Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006540.1 Hibiscus syriacus cultivar Beakdansim tig00015967_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: 68519
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2232 original size:2 final size:2
Alignment explanation
Indices: 2227--2253 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2217 ACACACACTA
2227 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 A
2254 ATTGTTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4331 original size:18 final size:18
Alignment explanation
Indices: 4308--4382 Score: 80
Period size: 18 Copynumber: 4.2 Consensus size: 18
4298 GGTCACAACC
*
4308 CGACCCGACCCGTTTACA
1 CGACCCGACCCGTTGACA
* *
4326 CGACCCGACCAGTTGACC
1 CGACCCGACCCGTTGACA
*
4344 CAACCCGACCCGTTGAC-
1 CGACCCGACCCGTTGACA
* * *
4361 CAAACCGACCCGTTGACC
1 CGACCCGACCCGTTGACA
4379 CGAC
1 CGAC
4383 TCGTTGACCG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
17 16 0.33
18 32 0.67
ACGTcount: A:0.24, C:0.45, G:0.19, T:0.12
Consensus pattern (18 bp):
CGACCCGACCCGTTGACA
Found at i:4357 original size:36 final size:35
Alignment explanation
Indices: 4305--4379 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 35
4295 ACCGGTCACA
* * * *
4305 ACCCGACCCGACCCGTTTACACGACCCGACCAGTTG
1 ACCCAACCCGACCCGTTGAC-CAAACCGACCAGTTG
*
4341 ACCCAACCCGACCCGTTGACCAAACCGACCCGTTG
1 ACCCAACCCGACCCGTTGACCAAACCGACCAGTTG
4376 ACCC
1 ACCC
4380 GACTCGTTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 16 0.47
36 18 0.53
ACGTcount: A:0.24, C:0.47, G:0.17, T:0.12
Consensus pattern (35 bp):
ACCCAACCCGACCCGTTGACCAAACCGACCAGTTG
Found at i:4368 original size:17 final size:17
Alignment explanation
Indices: 4330--4378 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
4320 TTTACACGAC
* *
4330 CCGACCAGTTGACCCAAC
1 CCGACCCGTTGA-CCAAA
4348 CCGACCCGTTGACCAAA
1 CCGACCCGTTGACCAAA
4365 CCGACCCGTTGACC
1 CCGACCCGTTGACC
4379 CGACTCGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 18 0.62
18 11 0.38
ACGTcount: A:0.24, C:0.45, G:0.18, T:0.12
Consensus pattern (17 bp):
CCGACCCGTTGACCAAA
Found at i:4404 original size:14 final size:15
Alignment explanation
Indices: 4380--4411 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
4370 CCGTTGACCC
4380 GACTCGTTGACCGTT
1 GACTCGTTGACCGTT
4395 GACT-GTTGACCGTT
1 GACTCGTTGACCGTT
4409 GAC
1 GAC
4412 CAAAGTTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.16, C:0.25, G:0.28, T:0.31
Consensus pattern (15 bp):
GACTCGTTGACCGTT
Found at i:6416 original size:24 final size:25
Alignment explanation
Indices: 6388--6445 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
6378 GAATATTTTA
6388 TCTGATTTCCGATT-TGAAATATGT
1 TCTGATTTCCGATTCTGAAATATGT
* *
6412 TCTGATTTCTGATTCTGAACTATGT
1 TCTGATTTCCGATTCTGAAATATGT
6437 TCTGATTTC
1 TCTGATTTC
6446 TGATCTGGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 13 0.42
25 18 0.58
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.48
Consensus pattern (25 bp):
TCTGATTTCCGATTCTGAAATATGT
Found at i:6436 original size:25 final size:25
Alignment explanation
Indices: 6388--6485 Score: 101
Period size: 24 Copynumber: 4.0 Consensus size: 25
6378 GAATATTTTA
*
6388 TCTGATTTCCGATT-TGAAATATGT
1 TCTGATTTCTGATTCTGAAATATGT
*
6412 TCTGATTTCTGATTCTGAACTATGT
1 TCTGATTTCTGATTCTGAAATATGT
* *
6437 TCTGATTTCTGA-TCTGGATTATGT
1 TCTGATTTCTGATTCTGAAATATGT
* * * *
6461 TTTGATATATGATATCTGATATATG
1 TCTGATTTCTGAT-TCTGAAATATG
6486 ATATGAATTC
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
24 32 0.52
25 21 0.34
26 8 0.13
ACGTcount: A:0.23, C:0.11, G:0.17, T:0.48
Consensus pattern (25 bp):
TCTGATTTCTGATTCTGAAATATGT
Found at i:6482 original size:14 final size:14
Alignment explanation
Indices: 6463--6489 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6453 GATTATGTTT
6463 TGATATATGATATC
1 TGATATATGATATC
6477 TGATATATGATAT
1 TGATATATGATAT
6490 GAATTCTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (14 bp):
TGATATATGATATC
Found at i:8467 original size:21 final size:19
Alignment explanation
Indices: 8431--8472 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 19
8421 TATTATACTT
8431 ATTTTGTCTTTTCTTGTACA
1 ATTTTGTCTTTTCTTG-ACA
8451 ATTTT-TCTTTTTGCTTGACA
1 ATTTTGTC-TTTT-CTTGACA
8471 AT
1 AT
8473 ATAAGTTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 2 0.10
20 14 0.70
21 4 0.20
ACGTcount: A:0.17, C:0.14, G:0.10, T:0.60
Consensus pattern (19 bp):
ATTTTGTCTTTTCTTGACA
Found at i:10755 original size:12 final size:12
Alignment explanation
Indices: 10727--10764 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
10717 TTTATTATTT
10727 TATTATTAT-AA
1 TATTATTATAAA
*
10738 TAATTACTATAAA
1 T-ATTATTATAAA
10751 TATTATTATAAA
1 TATTATTATAAA
10763 TA
1 TA
10765 ATAATATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 1 0.04
12 19 0.83
13 3 0.13
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (12 bp):
TATTATTATAAA
Found at i:10778 original size:24 final size:24
Alignment explanation
Indices: 10722--10779 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
10712 TTATTTTTAT
*
10722 TATT-TTATTATTATAATAATTAC
1 TATTATTATTATTATAATAATTAA
* *
10745 TATAAATATTATTATAAATAA-TAA
1 TATTATTATTATTAT-AATAATTAA
10769 TATTATTATTA
1 TATTATTATTA
10780 CAGGCCATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 3 0.11
24 20 0.71
25 5 0.18
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
TATTATTATTATTATAATAATTAA
Found at i:18125 original size:17 final size:17
Alignment explanation
Indices: 18103--18138 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
18093 ATCAAAGGCG
18103 TGTGAATGGAATTTTTA
1 TGTGAATGGAATTTTTA
18120 TGTGAATGGAATTTTTA
1 TGTGAATGGAATTTTTA
18137 TG
1 TG
18139 GTCGATCAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (17 bp):
TGTGAATGGAATTTTTA
Found at i:19026 original size:16 final size:17
Alignment explanation
Indices: 19005--19037 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
18995 TTGAAATGTC
*
19005 TGGAA-TAAATGATAAG
1 TGGAATTAAATAATAAG
19021 TGGAATTAAATAATAAG
1 TGGAATTAAATAATAAG
19038 ACAGAATGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.52, C:0.00, G:0.21, T:0.27
Consensus pattern (17 bp):
TGGAATTAAATAATAAG
Found at i:21391 original size:21 final size:20
Alignment explanation
Indices: 21241--21382 Score: 117
Period size: 20 Copynumber: 7.0 Consensus size: 20
21231 ATAACCAACG
* * *
21241 AATTCGCAACGC-GATTTCA
1 AATTCGCAACACAAATTTGA
* **
21260 AATTCGCAACACAAACTCCA
1 AATTCGCAACACAAATTTGA
* * *
21280 ATTTCGCAACAC-AGTTTCCA
1 AATTCGCAACACAAATTT-GA
*
21300 AATTCGCAACGCAAATTTGA
1 AATTCGCAACACAAATTTGA
*
21320 AATTCACAACACAGAATTTGA
1 AATTCGCAACACA-AATTTGA
21341 AATTCGCAACACAAATTTGA
1 AATTCGCAACACAAATTTGA
* * *
21361 ATTTTTGCAACGCAAATTTGA
1 A-ATTCGCAACACAAATTTGA
21382 A
1 A
21383 TTTTCGCAAA
Statistics
Matches: 100, Mismatches: 18, Indels: 8
0.79 0.14 0.06
Matches are distributed among these distances:
19 13 0.13
20 47 0.47
21 40 0.40
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.26
Consensus pattern (20 bp):
AATTCGCAACACAAATTTGA
Found at i:21398 original size:20 final size:20
Alignment explanation
Indices: 21333--21399 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 20
21323 TCACAACACA
*
21333 GAATTTGAA-ATTCGCAACAC
1 GAATTTGAATTTTCGCAA-AC
* *
21353 AAATTTGAATTTTTGC-AAC
1 GAATTTGAATTTTCGCAAAC
21372 GCAAATTTGAATTTTCGCAAAC
1 G--AATTTGAATTTTCGCAAAC
21394 GAATTT
1 GAATTT
21400 CTTTTTAATC
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
19 2 0.05
20 14 0.37
21 18 0.47
22 4 0.11
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.34
Consensus pattern (20 bp):
GAATTTGAATTTTCGCAAAC
Found at i:21969 original size:15 final size:16
Alignment explanation
Indices: 21949--21978 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21939 TATATGAAAT
21949 AAAGTT-AAATAAAAA
1 AAAGTTAAAATAAAAA
21964 AAAGTTAAAATAAAA
1 AAAGTTAAAATAAAA
21979 TAGAGTCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (16 bp):
AAAGTTAAAATAAAAA
Found at i:22248 original size:21 final size:21
Alignment explanation
Indices: 22224--22270 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
22214 TGCAAATTTT
*
22224 AAATTTTGTATAGCGAATTCC
1 AAATTTTATATAGCGAATTCC
* * *
22245 AAATTTTATGTTGCGAATTCT
1 AAATTTTATATAGCGAATTCC
22266 AAATT
1 AAATT
22271 CACGTTACGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.43
Consensus pattern (21 bp):
AAATTTTATATAGCGAATTCC
Found at i:22297 original size:20 final size:20
Alignment explanation
Indices: 22274--22328 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
22264 CTAAATTCAC
22274 GTTACGAATTTGAAAGCT-GT
1 GTTACGAATTTGAAA-CTCGT
* * * *
22294 GTTACAAAATTGGAATTCGT
1 GTTACGAATTTGAAACTCGT
22314 GTTACGAATTTGAAA
1 GTTACGAATTTGAAA
22329 TCACATTGCG
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.35
Consensus pattern (20 bp):
GTTACGAATTTGAAACTCGT
Found at i:22489 original size:17 final size:17
Alignment explanation
Indices: 22464--22498 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
22454 TTTGTCCGGA
*
22464 ATATAATTATTATTATT
1 ATATAATTAATATTATT
*
22481 ATATTATTAATATTATT
1 ATATAATTAATATTATT
22498 A
1 A
22499 ATACTGTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATATAATTAATATTATT
Found at i:22493 original size:9 final size:9
Alignment explanation
Indices: 22463--22501 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
22453 TTTTGTCCGG
*
22463 AATATAATT
1 AATATTATT
*
22472 ATTATTATT
1 AATATTATT
22481 -ATATTATT
1 AATATTATT
22489 AATATTATT
1 AATATTATT
22498 AATA
1 AATA
22502 CTGTTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
AATATTATT
Found at i:22871 original size:13 final size:13
Alignment explanation
Indices: 22838--22864 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
22828 AAAACCCACT
22838 ACACCACTCAAAA
1 ACACCACTCAAAA
22851 ACACCACTCAAAA
1 ACACCACTCAAAA
22864 A
1 A
22865 GATCACTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.37, G:0.00, T:0.07
Consensus pattern (13 bp):
ACACCACTCAAAA
Found at i:25593 original size:13 final size:13
Alignment explanation
Indices: 25575--25618 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
25565 TTTAGTTGTA
25575 ATTTTATTATTTT
1 ATTTTATTATTTT
*
25588 ATTTTATTTTTTGT
1 ATTTTATTATTT-T
*
25602 ATTTTA-AATTTT
1 ATTTTATTATTTT
25614 ATTTT
1 ATTTT
25619 TGGATTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 6 0.22
13 14 0.52
14 7 0.26
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (13 bp):
ATTTTATTATTTT
Found at i:25632 original size:21 final size:21
Alignment explanation
Indices: 25588--25633 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
25578 TTATTATTTT
* *
25588 ATTTTATTTTTTGTATTTTAA
1 ATTTTATTTTTTGGATTATAA
25609 ATTTTA-TTTTTGGATTATATA
1 ATTTTATTTTTTGGATTATA-A
25630 ATTT
1 ATTT
25634 AGATTTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (21 bp):
ATTTTATTTTTTGGATTATAA
Found at i:26517 original size:228 final size:227
Alignment explanation
Indices: 26115--26562 Score: 790
Period size: 228 Copynumber: 2.0 Consensus size: 227
26105 GTAAATTATC
* * *
26115 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
26180 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATAATT
26245 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
26310 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
26343 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
26408 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAA-AAT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATAAT
* *
26472 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
26537 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
26563 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
227 4 0.02
228 122 0.58
229 84 0.40
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATAATT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:26816 original size:20 final size:19
Alignment explanation
Indices: 26793--26839 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
26783 CGATATAACA
26793 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
26813 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
26833 GGTAAAA
1 GGTAAAA
26840 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:26841 original size:17 final size:19
Alignment explanation
Indices: 26802--26844 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
26792 AGGTAAAAAT
26802 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
26822 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
26839 ATGATA
1 ATGATA
26845 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:29120 original size:21 final size:21
Alignment explanation
Indices: 29073--29137 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
29063 AAGACAATCA
* *
29073 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
29095 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
29115 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
29136 AG
1 AG
29138 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:29213 original size:33 final size:33
Alignment explanation
Indices: 29171--29236 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
29161 AAATAGATGG
*
29171 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
29204 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
29237 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:30795 original size:18 final size:18
Alignment explanation
Indices: 30774--30810 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
30764 GTAATTGGAG
30774 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
30792 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
30810 T
1 T
30811 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:30818 original size:24 final size:24
Alignment explanation
Indices: 30766--30812 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
30756 TTTCATATGT
* *
30766 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
30790 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
30813 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:31112 original size:39 final size:39
Alignment explanation
Indices: 31069--31155 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
31059 TCCGATGCTC
*
31069 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
31108 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
31147 ATCAAAATC
1 ATCAAAATC
31156 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:31591 original size:23 final size:23
Alignment explanation
Indices: 31560--31632 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
31550 ATAGGTAAAC
*
31560 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
31583 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
31606 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
31629 ATAT
1 ATAT
31633 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:32457 original size:333 final size:334
Alignment explanation
Indices: 31675--32676 Score: 1952
Period size: 334 Copynumber: 3.0 Consensus size: 334
31665 CATACTTTTT
*
31675 TCACTGTAGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
1 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
31740 TATAGGCGTCTAATGATTTATTTTTTTCGTTACGATATATATTATTATTAAATTAAAAATTCTAA
66 TATAGGCGTCTAATGATTTATTTTTTTCGTTACGATATATATTATTATTAAATTAAAAATTCTAA
31805 ATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAA
131 ATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAA
31870 TATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAA
196 TATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAA
31935 GAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATATAATGTAATAGGTAAAT
261 GAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATATAATGTAATAGGTAAAT
32000 TTGCAATGC
326 TTGCAATGC
32009 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
1 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
32074 TATAGGCGTCTAATGATTTATTTTTTTCGTTACGATATATATTATTATTAAATTAAAAATTCTAA
66 TATAGGCGTCTAATGATTTATTTTTTTCGTTACGATATATATTATTATTAAATTAAAAATTCTAA
32139 ATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAA
131 ATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAA
32204 TATTGTAGGTGGAAAACATGAAACACTATT-AAAAAATTGAAACATAAATTACATAACTTTAAAA
196 TATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAA
32268 GAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATATAATGTAATAGGTAAAT
261 GAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATATAATGTAATAGGTAAAT
32333 TTGCAATGC
326 TTGCAATGC
32342 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
1 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
*
32407 TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAA
66 TATAGGCGTCTAATGATTTATTTTTTTCGTTACGATATATATTATTATTAAATTAAAAATTCTAA
*
32472 ATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAA
131 ATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAA
*
32537 TATTGTAGGTAGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAA
196 TATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAA
*
32602 GAAATATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATATAATGTAATAGGTAAAT
261 GAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATATAATGTAATAGGTAAAT
32667 TTGCAATGC
326 TTGCAATGC
32676 T
1 T
32677 ATCGGTATAA
Statistics
Matches: 662, Mismatches: 5, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
333 330 0.50
334 332 0.50
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (334 bp):
TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
TATAGGCGTCTAATGATTTATTTTTTTCGTTACGATATATATTATTATTAAATTAAAAATTCTAA
ATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAA
TATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAA
GAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATATAATGTAATAGGTAAAT
TTGCAATGC
Found at i:32833 original size:16 final size:15
Alignment explanation
Indices: 32800--32842 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
32790 TAATATAACA
*
32800 TAACCGGTCTAATTTT
1 TAACCGGTC-ACTTTT
32816 TAACCGGTCACTTGTT
1 TAACCGGTCACTT-TT
*
32832 TAATCGGTCAC
1 TAACCGGTCAC
32843 GCCGTATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 3 0.12
16 21 0.88
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.37
Consensus pattern (15 bp):
TAACCGGTCACTTTT
Found at i:34041 original size:12 final size:13
Alignment explanation
Indices: 34005--34038 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
33995 GTACTCAATA
34005 AATAAATATTATT
1 AATAAATATTATT
*
34018 AA-AAGTATTATT
1 AATAAATATTATT
34030 AATAAATAT
1 AATAAATAT
34039 ATTTTAAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (13 bp):
AATAAATATTATT
Found at i:34306 original size:23 final size:23
Alignment explanation
Indices: 34264--34319 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
34254 ATTATTATAT
34264 TATATTATTAAAAATATTAATAAA
1 TATATT-TTAAAAATATTAATAAA
* * *
34288 TATATTTTAAATATGTTAATAAT
1 TATATTTTAAAAATATTAATAAA
34311 TAATATTTT
1 T-ATATTTT
34320 TATTAAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATAAA
Found at i:49995 original size:19 final size:19
Alignment explanation
Indices: 49978--50036 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
49968 TGAAAAGATT
49978 TAATAAAATAAAATAGATAA
1 TAAT-AAATAAAATAGATAA
*
49998 TAATAAATAAAA-AGGAAAA
1 TAATAAATAAAATA-GATAA
* *
50017 TAATAAA-ATAATAAATAA
1 TAATAAATAAAATAGATAA
50035 TA
1 TA
50037 GTAGTAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.27
19 20 0.61
20 4 0.12
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (19 bp):
TAATAAATAAAATAGATAA
Found at i:50003 original size:20 final size:20
Alignment explanation
Indices: 49978--50027 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
49968 TGAAAAGATT
*
49978 TAATAAAATAAAATA-GATAA
1 TAATAAAATAAAA-AGGAAAA
49998 TAAT-AAATAAAAAGGAAAA
1 TAATAAAATAAAAAGGAAAA
50017 TAATAAAATAA
1 TAATAAAATAA
50028 TAAATAATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 1 0.04
19 16 0.59
20 10 0.37
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (20 bp):
TAATAAAATAAAAAGGAAAA
Found at i:50105 original size:17 final size:18
Alignment explanation
Indices: 50072--50113 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
50062 AGTTTTTTTA
50072 AAATAAAAGATAATAATT
1 AAATAAAAGATAATAATT
*
50090 AAATAAAATA-AATAATT
1 AAATAAAAGATAATAATT
50107 AAATAAA
1 AAATAAA
50114 TAATTTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
AAATAAAAGATAATAATT
Found at i:50749 original size:24 final size:25
Alignment explanation
Indices: 50722--50833 Score: 79
Period size: 24 Copynumber: 4.5 Consensus size: 25
50712 AAATAATTCC
*
50722 TAAAATAAT-AACTTAAATCCTAAT
1 TAAAATAATAAACTAAAATCCTAAT
*
50746 TAAAACTATTTAAACTAAAATACCTAA-
1 TAAAA-TA-ATAAACTAAAAT-CCTAAT
* * * *
50773 AACAAAT-ATAAAATAAAATACTATT
1 TA-AAATAATAAACTAAAATCCTAAT
**
50798 TAAAATAATATCCT-AAATCCTAAT
1 TAAAATAATAAACTAAAATCCTAAT
*
50822 TAAAATACTAAA
1 TAAAATAATAAA
50834 ACCTATTTAA
Statistics
Matches: 65, Mismatches: 16, Indels: 14
0.68 0.17 0.15
Matches are distributed among these distances:
24 29 0.45
25 17 0.26
26 1 0.02
27 10 0.15
28 8 0.12
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.30
Consensus pattern (25 bp):
TAAAATAATAAACTAAAATCCTAAT
Found at i:50849 original size:76 final size:73
Alignment explanation
Indices: 50698--50925 Score: 225
Period size: 75 Copynumber: 3.1 Consensus size: 73
50688 CTTCAAATTC
* * * * * *
50698 CTAAAAC-AAGTTAAAA-ATAAT-TCCTAAAATAATAACTTAAATCCTAATTAAAACTATTTAAA
1 CTAAAACAAAGATAAAATATAATAT-TTAAAATAATATCCTAAATCCTAATTAAAA-TACTAAAA
*
50760 -CTA--AAATA
64 CCTATTTAA-A
* *
50768 CCTAAAACAAATATAAAATAAAATACTATTTAAAATAATATCCTAAATCCTAATTAAAATACTAA
1 -CTAAAACAAAGATAAAAT---ATAATATTTAAAATAATATCCTAAATCCTAATTAAAATACTAA
50833 AACCTATTTAAA
62 AACCTATTTAAA
* * *
50845 CTAAAATACAAAGATAAAATATAATATTTAAAATATTATCCTAAAACTTAATTAAAATACTAAAA
1 CT-AAA-ACAAAGATAAAATATAATATTTAAAATAATATCCTAAATCCTAATTAAAATACTAAAA
50910 CCTATTTAAA
64 CCTATTTAAA
50920 CTAAAA
1 CTAAAA
50926 TACCTAAAAC
Statistics
Matches: 132, Mismatches: 14, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
71 7 0.05
72 7 0.05
73 1 0.01
74 3 0.02
75 59 0.45
76 36 0.27
77 5 0.04
78 14 0.11
ACGTcount: A:0.56, C:0.13, G:0.01, T:0.30
Consensus pattern (73 bp):
CTAAAACAAAGATAAAATATAATATTTAAAATAATATCCTAAATCCTAATTAAAATACTAAAACC
TATTTAAA
Found at i:53019 original size:59 final size:59
Alignment explanation
Indices: 52896--53116 Score: 218
Period size: 59 Copynumber: 3.8 Consensus size: 59
52886 TCATTATTGG
* ** ** *
52896 AATCCATACATTCCA-TATGATTTCCTTATCA-TTTAGCACCGT-TAGGGCTTTATTTGGA
1 AATCCATACATT-CAGTATGATTTCCTTATCATTTTAGCA-CATATAATGCTCCATATGGA
* * *
52954 AATCCATACATTCAGTATGATTCCCTTACCATTTTAGCACATATAATGC-CCTATCTGGA
1 AATCCATACATTCAGTATGATTTCCTTATCATTTTAGCACATATAATGCTCC-ATATGGA
* * * * *
53013 AATCCATATATTCAATATGATTTCCTTATCATTTTAGCACACT-CAGTTCTCCATATGGA
1 AATCCATACATTCAGTATGATTTCCTTATCATTTTAGCACA-TATAATGCTCCATATGGA
* * *
53072 AATCCATACACTCAGTATGCTTTTCTTATCATTTTAGCACATATA
1 AATCCATACATTCAGTATGATTTCCTTATCATTTTAGCACATATA
53117 GTGTCATTTG
Statistics
Matches: 134, Mismatches: 22, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
57 2 0.01
58 29 0.22
59 100 0.75
60 3 0.02
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (59 bp):
AATCCATACATTCAGTATGATTTCCTTATCATTTTAGCACATATAATGCTCCATATGGA
Found at i:53088 original size:118 final size:117
Alignment explanation
Indices: 52896--53116 Score: 300
Period size: 118 Copynumber: 1.9 Consensus size: 117
52886 TCATTATTGG
* * ** *
52896 AATCCATACATTCCATATGATTTCCTTATCATTTAGCACCGTTAGGGCTTTATTTGGAAATCCAT
1 AATCCATACATTCAATATGATTTCCTTATCATTTAGCACCGTCAGGGCTCCATATGGAAATCCAT
*
52961 ACATTCAGTATGATTCCCTTACCATTTTAGCACATATAATGCCCTATCTGGA
66 ACACTCAGTATGATTCCCTTACCATTTTAGCACATATAATGCCCTATCTGGA
* **
53013 AATCCATATATTCAATATGATTTCCTTATCATTTTAGCACAC-TCAGTTCTCCATATGGAAATCC
1 AATCCATACATTCAATATGATTTCCTTATCA-TTTAGCAC-CGTCAGGGCTCCATATGGAAATCC
* ** *
53077 ATACACTCAGTATGCTTTTCTTATCATTTTAGCACATATA
64 ATACACTCAGTATGATTCCCTTACCATTTTAGCACATATA
53117 GTGTCATTTG
Statistics
Matches: 89, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
117 29 0.33
118 59 0.66
119 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (117 bp):
AATCCATACATTCAATATGATTTCCTTATCATTTAGCACCGTCAGGGCTCCATATGGAAATCCAT
ACACTCAGTATGATTCCCTTACCATTTTAGCACATATAATGCCCTATCTGGA
Found at i:55673 original size:31 final size:29
Alignment explanation
Indices: 55606--55668 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
55596 CTGCTGTGTA
* *
55606 TTTTTCTGCACTGTTCGAACCAAATCAGT
1 TTTTTCTGCACAGTTCAAACCAAATCAGT
*
55635 TTTTTCTGCACAGTTCAAACCAAATCTGT
1 TTTTTCTGCACAGTTCAAACCAAATCAGT
55664 TTTTT
1 TTTTT
55669 TTCTGTACTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.43
Consensus pattern (29 bp):
TTTTTCTGCACAGTTCAAACCAAATCAGT
Found at i:55684 original size:15 final size:15
Alignment explanation
Indices: 55664--55693 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55654 CCAAATCTGT
*
55664 TTTTTTTCTGTACTG
1 TTTTTTTCTGCACTG
55679 TTTTTTTCTGCACTG
1 TTTTTTTCTGCACTG
55694 CATTGTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.17, G:0.13, T:0.63
Consensus pattern (15 bp):
TTTTTTTCTGCACTG
Found at i:55738 original size:14 final size:14
Alignment explanation
Indices: 55712--55751 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
55702 AAATCTGCTC
55712 AATAAAATAAAATAA
1 AATAAAAT-AAATAA
*
55727 AATAAAATAAATAG
1 AATAAAATAAATAA
55741 AATAAAATAAA
1 AATAAAATAAA
55752 GTTTGCTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (14 bp):
AATAAAATAAATAA
Found at i:55768 original size:5 final size:5
Alignment explanation
Indices: 55712--55751 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
55702 AAATCTGCTC
*
55712 AATAA AATAA AATAA AATAA AAT-A AATAG AATAA AATAA A
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA A
55752 GTTTGCTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:55774 original size:10 final size:10
Alignment explanation
Indices: 55761--55799 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
55751 AGTTTGCTAA
55761 AAATAAAACG
1 AAATAAAACG
*
55771 AAATAAAACAA
1 AAATAAAAC-G
*
55782 AAATAAAAGG
1 AAATAAAACG
55792 AAATAAAA
1 AAATAAAA
55800 TAGAACGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.77, C:0.05, G:0.08, T:0.10
Consensus pattern (10 bp):
AAATAAAACG
Found at i:55783 original size:21 final size:21
Alignment explanation
Indices: 55759--55799 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
55749 AAAGTTTGCT
55759 AAAAATAAAACGAAATAAAAC
1 AAAAATAAAACGAAATAAAAC
*
55780 AAAAATAAAAGGAAATAAAA
1 AAAAATAAAACGAAATAAAA
55800 TAGAACGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.78, C:0.05, G:0.07, T:0.10
Consensus pattern (21 bp):
AAAAATAAAACGAAATAAAAC
Found at i:66600 original size:85 final size:82
Alignment explanation
Indices: 66473--66705 Score: 268
Period size: 75 Copynumber: 2.9 Consensus size: 82
66463 AAATAATTCC
* *
66473 TAAAATAATAACTTAAATCCTAATTAAAACT-CTTAAAA-CTATTTAAACTAAAATACCTAAAAC
1 TAAAATAATATCCTAAATCCTAATTAAAA-TAC-TAAAACCTATTTAAACTAAAATACCTAAAAC
*
66536 AAATATAAAATAAAATGCTATT
64 AAAGATAAAATAAAA---TATT
* *
66558 TAAAATAATATCCTAAATCCTAATTAAATTACTAAAACCTATTTAAAAT-AAA-A--T---ACAA
1 TAAAATAATATCCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAA
*
66616 AGATAAAATATAATATT
66 AGATAAAATAAAATATT
* * * *
66633 TAAAATATTATCCTAAAACTTAATTAAAATACTAAAACATATTTAAACTAAAATACCTAAAACAA
1 TAAAATAATATCCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAA
66698 AGATAAAA
66 AGATAAAA
66706 AATATTATCC
Statistics
Matches: 127, Mismatches: 12, Indels: 21
0.79 0.08 0.13
Matches are distributed among these distances:
75 47 0.37
76 3 0.02
77 1 0.01
78 15 0.12
79 1 0.01
81 1 0.01
82 12 0.09
83 1 0.01
84 9 0.07
85 37 0.29
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.30
Consensus pattern (82 bp):
TAAAATAATATCCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAA
AGATAAAATAAAATATT
Found at i:66704 original size:25 final size:24
Alignment explanation
Indices: 66657--66704 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
66647 AAAACTTAAT
* **
66657 TAAAATACTAAAACATATTTAAAC
1 TAAAATACTAAAACAAAGATAAAC
66681 TAAAATACCTAAAACAAAGATAAA
1 TAAAATA-CTAAAACAAAGATAAA
66705 AAATATTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.23
Consensus pattern (24 bp):
TAAAATACTAAAACAAAGATAAAC
Found at i:66722 original size:70 final size:72
Alignment explanation
Indices: 66559--66723 Score: 190
Period size: 75 Copynumber: 2.3 Consensus size: 72
66549 AATGCTATTT
* * * * *
66559 AAAATAATATCCTAAATCCTAATTAAATTACTAAAACCTATTTAAAATAAAATACAAAGATAAAA
1 AAAATATTATCCTAAAACTTAATTAAAATACTAAAACATATTTAAAATAAAATAC--A-ATAAAA
* * **
66624 TATAATATTT
63 CATAAGATAA
* *
66634 AAAATATTATCCTAAAACTTAATTAAAATACTAAAACATATTTAAACTAAAATAC-CTAAAACA-
1 AAAATATTATCCTAAAACTTAATTAAAATACTAAAACATATTTAAAATAAAATACAATAAAACAT
66697 AAGATAA
66 AAGATAA
66704 AAAATATTATCCTAAAACTT
1 AAAATATTATCCTAAAACTT
66724 GAGTTTAATT
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
70 24 0.30
71 6 0.08
75 49 0.62
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.30
Consensus pattern (72 bp):
AAAATATTATCCTAAAACTTAATTAAAATACTAAAACATATTTAAAATAAAATACAATAAAACAT
AAGATAA
Done.