Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003403.1 Hibiscus syriacus cultivar Beakdansim tig00007168_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: 86962
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:2358 original size:20 final size:21
Alignment explanation
Indices: 2315--2366 Score: 81
Period size: 20 Copynumber: 2.5 Consensus size: 21
2305 ATTGTTGGGT
2315 AGTATCGATACTGATTGAATC
1 AGTATCGATACTGATTGAATC
2336 AGTATCGATACTG-TTGAGA-C
1 AGTATCGATACTGATTGA-ATC
2356 AGTATCGATAC
1 AGTATCGATAC
2367 CATGGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (21 bp):
AGTATCGATACTGATTGAATC
Found at i:2471 original size:21 final size:20
Alignment explanation
Indices: 2429--2485 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
2419 TACCGTAAGG
* * *
2429 GGGTATCGGTACCTTAGTAA
1 GGGTATCGATACCATGGTAA
2449 GGTAGTATCGAT-CCATGGTAA
1 GG--GTATCGATACCATGGTAA
2470 GGGTATCGATACCATG
1 GGGTATCGATACCATG
2486 AAACATCGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
21 9 0.29
22 7 0.23
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (20 bp):
GGGTATCGATACCATGGTAA
Found at i:2529 original size:94 final size:96
Alignment explanation
Indices: 2356--2536 Score: 262
Period size: 94 Copynumber: 1.9 Consensus size: 96
2346 CTGTTGAGAC
* * *
2356 AGTATCGATACCATGGTAAGGGTATCGATACCAAGCAAACATCTAATCTAATTTTGGTATTGATA
1 AGTATCGATACCATGGTAAGGGTATCGATACCAAGCAAACATCGAACCTAATTTTGGTATCGATA
* *
2421 CCGTAAGGGGGTATCGGTACCTTAGTAAGGT
66 CCGTAAGGGAGTATCAGTACCTTAGTAAGGT
*
2452 AGTATCGAT-CCATGGTAAGGGTATCGATACCATG-AAACATCGAACCTAATTTTGGTATCGATA
1 AGTATCGATACCATGGTAAGGGTATCGATACCAAGCAAACATCGAACCTAATTTTGGTATCGATA
2515 CCAGGT-A-GGAGTATCAGTACCT
66 CC--GTAAGGGAGTATCAGTACCT
2537 AGTGTATAAG
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
94 41 0.53
95 25 0.32
96 11 0.14
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.28
Consensus pattern (96 bp):
AGTATCGATACCATGGTAAGGGTATCGATACCAAGCAAACATCGAACCTAATTTTGGTATCGATA
CCGTAAGGGAGTATCAGTACCTTAGTAAGGT
Found at i:3024 original size:34 final size:34
Alignment explanation
Indices: 2986--3050 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
2976 ACAAAGCTGA
*
2986 AATGCATATGGGTGCATTATCGGCATAAAAGAAT
1 AATGCATATGGATGCATTATCGGCATAAAAGAAT
* *
3020 AATGCATATGGATGCATTATTGGCATGAAAG
1 AATGCATATGGATGCATTATCGGCATAAAAG
3051 GATGTCATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.28
Consensus pattern (34 bp):
AATGCATATGGATGCATTATCGGCATAAAAGAAT
Found at i:3083 original size:78 final size:78
Alignment explanation
Indices: 2952--3117 Score: 262
Period size: 78 Copynumber: 2.1 Consensus size: 78
2942 GGCACTGTGT
** *
2952 GTGCATTATTGGCATGAAAGGATGACAAAGCTGAAATGCATATGGGTGCATTATCGGCATAAAAG
1 GTGCATTATTGGCATGAAAGGATGACAAAGCTGAAATGCATATGGGTGCATTATCAACAAAAAAG
3017 AATAATGCATATG
66 AATAATGCATATG
* *
3030 GATGCATTATTGGCATGAAAGGATGTCATAG-TGAAATGCATATGGGTGCATTATCAACAAAAAA
1 G-TGCATTATTGGCATGAAAGGATGACAAAGCTGAAATGCATATGGGTGCATTATCAACAAAAAA
3094 GAATAATGCATATG
65 GAATAATGCATATG
*
3108 GTGTATTATT
1 GTGCATTATT
3118 AACCTAAAGG
Statistics
Matches: 81, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
77 8 0.10
78 46 0.57
79 27 0.33
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.28
Consensus pattern (78 bp):
GTGCATTATTGGCATGAAAGGATGACAAAGCTGAAATGCATATGGGTGCATTATCAACAAAAAAG
AATAATGCATATG
Found at i:5439 original size:2 final size:2
Alignment explanation
Indices: 5432--5524 Score: 177
Period size: 2 Copynumber: 46.5 Consensus size: 2
5422 AGGTCAAAAG
*
5432 AT AT AT AT AT AT AT AT AT AT CT 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
5474 AT AT AT AT 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 AT AT AT AT
5516 AT AT AT AT A
1 AT AT AT AT A
5525 ACTTTTCTGG
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6454 original size:18 final size:18
Alignment explanation
Indices: 6431--6465 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6421 GAAGCACGTC
6431 ATTATTTAAAAAAATATG
1 ATTATTTAAAAAAATATG
*
6449 ATTATTTAAAATAATAT
1 ATTATTTAAAAAAATAT
6466 CTAACTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
ATTATTTAAAAAAATATG
Found at i:6559 original size:18 final size:17
Alignment explanation
Indices: 6536--6569 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
6526 GGAGACCATA
6536 ATATTATATTTTTATATT
1 ATATTATA-TTTTATATT
6554 ATATTATATTTTATAT
1 ATATTATATTTTATAT
6570 AAATAAATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:6730 original size:13 final size:14
Alignment explanation
Indices: 6707--6735 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
6697 TTTTCATTCA
6707 AATATTTATAATTT
1 AATATTTATAATTT
6721 AATA-TTATAATTT
1 AATATTTATAATTT
6734 AA
1 AA
6736 CTCGTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AATATTTATAATTT
Found at i:7434 original size:14 final size:14
Alignment explanation
Indices: 7411--7446 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
7401 ACCATTTGAG
*
7411 AGGGGATTCGGTGT
1 AGGGGATTCGATGT
*
7425 AGGTGATTCGATGT
1 AGGGGATTCGATGT
7439 AGGGGATT
1 AGGGGATT
7447 ATTCAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.19, C:0.06, G:0.44, T:0.31
Consensus pattern (14 bp):
AGGGGATTCGATGT
Found at i:18354 original size:22 final size:22
Alignment explanation
Indices: 18319--18424 Score: 77
Period size: 22 Copynumber: 5.0 Consensus size: 22
18309 CAATCAGAAT
18319 AAAGAGAAAA-AAAAAAGCAAAA
1 AAAGA-AAAATAAAAAAGCAAAA
18341 AAAGAAAAAT--AAAAGC--AA
1 AAAGAAAAATAAAAAAGCAAAA
*
18359 AAAG-AAAATAAAAGAGCAACAA
1 AAAGAAAAATAAAAAAGCAA-AA
* **
18381 AAAGAAAAA-AGAAAAG-AAGC
1 AAAGAAAAATAAAAAAGCAAAA
18401 AAAGAGAAAATAAACAAAG-AAAA
1 AAAGA-AAAATAAA-AAAGCAAAA
18424 A
1 A
18425 GAGACAATAA
Statistics
Matches: 66, Mismatches: 8, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
17 5 0.08
18 6 0.09
19 5 0.08
20 11 0.17
21 10 0.15
22 18 0.27
23 11 0.17
ACGTcount: A:0.77, C:0.06, G:0.14, T:0.03
Consensus pattern (22 bp):
AAAGAAAAATAAAAAAGCAAAA
Found at i:18360 original size:17 final size:17
Alignment explanation
Indices: 18339--18372 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
18329 AAAAAAGCAA
18339 AAAAAGAAAAATAAAAGC
1 AAAAAG-AAAATAAAAGC
18357 AAAAAGAAAATAAAAG
1 AAAAAGAAAATAAAAG
18373 AGCAACAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.79, C:0.03, G:0.12, T:0.06
Consensus pattern (17 bp):
AAAAAGAAAATAAAAGC
Found at i:18410 original size:15 final size:15
Alignment explanation
Indices: 18390--18431 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
18380 AAAAGAAAAA
*
18390 AGAAAAGAAGCAAAG
1 AGAAAAGAAACAAAG
*
18405 AGAAAATAAACAAAG
1 AGAAAAGAAACAAAG
*
18420 A-AAAAGAGACAA
1 AGAAAAGAAACAA
18432 TAAGCACATG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 9 0.39
15 14 0.61
ACGTcount: A:0.71, C:0.07, G:0.19, T:0.02
Consensus pattern (15 bp):
AGAAAAGAAACAAAG
Found at i:18412 original size:44 final size:39
Alignment explanation
Indices: 18319--18424 Score: 117
Period size: 44 Copynumber: 2.6 Consensus size: 39
18309 CAATCAGAAT
*
18319 AAAGAGAAAA-AAAAAAGCAAAAAAAGAAAAATAAAAGC
1 AAAGAGAAAATAAAAAAGCAAAAAAAGAAAAAAAAAAGC
* *
18357 AAAAAGAAAATAAAAGAGCAACAAAAAGAAAAAAGAAAAGAAGC
1 AAAGAGAAAATAAAAAAGCAA-AAAAAG--AAAA-AAAA-AAGC
18401 AAAGAGAAAATAAACAAAG-AAAAA
1 AAAGAGAAAATAAA-AAAGCAAAAA
18425 GAGACAATAA
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
38 9 0.16
39 9 0.16
40 6 0.11
42 4 0.07
43 6 0.11
44 19 0.34
45 3 0.05
ACGTcount: A:0.77, C:0.06, G:0.14, T:0.03
Consensus pattern (39 bp):
AAAGAGAAAATAAAAAAGCAAAAAAAGAAAAAAAAAAGC
Found at i:19346 original size:24 final size:23
Alignment explanation
Indices: 19289--19348 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 23
19279 CTAGAAAGGA
19289 TAAATATTTTCAAAACTTTTTAT
1 TAAATATTTTCAAAACTTTTTAT
*
19312 TAAACATTTTTCAAAACTCTTTTAAT
1 TAAATA-TTTTCAAAACT-TTTT-AT
*
19338 T-GATATTTTCA
1 TAAATATTTTCA
19349 GATCTTGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 5 0.16
24 17 0.55
25 6 0.19
26 3 0.10
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.50
Consensus pattern (23 bp):
TAAATATTTTCAAAACTTTTTAT
Found at i:19578 original size:32 final size:33
Alignment explanation
Indices: 19494--19578 Score: 95
Period size: 32 Copynumber: 2.6 Consensus size: 33
19484 ACAATGGGGA
* * *
19494 CATCTTTGAAGATTCAACATCAAATGTTGAGGT
1 CATCTTTGGAGATTTAACATCAAATATTGAGGT
* *
19527 -ATATTTGGAGA-TTAGACATCGAATATTG-GGT
1 CATCTTTGGAGATTTA-ACATCAAATATTGAGGT
19558 CATCTTTGGAGATTTAACATC
1 CATCTTTGGAGATTTAACATC
19579 CTGATACGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
31 5 0.12
32 35 0.81
33 3 0.07
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (33 bp):
CATCTTTGGAGATTTAACATCAAATATTGAGGT
Found at i:20110 original size:127 final size:126
Alignment explanation
Indices: 19846--20307 Score: 534
Period size: 127 Copynumber: 3.7 Consensus size: 126
19836 TCCCCTGACC
* * * * * **
19846 AAGACTCATGAACAAATAAGTAGTGTCATCACCTGACCAGATCTCCTCATTATGTAAGAGTTGTG
1 AAGACTCATGAACAAATAAGCAGTGTCATCACCTGACCTGATCTCCTCATCACGTAGGAGCCGTG
* * * * * *
19911 CCAA-CTTAGATAACCATCCATCCCCATCAGAGTGGAACAGTGTTATCACCCTTAGATGGCC
66 TCAACCTTTGATAACCAT-CGTCCCTATCAGAGTGGAATAGTGTTATCACCCTTAGATGGCA
* * * * *
19972 AAGACTCATGAACAGATGAGTAGTGTCATCACCCGACCTGATCTCCTCATCACGTAGGAGCCATG
1 AAGACTCATGAACAAATAAGCAGTGTCATCACCTGACCTGATCTCCTCATCACGTAGGAGCCGTG
* * * *
20037 TCAACCTTTGATAAACAGTCGTCCCTATCATAGTGGAATTGTGTTATCACCCTTATATGGCA
66 TCAACCTTTGATAACCA-TCGTCCCTATCAGAGTGGAATAGTGTTATCACCCTTAGATGGCA
* * * *
20099 AAGACTAATGAATAGATTAGCAGTGTCATCACCTGACCTGATCTCCTCATCACGTAGGAGCCGTG
1 AAGACTCATGAACAAATAAGCAGTGTCATCACCTGACCTGATCTCCTCATCACGTAGGAGCCGTG
* *
20164 TCAACCTTTGATAACCATCTGTCCCTAGCAGAGTGGAATCGTGTTATCACCCTTAGATGGCTA
66 TCAACCTTTGATAACCATC-GTCCCTATCAGAGTGGAATAGTGTTATCACCCTTAGATGGC-A
* * * * * *
20227 AA-ACTCTTGAAAAAATAAGCAATGTCATCACCTGATCT-ATTCTCCTCATCATGTAGGAGTCGT
1 AAGACTCATGAACAAATAAGCAGTGTCATCACCTGACCTGA-TCTCCTCATCACGTAGGAGCCGT
* *
20290 GTCAACCCTAGATAACCA
65 GTCAACCTTTGATAACCA
20308 AGACTTATCA
Statistics
Matches: 289, Mismatches: 42, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
126 61 0.21
127 224 0.78
128 4 0.01
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (126 bp):
AAGACTCATGAACAAATAAGCAGTGTCATCACCTGACCTGATCTCCTCATCACGTAGGAGCCGTG
TCAACCTTTGATAACCATCGTCCCTATCAGAGTGGAATAGTGTTATCACCCTTAGATGGCA
Found at i:23318 original size:24 final size:22
Alignment explanation
Indices: 23275--23318 Score: 52
Period size: 24 Copynumber: 1.9 Consensus size: 22
23265 TTGAGTCTTT
*
23275 TTTTCTTCTCTTGTTACACGCA
1 TTTTCTTCTCTTGTGACACGCA
*
23297 TTTTCTTTGCTCTTGTGGCACG
1 TTTTC-TT-CTCTTGTGACACG
23319 ATCCTTATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 2 0.11
24 11 0.61
ACGTcount: A:0.09, C:0.25, G:0.16, T:0.50
Consensus pattern (22 bp):
TTTTCTTCTCTTGTGACACGCA
Found at i:29035 original size:14 final size:14
Alignment explanation
Indices: 28979--29030 Score: 79
Period size: 14 Copynumber: 3.7 Consensus size: 14
28969 TTAACTCGAA
28979 CTGAGTCAACTCGT
1 CTGAGTCAACTCGT
28993 CTGAGTCAACTCGT
1 CTGAGTCAACTCGT
*
29007 CTGAGTAAACTCGT
1 CTGAGTCAACTCGT
29021 -TCGAGTCAAC
1 CT-GAGTCAAC
29031 CCGTTGACAC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
13 1 0.03
14 34 0.97
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (14 bp):
CTGAGTCAACTCGT
Found at i:34501 original size:18 final size:18
Alignment explanation
Indices: 34478--34519 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
34468 ATATGTACTA
*
34478 TTCATGTAGTATCGATAC
1 TTCATGCAGTATCGATAC
34496 TTCATGCAGTATCGATAC
1 TTCATGCAGTATCGATAC
34514 TTCATG
1 TTCATG
34520 AAGAAGTGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (18 bp):
TTCATGCAGTATCGATAC
Found at i:37171 original size:15 final size:15
Alignment explanation
Indices: 37151--37179 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
37141 AATACCTTTT
37151 AAAAATAATTTTAAG
1 AAAAATAATTTTAAG
37166 AAAAATAATTTTAA
1 AAAAATAATTTTAA
37180 ATGATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
AAAAATAATTTTAAG
Found at i:39753 original size:3 final size:3
Alignment explanation
Indices: 39745--39792 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
39735 AAATAAACGT
*
39745 TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
39792 T
1 T
39793 TGAATTGAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:40431 original size:50 final size:51
Alignment explanation
Indices: 40333--40437 Score: 124
Period size: 50 Copynumber: 2.1 Consensus size: 51
40323 ATGAGAGAGC
* * **
40333 CAAGTTGAGGAAAGATACTACTGAAAAGTTGACTCTTCTCCGTTAGAAAGT
1 CAAGTTGAGGAAAGACACTACTGAAAAGTTGACTCCTCTCCGCAAGAAAGT
* * *
40384 CAAGTTGA-GAATGACATTACT-AAAAGGTTGACTCCTCTTCGCAAGAAAGT
1 CAAGTTGAGGAAAGACACTACTGAAAA-GTTGACTCCTCTCCGCAAGAAAGT
40434 CAAG
1 CAAG
40438 AATAATACCA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
49 4 0.09
50 34 0.74
51 8 0.17
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (51 bp):
CAAGTTGAGGAAAGACACTACTGAAAAGTTGACTCCTCTCCGCAAGAAAGT
Found at i:40505 original size:45 final size:45
Alignment explanation
Indices: 40411--40705 Score: 263
Period size: 45 Copynumber: 6.5 Consensus size: 45
40401 TACTAAAAGG
* * * ** * * *
40411 TTGACTCCTCTTCGCAAGAAAGTCAAGAATAATACCACT-AGAAGG
1 TTGACTTCTCTTCACGAGAAAGTCAAGAAGGACAACACTGAG-AGA
* * * * *
40456 TTGACTTCTCTTCTCGAGAAAGTCAAGTAGGACAACACCGAAATA
1 TTGACTTCTCTTCACGAGAAAGTCAAGAAGGACAACACTGAGAGA
* * *
40501 TTGACTTCTCTTCACAAGAAAGTCAAGAAGGACAAAGATTGAGAGA
1 TTGACTTCTCTTCACGAGAAAGTCAAGAAGGAC-AACACTGAGAGA
* * * * *
40547 TTGACTTCTCTTCATGAGAAAGTTAAGAATGACAATACGGAGAGA
1 TTGACTTCTCTTCACGAGAAAGTCAAGAAGGACAACACTGAGAGA
* * *
40592 TTTACTCCTCTTCACGAGAAAGTCAAGGAA-GACAATACTGAGAGA
1 TTGACTTCTCTTCACGAGAAAGTCAA-GAAGGACAACACTGAGAGA
* * * *
40637 TTGAC-TCTTCTTCGCAAGAAAGTCAAGAAGGACAACACTAAAAGA
1 TTGACTTC-TCTTCACGAGAAAGTCAAGAAGGACAACACTGAGAGA
* *
40682 TTGAATCCTCTTCACGAGAAAGTC
1 TTGACTTCTCTTCACGAGAAAGTC
40706 CAAGGAAGAA
Statistics
Matches: 201, Mismatches: 43, Indels: 12
0.79 0.17 0.05
Matches are distributed among these distances:
44 4 0.02
45 156 0.78
46 41 0.20
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (45 bp):
TTGACTTCTCTTCACGAGAAAGTCAAGAAGGACAACACTGAGAGA
Found at i:40665 original size:90 final size:91
Alignment explanation
Indices: 40456--40714 Score: 290
Period size: 91 Copynumber: 2.8 Consensus size: 91
40446 CACTAGAAGG
* * * * * *
40456 TTGACTTCTCTTCTCGAGAAAGTCAAGTAGGACAACACCGAAATATTGACTTCTCTTCACAAGAA
1 TTGACTTCTCTTCACAAGAAAGTCAAGAAGGACAACACCGAAAGATTGACTCCTCTTCACGAGAA
*
40521 AGTCAA-GAAGGACAAAGATTGAGAGA
66 AGTCAAGGAA-GACAAAGACTGAGAGA
** * * * * * *
40547 TTGACTTCTCTTCATGAGAAAGTTAAGAATGACAATACGGAGAGATTTACTCCTCTTCACGAGAA
1 TTGACTTCTCTTCACAAGAAAGTCAAGAAGGACAACACCGAAAGATTGACTCCTCTTCACGAGAA
*
40612 AGTCAAGGAAGAC-AATACTGAGAGA
66 AGTCAAGGAAGACAAAGACTGAGAGA
* ** *
40637 TTGAC-TCTTCTTCGCAAGAAAGTCAAGAAGGACAACACTAAAAGATTGAATCCTCTTCACGAGA
1 TTGACTTC-TCTTCACAAGAAAGTCAAGAAGGACAACACCGAAAGATTGACTCCTCTTCACGAGA
40701 AAGTCCAAGGAAGA
65 AAGT-CAAGGAAGA
40715 AAAATATTGA
Statistics
Matches: 140, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
89 2 0.01
90 64 0.46
91 71 0.51
92 3 0.02
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.23
Consensus pattern (91 bp):
TTGACTTCTCTTCACAAGAAAGTCAAGAAGGACAACACCGAAAGATTGACTCCTCTTCACGAGAA
AGTCAAGGAAGACAAAGACTGAGAGA
Found at i:41137 original size:38 final size:38
Alignment explanation
Indices: 40677--41138 Score: 534
Period size: 38 Copynumber: 12.0 Consensus size: 38
40667 GACAACACTA
* * * *
40677 AAAGATTGAATCCTCTTCACGAGAAAGTCCAAGGAAGAA-
1 AAAGATTGACTTCTCTTCACGAGGAAGT-CAA-GAATAAC
* * * *
40716 AAATATTGACTTCTCTTCATGAGGAAATCAAGAATAAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * *
40754 AAAGATTGATTTCTCTTCATGAGGAAATCAAGAATAAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
40792 AAAGATTGACTTCTCTTCATGAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
40830 ATAGAAAGATTGACTCCTCTTCACGAGTG-AGTCAAGAATAAA
1 ----AAAGATTGACTTCTCTTCACGAG-GAAGTCAAGAATAAC
* *
40872 AAAGGTTGACTTCTCTTCACGAGGAAGTCAAGAAGGAA-
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAA-TAAC
** * **
40910 AAAGATCAACTGCTCTTCACGAGGAAGTCTTGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
40948 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAGC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
40986 AAAGATCGACTTCTCTTCACGAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * *
41024 AAATATTGACTTCCCTTCACGAAGAAGTCAAGAATGAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
41062 AAATATTGACTTCTCTTCATGAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
41100 AAAGATTGACTCCTCTTCACTAGGAGGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
41138 A
1 A
41139 TTGAAAGATT
Statistics
Matches: 367, Mismatches: 47, Indels: 19
0.85 0.11 0.04
Matches are distributed among these distances:
37 8 0.02
38 301 0.82
39 24 0.07
42 33 0.09
43 1 0.00
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.24
Consensus pattern (38 bp):
AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
Found at i:43084 original size:19 final size:19
Alignment explanation
Indices: 43060--43101 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
43050 ACTTGATTTA
*
43060 TTTTATCTCATTTTTTTCT
1 TTTTATCTCATTTTCTTCT
43079 TTTTATCTCATTTTCTTCT
1 TTTTATCTCATTTTCTTCT
43098 TTTT
1 TTTT
43102 CTTTTTCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTATCTCATTTTCTTCT
Found at i:43118 original size:10 final size:10
Alignment explanation
Indices: 43103--43128 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
43093 CTTCTTTTTC
43103 TTTTTCTATA
1 TTTTTCTATA
43113 TTTTTCTATA
1 TTTTTCTATA
43123 TTTTTC
1 TTTTTC
43129 CTTTTCTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTTCTATA
Found at i:43175 original size:22 final size:21
Alignment explanation
Indices: 43113--43184 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 21
43103 TTTTTCTATA
*
43113 TTTTTCTATATTTTTCCTTTTC
1 TTTTT-TATATTTTTTCTTTTC
* * * *
43135 TTATTCTATCTATTCTCTTTTC
1 TT-TTTTATATTTTTTCTTTTC
43157 ATTTTTTATATTTTTTCTTTTC
1 -TTTTTTATATTTTTTCTTTTC
43179 TTTTTT
1 TTTTTT
43185 CTCTATATCT
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 6 0.15
22 29 0.74
23 4 0.10
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTTATATTTTTTCTTTTC
Found at i:50246 original size:23 final size:22
Alignment explanation
Indices: 50175--50246 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 22
50165 TAACATAGTA
50175 CATCGATGCACATTCAAGGACTG
1 CATCGATGCACATTCAAGGA-TG
* *
50198 CATCGGAT-CACCTTCATGG-TG
1 CATC-GATGCACATTCAAGGATG
*
50219 AATCGATGCACATTCAAGGGATG
1 CATCGATGCACATTCAA-GGATG
50242 CATCG
1 CATCG
50247 GTACACTCTC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
20 3 0.08
21 12 0.31
22 2 0.05
23 19 0.49
24 3 0.08
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.24
Consensus pattern (22 bp):
CATCGATGCACATTCAAGGATG
Found at i:54110 original size:22 final size:21
Alignment explanation
Indices: 54068--54107 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54058 GAGATTATTT
*
54068 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
*
54089 TCATTTTTGAATTTTAAAA
1 TCATTTTTCAATTTTAAAA
54108 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:54114 original size:20 final size:21
Alignment explanation
Indices: 54070--54114 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
54060 GATTATTTTC
* *
54070 ATTTTTCAATTTTGAAATATC
1 ATTTTTCAATTTTGAAAAATA
*
54091 ATTTTTGAATTTT-AAAAATA
1 ATTTTTCAATTTTGAAAAATA
54111 ATTT
1 ATTT
54115 CTCATAATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (21 bp):
ATTTTTCAATTTTGAAAAATA
Found at i:56132 original size:65 final size:65
Alignment explanation
Indices: 56038--56194 Score: 215
Period size: 65 Copynumber: 2.4 Consensus size: 65
56028 ACACTAGGGG
* * * * * *
56038 GTGCATCGGTACACTAATTACATTAGATGTTTCAAAAGAGCCAGGAGTGCATCGATGCATGGAAT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCAAGGAAT
* ** **
56103 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCAAGGCTT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCAAGGAAT
56168 GTGCATCGGTACACAAAATGCATTCGA
1 GTGCATCGGTACACAAAATGCATTCGA
56195 AATATATGTG
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 81 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.26
Consensus pattern (65 bp):
GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCAAGGAAT
Found at i:60217 original size:3 final size:3
Alignment explanation
Indices: 60209--60257 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
60199 AAGAAAAAAT
60209 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
60257 T
1 T
60258 TGAAACGAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:63559 original size:2 final size:2
Alignment explanation
Indices: 63552--63580 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
63542 GAAGGAATTA
63552 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 A
63581 CAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:64868 original size:14 final size:14
Alignment explanation
Indices: 64849--64886 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
64839 ACTATAATTA
64849 AAATAT-ATATTTTC
1 AAATATAAT-TTTTC
64863 AAATATAATTTTTC
1 AAATATAATTTTTC
64877 AAA-ATAATTT
1 AAATATAATTT
64887 GAATCATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.30
14 14 0.61
15 2 0.09
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATATAATTTTTC
Found at i:65454 original size:15 final size:16
Alignment explanation
Indices: 65423--65455 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
65413 AATTTTTTTG
*
65423 TTATAATTACGAAAAC
1 TTATAATTACAAAAAC
65439 TTATAATTA-AAAAAC
1 TTATAATTACAAAAAC
65454 TT
1 TT
65456 GTCACTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (16 bp):
TTATAATTACAAAAAC
Found at i:66223 original size:31 final size:31
Alignment explanation
Indices: 66181--66242 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
66171 GATTTATGAG
* *
66181 ATAAAAGTATTATTATTTATGCGACAAATTT
1 ATAAAAATATTATTATTCATGCGACAAATTT
66212 ATAAAAATATTATTATTCATGCGACAAATTT
1 ATAAAAATATTATTATTCATGCGACAAATTT
66243 TGAAATGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (31 bp):
ATAAAAATATTATTATTCATGCGACAAATTT
Found at i:69593 original size:35 final size:35
Alignment explanation
Indices: 69546--69627 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
69536 TAGTAGTGTA
* *
69546 GTATCAACACTAGAGCAATAGCGTCGATAC-ATAGG
1 GTATCAATACTAGAGCAATAGCATCGATACTA-AGG
* * *
69581 GTATCAATACTAGAGGAGTAGCATTGATACTAAGG
1 GTATCAATACTAGAGCAATAGCATCGATACTAAGG
*
69616 GTATCGATACTA
1 GTATCAATACTA
69628 TAATAATGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
35 39 0.98
36 1 0.03
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (35 bp):
GTATCAATACTAGAGCAATAGCATCGATACTAAGG
Found at i:70223 original size:20 final size:20
Alignment explanation
Indices: 70187--70224 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
70177 ATGTGATTAC
*
70187 ATGTGGATATAATATAAGCT
1 ATGTGGATATAACATAAGCT
70207 ATGT-GATATGAACATAAG
1 ATGTGGATAT-AACATAAG
70225 GAATTATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (20 bp):
ATGTGGATATAACATAAGCT
Found at i:70646 original size:21 final size:21
Alignment explanation
Indices: 70620--70696 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
70610 GTCCTTCGGG
*
70620 ACATATATGTGATCTTTTGGA
1 ACATATATGTGGTCTTTTGGA
* *
70641 ACATATATGCGGTCTTTTGGG
1 ACATATATGTGGTCTTTTGGA
* * *
70662 ACTTATATTTGGTCCTTTGGA
1 ACATATATGTGGTCTTTTGGA
*
70683 ATATATATGTGGTC
1 ACATATATGTGGTC
70697 CTTAGGGACA
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.23, C:0.12, G:0.22, T:0.43
Consensus pattern (21 bp):
ACATATATGTGGTCTTTTGGA
Found at i:70669 original size:42 final size:42
Alignment explanation
Indices: 70607--70706 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
70597 AGGGTTCTAC
* *
70607 GCGGTCCTTCGGGACATATATGTGATCTTTTGGAACATATAT
1 GCGGTCCTTAGGGACATATATGTGATCCTTTGGAACATATAT
* * * * * *
70649 GCGGTCTTTTGGGACTTATATTTGGTCCTTTGGAATATATAT
1 GCGGTCCTTAGGGACATATATGTGATCCTTTGGAACATATAT
*
70691 GTGGTCCTTAGGGACA
1 GCGGTCCTTAGGGACA
70707 ATTTTATATG
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (42 bp):
GCGGTCCTTAGGGACATATATGTGATCCTTTGGAACATATAT
Found at i:70988 original size:18 final size:18
Alignment explanation
Indices: 70965--71010 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
70955 TAACTGGAAT
*
70965 TAATGATAATACTATTCA
1 TAATGATAATAATATTCA
* *
70983 TAATGATAAGAATATTGA
1 TAATGATAATAATATTCA
*
71001 TGATGATAAT
1 TAATGATAAT
71011 GATGGCATAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.46, C:0.04, G:0.13, T:0.37
Consensus pattern (18 bp):
TAATGATAATAATATTCA
Found at i:75777 original size:21 final size:21
Alignment explanation
Indices: 75740--75797 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
75730 GTGACCCTAT
*
75740 GGAACATATATGCGGTCATTC
1 GGAACATATATGTGGTCATTC
* * * *
75761 GGGACATATATTTGGTCCTTT
1 GGAACATATATGTGGTCATTC
75782 GGAACATATATGTGGT
1 GGAACATATATGTGGT
75798 ACATAGGGAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (21 bp):
GGAACATATATGTGGTCATTC
Found at i:75816 original size:23 final size:23
Alignment explanation
Indices: 75790--75837 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
75780 TTGGAACATA
75790 TATGTGGTACATAGGGATAATTC
1 TATGTGGTACATAGGGATAATTC
* *
75813 TATGTGGTCCATTGGGATAATTC
1 TATGTGGTACATAGGGATAATTC
75836 TA
1 TA
75838 CGAGGTCCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.38
Consensus pattern (23 bp):
TATGTGGTACATAGGGATAATTC
Found at i:76096 original size:18 final size:18
Alignment explanation
Indices: 76073--76118 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
76063 TAACTGGGAT
*
76073 TAATGATAATACTAATGA
1 TAATGATAATAATAATGA
* *
76091 TAATGATAAGAATATTGA
1 TAATGATAATAATAATGA
*
76109 TGATGATAAT
1 TAATGATAAT
76119 GACATAGGTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.48, C:0.02, G:0.15, T:0.35
Consensus pattern (18 bp):
TAATGATAATAATAATGA
Found at i:81141 original size:21 final size:21
Alignment explanation
Indices: 81108--81202 Score: 118
Period size: 21 Copynumber: 4.5 Consensus size: 21
81098 TCGAGGGTTC
* * *
81108 TATGCGGTTCTTTGGCACATA
1 TATGTGGTCCTTTGGAACATA
*
81129 TATGTGATCCTTTGGAACATA
1 TATGTGGTCCTTTGGAACATA
* * *
81150 TATGCGGTCCTTCGGGACATA
1 TATGTGGTCCTTTGGAACATA
*
81171 TATTTGGTCCTTTGGAACATA
1 TATGTGGTCCTTTGGAACATA
81192 TATGTGGTCCT
1 TATGTGGTCCT
81203 CAGGGACAAT
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (21 bp):
TATGTGGTCCTTTGGAACATA
Found at i:81170 original size:42 final size:42
Alignment explanation
Indices: 81108--81210 Score: 136
Period size: 42 Copynumber: 2.5 Consensus size: 42
81098 TCGAGGGTTC
* * *
81108 TATGCGGTTCTTTGGCACATATATGTGATCCTTTGGAACATA
1 TATGCGGTCCTTCGGGACATATATGTGATCCTTTGGAACATA
* *
81150 TATGCGGTCCTTCGGGACATATATTTGGTCCTTTGGAACATA
1 TATGCGGTCCTTCGGGACATATATGTGATCCTTTGGAACATA
*
81192 TATGTGGTCC-TCAGGGACA
1 TATGCGGTCCTTC-GGGACA
81211 ATTCTATGTG
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 2 0.04
42 52 0.96
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (42 bp):
TATGCGGTCCTTCGGGACATATATGTGATCCTTTGGAACATA
Found at i:81259 original size:23 final size:23
Alignment explanation
Indices: 81205--81259 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 23
81195 GTGGTCCTCA
* ** *
81205 GGGACAATTCTATGTGGTCTTTC
1 GGGAAAATTCTATGAAGTCCTTC
* *
81228 GAGATAATTCTATGAAGTCCTTC
1 GGGAAAATTCTATGAAGTCCTTC
81251 GGGAAAATT
1 GGGAAAATT
81260 TTATATGGAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.35
Consensus pattern (23 bp):
GGGAAAATTCTATGAAGTCCTTC
Found at i:81499 original size:18 final size:19
Alignment explanation
Indices: 81476--81520 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
81466 AATTGGGATT
*
81476 AATGATAATACTATTGA-G
1 AATGATAATAATATTGATG
*
81494 AATGATAAGAATATTGATG
1 AATGATAATAATATTGATG
81513 -ATGATAAT
1 AATGATAAT
81521 GATGTCATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.18, T:0.33
Consensus pattern (19 bp):
AATGATAATAATATTGATG
Found at i:81571 original size:25 final size:29
Alignment explanation
Indices: 81536--81588 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 29
81526 CATAGGTATA
81536 TATATGCATTTTGT-T-ATATG-TGATAT
1 TATATGCATTTTGTATGATATGATGATAT
81562 TATATG-ATTTTGTATGATATGATGATA
1 TATATGCATTTTGTATGATATGATGATA
81589 GGAAATATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 7 0.29
26 7 0.29
27 5 0.21
28 5 0.21
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.51
Consensus pattern (29 bp):
TATATGCATTTTGTATGATATGATGATAT
Done.