTCAA
Found at i:84007 original size:64 final size:63
Alignment explanation
Indices: 83934--84054 Score: 152
Period size: 64 Copynumber: 1.9 Consensus size: 63
83924 CAAATAAATG
* * *
83934 AACATCGAATGCCATTAATGCATCGATGCATAAGGAGTGCATCGATGCACCCGCTTAAAATACA
1 AACATCGAATGACATTAATGCACCGATGCACAAGGAGTGCATCGATGCACCCG-TTAAAATACA
* ** * * *
83998 AACATCGAATGAGATTTGTGTACCGATGCACATGTAGTGCATCGATGCACCCGTTAA
1 AACATCGAATGACATTAATGCACCGATGCACAAGGAGTGCATCGATGCACCCGTTAA
84055 GGAATGCATC
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
63 4 0.08
64 44 0.92
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (63 bp):
AACATCGAATGACATTAATGCACCGATGCACAAGGAGTGCATCGATGCACCCGTTAAAATACA
Found at i:87943 original size:23 final size:23
Alignment explanation
Indices: 87913--87959 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
87903 ACTCAATCAT
* *
87913 ACACAATCCCAAGACTTTCGCAA
1 ACACAATCCCAAAACTTTCACAA
87936 ACACAATCCCAAAACTTTCACAA
1 ACACAATCCCAAAACTTTCACAA
87959 A
1 A
87960 ACTTTGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.45, C:0.34, G:0.04, T:0.17
Consensus pattern (23 bp):
ACACAATCCCAAAACTTTCACAA
Found at i:88177 original size:24 final size:25
Alignment explanation
Indices: 88145--88192 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 25
88135 TTTAGATTTG
88145 ATAAAATTATTAATATCAT-TTTTC
1 ATAAAATTATTAATATCATATTTTC
88169 ATAAAATTATTAATATCATATTTT
1 ATAAAATTATTAATATCATATTTT
88193 TATTTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (25 bp):
ATAAAATTATTAATATCATATTTTC
Done.