Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 204 of 444
Found at i:57031390 original size:30 final size:30
Alignment explanation
Indices: 57031356--57031453 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
57031346 AGCTCACTCC
57031356 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
57031386 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
57031416 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
57031446 TAGCTCAT
1 TAGCTCAT
57031454 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:57033077 original size:10 final size:10
Alignment explanation
Indices: 57033062--57033110 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
57033052 ATACAAGTTA
57033062 AAAAAAAATC
1 AAAAAAAATC
57033072 AAAAAAAATTC
1 AAAAAAAA-TC
*
57033083 GAAAAAAAATT
1 -AAAAAAAATC
*
57033094 GAAAAAAAT-
1 AAAAAAAATC
57033103 AAAAAAAA
1 AAAAAAAA
57033111 AAAGAAAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
9 7 0.21
10 16 0.47
11 3 0.09
12 8 0.24
ACGTcount: A:0.80, C:0.04, G:0.04, T:0.12
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:57033109 original size:22 final size:22
Alignment explanation
Indices: 57033061--57033113 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
57033051 TATACAAGTT
**
57033061 AAAAAAAAATCAAAAAAAATTC
1 AAAAAAAAATCAAAAAAAATAA
* **
57033083 GAAAAAAAATTGAAAAAAATAA
1 AAAAAAAAATCAAAAAAAATAA
57033105 AAAAAAAAA
1 AAAAAAAAA
57033114 GAAAAAGAGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.81, C:0.04, G:0.04, T:0.11
Consensus pattern (22 bp):
AAAAAAAAATCAAAAAAAATAA
Found at i:57033112 original size:11 final size:11
Alignment explanation
Indices: 57033061--57033111 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
57033051 TATACAAGTT
57033061 AAAAAAAAATC
1 AAAAAAAAATC
*
57033072 AAAAAAAATTC
1 AAAAAAAAATC
*
57033083 GAAAAAAAAT-
1 AAAAAAAAATC
**
57033093 TGAAAAAAAT-
1 AAAAAAAAATC
57033103 AAAAAAAAA
1 AAAAAAAAA
57033112 AAGAAAAAGA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
10 15 0.45
11 18 0.55
ACGTcount: A:0.80, C:0.04, G:0.04, T:0.12
Consensus pattern (11 bp):
AAAAAAAAATC
Found at i:57034048 original size:21 final size:20
Alignment explanation
Indices: 57034014--57034081 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
57034004 ACATTCTTGT
57034014 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
57034035 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
57034056 AAAGAAAACGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
57034077 AAAGA
1 AAAGA
57034082 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.01
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:57034049 original size:6 final size:5
Alignment explanation
Indices: 57034025--57034081 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
57034015 AAGAGAAAAC
*
57034025 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
57034072 AAAGA AAAGA
1 AAAGA AAAGA
57034082 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:57034056 original size:15 final size:14
Alignment explanation
Indices: 57034025--57034081 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
57034015 AAGAGAAAAC
57034025 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
57034041 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
57034056 AAAGAAAACGAAATAA
1 AAAGAAAA-G-AAGAA
57034072 AAAGAAAAGA
1 AAAGAAAAGA
57034082 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:57034160 original size:11 final size:12
Alignment explanation
Indices: 57034129--57034159 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
57034119 TTGAGAGAAC
57034129 TTGAAAAAGCCT
1 TTGAAAAAGCCT
*
57034141 TTGAAAAAGTCT
1 TTGAAAAAGCCT
57034153 TTGAAAA
1 TTGAAAA
57034160 GCAAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:57034170 original size:12 final size:12
Alignment explanation
Indices: 57034162--57034186 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57034152 TTTGAAAAGC
57034162 AAAAAGAAAATG
1 AAAAAGAAAATG
57034174 AAAAAGAAAATG
1 AAAAAGAAAATG
57034186 A
1 A
57034187 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:57034183 original size:18 final size:18
Alignment explanation
Indices: 57034156--57034211 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
57034146 AAAGTCTTTG
57034156 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
57034175 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
57034193 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
57034210 AA
1 AA
57034212 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:57034196 original size:30 final size:31
Alignment explanation
Indices: 57034162--57034243 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
57034152 TTTGAAAAGC
*
57034162 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
57034192 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
57034222 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
57034244 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:57035714 original size:18 final size:18
Alignment explanation
Indices: 57035687--57035733 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
57035677 ATCTTTACTC
*
57035687 AATTCGATTGAAGTTGAA
1 AATTCCATTGAAGTTGAA
57035705 AATTCCATTGAAGTTGAA
1 AATTCCATTGAAGTTGAA
57035723 AATTCCATTGA
1 AATTCCATTGA
57035734 TTTGTTGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (18 bp):
AATTCCATTGAAGTTGAA
Found at i:57036508 original size:30 final size:30
Alignment explanation
Indices: 57036474--57036571 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
57036464 AGCTCACTCC
57036474 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
57036504 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
57036534 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
57036564 TAGCTCAT
1 TAGCTCAT
57036572 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:57038046 original size:19 final size:19
Alignment explanation
Indices: 57038022--57038061 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
57038012 AGCTCCCATG
*
57038022 TAGCTCCACACCAGCTCAT
1 TAGCTCCAAACCAGCTCAT
*
57038041 TAGCTCGAAACCAGCTCAT
1 TAGCTCCAAACCAGCTCAT
57038060 TA
1 TA
57038062 TCAGCTCGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.35, G:0.12, T:0.23
Consensus pattern (19 bp):
TAGCTCCAAACCAGCTCAT
Found at i:57039289 original size:14 final size:14
Alignment explanation
Indices: 57039267--57039314 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
57039257 ACCTAAACTG
*
57039267 ACCAATTTGTTCAT
1 ACCATTTTGTTCAT
*
57039281 ACCATTTTGTTCCT
1 ACCATTTTGTTCAT
* * *
57039295 ACCCTTTCGTTCTT
1 ACCATTTTGTTCAT
57039309 ACCATT
1 ACCATT
57039315 CCATTCGTGC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.19, C:0.29, G:0.06, T:0.46
Consensus pattern (14 bp):
ACCATTTTGTTCAT
Found at i:57044054 original size:19 final size:19
Alignment explanation
Indices: 57044030--57044069 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
57044020 AGCTCCCATG
57044030 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
57044049 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
57044068 TA
1 TA
57044070 TCAGCTCGCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:57045689 original size:14 final size:14
Alignment explanation
Indices: 57045642--57045689 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
57045632 GTACGAATGG
*
57045642 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
57045656 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
57045670 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
57045684 ATTGGT
1 AATGGT
57045690 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:57050774 original size:30 final size:31
Alignment explanation
Indices: 57050740--57050836 Score: 103
Period size: 30 Copynumber: 3.2 Consensus size: 31
57050730 AGCTCACTCC
* *
57050740 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAAGCT
* * **
57050770 TAGCTCAAC-TTCAGCTTAGGAG-TTTAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAAGCT
57050799 TCAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 T-AGCTCAACTTTCAGCTCACGAGCTAAAGCT
57050830 TAGCTCA
1 TAGCTCA
57050837 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
29 5 0.09
30 38 0.72
31 10 0.19
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAAGCT
Found at i:57052675 original size:11 final size:11
Alignment explanation
Indices: 57052659--57052687 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
57052649 TACAAGTCAA
57052659 AAAAAAATTTC
1 AAAAAAATTTC
57052670 AAAAAAA-TTC
1 AAAAAAATTTC
57052680 AAAAAAAT
1 AAAAAAAT
57052688 CGAAAAGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAAAAATTTC
Found at i:57053636 original size:9 final size:10
Alignment explanation
Indices: 57053629--57053685 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
57053619 AAGAGAAAAC
57053629 AAAGAAAAGA
1 AAAGAAAAGA
*
57053639 AAAGAAAAAGT
1 AAAG-AAAAGA
57053650 AAAG-AAAGAA
1 AAAGAAAAG-A
57053660 AAAGAAAATGA
1 AAAGAAAA-GA
57053671 AATA-AAAAGA
1 AA-AGAAAAGA
57053681 AAAGA
1 AAAGA
57053686 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 5 0.13
10 13 0.33
11 19 0.49
12 2 0.05
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:57053639 original size:5 final size:5
Alignment explanation
Indices: 57053629--57053685 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
57053619 AAGAGAAAAC
*
57053629 AAAGA AAAGA AAAGAA AAAGT AAAG- AAAGAA AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAGA AAAGA AAAG-A AAAGA AAA-GA AA-AGA
57053676 AAAGA AAAGA
1 AAAGA AAAGA
57053686 GAGGCAAGAG
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
4 5 0.11
5 26 0.58
6 13 0.29
7 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (5 bp):
AAAGA
Found at i:57053648 original size:16 final size:15
Alignment explanation
Indices: 57053629--57053685 Score: 78
Period size: 16 Copynumber: 3.7 Consensus size: 15
57053619 AAGAGAAAAC
57053629 AAAGAAAAGAAAAGAA
1 AAAGAAAAG-AAAGAA
*
57053645 AAAGTAAAGAAAGAA
1 AAAGAAAAGAAAGAA
*
57053660 AAAGAAAATGAAATAA
1 AAAGAAAA-GAAAGAA
57053676 AAAGAAAAGA
1 AAAGAAAAGA
57053686 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
15 15 0.41
16 22 0.59
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (15 bp):
AAAGAAAAGAAAGAA
Found at i:57053653 original size:21 final size:20
Alignment explanation
Indices: 57053618--57053685 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
57053608 ACATTCTTGT
*
57053618 AAAGAGAAAACAAAGAAAAGA
1 AAAGA-AAAAGAAAGAAAAGA
57053639 AAAGAAAAAGTAAAG-AAAGAA
1 AAAGAAAAAG-AAAGAAAAG-A
* *
57053660 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGAAA-GAAAAGA
57053681 AAAGA
1 AAAGA
57053686 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 11 0.28
21 25 0.62
22 4 0.10
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.04
Consensus pattern (20 bp):
AAAGAAAAAGAAAGAAAAGA
Found at i:57053765 original size:11 final size:12
Alignment explanation
Indices: 57053733--57053763 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
57053723 TTGAGAGAAC
57053733 TTGAAAAAGCCT
1 TTGAAAAAGCCT
57053745 TTGAAAAAGCCT
1 TTGAAAAAGCCT
57053757 TTGAAAA
1 TTGAAAA
57053764 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:57053774 original size:12 final size:12
Alignment explanation
Indices: 57053766--57053790 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57053756 TTTGAAAAGC
57053766 AAAAAGAAAATG
1 AAAAAGAAAATG
57053778 AAAAAGAAAATG
1 AAAAAGAAAATG
57053790 A
1 A
57053791 TATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:57053787 original size:18 final size:18
Alignment explanation
Indices: 57053760--57053815 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
57053750 AAAGCCTTTG
57053760 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
57053779 AAAAGAAAATGATATTGA
1 AAAAGAAAAAGAAAATGA
* *
57053797 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
57053814 AA
1 AA
57053816 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.18, T:0.09
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:57053800 original size:30 final size:31
Alignment explanation
Indices: 57053766--57053847 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
57053756 TTTGAAAAGC
* *
57053766 AAAAAGAAAATGAAAAAGAAA-ATGATATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
57053796 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
57053826 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
57053848 TGAAACAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 8 0.19
30 25 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.21, T:0.13
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:57055983 original size:32 final size:31
Alignment explanation
Indices: 57055918--57055986 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 31
57055908 AGCTCACTCC
57055918 TAGCTC-ACTTTCAACTCACAAGCTAAACCT
1 TAGCTCAACTTTCAACTCACAAGCTAAACCT
* *
57055948 TAGCTCAACTTT-AGCTCACGAGCTAAAAACCT
1 TAGCTCAACTTTCAACTCACAAGCT--AAACCT
57055980 TAGCTCA
1 TAGCTCA
57055987 TTTTAGTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 16 0.47
31 5 0.15
32 13 0.38
ACGTcount: A:0.33, C:0.30, G:0.10, T:0.26
Consensus pattern (31 bp):
TAGCTCAACTTTCAACTCACAAGCTAAACCT
Found at i:57057825 original size:20 final size:20
Alignment explanation
Indices: 57057802--57057849 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
57057792 AGCTCCGTCC
*
57057802 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTA
***
57057822 AGCTCGTTTCAGCTCATTTA
1 AGCTCAACTCAGCTCATTTA
57057842 AGCTCAAC
1 AGCTCAAC
57057850 CGAGCTTACT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTA
Found at i:57060906 original size:30 final size:30
Alignment explanation
Indices: 57060872--57060968 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
57060862 TAAACTAAAA
57060872 TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
* * * * * *
57060902 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCATGAGCTAAAGT
* * *
57060932 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCATGAGCT-AAAGT
57060962 TGAGCTA
1 TGAGCTA
57060969 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
Found at i:57061021 original size:20 final size:21
Alignment explanation
Indices: 57060985--57061029 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
57060975 AGCTCGGTTT
57060985 AGCTCAGAAAAGATGGA-TTG
1 AGCTCAGAAAAGATGGATTTG
*
57061005 AGCTC-GAATAAGCTGGATTTG
1 AGCTCAGAA-AAGATGGATTTG
57061026 AGCT
1 AGCT
57061030 GGACGGAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 12 0.55
21 7 0.32
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.24
Consensus pattern (21 bp):
AGCTCAGAAAAGATGGATTTG
Found at i:57061485 original size:14 final size:14
Alignment explanation
Indices: 57061438--57061485 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
57061428 GTACGAATGG
* *
57061438 AATGGTAGGAACGA
1 AATGGTATGAACAA
*
57061452 AAGGGTATGAACAA
1 AATGGTATGAACAA
57061466 AATGGTATGAACAA
1 AATGGTATGAACAA
*
57061480 ATTGGT
1 AATGGT
57061486 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.29, T:0.21
Consensus pattern (14 bp):
AATGGTATGAACAA
Found at i:57063047 original size:15 final size:15
Alignment explanation
Indices: 57063027--57063074 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
57063017 TCAAAGATGG
57063027 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
57063042 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
57063056 GTTTATGGATATAAA
1 GTTTATGGATATGAA
57063071 GTTT
1 GTTT
57063075 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:57063061 original size:14 final size:14
Alignment explanation
Indices: 57063021--57063064 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
57063011 AAGGATTCAA
57063021 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
57063035 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
57063050 AGATGGGTTTATGG
1 AGATGGGTTTATGG
57063064 A
1 A
57063065 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:57063090 original size:29 final size:29
Alignment explanation
Indices: 57063021--57063080 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
57063011 AAGGATTCAA
*
57063021 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
57063050 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
57063079 AG
1 AG
57063081 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:57064095 original size:14 final size:14
Alignment explanation
Indices: 57064053--57064097 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
57064043 TTAAAGAAGC
57064053 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
57064067 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
57064080 AACTCATTTAATTA
1 AACTCATTAAATTA
57064094 AACT
1 AACT
57064098 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:57067832 original size:15 final size:15
Alignment explanation
Indices: 57067812--57067859 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
57067802 TCAAAGATGG
57067812 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
57067827 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
57067841 GTTTATGGATATAAA
1 GTTTATGGATATGAA
57067856 GTTT
1 GTTT
57067860 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:57067846 original size:14 final size:14
Alignment explanation
Indices: 57067806--57067849 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
57067796 AAGGATTCAA
57067806 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
57067820 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
57067835 AGATGGGTTTATGG
1 AGATGGGTTTATGG
57067849 A
1 A
57067850 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:57067875 original size:29 final size:29
Alignment explanation
Indices: 57067806--57067865 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
57067796 AAGGATTCAA
*
57067806 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
57067835 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
57067864 AG
1 AG
57067866 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:57068880 original size:14 final size:14
Alignment explanation
Indices: 57068838--57068882 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
57068828 TTAAAGAAGC
57068838 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
57068852 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
57068865 AACTCATTTAATTA
1 AACTCATTAAATTA
57068879 AACT
1 AACT
57068883 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:57071501 original size:30 final size:30
Alignment explanation
Indices: 57071465--57071561 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
57071455 AGCTCACTCC
57071465 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
57071495 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
57071525 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
57071555 TAGCTCA
1 TAGCTCA
57071562 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:57074075 original size:9 final size:10
Alignment explanation
Indices: 57074068--57074124 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
57074058 AAGAGAAAAT
57074068 AAAGAAAAGA
1 AAAGAAAAGA
57074078 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
57074090 AAAGAAGA-A
1 AAAGAAAAGA
57074099 AAAGAAAATGA
1 AAAGAAAA-GA
57074110 AATA-AAAAGA
1 AA-AGAAAAGA
57074120 AAAGA
1 AAAGA
57074125 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:57074092 original size:6 final size:5
Alignment explanation
Indices: 57074068--57074124 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
57074058 AAGAGAAAAT
*
57074068 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
57074115 AAAGA AAAGA
1 AAAGA AAAGA
57074125 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:57074099 original size:15 final size:14
Alignment explanation
Indices: 57074068--57074124 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
57074058 AAGAGAAAAT
57074068 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
57074084 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
57074099 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
57074115 AAAGAAAAGA
1 AAAGAAAAGA
57074125 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:57074201 original size:12 final size:12
Alignment explanation
Indices: 57074193--57074217 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57074183 TTTGAAAAGC
57074193 AAAAAGAAAATG
1 AAAAAGAAAATG
57074205 AAAAAGAAAATG
1 AAAAAGAAAATG
57074217 A
1 A
57074218 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:57074214 original size:18 final size:18
Alignment explanation
Indices: 57074187--57074229 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
57074177 AAAGCCTTTG
57074187 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
57074206 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
57074224 AAAAGA
1 AAAAGA
57074230 GATTGAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:57074225 original size:12 final size:12
Alignment explanation
Indices: 57074210--57074243 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
57074200 AAATGAAAAA
*
57074210 GAAAATGAGATT
1 GAAAAAGAGATT
57074222 GAAAAAGAGATT
1 GAAAAAGAGATT
57074234 GAAAAAGAGA
1 GAAAAAGAGA
57074244 ACGAAAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (12 bp):
GAAAAAGAGATT
Found at i:57074280 original size:30 final size:31
Alignment explanation
Indices: 57074228--57074287 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
57074218 GATTGAAAAA
*
57074228 GAGATTGAAAAAGAGAACG-AAAAGAAATTT
1 GAGAGTGAAAAAGAGAACGAAAAAGAAATTT
*
57074258 GAGAGTGAAAAAGA-AGATGAAAAAGAAATT
1 GAGAGTGAAAAAGAGA-ACGAAAAAGAAATT
57074288 GAAACAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 1 0.04
30 15 0.58
31 10 0.38
ACGTcount: A:0.58, C:0.02, G:0.25, T:0.15
Consensus pattern (31 bp):
GAGAGTGAAAAAGAGAACGAAAAAGAAATTT
Found at i:57075606 original size:14 final size:14
Alignment explanation
Indices: 57075587--57075631 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
57075577 AACTCATCTT
*
57075587 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
57075601 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
57075614 AATTTAATTTAATG
1 AGTTTAATTTAATG
57075628 AGTT
1 AGTT
57075632 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:57077840 original size:18 final size:18
Alignment explanation
Indices: 57077817--57077866 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
57077807 GAAAGAAAAA
*
57077817 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGAATGAGAGT
* *
57077835 GAAAAAGAAAATGAGATT
1 GAAAAAGAGAATGAGAGT
57077853 GAAAAAGAGAATGA
1 GAAAAAGAGAATGA
57077867 AAAAGAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.14
Consensus pattern (18 bp):
GAAAAAGAGAATGAGAGT
Found at i:57077843 original size:24 final size:24
Alignment explanation
Indices: 57077810--57077891 Score: 92
Period size: 24 Copynumber: 3.4 Consensus size: 24
57077800 AAGAAATGAA
57077810 AGAAAAAGAAAAAGAGATTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
* * * *
57077834 TGAAAAAGAAAATGAGATTGAAAA
1 AGAAAAAGAAAAAGAGATTGAGAG
* * *
57077858 AGAGAATGAAAAAGAGTTTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
*
57077882 AGAGAAAGAA
1 AGAAAAAGAA
57077892 TGTGAACAAG
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.60, C:0.00, G:0.28, T:0.12
Consensus pattern (24 bp):
AGAAAAAGAAAAAGAGATTGAGAG
Found at i:57077922 original size:18 final size:19
Alignment explanation
Indices: 57077886--57077922 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
57077876 TGAGAGAGAG
*
57077886 AAAGAATGTGAACAAGAAA
1 AAAGAATGTGAAAAAGAAA
57077905 AAAGAATG-GAAAAAGAAA
1 AAAGAATGTGAAAAAGAAA
57077923 TTGAGATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.68, C:0.03, G:0.22, T:0.08
Consensus pattern (19 bp):
AAAGAATGTGAAAAAGAAA
Found at i:57079377 original size:29 final size:29
Alignment explanation
Indices: 57079345--57079404 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
57079335 ATAACCAAAC
* *
57079345 CTACAAAAACTTTATATTCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
* *
57079374 CTACATAAACTTCATATCCATAAACCTAT
1 CTACAAAAACTTCATATCCATAAACCCAT
57079403 CT
1 CT
57079405 TTGAATCCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.32
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:57080520 original size:14 final size:14
Alignment explanation
Indices: 57080501--57080545 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
57080491 AACTCATCTT
*
57080501 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
57080515 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
57080528 AATTTAATTTAATG
1 AGTTTAATTTAATG
57080542 AGTT
1 AGTT
57080546 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:57081555 original size:29 final size:29
Alignment explanation
Indices: 57081522--57081581 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
57081512 ATAACCAAAC
* *
57081522 CTACAAAAACTTTATACGCATAAACCCAT
1 CTACAAAAACTTCATACCCATAAACCCAT
*
57081551 CTACATAAACTTCATACCCATAAACCCAT
1 CTACAAAAACTTCATACCCATAAACCCAT
57081580 CT
1 CT
57081582 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.32, G:0.02, T:0.25
Consensus pattern (29 bp):
CTACAAAAACTTCATACCCATAAACCCAT
Found at i:57083080 original size:14 final size:14
Alignment explanation
Indices: 57083061--57083105 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
57083051 AACTCATCTT
*
57083061 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
57083075 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
57083088 AATTTAATTTAATG
1 AGTTTAATTTAATG
57083102 AGTT
1 AGTT
57083106 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:57084115 original size:29 final size:29
Alignment explanation
Indices: 57084082--57084141 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
57084072 ATAACCAAAC
*
57084082 CTACAAAAACTTTATA-CGCATAAACCCAT
1 CTACAAAAACTTCATATC-CATAAACCCAT
*
57084111 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
57084140 CT
1 CT
57084142 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.42, C:0.30, G:0.02, T:0.27
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:57085645 original size:14 final size:14
Alignment explanation
Indices: 57085626--57085670 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
57085616 AACTCATCTT
*
57085626 AGTTTAATTAAATG
1 AGTTTAATTTAATG
57085640 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
57085653 AATTTAATTTAATG
1 AGTTTAATTTAATG
57085667 AGTT
1 AGTT
57085671 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:57086848 original size:11 final size:12
Alignment explanation
Indices: 57086833--57086861 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
57086823 TCAAGTAAGT
57086833 TTCAAAAAAAAA
1 TTCAAAAAAAAA
57086845 -TCAAAAAAAAA
1 TTCAAAAAAAAA
57086856 TTCAAA
1 TTCAAA
57086862 TTAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.17
Consensus pattern (12 bp):
TTCAAAAAAAAA
Found at i:57086890 original size:28 final size:28
Alignment explanation
Indices: 57086836--57086888 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
57086826 AGTAAGTTTC
*
57086836 AAAAAAAAATCAAAAAAAAATTCAAATT
1 AAAAAAAAATCAAAAAAAAATACAAATT
* *
57086864 AAAAAAAATTGAAAAAAAAA-ACAAA
1 AAAAAAAAATCAAAAAAAAATACAAA
57086889 ATCTGAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.79, C:0.06, G:0.02, T:0.13
Consensus pattern (28 bp):
AAAAAAAAATCAAAAAAAAATACAAATT
Found at i:57093713 original size:42 final size:42
Alignment explanation
Indices: 57093654--57093759 Score: 203
Period size: 42 Copynumber: 2.5 Consensus size: 42
57093644 CATTTAAGCC
57093654 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
57093696 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
57093738 TCTTAGTTTAATTAAATGAGTT
1 TCTTAGTTTAA-TAAATGAGTT
57093760 TATTTAATGA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 53 0.84
43 10 0.16
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (42 bp):
TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
Found at i:57093761 original size:14 final size:14
Alignment explanation
Indices: 57093742--57093786 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
57093732 AACTCATCTT
*
57093742 AGTTTAATTAAATG
1 AGTTTAATTTAATG
57093756 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
57093769 AATTTAATTTAATG
1 AGTTTAATTTAATG
57093783 AGTT
1 AGTT
57093787 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:57094795 original size:29 final size:29
Alignment explanation
Indices: 57094762--57094821 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
57094752 ATAACCAAAC
*
57094762 CTACAAAAACTTTATACCCATAAACCCAT
1 CTACAAAAACTTCATACCCATAAACCCAT
* *
57094791 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATACCCATAAACCCAT
57094820 CT
1 CT
57094822 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.27
Consensus pattern (29 bp):
CTACAAAAACTTCATACCCATAAACCCAT
Found at i:57095062 original size:18 final size:17
Alignment explanation
Indices: 57095036--57095070 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
57095026 AGTAATTTTC
*
57095036 AAAAAAAAATTTGAAAA
1 AAAAAAAAATCTGAAAA
57095053 AAAAACAAAATCTGAAAA
1 AAAAA-AAAATCTGAAAA
57095071 TTTGAACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.14
Consensus pattern (17 bp):
AAAAAAAAATCTGAAAA
Found at i:57095993 original size:18 final size:18
Alignment explanation
Indices: 57095970--57096019 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
57095960 GAAAGAAAAA
*
57095970 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGAATGAGAGT
* *
57095988 GAAAAAGAAAATGAGATT
1 GAAAAAGAGAATGAGAGT
57096006 GAAAAAGAGAATGA
1 GAAAAAGAGAATGA
57096020 AAAAGAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.14
Consensus pattern (18 bp):
GAAAAAGAGAATGAGAGT
Found at i:57095996 original size:24 final size:24
Alignment explanation
Indices: 57095963--57096044 Score: 92
Period size: 24 Copynumber: 3.4 Consensus size: 24
57095953 AAGAAATGAA
57095963 AGAAAAAGAAAAAGAGATTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
* * * *
57095987 TGAAAAAGAAAATGAGATTGAAAA
1 AGAAAAAGAAAAAGAGATTGAGAG
* * *
57096011 AGAGAATGAAAAAGAGTTTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
*
57096035 AGAGAAAGAA
1 AGAAAAAGAA
57096045 TGTGAACAAG
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.60, C:0.00, G:0.28, T:0.12
Consensus pattern (24 bp):
AGAAAAAGAAAAAGAGATTGAGAG
Found at i:57097529 original size:29 final size:29
Alignment explanation
Indices: 57097497--57097556 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
57097487 ATAACCAAAC
* *
57097497 CTACAAAAACTTTATATTCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
* *
57097526 CTACATAAACTTCATATCCATAAACCTAT
1 CTACAAAAACTTCATATCCATAAACCCAT
57097555 CT
1 CT
57097557 TTGAATCCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.32
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:57098672 original size:14 final size:14
Alignment explanation
Indices: 57098653--57098697 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
57098643 AACTCATCTT
*
57098653 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
57098667 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
57098680 AATTTAATTTAATG
1 AGTTTAATTTAATG
57098694 AGTT
1 AGTT
57098698 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:57099705 original size:29 final size:29
Alignment explanation
Indices: 57099672--57099731 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
57099662 ATAACCAAAC
*
57099672 CTACAAAAACTTTATACCCATAAACCCAT
1 CTACAAAAACTTCATACCCATAAACCCAT
* *
57099701 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATACCCATAAACCCAT
57099730 CT
1 CT
57099732 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.27
Consensus pattern (29 bp):
CTACAAAAACTTCATACCCATAAACCCAT
Found at i:57101232 original size:14 final size:14
Alignment explanation
Indices: 57101213--57101257 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
57101203 AACTCATCTT
*
57101213 AGTTTAATTAAATG
1 AGTTTAATTTAATG
57101227 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
57101240 AATTTAATTTAATG
1 AGTTTAATTTAATG
57101254 AGTT
1 AGTT
57101258 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:57102479 original size:28 final size:28
Alignment explanation
Indices: 57102423--57102477 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
57102413 TCAAGTAAGT
*
57102423 TTAAAAAAAAATCAAAAAAAAATTCAAA
1 TTAAAAAAAAATCAAAAAAAAATACAAA
* *
57102451 TTAAAAAAAATTGAAAAAAAAA-ACAAA
1 TTAAAAAAAAATCAAAAAAAAATACAAA
57102478 ATCTGAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.16
Consensus pattern (28 bp):
TTAAAAAAAAATCAAAAAAAAATACAAA
Found at i:57106260 original size:21 final size:21
Alignment explanation
Indices: 57106196--57106269 Score: 50
Period size: 21 Copynumber: 3.6 Consensus size: 21
57106186 AAAAAAATCA
57106196 GAAAAAGAAAACAAAAGAG-AG
1 GAAAAAGAAAA-AAAAGAGAAG
**
57106217 TG-AAAAG-AAAATCAGTA-AA-
1 -GAAAAAGAAAAAAAAG-AGAAG
57106236 GAAAAAGAAAAAAAAGAGAAG
1 GAAAAAGAAAAAAAAGAGAAG
**
57106257 GAAATTGAAAAAA
1 GAAAAAGAAAAAA
57106270 TGAGTGTCTT
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
18 1 0.03
19 9 0.22
20 13 0.32
21 16 0.40
22 1 0.03
ACGTcount: A:0.70, C:0.03, G:0.20, T:0.07
Consensus pattern (21 bp):
GAAAAAGAAAAAAAAGAGAAG
Found at i:57109390 original size:42 final size:42
Alignment explanation
Indices: 57109331--57109436 Score: 194
Period size: 42 Copynumber: 2.5 Consensus size: 42
57109321 CATTTAAGCC
*
57109331 TCTTAATTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
57109373 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
57109415 TCTTAGTTTAATTAAATGAGTT
1 TCTTAGTTTAA-TAAATGAGTT
57109437 TATTTAATGA
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
42 52 0.84
43 10 0.16
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (42 bp):
TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
Found at i:57109438 original size:14 final size:14
Alignment explanation
Indices: 57109419--57109463 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
57109409 AACTCATCTT
*
57109419 AGTTTAATTAAATG
1 AGTTTAATTTAATG
57109433 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
57109446 AATTTAATTTAATG
1 AGTTTAATTTAATG
57109460 AGTT
1 AGTT
57109464 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:57111158 original size:62 final size:61
Alignment explanation
Indices: 57111061--57111185 Score: 187
Period size: 62 Copynumber: 2.0 Consensus size: 61
57111051 AGGACTTTGC
* * * *
57111061 CTATGAGAGCTACGTTCCTTATAAGTTGTCTTGGTAATCCCTCGTTTATGTTATGTTTCGGA
1 CTATGAGAGCTACGTTCCTTACAAGTTGGCTTGGTAAACCCTCGTTTATGTTA-GTTCCGGA
* *
57111123 CTATGAGAGCTACGTTCCTTACAGGTTGGCTTGGTAAACCCTTGTTTATGTTAGTTCCGGA
1 CTATGAGAGCTACGTTCCTTACAAGTTGGCTTGGTAAACCCTCGTTTATGTTAGTTCCGGA
57111184 CT
1 CT
57111186 TCGCGACATG
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
61 9 0.16
62 48 0.84
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.39
Consensus pattern (61 bp):
CTATGAGAGCTACGTTCCTTACAAGTTGGCTTGGTAAACCCTCGTTTATGTTAGTTCCGGA
Found at i:57113084 original size:30 final size:30
Alignment explanation
Indices: 57113050--57113133 Score: 107
Period size: 30 Copynumber: 2.8 Consensus size: 30
57113040 GCTAAGTTTG
**
57113050 AGCTCGTGAGCTGGAAG-TGAGCTGAGTCCA
1 AGCTCGTGAGCT-GAAGTTGAGCTGAGAACA
*
57113080 AGCTCGAGAGCTGAAGTTGAGCTGAGAACA
1 AGCTCGTGAGCTGAAGTTGAGCTGAGAACA
* *
57113110 AGCTCATGAGCTCAAGTTGAGCTG
1 AGCTCGTGAGCTGAAGTTGAGCTG
57113134 GATGTGAACA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 4 0.09
30 43 0.91
ACGTcount: A:0.27, C:0.19, G:0.33, T:0.20
Consensus pattern (30 bp):
AGCTCGTGAGCTGAAGTTGAGCTGAGAACA
Found at i:57117168 original size:21 final size:21
Alignment explanation
Indices: 57117144--57117211 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
57117134 GATTTTCAAT
57117144 GAAATCGAGAGAAGAAACAAA
1 GAAATCGAGAGAAGAAACAAA
***** *
57117165 GAAAAT-GAGAGAATCTTGAAT
1 G-AAATCGAGAGAAGAAACAAA
*
57117186 GAAATCGAGAAAAGAAACAAA
1 GAAATCGAGAGAAGAAACAAA
57117207 GAAAT
1 GAAAT
57117212 GAAAGAAAAA
Statistics
Matches: 32, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
20 4 0.12
21 24 0.75
22 4 0.12
ACGTcount: A:0.59, C:0.07, G:0.22, T:0.12
Consensus pattern (21 bp):
GAAATCGAGAGAAGAAACAAA
Found at i:57117187 original size:42 final size:42
Alignment explanation
Indices: 57117122--57117218 Score: 135
Period size: 42 Copynumber: 2.3 Consensus size: 42
57117112 AGATTATGAG
* *
57117122 AGAAAATGAGACG-ATTTTCAATGAAATCGAGAGAAGAAACAA
1 AGAAAATGAGA-GAATCTTCAATGAAATCGAGAAAAGAAACAA
*
57117164 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
1 AGAAAATGAGAGAATCTTCAATGAAATCGAGAAAAGAAACAA
*
57117206 AG-AAATGAAAGAA
1 AGAAAATGAGAGAA
57117219 AAAGAAAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
41 11 0.22
42 39 0.78
ACGTcount: A:0.57, C:0.07, G:0.22, T:0.14
Consensus pattern (42 bp):
AGAAAATGAGAGAATCTTCAATGAAATCGAGAAAAGAAACAA
Found at i:57117245 original size:18 final size:18
Alignment explanation
Indices: 57117222--57117271 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
57117212 GAAAGAAAAA
* *
57117222 GAAAAAGAGATTGGGAGT
1 GAAAAAGAGAATGAGAGT
* *
57117240 GAAAAAGAAAATGAGATT
1 GAAAAAGAGAATGAGAGT
57117258 GAAAAAGAGAATGA
1 GAAAAAGAGAATGA
57117272 AAAAGTTTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.30, T:0.14
Consensus pattern (18 bp):
GAAAAAGAGAATGAGAGT
Found at i:57117323 original size:18 final size:19
Alignment explanation
Indices: 57117287--57117325 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
57117277 TTTGAGAGAG
*
57117287 AAAAAGAATGTGAACAAGA
1 AAAAAGAATGTGAAAAAGA
*
57117306 AAAAAGAGTG-GAAAAAGA
1 AAAAAGAATGTGAAAAAGA
57117324 AA
1 AA
57117326 TTAAGATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.08
Consensus pattern (19 bp):
AAAAAGAATGTGAAAAAGA
Found at i:57121387 original size:19 final size:19
Alignment explanation
Indices: 57121363--57121402 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
57121353 AGCTCCCATG
57121363 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
* *
57121382 TAGCTCGAGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
57121401 TA
1 TA
57121403 TTAGCTCACG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:57124026 original size:30 final size:30
Alignment explanation
Indices: 57123992--57124089 Score: 74
Period size: 30 Copynumber: 3.3 Consensus size: 30
57123982 AGCTCACTCC
57123992 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
57124022 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
57124052 CAGCTCA-ACTAT-ATCTCACGAGCTAAAGCT
1 TAGCTCATA-T-TCAGCTCACGAGCTAAACCT
57124082 TAGCTCAT
1 TAGCTCAT
57124090 TTTAGTTTAA
Statistics
Matches: 49, Mismatches: 16, Indels: 5
0.70 0.23 0.07
Matches are distributed among these distances:
30 48 0.98
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:57133741 original size:30 final size:30
Alignment explanation
Indices: 57133656--57133752 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
57133646 TAAACTAAAA
* *
57133656 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
57133686 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
57133716 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
57133745 ATGAGCTA
1 -TGAGCTA
57133753 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:57134461 original size:21 final size:20
Alignment explanation
Indices: 57134425--57134473 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
57134415 ATCAGCTCAC
*
57134425 TTGAGCTCGTTTTAGCTCGT
1 TTGAGCTCGATTTAGCTCGT
*
57134445 TTGAGCTCGAATTTAGCTTGT
1 TTGAGCTCG-ATTTAGCTCGT
*
57134466 TTCAGCTC
1 TTGAGCTC
57134474 ATTCCTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.43
Consensus pattern (20 bp):
TTGAGCTCGATTTAGCTCGT
Found at i:57134714 original size:13 final size:13
Alignment explanation
Indices: 57134696--57134720 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57134686 TGAATAGTTG
57134696 TGTTATTTAATTA
1 TGTTATTTAATTA
57134709 TGTTATTTAATT
1 TGTTATTTAATT
57134721 TTGTAGGTTA
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:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:57136872 original size:21 final size:20
Alignment explanation
Indices: 57136848--57136932 Score: 53
Period size: 21 Copynumber: 4.1 Consensus size: 20
57136838 GATTTTGAAT
57136848 GAAATCGAGAGAAGAAACAAA
1 GAAAT-GAGAGAAGAAACAAA
***** *
57136869 GAAAATGAGAGAATCTTGAAT
1 G-AAATGAGAGAAGAAACAAA
*
57136890 GAAATCGAGAAAAGAAACAAA
1 GAAAT-GAGAGAAGAAACAAA
* * *
57136911 GAAATGAAAGAAAAAAAAAA
1 GAAATGAGAGAAGAAACAAA
57136931 GA
1 GA
57136933 GATTGAGAGT
Statistics
Matches: 45, Mismatches: 17, Indels: 5
0.67 0.25 0.07
Matches are distributed among these distances:
20 17 0.38
21 24 0.53
22 4 0.09
ACGTcount: A:0.64, C:0.06, G:0.21, T:0.09
Consensus pattern (20 bp):
GAAATGAGAGAAGAAACAAA
Found at i:57136888 original size:42 final size:42
Alignment explanation
Indices: 57136826--57136922 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
57136816 AGATTATGAG
* * *
57136826 AGAAAATGAGAGGATTTTGAATGAAATCGAGAGAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
57136868 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
*
57136910 AG-AAATGAAAGAA
1 AGAAAATGAGAGAA
57136923 AAAAAAAAGA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 10 0.20
42 41 0.80
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (42 bp):
AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
Found at i:57138613 original size:20 final size:20
Alignment explanation
Indices: 57138590--57138637 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
57138580 AGCTCTGTCC
57138590 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
*** *
57138610 AGCTCGTTTCAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTG
57138630 AGCTCAAC
1 AGCTCAAC
57138638 CGAGCTTACT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:57141062 original size:21 final size:21
Alignment explanation
Indices: 57141038--57141105 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
57141028 GATTTTGAAT
57141038 GAAATCGAGAGAAGAAACAAA
1 GAAATCGAGAGAAGAAACAAA
***** *
57141059 GAAAAT-GAGAGAATCTTGAAT
1 G-AAATCGAGAGAAGAAACAAA
*
57141080 GAAATCGAGAAAAGAAACAAA
1 GAAATCGAGAGAAGAAACAAA
57141101 GAAAT
1 GAAAT
57141106 GAAAGAAAAA
Statistics
Matches: 32, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
20 4 0.12
21 24 0.75
22 4 0.12
ACGTcount: A:0.59, C:0.07, G:0.22, T:0.12
Consensus pattern (21 bp):
GAAATCGAGAGAAGAAACAAA
Found at i:57141078 original size:42 final size:42
Alignment explanation
Indices: 57141016--57141112 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
57141006 AGATTATGAG
* * *
57141016 AGAAAATGAGAGGATTTTGAATGAAATCGAGAGAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
57141058 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
*
57141100 AG-AAATGAAAGAA
1 AGAAAATGAGAGAA
57141113 AAAGAAAAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 10 0.20
42 41 0.80
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (42 bp):
AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
Found at i:57141139 original size:18 final size:18
Alignment explanation
Indices: 57141116--57141168 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
57141106 GAAAGAAAAA
57141116 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGATTGAGAGT
* ** *
57141134 GAAAAAGAAAAAGAGAAT
1 GAAAAAGAGATTGAGAGT
*
57141152 GAAAAAGAGTTTGAGAG
1 GAAAAAGAGATTGAGAG
57141169 ACAAAAAGAA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.30, T:0.13
Consensus pattern (18 bp):
GAAAAAGAGATTGAGAGT
Found at i:57141156 original size:36 final size:36
Alignment explanation
Indices: 57141107--57141178 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
57141097 CAAAGAAATG
**
57141107 AAAGAAAAAGAAAAAGAGATTGAGAGTGAAAAAGAA
1 AAAGAAAAAGAAAAAGAGATTGAGAGACAAAAAGAA
* * *
57141143 AAAGAGAATGAAAAAGAGTTTGAGAGACAAAAAGAA
1 AAAGAAAAAGAAAAAGAGATTGAGAGACAAAAAGAA
57141179 TGTGAACAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.64, C:0.01, G:0.25, T:0.10
Consensus pattern (36 bp):
AAAGAAAAAGAAAAAGAGATTGAGAGACAAAAAGAA
Found at i:57141207 original size:18 final size:19
Alignment explanation
Indices: 57141171--57141209 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
57141161 TTTGAGAGAC
*
57141171 AAAAAGAATGTGAACAAGA
1 AAAAAGAATGTGAAAAAGA
*
57141190 AAAAAGAGTG-GAAAAAGA
1 AAAAAGAATGTGAAAAAGA
57141208 AA
1 AA
57141210 TTGAGATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.08
Consensus pattern (19 bp):
AAAAAGAATGTGAAAAAGA
Found at i:57141889 original size:10 final size:10
Alignment explanation
Indices: 57141876--57141910 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
57141866 AAGCTCGGTT
57141876 GAGCTCAAAC
1 GAGCTCAAAC
*
57141886 GAGCTAAAAC
1 GAGCTCAAAC
*
57141896 GAGCTCAAAT
1 GAGCTCAAAC
57141906 GAGCT
1 GAGCT
57141911 GAGTTGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:57141919 original size:20 final size:20
Alignment explanation
Indices: 57141873--57141920 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
57141863 AGTAAGCTCG
57141873 GTTGAGCTCAAACGAGCTAA
1 GTTGAGCTCAAACGAGCTAA
*** * *
57141893 AACGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTAA
57141913 GTTGAGCT
1 GTTGAGCT
57141921 GGACAGAGCT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTAA
Found at i:57141949 original size:20 final size:20
Alignment explanation
Indices: 57141902--57141950 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
57141892 AAACGAGCTC
57141902 AAATGAGCTGAGTTGAGCTGG
1 AAATGAGCTGAG-TGAGCTGG
*
57141923 ACA-GAGCTCGAG-GAGCTGG
1 AAATGAGCT-GAGTGAGCTGG
57141942 AAATGAGCT
1 AAATGAGCT
57141951 AGGATCAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 9 0.38
20 10 0.42
21 5 0.21
ACGTcount: A:0.31, C:0.14, G:0.37, T:0.18
Consensus pattern (20 bp):
AAATGAGCTGAGTGAGCTGG
Found at i:57142828 original size:22 final size:24
Alignment explanation
Indices: 57142798--57142841 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
57142788 TTCTCTTTTT
57142798 ATTTATTTA-TTTTATTTTTTTGA
1 ATTTATTTATTTTTATTTTTTTGA
57142821 ATTT-TTTATTTTTATTTTTTT
1 ATTTATTTATTTTTATTTTTTT
57142842 CTTTATATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (24 bp):
ATTTATTTATTTTTATTTTTTTGA
Found at i:57143207 original size:14 final size:14
Alignment explanation
Indices: 57143188--57143243 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
57143178 AAAGAATGGT
*
57143188 CGAAATTGTATGAA
1 CGAAATGGTATGAA
57143202 CGAAATGGTATGAA
1 CGAAATGGTATGAA
* *
57143216 TGGAATGGTATGAA
1 CGAAATGGTATGAA
* **
57143230 TGAAGGGGTATGAA
1 CGAAATGGTATGAA
57143244 TAATTGGTCG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.39, C:0.04, G:0.32, T:0.25
Consensus pattern (14 bp):
CGAAATGGTATGAA
Found at i:57143819 original size:17 final size:17
Alignment explanation
Indices: 57143797--57143831 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
57143787 TCGGCCTCCC
57143797 TTGTTTAATGAAGCAAT
1 TTGTTTAATGAAGCAAT
57143814 TTGTTTAATGAAGCAAT
1 TTGTTTAATGAAGCAAT
57143831 T
1 T
57143832 AAGTGACAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (17 bp):
TTGTTTAATGAAGCAAT
Found at i:57145714 original size:20 final size:20
Alignment explanation
Indices: 57145691--57145735 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
57145681 AGCTCCGTCC
57145691 AGCTCAATTCAGCTCATTTG
1 AGCTCAATTCAGCTCATTTG
** **
57145711 AGCTCGTTTCAGCTTGTTTG
1 AGCTCAATTCAGCTCATTTG
57145731 AGCTC
1 AGCTC
57145736 GTTTCAACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (20 bp):
AGCTCAATTCAGCTCATTTG
Found at i:57145729 original size:10 final size:10
Alignment explanation
Indices: 57145698--57145755 Score: 53
Period size: 10 Copynumber: 5.8 Consensus size: 10
57145688 TCCAGCTCAA
*
57145698 TTCAGCTCAT
1 TTCAGCTCGT
*
57145708 TTGAGCTCGT
1 TTCAGCTCGT
*
57145718 TTCAGCTTGT
1 TTCAGCTCGT
*
57145728 TTGAGCTCGT
1 TTCAGCTCGT
* *
57145738 TTCAACTTGT
1 TTCAGCTCGT
*
57145748 TTGAGCTC
1 TTCAGCTC
57145756 AACCGAGCTT
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
10 36 1.00
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.43
Consensus pattern (10 bp):
TTCAGCTCGT
Found at i:57145736 original size:20 final size:20
Alignment explanation
Indices: 57145707--57145755 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
57145697 ATTCAGCTCA
*
57145707 TTTGAGCTCGTTTCAGCTTG
1 TTTGAGCTCGTTTCAACTTG
57145727 TTTGAGCTCGTTTCAACTTG
1 TTTGAGCTCGTTTCAACTTG
57145747 TTTGAGCTC
1 TTTGAGCTC
57145756 AACCGAGCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.45
Consensus pattern (20 bp):
TTTGAGCTCGTTTCAACTTG
Found at i:57146419 original size:11 final size:12
Alignment explanation
Indices: 57146400--57146432 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
57146390 CATTCTAATA
57146400 AATTAAGTTT-T
1 AATTAAGTTTAT
*
57146411 AATTCAGTTTAT
1 AATTAAGTTTAT
57146423 AATTAAGTTT
1 AATTAAGTTT
57146433 GCTACAGCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (12 bp):
AATTAAGTTTAT
Found at i:57146815 original size:40 final size:41
Alignment explanation
Indices: 57146770--57146861 Score: 168
Period size: 42 Copynumber: 2.2 Consensus size: 41
57146760 CATCTTGCCT
57146770 GAGCTAAACCGAGCTCACTCCTAG-CTCACTTTCAACTCAC
1 GAGCTAAACCGAGCTCACTCCTAGCCTCACTTTCAACTCAC
57146810 GAGCTAAACCGAGCTCACTCCTAGCTCTCACTTTCAACTCAC
1 GAGCTAAACCGAGCTCACTCCTAGC-CTCACTTTCAACTCAC
57146852 GAGCTAAACC
1 GAGCTAAACC
57146862 TTAGCTCAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 24 0.48
42 26 0.52
ACGTcount: A:0.28, C:0.37, G:0.13, T:0.22
Consensus pattern (41 bp):
GAGCTAAACCGAGCTCACTCCTAGCCTCACTTTCAACTCAC
Found at i:57148589 original size:11 final size:11
Alignment explanation
Indices: 57148573--57148609 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
57148563 ATACAAGTCA
57148573 AAAAAAATTCG
1 AAAAAAATTCG
57148584 AAAAAAATTC-
1 AAAAAAATTCG
57148594 AAAAAAATTTCG
1 AAAAAAA-TTCG
57148606 AAAA
1 AAAA
57148610 GAAAAAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 7 0.29
11 13 0.54
12 4 0.17
ACGTcount: A:0.68, C:0.08, G:0.05, T:0.19
Consensus pattern (11 bp):
AAAAAAATTCG
Found at i:57149531 original size:9 final size:10
Alignment explanation
Indices: 57149524--57149580 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
57149514 AAGAGAAAAT
57149524 AAAGAAAAGA
1 AAAGAAAAGA
57149534 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
57149546 AAAGAAGA-A
1 AAAGAAAAGA
57149555 AAAGAAAATGA
1 AAAGAAAA-GA
57149566 AATA-AAAAGA
1 AA-AGAAAAGA
57149576 AAAGA
1 AAAGA
57149581 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:57149548 original size:6 final size:5
Alignment explanation
Indices: 57149524--57149580 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
57149514 AAGAGAAAAT
*
57149524 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
57149571 AAAGA AAAGA
1 AAAGA AAAGA
57149581 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:57149555 original size:15 final size:14
Alignment explanation
Indices: 57149524--57149580 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
57149514 AAGAGAAAAT
57149524 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
57149540 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
57149555 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
57149571 AAAGAAAAGA
1 AAAGAAAAGA
57149581 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:57149657 original size:12 final size:12
Alignment explanation
Indices: 57149649--57149673 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57149639 TTTGAAAAGC
57149649 AAAAAGAAAATG
1 AAAAAGAAAATG
57149661 AAAAAGAAAATG
1 AAAAAGAAAATG
57149673 A
1 A
57149674 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:57149670 original size:18 final size:18
Alignment explanation
Indices: 57149643--57149698 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
57149633 AAAGCCTTTG
*
57149643 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAATGAAAATGA
* *
57149662 AAAAGAAAATGAGATTGA
1 AAAAGAAAATGAAAATGA
*
57149680 AAAAGAGAATGAAAA-GA
1 AAAAGAAAATGAAAATGA
57149697 AA
1 AA
57149699 TTTGAGAGTG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
17 4 0.13
18 22 0.71
19 5 0.16
ACGTcount: A:0.70, C:0.02, G:0.20, T:0.09
Consensus pattern (18 bp):
AAAAGAAAATGAAAATGA
Found at i:57149683 original size:30 final size:31
Alignment explanation
Indices: 57149649--57149730 Score: 114
Period size: 30 Copynumber: 2.7 Consensus size: 31
57149639 TTTGAAAAGC
*
57149649 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* *
57149679 AAAAAGAGAATG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
57149709 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
57149731 TGAAACAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 8 0.18
30 28 0.62
31 9 0.20
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.13
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:57151845 original size:30 final size:31
Alignment explanation
Indices: 57151811--57151907 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
57151801 AGCTCACTCC
*
57151811 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
57151841 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
57151871 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
57151901 TAGCTCA
1 TAGCTCA
57151908 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:57154674 original size:30 final size:30
Alignment explanation
Indices: 57154589--57154685 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
57154579 TAAACTAAAA
* * * *
57154589 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGTTGAAGT
* * * * *
57154619 TGAGCTGAGATTAAACTCCTAAGTTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGTTGAAGT
*
57154649 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGATTTAGCTCGTGAGTTG-AAGT
57154679 TGAGCTA
1 TGAGCTA
57154686 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
30 48 0.94
31 3 0.06
ACGTcount: A:0.29, C:0.12, G:0.28, T:0.31
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGTTGAAGT
Found at i:57156854 original size:30 final size:30
Alignment explanation
Indices: 57156783--57156865 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
57156773 CTTTTGTTTC
* *
57156783 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
57156814 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
57156843 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
57156866 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:57156865 original size:18 final size:18
Alignment explanation
Indices: 57156816--57156871 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
57156806 CACTCTCAAA
* *
57156816 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
57156833 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
57156851 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
57156870 TT
1 TT
57156872 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:57156872 original size:12 final size:12
Alignment explanation
Indices: 57156841--57156865 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57156831 TTTTTCAATC
57156841 TCATTTTCTTTT
1 TCATTTTCTTTT
57156853 TCATTTTCTTTT
1 TCATTTTCTTTT
57156865 T
1 T
57156866 GCTTTTCAAA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:57156883 original size:12 final size:12
Alignment explanation
Indices: 57156868--57156898 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
57156858 TTCTTTTTGC
*
57156868 TTTTCAAAGGCT
1 TTTTCAAAGACT
57156880 TTTTCAAAGACT
1 TTTTCAAAGACT
57156892 TTTTCAA
1 TTTTCAA
57156899 GTTCTCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGACT
Found at i:57156956 original size:5 final size:5
Alignment explanation
Indices: 57156946--57157002 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
57156936 CTCTTGCCTC
*
57156946 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
57156993 TCTTT TCTTT
1 TCTTT TCTTT
57157003 ATTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:57156986 original size:15 final size:14
Alignment explanation
Indices: 57156946--57157002 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
57156936 CTCTTGCCTC
*
57156946 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
57156961 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
57156976 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
57156993 TCTTTTCTTT
1 TCTTTTCTTT
57157003 ATTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:57157012 original size:21 final size:20
Alignment explanation
Indices: 57156944--57157013 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
57156934 GCCTCTTGCC
57156944 TCTCTTTTCTTTTTATTTCATTT
1 TCTCTTTTC-TTTT-TTT-ATTT
**
57156967 TCT-TTTTCTTCTTTTGCTTT
1 TCTCTTTTCTT-TTTTTATTT
57156987 T-TCTTTTCTTTTCTTTATTT
1 TCTCTTTTCTTTT-TTTATTT
57157007 TCTCTTT
1 TCTCTTT
57157014 ACAAGAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
19 3 0.08
20 17 0.44
21 9 0.23
22 7 0.18
23 3 0.08
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.76
Consensus pattern (20 bp):
TCTCTTTTCTTTTTTTATTT
Done.