Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005160.1 Hibiscus syriacus cultivar Beakdansim tig00011637_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: 70821
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:3257 original size:2 final size:2
Alignment explanation
Indices: 3250--3318 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
3240 AAATATGTAT
3250 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3292 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
3319 TTAATACATG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5341 original size:19 final size:20
Alignment explanation
Indices: 5319--5361 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
5309 GAAAAGATAT
5319 TCTCT-ATTTGAGG-AAAATA
1 TCTCTCATTTG-GGTAAAATA
5338 TCTCTCATTTGGGTTAAAATA
1 TCTCTCATTTGGG-TAAAATA
5359 TCT
1 TCT
5362 GTAAGTCCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
21 9 0.43
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (20 bp):
TCTCTCATTTGGGTAAAATA
Found at i:19191 original size:20 final size:19
Alignment explanation
Indices: 19166--19219 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
19156 GCAAAATAAA
19166 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
19186 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
19206 AATCGCAACGCGAT
1 AATCGCAACGCGAT
19220 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:19230 original size:21 final size:20
Alignment explanation
Indices: 19206--19382 Score: 94
Period size: 21 Copynumber: 8.6 Consensus size: 20
19196 CAGTTCCCAG
19206 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
*
19226 GAATCGCAATGCGA-TA-GTACA
1 -AATCGCAACGCGATTATG-A-A
** * *
19247 AATTCGCATTGCGATTTTCCAA
1 AA-TCGCAACGCGATTAT-GAA
*
19269 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGATTATGAA
**
19289 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGATTATGA-A
* *
19309 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGATTATGAA
* * *
19329 TATCGCAACGAGTATCCAT-AA
1 AATCGCAACGCG-AT-TATGAA
* *
19350 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGATTATG-AA
19371 AATCGCAACGCG
1 AATCGCAACGCG
19383 TATCCGTAAA
Statistics
Matches: 118, Mismatches: 24, Indels: 28
0.69 0.14 0.16
Matches are distributed among these distances:
19 3 0.03
20 50 0.42
21 59 0.50
22 5 0.04
23 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:19292 original size:20 final size:20
Alignment explanation
Indices: 19268--19600 Score: 289
Period size: 20 Copynumber: 16.6 Consensus size: 20
19258 CGATTTTCCA
* *
19268 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATACGT
* **
19288 AAATCGCAACGCGAACATAT
1 AAATCGCAACGCGAATACGT
*
19308 AAATCGCAACGCG-ATTC-T
1 AAATCGCAACGCGAATACGT
* * * * *
19326 GACTATCGCAACGAGTATCCAT
1 -A-AATCGCAACGCGAATACGT
19348 AAAATCGCAACGAC-AATACGT
1 -AAATCGCAACG-CGAATACGT
* *
19369 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGAATACGT
* *
19390 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATACGT
*
19410 AAATCGCAACGAGAATACGT
1 AAATCGCAACGCGAATACGT
* * *
19430 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATACGT
* * *
19450 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATACGT
* * *
19470 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATACGT
*
19490 AAATCGCAATGCGAATACGT
1 AAATCGCAACGCGAATACGT
*
19510 AAATCGCAATGCGAATACGT
1 AAATCGCAACGCGAATACGT
*
19530 AAATCGCAATGCGAATACGT
1 AAATCGCAACGCGAATACGT
*
19550 AAATCGCAATGCGAAT-CTGT
1 AAATCGCAACGCGAATAC-GT
* *
19570 AAATCGCAATGTGAAT-CTGT
1 AAATCGCAACGCGAATAC-GT
19590 AAATCGCAACG
1 AAATCGCAACG
19601 AGATTCTGAC
Statistics
Matches: 278, Mismatches: 28, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
18 1 0.00
19 3 0.01
20 239 0.86
21 33 0.12
22 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGAATACGT
Found at i:19452 original size:60 final size:60
Alignment explanation
Indices: 19330--19603 Score: 341
Period size: 60 Copynumber: 4.5 Consensus size: 60
19320 GATTCTGACT
* * * * * *
19330 ATCGCAACGAGTATCCATAAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAATGCGTATCCGT-AAATCGCAACGAGAATACGT-AAATCGCAATGCGAATCCGTAA
* *
19392 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAA
1 ATCGCAATGCGTATCCGTAAATCGCAACGAGAATACGTAAATCGCAATGCGAATCCGTAA
* * * * *
19452 ATCGCAATGCGTATCCGTAAATCGCAATGCGTATCCGTAAATCGCAATGCGAATACGTAA
1 ATCGCAATGCGTATCCGTAAATCGCAACGAGAATACGTAAATCGCAATGCGAATCCGTAA
* * * * *
19512 ATCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAATCGCAATGCGAATCTGTAA
1 ATCGCAATGCGTATCCGTAAATCGCAACGAGAATACGTAAATCGCAATGCGAATCCGTAA
* * *
19572 ATCGCAATGTGAATCTGTAAATCGCAACGAGA
1 ATCGCAATGCGTATCCGTAAATCGCAACGAGA
19604 TTCTGACTAT
Statistics
Matches: 190, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
60 155 0.82
61 19 0.10
62 16 0.08
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (60 bp):
ATCGCAATGCGTATCCGTAAATCGCAACGAGAATACGTAAATCGCAATGCGAATCCGTAA
Found at i:20493 original size:24 final size:24
Alignment explanation
Indices: 20461--20514 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
20451 GTATTCAAAA
20461 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
20485 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
20509 TTTGAT
1 TTTGAT
20515 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:23049 original size:19 final size:19
Alignment explanation
Indices: 23027--23096 Score: 131
Period size: 19 Copynumber: 3.7 Consensus size: 19
23017 AATTCACTCG
*
23027 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
23046 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
23065 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
23084 TTGCGATTTTCAT
1 TTGCGATTTTCAT
23097 CTTTTCCTCT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.14, C:0.20, G:0.17, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:23353 original size:20 final size:20
Alignment explanation
Indices: 23304--23357 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
23294 GACATTCATT
* * *
23304 TGACTATCACAATGCGGAAT
1 TGACTATCGCAACGCGGAAA
23324 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
*
23344 TGACTTTCGCAACG
1 TGACTATCGCAACG
23358 AGAGAATCGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:23387 original size:33 final size:34
Alignment explanation
Indices: 23350--23423 Score: 132
Period size: 33 Copynumber: 2.2 Consensus size: 34
23340 GAAATGACTT
23350 TCGCAACGAGAGAATCGTAATGCG-AAATGAAAA
1 TCGCAACGAGAGAATCGTAATGCGAAAATGAAAA
*
23383 TCGCAACGAGTGAATCGTAATGCGAAAATGAAAA
1 TCGCAACGAGAGAATCGTAATGCGAAAATGAAAA
23417 TCGCAAC
1 TCGCAAC
23424 ACGAAATTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 23 0.59
34 16 0.41
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (34 bp):
TCGCAACGAGAGAATCGTAATGCGAAAATGAAAA
Found at i:23621 original size:14 final size:14
Alignment explanation
Indices: 23602--23638 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
23592 TATCAATTAA
23602 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
23616 ACAAATCATCTTTT
1 ACAAATCAACATTT
23630 ACAAATCAA
1 ACAAATCAA
23639 TTAAAAAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:25171 original size:31 final size:31
Alignment explanation
Indices: 25133--25227 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
25123 GAACCTCGGC
* *
25133 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* **
25164 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* *
25195 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
25226 AA
1 AA
25228 GCCCTCGACT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 49 0.94
32 3 0.06
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:25393 original size:17 final size:19
Alignment explanation
Indices: 25361--25396 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
25351 CATATATCTC
25361 ATATCATATCACATGTATT
1 ATATCATATCACATGTATT
25380 ATAT-ATAT-ACATGTATT
1 ATATCATATCACATGTATT
25397 CATGTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATCATATCACATGTATT
Found at i:25991 original size:64 final size:65
Alignment explanation
Indices: 25880--26028 Score: 196
Period size: 64 Copynumber: 2.3 Consensus size: 65
25870 TCTTTCAATG
* ** * *
25880 AAGGTATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTT-TTTATTTTA
1 AAGGAATGCATCGATGCACTACTAATGCATCGATGCATAAAAGGCATTCGATGTTCTTTATTTT-
25944 A
65 A
* *
25945 AAGG-ATGCATCGATGCA-TAGCTAATGCATCGATGCATCAAAGGCATTCGATGTTCTTTCTTTT
1 AAGGAATGCATCGATGCACTA-CTAATGCATCGATGCATAAAAGGCATTCGATGTTCTTTATTTT
26008 A
65 A
26009 AAGGAATGCATCGATGCACT
1 AAGGAATGCATCGATGCACT
26029 TATGAATGTG
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
63 2 0.03
64 47 0.64
65 24 0.32
66 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (65 bp):
AAGGAATGCATCGATGCACTACTAATGCATCGATGCATAAAAGGCATTCGATGTTCTTTATTTTA
Found at i:28588 original size:21 final size:22
Alignment explanation
Indices: 28546--28602 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 22
28536 AATAACAAAC
*
28546 ATTAGTAATTGTTAAATAATTA
1 ATTAGTAATTGTTAAAAAATTA
28568 ATTA-TAATT-TTAAAAACATT-
1 ATTAGTAATTGTTAAAAA-ATTA
*
28588 ATATAGAAATTGTTA
1 AT-TAGTAATTGTTA
28603 CCTTAAAGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
20 8 0.28
21 10 0.34
22 8 0.28
23 3 0.10
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (22 bp):
ATTAGTAATTGTTAAAAAATTA
Found at i:29464 original size:20 final size:20
Alignment explanation
Indices: 29439--29549 Score: 78
Period size: 19 Copynumber: 6.0 Consensus size: 20
29429 TTTTGGTTGA
*
29439 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGCGAG
*
29459 AATGAAAATCACAACGCG-G
1 AATGAAAATCGCAACGCGAG
** *
29478 AAATGACTATCG-AA-ACGAG
1 -AATGAAAATCGCAACGCGAG
*
29497 -A-G--AATTGCAACGCGA-
1 AATGAAAATCGCAACGCGAG
*
29512 AATTAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGCGAG
*
29531 AATGAAAATCGCAATGCGA
1 AATGAAAATCGCAACGCGA
29550 TTTTGGTTTC
Statistics
Matches: 70, Mismatches: 13, Indels: 17
0.70 0.13 0.17
Matches are distributed among these distances:
14 3 0.04
15 2 0.03
16 5 0.07
17 1 0.01
18 2 0.03
19 33 0.47
20 24 0.34
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (20 bp):
AATGAAAATCGCAACGCGAG
Found at i:29595 original size:21 final size:21
Alignment explanation
Indices: 29569--29632 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
29559 CGCGTTGCGA
29569 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
29590 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
* *
29611 TTTTGT-GTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
29631 TT
1 TT
29633 TCATGTTGTG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 14 0.38
21 23 0.62
ACGTcount: A:0.11, C:0.19, G:0.17, T:0.53
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:29630 original size:20 final size:20
Alignment explanation
Indices: 29576--29647 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
29566 CGATTCTCTC
* *
29576 GTTGCGATTTTCATTTCTCT
1 GTTGCGATTTTCATTTTTAT
** *
29596 CGTTGCGATAGTCATTTTTGT
1 -GTTGCGATTTTCATTTTTAT
*
29617 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTTAT
*
29637 GTTGTGATTTT
1 GTTGCGATTTT
29648 AAGTTTAGAA
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
20 26 0.62
21 16 0.38
ACGTcount: A:0.12, C:0.14, G:0.19, T:0.54
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTTAT
Found at i:30233 original size:20 final size:20
Alignment explanation
Indices: 30208--30401 Score: 210
Period size: 20 Copynumber: 9.6 Consensus size: 20
30198 CTTTAAAAAT
*
30208 CGCGTTGTGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
30228 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* * *
30248 TGTCATTGCGCTTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
30269 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
30289 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
30309 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
30329 CGCGTTGCGATTTTACGTATT
1 CGCGTTGCGA-TTTACGGATA
**
30350 TTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
30370 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
30391 CTCGTTGCGAT
1 CGCGTTGCGAT
30402 AGTCAGAATT
Statistics
Matches: 143, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
20 93 0.65
21 50 0.35
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:30356 original size:41 final size:41
Alignment explanation
Indices: 30208--30401 Score: 198
Period size: 41 Copynumber: 4.8 Consensus size: 41
30198 CTTTAAAAAT
* * *
30208 CGCGTTGTGA-TTTACGGATACGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGATTTTACGGATACTCGTTGCGA-TTTACGGATA
* * * * * * *
30248 TGTCATTGCG-CTTTACGGATACGCATTGCGATTTACGTATT
1 CG-CGTTGCGATTTTACGGATACTCGTTGCGATTTACGGATA
* * *
30289 CTCGTTGCGA-TTTACAGATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGGATACTCGTTGCGATTTACGGATA
* **
30329 CGCGTTGCGATTTTACGTATTTTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGGATACTCGTTGCGATTTACGGATA
30370 CGCGTTGCGATTTTACGGATACTCGTTGCGAT
1 CGCGTTGCGATTTTACGGATACTCGTTGCGAT
30402 AGTCAGAATT
Statistics
Matches: 129, Mismatches: 20, Indels: 9
0.82 0.13 0.06
Matches are distributed among these distances:
40 51 0.40
41 78 0.60
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (41 bp):
CGCGTTGCGATTTTACGGATACTCGTTGCGATTTACGGATA
Found at i:30370 original size:61 final size:61
Alignment explanation
Indices: 30253--30401 Score: 237
Period size: 61 Copynumber: 2.4 Consensus size: 61
30243 CGTATTGTCA
* *
30253 TTGCGCTTTACGGATACGCATTGCGA-TTTACGTATTCTCGTTGCGATTTACAGATACGCG
1 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACAGATACGCG
* *
30313 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTTTCGTTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACAGATACGCG
*
30374 TTGCGATTTTACGGATACTCGTTGCGAT
1 TTGCGA-TTTACGGATACGCGTTGCGAT
30402 AGTCAGAATT
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
60 24 0.29
61 38 0.46
62 20 0.24
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (61 bp):
TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACAGATACGCG
Found at i:30417 original size:61 final size:61
Alignment explanation
Indices: 30253--30443 Score: 203
Period size: 61 Copynumber: 3.1 Consensus size: 61
30243 CGTATTGTCA
* * * *
30253 TTGCGCTTTACGGATACGCATTGCGAT-TTACGT-ATTCTCGTTGCGATTTACAGATACGCG
1 TTGCGATTTACGGATACGCGTTGCGATGTCACGTAATT-GCGTTGCGATTTACAGATACGCG
* * * * *
30313 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTTTCGTTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCGTTGCGATGTCACGTAATTGCGTTGCGATTTACAGATACGCG
* * *
30374 TTGCGATTTTACGGATACTCGTTGCGATAGTCA-G-AATTGCGTTGCGATTTATATG-TTCGCG
1 TTGCGA-TTTACGGATACGCGTTGCGAT-GTCACGTAATTGCGTTGCGATTTACA-GATACGCG
30435 TTGCGATTT
1 TTGCGATTT
30444 TCATATTCGC
Statistics
Matches: 114, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
60 28 0.25
61 60 0.53
62 24 0.21
63 2 0.02
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (61 bp):
TTGCGATTTACGGATACGCGTTGCGATGTCACGTAATTGCGTTGCGATTTACAGATACGCG
Found at i:30435 original size:20 final size:20
Alignment explanation
Indices: 30412--30458 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
30402 AGTCAGAATT
*
30412 GCGTTGCGATTTAT-ATGTTC
1 GCGTTGCGATTT-TCATATTC
30432 GCGTTGCGATTTTCATATTC
1 GCGTTGCGATTTTCATATTC
30452 GCGTTGC
1 GCGTTGC
30459 AATTATGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.13, C:0.19, G:0.26, T:0.43
Consensus pattern (20 bp):
GCGTTGCGATTTTCATATTC
Found at i:34643 original size:20 final size:20
Alignment explanation
Indices: 34618--34713 Score: 82
Period size: 20 Copynumber: 5.2 Consensus size: 20
34608 TTTTGGTTGA
34618 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
34638 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
** *
34657 AAATGACTATCGCAA--TGAG
1 -AATGAAAATCGCAACGAGAG
*
34676 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
34691 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
34711 AAT
1 AAT
34714 CGCAACGCAA
Statistics
Matches: 60, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
14 7 0.12
16 4 0.07
17 2 0.03
18 1 0.02
19 14 0.23
20 32 0.53
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:34702 original size:19 final size:19
Alignment explanation
Indices: 34616--34775 Score: 107
Period size: 19 Copynumber: 9.1 Consensus size: 19
34606 TCTTTTGGTT
*
34616 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
34635 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
34655 GGAAATGACTATCGCAA--T
1 -GAAATGAAAATCGCAACGC
*
34673 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
34689 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
34706 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
34722 AAAATTAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
34739 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
34755 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
34774 GA
1 GA
34776 TTTTGGTTTC
Statistics
Matches: 107, Mismatches: 17, Indels: 34
0.68 0.11 0.22
Matches are distributed among these distances:
14 28 0.26
15 3 0.03
16 4 0.04
17 4 0.04
18 3 0.03
19 35 0.33
20 28 0.26
21 2 0.02
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:34702 original size:33 final size:33
Alignment explanation
Indices: 34616--34770 Score: 202
Period size: 33 Copynumber: 4.5 Consensus size: 33
34606 TCTTTTGGTT
34616 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-G--AATCGCAACGC
** *
34655 GGAAATGACTATCGCAATGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
34689 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
34722 AAAATTAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
34755 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
34771 TGCGATTTTG
Statistics
Matches: 105, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
33 75 0.71
34 11 0.10
36 1 0.01
37 1 0.01
38 3 0.03
40 14 0.13
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:34716 original size:14 final size:14
Alignment explanation
Indices: 34665--34753 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 14
34655 GGAAATGACT
*
34665 ATCGCAATGAGAGA
1 ATCGCAACGAGAGA
*
34679 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
34698 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
* *
34712 ATCGCAACGCAAAATTAAA
1 ATCGCAACG----A-GAGA
34731 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
34745 ATCGCAACG
1 ATCGCAACG
34754 CGAAATGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 30 0.52
15 2 0.03
16 1 0.02
17 2 0.03
18 2 0.03
19 21 0.36
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:34821 original size:21 final size:21
Alignment explanation
Indices: 34795--34858 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
34785 CGCGTTGCGA
*
34795 TTCTCTCATTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
34816 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
34837 TT-TCGT-GTTGCGATTTTCAT
1 TTCTC-TCGTTGCGATTTTCAT
34857 TT
1 TT
34859 TCATGTTGTG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
20 16 0.43
21 21 0.57
ACGTcount: A:0.12, C:0.20, G:0.16, T:0.52
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:34871 original size:20 final size:20
Alignment explanation
Indices: 34803--34873 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
34793 GATTCTCTCA
34803 TTGCGATTTTCATTTCTC-TCG
1 TTGCGATTTTCATTT-TCAT-G
** *
34824 TTGCGATAGTCATTTTCGTG
1 TTGCGATTTTCATTTTCATG
34844 TTGCGATTTTCATTTTCATG
1 TTGCGATTTTCATTTTCATG
*
34864 TTGTGATTTT
1 TTGCGATTTT
34874 AAGTTTAGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
20 29 0.67
21 14 0.33
ACGTcount: A:0.13, C:0.15, G:0.18, T:0.54
Consensus pattern (20 bp):
TTGCGATTTTCATTTTCATG
Found at i:35490 original size:20 final size:19
Alignment explanation
Indices: 35455--35608 Score: 76
Period size: 20 Copynumber: 7.6 Consensus size: 19
35445 TTACGGATAC
35455 GCATTGCGATTTTACGTATT
1 GCATTGCGA-TTTACGTATT
* * *
35475 GTCATTGCGCTTTACGGATAC
1 G-CATTGCGATTTACGTAT-T
35496 GCATTGCGATTTACGTATT
1 GCATTGCGATTTACGTATT
* * * *
35515 CTCGTTGTGATTTACAG-ATAC
1 -GCATTGCGATTTAC-GTAT-T
* * *
35536 GCGTTGCGATTTACGGATAC
1 GCATTGCGATTTACGTAT-T
*
35556 GCGTTGCGATTTTACGTATTT
1 GCATTGCGA-TTTACGTA-TT
* * * *
35577 TCGTTGCGATTTACGGATAC
1 GCATTGCGATTTACGTAT-T
35597 GCATTGCGATTT
1 GCATTGCGATTT
35609 TACGGATACT
Statistics
Matches: 106, Mismatches: 19, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
19 2 0.02
20 79 0.75
21 24 0.23
22 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.39
Consensus pattern (19 bp):
GCATTGCGATTTACGTATT
Found at i:35529 original size:40 final size:40
Alignment explanation
Indices: 35436--35550 Score: 167
Period size: 40 Copynumber: 2.9 Consensus size: 40
35426 TTAAAAATCG
*
35436 CGTTGTGATTTACGGATACGCATTGCGATTTTACGTATTGT
1 CGTTGTGATTTACGGATACGCATTGCGA-TTTACGTATTCT
* * *
35477 CATTGCGCTTTACGGATACGCATTGCGATTTACGTATTCT
1 CGTTGTGATTTACGGATACGCATTGCGATTTACGTATTCT
* *
35517 CGTTGTGATTTACAGATACGCGTTGCGATTTACG
1 CGTTGTGATTTACGGATACGCATTGCGATTTACG
35551 GATACGCGTT
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
40 40 0.62
41 25 0.38
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.38
Consensus pattern (40 bp):
CGTTGTGATTTACGGATACGCATTGCGATTTACGTATTCT
Found at i:35596 original size:61 final size:60
Alignment explanation
Indices: 35477--35623 Score: 213
Period size: 61 Copynumber: 2.4 Consensus size: 60
35467 TACGTATTGT
* * *
35477 CATTGCGCTTTACGGATACGCATTGCGATTTACGTATTCTCGTTGTGATTTACAGATACG
1 CATTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACAGATACG
* * *
35537 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTTTCGTTGCGATTTACGGATACG
1 CATTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACAGATACG
*
35598 CATTGCGATTTTACGGATACTCGTTG
1 CATTGCGA-TTTACGGATACGCGTTG
35624 TGACACATTT
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
60 25 0.32
61 36 0.47
62 16 0.21
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (60 bp):
CATTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACAGATACG
Found at i:35622 original size:41 final size:41
Alignment explanation
Indices: 35444--35623 Score: 168
Period size: 41 Copynumber: 4.4 Consensus size: 41
35434 CGCGTTGTGA
* * * *
35444 TTTACGGATACGCATTGCGATTTTACGTAT-TGTCATTGCG-C
1 TTTACGGATACGCGTTGCGA-TTTACGGATACG-CATTGCGAT
* * * * * *
35485 TTTACGGATACGCATTGCGATTTACGTATTCTCGTTGTGA-
1 TTTACGGATACGCGTTGCGATTTACGGATACGCATTGCGAT
* *
35525 TTTACAGATACGCGTTGCGATTTACGGATACGCGTTGCGAT
1 TTTACGGATACGCGTTGCGATTTACGGATACGCATTGCGAT
* ***
35566 TTTACGTATTTTCGTTGCGATTTACGGATACGCATTGCGAT
1 TTTACGGATACGCGTTGCGATTTACGGATACGCATTGCGAT
*
35607 TTTACGGATACTCGTTG
1 TTTACGGATACGCGTTG
35624 TGACACATTT
Statistics
Matches: 117, Mismatches: 19, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
40 48 0.41
41 69 0.59
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.38
Consensus pattern (41 bp):
TTTACGGATACGCGTTGCGATTTACGGATACGCATTGCGAT
Found at i:37231 original size:18 final size:18
Alignment explanation
Indices: 37208--37243 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
37198 ACCGGTCAAC
37208 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
37226 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
37244 TGACCGGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.50, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:44459 original size:18 final size:18
Alignment explanation
Indices: 44434--44485 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
44424 CGGTCAACAT
44434 TCAACGGGTCGGGTCGGG
1 TCAACGGGTCGGGTCGGG
* *
44452 TTAACGGGTCGGGTTGGG
1 TCAACGGGTCGGGTCGGG
44470 TCAACGGGTCGGGTCG
1 TCAACGGGTCGGGTCG
44486 TGGCAGGTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.12, C:0.19, G:0.48, T:0.21
Consensus pattern (18 bp):
TCAACGGGTCGGGTCGGG
Found at i:46690 original size:17 final size:17
Alignment explanation
Indices: 46652--46690 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
46642 CACATGTCAA
46652 TTTTTGTCTTAAAAGTG
1 TTTTTGTCTTAAAAGTG
*
46669 ATTTTT-TCTTAAAATTG
1 -TTTTTGTCTTAAAAGTG
46686 TTTTT
1 TTTTT
46691 AGAAAACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 10 0.50
18 5 0.25
ACGTcount: A:0.23, C:0.05, G:0.10, T:0.62
Consensus pattern (17 bp):
TTTTTGTCTTAAAAGTG
Found at i:46828 original size:18 final size:18
Alignment explanation
Indices: 46791--46828 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
46781 TTTTCTAAAA
*
46791 TTAAAATAATAACTATTT
1 TTAAAATAATAACTAATT
*
46809 TTAAAATAATAATTAATT
1 TTAAAATAATAACTAATT
46827 TT
1 TT
46829 TTTTGTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAAATAATAACTAATT
Found at i:53793 original size:2 final size:2
Alignment explanation
Indices: 53788--53818 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
53778 CACACACATA
53788 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
53819 CACACACACA
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:57558 original size:54 final size:54
Alignment explanation
Indices: 57422--58012 Score: 613
Period size: 54 Copynumber: 11.1 Consensus size: 54
57412 CTTGAAAAAC
* * *
57422 CTTCTGTC-AACGGGTTCGTTCCCTCTTCCT-TCAGGGAGTATAGAACTTGAACAAT
1 CTTCT-TCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAAC-AT
* * * *
57477 CATT-TGCAAACGAGTTTGCTCCCTCTTTCTCTAGGGAGTATAGAACTCAAACAT
1 C-TTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACAT
** * * *
57531 CTTCTTCTTACGAGTTCGTTCCCTCTTTATCTAGGGAGTATAGAACTCGAACA-
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACAT
* * *
57584 --TCTTCAAACGGGTTTGCTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAACA-
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAACAT
* * *
57636 --TCTTCAAACGGGTTCGCTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAATAAT
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAA-CAT
* * * * *
57690 CTTCTGCAAACAGGTTCGTTCCCTCTTTATCTAGGGAGTAT-GAAACTCGAATAAT
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAG-AACTCGAA-CAT
*
57745 CTTCTGCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACAT
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACAT
** * * *
57799 CTTCTTCTTACGGGTTCGTTCCCTCTTTATCTAGGGAGTATGGAACTCGAACA-
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACAT
* * * *
57852 --TCTTCAAACGGGTTTGCTCCCTCTTTCT-TCAGGGAGAATAGAACTCAAATAT
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAACAT
** * *
57904 CTTCTTCAAACGGGTTCATTCCCTCTTTATCTAGGGAGTATGGAACTCGAACAT
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACAT
* * *
57958 CTTC-T--AACAGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAAAAT
1 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACAT
58009 CTTC
1 CTTC
58013 AAACGTGTCT
Statistics
Matches: 456, Mismatches: 64, Indels: 36
0.82 0.12 0.06
Matches are distributed among these distances:
50 1 0.00
51 106 0.23
52 69 0.15
53 4 0.01
54 142 0.31
55 105 0.23
56 29 0.06
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (54 bp):
CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACAT
Found at i:57692 original size:105 final size:103
Alignment explanation
Indices: 57430--58017 Score: 606
Period size: 105 Copynumber: 5.5 Consensus size: 103
57420 ACCTTCTGTC
* * * * * * *
57430 AACGGGTTCGTTCCCTCTTCCTTCAGGGAGTATAGAACTTGAACAATCATTTGCAAACGAGTTTG
1 AACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAATAATC--TT-CAAACGGGTTCG
* * *
57495 CTCCCTCTTTCTCTAGGGAGTATAGAACTCAAACATCTTCTTCT
63 CTCCCTCTTTATCTAGGGAGTATAGAACTCGAACA---TCTTCA
* * * * * * *
57539 TACGAGTTCGTTCCCTCTTTATCTAGGGAGTATAGAACTCGAA-CATCTTCAAACGGGTTTGCTC
1 AACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAATAATCTTCAAACGGGTTCGCTC
* * *
57603 CCTCTTTCTTTCAGGAAGTATAGAACTCGAACATCTTCA
66 CCTCTTTATCT-AGGGAGTATAGAACTCGAACATCTTCA
* *
57642 AACGGGTTCGCTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAATAATCTTCTGCAAACAGGTTC
1 AACGGGTTCGCTCCCTCTTTCTTT-AGGGAGTATAGAACTCGAATAATC-T-T-CAAACGGGTTC
* *
57707 GTTCCCTCTTTATCTAGGGAGTAT-GAAACTCGAATAATCTTCTGCA
62 GCTCCCTCTTTATCTAGGGAGTATAG-AACTCGAA-CATC-T-T-CA
* ** ** *
57753 AACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGT
1 AACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCG-A-ATAATCTTCAAACGGGTTCGC
*
57818 TCCCTCTTTATCTAGGGAGTATGGAACTCGAACATCTTCA
64 TCCCTCTTTATCTAGGGAGTATAGAACTCGAACATCTTCA
* * * * * **
57858 AACGGGTTTGCTCCCTCTTTCTTCAGGGAGAATAGAACTCAAATATCTTCTTCAAACGGGTTCAT
1 AACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAATA--ATCTTCAAACGGGTTCGC
* *
57923 TCCCTCTTTATCTAGGGAGTATGGAACTCGAACATCTTCT
64 TCCCTCTTTATCTAGGGAGTATAGAACTCGAACATCTTCA
*
57963 AACAGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAA-AATCTTCAAACG
1 AACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAATAATCTTCAAACG
58018 TGTCTGCTCC
Statistics
Matches: 412, Mismatches: 51, Indels: 39
0.82 0.10 0.08
Matches are distributed among these distances:
102 10 0.02
103 26 0.06
104 20 0.05
105 157 0.38
106 24 0.06
107 18 0.04
108 30 0.07
109 77 0.19
110 19 0.05
111 27 0.07
112 4 0.01
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (103 bp):
AACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAATAATCTTCAAACGGGTTCGCTC
CCTCTTTATCTAGGGAGTATAGAACTCGAACATCTTCA
Found at i:57962 original size:268 final size:263
Alignment explanation
Indices: 57434--58012 Score: 819
Period size: 268 Copynumber: 2.2 Consensus size: 263
57424 TCTGTCAACG
* *
57434 GGTTCGTTCCCTCTTCCTTC-AGGGAGTATAGAACTTGAACAATCATT-TGCAAACGAGTTTGCT
1 GGTTCGTTCCCTCTT--TTCTAGGGAGTATAGAACTCGAA-AATC-TTCTGCAAACGAGTTCGCT
57497 CCCTCTTTCTCTAGGGAGTATAGAACTCAAACATCTTCTTCTTACGAGTTCGTTCCCTCTTTATC
62 CCCTCTTTCTCTAGGGAGTATAGAACTCAAACATCTTCTTCTTACGAGTTCGTTCCCTCTTTATC
*
57562 TAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTTGCTCCCTCTTTCTTTCAGGAAGTATAGA
127 TAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTTGCTCCCTCTTTCTTTCAGGAAGAATAGA
* * * *
57627 ACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAATAATCT
192 ACTCAAACATCTTCAAACGGGTTCACTCCCTCTTTATCTCAGGAAGTATAGAACTCGAATAATCT
57692 TCTGCAAACA
257 TCT---AACA
*
57702 GGTTCGTTCCCTCTTTATCTAGGGAGTAT-GAAACTCGAATAATCTTCTGCAAACGGGTTCGCTC
1 GGTTCGTTCCCTCTTT-TCTAGGGAGTATAG-AACTCGAA-AATCTTCTGCAAACGAGTTCGCTC
* *
57766 CCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGTTCCCTCTTTATCT
63 CCTCTTTCTCTAGGGAGTATAGAACTCAAACATCTTCTTCTTACGAGTTCGTTCCCTCTTTATCT
* *
57831 AGGGAGTATGGAACTCGAACATCTTCAAACGGGTTTGCTCCCTCTTTC-TTCAGGGAGAATAGAA
128 AGGGAGTATAGAACTCGAACATCTTCAAACGGGTTTGCTCCCTCTTTCTTTCAGGAAGAATAGAA
* * * * *
57895 CTCAAATATCTTCTTCAAACGGGTTCATTCCCTCTTTATCT-AGGGAGTATGGAACTCGAA-CAT
193 CTC-AA-A-CATCTTCAAACGGGTTCACTCCCTCTTTATCTCAGGAAGTATAGAACTCGAATAAT
57958 CTTCTAACA
255 CTTCTAACA
* *
57967 GGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAAAATCTTC
1 GGTTCGTTCCCTCTTT-TCTAGGGAGTATAGAACTCGAAAATCTTC
58013 AAACGTGTCT
Statistics
Matches: 282, Mismatches: 21, Indels: 20
0.87 0.07 0.06
Matches are distributed among these distances:
264 7 0.02
265 38 0.13
266 2 0.01
267 22 0.08
268 168 0.60
269 18 0.06
270 27 0.10
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (263 bp):
GGTTCGTTCCCTCTTTTCTAGGGAGTATAGAACTCGAAAATCTTCTGCAAACGAGTTCGCTCCCT
CTTTCTCTAGGGAGTATAGAACTCAAACATCTTCTTCTTACGAGTTCGTTCCCTCTTTATCTAGG
GAGTATAGAACTCGAACATCTTCAAACGGGTTTGCTCCCTCTTTCTTTCAGGAAGAATAGAACTC
AAACATCTTCAAACGGGTTCACTCCCTCTTTATCTCAGGAAGTATAGAACTCGAATAATCTTCTA
ACA
Found at i:58191 original size:55 final size:55
Alignment explanation
Indices: 58019--58398 Score: 507
Period size: 55 Copynumber: 7.0 Consensus size: 55
58009 CTTCAAACGT
* * *
58019 GTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCC--ACAATCTTCATCAATCAC
1 GTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGC
* * *
58072 GTCTTCCCCCTATTTCTTCAGAGAGTATAAGACCC--ACAATCTTCATCAATCAC
1 GTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGC
* *
58125 GTTTGCCCCCTATTTCTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGT
1 GTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGC
* * * *
58180 GTCCGCCCCCTATTTCTTCAGAGAGTATAACACTCGAACAATCTTCAACGATCGC
1 GTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGC
* * *
58235 GTCTGCCCTCTATTTCTTCAGAGAGTATAAGACCTGAACAATCTTCAACAATCGT
1 GTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGC
* * ** *
58290 GTCCGCCCCCTATTTCCTCAGAGAGTATAAGACTTGAACAATCTTCAACGATCGC
1 GTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGC
* * ** *
58345 GTCCGCCCCCTATTTCTTCAGAGAGTATGAGACTTGAACAATCTTCAACGATCG
1 GTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCG
58399 TAGGGAACCT
Statistics
Matches: 297, Mismatches: 28, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
53 84 0.28
55 213 0.72
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.28
Consensus pattern (55 bp):
GTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGC
Found at i:58268 original size:110 final size:110
Alignment explanation
Indices: 57975--58399 Score: 553
Period size: 110 Copynumber: 3.9 Consensus size: 110
57965 CAGGTTCGCT
* * * * *
57975 CCCTCTTTCTTTAGGGAGTAT-AGAACTCGAA-AATCTTCAA--A-CGTGTCTGCTCCCTATTTC
1 CCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTC
* ** **
58035 TTCAGAGAGTATAAGACCC--ACAATCTTCATCAATCACGTCTTCC
65 TTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCCGCC
* * * * *
58079 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCACGTTTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCT
58142 TCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCCGCC
66 TCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCCGCC
* *
58187 CCCTATTTCTTCAGAGAGTATAACACTCGAACAATCTTCAACGATCGCGTCTGCCCTCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCT
*
58252 TCAGAGAGTATAAGACCTGAACAATCTTCAACAATCGTGTCCGCC
66 TCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCCGCC
* * *
58297 CCCTATTTCCTCAGAGAGTATAAGACTTGAACAATCTTCAACGATCGCGTCCGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCT
* ** *
58362 TCAGAGAGTATGAGACTTGAACAATCTTCAACGATCGT
66 TCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGT
58400 AGGGAACCTG
Statistics
Matches: 282, Mismatches: 30, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
102 1 0.00
103 9 0.03
104 20 0.07
105 3 0.01
106 34 0.12
108 45 0.16
109 1 0.00
110 169 0.60
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (110 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCT
TCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCCGCC
Found at i:59396 original size:8 final size:8
Alignment explanation
Indices: 59383--59460 Score: 54
Period size: 8 Copynumber: 9.4 Consensus size: 8
59373 TCTTGAACCC
59383 TCATTTTT
1 TCATTTTT
59391 TCATTTTT
1 TCATTTTT
59399 TCATTCATTT
1 TCATT--TTT
59409 T--TTATTAT
1 TCATT-TT-T
59417 T-ATTTTT
1 TCATTTTT
*
59424 TTATTTTTT
1 TCA-TTTTT
*
59433 TTATTTTTT
1 TCA-TTTTT
*
59442 TTATTTTT
1 TCATTTTT
59450 TCATTTTT
1 TCATTTTT
59458 TCA
1 TCA
59461 CTCATTTTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 12
0.83 0.01 0.16
Matches are distributed among these distances:
7 5 0.08
8 35 0.56
9 19 0.30
10 4 0.06
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (8 bp):
TCATTTTT
Found at i:59406 original size:20 final size:20
Alignment explanation
Indices: 59383--59471 Score: 78
Period size: 20 Copynumber: 4.5 Consensus size: 20
59373 TCTTGAACCC
59383 TCATTTTTTCATTTTTTCAT
1 TCATTTTTTCATTTTTTCAT
**
59403 TCATTTTTT-ATTATTATTTTT
1 TCATTTTTTCATT-TT-TTCAT
* *
59424 TTATTTTTTTTATTTTTT--T
1 TCA-TTTTTTCATTTTTTCAT
*
59443 T-ATTTTTTCATTTTTTCAC
1 TCATTTTTTCATTTTTTCAT
59462 TCATTTTTTC
1 TCATTTTTTC
59472 TTCTTCTTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 14
0.75 0.07 0.18
Matches are distributed among these distances:
17 13 0.23
18 1 0.02
19 6 0.11
20 19 0.33
21 7 0.12
22 8 0.14
23 3 0.05
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (20 bp):
TCATTTTTTCATTTTTTCAT
Found at i:59458 original size:9 final size:9
Alignment explanation
Indices: 59386--59450 Score: 67
Period size: 9 Copynumber: 6.6 Consensus size: 9
59376 TGAACCCTCA
*
59386 TTTTTTCAT
1 TTTTTTTAT
59395 TTTTTCATTCAT
1 TTTTT--TT-AT
59407 TTTTTATTATT
1 TTTTT-TTA-T
59418 ATTTTTTTAT
1 -TTTTTTTAT
59428 TTTTTTTAT
1 TTTTTTTAT
59437 TTTTTTTAT
1 TTTTTTTAT
59446 TTTTT
1 TTTTT
59451 CATTTTTTCA
Statistics
Matches: 50, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
9 28 0.56
10 2 0.04
11 8 0.16
12 12 0.24
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTTAT
Done.