Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 167 of 344
Found at i:55798655 original size:10 final size:10
Alignment explanation
Indices: 55798640--55798677 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
55798630 TTGGGTTAAG
55798640 ATTGAGCTGA
1 ATTGAGCTGA
55798650 ATTGAGCTCGA
1 ATTGAGCT-GA
55798661 A-TGAGCTGA
1 ATTGAGCTGA
*
55798670 CTTGAGCT
1 ATTGAGCT
55798678 CGATGAGCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 20 0.80
11 3 0.12
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:55798665 original size:20 final size:19
Alignment explanation
Indices: 55798642--55798687 Score: 74
Period size: 20 Copynumber: 2.4 Consensus size: 19
55798632 GGGTTAAGAT
55798642 TGAGCTGAATTGAGCTCGAA
1 TGAGCTGAATTGAGCTCG-A
*
55798662 TGAGCTGACTTGAGCTCGA
1 TGAGCTGAATTGAGCTCGA
55798681 TGAGCTG
1 TGAGCTG
55798688 GAAACGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (19 bp):
TGAGCTGAATTGAGCTCGA
Found at i:55800703 original size:20 final size:20
Alignment explanation
Indices: 55800678--55800715 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
55800668 TTTTGAACCA
*
55800678 TTACCATTTCGTACCAATCC
1 TTACCATTTAGTACCAATCC
55800698 TTACCATTTAGTACCAAT
1 TTACCATTTAGTACCAAT
55800716 TCCCAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.05, T:0.37
Consensus pattern (20 bp):
TTACCATTTAGTACCAATCC
Found at i:55803150 original size:26 final size:26
Alignment explanation
Indices: 55803097--55803151 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
55803087 ATTAGTATGT
*
55803097 TTTTAATGTGTCTAATTAGGATATAA
1 TTTTAATGTGTCTAATTAGGACATAA
*
55803123 TTTTAATGTGTCTAGTTTAGGACA-AA
1 TTTTAATGTGTCTA-ATTAGGACATAA
55803149 TTT
1 TTT
55803152 ATTAGCTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.31, C:0.05, G:0.16, T:0.47
Consensus pattern (26 bp):
TTTTAATGTGTCTAATTAGGACATAA
Found at i:55805117 original size:22 final size:22
Alignment explanation
Indices: 55805087--55805130 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
55805077 TTTGGTATTT
55805087 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
55805109 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
55805131 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:55809339 original size:17 final size:17
Alignment explanation
Indices: 55809314--55809368 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
55809304 TCTCTTTTCA
*
55809314 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
55809331 TTCTTTTTTTTTTCATTT
1 TTC-TTTTTTTTTGAATT
* *
55809349 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
55809366 TTC
1 TTC
55809369 GCTCTTTTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 16 0.53
18 14 0.47
ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:55809342 original size:18 final size:18
Alignment explanation
Indices: 55809319--55809360 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
55809309 TTTCATTCTC
*
55809319 TTTTTTTGAATTTTCTTT
1 TTTTTTTCAATTTTCTTT
*
55809337 TTTTTTTCATTTTTCTTT
1 TTTTTTTCAATTTTCTTT
55809355 TCTTTT
1 T-TTTT
55809361 GTATTTTCGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.07, C:0.10, G:0.02, T:0.81
Consensus pattern (18 bp):
TTTTTTTCAATTTTCTTT
Found at i:55811919 original size:22 final size:22
Alignment explanation
Indices: 55811889--55811932 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
55811879 TTTGGTATTT
55811889 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
55811911 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
55811933 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:55815348 original size:20 final size:20
Alignment explanation
Indices: 55815321--55815358 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55815311 AGACACATTA
55815321 ATAAACATATAAT-TAAATT
1 ATAAACATATAATATAAATT
*
55815340 ATAACACATTTAATATAAA
1 ATAA-ACATATAATATAAA
55815359 CTTAGCTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 8 0.50
21 4 0.25
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (20 bp):
ATAAACATATAATATAAATT
Found at i:55815543 original size:31 final size:30
Alignment explanation
Indices: 55815500--55815560 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
55815490 AGAAATTAAG
*
55815500 TAATTGAGCTGAAATGAAGCTAAAATGAGCT
1 TAATCGAGCTGAAAT-AAGCTAAAATGAGCT
* *
55815531 TAATCGAGCTGAAATAAGCTCAAGTGAGCT
1 TAATCGAGCTGAAATAAGCTAAAATGAGCT
55815561 GATTTGAGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.25
Consensus pattern (30 bp):
TAATCGAGCTGAAATAAGCTAAAATGAGCT
Found at i:55815570 original size:30 final size:31
Alignment explanation
Indices: 55815501--55815573 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
55815491 GAAATTAAGT
*
55815501 AATTGAGCTGAAATGAAGCTAAAATGAGCTT
1 AATTGAGCTGAAATGAAGCTAAAATGAGCTG
* * *
55815532 AATCGAGCTGAAAT-AAGCTCAAGTGAGCTG
1 AATTGAGCTGAAATGAAGCTAAAATGAGCTG
*
55815562 ATTTGAGCTGAA
1 AATTGAGCTGAA
55815574 TGGAGCTCAG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 23 0.64
31 13 0.36
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (31 bp):
AATTGAGCTGAAATGAAGCTAAAATGAGCTG
Found at i:55815889 original size:29 final size:29
Alignment explanation
Indices: 55815823--55815879 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
55815813 GATTCAAAGA
*
55815823 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
*
55815852 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
55815880 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.46
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:55823866 original size:23 final size:22
Alignment explanation
Indices: 55823814--55823866 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
55823804 TCCACGTCTT
*
55823814 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
55823836 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
55823859 TTTCTTTT
1 TTTCTTTT
55823867 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:55825137 original size:13 final size:13
Alignment explanation
Indices: 55825119--55825143 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55825109 TGGTCATCAT
55825119 GGTGTGAACACAA
1 GGTGTGAACACAA
55825132 GGTGTGAACACA
1 GGTGTGAACACA
55825144 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:55826047 original size:10 final size:10
Alignment explanation
Indices: 55826032--55826069 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
55826022 GCTCGTTTCC
*
55826032 AGCTCACTCG
1 AGCTCAATCG
55826042 AGCTCAAGTC-
1 AGCTCAA-TCG
55826052 AGCTCAATCG
1 AGCTCAATCG
55826062 AGCTCAAT
1 AGCTCAAT
55826070 TTAGCTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:55826075 original size:20 final size:20
Alignment explanation
Indices: 55826031--55826068 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
55826021 AGCTCGTTTC
*
55826031 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
55826051 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
55826069 TTTAGCTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:55829120 original size:21 final size:22
Alignment explanation
Indices: 55829077--55829125 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
55829067 TCTTTTTGGA
55829077 TTTCTTTTCTTTTTCAATCTCTT
1 TTTCTTTTC-TTTTCAATCTCTT
* *
55829100 TTTCTTTTC-TTTCGATTTCTT
1 TTTCTTTTCTTTTCAATCTCTT
55829121 TTTCT
1 TTTCT
55829126 CGCTCGTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 15 0.62
23 9 0.38
ACGTcount: A:0.06, C:0.20, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTCTTTTCTTTTCAATCTCTT
Found at i:55830183 original size:27 final size:27
Alignment explanation
Indices: 55830153--55830205 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
55830143 TTTTCCTTCT
*
55830153 CTTTTTTTTCGGA-TTTTTTTTTCGAAA
1 CTTTTTTTT-GAACTTTTTTTTTCGAAA
*
55830180 CTTTTTTTTTAACTTTTTTTTTCGAA
1 CTTTTTTTTGAACTTTTTTTTTCGAA
55830206 GCTACGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.15, C:0.11, G:0.08, T:0.66
Consensus pattern (27 bp):
CTTTTTTTTGAACTTTTTTTTTCGAAA
Found at i:55831067 original size:13 final size:13
Alignment explanation
Indices: 55831049--55831073 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55831039 TGGTCATCAT
55831049 GGTGTGAACACAA
1 GGTGTGAACACAA
55831062 GGTGTGAACACA
1 GGTGTGAACACA
55831074 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:55834401 original size:15 final size:15
Alignment explanation
Indices: 55834383--55834411 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
55834373 CTAGACCGTA
55834383 TGCAATTTTTTTTTT
1 TGCAATTTTTTTTTT
55834398 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
55834412 CCTTCTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (15 bp):
TGCAATTTTTTTTTT
Found at i:55834451 original size:15 final size:15
Alignment explanation
Indices: 55834419--55834473 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
55834409 TTTCCTTCTC
* **
55834419 TTTTTTTTCGGATTT
1 TTTTTTTTCGAAACT
55834434 TTTTTTTTCGAAACT
1 TTTTTTTTCGAAACT
55834449 TTTTTTTT---AACTT
1 TTTTTTTTCGAAAC-T
55834462 TTTTTTTTCGAA
1 TTTTTTTTCGAA
55834474 GCTACGATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 3 0.09
13 9 0.27
15 20 0.61
16 1 0.03
ACGTcount: A:0.15, C:0.09, G:0.07, T:0.69
Consensus pattern (15 bp):
TTTTTTTTCGAAACT
Found at i:55834451 original size:28 final size:28
Alignment explanation
Indices: 55834420--55834473 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
55834410 TTCCTTCTCT
* *
55834420 TTTTTTTCGGATTTTTTTTTTTCGAAAC
1 TTTTTTTCGAACTTTTTTTTTTCGAAAC
**
55834448 TTTTTTTTTAACTTTTTTTTTTCGAA
1 TTTTTTTCGAACTTTTTTTTTTCGAA
55834474 GCTACGATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.15, C:0.09, G:0.07, T:0.69
Consensus pattern (28 bp):
TTTTTTTCGAACTTTTTTTTTTCGAAAC
Found at i:55835334 original size:13 final size:13
Alignment explanation
Indices: 55835316--55835340 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55835306 TGGTCATCAT
55835316 GGTGTGAACACAA
1 GGTGTGAACACAA
55835329 GGTGTGAACACA
1 GGTGTGAACACA
55835341 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:55837970 original size:5 final size:4
Alignment explanation
Indices: 55837936--55837969 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
55837926 TTAAACTAAG
55837936 TAAA TAAA TAAA TAAA TAAA TAAAA TAAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA T-AAA T-AAA TAAA
55837970 ACTTTACAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 20 0.69
5 9 0.31
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:55838266 original size:19 final size:19
Alignment explanation
Indices: 55838239--55838329 Score: 68
Period size: 19 Copynumber: 4.9 Consensus size: 19
55838229 TTATTCCAGC
*
55838239 AACTAAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
*
55838258 AACTTAATTAACTAACATG
1 AACTTAATTAACTAAGATG
*
55838277 AA--TAATTTATTCT-AGCAT-
1 AACTTAA-TTA-ACTAAG-ATG
55838295 --CTTAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
* *
55838312 AACTCAATTAAGTAAGAT
1 AACTTAATTAACTAAGAT
55838330 AAGTAATTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 18
0.69 0.09 0.22
Matches are distributed among these distances:
16 4 0.07
17 8 0.14
18 7 0.12
19 37 0.66
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (19 bp):
AACTTAATTAACTAAGATG
Found at i:55838302 original size:54 final size:54
Alignment explanation
Indices: 55838229--55838357 Score: 172
Period size: 54 Copynumber: 2.4 Consensus size: 54
55838219 CATCATTAAA
* * *
55838229 TTATTCCAGCAACTAAATTAACTAAGATGAACTTAATTAACTAACATGAA-TAAT
1 TTATTCCAGCATCTTAATTAACTAAGATGAACTCAATTAACTAACAT-AAGTAAT
* * *
55838283 TTATTCTAGCATCTTAATTAACTAAGATGAACTCAATTAAGTAAGATAAGTAAT
1 TTATTCCAGCATCTTAATTAACTAAGATGAACTCAATTAACTAACATAAGTAAT
55838337 TTATTCCAGCAAT-TTAATTAA
1 TTATTCCAGC-ATCTTAATTAA
55838358 TTAAACTAAG
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
53 2 0.03
54 62 0.94
55 2 0.03
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (54 bp):
TTATTCCAGCATCTTAATTAACTAAGATGAACTCAATTAACTAACATAAGTAAT
Found at i:55840050 original size:27 final size:27
Alignment explanation
Indices: 55840020--55840196 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
55840010 ATATTGAGTC
* *
55840020 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
55840047 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
55840074 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
55840102 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
55840129 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
55840156 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
55840183 -GCACACTTAGTGCT
1 CGCACACTTAGTGCT
55840197 GTACAATTTA
Statistics
Matches: 128, Mismatches: 19, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
26 13 0.10
27 91 0.71
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:55840112 original size:55 final size:54
Alignment explanation
Indices: 55840020--55840196 Score: 205
Period size: 54 Copynumber: 3.3 Consensus size: 54
55840010 ATATTGAGTC
* * * * *
55840020 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* ** * *
55840074 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCAACATAGTCAAAT
* **
55840129 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
55840183 -GCACACTTAGTGCT
1 CGCACACTTAGTGCT
55840197 GTACAATTTA
Statistics
Matches: 104, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
53 13 0.12
54 46 0.44
55 45 0.43
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:55840159 original size:82 final size:80
Alignment explanation
Indices: 55840041--55840195 Score: 222
Period size: 82 Copynumber: 1.9 Consensus size: 80
55840031 TGCTATATAA
* *
55840041 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-T-GCA
55840106 CACTTAGTGCCGCATGG
64 CACTTAGTGCCGCATGG
* * **
55840123 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATGCAC
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATGCAC
55840187 ACTTAGTGC
65 ACTTAGTGC
55840196 TGTACAATTT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
80 13 0.20
81 2 0.03
82 51 0.77
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (80 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATGCACA
CTTAGTGCCGCATGG
Found at i:55853647 original size:46 final size:46
Alignment explanation
Indices: 55853482--55853654 Score: 136
Period size: 46 Copynumber: 3.7 Consensus size: 46
55853472 TGTAACCCGC
* *** *
55853482 CCATAAGCGAACTCGGACTCAACTCAAC-AGGCTCAGGCGTTCTCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGA-GTTCAGATATTCGCAT
* * ** ** * *
55853528 CCATAGGTGAACTCGGACTCAACTCAACGAGTTTGGATGCCTAG-TT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCAGAT-ATTCGCAT
* * *
55853574 ACATTTCA-CGAACTCAGACTCAACTCAACGAGTTCAGATATTCGCAT
1 CCA--TAAGCGAACTCGGACTCAACTCAACGAGTTCAGATATTCGCAT
*
55853621 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC
55853655 GGATGCCCAA
Statistics
Matches: 94, Mismatches: 27, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
45 2 0.02
46 59 0.63
47 32 0.34
48 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.23
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCAGATATTCGCAT
Found at i:55853648 original size:93 final size:93
Alignment explanation
Indices: 55853489--55853661 Score: 258
Period size: 93 Copynumber: 1.9 Consensus size: 93
55853479 CGCCCATAAG
* * * * *
55853489 CGAACTCGGACTCAACTCAACAGGCTCAGGCGTTCTCATCCATAGGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACAGGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
55853554 ACGAGTTTGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
* *
55853582 CGAACTCAGACTCAACTCAAC-GAGTTCAGATATTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCAGACTCAACTCAACAG-GCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
55853646 AACGAGTTCGGATGCC
65 AACGAGTTCGGATGCC
55853662 CAAATATCCC
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
92 1 0.01
93 70 0.99
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (93 bp):
CGAACTCAGACTCAACTCAACAGGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATTTCA
Found at i:55856111 original size:15 final size:15
Alignment explanation
Indices: 55856043--55856122 Score: 74
Period size: 15 Copynumber: 5.4 Consensus size: 15
55856033 CAAAGATAAC
*
55856043 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
55856057 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* * *
55856072 GAGAAACCCGGAATA
1 AAGAAATCCAGAATA
55856087 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
** *
55856102 AAGAGTTCCAGGATA
1 AAGAAATCCAGAATA
55856117 AAGAAA
1 AAGAAA
55856123 CCCAAGATAC
Statistics
Matches: 51, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
14 9 0.18
15 41 0.80
16 1 0.02
ACGTcount: A:0.56, C:0.14, G:0.19, T:0.11
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:55856131 original size:15 final size:15
Alignment explanation
Indices: 55856054--55856131 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
55856044 AGAAAACCGA
55856054 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* **
55856069 ATAGAGAAA-CCCGG
1 ATAAAGAAATCCAAG
55856083 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
** *
55856098 AATAAAGAGTTCCAGG
1 -ATAAAGAAATCCAAG
*
55856114 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
55856129 ATA
1 ATA
55856132 CGATACTATG
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
14 3 0.06
15 42 0.88
16 3 0.06
ACGTcount: A:0.54, C:0.15, G:0.18, T:0.13
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:55866515 original size:42 final size:42
Alignment explanation
Indices: 55866451--55866543 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
55866441 CAAATCAGTG
* * *
55866451 CCGACGCCATGTCCCAGACATGGTCTTATACGAGACCTCATA
1 CCGATGCCATGTCCCAGACATGGTCTTATACGAAACCACATA
* *
55866493 CCGATGCCATGTCCCAGACATGGTCTTATACGAAATCACTTA
1 CCGATGCCATGTCCCAGACATGGTCTTATACGAAACCACATA
55866535 CCGATGCCA
1 CCGATGCCA
55866544 AAGCCATATA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.23
Consensus pattern (42 bp):
CCGATGCCATGTCCCAGACATGGTCTTATACGAAACCACATA
Found at i:55869484 original size:13 final size:13
Alignment explanation
Indices: 55869466--55869492 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55869456 GCCAAATAGA
55869466 TATCACATACATG
1 TATCACATACATG
55869479 TATCACATACATG
1 TATCACATACATG
55869492 T
1 T
55869493 TTTTCATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.33
Consensus pattern (13 bp):
TATCACATACATG
Found at i:55869523 original size:21 final size:21
Alignment explanation
Indices: 55869497--55869547 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
55869487 ACATGTTTTT
55869497 CATATAACAAATCATACTCAG
1 CATATAACAAATCATACTCAG
* *
55869518 CATATAACATATCATACTTAG
1 CATATAACAAATCATACTCAG
55869539 CATATAACA
1 CATATAACA
55869548 GACTAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.47, C:0.22, G:0.04, T:0.27
Consensus pattern (21 bp):
CATATAACAAATCATACTCAG
Found at i:55878483 original size:6 final size:6
Alignment explanation
Indices: 55878472--55878505 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
55878462 ACTGTGATGC
55878472 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGT
55878506 TCTGATCTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (6 bp):
ATGTAT
Found at i:55878732 original size:40 final size:38
Alignment explanation
Indices: 55878681--55878776 Score: 102
Period size: 40 Copynumber: 2.5 Consensus size: 38
55878671 ACGATATTCT
* ** * *
55878681 ATGGTATGTAGGGTTGGATGGGTTTATTTTATCCCTAT
1 ATGGTGTGTAGGGTTGGATGGGTCAATTTTATCCCCAC
* *
55878719 ATTTGGTGTGTAGGGATGGGTGGGTCAATTTTATCCCCAC
1 A--TGGTGTGTAGGGTTGGATGGGTCAATTTTATCCCCAC
*
55878759 ATGGTGTGTTGGGTTGGA
1 ATGGTGTGTAGGGTTGGA
55878777 CGGAGTTGGC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
38 15 0.33
40 31 0.67
ACGTcount: A:0.17, C:0.09, G:0.34, T:0.40
Consensus pattern (38 bp):
ATGGTGTGTAGGGTTGGATGGGTCAATTTTATCCCCAC
Found at i:55881168 original size:29 final size:27
Alignment explanation
Indices: 55881150--55881219 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
55881140 ATATTAAGTC
55881150 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
55881177 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
55881205 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
55881220 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:55881213 original size:28 final size:28
Alignment explanation
Indices: 55881150--55881247 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
55881140 ATATTAAGTC
*
55881150 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
55881177 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
55881205 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
55881234 CGCACACTTAGTGC
1 CGCACACTTAGTGC
55881248 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:55885902 original size:17 final size:19
Alignment explanation
Indices: 55885880--55885916 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
55885870 TTGGGCTTAT
55885880 TGGG-CCACACGGG-CGTG
1 TGGGCCCACACGGGCCGTG
*
55885897 TGGGCCCACATGGGCCGTG
1 TGGGCCCACACGGGCCGTG
55885916 T
1 T
55885917 TGTGGGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 4 0.24
18 8 0.47
19 5 0.29
ACGTcount: A:0.11, C:0.30, G:0.43, T:0.16
Consensus pattern (19 bp):
TGGGCCCACACGGGCCGTG
Found at i:55886964 original size:38 final size:38
Alignment explanation
Indices: 55886916--55887009 Score: 125
Period size: 40 Copynumber: 2.4 Consensus size: 38
55886906 AACTCCGTCT
* * *
55886916 AACCCGACACACCATATGGGGATAAAATCGACCTACCC
1 AACCCTACACACCATATGGGGATAAAATCAACCCACCC
* *
55886954 ATCCCTACACACCAAATATGGGGATAAAATCAACCCATCC
1 AACCCTACACACC--ATATGGGGATAAAATCAACCCACCC
55886994 AACCCTACACACCATA
1 AACCCTACACACCATA
55887010 GAGTACCGTA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
38 14 0.29
40 34 0.71
ACGTcount: A:0.39, C:0.35, G:0.11, T:0.15
Consensus pattern (38 bp):
AACCCTACACACCATATGGGGATAAAATCAACCCACCC
Found at i:55889922 original size:26 final size:25
Alignment explanation
Indices: 55889866--55889922 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
55889856 AATCTAAAAT
*
55889866 AAATTC-AAAATCTAATTTCATTTA
1 AAATTCTAAAATCTAATTTCACTTA
* *
55889890 AAGTTCTAAAATCTATTTTACACTTA
1 AAATTCTAAAATCTAATTT-CACTTA
55889916 AAATTCT
1 AAATTCT
55889923 TATAACGTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 5 0.19
25 11 0.41
26 11 0.41
ACGTcount: A:0.42, C:0.14, G:0.02, T:0.42
Consensus pattern (25 bp):
AAATTCTAAAATCTAATTTCACTTA
Found at i:55893582 original size:22 final size:22
Alignment explanation
Indices: 55893553--55893604 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
55893543 GGATAGTAAA
55893553 CTGCATCTATATCT-GATCTATT
1 CTGCATCTATAT-TAGATCTATT
* * *
55893575 TTGCATCTGTATTAGATCTGTT
1 CTGCATCTATATTAGATCTATT
55893597 CTGCATCT
1 CTGCATCT
55893605 TACCTGAACG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.19, C:0.21, G:0.13, T:0.46
Consensus pattern (22 bp):
CTGCATCTATATTAGATCTATT
Found at i:55895931 original size:43 final size:41
Alignment explanation
Indices: 55895884--55895981 Score: 110
Period size: 43 Copynumber: 2.4 Consensus size: 41
55895874 ATTATTTTAC
* *
55895884 ATTTTAATAATATATTATTTCATATTATTATTTATTATATATT
1 ATTTTAATAAT-TATTATTTCACATTATTATCTA-TATATATT
* *
55895927 ATTTTACACAATTATTATTTTACATTATTATCTATATATA-T
1 ATTTTA-ATAATTATTATTTCACATTATTATCTATATATATT
*
55895968 -TTTTATTAATTATT
1 ATTTTAATAATTATT
55895982 TGTACATATT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
39 7 0.15
40 5 0.10
41 1 0.02
42 6 0.12
43 25 0.52
44 4 0.08
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (41 bp):
ATTTTAATAATTATTATTTCACATTATTATCTATATATATT
Found at i:55895956 original size:16 final size:16
Alignment explanation
Indices: 55895906--55895957 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
55895896 TATTATTTCA
55895906 TATTATTA-TTT--AT
1 TATTATTATTTTACAT
*
55895919 TATATATTATTTTACAC
1 TAT-TATTATTTTACAT
*
55895936 AATTATTATTTTACAT
1 TATTATTATTTTACAT
55895952 TATTAT
1 TATTAT
55895958 CTATATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 3 0.10
14 5 0.16
15 3 0.10
16 17 0.55
17 3 0.10
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTATTATTTTACAT
Found at i:55899964 original size:15 final size:15
Alignment explanation
Indices: 55899928--55899977 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 15
55899918 GATATTCTTT
55899928 TTTGCAT-TCATACA
1 TTTGCATCTCATACA
55899942 TTTGCATCTCATAGCA
1 TTTGCATCTCATA-CA
55899958 TTT-CA--TCATATCA
1 TTTGCATCTCATA-CA
55899971 TTTGCAT
1 TTTGCAT
55899978 TCAAAGTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 10 0.32
14 9 0.29
15 7 0.23
16 5 0.16
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.44
Consensus pattern (15 bp):
TTTGCATCTCATACA
Found at i:55904625 original size:93 final size:93
Alignment explanation
Indices: 55904512--55904682 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
55904502 GCCCATAAGT
*
55904512 GAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
55904576 ACGAGTTCGGATGCCTAGTTACATTTCAC
65 ACGAGTTCGGATGCCTAGTTACATTTCAC
* *
55904605 GAACTTGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
55904670 CGAGTTCGGATGC
66 CGAGTTCGGATGC
55904683 TCAACCATCC
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 72 0.97
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:55904677 original size:46 final size:46
Alignment explanation
Indices: 55904504--55904679 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
55904494 TGTAACCCGC
* *
55904504 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
*
55904550 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* * * *
55904600 --TTCA-CGAACTTGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
55904643 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
55904680 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 12, Indels: 20
0.77 0.09 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 4 0.04
46 61 0.56
47 28 0.26
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:55904946 original size:34 final size:34
Alignment explanation
Indices: 55904905--55904975 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
55904895 TATAATTAAC
55904905 ATTAATAACTTAAAAATAACATTTATGCTACATT
1 ATTAATAACTTAAAAATAACATTTATGCTACATT
55904939 ATTAATAACTTAAAAATAACATTTATGCTACATT
1 ATTAATAACTTAAAAATAACATTTATGCTACATT
55904973 ATT
1 ATT
55904976 TACACATGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.39
Consensus pattern (34 bp):
ATTAATAACTTAAAAATAACATTTATGCTACATT
Found at i:55905170 original size:30 final size:30
Alignment explanation
Indices: 55905136--55905194 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
55905126 ATTTAATACG
55905136 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
55905166 AACTTTTGCATAATTACACTTTTGCCCCT
1 AACTTTGGAAAAATTACACTTTTGCCCCT
55905195 TGGCTCAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:55912273 original size:46 final size:45
Alignment explanation
Indices: 55912180--55912265 Score: 120
Period size: 46 Copynumber: 1.9 Consensus size: 45
55912170 TACATTTCAC
* *
55912180 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
1 GAACTCGAACTCAACTCAACGAGTTCGGA-ATGCGCAACCATAAGT
* *
55912226 GAACTCGGACTCAACTCAACGAGTTCGG-ATGCTCAACCAT
1 GAACTCGAACTCAACTCAACGAGTTCGGAATGCGCAACCAT
55912266 CCTAGTGACA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 9 0.25
46 27 0.75
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (45 bp):
GAACTCGAACTCAACTCAACGAGTTCGGAATGCGCAACCATAAGT
Found at i:55918671 original size:210 final size:210
Alignment explanation
Indices: 55918300--55918893 Score: 724
Period size: 210 Copynumber: 2.8 Consensus size: 210
55918290 TAAGCCGCAG
* *
55918300 CATAGCAGATCTCACCTTTAGATGTTTACACTGAAGCAGATCCAAGATGACAGATCTTATCTCTC
1 CATAGCAGATCTCACCTTCAGATGTTTACGCTGAAGCAGATCCAAGATGACAGATCTTATCTCTC
* * *
55918365 TGTAGTCGGCAGGGAACAGATCGAAGATATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCA
66 TGTATTCGGCAGGGAGCAAATCGAAGATATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCA
* * * * * *
55918430 AATCTAAGATGCTTTGTCACCTCTATATTGTCAGAGAACAAATCGAAGTCTGGCATTTCCACTTT
131 AATCTAAGATGATTTGTCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTAGCATCTCCACTTC
* *
55918495 GATGGA-AGGTAGACA
196 AATGGAGA-GCAGACA
*
55918510 CATAGCAGGTCTCACCTTCAGATGTTTACGCTGAAGCAGATCCAAGATGACAGATCTTATCTCTC
1 CATAGCAGATCTCACCTTCAGATGTTTACGCTGAAGCAGATCCAAGATGACAGATCTTATCTCTC
* *
55918575 TGTATTCGGCGGGGAGCAAATCGAAGATATAGCTGATTTGGCTTTCACGTGTTTACGATGAGGCA
66 TGTATTCGGCAGGGAGCAAATCGAAGATATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCA
* * *
55918640 AATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAATAGATCGAAGTCTAGCATCTCCACTTC
131 AATCTAAGATGATTTGTCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTAGCATCTCCACTTC
*
55918705 AATGGAGAGCAGATA
196 AATGGAGAGCAGACA
** *
55918720 CATAGCAGATCAGACCTTCAGATGATTA-GACTGAAGCAAGATCCAAGATG---G-T-TTGGCAT
1 CATAGCAGATCTCACCTTCAGATGTTTACG-CTGAAGC-AGATCCAAGATGACAGATCTT---AT
* * * * * * * *
55918779 C-CT-TGTGCTT--ACAAGGAGAAAATCAAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTT
61 CTCTCTGT-ATTCGGCAGGGAGCAAATCGAAGATATAGCTGATTTGGCTTTCACGTGTTTACGAT
* * * * *
55918840 AAAGCAAATCTAAGACGAATTGTTATCTTTGTATTGTCAGAGAACAAATCGAAG
125 GAAGCAAATCTAAGATGATTTGTCATCTCTGTATTGTCAGAGAACAAATCGAAG
55918894 AAACGGATTT
Statistics
Matches: 335, Mismatches: 42, Indels: 18
0.85 0.11 0.05
Matches are distributed among these distances:
206 90 0.27
207 4 0.01
208 5 0.01
209 4 0.01
210 219 0.65
211 13 0.04
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (210 bp):
CATAGCAGATCTCACCTTCAGATGTTTACGCTGAAGCAGATCCAAGATGACAGATCTTATCTCTC
TGTATTCGGCAGGGAGCAAATCGAAGATATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCA
AATCTAAGATGATTTGTCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTAGCATCTCCACTTC
AATGGAGAGCAGACA
Found at i:55923117 original size:18 final size:20
Alignment explanation
Indices: 55923080--55923134 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
55923070 TACAATATTT
*
55923080 TTATTTTAAATTTATGTTT-AA
1 TTATTTTTAA-TT-TGTTTAAA
55923101 TTATTTTT-ATTTGTTTAAA
1 TTATTTTTAATTTGTTTAAA
*
55923120 TTCTTTTTAATTTGT
1 TTATTTTTAATTTGT
55923135 AGGTTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 5 0.17
19 11 0.37
20 7 0.23
21 7 0.23
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.67
Consensus pattern (20 bp):
TTATTTTTAATTTGTTTAAA
Found at i:55930693 original size:37 final size:37
Alignment explanation
Indices: 55930604--55930693 Score: 135
Period size: 37 Copynumber: 2.4 Consensus size: 37
55930594 TCCATTCAAA
* * * *
55930604 AACATTCCAATTGCTAATAAGAGCTCATCCACCCGAT
1 AACATACCAATTGCTCATAAGAGCTCAGCCACCCAAT
55930641 AACATACCAATTGCTCATAAGAGCTCAGCCACCCAAT
1 AACATACCAATTGCTCATAAGAGCTCAGCCACCCAAT
*
55930678 AACATGCCAATTGCTC
1 AACATACCAATTGCTC
55930694 TGAAGAGTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.36, C:0.31, G:0.11, T:0.22
Consensus pattern (37 bp):
AACATACCAATTGCTCATAAGAGCTCAGCCACCCAAT
Found at i:55934173 original size:29 final size:30
Alignment explanation
Indices: 55934125--55934182 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
55934115 TTTTAATCCT
*
55934125 TTTTAAAAAATTTTATATATAATTTATTTA
1 TTTTAAAAAATTTTAAATATAATTTATTTA
* *
55934155 TTTT-AAATATTTTAAATATTATTTATTT
1 TTTTAAAAAATTTTAAATATAATTTATTT
55934183 TTACTATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTTAAAAAATTTTAAATATAATTTATTTA
Found at i:55934246 original size:29 final size:28
Alignment explanation
Indices: 55934214--55934370 Score: 108
Period size: 31 Copynumber: 5.2 Consensus size: 28
55934204 TATGTAAAAA
55934214 ATTATTATATATATTATTTTTATTTATGT
1 ATTATTATATATATTATTTTTATTTAT-T
55934243 ATTATTTATTATATTATTTATATTTTATTATATT
1 ATTA-TTA-TATA-TA-TTAT-TTTTATT-TATT
*
55934277 -TTATT-TATATATT-TTATTATATATCATT
1 ATTATTATATATATTATT-TT-TAT-TTATT
*
55934305 -TTATTATATATATTATTCATTATATTTTTT
1 ATTATTATATATATTATT--TT-TATTTATT
* *
55934335 ATTGTTATATATATTA-TATTATATTATT
1 ATTATTATATATATTATTTTTAT-TTATT
55934363 ATTTATTA
1 A-TTATTA
55934371 CTTATTATTA
Statistics
Matches: 106, Mismatches: 7, Indels: 30
0.74 0.05 0.21
Matches are distributed among these distances:
26 1 0.01
27 6 0.06
28 19 0.18
29 20 0.19
30 13 0.12
31 25 0.24
32 4 0.04
33 7 0.07
34 8 0.08
35 3 0.03
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (28 bp):
ATTATTATATATATTATTTTTATTTATT
Found at i:55934249 original size:11 final size:11
Alignment explanation
Indices: 55934214--55934368 Score: 93
Period size: 12 Copynumber: 14.8 Consensus size: 11
55934204 TATGTAAAAA
55934214 ATTA-TTATAT
1 ATTATTTATAT
55934224 A-TA-TTAT-T
1 ATTATTTATAT
* *
55934232 TTTATTTATGT
1 ATTATTTATAT
55934243 ATTATTTATTAT
1 ATTATTTA-TAT
55934255 ATTATTTATAT
1 ATTATTTATAT
*
55934266 TTTA-TTATAT
1 ATTATTTATAT
*
55934276 TTTATTTATAT
1 ATTATTTATAT
*
55934287 ATTTTATTATAT
1 ATTAT-TTATAT
*
55934299 ATCA-TT-T-T
1 ATTATTTATAT
55934307 ATTA--TATAT
1 ATTATTTATAT
*
55934316 ATTATTCAT-T
1 ATTATTTATAT
*
55934326 A-TATTT-TTT
1 ATTATTTATAT
*
55934335 ATTGTTATATAT
1 ATTATT-TATAT
55934347 ATTATATTATATT
1 ATTAT-TTATA-T
55934360 ATTATTTAT
1 ATTATTTAT
55934369 TACTTATTAT
Statistics
Matches: 115, Mismatches: 14, Indels: 30
0.72 0.09 0.19
Matches are distributed among these distances:
7 1 0.01
8 7 0.06
9 20 0.17
10 22 0.19
11 26 0.23
12 32 0.28
13 7 0.06
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (11 bp):
ATTATTTATAT
Found at i:55934252 original size:21 final size:20
Alignment explanation
Indices: 55934218--55934294 Score: 86
Period size: 21 Copynumber: 3.8 Consensus size: 20
55934208 TAAAAAATTA
55934218 TTATATA-TATTATTTTTAT
1 TTATATATTATTATTTTTAT
*
55934237 TTATGTATTATTTATTATATTAT
1 TTATATATTA-TTATT-T-TTAT
*
55934260 TTATATTTTATTATATTTTAT
1 TTATATATTATTAT-TTTTAT
55934281 TTATATATT-TTATT
1 TTATATATTATTATT
55934295 ATATATCATT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
19 7 0.14
20 6 0.12
21 17 0.35
22 6 0.12
23 13 0.27
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (20 bp):
TTATATATTATTATTTTTAT
Found at i:55934281 original size:33 final size:35
Alignment explanation
Indices: 55934215--55934369 Score: 142
Period size: 37 Copynumber: 4.4 Consensus size: 35
55934205 ATGTAAAAAA
*
55934215 TTATTATA-TATATTAT-TTTTATT-TATGTATTAT
1 TTATTATATTAT-TTATATTTTATTATATATATTAT
*
55934248 TTATTATATTATTTATATTTTATTATATTTTATTTAT
1 TTATTATATTATTTATATTTTATTATA-TATA-TTAT
* * *
55934285 ATATTTTATTATATATCATTTTATTATATATATTAT
1 TTATTATATTATTTAT-ATTTTATTATATATATTAT
*
55934321 TCATTATATT-TTT-TATTGTTATATATATTATATTAT
1 TTATTATATTATTTATATT-TTAT-TATA-TATATTAT
55934357 ATTATTAT-TTATT
1 -TTATTATATTATT
55934370 ACTTATTATT
Statistics
Matches: 101, Mismatches: 10, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
33 15 0.15
34 15 0.15
35 8 0.08
36 24 0.24
37 28 0.28
38 11 0.11
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (35 bp):
TTATTATATTATTTATATTTTATTATATATATTAT
Found at i:55934327 original size:31 final size:28
Alignment explanation
Indices: 55934242--55934370 Score: 112
Period size: 31 Copynumber: 4.7 Consensus size: 28
55934232 TTTATTTATG
*
55934242 TATTAT-TTATTA-TATTATTTATATTT
1 TATTATATTATTATTATTATATATATTT
55934268 TATT--A-TATT-TTATT-TATATATTT
1 TATTATATTATTATTATTATATATATTT
55934291 TATTATATATCATT-TTATTATATATATTAT
1 TATTATAT-T-ATTATTATTATATATATT-T
* * *
55934321 TCATTATATTTTTTATTGTTATATATATTA
1 T-ATTATA-TTATTATTATTATATATATTT
55934351 TATTATATTATTATTTATTA
1 TATTATATTATTA-TTATTA
55934371 CTTATTATTA
Statistics
Matches: 84, Mismatches: 6, Indels: 23
0.74 0.05 0.20
Matches are distributed among these distances:
23 12 0.14
24 8 0.10
25 1 0.01
26 4 0.05
27 1 0.01
28 13 0.15
29 19 0.23
30 5 0.06
31 20 0.24
32 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.65
Consensus pattern (28 bp):
TATTATATTATTATTATTATATATATTT
Found at i:55934327 original size:73 final size:72
Alignment explanation
Indices: 55934221--55934358 Score: 183
Period size: 73 Copynumber: 1.9 Consensus size: 72
55934211 AAAATTATTA
* * * *
55934221 TATATATTATTTTTATTTATGTATTATTTATTATATTATTTATATT-TTAT-TATATTTTATTTA
1 TATATATCATTTTTATTTATATATTATTCATTATATT-TTT-TATTGTTATATATATTATA-TTA
55934284 TATATTTTAT
63 TATATTTTAT
55934294 TATATATCA-TTTTATTATATATATTATTCATTATATTTTTTATTGTTATATATATTATATTATA
1 TATATATCATTTTTATT-TATATATTATTCATTATATTTTTTATTGTTATATATATTATATTATA
55934358 T
65 T
55934359 TATTATTTAT
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
71 4 0.07
72 20 0.34
73 34 0.59
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (72 bp):
TATATATCATTTTTATTTATATATTATTCATTATATTTTTTATTGTTATATATATTATATTATAT
ATTTTAT
Found at i:55934386 original size:29 final size:27
Alignment explanation
Indices: 55934214--55934386 Score: 111
Period size: 27 Copynumber: 6.3 Consensus size: 27
55934204 TATGTAAAAA
55934214 ATTATTATATATATTATTT-TTA-T-TT
1 ATTATTATAT-TATTATTTATTATTATT
55934239 ATGTATTAT-TTATTATATTATT-TATATT
1 AT-TATTATATTATTAT-TTATTAT-TATT
55934267 -TTATTATATT-TTATTTATATATT-TT
1 ATTATTATATTATTATTTAT-TATTATT
55934292 ATTATATATCATT-TTA-TTA-TATATATT
1 ATTAT-TAT-ATTATTATTTATTAT-TATT
*
55934319 ATTCATTATATTTTTTATTGT-TATATATATT
1 ATT-ATTATA-TTATTATT-TAT-TAT-TATT
55934350 A-TATTATATTATTATTTATTACTTATT
1 ATTATTATATTATTATTTATTA-TTATT
55934377 ATTATGTATA
1 ATTAT-TATA
55934387 ATTTTTAAAA
Statistics
Matches: 122, Mismatches: 1, Indels: 46
0.72 0.01 0.27
Matches are distributed among these distances:
24 6 0.05
25 14 0.11
26 26 0.21
27 29 0.24
28 25 0.20
29 11 0.09
30 2 0.02
31 9 0.07
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (27 bp):
ATTATTATATTATTATTTATTATTATT
Found at i:55934873 original size:7 final size:7
Alignment explanation
Indices: 55934863--55934912 Score: 66
Period size: 7 Copynumber: 7.0 Consensus size: 7
55934853 GTACCATGTA
55934863 ATTTTAT
1 ATTTTAT
55934870 ATTTTAT
1 ATTTTAT
55934877 ATTTTAT
1 ATTTTAT
55934884 ATTTTAT
1 ATTTTAT
55934891 A-TTTATT
1 ATTTTA-T
*
55934898 ATTTTCT
1 ATTTTAT
55934905 ATGTTTAT
1 AT-TTTAT
55934913 TTGCATGACA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
6 4 0.11
7 27 0.71
8 7 0.18
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (7 bp):
ATTTTAT
Found at i:55935797 original size:9 final size:9
Alignment explanation
Indices: 55935779--55935815 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
55935769 TATAGTTTGA
*
55935779 TATTCAAAT
1 TATTCGAAT
55935788 TATTCGAAT
1 TATTCGAAT
*
55935797 TATTCGAGT
1 TATTCGAAT
55935806 TATTCGAAT
1 TATTCGAAT
55935815 T
1 T
55935816 CAAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:55940852 original size:21 final size:21
Alignment explanation
Indices: 55940822--55940861 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
55940812 GACTTCTCAG
55940822 TCAATCAGACAATCAAATAAT
1 TCAATCAGACAATCAAATAAT
*
55940843 TCAATTAGACAATCAAATA
1 TCAATCAGACAATCAAATA
55940862 GATATTGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.17, G:0.05, T:0.25
Consensus pattern (21 bp):
TCAATCAGACAATCAAATAAT
Found at i:55944418 original size:44 final size:45
Alignment explanation
Indices: 55944306--55944419 Score: 124
Period size: 45 Copynumber: 2.6 Consensus size: 45
55944296 AAAATTTATA
* *
55944306 GCTTCAATCTGCTCCATTGCAACTTCAGGGAGATAAGATTCACTG
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTCACTG
* * ** * **
55944351 TCTTCAGTCTGCTCTGCTACAACTTCAGGGAGATTAAG-CT-GGTG
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGA-TAAGACTCACTG
55944395 GCTTCAATCTGCTCCACTGCAACTT
1 GCTTCAATCTGCTCCACTGCAACTT
55944420 TAGAAAGATA
Statistics
Matches: 54, Mismatches: 14, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
44 22 0.41
45 28 0.52
46 4 0.07
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (45 bp):
GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTCACTG
Found at i:55944428 original size:143 final size:141
Alignment explanation
Indices: 55944167--55944564 Score: 423
Period size: 143 Copynumber: 2.8 Consensus size: 141
55944157 TTGCGACTTG
* * * *
55944167 TAGCTTCAATTTGTTCCACTGTAACTTCAGGGAAATAAGATT-C-G-C-T-AGTCTGCTCCGCTG
1 TAGCTTCAATCTGTTCCACTGCAACTTCAGGG-AATAAGATTCCTGTCTTCAGTCTGCTCTGCTA
* * * * *
55944227 CAACTTTAGGGAGATAAGGCTGGTGGCTTAAATCTACTCTACTGCAGCTTCAAGAAGATAAGATT
65 CAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTGCAACTTCAAGAAGATAAGATC
55944292 AGCCAAAATTTA
130 AGCCAAAATTTA
* *
55944304 TAGCTTCAATCTGCTCCATTGCAACTTCAGGGAGATAAGATTCACTGTCTTCAGTCTGCTCTGCT
1 TAGCTTCAATCTGTTCCACTGCAACTTCAGGGA-ATAAGATTC-CTGTCTTCAGTCTGCTCTGCT
* *
55944369 ACAACTTCAGGGAGATTAA-GCTGGTGGCTTCAATCTGCTCCACTGCAACTT-TAGAAAGATAAG
64 ACAACTTCAGGGAGA-TAAGGCTGGTGGCTTCAATCTACTCCACTGCAACTTCAAG-AAGATAAG
* * *
55944432 ATCCGCCATAATTTG
127 ATCAGCCAAAATTTA
* * * ** * * * * *
55944447 TGGCTTTAATCTATTCTGCTGCAACGTCGGGGAATTAAGGTTCGTTGTCTTCAGTCTGCTCTACT
1 TAGCTTCAATCTGTTCCACTGCAACTTCAGGGAA-TAAGATTC-CTGTCTTCAGTCTGCTCTGCT
* * *
55944512 ATAACTTCAGGGAGATAAGGTTGGTGGCTTCAATCTACTTCACTGCAACTTCA
64 ACAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTGCAACTTCA
55944565 GGGAGATGAG
Statistics
Matches: 215, Mismatches: 34, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
136 1 0.00
137 36 0.17
139 1 0.00
140 1 0.00
141 1 0.00
142 7 0.03
143 165 0.77
144 3 0.01
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (141 bp):
TAGCTTCAATCTGTTCCACTGCAACTTCAGGGAATAAGATTCCTGTCTTCAGTCTGCTCTGCTAC
AACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTGCAACTTCAAGAAGATAAGATCA
GCCAAAATTTA
Found at i:55956182 original size:38 final size:37
Alignment explanation
Indices: 55956098--55956210 Score: 160
Period size: 38 Copynumber: 3.1 Consensus size: 37
55956088 CGAAGCTTTG
* * *
55956098 CTAATTCCGGGCTAAGCCGAA-GCATGGTGCGAG-TA
1 CTAAATCCGGGTTAAGCCGAAGGCATTGTGCGAGTTA
55956133 CT-AATCCGGGTTAAGCCGAAGGCATTTGTGCGAGTTA
1 CTAAATCCGGGTTAAGCCGAAGGCA-TTGTGCGAGTTA
55956170 CTAAATCCGGGTTAAGTCCGAAGGCATTGTGCGAGTTA
1 CTAAATCCGGGTTAAG-CCGAAGGCATTGTGCGAGTTA
55956208 CTA
1 CTA
55956211 TAACGGCTAT
Statistics
Matches: 70, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
34 16 0.23
35 5 0.07
36 8 0.11
37 4 0.06
38 28 0.40
39 9 0.13
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (37 bp):
CTAAATCCGGGTTAAGCCGAAGGCATTGTGCGAGTTA
Found at i:55956232 original size:36 final size:37
Alignment explanation
Indices: 55956104--55956234 Score: 148
Period size: 36 Copynumber: 3.6 Consensus size: 37
55956094 TTTGCTAATT
* *
55956104 CCGGGCTAAG-CCGAA-GCATGGTGCGAG-TACTAAT
1 CCGGGCTAAGTCCGAAGGCATTGTGCGAGTTACTAAA
*
55956138 CCGGGTTAAG-CCGAAGGCATTTGTGCGAGTTACTAAA
1 CCGGGCTAAGTCCGAAGGCA-TTGTGCGAGTTACTAAA
*
55956175 TCCGGGTTAAGTCCGAAGGCATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCGAAGGCATTGTGCGAGTTACTA-AA
*
55956214 -C-GGCTATGTCCGAAGGCATTG
1 CCGGGCTAAGTCCGAAGGCATTG
55956235 AACGAGGAGC
Statistics
Matches: 86, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
34 14 0.16
35 3 0.03
36 26 0.30
37 7 0.08
38 25 0.29
39 11 0.13
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.24
Consensus pattern (37 bp):
CCGGGCTAAGTCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:55964102 original size:40 final size:40
Alignment explanation
Indices: 55964018--55964242 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
55964008 TTGAATGATT
* * * *
55964018 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
55964058 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
55964098 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
55964137 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
55964177 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
55964218 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
55964243 AACGAGGAGC
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 121 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:55964264 original size:119 final size:119
Alignment explanation
Indices: 55964018--55964275 Score: 283
Period size: 119 Copynumber: 2.2 Consensus size: 119
55964008 TTGAATGATT
* *
55964018 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* ** *
55964083 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
* * * **
55964137 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
55964200 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATA
64 TTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTGA-CTAAA
* *
55964257 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
55964276 TACGTGATTT
Statistics
Matches: 117, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
118 3 0.03
119 83 0.71
120 31 0.26
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTGACTAAA
Found at i:55965889 original size:53 final size:53
Alignment explanation
Indices: 55965826--55965929 Score: 172
Period size: 53 Copynumber: 2.0 Consensus size: 53
55965816 GGGAGCATAG
55965826 CTCGAAATGAATAAATTAATCAAAGATAGCAAATGCAATAAGAAGGAAATTAA
1 CTCGAAATGAATAAATTAATCAAAGATAGCAAATGCAATAAGAAGGAAATTAA
* * * *
55965879 CTCGAAATGAATAAGTTAATCAATGATAGCAAATGTAATAAGAAGTAAATT
1 CTCGAAATGAATAAATTAATCAAAGATAGCAAATGCAATAAGAAGGAAATT
55965930 GATTAGGAGC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (53 bp):
CTCGAAATGAATAAATTAATCAAAGATAGCAAATGCAATAAGAAGGAAATTAA
Found at i:55965932 original size:27 final size:26
Alignment explanation
Indices: 55965850--55965932 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 26
55965840 ATTAATCAAA
*
55965850 GATAGCAAATGCAATAAGAAGGAAATT
1 GATAGCAAATG-AATAAGAAGTAAATT
* * *
55965877 AACTCG-AAATGAATAAGTTAA-TCAA-T
1 GA-TAGCAAATGAATAAG--AAGTAAATT
55965903 GATAGCAAATGTAATAAGAAGTAAATT
1 GATAGCAAATG-AATAAGAAGTAAATT
55965930 GAT
1 GAT
55965933 TAGGAGCAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 14
0.67 0.11 0.22
Matches are distributed among these distances:
25 4 0.10
26 16 0.38
27 18 0.43
28 4 0.10
ACGTcount: A:0.51, C:0.07, G:0.18, T:0.24
Consensus pattern (26 bp):
GATAGCAAATGAATAAGAAGTAAATT
Found at i:55967837 original size:25 final size:25
Alignment explanation
Indices: 55967809--55967857 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
55967799 ATTGAAAAAA
55967809 AGATTTTGGACATAGCCTATTTCAG
1 AGATTTTGGACATAGCCTATTTCAG
55967834 AGATTTTGGACATAGCCTATTTCA
1 AGATTTTGGACATAGCCTATTTCA
55967858 CAGAAGGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (25 bp):
AGATTTTGGACATAGCCTATTTCAG
Found at i:55969830 original size:24 final size:24
Alignment explanation
Indices: 55969792--55969840 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
55969782 CATATTGTTG
* *
55969792 TTGCATTTATGTTTGCAGTTGCTC
1 TTGCATTTATGTTTGAAGCTGCTC
* *
55969816 TTGCATTTCTTTTTGAAGCTGCTC
1 TTGCATTTATGTTTGAAGCTGCTC
55969840 T
1 T
55969841 AGCCTTTCCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.12, C:0.18, G:0.18, T:0.51
Consensus pattern (24 bp):
TTGCATTTATGTTTGAAGCTGCTC
Found at i:55979595 original size:37 final size:37
Alignment explanation
Indices: 55979535--55979671 Score: 177
Period size: 37 Copynumber: 4.0 Consensus size: 37
55979525 TTTAGCTTGA
* *
55979535 ATAATCCCCACACGTAGTTATCGGGTCTTACCCGGAC
1 ATAATCTCCACACGTAGTCATCGGGTCTTACCCGGAC
*
55979572 AAAATCTCCACACGTAGTCATCGGG---T-------C
1 ATAATCTCCACACGTAGTCATCGGGTCTTACCCGGAC
55979599 ATAATCTCCACACGTAGTCATCGGGTCTTACCCGGAC
1 ATAATCTCCACACGTAGTCATCGGGTCTTACCCGGAC
55979636 ATAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 ATAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
55979672 ATATATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 20
0.78 0.04 0.18
Matches are distributed among these distances:
27 25 0.29
30 1 0.01
34 1 0.01
37 59 0.69
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
ATAATCTCCACACGTAGTCATCGGGTCTTACCCGGAC
Found at i:55979610 original size:64 final size:64
Alignment explanation
Indices: 55979535--55979662 Score: 229
Period size: 64 Copynumber: 2.0 Consensus size: 64
55979525 TTTAGCTTGA
*
55979535 ATAATCCCCACACGTAGTTATCGGGTCTTACCCGGACAAAATCTCCACACGTAGTCATCGGGTC
1 ATAATCCCCACACGTAGTCATCGGGTCTTACCCGGACAAAATCTCCACACGTAGTCATCGGGTC
* *
55979599 ATAATCTCCACACGTAGTCATCGGGTCTTACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 ATAATCCCCACACGTAGTCATCGGGTCTTACCCGGACAAAATCTCCACACGTAGTCATCGGGTC
55979663 TTACCCGGAA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (64 bp):
ATAATCCCCACACGTAGTCATCGGGTCTTACCCGGACAAAATCTCCACACGTAGTCATCGGGTC
Found at i:55979612 original size:27 final size:27
Alignment explanation
Indices: 55979574--55979625 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
55979564 ACCCGGACAA
55979574 AATCTCCACACGTAGTCATCGGGTCAT
1 AATCTCCACACGTAGTCATCGGGTCAT
55979601 AATCTCCACACGTAGTCATCGGGTC
1 AATCTCCACACGTAGTCATCGGGTC
55979626 TTACCCGGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (27 bp):
AATCTCCACACGTAGTCATCGGGTCAT
Found at i:55979870 original size:48 final size:48
Alignment explanation
Indices: 55979812--55980053 Score: 376
Period size: 48 Copynumber: 5.0 Consensus size: 48
55979802 ATATACACAC
* * *
55979812 ATCTCCTACATATTTCACATTAGCCATTCGGCTTTACCAAATATACAC
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* * * *
55979860 ATCTCATACATATTTCACACTAGCCATTTGGATTTACCACATATATAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
55979908 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
55979956 ATCTCATACATATTTCATATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* * *
55980004 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACACATATAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
55980052 AT
1 AT
55980054 TTATCTTGTA
Statistics
Matches: 178, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 178 1.00
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (48 bp):
ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
Found at i:55987772 original size:27 final size:27
Alignment explanation
Indices: 55987734--55987787 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
55987724 AAGTTGGTGG
55987734 GCTGATTTTTTATATTTTTCCAACTAC
1 GCTGATTTTTTATATTTTTCCAACTAC
55987761 GCTGATTTTTTATATTTTTCCAACTAC
1 GCTGATTTTTTATATTTTTCCAACTAC
55987788 AAGGACCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.52
Consensus pattern (27 bp):
GCTGATTTTTTATATTTTTCCAACTAC
Found at i:55990170 original size:47 final size:46
Alignment explanation
Indices: 55990058--55990329 Score: 198
Period size: 47 Copynumber: 5.8 Consensus size: 46
55990048 AATTTCTTGT
** *
55990058 GTGCCAGTGTAAGACATGTCTGGGACATGCAAT-GGCCACA-TTATGA
1 GTGCCAGTGTAAGACATGTCTGGGACATGC-ATCGG-CACAGAGACGA
* *
55990104 GTGCTAGTATAAGACCATGTCTGGGACATGGCATCGGCACAGAGACGA
1 GTGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCACAGAGACGA
* * **
55990152 GTGCCAGTGTAAGACATGTCTAGGACATGCATCAGC-CTCA-ACGA
1 GTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCACAGAGACGA
* ** **
55990196 TGATAGCCAGTGTAAGACGTGTCTGGGACACACATCGGCTA-AGAG--TT
1 -G-T-GCCAGTGTAAGACATGTCTGGGACATGCATCGGC-ACAGAGACGA
* * * *
55990243 GTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCACATATATACGA
1 GTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCAC--AGAGACGA
* * *
55990291 GAGCTAGTATAAGACCATGTCTGGGACATGGCATCGGCA
1 GTGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCA
55990330 ACTTATTCCA
Statistics
Matches: 177, Mismatches: 32, Indels: 30
0.74 0.13 0.13
Matches are distributed among these distances:
43 1 0.01
44 33 0.19
45 4 0.02
46 23 0.13
47 62 0.35
48 32 0.18
49 14 0.08
50 8 0.05
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (46 bp):
GTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCACAGAGACGA
Found at i:55990178 original size:94 final size:91
Alignment explanation
Indices: 55990058--55990330 Score: 295
Period size: 94 Copynumber: 2.9 Consensus size: 91
55990048 AATTTCTTGT
*
55990058 GTGCCAGTGTAAGACATGTCTGGGACATGCAAT-GGCCACATTATGAGTGCTAGTATAAGACCAT
1 GTGCCAGTGTAAGACATGTCTGGGACATGC-ATCAGCCACATTATGAGTGCTAGTATAAGACCAT
55990122 GTCTGGGACATGGCATCGGCACAGAGACGA
65 GTCTGGGACATGGCATCGGCA-AGAG--GA
* * ** * * *
55990152 GTGCCAGTGTAAGACATGTCTAGGACATGCATCAGCCTCAACGATGA-TAGCCAGTGTAAGA-CG
1 GTGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCAC-ATTATGAGT-GCTAGTATAAGACCA
** **
55990215 TGTCTGGGACA-CACATCGGCTAAGAGTT
64 TGTCTGGGACATGGCATCGGC-AAGAGGA
* *
55990243 GTGCTAGTGTAAGACATGTCTGGGACATGCATCAG-CACATATATACGAGAGCTAGTATAAGACC
1 GTGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACAT-TAT--GAGTGCTAGTATAAGACC
55990307 ATGTCTGGGACATGGCATCGGCAA
63 ATGTCTGGGACATGGCATCGGCAA
55990331 CTTATTCCAT
Statistics
Matches: 146, Mismatches: 23, Indels: 21
0.77 0.12 0.11
Matches are distributed among these distances:
89 1 0.01
90 4 0.03
91 33 0.23
92 12 0.08
93 27 0.18
94 54 0.37
95 15 0.10
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (91 bp):
GTGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGTGCTAGTATAAGACCATG
TCTGGGACATGGCATCGGCAAGAGGA
Found at i:55992522 original size:75 final size:75
Alignment explanation
Indices: 55992409--55992736 Score: 342
Period size: 75 Copynumber: 4.4 Consensus size: 75
55992399 GTAAAAGAGA
* * * * *
55992409 TTGCACCCAGCGCTAG-CGGATTAACTGACAGTT-TTGAATATGAGCCCAGCTCTAATTGGATAA
1 TTGCACCCAGTGCTAGTCGGATTAACCGATA-TTATTGAATGTGAGCCCAGCTCTAGTTGGATAA
55992472 ACCAACGATAT
65 ACCAACGATAT
55992483 TTGCACCCAGTGCTAGTCGGATTAACCGATATTATTGAATGTGAGCCCAGCTCTAGTTGGATAAA
1 TTGCACCCAGTGCTAGTCGGATTAACCGATATTATTGAATGTGAGCCCAGCTCTAGTTGGATAAA
*
55992548 CCAATGATAT
66 CCAACGATAT
** * * * * * * *
55992558 TCACACCCAATGCTAGTCGGATTAGCCGATAGTATTGAATGTGAACCCAACTCTAGTCGGATATA
1 TTGCACCCAGTGCTAGTCGGATTAACCGATATTATTGAATGTGAGCCCAGCTCTAGTTGGATAAA
55992623 CCAACGATAT
66 CCAACGATAT
* * * * **
55992633 TTGCACCCAGTGCTAGTCGG-GTATACCAACGATTA-T-AATTGTGAGCCCAGCGCTAGTCAGAT
1 TTGCACCCAGTGCTAGTCGGATTA-ACCGA-TATTATTGAA-TGTGAGCCCAGCTCTAGTTGGAT
* *
55992695 AAACCAATGATAA
63 AAACCAACGATAT
* ** *
55992708 TTGCATCCAGCACTAGTCGGATAAACCGA
1 TTGCACCCAGTGCTAGTCGGATTAACCGA
55992737 CAGTTGTGTG
Statistics
Matches: 211, Mismatches: 37, Indels: 11
0.81 0.14 0.04
Matches are distributed among these distances:
74 21 0.10
75 186 0.88
76 4 0.02
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (75 bp):
TTGCACCCAGTGCTAGTCGGATTAACCGATATTATTGAATGTGAGCCCAGCTCTAGTTGGATAAA
CCAACGATAT
Found at i:55992617 original size:40 final size:40
Alignment explanation
Indices: 55992495--55992619 Score: 111
Period size: 40 Copynumber: 3.2 Consensus size: 40
55992485 GCACCCAGTG
* * *
55992495 CTAGTCGGATTAACCGATATTATTGAATGTGAGCCCAGCT
1 CTAGTCGGATTAACCGATAGTATTGAATGTGAACCCAACT
* * * *
55992535 CTAGTTGGATAAACCAAT-G-A-T--AT-TCACACCCAA-T
1 CTAGTCGGATTAACCGATAGTATTGAATGTGA-ACCCAACT
*
55992569 GCTAGTCGGATTAGCCGATAGTATTGAATGTGAACCCAACT
1 -CTAGTCGGATTAACCGATAGTATTGAATGTGAACCCAACT
55992610 CTAGTCGGAT
1 CTAGTCGGAT
55992620 ATACCAACGA
Statistics
Matches: 64, Mismatches: 12, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
34 3 0.05
35 20 0.31
36 1 0.02
37 2 0.03
38 2 0.03
40 33 0.52
41 3 0.05
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (40 bp):
CTAGTCGGATTAACCGATAGTATTGAATGTGAACCCAACT
Found at i:55992649 original size:35 final size:35
Alignment explanation
Indices: 55992610--55992730 Score: 116
Period size: 35 Copynumber: 3.3 Consensus size: 35
55992600 GAACCCAACT
*
55992610 CTAGTCGGATATACCAACGATATTTGCACCCAGTG
1 CTAGTCGGATATACCAACGATATTTGCACCCAGCG
* *
55992645 CTAGTCGGGTATACCAACGATTATAATTGTGAGCCCAGCG
1 CTAGTCGGATATACCAACGA-TAT--TTG-CA-CCCAGCG
* * * * * *
55992685 CTAGTCAGATAAACCAATGATAATTGCATCCAGCA
1 CTAGTCGGATATACCAACGATATTTGCACCCAGCG
55992720 CTAGTCGGATA
1 CTAGTCGGATA
55992731 AACCGACAGT
Statistics
Matches: 69, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
35 34 0.49
36 4 0.06
37 3 0.04
38 3 0.04
39 3 0.04
40 22 0.32
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (35 bp):
CTAGTCGGATATACCAACGATATTTGCACCCAGCG
Found at i:55992724 original size:150 final size:149
Alignment explanation
Indices: 55992408--55992740 Score: 395
Period size: 150 Copynumber: 2.2 Consensus size: 149
55992398 CGTAAAAGAG
* * * * *
55992408 ATTGCACCCAGCGCTAG-CGGATTAACTGACAGTTTTGAATATGAGCCCAGCTCTAATTGGATAA
1 ATTGCACCCAGCGCTAGTCGGATTAACCGACAGTATTGAATATGAACCCAACTCTAATCGGATAA
* * *
55992472 ACCAACGATATTTGCACCCAGTGCTAGTCGGATTAACCGATATTATTGAATGTGAGCCCAGCTCT
66 ACCAACGATATTTGCACCCAGTGCTAGTCGGATTAACCAAGATTATTGAATGTGAGCCCAGCGCT
**
55992537 AGTTGGATAAACCAATGAT
131 AGTCAGATAAACCAATGAT
* ** * * * *
55992556 ATTCACACCCAATGCTAGTCGGATTAGCCGATAGTATTGAATGTGAACCCAACTCTAGTCGGATA
1 ATT-GCACCCAGCGCTAGTCGGATTAACCGACAGTATTGAATATGAACCCAACTCTAATCGGATA
* *
55992621 TACCAACGATATTTGCACCCAGTGCTAGTCGG-GTATACCAACGATTA-T-AATTGTGAGCCCAG
65 AACCAACGATATTTGCACCCAGTGCTAGTCGGATTA-ACCAA-GATTATTGAA-TGTGAGCCCAG
55992683 CGCTAGTCAGATAAACCAATGAT
127 CGCTAGTCAGATAAACCAATGAT
* * *
55992706 AATTGCATCCAGCACTAGTCGGATAAACCGACAGT
1 -ATTGCACCCAGCGCTAGTCGGATTAACCGACAGT
55992741 TGTGTGCCGA
Statistics
Matches: 152, Mismatches: 27, Indels: 10
0.80 0.14 0.05
Matches are distributed among these distances:
148 3 0.02
149 15 0.10
150 127 0.84
151 7 0.05
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (149 bp):
ATTGCACCCAGCGCTAGTCGGATTAACCGACAGTATTGAATATGAACCCAACTCTAATCGGATAA
ACCAACGATATTTGCACCCAGTGCTAGTCGGATTAACCAAGATTATTGAATGTGAGCCCAGCGCT
AGTCAGATAAACCAATGAT
Found at i:55997613 original size:18 final size:18
Alignment explanation
Indices: 55997571--55997613 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
55997561 GCCCATTCCG
*
55997571 AAGTATATATATATACAT
1 AAGTATGTATATATACAT
55997589 ATA-TATGTATATATACAT
1 A-AGTATGTATATATACAT
55997607 AAGTATG
1 AAGTATG
55997614 CCCATTCGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 20 0.91
19 1 0.05
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.40
Consensus pattern (18 bp):
AAGTATGTATATATACAT
Found at i:55998120 original size:28 final size:28
Alignment explanation
Indices: 55998052--55998146 Score: 120
Period size: 28 Copynumber: 3.4 Consensus size: 28
55998042 CATGAGACTG
* * * *
55998052 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
55998081 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
55998109 GCACTAAGTGTGCGAG-ATGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
55998136 GCACTGAGTGT
1 GCACTAAGTGT
55998147 ACGGACTTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 20 0.33
28 22 0.37
29 18 0.30
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:55998160 original size:27 final size:27
Alignment explanation
Indices: 55998080--55998162 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
55998070 TAAATTGTAC
* * *
55998080 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTACGAG-ATGAATATAT
* *
55998108 AGCACTAAGTGTGCGAGATGATTATAT
1 AGCACTAAGTGTACGAGATGAATATAT
* *
55998135 AGCACTGAGTGTACG-GACTTAATATAT
1 AGCACTAAGTGTACGAGA-TGAATATAT
55998162 A
1 A
55998163 TTTTTGAATC
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
26 2 0.04
27 30 0.61
28 17 0.35
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTACGAGATGAATATAT
Found at i:56004137 original size:13 final size:13
Alignment explanation
Indices: 56004119--56004144 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56004109 TAAAGACTAA
56004119 AATGCAATCCACT
1 AATGCAATCCACT
56004132 AATGCAATCCACT
1 AATGCAATCCACT
56004145 CTAAGTACTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (13 bp):
AATGCAATCCACT
Found at i:56004673 original size:13 final size:13
Alignment explanation
Indices: 56004655--56004679 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56004645 TTGATAATAA
56004655 TTTTTATTTTTAT
1 TTTTTATTTTTAT
56004668 TTTTTATTTTTA
1 TTTTTATTTTTA
56004680 AAAATATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:56009151 original size:47 final size:47
Alignment explanation
Indices: 56009097--56009501 Score: 666
Period size: 47 Copynumber: 8.6 Consensus size: 47
56009087 TATTTGAATA
56009097 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
56009144 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGTCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
56009191 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
56009240 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
56009287 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
56009334 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
56009381 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * *
56009428 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
56009475 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
56009502 TCCCGAAGGG
Statistics
Matches: 338, Mismatches: 18, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
47 294 0.87
49 44 0.13
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:56010620 original size:40 final size:40
Alignment explanation
Indices: 56010571--56010647 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
56010561 CCAACACACC
* * *
56010571 ATGTAGGGATAAAATCGATCCACCCATCCCTACACACAAA
1 ATGTAGGGATAAAATCAACCCACCCAACCCTACACACAAA
* *
56010611 ATGTGGGGATAAAATCAACCCATCCAACCCTACACAC
1 ATGTAGGGATAAAATCAACCCACCCAACCCTACACAC
56010648 CATAGAGTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.39, C:0.31, G:0.13, T:0.17
Consensus pattern (40 bp):
ATGTAGGGATAAAATCAACCCACCCAACCCTACACACAAA
Found at i:56012418 original size:19 final size:19
Alignment explanation
Indices: 56012391--56012427 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
56012381 AAGGTATATT
*
56012391 AAAAGAATGATAAAGTGAC
1 AAAAAAATGATAAAGTGAC
*
56012410 AAAAAAATGATAATGTGA
1 AAAAAAATGATAAAGTGA
56012428 ATTAAGATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.19, T:0.19
Consensus pattern (19 bp):
AAAAAAATGATAAAGTGAC
Found at i:56012561 original size:13 final size:13
Alignment explanation
Indices: 56012543--56012568 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56012533 TAATGGGTTC
56012543 AAATTTATTATAT
1 AAATTTATTATAT
56012556 AAATTTATTATAT
1 AAATTTATTATAT
56012569 TTTATTTGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAATTTATTATAT
Found at i:56015327 original size:16 final size:16
Alignment explanation
Indices: 56015302--56015335 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
56015292 ATGAATATAT
* *
56015302 ATGTGTAAATGTGATA
1 ATGTGCAAATATGATA
56015318 ATGTGCAAATATGATA
1 ATGTGCAAATATGATA
56015334 AT
1 AT
56015336 TGGATATTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (16 bp):
ATGTGCAAATATGATA
Found at i:56023144 original size:21 final size:21
Alignment explanation
Indices: 56023093--56023132 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
56023083 CTTGAGTTCT
* *
56023093 TAAATGTTTATTGATAGATTA
1 TAAAGGTTTAATGATAGATTA
56023114 TAAAGGTTTAATGATAGAT
1 TAAAGGTTTAATGATAGAT
56023133 ATACAAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.42
Consensus pattern (21 bp):
TAAAGGTTTAATGATAGATTA
Found at i:56023837 original size:22 final size:23
Alignment explanation
Indices: 56023764--56023887 Score: 112
Period size: 22 Copynumber: 5.4 Consensus size: 23
56023754 TCAGCTCGTA
* *
56023764 AGAGCTTACTGTTTTTAGCTCATT
1 AGAGCTTACTG-TTTCAGCTCAAT
* * *
56023788 AGAGCTTACCGTTTTAGCTC-GT
1 AGAGCTTACTGTTTCAGCTCAAT
56023810 ATGAGCTTACTG-TTCAGCTCAAT
1 A-GAGCTTACTGTTTCAGCTCAAT
* **
56023833 AGAGCTTACTG-TTCACCTGGAT
1 AGAGCTTACTGTTTCAGCTCAAT
*
56023855 AGAGCTTACCGTTTCAGCTCAA-
1 AGAGCTTACTGTTTCAGCTCAAT
56023877 ATGAGCTTACT
1 A-GAGCTTACT
56023888 ATTCATCAGC
Statistics
Matches: 83, Mismatches: 13, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
22 38 0.46
23 35 0.42
24 10 0.12
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.35
Consensus pattern (23 bp):
AGAGCTTACTGTTTCAGCTCAAT
Found at i:56042978 original size:48 final size:48
Alignment explanation
Indices: 56042885--56042979 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 48
56042875 CGGCAGTGAC
* * *
56042885 ATGTGATCCCATGTAAAACCATGTCTGAGATAAGGCTTTGGCATCATT
1 ATGTGATCCCATGTAAAACCATGTCTGAGACAAGGCATTGACATCATT
* * * *
56042933 ATGTGATCCCATGTAAGATCATGTTTGAGACATGGCATTGACATCAT
1 ATGTGATCCCATGTAAAACCATGTCTGAGACAAGGCATTGACATCAT
56042980 AATGAGACAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (48 bp):
ATGTGATCCCATGTAAAACCATGTCTGAGACAAGGCATTGACATCATT
Found at i:56050641 original size:16 final size:16
Alignment explanation
Indices: 56050620--56050653 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
56050610 TCTCAATTAG
*
56050620 GAAAAAAAAAATAAAA
1 GAAAAAAAAAAGAAAA
*
56050636 GAAAAAAAGAAGAAAA
1 GAAAAAAAAAAGAAAA
56050652 GA
1 GA
56050654 GAAGGAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (16 bp):
GAAAAAAAAAAGAAAA
Found at i:56050739 original size:26 final size:26
Alignment explanation
Indices: 56050690--56050755 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
56050680 ATATGTTTTT
* *
56050690 TAATTTTT-T-ATTTATTTATCTTTA
1 TAATTTTTATAATTTATATATATTTA
56050714 TAATTTTTATAATTTATATATATTTA
1 TAATTTTTATAATTTATATATATTTA
56050740 -AATTTATTATATATTT
1 TAATTT-TTATA-ATTT
56050756 TTGAAAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
24 8 0.22
25 6 0.17
26 18 0.50
27 4 0.11
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (26 bp):
TAATTTTTATAATTTATATATATTTA
Found at i:56050750 original size:17 final size:17
Alignment explanation
Indices: 56050710--56050755 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
56050700 TTTATTTATC
*
56050710 TTTATA-ATTTTTATAA
1 TTTATATATATTTATAA
56050726 TTTATATATATTTA-AA
1 TTTATATATATTTATAA
56050742 TTTATTATATATTT
1 TTTA-TATATATTT
56050756 TTGAAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTATATATATTTATAA
Found at i:56050766 original size:19 final size:18
Alignment explanation
Indices: 56050711--56050766 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
56050701 TTATTTATCT
*
56050711 TTATA-ATTTTTATAAT-
1 TTATATATTTTTAAAATA
* *
56050727 TTATATATATTTAAATTTA
1 TTATATATTTTTAAA-ATA
56050746 TTATATATTTTTGAAAATA
1 TTATATATTTTT-AAAATA
56050765 TT
1 TT
56050767 TATGTATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 5 0.16
17 7 0.23
18 1 0.03
19 15 0.48
20 3 0.10
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TTATATATTTTTAAAATA
Found at i:56052430 original size:42 final size:43
Alignment explanation
Indices: 56052382--56052467 Score: 165
Period size: 42 Copynumber: 2.0 Consensus size: 43
56052372 ATTTACTTAA
56052382 TTTTTTTGTATAAATCGAGTTAAAATAGGTAAAA-AAAATCTT
1 TTTTTTTGTATAAATCGAGTTAAAATAGGTAAAAGAAAATCTT
56052424 TTTTTTTGTATAAATCGAGTTAAAATAGGTAAAAGAAAATCTT
1 TTTTTTTGTATAAATCGAGTTAAAATAGGTAAAAGAAAATCTT
56052467 T
1 T
56052468 ATTTGAGCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 34 0.79
43 9 0.21
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.41
Consensus pattern (43 bp):
TTTTTTTGTATAAATCGAGTTAAAATAGGTAAAAGAAAATCTT
Found at i:56059973 original size:178 final size:174
Alignment explanation
Indices: 56059678--56060014 Score: 462
Period size: 178 Copynumber: 1.9 Consensus size: 174
56059668 AGCATTTTAA
* **
56059678 TCTAAATTATGTCAAAATTATAGAGATTAAATCTCAAATTTGAGTGAAATATAGGGATCAGCACT
1 TCTAAATTATGTCAAAATTATAGAGATTAAATCTCAAATTTGAGTGAAATATAGAGATCAAAACT
* * ** * *
56059743 GAAATTTAATCATTCTTATATAATCTTAAAAAAGTATTGTGACTAGAACTGAAATTTAGCCATTA
66 AAAATTTAACCATTCTTATATAATCTTAAAAAAGTAGAGGGACTAGAACTGAAATTTAACCATTA
*
56059808 -TTTTCTCATGTGAAAAGAAAAGGAAAAAAAAAGAACAGTCAGGT
131 TTTTTCTCATGTCAAAAGAAAA-GAAAAAAAAAGAACAGTCAGGT
56059852 TCTAAATTATGTCAAAATAAAGTATAGAGATTAAATCTCAAATTTGAGTGAAATATA-AGACTCA
1 TCTAAATTATGTCAAAAT----TATAGAGATTAAATCTCAAATTTGAGTGAAATATAGAGA-TCA
* * * * *
56059916 AAACTAAAATTTAACCGTTCTTATATAATCTTGAGAAGGTAGAGGGATTAGAACTGAAATTTAAC
61 AAACTAAAATTTAACCATTCTTATATAATCTTAAAAAAGTAGAGGGACTAGAACTGAAATTTAAC
*
56059981 CATTATTTTTTTCATGTCAAAAGAAAAGAAAAAA
126 CATTATTTTTCTCATGTCAAAAGAAAAGAAAAAA
56060015 GAATGGGCGG
Statistics
Matches: 141, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
174 18 0.13
177 2 0.01
178 102 0.72
179 19 0.13
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (174 bp):
TCTAAATTATGTCAAAATTATAGAGATTAAATCTCAAATTTGAGTGAAATATAGAGATCAAAACT
AAAATTTAACCATTCTTATATAATCTTAAAAAAGTAGAGGGACTAGAACTGAAATTTAACCATTA
TTTTTCTCATGTCAAAAGAAAAGAAAAAAAAAGAACAGTCAGGT
Found at i:56061433 original size:17 final size:16
Alignment explanation
Indices: 56061413--56061455 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
56061403 ATTTAAAGTC
56061413 AAAATTAATTTAAACAT
1 AAAATTAATTT-AACAT
*
56061430 AAAATTAATATAACAT
1 AAAATTAATTTAACAT
56061446 AAAA-TAATTT
1 AAAATTAATTT
56061456 TAAAATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 5 0.21
16 9 0.38
17 10 0.42
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATTAATTTAACAT
Found at i:56061446 original size:16 final size:17
Alignment explanation
Indices: 56061413--56061450 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
56061403 ATTTAAAGTC
*
56061413 AAAATTAATTTAAACAT
1 AAAATTAATATAAACAT
56061430 AAAATTAATAT-AACAT
1 AAAATTAATATAAACAT
56061446 AAAAT
1 AAAAT
56061451 AATTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATTAATATAAACAT
Found at i:56066041 original size:124 final size:124
Alignment explanation
Indices: 56065821--56066066 Score: 483
Period size: 124 Copynumber: 2.0 Consensus size: 124
56065811 TGTGCCCTCA
*
56065821 TTGACACCACAATTCAAACACCTAAACAAAATCACATTCATCTATCACGATTTCACTCATCAATT
1 TTGACACCACAATTCAAACACCTAAACAAAATCACATTCATCTATCACAATTTCACTCATCAATT
56065886 CATCCATTTAACCATTAAATACCAAAGCAATATGAGCTATACTATATATGACCAAAACG
66 CATCCATTTAACCATTAAATACCAAAGCAATATGAGCTATACTATATATGACCAAAACG
56065945 TTGACACCACAATTCAAACACCTAAACAAAATCACATTCATCTATCACAATTTCACTCATCAATT
1 TTGACACCACAATTCAAACACCTAAACAAAATCACATTCATCTATCACAATTTCACTCATCAATT
56066010 CATCCATTTAACCATTAAATACCAAAGCAATATGAGCTATACTATATATGACCAAAA
66 CATCCATTTAACCATTAAATACCAAAGCAATATGAGCTATACTATATATGACCAAAA
56066067 GATCAAACTT
Statistics
Matches: 121, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
124 121 1.00
ACGTcount: A:0.43, C:0.26, G:0.05, T:0.27
Consensus pattern (124 bp):
TTGACACCACAATTCAAACACCTAAACAAAATCACATTCATCTATCACAATTTCACTCATCAATT
CATCCATTTAACCATTAAATACCAAAGCAATATGAGCTATACTATATATGACCAAAACG
Found at i:56067095 original size:35 final size:35
Alignment explanation
Indices: 56067055--56067125 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
56067045 AATTTAATCC
* *
56067055 ATTTAAACTTTATAAATACTCAATTTATACAATTA
1 ATTTAAACCTCATAAATACTCAATTTATACAATTA
56067090 ATTTAAACCTCATAAATACTCAATTTATACAATTA
1 ATTTAAACCTCATAAATACTCAATTTATACAATTA
56067125 A
1 A
56067126 GTCTTTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.39
Consensus pattern (35 bp):
ATTTAAACCTCATAAATACTCAATTTATACAATTA
Found at i:56071845 original size:43 final size:43
Alignment explanation
Indices: 56071761--56071900 Score: 124
Period size: 43 Copynumber: 3.3 Consensus size: 43
56071751 TCTGAGATAT
* * * * * *
56071761 CGTGTAAGACCGTGTCTGGGACACAGACCTCGAT-TGAGATTTA
1 CGTGTAAGACCATATCTGGGACAGAGGCATCGATAT-TGATTTA
* **
56071804 CGTATAAGACCATATCTGGGACATCGGCATCG-TATCTGATTT-
1 CGTGTAAGACCATATCTGGGACAGAGGCATCGATAT-TGATTTA
* * *
56071846 CGTGTAAGACCCTGTCTGGGACAGAGGCATCGATATTGAATTA
1 CGTGTAAGACCATATCTGGGACAGAGGCATCGATATTGATTTA
*
56071889 CATGTAAGACCA
1 CGTGTAAGACCA
56071901 CGTCCAGGAC
Statistics
Matches: 77, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
42 33 0.43
43 44 0.57
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (43 bp):
CGTGTAAGACCATATCTGGGACAGAGGCATCGATATTGATTTA
Found at i:56078724 original size:18 final size:18
Alignment explanation
Indices: 56078697--56078731 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
56078687 TTGATAATTA
*
56078697 TTAAGTATTTTAAGTTAT
1 TTAAGAATTTTAAGTTAT
*
56078715 TTAAGAATTTTATGTTA
1 TTAAGAATTTTAAGTTA
56078732 ACAAGAAAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.54
Consensus pattern (18 bp):
TTAAGAATTTTAAGTTAT
Found at i:56079115 original size:11 final size:12
Alignment explanation
Indices: 56079099--56079127 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
56079089 TGCCACGTTC
56079099 TATCTTTCCA-T
1 TATCTTTCCATT
56079110 TATCTTTCCATT
1 TATCTTTCCATT
56079122 TATCTT
1 TATCTT
56079128 CTTTATTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.17, C:0.24, G:0.00, T:0.59
Consensus pattern (12 bp):
TATCTTTCCATT
Found at i:56083081 original size:69 final size:69
Alignment explanation
Indices: 56082995--56083132 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
56082985 CTATTACTGC
56082995 TCCATTAACTGAGATTATTAAAAAATATGTGGGTTTTAAATGGAGAGAAGTTCAGGAAAAGGCTT
1 TCCATTAACTGAGATTATTAAAAAATATGTGGGTTTTAAATGGAGAGAAGTTCAGGAAAAGGCTT
56083060 TTCA
66 TTCA
* * *
56083064 TCCATTAACTGATATTATTAAAAAATCTGTGGGTTTTAAATGGGGAGAAGTTCAGGAAAAGGCTT
1 TCCATTAACTGAGATTATTAAAAAATATGTGGGTTTTAAATGGAGAGAAGTTCAGGAAAAGGCTT
56083129 TTCA
66 TTCA
56083133 AACTTTAAAG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (69 bp):
TCCATTAACTGAGATTATTAAAAAATATGTGGGTTTTAAATGGAGAGAAGTTCAGGAAAAGGCTT
TTCA
Found at i:56085678 original size:12 final size:12
Alignment explanation
Indices: 56085646--56085679 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
56085636 CTACACGCCA
56085646 CATTCTATCTTTC
1 CATT-TATCTTTC
56085659 CA-TTATCTTTC
1 CATTTATCTTTC
56085670 CATTTATCTT
1 CATTTATCTT
56085680 CTTTATTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 10 0.50
12 8 0.40
13 2 0.10
ACGTcount: A:0.18, C:0.26, G:0.00, T:0.56
Consensus pattern (12 bp):
CATTTATCTTTC
Found at i:56087533 original size:43 final size:44
Alignment explanation
Indices: 56087453--56087537 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 44
56087443 GTAATGCCTC
* * *
56087453 GTAACCCTAATCTGATGTTAATTACGGGTTAGGGGTGTTACACT
1 GTAACCCTAATCCGATGTTAATTACGGGTGAGCGGTGTTACACT
*
56087497 GTAACCCT-ATCCGGTGTTGAA-TACGGGTGAGCGGTGTTACA
1 GTAACCCTAATCCGATGTT-AATTACGGGTGAGCGGTGTTACA
56087538 GGTTATGCTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
43 26 0.72
44 10 0.28
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.31
Consensus pattern (44 bp):
GTAACCCTAATCCGATGTTAATTACGGGTGAGCGGTGTTACACT
Found at i:56090492 original size:13 final size:13
Alignment explanation
Indices: 56090463--56090495 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
56090453 ATTCCAAGTC
*
56090463 ATGTTTT-AAGCT
1 ATGTTTTAAAGAT
56090475 ATGTTTTAAAGAT
1 ATGTTTTAAAGAT
56090488 ATGTTTTA
1 ATGTTTTA
56090496 CACGTGCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.30, C:0.03, G:0.15, T:0.52
Consensus pattern (13 bp):
ATGTTTTAAAGAT
Found at i:56092122 original size:42 final size:41
Alignment explanation
Indices: 56092006--56092154 Score: 185
Period size: 42 Copynumber: 3.5 Consensus size: 41
56091996 TACCAATGGT
* *
56092006 ATATCCCAGATATGGTCTTACATGTAATCTCATATCGATACC
1 ATATCCCAAATATGGTCTTACATG-AATCTCATATCGATGCC
* *
56092048 AATAGT-CCAACTATGGTCTTACACGAAATCTCATATCGATGCC
1 -ATA-TCCCAAATATGGTCTTACATG-AATCTCATATCGATGCC
56092091 ATATCCCAAATATGGTCTTACATGAAGTCTCATA-CTGATGCC
1 ATATCCCAAATATGGTCTTACATGAA-TCTCATATC-GATGCC
*
56092133 ATATCCCAGATATGGTCTTACA
1 ATATCCCAAATATGGTCTTACA
56092155 CATAAACTTA
Statistics
Matches: 94, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
41 4 0.04
42 54 0.57
43 35 0.37
44 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (41 bp):
ATATCCCAAATATGGTCTTACATGAATCTCATATCGATGCC
Found at i:56096540 original size:42 final size:42
Alignment explanation
Indices: 56096482--56096571 Score: 119
Period size: 42 Copynumber: 2.1 Consensus size: 42
56096472 AACTACGGTA
* *
56096482 TTACACGAAATCTCATA-TCGATGCCATATTCCAAATATGGTC
1 TTACACGAAATATCATACT-GATGCCATATCCCAAATATGGTC
* * *
56096524 TTACACGAAGTATCATACTGATGCCATATCCCAGATATGGTT
1 TTACACGAAATATCATACTGATGCCATATCCCAAATATGGTC
56096566 TTACAC
1 TTACAC
56096572 ATAAACTTAG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 41 0.98
43 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.31
Consensus pattern (42 bp):
TTACACGAAATATCATACTGATGCCATATCCCAAATATGGTC
Found at i:56106362 original size:46 final size:47
Alignment explanation
Indices: 56106216--56106417 Score: 166
Period size: 46 Copynumber: 4.4 Consensus size: 47
56106206 GTGCTAATGT
* ** *
56106216 AAGACATGTCTGGGACATGCATCGGCCACATTATG-AGAGCCAGTGT
1 AAGACATGTCTGGGACATGCATCGGCCTCAAGATGTAGAGCCAGTGA
* * * * ** ** * *
56106262 GAGACCATGTCTAGGACATGGCATCGACATTGAGA-CAAGAGCTAGTGT
1 AAGA-CATGTCTGGGACAT-GCATCGGCCTCAAGATGTAGAGCCAGTGA
56106310 AAGACATGTCTGGGACATGCATCGGCCTCAAGATGTA-AGCCAGTGA
1 AAGACATGTCTGGGACATGCATCGGCCTCAAGATGTAGAGCCAGTGA
* *
56106356 AAGACATATCTGGGACATGCATCGG-CTACAAGATGT---GTCAGTGA
1 AAGACATGTCTGGGACATGCATCGGCCT-CAAGATGTAGAGCCAGTGA
*
56106400 ATGACCATGTCTGGGACA
1 AAGA-CATGTCTGGGACA
56106418 AGGCTTCGAT
Statistics
Matches: 125, Mismatches: 25, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
44 10 0.08
45 14 0.11
46 53 0.42
47 27 0.22
48 21 0.17
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.21
Consensus pattern (47 bp):
AAGACATGTCTGGGACATGCATCGGCCTCAAGATGTAGAGCCAGTGA
Done.