Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003045.1 Hibiscus syriacus cultivar Beakdansim tig00006338_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: 84829
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:485 original size:2 final size:2
Alignment explanation
Indices: 473--514 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
463 ACTTTATCTA
*
473 AT AT A- AT AT AT AT AT AT AT AA AT AT AT -T 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
513 AT
1 AT
515 TATTTTTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:498 original size:21 final size:21
Alignment explanation
Indices: 472--513 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
462 GACTTTATCT
472 AATATAATATATATATATATA
1 AATATAATATATATATATATA
*
493 AATATATTATATATATATATA
1 AATATAATATATATATATATA
514 TTATTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATATAATATATATATATATA
Found at i:515 original size:15 final size:15
Alignment explanation
Indices: 473--517 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
463 ACTTTATCTA
473 ATATA-ATATATA-T
1 ATATATATATATATT
*
486 ATATATAAATATATT
1 ATATATATATATATT
501 ATATATATATATATT
1 ATATATATATATATT
516 AT
1 AT
518 TTTTTCACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 5 0.18
14 6 0.21
15 17 0.61
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATATATATATATT
Found at i:1851 original size:56 final size:57
Alignment explanation
Indices: 1761--1875 Score: 196
Period size: 56 Copynumber: 2.0 Consensus size: 57
1751 GTCCTCTAAA
1761 TTATTTTGTTGTTTGAACAAGTGCGTTATGCATTGGAAGTTGGAACTGAAATATTATACC
1 TTATTTTGTTGTTTG---AAGTGCGTTATGCATTGGAAGTTGGAACTGAAATATTATACC
1821 TTATTTTGTTGTTTG-AGTGCGTTATGCATTGGAAGTTGGAACTGAAATATTATAC
1 TTATTTTGTTGTTTGAAGTGCGTTATGCATTGGAAGTTGGAACTGAAATATTATAC
1876 TTGATGTTAT
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
56 40 0.73
60 15 0.27
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.42
Consensus pattern (57 bp):
TTATTTTGTTGTTTGAAGTGCGTTATGCATTGGAAGTTGGAACTGAAATATTATACC
Found at i:1889 original size:56 final size:56
Alignment explanation
Indices: 1780--1889 Score: 186
Period size: 56 Copynumber: 2.0 Consensus size: 56
1770 TGTTTGAACA
* *
1780 AGTGCGTTATGCATTGGAAGTTGGAACTGAAATATTATACCTTATTTTGTTGTTTG
1 AGTGCGTTATGCATTGGAAGTTGGAACTGAAATATTATACCTTATGTTATTGTTTG
1836 AGTGCGTTATGCATTGGAAGTTGGAACTGAAATATTATA-CTTGATGTTATTGTT
1 AGTGCGTTATGCATTGGAAGTTGGAACTGAAATATTATACCTT-ATGTTATTGTT
1890 GAAAGATACT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
55 3 0.06
56 48 0.94
ACGTcount: A:0.26, C:0.08, G:0.24, T:0.42
Consensus pattern (56 bp):
AGTGCGTTATGCATTGGAAGTTGGAACTGAAATATTATACCTTATGTTATTGTTTG
Found at i:5582 original size:15 final size:15
Alignment explanation
Indices: 5562--5592 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5552 CATGGAAGCC
5562 AAAAAAAGTTCATAT
1 AAAAAAAGTTCATAT
5577 AAAAAAAGTTCATAT
1 AAAAAAAGTTCATAT
5592 A
1 A
5593 CCAACAGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.26
Consensus pattern (15 bp):
AAAAAAAGTTCATAT
Found at i:7015 original size:14 final size:15
Alignment explanation
Indices: 6996--7027 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
6986 CTTTTTTTAA
6996 ATAATTTTAAAA-AT
1 ATAATTTTAAAAGAT
7010 ATAATTTTAAAAGAT
1 ATAATTTTAAAAGAT
7025 ATA
1 ATA
7028 TTAATTTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
ATAATTTTAAAAGAT
Found at i:7323 original size:21 final size:21
Alignment explanation
Indices: 7291--7345 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
7281 ATCGTGATTG
*
7291 CGGCCGTCGCGGGCGCTATTA
1 CGGCCATCGCGGGCGCTATTA
* * *
7312 CGGTCATCGCGGACGCTATTG
1 CGGCCATCGCGGGCGCTATTA
*
7333 CGGCCGTCGCGGG
1 CGGCCATCGCGGG
7346 TAACTCGGAC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.09, C:0.33, G:0.40, T:0.18
Consensus pattern (21 bp):
CGGCCATCGCGGGCGCTATTA
Found at i:8790 original size:2 final size:2
Alignment explanation
Indices: 8785--8821 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
8775 GTCATTTAGG
8785 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8822 TCTAAATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10045 original size:26 final size:24
Alignment explanation
Indices: 10006--10073 Score: 59
Period size: 26 Copynumber: 2.8 Consensus size: 24
9996 ATAATATAAT
**
10006 AAAACAAACTCAAATAAAGTGAAATA
1 AAAACAAAAACAAATAAAGT-AAA-A
10032 AAAACAAAAACAAA-ATAAGTAAAA
1 AAAACAAAAACAAATA-AAGTAAAA
*
10056 AAAA-AGAGAACAAATAAA
1 AAAACA-AAAACAAATAAA
10074 CAAAATAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
23 1 0.03
24 14 0.39
25 5 0.14
26 16 0.44
ACGTcount: A:0.74, C:0.09, G:0.07, T:0.10
Consensus pattern (24 bp):
AAAACAAAAACAAATAAAGTAAAA
Found at i:10144 original size:2 final size:2
Alignment explanation
Indices: 10137--10161 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10127 CAAAAAGGTA
10137 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 A
10162 ATAAGATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10274 original size:2 final size:2
Alignment explanation
Indices: 10267--10297 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
10257 AAATAAAATA
10267 AT 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 AT A
10298 AACGTTAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10379 original size:20 final size:18
Alignment explanation
Indices: 10335--10407 Score: 60
Period size: 18 Copynumber: 3.9 Consensus size: 18
10325 CCAAAAAGAA
*
10335 AAAATAGAGAAAAATAAAT
1 AAAATAGA-TAAAATAAAT
10354 AAAATAGATAAAATAAAT
1 AAAATAGATAAAATAAAT
* *
10372 AGAAAATATATATAAT-AAT
1 --AAAATAGATAAAATAAAT
10391 AATAATA-ATAATAATAA
1 AA-AATAGATAA-AATAA
10408 TAGGGACAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
17 5 0.11
18 16 0.36
19 12 0.27
20 12 0.27
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (18 bp):
AAAATAGATAAAATAAAT
Found at i:10391 original size:3 final size:3
Alignment explanation
Indices: 10383--10409 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
10373 GAAAATATAT
10383 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
10410 GGGACAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:13321 original size:11 final size:10
Alignment explanation
Indices: 13306--13366 Score: 53
Period size: 8 Copynumber: 6.6 Consensus size: 10
13296 CCTTATTTCC
13306 TTTTTTCCTT
1 TTTTTTCCTT
13316 CTTTTTTCC--
1 -TTTTTTCCTT
13325 TTTTTTCC--
1 TTTTTTCCTT
*
13333 TTTTCT-CTT
1 TTTTTTCCTT
13342 TTTTTTCCTT
1 TTTTTTCCTT
*
13352 TTTTTT-ATT
1 TTTTTTCCTT
13361 TTTTTT
1 TTTTTT
13367 TGATTTGGGG
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
7 1 0.02
8 13 0.30
9 13 0.30
10 9 0.20
11 8 0.18
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTTCCTT
Found at i:13326 original size:27 final size:25
Alignment explanation
Indices: 13296--13351 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 25
13286 CTTGAACCCA
*
13296 CCTTATTTCCTTTTTTCCTTCTTTTTT
1 CCTTATTTCCTTTTCT-CTT-TTTTTT
*
13323 CCTTTTTTCCTTTTCTCTTTTTTTT
1 CCTTATTTCCTTTTCTCTTTTTTTT
13348 CCTT
1 CCTT
13352 TTTTTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 10 0.37
26 3 0.11
27 14 0.52
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (25 bp):
CCTTATTTCCTTTTCTCTTTTTTTT
Found at i:13336 original size:7 final size:8
Alignment explanation
Indices: 13296--13355 Score: 57
Period size: 8 Copynumber: 7.0 Consensus size: 8
13286 CTTGAACCCA
*
13296 CCTTATTT
1 CCTTTTTT
13304 CCTTTTTT
1 CCTTTTTT
13312 CCTTCTTTTTT
1 -C--CTTTTTT
13323 CCTTTTTT
1 CCTTTTTT
*
13331 CCTTTTCT
1 CCTTTTTT
*
13339 CTTTTTTTT
1 C-CTTTTTT
13348 CCTTTTTT
1 CCTTTTTT
13356 TTATTTTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
8 28 0.65
9 7 0.16
10 1 0.02
11 7 0.16
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (8 bp):
CCTTTTTT
Found at i:16913 original size:2 final size:2
Alignment explanation
Indices: 16908--16956 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
16898 AATAAAACTA
16908 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
16950 AT AT AT A
1 AT AT AT A
16957 AACGTTAGGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21055 original size:25 final size:25
Alignment explanation
Indices: 21014--21071 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
21004 AAATGTACTC
* *
21014 ATGGCAAGGCCCTTAGCTGAGGATTA
1 ATGG-AAGACCCTTAGCAGAGGATTA
*
21040 ATGGAAGACCCTTAGCAGATGATTA
1 ATGGAAGACCCTTAGCAGAGGATTA
21065 ATGGAAG
1 ATGGAAG
21072 CATAACACCC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 25 0.86
26 4 0.14
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (25 bp):
ATGGAAGACCCTTAGCAGAGGATTA
Found at i:21624 original size:20 final size:21
Alignment explanation
Indices: 21599--21640 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
21589 TTACACAAGG
21599 TAATCATTCAACTCT-TTTTT
1 TAATCATTCAACTCTGTTTTT
*
21619 TAATCATTCAGCTCTGTTTTT
1 TAATCATTCAACTCTGTTTTT
21640 T
1 T
21641 TCTTTATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.21, C:0.19, G:0.05, T:0.55
Consensus pattern (21 bp):
TAATCATTCAACTCTGTTTTT
Found at i:27805 original size:25 final size:25
Alignment explanation
Indices: 27775--27827 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
27765 ATTTGGTTGT
27775 TTTCCAATGAATTGCCTAATTTTGC
1 TTTCCAATGAATTGCCTAATTTTGC
*
27800 TTTCCAATGAATTGTCTAATTTTGC
1 TTTCCAATGAATTGCCTAATTTTGC
27825 TTT
1 TTT
27828 GAATTGACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.23, C:0.17, G:0.11, T:0.49
Consensus pattern (25 bp):
TTTCCAATGAATTGCCTAATTTTGC
Found at i:30647 original size:131 final size:128
Alignment explanation
Indices: 30494--30893 Score: 547
Period size: 127 Copynumber: 3.1 Consensus size: 128
30484 TATTTCAAGT
* *
30494 TAACTACTAACTTTTATTTTATTACACTCTAACCGTTATTTATTTATTTACTTATTGTTTCTAAT
1 TAACTACTAACTTTTATTTTATTGCACTCTAACCATTATTTATTTATTTA--TATT-TTTCTAAT
*
30559 ATTTTATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTTCAGACTCAG
63 ATTTGATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTTCAGACTCAG
30624 C
128 C
* *
30625 TAACTACTGACTTTTATTTTATTGCACTCTAACCATTATTTATTTATTTAT-TTATTCTAATATT
1 TAACTACTAACTTTTATTTTATTGCACTCTAACCATTATTTATTTATTTATATTTTTCTAATATT
* * * * *
30689 TGATTCGACCTTGTGGTGACCAGATCCGGTGTACGATCCACATTATTTTGGTTCGGACTCTGC
66 TGATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTTCAGACTCAGC
* * *
30752 TAACTACTAACTTTTATTTTATTGCACTCTAACCATTAATTAATTATTTA-ATATTTT-TATTAT
1 TAACTACTAACTTTTATTTTATTGCACTCTAACCATTATTTATTTATTTATAT-TTTTCTAATAT
* * * * **
30815 TCGATTTGACCTTGTGGTGATCAGATCAGGGGTATGATCCACATTATTATGGTTC-GAACTCTTC
65 TTGATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTTCAG-ACTCAGC
*
30879 TAACCACTAACTTTT
1 TAACTACTAACTTTT
30894 TTATATTTAT
Statistics
Matches: 242, Mismatches: 24, Indels: 10
0.88 0.09 0.04
Matches are distributed among these distances:
126 1 0.00
127 188 0.78
128 5 0.02
129 1 0.00
131 47 0.19
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.44
Consensus pattern (128 bp):
TAACTACTAACTTTTATTTTATTGCACTCTAACCATTATTTATTTATTTATATTTTTCTAATATT
TGATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTTCAGACTCAGC
Found at i:31016 original size:16 final size:16
Alignment explanation
Indices: 30997--31033 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
30987 TCTACTGACC
*
30997 GCTAACTTTTCTAACA
1 GCTAACCTTTCTAACA
*
31013 GCTAACCTTTCTAACT
1 GCTAACCTTTCTAACA
31029 GCTAA
1 GCTAA
31034 TTGCTAACGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.30, C:0.27, G:0.08, T:0.35
Consensus pattern (16 bp):
GCTAACCTTTCTAACA
Found at i:31105 original size:16 final size:16
Alignment explanation
Indices: 31080--31115 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
31070 ATTTCTGCTA
*
31080 TTTAACTTTATGCACT
1 TTTAAATTTATGCACT
*
31096 TTTAAATTTATGCATT
1 TTTAAATTTATGCACT
31112 TTTA
1 TTTA
31116 TTTTCTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.06, T:0.56
Consensus pattern (16 bp):
TTTAAATTTATGCACT
Found at i:33515 original size:10 final size:10
Alignment explanation
Indices: 33500--33534 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
33490 TTGGGTAGTG
33500 GGAAAGTGAA
1 GGAAAGTGAA
33510 GGAAAGTGAA
1 GGAAAGTGAA
*
33520 GGAAAATGAAA
1 GGAAAGTG-AA
33531 GGAA
1 GGAA
33535 TGGTAATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 17 0.74
11 6 0.26
ACGTcount: A:0.54, C:0.00, G:0.37, T:0.09
Consensus pattern (10 bp):
GGAAAGTGAA
Found at i:36638 original size:2 final size:2
Alignment explanation
Indices: 36633--36667 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
36623 AAAAAAAAGT
36633 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
36668 TGGTATTTGT
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
Found at i:44414 original size:24 final size:24
Alignment explanation
Indices: 44382--44478 Score: 140
Period size: 24 Copynumber: 4.0 Consensus size: 24
44372 GTGCTTCCTG
*
44382 TTCTTGATTAATCTGGCATATTGC
1 TTCTTGATTATTCTGGCATATTGC
*
44406 TTCTTGATTGTTCTGGCATATTGC
1 TTCTTGATTATTCTGGCATATTGC
* *
44430 TTCTTGATTTTTCTGGCATACTGC
1 TTCTTGATTATTCTGGCATATTGC
* *
44454 TTCTTGATTAGTCTGGTATATTGC
1 TTCTTGATTATTCTGGCATATTGC
44478 T
1 T
44479 GCCTTGTTGT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.15, C:0.16, G:0.19, T:0.49
Consensus pattern (24 bp):
TTCTTGATTATTCTGGCATATTGC
Found at i:45639 original size:27 final size:26
Alignment explanation
Indices: 45608--45689 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 26
45598 TCACCCACCA
45608 ACAGCTCCTCAAGCTCATCAGTTTTCT
1 ACAGCTCCTCAAG-TCATCAGTTTTCT
* ** *
45635 ACAGCCCCTCTTGTTCACCAGTTTTCT
1 ACAGCTCCTCAAG-TCATCAGTTTTCT
* * *
45662 GCAGTTCCTCAAAGTCCTCAGTTTTCT
1 ACAGCTCCTC-AAGTCATCAGTTTTCT
45689 A
1 A
45690 TTTTTCCACC
Statistics
Matches: 41, Mismatches: 13, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
27 40 0.98
28 1 0.02
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (26 bp):
ACAGCTCCTCAAGTCATCAGTTTTCT
Found at i:47376 original size:15 final size:15
Alignment explanation
Indices: 47340--47381 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
47330 ATCCACTACA
*
47340 TCATCAACATCATTG
1 TCATCACCATCATTG
*
47355 TCTTCACCA-CATATG
1 TCATCACCATCAT-TG
47370 TCATCACCATCA
1 TCATCACCATCA
47382 CAACAACTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 3 0.14
15 17 0.77
16 2 0.09
ACGTcount: A:0.31, C:0.33, G:0.05, T:0.31
Consensus pattern (15 bp):
TCATCACCATCATTG
Found at i:50597 original size:36 final size:36
Alignment explanation
Indices: 50548--50678 Score: 149
Period size: 36 Copynumber: 3.6 Consensus size: 36
50538 TACGAAAATA
** *
50548 AAGCATCAGCACTTTTAATTCAAAGTGAACGGAAGG
1 AAGCATCAGCACTTTCGATTCAAAGTGAACGAAAGG
*
50584 AAGCATC-GACACTTTCGATTCAATA-AGAACGAAAGG
1 AAGCATCAG-CACTTTCGATTCAA-AGTGAACGAAAGG
* * *
50620 AAGCATCAGCTCTTTCGATTCAAAGTGAATGAAATG
1 AAGCATCAGCACTTTCGATTCAAAGTGAACGAAAGG
* *
50656 AAGCATCATCACTTTCGACTCAA
1 AAGCATCAGCACTTTCGATTCAA
50679 TTGTTCATCT
Statistics
Matches: 80, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
35 2 0.03
36 76 0.95
37 2 0.03
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (36 bp):
AAGCATCAGCACTTTCGATTCAAAGTGAACGAAAGG
Found at i:52818 original size:21 final size:22
Alignment explanation
Indices: 52789--52837 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
52779 AAATAATTAA
*
52789 AATAG-TTTGTAAA-TTAATTT
1 AATAGTTTTGGAAAGTTAATTT
*
52809 AATAGTTTTGGAAAGTTATTTT
1 AATAGTTTTGGAAAGTTAATTT
*
52831 AGTAGTT
1 AATAGTT
52838 GCAAAGTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 7 0.29
22 12 0.50
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (22 bp):
AATAGTTTTGGAAAGTTAATTT
Found at i:53018 original size:60 final size:58
Alignment explanation
Indices: 52879--53066 Score: 178
Period size: 60 Copynumber: 3.1 Consensus size: 58
52869 GCATCATGTG
* * * * *
52879 TCCCTAAACTATGACTCTCATTCCAAGTTAGTTCTTAAACTTTTAAATATTCTAATTTCA
1 TCCCCAAACTATGACTCTCATTCTAA-TTAGTCCTTAAACTTTTGAACATTC-AATTTCA
** *
52939 TCCTTAAACTAAGACTCTCATTCTATATTAGTCCTTAAACTTTTGAACATTCGAATTTCA
1 TCCCCAAACTATGACTCTCATTCTA-ATTAGTCCTTAAACTTTTGAACATTC-AATTTCA
* * * * * * *
52999 TCCCCAAATTATGAATCTCATGCTAAATTAGACCCTAAACTTTTAGATCTTTCAATTTCA
1 TCCCCAAACTATGACTCTCATTCT-AATTAGTCCTTAAACTTTT-GAACATTCAATTTCA
*
53059 TACCCAAA
1 TCCCCAAA
53067 TTCATCCAAA
Statistics
Matches: 107, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
60 99 0.93
61 8 0.07
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (58 bp):
TCCCCAAACTATGACTCTCATTCTAATTAGTCCTTAAACTTTTGAACATTCAATTTCA
Found at i:53632 original size:21 final size:21
Alignment explanation
Indices: 53606--53768 Score: 217
Period size: 21 Copynumber: 7.8 Consensus size: 21
53596 AAAAGGTGTC
53606 GCAGTGCATCCATGCACCCCT
1 GCAGTGCATCCATGCACCCCT
53627 GCAGTGCATCCATGCACCCCT
1 GCAGTGCATCCATGCACCCCT
*
53648 GCAGTGCATCCATGCACCCGT
1 GCAGTGCATCCATGCACCCCT
*
53669 GCAGTGCATCCATGCATCCCT
1 GCAGTGCATCCATGCACCCCT
53690 GCAGTGCATCCATGCA--CCT
1 GCAGTGCATCCATGCACCCCT
* *
53709 GCACTAGTGCATCGATGCA-CCAT
1 G--C-AGTGCATCCATGCACCCCT
* *
53732 GCAGTGCATCGATGCA-CCAT
1 GCAGTGCATCCATGCACCCCT
53752 GCAGTGCATCCATGCAC
1 GCAGTGCATCCATGCAC
53769 TCAAACACCG
Statistics
Matches: 131, Mismatches: 6, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
19 4 0.03
20 33 0.25
21 78 0.60
22 13 0.10
23 3 0.02
ACGTcount: A:0.21, C:0.37, G:0.21, T:0.20
Consensus pattern (21 bp):
GCAGTGCATCCATGCACCCCT
Found at i:53856 original size:20 final size:20
Alignment explanation
Indices: 53789--53856 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
53779 AATGCAATTA
* *
53789 GTGCATCGATGCATCCTTCC
1 GTGCATCGATGCATCCTACT
*
53809 GTGCATCGATGCAT-CAAGGCT
1 GTGCATCGATGCATCCTA--CT
*
53830 GTACATCGATGCATCCTACT
1 GTGCATCGATGCATCCTACT
53850 GTGCATC
1 GTGCATC
53857 TATGTACGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.03
20 22 0.56
21 14 0.36
22 2 0.05
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (20 bp):
GTGCATCGATGCATCCTACT
Found at i:53994 original size:21 final size:21
Alignment explanation
Indices: 53965--54004 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
53955 TTTGAGTAGA
53965 AAAATCATCACCAAACGGCTTC
1 AAAATCATC-CCAAACGGCTTC
*
53987 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCAAACGGCT
54005 ATATACAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 4 0.24
22 4 0.24
ACGTcount: A:0.40, C:0.35, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCAAACGGCTTC
Found at i:57133 original size:34 final size:30
Alignment explanation
Indices: 57095--57163 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
57085 TTGATATAAC
57095 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
57129 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
57158 AATTTA
1 AATTTA
57164 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:57175 original size:29 final size:30
Alignment explanation
Indices: 57104--57163 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
57094 CAATTTAAGG
57104 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
57135 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
57164 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:57270 original size:21 final size:20
Alignment explanation
Indices: 57244--57300 Score: 96
Period size: 21 Copynumber: 2.8 Consensus size: 20
57234 AGGGTGTCAA
57244 AGTGCATCCATGCACCTCTGC
1 AGTGCATCCATGCACC-CTGC
57265 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
57286 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
57301 GAAGGCTGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
20 1 0.03
21 32 0.91
22 2 0.06
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:58818 original size:16 final size:16
Alignment explanation
Indices: 58797--58829 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
58787 TAATAAATAA
58797 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
58813 ACGAACATAAACTAAC
1 ACGAACATAAACGAAC
58829 A
1 A
58830 AATTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.24, G:0.09, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:58877 original size:31 final size:31
Alignment explanation
Indices: 58839--58915 Score: 154
Period size: 31 Copynumber: 2.5 Consensus size: 31
58829 AAATTTTTTT
58839 TTGTTCATGTTCGTTTATTAAAGAATATAAC
1 TTGTTCATGTTCGTTTATTAAAGAATATAAC
58870 TTGTTCATGTTCGTTTATTAAAGAATATAAC
1 TTGTTCATGTTCGTTTATTAAAGAATATAAC
58901 TTGTTCATGTTCGTT
1 TTGTTCATGTTCGTT
58916 CATTTAATAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.48
Consensus pattern (31 bp):
TTGTTCATGTTCGTTTATTAAAGAATATAAC
Found at i:59010 original size:16 final size:16
Alignment explanation
Indices: 58922--59003 Score: 132
Period size: 16 Copynumber: 5.2 Consensus size: 16
58912 CGTTCATTTA
58922 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
58936 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
*
58952 ATAAACGAACACGAAC
1 ATAAATGAACACGAAC
*
58968 ATAAATGAACAAGAAC
1 ATAAATGAACACGAAC
58984 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
59000 ATAA
1 ATAA
59004 GCGAACATAA
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
14 6 0.10
15 2 0.03
16 54 0.87
ACGTcount: A:0.60, C:0.17, G:0.11, T:0.12
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:59736 original size:14 final size:14
Alignment explanation
Indices: 59719--59755 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
59709 GATTGGGTTA
* *
59719 AACATAAATGAATG
1 AACATAAACGAACG
59733 AACATAAACGAACG
1 AACATAAACGAACG
59747 AACATAAAC
1 AACATAAAC
59756 AAACATAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.59, C:0.16, G:0.11, T:0.14
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:60270 original size:22 final size:22
Alignment explanation
Indices: 60231--60289 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
60221 CTAAAAATTA
*
60231 TTAATAAA-T-ATATTATATATAT
1 TTAATAAATTAATAATAT-TAT-T
*
60253 TTAATAACTTAATAATATTATT
1 TTAATAAATTAATAATATTATT
*
60275 TTATTAAATTAATAA
1 TTAATAAATTAATAA
60290 ATAAAATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 21 0.68
23 4 0.13
24 6 0.19
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAATAAATTAATAATATTATT
Found at i:60292 original size:26 final size:26
Alignment explanation
Indices: 60230--60307 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 26
60220 TCTAAAAATT
* *
60230 ATTAATAAAT-ATATTATATATATTTA
1 ATTAATAAATAATATTAT-TTTATTAA
*
60256 A-TAACTTAATAATATTATTTTATTAA
1 ATTAA-TAAATAATATTATTTTATTAA
* * *
60282 ATTAATAAATAAAATAAATTTATTAA
1 ATTAATAAATAATATTATTTTATTAA
60308 TAATTTATTA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
25 3 0.07
26 29 0.69
27 10 0.24
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (26 bp):
ATTAATAAATAATATTATTTTATTAA
Found at i:60367 original size:23 final size:23
Alignment explanation
Indices: 60341--60386 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
60331 GATGTAATTT
*
60341 AATATATTATTATAATACTAAAA
1 AATATAATATTATAATACTAAAA
* *
60364 AATATAATATTATATTATTAAAA
1 AATATAATATTATAATACTAAAA
60387 TTATTAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
AATATAATATTATAATACTAAAA
Found at i:60394 original size:23 final size:23
Alignment explanation
Indices: 60368--60412 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
60358 CTAAAAAATA
*
60368 TAATATTATATTATTAA-AATTAT
1 TAATAATATATT-TTAATAATTAT
60391 TAATAATATATTTTAATAATTA
1 TAATAATATATTTTAATAATTA
60413 ATATTCTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TAATAATATATTTTAATAATTAT
Found at i:60618 original size:19 final size:19
Alignment explanation
Indices: 60594--60634 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
60584 TGTTTTGGTG
60594 AGTTGTCAGCCACGTCGAA
1 AGTTGTCAGCCACGTCGAA
*
60613 AGTTGTCAGCCACGTCGGA
1 AGTTGTCAGCCACGTCGAA
60632 AGT
1 AGT
60635 CATCAATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.22
Consensus pattern (19 bp):
AGTTGTCAGCCACGTCGAA
Found at i:61752 original size:16 final size:15
Alignment explanation
Indices: 61716--61754 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
61706 TTTCTGCGTG
61716 AGGTTTAATTTGTTT
1 AGGTTTAATTTGTTT
*
61731 ATGTTTAATTTAGTTT
1 AGGTTTAATTT-GTTT
61747 AGGTTTAA
1 AGGTTTAA
61755 GATTTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (15 bp):
AGGTTTAATTTGTTT
Found at i:62075 original size:2 final size:2
Alignment explanation
Indices: 62068--62115 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
62058 TCTTAACATG
62068 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
62110 TA TA TA
1 TA TA TA
62116 AAATTTATAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:73563 original size:7 final size:7
Alignment explanation
Indices: 73561--73702 Score: 77
Period size: 7 Copynumber: 18.4 Consensus size: 7
73551 TGAAAAAGAA
73561 AAAAAAGG
1 AAAAAA-G
*
73569 AAAATGAG
1 AAAA-AAG
73577 AAAAATAG
1 AAAAA-AG
73585 AAGAAAAG
1 AA-AAAAG
*
73593 AAAAATGAA
1 AAAAA--AG
73602 AAAAAATG
1 AAAAAA-G
*
73610 AAAAGAG
1 AAAAAAG
73617 AAAAAAGAG
1 -AAAAA-AG
73626 AAAATAAG
1 AAAA-AAG
73634 AAAATGGAAG
1 AAAA---AAG
*
73644 AAAAATG
1 AAAAAAG
*
73651 AAAAATG
1 AAAAAAG
*
73658 AAAAAAT
1 AAAAAAG
*
73665 AAAAAGG
1 AAAAAAG
*
73672 AAAAATG
1 AAAAAAG
73679 AAAAAAG
1 AAAAAAG
*
73686 AAAAATG
1 AAAAAAG
*
73693 AAAAAGG
1 AAAAAAG
73700 AAA
1 AAA
73703 TAAAAGGGGG
Statistics
Matches: 107, Mismatches: 16, Indels: 23
0.73 0.11 0.16
Matches are distributed among these distances:
7 51 0.48
8 36 0.34
9 13 0.12
10 7 0.07
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (7 bp):
AAAAAAG
Found at i:73583 original size:41 final size:40
Alignment explanation
Indices: 73552--73684 Score: 125
Period size: 41 Copynumber: 3.4 Consensus size: 40
73542 AAAAAATGTT
73552 GAAAAA-GAAAAAAAAGGAAAATGAGAAAAATAGAAGAAAA
1 GAAAAATGAAAAAAAAGGAAAA-GAGAAAAATAGAAGAAAA
*
73592 GAAAAATGAAAAAAAATGAAAAGAGAAAAA-AG-AGAAAA
1 GAAAAATGAAAAAAAAGGAAAAGAGAAAAATAGAAGAAAA
* * * * *
73630 TAAGAAAATGGAAGAAAAATGAAAA-ATGAAAAA-ATAA-AAAG
1 -GA-AAAAT-GAAAAAAAAGGAAAAGA-GAAAAATAGAAGAAAA
73671 GAAAAATGAAAAAA
1 GAAAAATGAAAAAA
73685 GAAAAATGAA
Statistics
Matches: 80, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
38 12 0.15
39 8 0.10
40 21 0.26
41 38 0.47
42 1 0.01
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (40 bp):
GAAAAATGAAAAAAAAGGAAAAGAGAAAAATAGAAGAAAA
Found at i:73591 original size:57 final size:57
Alignment explanation
Indices: 73515--73663 Score: 162
Period size: 57 Copynumber: 2.6 Consensus size: 57
73505 TGAAGAAGAG
* * **
73515 ATGA-AAAAATGAAAAGAAAAGAGAAAT-AAAAAATGTTGAAAAAGAAAAAAAAG-GAAA
1 ATGAGAAAAAT-AGAAGAAAAGAAAAATGAAAAAA-AATG-AAAAGAAAAAAAAGAGAAA
*
73572 ATGAGAAAAATAGAAGAAAAGAAAAATGAAAAAAAATGAAAAGAGAAAAAAGAGAAA
1 ATGAGAAAAATAGAAGAAAAGAAAAATGAAAAAAAATGAAAAGAAAAAAAAGAGAAA
* *
73629 ATAAG-AAAATGGAAGAAAAATGAAAAATGAAAAAA
1 ATGAGAAAAATAGAAG-AAAA-GAAAAATGAAAAAA
73664 TAAAAAGGAA
Statistics
Matches: 80, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
56 22 0.28
57 32 0.40
58 26 0.32
ACGTcount: A:0.72, C:0.00, G:0.18, T:0.09
Consensus pattern (57 bp):
ATGAGAAAAATAGAAGAAAAGAAAAATGAAAAAAAATGAAAAGAAAAAAAAGAGAAA
Found at i:73664 original size:56 final size:55
Alignment explanation
Indices: 73553--73691 Score: 162
Period size: 56 Copynumber: 2.5 Consensus size: 55
73543 AAAAATGTTG
* *
73553 AAAAAGAAAAAAAAGGAAAATGAGAAAAATAGAAGAAAAGAAAAATGAAAAAAAAT
1 AAAAAGAGAAAAAAGGAAAATAAGAAAAATAGAAGAAAAGAAAAATG-AAAAAAAT
* *
73609 GAAAAGAGAAAAAAGAGAAAATAAG-AAAATGGAAGAAAAATGAAAAATG-AAAAAAT
1 AAAAAGAGAAAAAAG-GAAAATAAGAAAAATAGAAG-AAAA-GAAAAATGAAAAAAAT
*
73665 AAAAAG-G-AAAAATGAAAA-AAGAAAAAT
1 AAAAAGAGAAAAAAGGAAAATAAGAAAAAT
73692 GAAAAAGGAA
Statistics
Matches: 73, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
52 3 0.04
53 10 0.14
54 5 0.07
55 1 0.01
56 34 0.47
57 12 0.16
58 8 0.11
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (55 bp):
AAAAAGAGAAAAAAGGAAAATAAGAAAAATAGAAGAAAAGAAAAATGAAAAAAAT
Found at i:73674 original size:21 final size:21
Alignment explanation
Indices: 73604--73702 Score: 99
Period size: 21 Copynumber: 4.4 Consensus size: 21
73594 AAAATGAAAA
* *
73604 AAAATGAAAAGAGAAAAAAGA
1 AAAATGAAAAAAGAAAAATGA
73625 GAAAATAAGAAAATGGAAGAAAAATGA
1 -AAAAT--GAAAA---AAGAAAAATGA
* *
73652 AAAATGAAAAAATAAAAAGGA
1 AAAATGAAAAAAGAAAAATGA
73673 AAAATGAAAAAAGAAAAATGA
1 AAAATGAAAAAAGAAAAATGA
*
73694 AAAAGGAAA
1 AAAATGAAA
73703 TAAAAGGGGG
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
21 36 0.55
22 5 0.08
24 10 0.15
26 5 0.08
27 9 0.14
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (21 bp):
AAAATGAAAAAAGAAAAATGA
Found at i:75039 original size:37 final size:36
Alignment explanation
Indices: 74983--75053 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 36
74973 AAACAATTTA
*
74983 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC
1 ATCTTAAGCCTTCACGGAAGAATAGTGAAGCAAATC
* *
75019 ATCTATAAGCCTTTAGGGAAGAATAGTGAAGCAAA
1 ATCT-TAAGCCTTCACGGAAGAATAGTGAAGCAAA
75054 CCCGTTTGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
36 4 0.13
37 27 0.87
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (36 bp):
ATCTTAAGCCTTCACGGAAGAATAGTGAAGCAAATC
Found at i:75113 original size:55 final size:55
Alignment explanation
Indices: 75056--75539 Score: 537
Period size: 55 Copynumber: 8.9 Consensus size: 55
75046 GAAGCAAACC
* * * *
75056 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTTTGAAGGACTAGAGAGCGGACC
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
*
75111 CGTTATATT-AAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTT-TGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * *
75166 CGTTTGTTGAAGA----TCGAGTCCTATACTCTCTGAAGAAATAGGGAGCGAACC
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
* **
75217 CGTTTTTATGAAGATTGTTCGAGTTCTATACTCTCTGAAAAAATAGGGAGCGGACA
1 CGTTTGT-TGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
* ** *
75273 CGTTTGTTGAAGA---TT-GAG-TCTTATACTCTCTGAAGGAATAGGCAGCATACC
1 CGTTTGTTGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
75324 CGTTTATTGAAGATTGTTCAAG-TCATATACTCTCTGAAGGAATAGGGAGCGAACA
1 CGTTTGTTGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGGGAGCGGACA
* * * *
75379 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCCCCGAACGAATAGGGAGCAGACA
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * * *
75434 CGTTTGCTGAAGATTGTTTGAG-TCTTATACTCCCTGAACGAATAGGGAGCAGACA
1 CGTTTGTTGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGGGAGCGGACA
* *
75489 CATTTGCTGAAGATTGTTCGAG-TCTTATACTC-CTTGAAGGAATAGGGAGCG
1 CGTTTGTTGAAGATTGTTCGAGTTC-TATACTCTC-TGAAGGAATAGGGAGCG
75540 AACCCGTCAT
Statistics
Matches: 371, Mismatches: 43, Indels: 30
0.84 0.10 0.07
Matches are distributed among these distances:
50 2 0.01
51 79 0.21
52 8 0.02
54 8 0.02
55 229 0.62
56 45 0.12
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (55 bp):
CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
Found at i:76732 original size:16 final size:15
Alignment explanation
Indices: 76696--76734 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
76686 TTTCTGTGTG
76696 AGGTTTAATTTGTTT
1 AGGTTTAATTTGTTT
*
76711 ATGTTTAATTTAGTTT
1 AGGTTTAATTT-GTTT
76727 AGGTTTAA
1 AGGTTTAA
76735 GATTTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (15 bp):
AGGTTTAATTTGTTT
Found at i:77056 original size:2 final size:2
Alignment explanation
Indices: 77049--77117 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
77039 TCTTAACATG
77049 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
77091 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 T
77118 TAAAATTTAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:82427 original size:10 final size:11
Alignment explanation
Indices: 82398--82437 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
82388 CTGAGCTGAG
82398 CCGTTGACCGA
1 CCGTTGACCGA
82409 CCGTTGACCG-
1 CCGTTGACCGA
*
82419 CCTTTGACCGA
1 CCGTTGACCGA
*
82430 CCATTGAC
1 CCGTTGAC
82438 TTTTTTTGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.17, C:0.38, G:0.23, T:0.23
Consensus pattern (11 bp):
CCGTTGACCGA
Found at i:84134 original size:19 final size:21
Alignment explanation
Indices: 84107--84150 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
84097 CTCTGATTTT
*
84107 TGTTTTGATTTATG-T-TCTC
1 TGTTCTGATTTATGATATCTC
*
84126 TGTTCTGATTTCTGATATCTC
1 TGTTCTGATTTATGATATCTC
84147 TGTT
1 TGTT
84151 TATTGACTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
20 1 0.05
21 8 0.38
ACGTcount: A:0.11, C:0.14, G:0.16, T:0.59
Consensus pattern (21 bp):
TGTTCTGATTTATGATATCTC
Done.