Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000158.1 Hibiscus syriacus cultivar Beakdansim tig00000280_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: 55328
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:1865 original size:21 final size:21
Alignment explanation
Indices: 1841--1880 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1831 TATAGTAATT
1841 ATATTTTTCAATAAT-TAAATA
1 ATATTTTT-AATAATATAAATA
1862 ATATTTTTAATAATATAAA
1 ATATTTTTAATAATATAAA
1881 AAAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATTTTTAATAATATAAATA
Found at i:1873 original size:20 final size:19
Alignment explanation
Indices: 1803--1880 Score: 61
Period size: 21 Copynumber: 3.9 Consensus size: 19
1793 ATCATTTATT
*
1803 ATATTTTTACAATTAAAATA
1 ATATTTTTATAATT-AAATA
* *
1823 ATATATTTTAT-AGT-AATT
1 ATAT-TTTTATAATTAAATA
1841 ATATTTTTCAATAATTAAATA
1 ATATTTTT--ATAATTAAATA
1862 ATATTTTTAATAATATAAA
1 ATATTTTT-ATAAT-TAAA
1881 AAAAAAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
17 4 0.09
18 7 0.15
19 2 0.04
20 14 0.30
21 20 0.43
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (19 bp):
ATATTTTTATAATTAAATA
Found at i:8098 original size:2 final size:2
Alignment explanation
Indices: 8093--8124 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
8083 ACCGAATTGA
8093 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
8125 TACATTAACA
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:8747 original size:44 final size:44
Alignment explanation
Indices: 8684--8773 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
8674 ATAAATTACT
8684 AAAGATAGATTGAATTCAAAACAAACAACATTTAACTAAAAGTA
1 AAAGATAGATTGAATTCAAAACAAACAACATTTAACTAAAAGTA
8728 AAAGATAGATTGAATTCAAAACAAACAACATTTAACTAAAAGTA
1 AAAGATAGATTGAATTCAAAACAAACAACATTTAACTAAAAGTA
8772 AA
1 AA
8774 GGTCAAAGTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.58, C:0.11, G:0.09, T:0.22
Consensus pattern (44 bp):
AAAGATAGATTGAATTCAAAACAAACAACATTTAACTAAAAGTA
Found at i:9697 original size:17 final size:18
Alignment explanation
Indices: 9675--9710 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
9665 AACCATAAAG
9675 TTTT-AAAAATAAATTAA
1 TTTTAAAAAATAAATTAA
9692 TTTTAAAAAATAAATTAA
1 TTTTAAAAAATAAATTAA
9710 T
1 T
9711 AAATTCTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTTAAAAAATAAATTAA
Found at i:25886 original size:44 final size:44
Alignment explanation
Indices: 25793--25887 Score: 163
Period size: 44 Copynumber: 2.2 Consensus size: 44
25783 ATTTAAACAA
25793 TAAATATGATTTATTGATTTGATTAATTTAAAAATTAATTAAAT
1 TAAATATGATTTATTGATTTGATTAATTTAAAAATTAATTAAAT
* **
25837 GAAATATGATTTATTGATTTGATTAATTTAAAAATTAATTCGAT
1 TAAATATGATTTATTGATTTGATTAATTTAAAAATTAATTAAAT
25881 TAAATAT
1 TAAATAT
25888 TCACACTTGA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.44, C:0.01, G:0.08, T:0.46
Consensus pattern (44 bp):
TAAATATGATTTATTGATTTGATTAATTTAAAAATTAATTAAAT
Found at i:26375 original size:15 final size:15
Alignment explanation
Indices: 26355--26386 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
26345 GAAAAAATCG
26355 AAAAATATACCACAA
1 AAAAATATACCACAA
*
26370 AAAAATATATCACAA
1 AAAAATATACCACAA
26385 AA
1 AA
26387 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.16, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAAATATACCACAA
Found at i:26952 original size:16 final size:16
Alignment explanation
Indices: 26915--26952 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
26905 AAATATTTAT
26915 AATAAATAAAAATCTA
1 AATAAATAAAAATCTA
*
26931 ATTAAATTAAAAAT-TA
1 AATAAA-TAAAAATCTA
26947 AATAAA
1 AATAAA
26953 ATTTAAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAAATAAAAATCTA
Found at i:27861 original size:20 final size:21
Alignment explanation
Indices: 27836--27874 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
27826 ATATATATAA
27836 TTTAAAATAATA-TAATTATG
1 TTTAAAATAATACTAATTATG
*
27856 TTTAAAATTATACTAATTA
1 TTTAAAATAATACTAATTA
27875 AAATAGTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (21 bp):
TTTAAAATAATACTAATTATG
Found at i:28406 original size:8 final size:8
Alignment explanation
Indices: 28393--28421 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
28383 AAGAAGGAAA
28393 AATAAAAT
1 AATAAAAT
28401 AATAAAAT
1 AATAAAAT
28409 AATAAAAT
1 AATAAAAT
28417 AATAA
1 AATAA
28422 TAAAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:28409 original size:13 final size:12
Alignment explanation
Indices: 28391--28430 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 12
28381 TGAAGAAGGA
28391 AAAATAAAATAAT
1 AAAATAAAA-AAT
28404 AAAATAATAAAAT
1 AAAATAA-AAAAT
28417 AATAATAAAAAAT
1 AA-AATAAAAAAT
28430 A
1 A
28431 TTAATAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 18 0.72
14 7 0.28
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:28435 original size:13 final size:12
Alignment explanation
Indices: 28390--28439 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
28380 ATGAAGAAGG
*
28390 AAAAATAAAATA
1 AAAAATATAATA
*
28402 ATAAA-ATAATA
1 AAAAATATAATA
*
28413 AAATA-ATAATA
1 AAAAATATAATA
28424 AAAAATATTAATA
1 AAAAATA-TAATA
28437 AAA
1 AAA
28440 GATTAGTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
11 18 0.58
12 5 0.16
13 8 0.26
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAATATAATA
Found at i:28490 original size:11 final size:11
Alignment explanation
Indices: 28398--28490 Score: 62
Period size: 11 Copynumber: 8.0 Consensus size: 11
28388 GGAAAAATAA
*
28398 AATAATAAAAT
1 AATAAAAAAAT
*
28409 AATAAAATAAT
1 AATAAAAAAAT
28420 AATAAAAAATATT
1 AATAAAAAA-A-T
* *
28433 AATAAAAGATT
1 AATAAAAAAAT
* *
28444 AGTTAAAAAAAC
1 A-ATAAAAAAAT
28456 AA-ACAAATAAAT
1 AATA-AAA-AAAT
*
28468 AAGAATAAAAAT
1 AATAA-AAAAAT
28480 AATAAAAAAAT
1 AATAAAAAAAT
28491 GTAGTAAAGT
Statistics
Matches: 63, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
10 1 0.02
11 28 0.44
12 22 0.35
13 12 0.19
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.23
Consensus pattern (11 bp):
AATAAAAAAAT
Found at i:29668 original size:3 final size:3
Alignment explanation
Indices: 29660--29697 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
29650 ACCTGCAAAC
* *
29660 ATA ATA ATA AAA ATA ATA ATA ATA A-A AAA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
29698 TTTTTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (3 bp):
ATA
Found at i:29690 original size:17 final size:18
Alignment explanation
Indices: 29660--29697 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
29650 ACCTGCAAAC
29660 ATAATAATAAAAATAATA
1 ATAATAATAAAAATAATA
29678 ATAATAA-AAAAATAATA
1 ATAATAATAAAAATAATA
29695 ATA
1 ATA
29698 TTTTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
ATAATAATAAAAATAATA
Found at i:30323 original size:37 final size:37
Alignment explanation
Indices: 30272--30482 Score: 381
Period size: 37 Copynumber: 5.8 Consensus size: 37
30262 GGGTTTTTTG
*
30272 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
*
30309 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA-AATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
30345 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
*
30382 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA-AATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
30418 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
30455 TGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGGGAAACTGTCTCAAGAGAG
30483 TCAAAACTTG
Statistics
Matches: 167, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
36 70 0.42
37 97 0.58
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
Found at i:30349 original size:73 final size:73
Alignment explanation
Indices: 30272--30488 Score: 416
Period size: 73 Copynumber: 3.0 Consensus size: 73
30262 GGGTTTTTTG
*
30272 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
30337 ACAAAATT
66 ACAAAATT
30345 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
30410 ACAAAATT
66 ACAAAATT
30418 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
*
30483 TCAAAA
66 ACAAAA
30489 CTTGGAAATT
Statistics
Matches: 142, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 142 1.00
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (73 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
ACAAAATT
Found at i:30971 original size:252 final size:250
Alignment explanation
Indices: 30521--31186 Score: 961
Period size: 252 Copynumber: 2.7 Consensus size: 250
30511 ACAATGGTGA
* * * *
30521 GCACAATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCATTGTGAAGTTGAACCTTG
1 GCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGG-TGGCCCCTTCGTCGTGAAGTTGAGCC-TG
*
30586 GAATTGGATATCCTTCGTCGTGAAGTTGAAATCC-AGT-A--TG--TTGTTTCGAGGCCAATATC
64 GAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGTAAGTTGTATTGTTTCGAGTCCAATATC
* * * *
30645 ATTCGCTGTGAAGTTGAAATTGACTTC-GAAACTGGAAAGTTTATTGACAGACACTCCTTCTCTG
129 CTCCGC-GTGAAGTTGAAATTG-GTTCTGAAACTGGGAAGTTTATTGACAGACACTCCTTCTCTG
* * *
30709 AGTTGGATATCC-TCTGCCGTGAAGTTGAAATTCAATCTGGAGATGGATGTTGCTTGTGT
192 AGTTGGATATCCTTC-GCCGTGAAGTTGAAATCCAATCTAGAGATGGATGCTGCTTGTGT
* * * * *
30768 GTACGATTCACTTCGTCGTGAAGTTGAAACCGTAGGTTGCCCCTTCGCCGTGAAGTTGAGCCAGG
1 GCACGATTCCCTTCGTCGTGAAGTTGAAACCGT-GGTGGCCCCTTCGTCGTGAAGTTGAGCCTGG
*
30833 AATTGGATATCCTTCGTCATGAAGTTGAAATCCAAGTAAGTTGTATTGTTTCGAGTCCAATATCC
65 AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGTAAGTTGTATTGTTTCGAGTCCAATATCC
*
30898 TCCGTCGTGAAGTTGAAATTGGTTCTGAAACTGGGAAGTTTATTGACAGACACTCCTTCTTTGAG
130 TCCG-CGTGAAGTTGAAATTGGTTCTGAAACTGGGAAGTTTATTGACAGACACTCCTTCTCTGAG
*
30963 TTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGATGGATGCTGCTTGTGT
194 TTGGATATCCTTCGCCGTGAAGTTGAAATCCAATCTAGAGATGGATGCTGCTTGTGT
*
31020 GCACGATTCCCTTTGTCGTGAAGTTGAAACCGTGGGTGGCCCCTTCGTCGTGAAGTTGAGCCTGG
1 GCACGATTCCCTTCGTCGTGAAGTTGAAACCGT-GGTGGCCCCTTCGTCGTGAAGTTGAGCCTGG
* * *
31085 AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGTAAGTTATATTGCTCCGAGTCCAATATCC
65 AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGTAAGTTGTATTGTTTCGAGTCCAATATCC
* *
31150 TCCGCCGTGAAGTTGAAATTGGCTCTGGAACTGGGAA
130 TCCG-CGTGAAGTTGAAATTGGTTCTGAAACTGGGAA
31187 ATTGTTTGTT
Statistics
Matches: 375, Mismatches: 34, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
246 34 0.09
247 54 0.14
248 3 0.01
250 2 0.01
251 3 0.01
252 276 0.74
253 3 0.01
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (250 bp):
GCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGTGGCCCCTTCGTCGTGAAGTTGAGCCTGGA
ATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGTAAGTTGTATTGTTTCGAGTCCAATATCCT
CCGCGTGAAGTTGAAATTGGTTCTGAAACTGGGAAGTTTATTGACAGACACTCCTTCTCTGAGTT
GGATATCCTTCGCCGTGAAGTTGAAATCCAATCTAGAGATGGATGCTGCTTGTGT
Found at i:31340 original size:110 final size:109
Alignment explanation
Indices: 31137--31395 Score: 371
Period size: 110 Copynumber: 2.4 Consensus size: 109
31127 ATATTGCTCC
* ** * *
31137 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTG---GAACTGGGAAATTGTTTGTTGA
1 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAAGAAATGGAAAATTGTTTGTTGA
*
31199 CAATCAGCCTCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTT
66 CAATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTT
* * *
31243 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAAGAAATTGAAAAGTTGTTTGTTG
1 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAAGAAATGGAAAA-TTGTTTGTTG
* *
31308 ACAATCAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTT
65 ACAATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTT
* *
31353 GGGTCCAATATCTTTCGATGTGAAGTTGAAATTGGCTCTGAAA
1 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAA
31396 TTGGGAAGCC
Statistics
Matches: 135, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
106 36 0.27
109 8 0.06
110 91 0.67
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (109 bp):
GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAAGAAATGGAAAATTGTTTGTTGA
CAATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTT
Found at i:35118 original size:12 final size:13
Alignment explanation
Indices: 35101--35129 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
35091 TTTATTTGCG
35101 AAAATTAAAA-TT
1 AAAATTAAAATTT
35113 AAAATTAAAATTT
1 AAAATTAAAATTT
35126 AAAA
1 AAAA
35130 AACTCGATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:35315 original size:12 final size:11
Alignment explanation
Indices: 35290--35370 Score: 56
Period size: 12 Copynumber: 7.0 Consensus size: 11
35280 GGAAAAAGAA
*
35290 AATAATAAAAT
1 AATAAAAAAAT
35301 AATAAAAATAAT
1 AATAAAAA-AAT
* *
35313 AATAAAAGATT
1 AATAAAAAAAT
* *
35324 AGTTAAAAAAAC
1 A-ATAAAAAAAT
35336 AA-ACAAATAAAT
1 AATA-AAA-AAAT
*
35348 AAGAATAAAAAT
1 AATAA-AAAAAT
35360 AATAAAAAAAT
1 AATAAAAAAAT
35371 GTAGTAAAGT
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
10 1 0.02
11 19 0.35
12 31 0.57
13 3 0.06
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (11 bp):
AATAAAAAAAT
Found at i:36328 original size:34 final size:33
Alignment explanation
Indices: 36290--36356 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
36280 GCTGTTTGTT
* *
36290 CCCGTTGTGGGTTCTGTTGGTTTTTTGGATTCCC
1 CCCGTTGT-GGATCTGTTGGATTTTTGGATTCCC
*
36324 CCCGTTGTTGATCTGTTGGATTTTTGGATTCCC
1 CCCGTTGTGGATCTGTTGGATTTTTGGATTCCC
36357 ACAACATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 22 0.73
34 8 0.27
ACGTcount: A:0.06, C:0.21, G:0.27, T:0.46
Consensus pattern (33 bp):
CCCGTTGTGGATCTGTTGGATTTTTGGATTCCC
Found at i:36560 original size:15 final size:15
Alignment explanation
Indices: 36526--36561 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
36516 ACCTGCAAAC
*
36526 ATAATAATAAAAATA
1 ATAATAATAAAAAAA
*
36541 TTAATAATAAAAAAA
1 ATAATAATAAAAAAA
36556 ATAATA
1 ATAATA
36562 TTTTTTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAATAATAAAAAAA
Found at i:37143 original size:19 final size:20
Alignment explanation
Indices: 37106--37144 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
37096 TAGTAGTATC
37106 AATTTTATGAATTTAATTTA
1 AATTTTATGAATTTAATTTA
*
37126 AATTTTAT-AATTTTATTTA
1 AATTTTATGAATTTAATTTA
37145 TTATACACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
AATTTTATGAATTTAATTTA
Found at i:42150 original size:41 final size:41
Alignment explanation
Indices: 42085--42164 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
42075 ACAGATGGGC
* *
42085 ATGGGACCCGAATCCGACGGGTTCCAACCAGACCCGACCCG
1 ATGGGACCCGAATCCGACGAGTTCCAACCAGACCAGACCCG
*
42126 ATGGGACCCGAATCTGACGAGTTCCAACCAGACCAGACC
1 ATGGGACCCGAATCCGACGAGTTCCAACCAGACCAGACC
42165 TGACCCGATC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.28, C:0.36, G:0.25, T:0.11
Consensus pattern (41 bp):
ATGGGACCCGAATCCGACGAGTTCCAACCAGACCAGACCCG
Found at i:44410 original size:14 final size:13
Alignment explanation
Indices: 44389--44427 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
44379 AATAGAAGAT
44389 AATAAATAAAAAA
1 AATAAATAAAAAA
*
44402 AATAGAATAAAAGA
1 AATA-AATAAAAAA
*
44416 AATAATTAAAAA
1 AATAAATAAAAA
44428 TAAAGAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (13 bp):
AATAAATAAAAAA
Found at i:44418 original size:23 final size:24
Alignment explanation
Indices: 44373--44436 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 24
44363 GTGCAAAAAC
* * *
44373 ATAACAAATAGAAGATAATAAATA
1 ATAAAAAATAGAAGAAAAGAAATA
*
44397 A-AAAAAATAGAATAAAAGAAATA
1 ATAAAAAATAGAAGAAAAGAAATA
*
44420 ATTAAAAATA-AAGAAAA
1 ATAAAAAATAGAAGAAAA
44437 TTTAAATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
23 25 0.76
24 8 0.24
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (24 bp):
ATAAAAAATAGAAGAAAAGAAATA
Found at i:45211 original size:23 final size:24
Alignment explanation
Indices: 45167--45211 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
45157 ATGTTGTTTC
45167 TTGGTTTTGTTTTGGTGTTTGGCT
1 TTGGTTTTGTTTTGGTGTTTGGCT
45191 TTGGTTTT-TTGTT-GTGTTTGG
1 TTGGTTTTGTT-TTGGTGTTTGG
45212 TCTCTGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.00, C:0.02, G:0.33, T:0.64
Consensus pattern (24 bp):
TTGGTTTTGTTTTGGTGTTTGGCT
Found at i:45767 original size:17 final size:16
Alignment explanation
Indices: 45730--45761 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
45720 TGAAACAAAA
45730 AATAAAAATAAGTAAT
1 AATAAAAATAAGTAAT
45746 AATAAAAATAA-TAAT
1 AATAAAAATAAGTAAT
45761 A
1 A
45762 TAATAACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (16 bp):
AATAAAAATAAGTAAT
Found at i:45846 original size:37 final size:36
Alignment explanation
Indices: 45792--46102 Score: 211
Period size: 37 Copynumber: 8.6 Consensus size: 36
45782 AAAAATTTAT
*
45792 TTTTTAAAAAACCATATAATATAAATTTTTAAAAATG
1 TTTTT-AAAAACTATATAATATAAATTTTTAAAAATG
*
45829 TTTTTTAAAAACTATATATTATATATAAATTTTCAAAAATG
1 -TTTTTAAAAAC--TATA-TA-ATATAAATTTTTAAAAATG
* *
45870 TTTTTTTAAAACTATAT-A-AT---TTTTAAAAAATG
1 -TTTTTAAAAACTATATAATATAAATTTTTAAAAATG
45902 TTTTTAAAAAC----T-ATAT-AATTTTTAAAAATG
1 TTTTTAAAAACTATATAATATAAATTTTTAAAAATG
* *
45932 -TTTTAAAAATTATATATTATATATAAGTTTTCAAAAATG
1 TTTTTAAAAACTATATA--ATATA-AA-TTTTTAAAAATG
* * * *
45971 TTTTCAAAAACTATATATTATATAAGTTTTCAAAATG
1 TTTTTAAAAACTATATAATATA-AATTTTTAAAAATG
* *
46008 ATTTTAAAAACTATATATTATATATATTTTCT-AAAATG
1 TTTTTAAAAACTATATA--ATATAAATTTT-TAAAAATG
* * * * *
46046 -TTTAAAAAACTATATATTATATAGTTTTCAAACATG
1 TTTTTAAAAACTATATAATATA-AATTTTTAAAAATG
*
46082 -TTTTAAAAACTATATATTATA
1 TTTTTAAAAACTATATAATATA
46103 TAAGTATTTT
Statistics
Matches: 224, Mismatches: 26, Indels: 48
0.75 0.09 0.16
Matches are distributed among these distances:
27 2 0.01
28 2 0.01
29 9 0.04
30 11 0.05
31 10 0.04
32 11 0.05
33 1 0.00
35 6 0.03
36 34 0.15
37 45 0.20
38 25 0.11
39 23 0.10
40 16 0.07
41 29 0.13
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (36 bp):
TTTTTAAAAACTATATAATATAAATTTTTAAAAATG
Found at i:45899 original size:32 final size:31
Alignment explanation
Indices: 45850--45947 Score: 130
Period size: 31 Copynumber: 3.2 Consensus size: 31
45840 CTATATATTA
* *
45850 TATATAAATTTTCAAAAATGTTTTTTTAAAAC
1 TATAT-AATTTTTAAAAATGTTTTTTAAAAAC
45882 TATATAATTTTTAAAAAATG-TTTTTAAAAAC
1 TATATAATTTTT-AAAAATGTTTTTTAAAAAC
*
45913 TATATAATTTTTAAAAATG--TTTTAAAAAT
1 TATATAATTTTTAAAAATGTTTTTTAAAAAC
45942 TATATA
1 TATATA
45948 TTATATATAA
Statistics
Matches: 62, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
29 15 0.24
30 7 0.11
31 28 0.45
32 12 0.19
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (31 bp):
TATATAATTTTTAAAAATGTTTTTTAAAAAC
Found at i:45986 original size:38 final size:37
Alignment explanation
Indices: 45913--46145 Score: 276
Period size: 37 Copynumber: 6.2 Consensus size: 37
45903 TTTTAAAAAC
* *
45913 TATATAA-TTTTTAAAAATGTTTTAAAAATTATATATT
1 TATATAAGTTTTCAAAAATGTTTTAAAAACTATATA-T
45950 ATATATAAGTTTTCAAAAATGTTTTCAAAAACTATATAT
1 -TATATAAGTTTTCAAAAATGTTTT-AAAAACTATATAT
45989 TATATAAGTTTTC-AAAATGATTTTAAAAACTATATAT
1 TATATAAGTTTTCAAAAATG-TTTTAAAAACTATATAT
* *
46026 TATATATA-TTTTCTAAAATGTTTAAAAAACTATATAT
1 TATATA-AGTTTTCAAAAATGTTTTAAAAACTATATAT
*
46063 TATAT-AGTTTTCAAACATGTTTTAAAAACTATATAT
1 TATATAAGTTTTCAAAAATGTTTTAAAAACTATATAT
*** *
46099 TATATAAGTATTTTCAAAAACCATTTGAAAACTATAATAT
1 TATATAAG--TTTTCAAAAATGTTTTAAAAACTAT-ATAT
46139 ATATATA
1 -TATATA
46146 TATATATATA
Statistics
Matches: 173, Mismatches: 11, Indels: 19
0.85 0.05 0.09
Matches are distributed among these distances:
35 1 0.01
36 31 0.18
37 53 0.31
38 31 0.18
39 36 0.21
40 15 0.09
41 6 0.03
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (37 bp):
TATATAAGTTTTCAAAAATGTTTTAAAAACTATATAT
Found at i:46862 original size:84 final size:84
Alignment explanation
Indices: 46709--48001 Score: 1433
Period size: 84 Copynumber: 15.4 Consensus size: 84
46699 ATTTTGTTAA
* * * * ** * * *
46709 CAGATAACCCTTCTTGCCTTGAGTTATGCTGTAAAATTACGTGCCTTTGAGATGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATACTG-CAAATGATATGCCTTTGAGCTGAGCGTAGTCGA
*
46774 ACTCAAAGGTCTTTGGTTGG
65 ACTCGAAGGTCTTTGGTTGG
* * * *
46794 CAGATACCCCTTCTCGACTTAAGTTATACTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGAA
* * *
46859 CTCAAAGGTCTCTCGTTGG
66 CTCGAAGGTCTTTGGTTGG
* ** * ** * * * *
46878 CAAATAACCCTTCTTTCCTTGAGCTATGTTACAAATAATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGAA
*
46943 CTCAAAGGTCTTTGGTTGG
66 CTCGAAGGTCTTTGGTTGG
* * * * *
46962 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATTATATGTCTTTGAGCTGAGCGTAGTCAAA
1 CAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGAA
**
47027 CTCGAAGGTCTTTTATTGG
66 CTCGAAGGTCTTTGGTTGG
* * * * * * *
47046 CAGATAGCCCTTCTCGCCTTGAGCTATATTGCAAATGATATGCATTTGAGCTGAGTGTAATCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGAA
47111 CTCGAAGGTCTTTGGTTGG
66 CTCGAAGGTCTTTGGTTGG
*
47130 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGAA
*
47195 CTCGAATGTCTTTTGG-TGG
66 CTCGAAGGTC-TTTGGTTGG
* * * * *
47214 CAGATAACCTTTATAGCCTTGA-TCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAA
1 CAGATAACCCTTCTAGCCTTGAGT-TATACTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGA
47278 ACTCGAAGGTCTTTGGTTGG
65 ACTCGAAGGTCTTTGGTTGG
* * * *
47298 CAGATAACCCTTATAGCCTTGAGTTATGCTGCAAATGATGTGCC-TTGAAACTGAGCGTAGTCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCTTTG-AGCTGAGCGTAGTCGA
47362 ACTCGAAGGTCTTTTGG-TGG
65 ACTCGAAGGTC-TTTGGTTGG
* * * ** *
47382 GAGATAGCCCTTCTAGCCTTGAGCTATACTATAAATGATGTGCC-TTGAAGCTGAGCGTAGTCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCTTTG-AGCTGAGCGTAGTCGA
47446 ACTCGAAGGTCTTTGGTTGG
65 ACTCGAAGGTCTTTGGTTGG
* * * *
47466 CAAATAACCCTTCTAGCCTTGAGTTATGA-TGCAAATGATATACCTTGGAGCTGAGCGTAGTCAA
1 CAGATAACCCTTCTAGCCTTGAGTTAT-ACTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGA
*
47530 ACTCGAAGGTCTTTTAG-TGG
65 ACTCGAAGGTC-TTTGGTTGG
* * * *
47550 CAGATAACCCTTTTAGCCTTGAGCTATGCTGCAAATGATGA-GCC-TTGAAGCTGAGCGTAGTCA
1 CAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGAT-ATGCCTTTG-AGCTGAGCGTAGTCG
* *
47613 AACTCGAAAGTCTTTGGTTGA
64 AACTCGAAGGTCTTTGGTTGG
* * * *
47634 CAGATAAGCCTTCTAGCCTTGAGTTATACTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGAA
* * *
47699 CTCAAAGGTATTT-TTGTGG
66 CTCGAAGGTCTTTGGT-TGG
* * * * *
47718 AAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATGTGTCTTGGAGCTGAGCATAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGAA
** *
47783 CTTAAAGGTCTTTGGTTGA
66 CTCGAAGGTCTTTGGTTGG
* * * * * * *
47802 CAGATAACCCTTATAACCTTGAGTTATGCTACAAATGATATGCCTTAGGGCTGAGCGTAGTCAAA
1 CAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGAA
*
47867 CTCGAAGGTCTTTTGTTGG
66 CTCGAAGGTCTTTGGTTGG
* * * * * * * *
47886 CAAATAACCCTTCTTGCCTTGAGTTAT-CTTGCAAAAGTATCTACATTGGAGCTTAGCGTAGTCG
1 CAGATAACCCTTCTAGCCTTGAGTTATAC-TGCAAATG-ATATGCCTTTGAGCTGAGCGTAGTCG
* *
47950 AACTCGAAGGTCTTT-GCTGA
64 AACTCGAAGGTCTTTGGTTGG
*
47970 CAGATAACCCTTCTCA-CCTTGAGTTATGCTGC
1 CAGATAACCCTTCT-AGCCTTGAGTTATACTGC
48002 TGATAGTTTC
Statistics
Matches: 1025, Mismatches: 161, Indels: 45
0.83 0.13 0.04
Matches are distributed among these distances:
83 21 0.02
84 921 0.90
85 83 0.08
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (84 bp):
CAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTGGTTGG
Found at i:46949 original size:168 final size:168
Alignment explanation
Indices: 46700--48001 Score: 1585
Period size: 168 Copynumber: 7.7 Consensus size: 168
46690 AACTCGATAA
** * * * * * * *
46700 TTTTGTTAACAGATAACCCTTCTTGCCTTGAGTTATGCTGTAAAATTACGTGCCTTTGAGATGAG
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATACTG-CAAATGATGTGCCTTGGAGCTGAG
* * * * * * *
46765 TGTAATCGAACTCAAAGGTCTTTGGTTGGCAGATACCCCTTCTCGACTTAAGTTATACTGCAAAT
65 CGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
*
46830 GATATGCCTTTGAGCTGAGCGTAGTCGAACTCAAAGGTC
130 GATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTC
* * * * ** * *
46869 TCTCGTTGGCAAATAACCCTTCTTTCCTTGAGCTATGTTACAAATAATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGC
* *
46934 GTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATT
66 GTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
* *
46999 ATATGTCTTTGAGCTGAGCGTAGTCAAACTCGAAGGTC
131 ATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTC
* * * * * * * *
47037 TTTTATTGGCAGATAGCCCTTCTCGCCTTGAGCTATATTGCAAATGATATGCATTTGAGCTGAGT
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGC
* *
47102 GTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
66 GTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
*
47167 ATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAATGTC
131 ATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTC
* * * * *
47205 TTTTGGTGGCAGATAACCTTTATAGCCTTGATCTATACTGCAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGC
* * *
47270 GTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTATAGCCTTGAGTTATGCTGCAAATG
66 GTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
* *
47335 ATGTGCC-TTGAAACTGAGCGTAGTCGAACTCGAAGGTC
131 ATATGCCTTTG-AGCTGAGCGTAGTCGAACTCGAAGGTC
* * * * ** *
47373 TTTTGGTGGGAGATAGCCCTTCTAGCCTTGAGCTATACTATAAATGATGTGCCTTGAAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGC
* * *
47438 GTAGTCGAACTCGAAGGTCTTTGGTTGGCAAATAACCCTTCTAGCCTTGAGTTATGATGCAAATG
66 GTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
* * *
47503 ATATACCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTC
131 ATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTC
* * *
47541 TTTTAG-TGGCAGATAACCCTT-TTAGCCTTGAGCTATGCTGCAAATGATGAGCCTTGAAGCTGA
1 TTTT-GTTGGCAGATAACCCTTCTT-GCCTTGAGCTATACTGCAAATGATGTGCCTTGGAGCTGA
* * * * *
47604 GCGTAGTCAAACTCGAAA-GTCTTTGGTTGACAGATAAGCCTTCTAGCCTTGAGTTATACTGTAA
64 GCGTAGTCGAACTC-AAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAA
* * * *
47668 ATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTA
128 ATGATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTC
* * * *
47709 TTTT-TGTGGAAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATGTGTCTTGGAGCTGAG
1 TTTTGT-TGGCAGATAACCCTTCTTGCCTTGAGCTATACTGCAAATGATGTGCCTTGGAGCTGAG
* * * * * *
47773 CATAGTCGAACTTAAAGGTCTTTGGTTGACAGATAACCCTTATAACCTTGAGTTATGCTACAAAT
65 CGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
* * *
47838 GATATGCCTTAGGGCTGAGCGTAGTCAAACTCGAAGGTC
130 GATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTC
* * * * * * *
47877 TTTTGTTGGCAAATAACCCTTCTTGCCTTGAGTTAT-CTTGCAAAAGTATCTACATTGGAGCTTA
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATAC-TGCAAATG-ATGTGCCTTGGAGCTGA
* * *
47941 GCGTAGTCGAACTCGAAGGTCTTT-GCTGACAGATAACCCTTCTCA-CCTTGAGTTATGCTGC
64 GCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCT-AGCCTTGAGTTATGCTGC
48002 TGATAGTTTC
Statistics
Matches: 981, Mismatches: 139, Indels: 27
0.86 0.12 0.02
Matches are distributed among these distances:
167 8 0.01
168 901 0.92
169 72 0.07
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (168 bp):
TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGC
GTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
ATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTC
Found at i:48652 original size:5 final size:5
Alignment explanation
Indices: 48642--48666 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
48632 TCAGGCTTAC
48642 AATCA AATCA AATCA AATCA AATCA
1 AATCA AATCA AATCA AATCA AATCA
48667 TAAACATGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
AATCA
Found at i:49293 original size:95 final size:95
Alignment explanation
Indices: 49092--49354 Score: 305
Period size: 95 Copynumber: 2.7 Consensus size: 95
49082 GGCTACCTGA
* * * * * * * *
49092 ATCCATAAAGCCGGAGTGTTTAACCAATTGCTCTAGATGGACAATTTAATATCATTGTATAG-AT
1 ATCCATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAA-CTCA-AGC-TT-TATTGTAT
* *
49156 ATTATAATCGCCTTTATCAGGCTAGCTGAATATT
62 ATTATAATCACCTTTATCAGGCTAACTGAATATT
49190 ATCCATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
*
49255 TAATCACCTTTATCAGGCTAACTGAATCTT
66 TAATCACCTTTATCAGGCTAACTGAATATT
* * * * * *
49285 ATTCATAAAG-TCGCGTCGCTTAACCAATTGCTTTAGTGGGACAACTCAAGCTTTATTGTATATA
1 ATCCATAAAGCT-GGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT-
49349 TATAAT
64 TATAAT
49355 ATTATAATCT
Statistics
Matches: 145, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
94 5 0.03
95 90 0.62
96 8 0.06
97 2 0.01
98 40 0.28
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (95 bp):
ATCCATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
TAATCACCTTTATCAGGCTAACTGAATATT
Found at i:52815 original size:4 final size:4
Alignment explanation
Indices: 52806--52848 Score: 50
Period size: 4 Copynumber: 10.0 Consensus size: 4
52796 CAAATAGAAG
*
52806 ATAA ATAA ATAAA ATAT ATAA ATAAA ATAAA ATAA ATAA ATAA
1 ATAA ATAA AT-AA ATAA ATAA AT-AA AT-AA ATAA ATAA ATAA
52849 GCAAAGAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 22 0.63
5 13 0.37
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:52820 original size:9 final size:9
Alignment explanation
Indices: 52808--52845 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
52798 AATAGAAGAT
52808 AAATAAATA
1 AAATAAATA
*
52817 AAATATAT-
1 AAATAAATA
52825 AAATAAAATA
1 AAAT-AAATA
52835 AAATAAATA
1 AAATAAATA
52844 AA
1 AA
52846 TAAGCAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 4 0.16
9 17 0.68
10 4 0.16
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAATAAATA
Found at i:52835 original size:18 final size:18
Alignment explanation
Indices: 52806--52848 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
52796 CAAATAGAAG
*
52806 ATAAAT-AAATAAAATAT
1 ATAAATAAAATAAAATAA
52823 ATAAATAAAATAAAATAA
1 ATAAATAAAATAAAATAA
52841 ATAAATAA
1 ATAAATAA
52849 GCAAAGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
ATAAATAAAATAAAATAA
Found at i:52885 original size:30 final size:30
Alignment explanation
Indices: 52808--52887 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 30
52798 AATAGAAGAT
* * *
52808 AAATAAATAAAATATATAAATAAAATAAAAT
1 AAATAAATAAAA-AAAGAAATAAAATAAAAG
** *
52839 AAATAAATAAGCAAAGAAATATAATAAAAG
1 AAATAAATAAAAAAAGAAATAAAATAAAAG
52869 AAAT-AATAAAAAAAAGAAA
1 AAATAAAT-AAAAAAAGAAA
52888 ATTTAAATAA
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 3 0.08
30 27 0.68
31 10 0.25
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.19
Consensus pattern (30 bp):
AAATAAATAAAAAAAGAAATAAAATAAAAG
Found at i:54092 original size:22 final size:23
Alignment explanation
Indices: 54065--54124 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
54055 CCTGAAACAA
*
54065 AAAATAATAATAAGT-AAT-AATA
1 AAAATAAAAATAA-TAAATAAATA
54087 AAAATAAAAATAATAAATAAATA
1 AAAATAAAAATAATAAATAAATA
* *
54110 AATATAAAAAAAATA
1 AAAATAAAAATAATA
54125 TTTTTTCTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.03
22 15 0.45
23 17 0.52
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (23 bp):
AAAATAAAAATAATAAATAAATA
Found at i:54100 original size:15 final size:15
Alignment explanation
Indices: 54080--54124 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
54070 AATAATAAGT
54080 AATAATAAAAATAAA
1 AATAATAAAAATAAA
54095 AATAATAAATAAATAAA
1 AATAAT-AA-AAATAAA
* *
54112 TATAAAAAAAATA
1 AATAATAAAAATA
54125 TTTTTTCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 11 0.42
16 4 0.15
17 11 0.42
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (15 bp):
AATAATAAAAATAAA
Found at i:54105 original size:29 final size:28
Alignment explanation
Indices: 54064--54119 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
54054 CCCTGAAACA
*
54064 AAAAATAATAATAAGT-AATAATAAAAAT
1 AAAAATAATAATAAATAAAT-ATAAAAAT
54092 AAAAATAATAAATAAATAAATATAAAAA
1 AAAAATAAT-AATAAATAAATATAAAAA
54120 AAATATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 9 0.36
29 13 0.52
30 3 0.12
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (28 bp):
AAAAATAATAATAAATAAATATAAAAAT
Found at i:54239 original size:30 final size:29
Alignment explanation
Indices: 54183--54277 Score: 113
Period size: 28 Copynumber: 3.2 Consensus size: 29
54173 CTATATATTA
*
54183 TATATAAATTTTCAAAAATATTTTTAAAAAAT
1 TATAT-AATTTTTAAAAA-ATTTTT-AAAAAT
* *
54215 TATATAATTTTTAAAAAGTTTTTAAAAAC
1 TATATAATTTTTAAAAAATTTTTAAAAAT
54244 TA-ATAA-TTTTAAAAAATGTTTTAAAAAT
1 TATATAATTTTTAAAAAAT-TTTTAAAAAT
54272 TATATA
1 TATATA
54278 TTATATATAA
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
27 10 0.18
28 15 0.27
29 10 0.18
30 5 0.09
31 11 0.20
32 5 0.09
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (29 bp):
TATATAATTTTTAAAAAATTTTTAAAAAT
Found at i:54368 original size:69 final size:69
Alignment explanation
Indices: 54135--54472 Score: 219
Period size: 69 Copynumber: 4.9 Consensus size: 69
54125 TTTTTTCTAA
* * * *
54135 AAAAAC-ATATAATATAAATTTTCAAAAATGTTTT-AAAACTATATATTATATATAAATTTTCAA
1 AAAAACTATATTATAT-AA-TTTCTAAAATGTTTTAAAAAATATATA-T-TATATAAGTTTTC-A
*
54198 AAATATTTT
61 AAATGTTTT
* * * * * **
54207 TAAAA--A-ATTATATAATTTTTAAAAAGTTTTTAAAAA-CTA-A-TA-AT---TTTAAAAAATG
1 AAAAACTATATTATATAATTTCTAAAATGTTTTAAAAAATATATATTATATAAGTTTTCAAAATG
54262 TTTT
66 TTTT
* *
54266 AAAAATTATATATTATATATAAAATTTCAAAAATGTTTTCAAAAAAATATATATTATATAAGTTT
1 AAAAA--CTATA-T-TATAT--AATTTCTAAAATGTTTT--AAAAAATATATATTATATAAGTTT
54331 TCAAAATGATTTT
58 TCAAAATG-TTTT
* *
54344 -AAAACTATATT-TAT-ATTTCTAAAATGTTTTAAAAATTATATA-TATAT-AGTTTTCAAAGGT
1 AAAAACTATATTATATAATTTCTAAAATGTTTTAAAAAATATATATTATATAAGTTTTCAAA-AT
54404 GTTTT
65 GTTTT
* *
54409 AAAAACTATATTATATACATTT-TCAAAATGTTTTTAAAAAT-TATATTATATACATTTTTCAAA
1 AAAAACTATATTATATA-ATTTCT-AAAATGTTTTAAAAAATATATATTATATA-AGTTTTCAAA
54472 A
63 A
54473 ACTGTTTGCA
Statistics
Matches: 211, Mismatches: 26, Indels: 60
0.71 0.09 0.20
Matches are distributed among these distances:
59 13 0.06
60 3 0.01
63 3 0.01
64 3 0.01
65 15 0.07
66 23 0.11
67 15 0.07
68 33 0.16
69 45 0.21
70 11 0.05
71 12 0.06
72 8 0.04
73 3 0.01
74 3 0.01
75 4 0.02
77 13 0.06
78 4 0.02
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.44
Consensus pattern (69 bp):
AAAAACTATATTATATAATTTCTAAAATGTTTTAAAAAATATATATTATATAAGTTTTCAAAATG
TTTT
Found at i:54460 original size:35 final size:34
Alignment explanation
Indices: 54141--54472 Score: 203
Period size: 35 Copynumber: 9.6 Consensus size: 34
54131 CTAAAAAAAC
* *
54141 ATATAATATAAATTTTCAAAAATG-TTTTAAAACTAT
1 ATATTATAT-AATTTTC-AAAATGTTTTTAAAAAT-T
*
54177 ATATTATATATAAATTTTCAAAAATATTTTT-AAAA--
1 ATA-T-TATAT-AATTTTC-AAAATGTTTTTAAAAATT
* * *
54212 A-ATTATATAATTTTTAAAAAGTTTTTAAAAACT
1 ATATTATATAATTTTCAAAATGTTTTTAAAAATT
**
54245 A-A-TA-AT--TTTAAAAAATG-TTTTAAAAATTAT
1 ATATTATATAATTTTCAAAATGTTTTTAAAAA-T-T
* *
54275 ATATTATATATAAAATTTCAAAAATGTTTTCAAAAAAATAT
1 ATA-T-TATAT-AATTTTC-AAAATGTTTT--TAAAAAT-T
* *
54316 ATATTATATAAGTTTTCAAAATGATTTT-AAAACT
1 ATATTATATAA-TTTTCAAAATGTTTTTAAAAATT
54350 ATATT-TAT-A-TTTCTAAAATG-TTTTAAAAATT
1 ATATTATATAATTTTC-AAAATGTTTTTAAAAATT
* * *
54381 ATATATATATAGTTTTC-AAAGGTGTTTTAAAAACT
1 ATAT-TATATAATTTTCAAAATGT-TTTTAAAAATT
54416 ATATTATATACATTTTCAAAATGTTTTTAAAAATT
1 ATATTATATA-ATTTTCAAAATGTTTTTAAAAATT
54451 ATATTATATACATTTTTCAAAA
1 ATATTATATA-A-TTTTCAAAA
54473 ACTGTTTGCA
Statistics
Matches: 239, Mismatches: 25, Indels: 64
0.73 0.08 0.20
Matches are distributed among these distances:
28 9 0.04
29 8 0.03
30 19 0.08
31 28 0.12
32 9 0.04
33 13 0.05
34 15 0.06
35 52 0.22
36 17 0.07
37 1 0.00
38 34 0.14
39 19 0.08
40 4 0.02
41 6 0.03
42 5 0.02
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.45
Consensus pattern (34 bp):
ATATTATATAATTTTCAAAATGTTTTTAAAAATT
Found at i:54500 original size:2 final size:2
Alignment explanation
Indices: 54493--54527 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
54483 ACTAAAACTC
54493 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54528 GCGAAATGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.