Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000642.1 Hibiscus syriacus cultivar Beakdansim tig00001242_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: 88049
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:260 original size:14 final size:14
Alignment explanation
Indices: 241--271 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
231 ATGGATGTTG
241 GATACTTGAACTTA
1 GATACTTGAACTTA
255 GATACTTGAACTTA
1 GATACTTGAACTTA
269 GAT
1 GAT
272 GCTTATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (14 bp):
GATACTTGAACTTA
Found at i:282 original size:2 final size:2
Alignment explanation
Indices: 275--320 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
265 CTTAGATGCT
275 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
316 TA TA T
1 TA TA T
321 TTGGTTTTGA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:584 original size:13 final size:13
Alignment explanation
Indices: 564--599 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
554 AAGGGGGGAG
*
564 TAATTTTCAAAAT
1 TAATTTTCAAAAA
*
577 TGATTTTCAAAAA
1 TAATTTTCAAAAA
590 TAATTTTCAA
1 TAATTTTCAA
600 TAAGAAAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (13 bp):
TAATTTTCAAAAA
Found at i:989 original size:54 final size:54
Alignment explanation
Indices: 921--1043 Score: 201
Period size: 54 Copynumber: 2.3 Consensus size: 54
911 CTCATAGGGT
* *
921 GTACTGATACCCCTATGCCAATTTTGGCTCTGAGAAAAACAGAATGCCAAATGG
1 GTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAACAGAATGCCAAATGG
* *
975 GTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAACAGAATGGCTAATGG
1 GTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAACAGAATGCCAAATGG
*
1029 GTACCTATACCCCTA
1 GTACCGATACCCCTA
1044 GTCATTTAAC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 64 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.24
Consensus pattern (54 bp):
GTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAACAGAATGCCAAATGG
Found at i:3690 original size:60 final size:60
Alignment explanation
Indices: 3567--3699 Score: 137
Period size: 60 Copynumber: 2.2 Consensus size: 60
3557 TCGGGTGATC
* * * * *
3567 ATTTTGTAACTTTTAATAGTCGGTGGACTCAACAAATCAACACCCTACAGTCAAAGGATT
1 ATTTTGTAACTTTTAATAATCAGTGAACTCAACAAATCAACACCCTACAATCAAAGGACT
* * * *
3627 ATTTTGTAACTTTTAATAATCAAG-GAACTCAACAAA-GAATCATCCTATAATCAAGGGACT
1 ATTTTGTAACTTTTAATAATC-AGTGAACTCAACAAATCAA-CACCCTACAATCAAAGGACT
3687 ATTTGTGT-ACTTT
1 ATTT-TGTAACTTT
3700 ACCCTAATTA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
59 2 0.03
60 55 0.90
61 4 0.07
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (60 bp):
ATTTTGTAACTTTTAATAATCAGTGAACTCAACAAATCAACACCCTACAATCAAAGGACT
Found at i:9460 original size:11 final size:11
Alignment explanation
Indices: 9444--9468 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9434 TATTCATAAC
9444 AAATTTAAAAT
1 AAATTTAAAAT
9455 AAATTTAAAAT
1 AAATTTAAAAT
9466 AAA
1 AAA
9469 ATAATTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATTTAAAAT
Found at i:10227 original size:23 final size:23
Alignment explanation
Indices: 10201--10245 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
10191 CACCACAGCT
*
10201 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
10224 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
10246 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:10483 original size:149 final size:149
Alignment explanation
Indices: 10213--10527 Score: 605
Period size: 149 Copynumber: 2.1 Consensus size: 149
10203 TATAATTGCA
10213 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
10277 TTCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTT
10342 CCAAAGAATATACATATGTC
130 CCAAAGAATATACATATGTC
10362 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
10427 TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTC
*
10492 CAAAGAATATATATATGTC
131 CAAAGAATATACATATGTC
10511 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
10528 CCCTCGACTC
Statistics
Matches: 164, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
148 1 0.01
149 163 0.99
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTC
CAAAGAATATACATATGTC
Found at i:11438 original size:18 final size:18
Alignment explanation
Indices: 11417--11451 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
11407 TCCCATCTAG
11417 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
11435 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
11452 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:12056 original size:21 final size:21
Alignment explanation
Indices: 12032--12076 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
12022 TGTTGTTCGT
* *
12032 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
12053 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
12074 TTG
1 TTG
12077 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:15353 original size:23 final size:23
Alignment explanation
Indices: 15327--15371 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
15317 CACCACAGCT
*
15327 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
15350 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
15372 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:15609 original size:149 final size:149
Alignment explanation
Indices: 15339--15653 Score: 596
Period size: 149 Copynumber: 2.1 Consensus size: 149
15329 TATAATTGCA
15339 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
*
15403 TTCCTTAAGAATCATATAAATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTT
65 TTCCTTAAGAATCATATAAATATGATAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTT
15468 CCAAAGAATATACATATGTC
130 CCAAAGAATATACATATGTC
15488 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
*
15553 TCCTTAAGAATCATATACATATGATAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTC
66 TCCTTAAGAATCATATAAATATGATAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTC
15618 CAAAGAATATACATATGTC
131 CAAAGAATATACATATGTC
15637 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
15654 CCCTCGACTC
Statistics
Matches: 163, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
148 1 0.01
149 162 0.99
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATAAATATGATAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTC
CAAAGAATATACATATGTC
Found at i:16563 original size:18 final size:18
Alignment explanation
Indices: 16540--16574 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
16530 TTCCATCTAG
16540 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
16558 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
16575 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:17178 original size:21 final size:21
Alignment explanation
Indices: 17154--17198 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
17144 TGTTGTTCGT
* *
17154 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
17175 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
17196 TTG
1 TTG
17199 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:18418 original size:14 final size:15
Alignment explanation
Indices: 18393--18422 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
18383 TATTAGATAA
18393 AATTTAAAATATATT
1 AATTTAAAATATATT
18408 AATTT-AAATATATT
1 AATTTAAAATATATT
18422 A
1 A
18423 TAAATAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTTAAAATATATT
Found at i:18447 original size:24 final size:24
Alignment explanation
Indices: 18389--18452 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
18379 ATATTATTAG
18389 ATAAA-ATTTA-AAATATATTAAT
1 ATAAATATTTATAAATATATTAAT
*
18411 TTAAATATATTATAAATA-ATTAAT
1 ATAAATAT-TTATAAATATATTAAT
18435 ATAAATTATTTATCAAAT
1 ATAAA-TATTTAT-AAAT
18453 TTAGTTTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
22 4 0.11
23 2 0.06
24 17 0.49
25 12 0.34
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAAATATTTATAAATATATTAAT
Found at i:24303 original size:18 final size:18
Alignment explanation
Indices: 24282--24320 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
24272 GCACTTGATA
*
24282 CTCTGGACGAGGTTGTTC
1 CTCTGGACGAGCTTGTTC
* *
24300 CTCTGGAGGTGCTTGTTC
1 CTCTGGACGAGCTTGTTC
24318 CTC
1 CTC
24321 GTGCTGCTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.26, G:0.31, T:0.36
Consensus pattern (18 bp):
CTCTGGACGAGCTTGTTC
Found at i:25985 original size:21 final size:22
Alignment explanation
Indices: 25903--25984 Score: 103
Period size: 23 Copynumber: 3.7 Consensus size: 22
25893 TAACCTCTAG
* *
25903 GGGGGTATCGATTCCCCTAC-A
1 GGGGGAATCGATTCCCCTTCAA
*
25924 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATTCCCCTTC-AA
*
25947 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATTCCCCTTCAA
*
25969 GGGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
25985 TCTGCACCAA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
21 17 0.31
22 16 0.30
23 21 0.39
ACGTcount: A:0.18, C:0.27, G:0.32, T:0.23
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:28357 original size:76 final size:76
Alignment explanation
Indices: 28225--28430 Score: 283
Period size: 76 Copynumber: 2.7 Consensus size: 76
28215 CAAAGCCAAA
* * * **
28225 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
28289 TTTGGCTCCGAG
65 TTTGGCTCCGAG
*
28301 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
* *
28366 TTTGTTCCGAG
66 TTGGCTCCGAG
* * *
28377 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGG-GGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCC
28431 TTGTACAACG
Statistics
Matches: 117, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
74 14 0.12
75 25 0.21
76 78 0.67
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.20
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTGGCTCCGAG
Found at i:34265 original size:21 final size:21
Alignment explanation
Indices: 34212--34271 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
34202 CCCCCCATGA
34212 GGGAACCGATTCCCCCTTTGA-AG
1 GGGAACCGATTCCCCC--T-ACAG
34235 GGGAACCGATTCCCCCTACAG
1 GGGAACCGATTCCCCCTACAG
* *
34256 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
34272 CTGGGGTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.03
21 17 0.50
23 16 0.47
ACGTcount: A:0.23, C:0.35, G:0.25, T:0.17
Consensus pattern (21 bp):
GGGAACCGATTCCCCCTACAG
Found at i:36224 original size:9 final size:8
Alignment explanation
Indices: 36203--36252 Score: 50
Period size: 9 Copynumber: 6.1 Consensus size: 8
36193 TGTTTCAACA
36203 TTTGGATAT
1 TTTGGAT-T
36212 TTTGGATT
1 TTTGGATT
36220 GTTT-GATT
1 -TTTGGATT
36228 TTGTGGATT
1 TT-TGGATT
*
36237 GTTGGA-T
1 TTTGGATT
36244 TTTGGATT
1 TTTGGATT
36252 T
1 T
36253 ATGAATGGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
7 8 0.23
8 12 0.34
9 15 0.43
ACGTcount: A:0.14, C:0.00, G:0.28, T:0.58
Consensus pattern (8 bp):
TTTGGATT
Found at i:36236 original size:17 final size:17
Alignment explanation
Indices: 36204--36247 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
36194 GTTTCAACAT
36204 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
36221 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
36238 TTGGATTTTG
1 TTGGATTTTG
36248 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:37004 original size:75 final size:76
Alignment explanation
Indices: 36852--37062 Score: 264
Period size: 75 Copynumber: 2.8 Consensus size: 76
36842 CAAAGCCAAA
* * * * *
36852 AATTCCAGATTGCTCAGAGGGAACCAATTCCCCCCCCCATAGGAGGAACCGATTCCCCCCTGAAT
1 AATTCCAGAATGCTCGGAGGGAACCGA-T--CCCCCCCATAGGAGGAACCGATTCCCCCCTAAAC
*
36917 GGTTTGGCTCCGAG
63 AGTTTGGCTCCGAG
* *
36931 ATTTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
* *
36995 TTTGTTCCGAG
66 TTGGCTCCGAG
* * *
37006 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCCT
37063 TGTACAACGG
Statistics
Matches: 116, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
75 86 0.74
76 6 0.05
78 1 0.01
79 23 0.20
ACGTcount: A:0.24, C:0.33, G:0.23, T:0.20
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTGGCTCCGAG
Found at i:39608 original size:22 final size:21
Alignment explanation
Indices: 39566--39605 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
39556 GAGATTCATT
*
39566 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
39587 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
39606 ATAACTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:46185 original size:17 final size:17
Alignment explanation
Indices: 46159--46199 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
46149 TTTTCAACAA
*
46159 AGTTGGTCTTTGCTTTG
1 AGTTGCTCTTTGCTTTG
46176 AGTTGCTCTTTGCTTTG
1 AGTTGCTCTTTGCTTTG
46193 AGTTGCT
1 AGTTGCT
46200 TCCCGTTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.07, C:0.15, G:0.27, T:0.51
Consensus pattern (17 bp):
AGTTGCTCTTTGCTTTG
Found at i:46594 original size:31 final size:31
Alignment explanation
Indices: 46559--46646 Score: 149
Period size: 31 Copynumber: 2.8 Consensus size: 31
46549 AAAGTAGATG
*
46559 CTTAAATTTTAGATAAAATATTAATTTAACT
1 CTTAAATTTTAAATAAAATATTAATTTAACT
*
46590 CTTAAATTTTAAATAAATTATTAATTTAACT
1 CTTAAATTTTAAATAAAATATTAATTTAACT
*
46621 CTTGAATTTTAAATAAAATATTAATT
1 CTTAAATTTTAAATAAAATATTAATT
46647 AACAATATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (31 bp):
CTTAAATTTTAAATAAAATATTAATTTAACT
Found at i:49391 original size:15 final size:15
Alignment explanation
Indices: 49369--49410 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
49359 TTTAATTTAA
49369 TATATATATATAATT
1 TATATATATATAATT
* *
49384 TTTATATATTTAATT
1 TATATATATATAATT
*
49399 TAAATATATATA
1 TATATATATATA
49411 TAGCCGGCCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATATATATATAATT
Found at i:49410 original size:38 final size:37
Alignment explanation
Indices: 49327--49412 Score: 120
Period size: 38 Copynumber: 2.3 Consensus size: 37
49317 AAATAATTAT
49327 TATATATATATATATAATATTAATAAATTTAATTTAA
1 TATATATATATATATAATATTAATAAATTTAATTTAA
* * * *
49364 TTTAATATATATATATAATTTTTATATATTTAATTTAA
1 TAT-ATATATATATATAATATTAATAAATTTAATTTAA
49402 -ATATATATATA
1 TATATATATATA
49413 GCCGGCCCGA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 9 0.21
37 3 0.07
38 31 0.72
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (37 bp):
TATATATATATATATAATATTAATAAATTTAATTTAA
Found at i:49556 original size:25 final size:25
Alignment explanation
Indices: 49518--49586 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
49508 AATCCCCGCG
*
49518 GTTTTTTAAGTGGGGAC-GAGTATGA
1 GTTTTTTAAATGGGGACGGA-TATGA
*
49543 GTTTTTTAAATGGGGATGGATATGA
1 GTTTTTTAAATGGGGACGGATATGA
* *
49568 ATTTTTTAAACGGGGACGG
1 GTTTTTTAAATGGGGACGG
49587 GGAGACCAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
25 36 0.95
26 2 0.05
ACGTcount: A:0.26, C:0.04, G:0.33, T:0.36
Consensus pattern (25 bp):
GTTTTTTAAATGGGGACGGATATGA
Found at i:50262 original size:134 final size:128
Alignment explanation
Indices: 50008--50272 Score: 476
Period size: 134 Copynumber: 2.0 Consensus size: 128
49998 AAAAACATAA
50008 TTTTATAAAAATTACAGTTTGACAATTTATATACAAAAAGTTCAAAAAAAAGTTCAATAACTTAT
1 TTTTATAAAAATTACAGTTTGACAATTTATATACAAAAAGTTCAAAAAAAAGTTCAATAACTTAT
50073 ATGTAATAAATAAACCAAAACTAATTATTTAAATTCACATATTTACTAACAAGTAGACTAACT
66 ATGTAATAAATAAACCAAAACTAATTATTTAAATTCACATATTTACTAACAAGTAGACTAACT
50136 TTTTATAAAAATTACAGTTTGACAATTTATATACAAAAAGTTCAAAAAAAAAAGTTCAATAACTT
1 TTTTATAAAAATTACAGTTTGACAATTTATATACAAAAAGTTC--AAAAAAAAGTTCAATAACTT
50201 ATATGTAATAAATAAACAAACCAAAACTAATTATTTAAATTCACATATTTACTAACAAGTAGACT
64 ATATGTAATAAAT----AAACCAAAACTAATTATTTAAATTCACATATTTACTAACAAGTAGACT
50266 AACT
125 AACT
50270 TTT
1 TTT
50273 CATTTTTTTT
Statistics
Matches: 131, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
128 43 0.33
130 33 0.25
134 55 0.42
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34
Consensus pattern (128 bp):
TTTTATAAAAATTACAGTTTGACAATTTATATACAAAAAGTTCAAAAAAAAGTTCAATAACTTAT
ATGTAATAAATAAACCAAAACTAATTATTTAAATTCACATATTTACTAACAAGTAGACTAACT
Found at i:69292 original size:25 final size:24
Alignment explanation
Indices: 69246--69292 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
69236 AAACTCAATA
* *
69246 ATTTGAAAATTAATAAATTTTTTT
1 ATTTGAAAATTAAGAAAATTTTTT
*
69270 ATTTCGAAAATTTAGAAAATTTT
1 ATTT-GAAAATTAAGAAAATTTT
69293 GGAAAAATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 4 0.21
25 15 0.79
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (24 bp):
ATTTGAAAATTAAGAAAATTTTTT
Found at i:69720 original size:21 final size:20
Alignment explanation
Indices: 69679--69739 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
69669 TCCCCTGTGG
69679 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT--CCTTC-AA
*
69702 GGTGGAATCGGTTCCTTCAA
1 GGGGGAATCGGTTCCTTCAA
* *
69722 GGGGGGATCGATTCCTTC
1 GGGGGAATCGGTTCCTTC
69740 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.50
21 5 0.15
23 12 0.35
ACGTcount: A:0.18, C:0.23, G:0.33, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGGTTCCTTCAA
Found at i:75092 original size:24 final size:26
Alignment explanation
Indices: 75037--75089 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
75027 ACTTAATGCA
75037 TATGGTGGGCACGACCTTATATGTAT
1 TATGGTGGGCACGACCTTATATGTAT
*
75063 TATGGTGGGCACGACCTTATGTGTAT
1 TATGGTGGGCACGACCTTATATGTAT
75089 T
1 T
75090 GGTATTTCGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.36
Consensus pattern (26 bp):
TATGGTGGGCACGACCTTATATGTAT
Found at i:76474 original size:3 final size:3
Alignment explanation
Indices: 76466--76491 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
76456 AAGAGGATAT
76466 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
76492 CAAAACTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:79387 original size:3 final size:3
Alignment explanation
Indices: 79376--79408 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
79366 ATGACATGAC
79376 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
79409 ATGATGTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:86829 original size:64 final size:64
Alignment explanation
Indices: 86737--86895 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 64
86727 GAATAAATTG
* * * *
86737 AACATCGAATGCATTTTATGCATTGATGCACATACCATGTATCGATACACTCAAGG-TT-TTATG
1 AACATCGAATGCACTTTATGCATCGATGCACAGACCATGCATCGATACACTC-AGGCTTGTT-TG
86800 A
64 A
* * *
86801 AATCATCGAATGCA-TTTATGCATCGATGCGCAGACCATGCATCGATGCACTCTGGCTTGTTTGA
1 AA-CATCGAATGCACTTTATGCATCGATGCACAGACCATGCATCGATACACTCAGGCTTGTTTGA
*
86865 AACATCGAATGCACTTCT-TTCATCGATGCAC
1 AACATCGAATGCACTT-TATGCATCGATGCAC
86896 TCTTAGTGCA
Statistics
Matches: 82, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
63 13 0.16
64 55 0.67
65 14 0.17
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (64 bp):
AACATCGAATGCACTTTATGCATCGATGCACAGACCATGCATCGATACACTCAGGCTTGTTTGA
Done.