Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 179 of 320
Found at i:59347233 original size:30 final size:28
Alignment explanation
Indices: 59347197--59347252 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
59347187 AAGCGAAAAA
* *
59347197 GAAAAAGAGTGTGTGCAAGAAAGTAAAGTT
1 GAAAAAGAGAGTGAGCAA-AAAG-AAAGTT
59347227 GAAAAAGAGAGTGAGCAAAAAGAAAG
1 GAAAAAGAGAGTGAGCAAAAAGAAAG
59347253 CGTGGAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.54, C:0.04, G:0.30, T:0.12
Consensus pattern (28 bp):
GAAAAAGAGAGTGAGCAAAAAGAAAGTT
Found at i:59350524 original size:29 final size:29
Alignment explanation
Indices: 59350491--59350547 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
59350481 ATAACCAAAC
*
59350491 CTACAAAAACTTTATATCCATAAACCCAA
1 CTACAAAAACTTCATATCCATAAACCCAA
*
59350520 CTACATAAACTTCATATCCATAAACCCA
1 CTACAAAAACTTCATATCCATAAACCCA
59350548 TCTTTGAATC
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:0.46, C:0.30, G:0.00, T:0.25
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAA
Found at i:59355805 original size:30 final size:30
Alignment explanation
Indices: 59355707--59355807 Score: 87
Period size: 30 Copynumber: 3.4 Consensus size: 30
59355697 AGTTTAAACT
*
59355707 AAAATGAGCTAAGCTTTAGCTCGTGAGCT-
1 AAAATGAGCTAAGGTTTAGCTCGTGAGCTG
* * * * * * *
59355736 AAAGTTGAGCTGAGGCTAAACTCCTAAGCTG
1 AAA-ATGAGCTAAGGTTTAGCTCGTGAGCTG
** *
59355767 AAGTTGAGCTAAGGTTTAGCTCGTGAGTTG
1 AAAATGAGCTAAGGTTTAGCTCGTGAGCTG
59355797 AAAATGAGCTA
1 AAAATGAGCTA
59355808 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 18, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
29 3 0.06
30 47 0.90
31 2 0.04
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.27
Consensus pattern (30 bp):
AAAATGAGCTAAGGTTTAGCTCGTGAGCTG
Found at i:59360065 original size:50 final size:49
Alignment explanation
Indices: 59359947--59360122 Score: 194
Period size: 50 Copynumber: 3.5 Consensus size: 49
59359937 CTGGTACGCA
* * **
59359947 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAGTCTAATACACG
*
59359996 TAGTAGCCTGCACTTAGTACTACACACGTGACCTCACCA-TCTAATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAACAGTCTAATACACG
* *** * *
59360046 TAGTAGCCTGCACTTAGTACTACACACGTGATC-ACAGTTTTCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAG---TCTAATACACG
59360097 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
59360123 TGCGACCTCA
Statistics
Matches: 109, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
49 29 0.27
50 41 0.38
51 36 0.33
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAGTCTAATACACG
Found at i:59360120 original size:101 final size:99
Alignment explanation
Indices: 59359947--59360133 Score: 268
Period size: 101 Copynumber: 1.9 Consensus size: 99
59359937 CTGGTACGCA
* * *
59359947 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCGGGTACACATAGTAGCCTGCACTTA
*
59360012 GTACTACACACGTGACCTCACCATCTAATACACG
66 GTACTACACACGCGACCTCACCATCTAATACACG
* * *
59360046 TAGTAGCCTGCACTTAGTACTACACACGTGATC-ACAGTTTTCGGGTACGCATAGTAGCCTGCAC
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAG---TCGGGTACACATAGTAGCCTGCAC
*
59360110 TTAGTACTACACATGCGACCTCAC
63 TTAGTACTACACACGCGACCTCAC
59360134 AATAGATCAT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
98 4 0.05
99 30 0.39
101 43 0.56
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCGGGTACACATAGTAGCCTGCACTTA
GTACTACACACGCGACCTCACCATCTAATACACG
Found at i:59362343 original size:9 final size:10
Alignment explanation
Indices: 59362336--59362392 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
59362326 AAGAGAAAAT
59362336 AAAGAAAAGA
1 AAAGAAAAGA
59362346 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
59362358 AAAGAAGA-A
1 AAAGAAAAGA
59362367 AAAGAAAATGA
1 AAAGAAAA-GA
59362378 AATA-AAAAGA
1 AA-AGAAAAGA
59362388 AAAGA
1 AAAGA
59362393 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:59362360 original size:6 final size:5
Alignment explanation
Indices: 59362336--59362392 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
59362326 AAGAGAAAAT
*
59362336 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
59362383 AAAGA AAAGA
1 AAAGA AAAGA
59362393 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:59362367 original size:15 final size:14
Alignment explanation
Indices: 59362336--59362392 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
59362326 AAGAGAAAAT
59362336 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
59362352 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
59362367 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
59362383 AAAGAAAAGA
1 AAAGAAAAGA
59362393 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:59362495 original size:30 final size:31
Alignment explanation
Indices: 59362461--59362542 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
59362451 TTTGAAAAGC
*
59362461 AAAAAGAAAAAGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAAAGAAAAAGAAATATGAGAGTG
* * *
59362491 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAAAGAAAAAGAAATATGAGAGTG
* *
59362521 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAAAGAAAAAGAAAT
59362543 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.66, C:0.01, G:0.22, T:0.11
Consensus pattern (31 bp):
AAAAAGAAAAAGAAAAAGAAATATGAGAGTG
Found at i:59362515 original size:24 final size:24
Alignment explanation
Indices: 59362466--59362535 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
59362456 AAAGCAAAAA
*
59362466 GAAAAAGAAAAAGAAAATGAGATT
1 GAAAAAGAAAAAGAAAATGAAATT
* *
59362490 GAAAAAGAGAACGAAAA-GAAATTT
1 GAAAAAGAAAAAGAAAATGAAA-TT
* ** *
59362514 GAGAGTGAAAAAGAAGATGAAA
1 GAAAAAGAAAAAGAAAATGAAA
59362536 AAGAAATTGA
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
23 3 0.09
24 28 0.80
25 4 0.11
ACGTcount: A:0.63, C:0.01, G:0.24, T:0.11
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAATGAAATT
Found at i:59364680 original size:30 final size:30
Alignment explanation
Indices: 59364646--59364742 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
59364636 AGCTCACTCC
59364646 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
59364676 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
59364706 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
59364736 TAGCTCA
1 TAGCTCA
59364743 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:59373517 original size:12 final size:12
Alignment explanation
Indices: 59373500--59373542 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
59373490 CATAAATCAC
59373500 TTTTTTTTCGAT
1 TTTTTTTTCGAT
* *
59373512 TTTTTTTTTGAA
1 TTTTTTTTCGAT
59373524 TTTTTTTTCGAT
1 TTTTTTTTCGAT
59373536 TTTTTTT
1 TTTTTTT
59373543 AACTTGTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.09, C:0.05, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTTTTCGAT
Found at i:59373916 original size:14 final size:14
Alignment explanation
Indices: 59373899--59373938 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
59373889 CGAATGGAAT
*
59373899 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
59373913 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
59373927 GATATGAACAAA
1 GGTAGGAACAAA
59373939 TTGGTCAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:59381679 original size:11 final size:12
Alignment explanation
Indices: 59381647--59381679 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
59381637 GAGCTACAGC
59381647 AAACTTAATTAT
1 AAACTTAATTAT
*
59381659 AAACTGAATTA-
1 AAACTTAATTAT
59381670 AAACTTAATT
1 AAACTTAATT
59381680 TATTAGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (12 bp):
AAACTTAATTAT
Found at i:59381747 original size:20 final size:21
Alignment explanation
Indices: 59381711--59381749 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
59381701 AGCTGAATCA
*
59381711 AGCTGAATTCTAGCTCAAACG
1 AGCTGAATTCGAGCTCAAACG
59381732 AGCTGAA-TCGAGCTCAAA
1 AGCTGAATTCGAGCTCAAA
59381750 TGAACTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (21 bp):
AGCTGAATTCGAGCTCAAACG
Found at i:59384068 original size:26 final size:26
Alignment explanation
Indices: 59384048--59384223 Score: 298
Period size: 26 Copynumber: 6.8 Consensus size: 26
59384038 AAAATTACTA
59384048 AAATACCCCTATAGGGTAAATTATCG
1 AAATACCCCTATAGGGTAAATTATCG
*
59384074 AAATACCCTTATAGGGTAAATTATCG
1 AAATACCCCTATAGGGTAAATTATCG
59384100 AAATACCCCTATAGGGTAAATTATCG
1 AAATACCCCTATAGGGTAAATTATCG
* *
59384126 AAATACCCTTATAGTGTAAATTATCG
1 AAATACCCCTATAGGGTAAATTATCG
*
59384152 AAATACCCCTACAGGGTAAATTATCG
1 AAATACCCCTATAGGGTAAATTATCG
* *
59384178 AAATACCCTTATAGTGTAAATTATCG
1 AAATACCCCTATAGGGTAAATTATCG
59384204 AAATACCCCTATAGGGTAAA
1 AAATACCCCTATAGGGTAAA
59384224 ATGACTGTTT
Statistics
Matches: 138, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 138 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.28
Consensus pattern (26 bp):
AAATACCCCTATAGGGTAAATTATCG
Found at i:59384115 original size:52 final size:52
Alignment explanation
Indices: 59384048--59384223 Score: 334
Period size: 52 Copynumber: 3.4 Consensus size: 52
59384038 AAAATTACTA
*
59384048 AAATACCCCTATAGGGTAAATTATCGAAATACCCTTATAGGGTAAATTATCG
1 AAATACCCCTATAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
59384100 AAATACCCCTATAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
1 AAATACCCCTATAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
*
59384152 AAATACCCCTACAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
1 AAATACCCCTATAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
59384204 AAATACCCCTATAGGGTAAA
1 AAATACCCCTATAGGGTAAA
59384224 ATGACTGTTT
Statistics
Matches: 121, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 121 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.28
Consensus pattern (52 bp):
AAATACCCCTATAGGGTAAATTATCGAAATACCCTTATAGTGTAAATTATCG
Found at i:59387095 original size:27 final size:26
Alignment explanation
Indices: 59387065--59387241 Score: 149
Period size: 27 Copynumber: 6.5 Consensus size: 26
59387055 AAATTGTACA
* *
59387065 GCACTAAGTGTACGATTCGACTATGTT
1 GCACTAAGTGTGCGATT-GACTATGTG
* *
59387092 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCG-ATTGACTATG-TG
* *
59387119 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCG-ATTGACTATGTG
* *
59387146 GCACTAAGTGTGCGAGTCCGACTATGTA
1 GCACTAAGTGTGCGA-T-TGACTATGTG
* *
59387174 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGA-TTGACTATGTG
* * *
59387201 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGA-TTGACTATGTG
*
59387228 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
59387242 GGCTCAATAT
Statistics
Matches: 124, Mismatches: 21, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
26 1 0.01
27 98 0.79
28 25 0.20
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (26 bp):
GCACTAAGTGTGCGATTGACTATGTG
Found at i:59387178 original size:82 final size:81
Alignment explanation
Indices: 59387065--59387220 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
59387055 AAATTGTACA
* * *
59387065 GCACTAAGTGTACGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTACGATCCGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
59387129 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
59387146 GCACTAAGTGTGCGAGTCCGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTACGA-TCCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
59387211 TGCGAGTTGA
65 TGCGAATTGA
59387221 TTATATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.77
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTACGATCCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:59387232 original size:82 final size:81
Alignment explanation
Indices: 59387061--59387241 Score: 211
Period size: 82 Copynumber: 2.2 Consensus size: 81
59387051 GATTAAATTG
* * * *
59387061 TACAGCACTAAGTGTACGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATCCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
59387126 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
59387142 TGCGGCACTAAGTGTGCGAGTCCGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGA-TCCGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
59387206 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
59387224 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
59387242 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
81 17 0.21
82 65 0.79
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATCCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:59389372 original size:30 final size:30
Alignment explanation
Indices: 59389325--59389418 Score: 172
Period size: 30 Copynumber: 3.2 Consensus size: 30
59389315 CAAGTAGCCG
59389325 AAGCTAG-TTAAATCGCACACTTAGTGCCA
1 AAGCTAGTTTAAATCGCACACTTAGTGCCA
*
59389354 AAGCTAGTTTAGATCGCACACTTAGTGCCA
1 AAGCTAGTTTAAATCGCACACTTAGTGCCA
59389384 AAGCTAGTTTAAATCGCACACTTAGTGCCA
1 AAGCTAGTTTAAATCGCACACTTAGTGCCA
59389414 AAGCT
1 AAGCT
59389419 TCCGATTCAT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
29 7 0.11
30 55 0.89
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (30 bp):
AAGCTAGTTTAAATCGCACACTTAGTGCCA
Found at i:59392590 original size:14 final size:14
Alignment explanation
Indices: 59392571--59392613 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
59392561 AACCGGCCAA
*
59392571 TTTGTTCATACCAT
1 TTTGTTCCTACCAT
*
59392585 TTTGTTCCTACCCT
1 TTTGTTCCTACCAT
*
59392599 TTCGTTCCTACCAT
1 TTTGTTCCTACCAT
59392613 T
1 T
59392614 CCATTCGTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.14, C:0.30, G:0.07, T:0.49
Consensus pattern (14 bp):
TTTGTTCCTACCAT
Found at i:59393389 original size:9 final size:9
Alignment explanation
Indices: 59393377--59393421 Score: 63
Period size: 9 Copynumber: 4.7 Consensus size: 9
59393367 TATACAAGTT
59393377 AAAAAAATA
1 AAAAAAATA
59393386 AAAAAAATTCGA
1 AAAAAAA-T--A
59393398 AAAAAAATA
1 AAAAAAATA
59393407 AAAAAAATA
1 AAAAAAATA
59393416 AAAAAA
1 AAAAAA
59393422 GAGTGATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
9 23 0.70
10 1 0.03
11 1 0.03
12 8 0.24
ACGTcount: A:0.84, C:0.02, G:0.02, T:0.11
Consensus pattern (9 bp):
AAAAAAATA
Found at i:59393421 original size:21 final size:21
Alignment explanation
Indices: 59393377--59393421 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
59393367 TATACAAGTT
***
59393377 AAAAAAATAAAAAAAATTCGA
1 AAAAAAATAAAAAAAATAAAA
59393398 AAAAAAATAAAAAAAATAAAA
1 AAAAAAATAAAAAAAATAAAA
59393419 AAA
1 AAA
59393422 GAGTGATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.84, C:0.02, G:0.02, T:0.11
Consensus pattern (21 bp):
AAAAAAATAAAAAAAATAAAA
Found at i:59405152 original size:14 final size:14
Alignment explanation
Indices: 59405130--59405177 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
59405120 ACCTAAACCG
*
59405130 ACCAATTTGTTCAT
1 ACCATTTTGTTCAT
*
59405144 ACCATTTTGTTCCT
1 ACCATTTTGTTCAT
* * *
59405158 ACCCTTTCGTTCTT
1 ACCATTTTGTTCAT
59405172 ACCATT
1 ACCATT
59405178 CCATTCGTAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.19, C:0.29, G:0.06, T:0.46
Consensus pattern (14 bp):
ACCATTTTGTTCAT
Found at i:59405845 original size:20 final size:22
Alignment explanation
Indices: 59405815--59405861 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
59405805 AAAGTACATA
59405815 AAAAAAGAATTAC-AAAAATAC
1 AAAAAAGAATTACGAAAAATAC
59405836 AAAAAA-AATTACGAAAAATAC
1 AAAAAAGAATTACGAAAAATAC
59405857 AAAAA
1 AAAAA
59405862 GAAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.74, C:0.09, G:0.04, T:0.13
Consensus pattern (22 bp):
AAAAAAGAATTACGAAAAATAC
Found at i:59405866 original size:24 final size:23
Alignment explanation
Indices: 59405803--59405867 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 23
59405793 TGTAAATTTT
*
59405803 GAAAAGTACATAAAAAAAGAATTAC
1 GAAAAATACA-AAAAAAA-AATTAC
59405828 -AAAAATAC--AAAAAAAATTAC
1 GAAAAATACAAAAAAAAAATTAC
59405848 GAAAAATACAAAAAGAAAAA
1 GAAAAATACAAAAA-AAAAA
59405868 AAAAGAAGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
20 6 0.17
21 14 0.40
23 3 0.09
24 12 0.34
ACGTcount: A:0.72, C:0.08, G:0.08, T:0.12
Consensus pattern (23 bp):
GAAAAATACAAAAAAAAAATTAC
Found at i:59406844 original size:30 final size:30
Alignment explanation
Indices: 59406810--59406897 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
59406800 CTAGCTTATA
* *
59406810 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
1 TTCAGCTTAAGAGCTAAACCTTAGCTCAAC
* * *
59406840 TTCAGCTTAGGAG-TATAATCTCAGCTCAAC
1 TTCAGCTTAAGAGCTA-AACCTTAGCTCAAC
* * *
59406870 TTTAGCTTAAGGGCTAAAGCTTAGCTCA
1 TTCAGCTTAAGAGCTAAACCTTAGCTCA
59406898 TTTTAGCTCA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
29 2 0.04
30 43 0.91
31 2 0.04
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (30 bp):
TTCAGCTTAAGAGCTAAACCTTAGCTCAAC
Found at i:59409261 original size:30 final size:31
Alignment explanation
Indices: 59409169--59409263 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 31
59409159 AACTAAAATA
*
59409169 AGCTAAGCTTTAGCTCGTGAGCT-AAAGTTG
1 AGCTAAGGTTTAGCTCGTGAGCTGAAAGTTG
* * * * * *
59409199 AGCTGAGGCTAAACTCCTAAGCTG-AAGTTG
1 AGCTAAGGTTTAGCTCGTGAGCTGAAAGTTG
*
59409229 AGCTAAGGTTTAGCTCGTGAGTTGAAAG-TG
1 AGCTAAGGTTTAGCTCGTGAGCTGAAAGTTG
59409259 AGCTA
1 AGCTA
59409264 GGAGTGAGCT
Statistics
Matches: 49, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
30 46 0.94
31 3 0.06
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.27
Consensus pattern (31 bp):
AGCTAAGGTTTAGCTCGTGAGCTGAAAGTTG
Found at i:59411837 original size:30 final size:30
Alignment explanation
Indices: 59411803--59411885 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 30
59411793 TAAACTAAAA
* *
59411803 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGC
* * * * * *
59411833 TGAGCTGAGATTAAACTCCTAAGCTGAAGC
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGC
59411863 TGAGCTAAGATTTAGCTCGTGAG
1 TGAGCTAAGATTTAGCTCGTGAG
59411886 TTGAATATAA
Statistics
Matches: 40, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGC
Found at i:59414155 original size:30 final size:29
Alignment explanation
Indices: 59414110--59414195 Score: 111
Period size: 30 Copynumber: 2.9 Consensus size: 29
59414100 TTCTTTTGTT
*
59414110 TCAATTTCTTTTTCATCTTCTTTTTCACTC
1 TCAATTTCTTTTTCAT-TTCTTTTTCAATC
59414140 TCAAATTTC-TTTTCATTCTCTTTTTCAATC
1 TC-AATTTCTTTTTCATT-TCTTTTTCAATC
*
59414170 TCATTTTCTTTTTCATTTTCTTTTTC
1 TCAATTTCTTTTTCA-TTTCTTTTTC
59414196 TTTTCAAAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
29 6 0.12
30 36 0.72
31 8 0.16
ACGTcount: A:0.14, C:0.23, G:0.00, T:0.63
Consensus pattern (29 bp):
TCAATTTCTTTTTCATTTCTTTTTCAATC
Found at i:59414185 original size:12 final size:12
Alignment explanation
Indices: 59414170--59414200 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
59414160 TTTTTCAATC
59414170 TCATTTTCTTTT
1 TCATTTTCTTTT
59414182 TCATTTTCTTTT
1 TCATTTTCTTTT
59414194 TC-TTTTC
1 TCATTTTC
59414201 AAAGACTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.74
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:59414194 original size:18 final size:18
Alignment explanation
Indices: 59414145--59414199 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
59414135 CACTCTCAAA
*
59414145 TTTC-TTTTCATTCTCTT
1 TTTCATTTTCATTTTCTT
* *
59414162 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
59414180 TTTCATTTTCTTTTTCTT
1 TTTCATTTTCATTTTCTT
59414198 TT
1 TT
59414200 CAAAGACTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
17 4 0.13
18 27 0.87
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:59414283 original size:5 final size:5
Alignment explanation
Indices: 59414273--59414329 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
59414263 CTCTTGCCTC
*
59414273 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
59414320 TCTTT TCTTT
1 TCTTT TCTTT
59414330 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:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:59414313 original size:15 final size:14
Alignment explanation
Indices: 59414273--59414329 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
59414263 CTCTTGCCTC
*
59414273 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
59414288 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
59414303 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
59414320 TCTTTTCTTT
1 TCTTTTCTTT
59414330 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:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:59414330 original size:21 final size:21
Alignment explanation
Indices: 59414273--59414340 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
59414263 CTCTTGCCTC
* *
59414273 TCTTTTCTTTT-TATTTCATTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
59414294 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
59414315 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
59414335 CTCTTT
1 -TCTTT
59414341 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:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:59418099 original size:30 final size:31
Alignment explanation
Indices: 59418019--59418101 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 31
59418009 CTTTTGTTTC
* *
59418019 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCATTTTCTTTTTCAATCTCA
* * *
59418050 AATTTC-TGTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTCATTTTCTTTTTCAATCTCA
* *
59418079 ATTTTCTTTTTCTTTTTCTTTTT
1 AATTTCTTTTTCATTTTCTTTTT
59418102 TCTTTTCAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
29 5 0.12
30 31 0.74
31 6 0.14
ACGTcount: A:0.12, C:0.22, G:0.02, T:0.64
Consensus pattern (31 bp):
AATTTCTTTTTCATTTTCTTTTTCAATCTCA
Found at i:59418200 original size:26 final size:25
Alignment explanation
Indices: 59418170--59418233 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 25
59418160 CTCTTGCCTC
59418170 TTCTTTCTTTT-TATTTCATTTTCTT
1 TTCTTTCTTTTCTATTTC-TTTTCTT
*
59418195 TT-TCTTCTTTTGCTTTTTCTTTTCTT
1 TTCT-TTCTTTT-CTATTTCTTTTCTT
*
59418221 TTCTTTGTTTTCT
1 TTCTTTCTTTTCT
59418234 CTTAACAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
24 1 0.03
25 11 0.33
26 15 0.45
27 6 0.18
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (25 bp):
TTCTTTCTTTTCTATTTCTTTTCTT
Found at i:59418210 original size:15 final size:14
Alignment explanation
Indices: 59418168--59418226 Score: 57
Period size: 16 Copynumber: 3.9 Consensus size: 14
59418158 GCCTCTTGCC
59418168 TCTTC-TTTCTTTT
1 TCTTCTTTTCTTTT
*
59418181 TATTTCATTTTCTTTT
1 T-CTTC-TTTTCTTTT
59418197 TCTTCTTTTGCTTTT
1 TCTTCTTTT-CTTTT
59418212 TCTTTTCTTTTCTTT
1 TC--TTCTTTTCTTT
59418227 GTTTTCTCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
13 1 0.03
14 7 0.18
15 10 0.26
16 13 0.34
17 7 0.18
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (14 bp):
TCTTCTTTTCTTTT
Found at i:59418227 original size:21 final size:20
Alignment explanation
Indices: 59418188--59418236 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
59418178 TTTTATTTCA
59418188 TTTTCTTTTTCTTCTTTTGCT
1 TTTTCTTTTTCTTCTTTTG-T
*
59418209 TTTTC-TTTTCTTTTCTTTGT
1 TTTTCTTTTTCTTCT-TTTGT
59418229 TTTCTCTT
1 TTT-TCTT
59418237 AACAAGAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 12 0.50
21 11 0.46
22 1 0.04
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (20 bp):
TTTTCTTTTTCTTCTTTTGT
Found at i:59420801 original size:30 final size:30
Alignment explanation
Indices: 59420767--59420863 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
59420757 TAAACTAAAA
59420767 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
59420797 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
59420827 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
59420857 TGAGCTA
1 TGAGCTA
59420864 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:59422067 original size:30 final size:30
Alignment explanation
Indices: 59422033--59422129 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
59422023 TAAACTAAAC
59422033 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
59422063 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
59422093 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
59422123 TGAGCTA
1 TGAGCTA
59422130 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:59440375 original size:27 final size:27
Alignment explanation
Indices: 59440336--59440513 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
59440326 AAATTGAGTC
* * * *
59440336 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
59440363 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
59440390 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
59440418 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
59440445 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
59440472 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
59440499 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
59440514 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:59440475 original size:82 final size:81
Alignment explanation
Indices: 59440357--59440512 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
59440347 TGCTATATAA
* *
59440357 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
59440422 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
59440439 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
59440503 CACTTAGTGC
65 CACTTAGTGC
59440513 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:59445222 original size:25 final size:25
Alignment explanation
Indices: 59445193--59445240 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
59445183 TTAAAATATG
* * *
59445193 AAAATAACCGTTTTGCCCCTAGGTA
1 AAAATAACCATTATACCCCTAGGTA
*
59445218 AAAATGACCATTATACCCCTAGG
1 AAAATAACCATTATACCCCTAGG
59445241 GTTTAAATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (25 bp):
AAAATAACCATTATACCCCTAGGTA
Found at i:59445324 original size:11 final size:11
Alignment explanation
Indices: 59445288--59445343 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
59445278 CATGGTATGT
59445288 ATGATATGCAC
1 ATGATATGCAC
* *
59445299 ATGACATG--T
1 ATGATATGCAC
59445308 ATGATATGCAC
1 ATGATATGCAC
*
59445319 ATGATATG--T
1 ATGATATGCAC
59445328 ATGATATGCAC
1 ATGATATGCAC
59445339 ATGAT
1 ATGAT
59445344 GTATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:59445343 original size:20 final size:20
Alignment explanation
Indices: 59445277--59445343 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
59445267 ATTTTGATAA
*
59445277 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
59445297 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
59445317 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
59445337 ACATGAT
1 ACATGAT
59445344 GTATTCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:59445422 original size:25 final size:25
Alignment explanation
Indices: 59445394--59445513 Score: 208
Period size: 25 Copynumber: 4.9 Consensus size: 25
59445384 AGGAAGTGTA
59445394 AAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTATGAT
*
59445419 AAAGGGCTTATGCCCTAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTATGAT
59445444 AAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTATGAT
*
59445469 AAAGGGCTTATGCCCCAGTTATTA-
1 AAAGGGCTTATGCCCCAGTTATGAT
59445493 AAAGGGCTT-TGCCCCAGTTAT
1 AAAGGGCTTATGCCCCAGTTAT
59445514 TAAAAGAGGC
Statistics
Matches: 92, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
23 12 0.13
24 9 0.10
25 71 0.77
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (25 bp):
AAAGGGCTTATGCCCCAGTTATGAT
Found at i:59445547 original size:75 final size:75
Alignment explanation
Indices: 59445394--59445537 Score: 206
Period size: 75 Copynumber: 1.9 Consensus size: 75
59445384 AGGAAGTGTA
* *
59445394 AAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTATGCCCTAGTTATGATAAAGGGCTTATGCCC
1 AAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTAGGCCC
59445459 CAGTTATGAT
66 CAGTTATGAT
* *
59445469 AAAGGGCTTATGCCCCAGTTATTA-AAAGGGCTT-TGCCCCAGTTATTA-AAAGAGGC-TAGGCC
1 AAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTATGCCCCAGTTATGATAAAG-GGCTTAGGCC
59445530 TCCAGTTA
65 -CCAGTTA
59445538 AATGGTAAAG
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
72 9 0.14
73 22 0.35
74 9 0.14
75 23 0.37
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (75 bp):
AAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTAGGCCC
CAGTTATGAT
Found at i:59445767 original size:31 final size:31
Alignment explanation
Indices: 59445732--59445794 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
59445722 CGTTTACAGT
*
59445732 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATACGAAATATGA
* **
59445763 AAAGGCTTCGGCCTAGTGTTACGAAATATGA
1 AAAGGCTTCGGCCCAGTAATACGAAATATGA
59445794 A
1 A
59445795 GTGTGAAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATACGAAATATGA
Found at i:59452909 original size:17 final size:18
Alignment explanation
Indices: 59452887--59452924 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
59452877 TATAATAAGG
59452887 TTATTAAGGTAAAT-TTA
1 TTATTAAGGTAAATATTA
* *
59452904 TTATTAATGTTAATATTA
1 TTATTAAGGTAAATATTA
59452922 TTA
1 TTA
59452925 AAAGAAAGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (18 bp):
TTATTAAGGTAAATATTA
Found at i:59453848 original size:22 final size:22
Alignment explanation
Indices: 59453822--59453885 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
59453812 AGCTTACCAT
*
59453822 TTCAGCACGTATGAA-CTTACTG
1 TTCAGCACG-ATAAAGCTTACTG
* *
59453844 TTCAGCTCGATAAAGCTTATTG
1 TTCAGCACGATAAAGCTTACTG
** *
59453866 TTCAGCTTGATAGAGCTTAC
1 TTCAGCACGATAAAGCTTAC
59453886 CCTTTCATCT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 4 0.11
22 31 0.89
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (22 bp):
TTCAGCACGATAAAGCTTACTG
Found at i:59461996 original size:14 final size:14
Alignment explanation
Indices: 59461977--59462003 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
59461967 TTGGTAACCT
59461977 GTAAAAGCTTTTCC
1 GTAAAAGCTTTTCC
59461991 GTAAAAGCTTTTC
1 GTAAAAGCTTTTC
59462004 AGGTATTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (14 bp):
GTAAAAGCTTTTCC
Found at i:59464779 original size:20 final size:20
Alignment explanation
Indices: 59464733--59464796 Score: 112
Period size: 20 Copynumber: 3.2 Consensus size: 20
59464723 TCCAAACACC
59464733 AGAAAAGTAAATCATTTTCA
1 AGAAAAGTAAATCATTTTCA
59464753 A-AAAAGTAAATCATTTTCA
1 AGAAAAGTAAATCATTTTCA
*
59464772 AGAAAAGTAAATCATTTTCC
1 AGAAAAGTAAATCATTTTCA
59464792 AGAAA
1 AGAAA
59464797 TAATTTTCTG
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
19 19 0.45
20 23 0.55
ACGTcount: A:0.52, C:0.11, G:0.09, T:0.28
Consensus pattern (20 bp):
AGAAAAGTAAATCATTTTCA
Found at i:59466117 original size:27 final size:28
Alignment explanation
Indices: 59466087--59466238 Score: 100
Period size: 27 Copynumber: 5.6 Consensus size: 28
59466077 CTGCAATGGC
59466087 ATTTCGA-TAATTTTACAAATTGGGGGT
1 ATTTCGAGTAATTTTACAAATTGGGGGT
* * *
59466114 ATTTC-AGTTATTTTACAAGTTGGGCGT
1 ATTTCGAGTAATTTTACAAATTGGGGGT
* * * ** * *
59466141 CTTTAGA-TAATTTCATGAATCGAGGGT
1 ATTTCGAGTAATTTTACAAATTGGGGGT
* **
59466168 ATTTCG-GTAATTTCACAAATCAGGGGT
1 ATTTCGAGTAATTTTACAAATTGGGGGT
* * **
59466195 A-TTCCAGTAATTTAACAACCTGGGGGT
1 ATTTCGAGTAATTTTACAAATTGGGGGT
*
59466222 ATTT-TAGTAATTTTACA
1 ATTTCGAGTAATTTTACA
59466239 GATCGAGGGT
Statistics
Matches: 93, Mismatches: 27, Indels: 10
0.72 0.21 0.08
Matches are distributed among these distances:
26 4 0.04
27 86 0.92
28 3 0.03
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (28 bp):
ATTTCGAGTAATTTTACAAATTGGGGGT
Found at i:59466248 original size:27 final size:26
Alignment explanation
Indices: 59466158--59466248 Score: 76
Period size: 27 Copynumber: 3.4 Consensus size: 26
59466148 TAATTTCATG
* *
59466158 AATCGAGGGTATTTCGGTAATTTCAC
1 AATCGAGGGTATTTCAGTAATTTAAC
*
59466184 AAATC-AGGGGTATTCCAGTAATTTAAC
1 -AATCGA-GGGTATTTCAGTAATTTAAC
* * * *
59466211 AACCTGGGGGTATTTTAGTAATTTTAC
1 AATC-GAGGGTATTTCAGTAATTTAAC
59466238 AGATCGAGGGT
1 A-ATCGAGGGT
59466249 CTTAACGACC
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
26 4 0.08
27 44 0.88
28 2 0.04
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (26 bp):
AATCGAGGGTATTTCAGTAATTTAAC
Found at i:59467310 original size:53 final size:53
Alignment explanation
Indices: 59467230--59467336 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
59467220 TAACACCCTT
59467230 ACATAGCACCCGATTCCAAAATGGTACTGACTGCCTACCTTGAATAGCAATCG
1 ACATAGCACCCGATTCCAAAATGGTACTGACTGCCTACCTTGAATAGCAATCG
59467283 ACATAGCACCCGATTCCAAAATGGTACTGACTGCCTACCTTGAATAGCAATCG
1 ACATAGCACCCGATTCCAAAATGGTACTGACTGCCTACCTTGAATAGCAATCG
59467336 A
1 A
59467337 TTCCTCTTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (53 bp):
ACATAGCACCCGATTCCAAAATGGTACTGACTGCCTACCTTGAATAGCAATCG
Found at i:59471444 original size:28 final size:29
Alignment explanation
Indices: 59471400--59471479 Score: 78
Period size: 28 Copynumber: 2.8 Consensus size: 29
59471390 CATACATGCT
*
59471400 TATGGCCCACTAAGCCC-AATCTCAT-TCA
1 TATGGCCCACTAAGCCCAAATCACATCT-A
*
59471428 TATGGCCCA-TCAGGCCCAAATCACATCTA
1 TATGGCCCACT-AAGCCCAAATCACATCTA
* *
59471457 TATGGCCAACT-AGGCCAAATCAC
1 TATGGCCCACTAAGCCCAAATCAC
59471480 TTTTACAGTC
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
27 1 0.02
28 24 0.56
29 16 0.37
30 2 0.05
ACGTcount: A:0.31, C:0.34, G:0.14, T:0.21
Consensus pattern (29 bp):
TATGGCCCACTAAGCCCAAATCACATCTA
Found at i:59471727 original size:16 final size:16
Alignment explanation
Indices: 59471706--59471750 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
59471696 AACTTTCAGC
59471706 TTTTCGGCATTTAAGA
1 TTTTCGGCATTTAAGA
* *
59471722 TTTTCGGCATTTCAGT
1 TTTTCGGCATTTAAGA
*
59471738 TTTTCGGGATTTA
1 TTTTCGGCATTTA
59471751 CCGATCTACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.18, C:0.13, G:0.20, T:0.49
Consensus pattern (16 bp):
TTTTCGGCATTTAAGA
Found at i:59473931 original size:93 final size:93
Alignment explanation
Indices: 59473803--59473973 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
59473793 GCCCATAAGC
* * * *
59473803 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACGCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
59473868 CGAGTTCGGATGCCTAGTTACATCTCAT
66 CGAGTTCGGATGCCTAGTTACATCTCAT
*
59473896 GAACTCGGACTCAACGCAACAAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACGCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
59473961 CGAGTTCGGATGC
66 CGAGTTCGGATGC
59473974 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACGCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAT
Found at i:59473970 original size:46 final size:46
Alignment explanation
Indices: 59473795--59473970 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
59473785 TGTAACCCGC
* * * *
59473795 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
59473841 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* * *
59473891 -C-TCA-TGAACTCGGACTCAACGCAACAAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
59473934 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
59473971 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 62 0.57
47 28 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:59479534 original size:28 final size:28
Alignment explanation
Indices: 59479493--59479579 Score: 95
Period size: 28 Copynumber: 3.1 Consensus size: 28
59479483 AAGTCCACAT
*
59479493 ACATTCTTATGGCCCACTAGGCCCAATC
1 ACATTCATATGGCCCACTAGGCCCAATC
* * *
59479521 TCATTCATATGGCCTATTAGGCCCAAATC
1 ACATTCATATGGCCCACTAGGCCC-AATC
* *
59479550 ACA-ACTATATGGCCCACTAGGCCTAATC
1 ACATTC-ATATGGCCCACTAGGCCCAATC
59479578 AC
1 AC
59479580 TTTTACAGTC
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
28 27 0.56
29 21 0.44
ACGTcount: A:0.29, C:0.32, G:0.14, T:0.25
Consensus pattern (28 bp):
ACATTCATATGGCCCACTAGGCCCAATC
Found at i:59479667 original size:17 final size:18
Alignment explanation
Indices: 59479645--59479679 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
59479635 TTTCCTATTA
59479645 TGGGCCCA-ATAGCCCAT
1 TGGGCCCATATAGCCCAT
*
59479662 TGGGCCCATTTAGCCCAT
1 TGGGCCCATATAGCCCAT
59479680 GTTGGCCCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.20, C:0.34, G:0.23, T:0.23
Consensus pattern (18 bp):
TGGGCCCATATAGCCCAT
Found at i:59480621 original size:4 final size:4
Alignment explanation
Indices: 59480614--59480639 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
59480604 ATATATAATA
59480614 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
59480640 CATACAAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:59483694 original size:67 final size:65
Alignment explanation
Indices: 59483554--59483801 Score: 213
Period size: 64 Copynumber: 3.8 Consensus size: 65
59483544 ATATAGTTCG
* * * * *
59483554 GCTCTCTTGTAC-ACATGGTG-AACAC-TCAGTACCACGCATGTGACCTAGCCA-ATTTAT-CTC
1 GCTCTCTTGT-CTACATGGTGTTACACAT-AGAACCACGCATGCGACCTAGCTACATATATCCT-
59483614 GTA
63 GTA
* * * *
59483617 GCTCTCTTGTCTACATGGTGTCCTTCACCTGGAACCACGTATGCGACCTAGCTACATATATCCTG
1 GCTCTCTTGTCTACATGGTGT--TACACATAGAACCACGCATGCGACCTAGCTACATATATCCTG
59483682 TA
64 TA
** * * * * *
59483684 GCTCTCTTGTCTACATGGTG-TACACATATTATCACCCATGCAACCTAGCTGCATATATCCCGTA
1 GCTCTCTTGTCTACATGGTGTTACACATAGAACCACGCATGCGACCTAGCTACATATATCCTGTA
** * * *
59483748 GCTCTCTTGTCTACATGGTG-TACACATATTATCACCCATGCAACCTAGCTACAT
1 GCTCTCTTGTCTACATGGTGTTACACATAGAACCACGCATGCGACCTAGCTACAT
59483802 CATAATGTTT
Statistics
Matches: 158, Mismatches: 20, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
62 1 0.01
63 18 0.11
64 86 0.54
66 22 0.14
67 29 0.18
68 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (65 bp):
GCTCTCTTGTCTACATGGTGTTACACATAGAACCACGCATGCGACCTAGCTACATATATCCTGTA
Found at i:59483751 original size:64 final size:64
Alignment explanation
Indices: 59483657--59483801 Score: 263
Period size: 64 Copynumber: 2.3 Consensus size: 64
59483647 GGAACCACGT
* *
59483657 ATGCGACCTAGCTACATATATCCTGTAGCTCTCTTGTCTACATGGTGTACACATATTATCACCC
1 ATGCAACCTAGCTACATATATCCCGTAGCTCTCTTGTCTACATGGTGTACACATATTATCACCC
*
59483721 ATGCAACCTAGCTGCATATATCCCGTAGCTCTCTTGTCTACATGGTGTACACATATTATCACCC
1 ATGCAACCTAGCTACATATATCCCGTAGCTCTCTTGTCTACATGGTGTACACATATTATCACCC
59483785 ATGCAACCTAGCTACAT
1 ATGCAACCTAGCTACAT
59483802 CATAATGTTT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 77 1.00
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (64 bp):
ATGCAACCTAGCTACATATATCCCGTAGCTCTCTTGTCTACATGGTGTACACATATTATCACCC
Found at i:59484571 original size:30 final size:30
Alignment explanation
Indices: 59484536--59484596 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
59484526 TCCTTAACTC
*
59484536 AAACTTTTGCAAAATTATAATTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
* * *
59484566 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
59484596 A
1 A
59484597 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.41
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACAATTTTGCCCCT
Found at i:59486807 original size:47 final size:47
Alignment explanation
Indices: 59486744--59487273 Score: 853
Period size: 47 Copynumber: 11.3 Consensus size: 47
59486734 CCCTTCGGGA
* * *
59486744 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * * * *
59486791 CTTATCACATATATACACCTCCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
59486838 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
59486885 CTTATCACATATATACACTTTCACATTCATTACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
59486932 CTTGTCACATATATACACTTTCACATTAATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * *
59486979 TTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
59487026 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
59487073 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
59487120 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
59487167 TTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
59487214 CTTGTCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
59487261 CTTATCACATATA
1 CTTATCACATATA
59487274 CATATCTTGT
Statistics
Matches: 444, Mismatches: 39, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 444 1.00
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
Found at i:59487082 original size:22 final size:22
Alignment explanation
Indices: 59487054--59487129 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
59487044 TTTCACATTC
59487054 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
59487076 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
59487100 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
59487123 ATCACAT
1 ATCACAT
59487130 ATATACACTT
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 18 0.46
23 5 0.13
24 5 0.13
25 11 0.28
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:59492013 original size:44 final size:44
Alignment explanation
Indices: 59491942--59492092 Score: 159
Period size: 43 Copynumber: 3.5 Consensus size: 44
59491932 TATGTGTTAT
* * *
59491942 CGTGTAAGACCACGTCTAGGACGTTGGCATCGACT-TATGATTTA
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGA-TATTTGATTTA
*
59491986 CGTGTAAGACCATGTCTGGGACATTGGCATC-ATATTTGATTT-
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGATATTTGATTTA
* * * *
59492028 TGTGTAAGACC-CTATCTGGGACAGTGGCATTGATATTTGA-TTA
1 CGTGTAAGACCAC-GTCTGGGACATTGGCATCGATATTTGATTTA
* *
59492071 CATGTAAGACCACGTCTCGGAC
1 CGTGTAAGACCACGTCTGGGAC
59492093 GTTGCCATTG
Statistics
Matches: 89, Mismatches: 13, Indels: 11
0.79 0.12 0.10
Matches are distributed among these distances:
42 28 0.31
43 32 0.36
44 29 0.33
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (44 bp):
CGTGTAAGACCACGTCTGGGACATTGGCATCGATATTTGATTTA
Found at i:59492078 original size:43 final size:42
Alignment explanation
Indices: 59491983--59492082 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 42
59491973 GACTTATGAT
* *
59491983 TTACGTGTAAGACCATGTCTGGGACATTGGCATCATATTTGA
1 TTACGTGTAAGACCATATCTGGGACAGTGGCATCATATTTGA
** * *
59492025 TTTTGTGTAAGACCCTATCTGGGACAGTGGCATTGATATTTGA
1 TTACGTGTAAGACCATATCTGGGACAGTGGCA-TCATATTTGA
*
59492068 TTACATGTAAGACCA
1 TTACGTGTAAGACCA
59492083 CGTCTCGGAC
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
42 27 0.57
43 20 0.43
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (42 bp):
TTACGTGTAAGACCATATCTGGGACAGTGGCATCATATTTGA
Found at i:59495765 original size:47 final size:47
Alignment explanation
Indices: 59495706--59495990 Score: 430
Period size: 47 Copynumber: 6.1 Consensus size: 47
59495696 GAAATGATAG
* *
59495706 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
59495753 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
59495800 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
59495847 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
59495894 TAAGGCCTAATGGCCGATGTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * *
59495940 -CAGGGCTGATTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCT-AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
59495987 TAAG
1 TAAG
59495991 TCCCGAAGGG
Statistics
Matches: 222, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
45 5 0.02
46 35 0.16
47 180 0.81
48 2 0.01
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:59496165 original size:37 final size:37
Alignment explanation
Indices: 59496109--59496187 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
59496099 CCGAGCTCTA
* * * *
59496109 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCAATAACTACGTGTGGAGATTATGTCCGGGT
*
59496146 AAGACCCAATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCAATAACTACGTGTGGAGATTATGTCCGGGT
59496183 AAGAC
1 AAGAC
59496188 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCAATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:59498085 original size:43 final size:43
Alignment explanation
Indices: 59498037--59498182 Score: 274
Period size: 43 Copynumber: 3.4 Consensus size: 43
59498027 TTGGTTTTCA
59498037 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
*
59498080 GCACTAAGTGTGCGGGCAATAAGTGTTCGCGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
59498123 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
*
59498166 GCACTAAGTGTGTGGGC
1 GCACTAAGTGTGCGGGC
59498183 TTGAAATGCA
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 100 1.00
ACGTcount: A:0.22, C:0.14, G:0.36, T:0.27
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:59498199 original size:29 final size:29
Alignment explanation
Indices: 59498164--59498237 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
59498154 GTTGTGAGAT
* * *
59498164 TGGCACTAAGTGTGTGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
59498193 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
59498222 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
59498238 TGGTTGATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 5 0.12
29 35 0.88
ACGTcount: A:0.26, C:0.15, G:0.32, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:59498676 original size:40 final size:40
Alignment explanation
Indices: 59498627--59498823 Score: 259
Period size: 40 Copynumber: 4.9 Consensus size: 40
59498617 GAATTACTAA
* *
59498627 ATCCAGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
*
59498667 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
* *
59498707 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
* ** * * *
59498747 ATCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
* * * *
59498787 GTCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
59498824 CGTGTATTCG
Statistics
Matches: 139, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 139 1.00
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
Found at i:59498685 original size:80 final size:80
Alignment explanation
Indices: 59498585--59498823 Score: 223
Period size: 80 Copynumber: 3.0 Consensus size: 80
59498575 CTAAGCGACC
* ** *
59498585 ATATCCGGACTAAGACCCGAAG-GCATTGGTG-TGAATTACTAAATCCAGGCTAAGTCCCGAAGA
1 ATATCCGGGCTAAGACCCGAAGAGCATTCATGCT-AATGA-TAAATCCAGGCTAAGTCCCGAAGA
59498648 GCATTCATGCTAGTGAT
64 GCATTCATGCTAGTGAT
* * * ** * *
59498665 GTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGC
1 ATATCCGGGCTAAGACCCGAAGAGCATTCATGCTAATGATAAATCCAGGCTAAGTCCCGAAGAGC
*
59498730 ATTCGTGCTAGTGAT
66 ATTCATGCTAGTGAT
* * ** * ** * *
59498745 ATATCCGTGCTAA-ACCCCGAAGAGCATTCGTGCTGGTGTTATGTCCGGGCTAGGTCCCGAAGAG
1 ATATCCGGGCTAAGA-CCCGAAGAGCATTCATGCTAATGATAAATCCAGGCTAAGTCCCGAAGAG
* *
59498809 CAATCATGCTGGTGA
65 CATTCATGCTAGTGA
59498824 CGTGTATTCG
Statistics
Matches: 131, Mismatches: 25, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
80 120 0.92
81 10 0.08
82 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGAGCATTCATGCTAATGATAAATCCAGGCTAAGTCCCGAAGAGC
ATTCATGCTAGTGAT
Found at i:59502415 original size:47 final size:47
Alignment explanation
Indices: 59502356--59502640 Score: 428
Period size: 47 Copynumber: 6.1 Consensus size: 47
59502346 GAAATGATAG
* *
59502356 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
59502403 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
59502450 TAAGGCCTAATGGCCGATGTGATGAATATGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
59502497 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
59502544 TAAGGCCTAATGGCCGATGTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * * *
59502590 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
59502637 TAAG
1 TAAG
59502641 TCCCGAAGGG
Statistics
Matches: 220, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
46 40 0.18
47 180 0.82
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:59502816 original size:37 final size:37
Alignment explanation
Indices: 59502760--59502838 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
59502750 CCGAGCTCTA
* * *
59502760 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
59502797 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
59502834 AAGAC
1 AAGAC
59502839 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:59514281 original size:43 final size:43
Alignment explanation
Indices: 59514220--59514334 Score: 187
Period size: 43 Copynumber: 2.7 Consensus size: 43
59514210 AATAAACTCG
*
59514220 CACACTTAGTGCTAATTAATTAACCGAAGCTATAATTGTATCC
1 CACACTTAGTGCCAATTAATTAACCGAAGCTATAATTGTATCC
*
59514263 CACACTTAGTGCCAATTAATTAACCGAAGCTATAATTGTATCG
1 CACACTTAGTGCCAATTAATTAACCGAAGCTATAATTGTATCC
59514306 CACACTTAGTGCCAA-TAGATTAAACCGAA
1 CACACTTAGTGCCAATTA-ATT-AACCGAA
59514335 CTTATATCGG
Statistics
Matches: 68, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
42 2 0.03
43 59 0.87
44 7 0.10
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.29
Consensus pattern (43 bp):
CACACTTAGTGCCAATTAATTAACCGAAGCTATAATTGTATCC
Found at i:59519513 original size:29 final size:29
Alignment explanation
Indices: 59519481--59519537 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
59519471 ATTTACTCAT
59519481 ACATGATCAACATCTCATAATTTAACCCC
1 ACATGATCAACATCTCATAATTTAACCCC
** * *
59519510 ACATTTTCATCATTTCATAATTTAACCC
1 ACATGATCAACATCTCATAATTTAACCC
59519538 TTAAATGGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.35
Consensus pattern (29 bp):
ACATGATCAACATCTCATAATTTAACCCC
Found at i:59523062 original size:47 final size:47
Alignment explanation
Indices: 59523009--59523265 Score: 361
Period size: 47 Copynumber: 5.5 Consensus size: 47
59522999 ATTCAGCCAA
*
59523009 GAAAGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGACGTGATGAATGT
*
59523056 GAAAGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGACGTGATGAATGT
* *
59523103 GAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGACGTGATGAATGT
* * *
59523150 GAAAGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGACGTGATGAATGT
* * * * * * * *
59523197 GAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTAATGGATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGACGTGATGAATGT
* *
59523244 GAAAGTGCATAAATGTGATAAG
1 GAAAGTGTATATATGTGATAAG
59523266 TCCCGAAAGG
Statistics
Matches: 193, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 193 1.00
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.27
Consensus pattern (47 bp):
GAAAGTGTATATATGTGATAAGGCCTAATAGCCGACGTGATGAATGT
Found at i:59523373 original size:37 final size:37
Alignment explanation
Indices: 59523317--59523395 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
59523307 CCGAGCTCTA
* * *
59523317 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
59523354 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
59523391 AAGAC
1 AAGAC
59523396 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:59525300 original size:43 final size:43
Alignment explanation
Indices: 59525239--59525341 Score: 197
Period size: 43 Copynumber: 2.4 Consensus size: 43
59525229 TTGGTTTTCA
59525239 GCACTAAGTGTGCGGGCAATAAGTGTTCACAGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACAGTTGTGAGATTG
*
59525282 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACAGTTGTGAGATTG
59525325 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
59525342 TTGAAATGCA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.23, C:0.16, G:0.35, T:0.26
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACAGTTGTGAGATTG
Found at i:59525358 original size:29 final size:29
Alignment explanation
Indices: 59525323--59525396 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
59525313 GTTGTGAGAT
* *
59525323 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
* *
59525352 TGGCACTAAGTGTGCAAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
59525381 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
59525397 TGGTTGATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.13
29 34 0.87
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:59525834 original size:40 final size:40
Alignment explanation
Indices: 59525711--59525986 Score: 279
Period size: 40 Copynumber: 6.9 Consensus size: 40
59525701 TTGAATGATG
** *
59525711 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGA-TATA
* * ** * * * *
59525751 TCCGGACTAAGACCCGAAG-GCATTGGTGCGAGTTACAAAA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA-TATA
*
59525791 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
*
59525831 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* *
59525871 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* ** * * * *
59525911 TCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTATG
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* * *
59525951 TCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
59525987 CGTGTATTCG
Statistics
Matches: 201, Mismatches: 33, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
40 183 0.91
41 18 0.09
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
Found at i:59528688 original size:47 final size:47
Alignment explanation
Indices: 59528635--59529036 Score: 579
Period size: 47 Copynumber: 8.5 Consensus size: 47
59528625 ATTCAGCCAA
* * *
59528635 GAAAGTGTATCTGTGTGATAAGGCCTAATAGCCGACGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGT
*
59528682 GAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGT
*
59528729 GAAAGTGTATGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGT
1 GAAA--G--TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGT
* *
59528780 GAAAGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGT
*
59528827 GAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGT
* *
59528874 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGCGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGT
*
59528921 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGT
* * * * * * * *
59528968 GAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTAATGGATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGT
* *
59529015 GAAAGTGCATAAATGTGATAAG
1 GAAAGTGTATATATGTGATAAG
59529037 TCCCGAAAGG
Statistics
Matches: 329, Mismatches: 22, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
47 283 0.86
49 2 0.01
51 44 0.13
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
GAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGT
Found at i:59529211 original size:37 final size:37
Alignment explanation
Indices: 59529155--59529233 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
59529145 CCGAGCTCTA
* * *
59529155 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
59529192 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
59529229 AAGAC
1 AAGAC
59529234 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:59531916 original size:46 final size:46
Alignment explanation
Indices: 59531849--59532023 Score: 203
Period size: 46 Copynumber: 3.8 Consensus size: 46
59531839 AACCCGCCCC
* *
59531849 TAAGTGAACTCGGGCTCAACTCAACGAGCTCAGG-TGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-GGATGTTCGCATCCA
* * * *
59531895 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAG-TTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG-TTCGCATCCA
* * **
59531941 TTTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 --TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCGCATCCA
59531988 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG
59532024 CTCAACCATC
Statistics
Matches: 105, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
45 4 0.04
46 65 0.62
47 34 0.32
48 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCGCATCCA
Found at i:59531967 original size:93 final size:93
Alignment explanation
Indices: 59531854--59532024 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
59531844 GCCCCTAAGT
* **
59531854 GAACTCGGGCTCAACTCAACGAGCTCAGG-TGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
59531918 ACGAGTTCGGATGCCTAGTTACATTTCAC
65 ACGAGTTCGGATGCCTAGTTACATTTCAC
*
59531947 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
59532012 CGAGTTCGGATGC
66 CGAGTTCGGATGC
59532025 TCAACCATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:59535253 original size:43 final size:43
Alignment explanation
Indices: 59535142--59535295 Score: 132
Period size: 43 Copynumber: 3.6 Consensus size: 43
59535132 AATGCTAACA
* ** **
59535142 TCCCAGACGTGGTCTTACATGT-AATCAAATATCGATGCCTCTG
1 TCCCAGACATGGTCTTACACATAAATCAAATAT-GATGCCAATG
* * * * *
59535185 CCCCAAACAGGGTCTTACAC-GAAATCAAATATGATGCGAATG
1 TCCCAGACATGGTCTTACACATAAATCAAATATGATGCCAATG
* ** * *
59535227 TCCCAGACATGGTCTTACACATAAATCATAGGTCATTGCCAACG
1 TCCCAGACATGGTCTTACACATAAATCAAATATGA-TGCCAATG
59535271 TCCCAGACATGGTCTTACACGATAA
1 TCCCAGACATGGTCTTACAC-ATAA
59535296 CACATATCGG
Statistics
Matches: 88, Mismatches: 19, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
42 24 0.27
43 34 0.39
44 26 0.30
45 4 0.05
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.25
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACACATAAATCAAATATGATGCCAATG
Found at i:59551949 original size:42 final size:44
Alignment explanation
Indices: 59551858--59551963 Score: 119
Period size: 42 Copynumber: 2.5 Consensus size: 44
59551848 AGACCACATT
* * *
59551858 TGGGACATTGGCATCGATTTGAGATTTACGTATAAGACCATGTT
1 TGGGATATTGGCATCGATATGAGATTTACGTATAAGACCATGTC
* *
59551902 TGGGATATTGGCATC-ATAT-ATGATTT-CGTTTAAGACCCTGTC
1 TGGGATATTGGCATCGATATGA-GATTTACGTATAAGACCATGTC
* *
59551944 TGGGATAATGGCATTGATAT
1 TGGGATATTGGCATCGATAT
59551964 TTGATTACAT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
42 27 0.51
43 12 0.23
44 14 0.26
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (44 bp):
TGGGATATTGGCATCGATATGAGATTTACGTATAAGACCATGTC
Found at i:59559633 original size:42 final size:43
Alignment explanation
Indices: 59559516--59559666 Score: 126
Period size: 43 Copynumber: 3.5 Consensus size: 43
59559506 TAGGATTCCA
* * *** * *
59559516 ATATGTGACTTCGTGTAAGACCACATCTGGGACATTGGCATCA
1 ATATATGATTTCGTGTAAGACCATGGCTGGGACAGTGGCATCG
* ** * *
59559559 ATTTGA-GATTTACGTGTAAGACCATGTTTGGGATATTGGCATCG
1 ATAT-ATGATTT-CGTGTAAGACCATGGCTGGGACAGTGGCATCG
*
59559603 -TATATGATTTCGTGTAAGACCCTGGCTGGGACAGTGGCATCG
1 ATATATGATTTCGTGTAAGACCATGGCTGGGACAGTGGCATCG
* * *
59559645 ATATCTGATTACATGTAAGACC
1 ATATATGATTTCGTGTAAGACC
59559667 TCGTCTGGGA
Statistics
Matches: 87, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
42 28 0.32
43 32 0.37
44 27 0.31
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.31
Consensus pattern (43 bp):
ATATATGATTTCGTGTAAGACCATGGCTGGGACAGTGGCATCG
Found at i:59559665 original size:43 final size:42
Alignment explanation
Indices: 59559568--59559691 Score: 117
Period size: 42 Copynumber: 2.9 Consensus size: 42
59559558 AATTTGAGAT
** * *
59559568 TTACGTGTAAGACCATGTTTGGGATATTGGCATCGTATATGA
1 TTACGTGTAAGACCATGGCTGGGACAGTGGCATCGTATATGA
* * *
59559610 TTTCGTGTAAGACCCTGGCTGGGACAGTGGCATCGATATCTGA
1 TTACGTGTAAGACCATGGCTGGGACAGTGGCATCG-TATATGA
* * *
59559653 TTACATGTAAGACC-TCGTCTGGGAC-GTTGGCATTGTATA
1 TTACGTGTAAGACCAT-GGCTGGGACAG-TGGCATCGTATA
59559692 AGCTTTTCGA
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
42 34 0.51
43 33 0.49
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.32
Consensus pattern (42 bp):
TTACGTGTAAGACCATGGCTGGGACAGTGGCATCGTATATGA
Found at i:59562641 original size:27 final size:26
Alignment explanation
Indices: 59562585--59562641 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
59562575 CAACCTTAAC
* * *
59562585 CCTAGGGGTATATCAGTAATTTTGCT
1 CCTAGGGGTAAATCAGTAATTTTCCA
59562611 CCTAGGGGTAAATCTA-TAAATTTTCCA
1 CCTAGGGGTAAATC-AGT-AATTTTCCA
59562638 CCTA
1 CCTA
59562642 TAAAGGTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (26 bp):
CCTAGGGGTAAATCAGTAATTTTCCA
Found at i:59564881 original size:3 final size:3
Alignment explanation
Indices: 59564873--59564901 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
59564863 TTTTTCCTAT
59564873 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
59564902 TTTATAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:59564919 original size:24 final size:23
Alignment explanation
Indices: 59564892--59564950 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
59564882 ATAATAATAA
*
59564892 TAATAATAATTTTATAAATATATC
1 TAATAATAAATTTA-AAATATATC
* * *
59564916 TAATAAAAAAATTTAAAATATCTG
1 TAAT-AATAAATTTAAAATATATC
59564940 TAATAATAAAT
1 TAATAATAAAT
59564951 ACAGTAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 6 0.21
24 15 0.52
25 8 0.28
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (23 bp):
TAATAATAAATTTAAAATATATC
Found at i:59569063 original size:27 final size:27
Alignment explanation
Indices: 59569033--59569111 Score: 115
Period size: 27 Copynumber: 3.0 Consensus size: 27
59569023 AATCTCATAT
* *
59569033 CTGTAGGCTAGCATTACTGAAATACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
*
59569060 CTGTAGGGTAGAATTACTGAAATGCCC
1 CTGTAGGGTAGAATTACTGAAATACCC
*
59569087 CTGTAGGGTAGAATTAC-CAAATACC
1 CTGTAGGGTAGAATTACTGAAATACC
59569112 TTTGGTTTAC
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
26 6 0.13
27 41 0.87
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (27 bp):
CTGTAGGGTAGAATTACTGAAATACCC
Found at i:59569127 original size:26 final size:27
Alignment explanation
Indices: 59569098--59569220 Score: 124
Period size: 27 Copynumber: 4.6 Consensus size: 27
59569088 TGTAGGGTAG
** *
59569098 AATTACC-AAATACCTTTGGTTTACAA
1 AATTACCAAAATACCCCTAGTTTACAA
**
59569124 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTACAA
**
59569151 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTACAA
* ***
59569178 AATAACCAAAATACCCCT-GATTTGTGA
1 AATTACCAAAATACCCCTAG-TTTACAA
59569205 AATTACCAAAATACCC
1 AATTACCAAAATACCC
59569221 TCGACCTGTA
Statistics
Matches: 87, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
26 8 0.09
27 79 0.91
ACGTcount: A:0.41, C:0.23, G:0.07, T:0.28
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAGTTTACAA
Found at i:59569146 original size:27 final size:27
Alignment explanation
Indices: 59569122--59569355 Score: 192
Period size: 27 Copynumber: 8.7 Consensus size: 27
59569112 TTTGGTTTAC
59569122 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
59569149 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
*
59569176 AAAATAACCAAAATACCCCT-GATTTGT
1 AAAATTACCAAAATACCCCTAG-TTTGT
* * **
59569203 GAAATTACCAAAATA-CCCTCGACCTGT
1 AAAATTACCAAAATACCCCTAG-TTTGT
* * * *
59569230 AAAATTACCGAAATA-CCTTCGACTTGT
1 AAAATTACCAAAATACCCCTAG-TTTGT
* * *
59569257 AAAATTATCGAAATACCCGCGA-TTTGT
1 AAAATTACCAAAATACCC-CTAGTTTGT
* *
59569284 AAAGTTACCAAAATACCCCTAATTT-T
1 AAAATTACCAAAATACCCCTAGTTTGT
* * * * *
59569310 GAAAAGTACCGAAATACCCTTAATTTGG
1 -AAAATTACCAAAATACCCCTAGTTTGT
*
59569338 AAAGTTA-CAGAAATACCC
1 AAAATTACCA-AAATACCC
59569356 TTGACTTTCA
Statistics
Matches: 173, Mismatches: 26, Indels: 16
0.80 0.12 0.07
Matches are distributed among these distances:
26 9 0.05
27 162 0.94
28 2 0.01
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTAGTTTGT
Found at i:59569351 original size:81 final size:82
Alignment explanation
Indices: 59569123--59569355 Score: 230
Period size: 81 Copynumber: 2.9 Consensus size: 82
59569113 TTGGTTTACA
* * * * *
59569123 AAATTACCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATAACCA-
1 AAATTACCAAAATACCCCTAACTTTG-AAAATTACCGAAATACCCTTAATTTGTAAAATTACCAG
59569186 AAATACCCCTGATTTGTG
65 AAATACCCCTGATTTGTG
* * * * * *
59569204 AAATTACCAAAATACCCTCGACCTGT-AAAATTACCGAAATA-CCTTCGACTTGTAAAATTATC-
1 AAATTACCAAAATACCC-CTAACTTTGAAAATTACCGAAATACCCTT-AATTTGTAAAATTACCA
59569266 GAAATACCCGC-GATTTGT-
64 GAAATACCC-CTGATTTGTG
* * * *
59569284 AAAGTTACCAAAATACCCCTAATTTTGAAAAGTACCGAAATACCCTTAATTTGGAAAGTTA-CAG
1 AAA-TTACCAAAATACCCCTAACTTTGAAAATTACCGAAATACCCTTAATTTGTAAAATTACCAG
59569348 AAATACCC
65 AAATACCC
59569356 TTGACTTTCA
Statistics
Matches: 123, Mismatches: 20, Indels: 18
0.76 0.12 0.11
Matches are distributed among these distances:
80 11 0.09
81 104 0.85
82 6 0.05
83 2 0.02
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.27
Consensus pattern (82 bp):
AAATTACCAAAATACCCCTAACTTTGAAAATTACCGAAATACCCTTAATTTGTAAAATTACCAGA
AATACCCCTGATTTGTG
Found at i:59569427 original size:27 final size:27
Alignment explanation
Indices: 59569376--59569432 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
59569366 AAAATTATAT
* *
59569376 AAATACCATTGGTTTGCATAATTACTA
1 AAATACCATTGGTTTGCAGAATTACCA
* *
59569403 AAATACCATTGGTTTGTAGATTTACCA
1 AAATACCATTGGTTTGCAGAATTACCA
59569430 AAA
1 AAA
59569433 CATCCTTGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (27 bp):
AAATACCATTGGTTTGCAGAATTACCA
Found at i:59569510 original size:27 final size:26
Alignment explanation
Indices: 59569480--59569556 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 26
59569470 AGGTAAAAAA
59569480 ACCGTAATGCCCCTGTAGGGTGAAATG
1 ACCGTAATGCCCCTGTAGGGT-AAATG
* *
59569507 ACCGTAAAGCCCCTGTAGAGTAAATTG
1 ACCGTAATGCCCCTGTAGGGTAAA-TG
* *
59569534 ACC-TAATACCCCTGTATGGTAAA
1 ACCGTAATGCCCCTGTAGGGTAAA
59569557 ATGATGATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
26 19 0.44
27 24 0.56
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.23
Consensus pattern (26 bp):
ACCGTAATGCCCCTGTAGGGTAAATG
Found at i:59569779 original size:27 final size:27
Alignment explanation
Indices: 59569702--59569780 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
59569692 GGAAGTTCTG
* * *
59569702 TACTGGTGACTATGCCACATTCACTGT
1 TACTGGTGGCTATGCCACATTTACTGA
* *
59569729 TAGTGGTGGCTATGCCACAATTACTGA
1 TACTGGTGGCTATGCCACATTTACTGA
*
59569756 TACTGGTGGCTTTGCCACATTTACT
1 TACTGGTGGCTATGCCACATTTACT
59569781 ATTTCTGGCA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.34
Consensus pattern (27 bp):
TACTGGTGGCTATGCCACATTTACTGA
Found at i:59571109 original size:31 final size:31
Alignment explanation
Indices: 59571074--59571135 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
59571064 CTAGGAAATA
*
59571074 TGGAATGTTGAAAAAGATTTAGGCAACTATT
1 TGGAATGTTGAAAAAGAATTAGGCAACTATT
*
59571105 TGGAATGTTGAAAATGAATTAGGCAACTATT
1 TGGAATGTTGAAAAAGAATTAGGCAACTATT
59571136 GTTTGGATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (31 bp):
TGGAATGTTGAAAAAGAATTAGGCAACTATT
Found at i:59572110 original size:10 final size:10
Alignment explanation
Indices: 59572073--59572109 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
59572063 GAACATGTTG
59572073 AATTTTAATT
1 AATTTTAATT
59572083 AATTTATAATT
1 AATTT-TAATT
*
59572094 AATTTTGATT
1 AATTTTAATT
59572104 AATTTT
1 AATTTT
59572110 GGTTTTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (10 bp):
AATTTTAATT
Found at i:59579820 original size:20 final size:20
Alignment explanation
Indices: 59579795--59579857 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
59579785 ATTTTGATAA
59579795 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
59579815 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
*
59579835 ACATGATATGTGTGATATGC
1 ACATGATATGTATGATATGC
59579855 ACA
1 ACA
59579858 CGAGATGTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:59579936 original size:24 final size:24
Alignment explanation
Indices: 59579909--59580052 Score: 197
Period size: 24 Copynumber: 6.0 Consensus size: 24
59579899 GGAGGAAGTG
59579909 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
59579933 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
59579957 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
59579981 -TAAAGGGCTTATGCCCCAGTTATT
1 CAAAAGGGCTTATGCCCCAGTTA-T
*
59580005 AAAAAGGGCTT-TGCCCCAGTTA-
1 CAAAAGGGCTTATGCCCCAGTTAT
*
59580027 CTAAAAGAGGC-TAGGCCTCCAGTTAT
1 C-AAAAG-GGCTTATGCC-CCAGTTAT
59580053 ATGATAAAGC
Statistics
Matches: 109, Mismatches: 4, Indels: 12
0.87 0.03 0.10
Matches are distributed among these distances:
23 27 0.25
24 66 0.61
25 16 0.15
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.26
Consensus pattern (24 bp):
CAAAAGGGCTTATGCCCCAGTTAT
Found at i:59580033 original size:71 final size:72
Alignment explanation
Indices: 59579911--59580052 Score: 211
Period size: 71 Copynumber: 2.0 Consensus size: 72
59579901 AGGAAGTGCA
* *
59579911 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-C
1 AAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCTC
59579974 CAGTTATT
65 CAGTTATT
59579982 AAAGGGCTTATGCCCCAGTTATTAAAAAGGGCTT-TGCCCCAGTTA-CTAAAAGAGGCTAGGCCT
1 AAAGGGCTTATGCCCCAGTTA-TAAAAAGGGCTTATGCCCCAGTTATC-AAAAGAGGCTAGGCCT
59580045 CCAGTTAT
64 CCAGTTAT
59580053 ATGATAAAGC
Statistics
Matches: 65, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
70 1 0.02
71 42 0.65
72 22 0.34
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (72 bp):
AAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTCC
AGTTATT
Found at i:59586145 original size:40 final size:40
Alignment explanation
Indices: 59586090--59586400 Score: 446
Period size: 40 Copynumber: 7.8 Consensus size: 40
59586080 GGATATAGCT
* * *
59586090 ACTCGCTCAAATGCCTTCGGGACATAGCCCGG-TTAGAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
*
59586130 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
*
59586170 ACTCGCACAAATGCCTTCGGGACTTAGCCTGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
*
59586210 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * *
59586250 ACTCACACAATTGCCTTCGGGACTTAGCGCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
*
59586290 ACTCGCACAAATGCCTTCGGGACTTAGCTCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
** *
59586330 ACTCGCACAAATGCCTTCGGGACTT-GCCCGGAACTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* ** *
59586369 ACTAGTGCAGATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
59586401 TTTTCATCCA
Statistics
Matches: 248, Mismatches: 21, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
39 31 0.12
40 215 0.87
41 2 0.01
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:59593446 original size:27 final size:27
Alignment explanation
Indices: 59593416--59593593 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
59593406 ATATTGAGCC
* *
59593416 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
59593443 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
59593470 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
59593498 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
59593525 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
59593552 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
59593579 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
59593594 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:59593528 original size:55 final size:54
Alignment explanation
Indices: 59593416--59593593 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
59593406 ATATTGAGCC
* * * * *
59593416 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
59593470 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
59593525 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
59593579 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
59593594 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:59596993 original size:39 final size:40
Alignment explanation
Indices: 59596700--59597010 Score: 428
Period size: 40 Copynumber: 7.8 Consensus size: 40
59596690 GGATATAGCT
* * * *
59596700 ACTCGCTCAAATGCCTTTGGGACATAGCCCGG-TTAGAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
* *
59596740 ACTCGCACAATTGCCTTCGGGACTTAGCTCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
*
59596780 ACTCGCACAAATGCCTTCGGGACTTAGCCCGAATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * *
59596820 ACTCGCACAATTGCCTTCAGGACTTAGCCTGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * *
59596860 ACTCACACAATTGCCTTCGGGACTTAGCGCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
59596900 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
** *
59596940 ACTCGCACAAATGCCTTCGGGACTT-GCCCGGAACTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * *
59596979 ACTAGCGCAGATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
59597011 TTTTCATCCA
Statistics
Matches: 243, Mismatches: 26, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
39 33 0.14
40 208 0.86
41 2 0.01
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:59601094 original size:9 final size:9
Alignment explanation
Indices: 59601082--59601138 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
59601072 TTTGATAAAC
59601082 ATGATATGT
1 ATGATATGT
*
59601091 ATGATATGCAC
1 ATGATATG--T
*
59601102 ATGACATGT
1 ATGATATGT
*
59601111 ATGATATGCAC
1 ATGATATG--T
59601122 ATGATATGT
1 ATGATATGT
59601131 ATGATATG
1 ATGATATG
59601139 CACACGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:59601105 original size:20 final size:20
Alignment explanation
Indices: 59601080--59601142 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
59601070 ATTTTGATAA
59601080 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
59601100 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
59601120 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
59601140 ACA
1 ACA
59601143 CGAGATGTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:59601221 original size:24 final size:24
Alignment explanation
Indices: 59601194--59601337 Score: 188
Period size: 24 Copynumber: 6.0 Consensus size: 24
59601184 GGAGGAAGTG
59601194 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
59601218 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
59601242 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
59601266 -TAAAGGGCTTATGCCCCAGTTATT
1 CAAAAGGGCTTATGCCCCAGTTA-T
* *
59601290 AAAAAGGGCAT-TGCCCCAGTTA-
1 CAAAAGGGCTTATGCCCCAGTTAT
*
59601312 CTAAAAGAGGC-TAGGCCTCCAGTTAT
1 C-AAAAG-GGCTTATGCC-CCAGTTAT
59601338 ATGATAAAGC
Statistics
Matches: 108, Mismatches: 5, Indels: 12
0.86 0.04 0.10
Matches are distributed among these distances:
23 27 0.25
24 66 0.61
25 15 0.14
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.25
Consensus pattern (24 bp):
CAAAAGGGCTTATGCCCCAGTTAT
Found at i:59601318 original size:71 final size:72
Alignment explanation
Indices: 59601196--59601337 Score: 202
Period size: 71 Copynumber: 2.0 Consensus size: 72
59601186 AGGAAGTGCA
* * *
59601196 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-C
1 AAAGGGCTTATGCCCCAGTTATAAAAAGGGCATATGCCCCAGTTATCAAAAGAGGC-TAGGCCTC
59601259 CAGTTATT
65 CAGTTATT
59601267 AAAGGGCTTATGCCCCAGTTATTAAAAAGGGCAT-TGCCCCAGTTA-CTAAAAGAGGCTAGGCCT
1 AAAGGGCTTATGCCCCAGTTA-TAAAAAGGGCATATGCCCCAGTTATC-AAAAGAGGCTAGGCCT
59601330 CCAGTTAT
64 CCAGTTAT
59601338 ATGATAAAGC
Statistics
Matches: 64, Mismatches: 3, Indels: 7
0.86 0.04 0.09
Matches are distributed among these distances:
70 1 0.02
71 42 0.66
72 21 0.33
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (72 bp):
AAAGGGCTTATGCCCCAGTTATAAAAAGGGCATATGCCCCAGTTATCAAAAGAGGCTAGGCCTCC
AGTTATT
Found at i:59607443 original size:30 final size:30
Alignment explanation
Indices: 59607409--59607469 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
59607399 TCCTTAACTC
59607409 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
59607439 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
59607469 A
1 A
59607470 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:59613822 original size:43 final size:42
Alignment explanation
Indices: 59613775--59613912 Score: 136
Period size: 43 Copynumber: 3.2 Consensus size: 42
59613765 TCTCAAATAG
*
59613775 GGTCTTACACAAAAATCTCAATCGAGGCCTGTGTCCCAGACAC
1 GGTCTTACAC-AAAATCTCAATCGAGGCCTGTGTCCCAAACAC
* * ** *
59613818 GGTCTTACACGAAA--TCAGATACGATGCCCATGTCCCAAACAT
1 GGTCTTACACAAAATCTCA-AT-CGAGGCCTGTGTCCCAAACAC
* **
59613860 GGTCTTATATGTAAATCTCAATCGAGGCCTGTGTCCCAAACAC
1 GGTCTTACA-CAAAATCTCAATCGAGGCCTGTGTCCCAAACAC
*
59613903 AGTCTTACAC
1 GGTCTTACAC
59613913 GATGTCTCAG
Statistics
Matches: 74, Mismatches: 16, Indels: 11
0.73 0.16 0.11
Matches are distributed among these distances:
40 3 0.04
41 2 0.03
42 27 0.36
43 37 0.50
44 2 0.03
45 3 0.04
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (42 bp):
GGTCTTACACAAAATCTCAATCGAGGCCTGTGTCCCAAACAC
Found at i:59617900 original size:39 final size:39
Alignment explanation
Indices: 59617856--59617944 Score: 160
Period size: 39 Copynumber: 2.3 Consensus size: 39
59617846 TTAAGCCTGA
*
59617856 ATATAATACCAGCACAAATGCCTTCGGGGCTTAGCCCGG
1 ATATAACACCAGCACAAATGCCTTCGGGGCTTAGCCCGG
*
59617895 ATATAACACCAGCACGAATGCCTTCGGGGCTTAGCCCGG
1 ATATAACACCAGCACAAATGCCTTCGGGGCTTAGCCCGG
59617934 ATATAACACCA
1 ATATAACACCA
59617945 AATCATATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.19
Consensus pattern (39 bp):
ATATAACACCAGCACAAATGCCTTCGGGGCTTAGCCCGG
Done.