Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 134 of 228
Found at i:40047860 original size:30 final size:30
Alignment explanation
Indices: 40047825--40047898 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
40047815 AGTTTTTCCC
40047825 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
40047855 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
40047885 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
40047899 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:40047888 original size:20 final size:20
Alignment explanation
Indices: 40047825--40047889 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
40047815 AGTTTTTCCC
* * * *
40047825 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
40047845 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
40047864 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
40047885 AGCTC
1 AGCTC
40047890 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:40050134 original size:20 final size:20
Alignment explanation
Indices: 40050109--40050146 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40050099 TTGAGCTGAA
* *
40050109 TTGAGCTTGAGTGGGTTGAC
1 TTGAGCTCGAGTGAGTTGAC
40050129 TTGAGCTCGAGTGAGTTG
1 TTGAGCTCGAGTGAGTTG
40050147 GAAACGAGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.11, G:0.39, T:0.34
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGTTGAC
Found at i:40051743 original size:20 final size:20
Alignment explanation
Indices: 40051697--40051743 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
40051687 AGCTCGTTTC
*
40051697 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
40051717 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
40051737 CAGCTCA
1 CAGCTCA
40051744 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:40055072 original size:29 final size:29
Alignment explanation
Indices: 40055006--40055062 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
40054996 GATTCAAAGA
*
40055006 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
*
40055035 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
40055063 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.46
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:40056081 original size:14 final size:14
Alignment explanation
Indices: 40056039--40056083 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
40056029 TTAAAGAAGC
40056039 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
40056053 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
40056066 AACTCATTTAATTA
1 AACTCATTAAATTA
40056080 AACT
1 AACT
40056084 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:40058684 original size:20 final size:19
Alignment explanation
Indices: 40058661--40058725 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
40058651 AAGCTCAAAC
40058661 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
40058681 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
40058701 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
40058721 GAGCT
1 GAGCT
40058726 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:40060440 original size:20 final size:20
Alignment explanation
Indices: 40060417--40060473 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
40060407 GGGTTAAGAT
**
40060417 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCAAG
* *
40060437 TGAGTTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
*
40060457 TGAGCTGGAAATGAGCT
1 TGAGCT-GAATTGAGCT
40060474 AAACGGAGCT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 21 0.72
21 8 0.28
ACGTcount: A:0.26, C:0.12, G:0.33, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:40064684 original size:20 final size:20
Alignment explanation
Indices: 40064661--40064717 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
40064651 GGGTTAAGAT
**
40064661 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCAAG
* *
40064681 TGAGTTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
*
40064701 TGAGCTGGAAATGAGCT
1 TGAGCT-GAATTGAGCT
40064718 AAACGGAGCT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 21 0.72
21 8 0.28
ACGTcount: A:0.26, C:0.12, G:0.33, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:40068928 original size:20 final size:20
Alignment explanation
Indices: 40068905--40068961 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
40068895 GGGTTAAGAT
*
40068905 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
40068925 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
*
40068945 TGAGCTGGAAATGAGCT
1 TGAGCT-GAATTGAGCT
40068962 AAACAGAGCT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 22 0.73
21 8 0.27
ACGTcount: A:0.25, C:0.12, G:0.35, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:40070417 original size:33 final size:33
Alignment explanation
Indices: 40070379--40070441 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
40070369 GATTACTCAC
40070379 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
40070412 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
40070442 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:40070501 original size:27 final size:28
Alignment explanation
Indices: 40070459--40070522 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
40070449 TTTTTCGCTT
40070459 TTTC-TTTTCAATTTTT-TTCATTC-TCAA
1 TTTCTTTTTCAATTTTTCTT--TTCTTCAA
*
40070486 TTTCTTTTTCAA-TTTTCTTTTCTTCAT
1 TTTCTTTTTCAATTTTTCTTTTCTTCAA
40070513 TTTCTTTTTC
1 TTTCTTTTTC
40070523 TCTCACTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 3 0.09
27 21 0.64
28 9 0.27
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.69
Consensus pattern (28 bp):
TTTCTTTTTCAATTTTTCTTTTCTTCAA
Found at i:40070554 original size:12 final size:12
Alignment explanation
Indices: 40070482--40070555 Score: 58
Period size: 12 Copynumber: 5.9 Consensus size: 12
40070472 TTTTTCATTC
40070482 TCAATTTCTTTT
1 TCAATTTCTTTT
40070494 TCAATTTTCTTTTCT
1 TCAA-TTTC-TTT-T
*
40070509 TCATTTTCTTTT
1 TCAATTTCTTTT
** **
40070521 TCTCTCACTTTT
1 TCAATTTCTTTT
*
40070533 TCGATTTCTTTT
1 TCAATTTCTTTT
*
40070545 TCAATCTCTTT
1 TCAATTTCTTT
40070556 CTCCTTTTCT
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
12 30 0.62
13 7 0.15
14 7 0.15
15 4 0.08
ACGTcount: A:0.12, C:0.22, G:0.01, T:0.65
Consensus pattern (12 bp):
TCAATTTCTTTT
Found at i:40070564 original size:24 final size:24
Alignment explanation
Indices: 40070479--40070565 Score: 68
Period size: 24 Copynumber: 3.5 Consensus size: 24
40070469 ATTTTTTTCA
* *
40070479 TTCTCAATTTCTTTTTCAATTTTCTT
1 TTCTCATTTTCTTTTTCAA-TCTC-T
** *
40070505 TTCTTCATTTTCTTTTTCTCTCACT
1 TTC-TCATTTTCTTTTTCAATCTCT
*
40070530 TTTTCGA-TTTCTTTTTCAATCTCT
1 TTCTC-ATTTTCTTTTTCAATCTCT
*
40070554 TTCTCCTTTTCT
1 TTCTCATTTTCT
40070566 CGCTCAATGG
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
24 25 0.53
25 4 0.09
26 5 0.11
27 13 0.28
ACGTcount: A:0.10, C:0.24, G:0.01, T:0.64
Consensus pattern (24 bp):
TTCTCATTTTCTTTTTCAATCTCT
Found at i:40071610 original size:12 final size:11
Alignment explanation
Indices: 40071587--40071630 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
40071577 TTGTCACTTC
40071587 TTTTTTTC--T
1 TTTTTTTCAAT
40071596 TTTTTTTCAAT
1 TTTTTTTCAAT
*
40071607 TTTTTTTGAAT
1 TTTTTTTCAAT
*
40071618 TTTTTTTGAAT
1 TTTTTTTCAAT
40071629 TT
1 TT
40071631 CTTCTCTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 8 0.25
11 24 0.75
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.77
Consensus pattern (11 bp):
TTTTTTTCAAT
Found at i:40071733 original size:11 final size:12
Alignment explanation
Indices: 40071717--40071746 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
40071707 CCAACTCAAA
40071717 TTTTTTTTGA-T
1 TTTTTTTTGACT
40071728 TTTTTTTTGACT
1 TTTTTTTTGACT
40071740 TTTTTTT
1 TTTTTTT
40071747 CGTTACGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (12 bp):
TTTTTTTTGACT
Found at i:40074754 original size:20 final size:19
Alignment explanation
Indices: 40074731--40074795 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
40074721 AAGCTCAAAC
40074731 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
40074751 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
40074771 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
40074791 GAGCT
1 GAGCT
40074796 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:40076245 original size:18 final size:18
Alignment explanation
Indices: 40076218--40076267 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
40076208 CAAACTCTTT
40076218 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
40076236 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
40076254 TCAATCTCTTTTTC
1 TCATTCTCTTTTTC
40076268 TTTGTCTTTC
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:0.14, C:0.28, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:40077357 original size:19 final size:19
Alignment explanation
Indices: 40077316--40077356 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
40077306 TATGTTCAAA
40077316 TTTTCAGATTTTGTTTTTT
1 TTTTCAGATTTTGTTTTTT
40077335 TTTTCA-ATTTT-TTTTCTT
1 TTTTCAGATTTTGTTTT-TT
40077353 TTTT
1 TTTT
40077357 TTTGAAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.19
18 11 0.52
19 6 0.29
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.78
Consensus pattern (19 bp):
TTTTCAGATTTTGTTTTTT
Found at i:40087100 original size:13 final size:13
Alignment explanation
Indices: 40087082--40087106 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40087072 GTATTGATCA
40087082 TGTGTTCACACCT
1 TGTGTTCACACCT
40087095 TGTGTTCACACC
1 TGTGTTCACACC
40087107 ATGATGACCA
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:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:40088302 original size:6 final size:6
Alignment explanation
Indices: 40088291--40088316 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
40088281 AGTTGTAAAG
40088291 TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TT
40088317 ATTTATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:40097501 original size:14 final size:14
Alignment explanation
Indices: 40097459--40097503 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
40097449 TTAAAGAAGC
40097459 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
40097473 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
40097486 AACTCATTTAATTA
1 AACTCATTAAATTA
40097500 AACT
1 AACT
40097504 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:40099990 original size:24 final size:24
Alignment explanation
Indices: 40099963--40100031 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 24
40099953 TTCACATTCT
*
40099963 TTCTCTCTCTCAAACTCTTTTTCA
1 TTCTCTCTCTCAATCTCTTTTTCA
* * * *
40099987 TTCTCTTTTTCAATCTCATTTTCT
1 TTCTCTCTCTCAATCTCTTTTTCA
* *
40100011 TTTTCACTCTCAATCTCTTTT
1 TTCTCTCTCTCAATCTCTTTT
40100032 CTTTATCTTT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.14, C:0.29, G:0.00, T:0.57
Consensus pattern (24 bp):
TTCTCTCTCTCAATCTCTTTTTCA
Found at i:40100005 original size:18 final size:18
Alignment explanation
Indices: 40099984--40100031 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
40099974 AAACTCTTTT
40099984 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
40100002 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
40100020 TCAATCTCTTTT
1 TCATTCTCTTTT
40100032 CTTTATCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.15, C:0.27, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:40101408 original size:29 final size:29
Alignment explanation
Indices: 40101342--40101398 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
40101332 GATTCAAAGA
*
40101342 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
* *
40101371 TGGGTTTATGGATGTAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
40101399 GTTTGGTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.46
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:40102420 original size:14 final size:14
Alignment explanation
Indices: 40102378--40102422 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
40102368 TTAAAGAAGC
40102378 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
40102392 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
40102405 AACTCATTTAATTA
1 AACTCATTAAATTA
40102419 AACT
1 AACT
40102423 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:40103551 original size:30 final size:30
Alignment explanation
Indices: 40103526--40103613 Score: 113
Period size: 30 Copynumber: 2.9 Consensus size: 30
40103516 CTAGCTTATA
40103526 TTTAGCTCACGAGCTAAACCTTAGCTCAAC
1 TTTAGCTCACGAGCTAAACCTTAGCTCAAC
* * * * * *
40103556 TTCAGCTTAGGAGTTTAACCTCAGCTCAAC
1 TTTAGCTCACGAGCTAAACCTTAGCTCAAC
*
40103586 TTTAGCTCACGAGCTAAAACTTAGCTCA
1 TTTAGCTCACGAGCTAAACCTTAGCTCA
40103614 TTTTAGTTTA
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (30 bp):
TTTAGCTCACGAGCTAAACCTTAGCTCAAC
Found at i:40104543 original size:22 final size:20
Alignment explanation
Indices: 40104511--40104559 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
40104501 GCCGAATTTA
40104511 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
40104534 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
40104554 TGAACA
1 TGAACA
40104560 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:40106858 original size:13 final size:12
Alignment explanation
Indices: 40106840--40106877 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
40106830 AAAGGAGAAG
40106840 AAATTCAGAAAAA
1 AAATTCA-AAAAA
40106853 AAATTC-AAAAA
1 AAATTCAAAAAA
40106864 AAA-TCAAAAAA
1 AAATTCAAAAAA
40106875 AAA
1 AAA
40106878 GGAAAAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.08
11 16 0.67
13 6 0.25
ACGTcount: A:0.76, C:0.08, G:0.03, T:0.13
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:40107864 original size:37 final size:37
Alignment explanation
Indices: 40107813--40107883 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
40107803 CATTCTTGTA
40107813 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
40107850 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
40107884 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:40107883 original size:6 final size:6
Alignment explanation
Indices: 40107823--40107872 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
40107813 AAGAGAAAAC
*
40107823 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
40107872 A
1 A
40107873 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:40107965 original size:11 final size:12
Alignment explanation
Indices: 40107933--40107963 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
40107923 TTGAGAGAAC
40107933 TTGAAAAAGCCT
1 TTGAAAAAGCCT
40107945 TTGAAAAAGCCT
1 TTGAAAAAGCCT
40107957 TTGAAAA
1 TTGAAAA
40107964 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:40110176 original size:30 final size:30
Alignment explanation
Indices: 40110142--40110238 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
40110132 AGCTCACTCC
40110142 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
40110172 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
40110202 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
40110232 TAGCTCA
1 TAGCTCA
40110239 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:40111168 original size:22 final size:20
Alignment explanation
Indices: 40111136--40111184 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
40111126 GCCGAATTTA
40111136 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
40111159 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
40111179 TGAACA
1 TGAACA
40111185 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:40114637 original size:15 final size:14
Alignment explanation
Indices: 40114617--40114669 Score: 72
Period size: 13 Copynumber: 3.7 Consensus size: 14
40114607 ATAGGTACGT
*
40114617 AAAAAAAAAGTTTG
1 AAAAAAAAAATTTG
40114631 AAAAAAAAAA-TTG
1 AAAAAAAAAATTTG
40114644 AAAAAAAAAATTTTG
1 AAAAAAAAAA-TTTG
40114659 AAAAGAAAAAA
1 AAAA-AAAAAA
40114670 AAATTGCATA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
13 13 0.37
14 9 0.26
15 7 0.20
16 6 0.17
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (14 bp):
AAAAAAAAAATTTG
Found at i:40115832 original size:17 final size:18
Alignment explanation
Indices: 40115800--40115833 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40115790 AAAAGAGAGT
*
40115800 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
40115818 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
40115834 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:40120823 original size:27 final size:26
Alignment explanation
Indices: 40120761--40120872 Score: 107
Period size: 27 Copynumber: 4.2 Consensus size: 26
40120751 AGCATGGCTG
* * *
40120761 CCAGAACAGATAATGAGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
40120787 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
* **
40120815 CTAGAACAGATATATGTGGTGGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
40120842 CCAGATCAGACAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
40120869 CCAG
1 CCAG
40120873 GACCCTTCCT
Statistics
Matches: 70, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
26 6 0.09
27 49 0.70
28 15 0.21
ACGTcount: A:0.37, C:0.22, G:0.25, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:40121040 original size:28 final size:26
Alignment explanation
Indices: 40120978--40121040 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
40120968 AAAGTAACCC
** * *
40120978 TAGGGGTATAATGGTAATTTTGCACC
1 TAGGGGTATAACAGTAATTTTCCACA
40121004 TAGGGGTATAACAGTAATTTTCCATACA
1 TAGGGGTATAACAGTAATTTTCC--ACA
40121032 TAGGGGTAT
1 TAGGGGTAT
40121041 TCAAGTAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 20 0.65
28 11 0.35
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.33
Consensus pattern (26 bp):
TAGGGGTATAACAGTAATTTTCCACA
Found at i:40124051 original size:30 final size:30
Alignment explanation
Indices: 40124017--40124113 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
40124007 TAAACTAAAA
*
40124017 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
40124047 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
*
40124077 TGAGCTAAGGTTTAGCTTGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
40124106 ATGAGCTA
1 -TGAGCTA
40124114 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:40126387 original size:6 final size:6
Alignment explanation
Indices: 40126371--40126420 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
40126361 TTTCTTTTTA
*
40126371 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
40126420 T
1 T
40126421 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:40126403 original size:37 final size:37
Alignment explanation
Indices: 40126360--40126430 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
40126350 CTTGCCTCTC
40126360 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
40126397 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
40126431 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:40126431 original size:16 final size:16
Alignment explanation
Indices: 40126356--40126416 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
40126346 GCCTCTTGCC
*
40126356 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
40126372 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
40126388 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
40126404 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
40126417 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:40127372 original size:17 final size:16
Alignment explanation
Indices: 40127309--40127372 Score: 51
Period size: 17 Copynumber: 3.9 Consensus size: 16
40127299 CTCACAAGAC
*
40127309 TTTTCACTTTTGTTTTT
1 TTTTAACTTTT-TTTTT
40127326 TTTT--CTTTTTCTTTT
1 TTTTAACTTTTT-TTTT
**
40127341 TTTTAACTCGATTTTTT
1 TTTTAACT-TTTTTTTT
*
40127358 TTGTAACTTTTTTTT
1 TTTTAACTTTTTTTT
40127373 CCTTTTTTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
14 1 0.03
15 13 0.34
16 5 0.13
17 17 0.45
18 2 0.05
ACGTcount: A:0.09, C:0.11, G:0.05, T:0.75
Consensus pattern (16 bp):
TTTTAACTTTTTTTTT
Found at i:40127390 original size:12 final size:13
Alignment explanation
Indices: 40127375--40127413 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
40127365 TTTTTTTTCC
40127375 TTTTTTTCG-ATT
1 TTTTTTTCGAATT
40127387 TTTTTTT-GAATT
1 TTTTTTTCGAATT
40127399 TTTTTTTCTGAATT
1 TTTTTTTC-GAATT
40127413 T
1 T
40127414 CTTCTCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.04
12 17 0.71
14 6 0.25
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (13 bp):
TTTTTTTCGAATT
Found at i:40127402 original size:14 final size:14
Alignment explanation
Indices: 40127385--40127413 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
40127375 TTTTTTTCGA
40127385 TTTTTTTT-TGAAT
1 TTTTTTTTCTGAAT
40127398 TTTTTTTTCTGAAT
1 TTTTTTTTCTGAAT
40127412 TT
1 TT
40127414 CTTCTCCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.14, C:0.03, G:0.07, T:0.76
Consensus pattern (14 bp):
TTTTTTTTCTGAAT
Found at i:40129164 original size:30 final size:30
Alignment explanation
Indices: 40129130--40129226 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
40129120 TAAACTAAAA
*
40129130 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
40129160 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
*
40129190 TGAGCTAAGGTTTAGCTTGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
40129219 ATGAGCTA
1 -TGAGCTA
40129227 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:40130667 original size:16 final size:16
Alignment explanation
Indices: 40130642--40130673 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40130632 CTAAAAGAAA
40130642 AAGAAAAGATGAGCAG
1 AAGAAAAGATGAGCAG
*
40130658 AAGAAGAGATGAGCAG
1 AAGAAAAGATGAGCAG
40130674 GGAGTTCGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.34, T:0.06
Consensus pattern (16 bp):
AAGAAAAGATGAGCAG
Found at i:40138194 original size:13 final size:12
Alignment explanation
Indices: 40138176--40138251 Score: 55
Period size: 13 Copynumber: 5.8 Consensus size: 12
40138166 TATGCAATTT
40138176 TTTTTTTTTGCAA
1 TTTTTTTTT-CAA
**
40138189 TTTTTTTTTCCTTC
1 TTTTTTTTT-C-AA
40138203 TTTTTTTTTCAGA
1 TTTTTTTTTCA-A
40138216 TTTTTTTTTCGAAA
1 TTTTTTTTTC--AA
40138230 CTTTTTTTTT-AA
1 -TTTTTTTTTCAA
40138242 CTTTTTTTTT
1 -TTTTTTTTT
40138252 TGAAGCTACG
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
12 12 0.23
13 21 0.40
14 10 0.19
15 10 0.19
ACGTcount: A:0.12, C:0.11, G:0.04, T:0.74
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:40141475 original size:22 final size:22
Alignment explanation
Indices: 40141445--40141488 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
40141435 TTTGGTATTT
40141445 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
40141467 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
40141489 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:40145925 original size:68 final size:64
Alignment explanation
Indices: 40145815--40146055 Score: 177
Period size: 68 Copynumber: 3.7 Consensus size: 64
40145805 ATACAGATGG
* * *
40145815 TATGTAGCTAGGTCACATGTATAGTGCTAAGTGCACATCATGT-GTACAAGAGAGCTACAAGACA
1 TATGTAGCTAGGTCACATGGATAGTACTAAGTGCACACCATGTAG-ACAAGAGAGCTAC--GACA
40145879 TTA
63 -TA
* * * **
40145882 TGATGTAGCTAGGTCACATGGGT-GATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGAT
1 T-ATGTAGCTAGGTCACATGGATAG-TACTAAGTGCACACCATGTAGACAAGAGAGCTACGACAT
40145946 A
64 A
* * * * * *
40145947 TATGTAGCTAGGTCACATGCG-TGGTTCCAAGTGAAGGACACCATGAAGACAAGAGAGCTACGAG
1 TATGTAGCTAGGTCACATG-GATAGTACTAAGT---GCACACCATGTAGACAAGAGAGCTACGAC
40146011 ATA
62 ATA
* * * **
40146014 AACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT
1 TA-TGTAGCTAGGTCACATGGATAGTACTAAGTGCACACCATGT
40146056 GTACAAAAGA
Statistics
Matches: 144, Mismatches: 20, Indels: 24
0.77 0.11 0.13
Matches are distributed among these distances:
63 8 0.06
64 24 0.17
65 6 0.04
66 24 0.17
67 32 0.22
68 49 0.34
69 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (64 bp):
TATGTAGCTAGGTCACATGGATAGTACTAAGTGCACACCATGTAGACAAGAGAGCTACGACATA
Found at i:40149791 original size:35 final size:35
Alignment explanation
Indices: 40149745--40149815 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
40149735 CTAAGCTAGT
40149745 TGAACAGATCATCAATCCTTAGCAGTGGATACTTA
1 TGAACAGATCATCAATCCTTAGCAGTGGATACTTA
40149780 TGAACAGATCATCAATCCTTAGCAGTGGATACTTA
1 TGAACAGATCATCAATCCTTAGCAGTGGATACTTA
40149815 T
1 T
40149816 TCTTAATCGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Consensus pattern (35 bp):
TGAACAGATCATCAATCCTTAGCAGTGGATACTTA
Found at i:40152525 original size:17 final size:18
Alignment explanation
Indices: 40152503--40152536 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40152493 ACAACACTCC
*
40152503 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
40152520 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
40152537 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:40152644 original size:15 final size:16
Alignment explanation
Indices: 40152619--40152650 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
40152609 TATCTCACAC
40152619 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
40152635 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
40152650 T
1 T
40152651 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:40153602 original size:31 final size:28
Alignment explanation
Indices: 40153558--40153632 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 28
40153548 CTCGCAAGAC
*
40153558 TTTTCACTTTTTTTTTAACTTGATTTTT
1 TTTTCACTTTTTTTTTAACTCGATTTTT
**
40153586 TTTGCTCACCTTTTTTTTTTGCTCGATTTTT
1 TTT--TCA-CTTTTTTTTTAACTCGATTTTT
40153617 TTTTCACTTTTTTTTT
1 TTTTCACTTTTTTTTT
40153633 GAATTTTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 13 0.32
29 3 0.07
30 3 0.07
31 22 0.54
ACGTcount: A:0.09, C:0.15, G:0.05, T:0.71
Consensus pattern (28 bp):
TTTTCACTTTTTTTTTAACTCGATTTTT
Found at i:40153615 original size:16 final size:16
Alignment explanation
Indices: 40153581--40153620 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
40153571 TTTAACTTGA
40153581 TTTTTTTTGCTCACCTT
1 TTTTTTTTGCTCA-CTT
40153598 TTTTTTTTGCTCGA-TT
1 TTTTTTTTGCTC-ACTT
40153614 TTTTTTT
1 TTTTTTT
40153621 CACTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.41
17 12 0.55
18 1 0.05
ACGTcount: A:0.05, C:0.15, G:0.07, T:0.72
Consensus pattern (16 bp):
TTTTTTTTGCTCACTT
Found at i:40153627 original size:12 final size:12
Alignment explanation
Indices: 40153611--40153685 Score: 53
Period size: 13 Copynumber: 5.8 Consensus size: 12
40153601 TTTTTGCTCG
40153611 ATTTTTTTTTCA
1 ATTTTTTTTTCA
* *
40153623 CTTTTTTTTTGA
1 ATTTTTTTTTCA
40153635 ATTTTTTATTTCAATCA
1 A-TTTTT-TTT---TCA
40153652 ATTTTTTTTTTCGA
1 A-TTTTTTTTTC-A
*
40153666 ATTTTTTTTT-G
1 ATTTTTTTTTCA
40153677 ATTTTTTTT
1 ATTTTTTTT
40153686 GTTACTCCAA
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
11 9 0.17
12 10 0.19
13 16 0.31
14 5 0.10
16 3 0.06
17 9 0.17
ACGTcount: A:0.16, C:0.07, G:0.04, T:0.73
Consensus pattern (12 bp):
ATTTTTTTTTCA
Found at i:40153640 original size:13 final size:13
Alignment explanation
Indices: 40153624--40153685 Score: 56
Period size: 13 Copynumber: 4.5 Consensus size: 13
40153614 TTTTTTTCAC
40153624 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
*
40153637 TTTTTATTTCAATCAAT
1 TTTTT-TTT---TGAAT
40153654 TTTTTTTTTCGAA-
1 TTTTTTTTT-GAAT
40153667 TTTTTTTTTG-AT
1 TTTTTTTTTGAAT
40153679 TTTTTTT
1 TTTTTTT
40153686 GTTACTCCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
11 1 0.02
12 8 0.20
13 15 0.37
14 5 0.12
16 3 0.07
17 9 0.22
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:40153680 original size:11 final size:13
Alignment explanation
Indices: 40153598--40153685 Score: 60
Period size: 12 Copynumber: 6.6 Consensus size: 13
40153588 TGCTCACCTT
40153598 TTTTTTTTGCTCG-A
1 TTTTTTTT--TCGAA
*
40153612 TTTTTTTTTC-AC
1 TTTTTTTTTCGAA
40153624 TTTTTTTTT-GAA
1 TTTTTTTTTCGAA
*
40153636 TTTTTTATTTCAATCAA
1 TTTTTT-TTTC---GAA
40153653 TTTTTTTTTTCGAA
1 -TTTTTTTTTCGAA
40153667 TTTTTTTTT-G-A
1 TTTTTTTTTCGAA
40153678 TTTTTTTT
1 TTTTTTTT
40153686 GTTACTCCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 19
0.73 0.05 0.22
Matches are distributed among these distances:
11 9 0.15
12 19 0.31
13 12 0.19
14 10 0.16
17 6 0.10
18 6 0.10
ACGTcount: A:0.14, C:0.08, G:0.06, T:0.73
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:40158546 original size:13 final size:12
Alignment explanation
Indices: 40158530--40158574 Score: 63
Period size: 13 Copynumber: 3.6 Consensus size: 12
40158520 ACGGTATTGT
40158530 AAAAAAAATATAA
1 AAAAAAAAT-TAA
*
40158543 AAAAAAATTTGAA
1 AAAAAAAATT-AA
40158556 AAAAAAAATTAA
1 AAAAAAAATTAA
40158568 AAAAAAA
1 AAAAAAA
40158575 GTTTGTATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.34
13 19 0.66
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTAA
Found at i:40158547 original size:12 final size:12
Alignment explanation
Indices: 40158530--40158574 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
40158520 ACGGTATTGT
40158530 AAAAAAAATATA
1 AAAAAAAATATA
*
40158542 AAAAAAAATTTGA
1 AAAAAAAATAT-A
40158555 AAAAAAAA-ATTA
1 AAAAAAAATA-TA
40158567 AAAAAAAA
1 AAAAAAAA
40158575 GTTTGTATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 19 0.66
13 10 0.34
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (12 bp):
AAAAAAAATATA
Found at i:40158564 original size:26 final size:26
Alignment explanation
Indices: 40158530--40158579 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
40158520 ACGGTATTGT
40158530 AAAAAAAATATAAAAAAAAA-TTTGAA
1 AAAAAAAAT-TAAAAAAAAAGTTTGAA
40158556 AAAAAAAATTAAAAAAAAAGTTTG
1 AAAAAAAATTAAAAAAAAAGTTTG
40158580 TATTCAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (26 bp):
AAAAAAAATTAAAAAAAAAGTTTGAA
Found at i:40158668 original size:33 final size:33
Alignment explanation
Indices: 40158626--40158688 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
40158616 AAGAAAAAAA
**
40158626 AAGAAAAAAAAATTCGGAATT-AAAAAAAAAGGG
1 AAGAAAAAAAAA-TCAAAATTGAAAAAAAAAGGG
40158659 AAGAAAAAAAAATCAAAATTGAAAAAAAAA
1 AAGAAAAAAAAATCAAAATTGAAAAAAAAA
40158689 AGAGTGATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 6 0.22
33 21 0.78
ACGTcount: A:0.73, C:0.03, G:0.13, T:0.11
Consensus pattern (33 bp):
AAGAAAAAAAAATCAAAATTGAAAAAAAAAGGG
Found at i:40159617 original size:21 final size:21
Alignment explanation
Indices: 40159577--40159635 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
40159567 AATCTTGAAT
*
40159577 GAAATTGAGAGAAGAA-AAAAA
1 GAAA-TGAGAGAAAAAGAAAAA
40159598 GAAATGAGAGAAAAAGAAAAA
1 GAAATGAGAGAAAAAGAAAAA
* *
40159619 GAAATAAAAGAAAAAGA
1 GAAATGAGAGAAAAAGA
40159636 TGAAAATGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 10 0.29
21 24 0.71
ACGTcount: A:0.71, C:0.00, G:0.22, T:0.07
Consensus pattern (21 bp):
GAAATGAGAGAAAAAGAAAAA
Found at i:40159627 original size:15 final size:14
Alignment explanation
Indices: 40159588--40159635 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
40159578 AAATTGAGAG
40159588 AAGAAAAAAAGAAA
1 AAGAAAAAAAGAAA
* *
40159602 TGAGAGAAAAAGAAA
1 -AAGAAAAAAAGAAA
40159617 AAGAAATAAAAGAAA
1 AAGAAA-AAAAGAAA
40159632 AAGA
1 AAGA
40159636 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (14 bp):
AAGAAAAAAAGAAA
Found at i:40167941 original size:27 final size:27
Alignment explanation
Indices: 40167910--40167982 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 27
40167900 TCTTCTTCAA
40167910 CATCTTTTTCTTTTTCAATTTT-TTCT
1 CATCTTTTTCTTTTTCAATTTTCTTCT
* *
40167936 CAATCTCAATTTCTTTTTCAATTTTCTTTT
1 C-ATCT--TTTTCTTTTTCAATTTTCTTCT
* *
40167966 CTTCATTTTCTTTTTCA
1 CATCTTTTTCTTTTTCA
40167983 CTACAATGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.03
27 15 0.39
29 18 0.47
30 4 0.11
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (27 bp):
CATCTTTTTCTTTTTCAATTTTCTTCT
Found at i:40167946 original size:17 final size:18
Alignment explanation
Indices: 40167924--40167957 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40167914 TTTTTCTTTT
40167924 TCAATTT-TTTCTCAATC
1 TCAATTTCTTTCTCAATC
*
40167941 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTCTCAAT
40167958 TTTCTTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.56
Consensus pattern (18 bp):
TCAATTTCTTTCTCAATC
Found at i:40171988 original size:18 final size:18
Alignment explanation
Indices: 40171967--40172001 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
40171957 TTTTTCTTTT
40171967 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
40171985 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
40172002 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:40172889 original size:31 final size:29
Alignment explanation
Indices: 40172844--40172915 Score: 85
Period size: 31 Copynumber: 2.5 Consensus size: 29
40172834 CTCGCAAGAC
*
40172844 TTTTCAC--TTTTTTTTAACTTGATTTTT
1 TTTTCACTTTTTTTTTTAACTGGATTTTT
**
40172871 TTTGTCACCTTTTTTTTTTTGCTGGATTTTT
1 TTT-TCA-CTTTTTTTTTTAACTGGATTTTT
40172902 TTTTCACTTTTTTT
1 TTTTCACTTTTTTT
40172916 GAATTTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
27 3 0.08
28 3 0.08
29 9 0.24
30 3 0.08
31 20 0.53
ACGTcount: A:0.10, C:0.12, G:0.07, T:0.71
Consensus pattern (29 bp):
TTTTCACTTTTTTTTTTAACTGGATTTTT
Found at i:40179668 original size:45 final size:45
Alignment explanation
Indices: 40179619--40179813 Score: 291
Period size: 45 Copynumber: 4.3 Consensus size: 45
40179609 TCGGCCATGG
* * * *
40179619 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
* *
40179664 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
* * * *
40179709 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAG
1 TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
*
40179754 TGCTTCCTTAATTTGTTCCATAAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
40179799 TGCTTCCTTAATTTC
1 TGCTTCCTTAATTTC
40179814 ATGCCGTTCA
Statistics
Matches: 136, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 136 1.00
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (45 bp):
TGCTTCCTTAATTTCTTCCATAAATTATGCATGATGTTGGTCAAA
Found at i:40180171 original size:20 final size:20
Alignment explanation
Indices: 40180146--40180200 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
40180136 ACGAGTTAAA
* *
40180146 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
40180166 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
40180186 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
40180201 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:40185186 original size:21 final size:22
Alignment explanation
Indices: 40185160--40185203 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
40185150 AAACGAGCTC
40185160 GTTGAGCTAAGTTGAG-TTGAA
1 GTTGAGCTAAGTTGAGCTTGAA
* *
40185181 GTTGAGCTGATTTGAGCTTGAA
1 GTTGAGCTAAGTTGAGCTTGAA
40185203 G
1 G
40185204 GAGTATGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.25, C:0.07, G:0.34, T:0.34
Consensus pattern (22 bp):
GTTGAGCTAAGTTGAGCTTGAA
Found at i:40187165 original size:27 final size:26
Alignment explanation
Indices: 40187125--40187236 Score: 134
Period size: 27 Copynumber: 4.2 Consensus size: 26
40187115 TGCATGGCTG
* *
40187125 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
* *
40187151 CCAGATACAGATAATCTTGGTAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
40187179 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
40187206 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
40187233 CCAG
1 CCAG
40187237 GACGCTTCCT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
26 6 0.08
27 53 0.72
28 15 0.20
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:40187189 original size:54 final size:54
Alignment explanation
Indices: 40187125--40187236 Score: 156
Period size: 54 Copynumber: 2.1 Consensus size: 54
40187115 TGCATGGCTG
* *
40187125 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCT-TGGTAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAAT-TGTGGCAGAGCCA
* *
40187179 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATTGTGGCAGAGCCA
40187233 CCAG
1 CCAG
40187237 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
53 1 0.02
54 33 0.63
55 18 0.35
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATTGTGGCAGAGCCA
Found at i:40187404 original size:28 final size:26
Alignment explanation
Indices: 40187342--40187404 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
40187332 AAAGTAACCC
** * *
40187342 TAGGGGTATAATGGTAATTTTGCACC
1 TAGGGGTATAACAGTAATTTTCCACA
40187368 TAGGGGTATAACAGTAATTTTCCATACA
1 TAGGGGTATAACAGTAATTTTCC--ACA
40187396 TAGGGGTAT
1 TAGGGGTAT
40187405 TCAAGTAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 20 0.65
28 11 0.35
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.33
Consensus pattern (26 bp):
TAGGGGTATAACAGTAATTTTCCACA
Found at i:40194727 original size:14 final size:14
Alignment explanation
Indices: 40194699--40194740 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
40194689 CTTTTCTTTC
*
40194699 TTTTCTTTTCACTCT
1 TTTTCTTTT-TCTCT
*
40194714 TTTTGTTTTTCTCT
1 TTTTCTTTTTCTCT
40194728 TTTTCTTTTTCTC
1 TTTTCTTTTTCTC
40194741 GCTCAATAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTTCTTTTTCTCT
Found at i:40198977 original size:12 final size:12
Alignment explanation
Indices: 40198944--40199024 Score: 53
Period size: 12 Copynumber: 6.8 Consensus size: 12
40198934 TTTCCACTCG
40198944 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
40198955 AGCTCTCTTTCA
1 ATTTCTTTTTCA
40198967 ATTTCTTTTTCCA
1 ATTTCTTTTT-CA
*
40198980 CTCTTTCTTTTTC-
1 --ATTTCTTTTTCA
*
40198993 --TTCTCTTTCA
1 ATTTCTTTTTCA
40199003 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
40199015 ATCTCTTTTT
1 ATTTCTTTTT
40199025 GCTTTTCACT
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
9 8 0.15
11 3 0.06
12 30 0.57
13 2 0.04
14 1 0.02
15 9 0.17
ACGTcount: A:0.12, C:0.25, G:0.01, T:0.62
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:40198985 original size:21 final size:20
Alignment explanation
Indices: 40198959--40199014 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 20
40198949 TTTTCAAGCT
40198959 CTCTTTCAATTTCTTTTTCCA
1 CTCTTTCAATTTCTTTTT-CA
*
40198980 CTCTTTC--TTT-TTCTT--
1 CTCTTTCAATTTCTTTTTCA
40198995 CTCTTTCAATTTCTTTTTCA
1 CTCTTTCAATTTCTTTTTCA
40199015 ATCTCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
15 7 0.25
17 3 0.11
18 8 0.29
19 3 0.11
21 7 0.25
ACGTcount: A:0.11, C:0.27, G:0.00, T:0.62
Consensus pattern (20 bp):
CTCTTTCAATTTCTTTTTCA
Found at i:40199075 original size:14 final size:15
Alignment explanation
Indices: 40199053--40199098 Score: 60
Period size: 14 Copynumber: 3.1 Consensus size: 15
40199043 TTTTGAAATC
40199053 TCATTTTCATATT-TT
1 TCATTTTCAT-TTCTT
40199068 TC-TTTTCATTTCTT
1 TCATTTTCATTTCTT
40199082 TCATTTTCATTTTCTT
1 TCATTTTCA-TTTCTT
40199098 T
1 T
40199099 ATTCTTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.07
14 11 0.39
15 8 0.29
16 7 0.25
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (15 bp):
TCATTTTCATTTCTT
Found at i:40200174 original size:21 final size:20
Alignment explanation
Indices: 40200144--40200182 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
40200134 CTTTTCACTT
*
40200144 CTTTTTTTTCTTCTTTTTTTA
1 CTTTTGTTTCTT-TTTTTTTA
40200165 CTTTTGTTTCTTTTTTTT
1 CTTTTGTTTCTTTTTTTT
40200183 GCTCATTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.03, C:0.13, G:0.03, T:0.82
Consensus pattern (20 bp):
CTTTTGTTTCTTTTTTTTTA
Found at i:40201788 original size:20 final size:20
Alignment explanation
Indices: 40201765--40201811 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
40201755 GGGTTAAAAT
40201765 TGAGCTGAATTGAGCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
* *
40201785 TGAGCTTACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
40201805 TGAGCTG
1 TGAGCTG
40201812 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:40203368 original size:38 final size:38
Alignment explanation
Indices: 40203317--40203393 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
40203307 CGCATTTCAT
40203317 AGCCTGCACAAAAAATAACGATGCGGTTCATGTTTCTA
1 AGCCTGCACAAAAAATAACGATGCGGTTCATGTTTCTA
*
40203355 AGCCTGCACAAAAAATGACGATGCGGTTCATGTTTCTA
1 AGCCTGCACAAAAAATAACGATGCGGTTCATGTTTCTA
40203393 A
1 A
40203394 CTTATTCTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (38 bp):
AGCCTGCACAAAAAATAACGATGCGGTTCATGTTTCTA
Found at i:40210103 original size:13 final size:12
Alignment explanation
Indices: 40210085--40210127 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
40210075 AAAATTCATA
40210085 TTTTTTTTAAAT
1 TTTTTTTTAAAT
*
40210097 CTTTTTTTTAGAT
1 -TTTTTTTTAAAT
*
40210110 TTTTTTTCAAAT
1 TTTTTTTTAAAT
40210122 ATTTTT
1 -TTTTT
40210128 AATATATTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (12 bp):
TTTTTTTTAAAT
Found at i:40210136 original size:25 final size:24
Alignment explanation
Indices: 40210082--40210136 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
40210072 AAAAAAATTC
* **
40210082 ATATTTTTTTTAAATCTTTTTTTT
1 ATATTTTTTTTAAATATTTTTAAT
*
40210106 AGATTTTTTTTCAAATATTTTTAAT
1 ATATTTTTTTT-AAATATTTTTAAT
40210131 ATATTT
1 ATATTT
40210137 CAATACAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (24 bp):
ATATTTTTTTTAAATATTTTTAAT
Found at i:40210194 original size:12 final size:11
Alignment explanation
Indices: 40210172--40210196 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40210162 TAAAAACAAA
40210172 TACTATTTTTT
1 TACTATTTTTT
40210183 TACTATTTTTT
1 TACTATTTTTT
40210194 TAC
1 TAC
40210197 AAACTTACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (11 bp):
TACTATTTTTT
Found at i:40211518 original size:18 final size:19
Alignment explanation
Indices: 40211478--40211523 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
40211468 TTTGTCCAAT
*
40211478 TTTAAAC-AAATTAATTAA
1 TTTAAACTAAATTAACTAA
*
40211496 CTTAAACTAAA-TAACTAA
1 TTTAAACTAAATTAACTAA
40211514 TTT-AACTAAA
1 TTTAAACTAAA
40211524 AGCAAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 7 0.29
18 14 0.58
19 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (19 bp):
TTTAAACTAAATTAACTAA
Found at i:40215222 original size:13 final size:13
Alignment explanation
Indices: 40215173--40215223 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
40215163 AAGTATGTAA
40215173 ATCTGTTATTTCTGT
1 ATCTG-TATTT-TGT
* *
40215188 ATTTGTATATTGT
1 ATCTGTATTTTGT
*
40215201 ATATGTATTTTGT
1 ATCTGTATTTTGT
40215214 ATCTGTATTT
1 ATCTGTATTT
40215224 GGGGTGGGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
13 23 0.74
14 4 0.13
15 4 0.13
ACGTcount: A:0.20, C:0.06, G:0.14, T:0.61
Consensus pattern (13 bp):
ATCTGTATTTTGT
Found at i:40216392 original size:19 final size:19
Alignment explanation
Indices: 40216358--40216394 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
40216348 GGATTGATGT
* *
40216358 ATAAAATTTTATAATTTAG
1 ATAAAATTTGAAAATTTAG
40216377 ATAAAATTTGAAAATTTA
1 ATAAAATTTGAAAATTTA
40216395 CGATGAGCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (19 bp):
ATAAAATTTGAAAATTTAG
Found at i:40220008 original size:39 final size:40
Alignment explanation
Indices: 40219913--40220135 Score: 239
Period size: 39 Copynumber: 5.7 Consensus size: 40
40219903 TTGAATGATG
*
40219913 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAA-A
* * *
40219952 TCTGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAA
40219992 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* *
40220031 TCCGAGCTAAG-GCCGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* * *
40220070 TCCGGGTTAAGTTCCGAAGGCATTTGTGC-AAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTA-AA
*
40220111 T-CGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40220136 AACGAGGAGC
Statistics
Matches: 159, Mismatches: 16, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
39 91 0.57
40 54 0.34
41 13 0.08
42 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:40220157 original size:79 final size:79
Alignment explanation
Indices: 40219965--40220168 Score: 202
Period size: 79 Copynumber: 2.6 Consensus size: 79
40219955 GGACTAAGAT
** * * ** *
40219965 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCT-AAGCCCGAAGGCATTTGTGCGAGATACTA
1 CCGAAGGCATTTGAACGAGATACTAAATCCGGGTTAAATTCCGAAGGCATTTGTGCGAAATACTA
*
40220029 AATCCGAGCTAAGG
66 AATCCGAGCTAAGC
** *
40220043 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTTCCGAAGGCATTTGTGC-AAATTACT
1 CCGAAGGCATTTGAACGAGATACTAAATCCGGGTTAAATTCCGAAGGCATTTGTGCGAAA-TACT
* *
40220107 ATAAT-CGGGCTATGTC
65 A-AATCCGAGCTAAG-C
* *
40220123 CCGAAGGCATTTGAACGAGGA-GCTATATCC-GGTTAAATTCCGAAGG
1 CCGAAGGCATTTGAACGA-GATACTAAATCCGGGTTAAATTCCGAAGG
40220169 TACGTGATTT
Statistics
Matches: 107, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
78 35 0.33
79 44 0.41
80 26 0.24
81 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGAACGAGATACTAAATCCGGGTTAAATTCCGAAGGCATTTGTGCGAAATACTA
AATCCGAGCTAAGC
Found at i:40222514 original size:27 final size:27
Alignment explanation
Indices: 40222483--40222660 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
40222473 TAAATTGTAC
40222483 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
40222510 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40222536 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
40222564 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
40222592 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40222619 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
40222646 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40222661 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:40222597 original size:82 final size:81
Alignment explanation
Indices: 40222484--40222639 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40222474 AAATTGTACA
* *
40222484 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
40222548 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
40222565 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
40222630 TGCGAGTTGA
65 TGCGAATTGA
40222640 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:40222651 original size:82 final size:81
Alignment explanation
Indices: 40222480--40222660 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
40222470 GATTAAATTG
* *
40222480 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
40222545 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
40222561 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
40222625 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
40222643 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
40222661 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:40241115 original size:27 final size:26
Alignment explanation
Indices: 40241085--40241288 Score: 192
Period size: 27 Copynumber: 7.5 Consensus size: 26
40241075 AAATTGTACA
40241085 GCACTAAGTGTGCGATTCGACTATGTT
1 GCACTAAGTGTGCGATT-GACTATGTT
* *
40241112 GCACTAAGTGTGCGAAATGAATATGTT
1 GCACTAAGTGTGCG-ATTGACTATGTT
* * *
40241139 GCACTAAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCG-ATTGACTATGTT
* **
40241166 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCG-ATTGACTATGTT
*
40241193 GCACTAAGTGTGCGAGTCTGACTATGTA
1 GCACTAAGTGTGCGA-T-TGACTATGTT
* * *
40241221 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGA-TTGACTATGTT
* * *
40241248 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGA-TTGACTATGTT
*
40241275 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
40241289 GACTCGATAT
Statistics
Matches: 154, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
26 1 0.01
27 128 0.83
28 25 0.16
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (26 bp):
GCACTAAGTGTGCGATTGACTATGTT
Found at i:40241145 original size:54 final size:53
Alignment explanation
Indices: 40241085--40241288 Score: 221
Period size: 54 Copynumber: 3.8 Consensus size: 53
40241075 AAATTGTACA
* * *
40241085 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGTT
1 GCACTAAGTGTGCGATT-GACTATGTAGCACTAAGTGTGCGAATTGAATATGTG
* * ** *
40241139 GCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCG-ATTGACTATGTA-GCACTAAGTGTGCGAATTGAATATGTG
* * *
40241193 GCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGA-T-TGACTATGTAGCACTAAGTGTGCGAATTGAATATGTG
* * *
40241248 GCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAGTGTGCGA-TTGACTATGTAGCACTAAGTGTGCG
40241289 GACTCGATAT
Statistics
Matches: 127, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
53 1 0.01
54 77 0.61
55 48 0.38
56 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (53 bp):
GCACTAAGTGTGCGATTGACTATGTAGCACTAAGTGTGCGAATTGAATATGTG
Found at i:40241279 original size:109 final size:108
Alignment explanation
Indices: 40241085--40241288 Score: 284
Period size: 109 Copynumber: 1.9 Consensus size: 108
40241075 AAATTGTACA
* * * *
40241085 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGTTGCACTAAGTGT
1 GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
40241150 GCGAAATGAATATGATGCACTAAGTGTGCGAATTGACCATGCG
66 GCGAAATGAATATGATGCACTAAGTGTGCGAATTGACCATGCG
** *
40241193 GCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-GACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
** * *
40241258 TGCGAGTTGATTAT-ATAGCACTGAGTGTGCG
65 TGCGAAATGAATATGAT-GCACTAAGTGTGCG
40241289 GACTCGATAT
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
108 19 0.23
109 64 0.77
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (108 bp):
GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAAATGAATATGATGCACTAAGTGTGCGAATTGACCATGCG
Found at i:40244047 original size:18 final size:19
Alignment explanation
Indices: 40244024--40244062 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
40244014 GGGGTGTTCC
40244024 AAAGGTT-CACTTA-AAGAA
1 AAAGGTTGCA-TTACAAGAA
40244042 AAAGGTTGCATTACAAGAA
1 AAAGGTTGCATTACAAGAA
40244061 AA
1 AA
40244063 CCAAGACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.51, C:0.10, G:0.18, T:0.21
Consensus pattern (19 bp):
AAAGGTTGCATTACAAGAA
Found at i:40252646 original size:23 final size:23
Alignment explanation
Indices: 40252616--40252663 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
40252606 AAGACATTGT
40252616 TTAATTCTATTCAATGAATTTTC
1 TTAATTCTATTCAATGAATTTTC
40252639 TTAATTCTATTCAATGAATTTTC
1 TTAATTCTATTCAATGAATTTTC
40252662 TT
1 TT
40252664 GCTCATATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.54
Consensus pattern (23 bp):
TTAATTCTATTCAATGAATTTTC
Found at i:40253744 original size:15 final size:16
Alignment explanation
Indices: 40253713--40253747 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
40253703 CACACTTATT
40253713 TTCTCAATTTATTTTC
1 TTCTCAATTTATTTTC
*
40253729 TTCTCCATTT-TTTTC
1 TTCTCAATTTATTTTC
40253744 TTCT
1 TTCT
40253748 TTTTCTTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.11, C:0.23, G:0.00, T:0.66
Consensus pattern (16 bp):
TTCTCAATTTATTTTC
Found at i:40261008 original size:17 final size:17
Alignment explanation
Indices: 40260988--40261029 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
40260978 TCTATTCTTT
* *
40260988 ACTTGAATATATTGCAA
1 ACTTGAATATATCGAAA
40261005 ACTTG-ATATATCGAAA
1 ACTTGAATATATCGAAA
40261021 ACTTGAATA
1 ACTTGAATA
40261030 ATTTCTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (17 bp):
ACTTGAATATATCGAAA
Found at i:40262431 original size:29 final size:29
Alignment explanation
Indices: 40262360--40262431 Score: 69
Period size: 28 Copynumber: 2.6 Consensus size: 29
40262350 ATTCCATAGC
* * *
40262360 TTTTAAATTGTGTC-TTGTTATTACATAG
1 TTTTTAATTGTGTCTTTGTCATTACATAA
**
40262388 TTTTT-ATTACGTCTTTGTCATGT-CATAA
1 TTTTTAATTGTGTCTTTGTCAT-TACATAA
40262416 TTTTTAATTGTGTCTT
1 TTTTTAATTGTGTCTT
40262432 AGTTTGCAGC
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
27 6 0.18
28 19 0.56
29 9 0.26
ACGTcount: A:0.21, C:0.10, G:0.12, T:0.57
Consensus pattern (29 bp):
TTTTTAATTGTGTCTTTGTCATTACATAA
Found at i:40265322 original size:104 final size:104
Alignment explanation
Indices: 40265142--40265351 Score: 420
Period size: 104 Copynumber: 2.0 Consensus size: 104
40265132 CCAAAAATCG
40265142 GGGGTTAGCAAAATTGGGTTTGTGAAGTGAGAGAGAGTGGTCATTCCTTAATTTTTAAGATTATC
1 GGGGTTAGCAAAATTGGGTTTGTGAAGTGAGAGAGAGTGGTCATTCCTTAATTTTTAAGATTATC
40265207 TATGCATTTTTAGGAATTAAATGAGTTATTTGTTTAGTT
66 TATGCATTTTTAGGAATTAAATGAGTTATTTGTTTAGTT
40265246 GGGGTTAGCAAAATTGGGTTTGTGAAGTGAGAGAGAGTGGTCATTCCTTAATTTTTAAGATTATC
1 GGGGTTAGCAAAATTGGGTTTGTGAAGTGAGAGAGAGTGGTCATTCCTTAATTTTTAAGATTATC
40265311 TATGCATTTTTAGGAATTAAATGAGTTATTTGTTTAGTT
66 TATGCATTTTTAGGAATTAAATGAGTTATTTGTTTAGTT
40265350 GG
1 GG
40265352 TTAAGTGTTA
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 106 1.00
ACGTcount: A:0.28, C:0.06, G:0.26, T:0.41
Consensus pattern (104 bp):
GGGGTTAGCAAAATTGGGTTTGTGAAGTGAGAGAGAGTGGTCATTCCTTAATTTTTAAGATTATC
TATGCATTTTTAGGAATTAAATGAGTTATTTGTTTAGTT
Found at i:40277319 original size:18 final size:18
Alignment explanation
Indices: 40277296--40277343 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
40277286 AAACCCTAGA
40277296 ATTCTTTTGAATCTGATT
1 ATTCTTTTGAATCTGATT
40277314 ATTCTTTGTG-ATCTGATT
1 ATTCTTT-TGAATCTGATT
40277332 -TT-TTTT-AATCTG
1 ATTCTTTTGAATCTG
40277344 TTTTGGATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 6 0.21
16 3 0.11
17 2 0.07
18 15 0.54
19 2 0.07
ACGTcount: A:0.19, C:0.10, G:0.12, T:0.58
Consensus pattern (18 bp):
ATTCTTTTGAATCTGATT
Found at i:40291860 original size:16 final size:17
Alignment explanation
Indices: 40291841--40291874 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
40291831 AAATATTATG
40291841 AAATAAAAAT-AAACAA
1 AAATAAAAATCAAACAA
*
40291857 AAATAAACATCAAACAA
1 AAATAAAAATCAAACAA
40291874 A
1 A
40291875 CACCATCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (17 bp):
AAATAAAAATCAAACAA
Found at i:40306273 original size:33 final size:33
Alignment explanation
Indices: 40306231--40306294 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
40306221 TATTTTGCTG
40306231 TAGTAAATTGTTGGTAAGCATTTTCAATAGTAA
1 TAGTAAATTGTTGGTAAGCATTTTCAATAGTAA
40306264 TAGTAAATTGTTGGTAAGCATTTTCAATAGT
1 TAGTAAATTGTTGGTAAGCATTTTCAATAGT
40306295 TCCAATTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.41
Consensus pattern (33 bp):
TAGTAAATTGTTGGTAAGCATTTTCAATAGTAA
Found at i:40309704 original size:24 final size:24
Alignment explanation
Indices: 40309677--40309753 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
40309667 AAATGAATGC
40309677 ATATTAGCTGCAAATAATGATGGA
1 ATATTAGCTGCAAATAATGATGGA
* * *
40309701 ATA-TGGCTTGCACTAGTATAT-AT-GC
1 ATATTAGC-TGCA--AATA-ATGATGGA
40309726 ATATTAGCTGCAAATAATGATGGA
1 ATATTAGCTGCAAATAATGATGGA
40309750 ATAT
1 ATAT
40309754 GGCTTGCACT
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 2 0.05
23 8 0.20
24 12 0.30
25 8 0.20
26 8 0.20
27 2 0.05
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.32
Consensus pattern (24 bp):
ATATTAGCTGCAAATAATGATGGA
Found at i:40309730 original size:49 final size:49
Alignment explanation
Indices: 40309673--40309772 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
40309663 ATTCAAATGA
40309673 ATGCATATTAGCTGCAAATAATGATGGAATATGGCTTGCACTAGTATAT
1 ATGCATATTAGCTGCAAATAATGATGGAATATGGCTTGCACTAGTATAT
40309722 ATGCATATTAGCTGCAAATAATGATGGAATATGGCTTGCACTAGTATAT
1 ATGCATATTAGCTGCAAATAATGATGGAATATGGCTTGCACTAGTATAT
40309771 AT
1 AT
40309773 CTTTCTTTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (49 bp):
ATGCATATTAGCTGCAAATAATGATGGAATATGGCTTGCACTAGTATAT
Found at i:40309761 original size:24 final size:24
Alignment explanation
Indices: 40309685--40309761 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
40309675 GCATATTAGC
40309685 TGCAAATAATGATGGAATATGGCT
1 TGCAAATAATGATGGAATATGGCT
* * *
40309709 TGCACTAGTATAT-AT-GCATATTAGC-
1 TGCA--AATA-ATGATGGAATA-TGGCT
40309734 TGCAAATAATGATGGAATATGGCT
1 TGCAAATAATGATGGAATATGGCT
40309758 TGCA
1 TGCA
40309762 CTAGTATATA
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 2 0.05
23 8 0.20
24 12 0.30
25 8 0.20
26 8 0.20
27 2 0.05
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (24 bp):
TGCAAATAATGATGGAATATGGCT
Found at i:40311759 original size:17 final size:17
Alignment explanation
Indices: 40311737--40311769 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
40311727 CTAATTTTCT
40311737 AAAAAAAATC-TAAAAG
1 AAAAAAAATCTTAAAAG
40311753 AAAAAAAATCTTAAAAG
1 AAAAAAAATCTTAAAAG
40311770 CCATTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.73, C:0.06, G:0.06, T:0.15
Consensus pattern (17 bp):
AAAAAAAATCTTAAAAG
Found at i:40322506 original size:40 final size:39
Alignment explanation
Indices: 40322422--40322606 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 39
40322412 TTGAATGATG
* * * *
40322422 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
40322462 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
40322502 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* *
40322541 TCCGGGTTAAGTCCCGAAGGCATTAGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
* *
40322582 -CCGGGCTATGTCCCGAAGGTATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
40322607 AACGAGGAGC
Statistics
Matches: 123, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
39 35 0.28
40 78 0.63
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40322558 original size:79 final size:81
Alignment explanation
Indices: 40322422--40322606 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
40322412 TTGAATGATG
*
40322422 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
*
40322486 TGTGCGAGATACTA-A
66 AGTGCGAGATACTATA
* * * **
40322501 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
40322563 TTAGTGCGAGTTACTATA
64 TTAGTGCGAGATACTATA
* * *
40322581 ACCGGGCTATGTCCCGAAGGTATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40322607 AACGAGGAGC
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 32 0.36
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
AGTGCGAGATACTATA
Found at i:40322628 original size:79 final size:79
Alignment explanation
Indices: 40322423--40322639 Score: 183
Period size: 79 Copynumber: 2.7 Consensus size: 79
40322413 TGAATGATGT
** * * * **
40322423 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTGACTAAATCCGGGTTAA-ATCCCGAAGGCATT
* *
40322486 TGTGCGAGATACTAATT
63 AGTGCGAGATACTAATA
** * *
40322503 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTAGT
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTAGT
*
40322568 GCGAGTTACT-ATAA
66 GCGAGATACTAAT-A
* * * *
40322582 CCGGGCTATGTCCCGAAGGTATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAATCCCGAAGG
40322640 TACGTGATTT
Statistics
Matches: 114, Mismatches: 18, Indels: 11
0.80 0.13 0.08
Matches are distributed among these distances:
78 3 0.03
79 70 0.61
80 41 0.36
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTAGT
GCGAGATACTAATA
Found at i:40325134 original size:16 final size:16
Alignment explanation
Indices: 40325115--40325148 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
40325105 GCATATATGA
*
40325115 ATGGTTGGATTCATGG
1 ATGGCTGGATTCATGG
40325131 ATGGCTGGATTCATGG
1 ATGGCTGGATTCATGG
40325147 AT
1 AT
40325149 ATGGCTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.09, G:0.35, T:0.35
Consensus pattern (16 bp):
ATGGCTGGATTCATGG
Found at i:40330790 original size:17 final size:17
Alignment explanation
Indices: 40330768--40330800 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40330758 TAGACTATAG
*
40330768 CACCTGGTAAATAGTAT
1 CACCTGGCAAATAGTAT
40330785 CACCTGGCAAATAGTA
1 CACCTGGCAAATAGTA
40330801 CCGCTTGACG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.24
Consensus pattern (17 bp):
CACCTGGCAAATAGTAT
Found at i:40332618 original size:6 final size:6
Alignment explanation
Indices: 40332550--40332604 Score: 110
Period size: 6 Copynumber: 9.2 Consensus size: 6
40332540 TTTATTATAG
40332550 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
40332598 ACATAT A
1 ACATAT A
40332605 GAAATATATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (6 bp):
ACATAT
Found at i:40335977 original size:27 final size:27
Alignment explanation
Indices: 40335936--40335987 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
40335926 TCATTGAAGC
* *
40335936 ATCTTCATTGCTGTCCATGCATGTATT
1 ATCTTCAATGATGTCCATGCATGTATT
40335963 ATCTTCAATGATGTCCATGCATGTA
1 ATCTTCAATGATGTCCATGCATGTA
40335988 CCTACAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.40
Consensus pattern (27 bp):
ATCTTCAATGATGTCCATGCATGTATT
Found at i:40338099 original size:6 final size:6
Alignment explanation
Indices: 40338090--40338213 Score: 72
Period size: 6 Copynumber: 20.0 Consensus size: 6
40338080 TCATTCTCAA
* * * **
40338090 TTTCTT TTTCAAT TTTCTAT TCTTCAT TTTCTT TTTCTC TCACTT TTT-TT
1 TTTCTT TTTC-TT TTTCT-T T-TTCTT TTTCTT TTTCTT TTTCTT TTTCTT
* ** *
40338140 ATTTCTTT TTTCTT TTACAA TTTCTT TTTCTT TTT-TCT TTTCTA TTTCTT
1 -TTTC-TT TTTCTT TTTCTT TTTCTT TTTCTT TTTCT-T TTTCTT TTTCTT
** *
40338190 TTTCAC TTTCCT TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT
40338214 CTTTTTCATT
Statistics
Matches: 87, Mismatches: 23, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
5 3 0.03
6 65 0.75
7 14 0.16
8 5 0.06
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (6 bp):
TTTCTT
Found at i:40338105 original size:27 final size:27
Alignment explanation
Indices: 40338075--40338126 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
40338065 TTTTTAGTTT
40338075 TTTTCTCATTC-TCAATTTCTTTTTCAA
1 TTTTCT-ATTCTTCAATTTCTTTTTCAA
*
40338102 TTTTCTATTCTTCATTTTCTTTTTC
1 TTTTCTATTCTTCAATTTCTTTTTC
40338127 TCTCACTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.13, C:0.21, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTTCTATTCTTCAATTTCTTTTTCAA
Found at i:40338155 original size:18 final size:17
Alignment explanation
Indices: 40338134--40338229 Score: 70
Period size: 18 Copynumber: 5.5 Consensus size: 17
40338124 TTCTCTCACT
40338134 TTTTTTATTTCTTTTTTC
1 TTTTTTATTTC-TTTTTC
**
40338152 TTTTACAATTTCTTTTTC
1 TTTT-TTATTTCTTTTTC
* *
40338170 TTTTTTCTTTTCTATTTC
1 TTTTTT-ATTTCTTTTTC
* *
40338188 TTTTTCACTTTCCTTTTC
1 TTTTTTA-TTTCTTTTTC
*
40338206 -TTTTT-CTTCTTTTTC
1 TTTTTTATTTCTTTTTC
*
40338221 ATTTTTATT
1 TTTTTTATT
40338230 ACAATGTGAG
Statistics
Matches: 59, Mismatches: 14, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
15 8 0.14
16 5 0.08
17 5 0.08
18 36 0.61
19 5 0.08
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTTATTTCTTTTTC
Found at i:40338169 original size:25 final size:24
Alignment explanation
Indices: 40338141--40338193 Score: 88
Period size: 25 Copynumber: 2.2 Consensus size: 24
40338131 ACTTTTTTTA
40338141 TTTCTTTTTTCTTTTACAATTTCTT
1 TTTCTTTTTTCTTTT-CAATTTCTT
*
40338166 TTTCTTTTTTCTTTTCTATTTCTT
1 TTTCTTTTTTCTTTTCAATTTCTT
40338190 TTTC
1 TTTC
40338194 ACTTTCCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTCTTTTTTCTTTTCAATTTCTT
Found at i:40338186 original size:24 final size:24
Alignment explanation
Indices: 40338141--40338213 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
40338131 ACTTTTTTTA
*
40338141 TTTCTTTTTTCTTTTACAATTTCTT
1 TTTCTTTTTTCTTTT-CTATTTCTT
40338166 TTTCTTTTTTCTTTTCTATTTCTT
1 TTTCTTTTTTCTTTTCTATTTCTT
** * *
40338190 TTTCACTTTCCTTTTCTTTTTCTT
1 TTTCTTTTTTCTTTTCTATTTCTT
40338214 CTTTTTCATT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
24 28 0.65
25 15 0.35
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (24 bp):
TTTCTTTTTTCTTTTCTATTTCTT
Done.