Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000703.1 Hibiscus syriacus cultivar Beakdansim tig00001368_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: 66237
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.31
Found at i:850 original size:19 final size:20
Alignment explanation
Indices: 800--850 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
790 CTGTTGATAG
* *
800 TGGTATCGATATTGTAAGGG
1 TGGTATCGATACTGTAAGGA
* *
820 TAGTATCAATACTGT-AGGA
1 TGGTATCGATACTGTAAGGA
839 TGGTATCGATAC
1 TGGTATCGATAC
851 CCTTAAAACA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.29, C:0.10, G:0.27, T:0.33
Consensus pattern (20 bp):
TGGTATCGATACTGTAAGGA
Found at i:1026 original size:20 final size:20
Alignment explanation
Indices: 1001--1038 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
991 TTTGGTTCAC
1001 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
1021 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
1039 GAAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:2048 original size:21 final size:21
Alignment explanation
Indices: 2022--2093 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
2012 ATGTTATGGA
2022 AATGTGAACCTTGAACAAGTG
1 AATGTGAACCTTGAACAAGTG
** *
2043 AATGTGAACAGTGAACTAGTG
1 AATGTGAACCTTGAACAAGTG
*
2064 AATGTGAA-CTGTGAACCAGTG
1 AATGTGAACCT-TGAACAAGTG
2085 AATGTGAAC
1 AATGTGAAC
2094 ATACTATGAC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.24
Consensus pattern (21 bp):
AATGTGAACCTTGAACAAGTG
Found at i:2052 original size:14 final size:15
Alignment explanation
Indices: 2033--2094 Score: 62
Period size: 14 Copynumber: 4.4 Consensus size: 15
2023 ATGTGAACCT
2033 TGAACAAGTGAA-TG
1 TGAACAAGTGAACTG
2047 TGAAC-AGTGAACTAG
1 TGAACAAGTGAACT-G
*
2062 TG-A-ATGTGAACTG
1 TGAACAAGTGAACTG
*
2075 TGAACCAGTGAA-TG
1 TGAACAAGTGAACTG
2089 TGAACA
1 TGAACA
2095 TACTATGACA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
13 9 0.23
14 22 0.56
15 8 0.21
ACGTcount: A:0.39, C:0.11, G:0.27, T:0.23
Consensus pattern (15 bp):
TGAACAAGTGAACTG
Found at i:2247 original size:21 final size:21
Alignment explanation
Indices: 2222--2271 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
2212 GAGTCGAGGG
*
2222 TTATGTGGTCTTTCGAGATAA
1 TTATGTGGTCTTTCGAGACAA
*
2243 TTATGTGGTCTTTCGGGACAA
1 TTATGTGGTCTTTCGAGACAA
2264 TTATGTGG
1 TTATGTGG
2272 CACTTCGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.20, C:0.10, G:0.28, T:0.42
Consensus pattern (21 bp):
TTATGTGGTCTTTCGAGACAA
Found at i:2278 original size:21 final size:21
Alignment explanation
Indices: 2241--2346 Score: 56
Period size: 21 Copynumber: 4.9 Consensus size: 21
2231 CTTTCGAGAT
*
2241 AATTATGTGGTC-TTTCGGGAC
1 AATTATGTGG-CACTTCGGGAC
2262 AATTATGTGGCACTTCGGTGTA-
1 AATTATGTGGCACTTCGG-G-AC
* * *
2284 ACTCTATGTGGCACTTTAGTG-C
1 AAT-TATGTGGCAC-TTCGGGAC
* * **
2306 AAACCTATTTGGGTCTTCGGGAC
1 -AA-TTATGTGGCACTTCGGGAC
2329 AATTATGTGGCACTTCGG
1 AATTATGTGGCACTTCGG
2347 TGCAAATTAC
Statistics
Matches: 61, Mismatches: 15, Indels: 18
0.65 0.16 0.19
Matches are distributed among these distances:
20 1 0.02
21 27 0.44
22 9 0.15
23 21 0.34
24 3 0.05
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (21 bp):
AATTATGTGGCACTTCGGGAC
Found at i:2313 original size:23 final size:23
Alignment explanation
Indices: 2265--2313 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
2255 TCGGGACAAT
* *
2265 TATGTGGCACTTCGGTGTAACTC
1 TATGTGGCACTTCAGTGAAACTC
*
2288 TATGTGGCACTTTAGTGCAAAC-C
1 TATGTGGCACTTCAGTG-AAACTC
2311 TAT
1 TAT
2314 TTGGGTCTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (23 bp):
TATGTGGCACTTCAGTGAAACTC
Found at i:2795 original size:25 final size:25
Alignment explanation
Indices: 2749--2796 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
2739 TGCTCTGATC
* *
2749 ATTTTTGTAAACTTATATATTTTGT
1 ATTTTTGTAAACTCATAAATTTTGT
2774 ATTTTTGTAAAC-CATCAAATTTT
1 ATTTTTGTAAACTCAT-AAATTTT
2797 TTTATGCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 18 0.90
ACGTcount: A:0.31, C:0.08, G:0.06, T:0.54
Consensus pattern (25 bp):
ATTTTTGTAAACTCATAAATTTTGT
Found at i:3390 original size:18 final size:17
Alignment explanation
Indices: 3335--3390 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 17
3325 ATGTTACTTT
*
3335 ATTTAAGCATG-AGTTC
1 ATTTAAACATGCAGTTC
3351 ATTTAAACATGCA-TTGC
1 ATTTAAACATGCAGTT-C
3368 ATTTAAAGCAT-CTAGTTC
1 ATTTAAA-CATGC-AGTTC
3386 ATTTA
1 ATTTA
3391 GGGAAGTAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
16 12 0.35
17 10 0.29
18 10 0.29
19 2 0.06
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.39
Consensus pattern (17 bp):
ATTTAAACATGCAGTTC
Found at i:3468 original size:17 final size:17
Alignment explanation
Indices: 3447--3507 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
3437 ATTCATGCAT
3447 CTAGTTCATTAATAAAG
1 CTAGTTCATTAATAAAG
* *
3464 TTAGTTTATTAATTAAA-
1 CTAGTTCATTAA-TAAAG
* * *
3481 CTAGTTCACTCATCAAG
1 CTAGTTCATTAATAAAG
3498 CTAGTTCATT
1 CTAGTTCATT
3508 TATTAAACTA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
16 3 0.09
17 27 0.79
18 4 0.12
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (17 bp):
CTAGTTCATTAATAAAG
Found at i:3485 original size:34 final size:34
Alignment explanation
Indices: 3447--3517 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
3437 ATTCATGCAT
* * *
3447 CTAGTTCATTAATAAAGTTAGTTTATTAATTAAA
1 CTAGTTCACTAATAAAGCTAGTTCATTAATTAAA
* * *
3481 CTAGTTCACTCATCAAGCTAGTTCATTTATTAAA
1 CTAGTTCACTAATAAAGCTAGTTCATTAATTAAA
3515 CTA
1 CTA
3518 ACTCTTAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (34 bp):
CTAGTTCACTAATAAAGCTAGTTCATTAATTAAA
Found at i:4647 original size:64 final size:63
Alignment explanation
Indices: 4542--4661 Score: 159
Period size: 64 Copynumber: 1.9 Consensus size: 63
4532 ATTGTTCAAG
* * * * *
4542 GTGTATCGATGCACATGAAGTGTATCGATGCACTACTTTAAAATAAAAACATTGAATGCCATCA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCACCTT-AAATAAAAACATCGAATGCCATCA
* * *
4606 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAATACAAACATCGAAT
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCACCTTAAATAAAAACATCGAAT
4662 ATGATTTATG
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
63 15 0.31
64 33 0.69
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCACCTTAAATAAAAACATCGAATGCCATCA
Found at i:5397 original size:23 final size:23
Alignment explanation
Indices: 5344--5427 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 23
5334 CAATCTCATA
*
5344 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
** * *
5367 AAGTACTTCGGTGCAATTCTATG
1 TGGCACTTCGGTGCAATTCTACG
* *
5390 TGGCACTTCAGTACAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
5413 TGGTACTTCGATGCA
1 TGGCACTTCGGTGCA
5428 TTTATACGAG
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:5502 original size:21 final size:21
Alignment explanation
Indices: 5478--5521 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
5468 AGTACTCACA
5478 TACCTTAGGTTCTCAGTATGG
1 TACCTTAGGTTCTCAGTATGG
5499 TACCTTAGGTTCTCAGTATGG
1 TACCTTAGGTTCTCAGTATGG
5520 TA
1 TA
5522 TCATGAGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (21 bp):
TACCTTAGGTTCTCAGTATGG
Found at i:12352 original size:23 final size:23
Alignment explanation
Indices: 12294--12354 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
12284 CAATCTTATA
*
12294 TGGCACTTCGGTACAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
12317 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
12340 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
12355 TTTATACAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:12874 original size:20 final size:21
Alignment explanation
Indices: 12837--12876 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
12827 AAATTAAGTT
12837 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
12858 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
12877 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:13170 original size:63 final size:64
Alignment explanation
Indices: 13093--13234 Score: 171
Period size: 63 Copynumber: 2.2 Consensus size: 64
13083 GAATTAATTG
*** * *
13093 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGC-TCTGAATA-TTTTCAA
1 AACATCGAATGCATTCCATGCACCGATGCACAAGCCATGCATCGATGCACCAGAATATTTTTC-A
** * **
13156 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACCAGGCTATTTTTCA
1 AACATCGAATGCATTCCATGCACCGATGCACAAGCCATGCATCGATGCACCAGAATATTTTTCA
13220 AACATCGAATGCATT
1 AACATCGAATGCATT
13235 TCGCATCGAT
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
63 42 0.63
64 20 0.30
65 5 0.07
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTCCATGCACCGATGCACAAGCCATGCATCGATGCACCAGAATATTTTTCA
Found at i:19054 original size:20 final size:21
Alignment explanation
Indices: 19025--19080 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
19015 TTTGTGCTTC
*
19025 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
19045 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
19067 ATGCATCGATGCAT
1 ATGCATCGATGCAT
19081 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:21497 original size:20 final size:21
Alignment explanation
Indices: 21460--21499 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
21450 AAATTAAGTT
21460 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
21481 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
21500 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:21893 original size:64 final size:64
Alignment explanation
Indices: 21717--21878 Score: 211
Period size: 64 Copynumber: 2.5 Consensus size: 64
21707 AAATTAATTG
* * *
21717 AACATCGAATGCATTCTATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTC-ATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* ** **
21782 AACATCGAATGCATTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-A
1 AACATCGAATGCATTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCAA
21845 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCA-TTCATGCATCGATGCACACT
21879 TGGTGCACCG
Statistics
Matches: 84, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
63 18 0.21
64 51 0.61
65 15 0.18
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:25211 original size:14 final size:14
Alignment explanation
Indices: 25188--25234 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
25178 CATTTCATTA
*
25188 AACCATTTTATCAT
1 AACCACTTTATCAT
*
25202 AACCACTTTATCTT
1 AACCACTTTATCAT
25216 CAAACCAC-TTATCAT
1 --AACCACTTTATCAT
25231 AACC
1 AACC
25235 TATAACCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 4 0.14
14 12 0.43
15 6 0.21
16 6 0.21
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.34
Consensus pattern (14 bp):
AACCACTTTATCAT
Found at i:25477 original size:18 final size:19
Alignment explanation
Indices: 25454--25489 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
25444 CCGAATTAGT
*
25454 AAAAAATAAAA-AAAAATC
1 AAAAAAGAAAAGAAAAATC
25472 AAAAAAGAAAAGAAAAAT
1 AAAAAAGAAAAGAAAAAT
25490 TTAAAGAGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.83, C:0.03, G:0.06, T:0.08
Consensus pattern (19 bp):
AAAAAAGAAAAGAAAAATC
Found at i:27500 original size:17 final size:17
Alignment explanation
Indices: 27480--27533 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
27470 ATTCATGCAT
27480 CTAGTTCATTAATTAAA
1 CTAGTTCATTAATTAAA
* * * *
27497 CTAGTTCACTCATCAAG
1 CTAGTTCATTAATTAAA
* *
27514 CTATTTCATTTATTAAA
1 CTAGTTCATTAATTAAA
27531 CTA
1 CTA
27534 ACTCTTAATT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.41
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:40236 original size:41 final size:41
Alignment explanation
Indices: 40152--40236 Score: 107
Period size: 41 Copynumber: 2.1 Consensus size: 41
40142 CTTTTAAATG
* ****
40152 TTTAAATTATAATTTAAATTAATTTTTTATGTTTATTTTTT
1 TTTAAATTATAATCTAAATTAATTTTTTATGTTTAAAGATT
* *
40193 TTTAAATTATACTCTAAATTGATTTTTTATGTTTAAAGATT
1 TTTAAATTATAATCTAAATTAATTTTTTATGTTTAAAGATT
40234 TTT
1 TTT
40237 TTCTAAAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (41 bp):
TTTAAATTATAATCTAAATTAATTTTTTATGTTTAAAGATT
Found at i:44507 original size:19 final size:19
Alignment explanation
Indices: 44483--44523 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
44473 TGGTTGTTGT
*
44483 ATACTCAAGTTCTATATAA
1 ATACTCAAATTCTATATAA
44502 ATACTCAAATTCTATATAA
1 ATACTCAAATTCTATATAA
44521 ATA
1 ATA
44524 TGGCAAGGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (19 bp):
ATACTCAAATTCTATATAA
Found at i:47705 original size:15 final size:15
Alignment explanation
Indices: 47685--47715 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
47675 ATCTTGTATG
47685 CCTATTTATAATTTC
1 CCTATTTATAATTTC
47700 CCTATTTATAATTTC
1 CCTATTTATAATTTC
47715 C
1 C
47716 TGTTGGTCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.52
Consensus pattern (15 bp):
CCTATTTATAATTTC
Found at i:56731 original size:33 final size:31
Alignment explanation
Indices: 56675--56796 Score: 110
Period size: 33 Copynumber: 3.8 Consensus size: 31
56665 TTACCTAAAG
56675 ATGAAAATGATGAAAAAGAAGAAAAAAATGAAAA
1 ATGAAAATG--GAAAAA-AAGAAAAAAATGAAAA
56709 ATGGAAAATGGAAAAAATAGAAAAAAATGGAAAAA
1 AT-GAAAATGGAAAAAA-AGAAAAAAAT-G-AAAA
* *
56744 AT-AAAATAGAAAAAAATG-AAAAAATAGGAAA
1 ATGAAAATGGAAAAAAA-GAAAAAAAT-GAAAA
56775 A--AAAA-GGAAAAAAAGAAAAAAA
1 ATGAAAATGGAAAAAAAGAAAAAAA
56797 AAAGAATAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 17
0.79 0.04 0.17
Matches are distributed among these distances:
28 1 0.01
29 14 0.18
30 4 0.05
31 4 0.05
32 10 0.13
33 29 0.37
34 3 0.04
35 13 0.17
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.10
Consensus pattern (31 bp):
ATGAAAATGGAAAAAAAGAAAAAAATGAAAA
Found at i:56735 original size:10 final size:10
Alignment explanation
Indices: 56720--56796 Score: 63
Period size: 9 Copynumber: 7.6 Consensus size: 10
56710 TGGAAAATGG
56720 AAAAAATAGA
1 AAAAAATAGA
*
56730 AAAAAATGGAAAA
1 AAAAAAT---AGA
56743 AATAAAATAGA
1 AA-AAAATAGA
56754 AAAAAAT-G-
1 AAAAAATAGA
56762 AAAAAATAGGA
1 AAAAAATA-GA
*
56773 AAAAAA-AGG
1 AAAAAATAGA
56782 AAAAAA-AGA
1 AAAAAATAGA
56791 AAAAAA
1 AAAAAA
56797 AAAGAATAGA
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
8 7 0.12
9 16 0.29
10 14 0.25
11 10 0.18
13 4 0.07
14 5 0.09
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (10 bp):
AAAAAATAGA
Found at i:56779 original size:23 final size:24
Alignment explanation
Indices: 56705--56769 Score: 89
Period size: 24 Copynumber: 2.7 Consensus size: 24
56695 GAAAAAAATG
56705 AAAAATGGAAAATGGAA-AAAATAGAA
1 AAAAATGGAAAA---AATAAAATAGAA
56731 AAAAATGGAAAAAATAAAATAGAA
1 AAAAATGGAAAAAATAAAATAGAA
56755 AAAAAT-GAAAAAATA
1 AAAAATGGAAAAAATA
56770 GGAAAAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
23 11 0.29
24 15 0.39
26 12 0.32
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (24 bp):
AAAAATGGAAAAAATAAAATAGAA
Found at i:56796 original size:11 final size:11
Alignment explanation
Indices: 56782--56838 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
56772 AAAAAAAAGG
56782 AAAAAAAGAAA
1 AAAAAAAGAAA
56793 AAAAAAAG-AA
1 AAAAAAAGAAA
* *
56803 TAGAAAAGAAA
1 AAAAAAAGAAA
* *
56814 AACAAAACAAA
1 AAAAAAAGAAA
*
56825 AACAAAAACAAA
1 AA-AAAAAGAAA
56837 AA
1 AA
56839 CAAATAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
10 8 0.21
11 20 0.53
12 10 0.26
ACGTcount: A:0.84, C:0.07, G:0.07, T:0.02
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:56797 original size:10 final size:10
Alignment explanation
Indices: 56687--56831 Score: 69
Period size: 10 Copynumber: 13.5 Consensus size: 10
56677 GAAAATGATG
56687 AAAAAGAAGAA
1 AAAAAGAA-AA
56698 AAAAATGAAAA
1 AAAAA-GAAAA
*
56709 ATGGAAAATGGAAA
1 A---AAAA-GAAAA
*
56723 AAATAGAAAA
1 AAAAAGAAAA
**
56733 AAATGGAAAA
1 AAAAAGAAAA
56743 AATAAA-ATAGAA
1 AA-AAAGA-A-AA
56755 AAAAATGAAAA
1 AAAAA-GAAAA
* *
56766 AATAGGAAAA
1 AAAAAGAAAA
*
56776 AAAAGGAAAA
1 AAAAAGAAAA
*
56786 AAAGA-AAAA
1 AAAAAGAAAA
*
56795 AAAAAGAATA
1 AAAAAGAAAA
*
56805 GAAAAGAAAA
1 AAAAAGAAAA
*
56815 ACAAAACAAAA
1 A-AAAAGAAAA
56826 ACAAAA
1 A-AAAA
56832 ACAAAAACAA
Statistics
Matches: 106, Mismatches: 17, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
9 8 0.08
10 44 0.42
11 35 0.33
12 8 0.08
13 1 0.01
14 10 0.09
ACGTcount: A:0.77, C:0.02, G:0.14, T:0.07
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:56809 original size:21 final size:19
Alignment explanation
Indices: 56753--56826 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
56743 AATAAAATAG
* *
56753 AAAAAAATGAAAAAATAGGA
1 AAAAAAAAGAAAAAA-AGAA
*
56773 AAAAAAAGGAAAAAAAGAA
1 AAAAAAAAGAAAAAAAGAA
56792 AAAAAAAAGAATAGAAAAGAA
1 AAAAAAAAGAA-A-AAAAGAA
* *
56813 AAACAAAACAAAAA
1 AAAAAAAAGAAAAA
56827 CAAAAACAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 15 0.32
20 16 0.34
21 16 0.34
ACGTcount: A:0.81, C:0.03, G:0.12, T:0.04
Consensus pattern (19 bp):
AAAAAAAAGAAAAAAAGAA
Found at i:56839 original size:6 final size:6
Alignment explanation
Indices: 56806--56842 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
56796 AAAAGAATAG
*
56806 AAAAGA AAAAC- AAAACA AAAACA AAAACA AAAACA AA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AA
56843 TAAAATTGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.84, C:0.14, G:0.03, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:58009 original size:37 final size:37
Alignment explanation
Indices: 57968--58052 Score: 170
Period size: 37 Copynumber: 2.3 Consensus size: 37
57958 TCACGAAAGG
57968 GTAGTGAAGCAAATCATCTGAAAATCTTCACAAGGAA
1 GTAGTGAAGCAAATCATCTGAAAATCTTCACAAGGAA
58005 GTAGTGAAGCAAATCATCTGAAAATCTTCACAAGGAA
1 GTAGTGAAGCAAATCATCTGAAAATCTTCACAAGGAA
58042 GTAGTGAAGCA
1 GTAGTGAAGCA
58053 TAAGAAGATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.21
Consensus pattern (37 bp):
GTAGTGAAGCAAATCATCTGAAAATCTTCACAAGGAA
Found at i:58123 original size:53 final size:53
Alignment explanation
Indices: 58054--58793 Score: 935
Period size: 53 Copynumber: 13.9 Consensus size: 53
58044 AGTGAAGCAT
* * *
58054 AAGAAGATTGTTCGAGTTCTACACCCTGAAGAAAAAGAGAGCGGACCCGTAAG
1 AAGATGATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGG
* *
58107 AAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGG
1 AAGATGATTGTTCGAGTTC-TACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGG
* * *
58161 AAGATTATTGTTCGAGTTCTACTCCTTGAAG-AAAAGGGAGCGGACCCGTAGG
1 AAGATGATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGG
*
58213 AAGATGATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGC-GAGCCCGTAGG
1 AAGATGATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGA-CCCGTAGG
* * *
58266 AAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGCGGACTCGTAGG
1 AAGATGATTGTTCGAGTTC-TACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGG
* *
58320 AAGATTATTGTTCGAGTTCTACTCCCTGAAG-AAAAGAGAGAGGACCCGTAGG
1 AAGATGATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGG
*
58372 AAGATGATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGC-GAGCCCGTAGG
1 AAGATGATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGA-CCCGTAGG
* * * *
58425 AAGATTATCGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGC-GAGCCCATAGG
1 AAGATGATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGA-CCCGTAGG
*
58478 CAGATGATTGTTCGAGTTCTACTCCCTGAA-AAAAGAGAGAGC-GAGCCCGTAGG
1 AAGATGATTGTTCGAGTTCTACTCCCTGAAGAAAA-AGAGAGCGGA-CCCGTAGG
* *
58531 CAGATGATTGTTCGAGTTCTACTCCCTGAA-AAAAGAGAGAGTGGACCCGTAGG
1 AAGATGATTGTTCGAGTTCTACTCCCTGAAGAAAA-AGAGAGCGGACCCGTAGG
* * * * *
58584 AAGATTATTGATCGAGTGCTTACTCCCTGAAGAAAGAGAGAGC-GAGCCCGTAAG
1 AAGATGATTGTTCGAGTTC-TACTCCCTGAAGAAAAAGAGAGCGGA-CCCGTAGG
* *
58638 AACAAGATTGTTCGAGTTCTACTCCCTGAA-AAAAGAGAGAGC-GAGCCCGTAGG
1 AAGATGATTGTTCGAGTTCTACTCCCTGAAGAAAA-AGAGAGCGGA-CCCGTAGG
* * * * *
58691 AAGAAGATTTTTCGAGTTCTACTCCTTGAAGAAAGAGAGAGTGGACCCGTAGG
1 AAGATGATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGG
* ** * *
58744 AAGAAGATTGTTCGAGTTCTTACTCCCTGAAGCGATAGAGAGCGAACCCG
1 AAGATGATTGTTCGAGTTC-TACTCCCTGAAGAAAAAGAGAGCGGACCCG
58794 ATTTTGGAGA
Statistics
Matches: 615, Mismatches: 56, Indels: 31
0.88 0.08 0.04
Matches are distributed among these distances:
52 106 0.17
53 336 0.55
54 168 0.27
55 5 0.01
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.22
Consensus pattern (53 bp):
AAGATGATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGG
Found at i:58350 original size:159 final size:161
Alignment explanation
Indices: 58054--58787 Score: 1060
Period size: 159 Copynumber: 4.6 Consensus size: 161
58044 AGTGAAGCAT
* * * *
58054 AAGAAGATTGTTCGAGTTCTACACCCTGAAGAAAAAGAGAGCGGACCCGTAAGAAGATTATTGTT
1 AAGATGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGGACCCGTAGGAAGATTATTGTT
*
58119 CGAGTTCTTACTCCCTGAAGAAATAGAGAGCGGA-CCCGTAGGAAGATTATTGTTCGAGTTCTAC
66 CGAGTTCTTACTCCCTGAAGAAATAGAGAGCGGAGCCCGTAGGAAGATGATTGTTCGAGTTCTAC
*
58183 TCCTTGAAGAAAAG-G-GAGCG-GACCCGTAGG
131 TCCCTGAA-AAAAGAGAGAGCGAG-CCCGTAGG
*
58213 AAGATGATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGC-GAGCCCGTAGGAAGATTATTGT
1 AAGATGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGGA-CCCGTAGGAAGATTATTGT
* *
58277 TCGAGTTCTTACTCCCTGAAGAAATAGAGAGCGGA-CTCGTAGGAAGATTATTGTTCGAGTTCTA
65 TCGAGTTCTTACTCCCTGAAGAAATAGAGAGCGGAGCCCGTAGGAAGATGATTGTTCGAGTTCTA
58341 CTCCCTGAAGAAAAGAGAGAG-GA-CCCGTAGG
130 CTCCCTGAA-AAAAGAGAGAGCGAGCCCGTAGG
* *
58372 AAGATGATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGC-GAGCCCGTAGGAAGATTATCGT
1 AAGATGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGGA-CCCGTAGGAAGATTATTGT
* * *
58436 TCGAGTTC-TACTCCCTGAAGAAAGAGAGAGC-GAGCCCATAGGCAGATGATTGTTCGAGTTCTA
65 TCGAGTTCTTACTCCCTGAAGAAATAGAGAGCGGAGCCCGTAGGAAGATGATTGTTCGAGTTCTA
58499 CTCCCTGAAAAAAGAGAGAGCGAGCCCGTAGG
130 CTCCCTGAAAAAAGAGAGAGCGAGCCCGTAGG
* * * *
58531 CAGATGATTGTTCGAGTTCTACTCCCTGAAAAAAGAGAGAGTGGACCCGTAGGAAGATTATTGAT
1 AAGATGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGGACCCGTAGGAAGATTATTGTT
* * * * *
58596 CGAGTGCTTACTCCCTGAAGAAAGAGAGAGC-GAGCCCGTAAGAACAAGATTGTTCGAGTTCTAC
66 CGAGTTCTTACTCCCTGAAGAAATAGAGAGCGGAGCCCGTAGGAAGATGATTGTTCGAGTTCTAC
58660 TCCCTGAAAAAAGAGAGAGCGAGCCCGTAGG
131 TCCCTGAAAAAAGAGAGAGCGAGCCCGTAGG
* * * * **
58691 AAGAAGATTTTTCGAGTTCTACTCCTTGAAGAAAGAGAGAGTGGACCCGTAGGAAGAAGATTGTT
1 AAGATGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGGACCCGTAGGAAGATTATTGTT
**
58756 CGAGTTCTTACTCCCTGAAGCGATAGAGAGCG
66 CGAGTTCTTACTCCCTGAAGAAATAGAGAGCG
58788 AACCCGATTT
Statistics
Matches: 529, Mismatches: 36, Indels: 18
0.91 0.06 0.03
Matches are distributed among these distances:
157 13 0.02
158 60 0.11
159 283 0.53
160 170 0.32
161 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (161 bp):
AAGATGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGGACCCGTAGGAAGATTATTGTT
CGAGTTCTTACTCCCTGAAGAAATAGAGAGCGGAGCCCGTAGGAAGATGATTGTTCGAGTTCTAC
TCCCTGAAAAAAGAGAGAGCGAGCCCGTAGG
Found at i:64439 original size:379 final size:384
Alignment explanation
Indices: 63842--64606 Score: 1387
Period size: 379 Copynumber: 2.0 Consensus size: 384
63832 TTAATTTTGT
63842 CTTGCTCCCCCTTACTATAACACTTTTCCCCCTTTTTGTTAAATCAAAAAGACTCTATAAACGTT
1 CTTGCTCCCCCTTACTATAACACTTTTCCCCCTTTTTGTTAAATCAAAAAGACTCTATAAACGTT
63907 TTGAAACAAGAGTTTTGAAAAACTTAGCCAATTGATATTTAGAAATTTAAAGCTTAAGCTACTAA
66 TTGAAACAAGAGTTTTGAAAAACTTAGCCAATTGATATTTAGAAATTTAAAGCTTAAGCTACTAA
*
63972 GAACACAATCAAGAGAAAGGTTAGCCATTAGTTTCATGAATCAATATTCATTAATAATATGCAAT
131 GAACACAATCAAGAGAAAGGTTAGCCATTAGTTTCATAAATCAATATTCATTAATAATATGCAAT
64037 GGTAATTGGTCATATTCTAATATGATGCAAAACTTAAAATCAAATTTAAAAAATTCAAACAAACC
196 GGTAATTGGTCATATTCTAATATGATGCAAAACTTAAAATCAAATTTAAAAAATTCAAACAAACC
64102 AAATACATATTAAG-T-T-CA-AACATCCAGAACAAACAAATCCAAAAACATCAAAATGTTTAAC
261 AAATACATATTAAGTTATCCAGAACATCCAGAACAAACAAATCCAAAAACATCAAAATGTTTAAC
*
64163 AATAAGTTCTAAATCAAACCAAGAGAAAACTAAAGCAAGGCAAGGTTTAATCCATAGGA
326 AATAAGTTCTAAATCAAACCAAGAGAAAACTAAAGCAAGACAAGGTTTAATCCATAGGA
64222 CTTGCTCCCCCTTACTATAACACTTTTCCCCCTTTTTGTTAAATC-AAAAGACTCTATAAACGTT
1 CTTGCTCCCCCTTACTATAACACTTTTCCCCCTTTTTGTTAAATCAAAAAGACTCTATAAACGTT
* * * *
64286 TTGAAACAAGGGTTTTGAAAAACTTATCCAATTGATATTTAGATATTTAAAGCTTAAGCTGCTAA
66 TTGAAACAAGAGTTTTGAAAAACTTAGCCAATTGATATTTAGAAATTTAAAGCTTAAGCTACTAA
*
64351 GAACACAATCAAGAGAAATGTTAGCCATTAGTTTCATAAATCAATATTCATTAATAATATGCAAT
131 GAACACAATCAAGAGAAAGGTTAGCCATTAGTTTCATAAATCAATATTCATTAATAATATGCAAT
64416 GGTAATTGGTCATATTCTAATATGATGCAAAACTTAAAATCAAATTTAAAAAATTCAAACAAACC
196 GGTAATTGGTCATATTCTAATATGATGCAAAACTTAAAATCAAATTTAAAAAATTCAAACAAACC
64481 AAATACATATTAAGTTCAAACATCCAGAACATCCAGAACAAACAAATCCAAAAACATCAAAATGT
261 AAATACATATTAAGTT-----ATCCAGAACATCCAGAACAAACAAATCCAAAAACATCAAAATGT
64546 TTAACAATAAGTTCTAAATCAAACCAAGAGAAAACTAAAGCAAGACAAGGTTTAATCCATA
321 TTAACAATAAGTTCTAAATCAAACCAAGAGAAAACTAAAGCAAGACAAGGTTTAATCCATA
64607 TGAGGATCGG
Statistics
Matches: 369, Mismatches: 7, Indels: 10
0.96 0.02 0.03
Matches are distributed among these distances:
379 222 0.60
380 46 0.12
386 1 0.00
387 2 0.01
388 98 0.27
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.28
Consensus pattern (384 bp):
CTTGCTCCCCCTTACTATAACACTTTTCCCCCTTTTTGTTAAATCAAAAAGACTCTATAAACGTT
TTGAAACAAGAGTTTTGAAAAACTTAGCCAATTGATATTTAGAAATTTAAAGCTTAAGCTACTAA
GAACACAATCAAGAGAAAGGTTAGCCATTAGTTTCATAAATCAATATTCATTAATAATATGCAAT
GGTAATTGGTCATATTCTAATATGATGCAAAACTTAAAATCAAATTTAAAAAATTCAAACAAACC
AAATACATATTAAGTTATCCAGAACATCCAGAACAAACAAATCCAAAAACATCAAAATGTTTAAC
AATAAGTTCTAAATCAAACCAAGAGAAAACTAAAGCAAGACAAGGTTTAATCCATAGGA
Found at i:65933 original size:14 final size:14
Alignment explanation
Indices: 65914--65947 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
65904 ATGGGAAAAT
*
65914 TTTGAAAAACTATG
1 TTTGAAAAACAATG
65928 TTTG-AAAACAATG
1 TTTGAAAAACAATG
65941 TTTGAAA
1 TTTGAAA
65948 TCAATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (14 bp):
TTTGAAAAACAATG
Found at i:65941 original size:13 final size:13
Alignment explanation
Indices: 65914--65952 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
65904 ATGGGAAAAT
*
65914 TTTGAAAAACTATG
1 TTTG-AAAACAATG
65928 TTTGAAAACAATG
1 TTTGAAAACAATG
*
65941 TTTGAAATCAAT
1 TTTGAAAACAAT
65953 ATATAGTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.36
Consensus pattern (13 bp):
TTTGAAAACAATG
Done.