Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 101 of 770
Found at i:29359205 original size:21 final size:20
Alignment explanation
Indices: 29359161--29359209 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
29359151 TCAGCTCCCA
* *
29359161 TCAGCTCACTTGAGCTCGAT
1 TCAGCTCGCTTGAGCTAGAT
*
29359181 TCAGCTCGTTTGAGCTAGAAT
1 TCAGCTCGCTTGAGCTAG-AT
29359202 TCAGCTCG
1 TCAGCTCG
29359210 ATCTAGCTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (20 bp):
TCAGCTCGCTTGAGCTAGAT
Found at i:29360645 original size:28 final size:28
Alignment explanation
Indices: 29360563--29360652 Score: 119
Period size: 29 Copynumber: 3.1 Consensus size: 28
29360553 TGAGCATGAC
29360563 TATAAATGTGAATTGGGCCT-GATGGGCCA
1 TATAAATGTG-ATTGGGCCTAG-TGGGCCA
* *
29360592 TATAAACGTGATTTGGGCCTAATGGGCCA
1 TATAAATGTGA-TTGGGCCTAGTGGGCCA
*
29360621 TATAAATATGATTGGGCCTAGTGGGCCA
1 TATAAATGTGATTGGGCCTAGTGGGCCA
29360649 TATA
1 TATA
29360653 TAGGTATGTG
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
28 21 0.39
29 33 0.61
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (28 bp):
TATAAATGTGATTGGGCCTAGTGGGCCA
Found at i:29363493 original size:4 final size:4
Alignment explanation
Indices: 29363484--29363513 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
29363474 TGTTGGTGTA
29363484 TTAT TTAT TTAT TTAT TTAT TTAT TT-T TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA
29363514 GTTCAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:29366150 original size:10 final size:10
Alignment explanation
Indices: 29366135--29366161 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
29366125 TACTCCTTCA
29366135 AGCTCAAATC
1 AGCTCAAATC
29366145 AGCTCAAATC
1 AGCTCAAATC
29366155 AGCTCAA
1 AGCTCAA
29366162 CTTCAGCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:29366169 original size:21 final size:21
Alignment explanation
Indices: 29366135--29366183 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
29366125 TACTCCTTCA
29366135 AGCTCAA-ATCAGCTCAAATC
1 AGCTCAACATCAGCTCAAATC
* * * *
29366155 AGCTCAACTTCAGCTTAACTT
1 AGCTCAACATCAGCTCAAATC
29366176 AGCTCAAC
1 AGCTCAAC
29366184 GAGCTCGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.35, C:0.31, G:0.10, T:0.24
Consensus pattern (21 bp):
AGCTCAACATCAGCTCAAATC
Found at i:29367217 original size:30 final size:31
Alignment explanation
Indices: 29367181--29367278 Score: 94
Period size: 30 Copynumber: 3.2 Consensus size: 31
29367171 AGCTCACTCC
*
29367181 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
29367211 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
29367241 CAGCTCAACTTT-AGCTCACGAGCTAAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCT-AAACCT
29367272 TAGCTCA
1 TAGCTCA
29367279 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
30 38 0.75
31 13 0.25
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:29369806 original size:9 final size:10
Alignment explanation
Indices: 29369799--29369855 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
29369789 AAGAGAAAAC
29369799 AAAGAAAAGA
1 AAAGAAAAGA
29369809 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
29369821 AAAGAAGA-A
1 AAAGAAAAGA
29369830 AAAGAAAATGA
1 AAAGAAAA-GA
29369841 AATA-AAAAGA
1 AA-AGAAAAGA
29369851 AAAGA
1 AAAGA
29369856 GAGGCAAAAG
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:29369822 original size:21 final size:20
Alignment explanation
Indices: 29369788--29369855 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
29369778 ACATTTTTGT
29369788 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
29369809 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
29369830 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
29369851 AAAGA
1 AAAGA
29369856 GAGGCAAAAG
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:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:29369823 original size:6 final size:5
Alignment explanation
Indices: 29369799--29369855 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
29369789 AAGAGAAAAC
*
29369799 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
29369846 AAAGA AAAGA
1 AAAGA AAAGA
29369856 GAGGCAAAAG
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:29369830 original size:15 final size:14
Alignment explanation
Indices: 29369799--29369855 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
29369789 AAGAGAAAAC
29369799 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
29369815 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
29369830 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
29369846 AAAGAAAAGA
1 AAAGAAAAGA
29369856 GAGGCAAAAG
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:29371263 original size:71 final size:71
Alignment explanation
Indices: 29371175--29371338 Score: 319
Period size: 71 Copynumber: 2.3 Consensus size: 71
29371165 GAGATGTATC
29371175 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATACGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATACGTGATTCCAAGTGA
29371240 AGGACA
66 AGGACA
*
29371246 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATACGTGATTCCAAGTGA
29371311 AGGACA
66 AGGACA
29371317 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
29371339 AGACAAATCG
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 92 1.00
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATACGTGATTCCAAGTGA
AGGACA
Found at i:29372723 original size:12 final size:12
Alignment explanation
Indices: 29372693--29372724 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
29372683 AAAAGCCTTT
*
29372693 GAAAATCAAAAA
1 GAAAATGAAAAA
29372705 GAAAATGAAAAA
1 GAAAATGAAAAA
29372717 GAAAATGA
1 GAAAATGA
29372725 GATTGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.72, C:0.03, G:0.16, T:0.09
Consensus pattern (12 bp):
GAAAATGAAAAA
Found at i:29372734 original size:30 final size:31
Alignment explanation
Indices: 29372700--29372781 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
29372690 TTTGAAAATC
* *
29372700 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAGAATGAAAAAGAAATATGAGAGTG
* *
29372730 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAGAATGAAAAAGAAATATGAGAGTG
*
29372760 AAAAAGAGGATGAAAAAGAAAT
1 AAAAAGAGAATGAAAAAGAAAT
29372782 TGAAACAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 8 0.18
30 27 0.61
31 9 0.20
ACGTcount: A:0.63, C:0.01, G:0.23, T:0.12
Consensus pattern (31 bp):
AAAAAGAGAATGAAAAAGAAATATGAGAGTG
Found at i:29375052 original size:30 final size:31
Alignment explanation
Indices: 29375018--29375114 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
29375008 AGCTCACTCC
*
29375018 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
29375048 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
29375078 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
29375108 TAGCTCA
1 TAGCTCA
29375115 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:29378962 original size:30 final size:30
Alignment explanation
Indices: 29378928--29379025 Score: 74
Period size: 30 Copynumber: 3.3 Consensus size: 30
29378918 AGCTCACTCC
29378928 TAGCTCATATTCAGTTCACGAGCTAAACCT
1 TAGCTCATATTCAGTTCACGAGCTAAACCT
** * * * *
29378958 TAGCTCAGCTTCAGCTT-AGGAGTTTAATCT
1 TAGCTCATATTCAG-TTCACGAGCTAAACCT
* * * *
29378988 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGTTCACGAGCTAAACCT
29379018 TAGCTCAT
1 TAGCTCAT
29379026 TTTAGTTTAA
Statistics
Matches: 49, Mismatches: 15, Indels: 7
0.69 0.21 0.10
Matches are distributed among these distances:
29 1 0.02
30 46 0.94
31 2 0.04
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.31
Consensus pattern (30 bp):
TAGCTCATATTCAGTTCACGAGCTAAACCT
Found at i:29397992 original size:30 final size:30
Alignment explanation
Indices: 29397906--29398003 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 30
29397896 TTAAACTAAA
* *
29397906 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * * *
29397936 TTGAGCTGAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * *
29397966 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
29397996 ATGAGCTA
1 ATGAGCTA
29398004 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:29400286 original size:30 final size:30
Alignment explanation
Indices: 29400215--29400297 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
29400205 CTTTTGTTTC
* *
29400215 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
29400246 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
29400275 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
29400298 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:29400297 original size:18 final size:18
Alignment explanation
Indices: 29400248--29400303 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
29400238 CACTCTCAAA
* *
29400248 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
29400265 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
29400283 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
29400302 TT
1 TT
29400304 CAAAGACTTT
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:29400304 original size:12 final size:12
Alignment explanation
Indices: 29400273--29400297 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29400263 TTTTTCAATC
29400273 TCATTTTCTTTT
1 TCATTTTCTTTT
29400285 TCATTTTCTTTT
1 TCATTTTCTTTT
29400297 T
1 T
29400298 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:29400315 original size:12 final size:12
Alignment explanation
Indices: 29400300--29400330 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
29400290 TTCTTTTTGC
29400300 TTTTCAAAGACT
1 TTTTCAAAGACT
*
29400312 TTTTCAAAGGCT
1 TTTTCAAAGACT
29400324 TTTTCAA
1 TTTTCAA
29400331 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:29400388 original size:5 final size:5
Alignment explanation
Indices: 29400378--29400434 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
29400368 CTCTTGCCTC
*
29400378 TCTTT TCTTT T-TATT TCGTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
29400425 TCTTT TCTTT
1 TCTTT TCTTT
29400435 GTTTTCTCTT
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:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:29400418 original size:15 final size:14
Alignment explanation
Indices: 29400378--29400434 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
29400368 CTCTTGCCTC
*
29400378 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
29400393 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
29400408 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
29400425 TCTTTTCTTT
1 TCTTTTCTTT
29400435 GTTTTCTCTT
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:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:29400435 original size:21 final size:21
Alignment explanation
Indices: 29400378--29400445 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
29400368 CTCTTGCCTC
* *
29400378 TCTTTTCTTTT-TATTTCGTTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
29400399 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
29400420 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
29400440 CTCTTT
1 -TCTTT
29400446 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.01, C:0.18, G:0.04, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:29403135 original size:30 final size:30
Alignment explanation
Indices: 29403049--29403146 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 30
29403039 TTAAACTAAA
* *
29403049 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * * *
29403079 TTGAGCTGAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * *
29403109 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
29403139 ATGAGCTA
1 ATGAGCTA
29403147 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:29405762 original size:10 final size:10
Alignment explanation
Indices: 29405747--29405781 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
29405737 TACAAGTCAA
29405747 AAAAAATTCG
1 AAAAAATTCG
*
29405757 AAAAAAATTCA
1 -AAAAAATTCG
29405768 AAAAAATTCG
1 AAAAAATTCG
29405778 AAAA
1 AAAA
29405782 GAAAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.17
Consensus pattern (10 bp):
AAAAAATTCG
Found at i:29405762 original size:11 final size:11
Alignment explanation
Indices: 29405746--29405781 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
29405736 ATACAAGTCA
29405746 AAAAAAATTCG
1 AAAAAAATTCG
29405757 AAAAAAATTC-
1 AAAAAAATTCG
29405767 AAAAAAATTCG
1 AAAAAAATTCG
29405778 AAAA
1 AAAA
29405782 GAAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.69, C:0.08, G:0.06, T:0.17
Consensus pattern (11 bp):
AAAAAAATTCG
Found at i:29405791 original size:21 final size:21
Alignment explanation
Indices: 29405745--29405791 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
29405735 TATACAAGTC
*
29405745 AAAAAAAATTCGAAAAAAATT
1 AAAAAAAATTCGAAAAAAATA
* *
29405766 CAAAAAAATTCGAAAAGAA-A
1 AAAAAAAATTCGAAAAAAATA
29405786 AAAAAA
1 AAAAAA
29405792 TCTGAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.13
Consensus pattern (21 bp):
AAAAAAAATTCGAAAAAAATA
Found at i:29405798 original size:18 final size:17
Alignment explanation
Indices: 29405745--29405803 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 17
29405735 TATACAAGTC
29405745 AAAAAAAATTCGAAAAAA
1 AAAAAAAATTCG-AAAAA
29405763 ATTCAAAAAAATTCGAAAAGA
1 A---AAAAAAATTCGAAAA-A
29405784 AAAAAAAA-TCTGAAAAA
1 AAAAAAAATTC-GAAAAA
29405801 AAA
1 AAA
29405804 GTGTTTAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
17 6 0.17
18 13 0.36
20 4 0.11
21 13 0.36
ACGTcount: A:0.73, C:0.07, G:0.07, T:0.14
Consensus pattern (17 bp):
AAAAAAAATTCGAAAAA
Found at i:29406743 original size:15 final size:14
Alignment explanation
Indices: 29406720--29406773 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
29406710 AAGAGAAAAC
29406720 AAAGAAAAAAAAGAA
1 AAAG-AAAAAAAGAA
*
29406735 AAAGCAAAAGAAGAA
1 AAAG-AAAAAAAGAA
*
29406750 AAAGAAAATGAAATAA
1 AAAGAAAA--AAAGAA
29406766 AAAGAAAA
1 AAAGAAAA
29406774 GAGAGGCAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 4 0.12
15 17 0.52
16 12 0.36
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.04
Consensus pattern (14 bp):
AAAGAAAAAAAGAA
Found at i:29406838 original size:12 final size:12
Alignment explanation
Indices: 29406823--29406852 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
29406813 TTGAAAGAAC
29406823 TTGAAAAAGCCT
1 TTGAAAAAGCCT
29406835 TTG-AAAAGCCT
1 TTGAAAAAGCCT
29406846 TTGAAAA
1 TTGAAAA
29406853 GGAAAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:29406843 original size:11 final size:11
Alignment explanation
Indices: 29406827--29406853 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
29406817 AAGAACTTGA
29406827 AAAAGCCTTTG
1 AAAAGCCTTTG
29406838 AAAAGCCTTTG
1 AAAAGCCTTTG
29406849 AAAAG
1 AAAAG
29406854 GAAAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (11 bp):
AAAAGCCTTTG
Found at i:29406869 original size:12 final size:12
Alignment explanation
Indices: 29406848--29406879 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
29406838 AAAAGCCTTT
*
29406848 GAAAAGGAAAAA
1 GAAAATGAAAAA
29406860 GAAAATGAAAAA
1 GAAAATGAAAAA
29406872 GAAAATGA
1 GAAAATGA
29406880 GATTGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (12 bp):
GAAAATGAAAAA
Found at i:29406886 original size:18 final size:18
Alignment explanation
Indices: 29406846--29406891 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
29406836 TGAAAAGCCT
*
29406846 TTGAAAAGGAAAAAGAAA
1 TTGAAAAAGAAAAAGAAA
* * *
29406864 ATGAAAAAGAAAATGAGA
1 TTGAAAAAGAAAAAGAAA
29406882 TTGAAAAAGA
1 TTGAAAAAGA
29406892 GAACGAAAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.13
Consensus pattern (18 bp):
TTGAAAAAGAAAAAGAAA
Found at i:29406888 original size:30 final size:30
Alignment explanation
Indices: 29406854--29406922 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
29406844 CTTTGAAAAG
* *
29406854 GAAAAAGAAAATGAAAAAGAAA-ATGAGATT
1 GAAAAAGAAAACG-AAAAGAAATATGAGAGT
* *
29406884 GAAAAAGAGAACGAAAAGAAATTTGAGAGT
1 GAAAAAGAAAACGAAAAGAAATATGAGAGT
29406914 GAAAAAGAA
1 GAAAAAGAA
29406923 GAAAAAGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 8 0.24
30 25 0.76
ACGTcount: A:0.64, C:0.01, G:0.23, T:0.12
Consensus pattern (30 bp):
GAAAAAGAAAACGAAAAGAAATATGAGAGT
Found at i:29406928 original size:28 final size:27
Alignment explanation
Indices: 29406866--29406934 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 27
29406856 AAAAGAAAAT
* *
29406866 GAAAAAGAAA-ATGAGATTGAAAAAGA
1 GAAAAAGAAATTTGAGAGTGAAAAAGA
29406892 GAACGAAAAGAAATTTGAGAGTGAAAAAGAA
1 G-A--AAAAGAAATTTGAGAGTGAAAAAG-A
29406923 GAAAAAGAAATT
1 GAAAAAGAAATT
29406935 GAAACAAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
26 1 0.03
27 1 0.03
28 10 0.28
29 8 0.22
30 14 0.39
31 2 0.06
ACGTcount: A:0.62, C:0.01, G:0.23, T:0.13
Consensus pattern (27 bp):
GAAAAAGAAATTTGAGAGTGAAAAAGA
Found at i:29412938 original size:20 final size:19
Alignment explanation
Indices: 29412915--29412954 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
29412905 CAGTTCCATG
29412915 AGCTCAACTCAGCTCCATCT
1 AGCTCAACTCAGCT-CATCT
* *
29412935 AGCTCAATTGAGCTCATCT
1 AGCTCAACTCAGCTCATCT
29412954 A
1 A
29412955 TAATTTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.28, C:0.33, G:0.12, T:0.28
Consensus pattern (19 bp):
AGCTCAACTCAGCTCATCT
Found at i:29413309 original size:18 final size:18
Alignment explanation
Indices: 29413285--29413332 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
29413275 GAGTAGCCGA
29413285 AAATTAATGTGTCTAAATT
1 AAATTAATGTGT-TAAATT
* *
29413304 -AATTAATTTGTTGAATT
1 AAATTAATGTGTTAAATT
*
29413321 AAATTTATGTGT
1 AAATTAATGTGT
29413333 GCAGGTGCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (18 bp):
AAATTAATGTGTTAAATT
Found at i:29417771 original size:11 final size:11
Alignment explanation
Indices: 29417755--29417784 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
29417745 ATACAAGTAT
29417755 AAAAAAAATTC
1 AAAAAAAATTC
29417766 AAAAAAAATTC
1 AAAAAAAATTC
29417777 AAAAAAAA
1 AAAAAAAA
29417785 AAGCTTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:29417784 original size:15 final size:15
Alignment explanation
Indices: 29417766--29417800 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
29417756 AAAAAAATTC
29417766 AAAAAAAATTCAAAA
1 AAAAAAAATTCAAAA
**
29417781 AAAAAAGCTTCAAAA
1 AAAAAAAATTCAAAA
29417796 AAAAA
1 AAAAA
29417801 GATTTGTGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.77, C:0.09, G:0.03, T:0.11
Consensus pattern (15 bp):
AAAAAAAATTCAAAA
Found at i:29418730 original size:21 final size:20
Alignment explanation
Indices: 29418704--29418771 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 20
29418694 ACATTCTTGT
29418704 AAAGAAAAAACAAAGAAAAGA
1 AAAGAAAAAACAAA-AAAAGA
* *
29418725 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAACAAAAAAAG-A
29418746 AAAGAAAAAGA-AATAAAAAGA
1 AAAGAAAAA-ACAA-AAAAAGA
29418767 AAAGA
1 AAAGA
29418772 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 4 0.10
21 31 0.77
22 5 0.12
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.01
Consensus pattern (20 bp):
AAAGAAAAAACAAAAAAAGA
Found at i:29418739 original size:6 final size:5
Alignment explanation
Indices: 29418704--29418771 Score: 59
Period size: 5 Copynumber: 13.0 Consensus size: 5
29418694 ACATTCTTGT
* *
29418704 AAAGA AAAAA CAAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGAA
1 AAAGA AAAGA -AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAG-A
29418752 AAAGA AATA-A AAAGA AAAGA
1 AAAGA AA-AGA AAAGA AAAGA
29418772 GAGGCAAGAG
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
4 4 0.08
5 28 0.54
6 20 0.38
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.01
Consensus pattern (5 bp):
AAAGA
Found at i:29424447 original size:29 final size:29
Alignment explanation
Indices: 29424414--29424473 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
29424404 ATAACCAAAC
* *
29424414 CTACAAAAAATTTATATCCATAAATCCAT
1 CTACAAAAAATTCATATCCATAAACCCAT
* *
29424443 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAAATTCATATCCATAAACCCAT
29424472 CT
1 CT
29424474 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:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAAATTCATATCCATAAACCCAT
Found at i:29433702 original size:30 final size:30
Alignment explanation
Indices: 29433668--29433766 Score: 94
Period size: 30 Copynumber: 3.3 Consensus size: 30
29433658 TAAACTAAAA
29433668 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
29433698 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
29433728 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
29433758 TGAGCTAAG
1 TGAGCTAAG
29433767 AGTGAGCTCG
Statistics
Matches: 52, Mismatches: 14, Indels: 6
0.72 0.19 0.08
Matches are distributed among these distances:
29 2 0.04
30 44 0.85
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.27
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:29435935 original size:30 final size:30
Alignment explanation
Indices: 29435864--29435946 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
29435854 CTTTTGTTTC
* *
29435864 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
29435895 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
29435924 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
29435947 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:29435946 original size:18 final size:18
Alignment explanation
Indices: 29435897--29435952 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
29435887 CACTCTCAAA
* *
29435897 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
29435914 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
29435932 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
29435951 TT
1 TT
29435953 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:29435953 original size:12 final size:12
Alignment explanation
Indices: 29435922--29435946 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29435912 TTTTTCAATC
29435922 TCATTTTCTTTT
1 TCATTTTCTTTT
29435934 TCATTTTCTTTT
1 TCATTTTCTTTT
29435946 T
1 T
29435947 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:29436025 original size:5 final size:5
Alignment explanation
Indices: 29436015--29436071 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
29436005 CTCTTGCCTC
*
29436015 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
29436062 TCTTT TCTTT
1 TCTTT TCTTT
29436072 ATTTACTCTT
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:29436055 original size:15 final size:14
Alignment explanation
Indices: 29436015--29436071 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
29436005 CTCTTGCCTC
*
29436015 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
29436030 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
29436045 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
29436062 TCTTTTCTTT
1 TCTTTTCTTT
29436072 ATTTACTCTT
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:29437000 original size:11 final size:13
Alignment explanation
Indices: 29436984--29437037 Score: 73
Period size: 12 Copynumber: 4.5 Consensus size: 13
29436974 CATTAAACAC
29436984 TTTTTTTCAG-AT
1 TTTTTTTCAGAAT
29436996 TTTTTTTC-GAAT
1 TTTTTTTCAGAAT
29437008 TTTTTTT--GAAT
1 TTTTTTTCAGAAT
29437019 TTTTTTTCA-AAT
1 TTTTTTTCAGAAT
29437031 TTTTTTT
1 TTTTTTT
29437038 TACTTGTATA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
11 12 0.31
12 27 0.69
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.72
Consensus pattern (13 bp):
TTTTTTTCAGAAT
Found at i:29437010 original size:10 final size:11
Alignment explanation
Indices: 29436984--29437036 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
29436974 CATTAAACAC
*
29436984 TTTTTTTCAGAT
1 TTTTTTTC-GAA
29436996 TTTTTTTCGAA
1 TTTTTTTCGAA
*
29437007 TTTTTTTTGAA
1 TTTTTTTCGAA
*
29437018 TTTTTTTTCAAA
1 -TTTTTTTCGAA
29437030 TTTTTTT
1 TTTTTTT
29437037 TTACTTGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
11 19 0.53
12 17 0.47
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.72
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:29437020 original size:23 final size:24
Alignment explanation
Indices: 29436984--29437037 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
29436974 CATTAAACAC
*
29436984 TTTTTTTCAGATTTTTTTTCGAAT
1 TTTTTTTCAGATTTTTTTTCAAAT
*
29437008 TTTTTTTGA-ATTTTTTTTCAAAT
1 TTTTTTTCAGATTTTTTTTCAAAT
29437031 TTTTTTT
1 TTTTTTT
29437038 TACTTGTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 20 0.71
24 8 0.29
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.72
Consensus pattern (24 bp):
TTTTTTTCAGATTTTTTTTCAAAT
Found at i:29438780 original size:30 final size:30
Alignment explanation
Indices: 29438746--29438842 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
29438736 TAAACTAAAA
29438746 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
29438776 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
29438806 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
29438836 TGAGCTA
1 TGAGCTA
29438843 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:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:29439577 original size:14 final size:14
Alignment explanation
Indices: 29439558--29439602 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
29439548 AACTCATCTT
*
29439558 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
29439572 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
29439585 AATTTAATTTAATG
1 AGTTTAATTTAATG
29439599 AGTT
1 AGTT
29439603 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:29440629 original size:15 final size:15
Alignment explanation
Indices: 29440583--29440630 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
29440573 AAACCTATAA
*
29440583 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
29440598 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
29440612 AAACTTCATATCCAT
1 AAACTTCATATCCAT
29440627 AAAC
1 AAAC
29440631 CCATCTTTGA
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:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:29441204 original size:15 final size:15
Alignment explanation
Indices: 29441184--29441231 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
29441174 TCAAAGATGG
29441184 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
29441199 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
29441213 GTTTATGGATATAAA
1 GTTTATGGATATGAA
29441228 GTTT
1 GTTT
29441232 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:29441218 original size:14 final size:14
Alignment explanation
Indices: 29441178--29441221 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
29441168 AAGGATTCAA
29441178 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
29441192 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
29441207 AGATGGGTTTATGG
1 AGATGGGTTTATGG
29441221 A
1 A
29441222 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:29441247 original size:29 final size:29
Alignment explanation
Indices: 29441178--29441237 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
29441168 AAGGATTCAA
*
29441178 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
29441207 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
29441236 AG
1 AG
29441238 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:29442253 original size:14 final size:14
Alignment explanation
Indices: 29442211--29442255 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
29442201 TTAAAGAAGC
29442211 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
29442225 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
29442238 AACTCATTTAATTA
1 AACTCATTAAATTA
29442252 AACT
1 AACT
29442256 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:29447134 original size:2 final size:2
Alignment explanation
Indices: 29447127--29447159 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
29447117 GGATGAATGA
29447127 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29447160 GAATACTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29451072 original size:45 final size:45
Alignment explanation
Indices: 29450973--29451145 Score: 221
Period size: 45 Copynumber: 3.9 Consensus size: 45
29450963 TTCATCCACT
* *
29450973 AGCATT-TTGCCTGCTAGGCTCGAA-GCCCG-ATA-TCATTTCACC
1 AGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGT-ATCTCACC
*
29451015 GGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGTATCTCACC
1 AGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGTATCTCACC
* *
29451060 AGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACT
1 AGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGTATCTCACC
* * *
29451105 GGCATCATAGCCTACTAGGCTC-AGAGGCCCGAATAGTATCT
1 AGCATTATAGCCTGCTAGGCTCGA-AGGCCCGAATAGTATCT
29451146 GTGACAGCCC
Statistics
Matches: 117, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
42 5 0.04
43 17 0.15
44 6 0.05
45 88 0.75
46 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (45 bp):
AGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGTATCTCACC
Found at i:29452068 original size:15 final size:15
Alignment explanation
Indices: 29452025--29452071 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
29452015 ACAATTAAAG
29452025 AGATATGCTTTGATT
1 AGATATGCTTTGATT
* *
29452040 AGATA---ATAGATT
1 AGATATGCTTTGATT
29452052 AGATATGCTTTGATT
1 AGATATGCTTTGATT
29452067 AGATA
1 AGATA
29452072 ATAAGTTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
12 10 0.40
15 15 0.60
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.40
Consensus pattern (15 bp):
AGATATGCTTTGATT
Found at i:29457758 original size:30 final size:30
Alignment explanation
Indices: 29457662--29457758 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
29457652 AGCTCACTCC
* *
29457662 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* * * **
29457692 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
**
29457722 CGGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
29457752 TAGCTCA
1 TAGCTCA
29457759 TTTTAGTTTA
Statistics
Matches: 48, Mismatches: 16, Indels: 6
0.69 0.23 0.09
Matches are distributed among these distances:
29 2 0.04
30 39 0.81
31 7 0.15
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:29458205 original size:17 final size:16
Alignment explanation
Indices: 29458155--29458215 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 16
29458145 AAGGCTAGTC
*
29458155 CATGAATGGATCAAATG
1 CATGAATGG-TTAAATG
*
29458172 CATGGAAT-GATAGAATG
1 CAT-GAATGGTTA-AATG
29458189 CATGAATGGCTTAAATG
1 CATGAATGG-TTAAATG
*
29458206 CATGTATGGT
1 CATGAATGGT
29458216 GGCTGATACA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
16 6 0.17
17 24 0.67
18 6 0.17
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.28
Consensus pattern (16 bp):
CATGAATGGTTAAATG
Found at i:29460061 original size:13 final size:12
Alignment explanation
Indices: 29460043--29460075 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
29460033 AAGTTTGAAA
29460043 AAAAAAAATTCCG
1 AAAAAAAATT-CG
29460056 AAAAAAAATTCG
1 AAAAAAAATTCG
29460068 AAAAAAAA
1 AAAAAAAA
29460076 AGTGATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.73, C:0.09, G:0.06, T:0.12
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:29460076 original size:13 final size:14
Alignment explanation
Indices: 29460042--29460076 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
29460032 CAAGTTTGAA
29460042 AAAAAAAAATTCCG
1 AAAAAAAAATTCCG
29460056 -AAAAAAAATT-CG
1 AAAAAAAAATTCCG
29460068 AAAAAAAAA
1 AAAAAAAAA
29460077 GTGATTTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 2 0.10
13 18 0.90
ACGTcount: A:0.74, C:0.09, G:0.06, T:0.11
Consensus pattern (14 bp):
AAAAAAAAATTCCG
Found at i:29468720 original size:6 final size:5
Alignment explanation
Indices: 29468696--29468752 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
29468686 AAGAGAAAAT
*
29468696 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGAA AAAGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAG-A AAAGA AA-AGA
29468743 AAAGA AAAGA
1 AAAGA AAAGA
29468753 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 24 0.55
6 16 0.36
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:29468745 original size:25 final size:25
Alignment explanation
Indices: 29468700--29468748 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
29468690 GAAAATAAAG
29468700 AAAAGAAAAGAAAAAGCAAAAGAAGA
1 AAAAGAAAAGAAAAA-CAAAAGAAGA
*
29468726 AAAAGAAAAAGAAATA-AAAAGAA
1 AAAAG-AAAAGAAAAACAAAAGAA
29468749 AAGAGAGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 5 0.24
27 9 0.43
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (25 bp):
AAAAGAAAAGAAAAACAAAAGAAGA
Found at i:29468832 original size:11 final size:12
Alignment explanation
Indices: 29468800--29468830 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
29468790 TTGAGAGAAC
29468800 TTGAAAAAGCCT
1 TTGAAAAAGCCT
29468812 TTGAAAAAGCCT
1 TTGAAAAAGCCT
29468824 TTGAAAA
1 TTGAAAA
29468831 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:29471036 original size:30 final size:31
Alignment explanation
Indices: 29471002--29471098 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
29470992 AGCTCACTCC
*
29471002 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
29471032 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
29471062 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
29471092 TAGCTCA
1 TAGCTCA
29471099 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:29472706 original size:18 final size:19
Alignment explanation
Indices: 29472683--29472721 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
29472673 TTTATCTCAA
*
29472683 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
29472701 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
29472720 TT
1 TT
29472722 CTCTCTCAAA
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:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:29472737 original size:48 final size:49
Alignment explanation
Indices: 29472685--29472788 Score: 115
Period size: 48 Copynumber: 2.2 Consensus size: 49
29472675 TATCTCAATT
* * *
29472685 TCTTTTTCCACTCT-TTTTTC-TTGTTCACATTCTTTTTCTCTCTCAAAC
1 TCTTTTTCCACTCTCTTTTTCAATCTT-ACATTCTTTTTCACTCTCAAAC
* ** *
29472733 TCTTTTT-CATTCTCTTTTTCAATCTTATTTTCTTTTTCACTCTCAATC
1 TCTTTTTCCACTCTCTTTTTCAATCTTACATTCTTTTTCACTCTCAAAC
29472781 TCTTTTTC
1 TCTTTTTC
29472789 TTTTTCTTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
47 5 0.11
48 38 0.83
49 3 0.07
ACGTcount: A:0.12, C:0.27, G:0.01, T:0.60
Consensus pattern (49 bp):
TCTTTTTCCACTCTCTTTTTCAATCTTACATTCTTTTTCACTCTCAAAC
Found at i:29472784 original size:18 final size:18
Alignment explanation
Indices: 29472743--29472788 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
29472733 TCTTTTTCAT
* *
29472743 TCTCTTTTTCAATCTTAT
1 TCTCTTTTTCAATCTCAA
* *
29472761 TTTCTTTTTCACTCTCAA
1 TCTCTTTTTCAATCTCAA
29472779 TCTCTTTTTC
1 TCTCTTTTTC
29472789 TTTTTCTTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.61
Consensus pattern (18 bp):
TCTCTTTTTCAATCTCAA
Found at i:29472847 original size:42 final size:42
Alignment explanation
Indices: 29472792--29472888 Score: 135
Period size: 42 Copynumber: 2.3 Consensus size: 42
29472782 CTTTTTCTTT
* *
29472792 TTCTTTCA-TTTCTTTGTTTCTTTTCTCGATTTCAAT-AAAGA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCAATCAAA-A
*
29472833 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCAATCAAAA
*
29472875 TCCTCTCATTTTCT
1 TTCTCTCATTTTCT
29472889 CTCATAATCT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
41 7 0.14
42 40 0.80
43 3 0.06
ACGTcount: A:0.16, C:0.23, G:0.05, T:0.56
Consensus pattern (42 bp):
TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCAATCAAAA
Found at i:29475821 original size:11 final size:11
Alignment explanation
Indices: 29475805--29475870 Score: 71
Period size: 11 Copynumber: 5.8 Consensus size: 11
29475795 ATACAAGTTT
*
29475805 GAAAAAAAACC
1 GAAAAAAAATC
29475816 GAAAAAAAAATTC
1 G-AAAAAAAA-TC
29475829 -AAAAAAAATTC
1 GAAAAAAAA-TC
*
29475840 GAAAAAAAATT
1 GAAAAAAAATC
*
29475851 GAAAAAAAATT
1 GAAAAAAAATC
29475862 GAAAAAAAA
1 GAAAAAAAA
29475871 GTGATTTATG
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
11 33 0.66
12 16 0.32
13 1 0.02
ACGTcount: A:0.74, C:0.06, G:0.08, T:0.12
Consensus pattern (11 bp):
GAAAAAAAATC
Found at i:29475823 original size:12 final size:12
Alignment explanation
Indices: 29475806--29475870 Score: 64
Period size: 12 Copynumber: 5.6 Consensus size: 12
29475796 TACAAGTTTG
*
29475806 AAAAAAAACCGA
1 AAAAAAAATCGA
29475818 AAAAAAAATTC-A
1 AAAAAAAA-TCGA
*
29475830 AAAAAAATTCG-
1 AAAAAAAATCGA
*
29475841 AAAAAAAATTG-
1 AAAAAAAATCGA
*
29475852 AAAAAAAATTGA
1 AAAAAAAATCGA
29475864 AAAAAAA
1 AAAAAAA
29475871 GTGATTTATG
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
11 22 0.48
12 23 0.50
13 1 0.02
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.12
Consensus pattern (12 bp):
AAAAAAAATCGA
Found at i:29475832 original size:23 final size:23
Alignment explanation
Indices: 29475806--29475870 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
29475796 TACAAGTTTG
*
29475806 AAAAAAAACCGAAAAAAAAATTC
1 AAAAAAAATCGAAAAAAAAATTC
*
29475829 AAAAAAAATTCG-AAAAAAAATTG
1 AAAAAAAA-TCGAAAAAAAAATTC
*
29475852 AAAAAAAATTGAAAAAAAA
1 AAAAAAAATCGAAAAAAAA
29475871 GTGATTTATG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 2 0.05
23 33 0.89
24 2 0.05
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.12
Consensus pattern (23 bp):
AAAAAAAATCGAAAAAAAAATTC
Found at i:29476219 original size:15 final size:15
Alignment explanation
Indices: 29476199--29476246 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
29476189 TCAAAGATGG
29476199 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
29476214 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
29476228 GTTTATGGATATAAA
1 GTTTATGGATATGAA
29476243 GTTT
1 GTTT
29476247 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:29476226 original size:29 final size:29
Alignment explanation
Indices: 29476193--29476252 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
29476183 AAGGATTCAA
*
29476193 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
29476222 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
29476251 AG
1 AG
29476253 GTTTGCTTAT
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:29476233 original size:14 final size:14
Alignment explanation
Indices: 29476193--29476236 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
29476183 AAGGATTCAA
29476193 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
29476207 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
29476222 AGATGGGTTTATGG
1 AGATGGGTTTATGG
29476236 A
1 A
29476237 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:29478355 original size:9 final size:10
Alignment explanation
Indices: 29478348--29478404 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
29478338 AAGAGAAAAT
29478348 AAAGAAAAGA
1 AAAGAAAAGA
29478358 AAAGAAAAAGA
1 AAAG-AAAAGA
*
29478369 AAA-AGAAGAA
1 AAAGAAAAG-A
29478379 AAAGAAAATGA
1 AAAGAAAA-GA
29478390 AATA-AAAAGA
1 AA-AGAAAAGA
29478400 AAAGA
1 AAAGA
29478405 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:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:29478358 original size:5 final size:5
Alignment explanation
Indices: 29478348--29478404 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
29478338 AAGAGAAAAT
*
29478348 AAAGA AAAGA AAAGAA AAAGA AAA-A GAAGAA AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAGA AAAGA AAAG-A AAAGA AAA-GA AA-AGA
29478395 AAAGA AAAGA
1 AAAGA AAAGA
29478405 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 26 0.59
6 13 0.30
7 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:29478484 original size:11 final size:12
Alignment explanation
Indices: 29478452--29478482 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
29478442 TTAAGAGAAC
29478452 TTGAAAAAGCCT
1 TTGAAAAAGCCT
29478464 TTGAAAAAGCCT
1 TTGAAAAAGCCT
29478476 TTGAAAA
1 TTGAAAA
29478483 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:29481119 original size:20 final size:21
Alignment explanation
Indices: 29481094--29481141 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
29481084 GTAAGCTCGG
*
29481094 TTGAGCTCAAATGAGATGGA-
1 TTGAGCTCAAATAAGATGGAT
* *
29481114 TTGAGCTCGAATAAGCTGGAT
1 TTGAGCTCAAATAAGATGGAT
29481135 TTGAGCT
1 TTGAGCT
29481142 GGACGGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAGCTCAAATAAGATGGAT
Found at i:29483262 original size:30 final size:30
Alignment explanation
Indices: 29483191--29483273 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
29483181 CTTTTGTTTC
* *
29483191 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
29483222 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
29483251 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
29483274 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:29483273 original size:18 final size:18
Alignment explanation
Indices: 29483224--29483279 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
29483214 CACTCTCAAA
* *
29483224 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
29483241 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
29483259 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
29483278 TT
1 TT
29483280 CAAAGGATTT
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:29483280 original size:12 final size:12
Alignment explanation
Indices: 29483249--29483273 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29483239 TTTTTCAATC
29483249 TCATTTTCTTTT
1 TCATTTTCTTTT
29483261 TCATTTTCTTTT
1 TCATTTTCTTTT
29483273 T
1 T
29483274 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:29483291 original size:12 final size:12
Alignment explanation
Indices: 29483276--29483306 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
29483266 TTCTTTTTGC
29483276 TTTTCAAAGGAT
1 TTTTCAAAGGAT
*
29483288 TTTTCAAAGGTT
1 TTTTCAAAGGAT
29483300 TTTTCAA
1 TTTTCAA
29483307 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:0.10, G:0.13, T:0.48
Consensus pattern (12 bp):
TTTTCAAAGGAT
Found at i:29483362 original size:5 final size:5
Alignment explanation
Indices: 29483352--29483416 Score: 62
Period size: 5 Copynumber: 12.4 Consensus size: 5
29483342 GCCTCTTGCC
*
29483352 TTTCT TTTCT TTT-T ATTTCAT TTTCT TTT-T CTTCT TTTGCT TTTGCTT
1 TTTCT TTTCT TTTCT -TTTC-T TTTCT TTTCT TTTCT TTT-CT TTT-C-T
29483400 TTTCT TTTCT TTTCT TT
1 TTTCT TTTCT TTTCT TT
29483417 GTTTTCTCTT
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
4 4 0.08
5 31 0.60
6 12 0.23
7 5 0.10
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:29485891 original size:20 final size:20
Alignment explanation
Indices: 29485833--29485899 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
29485823 AAGAAAGAAG
*
29485833 GAGCTGAAAGTAAGCTCGG-TT
1 GAGCTCAAA-TAAGCT-GGATT
** *
29485854 GAGCTCAAACGAGATGGATT
1 GAGCTCAAATAAGCTGGATT
*
29485874 GAGCTCAAATAAGCTGGATG
1 GAGCTCAAATAAGCTGGATT
29485894 GAGCTC
1 GAGCTC
29485900 GTGGAGCTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
19 2 0.05
20 27 0.73
21 8 0.22
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (20 bp):
GAGCTCAAATAAGCTGGATT
Found at i:29486662 original size:19 final size:19
Alignment explanation
Indices: 29486632--29486677 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
29486622 CAAGTTAGCT
29486632 CTCATGTAGCTCCACACCAG
1 CTCAT-TAGCTCCACACCAG
***
29486652 CTCATTAGCTCGGGACCAG
1 CTCATTAGCTCCACACCAG
29486671 CTCATTA
1 CTCATTA
29486678 TCAGCTCACG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.24, C:0.35, G:0.17, T:0.24
Consensus pattern (19 bp):
CTCATTAGCTCCACACCAG
Found at i:29487767 original size:10 final size:10
Alignment explanation
Indices: 29487752--29487778 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
29487742 TACTCCTTCA
29487752 AGCTCAAATC
1 AGCTCAAATC
29487762 AGCTCAAATC
1 AGCTCAAATC
29487772 AGCTCAA
1 AGCTCAA
29487779 CTTCAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:29489626 original size:15 final size:15
Alignment explanation
Indices: 29489606--29489653 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
29489596 TCAAAGATGG
29489606 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
29489621 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
29489636 -TTTATGGATATAAA
1 GTTTATGGATATGAA
29489650 GTTT
1 GTTT
29489654 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:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:29489633 original size:29 final size:29
Alignment explanation
Indices: 29489600--29489659 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
29489590 AAGGATTCAA
* *
29489600 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATGGATATAAAGTTTATGT
*
29489629 AGATGGATTTATGGATATAAAGTTTTTGT
1 AGATGGATTTATGGATATAAAGTTTATGT
29489658 AG
1 AG
29489660 GTTTGGTTAT
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:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATGGATATAAAGTTTATGT
Found at i:29491787 original size:6 final size:5
Alignment explanation
Indices: 29491763--29491827 Score: 62
Period size: 5 Copynumber: 12.4 Consensus size: 5
29491753 AAGAGAAAAC
*
29491763 AAAGA AAAGA AAAGAA AAAGCA AAAGCA AAAGA AGA-A AAAGA AAATGA
1 AAAGA AAAGA AAAG-A AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA
29491811 AATA-A AAAGA AAAGA AA
1 AA-AGA AAAGA AAAGA AA
29491828 GGCAAGAGGC
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
4 4 0.08
5 27 0.52
6 20 0.38
7 1 0.02
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:29491793 original size:12 final size:10
Alignment explanation
Indices: 29491763--29491827 Score: 62
Period size: 11 Copynumber: 6.2 Consensus size: 10
29491753 AAGAGAAAAC
29491763 AAAGAAAAGA
1 AAAGAAAAGA
29491773 AAAGAAAAAGCA
1 AAAG-AAAAG-A
29491785 AAAGCAAAAGA
1 AAAG-AAAAGA
*
29491796 AGA-AAAAGA
1 AAAGAAAAGA
29491805 AAATGAAATA-A
1 AAA-GAAA-AGA
29491816 AAAGAAAAGA
1 AAAGAAAAGA
29491826 AA
1 AA
29491828 GGCAAGAGGC
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
9 9 0.20
10 11 0.24
11 15 0.33
12 11 0.24
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.03
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:29491905 original size:11 final size:12
Alignment explanation
Indices: 29491873--29491903 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
29491863 TTGAGAGAAC
29491873 TTGAAAAAGCCT
1 TTGAAAAAGCCT
29491885 TTGAAAAAGCCT
1 TTGAAAAAGCCT
29491897 TTGAAAA
1 TTGAAAA
29491904 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:29491914 original size:12 final size:12
Alignment explanation
Indices: 29491906--29491930 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29491896 TTTGAAAAGC
29491906 AAAAAGAAAATG
1 AAAAAGAAAATG
29491918 AAAAAGAAAATG
1 AAAAAGAAAATG
29491930 A
1 A
29491931 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:29491927 original size:18 final size:18
Alignment explanation
Indices: 29491900--29491955 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
29491890 AAAGCCTTTG
*
29491900 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAATGAAAATGA
* *
29491919 AAAAGAAAATGAGATTGA
1 AAAAGAAAATGAAAATGA
*
29491937 AAAAGAGAATGAAAA-GA
1 AAAAGAAAATGAAAATGA
29491954 AA
1 AA
29491956 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:29491940 original size:30 final size:31
Alignment explanation
Indices: 29491906--29491987 Score: 114
Period size: 30 Copynumber: 2.7 Consensus size: 31
29491896 TTTGAAAAGC
*
29491906 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* *
29491936 AAAAAGAGAATG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
29491966 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
29491988 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:29494196 original size:30 final size:30
Alignment explanation
Indices: 29494101--29494197 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
29494091 AGCTCACTCC
* *
29494101 TAGCTC-ACTTTCAACTCATGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAACCT
* * * * * *
29494131 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
29494161 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
29494191 TAGCTCA
1 TAGCTCA
29494198 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 46 0.92
31 4 0.08
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:29496180 original size:27 final size:27
Alignment explanation
Indices: 29496140--29496280 Score: 173
Period size: 27 Copynumber: 5.2 Consensus size: 27
29496130 GAGAAGCGTC
*
29496140 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
29496167 CTGGTGGCTCTGCCAC-ATATATCTG-T
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
* *
29496193 CCTGGTGGCTATGCCACAATTATCTAAT
1 -CTGGTGGCTCTGCCACAATTATCTGAT
*
29496221 CTGGTGGCTCTGCCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
29496248 CTGGTGGCTCTACCACAA-TATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
29496275 CTGGTG
1 CTGGTG
29496281 ACTTCGTCAC
Statistics
Matches: 99, Mismatches: 8, Indels: 14
0.82 0.07 0.12
Matches are distributed among these distances:
26 11 0.11
27 84 0.85
28 4 0.04
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:29496223 original size:54 final size:54
Alignment explanation
Indices: 29496137--29496280 Score: 227
Period size: 54 Copynumber: 2.7 Consensus size: 54
29496127 ATGGAGAAGC
*
29496137 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTAATCTGGTGGCTCTGCCACATATATCT
29496191 GTCCTGGTGGCTATGCCACAATTATCTAATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTAATCTGGTGGCTCTGCCACATATATCT
* * * *
29496245 GTTCTGGTGGCTCTACCACAA-TATCTGTATCTGGTG
1 GTCCTGGTGGCTATGCCACAATTATCT-AATCTGGTG
29496281 ACTTCGTCAC
Statistics
Matches: 84, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
53 5 0.06
54 79 0.94
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCTAATCTGGTGGCTCTGCCACATATATCT
Found at i:29496292 original size:81 final size:80
Alignment explanation
Indices: 29496140--29496298 Score: 207
Period size: 81 Copynumber: 2.0 Consensus size: 80
29496130 GAGAAGCGTC
* *
29496140 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTCCTGGTGGCTAT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTACCACATATATCTGTCCTGGTGACTAT
29496205 GCCACAATTATCTAAT
66 GCCACAA-TATCTAAT
* * *
29496221 CTGGTGGCTCTGCCAC-ATATATCTGTTCTGGTGGCTCTACCACA-ATATCTGTATCTGGTGACT
1 CTGGTGGCTATGCCACAAT-TATCTGATCTGGTGGCTCTACCACATATATCTGT-CCTGGTGACT
*
29496284 -TCGTCACAATATCTA
64 AT-GCCACAATATCTA
29496299 GCAGCCTCGC
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
80 17 0.25
81 52 0.75
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (80 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTACCACATATATCTGTCCTGGTGACTAT
GCCACAATATCTAAT
Found at i:29500289 original size:21 final size:21
Alignment explanation
Indices: 29500265--29500320 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
29500255 AAGAAGAAAT
* *
29500265 GAGCTGAAATGAGCTAAATTC
1 GAGCTCAAGTGAGCTAAATTC
*
29500286 GAGCTCAAGCGAGCTAAA-TC
1 GAGCTCAAGTGAGCTAAATTC
29500306 GAGCTCAAGTGAGCT
1 GAGCTCAAGTGAGCT
29500321 GATTGGAGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.20
Consensus pattern (21 bp):
GAGCTCAAGTGAGCTAAATTC
Found at i:29500977 original size:15 final size:15
Alignment explanation
Indices: 29500957--29500990 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
29500947 ATACCTGTAG
29500957 GAATTCTCAAAAGCA
1 GAATTCTCAAAAGCA
*
29500972 GAATTCTCACAAGCA
1 GAATTCTCAAAAGCA
29500987 GAAT
1 GAAT
29500991 AGATATCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.21
Consensus pattern (15 bp):
GAATTCTCAAAAGCA
Found at i:29505094 original size:11 final size:11
Alignment explanation
Indices: 29505078--29505121 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
29505068 TTATACAAGT
29505078 AAAAAAAATCA
1 AAAAAAAATCA
*
29505089 AAAAAAATTCA
1 AAAAAAAATCA
*
29505100 AAAAAAAATTCG
1 AAAAAAAA-TCA
29505112 AAAAAAAATC
1 AAAAAAAATC
29505122 TGGAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.75, C:0.09, G:0.02, T:0.14
Consensus pattern (11 bp):
AAAAAAAATCA
Found at i:29505127 original size:13 final size:12
Alignment explanation
Indices: 29505078--29505131 Score: 67
Period size: 12 Copynumber: 4.6 Consensus size: 12
29505068 TTATACAAGT
29505078 AAAAAAAA-TC-
1 AAAAAAAATTCG
*
29505088 AAAAAAAATTCA
1 AAAAAAAATTCG
29505100 AAAAAAAATTCG
1 AAAAAAAATTCG
*
29505112 AAAAAAAATCTGG
1 AAAAAAAAT-TCG
29505125 AAAAAAA
1 AAAAAAA
29505132 GTGTTTAATG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
10 8 0.21
11 2 0.05
12 20 0.51
13 9 0.23
ACGTcount: A:0.74, C:0.07, G:0.06, T:0.13
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:29506007 original size:21 final size:21
Alignment explanation
Indices: 29505973--29506044 Score: 62
Period size: 21 Copynumber: 3.4 Consensus size: 21
29505963 ACATTCTTGT
29505973 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAAGAAAAGA
29505994 AAAGAAAAAGCAAAAGCAAAAG-
1 AAAGAAAAAGC-AAAG-AAAAGA
*
29506016 -AAGAAAAAGGAAACGAAATA-A
1 AAAGAAAAAGCAAA-GAAA-AGA
29506037 AAAGAAAA
1 AAAGAAAA
29506045 GAGAGGCAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
20 10 0.23
21 17 0.40
22 11 0.26
23 5 0.12
ACGTcount: A:0.75, C:0.06, G:0.18, T:0.01
Consensus pattern (21 bp):
AAAGAAAAAGCAAAGAAAAGA
Found at i:29506123 original size:12 final size:12
Alignment explanation
Indices: 29506115--29506139 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29506105 TTTGAAAAGC
29506115 AAAAAGAAAATG
1 AAAAAGAAAATG
29506127 AAAAAGAAAATG
1 AAAAAGAAAATG
29506139 A
1 A
29506140 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:29506136 original size:18 final size:18
Alignment explanation
Indices: 29506109--29506151 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
29506099 AAAGCCTTTG
29506109 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
29506128 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
29506146 AAAAGA
1 AAAAGA
29506152 GAGTGAAAAG
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:29506149 original size:30 final size:31
Alignment explanation
Indices: 29506115--29506196 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 31
29506105 TTTGAAAAGC
**
29506115 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGACAG
* * *
29506145 AAAAAGAGAGTG-AAAAGAAATTTGAGACAG
1 AAAAAGAAAATGAAAAAGAAATATGAGACAG
**
29506175 AAAAAGAAGTTGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
29506197 TGAAAAAGAG
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:0.63, C:0.01, G:0.22, T:0.13
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGACAG
Found at i:29506191 original size:12 final size:12
Alignment explanation
Indices: 29506174--29506218 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
29506164 ATTTGAGACA
*
29506174 GAAAAAGAAGTT
1 GAAAAAGAAATT
29506186 GAAAAAGAAATT
1 GAAAAAGAAATT
*
29506198 GAAAAAGAGATT
1 GAAAAAGAAATT
*
29506210 -AAAGAGAAA
1 GAAAAAGAAA
29506219 GAAATTGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 7 0.24
12 22 0.76
ACGTcount: A:0.64, C:0.00, G:0.22, T:0.13
Consensus pattern (12 bp):
GAAAAAGAAATT
Found at i:29508363 original size:30 final size:31
Alignment explanation
Indices: 29508329--29508425 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
29508319 AGCTCACTCC
*
29508329 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
29508359 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
29508389 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
29508419 TAGCTCA
1 TAGCTCA
29508426 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:29518949 original size:30 final size:30
Alignment explanation
Indices: 29518915--29519011 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
29518905 TAAACTAAAA
*
29518915 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * * * * *
29518945 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* *
29518975 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGATTTAGCTCGTGAGCT-AAAGT
29519005 TGAGCTA
1 TGAGCTA
29519012 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:0.14, G:0.28, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
Found at i:29519804 original size:20 final size:20
Alignment explanation
Indices: 29519781--29519822 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
29519771 CTCGGTTGAA
29519781 CTCAAACGAGCTGAAATGAG
1 CTCAAACGAGCTGAAATGAG
* *
29519801 CTCAAATGAGCTGAATTGAG
1 CTCAAACGAGCTGAAATGAG
29519821 CT
1 CT
29519823 GGACAGAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (20 bp):
CTCAAACGAGCTGAAATGAG
Found at i:29519823 original size:10 final size:10
Alignment explanation
Indices: 29519788--29519823 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
29519778 GAACTCAAAC
29519788 GAGCTGAAAT
1 GAGCTGAAAT
*
29519798 GAGCTCAAAT
1 GAGCTGAAAT
*
29519808 GAGCTGAATT
1 GAGCTGAAAT
29519818 GAGCTG
1 GAGCTG
29519824 GACAGAGCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.33, C:0.14, G:0.31, T:0.22
Consensus pattern (10 bp):
GAGCTGAAAT
Found at i:29521086 original size:36 final size:36
Alignment explanation
Indices: 29521034--29521104 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
29521024 CGAATGAGGC
* *
29521034 TGATCTGTTTTAAAAACTTCAAAACTCGTACCTTGT
1 TGATATGTTTTAAAAACTTCAAAACTCATACCTTGT
29521070 TGATATGTTTTAAAAACTTCAAAACTCATACCTTG
1 TGATATGTTTTAAAAACTTCAAAACTCATACCTTG
29521105 CTTACCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (36 bp):
TGATATGTTTTAAAAACTTCAAAACTCATACCTTGT
Found at i:29521374 original size:12 final size:12
Alignment explanation
Indices: 29521357--29521382 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29521347 CTCTTGAAAC
29521357 TCAATTTCTTTT
1 TCAATTTCTTTT
29521369 TCAATTTCTTTT
1 TCAATTTCTTTT
29521381 TC
1 TC
29521383 TTCCACATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.65
Consensus pattern (12 bp):
TCAATTTCTTTT
Found at i:29521430 original size:12 final size:12
Alignment explanation
Indices: 29521413--29521447 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
29521403 TTGATCTCTT
*
29521413 TTTCTTTTTCAC
1 TTTCTTTTTCAA
29521425 TTTCTTTTTCAA
1 TTTCTTTTTCAA
29521437 TTTCATTTTTC
1 TTTC-TTTTTC
29521448 TTTTTCTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:29521430 original size:18 final size:19
Alignment explanation
Indices: 29521409--29521454 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
29521399 ACTCTTGATC
*
29521409 TCTTTTTCTTTTTCA-CTT
1 TCTTTTTCTATTTCATCTT
* *
29521427 TCTTTTTCAATTTCATTTT
1 TCTTTTTCTATTTCATCTT
29521446 TCTTTTTCT
1 TCTTTTTCT
29521455 CATTCTCTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.72
Consensus pattern (19 bp):
TCTTTTTCTATTTCATCTT
Done.