Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002885.1 Hibiscus syriacus cultivar Beakdansim tig00005967_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: 60303
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5383 original size:85 final size:85
Alignment explanation
Indices: 5235--5400 Score: 262
Period size: 85 Copynumber: 2.0 Consensus size: 85
5225 CTATGACGCA
*
5235 TTATGACACGCATTTATGACGCTCATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAGATGACA
1 TTATGACACGCATTTATGACGCTCATTGCGCGTCATTGAAGCCACCGTCATAAATGAAGATGACA
* *
5300 CACATTTGTGTTTCATAAAT
66 CACATTCGTGTGTCATAAAT
* * *
5320 TTATTACACGCATTTATGAC-TTACATTGCGTGTCATTGAAGCCACCGTCATAAATGAAGATGAC
1 TTATGACACGCATTTATGACGCT-CATTGCGCGTCATTGAAGCCACCGTCATAAATGAAGATGAC
5384 ACACATTCGTGTGTCAT
65 ACACATTCGTGTGTCAT
5401 GATTGTATTT
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
84 1 0.01
85 73 0.99
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (85 bp):
TTATGACACGCATTTATGACGCTCATTGCGCGTCATTGAAGCCACCGTCATAAATGAAGATGACA
CACATTCGTGTGTCATAAAT
Found at i:5425 original size:2 final size:2
Alignment explanation
Indices: 5418--5450 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5408 TTTCGTAAAT
5418 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5451 TGTAGATTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11227 original size:650 final size:650
Alignment explanation
Indices: 9979--11280 Score: 2304
Period size: 650 Copynumber: 2.0 Consensus size: 650
9969 AATAGGTATT
* *
9979 CCTTTGGTATTTATTTCATTTTCACGTTGTAATAGTATCATAAGTGTCTGACGACTTGGGTCATG
1 CCTTTGGTATTTATTTCATTTTCACGTTGTAATAGCATCATAAATGTCTGACGACTTGGGTCATG
* *
10044 CTCTATAATCTTTAGAGGTACTACATCATTCAGGTTCATCTGTGTTTCCATAGTCTATCCAAAGA
66 CTCCATAATCTTTAGAGGCACTACATCATTCAGGTTCATCTGTGTTTCCATAGTCTATCCAAAGA
10109 CATTCACTTGATCCAAGTCATAAATGTATTAGGTCATCTTGGTATTCGAGGTTATTTTAGTCATT
131 CATTCACTTGATCCAAGTCATAAATGTATTAGGTCATCTTGGTATTCGAGGTTATTTTAGTCATT
* * *
10174 TGGGGCCCAAACATATTAGCTATTTCAAAACTTGAGGATAATCCATCATTTAAATACTCCAGTGA
196 TGGGGCCAAAACACATTAGCTATTTCAAAACTTGAGGATAATCAATCATTTAAATACTCCAGTGA
* *
10239 TGTGTCGTACATTCAGTAATCCAGTCCTCAGACGATCATTCAAAAACAAGGAGATTGATGTATTA
261 TGTGTCG-ACATTAAGTAATCCAGTCCTCAGACGATCATTCAAAAACAAGGAGATTGACGTATTA
*
10304 AGAATTTTCAAATATAGAAGTTTGTTTTTGGGTTTTTCAAATAGATCAGGAATTTAATCGGTGGT
325 AGAATTTTCAAATATAGAAGTTTATTTTTGGGTTTTTCAAATAGATCAGGAATTTAATCGGTGGT
* * *
10369 TTCAAGATTCAAGTGAATCAAAATATGAGTTCTCAGCTCGTTTTCATTATCATAGTCATTCATAG
390 TTCAAGATTCAAATGAATCAAAATATGAGTTCTCAGCTCGTCTTCATTATCATAGTCATCCATAG
10434 TCCTTTTTACACTTTAAGGGTATTATCGTCATTCCATTCAATTCTATCAGTGACATTACTTCCGA
455 TCCTTTTTACACTTTAAGGGTATTATCGTCATTCCATTCAATTCTATCAGTGACATTACTTCCGA
*
10499 TAAATTAGACTTCAAAGTATTCTAGTTCTTTTAGAGTTCAAGGTATTGGTCATTTGAACATTAGA
520 TAAATTAGACTTCAAAGTATTCTAGTTCCTTTAGAGTTCAAGGTATTGGTCATTTGAACATTAGA
10564 AGTTATTTTAGTTATTTCGTAGCTCGAGGACAGTTCTGTAATTT-AGATCAACACAAACATATGT
585 AGTTATTTTAGTTATTTCGTAGCTCGAGGACAGTTCTGTAATTTAAGATCAACACAAACATATGT
10628 A
650 A
* * *
10629 CCTTTGTTATTTATTTCATTTTCACGTTGTAATAGCATCCTAAATGTCTGACTACTTGGGTCATG
1 CCTTTGGTATTTATTTCATTTTCACGTTGTAATAGCATCATAAATGTCTGACGACTTGGGTCATG
*
10694 CTCCATAATCTTTAGAGGCACTACATCATTCAGGTTCATTTGTGTTTCCATAGTCTATCCAAAGA
66 CTCCATAATCTTTAGAGGCACTACATCATTCAGGTTCATCTGTGTTTCCATAGTCTATCCAAAGA
*
10759 CATTCACTTGATCTAAGTCATAAATGTATTAGGTCATCTTGGTATTCGAGGTTATTTTAGTCATT
131 CATTCACTTGATCCAAGTCATAAATGTATTAGGTCATCTTGGTATTCGAGGTTATTTTAGTCATT
10824 TGGGGCCAAAACACATTAGCTATTTCAAAACTTGAGGATAATCAATCATTTAAATACTCCAGTGA
196 TGGGGCCAAAACACATTAGCTATTTCAAAACTTGAGGATAATCAATCATTTAAATACTCCAGTGA
*
10889 TGTGTC-ACACTTAAAGTAATCCAGTCCTCAGACGATCATTCAAAAACAAGGGGATTGACGTATT
261 TGTGTCGACA-TT-AAGTAATCCAGTCCTCAGACGATCATTCAAAAACAAGGAGATTGACGTATT
10953 AAGAATTTTCAAATATAGAAGTTTATTTTTAGGG-TTTTCAAATAGATCAGGAATTTAATCGGTG
324 AAGAATTTTCAAATATAGAAGTTTATTTTT-GGGTTTTTCAAATAGATCAGGAATTTAATCGGTG
* *
11017 GTTTCAAGATTCAAATGAATCAAAATATGGGTTCTCAGGTCGTCTTCATTATCATAGTCATCCAT
388 GTTTCAAGATTCAAATGAATCAAAATATGAGTTCTCAGCTCGTCTTCATTATCATAGTCATCCAT
* *
11082 AGTCCTTTTTACACTTTAAGTGTATTATCGTCATTCCATTCAATTCTATCAGTGACATTACTTCT
453 AGTCCTTTTTACACTTTAAGGGTATTATCGTCATTCCATTCAATTCTATCAGTGACATTACTTCC
*
11147 GATAAATTAGACTTCAAAGTATTCTAGTTCCTTTAGAGTTCAAGGTATTGGTCATTTGAACATTG
518 GATAAATTAGACTTCAAAGTATTCTAGTTCCTTTAGAGTTCAAGGTATTGGTCATTTGAACATTA
* *
11212 GAGGTTATTTTAGTTATTTCGTAGCTCGAGGACATTTCTGTAATTTAAGATCAACACAAACATAT
583 GAAGTTATTTTAGTTATTTCGTAGCTCGAGGACAGTTCTGTAATTTAAGATCAACACAAACATAT
11277 GTA
648 GTA
11280 C
1 C
11281 ATTTTCTGAT
Statistics
Matches: 621, Mismatches: 27, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
648 3 0.00
649 2 0.00
650 591 0.95
651 25 0.04
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Consensus pattern (650 bp):
CCTTTGGTATTTATTTCATTTTCACGTTGTAATAGCATCATAAATGTCTGACGACTTGGGTCATG
CTCCATAATCTTTAGAGGCACTACATCATTCAGGTTCATCTGTGTTTCCATAGTCTATCCAAAGA
CATTCACTTGATCCAAGTCATAAATGTATTAGGTCATCTTGGTATTCGAGGTTATTTTAGTCATT
TGGGGCCAAAACACATTAGCTATTTCAAAACTTGAGGATAATCAATCATTTAAATACTCCAGTGA
TGTGTCGACATTAAGTAATCCAGTCCTCAGACGATCATTCAAAAACAAGGAGATTGACGTATTAA
GAATTTTCAAATATAGAAGTTTATTTTTGGGTTTTTCAAATAGATCAGGAATTTAATCGGTGGTT
TCAAGATTCAAATGAATCAAAATATGAGTTCTCAGCTCGTCTTCATTATCATAGTCATCCATAGT
CCTTTTTACACTTTAAGGGTATTATCGTCATTCCATTCAATTCTATCAGTGACATTACTTCCGAT
AAATTAGACTTCAAAGTATTCTAGTTCCTTTAGAGTTCAAGGTATTGGTCATTTGAACATTAGAA
GTTATTTTAGTTATTTCGTAGCTCGAGGACAGTTCTGTAATTTAAGATCAACACAAACATATGTA
Found at i:12229 original size:22 final size:22
Alignment explanation
Indices: 12204--12257 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
12194 ATAAGATATG
*
12204 AAGTCAACGATCAGACCGGTCA
1 AAGTCAACGATCAGACCAGTCA
*
12226 AAGTCAACAATCAGACCAGTCA
1 AAGTCAACGATCAGACCAGTCA
*
12248 ACGGTCAACG
1 A-AGTCAACG
12258 GGTTTGATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 21 0.78
23 6 0.22
ACGTcount: A:0.39, C:0.28, G:0.20, T:0.13
Consensus pattern (22 bp):
AAGTCAACGATCAGACCAGTCA
Found at i:15436 original size:15 final size:16
Alignment explanation
Indices: 15408--15442 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
15398 TTAAATGCAT
15408 TTTTCTTTTAAAATTA
1 TTTTCTTTTAAAATTA
*
15424 TTTT-TTTTGAAATTA
1 TTTTCTTTTAAAATTA
15439 TTTT
1 TTTT
15443 AAAGGATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (16 bp):
TTTTCTTTTAAAATTA
Found at i:18893 original size:18 final size:18
Alignment explanation
Indices: 18870--18916 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
18860 AGTGCACATA
18870 ATATCTCCTAATTATAAG
1 ATATCTCCTAATTATAAG
18888 ATATCTCCTAATTATAAG
1 ATATCTCCTAATTATAAG
18906 ATATCTCCTAA
1 ATATCTCCTAA
18917 GGTAATACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.38
Consensus pattern (18 bp):
ATATCTCCTAATTATAAG
Found at i:23382 original size:21 final size:21
Alignment explanation
Indices: 23356--23403 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
23346 CTTAAACTAA
23356 ATGCTGCCAAATGTGAATTTT
1 ATGCTGCCAAATGTGAATTTT
*
23377 ATGCTGCTAAATGTGAATTTT
1 ATGCTGCCAAATGTGAATTTT
23398 ATGCTG
1 ATGCTG
23404 TTGGAATCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (21 bp):
ATGCTGCCAAATGTGAATTTT
Found at i:25019 original size:2 final size:2
Alignment explanation
Indices: 25012--25162 Score: 284
Period size: 2 Copynumber: 75.5 Consensus size: 2
25002 GATGTATGTA
25012 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
25054 TG TG TG TG AG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
25096 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
25138 TG TG TG TG CG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
25163 TATTAATTAG
Statistics
Matches: 145, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 145 1.00
ACGTcount: A:0.01, C:0.01, G:0.50, T:0.49
Consensus pattern (2 bp):
TG
Found at i:25236 original size:2 final size:2
Alignment explanation
Indices: 25229--25253 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25219 TTATATTGTA
25229 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
25254 AAAGCTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30231 original size:2 final size:2
Alignment explanation
Indices: 30224--30277 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
30214 ATTAATATTA
30224 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30266 AT AT AT AT -T AT A
1 AT AT AT AT AT AT A
30278 ATTACGATGA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30281 original size:6 final size:7
Alignment explanation
Indices: 30214--30281 Score: 63
Period size: 8 Copynumber: 9.6 Consensus size: 7
30204 ATCGTAACCC
30214 ATTA-AT
1 ATTATAT
30220 ATTA-AT
1 ATTATAT
30226 A-TATAT
1 ATTATAT
30232 ATATATAT
1 AT-TATAT
30240 ATATATAT
1 AT-TATAT
30248 ATATATAT
1 AT-TATAT
30256 ATATATAT
1 AT-TATAT
30264 ATATATAT
1 AT-TATAT
30272 ATTATA-
1 ATTATAT
30278 ATTA
1 ATTA
30282 CGATGATAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
5 2 0.03
6 14 0.24
7 4 0.07
8 39 0.66
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (7 bp):
ATTATAT
Found at i:34357 original size:60 final size:60
Alignment explanation
Indices: 34243--34359 Score: 148
Period size: 60 Copynumber: 1.9 Consensus size: 60
34233 ATAAAATTGG
* * * *
34243 AATGTTAAAAAATTTGGGGGCCAATTTAAAATGAAGGTCATAGTTTGATGATGAAATCAA
1 AATGTTAAAAAAATTGGGGACCAATTTAAAATGAAAGTCATAGTTTGATAATGAAATCAA
**
34303 AATGTTAAAAAAATTGGGGATTAATTTAAAAT-AATAGTCATAGTTT-ATAAATGAAAT
1 AATGTTAAAAAAATTGGGGACCAATTTAAAATGAA-AGTCATAGTTTGAT-AATGAAAT
34360 TGAAACATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 4 0.08
60 45 0.92
ACGTcount: A:0.45, C:0.04, G:0.18, T:0.32
Consensus pattern (60 bp):
AATGTTAAAAAAATTGGGGACCAATTTAAAATGAAAGTCATAGTTTGATAATGAAATCAA
Found at i:48463 original size:17 final size:19
Alignment explanation
Indices: 48441--48481 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
48431 TCATAGTAAA
48441 TATTTTTA-T-TAATAATT
1 TATTTTTATTCTAATAATT
48458 TATTTTTATTCGTAATAATT
1 TATTTTTATTC-TAATAATT
48478 TATT
1 TATT
48482 ATTTTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.38
18 1 0.05
20 12 0.57
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
TATTTTTATTCTAATAATT
Found at i:48559 original size:11 final size:12
Alignment explanation
Indices: 48543--48571 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
48533 CTTCTTTTGG
48543 AAAAATAAAA-T
1 AAAAATAAAACT
48554 AAAAATAAAACT
1 AAAAATAAAACT
48566 AAAAAT
1 AAAAAT
48572 TATTTGAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAAATAAAACT
Found at i:49130 original size:107 final size:107
Alignment explanation
Indices: 49009--49226 Score: 382
Period size: 107 Copynumber: 2.0 Consensus size: 107
48999 AATAAATTAA
* * * *
49009 AATATAAATAAACTGATTTTTTAAACTTAAAAGAGTTTTGTAATATTGAGATTTAAATCATTTTA
1 AATATAAATAAACTGATTTTTTAAACTTAAAAGAGTTTTGAAATACTGAAATTTAAATAATTTTA
*
49074 GTTTTACAATACTGAAATTTAAATAATCCATACAACTACAAT
66 GTTTTACAAAACTGAAATTTAAATAATCCATACAACTACAAT
49116 AATATAAATAAACTGATTTTTTAAACTTAAAAGAGTTTTGAAATACTGAAATTTAAATAATTTTA
1 AATATAAATAAACTGATTTTTTAAACTTAAAAGAGTTTTGAAATACTGAAATTTAAATAATTTTA
*
49181 GTTTTACAAAACTGAAATTTAAATAATCGATACAACTACAAT
66 GTTTTACAAAACTGAAATTTAAATAATCCATACAACTACAAT
49223 AATA
1 AATA
49227 ATTTTTTTAA
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
107 105 1.00
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (107 bp):
AATATAAATAAACTGATTTTTTAAACTTAAAAGAGTTTTGAAATACTGAAATTTAAATAATTTTA
GTTTTACAAAACTGAAATTTAAATAATCCATACAACTACAAT
Found at i:49343 original size:201 final size:189
Alignment explanation
Indices: 49116--49635 Score: 735
Period size: 201 Copynumber: 2.7 Consensus size: 189
49106 CAACTACAAT
49116 AATATAAATAAACTGATTTTTTAAACTTAAAAGAGTTTTGAAATACTGAAATTTAAATAATTTTA
1 AATATAAATAAACTGATTTTTTAAACTTAAAAGAGTTTTGAAATACTGAAATTTAAATAATTTTA
* *
49181 GTTTTACAAAACTGAAATTTAAATAATCGATACAACTACAATAATAATTTTTTTAAAATAAATCA
66 GTTTTACAATATTGAAATTTAAATAATC-ATACAACTACAATAATAATTTTTTTAAAATAAATCA
*
49246 ATTCATACTAATAAATTATTTAATAAATAAACTTATTAAATTAACGTCTGCAGACTGTTAAAATA
130 ATTCATACTAATAAATTATTTAATAAATAAACTTATTAAATTAACATCTGCAGACTG--------
*
49311 AATTAA
187 --CT-A
* * * * *
49317 AATATAAATAAACTAATTTTTTAAACTTAAAAGAGTTTTGTAATATTGAGATTTAAATCATTTTA
1 AATATAAATAAACTGATTTTTTAAACTTAAAAGAGTTTTGAAATACTGAAATTTAAATAATTTTA
49382 GTTTTACAATATTGAAATTTAAATAATCCATACAACTACAATAATATATTTTTTTAAAATAAATC
66 GTTTTACAATATTGAAATTTAAATAAT-CATACAACTACAATAATA-ATTTTTTTAAAATAAATC
*
49447 AATTCATACTAATAAATTATTTAATAAATAATCTTATTAAATTAACATCTGCAGACTGCTA
129 AATTCATACTAATAAATTATTTAATAAATAAACTTATTAAATTAACATCTGCAGACTGCTA
* * * *
49508 AA-AT--A-AAA-TGATTTTTTAAACATATAAGTATTTTTGCAATACTGAAATTTAAATAATTTT
1 AATATAAATAAACTGATTTTTTAAACTTAAAAG-AGTTTTGAAATACTGAAATTTAAATAATTTT
49568 AGTTTTACAATATTGAAATTTAAATAATTCATACAACTACAATAATAATTTTTTTAAAATAAATC
65 AGTTTTACAATATTGAAATTTAAATAA-TCATACAACTACAATAATAATTTTTTTAAAATAAATC
49633 AAT
129 AAT
49636 CTATATTTTT
Statistics
Matches: 297, Mismatches: 18, Indels: 23
0.88 0.05 0.07
Matches are distributed among these distances:
186 38 0.13
187 74 0.25
188 2 0.01
190 2 0.01
191 3 0.01
192 1 0.00
201 102 0.34
202 75 0.25
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.39
Consensus pattern (189 bp):
AATATAAATAAACTGATTTTTTAAACTTAAAAGAGTTTTGAAATACTGAAATTTAAATAATTTTA
GTTTTACAATATTGAAATTTAAATAATCATACAACTACAATAATAATTTTTTTAAAATAAATCAA
TTCATACTAATAAATTATTTAATAAATAAACTTATTAAATTAACATCTGCAGACTGCTA
Found at i:49366 original size:308 final size:308
Alignment explanation
Indices: 48808--49429 Score: 1154
Period size: 308 Copynumber: 2.0 Consensus size: 308
48798 AATAAACTGA
*
48808 AATATAAATAAACTGATTTTTTAAACTTAAAAGAGTTTTGCAATACTGAAATTTAAATAATTTTA
1 AATATAAATAAACTGATTTTTTAAACTTAAAAGAGTTTTGAAATACTGAAATTTAAATAATTTTA
*
48873 GTTTTAAAAAACTGAAATTTAAATAATCGATACAACTACAATAATGATTTTTTTAAAATAAATCA
66 GTTTTAAAAAACTGAAATTTAAATAATCGATACAACTACAATAATAATTTTTTTAAAATAAATCA
* *
48938 ATCCATACTAATAAATTATTTAATAAATAACCTTATTAAATTAGCATCTACAGACTGTTAAAATA
131 ATCCATACTAATAAATTATTTAATAAATAAACTTATTAAATTAACATCTACAGACTGTTAAAATA
*
49003 AATTAAAATATAAATAAACTGATTTTTTAAACTTAAAAGAGTTTTGTAATATTGAGATTTAAATC
196 AATTAAAATATAAATAAACTAATTTTTTAAACTTAAAAGAGTTTTGTAATATTGAGATTTAAATC
49068 ATTTTAGTTTTACAATACTGAAATTTAAATAATCCATACAACTACAAT
261 ATTTTAGTTTTACAATACTGAAATTTAAATAATCCATACAACTACAAT
49116 AATATAAATAAACTGATTTTTTAAACTTAAAAGAGTTTTGAAATACTGAAATTTAAATAATTTTA
1 AATATAAATAAACTGATTTTTTAAACTTAAAAGAGTTTTGAAATACTGAAATTTAAATAATTTTA
*
49181 GTTTTACAAAACTGAAATTTAAATAATCGATACAACTACAATAATAATTTTTTTAAAATAAATCA
66 GTTTTAAAAAACTGAAATTTAAATAATCGATACAACTACAATAATAATTTTTTTAAAATAAATCA
* * *
49246 ATTCATACTAATAAATTATTTAATAAATAAACTTATTAAATTAACGTCTGCAGACTGTTAAAATA
131 ATCCATACTAATAAATTATTTAATAAATAAACTTATTAAATTAACATCTACAGACTGTTAAAATA
49311 AATTAAAATATAAATAAACTAATTTTTTAAACTTAAAAGAGTTTTGTAATATTGAGATTTAAATC
196 AATTAAAATATAAATAAACTAATTTTTTAAACTTAAAAGAGTTTTGTAATATTGAGATTTAAATC
*
49376 ATTTTAGTTTTACAATATTGAAATTTAAATAATCCATACAACTACAAT
261 ATTTTAGTTTTACAATACTGAAATTTAAATAATCCATACAACTACAAT
49424 AATATA
1 AATATA
49430 TTTTTTTAAA
Statistics
Matches: 304, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
308 304 1.00
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (308 bp):
AATATAAATAAACTGATTTTTTAAACTTAAAAGAGTTTTGAAATACTGAAATTTAAATAATTTTA
GTTTTAAAAAACTGAAATTTAAATAATCGATACAACTACAATAATAATTTTTTTAAAATAAATCA
ATCCATACTAATAAATTATTTAATAAATAAACTTATTAAATTAACATCTACAGACTGTTAAAATA
AATTAAAATATAAATAAACTAATTTTTTAAACTTAAAAGAGTTTTGTAATATTGAGATTTAAATC
ATTTTAGTTTTACAATACTGAAATTTAAATAATCCATACAACTACAAT
Found at i:54576 original size:24 final size:23
Alignment explanation
Indices: 54549--54595 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
54539 TAGAGATTTT
* *
54549 TATAAAAATAGATAATTAAAATAA
1 TATAAAAATA-AAAAATAAAATAA
*
54573 TATAATAATAAAAAATAAAATAA
1 TATAAAAATAAAAAATAAAATAA
54596 AAATTTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (23 bp):
TATAAAAATAAAAAATAAAATAA
Found at i:55741 original size:23 final size:21
Alignment explanation
Indices: 55696--55750 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
55686 TATTTATATG
* *
55696 AATATATAAAATATTAAATTA
1 AATATATAAAATAATAAAATA
55717 AATATATATAAATAATAATAATA
1 AATATATA-AAATAATAA-AATA
*
55740 AAAATA-AAAAT
1 AATATATAAAAT
55751 GAATTTTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 12 0.41
22 9 0.31
23 8 0.28
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AATATATAAAATAATAAAATA
Found at i:57486 original size:43 final size:43
Alignment explanation
Indices: 57421--57506 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
57411 CCGTGCATCA
* *
57421 AACAAAACTTTACATATTGGGGACAGCTTTCAGTCCTAACTTC
1 AACAAAACTTTACATATTGGGGACAACTTTCACTCCTAACTTC
* *
57464 AACAAAACTTTACAT-TTAGGGGATAACTTTCCCTCCTAACTTC
1 AACAAAACTTTACATATT-GGGGACAACTTTCACTCCTAACTTC
57507 TCTAAAGCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 2 0.05
43 36 0.95
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (43 bp):
AACAAAACTTTACATATTGGGGACAACTTTCACTCCTAACTTC
Done.