Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 97 of 168
Found at i:28688556 original size:5 final size:6
Alignment explanation
Indices: 28688539--28688564 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
28688529 TATACAAGTC
28688539 AGAAAA AGAAAA AGAAAA AGAAAA AG
1 AGAAAA AGAAAA AGAAAA AGAAAA AG
28688565 TAGGTGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:28688904 original size:7 final size:7
Alignment explanation
Indices: 28688886--28688928 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
28688876 AATATAATAG
28688886 TTAA-TT
1 TTAAGTT
28688892 TT-AGTT
1 TTAAGTT
28688898 TTAAGTT
1 TTAAGTT
28688905 TTAAGTT
1 TTAAGTT
28688912 TTAAGTT
1 TTAAGTT
*
28688919 TTTAGTT
1 TTAAGTT
28688926 TTA
1 TTA
28688929 TTTTTCAGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
5 1 0.03
6 6 0.18
7 26 0.79
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.63
Consensus pattern (7 bp):
TTAAGTT
Found at i:28689668 original size:10 final size:10
Alignment explanation
Indices: 28689650--28689681 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
28689640 TGTCATCCCC
28689650 ATCATTATAT
1 ATCATTATAT
*
28689660 ATTATTATAT
1 ATCATTATAT
28689670 ATCATTATAT
1 ATCATTATAT
28689680 AT
1 AT
28689682 AATTTTAGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (10 bp):
ATCATTATAT
Found at i:28689674 original size:29 final size:29
Alignment explanation
Indices: 28689619--28689674 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
28689609 TGAGCATGAG
* *
28689619 CCATCATTATATATCATTATGTGTCATCC
1 CCATCATTATATATCATTATATATCATCC
*
28689648 CCATCATTATATATTATTATATATCAT
1 CCATCATTATATATCATTATATATCAT
28689675 TATATATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.32, C:0.20, G:0.04, T:0.45
Consensus pattern (29 bp):
CCATCATTATATATCATTATATATCATCC
Found at i:28691181 original size:45 final size:45
Alignment explanation
Indices: 28691130--28691225 Score: 158
Period size: 45 Copynumber: 2.1 Consensus size: 45
28691120 TATAAATGGA
28691130 ACATTAGCCGATTGTTTATATAATGGAAAATTAGCTCA-AAATTTC
1 ACATTAGCCGATTGTTTATATAATGGAAAATTAGCT-AGAAATTTC
* *
28691175 ACATTAGCCTATTGTTTATATAATGGAACATTAGCTAGAAATTTC
1 ACATTAGCCGATTGTTTATATAATGGAAAATTAGCTAGAAATTTC
28691220 ACATTA
1 ACATTA
28691226 TTGCCTTGCT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 1 0.02
45 47 0.98
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (45 bp):
ACATTAGCCGATTGTTTATATAATGGAAAATTAGCTAGAAATTTC
Found at i:28691972 original size:9 final size:9
Alignment explanation
Indices: 28691958--28691983 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
28691948 TTGCAAAAGG
28691958 GACGATGAC
1 GACGATGAC
28691967 GACGATGAC
1 GACGATGAC
28691976 GACGATGA
1 GACGATGA
28691984 GGATGATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.19, G:0.35, T:0.12
Consensus pattern (9 bp):
GACGATGAC
Found at i:28692198 original size:16 final size:16
Alignment explanation
Indices: 28692177--28692210 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
28692167 GGTGACAGGA
28692177 TAAAATTAAGTATGTT
1 TAAAATTAAGTATGTT
28692193 TAAAATTAAGTATGTT
1 TAAAATTAAGTATGTT
28692209 TA
1 TA
28692211 TTGCTATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (16 bp):
TAAAATTAAGTATGTT
Found at i:28692681 original size:16 final size:16
Alignment explanation
Indices: 28692662--28692702 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
28692652 AATTTGATAC
28692662 AATTTTAATAACAATT
1 AATTTTAATAACAATT
*
28692678 AATTTTGATAACAATT
1 AATTTTAATAACAATT
*
28692694 AGTTTTAAT
1 AATTTTAAT
28692703 TTTATTACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (16 bp):
AATTTTAATAACAATT
Found at i:28692704 original size:22 final size:23
Alignment explanation
Indices: 28692676--28692729 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
28692666 TTAATAACAA
*
28692676 TTAATTTTGATAAC-AAT-TAGTT
1 TTAATTTT-ATAACAAATATAATT
*
28692698 TTAATTTTATTACAAATATAATT
1 TTAATTTTATAACAAATATAATT
28692721 TTAATTTTA
1 TTAATTTTA
28692730 ATTAAAAACG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 4 0.14
22 11 0.39
23 13 0.46
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
TTAATTTTATAACAAATATAATT
Found at i:28696340 original size:21 final size:19
Alignment explanation
Indices: 28696304--28696418 Score: 167
Period size: 19 Copynumber: 5.8 Consensus size: 19
28696294 AATCATATCT
28696304 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
28696323 TCCAAGATTGCACATATCATA
1 TCTAAGATTG--CATATCATA
28696344 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
28696363 ACTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
28696384 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
28696403 TCTAAGATTTCATATC
1 TCTAAGATTGCATATC
28696419 CTCAAAAATT
Statistics
Matches: 87, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
19 51 0.59
21 36 0.41
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:28696417 original size:40 final size:40
Alignment explanation
Indices: 28696304--28696417 Score: 192
Period size: 40 Copynumber: 2.9 Consensus size: 40
28696294 AATCATATCT
* *
28696304 TCTAAGATTGCATATCATATCCAAGATTGCACATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
*
28696344 TCTAAGATTGCATATCATAACTAAGATTGCATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
*
28696384 TCTAAGATTGCATATCATATCTAAGATTTCATAT
1 TCTAAGATTGCATATCATATCTAAGATTGCATAT
28696418 CCTCAAAAAT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 69 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.36
Consensus pattern (40 bp):
TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
Found at i:28698609 original size:7 final size:7
Alignment explanation
Indices: 28698599--28698657 Score: 50
Period size: 7 Copynumber: 8.4 Consensus size: 7
28698589 CACTAACTCT
28698599 TAACCTC
1 TAACCTC
28698606 TAACCTC
1 TAACCTC
*
28698613 TAACCCC
1 TAACCTC
*
28698620 TAACCCC
1 TAACCTC
*
28698627 AAACC-C
1 TAACCTC
28698633 TTAACCTC
1 -TAACCTC
28698641 TAA-CTAC
1 TAACCT-C
*
28698648 TAACCCC
1 TAACCTC
28698655 TAA
1 TAA
28698658 ACCTTATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
6 3 0.07
7 39 0.89
8 2 0.05
ACGTcount: A:0.34, C:0.44, G:0.00, T:0.22
Consensus pattern (7 bp):
TAACCTC
Found at i:28698616 original size:14 final size:14
Alignment explanation
Indices: 28698599--28698644 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
28698589 CACTAACTCT
*
28698599 TAACCTCTAACCTC
1 TAACCCCTAACCTC
*
28698613 TAACCCCTAACCCC
1 TAACCCCTAACCTC
* *
28698627 AAACCCTTAACCTC
1 TAACCCCTAACCTC
28698641 TAAC
1 TAAC
28698645 TACTAACCCC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.33, C:0.46, G:0.00, T:0.22
Consensus pattern (14 bp):
TAACCCCTAACCTC
Found at i:28698631 original size:28 final size:30
Alignment explanation
Indices: 28698600--28698661 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 30
28698590 ACTAACTCTT
*
28698600 AACCTC-TAACCTCTAACCCCTAACCCC-A
1 AACCTCTTAACCTCTAACCACTAACCCCTA
*
28698628 AACC-CTTAACCTCTAACTACTAACCCCTA
1 AACCTCTTAACCTCTAACCACTAACCCCTA
28698657 AACCT
1 AACCT
28698662 TATTTAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 1 0.03
28 23 0.79
29 5 0.17
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.21
Consensus pattern (30 bp):
AACCTCTTAACCTCTAACCACTAACCCCTA
Found at i:28698758 original size:90 final size:88
Alignment explanation
Indices: 28698607--28698803 Score: 277
Period size: 88 Copynumber: 2.2 Consensus size: 88
28698597 CTTAACCTCT
* * * * *
28698607 AACCTCTAACCCCTAACCCCAAACCCTTAACCTCTAACTACTAACCCCTAAACCTTATTTAATAT
1 AACC-CTAAACCCTAA-CCCGAATCCTTAACCCCTAACCACTAACCCCTAAACCTTATTT-A-AT
*
28698672 ATAAATTAAAAAATACTAATTAATCTA
62 ATAAATTAAAAAACACTAATTAATCTA
*
28698699 AACCCTAAACTCTAACCCGAATCCTTAACCCCTAACCACTAACCCCTAAACCTTATTTAATATAA
1 AACCCTAAACCCTAACCCGAATCCTTAACCCCTAACCACTAACCCCTAAACCTTATTTAATATAA
*
28698764 ATTAAAATACACTAATTAATCTA
66 ATTAAAAAACACTAATTAATCTA
*
28698787 AACCTTAAACCCTAACC
1 AACCCTAAACCCTAACC
28698804 TGACACCGAA
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
88 42 0.44
89 1 0.01
90 39 0.41
91 9 0.09
92 4 0.04
ACGTcount: A:0.42, C:0.30, G:0.01, T:0.27
Consensus pattern (88 bp):
AACCCTAAACCCTAACCCGAATCCTTAACCCCTAACCACTAACCCCTAAACCTTATTTAATATAA
ATTAAAAAACACTAATTAATCTA
Found at i:28698990 original size:14 final size:14
Alignment explanation
Indices: 28698971--28699007 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
28698961 ATCCTAAATT
28698971 AACCATATACCCTA
1 AACCATATACCCTA
*
28698985 AACCATAAACCCTA
1 AACCATATACCCTA
*
28698999 AACAATATA
1 AACCATATA
28699008 TATTAAACCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.19
Consensus pattern (14 bp):
AACCATATACCCTA
Found at i:28699396 original size:41 final size:40
Alignment explanation
Indices: 28699338--28699573 Score: 296
Period size: 41 Copynumber: 5.8 Consensus size: 40
28699328 AAATGTTTTT
*
28699338 GCGGCGCTTATCCAAAAACGCCGCTAAAGCCTTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCC-TGAGCATTA
* * *
28699379 ACGGCGCTTTTCCAAAAATGCTGCTAAAGCCCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAG-CCTGAGCATTA
*
28699420 GCGGCGCTTATCCAAAAACGCCGCTAAAGCCCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAG-CCTGAGCATTA
** *
28699461 GCGGCGCTTTAGCAAAAACGCCGCTGAAGGCCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCT-AAAGCCTGAGCATTA
* *
28699502 GCTGCGC-TTTCGCAAAAACGCTGCTAAAGGCCTGAGCATTA
1 GCGGCGCTTTTC-CAAAAACGCCGCTAAA-GCCTGAGCATTA
*
28699543 GCGGCGC-TTTCGTAAAAACGCCGCTAAAGCC
1 GCGGCGCTTTTC-CAAAAACGCCGCTAAAGCC
28699574 CCAAAAGGTC
Statistics
Matches: 171, Mismatches: 20, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
40 7 0.04
41 159 0.93
42 5 0.03
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.19
Consensus pattern (40 bp):
GCGGCGCTTTTCCAAAAACGCCGCTAAAGCCTGAGCATTA
Found at i:28699477 original size:82 final size:82
Alignment explanation
Indices: 28699338--28699574 Score: 341
Period size: 82 Copynumber: 2.9 Consensus size: 82
28699328 AAATGTTTTT
* * ** * *
28699338 GCGGCGCTTATCCAAAAACGCCGCTAAAGCCTTGAGCATTAACGGCGCTTTTCCAAAAATGCTGC
1 GCGGCGCTTATCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTAGCAAAAACGCCGC
28699403 TAAAGCCCTGAGCATTA
66 TAAAGCCCTGAGCATTA
28699420 GCGGCGCTTATCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTAGCAAAAACGCCGC
1 GCGGCGCTTATCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTAGCAAAAACGCCGC
* *
28699485 TGAAGGCCTGAGCATTA
66 TAAAGCCCTGAGCATTA
* * * * *
28699502 GCTGCGCTT-TCGCAAAAACGCTGCTAAAGGCCTGAGCATTAGCGGCGCTTTCGTAAAAACGCCG
1 GCGGCGCTTATC-CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTAGCAAAAACGCCG
28699566 CTAAAGCCC
65 CTAAAGCCC
28699575 CAAAAGGTCA
Statistics
Matches: 139, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
81 2 0.01
82 137 0.99
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.19
Consensus pattern (82 bp):
GCGGCGCTTATCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTAGCAAAAACGCCGC
TAAAGCCCTGAGCATTA
Found at i:28699560 original size:123 final size:123
Alignment explanation
Indices: 28699350--28699574 Score: 348
Period size: 123 Copynumber: 1.8 Consensus size: 123
28699340 GGCGCTTATC
*
28699350 CAAAAACGCCGCTAAAGCCTTGAGCATTAACGGCGCTTTTCCAAAAATGCTGCTAAAGCCCTGAG
1 CAAAAACGCCGCTAAAGCCTTGAGCATTAACGGCGCTTTTCCAAAAACGCTGCTAAAGCCCTGAG
28699415 CATTAGCGGCGCTTATCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTAG
66 CATTAGCGGCGCTTATCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTAG
* * * *
28699473 CAAAAACGCCGCTGAAGGCC-TGAGCATTAGCTGCGC-TTTCGCAAAAACGCTGCTAAAGGCCTG
1 CAAAAACGCCGCT-AAAGCCTTGAGCATTAACGGCGCTTTTC-CAAAAACGCTGCTAAAGCCCTG
*
28699536 AGCATTAGCGGCGCTT-TCGTAAAAACGCCGCTAAAGCCC
64 AGCATTAGCGGCGCTTATC-CAAAAACGCCGCTAAAGCCC
28699575 CAAAAGGTCA
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
122 6 0.06
123 82 0.88
124 5 0.05
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.19
Consensus pattern (123 bp):
CAAAAACGCCGCTAAAGCCTTGAGCATTAACGGCGCTTTTCCAAAAACGCTGCTAAAGCCCTGAG
CATTAGCGGCGCTTATCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTAG
Found at i:28700020 original size:107 final size:104
Alignment explanation
Indices: 28699813--28700027 Score: 261
Period size: 107 Copynumber: 2.0 Consensus size: 104
28699803 ATTTTTTTTT
* * *
28699813 TTACATAACGGTGGTGCCGGCCATTTCCAGACCACCGCCAAAAAAATATTTTGAATTTTTTCGTA
1 TTACATAAAGGTGGTGCCGGCCATTGCCAGACCACCACCAAAAAAATATTTTGAATTTTTTCGTA
* *
28699878 TACTGGTGCCCCCAATGACAGCCAAAATGTAAAAAAAAA
66 TACTGGTGCCCCCAAAGACAGCCAAAATATAAAAAAAAA
* * *
28699917 TTACATAAAGGTGGTG-CTGCCATTGCCAGGCCACCACCAAAAAAATTTTTTTTTTGAATTTTTT
1 TTACATAAAGGTGGTGCCGGCCATTGCCAGACCACCACCAAAAAAA----TATTTTGAATTTTTT
* * * *
28699981 CGTATATTGGTGCCTGCCAAAGATAGCCATAATATAAAAAATAAA
62 CGTATACTGGTGCC-CCCAAAGACAGCCAAAATATAAAAAA-AAA
28700026 TT
1 TT
28700028 TGTGGTGGCT
Statistics
Matches: 93, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
103 25 0.27
104 15 0.16
107 27 0.29
108 21 0.23
109 5 0.05
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (104 bp):
TTACATAAAGGTGGTGCCGGCCATTGCCAGACCACCACCAAAAAAATATTTTGAATTTTTTCGTA
TACTGGTGCCCCCAAAGACAGCCAAAATATAAAAAAAAA
Found at i:28701788 original size:2 final size:2
Alignment explanation
Indices: 28701777--28701806 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
28701767 AGATAAAAAT
28701777 TA TA -A 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 T
28701807 GTACATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28701980 original size:36 final size:36
Alignment explanation
Indices: 28701940--28702015 Score: 84
Period size: 36 Copynumber: 2.1 Consensus size: 36
28701930 TGAAACATAG
*
28701940 AAAATATATAAAAGTATGT-GTATATATATAT-TTATA
1 AAAAT-TA-AAAAATATGTAGTATATATATATATTATA
* *
28701976 AAAATTAAAAAATGTGTACGTATATGTATATATTATA
1 AAAATTAAAAAATATGTA-GTATATATATATATTATA
28702013 AAA
1 AAA
28702016 CGTATGTATG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 8 0.24
35 2 0.06
36 16 0.47
37 8 0.24
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.38
Consensus pattern (36 bp):
AAAATTAAAAAATATGTAGTATATATATATATTATA
Found at i:28702609 original size:21 final size:21
Alignment explanation
Indices: 28702583--28702622 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
28702573 CTAAGCATAC
28702583 CATATCTAAGATTGCATATAT
1 CATATCTAAGATTGCATATAT
28702604 CATATCTAAGATTGCATAT
1 CATATCTAAGATTGCATAT
28702623 CCTTGAAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (21 bp):
CATATCTAAGATTGCATATAT
Found at i:28703355 original size:132 final size:132
Alignment explanation
Indices: 28703118--28703452 Score: 458
Period size: 132 Copynumber: 2.5 Consensus size: 132
28703108 AATGACAAGG
* * * * * *
28703118 AGATAAGATTCGCTGCCTTCTATCTTCTCCATTACTACTTAGGGATACAGGATCTACAATCTTCG
1 AGATAAGATTTGCTGCCTTCGATCTGCTCCACTACTACTTAGGGAGACAGGATCTACAATCTTCA
* * * *
28703183 ACCTACTCCACTGCTGCTCAGGGAGAAGGGATTGGTGGCTTAAATTTGCTTCCCTACTACCTTGG
66 ACCTACTCCACCGCTGCTCAAGGAGAAGGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGG
28703248 GA
131 GA
* * *
28703250 AGATAGGATTTGCTGCCTTCGATCTGGTCCACTACTTCTTAGGGAGACAGGATCTACAATCTTCA
1 AGATAAGATTTGCTGCCTTCGATCTGCTCCACTACTACTTAGGGAGACAGGATCTACAATCTTCA
28703315 ACCTACTCCACCGCTGCTCAAGGAGATA-GGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTG
66 ACCTACTCCACCGCTGCTCAAGGAGA-AGGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTG
28703379 GGA
130 GGA
* * *** * *
28703382 ATATAAGATTTACCATCTTCGATCTGCTCCAC-ACTGCTTAGGGAGACAAGATCTACAATCTTCA
1 AGATAAGATTTGCTGCCTTCGATCTGCTCCACTACTACTTAGGGAGACAGGATCTACAATCTTCA
*
28703446 ATCTACT
66 ACCTACT
28703453 TCACTGCCAA
Statistics
Matches: 179, Mismatches: 23, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
131 36 0.20
132 142 0.79
133 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (132 bp):
AGATAAGATTTGCTGCCTTCGATCTGCTCCACTACTACTTAGGGAGACAGGATCTACAATCTTCA
ACCTACTCCACCGCTGCTCAAGGAGAAGGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGG
GA
Found at i:28703476 original size:45 final size:45
Alignment explanation
Indices: 28703425--28703579 Score: 229
Period size: 45 Copynumber: 3.4 Consensus size: 45
28703415 CTGCTTAGGG
* * * *
28703425 AGACAAGATCTACAATCTTCAATCTACTTCACTGCCAATACATGA
1 AGACAAGATCTGCTATCTTCAATCTACTTCGCTGCCAATACAGGA
*
28703470 AGACAAGATCTGTTATCTTCAATCTACTTCGCTGCCAATACAGGA
1 AGACAAGATCTGCTATCTTCAATCTACTTCGCTGCCAATACAGGA
* * *
28703515 AGACAAGATTTGCTATTTTCGATCTACTTCGCTGCCAATACAGGA
1 AGACAAGATCTGCTATCTTCAATCTACTTCGCTGCCAATACAGGA
*
28703560 AGACAAGATTTGCTATCTTC
1 AGACAAGATCTGCTATCTTC
28703580 GCTACGAGTA
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 100 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (45 bp):
AGACAAGATCTGCTATCTTCAATCTACTTCGCTGCCAATACAGGA
Found at i:28703699 original size:10 final size:10
Alignment explanation
Indices: 28703684--28703713 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
28703674 GCAAAGGTAT
28703684 CTCATGGGAC
1 CTCATGGGAC
28703694 CTCATGGGAC
1 CTCATGGGAC
28703704 CTCATGGGAC
1 CTCATGGGAC
28703714 AATGGAGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.20, C:0.30, G:0.30, T:0.20
Consensus pattern (10 bp):
CTCATGGGAC
Found at i:28704410 original size:54 final size:54
Alignment explanation
Indices: 28704311--28704482 Score: 276
Period size: 54 Copynumber: 3.2 Consensus size: 54
28704301 CTTTTTTTTT
* *
28704311 TCATTCATTTCAA-TGT-TTTTTCTACATCTAACACCCTTTTTTTTTCATTCAATC
1 TCATTTATTTCAATTTTATTTTTCTACATCTAACACCC--TTTTTTTCATTCAATC
* *
28704365 TCATTTATTTCAATTTTATTTTTCTATATCTAACACCCTTCTTTTCATTCAATC
1 TCATTTATTTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTCATTCAATC
28704419 TCATTTATTTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTCATTCAATC
1 TCATTTATTTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTCATTCAATC
28704473 TCATTTATTT
1 TCATTTATTT
28704483 TAACTTTTTG
Statistics
Matches: 110, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
54 89 0.81
55 2 0.02
56 19 0.17
ACGTcount: A:0.23, C:0.22, G:0.01, T:0.54
Consensus pattern (54 bp):
TCATTTATTTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTCATTCAATC
Found at i:28705893 original size:54 final size:54
Alignment explanation
Indices: 28705775--28705947 Score: 285
Period size: 54 Copynumber: 3.2 Consensus size: 54
28705765 ACTTTTTTTA
*
28705775 TCATTCATTTCAATTTT-TTATTTCTACATCTAACACCCCTTTTTTTCATTCAATC
1 TCATTTATTTCAATTTTATT-TTTCTACATCTAACA-CCCTTTTTTTCATTCAATC
*
28705830 TCATTTATTTCAATTTTATTTTTCTATATCTAACACCCTTTTTTTCATTCAATC
1 TCATTTATTTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTCATTCAATC
* *
28705884 TCATTTATTTCAGTTTTATTTTTCTACATCTAACACCCTTTTTTTCATTCAATG
1 TCATTTATTTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTCATTCAATC
28705938 TCATTTATTT
1 TCATTTATTT
28705948 TAACTTCTTG
Statistics
Matches: 112, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
54 80 0.71
55 30 0.27
56 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.01, T:0.54
Consensus pattern (54 bp):
TCATTTATTTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTCATTCAATC
Found at i:28706088 original size:107 final size:106
Alignment explanation
Indices: 28705966--28706179 Score: 304
Period size: 107 Copynumber: 2.0 Consensus size: 106
28705956 TGAATTTTTT
* *
28705966 TTTACATAAAGGTGGTGTCGACCATTGCCAAGCCACCAC-CAAAATTTTTTTTTTGAATTTTTTC
1 TTTACATAAAGGTGGTGTCGACCATTGCCAAGCCACCACAAAAAATTGTTTTTTT--ATTTTTTC
* *
28706030 ATATACTGTTGCCGGCAAATTACAGCCAAAATGTAAAAAAAAA
64 ATATACTGGTGCCGGCAAATGACAGCCAAAATGTAAAAAAAAA
* * *
28706073 TTTACATAAAGGTGGTGTCGGCCATTGCCAGGCCACCACAAAAAAATTGTTTTTTTATTTTTTCG
1 TTTACATAAAGGTGGTGTCGACCATTGCCAAGCCACCAC-AAAAAATTGTTTTTTTATTTTTTCA
** *
28706138 TATACTGGTGCCGGCCTATGATAGCCAAAATGTAAAAAAAAA
65 TATACTGGTGCCGGCAAATGACAGCCAAAATGTAAAAAAAAA
28706180 ATGGTGGTGG
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 82 0.86
109 13 0.14
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (106 bp):
TTTACATAAAGGTGGTGTCGACCATTGCCAAGCCACCACAAAAAATTGTTTTTTTATTTTTTCAT
ATACTGGTGCCGGCAAATGACAGCCAAAATGTAAAAAAAAA
Found at i:28707339 original size:54 final size:53
Alignment explanation
Indices: 28707274--28707446 Score: 231
Period size: 54 Copynumber: 3.2 Consensus size: 53
28707264 ACTTTTTTTA
* *
28707274 TCATTCATTTCAATTTTTTATTTCTACATCTAACACGCTTTTTTTCATTCAATC
1 TCATTTATTTCAATTTTTT-TTTCTACATCTAACACCCTTTTTTTCATTCAATC
* * *
28707328 TCATTTATTTCAATTTTATTTTTCTATATATAACACCCTTTTTTTCTTTCAATC
1 TCATTTATTTCAATTTT-TTTTTCTACATCTAACACCCTTTTTTTCATTCAATC
* *
28707382 TCATTTATTT-AAGTATTATTTTTCTACATCTAACACCCTTTTTTTTCATTCAATG
1 TCATTTATTTCAA-T-TTTTTTTTCTACATCTAACACCC-TTTTTTTCATTCAATC
28707437 TCATTTATTT
1 TCATTTATTT
28707447 TAACTTCTTA
Statistics
Matches: 105, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
53 2 0.02
54 75 0.71
55 28 0.27
ACGTcount: A:0.24, C:0.19, G:0.02, T:0.55
Consensus pattern (53 bp):
TCATTTATTTCAATTTTTTTTTCTACATCTAACACCCTTTTTTTCATTCAATC
Found at i:28707677 original size:107 final size:104
Alignment explanation
Indices: 28707465--28707679 Score: 268
Period size: 111 Copynumber: 2.0 Consensus size: 104
28707455 TAAAATTTTT
* *
28707465 TTTACATAAAGGTGGTGTCGGCCATTGCCAAGCCACCACCAAAAAAAATATTTGAATTTTTTCGT
1 TTTACATAAAGGTGATGCCGGCCATTGCCAAGCCACCACCAAAAAAAATATTTGAATTTTTTCGT
* ***
28707530 ATACTGTTGCCAGCAAATGACAGCCAAAATGTAAAAAAAAAA
66 ATACTGGTGCCAGCAAATGACAAAAAAAATGT---AAAAAAA
* *
28707572 TTTACATAAAGGTGATGCCGGCCATTGCCAGGCCACCACCAAAAAAAAATTGTTTTTGAATTTTT
1 TTTACATAAAGGTGATGCCGGCCATTGCCAAGCCACCACC-AAAAAAAA---TATTTGAATTTTT
* **
28707637 TCGTATACTGGTGCCGGCCTATGACAAAAAAAATGTAAAAAAA
62 TCGTATACTGGTGCCAGCAAATGACAAAAAAAATGTAAAAAAA
28707680 AATTGGTGGT
Statistics
Matches: 93, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
107 37 0.40
108 15 0.16
111 41 0.44
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.26
Consensus pattern (104 bp):
TTTACATAAAGGTGATGCCGGCCATTGCCAAGCCACCACCAAAAAAAATATTTGAATTTTTTCGT
ATACTGGTGCCAGCAAATGACAAAAAAAATGTAAAAAAA
Found at i:28708857 original size:41 final size:41
Alignment explanation
Indices: 28708807--28708894 Score: 131
Period size: 41 Copynumber: 2.1 Consensus size: 41
28708797 TCTCATTTAT
* ***
28708807 TTCAATTTTATTTTTTTACATCTAATTTCCTTTTATTTTCA
1 TTCAATTTTATTTTTCTACATCTAACACCCTTTTATTTTCA
*
28708848 TTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTTTCA
1 TTCAATTTTATTTTTCTACATCTAACACCCTTTTATTTTCA
28708889 TTCAAT
1 TTCAAT
28708895 CTCATTTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.23, C:0.18, G:0.00, T:0.59
Consensus pattern (41 bp):
TTCAATTTTATTTTTCTACATCTAACACCCTTTTATTTTCA
Found at i:28708861 original size:21 final size:20
Alignment explanation
Indices: 28708807--28708868 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
28708797 TCTCATTTAT
28708807 TTCAATTTTATTTTTTTACA
1 TTCAATTTTATTTTTTTACA
** *
28708827 -TCTAATTTCCTTTTATTTTCA
1 TTC-AATTTTATTTT-TTTACA
*
28708848 TTCAATTTTATTTTTCTACA
1 TTCAATTTTATTTTTTTACA
28708868 T
1 T
28708869 CTAACACCCT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
19 2 0.06
20 14 0.44
21 14 0.44
22 2 0.06
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.63
Consensus pattern (20 bp):
TTCAATTTTATTTTTTTACA
Found at i:28708883 original size:97 final size:94
Alignment explanation
Indices: 28708741--28708948 Score: 301
Period size: 97 Copynumber: 2.2 Consensus size: 94
28708731 CTGAAACACT
*
28708741 TTTTTTTTCATTC-ATTTCAATTTTTTTCTACATCTAACACCTTTTTTTTCATTCAATCTCATTT
1 TTTTTTTTCATTCAATTT---TATTTTTCTACATCTAACACCTTTTTTTTCATTCAATCTCATTT
* ***
28708805 ATTTCAATTTTATTTTTTTACATCTAATTTCC
63 ATTTCAATTTTATTTTTCTACATCTAACACCC
28708837 TTTTATTTTCATTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTTTCATTCAATCTCATTT
1 TTTT-TTTTCATTCAATTTTATTTTTCTACATCTAACA-CC-TTTTTTTTCATTCAATCTCATTT
*
28708902 ATTTTAATTTTATTTTTCTACATCTAACACCC
63 ATTTCAATTTTATTTTTCTACATCTAACACCC
28708934 TTTTTTTTCATTCAA
1 TTTTTTTTCATTCAA
28708949 ACTCATTTAT
Statistics
Matches: 102, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
95 18 0.18
96 17 0.17
97 63 0.62
98 4 0.04
ACGTcount: A:0.23, C:0.19, G:0.00, T:0.58
Consensus pattern (94 bp):
TTTTTTTTCATTCAATTTTATTTTTCTACATCTAACACCTTTTTTTTCATTCAATCTCATTTATT
TCAATTTTATTTTTCTACATCTAACACCC
Found at i:28708926 original size:56 final size:56
Alignment explanation
Indices: 28708848--28708995 Score: 262
Period size: 55 Copynumber: 2.7 Consensus size: 56
28708838 TTTATTTTCA
*
28708848 TTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTTTCATTCAATCTCATTTAT
1 TTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTTTCATTCAAACTCATTTAT
*
28708904 TTTAATTTTATTTTTCTACATCTAACACCC-TTTTTTTTCATTCAAACTCATTTAT
1 TTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTTTCATTCAAACTCATTTAT
*
28708959 TTCAGTTTTATTTTTCTACATCTAACACCCTTTTTTT
1 TTCAATTTTATTTTTCTACATCTAACACCCTTTTTTT
28708996 GGTTTTTTAG
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
55 52 0.60
56 35 0.40
ACGTcount: A:0.23, C:0.21, G:0.01, T:0.55
Consensus pattern (56 bp):
TTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTTTCATTCAAACTCATTTAT
Found at i:28709076 original size:13 final size:13
Alignment explanation
Indices: 28709060--28709095 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
28709050 AATTTCATTT
28709060 TTTTATTTTAATA
1 TTTTATTTTAATA
*
28709073 TTTTATTTAAATA
1 TTTTATTTTAATA
*
28709086 TTTTAATTTA
1 TTTTATTTTA
28709096 TTTATTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTATTTTAATA
Found at i:28709080 original size:21 final size:21
Alignment explanation
Indices: 28709051--28709107 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
28709041 AATAAATCTA
*
28709051 ATTTCATTTTTTTATTTTAAT
1 ATTTTATTTTTTTATTTTAAT
***
28709072 ATTTTATTTAAATATTTTAAT
1 ATTTTATTTTTTTATTTTAAT
*
28709093 TTATTTATTATTTTT
1 AT-TTTATT-TTTTT
28709108 GTCAATTGAA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
21 18 0.69
22 6 0.23
23 2 0.08
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTTTATTTTTTTATTTTAAT
Found at i:28714808 original size:30 final size:30
Alignment explanation
Indices: 28714724--28714808 Score: 152
Period size: 30 Copynumber: 2.8 Consensus size: 30
28714714 CTAATATCTC
*
28714724 GATACCCATATCTTTGACTTTCCAATATTT
1 GATACCCATATCTTTGACTTTCCATTATTT
*
28714754 GATACCTATATCTTTGACTTTCCATTATTT
1 GATACCCATATCTTTGACTTTCCATTATTT
28714784 GATACCCATATCTTTGACTTTCCAT
1 GATACCCATATCTTTGACTTTCCAT
28714809 AAATATTGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.25, C:0.24, G:0.07, T:0.45
Consensus pattern (30 bp):
GATACCCATATCTTTGACTTTCCATTATTT
Found at i:28715977 original size:43 final size:43
Alignment explanation
Indices: 28715856--28715966 Score: 150
Period size: 43 Copynumber: 2.6 Consensus size: 43
28715846 CTGAAAAAGT
* * *
28715856 GCCGCTTAAGGTCATGTTCTTTAGTGGCGTTTATGATGAATGC
1 GCCGCTAAAGGTCATGTTCTTTAGTGGCGTTTGTGATGAACGC
* * * *
28715899 GTCACTAAATGTCATGTTCTTTAGCGGCGTTTGTGATGAACGC
1 GCCGCTAAAGGTCATGTTCTTTAGTGGCGTTTGTGATGAACGC
*
28715942 GCCGCTAAAGGTCATATTCTTTAGT
1 GCCGCTAAAGGTCATGTTCTTTAGT
28715967 AACATTTGTG
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (43 bp):
GCCGCTAAAGGTCATGTTCTTTAGTGGCGTTTGTGATGAACGC
Found at i:28717065 original size:11 final size:11
Alignment explanation
Indices: 28717051--28717082 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
28717041 TTTAAATAGA
28717051 AATTTGAGAGG
1 AATTTGAGAGG
*
28717062 AATTTGAAAGG
1 AATTTGAGAGG
28717073 AATTTGAGAG
1 AATTTGAGAG
28717083 AATATTAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (11 bp):
AATTTGAGAGG
Found at i:28718643 original size:5 final size:5
Alignment explanation
Indices: 28718631--28718673 Score: 79
Period size: 5 Copynumber: 8.8 Consensus size: 5
28718621 ATTTTATTGC
28718631 TATA- TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA
28718674 AAGTCTAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.11
5 34 0.89
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:28719981 original size:3 final size:3
Alignment explanation
Indices: 28719961--28720011 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
28719951 CATTTGTTTT
* *
28719961 TTA TTT TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28720009 TTA
1 TTA
28720012 CTATACATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:28722171 original size:13 final size:13
Alignment explanation
Indices: 28722153--28722178 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28722143 AAAGAGATTT
28722153 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
28722166 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
28722179 AAATTGAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
GTTTTCTAGTAAA
Found at i:28730426 original size:44 final size:44
Alignment explanation
Indices: 28730368--28730854 Score: 334
Period size: 44 Copynumber: 11.0 Consensus size: 44
28730358 GAGCAGGTTG
*** * *
28730368 AAAGAAAGCAGATCTTGTCTTCATGTACTAGTGGCGAAGCAGATC
1 AAAGAAA-CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
* * *
28730413 AAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATC
1 AAAGAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
* *** ** *
28730457 GAAGAAAACAGATCTTGTCTTCATGTACT-GCCGTGAAGTAGATC
1 AAAG-AAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
* * *
28730501 AAAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATC
1 AAAGA-AACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
* * *
28730546 AAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATC
1 AAAGAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
* * * *** * * *
28730590 GAAGAAAACATATATTGTCTTCATGTATTGG-CGTGAAGTAGATC
1 AAAG-AAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
* * * *
28730634 AAAGGTACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATC
1 AAA-GAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
* * *
28730679 AAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATC
1 AAAGAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
* * * *** ** * *
28730723 GAAGAAAATAGATCTTATCTTCATGTACT-GACGTGAAGTAAATC
1 AAAG-AAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
* * * * * * *
28730767 AAAGATAGCAGGTCCTGTCTTCCTATA-TCGGTAGCGAATTGGATC
1 AAAGA-AACAGATCTTGTCTTCCCATACT-GGTGGCGAAGTAGATC
* * * * * *
28730812 GAATATATAGATTTTATCTTCCCATACTGGTGGCGAAGTAGAT
1 AAAGAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGAT
28730855 TGAAGATTAC
Statistics
Matches: 331, Mismatches: 100, Indels: 23
0.73 0.22 0.05
Matches are distributed among these distances:
43 3 0.01
44 221 0.67
45 107 0.32
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (44 bp):
AAAGAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
Found at i:28730786 original size:89 final size:89
Alignment explanation
Indices: 28730368--28730771 Score: 375
Period size: 89 Copynumber: 4.6 Consensus size: 89
28730358 GAGCAGGTTG
* * * *
28730368 AAAGAAAGCAGATCTTGTCTTCATGTACTAGTGGCGAAGCAGATCAAAGAAACAGATCTTGTCTC
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGTGGTGAAGTAGATCAAAGAAACAGATCTTGTCTC
*
28730433 CCCATACTGGTGGTGGAGTAGATC
66 CCCATACTGGTGGTGAAGTAGATC
* ** * *
28730457 GAAGAAAACAGATCTTGTCTTCATGTACT-GCCGTGAAGTAGATCAAAGATACCAGATCTTGCCT
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGTGGTGAAGTAGATCAAAGA-AACAGATCTTGTCT
* * *
28730521 TCCCATACTGGTGGCGAAGCAGATC
65 CCCCATACTGGTGGTGAAGTAGATC
* *** * * * *
28730546 AAAG-AAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAAAACATATATTGTCT
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGTGGTGAAGTAGATCAAAG-AAACAGATCTTGTCT
* *** * *
28730610 TCATGTATTGG-CGTGAAGTAGATC
65 CCCCATACTGGTGGTGAAGTAGATC
** * * *** * *
28730634 AAAGGTACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAACAGATCTTGTCTC
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGTGGTGAAGTAGATCAAAGAAACAGATCTTGTCTC
*
28730699 CCCATACTGGTGGTGGAGTAGATC
66 CCCATACTGGTGGTGAAGTAGATC
* * * ** *
28730723 GAAGAAAATAGATCTTATCTTCATGTACT-GACGTGAAGTAAATCAAAGA
1 AAAGAAAACAGATCTTGTCTTCATGTACTGGTGGTGAAGTAGATCAAAGA
28730772 TAGCAGGTCC
Statistics
Matches: 246, Mismatches: 64, Indels: 11
0.77 0.20 0.03
Matches are distributed among these distances:
88 84 0.34
89 161 0.65
90 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.25
Consensus pattern (89 bp):
AAAGAAAACAGATCTTGTCTTCATGTACTGGTGGTGAAGTAGATCAAAGAAACAGATCTTGTCTC
CCCATACTGGTGGTGAAGTAGATC
Found at i:28730860 original size:133 final size:133
Alignment explanation
Indices: 28730393--28730773 Score: 672
Period size: 133 Copynumber: 2.9 Consensus size: 133
28730383 TGTCTTCATG
*
28730393 TACTAGTGGCGAAGCAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCG
1 TACTGGTGGCGAAGCAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCG
*
28730458 AAGAAAACAGATCTTGTCTTCATGTACTGCCGTGAAGTAGATCAAAGATACCAGATCTTGCCTTC
66 AAGAAAACAGATCTTGTCTTCATGTACTGACGTGAAGTAGATCAAAGATACCAGATCTTGCCTTC
28730523 CCA
131 CCA
28730526 TACTGGTGGCGAAGCAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCG
1 TACTGGTGGCGAAGCAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCG
* * * * *
28730591 AAGAAAACATATATTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGGTACCAGATCTTGCCTTC
66 AAGAAAACAGATCTTGTCTTCATGTACTGACGTGAAGTAGATCAAAGATACCAGATCTTGCCTTC
28730656 CCA
131 CCA
28730659 TACTGGTGGCGAAGCAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCG
1 TACTGGTGGCGAAGCAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCG
* * *
28730724 AAGAAAATAGATCTTATCTTCATGTACTGACGTGAAGTAAATCAAAGATA
66 AAGAAAACAGATCTTGTCTTCATGTACTGACGTGAAGTAGATCAAAGATA
28730774 GCAGGTCCTG
Statistics
Matches: 234, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
133 234 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.25
Consensus pattern (133 bp):
TACTGGTGGCGAAGCAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCG
AAGAAAACAGATCTTGTCTTCATGTACTGACGTGAAGTAGATCAAAGATACCAGATCTTGCCTTC
CCA
Found at i:28730901 original size:266 final size:265
Alignment explanation
Indices: 28730393--28730903 Score: 641
Period size: 266 Copynumber: 1.9 Consensus size: 265
28730383 TGTCTTCATG
28730393 TACTAGTGGCGAAGCAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCG
1 TACTAGTGGCGAAGCAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCG
* * * *
28730458 AAGAAAACAGATCTTGTCTTCATGTACTGCCGTGAAGTAGATCAAAGATACCAGATCTTGCCTTC
66 AAGAAAACAGATCTTATCTTCATGTACTGACGTGAAGTAAATCAAAGATACCAGATCCTGCCTTC
* * * *
28730523 CCATACTGGTGGCGAAGCAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGA
131 CCATACTGGTAGCGAAGCAGATCAAAGAAACAGATCTTATCTCCCCATACTGGTGGCGAAGTAGA
* * * * * * *
28730588 TCGAAGAAAACATATATTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGGTACCAGATCTTGCC
196 TCGAAGAAAACAGATAGTATCTCCAAGCA-TGGCGTGAAGCAGATCAAAGGTACCAGATCTTGCC
28730653 TTCCCA
260 TTCCCA
*
28730659 TACTGGTGGCGAAGCAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCG
1 TACTAGTGGCGAAGCAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCG
* * * *
28730724 AAGAAAATAGATCTTATCTTCATGTACTGACGTGAAGTAAATCAAAGATAGCAGGTCCTGTCTTC
66 AAGAAAACAGATCTTATCTTCATGTACTGACGTGAAGTAAATCAAAGATACCAGATCCTGCCTTC
* *** * * * * * *
28730789 CTATA-TCGGTAGCGAATTGGATCGAATATATAGATTTTATCTTCCCATACTGGTGGCGAAGTAG
131 CCATACT-GGTAGCGAAGCAGATCAAAGAAACAGATCTTATCTCCCCATACTGGTGGCGAAGTAG
* ** * *
28730853 ATTGAAGATTACAGATCGTATCTCCCTAAGCA-GAG-GTGGAGCAGATCAAAG
195 ATCGAAGAAAACAGATAGTATCT-CC-AAGCATG-GCGTGAAGCAGATCAAAG
28730904 ATGGCAGATT
Statistics
Matches: 206, Mismatches: 35, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
265 1 0.00
266 200 0.97
267 2 0.01
268 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (265 bp):
TACTAGTGGCGAAGCAGATCAAAGAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCG
AAGAAAACAGATCTTATCTTCATGTACTGACGTGAAGTAAATCAAAGATACCAGATCCTGCCTTC
CCATACTGGTAGCGAAGCAGATCAAAGAAACAGATCTTATCTCCCCATACTGGTGGCGAAGTAGA
TCGAAGAAAACAGATAGTATCTCCAAGCATGGCGTGAAGCAGATCAAAGGTACCAGATCTTGCCT
TCCCA
Found at i:28732650 original size:21 final size:20
Alignment explanation
Indices: 28732596--28732651 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
28732586 ATATTTATCA
* *
28732596 TTATACCATTATTTATTATTG
1 TTATATCATTA-TTATTATGG
*
28732617 TTATATTATTTATTATTATGG
1 TTATATCA-TTATTATTATGG
28732638 TTATTATCATTATT
1 TTA-TATCATTATT
28732652 TCTATATTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 22 0.76
22 7 0.24
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (20 bp):
TTATATCATTATTATTATGG
Found at i:28732753 original size:25 final size:24
Alignment explanation
Indices: 28732682--28732766 Score: 91
Period size: 25 Copynumber: 3.5 Consensus size: 24
28732672 GTTTTTACAA
*
28732682 TATATATATATATATGCATTTTTT
1 TATATATATATATACGCATTTTTT
* * * * *
28732706 TATGTAT-TAAACACACATATTTT
1 TATATATATATATACGCATTTTTT
28732729 TATATATAATATATACGCATTTTTT
1 TATATAT-ATATATACGCATTTTTT
*
28732754 TAAATATATATAT
1 TATATATATATAT
28732767 TTTTTAAAGC
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
23 17 0.36
24 12 0.26
25 18 0.38
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.51
Consensus pattern (24 bp):
TATATATATATATACGCATTTTTT
Found at i:28733121 original size:11 final size:11
Alignment explanation
Indices: 28733105--28733129 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28733095 TTAAAATCGT
28733105 TTTTTTAAATA
1 TTTTTTAAATA
28733116 TTTTTTAAATA
1 TTTTTTAAATA
28733127 TTT
1 TTT
28733130 GGCAATCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTTTAAATA
Found at i:28735028 original size:137 final size:134
Alignment explanation
Indices: 28734898--28735260 Score: 343
Period size: 149 Copynumber: 2.6 Consensus size: 134
28734888 AAAAATTAAG
* * *
28734898 TATATTTTTTAA-TTTGGTTATATATTTTAAATATTGTTTTATTAATAATTTTATTTAATATATC
1 TATATTTTTTAAGTTTGATTATATCTTTTAAATATTGTTTTATCAATAATTTTATTTAATATATC
* * * * ** *
28734962 GTTATTTAAATAAAAAAATTATAAAAACATATATATGAGTAACCTGTGCATCACACGGGATA-AA
66 GTTATTTAAATAAAAAAATTAT-AAAAC--ACACA--AGCAACCCGTAAATCACACGAGATAGAA
28735026 AAATTAGTATAT
126 AAA--A-TATAT
* ** *
28735038 TATATTTCAAAAACTTAAGTATTTTTTAATATCTTTTAAATATTATTTTATCAATAATTTTATTT
1 TATATTT------TTTAAGT-TTGATT-ATATCTTTTAAATATTGTTTTATCAATAATTTTATTT
* * **
28735103 AATATATTGTTATTTAAATAATAATTTTATAAAACACACAAGCAACCCGTAAATCACACGAGATA
58 AATATATCGTTATTTAAATAAAAAAATTATAAAACACACAAGCAACCCGTAAATCACACGAGATA
28735168 GAAAACTAATATAT
123 GAAAA--AATATAT
* * *
28735182 TATATATTTTAAATTTTGATTATATCTTTTAAATATTGTTTAATCAATAATTTTATTTAATATAT
1 TATAT-TTTTTAAGTTTGATTATATCTTTTAAATATTGTTTTATCAATAATTTTATTTAATATAT
*
28735247 CATTATTTAAATAA
65 CGTTATTTAAATAA
28735261 TAATTTTATA
Statistics
Matches: 184, Mismatches: 26, Indels: 29
0.77 0.11 0.12
Matches are distributed among these distances:
137 54 0.29
138 4 0.02
139 4 0.02
140 7 0.04
144 30 0.16
145 7 0.04
146 7 0.04
147 2 0.01
148 9 0.05
149 60 0.33
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (134 bp):
TATATTTTTTAAGTTTGATTATATCTTTTAAATATTGTTTTATCAATAATTTTATTTAATATATC
GTTATTTAAATAAAAAAATTATAAAACACACAAGCAACCCGTAAATCACACGAGATAGAAAAAAT
ATAT
Found at i:28737817 original size:7 final size:7
Alignment explanation
Indices: 28737805--28737835 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
28737795 TATTGGATCA
28737805 CTTTGAT
1 CTTTGAT
28737812 CTTTGAT
1 CTTTGAT
28737819 CTTTGAT
1 CTTTGAT
*
28737826 CTTTAAT
1 CTTTGAT
28737833 CTT
1 CTT
28737836 CAAAATTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.10, T:0.58
Consensus pattern (7 bp):
CTTTGAT
Found at i:28738683 original size:13 final size:13
Alignment explanation
Indices: 28738658--28738712 Score: 62
Period size: 13 Copynumber: 4.2 Consensus size: 13
28738648 GAATAACATA
28738658 TAAATATTAATAAT
1 TAAATA-TAATAAT
28738672 TAAATATAATAAT
1 TAAATATAATAAT
28738685 T--A-ATAATACATT
1 TAAATATAATA-A-T
28738697 TAAATATAATAAT
1 TAAATATAATAAT
28738710 TAA
1 TAA
28738713 TAATAAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
10 6 0.17
11 2 0.06
12 2 0.06
13 12 0.33
14 8 0.22
15 6 0.17
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAATATAATAAT
Found at i:28738699 original size:25 final size:25
Alignment explanation
Indices: 28738671--28738728 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
28738661 ATATTAATAA
*
28738671 TTAAATATAATAATTAATAATACAT
1 TTAAATATAATAATTAATAATAAAT
28738696 TTAAATATAATAATTAATAATAAAT
1 TTAAATATAATAATTAATAATAAAT
28738721 TTAAATAT
1 TTAAATAT
28738729 GTCTAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
TTAAATATAATAATTAATAATAAAT
Found at i:28738718 original size:13 final size:13
Alignment explanation
Indices: 28738660--28738718 Score: 54
Period size: 13 Copynumber: 4.6 Consensus size: 13
28738650 ATAACATATA
*
28738660 AATATTAATAATT
1 AATAATAATAATT
28738673 AA-ATATAATAATT
1 AATA-ATAATAATT
28738686 AATAATACAT--TT
1 AATAATA-ATAATT
28738698 AA-ATATAATAATT
1 AATA-ATAATAATT
28738711 AATAATAA
1 AATAATAA
28738719 ATTTAAATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
11 3 0.08
12 8 0.21
13 23 0.61
14 4 0.11
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (13 bp):
AATAATAATAATT
Found at i:28739356 original size:43 final size:42
Alignment explanation
Indices: 28739296--28739549 Score: 283
Period size: 42 Copynumber: 6.0 Consensus size: 42
28739286 CAGCGTTTAC
* *
28739296 AGAAAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGGTT
1 AGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
* * *
28739338 AAAAAAAAGACGCCGCTAAAGATCATGTTCTTAAGCAGCGCTT
1 AGAAAAAA-ACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
* * * *
28739381 AAAAAAAAGACACCGCTAAAGATCTTGTTCTTTAGCGGCGCAT
1 AGAAAAAA-ACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
* * * * * *
28739424 GGAGAAAAATGCCACTAAAGATCATCTTCTTTAGCGGTGCTT
1 AGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
* * * *
28739466 AGACAAAAACGCCGCTAAAAATCATATTCTTTAGCGGCACTT
1 AGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
* * * *
28739508 GGTAAAAAACGCCACTATAGATCATGTTCTTTAGCGGCGCTT
1 AGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
28739550 TCTTCACAAA
Statistics
Matches: 175, Mismatches: 36, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
42 102 0.58
43 73 0.42
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (42 bp):
AGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
Found at i:28740039 original size:21 final size:21
Alignment explanation
Indices: 28739979--28740050 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
28739969 TTCTTTTGAA
* *
28739979 CCTCTACTTCTCTTGCTGCAG
1 CCTCTGCTTCTCTTGCTGTAG
*
28740000 CCTCTGCTTCTCTCGCTGTAG
1 CCTCTGCTTCTCTTGCTGTAG
* * *
28740021 CCTCTGCTTCCCTTACTGTCG
1 CCTCTGCTTCTCTTGCTGTAG
28740042 CCTCTGCTT
1 CCTCTGCTT
28740051 TAAGTTGTAG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.06, C:0.40, G:0.15, T:0.39
Consensus pattern (21 bp):
CCTCTGCTTCTCTTGCTGTAG
Found at i:28745577 original size:9 final size:9
Alignment explanation
Indices: 28745563--28745857 Score: 343
Period size: 9 Copynumber: 33.4 Consensus size: 9
28745553 ACGCCAGTTA
28745563 TTATGTAAG
1 TTATGTAAG
28745572 TTATGTAAG
1 TTATGTAAG
*
28745581 TTATTTAAG
1 TTATGTAAG
28745590 TTATGTAAG
1 TTATGTAAG
28745599 TTATGTAAG
1 TTATGTAAG
* *
28745608 TTATTTAAT
1 TTATGTAAG
28745617 TTATGTAAG
1 TTATGTAAG
28745626 TTATGTAAG
1 TTATGTAAG
28745635 TTATGTAAG
1 TTATGTAAG
* *
28745644 TTATTTAAT
1 TTATGTAAG
28745653 TTATGTAAG
1 TTATGTAAG
28745662 TTATGTAAG
1 TTATGTAAG
* *
28745671 TTATTTAAT
1 TTATGTAAG
*
28745680 TTATATAAG
1 TTATGTAAG
28745689 TTATGTAAG
1 TTATGTAAG
28745698 TTATGTAAG
1 TTATGTAAG
* *
28745707 TTATTTAAT
1 TTATGTAAG
28745716 TTATGTAAG
1 TTATGTAAG
*
28745725 TTATGTAGG
1 TTATGTAAG
**
28745734 CAATGT-A-
1 TTATGTAAG
*
28745741 TTATGTAAA
1 TTATGTAAG
*
28745750 TAATGTAAG
1 TTATGTAAG
*
28745759 TTA-GGAAGG
1 TTATGTAA-G
28745768 TTATGT-A-
1 TTATGTAAG
28745775 TTATGTAAG
1 TTATGTAAG
*
28745784 TTATTTAAG
1 TTATGTAAG
28745793 TTATGTAAG
1 TTATGTAAG
* *
28745802 TTATTTAAT
1 TTATGTAAG
28745811 TTATGTAAG
1 TTATGTAAG
28745820 TTATGTAAG
1 TTATGTAAG
*
28745829 TTATGTAGG
1 TTATGTAAG
28745838 TTATGT-A-
1 TTATGTAAG
*
28745845 TTATGTTAG
1 TTATGTAAG
28745854 TTAT
1 TTAT
28745858 TATGTTATTA
Statistics
Matches: 240, Mismatches: 38, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
7 16 0.07
8 6 0.03
9 217 0.90
10 1 0.00
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:28745875 original size:20 final size:19
Alignment explanation
Indices: 28745838--28745877 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
28745828 GTTATGTAGG
* *
28745838 TTATGTATTATGTTAGTTA
1 TTATGTATTATATAAGTTA
28745857 TTATGTTATTATATAAGTTA
1 TTATG-TATTATATAAGTTA
28745877 T
1 T
28745878 GCAAGTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (19 bp):
TTATGTATTATATAAGTTA
Found at i:28745896 original size:25 final size:26
Alignment explanation
Indices: 28745866--28745919 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
28745856 ATTATGTTAT
*
28745866 TATATAAG-TTATGCAAGTTTCTATA
1 TATATAAGATTATGCAAGTTTATATA
* *
28745891 TATATATGTATTATGTAAGTTTATATA
1 TATATAAG-ATTATGCAAGTTTATATA
28745918 TA
1 TA
28745920 AGTTATGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.29
27 17 0.71
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (26 bp):
TATATAAGATTATGCAAGTTTATATA
Found at i:28746010 original size:17 final size:18
Alignment explanation
Indices: 28745978--28746011 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28745968 TGATTGATAA
28745978 ATTTTGAAAAAAATATAG
1 ATTTTGAAAAAAATATAG
*
28745996 ATTTT-AAAAATATATA
1 ATTTTGAAAAAAATATA
28746012 CATTAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
ATTTTGAAAAAAATATAG
Found at i:28746210 original size:2 final size:2
Alignment explanation
Indices: 28746205--28746235 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28746195 AAGAGAGGTT
28746205 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 T
28746236 GATTTGCTTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28746556 original size:20 final size:20
Alignment explanation
Indices: 28746531--28746580 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
28746521 CCTTAAACCT
*
28746531 GAACTCGAATATTAAACCCC
1 GAACTCGAACATTAAACCCC
* * *
28746551 GAACTCTAACCTTAGACCCC
1 GAACTCGAACATTAAACCCC
*
28746571 AAACTCGAAC
1 GAACTCGAAC
28746581 TCTAAATCTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.34, G:0.10, T:0.18
Consensus pattern (20 bp):
GAACTCGAACATTAAACCCC
Found at i:28746649 original size:20 final size:20
Alignment explanation
Indices: 28746599--28746655 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
28746589 TCGAATCCAA
*
28746599 GTTTAGGGTTCAAGGTTCGGG
1 GTTTAGGGTTCAAGGTT-TGG
* *
28746620 GTTCA-AGTTCAAGGTTTGG
1 GTTTAGGGTTCAAGGTTTGG
28746639 GTTTAGGGTTC-AGGTTT
1 GTTTAGGGTTCAAGGTTT
28746656 AAGATTTAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 12 0.40
20 14 0.47
21 4 0.13
ACGTcount: A:0.16, C:0.09, G:0.37, T:0.39
Consensus pattern (20 bp):
GTTTAGGGTTCAAGGTTTGG
Found at i:28747356 original size:11 final size:12
Alignment explanation
Indices: 28747340--28747373 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
28747330 TGTTATAAAA
28747340 AATTAC-GAGTT
1 AATTACAGAGTT
*
28747351 AATTACAGAGCT
1 AATTACAGAGTT
28747363 AATTACAGAGT
1 AATTACAGAGT
28747374 GCTGGAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (12 bp):
AATTACAGAGTT
Found at i:28748937 original size:336 final size:332
Alignment explanation
Indices: 28748221--28749152 Score: 945
Period size: 336 Copynumber: 2.8 Consensus size: 332
28748211 TCAATTATGC
* * * * *
28748221 TTTAATGCACAGTTCTGGCGTTTTCTGTAAAAATGCCAGTAAAAATTAATTTGCTTAAGCTATAT
1 TTTAATGCACATTTCTGGCGTTTTCTGT-TAAACGCCAGTAAAAATTAATTTGCTTAAGCTAAAC
** * * * *
28748286 GGGGTCGTTTAGACAATATTTTAAGTCA-TTTTGCGGCGTTTTGTGCAAAAACGCCATTATAAAT
65 GAAGACGTTTAGACAATATTTTAAGTCACTTTTGCGGCG-TTTGTTCAAAAACGCCA-CAAAAAT
* * *
28748350 TAAGAGAAACGGCGCCGTTGGATTAATTTAGAGAAAATGCTAAGTTAAAAACTAGTACAGAAACG
128 TAACAGAAACGGCGCCGTTGAATTAATATAGAGAAAATGCTAAGTTAAAAACT-GTACAGAAACG
* * ** *
28748415 ACGTCGTTTAG-ACAAAATTTTAAGACAATTTTGCAGCGCATCCTGAACAAACGCCGCTATTGCT
192 GCGTCGTTTAGCA-AAAATTTTAAGACACTTTTGCAGCGTTTCTTGAACAAACGCCGCTATTGCT
* * * * *
28748479 TGTACGTTTACGGCGTTTTCTAAAAAGCGCCACTAAAATTTAAAGTTCTAATCCAAAACGACGCC
256 TGTACATTTACAGCGTTTTCTAAAAAGAGCCACTAAAAATGAAAGTTCTAATCCAAAACGACGCC
*
28748544 ATTTTATTAAGC
321 ATTTTATTAAGA
* * * *
28748556 TGTAAAGCACATTTTTGGCGTTTTCTGATTAAACGCTAGTAAAAATTAATTTGCTTAAGCTAAAC
1 TTTAATGCACATTTCTGGCGTTTTCTG-TTAAACGCCAGTAAAAATTAATTTGCTTAAGCTAAAC
* * * * * *
28748621 GAAGCCGTTTAGGCAATATTTTATGTCACTTTTGTGGCGTTTGGTTTAAAAACGCTACAAAAATT
65 GAAGACGTTTAGACAATATTTTAAGTCACTTTTGCGGCGTTT-GTTCAAAAACGCCACAAAAATT
* * * *
28748686 AACAGAAACGGTGTCGTTGAATTAATATAGAGAAAATGCTAAGTATAAAAGCATGTACAGAGACG
129 AACAGAAACGGCGCCGTTGAATTAATATAGAGAAAATGCTAAGT-TAAAAAC-TGTACAGAAACG
* * * * * * *
28748751 GCGCCGTTTAGCAAAAATTTTAAGACACTTTCGCTGCTTTTATTGAACAAACGCCACTATAGCTT
192 GCGTCGTTTAGCAAAAATTTTAAGACACTTTTGCAGCGTTTCTTGAACAAACGCCGCTATTGCTT
** * ** * * **
28748816 GTGTATTTGCAGCG-TTTCTAGACCAGAGCCAC-AAAGAATGAAGGTTCTAATCCGAAACGGTGC
257 GTACATTTACAGCGTTTTCTA-AAAAGAGCCACTAAA-AATGAAAGTTCTAATCCAAAACGACGC
* *
28748879 CGTTTTGTTAAGA
320 CATTTTATTAAGA
* * * * *
28748892 TTTAATGCACATTTCTGGCGTTTTCCGTTAAAGCACCACTAAAAATTAATTTGCTTAAGTTAGAC
1 TTTAATGCACATTTCTGGCGTTTTCTGTTAAA-CGCCAGTAAAAATTAATTTGCTTAAGCTAAAC
** * * ** *
28748957 GTCGACGTTTAGCCAATATTTCAAGTCACTTTTGCGGCGTTTCCTGAACAAACGCCACGAAAAAT
65 GAAGACGTTTAGACAATATTTTAAGTCACTTTTGCGGCGTTTGTTCAA-AAACGCCAC-AAAAAT
* * * *** *
28749022 TATCATAAATGGCGCCGTTTTGTTAATATAGAGAAAATGCTAAGTTAAAAATCGTGGACAGAAAC
128 TAACAGAAACGGCGCCGTTGAATTAATATAGAGAAAATGCTAAGTTAAAAA-C-TGTACAGAAAC
* * * * * * *
28749087 AGCGTCGTTCAACCAAAATTTTAAGTCACTTTTGCGGCGTTTCTTGCACAAACGCCGCTATTGCT
191 GGCGTCGTTTAGCAAAAATTTTAAGACACTTTTGCAGCGTTTCTTGAACAAACGCCGCTATTGCT
28749152 T
256 T
28749153 AAGCATTAGC
Statistics
Matches: 484, Mismatches: 101, Indels: 22
0.80 0.17 0.04
Matches are distributed among these distances:
335 142 0.29
336 234 0.48
337 108 0.22
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (332 bp):
TTTAATGCACATTTCTGGCGTTTTCTGTTAAACGCCAGTAAAAATTAATTTGCTTAAGCTAAACG
AAGACGTTTAGACAATATTTTAAGTCACTTTTGCGGCGTTTGTTCAAAAACGCCACAAAAATTAA
CAGAAACGGCGCCGTTGAATTAATATAGAGAAAATGCTAAGTTAAAAACTGTACAGAAACGGCGT
CGTTTAGCAAAAATTTTAAGACACTTTTGCAGCGTTTCTTGAACAAACGCCGCTATTGCTTGTAC
ATTTACAGCGTTTTCTAAAAAGAGCCACTAAAAATGAAAGTTCTAATCCAAAACGACGCCATTTT
ATTAAGA
Found at i:28750865 original size:114 final size:114
Alignment explanation
Indices: 28750685--28750999 Score: 431
Period size: 114 Copynumber: 2.8 Consensus size: 114
28750675 ACTTACCCAT
28750685 AAACGCCACTAAATCCCCCGAAAGCT-CAGAAAACGGCGTCGTTGGGCTTAGGTATTTTTGCGGC
1 AAACGCCACTAAAT-CCCCGAAAGCTCCA-AAAACGGCGTCGTTGGGCTTAGGTATTTTTGCGGC
*
28750749 GCTTTCTCAAAAACGCCGCTAAAGCCCTGGGCATTAG-AGGTGCTTA-ATTAA
64 GCTTTCTCAAAAACGCCACTAAAGCCCTGGGCATTAGCA-GTGCTTACA-TAA
* * *
28750800 AAATGCCACTAAATCCCCGAAAGCTCCAAAAATGGTGTCGTTGGGCTTAGGTATTTTTGCGGCGC
1 AAACGCCACTAAATCCCCGAAAGCTCCAAAAACGGCGTCGTTGGGCTTAGGTATTTTTGCGGCGC
* *
28750865 TTTCTCAAAAACGCCACTAAAGCCCTTGGCATTTGCAGTGCTTACATAA
66 TTTCTCAAAAACGCCACTAAAGCCCTGGGCATTAGCAGTGCTTACATAA
* * * * * * *
28750914 AAACACCACTAAATCGCCAAAAGCTCAAAAAACGGCGTCGTTAGGCTGAGGTATTTTTACGGCGC
1 AAACGCCACTAAATCCCCGAAAGCTCCAAAAACGGCGTCGTTGGGCTTAGGTATTTTTGCGGCGC
*
28750979 TTAACT-AAAAACGCCACTAAA
66 TT-TCTCAAAAACGCCACTAAA
28751000 TCCGCGAAAA
Statistics
Matches: 179, Mismatches: 17, Indels: 9
0.87 0.08 0.04
Matches are distributed among these distances:
114 160 0.89
115 19 0.11
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (114 bp):
AAACGCCACTAAATCCCCGAAAGCTCCAAAAACGGCGTCGTTGGGCTTAGGTATTTTTGCGGCGC
TTTCTCAAAAACGCCACTAAAGCCCTGGGCATTAGCAGTGCTTACATAA
Found at i:28751034 original size:188 final size:186
Alignment explanation
Indices: 28750790--28751147 Score: 452
Period size: 188 Copynumber: 1.9 Consensus size: 186
28750780 CATTAGAGGT
* * **
28750790 GCTTAATTAAAAATGCCACTAAATCCCCGAAAGCTCCAAAAATGGTGTCGTTGGGCTTAGGTATT
1 GCTTAACTAAAAACGCCACTAAATCCCCGAAAGCTCCAAAAACAGTGTCGTTGGGCTTAGGT-TT
* *
28750855 -TTTGCGGCGCTTT-CTCAAAAACGCCACTAAAGCCCTTGGCATTTGCAGTGCTTACATAAAAAC
65 CTTTGCGGCGCTTTAC-CAAAAACGCCACTAAAGCCCTTAGCATTAGCAGTGCTTACATAAAAAC
28750918 ACCACTAAATCGCCAAAAGCTCAAAAAACGGCGTCGTTAGGCTGAGGTATTTTTACGGC
129 ACCACTAAATCGCCAAAAGCTC-AAAAACGGCGTCGTTAGGCTGAGGTATTTTTACGGC
* * *
28750977 GCTTAACTAAAAACGCCACTAAATCCGCGAAAAGCT-TAGAAAACAGTGTCGTTGGGCTTATGTT
1 GCTTAACTAAAAACGCCACTAAATCCCCG-AAAGCTCCA-AAAACAGTGTCGTTGGGCTTAGGTT
** * * * * *
28751041 TCTTTGCGGCGCTTTACCGTAAATGCCGCTAAAGCCCTTAGCGTTAGCGGTGCTTACCTAAAAAC
64 TCTTTGCGGCGCTTTACCAAAAACGCCACTAAAGCCCTTAGCATTAGCAGTGCTTACATAAAAAC
* * * ** *
28751106 GCCGCTAAATCTCTGAAAGCTCAGAAACGGCGTCGTTAGGCT
129 ACCACTAAATCGCCAAAAGCTCAAAAACGGCGTCGTTAGGCT
28751148 TACGTTTTTT
Statistics
Matches: 145, Mismatches: 22, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
187 48 0.33
188 96 0.66
189 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (186 bp):
GCTTAACTAAAAACGCCACTAAATCCCCGAAAGCTCCAAAAACAGTGTCGTTGGGCTTAGGTTTC
TTTGCGGCGCTTTACCAAAAACGCCACTAAAGCCCTTAGCATTAGCAGTGCTTACATAAAAACAC
CACTAAATCGCCAAAAGCTCAAAAACGGCGTCGTTAGGCTGAGGTATTTTTACGGC
Found at i:28751529 original size:15 final size:16
Alignment explanation
Indices: 28751495--28751529 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
28751485 GAAATTAGGG
*
28751495 ATTTCAGGGGGGAAAG
1 ATTTCAGGGGGGAAAA
28751511 ATTTCA-GGGGGAAAA
1 ATTTCAGGGGGGAAAA
28751526 ATTT
1 ATTT
28751530 ATAAATGGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.34, C:0.06, G:0.34, T:0.26
Consensus pattern (16 bp):
ATTTCAGGGGGGAAAA
Found at i:28752481 original size:14 final size:14
Alignment explanation
Indices: 28752454--28752492 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
28752444 ACATAATCCT
*
28752454 TAACCCCTAGACCCC
1 TAACCCTTA-ACCCC
28752469 TAACCCTTAACCCC
1 TAACCCTTAACCCC
*
28752483 CAACCCTTAA
1 TAACCCTTAA
28752493 ACCATAAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.31, C:0.49, G:0.03, T:0.18
Consensus pattern (14 bp):
TAACCCTTAACCCC
Found at i:28752502 original size:15 final size:14
Alignment explanation
Indices: 28752484--28752543 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
28752474 CTTAACCCCC
28752484 AACCCTTAAACCATA
1 AACCC-TAAACCATA
* *
28752499 AACCATAATCCATA
1 AACCCTAAACCATA
*
28752513 ATCCCTAAACACATA
1 AACCCTAAAC-CATA
* *
28752528 ATCCCTAAACCTTA
1 AACCCTAAACCATA
28752542 AA
1 AA
28752544 ATTTGGATAT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
14 19 0.51
15 18 0.49
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.22
Consensus pattern (14 bp):
AACCCTAAACCATA
Found at i:28752543 original size:22 final size:21
Alignment explanation
Indices: 28752490--28752543 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
28752480 CCCCAACCCT
28752490 TAAACCATAAACCATAATCCA
1 TAAACCATAAACCATAATCCA
* * *
28752511 TAATCCCTAAACACATAATCCC
1 TAAACCATAAAC-CATAATCCA
*
28752533 TAAACCTTAAA
1 TAAACCATAAA
28752544 ATTTGGATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (21 bp):
TAAACCATAAACCATAATCCA
Found at i:28752975 original size:14 final size:14
Alignment explanation
Indices: 28752955--28753003 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
28752945 AATGGTAACA
*
28752955 CCTAAACCTTAAAC
1 CCTAAACCATAAAC
* *
28752969 TCTAAACCATATAC
1 CCTAAACCATAAAC
*
28752983 CCTAAACCAAAAAC
1 CCTAAACCATAAAC
28752997 CCTAAAC
1 CCTAAAC
28753004 TCTAGTGATA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.18
Consensus pattern (14 bp):
CCTAAACCATAAAC
Found at i:28753244 original size:41 final size:41
Alignment explanation
Indices: 28753186--28753430 Score: 312
Period size: 41 Copynumber: 6.0 Consensus size: 41
28753176 TTTAAATCCT
** *
28753186 TGAGCATTAGCGGCGCTTTATCAAAAACGCCACTAAAGCCC
1 TGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCC
* * * *
28753227 CGAGCATTAGCGGCGCTTTTCCAAAAACTCCGCTAAAGCCA
1 TGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCC
* *
28753268 GGAGCATTAGCGGCGCTTTCCCAAAAACGCCGTTAAAAG-CC
1 TGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCT-AAAGCCC
* *
28753309 TGAGCATTAGCGGCACTTTCCCAAAAACGCCGCTAAAGCCT
1 TGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCC
* * * *
28753350 TGAGCATTAGCGGCGCTTTCACAGAAACGTCGCTAAATCCC
1 TGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCC
* * *
28753391 TGGGCATTAGTGGCGCTTTCCCAAAAATGCCGCTAAAGCC
1 TGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCC
28753431 TCGAAAGCTC
Statistics
Matches: 174, Mismatches: 28, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
40 4 0.02
41 166 0.95
42 4 0.02
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.20
Consensus pattern (41 bp):
TGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCC
Found at i:28754642 original size:19 final size:19
Alignment explanation
Indices: 28754618--28754663 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
28754608 TTAAAGAAAA
28754618 AATTAATTAATATTTAT-AT
1 AATTAATTAATA-TTATGAT
**
28754637 AATTAAAAAATATTATGAT
1 AATTAATTAATATTATGAT
28754656 -ATTAATTA
1 AATTAATTA
28754664 TTTTGTATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
AATTAATTAATATTATGAT
Found at i:28757215 original size:19 final size:20
Alignment explanation
Indices: 28757191--28757231 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
28757181 TCTGTTTTGA
*
28757191 TTTTA-TTTATTCTACTCTG
1 TTTTATTTTATTCTACTATG
*
28757210 TTTTATTTTGTTCTACTATG
1 TTTTATTTTATTCTACTATG
28757230 TT
1 TT
28757232 GTAGTACCGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.15, C:0.12, G:0.07, T:0.66
Consensus pattern (20 bp):
TTTTATTTTATTCTACTATG
Found at i:28766022 original size:14 final size:16
Alignment explanation
Indices: 28765992--28766023 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
28765982 TAAAAAGTTA
28765992 TGTACTAGGGAATTTT
1 TGTACTAGGGAATTTT
28766008 TGTA-TAGGG-ATTTT
1 TGTACTAGGGAATTTT
28766022 TG
1 TG
28766024 GCTCTAGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 5 0.31
16 4 0.25
ACGTcount: A:0.22, C:0.03, G:0.28, T:0.47
Consensus pattern (16 bp):
TGTACTAGGGAATTTT
Found at i:28800682 original size:27 final size:27
Alignment explanation
Indices: 28800652--28800905 Score: 312
Period size: 27 Copynumber: 9.4 Consensus size: 27
28800642 GGGTATAATA
28800652 GTCATTTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTTG
* *
28800679 GTCATTTTACCCTATATGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTTG
* * * * **
28800706 CTCATTCTAACCTATGGGGGTATTTCA
1 GTCATTTTACCCTATAGGGGTATTTTG
* *
28800733 GTCATTTTACCCTATAAGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTTG
* * *
28800760 GTCATTTTACCTTATGGGGGTATTTCG
1 GTCATTTTACCCTATAGGGGTATTTTG
* *
28800787 GTAATTTTACCCTATTGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTTG
* *
28800814 GTCATTTTACCCTATGGGGGTATTTTA
1 GTCATTTTACCCTATAGGGGTATTTTG
** *
28800841 GTCATTTTACTTTATTGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTTG
28800868 GTCATTTTACCCTAT-GAGGGTATTTTG
1 GTCATTTTACCCTATAG-GGGTATTTTG
28800895 GTCATTTTACC
1 GTCATTTTACC
28800906 TATTTTAGGG
Statistics
Matches: 196, Mismatches: 30, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
26 1 0.01
27 195 0.99
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.45
Consensus pattern (27 bp):
GTCATTTTACCCTATAGGGGTATTTTG
Found at i:28802503 original size:24 final size:23
Alignment explanation
Indices: 28802458--28802506 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
28802448 AATTTATCGT
*
28802458 ATTTTTACTGGCAGCTTGTTTGC
1 ATTTTTACTGGCAGATTGTTTGC
* *
28802481 ATTTTTACTGGTAGAATTTTTTGC
1 ATTTTTACTGGCAG-ATTGTTTGC
28802505 AT
1 AT
28802507 ATTGTTATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.51
Consensus pattern (23 bp):
ATTTTTACTGGCAGATTGTTTGC
Found at i:28808887 original size:19 final size:19
Alignment explanation
Indices: 28808860--28808914 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 19
28808850 AAATCCCAAA
28808860 TTTTGATACCCATATCTTT
1 TTTTGATACCCATATCTTT
* *
28808879 TTTTTATACTCATATC--T
1 TTTTGATACCCATATCTTT
*
28808896 TTCTGATACCCATATCTTT
1 TTTTGATACCCATATCTTT
28808915 GACTTTTCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 14 0.48
19 15 0.52
ACGTcount: A:0.22, C:0.22, G:0.04, T:0.53
Consensus pattern (19 bp):
TTTTGATACCCATATCTTT
Found at i:28808909 original size:17 final size:17
Alignment explanation
Indices: 28808863--28808914 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
28808853 TCCCAAATTT
*
28808863 TGATACCCATATCTTTTTT
1 TGATACCCATATC--TTTC
* *
28808882 TTATACTCATATCTTTC
1 TGATACCCATATCTTTC
28808899 TGATACCCATATCTTT
1 TGATACCCATATCTTT
28808915 GACTTTTCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
17 17 0.61
19 11 0.39
ACGTcount: A:0.23, C:0.23, G:0.04, T:0.50
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:28830990 original size:23 final size:23
Alignment explanation
Indices: 28830960--28831007 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
28830950 TTAAAACATA
* *
28830960 TAAATATTTCATAT-ATTAATAT
1 TAAATATTTAATATAATTAAGAT
28830982 TAAAGTATTTAATATAATTAAGAT
1 TAAA-TATTTAATATAATTAAGAT
28831006 TA
1 TA
28831008 TATAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 9 0.41
24 9 0.41
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (23 bp):
TAAATATTTAATATAATTAAGAT
Found at i:28841812 original size:13 final size:13
Alignment explanation
Indices: 28841791--28841821 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
28841781 GCTTAGATCA
*
28841791 TCATCAAATAAAT
1 TCATAAAATAAAT
28841804 TCATAAAATAAAT
1 TCATAAAATAAAT
28841817 TCATA
1 TCATA
28841822 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:28842069 original size:30 final size:30
Alignment explanation
Indices: 28842034--28842091 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
28842024 CCTTGACTCT
*
28842034 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
28842064 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
28842092 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:28848027 original size:63 final size:62
Alignment explanation
Indices: 28847897--28848027 Score: 149
Period size: 62 Copynumber: 2.1 Consensus size: 62
28847887 GAGACACAGA
* * ** * *
28847897 CGTGTGTCCAAGTCGTGTGACACATTATTGTTATTAGAGACCACACGAGTCAGAGACATGGG
1 CGTGTGTCCAAGCCGTGTGACACACTATTGCGATTAGAGACCACACGAGGCAGAAACATGGG
* *
28847959 TGTGTGTCCAAGCCGTGTGACTCACTATTTGCGATCTA-AGACCACAC-AGGCAGACAACATGGG
1 CGTGTGTCCAAGCCGTGTGACACACTA-TTGCGAT-TAGAGACCACACGAGGCAGA-AACATGGG
28848022 CGTGTG
1 CGTGTG
28848028 ACAGGCCGTG
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
62 29 0.51
63 26 0.46
64 2 0.04
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (62 bp):
CGTGTGTCCAAGCCGTGTGACACACTATTGCGATTAGAGACCACACGAGGCAGAAACATGGG
Found at i:28849221 original size:22 final size:22
Alignment explanation
Indices: 28849204--28849270 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
28849194 GAACTAAACC
28849204 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
28849226 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
** *
28849248 CTCATGTTTCACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
28849270 C
1 C
28849271 ATAATTGGAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.30
Consensus pattern (22 bp):
CTCATGGCTAACGTACTAAGCT
Found at i:28849511 original size:18 final size:19
Alignment explanation
Indices: 28849484--28849519 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
28849474 CAAAAAAACT
28849484 AAAATAATTTTTAAAATTC
1 AAAATAATTTTTAAAATTC
28849503 AAAAT-ATTTTTAAAATT
1 AAAATAATTTTTAAAATT
28849520 TTCAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAATAATTTTTAAAATTC
Found at i:28856014 original size:23 final size:24
Alignment explanation
Indices: 28855984--28856037 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
28855974 TTACATCTCA
*
28855984 AAAAATTATAAA-A-AATTATATAT
1 AAAAATTA-AAACATAAATATATAT
28856007 AAAAATTAAAACTATAAATATATAT
1 AAAAATTAAAAC-ATAAATATATAT
28856032 AAAAAT
1 AAAAAT
28856038 AAATCTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 3 0.11
23 8 0.30
24 1 0.04
25 15 0.56
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (24 bp):
AAAAATTAAAACATAAATATATAT
Found at i:28859787 original size:60 final size:59
Alignment explanation
Indices: 28859671--28859787 Score: 128
Period size: 60 Copynumber: 2.0 Consensus size: 59
28859661 AGTATTTAAG
** * * ** *
28859671 ATTTTTTTTTGTCCAATTAGGTACCTAAAGTTAGTTTTAAGGTTCAATTTGGTACCTCA
1 ATTTTTTTTTGTCCAATTAAATACATAAACTTAGTTTTAAGGTTCAAAATGATACCTCA
* *
28859730 ATTTTTTTTTGGTCCACTTAAATACATAAACTTAGCTTTT-TGGTTCAAAATGATACCT
1 ATTTTTTTTT-GTCCAATTAAATACATAAACTTAG-TTTTAAGGTTCAAAATGATACCT
28859788 GAACTTGGTT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
59 10 0.21
60 33 0.70
61 4 0.09
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (59 bp):
ATTTTTTTTTGTCCAATTAAATACATAAACTTAGTTTTAAGGTTCAAAATGATACCTCA
Found at i:28864598 original size:37 final size:37
Alignment explanation
Indices: 28864557--28864795 Score: 433
Period size: 37 Copynumber: 6.5 Consensus size: 37
28864547 TTGTAATAAC
28864557 TCAAATTATATAAAATTATAAATGGTTAGTAAAATTA
1 TCAAATTATATAAAATTATAAATGGTTAGTAAAATTA
*
28864594 TCAAATTATATAAAATTATTAATGGTTAGTAAAATTA
1 TCAAATTATATAAAATTATAAATGGTTAGTAAAATTA
*
28864631 TCAAATTATATAAAATTATTAATGGTTAGTAAAATTA
1 TCAAATTATATAAAATTATAAATGGTTAGTAAAATTA
*
28864668 TCAAATTATATAAAATTATAAATGGTCAGTAAAATTA
1 TCAAATTATATAAAATTATAAATGGTTAGTAAAATTA
*
28864705 TCAAATTATATAAAATTATTAATGGTTAGTAAAATTA
1 TCAAATTATATAAAATTATAAATGGTTAGTAAAATTA
*
28864742 TCAAATTATATAAAATTATAAATGGTTAATAAAATTA
1 TCAAATTATATAAAATTATAAATGGTTAGTAAAATTA
28864779 TCAAATTATATAAAATT
1 TCAAATTATATAAAATT
28864796 GGGTTAGGGT
Statistics
Matches: 195, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 195 1.00
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (37 bp):
TCAAATTATATAAAATTATAAATGGTTAGTAAAATTA
Found at i:28864842 original size:29 final size:29
Alignment explanation
Indices: 28864794--28865162 Score: 505
Period size: 29 Copynumber: 12.7 Consensus size: 29
28864784 TTATATAAAA
28864794 TTGGGTTAGGGTTAGGGTTTTTAATTAAG
1 TTGGGTTAGGGTTAGGGTTTTTAATTAAG
* * *
28864823 TTTGGATAGGGTTAGGGTTTTTAATTAAA
1 TTGGGTTAGGGTTAGGGTTTTTAATTAAG
28864852 TTGGGTTA-GGTTAGGGTTTTTAATTAAG
1 TTGGGTTAGGGTTAGGGTTTTTAATTAAG
*
28864880 TTAGGTTAGGGTTAGGGTTTTTAATTGAA-
1 TTGGGTTAGGGTTAGGGTTTTTAATT-AAG
*
28864909 TTGGGTTAGGGTTAGGGTTTTTAATTAAA
1 TTGGGTTAGGGTTAGGGTTTTTAATTAAG
*
28864938 TTAGGTTAGGGTTAGGGTTTTTAATTAAG
1 TTGGGTTAGGGTTAGGGTTTTTAATTAAG
* *
28864967 TTAGGTTAGGGTTAGGATTTTTAATTAAG
1 TTGGGTTAGGGTTAGGGTTTTTAATTAAG
* * * *
28864996 TTAATTAGGTTAGGGTTAGGGCTTTTATTTAAA
1 ----TTGGGTTAGGGTTAGGGTTTTTAATTAAG
28865029 TTGGGTTAGGGTTAGGGTTTTTAATTGAA-
1 TTGGGTTAGGGTTAGGGTTTTTAATT-AAG
28865058 TTGGGTTAGGGTTAGGGTTTTTAATTAAG
1 TTGGGTTAGGGTTAGGGTTTTTAATTAAG
*
28865087 TTTGGTTAGGGTTAGGGTTTTTAATTTAA-
1 TTGGGTTAGGGTTAGGGTTTTTAA-TTAAG
28865116 TTGGGTTAGGGTTAGGGTTTTTAATTAAG
1 TTGGGTTAGGGTTAGGGTTTTTAATTAAG
* *
28865145 TTAGGTTAGAGTT-GGGTT
1 TTGGGTTAGGGTTAGGGTT
28865163 AGGGTTAGGG
Statistics
Matches: 307, Mismatches: 22, Indels: 23
0.87 0.06 0.07
Matches are distributed among these distances:
28 39 0.13
29 235 0.77
30 8 0.03
33 25 0.08
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (29 bp):
TTGGGTTAGGGTTAGGGTTTTTAATTAAG
Found at i:28864856 original size:58 final size:58
Alignment explanation
Indices: 28864791--28865258 Score: 582
Period size: 58 Copynumber: 7.8 Consensus size: 58
28864781 AAATTATATA
* *
28864791 AAATTGGGTTAGGGTTAGGGTTTTTAATTAAGTTTGGATAGGGTTAGGGTTTTTAATT
1 AAATTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATT
28864849 AAATTGGGTTA-GGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATT
* *
28864906 GAATTGGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATT
* * * * *
28864964 AAGTTAGGTTAGGGTTAGGATTTTTAATTAAGTTAATTAGGTTAGGGTTAGGGCTTTTATTT
1 AAATTGGGTTAGGGTTAGGGTTTTTAATTAAG----TTAGGTTAGGGTTAGGGTTTTTAATT
*
28865026 AAATTGGGTTAGGGTTAGGGTTTTTAATTGAA-TTGGGTTAGGGTTAGGGTTTTTAATT
1 AAATTGGGTTAGGGTTAGGGTTTTTAATT-AAGTTAGGTTAGGGTTAGGGTTTTTAATT
* * *
28865084 AAGTTTGGTTAGGGTTAGGGTTTTTAATTTAA-TTGGGTTAGGGTTAGGGTTTTTAATTAAGTT
1 AAATTGGGTTAGGGTTAGGGTTTTTAA-TTAAGTTAGGTTAGGGTTAGGG--TTT--TTAA-TT
* * *
28865147 AGGTTAGAGTTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTGGGGGTTTTAACT
1 A----A-A-TTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATT
* * * *
28865211 GAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTGGGTTAGGGTTAGG
1 AAATTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGG
28865259 AATAAATTTC
Statistics
Matches: 361, Mismatches: 30, Indels: 38
0.84 0.07 0.09
Matches are distributed among these distances:
57 54 0.15
58 191 0.53
59 3 0.01
60 4 0.01
62 54 0.15
63 5 0.01
64 1 0.00
65 4 0.01
67 3 0.01
68 4 0.01
69 38 0.11
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (58 bp):
AAATTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATT
Found at i:28865072 original size:149 final size:149
Alignment explanation
Indices: 28864791--28865258 Score: 678
Period size: 149 Copynumber: 3.1 Consensus size: 149
28864781 AAATTATATA
* *
28864791 AAATTGGGTTAGGGTTAGGGTTTTTAATTAAGTTTGGATAGGGTTAGGGTTTTTAATT-A---AA
1 AAATTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAA
28864852 TTGGGTTA-GGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTGAATTGGGTT
66 TTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTGAATTGGGTT
28864916 AGGGTTAGGGTTTTTAATT
131 AGGGTTAGGGTTTTTAATT
* *
28864935 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGATTTTTAATTAAGTTAA
1 AAATTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAA
* * * * *
28865000 TTAGGTTAGGGTTAGGGCTTTTATTTAAATTGGGTTAGGGTTAGGGTTTTTAATTGAATTGGGTT
66 TTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTGAATTGGGTT
28865065 AGGGTTAGGGTTTTTAATT
131 AGGGTTAGGGTTTTTAATT
* * *
28865084 AAGTTTGGTTAGGGTTAGGGTTTTTAATTTAA-TTGGGTTAGGGTTAGGGTTTTTAATTAAGTTA
1 AAATTGGGTTAGGGTTAGGGTTTTTAA-TTAAGTTAGGTTAGGGTTAGGGTTTTTAATT-A---A
* * *
28865148 GGTTAGAGTTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTGGGGGTTTTAACTGA
61 -GTTA-A-TTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTGA
*
28865213 ATTAGGTTAGGGTTAGGGTTTTTAATT
123 ATTGGGTTAGGGTTAGGGTTTTTAATT
28865240 AAATTGGGTTAGGGTTAGG
1 AAATTGGGTTAGGGTTAGG
28865259 AATAAATTTC
Statistics
Matches: 287, Mismatches: 24, Indels: 14
0.88 0.07 0.04
Matches are distributed among these distances:
144 54 0.19
145 1 0.00
148 9 0.03
149 120 0.42
150 5 0.02
153 1 0.00
154 4 0.01
155 1 0.00
156 92 0.32
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (149 bp):
AAATTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAA
TTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTGAATTGGGTT
AGGGTTAGGGTTTTTAATT
Found at i:28865169 original size:69 final size:69
Alignment explanation
Indices: 28865085--28865232 Score: 201
Period size: 69 Copynumber: 2.1 Consensus size: 69
28865075 TTTTTAATTA
* * * *
28865085 AGTTTGGTTAGGGTTAGGGTTTTTAATTTAA-TTGGGTTAGGGTTAGGGTTTTTAA-TTAAGTTA
1 AGTTGGGTTAGGGTTAGGGTTTTTAA-TTAAGTTAGGTTAGGGTTAGGGGTTTTAACTGAA-TTA
28865148 GGTTAG
64 GGTTAG
*
28865154 AGTTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTGGGGGTTTTAACTGAATTAGG
1 AGTTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGGTTTTAACTGAATTAGG
28865219 TTAG
66 TTAG
*
28865223 GGTTAGGGTT
1 AGTT-GGGTT
28865233 TTTAATTAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
68 4 0.06
69 58 0.83
70 8 0.11
ACGTcount: A:0.21, C:0.01, G:0.35, T:0.43
Consensus pattern (69 bp):
AGTTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGGTTTTAACTGAATTAGG
TTAG
Found at i:28865171 original size:40 final size:40
Alignment explanation
Indices: 28865116--28865200 Score: 161
Period size: 40 Copynumber: 2.1 Consensus size: 40
28865106 TTTAATTTAA
28865116 TTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGAG
1 TTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGAG
*
28865156 TTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGG
1 TTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGAG
28865196 TTGGG
1 TTGGG
28865201 GGTTTTAACT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.42
Consensus pattern (40 bp):
TTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGAG
Found at i:28865171 original size:98 final size:98
Alignment explanation
Indices: 28865058--28865251 Score: 316
Period size: 98 Copynumber: 2.0 Consensus size: 98
28865048 TTTAATTGAA
* * * * *
28865058 TTGGGTTAGGGTTAGGGTTTTTAATTAAGTTTGGTTAGGGTTAGGGTTTTTAATTTAATTGGGTT
1 TTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGGTTTTAACTGAATTAGGTT
*
28865123 AGGGTTAGGGTTTTTAATTAAGTTAGGTTAGAG
66 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGAG
*
28865156 TTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTGGGGGTTTTAACTGAATTAGGTT
1 TTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGGTTTTAACTGAATTAGGTT
*
28865221 AGGGTTAGGGTTTTTAATTAAATTGGGTTAG
66 AGGGTTAGGGTTTTTAATTAAATTAGGTTAG
28865252 GGTTAGGAAT
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 88 1.00
ACGTcount: A:0.22, C:0.01, G:0.34, T:0.44
Consensus pattern (98 bp):
TTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGGTTTTAACTGAATTAGGTT
AGGGTTAGGGTTTTTAATTAAATTAGGTTAGAG
Found at i:28865208 original size:127 final size:115
Alignment explanation
Indices: 28864791--28865258 Score: 573
Period size: 120 Copynumber: 3.9 Consensus size: 115
28864781 AAATTATATA
* * * *
28864791 AAATTGGGTTAGGGTTAGGGTTTTTAATTAAGTTTGGATAGGGTTAGGGTTTTTAATTAAATTGG
1 AAATTGGGTTAGGGTTAGGGTTTTTAATTAA-TTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAG
* * *
28864856 GTTA-GGTTAGGGTTTTTAA-TTAAGTTAGGTTAGGGTTAGGGTTTTTAATT
65 GTTAGGGTTAGGGTTTTTAATTTAA-TTGGGTTAGGGTTAGGGCTTTTATTT
*
28864906 GAATTGGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAG
1 AAATTGGGTTAGGGTTAGGGTTTTTAATT-AATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAG
* *
28864971 GTTAGGGTTAGGATTTTTAATTAAGTTAATTAGGTTAGGGTTAGGGCTTTTATTT
65 GTTAGGGTTAGGGTTTTTAA-T---TTAATTGGGTTAGGGTTAGGGCTTTTATTT
* *
28865026 AAATTGGGTTAGGGTTAGGGTTTTTAATTGAATTGGGTTAGGGTTAGGGTTTTTAATTAAGTTTG
1 AAATTGGGTTAGGGTTAGGGTTTTTAATT-AATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAG
*
28865091 GTTAGGGTTAGGGTTTTTAATTTAATTGGGTTAGGGTTAGGGTTTTTAATTAAGTT
65 GTTAGGGTTAGGGTTTTTAATTTAATTGGGTTAGGGTTAGGGCTTTT-A-T---TT
* * *
28865147 AGGTTAGAGTTGGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTGGGGGTTTTAACTG
1 A----A-A-TTGGGTTAGGGTTAGGGTTTTTAATTAA-TTAGGTTAGGGTTAGGGTTTTTAA-TT
*
28865212 AA-TTAGGTTAGGGTTAGGGTTTTTAATTAAATTGGGTTAGGGTTAGG
58 AAGTTAGGTTAGGGTTAGGGTTTTTAATTTAATTGGGTTAGGGTTAGG
28865259 AATAAATTTC
Statistics
Matches: 312, Mismatches: 21, Indels: 28
0.86 0.06 0.08
Matches are distributed among these distances:
115 61 0.20
116 40 0.13
117 1 0.00
118 1 0.00
119 1 0.00
120 104 0.33
121 7 0.02
125 1 0.00
126 3 0.01
127 90 0.29
128 3 0.01
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (115 bp):
AAATTGGGTTAGGGTTAGGGTTTTTAATTAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGG
TTAGGGTTAGGGTTTTTAATTTAATTGGGTTAGGGTTAGGGCTTTTATTT
Found at i:28865217 original size:29 final size:28
Alignment explanation
Indices: 28865159--28865258 Score: 128
Period size: 29 Copynumber: 3.5 Consensus size: 28
28865149 GTTAGAGTTG
*
28865159 GGTTAGGGTTAGGGTTTTTAATTAAGTTA
1 GGTTAGGGTTAGGGTTTTTAA-TAAATTA
* * *
28865188 GGTTAGGGTTGGGGGTTTTAACTGAATTA
1 GGTTAGGGTTAGGGTTTTTAA-TAAATTA
*
28865217 GGTTAGGGTTAGGGTTTTTAATTAAATTG
1 GGTTAGGGTTAGGGTTTTTAA-TAAATTA
28865246 GGTTAGGGTTAGG
1 GGTTAGGGTTAGG
28865259 AATAAATTTC
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 61 1.00
ACGTcount: A:0.22, C:0.01, G:0.36, T:0.41
Consensus pattern (28 bp):
GGTTAGGGTTAGGGTTTTTAATAAATTA
Found at i:28865484 original size:21 final size:21
Alignment explanation
Indices: 28865458--28865507 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
28865448 CTTTCTCTAG
* *
28865458 CTTCCGGTGGCGG-TTGTTGTT
1 CTTCCGGTGG-GGATTCTGGTT
28865479 CTTCCGGTGGGGATTCTGGTT
1 CTTCCGGTGGGGATTCTGGTT
28865500 CTTCCGGT
1 CTTCCGGT
28865508 ACGACATCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 24 0.92
ACGTcount: A:0.02, C:0.22, G:0.36, T:0.40
Consensus pattern (21 bp):
CTTCCGGTGGGGATTCTGGTT
Found at i:28865787 original size:18 final size:18
Alignment explanation
Indices: 28865761--28865801 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
28865751 GGACTCGAAA
28865761 AAGGATACATATAAGGGT
1 AAGGATACATATAAGGGT
*
28865779 AAGGGTACATATAAGGGT
1 AAGGATACATATAAGGGT
*
28865797 TAGGA
1 AAGGA
28865802 AACGCACCTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.32, T:0.22
Consensus pattern (18 bp):
AAGGATACATATAAGGGT
Found at i:28866458 original size:7 final size:7
Alignment explanation
Indices: 28866446--28866470 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28866436 TATACATAAT
28866446 AATACTA
1 AATACTA
28866453 AATACTA
1 AATACTA
28866460 AATACTA
1 AATACTA
28866467 AATA
1 AATA
28866471 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:28867664 original size:51 final size:51
Alignment explanation
Indices: 28867609--28867724 Score: 214
Period size: 51 Copynumber: 2.3 Consensus size: 51
28867599 TATTTTAAAA
*
28867609 AAGGAAATTGAGAGGAAATTGAAATCAAATATGGATTTGAGAGAATTTTGG
1 AAGGAAATTGAGAGGAAATTGAAATCAAATATGCATTTGAGAGAATTTTGG
*
28867660 AAGGAAATTGAGAGGAAATTGAAATTAAATATGCATTTGAGAGAATTTTGG
1 AAGGAAATTGAGAGGAAATTGAAATCAAATATGCATTTGAGAGAATTTTGG
28867711 AAGGAAATTGAGAG
1 AAGGAAATTGAGAG
28867725 AATTTTGGAA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.44, C:0.02, G:0.28, T:0.27
Consensus pattern (51 bp):
AAGGAAATTGAGAGGAAATTGAAATCAAATATGCATTTGAGAGAATTTTGG
Found at i:28867667 original size:29 final size:29
Alignment explanation
Indices: 28867635--28867718 Score: 74
Period size: 29 Copynumber: 3.1 Consensus size: 29
28867625 AATTGAAATC
28867635 AAATATGGATTTGAGAGAATTTTGGAAGG
1 AAATATGGATTTGAGAGAATTTTGGAAGG
* * **
28867664 AAAT-T-GA---GAG-GAA-ATTGAAATT
1 AAATATGGATTTGAGAGAATTTTGGAAGG
*
28867686 AAATATGCATTTGAGAGAATTTTGGAAGG
1 AAATATGGATTTGAGAGAATTTTGGAAGG
28867715 AAAT
1 AAAT
28867719 TGAGAGAATT
Statistics
Matches: 39, Mismatches: 9, Indels: 14
0.63 0.15 0.23
Matches are distributed among these distances:
22 9 0.23
23 4 0.10
24 4 0.10
27 5 0.13
28 4 0.10
29 13 0.33
ACGTcount: A:0.43, C:0.01, G:0.26, T:0.30
Consensus pattern (29 bp):
AAATATGGATTTGAGAGAATTTTGGAAGG
Found at i:28867673 original size:22 final size:22
Alignment explanation
Indices: 28867645--28867751 Score: 81
Period size: 22 Copynumber: 4.5 Consensus size: 22
28867635 AAATATGGAT
28867645 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
* * **
28867667 TTGAGAGGAA-ATTGAAATTAAA
1 TTGAGA-GAATTTTGGAAGGAAA
28867689 TATGCATTTGAGAGAATTTTGGAAGGAAA
1 T-TG-A---GAG--AATTTTGGAAGGAAA
*
28867718 TTGAGAGAATTTTGGAAAGAAA
1 TTGAGAGAATTTTGGAAGGAAA
28867740 TTGAGAGGAATT
1 TTGAGA-GAATT
28867752 GAGAGGAAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
22 35 0.53
23 10 0.15
24 4 0.06
26 1 0.02
27 3 0.05
28 4 0.06
29 9 0.14
ACGTcount: A:0.42, C:0.01, G:0.28, T:0.29
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:28867768 original size:12 final size:11
Alignment explanation
Indices: 28867736--28867768 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
28867726 ATTTTGGAAA
28867736 GAAATTGAGAG
1 GAAATTGAGAG
28867747 G-AATTGAGAG
1 GAAATTGAGAG
28867757 GAAATATGAGAG
1 GAAAT-TGAGAG
28867769 AGGATTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 4 0.20
12 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.18
Consensus pattern (11 bp):
GAAATTGAGAG
Found at i:28873206 original size:24 final size:24
Alignment explanation
Indices: 28873174--28873223 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
28873164 TGGTGGAGGT
*
28873174 GACACGTGTGTTGCAACCAAATCA
1 GACACGTGTGGTGCAACCAAATCA
*
28873198 GACACGTGTGGTGCAACCGAATCA
1 GACACGTGTGGTGCAACCAAATCA
28873222 GA
1 GA
28873224 TCACATGGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (24 bp):
GACACGTGTGGTGCAACCAAATCA
Found at i:28877961 original size:16 final size:17
Alignment explanation
Indices: 28877942--28877974 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28877932 AAATTTATAC
*
28877942 ATATATA-ATATGAAAA
1 ATATATAGAAATGAAAA
28877958 ATATATAGAAATGAAAA
1 ATATATAGAAATGAAAA
28877975 TTATTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (17 bp):
ATATATAGAAATGAAAA
Found at i:28878252 original size:2 final size:2
Alignment explanation
Indices: 28878245--28878283 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
28878235 CATAATCACC
28878245 TA TA 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 TA TA T
28878284 GTATGTATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28878869 original size:20 final size:20
Alignment explanation
Indices: 28878846--28878884 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28878836 GTGTCGTGAC
*
28878846 TCTGGTCCTGATGTCGCGAT
1 TCTGGTCCTGATGTAGCGAT
28878866 TCTGGTCCTGATGTAGCGA
1 TCTGGTCCTGATGTAGCGA
28878885 CTTTAGCTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.31, T:0.33
Consensus pattern (20 bp):
TCTGGTCCTGATGTAGCGAT
Found at i:28883176 original size:31 final size:31
Alignment explanation
Indices: 28883138--28883198 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
28883128 TACATAGACG
28883138 AAAATACTACACTTAGGACACCAGATCCATT
1 AAAATACTACACTTAGGACACCAGATCCATT
*
28883169 AAAATACTACACTTAGGGCACCAGATCCAT
1 AAAATACTACACTTAGGACACCAGATCCAT
28883199 CGGAATATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.41, C:0.26, G:0.11, T:0.21
Consensus pattern (31 bp):
AAAATACTACACTTAGGACACCAGATCCATT
Found at i:28888142 original size:3 final size:3
Alignment explanation
Indices: 28888136--28888168 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
28888126 GTTGCTGTTG
*
28888136 TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28888169 CTCTTATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:28890034 original size:3 final size:3
Alignment explanation
Indices: 28890026--28890105 Score: 151
Period size: 3 Copynumber: 26.7 Consensus size: 3
28890016 CGACTTCGTT
*
28890026 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28890074 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28890106 TCTTTCATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28890676 original size:19 final size:19
Alignment explanation
Indices: 28890639--28890677 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
28890629 CTTTGTATTT
*
28890639 ATTTCAATTTGGCTCTCAA
1 ATTTCAATTTGGATCTCAA
* *
28890658 ATTTCAATTTTGATTTCAA
1 ATTTCAATTTGGATCTCAA
28890677 A
1 A
28890678 ATTAGTCTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (19 bp):
ATTTCAATTTGGATCTCAA
Found at i:28890720 original size:3 final size:3
Alignment explanation
Indices: 28890714--28890746 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
28890704 GTTGTTGTTG
*
28890714 TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28890747 CTCTTATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:28890974 original size:22 final size:21
Alignment explanation
Indices: 28890918--28890974 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
28890908 AAGATGTAGT
28890918 ATGCTATTATTTTTAAATTATC
1 ATGC-ATTATTTTTAAATTATC
* **
28890940 AT-TAACATGTTTTAAATTTATC
1 ATGCATTAT-TTTTAAA-TTATC
28890962 ATGCATTATTTTT
1 ATGCATTATTTTT
28890975 TAGTCTATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
20 3 0.12
21 7 0.27
22 13 0.50
23 3 0.12
ACGTcount: A:0.32, C:0.09, G:0.05, T:0.54
Consensus pattern (21 bp):
ATGCATTATTTTTAAATTATC
Found at i:28894154 original size:42 final size:42
Alignment explanation
Indices: 28894095--28894178 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
28894085 GCAGTTTTCG
*
28894095 TTACCTCTGCAACATCATGTAGTTGTCCGGTAGTGAAATTGA
1 TTACCTCTGCAACATCATATAGTTGTCCGGTAGTGAAATTGA
* *
28894137 TTACCTCTGCAACATCATATAGTTGTTCTGTAGTGAAATTGA
1 TTACCTCTGCAACATCATATAGTTGTCCGGTAGTGAAATTGA
28894179 ACACTGCAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (42 bp):
TTACCTCTGCAACATCATATAGTTGTCCGGTAGTGAAATTGA
Found at i:28896113 original size:55 final size:55
Alignment explanation
Indices: 28896013--28896191 Score: 292
Period size: 55 Copynumber: 3.3 Consensus size: 55
28896003 ACTTTTTTTT
* *
28896013 TCATTCATTTCAATTTT-TTTTTCTACATCTAACA--CTTTTTTTTCATTTAATC
1 TCATTTATTTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTTCATTCAATC
28896065 TCATTTATTTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTTCATTCAATC
1 TCATTTATTTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTTCATTCAATC
* *
28896120 TCATTTATTTCAATTTAATTTTTCTACATCTAACACCCTGTTTTTTCATTCAATC
1 TCATTTATTTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTTCATTCAATC
*
28896175 TCATTTATTTTAATTTT
1 TCATTTATTTCAATTTT
28896192 TTGAATTTTA
Statistics
Matches: 118, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
52 16 0.14
53 17 0.14
55 85 0.72
ACGTcount: A:0.24, C:0.20, G:0.01, T:0.56
Consensus pattern (55 bp):
TCATTTATTTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTTCATTCAATC
Found at i:28897475 original size:56 final size:55
Alignment explanation
Indices: 28897388--28897550 Score: 215
Period size: 55 Copynumber: 3.0 Consensus size: 55
28897378 CACTTTTTTT
* *
28897388 TCATTCATTTCAA--TT-TTTTTCTACGTCTAACACCCTTTTTTTTTCATTCAATC
1 TCATTTATTTCAATTTTATTTTTCTACATCTAACACCC-TTTTTTTTCATTCAATC
*
28897441 TCATTTATTTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTTCTTTCAATC
1 TCATTTATTTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTTCATTCAATC
* * ** *
28897496 TAATTTATTTCAATTTTATTTTTTTACATCTAATTTCCCTTTATTTTCATTCAAT
1 TCATTTATTTCAATTTTATTTTTCTACATCTAA-CACCCTTTTTTTTCATTCAAT
28897551 TTTATTTTTC
Statistics
Matches: 97, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
53 12 0.12
55 49 0.51
56 36 0.37
ACGTcount: A:0.23, C:0.20, G:0.01, T:0.56
Consensus pattern (55 bp):
TCATTTATTTCAATTTTATTTTTCTACATCTAACACCCTTTTTTTTCATTCAATC
Found at i:28898805 original size:30 final size:30
Alignment explanation
Indices: 28898759--28898852 Score: 161
Period size: 30 Copynumber: 3.1 Consensus size: 30
28898749 ATTTCTTATG
*
28898759 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
28898790 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
*
28898820 CCATTATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
28898850 CCA
1 CCA
28898853 TAAATATGGA
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
30 54 0.89
31 7 0.11
ACGTcount: A:0.26, C:0.27, G:0.06, T:0.41
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:28898814 original size:15 final size:15
Alignment explanation
Indices: 28898769--28898845 Score: 68
Period size: 15 Copynumber: 5.1 Consensus size: 15
28898759 CCAATATCTC
28898769 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
28898784 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
28898799 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
28898814 GACTTTCCAT-TATTT
1 GA-TACCCATATCTTT
28898829 GATACCCATATCTTT
1 GATACCCATATCTTT
28898844 GA
1 GA
28898846 CTTTCCATAA
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 9 0.20
15 28 0.61
16 9 0.20
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.43
Consensus pattern (15 bp):
GATACCCATATCTTT
Done.