Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004749.1 Hibiscus syriacus cultivar Beakdansim tig00010720_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: 53078
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:337 original size:3 final size:3
Alignment explanation
Indices: 320--410 Score: 91
Period size: 3 Copynumber: 31.7 Consensus size: 3
310 ATAAGAAGTT
* *
320 TTA TTA -TA TTG TTA TTA TTA TTA -TA TTA TTA TTA TTG TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
365 TTT TTA TT- GTA TTA TTA TTA TTA TTG TTA TTG TTA TTG TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
411 GTTTTTGTTG
Statistics
Matches: 71, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
2 7 0.10
3 64 0.90
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:427 original size:6 final size:6
Alignment explanation
Indices: 326--430 Score: 79
Period size: 6 Copynumber: 17.5 Consensus size: 6
316 AGTTTTATTA
* * * * *
326 TATTGT TATTAT TATTATAT TATTAT TATTGT T-TTAT TATTTT TATTG-
1 TATTGT TATTGT TA-T-TGT TATTGT TATTGT TATTGT TATTGT TATTGT
* * * * * *
374 TATTAT TATTAT TATTGT TATTGT TATTGT TATTAT TGTTTT TGTTGT
1 TATTGT TATTGT TATTGT TATTGT TATTGT TATTGT TATTGT TATTGT
422 TATTGT TAT
1 TATTGT TAT
431 ATTTACTTGT
Statistics
Matches: 83, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
5 8 0.10
6 68 0.82
7 2 0.02
8 5 0.06
ACGTcount: A:0.22, C:0.00, G:0.10, T:0.69
Consensus pattern (6 bp):
TATTGT
Found at i:428 original size:9 final size:9
Alignment explanation
Indices: 326--425 Score: 89
Period size: 9 Copynumber: 11.1 Consensus size: 9
316 AGTTTTATTA
326 TATTGTTAT
1 TATTGTTAT
*
335 TATTATTA-
1 TATTGTTAT
*
343 TATTATTAT
1 TATTGTTAT
352 TATTGTT-T
1 TATTGTTAT
* *
360 TATTATTTT
1 TATTGTTAT
369 TATTG-TAT
1 TATTGTTAT
*
377 TATTATTAT
1 TATTGTTAT
386 TATTGTTATTGT
1 TATTGTTA---T
398 TATTGTTAT
1 TATTGTTAT
*
407 TATTGTTTT
1 TATTGTTAT
*
416 TGTTGTTAT
1 TATTGTTAT
425 T
1 T
426 GTTATATTTA
Statistics
Matches: 75, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
8 21 0.28
9 45 0.60
12 9 0.12
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (9 bp):
TATTGTTAT
Found at i:7167 original size:30 final size:30
Alignment explanation
Indices: 7133--7213 Score: 135
Period size: 30 Copynumber: 2.6 Consensus size: 30
7123 AAGGTTCGAC
7133 GTGCTAATGCTACGATATTATCCAATGATT
1 GTGCTAATGCTACGATATTATCCAATGATT
*
7163 GTGCTAATGCTACGATAGTATCCAATGATT
1 GTGCTAATGCTACGATATTATCCAATGATT
7193 GTGCAATAATGCTACGATATT
1 GTGC--TAATGCTACGATATT
7214 TTATTTAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 33 0.70
32 14 0.30
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (30 bp):
GTGCTAATGCTACGATATTATCCAATGATT
Found at i:8198 original size:2 final size:2
Alignment explanation
Indices: 8191--8220 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
8181 AGATTTCAAC
8191 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
8221 AAGTTAACAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8987 original size:21 final size:23
Alignment explanation
Indices: 8962--9007 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
8952 AACCACTAAT
8962 TTTTTTAT-TAAAATATACTTAC
1 TTTTTTATATAAAATATACTTAC
8984 TTTTTTATAAATAAAATATACTTA
1 TTTTTTAT--ATAAAATATACTTA
9008 TTTAAGTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.38
25 13 0.62
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTTTATATAAAATATACTTAC
Found at i:10081 original size:19 final size:18
Alignment explanation
Indices: 10053--10089 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
10043 AATTAGAAGT
10053 TAAATGACCAAAATAAAAA
1 TAAATGACCAAAA-AAAAA
*
10072 TAAATTACCAAAAAAAAA
1 TAAATGACCAAAAAAAAA
10090 GGACTACATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.70, C:0.11, G:0.03, T:0.16
Consensus pattern (18 bp):
TAAATGACCAAAAAAAAA
Found at i:11075 original size:22 final size:23
Alignment explanation
Indices: 11011--11075 Score: 87
Period size: 22 Copynumber: 2.8 Consensus size: 23
11001 CTAATAATTA
*
11011 TGTCTTTATGACATGTTTTTTCTC
1 TGTCTTTATAACATG-TTTTTCTC
*
11035 TGTCTTTATAACATATTTTT-TC
1 TGTCTTTATAACATGTTTTTCTC
*
11057 TGTCTTTATAACACGTTTT
1 TGTCTTTATAACATGTTTT
11076 CGGTCGTTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
22 19 0.51
23 5 0.14
24 13 0.35
ACGTcount: A:0.18, C:0.15, G:0.09, T:0.57
Consensus pattern (23 bp):
TGTCTTTATAACATGTTTTTCTC
Found at i:11476 original size:19 final size:19
Alignment explanation
Indices: 11452--11492 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
11442 ATTATATATT
11452 TAATTTATAAAT-TTTATAA
1 TAATTT-TAAATATTTATAA
*
11471 TAATTTTAAATATTTTTAA
1 TAATTTTAAATATTTATAA
11490 TAA
1 TAA
11493 AATTAACGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TAATTTTAAATATTTATAA
Found at i:11907 original size:12 final size:13
Alignment explanation
Indices: 11881--11905 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11871 TATTATTAAA
11881 AAATATATTTTTT
1 AAATATATTTTTT
11894 AAATATATTTTT
1 AAATATATTTTT
11906 AACTACGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AAATATATTTTTT
Found at i:16597 original size:14 final size:14
Alignment explanation
Indices: 16578--16641 Score: 56
Period size: 14 Copynumber: 4.5 Consensus size: 14
16568 GTCTGAACCT
*
16578 AGTCAACTCGGCTG
1 AGTCAACTCGACTG
* *
16592 AGTCAACTCGCCTA
1 AGTCAACTCGACTG
* *
16606 AGTCAACCCGAATTG
1 AGTCAACTCG-ACTG
* *
16621 AGTCAACTCGTCCG
1 AGTCAACTCGACTG
16635 AGTCAAC
1 AGTCAAC
16642 CCGTTGACTT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
14 29 0.74
15 10 0.26
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.20
Consensus pattern (14 bp):
AGTCAACTCGACTG
Found at i:17426 original size:32 final size:32
Alignment explanation
Indices: 17385--17469 Score: 154
Period size: 32 Copynumber: 2.7 Consensus size: 32
17375 AAGGTGACCT
17385 TTGGGTAGGCTCCGAGGCCCCGAGAAATATTC
1 TTGGGTAGGCTCCGAGGCCCCGAGAAATATTC
17417 TTGGGTAGGCTCCGAGGCCCCGAGAAATATTC
1 TTGGGTAGGCTCCGAGGCCCCGAGAAATATTC
17449 TTGGGTAGGCTCTC-AGGCCCC
1 TTGGGTAGGCTC-CGAGGCCCC
17470 AAGGCACTCC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
32 51 0.98
33 1 0.02
ACGTcount: A:0.19, C:0.27, G:0.32, T:0.22
Consensus pattern (32 bp):
TTGGGTAGGCTCCGAGGCCCCGAGAAATATTC
Found at i:20232 original size:22 final size:23
Alignment explanation
Indices: 20181--20235 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
20171 ACATTTAAAA
20181 TTTAGTCCTTTTATTCTTTTAGT
1 TTTAGTCCTTTTATTCTTTTAGT
20204 TTTAGTCCTTTTATTCTTTTAG-
1 TTTAGTCCTTTTATTCTTTTAGT
20226 TTTAGTCCTT
1 TTTAGTCCTT
20236 CCATAATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 10 0.31
23 22 0.69
ACGTcount: A:0.13, C:0.15, G:0.09, T:0.64
Consensus pattern (23 bp):
TTTAGTCCTTTTATTCTTTTAGT
Found at i:21130 original size:38 final size:38
Alignment explanation
Indices: 21079--21153 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
21069 CTTGTATTGT
* *
21079 TATTTGGGTATTGTGCTTGCTCTAGTTTGAGCAAAGGA
1 TATTTGGATATTGTGCTTGCTCTAATTTGAGCAAAGGA
*
21117 TATTTGGATATTGTGCTTGTTCTAATTTGAGCAAAGG
1 TATTTGGATATTGTGCTTGCTCTAATTTGAGCAAAGG
21154 GAATGTTACT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.23, C:0.09, G:0.27, T:0.41
Consensus pattern (38 bp):
TATTTGGATATTGTGCTTGCTCTAATTTGAGCAAAGGA
Found at i:24779 original size:14 final size:12
Alignment explanation
Indices: 24730--24776 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
24720 AACTTTTTTG
24730 ATCTCATGATCT
1 ATCTCATGATCT
24742 ATCTCATGATCT
1 ATCTCATGATCT
24754 ATCTCATGACTCAT
1 ATCTCATGA-TC-T
*
24768 AACTCATGA
1 ATCTCATGA
24777 CTCGTGTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 21 0.66
13 2 0.06
14 9 0.28
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.36
Consensus pattern (12 bp):
ATCTCATGATCT
Found at i:27262 original size:21 final size:21
Alignment explanation
Indices: 27237--27276 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
27227 GTCTGGTGAT
*
27237 GAACCGAATTGAGTAGATGAC
1 GAACCCAATTGAGTAGATGAC
27258 GAACCCAATTGAGTAGATG
1 GAACCCAATTGAGTAGATG
27277 TTGCCTTCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.20
Consensus pattern (21 bp):
GAACCCAATTGAGTAGATGAC
Found at i:28109 original size:312 final size:305
Alignment explanation
Indices: 27252--28351 Score: 1237
Period size: 299 Copynumber: 3.7 Consensus size: 305
27242 GAATTGAGTA
* * * *
27252 GATGACGAACCCAATTGAGTAGATGTTGCCTTCGTCTTTGATAATGGTCGAGATTTGGAGGAAGA
1 GATGACGAACCCAATTGAGTAGATGTTTCCTTCGTCTTTGATAATCGTTGAGATTTCGAGGAAGA
** * * * * *
27317 AGACTTGGCAAGGGAAGTTCTCTTCTT-T-CTTTTTCGTTTT-TCCGTGACATTTAGAGGATCAA
66 AGACTCAGCAATGGAAGTTCTCTTCTTCTCCTTTTTCATTTTCTCCGTAACATTTGGAAGATCAA
* * *
27379 TGCAAGACTGGTTTCTCGTTTTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATATCTGTA
131 TGCAAGACTGGTTTCTCATCTTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATACCTGTA
* * * * *
27444 AC--AA-AGT--TTAAA-TGATTTCGACTTTCTTATGTTAATGAGAATATTAAATATATTAATAA
196 ACAAAATAGTAATGAAATTGATTTCGACTTTGTTGTGTTCATGAGAATCTTAAATATATTAATAA
*
27503 GAAATAATCATGCATGATGATCTTTATATTTTGAAGT-C--T-A-
261 GAAATAATCATGCATGATGATCTCTATATTTTGAAGTACGTTGAC
* * * * * * * * *
27543 G-TGACGAACCCAGTTGAGAAGATATTTTCTTCATCTTGGATAATCGTTTATATTTCGAAGAAGA
1 GATGACGAACCCAATTGAGTAGATGTTTCCTTCGTCTTTGATAATCGTTGAGATTTCGAGGAAGA
* ** * * * *
27607 AGAGTCAGCAATGGAAGAGCTCTTTCTTCTTCTTTTTC-GTTTCTCTGCAACATTTGGAAGATCA
66 AGACTCAGCAATGGAAGTTCTC-TTCTTCTCCTTTTTCATTTTCTCCGTAACATTTGGAAGATCA
* * *
27671 ATGCAAGATTGGTTACTCATCTTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATATCTGT
130 ATGCAAGACTGGTTTCTCATCTTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATACCTGT
* * * * * ** * *
27736 AACAAAATATTAATGAAATTGACTTCAAATTTATTGTGTTTGTGAGAATTTTAAATATATTAGTA
195 AACAAAATAGTAATGAAATTGATTTCGACTTTGTTGTGTTCATGAGAATCTTAAATATATTAATA
27801 AGAAATAATCATGCATGAT-ACTCTCTATATTTTGAAGTCAAACTGATTGAGTC
260 AGAAATAATCATGCATGATGA-TCTCTATATTTTGAAGT---AC-G-TTGA--C
* *
27854 GATGACGAACCTAATTGAGTAGATGTTTCCTTCGTCTTCGATAATCGTTGAGATTTCGAGGAAGA
1 GATGACGAACCCAATTGAGTAGATGTTTCCTTCGTCTTTGATAATCGTTGAGATTTCGAGGAAGA
* *
27919 TGACTCAG-AAGTGGAAGTTCTCTTGCTTCTCCTTTTT-ATTTTCTCCCTAACATTTGGAAGATC
66 AGACTCAGCAA-TGGAAGTTCTCTT-CTTCTCCTTTTTCATTTTCTCCGTAACATTTGGAAGATC
* * *
27982 AATGCAAGACTGGTTTCTCATCTTCTCTGCTTCTGGTCCAGATCCCGTTGATTGATCAATACCTG
129 AATGCAAGACTGGTTTCTCATCTTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATACCTG
* * *
28047 TAACATAATAGTAATGAAATTGATTTCGACTTTGTCGTGTTCTTGAGAATCTTAAATATATTAAT
194 TAACAAAATAGTAATGAAATTGATTTCGACTTTGTTGTGTTCATGAGAATCTTAAATATATTAAT
* * * *
28112 AAGAAATAATAATGTACGATGATCTCTATATATTG-A--A-GTT--C
259 AAGAAATAATCATGCATGATGATCTCTATATTTTGAAGTACGTTGAC
* *
28153 GTTGACGAACCCAATTGAGTAGATGTTTCCTTCGTCTTTGACAATCGTTGAGATTTCGAGGAAGA
1 GATGACGAACCCAATTGAGTAGATGTTTCCTTCGTCTTTGATAATCGTTGAGATTTCGAGGAAGA
* *
28218 AGACTCAGCAATGGAAGTGT-TCTTCCTTCTCCTTTTTCGTTTT-TCCGTAACATTTGAAAGATC
66 AGACTCAGCAATGGAAGT-TCTCTT-CTTCTCCTTTTTCATTTTCTCCGTAACATTTGGAAGATC
* * * * * * *
28281 AGTGCAAGACTGTTTTCCCGTATTCTCTGTTTCTGGTTCAGATCCTACTGATTGATCAATACCTG
129 AATGCAAGACTGGTTTCTCATCTTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATACCTG
28346 TAACAA
194 TAACAA
28352 GGTCGTATAG
Statistics
Matches: 677, Mismatches: 101, Indels: 54
0.81 0.12 0.06
Matches are distributed among these distances:
290 66 0.10
291 6 0.01
292 4 0.01
293 87 0.13
295 2 0.00
296 2 0.00
298 5 0.01
299 242 0.36
300 7 0.01
303 3 0.00
304 1 0.00
306 1 0.00
307 1 0.00
308 1 0.00
311 6 0.01
312 242 0.36
313 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (305 bp):
GATGACGAACCCAATTGAGTAGATGTTTCCTTCGTCTTTGATAATCGTTGAGATTTCGAGGAAGA
AGACTCAGCAATGGAAGTTCTCTTCTTCTCCTTTTTCATTTTCTCCGTAACATTTGGAAGATCAA
TGCAAGACTGGTTTCTCATCTTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATACCTGTA
ACAAAATAGTAATGAAATTGATTTCGACTTTGTTGTGTTCATGAGAATCTTAAATATATTAATAA
GAAATAATCATGCATGATGATCTCTATATTTTGAAGTACGTTGAC
Found at i:28219 original size:611 final size:603
Alignment explanation
Indices: 26939--28351 Score: 1646
Period size: 611 Copynumber: 2.3 Consensus size: 603
26929 GTCTGATGAT
* * * *** * * *
26939 GAACCCAATTGAGTAGATGTTGCCTTTATCTTCAACAATCAACGTGATTTTGAGGAAGAAGATCT
1 GAACCCAATTGAGTAGATGTTTCCTTCATCTTCGACAATCGTTGAGATTTCGAGGAAGAAGATCA
* * *
27004 GGATATGGAAGTTCTC-TTCTTTCTCCTTTTTCATTTCT-TCGTAACATTTGAAAGATCAGTGCA
66 GCA-ATGGAAGTGCTCTTTC-TTCTCCTTTTTCGTTTCTCT-GTAACATTTGAAAGATCAGTGCA
* * * *
27067 AGACTGATTTTTTATCTCCTCTGTTGT-TGGTTCAGATCCCATCGATTGATCAATACCTGTAACA
128 AGACTGATTTCTCATCTTCTCTGTT-TCTGGTTCAGATCCCATTGATTGATCAATACCTGTAACA
* * * * *
27131 AAATAGTACTAAATTAATTTCGAGTTTGTTGAGTTCATGAATATCTTTAATACATTAATAAGAAA
192 AAATAGTAATAAATTAACTTCAAATTTATTGAGTTCATGAATATCTTTAATACATTAATAAGAAA
27196 TAATCATGCATGATGATCTCTATATTTTAATGTCTGGTGATGAACCGAATTGAGTAGATGACGAA
257 TAATCATGCATGATGATCTCTATATTTTAATGTC----GA-GAACCGAATTGAGTAGATGACGAA
* * * **
27261 CCCAATTGAGTAGATGTTGCCTTCGTCTTTGATAATGGTCGAGATTTGGAGGAAGAAGACTTGGC
317 CCCAATTGAGTAGATGTTGCCTTCGTCTTCGATAATCGTCGAGATTTCGAGGAAGAAGACTCAGC
* * * *
27326 AAGGGAAGTTCTCTTCTTTCTTTTTCGTTTTTCCGTGACATTTAGAGGATCAATGCAAGACTGGT
382 AAGGGAAGTTCTCTTCTTTCTTTTTCATTTTTCCCTAACATTTAGAAGATCAATGCAAGACTGGT
* * * * * *
27391 TTCTCGTTTTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATATCTGTAACAAAGTTTAAA
447 TTCTCATCTTCTCTGCTTCTGGTCCAGATCCCATTGATTGATCAATACCTGTAACAAAGTTGAAA
* * *
27456 TGATTTCGACTTTCTTATGTTAATGAGAATATTAAATATATTAATAAGAAATAATCATGCATGAT
512 TGATTTCGACTTTCTCATGTTAATGAGAATATTAAATATATTAATAAGAAATAATAATGCACGAT
* *
27521 GATCTTTATATTTTGAAGTCTAGTGAC
577 GATCTCTATATATTGAAGTCTAGTGAC
* * * * * * * * *
27548 GAACCCAGTTGAGAAGATATTTTCTTCATCTTGGATAATCGTTTATATTTCGAAGAAGAAGAGTC
1 GAACCCAATTGAGTAGATGTTTCCTTCATCTTCGACAATCGTTGAGATTTCGAGGAAGAAGA-TC
* * * * *
27613 AGCAATGGAAGAGCTCTTTCTTCTTCTTTTTCGTTTCTCTGCAACATTTGGAAGATCAATGCAAG
65 AGCAATGGAAGTGCTCTTTCTTCTCCTTTTTCGTTTCTCTGTAACATTTGAAAGATCAGTGCAAG
* * * *
27678 ATTGGTTACTCATCTTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATATCTGTAACAAAA
130 ACTGATTTCTCATCTTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATACCTGTAACAAAA
* * * ** * *
27743 TATTAATGAAATTGACTTCAAATTTATTGTGTTTGTGAGA-AT-TTTAAATATATTAGTAAGAAA
195 TAGTAAT-AAATTAACTTCAAATTTATTGAGTTCATGA-ATATCTTT-AATACATTAATAAGAAA
* * *
27806 TAATCATGCATGAT-ACTCTCTATATTTTGAA-GTC-A-AACTG-ATTGAGTCGATGACGAACCT
257 TAATCATGCATGATGA-TCTCTATATTTT-AATGTCGAGAACCGAATTGAGTAGATGACGAACCC
* * *
27866 AATTGAGTAGATGTTTCCTTCGTCTTCGATAATCGTTGAGATTTCGAGGAAGATGACTCAG-AAG
320 AATTGAGTAGATGTTGCCTTCGTCTTCGATAATCGTCGAGATTTCGAGGAAGAAGACTCAGCAAG
*
27930 TGGAAGTTCTCTTGCTTCTCCTTTTT-ATTTTCTCCCTAACATTTGGAAGATCAATGCAAGACTG
385 -GGAAGTTCTCTT-CTT-T-CTTTTTCATTTT-TCCCTAACATTTAGAAGATCAATGCAAGACTG
*
27994 GTTTCTCATCTTCTCTGCTTCTGGTCCAGATCCCGTTGATTGATCAATACCTGTAACATAATAGT
445 GTTTCTCATCTTCTCTGCTTCTGGTCCAGATCCCATTGATTGATCAATACCTGTAAC--AA-AGT
* * ** *
28059 AATGAAATTGATTTCGACTTTGTCGTGTTCTTGAGAATCTTAAATATATTAATAAGAAATAATAA
507 --TGAAA-TGATTTCGACTTTCTCATGTTAATGAGAATATTAAATATATTAATAAGAAATAATAA
* *
28124 TGTACGATGATCTCTATATATTGAAGT-TCGTTGAC
569 TGCACGATGATCTCTATATATTGAAGTCTAG-TGAC
* *
28159 GAACCCAATTGAGTAGATGTTTCCTTCGTCTTTGACAATCGTTGAGATTTCGAGGAAGAAGACTC
1 GAACCCAATTGAGTAGATGTTTCCTTCATCTTCGACAATCGTTGAGATTTCGAGGAAGAAGA-TC
* * * *
28224 AGCAATGGAAGTGTTCTTCCTTCTCCTTTTTCGTTTTTCCGTAACATTTGAAAGATCAGTGCAAG
65 AGCAATGGAAGTGCTCTTTCTTCTCCTTTTTCGTTTCTCTGTAACATTTGAAAGATCAGTGCAAG
* * * * * *
28289 ACTGTTTTCCCGTATTCTCTGTTTCTGGTTCAGATCCTACTGATTGATCAATACCTGTAACAA
130 ACTGATTTCTCATCTTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATACCTGTAACAA
28352 GGTCGTATAG
Statistics
Matches: 673, Mismatches: 110, Indels: 40
0.82 0.13 0.05
Matches are distributed among these distances:
601 3 0.00
602 83 0.12
603 7 0.01
604 5 0.01
605 86 0.13
607 2 0.00
608 4 0.01
609 157 0.23
610 82 0.12
611 244 0.36
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.38
Consensus pattern (603 bp):
GAACCCAATTGAGTAGATGTTTCCTTCATCTTCGACAATCGTTGAGATTTCGAGGAAGAAGATCA
GCAATGGAAGTGCTCTTTCTTCTCCTTTTTCGTTTCTCTGTAACATTTGAAAGATCAGTGCAAGA
CTGATTTCTCATCTTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATACCTGTAACAAAAT
AGTAATAAATTAACTTCAAATTTATTGAGTTCATGAATATCTTTAATACATTAATAAGAAATAAT
CATGCATGATGATCTCTATATTTTAATGTCGAGAACCGAATTGAGTAGATGACGAACCCAATTGA
GTAGATGTTGCCTTCGTCTTCGATAATCGTCGAGATTTCGAGGAAGAAGACTCAGCAAGGGAAGT
TCTCTTCTTTCTTTTTCATTTTTCCCTAACATTTAGAAGATCAATGCAAGACTGGTTTCTCATCT
TCTCTGCTTCTGGTCCAGATCCCATTGATTGATCAATACCTGTAACAAAGTTGAAATGATTTCGA
CTTTCTCATGTTAATGAGAATATTAAATATATTAATAAGAAATAATAATGCACGATGATCTCTAT
ATATTGAAGTCTAGTGAC
Found at i:33644 original size:15 final size:15
Alignment explanation
Indices: 33626--33669 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 15
33616 TAACCGGTTT
33626 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
33641 CGGTTTTTTAAAAAAC
1 CGG-TTTTAAAAAAAC
*
33657 CGGTTATAAAAAA
1 CGGTTTTAAAAAA
33670 TCGATTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:33793 original size:21 final size:21
Alignment explanation
Indices: 33767--33832 Score: 132
Period size: 21 Copynumber: 3.1 Consensus size: 21
33757 TTCCAGAATG
33767 CCCATAGGGGGTACCGATTCC
1 CCCATAGGGGGTACCGATTCC
33788 CCCATAGGGGGTACCGATTCC
1 CCCATAGGGGGTACCGATTCC
33809 CCCATAGGGGGTACCGATTCC
1 CCCATAGGGGGTACCGATTCC
33830 CCC
1 CCC
33833 CTATTCAACG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.18, C:0.36, G:0.27, T:0.18
Consensus pattern (21 bp):
CCCATAGGGGGTACCGATTCC
Found at i:33896 original size:21 final size:21
Alignment explanation
Indices: 33872--33924 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
33862 ACACTTAGGG
33872 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
33893 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
33914 TACCGATTCCC
1 AACCGATTCCC
33925 CCACGCTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:34141 original size:13 final size:13
Alignment explanation
Indices: 34120--34174 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
34110 AAGTTCGATA
*
34120 AATTCAAATACTT
1 AATTGAAATACTT
34133 AATTGAAATACTT
1 AATTGAAATACTT
* *
34146 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
34160 AATTGAAATACTT
1 AATTGAAATACTT
34173 AA
1 AA
34175 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:34256 original size:32 final size:33
Alignment explanation
Indices: 34160--34258 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
34150 AACTCAACAT
* * *
34160 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
34193 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
34226 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
34258 A
1 A
34259 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:34277 original size:21 final size:21
Alignment explanation
Indices: 34253--34292 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
34243 ACTTCAAGTT
34253 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
34274 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
34293 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:36615 original size:12 final size:13
Alignment explanation
Indices: 36597--36636 Score: 55
Period size: 12 Copynumber: 3.0 Consensus size: 13
36587 TTCCGGATAA
36597 AAACCGGTTTTTT
1 AAACCGGTTTTTT
36610 -AACCGGTTTTTTT
1 AAACCGG-TTTTTT
36623 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
36637 GTCTGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
14 6 0.25
15 6 0.25
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (13 bp):
AAACCGGTTTTTT
Found at i:36628 original size:15 final size:14
Alignment explanation
Indices: 36597--36636 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
36587 TTCCGGATAA
36597 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
36610 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
36623 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
36637 GTCTGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:46855 original size:228 final size:227
Alignment explanation
Indices: 46516--47094 Score: 721
Period size: 228 Copynumber: 2.5 Consensus size: 227
46506 AATCAACCTT
* * * * * * * *
46516 TGCTGATCTGG-GGGAATCCCTTCTTTGTCCTGAATCTTCGCCTTAACATTATCGATCGTATCAG
1 TGCTGATCCGGTGGG-ATCCCTTCCTTGTCTTGGATCTTGGCCTTAACGTTGTCGATCGTATCGG
* * **
46580 AACTCTCCACTTCCAGGGTAATGGTTTTTCCAGTCAAAGTCTTGACGAAGATCTGCATCCCACCA
65 AACTCTCGACTTCCAGGGTAATGG-TTTTCCGGTCAGGGTCTTGACGAAGATCTGCATCCCACCA
* * *
46645 CGAAGCCTCAAAACCAGATGAAGGGTCGATTCCTTCTGGATGTTGTAATCGGCCAAGGTCCGGCC
129 CGAAGACGCAAAACCAGATGAAGGGTCGACTCCTTCTGGATGTTGTAATCGGCCAAGGTCCGGCC
* *
46710 GTCCTCGAGCTGCTTTCCGGCAAAGATGAGCCTC
194 GTCCTCGAGCTGCTTTCCGGCAAAGATGAGACGC
* *
46744 TGCTGATCCGGTGGGATGCCC-TCCTTGTCTTGGATCTTGGCCTTCACGTTGTCGATCGTGTCGG
1 TGCTGATCCGGTGGGAT-CCCTTCCTTGTCTTGGATCTTGGCCTTAACGTTGTCGATCGTATCGG
* * * * * * *
46808 AGCTCTCGACTTCCAAGGTTATGGTTTTACCGGTCAGGGTTTTGACGAAGATTTGCATGCCTCCA
65 AACTCTCGACTTCCAGGGTAATGGTTTT-CCGGTCAGGGTCTTGACGAAGATCTGCATCCCACCA
* ** * * * *
46873 CGAAGACGGAGGACGAGGTGGAGGGTTGACTCCTTCTGGATGTTGTAATCGGCCAAGGTCCGGCC
129 CGAAGACGCAAAACCAGATGAAGGGTCGACTCCTTCTGGATGTTGTAATCGGCCAAGGTCCGGCC
* *
46938 GTCCTCTAGCTGTTTTCCGGCAAAGATGAGACGC
194 GTCCTCGAGCTGCTTTCCGGCAAAGATGAGACGC
* * *
46972 TGCTGGTCCGGTGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTGTCGATGGTATCGGA
1 TGCTGATCCGGTGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTAACGTTGTCGATCGTATCGGA
* * * *
47037 ACTCTCGACTTCGAGGGTGATTGTCTTTCCGGTCAGGGTCTTGACGAAAATCTGCATC
66 ACTCTCGACTTCCAGGGTAATGGT-TTTCCGGTCAGGGTCTTGACGAAGATCTGCATC
47095 TTGTTTGGCT
Statistics
Matches: 298, Mismatches: 48, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
227 7 0.02
228 282 0.95
229 9 0.03
ACGTcount: A:0.18, C:0.25, G:0.27, T:0.29
Consensus pattern (227 bp):
TGCTGATCCGGTGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTAACGTTGTCGATCGTATCGGA
ACTCTCGACTTCCAGGGTAATGGTTTTCCGGTCAGGGTCTTGACGAAGATCTGCATCCCACCACG
AAGACGCAAAACCAGATGAAGGGTCGACTCCTTCTGGATGTTGTAATCGGCCAAGGTCCGGCCGT
CCTCGAGCTGCTTTCCGGCAAAGATGAGACGC
Found at i:47589 original size:5 final size:5
Alignment explanation
Indices: 47579--47604 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
47569 AAATCAATAA
47579 ATTTT ATTTT ATTTT ATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT A
47605 ACGTTATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Done.