Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006116.1 Hibiscus syriacus cultivar Beakdansim tig00014496_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: 58799
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6147 original size:58 final size:58
Alignment explanation
Indices: 6082--6197 Score: 205
Period size: 58 Copynumber: 2.0 Consensus size: 58
6072 TGATCTGGCC
*
6082 TCATGTCATTGACGTGTTTGTATTGTTCCAGAAACGACTTGGCTAAATCCTTCCAAGT
1 TCATGTCATTGACGTGTTTGTATTGTTCCAGAAAAGACTTGGCTAAATCCTTCCAAGT
* *
6140 TCATGTCATTGACGTGTTTGTATTGTTCCATAAAAGACTTGGTTAAATCCTTCCAAGT
1 TCATGTCATTGACGTGTTTGTATTGTTCCAGAAAAGACTTGGCTAAATCCTTCCAAGT
6198 CTTGATATGG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (58 bp):
TCATGTCATTGACGTGTTTGTATTGTTCCAGAAAAGACTTGGCTAAATCCTTCCAAGT
Found at i:10277 original size:11 final size:10
Alignment explanation
Indices: 10246--10291 Score: 69
Period size: 9 Copynumber: 4.7 Consensus size: 10
10236 ATAAAAAAGA
10246 TAAAGAAAAT
1 TAAAGAAAAT
10256 TAAAG-AAAT
1 TAAAGAAAAT
10265 TAAAGAAAAAT
1 TAAAG-AAAAT
10276 TAAAGAAAA-
1 TAAAGAAAAT
10285 TAAAGAA
1 TAAAGAA
10292 TATAATAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
9 16 0.47
10 9 0.26
11 9 0.26
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (10 bp):
TAAAGAAAAT
Found at i:10296 original size:9 final size:9
Alignment explanation
Indices: 10234--10433 Score: 68
Period size: 9 Copynumber: 20.3 Consensus size: 9
10224 GTACCCTTAG
10234 AAATAAA-A
1 AAATAAAGA
10242 AAGATAAAGA
1 AA-ATAAAGA
10252 AAATTAAAGA
1 AAA-TAAAGA
*
10262 AATTAAAGAA
1 AAATAAAG-A
10272 AAATTAAAGA
1 AAA-TAAAGA
10282 AAATAAAGA
1 AAATAAAGA
*
10291 ATATAATA-A
1 AAATAA-AGA
*
10300 TAATATAATAAA
1 -AA-ATAA-AGA
*
10312 TAAATAAATA
1 -AAATAAAGA
10322 AAA-ACAAGA
1 AAATA-AAGA
*
10331 ATAA-AATGA
1 A-AATAAAGA
*
10340 AAATAAATA
1 AAATAAAGA
*
10349 ATGAATAAATA
1 A--AATAAAGA
*
10360 TAAATGAAATAA
1 -AAAT-AAA-GA
10372 AAATAAAGTA
1 AAATAAAG-A
10382 AAGATAAAGA
1 AA-ATAAAGA
10392 AAA-ATAAGAA
1 AAATA-AAG-A
10402 ATAATAAAGA
1 A-AATAAAGA
* *
10412 AAAAAAAAA
1 AAATAAAGA
*
10421 AGAAAAAAGA
1 A-AATAAAGA
10431 AAA
1 AAA
10434 AATAAATATA
Statistics
Matches: 154, Mismatches: 14, Indels: 47
0.72 0.07 0.22
Matches are distributed among these distances:
8 6 0.04
9 51 0.33
10 49 0.32
11 41 0.27
12 7 0.05
ACGTcount: A:0.73, C:0.01, G:0.09, T:0.17
Consensus pattern (9 bp):
AAATAAAGA
Found at i:10307 original size:8 final size:7
Alignment explanation
Indices: 10283--10409 Score: 50
Period size: 7 Copynumber: 17.9 Consensus size: 7
10273 AATTAAAGAA
*
10283 AATAAAG
1 AATAAAT
10290 AATATAAT
1 AATA-AAT
10298 AATAATAT
1 AATAA-AT
10306 AATAAAT
1 AATAAAT
10313 AAATAAAT
1 -AATAAAT
*
10321 AA-AAAC
1 AATAAAT
* *
10327 AAGAATAA
1 AATAA-AT
*
10335 AATGAA-
1 AATAAAT
10341 AATAAAT
1 AATAAAT
*
10348 AATGAAT
1 AATAAAT
*
10355 AA-ATAT
1 AATAAAT
10361 AAATGAAAT
1 -AAT-AAAT
10370 AA-AAAT
1 AATAAAT
10376 AAAGTAAA-
1 -AA-TAAAT
* *
10384 GATAAAG
1 AATAAAT
10391 AA-AAAT
1 AATAAAT
*
10397 AAGAAAT
1 AATAAAT
10404 AATAAA
1 AATAAA
10410 GAAAAAAAAA
Statistics
Matches: 92, Mismatches: 14, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
6 25 0.27
7 35 0.38
8 26 0.28
9 6 0.07
ACGTcount: A:0.71, C:0.01, G:0.07, T:0.21
Consensus pattern (7 bp):
AATAAAT
Found at i:10318 original size:11 final size:11
Alignment explanation
Indices: 10282--10378 Score: 60
Period size: 11 Copynumber: 8.6 Consensus size: 11
10272 AAATTAAAGA
*
10282 AAATAAAGAAT
1 AAATAAATAAT
10293 ATAAT-AATAAT
1 A-AATAAATAAT
10304 ATAATAAATAAAT
1 A-AATAAAT-AAT
*
10317 AAATAAA-AACA
1 AAATAAATAA-T
*
10328 AGAATAAAATGA-
1 A-AAT-AAATAAT
10340 AAATAAATAAT
1 AAATAAATAAT
*
10351 GAATAAAT-AT
1 AAATAAATAAT
10361 AAATGAAATAA-
1 AAAT-AAATAAT
10372 AAATAAA
1 AAATAAA
10379 GTAAAGATAA
Statistics
Matches: 70, Mismatches: 6, Indels: 21
0.72 0.06 0.22
Matches are distributed among these distances:
10 15 0.21
11 30 0.43
12 17 0.24
13 7 0.10
14 1 0.01
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.23
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:10369 original size:26 final size:26
Alignment explanation
Indices: 10261--10393 Score: 72
Period size: 26 Copynumber: 5.3 Consensus size: 26
10251 AAAATTAAAG
* *
10261 AAATTAAAGAAAAATTAAAG-AAA-AT
1 AAATGAAATAAAAA-TAAAGTAAATAT
* *
10286 AAA-GAATATAATAATAATA-TAATAAAT
1 AAATGAA-ATAAAAATAA-AGTAA-ATAT
*
10313 AAAT-AAATAAAAA-CAAG--AATA-
1 AAATGAAATAAAAATAAAGTAAATAT
*
10334 AAATGAAAATAAATAATGAA-TAAATAT
1 AAATG-AAATAAA-AATAAAGTAAATAT
*
10361 AAATGAAATAAAAATAAAGTAAAGAT
1 AAATGAAATAAAAATAAAGTAAATAT
10387 AAA-GAAA
1 AAATGAAA
10394 AATAAGAAAT
Statistics
Matches: 84, Mismatches: 9, Indels: 30
0.68 0.07 0.24
Matches are distributed among these distances:
21 4 0.05
22 2 0.02
23 8 0.10
24 8 0.10
25 23 0.27
26 27 0.32
27 12 0.14
ACGTcount: A:0.71, C:0.01, G:0.08, T:0.21
Consensus pattern (26 bp):
AAATGAAATAAAAATAAAGTAAATAT
Found at i:10383 original size:11 final size:11
Alignment explanation
Indices: 10339--10415 Score: 51
Period size: 11 Copynumber: 7.4 Consensus size: 11
10329 GAATAAAATG
10339 AAAATAAA-TA
1 AAAATAAAGTA
*
10349 ATGAATAAA-TA
1 A-AAATAAAGTA
*
10360 TAAATGAAA-TA
1 AAAAT-AAAGTA
10371 AAAATAAAGTA
1 AAAATAAAGTA
*
10382 AAGATAAAG-A
1 AAAATAAAGTA
10392 AAAAT-AAG-A
1 AAAATAAAGTA
10401 AATAATAAAG-A
1 AA-AATAAAGTA
10412 AAAA
1 AAAA
10416 AAAAAAGAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
9 6 0.11
10 17 0.30
11 33 0.59
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (11 bp):
AAAATAAAGTA
Found at i:10397 original size:49 final size:48
Alignment explanation
Indices: 10265--10408 Score: 127
Period size: 49 Copynumber: 2.9 Consensus size: 48
10255 TTAAAGAAAT
*
10265 TAAAGAAAAATTAAAG-AAAATAAAGAATATAATAATAATATAATAAATAAA
1 TAAATAAAAA-TAAAGTAAAATAAAGAA-A-AATAATAATATAAT-AATAAA
* * *
10316 TAAATAAAAACAAGAATAAAATGAAA-ATAAATAATGAATA-AAT-ATAAA
1 TAAATAAAAATAA-AGTAAAAT-AAAGAAAAATAAT-AATATAATAATAAA
*
10364 TGAAATAAAAATAAAGTAAAGATAAAGAAAAATAAGAA-ATAATAA
1 T-AAATAAAAATAAAGTAAA-ATAAAGAAAAATAATAATATAATAA
10409 AGAAAAAAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
47 1 0.01
48 19 0.25
49 21 0.28
50 11 0.14
51 15 0.20
52 6 0.08
53 3 0.04
ACGTcount: A:0.71, C:0.01, G:0.08, T:0.21
Consensus pattern (48 bp):
TAAATAAAAATAAAGTAAAATAAAGAAAAATAATAATATAATAATAAA
Found at i:10408 original size:20 final size:19
Alignment explanation
Indices: 10234--10447 Score: 84
Period size: 20 Copynumber: 10.8 Consensus size: 19
10224 GTACCCTTAG
10234 AAATAAAAA-AGATAAAGAA
1 AAATAAAAATA-ATAAAGAA
* *
10253 AATTAAAGAA-ATTAAAGAA
1 AAATAAA-AATAATAAAGAA
10272 AAATTAAAGAA-AATAAAGAA
1 AAA-TAAA-AATAATAAAGAA
*
10292 TATAATAATAATATAATAAATAAA
1 -A-AATAA-AA-ATAATAAA-GAA
* * *
10316 TAAATAAAAACAA-GAA-TA
1 -AAATAAAAATAATAAAGAA
* *
10334 AAATGAAAATAAATAATGAA
1 AAATAAAAAT-AATAAAGAA
* * *
10354 TAAATATAAAT--GAAATAA
1 -AAATAAAAATAATAAAGAA
10372 AAATAAAGTAA-AGATAAAGAA
1 AAATAAA--AATA-ATAAAGAA
10393 AAATAAGAAATAATAAAGAA
1 AAATAA-AAATAATAAAGAA
* * *
10413 AAAAAAAAAGAAAAAAGAAA
1 AAATAAAAATAATAAAG-AA
*
10433 AAATAAATATAATAA
1 AAATAAAAATAATAA
10448 TATATATAAT
Statistics
Matches: 147, Mismatches: 28, Indels: 39
0.69 0.13 0.18
Matches are distributed among these distances:
17 14 0.10
18 7 0.05
19 27 0.18
20 49 0.33
21 28 0.19
22 7 0.05
23 11 0.07
24 4 0.03
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.18
Consensus pattern (19 bp):
AAATAAAAATAATAAAGAA
Found at i:10424 original size:12 final size:13
Alignment explanation
Indices: 10387--10434 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
10377 AAGTAAAGAT
* *
10387 AAAGAAAAATAAG
1 AAAGAAAAAGAAA
*
10400 AAATAATAAAGAAA
1 AAAGAA-AAAGAAA
10414 AAA-AAAAAGAAA
1 AAAGAAAAAGAAA
10426 AAAGAAAAA
1 AAAGAAAAA
10435 ATAAATATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 10 0.33
13 12 0.40
14 8 0.27
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.06
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:10429 original size:19 final size:19
Alignment explanation
Indices: 10387--10435 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
10377 AAGTAAAGAT
* * *
10387 AAAGAAAAATAAGAAATAAT
1 AAAGAAAAA-AAAAAAGAAA
10407 AAAGAAAAAAAAAAAGAAA
1 AAAGAAAAAAAAAAAGAAA
10426 AAAGAAAAAA
1 AAAGAAAAAA
10436 TAAATATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (19 bp):
AAAGAAAAAAAAAAAGAAA
Found at i:10452 original size:2 final size:2
Alignment explanation
Indices: 10439--10500 Score: 103
Period size: 2 Copynumber: 32.5 Consensus size: 2
10429 GAAAAAATAA
10439 AT AT A- AT A- AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10478 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
10501 AATGTTAGGA
Statistics
Matches: 57, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.05
2 54 0.95
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10634 original size:3 final size:3
Alignment explanation
Indices: 10583--10647 Score: 53
Period size: 3 Copynumber: 21.3 Consensus size: 3
10573 ATAGAAATGT
* * * *
10583 ATA ATG ATA ATG ATA ATA A-A A-A ACA ATA AAA ATAA ATA TATA TATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA -ATA -ATA
10629 ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
10648 AAGGGCTAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
2 4 0.08
3 38 0.73
4 10 0.19
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:12935 original size:18 final size:18
Alignment explanation
Indices: 12914--12950 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
12904 AGAGTGTAAG
*
12914 CAAGGTTTTGAGTATAAA
1 CAAGGTTTTAAGTATAAA
12932 CAAGGTTTTAAGTATAAA
1 CAAGGTTTTAAGTATAAA
12950 C
1 C
12951 TTTATGTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (18 bp):
CAAGGTTTTAAGTATAAA
Found at i:13176 original size:2 final size:2
Alignment explanation
Indices: 13171--13204 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
13161 TAAAAAATTA
13171 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13205 TTGTATTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16173 original size:20 final size:22
Alignment explanation
Indices: 16148--16202 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
16138 AGGCTTAATA
*
16148 GTATCGGTAC-CCT-TACTATG
1 GTATCGATACTCCTATACTATG
*
16168 GTATCGATACTTCTATACTATG
1 GTATCGATACTCCTATACTATG
16190 GTATCGATACTCC
1 GTATCGATACTCC
16203 CTTCAGTATC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 9 0.30
21 2 0.07
22 19 0.63
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (22 bp):
GTATCGATACTCCTATACTATG
Found at i:16300 original size:19 final size:21
Alignment explanation
Indices: 16273--16322 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
16263 CTTTCCTCTT
* *
16273 AGTACCGATACC-C-TACTTC
1 AGTATCGATACCACTTACATC
*
16292 AGTATCGATACCACTTGCATC
1 AGTATCGATACCACTTACATC
16313 AGTATCGATA
1 AGTATCGATA
16323 TTGTTCATCG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 11 0.42
20 1 0.04
21 14 0.54
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (21 bp):
AGTATCGATACCACTTACATC
Found at i:22971 original size:22 final size:22
Alignment explanation
Indices: 22943--22989 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
22933 CAGTCTAAAT
*
22943 GCTGAACGATTCAGCATTCAGC
1 GCTGAACGATTCAACATTCAGC
* *
22965 GCTGAACGGTTCAACATTTAGC
1 GCTGAACGATTCAACATTCAGC
22987 GCT
1 GCT
22990 AAATGGTTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (22 bp):
GCTGAACGATTCAACATTCAGC
Found at i:22997 original size:22 final size:22
Alignment explanation
Indices: 22947--22998 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
22937 CTAAATGCTG
* * *
22947 AACGATTCAGCATTCAGCGCTG
1 AACGGTTCAACATTCAGCGCTA
*
22969 AACGGTTCAACATTTAGCGCTA
1 AACGGTTCAACATTCAGCGCTA
*
22991 AATGGTTC
1 AACGGTTC
22999 CATTCAAAGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (22 bp):
AACGGTTCAACATTCAGCGCTA
Found at i:27253 original size:18 final size:18
Alignment explanation
Indices: 27230--27265 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
27220 TCTATCTTCT
27230 TGAGGAGGTAGAAGAGAG
1 TGAGGAGGTAGAAGAGAG
27248 TGAGGAGGTAGAAGAGAG
1 TGAGGAGGTAGAAGAGAG
27266 ATAGTCAAAA
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:0.39, C:0.00, G:0.50, T:0.11
Consensus pattern (18 bp):
TGAGGAGGTAGAAGAGAG
Found at i:29753 original size:2 final size:2
Alignment explanation
Indices: 29701--29744 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
29691 ATCTCAGCTT
29701 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
29743 TA
1 TA
29745 CAGATATATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32074 original size:10 final size:10
Alignment explanation
Indices: 32059--32083 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
32049 TCTATTTCGA
32059 AAATCAACCT
1 AAATCAACCT
32069 AAATCAACCT
1 AAATCAACCT
32079 AAATC
1 AAATC
32084 TCTTACTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.20
Consensus pattern (10 bp):
AAATCAACCT
Found at i:39370 original size:23 final size:22
Alignment explanation
Indices: 39344--39407 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 22
39334 CCTTCGGGAC
39344 ATGTGGCACTTTGGTGCAAACCT
1 ATGTGGCACTTTGGTGCAAA-CT
*
39367 ATGTGGTC-CTTTGG-G-ACAATT
1 ATGTGG-CACTTTGGTGCA-AACT
*
39388 ATGTGGCACTTCGGTGCAAA
1 ATGTGGCACTTTGGTGCAAA
39408 TTACGAGCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
20 1 0.03
21 13 0.38
22 6 0.18
23 13 0.38
24 1 0.03
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (22 bp):
ATGTGGCACTTTGGTGCAAACT
Found at i:39383 original size:40 final size:41
Alignment explanation
Indices: 39325--39407 Score: 114
Period size: 44 Copynumber: 2.0 Consensus size: 41
39315 GTCGAGGGTT
*
39325 CTATGTGGTCCTTCGGGAC-ATGTGGCACTTTGGTGCAAAC
1 CTATGTGGTCCTTCGGGACAATGTGGCACTTCGGTGCAAAC
*
39365 CTATGTGGTCCTTTGGGACAATTATGTGGCACTTCGGTGCAAA
1 CTATGTGGTCCTTCGGGAC-A--ATGTGGCACTTCGGTGCAAA
39408 TTACGAGCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
40 18 0.49
44 19 0.51
ACGTcount: A:0.19, C:0.20, G:0.29, T:0.31
Consensus pattern (41 bp):
CTATGTGGTCCTTCGGGACAATGTGGCACTTCGGTGCAAAC
Found at i:46242 original size:44 final size:44
Alignment explanation
Indices: 46174--46296 Score: 201
Period size: 44 Copynumber: 2.8 Consensus size: 44
46164 GTCGAGGGTT
* *
46174 CTATGTGGTCCTTCGGAACAATTATGTGGCACTTCGGTGCAAAC
1 CTATGTGGTCCTTCGGGACAATTATGTGGCACTTCGGTACAAAC
* *
46218 CTATTTGGTCCTTCGGGACAATTATGTGGCACTTTGGTACAAAC
1 CTATGTGGTCCTTCGGGACAATTATGTGGCACTTCGGTACAAAC
*
46262 CTATGTGGTCCTTCGGGATAATTATGTGGCACTTC
1 CTATGTGGTCCTTCGGGACAATTATGTGGCACTTC
46297 AGTGTAAATT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 72 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.33
Consensus pattern (44 bp):
CTATGTGGTCCTTCGGGACAATTATGTGGCACTTCGGTACAAAC
Found at i:46296 original size:21 final size:21
Alignment explanation
Indices: 46175--46290 Score: 85
Period size: 21 Copynumber: 5.3 Consensus size: 21
46165 TCGAGGGTTC
*
46175 TATGTGGTCCTTCGGAACAAT
1 TATGTGGTCCTTCGGGACAAT
*
46196 TATGTGG-CACTTCGGTG-CAAACC
1 TATGTGGTC-CTTCGG-GAC-AA-T
*
46219 TATTTGGTCCTTCGGGACAAT
1 TATGTGGTCCTTCGGGACAAT
* * *
46240 TATGTGG-CACTTTGGTACAAACC
1 TATGTGGTC-CTTCGGGAC-AA-T
*
46263 TATGTGGTCCTTCGGGATAAT
1 TATGTGGTCCTTCGGGACAAT
46284 TATGTGG
1 TATGTGG
46291 CACTTCAGTG
Statistics
Matches: 73, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
20 2 0.03
21 34 0.47
22 9 0.12
23 26 0.36
24 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGACAAT
Found at i:47879 original size:2 final size:2
Alignment explanation
Indices: 47872--47918 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
47862 AGTCCTTATC
47872 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
47914 TA TA T
1 TA TA T
47919 TTAGGATAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53697 original size:125 final size:124
Alignment explanation
Indices: 53555--53794 Score: 392
Period size: 125 Copynumber: 1.9 Consensus size: 124
53545 TTCTCCAATG
* *
53555 AAAAAAAATCATATATTCAAAGCATGACCTTGATCG-GATATTTGGCAGTTCGGTGTTTGCTCCA
1 AAAAAAAACCATATATTCAAAGCATAACCTTGATCGAG-TATTTGGCAGTTCGGTGTTTGCTCCA
*
53619 CTATGATTGTCAAGTCAAAGACATTGTGATGAGTTGAACCCTTTAATTAGTTTAATGAAA
65 CTATGATTGTCAAATCAAAGACATTGTGATGAGTTGAACCCTTTAATTAGTTTAATGAAA
*
53679 AAAAAGAAACCATATATTCAAAGCATAACCTTGATCGAGTATTTGGTAGTTCGGTGTTTGCTCCA
1 AAAAA-AAACCATATATTCAAAGCATAACCTTGATCGAGTATTTGGCAGTTCGGTGTTTGCTCCA
* * *
53744 CTGTGATTGTTAAATCGAAGACATTGTGATGAGTTGAACCCTTTAATTAGT
65 CTATGATTGTCAAATCAAAGACATTGTGATGAGTTGAACCCTTTAATTAGT
53795 CCGATGAAGG
Statistics
Matches: 107, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
124 5 0.05
125 101 0.94
126 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (124 bp):
AAAAAAAACCATATATTCAAAGCATAACCTTGATCGAGTATTTGGCAGTTCGGTGTTTGCTCCAC
TATGATTGTCAAATCAAAGACATTGTGATGAGTTGAACCCTTTAATTAGTTTAATGAAA
Found at i:57042 original size:20 final size:22
Alignment explanation
Indices: 56991--57073 Score: 134
Period size: 22 Copynumber: 3.9 Consensus size: 22
56981 TCTACATTTA
* *
56991 TCAAAGATAATAGATTCTCTCC
1 TCAAAGATGATAGATTCTCTCT
57013 TCAAAGATGATAGATTCTCTCT
1 TCAAAGATGATAGATTCTCTCT
57035 TC-AA-ATGATAGATTCTCTCT
1 TCAAAGATGATAGATTCTCTCT
57055 TCAAAGATGATAGATTCTC
1 TCAAAGATGATAGATTCTC
57074 GTTTTAAATT
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
20 18 0.32
21 4 0.07
22 35 0.61
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (22 bp):
TCAAAGATGATAGATTCTCTCT
Found at i:57944 original size:46 final size:46
Alignment explanation
Indices: 57865--57976 Score: 145
Period size: 46 Copynumber: 2.4 Consensus size: 46
57855 GGGAGTTTTT
* ** *
57865 TGATGTTTTC-AAAACCTTCTGGCCATCTGTAAGACCTTCAGTACA
1 TGATGTTTTCAAAAACCTTCAGGCCATCCATAAGACCTACAGTACA
* *
57910 TGATGTTTTCAAAAACCTTCAGGTCATCCATAAGACCTACAGTGCA
1 TGATGTTTTCAAAAACCTTCAGGCCATCCATAAGACCTACAGTACA
*
57956 GGATGTTTTCAAAAAGCCTTC
1 TGATGTTTTCAAAAA-CCTTC
57977 GAGAGCTTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 10 0.17
46 43 0.74
47 5 0.09
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.31
Consensus pattern (46 bp):
TGATGTTTTCAAAAACCTTCAGGCCATCCATAAGACCTACAGTACA
Found at i:57987 original size:122 final size:121
Alignment explanation
Indices: 57766--58163 Score: 611
Period size: 122 Copynumber: 3.3 Consensus size: 121
57756 AAACTATTTC
* * *
57766 CCATCTGTAAGACCTTCAGTGCATGATGTTATCAAAACCTTTGGGTCATCCACAAGACCTACAGT
1 CCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGT
* * *
57831 GCAGGATGTTTTCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAAAACCTTCTGG
66 GCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGG
* *
57887 CCATCTGTAAGACCTTCAGTACATGATGTTTTCAAAAACCTTCAGGTCATCCATAAGACCTACAG
1 CCATCTGTAAGACCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGTCATCCATAAGACCTACAG
* *
57952 TGCAGGATGTTTTCAAAAAGCCTTCGAGAGCTTTTTAATGTTTTCAAAGCCTTCGGG
65 TGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGG
* * **
58009 TCATCTGTAACACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGT
1 CCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGT
*
58074 GCAGGATGTTTTC-AAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGG
66 GCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGG
* * *
58129 TCATTTGTAAGA-CTACAGTGCATGATGTTTTCAAA
1 CCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAA
58164 GAGCCTTTGG
Statistics
Matches: 254, Mismatches: 22, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
119 22 0.09
120 49 0.19
121 73 0.29
122 110 0.43
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (121 bp):
CCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGT
GCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGG
Found at i:58040 original size:45 final size:45
Alignment explanation
Indices: 57989--58099 Score: 177
Period size: 45 Copynumber: 2.4 Consensus size: 45
57979 GAGCTTTTTA
* *
57989 ATGTTTTCAAAGCCTTCGGGTCATCTGTAACACCTTCAGTGCATG
1 ATGTTTTCAAAGCCTTCGGGTCATCTGTAACACCTACAGTGCAGG
* *
58034 ATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCAGG
1 ATGTTTTCAAAGCCTTCGGGTCATCTGTAACACCTACAGTGCAGG
58079 ATGTTTTCAAAAGCCTTCGGG
1 ATGTTTTC-AAAGCCTTCGGG
58100 AGCTTTTTGA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
45 49 0.82
46 11 0.18
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.32
Consensus pattern (45 bp):
ATGTTTTCAAAGCCTTCGGGTCATCTGTAACACCTACAGTGCAGG
Found at i:58191 original size:74 final size:75
Alignment explanation
Indices: 58032--58247 Score: 357
Period size: 75 Copynumber: 2.9 Consensus size: 75
58022 CTTCAGTGCA
* * * *
58032 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAGCCTTC
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAGCCTTT
58097 GGGAGCTTTT
66 GGGAGCTTTT
*
58107 TGATATTTTCAAAGCCTTCGGGTCATTTGTAAGA-CTACAGTGCATGATGTTTTCAAAGAGCCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAA-AGCCTT
58171 TGGGAGCTTTT
65 TGGGAGCTTTT
58182 TGATA-TTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAA-CCTTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAGCCTTT
58245 GGG
66 GGG
58248 TCATCCATAA
Statistics
Matches: 133, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
73 8 0.06
74 50 0.38
75 75 0.56
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.35
Consensus pattern (75 bp):
TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAGCCTTT
GGGAGCTTTT
Found at i:58251 original size:45 final size:43
Alignment explanation
Indices: 58187--58291 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 43
58177 CTTTTTGATA
* ** *
58187 TTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGT
1 TTTCAAAACCTTCGGGTCATCCATAAGACCT--AGTGCAGGATGT
* *
58232 TTTCAAAACCTTTGGGTCATCCATAAGACCTAGTGGAGGATGT
1 TTTCAAAACCTTCGGGTCATCCATAAGACCTAGTGCAGGATGT
58275 TTTCAAAAAGCCTTCGG
1 TTTC-AAAA-CCTTCGG
58292 AGCTTTTGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
43 14 0.27
44 4 0.08
45 33 0.65
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (43 bp):
TTTCAAAACCTTCGGGTCATCCATAAGACCTAGTGCAGGATGT
Found at i:58321 original size:117 final size:118
Alignment explanation
Indices: 58112--58410 Score: 406
Period size: 117 Copynumber: 2.5 Consensus size: 118
58102 CTTTTTGATA
* * *** * * *
58112 TTTTCAAAGCCTTCGGGTCATTTGTAAGA-CTACAGTGCATGATGTTTTCAAAGAGCCTTTGGGA
1 TTTTCAAAACCTTCAGGTCATCCATAAGACCTA-AGTGCAGGATGTTTTCAAAAAGCC-TTCGGA
* *
58176 GCTTTTTGATATTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATG
64 GCTTTTTGATATTTCAAAGCCTTAGGGTCATCTGTAAGACCTACAGTGCATAATG
** *
58231 TTTTCAAAACCTTTGGGTCATCCATAAGACCT-AGTGGAGGATGTTTTCAAAAAGCCTTCGGAGC
1 TTTTCAAAACCTTCAGGTCATCCATAAGACCTAAGTGCAGGATGTTTTCAAAAAGCCTTCGGAGC
58295 -TTTTGATATTTTCAAAGCCTTAGGGTCATCTGTAAGACCTACAGTGCATAATG
66 TTTTTGATA-TTTCAAAGCCTTAGGGTCATCTGTAAGACCTACAGTGCATAATG
* *
58348 TTTTCTAATCCTTCAGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGG
1 TTTTCAAAACCTTCAGGTCATCCATAAGACCTA-AGTGCAGGATGTTTTCAAAAAGCCTTCGG
58411 GTCATCTGTA
Statistics
Matches: 160, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
116 8 0.05
117 77 0.48
118 21 0.13
119 52 0.32
120 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (118 bp):
TTTTCAAAACCTTCAGGTCATCCATAAGACCTAAGTGCAGGATGTTTTCAAAAAGCCTTCGGAGC
TTTTTGATATTTCAAAGCCTTAGGGTCATCTGTAAGACCTACAGTGCATAATG
Found at i:58393 original size:311 final size:318
Alignment explanation
Indices: 57819--58411 Score: 912
Period size: 311 Copynumber: 1.9 Consensus size: 318
57809 GGTCATCCAC
* *
57819 AAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAAAACCTTC
1 AAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGATTTCAAAACCTTC
* *
57884 TGGCCATCTGTAAGACCTTCAGTACATGATGTTTTCAAAAACCTTCAGGTCATCCATAAGACCTA
66 GGGCCATCTGTAAGACCTACAGTACATGATGTTTTCAAAAACCTTCAGGTCATCCATAAGACCTA
* *
57949 CAGTGCAGGATGTTTTCAAAAAGCCTTCGAGAGCTTTTTAATGTTTTCAAAGCCTTCGGGTCATC
131 -AGTGCAGGATGTTTTCAAAAAGCCTTCGAGAGCTTTTTAATATTTTCAAAGCCTTAGGGTCATC
* * * **
58014 TGTAACACCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCAGG
195 TGTAACACCTACAGTGCATAATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACAGTGCAGG
58079 ATGTTTTC-AAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATTTGT
260 ATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATTTGT
* * * *
58137 AAGA-CTACAGTGCATGATGTTTTCAAAGAGCCTTTGGGAGCTTTTTGAT-ATTTCAAAGCCTTC
1 AAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGATTTCAAAACCTTC
* * **
58200 GGGTCATCTGTAAGACCTACAGTGCATGATGTTTTC-AAAACCTTTGGGTCATCCATAAGACCT-
66 GGGCCATCTGTAAGACCTACAGTACATGATGTTTTCAAAAACCTTCAGGTCATCCATAAGACCTA
* *
58263 AGTGGAGGATGTTTTCAAAAAGCCTTCG-GAGC-TTTTGATATTTTCAAAGCCTTAGGGTCATCT
131 AGTGCAGGATGTTTTCAAAAAGCCTTCGAGAGCTTTTTAATATTTTCAAAGCCTTAGGGTCATCT
* * *
58326 GTAAGACCTACAGTGCATAATGTTTTCTAATCCTTCAGGTCATCCATAAGACCTACAGTGCAGGA
196 GTAACACCTACAGTGCATAATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACAGTGCAGGA
58391 TGTTTTCAAAAAGCCTTCGGG
261 TGTTTTCAAAAAGCCTTCGGG
58412 TCATCTGTAA
Statistics
Matches: 250, Mismatches: 24, Indels: 8
0.89 0.09 0.03
Matches are distributed among these distances:
311 92 0.37
312 17 0.07
313 27 0.11
315 25 0.10
316 44 0.18
317 41 0.16
318 4 0.02
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (318 bp):
AAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGATTTCAAAACCTTC
GGGCCATCTGTAAGACCTACAGTACATGATGTTTTCAAAAACCTTCAGGTCATCCATAAGACCTA
AGTGCAGGATGTTTTCAAAAAGCCTTCGAGAGCTTTTTAATATTTTCAAAGCCTTAGGGTCATCT
GTAACACCTACAGTGCATAATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACAGTGCAGGA
TGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCATTTGT
Found at i:58426 original size:47 final size:46
Alignment explanation
Indices: 58303--58504 Score: 239
Period size: 45 Copynumber: 4.4 Consensus size: 46
58293 GCTTTTGATA
* ** **
58303 TTTTC-AAAGCCTTAGGGTCATCTGTAAGACCTACAGTGCATAATG
1 TTTTCAAAAGCCTTCGGGTCATCCATAAGACCTACAGTGCAGGATG
* * *
58348 TTTTC-TAATCCTTCAGGTCATCCATAAGACCTACAGTGCAGGATG
1 TTTTCAAAAGCCTTCGGGTCATCCATAAGACCTACAGTGCAGGATG
** *
58393 TTTTCAAAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATG
1 TTTTC-AAAAGCCTTCGGGTCATCCATAAGACCTACAGTGCAGGATG
*
58440 TTTTCAAAA-CCTTCGGGTCATCCATAAGACCTACAGTGAAGGATG
1 TTTTCAAAAGCCTTCGGGTCATCCATAAGACCTACAGTGCAGGATG
*
58485 TGTTCAAACAAGCCTTCGGG
1 TTTTC-AA-AAGCCTTCGGG
58505 AGCTTTTTGA
Statistics
Matches: 133, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
45 78 0.59
46 6 0.05
47 41 0.31
48 8 0.06
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (46 bp):
TTTTCAAAAGCCTTCGGGTCATCCATAAGACCTACAGTGCAGGATG
Found at i:58465 original size:92 final size:92
Alignment explanation
Indices: 58308--58504 Score: 322
Period size: 92 Copynumber: 2.1 Consensus size: 92
58298 TGATATTTTC
* * *
58308 AAAGCCTTAGGGTCATCTGTAAGACCTACAGTGCATAATGTTTTCTAATCCTTCAGGTCATCCAT
1 AAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATAATGTTTTCAAAACCTTCAGGTCATCCAT
* *
58373 AAGACCTACAGTGCAGGATGTTTTCAA
66 AAGACCTACAGTGAAGGATGTGTTCAA
* *
58400 AAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCAT
1 AAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATAATGTTTTCAAAACCTTCAGGTCATCCAT
58465 AAGACCTACAGTGAAGGATGTGTTCAA
66 AAGACCTACAGTGAAGGATGTGTTCAA
58492 ACAAGCCTTCGGG
1 A-AAGCCTTCGGG
58505 AGCTTTTTGA
Statistics
Matches: 97, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
92 86 0.89
93 11 0.11
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (92 bp):
AAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATAATGTTTTCAAAACCTTCAGGTCATCCAT
AAGACCTACAGTGAAGGATGTGTTCAA
Done.