Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006179.1 Hibiscus syriacus cultivar Beakdansim tig00014694_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: 101378
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:5496 original size:18 final size:19
Alignment explanation
Indices: 5473--5511 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
5463 AATTTAATCG
*
5473 AATATATAA-TTAAAATTC
1 AATATAAAACTTAAAATTC
5491 AATATAAAATCTTAAAATTC
1 AATATAAAA-CTTAAAATTC
5511 A
1 A
5512 TTAACACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (19 bp):
AATATAAAACTTAAAATTC
Found at i:7135 original size:3 final size:3
Alignment explanation
Indices: 7113--7189 Score: 55
Period size: 3 Copynumber: 23.7 Consensus size: 3
7103 TGTAACCAAA
* * *
7113 AAT ATAT AAC AAT AAAT AAT AAT AAT AAT AAAT ATT AAAT ATT AAAT
1 AAT A-AT AAT AAT -AAT AAT AAT AAT AAT -AAT AAT -AAT AAT -AAT
* *
7160 AAT AAT AAT AAT AAAT ATT AAT AAT GAT AA
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AA
7190 CCCGGAAAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
3 42 0.72
4 16 0.28
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:7136 original size:6 final size:6
Alignment explanation
Indices: 7113--7189 Score: 55
Period size: 7 Copynumber: 11.8 Consensus size: 6
7103 TGTAACCAAA
* * *
7113 AATATAT AACAAT AAATAAT AATAAT AATAAAT ATTAAAT ATTAAAT AATAAT
1 AATA-AT AATAAT -AATAAT AATAAT AAT-AAT AAT-AAT AAT-AAT AATAAT
* *
7166 AATAAT AAATATT AATAAT GATAA
1 AATAAT -AATAAT AATAAT AATAA
7190 CCCGGAAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
6 29 0.48
7 31 0.52
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (6 bp):
AATAAT
Found at i:7139 original size:13 final size:13
Alignment explanation
Indices: 7112--7184 Score: 59
Period size: 13 Copynumber: 6.0 Consensus size: 13
7102 TTGTAACCAA
*
7112 AAATATATAACAAT
1 AAATA-ATAATAAT
7126 AAATAATAATAAT
1 AAATAATAATAAT
*
7139 -AAT-A-AATATT
1 AAATAATAATAAT
*
7149 AAAT-ATTA-AAT
1 AAATAATAATAAT
7160 -AATAATAATAAT
1 AAATAATAATAAT
*
7172 AAATATTAATAAT
1 AAATAATAATAAT
7185 GATAACCCGG
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
10 8 0.17
11 10 0.21
12 7 0.15
13 18 0.38
14 5 0.10
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:7475 original size:21 final size:22
Alignment explanation
Indices: 7429--7475 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
7419 AATATTTGAT
* * *
7429 AAATTAATGTATAATATGATTA
1 AAATAAATGTATAATACGAATA
7451 AAATAAATGTATAA-ACGAATA
1 AAATAAATGTATAATACGAATA
7472 AAAT
1 AAAT
7476 TTTTATGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (22 bp):
AAATAAATGTATAATACGAATA
Found at i:8682 original size:2 final size:2
Alignment explanation
Indices: 8671--8763 Score: 179
Period size: 2 Copynumber: 47.0 Consensus size: 2
8661 TATACTTCAA
8671 AT AT -T 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
8712 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
8754 AT AT AT AT AT
1 AT AT AT AT AT
8764 TTGATTATTT
Statistics
Matches: 90, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 89 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:11466 original size:2 final size:2
Alignment explanation
Indices: 11459--11486 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11449 TAACTAAGGG
11459 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
11487 ACAAACCCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:11603 original size:31 final size:32
Alignment explanation
Indices: 11541--11604 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
11531 AACAAGACCC
*
11541 ATCAATCCCACGCTTCCACCTCCATACACCAA
1 ATCAATCCCACGCTTCCACCTCCATAAACCAA
* * *
11573 ATCAATCCCTCTC-TCCACCTTCATAAACCAA
1 ATCAATCCCACGCTTCCACCTCCATAAACCAA
11604 A
1 A
11605 ACAACACGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 17 0.61
32 11 0.39
ACGTcount: A:0.33, C:0.44, G:0.02, T:0.22
Consensus pattern (32 bp):
ATCAATCCCACGCTTCCACCTCCATAAACCAA
Found at i:13572 original size:23 final size:24
Alignment explanation
Indices: 13534--13581 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
13524 TTTGTTATAG
13534 TTTGATAAAATTTAAT-AATATTT
1 TTTGATAAAATTTAATGAATATTT
*
13557 TTTGAT-AAATTATAATGATTATTT
1 TTTGATAAAATT-TAATGAATATTT
13581 T
1 T
13582 ATAATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 10 0.45
24 7 0.32
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (24 bp):
TTTGATAAAATTTAATGAATATTT
Found at i:14803 original size:58 final size:59
Alignment explanation
Indices: 14697--14812 Score: 155
Period size: 58 Copynumber: 2.0 Consensus size: 59
14687 GAACATATGA
* * *
14697 ATAGTCGAGTGATCATTTTGTAACTTTTAATAATCGGGAGACTCAACAAA-ATAACACCT
1 ATAGTCGAGAGATCATTTTGTAACTTTTAATAATAGAGAGACTCAACAAAGA-AACACCT
* * *
14756 ATAGTCGAGAGATCA-TTTGTAACTTTTAATAGTAGAGAGGCTTAACAAAGAAACACC
1 ATAGTCGAGAGATCATTTTGTAACTTTTAATAATAGAGAGACTCAACAAAGAAACACC
14813 CTAGAGTCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
58 35 0.70
59 15 0.30
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (59 bp):
ATAGTCGAGAGATCATTTTGTAACTTTTAATAATAGAGAGACTCAACAAAGAAACACCT
Found at i:18243 original size:260 final size:255
Alignment explanation
Indices: 17570--18439 Score: 1253
Period size: 260 Copynumber: 3.4 Consensus size: 255
17560 CTTATTCATA
*
17570 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGGTTTCTAATTCATATATTCGGGT
1 TATTGAATAAAAATA-TTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGT
* *
17635 CCGGTCGTGTGAAACTTTATTTTGGTCGGGTCGGGTCGG-TTTTTTAAGTATGATATTCGGGTCG
65 CGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTATGATATTCGGGTCG
* *
17699 GGTCGAATTCGGGTTTAGGGTGAAAAATACCCGACCCAAAAATATATATAATTTTACCTTATATA
130 GGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAATATATATAATTTTACCTTATATA
* *
17764 TTTAAGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTTACTATTTT
195 TTTAGGAATAATTACAATAATA-CCCTCTATATATAATTTTTTTCAATTAAGTCACTATTTT
*
17826 TATTGAATAAAAATATTTTTT-TTATTTCGGGTCGGGTCGAATTTCTAATTCATATATTCGGGTC
1 TATTGAATAAAAATATTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTC
* * *
17890 GGGTCGGGTGAAATTTTATTTTGGTCTGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGG
66 GGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTATGATATTCGGGTCGG
* *
17955 GTTGAGTTCGGGATTAGGGTGAAAAATACCCGACCCGAAAATATATATAATTTTACCTTATATAT
131 GTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAATATATATAATTTTACCTTATATAT
* *
18020 TTAGGAATAATTACAATAATACCTCTCTATATATAATTTTTTTTCAATTAAGTCATTGTTTT
196 TTAGGAATAATTACAATAATACC-CTCTATATATAA-TTTTTTTCAATTAAGTCACTATTTT
18082 TATTGAATAAAAATAATTTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGG
1 TATTGAATAAAAAT-A--TTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGG
* *
18147 GTCGGGTCGGGTGAAACTTTATTTTGGTTGGGTCGGGTCGGTTTTTTTAAGTATGATATTTGGGT
63 GTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTATGATATTCGGGT
* * * *
18212 CTGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGATCCGACCCGACCCAAGAAATATATAATAT
128 CGGGTCGAGTTCGGGTTTAGGGTGAAAAATA--C---CCGACCCGA---AA-ATATATATAATTT
* * *
18277 TACATTATATATTTAGGAATAATTACAATAATACCC-CTATATGTACTTTTTTTCAATTAAGTCA
184 TACCTTATATATTTAGGAATAATTACAATAATACCCTCTATATATAATTTTTTTCAATTAAGTCA
18341 CTATTTT
249 CTATTTT
* *
18348 TATTGAATAAAAATAATTTTTTATTATTT----T-GGGTCGGGTTTATAATTCATATA-T----T
1 TATTGAATAAAAAT-ATTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGT
*
18403 CGGGTCGGGTGAAACTTTATTTTGGTCGGGTCAGGTC
65 CGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTC
18440 TCGGATGGAG
Statistics
Matches: 562, Mismatches: 36, Indels: 34
0.89 0.06 0.05
Matches are distributed among these distances:
254 113 0.20
255 124 0.22
256 51 0.09
257 1 0.00
258 1 0.00
259 27 0.05
260 127 0.23
262 1 0.00
264 13 0.02
265 9 0.02
266 39 0.07
267 8 0.01
268 3 0.01
269 45 0.08
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (255 bp):
TATTGAATAAAAATATTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTC
GGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTATGATATTCGGGTCGG
GTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAATATATATAATTTTACCTTATATAT
TTAGGAATAATTACAATAATACCCTCTATATATAATTTTTTTCAATTAAGTCACTATTTT
Found at i:23494 original size:55 final size:54
Alignment explanation
Indices: 23433--23923 Score: 542
Period size: 55 Copynumber: 8.9 Consensus size: 54
23423 AATAAGAGCC
* * *
23433 CGCTCCCTATTCCTTCAGGGAGTATAGGACTCGAA-AAACATTCGACAAACAGGTT
1 CGCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATC-TTCAACAAAC-GGTT
*
23488 CGCTCCCTATTCCTTCAGGGAGTATAGAACTCGAATAATCTTCTAA-AAACGAGTT
1 CGCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTC-AACAAACG-GTT
* * * **
23543 CGCTCCCTATTTCTTCAGGGAGTACAGAACTCGAACTATCTTCAGTAAACGTGTAT
1 CGCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACG-GT-T
* *
23599 -GCTCCCTATTCGTTCAGGGAGTATA-AGACTCGAACAATCTTCAATAAACGGGTT
1 CGCTCCCTATTCCTTCAGGGAGTATAGA-ACTCGAACAATCTTCAACAAAC-GGTT
*
23653 CGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAAC-GTGT
1 CGCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGT-T
* * **
23707 CTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGCC
1 C-GCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAAC-GGTT
** * * * **
23763 CGCTCTATATTCTTTCAGAGAGTATAGAACTCGAACAATCTTTAACAAACGGGCC
1 CGCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAAC-GGTT
* * * * **
23818 CGCTCTCTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAACGCAT
1 CGCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGTT
* * *
23872 CTGCTCCCTATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCAACAAACG
1 C-GCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACG
23924 TGTTTGCTTC
Statistics
Matches: 388, Mismatches: 34, Indels: 28
0.86 0.08 0.06
Matches are distributed among these distances:
53 2 0.01
54 8 0.02
55 369 0.95
56 8 0.02
57 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (54 bp):
CGCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGTT
Found at i:23739 original size:165 final size:164
Alignment explanation
Indices: 23434--23931 Score: 608
Period size: 165 Copynumber: 3.0 Consensus size: 164
23424 ATAAGAGCCC
* * * *
23434 GCTCCCTATTCCTTCAGGGAGTATAGGACTCGAA-AAACATTCGACAAACAGGTTCGCTCCCTAT
1 GCTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATC-TTCAACAAACGGGTTCGCTCCCTAT
* * *
23498 TCCTTCAGGGAGTATAGAACTCGAATAATCTTCTAAAAACGAGT-TCGCTCCCTATTTCTTCAGG
65 TCCTTCAGGGAGTATAGAACTCGAACAATCTTC-AAAAACGAGTCT-GCTCCCTATTCCTTCAGA
* * **
23562 GAGTACAGAACTCGAACTATCTTCAGTAAACGTGTAT
128 GAGTATAGAACTCGAACAATCTTCAACAAACGTGTAT
* *
23599 GCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAATAAACGGGTTCGCTCCCTATT
1 GCTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGGGTTCGCTCCCTATT
* * *
23664 CGTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCTGCTCTCTATTCCTTCAGAGA
66 CCTTCAGGGAGTATAGAACTCGAACAATCTTCAA-AAACGAGTCTGCTCCCTATTCCTTCAGAGA
* ***
23729 GTATAGAACTCGAACAATCTTCAACAAACGGGCCC
130 GTATAGAACTCGAACAATCTTCAACAAACGTGTAT
** * * * ** *
23764 GCTCTATATTCTTTCAGAGAGTAT-AGAACTCGAACAATCTTTAACAAACGGGCCCGCTCTCTAT
1 GCTCCCTATTCCTTCAGGGAGTATAAG-ACTCGAACAATCTTCAACAAACGGGTTCGCTCCCTAT
* *
23828 TCTTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAACGCA-TCTGCTCCCTATTCCTTCAGA
65 TCCTTCAGGGAGTATAGAACTCGAACAATCTTCAA-AAACG-AGTCTGCTCCCTATTCCTTCAGA
* * *
23892 GAGTATAGGACTTGAACAATCTTCAACAAACGTGTTT
128 GAGTATAGAACTCGAACAATCTTCAACAAACGTGTAT
23929 GCT
1 GCT
23932 TCACTACTCC
Statistics
Matches: 288, Mismatches: 40, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
164 4 0.01
165 280 0.97
166 4 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (164 bp):
GCTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGGGTTCGCTCCCTATT
CCTTCAGGGAGTATAGAACTCGAACAATCTTCAAAAACGAGTCTGCTCCCTATTCCTTCAGAGAG
TATAGAACTCGAACAATCTTCAACAAACGTGTAT
Found at i:23976 original size:37 final size:36
Alignment explanation
Indices: 23926--24033 Score: 144
Period size: 37 Copynumber: 2.9 Consensus size: 36
23916 AACAAACGTG
*
23926 TTTGCTTCACTACTCCTCCGTGAAGGCTTATAGATGA
1 TTTGCTTCACTACTCTTCCGTGAAGGCTTA-AGATGA
*
23963 TTTGCTTCACTACTCTTCTGTGAAGGCTTAAGACTGA
1 TTTGCTTCACTACTCTTCCGTGAAGGCTTAAGA-TGA
* * * *
24000 ATTACTTCACTGCTCTTTCGTGAAGGCTTAAGAT
1 TTTGCTTCACTACTCTTCCGTGAAGGCTTAAGAT
24034 TGACTTGTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
36 4 0.06
37 59 0.94
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (36 bp):
TTTGCTTCACTACTCTTCCGTGAAGGCTTAAGATGA
Found at i:26531 original size:2 final size:2
Alignment explanation
Indices: 26524--26555 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
26514 ATATCTCCTA
26524 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
26556 TTCCCATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27277 original size:21 final size:21
Alignment explanation
Indices: 27245--27318 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
27235 AGGGGGGTAT
27245 CGATTCCCCCTTGAATGAGTAC
1 CGATT-CCCCTTGAATGAGTAC
*
27267 CGATTCCCCTTGAATGGGTAC
1 CGATTCCCCTTGAATGAGTAC
* * *
27288 TGATTCCCATTGAATGTGTAC
1 CGATTCCCCTTGAATGAGTAC
27309 CGATTCCCCT
1 CGATTCCCCT
27319 AGCCCAGAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
21 41 0.89
22 5 0.11
ACGTcount: A:0.20, C:0.30, G:0.19, T:0.31
Consensus pattern (21 bp):
CGATTCCCCTTGAATGAGTAC
Found at i:28761 original size:10 final size:9
Alignment explanation
Indices: 28742--28846 Score: 72
Period size: 9 Copynumber: 11.3 Consensus size: 9
28732 CTTGAACCCC
*
28742 CTTTTATTT
1 CTTTTTTTT
28751 CTTTTTCTTT
1 CTTTTT-TTT
*
28761 CTCTTTTTT
1 CTTTTTTTT
*
28770 CATCATTTTTT
1 C-T-TTTTTTT
28781 C--TTTTTT
1 CTTTTTTTT
*
28788 CTTTTTTCT
1 CTTTTTTTT
28797 -TTTTTTTT
1 CTTTTTTTT
*
28805 ATTTTTTTT
1 CTTTTTTTT
28814 CATTATTTTTT
1 C-TT-TTTTTT
* *
28825 CATTTTTCT
1 CTTTTTTTT
28834 CTTTTTATTT
1 CTTTTT-TTT
28844 CTT
1 CTT
28847 CTTCAAGTGA
Statistics
Matches: 77, Mismatches: 10, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
7 7 0.09
8 7 0.09
9 32 0.42
10 17 0.22
11 14 0.18
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:28787 original size:7 final size:7
Alignment explanation
Indices: 28775--28849 Score: 62
Period size: 7 Copynumber: 10.3 Consensus size: 7
28765 TTTTTCATCA
28775 TTTTTTC
1 TTTTTTC
28782 TTTTTTC
1 TTTTTTC
28789 TTTTTTC
1 TTTTTTC
28796 TTTTTT-
1 TTTTTTC
*
28802 TTTATTTT
1 TTT-TTTC
*
28810 TTTTCATTA
1 TTTT--TTC
28819 TTTTTTC
1 TTTTTTC
*
28826 ATTTTTC
1 TTTTTTC
*
28833 TCTTTTTA
1 T-TTTTTC
*
28841 TTTCTTC
1 TTTTTTC
28848 TT
1 TT
28850 CAAGTGAAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
6 3 0.05
7 38 0.68
8 9 0.16
9 6 0.11
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTTC
Found at i:28799 original size:44 final size:45
Alignment explanation
Indices: 28748--28849 Score: 134
Period size: 44 Copynumber: 2.3 Consensus size: 45
28738 CCCCCTTTTA
* *
28748 TTTCTTTTTCTTTCTCTTTTTTCATCATTTTTTCTTTTTTCT-TT
1 TTTCTTTTTCTTTATCTTTTTTCATCATTTTTTCATTTTTCTCTT
* * *
28792 TTTCTTTTTTTTTATTTTTTTTCATTATTTTTTCATTTTTCTCTT
1 TTTCTTTTTCTTTATCTTTTTTCATCATTTTTTCATTTTTCTCTT
*
28837 TTTATTTCTTCTT
1 TTTCTTT-TTCTT
28850 CAAGTGAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
44 37 0.76
45 8 0.16
46 4 0.08
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (45 bp):
TTTCTTTTTCTTTATCTTTTTTCATCATTTTTTCATTTTTCTCTT
Found at i:28825 original size:11 final size:10
Alignment explanation
Indices: 28789--28831 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
28779 TTCTTTTTTC
28789 TTTTTTC-TT
1 TTTTTTCATT
*
28798 TTTTTTTATT
1 TTTTTTCATT
28808 TTTTTTCATT
1 TTTTTTCATT
28818 ATTTTTTCATT
1 -TTTTTTCATT
28829 TTT
1 TTT
28832 CTCTTTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
9 6 0.20
10 14 0.47
11 10 0.33
ACGTcount: A:0.09, C:0.07, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTCATT
Found at i:47227 original size:3 final size:3
Alignment explanation
Indices: 47219--47279 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
47209 CTCCTTACTC
47219 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
47267 TCA TCA TCA TCA T
1 TCA TCA TCA TCA T
47280 AAGGAGCATA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:49170 original size:23 final size:23
Alignment explanation
Indices: 49142--49202 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
49132 CTCATATAAA
*
49142 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* * * *
49165 TTCACCGTAGTGTCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
49188 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
49203 TATAATAATG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:49389 original size:103 final size:103
Alignment explanation
Indices: 49218--49435 Score: 436
Period size: 103 Copynumber: 2.1 Consensus size: 103
49208 TAATGTCCAT
49218 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
49283 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
49321 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
49386 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
49424 AAGGACCACATA
1 AAGGACCACATA
49436 GACCCTCGAC
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 115 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:51003 original size:21 final size:21
Alignment explanation
Indices: 50985--51040 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
50975 TCGTTTGAGA
50985 GGGTATCGATTCCCCTTGAAT
1 GGGTATCGATTCCCCTTGAAT
51006 GGGTATCGATTCCCCTTGAAT
1 GGGTATCGATTCCCCTTGAAT
*
51027 GGGTATCAATTCCC
1 GGGTATCGATTCCC
51041 TTAGCCCAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (21 bp):
GGGTATCGATTCCCCTTGAAT
Found at i:54290 original size:23 final size:23
Alignment explanation
Indices: 54264--54324 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
54254 CTCATATAAA
*
54264 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* * *
54287 TGCACAGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
54310 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
54325 TATAATAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:57527 original size:17 final size:17
Alignment explanation
Indices: 57487--57537 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
57477 TAAACCAAAT
57487 AAATA-AATTAAATATTA
1 AAATATAATTAAA-ATTA
*
57504 ACA-ATAATTAAAATTA
1 AAATATAATTAAAATTA
57520 AAATATAATTTAAAATTA
1 AAATATAA-TTAAAATTA
57538 TTATCGTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 7 0.24
17 13 0.45
18 9 0.31
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATATAATTAAAATTA
Found at i:57532 original size:18 final size:16
Alignment explanation
Indices: 57487--57537 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 16
57477 TAAACCAAAT
57487 AAATAAATTAAATATTAA
1 AAAT-AATTAAA-ATTAA
*
57505 CAATAATTAAAATTAA
1 AAATAATTAAAATTAA
57521 AATATAATTTAAAATTA
1 AA-ATAA-TTAAAATTA
57538 TTATCGTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 6 0.21
17 11 0.38
18 12 0.41
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATAATTAAAATTAA
Found at i:59845 original size:44 final size:43
Alignment explanation
Indices: 59793--59899 Score: 110
Period size: 44 Copynumber: 2.5 Consensus size: 43
59783 CGTTTGTGAA
* * *
59793 TGTA-AAACGCCGCTATTGACTACGT-ATATAGTGGCGTTTTATT
1 TGTACAAACGCCGCTATTAACTAAGTAAT-TAGTGGCATTTTA-T
* * *
59836 TTTACAAACGCCGATATTAACTAAGTAATTTGTGGCATTTTAT
1 TGTACAAACGCCGCTATTAACTAAGTAATTAGTGGCATTTTAT
*
59879 TGTACAAACTCCGCTAATTAA
1 TGTACAAACGCCGCT-ATTAA
59900 AACTGAATTT
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
43 16 0.31
44 34 0.65
45 2 0.04
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (43 bp):
TGTACAAACGCCGCTATTAACTAAGTAATTAGTGGCATTTTAT
Found at i:63430 original size:16 final size:16
Alignment explanation
Indices: 63405--63446 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
63395 GCAACAATAT
*
63405 TAAAAGTGAAAAGAAA
1 TAAAAATGAAAAGAAA
*
63421 TAAAAATGAAATGAAA
1 TAAAAATGAAAAGAAA
*
63437 T-GAAATGAAA
1 TAAAAATGAAA
63447 TTAAGAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (16 bp):
TAAAAATGAAAAGAAA
Found at i:63573 original size:3 final size:3
Alignment explanation
Indices: 63565--63613 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
63555 ATAAATGAGT
63565 ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
63611 ATA
1 ATA
63614 TAAATACTGC
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.09
3 40 0.91
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:64821 original size:38 final size:38
Alignment explanation
Indices: 64686--64995 Score: 262
Period size: 38 Copynumber: 7.9 Consensus size: 38
64676 AAAAATCCTT
* *
64686 TTTTTAAAAA-TAAACTATATAT-TATACGTTTTCAAAAAAG
1 TTTTTAAAAACTATA-TATATATATATA--TTTTC-AAAATG
** * *
64726 TATTTTCGAAACTATAT-TATATATATATATT-AAAATA
1 T-TTTTAAAAACTATATATATATATATATTTTCAAAATG
*
64763 TTTTCAAAAACTATATTATATATATATATATATATTCAAAATG
1 TTTTTAAAAAC--TA-TATATATATATATAT-T-TTCAAAATG
*
64806 TTTTTAAAAACTATATAT-TAAATATAAGTTTTCAAAATG
1 TTTTTAAAAACTATATATATATATAT-A-TTTTCAAAATG
* *
64845 -TTTTAAAAACTATATAATATATAAATGTTTTCAAAAT-
1 TTTTTAAAAACTATAT-ATATATATATATTTTCAAAATG
* *
64882 ATTTTAAAAACTATATTATATATATATATATTCAAAATG
1 TTTTTAAAAACTATA-TATATATATATATTTTCAAAATG
*
64921 -TTTTAAAAACTATATA-ATATATATTTTTTCAAAAAT-
1 TTTTTAAAAACTATATATATATATATATTTTC-AAAATG
*
64957 TTTTTAAAAAAACTATATAATATATATCTATTTTCAAAA
1 TTTTT--AAAAACTATAT-ATATATATATATTTTCAAAA
64996 ACCGATTTTT
Statistics
Matches: 224, Mismatches: 23, Indels: 46
0.76 0.08 0.16
Matches are distributed among these distances:
36 19 0.08
37 16 0.07
38 73 0.33
39 35 0.16
40 34 0.15
41 27 0.12
42 5 0.02
43 15 0.07
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (38 bp):
TTTTTAAAAACTATATATATATATATATTTTCAAAATG
Found at i:64916 original size:76 final size:75
Alignment explanation
Indices: 64734--64995 Score: 291
Period size: 76 Copynumber: 3.4 Consensus size: 75
64724 AGTATTTTCG
* *
64734 AAACTATAT-TATATATATATATT-AAAATATTTTCAAAAACTATATTATATATATATATATATA
1 AAACTATATATATATATATATATTCAAAATGTTTT-AAAAACTATA-TA-ATATATA-A-ATATT
64797 TTCAAAATGTTTTTAA
61 TTCAAAAT-TTTTTAA
* * *
64813 AAACTATATAT-TAAATATAAGTTTTCAAAATGTTTTAAAAACTATATAATATATAAATGTTTTC
1 AAACTATATATATATATAT-A-TATTCAAAATGTTTTAAAAACTATATAATATATAAATATTTTC
*
64877 AAAATATTTTAA
64 AAAATTTTTTAA
*
64889 AAACTATATTATATATATATATATTCAAAATGTTTTAAAAACTATATAATATAT--ATTTTTTCA
1 AAACTATA-TATATATATATATATTCAAAATGTTTTAAAAACTATATAATATATAAATATTTTC-
64952 AAAATTTTTTAAAA
64 AAAATTTTTT--AA
* *
64966 AAACTATATAATATATATCTATTTTCAAAA
1 AAACTATAT-ATATATATATATATTCAAAA
64996 ACCGATTTTT
Statistics
Matches: 161, Mismatches: 12, Indels: 22
0.83 0.06 0.11
Matches are distributed among these distances:
74 7 0.04
75 9 0.06
76 47 0.29
77 43 0.27
78 7 0.04
79 22 0.14
80 4 0.02
81 13 0.08
82 9 0.06
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (75 bp):
AAACTATATATATATATATATATTCAAAATGTTTTAAAAACTATATAATATATAAATATTTTCAA
AATTTTTTAA
Found at i:66017 original size:41 final size:41
Alignment explanation
Indices: 65921--66286 Score: 234
Period size: 41 Copynumber: 8.7 Consensus size: 41
65911 TTTGTAAATG
* * * * *
65921 AAAATGCCAATAAAGTATGAGACTTTAGCGGCATTTGCATA
1 AAAACGCCACTAAAGTACGAGTCTTTAGCGGCATTTGTATA
* *
65962 AAAACACCGCTAAAGTACGAGTCTTTAGCGGCATTTGTATA
1 AAAACGCCACTAAAGTACGAGTCTTTAGCGGCATTTGTATA
* * * * *
66003 TAAACGCCATTAAAGCACAAGTCTTTAGCAACATTTTTGTGGCGTTTGTATA
1 AAAACGCCACTAAAGTACGAGTCTTTAG---C--------GGCATTTGTATA
* * * * * *
66055 AAAACGCCGCTAAAATACGAATCTATAGCGGCGTCTGTATA
1 AAAACGCCACTAAAGTACGAGTCTTTAGCGGCATTTGTATA
* *
66096 AAAATGCCACTAAAGTACGAGTCTTTAGCGGCATTTTTATA
1 AAAACGCCACTAAAGTACGAGTCTTTAGCGGCATTTGTATA
* * ** *
66137 TAAACGCCACTAAAGTGCGAGTCTTTAGCAACATTTTTATA
1 AAAACGCCACTAAAGTACGAGTCTTTAGCGGCATTTGTATA
* * * * * ** * *
66178 CAAATGTCGCTAAAGTATGAGTCTACAACGGC-GTT-TATA
1 AAAACGCCACTAAAGTACGAGTCTTTAGCGGCATTTGTATA
* ** * *
66217 TAAACGCCACTAAAGTAC-AGTCTTTAGCAACGTTTATATA
1 AAAACGCCACTAAAGTACGAGTCTTTAGCGGCATTTGTATA
* * *
66257 AAAACACCACCAAAGTACGAGTATTTAGCG
1 AAAACGCCACTAAAGTACGAGTCTTTAGCG
66287 ATGTTTGTTA
Statistics
Matches: 247, Mismatches: 64, Indels: 28
0.73 0.19 0.08
Matches are distributed among these distances:
38 8 0.03
39 19 0.08
40 21 0.09
41 166 0.67
44 1 0.00
49 1 0.00
52 31 0.13
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (41 bp):
AAAACGCCACTAAAGTACGAGTCTTTAGCGGCATTTGTATA
Found at i:66119 original size:93 final size:93
Alignment explanation
Indices: 65954--66133 Score: 234
Period size: 93 Copynumber: 1.9 Consensus size: 93
65944 TTTAGCGGCA
* * * * * *
65954 TTTGCATAAAAACACCGCTAAAGTACGAGTCTTTAGCGGCATTTGTATATAAACGCCATTAAAGC
1 TTTGCATAAAAACACCGCTAAAATACGAATCTATAGCGGCATCTGTATAAAAACGCCACTAAAGC
66019 ACAAGTCTTTAGCAACATTTTTGTGGCG
66 ACAAGTCTTTAGCAACATTTTTGTGGCG
* * * * *
66047 TTTGTATAAAAACGCCGCTAAAATACGAATCTATAGCGGCGTCTGTATAAAAATGCCACTAAAGT
1 TTTGCATAAAAACACCGCTAAAATACGAATCTATAGCGGCATCTGTATAAAAACGCCACTAAAGC
* **
66112 ACGAGTCTTTAGCGGCATTTTT
66 ACAAGTCTTTAGCAACATTTTT
66134 ATATAAACGC
Statistics
Matches: 73, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (93 bp):
TTTGCATAAAAACACCGCTAAAATACGAATCTATAGCGGCATCTGTATAAAAACGCCACTAAAGC
ACAAGTCTTTAGCAACATTTTTGTGGCG
Found at i:68982 original size:21 final size:21
Alignment explanation
Indices: 68956--68999 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
68946 GCTATAACGT
68956 CAAGGATAGCTCCACATTAAG
1 CAAGGATAGCTCCACATTAAG
68977 CAAGGATAGCTCCACATTAAG
1 CAAGGATAGCTCCACATTAAG
68998 CA
1 CA
69000 TTGAGGCCAT
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:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (21 bp):
CAAGGATAGCTCCACATTAAG
Found at i:69436 original size:19 final size:18
Alignment explanation
Indices: 69393--69441 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
69383 TTTGCTTGAG
*
69393 ATGTTATCC-TCCGTGAA
1 ATGTTATCCTTCAGTGAA
69410 ATAAGTTATCCTTCAAGTGAA
1 AT--GTTATCCTTC-AGTGAA
69431 ATGTTATCCTT
1 ATGTTATCCTT
69442 TTTGAGAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 2 0.07
19 16 0.59
20 2 0.07
21 7 0.26
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (18 bp):
ATGTTATCCTTCAGTGAA
Found at i:77618 original size:111 final size:112
Alignment explanation
Indices: 77486--77714 Score: 379
Period size: 112 Copynumber: 2.1 Consensus size: 112
77476 GTCATAGGCG
* * * *
77486 CATTTCGACATACTTTGTGTATGATAG-TATCGATCGATTTTGTTTAATGCATAACGGTGCATTT
1 CATTTCAACATACTTCGTGTATGAAAGTTATCGATCGATTTTGCTTAATGCATAACGGTGCATTT
** * *
77550 TTGGCATAAAAGGTGTCACCCATGGTATTCATGATGAGGTGAATTAC
66 TCAGCATAAAAGGTGCCACCCATGGTATTCATAATGAGGTGAATTAC
77597 CATTTCAACATACTTCGTGTATGAAAGTTATCGATCGATTTTGCTTAATGCATAACGGTGCATTT
1 CATTTCAACATACTTCGTGTATGAAAGTTATCGATCGATTTTGCTTAATGCATAACGGTGCATTT
77662 TCAGCATAAAAGGTGCCACCCATGGTATTCATAATGAGGTGAATTAC
66 TCAGCATAAAAGGTGCCACCCATGGTATTCATAATGAGGTGAATTAC
77709 CATTTC
1 CATTTC
77715 CGCACTTCGG
Statistics
Matches: 109, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
111 24 0.22
112 85 0.78
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (112 bp):
CATTTCAACATACTTCGTGTATGAAAGTTATCGATCGATTTTGCTTAATGCATAACGGTGCATTT
TCAGCATAAAAGGTGCCACCCATGGTATTCATAATGAGGTGAATTAC
Found at i:78872 original size:29 final size:29
Alignment explanation
Indices: 78786--78880 Score: 111
Period size: 34 Copynumber: 3.1 Consensus size: 29
78776 TTTTTGCTTC
*
78786 AATT-AATTCGGTTAATAATTTTCAAAAA
1 AATTCAATTCGGTTAATAATTTTCAAATA
*
78814 AATTCGATTGAGTTCGGTTAATAATTTTCAAATT
1 AATTC-A---A-TTCGGTTAATAATTTTCAAATA
*
78848 AATTCAATTCAGTTAATAATTTTCAAATA
1 AATTCAATTCGGTTAATAATTTTCAAATA
78877 AATT
1 AATT
78881 TTGGTTCGTT
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
28 4 0.07
29 24 0.42
30 2 0.04
33 2 0.04
34 25 0.44
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.42
Consensus pattern (29 bp):
AATTCAATTCGGTTAATAATTTTCAAATA
Found at i:87031 original size:19 final size:20
Alignment explanation
Indices: 87007--87059 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
86997 CTTAGCATAT
87007 TAAAAATAAAAACTT-AAAA
1 TAAAAATAAAAACTTGAAAA
*
87026 TAAAAATGAAAACTTGAAAA
1 TAAAAATAAAAACTTGAAAA
*
87046 TAAAGA-AAAAACTT
1 TAAAAATAAAAACTT
87060 TATAAAACCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 21 0.70
20 9 0.30
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.21
Consensus pattern (20 bp):
TAAAAATAAAAACTTGAAAA
Found at i:90720 original size:22 final size:23
Alignment explanation
Indices: 90693--90754 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
90683 CGATTCCCCT
90693 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
*
90716 AGGGGGAATCAGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCCTTCAA
* *
90738 AGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
90755 TCTGCCCTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
22 15 0.43
23 20 0.57
ACGTcount: A:0.21, C:0.26, G:0.31, T:0.23
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:99446 original size:4 final size:4
Alignment explanation
Indices: 99437--99471 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
99427 TCAGTTTTGT
*
99437 AATA AATA AAGTA AATA AATG AATA AATA AATA AA
1 AATA AATA AA-TA AATA AATA AATA AATA AATA AA
99472 ATATTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (4 bp):
AATA
Done.