Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 17 of 316
Found at i:5212484 original size:26 final size:26
Alignment explanation
Indices: 5212416--5212599 Score: 105
Period size: 26 Copynumber: 7.0 Consensus size: 26
5212406 TCAATAATAT
* **
5212416 AAAACAATTTCAAGA-AAATAATATGC
1 AAAACAATTT-AAAATAAATAATAAAC
5212442 AAAACAAATTTAAAATAAATAATAAAC
1 AAAAC-AATTTAAAATAAATAATAAAC
* *
5212469 AAAACAATTTAAAATAAATAATATAT
1 AAAACAATTTAAAATAAATAATAAAC
* *
5212495 AAGACACTTTAAAATAACAT-AT----
1 AAAACAATTTAAAATAA-ATAATAAAC
* * *
5212517 AAAAGAGTTTAAGATAAATAATATGTAA-
1 AAAACAATTTAAAATAAATAATA---AAC
*
5212545 AAAGA-AATTTAAAATAAATAATATAC
1 AAA-ACAATTTAAAATAAATAATAAAC
*
5212571 AAAAACAGTTTAAAAATAATATATATAAA
1 -AAAACAATTT-AAAATAA-ATA-ATAAA
5212600 TATATATATA
Statistics
Matches: 125, Mismatches: 16, Indels: 30
0.73 0.09 0.18
Matches are distributed among these distances:
21 2 0.02
22 15 0.12
25 1 0.01
26 45 0.36
27 28 0.22
28 26 0.21
29 4 0.03
30 4 0.03
ACGTcount: A:0.62, C:0.06, G:0.05, T:0.27
Consensus pattern (26 bp):
AAAACAATTTAAAATAAATAATAAAC
Found at i:5212573 original size:102 final size:101
Alignment explanation
Indices: 5212412--5212598 Score: 263
Period size: 102 Copynumber: 1.8 Consensus size: 101
5212402 GAAGTCAATA
*
5212412 ATATAAAACAATTTCAAGAAAATAATATGCAAAACAAATTTAAAATAAATAATAAAC-AAAACAA
1 ATATAAAACAATTTCAAGAAAATAATATGAAAAACAAATTTAAAATAAATAATAAACAAAAACAA
5212476 TTT-AAAATAAATAATATATAAGACACTTTAAAATAAC
66 TTTAAAAAT-AAT-ATATATAAGACACTTTAAAATAAC
* * * *
5212513 ATATAAAAGAGTTT-AAGATAAATAATATGTAAAAAGAAATTTAAAATAAATAATATACAAAAAC
1 ATATAAAACAATTTCAAGA-AAATAATATG-AAAAACAAATTTAAAATAAATAATAAACAAAAAC
*
5212577 AGTTTAAAAATAATATATATAA
64 AATTTAAAAATAATATATATAA
5212599 ATATATATAT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
100 4 0.05
101 22 0.29
102 33 0.43
103 12 0.16
104 5 0.07
ACGTcount: A:0.62, C:0.06, G:0.05, T:0.27
Consensus pattern (101 bp):
ATATAAAACAATTTCAAGAAAATAATATGAAAAACAAATTTAAAATAAATAATAAACAAAAACAA
TTTAAAAATAATATATATAAGACACTTTAAAATAAC
Found at i:5212604 original size:12 final size:12
Alignment explanation
Indices: 5212584--5212613 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
5212574 AACAGTTTAA
5212584 AAATAATATATAT
1 AAAT-ATATATAT
5212597 AAATATATATAT
1 AAATATATATAT
5212609 AAATA
1 AAATA
5212614 ATCCAAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AAATATATATAT
Found at i:5212722 original size:25 final size:25
Alignment explanation
Indices: 5212685--5212775 Score: 89
Period size: 25 Copynumber: 3.6 Consensus size: 25
5212675 TGATAATAGT
* *
5212685 TTAAAATACATAATATGTGAAAAAC
1 TTAAAATAAATAATATATGAAAAAC
*
5212710 TTAAAACAAATAATA-AT--AAAAC
1 TTAAAATAAATAATATATGAAAAAC
*
5212732 GGTTTAAAATAAATAATATAAGAAAAAAC
1 ---TTAAAATAAATAATATATG-AAAAAC
5212761 TTAAAATAAATAATA
1 TTAAAATAAATAATA
5212776 ATAACAAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
22 5 0.09
24 1 0.02
25 27 0.50
26 16 0.30
29 5 0.09
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (25 bp):
TTAAAATAAATAATATATGAAAAAC
Found at i:5212741 original size:50 final size:51
Alignment explanation
Indices: 5212683--5212779 Score: 151
Period size: 51 Copynumber: 1.9 Consensus size: 51
5212673 CTTGATAATA
* **
5212683 GTTTAAAATACATAATATGTG-AAAAACTTAAAACAAATAATAATAAAACG
1 GTTTAAAATAAATAATATAAGAAAAAACTTAAAACAAATAATAATAAAACG
*
5212733 GTTTAAAATAAATAATATAAGAAAAAACTTAAAATAAATAATAATAA
1 GTTTAAAATAAATAATATAAGAAAAAACTTAAAACAAATAATAATAA
5212780 CAAAAAAGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
50 18 0.43
51 24 0.57
ACGTcount: A:0.62, C:0.05, G:0.06, T:0.27
Consensus pattern (51 bp):
GTTTAAAATAAATAATATAAGAAAAAACTTAAAACAAATAATAATAAAACG
Found at i:5212768 original size:26 final size:27
Alignment explanation
Indices: 5212704--5212786 Score: 91
Period size: 26 Copynumber: 3.2 Consensus size: 27
5212694 ATAATATGTG
*
5212704 AAAAACTTAAAACAAATAATAAT-A-A
1 AAAAACTTAAAATAAATAATAATAACA
**** *
5212729 AACGGTTTAAAATAAATAAT-ATAAGA
1 AAAAACTTAAAATAAATAATAATAACA
5212755 AAAAACTTAAAATAAATAATAATAACA
1 AAAAACTTAAAATAAATAATAATAACA
5212782 AAAAA
1 AAAAA
5212787 GTTTTAAAAA
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
24 2 0.04
25 16 0.36
26 17 0.38
27 10 0.22
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.22
Consensus pattern (27 bp):
AAAAACTTAAAATAAATAATAATAACA
Found at i:5212793 original size:29 final size:27
Alignment explanation
Indices: 5212704--5212819 Score: 87
Period size: 26 Copynumber: 4.2 Consensus size: 27
5212694 ATAATATGTG
* *
5212704 AAAAACTTAAAACAAATAATAAT-A-A
1 AAAAATTTAAAATAAATAATAATAACA
*** *
5212729 AACGGTTTAAAATAAATAAT-ATAAGA
1 AAAAATTTAAAATAAATAATAATAACA
*
5212755 AAAAACTTAAAATAAATAATAATAACA
1 AAAAATTTAAAATAAATAATAATAACA
5212782 AAAAAGTTTTAAAA-AAATGAATAACTAAACA
1 AAAAA--TTTAAAATAAAT-AATAA-T-AACA
5212813 AATAAAT
1 AA-AAAT
5212820 AAATTAGATA
Statistics
Matches: 71, Mismatches: 11, Indels: 13
0.75 0.12 0.14
Matches are distributed among these distances:
24 2 0.03
25 16 0.23
26 17 0.24
27 10 0.14
28 4 0.06
29 11 0.15
30 2 0.03
31 6 0.08
32 3 0.04
ACGTcount: A:0.66, C:0.06, G:0.04, T:0.23
Consensus pattern (27 bp):
AAAAATTTAAAATAAATAATAATAACA
Found at i:5213968 original size:11 final size:12
Alignment explanation
Indices: 5213940--5213975 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
5213930 GGGCCTGGGG
5213940 TTAATTTGGGTT
1 TTAATTTGGGTT
5213952 TGTAA-TTGGGTT
1 T-TAATTTGGGTT
5213964 TTAATTTGGGTT
1 TTAATTTGGGTT
5213976 ATTTGTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.14
12 16 0.73
13 3 0.14
ACGTcount: A:0.17, C:0.00, G:0.28, T:0.56
Consensus pattern (12 bp):
TTAATTTGGGTT
Found at i:5217413 original size:23 final size:25
Alignment explanation
Indices: 5217387--5217433 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
5217377 TATCATTCAT
*
5217387 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
5217410 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
5217434 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:5217754 original size:46 final size:45
Alignment explanation
Indices: 5217694--5217997 Score: 341
Period size: 46 Copynumber: 7.0 Consensus size: 45
5217684 TTTGACGTGA
* * * * *
5217694 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCA-GT
** * *
5217740 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA-GT
*
5217786 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG-T
5217832 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA-GT
* *
5217878 TGCCATGGTATCTTTCAATCATGGTCTTACACA---C--A--GGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGT
*
5217916 TGCCATGGTATCTTTCAACCATGGTCTTACACA---C--A--GGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGT
5217954 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
5217998 AGAGCACACT
Statistics
Matches: 232, Mismatches: 16, Indels: 21
0.86 0.06 0.08
Matches are distributed among these distances:
38 72 0.31
41 2 0.01
43 2 0.01
45 6 0.03
46 149 0.64
47 1 0.00
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.38
Consensus pattern (45 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGT
Found at i:5217924 original size:38 final size:38
Alignment explanation
Indices: 5217873--5217986 Score: 219
Period size: 38 Copynumber: 3.0 Consensus size: 38
5217863 CATTTCATAT
*
5217873 CAGGTTGCCATGGTATCTTTCAATCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
5217911 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
5217949 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
5217987 TTTCATATCA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
38 75 1.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.32
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
Found at i:5222712 original size:18 final size:19
Alignment explanation
Indices: 5222674--5222712 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
5222664 TCAAAATGGA
*
5222674 TTATTTTAAATTTTTAAAT
1 TTATTTTAAATTTATAAAT
*
5222693 TTATTTT-AATTTATATAT
1 TTATTTTAAATTTATAAAT
5222711 TT
1 TT
5222713 TGATTTTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTTTAAATTTATAAAT
Found at i:5234059 original size:18 final size:19
Alignment explanation
Indices: 5234017--5234059 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5234007 AAATTTTCTA
**
5234017 TTTCATTCAAACAAGTAGT
1 TTTCATTCAAACAAGTAAC
*
5234036 TTTCATTCACACAA-TAAC
1 TTTCATTCAAACAAGTAAC
5234054 TTTCAT
1 TTTCAT
5234060 ATAAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.40
Consensus pattern (19 bp):
TTTCATTCAAACAAGTAAC
Found at i:5237506 original size:39 final size:39
Alignment explanation
Indices: 5237462--5237733 Score: 454
Period size: 39 Copynumber: 7.0 Consensus size: 39
5237452 ATTATATTAT
* *
5237462 CAGCACAAAGCCTGCGGGACTTTAACCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* *
5237501 TAGCACGAAGCCTGCGGGACTTTGGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
5237540 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
5237579 CAGCACGAAGCCTGCGGGACTTTAGTCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* * *
5237618 CAGCACGAAGCCTGTGGGACTTTGGCCCGGATATATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
5237657 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
5237696 CAGCACGAAGCCTGAGGGACTTTAGCCCGGATACATTT
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
5237734 TTAGTGTCTT
Statistics
Matches: 218, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 218 1.00
ACGTcount: A:0.23, C:0.29, G:0.26, T:0.22
Consensus pattern (39 bp):
CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
Found at i:5239675 original size:5 final size:5
Alignment explanation
Indices: 5239665--5239702 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
5239655 TTCATTTTTC
5239665 TTCTT TTC-T TTCTT TTCTTT TTCTT TTCTTT TTCTT TT
1 TTCTT TTCTT TTCTT TTC-TT TTCTT TTC-TT TTCTT TT
5239703 TGTTGTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 4 0.13
5 16 0.53
6 10 0.33
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTCTT
Found at i:5239688 original size:6 final size:6
Alignment explanation
Indices: 5239653--5239703 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
5239643 TTAGTTTAGG
*
5239653 TTTTCAT TTTTCT TCTTT-T CTTTC- TTTTCT TTTTC- TTTTCT TTTTCT
1 TTTTC-T TTTTCT T-TTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
5239700 TTTT
1 TTTT
5239704 GTTGTTGAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
5 12 0.32
6 18 0.47
7 8 0.21
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:5239689 original size:11 final size:11
Alignment explanation
Indices: 5239653--5239702 Score: 66
Period size: 11 Copynumber: 4.4 Consensus size: 11
5239643 TTAGTTTAGG
5239653 TTTTCATTTTTC
1 TTTTC-TTTTTC
5239665 TTCTT-TTCTTTC
1 TT-TTCTT-TTTC
5239677 TTTTCTTTTTC
1 TTTTCTTTTTC
5239688 TTTTCTTTTTC
1 TTTTCTTTTTC
5239699 TTTT
1 TTTT
5239703 TGTTGTTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
11 23 0.66
12 10 0.29
13 2 0.06
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:5240815 original size:19 final size:21
Alignment explanation
Indices: 5240791--5240831 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
5240781 TAATTATGAT
5240791 TTATAAATTTA-TT-TTAACA
1 TTATAAATTTACTTATTAACA
*
5240810 TTATAACTTTACTTATTAACA
1 TTATAAATTTACTTATTAACA
5240831 T
1 T
5240832 GTAAATTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 2 0.11
21 7 0.37
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (21 bp):
TTATAAATTTACTTATTAACA
Found at i:5243722 original size:36 final size:38
Alignment explanation
Indices: 5243667--5243740 Score: 109
Period size: 36 Copynumber: 2.0 Consensus size: 38
5243657 TAGTATTACA
5243667 CTCAACTTTAACAATGCTTAA-AGATAT-AAAAAGTTGG
1 CTCAACTTTAACAATGCTTAATA-ATATAAAAAAGTTGG
5243704 CTCAACTTT-ACAATGCTTAATAATATACAAAAAGTTG
1 CTCAACTTTAACAATGCTTAATAATATA-AAAAAGTTG
5243741 TCTCGATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
36 15 0.44
37 10 0.29
38 9 0.26
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (38 bp):
CTCAACTTTAACAATGCTTAATAATATAAAAAAGTTGG
Found at i:5247015 original size:48 final size:47
Alignment explanation
Indices: 5246865--5247226 Score: 284
Period size: 48 Copynumber: 7.6 Consensus size: 47
5246855 GGTAAAATAC
* * * ** **
5246865 CGATGCCATGTCCCAGACATGGTCTTACACTGACACAT-ATAACAATAC
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTC-TCATAA-TGTGG
* * * * * *
5246913 CGATGCCATGTTCCAAGCATGATCTTACACTGGC-CGCATATTGAGG
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTGG
* *
5246959 CCGATGCCATATCCCAAACATGGTCTTACATTGGCTCTCATAATGTGG
1 -CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTGG
* * * * *
5247007 CAGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAAAGT--
1 C-GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTC--AT-AATGTGG
* * *
5247056 CGATGCCATGTCCCAGACATAGTCTTACATTGGCTCTCATAATGTGG
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTGG
* * * * * ****
5247103 TCGATGCCATGTCTCAGACATGGTCTTACACTAGCACACAT-ATCAACAC
1 -CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAAT--GTGG
*
5247152 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATATGG
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTGG
*
5247199 CCGATGCCATGTCCCAAATATGGTCTTA
1 -CGATGCCATGTCCCAAACATGGTCTTA
5247227 TGTTAGCACA
Statistics
Matches: 248, Mismatches: 52, Indels: 28
0.76 0.16 0.09
Matches are distributed among these distances:
45 4 0.02
46 2 0.01
47 37 0.15
48 196 0.79
49 3 0.01
50 2 0.01
51 4 0.02
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (47 bp):
CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTGG
Found at i:5247083 original size:96 final size:95
Alignment explanation
Indices: 5246863--5247245 Score: 423
Period size: 96 Copynumber: 4.0 Consensus size: 95
5246853 AGGGTAAAAT
* * * * ** ** *
5246863 ACCGATGCCATGTCCCAGACATGGTCTTACACTGACACAT-ATAACAATACCGATGCCATGTTCC
1 ACCGATGCCATGTCCCAAACATGGTCTTACATTGGCTC-TCATAA-TGTGGCGATGCCATGTCCC
* * * ** *
5246927 A-AGCATGATCTTACACTGGC-CGCATATTGAG
64 AGA-CATGGTCTTACACTAGCACACATATCAAC
* *
5246958 GCCGATGCCATATCCCAAACATGGTCTTACATTGGCTCTCATAATGTGGCAGATGCCATGTCCCA
1 ACCGATGCCATGTCCCAAACATGGTCTTACATTGGCTCTCATAATGTGGC-GATGCCATGTCCCA
5247023 GACATGGTCTTACACTAGCACACATATCAA-
65 GACATGGTCTTACACTAGCACACATATCAAC
* * * *
5247053 AGTCGATGCCATGTCCCAGACATAGTCTTACATTGGCTCTCATAATGTGGTCGATGCCATGTCTC
1 A-CCGATGCCATGTCCCAAACATGGTCTTACATTGGCTCTCATAATGTGG-CGATGCCATGTCCC
5247118 AGACATGGTCTTACACTAGCACACATATCAAC
64 AGACATGGTCTTACACTAGCACACATATCAAC
* *
5247150 ACCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATATGGCCGATGCCATGTCCCA
1 ACCGATGCCATGTCCCAAACATGGTCTTACATTGGCTCTCATAATGTGG-CGATGCCATGTCCCA
* * ***
5247215 AATATGGTCTTATGTTAGCACACATATCAAC
65 GACATGGTCTTACACTAGCACACATATCAAC
5247246 CGAATGTCTT
Statistics
Matches: 247, Mismatches: 34, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
94 3 0.01
95 64 0.26
96 178 0.72
97 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (95 bp):
ACCGATGCCATGTCCCAAACATGGTCTTACATTGGCTCTCATAATGTGGCGATGCCATGTCCCAG
ACATGGTCTTACACTAGCACACATATCAAC
Found at i:5247225 original size:144 final size:144
Alignment explanation
Indices: 5246863--5247226 Score: 362
Period size: 144 Copynumber: 2.5 Consensus size: 144
5246853 AGGGTAAAAT
* * * *
5246863 ACCGATGCCATGTCCCAGACATGGTCTTACACTGACACAT-ATAACAATACCGATGCCATGTTCC
1 ACCGATGCCATGTCCCAGACATGGTCTTACACTGGCAC-TCATAA-TATGCCGATGCCATGTCCC
* * * * *
5246927 AAGCATGATCTTACACTGGCCGCATATTGAGGCCGATGCCATATCCCAAACATGGTCTTACATTG
64 AAACATGGTCTTACACTGGCCGCATAATGAGGCCGATGCCATATCCCAAACATGGTCTTACACTA
* * ***
5246992 GCTCTCATAATGTGGC
129 GCACACATAATGCAAC
* * * *
5247008 A--GATGCCATGTCCCAGACATGGTCTTACACTAGCACACAT-ATCAAAGTCGATGCCATGTCCC
1 ACCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCATAAT--ATGCCGATGCCATGTCCC
* * * * * * * * *
5247070 AGACATAGTCTTACATTGGCTCTCATAATGTGGTCGATGCCATGTCTCAGACATGGTCTTACACT
64 AAACATGGTCTTACACTGGC-CGCATAATGAGGCCGATGCCATATCCCAAACATGGTCTTACACT
5247135 AGCACACAT-AT-CAAC
128 AGCACACATAATGCAAC
* *
5247150 ACCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAATATGGCCGATGCCATGTCCCA
1 ACCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCATAATAT-GCCGATGCCATGTCCCA
*
5247215 AATATGGTCTTA
65 AACATGGTCTTA
5247227 TGTTAGCACA
Statistics
Matches: 175, Mismatches: 36, Indels: 17
0.77 0.16 0.07
Matches are distributed among these distances:
142 3 0.02
143 67 0.38
144 102 0.58
145 3 0.02
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (144 bp):
ACCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCATAATATGCCGATGCCATGTCCCAA
ACATGGTCTTACACTGGCCGCATAATGAGGCCGATGCCATATCCCAAACATGGTCTTACACTAGC
ACACATAATGCAAC
Found at i:5252612 original size:54 final size:56
Alignment explanation
Indices: 5252553--5252660 Score: 166
Period size: 54 Copynumber: 1.9 Consensus size: 56
5252543 ATTTTCCTAT
*
5252553 AGTTTTCTGAATTTAGATTG-TGTATATATATT-TAGAATTGGTTTTGGTATGACA
1 AGTTTTCTGAATTTAGATTGATATATATATATTGTAGAATTGGTTTTGGTATGACA
* *
5252607 AGTTTTCTGAATTTAGATTGCATATATATTTTTTGTAGAATTGGTTTTGGTATG
1 AGTTTTCTGAATTTAGATTG-ATATATATATATTGTAGAATTGGTTTTGGTATG
5252661 GCAACTTACA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
54 20 0.42
56 9 0.19
57 19 0.40
ACGTcount: A:0.26, C:0.04, G:0.20, T:0.50
Consensus pattern (56 bp):
AGTTTTCTGAATTTAGATTGATATATATATATTGTAGAATTGGTTTTGGTATGACA
Found at i:5253813 original size:34 final size:34
Alignment explanation
Indices: 5253774--5253841 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
5253764 CAAACTTTAA
5253774 ATGCAATGGTTCTCCTTCAAAACTGTCACTAAGT
1 ATGCAATGGTTCTCCTTCAAAACTGTCACTAAGT
5253808 ATGCAATGGTTCTCCTTCAAAACTGTCACTAAGT
1 ATGCAATGGTTCTCCTTCAAAACTGTCACTAAGT
5253842 CTACCATTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (34 bp):
ATGCAATGGTTCTCCTTCAAAACTGTCACTAAGT
Found at i:5254693 original size:49 final size:49
Alignment explanation
Indices: 5254633--5254734 Score: 125
Period size: 49 Copynumber: 2.1 Consensus size: 49
5254623 GGCTCGCACC
* * * *
5254633 TAATAAAAAAATTATTATTTTTATTGTTATAATTTAT-AAAATTTTAAAT
1 TAATAAAAAAATTA-TACTTTAATTGTTAAAATTGATAAAAATTTTAAAT
* * *
5254682 TAATAATAAAATTATACTTTAATTTTTAAAATTGATAAAAATTTTAATT
1 TAATAAAAAAATTATACTTTAATTGTTAAAATTGATAAAAATTTTAAAT
5254731 TAAT
1 TAAT
5254735 CTTTAAAAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 17 0.38
49 28 0.62
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (49 bp):
TAATAAAAAAATTATACTTTAATTGTTAAAATTGATAAAAATTTTAAAT
Found at i:5254706 original size:30 final size:28
Alignment explanation
Indices: 5254672--5254768 Score: 79
Period size: 31 Copynumber: 3.2 Consensus size: 28
5254662 TAATTTATAA
*
5254672 AATTTTAAATTAATAATAAAATTATACTTT
1 AATTTTAAATTAAT-A-AAAATTATAATTT
* *
5254702 AATTTTTAAAATTGATAAAAATTTTAATTT
1 AA-TTTT-AAATTAATAAAAATTATAATTT
5254732 AATCTTTAAAAACTT-ATAAAAATATATAATTT
1 AAT-TTT--AAA-TTAATAAAAAT-TATAATTT
5254764 AATTT
1 AATTT
5254769 CGATTAAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
29 1 0.02
30 18 0.32
31 19 0.33
32 19 0.33
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (28 bp):
AATTTTAAATTAATAAAAATTATAATTT
Found at i:5254765 original size:32 final size:30
Alignment explanation
Indices: 5254689--5254768 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 30
5254679 AATTAATAAT
* *
5254689 AAAATTATACTTTAATTTTTAAAATTGATA
1 AAAATTATAATTTAATTTTAAAAATTGATA
*
5254719 AAAATTTTAATTTAATCTTTAAAAACTT-ATA
1 AAAATTATAATTTAAT-TTTAAAAA-TTGATA
5254750 AAAATATATAATTTAATTT
1 AAAAT-TATAATTTAATTT
5254769 CGATTAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
30 14 0.33
31 17 0.40
32 12 0.28
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (30 bp):
AAAATTATAATTTAATTTTAAAAATTGATA
Found at i:5254883 original size:19 final size:17
Alignment explanation
Indices: 5254844--5254883 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
5254834 GAAATATGTC
*
5254844 AAAAATATTTTTTAATG
1 AAAAATATTTTTTAATA
5254861 AAAAATATTTTAATTAATA
1 AAAAATATTTT--TTAATA
5254880 AAAA
1 AAAA
5254884 CTATAAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 11 0.55
19 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
AAAAATATTTTTTAATA
Found at i:5259071 original size:106 final size:106
Alignment explanation
Indices: 5258935--5259135 Score: 366
Period size: 106 Copynumber: 1.9 Consensus size: 106
5258925 AGAATTTTTC
5258935 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
1 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
* *
5259000 TTCTCGTTTGACCAAATAGCCAAATATCCTTTTTAAACTTT
66 TTCTCGTTCGACCAAACAGCCAAATATCCTTTTTAAACTTT
*
5259041 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTCGAT
1 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
*
5259106 TTCTCGTTCGACTAAACAGCCAAATATCCT
66 TTCTCGTTCGACCAAACAGCCAAATATCCT
5259136 CTTAAAGCTT
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 91 1.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (106 bp):
TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
TTCTCGTTCGACCAAACAGCCAAATATCCTTTTTAAACTTT
Found at i:5276012 original size:29 final size:29
Alignment explanation
Indices: 5275970--5276030 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
5275960 TTGATAGTAA
5275970 GTACTGAACAAGAGTACTTAATGAGACAC
1 GTACTGAACAAGAGTACTTAATGAGACAC
*
5275999 GTACTGAACAAGAGTACTTAATGAGACCC
1 GTACTGAACAAGAGTACTTAATGAGACAC
5276028 GTA
1 GTA
5276031 ACTGTTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (29 bp):
GTACTGAACAAGAGTACTTAATGAGACAC
Found at i:5286450 original size:178 final size:178
Alignment explanation
Indices: 5286143--5286484 Score: 537
Period size: 178 Copynumber: 1.9 Consensus size: 178
5286133 TAGAAGTCTA
* *
5286143 AGAAACACACTCTCAGAGGTGATCCAATCATAGGGAATGAACCACTTCAAAGTGATAAAACCATG
1 AGAAACACACTCTCAGAGCTGATCCAATAATAGGGAATGAACCACTTCAAAGTGATAAAACCATG
* *
5286208 AGACCTATTAGAATCAAATGCAATCAATCTTTAATACAAACATCTATACAAATGAGGATTTTTTG
66 AGACCTATTAGAATCAAATGCAATCAATCTTAAATACAAACATCTATACAAATAAGGATTTTTTG
* * *
5286273 TTTTTATTTTTCCAGCTTTGCTTTAATAATAAGCTTTATAAAAGTTAG
131 TTTTTATTTTGCCAACTTTGCTTCAATAATAAGCTTTATAAAAGTTAG
* * *
5286321 AGAAACACACTCTCAGAGCTGATCTAATAATAGGGAATTAACCACTTCAAAGTGATAAAATCATG
1 AGAAACACACTCTCAGAGCTGATCCAATAATAGGGAATGAACCACTTCAAAGTGATAAAACCATG
5286386 AGACCTATTAGAATCAAATGCAA-CACATCTTAAATACAAACA-C-ATACAAATAAGGATTTTTT
66 AGACCTATTAGAATCAAATGCAATCA-ATCTTAAATACAAACATCTATACAAATAAGGA--TTTT
*
5286448 TTGTTTTTATTTTGCCAACTTTTCTTCAATAATAAGC
128 TTGTTTTTATTTTGCCAACTTTGCTTCAATAATAAGC
5286485 ATCACTTCCC
Statistics
Matches: 150, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
176 12 0.08
177 3 0.02
178 135 0.90
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (178 bp):
AGAAACACACTCTCAGAGCTGATCCAATAATAGGGAATGAACCACTTCAAAGTGATAAAACCATG
AGACCTATTAGAATCAAATGCAATCAATCTTAAATACAAACATCTATACAAATAAGGATTTTTTG
TTTTTATTTTGCCAACTTTGCTTCAATAATAAGCTTTATAAAAGTTAG
Found at i:5297691 original size:3 final size:3
Alignment explanation
Indices: 5297683--5297730 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
5297673 TTCTTACCTT
5297683 TTA TTA TTA TTA 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
5297731 AGAAGTCTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5303741 original size:47 final size:47
Alignment explanation
Indices: 5303672--5303767 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 47
5303662 TGCACGTTTG
* *
5303672 TTCTATGGTCCATGTCCGAGTTCGTGATTGTCTCTCCCAGTAATATT
1 TTCTATGATCCATGTCCGAGTTCATGATTGTCTCTCCCAGTAATATT
*
5303719 TTCTATGATCCATGTCCGAGTTCATGATTGTCTCTCCCAGTAATGTT
1 TTCTATGATCCATGTCCGAGTTCATGATTGTCTCTCCCAGTAATATT
5303766 TT
1 TT
5303768 AAAATTATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.42
Consensus pattern (47 bp):
TTCTATGATCCATGTCCGAGTTCATGATTGTCTCTCCCAGTAATATT
Found at i:5304328 original size:5 final size:6
Alignment explanation
Indices: 5304306--5304352 Score: 69
Period size: 6 Copynumber: 7.8 Consensus size: 6
5304296 TGCACTTTTT
*
5304306 TTTTCC TTTTCCC TTTTCC -TTTCC TTTTCC TTTTCC TTTTCC CTTTC
1 TTTTCC TTTT-CC TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTTC
5304353 GCTTCTCTCT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
5 5 0.13
6 27 0.71
7 6 0.16
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (6 bp):
TTTTCC
Found at i:5304328 original size:18 final size:17
Alignment explanation
Indices: 5304307--5304344 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
5304297 GCACTTTTTT
5304307 TTTCCTTTTCCCTTTTCC
1 TTTCCTTTT-CCTTTTCC
5304325 TTTCCTTTTCCTTTTCC
1 TTTCCTTTTCCTTTTCC
5304342 TTT
1 TTT
5304345 TCCCTTTCGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTCCTTTTCCTTTTCC
Found at i:5304333 original size:24 final size:24
Alignment explanation
Indices: 5304306--5304370 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 24
5304296 TGCACTTTTT
5304306 TTTTCCTTTTCCCTTTT-CCTTTCC
1 TTTTCCTTTT-CCTTTTCCCTTTCC
5304330 TTTTCCTTTTCCTTTTCCCTTTCGC
1 TTTTCCTTTTCCTTTTCCCTTTC-C
* *
5304355 TTCTCTCTTTTACTTT
1 TTTTC-CTTTTCCTTT
5304371 CTTGGAAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
23 6 0.17
24 16 0.44
25 5 0.14
26 9 0.25
ACGTcount: A:0.02, C:0.34, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTTCCTTTTCCTTTTCCCTTTCC
Found at i:5305346 original size:60 final size:60
Alignment explanation
Indices: 5305223--5305348 Score: 137
Period size: 60 Copynumber: 2.1 Consensus size: 60
5305213 AAAAATTAAC
* * * * ** * *
5305223 TTTTTAGAGTTAGGACTAATTGACAGATTTTGTAAATGTTGAGTGTTAAATTTATTGAAT
1 TTTTTAGAATTAGAACTAAATGACAAATTTTGTAAATCATGAGAGCTAAATTTATTGAAT
* * *
5305283 TTTTTAGAATTAGAACTAAAATGACAAATTTTGTAAA-CATGAGAGCTAATTTTGTTGATT
1 TTTTTAGAATTAGAACT-AAATGACAAATTTTGTAAATCATGAGAGCTAAATTTATTGAAT
5305343 TTTTTA
1 TTTTTA
5305349 TATTTTGGAT
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 37 0.69
61 17 0.31
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (60 bp):
TTTTTAGAATTAGAACTAAATGACAAATTTTGTAAATCATGAGAGCTAAATTTATTGAAT
Found at i:5307443 original size:28 final size:26
Alignment explanation
Indices: 5307399--5307450 Score: 61
Period size: 28 Copynumber: 1.9 Consensus size: 26
5307389 AAAACTTAAT
5307399 TAAGTTAATTAAATGAAACTTACATAGA
1 TAAGTTAATTAAATG-AAC-TACATAGA
*
5307427 TAAGTATAATT-ATTGAACTACATA
1 TAAGT-TAATTAAATGAACTACATA
5307451 AACAATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 6 0.27
27 3 0.14
28 8 0.36
29 5 0.23
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.35
Consensus pattern (26 bp):
TAAGTTAATTAAATGAACTACATAGA
Found at i:5307744 original size:17 final size:17
Alignment explanation
Indices: 5307722--5307755 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5307712 ATTTTGGGCC
5307722 CTAAACCAAACAACCCA
1 CTAAACCAAACAACCCA
5307739 CTAAACCAAACAACCCA
1 CTAAACCAAACAACCCA
5307756 ATAACCCGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.41, G:0.00, T:0.06
Consensus pattern (17 bp):
CTAAACCAAACAACCCA
Found at i:5308979 original size:15 final size:17
Alignment explanation
Indices: 5308959--5308999 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
5308949 GTTACTATTA
5308959 TATTTATTATT-A-TAT
1 TATTTATTATTCACTAT
5308974 TATTTATT-TTCACTAT
1 TATTTATTATTCACTAT
5308990 TA-TTATTATT
1 TATTTATTATT
5309000 TTCATCATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 2 0.09
15 14 0.61
16 7 0.30
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTATTATTCACTAT
Found at i:5309000 original size:18 final size:18
Alignment explanation
Indices: 5308971--5309013 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 18
5308961 TTTATTATTA
5308971 TATTATTTATTTTCA-CTAT
1 TATTA-TTATTTTCATC-AT
5308990 TATTATTATTTTCATCAT
1 TATTATTATTTTCATCAT
5309008 TATTAT
1 TATTAT
5309014 ACATATATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTATTATTTTCATCAT
Found at i:5312401 original size:29 final size:30
Alignment explanation
Indices: 5312342--5312399 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
5312332 TCCGAGCCTT
*
5312342 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
5312372 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
5312400 AGAGTCGAGG
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:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:5312629 original size:13 final size:13
Alignment explanation
Indices: 5312611--5312642 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5312601 TTTCCAGCAA
5312611 TTATGAATTTATT
1 TTATGAATTTATT
5312624 TTATGAATTTATT
1 TTATGAATTTATT
*
5312637 TGATGA
1 TTATGA
5312643 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:5312850 original size:50 final size:50
Alignment explanation
Indices: 5312737--5312978 Score: 263
Period size: 50 Copynumber: 4.7 Consensus size: 50
5312727 ATTTGGGTAA
* * * *
5312737 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCA-TGGGAACC--GAGA-C--G
*
5312793 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
* * * *
5312843 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
* * *
5312893 AGAGGTCCCCA-ATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGT-CCCATGTAAGACCATGTCTGGGACATGGCATGGGAACCGA-GACG
**
5312943 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
5312979 TTTGGCATGT
Statistics
Matches: 164, Mismatches: 18, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
49 1 0.01
50 90 0.55
51 29 0.18
52 1 0.01
53 3 0.02
55 6 0.04
56 34 0.21
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.19
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
Found at i:5312927 original size:100 final size:103
Alignment explanation
Indices: 5312737--5312986 Score: 346
Period size: 100 Copynumber: 2.4 Consensus size: 103
5312727 ATTTGGGTAA
5312737 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
** *
5312802 CTGTAAGACCATGTCTGGGACATGGCATGGGAACCGA-GACG
63 CAATAAGACCATGTCTGGGACATGGCATGGGAACC-ATCACG
* * *
5312843 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCAA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCAA
*
5312905 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGAACCATCACG
* *
5312943 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
5312987 GTTATTATCA
Statistics
Matches: 131, Mismatches: 10, Indels: 10
0.87 0.07 0.07
Matches are distributed among these distances:
99 1 0.01
100 49 0.37
101 39 0.30
105 2 0.02
106 40 0.31
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCAA
TAAGACCATGTCTGGGACATGGCATGGGAACCATCACG
Found at i:5328300 original size:15 final size:17
Alignment explanation
Indices: 5328280--5328320 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
5328270 GTTACTATTA
5328280 TATTTATTATT-A-TAT
1 TATTTATTATTCACTAT
5328295 TATTTATT-TTCACTAT
1 TATTTATTATTCACTAT
5328311 TA-TTATTATT
1 TATTTATTATT
5328321 TCATCATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 2 0.09
15 14 0.61
16 7 0.30
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTATTATTCACTAT
Found at i:5334298 original size:14 final size:15
Alignment explanation
Indices: 5334273--5334306 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5334263 TTTTTTTTAA
*
5334273 AATTATTAATTAATT
1 AATTATTAATTAAAT
5334288 AATTA-TAATTAAAT
1 AATTATTAATTAAAT
5334302 AATTA
1 AATTA
5334307 AAGTTCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTATTAATTAAAT
Found at i:5336590 original size:5 final size:5
Alignment explanation
Indices: 5336580--5336604 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5336570 TTCTATACCA
5336580 ATCCC ATCCC ATCCC ATCCC ATCCC
1 ATCCC ATCCC ATCCC ATCCC ATCCC
5336605 CTCTTTCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.60, G:0.00, T:0.20
Consensus pattern (5 bp):
ATCCC
Found at i:5342198 original size:17 final size:17
Alignment explanation
Indices: 5342176--5342209 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5342166 ATCCACTAAT
*
5342176 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
5342193 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
5342210 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:5346837 original size:17 final size:17
Alignment explanation
Indices: 5346815--5346848 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5346805 ATCCACTAAT
*
5346815 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
5346832 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
5346849 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:5351487 original size:25 final size:24
Alignment explanation
Indices: 5351407--5351487 Score: 72
Period size: 25 Copynumber: 3.1 Consensus size: 24
5351397 GACAAAAAAG
*
5351407 AAAGATTAAGTACCAAATTAGGAA
1 AAAGATTAAGTACCAAATTAGAAA
* *
5351431 AAAGAATAAAGTATCAAATTAGACCCCAAA
1 AAAG-ATTAAGTACCAAATTAG-----AAA
5351461 AAAGATTAAGTACCAAATTCAGAAA
1 AAAGATTAAGTACCAAATT-AGAAA
5351486 AA
1 AA
5351488 GTGTTAAGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
24 4 0.09
25 20 0.44
29 13 0.29
30 8 0.18
ACGTcount: A:0.57, C:0.12, G:0.12, T:0.19
Consensus pattern (24 bp):
AAAGATTAAGTACCAAATTAGAAA
Found at i:5354970 original size:3 final size:3
Alignment explanation
Indices: 5354962--5354993 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5354952 ATTTCATTTT
5354962 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
5354994 GTTGATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5355755 original size:3 final size:3
Alignment explanation
Indices: 5355747--5355774 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5355737 CCGCCATCGT
5355747 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5355775 TTTTATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:5356623 original size:30 final size:30
Alignment explanation
Indices: 5356589--5356650 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
5356579 TTTGAAAATC
*
5356589 AAAA-CTTAAAAATATTTAAAATACAAAAAA
1 AAAACCTT-AAAATATATAAAATACAAAAAA
* *
5356619 AAAACCTTAAAATATATAAAATTCAAGAAA
1 AAAACCTTAAAATATATAAAATACAAAAAA
5356649 AA
1 AA
5356651 TTCTATTAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 25 0.89
31 3 0.11
ACGTcount: A:0.68, C:0.08, G:0.02, T:0.23
Consensus pattern (30 bp):
AAAACCTTAAAATATATAAAATACAAAAAA
Found at i:5358207 original size:37 final size:37
Alignment explanation
Indices: 5358166--5358240 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
5358156 TACTTACCAT
*
5358166 ATGTGTCCTAATAAGGATTGGTTTTCTAGTCTTAAAG
1 ATGTGTCCTAATAAAGATTGGTTTTCTAGTCTTAAAG
5358203 ATGTGTCCTAATAAAGATTGGTTTTCTAGTCTTAAAG
1 ATGTGTCCTAATAAAGATTGGTTTTCTAGTCTTAAAG
5358240 A
1 A
5358241 GCTAGAAGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (37 bp):
ATGTGTCCTAATAAAGATTGGTTTTCTAGTCTTAAAG
Found at i:5358240 original size:21 final size:21
Alignment explanation
Indices: 5358181--5358240 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 21
5358171 TCCTAATAAG
5358181 GATTGGTTTTCTAGTCTTAAA
1 GATTGGTTTTCTAGTCTTAAA
* * *
5358202 GA-T-GTGTCCTA---ATAAA
1 GATTGGTTTTCTAGTCTTAAA
5358218 GATTGGTTTTCTAGTCTTAAA
1 GATTGGTTTTCTAGTCTTAAA
5358239 GA
1 GA
5358241 GCTAGAAGGT
Statistics
Matches: 28, Mismatches: 6, Indels: 10
0.64 0.14 0.23
Matches are distributed among these distances:
16 6 0.21
17 1 0.04
18 6 0.21
19 6 0.21
20 1 0.04
21 8 0.29
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (21 bp):
GATTGGTTTTCTAGTCTTAAA
Found at i:5360043 original size:46 final size:46
Alignment explanation
Indices: 5359993--5360168 Score: 180
Period size: 46 Copynumber: 3.8 Consensus size: 46
5359983 TGGTTGAGCA
5359993 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
5360039 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* * *
5360084 CATCCGAGCTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
5360132 CCCGAGCTCGTTGAGTTGAGCCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5360169 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 62 0.58
47 27 0.25
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:5360149 original size:93 final size:93
Alignment explanation
Indices: 5359990--5360161 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
5359980 GGATGGTTGA
* * *
5359990 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
5360055 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGCCCGAGTTCGTGAAATGTAACTAG
* *
5360083 GCATCCGAGCTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
5360148 TGAGCCCGAGTTCG
66 TGAGCCCGAGTTCG
5360162 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGCCCGAGTTCGTGAAATGTAACTAG
Found at i:5364483 original size:24 final size:22
Alignment explanation
Indices: 5364450--5364493 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
5364440 GAATTCTTAA
5364450 TTTTTAAATTCTTTTAAAATATAT
1 TTTTTAAA-T-TTTTAAAATATAT
*
5364474 TTTTTGAATTTTTAAAATAT
1 TTTTTAAATTTTTAAAATAT
5364494 GTGTTGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 1 0.05
24 7 0.37
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTTTAAATTTTTAAAATATAT
Found at i:5365377 original size:90 final size:90
Alignment explanation
Indices: 5365275--5365451 Score: 230
Period size: 90 Copynumber: 2.0 Consensus size: 90
5365265 ATATTTTTAA
* * * * * **
5365275 AAAATGTCTAATGTGTTACTTGAACTATTAATTTTTATATTATTTGG-AACTTATATTTTCATAA
1 AAAATGACTAATGTGGTACTCGAACTATCAATTTGTATATTATTTGGTAACTT-TACATTCATAA
*
5365339 AACATATAATGTGATACTTATACTTT
65 AACATACAATGTGATACTTATACTTT
*
5365365 AAAATGACTAATGTGGTACTCGAACTATCAATTTGTATATTATTTGGTACCTTTACATTCATAAA
1 AAAATGACTAATGTGGTACTCGAACTATCAATTTGTATATTATTTGGTAACTTTACATTCATAAA
** *
5365430 ATGTACAATGTGGTACTTATAC
66 ACATACAATGTGATACTTATAC
5365452 ATTGGAAATG
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
90 70 0.95
91 4 0.05
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.42
Consensus pattern (90 bp):
AAAATGACTAATGTGGTACTCGAACTATCAATTTGTATATTATTTGGTAACTTTACATTCATAAA
ACATACAATGTGATACTTATACTTT
Found at i:5365994 original size:20 final size:22
Alignment explanation
Indices: 5365964--5366004 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
5365954 TATCATACTA
5365964 GTATACATATT-AATAGTTCAG
1 GTATACATATTGAATAGTTCAG
*
5365985 GTAT-CATATTGAATATTTCA
1 GTATACATATTGAATAGTTCA
5366005 AAGACCAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (22 bp):
GTATACATATTGAATAGTTCAG
Found at i:5370525 original size:10 final size:11
Alignment explanation
Indices: 5370509--5370550 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
5370499 TGACCTTTCC
5370509 AAGGTATGGG-
1 AAGGTATGGGA
*
5370519 TAGGTATGGGA
1 AAGGTATGGGA
*
5370530 AAGGTATGGGC
1 AAGGTATGGGA
*
5370541 AAGGAATGGG
1 AAGGTATGGG
5370551 TATATTCTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.31, C:0.02, G:0.48, T:0.19
Consensus pattern (11 bp):
AAGGTATGGGA
Found at i:5372937 original size:18 final size:18
Alignment explanation
Indices: 5372914--5372986 Score: 83
Period size: 18 Copynumber: 4.1 Consensus size: 18
5372904 CAATCCCAAC
*
5372914 TACTGTATACGTGAACAG
1 TACTGTATACGTGAATAG
*
5372932 TACTGTATACGTAAATAG
1 TACTGTATACGTGAATAG
* * *
5372950 TGCTATATACATGAATAG
1 TACTGTATACGTGAATAG
* *
5372968 TGCCGTATACGTGAATAG
1 TACTGTATACGTGAATAG
5372986 T
1 T
5372987 GTCGTAAATG
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.32
Consensus pattern (18 bp):
TACTGTATACGTGAATAG
Found at i:5373548 original size:33 final size:33
Alignment explanation
Indices: 5373506--5373572 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
5373496 AATATTTGGT
5373506 GCCCATAACTTTGACCTTTCCTAGGTATGGGCA
1 GCCCATAACTTTGACCTTTCCTAGGTATGGGCA
5373539 GCCCATAACTTTGACCTTTCCTAGGTATGGGCA
1 GCCCATAACTTTGACCTTTCCTAGGTATGGGCA
5373572 G
1 G
5373573 GTATGGGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.30
Consensus pattern (33 bp):
GCCCATAACTTTGACCTTTCCTAGGTATGGGCA
Found at i:5373590 original size:11 final size:11
Alignment explanation
Indices: 5373561--5373623 Score: 92
Period size: 11 Copynumber: 5.8 Consensus size: 11
5373551 GACCTTTCCT
5373561 AGGTATGGGC-
1 AGGTATGGGCA
*
5373571 AGGTATGGGAA
1 AGGTATGGGCA
*
5373582 AGATATGGGCA
1 AGGTATGGGCA
5373593 AGGTATGGGCA
1 AGGTATGGGCA
5373604 AGGTATGGGCA
1 AGGTATGGGCA
*
5373615 AGGAATGGG
1 AGGTATGGG
5373624 TATATTCTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
10 9 0.19
11 38 0.81
ACGTcount: A:0.30, C:0.06, G:0.46, T:0.17
Consensus pattern (11 bp):
AGGTATGGGCA
Found at i:5374399 original size:21 final size:19
Alignment explanation
Indices: 5374375--5374419 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
5374365 AAATTATAAA
5374375 TTTTTTTAAAAGTATTATTCT
1 TTTTTTTAAAAGTA-TATT-T
* *
5374396 TTTTTTTGAAATTATATTT
1 TTTTTTTAAAAGTATATTT
5374415 TTTTT
1 TTTTT
5374420 AAAAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 4 0.18
21 12 0.55
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.69
Consensus pattern (19 bp):
TTTTTTTAAAAGTATATTT
Found at i:5374409 original size:18 final size:18
Alignment explanation
Indices: 5374356--5374419 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
5374346 TTAAAATTGA
*
5374356 TTTTTTTTGAAATTATAA
1 TTTTTTTTGAAATTATAT
* * *
5374374 ATTTTTTTAAAAGTATTATT
1 TTTTTTTTGAAATTA-TA-T
5374394 CTTTTTTTTGAAATTATAT
1 -TTTTTTTTGAAATTATAT
5374413 TTTTTTT
1 TTTTTTT
5374420 AAAAAATAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
18 19 0.53
19 3 0.08
20 2 0.06
21 12 0.33
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTTTTTTGAAATTATAT
Found at i:5374455 original size:16 final size:17
Alignment explanation
Indices: 5374436--5374467 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5374426 TAAAATTTTG
5374436 TAAAAAAAT-TAAAAAC
1 TAAAAAAATCTAAAAAC
5374452 TAAAAAAATCTAAAAA
1 TAAAAAAATCTAAAAA
5374468 GTGTTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (17 bp):
TAAAAAAATCTAAAAAC
Found at i:5378843 original size:30 final size:30
Alignment explanation
Indices: 5378807--5378864 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
5378797 AGGCAATCCT
5378807 CCTATCTAAGTCTGCAAATGAAGCTTGTCG
1 CCTATCTAAGTCTGCAAATGAAGCTTGTCG
5378837 CCTATCTAAGTCTGCAAATGAAGCTTGT
1 CCTATCTAAGTCTGCAAATGAAGCTTGT
5378865 TTCGACGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (30 bp):
CCTATCTAAGTCTGCAAATGAAGCTTGTCG
Found at i:5382905 original size:28 final size:31
Alignment explanation
Indices: 5382864--5382926 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
5382854 TATTAATGAT
*
5382864 AAAATTATACTTTAGCCC-TAAAAATAATAA
1 AAAATTATACTTTAACCCTTAAAAATAATAA
*
5382894 AAAATTA-A-TTTAACCCTTTAAAAATTATAA
1 AAAATTATACTTTAACCC-TTAAAAATAATAA
5382924 AAA
1 AAA
5382927 TATAAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 7 0.24
29 1 0.03
30 21 0.72
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.32
Consensus pattern (31 bp):
AAAATTATACTTTAACCCTTAAAAATAATAA
Found at i:5384089 original size:273 final size:273
Alignment explanation
Indices: 5383602--5384146 Score: 722
Period size: 273 Copynumber: 2.0 Consensus size: 273
5383592 CATCGACGTT
*
5383602 GGAAAAATATACTCCAAACCATAACAATTAGATATGCTGACGTCTCCTAACTCTGGGAAGCACAA
1 GGAAAAATATACTCCAAACCATAACAAGTAGATATGCTGACGTCTCCTAACTCTGGGAAGCACAA
* *
5383667 AGAATTATGAGAAGTGATGGTCGATGATATTTCTCCCTCGTCACCTTCCAATTCTGTCACTATTT
66 AGAAGTATGAGAAGTGATGGTCGATGATATTTCTCCCTCGTCACCTTCCAATTCTGTCACTACTT
* * * * ** *
5383732 GCTTCATTTCATCACAGTAGCTTACTTCAAGGCCTTTCAATTGTACTAGACTTTGAGCAAGAGAG
131 GCTTCAATTCAGCACAATAGATTACTTCAAGGCCTTTCAAGAGTACGAGACTTTGAGCAAGAGAG
* * * **
5383797 ACTGAACAGAGTGATTTCAAACGTGGGCACTTTTTTATAGTCAAAACAACTAAGCTTTCAAGTCT
196 ACTGAAAAGAGTGATTTCAAACGTCGGCACTGTAGTATAGTCAAAACAACTAAGCTTTCAAGTCT
5383862 TACATGTTGGGTC
261 TACATGTTGGGTC
* * ** * *
5383875 GGAAAAATATATTCCAAACCATCACAAGTAGATATG-TAGACCGT-TGTTAACTTTGGGAAGGAC
1 GGAAAAATATACTCCAAACCATAACAAGTAGATATGCT-GA-CGTCTCCTAACTCTGGGAAGCAC
* *
5383938 AAAGAAGTATGAGAATTGATGGTCGATGATATTTCTCCCTCGTCACCTTCTAATTCTGTCACTAC
64 AAAGAAGTATGAGAAGTGATGGTCGATGATATTTCTCCCTCGTCACCTTCCAATTCTGTCACTAC
* **
5384003 TTGCTTCAATTCAGGACAATAGATTA-TCTCAA-GTTTTTCCAAGAGTACGAGACTTTGAGCAAG
129 TTGCTTCAATTCAGCACAATAGATTACT-TCAAGGCCTTT-CAAGAGTACGAGACTTTGAGCAAG
* * * * **
5384066 CGA-ATGTGAAAAGAGTGATTTCAAATGTCGGCAGTGTAGTATAGTCAATTCAACTAAGCTTTCA
192 AGAGA-CTGAAAAGAGTGATTTCAAACGTCGGCACTGTAGTATAGTCAAAACAACTAAGCTTTCA
5384130 AGTCTTACATGTTGGGT
256 AGTCTTACATGTTGGGT
5384147 TGGCAATTCC
Statistics
Matches: 235, Mismatches: 32, Indels: 10
0.85 0.12 0.04
Matches are distributed among these distances:
272 7 0.03
273 225 0.96
274 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (273 bp):
GGAAAAATATACTCCAAACCATAACAAGTAGATATGCTGACGTCTCCTAACTCTGGGAAGCACAA
AGAAGTATGAGAAGTGATGGTCGATGATATTTCTCCCTCGTCACCTTCCAATTCTGTCACTACTT
GCTTCAATTCAGCACAATAGATTACTTCAAGGCCTTTCAAGAGTACGAGACTTTGAGCAAGAGAG
ACTGAAAAGAGTGATTTCAAACGTCGGCACTGTAGTATAGTCAAAACAACTAAGCTTTCAAGTCT
TACATGTTGGGTC
Found at i:5386097 original size:32 final size:31
Alignment explanation
Indices: 5386026--5386098 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 31
5386016 AAAAGATTAA
*
5386026 GTACCAAATTAAGAAAAAGTGTTAAGTTTAG
1 GTACCAAATTAAGAAAAAGTGTTAAATTTAG
** *
5386057 GTGTCAAATTAGGGAGAAAA-TGTTAAATTTAG
1 GTACCAAATTA-AGA-AAAAGTGTTAAATTTAG
5386089 GTACCAAATT
1 GTACCAAATT
5386099 GGAAAAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
31 9 0.26
32 21 0.62
33 4 0.12
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.30
Consensus pattern (31 bp):
GTACCAAATTAAGAAAAAGTGTTAAATTTAG
Found at i:5386336 original size:15 final size:15
Alignment explanation
Indices: 5386305--5386335 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
5386295 ATCATTAAAA
5386305 TATTTTTAATATTTT
1 TATTTTTAATATTTT
5386320 TATTTATTAATATTTT
1 TATTT-TTAATATTTT
5386336 AATGGGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTTTTAATATTTT
Found at i:5386594 original size:2 final size:2
Alignment explanation
Indices: 5386587--5386611 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5386577 AATTTGGACC
5386587 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5386612 GCTTTGCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5388245 original size:21 final size:22
Alignment explanation
Indices: 5388219--5388260 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
5388209 TGACCTTTCC
*
5388219 AAGGTATGGG-TAGGTATGGGA
1 AAGGTATGGGCAAGGTATGGGA
5388240 AAGGTATGGGCAAGGTATGGG
1 AAGGTATGGGCAAGGTATGGG
5388261 GTATATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.29, C:0.02, G:0.48, T:0.21
Consensus pattern (22 bp):
AAGGTATGGGCAAGGTATGGGA
Found at i:5388246 original size:11 final size:10
Alignment explanation
Indices: 5388219--5388260 Score: 57
Period size: 11 Copynumber: 4.0 Consensus size: 10
5388209 TGACCTTTCC
5388219 AAGGTATGGG
1 AAGGTATGGG
*
5388229 TAGGTATGGG
1 AAGGTATGGG
5388239 AAAGGTATGGG
1 -AAGGTATGGG
5388250 CAAGGTATGGG
1 -AAGGTATGGG
5388261 GTATATTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.29, C:0.02, G:0.48, T:0.21
Consensus pattern (10 bp):
AAGGTATGGG
Found at i:5392332 original size:18 final size:18
Alignment explanation
Indices: 5392309--5392383 Score: 89
Period size: 18 Copynumber: 4.2 Consensus size: 18
5392299 CCCAACTACT
*
5392309 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
* ***
5392327 GTATACGTAAATAGTGTT
1 GTATACGTGAATAGTACC
5392345 GTATACGTGAATA-TGACC
1 GTATACGTGAATAGT-ACC
5392363 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
5392381 GTA
1 GTA
5392384 AACAGTTGTA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
17 1 0.02
18 44 0.96
19 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:5392355 original size:36 final size:36
Alignment explanation
Indices: 5392308--5392377 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
5392298 TCCCAACTAC
5392308 TGTATACGTGAACA-GTACCGTATACGTAAATAGTGT
1 TGTATACGTGAACATG-ACCGTATACGTAAATAGTGT
* *
5392344 TGTATACGTGAATATGACCGTATACGTGAATAGT
1 TGTATACGTGAACATGACCGTATACGTAAATAGT
5392378 ACCGTAAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 30 0.97
37 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (36 bp):
TGTATACGTGAACATGACCGTATACGTAAATAGTGT
Found at i:5396022 original size:15 final size:16
Alignment explanation
Indices: 5396002--5396031 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5395992 ACATTATGTG
5396002 ACAAAAA-TAAATAAA
1 ACAAAAAGTAAATAAA
5396017 ACAAAAAGTAAATAA
1 ACAAAAAGTAAATAA
5396032 CTAAACCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.77, C:0.07, G:0.03, T:0.13
Consensus pattern (16 bp):
ACAAAAAGTAAATAAA
Found at i:5399638 original size:35 final size:35
Alignment explanation
Indices: 5399599--5399670 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
5399589 ACAAATAGCA
5399599 GTCAAATATTTAACCCATTAGAATACATTTACATC
1 GTCAAATATTTAACCCATTAGAATACATTTACATC
* *
5399634 GTCAAATATTTAACCCATTGGAATACATTTACTTC
1 GTCAAATATTTAACCCATTAGAATACATTTACATC
5399669 GT
1 GT
5399671 TTATTGTGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.36
Consensus pattern (35 bp):
GTCAAATATTTAACCCATTAGAATACATTTACATC
Found at i:5402064 original size:19 final size:17
Alignment explanation
Indices: 5402039--5402090 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
5402029 TTTAAAAAAT
5402039 ATTTTTAAATATTTTTA
1 ATTTTTAAATATTTTTA
*
5402056 TACTTTTT-AATAATTTTA
1 -A-TTTTTAAATATTTTTA
*
5402074 ATTTCTAAATTATTTTT
1 ATTTTTAAA-TATTTTT
5402091 TTGCATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 4 0.14
17 3 0.11
18 16 0.57
19 5 0.18
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTTTTAAATATTTTTA
Found at i:5402919 original size:40 final size:41
Alignment explanation
Indices: 5402874--5402995 Score: 124
Period size: 40 Copynumber: 3.0 Consensus size: 41
5402864 GAAAAAATCA
* *
5402874 AATAGATGGAGTTTTAGCAGCGTTTTTAAAAAAACGCCGC-
1 AATAGATCGAGTTTTAGCGGCGTTTTTAAAAAAACGCCGCT
* * * * *
5402914 AATAGATCGAGCTTTAGTGGCATTTTTGAAAAAGCGCCGCT
1 AATAGATCGAGTTTTAGCGGCGTTTTTAAAAAAACGCCGCT
* * **
5402955 AAAAG-TCGACTTTTAGCGGCG-TTTTAGTAAAACGCCGCT
1 AATAGATCGAGTTTTAGCGGCGTTTTTAAAAAAACGCCGCT
5402994 AA
1 AA
5402996 AAGTTTAAGC
Statistics
Matches: 65, Mismatches: 16, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
39 16 0.25
40 45 0.69
41 4 0.06
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (41 bp):
AATAGATCGAGTTTTAGCGGCGTTTTTAAAAAAACGCCGCT
Found at i:5403274 original size:41 final size:41
Alignment explanation
Indices: 5403195--5403291 Score: 108
Period size: 41 Copynumber: 2.4 Consensus size: 41
5403185 CTTCAATGAC
** *
5403195 ATTAGCGGCGCTTTCCT-AAAAACGCCGCAATAGCTCGCACT
1 ATTAGCGGCATTTTTCTAAAAAACGCCGCAATAGCTCGCA-T
* * *
5403236 -TTAGTGGCATTTTTCTAAAAAACGCCGCTATAGGTCGCAT
1 ATTAGCGGCATTTTTCTAAAAAACGCCGCAATAGCTCGCAT
5403276 AATTAGCGGCATTTTT
1 -ATTAGCGGCATTTTT
5403292 TTGTAAACGC
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
40 13 0.28
41 20 0.43
42 13 0.28
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.30
Consensus pattern (41 bp):
ATTAGCGGCATTTTTCTAAAAAACGCCGCAATAGCTCGCAT
Found at i:5403394 original size:156 final size:149
Alignment explanation
Indices: 5402903--5403422 Score: 491
Period size: 156 Copynumber: 3.4 Consensus size: 149
5402893 GCGTTTTTAA
* * * * *
5402903 AAAAACGCCGCAATAGATCGAGCTTTAGTGGCATTTTTGAAAAAGCGCCGCTAAAAGTCGACTTT
1 AAAAACGCCGCAATAGATC-AACTTTAGTGGCATTTTTAAAAAAACGCCGCTAAAGGTCG-CATT
* * *
5402968 TAGCGGCGTTTTAGTAAAACGCCGCTAAAAGTTTAAGCAAGACGACGTCGTTTTACATGAGCTTC
64 TAGCGGCTTTTTAGT-AAACGCCGCTAAAAGGTTAAGCAA-ACGACGTCGTTTTAAATGAGCTTC
* * * *
5403033 ATTGGCAGTAGCGGCGTTTTCCC
127 AATGGCATTAGCGGCGCTTTCCT
* * * * *
5403056 AAAAACGCCGTAACAGATCAAACTTTAGTGGCGTTTTTAAAAAAGACGCCGCTAGAGGTTCGCCT
1 AAAAACGCCGCAATAGATC-AACTTTAGTGGCATTTTTAAAAAA-ACGCCGCTAAAGG-TCGCAT
* ** * * * *
5403121 TTTGCGGCGTTTTTGGAAAAAACACCGCTAAAATGTTAAACAAAACGACGTCGTTTTATATGAGC
63 TTAGCGGC-TTTTT--AGTAAACGCCGCTAAAAGGTTAAGC-AAACGACGTCGTTTTAAATGAGC
*
5403186 TTCAATGACATTAGCGGCGCTTTCCT
124 TTCAATGGCATTAGCGGCGCTTTCCT
* * * *
5403212 AAAAACGCCGCAATAGCTCGCACTTTAGTGGCATTTTTCTAAAAAACGCCGCTATAGGTCGCATA
1 AAAAACGCCGCAATAGATC-AACTTTAGTGGCATTTTT-AAAAAAACGCCGCTAAAGGTCGCAT-
* * * *
5403277 ATTAGCGGCATTTTTTTGTAAACGCCGCTAATAGGTTAAGGCAAACGACGTCATTTTAAATTAGC
63 -TTAGCGGC--TTTTTAGTAAACGCCGCTAAAAGGTTAA-GCAAACGACGTCGTTTTAAATGAGC
*
5403342 TTCAATGGCATTAGCGGCGCTTTACT
124 TTCAATGGCATTAGCGGCGCTTTCCT
* * ** * * * *
5403368 TAAAACGCCGCAATATATCAATCTTTAACGGCGTCTTTACAAAAACGACGCTAAA
1 AAAAACGCCGCAATAGATCAA-CTTTAGTGGCATTTTTAAAAAAACGCCGCTAAA
5403423 ACATTAAGCA
Statistics
Matches: 296, Mismatches: 59, Indels: 22
0.79 0.16 0.06
Matches are distributed among these distances:
153 38 0.13
154 19 0.06
155 26 0.09
156 192 0.65
157 16 0.05
158 5 0.02
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (149 bp):
AAAAACGCCGCAATAGATCAACTTTAGTGGCATTTTTAAAAAAACGCCGCTAAAGGTCGCATTTA
GCGGCTTTTTAGTAAACGCCGCTAAAAGGTTAAGCAAACGACGTCGTTTTAAATGAGCTTCAATG
GCATTAGCGGCGCTTTCCT
Found at i:5404079 original size:14 final size:13
Alignment explanation
Indices: 5404056--5404102 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
5404046 TATAGGTTTA
5404056 AGGGTTATGATTT
1 AGGGTTATGATTT
5404069 AGGGTTGATGATTT
1 AGGGTT-ATGATTT
**
5404083 ATGTTTTATGATTT
1 A-GGGTTATGATTT
5404097 AGGGTT
1 AGGGTT
5404103 TGAGGTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 9 0.32
14 16 0.57
15 3 0.11
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (13 bp):
AGGGTTATGATTT
Found at i:5404276 original size:14 final size:14
Alignment explanation
Indices: 5404259--5404288 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5404249 GTGTTTTAAA
*
5404259 GTTTATTGTTTAGG
1 GTTTATTATTTAGG
5404273 GTTTATTATTTAGG
1 GTTTATTATTTAGG
5404287 GT
1 GT
5404289 CTAAGATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.27, T:0.57
Consensus pattern (14 bp):
GTTTATTATTTAGG
Found at i:5404325 original size:7 final size:7
Alignment explanation
Indices: 5404313--5404374 Score: 54
Period size: 7 Copynumber: 8.4 Consensus size: 7
5404303 TTTAGTGATA
5404313 TTAAGGT
1 TTAAGGT
5404320 TTAAGGGT
1 TTAA-GGT
5404328 TTAAGGT
1 TTAAGGT
* *
5404335 TTAGGGG
1 TTAAGGT
5404342 TTAAGAGT
1 TTAAG-GT
5404350 TTAGAGG-
1 TTA-AGGT
*
5404357 TTAAGGG
1 TTAAGGT
5404364 TTAATGGT
1 TTAA-GGT
5404372 TTA
1 TTA
5404375 TGAATTATGT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
6 3 0.07
7 23 0.51
8 17 0.38
9 2 0.04
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (7 bp):
TTAAGGT
Found at i:5404333 original size:15 final size:14
Alignment explanation
Indices: 5404313--5404405 Score: 62
Period size: 14 Copynumber: 6.4 Consensus size: 14
5404303 TTTAGTGATA
5404313 TTAAGGTTTAAGGGT
1 TTAAGGTTT-AGGGT
*
5404328 TTAAGGTTTAGGGG
1 TTAAGGTTTAGGGT
5404342 TTAAGAGTTTAGAGG-
1 TTAAG-GTTTAG-GGT
* *
5404357 TTAAGGGTTAATGGT
1 TTAA-GGTTTAGGGT
* ** * *
5404372 TTATGAATTATGTT
1 TTAAGGTTTAGGGT
*
5404386 TTATGGTTTAGGGT
1 TTAAGGTTTAGGGT
5404400 TTAAGG
1 TTAAGG
5404406 GATAGATGTT
Statistics
Matches: 61, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
14 32 0.52
15 26 0.43
16 3 0.05
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (14 bp):
TTAAGGTTTAGGGT
Found at i:5404346 original size:22 final size:22
Alignment explanation
Indices: 5404313--5404374 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
5404303 TTTAGTGATA
*
5404313 TTAAGGTTTAAGGGTTTA-AGG
1 TTAAGGGTTAAGGGTTTAGAGG
* *
5404334 TTTAGGGGTTAAGAGTTTAGAGG
1 -TTAAGGGTTAAGGGTTTAGAGG
*
5404357 TTAAGGGTTAATGGTTTA
1 TTAAGGGTTAAGGGTTTA
5404375 TGAATTATGT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 30 0.91
23 3 0.09
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (22 bp):
TTAAGGGTTAAGGGTTTAGAGG
Found at i:5404469 original size:7 final size:7
Alignment explanation
Indices: 5404459--5404514 Score: 58
Period size: 7 Copynumber: 8.0 Consensus size: 7
5404449 TAGGGGTTAA
*
5404459 TTAGGGC
1 TTAGGGT
5404466 TTAGGGT
1 TTAGGGT
*
5404473 TTGGGGT
1 TTAGGGT
5404480 TTAGGGT
1 TTAGGGT
**
5404487 TTATAGT
1 TTAGGGT
5404494 TTAGGGT
1 TTAGGGT
*
5404501 TTATGGT
1 TTAGGGT
*
5404508 ATAGGGT
1 TTAGGGT
5404515 CAGGGTCTTA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.16, C:0.02, G:0.39, T:0.43
Consensus pattern (7 bp):
TTAGGGT
Found at i:5404738 original size:14 final size:14
Alignment explanation
Indices: 5404719--5404784 Score: 53
Period size: 14 Copynumber: 4.7 Consensus size: 14
5404709 GATTTAGGGT
5404719 TTTAGGGTTTATGG
1 TTTAGGGTTTATGG
*
5404733 TTTAGGGATTA-GG
1 TTTAGGGTTTATGG
*
5404746 TTTTGTGGTTTATGG
1 TTTAG-GGTTTATGG
** * *
5404761 CATGGGGCTTATGG
1 TTTAGGGTTTATGG
*
5404775 TTTGGGGTTT
1 TTTAGGGTTT
5404785 GGGATTGAGG
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
13 6 0.15
14 30 0.75
15 4 0.10
ACGTcount: A:0.12, C:0.03, G:0.38, T:0.47
Consensus pattern (14 bp):
TTTAGGGTTTATGG
Found at i:5404754 original size:21 final size:22
Alignment explanation
Indices: 5404711--5404757 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
5404701 GTTAGGGAGA
*
5404711 TTTAGGGTTTTAGGGTTTATGG
1 TTTAGGGTATTAGGGTTTATGG
* *
5404733 TTTAGGG-ATTAGGTTTTGTGG
1 TTTAGGGTATTAGGGTTTATGG
5404754 TTTA
1 TTTA
5404758 TGGCATGGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.15, C:0.00, G:0.34, T:0.51
Consensus pattern (22 bp):
TTTAGGGTATTAGGGTTTATGG
Found at i:5405062 original size:41 final size:41
Alignment explanation
Indices: 5404975--5405061 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 41
5404965 GTGTTTTTTC
* **
5404975 AAAAACGCCACAAAAAATGAGCTATAGTGGCGTTTATAATA
1 AAAAACGCCACAAAAAATGACCTATACCGGCGTTTATAATA
**
5405016 AAAAACGCCACTAAAAGTTGACCTATACCGGCGTTT-TAAATA
1 AAAAACGCCAC-AAAAAATGACCTATACCGGCGTTTAT-AATA
5405058 AAAA
1 AAAA
5405062 CACCGCAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 12 0.31
42 27 0.69
ACGTcount: A:0.46, C:0.17, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAAACGCCACAAAAAATGACCTATACCGGCGTTTATAATA
Found at i:5405742 original size:24 final size:24
Alignment explanation
Indices: 5405712--5405757 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
5405702 GTCAGGTAAC
5405712 TTTAATTTCTAAGTCTCTGTTTCT
1 TTTAATTTCTAAGTCTCTGTTTCT
5405736 TTTAATTTCTAAGTCTCTGTTT
1 TTTAATTTCTAAGTCTCTGTTT
5405758 ACAAATACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.17, C:0.15, G:0.09, T:0.59
Consensus pattern (24 bp):
TTTAATTTCTAAGTCTCTGTTTCT
Found at i:5406534 original size:24 final size:24
Alignment explanation
Indices: 5406471--5406540 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 24
5406461 TTTGTGACTG
*
5406471 TGAAAATCGTATTATAATAATGTTA
1 TGAAAATTGTATTATAAT-ATGTTA
**
5406496 T-ACTATCT-TATTTATAATATGTTA
1 TGAAAAT-TGTA-TTATAATATGTTA
5406520 TGAAAATTGTATTATAATATG
1 TGAAAATTGTATTATAATATG
5406541 CTTTTGTTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
24 23 0.64
25 13 0.36
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (24 bp):
TGAAAATTGTATTATAATATGTTA
Found at i:5409367 original size:21 final size:21
Alignment explanation
Indices: 5409341--5409380 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5409331 CTTAGAGCGA
* *
5409341 AGGCAGCAGCGCGGGAGGCGG
1 AGGCAGCAACGAGGGAGGCGG
5409362 AGGCAGCAACGAGGGAGGC
1 AGGCAGCAACGAGGGAGGC
5409381 AGAGCAGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.23, G:0.53, T:0.00
Consensus pattern (21 bp):
AGGCAGCAACGAGGGAGGCGG
Found at i:5409746 original size:44 final size:44
Alignment explanation
Indices: 5409678--5409883 Score: 167
Period size: 44 Copynumber: 4.7 Consensus size: 44
5409668 ACTGGGCAAA
*
5409678 TTAGCGGCG-TTTTTT--AAAAGCGCCGCTAAAAGTGC-TGGTCT
1 TTAGCAGCGCTTTTTTAAAAAAGCGCCGCTAAAAGT-CATGGTCT
****
5409719 TTAGCAGCGCTTTTTTAAAAAAGCGCCGCTAAAAGT-ACTGCAAA
1 TTAGCAGCGCTTTTTTAAAAAAGCGCCGCTAAAAGTCA-TGGTCT
** * *
5409763 TTAGCAGCATTTTTTTGAAAAAAAACGCCGCTAAAAGTCATTGTCT
1 TTAGCAGCGCTTTTTT--AAAAAAGCGCCGCTAAAAGTCATGGTCT
* * * * *
5409809 TTAG-TG-GCATTTTTTTAAAAAGCGCCGCTAAAAATCGTAGTCT
1 TTAGCAGCGC-TTTTTTAAAAAAGCGCCGCTAAAAGTCATGGTCT
*
5409852 TTAGCGGCGCTTTTTTCAAAAAA-CGCCGCTAA
1 TTAGCAGCGCTTTTTT-AAAAAAGCGCCGCTAA
5409884 TTTTACCGGC
Statistics
Matches: 130, Mismatches: 23, Indels: 21
0.75 0.13 0.12
Matches are distributed among these distances:
41 8 0.06
42 6 0.05
43 27 0.21
44 50 0.38
45 14 0.11
46 24 0.18
47 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (44 bp):
TTAGCAGCGCTTTTTTAAAAAAGCGCCGCTAAAAGTCATGGTCT
Found at i:5409852 original size:43 final size:44
Alignment explanation
Indices: 5409782--5409883 Score: 134
Period size: 43 Copynumber: 2.3 Consensus size: 44
5409772 TTTTTTTGAA
* * * *
5409782 AAAAAACGCCGCTAAAAGTCATTGTCTTTAGTGGC-ATTTTTTT
1 AAAAAACGCCGCTAAAAATCATAGTCTTTAGCGGCGATTTTTTC
* * *
5409825 AAAAAGCGCCGCTAAAAATCGTAGTCTTTAGCGGCGCTTTTTTC
1 AAAAAACGCCGCTAAAAATCATAGTCTTTAGCGGCGATTTTTTC
5409869 AAAAAACGCCGCTAA
1 AAAAAACGCCGCTAA
5409884 TTTTACCGGC
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
43 30 0.60
44 20 0.40
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (44 bp):
AAAAAACGCCGCTAAAAATCATAGTCTTTAGCGGCGATTTTTTC
Found at i:5413424 original size:39 final size:39
Alignment explanation
Indices: 5413360--5413468 Score: 121
Period size: 39 Copynumber: 2.7 Consensus size: 39
5413350 CGGCGTTTTC
* * *
5413360 AGCGGCGTTTGGATGAAAAACGCCGCAAAAT-TTACACATT
1 AGCGGCGTTTGTAT-AAAAATGCCGCAAAATATCA-ACATT
* *
5413400 AGTGGCGTTTGTATAAAAATGCCGCAAAATATCAATATT
1 AGCGGCGTTTGTATAAAAATGCCGCAAAATATCAACATT
* *
5413439 AGCGGCGCTTATATAGAAAATGCCGCAAAA
1 AGCGGCGTTTGTATA-AAAATGCCGCAAAA
5413469 AAGTGAGAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 31 0.53
40 28 0.47
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (39 bp):
AGCGGCGTTTGTATAAAAATGCCGCAAAATATCAACATT
Found at i:5414456 original size:28 final size:28
Alignment explanation
Indices: 5414424--5414490 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
5414414 TGTGAATGGT
5414424 TTTTGGGTTTAAAGTTTAGGGTTATA-GG
1 TTTTGGGTTTAAAGTTTAGGGTT-TAGGG
* **
5414452 TTTTGTGTTTGTAGTTTAGGGTTTAGGG
1 TTTTGGGTTTAAAGTTTAGGGTTTAGGG
*
5414480 TTTTAGGTTTA
1 TTTTGGGTTTA
5414491 GGGTTTTAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
27 2 0.06
28 30 0.94
ACGTcount: A:0.16, C:0.00, G:0.31, T:0.52
Consensus pattern (28 bp):
TTTTGGGTTTAAAGTTTAGGGTTTAGGG
Found at i:5414474 original size:21 final size:21
Alignment explanation
Indices: 5414450--5414503 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
5414440 TAGGGTTATA
*
5414450 GGTTTTGTGTTTGTA-GTTTAG
1 GGTTTTGGGTTT-TAGGTTTAG
*
5414471 GGTTTAGGGTTTTAGGTTTAG
1 GGTTTTGGGTTTTAGGTTTAG
*
5414492 GGTTTTAGGTTT
1 GGTTTTGGGTTT
5414504 AGAGTGTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.11, C:0.00, G:0.35, T:0.54
Consensus pattern (21 bp):
GGTTTTGGGTTTTAGGTTTAG
Found at i:5414482 original size:14 final size:14
Alignment explanation
Indices: 5414466--5414505 Score: 71
Period size: 14 Copynumber: 2.8 Consensus size: 14
5414456 GTGTTTGTAG
5414466 TTTAGGGTTTAGGGT
1 TTTA-GGTTTAGGGT
5414481 TTTAGGTTTAGGGT
1 TTTAGGTTTAGGGT
5414495 TTTAGGTTTAG
1 TTTAGGTTTAG
5414506 AGTGTAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 21 0.84
15 4 0.16
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTTAGGTTTAGGGT
Found at i:5414486 original size:8 final size:7
Alignment explanation
Indices: 5414465--5414505 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
5414455 TGTGTTTGTA
5414465 GTTTAGG
1 GTTTAGG
5414472 GTTTAGG
1 GTTTAGG
5414479 GTTTTA-G
1 G-TTTAGG
5414486 GTTTAGG
1 GTTTAGG
5414493 GTTTTA-G
1 G-TTTAGG
5414500 GTTTAG
1 GTTTAG
5414506 AGTGTAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 8 0.27
7 14 0.47
8 8 0.27
ACGTcount: A:0.15, C:0.00, G:0.37, T:0.49
Consensus pattern (7 bp):
GTTTAGG
Found at i:5414550 original size:15 final size:15
Alignment explanation
Indices: 5414530--5414561 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5414520 TTTAATTTAG
5414530 AAGATAAATATAAAT
1 AAGATAAATATAAAT
*
5414545 AAGATAAATATATAT
1 AAGATAAATATAAAT
5414560 AA
1 AA
5414562 ATTATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (15 bp):
AAGATAAATATAAAT
Found at i:5414586 original size:37 final size:37
Alignment explanation
Indices: 5414536--5414616 Score: 153
Period size: 37 Copynumber: 2.2 Consensus size: 37
5414526 TTAGAAGATA
5414536 AATATAAATAAGATAAATATATATAAATTATTATTTT
1 AATATAAATAAGATAAATATATATAAATTATTATTTT
5414573 AATATAAATAAGATAAATATATATAAATTATTATTTT
1 AATATAAATAAGATAAATATATATAAATTATTATTTT
*
5414610 AAAATAA
1 AATATAA
5414617 TATATATCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (37 bp):
AATATAAATAAGATAAATATATATAAATTATTATTTT
Found at i:5416600 original size:39 final size:39
Alignment explanation
Indices: 5416546--5416624 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
5416536 GATATGACTG
*
5416546 TCTTAAATTTGTTATTTTGCATGATTATTTGAGATCTGC
1 TCTTAAATTTGTTATTCTGCATGATTATTTGAGATCTGC
5416585 TCTTAAATTTGTTATTCTGCATGATTATTTGAGATCTGC
1 TCTTAAATTTGTTATTCTGCATGATTATTTGAGATCTGC
5416624 T
1 T
5416625 TCTGTCAATG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.23, C:0.11, G:0.15, T:0.51
Consensus pattern (39 bp):
TCTTAAATTTGTTATTCTGCATGATTATTTGAGATCTGC
Found at i:5416614 original size:20 final size:20
Alignment explanation
Indices: 5416552--5416615 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
5416542 ACTGTCTTAA
*
5416552 ATTTGTTATTTTGCATGATT
1 ATTTGTTATTCTGCATGATT
** *
5416572 ATTTGAGA-TCTGC-T-CTT
1 ATTTGTTATTCTGCATGATT
5416589 AAATTTGTTATTCTGCATGATT
1 --ATTTGTTATTCTGCATGATT
5416611 ATTTG
1 ATTTG
5416616 AGATCTGCTT
Statistics
Matches: 32, Mismatches: 7, Indels: 10
0.65 0.14 0.20
Matches are distributed among these distances:
17 2 0.06
18 1 0.03
19 10 0.31
20 16 0.50
21 1 0.03
22 2 0.06
ACGTcount: A:0.22, C:0.09, G:0.16, T:0.53
Consensus pattern (20 bp):
ATTTGTTATTCTGCATGATT
Found at i:5418180 original size:54 final size:54
Alignment explanation
Indices: 5418098--5418205 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
5418088 TGGGCCTAAT
*
5418098 TTTATTTCCATGTTCTTTTGTAGAAATTAGTTATGAACAAGGTAATATATATAG
1 TTTATTTCCATGTTCTTTTGTACAAATTAGTTATGAACAAGGTAATATATATAG
5418152 TTTATTTCCATGTTCTTTTGTACAAATTAGTTATGAACAAGGTAATATATATAG
1 TTTATTTCCATGTTCTTTTGTACAAATTAGTTATGAACAAGGTAATATATATAG
5418206 ATATAGTTTA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.44
Consensus pattern (54 bp):
TTTATTTCCATGTTCTTTTGTACAAATTAGTTATGAACAAGGTAATATATATAG
Found at i:5418787 original size:106 final size:105
Alignment explanation
Indices: 5418544--5419083 Score: 774
Period size: 106 Copynumber: 5.2 Consensus size: 105
5418534 ATTTTAAAAT
* * * * *
5418544 TTTTATTTTATTTTGAAATTACCGAATTAAATTAAAATGTATTTAAAGTTTTA-TTTGAATATTT
1 TTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTCTTTAAAGTTTTATTTTAAATATTT
* **
5418608 TATTTGATTTTAATTTAATCACGGAAAATATTTTGTCTAC
66 TACTTGATTTTAATTTAATCACTAAAAATATTTTGTCTAC
** *
5418648 TTTTA--TT-TTTTTAAATTATTTAATTAAATTAAATTGTCTTTAAAATTTTATTTTAAATATTT
1 TTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTCTTTAAAGTTTTATTTTAAATATTT
* * * *
5418710 TACTTGGTTTGAATTTACTCACTAAAAATATTTTGTATAC
66 TACTTGATTTTAATTTAATCACTAAAAATATTTTGTCTAC
*
5418750 TTTTATTTTAATTTTTAAATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATT
1 TTTTATTTT-ATTTTTAAATTACCTAATTAAATTAAATTGTCTTTAAAGTTTTATTTTAAATATT
* * *
5418815 TT-TTTAGATTTTAATTTAATCACAAAAAATATTTTGTCTAT
65 TTACTT-GATTTTAATTTAATCACTAAAAATATTTTGTCTAC
*
5418856 TTTTATTTTATTTTTTAAATTACCTAACTAAATTTAAA-TGTCTTTAAAGTTTTATTTTAAATAT
1 TTTTATTTTA-TTTTTAAATTACCTAATTAAA-TTAAATTGTCTTTAAAGTTTTATTTTAAATAT
5418920 TTTACTTGATTTTAATTTAATCACTAAAAATATTTTGTCTAC
64 TTTACTTGATTTTAATTTAATCACTAAAAATATTTTGTCTAC
* *
5418962 TTTTATTTTATTTTTTAAATTACCTAATTAAATTAATTTTTCTTTAAAGTTTTATTTTAAATATT
1 TTTTATTTTA-TTTTTAAATTACCTAATTAAATTAAATTGTCTTTAAAGTTTTATTTTAAATATT
5419027 TTACTTGATTTTAATTTAATCACTAAAAATA--TTGTCTAC
65 TTACTTGATTTTAATTTAATCACTAAAAATATTTTGTCTAC
5419066 -TTTATTTTATTTTTAAAT
1 TTTTATTTTATTTTTAAAT
5419084 ATTTTATTTT
Statistics
Matches: 392, Mismatches: 34, Indels: 22
0.88 0.08 0.05
Matches are distributed among these distances:
101 36 0.09
102 59 0.15
103 9 0.02
104 15 0.04
105 7 0.02
106 259 0.66
107 7 0.02
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (105 bp):
TTTTATTTTATTTTTAAATTACCTAATTAAATTAAATTGTCTTTAAAGTTTTATTTTAAATATTT
TACTTGATTTTAATTTAATCACTAAAAATATTTTGTCTAC
Found at i:5420451 original size:16 final size:15
Alignment explanation
Indices: 5420418--5420460 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
5420408 GTTACTATTA
5420418 TATTTATTATTATAT
1 TATTTATTATTATAT
5420433 TATTTATT-TTCACTAT
1 TATTTATTATT-A-TAT
5420449 TA-TTATTATTAT
1 TATTTATTATTAT
5420461 TTTCATCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 3 0.12
15 15 0.60
16 7 0.28
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTTATTATTATAT
Found at i:5420460 original size:21 final size:21
Alignment explanation
Indices: 5420425--5420475 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
5420415 TTATATTTAT
5420425 TATTA-TATTATTTATTTTCA
1 TATTATTATTATTTATTTTCA
5420445 CTATTATTATTA-TTATTTTCA
1 -TATTATTATTATTTATTTTCA
5420466 TCATTATTAT
1 T-ATTATTAT
5420476 ACATATATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 1 0.04
21 22 0.79
22 5 0.18
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (21 bp):
TATTATTATTATTTATTTTCA
Found at i:5421586 original size:14 final size:14
Alignment explanation
Indices: 5421567--5421600 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
5421557 ACAATTAGCG
5421567 ACATTGATAACAGA
1 ACATTGATAACAGA
5421581 ACATTGATAACAGA
1 ACATTGATAACAGA
*
5421595 AGATTG
1 ACATTG
5421601 CCACAATCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.24
Consensus pattern (14 bp):
ACATTGATAACAGA
Found at i:5426535 original size:21 final size:21
Alignment explanation
Indices: 5426506--5426553 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
5426496 ACTTAGAGGG
* *
5426506 GAGGTAGCAGAGAGGGAGGCA
1 GAGGCAGCAGAGAGAGAGGCA
* *
5426527 GCGGCAGCAGTGAGAGAGGCA
1 GAGGCAGCAGAGAGAGAGGCA
5426548 GAGGCA
1 GAGGCA
5426554 CGAGCGATGG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.15, G:0.50, T:0.04
Consensus pattern (21 bp):
GAGGCAGCAGAGAGAGAGGCA
Found at i:5427028 original size:44 final size:43
Alignment explanation
Indices: 5426927--5427028 Score: 159
Period size: 43 Copynumber: 2.3 Consensus size: 43
5426917 TCTGCCAAAA
* *
5426927 TTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAGCCGTCACTT
1 TTAGCGGCGCTTTTTCCACAAACGCCGCTAAAAGCCATCACTT
* *
5426970 TTAGCGGCGCTTTTTCCACAAACGCCGCTAAAATCTATCACTT
1 TTAGCGGCGCTTTTTCCACAAACGCCGCTAAAAGCCATCACTT
5427013 TTAGCGGCGTCTTTTT
1 TTAGCGGCG-CTTTTT
5427029 TCAATAAACG
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
43 48 0.89
44 6 0.11
ACGTcount: A:0.22, C:0.30, G:0.18, T:0.30
Consensus pattern (43 bp):
TTAGCGGCGCTTTTTCCACAAACGCCGCTAAAAGCCATCACTT
Found at i:5440166 original size:23 final size:24
Alignment explanation
Indices: 5440118--5440168 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
5440108 TCAGGTACTG
5440118 AATTAGACAAAAAAAAAGGTACCA
1 AATTAGACAAAAAAAAAGGTACCA
*
5440142 AATTAGA-AAAAAATAAA-GTATCA
1 AATTAGACAAAAAA-AAAGGTACCA
5440165 AATT
1 AATT
5440169 GGACCCCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.63, C:0.08, G:0.10, T:0.20
Consensus pattern (24 bp):
AATTAGACAAAAAAAAAGGTACCA
Found at i:5441430 original size:49 final size:49
Alignment explanation
Indices: 5441375--5441475 Score: 166
Period size: 49 Copynumber: 2.1 Consensus size: 49
5441365 ATGATTTAAG
* *
5441375 TATGACTATTTAAAACCATGACTAACAATGGCATGTCTACGATTGCCAA
1 TATGACTATTTAAAACCATGACTAACAATGACATCTCTACGATTGCCAA
* *
5441424 TATGACTATTTAAAACCATGATTGACAATGACATCTCTACGATTGCCAA
1 TATGACTATTTAAAACCATGACTAACAATGACATCTCTACGATTGCCAA
5441473 TAT
1 TAT
5441476 TATATGATTG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.31
Consensus pattern (49 bp):
TATGACTATTTAAAACCATGACTAACAATGACATCTCTACGATTGCCAA
Found at i:5442780 original size:17 final size:18
Alignment explanation
Indices: 5442758--5442793 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5442748 GGCCAAGATG
*
5442758 GGTGTGT-GGGCCACACA
1 GGTGTGTAGGCCCACACA
5442775 GGTGTGTAGGCCCACACA
1 GGTGTGTAGGCCCACACA
5442793 G
1 G
5442794 TCATGCCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.19, C:0.25, G:0.39, T:0.17
Consensus pattern (18 bp):
GGTGTGTAGGCCCACACA
Found at i:5445288 original size:14 final size:14
Alignment explanation
Indices: 5445233--5445294 Score: 53
Period size: 13 Copynumber: 4.7 Consensus size: 14
5445223 TTTAGTATTG
*
5445233 AAATAATTTTGTAT
1 AAATAATTTTTTAT
5445247 -AA-AATTTTTTAT
1 AAATAATTTTTTAT
*
5445259 --TTGAATTTTTTA-
1 AAAT-AATTTTTTAT
5445271 AAATAATTTTTTAT
1 AAATAATTTTTTAT
*
5445285 AAATTATTTT
1 AAATAATTTT
5445295 CAGTGAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
12 9 0.23
13 20 0.51
14 10 0.26
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (14 bp):
AAATAATTTTTTAT
Found at i:5445392 original size:17 final size:17
Alignment explanation
Indices: 5445370--5445404 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5445360 AATCAAAAAT
5445370 TATTTT-TAATAAAATAA
1 TATTTTGTAAT-AAATAA
5445387 TATTTTGTAATAAATAA
1 TATTTTGTAATAAATAA
5445404 T
1 T
5445405 GTATTATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
TATTTTGTAATAAATAA
Found at i:5449583 original size:6 final size:6
Alignment explanation
Indices: 5449572--5449621 Score: 100
Period size: 6 Copynumber: 8.3 Consensus size: 6
5449562 GAAAAGAGAA
5449572 TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG
1 TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG
5449620 TG
1 TG
5449622 AAGAAAAAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.16, C:0.00, G:0.66, T:0.18
Consensus pattern (6 bp):
TGGGAG
Done.