Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397274.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_228.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2969030
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 66526 characters in sequence are not A, C, G, or T
File 2 of 8
Found at i:675689 original size:33 final size:32
Alignment explanation
Indices: 675651--675722 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 32
675641 TAGAATATAT
*
675651 AATATA-AGAAATTATATTAAAAAATAAAAATAA
1 AATATATA-AAATTATAATAAAAAAT-AAAATAA
* *
675684 AATATATAAGATTATAATAAGAAATAAAATAA
1 AATATATAAAATTATAATAAAAAATAAAATAA
675716 AATATAT
1 AATATAT
675723 GACATTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 14 0.40
33 20 0.57
34 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (32 bp):
AATATATAAAATTATAATAAAAAATAAAATAA
Found at i:675718 original size:32 final size:34
Alignment explanation
Indices: 675652--675722 Score: 101
Period size: 32 Copynumber: 2.1 Consensus size: 34
675642 AGAATATATA
*
675652 ATATAAGAAATTATATTAAAAAATAAAAATAAAAT
1 ATATAAG-AATTATAATAAAAAATAAAAATAAAAT
*
675687 ATATAAG-ATTATAATAAGAAAT-AAAATAAAAT
1 ATATAAGAATTATAATAAAAAATAAAAATAAAAT
675719 ATAT
1 ATAT
675723 GACATTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 14 0.41
33 13 0.38
35 7 0.21
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (34 bp):
ATATAAGAATTATAATAAAAAATAAAAATAAAAT
Found at i:677157 original size:53 final size:53
Alignment explanation
Indices: 677077--677182 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
677067 AAATTGTGCT
677077 AGGAAATAAGTTTAATATCTTCTACCCAGACCTTGTCGACAAGACAAAGGCTC
1 AGGAAATAAGTTTAATATCTTCTACCCAGACCTTGTCGACAAGACAAAGGCTC
677130 AGGAAATAAGTTTAATATCTTCTACCCAGACCTTGTCGACAAGACAAAGGCTC
1 AGGAAATAAGTTTAATATCTTCTACCCAGACCTTGTCGACAAGACAAAGGCTC
677183 CTGCATATGC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (53 bp):
AGGAAATAAGTTTAATATCTTCTACCCAGACCTTGTCGACAAGACAAAGGCTC
Found at i:680098 original size:50 final size:50
Alignment explanation
Indices: 680039--680137 Score: 126
Period size: 50 Copynumber: 2.0 Consensus size: 50
680029 TTTAATAGTT
*
680039 ATATAAAACTCTATAGAGTTAATAGAAAGGCACATTCAAGTTGAGAATAA
1 ATATAAAACTCTATAGAGTTAATAGAAAGGCACATTCAAGATGAGAATAA
* * * * ** *
680089 ATATAAAACTTTATTGGGTTAATTGTTAGGCACATTTAAGATGAGAATA
1 ATATAAAACTCTATAGAGTTAATAGAAAGGCACATTCAAGATGAGAATA
680138 TTTTGACTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.31
Consensus pattern (50 bp):
ATATAAAACTCTATAGAGTTAATAGAAAGGCACATTCAAGATGAGAATAA
Found at i:682097 original size:50 final size:51
Alignment explanation
Indices: 682021--682142 Score: 176
Period size: 50 Copynumber: 2.4 Consensus size: 51
682011 TGCACATAGA
* *
682021 TTGGACTG-TTATAATATTGAAAAGTCAAATAAATGTAGGACAGATGTAGG
1 TTGGACAGATTATAATATTGAAAAGTCAAATAAATCTAGGACAGATGTAGG
* * *
682071 TTGGACAGATTA-AATATTGAAGAGTCAAATAAATCTAGTATAGATGTAGG
1 TTGGACAGATTATAATATTGAAAAGTCAAATAAATCTAGGACAGATGTAGG
*
682121 TTGGACAGGTTATAATATTGAA
1 TTGGACAGATTATAATATTGAA
682143 CAGCCAAGTT
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
50 52 0.81
51 12 0.19
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (51 bp):
TTGGACAGATTATAATATTGAAAAGTCAAATAAATCTAGGACAGATGTAGG
Found at i:690647 original size:19 final size:19
Alignment explanation
Indices: 690623--690659 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
690613 GGACTCCAAA
690623 GAAATCCAAGTTGTGCTAG
1 GAAATCCAAGTTGTGCTAG
690642 GAAATCCAAGTTGTGCTA
1 GAAATCCAAGTTGTGCTA
690660 ACATTTAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.27
Consensus pattern (19 bp):
GAAATCCAAGTTGTGCTAG
Found at i:693559 original size:4 final size:4
Alignment explanation
Indices: 693550--693600 Score: 52
Period size: 4 Copynumber: 13.2 Consensus size: 4
693540 GTTCAATTTT
* * * *
693550 ATAC ATAC ATAC ATAC ATAC ATAT ACAA ATAC A-A- ATAC ATAC ACAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
693596 ATAC A
1 ATAC A
693601 CACACACACA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
2 1 0.03
3 2 0.05
4 35 0.92
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.22
Consensus pattern (4 bp):
ATAC
Found at i:693587 original size:18 final size:18
Alignment explanation
Indices: 693566--693600 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
693556 ACATACATAC
*
693566 ATACATATACAAATACAA
1 ATACATACACAAATACAA
*
693584 ATACATACACACATACA
1 ATACATACACAAATACA
693601 CACACACACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (18 bp):
ATACATACACAAATACAA
Found at i:693601 original size:8 final size:8
Alignment explanation
Indices: 693552--693618 Score: 53
Period size: 8 Copynumber: 8.1 Consensus size: 8
693542 TCAATTTTAT
*
693552 ACATACAT
1 ACATACAC
*
693560 ACATACAT
1 ACATACAC
*
693568 ACATATAC
1 ACATACAC
* *
693576 AAATACAAAT
1 ACATAC--AC
693586 ACATACAC
1 ACATACAC
693594 ACATACAC
1 ACATACAC
*
693602 ACACACAC
1 ACATACAC
*
693610 ACACACAC
1 ACATACAC
693618 A
1 A
693619 TATATAGTTA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
8 43 0.88
10 6 0.12
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (8 bp):
ACATACAC
Found at i:708081 original size:30 final size:30
Alignment explanation
Indices: 708023--708082 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
708013 ATTGTTATTC
* *
708023 ATAAAAATTTATTTAATTTAAAATAAAAAT
1 ATAAAAATTTATTCAATATAAAATAAAAAT
*
708053 ATAAAAATTTTATTCAATATAATA-AAAAAT
1 ATAAAAA-TTTATTCAATATAAAATAAAAAT
708083 TTATTTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (30 bp):
ATAAAAATTTATTCAATATAAAATAAAAAT
Found at i:711549 original size:29 final size:29
Alignment explanation
Indices: 711504--711566 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
711494 CATGATGAAT
* *
711504 TGTCACTTTCTCCCTATTCAA-AAAAGAAG
1 TGTCAATTTCTCCCTATTCAATAAAA-AAA
711533 TGTCAATTTC-CCACTATTCAATAAAAAAA
1 TGTCAATTTCTCC-CTATTCAATAAAAAAA
711562 TGTCA
1 TGTCA
711567 CTTTTCTCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 2 0.07
29 24 0.80
30 4 0.13
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.32
Consensus pattern (29 bp):
TGTCAATTTCTCCCTATTCAATAAAAAAA
Found at i:711904 original size:30 final size:27
Alignment explanation
Indices: 711867--711933 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
711857 TAATTTGACT
711867 ATTTAT-TTTAATTTAAAAAATATTAATA
1 ATTTATATTTAATTT--AAAATATTAATA
* *
711895 ATTTATATTTCATTTAAAATATTAGTA
1 ATTTATATTTAATTTAAAATATTAATA
*
711922 ATTTATAATTAA
1 ATTTATATTTAA
711934 AACATTAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 21 0.62
28 6 0.18
29 7 0.21
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (27 bp):
ATTTATATTTAATTTAAAATATTAATA
Found at i:712108 original size:20 final size:20
Alignment explanation
Indices: 712083--712121 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
712073 TTTTAAATTC
712083 ATTTTAATTT-TTTCTTTTGA
1 ATTTT-ATTTATTTCTTTTGA
712103 ATTTTATTTACTTTCTTTT
1 ATTTTATTTA-TTTCTTTT
712122 TTATAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 5 0.29
21 8 0.47
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.72
Consensus pattern (20 bp):
ATTTTATTTATTTCTTTTGA
Found at i:712445 original size:18 final size:17
Alignment explanation
Indices: 712398--712448 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
712388 AACCTTTTTA
712398 TTTTAAATTCTTTTTAA-
1 TTTTAAATTC-TTTTAAT
712415 TTTT---TTCTTTTAAT
1 TTTTAAATTCTTTTAAT
712429 TTTTAAATTCATTTTAAT
1 TTTTAAATTC-TTTTAAT
712447 TT
1 TT
712449 AATGAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
13 6 0.21
14 7 0.24
17 7 0.24
18 9 0.31
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTAAATTCTTTTAAT
Found at i:716602 original size:21 final size:22
Alignment explanation
Indices: 716569--716612 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
716559 GACTCTCTGA
*
716569 TTTGTTGCTATGTTAACCTCAT
1 TTTGTTGCAATGTTAACCTCAT
* *
716591 TTTG-TGCAATGTTCACTTCAT
1 TTTGTTGCAATGTTAACCTCAT
716612 T
1 T
716613 GTTTGCCTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.18, C:0.18, G:0.14, T:0.50
Consensus pattern (22 bp):
TTTGTTGCAATGTTAACCTCAT
Found at i:727505 original size:23 final size:21
Alignment explanation
Indices: 727435--727506 Score: 108
Period size: 21 Copynumber: 3.3 Consensus size: 21
727425 TTTTCTTTTT
*
727435 AAACCTCTGGGTACATCTCTA
1 AAACCTCTGGGTACATCTTTA
727456 AAACCTCTGGGTACATCTTTA
1 AAACCTCTGGGTACATCTTTA
*
727477 AAACCTCTAGGTACATTCTTGTA
1 AAACCTCTGGGTACA-TCTT-TA
727500 AAACCTC
1 AAACCTC
727507 CAAGTAATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 34 0.72
22 4 0.09
23 9 0.19
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (21 bp):
AAACCTCTGGGTACATCTTTA
Found at i:727645 original size:21 final size:22
Alignment explanation
Indices: 727615--727660 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
727605 CTTTAAGTAT
*
727615 ATTTTCTAAAACCTCCGGGTAC
1 ATTTTCTAAAACCTCCAGGTAC
*
727637 ATTTT-TAAAACCTCTAGGTAC
1 ATTTTCTAAAACCTCCAGGTAC
727658 ATT
1 ATT
727661 CTTATGACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (22 bp):
ATTTTCTAAAACCTCCAGGTAC
Found at i:727770 original size:21 final size:21
Alignment explanation
Indices: 727742--727814 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
727732 CAACATTTTC
727742 TTTT-AAAACCTCTTGGTATA
1 TTTTCAAAACCTCTTGGTATA
* * *
727762 TCTTCAAAA-CTTTTGGATACA
1 TTTTCAAAACCTCTTGG-TATA
* *
727783 TTTTCTAAAACCTCTAGATATA
1 TTTTC-AAAACCTCTTGGTATA
727805 TTTTCAAAAC
1 TTTTCAAAAC
727815 TTCTAAGTAC
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
20 9 0.22
21 16 0.39
22 12 0.29
23 4 0.10
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41
Consensus pattern (21 bp):
TTTTCAAAACCTCTTGGTATA
Found at i:727792 original size:22 final size:21
Alignment explanation
Indices: 727764--727827 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
727754 TTGGTATATC
* *
727764 TTCAAAACTTTTGGATACATT
1 TTCAAAACTTCTAGATACATT
* *
727785 TTCTAAAACCTCTAGATATATT
1 TTC-AAAACTTCTAGATACATT
727807 TTCAAAACTTCTA-AGTACATT
1 TTCAAAACTTCTAGA-TACATT
727828 CTTATGACAC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 1 0.03
21 17 0.49
22 17 0.49
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.41
Consensus pattern (21 bp):
TTCAAAACTTCTAGATACATT
Found at i:727819 original size:21 final size:21
Alignment explanation
Indices: 727758--727819 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 21
727748 AACCTCTTGG
* * *
727758 TATATCTTCAAAACTTTTGGA
1 TATATTTTCAAAACTTCTAGA
* *
727779 TACATTTTCTAAAACCTCTAGA
1 TATATTTTC-AAAACTTCTAGA
727801 TATATTTTCAAAACTTCTA
1 TATATTTTCAAAACTTCTA
727820 AGTACATTCT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
21 16 0.48
22 17 0.52
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.42
Consensus pattern (21 bp):
TATATTTTCAAAACTTCTAGA
Found at i:727826 original size:43 final size:43
Alignment explanation
Indices: 727745--727827 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
727735 CATTTTCTTT
* * **
727745 TAAAACCTCTTGGTATATCTTCAAAACTTTTGGATACATTTTC
1 TAAAACCTCTAGATATATCTTCAAAACTTTAAGATACATTTTC
*
727788 TAAAACCTCTAGATATATTTTCAAAACTTCTAAG-TACATT
1 TAAAACCTCTAGATATATCTTCAAAACTT-TAAGATACATT
727828 CTTATGACAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 32 0.94
44 2 0.06
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.40
Consensus pattern (43 bp):
TAAAACCTCTAGATATATCTTCAAAACTTTAAGATACATTTTC
Found at i:727937 original size:167 final size:164
Alignment explanation
Indices: 727452--727938 Score: 528
Period size: 167 Copynumber: 2.9 Consensus size: 164
727442 TGGGTACATC
* * * *
727452 TCTAAAACCTCTGGGTACATCTTTAAAACCTCTAGGTACATTCTTGTAAAACCTCCAAGTAATTA
1 TCTAAAACCTCTGGGTACAT-TTTAAAACCTCTAGGTACATTCTTATGACACCTCCGAGTAATTA
* * * * **
727517 GTATTAATATTTATTTAAAGTTACGTAGCCTCATATTAAGATGATGAGCAATTTTTTCTTTTAAA
65 GCATTAATATTTCTTTAAAGTTACATAGCCTCAT-TTAAGATGAGGAGCAACATTTTCTTTTAAA
** * *
727582 ACCTCCGAGTGCATCTCCAAAAACTTTAAGTATATTT
129 ACCTCCGAGTATATCTTC-AAAACTTTAAGTACATTT
* * *
727619 TCTAAAACCTCCGGGTACATTTTTAAAACCTCTAGGTACATTCTTATGACACTTTCGAGTAATTA
1 TCTAAAACCTCTGGGTACA-TTTTAAAACCTCTAGGTACATTCTTATGACACCTCCGAGTAATTA
* * * *
727684 ACATTAATATTTCTTTAAAGTTA-AGTAGCTTCATTTTGAGATGGGGAGCAACATTTTCTTTTAA
65 GCATTAATATTTCTTTAAAGTTACA-TAGCCTCA-TTTAAGATGAGGAGCAACATTTTCTTTTAA
* **
727748 AACCTCTTG-GTATATCTTCAAAACTTTTGGATACATTT
128 AACCTC-CGAGTATATCTTCAAAACTTTAAG-TACATTT
* * * * * * *
727786 TCTAAAACCTCTAGATATATTTTCAAAACTTCTAAGTACATTCTTATGACACCTCCGGGTAACTA
1 TCTAAAACCTCTGGGTACATTTT-AAAACCTCTAGGTACATTCTTATGACACCTCCGAGTAATTA
* * * * * *
727851 GCATTAATATTTCTTTAAAGTTACACAACCTCGTTTAAAAATGAGGAGCAACCTTTTCTTATAAA
65 GCATTAATATTTCTTTAAAGTTACATAGCCTCATTT-AAGATGAGGAGCAACATTTTCTTTTAAA
*
727916 ACCTCCGAGTATATTTTCAAAAC
129 ACCTCCGAGTATATCTTCAAAAC
727939 CTTCGAGTAC
Statistics
Matches: 265, Mismatches: 46, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
166 17 0.06
167 244 0.92
168 4 0.02
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.37
Consensus pattern (164 bp):
TCTAAAACCTCTGGGTACATTTTAAAACCTCTAGGTACATTCTTATGACACCTCCGAGTAATTAG
CATTAATATTTCTTTAAAGTTACATAGCCTCATTTAAGATGAGGAGCAACATTTTCTTTTAAAAC
CTCCGAGTATATCTTCAAAACTTTAAGTACATTT
Found at i:727955 original size:21 final size:21
Alignment explanation
Indices: 727913--727958 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
727903 CTTTTCTTAT
* **
727913 AAAACCTCCGAGTATATTTTC
1 AAAACCTCCGAGTACAACTTC
*
727934 AAAACCTTCGAGTACAACTTC
1 AAAACCTCCGAGTACAACTTC
727955 AAAA
1 AAAA
727959 TCTTTGGGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.24, G:0.09, T:0.26
Consensus pattern (21 bp):
AAAACCTCCGAGTACAACTTC
Found at i:728042 original size:29 final size:29
Alignment explanation
Indices: 728000--728080 Score: 153
Period size: 29 Copynumber: 2.8 Consensus size: 29
727990 ATCATTTATT
728000 TTCTTTAAAGTTGTGGAGCCTTCTTAATA
1 TTCTTTAAAGTTGTGGAGCCTTCTTAATA
728029 TTCTTTAAAGTTGTGGAGCCTTCTTAATA
1 TTCTTTAAAGTTGTGGAGCCTTCTTAATA
*
728058 TTCTTTAAAGTTGTGAAGCCTTC
1 TTCTTTAAAGTTGTGGAGCCTTC
728081 AAATGAGGAG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.44
Consensus pattern (29 bp):
TTCTTTAAAGTTGTGGAGCCTTCTTAATA
Found at i:728243 original size:16 final size:15
Alignment explanation
Indices: 728236--728273 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 15
728226 AATGAATAAA
728236 AAATAAAAGAAAAAT
1 AAATAAAAGAAAAAT
728251 AAAGTAAAAGGAAAAAT
1 AAA-TAAAA-GAAAAAT
728268 AAATAA
1 AAATAA
728274 TGAAAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.14
16 8 0.38
17 10 0.48
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (15 bp):
AAATAAAAGAAAAAT
Found at i:728562 original size:22 final size:22
Alignment explanation
Indices: 728535--728584 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
728525 CAAAACTTTA
728535 CATTTTTG-TTGATGAAAAACTC
1 CATTTTTGATTGAT-AAAAACTC
*
728557 CA-TTTTGATTGCTAAAAACTC
1 CATTTTTGATTGATAAAAACTC
728578 CATTTTT
1 CATTTTT
728585 CTACTGCTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (22 bp):
CATTTTTGATTGATAAAAACTC
Found at i:737615 original size:34 final size:34
Alignment explanation
Indices: 737572--737659 Score: 167
Period size: 34 Copynumber: 2.6 Consensus size: 34
737562 AGTCCTCTAC
*
737572 TTGAATCAAATATATAACTTTTTTATTTTGAAAT
1 TTGAATCAAATTTATAACTTTTTTATTTTGAAAT
737606 TTGAATCAAATTTATAACTTTTTTATTTTGAAAT
1 TTGAATCAAATTTATAACTTTTTTATTTTGAAAT
737640 TTGAATCAAATTTATAACTT
1 TTGAATCAAATTTATAACTT
737660 AAAGAGAAAG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.38, C:0.07, G:0.06, T:0.50
Consensus pattern (34 bp):
TTGAATCAAATTTATAACTTTTTTATTTTGAAAT
Found at i:740850 original size:12 final size:12
Alignment explanation
Indices: 740833--740857 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
740823 TCAACAGTGA
740833 TATATATATAAT
1 TATATATATAAT
740845 TATATATATAAT
1 TATATATATAAT
740857 T
1 T
740858 TTTAGATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TATATATATAAT
Found at i:741133 original size:14 final size:14
Alignment explanation
Indices: 741114--741140 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
741104 ATGTCCAAGA
741114 TCAATCAAATTTGG
1 TCAATCAAATTTGG
741128 TCAATCAAATTTG
1 TCAATCAAATTTG
741141 TATAAAGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (14 bp):
TCAATCAAATTTGG
Found at i:744194 original size:3 final size:3
Alignment explanation
Indices: 744181--744211 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
744171 GAGAATTACC
744181 CTT CTTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT
744212 GTTTATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
CTT
Found at i:754364 original size:84 final size:84
Alignment explanation
Indices: 754252--754687 Score: 497
Period size: 84 Copynumber: 5.2 Consensus size: 84
754242 GCATGCAACT
** * * *
754252 TTTCTTCAACAGCC-TC--CTTAGTGGCTTCTGCAATCTTCTTTTGCTCCTCTACATTAGCCACC
1 TTTCTTCAACAGCCTTCTTCTTAGTTTCTTCTGCAATCTTCTTTTGCTCCTCTGCTTTAGCCATC
*
754314 TCCAAAT-TGGCAAGTTTTC
66 TCCAAATCT-GCATGTTTTC
* * *
754333 TTTCTTCAACAGCCTTCTTCGTAGTTTCTTCTGCGAGCTT-TCTTTGCTCCTCTGCTTTAGCCAT
1 TTTCTTCAACAGCCTTCTTCTTAGTTTCTTCTGCAATCTTCT-TTTGCTCCTCTGCTTTAGCCAT
*
754397 CTCCATATCTGCATGTTTTC
65 CTCCAAATCTGCATGTTTTC
* * **
754417 TTTCTTCAACAGCCTTCTTCTTAGCTTCTTCTGCAAGCTTCCTTTT-CTCCTCCACTTTAGCCAT
1 TTTCTTCAACAGCCTTCTTCTTAGTTTCTTCTGCAATCTT-CTTTTGCTCCTCTGCTTTAGCCAT
*
754481 CTCCATATCTGCATGTTTTC
65 CTCCAAATCTGCATGTTTTC
* * * *
754501 TTTCTTCAACAGCCTCCTTCTTAGTTTCTTCTGCAATCTTCCTTTGCTCCTCTGCTTGAGTCATC
1 TTTCTTCAACAGCCTTCTTCTTAGTTTCTTCTGCAATCTTCTTTTGCTCCTCTGCTTTAGCCATC
* *
754566 TCCAAATCAGCACGTTTTC
66 TCCAAATCTGCATGTTTTC
* * * * * * *
754585 TTTCTTCAGCCGCTTTCTTCGTAGCTTCTTCTGCAATCTTCCTTTGCTCCTCTGCTTTAGCCATA
1 TTTCTTCAACAGCCTTCTTCTTAGTTTCTTCTGCAATCTTCTTTTGCTCCTCTGCTTTAGCCATC
* * *
754650 TACAAATCAGCACGTTTTC
66 TCCAAATCTGCATGTTTTC
* * *
754669 TTTGTTCAACTGTCTTCTT
1 TTTCTTCAACAGCCTTCTT
754688 TTTCTCTTCT
Statistics
Matches: 306, Mismatches: 41, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
81 14 0.05
82 2 0.01
83 5 0.02
84 280 0.92
85 4 0.01
86 1 0.00
ACGTcount: A:0.15, C:0.31, G:0.11, T:0.43
Consensus pattern (84 bp):
TTTCTTCAACAGCCTTCTTCTTAGTTTCTTCTGCAATCTTCTTTTGCTCCTCTGCTTTAGCCATC
TCCAAATCTGCATGTTTTC
Found at i:757111 original size:28 final size:28
Alignment explanation
Indices: 757080--757135 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
757070 TAATTCATTT
757080 ACACCAACAACTCAAGGCATAGATAGGA
1 ACACCAACAACTCAAGGCATAGATAGGA
757108 ACACCAACAACTCAAGGCATAGATAGGA
1 ACACCAACAACTCAAGGCATAGATAGGA
757136 GACCATCCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.25, G:0.18, T:0.11
Consensus pattern (28 bp):
ACACCAACAACTCAAGGCATAGATAGGA
Found at i:762441 original size:29 final size:29
Alignment explanation
Indices: 762387--762442 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
762377 TTTGGCTTAA
* *
762387 AATAAAAATATAAATACTTGATTGAATGT
1 AATAAAAATATAAAAACTTAATTGAATGT
*
762416 AATAAAAGTATAAAAAC-TAATCTGAAT
1 AATAAAAATATAAAAACTTAAT-TGAAT
762443 TTTCTTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 3 0.13
29 20 0.87
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.30
Consensus pattern (29 bp):
AATAAAAATATAAAAACTTAATTGAATGT
Found at i:762583 original size:22 final size:23
Alignment explanation
Indices: 762540--762583 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
762530 ATATTTAAAA
* *
762540 TTAAAAATTAAACTTAATTTGAT
1 TTAAAAATTAAACATAAATTGAT
762563 TTAAAAATTAAA-ATAAATTGA
1 TTAAAAATTAAACATAAATTGA
762584 ATTCTAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (23 bp):
TTAAAAATTAAACATAAATTGAT
Found at i:764794 original size:126 final size:126
Alignment explanation
Indices: 764569--764804 Score: 298
Period size: 126 Copynumber: 1.9 Consensus size: 126
764559 TAATGCGTAT
* * * * *
764569 AAAATCCTCGAATAAAGAAATAGAAGAAAGGCTCTGTTTCTCTTTGTCTCTGCCTCGCATTGTTA
1 AAAATCCTCGAAGAAAGAAACAAAAGAAAGGCTCTGTTTCTCTCTATCTCTGCCTCGCATTGTTA
* * *
764634 TTTCAAGAAAACAAGGAAAGAAGAGTTAATTTTGTTTGGCACAAGGCAATAATGAGGGTAG
66 TTTCAAGAAAACAAGGAAAAAAAAATTAATTTTGTTTGGCACAAGGCAATAATGAGGGTAG
* * * * * *
764695 AAAATCCTTGAAGAAAGAAACAAAAGAAATGCTCTGTTTTTCTCTATCTCTG-TTGGCCGTTGTT
1 AAAATCCTCGAAGAAAGAAACAAAAGAAAGGCTCTGTTTCTCTCTATCTCTGCCTCG-CATTGTT
764759 ATTTCAA-AAGAATCAA-GAAAAAAAAATTAATTTTGTTTGGCACAAG
65 ATTTCAAGAA-AA-CAAGGAAAAAAAAATTAATTTTGTTTGGCACAAG
764805 ACATCATTGC
Statistics
Matches: 93, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
125 4 0.04
126 86 0.92
127 3 0.03
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (126 bp):
AAAATCCTCGAAGAAAGAAACAAAAGAAAGGCTCTGTTTCTCTCTATCTCTGCCTCGCATTGTTA
TTTCAAGAAAACAAGGAAAAAAAAATTAATTTTGTTTGGCACAAGGCAATAATGAGGGTAG
Found at i:766108 original size:47 final size:47
Alignment explanation
Indices: 766039--766128 Score: 153
Period size: 47 Copynumber: 1.9 Consensus size: 47
766029 CCCATAATGG
*
766039 AGAGAAACTCTTACACTGGTTTGAGTCTACCTCGACCCTTATAAATA
1 AGAGAAACTCTTACACTAGTTTGAGTCTACCTCGACCCTTATAAATA
* *
766086 AGAGAAACTCTTACACTAGTTTGAGTTTATCTCGACCCTTATA
1 AGAGAAACTCTTACACTAGTTTGAGTCTACCTCGACCCTTATA
766129 TCTCTCATGG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.32
Consensus pattern (47 bp):
AGAGAAACTCTTACACTAGTTTGAGTCTACCTCGACCCTTATAAATA
Found at i:766862 original size:8 final size:8
Alignment explanation
Indices: 766836--766873 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
766826 TAAACGAATT
766836 TAATTAAA
1 TAATTAAA
*
766844 TATAATAAA
1 TA-ATTAAA
766853 TAATTAAA
1 TAATTAAA
766861 TAATTAAA
1 TAATTAAA
766869 TAATT
1 TAATT
766874 TTTTTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
TAATTAAA
Found at i:767895 original size:36 final size:36
Alignment explanation
Indices: 767820--767893 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 36
767810 TCGTTCTTGG
* *
767820 TTATTTTAGTTGAATTAGGATTTTTTTATTTATATT
1 TTATTTTAGTCGAATTAAGATTTTTTTATTTATATT
* *
767856 TTATTTCTAGTCGAATTAAGATTTTTTTCTTTTTATT
1 TTATTT-TAGTCGAATTAAGATTTTTTTATTTATATT
767893 T
1 T
767894 ATAAATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
36 6 0.18
37 27 0.82
ACGTcount: A:0.23, C:0.04, G:0.09, T:0.64
Consensus pattern (36 bp):
TTATTTTAGTCGAATTAAGATTTTTTTATTTATATT
Found at i:781741 original size:14 final size:15
Alignment explanation
Indices: 781709--781745 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
781699 TAATATATAA
*
781709 TAATAAATAATATTT
1 TAATTAATAATATTT
781724 TAATTAATAATA-TT
1 TAATTAATAATATTT
781738 TAATTAAT
1 TAATTAAT
781746 TATTAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TAATTAATAATATTT
Found at i:781744 original size:18 final size:18
Alignment explanation
Indices: 781699--781764 Score: 59
Period size: 18 Copynumber: 3.9 Consensus size: 18
781689 CAACGTCATT
* *
781699 TAATATATAA-TAATAAA
1 TAATATTTAATTAATTAA
781716 TAATA-TT--TTAATTAA
1 TAATATTTAATTAATTAA
*
781731 TAATATTTAATTAATTAT
1 TAATATTTAATTAATTAA
* *
781749 TAAAATTTATTTAATT
1 TAATATTTAATTAATT
781765 TAAAATAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
15 11 0.28
16 3 0.08
17 5 0.12
18 21 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATATTTAATTAATTAA
Found at i:783833 original size:4 final size:4
Alignment explanation
Indices: 783824--783850 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
783814 CTTCTCCTCT
783824 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
783851 TCTCAGACGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:784276 original size:12 final size:12
Alignment explanation
Indices: 784256--784293 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
784246 ATTCTATTTG
784256 AATTTAAATTAA
1 AATTTAAATTAA
*
784268 AATTCAAATTATA
1 AATTTAAATTA-A
784281 AATTTAAA-TAA
1 AATTTAAATTAA
784292 AA
1 AA
784294 AAATATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 3 0.13
12 12 0.52
13 8 0.35
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (12 bp):
AATTTAAATTAA
Found at i:793410 original size:16 final size:17
Alignment explanation
Indices: 793391--793428 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
793381 ATAAAAAAAA
*
793391 ATTATATAATT-ATATT
1 ATTATATAATTAATATC
*
793407 ATTATATCATTAATATC
1 ATTATATAATTAATATC
793424 ATTAT
1 ATTAT
793429 TTATTATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTATATAATTAATATC
Found at i:793427 original size:20 final size:18
Alignment explanation
Indices: 793391--793453 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 18
793381 ATAAAAAAAA
*
793391 ATTATATAAT-TAT-ATT
1 ATTATATCATATATCATT
793407 ATTATATCATTAATATCATT
1 ATTATATCA-T-ATATCATT
*
793427 ATTTATTATCATATATCAAT
1 A-TTA-TATCATATATCATT
793447 ATTATAT
1 ATTATAT
793454 TAAATAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
16 8 0.21
17 1 0.03
18 3 0.08
19 6 0.15
20 12 0.31
21 4 0.10
22 5 0.13
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTATATCATATATCATT
Found at i:808476 original size:13 final size:15
Alignment explanation
Indices: 808458--808496 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
808448 AATGGTAAAG
808458 TTTTTATTTA-ATT-
1 TTTTTATTTATATTA
808471 TTTTTATTTATATTA
1 TTTTTATTTATATTA
*
808486 TTATTATTTAT
1 TTTTTATTTAT
808497 GTTTTTCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.43
14 3 0.13
15 10 0.43
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTATTTATATTA
Found at i:809239 original size:16 final size:17
Alignment explanation
Indices: 809220--809253 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
809210 TTTTAAAAAA
809220 TTTAATTTTTAA-TTTT
1 TTTAATTTTTAACTTTT
809236 TTTAATTTTTAACTTTT
1 TTTAATTTTTAACTTTT
809253 T
1 T
809254 AATAAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTAATTTTTAACTTTT
Found at i:810295 original size:27 final size:27
Alignment explanation
Indices: 810263--810317 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
810253 AGAATGCAAT
* * *
810263 AAAATAATATAAAATTAATATTCTATA
1 AAAATAAAATAAAAATAATATTATATA
*
810290 AAAATAAAATAAAAATATTATTATATA
1 AAAATAAAATAAAAATAATATTATATA
810317 A
1 A
810318 TTTGATTAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (27 bp):
AAAATAAAATAAAAATAATATTATATA
Found at i:810559 original size:16 final size:16
Alignment explanation
Indices: 810540--810582 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
810530 ATTACTATGA
810540 TTAAATATTGATAAAT
1 TTAAATATTGATAAAT
**
810556 TTAAATAATTTTTAAAT
1 TTAAAT-ATTGATAAAT
810573 TTAAACTATT
1 TTAAA-TATT
810583 AATTTTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 6 0.26
17 16 0.70
18 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (16 bp):
TTAAATATTGATAAAT
Found at i:819387 original size:29 final size:30
Alignment explanation
Indices: 819355--819413 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
819345 TGTCTTGATA
819355 TTTTAT-TATTTATTTT-AACTCAAATAAAT
1 TTTTATATATTTATTTTGAA-TCAAATAAAT
*
819384 TTTTATATTTTTATTTTGAATCAAATAAAT
1 TTTTATATATTTATTTTGAATCAAATAAAT
819414 CATTAACTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 6 0.22
30 19 0.70
31 2 0.07
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (30 bp):
TTTTATATATTTATTTTGAATCAAATAAAT
Found at i:822532 original size:2 final size:2
Alignment explanation
Indices: 822525--822555 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
822515 TATGTTGATG
*
822525 CT CT CT CT CT CT CT CT CG CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
822556 ACAGTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.03, T:0.45
Consensus pattern (2 bp):
CT
Found at i:838202 original size:15 final size:16
Alignment explanation
Indices: 838171--838203 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
838161 AGTTAAAATG
*
838171 AAAAATAAACAATTAT
1 AAAAAGAAACAATTAT
838187 AAAAAGAAACAA-TAT
1 AAAAAGAAACAATTAT
838202 AA
1 AA
838204 GGTTAATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.18
Consensus pattern (16 bp):
AAAAAGAAACAATTAT
Found at i:838700 original size:11 final size:12
Alignment explanation
Indices: 838670--838711 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
838660 GATGTTATTT
838670 TTATTTT-ATT-
1 TTATTTTAATTA
*
838680 TTATTATAATTA
1 TTATTTTAATTA
838692 TT-TTTTAATTA
1 TTATTTTAATTA
838703 TTATTTTAA
1 TTATTTTAA
838712 ATTTAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 6 0.22
11 13 0.48
12 8 0.30
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATTTTAATTA
Found at i:839685 original size:32 final size:28
Alignment explanation
Indices: 839621--839675 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
839611 ATATTACAAA
839621 CAAATAAATTACATCAAAAATAAATAAG
1 CAAATAAATTACATCAAAAATAAATAAG
* *
839649 CAAATACATTACATCAAATATAAATAA
1 CAAATAAATTACATCAAAAATAAATAA
839676 AATTTCAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.62, C:0.13, G:0.02, T:0.24
Consensus pattern (28 bp):
CAAATAAATTACATCAAAAATAAATAAG
Found at i:840911 original size:24 final size:27
Alignment explanation
Indices: 840853--840905 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
840843 ACATATTACA
840853 AACAAATAAATTACATCAAAAATAAAT
1 AACAAATAAATTACATCAAAAATAAAT
* *
840880 AAGCAAATACATTACATCAAATATAA
1 AA-CAAATAAATTACATCAAAAATAA
840906 TAAAATTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 2 0.09
28 21 0.91
ACGTcount: A:0.62, C:0.13, G:0.02, T:0.23
Consensus pattern (27 bp):
AACAAATAAATTACATCAAAAATAAAT
Found at i:845770 original size:21 final size:22
Alignment explanation
Indices: 845720--845770 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
845710 AGATGAGGGA
845720 GAAAAAATAGTAAGTAAATGAC
1 GAAAAAATAGTAAGTAAATGAC
845742 GAAAAAATAGTAAGTAAATGAC
1 GAAAAAATAGTAAGTAAATGAC
845764 -AAAAAAT
1 GAAAAAAT
845771 TAGCATTCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 7 0.24
22 22 0.76
ACGTcount: A:0.63, C:0.04, G:0.16, T:0.18
Consensus pattern (22 bp):
GAAAAAATAGTAAGTAAATGAC
Found at i:853232 original size:15 final size:16
Alignment explanation
Indices: 853184--853238 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 16
853174 CATGCAAATC
853184 ATATATCTATATC-TAT
1 ATATAT-TATATCTTAT
* * *
853200 ATATGTTATATATAAT
1 ATATATTATATCTTAT
853216 ATA-ATTATATCTTAT
1 ATATATTATATCTTAT
853231 ATTATATT
1 A-TATATT
853239 TAAATACATA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
15 15 0.50
16 12 0.40
17 3 0.10
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (16 bp):
ATATATTATATCTTAT
Found at i:868555 original size:3 final size:3
Alignment explanation
Indices: 868547--868610 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
868537 TTTCATCTGC
*
868547 TTA TTA TTA TTA TTA TTA CTA 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
868595 TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
868611 ATGAATGAGT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:875623 original size:18 final size:19
Alignment explanation
Indices: 875600--875635 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
875590 CGAGATTAGA
875600 TATAATT-CAAATAATATC
1 TATAATTACAAATAATATC
*
875618 TATAATTATAAATAATAT
1 TATAATTACAAATAATAT
875636 TATTAAGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (19 bp):
TATAATTACAAATAATATC
Found at i:881864 original size:2 final size:2
Alignment explanation
Indices: 881857--881887 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
881847 TTATAAATAA
881857 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
881888 TGTCACATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:882755 original size:16 final size:18
Alignment explanation
Indices: 882724--882756 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
882714 TACTTTTTGT
882724 TTAATCCTGTTAAATGTA
1 TTAATCCTGTTAAATGTA
882742 TTAAT-CTG-TAAATGT
1 TTAATCCTGTTAAATGT
882757 GTCAAGTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (18 bp):
TTAATCCTGTTAAATGTA
Found at i:891000 original size:16 final size:16
Alignment explanation
Indices: 890970--891007 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
890960 ATAATATAAT
*
890970 TATTT-ATATTTAAAA
1 TATTTAATAATTAAAA
890985 TATTTAATAATTAAAA
1 TATTTAATAATTAAAA
*
891001 TAATTAA
1 TATTTAA
891008 GAAAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTTAATAATTAAAA
Found at i:892155 original size:16 final size:16
Alignment explanation
Indices: 892134--892166 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
892124 TCCTATTGAC
892134 AACACTTACATTTAGA
1 AACACTTACATTTAGA
*
892150 AACACTTGCATTTAGA
1 AACACTTACATTTAGA
892166 A
1 A
892167 GCTAGGTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.30
Consensus pattern (16 bp):
AACACTTACATTTAGA
Found at i:892865 original size:26 final size:26
Alignment explanation
Indices: 892836--892885 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
892826 TATTGTTGTA
*
892836 TTAA-GAAAATTATTTTTATATAAATT
1 TTAATGAAAA-TATTTATATATAAATT
*
892862 TTAATTAAAATATTTATATATAAA
1 TTAATGAAAATATTTATATATAAA
892886 AATAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
TTAATGAAAATATTTATATATAAATT
Found at i:893204 original size:14 final size:13
Alignment explanation
Indices: 893179--893213 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
893169 TGAGGATTCA
*
893179 GAGAGAGGAAGAG
1 GAGAGAGAAAGAG
893192 GAGGAGAGAAAGAG
1 GA-GAGAGAAAGAG
893206 GAGAGAGA
1 GAGAGAGA
893214 TAGCGTTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (13 bp):
GAGAGAGAAAGAG
Found at i:893306 original size:15 final size:16
Alignment explanation
Indices: 893283--893316 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
893273 AGGAAAGCTC
893283 AAGAAGAGGAGGA-AA
1 AAGAAGAGGAGGAGAA
*
893298 AAGAGGAGGAGGAGAA
1 AAGAAGAGGAGGAGAA
893314 AAG
1 AAG
893317 GAAGGATCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (16 bp):
AAGAAGAGGAGGAGAA
Found at i:896104 original size:3 final size:3
Alignment explanation
Indices: 896025--896084 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
896015 CCCTATGTAC
*
896025 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
896073 ATA ATA ATA ATA
1 ATA ATA ATA ATA
896085 GAGAAGAAAG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:899145 original size:135 final size:134
Alignment explanation
Indices: 898900--899839 Score: 1169
Period size: 135 Copynumber: 7.0 Consensus size: 134
898890 AGTCGTAGTC
* * * * * *
898900 AAAGGGGCAAGAATAATGATA-AAAAGCAAACAAAAAGTTTAGATGGAAGATCATATAGAGAGAA
1 AAAGGGGCAAGAAAAATGACAGAAAA-C-AACAAAAACTTTAGATGGAAGATCAGACAGACAG-A
* * * *
898964 CCAAAGTTTAAGATGGGATCAAAACAGTGAGAAAAGCCATGATACCAGTTCTGATGGAGGTTATT
63 --GAAGTTTAAAATGGGATCAAAACAGTGAGAAAATCCATGATACCAGTTCTGATGGAGGTTACT
899029 CAGACAGCA
126 CAGACAGCA
* *
899038 AAAGGGGCAAGAAATATGACAGAAAACGAACCAAAACTTTAGATGGAAGATCAGACAGACAGAGA
1 AAAGGGGCAAGAAAAATGACAGAAAAC-AACAAAAACTTTAGATGGAAGATCAGACAGACAGAGA
* * * *
899103 AGTTTAAAATGGGACCAAAACAGTGAGGAAATCCATGATACCAGTTCTGATGGAAGCTACTCAGA
65 AGTTTAAAATGGGATCAAAACAGTGAGAAAATCCATGATACCAGTTCTGATGGAGGTTACTCAGA
899168 CAGCA
130 CAGCA
* * *
899173 AAAGGGGCAAGAAAAATGACAGAAAACAAGAAAAAGTTTTAGATGGAGGAAGATCAGACAGGCAG
1 AAAGGGGCAAGAAAAATGACAGAAAACAACAAAAA-CTTTAGAT---GGAAGATCAGACAGACAG
* * *
899238 AGAAGTTTAAAGTGGGATGAAAACAGTGAGAAAATCCATGATACTAGTTCTGATGGAGGTTACTC
62 AGAAGTTTAAAATGGGATCAAAACAGTGAGAAAATCCATGATACCAGTTCTGATGGAGGTTACTC
* *
899303 AGACGGTA
127 AGACAGCA
*
899311 AAAGGGGCAAGAAAAATGACAGAAAACAAGCAAAAACTTTGGATGGAAGATCAGACAGACAGAGA
1 AAAGGGGCAAGAAAAATGACAGAAAACAA-CAAAAACTTTAGATGGAAGATCAGACAGACAGAGA
* *
899376 AGTTTAAAATGGGATGAAAACAGTGAGAAAATCCATGATACCGGTTCTGATGGAGGTTACTCAGA
65 AGTTTAAAATGGGATCAAAACAGTGAGAAAATCCATGATACCAGTTCTGATGGAGGTTACTCAGA
899441 CAGCA
130 CAGCA
* * ** *
899446 GAAGGGGCAAGAAAAATGACAGAAAACGAGCAAAAGGTTTAGATGAAGGAAGATCACACAGACAG
1 AAAGGGGCAAGAAAAATGACAGAAAAC-AACAAAAACTTTAGAT---GGAAGATCAGACAGACAG
* * * *
899511 AGAAGGTTAACATGGGATCAAAACAGTGAGGAAATCCATGATAACAGTTCTGATGGAGGTTACTC
62 AGAAGTTTAAAATGGGATCAAAACAGTGAGAAAATCCATGATACCAGTTCTGATGGAGGTTACTC
*
899576 AGACAGTA
127 AGACAGCA
* * * *
899584 AAAGGGGCAAGAAAAGTGACAGAAAACGAGCAAAAACTTTGGATGGAAGATCAGGCAGAC-GAAG
1 AAAGGGGCAAGAAAAATGACAGAAAAC-AACAAAAACTTTAGATGGAAGATCAGACAGACAG-AG
* * *
899648 AAGTTTAAAATGGGATGAAAACAGTGAGAAAATCCATGATACCGGTTCTGATGGGGGTTACTCAG
64 AAGTTTAAAATGGGATCAAAACAGTGAGAAAATCCATGATACCAGTTCTGATGGAGGTTACTCAG
899713 ACAGCA
129 ACAGCA
* * *
899719 AAAGGGGCAAGAAAAATGACAG-----AA-AAAATC-TTAGATGGAAGATCAGACAGAGACAGAA
1 AAAGGGGCAAGAAAAATGACAGAAAACAACAAAAACTTTAGATGGAAGATCAGACAGACAGAGAA
* * * * * * * *
899777 ATTTAAAATGGGATCAAAACAGAGAGAGAACCCTTGATACAAGTTCTGATGAAGGTTATTCAG
66 GTTTAAAATGGGATCAAAACAGTGAGAAAATCCATGATACCAGTTCTGATGGAGGTTACTCAG
899840 GGAGGGACAT
Statistics
Matches: 704, Mismatches: 86, Indels: 35
0.85 0.10 0.04
Matches are distributed among these distances:
127 75 0.11
128 5 0.01
129 1 0.00
134 7 0.01
135 319 0.45
136 1 0.00
137 1 0.00
138 286 0.41
139 9 0.01
ACGTcount: A:0.44, C:0.13, G:0.26, T:0.17
Consensus pattern (134 bp):
AAAGGGGCAAGAAAAATGACAGAAAACAACAAAAACTTTAGATGGAAGATCAGACAGACAGAGAA
GTTTAAAATGGGATCAAAACAGTGAGAAAATCCATGATACCAGTTCTGATGGAGGTTACTCAGAC
AGCA
Found at i:899387 original size:273 final size:272
Alignment explanation
Indices: 898967--899744 Score: 1222
Period size: 273 Copynumber: 2.8 Consensus size: 272
898957 GAGAGAACCA
* *
898967 AAGTTT-AAGATGGGATCAAAACAGTGAGAAAAGCCATGATACCAGTTCTGATGGAGGTTATTCA
1 AAGTTTAAAG-TGGGATCAAAACAGTGAGAAAATCCATGATA-CAGTTCTGATGGAGGTTACTCA
* * * *
899031 GACAGCAAAAGGGGCAAGAAATATGACAGAAAACGAA-CCAAAACTTTAGATGGAAGATCAGACA
64 GACAGTAAAAGGGGCAAGAAAAATGACAGAAAAC-AAGCAAAAACTTTGGATGGAAGATCAGACA
** * * * *
899095 GACAGAGAAGTTTAAAATGGGACCAAAACAGTGAGGAAATCCATGATACCAGTTCTGATGGAAGC
128 GACAGAGAAGTTTAAAATGGGATGAAAACAGTGAGAAAATCCATGATACCGGTTCTGATGGAGGT
* *
899160 TACTCAGACAGCAAAAGGGGCAAGAAAAATGACAGAAAACAAGAAAAAGTTTTAGATGGAGGAAG
193 TACTCAGACAGCAAAAGGGGCAAGAAAAATGACAGAAAACAAGAAAAAGGTTTAGATGAAGGAAG
* *
899225 ATCAGACAGGCAGAG
258 ATCACACAGACAGAG
*
899240 AAGTTTAAAGTGGGATGAAAACAGTGAGAAAATCCATGATACTAGTTCTGATGGAGGTTACTCAG
1 AAGTTTAAAGTGGGATCAAAACAGTGAGAAAATCCATGATAC-AGTTCTGATGGAGGTTACTCAG
*
899305 ACGGTAAAAGGGGCAAGAAAAATGACAGAAAACAAGCAAAAACTTTGGATGGAAGATCAGACAGA
65 ACAGTAAAAGGGGCAAGAAAAATGACAGAAAACAAGCAAAAACTTTGGATGGAAGATCAGACAGA
899370 CAGAGAAGTTTAAAATGGGATGAAAACAGTGAGAAAATCCATGATACCGGTTCTGATGGAGGTTA
130 CAGAGAAGTTTAAAATGGGATGAAAACAGTGAGAAAATCCATGATACCGGTTCTGATGGAGGTTA
* * *
899435 CTCAGACAGCAGAAGGGGCAAGAAAAATGACAGAAAACGAGCAAAAGGTTTAGATGAAGGAAGAT
195 CTCAGACAGCAAAAGGGGCAAGAAAAATGACAGAAAACAAGAAAAAGGTTTAGATGAAGGAAGAT
899500 CACACAGACAGAG
260 CACACAGACAGAG
* *
899513 AAGGTTAACA-TGGGATCAAAACAGTGAGGAAATCCATGATAACAGTTCTGATGGAGGTTACTCA
1 AAGTTTAA-AGTGGGATCAAAACAGTGAGAAAATCCATGAT-ACAGTTCTGATGGAGGTTACTCA
* * *
899577 GACAGTAAAAGGGGCAAGAAAAGTGACAGAAAACGAGCAAAAACTTTGGATGGAAGATCAGGCAG
64 GACAGTAAAAGGGGCAAGAAAAATGACAGAAAACAAGCAAAAACTTTGGATGGAAGATCAGACAG
*
899642 AC-GAAGAAGTTTAAAATGGGATGAAAACAGTGAGAAAATCCATGATACCGGTTCTGATGGGGGT
129 ACAG-AGAAGTTTAAAATGGGATGAAAACAGTGAGAAAATCCATGATACCGGTTCTGATGGAGGT
899706 TACTCAGACAGCAAAAGGGGCAAGAAAAATGACAGAAAA
193 TACTCAGACAGCAAAAGGGGCAAGAAAAATGACAGAAAA
899745 AATCTTAGAT
Statistics
Matches: 469, Mismatches: 30, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
272 4 0.01
273 459 0.98
274 6 0.01
ACGTcount: A:0.44, C:0.13, G:0.27, T:0.17
Consensus pattern (272 bp):
AAGTTTAAAGTGGGATCAAAACAGTGAGAAAATCCATGATACAGTTCTGATGGAGGTTACTCAGA
CAGTAAAAGGGGCAAGAAAAATGACAGAAAACAAGCAAAAACTTTGGATGGAAGATCAGACAGAC
AGAGAAGTTTAAAATGGGATGAAAACAGTGAGAAAATCCATGATACCGGTTCTGATGGAGGTTAC
TCAGACAGCAAAAGGGGCAAGAAAAATGACAGAAAACAAGAAAAAGGTTTAGATGAAGGAAGATC
ACACAGACAGAG
Found at i:900489 original size:2 final size:2
Alignment explanation
Indices: 900482--900513 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
900472 AGTGACGATA
*
900482 AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
900514 TCGTAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:929878 original size:2 final size:2
Alignment explanation
Indices: 929871--929908 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
929861 ATCACGCGTT
* *
929871 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
929909 ATTCATGAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:932498 original size:29 final size:30
Alignment explanation
Indices: 932456--932516 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
932446 ATAATACAAA
*
932456 ATAATTATTTTTTATAAAGTTTT-AATTTC
1 ATAATTATTCTTTATAAAGTTTTCAATTTC
*
932485 ATAATTATTCTTTATAAATTTTTCGAATTTC
1 ATAATTATTCTTTATAAAGTTTTC-AATTTC
932516 A
1 A
932517 AGTTAAATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 21 0.75
31 7 0.25
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (30 bp):
ATAATTATTCTTTATAAAGTTTTCAATTTC
Found at i:943081 original size:43 final size:41
Alignment explanation
Indices: 943026--943114 Score: 108
Period size: 41 Copynumber: 2.1 Consensus size: 41
943016 AATAAGAAAG
*
943026 AAATATATATATATAAACAGATGTGTTACATAAA-GAATTATGA
1 AAATAT-TA-ATATAAACAGATGCGTTACA-AAAGGAATTATGA
** *
943069 AAATATTAATATAAATGGATGCGTTATAAAAGGAATTATGA
1 AAATATTAATATAAACAGATGCGTTACAAAAGGAATTATGA
943110 AAATA
1 AAATA
943115 CAAATACGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 3 0.07
41 30 0.73
42 2 0.05
43 6 0.15
ACGTcount: A:0.52, C:0.03, G:0.13, T:0.31
Consensus pattern (41 bp):
AAATATTAATATAAACAGATGCGTTACAAAAGGAATTATGA
Found at i:943771 original size:41 final size:42
Alignment explanation
Indices: 943692--943798 Score: 105
Period size: 41 Copynumber: 2.5 Consensus size: 42
943682 ACCCAAGTGA
* * *
943692 TACAGAAAGAATTATGAAA-ATATAGATATGACCTAATGCGT
1 TACAGAAAGAATTATGAAATACATACATATGACCTAATGCAT
943733 TACAG-AAGAAATTATGGAAATACATACATATG-CC-AATGCAT
1 TACAGAAAG-AATTAT-GAAATACATACATATGACCTAATGCAT
* *
943774 CACATAAAAGAATTATAGAAATACA
1 TACA-GAAAGAATTAT-GAAATACA
943799 AATTAGTGCC
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
40 3 0.05
41 20 0.36
42 20 0.36
43 12 0.22
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.24
Consensus pattern (42 bp):
TACAGAAAGAATTATGAAATACATACATATGACCTAATGCAT
Found at i:946884 original size:12 final size:12
Alignment explanation
Indices: 946867--946904 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
946857 CTTAGGTAAG
946867 ATACATGAAGAA
1 ATACATGAAGAA
*
946879 ATACATG-GGAAA
1 ATACATGAAG-AA
946891 ATACATGAAGAA
1 ATACATGAAGAA
946903 AT
1 AT
946905 TAAGAATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 1 0.05
12 20 0.91
13 1 0.05
ACGTcount: A:0.55, C:0.08, G:0.18, T:0.18
Consensus pattern (12 bp):
ATACATGAAGAA
Found at i:951560 original size:40 final size:43
Alignment explanation
Indices: 951515--951599 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 43
951505 TTTAATATTA
951515 AAATATTTATAATTAAAAAT-AAAA-AAATTAAA-AAAAAACT
1 AAATATTTATAATTAAAAATAAAAAGAAATTAAATAAAAAACT
*
951555 AAATATTTATAATTGAAAATAAAAAGAAATTAAATAAAAAACT
1 AAATATTTATAATTAAAAATAAAAAGAAATTAAATAAAAAACT
951598 AA
1 AA
951600 CACCTTAAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
40 19 0.46
41 4 0.10
42 8 0.20
43 10 0.24
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (43 bp):
AAATATTTATAATTAAAAATAAAAAGAAATTAAATAAAAAACT
Found at i:955901 original size:47 final size:46
Alignment explanation
Indices: 955835--955990 Score: 136
Period size: 47 Copynumber: 3.4 Consensus size: 46
955825 TTCTCTTCTT
* *
955835 GTAACATGGTATCAGAGTTTCGAGTTTGATAGATCAATTATTTTTTC
1 GTAACATAGTATCAGAGTTT-AAGTTTGATAGATCAATTATTTTTTC
* * * * * *
955882 GTAACATAATATCAGAGTTTTAGATTCGATAGATTAATTTTTTTTTT
1 GTAACATAGTATCAGAGTTTAAG-TTTGATAGATCAATTATTTTTTC
* * * * *
955929 GTAATATAGTATCAAAGTTTAAAATTTGACAGATCAAATATTTTTT-
1 GTAACATAGTATCAGAGTTT-AAGTTTGATAGATCAATTATTTTTTC
* *
955975 -TAATATGGTATCAGAG
1 GTAACATAGTATCAGAG
955991 CCATTTAGGG
Statistics
Matches: 88, Mismatches: 19, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
45 14 0.16
46 2 0.02
47 71 0.81
48 1 0.01
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (46 bp):
GTAACATAGTATCAGAGTTTAAGTTTGATAGATCAATTATTTTTTC
Found at i:957971 original size:30 final size:29
Alignment explanation
Indices: 957937--958045 Score: 112
Period size: 30 Copynumber: 3.7 Consensus size: 29
957927 AATAATTAAT
*
957937 TATAAGAATTTATTTGATTTAAAATAAAAA
1 TATAAGAATTTATTTGA-ATAAAATAAAAA
* *
957967 TATAAAAACTTATTTGACATAAAATAAAAA
1 TATAAGAATTTATTTGA-ATAAAATAAAAA
* * * *
957997 TATAAGATTTTAATTGAATATAATAAAAG
1 TATAAGAATTTATTTGAATAAAATAAAAA
*
958026 TATAA-ATATTTATTTAAATA
1 TATAAGA-ATTTATTTGAATA
958046 TTTTAAAATA
Statistics
Matches: 65, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
28 1 0.02
29 25 0.38
30 39 0.60
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.39
Consensus pattern (29 bp):
TATAAGAATTTATTTGAATAAAATAAAAA
Found at i:958061 original size:11 final size:11
Alignment explanation
Indices: 958041--958072 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
958031 ATATTTATTT
958041 AAAT-ATTTTA
1 AAATAATTTTA
958051 AAATAATTTTA
1 AAATAATTTTA
958062 AAATAATTTTA
1 AAATAATTTTA
958073 GATAATACGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.19
11 17 0.81
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
AAATAATTTTA
Found at i:958478 original size:2 final size:2
Alignment explanation
Indices: 958466--958507 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
958456 CTAAACTGGT
*
958466 GA GA GA CA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
958508 AACCCTAGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:972193 original size:13 final size:13
Alignment explanation
Indices: 972175--972199 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
972165 AATGCACGTG
972175 TTAAGCTCACACC
1 TTAAGCTCACACC
972188 TTAAGCTCACAC
1 TTAAGCTCACAC
972200 ATCTTGTTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.36, G:0.08, T:0.24
Consensus pattern (13 bp):
TTAAGCTCACACC
Found at i:977697 original size:19 final size:18
Alignment explanation
Indices: 977652--977699 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 18
977642 TTTTTAAAGC
977652 TTTTTTTTAAAAAAATTT
1 TTTTTTTTAAAAAAATTT
*
977670 TATTCTTTTAAAAAAATTGT
1 T-TTTTTTTAAAAAAATT-T
977690 TTTTTTTTAA
1 TTTTTTTTAA
977700 GAGCTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 1 0.04
19 23 0.88
20 2 0.08
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTTTTTAAAAAAATTT
Found at i:983290 original size:16 final size:16
Alignment explanation
Indices: 983255--983296 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
983245 ATGAAATTTT
*
983255 ATTAATTAATTGAGAT
1 ATTAATTAATTGAGAA
* *
983271 ATTATTTAATTGATAA
1 ATTAATTAATTGAGAA
983287 ATTAA-TAATT
1 ATTAATTAATT
983297 TATTAAGTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (16 bp):
ATTAATTAATTGAGAA
Found at i:989929 original size:25 final size:22
Alignment explanation
Indices: 989900--989967 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 22
989890 CTCCGCCAAC
989900 CTGTCTATATTAGTTTCCTCCATAT
1 CTGTCTATATTA-TTT--TCCATAT
*
989925 CTGTCTTTATTTATTTTCCATAT
1 CTGTCTATA-TTATTTTCCATAT
* *
989948 CCGTCTATATTTTTTTCCAT
1 CTGTCTATATTATTTTCCAT
989968 TGGTAACTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
22 10 0.26
23 14 0.37
25 11 0.29
26 3 0.08
ACGTcount: A:0.18, C:0.22, G:0.06, T:0.54
Consensus pattern (22 bp):
CTGTCTATATTATTTTCCATAT
Found at i:989966 original size:22 final size:23
Alignment explanation
Indices: 989918--989967 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
989908 ATTAGTTTCC
* *
989918 TCCATATCTGTCTTTATTTATTT
1 TCCATATCCGTCTATATTTATTT
989941 TCCATATCCGTCTATATTT-TTT
1 TCCATATCCGTCTATATTTATTT
989963 TCCAT
1 TCCAT
989968 TGGTAACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.18, C:0.22, G:0.04, T:0.56
Consensus pattern (23 bp):
TCCATATCCGTCTATATTTATTT
Found at i:1000493 original size:116 final size:119
Alignment explanation
Indices: 1000336--1000571 Score: 300
Period size: 116 Copynumber: 2.0 Consensus size: 119
1000326 AAACAGAAGC
* * * * * *** **
1000336 CAAAATTGACATTCAGAAACTGCAATCTAATACTGAGGTGTATTATGGGCTTGTATTCTAATT-G
1 CAAAATTGACATACAAAAACTACAAACTAACACTGAGGTGTATTATAAACTCATATTCTAATTGG
*
1000400 T-AGCAGAAATGTTGTACTCTTGTTATGAAGCAATTGCTG-T-CAACTCCAAATT
66 TGA-CAGAAATGTTGTACTCTTGTTATGAAGAAATTGCTGTTACAACTCCAAATT
* *
1000452 CAAAATTGGCATACAAAAACTACAAACTAACACTGAGGTGTATTATAAACTCATGTTCTAATTGG
1 CAAAATTGACATACAAAAACTACAAACTAACACTGAGGTGTATTATAAACTCATATTCTAATTGG
*
1000517 TGTACAGAAATGTTGTACTCTTGTTATGAAGAAATTGCTGTTATAACTCCAAATT
66 TG-ACAGAAATGTTGTACTCTTGTTATGAAGAAATTGCTGTTACAACTCCAAATT
1000572 TGCTTTTATG
Statistics
Matches: 101, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
116 51 0.50
117 2 0.02
118 35 0.35
119 2 0.02
120 11 0.11
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (119 bp):
CAAAATTGACATACAAAAACTACAAACTAACACTGAGGTGTATTATAAACTCATATTCTAATTGG
TGACAGAAATGTTGTACTCTTGTTATGAAGAAATTGCTGTTACAACTCCAAATT
Found at i:1009022 original size:2 final size:2
Alignment explanation
Indices: 1009015--1009048 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1009005 ACATTATGAA
*
1009015 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1009049 GGATTTTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1009284 original size:2 final size:2
Alignment explanation
Indices: 1009279--1009304 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1009269 ACACACACAC
1009279 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1009305 GAGTCACTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1012118 original size:282 final size:282
Alignment explanation
Indices: 1011606--1012164 Score: 719
Period size: 282 Copynumber: 2.0 Consensus size: 282
1011596 ACTTGTAGAC
* * * * * *
1011606 TGCTGAGATGTCCAATAGAAGAGGGAAGTTCTTCAATACTTGTGCCATCTAAATGGAGCTCCAGC
1 TGCTGAGATGTCAAATAGAAGAGGGAAGTTCTTCAACACTTGTCCCATCCAAATAGAGCTCCACC
* ** * *
1011671 AAACGTTCCATTTTTCCGGTAATCTCTGGAAACCTTTGAAGATTCATGCAGCCTGAAAGAATCAA
66 AAACATTCCATTTCCCCGGTAATCTCTGGAAACCTTCGAAGATTCATGCAGCCTGAAAGAATAAA
* *
1011736 CGTTTCAAGAGACTGCATTCCAATATTGGTTGAGAGACTCCTAAGACTTGTGCAGTTTCTTAAAT
131 CGTTTCAAGAGACTCCATTCCAATATTGGTTGAGAAACTCCTAAGACTTGTGCAGTTTCTTAAAT
* * *
1011801 TCAAAAGTTTGAGCTTGGGTAAAAATAATATGGATGGATGGACATCTAATAAGCTGGTACAACCT
196 TCAAAAGCTTAAGCTTGGGTAAAAATAATATGGATGGATGGACATCTAATAAACTGGTACAACCT
1011866 TCCAAATTCAAACTTTCGAGAT
261 TCCAAATTCAAACTTTCGAGAT
* *
1011888 TGCTGAGATGTCTAAAT-GAAGAGGGAAGTTCTTTAACACTTGTCCCGTCCAAATAGAGCTCCAC
1 TGCTGAGATGTC-AAATAGAAGAGGGAAGTTCTTCAACACTTGTCCCATCCAAATAGAGCTCCAC
* * * *
1011952 CAAACATTCCATTTCCCCGGTGATCTCTGGCAACCTTCGGAGATTTGA-GCAGCCTGAAAGAATA
65 CAAACATTCCATTTCCCCGGTAATCTCTGGAAACCTTCGAAGA-TTCATGCAGCCTGAAAGAATA
* * * * * * * *
1012016 AATGTTTTAAGAGATTCCATTCTAATTTTGGTTGGGAAACTCCTAAGGCTTTTGCAGTTTCTTAA
129 AACGTTTCAAGAGACTCCATTCCAATATTGGTTGAGAAACTCCTAAGACTTGTGCAGTTTCTTAA
* * * * ** * *
1012081 ATTCAAAAGCTTAAGGTTTGGTAAAAATGCA-ATGGATGGATGGACATGTGCTAAACTGGTGCAG
194 ATTCAAAAGCTTAAGCTTGGGTAAAAAT-AATATGGATGGATGGACATCTAATAAACTGGTACAA
*
1012145 TCTTCCAAATTCAAACTTTC
258 CCTTCCAAATTCAAACTTTC
1012165 CAAATTTTCG
Statistics
Matches: 235, Mismatches: 39, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
282 228 0.97
283 7 0.03
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (282 bp):
TGCTGAGATGTCAAATAGAAGAGGGAAGTTCTTCAACACTTGTCCCATCCAAATAGAGCTCCACC
AAACATTCCATTTCCCCGGTAATCTCTGGAAACCTTCGAAGATTCATGCAGCCTGAAAGAATAAA
CGTTTCAAGAGACTCCATTCCAATATTGGTTGAGAAACTCCTAAGACTTGTGCAGTTTCTTAAAT
TCAAAAGCTTAAGCTTGGGTAAAAATAATATGGATGGATGGACATCTAATAAACTGGTACAACCT
TCCAAATTCAAACTTTCGAGAT
Found at i:1023298 original size:62 final size:62
Alignment explanation
Indices: 1023201--1023324 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
1023191 TCAAACACAT
1023201 AAATTATGTATCACCATAAAAATGTTCACTAATTTAACAAGAAGCAAACTTCCATACCTTCC
1 AAATTATGTATCACCATAAAAATGTTCACTAATTTAACAAGAAGCAAACTTCCATACCTTCC
1023263 AAATTATGTATCACCATAAAAATGTTCACTAATTTAACAAGAAGCAAACTTCCATACCTTCC
1 AAATTATGTATCACCATAAAAATGTTCACTAATTTAACAAGAAGCAAACTTCCATACCTTCC
1023325 GCAGGAATCC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.42, C:0.23, G:0.06, T:0.29
Consensus pattern (62 bp):
AAATTATGTATCACCATAAAAATGTTCACTAATTTAACAAGAAGCAAACTTCCATACCTTCC
Found at i:1026432 original size:24 final size:22
Alignment explanation
Indices: 1026392--1026437 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
1026382 TGAACAAGAG
*
1026392 TTAAAAGATAAATCAGAAGAAT
1 TTAAAAGATAAAACAGAAGAAT
*
1026414 TTAAAGAGAATAAAACAGAGGAAT
1 TTAAA-AG-ATAAAACAGAAGAAT
1026438 AAGCTAGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 2 0.10
24 13 0.65
ACGTcount: A:0.59, C:0.04, G:0.17, T:0.20
Consensus pattern (22 bp):
TTAAAAGATAAAACAGAAGAAT
Found at i:1031298 original size:29 final size:30
Alignment explanation
Indices: 1031249--1031305 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
1031239 ATATATTTTT
* * *
1031249 GTTAATTTAGTTTTTACA-TTTAAAAATCA
1 GTTAATTTAATTTCTAAATTTTAAAAATCA
1031278 GTTAATTTAATTTCTAAATTTTAAAAAT
1 GTTAATTTAATTTCTAAATTTTAAAAAT
1031306 TAAAATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.49
Consensus pattern (30 bp):
GTTAATTTAATTTCTAAATTTTAAAAATCA
Found at i:1032565 original size:27 final size:28
Alignment explanation
Indices: 1032517--1032578 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 28
1032507 AAGATTTTTT
1032517 AAATATTAATAATCTAGAATTT-AATAA
1 AAATATTAATAATCTAGAATTTAAATAA
*
1032544 AAATATTAATAAT-TA-ATCATTTAAATAT
1 AAATATTAATAATCTAGA--ATTTAAATAA
1032572 AAATATT
1 AAATATT
1032579 TCATTTATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
25 1 0.03
26 2 0.06
27 17 0.55
28 11 0.35
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (28 bp):
AAATATTAATAATCTAGAATTTAAATAA
Found at i:1032617 original size:16 final size:16
Alignment explanation
Indices: 1032596--1032644 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1032586 TAATTTAATC
1032596 ATTAATATTTTCAAAT
1 ATTAATATTTTCAAAT
1032612 ATTAATATTTT---AT
1 ATTAATATTTTCAAAT
1032625 -TT-A-ATTTTCAAAT
1 ATTAATATTTTCAAAT
1032638 ATTAATA
1 ATTAATA
1032645 ATTGATAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 12
0.69 0.00 0.31
Matches are distributed among these distances:
10 5 0.19
11 1 0.04
12 2 0.07
13 4 0.15
14 2 0.07
15 1 0.04
16 12 0.44
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTAATATTTTCAAAT
Found at i:1032636 original size:26 final size:25
Alignment explanation
Indices: 1032602--1032697 Score: 92
Period size: 26 Copynumber: 3.8 Consensus size: 25
1032592 AATCATTAAT
1032602 ATTTTCAAATATTAATATTTTATTTA
1 ATTTT-AAATATTAATATTTTATTTA
* *
1032628 ATTTTCAAATATTAATAATTGA--TA
1 ATTTT-AAATATTAATATTTTATTTA
*
1032652 A-TTTAAATTTTAATATTTTATTTA
1 ATTTTAAATATTAATATTTTATTTA
*
1032676 TAATTT-AATCATTAATATTTTA
1 -ATTTTAAAT-ATTAATATTTTA
1032698 AAATATTAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
22 13 0.22
23 3 0.05
24 5 0.08
25 4 0.07
26 34 0.58
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (25 bp):
ATTTTAAATATTAATATTTTATTTA
Found at i:1032656 original size:29 final size:27
Alignment explanation
Indices: 1032588--1032662 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 27
1032578 TTCATTTATA
1032588 ATTTAATCATTAATATTTTCAAATATTAAT
1 ATTTAAT--TTAA-ATTTTCAAATATTAAT
*
1032618 ATTTTATTT-AATTTTCAAATATTAAT
1 ATTTAATTTAAATTTTCAAATATTAAT
1032644 AATTGATAATTTAAATTTT
1 -ATT--TAATTTAAATTTT
1032663 AATATTTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 16 0.41
27 4 0.10
28 2 0.05
29 5 0.13
30 12 0.31
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.53
Consensus pattern (27 bp):
ATTTAATTTAAATTTTCAAATATTAAT
Found at i:1032656 original size:90 final size:90
Alignment explanation
Indices: 1032544--1032712 Score: 284
Period size: 90 Copynumber: 1.9 Consensus size: 90
1032534 AATTTAATAA
* *
1032544 AAATATTAATAATTAATCATTTAAATATAAATATTTCATTTATAATTTAATCATTAATATTTTCA
1 AAATATTAATAATTAATAATTTAAATATAAATATTTCATTTATAATTTAATCATTAATATTTTAA
1032609 AATATTAATATTTTATTTAATTTTC
66 AATATTAATATTTTATTTAATTTTC
* * * *
1032634 AAATATTAATAATTGATAATTTAAATTTTAATATTTTATTTATAATTTAATCATTAATATTTTAA
1 AAATATTAATAATTAATAATTTAAATATAAATATTTCATTTATAATTTAATCATTAATATTTTAA
1032699 AATATTAATATTTT
66 AATATTAATATTTT
1032713 TAATTTAAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 73 1.00
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.52
Consensus pattern (90 bp):
AAATATTAATAATTAATAATTTAAATATAAATATTTCATTTATAATTTAATCATTAATATTTTAA
AATATTAATATTTTATTTAATTTTC
Found at i:1032736 original size:21 final size:21
Alignment explanation
Indices: 1032650--1032738 Score: 58
Period size: 21 Copynumber: 4.2 Consensus size: 21
1032640 TAATAATTGA
*
1032650 TAATTTAAATTTTAATAT--T
1 TAATTTAAATATTAATATCAT
* * *
1032669 TTATTTATAAT-TTAATCATTAA
1 TAATTTA-AATATTAAT-ATCAT
* **
1032691 TATTTTAAAATATTAATATTTT
1 TAATTT-AAATATTAATATCAT
*
1032713 TAATTTAAATATTATTATCAT
1 TAATTTAAATATTAATATCAT
1032734 TAATT
1 TAATT
1032739 ATTTTATTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
19 11 0.20
20 5 0.09
21 17 0.31
22 15 0.28
23 6 0.11
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TAATTTAAATATTAATATCAT
Found at i:1032806 original size:27 final size:26
Alignment explanation
Indices: 1032749--1032806 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 26
1032739 ATTTTATTTT
*
1032749 ATTT-TTTAAAATATTAATAATTGAT
1 ATTTATTTAAAATATTAATAATTGAC
1032774 AGTTTATTTAAAATATTAATAATTGACC
1 A-TTTATTTAAAATATTAATAATTGA-C
1032802 ATTTA
1 ATTTA
1032807 AATATTAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 1 0.03
26 3 0.10
27 24 0.83
28 1 0.03
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (26 bp):
ATTTATTTAAAATATTAATAATTGAC
Found at i:1032928 original size:40 final size:38
Alignment explanation
Indices: 1032884--1032979 Score: 95
Period size: 40 Copynumber: 2.4 Consensus size: 38
1032874 TTTATATAAA
*
1032884 TTATTTTATTATT-TATTTTTAAATATTAATAATTGATTAT
1 TTATTTTATTATTATATTTTCAAATATTAAT-ATT--TTAT
* *
1032924 TTATTTAAAATATTAATATTTTCAAATATTAATATTTTAT
1 TTATTT-TATTATT-ATATTTTCAAATATTAATATTTTAT
*
1032964 TTAATTTATATATTAT
1 TTATTTTAT-TATTAT
1032980 TATGATTAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
39 3 0.07
40 19 0.41
41 5 0.11
42 3 0.07
43 16 0.35
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (38 bp):
TTATTTTATTATTATATTTTCAAATATTAATATTTTAT
Found at i:1032950 original size:16 final size:16
Alignment explanation
Indices: 1032931--1032961 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1032921 TATTTATTTA
1032931 AAATATTAATATTTTC
1 AAATATTAATATTTTC
1032947 AAATATTAATATTTT
1 AAATATTAATATTTT
1032962 ATTTAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
AAATATTAATATTTTC
Found at i:1032959 original size:147 final size:148
Alignment explanation
Indices: 1032601--1032941 Score: 441
Period size: 147 Copynumber: 2.3 Consensus size: 148
1032591 TAATCATTAA
* * * *
1032601 TATTTTCAAATATTAAT-ATT--TTATTTAATTTTCAAATATTAATAATTGATAATTTAAATTTT
1 TATTTTTAAATATTAATAATTGATTATTT-A-TTTAAAATATTAATAATTGACAATTTAAATATT
*
1032663 AATATTTTATTTATAATTTAATCATTAATATTTTAAAATATTAATATTTTTAATTTAAATATTAT
64 AATATTTTATTTATAATTTAATCATTAATATTTTAAAATACTAATATTTTTAATTTAAATATTAT
*
1032728 TATCATTAATTATTTTATTT
129 TATCATAAATTATTTTATTT
*
1032748 TATTTTTTAAAATATTAATAATTGA-TAGTTTATTTAAAATATTAATAATTGACCATTTAAATAT
1 TA-TTTTT-AAATATTAATAATTGATTA-TTTATTTAAAATATTAATAATTGACAATTTAAATAT
* *
1032812 TAATA-TTTA-TTATAATTTAGTCATTAATA-TTTAAAATTACT-ATTTTATTTAATTT-AATAT
63 TAATATTTTATTTATAATTTAATCATTAATATTTTAAAA-TACTAATATT-TTTAATTTAAATAT
1032872 TATTTAT-ATAAATTATTTTATTATT
126 TA-TTATCATAAATTATTTTA-T-TT
1032897 TATTTTTAAATATTAATAATTGATTATTTATTTAAAATATTAATA
1 TATTTTTAAATATTAATAATTGATTATTTATTTAAAATATTAATA
1032942 TTTTCAAATA
Statistics
Matches: 173, Mismatches: 9, Indels: 24
0.84 0.04 0.12
Matches are distributed among these distances:
147 67 0.39
148 46 0.27
149 18 0.10
150 36 0.21
151 3 0.02
152 3 0.02
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (148 bp):
TATTTTTAAATATTAATAATTGATTATTTATTTAAAATATTAATAATTGACAATTTAAATATTAA
TATTTTATTTATAATTTAATCATTAATATTTTAAAATACTAATATTTTTAATTTAAATATTATTA
TCATAAATTATTTTATTT
Found at i:1032981 original size:43 final size:42
Alignment explanation
Indices: 1032890--1032982 Score: 104
Period size: 43 Copynumber: 2.2 Consensus size: 42
1032880 TAAATTATTT
*
1032890 TATTATT-TATTTTTAAATATTAATAATTGATTATTTATTTAA
1 TATTATTATATTTTCAAATATTAATAATT-ATTATTTATTTAA
*
1032932 -AATATTAATATTTTCAAATATTAAT-ATT-TTATTTAATTTATA
1 TATTATT-ATATTTTCAAATATTAATAATTATTATTT-ATTTA-A
1032974 TATTATTAT
1 TATTATTAT
1032983 GATTAATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
40 6 0.14
41 10 0.23
42 6 0.14
43 21 0.49
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (42 bp):
TATTATTATATTTTCAAATATTAATAATTATTATTTATTTAA
Found at i:1032996 original size:240 final size:238
Alignment explanation
Indices: 1032510--1032994 Score: 541
Period size: 240 Copynumber: 2.0 Consensus size: 238
1032500 TTTTAATAAG
*
1032510 ATTTTTT-AAATATTAATAATCTAGAATTTAATAAAAATATTAATAATTAATCATTTAAATATAA
1 ATTTTTTAAAATATTAATAATCTAGAATTTAATAAAAATATTAATAATTAACCATTTAAATATAA
1032574 ATATTTCATTTATAATTTAATCATTAATATTTTCAAATATTAATATTTTATTTAATTTTCAAATA
66 ATATTTCATTTATAATTTAATCATTAATATTTTCAAATATTAATATTTTATTTAATTTT-AAATA
* *
1032639 TTAATAATTGATAATTTAAATTTTAATATTTTATTTATAATTTAATCATTAATATTTTAAAATAT
130 TTAATAATTGATAAATT-AATTTTAATATTTTATTTATAATTTAATAATTAATATTTTAAAATAT
* * *
1032704 TAATATTTTTAATTTAAATATTATTATCATTAATTATTTTATTTT
194 TAATATTTTAAATTTAAATATTATTATAATTAATTATTTTATTTA
* * *
1032749 ATTTTTTAAAATATTAATAAT-T-GATAGTTTATTTAAAATATTAATAATTGACCATTTAAATAT
1 ATTTTTTAAAATATTAATAATCTAGA-A-TTTAATAAAAATATTAATAATTAACCATTTAAATAT
* * *
1032812 TAATATTT-A-TTATAATTTAGTCATTAATA-TTT-AAA-ATTACTATTTTATTTAA-TTT-AAT
64 AAATATTTCATTTATAATTTAATCATTAATATTTTCAAATATTAATATTTTATTTAATTTTAAAT
* * * * *
1032870 ATTATTTA-T-ATAAATT-ATTTTATTA-TTTATTTTTAAATATTAATAATTGATTATTTATTTA
129 ATTAATAATTGATAAATTAATTTTAATATTTTATTTAT-AAT-TTAATAATT-A--ATAT-TTTA
* *
1032931 AAATATTAATATTTTCAAATATTAATATTTTATT-TAATTTATATATTATTATGATTA
188 AAATATTAATATTTT-AAAT-TTAA-ATATTATTATAATTAAT-TATT-TTAT--TTA
1032988 ATTTTTT
1 ATTTTTT
1032995 TATTTTATTT
Statistics
Matches: 211, Mismatches: 19, Indels: 32
0.81 0.07 0.12
Matches are distributed among these distances:
227 8 0.04
228 11 0.05
229 8 0.04
230 7 0.03
231 1 0.00
232 12 0.06
233 19 0.09
234 6 0.03
235 26 0.12
236 14 0.07
237 7 0.03
238 21 0.10
239 19 0.09
240 52 0.25
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.54
Consensus pattern (238 bp):
ATTTTTTAAAATATTAATAATCTAGAATTTAATAAAAATATTAATAATTAACCATTTAAATATAA
ATATTTCATTTATAATTTAATCATTAATATTTTCAAATATTAATATTTTATTTAATTTTAAATAT
TAATAATTGATAAATTAATTTTAATATTTTATTTATAATTTAATAATTAATATTTTAAAATATTA
ATATTTTAAATTTAAATATTATTATAATTAATTATTTTATTTA
Found at i:1033015 original size:107 final size:101
Alignment explanation
Indices: 1032834--1033048 Score: 306
Period size: 107 Copynumber: 2.1 Consensus size: 101
1032824 TAATTTAGTC
*
1032834 ATTAATATTTAAAATTACTATTTTATTTAATTTAATATTATTTATATAAATTATTTTATTATTTA
1 ATTAATATTTAAAATTAATATTTTATTTAATTTAATATTATTTATATAAATTATTTTATTATTTA
*
1032899 TTTTTAAATATTAATAATTGATTATTTATTTAAAAT
66 TTTTTAAATATTAATAATTGATAATTTATTTAAAAT
* *
1032935 ATTAATATTTTCAAATATTAATATTTTATTTAATTTATATATTA-TTATGATTAATTTTTTTATT
1 ATTAATA-TTT-AAA-ATTAATATTTTATTTAATTTA-ATATTATTTAT-ATAAATTATTTTA--
* *
1032999 TTATTTCTTTTTAAATATTAATAATTGGTAATTTATTTAAAAT
59 TTATTTATTTTTAAATATTAATAATTGATAATTTATTTAAAAT
1033042 ATTAATA
1 ATTAATA
1033049 ATTGATTATT
Statistics
Matches: 101, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
101 7 0.07
102 3 0.03
103 3 0.03
104 24 0.24
105 17 0.17
107 47 0.47
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (101 bp):
ATTAATATTTAAAATTAATATTTTATTTAATTTAATATTATTTATATAAATTATTTTATTATTTA
TTTTTAAATATTAATAATTGATAATTTATTTAAAAT
Found at i:1033092 original size:107 final size:111
Alignment explanation
Indices: 1032834--1033190 Score: 294
Period size: 107 Copynumber: 3.3 Consensus size: 111
1032824 TAATTTAGTC
* * * *
1032834 ATTAATAT-TT-AAA-ATTACTATTTTATTTAATTTA-ATATTAT--TTATATAA--ATTA-TT-
1 ATTAATATATTCAAATATTAATATTTTATTTAATATATATATTATAATGATATAATGTTTATTTA
* *
1032889 TTATTATTTATTTTTAAATATTAATAATTGATTATTTATTTAAAAT
66 TTTTTATTTATTTTTAAATATTAATAATTGATAATTTATTTAAAAT
* * *
1032935 ATTAATATTTTCAAATATTAATATTTTATTTAATTTATATATTATTATGAT-TAAT-TTT-TTTA
1 ATTAATATATTCAAATATTAATATTTTATTTAATATATATATTATAATGATATAATGTTTATTTA
* *
1032997 -TTTTATTTCTTTTTAAATATTAATAATTGGTAATTTATTTAAAAT
66 TTTTTATTTATTTTTAAATATTAATAATTGATAATTTATTTAAAAT
* * * *
1033042 ATTAATA-ATT-GATTATTTAATTATTTATATTTTATATATA-ATT-TAAATGATATTATGTTTA
1 ATTAATATATTCAAATA-TTAA-TATTT-TATTTAATATATATATTAT-AATGATATAATGTTTA
* *
1033103 TTTATTTTTAATTTATTTTTTAAATA--AGATAATTTATAATTTATTTATTAAT
62 TTTATTTTT-ATTTA-TTTTTAAATATTA-ATAATTGATAATTTATTTA-AAAT
*
1033155 AACTT-ATA-ATTTAAATATTAATA-TTTATTT-ATATAT
1 -A-TTAATATATTCAAATATTAATATTTTATTTAATATAT
1033191 TTAATTTTAT
Statistics
Matches: 212, Mismatches: 20, Indels: 39
0.78 0.07 0.14
Matches are distributed among these distances:
101 8 0.04
102 2 0.01
103 3 0.01
104 20 0.09
105 10 0.05
106 10 0.05
107 68 0.32
108 14 0.07
109 3 0.01
110 10 0.05
111 10 0.05
112 23 0.11
113 15 0.07
114 11 0.05
115 5 0.02
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (111 bp):
ATTAATATATTCAAATATTAATATTTTATTTAATATATATATTATAATGATATAATGTTTATTTA
TTTTTATTTATTTTTAAATATTAATAATTGATAATTTATTTAAAAT
Found at i:1033161 original size:22 final size:22
Alignment explanation
Indices: 1033131--1033177 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1033121 TTTAAATAAG
* **
1033131 ATAATTTATAATTTATTTATTA
1 ATAACTTATAATTTAAATATTA
1033153 ATAACTTATAATTTAAATATTA
1 ATAACTTATAATTTAAATATTA
1033175 ATA
1 ATA
1033178 TTTATTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
ATAACTTATAATTTAAATATTA
Found at i:1033184 original size:18 final size:18
Alignment explanation
Indices: 1033163--1033200 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1033153 ATAACTTATA
1033163 ATTTAAATA-TTAATATTT
1 ATTTAAATATTTAAT-TTT
*
1033181 ATTTATATATTTAATTTT
1 ATTTAAATATTTAATTTT
1033199 AT
1 AT
1033201 ATATTTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTAAATATTTAATTTT
Found at i:1033199 original size:14 final size:14
Alignment explanation
Indices: 1033158--1033206 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
1033148 TATTAATAAC
*
1033158 TTATA-ATTTAAATA
1 TTATATATTT-AATT
1033172 TTA-ATATTT-A-T
1 TTATATATTTAATT
1033183 TTATATATTTAATT
1 TTATATATTTAATT
1033197 TTATATATTT
1 TTATATATTT
1033207 TAACTACATT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
11 3 0.10
12 7 0.23
13 2 0.07
14 18 0.60
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTATATATTTAATT
Found at i:1033209 original size:41 final size:41
Alignment explanation
Indices: 1033159--1033263 Score: 117
Period size: 42 Copynumber: 2.5 Consensus size: 41
1033149 ATTAATAACT
* *
1033159 TATAATTTAAATATTAATATTT-ATTTATATATTTAATTTTA
1 TATATTTTAAATATTAATATTTCATTTATA-ATTTAATATTA
*
1033200 TATATTTTAACTACATT-ATATTTCATTTATAATTTAATATTA
1 TATATTTTAA--ATATTAATATTTCATTTATAATTTAATATTA
*
1033242 -ATATGTTAAAATATTAATATTT
1 TATAT-TTTAAATATTAATATTT
1033264 TATTAAAAGT
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
40 4 0.07
41 19 0.35
42 20 0.37
43 11 0.20
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (41 bp):
TATATTTTAAATATTAATATTTCATTTATAATTTAATATTA
Found at i:1036001 original size:22 final size:23
Alignment explanation
Indices: 1035959--1036001 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1035949 CTTTTTATAC
*
1035959 TATTTCTTTTTTTAATTTGTTAT
1 TATTTCTTTATTTAATTTGTTAT
*
1035982 TATTT-TTTATTTCATTTGTT
1 TATTTCTTTATTTAATTTGTT
1036002 GTAAAGTAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (23 bp):
TATTTCTTTATTTAATTTGTTAT
Found at i:1038346 original size:26 final size:26
Alignment explanation
Indices: 1038310--1038362 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1038300 ATCATAACAA
1038310 TGCAAGTACCATTTTTGAAGGAACTT
1 TGCAAGTACCATTTTTGAAGGAACTT
1038336 TGCAAGTACCATTTTTGAAGGAACTT
1 TGCAAGTACCATTTTTGAAGGAACTT
1038362 T
1 T
1038363 TGAAATTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (26 bp):
TGCAAGTACCATTTTTGAAGGAACTT
Found at i:1038498 original size:39 final size:39
Alignment explanation
Indices: 1038455--1038576 Score: 113
Period size: 39 Copynumber: 3.1 Consensus size: 39
1038445 GTTTTCAAGG
1038455 CTACTAGCAATGTTTCTTCTTCTAGGGGTGTTCCGAATA
1 CTACTAGCAATGTTTCTTCTTCTAGGGGTGTTCCGAATA
* * ***
1038494 CTACTTA-CAATGCCTT-TTCTTTTAAAAGTGTTCCGAATA
1 CTAC-TAGCAATG-TTTCTTCTTCTAGGGGTGTTCCGAATA
* * * * * *
1038533 CTACTTGTAATGTTTCTTCTTCTTGGGTTGTTTCGAATT
1 CTACTAGCAATGTTTCTTCTTCTAGGGGTGTTCCGAATA
1038572 CTACT
1 CTACT
1038577 CATAATGGTT
Statistics
Matches: 63, Mismatches: 16, Indels: 8
0.72 0.18 0.09
Matches are distributed among these distances:
38 3 0.05
39 56 0.89
40 4 0.06
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.44
Consensus pattern (39 bp):
CTACTAGCAATGTTTCTTCTTCTAGGGGTGTTCCGAATA
Found at i:1038583 original size:39 final size:37
Alignment explanation
Indices: 1038521--1038666 Score: 91
Period size: 39 Copynumber: 3.8 Consensus size: 37
1038511 TCTTTTAAAA
* * ** *
1038521 GTGTTCCGAATACTACTTGTAATGTTTCTTCTTCTTGG
1 GTGTTTCGAATTCTACTCATAAT-TTTCTTCTTCTAGG
* * *
1038559 GTTGTTTCGAATTCTACTCATAATGGTTCTTTTTCTGGG
1 G-TGTTTCGAATTCTACTCATAAT-TTTCTTCTTCTAGG
** * *
1038598 GATGTTTTAAATTTTACGCATAA--TTCTTCTTCTAAGG
1 G-TGTTTCGAATTCTACTCATAATTTTCTTCTTCT-AGG
*
1038635 GTG-TTCTGAATTCTACTCGTAATTCTTCTTCT
1 GTGTTTC-GAATTCTACTCATAATT-TTCTTCT
1038667 AAGGGTATTC
Statistics
Matches: 83, Mismatches: 19, Indels: 11
0.73 0.17 0.10
Matches are distributed among these distances:
35 2 0.02
36 22 0.27
37 3 0.04
38 1 0.01
39 55 0.66
ACGTcount: A:0.18, C:0.17, G:0.16, T:0.48
Consensus pattern (37 bp):
GTGTTTCGAATTCTACTCATAATTTTCTTCTTCTAGG
Found at i:1038658 original size:36 final size:35
Alignment explanation
Indices: 1038618--1038697 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 35
1038608 ATTTTACGCA
* * *
1038618 TAATTCTTCTTCTAAGGGTGTTCTGAATTCTACTC
1 TAATTCTTCTTCTAAGGGTATTCTAAATACTACTC
1038653 GTAATTCTTCTTCTAAGGGTATTCTAAATACTACTC
1 -TAATTCTTCTTCTAAGGGTATTCTAAATACTACTC
1038689 TCAATTCTT
1 T-AATTCTT
1038698 TCTCTTCTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 1 0.03
36 39 0.98
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.45
Consensus pattern (35 bp):
TAATTCTTCTTCTAAGGGTATTCTAAATACTACTC
Found at i:1042620 original size:25 final size:28
Alignment explanation
Indices: 1042592--1042642 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
1042582 GGGGCCATTT
1042592 CCACA-AAACC-TAA-CAACCAATTTCA
1 CCACAGAAACCTTAAGCAACCAATTTCA
*
1042617 CCACAGAAGCCTTAAGCAACCAATTT
1 CCACAGAAACCTTAAGCAACCAATTT
1042643 AAAANNNNNN
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
26 4 0.18
27 3 0.14
28 10 0.45
ACGTcount: A:0.43, C:0.33, G:0.06, T:0.18
Consensus pattern (28 bp):
CCACAGAAACCTTAAGCAACCAATTTCA
Found at i:1043425 original size:9 final size:9
Alignment explanation
Indices: 1043413--1043448 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
1043403 GTAGAAAACT
1043413 ATAAAAATA
1 ATAAAAATA
*
1043422 ATAATAATA
1 ATAAAAATA
*
1043431 ACAAAAATA
1 ATAAAAATA
1043440 ATAAAAATA
1 ATAAAAATA
1043449 GTTTAAATAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (9 bp):
ATAAAAATA
Found at i:1048375 original size:361 final size:352
Alignment explanation
Indices: 1047757--1048802 Score: 1276
Period size: 350 Copynumber: 2.9 Consensus size: 352
1047747 TTATATATAT
* * * *
1047757 ACTTTAAATATAAATATATTTA-TTTTTATTTTATATTAACATTACAAAAATTTTAATTTATAAA
1 ACTTTAAATATAAACATATTTACTTTTTATTTTATATTAACATTACAAAAATTATAACTTAAAAA
* * * * *
1047821 ATTATTATTTAAAATATATACACCTTTGTTTATATAAACTTATAATATATAAACCTTAAGAGAAG
66 ATTATTAATTATAATATATATACTTTTGTTTATATAAACTTATAATATATAAA-CTTAAAAGAAG
* * * * * *
1047886 TTGTGATATTAGAATAGTTTTAAAACCTAGTTATTTTTTTTAATTTGATGTAATTAAAGATAAAT
130 TTAT-AAATTAGAATAGTTTTAAAACTTAGCTA-TTTTTTTAATTTCATGTAATTAAAGAAAAAT
* * * *
1047951 TTATATACTTAATTAAATTAATTCATGAAATTATGATTATTAATTACCTTGTAATGCCTTTTAAT
193 TCATATAATTAATTAAATTAATTCATGAAACTATGATTATTAATTACCTTGTAATGTCTTTTAAT
*
1048016 ATATTTACTTTATATATTTTGGGCTTATTTATAAAGAATATATTTACTATTATATATATACTAAA
258 ATATTTACTTTATATATTTTGGGCTTATTTATAAAGAATATAATTACTATTATATATATACTAAA
1048081 ATACTTTTAG-T-GTGTGTGTGTATATGTCC
323 ATACTTTTAGTTAGTGTGTGTGTATATGT-C
* * *
1048110 ACTTTAAATATAAACATATATACTTTTTATTTTGTATTAATATTACAAAAATTATAACTTAAAAA
1 ACTTTAAATATAAACATATTTACTTTTTATTTTATATTAACATTACAAAAATTATAACTTAAAAA
1048175 ATTATTAATTATAATATATATACTTTTGTTTATATAAACTTATAATATATAAACTTAATTATTTA
66 ATTATTAATTATAATATATATACTTTTGTTTATATAAACTTATAATATATAAAC--------TT-
* * *
1048240 AAAAGAAGTTATAAGATTAGAATAATTTTGAAACTTAACTATTTTTTTAATTTCATGTAATTAAA
122 AAAAGAAGTTATAA-ATTAGAATAGTTTTAAAACTTAGCTATTTTTTTAATTTCATGTAATTAAA
*
1048305 GAAAAATTCATATAATTAATTAAATTAATTCATGAAACTATGATTACTAATTACCTTGTAATGTC
186 GAAAAATTCATATAATTAATTAAATTAATTCATGAAACTATGATTATTAATTACCTTGTAATGTC
* ** * *
1048370 TTTTAATATATTTACTTTATATATATTAAG-TTCATTTATAAAGAATATACTTACTACTATATAT
251 TTTTAATATATTTACTTTATATATTTTGGGCTT-ATTTATAAAGAATATAATTACTATTATATAT
* * *
1048434 ATACTAAAATACTTTTAGTTTTAGTGTGTGTGTGTGTGTG
315 ATACTAAAATACTTTTAG--TTAGTGTGTGTGTATATGTC
** * * * *
1048474 TGTGTATACTTTAAAACATATTTACTTTCTATTTTATATTAACATTACAAAAATTATAACTTAAA
1 ACTTTA-AATAT-AAACATATTTACTTTTTATTTTATATTAACATTACAAAAATTATAACTTAAA
* *
1048539 AAA-TATTAATTATAATGTATATA-TCTTTGTTTATATAAAC-T-TAAT-TAT---CTCAAAAGA
64 AAATTATTAATTATAATATATATACT-TTTGTTTATATAAACTTATAATATATAAACTTAAAAGA
* * *
1048596 AGTTATGAAATTAGAATAGTTTTAAAACTTAGCTATTTTTTTAATTTCATGTAATTAAGGACATA
128 AGTTAT-AAATTAGAATAGTTTTAAAACTTAGCTATTTTTTTAATTTCATGTAATTAAAGAAAAA
** * *
1048661 CCCGTATAATTAATTAGATTAATTCATGAAACTATGATTATTAATTACCTTGTAATGTCTTTTAA
192 TTCATATAATTAATTAAATTAATTCATGAAACTATGATTATTAATTACCTTGTAATGTCTTTTAA
* **
1048726 TATATTTACTTTATATATATTAGGTGC--ATTTAT-AAGAAATATAATTGTTATTATATATATAC
257 TATATTTACTTTATATAT-TTTGG-GCTTATTTATAAAG-AATATAATTACTATTATATATAT--
1048788 ACTAAAATACTTTTA
317 ACTAAAATACTTTTA
1048803 ATATATATAG
Statistics
Matches: 603, Mismatches: 64, Indels: 53
0.84 0.09 0.07
Matches are distributed among these distances:
349 3 0.00
350 165 0.27
351 4 0.01
352 16 0.03
353 21 0.03
354 86 0.14
359 1 0.00
360 2 0.00
361 159 0.26
362 34 0.06
363 4 0.01
364 6 0.01
365 51 0.08
366 51 0.08
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (352 bp):
ACTTTAAATATAAACATATTTACTTTTTATTTTATATTAACATTACAAAAATTATAACTTAAAAA
ATTATTAATTATAATATATATACTTTTGTTTATATAAACTTATAATATATAAACTTAAAAGAAGT
TATAAATTAGAATAGTTTTAAAACTTAGCTATTTTTTTAATTTCATGTAATTAAAGAAAAATTCA
TATAATTAATTAAATTAATTCATGAAACTATGATTATTAATTACCTTGTAATGTCTTTTAATATA
TTTACTTTATATATTTTGGGCTTATTTATAAAGAATATAATTACTATTATATATATACTAAAATA
CTTTTAGTTAGTGTGTGTGTATATGTC
Found at i:1050311 original size:17 final size:17
Alignment explanation
Indices: 1050289--1050342 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
1050279 TAATCAATTT
1050289 ATTTAAAACTAAAGATA
1 ATTTAAAACTAAAGATA
* * *
1050306 ATTT--AATTTAATAT-
1 ATTTAAAACTAAAGATA
*
1050320 ATTTAAAACTAAAGACA
1 ATTTAAAACTAAAGATA
1050337 ATTTAA
1 ATTTAA
1050343 TATATTTATC
Statistics
Matches: 27, Mismatches: 7, Indels: 6
0.68 0.17 0.15
Matches are distributed among these distances:
14 4 0.15
15 7 0.26
16 6 0.22
17 10 0.37
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (17 bp):
ATTTAAAACTAAAGATA
Found at i:1050315 original size:26 final size:26
Alignment explanation
Indices: 1050284--1050350 Score: 71
Period size: 31 Copynumber: 2.4 Consensus size: 26
1050274 AATGATAATC
*
1050284 AATTTATTTAAAACTAAAGATAATTT
1 AATTTATTTAAAACTAAAGACAATTT
1050310 AATTTAATATATTTAAAACTAAAGACAATTT
1 AA--T--T-TATTTAAAACTAAAGACAATTT
*
1050341 AATATATTTA
1 AATTTATTTA
1050351 TCCCAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
26 8 0.24
28 1 0.03
29 1 0.03
30 1 0.03
31 23 0.68
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (26 bp):
AATTTATTTAAAACTAAAGACAATTT
Found at i:1060675 original size:27 final size:27
Alignment explanation
Indices: 1060644--1060697 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1060634 AATAACAATA
1060644 ATTTTTA-ATATAAAATTTTTACTATT
1 ATTTTTATATATAAAATTTTTACTATT
* * *
1060670 ATTTTTATTTATAAATTTTTTATTATT
1 ATTTTTATATATAAAATTTTTACTATT
1060697 A
1 A
1060698 ACATAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (27 bp):
ATTTTTATATATAAAATTTTTACTATT
Done.