Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008415.1 Hibiscus syriacus cultivar Beakdansim tig00111193_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: 525802
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:372192 original size:22 final size:22
Alignment explanation
Indices: 372167--372213 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
372157 TCATGTTCTC
* *
372167 TTCACTTATGGTAATCTTACAA
1 TTCACTTATGATAATATTACAA
372189 TTCACTTATGATAATATTACAA
1 TTCACTTATGATAATATTACAA
372211 TTC
1 TTC
372214 TAAGCTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (22 bp):
TTCACTTATGATAATATTACAA
Found at i:373700 original size:18 final size:18
Alignment explanation
Indices: 373677--373715 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
373667 GCTCCGGTGT
373677 CAATATATATATATATAA
1 CAATATATATATATATAA
373695 CAATATATATATATATAA
1 CAATATATATATATATAA
373713 CAA
1 CAA
373716 AACAATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (18 bp):
CAATATATATATATATAA
Found at i:377438 original size:2 final size:2
Alignment explanation
Indices: 377431--377458 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
377421 GTATGGCTGA
377431 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
377459 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:377463 original size:2 final size:2
Alignment explanation
Indices: 377458--377487 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
377448 TATATATATA
377458 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
377488 GTTCTCTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:393981 original size:18 final size:18
Alignment explanation
Indices: 393954--393993 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
393944 ATGCCATTGG
*
393954 ACCTCGATAACTAAAGTA
1 ACCTCAATAACTAAAGTA
* *
393972 ACCTCAATAACTGAAGTG
1 ACCTCAATAACTAAAGTA
393990 ACCT
1 ACCT
393994 AAACACCCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.25, G:0.12, T:0.23
Consensus pattern (18 bp):
ACCTCAATAACTAAAGTA
Found at i:396643 original size:21 final size:21
Alignment explanation
Indices: 396592--396644 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
396582 ATTATTACTA
396592 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
396613 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
396634 TCGCAATGCGA
1 TCGCAATGCGA
396645 ATTTGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:396679 original size:20 final size:20
Alignment explanation
Indices: 396654--396768 Score: 124
Period size: 20 Copynumber: 5.7 Consensus size: 20
396644 AATTTGGAAA
*
396654 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
396674 ATCGCAACGCAATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
396695 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
396715 TTCGCAACGCGATACTTACT
1 ATCGCAACGCGATACTGACT
*
396735 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
396755 TTCGCAACGAGATA
1 ATCGCAACGCGATA
396769 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 63 0.78
21 14 0.17
22 2 0.02
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:396751 original size:40 final size:40
Alignment explanation
Indices: 396652--396788 Score: 168
Period size: 41 Copynumber: 3.4 Consensus size: 40
396642 CGAATTTGGA
* * *
396652 AAATCGCAATGCGATACTGACTATCGCAACGCAATAATAC
1 AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
*
396692 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATACTTAC
1 -AAATCGCAACGCGATACTGACTTTCGCAACGCGATA-ATAC
** *
396734 -TTTCGCAACGCGATACTGACTTTCGCAACGAGATAATAC
1 AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
*
396773 ATAATCGCAATGCGAT
1 A-AATCGCAACGCGAT
396789 TTTCAAAGCG
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 3 0.04
40 32 0.39
41 44 0.54
42 3 0.04
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.23
Consensus pattern (40 bp):
AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:396983 original size:22 final size:22
Alignment explanation
Indices: 396955--396998 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
396945 CACTCTCTCA
396955 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
396977 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
396999 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:397310 original size:20 final size:20
Alignment explanation
Indices: 397261--397319 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
397251 TTTATTCTCT
* **
397261 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
397281 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
397301 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
397320 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:398660 original size:18 final size:18
Alignment explanation
Indices: 398639--398686 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
398629 TCCACTTTGG
*
398639 GAGCCATCACCTCACCCA
1 GAGCTATCACCTCACCCA
*
398657 GAGCTATCACCTCACCTA
1 GAGCTATCACCTCACCCA
398675 GAGCTATCACCT
1 GAGCTATCACCT
398687 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.42, G:0.12, T:0.19
Consensus pattern (18 bp):
GAGCTATCACCTCACCCA
Found at i:399274 original size:19 final size:20
Alignment explanation
Indices: 399231--399275 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
399221 CGCAACACGA
399231 AAATGACTATCGCAATGCAG
1 AAATGACTATCGCAATGCAG
* *
399251 AAATGGCTATCGTAATGC-G
1 AAATGACTATCGCAATGCAG
399270 AAATGA
1 AAATGA
399276 AAATCGCAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (20 bp):
AAATGACTATCGCAATGCAG
Found at i:399281 original size:19 final size:19
Alignment explanation
Indices: 399239--399322 Score: 70
Period size: 19 Copynumber: 4.6 Consensus size: 19
399229 GAAAATGACT
***
399239 ATCGCAATGCAGAAATGGCT
1 ATCGCAATGC-GAAATGAAA
*
399259 ATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
399278 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
399292 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
399311 ATCGCAATGCGA
1 ATCGCAATGCGA
399323 TTTGTGTTTC
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 26 0.51
20 9 0.18
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:399355 original size:14 final size:14
Alignment explanation
Indices: 399336--399392 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
399326 GTGTTTCGCG
399336 TTGCGATTTTATCA
1 TTGCGATTTTATCA
399350 TTGCGATTTTCATTTCGCA
1 TTGCGATTTT-A--T--CA
* *
399369 TTGCGATTTTTTCG
1 TTGCGATTTTATCA
399383 TTGCGATTTT
1 TTGCGATTTT
399393 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 21 0.58
15 1 0.03
16 1 0.03
17 1 0.03
19 12 0.33
ACGTcount: A:0.14, C:0.16, G:0.18, T:0.53
Consensus pattern (14 bp):
TTGCGATTTTATCA
Found at i:399366 original size:33 final size:33
Alignment explanation
Indices: 399329--399408 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
399319 GCGATTTGTG
*
399329 TTTCGCGTTGCGATTTTATCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTATCATTGCGATTTTCA
* *
399362 TTTCGCATTGCGATTTTTTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTATCATTGCGATTTTCA
*
399395 TTTCGCATTACGAT
1 TTTCGCATTGCGAT
399409 AGCCATTTCC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.15, C:0.19, G:0.17, T:0.49
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTATCATTGCGATTTTCA
Found at i:399372 original size:19 final size:19
Alignment explanation
Indices: 399348--399408 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 19
399338 GCGATTTTAT
399348 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
399367 CATTGCGA-TTT--TTTCG
1 CATTGCGATTTTCATTTCG
399383 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
399400 CATTACGAT
1 CATTGCGAT
399409 AGCCATTTCC
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 6 0.17
15 3 0.08
16 5 0.14
17 5 0.14
18 3 0.08
19 14 0.39
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.48
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:399427 original size:20 final size:20
Alignment explanation
Indices: 399393--399463 Score: 99
Period size: 20 Copynumber: 3.6 Consensus size: 20
399383 TTGCGATTTT
*
399393 CATTT-CGCATTACGATAGC
1 CATTTCCGCGTTACGATAGC
399412 CATTTCCGCGTTACGATAGC
1 CATTTCCGCGTTACGATAGC
* *
399432 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTACGATAGC
*
399452 CATTTTCGCGTT
1 CATTTCCGCGTT
399464 GCGAAAGTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 5 0.11
20 42 0.89
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (20 bp):
CATTTCCGCGTTACGATAGC
Found at i:399464 original size:20 final size:20
Alignment explanation
Indices: 399381--399487 Score: 90
Period size: 20 Copynumber: 5.4 Consensus size: 20
399371 GCGATTTTTT
**
399381 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATAGTCATTTTCG
* * * *
399400 CATTACGATAGCCATTTCCG
1 CGTTGCGATAGTCATTTTCG
* * *
399420 CGTTACGATAGCCATTTCCG
1 CGTTGCGATAGTCATTTTCG
399440 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* * *
399460 CGTTGCGAAAGTAAGTTTCG
1 CGTTGCGATAGTCATTTTCG
*
399480 TGTTGCGA
1 CGTTGCGA
399488 AAGTAAACTA
Statistics
Matches: 73, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
19 9 0.12
20 64 0.88
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:399488 original size:20 final size:20
Alignment explanation
Indices: 399438--399493 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
399428 TAGCCATTTC
* * *
399438 CGCGTTGCGATAGTCATTTT
1 CGCGTTGCGAAAGTAAGTTT
399458 CGCGTTGCGAAAGTAAGTTT
1 CGCGTTGCGAAAGTAAGTTT
*
399478 CGTGTTGCGAAAGTAA
1 CGCGTTGCGAAAGTAA
399494 ACTATTCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGAAAGTAAGTTT
Found at i:399922 original size:41 final size:42
Alignment explanation
Indices: 399832--399922 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 42
399822 CCCGGCTCAC
* * *
399832 CTGTCATCCCTTAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
* *
399874 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
399915 CTGTCATC
1 CTGTCATC
399923 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 23 0.53
42 20 0.47
ACGTcount: A:0.22, C:0.41, G:0.15, T:0.22
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:401366 original size:14 final size:14
Alignment explanation
Indices: 401332--401370 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
401322 TTGATTGTTT
401332 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
401346 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
401360 TGTTGATTTGT
1 AATTGATTTGT
401371 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:401500 original size:20 final size:20
Alignment explanation
Indices: 401475--401512 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
401465 GCAAAGCAGA
*
401475 CTATCGCAACGCGAAAATTG
1 CTATCGCAACGAGAAAATTG
401495 CTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
401513 CGCAATGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATTG
Found at i:401531 original size:19 final size:19
Alignment explanation
Indices: 401507--401593 Score: 139
Period size: 19 Copynumber: 4.8 Consensus size: 19
401497 ATCGCAACGA
401507 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
401526 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
401545 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
401564 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
401578 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
401594 TTTTTATTTC
Statistics
Matches: 65, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
14 11 0.17
15 1 0.02
16 2 0.03
17 2 0.03
19 49 0.75
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:401551 original size:38 final size:33
Alignment explanation
Indices: 401497--401593 Score: 149
Period size: 38 Copynumber: 2.8 Consensus size: 33
401487 GAAAATTGCT
401497 ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
401530 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAAA
401568 ATCGCAACGAGAAAATCGCAATGCGA
1 ATCGCAACGAGAAAATCGCAATGCGA
401594 TTTTTATTTC
Statistics
Matches: 59, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
33 23 0.39
34 1 0.02
35 2 0.03
36 2 0.03
37 1 0.02
38 30 0.51
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
Found at i:401637 original size:20 final size:20
Alignment explanation
Indices: 401612--401651 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
401602 TCGCATTGCG
*
401612 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
401632 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
401652 CCATTGCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.25, G:0.23, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:402303 original size:20 final size:20
Alignment explanation
Indices: 402192--402306 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
402182 GATTCTGTAT
*
402192 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * * *
402212 AATCTCGTTGCAAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
402232 AATTGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
402252 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
*
402273 TATCGTGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
402293 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
402307 TTTCCAAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
19 3 0.04
20 58 0.76
21 13 0.17
22 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:402325 original size:41 final size:41
Alignment explanation
Indices: 402239--402327 Score: 99
Period size: 41 Copynumber: 2.2 Consensus size: 41
402229 CAGAATTGCG
* ** * **
402239 TTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATTATCGTG
1 TTGCGAAAGTCAGTATCGCATTGCGATTTTCAAATATCGCA
*
402280 TTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT-TCGCA
1 TTGCGAAAGTCAGTATCGCATTGCGATTTT-CAAATATCGCA
402321 TTGCGAA
1 TTGCGAA
402328 TTGGGAAAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 37 0.95
42 2 0.05
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (41 bp):
TTGCGAAAGTCAGTATCGCATTGCGATTTTCAAATATCGCA
Found at i:402340 original size:21 final size:20
Alignment explanation
Indices: 402316--402397 Score: 76
Period size: 21 Copynumber: 4.0 Consensus size: 20
402306 TTTTCCAAAT
402316 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
**
402337 TCGCAACGCGAAATTGGAAAA
1 TCGCATTGCG-AATTGGAAAA
* *
402358 TCGCATTGCG-ATAGTAATAA
1 TCGCATTGCGAATTGGAA-AA
*
402378 TCGCGTTGCGAATCTGGAAA
1 TCGCATTGCGAAT-TGGAAA
402398 CTGATTTGCG
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
19 5 0.10
20 11 0.23
21 25 0.52
22 7 0.15
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:404898 original size:20 final size:19
Alignment explanation
Indices: 404869--404909 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
404859 ATGGATGTAT
* *
404869 ATTTTTAAATTACATTTAA
1 ATTTTTAAATAAAATTTAA
404888 ATTTGTTAAATAAAATTTAA
1 ATTT-TTAAATAAAATTTAA
404908 AT
1 AT
404910 GCTTCAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
ATTTTTAAATAAAATTTAA
Found at i:405420 original size:2 final size:2
Alignment explanation
Indices: 405413--405439 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
405403 ATATCACTTT
405413 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 T
405440 GGATGAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:407684 original size:39 final size:38
Alignment explanation
Indices: 407602--407690 Score: 92
Period size: 39 Copynumber: 2.3 Consensus size: 38
407592 AAAGCATGTG
* * *
407602 GTAAGGACTTATCTGTGTACAAAGCAGAGGGGCCTTCA
1 GTAAGGACTTACCTGTGTACAAAGCAGAGGAGCCTACA
*
407640 GTAAGGACTTACCTTGTGCTA-AAAGTAGAGGAGCCTAC-
1 GTAAGGACTTACC-TGTG-TACAAAGCAGAGGAGCCTACA
*
407678 GATAAGGTCTTAC
1 G-TAAGGACTTAC
407691 AAGTCATAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
38 13 0.30
39 28 0.65
40 2 0.05
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (38 bp):
GTAAGGACTTACCTGTGTACAAAGCAGAGGAGCCTACA
Found at i:410689 original size:64 final size:65
Alignment explanation
Indices: 410552--410694 Score: 184
Period size: 64 Copynumber: 2.2 Consensus size: 65
410542 AATTGTTCAG
* *
410552 TGTGTATCGATGCA-CAGGAAGTGCATCGATGCACCCATTAACAATTAAAACATCAAATGCAATT
1 TGTGTATCGATGCATAAGGAAGTGCATCGATGCACCCATTAACAATTAAAACATCAAAGGCAATT
* * * * **
410616 AGTGCATCGATGCATAAGG-AGTGCATCGATGCACCCCCTTAA-AATTAAAACATCGAAGGTGAT
1 TGTGTATCGATGCATAAGGAAGTGCATCGATGCA-CCCATTAACAATTAAAACATCAAAGGCAAT
410679 T
65 T
410680 TGTGTATCGATGCAT
1 TGTGTATCGATGCAT
410695 GGGTAGTGTA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
64 57 0.85
65 10 0.15
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (65 bp):
TGTGTATCGATGCATAAGGAAGTGCATCGATGCACCCATTAACAATTAAAACATCAAAGGCAATT
Found at i:410746 original size:20 final size:20
Alignment explanation
Indices: 410721--410758 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
410711 TACATGTTAA
410721 AGAATGCATCGATACACTGT
1 AGAATGCATCGATACACTGT
* *
410741 AGAATGTATCGATGCACT
1 AGAATGCATCGATACACT
410759 TCAAGGGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATACACTGT
Found at i:411505 original size:23 final size:23
Alignment explanation
Indices: 411475--411534 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
411465 CATTTTATAT
411475 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* *
411498 GGCACTTCGGTGTAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
*
411521 GACACTTCGGTGCA
1 GGCACTTCGGTGCA
411535 TTTATACGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:416665 original size:20 final size:18
Alignment explanation
Indices: 416640--416679 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
416630 TTGTACTAAC
416640 TTGTTTCTATGTTGTTTTTT
1 TTGTTT-TATGTT-TTTTTT
*
416660 TTGTTTTTTGTTTTTTTT
1 TTGTTTTATGTTTTTTTT
416678 TT
1 TT
416680 CCTCTTTGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 5 0.26
20 6 0.32
ACGTcount: A:0.03, C:0.03, G:0.12, T:0.82
Consensus pattern (18 bp):
TTGTTTTATGTTTTTTTT
Found at i:418189 original size:40 final size:40
Alignment explanation
Indices: 418145--418225 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
418135 TGTGGCTCAG
418145 AAATGGGTTGATTTAGCTGGCTTTGCAAGAGAATTAAAGC
1 AAATGGGTTGATTTAGCTGGCTTTGCAAGAGAATTAAAGC
418185 AAATGGGTTGATTTAGCTGGCTTTGCAAGAGAATTAAAGC
1 AAATGGGTTGATTTAGCTGGCTTTGCAAGAGAATTAAAGC
418225 A
1 A
418226 GATTGACAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.30
Consensus pattern (40 bp):
AAATGGGTTGATTTAGCTGGCTTTGCAAGAGAATTAAAGC
Found at i:422832 original size:41 final size:42
Alignment explanation
Indices: 422730--422836 Score: 128
Period size: 42 Copynumber: 2.6 Consensus size: 42
422720 TTCACAATTT
* * *
422730 ATAAGTCCTTCGGGCCAT-TAGTAAGTCTTTCGAGCATGATGC
1 ATAAGTCCTTCGGGCCATCT-GTAAGCCTTTAGAGCAAGATGC
* * *
422772 TTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG-
1 ATAAGTCCTTCGGGCCATCTGTAAGCCTTTAGAGCAAGATGC
*
422813 ATGAGTCCTTCGGGCCATCTGTAA
1 ATAAGTCCTTCGGGCCATCTGTAA
422837 AACCTTCGGG
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 20 0.37
42 33 0.61
43 1 0.02
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.31
Consensus pattern (42 bp):
ATAAGTCCTTCGGGCCATCTGTAAGCCTTTAGAGCAAGATGC
Found at i:423116 original size:59 final size:59
Alignment explanation
Indices: 423024--423141 Score: 209
Period size: 59 Copynumber: 2.0 Consensus size: 59
423014 CTTCACGGAA
* **
423024 GAGTAGTGAAGTAAATTCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGT
1 GAGTAGTGAAGCAAACCCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGT
423083 GAGTAGTGAAGCAAACCCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGT
1 GAGTAGTGAAGCAAACCCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGT
423142 AATTTTTAAG
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (59 bp):
GAGTAGTGAAGCAAACCCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGT
Found at i:423261 original size:42 final size:41
Alignment explanation
Indices: 423198--423284 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 41
423188 AGTGCCATCA
* * *
423198 GTAAGTCTTTTGAGCATGATGATTAAATCCTTCGGGTCATTT
1 GTAAGTCTTTCGAGCATGATGA-TAAATCCTCCGGGCCATTT
* *
423240 GTAAGTCTTTCGAGTGA-GATGATAAGTCCTCCGGGCCATTT
1 GTAAGTCTTTCGAG-CATGATGATAAATCCTCCGGGCCATTT
423281 -TAAG
1 GTAAG
423285 CCTTCTCGGA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
40 4 0.10
41 16 0.41
42 18 0.46
43 1 0.03
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (41 bp):
GTAAGTCTTTCGAGCATGATGATAAATCCTCCGGGCCATTT
Found at i:423717 original size:53 final size:53
Alignment explanation
Indices: 423654--423855 Score: 280
Period size: 53 Copynumber: 3.8 Consensus size: 53
423644 AGAATTACAC
* *
423654 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACTCGTAAG
423707 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACTCGTAAG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACTCGTAAG
* * * ***
423760 CAGAAGATTGTTCGAGTTCTACTTCCTGAAGAAATAGGGAGCGAACTCGTTTT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACTCGTAAG
* * *
423813 TAGAAGATTGTTCAAGTTCCTTAATCCCTGAA-CAAGAGGGAGC
1 CAGAAGATTGTTCGAGTT-C-TACTCCCTGAAGCAAGAGGGAGC
423856 AGACACATCA
Statistics
Matches: 133, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
53 114 0.86
54 10 0.08
55 9 0.07
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.24
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACTCGTAAG
Found at i:427480 original size:64 final size:66
Alignment explanation
Indices: 427343--427504 Score: 183
Period size: 64 Copynumber: 2.5 Consensus size: 66
427333 AATTGTTCAG
* *
427343 TGTGTATCGATGCA-AAGGAAGTGCATCGACGCA-CCCATTAAAAATTGAAAAATCGAATGCAAT
1 TGTGTATCGATGCATAAGGAAGTGCATCGATGCACCCCATTAAAAATTGAAAAATCGAAGGCAAT
427406 T
66 T
* * * **
427407 AGTGAATCGATGCATAAGG-AGTGCATCGATGCACCCCCTT-AAAATT-AAAACATCGAAGGTGA
1 TGTGTATCGATGCATAAGGAAGTGCATCGATGCACCCCATTAAAAATTGAAAA-ATCGAAGGCAA
427469 TT
65 TT
* * *
427471 TGTGTATCGATGCAT-GGGTAGTGTATCGATGCAC
1 TGTGTATCGATGCATAAGGAAGTGCATCGATGCAC
427505 ATGTTAAAGA
Statistics
Matches: 83, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
63 6 0.07
64 68 0.82
65 9 0.11
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.25
Consensus pattern (66 bp):
TGTGTATCGATGCATAAGGAAGTGCATCGATGCACCCCATTAAAAATTGAAAAATCGAAGGCAAT
T
Found at i:428283 original size:23 final size:23
Alignment explanation
Indices: 428256--428323 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
428246 CATTTTATAT
428256 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * ** *
428279 GGCACTTCGATGCAATTCTTTGT
1 GGCACTTCGGTGCATTTCTACGC
* *
428302 GGCACTTTGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
428324 AGCTGTGGTG
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.16, C:0.24, G:0.25, T:0.35
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:430805 original size:41 final size:42
Alignment explanation
Indices: 430760--430859 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 42
430750 TTATTTATAA
* * * * *
430760 TTGTGAAGA-AAATATTTTTTTTATTAATCTTAGTTGGTGAT
1 TTGTGAAGACAAATATTTTTGTCACTAATCTTAATCGGTGAT
* * *
430801 TTGTGACGACAATTATTTTTGTCACTAGTCTTAATCGGTGAT
1 TTGTGAAGACAAATATTTTTGTCACTAATCTTAATCGGTGAT
* *
430843 TTGTGATGACAATTATT
1 TTGTGAAGACAAATATT
430860 CTTATCACCA
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 8 0.16
42 41 0.84
ACGTcount: A:0.27, C:0.08, G:0.18, T:0.47
Consensus pattern (42 bp):
TTGTGAAGACAAATATTTTTGTCACTAATCTTAATCGGTGAT
Found at i:432493 original size:104 final size:105
Alignment explanation
Indices: 432301--432503 Score: 282
Period size: 104 Copynumber: 1.9 Consensus size: 105
432291 ATAATAATAA
* * * *
432301 CGAACATTTGGTCACTAAAAAATACTTAGCGTGACAATATTGGTGGTCACAAAATATAGTTTTAG
1 CGAACATTTGATCACTAAAAAATACTTAACGTGACAATATTGATGGTCACAAAATATACTTTTAG
* **** * *
432366 TGTCAAACAAATTTATTGTAATTTTTATTGATAAAAGTAT
66 TGTCAAACAAATTCAAAACAATTTATAGTGATAAAAGTAT
*
432406 CGAACATTTGATCACT-AAAAATACTTAATGTGACAATATTGATGGTCACAAAATATACTTTTAG
1 CGAACATTTGATCACTAAAAAATACTTAACGTGACAATATTGATGGTCACAAAATATACTTTTAG
*
432470 TGTCAAATAAATTCAAAACAATTTATAGTGATAA
66 TGTCAAACAAATTCAAAACAATTTATAGTGATAA
432504 TTGTGTCAAA
Statistics
Matches: 85, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
104 70 0.82
105 15 0.18
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.34
Consensus pattern (105 bp):
CGAACATTTGATCACTAAAAAATACTTAACGTGACAATATTGATGGTCACAAAATATACTTTTAG
TGTCAAACAAATTCAAAACAATTTATAGTGATAAAAGTAT
Found at i:432530 original size:104 final size:103
Alignment explanation
Indices: 432311--432532 Score: 246
Period size: 104 Copynumber: 2.1 Consensus size: 103
432301 CGAACATTTG
* * *
432311 GTCACTAAAAAATACTTAGCGTGACAATATTGGTGGTCACAAAATATAGTTTTAGTGTCAAACAA
1 GTCAC-AAAAAATACTTAACGTGACAATATTGATGGTCACAAAATATACTTTTAGTGTCAAACAA
* **** * * * *
432376 ATTTATTGTAATTTTTATTGATAAAAGTATCGAACATTT
65 ATTCAAAACAATTTATAGTGATAAAAGTATCAAACAATT
* * *
432415 GATCACTAAAAATACTTAATGTGACAATATTGATGGTCACAAAATATACTTTTAGTGTCAAATAA
1 G-TCACAAAAAATACTTAACGTGACAATATTGATGGTCACAAAATATACTTTTAGTGTCAAACAA
** * *
432480 ATTCAAAACAATTTATAGTGATAATTGTGTCAAATAGATT
65 ATTCAAAACAATTTATAGTGATAAAAGTATCAAACA-ATT
432520 GTCACAAAAAATA
1 GTCACAAAAAATA
432533 TGAACAATTG
Statistics
Matches: 96, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
104 89 0.93
105 7 0.07
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (103 bp):
GTCACAAAAAATACTTAACGTGACAATATTGATGGTCACAAAATATACTTTTAGTGTCAAACAAA
TTCAAAACAATTTATAGTGATAAAAGTATCAAACAATT
Found at i:433801 original size:20 final size:20
Alignment explanation
Indices: 433776--433828 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
433766 TCAATTGAAA
433776 AGTGCTTGAGCAGTAAGTGT
1 AGTGCTTGAGCAGTAAGTGT
433796 AGTGCTTGAGCAGTAAGTGT
1 AGTGCTTGAGCAGTAAGTGT
*
433816 TGTGCTTGAGCAG
1 AGTGCTTGAGCAG
433829 CCCTCCGTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.11, G:0.36, T:0.30
Consensus pattern (20 bp):
AGTGCTTGAGCAGTAAGTGT
Found at i:438453 original size:44 final size:44
Alignment explanation
Indices: 438391--438605 Score: 274
Period size: 44 Copynumber: 5.0 Consensus size: 44
438381 GCGAAAAGCA
* * * * *
438391 GTAAGGTCTCACCTTTGCACATAGCAGAGGAGCATTTAGAAACG
1 GTAAGGTCTTACCCTTGCACATAGCAGAGGAGCCTTCAGAAATG
* * *
438435 GTAAGTTCTTACCCTTGCACATAGCAAAGGAGCCTTCAGAAATT
1 GTAAGGTCTTACCCTTGCACATAGCAGAGGAGCCTTCAGAAATG
* *
438479 GTAAGGTCTTAACCTTGCACATAGC--A-GAGCCTTCAGAAATT
1 GTAAGGTCTTACCCTTGCACATAGCAGAGGAGCCTTCAGAAATG
* *
438520 GTAAGGTCTTAACCTTGCACATAGCAGAGGAGCCTTCAAAAATG
1 GTAAGGTCTTACCCTTGCACATAGCAGAGGAGCCTTCAGAAATG
* * *
438564 GTAAGGTCTTACCCTTGCACAAAGCAAATGAGCCTTCAGAAA
1 GTAAGGTCTTACCCTTGCACATAGCAGAGGAGCCTTCAGAAA
438606 CTTCCTACAA
Statistics
Matches: 151, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
41 40 0.26
42 1 0.01
43 1 0.01
44 109 0.72
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (44 bp):
GTAAGGTCTTACCCTTGCACATAGCAGAGGAGCCTTCAGAAATG
Found at i:438540 original size:85 final size:87
Alignment explanation
Indices: 438391--438606 Score: 267
Period size: 85 Copynumber: 2.5 Consensus size: 87
438381 GCGAAAAGCA
* * * * *
438391 GTAAGGTC-TCACCTTTGCACATAGCAGAGGAGCATTTAGAAACGGTAAGTTCTTACCCTTGCAC
1 GTAAGGTCTTAACC-TTGCACATAGCA-AGGAGCCTTCAGAAACGGTAAGGTCTTAACCTTGCAC
* *
438455 ATAGCAAAGGAGCCTTCAGAAATT
64 ATAGCAAAGGAGCCTTCAAAAATG
**
438479 GTAAGGTCTTAACCTTGCACATAGC-A-GAGCCTTCAGAAATTGTAAGGTCTTAACCTTGCACAT
1 GTAAGGTCTTAACCTTGCACATAGCAAGGAGCCTTCAGAAACGGTAAGGTCTTAACCTTGCACAT
*
438542 AGCAGAGGAGCCTTCAAAAATG
66 AGCAAAGGAGCCTTCAAAAATG
* * *
438564 GTAAGGTCTTACCCTTGCACAAAGCAAATGAGCCTTCAGAAAC
1 GTAAGGTCTTAACCTTGCACATAGC-AAGGAGCCTTCAGAAAC
438607 TTCCTACAAC
Statistics
Matches: 111, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
85 73 0.66
86 1 0.01
87 1 0.01
88 32 0.29
89 4 0.04
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (87 bp):
GTAAGGTCTTAACCTTGCACATAGCAAGGAGCCTTCAGAAACGGTAAGGTCTTAACCTTGCACAT
AGCAAAGGAGCCTTCAAAAATG
Found at i:439407 original size:41 final size:41
Alignment explanation
Indices: 439361--439441 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
439351 CATTAAACCG
* *
439361 GGTCGGATCTGGTCAGGCATATGGGTCGGATTAACGGGTCA
1 GGTCGGATCTGGTCAGGCAGACGGGTCGGATTAACGGGTCA
439402 GGTCGGATCTGGTCAGGCAGACGGGTCGGATTAACGGGTC
1 GGTCGGATCTGGTCAGGCAGACGGGTCGGATTAACGGGTC
439442 GGGTTGGACA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.19, C:0.19, G:0.41, T:0.22
Consensus pattern (41 bp):
GGTCGGATCTGGTCAGGCAGACGGGTCGGATTAACGGGTCA
Found at i:444907 original size:2 final size:2
Alignment explanation
Indices: 444900--444930 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
444890 CCCAAACTCA
444900 AT AT AT 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 AT AT AT A
444931 AAAGTTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:445646 original size:178 final size:176
Alignment explanation
Indices: 445332--445688 Score: 655
Period size: 178 Copynumber: 2.0 Consensus size: 176
445322 GTGGTTAAAA
445332 AATTATTATTATTATTAAAGTTCACATGTTCCAACACGGAAATTGCAAGGTATTTGAGTGTTCAT
1 AATTATTATTATTATTAAAGTTCACATGTTCCAACACGGAAATTGCAAGGTATTTGAGTGTTCA-
445397 TTTAAAAATGGTTACGAGTCTTTAAAACATACTATCACTTGCAAACACTTAGATTAATAACAAAA
65 TTTAAAAATGGTTACGAGTCTTTAAAACATACTATCACTTGCAAACACTTAGATTAATAACAAAA
445462 TATGTTTATTTATTTATTTTAGTTTACTGATGAGATTTTAATTTAATTAT
130 TATGTTTA-TTATTTATTTTAG-TTACTGATGAGATTTTAA-TTAATTAT
445512 AATTATTATTATTATTAAAGTTCACATGTTCCAACACCGGAAATTGCAAGGTATTTGAGTGTTCA
1 AATTATTATTATTATTAAAGTTCACATGTTCCAACA-CGGAAATTGCAAGGTATTTGAGTGTTCA
445577 -TTAAAAATGGTTACGAGTCTTTAAAA-ATACTATCACTTGCAAACACTTAGATTAATAACAAAA
65 TTTAAAAATGGTTACGAGTCTTTAAAACATACTATCACTTGCAAACACTTAGATTAATAACAAAA
445640 TATGTTTATTATTTATTTTAGTTACTGATGAGATTTTAATTAATTAT
130 TATGTTTATTATTTATTTTAGTTACTGATGAGATTTTAATTAATTAT
445687 AA
1 AA
445689 GTTTAAAAGA
Statistics
Matches: 176, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
175 10 0.06
176 18 0.10
177 13 0.07
178 45 0.26
179 26 0.15
180 36 0.20
181 28 0.16
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.41
Consensus pattern (176 bp):
AATTATTATTATTATTAAAGTTCACATGTTCCAACACGGAAATTGCAAGGTATTTGAGTGTTCAT
TTAAAAATGGTTACGAGTCTTTAAAACATACTATCACTTGCAAACACTTAGATTAATAACAAAAT
ATGTTTATTATTTATTTTAGTTACTGATGAGATTTTAATTAATTAT
Found at i:445792 original size:76 final size:74
Alignment explanation
Indices: 445625--445774 Score: 243
Period size: 76 Copynumber: 2.0 Consensus size: 74
445615 GCAAACACTT
445625 AGATTAATAAC-AAAATATGTTTA-TTA-TTTATTTTAGTTACTGATGAGATTTTAATTAATTAT
1 AGATTAATAACAAAAATATGTTTATTTATTTTATTTTAGTTACTGATGAGATTTTAATTAATTAT
445687 AAGTTTAAA
66 AAGTTTAAA
445696 AGATTAATAACAAAATATATGTTTATTTATTTTATTTTAGTTTACTGATGAGATTTTAATTTAAT
1 AGATTAATAACAAAA-ATATGTTTATTTATTTTATTTTAG-TTACTGATGAGATTTTAA-TTAAT
445761 TATAAAGTTTAAA
63 TAT-AAGTTTAAA
445774 A
1 A
445775 TATTTATGTT
Statistics
Matches: 72, Mismatches: 0, Indels: 7
0.91 0.00 0.09
Matches are distributed among these distances:
71 11 0.15
72 3 0.04
73 9 0.12
74 3 0.04
75 10 0.14
76 18 0.25
77 8 0.11
78 10 0.14
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (74 bp):
AGATTAATAACAAAAATATGTTTATTTATTTTATTTTAGTTACTGATGAGATTTTAATTAATTAT
AAGTTTAAA
Found at i:447768 original size:13 final size:13
Alignment explanation
Indices: 447750--447775 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
447740 AATTAACTAA
447750 ACATTTTATATAT
1 ACATTTTATATAT
447763 ACATTTTATATAT
1 ACATTTTATATAT
447776 TGTTAGATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
ACATTTTATATAT
Found at i:447860 original size:2 final size:2
Alignment explanation
Indices: 447853--447883 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
447843 ATCGTTAAAT
447853 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 T
447884 TTCAATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:458695 original size:16 final size:16
Alignment explanation
Indices: 458671--458703 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
458661 TATCGCCGAC
*
458671 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
458687 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
458703 C
1 C
458704 ACGAATAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:459164 original size:20 final size:22
Alignment explanation
Indices: 459139--459180 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
459129 GGGCACGAAT
459139 TCGGTG-CCCCCC-TTTTGCAG
1 TCGGTGCCCCCCCTTTTTGCAG
459159 TCGGTGCCCCCCCTTTTTGCAG
1 TCGGTGCCCCCCCTTTTTGCAG
459181 CTATTGTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
21 6 0.30
22 8 0.40
ACGTcount: A:0.05, C:0.40, G:0.24, T:0.31
Consensus pattern (22 bp):
TCGGTGCCCCCCCTTTTTGCAG
Found at i:464411 original size:39 final size:39
Alignment explanation
Indices: 464357--464453 Score: 153
Period size: 39 Copynumber: 2.5 Consensus size: 39
464347 TTGATCTAAC
464357 GACACGAAATGTTCAAAATTTAAGAATCCATAAATTTAA
1 GACACGAAATGTTCAAAATTTAAGAATCCATAAATTTAA
*
464396 GACACGAAATGTTCAAAATTTAAGAATTCATAAATTTAA
1 GACACGAAATGTTCAAAATTTAAGAATCCATAAATTTAA
* *
464435 GA-ATGGAA-GTTCAAAATTT
1 GACACGAAATGTTCAAAATTT
464454 TAATATTATT
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
37 11 0.20
38 4 0.07
39 40 0.73
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.30
Consensus pattern (39 bp):
GACACGAAATGTTCAAAATTTAAGAATCCATAAATTTAA
Found at i:464432 original size:16 final size:15
Alignment explanation
Indices: 464407--464438 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
464397 ACACGAAATG
464407 TTCAAAATTTAAGAA
1 TTCAAAATTTAAGAA
464422 TTCATAAATTTAAGAA
1 TTCA-AAATTTAAGAA
464438 T
1 T
464439 GGAAGTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (15 bp):
TTCAAAATTTAAGAA
Found at i:465128 original size:22 final size:22
Alignment explanation
Indices: 465111--465158 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
465101 TAATATTTTG
465111 TTATAAATGTAT-TTATATTATA
1 TTATAAAT-TATATTATATTATA
*
465133 TTATATATTATATTATATTAT-
1 TTATAAATTATATTATATTATA
465154 TTATA
1 TTATA
465159 CTTTTCGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TTATAAATTATATTATATTATA
Found at i:465139 original size:12 final size:12
Alignment explanation
Indices: 465120--465150 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
465110 GTTATAAATG
465120 TATT-TATATTA
1 TATTATATATTA
465131 TATTATATATTA
1 TATTATATATTA
465143 TATTATAT
1 TATTATAT
465151 TATTTATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTATATATTA
Found at i:470708 original size:22 final size:22
Alignment explanation
Indices: 470685--470757 Score: 137
Period size: 22 Copynumber: 3.3 Consensus size: 22
470675 ATGAGTTACG
*
470685 GGAGTTACATGATATAATTTCG
1 GGAGTTACATGATATAATTTCA
470707 GGAGTTACATGATATAATTTCA
1 GGAGTTACATGATATAATTTCA
470729 GGAGTTACATGATATAATTTCA
1 GGAGTTACATGATATAATTTCA
470751 GGAGTTA
1 GGAGTTA
470758 TAATAGCTGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.36
Consensus pattern (22 bp):
GGAGTTACATGATATAATTTCA
Found at i:484264 original size:17 final size:16
Alignment explanation
Indices: 484242--484280 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
484232 AAATTATCAA
* *
484242 TTTTATTTAAATTAAT
1 TTTTATTGAAAATAAT
484258 TTATTATTGAAAATAAT
1 TT-TTATTGAAAATAAT
484275 TTTTAT
1 TTTTAT
484281 CAATTTCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TTTTATTGAAAATAAT
Found at i:484676 original size:3 final size:3
Alignment explanation
Indices: 484668--484705 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
484658 CGGAAGATAG
484668 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
484706 TGCCATTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:485732 original size:25 final size:26
Alignment explanation
Indices: 485703--485763 Score: 99
Period size: 25 Copynumber: 2.4 Consensus size: 26
485693 TATTTGTAGT
*
485703 AGAAAAATAATATTTATTATAATGA-
1 AGAAAAATAATATTAATTATAATGAC
485728 AGAAAAATAATATTAATTATAATGAC
1 AGAAAAATAATATTAATTATAATGAC
485754 A-AAAAATAAT
1 AGAAAAATAAT
485764 GACACCGTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
25 33 0.97
26 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.31
Consensus pattern (26 bp):
AGAAAAATAATATTAATTATAATGAC
Found at i:488039 original size:2 final size:2
Alignment explanation
Indices: 488032--488059 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
488022 AGTTGCAGCA
488032 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
488060 GGAGGCATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:489724 original size:17 final size:17
Alignment explanation
Indices: 489674--489724 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
489664 GTAAATTAAT
*
489674 ATTAAAATAA-ATAAATA
1 ATTAAAATAACA-CAATA
* *
489691 AATAAAATATTCACAATA
1 ATTAAAATA-ACACAATA
489709 ATTAAAATAACACAAT
1 ATTAAAATAACACAAT
489725 TTAAATTTGT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 14 0.52
18 12 0.44
19 1 0.04
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (17 bp):
ATTAAAATAACACAATA
Found at i:495711 original size:8 final size:8
Alignment explanation
Indices: 495698--495738 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
495688 CTCATTTTCA
495698 GAGAATTT
1 GAGAATTT
495706 GAGAATTT
1 GAGAATTT
*
495714 -AGAGTTT
1 GAGAATTT
*
495721 GGGAATTT
1 GAGAATTT
495729 GAGAATTT
1 GAGAATTT
495737 GA
1 GA
495739 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:495984 original size:127 final size:128
Alignment explanation
Indices: 495819--496425 Score: 1069
Period size: 127 Copynumber: 4.8 Consensus size: 128
495809 ACTATTCACA
495819 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGG-GCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
495884 TTATGTCACTCATGTCCATCGGGGACACTAGAT-ATATCAGTACCTATTATTTCTCAGGGGACT
65 TTATGTCACTCATGTCCCTCGGGGACACTAGATCATATCAGTACCTATTATTTCTCAGGGGACT
** * *
495947 TGAAGGCGATTTCCCGGGGGGCGCCTTCCATTATTTTGTCAAAGAATATATTATCATTGCCCTAT
1 TGAAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
*
496012 TATGTCACTCATGTCCCTCGGGGACACTA-TTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TATGTCACTCATGTCCCTCGGGGACACTAGATCATATCAGTACCTATTATTTCTCAGGGGACT
*
496074 TGAAGGCGCGTTCCCGGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGG-GCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
496139 TTATGTCACTCATGTCCCTTGGGGACACTAGAT-ATATCAGTACCTATTATTTCTCAGGGGACT
65 TTATGTCACTCATGTCCCTCGGGGACACTAGATCATATCAGTACCTATTATTTCTCAGGGGACT
*
496202 TGAAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATATTATCATTGCCCTAT
1 TGAAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
*
496267 TATGTCACTCATGTCCCTCGGGGACACTA-TTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TATGTCACTCATGTCCCTCGGGGACACTAGATCATATCAGTACCTATTATTTCTCAGGGGACT
*
496329 TGAAGGAGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
1 TGAAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
496394 TATGTCACTCATGTCCCTCGGGGACACTAGAT
66 TATGTCACTCATGTCCCTCGGGGACACTAGAT
496426 GGATTGTGAA
Statistics
Matches: 454, Mismatches: 20, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
126 2 0.00
127 312 0.69
128 139 0.31
129 1 0.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.33
Consensus pattern (128 bp):
TGAAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
TATGTCACTCATGTCCCTCGGGGACACTAGATCATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:496270 original size:255 final size:255
Alignment explanation
Indices: 495819--496425 Score: 1144
Period size: 255 Copynumber: 2.4 Consensus size: 255
495809 ACTATTCACA
495819 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
495884 TTATGTCACTCATGTCCATCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACTTG
66 TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACTTG
*
495949 AAGGCGATTTCCCGGGGGGCGCCTTCCATTATTTTGTCAAAGAATATATTATCATTGCCCTATTA
131 AAGGCGAGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAAAGAATATATTATCATTGCCCTATTA
496014 TGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
196 TGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
*
496074 TGAAGGCGCGTTCCCGGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
496139 TTATGTCACTCATGTCCCTTGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACTTG
66 TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACTTG
* *
496204 AAGGCGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATATTATCATTGCCCTATTA
131 AAGGCGAGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAAAGAATATATTATCATTGCCCTATTA
496269 TGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
196 TGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
*
496329 TGAAGGAGCGTTCCCGGGGG-GCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
496393 TTATGTCACTCATGTCCCTCGGGGACACTAGAT
66 TTATGTCACTCATGTCCCTCGGGGACACTAGAT
496426 GGATTGTGAA
Statistics
Matches: 343, Mismatches: 9, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
254 75 0.22
255 268 0.78
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.33
Consensus pattern (255 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACTTG
AAGGCGAGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAAAGAATATATTATCATTGCCCTATTA
TGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:496826 original size:34 final size:34
Alignment explanation
Indices: 496787--496859 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 34
496777 TAAGTTGAAA
*
496787 TTTAATGTTAAATTTTGAATACA-ATAATTTATAT
1 TTTAATGTTAAATTTCGAATA-ATATAATTTATAT
* *
496821 TTTAATTTTAAATTTCGAATAATATAATTTGTAT
1 TTTAATGTTAAATTTCGAATAATATAATTTATAT
496855 TTTAA
1 TTTAA
496860 AAACATTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
33 1 0.03
34 34 0.97
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (34 bp):
TTTAATGTTAAATTTCGAATAATATAATTTATAT
Found at i:497401 original size:21 final size:21
Alignment explanation
Indices: 497377--497446 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
497367 ATAAAACCCT
*
497377 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
497398 GCGGGCTAGGAATGTAACCCT-
1 GCGGGCTAGGAATGTAA-CCTG
* * *
497419 GCGGGCTCGTAATGTAAACTG
1 GCGGGCTAGGAATGTAACCTG
*
497440 GTGGGCT
1 GCGGGCT
497447 TGGCATATGA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 2 0.05
21 37 0.88
22 3 0.07
ACGTcount: A:0.20, C:0.21, G:0.37, T:0.21
Consensus pattern (21 bp):
GCGGGCTAGGAATGTAACCTG
Found at i:498054 original size:23 final size:22
Alignment explanation
Indices: 498014--498058 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
498004 ACTGAAACTG
498014 AAATATAAATATACAATTCAAAT
1 AAATATAAATATACAATT-AAAT
*
498037 AAATA-AAATATTCTAATTAAAT
1 AAATATAAATATAC-AATTAAAT
498059 CTAGCATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATATAAATATACAATTAAAT
Found at i:499257 original size:31 final size:33
Alignment explanation
Indices: 499192--499271 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 33
499182 TTAATAATTC
* *
499192 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTACATAAATATTA-TTTAA
*
499226 TAAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAAATAATAATTACATAAATATTATTTAA
*
499257 TATAAAATATAATAA
1 TA-AAAAAATAATAA
499272 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 6 0.15
32 10 0.25
33 2 0.05
34 22 0.55
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
TAAAAAAATAATAATTACATAAATATTATTTAA
Found at i:501532 original size:31 final size:30
Alignment explanation
Indices: 501497--501557 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
501487 ATTTTAGTGG
501497 TCAATACGCTATAAAATAATAATAAAAATAA
1 TCAATACGCTAT-AAATAATAATAAAAATAA
* * *
501528 TCAATATGTTATAAATAATAATATAAATAA
1 TCAATACGCTATAAATAATAATAAAAATAA
501558 ATAAAATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.59, C:0.07, G:0.03, T:0.31
Consensus pattern (30 bp):
TCAATACGCTATAAATAATAATAAAAATAA
Found at i:508588 original size:153 final size:153
Alignment explanation
Indices: 508310--508616 Score: 361
Period size: 153 Copynumber: 2.0 Consensus size: 153
508300 GGAACTCCAT
* ** **
508310 TCCCTCTGGTGTTAAAGAAATGGATACTAGGAATTCTGTTCCTTCATCTCCAGAACATGTAAATG
1 TCCCTCTGGTGTTAAAGAAATGGATACTAGGAACTCCATTCCTTCATCTCCAGAACACATAAATG
* * * * *
508375 TTGCTAAGGATGAACTGGATATGACAAATACGACTAGTCCCGTGACAGTTGCGTCAAATTTATTT
66 TTGCTAAGGATGAACTGGATATAACAAATACGACTAGTCCAGTGACAGTTACATCAAATTTATCT
* * * *
508440 GGAGCTTTAAGTTCAACCCCAAA
131 GAAACTTCAAGTTCAACACCAAA
* *
508463 TCCCTCTGGTGTTAAAGAAATGGATA-TAGGCAACTCCATTTCTTCATCTCCAGAACCCATAGAA
1 TCCCTCTGGTGTTAAAGAAATGGATACTAGG-AACTCCATTCCTTCATCTCCAGAACACATA-AA
* * * *
508527 -GTTG-TGAGGAATGAATTGGATATAAGAAAGT-CGACTAGTCCAGTGACCGTTACATCAAATTT
64 TGTTGCTAAGG-ATGAACTGGATATAACAAA-TACGACTAGTCCAGTGACAGTTACATCAAATTT
*
508589 CTCTGAAACTTCAAGTTCAACACCAAA
127 ATCTGAAACTTCAAGTTCAACACCAAA
508616 T
1 T
508617 ATTTTGGATT
Statistics
Matches: 129, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
152 8 0.06
153 118 0.91
154 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (153 bp):
TCCCTCTGGTGTTAAAGAAATGGATACTAGGAACTCCATTCCTTCATCTCCAGAACACATAAATG
TTGCTAAGGATGAACTGGATATAACAAATACGACTAGTCCAGTGACAGTTACATCAAATTTATCT
GAAACTTCAAGTTCAACACCAAA
Found at i:508766 original size:354 final size:352
Alignment explanation
Indices: 508109--508767 Score: 758
Period size: 354 Copynumber: 1.9 Consensus size: 352
508099 GGAACTCTAT
* * * *
508109 TCCCTATGGTGTTAAAGAAATGGATACTAGGTATTGCACTTCCTCATCTCCAGAACTCATAAATG
1 TCCCTATGGTGTTAAAGAAATGGATACTAGGAACTCCACTTCCTCATCTCCAGAACCCATAAATG
* * ** ** *
508174 TTGTGAGGGATGAATTGGATATGAGAACCATAACTAGTCCAGTGGTTCTTATGTCAAGTTGCTCT
66 TTGTGAGGAATGAATTGGATATAAGAA-CATAACTAGTCCAGTGGACCTTACATCAAATTGCTCT
* * * ** * * * * *
508239 GAAGCTTTAAGTTCAAGATTAAATGCTTCAGATTATTCTGGCGTCGAAGAACTGGATGTTAGGAA
130 GAAACTTCAAGTTCAACACCAAATACTTCAGATTATTCTGGCGTCAAAGAAATGGAGGGTAGGAA
* * *
508304 CTCCATTCCCTCTGGTGTTAAAGAAATGGATACTAGGAATTCTGTTCCTTCATCTCCAGAACATG
195 CTCCATTCCCACTGGTGCTAAAGAAATGGATACTAGGAAATCTGTTCCTTCATCTCCAGAACATG
* *
508369 TAAATGTTGCTAAGGATGAACTGGATATGACAAATACGACTAGTCCCGTGACAGTTGCGTCAAAT
260 -AAATGTTGCTAAGGATGAACTGGATATAACAAACACGACTAGTCCCGTGACAGTTGCGTCAAAT
508434 TTATTTGGAGCTTTAAGTTCAACCCCAAA
324 TTATTTGGAGCTTTAAGTTCAACCCCAAA
* * *
508463 TCCCTCTGGTGTTAAAGAAATGGATA-TAGGCAACTCCATTTCTTCATCTCCAGAACCCATAGAA
1 TCCCTATGGTGTTAAAGAAATGGATACTAGG-AACTCCACTTCCTCATCTCCAGAACCCATA-AA
* *
508527 -GTTGTGAGGAATGAATTGGATATAAGAA-AGTCGACTAGTCCAGT-GACCGTTACATCAAATTT
64 TGTTGTGAGGAATGAATTGGATATAAGAACA-T-AACTAGTCCAGTGGACC-TTACATCAAATTG
* ** *
508589 CTCTGAAACTTCAAGTTCAACACCAAATATTTTGGATTATTCTGGTGTCAAAGAAATGGAGGGTA
126 CTCTGAAACTTCAAGTTCAACACCAAATACTTCAGATTATTCTGGCGTCAAAGAAATGGAGGGTA
** * * *
508654 GGAACTCTGTTCCCACTGGTGCTCAAGAAATGGATATTGGGAACATCAT-TTCC-TCATCTCCAG
191 GGAACTCCATTCCCACTGGTGCTAAAGAAATGGATACTAGGAA-ATC-TGTTCCTTCATCTCCAG
* * * *
508717 AACCCATG-AATGTTG-TGAGGGATGAATTGGATATAAGAAACATGACTAGTC
254 AA--CATGAAATGTTGCT-AAGGATGAACTGGATATAACAAACACGACTAGTC
508768 GAGCAATCCT
Statistics
Matches: 251, Mismatches: 44, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
352 1 0.00
353 8 0.03
354 229 0.91
355 8 0.03
356 5 0.02
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (352 bp):
TCCCTATGGTGTTAAAGAAATGGATACTAGGAACTCCACTTCCTCATCTCCAGAACCCATAAATG
TTGTGAGGAATGAATTGGATATAAGAACATAACTAGTCCAGTGGACCTTACATCAAATTGCTCTG
AAACTTCAAGTTCAACACCAAATACTTCAGATTATTCTGGCGTCAAAGAAATGGAGGGTAGGAAC
TCCATTCCCACTGGTGCTAAAGAAATGGATACTAGGAAATCTGTTCCTTCATCTCCAGAACATGA
AATGTTGCTAAGGATGAACTGGATATAACAAACACGACTAGTCCCGTGACAGTTGCGTCAAATTT
ATTTGGAGCTTTAAGTTCAACCCCAAA
Found at i:508835 original size:201 final size:200
Alignment explanation
Indices: 508463--509017 Score: 654
Period size: 201 Copynumber: 2.8 Consensus size: 200
508453 CAACCCCAAA
* * * *
508463 TCCCTCTGGTGTTAAAGAAATGGATATAGGCAACTCCATTTCTTCATCTCCAGAACCCATAGAA-
1 TCCCTCTGGTGTTCAAGAAATGGATATTGGGAACTCCATTTCCTCATCTCCAGAACCCAT-GAAT
* * * * *
508527 GTTGTGAGGAATGAATTGGATATAAGAAA-GTCGACTAGTCCAGTGACCGTTACATCAAATTTCT
65 GTTGTGAGGGATGAATTGGATATAAGAAACAT-GACTAGTCCAGTGACC-TTGCATCAAGTTCCT
* *
508591 CTGAAACTTCAAGTTCAACACCAAATATTTTGGATTATTCTGGTGTCAAAGAAATGGAGGGT-AG
128 CTGAAGCTTCAAGTTCAACACCAAATATTTCGGATTATTCTGGTGTCAAAGAAATGGA-GGTCAG
*
508655 GAACTCTGT
192 GAACTCCGT
* *
508664 TCCCACTGGTGCTCAAGAAATGGATATTGGGAACAT-CATTTCCTCATCTCCAGAACCCATGAAT
1 TCCCTCTGGTGTTCAAGAAATGGATATTGGGAAC-TCCATTTCCTCATCTCCAGAACCCATGAAT
* **
508728 GTTGTGAGGGATGAATTGGATATAAGAAACATGACTAGTCGAGCAATCCTTGCATCAAGTTCCTC
65 GTTGTGAGGGATGAATTGGATATAAGAAACATGACTAGTCCAGTGA-CCTTGCATCAAGTTCCTC
* *
508793 TGAAGCTTCAAGTTCAACACCAAATATTTCGGATTGTTCTGGTGTCAAAGAAATGGATGTCAGGA
129 TGAAGCTTCAAGTTCAACACCAAATATTTCGGATTATTCTGGTGTCAAAGAAATGGAGGTCAGGA
*
508858 ATTCCGT
194 ACTCCGT
* * * * *
508865 TCCCTCT-GTGGTTCAAAAAACGGATGTTGTGAACTCCATTTTCTCATCTCCAGAACCCAT-AGA
1 TCCCTCTGGT-GTTCAAGAAATGGATATTGGGAACTCCATTTCCTCATCTCCAGAACCCATGA-A
** ** * * * * * * *
508928 TGTTGTGATAGATGAATTCAATGTGAGAACCATGGCTAGTCCAGTGACCCTGGCATCAAGCTGCT
64 TGTTGTGAGGGATGAATTGGATATAAGAAACATGACTAGTCCAGTGA-CCTTGCATCAAGTTCCT
*
508993 CTGAAGCTTTAAGTTCAACACCAAA
128 CTGAAGCTTCAAGTTCAACACCAAA
509018 CGTCTCAGAT
Statistics
Matches: 303, Mismatches: 43, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
200 9 0.03
201 290 0.96
202 4 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (200 bp):
TCCCTCTGGTGTTCAAGAAATGGATATTGGGAACTCCATTTCCTCATCTCCAGAACCCATGAATG
TTGTGAGGGATGAATTGGATATAAGAAACATGACTAGTCCAGTGACCTTGCATCAAGTTCCTCTG
AAGCTTCAAGTTCAACACCAAATATTTCGGATTATTCTGGTGTCAAAGAAATGGAGGTCAGGAAC
TCCGT
Found at i:510084 original size:24 final size:24
Alignment explanation
Indices: 510041--510098 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
510031 AAATGTAATA
*
510041 AATAATATTATTTATTAATAAAAT
1 AATAATATTATTTATAAATAAAAT
**
510065 AATAATATTATTT-TCAAATATTAT
1 AATAATATTATTTAT-AAATAAAAT
510089 AATAAT-TTAT
1 AATAATATTAT
510099 CTAATATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.17
24 25 0.83
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AATAATATTATTTATAAATAAAAT
Found at i:510161 original size:27 final size:31
Alignment explanation
Indices: 510131--510229 Score: 82
Period size: 36 Copynumber: 3.1 Consensus size: 31
510121 TATTATTATT
510131 AAATATTATATCTA-TA-A-TT-TTA-AATAA
1 AAATATTATAT-TATTATATTTATTAGAATAA
510158 AAATATTAATATTATTATATTTTATTAGAATAA
1 AAATATT-ATATTATTATA-TTTATTAGAATAA
*
510191 AAATATTATAATTATATTAAATATTTATTAAAATAA
1 AAATATTAT-A-T-TATT--ATATTTATTAGAATAA
510227 AAA
1 AAA
510230 ATAATATGTT
Statistics
Matches: 59, Mismatches: 1, Indels: 15
0.79 0.01 0.20
Matches are distributed among these distances:
27 9 0.15
28 6 0.10
29 1 0.02
31 2 0.03
32 5 0.08
33 13 0.22
34 1 0.02
35 4 0.07
36 15 0.25
37 3 0.05
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (31 bp):
AAATATTATATTATTATATTTATTAGAATAA
Found at i:510170 original size:33 final size:34
Alignment explanation
Indices: 510127--510236 Score: 97
Period size: 33 Copynumber: 3.3 Consensus size: 34
510117 TCAATATTAT
*
510127 TATTAAATATTATATCTATAATT-TTA-AATAAAAA
1 TATT-AATATTATATATAT-ATTATTAGAATAAAAA
*
510161 TATTAATATTAT-TATATTTTATTAGAATAAAAA
1 TATTAATATTATATATATATTATTAGAATAAAAA
* *
510194 TATT-ATAATTATATTAAATATTTATTAAAATAAAAA
1 TATTAAT-ATTATA-TATATA-TTATTAGAATAAAAA
510230 -A-TAATAT
1 TATTAATAT
510237 GTTGTTAAGT
Statistics
Matches: 64, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
31 2 0.03
32 9 0.14
33 25 0.39
34 7 0.11
35 7 0.11
36 14 0.22
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (34 bp):
TATTAATATTATATATATATTATTAGAATAAAAA
Found at i:510226 original size:36 final size:33
Alignment explanation
Indices: 510152--510236 Score: 95
Period size: 36 Copynumber: 2.5 Consensus size: 33
510142 CTATAATTTT
*
510152 AAATAAAAATATTAATATTATTATATTTTATTA
1 AAATAAAAATATTAATATTATTAAATTTTATTA
*
510185 GAATAAAAATATT-ATAATTATATTAAATATTTATTA
1 AAATAAAAATATTAAT-A-T-TATTAAAT-TTTATTA
510221 AAATAAAAA-A-TAATAT
1 AAATAAAAATATTAATAT
510237 GTTGTTAAGT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
32 2 0.05
33 14 0.32
34 3 0.07
35 10 0.23
36 15 0.34
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (33 bp):
AAATAAAAATATTAATATTATTAAATTTTATTA
Found at i:510502 original size:17 final size:17
Alignment explanation
Indices: 510465--510502 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
510455 TTTTTAGTAA
*
510465 ATATAATTTTAATAATT
1 ATATAATTTTAATAATG
510482 ATATAATTATTAA-AATG
1 ATATAATT-TTAATAATG
510499 ATAT
1 ATAT
510503 CAAAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
ATATAATTTTAATAATG
Found at i:510538 original size:19 final size:19
Alignment explanation
Indices: 510492--510539 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
510482 ATATAATTAT
*
510492 TAAAATGATATCAAAATAA
1 TAAAATAATATCAAAATAA
* *
510511 TATATTAATATC-AAATATA
1 TAAAATAATATCAAAATA-A
510530 TAAAATAATA
1 TAAAATAATA
510540 ATATTTTCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (19 bp):
TAAAATAATATCAAAATAA
Found at i:511644 original size:15 final size:15
Alignment explanation
Indices: 511602--511664 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
511592 AGTAATATCA
511602 TTATATAAATATTATT
1 TTATATAAATATTA-T
* *
511618 TTTTATTAAAATAATAT
1 TTATA-T-AAATATTAT
*
511635 TTATATAAATGTTAT
1 TTATATAAATATTAT
*
511650 TTATTTAAAT-TTAT
1 TTATATAAATATTAT
511664 T
1 T
511665 AATTATTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
14 5 0.13
15 16 0.41
16 5 0.13
17 6 0.15
18 7 0.18
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
TTATATAAATATTAT
Found at i:511825 original size:23 final size:24
Alignment explanation
Indices: 511777--511831 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
511767 AGTGATATGA
511777 TAATATTT-TTTTATAATTAATGT
1 TAATATTTATTTTATAATTAATGT
*
511800 TAATATTTATTATTAT-TTTAAT-T
1 TAATATTTATT-TTATAATTAATGT
511823 TAA-ATTTAT
1 TAATATTTAT
511832 AATGAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 6 0.21
23 12 0.41
24 7 0.24
25 4 0.14
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TAATATTTATTTTATAATTAATGT
Found at i:511841 original size:22 final size:24
Alignment explanation
Indices: 511793--511841 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 24
511783 TTTTTTATAA
* * *
511793 TTAATGTTAATATTTATTATTATT
1 TTAATGTTAATATTTATAATGAAT
511817 TTAAT-TTAA-ATTTATAATGAAT
1 TTAATGTTAATATTTATAATGAAT
511839 TTA
1 TTA
511842 TATTAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 13 0.59
23 4 0.18
24 5 0.23
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
TTAATGTTAATATTTATAATGAAT
Found at i:513470 original size:42 final size:42
Alignment explanation
Indices: 513388--513470 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
513378 GCTCAACCCT
* *
513388 CCAGTTCATATGTCATCTCCTCAGGGGTATATGCCAAGCCCA
1 CCAGTTCATATGTCATCTCCACAGGGGTACATGCCAAGCCCA
* * * *
513430 CCAGTTTATATGTCATCTCCACAGGGTTACATTCCTAGCCC
1 CCAGTTCATATGTCATCTCCACAGGGGTACATGCCAAGCCC
513471 TCAGGGTTAC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.29
Consensus pattern (42 bp):
CCAGTTCATATGTCATCTCCACAGGGGTACATGCCAAGCCCA
Found at i:513477 original size:21 final size:21
Alignment explanation
Indices: 513451--513499 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
513441 GTCATCTCCA
*
513451 CAGGGTTACATTCCTAGCCCT
1 CAGGGTTACATTCCTAGCCCG
513472 CAGGGTTACATTCCTAGCCCG
1 CAGGGTTACATTCCTAGCCCG
513493 CAGGGTT
1 CAGGGTT
513500 TTATGACACC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.18, C:0.31, G:0.24, T:0.27
Consensus pattern (21 bp):
CAGGGTTACATTCCTAGCCCG
Found at i:514051 original size:34 final size:34
Alignment explanation
Indices: 514008--514080 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
513998 TTAAATGTTT
*
514008 TTAATATACAAATTATAGTATTCAAAATTTAAAA
1 TTAAAATACAAATTATAGTATTCAAAATTTAAAA
* * *
514042 TTAAAATACAAATTATGGTATTCGAAATTTAACA
1 TTAAAATACAAATTATAGTATTCAAAATTTAAAA
514076 TTAAA
1 TTAAA
514081 TTCAACTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (34 bp):
TTAAAATACAAATTATAGTATTCAAAATTTAAAA
Found at i:514206 original size:14 final size:14
Alignment explanation
Indices: 514187--514217 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
514177 TTTTATCCTT
514187 AACATATACATTAA
1 AACATATACATTAA
514201 AACATATACATTAA
1 AACATATACATTAA
514215 AAC
1 AAC
514218 TAACTTATCA
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:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (14 bp):
AACATATACATTAA
Found at i:514331 original size:23 final size:22
Alignment explanation
Indices: 514302--514407 Score: 89
Period size: 23 Copynumber: 4.9 Consensus size: 22
514292 TTATCACTTC
514302 ACATTTATTCAATTTATTCATA
1 ACATTTATTCAATTTATTCATA
* *
514324 ACATTTTATCCAATATATTCA-A
1 ACA-TTTATTCAATTTATTCATA
* *
514346 ACA---ACT-AATTGA-TCACTTA
1 ACATTTATTCAATTTATTCA--TA
514365 ACATTTATTCAATTTATTCATA
1 ACATTTATTCAATTTATTCATA
*
514387 ACATTTTATCCAATTTATTCA
1 ACA-TTTATTCAATTTATTCA
514408 AACTTCACAT
Statistics
Matches: 65, Mismatches: 9, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
16 3 0.05
17 4 0.06
18 1 0.02
19 4 0.06
22 14 0.22
23 36 0.55
24 3 0.05
ACGTcount: A:0.38, C:0.17, G:0.01, T:0.44
Consensus pattern (22 bp):
ACATTTATTCAATTTATTCATA
Found at i:514901 original size:138 final size:139
Alignment explanation
Indices: 514548--515021 Score: 819
Period size: 139 Copynumber: 3.4 Consensus size: 139
514538 ATCTATAGTT
514548 CCCCGAGGGACATGAGTGACATAATAGGGCAA-GAATAACATATTCTCTGACAAAATAATTGAAG
1 CCCCGAGGGACATGAGTGACATAATAGGGCAATG-ATAACATATTCTCTGACAAAATAATTGAAG
* *
514612 GCGCGTCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATATTAGGTACTGACA
65 GCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTACTGACA
514677 TGAATAGTGC
130 TGAATAGTGC
514687 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATTGAAGG
1 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATTGAAGG
*
514752 CGCGCCTCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTACTGACAT
66 CGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTACTGACAT
514817 GAATAGTG-
131 GAATAGTGC
* * *
514825 CCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTATCTGAAAAAATAATTGAAGG
1 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATTGAAGG
* * *
514890 CGTGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCTCTCATAAATAATAGGTACTGACAT
66 CGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTACTGACAT
514955 GAATAGTGC
131 GAATAGTGC
*
514964 CCCCGAGGGAC-TCGAGTGACATAATAGGGCAATGATAACATATTCTCGGACAAAATAA
1 CCCCGAGGGACAT-GAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAA
515022 CCGTAGGTGC
Statistics
Matches: 318, Mismatches: 14, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
138 132 0.42
139 185 0.58
140 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (139 bp):
CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATTGAAGG
CGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAGAAATAATAGGTACTGACAT
GAATAGTGC
Found at i:518032 original size:22 final size:23
Alignment explanation
Indices: 518004--518051 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
517994 TTTATGATAT
* *
518004 TTATTTAATGTAATAATTAA-TA
1 TTATTTAATATAAAAATTAATTA
*
518026 TTATTTATTATAAAAATTAATTA
1 TTATTTAATATAAAAATTAATTA
518049 TTA
1 TTA
518052 ATTTTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTATTTAATATAAAAATTAATTA
Found at i:519445 original size:21 final size:21
Alignment explanation
Indices: 519412--519471 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 21
519402 TAATTATTAA
* * *
519412 AATATTTAAAATATGTTTATT
1 AATATTTATAATATATATATT
*
519433 AATATTTCTAATAATATATATT
1 AATATTTATAAT-ATATATATT
*
519455 -ATATTTTTAATAT-TATA
1 AATATTTATAATATATATA
519472 ATAAAAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 4 0.12
20 2 0.06
21 20 0.61
22 7 0.21
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
AATATTTATAATATATATATT
Found at i:519841 original size:22 final size:23
Alignment explanation
Indices: 519811--519858 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
519801 TAATAAATTT
519811 TTAATATTTTA-GAAATAATAATA
1 TTAATATTTTATGAAA-AATAATA
*
519834 TTAA-ATTTTATGATAAATAATA
1 TTAATATTTTATGAAAAATAATA
519856 TTA
1 TTA
519859 TTTATTGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (23 bp):
TTAATATTTTATGAAAAATAATA
Found at i:520052 original size:20 final size:20
Alignment explanation
Indices: 520013--520053 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
520003 TTCCAGAAAA
**
520013 CGTTTTCCAGAAATGTAATT
1 CGTTTTCCAGAAATCAAATT
*
520033 CGTTTTCCAGAATTCAAATT
1 CGTTTTCCAGAAATCAAATT
520053 C
1 C
520054 CAGTAATTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (20 bp):
CGTTTTCCAGAAATCAAATT
Found at i:520069 original size:29 final size:29
Alignment explanation
Indices: 520027--520107 Score: 144
Period size: 29 Copynumber: 2.8 Consensus size: 29
520017 TTCCAGAAAT
*
520027 GTAATTCGTTTTCCAGAATTCAAATTCCA
1 GTAATTCATTTTCCAGAATTCAAATTCCA
*
520056 GTAATTCATTTTCCAGAATTTAAATTCCA
1 GTAATTCATTTTCCAGAATTCAAATTCCA
520085 GTAATTCATTTTCCAGAATTCAA
1 GTAATTCATTTTCCAGAATTCAA
520108 TTTCTAGAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.40
Consensus pattern (29 bp):
GTAATTCATTTTCCAGAATTCAAATTCCA
Found at i:520110 original size:15 final size:15
Alignment explanation
Indices: 520035--520110 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
520025 ATGTAATTCG
520035 TTTTCCAGAATTCAA
1 TTTTCCAGAATTCAA
*
520050 -ATTCCAGTAATTC-A
1 TTTTCCAG-AATTCAA
*
520064 TTTTCCAGAATTTAA
1 TTTTCCAGAATTCAA
*
520079 -ATTCCAGTAATTC-A
1 TTTTCCAG-AATTCAA
520093 TTTTCCAGAATTCAA
1 TTTTCCAGAATTCAA
520108 TTT
1 TTT
520111 CTAGAAAACC
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
14 23 0.47
15 26 0.53
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (15 bp):
TTTTCCAGAATTCAA
Found at i:520111 original size:14 final size:14
Alignment explanation
Indices: 520036--520116 Score: 90
Period size: 14 Copynumber: 5.6 Consensus size: 14
520026 TGTAATTCGT
520036 TTTCCAGAATTCAA
1 TTTCCAGAATTCAA
* *
520050 ATTCCAGTAATTCAT
1 TTTCCAG-AATTCAA
*
520065 TTTCCAGAATTTAA
1 TTTCCAGAATTCAA
* *
520079 ATTCCAGTAATTCAT
1 TTTCCAG-AATTCAA
520094 TTTCCAGAATTCAA
1 TTTCCAGAATTCAA
*
520108 TTTCTAGAA
1 TTTCCAGAA
520117 AACCAATTAC
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
14 31 0.57
15 23 0.43
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.40
Consensus pattern (14 bp):
TTTCCAGAATTCAA
Found at i:521014 original size:15 final size:15
Alignment explanation
Indices: 520994--521028 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
520984 TCTGAGCCTA
520994 CAACGAACATGTCAT
1 CAACGAACATGTCAT
521009 CAACGAACATGTCAT
1 CAACGAACATGTCAT
521024 CAACG
1 CAACG
521029 TACAATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.40, C:0.29, G:0.14, T:0.17
Consensus pattern (15 bp):
CAACGAACATGTCAT
Found at i:522160 original size:30 final size:30
Alignment explanation
Indices: 522126--522198 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
522116 CCCAAAGGAC
522126 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
522156 CTATCCAGAGGTCATAAAGATCCTTGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
522186 CTGTCCATAGGTC
1 CTATCCAGAGGTC
522199 CCGAAGAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:522222 original size:31 final size:31
Alignment explanation
Indices: 522184--522248 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
522174 GATCCTTGGT
*
522184 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
* * **
522215 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
522246 AAC
1 AAC
522249 CCTCGACTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACATAGGTA
Found at i:524178 original size:15 final size:15
Alignment explanation
Indices: 524158--524191 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
524148 TTATGGTGTG
524158 ACTGGTTCTTCTTGA
1 ACTGGTTCTTCTTGA
524173 ACTGGTTCTTCTTGA
1 ACTGGTTCTTCTTGA
524188 ACTG
1 ACTG
524192 CTTCAGGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.44
Consensus pattern (15 bp):
ACTGGTTCTTCTTGA
Done.