Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003389.1 Hibiscus syriacus cultivar Beakdansim tig00007134_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: 60461
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:328 original size:40 final size:41
Alignment explanation
Indices: 257--533 Score: 219
Period size: 40 Copynumber: 6.6 Consensus size: 41
247 CAACGCGATT
** * *
257 TTGCGATAGTCCAAGTTCACGTTGCGATAGTCGAAGTTCGCG
1 TTGCGATTTTCCAAATT-ACGTTGCGATAGTCCAAGTTCGCG
*
299 TTGCGATTTTCCAAATT-TGTTGCGATAGTCCAAGTTCACGTCGAAG
1 TTGCGATTTTCCAAATTACGTTGCGATAGTCCAAGTT--CG-C---G
** * *
345 TTGCGATAGTCCAAGTTCACGTT-CGA-AGTTTTCCAAATT--CG
1 TTGCGATTTTCCAAATT-ACGTTGCGATAG---TCCAAGTTCGCG
** * * *
386 TTGCGATAGTCCAAGTTCACATTGCGATAGTCGAAGTTCGCG
1 TTGCGATTTTCCAAATT-ACGTTGCGATAGTCCAAGTTCGCG
428 TTGCGATTTTCCAAATT-CGTTGCGATAGTCCAAGTTCGCG
1 TTGCGATTTTCCAAATTACGTTGCGATAGTCCAAGTTCGCG
* * * *
468 TTGCGATAGTT-GAAGTTGCGTTGCGATAGTCCAAGTTCGCG
1 TTGCGAT-TTTCCAAATTACGTTGCGATAGTCCAAGTTCGCG
509 TTGCGATTTTCCAAATT-CGTTGCGA
1 TTGCGATTTTCCAAATTACGTTGCGA
534 ATTGCATTTG
Statistics
Matches: 193, Mismatches: 24, Indels: 38
0.76 0.09 0.15
Matches are distributed among these distances:
40 65 0.34
41 59 0.31
42 35 0.18
43 3 0.02
44 1 0.01
46 17 0.09
47 3 0.02
48 3 0.02
49 7 0.04
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.33
Consensus pattern (41 bp):
TTGCGATTTTCCAAATTACGTTGCGATAGTCCAAGTTCGCG
Found at i:355 original size:27 final size:28
Alignment explanation
Indices: 317--374 Score: 109
Period size: 27 Copynumber: 2.1 Consensus size: 28
307 TTCCAAATTT
317 GTTGCGATAGTCCAAGTTCACG-TCGAA
1 GTTGCGATAGTCCAAGTTCACGTTCGAA
344 GTTGCGATAGTCCAAGTTCACGTTCGAA
1 GTTGCGATAGTCCAAGTTCACGTTCGAA
372 GTT
1 GTT
375 TTCCAAATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 22 0.73
28 8 0.27
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (28 bp):
GTTGCGATAGTCCAAGTTCACGTTCGAA
Found at i:450 original size:61 final size:61
Alignment explanation
Indices: 257--494 Score: 327
Period size: 61 Copynumber: 3.8 Consensus size: 61
247 CAACGCGATT
* *
257 TTGCGATAGTCCAAGTTCACGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTTG
1 TTGCGATAGTCCAAGTTCACATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCG
* *
318 TTGCGATAGTCCAAGTTCACGTCGAAGTTGCGATAGTCCAAGTTCACGTT-CGAAGTTTTCCAAA
1 TTGCGATAGTCCAAGTTCA---C--A-TTGCGATAGTCGAAGTTCGCGTTGCG-A-TTTTCCAAA
382 TTCG
58 TTCG
386 TTGCGATAGTCCAAGTTCACATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCG
1 TTGCGATAGTCCAAGTTCACATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCG
* * *
447 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTTGAAGTT-GCGTTGCGAT
1 TTGCGATAGTCCAAGTTCACATTGCGATAGTCGAAGTTCGCGTTGCGAT
495 AGTCCAAGTT
Statistics
Matches: 159, Mismatches: 9, Indels: 19
0.85 0.05 0.10
Matches are distributed among these distances:
60 10 0.06
61 67 0.42
62 22 0.14
63 3 0.02
64 1 0.01
65 1 0.01
66 2 0.01
67 22 0.14
68 31 0.19
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (61 bp):
TTGCGATAGTCCAAGTTCACATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCG
Found at i:505 original size:81 final size:82
Alignment explanation
Indices: 384--533 Score: 248
Period size: 81 Copynumber: 1.8 Consensus size: 82
374 TTTCCAAATT
*
384 CGTTGCGATAGTCCAAGTTCACATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTT
1 CGTTGCGATAGTCCAAGTTCACATTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTT
449 GCGATAGTCCAAGTTCG
66 GCGATAGTCCAAGTTCG
** * *
466 CGTTGCGATAGTTGAAGTT-GCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTT
1 CGTTGCGATAGTCCAAGTTCACATTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTT
530 GCGA
66 GCGA
534 ATTGCATTTG
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
81 46 0.73
82 17 0.27
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.33
Consensus pattern (82 bp):
CGTTGCGATAGTCCAAGTTCACATTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTT
GCGATAGTCCAAGTTCG
Found at i:527 original size:21 final size:21
Alignment explanation
Indices: 257--515 Score: 230
Period size: 21 Copynumber: 12.3 Consensus size: 21
247 CAACGCGATT
*
257 TTGCGATAGTCCAAGTTCACG
1 TTGCGATAGTCCAAGTTCGCG
*
278 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
** * *
299 TTGCGATTTTCCAAATT--TG
1 TTGCGATAGTCCAAGTTCGCG
318 TTGCGATAGTCCAAGTTCACGTCGAAG
1 TTGCGATAGTCCAAGTT--CG-C---G
*
345 TTGCGATAGTCCAAGTTCACG
1 TTGCGATAGTCCAAGTTCGCG
*
366 TT-CGA-AGTTTTCCAAATT--CG
1 TTGCGATAG---TCCAAGTTCGCG
* *
386 TTGCGATAGTCCAAGTTCACA
1 TTGCGATAGTCCAAGTTCGCG
*
407 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
** *
428 TTGCGATTTTCCAAATT--CG
1 TTGCGATAGTCCAAGTTCGCG
447 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
**
468 TTGCGATAGTTGAAGTT-GCG
1 TTGCGATAGTCCAAGTTCGCG
488 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
509 TTGCGAT
1 TTGCGAT
516 TTTCCAAATT
Statistics
Matches: 191, Mismatches: 29, Indels: 36
0.75 0.11 0.14
Matches are distributed among these distances:
19 40 0.21
20 25 0.13
21 97 0.51
22 9 0.05
24 1 0.01
25 1 0.01
27 18 0.09
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.32
Consensus pattern (21 bp):
TTGCGATAGTCCAAGTTCGCG
Found at i:873 original size:65 final size:65
Alignment explanation
Indices: 764--942 Score: 295
Period size: 65 Copynumber: 2.8 Consensus size: 65
754 ATTGCCAACA
* *
764 CTTGGGAATCTTTTACACTATCGCAACATATTCTTTATTGTTTCAAACTAAGATCTTACAAATGG
1 CTTGAGAATCTTTTACACTATCGCAACACATTCTTTATTGTTTCAAACTAAGATCTTACAAATGG
* *
829 CTTGAGAATCTTTTATACTATCGCAACACAATCTTTATTGTTTCAAACTAAGATCTTACAAATGG
1 CTTGAGAATCTTTTACACTATCGCAACACATTCTTTATTGTTTCAAACTAAGATCTTACAAATGG
* * *
894 CTTGAGAATCTTATACACTATTGTAACACATTCTTTATTGTTTCAAACT
1 CTTGAGAATCTTTTACACTATCGCAACACATTCTTTATTGTTTCAAACT
943 CCACGTGAAT
Statistics
Matches: 105, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 105 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (65 bp):
CTTGAGAATCTTTTACACTATCGCAACACATTCTTTATTGTTTCAAACTAAGATCTTACAAATGG
Found at i:1060 original size:19 final size:19
Alignment explanation
Indices: 986--1070 Score: 82
Period size: 19 Copynumber: 4.2 Consensus size: 19
976 TATTTTGGAT
*
986 TTTTCACTATCGCAACAC-
1 TTTTAACTATCGCAACACA
*
1004 TTTTCACTATCGCAACAACA
1 TTTTAACTATCGCAAC-ACA
*
1024 CGTTTTTCAAACTCTCGCAACACA
1 ---TTTT--AACTATCGCAACACA
1048 TTTTAACTATCGCAACACA
1 TTTTAACTATCGCAACACA
1067 TTTT
1 TTTT
1071 TCAAAATCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
18 16 0.28
19 20 0.35
21 4 0.07
23 4 0.07
24 3 0.05
25 10 0.18
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.34
Consensus pattern (19 bp):
TTTTAACTATCGCAACACA
Found at i:1061 original size:44 final size:40
Alignment explanation
Indices: 995--1075 Score: 117
Period size: 44 Copynumber: 1.9 Consensus size: 40
985 TTTTTCACTA
*
995 TCGCAACACTTTTCACTATCGCAACAACACGTTTTTCAAACTC
1 TCGCAACACTTTTAACTATCGCAAC-ACA--TTTTTCAAACTC
1038 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
1 TCGCAACAC-TTTTAACTATCGCAACACATTTTTCAAA
1076 ATCGCGTTGC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
41 9 0.25
43 12 0.33
44 15 0.42
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.31
Consensus pattern (40 bp):
TCGCAACACTTTTAACTATCGCAACACATTTTTCAAACTC
Found at i:1064 original size:41 final size:41
Alignment explanation
Indices: 995--1075 Score: 110
Period size: 41 Copynumber: 1.9 Consensus size: 41
985 TTTTTCACTA
* *
995 TCGCAACACTTTTCACTATCGCAACAACACGTTTTTCAAACTC
1 TCGCAACACTTTTAACTATCG--ACAACACATTTTTCAAACTC
1038 TCGCAACACATTTTAACTATCG-CAACACATTTTTCAAA
1 TCGCAACAC-TTTTAACTATCGACAACACATTTTTCAAA
1076 ATCGCGTTGC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 15 0.43
43 9 0.26
44 11 0.31
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.31
Consensus pattern (41 bp):
TCGCAACACTTTTAACTATCGACAACACATTTTTCAAACTC
Found at i:2171 original size:181 final size:180
Alignment explanation
Indices: 1944--2416 Score: 716
Period size: 181 Copynumber: 2.6 Consensus size: 180
1934 ATCAACAGCC
* *
1944 ATATAACAGGTAAAAATATGATAAAACCGGTGTCATTATAATAAAACTGGTAAACCGCTACCGGA
1 ATATAACAGGT-AAAATATGATAAAA-CGGTGTCATTATGATAAAACCGGTAAACCGCTACCGGA
**
2009 TATATTGAAAGTGTCGATAAATTAATATAAGTATTAACACTTTTGTAATTTAAAAGAGAAGAAGT
64 TATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTTGTAATTTAAAAGAGAAGAAGT
* * *
2074 TATAGCGCCTATAAAGTGTCGATACTTTATACAAATGTATCGATATATAGTA
129 TATAGCGCCTAAAAAGTGTCGATACTTTATACAAATGTATCGATACATAGCA
*
2126 ATATAACAGGTAAAATATGATAAAATCGGTGTCATTATGATAAAACCGGTAAACCACTACCGGAT
1 ATATAACAGGTAAAATATGATAAAA-CGGTGTCATTATGATAAAACCGGTAAACCGCTACCGGAT
*
2191 ATATTGAAAATGTCGATAAATTAATATAAGTATCGACACTTTTGTAATTTAAAAGAGAAGAAGTT
65 ATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTTGTAATTTAAAAGAGAAGAAGTT
* *
2256 ATAGCGCCTAAAAAGTGTCGATATTTTATACAAATGTATCGATCCATAGCA
130 ATAGCGCCTAAAAAGTGTCGATACTTTATACAAATGTATCGATACATAGCA
* * * * *
2307 ATATAACAGGTAATAATATGACAAAACAGGTCTCGA-AATGATAAAACCGGTAATA-AGCTACCA
1 ATATAACAGGTAA-AATATGATAAAAC-GGTGTC-ATTATGATAAAACCGGTAA-ACCGCTACCG
*
2370 GATATATTGAAAGTGTCAATAAATTAATATAAGTATCGACACTTTTG
62 GATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTTG
2417 ATGGAGTTAA
Statistics
Matches: 267, Mismatches: 20, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
181 172 0.64
182 93 0.35
183 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (180 bp):
ATATAACAGGTAAAATATGATAAAACGGTGTCATTATGATAAAACCGGTAAACCGCTACCGGATA
TATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTTGTAATTTAAAAGAGAAGAAGTTA
TAGCGCCTAAAAAGTGTCGATACTTTATACAAATGTATCGATACATAGCA
Found at i:4133 original size:18 final size:19
Alignment explanation
Indices: 4087--4134 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
4077 AATGTAGGGT
* *
4087 TAATTTTGTATAAGCTTTT
1 TAATTTTGTATAAGATTTA
*
4106 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
4125 TAA-TTTGTAT
1 TAATTTTGTAT
4135 GTGAATGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.29, C:0.04, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:4624 original size:202 final size:197
Alignment explanation
Indices: 4276--4787 Score: 823
Period size: 202 Copynumber: 2.6 Consensus size: 197
4266 CATTCCAAGT
4276 ATACTTTGTGTCCAGAATGATTTCCTTACCAA-GTGCA-TGGAAATGTGTCGATACATTTATAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGT-CACT--AAATGTGTCGATACATTTATAAA
* *
4339 AAGTATCGATTCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAAC
63 AAGTATCGATCCAAAAAATATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAAC
*
4404 CGGTCTAAATATACCGGTTTATGAGAAAACAGGTGTACATAAAGTATCGACACTTGTTTAATTTG
128 CGGTCTAAATAAACCGGTTTATGAGAAAACAGGTGTACATAAAGTATCGACACTTGTTTAATTTG
4469 TGCCG
193 TGCCG
*
4474 ATCCCGTACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACTATAATGTGTCGATACCTTTAT
1 A-----TACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACTA-AATGTGTCGATACATTTAT
4539 -AAAAGTATCGATCCAAAAAATATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCT
60 AAAAAGTATCGATCCAAAAAATATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCT
* * *
4603 AACCGGTCTAAATAAACCGGTTTATGAGAAAACATGTGTACATGAAGTATCGACACTTTTTTAAT
125 AACCGGTCTAAATAAACCGGTTTATGAGAAAACAGGTGTACATAAAGTATCGACACTTGTTTAAT
*
4668 TTGTGTCG
190 TTGTGCCG
* *
4676 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTGTAAAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACTA-AATGTGTCGATACATTTATAAAAA
4741 GTATCGATCCAAAAAATATCGAGACCCATAATTATAATGTAATAGGT
65 GTATCGATCCAAAAAATATCGAGACCCATAATTATAATGTAATAGGT
4788 CATTTTGCAA
Statistics
Matches: 293, Mismatches: 12, Indels: 18
0.91 0.04 0.06
Matches are distributed among these distances:
197 55 0.19
198 52 0.18
202 132 0.45
203 51 0.17
204 3 0.01
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Consensus pattern (197 bp):
ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACTAAATGTGTCGATACATTTATAAAAAG
TATCGATCCAAAAAATATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCGG
TCTAAATAAACCGGTTTATGAGAAAACAGGTGTACATAAAGTATCGACACTTGTTTAATTTGTGC
CG
Found at i:4872 original size:198 final size:193
Alignment explanation
Indices: 4276--4877 Score: 764
Period size: 202 Copynumber: 3.0 Consensus size: 193
4266 CATTCCAAGT
**
4276 ATACTTTGTGTCCAGAATGATTTCCTTACCAA-GTGCATGGAAATGTGTCGATACATTTATAAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGT-CA-CCAAATGTGTCGATACATTTATAAAA
* *
4340 AGTATCGATTCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACC
64 AGTATCGATCCAAAAAATATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACC
4405 GGTCTAAATATACCGGTTTATGAGAAAACAGGTGTACATAAAGTATCGACACTTGTT-TAATTTG
129 GGTCTAAATATACCGGTTTATGAGAAAACA-G-GTACAT-AAGTATCGACACTT-TTAT-ATTTG
*
4469 TGCCG
189 TGTCG
* *
4474 ATCCCGTACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACTATAATGTGTCGATACCTTTAT
1 A-----TACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCA-AATGTGTCGATACATTTAT
4539 -AAAAGTATCGATCCAAAAAATATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCT
60 AAAAAGTATCGATCCAAAAAATATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCT
* *
4603 AACCGGTCTAAATAAACCGGTTTATGAGAAAACATGTGTACATGAAGTATCGACACTTTTTTAAT
125 AACCGGTCTAAATATACCGGTTTATGAGAAAACA-G-GTACAT-AAGTATCGACACTTTTAT-AT
4668 TTGTGTCG
186 TTGTGTCG
*
4676 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTGTAAAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCA-AATGTGTCGATACATTTATAAAAA
* * ** *
4741 GTATCGATCCAAAAAATATCGAGACCCATAATTATAATGTAATAGGT-CATTTTGCAAAGTAATC
65 GTATCGATCCAAAAAATATCGAGACCCATAATTATAATGTAATAGGTAAATTAT-CAATCTAACC
* ** ** *
4805 GGTATAAATATACCTATTTAATTTG-AAACAGGTCACCATAATGTATCGACACATTTTATAGTTG
129 GGTCTAAATATACCGGTTT-ATGAGAAAACAGGT-A-CATAA-GTATCGACAC-TTTTATATTTG
4869 TGTCG
189 TGTCG
4874 ATAC
1 ATAC
4878 ATTTTTAAAT
Statistics
Matches: 363, Mismatches: 26, Indels: 30
0.87 0.06 0.07
Matches are distributed among these distances:
196 2 0.01
197 63 0.17
198 105 0.29
199 8 0.02
201 2 0.01
202 130 0.36
203 51 0.14
204 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Consensus pattern (193 bp):
ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCAAATGTGTCGATACATTTATAAAAAG
TATCGATCCAAAAAATATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCGG
TCTAAATATACCGGTTTATGAGAAAACAGGTACATAAGTATCGACACTTTTATATTTGTGTCG
Found at i:5198 original size:15 final size:15
Alignment explanation
Indices: 5178--5206 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5168 AGAATCAGGG
5178 CTCTTCTCAACCCAT
1 CTCTTCTCAACCCAT
5193 CTCTTCTCAACCCA
1 CTCTTCTCAACCCA
5207 GATCTTCTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.48, G:0.00, T:0.31
Consensus pattern (15 bp):
CTCTTCTCAACCCAT
Found at i:5212 original size:15 final size:15
Alignment explanation
Indices: 5179--5214 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
5169 GAATCAGGGC
**
5179 TCTTCTCAACCCATC
1 TCTTCTCAACCCAGA
5194 TCTTCTCAACCCAGA
1 TCTTCTCAACCCAGA
5209 TCTTCT
1 TCTTCT
5215 GAGGAAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.19, C:0.42, G:0.03, T:0.36
Consensus pattern (15 bp):
TCTTCTCAACCCAGA
Found at i:7633 original size:24 final size:24
Alignment explanation
Indices: 7582--7634 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
7572 TTTCATTTAT
* * *
7582 AATTAGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATGTA
7606 AATTTGAGTTTGAATTTAAATGTA
1 AATTTGAGTTTGAATTTAAATGTA
7630 AATTT
1 AATTT
7635 TGGCTCCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATGTA
Found at i:8074 original size:12 final size:12
Alignment explanation
Indices: 8057--8081 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8047 CAACCAAAAC
8057 AAGTTCACAAAT
1 AAGTTCACAAAT
8069 AAGTTCACAAAT
1 AAGTTCACAAAT
8081 A
1 A
8082 TCAACACTTT
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:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (12 bp):
AAGTTCACAAAT
Found at i:8439 original size:201 final size:200
Alignment explanation
Indices: 8080--8914 Score: 936
Period size: 197 Copynumber: 4.2 Consensus size: 200
8070 AGTTCACAAA
* * **
8080 TATCAACACTTTATACATTTGTGTCGATACTTTGTGTCCATAATGTATTTTCCAACCAAAACAAG
1 TATCGACACTTTATACATTTGTGTCGATACTTTATGTCCATAATAAATTTT----CC-AAACAAG
* * * * * *
8145 TTCAC-AAATAAGTGTCGACACATTTATATCAAGTATCGATCCCAAAAACATCGAAACCCGTAAC
61 TTCACGAAA-AAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAAT
* * * * * *
8209 TATAATATAATAGGTCACTTTACAATGTAACCAGTTTAAATTTATAGGTTTTATGAGAAAATAGG
125 TATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAATTTATAGGTTTTATGAGAAAATAGG
*
8274 TCTACA-ATATG
190 TATACATA-ATG
* * * ** *
8285 TATCGACACTTTATTCATTTGTGTCGATACATGT-TGTCCAGAATGTA-TTTCCAAACCAAGTGC
1 TATCGACACTTTATACATTTGTGTCGATAC-TTTATGTCCATAATAAATTTTCCAAA-CAAGTTC
8348 ACGAAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTAT
64 ACG-AAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTAT
* * *** * * *
8413 AATGTAATAAGTAACATAAAAATGTAACCGGTCTAAA--TATACCATTTATTAAAAAAGAAAGGT
128 AATGTAATAGGTAACATAACAATGTAACCGGTCTAAATTTATAGGTTTTA-TGAGAAA-ATAGGT
8476 ATACATAATG
191 ATACATAATG
* * *
8486 TATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCAT
1 TATCGACACTTTATACATTTGTGTCGATACTTTATGTCCATAATAAATTTTCCAAACAAGTTCAC
* *
8551 GAAAAAGTGTCGATACATTTATAACAATTTTCGATCCCAAAAACATCGAAACACATAATTATAAT
66 GAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAAT
** **
8616 GTAATAGGTAACATAACAATGTAACCGGTCTAAACATACCGGTTATTA--A-AAAA-AGGTATAC
131 GTAATAGGTAACATAACAATGTAACCGGTCTAAATTTATAGGTT-TTATGAGAAAATAGGTATAC
8677 ATAATG
195 ATAATG
* *
8683 TATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCAC
1 TATCGACACTTTATACATTTGTGTCGATACTTTATGTCCATAATAAATTTTCCAAACAAGTTCAC
* * * * *
8748 GAAAAAGTGTCGATACGTTTAGAAAAAGTGTCGATCCTAAAAACATCGAAACCCATAATTATAAT
66 GAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAAT
* * * * * * * * *
8813 GTAATAGGTCACTTTACAATGTAACCGGTTTAATTTTCT-GATTTCATGAGAAAATAGGTCTACA
131 GTAATAGGTAACATAACAATGTAACCGGTCTAAATTTATAGGTTTTATGAGAAAATAGGTATACA
8877 TAATG
196 TAATG
* * * *
8882 CATCGACACTTTTTAAATTTATGTCGATACTTT
1 TATCGACACTTTATACATTTGTGTCGATACTTT
8915 TTAAAATTAC
Statistics
Matches: 544, Mismatches: 70, Indels: 38
0.83 0.11 0.06
Matches are distributed among these distances:
195 2 0.00
196 3 0.01
197 167 0.31
198 5 0.01
199 54 0.10
200 112 0.21
201 138 0.25
202 15 0.03
203 3 0.01
204 3 0.01
205 40 0.07
206 2 0.00
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.32
Consensus pattern (200 bp):
TATCGACACTTTATACATTTGTGTCGATACTTTATGTCCATAATAAATTTTCCAAACAAGTTCAC
GAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAAT
GTAATAGGTAACATAACAATGTAACCGGTCTAAATTTATAGGTTTTATGAGAAAATAGGTATACA
TAATG
Found at i:8501 original size:22 final size:21
Alignment explanation
Indices: 8475--8520 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
8465 AAAAGAAAGG
*
8475 TATACATAATGTATCGATACTT
1 TATACAT-ATGTATCGACACTT
* *
8497 TATACATTTGTGTCGACACTT
1 TATACATATGTATCGACACTT
8518 TAT
1 TAT
8521 GTCCATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.43
Consensus pattern (21 bp):
TATACATATGTATCGACACTT
Found at i:8697 original size:22 final size:21
Alignment explanation
Indices: 8672--8717 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
8662 TAAAAAAAGG
*
8672 TATACATAATGTATCGATACTT
1 TATACAT-ATGTATCGACACTT
* *
8694 TATACATTTGTGTCGACACTT
1 TATACATATGTATCGACACTT
8715 TAT
1 TAT
8718 GTCCATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.43
Consensus pattern (21 bp):
TATACATATGTATCGACACTT
Found at i:12432 original size:198 final size:198
Alignment explanation
Indices: 12071--12549 Score: 567
Period size: 198 Copynumber: 2.4 Consensus size: 198
12061 AATCAAAGAG
* *
12071 ACCGATAATTATAATGTAATAGGTAAATTTTCAATGTAACCGG-TAGAAATATACCGGGTTCATG
1 ACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTTA-AAATATACCGGGTTAATG
* * *
12135 AGAGAATAGGTCAACATAAAGTATCGACACTTTTTTAATTTGTGTCGATACATTTTTCCAAAATG
65 AGAGAATAGGTCAACATAAAGTATCGACACTCTTTAAATATGTGTCGATACATTTTTCCAAAATG
* * * *
12200 AATGGCAAACGAGGTGTACGCATAAAGTGTCGATACATTTGTAAAA-AGTATCGATCCTCG-AAA
130 AAAGACAAACGAGGTGCACACATAAAGTGTCGATACA-TT-TAAAATAGTATCGATCC-CGAAAA
*
12263 CATCGAA
192 CATCAAA
* * * *
12270 ATCGATAATTATTATGTAACAGGTAAATTTACAATGTAACCGGTTAAAATATACC-GGTTAATTA
1 ACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTTAAAATATACCGGGTTAATGA
* * * *
12334 GCA-AATAGGTCTACATTATGTATCGACACTCTTTAAATATGTGTCGATACTTTTTTCCAAAAT-
66 G-AGAATAGGTCAACATAAAGTATCGACACTCTTTAAATATGTGTCGATACATTTTTCCAAAATG
* *
12397 AAAGAACAAACGAGTTGCACACATAAAGTGTCGATACATTTAAAATTGTATCGATCCCGAAAACA
130 AAAG-ACAAACGAGGTGCACACATAAAGTGTCGATACATTTAAAATAGTATCGATCCCGAAAACA
12462 TCAAA
194 TCAAA
* * * * * ** * *
12467 ACCGAT-ATACATAATGTAATAGGTCAATTTATAATGTAACCGGTTTAAATTTACTAGTTTTATG
1 ACCGATAAT-TATAATGTAATAGGTAAATTTACAATGTAACCGGTTAAAATATACCGGGTTAATG
* *
12531 AGAAAATAGGTCAATATAA
65 AGAGAATAGGTCAACATAA
12550 GCACTACTTA
Statistics
Matches: 237, Mismatches: 35, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
196 9 0.04
197 68 0.29
198 109 0.46
199 49 0.21
200 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (198 bp):
ACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTTAAAATATACCGGGTTAATGA
GAGAATAGGTCAACATAAAGTATCGACACTCTTTAAATATGTGTCGATACATTTTTCCAAAATGA
AAGACAAACGAGGTGCACACATAAAGTGTCGATACATTTAAAATAGTATCGATCCCGAAAACATC
AAA
Found at i:22051 original size:24 final size:23
Alignment explanation
Indices: 21995--22051 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
21985 TATTAGTATT
21995 CATTTATTTATTATTTACGAACG
1 CATTTATTTATTATTTACGAACG
* *
22018 TATTCT-TTTATATGTTTACGAACG
1 CATT-TATTTAT-TATTTACGAACG
*
22042 CGTTTATTTA
1 CATTTATTTA
22052 ACGTTCGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.26, C:0.12, G:0.11, T:0.51
Consensus pattern (23 bp):
CATTTATTTATTATTTACGAACG
Found at i:33775 original size:8 final size:8
Alignment explanation
Indices: 33764--33789 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
33754 TCAAAGAAAC
33764 AAACTTGA
1 AAACTTGA
33772 AAACTTGA
1 AAACTTGA
33780 AAACTTGA
1 AAACTTGA
33788 AA
1 AA
33790 TTTTGGTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.23
Consensus pattern (8 bp):
AAACTTGA
Found at i:36426 original size:15 final size:15
Alignment explanation
Indices: 36406--36441 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
36396 ATATATTTAT
36406 TATTTAATACTACAA
1 TATTTAATACTACAA
36421 TATTTAATACTACAA
1 TATTTAATACTACAA
36436 TATTTA
1 TATTTA
36442 CATTATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (15 bp):
TATTTAATACTACAA
Found at i:39749 original size:13 final size:13
Alignment explanation
Indices: 39731--39755 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39721 ACTAGGGCAG
39731 GCTGAAATTTTCA
1 GCTGAAATTTTCA
39744 GCTGAAATTTTC
1 GCTGAAATTTTC
39756 GACAGTGACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
GCTGAAATTTTCA
Found at i:47252 original size:19 final size:20
Alignment explanation
Indices: 47228--47301 Score: 84
Period size: 19 Copynumber: 3.8 Consensus size: 20
47218 GTCTATTCAA
47228 AATAAATAT-ATAGATACAC
1 AATAAATATAATAGATACAC
* *
47247 AATAAATATAATCGATATGA-
1 AATAAATATAATAGATA-CAC
47267 AATAGAA-AT-ATAGATACAC
1 AATA-AATATAATAGATACAC
47286 AATAAATATAATAGAT
1 AATAAATATAATAGAT
47302 TTGGAATAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
18 3 0.07
19 21 0.47
20 18 0.40
21 3 0.07
ACGTcount: A:0.58, C:0.07, G:0.08, T:0.27
Consensus pattern (20 bp):
AATAAATATAATAGATACAC
Found at i:47270 original size:39 final size:38
Alignment explanation
Indices: 47227--47334 Score: 135
Period size: 39 Copynumber: 2.7 Consensus size: 38
47217 TGTCTATTCA
*
47227 AAATAAATATATAGATACACAATAAATATAATCGATATG
1 AAATAAA-ATATAGATACACAATAAATATAATAGATATG
*
47266 AAATAGAAATATAGATACACAATAAATATAATAGATTTGG
1 AAATA-AAATATAGATACACAATAAATATAATAGATAT-G
* * *
47306 AATAAAAAATATAGATGCACGATAAATAT
1 AA-ATAAAATATAGATACACAATAAATAT
47335 GACATCTATA
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
39 33 0.54
40 26 0.43
41 2 0.03
ACGTcount: A:0.56, C:0.06, G:0.10, T:0.27
Consensus pattern (38 bp):
AAATAAAATATAGATACACAATAAATATAATAGATATG
Found at i:47294 original size:17 final size:17
Alignment explanation
Indices: 47235--47295 Score: 52
Period size: 17 Copynumber: 3.3 Consensus size: 17
47225 CAAAATAAAT
47235 ATATAGATACACAATAA
1 ATATAGATACACAATAA
*
47252 ATATAATCGATATGA-AATAGAA
1 ATAT-A--GATA-CACAAT--AA
47274 ATATAGATACACAATAA
1 ATATAGATACACAATAA
47291 ATATA
1 ATATA
47296 ATAGATTTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
17 11 0.31
18 2 0.06
19 7 0.20
20 7 0.20
21 2 0.06
22 6 0.17
ACGTcount: A:0.57, C:0.08, G:0.08, T:0.26
Consensus pattern (17 bp):
ATATAGATACACAATAA
Found at i:50510 original size:20 final size:20
Alignment explanation
Indices: 50482--50524 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
50472 TTTATATAAA
*
50482 ATTTTCAAA-AATTAAAATTT
1 ATTTACAAATAATT-AAATTT
50502 ATTTACAAATAATTAAATTT
1 ATTTACAAATAATTAAATTT
50522 ATT
1 ATT
50525 AAATTAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTACAAATAATTAAATTT
Found at i:50535 original size:8 final size:9
Alignment explanation
Indices: 50511--50547 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
50501 TATTTACAAA
50511 TAATTAAAT
1 TAATTAAAT
*
50520 TTATTAAAT
1 TAATTAAAT
50529 TAA-TAAA-
1 TAATTAAAT
50536 TAATTAAAT
1 TAATTAAAT
50545 TAA
1 TAA
50548 AAAAATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
7 3 0.12
8 8 0.33
9 13 0.54
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
TAATTAAAT
Found at i:58221 original size:20 final size:20
Alignment explanation
Indices: 58161--58231 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
58151 AAATAACCAA
58161 CAAATTCGCAACACAATCT-
1 CAAATTCGCAACACAATCTC
58180 CAAATTCGCAACACGAA-CTC
1 CAAATTCGCAACAC-AATCTC
* * *
58200 CAATTTTGCAACACAATTTC
1 CAAATTCGCAACACAATCTC
58220 CAAATTCGCAAC
1 CAAATTCGCAAC
58232 TCAGTTTTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
19 18 0.41
20 26 0.59
ACGTcount: A:0.39, C:0.31, G:0.07, T:0.23
Consensus pattern (20 bp):
CAAATTCGCAACACAATCTC
Found at i:58285 original size:20 final size:20
Alignment explanation
Indices: 58262--58307 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
58252 GCTAATTTGG
*
58262 AATTCGCAACACAGAGGTCA
1 AATTCGCAACACAGAAGTCA
* *
58282 AATTCGCAACATATAAGTCA
1 AATTCGCAACACAGAAGTCA
58302 AATTCG
1 AATTCG
58308 TAAAGCGCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (20 bp):
AATTCGCAACACAGAAGTCA
Found at i:58899 original size:20 final size:21
Alignment explanation
Indices: 58879--58929 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
58869 TCGCAACGCG
* *
58879 ATTTTAGTTTTCGTGTTGCGA
1 ATTTAAGTTTTCGAGTTGCGA
*
58900 ATTTCA-TTTTCGAGTTGCGA
1 ATTTAAGTTTTCGAGTTGCGA
58920 ATTTAAGTTT
1 ATTTAAGTTT
58930 CAAGAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.20, C:0.10, G:0.20, T:0.51
Consensus pattern (21 bp):
ATTTAAGTTTTCGAGTTGCGA
Done.