Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001872.1 Hibiscus syriacus cultivar Beakdansim tig00003795_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: 82925
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:3430 original size:103 final size:106
Alignment explanation
Indices: 3246--3456 Score: 374
Period size: 103 Copynumber: 2.0 Consensus size: 106
3236 ACTCTATCGA
3246 ACATGTTAATCTACTTAAGTCATCCTATCAAATATAAGATCTCTATTAGACTCTTCAATTGTATG
1 ACATGTTAATCTACTTAAGTCATCCTATCAAATAT-A-ATCTCTATTAGACTCTTCAATTGTATG
*
3311 AAATCTCTTTTAATATTTAAGCGTCACCTGACATTTCGAGAAT
64 AAATATCTTTTAATATTTAAGCGTCACCTGACATTTCGAGAAT
3354 ACATGTTAATCTACTTAAGTCATCCTATC-AA-AT-ATCTCTATTAGACTCTTCAATTGTATGAA
1 ACATGTTAATCTACTTAAGTCATCCTATCAAATATAATCTCTATTAGACTCTTCAATTGTATGAA
3416 ATATCTTTTAATATTTAAGCGTCACCTGACATTTCGAGAAT
66 ATATCTTTTAATATTTAAGCGTCACCTGACATTTCGAGAAT
3457 GTATAAAATA
Statistics
Matches: 102, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
103 69 0.68
106 2 0.02
107 2 0.02
108 29 0.28
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.38
Consensus pattern (106 bp):
ACATGTTAATCTACTTAAGTCATCCTATCAAATATAATCTCTATTAGACTCTTCAATTGTATGAA
ATATCTTTTAATATTTAAGCGTCACCTGACATTTCGAGAAT
Found at i:5659 original size:2 final size:2
Alignment explanation
Indices: 5652--5746 Score: 183
Period size: 2 Copynumber: 48.0 Consensus size: 2
5642 ATATACTCAC
5652 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
5694 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A 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
5735 TA TA TA TA TA TA
1 TA TA TA TA TA TA
5747 ATTAGAATTA
Statistics
Matches: 92, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 91 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5783 original size:18 final size:19
Alignment explanation
Indices: 5762--5798 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
5752 AATTAGAGAG
5762 ATAAAAGAGAAAAA-ATAA
1 ATAAAAGAGAAAAACATAA
5780 ATAAAAGAGAAAAACATAA
1 ATAAAAGAGAAAAACATAA
5799 CCAAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.76, C:0.03, G:0.11, T:0.11
Consensus pattern (19 bp):
ATAAAAGAGAAAAACATAA
Found at i:5804 original size:19 final size:18
Alignment explanation
Indices: 5764--5804 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
5754 TTAGAGAGAT
*
5764 AAAAGAGAAAAAATAAAT
1 AAAAGAGAAAAAATAAAC
*
5782 AAAAGAGAAAAACATAACC
1 AAAAGAGAAAAA-ATAAAC
5801 AAAA
1 AAAA
5805 ATTACGACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.76, C:0.07, G:0.10, T:0.07
Consensus pattern (18 bp):
AAAAGAGAAAAAATAAAC
Found at i:12230 original size:30 final size:30
Alignment explanation
Indices: 12171--12231 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
12161 TATAACAATA
12171 TTGAATATTTTTATGACATGATACATGATTTT
1 TTGAATATTTTTAT-A-ATGATACATGATTTT
12203 TTGAATATTGTTTAT-ATGATATC-TGATTT
1 TTGAATATT-TTTATAATGATA-CATGATTT
12232 ACCGTATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
30 12 0.44
31 1 0.04
32 9 0.33
33 5 0.19
ACGTcount: A:0.30, C:0.05, G:0.13, T:0.52
Consensus pattern (30 bp):
TTGAATATTTTTATAATGATACATGATTTT
Found at i:15384 original size:24 final size:23
Alignment explanation
Indices: 15343--15388 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
15333 TTATAACTTA
15343 AATTATAAAATAATTTAAGAATAC
1 AATTATAAAATAATTTAA-AATAC
*
15367 AATTATAACATCAA-TTAAAATA
1 AATTATAAAAT-AATTTAAAATA
15389 TATTTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 14 0.70
25 2 0.10
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (23 bp):
AATTATAAAATAATTTAAAATAC
Found at i:20459 original size:17 final size:17
Alignment explanation
Indices: 20439--20475 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
20429 AAGTCAACGA
20439 TCAACGGTCGGGTCGGG
1 TCAACGGTCGGGTCGGG
20456 TCAACGGTCGGGTCGGG
1 TCAACGGTCGGGTCGGG
20473 TCA
1 TCA
20476 GACCGGTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.14, C:0.24, G:0.43, T:0.19
Consensus pattern (17 bp):
TCAACGGTCGGGTCGGG
Found at i:20518 original size:19 final size:18
Alignment explanation
Indices: 20471--20520 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
20461 GGTCGGGTCG
20471 GGTCAGACCGGTCAAACT
1 GGTCAGACCGGTCAAACT
20489 GGTTCAGACCGGTCAAA-T
1 GG-TCAGACCGGTCAAACT
20507 CGGTCAGAACCGGT
1 -GGTCAG-ACCGGT
20521 TTCCAGTAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.24
19 22 0.76
ACGTcount: A:0.26, C:0.26, G:0.30, T:0.18
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACT
Found at i:27721 original size:17 final size:17
Alignment explanation
Indices: 27701--27737 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
27691 GAAAGTCAAC
27701 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
27718 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
27735 GGT
1 GGT
27738 GAGACCGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.22, G:0.49, T:0.19
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:27761 original size:19 final size:20
Alignment explanation
Indices: 27741--27804 Score: 80
Period size: 19 Copynumber: 3.3 Consensus size: 20
27731 GTCGGGTGAG
27741 ACCGGTCAAACCGGTTCAG-
1 ACCGGTCAAACCGGTTCAGA
*
27760 ACTGGTCAAACCGGTTC-GA
1 ACCGGTCAAACCGGTTCAGA
*
27779 ACCGGTTGAAACCGG-TCAGA
1 ACCGG-TCAAACCGGTTCAGA
27799 ACCGGT
1 ACCGGT
27805 TGAAAACCGG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
18 1 0.03
19 23 0.59
20 15 0.38
ACGTcount: A:0.27, C:0.28, G:0.28, T:0.17
Consensus pattern (20 bp):
ACCGGTCAAACCGGTTCAGA
Found at i:27825 original size:9 final size:10
Alignment explanation
Indices: 27741--27825 Score: 79
Period size: 10 Copynumber: 8.7 Consensus size: 10
27731 GTCGGGTGAG
27741 ACCGG-TCAA
1 ACCGGTTCAA
*
27750 ACCGGTTCAG
1 ACCGGTTCAA
*
27760 ACTGG-TCAA
1 ACCGGTTCAA
*
27769 ACCGGTTCGA
1 ACCGGTTCAA
*
27779 ACCGGTTGAA
1 ACCGGTTCAA
27789 ACCGG-TCAGA
1 ACCGGTTCA-A
*
27799 ACCGGTTGAAA
1 ACCGGTT-CAA
27810 ACCGGTT-AA
1 ACCGGTTCAA
27819 ACCGGTT
1 ACCGGTT
27826 TCCAGCAGCC
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
9 23 0.37
10 29 0.47
11 9 0.15
12 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.27, T:0.19
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:29756 original size:22 final size:23
Alignment explanation
Indices: 29712--29771 Score: 61
Period size: 25 Copynumber: 2.6 Consensus size: 23
29702 CAGACATATA
*
29712 AAAATTTGTTTTTTTAAATAAACTT
1 AAAATTT-TTTTTTT-AATAAACTC
29737 AAAATTTATTTTTTT-A-AAACTC
1 AAAATTT-TTTTTTTAATAAACTC
*
29759 AATATTTTTTTTT
1 AAAATTTTTTTTT
29772 GAAATTATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 6 0.19
22 11 0.34
23 1 0.03
25 14 0.44
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.57
Consensus pattern (23 bp):
AAAATTTTTTTTTTAATAAACTC
Found at i:30067 original size:46 final size:46
Alignment explanation
Indices: 30014--30105 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
30004 GTGTTCAACC
*
30014 GGTCACAAAAATAAGGAGTTCCAACCGTTGGGTGGTTGTCCAATCG
1 GGTCACAAAAATAAGGAGCTCCAACCGTTGGGTGGTTGTCCAATCG
30060 GGTCACAAAAATAAGGAGCTCCAACCGTTGGGTGGTTGTCCAATCG
1 GGTCACAAAAATAAGGAGCTCCAACCGTTGGGTGGTTGTCCAATCG
30106 AACGATGTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (46 bp):
GGTCACAAAAATAAGGAGCTCCAACCGTTGGGTGGTTGTCCAATCG
Found at i:35418 original size:11 final size:11
Alignment explanation
Indices: 35393--35432 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 11
35383 TATGAAAAAA
*
35393 TTAAAATCA-T
1 TTAAAATTATT
35403 TTAAAATTATT
1 TTAAAATTATT
35414 TTAAAATTTATT
1 TTAAAA-TTATT
35426 TTAAAAT
1 TTAAAAT
35433 ATGAATTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 8 0.30
11 8 0.30
12 11 0.41
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (11 bp):
TTAAAATTATT
Found at i:35444 original size:22 final size:22
Alignment explanation
Indices: 35418--35718 Score: 285
Period size: 22 Copynumber: 13.6 Consensus size: 22
35408 ATTATTTTAA
35418 AATTTATTTTAAAATATGAATT
1 AATTTATTTTAAAATATGAATT
*
35440 GATTTATTTTAAAATAT-AGATT
1 AATTTATTTTAAAATATGA-ATT
*
35462 GATTTATTTTAAAATAT-AGATT
1 AATTTATTTTAAAATATGA-ATT
* **
35484 TATTTATTTTAAAATATGAAAAA
1 AATTTATTTTAAAATATG-AATT
** *
35507 AAAATATTTTAAAATACGAATT
1 AATTTATTTTAAAATATGAATT
*
35529 GATTTATTTTAAAATATGGAA--
1 AATTTATTTTAAAATAT-GAATT
* *
35550 AATTTTGTTTTAAAATATGGATT
1 AA-TTTATTTTAAAATATGAATT
*
35573 GATTTATTTTAAAATAT-AGATT
1 AATTTATTTTAAAATATGA-ATT
* *
35595 GATTTATTTTAAAATATAGAA-A
1 AATTTATTTTAAAATAT-GAATT
*
35617 AAGTTATTTTAAAATATGAATT
1 AATTTATTTTAAAATATGAATT
*
35639 AATTTATTTTAAAATATGGATT
1 AATTTATTTTAAAATATGAATT
*
35661 AATTTATTTTAAAATATGGAA-A
1 AATTTATTTTAAAATAT-GAATT
* *
35683 AAGTTATTTTAAAAGAT-AGATT
1 AATTTATTTTAAAATATGA-ATT
*
35705 GATTTATTTTAAAA
1 AATTTATTTTAAAA
35719 AATTTATTAT
Statistics
Matches: 232, Mismatches: 33, Indels: 28
0.79 0.11 0.10
Matches are distributed among these distances:
20 1 0.00
21 8 0.03
22 199 0.86
23 22 0.09
24 2 0.01
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.46
Consensus pattern (22 bp):
AATTTATTTTAAAATATGAATT
Found at i:35492 original size:66 final size:66
Alignment explanation
Indices: 35416--35718 Score: 385
Period size: 66 Copynumber: 4.6 Consensus size: 66
35406 AAATTATTTT
35416 AAAATTTATTTTAAAATATGAATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAATATAG
1 AAAATTTATTTTAAAATATGAATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAATATAG
35481 A
66 A
*** *** ** *
35482 TTTATTTATTTTAAAATATGAAAAAAAAATATTTTAAAATA-CGAATTGATTTATTTTAAAATAT
1 AAAATTTATTTTAAAATATG-AATTGATTTATTTTAAAATATAG-ATTGATTTATTTTAAAATAT
*
35546 GGA
64 AGA
* * *
35549 AAATTTTGTTTTAAAATATGGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAATATAG
1 AAAATTTATTTTAAAATATGAATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAATATAG
35614 A
66 A
* * * * *
35615 AAAAGTTATTTTAAAATATGAATTAATTTATTTTAAAATATGGATTAATTTATTTTAAAATATGG
1 AAAATTTATTTTAAAATATGAATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAATATAG
35680 A
66 A
* *
35681 AAAAGTTATTTTAAAAGAT-AGATTGATTTATTTTAAAA
1 AAAATTTATTTTAAAATATGA-ATTGATTTATTTTAAAA
35719 AATTTATTAT
Statistics
Matches: 200, Mismatches: 33, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
65 1 0.00
66 146 0.73
67 53 0.26
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.46
Consensus pattern (66 bp):
AAAATTTATTTTAAAATATGAATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAATATAG
A
Found at i:35776 original size:31 final size:31
Alignment explanation
Indices: 35741--35800 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
35731 TAGTTGTATG
35741 AATTATTTAAATTTCAGTATTATAAAACTAA
1 AATTATTTAAATTTCAGTATTATAAAACTAA
*
35772 AATTATTTAAATTTCAGTATTGTAAAACT
1 AATTATTTAAATTTCAGTATTATAAAACT
35801 CCTTTAAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (31 bp):
AATTATTTAAATTTCAGTATTATAAAACTAA
Found at i:38073 original size:147 final size:147
Alignment explanation
Indices: 37894--38165 Score: 404
Period size: 147 Copynumber: 1.9 Consensus size: 147
37884 TGGAGACTCT
37894 AACCTTATCTAATTAAAAAAAGTCAATAGAGACTCCAAAAAGATAAAATCATTCATATTAGG-TC
1 AACCTTATCTAATTAAAAAAAGTCAATAGAGACTCCAAAAAGATAAAATCATTCATATTAGGTTC
**
37958 AAATCATGATCTTAAGCCACCCGAAAGACAGTTACAACAATCATCATAAAATAATATCACGTCAT
66 AAA-CATGATCCCAAGCCACCCGAAAGACAGTTACAACAATCATCATAAAATAATATCACGTCAT
38023 CGTCGAAAAATCTTATCC
130 CGTCGAAAAATCTTATCC
* *
38041 AACCTTATCTAATTCAAAAAAA-TCAGTGGAGACTCCAAAAAGATAAAATCATTCATATTAGGTT
1 AACCTTATCTAATT-AAAAAAAGTCAATAGAGACTCCAAAAAGATAAAATCATTCATATTAGGTT
* * * * * * * *
38105 GAAACATGATCCCAAGCCACTCGAAGGACTGTTACAATAATTATCATAAGATAATGTCACG
65 CAAACATGATCCCAAGCCACCCGAAAGACAGTTACAACAATCATCATAAAATAATATCACG
38166 CCATTTTTGA
Statistics
Matches: 111, Mismatches: 12, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
147 100 0.90
148 11 0.10
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.25
Consensus pattern (147 bp):
AACCTTATCTAATTAAAAAAAGTCAATAGAGACTCCAAAAAGATAAAATCATTCATATTAGGTTC
AAACATGATCCCAAGCCACCCGAAAGACAGTTACAACAATCATCATAAAATAATATCACGTCATC
GTCGAAAAATCTTATCC
Found at i:38291 original size:2 final size:2
Alignment explanation
Indices: 38284--38312 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38274 ACGGAACAAA
38284 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
38313 ATTGAATAAT
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:39196 original size:16 final size:17
Alignment explanation
Indices: 39169--39201 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
39159 ATTCTAGCAA
39169 GTTTGTATTCTGGAACT
1 GTTTGTATTCTGGAACT
39186 GTTTGTA-TCTGGAACT
1 GTTTGTATTCTGGAACT
39202 ACCAGTCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.18, C:0.12, G:0.24, T:0.45
Consensus pattern (17 bp):
GTTTGTATTCTGGAACT
Found at i:39356 original size:45 final size:45
Alignment explanation
Indices: 39292--39381 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
39282 TGTTGTCTAA
39292 AACTTAGTTAGCTAAATATCTTGTTTGCTTCTTTCTAACAATTTT
1 AACTTAGTTAGCTAAATATCTTGTTTGCTTCTTTCTAACAATTTT
*
39337 AACTTAGTTAGCTAAATATCTTGTTTGCTTCTTTCTAACATTTTT
1 AACTTAGTTAGCTAAATATCTTGTTTGCTTCTTTCTAACAATTTT
39382 TTCTTCATAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.26, C:0.16, G:0.09, T:0.50
Consensus pattern (45 bp):
AACTTAGTTAGCTAAATATCTTGTTTGCTTCTTTCTAACAATTTT
Found at i:42295 original size:20 final size:21
Alignment explanation
Indices: 42270--42309 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
42260 TCTATTAGTT
*
42270 ATTAGATAGGATCA-TTTTTA
1 ATTAGATAGAATCAGTTTTTA
42290 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTT
42310 TATTCTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (21 bp):
ATTAGATAGAATCAGTTTTTA
Found at i:42326 original size:53 final size:52
Alignment explanation
Indices: 42238--42366 Score: 224
Period size: 53 Copynumber: 2.5 Consensus size: 52
42228 TAAATTAAAT
42238 ATTAGATAGAATCAGTTTTTATTCTATTAGTTATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTTATTCTATTAGTTATTAGATAGGATCATTTTTA
* *
42290 ATTAGATAGAATCAGTTTTTTATTCTTTTAGTTATTAGATATGATCATTTTTA
1 ATTAGATAGAATCAG-TTTTTATTCTATTAGTTATTAGATAGGATCATTTTTA
42343 ATTAGATAGAATCA-TTTTTATTCT
1 ATTAGATAGAATCAGTTTTTATTCT
42367 GTTTCTAATT
Statistics
Matches: 74, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
51 10 0.14
52 15 0.20
53 49 0.66
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.50
Consensus pattern (52 bp):
ATTAGATAGAATCAGTTTTTATTCTATTAGTTATTAGATAGGATCATTTTTA
Found at i:42348 original size:20 final size:20
Alignment explanation
Indices: 42323--42362 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
42313 TCTTTTAGTT
42323 ATTAGATATG-ATCATTTTTA
1 ATTAGATA-GAATCATTTTTA
42343 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
42363 TTCTGTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:48190 original size:20 final size:20
Alignment explanation
Indices: 48165--48203 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
48155 TAAATTAAAT
*
48165 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
48185 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
48204 TATTCTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:48242 original size:20 final size:21
Alignment explanation
Indices: 48217--48256 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
48207 TCTATTAGTT
*
48217 ATTAGATAGGATC-ATTTTTA
1 ATTAGATAGAATCAATTTTTA
48237 ATTAGATAGAATCAATTTTT
1 ATTAGATAGAATCAATTTTT
48257 TATTCTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (21 bp):
ATTAGATAGAATCAATTTTTA
Found at i:48280 original size:53 final size:51
Alignment explanation
Indices: 48164--48313 Score: 264
Period size: 53 Copynumber: 2.9 Consensus size: 51
48154 CTAAATTAAA
*
48164 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTATTCTATTAGT
48216 TATTAGATAGGATCATTTTTAATTAGATAGAATCAATTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATC-A-TTTTTATTCTATTAGT
48269 TATTAGATAGGATCATTTTTAATTAGATAGAATCATTTTTATTCT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCATTTTTATTCT
48314 GTTGCTAATT
Statistics
Matches: 95, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
51 10 0.11
52 34 0.36
53 51 0.54
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (51 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCATTTTTATTCTATTAGT
Found at i:48295 original size:20 final size:20
Alignment explanation
Indices: 48270--48309 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
48260 TCTATTAGTT
*
48270 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
48290 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
48310 TTCTGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:60819 original size:159 final size:158
Alignment explanation
Indices: 60223--60851 Score: 583
Period size: 159 Copynumber: 4.0 Consensus size: 158
60213 ATTCTCTTAT
* * * * *
60223 GATCATCATGCTTTTGAGATTCTTTACCATTTCCAAGATTTCTTCTTTCATCATAACTGTTTCCT
1 GATCACCATGTTTTTGAGATTCTTTACCATTT-CAATATTTCTTCTTTCACCATAACTGTTCCCT
* * * * * * * * *
60288 GATTCACTATCATCATTTCTTCCACTGAATCCAGATCTCTCAATGCTGTGTTGTTCATAGGTAC-
65 GAATCTCTTTCATCACTTCTTCCACTAAATCCAGATCTCTCAACGCTGAGTTTTTCATAGAT-CT
* * *
60352 CTGAATAAAGCATTCTATGAAGATCACTGC
129 CTGAAGAAAGCATACTATGAAGGTCACTGC
** * * *
60382 GATCACTGTTTTTTTGAGATTCTTTACCATCTCCATTATTTCTTCTTTCA-CAGTAACTG-TCTC
1 GATCACCATGTTTTTGAGATTCTTTACCAT-TTCAATATTTCTTCTTTCACCA-TAACTGTTC-C
* * * * * *
60445 CTGAATCTGATTT-ATCGCTACTTCCACTAAATCCAGATCTCTCAATGCTG-CTTTGTTCATAGG
63 CTGAATCT-CTTTCATCACTTCTTCCACTAAATCCAGATCTCTCAACGCTGAGTTT-TTCATAGA
* * *
60508 TATCCGAA-AAGAGCATTCTATGAAGGTCACTGC
126 TCTCTGAAGAA-AGCATACTATGAAGGTCACTGC
* * * * * * * * *
60541 AATGAACGTGTTTTTGAGATTCTTTACAATTTCTATTATTTCTTCTTTCCCCACAACTGTTTCCT
1 GATCACCATGTTTTTGAGATTCTTTACCATTTC-AATATTTCTTCTTTCACCATAACTGTTCCCT
* * * * *
60606 GAATCTCTTTCAGCACTTCCTCTACTAAATCCAGATCTCTCAGCACTGCA-TTTTTCGA-AGATC
65 GAATCTCTTTCATCACTTCTTCCACTAAATCCAGATCTCTCAACGCTG-AGTTTTTC-ATAGATC
* *
60669 TCTGAAGAAAGCATAATATGAAGGTGACTGC
128 TCTGAAGAAAGCATACTATGAAGGTCACTGC
* * *
60700 GATCACCATGATTTTGAGATTCTTTACCATCTTCAATATTTCTTCTTTCCCCGTAACTGTTCCCT
1 GATCACCATGTTTTTGAGATTCTTTACCAT-TTCAATATTTCTTCTTTCACCATAACTGTTCCCT
* * *
60765 GAATCTCTTTCATCACATCTTCCACTAAATCCAAATCTCTCAACGCTGAGTTTTT-TTAGGATCT
65 GAATCTCTTTCATCACTTCTTCCACTAAATCCAGATCTCTCAACGCTGAGTTTTTCATA-GATCT
* *
60829 CTGAAGAAAGCATATTACGAAGG
129 CTGAAGAAAGCATACTATGAAGG
60852 CCATTGTGAT
Statistics
Matches: 384, Mismatches: 67, Indels: 38
0.79 0.14 0.08
Matches are distributed among these distances:
158 14 0.04
159 355 0.92
160 15 0.04
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (158 bp):
GATCACCATGTTTTTGAGATTCTTTACCATTTCAATATTTCTTCTTTCACCATAACTGTTCCCTG
AATCTCTTTCATCACTTCTTCCACTAAATCCAGATCTCTCAACGCTGAGTTTTTCATAGATCTCT
GAAGAAAGCATACTATGAAGGTCACTGC
Found at i:77775 original size:60 final size:60
Alignment explanation
Indices: 77638--77784 Score: 153
Period size: 60 Copynumber: 2.5 Consensus size: 60
77628 AACATAATGA
* * *
77638 ATAGTCAGGTG-ACCATTTTGTAACTTTTACTAGTTGAGGAACTCAACAAAGTAACTCCCT
1 ATAGTCAGG-GAACCATTTTGTAACTTTTAATAGTGGAGGAACTCAACAAAATAACTCCCT
*
77698 ATAGTC-GGGAAACCATTTTGTAACTTTTAATAGTCGGA-GAACTCAACAAAATAGTA-T-CTT
1 ATAGTCAGGG-AACCATTTTGTAACTTTTAATAGT-GGAGGAACTCAACAAAATA--ACTCCCT
*
77758 ATAGTCAGGGAATCATTTGTGT-ACTTT
1 ATAGTCAGGGAACCATTT-TGTAACTTT
77785 ACCCTATCTT
Statistics
Matches: 75, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
58 1 0.01
59 2 0.03
60 62 0.83
61 9 0.12
62 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (60 bp):
ATAGTCAGGGAACCATTTTGTAACTTTTAATAGTGGAGGAACTCAACAAAATAACTCCCT
Found at i:80092 original size:35 final size:35
Alignment explanation
Indices: 80046--80121 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
80036 AAAACAGTCC
* *
80046 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
80081 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
80116 TCAATT
1 TCAATT
80122 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:80692 original size:126 final size:127
Alignment explanation
Indices: 80513--80754 Score: 362
Period size: 126 Copynumber: 1.9 Consensus size: 127
80503 TATTTATATA
* **
80513 ATCAATTTGGTCCTAAATTAAATAGATTTAATAAATTAATCATTTAATTAGGATCTAACATGTGT
1 ATCAATTTGGTCCTAAATTAAATAAATTT-ATAAATTAATCATTTAACCAGGATCTAACATGTGT
* *
80578 TAGCACATGATCATGACACGTGTCATTGGTGACACATGTCAC-CCTAATTATTTATATATGCT
65 TAACACATGATCATGACACATGTCATTGGTGACACATGTCACACCTAATTATTTATATATGCT
*
80640 ATCAATTTGGTCCTAAATTAAATAAAATTT-TAAATTAATCATTTAACCAGGATCTGACATGTGT
1 ATCAATTTGGTCCTAAATTAAAT-AAATTTATAAATTAATCATTTAACCAGGATCTAACATGTGT
* * * *
80704 TAACACATGATCATGATATATGTTATTGGTGACACATGTCCCACCTAATTA
65 TAACACATGATCATGACACATGTCATTGGTGACACATGTCACACCTAATTA
80755 GAAGAAAATT
Statistics
Matches: 103, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
126 67 0.65
127 31 0.30
128 5 0.05
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (127 bp):
ATCAATTTGGTCCTAAATTAAATAAATTTATAAATTAATCATTTAACCAGGATCTAACATGTGTT
AACACATGATCATGACACATGTCATTGGTGACACATGTCACACCTAATTATTTATATATGCT
Found at i:82672 original size:20 final size:21
Alignment explanation
Indices: 82635--82673 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
82625 CAATTTCGAC
82635 ACCTAATAAGCATCGATACAT
1 ACCTAATAAGCATCGATACAT
* *
82656 ACCT-ATAAGTATTGATAC
1 ACCTAATAAGCATCGATAC
82674 TAATGATGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (21 bp):
ACCTAATAAGCATCGATACAT
Done.