Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 101 of 438
Found at i:28617358 original size:35 final size:35
Alignment explanation
Indices: 28617318--28617387 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
28617308 CTTCATGACC
*
28617318 AAACTTTATCAATTACCATAGCTAACCTGCCAAAA
1 AAACTTTATCAATTACCATAGCTAACCTACCAAAA
*
28617353 AAACTTTTTCAATTACCATAGCTAACCTACCAAAA
1 AAACTTTATCAATTACCATAGCTAACCTACCAAAA
28617388 GCTTACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.43, C:0.26, G:0.04, T:0.27
Consensus pattern (35 bp):
AAACTTTATCAATTACCATAGCTAACCTACCAAAA
Found at i:28625242 original size:29 final size:29
Alignment explanation
Indices: 28625200--28625257 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
28625190 TTCAACTGAC
28625200 GATAATCTATACACATTCTCATCGTACCT
1 GATAATCTATACACATTCTCATCGTACCT
28625229 GATAATCTATACACATTCTCATCGTACCT
1 GATAATCTATACACATTCTCATCGTACCT
28625258 TCTTTCTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (29 bp):
GATAATCTATACACATTCTCATCGTACCT
Found at i:28627185 original size:569 final size:569
Alignment explanation
Indices: 28626100--28627236 Score: 1582
Period size: 569 Copynumber: 2.0 Consensus size: 569
28626090 CTAACTACCG
** * ** * * *
28626100 CTTACATTTCCTGCATTTCTGGGAGGTCTACCATGAGAAACGTTGCCACTTGATCTCTGATTCAT
1 CTTACATTTCCCACATTTCTGGAAGGTCTACCACAAGAAACGTTGCCACTCGACCTCGGATTCAT
* * * *
28626165 AAAATTATCTTTTTTAGCTAAATCTGGGCAATCTTTTATAAAATGATTTTGTGAACCACAACTAT
66 AAAATTATCTTTTTCAGCTAAATCTAGGCAATATTTTATAAAATGATTTCGTGAACCACAACTAT
* * * * * * *
28626230 AACAAGCTCGGTTATTACTTTTTCCCTAGCTCTCTACAAAATGTCGTCTTCCACATTGATCACAC
131 AACAAGCTCAGTAATTACTCTATCCCTAGCACTCTACAAAATGCCATCTTCCACATTGATCACAC
* * * *
28626295 TCAGGTTTTTCATTCTTTGCATTACCAACACTGGCAACAGTCGTAGCTAGAGCTTCAAAGCTCGG
196 TCAGGTTTTTCATTCTTTGCATTACCAACACTAGCAACAGACATAGCTAGAGCTTCAAAGCTCGA
*
28626360 TTGCTATCTAGCACGATCTCTATTCGAATGTCCCACAATAGCCTTTGAACAGCTATTATCATCTC
261 TTGCAATCTAGCACGATCTCTATTCGAATGTCCCACAATAGCCTTTGAACAGCTATTATCATCTC
* * * * *
28626425 TAAACTTCTTGGATACAGATTGAAATGACTTGCCCGATGATCTCTTTCGTACATCTTTAGCTTCA
326 TAAACTTCTTGGATACAGACTAAAATGACTTGCCCAATGATCTCATTCGTACATCTCTAGCTTCA
* * * ** *
28626490 GAATCAGCTTTTCTTTTCTCTTTCTTAAGATCATCAGCTTTACATGCTTGTTTAACAAGCACAAC
391 AAATCAGCTTTTCTTTTCTCTTTCCTAAGATCATCAGCTGTACATGCTCATTCAACAAGCACAAC
** * *
28626555 AAATTCTTTGATTTCCAGAATTTTGACTAATAGATGAATGTCTCCAGTTAAGCCATCCTCTAATC
456 AAATTCTTTGATTTCCAGAATTTCAACTAACAGATGAATATCTCCAGTTAAGCCATCCTCTAATC
* * *
28626620 TTTTGTACATTATTGCCTCTGTAGATACACATTCACGAGCATATTGGCA
521 TTTTGCACATTATTGCCTCCGTAGATACACATTCACGAGCATACTGGCA
* * * *
28626669 CTTACATTTCCCATATTTCTGGAAGGTCTACCACAAGAAGCGTTGTCACTCGGCCTCGGATTC-T
1 CTTACATTTCCCACATTTCTGGAAGGTCTACCACAAGAAACGTTGCCACTCGACCTCGGATTCAT
* *
28626733 GAACATTATCTTTTTCAGCTAAATCTAGGCAATATTTTATAAAATGATTTCGTGAACCACAACTG
66 -AAAATTATCTTTTTCAGCTAAATCTAGGCAATATTTTATAAAATGATTTCGTGAACCACAACTA
*
28626798 TAACAAGCTCAGTAATTACTCTATCCCTAGCACTCT-CTAAAATGCCATCTTTCACATTGATCAC
130 TAACAAGCTCAGTAATTACTCTATCCCTAGCACTCTAC-AAAATGCCATCTTCCACATTGATCAC
* *
28626862 ACTCAGGTTTTTCATTCTTTGCATTACCAACACTAGCAACAGACATAGCT-GAAGTTTTAAAGCT
194 ACTCAGGTTTTTCATTCTTTGCATTACCAACACTAGCAACAGACATAGCTAG-AGCTTCAAAGCT
* **
28626926 CGATTGCAATCTAGCACGATCTCTATTTGAATGTCCCACAATAGCCTTTGAATGGCTATTATCAT
258 CGATTGCAATCTAGCACGATCTCTATTCGAATGTCCCACAATAGCCTTTGAACAGCTATTATCAT
* * * * * * *
28626991 CTCTGAATTTCTT-TATTGCAGACTAAAATGGCTTGCCCAATGATCTCATTCGTACCTCTCTAGT
323 CTCTAAACTTCTTGGA-TACAGACTAAAATGACTTGCCCAATGATCTCATTCGTACATCTCTAGC
*
28627055 TTCAAAATTAGCTTTTCTTTTCTCTTTCCTAAGAT-ATTCAGCTGTACATGCTCATTCAACAAGC
387 TTCAAAATCAGCTTTTCTTTTCTCTTTCCTAAGATCA-TCAGCTGTACATGCTCATTCAACAAGC
* * * ** *
28627119 ACAACAAATTCTTTGATTTTCAGAATTTCAACTAACAGATGAATATCTCTATTTAATTCGTCCTC
451 ACAACAAATTCTTTGATTTCCAGAATTTCAACTAACAGATGAATATCTCCAGTTAAGCCATCCTC
28627184 TAATCTTTTGCACATTATTGCCTCCGTAGATACACATTCACGAGCATACTGGC
516 TAATCTTTTGCACATTATTGCCTCCGTAGATACACATTCACGAGCATACTGGC
28627237 TTAATCTTAT
Statistics
Matches: 495, Mismatches: 68, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
568 5 0.01
569 490 0.99
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.35
Consensus pattern (569 bp):
CTTACATTTCCCACATTTCTGGAAGGTCTACCACAAGAAACGTTGCCACTCGACCTCGGATTCAT
AAAATTATCTTTTTCAGCTAAATCTAGGCAATATTTTATAAAATGATTTCGTGAACCACAACTAT
AACAAGCTCAGTAATTACTCTATCCCTAGCACTCTACAAAATGCCATCTTCCACATTGATCACAC
TCAGGTTTTTCATTCTTTGCATTACCAACACTAGCAACAGACATAGCTAGAGCTTCAAAGCTCGA
TTGCAATCTAGCACGATCTCTATTCGAATGTCCCACAATAGCCTTTGAACAGCTATTATCATCTC
TAAACTTCTTGGATACAGACTAAAATGACTTGCCCAATGATCTCATTCGTACATCTCTAGCTTCA
AAATCAGCTTTTCTTTTCTCTTTCCTAAGATCATCAGCTGTACATGCTCATTCAACAAGCACAAC
AAATTCTTTGATTTCCAGAATTTCAACTAACAGATGAATATCTCCAGTTAAGCCATCCTCTAATC
TTTTGCACATTATTGCCTCCGTAGATACACATTCACGAGCATACTGGCA
Found at i:28628942 original size:23 final size:23
Alignment explanation
Indices: 28628885--28628943 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
28628875 ACATCGCAGT
*
28628885 AAAGCTGCTAACAGTAACGCAAC
1 AAAGCTGCTAATAGTAACGCAAC
*
28628908 AAAGCTGCTAATAGTAATGCAAC
1 AAAGCTGCTAATAGTAACGCAAC
28628931 AAAGCTGCTAATA
1 AAAGCTGCTAATA
28628944 ACAGTAAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.19
Consensus pattern (23 bp):
AAAGCTGCTAATAGTAACGCAAC
Found at i:28636048 original size:27 final size:27
Alignment explanation
Indices: 28635982--28636048 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
28635972 TGGAAATCAT
*
28635982 CTTTTCCAAAA-CCAAATTTTAGGAAAA
1 CTTTT-CAAAACCCTAATTTTAGGAAAA
*
28636009 CTTTTCAATACCCTAATTTT-GAGAAAA
1 CTTTTCAAAACCCTAATTTTAG-GAAAA
28636036 -TTTTCAGAAACCC
1 CTTTTCA-AAACCC
28636049 ATTCCACAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 11 0.32
27 23 0.68
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.33
Consensus pattern (27 bp):
CTTTTCAAAACCCTAATTTTAGGAAAA
Found at i:28643300 original size:40 final size:40
Alignment explanation
Indices: 28643256--28643480 Score: 272
Period size: 40 Copynumber: 5.6 Consensus size: 40
28643246 CGACAAAAAA
* * * *
28643256 TCGGCTATTTGTGGCATTTAGTGTGAGATTCGACATAGTT
1 TCGGCTATATATGGCACTTAGTGTGAGATTCGACATAGCT
*
28643296 TCGGCTATATATGGCACTTAGTGT-ACAATTCGACATAGCT
1 TCGGCTATATATGGCACTTAGTGTGA-GATTCGACATAGCT
* *
28643336 TCGGCTATATATGGCACTTAGTGTGTGATTTGACATAGCT
1 TCGGCTATATATGGCACTTAGTGTGAGATTCGACATAGCT
* * * * *
28643376 TCAGCTATTTCTAGCACTTAGTGTGCGATTCGACATAGCT
1 TCGGCTATATATGGCACTTAGTGTGAGATTCGACATAGCT
* * * * *
28643416 TTGGCTATATATGGCACTTAGTGTGTGATTTGAGATAACT
1 TCGGCTATATATGGCACTTAGTGTGAGATTCGACATAGCT
*
28643456 TCGGCTATGTATGGCACTTAGTGTG
1 TCGGCTATATATGGCACTTAGTGTG
28643481 CGTGAAATTG
Statistics
Matches: 158, Mismatches: 25, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
39 1 0.01
40 157 0.99
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (40 bp):
TCGGCTATATATGGCACTTAGTGTGAGATTCGACATAGCT
Found at i:28643472 original size:120 final size:120
Alignment explanation
Indices: 28643259--28643480 Score: 329
Period size: 120 Copynumber: 1.9 Consensus size: 120
28643249 CAAAAAATCG
* * *
28643259 GCTATTTGTGGCATTTAGTGTGAGATTCGACATAGTTTCGGCTATATATGGCACTTAGTGTACAA
1 GCTATTTCTAGCACTTAGTGTGAGATTCGACATAGTTTCGGCTATATATGGCACTTAGTGTACAA
*
28643324 TTCGACATAGCTTCGGCTATATATGGCACTTAGTGTGTGATTTGACATAGCTTCA
66 TTCGACATAACTTCGGCTATATATGGCACTTAGTGTGTGATTTGACATAGCTTCA
* ***
28643379 GCTATTTCTAGCACTTAGTGTGCGATTCGACATAGCTTT-GGCTATATATGGCACTTAGTGTGTG
1 GCTATTTCTAGCACTTAGTGTGAGATTCGACATAG-TTTCGGCTATATATGGCACTTAGTGTACA
* * *
28643443 ATTTGAGATAACTTCGGCTATGTATGGCACTTAGTGTG
65 ATTCGACATAACTTCGGCTATATATGGCACTTAGTGTG
28643481 CGTGAAATTG
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
120 87 0.97
121 3 0.03
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (120 bp):
GCTATTTCTAGCACTTAGTGTGAGATTCGACATAGTTTCGGCTATATATGGCACTTAGTGTACAA
TTCGACATAACTTCGGCTATATATGGCACTTAGTGTGTGATTTGACATAGCTTCA
Found at i:28643480 original size:80 final size:80
Alignment explanation
Indices: 28643256--28643482 Score: 310
Period size: 80 Copynumber: 2.8 Consensus size: 80
28643246 CGACAAAAAA
* * * * * * *
28643256 TCGGCTATTTGTGGCATTTAGTGTGAGATTCGACATAGTTTCGGCTATATATGGCACTTAGTGTA
1 TCGGCTATATATGGCACTTAGTGTGTGATTTGACATAGCTTCGGCTATATATGGCACTTAGTGTG
*
28643321 CAATTCGACATAGCT
66 CGATTCGACATAGCT
* * * *
28643336 TCGGCTATATATGGCACTTAGTGTGTGATTTGACATAGCTTCAGCTATTTCTAGCACTTAGTGTG
1 TCGGCTATATATGGCACTTAGTGTGTGATTTGACATAGCTTCGGCTATATATGGCACTTAGTGTG
28643401 CGATTCGACATAGCT
66 CGATTCGACATAGCT
* * * *
28643416 TTGGCTATATATGGCACTTAGTGTGTGATTTGAGATAACTTCGGCTATGTATGGCACTTAGTGTG
1 TCGGCTATATATGGCACTTAGTGTGTGATTTGACATAGCTTCGGCTATATATGGCACTTAGTGTG
28643481 CG
66 CG
28643483 TGAAATTGAA
Statistics
Matches: 128, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
80 128 1.00
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (80 bp):
TCGGCTATATATGGCACTTAGTGTGTGATTTGACATAGCTTCGGCTATATATGGCACTTAGTGTG
CGATTCGACATAGCT
Found at i:28645755 original size:2 final size:2
Alignment explanation
Indices: 28645748--28645774 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28645738 TCGATCGGAG
28645748 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
28645775 GTACGCACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28648370 original size:39 final size:38
Alignment explanation
Indices: 28648312--28648493 Score: 154
Period size: 40 Copynumber: 4.6 Consensus size: 38
28648302 CCGCACCAAG
* * * *
28648312 GCCTACGGGACTTAACCCGGATATCACGATTTG-ACAAAT
1 GCCTTCGGGTCTTAGCCCGGATAT-AC-ACTTGCACAAAT
* *
28648351 GCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATAT-AC-ACTTGCACAAAT
* *
28648391 GCCTTCGGGTCTTAGCCCGGATATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATA-C-ACTTGCACAAAT
* *
28648431 GCCTTCGGGTCTTAACCCGGATATA-A-TTTCAGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATACACTTGCA-CA-AA-T
* *
28648470 GTCTTCGGGGCTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
28648494 CATTCAATTT
Statistics
Matches: 118, Mismatches: 20, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
36 3 0.03
37 3 0.03
38 1 0.01
39 49 0.42
40 62 0.53
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.28
Consensus pattern (38 bp):
GCCTTCGGGTCTTAGCCCGGATATACACTTGCACAAAT
Found at i:28648394 original size:40 final size:39
Alignment explanation
Indices: 28648348--28648493 Score: 159
Period size: 40 Copynumber: 3.7 Consensus size: 39
28648338 CGATTTGACA
* *
28648348 AATGCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCAC
1 AATGCCTTCGGGTCTTAGCCCGGATATAACAACTAGCAC
* *
28648387 GAATGCCTTCGGGTCTTAGCCCGGATATAGCTACTAGCAC
1 -AATGCCTTCGGGTCTTAGCCCGGATATAACAACTAGCAC
* *** *
28648427 AATTGCCTTCGGGTCTTAACCCGGATATAATTTC-AGCAT
1 AA-TGCCTTCGGGTCTTAGCCCGGATATAACAACTAGCAC
* *
28648466 AATTGTCTTCGGGGCTTAGCCCGGATAT
1 AA-TGCCTTCGGGTCTTAGCCCGGATAT
28648494 CATTCAATTT
Statistics
Matches: 93, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
39 31 0.33
40 62 0.67
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (39 bp):
AATGCCTTCGGGTCTTAGCCCGGATATAACAACTAGCAC
Found at i:28656981 original size:2 final size:2
Alignment explanation
Indices: 28656974--28656998 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28656964 TCGATCGGAG
28656974 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
28656999 GTACGCACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28663780 original size:46 final size:46
Alignment explanation
Indices: 28663720--28664035 Score: 429
Period size: 46 Copynumber: 6.9 Consensus size: 46
28663710 TTTGACATGA
* * * * *
28663720 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATATCAGGT
* * *
28663766 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
* * *** *
28663812 TGCCATAGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
* *
28663858 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATACCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
*
28663904 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
* *
28663949 TGTCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
*
28663995 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATAT
28664036 TAGAGAACAC
Statistics
Matches: 248, Mismatches: 20, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
45 47 0.19
46 201 0.81
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGT
Found at i:28664014 original size:137 final size:138
Alignment explanation
Indices: 28663720--28664034 Score: 427
Period size: 137 Copynumber: 2.3 Consensus size: 138
28663710 TTTGACATGA
* * * ** *
28663720 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTATCTTTCAA
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATACCAGGTTGCCATGGTATCTTTCAA
** * **
28663784 CCATGGTCTTATTCATTTCATGTCACGTTGCCATAGTATCTTTCAACCATGGTCTTATTCATTTC
65 CCATGGTCTTACACATTTCATATCACGTTGCCATAGTATCTTTCAACCATGGTCTTACACATTTC
* * *
28663849 CCGTCATGT
130 ACATCAGGT
*
28663858 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATACCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATACCAGGTTGCCATGGTATCTTTCAAC
* * *
28663923 CATGGTCTTACACA-TTCATATCAGGTTGTCATGGTATCTTTCAACCATGGTCTTACACATTTCA
66 CATGGTCTTACACATTTCATATCACGTTGCCATAGTATCTTTCAACCATGGTCTTACACATTTCA
*
28663987 TATCAGGT
131 CATCAGGT
*
28663995 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATA
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATA
28664035 TTAGAGAACA
Statistics
Matches: 155, Mismatches: 21, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
137 90 0.58
138 65 0.42
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.40
Consensus pattern (138 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATACCAGGTTGCCATGGTATCTTTCAAC
CATGGTCTTACACATTTCATATCACGTTGCCATAGTATCTTTCAACCATGGTCTTACACATTTCA
CATCAGGT
Found at i:28669841 original size:11 final size:11
Alignment explanation
Indices: 28669822--28669852 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
28669812 TAAATGAAAT
*
28669822 TATGTGTAACG
1 TATGAGTAACG
28669833 TATGAGTAACG
1 TATGAGTAACG
28669844 TATGAGTAA
1 TATGAGTAA
28669853 TAAGCTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.32
Consensus pattern (11 bp):
TATGAGTAACG
Found at i:28670491 original size:21 final size:22
Alignment explanation
Indices: 28670465--28670523 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
28670455 GTTTTAAGAA
*
28670465 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
*
28670486 TTGTTTTAATATTTGTTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
28670508 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
28670524 GATTTATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 6 0.19
21 16 0.50
22 10 0.31
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:28670538 original size:26 final size:24
Alignment explanation
Indices: 28670494--28670543 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
28670484 ATTTGTTTTA
*
28670494 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
28670518 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTG-TTT-TTATATTTTTAAAT
28670544 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:28675990 original size:46 final size:46
Alignment explanation
Indices: 28675934--28676200 Score: 274
Period size: 46 Copynumber: 5.7 Consensus size: 46
28675924 GACGAGGGCT
28675934 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGAGAGCC
* * *
28675980 AGTGTAAGACATGTCTGGGACATGCATCATGGCATTGGCATTGA-GACGAGGGCT
1 AGTGTAAGACATGTCTGGGACATGCATCA-GCCA----CAGT-ATGA-GA--GCC
28676034 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGAGAGCC
* * * *
28676080 AGTGTAAGACATGTCAGGGACATGCATCGGCCTCGAG-ATGATAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGTATGAGAGCC
* * * * * *
28676126 AGTGTCAGACATGTCTGGGACATGCGTCGGCTAC-G-A-GATGTGCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGA-GAGCC
*
28676170 AGTGTAAGACATGTCTGGGACATGCGTCAGC
1 AGTGTAAGACATGTCTGGGACATGCATCAGC
28676201 ATGGTTACAT
Statistics
Matches: 189, Mismatches: 20, Indels: 26
0.80 0.09 0.11
Matches are distributed among these distances:
43 2 0.01
44 33 0.17
46 99 0.52
47 5 0.03
48 3 0.02
49 5 0.03
51 5 0.03
52 3 0.02
53 3 0.02
54 31 0.16
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGAGAGCC
Found at i:28676050 original size:100 final size:100
Alignment explanation
Indices: 28675907--28676107 Score: 393
Period size: 100 Copynumber: 2.0 Consensus size: 100
28675897 ATGTATGAGA
28675907 CATGGCATTGGCATTGAGACGAGGGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTA
1 CATGGCATTGGCATTGAGACGAGGGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTA
*
28675972 TGAGAGCCAGTGTAAGACATGTCTGGGACATGCAT
66 TGAGAGCCAGTGTAAGACATGTCAGGGACATGCAT
28676007 CATGGCATTGGCATTGAGACGAGGGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTA
1 CATGGCATTGGCATTGAGACGAGGGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTA
28676072 TGAGAGCCAGTGTAAGACATGTCAGGGACATGCAT
66 TGAGAGCCAGTGTAAGACATGTCAGGGACATGCAT
28676107 C
1 C
28676108 GGCCTCGAGA
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.21
Consensus pattern (100 bp):
CATGGCATTGGCATTGAGACGAGGGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTA
TGAGAGCCAGTGTAAGACATGTCAGGGACATGCAT
Found at i:28678882 original size:40 final size:40
Alignment explanation
Indices: 28678755--28678884 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
28678745 ATGCTGGAAA
* *
28678755 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * **
28678795 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
28678835 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
28678875 TTATATCCGG
1 TTATATCCGG
28678885 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 72 0.95
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:28686513 original size:40 final size:40
Alignment explanation
Indices: 28686386--28686515 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
28686376 ATGCTGGAAA
* *
28686386 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * **
28686426 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
28686466 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
28686506 TTATATCCGG
1 TTATATCCGG
28686516 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 72 0.95
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:28693236 original size:39 final size:40
Alignment explanation
Indices: 28693136--28693317 Score: 167
Period size: 40 Copynumber: 4.6 Consensus size: 40
28693126 TCGAATGATG
* * *
28693136 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-AAGTTACTAAA
* * * *
28693176 TCCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTCGTGCAAGTTACTAAA
28693216 TCCGGGCTAAG-CCCGAAGGCATT-GTGCAAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
* * * **
28693254 CCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCGCTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTA-AA
** *
28693295 -CCGGGCTTCGACCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
28693318 TGAGCGAGTC
Statistics
Matches: 116, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
38 22 0.19
39 23 0.20
40 62 0.53
41 9 0.08
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.23
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
Found at i:28693281 original size:78 final size:80
Alignment explanation
Indices: 28693136--28693286 Score: 209
Period size: 78 Copynumber: 1.9 Consensus size: 80
28693126 TCGAATGATG
* * * *
28693136 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
28693201 GTGCGAGTTAATAAA
66 GTGCGAGTTAATAAA
* **
28693216 TCCGGGCTAAG-CCCGAAGGCATTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCATT
28693278 CGTGCGAGT
65 CGTGCGAGT
28693287 CGCTATAACC
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
77 1 0.02
78 36 0.57
79 15 0.24
80 11 0.17
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.23
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
GTGCGAGTTAATAAA
Found at i:28693299 original size:78 final size:80
Alignment explanation
Indices: 28693136--28693317 Score: 201
Period size: 78 Copynumber: 2.3 Consensus size: 80
28693126 TCGAATGATG
* * * * *
28693136 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATTC
1 TCCGGGCTAAGACCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
*
28693201 GTGCGAGTTAATAAA
66 GTGCGAGTCAATAAA
* **
28693216 TCCGGGCTAAG-CCCGAAGGCATTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGGCTAAGACCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCATT
**
28693278 CGTGCGAGTCGCTATAA
65 CGTGCGAGTCAATA-AA
**
28693295 -CCGGGCTTCGACCCGAAGGCATT
1 TCCGGGCTAAGACCCGAAGGCATT
28693318 TGAGCGAGTC
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
77 1 0.01
78 46 0.53
79 29 0.33
80 11 0.13
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.23
Consensus pattern (80 bp):
TCCGGGCTAAGACCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
GTGCGAGTCAATAAA
Found at i:28698170 original size:29 final size:29
Alignment explanation
Indices: 28698146--28698239 Score: 161
Period size: 29 Copynumber: 3.2 Consensus size: 29
28698136 TCGCACACCC
*
28698146 AGTGCCGTATATTTCCAGCATGCACACTT
1 AGTGCCATATATTTCCAGCATGCACACTT
*
28698175 AGTGCTATATATTTCCAGCATGCACACTT
1 AGTGCCATATATTTCCAGCATGCACACTT
*
28698204 AGTGCCATATATTTCCAGCACGCACACTT
1 AGTGCCATATATTTCCAGCATGCACACTT
28698233 AGTGCCA
1 AGTGCCA
28698240 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 61 1.00
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.30
Consensus pattern (29 bp):
AGTGCCATATATTTCCAGCATGCACACTT
Found at i:28698171 original size:58 final size:58
Alignment explanation
Indices: 28698108--28698239 Score: 158
Period size: 58 Copynumber: 2.3 Consensus size: 58
28698098 GATTTAAGCC
* * * *
28698108 CGCACACATAGTGCCATACCCTTCGAGC-TCGCACACCCAGTGCCGTATATTTCCAGCA
1 CGCACACTTAGTGCCATACACTTCCAGCAT-GCACACCCAGTGCCATATATTTCCAGCA
* * * * **
28698166 TGCACACTTAGTGCTATATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATACACTTCCAGCATGCACACCCAGTGCCATATATTTCCAGCA
28698224 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
28698240 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
58 60 0.98
59 1 0.02
ACGTcount: A:0.26, C:0.33, G:0.16, T:0.26
Consensus pattern (58 bp):
CGCACACTTAGTGCCATACACTTCCAGCATGCACACCCAGTGCCATATATTTCCAGCA
Found at i:28698727 original size:2 final size:2
Alignment explanation
Indices: 28698720--28698744 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28698710 TAATGGCCGA
28698720 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
28698745 CAATGTCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28705834 original size:67 final size:64
Alignment explanation
Indices: 28705697--28705879 Score: 219
Period size: 67 Copynumber: 2.8 Consensus size: 64
28705687 ATATAGTTCG
* * * * *
28705697 GCTCTCTTGTAC-ACATGGTGAACA-CTAGTACCACCCATGTGACCTAGCCA-ATTTATCTCGTA
1 GCTCTCTTGT-CTACATGGTGTACACCTAGTACCACCCATGCGACCTAGCTACATATATCCCGTA
* * *
28705759 GCTCTCTTGTCTACATGGTGTCCTTCACCTAGAACCACGCATGCGACCTAGCTACATATATCCCG
1 GCTCTCTTGTCTACATGGTG---TACACCTAGTACCACCCATGCGACCTAGCTACATATATCCCG
28705824 TA
63 TA
* *
28705826 GCTCTCTTGTCTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACAT
1 GCTCTCTTGTCTACATGGTGTACACCTAGTACCACCCATGCGACCTAGCTACAT
28705880 CATAATGTCT
Statistics
Matches: 102, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
61 1 0.01
62 18 0.18
64 29 0.28
65 2 0.02
66 22 0.22
67 30 0.29
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (64 bp):
GCTCTCTTGTCTACATGGTGTACACCTAGTACCACCCATGCGACCTAGCTACATATATCCCGTA
Found at i:28706641 original size:30 final size:30
Alignment explanation
Indices: 28706605--28706665 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
28706595 TCCTTAACTC
28706605 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
28706635 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
28706665 A
1 A
28706666 GGCTCATGAA
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:28710713 original size:27 final size:28
Alignment explanation
Indices: 28710657--28710726 Score: 124
Period size: 27 Copynumber: 2.5 Consensus size: 28
28710647 AAATTTGTAC
28710657 AGCACTAAGTGTGCGAGTTTGATCATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
28710685 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
28710712 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
28710727 GACTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 24 0.59
28 17 0.41
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATCATAT
Found at i:28710737 original size:27 final size:27
Alignment explanation
Indices: 28710657--28710738 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
28710647 AAATTTGTAC
* *
28710657 AGCACTAAGTGTGCGAGTTTGA-TCATAT
1 AGCACTAAGTGTGCGAG-CTCACT-ATAT
* * *
28710685 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
28710712 AGCACTAAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
28710739 GCTTTTGAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
26 1 0.02
27 30 0.61
28 18 0.37
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:28718650 original size:27 final size:28
Alignment explanation
Indices: 28718594--28718663 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
28718584 AAATTTGTAC
28718594 AGCACTAAGTGTGCGAGTTTGATCATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
28718622 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
28718649 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28718664 GACTCACTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 23 0.57
28 17 0.43
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATCATAT
Found at i:28718674 original size:27 final size:27
Alignment explanation
Indices: 28718594--28718675 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
28718584 AAATTTGTAC
* *
28718594 AGCACTAAGTGTGCGAGTTTGA-TCATAT
1 AGCACTAAGTGTGCGAG-CTCACT-ATAT
* * *
28718622 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
*
28718649 AGCACTGAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
28718676 GCTTTTGAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.02
27 29 0.60
28 18 0.38
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:28722507 original size:29 final size:26
Alignment explanation
Indices: 28722450--28722654 Score: 146
Period size: 27 Copynumber: 7.6 Consensus size: 26
28722440 AAACCAAGGC
* *
28722450 TATTTC-GATAATTTTGTAAACCAATGG
1 TATTTCTG-TAATTTTGTAAATC-AGGG
* *
28722477 TATTTCTATAATTTTTTGAAAGTCATGGG
1 TATTTCTGTAATTTTGT-AAA-TCA-GGG
28722506 TATTTCTGTAATTTTGTAAATCAGGG
1 TATTTCTGTAATTTTGTAAATCAGGG
** **
28722532 TATTTCTGTAATTTTCCAAATTGGGGG
1 TATTTCTGTAATTTTGTAAA-TCAGGG
**
28722559 TATTTC-GATAATTTTACAAATCGAGGG
1 TATTTCTG-TAATTTTGTAAATC-AGGG
* ** **
28722586 TATTTCAGTAATTTTACAGGTCAAGGG
1 TATTTCTGTAATTTTGTAAATC-AGGG
*
28722613 TATCTCTGTAATTTTGTAAATCAGGGG
1 TATTTCTGTAATTTTGTAAATCA-GGG
28722640 TATTT-TGGTAATTTT
1 TATTTCT-GTAATTTT
28722655 ACTAATCGAG
Statistics
Matches: 145, Mismatches: 23, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
26 25 0.17
27 94 0.65
28 8 0.06
29 18 0.12
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (26 bp):
TATTTCTGTAATTTTGTAAATCAGGG
Found at i:28722570 original size:27 final size:27
Alignment explanation
Indices: 28722450--28722680 Score: 116
Period size: 27 Copynumber: 8.5 Consensus size: 27
28722440 AAACCAAGGC
** * * *
28722450 TATTTCGATAATTTTGTAAACCAATGG
1 TATTTCGATAATTTTACAAATCGAGGG
* **
28722477 TATTTCTATAATTTTTTGAAAGTC-ATGGG
1 TATTTCGATAA-TTTTACAAA-TCGA-GGG
**
28722506 TATTTCTG-TAATTTTGTAAATC-AGGG
1 TATTTC-GATAATTTTACAAATCGAGGG
* * *
28722532 TATTTCTG-TAATTTTCCAAATTGGGGG
1 TATTTC-GATAATTTTACAAATCGAGGG
28722559 TATTTCGATAATTTTACAAATCGAGGG
1 TATTTCGATAATTTTACAAATCGAGGG
** *
28722586 TATTTC-AGTAATTTTACAGGTCAAGGG
1 TATTTCGA-TAATTTTACAAATCGAGGG
* **
28722613 TATCTCTG-TAATTTTGTAAATC-AGGGG
1 TATTTC-GATAATTTTACAAATCGA-GGG
* * * *
28722640 TATTTTGGTAATTTTACTAATCGAGGA
1 TATTTCGATAATTTTACAAATCGAGGG
* *
28722667 TATTTTGGTAATTT
1 TATTTCGATAATTT
28722681 ACAGGTTAAG
Statistics
Matches: 163, Mismatches: 29, Indels: 24
0.75 0.13 0.11
Matches are distributed among these distances:
26 26 0.16
27 109 0.67
28 16 0.10
29 12 0.07
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (27 bp):
TATTTCGATAATTTTACAAATCGAGGG
Found at i:28722614 original size:54 final size:53
Alignment explanation
Indices: 28722444--28722656 Score: 173
Period size: 54 Copynumber: 3.9 Consensus size: 53
28722434 ATCTACAAAC
* * *
28722444 CAAGGCTATTTC-GATAATTTTGTAAACCAATGGTATTTCTA-TAATTTTTTGA-AAGT
1 CAAGGGTATTTCTG-TAATTTTGTAAATC-AGGGTATTTC-AGTAA--TTTT-ACAAGT
* * * *
28722500 CATGGGTATTTCTGTAATTTTGTAAATCAGGGTATTTCTGTAATTTTCCAAAT
1 CAAGGGTATTTCTGTAATTTTGTAAATCAGGGTATTTCAGTAATTTTACAAGT
*** ** *
28722553 TGGGGGTATTTC-GATAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAGGT
1 CAAGGGTATTTCTG-TAATTTTGTAAATC-AGGGTATTTCAGTAATTTTACAAGT
* **
28722607 CAAGGGTATCTCTGTAATTTTGTAAATCAGGGGTATTTTGGTAATTTTAC
1 CAAGGGTATTTCTGTAATTTTGTAAATCA-GGGTATTTCAGTAATTTTAC
28722657 TAATCGAGGA
Statistics
Matches: 126, Mismatches: 24, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
52 1 0.01
53 29 0.23
54 59 0.47
55 13 0.10
56 23 0.18
57 1 0.01
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.42
Consensus pattern (53 bp):
CAAGGGTATTTCTGTAATTTTGTAAATCAGGGTATTTCAGTAATTTTACAAGT
Found at i:28722721 original size:107 final size:107
Alignment explanation
Indices: 28722503--28722761 Score: 258
Period size: 107 Copynumber: 2.4 Consensus size: 107
28722493 TGAAAGTCAT
* * * *
28722503 GGGTATTTCTGTAATTTTGTAAATCA-GGGTATTTCT-GTAATTTTCCAAATTGGGGGTATTTCG
1 GGGTA-TTCTGTAATTTTGTAAATCAGGGGTATTT-TGGTAATTTTACAAATCGAGGATATTTCG
* * * **
28722566 ATAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAGGTCAA
64 ATAATTTTACAAATCAAGGGTATGTCAGTAATTTCACAAATCAA
* * *
28722610 GGGTATCTCTGTAATTTTGTAAATCAGGGGTATTTTGGTAATTTTACTAATCGAGGATATTTTGG
1 GGGTAT-TCTGTAATTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAATCGAGGATATTTCGA
** * *
28722675 TAA-TTTACAGGTTAAGGGTATGTCAGTAATTTCACAAATCAG
65 TAATTTTACAAATCAAGGGTATGTCAGTAATTTCACAAATCAA
* * *
28722717 GGGTATTTTGGTAATTCTGCT-AATC-GAGGATATTTTGGTAATTTT
1 GGGTATTCT-GTAATTTTG-TAAATCAG-GGGTATTTTGGTAATTTT
28722762 GTAAACCAAG
Statistics
Matches: 127, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
106 4 0.03
107 90 0.71
108 33 0.26
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.41
Consensus pattern (107 bp):
GGGTATTCTGTAATTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAATCGAGGATATTTCGAT
AATTTTACAAATCAAGGGTATGTCAGTAATTTCACAAATCAA
Found at i:28722723 original size:80 final size:79
Alignment explanation
Indices: 28722528--28722760 Score: 286
Period size: 80 Copynumber: 2.9 Consensus size: 79
28722518 TTTGTAAATC
* ** * * * * **
28722528 AGGGTATTTCTGTAATTTTCCAAATTGGGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCA
1 AGGGTATCTCTGTAA-TTTCCAAATCAGGGGTATTTTGGTAATTTTACTAATCGAGGATATTTTG
28722593 GTAATTTTACAGGTCA
65 GTAA-TTTACAGGTCA
**
28722609 AGGGTATCTCTGTAATTTTGTAAATCAGGGGTATTTTGGTAATTTTACTAATCGAGGATATTTTG
1 AGGGTATCTCTGTAA-TTTCCAAATCAGGGGTATTTTGGTAATTTTACTAATCGAGGATATTTTG
*
28722674 GTAATTTACAGGTTA
65 GTAATTTACAGGTCA
* * * *
28722689 AGGGTATGTCAGTAATTTCACAAATCAGGGGTATTTTGGTAATTCTGCTAATCGAGGATATTTTG
1 AGGGTATCTCTGTAATTTC-CAAATCAGGGGTATTTTGGTAATTTTACTAATCGAGGATATTTTG
28722754 GTAATTT
65 GTAATTT
28722761 TGTAAACCAA
Statistics
Matches: 133, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
79 3 0.02
80 72 0.54
81 58 0.44
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.40
Consensus pattern (79 bp):
AGGGTATCTCTGTAATTTCCAAATCAGGGGTATTTTGGTAATTTTACTAATCGAGGATATTTTGG
TAATTTACAGGTCA
Found at i:28722730 original size:27 final size:27
Alignment explanation
Indices: 28722503--28722786 Score: 152
Period size: 27 Copynumber: 10.6 Consensus size: 27
28722493 TGAAAGTCAT
**
28722503 GGGTATTTCT-GTAATTTTGTAAATCA-
1 GGGTATTT-TGGTAATTTTACAAATCAG
* **
28722529 GGGTATTTCT-GTAATTTTCCAAATTGG
1 GGGTATTT-TGGTAATTTTACAAATCAG
* *
28722556 GGGTATTTCGATAATTTTACAAATC-G
1 GGGTATTTTGGTAATTTTACAAATCAG
** ** *
28722582 AGGGTATTTCAGTAATTTTACAGGTCAA
1 -GGGTATTTTGGTAATTTTACAAATCAG
* **
28722610 GGGTATCTCT-GTAATTTTGTAAATCAG
1 GGGTAT-TTTGGTAATTTTACAAATCAG
*
28722637 GGGTATTTTGGTAATTTTACTAATC-G
1 GGGTATTTTGGTAATTTTACAAATCAG
* ** * *
28722663 AGGATATTTTGGTAA-TTTACAGGTTAA
1 -GGGTATTTTGGTAATTTTACAAATCAG
* ** *
28722690 GGGTATGTCAGTAATTTCACAAATCAG
1 GGGTATTTTGGTAATTTTACAAATCAG
* * *
28722717 GGGTATTTTGGTAATTCTGCTAATC-G
1 GGGTATTTTGGTAATTTTACAAATCAG
* ** * *
28722743 AGGATATTTTGGTAATTTTGTAAACCAA
1 -GGGTATTTTGGTAATTTTACAAATCAG
*
28722771 GGGTATTTTAGTAATT
1 GGGTATTTTGGTAATT
28722787 CTACCTTACA
Statistics
Matches: 193, Mismatches: 54, Indels: 21
0.72 0.20 0.08
Matches are distributed among these distances:
26 43 0.22
27 149 0.77
28 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAATCAG
Found at i:28725228 original size:27 final size:26
Alignment explanation
Indices: 28725188--28725299 Score: 125
Period size: 27 Copynumber: 4.2 Consensus size: 26
28725178 AGCATGGCTG
* * *
28725188 CCAGAACAGCTAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
28725214 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
* *
28725242 CCAGAATAGAAATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
28725269 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
28725296 CCAG
1 CCAG
28725300 TACACTTCCT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
26 6 0.08
27 50 0.68
28 17 0.23
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:28726746 original size:24 final size:24
Alignment explanation
Indices: 28726716--28726775 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
28726706 TCCCTTACTG
28726716 CTCCTAAATCCTATCCCTTATCAA
1 CTCCTAAATCCTATCCCTTATCAA
28726740 CTCCTAAATCCTATCCCTTATCAA
1 CTCCTAAATCCTATCCCTTATCAA
28726764 CTCCTAAATCCT
1 CTCCTAAATCCT
28726776 CTCCTGACAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.28, C:0.38, G:0.00, T:0.33
Consensus pattern (24 bp):
CTCCTAAATCCTATCCCTTATCAA
Found at i:28733044 original size:27 final size:26
Alignment explanation
Indices: 28733009--28733120 Score: 134
Period size: 27 Copynumber: 4.2 Consensus size: 26
28732999 AGCATGGCTG
* *
28733009 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
28733035 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
* *
28733063 CCAGAATAGAAATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
28733090 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
28733117 CCAG
1 CCAG
28733121 GACGCTTCCT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
26 6 0.08
27 51 0.69
28 17 0.23
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:28734568 original size:23 final size:24
Alignment explanation
Indices: 28734539--28734597 Score: 111
Period size: 23 Copynumber: 2.5 Consensus size: 24
28734529 CCCTTACCTG
28734539 CTCCTAAATCCTATCCCTTATC-A
1 CTCCTAAATCCTATCCCTTATCAA
28734562 CTCCTAAATCCTATCCCTTATCAA
1 CTCCTAAATCCTATCCCTTATCAA
28734586 CTCCTAAATCCT
1 CTCCTAAATCCT
28734598 CTCCTGATAG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 22 0.63
24 13 0.37
ACGTcount: A:0.27, C:0.39, G:0.00, T:0.34
Consensus pattern (24 bp):
CTCCTAAATCCTATCCCTTATCAA
Found at i:28739041 original size:25 final size:25
Alignment explanation
Indices: 28739012--28739063 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
28739002 TTTAATTGAG
28739012 TTAATTTTTTTGTATATTTTGTCCT
1 TTAATTTTTTTGTATATTTTGTCCT
28739037 TTAATTTTTTTGTATATTTTGTCCT
1 TTAATTTTTTTGTATATTTTGTCCT
28739062 TT
1 TT
28739064 TTTGGCTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (25 bp):
TTAATTTTTTTGTATATTTTGTCCT
Found at i:28741796 original size:29 final size:29
Alignment explanation
Indices: 28741757--28741830 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
28741747 GGTTGAGAGA
* *
28741757 ATGGCACTAAGTGTGCGGGCTTGAAA-TGC
1 ATGGCACTAAGTGTGCGAG-TTGAAAGTAC
*
28741786 ATGGCACTAAGTGTGCGAGTTTAAAGTAC
1 ATGGCACTAAGTGTGCGAGTTGAAAGTAC
28741815 ATGGCACTAAGTGTGC
1 ATGGCACTAAGTGTGC
28741831 ATGGTTGATT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
ATGGCACTAAGTGTGCGAGTTGAAAGTAC
Found at i:28746277 original size:42 final size:43
Alignment explanation
Indices: 28746183--28746336 Score: 111
Period size: 43 Copynumber: 3.6 Consensus size: 43
28746173 CAACTACAAC
* * * *
28746183 GCCGACGTCCCGGAC-GTGGTCTTACATGTAATTCAATATCGAT
1 GCCGATGTCCCAGACAG-GGTCTTACAAGTAAATCAATATCGAT
** *
28746226 GCCTCTGTCCTAGACAGGGTCTTACAAG-AAATCAGATA-CGAT
1 GCCGATGTCCCAGACAGGGTCTTACAAGTAAATCA-ATATCGAT
* * * * *
28746268 GCCGATGTCCCAGACATGGTCTTATATGTAAATCTCA-ATCGAG
1 GCCGATGTCCCAGACAGGGTCTTACAAGTAAATC-AATATCGAT
* *
28746311 GCCTGA-GTCCTAGACACGGTCTTACA
1 GCC-GATGTCCCAGACAGGGTCTTACA
28746337 CTATATCTCA
Statistics
Matches: 87, Mismatches: 18, Indels: 12
0.74 0.15 0.10
Matches are distributed among these distances:
42 32 0.37
43 52 0.60
44 3 0.03
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.26
Consensus pattern (43 bp):
GCCGATGTCCCAGACAGGGTCTTACAAGTAAATCAATATCGAT
Found at i:28752209 original size:40 final size:40
Alignment explanation
Indices: 28752082--28752211 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
28752072 ATGCTGGAAA
* *
28752082 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * **
28752122 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
28752162 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
28752202 TTATATCCGG
1 TTATATCCGG
28752212 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.05
40 72 0.95
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:28760115 original size:40 final size:40
Alignment explanation
Indices: 28760049--28760199 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
28760039 AAATTGAATG
* * *
28760049 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
28760088 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
28760128 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* *
28760168 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
28760200 ACGTGGTTAT
Statistics
Matches: 91, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
39 16 0.18
40 73 0.80
41 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:28760213 original size:40 final size:40
Alignment explanation
Indices: 28760086--28760215 Score: 163
Period size: 40 Copynumber: 3.2 Consensus size: 40
28760076 ATGCTGGAAA
* * *
28760086 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * * **
28760126 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
*
28760166 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
28760206 TTATATCCGG
1 TTATATCCGG
28760216 TTTATTCCGA
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 73 0.99
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:28762028 original size:39 final size:40
Alignment explanation
Indices: 28761970--28762070 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 40
28761960 AAATTGAATG
* *
28761970 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * * *
28762009 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
28762049 ATATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
28762071 GCATTCGTGC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 29 0.55
40 24 0.45
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:28762063 original size:40 final size:40
Alignment explanation
Indices: 28761970--28762152 Score: 181
Period size: 40 Copynumber: 4.6 Consensus size: 40
28761960 AAATTGAATG
* * * * *
28761970 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
28762009 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
28762049 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
28762089 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* * *
28762129 ATATCCGGGTTAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
28762153 CTTGGTGCGG
Statistics
Matches: 121, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
39 32 0.26
40 87 0.72
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:28770229 original size:40 final size:40
Alignment explanation
Indices: 28770118--28770230 Score: 163
Period size: 40 Copynumber: 2.8 Consensus size: 40
28770108 GCTGAAAATT
* * *
28770118 AATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCTA
1 AATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAGCTA
* * * *
28770158 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTA
1 AATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAGCTA
28770198 AATCCGGGCTAAGACCCGAAGGCATTTGTGCAA
1 AATCCGGGCTAAGACCCGAAGGCATTTGTGCAA
28770231 ATCGTGATAT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 64 1.00
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.22
Consensus pattern (40 bp):
AATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAGCTA
Found at i:28770243 original size:40 final size:38
Alignment explanation
Indices: 28770074--28770260 Score: 155
Period size: 40 Copynumber: 4.8 Consensus size: 38
28770064 TGAGAAATTG
* * *
28770074 AATG-ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGAA
1 AATGTATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCA
* * *
28770114 AAT-TA-ATCCGGGTTAAGACCCGAAGGCAATTGTGCT
1 AATGTATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
* *
28770150 AGTAGCTATATCCGGGCTAAGACCCGAAGGCATTCGTGCA
1 AAT-G-TATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
* *
28770190 AGTTGTTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCA
1 A-ATG-TATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
* * *
28770230 AATCGTGATATCCGGGTTAAGTCCCGTAGGC
1 AAT-GT-ATATCCGGGCTAAGACCCGAAGGC
28770261 CTTGGTGCGG
Statistics
Matches: 119, Mismatches: 20, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
36 4 0.03
37 2 0.02
38 2 0.02
39 23 0.19
40 87 0.73
41 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (38 bp):
AATGTATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
Found at i:28774016 original size:26 final size:24
Alignment explanation
Indices: 28773986--28774055 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 24
28773976 GCCGTAATCG
* *
28773986 GTAAGCTCCTCTTGAGTTGATGAACA
1 GTAAGCTCCTATTGAGCTGA--AACA
28774012 GTAAGCT-CTATTGAGCTGAAACA
1 GTAAGCTCCTATTGAGCTGAAACA
* *
28774035 ATAAGCTCC-AATGAGCTGAAA
1 GTAAGCTCCTATTGAGCTGAAA
28774056 ATAGCTCATA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
23 21 0.54
24 1 0.03
25 10 0.26
26 7 0.18
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (24 bp):
GTAAGCTCCTATTGAGCTGAAACA
Found at i:28778776 original size:2 final size:2
Alignment explanation
Indices: 28778769--28778794 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28778759 TTGAGACTAG
28778769 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
28778795 CATGTCATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28780824 original size:30 final size:30
Alignment explanation
Indices: 28780790--28780850 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
28780780 TCCTTAACTC
28780790 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
28780820 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
28780850 A
1 A
28780851 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:28785239 original size:30 final size:30
Alignment explanation
Indices: 28785205--28785265 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
28785195 TCCTTAACTC
28785205 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
28785235 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
28785265 A
1 A
28785266 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:28787788 original size:27 final size:27
Alignment explanation
Indices: 28787758--28787827 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
28787748 CGATTTACAA
* *
28787758 AATTATTGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCATATAGGGTAG
* *
28787785 AATTACTGAAATACCTATGTAGGGTAG
1 AATTACTGAAATACCCATATAGGGTAG
* *
28787812 AATTACCGAGATACCC
1 AATTACTGAAATACCC
28787828 TTGTGGGGTA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (27 bp):
AATTACTGAAATACCCATATAGGGTAG
Found at i:28787836 original size:27 final size:27
Alignment explanation
Indices: 28787777--28787845 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
28787767 AATACCCCTA
*
28787777 TAGGGTAGAATTACTGAAATACCTATG
1 TAGGGTAGAATTACCGAAATACCTATG
*
28787804 TAGGGTAGAATTACCGAGATACCCT-TG
1 TAGGGTAGAATTACCGAAATA-CCTATG
* *
28787831 TGGGGTAAAATTACC
1 TAGGGTAGAATTACC
28787846 ATTTTTCCCT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 34 0.92
28 3 0.08
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (27 bp):
TAGGGTAGAATTACCGAAATACCTATG
Found at i:28788476 original size:26 final size:26
Alignment explanation
Indices: 28788399--28788479 Score: 108
Period size: 27 Copynumber: 3.0 Consensus size: 26
28788389 ATTCTGTTAA
* *
28788399 GTGGATTTGCCACATTATCTGTTTCTG
1 GTGGCTTTGCCACAATATCTG-TTCTG
* *
28788426 GTGGCTATGCCACAAATATTTGTTCTG
1 GTGGCTTTGCCAC-AATATCTGTTCTG
28788453 GTGGCTTTGCCACAATATCTGTTCTG
1 GTGGCTTTGCCACAATATCTGTTCTG
28788479 G
1 G
28788480 CAACCATGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
26 13 0.28
27 28 0.60
28 6 0.13
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.40
Consensus pattern (26 bp):
GTGGCTTTGCCACAATATCTGTTCTG
Found at i:28788627 original size:6 final size:6
Alignment explanation
Indices: 28788596--28788754 Score: 94
Period size: 6 Copynumber: 25.7 Consensus size: 6
28788586 TTGCATTCAC
* * * *
28788596 ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG -TCACCTA
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG AT--TCTG
*
28788646 ATTCTG ATTCTG ATTCTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG
* * * * * *
28788695 -TCACCTA ATTTTG ATTCTG ATTCTG ATTTTG ATTCTG -TCACCTG ATTTTG
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG
28788745 ATTCTG ATTC
1 ATTCTG ATTC
28788755 CCATTTTGAT
Statistics
Matches: 116, Mismatches: 22, Indels: 30
0.69 0.13 0.18
Matches are distributed among these distances:
5 7 0.06
6 91 0.78
7 13 0.11
8 5 0.04
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:28788627 original size:25 final size:25
Alignment explanation
Indices: 28788599--28788719 Score: 125
Period size: 25 Copynumber: 4.6 Consensus size: 25
28788589 CATTCACATT
*
28788599 CTGATTTTGATTCTGTTACCTGATA
1 CTGATTCTGATTCTGTTACCTGATA
* *
28788624 CTGATTCTGATTCTGTCACCTAATTCTGATT
1 CTGATTCTGATTCTGT----T-A-CCTGATA
28788655 CTGATTCTGATTCTGTTACCTGATA
1 CTGATTCTGATTCTGTTACCTGATA
* * *
28788680 CTGATTCTGATTCTGTCACCTAATT
1 CTGATTCTGATTCTGTTACCTGATA
*
28788705 TTGATTCTGATTCTG
1 CTGATTCTGATTCTG
28788720 ATTTTGATTC
Statistics
Matches: 81, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
25 56 0.69
26 1 0.01
27 1 0.01
29 1 0.01
30 1 0.01
31 21 0.26
ACGTcount: A:0.19, C:0.20, G:0.15, T:0.46
Consensus pattern (25 bp):
CTGATTCTGATTCTGTTACCTGATA
Found at i:28788634 original size:31 final size:31
Alignment explanation
Indices: 28788596--28788754 Score: 138
Period size: 31 Copynumber: 5.3 Consensus size: 31
28788586 TTGCATTCAC
*
28788596 ATTCTGATTTTGATTCTGTTACCTGA---T-
1 ATTCTGATTCTGATTCTGTTACCTGATTCTG
* *
28788623 A--CTGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTCTGATTCTGTTACCTGATTCTG
*
28788652 ATTCTGATTCTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGATTCTGTTACCTGATTCTG
* * *
28788683 ATTCTGATTCTG-TCACCTAATT--TTGATTCTG
1 ATTCTGATTCTGAT--TCT-GTTACCTGATTCTG
* * *
28788714 ATTCTGATTTTGATTCTGTCACCTGATTTTG
1 ATTCTGATTCTGATTCTGTTACCTGATTCTG
28788745 ATTCTGATTC
1 ATTCTGATTC
28788755 CCATTTTGAT
Statistics
Matches: 103, Mismatches: 17, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
25 20 0.19
27 1 0.01
28 1 0.01
29 2 0.02
30 3 0.03
31 71 0.69
32 3 0.03
33 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.48
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTTACCTGATTCTG
Found at i:28788682 original size:56 final size:56
Alignment explanation
Indices: 28788596--28788722 Score: 236
Period size: 56 Copynumber: 2.3 Consensus size: 56
28788586 TTGCATTCAC
*
28788596 ATTCTGATTTTGATTCTGTTACCTGATACTGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTCACCTAATTCTG
*
28788652 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTCACCTAATTTTG
1 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTCACCTAATTCTG
28788708 ATTCTGATTCTGATT
1 ATTCTGATTCTGATT
28788723 TTGATTCTGT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 69 1.00
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (56 bp):
ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTCACCTAATTCTG
Found at i:28788711 original size:19 final size:19
Alignment explanation
Indices: 28788680--28788750 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
28788670 TTACCTGATA
*
28788680 CTGATTCTGATTCTGTCAC
1 CTGATTTTGATTCTGTCAC
* *
28788699 CTAATTTTGATTCTG--ATT
1 CTGATTTTGATTCTGTCA-C
28788717 CTGATTTTGATTCTGTCAC
1 CTGATTTTGATTCTGTCAC
28788736 CTGATTTTGATTCTG
1 CTGATTTTGATTCTG
28788751 ATTCCCATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
17 1 0.02
18 14 0.32
19 28 0.64
20 1 0.02
ACGTcount: A:0.17, C:0.18, G:0.15, T:0.49
Consensus pattern (19 bp):
CTGATTTTGATTCTGTCAC
Found at i:28788753 original size:37 final size:37
Alignment explanation
Indices: 28788674--28788767 Score: 143
Period size: 37 Copynumber: 2.5 Consensus size: 37
28788664 ATTCTGTTAC
* *
28788674 CTGATACTGATTCTGATTCTGTCACCTAATTTTGATT
1 CTGATTCTGATTTTGATTCTGTCACCTAATTTTGATT
*
28788711 CTGATTCTGATTTTGATTCTGTCACCTGATTTTGATT
1 CTGATTCTGATTTTGATTCTGTCACCTAATTTTGATT
**
28788748 CTGATTCCCATTTTGATTCT
1 CTGATTCTGATTTTGATTCT
28788768 AGTTTTGATA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.18, C:0.19, G:0.14, T:0.49
Consensus pattern (37 bp):
CTGATTCTGATTTTGATTCTGTCACCTAATTTTGATT
Found at i:28791676 original size:36 final size:36
Alignment explanation
Indices: 28791636--28791736 Score: 118
Period size: 36 Copynumber: 2.9 Consensus size: 36
28791626 GCTAAATTGG
* *
28791636 GCACACCACCACCACCAGCAACATTCCTTTTGGGGC
1 GCACACCACCACCACCAGCAACATTCCTTTCGAGGC
* * *
28791672 GCACACCACCACCGCTAGCAACATTCCTTTCGAGGT
1 GCACACCACCACCACCAGCAACATTCCTTTCGAGGC
* *
28791708 GCACACCACGATCA--A-CAACATTCCTTTCG
1 GCACACCACCACCACCAGCAACATTCCTTTCG
28791737 GGACTTCGAG
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
33 14 0.25
34 1 0.02
36 42 0.74
ACGTcount: A:0.27, C:0.40, G:0.15, T:0.19
Consensus pattern (36 bp):
GCACACCACCACCACCAGCAACATTCCTTTCGAGGC
Found at i:28793412 original size:40 final size:40
Alignment explanation
Indices: 28793367--28793465 Score: 141
Period size: 38 Copynumber: 2.5 Consensus size: 40
28793357 GACAAACATC
*
28793367 AATGATG-TCAAAATTAAGACACATAATAAAAACACATATT
1 AATGATGTTC-AAACTAAGACACATAATAAAAACACATATT
* *
28793407 CATGATGTTCAAACTAAG--ACATAATTAAAACACATATT
1 AATGATGTTCAAACTAAGACACATAATAAAAACACATATT
28793445 AATGATGTTCAAACTAAGACA
1 AATGATGTTCAAACTAAGACA
28793466 TAATTAAAGA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
38 36 0.69
40 14 0.27
41 2 0.04
ACGTcount: A:0.51, C:0.14, G:0.09, T:0.26
Consensus pattern (40 bp):
AATGATGTTCAAACTAAGACACATAATAAAAACACATATT
Found at i:28793438 original size:38 final size:38
Alignment explanation
Indices: 28793387--28793479 Score: 159
Period size: 38 Copynumber: 2.4 Consensus size: 38
28793377 AAATTAAGAC
* *
28793387 ACATAATAAAAACACATATTCATGATGTTCAAACTAAG
1 ACATAATTAAAACACATATTAATGATGTTCAAACTAAG
28793425 ACATAATTAAAACACATATTAATGATGTTCAAACTAAG
1 ACATAATTAAAACACATATTAATGATGTTCAAACTAAG
28793463 ACATAATTAAAGACACA
1 ACATAATTAAA-ACACA
28793480 AACTAAAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
38 47 0.90
39 5 0.10
ACGTcount: A:0.52, C:0.15, G:0.08, T:0.26
Consensus pattern (38 bp):
ACATAATTAAAACACATATTAATGATGTTCAAACTAAG
Found at i:28794164 original size:20 final size:20
Alignment explanation
Indices: 28794139--28794177 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28794129 CAGCTTATCT
*
28794139 AGCTCGCTTCTAACTCATTG
1 AGCTCGATTCTAACTCATTG
*
28794159 AGCTCGATTCTATCTCATT
1 AGCTCGATTCTAACTCATT
28794178 TTAATTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.28, G:0.13, T:0.38
Consensus pattern (20 bp):
AGCTCGATTCTAACTCATTG
Found at i:28794313 original size:46 final size:46
Alignment explanation
Indices: 28794261--28794359 Score: 114
Period size: 46 Copynumber: 2.2 Consensus size: 46
28794251 GTCTTAAATA
* *
28794261 TGTCTTAAGTCT-ATTAA-TGCATCT-TAATTAGTATAGCATTTTAATG
1 TGTCTTAAGTCTAATTAATTG--T-TGTAATAAGTACAGCATTTTAATG
* *
28794307 TGTCTTAAGTTTAATTAATTGTTGTAATAAGTACAGCTTTTTAATG
1 TGTCTTAAGTCTAATTAATTGTTGTAATAAGTACAGCATTTTAATG
28794353 TGTCTTA
1 TGTCTTA
28794360 GATCAAGATA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
45 1 0.02
46 38 0.83
47 5 0.11
48 2 0.04
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.47
Consensus pattern (46 bp):
TGTCTTAAGTCTAATTAATTGTTGTAATAAGTACAGCATTTTAATG
Found at i:28797595 original size:47 final size:47
Alignment explanation
Indices: 28797537--28797974 Score: 687
Period size: 47 Copynumber: 9.3 Consensus size: 47
28797527 GTATGAGATA
* *
28797537 TATATATGTGATAAGGCCGAATGGCCAATTTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG
* *
28797584 CATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG
* * *
28797631 CATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATG
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG
* *
28797678 TATATATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG
*
28797725 TATATATGTGACAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG
* * *
28797772 CATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG
* *
28797819 TATATATGTGACAAGGCCTAATGGCCCATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG
* *
28797866 CATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG
* * *
28797913 TATATATGTGATAAGGCCGAGTGGCCAATGTGATGGATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG
*
28797960 TATAAATGTGATAAG
1 TATATATGTGATAAG
28797975 TCCCGAAGGG
Statistics
Matches: 366, Mismatches: 25, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 366 1.00
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.28
Consensus pattern (47 bp):
TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTG
Found at i:28798151 original size:37 final size:37
Alignment explanation
Indices: 28798092--28798174 Score: 130
Period size: 37 Copynumber: 2.2 Consensus size: 37
28798082 CCGAGCTCTA
* *
28798092 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACCACGGGTGGAGATTATGTCCGGGT
*
28798129 AAGACCCGATGACCACGGGTGGAGATTTTGTCCGGGT
1 AAGACCCGATGACCACGGGTGGAGATTATGTCCGGGT
*
28798166 AAGCCCCGA
1 AAGACCCGA
28798175 ACTAAAGGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.24, C:0.23, G:0.33, T:0.20
Consensus pattern (37 bp):
AAGACCCGATGACCACGGGTGGAGATTATGTCCGGGT
Found at i:28800146 original size:40 final size:40
Alignment explanation
Indices: 28800087--28800408 Score: 504
Period size: 40 Copynumber: 8.1 Consensus size: 40
28800077 GAGAATTGAG
28800087 AGTGATATATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
*
28800127 AGTGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
*
28800167 AGTGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
*
28800207 AGTGATATATCCGGACTAAGTTCCAAAGAGCATTCGTGCT
1 AGTGATATATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
* *
28800247 AGTGATATAACCGGACTAAGTTCCGAAGAGCATTCATGCT
1 AGTGATATATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
* *
28800287 AGTGATATAACCGGACTAACTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
28800327 AGTGATATATCCAGG-CTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCC-GGACTAAGTTCCGAAGAGCATTCGTGCT
* * * **
28800367 AGTGATATATTCGGGCGAA-ACCTCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGACTAAGTTC-CGAAGAGCATTCGTGCT
28800407 AG
1 AG
28800409 AATTATGAGG
Statistics
Matches: 265, Mismatches: 14, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
39 3 0.01
40 260 0.98
41 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.26
Consensus pattern (40 bp):
AGTGATATATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
Found at i:28800514 original size:28 final size:28
Alignment explanation
Indices: 28800418--28800517 Score: 94
Period size: 28 Copynumber: 3.5 Consensus size: 28
28800408 GAATTATGAG
* * * *
28800418 GCACTGTGTGTGCAAGTTCTTCAACCGA
1 GCACTATGTGTGCGAGTTCTTTAATCGA
* ** * *
28800446 GCACTATGTGTGCCGA-ATCAGTAGTTGAA
1 GCACTATGTGTG-CGAGTTCTTTAATCG-A
28800475 GCACTATGTGTGCGAGTTCTTTAATCGA
1 GCACTATGTGTGCGAGTTCTTTAATCGA
28800503 GCACTATGTGTGCGA
1 GCACTATGTGTGCGA
28800518 AATCAGTCAG
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
28 34 0.62
29 21 0.38
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTATGTGTGCGAGTTCTTTAATCGA
Found at i:28808713 original size:46 final size:48
Alignment explanation
Indices: 28808662--28808792 Score: 157
Period size: 46 Copynumber: 2.8 Consensus size: 48
28808652 ATGGTTGAGC
28808662 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T-G
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAACTAG
* * * *
28808709 -TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATGTAACTAGG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAACTA-G
28808754 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 -ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28808793 GCGGGTTACA
Statistics
Matches: 69, Mismatches: 7, Indels: 13
0.78 0.08 0.15
Matches are distributed among these distances:
42 2 0.03
43 4 0.06
45 3 0.04
46 29 0.42
47 29 0.42
48 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (48 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAACTAG
Found at i:28812915 original size:47 final size:47
Alignment explanation
Indices: 28812857--28813247 Score: 640
Period size: 47 Copynumber: 8.3 Consensus size: 47
28812847 GTATGAGATA
* *
28812857 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
28812904 CATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
28812951 CATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
28812998 TATATATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
28813045 TATATATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
28813092 TATATATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* * *
28813139 CATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* * *
28813186 TATATATGTGATAAGGCCGAGTGG-CGAATGTGATGGATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCG-ATGTGATGAATGTGAAAGTG
*
28813233 TATAAATGTGATAAG
1 TATATATGTGATAAG
28813248 TCCCGAAGGC
Statistics
Matches: 329, Mismatches: 14, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
46 1 0.00
47 328 1.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
Found at i:28813423 original size:37 final size:37
Alignment explanation
Indices: 28813364--28813446 Score: 130
Period size: 37 Copynumber: 2.2 Consensus size: 37
28813354 CCGAGCTCTA
* *
28813364 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACCACGGGTGGAGATTATGTCCGGGT
*
28813401 AAGACCCGATGACCACGGGTGGAGATTTTGTCCGGGT
1 AAGACCCGATGACCACGGGTGGAGATTATGTCCGGGT
*
28813438 AAGCCCCGA
1 AAGACCCGA
28813447 ACTAAAGGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.24, C:0.23, G:0.33, T:0.20
Consensus pattern (37 bp):
AAGACCCGATGACCACGGGTGGAGATTATGTCCGGGT
Found at i:28823592 original size:40 final size:40
Alignment explanation
Indices: 28823547--28823713 Score: 158
Period size: 40 Copynumber: 4.2 Consensus size: 40
28823537 CGGAATATAA
28823547 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
28823587 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
28823627 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
*** * * * * *
28823667 CC-GATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
28823706 CCGGATAT
1 CCGGATAT
28823714 CATTCAATTT
Statistics
Matches: 102, Mismatches: 23, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
39 30 0.29
40 72 0.71
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:28831579 original size:40 final size:40
Alignment explanation
Indices: 28831534--28831701 Score: 167
Period size: 40 Copynumber: 4.2 Consensus size: 40
28831524 CGGAATATAA
28831534 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
28831574 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
28831614 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
*** * * * * *
28831654 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
28831694 CCGGATAT
1 CCGGATAT
28831702 CATTCAATTT
Statistics
Matches: 104, Mismatches: 23, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
39 1 0.01
40 103 0.99
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:28831684 original size:80 final size:80
Alignment explanation
Indices: 28831550--28831699 Score: 196
Period size: 80 Copynumber: 1.9 Consensus size: 80
28831540 ATAACCACGT
* *
28831550 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
28831615 CGGATGTAGCCACTA
66 CGGATGTAGCCACTA
* * ** * *
28831630 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGGCTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGGCTTAG
28831693 CCCGGAT
64 CCCGGAT
28831700 ATCATTCAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
79 3 0.05
80 57 0.95
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.26
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
CGGATGTAGCCACTA
Found at i:28835077 original size:30 final size:29
Alignment explanation
Indices: 28835041--28835106 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
28835031 TTGTAACCAT
**
28835041 TCTTTTTCTCTCTCAAACTCTTTTTCATTC
1 TCTTTTTCAATCTC-AACTCTTTTTCATTC
** *
28835071 TCTTTTTCAATCTCATTTCTTTTTCATTT
1 TCTTTTTCAATCTCAACTCTTTTTCATTC
28835100 TCTTTTT
1 TCTTTTT
28835107 GTTTTTCAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 19 0.61
30 12 0.39
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (29 bp):
TCTTTTTCAATCTCAACTCTTTTTCATTC
Found at i:28835197 original size:15 final size:14
Alignment explanation
Indices: 28835175--28835233 Score: 75
Period size: 14 Copynumber: 4.2 Consensus size: 14
28835165 CTTTTGCCTC
28835175 TCTTTTCTTTTTTT
1 TCTTTTCTTTTTTT
*
28835189 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTTT
*
28835204 TCTTTT-TCTTTTT
1 TCTTTTCTTTTTTT
*
28835217 TCTTTTCTTTGTTT
1 TCTTTTCTTTTTTT
28835231 TCT
1 TCT
28835234 CGTTACAAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
13 11 0.29
14 14 0.37
15 13 0.34
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (14 bp):
TCTTTTCTTTTTTT
Found at i:28835231 original size:16 final size:16
Alignment explanation
Indices: 28835177--28835220 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 16
28835167 TTTGCCTCTC
*
28835177 TTTTCTTTTTT-TTCG
1 TTTTCTTTTTTCTTCT
28835192 TTTTC-TTTTTCTTCT
1 TTTTCTTTTTTCTTCT
28835207 TTTTCTTTTTTCTT
1 TTTTCTTTTTTCTT
28835221 TTCTTTGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 5 0.19
15 13 0.50
16 8 0.31
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (16 bp):
TTTTCTTTTTTCTTCT
Found at i:28840223 original size:29 final size:29
Alignment explanation
Indices: 28840190--28840320 Score: 163
Period size: 29 Copynumber: 4.5 Consensus size: 29
28840180 TGACGAGATC
*
28840190 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
* *
28840219 GGCACTAAGTGTGCGTGCTGGAAATATAA
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
*
28840248 GGCACTAAGTGTGCATGCTGGAAAAATAT
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
* * ** *
28840277 GACACTATGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
**
28840306 GGCACTGGGTGTGCG
1 GGCACTAAGTGTGCG
28840321 AGCTCGGAGG
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 90 1.00
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (29 bp):
GGCACTAAGTGTGCGTGCTGGAAAAATAT
Found at i:28846609 original size:29 final size:29
Alignment explanation
Indices: 28846577--28846649 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
28846567 TGAAAAGTAT
* * *
28846577 GGCACTAAGTGTGCGAATTTAAATTATAC
1 GGCACTAAGTGTGCGAACTTAAATCACAC
* * *
28846606 GGCACTATGTGTGCGAGCTTAAATCACAT
1 GGCACTAAGTGTGCGAACTTAAATCACAC
28846635 GGCACTAAGTGTGCG
1 GGCACTAAGTGTGCG
28846650 TGATCGATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (29 bp):
GGCACTAAGTGTGCGAACTTAAATCACAC
Found at i:28849818 original size:32 final size:32
Alignment explanation
Indices: 28849777--28849838 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
28849767 TCCAAGAGAG
* *
28849777 TATAACATCAGTGCAAGTTTTAATGTATCTGA
1 TATAACATCAATGCAAGTTTTAACGTATCTGA
28849809 TATAACATCAATGCAAGTTTTAACGTATCT
1 TATAACATCAATGCAAGTTTTAACGTATCT
28849839 AATTTATCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (32 bp):
TATAACATCAATGCAAGTTTTAACGTATCTGA
Found at i:28850250 original size:38 final size:39
Alignment explanation
Indices: 28850208--28850283 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
28850198 TTTAGTTTGT
* *
28850208 GTCTTTAATTATTTCCTAG-TTGAACATCATTAATATGA
1 GTCTTTAATTATGTCATAGTTTGAACATCATTAATATGA
28850246 GTCTTTAATTATGTCATAGTTTGAACATCATTAATATG
1 GTCTTTAATTATGTCATAGTTTGAACATCATTAATATG
28850284 TGTTCTACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 17 0.49
39 18 0.51
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.45
Consensus pattern (39 bp):
GTCTTTAATTATGTCATAGTTTGAACATCATTAATATGA
Found at i:28850649 original size:28 final size:29
Alignment explanation
Indices: 28850602--28850680 Score: 92
Period size: 28 Copynumber: 2.8 Consensus size: 29
28850592 TACATGCATG
* *
28850602 CATATGGCCCACTAGG-CCCAATCT-TATT
1 CATATGGCCCA-TCGGCCCCAATCTACATT
28850630 CATATGGCCCATCGGCCCCAAT-TACATT
1 CATATGGCCCATCGGCCCCAATCTACATT
* *
28850658 CATATGGTCCATCGGCCCTAATC
1 CATATGGCCCATCGGCCCCAATC
28850681 ACGTCCATAG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
27 4 0.09
28 40 0.91
ACGTcount: A:0.24, C:0.34, G:0.15, T:0.27
Consensus pattern (29 bp):
CATATGGCCCATCGGCCCCAATCTACATT
Found at i:28850689 original size:28 final size:28
Alignment explanation
Indices: 28850602--28850689 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 28
28850592 TACATGCATG
* ** *
28850602 CATATGGCCCACTAGG-CCCAATCTTATT
1 CATATGGCCCA-TCGGCCCCAATCACATC
* *
28850630 CATATGGCCCATCGGCCCCAATTACATT
1 CATATGGCCCATCGGCCCCAATCACATC
* * *
28850658 CATATGGTCCATCGGCCCTAATCACGTC
1 CATATGGCCCATCGGCCCCAATCACATC
28850686 CATA
1 CATA
28850690 GTCATGCAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
27 3 0.06
28 47 0.94
ACGTcount: A:0.25, C:0.34, G:0.15, T:0.26
Consensus pattern (28 bp):
CATATGGCCCATCGGCCCCAATCACATC
Found at i:28874306 original size:28 final size:30
Alignment explanation
Indices: 28874249--28874306 Score: 68
Period size: 28 Copynumber: 2.0 Consensus size: 30
28874239 TTATTTTCAC
* *
28874249 TTTTATCTTTATTTATCTTCTTAAAGTATT
1 TTTTATCTTTACTTATCTTCTTAAACTATT
28874279 TTTTAT-TTTACTT-TCTT-TTAATACTATT
1 TTTTATCTTTACTTATCTTCTTAA-ACTATT
28874307 CATTTTTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
27 4 0.16
28 9 0.36
29 6 0.24
30 6 0.24
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (30 bp):
TTTTATCTTTACTTATCTTCTTAAACTATT
Found at i:28877974 original size:39 final size:39
Alignment explanation
Indices: 28877843--28878033 Score: 163
Period size: 40 Copynumber: 4.8 Consensus size: 39
28877833 GAATATAACG
* ** **
28877843 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGG-TTATAGCG
1 ACTCGCAC-AATGCCTTCGGGACTTAGCCCGGATT-TAGTA
* * *
28877883 ACTCGCACGAATGCCTTCGGGACTTAACTCGGGTTTAGTA
1 ACTCGCAC-AATGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
28877923 ACTTGCACAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * * *
28877961 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCAC-AATGCCTTCGGGA-CTTAGCCCGGATTTAGTA
* *
28878001 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAATGCCTTCGGGACTTAGCCCGGA
28878034 CATCATTCGA
Statistics
Matches: 122, Mismatches: 23, Indels: 12
0.78 0.15 0.08
Matches are distributed among these distances:
38 23 0.19
39 21 0.17
40 68 0.56
41 10 0.08
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (39 bp):
ACTCGCACAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:28877977 original size:78 final size:80
Alignment explanation
Indices: 28877883--28878033 Score: 202
Period size: 78 Copynumber: 1.9 Consensus size: 80
28877873 GGTTATAGCG
* * * *
28877883 ACTCGCACGAATGCCTTCGGGA-CTTAACT-CGGGTTTAGTAACTT-GCACAATGCCTTCGGG-C
1 ACTCGCACGAATGCCTTC-GGATCCT-ACTCCGGATATAGTAACTTAGCACAAAGCCTTCGGGAC
28877944 TTAGCCCGGATTTATTA
64 TTAGCCCGGATTTATTA
* *
28877961 ACTCGCACGAATGCCTTCGGATCCTAGTCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTT
1 ACTCGCACGAATGCCTTCGGATCCTACTCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTT
28878026 AGCCCGGA
66 AGCCCGGA
28878034 CATCATTCGA
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
77 5 0.08
78 32 0.51
79 15 0.24
80 11 0.17
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (80 bp):
ACTCGCACGAATGCCTTCGGATCCTACTCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTT
AGCCCGGATTTATTA
Found at i:28887545 original size:31 final size:31
Alignment explanation
Indices: 28887490--28887569 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 31
28887480 CTCAACATAT
** *
28887490 ACTGGGCTAAAGCC-TTTCATAATTCATAAC
1 ACTGGGCCGAAGCCTTTTCAAAATTCATAAC
* *
28887520 ACTGGGTCGAAGCCTTTTCAAAATTCATATC
1 ACTGGGCCGAAGCCTTTTCAAAATTCATAAC
28887551 ACTGGGCCGAAGCCTTTTC
1 ACTGGGCCGAAGCCTTTTC
28887570 TGTAAGCGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 11 0.26
31 32 0.74
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCAAAATTCATAAC
Found at i:28887820 original size:25 final size:26
Alignment explanation
Indices: 28887786--28887857 Score: 112
Period size: 25 Copynumber: 2.8 Consensus size: 26
28887776 CTCTTTTAAT
28887786 AACTGGGGCAAAGCCCTTTTTGA-TA
1 AACTGGGGCAAAGCCCTTTTTGAGTA
*
28887811 AACTGGGGCAAAGCCC-TTTTCAGTA
1 AACTGGGGCAAAGCCCTTTTTGAGTA
*
28887836 AACTGGAGCAAAGCCCTTTTTG
1 AACTGGGGCAAAGCCCTTTTTG
28887858 CCCTTCCTCG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
24 5 0.12
25 33 0.79
26 4 0.10
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (26 bp):
AACTGGGGCAAAGCCCTTTTTGAGTA
Found at i:28887948 original size:21 final size:21
Alignment explanation
Indices: 28887889--28887948 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
28887879 ACCCAACCCA
*
28887889 TGCATATAATGAGTATATCATG
1 TGCATATCAT-AGTATATCATG
* **
28887911 TGCATCTCATAACATATCATG
1 TGCATATCATAGTATATCATG
28887932 TGCCATATCAT-GTATAT
1 TG-CATATCATAGTATAT
28887949 TAAAATCTCA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
21 15 0.50
22 15 0.50
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (21 bp):
TGCATATCATAGTATATCATG
Found at i:28897250 original size:40 final size:39
Alignment explanation
Indices: 28897161--28897344 Score: 221
Period size: 40 Copynumber: 4.6 Consensus size: 39
28897151 CGAATGATGA
* *
28897161 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-AT
*
28897201 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
28897240 CCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACCAAAT
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTAAT
* *
28897280 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AT
*
28897320 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
28897345 AACGAGTAGC
Statistics
Matches: 125, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
39 34 0.27
40 83 0.66
41 8 0.06
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:28897296 original size:79 final size:81
Alignment explanation
Indices: 28897160--28897342 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
28897150 TCGAATGATG
* * *
28897160 ACCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 ACCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
28897224 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
28897239 TCCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACCAAATCCGGGTTAAG-TCCCGAAGGCA
1 -ACCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
28897301 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
*
28897319 ACCGGGCTATGTCCCGAAGGCATT
1 ACCGGGCTAAGTCCCGAAGGCATT
28897343 TGAACGAGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 29 0.33
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (81 bp):
ACCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:28897366 original size:79 final size:79
Alignment explanation
Indices: 28897160--28897367 Score: 230
Period size: 79 Copynumber: 2.6 Consensus size: 79
28897150 TCGAATGATG
* *
28897160 ACCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGT-GACTATATCCGGACTAAGATCCGAAGGCAT
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTAG-CTATATCCGG-TTAAGATCCGAAGGCAT
28897223 TTGTGCGAGTTACTAAT
63 TTGTGCGAGTTACTAAT
* * * *
28897240 CCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTA-CCAAATCCGGGTTAAG-TCCCGAAGGCAT
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TAGCTATATCC-GGTTAAGAT-CCGAAGGCAT
28897302 TTGTGCGAGTTACT-AT
63 TTGTGCGAGTTACTAAT
* **
28897318 AACCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATCCGGTTAA
1 -ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTTAA
28897368 ATTTCGAAGG
Statistics
Matches: 107, Mismatches: 13, Indels: 17
0.78 0.09 0.12
Matches are distributed among these distances:
78 3 0.03
79 62 0.58
80 42 0.39
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (79 bp):
ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTTAAGATCCGAAGGCATTTG
TGCGAGTTACTAAT
Found at i:28898879 original size:31 final size:31
Alignment explanation
Indices: 28898814--28898898 Score: 120
Period size: 31 Copynumber: 2.8 Consensus size: 31
28898804 TTCAGTCTGA
* *
28898814 ACATAT-ACTGGGTTGAAGCC-TTTCATAAT
1 ACATATCACTGGGCTGAAGCCTTTTCAAAAT
*
28898843 TCATATCACTGGGCTGAAGCCTTTTCAAAAT
1 ACATATCACTGGGCTGAAGCCTTTTCAAAAT
*
28898874 ACATATCACTGGGCCGAAGCCTTTT
1 ACATATCACTGGGCTGAAGCCTTTT
28898899 GTTTAAGCGG
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
29 5 0.10
30 13 0.27
31 31 0.63
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (31 bp):
ACATATCACTGGGCTGAAGCCTTTTCAAAAT
Found at i:28899130 original size:24 final size:24
Alignment explanation
Indices: 28899103--28899185 Score: 78
Period size: 25 Copynumber: 3.4 Consensus size: 24
28899093 CTGGAGGCCT
*
28899103 AGCCTCTTTTAAT-AATTGGGGCAA
1 AGCC-CTTTTAATAAACTGGGGCAA
*
28899127 AGCCCTTTTTGATAAACTGGGGCAA
1 AGCCC-TTTTAATAAACTGGGGCAA
** *
28899152 AGCCCTTTTCGGTAAACTAGGGCAA
1 AGCCCTTTT-AATAAACTGGGGCAA
*
28899177 AGCCTTTTT
1 AGCCCTTTT
28899186 TGCACTTCCT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.02
24 14 0.27
25 36 0.71
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (24 bp):
AGCCCTTTTAATAAACTGGGGCAA
Found at i:28899153 original size:25 final size:25
Alignment explanation
Indices: 28899119--28899187 Score: 102
Period size: 25 Copynumber: 2.8 Consensus size: 25
28899109 TTTTAATAAT
28899119 TGGGGCAAAGCCCTTTTTGATAAAC
1 TGGGGCAAAGCCCTTTTTGATAAAC
* *
28899144 TGGGGCAAAGCCCTTTTCGGTAAAC
1 TGGGGCAAAGCCCTTTTTGATAAAC
* *
28899169 TAGGGCAAAGCCTTTTTTG
1 TGGGGCAAAGCCCTTTTTG
28899188 CACTTCCTCC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (25 bp):
TGGGGCAAAGCCCTTTTTGATAAAC
Found at i:28913175 original size:40 final size:40
Alignment explanation
Indices: 28913120--28913329 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
28913110 AACATTGGAA
28913120 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
28913160 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
28913200 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
28913240 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
28913279 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
28913320 CTATATCCGG
1 ATATATCCGG
28913330 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:28921304 original size:40 final size:40
Alignment explanation
Indices: 28921249--28921458 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
28921239 AACATTGGAA
28921249 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
28921289 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
28921329 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
28921369 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
28921408 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
28921449 CTATATCCGG
1 ATATATCCGG
28921459 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:28931460 original size:40 final size:40
Alignment explanation
Indices: 28931405--28931614 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
28931395 AACATTGGAA
28931405 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
28931445 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
28931485 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
28931525 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
28931564 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
28931605 CTATATCCGG
1 ATATATCCGG
28931615 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:28939593 original size:40 final size:40
Alignment explanation
Indices: 28939538--28939747 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
28939528 AACATTGGAA
28939538 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
28939578 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
28939618 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
28939658 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
28939697 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
28939738 CTATATCCGG
1 ATATATCCGG
28939748 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:28941707 original size:10 final size:10
Alignment explanation
Indices: 28941694--28941725 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
28941684 AAATAAGTTT
28941694 AATTTATATC
1 AATTTATATC
28941704 AATTTATATC
1 AATTTATATC
28941714 AATTTATATC
1 AATTTATATC
28941724 AA
1 AA
28941726 GAAAAGAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (10 bp):
AATTTATATC
Found at i:28947446 original size:5 final size:5
Alignment explanation
Indices: 28947436--28947468 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
28947426 TTGTGTGTTA
28947436 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
28947469 TTCAGCTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:28955637 original size:18 final size:15
Alignment explanation
Indices: 28955593--28955640 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 15
28955583 TAATGGATGT
28955593 TATTTGATATATGCA
1 TATTTGATATATGCA
28955608 TAATTT-ATATATGCGGA
1 T-ATTTGATATATGC--A
28955625 GTATTTGATATATGCA
1 -TATTTGATATATGCA
28955641 ATATGACATG
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
15 9 0.32
16 5 0.18
17 5 0.18
18 9 0.32
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (15 bp):
TATTTGATATATGCA
Found at i:28959542 original size:42 final size:42
Alignment explanation
Indices: 28959427--28959560 Score: 135
Period size: 42 Copynumber: 3.1 Consensus size: 42
28959417 TATGTGTTTT
* * *
28959427 CATGTAAGACCATGTCTGGAACGTTGGCATCAATATTGAGATTA
1 CATGTAAGACCATGTCTGGGAC-ATGGCATCAATATT-TGATTA
* * ** *
28959471 CGTGTAATACCATGTCTCAGACATCGGCATC-ATATTTGATTT
1 CATGTAAGACCATGTCTGGGACAT-GGCATCAATATTTGATTA
* *
28959513 CATGTAAGACCCTGTCTGGGACAATGGCATCGATATTTGATTA
1 CATGTAAGACCATGTCTGGGAC-ATGGCATCAATATTTGATTA
28959556 CATGT
1 CATGT
28959561 GTAACACCCC
Statistics
Matches: 73, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
42 27 0.37
43 23 0.32
44 23 0.32
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (42 bp):
CATGTAAGACCATGTCTGGGACATGGCATCAATATTTGATTA
Found at i:28961019 original size:92 final size:92
Alignment explanation
Indices: 28960862--28961030 Score: 295
Period size: 92 Copynumber: 1.8 Consensus size: 92
28960852 GCCCATAAGT
* *
28960862 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAGTGAACTCGGACTCAACTCAAC
28960927 GAGTTCGGATGCCTAGTTACATCTCAC
66 GAGTTCGGATGCCTAGTTACATCTCAC
*
28960954 GAACTCGGACTCAACTCAACGAGTTCGGACATT-GCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCAT-AGTGAACTCGGACTCAACTCAA
28961018 CGAGTTCGGATGC
65 CGAGTTCGGATGC
28961031 TCAACCATCC
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
91 8 0.11
92 65 0.89
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCAC
Found at i:28961027 original size:45 final size:45
Alignment explanation
Indices: 28960854--28961027 Score: 212
Period size: 45 Copynumber: 3.8 Consensus size: 45
28960844 TGTAACCCGC
* * *
28960854 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATT-GCAT
*
28960900 CCAT-AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTGCAT
* *
28960949 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTGCAT
28960991 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
28961028 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 8, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
42 5 0.05
43 2 0.02
44 3 0.03
45 59 0.53
46 4 0.04
47 30 0.27
48 3 0.03
49 3 0.03
50 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTGCAT
Found at i:28964800 original size:11 final size:11
Alignment explanation
Indices: 28964781--28964823 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
28964771 GCAAATATGG
*
28964781 ATATTTATCAC
1 ATATGTATCAC
*
28964792 ATATGTATCAT
1 ATATGTATCAC
* *
28964803 AAATTTATCAC
1 ATATGTATCAC
28964814 ATATGTATCA
1 ATATGTATCA
28964824 TAAACTTTAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.42
Consensus pattern (11 bp):
ATATGTATCAC
Found at i:28964838 original size:22 final size:22
Alignment explanation
Indices: 28964783--28964833 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
28964773 AAATATGGAT
28964783 ATTTATCACATATGTATCATAA
1 ATTTATCACATATGTATCATAA
28964805 ATTTATCACATATGTATCATAA
1 ATTTATCACATATGTATCATAA
28964827 ACTTTAT
1 A-TTTAT
28964834 TCATACTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 23 0.82
23 5 0.18
ACGTcount: A:0.39, C:0.14, G:0.04, T:0.43
Consensus pattern (22 bp):
ATTTATCACATATGTATCATAA
Found at i:28966377 original size:45 final size:44
Alignment explanation
Indices: 28966314--28966484 Score: 172
Period size: 45 Copynumber: 3.8 Consensus size: 44
28966304 TGTAACCCGC
* *
28966314 CCATAAG-CAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGCGTT-GCAT
*
28966358 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-G--G-C--GTTGCAT
* * * *
28966408 -C-TCA-CGAACTC-GACTCAACTCAACGAGTTCGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGC-GTTGCAT
28966449 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
28966485 ATGCTCAACC
Statistics
Matches: 105, Mismatches: 11, Indels: 21
0.77 0.08 0.15
Matches are distributed among these distances:
41 6 0.06
42 2 0.02
43 2 0.02
44 13 0.12
45 45 0.43
46 20 0.19
47 6 0.06
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (44 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGCGTTGCAT
Found at i:28966433 original size:91 final size:92
Alignment explanation
Indices: 28966322--28966488 Score: 291
Period size: 91 Copynumber: 1.8 Consensus size: 92
28966312 GCCCATAAGC
* *
28966322 AACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
1 AACTCGGACTCAACTCAACGAGCTCGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
28966387 AGTTCGGATGCCTAGTTACATCTCACG
66 AGTTCGGATGCCTAGTTACATCTCACG
* *
28966414 AACTC-GACTCAACTCAACGAGTTCGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAACG
1 AACTCGGACTCAACTCAACGAGCTCGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
28966478 AGTTCGGATGC
66 AGTTCGGATGC
28966489 TCAACCATCC
Statistics
Matches: 71, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
91 66 0.93
92 5 0.07
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (92 bp):
AACTCGGACTCAACTCAACGAGCTCGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
AGTTCGGATGCCTAGTTACATCTCACG
Found at i:28969763 original size:14 final size:14
Alignment explanation
Indices: 28969744--28969777 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
28969734 TCTTGTAATG
28969744 AAAGAATGAGACAA
1 AAAGAATGAGACAA
*
28969758 AAAGAAATTAGACAA
1 AAAG-AATGAGACAA
28969773 AAAGA
1 AAAGA
28969778 GAGGCAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.68, C:0.06, G:0.18, T:0.09
Consensus pattern (14 bp):
AAAGAATGAGACAA
Found at i:28971779 original size:25 final size:27
Alignment explanation
Indices: 28971750--28971813 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 27
28971740 TTTTACTGTA
28971750 TTTATTATTACG-GATATTT-T-AAATT
1 TTTATTATTA-GAGATATTTATAAAATT
* *
28971775 TTTATGATTAGATATATTTATAAAATT
1 TTTATTATTAGAGATATTTATAAAATT
*
28971802 ATTATTATTAGA
1 TTTATTATTAGA
28971814 TGGGAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 1 0.03
25 15 0.47
26 1 0.03
27 15 0.47
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.53
Consensus pattern (27 bp):
TTTATTATTAGAGATATTTATAAAATT
Found at i:28971811 original size:27 final size:25
Alignment explanation
Indices: 28971763--28971814 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
28971753 ATTATTACGG
*
28971763 ATATTTTAAATTTTTATGATTAGAT
1 ATATTTTAAATTATTATGATTAGAT
*
28971788 ATATTTATAAAATTATTATTATTAGAT
1 ATATTT-T-AAATTATTATGATTAGAT
28971815 GGGAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 6 0.26
26 1 0.04
27 16 0.70
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (25 bp):
ATATTTTAAATTATTATGATTAGAT
Found at i:28972768 original size:15 final size:15
Alignment explanation
Indices: 28972748--28972796 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
28972738 AGTTTTATCT
28972748 TCTTCTTTTCTTTTC
1 TCTTCTTTTCTTTTC
*
28972763 TCTTCTTTTCTCTTC
1 TCTTCTTTTCTTTTC
*
28972778 ATCTACTTTCTCTTCTTC
1 -TCTTCTTT-TCTT-TTC
28972796 T
1 T
28972797 TTTCCCCCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 14 0.50
16 7 0.25
17 4 0.14
18 3 0.11
ACGTcount: A:0.04, C:0.31, G:0.00, T:0.65
Consensus pattern (15 bp):
TCTTCTTTTCTTTTC
Done.