Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 109 of 297
Found at i:39142217 original size:44 final size:41
Alignment explanation
Indices: 39142168--39142266 Score: 110
Period size: 40 Copynumber: 2.4 Consensus size: 41
39142158 GAACGATTCT
**
39142168 GCACACTTAGTGCCATCTCAACTAACCGAAGCTAAGTTGGTATC
1 GCACACTTAGTGCCAT-T-AACTAACCGAAGCTAA-TTGAAATC
* * * *
39142212 GCACACTTAGTGCC-TTTAGTAGCCGAAGCTAATTTAAATC
1 GCACACTTAGTGCCATTAACTAACCGAAGCTAATTGAAATC
39142252 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
39142267 AATACTTTCG
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
40 19 0.40
41 13 0.27
42 1 0.02
43 1 0.02
44 14 0.29
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (41 bp):
GCACACTTAGTGCCATTAACTAACCGAAGCTAATTGAAATC
Found at i:39149385 original size:42 final size:42
Alignment explanation
Indices: 39149283--39149434 Score: 137
Period size: 43 Copynumber: 3.6 Consensus size: 42
39149273 TACAATGTCG
* * * *
39149283 ATGTCCTAGACGTGGTCTTACATGTAATTCAATACCGATGCCT
1 ATGTCCCAGACATGGTCTTACACGTAAATCAATA-CGATGCCT
* * * * *
39149326 CTGTCCCAAATAGGGTCTTACACG-AAATCAAATACGATGCCA
1 ATGTCCCAGACATGGTCTTACACGTAAATC-AATACGATGCCT
* *
39149368 ATGTCCCAGACATGGTCTTATACGTAAATCTCAAT-CGAGGCCT
1 ATGTCCCAGACATGGTCTTACACGTAAA--TCAATACGATGCCT
* *
39149411 GTGTCCCAGACAAGGTCTTACACG
1 ATGTCCCAGACATGGTCTTACACG
39149435 ATATCTCAGA
Statistics
Matches: 86, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
42 30 0.35
43 51 0.59
44 3 0.03
45 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (42 bp):
ATGTCCCAGACATGGTCTTACACGTAAATCAATACGATGCCT
Found at i:39150506 original size:21 final size:21
Alignment explanation
Indices: 39150482--39150530 Score: 80
Period size: 22 Copynumber: 2.3 Consensus size: 21
39150472 ATTTTTTCAT
39150482 AATTAAGCACAGAAATAGACA
1 AATTAAGCACAGAAATAGACA
*
39150503 AATTAAATCACAGAAATAGACA
1 AATT-AAGCACAGAAATAGACA
39150525 AATTAA
1 AATTAA
39150531 ATCACATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.59, C:0.12, G:0.10, T:0.18
Consensus pattern (21 bp):
AATTAAGCACAGAAATAGACA
Found at i:39150516 original size:22 final size:22
Alignment explanation
Indices: 39150489--39150541 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
39150479 CATAATTAAG
39150489 CACAGAAATAGACAAATTAAAT
1 CACAGAAATAGACAAATTAAAT
39150511 CACAGAAATAGACAAATTAAAT
1 CACAGAAATAGACAAATTAAAT
*
39150533 CACATAAAT
1 CACAGAAAT
39150542 TTTCACAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.58, C:0.15, G:0.08, T:0.19
Consensus pattern (22 bp):
CACAGAAATAGACAAATTAAAT
Found at i:39164121 original size:79 final size:78
Alignment explanation
Indices: 39164019--39164241 Score: 272
Period size: 79 Copynumber: 2.8 Consensus size: 78
39164009 GCTCCTCGTT
* *
39164019 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
39164084 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
* *
39164099 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
*
39164163 ATTAGTATCTCGCA
65 ATTAGTAACTCGCA
* * * * *
39164177 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
39164240 GA
63 GA
39164242 CATCATTCAA
Statistics
Matches: 125, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
78 45 0.36
79 60 0.48
80 20 0.16
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:39164136 original size:39 final size:40
Alignment explanation
Indices: 39164019--39164241 Score: 280
Period size: 39 Copynumber: 5.7 Consensus size: 40
39164009 GCTCCTCGTT
* *
39164019 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
39164059 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
39164099 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
39164138 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * *
39164177 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAAC-TCGCA
39164218 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39164242 CATCATTCAA
Statistics
Matches: 167, Mismatches: 10, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
38 2 0.01
39 88 0.53
40 67 0.40
41 10 0.06
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:39172250 original size:29 final size:29
Alignment explanation
Indices: 39172187--39172254 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
39172177 TAATCAACCG
39172187 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
39172216 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
39172245 CGCACACTTA
1 CGCACACTTA
39172255 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:39172366 original size:174 final size:174
Alignment explanation
Indices: 39172076--39172403 Score: 629
Period size: 174 Copynumber: 1.9 Consensus size: 174
39172066 AACTCAAGGT
*
39172076 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
39172141 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
39172206 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
39172250 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
39172315 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
*
39172380 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
39172404 TGTACAATTT
Statistics
Matches: 151, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 151 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:39172395 original size:29 final size:30
Alignment explanation
Indices: 39172356--39172434 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
39172346 CTTAATAATC
39172356 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
39172386 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
39172415 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
39172435 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:39180189 original size:27 final size:27
Alignment explanation
Indices: 39180159--39180336 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
39180149 ATATTGAGTC
* * * *
39180159 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
39180186 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
39180213 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
39180241 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
39180268 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
39180295 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
39180322 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39180337 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:39180298 original size:82 final size:81
Alignment explanation
Indices: 39180180--39180335 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
39180170 TGCTATATAA
* *
39180180 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
39180245 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
39180262 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
39180326 CACTTAGTGC
65 CACTTAGTGC
39180336 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:39180837 original size:12 final size:12
Alignment explanation
Indices: 39180820--39180846 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
39180810 ATGGCATACT
39180820 TATGTATATATA
1 TATGTATATATA
39180832 TATGTATATATA
1 TATGTATATATA
39180844 TAT
1 TAT
39180847 ACTTCGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATGTATATATA
Found at i:39183704 original size:46 final size:47
Alignment explanation
Indices: 39183561--39183780 Score: 145
Period size: 46 Copynumber: 4.7 Consensus size: 47
39183551 GGTAGGATGT
* *
39183561 CGATGCCATGTCCCAAACATGGTCTTACGCTAGCT-T--TACTC-GTAGC
1 CGATG-CATGTCCCAAACAT-GTCTTACACTAGCTCTCGT-CTCAATAGC
* * * * * * *
39183607 CAATGCATGTCCCAGACATGTCTTACATTGGCT-TACATCTCGA-GGC
1 CGATGCATGTCCCAAACATGTCTTACACTAGCTCT-CGTCTCAATAGC
*
39183653 TGATGCATGTCCCAAACATGTCTTACACTAGCTCTCGTCTCAAT-GC
1 CGATGCATGTCCCAAACATGTCTTACACTAGCTCTCGTCTCAATAGC
*** * *
39183699 CGATGCCATGTCTTGAACATGGTCTTACACTGGCTCTCG--T-AATGTGGC
1 CGATG-CATGTCCCAAACAT-GTCTTACACTAGCTCTCGTCTCAA--TAGC
* *
39183747 CGATGCATGTCCTAGACATGTCTTACACTAGCTC
1 CGATGCATGTCCCAAACATGTCTTACACTAGCTC
39183781 ACAATAGTCC
Statistics
Matches: 140, Mismatches: 23, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
44 12 0.09
45 15 0.11
46 64 0.46
47 25 0.18
48 24 0.17
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.30
Consensus pattern (47 bp):
CGATGCATGTCCCAAACATGTCTTACACTAGCTCTCGTCTCAATAGC
Found at i:39188892 original size:38 final size:38
Alignment explanation
Indices: 39188850--39189030 Score: 254
Period size: 38 Copynumber: 4.8 Consensus size: 38
39188840 TTTGGGCTAA
**
39188850 ATCCCGCAGGCTTAATGCTGGTATTATATCCGGGTTTT
1 ATCCCGCAGGCTTCGTGCTGGTATTATATCCGGGTTTT
*
39188888 ATCCCGCAGGCTTCGTGCTGGTATTATATCCGAGTTTT
1 ATCCCGCAGGCTTCGTGCTGGTATTATATCCGGGTTTT
* * **
39188926 ATCCCACAGGCTTCGTGCTAGTATTATATTTGGGTTTT
1 ATCCCGCAGGCTTCGTGCTGGTATTATATCCGGGTTTT
** **
39188964 ATCCTACAGGCTTCGTGCTGGTATTATATCCGGGTTAA
1 ATCCCGCAGGCTTCGTGCTGGTATTATATCCGGGTTTT
*
39189002 ATCCCGCAGGCTTAGTGCTGGTATTATAT
1 ATCCCGCAGGCTTCGTGCTGGTATTATAT
39189031 TCGAGCTTAA
Statistics
Matches: 126, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 126 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (38 bp):
ATCCCGCAGGCTTCGTGCTGGTATTATATCCGGGTTTT
Found at i:39189060 original size:40 final size:38
Alignment explanation
Indices: 39188847--39189063 Score: 204
Period size: 38 Copynumber: 5.7 Consensus size: 38
39188837 ATATTTGGGC
** *
39188847 TAAATCCCGCAGGCTTAATGCTGGTATTATATCCGGGT
1 TAAATCCCGCAGGCTTCGTGCTGGTATTATATCCGGCT
**
39188885 TTTATCCCGCAGGCTTCGTGCTGGTATTATATCCGAG-T
1 TAAATCCCGCAGGCTTCGTGCTGGTATTATATCCG-GCT
** * * ** *
39188923 TTTATCCCACAGGCTTCGTGCTAGTATTATATTTGGGT
1 TAAATCCCGCAGGCTTCGTGCTGGTATTATATCCGGCT
** ** *
39188961 TTTATCCTACAGGCTTCGTGCTGGTATTATATCCGGGT
1 TAAATCCCGCAGGCTTCGTGCTGGTATTATATCCGGCT
* *
39188999 TAAATCCCGCAGGCTTAGTGCTGGTATTATATTCGAGCT
1 TAAATCCCGCAGGCTTCGTGCTGGTATTATATCCG-GCT
*
39189038 TAAAGTTCCGCAGG-TTCTGTGCTGGT
1 TAAA-TCCCGCAGGCTTC-GTGCTGGT
39189064 GACTGGATTC
Statistics
Matches: 153, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
37 1 0.01
38 127 0.83
39 9 0.06
40 16 0.10
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (38 bp):
TAAATCCCGCAGGCTTCGTGCTGGTATTATATCCGGCT
Found at i:39194561 original size:38 final size:37
Alignment explanation
Indices: 39194505--39194699 Score: 237
Period size: 38 Copynumber: 5.1 Consensus size: 37
39194495 ATATTTGATG
**
39194505 TATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTAT
1 TATATCC-GGTTTTATCCCGCAGGCTTAGTGCTGGTAT
*
39194543 TATATCCAGGTTTTATCCCGCAGGCTTCGTGCTGGTAT
1 TATATCC-GGTTTTATCCCGCAGGCTTAGTGCTGGTAT
* *
39194581 TATATCCGAGTTTTATCTCGCAGGCTTCGTGCTGGTAT
1 TATATCCG-GTTTTATCCCGCAGGCTTAGTGCTGGTAT
***
39194619 TATATCCGGGTTTTATCCTATAGGCTTAGTGCTGGTAT
1 TATATCC-GGTTTTATCCCGCAGGCTTAGTGCTGGTAT
** * *
39194657 TATATCCGAGTTAAATCCCACAGGCTTAGTGTTGGTAT
1 TATATCCG-GTTTTATCCCGCAGGCTTAGTGCTGGTAT
39194695 TATAT
1 TATAT
39194700 TCGAGCTTAA
Statistics
Matches: 139, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
37 2 0.01
38 136 0.98
39 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.37
Consensus pattern (37 bp):
TATATCCGGTTTTATCCCGCAGGCTTAGTGCTGGTAT
Found at i:39194631 original size:76 final size:76
Alignment explanation
Indices: 39194505--39194699 Score: 282
Period size: 76 Copynumber: 2.6 Consensus size: 76
39194495 ATATTTGATG
* *
39194505 TATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGGTATTATATCCAGGTTTTATCCCGCAGGCTT
1 TATATCCGAGTTAAATCCCGCAGGCTTAGTGCTGGTATTATATCCAGGTTTTATCCCACAGGCTT
*
39194570 CGTGCTGGTAT
66 AGTGCTGGTAT
** * * * * *
39194581 TATATCCGAGTTTTATCTCGCAGGCTTCGTGCTGGTATTATATCCGGGTTTTATCCTATAGGCTT
1 TATATCCGAGTTAAATCCCGCAGGCTTAGTGCTGGTATTATATCCAGGTTTTATCCCACAGGCTT
39194646 AGTGCTGGTAT
66 AGTGCTGGTAT
* *
39194657 TATATCCGAGTTAAATCCCACAGGCTTAGTGTTGGTATTATAT
1 TATATCCGAGTTAAATCCCGCAGGCTTAGTGCTGGTATTATAT
39194700 TCGAGCTTAA
Statistics
Matches: 103, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
76 103 1.00
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.37
Consensus pattern (76 bp):
TATATCCGAGTTAAATCCCGCAGGCTTAGTGCTGGTATTATATCCAGGTTTTATCCCACAGGCTT
AGTGCTGGTAT
Found at i:39197655 original size:47 final size:47
Alignment explanation
Indices: 39197586--39197755 Score: 197
Period size: 47 Copynumber: 3.6 Consensus size: 47
39197576 ATATTTGAGT
39197586 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
* * * *
39197633 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G--
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCA
**
39197679 TCTAAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
* *
39197726 TCCGAGCTCGTTGAGTTGAGTCTGAGTTCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCG
39197756 CTTATGGGCG
Statistics
Matches: 100, Mismatches: 14, Indels: 18
0.76 0.11 0.14
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
45 3 0.03
46 26 0.26
47 54 0.54
48 3 0.03
50 4 0.04
51 3 0.03
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.29
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
Found at i:39197753 original size:93 final size:93
Alignment explanation
Indices: 39197590--39197762 Score: 328
Period size: 93 Copynumber: 1.9 Consensus size: 93
39197580 TTGAGTTCCG
39197590 AACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCGAGCTCGTTGAGTTGAGTC
1 AACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCGAGCTCGTTGAGTTGAGTC
39197655 CGAGTTCACTTATGGATGCGAACGTCTA
66 CGAGTTCACTTATGGATGCGAACGTCTA
39197683 AACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCGAGCTCGTTGAGTTGAGTC
1 AACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCGAGCTCGTTGAGTTGAGTC
* *
39197748 TGAGTTCGCTTATGG
66 CGAGTTCACTTATGG
39197763 GCGGGTTACA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
93 78 1.00
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.30
Consensus pattern (93 bp):
AACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCGAGCTCGTTGAGTTGAGTC
CGAGTTCACTTATGGATGCGAACGTCTA
Found at i:39199805 original size:15 final size:16
Alignment explanation
Indices: 39199785--39199817 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
39199775 AAATATATGG
39199785 TTAATGCTAGCCC-AA
1 TTAATGCTAGCCCGAA
39199800 TTAATGCTAGCCCGAA
1 TTAATGCTAGCCCGAA
39199816 TT
1 TT
39199818 CCCCGAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (16 bp):
TTAATGCTAGCCCGAA
Found at i:39201927 original size:42 final size:42
Alignment explanation
Indices: 39201814--39201962 Score: 149
Period size: 42 Copynumber: 3.5 Consensus size: 42
39201804 TAAATTATCG
* * * *
39201814 TGTAAGGCCGTGTCTGGGACACAGGCATCGATTTGAAATTTACG
1 TGTAAGACCATGTCTGGGACACAGGCATCGATCTG-AATTT-CA
*
39201858 TGTAAAACCATGTCTGGGACATC-GGCATCGTATCTG-ATTTCA
1 TGTAAGACCATGTCTGGGACA-CAGGCATCG-ATCTGAATTTCA
* * * *
39201900 TATAAGACCCTGTCTGGGACAGAGGCATCGATACTGAATTACA
1 TGTAAGACCATGTCTGGGACACAGGCATCGAT-CTGAATTTCA
*
39201943 TGTAAGACCATATCTGGGAC
1 TGTAAGACCATGTCTGGGAC
39201963 GTTGGCATTA
Statistics
Matches: 87, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
41 2 0.02
42 29 0.33
43 26 0.30
44 25 0.29
45 5 0.06
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACACAGGCATCGATCTGAATTTCA
Found at i:39207566 original size:17 final size:17
Alignment explanation
Indices: 39207546--39207585 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
39207536 CAAAATCACA
39207546 AAATACACATAATTTGC
1 AAATACACATAATTTGC
39207563 AAATACACATAATTTGC
1 AAATACACATAATTTGC
*
39207580 ACATAC
1 AAATAC
39207586 TCATGCTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.47, C:0.20, G:0.05, T:0.28
Consensus pattern (17 bp):
AAATACACATAATTTGC
Found at i:39211427 original size:8 final size:8
Alignment explanation
Indices: 39211401--39211440 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
39211391 CTAGATCGGT
*
39211401 AAAAGCCA
1 AAAAGCCG
39211409 AAAAGCCG
1 AAAAGCCG
*
39211417 AAAAGCTG
1 AAAAGCCG
*
39211425 AAATGCCG
1 AAAAGCCG
39211433 AAAAGCCG
1 AAAAGCCG
39211441 GCATTTCGAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.50, C:0.23, G:0.23, T:0.05
Consensus pattern (8 bp):
AAAAGCCG
Found at i:39213187 original size:68 final size:66
Alignment explanation
Indices: 39213115--39213286 Score: 170
Period size: 67 Copynumber: 2.6 Consensus size: 66
39213105 CATCATGTGT
* * * *
39213115 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
39213178 TGTAG
62 TGTAG
** * *
39213183 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCATGT
39213248 AG
65 AG
* * * *
39213250 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATG
39213287 GGTGGTATTG
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
64 24 0.27
65 3 0.03
66 17 0.19
67 32 0.36
68 13 0.15
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:39213220 original size:64 final size:64
Alignment explanation
Indices: 39213139--39213320 Score: 190
Period size: 67 Copynumber: 2.8 Consensus size: 64
39213129 AGACATTATG
* * *
39213139 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
39213203 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
39213268 AA
63 AA
* * * *
39213270 AT-TGGCTAGGTCACATGGGTGGTATTGA-GTGTTCACCATGT-GTACAAGAGA
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGA
39213321 TCTGAACTCT
Statistics
Matches: 96, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
62 1 0.01
63 17 0.18
64 25 0.26
66 20 0.21
67 33 0.34
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:39215046 original size:20 final size:21
Alignment explanation
Indices: 39215003--39215048 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
39214993 ACTGTTTTGT
39215003 TATGGG-CCAACTGTATTGAA
1 TATGGGCCCAACTGTATTGAA
*
39215023 -ATGGGCCCAACTGTGTT-AA
1 TATGGGCCCAACTGTATTGAA
39215042 TATGGGC
1 TATGGGC
39215049 AAGGCCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGGGCCCAACTGTATTGAA
Found at i:39215141 original size:60 final size:61
Alignment explanation
Indices: 39215041--39215219 Score: 185
Period size: 60 Copynumber: 3.0 Consensus size: 61
39215031 AACTGTGTTA
* * * *
39215041 ATATGGGCAAGGCCCAATATA-TCTCGA-CTTGTAATAGGGCTACGGCCCAGATTGATACTG
1 ATATGGGCTAGGCCCAGTATACTCT-GATATTGTAATAGGGCTACGGCCCAGATTAATACTG
* * *
39215101 ATATGGGCTAGGCCCAGTATACTCTGATATTGTAA-GGGGCTATGGCCCAGATTAATATTG
1 ATATGGGCTAGGCCCAGTATACTCTGATATTGTAATAGGGCTACGGCCCAGATTAATACTG
*
39215161 ATATGGGCTAAGGCCCAGT-TAACTCTGAT-TTCTGAATAGGGCTTA-GGCCCAG--TAATACT
1 ATATGGGCT-AGGCCCAGTAT-ACTCTGATATTGT-AATAGGGC-TACGGCCCAGATTAATACT
39215220 TGAGCTGATT
Statistics
Matches: 102, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
60 61 0.60
61 28 0.27
62 11 0.11
63 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (61 bp):
ATATGGGCTAGGCCCAGTATACTCTGATATTGTAATAGGGCTACGGCCCAGATTAATACTG
Found at i:39215168 original size:28 final size:27
Alignment explanation
Indices: 39215077--39215182 Score: 81
Period size: 28 Copynumber: 3.7 Consensus size: 27
39215067 ACTTGTAATA
* *
39215077 GGGCTACGGCCCAGATTGATACTGATAT
1 GGGCTA-GGCCCAGATTAATATTGATAT
* *
39215105 GGGCTAGGCCCAGTATACTCTGATATTG-TAAG
1 GGGCTAGGCCCAG---A-T-TAATATTGAT-AT
39215137 GGGCTATGGCCCAGATTAATATTGATAT
1 GGGCTA-GGCCCAGATTAATATTGATAT
39215165 GGGCTAAGGCCCAG-TTAA
1 GGGCT-AGGCCCAGATTAA
39215183 CTCTGATTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 19
0.74 0.05 0.22
Matches are distributed among these distances:
27 11 0.17
28 26 0.40
29 3 0.05
30 2 0.03
31 2 0.03
32 14 0.22
33 7 0.11
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (27 bp):
GGGCTAGGCCCAGATTAATATTGATAT
Found at i:39215699 original size:78 final size:78
Alignment explanation
Indices: 39215606--39215761 Score: 285
Period size: 78 Copynumber: 2.0 Consensus size: 78
39215596 TTCAAAATTA
39215606 ATAACCTTTTTAAATGGTTTTAAACGAATTGGTTTTCCCTGAACAATCACTCAGTTAAAGTGTGG
1 ATAACCTTTTTAAATGGTTTTAAACGAATTGGTTTTCCCTGAACAATCACTCAGTTAAAGTGTGG
*
39215671 CAATGGTTTTGTG
66 CAATGGTTGTGTG
* *
39215684 ATAACCTTTTTAAATGGTTTTAAACGAATTGGTTTTCCCTGAATAATCACTCGGTTAAAGTGTGG
1 ATAACCTTTTTAAATGGTTTTAAACGAATTGGTTTTCCCTGAACAATCACTCAGTTAAAGTGTGG
39215749 CAATGGTTGTGTG
66 CAATGGTTGTGTG
39215762 CATGTCTAGG
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (78 bp):
ATAACCTTTTTAAATGGTTTTAAACGAATTGGTTTTCCCTGAACAATCACTCAGTTAAAGTGTGG
CAATGGTTGTGTG
Found at i:39215898 original size:17 final size:17
Alignment explanation
Indices: 39215876--39215909 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
39215866 AATCTATAAT
39215876 GAAGATATCCTTTAAAC
1 GAAGATATCCTTTAAAC
*
39215893 GAAGATATTCTTTAAAC
1 GAAGATATCCTTTAAAC
39215910 ACTAAGAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (17 bp):
GAAGATATCCTTTAAAC
Found at i:39220650 original size:56 final size:56
Alignment explanation
Indices: 39220590--39220715 Score: 162
Period size: 56 Copynumber: 2.2 Consensus size: 56
39220580 CCCAGACAGG
* * *
39220590 GTCTTACTCACACACATATAACGGAGTCACATATTGATGCCAACATATTAAACACA
1 GTCTTACTCGCACACATATAACGAAGTCACATATCGATGCCAACATATTAAACACA
* * * * * **
39220646 GTCTTAGTCGTACACATATATCGAATTCACATATCGATGCCAACGTATTAAACATG
1 GTCTTACTCGCACACATATAACGAAGTCACATATCGATGCCAACATATTAAACACA
39220702 GTCTTACTCGCACA
1 GTCTTACTCGCACA
39220716 TCACATATTG
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.28
Consensus pattern (56 bp):
GTCTTACTCGCACACATATAACGAAGTCACATATCGATGCCAACATATTAAACACA
Found at i:39221868 original size:14 final size:15
Alignment explanation
Indices: 39221851--39221879 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39221841 TCACGAAAAT
39221851 TTCACACAT-ATAAA
1 TTCACACATAATAAA
39221865 TTCACACATAATAAA
1 TTCACACATAATAAA
39221880 CACATAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:39224424 original size:40 final size:40
Alignment explanation
Indices: 39224340--39224524 Score: 227
Period size: 40 Copynumber: 4.7 Consensus size: 40
39224330 TCGAATGATG
* *
39224340 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
*
39224379 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
39224420 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
39224459 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
39224498 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
39224525 AACGAGTAGC
Statistics
Matches: 127, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
39 36 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:39224476 original size:79 final size:81
Alignment explanation
Indices: 39224340--39224522 Score: 241
Period size: 79 Copynumber: 2.3 Consensus size: 81
39224330 TCGAATGATG
* *
39224340 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATT
39224404 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * **
39224419 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGAT-CCGAAGGCA
39224481 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
39224499 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
39224523 TGAACGAGTA
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
78 1 0.01
79 60 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:39224546 original size:79 final size:78
Alignment explanation
Indices: 39224341--39224557 Score: 237
Period size: 79 Copynumber: 2.7 Consensus size: 78
39224331 CGAATGATGT
* *
39224341 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGT-GACTATATCCGGACTAAGATCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTAG-CTATATCCGG-TTAAG-TCCGAAGGCATT
*
39224404 TGTGCGAGTTACTAATT
62 TGTGCGAGTTACTAATA
* *
39224421 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTA-CTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TAGCTATATCC-GGTTAAGT-CCGAAGGCATTT
39224484 GTGCGAGTTACT-ATAA
63 GTGCGAGTTACTAAT-A
* ** *
39224500 CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATCCGGTTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTT-AAGTCCGAAGG
39224558 TACGTGATTC
Statistics
Matches: 117, Mismatches: 11, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
78 3 0.03
79 68 0.58
80 46 0.39
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (78 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTTAAGTCCGAAGGCATTTGTG
CGAGTTACTAATA
Found at i:39242693 original size:56 final size:56
Alignment explanation
Indices: 39242598--39242791 Score: 212
Period size: 56 Copynumber: 3.4 Consensus size: 56
39242588 TCCCAGACGG
* * * *
39242598 GGTCTTACTCGCACA-CACATATAACAGAGTCACATATCGATGCCAACATATTAAATGT
1 GGTCTTACTCGCAAATCACATAT--C-GATTCACATATCGATGCCAACGTATTAAACGT
* * * *
39242656 GGTCTTACTCGCATA-CATATATCTGATTCACGTATCGATGCTAACGTATTAAACGT
1 GGTCTTACTCGCAAATCACATATC-GATTCACATATCGATGCCAACGTATTAAACGT
* * * *
39242712 GGTCTTACTTGTAAATCACATATCGGTTCACATATTGATGCCAACGTATTAAACGT
1 GGTCTTACTCGCAAATCACATATCGATTCACATATCGATGCCAACGTATTAAACGT
* *
39242768 GGTCTTACTCGCACATCACGTATC
1 GGTCTTACTCGCAAATCACATATC
39242792 AGAATCCTAT
Statistics
Matches: 115, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
56 88 0.77
57 7 0.06
58 20 0.17
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.31
Consensus pattern (56 bp):
GGTCTTACTCGCAAATCACATATCGATTCACATATCGATGCCAACGTATTAAACGT
Found at i:39243936 original size:14 final size:15
Alignment explanation
Indices: 39243919--39243947 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39243909 TCACGAAAAT
39243919 TTCACACAT-ATAAA
1 TTCACACATAATAAA
39243933 TTCACACATAATAAA
1 TTCACACATAATAAA
39243948 CACAGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:39246632 original size:40 final size:40
Alignment explanation
Indices: 39246441--39246625 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
39246431 TTGAATGATG
* * * *
39246441 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
39246481 TCCGGACTAAGAT-CCGAAGACATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
39246521 TCTGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTTCTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
39246560 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
39246601 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39246626 AACGAGTAGC
Statistics
Matches: 121, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
39 32 0.26
40 79 0.65
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:39246647 original size:79 final size:79
Alignment explanation
Indices: 39246494--39246658 Score: 190
Period size: 79 Copynumber: 2.1 Consensus size: 79
39246484 GGACTAAGAT
* * * ** **
39246494 CCGAAGACATTTGTGCGAGATACTAATTCTGGGCTAAGCCCGAAGGCATTTGTGCGAGTTTCTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTAGCTAA
*
39246559 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
39246573 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCT
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTAGCT
* *
39246637 ATATCC-GGTTAAATT
64 AAATCCGGGTTAAATC
39246652 CCGAAGG
1 CCGAAGG
39246659 TACGTGATTT
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
78 2 0.03
79 44 0.61
80 26 0.36
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTAGCTAA
ATCCGGGTTAAATC
Found at i:39251980 original size:23 final size:23
Alignment explanation
Indices: 39251949--39251993 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
39251939 TAATATGCTG
39251949 AACAATAAGCTCCAACGAGCTAA
1 AACAATAAGCTCCAACGAGCTAA
* **
39251972 AACAGTAAGCTCTTACGAGCTA
1 AACAATAAGCTCCAACGAGCTA
39251994 TGTAACACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.18
Consensus pattern (23 bp):
AACAATAAGCTCCAACGAGCTAA
Found at i:39253251 original size:16 final size:16
Alignment explanation
Indices: 39253232--39253262 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39253222 CTTCTTCACT
39253232 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
39253248 TACTTACTTACTTAA
1 TACTCACTTACTTAA
39253263 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:39253268 original size:20 final size:20
Alignment explanation
Indices: 39253229--39253268 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
39253219 AAACTTCTTC
* *
39253229 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
39253249 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
39253269 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:39253549 original size:53 final size:53
Alignment explanation
Indices: 39253514--39253716 Score: 187
Period size: 55 Copynumber: 3.8 Consensus size: 53
39253504 GGTATCCTTG
* * *
39253514 CCTTGTGAACTCACCAATGCCATGCGTTTGTATGGTCTTACATGAGACCTTTA
1 CCTTATGAACTCACCAATGCCATGCCTTGGTATGGTCTTACATGAGACCTTTA
* *
39253567 CCTTATGAACTCACCAATGCCATGCCTTGGTATGGTCTTACATGAGACATTTG
1 CCTTATGAACTCACCAATGCCATGCCTTGGTATGGTCTTACATGAGACCTTTA
* * * ** * *
39253620 CCTTATAGTAACTTATCAATGCCATGTCTTGACATGGTATTACATG-GCATCC-TTG
1 CCTTAT-G-AACTCACCAATGCCATGCCTTGGTATGGTCTTACATGAG-A-CCTTTA
* * *
39253675 CGTTA-GAAACCTTACCAATTGCCATGCCTTGGCATGGTCTTA
1 CCTTATG-AA-CTCACCAA-TGCCATGCCTTGGTATGGTCTTA
39253717 TATGGTATCC
Statistics
Matches: 126, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
53 57 0.45
54 9 0.07
55 59 0.47
56 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (53 bp):
CCTTATGAACTCACCAATGCCATGCCTTGGTATGGTCTTACATGAGACCTTTA
Found at i:39260954 original size:16 final size:16
Alignment explanation
Indices: 39260935--39260965 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39260925 CTTCTTCACT
39260935 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
39260951 TACTTACTTACTTAA
1 TACTCACTTACTTAA
39260966 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:39260971 original size:20 final size:20
Alignment explanation
Indices: 39260932--39260971 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
39260922 AAACTTCTTC
* *
39260932 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
39260952 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
39260972 TTATTAATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:39261284 original size:53 final size:54
Alignment explanation
Indices: 39261196--39261411 Score: 215
Period size: 55 Copynumber: 4.0 Consensus size: 54
39261186 TACGTGGTAT
* * * *
39261196 CCTTTTGAAACTTACCACTGCCATGTCTCGACATGGTCTTACATAGTATCCTTG
1 CCTTATGAAACTTACCAATGCCATGCCTTGACATGGTCTTACATAGTATCCTTG
* * *
39261250 CCTTATG-AACTCACCAATGCCATGCCTTGGCATGGTCTTACATGAG-A-CATTTG
1 CCTTATGAAACTTACCAATGCCATGCCTTGACATGGTCTTACAT-AGTATC-CTTG
* * * * * *
39261303 CCTTATAGTAACTTATCAATGCCATGTCTTGACATGGTATTACATGGCATCCTTG
1 CCTTAT-GAAACTTACCAATGCCATGCCTTGACATGGTCTTACATAGTATCCTTG
* * *
39261358 CGTTA-GAAACCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 CCTTATGAAA-CTTACCAA-TGCCATGCCTTGACATGGTCTTACATAGTATCCTT
39261412 AAACCTTACT
Statistics
Matches: 133, Mismatches: 21, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
52 1 0.01
53 44 0.33
54 17 0.13
55 70 0.53
56 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (54 bp):
CCTTATGAAACTTACCAATGCCATGCCTTGACATGGTCTTACATAGTATCCTTG
Found at i:39261355 original size:108 final size:110
Alignment explanation
Indices: 39261204--39261403 Score: 298
Period size: 108 Copynumber: 1.8 Consensus size: 110
39261194 ATCCTTTTGA
* * *
39261204 AACTTACCACTGCCATGTCTCGACATGGTCTTACATAGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTCGACATGGTATTACATAGCATCCTTGCCTTA-GAAACCTCACCAA
39261267 -TGCCATGCCTTGGCATGGTCTTACATGAGACATTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACATGAGACATTTGCCTTATAGT
* * * * *
39261312 AACTTATCAATGCCATGTCTTGACATGGTATTACATGGCATCCTTGCGTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTCGACATGGTATTACATAGCATCCTTGCCTTAGAAACCTCACCAAT
39261377 TGCCATGCCTTGGCATGGTCTTACATG
66 TGCCATGCCTTGGCATGGTCTTACATG
39261404 GTATCCTTAA
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 1 0.01
108 46 0.57
109 7 0.09
110 27 0.33
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTCGACATGGTATTACATAGCATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGAGACATTTGCCTTATAGT
Found at i:39265468 original size:17 final size:17
Alignment explanation
Indices: 39265442--39265475 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
39265432 GCTGAAAATA
39265442 CACTCATACTAATTGAT
1 CACTCATACTAATTGAT
*
39265459 CACTCGTACTAATTGAT
1 CACTCATACTAATTGAT
39265476 ATCCTAGTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.35
Consensus pattern (17 bp):
CACTCATACTAATTGAT
Found at i:39280207 original size:98 final size:98
Alignment explanation
Indices: 39280072--39280256 Score: 237
Period size: 98 Copynumber: 1.9 Consensus size: 98
39280062 CTCAATATGT
* * * * * * *
39280072 GAGCCAGTGTAAGACCATGTTTGGAACATGGCTTCAGCATTGTTATATGTGTCAATGTAAGACCA
1 GAGCCAGTGTAAGACCATATCTGGAACATGGCATCAGCATCGATATATGAGCCAATGTAAGACCA
39280137 TGTCTAGG-ACATGGCATCGGCACCGATGTATAA
66 TGT-TAGGAACATGGCATCGGCACCGATGTATAA
* * * * *
39280170 GAGCTAGTGTAAGACCATATCTGGGACATGGCATCAGCCTCGATATGTGAGCCAGTGTAAGACCA
1 GAGCCAGTGTAAGACCATATCTGGAACATGGCATCAGCATCGATATATGAGCCAATGTAAGACCA
*
39280235 TGTTTGGAACATGGCATCGGCA
66 TGTTAGGAACATGGCATCGGCA
39280257 TTGATATTAG
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
97 3 0.04
98 70 0.96
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.25
Consensus pattern (98 bp):
GAGCCAGTGTAAGACCATATCTGGAACATGGCATCAGCATCGATATATGAGCCAATGTAAGACCA
TGTTAGGAACATGGCATCGGCACCGATGTATAA
Found at i:39280263 original size:48 final size:48
Alignment explanation
Indices: 39280021--39280263 Score: 220
Period size: 48 Copynumber: 5.0 Consensus size: 48
39280011 ACTAGGGTTG
* * * * *
39280021 TGTGAGCCAGTGTAAGACCATATCT-GAGACATGGCATTGGCCTCAATA
1 TGTGAGCCAGTGTAAGACCATGTTTGGA-ACATGGCATCGGCATCGATA
* * * *
39280069 TGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCTTCAGCATTGTTA
1 TGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCGATA
* * * * * *
39280117 TATGTGTCAATGTAAGACCATGTCTAGG-ACATGGCATCGGCACCGATGTA
1 TGTGAGCCAGTGTAAGACCATGT-TTGGAACATGGCATCGGCATCGA--TA
** * * * * * *
39280167 TAAGAGCTAGTGTAAGACCATATCTGGGACATGGCATCAGCCTCGATA
1 TGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCGATA
*
39280215 TGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGATA
1 TGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCGATA
39280263 T
1 T
39280264 TAGAGGTTTA
Statistics
Matches: 151, Mismatches: 39, Indels: 10
0.75 0.19 0.05
Matches are distributed among these distances:
48 110 0.73
49 7 0.05
50 34 0.23
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (48 bp):
TGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCGATA
Found at i:39284551 original size:17 final size:17
Alignment explanation
Indices: 39284525--39284565 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
39284515 TAATTGCGAA
*
39284525 AAAGGACTAAATCGCAT
1 AAAGGGCTAAATCGCAT
39284542 AAAGGGCTAAATCGCAT
1 AAAGGGCTAAATCGCAT
39284559 AAAGGGC
1 AAAGGGC
39284566 AAAAGTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (17 bp):
AAAGGGCTAAATCGCAT
Found at i:39285637 original size:48 final size:48
Alignment explanation
Indices: 39285559--39285937 Score: 329
Period size: 48 Copynumber: 7.8 Consensus size: 48
39285549 TAGAGTTGTG
* * * *
39285559 TGAGCCAATGTAAGACCATGTCTAGG-ACATGGCATCAGCCTCAATATA
1 TGAGCCAGTGTAAGACCATGT-TTGGAACATGGCATCGGCCTCGATATA
* *
39285607 TGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCAT-TATTATA
1 TGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCCTCGA-TATA
* * * * *
39285655 TGTGTCAATGTAAGACCATGTCTGCG-ACATGGCATCGGCAC-CGATGTA
1 TGAGCCAGTGTAAGACCATGTTTG-GAACATGGCATCGGC-CTCGATATA
* * * * * *
39285703 GGAGAGCTAGTGTAAGACCATATCTGGGACATGGCATCAGCCTCGATATA
1 --TGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCCTCGATATA
* * * *
39285753 TGAGCCAGTGTAAGACCATGTTTGGAACATGCCATCGGCATTGATATG
1 TGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCCTCGATATA
* * * * * *
39285801 GGAGCTAGTGTAAGACTATGTTTGGGACATGGCATCGGCCTCGACATG
1 TGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCCTCGATATA
* * *
39285849 TGGGCTAGTGTAAGACCATGTTTGGAACAT-GCAATCGGCACT-GAAATA
1 TGAGCCAGTGTAAGACCATGTTTGGAACATGGC-ATCGGC-CTCGATATA
* * *
39285897 TGAGAGCCAGTGTAAGACCATGTCTGGGACGTGGCATCGGC
1 T--GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGC
39285938 ATCTTACCCT
Statistics
Matches: 268, Mismatches: 49, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
47 6 0.02
48 188 0.70
49 6 0.02
50 66 0.25
51 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (48 bp):
TGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCCTCGATATA
Found at i:39285831 original size:146 final size:143
Alignment explanation
Indices: 39285567--39285939 Score: 434
Period size: 146 Copynumber: 2.6 Consensus size: 143
39285557 TGTGAGCCAA
* *
39285567 TGTAAGACCATGTCTAGGACATGGCATCAGCCTCAATATATGAGCCAGTGTAAGACCATGTTTGG
1 TGTAAGACCATGTCTGGGACATGGCATCAGCCTCGATATATGAGCCAGTGTAAGACCATGTTTGG
* *
39285632 AACATGGCATCGGCATTATTATATGTGTCAATGTAAGACCATGTCTGCGACATGGCATCGGCAC-
66 AACATGGCATCGGCATTATTATAGGAGTCAATGTAAGACCATGTCTGCGACATGGCATCGGC-CT
39285696 CG-ATGTAGGAGAGCTAG
130 CGAATGT--G-G-GCTAG
*
39285713 TGTAAGACCATATCTGGGACATGGCATCAGCCTCGATATATGAGCCAGTGTAAGACCATGTTTGG
1 TGTAAGACCATGTCTGGGACATGGCATCAGCCTCGATATATGAGCCAGTGTAAGACCATGTTTGG
* * * * * *
39285778 AACATGCCATCGGCATTGA-TATGGGAG-CTAGTGTAAGACTATGTTTGGGACATGGCATCGGCC
66 AACATGGCATCGGCATT-ATTATAGGAGTC-AATGTAAGACCATGTCTGCGACATGGCATCGGCC
39285841 TCGACATGTGGGCTAG
129 TCGA-ATGTGGGCTAG
* * * *
39285857 TGTAAGACCATGTTTGGAACAT-GCAATCGGCACT-GAAATATGAGAGCCAGTGTAAGACCATGT
1 TGTAAGACCATGTCTGGGACATGGC-ATCAGC-CTCGATATAT--GAGCCAGTGTAAGACCATGT
* * *
39285920 CTGGGACGTGGCATCGGCAT
62 TTGGAACATGGCATCGGCAT
39285940 CTTACCCTTT
Statistics
Matches: 198, Mismatches: 20, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
143 2 0.01
144 35 0.18
145 5 0.03
146 151 0.76
147 1 0.01
148 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (143 bp):
TGTAAGACCATGTCTGGGACATGGCATCAGCCTCGATATATGAGCCAGTGTAAGACCATGTTTGG
AACATGGCATCGGCATTATTATAGGAGTCAATGTAAGACCATGTCTGCGACATGGCATCGGCCTC
GAATGTGGGCTAG
Found at i:39312275 original size:46 final size:46
Alignment explanation
Indices: 39312222--39312397 Score: 219
Period size: 46 Copynumber: 3.8 Consensus size: 46
39312212 TATTTGGGCA
39312222 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
*** * * * *
39312268 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGA-GCG
* * *
39312315 TCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
39312361 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
39312398 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 19, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
46 72 0.67
47 36 0.33
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:39312377 original size:93 final size:93
Alignment explanation
Indices: 39312218--39312389 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
39312208 GGGATATTTG
* * *
39312218 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
39312283 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
39312311 GGCATCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
39312376 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
39312390 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:39315338 original size:15 final size:15
Alignment explanation
Indices: 39315318--39315386 Score: 75
Period size: 15 Copynumber: 4.6 Consensus size: 15
39315308 GTATCTTGGG
39315318 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* * *
39315333 TCTCTTTATTCTAGA
1 TTTCTTTATCCTGGA
* *
39315348 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
39315363 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
39315378 TTTCTTTAT
1 TTTCTTTAT
39315387 TCGGTTTTCT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.13, C:0.17, G:0.12, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:39315380 original size:30 final size:30
Alignment explanation
Indices: 39315309--39315396 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 30
39315299 CATAGTATTG
* * * *
39315309 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
* *
39315339 TAT-TCTAGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
39315369 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
39315397 TGTTATCTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
29 8 0.17
30 39 0.81
31 1 0.02
ACGTcount: A:0.11, C:0.17, G:0.15, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:39315397 original size:14 final size:14
Alignment explanation
Indices: 39315318--39315397 Score: 61
Period size: 15 Copynumber: 5.4 Consensus size: 14
39315308 GTATCTTGGG
*
39315318 TTTCTTTATCCTGGA
1 TTTCTTTATTC-GGA
* *
39315333 TCTCTTTATTCTAGA
1 TTTCTTTATTC-GGA
*
39315348 TTTCTTTATTCTGGG
1 TTTCTTTATTC-GGA
* *
39315363 TTTCTCTATCTTGGA
1 TTTCTTTAT-TCGGA
*
39315378 TTTCTTTATTCGGT
1 TTTCTTTATTCGGA
39315392 TTTCTT
1 TTTCTT
39315398 GTTATCTTTG
Statistics
Matches: 52, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
14 9 0.17
15 42 0.81
16 1 0.02
ACGTcount: A:0.11, C:0.17, G:0.12, T:0.59
Consensus pattern (14 bp):
TTTCTTTATTCGGA
Found at i:39322210 original size:73 final size:74
Alignment explanation
Indices: 39322047--39322470 Score: 411
Period size: 74 Copynumber: 5.4 Consensus size: 74
39322037 TTTTTTTTTG
39322047 TTGAGCCTCGGGACACGCTGAGGTAATTTTAATTTCTATTTTCAAAAAAATCAACTCATATTGCG
1 TTGAGCCTCGGGACACGCTGAGGTAATTTTAATTTCTATTTTCAAAAAAATCAACTCATATTGCG
* *
39322112 AGAGGTGAG
66 AGAGATGAA
* * *
39322121 GTGAGCCTCGGGACACGTTGAGGTAATTTTAATTTCTATTTTCAAAAAAATTAACTCAT-TTGCG
1 TTGAGCCTCGGGACACGCTGAGGTAATTTTAATTTCTATTTTCAAAAAAATCAACTCATATTGCG
39322185 AGAGATGAA
66 AGAGATGAA
*
39322194 TTGAGCCTCGGGACACGCTGAGGTAATTTTAATTTCTATTTTTTAAAAAAAATCAACTCATATTG
1 TTGAGCCTCGGGACACGCTGAGGTAATTTTAATTTCTA--TTTTCAAAAAAATCAACTCATATTG
*
39322259 CGAAAGATGAA
64 CGAGAGATGAA
* ** * * *** *
39322270 TTGAGCCTCGGGACA-GGTGAATTGAGCCTCGGGACACGCTGAGGTAATTTTAATTTCTATTTTA
1 TTGAGCCTCGGGACACGCTG-A--G-G--T----A-A-TTTTA-ATTTCTAT--TTTC-------
39322334 AAAAAAAATCAACTCATATTGCGAGAGATGAA
44 AAAAA-AATCAACTCATATTGCGAGAGATGAA
*
39322366 TTGAGCCTCGGGACACGCTGAGGTAATTTTAATTTCTATTTTTAAAAAAATCAACTCATATTGCG
1 TTGAGCCTCGGGACACGCTGAGGTAATTTTAATTTCTATTTTCAAAAAAATCAACTCATATTGCG
* *
39322431 AGAAATGAG
66 AGAGATGAA
* * *
39322440 TTGAGCCTCGGGGCACGCCGAGGTATTTTTA
1 TTGAGCCTCGGGACACGCTGAGGTAATTTTA
39322471 GTTTATGTTT
Statistics
Matches: 287, Mismatches: 36, Indels: 54
0.76 0.10 0.14
Matches are distributed among these distances:
73 48 0.17
74 108 0.38
75 27 0.09
76 29 0.10
78 1 0.00
79 1 0.00
81 1 0.00
82 3 0.01
84 3 0.01
85 3 0.01
86 3 0.01
87 3 0.01
88 5 0.02
91 1 0.00
93 1 0.00
94 1 0.00
95 5 0.02
96 41 0.14
97 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (74 bp):
TTGAGCCTCGGGACACGCTGAGGTAATTTTAATTTCTATTTTCAAAAAAATCAACTCATATTGCG
AGAGATGAA
Found at i:39322292 original size:21 final size:21
Alignment explanation
Indices: 39322266--39322305 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
39322256 TTGCGAAAGA
39322266 TGAATTGAGCCTCGGGACAGG
1 TGAATTGAGCCTCGGGACAGG
39322287 TGAATTGAGCCTCGGGACA
1 TGAATTGAGCCTCGGGACA
39322306 CGCTGAGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.20, G:0.35, T:0.20
Consensus pattern (21 bp):
TGAATTGAGCCTCGGGACAGG
Found at i:39322415 original size:170 final size:170
Alignment explanation
Indices: 39322122--39322451 Score: 576
Period size: 170 Copynumber: 1.9 Consensus size: 170
39322112 AGAGGTGAGG
* * *
39322122 TGAGCCTCGGGACACGTTGAGGTAATTTTAATTTCTATTTTCAAAAAAATTAACTCATTTGCGAG
1 TGAGCCTCGGGACACGCTGAGGTAATTTTAATTTCTATTTTAAAAAAAATCAACTCATTTGCGAG
39322187 AGATGAATTGAGCCTCGGGACACGCTGAGGTAATTTTAATTTCTATTTTTTAAAAAAAATCAACT
66 AGATGAATTGAGCCTCGGGACACGCTGAGGTAATTTTAATTTCTATTTTTTAAAAAAAATCAACT
39322252 CATATTGCGA-AAGATGAATTGAGCCTCGGGACAGGTGAAT
131 CATATTGCGAGAA-ATGAATTGAGCCTCGGGACAGGTGAAT
39322292 TGAGCCTCGGGACACGCTGAGGTAATTTTAATTTCTATTTTAAAAAAAAATCAACTCATATTGCG
1 TGAGCCTCGGGACACGCTGAGGTAATTTTAATTTCTATTTT-AAAAAAAATCAACTCAT-TTGCG
39322357 AGAGATGAATTGAGCCTCGGGACACGCTGAGGTAATTTTAATTTCTA-TTTTT-AAAAAAATCAA
64 AGAGATGAATTGAGCCTCGGGACACGCTGAGGTAATTTTAATTTCTATTTTTTAAAAAAAATCAA
*
39322420 CTCATATTGCGAGAAATGAGTTGAGCCTCGGG
129 CTCATATTGCGAGAAATGAATTGAGCCTCGGG
39322452 GCACGCCGAG
Statistics
Matches: 153, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
170 79 0.52
171 22 0.14
172 52 0.34
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (170 bp):
TGAGCCTCGGGACACGCTGAGGTAATTTTAATTTCTATTTTAAAAAAAATCAACTCATTTGCGAG
AGATGAATTGAGCCTCGGGACACGCTGAGGTAATTTTAATTTCTATTTTTTAAAAAAAATCAACT
CATATTGCGAGAAATGAATTGAGCCTCGGGACAGGTGAAT
Found at i:39322509 original size:69 final size:71
Alignment explanation
Indices: 39322291--39322516 Score: 242
Period size: 74 Copynumber: 3.1 Consensus size: 71
39322281 GACAGGTGAA
* * *
39322291 TTGAGCCTCGGGACACGCTGAGGTAATTTTAATTTCTATTTTAAAAAAAAATCAACTCATATTGC
1 TTGAGCCTCGGGACACGCCGAGGTAATTTTAAGTTCTATTTT----TAAAATCAACTCATATTGC
*
39322356 GAGAGATGAA
62 GAGAGATGAG
* *
39322366 TTGAGCCTCGGGACACGCTGAGGTAATTTTAATTTCTATTTTTAAAAAAATCAACTCATATTGCG
1 TTGAGCCTCGGGACACGCCGAGGTAATTTTAAGTTCTATTTTT---AAAATCAACTCATATTGCG
*
39322431 AGAAATGAG
63 AGAGATGAG
* * **
39322440 TTGAGCCTCGGGGCACGCCGAGGT-ATTTTTAGTT-TATGTTTT-AAATTGACTCATATTGCGAG
1 TTGAGCCTCGGGACACGCCGAGGTAATTTTAAGTTCTAT-TTTTAAAATCAACTCATATTGCGAG
*
39322502 AGGTGAG
65 AGATGAG
*
39322509 TTAAGCCT
1 TTGAGCCT
39322517 TTTAATTTTT
Statistics
Matches: 135, Mismatches: 12, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
69 30 0.22
72 3 0.02
73 12 0.09
74 48 0.36
75 42 0.31
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.33
Consensus pattern (71 bp):
TTGAGCCTCGGGACACGCCGAGGTAATTTTAAGTTCTATTTTTAAAATCAACTCATATTGCGAGA
GATGAG
Found at i:39322612 original size:17 final size:18
Alignment explanation
Indices: 39322590--39322624 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
39322580 TGCTGAGGTA
*
39322590 TTTTCAATTTATG-TTTT
1 TTTTCAATCTATGCTTTT
39322607 TTTTCAATCTATGCTTTT
1 TTTTCAATCTATGCTTTT
39322625 CAAAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.17, C:0.11, G:0.06, T:0.66
Consensus pattern (18 bp):
TTTTCAATCTATGCTTTT
Found at i:39323787 original size:152 final size:152
Alignment explanation
Indices: 39323511--39323814 Score: 599
Period size: 152 Copynumber: 2.0 Consensus size: 152
39323501 TAAAATTAGG
39323511 CCATATAAAAGCCACCCAAACAACAAACGAAAAGGGGGGAGGATGTACAAAAAGTTTGTATCAAA
1 CCATATAAAAGCCACCCAAACAACAAACGAAAAGGGGGGAGGATGTACAAAAAGTTTGTATCAAA
39323576 AACAAAAGAAAAAAGAAAAGCTTAGAAGGTGAACTTCAATTTTTTTCCTCTGTTATCTCAATCTT
66 AACAAAAGAAAAAAGAAAAGCTTAGAAGGTGAACTTCAATTTTTTTCCTCTGTTATCTCAATCTT
39323641 TCTGTTTATCTTTGCTTTGCTT
131 TCTGTTTATCTTTGCTTTGCTT
39323663 CCATATAAAAGCCACCCAAACAACAAACGAAAAGGGGGGAGGATGTACAAAAAGTTTGTATCAAA
1 CCATATAAAAGCCACCCAAACAACAAACGAAAAGGGGGGAGGATGTACAAAAAGTTTGTATCAAA
*
39323728 AACAAAAGAAAAAAGAAAAGCTTAGAAGGTGAACTTCAATTTTTTTCCTCTGTTATCTCAATTTT
66 AACAAAAGAAAAAAGAAAAGCTTAGAAGGTGAACTTCAATTTTTTTCCTCTGTTATCTCAATCTT
39323793 TCTGTTTATCTTTGCTTTGCTT
131 TCTGTTTATCTTTGCTTTGCTT
39323815 TATTTTTTTT
Statistics
Matches: 151, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
152 151 1.00
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (152 bp):
CCATATAAAAGCCACCCAAACAACAAACGAAAAGGGGGGAGGATGTACAAAAAGTTTGTATCAAA
AACAAAAGAAAAAAGAAAAGCTTAGAAGGTGAACTTCAATTTTTTTCCTCTGTTATCTCAATCTT
TCTGTTTATCTTTGCTTTGCTT
Found at i:39324430 original size:3 final size:3
Alignment explanation
Indices: 39324415--39324458 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
39324405 GTTATTTTCA
* *
39324415 TAT TAT TAA TAT TAT TATT TAT TAT TAT TAT TAT TGT TAT TAT T
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT T
39324459 GTTCATTAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:39324438 original size:16 final size:16
Alignment explanation
Indices: 39324417--39324449 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
39324407 TATTTTCATA
39324417 TTATTAATATTATTAT
1 TTATTAATATTATTAT
*
39324433 TTATTATTATTATTAT
1 TTATTAATATTATTAT
39324449 T
1 T
39324450 GTTATTATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTAATATTATTAT
Found at i:39324459 original size:9 final size:9
Alignment explanation
Indices: 39324433--39324466 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
39324423 ATATTATTAT
*
39324433 TTATTATTA
1 TTATTATTG
39324442 TTATTATTG
1 TTATTATTG
39324451 TTATTATTG
1 TTATTATTG
39324460 TTCATTA
1 TT-ATTA
39324467 GTGTATATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 19 0.83
10 4 0.17
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (9 bp):
TTATTATTG
Found at i:39324565 original size:3 final size:3
Alignment explanation
Indices: 39324557--39324589 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
39324547 TGTGTTTCAA
39324557 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39324590 ATATCCTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:39324628 original size:120 final size:122
Alignment explanation
Indices: 39324437--39324661 Score: 287
Period size: 120 Copynumber: 1.9 Consensus size: 122
39324427 TATTATTTAT
* * * * *
39324437 TATTATTATTATTGTTATTATTGTTCATTAGTGTATATCTTCATGTATGTATATATATATGTAGT
1 TATTATTATTATTATTATTATTATTCATTAGTATATATCTTCATGTATGTATACATATATATAGT
*
39324502 AATGTTTCTATTA-CTTTATTTTAATAT-TTTTATTATAATGGCTTTTGTGTTTCAA
66 AATGTTTCTAATACCTTTATTTTAATATATTTTATTATAATGGCTTTTGTGTTTCAA
* **
39324557 TATTATTATTATTATTATTATTATT-ATTATTATATATCCTTGTTAG-ATGTATACATATATATA
1 TATTATTATTATTATTATTATTATTCATTAGTATATAT-CTTCAT-GTATGTATACATATATATA
* * *
39324620 TTACTGTTTTTAATACCTTTATTTTAATATCATTTTATTATA
64 GTAATGTTTCTAATACCTTTATTTTAATAT-ATTTTATTATA
39324662 TTTACCTTTT
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
119 10 0.11
120 53 0.60
121 15 0.17
123 10 0.11
ACGTcount: A:0.29, C:0.06, G:0.08, T:0.57
Consensus pattern (122 bp):
TATTATTATTATTATTATTATTATTCATTAGTATATATCTTCATGTATGTATACATATATATAGT
AATGTTTCTAATACCTTTATTTTAATATATTTTATTATAATGGCTTTTGTGTTTCAA
Found at i:39324797 original size:22 final size:23
Alignment explanation
Indices: 39324769--39324823 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
39324759 AATTTTTTTC
39324769 ATATATATTATATGAATA-ATTT
1 ATATATATTATATGAATATATTT
* *
39324791 ATATATAATATTATGTATATATTT
1 ATATATATTA-TATGAATATATTT
39324815 -TA-ATATTAT
1 ATATATATTAT
39324824 CAGTTATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 1 0.04
22 14 0.50
23 9 0.32
24 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (23 bp):
ATATATATTATATGAATATATTT
Found at i:39330252 original size:15 final size:15
Alignment explanation
Indices: 39330232--39330271 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
39330222 AAGCCATCAA
39330232 ACGCCCGTGTCTATC
1 ACGCCCGTGTCTATC
39330247 ACGCCCGTGTCTATC
1 ACGCCCGTGTCTATC
*
39330262 GCGCCCGTGT
1 ACGCCCGTGT
39330272 GGCACGCGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.10, C:0.40, G:0.25, T:0.25
Consensus pattern (15 bp):
ACGCCCGTGTCTATC
Found at i:39340286 original size:16 final size:17
Alignment explanation
Indices: 39340265--39340297 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
39340255 TGTAATTGAT
*
39340265 ATATAGGCA-AACAATA
1 ATATAGACATAACAATA
39340281 ATATAGACATAACAATA
1 ATATAGACATAACAATA
39340298 GTTGCCCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.58, C:0.12, G:0.09, T:0.21
Consensus pattern (17 bp):
ATATAGACATAACAATA
Found at i:39342778 original size:61 final size:61
Alignment explanation
Indices: 39342709--39342832 Score: 248
Period size: 61 Copynumber: 2.0 Consensus size: 61
39342699 TAGAAAATAA
39342709 TATAAATGATTGAAGGAAATATAATTTATAAAAGAATGAAATTGGGAGAATTAACTTAGAT
1 TATAAATGATTGAAGGAAATATAATTTATAAAAGAATGAAATTGGGAGAATTAACTTAGAT
39342770 TATAAATGATTGAAGGAAATATAATTTATAAAAGAATGAAATTGGGAGAATTAACTTAGAT
1 TATAAATGATTGAAGGAAATATAATTTATAAAAGAATGAAATTGGGAGAATTAACTTAGAT
39342831 TA
1 TA
39342833 CTGGTTTGTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.49, C:0.02, G:0.18, T:0.31
Consensus pattern (61 bp):
TATAAATGATTGAAGGAAATATAATTTATAAAAGAATGAAATTGGGAGAATTAACTTAGAT
Found at i:39342808 original size:30 final size:30
Alignment explanation
Indices: 39342713--39342808 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 30
39342703 AAATAATATA
39342713 AATGATTGAAGGAAATATAATTTATAAAAG
1 AATGATTGAAGGAAATATAATTTATAAAAG
* * *
39342743 AATGAAATTG--GGAGAAT-TAACTTAGATTATA-
1 AATG--ATTGAAGGA-AATATAA-TT-TATAAAAG
39342774 AATGATTGAAGGAAATATAATTTATAAAAG
1 AATGATTGAAGGAAATATAATTTATAAAAG
39342804 AATGA
1 AATGA
39342809 AATTGGGAGA
Statistics
Matches: 51, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
29 8 0.16
30 20 0.39
31 15 0.29
32 8 0.16
ACGTcount: A:0.51, C:0.01, G:0.18, T:0.30
Consensus pattern (30 bp):
AATGATTGAAGGAAATATAATTTATAAAAG
Found at i:39345145 original size:17 final size:16
Alignment explanation
Indices: 39345115--39345149 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
39345105 TTAAAAAATT
*
39345115 TAAAAAAATTTAAAAA
1 TAAAAAAATATAAAAA
39345131 TAAAAAAACTATAAAAA
1 TAAAAAAA-TATAAAAA
39345148 TA
1 TA
39345150 CTTTCAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
TAAAAAAATATAAAAA
Found at i:39345814 original size:3 final size:3
Alignment explanation
Indices: 39345806--39345839 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
39345796 AATTGCAAAC
39345806 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
39345840 TAACAGATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:39355636 original size:22 final size:24
Alignment explanation
Indices: 39355608--39355654 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
39355598 ATTATTAAAA
*
39355608 TTAT-AAAAT-TATATTTTAATTT
1 TTATAAAAATATATAGTTTAATTT
39355630 TTATAAAAATATATAGTTTAATTT
1 TTATAAAAATATATAGTTTAATTT
39355654 T
1 T
39355655 ACTTTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.18
23 5 0.23
24 13 0.59
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
TTATAAAAATATATAGTTTAATTT
Found at i:39357441 original size:16 final size:17
Alignment explanation
Indices: 39357414--39357448 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
39357404 AAAAAAAGAC
39357414 TATTTTTATTGGCAAAT
1 TATTTTTATTGGCAAAT
*
39357431 TATTTTT-TTGGTAAAT
1 TATTTTTATTGGCAAAT
39357447 TA
1 TA
39357449 AAAAATACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (17 bp):
TATTTTTATTGGCAAAT
Found at i:39357711 original size:11 final size:11
Alignment explanation
Indices: 39357695--39357719 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39357685 ATATTTTTGT
39357695 AAAAAAAAAGA
1 AAAAAAAAAGA
39357706 AAAAAAAAAGA
1 AAAAAAAAAGA
39357717 AAA
1 AAA
39357720 CTAGAAGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:39372315 original size:43 final size:43
Alignment explanation
Indices: 39372268--39372353 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
39372258 ATCAGTGCAA
* *
39372268 CAATTAAAGGAATGATATTTTAGGATCTTTAGCTATATTAGTG
1 CAATTAAAAGAATGATATTCTAGGATCTTTAGCTATATTAGTG
39372311 CAATTAAAAGAATGATATTCTAGGATCTTTAGCTATATTAGTG
1 CAATTAAAAGAATGATATTCTAGGATCTTTAGCTATATTAGTG
39372354 GATGTATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.38
Consensus pattern (43 bp):
CAATTAAAAGAATGATATTCTAGGATCTTTAGCTATATTAGTG
Found at i:39376884 original size:28 final size:28
Alignment explanation
Indices: 39376836--39376890 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
39376826 TATGACATTT
39376836 TTTTATTTTATATGTTCAATTACTTTTAG
1 TTTTATTTTATATGTTCAATTA-TTTTAG
*
39376865 TTTTATTTATTTAT-TT-AATTATTTTA
1 TTTTATTT-TATATGTTCAATTATTTTA
39376891 TTAATTGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 5 0.21
28 5 0.21
29 10 0.42
30 4 0.17
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (28 bp):
TTTTATTTTATATGTTCAATTATTTTAG
Found at i:39377242 original size:27 final size:27
Alignment explanation
Indices: 39377201--39377252 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
39377191 AAGTGTCAAT
* * *
39377201 TTTAAGTATCGAATTAGGAAAAAAATA
1 TTTAAGTACCAAATTAAGAAAAAAATA
39377228 TTTAAGTACCAAATTAAGAAAAAAA
1 TTTAAGTACCAAATTAAGAAAAAAA
39377253 AATCAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.27
Consensus pattern (27 bp):
TTTAAGTACCAAATTAAGAAAAAAATA
Found at i:39378004 original size:9 final size:9
Alignment explanation
Indices: 39377979--39378039 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 9
39377969 TTTTCATTTT
39377979 TTAAA-TAA
1 TTAAATTAA
* *
39377987 TTTATTTAA
1 TTAAATTAA
39377996 TTAAATTAA
1 TTAAATTAA
**
39378005 AAAAATTAA
1 TTAAATTAA
*
39378014 TTAAACTAA
1 TTAAATTAA
39378023 TTAAATTAA
1 TTAAATTAA
39378032 --AAATTAA
1 TTAAATTAA
39378039 T
1 T
39378040 GATCTAACTA
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
7 7 0.17
8 3 0.07
9 31 0.76
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (9 bp):
TTAAATTAA
Found at i:39381566 original size:92 final size:91
Alignment explanation
Indices: 39381448--39381662 Score: 279
Period size: 92 Copynumber: 2.3 Consensus size: 91
39381438 CCTTTTTGCA
* * *
39381448 TATATTTATTTGATCTAGTAGTTAAGCTGCAAATTACCGGTATAGCGGTTTACCGCATCGCATTG
1 TATA-TTATCTGATCTGGCAGTTAAGCTGCAAATTACCGGTATAGCGGTTTACCGCATCGCATTG
*
39381513 TACCGTATGTACGTTAGCTAGGCTACG
65 TACCGCATGTACGTTAGCTAGGCTACG
* * * * *
39381540 TATCATTATCTGATCTGGCAGTTAAGCTACAAATTATCGGTATAGCGGTTTACTGTATTGCATTG
1 TAT-ATTATCTGATCTGGCAGTTAAGCTGCAAATTACCGGTATAGCGGTTTACCGCATCGCATTG
*
39381605 TACCGCATGTACGTTAGCTATGCTACG
65 TACCGCATGTACGTTAGCTAGGCTACG
* *
39381632 TATGTATATCTGATTTGGCAGTTCAA-CTGCA
1 TATAT-TATCTGATCTGGCAGTT-AAGCTGCA
39381663 TGTTGATAAG
Statistics
Matches: 107, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
91 1 0.01
92 103 0.96
93 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (91 bp):
TATATTATCTGATCTGGCAGTTAAGCTGCAAATTACCGGTATAGCGGTTTACCGCATCGCATTGT
ACCGCATGTACGTTAGCTAGGCTACG
Found at i:39383105 original size:14 final size:14
Alignment explanation
Indices: 39383086--39383119 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
39383076 TTGTTTCACT
39383086 GAAAATGACTTCTA
1 GAAAATGACTTCTA
* *
39383100 GAAAATGATTTCTG
1 GAAAATGACTTCTA
39383114 GAAAAT
1 GAAAAT
39383120 AATTTACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (14 bp):
GAAAATGACTTCTA
Found at i:39383638 original size:15 final size:15
Alignment explanation
Indices: 39383583--39383639 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
39383573 TTTATGCTAC
*
39383583 AAAACATTTATTATT
1 AAAATATTTATTATT
* *
39383598 AATATATTTATAATTGT
1 AAAATATTTATTA-T-T
39383615 AACAAATATTTATTATT
1 -A-AAATATTTATTATT
39383632 AAAATATT
1 AAAATATT
39383640 AATATTGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 17 0.52
16 2 0.06
17 2 0.06
18 2 0.06
19 10 0.30
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:39383760 original size:22 final size:22
Alignment explanation
Indices: 39383720--39383775 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
39383710 AATAAAATTG
*
39383720 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
39383740 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* * *
39383762 TATTAATAATTTAT
1 AAATAATAAATTAT
39383776 TATATGACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.30
21 2 0.07
22 19 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:39385111 original size:15 final size:15
Alignment explanation
Indices: 39385056--39385112 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
39385046 TTTATGCTAC
*
39385056 AAAACATTTATTATT
1 AAAATATTTATTATT
* *
39385071 AATATATTTATAATTGT
1 AAAATATTTATTA-T-T
39385088 AACAAATATTTATTATT
1 -A-AAATATTTATTATT
39385105 AAAATATT
1 AAAATATT
39385113 AATATTGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 17 0.52
16 2 0.06
17 2 0.06
18 2 0.06
19 10 0.30
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:39385233 original size:22 final size:22
Alignment explanation
Indices: 39385193--39385248 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
39385183 AATAAAATTG
*
39385193 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
39385213 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* * *
39385235 TATTAATAATTTAT
1 AAATAATAAATTAT
39385249 TATATGACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.30
21 2 0.07
22 19 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:39388143 original size:40 final size:41
Alignment explanation
Indices: 39388099--39388204 Score: 155
Period size: 40 Copynumber: 2.7 Consensus size: 41
39388089 TTGAATAGCC
* *
39388099 GACTATATCCGGGCTCAGTCCCGAAGGCATTTGTGCTAG-T
1 GACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTT
*
39388139 GACTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTT
1 GACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTT
*
39388180 G-CTATATCC-GGCTAATTCCCGAAGG
1 GACTATATCCGGGCTAAGTCCCGAAGG
39388205 TACTTGGGTT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
39 14 0.23
40 44 0.73
41 2 0.03
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (41 bp):
GACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTT
Found at i:39389784 original size:18 final size:18
Alignment explanation
Indices: 39389743--39389787 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
39389733 TCTTTATTGT
* *
39389743 TCAGTATTAGTCAGTCAA
1 TCAGTAATAATCAGTCAA
*
39389761 -CAGTAATAATCAGTTAA
1 TCAGTAATAATCAGTCAA
39389778 TCAGTAATAA
1 TCAGTAATAA
39389788 CCATTTATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (18 bp):
TCAGTAATAATCAGTCAA
Found at i:39389799 original size:18 final size:18
Alignment explanation
Indices: 39389761--39389800 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
39389751 AGTCAGTCAA
*
39389761 CAGTAATAATCAGTTAAT
1 CAGTAATAACCAGTTAAT
* *
39389779 CAGTAATAACCATTTATT
1 CAGTAATAACCAGTTAAT
39389797 CAGT
1 CAGT
39389801 TACAGTCATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (18 bp):
CAGTAATAACCAGTTAAT
Found at i:39389810 original size:18 final size:18
Alignment explanation
Indices: 39389789--39389837 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
39389779 CAGTAATAAC
*
39389789 CATTTATTCAGT-TACAGT
1 CATTTATTCAATAT-CAGT
39389807 CATTTATTCAATATCAGT
1 CATTTATTCAATATCAGT
*
39389825 CAATTATTCAATA
1 CATTTATTCAATA
39389838 GTAGGCAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 27 0.96
19 1 0.04
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (18 bp):
CATTTATTCAATATCAGT
Found at i:39389849 original size:18 final size:18
Alignment explanation
Indices: 39389810--39389852 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
39389800 TTACAGTCAT
*
39389810 TTATTCAATATCAGTCAA
1 TTATTCAATATCAGGCAA
*
39389828 TTATTCAATAGT-AGGCAG
1 TTATTCAATA-TCAGGCAA
39389846 TTATTCA
1 TTATTCA
39389853 GTACCTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (18 bp):
TTATTCAATATCAGGCAA
Found at i:39389984 original size:6 final size:6
Alignment explanation
Indices: 39389967--39389997 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
39389957 TACACCGTGT
*
39389967 CAGTAA CGGTAA CAGTAA CAGTAA CAGTAA C
1 CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA C
39389998 GGTACATAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.16
Consensus pattern (6 bp):
CAGTAA
Found at i:39389984 original size:12 final size:12
Alignment explanation
Indices: 39389967--39390001 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
39389957 TACACCGTGT
39389967 CAGTAACGGTAA
1 CAGTAACGGTAA
*
39389979 CAGTAACAGTAA
1 CAGTAACGGTAA
39389991 CAGTAACGGTA
1 CAGTAACGGTA
39390002 CATAGGGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.17
Consensus pattern (12 bp):
CAGTAACGGTAA
Found at i:39390083 original size:51 final size:53
Alignment explanation
Indices: 39389977--39390095 Score: 154
Period size: 51 Copynumber: 2.3 Consensus size: 53
39389967 CAGTAACGGT
* *
39389977 AACAGTAACAGTAACAGTAACGGTACATAGGGTACCTCATCGGAACAAATCCGG
1 AACAGTAACAGTAACAATAACGGTA-ATAGGGTACCTCATCAGAACAAATCCGG
* **
39390031 AACAGTAACAGTAACAATAA-GGT-AT-GGAGTACCTCTTCAGAATGAATCCGG
1 AACAGTAACAGTAACAATAACGGTAATAGG-GTACCTCATCAGAACAAATCCGG
39390082 AACAGTAACAGTAA
1 AACAGTAACAGTAA
39390096 GGCGACACTT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
50 2 0.03
51 35 0.59
53 3 0.05
54 19 0.32
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.18
Consensus pattern (53 bp):
AACAGTAACAGTAACAATAACGGTAATAGGGTACCTCATCAGAACAAATCCGG
Found at i:39397645 original size:24 final size:24
Alignment explanation
Indices: 39397618--39397663 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
39397608 AGGTATCGTG
39397618 ACCTTAATTTTATAAATTGAGTAT
1 ACCTTAATTTTATAAATTGAGTAT
*
39397642 ACCTTGATTTTATAAATTGAGT
1 ACCTTAATTTTATAAATTGAGT
39397664 CATAAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.46
Consensus pattern (24 bp):
ACCTTAATTTTATAAATTGAGTAT
Found at i:39398927 original size:42 final size:41
Alignment explanation
Indices: 39398862--39398982 Score: 109
Period size: 42 Copynumber: 2.9 Consensus size: 41
39398852 AGCTTCTGTT
* * ** *
39398862 AACTCATATGAGTTTCCGTTTAACCCTAATGGGTTTCAGTTC
1 AACTCATACGAGCTTCTATTTAACCCTTATGGGTTTCA-TTC
* ** *
39398904 AACTCTTTTGAGCTT-TAATTTAACCTTTATGGGTTTTCATTC
1 AACTCATACGAGCTTCT-ATTTAACCCTTATGGG-TTTCATTC
* *
39398946 ATCTCATACGAGCTTCTATTCAACCCTTATGGGTTTC
1 AACTCATACGAGCTTCTATTTAACCCTTATGGGTTTC
39398983 TGTTTAGCAG
Statistics
Matches: 63, Mismatches: 13, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
41 4 0.06
42 53 0.84
43 6 0.10
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.42
Consensus pattern (41 bp):
AACTCATACGAGCTTCTATTTAACCCTTATGGGTTTCATTC
Found at i:39399590 original size:12 final size:12
Alignment explanation
Indices: 39399559--39399592 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
39399549 CCCTGTTTTC
*
39399559 ACACGGCTTGTG
1 ACACGGGTTGTG
39399571 ACACGGGTTGTG
1 ACACGGGTTGTG
*
39399583 ACATGGGTTG
1 ACACGGGTTG
39399593 AGTTGGTACG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.18, C:0.18, G:0.38, T:0.26
Consensus pattern (12 bp):
ACACGGGTTGTG
Found at i:39407089 original size:20 final size:22
Alignment explanation
Indices: 39407045--39407095 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
39407035 AATAATTTGG
*
39407045 TTTATTATTTATTTTTGTTTGAT
1 TTTATTA-TTACTTTTGTTTGAT
39407068 TTTATTATTACTTTT-TTT-AT
1 TTTATTATTACTTTTGTTTGAT
*
39407088 TTTTTTAT
1 TTTATTAT
39407096 GGTTGTGGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 9 0.35
21 3 0.12
22 7 0.27
23 7 0.27
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (22 bp):
TTTATTATTACTTTTGTTTGAT
Found at i:39407486 original size:16 final size:16
Alignment explanation
Indices: 39407465--39407497 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
39407455 GATAATCTAT
39407465 AAAACATGGAAAGAAC
1 AAAACATGGAAAGAAC
39407481 AAAACATGGAAAGAAC
1 AAAACATGGAAAGAAC
39407497 A
1 A
39407498 CACAAAGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.18, T:0.06
Consensus pattern (16 bp):
AAAACATGGAAAGAAC
Found at i:39407858 original size:43 final size:43
Alignment explanation
Indices: 39407789--39407954 Score: 174
Period size: 43 Copynumber: 3.9 Consensus size: 43
39407779 AGCTCTTACA
* * * * *
39407789 ATGCC-ATATCCCAGATATGGTCTTACATGTTATCAC-ATATCG
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCACAATA-CG
* * * * ** *
39407831 ATGCCATTGTCCTAGATAGGGTTTTACACAAAATCATAATACG
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCACAATACG
*
39407874 ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCACAATACA
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCACAATACG
* *
39407917 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACA
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCACA
39407955 TCTCGATAAC
Statistics
Matches: 102, Mismatches: 20, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
42 5 0.05
43 94 0.92
44 3 0.03
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.28
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCACAATACG
Found at i:39415396 original size:16 final size:16
Alignment explanation
Indices: 39415377--39415407 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39415367 CTTCTTCACT
39415377 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
39415393 TACTTACTTACTTAA
1 TACTCACTTACTTAA
39415408 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:39415413 original size:20 final size:20
Alignment explanation
Indices: 39415374--39415413 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
39415364 AAACTTCTTC
* *
39415374 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
39415394 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
39415414 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:39419283 original size:42 final size:42
Alignment explanation
Indices: 39419236--39419339 Score: 172
Period size: 42 Copynumber: 2.5 Consensus size: 42
39419226 TATCGGGATG
* * *
39419236 TGAGATTCATGTAAGACCATGACTGGGACATTTGCATCGATA
1 TGAGATTCGTGTAAGACCATGACTAGGACATTGGCATCGATA
*
39419278 TGAGATTCGTGTAAGACCATGTCTAGGACATTGGCATCGATA
1 TGAGATTCGTGTAAGACCATGACTAGGACATTGGCATCGATA
39419320 TGAGATTCGTGTAAGACCAT
1 TGAGATTCGTGTAAGACCAT
39419340 AGCTAAGCTA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (42 bp):
TGAGATTCGTGTAAGACCATGACTAGGACATTGGCATCGATA
Found at i:39419353 original size:42 final size:42
Alignment explanation
Indices: 39419236--39419361 Score: 159
Period size: 42 Copynumber: 3.0 Consensus size: 42
39419226 TATCGGGATG
* * ** *
39419236 TGAGATTCATGTAAGACCATGACTGGGACATTTGCATCGATA
1 TGAGATTCGTGTAAGACCATGTCTAAGACATTGGCATCGATA
*
39419278 TGAGATTCGTGTAAGACCATGTCTAGGACATTGGCATCGATA
1 TGAGATTCGTGTAAGACCATGTCTAAGACATTGGCATCGATA
39419320 TGAGATTCGTGTAAGACCATAG-CTAAG-CTATTGG-ATCGATA
1 TGAGATTCGTGTAAGACCAT-GTCTAAGAC-ATTGGCATCGATA
39419361 T
1 T
39419362 ACTATAACAT
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
41 9 0.12
42 67 0.87
43 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (42 bp):
TGAGATTCGTGTAAGACCATGTCTAAGACATTGGCATCGATA
Found at i:39420274 original size:21 final size:21
Alignment explanation
Indices: 39420248--39420304 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 21
39420238 ATGGTATAAG
39420248 GTTGATGAATTGGTACATTTT
1 GTTGATGAATTGGTACATTTT
*
39420269 GTTGATGATGAATTGGTATATTTT
1 G-T--TGATGAATTGGTACATTTT
*
39420293 GTGGCATGAATT
1 GTTG-ATGAATT
39420305 ATATGATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
21 2 0.07
22 8 0.27
23 1 0.03
24 19 0.63
ACGTcount: A:0.25, C:0.04, G:0.26, T:0.46
Consensus pattern (21 bp):
GTTGATGAATTGGTACATTTT
Found at i:39426594 original size:29 final size:28
Alignment explanation
Indices: 39426558--39426635 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
39426548 TCATGAGATT
39426558 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
39426588 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
39426615 TGGCACTAAGTGTGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
39426636 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:39426853 original size:174 final size:174
Alignment explanation
Indices: 39426588--39426915 Score: 593
Period size: 174 Copynumber: 1.9 Consensus size: 174
39426578 AAATTGTACA
*
39426588 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* * *
39426653 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACCTTATCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
39426718 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
*
39426762 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* *
39426827 TGTGCGAACTCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
39426892 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
39426916 ACCTTGAGTT
Statistics
Matches: 147, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
174 147 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:39428462 original size:53 final size:54
Alignment explanation
Indices: 39428338--39428585 Score: 224
Period size: 55 Copynumber: 4.7 Consensus size: 54
39428328 GGGTGTTACA
* * * * *
39428338 ACCATTGCCATGACTTGTCATGGTGTTACGTGGTATCC-T---TT-TGAAACTT
1 ACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAACTT
* * * *
39428387 ACCATTGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATG-AACTC
1 ACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAACTT
* * * *
39428440 ACCAATGCCATGCCTTGGCATGGTCTTATATGGGA-CCTTTGCCTTATGGTAACTT
1 ACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTAT-GAAACTT
* * * * *
39428495 ATCAATGCGATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA-GAAACCTT
1 ACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA-CTT
* *
39428549 ACCAATTGTCATGCCTTGGCATGGTCTTACATGGTAT
1 ACCAA-TGCCATGCCTTGACATGGTCTTACATGGTAT
39428586 TCTTAAACCT
Statistics
Matches: 159, Mismatches: 29, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
49 33 0.21
50 1 0.01
52 2 0.01
53 47 0.30
54 10 0.06
55 64 0.40
56 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.36
Consensus pattern (54 bp):
ACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAACTT
Found at i:39428526 original size:108 final size:110
Alignment explanation
Indices: 39428382--39428582 Score: 291
Period size: 108 Copynumber: 1.8 Consensus size: 110
39428372 ATCCTTTTGA
* *
39428382 AACTTACCATTGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTCGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA
*
39428445 -TGCCATGCCTTGGCATGGTCTTATATGGGACCTTTGCCTTATGGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATGGT
* * * * *
39428490 AACTTATCAATGCGATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTCGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
*
39428555 TGTCATGCCTTGGCATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
39428583 TATTCTTAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
107 1 0.01
108 47 0.58
109 7 0.09
110 26 0.32
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTCGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATGGT
Found at i:39430894 original size:16 final size:16
Alignment explanation
Indices: 39430873--39430905 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
39430863 GATAATCTAT
39430873 AAAACATGGAAAGAAC
1 AAAACATGGAAAGAAC
39430889 AAAACATGGAAAGAAC
1 AAAACATGGAAAGAAC
39430905 A
1 A
39430906 CACAAAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.18, T:0.06
Consensus pattern (16 bp):
AAAACATGGAAAGAAC
Found at i:39431212 original size:43 final size:43
Alignment explanation
Indices: 39431143--39431308 Score: 192
Period size: 43 Copynumber: 3.9 Consensus size: 43
39431133 AGCTCTTACA
* * * *
39431143 ATGCC-ATATCCCAGATATGGTCTTACATGTTATCAC-ATATCG
1 ATGCCAATGTCCCAGATAGGGTCTTACACGTAATCACAATA-CG
* * * ** *
39431185 ATGACATTGTCCCAGACAGGGTCTTACACAAAATCATAATACG
1 ATGCCAATGTCCCAGATAGGGTCTTACACGTAATCACAATACG
*
39431228 ATGCCAATGTCCCAGATAGGGTCTTACACGTAATCACAATACA
1 ATGCCAATGTCCCAGATAGGGTCTTACACGTAATCACAATACG
* *
39431271 ATGCCAATGTCCCAGATATGGTCTTACATGTAATCACA
1 ATGCCAATGTCCCAGATAGGGTCTTACACGTAATCACA
39431309 TCTTGATAAC
Statistics
Matches: 103, Mismatches: 19, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
42 4 0.04
43 96 0.93
44 3 0.03
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (43 bp):
ATGCCAATGTCCCAGATAGGGTCTTACACGTAATCACAATACG
Found at i:39439405 original size:49 final size:50
Alignment explanation
Indices: 39439290--39439461 Score: 160
Period size: 50 Copynumber: 3.5 Consensus size: 50
39439280 GCCTCAAACG
* * * **
39439290 TGTCCCAGACATGGTCTTACATTGGCTCATC-C--ATCA-AGTCGATTCCA
1 TGTCCCAGACATGGTCTTACACTGACT-ATCGCAAATCAGAGCCGACGCCA
*
39439337 TGTCCCAGACATGGCCTTACACTGACTATCG-AAATCA-AGGCCGACGCCA
1 TGTCCCAGACATGGTCTTACACTGACTATCGCAAATCAGA-GCCGACGCCA
* * * * * *
39439386 TGTCCCAGAAATGGTCTTACACT-ACCTCTCGCATATCTGAGCCGATGACA
1 TGTCCCAGACATGGTCTTACACTGA-CTATCGCAAATCAGAGCCGACGCCA
39439436 TGTCCCAGACATGGTCTTACACTGAC
1 TGTCCCAGACATGGTCTTACACTGAC
39439462 ACATCTTGTA
Statistics
Matches: 103, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
46 3 0.03
47 24 0.23
48 6 0.06
49 33 0.32
50 35 0.34
51 2 0.02
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.25
Consensus pattern (50 bp):
TGTCCCAGACATGGTCTTACACTGACTATCGCAAATCAGAGCCGACGCCA
Found at i:39439512 original size:46 final size:46
Alignment explanation
Indices: 39439425--39439642 Score: 212
Period size: 46 Copynumber: 4.7 Consensus size: 46
39439415 CGCATATCTG
*
39439425 AGCCGATGACATGTCCCAGACATGGTCTTACACTGAC--ACATCTTGT
1 AGCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACATCTTGT
**
39439471 AGCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCCCG-
1 AGCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTTGT
* * * **
39439516 AGGCCGATGCATGTCCCAGACATGTCTTACACTAGCTTTCGT-TTCA
1 A-GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTTGT
* ** *
39439562 ATGCCGATGCCATGTCCTAGACATGGTCTTACACTGGCTCCCA-CAATGT
1 A-GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACATC-TTGT
* *
39439611 GGCCGATGCATGTCCCAGGCATGTCTTACACT
1 AGCCGATGCATGTCCCAGACATGTCTTACACT
39439643 AGCACACAAA
Statistics
Matches: 143, Mismatches: 21, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
44 12 0.08
45 15 0.10
46 69 0.48
47 25 0.17
48 21 0.15
49 1 0.01
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (46 bp):
AGCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTTGT
Found at i:39439591 original size:94 final size:92
Alignment explanation
Indices: 39439472--39439645 Score: 251
Period size: 94 Copynumber: 1.9 Consensus size: 92
39439462 ACATCTTGTA
* *
39439472 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATC-CCGAGGCCGATGCATGTCCCAGA
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCACA-CAACGAGGCCGATGCATGTCCCAGA
39439536 CATGTCTTACACTAGCTTTCGTTTCAAT
65 CATGTCTTACACTAGCTTTCGTTTCAAT
* * * *
39439564 GCCGATGCCATGTCCTAGACATGGTCTTACACTGGCTCCCACAATGTGGCCGATGCATGTCCCAG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCACACAACGAGGCCGATGCATGTCCCAG
*
39439629 GCATGTCTTACACTAGC
64 ACATGTCTTACACTAGC
39439646 ACACAAATAA
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
92 7 0.10
93 14 0.19
94 51 0.71
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.26
Consensus pattern (92 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCACACAACGAGGCCGATGCATGTCCCAGAC
ATGTCTTACACTAGCTTTCGTTTCAAT
Found at i:39446267 original size:46 final size:46
Alignment explanation
Indices: 39446217--39446390 Score: 210
Period size: 46 Copynumber: 3.8 Consensus size: 46
39446207 ATGGTTGAGC
*
39446217 GTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 GTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAT
* * * *
39446263 GTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAG
1 GTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--AT
* *
39446308 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAC
1 G--TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAT
* *
39446356 GCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 GTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
39446391 GGGGCGGGTT
Statistics
Matches: 110, Mismatches: 11, Indels: 14
0.81 0.08 0.10
Matches are distributed among these distances:
43 5 0.05
45 4 0.04
46 63 0.57
47 28 0.25
48 4 0.04
50 6 0.05
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
GTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAT
Found at i:39453860 original size:46 final size:46
Alignment explanation
Indices: 39453810--39453982 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
39453800 TGGTTGAGCA
* *
39453810 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
39453856 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* * *
39453903 TCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
39453949 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
39453983 GGGGCGGGGT
Statistics
Matches: 105, Mismatches: 15, Indels: 14
0.78 0.11 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 61 0.58
47 27 0.26
48 3 0.03
50 5 0.05
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:39453966 original size:93 final size:93
Alignment explanation
Indices: 39453807--39453977 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
39453797 GGATGGTTGA
* * *
39453807 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
39453872 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * *
39453900 GCATCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
39453965 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
39453978 ACTTAGGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Done.