Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002936.1 Hibiscus syriacus cultivar Beakdansim tig00006065_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: 51692
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:9209 original size:56 final size:53
Alignment explanation
Indices: 9144--9308 Score: 143
Period size: 56 Copynumber: 3.0 Consensus size: 53
9134 TATGCTTGAA
* *
9144 TTAACGATTGAAAACCTATGTGCTTCAATCGACAAACTGACACCTCTGTGTAG
1 TTAATGATTGAATACCTATGTGCTTCAATCGACAAACTGACACCTCTGTGTAG
* * * * * ** * * *
9197 TTAAAAATGATTGAGTACCTCTGTGCTTCAGTCTAGAATTTGGCACCTCTGTCCTTG
1 TT---AATGATTGAATACCTATGTGCTTCAATCGACAAACTGACACCTCTGT-GTAG
* * *
9254 GTAATGATT-AAGTACCTATGTGCTTCAATCGACAAACTGACACCTCCGTGCAG
1 TTAATGATTGAA-TACCTATGTGCTTCAATCGACAAACTGACACCTCTGTGTAG
9307 TT
1 TT
9309 GGAAATGACT
Statistics
Matches: 81, Mismatches: 26, Indels: 10
0.69 0.22 0.09
Matches are distributed among these distances:
53 5 0.06
54 36 0.44
56 37 0.46
57 3 0.04
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (53 bp):
TTAATGATTGAATACCTATGTGCTTCAATCGACAAACTGACACCTCTGTGTAG
Found at i:9335 original size:56 final size:55
Alignment explanation
Indices: 9157--9393 Score: 192
Period size: 54 Copynumber: 4.3 Consensus size: 55
9147 ACGATTGAAA
* * ** *
9157 ACCTATGTGCTTCAATCGACAAACTGACACCTCTGTGTAGTTAAAAATGATTGAGT
1 ACCTCTGTGCTTCAATCGACAAACTGACACCTCTGTG-CGTTGGAAATGATTGAGC
* * * ** * * * * *
9213 ACCTCTGTGCTTCAGTCTAGAATTTGGCACCTCTGT-CCTTGGTAATGATTAAGT
1 ACCTCTGTGCTTCAATCGACAAACTGACACCTCTGTGCGTTGGAAATGATTGAGC
* * *
9267 ACCTATGTGCTTCAATCGACAAACTGACACCTCCGTGCAGTTGGAAATGACTGAGC
1 ACCTCTGTGCTTCAATCGACAAACTGACACCTCTGTGC-GTTGGAAATGATTGAGC
* * * * * * *
9323 ACCTCTCTGCTTCAGTCTAGAATCTAGA-ACATCTATGCGTT-GAAATGATTGAGC
1 ACCTCTGTGCTTCAATCGACAAACT-GACACCTCTGTGCGTTGGAAATGATTGAGC
*
9377 ACCTCTTTGCTTCAATC
1 ACCTCTGTGCTTCAATC
9394 TAAAGTCTAG
Statistics
Matches: 140, Mismatches: 38, Indels: 8
0.75 0.20 0.04
Matches are distributed among these distances:
54 67 0.48
55 4 0.03
56 67 0.48
57 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (55 bp):
ACCTCTGTGCTTCAATCGACAAACTGACACCTCTGTGCGTTGGAAATGATTGAGC
Found at i:9370 original size:110 final size:110
Alignment explanation
Indices: 9157--9393 Score: 296
Period size: 110 Copynumber: 2.2 Consensus size: 110
9147 ACGATTGAAA
* * * * *
9157 ACCTATGTGCTTCAATCGACAAACTGACACCTCTGTGTAGTTAAAAATGATTGAGTACCTCTGTG
1 ACCTATGTGCTTCAATCGACAAACTGACACCTCCGTGCAGTTAAAAATGACTGAGCACCTCTCTG
* * * * * * *
9222 CTTCAGTCTAGAATTTGGCACCTCTGTCCTTGGTAATGATTAAGT
66 CTTCAGTCTAGAATCTAGAACATCTATCCTTGGAAATGATTAAGC
**
9267 ACCTATGTGCTTCAATCGACAAACTGACACCTCCGTGCAGTTGGAAATGACTGAGCACCTCTCTG
1 ACCTATGTGCTTCAATCGACAAACTGACACCTCCGTGCAGTTAAAAATGACTGAGCACCTCTCTG
* *
9332 CTTCAGTCTAGAATCTAGAACATCTATGCGTT-GAAATGATTGAGC
66 CTTCAGTCTAGAATCTAGAACATCTAT-CCTTGGAAATGATTAAGC
* *
9377 ACCTCTTTGCTTCAATC
1 ACCTATGTGCTTCAATC
9394 TAAAGTCTAG
Statistics
Matches: 108, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
110 105 0.97
111 3 0.03
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (110 bp):
ACCTATGTGCTTCAATCGACAAACTGACACCTCCGTGCAGTTAAAAATGACTGAGCACCTCTCTG
CTTCAGTCTAGAATCTAGAACATCTATCCTTGGAAATGATTAAGC
Found at i:9376 original size:54 final size:54
Alignment explanation
Indices: 9310--9435 Score: 146
Period size: 54 Copynumber: 2.3 Consensus size: 54
9300 CGTGCAGTTG
* *
9310 GAAATGACTGAGCACCTCTCTGCTTCAGTCTAGAA-TCTAGAACATCTATGCGTT
1 GAAATGATTGAGCACCTCTCTGCTTCAATCTA-AAGTCTAGAACATCTATGCGTT
* * * * * *
9364 GAAATGATTGAGCACCTCTTTGCTTCAATCTAAAGTCTAGCACCTTTGTGCTTT
1 GAAATGATTGAGCACCTCTCTGCTTCAATCTAAAGTCTAGAACATCTATGCGTT
*
9418 AAAATTGATTGAGCACCT
1 GAAA-TGATTGAGCACCT
9436 ATGTTCATAA
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
53 2 0.03
54 46 0.75
55 13 0.21
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (54 bp):
GAAATGATTGAGCACCTCTCTGCTTCAATCTAAAGTCTAGAACATCTATGCGTT
Found at i:9449 original size:55 final size:55
Alignment explanation
Indices: 9368--9472 Score: 140
Period size: 55 Copynumber: 1.9 Consensus size: 55
9358 TGCGTTGAAA
* * * * *
9368 TGATTGAGCACCTCTTTGCTTCAATCTAAAGTCTAGCACCTTTGTGCTTTAAAAT
1 TGATTGAGCACCTATTTGCATAAATCTAAAGTCAAGCACCTCTGTGCTTTAAAAT
*
9423 TGATTGAGCACCTATGTT-CATAAATCTAGAGTCAAGCACCTCTGTGCTTT
1 TGATTGAGCACCTAT-TTGCATAAATCTAAAGTCAAGCACCTCTGTGCTTT
9473 GACAACCAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
55 41 0.95
56 2 0.05
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (55 bp):
TGATTGAGCACCTATTTGCATAAATCTAAAGTCAAGCACCTCTGTGCTTTAAAAT
Found at i:19881 original size:3 final size:3
Alignment explanation
Indices: 19868--19921 Score: 81
Period size: 3 Copynumber: 17.0 Consensus size: 3
19858 TTATCATATA
19868 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATT ATT ATTT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT A-TT ATT
19916 ATT ATT
1 ATT ATT
19922 GTTAATAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
3 39 0.81
4 9 0.19
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:19886 original size:13 final size:13
Alignment explanation
Indices: 19868--19921 Score: 101
Period size: 13 Copynumber: 4.2 Consensus size: 13
19858 TTATCATATA
19868 ATTATTTATTATT
1 ATTATTTATTATT
19881 ATTA-TTATTATT
1 ATTATTTATTATT
19893 ATTATTTATTATT
1 ATTATTTATTATT
19906 ATTATTTATTATT
1 ATTATTTATTATT
19919 ATT
1 ATT
19922 GTTAATAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.30
13 28 0.70
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTATTTATTATT
Found at i:22775 original size:21 final size:21
Alignment explanation
Indices: 22753--22792 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
22743 GTTTTAACAT
22753 TTTTTC-TCTCAATTTATTTA
1 TTTTTCTTCTCAATTTATTTA
*
22773 TTTTTCTTTTCAATTTATTT
1 TTTTTCTTCTCAATTTATTT
22793 CGTATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTCTTCTCAATTTATTTA
Found at i:24553 original size:21 final size:20
Alignment explanation
Indices: 24467--24624 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
24457 AAATGACCAA
**
24467 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
24486 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
24506 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
24526 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
24547 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
24568 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
24588 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
24609 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
24625 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:24653 original size:20 final size:20
Alignment explanation
Indices: 24591--24784 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
24581 CGATTTTCCA
* ** *
24591 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
24611 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
24631 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
24651 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
24671 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
24691 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
24711 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
24731 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
24751 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
24772 AAATCGCAACGCG
1 AAATCGCAACGCG
24785 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:24675 original size:60 final size:60
Alignment explanation
Indices: 24591--24784 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
24581 CGATTTTCCA
* ** * *
24591 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
24651 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
24711 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
24772 AAATCGCAACGCG
1 AAATCGCAACGCG
24785 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:25205 original size:33 final size:33
Alignment explanation
Indices: 25166--25236 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
25156 TTCACTTAGA
*
25166 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
25199 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
25232 TTTCA
1 TTTCA
25237 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:25341 original size:21 final size:20
Alignment explanation
Indices: 25315--25420 Score: 91
Period size: 21 Copynumber: 5.5 Consensus size: 20
25305 TGCAGAAGAG
25315 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ****
25336 TCGCAACGAGAGAATGGCTG
1 TCGCAACGAGAAAATGAAAA
25356 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
25377 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
25391 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
25410 TCGCAACGAGA
1 TCGCAACGAGA
25421 GAATCGCAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
14 11 0.17
16 2 0.03
17 2 0.03
19 11 0.17
20 15 0.23
21 25 0.38
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.11
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:25372 original size:41 final size:37
Alignment explanation
Indices: 25314--25431 Score: 140
Period size: 41 Copynumber: 3.2 Consensus size: 37
25304 TTGCAGAAGA
*
25314 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGGCT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAA----T
25355 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAA-
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
*
25391 -TCGCAAC--GCGAAATGAAAATCGCAACGAGAGAA-
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
25424 -TCGCAACG
1 GTCGCAACG
25432 CGAAACCAAA
Statistics
Matches: 74, Mismatches: 2, Indels: 9
0.87 0.02 0.11
Matches are distributed among these distances:
33 32 0.43
35 7 0.09
41 35 0.47
ACGTcount: A:0.43, C:0.19, G:0.26, T:0.11
Consensus pattern (37 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
Found at i:25394 original size:14 final size:14
Alignment explanation
Indices: 25375--25431 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
25365 GAGAAATGAA
25375 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
25389 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
25408 AATCGCAACGAGAG
1 AATCGCAACGAGAG
25422 AATCGCAACG
1 AATCGCAACG
25432 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:25407 original size:33 final size:33
Alignment explanation
Indices: 25367--25447 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
25357 CGCAACGAGA
25367 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
25400 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
25433 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
25448 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:25465 original size:19 final size:19
Alignment explanation
Indices: 25443--25540 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
25433 GAAACCAAAA
*
25443 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
25462 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
25476 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
25495 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
25509 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
25528 TCGCGTTGCGATT
1 TCGCGTTGCGATT
25541 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:25484 original size:14 final size:14
Alignment explanation
Indices: 25465--25554 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
25455 TTTCATTTCG
25465 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
25479 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
25498 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
25512 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
25531 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
25545 CGTTGCGATT
1 CGTTGCGATT
25555 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:25490 original size:33 final size:33
Alignment explanation
Indices: 25448--25562 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
25438 CAAAATCGCA
25448 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
25481 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
25514 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
25547 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
25563 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:27473 original size:92 final size:93
Alignment explanation
Indices: 27259--27725 Score: 904
Period size: 92 Copynumber: 5.1 Consensus size: 93
27249 TAGATTGCTT
*
27259 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
27324 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
27352 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
27417 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
27444 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
27509 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
27537 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
27602 TTTGTC-TTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
27629 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
27694 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
27721 AGTAA
1 AGTAA
27726 TGCAATCCAT
Statistics
Matches: 371, Mismatches: 1, Indels: 5
0.98 0.00 0.01
Matches are distributed among these distances:
92 190 0.51
93 181 0.49
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:27489 original size:185 final size:185
Alignment explanation
Indices: 27259--27725 Score: 902
Period size: 185 Copynumber: 2.5 Consensus size: 185
27249 TAGATTGCTT
*
27259 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
27324 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
27389 GTGTATTCTTTAACACTGTGAAATAGTA-TTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTC-TTGTTTTGTCTTTTGGTTGAA
27444 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
27509 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
27574 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTGTTTTGTCTTTTGGTTGAA
27629 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
27694 TTTGTCTTTGTTTTGTCTTTTGGTTG-AAGTAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAA
27726 TGCAATCCAT
Statistics
Matches: 280, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
184 6 0.02
185 269 0.96
186 5 0.02
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (185 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTGTTTTGTCTTTTGGTTGAA
Found at i:27893 original size:19 final size:19
Alignment explanation
Indices: 27773--27887 Score: 141
Period size: 19 Copynumber: 6.3 Consensus size: 19
27763 TAGTTTACTT
* *
27773 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
27793 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
27812 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
27831 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
27845 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
27864 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
27883 TCGCA
1 TCGCA
27888 TTGCGATTCT
Statistics
Matches: 83, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
14 9 0.11
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 55 0.66
20 13 0.16
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:27907 original size:14 final size:14
Alignment explanation
Indices: 27888--27942 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
27878 CAAAATCGCA
27888 TTGCGATTCTTTCG
1 TTGCGATTCTTTCG
27902 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
*
27919 CATTGCGATTCTGTCG
1 --TTGCGATTCTTTCG
27935 TTGCGATT
1 TTGCGATT
27943 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 14 0.40
16 7 0.20
17 8 0.23
19 6 0.17
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (14 bp):
TTGCGATTCTTTCG
Found at i:27925 original size:33 final size:33
Alignment explanation
Indices: 27883--27961 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
27873 GAAACCAAAA
*
27883 TCGCATTGCGATTCTTTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTGTCGTTGCGATTTTCATT
27916 TCGCATTGCGATTCTGTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTGTCGTTGCGATTTTCATT
*
27949 TCGCGTTGCGATT
1 TCGCATTGCGATT
27962 TTGGTTTCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.46
Consensus pattern (33 bp):
TCGCATTGCGATTCTGTCGTTGCGATTTTCATT
Found at i:27926 original size:19 final size:17
Alignment explanation
Indices: 27894--27982 Score: 78
Period size: 19 Copynumber: 5.1 Consensus size: 17
27884 CGCATTGCGA
27894 TTCTTTCG-TTGCGATT
1 TTCTTTCGCTTGCGATT
27910 TTCATTTCGCATTGCGA--
1 TTC-TTTCGC-TTGCGATT
*
27927 TTCTGTCG-TTGCGATT
1 TTCTTTCGCTTGCGATT
27943 TTCATTTCGCGTTGCGATT
1 TTC-TTTCGC-TTGCGATT
*
27962 TTGGTTTCGCGTTGCGATT
1 TT-CTTTCGC-TTGCGATT
27981 TT
1 TT
27983 AAGTTTCGTG
Statistics
Matches: 61, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
14 6 0.10
16 10 0.16
17 12 0.20
19 33 0.54
ACGTcount: A:0.09, C:0.19, G:0.22, T:0.49
Consensus pattern (17 bp):
TTCTTTCGCTTGCGATT
Found at i:27990 original size:20 final size:19
Alignment explanation
Indices: 27933--27998 Score: 89
Period size: 19 Copynumber: 3.4 Consensus size: 19
27923 GCGATTCTGT
27933 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTT-AGTTTCG
*
27952 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAGTTTCG
27971 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT-AGTTTCG
*
27991 TGTTGCGA
1 CGTTGCGA
27999 AAGTAAACTA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 29 0.69
20 13 0.31
ACGTcount: A:0.11, C:0.17, G:0.27, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTAGTTTCG
Found at i:29924 original size:13 final size:14
Alignment explanation
Indices: 29916--29952 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
29906 TATTGTTTAA
29916 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
29930 ATGATTTGTAAAAG
1 TTGATTTGTAAAAG
29944 TTGATTTGT
1 TTGATTTGT
29953 GTAATTGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:30054 original size:19 final size:19
Alignment explanation
Indices: 30038--30082 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
30028 AAAAATGACT
30038 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
30057 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
30076 ATCGCAA
1 ATCGCAA
30083 CGAGAGAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:30153 original size:19 final size:19
Alignment explanation
Indices: 30129--30326 Score: 193
Period size: 19 Copynumber: 11.4 Consensus size: 19
30119 GATTCTCTCG
*
30129 TTGCGATTTTCATTTTGCA
1 TTGCGATTTTCATTTCGCA
30148 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
30167 TTGCGA--TTC-TCTAG--
1 TTGCGATTTTCATTTCGCA
30181 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
30200 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
30219 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
30233 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
30252 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
30266 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
30286 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
30300 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
30319 TTGCGATT
1 TTGCGATT
30327 CTCTCGTTGC
Statistics
Matches: 147, Mismatches: 11, Indels: 42
0.74 0.05 0.21
Matches are distributed among these distances:
14 29 0.20
16 22 0.15
17 19 0.13
18 3 0.02
19 62 0.42
20 12 0.08
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:30164 original size:52 final size:52
Alignment explanation
Indices: 30107--30340 Score: 306
Period size: 52 Copynumber: 4.6 Consensus size: 52
30097 TGCGTTTATA
*
30107 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTTGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
30159 ATTTCGCATTGCGATTCTCTAGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
30211 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT-T-TC
* * * *
30265 GTTGCG-ATTTTC-ATT-TC-CGCATTGCGATTTTCA--T-G--TTGGGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
30311 ATTTCGCATTGCGATTCTCTCGTTGCGATT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATT
30341 GTAATTTCCG
Statistics
Matches: 163, Mismatches: 10, Indels: 23
0.83 0.05 0.12
Matches are distributed among these distances:
46 9 0.06
47 13 0.08
48 9 0.06
49 2 0.01
50 1 0.01
51 3 0.02
52 100 0.61
53 17 0.10
54 9 0.06
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:30238 original size:14 final size:14
Alignment explanation
Indices: 30219--30273 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
30209 TCATTTCGCA
30219 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
30233 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
30250 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
30266 TTGCGATT
1 TTGCGATT
30274 TTCATTTCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:30348 original size:33 final size:33
Alignment explanation
Indices: 30107--30340 Score: 269
Period size: 33 Copynumber: 6.9 Consensus size: 33
30097 TGCGTTTATA
30107 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* * *
30140 ATTTTGCATTGCGATTTTCATTTCGCATTGCGATTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
* * * *
30178 TAGTT-GCGATTTTC-ATT-TCGCATTGCGATTTTC
1 -ATTTCGC-A-TTGCGATTCTCTCGTTGCGATTTTC
30211 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
30244 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* *
30277 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTC
30311 ATTTCGCATTGCGATTCTCTCGTTGCGATT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATT
30341 GTAATTTCCG
Statistics
Matches: 170, Mismatches: 17, Indels: 28
0.79 0.08 0.13
Matches are distributed among these distances:
31 3 0.02
32 8 0.05
33 98 0.58
34 29 0.17
35 6 0.04
36 4 0.02
37 2 0.01
38 12 0.07
39 5 0.03
40 3 0.02
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:31389 original size:24 final size:24
Alignment explanation
Indices: 31355--31401 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
31345 CTGAAACATC
31355 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
31379 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
31402 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:32112 original size:20 final size:20
Alignment explanation
Indices: 32084--32313 Score: 237
Period size: 20 Copynumber: 11.5 Consensus size: 20
32074 AAATTTCAGT
* * *
32084 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
32104 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
32124 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
32144 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
32164 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
32184 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
32204 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
32224 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
32244 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
32264 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
32284 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
32304 GTTGCGATTT
1 GTTGCGATTT
32314 TTTAAAATCG
Statistics
Matches: 182, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 181 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:32324 original size:21 final size:21
Alignment explanation
Indices: 32300--32356 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
32290 ATTTTCATAT
*
32300 TCGCGTTGCGATTTTTTAAAA
1 TCGCATTGCGATTTTTTAAAA
* * * **
32321 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTTTAAAA
32342 TCGCATTGCGATTTT
1 TCGCATTGCGATTTT
32357 CAAGAATTGC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTTTAAAA
Found at i:33260 original size:20 final size:21
Alignment explanation
Indices: 33235--33273 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
33225 ATATCGTTTT
33235 ACCGGTTTTGTCAT-TTTGAG
1 ACCGGTTTTGTCATATTTGAG
33255 ACCGGTTTTGTCATATTTG
1 ACCGGTTTTGTCATATTTG
33274 TACCTGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (21 bp):
ACCGGTTTTGTCATATTTGAG
Found at i:33392 original size:183 final size:181
Alignment explanation
Indices: 32715--33613 Score: 1191
Period size: 182 Copynumber: 4.9 Consensus size: 181
32705 TGTTGACATA
* * * * * * *
32715 TTTTCTCATATTTTTAGCTTTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACGCTT
1 TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAATATCGACACTT
* *
32780 TTTAGGCGCTATAACTTTTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATTTTAAATTATCGA
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
* * *
32845 CACTTTCAACATATATGGTATCGTATTACC-GTTTTGTCATTTTAAGACCGG
131 CACTTTCAACATATCTGGTA-CGTTTTACCGGTTTTGTCATTTTGAGACCGG
*
32896 TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAATATCGACACTT
1 TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAATATCGACACTT
* *
32961 TATAGGCGCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTCGATACTTATATTAAAGTATCG
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATT-CAGAAAGTGTCGATACTTATATTAAATTATCG
* * * **
33025 ACACGTTCAACATATCCGGTA-GTTATTTACCTGG-TTTGTCATTTTGAGATCTT
130 ACACTTTCAACATATCTGGTACG-T-TTTACC-GGTTTTGTCATTTTGAGACCGG
* * * * * *
33078 TTTTCTCATATTTTTAGCTGTTATATTGTTATCGATCGATACATTTTTATAAAGTGTCGATACTT
1 TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAATATCGACACTT
33143 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
* *
33208 CACTTTCAACATATCCGATATCGTTTTACCGGTTTTGTCATTTTGAGACCGG
131 CACTTTCAACATATCTGGTA-CGTTTTACCGGTTTTGTCATTTTGAGACCGG
* * * *
33260 TTTTGTCATATTTGTACCTGATATATTGTTATGGATCGATA-ATTTTTTTTTAAAATATCAACAC
1 TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACA--TTTTTATAAAATATCGACAC
* * * *
33324 TTTATAGGCGCTATAACTTTTTCTCTTTTAAATTCCA-AAAGTGTCGATAATTATATTAAAGTAT
64 TTTTTAGGCGCTATAACTTCTTCTCTTTTAAATT-CAGAAAGTGTCGATACTTATATTAAATTAT
** * *
33388 CGACACTTTCAACATATCTGGTA-GTTATTTACCTTTTTTATCATTTTGAGACCGA
128 CGACACTTTCAACATATCTGGTACG-T-TTTACCGGTTTTGTCATTTTGAGACCGG
* * * *
33443 TTTTGTCATATTTTTAGCTGTTATATTGTTATGGATCGATACATTTTCATAAAATTTTGACACTT
1 TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAATATCGACACTT
*** * *
33508 TTTAGATACTATAACATCTTCTCTTTTAAATTCAGAAAGTATCGATACTTATATTAAATTATCGA
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
*
33573 AACTTTCAACATATCTGGTAGCGTTTTACCGGTTTTGTCAT
131 CACTTTCAACATATCTGGTA-CGTTTTACCGGTTTTGTCAT
33614 ATTTTTACTT
Statistics
Matches: 625, Mismatches: 75, Indels: 35
0.85 0.10 0.05
Matches are distributed among these distances:
179 1 0.00
180 1 0.00
181 145 0.23
182 315 0.50
183 158 0.25
184 5 0.01
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.44
Consensus pattern (181 bp):
TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAATATCGACACTT
TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
CACTTTCAACATATCTGGTACGTTTTACCGGTTTTGTCATTTTGAGACCGG
Found at i:33459 original size:365 final size:364
Alignment explanation
Indices: 32714--33613 Score: 1444
Period size: 365 Copynumber: 2.5 Consensus size: 364
32704 ATGTTGACAT
* *
32714 ATTTTCTCATATTTTTAGCTTTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACGCT
1 ATTTTCTCATATTTTTAGCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACT
* *
32779 TTTTAGGCGCTATAACTTTTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATTTTAAATTATCG
66 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCG
* *
32844 ACACTTTCAACATATATGGTATCGTATTACC-GTTTTGTCATTTTAAGACCGGTTTTGTCATATT
131 ACACTTTCAACATATCTGGTATCGTTTTACCGGTTTTGTCATTTTAAGACCGGTTTTGTCATATT
* * *
32908 TTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAATATCGACACTTTATAGGCGCTAT
196 TGTACCTGATATATTGTTATGGATCGATACATTTTTTTAAAATATCAACACTTTATAGGCGCTAT
*
32973 AACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTATCGACACGTTCAACAT
261 AACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATAATTATATTAAAGTATCGACACGTTCAACAT
* * *
33038 ATCCGGTAGTTATTTACCTGGTTTGTCATTTTGAGATCT
326 ATCCGGTAGTTATTTACCTGGTTTATCATTTTGAGACCG
* * * *
33077 TTTTTCTCATATTTTTAGCTGTTATATTGTTATCGATCGATACATTTTTATAAAGTGTCGATACT
1 ATTTTCTCATATTTTTAGCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACT
33142 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCG
66 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCG
* * *
33207 ACACTTTCAACATATCCGATATCGTTTTACCGGTTTTGTCATTTTGAGACCGGTTTTGTCATATT
131 ACACTTTCAACATATCTGGTATCGTTTTACCGGTTTTGTCATTTTAAGACCGGTTTTGTCATATT
33272 TGTACCTGATATATTGTTATGGATCGATA-ATTTTTTTTTAAAATATCAACACTTTATAGGCGCT
196 TGTACCTGATATATTGTTATGGATCGATACA--TTTTTTTAAAATATCAACACTTTATAGGCGCT
* *
33336 ATAACTTTTTCTCTTTTAAATTCCAAAAGTGTCGATAATTATATTAAAGTATCGACACTTTCAAC
259 ATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATAATTATATTAAAGTATCGACACGTTCAAC
* **
33401 ATATCTGGTAGTTATTTACCTTTTTTATCATTTTGAGACCG
324 ATATCCGGTAGTTATTTACCTGGTTTATCATTTTGAGACCG
* * * *
33442 ATTTTGTCATATTTTTAGCTGTTATATTGTTATGGATCGATACATTTTCATAAAATTTTGACACT
1 ATTTTCTCATATTTTTAGCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACT
*** * *
33507 TTTTAGATACTATAACATCTTCTCTTTTAAATTCAGAAAGTATCGATACTTATATTAAATTATCG
66 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCG
* *
33572 AAACTTTCAACATATCTGGTAGCGTTTTACCGGTTTTGTCAT
131 ACACTTTCAACATATCTGGTATCGTTTTACCGGTTTTGTCAT
33614 ATTTTTACTT
Statistics
Matches: 492, Mismatches: 42, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
363 150 0.30
364 59 0.12
365 283 0.58
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (364 bp):
ATTTTCTCATATTTTTAGCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACT
TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCG
ACACTTTCAACATATCTGGTATCGTTTTACCGGTTTTGTCATTTTAAGACCGGTTTTGTCATATT
TGTACCTGATATATTGTTATGGATCGATACATTTTTTTAAAATATCAACACTTTATAGGCGCTAT
AACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATAATTATATTAAAGTATCGACACGTTCAACAT
ATCCGGTAGTTATTTACCTGGTTTATCATTTTGAGACCG
Found at i:36141 original size:42 final size:42
Alignment explanation
Indices: 36077--36161 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
36067 ACTGAATTAA
*
36077 ATGGGGACGGGGAAAAAACGTTTATACTAAACGGGGATGGGG
1 ATGGGGACGGGGAAAAAACGTTTATACTAAACGGGGACGGGG
* **
36119 ATGGGGACGGGGAAAAATCGTTTATGTTAAACGGGGACGGGG
1 ATGGGGACGGGGAAAAAACGTTTATACTAAACGGGGACGGGG
36161 A
1 A
36162 CGGGTTTAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.32, C:0.09, G:0.41, T:0.18
Consensus pattern (42 bp):
ATGGGGACGGGGAAAAAACGTTTATACTAAACGGGGACGGGG
Found at i:36223 original size:2 final size:2
Alignment explanation
Indices: 36216--36247 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
36206 TAAAAATAAT
36216 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36248 TAATAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42501 original size:21 final size:22
Alignment explanation
Indices: 42477--42528 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
42467 CTACAAGAGA
*
42477 AGAGGAA-TAATCGAAGAAAAT
1 AGAGGAATTAATCAAAGAAAAT
*
42498 AGAGGAAGATTAATCAAATAAAAT
1 AGAGG-A-ATTAATCAAAGAAAAT
42522 AGAGGAA
1 AGAGGAA
42529 ATATAGATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 5 0.19
22 2 0.08
23 2 0.08
24 17 0.65
ACGTcount: A:0.58, C:0.04, G:0.23, T:0.15
Consensus pattern (22 bp):
AGAGGAATTAATCAAAGAAAAT
Found at i:51047 original size:39 final size:39
Alignment explanation
Indices: 50967--51241 Score: 194
Period size: 39 Copynumber: 7.1 Consensus size: 39
50957 GGGGTTCACA
*
50967 ATCAATCTAGGACCAATGAACAGAATGATAGTGAGATTCAAC
1 ATCAATCTAGGACCAACGAAC--AA-GATAGTGAGATTCAAC
51009 ATCAATCTAGGACCAACGAACAAGATAGTGAGATTCAAC
1 ATCAATCTAGGACCAACGAACAAGATAGTGAGATTCAAC
* * * * * *** **
51048 ATCAACCTAGCACC-GCTGCACAAGAT-TTCTCATTCTTTC
1 ATCAATCTAGGACCAAC-GAACAAGATAGTGAGATTC-AAC
* * ** ** *
51087 -GCAAT-T-GTA--ATGGTAA-TGGCTA-TGAGATTCAAC
1 ATCAATCTAGGACCAACG-AACAAGATAGTGAGATTCAAC
51120 ATCAATCTAGGACCAACGAACAAGATAGTGAGATTCAAC
1 ATCAATCTAGGACCAACGAACAAGATAGTGAGATTCAAC
*
51159 ATCAATCTAGGACCAACGAACCAGATAGTGAGATTCAAC
1 ATCAATCTAGGACCAACGAACAAGATAGTGAGATTCAAC
* * * *
51198 ATCAACCTAGCACC-GCTGCACAAGAT-GATGAGATTCAAC
1 ATCAATCTAGGACCAAC-GAACAAGATAG-TGAGATTCAAC
51237 ATCAA
1 ATCAA
51242 CAACATGGCA
Statistics
Matches: 181, Mismatches: 38, Indels: 31
0.72 0.15 0.12
Matches are distributed among these distances:
33 1 0.01
34 12 0.07
35 2 0.01
36 4 0.02
37 3 0.02
38 16 0.09
39 121 0.67
40 2 0.01
42 20 0.11
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (39 bp):
ATCAATCTAGGACCAACGAACAAGATAGTGAGATTCAAC
Found at i:51242 original size:39 final size:38
Alignment explanation
Indices: 51107--51286 Score: 173
Period size: 39 Copynumber: 4.6 Consensus size: 38
51097 TGGTAATGGC
* *
51107 TATGAGATTCAACATCAATCTAGGACCAACGAACAAGA
1 TATGAGATTCAACATCAACCTAGCACCAACGAACAAGA
* * *
51145 TAGTGAGATTCAACATCAATCTAGGACCAACGAACCAGA
1 TA-TGAGATTCAACATCAACCTAGCACCAACGAACAAGA
* *
51184 TAGTGAGATTCAACATCAACCTAGCACC-GCTGCACAAGA
1 TA-TGAGATTCAACATCAACCTAGCACCAAC-GAACAAGA
* *** *
51223 TGATGAGATTCAACATCAACAACATGGCATTGATGAACAAGA
1 T-ATGAGATTCAACATCAAC--C-TAGCACCAACGAACAAGA
51265 TGATGAGATTCAACATCAACCT
1 T-ATGAGATTCAACATCAACCT
51287 GACATTGATG
Statistics
Matches: 123, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
38 3 0.02
39 86 0.70
40 2 0.02
41 1 0.01
42 31 0.25
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (38 bp):
TATGAGATTCAACATCAACCTAGCACCAACGAACAAGA
Found at i:51293 original size:39 final size:39
Alignment explanation
Indices: 51187--51299 Score: 138
Period size: 42 Copynumber: 2.8 Consensus size: 39
51177 AACCAGATAG
** * *
51187 TGAGATTCAACATCAACCT-AGCACCGCTGCACAAGATGA
1 TGAGATTCAACATCAACCTGA-CATTGATGAACAAGATGA
*
51226 TGAGATTCAACATCAACAACATGGCATTGATGAACAAGATGA
1 TGAGATTCAACATCAAC--C-TGACATTGATGAACAAGATGA
51268 TGAGATTCAACATCAACCTGACATTGATGAAC
1 TGAGATTCAACATCAACCTGACATTGATGAAC
51300 GATATGACGA
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
39 30 0.47
40 1 0.02
41 1 0.02
42 32 0.50
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (39 bp):
TGAGATTCAACATCAACCTGACATTGATGAACAAGATGA
Found at i:51659 original size:17 final size:17
Alignment explanation
Indices: 51637--51669 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
51627 CATATGATTT
51637 AAGAGACCCTTGACACG
1 AAGAGACCCTTGACACG
51654 AAGAGACCCTTGACAC
1 AAGAGACCCTTGACAC
51670 ACATAGGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.30, G:0.21, T:0.12
Consensus pattern (17 bp):
AAGAGACCCTTGACACG
Done.