Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 550 of 770
Found at i:171049428 original size:28 final size:27
Alignment explanation
Indices: 171049378--171049430 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
171049368 CTATTCAGAA
* *
171049378 ATCAGTGTTAACTGGGCCTTAGCCCAT
1 ATCAGTATTAACTGGGCCATAGCCCAT
171049405 ATCAGTATTAATCTGGGCCATAGCCC
1 ATCAGTATTAA-CTGGGCCATAGCCC
171049431 TATTACAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (27 bp):
ATCAGTATTAACTGGGCCATAGCCCAT
Found at i:171049433 original size:62 final size:60
Alignment explanation
Indices: 171049355--171049499 Score: 168
Period size: 61 Copynumber: 2.4 Consensus size: 60
171049345 TCAAGCTTTA
* * *
171049355 CTGGGCCTAAGCCCTATT-CAGAAATCAGTG-TTAACTGGGCCTTAGCCCATATCAGTATTAAT
1 CTGGGCCT-AGCCCTATTACA-AAATCAGAGCAT-ACTGGGCC-TAGCCCATATCAGTATCAAT
* *
171049417 CTGGGCCATAGCCCTATTACAATATCAGAGCATACTGGGCCTAGCCCATATCAGTATCAGT
1 CTGGGCC-TAGCCCTATTACAAAATCAGAGCATACTGGGCCTAGCCCATATCAGTATCAAT
*
171049478 CTGGGCCGTAGCTCTATTACAA
1 CTGGGCC-TAGCCCTATTACAA
171049500 GTCGAGATAT
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
61 38 0.52
62 31 0.42
63 4 0.05
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (60 bp):
CTGGGCCTAGCCCTATTACAAAATCAGAGCATACTGGGCCTAGCCCATATCAGTATCAAT
Found at i:171049574 original size:19 final size:20
Alignment explanation
Indices: 171049520--171049574 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
171049510 ATTGGGCCTT
*
171049520 GCCCATATTAACACAGTTGG
1 GCCCATATTAAAACAGTTGG
* *
171049540 GCCCATTTTAATACAGTT-G
1 GCCCATATTAAAACAGTTGG
*
171049559 GCCCATAATAAAACAG
1 GCCCATATTAAAACAG
171049575 CCTCATATGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (20 bp):
GCCCATATTAAAACAGTTGG
Found at i:171060501 original size:27 final size:26
Alignment explanation
Indices: 171060463--171060571 Score: 110
Period size: 27 Copynumber: 4.0 Consensus size: 26
171060453 AAGCGTCCTC
*
171060463 GTGGCTATGCCACAATTATCTGATCTG
1 GTGGCTCTGCCAC-ATTATCTGATCTG
* *
171060490 GTGGCTCTGCCACATGTTTCTGTTCTG
1 GTGGCTCTGCCACAT-TATCTGATCTG
* *
171060517 GTGGCTCTGCCACGATTATCTATATGTG
1 GTGGCTCTGCCAC-ATTATCT-GATCTG
* * *
171060545 GTGACTCTGTCACATTATCTGTTCTG
1 GTGGCTCTGCCACATTATCTGATCTG
171060571 G
1 G
171060572 CAGCCATGCT
Statistics
Matches: 67, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
26 6 0.09
27 45 0.67
28 16 0.24
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.38
Consensus pattern (26 bp):
GTGGCTCTGCCACATTATCTGATCTG
Found at i:171060566 original size:54 final size:54
Alignment explanation
Indices: 171060463--171060571 Score: 139
Period size: 54 Copynumber: 2.0 Consensus size: 54
171060453 AAGCGTCCTC
* *
171060463 GTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATGTTTCTGTTCTG
1 GTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATGTATCTGTTCTG
* * * * *
171060517 GTGGCTCTGCCACGATTATCTATATGTGGTGACTCTGTCACAT-TATCTGTTCTG
1 GTGGCTATGCCACAATTATCT-GATCTGGTGACTCTGCCACATGTATCTGTTCTG
171060571 G
1 G
171060572 CAGCCATGCT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
54 30 0.64
55 17 0.36
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.38
Consensus pattern (54 bp):
GTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATGTATCTGTTCTG
Found at i:171081042 original size:22 final size:22
Alignment explanation
Indices: 171080963--171081042 Score: 106
Period size: 22 Copynumber: 3.6 Consensus size: 22
171080953 GTGTTGATGA
* * *
171080963 CACACGGGTGTGCCCTTGTGCC
1 CACACGGGCGTGTCCTTGTGTC
*
171080985 CACACGGGCGTGTCCTTTTTGTC
1 CACACGGGCGTGTCC-TTGTGTC
*
171081008 CACATGGGCGTGTCCTTGTGTC
1 CACACGGGCGTGTCCTTGTGTC
171081030 CACACGGGCGTGT
1 CACACGGGCGTGT
171081043 GACCCTGTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
22 31 0.62
23 19 0.38
ACGTcount: A:0.10, C:0.31, G:0.31, T:0.28
Consensus pattern (22 bp):
CACACGGGCGTGTCCTTGTGTC
Found at i:171082668 original size:40 final size:39
Alignment explanation
Indices: 171082631--171082814 Score: 221
Period size: 40 Copynumber: 4.6 Consensus size: 39
171082621 GCTACTCGTT
*
171082631 CAAATGCCTTCGGGACATAGCCCGATTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGATT-TAGTAACTCGCA
*
171082671 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GATTTAGTAACTCGCA
* *
171082711 CTAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAG-CCCGATTTAGTAACTCGCA
* * *
171082751 CTAATGCCTTC-GGATCTTAGTCCAGATTTAGTAACTTAGCA
1 CAAATGCCTTCGGGA-CTTAG-CCCGATTTAGTAAC-TCGCA
171082792 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
171082815 GACATCATTC
Statistics
Matches: 130, Mismatches: 9, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
39 6 0.05
40 108 0.83
41 16 0.12
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGATTTAGTAACTCGCA
Found at i:171090042 original size:40 final size:39
Alignment explanation
Indices: 171089951--171090101 Score: 135
Period size: 40 Copynumber: 3.8 Consensus size: 39
171089941 ATAACCACGT
* *
171089951 GCACAAATGCCTTCGGGTCTTAGCCCGAATAGAATGACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATAGAATGACTA
*
171089991 GCACGAATGCCTTCGGGTCTTAGCCCGGAT-GTA-GCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATAGAATG--ACTA
* * ** *
171090031 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAA-TGCCTTCGGGTCTTAGCCCGGATAGAATGACTA
* * *
171090071 GCATAATTGTCTTCGGGGCTTAGCCCGGATA
1 GCACAA-TGCCTTCGGGTCTTAGCCCGGATA
171090102 TCATTCAATT
Statistics
Matches: 92, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
38 1 0.01
39 4 0.04
40 86 0.93
41 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (39 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTA
Found at i:171095002 original size:26 final size:27
Alignment explanation
Indices: 171094967--171095020 Score: 101
Period size: 26 Copynumber: 2.0 Consensus size: 27
171094957 ACTTTTCTTG
171094967 CACACTTTGTTGACAAGCA-GTAATGA
1 CACACTTTGTTGACAAGCACGTAATGA
171094993 CACACTTTGTTGACAAGCACGTAATGA
1 CACACTTTGTTGACAAGCACGTAATGA
171095020 C
1 C
171095021 CCAAGGGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 19 0.70
27 8 0.30
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (27 bp):
CACACTTTGTTGACAAGCACGTAATGA
Found at i:171099390 original size:4 final size:4
Alignment explanation
Indices: 171099381--171099408 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
171099371 TAAGTAAATA
171099381 TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT
171099409 ATTATTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:171099412 original size:3 final size:3
Alignment explanation
Indices: 171099404--171099438 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
171099394 ATTTATTTAT
171099404 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
171099439 TACAAATGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:171101659 original size:46 final size:44
Alignment explanation
Indices: 171101555--171101662 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
171101545 TGTCTTTGAC
** * * *
171101555 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
171101599 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
171101645 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
171101663 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:171109027 original size:46 final size:44
Alignment explanation
Indices: 171108923--171109030 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
171108913 TGTCTTTGAC
** * * *
171108923 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
171108967 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
171109013 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
171109031 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:171114376 original size:2 final size:2
Alignment explanation
Indices: 171114369--171114393 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
171114359 TATGTACATA
171114369 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
171114394 AATAGTAATA
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:171115259 original size:13 final size:13
Alignment explanation
Indices: 171115241--171115266 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
171115231 TAAATATAAC
171115241 AATAATAGTAAAA
1 AATAATAGTAAAA
171115254 AATAATAGTAAAA
1 AATAATAGTAAAA
171115267 TTAAAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (13 bp):
AATAATAGTAAAA
Found at i:171125181 original size:2 final size:2
Alignment explanation
Indices: 171125174--171125204 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
171125164 AATATTATGA
171125174 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
171125205 ATTTAACTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:171128718 original size:20 final size:20
Alignment explanation
Indices: 171128693--171128730 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
171128683 GTTTATTCGC
*
171128693 GATTTTCAATATTTTGTAAA
1 GATTTTCAAAATTTTGTAAA
*
171128713 GATTTTTAAAATTTTGTA
1 GATTTTCAAAATTTTGTA
171128731 TTTGGATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTTTCAAAATTTTGTAAA
Found at i:171130387 original size:28 final size:28
Alignment explanation
Indices: 171130355--171130423 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
171130345 GCGTAGATCA
171130355 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
171130383 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
171130411 CGATA-TACCCCTA
1 CGAAATTACCCCTA
171130424 GGGTTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 8 0.20
28 32 0.80
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:171136709 original size:20 final size:20
Alignment explanation
Indices: 171136684--171136721 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
171136674 GGTTTTTCGC
*
171136684 GATTTTCAATATTTTGTAAA
1 GATTTTCAAAATTTTGTAAA
*
171136704 GATTTTTAAAATTTTGTA
1 GATTTTCAAAATTTTGTA
171136722 TTTGGATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTTTCAAAATTTTGTAAA
Found at i:171142571 original size:40 final size:40
Alignment explanation
Indices: 171142478--171142628 Score: 153
Period size: 40 Copynumber: 3.8 Consensus size: 40
171142468 AAATTGAATG
* * * **
171142478 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GGAAAT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGCCAAT
* * **
171142517 TTATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGCCGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGCCAAT
* * *
171142557 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGCCAAT
* *
171142597 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
171142629 ACATGCTTAT
Statistics
Matches: 92, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
39 31 0.34
40 59 0.64
41 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGCCAAT
Found at i:171142642 original size:40 final size:39
Alignment explanation
Indices: 171142518--171142643 Score: 139
Period size: 40 Copynumber: 3.2 Consensus size: 39
171142508 GCTGGAAATT
* * *
171142518 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGCCGC-TA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGC-A-CAGCTTA
* * *
171142558 TATCCGGGCTAAGACCCGAAGGCATTCGTGC-GAGTCATTC
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCACAG-C-TTA
171142598 TATCCGGGCTAAGACCCGAAGGCATTTGTGCACATGCTTA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCACA-GCTTA
171142638 TATCCG
1 TATCCG
171142644 ATTATATTCC
Statistics
Matches: 72, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
37 1 0.01
38 1 0.01
40 67 0.93
41 2 0.03
42 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (39 bp):
TATCCGGGCTAAGACCCGAAGGCATTTGTGCACAGCTTA
Found at i:171147068 original size:21 final size:21
Alignment explanation
Indices: 171147051--171147116 Score: 89
Period size: 21 Copynumber: 3.1 Consensus size: 21
171147041 CATGCATAAA
171147051 ATGAGCATATCATAGCATATC
1 ATGAGCATATCATAGCATATC
* *
171147072 ATGTGCATATCATAACATATC
1 ATGAGCATATCATAGCATATC
*
171147093 ATGAGCATACCAT-GCCATATC
1 ATGAGCATATCATAG-CATATC
171147114 ATG
1 ATG
171147117 TATAACAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (21 bp):
ATGAGCATATCATAGCATATC
Found at i:171147069 original size:10 final size:10
Alignment explanation
Indices: 171147054--171147115 Score: 63
Period size: 10 Copynumber: 6.0 Consensus size: 10
171147044 GCATAAAATG
171147054 AGCATATCAT
1 AGCATATCAT
171147064 AGCATATCAT
1 AGCATATCAT
*
171147074 GTGCATATCAT
1 -AGCATATCAT
*
171147085 AACATATCAT
1 AGCATATCAT
*
171147095 GAGCATACCAT
1 -AGCATATCAT
171147106 -GCCATATCAT
1 AG-CATATCAT
171147116 GTATAACAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
9 1 0.02
10 25 0.58
11 17 0.40
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (10 bp):
AGCATATCAT
Found at i:171147191 original size:25 final size:25
Alignment explanation
Indices: 171147154--171147202 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
171147144 ATAATCAAAC
* * *
171147154 CCTAGGGGTAAAATGGTTATTTTTA
1 CCTAGGGGCAAAATAGTCATTTTTA
171147179 CCTAGGGGCAAAATAGTCATTTTT
1 CCTAGGGGCAAAATAGTCATTTTT
171147203 CATATTATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (25 bp):
CCTAGGGGCAAAATAGTCATTTTTA
Found at i:171156371 original size:37 final size:37
Alignment explanation
Indices: 171156321--171156398 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
171156311 TATAAAAGAA
171156321 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
171156358 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
171156395 GTCT
1 GTCT
171156399 CGCCCGGAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.21, C:0.32, G:0.19, T:0.28
Consensus pattern (37 bp):
GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
Found at i:171156561 original size:49 final size:49
Alignment explanation
Indices: 171156501--171156623 Score: 219
Period size: 49 Copynumber: 2.5 Consensus size: 49
171156491 CATATATTTT
*
171156501 ACATTGGCCATTAGGCCTCATCACATATACATACACTTTCACATTCACC
1 ACATCGGCCATTAGGCCTCATCACATATACATACACTTTCACATTCACC
*
171156550 ACATCGGCCATTAGGCCTCATCACATATACGTACACTTTCACATTCACC
1 ACATCGGCCATTAGGCCTCATCACATATACATACACTTTCACATTCACC
*
171156599 ACATCGGCCATTAGGCCTTATCACA
1 ACATCGGCCATTAGGCCTCATCACA
171156624 CATATATGTA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 71 1.00
ACGTcount: A:0.29, C:0.33, G:0.11, T:0.27
Consensus pattern (49 bp):
ACATCGGCCATTAGGCCTCATCACATATACATACACTTTCACATTCACC
Found at i:171170290 original size:40 final size:40
Alignment explanation
Indices: 171170184--171170367 Score: 147
Period size: 40 Copynumber: 4.6 Consensus size: 40
171170174 TGCTGGAAAT
* * * * * **
171170184 TATAACCGGGTTAAGACCCGAAGGCAATGGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
*
171170224 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAT
1 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
* * * *
171170264 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-AATC-G
1 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
* * * * * * *
171170302 TGATATCCGGGTTAAGTCCCGTAGGCCTTGGTGCGGGTTAC
1 T-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
* * *
171170343 CATATCCGGGCTATGTCCCGAAGGC
1 TATATCCGGGCTAAGACCCGAAGGC
171170368 GTTTGAACGA
Statistics
Matches: 115, Mismatches: 26, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
38 1 0.01
39 29 0.25
40 85 0.74
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.23
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC
Found at i:171178318 original size:40 final size:38
Alignment explanation
Indices: 171178269--171178412 Score: 137
Period size: 40 Copynumber: 3.7 Consensus size: 38
171178259 TGCTGGAAAT
* * *
171178269 TATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGC-AGTCG
*
171178308 CTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCAT
1 -TATATCCGGGCTAAGACCCGAAGGCAATT-GTGC-AGTC-G
* * *
171178349 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGCAATCG
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGCAGTCG
* * *
171178387 TGATATCCGGGTTAAGTCCCGTAGGC
1 T-ATATCCGGGCTAAGACCCGAAGGC
171178413 CTTGGTGCGG
Statistics
Matches: 87, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
38 1 0.01
39 26 0.30
40 58 0.67
41 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (38 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTGTGCAGTCG
Found at i:171178438 original size:79 final size:80
Alignment explanation
Indices: 171178274--171178457 Score: 194
Period size: 79 Copynumber: 2.3 Consensus size: 80
171178264 GAAATTATAA
* * * *
171178274 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTATATCCGGGCTAAGACCCGAAGGCATTCG
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAATCGCTATATCCGGGCTAAGACCCGAAGGCATTCG
*
171178339 TGCGAGTCATTCTAT
66 TGCGAGTCATCCTAT
* * * * *
171178354 CCGGGCTAAGACCCGAAGGCATTTGTGC-AATCG-TGATATCCGGGTTAAGTCCCGTAGGCCTTG
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAATCGCT-ATATCCGGGCTAAGACCCGAAGGCATTC
* *
171178417 GTGCGGGTTA-CCATAT
65 GTGCGAGTCATCC-TAT
* * *
171178433 CCGGGCTATGTCCCGAAGGCGTTTG
1 CCGGGCTAAGACCCGAAGGCATTTG
171178458 AACGAGTAGC
Statistics
Matches: 87, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
78 2 0.02
79 59 0.68
80 26 0.30
ACGTcount: A:0.21, C:0.24, G:0.30, T:0.24
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAATCGCTATATCCGGGCTAAGACCCGAAGGCATTCG
TGCGAGTCATCCTAT
Found at i:171182917 original size:24 final size:24
Alignment explanation
Indices: 171182650--171182915 Score: 480
Period size: 24 Copynumber: 11.1 Consensus size: 24
171182640 GCAAAGACCA
*
171182650 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
171182674 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
171182698 TATGGCACTATGTGTGCGA-TTAC
1 TATGGCACTATGTGTGCGATTTAC
171182721 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
171182745 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
*
171182769 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
171182793 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
171182817 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
171182841 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
*
171182865 TATGGCACTATGTGTGCGATTTGC
1 TATGGCACTATGTGTGCGATTTAC
* *
171182889 TATAGCACTATGTGTGCGATTTGC
1 TATGGCACTATGTGTGCGATTTAC
171182913 TAT
1 TAT
171182916 AGTCACATTC
Statistics
Matches: 236, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
23 23 0.10
24 213 0.90
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (24 bp):
TATGGCACTATGTGTGCGATTTAC
Found at i:171190944 original size:24 final size:24
Alignment explanation
Indices: 171190676--171190942 Score: 480
Period size: 24 Copynumber: 11.1 Consensus size: 24
171190666 GCAAAGACCA
*
171190676 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
171190700 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
171190724 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
171190748 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
171190772 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
**
171190796 TATGGCACTATGTGTGCGATACAC
1 TATGGCACTATGTGTGCGATTTAC
171190820 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
171190844 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
171190868 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
*
171190892 TATGGCACTATGTGTGCGATTTGC
1 TATGGCACTATGTGTGCGATTTAC
* *
171190916 TATAGCACTATGTGTGCGATTTGC
1 TATGGCACTATGTGTGCGATTTAC
171190940 TAT
1 TAT
171190943 AGTCACATTC
Statistics
Matches: 236, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 236 1.00
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (24 bp):
TATGGCACTATGTGTGCGATTTAC
Found at i:171194009 original size:9 final size:9
Alignment explanation
Indices: 171193993--171194028 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
171193983 AGGTTTTCGT
171193993 ATTCGAATA
1 ATTCGAATA
*
171194002 ACTCGAATA
1 ATTCGAATA
171194011 ATTCGAATA
1 ATTCGAATA
171194020 ATTCGAATA
1 ATTCGAATA
171194029 TCAAACTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (9 bp):
ATTCGAATA
Found at i:171194285 original size:30 final size:30
Alignment explanation
Indices: 171194240--171194298 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
171194230 AATTTTTTAT
171194240 TTTCCCCCAAAATTTTTAC-TCCCTCCCAC
1 TTTCCCCCAAAATTTTTACTTCCCTCCCAC
* *
171194269 TTTCCCCCTTAAATTTTTACTTCCTTCCCA
1 TTTCCCCC-AAAATTTTTACTTCCCTCCCA
171194299 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
30 10 0.38
31 8 0.31
ACGTcount: A:0.19, C:0.41, G:0.00, T:0.41
Consensus pattern (30 bp):
TTTCCCCCAAAATTTTTACTTCCCTCCCAC
Found at i:171194953 original size:5 final size:5
Alignment explanation
Indices: 171194943--171194971 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
171194933 GAACAAATAT
171194943 ATTCG ATTCG ATTCG ATTCG ATTCG ATTC
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTC
171194972 AAATTTTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (5 bp):
ATTCG
Found at i:171195113 original size:114 final size:114
Alignment explanation
Indices: 171194953--171195192 Score: 480
Period size: 114 Copynumber: 2.1 Consensus size: 114
171194943 ATTCGATTCG
171194953 ATTCGATTCGATTCGATTCAAATTTTATCTCACTCGACTCGATTCGAGAAAATTTCAAATCAAAT
1 ATTCGATTCGATTCGATTCAAATTTTATCTCACTCGACTCGATTCGAGAAAATTTCAAATCAAAT
171195018 TAGGATGATAAAATATGATTCGTCAACTCTATTAACTCAAAATTTTTTC
66 TAGGATGATAAAATATGATTCGTCAACTCTATTAACTCAAAATTTTTTC
171195067 ATTCGATTCGATTCGATTCAAATTTTATCTCACTCGACTCGATTCGAGAAAATTTCAAATCAAAT
1 ATTCGATTCGATTCGATTCAAATTTTATCTCACTCGACTCGATTCGAGAAAATTTCAAATCAAAT
171195132 TAGGATGATAAAATATGATTCGTCAACTCTATTAACTCAAAATTTTTTC
66 TAGGATGATAAAATATGATTCGTCAACTCTATTAACTCAAAATTTTTTC
171195181 ATTCGATTCGAT
1 ATTCGATTCGAT
171195193 CGAACGCTTA
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 126 1.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (114 bp):
ATTCGATTCGATTCGATTCAAATTTTATCTCACTCGACTCGATTCGAGAAAATTTCAAATCAAAT
TAGGATGATAAAATATGATTCGTCAACTCTATTAACTCAAAATTTTTTC
Found at i:171197826 original size:25 final size:25
Alignment explanation
Indices: 171197776--171197873 Score: 73
Period size: 24 Copynumber: 4.1 Consensus size: 25
171197766 GTCCGGGCTA
* *
171197776 CATAAT-GGGAAGCTCA-TAAGAGC
1 CATAATCGGGAAGCTCACAAAGAAC
*
171197799 CATAATCGGGAAGTTCACAAAGAAC
1 CATAATCGGGAAGCTCACAAAGAAC
* *
171197824 CAT-ATCAGGAAGCTCACGAAA-AGC
1 CATAATCGGGAAGCTCAC-AAAGAAC
** *
171197848 C-T-ATTAGGAAGCTCACAAAGAGC
1 CATAATCGGGAAGCTCACAAAGAAC
171197871 CAT
1 CAT
171197874 GTAAGCGGAA
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
22 3 0.05
23 24 0.38
24 25 0.40
25 11 0.17
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.16
Consensus pattern (25 bp):
CATAATCGGGAAGCTCACAAAGAAC
Found at i:171200955 original size:12 final size:11
Alignment explanation
Indices: 171200934--171200986 Score: 65
Period size: 12 Copynumber: 4.7 Consensus size: 11
171200924 TAATATCTTC
171200934 AAAAAT-AAAT
1 AAAAATAAAAT
171200944 AAAAGATAAAAT
1 AAAA-ATAAAAT
171200956 AAAAA-ATAAAT
1 AAAAATA-AAAT
171200967 AAAAATAAAAAT
1 AAAAAT-AAAAT
171200979 AAAAATAA
1 AAAAATAA
171200987 TAGTAAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
10 5 0.13
11 14 0.37
12 18 0.47
13 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:171200964 original size:23 final size:23
Alignment explanation
Indices: 171200934--171200983 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
171200924 TAATATCTTC
171200934 AAAAATAAATAAAAGAT-AAAATA
1 AAAAATAAATAAAA-ATAAAAATA
171200957 AAAAATAAATAAAAATAAAAATA
1 AAAAATAAATAAAAATAAAAATA
171200980 AAAA
1 AAAA
171200984 TAATAGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (23 bp):
AAAAATAAATAAAAATAAAAATA
Found at i:171200968 original size:16 final size:16
Alignment explanation
Indices: 171200935--171200981 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
171200925 AATATCTTCA
*
171200935 AAAATAAATAAA-AGAT
1 AAAATAAA-AAATAAAT
171200951 AAAATAAAAAATAAAT
1 AAAATAAAAAATAAAT
171200967 AAAA-ATAAAAATAAA
1 AAAATA-AAAAATAAA
171200982 AATAATAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 4 0.14
16 24 0.86
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (16 bp):
AAAATAAAAAATAAAT
Found at i:171200972 original size:6 final size:6
Alignment explanation
Indices: 171200940--171200986 Score: 62
Period size: 6 Copynumber: 8.0 Consensus size: 6
171200930 CTTCAAAAAT
*
171200940 AAATAA AAGAT-A AAATAA AAA-AT AAATAA AAATAA AAATAA AAATAA
1 AAATAA AA-ATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
171200987 TAGTAAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
5 6 0.17
6 28 0.78
7 2 0.06
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:171200994 original size:23 final size:22
Alignment explanation
Indices: 171200934--171200998 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 22
171200924 TAATATCTTC
*
171200934 AAAAATAAATAAAAGATAAAATA
1 AAAAATAAATAAAATA-AAAATA
171200957 AAAAATAAATAAAAATAAAAAT-
1 AAAAATAAAT-AAAATAAAAATA
171200979 AAAAATAATAGTAAAATAAA
1 AAAAATAA-A-TAAAATAAA
171200999 GGGACTCAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
22 8 0.21
23 24 0.63
24 6 0.16
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.18
Consensus pattern (22 bp):
AAAAATAAATAAAATAAAAATA
Found at i:171202895 original size:5 final size:5
Alignment explanation
Indices: 171202887--171202915 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
171202877 GGGGGAAGGG
171202887 AGAAA AGAAA AGAAA AGAAA AGAAA AGAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAA
171202916 GAAGGGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:171207817 original size:25 final size:25
Alignment explanation
Indices: 171207788--171207848 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
171207778 GAGCTATTAT
171207788 CGGGAAGCTCGGAAGAACCATATAA
1 CGGGAAGCTCGGAAGAACCATATAA
171207813 CGGGAAGCTCGGAAGAACCATATAA
1 CGGGAAGCTCGGAAGAACCATATAA
171207838 CGGGAAGCTCG
1 CGGGAAGCTCG
171207849 AGAGGGCTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.36, C:0.21, G:0.31, T:0.11
Consensus pattern (25 bp):
CGGGAAGCTCGGAAGAACCATATAA
Found at i:171210381 original size:24 final size:24
Alignment explanation
Indices: 171210353--171210410 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
171210343 CTATATAATA
* * *
171210353 GGAAGCTCATA-AGAGCCATAATTG
1 GGAAGCTCACATAGAACCAT-ATCG
*
171210377 GGAAGTTCACATAGAACCATATCG
1 GGAAGCTCACATAGAACCATATCG
171210401 GGAAGCTCAC
1 GGAAGCTCAC
171210411 GAAAAGCCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 21 0.75
25 7 0.25
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (24 bp):
GGAAGCTCACATAGAACCATATCG
Found at i:171210472 original size:73 final size:73
Alignment explanation
Indices: 171210402--171210546 Score: 175
Period size: 73 Copynumber: 2.0 Consensus size: 73
171210392 ACCATATCGG
* * * * *
171210402 GAAGCTCACGAAAAGC-CTATCAGGAAGCTTACAAAGAGCCATGTAACGGGAAGCTTCGGATAGC
1 GAAGCTCAAG-AAAGCACTATCAGGAAGCTCACAAAGAGCCATGTAACAGGAAGCTCCAGATAGC
171210466 CAATATCAA
65 CAATATCAA
** * ** *
171210475 GTTGTTCAAGCGAGCACTATCAGGAAGCTCACAAAGAGGCATGTAACAGGAAGCTCCAGATAGCC
1 GAAGCTCAAGAAAGCACTATCAGGAAGCTCACAAAGAGCCATGTAACAGGAAGCTCCAGATAGCC
171210540 AATATCA
66 AATATCA
171210547 GGTTATTTAA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
72 3 0.05
73 57 0.95
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.17
Consensus pattern (73 bp):
GAAGCTCAAGAAAGCACTATCAGGAAGCTCACAAAGAGCCATGTAACAGGAAGCTCCAGATAGCC
AATATCAA
Found at i:171210563 original size:73 final size:73
Alignment explanation
Indices: 171210418--171210588 Score: 243
Period size: 73 Copynumber: 2.3 Consensus size: 73
171210408 CACGAAAAGC
* * * * *
171210418 CTATCAGGAAGCTTACAAAGAGCCATGTAACGGGAAGCTTCGGATAGCCAATATCAAGTTGTTCA
1 CTATCAGGAAGCTCACAAAGAGCCATGTAACAGGAAGCTCCAGATAGCCAATATCAAGTTATTCA
171210483 AGCGAGCA
66 AGCGAGCA
* * *
171210491 CTATCAGGAAGCTCACAAAGAGGCATGTAACAGGAAGCTCCAGATAGCCAATATCAGGTTATTTA
1 CTATCAGGAAGCTCACAAAGAGCCATGTAACAGGAAGCTCCAGATAGCCAATATCAAGTTATTCA
*
171210556 AGTGAGCA
66 AGCGAGCA
* *
171210564 TTATCAGGAAGCTCCCAAAGAGCCA
1 CTATCAGGAAGCTCACAAAGAGCCA
171210589 ATTTAATGGG
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 86 1.00
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (73 bp):
CTATCAGGAAGCTCACAAAGAGCCATGTAACAGGAAGCTCCAGATAGCCAATATCAAGTTATTCA
AGCGAGCA
Found at i:171212308 original size:26 final size:25
Alignment explanation
Indices: 171212237--171212334 Score: 79
Period size: 26 Copynumber: 3.8 Consensus size: 25
171212227 AAATATGTAA
* *
171212237 ATGAAATGATAAAATGAAATGTTTAG
1 ATGAAATGATTAAATGAAATGTTT-T
* * **
171212263 ATGAAATGGTTATACAAAATAGTTTT
1 ATGAAATGATTAAATGAAAT-GTTTT
* *
171212289 ATGAAATGATTACATGAAATGTTAT
1 ATGAAATGATTAAATGAAATGTTTT
* *
171212314 ATGAATTGATTATAAGGAAAT
1 ATGAAATGATTA-AATGAAAT
171212335 AGATGTATGA
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
25 15 0.27
26 37 0.66
27 4 0.07
ACGTcount: A:0.46, C:0.02, G:0.17, T:0.35
Consensus pattern (25 bp):
ATGAAATGATTAAATGAAATGTTTT
Found at i:171212326 original size:13 final size:13
Alignment explanation
Indices: 171212237--171212327 Score: 69
Period size: 13 Copynumber: 7.1 Consensus size: 13
171212227 AAATATGTAA
* *
171212237 ATGAAATGATAAA
1 ATGAAATGATTAT
* *
171212250 ATGAAATGTTTAG
1 ATGAAATGATTAT
*
171212263 ATGAAATGGTTAT
1 ATGAAATGATTAT
** *
171212276 ACAAAAT-AGTTTT
1 ATGAAATGA-TTAT
*
171212289 ATGAAATGATTAC
1 ATGAAATGATTAT
171212302 ATGAAATG-TTAT
1 ATGAAATGATTAT
*
171212314 ATGAATTGATTAT
1 ATGAAATGATTAT
171212327 A
1 A
171212328 AGGAAATAGA
Statistics
Matches: 60, Mismatches: 15, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
12 10 0.17
13 49 0.82
14 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.16, T:0.36
Consensus pattern (13 bp):
ATGAAATGATTAT
Found at i:171212335 original size:52 final size:52
Alignment explanation
Indices: 171212237--171212345 Score: 123
Period size: 52 Copynumber: 2.1 Consensus size: 52
171212227 AAATATGTAA
* * *
171212237 ATGAAATGATAAAATGAAATGTTTAGATGAAATGGTTATACAAAATAGTTTT
1 ATGAAATGATAAAATGAAATGTTTAGATGAAATGATTATACAAAATAGATGT
* * * *
171212289 ATGAAATGATTACATGAAATG-TTATATGAATTGATTATA-AGGAAATAGATGT
1 ATGAAATGATAAAATGAAATGTTTAGATGAAATGATTATACA--AAATAGATGT
171212341 ATGAA
1 ATGAA
171212346 TTGAGACATT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
50 1 0.02
51 15 0.31
52 32 0.67
ACGTcount: A:0.46, C:0.02, G:0.18, T:0.34
Consensus pattern (52 bp):
ATGAAATGATAAAATGAAATGTTTAGATGAAATGATTATACAAAATAGATGT
Found at i:171215048 original size:40 final size:40
Alignment explanation
Indices: 171214989--171215157 Score: 180
Period size: 40 Copynumber: 4.2 Consensus size: 40
171214979 TGAATGATAC
* *
171214989 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATCATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATCATAT
* * * *
171215029 CCGGGCTAAGACCCAAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATCATAT
* * * *
171215069 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATCATAT
* * * *
171215109 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGT-GATCATAT
171215150 CC-GGCTAA
1 CCGGGCTAA
171215158 ATTCGAAGAA
Statistics
Matches: 104, Mismatches: 22, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
39 1 0.01
40 95 0.91
41 8 0.08
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATCATAT
Found at i:171215156 original size:80 final size:80
Alignment explanation
Indices: 171214989--171215157 Score: 207
Period size: 80 Copynumber: 2.1 Consensus size: 80
171214979 TGAATGATAC
* * * *
171214989 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATCATATCCGGGCTAAGACCCAAAGGCATTCG
1 CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAATCCGGGCTAAGACCCAAAGGCATTCG
*
171215054 TGCGAGTTGTTATAT
66 TGCGAGTGGTTATAT
* * * *
171215069 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAATCCGGGTTAAGACCCGAAGGCAATT-
1 CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAATCCGGGCTAAGACCCAAAGGC-ATTC
**
171215133 GTGCTTGTGGATTATAT
65 GTGCGAGTGG-TTATAT
171215150 CC-GGCTAA
1 CCGGGCTAA
171215158 ATTCGAAGAA
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
80 65 0.86
81 11 0.14
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAATCCGGGCTAAGACCCAAAGGCATTCG
TGCGAGTGGTTATAT
Found at i:171229968 original size:80 final size:80
Alignment explanation
Indices: 171229884--171230032 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
171229874 TATGGTAACC
* * * *
171229884 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
171229948 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
171229964 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
171230029 CCGG
66 CCGG
171230033 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:171229974 original size:40 final size:38
Alignment explanation
Indices: 171229925--171230032 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
171229915 ATCACGATTT
*
171229925 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
171229965 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
171230005 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
171230033 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:171233004 original size:27 final size:27
Alignment explanation
Indices: 171232974--171233036 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
171232964 TACTCTTAAC
* *
171232974 ATAAACTTATATTCTAACATAATTCCA
1 ATAAACTAATATGCTAACATAATTCCA
171233001 ATAAACTAATATGCTAACATAATTCCA
1 ATAAACTAATATGCTAACATAATTCCA
171233028 ATAAACTAA
1 ATAAACTAA
171233037 CACCTAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (27 bp):
ATAAACTAATATGCTAACATAATTCCA
Found at i:171241442 original size:2 final size:2
Alignment explanation
Indices: 171241431--171241459 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
171241421 GTGTAAGCCC
171241431 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
171241460 TTATGGCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:171242945 original size:42 final size:40
Alignment explanation
Indices: 171242804--171242984 Score: 143
Period size: 41 Copynumber: 4.4 Consensus size: 40
171242794 GTTGAACTAT
* * *
171242804 ACATACGTGCCCTTGTTCGTAC-TCCGATACCCCTGAATTGC
1 ACATATGTGCCC-TGTTTGTACTTCAG-TACCCCTGAATTGC
* * *
171242845 ACATCTGTGCCTCTATTTGTACTTCAGTACCCATGAATTGC
1 ACATATGTGCC-CTGTTTGTACTTCAGTACCCCTGAATTGC
**
171242886 ACATACATGCCCTTGTTTGTACTTCA-TCACCCCCTGAATTGC
1 ACATATGTGCCC-TGTTTGTACTTCAGT-A-CCCCTGAATTGC
* ** *
171242928 ACATTTGTGTCCCTGTTTGTACTTTGGTACCCTTGAA-TGC
1 ACATATGTG-CCCTGTTTGTACTTCAGTACCCCTGAATTGC
* * *
171242968 ACTTTTGTACCCTGTTT
1 ACATATGTGCCCTGTTT
171242985 AAACTTTGGT
Statistics
Matches: 114, Mismatches: 19, Indels: 16
0.77 0.13 0.11
Matches are distributed among these distances:
39 8 0.07
40 12 0.11
41 57 0.50
42 33 0.29
43 4 0.04
ACGTcount: A:0.19, C:0.29, G:0.15, T:0.37
Consensus pattern (40 bp):
ACATATGTGCCCTGTTTGTACTTCAGTACCCCTGAATTGC
Found at i:171242958 original size:83 final size:81
Alignment explanation
Indices: 171242804--171242969 Score: 210
Period size: 83 Copynumber: 2.0 Consensus size: 81
171242794 GTTGAACTAT
*
171242804 ACATACGTGCCCTTGTTCGTACTCCGATACCCCTGAATTGCACATCTGTGCCTCTATTTGTACTT
1 ACATACATGCCCTTGTTCGTACTCCGATACCCCTGAATTGCACATCTGTGCCTCTATTTGTACTT
171242869 CAGTACCCATGAATTGC
66 CAGTACCCATGAA-TGC
* * * *
171242886 ACATACATGCCCTTGTTTGTACTTC-ATCACCCCCTGAATTGCACATTTGTGTCC-CTGTTTGTA
1 ACATACATGCCCTTGTTCGTACTCCGAT-A-CCCCTGAATTGCACATCTGTG-CCTCTATTTGTA
** *
171242949 CTTTGGTACCCTTGAATGC
63 CTTCAGTACCCATGAATGC
171242968 AC
1 AC
171242970 TTTTGTACCC
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
81 2 0.03
82 28 0.38
83 41 0.56
84 2 0.03
ACGTcount: A:0.20, C:0.30, G:0.16, T:0.35
Consensus pattern (81 bp):
ACATACATGCCCTTGTTCGTACTCCGATACCCCTGAATTGCACATCTGTGCCTCTATTTGTACTT
CAGTACCCATGAATGC
Found at i:171242960 original size:19 final size:19
Alignment explanation
Indices: 171242938--171242995 Score: 53
Period size: 20 Copynumber: 3.0 Consensus size: 19
171242928 ACATTTGTGT
*
171242938 CCCTGTTTGTACTTTGGTA
1 CCCTGTTTGAACTTTGGTA
** * *
171242957 CCCTTGAATGCACTTTTGTA
1 CCC-TGTTTGAACTTTGGTA
*
171242977 CCCTGTTTAAACTTTGGTA
1 CCCTGTTTGAACTTTGGTA
171242996 ATTCTGAGTC
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.43
Consensus pattern (19 bp):
CCCTGTTTGAACTTTGGTA
Found at i:171250296 original size:27 final size:27
Alignment explanation
Indices: 171250266--171250456 Score: 192
Period size: 27 Copynumber: 7.2 Consensus size: 27
171250256 TACTGAAATG
**
171250266 CCCTCGATTTTTAGAATTACCATTTTA
1 CCCTCGATTTACAGAATTACCATTTTA
* *** *
171250293 CCCTCGATTTATAGAATTATTGTTTCA
1 CCCTCGATTTACAGAATTACCATTTTA
*
171250320 CCCTCGATTTACA-AATTACCGTTTTA
1 CCCTCGATTTACAGAATTACCATTTTA
* * *
171250346 CCCTCAATTTATAGAATTACCAGTTTA
1 CCCTCGATTTACAGAATTACCATTTTA
171250373 CCCTCGATTTACAGAATTACC--TTTA
1 CCCTCGATTTACAGAATTACCATTTTA
* *
171250398 CCCTCAATTTACAAAATTACCATTTTA
1 CCCTCGATTTACAGAATTACCATTTTA
* * **
171250425 CCCT-TAGTTTACAAAATTACTGTTTTA
1 CCCTCGA-TTTACAGAATTACCATTTTA
171250452 CCCTC
1 CCCTC
171250457 AATTCTGAAA
Statistics
Matches: 139, Mismatches: 20, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
25 23 0.17
26 22 0.16
27 94 0.68
ACGTcount: A:0.29, C:0.25, G:0.07, T:0.40
Consensus pattern (27 bp):
CCCTCGATTTACAGAATTACCATTTTA
Found at i:171250348 original size:53 final size:53
Alignment explanation
Indices: 171250266--171250460 Score: 218
Period size: 52 Copynumber: 3.7 Consensus size: 53
171250256 TACTGAAATG
** * **
171250266 CCCTCGATTTTTAGAATTACCATTTTACCCTCGATTTATAGAATTA-TTGTTTCA
1 CCCTCGATTTACAGAATTACC-TTTTACCCTCAATTTATAGAATTACCAGTTT-A
171250320 CCCTCGATTTACA-AATTACCGTTTTACCCTCAATTTATAGAATTACCAGTTTA
1 CCCTCGATTTACAGAATTACC-TTTTACCCTCAATTTATAGAATTACCAGTTTA
* * *
171250373 CCCTCGATTTACAGAATTACC-TTTACCCTCAATTTACAAAATTACCATTTTA
1 CCCTCGATTTACAGAATTACCTTTTACCCTCAATTTATAGAATTACCAGTTTA
* * *
171250425 CCCT-TAGTTTACAAAATTACTGTTTTACCCTCAATT
1 CCCTCGA-TTTACAGAATTAC-CTTTTACCCTCAATT
171250461 CTGAAATTAC
Statistics
Matches: 124, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
51 1 0.01
52 44 0.35
53 44 0.35
54 35 0.28
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (53 bp):
CCCTCGATTTACAGAATTACCTTTTACCCTCAATTTATAGAATTACCAGTTTA
Found at i:171250522 original size:27 final size:27
Alignment explanation
Indices: 171250492--171250753 Score: 262
Period size: 27 Copynumber: 9.7 Consensus size: 27
171250482 TGTAGGATAG
171250492 AATTACCAAAATACCCTTAGTTTGTAA
1 AATTACCAAAATACCCTTAGTTTGTAA
*
171250519 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCTTAGTTTGTAA
*
171250546 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCTTAGTTTGTAA
171250573 AATTACCAAAATACCC-TAGTTTGTAA
1 AATTACCAAAATACCCTTAGTTTGTAA
* * * *
171250599 AATTACCGAAGTACCCTGAATTTGTAA
1 AATTACCAAAATACCCTTAGTTTGTAA
**
171250626 AATTACCAAAATACCCTT-GATTTACAA
1 AATTACCAAAATACCCTTAG-TTTGTAA
* *
171250653 AATTA-CAGAAATACCCTTGACTTTCTAAA
1 AATTACCA-AAATACCCTT-AGTTTGT-AA
* * * **
171250682 AATTA-TAGAAATACCATTGGTTTACAA
1 AATTACCA-AAATACCCTTAGTTTGTAA
** * *
171250709 AATTACTGAAATACCCTTGGTTTGTAG
1 AATTACCAAAATACCCTTAGTTTGTAA
* *
171250736 ATTTACCAAAACACCCTT
1 AATTACCAAAATACCCTT
171250754 GTAGGATGAA
Statistics
Matches: 199, Mismatches: 29, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
26 26 0.13
27 148 0.74
28 7 0.04
29 18 0.09
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (27 bp):
AATTACCAAAATACCCTTAGTTTGTAA
Found at i:171250655 original size:80 final size:80
Alignment explanation
Indices: 171250492--171250669 Score: 245
Period size: 80 Copynumber: 2.2 Consensus size: 80
171250482 TGTAGGATAG
*
171250492 AATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAA
1 AATTACCAAAATACCC-TAGTTTGTAAAATTACCAAAATACCCCTAATTTGTAAAATTACCAAAA
**
171250557 TACCCCTAGTTTGTAA
65 TACCCCTAGTTTACAA
* *
171250573 AATTACCAAAATACCCTAGTTTGTAAAATTACCGAAGTA-CCCTGAATTTGTAAAATTACCAAAA
1 AATTACCAAAATACCCTAGTTTGTAAAATTACCAAAATACCCCT-AATTTGTAAAATTACCAAAA
*
171250637 TA-CCCTTGATTTACAA
65 TACCCCTAG-TTTACAA
171250653 AATTA-CAGAAATACCCT
1 AATTACCA-AAATACCCT
171250670 TGACTTTCTA
Statistics
Matches: 88, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
79 11 0.12
80 61 0.69
81 16 0.18
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.30
Consensus pattern (80 bp):
AATTACCAAAATACCCTAGTTTGTAAAATTACCAAAATACCCCTAATTTGTAAAATTACCAAAAT
ACCCCTAGTTTACAA
Found at i:171250813 original size:26 final size:26
Alignment explanation
Indices: 171250772--171250845 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 26
171250762 AAATGACTAA
*
171250772 AATACCCCTAATAGGTAAAAAGACCGT
1 AATACCCCT-GTAGGTAAAAAGACCGT
**
171250799 AA-AGCCCCTGTAGGTTAAAGTGACCGT
1 AATA-CCCCTGTAGG-TAAAAAGACCGT
*
171250826 AATACCCTTGTATGGTAAAA
1 AATACCCCTGTA-GGTAAAA
171250846 TGACGAATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
26 5 0.13
27 30 0.79
28 3 0.08
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (26 bp):
AATACCCCTGTAGGTAAAAAGACCGT
Found at i:171251583 original size:20 final size:20
Alignment explanation
Indices: 171251558--171251644 Score: 131
Period size: 20 Copynumber: 4.3 Consensus size: 20
171251548 GATATGATAT
*
171251558 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGAAATGC
*
171251578 ACATGATATGTATAAAATGC
1 ACATGATATGTATGAAATGC
171251598 ACATGATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
*
171251618 ACATGATATGTATGAAATCC
1 ACATGATATGTATGAAATGC
171251638 ACATGAT
1 ACATGAT
171251645 GTATTCATAA
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
20 60 0.97
21 2 0.03
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.31
Consensus pattern (20 bp):
ACATGATATGTATGAAATGC
Found at i:171264730 original size:39 final size:39
Alignment explanation
Indices: 171264673--171264771 Score: 110
Period size: 39 Copynumber: 2.5 Consensus size: 39
171264663 AAATTGAATG
* *
171264673 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCC-GGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
171264712 ATATCCGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGCTAAGACCCGAAGACAATTATGCTAGAAACT
171264751 ATATCCGGCTAAGACCCGAAG
1 ATATCCGGCTAAGACCCGAAG
171264772 GCATTCGTGC
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 6 0.12
39 44 0.88
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.22
Consensus pattern (39 bp):
ATATCCGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:171264772 original size:39 final size:39
Alignment explanation
Indices: 171264711--171264836 Score: 132
Period size: 39 Copynumber: 3.2 Consensus size: 39
171264701 TGCTGGAAAT
* * *
171264711 TATATCCGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGCTAAGACCCGAAGGCAATTGTGCGAGTGAC
* *
171264750 TATATCCGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTAT
1 TATATCCGGCTAAGACCCGAAGGCAATT-GTGCGAGTGAC
* * *
171264789 TCTATCCGGGCTAAGA-CCGAAGGCATTTGTGC-ACGTGAA
1 TATATCC-GGCTAAGACCCGAAGGCAATTGTGCGA-GTGAC
171264828 TATATCCGG
1 TATATCCGG
171264837 TTATATTCCG
Statistics
Matches: 73, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
38 6 0.08
39 57 0.78
40 10 0.14
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
TATATCCGGCTAAGACCCGAAGGCAATTGTGCGAGTGAC
Found at i:171267448 original size:28 final size:27
Alignment explanation
Indices: 171267385--171267454 Score: 131
Period size: 27 Copynumber: 2.6 Consensus size: 27
171267375 ATAGTGAGTC
171267385 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
171267412 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
171267440 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
171267455 GTACAAATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 23 0.55
28 19 0.45
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:171275314 original size:26 final size:28
Alignment explanation
Indices: 171275285--171275353 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
171275275 ATAGTGAGTC
*
171275285 CGCACGCTTAGTGC-ATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
171275311 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
171275339 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
171275354 GTACAAATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 13 0.32
27 8 0.20
28 19 0.47
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:171277816 original size:49 final size:49
Alignment explanation
Indices: 171277760--171278029 Score: 459
Period size: 49 Copynumber: 5.5 Consensus size: 49
171277750 TACATATATG
* * *
171277760 TGTGATAAGGCCGAATGGCCAATGCGATGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCAATGTGGTGAATGTGAAAGTGTATGTATA
* *
171277809 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCAATGTGGTGAATGTGAAAGTGTATGTATA
* *
171277858 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCAATGTGGTGAATGTGAAAGTGTATGTATA
171277907 TGTGATAAGGCCTAATGGCCAATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCAATGTGGTGAATGTGAAAGTGTATGTATA
*
171277956 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCAATGTGGTGAATGTGAAAGTGTATGTATA
*
171278005 TGTGATAAGGCCTAATGGCTAATGT
1 TGTGATAAGGCCTAATGGCCAATGT
171278030 AAAATATCTG
Statistics
Matches: 211, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 211 1.00
ACGTcount: A:0.30, C:0.09, G:0.31, T:0.30
Consensus pattern (49 bp):
TGTGATAAGGCCTAATGGCCAATGTGGTGAATGTGAAAGTGTATGTATA
Found at i:171278175 original size:37 final size:37
Alignment explanation
Indices: 171278125--171278246 Score: 226
Period size: 37 Copynumber: 3.3 Consensus size: 37
171278115 GGAATATGTT
*
171278125 CCGGGTGAGACCCGATGACTACGTGTGGAGATTATGA
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
171278162 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
*
171278199 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGT
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
171278236 CCGGGTAAGAC
1 CCGGGTAAGAC
171278247 TTCTTTTATA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 83 1.00
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21
Consensus pattern (37 bp):
CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
Found at i:171280773 original size:24 final size:24
Alignment explanation
Indices: 171280746--171280860 Score: 212
Period size: 24 Copynumber: 4.8 Consensus size: 24
171280736 CTTATTATGT
**
171280746 TCGCACACATAGTGCCATAGCGAA
1 TCGCACACATAGTGCCATAGTAAA
171280770 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
171280794 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
171280818 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
171280842 TCGCACACATAGTGCCATA
1 TCGCACACATAGTGCCATA
171280861 TATTTCCAGC
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 89 1.00
ACGTcount: A:0.36, C:0.27, G:0.17, T:0.20
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:171280907 original size:28 final size:29
Alignment explanation
Indices: 171280843--171280915 Score: 130
Period size: 29 Copynumber: 2.6 Consensus size: 29
171280833 CATAGTAAAT
*
171280843 CGCACACATAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
171280872 CGCACACTTAGTGCCATATATTT-CAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
171280900 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
171280916 ATCTCGTCAC
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 21 0.49
29 22 0.51
ACGTcount: A:0.29, C:0.32, G:0.15, T:0.25
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:171290196 original size:40 final size:40
Alignment explanation
Indices: 171290094--171290245 Score: 153
Period size: 40 Copynumber: 3.8 Consensus size: 40
171290084 AAATTGAATG
* * * * *
171290094 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGAAGTT
* * * *
171290134 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGCAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGAAGTT
* **
171290174 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGAAGTT
* * *
171290214 AAATCTGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
171290246 AAATCGTGAT
Statistics
Matches: 92, Mismatches: 18, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
39 3 0.03
40 87 0.95
41 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGAAGTT
Found at i:171293227 original size:40 final size:39
Alignment explanation
Indices: 171293183--171293308 Score: 139
Period size: 40 Copynumber: 3.2 Consensus size: 39
171293173 GGGACTCAAC
*
171293183 CCGGATTTAGTAGCTTGCTCGAAAGCCTTCGGATCTTAGT
1 CCGGATTTAGTA-CTTGCACGAAAGCCTTCGGATCTTAGT
* * * *
171293223 CCGGATTTAGTAACTCGCACGTATGCCGTCGGATCTTAGT
1 CCGGATTTAGT-ACTTGCACGAAAGCCTTCGGATCTTAGT
*
171293263 CCGGATTTAGTCACTTAGCAC-AAAGCCTTCGGGA-CTTAGC
1 CCGGATTTAGT-ACTT-GCACGAAAGCCTTC-GGATCTTAGT
171293303 CCGGAT
1 CCGGAT
171293309 ATCATTCGAA
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
40 64 0.89
41 8 0.11
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (39 bp):
CCGGATTTAGTACTTGCACGAAAGCCTTCGGATCTTAGT
Found at i:171293267 original size:80 final size:80
Alignment explanation
Indices: 171293122--171293308 Score: 204
Period size: 80 Copynumber: 2.3 Consensus size: 80
171293112 GCTACACATT
* * *
171293122 CAAATGCCTTCGGGACATAGCCCGG-TTACAGTAACTCGCACGAATGCCTTCGGGACTCAACCCG
1 CAAA-GCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACGAATGCCGTCGGGACTCAACCCG
*
171293186 GATTTAGT-AGCTT-GCT
64 GATTTAGTCA-CTTAGCA
* * * **
171293202 CGAAAGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCACGTATGCCGTC-GGATCTTAGTCC
1 C-AAAGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCACGAATGCCGTCGGGA-CTCAACCC
171293265 GGATTTAGTCACTTAGCA
63 GGATTTAGTCACTTAGCA
171293283 CAAAGCCTTCGGGACTTAGCCCGGAT
1 CAAAGCCTTCGGGACTTAGCCCGGAT
171293309 ATCATTCGAA
Statistics
Matches: 90, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
79 6 0.07
80 72 0.80
81 12 0.13
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (80 bp):
CAAAGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCGTCGGGACTCAACCCGGA
TTTAGTCACTTAGCA
Found at i:171312984 original size:39 final size:40
Alignment explanation
Indices: 171312860--171313028 Score: 216
Period size: 40 Copynumber: 4.2 Consensus size: 40
171312850 CGGGATTTAA
* * * * *
171312860 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
171312900 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
171312940 CCGGATATATCAACTCGCACGAATGCCTTC-GGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
171312979 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
171313019 CCGGATATAT
1 CCGGATATAT
171313029 TTCCAATGTT
Statistics
Matches: 111, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 40 0.36
40 71 0.64
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:171313023 original size:79 final size:80
Alignment explanation
Indices: 171312860--171313028 Score: 216
Period size: 79 Copynumber: 2.1 Consensus size: 80
171312850 CGGGATTTAA
* * * * * * *
171312860 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAACCCGGATTTGGTGACTTGCACAAAGG
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCATAACCCGGATATGATAACTCGCACAAAGG
171312925 CCTTCGGGTCTTAGC
66 CCTTCGGGTCTTAGC
* * * *
171312940 CCGGATATATCAACTCGCACGAATGCCTTC-GGTCTTAGCCCGGATAT-ATCAACTCGCACGAAT
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCATAACCCGGATATGAT-AACTCGCACAAAG
171313003 GCCTTCGGGTCTTAGC
65 GCCTTCGGGTCTTAGC
171313019 CCGGATATAT
1 CCGGATATAT
171313029 TTCCAATGTT
Statistics
Matches: 77, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
78 1 0.01
79 49 0.64
80 27 0.35
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.25
Consensus pattern (80 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCATAACCCGGATATGATAACTCGCACAAAGG
CCTTCGGGTCTTAGC
Found at i:171320673 original size:7 final size:7
Alignment explanation
Indices: 171320661--171320686 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
171320651 ACTTTTTCAA
171320661 TCATCCC
1 TCATCCC
171320668 TCATCCC
1 TCATCCC
171320675 TCATCCC
1 TCATCCC
171320682 TCATC
1 TCATC
171320687 ATTCTCTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.54, G:0.00, T:0.31
Consensus pattern (7 bp):
TCATCCC
Found at i:171325721 original size:45 final size:45
Alignment explanation
Indices: 171325657--171325875 Score: 295
Period size: 45 Copynumber: 4.9 Consensus size: 45
171325647 TGTTGATTTG
*
171325657 ATTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGAT
1 ATTATTCGAGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGAT
171325702 ATTATTCGAGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGAT
1 ATTATTCGAGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGAT
* *
171325747 ACTATTCGAGCCTTTGAGCCTAGCAGGCTACAATGCCGGTGAGAT
1 ATTATTCGAGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGAT
* * *
171325792 ACTATTCG-GGCTTTCGAGCCTAGCAGGCTATAATGCCTGTGA-A-
1 ATTATTCGAGCCTTT-GAGCCTAGCAGGCTATAATGCCGGTGAGAT
* * * *
171325835 ATGATATCGGGCC-TCGAGCCTAGCAGGC-AAAATGCCGGTGA
1 ATTAT-TCGAGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
171325876 ATGAATTCGG
Statistics
Matches: 159, Mismatches: 12, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
42 11 0.07
43 16 0.10
44 10 0.06
45 122 0.77
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (45 bp):
ATTATTCGAGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGAT
Found at i:171335646 original size:7 final size:7
Alignment explanation
Indices: 171335634--171335659 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
171335624 ACTTTTTCAA
171335634 TCATCCC
1 TCATCCC
171335641 TCATCCC
1 TCATCCC
171335648 TCATCCC
1 TCATCCC
171335655 TCATC
1 TCATC
171335660 ATTCTCTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.54, G:0.00, T:0.31
Consensus pattern (7 bp):
TCATCCC
Found at i:171339297 original size:15 final size:14
Alignment explanation
Indices: 171339280--171339306 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
171339270 TAAAATGACA
171339280 AAAAAAACAAAAAC
1 AAAAAAACAAAAAC
171339294 AAAAAAACAAAAA
1 AAAAAAACAAAAA
171339307 TAGCAACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAACAAAAAC
Found at i:171339646 original size:30 final size:30
Alignment explanation
Indices: 171339580--171339648 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
171339570 CGTAAAAATT
171339580 GTAAAACGCAGAGCAATAGCGGCGTTTTAC
1 GTAAAACGCAGAGCAATAGCGGCGTTTTAC
** * **
171339610 CAAAAACGCAGAGCAATAGTGGCGTTTTTG
1 GTAAAACGCAGAGCAATAGCGGCGTTTTAC
171339640 GTAAAACGC
1 GTAAAACGC
171339649 CGCTAAAAAC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.20
Consensus pattern (30 bp):
GTAAAACGCAGAGCAATAGCGGCGTTTTAC
Found at i:171339770 original size:41 final size:41
Alignment explanation
Indices: 171339621--171339901 Score: 131
Period size: 41 Copynumber: 6.9 Consensus size: 41
171339611 AAAAACGCAG
* * * * *
171339621 AGCAATAGTGGCGTTTTTGGTAAAACGCCG-CTAAAAACAG
1 AGCAATAGCGGCGTTTTAGGAAAAACGCCGCCAAAAAACAT
* * * * * **
171339661 AGTAATAGCGGCGTTTTTGGTAAAACGCAGCTAAAAATTAT
1 AGCAATAGCGGCGTTTTAGGAAAAACGCCGCCAAAAAACAT
* * *
171339702 AGAAATAGCGGCGTTTTA-TAGATAACGCCGCCAAAAAACAT
1 AGCAATAGCGGCGTTTTAGGA-AAAACGCCGCCAAAAAACAT
* ** * *** *
171339743 AGCAATAGTGGCGTTTTACCAAAAACGCCGCTAAATGCCAG
1 AGCAATAGCGGCGTTTTAGGAAAAACGCCGCCAAAAAACAT
* * * * * * *
171339784 AGCATTAGTGGCGCTTTT-GGTAAAACGCCACTAAAAACCAA
1 AGCAATAGCGGCG-TTTTAGGAAAAACGCCGCCAAAAAACAT
* * * * * *
171339825 AG-AATTAGCGGCGCTTT-GTGTAAAACGCCACTAAAAACCAG
1 AGCAA-TAGCGGCGTTTTAG-GAAAAACGCCGCCAAAAAACAT
* * * *
171339866 AGCATTAGCGGCGTTTTTGGTAAAACGCCGCTAAAA
1 AGCAATAGCGGCGTTTTAGGAAAAACGCCGCCAAAA
171339902 GTCATTTAAC
Statistics
Matches: 192, Mismatches: 41, Indels: 15
0.77 0.17 0.06
Matches are distributed among these distances:
40 32 0.17
41 153 0.80
42 7 0.04
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (41 bp):
AGCAATAGCGGCGTTTTAGGAAAAACGCCGCCAAAAAACAT
Found at i:171339811 original size:82 final size:82
Alignment explanation
Indices: 171339611--171339901 Score: 216
Period size: 82 Copynumber: 3.5 Consensus size: 82
171339601 GCGTTTTACC
* * * *
171339611 AAAAACGCAGAGCAATAGTGGCGTTTTTGGTAAAACGCCGCT-AAAAACAGAGTAA-TAGCGGCG
1 AAAAAC-CAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAAACAAAG-AATTAGCGGCG
* ****
171339674 TTTTTGGTAAAACG-CAGCT
64 CTTTACCAAAAACGCCA-CT
** * * * * * * *
171339693 AAAAATTATAGAAATAGCGGCG-TTTT-ATAGATAACGCCGCCAAAAAACATAGCAA-TAGTGGC
1 AAAAACCAGAGCATTAGCGGCGCTTTTGGTA-A-AACGCCGCTAAAAAACAAAG-AATTAGCGGC
* *
171339755 GTTTTACCAAAAACGCCGCT
63 GCTTTACCAAAAACGCCACT
** * * *
171339775 AAATGCCAGAGCATTAGTGGCGCTTTTGGTAAAACGCCACTAAAAACCAAAGAATTAGCGGCGCT
1 AAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAAACAAAGAATTAGCGGCGCT
****
171339840 TTGTGTAAAACGCCACT
66 TTACCAAAAACGCCACT
*
171339857 AAAAACCAGAGCATTAGCGGCGTTTTTGGTAAAACGCCGCTAAAA
1 AAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAA
171339902 GTCATTTAAC
Statistics
Matches: 162, Mismatches: 40, Indels: 14
0.75 0.19 0.06
Matches are distributed among these distances:
79 2 0.01
80 5 0.03
81 22 0.14
82 125 0.77
83 6 0.04
84 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (82 bp):
AAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAAACAAAGAATTAGCGGCGCT
TTACCAAAAACGCCACT
Found at i:171339852 original size:123 final size:122
Alignment explanation
Indices: 171339608--171339901 Score: 324
Period size: 123 Copynumber: 2.4 Consensus size: 122
171339598 GCGGCGTTTT
* *
171339608 ACCAAAAACGCAGAGCAATAGTGGCGTTTTTGGTAAAACGCCGCTAAAAACAGAGTAATAGCGGC
1 ACCAAAAA-ACAGAGCAATAGTGGCGTTTTTGGTAAAACGCCGCTAAAAACAGAGCAATAGCGGC
* ** *
171339673 GTTTTTGGTAAAACGCAGCTAAAAATTATAGAAATAGCGGCGTTTTATAGATAACGCC
65 GCTTTTGGTAAAACGCAGCTAAAAACCAAAGAAATAGCGGCGTTTTATAGATAACGCC
* * **** ** * *
171339731 GCCAAAAAACATAGCAATAGTGGCGTTTTACCAAAAACGCCGCTAAATGCCAGAGCATTAGTGGC
1 ACCAAAAAACAGAGCAATAGTGGCGTTTTTGGTAAAACGCCGCTAAA-AACAGAGCAATAGCGGC
* *
171339796 GCTTTTGGTAAAACGCCA-CTAAAAACCAAAGAATTAGCGGCGCTTTGTGTA-A-AACGCC
65 GCTTTTGGTAAAACG-CAGCTAAAAACCAAAGAAATAGCGGCG-TTT-TATAGATAACGCC
* * * *
171339854 ACTAAAAACCAGAGCATTAGCGGCGTTTTTGGTAAAACGCCGCTAAAA
1 ACCAAAAAACAGAGCAATAGTGGCGTTTTTGGTAAAACGCCGCTAAAA
171339902 GTCATTTAAC
Statistics
Matches: 138, Mismatches: 29, Indels: 9
0.78 0.16 0.05
Matches are distributed among these distances:
122 33 0.24
123 96 0.70
124 6 0.04
125 3 0.02
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (122 bp):
ACCAAAAAACAGAGCAATAGTGGCGTTTTTGGTAAAACGCCGCTAAAAACAGAGCAATAGCGGCG
CTTTTGGTAAAACGCAGCTAAAAACCAAAGAAATAGCGGCGTTTTATAGATAACGCC
Found at i:171339963 original size:7 final size:7
Alignment explanation
Indices: 171339934--171339972 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
171339924 AAACCCCAAA
171339934 AAACA-T
1 AAACACT
171339940 AAACACT
1 AAACACT
*
171339947 AAACCCCT
1 AAA-CACT
171339955 AAACACT
1 AAACACT
171339962 AAACACT
1 AAACACT
171339969 AAAC
1 AAAC
171339973 TATAACCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 5 0.17
7 18 0.62
8 6 0.21
ACGTcount: A:0.56, C:0.31, G:0.00, T:0.13
Consensus pattern (7 bp):
AAACACT
Found at i:171339967 original size:22 final size:23
Alignment explanation
Indices: 171339917--171339972 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
171339907 TTAACCCTTA
*
171339917 AAACCCTAAACCCCAAAAAACAT
1 AAACACTAAACCCCAAAAAACAT
* *
171339940 AAACACTAAACCCCTAAACAC-T
1 AAACACTAAACCCCAAAAAACAT
171339962 AAACACTAAAC
1 AAACACTAAAC
171339973 TATAACCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 12 0.40
23 18 0.60
ACGTcount: A:0.55, C:0.34, G:0.00, T:0.11
Consensus pattern (23 bp):
AAACACTAAACCCCAAAAAACAT
Found at i:171341317 original size:115 final size:115
Alignment explanation
Indices: 171340838--171341376 Score: 508
Period size: 114 Copynumber: 4.7 Consensus size: 115
171340828 AGACGACACC
* * *
171340838 GTTTTCTTTGGATTTTTAGTGGCGTTTTAGGTTAAAACGCCACAATAGGGTTG-ATTTAGCGGCG
1 GTTTT-TTTGGATTTTTAGTGGCGTTTTAGGTTAAAACGCCGCAATAGGTTTGCCTTTAGCGGCG
* * * * * *
171340902 C-AAGGTTATAAACGCCACTAAGGGTTATTTTGTTTAGATCAAAACGGTGTA
65 CTAAGG-TAAAAACGCCACTAAAGTTTATTCTGTTTATATCAAAACGATGTA
* * * * * *
171340953 GTTTTTATGGATTTTTAGTGGCGTTTTTGGTTCAAACGCCACAATAGGTTTG-ATTTAGTGGCGC
1 GTTTTTTTGGATTTTTAGTGGCGTTTTAGGTTAAAACGCCGCAATAGGTTTGCCTTTAGCGGCGC
* * *
171341017 TAAGGTATAAACGCCACTAATGGTTAATT-TGTTTATATCAAAACGATGTA
66 TAAGGTAAAAACGCCACTAA-AGTTTATTCTGTTTATATCAAAACGATGTA
* * * * * * *
171341067 GTTTTATTCGATTATTAGTGGTGTTTTAGGGTAAAACGCCGGAATA-GTTTCGCCTTTAGCAGCG
1 GTTTTTTTGGATTTTTAGTGGCGTTTTAGGTTAAAACGCCGCAATAGGTTT-GCCTTTAGCGGCG
* * * *
171341131 CTTA-GTGATAAAACGCCACTAAA-TGTTATTCTGTTCATATGAAAAC-ATCGTC
65 CTAAGGT-A-AAAACGCCACTAAAGT-TTATTCTGTTTATATCAAAACGAT-GTA
* * * * *
171341183 GTTTTTTTTGGATTTTTAGTGGCGTTTTAGGGTGAAACGCTGCAATTGATTTGCCTTTAGCGGCG
1 G-TTTTTTTGGATTTTTAGTGGCGTTTTAGGTTAAAACGCCGCAATAGGTTTGCCTTTAGCGGCG
* *
171341248 CTACGG-AAAAACGCCACTAAAGTTTATTCTGTTTATATCAAAACGGTGTCA
65 CTAAGGTAAAAACGCCACTAAAGTTTATTCTGTTTATATCAAAACGATGT-A
** * * * *
171341299 -TTTTGTTTGTTTTTTTAGTGGCG-TTTATGTTAAAACGTCGTAATTGGTTTGCCTTTAGCGGCG
1 GTTTT-TTTGGATTTTTAGTGGCGTTTTAGGTTAAAACGCCGCAATAGGTTTGCCTTTAGCGGCG
*
171341362 CT-AGGTGAAAACGCC
65 CTAAGGTAAAAACGCC
171341377 GCAAATGTTA
Statistics
Matches: 351, Mismatches: 56, Indels: 35
0.79 0.13 0.08
Matches are distributed among these distances:
113 6 0.02
114 175 0.50
115 84 0.24
116 31 0.09
117 51 0.15
118 4 0.01
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.37
Consensus pattern (115 bp):
GTTTTTTTGGATTTTTAGTGGCGTTTTAGGTTAAAACGCCGCAATAGGTTTGCCTTTAGCGGCGC
TAAGGTAAAAACGCCACTAAAGTTTATTCTGTTTATATCAAAACGATGTA
Found at i:171341512 original size:59 final size:59
Alignment explanation
Indices: 171341445--171341574 Score: 172
Period size: 59 Copynumber: 2.2 Consensus size: 59
171341435 ACACCGAGTT
* ** *
171341445 CCCCCTTCTCCCTGGTTTATTTCCCCT-ATTTTCCCTTCTTCGAATCCCTAAAATAATCA
1 CCCCCTTCTCCCTAGTTTA-TTCCCCTCATTTTCCCTAATTCGAAACCCTAAAATAATCA
* * *
171341504 CCCCCTTCTCCCTAGTTTATTCCCTTCATTTTCCCTAATTTGAAACCCTAAAATAATTA
1 CCCCCTTCTCCCTAGTTTATTCCCCTCATTTTCCCTAATTCGAAACCCTAAAATAATCA
*
171341563 CCCCTTTCTCCC
1 CCCCCTTCTCCC
171341575 CAATTTGAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
58 6 0.10
59 56 0.90
ACGTcount: A:0.20, C:0.38, G:0.04, T:0.38
Consensus pattern (59 bp):
CCCCCTTCTCCCTAGTTTATTCCCCTCATTTTCCCTAATTCGAAACCCTAAAATAATCA
Found at i:171343981 original size:13 final size:13
Alignment explanation
Indices: 171343963--171343992 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
171343953 TTACATAATA
171343963 CATAAATATATAT
1 CATAAATATATAT
171343976 CATAAATATATAT
1 CATAAATATATAT
171343989 CATA
1 CATA
171343993 TCATAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (13 bp):
CATAAATATATAT
Found at i:171344109 original size:113 final size:111
Alignment explanation
Indices: 171343939--171344148 Score: 350
Period size: 113 Copynumber: 1.9 Consensus size: 111
171343929 TAATAAGTTA
171343939 CATAACTTACAAAATTACATAATACATAAATATATATCATAAATATATATCATATCATAACTTAC
1 CATAACTTACAAAATTACATAATACATAAATATATATCATAAATATATATCATATCATAACTTAC
*
171344004 ACAACTAACATAATACATAAATATATTTCATAAATATGTATCATAT
66 ACAACTAACATAATACATAAATATATATCATAAATATGTATCATAT
* *
171344050 CATAACTTACACAACTTACATAATAC-TCCAAATATATATCATAAATATATATCTTATCATAACT
1 CATAACTTACA-AAATTACATAATACAT--AAATATATATCATAAATATATATCATATCATAACT
*
171344114 TACACAACTTACATAATACATAAATATATATCATA
63 TACACAACTAACATAATACATAAATATATATCATA
171344149 TCATAACTTA
Statistics
Matches: 92, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
111 12 0.13
112 13 0.14
113 67 0.73
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (111 bp):
CATAACTTACAAAATTACATAATACATAAATATATATCATAAATATATATCATATCATAACTTAC
ACAACTAACATAATACATAAATATATATCATAAATATGTATCATAT
Found at i:171344110 original size:57 final size:56
Alignment explanation
Indices: 171343939--171344148 Score: 343
Period size: 56 Copynumber: 3.8 Consensus size: 56
171343929 TAATAAGTTA
*
171343939 CATAACTTACA-AAATTACATAATACATAAATATATATCATAAATATATATCATAT
1 CATAACTTACACAACTTACATAATACATAAATATATATCATAAATATATATCATAT
* * *
171343994 CATAACTTACACAACTAACATAATACATAAATATATTTCATAAATATGTATCATAT
1 CATAACTTACACAACTTACATAATACATAAATATATATCATAAATATATATCATAT
*
171344050 CATAACTTACACAACTTACATAATAC-TCCAAATATATATCATAAATATATATCTTAT
1 CATAACTTACACAACTTACATAATACAT--AAATATATATCATAAATATATATCATAT
171344107 CATAACTTACACAACTTACATAATACATAAATATATATCATA
1 CATAACTTACACAACTTACATAATACATAAATATATATCATA
171344149 TCATAACTTA
Statistics
Matches: 143, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
55 12 0.08
56 79 0.55
57 51 0.36
58 1 0.01
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (56 bp):
CATAACTTACACAACTTACATAATACATAAATATATATCATAAATATATATCATAT
Found at i:171344185 original size:113 final size:106
Alignment explanation
Indices: 171343918--171344161 Score: 328
Period size: 113 Copynumber: 2.2 Consensus size: 106
171343908 TAATATTTAT
*
171343918 TATATATCATATAATAAGTTACATAACTTACAAAATTACATAATACATAAATATATATCATAAAT
1 TATATATCATAT-ATAACTTACATAACTTACAAAATTACATAATACATAAATATATATCATAAAT
171343983 ATATATCATATCATAACTTACACAACTAACATAATACATAAA
65 ATATATCATATCATAACTTACACAACTAACATAATACATAAA
* * * *
171344025 TATATTTCATAAATATGTATCATATCATAACTTACACAACTTACATAATAC-TCCAAATATATAT
1 TATATATCAT--ATA--TAACTTA-CATAACTTACA-AAATTACATAATACAT--AAATATATAT
* *
171344089 CATAAATATATATCTTATCATAACTTACACAACTTACATAATACATAAA
58 CATAAATATATATCATATCATAACTTACACAACTAACATAATACATAAA
171344138 TATATATCATATCATAACTTACAT
1 TATATATCATAT-ATAACTTACAT
171344162 GCCTTACATA
Statistics
Matches: 118, Mismatches: 10, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
107 9 0.08
108 1 0.01
109 5 0.04
110 9 0.08
111 14 0.12
112 14 0.12
113 66 0.56
ACGTcount: A:0.48, C:0.16, G:0.01, T:0.35
Consensus pattern (106 bp):
TATATATCATATATAACTTACATAACTTACAAAATTACATAATACATAAATATATATCATAAATA
TATATCATATCATAACTTACACAACTAACATAATACATAAA
Found at i:171344199 original size:9 final size:9
Alignment explanation
Indices: 171344102--171344222 Score: 63
Period size: 9 Copynumber: 13.6 Consensus size: 9
171344092 AAATATATAT
171344102 CTTATCATAA
1 CTTA-CATAA
*
171344112 CTTACACAA
1 CTTACATAA
171344121 CTTACATAA
1 CTTACATAA
171344130 --TACATAA
1 CTTACATAA
* * *
171344137 -ATATATAT
1 CTTACATAA
*
171344145 CATATCATAA
1 CTTA-CATAA
**
171344155 CTTACATGC
1 CTTACATAA
171344164 CTTACATAA
1 CTTACATAA
* * *
171344173 ATGTATATCA
1 CT-TACATAA
*
171344183 -TAACATAA
1 CTTACATAA
171344191 CTTACATAA
1 CTTACATAA
171344200 CTTACA-AA
1 CTTACATAA
*
171344208 GCTTACTTAA
1 -CTTACATAA
171344218 CTTAC
1 CTTAC
171344223 TTAATATAAA
Statistics
Matches: 85, Mismatches: 19, Indels: 15
0.71 0.16 0.13
Matches are distributed among these distances:
7 7 0.08
8 11 0.13
9 50 0.59
10 17 0.20
ACGTcount: A:0.43, C:0.21, G:0.02, T:0.34
Consensus pattern (9 bp):
CTTACATAA
Found at i:171344204 original size:36 final size:36
Alignment explanation
Indices: 171344119--171344205 Score: 124
Period size: 36 Copynumber: 2.5 Consensus size: 36
171344109 TAACTTACAC
*
171344119 AACTTACATAA--TACATAAATATATATCATATCAT
1 AACTTACATAACTTACATAAATATATATCATAACAT
** *
171344153 AACTTACATGCCTTACATAAATGTATATCATAACAT
1 AACTTACATAACTTACATAAATATATATCATAACAT
171344189 AACTTACATAACTTACA
1 AACTTACATAACTTACA
171344206 AAGCTTACTT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 9 0.20
36 36 0.80
ACGTcount: A:0.46, C:0.18, G:0.02, T:0.33
Consensus pattern (36 bp):
AACTTACATAACTTACATAAATATATATCATAACAT
Found at i:171344247 original size:30 final size:32
Alignment explanation
Indices: 171344211--171344271 Score: 108
Period size: 30 Copynumber: 2.0 Consensus size: 32
171344201 TTACAAAGCT
171344211 TACTTAACTTACTT-A-ATATAAATATACACC
1 TACTTAACTTACTTAATATATAAATATACACC
171344241 TACTTAACTTACTTAATATATAAATATACAC
1 TACTTAACTTACTTAATATATAAATATACAC
171344272 TTGAAAATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 14 0.48
31 1 0.03
32 14 0.48
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (32 bp):
TACTTAACTTACTTAATATATAAATATACACC
Found at i:171352086 original size:40 final size:40
Alignment explanation
Indices: 171352041--171352208 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
171352031 CGGAATATAA
171352041 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
171352081 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
171352121 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
171352161 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
171352201 CCGGATAT
1 CCGGATAT
171352209 CATTCAATTT
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 106 0.99
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:171360075 original size:40 final size:40
Alignment explanation
Indices: 171360030--171360197 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
171360020 CGGAATATAA
171360030 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
171360070 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
171360110 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
171360150 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
171360190 CCGGATAT
1 CCGGATAT
171360198 CATTCAATTT
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 106 0.99
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:171367071 original size:27 final size:25
Alignment explanation
Indices: 171367016--171367071 Score: 58
Period size: 27 Copynumber: 2.2 Consensus size: 25
171367006 CAACCTTAAC
* *
171367016 CCTAGGGTATATCAGTAATTTTACT
1 CCTAGGGTAAATCAGTAATTTTACA
* *
171367041 CCTAGGGGTAAATCTGTAAATTTTCCA
1 CCTA-GGGTAAATCAGT-AATTTTACA
171367068 CCTA
1 CCTA
171367072 TAAAGGTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 4 0.16
26 10 0.40
27 11 0.44
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.36
Consensus pattern (25 bp):
CCTAGGGTAAATCAGTAATTTTACA
Found at i:171380808 original size:46 final size:46
Alignment explanation
Indices: 171380741--171380830 Score: 171
Period size: 46 Copynumber: 2.0 Consensus size: 46
171380731 TGAAGCAAAG
*
171380741 TAAGTTGGTGTATTGAAGATAATTATTTTGAAGATCCGATTGAATC
1 TAAGTTGGTGTATTGAAGATAATTATTCTGAAGATCCGATTGAATC
171380787 TAAGTTGGTGTATTGAAGATAATTATTCTGAAGATCCGATTGAA
1 TAAGTTGGTGTATTGAAGATAATTATTCTGAAGATCCGATTGAA
171380831 GCTGAGTCTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.38
Consensus pattern (46 bp):
TAAGTTGGTGTATTGAAGATAATTATTCTGAAGATCCGATTGAATC
Found at i:171381618 original size:16 final size:17
Alignment explanation
Indices: 171381597--171381638 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
171381587 AATTATGTGT
171381597 ATTAATTTATAA-TATA
1 ATTAATTTATAATTATA
*
171381613 ATTAATTT-TAATTTTA
1 ATTAATTTATAATTATA
171381629 ATTCAATTTA
1 ATT-AATTTA
171381639 ATTTGGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 3 0.14
16 14 0.64
17 5 0.23
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTAATTTATAATTATA
Found at i:171382342 original size:20 final size:18
Alignment explanation
Indices: 171382309--171382345 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
171382299 TGTGATGTTG
171382309 ATATGTTTAATTTAATTA
1 ATATGTTTAATTTAATTA
171382327 ATATGTTTTCAATTTAATT
1 ATATG-TTT-AATTTAATT
171382346 TGTGTTAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 3 0.18
20 9 0.53
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (18 bp):
ATATGTTTAATTTAATTA
Found at i:171385031 original size:47 final size:45
Alignment explanation
Indices: 171384875--171385139 Score: 177
Period size: 47 Copynumber: 5.7 Consensus size: 45
171384865 CTGTTTTATC
* *
171384875 CCGATGCCATGTCCCAGACATGGTCTTACACTGGC-TCTCATATACGCGTG
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTAGCATCTC-T-T-CGAG-G
* *
171384925 CTGATGCATGTCCCAGACATGTCTTACACTAGCACAACTCTT--A-G
1 CCGATGCATGTCCCAGACATGTCTTACACTAG--CATCTCTTCGAGG
* *
171384969 CCGATGCGTGTCCCAGACACGTCTTACACTAGCTATCTCTGTCGAGG
1 CCGATGCATGTCCCAGACATGTCTTACACTAGC-ATCTCT-TCGAGG
* *
171385016 CCGATGCATGTCCCAGACATGTCTTACACTGGCA-CTCATCTCTG-TG
1 CCGATGCATGTCCCAGACATGTCTTACACTAGCATCTC-T-TC-GAGG
** * * * *
171385062 TTGATGCCATATCCTAGACATGGTCTTACACTGGC-TCTCATAAT-GTGG
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTAGCATCTC-T--TCGAGG
*
171385110 CCGAAGCATGTCCCAGACATGTCTTACACT
1 CCGATGCATGTCCCAGACATGTCTTACACT
171385140 GGCGCACAAA
Statistics
Matches: 176, Mismatches: 24, Indels: 34
0.75 0.10 0.15
Matches are distributed among these distances:
42 1 0.01
43 5 0.03
44 31 0.18
45 3 0.02
46 20 0.11
47 57 0.32
48 33 0.19
49 16 0.09
50 7 0.04
51 3 0.02
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (45 bp):
CCGATGCATGTCCCAGACATGTCTTACACTAGCATCTCTTCGAGG
Found at i:171385131 original size:94 final size:92
Alignment explanation
Indices: 171384875--171385142 Score: 294
Period size: 94 Copynumber: 2.9 Consensus size: 92
171384865 CTGTTTTATC
* * *
171384875 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATACGCGTGCTGATGCATGTCCCA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATA-ATGAG-GCCGATGCATGTCCCA
*
171384940 GACATGTCTTACACTAGCACAACTCTTAG
64 GACATGTCTTACACTGGCACAACTCTTAG
* * * *
171384969 CCGATG-CGTGTCCCAGACA-CGTCTTACACTAGCTATCTC-T-GTCGAGGCCGATGCATGTCCC
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGC--TCTCATAAT-GAGGCCGATGCATGTCCC
*
171385030 AGACATGTCTTACACTGGCACTCATCTCTGT-G
63 AGACATGTCTTACACTGGCA--CAACTCT-TAG
** * * * *
171385062 TTGATGCCATATCCTAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGAAGCATGTCCCAGA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGAGGCCGATGCATGTCCCAGA
171385127 CATGTCTTACACTGGC
66 CATGTCTTACACTGGC
171385143 GCACAAATCA
Statistics
Matches: 145, Mismatches: 19, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
91 33 0.23
92 14 0.10
93 28 0.19
94 57 0.39
95 13 0.09
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (92 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGAGGCCGATGCATGTCCCAGA
CATGTCTTACACTGGCACAACTCTTAG
Found at i:171385523 original size:30 final size:30
Alignment explanation
Indices: 171385482--171385539 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
171385472 AAATTTACAT
* *
171385482 CTTTGGTAAAATGACCATTTTGCCCCTAGA
1 CTTTGGCAAAATGACCATTTTACCCCTAGA
171385512 CTTTGGCAAAATGACCATTTTACCCCTA
1 CTTTGGCAAAATGACCATTTTACCCCTA
171385540 TGCCTGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CTTTGGCAAAATGACCATTTTACCCCTAGA
Found at i:171389057 original size:40 final size:40
Alignment explanation
Indices: 171389012--171389178 Score: 176
Period size: 40 Copynumber: 4.2 Consensus size: 40
171389002 CGGAATATAA
171389012 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
171389052 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
171389092 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
171389132 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
171389171 CCGGATAT
1 CCGGATAT
171389179 CATTCAATTT
Statistics
Matches: 105, Mismatches: 21, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
39 14 0.13
40 91 0.87
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:171399508 original size:71 final size:71
Alignment explanation
Indices: 171399424--171399587 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
171399414 CGATTTGTCT
171399424 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
171399489 CTTTCA
66 CTTTCA
171399495 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
171399560 CTTTCA
66 CTTTCA
171399566 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
171399588 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:171399625 original size:71 final size:70
Alignment explanation
Indices: 171399424--171399621 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
171399414 CGATTTGTCT
* * * *
171399424 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
171399489 CTTTCA
65 CTTTCA
* * * *
171399495 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
171399560 CTTTCA
65 CTTTCA
* *
171399566 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
171399622 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:171401117 original size:18 final size:19
Alignment explanation
Indices: 171401096--171401133 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
171401086 TTTTAATTAT
*
171401096 TTTTATGGTTTT-TTTTAC
1 TTTTATGATTTTATTTTAC
*
171401114 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
171401133 T
1 T
171401134 ATGGTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:171402513 original size:15 final size:16
Alignment explanation
Indices: 171402484--171402515 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
171402474 AGTTTATGCT
171402484 AAGTAAATGAAATGGA
1 AAGTAAATGAAATGGA
171402500 AAGTAAAT-AAATGGA
1 AAGTAAATGAAATGGA
171402515 A
1 A
171402516 TGACAAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (16 bp):
AAGTAAATGAAATGGA
Found at i:171402533 original size:20 final size:20
Alignment explanation
Indices: 171402483--171402534 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
171402473 AAGTTTATGC
*
171402483 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGGAATGGAAAG
*
171402503 TAAATAAATGGAAT-GACAAG
1 TAAGTAAATGGAATGGA-AAG
171402523 TAAGTAAATGGA
1 TAAGTAAATGGA
171402535 GTGTAACAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.54, C:0.02, G:0.23, T:0.21
Consensus pattern (20 bp):
TAAGTAAATGGAATGGAAAG
Found at i:171402933 original size:38 final size:38
Alignment explanation
Indices: 171402890--171402966 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
171402880 ATAAATAAGG
*
171402890 TTAGTAAAATAATGAAAACAAATGCCATCATCTTTGTT
1 TTAGTAAAATAATGAAAACAAAGGCCATCATCTTTGTT
171402928 TTAGTAAAATAATGAAAACAAAGGCCATCATCTTTGTT
1 TTAGTAAAATAATGAAAACAAAGGCCATCATCTTTGTT
171402966 T
1 T
171402967 GTCCATTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.34
Consensus pattern (38 bp):
TTAGTAAAATAATGAAAACAAAGGCCATCATCTTTGTT
Found at i:171404932 original size:27 final size:26
Alignment explanation
Indices: 171404897--171405008 Score: 143
Period size: 27 Copynumber: 4.2 Consensus size: 26
171404887 AGCATGGCTG
* *
171404897 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
171404923 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
171404951 CCAGAACAGAAATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
171404978 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
171405005 CCAG
1 CCAG
171405009 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 6 0.08
27 53 0.70
28 17 0.22
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:171404989 original size:54 final size:54
Alignment explanation
Indices: 171404897--171405008 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
171404887 AGCATGGCTG
* *
171404897 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* * *
171404951 CCAGAACAGAAATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGAACAGAAA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
171405005 CCAG
1 CCAG
171405009 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (54 bp):
CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
Found at i:171406298 original size:19 final size:19
Alignment explanation
Indices: 171406274--171406317 Score: 74
Period size: 17 Copynumber: 2.4 Consensus size: 19
171406264 AAAAAGGTTG
171406274 ATGAAGAGAGGGGAGAAAA
1 ATGAAGAGAGGGGAGAAAA
171406293 ATG-A-AGAGGGGAGAAAA
1 ATGAAGAGAGGGGAGAAAA
171406310 ATGAAGAG
1 ATGAAGAG
171406318 GGAAATGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 16 0.70
18 2 0.09
19 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.41, T:0.07
Consensus pattern (19 bp):
ATGAAGAGAGGGGAGAAAA
Found at i:171406320 original size:16 final size:17
Alignment explanation
Indices: 171406280--171406319 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
171406270 GTTGATGAAG
171406280 AGAGGGGAGAAAAATGA
1 AGAGGGGAGAAAAATGA
171406297 AGAGGGGAGAAAAATGA
1 AGAGGGGAGAAAAATGA
171406314 AGAGGG
1 AGAGGG
171406320 AAATGGTCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.45, T:0.05
Consensus pattern (17 bp):
AGAGGGGAGAAAAATGA
Found at i:171412833 original size:27 final size:26
Alignment explanation
Indices: 171412798--171412909 Score: 143
Period size: 27 Copynumber: 4.2 Consensus size: 26
171412788 AGCATGGCTG
* *
171412798 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
171412824 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
171412852 CCAGAACAGAAATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
171412879 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
171412906 CCAG
1 CCAG
171412910 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 6 0.08
27 53 0.70
28 17 0.22
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:171412890 original size:54 final size:54
Alignment explanation
Indices: 171412798--171412909 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
171412788 AGCATGGCTG
* *
171412798 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* * *
171412852 CCAGAACAGAAATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGAACAGAAA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
171412906 CCAG
1 CCAG
171412910 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (54 bp):
CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
Found at i:171416377 original size:35 final size:35
Alignment explanation
Indices: 171416331--171416400 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
171416321 TTTAGACCCT
171416331 ATTCAGAATGGTGGTTTCGAGACCACGAATCTGAG
1 ATTCAGAATGGTGGTTTCGAGACCACGAATCTGAG
171416366 ATTCAGAATGGTGGTTTCGAGACCACGAATCTGAG
1 ATTCAGAATGGTGGTTTCGAGACCACGAATCTGAG
171416401 TCAAAAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (35 bp):
ATTCAGAATGGTGGTTTCGAGACCACGAATCTGAG
Found at i:171416464 original size:15 final size:15
Alignment explanation
Indices: 171416432--171416460 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
171416422 ATTTTTAGTG
171416432 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
171416447 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
171416461 ATTTTTGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Done.