Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005254.1 Hibiscus syriacus cultivar Beakdansim tig00011878_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: 74332
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:3625 original size:61 final size:61
Alignment explanation
Indices: 3529--3804 Score: 336
Period size: 61 Copynumber: 4.6 Consensus size: 61
3519 GAGTCGAGGG
* * *
3529 TTACCTATATCTTTCGAGACATATGGACAGTATTACATATGTC-TTCGGACATATGGACAGA
1 TTACCTATGTCTTTCGGGACATATGGACAG-ATTACCTATGTCTTTCGGACATATGGACAGA
* *
3590 TTACCTACGTCTTTCGGGACATATGGACATGATTACCTATGTCTTTTGGGACATATGGACAGGA
1 TTACCTATGTCTTTCGGGACATATGGACA-GATTACCTATGTC-TTTCGGACATATGGACA-GA
* *
3654 TTACCTATGTCTTTCGGGACATATGG--ATATTACCTATGTCTTTCGGGACATATGGACAGT
1 TTACCTATGTCTTTCGGGACATATGGACAGATTACCTATGTCTTTC-GGACATATGGACAGA
* * *
3714 TTACCTATGT-TCTTC-GGACATATGAACAGTTTACCTATGTC--TCGGACATATGG-CAGT
1 TTACCTATGTCT-TTCGGGACATATGGACAGATTACCTATGTCTTTCGGACATATGGACAGA
3771 TTACCTATGT-TCTTCGGGACATATGGACAGATTA
1 TTACCTATGTCT-TTCGGGACATATGGACAGATTA
3805 TTAACGAGTT
Statistics
Matches: 192, Mismatches: 14, Indels: 21
0.85 0.06 0.09
Matches are distributed among these distances:
57 19 0.10
58 26 0.14
59 12 0.06
60 17 0.09
61 74 0.39
62 2 0.01
63 15 0.08
64 27 0.14
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (61 bp):
TTACCTATGTCTTTCGGGACATATGGACAGATTACCTATGTCTTTCGGACATATGGACAGA
Found at i:3634 original size:32 final size:31
Alignment explanation
Indices: 3529--3804 Score: 340
Period size: 32 Copynumber: 9.1 Consensus size: 31
3519 GAGTCGAGGG
* *
3529 TTACCTATATCTTTCGAGACATATGGACAGTA
1 TTACCTATGTCTTTCGGGACATATGGACAG-A
*
3561 TTACATATGTC-TTC-GGACATATGGACAGA
1 TTACCTATGTCTTTCGGGACATATGGACAGA
*
3590 TTACCTACGTCTTTCGGGACATATGGACATGA
1 TTACCTATGTCTTTCGGGACATATGGACA-GA
*
3622 TTACCTATGTCTTTTGGGACATATGGACAGGA
1 TTACCTATGTCTTTCGGGACATATGGACA-GA
*
3654 TTACCTATGTCTTTCGGGACATATGG--ATA
1 TTACCTATGTCTTTCGGGACATATGGACAGA
*
3683 TTACCTATGTCTTTCGGGACATATGGACAGT
1 TTACCTATGTCTTTCGGGACATATGGACAGA
* *
3714 TTACCTATGT-TCTTC-GGACATATGAACAGT
1 TTACCTATGTCT-TTCGGGACATATGGACAGA
*
3744 TTACCTATGTC--TC-GGACATATGG-CAGT
1 TTACCTATGTCTTTCGGGACATATGGACAGA
3771 TTACCTATGT-TCTTCGGGACATATGGACAGA
1 TTACCTATGTCT-TTCGGGACATATGGACAGA
3802 TTA
1 TTA
3805 TTAACGAGTT
Statistics
Matches: 217, Mismatches: 15, Indels: 25
0.84 0.06 0.10
Matches are distributed among these distances:
27 14 0.06
28 11 0.05
29 39 0.18
30 52 0.24
31 36 0.17
32 65 0.30
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (31 bp):
TTACCTATGTCTTTCGGGACATATGGACAGA
Found at i:3657 original size:93 final size:91
Alignment explanation
Indices: 3529--3804 Score: 355
Period size: 93 Copynumber: 3.0 Consensus size: 91
3519 GAGTCGAGGG
* * * * *
3529 TTACCTATATCTTTCGAGACATATGGACAGTATTACATATGTCTTCGGACATATGGACAGATTAC
1 TTACCTATGTCTTTTGGGACATATGGACAGGATTACCTATGTCTTCGGACATATGG-CAGATTAC
*
3594 CTACGTCTTTCGGGACATATGGACATGA
65 CTATGTCTTTCGGGACATATGGACA-GA
*
3622 TTACCTATGTCTTTTGGGACATATGGACAGGATTACCTATGTCTTTCGGGACATATGG-ATATTA
1 TTACCTATGTCTTTTGGGACATATGGACAGGATTACCTATGTC-TTC-GGACATATGGCAGATTA
*
3686 CCTATGTCTTTCGGGACATATGGACAGT
64 CCTATGTCTTTCGGGACATATGGACAGA
* * * * *
3714 TTACCTATGT-TCTTCGGACATATGAACA-GTTTACCTATGTC-TCGGACATATGGCAGTTTACC
1 TTACCTATGTCTTTTGGGACATATGGACAGGATTACCTATGTCTTCGGACATATGGCAGATTACC
3776 TATGT-TCTTCGGGACATATGGACAGA
66 TATGTCT-TTCGGGACATATGGACAGA
3802 TTA
1 TTA
3805 TTAACGAGTT
Statistics
Matches: 164, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
87 11 0.07
88 34 0.21
90 12 0.07
91 15 0.09
92 11 0.07
93 68 0.41
94 3 0.02
95 10 0.06
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (91 bp):
TTACCTATGTCTTTTGGGACATATGGACAGGATTACCTATGTCTTCGGACATATGGCAGATTACC
TATGTCTTTCGGGACATATGGACAGA
Found at i:4276 original size:23 final size:23
Alignment explanation
Indices: 4249--4295 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
4239 TAAGCAAGAC
4249 AGGTCAATTTCTCCTTTCCAAAG
1 AGGTCAATTTCTCCTTTCCAAAG
* *
4272 AGGTCAGTTTTTCCTTTCCAAAG
1 AGGTCAATTTCTCCTTTCCAAAG
4295 A
1 A
4296 TCAAATCAAA
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:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (23 bp):
AGGTCAATTTCTCCTTTCCAAAG
Found at i:8485 original size:15 final size:16
Alignment explanation
Indices: 8448--8497 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 16
8438 ATTATTATTT
8448 TTATTTAATAATAATA
1 TTATTTAATAATAATA
* *
8464 -AAATTAATAA-AATA
1 TTATTTAATAATAATA
*
8478 TTATTTAA-AATATTA
1 TTATTTAATAATAATA
8493 TTATT
1 TTATT
8498 ATTATTTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
14 6 0.22
15 21 0.78
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTATTTAATAATAATA
Found at i:8486 original size:12 final size:12
Alignment explanation
Indices: 8471--8513 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
8461 ATAAAATTAA
8471 TAAAATATTATT
1 TAAAATATTATT
8483 TAAAATATTA-T
1 TAAAATATTATT
*
8494 T--ATTATTATT
1 TAAAATATTATT
8504 TAAAATATTA
1 TAAAATATTA
8514 ATATATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 6 0.23
10 2 0.08
11 2 0.08
12 16 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TAAAATATTATT
Found at i:8496 original size:51 final size:51
Alignment explanation
Indices: 8396--8510 Score: 162
Period size: 51 Copynumber: 2.3 Consensus size: 51
8386 CGGTTATAAA
*
8396 TATTATTT-AAATAATAAAATTGATAAAAAAATTATATAAAAAATTATTAT
1 TATTATTTAAAATAATAAAATTAATAAAAAAATTATATAAAAAATTATTAT
* * * *
8446 TTTTATTTAATAATAATAAAATTAAT-AAAATATTATTTAAAATATTATTAT
1 TATTATTTAA-AATAATAAAATTAATAAAAAAATTATATAAAAAATTATTAT
8497 TATTATTTAAAATA
1 TATTATTTAAAATA
8511 TTAATATATT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
50 11 0.19
51 32 0.56
52 14 0.25
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (51 bp):
TATTATTTAAAATAATAAAATTAATAAAAAAATTATATAAAAAATTATTAT
Found at i:8524 original size:18 final size:21
Alignment explanation
Indices: 8476--8517 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
8466 ATTAATAAAA
*
8476 TATTATTTAAAATATTATTAT
1 TATTATTTAAAATATTAATAT
8497 TATTATTTAAAATATTAATAT
1 TATTATTTAAAATATTAATAT
8518 ATTTTAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTATTTAAAATATTAATAT
Found at i:8964 original size:20 final size:21
Alignment explanation
Indices: 8920--8964 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
8910 AATCTAGAAT
*
8920 TTATTTTCAAATATGAAATAA
1 TTATTTTCAAATATGAAAAAA
* *
8941 TTATTTTTAAA-ATTAAAAAA
1 TTATTTTCAAATATGAAAAAA
8961 TTAT
1 TTAT
8965 AATCTTTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
TTATTTTCAAATATGAAAAAA
Found at i:10365 original size:21 final size:21
Alignment explanation
Indices: 10327--10366 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
10317 ATTTTTACTC
* * *
10327 TAAAATATTATCTTATTTAAT
1 TAAAAAATTATATAATTTAAT
10348 TAAAAAATTATATAATTTA
1 TAAAAAATTATATAATTTA
10367 TAACATGTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAAAAATTATATAATTTAAT
Found at i:15516 original size:12 final size:12
Alignment explanation
Indices: 15499--15543 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
15489 ATGCATGCAT
15499 CATACATATATA
1 CATACATATATA
*
15511 CATACATACATA
1 CATACATATATA
*
15523 CATACATATATG
1 CATACATATATA
15535 CATACATAT
1 CATACATAT
15544 CCTAAAATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.47, C:0.20, G:0.02, T:0.31
Consensus pattern (12 bp):
CATACATATATA
Found at i:15559 original size:4 final size:4
Alignment explanation
Indices: 15499--15542 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
15489 ATGCATGCAT
* * *
15499 CATA CATA TATA CATA CATA CATA CATA CATA TATG CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
15543 TCCTAAAATC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.48, C:0.20, G:0.02, T:0.30
Consensus pattern (4 bp):
CATA
Found at i:16049 original size:6 final size:6
Alignment explanation
Indices: 16040--16064 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
16030 GGGATGATAA
16040 ACGGGG ACGGGG ACGGGG ACGGGG A
1 ACGGGG ACGGGG ACGGGG ACGGGG A
16065 AAACCCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.16, G:0.64, T:0.00
Consensus pattern (6 bp):
ACGGGG
Found at i:16164 original size:12 final size:13
Alignment explanation
Indices: 16128--16171 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
16118 GCCCCGATTA
16128 CCCGATTACCCGC
1 CCCGATTACCCGC
16141 CCCGATTACCCGC
1 CCCGATTACCCGC
*
16154 CCCGA-TACCCGA
1 CCCGATTACCCGC
16166 CCCGAT
1 CCCGAT
16172 AAATATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.18, C:0.52, G:0.16, T:0.14
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:16301 original size:24 final size:24
Alignment explanation
Indices: 16274--16325 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
16264 ATATATATAT
* * *
16274 ATACCCGACCCGATTCTCGGCCCA
1 ATACCCGACCCAATACCCGGCCCA
16298 ATACCCGACCCAATACCCGGCCCA
1 ATACCCGACCCAATACCCGGCCCA
16322 ATAC
1 ATAC
16326 TCGTTTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.46, G:0.13, T:0.13
Consensus pattern (24 bp):
ATACCCGACCCAATACCCGGCCCA
Found at i:16311 original size:12 final size:12
Alignment explanation
Indices: 16274--16325 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
16264 ATATATATAT
*
16274 ATACCCGACCCG
1 ATACCCGACCCA
* * *
16286 ATTCTCGGCCCA
1 ATACCCGACCCA
16298 ATACCCGACCCA
1 ATACCCGACCCA
*
16310 ATACCCGGCCCA
1 ATACCCGACCCA
16322 ATAC
1 ATAC
16326 TCGTTTAAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.27, C:0.46, G:0.13, T:0.13
Consensus pattern (12 bp):
ATACCCGACCCA
Found at i:17224 original size:4 final size:4
Alignment explanation
Indices: 17215--17271 Score: 69
Period size: 4 Copynumber: 14.0 Consensus size: 4
17205 ATGTATGCAT
* * * *
17215 CATA CATA CATA CATA CATG CATA CATG CATA CATG CATA CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
17263 CATA TCATA
1 CATA -CATA
17272 AAATGAAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
4 40 0.91
5 4 0.09
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:17228 original size:8 final size:8
Alignment explanation
Indices: 17209--17265 Score: 89
Period size: 8 Copynumber: 7.2 Consensus size: 8
17199 TATGTAATGT
17209 ATGCAT-C
1 ATGCATAC
*
17216 ATACATAC
1 ATGCATAC
*
17224 ATACATAC
1 ATGCATAC
17232 ATGCATAC
1 ATGCATAC
17240 ATGCATAC
1 ATGCATAC
17248 ATGCATAC
1 ATGCATAC
17256 ATGCATAC
1 ATGCATAC
17264 AT
1 AT
17266 ATCATAAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
7 5 0.11
8 42 0.89
ACGTcount: A:0.40, C:0.25, G:0.09, T:0.26
Consensus pattern (8 bp):
ATGCATAC
Found at i:17396 original size:13 final size:13
Alignment explanation
Indices: 17373--17442 Score: 59
Period size: 14 Copynumber: 5.2 Consensus size: 13
17363 CATGTAATAC
17373 ATGTATTAGGGTTT
1 ATGT-TTAGGGTTT
17387 ATGTTTAGGGTTT
1 ATGTTTAGGGTTT
* *
17400 AATATTTATGGTTT
1 -ATGTTTAGGGTTT
**
17414 AAAATTTAGGGTTT
1 -ATGTTTAGGGTTT
* *
17428 AGGTTTAGAGTTT
1 ATGTTTAGGGTTT
17441 AT
1 AT
17443 ATAAACTATA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
13 20 0.43
14 27 0.57
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (13 bp):
ATGTTTAGGGTTT
Found at i:17407 original size:14 final size:14
Alignment explanation
Indices: 17378--17428 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
17368 AATACATGTA
*
17378 TTAGGGTTT-ATGT
1 TTAGGGTTTAATAT
17391 TTAGGGTTTAATAT
1 TTAGGGTTTAATAT
* *
17405 TTATGGTTTAAAAT
1 TTAGGGTTTAATAT
17419 TTAGGGTTTA
1 TTAGGGTTTA
17429 GGTTTAGAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
13 9 0.27
14 24 0.73
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (14 bp):
TTAGGGTTTAATAT
Found at i:17534 original size:15 final size:15
Alignment explanation
Indices: 17529--17566 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
17519 AGTTTATATA
17529 TATATATATATAGGT
1 TATATATATATAGGT
*
17544 TATATATATATAGTT
1 TATATATATATAGGT
17559 TATATATA
1 TATATATA
17567 CTATTCATGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (15 bp):
TATATATATATAGGT
Found at i:17540 original size:21 final size:21
Alignment explanation
Indices: 17514--17555 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
17504 TAATTTACTT
*
17514 TATATAGTTTATATATATATA
1 TATATAGGTTATATATATATA
17535 TATATAGGTTATATATATATA
1 TATATAGGTTATATATATATA
17556 GTTTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (21 bp):
TATATAGGTTATATATATATA
Found at i:18095 original size:20 final size:20
Alignment explanation
Indices: 18072--18138 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 20
18062 ATAAAATCTC
*
18072 AATTCTCCATTTCCCTCCAA
1 AATTCTCAATTTCCCTCCAA
* * *
18092 AATTTTCTA-TTCCCTCTAA
1 AATTCTCAATTTCCCTCCAA
* * *
18111 ATTTCTCAATTTTCCT-CTA
1 AATTCTCAATTTCCCTCCAA
18130 AATTCTCAA
1 AATTCTCAA
18139 ATAAAATAAA
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
19 24 0.67
20 12 0.33
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (20 bp):
AATTCTCAATTTCCCTCCAA
Found at i:18218 original size:2 final size:2
Alignment explanation
Indices: 18211--18436 Score: 66
Period size: 2 Copynumber: 113.0 Consensus size: 2
18201 ACTTTGAATA
*
18211 AT AT AT AT AT AT AT AT AT AT AT -T AT ACT AT AT -T A- AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * * * * *
18251 AT -T AT AGT TT AT AA ACT AT AT ACT TT TT AT AGT TT AT AC AT AT
1 AT AT AT A-T AT AT AT A-T AT AT A-T AT AT AT A-T AT AT AT AT AT
* * * * *
18294 AGT TT AC AT AT AGT TT AT AT AT AT AGT -T CAT AT AA AC AT A- AT
1 A-T AT AT AT AT A-T AT AT AT AT AT A-T AT -AT AT AT AT AT AT AT
* *
18336 TT AT AT AT AT A- ACT -T AT A- AT A- AT -T AT AT AGT TT AT A- AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * * *
18374 AT AA AT AT AGT TT AT AT AT AT AGT TT AT AT AT AA ACT -T AT AT
1 AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT
18416 -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
18437 TTTTCAATTT
Statistics
Matches: 163, Mismatches: 33, Indels: 56
0.65 0.13 0.22
Matches are distributed among these distances:
1 14 0.09
2 136 0.83
3 13 0.08
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18303 original size:11 final size:11
Alignment explanation
Indices: 18287--18316 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
18277 TTATAGTTTA
18287 TACATATAGTT
1 TACATATAGTT
18298 TACATATAGTT
1 TACATATAGTT
*
18309 TATATATA
1 TACATATA
18317 TAGTTCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (11 bp):
TACATATAGTT
Found at i:18394 original size:13 final size:13
Alignment explanation
Indices: 18278--18435 Score: 89
Period size: 13 Copynumber: 12.3 Consensus size: 13
18268 ATATACTTTT
*
18278 TATAGTTTATACA
1 TATAGTTTATATA
*
18291 TATAG-TT-TACA
1 TATAGTTTATATA
18302 TATAGTTTATATA
1 TATAGTTTATATA
*
18315 TATAGTTCATATAAA
1 TATAGTT--TATATA
* *
18330 CATAATTTATATA
1 TATAGTTTATATA
**
18343 TATAACTTATA-A
1 TATAGTTTATATA
18355 TA-A--TTATATA
1 TATAGTTTATATA
* * *
18365 GTTTA-TAATATAAA
1 -TATAGT-TTATATA
18379 TATAGTTTATATA
1 TATAGTTTATATA
18392 TATAGTTTATATA
1 TATAGTTTATATA
* *
18405 TAAACTTATATTATA
1 TATAGTT-TA-TATA
*
18420 TATA-TATATATA
1 TATAGTTTATATA
18432 TATA
1 TATA
18436 TTTTTCAATT
Statistics
Matches: 116, Mismatches: 17, Indels: 25
0.73 0.11 0.16
Matches are distributed among these distances:
9 5 0.04
10 1 0.01
11 11 0.09
12 16 0.14
13 57 0.49
14 9 0.08
15 17 0.15
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:18538 original size:16 final size:16
Alignment explanation
Indices: 18519--18559 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
18509 TTAATTCTTT
*
18519 TTTTAATTTATATAAA
1 TTTTAAGTTATATAAA
*
18535 TTTTAAGTTATATCAA
1 TTTTAAGTTATATAAA
18551 TTTTAAGTT
1 TTTTAAGTT
18560 TTTCACTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (16 bp):
TTTTAAGTTATATAAA
Found at i:21942 original size:29 final size:28
Alignment explanation
Indices: 21903--21958 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
21893 AATTAATATT
21903 AAAAATAAACAT-AATAAAACAACATACC
1 AAAAATAAACATGAATAAAAC-ACATACC
*
21931 AAAAATAAAACATGAATCAAACACATAC
1 AAAAAT-AAACATGAATAAAACACATAC
21959 GTAATAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 6 0.24
29 12 0.48
30 7 0.28
ACGTcount: A:0.66, C:0.18, G:0.02, T:0.14
Consensus pattern (28 bp):
AAAAATAAACATGAATAAAACACATACC
Found at i:23721 original size:16 final size:16
Alignment explanation
Indices: 23681--23724 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
23671 ATTTTAAGGG
*
23681 TTAGGTATTGA-AATT
1 TTAGGTTTTGAGAATT
* *
23696 TAAGGATTTGAGAATT
1 TTAGGTTTTGAGAATT
23712 TTAGGTTTTGAGA
1 TTAGGTTTTGAGA
23725 TGATATTAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.32, C:0.00, G:0.25, T:0.43
Consensus pattern (16 bp):
TTAGGTTTTGAGAATT
Found at i:27666 original size:2 final size:2
Alignment explanation
Indices: 27659--27693 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
27649 CATACATCAT
27659 TA 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 TA T
27694 GATTGGTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28015 original size:15 final size:15
Alignment explanation
Indices: 27997--28027 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27987 AAATTCTAAA
27997 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
28012 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
28027 T
1 T
28028 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:35314 original size:23 final size:22
Alignment explanation
Indices: 35287--35333 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
35277 AACCCTAAAT
35287 AAGCCCAAAAATCGTATCTGCTA
1 AAGCCC-AAAATCGTATCTGCTA
* * *
35310 AAGCCCAGAATTGTATCTTCTA
1 AAGCCCAAAATCGTATCTGCTA
35332 AA
1 AA
35334 CTCGCGATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (22 bp):
AAGCCCAAAATCGTATCTGCTA
Found at i:39357 original size:17 final size:17
Alignment explanation
Indices: 39335--39381 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
39325 TGTTTTACTC
39335 ATTTAATATTTTATT-A
1 ATTTAATATTTTATTCA
*
39351 TATTTAATAATTTATTCA
1 -ATTTAATATTTTATTCA
39369 ATTTAATTATTTT
1 ATTTAA-TATTTT
39382 TATGATTCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 20 0.77
18 6 0.23
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTAATATTTTATTCA
Found at i:55012 original size:148 final size:149
Alignment explanation
Indices: 54742--55034 Score: 418
Period size: 148 Copynumber: 2.0 Consensus size: 149
54732 CATTCTAGGA
* *
54742 TGATTTTGCTTCTCTTTTTCATTTTTTATGTTACTGTTCTGAGAAGCCCGCAAATGCCAGTTCTT
1 TGATTTTGCTTCTCCTTTTCACTTTTTATGTTACTGTTCTGAGAAGCCCGCAAATGCCAGTTCTT
*
54807 GTTCTTTGCTTCTTCCAGTTTAGGGGGACACTTTGGTGTGGTTGATAACTGTGCTTCTT-ATCAA
66 GTTC-TTGCTTCTTCCAGTTTAGGGGGACAATTTGGTGTGGTTGATAACTGTGCTTCTTAATCAA
54871 GATAAATTCCTATCCCAGGC
130 GATAAATTCCTATCCCAGGC
*
54891 TGATTTTGCTTC-CCTTTTCGAACTTTTTATGTTACTGTTCTGAGAAGCCTGCAAATGTCCA-TT
1 TGATTTTGCTTCTCCTTTTC--ACTTTTTATGTTACTGTTCTGAGAAGCCCGCAAATG-CCAGTT
* * * *
54954 GCTT-TTC-TGTTTGTTCCAGTTTATGGGGACAATTTGGTGTGGTTGATAAGT-TGACTTCTTAA
63 -CTTGTTCTTGCTTCTTCCAGTTTAGGGGGACAATTTGGTGTGGTTGATAACTGTG-CTTCTTAA
55016 TCAAGATAAATTCCTATCC
126 TCAAGATAAATTCCTATCC
55035 TTTTGGACCA
Statistics
Matches: 130, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
147 2 0.02
148 51 0.39
149 32 0.25
150 39 0.30
151 6 0.05
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (149 bp):
TGATTTTGCTTCTCCTTTTCACTTTTTATGTTACTGTTCTGAGAAGCCCGCAAATGCCAGTTCTT
GTTCTTGCTTCTTCCAGTTTAGGGGGACAATTTGGTGTGGTTGATAACTGTGCTTCTTAATCAAG
ATAAATTCCTATCCCAGGC
Found at i:58095 original size:19 final size:19
Alignment explanation
Indices: 58071--58107 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
58061 ATTTATTGCA
58071 AATATTAAATATAATAAAT
1 AATATTAAATATAATAAAT
**
58090 AATATTATTTATAATAAA
1 AATATTAAATATAATAAA
58108 ACTTAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATATTAAATATAATAAAT
Found at i:58121 original size:25 final size:23
Alignment explanation
Indices: 58093--58150 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
58083 AATAAATAAT
*
58093 ATTATTTATAATAAAACTTAATATA
1 ATTATTTATAA-AAAA-TTAAAATA
* *
58118 ATTATTTTTAAAATATTAAAATA
1 ATTATTTATAAAAAATTAAAATA
58141 ATTTATTTAT
1 A-TTATTTAT
58151 TATTAAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 8 0.29
24 10 0.36
25 10 0.36
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTATTTATAAAAAATTAAAATA
Found at i:58141 original size:23 final size:26
Alignment explanation
Indices: 58076--58162 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 26
58066 TTGCAAATAT
* *
58076 TAAATATAATAAATAATATTATTTATAA
1 TAAATATTA-AAATAAT-TTATTTATTA
*
58104 TAAA-ACTTAATATAA-TTATTT-TTA
1 TAAATA-TTAAAATAATTTATTTATTA
58128 -AAATATTAAAATAATTTATTTATTA
1 TAAATATTAAAATAATTTATTTATTA
58153 TTAAATATTA
1 -TAAATATTA
58163 TTTTTATAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
23 11 0.22
24 9 0.18
25 9 0.18
27 14 0.29
28 6 0.12
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (26 bp):
TAAATATTAAAATAATTTATTTATTA
Found at i:58280 original size:19 final size:19
Alignment explanation
Indices: 58212--58280 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
58202 TTTTAAATCT
58212 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
58231 TTATTATATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
58250 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
58270 TTATTAATAAT
1 TTATTAATAAT
58281 TTAATAATAC
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
18 8 0.20
19 18 0.44
20 8 0.20
22 7 0.17
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:58442 original size:52 final size:50
Alignment explanation
Indices: 58335--58444 Score: 118
Period size: 52 Copynumber: 2.2 Consensus size: 50
58325 AATAATTTAT
* * **
58335 TATATATTATTAAAATAAAAATATATATCTTATATATTAAATATAATTGA
1 TATATTTTATTAAAATAAAAATATATATCTTATATATGAAATATAATAAA
*
58385 T-TATTTTATTATAATATTAAAAATATATATGTTAT-TA-GAAATATTAATAAA
1 TATATTTTATTA-AA-A-TAAAAATATATATCTTATATATGAAATA-TAATAAA
58436 TATATTTTA
1 TATATTTTA
58445 AATATTTTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
49 9 0.18
50 8 0.16
51 9 0.18
52 24 0.48
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (50 bp):
TATATTTTATTAAAATAAAAATATATATCTTATATATGAAATATAATAAA
Found at i:69580 original size:216 final size:216
Alignment explanation
Indices: 69008--69653 Score: 1248
Period size: 213 Copynumber: 3.0 Consensus size: 216
68998 TTGGTAATTA
69008 AAAATTTGGTGGAAGCTTTTGCA-AAAATTGAAAATATTTGCACAGCGATTTAGAGTGGTTCGAC
1 AAAATTTGGTGGAAGCTTTTGCAGAAAATTGAAAATATTTGCACAGCGATTTAGAGTGGTTCGAC
69072 TCTCTTAACCAAAGTCTACGTCCACTACCTTAGCTATCTACACTAAGGATTTTTCAACAAATTCA
66 TCTCTTAACCAAAGTCTACGTCCACTACCTTAGCTATCTACACTAAGGATTTTTCAACAAATTCA
69137 CTAATTTGTTC-TTTTTTTAGGACAAAGAGTAACCTTACAACTCCCTCAAGAATTATATCCCAAA
131 CTAATTTGTTCTTTTTTTTAGGACAAAGAGTAACCTTACAACTCCCTCAAGAATTATATCCCAAA
69201 TTC-TGAGCACACTCTCTCCC
196 TTCTTGAGCACACTCTCTCCC
69221 AAAATTTGGTGGAAGCTTTTGCAGAAAATTG-AAATATTTGCACAGCGATTTAGAGTGGTTCGAC
1 AAAATTTGGTGGAAGCTTTTGCAGAAAATTGAAAATATTTGCACAGCGATTTAGAGTGGTTCGAC
69285 TCTCTTAACCAAAGTCTACGTCCACTACCTTAGCTATCTACACTAAGGATTTTTCAACAAATTCA
66 TCTCTTAACCAAAGTCTACGTCCACTACCTTAGCTATCTACACTAAGGATTTTTCAACAAATTCA
69350 CTAATTTGTTCTTTTTTTTAGGACAAAGAGTAACCTTACAACTCCCTCAAGAATTATATCCCAAA
131 CTAATTTGTTCTTTTTTTTAGGACAAAGAGTAACCTTACAACTCCCTCAAGAATTATATCCCAAA
69415 TTCTTGAGCACACTCTCTCCC
196 TTCTTGAGCACACTCTCTCCC
69436 AAAATTTGGTGGAAGCTTTTGCAGAAAATTGAAAATATTTGCACAGCGATTTAGAGTGGTTCGAC
1 AAAATTTGGTGGAAGCTTTTGCAGAAAATTGAAAATATTTGCACAGCGATTTAGAGTGGTTCGAC
69501 TCTCTTAACCAAAGTCTACGTCCACTACCTTAGCTATCTACACTAAGGATTTTTCAACAAATTCA
66 TCTCTTAACCAAAGTCTACGTCCACTACCTTAGCTATCTACACTAAGGATTTTTCAACAAATTCA
69566 CTAATTTGTTCTTTTTTTTAGGACAAAGA-TAACCTTACAACTCCCTCAAGAATTATATCCCAAA
131 CTAATTTGTTCTTTTTTTTAGGACAAAGAGTAACCTTACAACTCCCTCAAGAATTATATCCCAAA
*
69630 TTCTTGAGCACACTTTCTCCC
196 TTCTTGAGCACACTCTCTCCC
69651 AAA
1 AAA
69654 GAGAATACAC
Statistics
Matches: 428, Mismatches: 1, Indels: 6
0.98 0.00 0.01
Matches are distributed among these distances:
213 132 0.31
214 63 0.15
215 106 0.25
216 127 0.30
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (216 bp):
AAAATTTGGTGGAAGCTTTTGCAGAAAATTGAAAATATTTGCACAGCGATTTAGAGTGGTTCGAC
TCTCTTAACCAAAGTCTACGTCCACTACCTTAGCTATCTACACTAAGGATTTTTCAACAAATTCA
CTAATTTGTTCTTTTTTTTAGGACAAAGAGTAACCTTACAACTCCCTCAAGAATTATATCCCAAA
TTCTTGAGCACACTCTCTCCC
Found at i:72883 original size:23 final size:23
Alignment explanation
Indices: 72840--72886 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
72830 ATGCACAACA
*
72840 GAGTGCATTGATGCACATTCAAG
1 GAGTGCATTGATACACATTCAAG
*
72863 GAGTGCATTGGTACATC-TTCAAG
1 GAGTGCATTGATACA-CATTCAAG
72886 G
1 G
72887 TGTATCGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (23 bp):
GAGTGCATTGATACACATTCAAG
Done.