Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 73 of 240
Found at i:23315815 original size:89 final size:88
Alignment explanation
Indices: 23315661--23316010 Score: 360
Period size: 89 Copynumber: 3.9 Consensus size: 88
23315651 GTAAAGCGAG
* * * * * * * * ** *
23315661 TTGAAGCTACAAGTCTTATCTCACTGAGGTTACAGTAGAGTAGACTGACCATAACAAGTCTTATC
1 TTGAAGATACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCAA-TCTTATC
*
23315726 TCCCTGAAGTTGCAGTGGAGCATA
65 TCCCTGAAGTTGCAGTGGAGCAGA
* * * *
23315750 CTGAAGATAGCAAACCTTATCTCCCTGAAGTTACAGTGGAGCACG-TTGAAGATACCAATATTAT
1 TTGAAGATA-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCA-GATTGAAGATACCAATCTTAT
23315814 CTCCCTGAAGTTGCAGTGGAGCAGA
64 CTCCCTGAAGTTGCAGTGGAGCAGA
* ** * * * * *
23315839 TTGAAGCTATTAATCTTATCTCCCAGAAGTTGCAATGGAGCAGACTGAAGATAACCAACCTTATT
1 TTGAAGATACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT-ACCAATCTTATC
* *
23315904 TTCCTGAAGTTGCAGTGGAGCAGG
65 TCCCTGAAGTTGCAGTGGAGCAGA
* * * ** *
23315928 TTGAAGATACCAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTATTAATCCTATCT
1 TTGAAGATACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCAATCTTATCT
*
23315993 CCCTGAAGTTGCAATGGA
66 CCCTGAAGTTGCAGTGGA
23316011 ACGGATTAAA
Statistics
Matches: 214, Mismatches: 43, Indels: 9
0.80 0.16 0.03
Matches are distributed among these distances:
87 1 0.00
88 58 0.27
89 118 0.55
90 36 0.17
91 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (88 bp):
TTGAAGATACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCAATCTTATCT
CCCTGAAGTTGCAGTGGAGCAGA
Found at i:23315831 original size:44 final size:44
Alignment explanation
Indices: 23315661--23316010 Score: 353
Period size: 44 Copynumber: 7.9 Consensus size: 44
23315651 GTAAAGCGAG
* * * * * *
23315661 TTGAAGCTA-CAAGTCTTATCTCACTGAGGTTACAGTAGAGTAGA
1 TTGAAGATACCAA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
* ** * *
23315705 CTGACCATAACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCATA
1 TTGAAGATACCAA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
* * * *
23315750 CTGAAGATAGCAAACCTTATCTCCCTGAAGTTACAGTGGAGCACG-
1 TTGAAGATA-CCAATCTTATCTCCCTGAAGTTGCAGTGGAGCA-GA
*
23315795 TTGAAGATACCAATATTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 TTGAAGATACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
* ** * *
23315839 TTGAAGCTATTAATCTTATCTCCCAGAAGTTGCAATGGAGCAGA
1 TTGAAGATACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
* * * * *
23315883 CTGAAGATAACCAACCTTATTTTCCTGAAGTTGCAGTGGAGCAGG
1 TTGAAGAT-ACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
*
23315928 TTGAAGATACCAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGA
1 TTGAAGATACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
* ** * *
23315972 TTGAAGCTATTAATCCTATCTCCCTGAAGTTGCAATGGA
1 TTGAAGATACCAATCTTATCTCCCTGAAGTTGCAGTGGA
23316011 ACGGATTAAA
Statistics
Matches: 251, Mismatches: 50, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
43 1 0.00
44 142 0.57
45 106 0.42
46 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (44 bp):
TTGAAGATACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
Found at i:23315899 original size:133 final size:133
Alignment explanation
Indices: 23315719--23316010 Score: 476
Period size: 133 Copynumber: 2.2 Consensus size: 133
23315709 CCATAACAAG
* * *
23315719 TCTTATCTCCCTGAAGTTGCAGTGGAGCATACTGAAGATAGCAAACCTTATCTCCCTGAAGTTAC
1 TCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAACAAACCTTATCTCCCTGAAGTTAC
*
23315784 AGTGGAGCACGTTGAAGATACCAATATTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAT
66 AGTGGAGCACGTTGAAGATACCAATATTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTAT
23315849 TAA
131 TAA
* * * * *
23315852 TCTTATCTCCCAGAAGTTGCAATGGAGCAGACTGAAGATAACCAACCTTATTTTCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAACAAACCTTATCTCCCTGAAGTTAC
* *
23315917 AGTGGAGCAGGTTGAAGATACCAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTAT
66 AGTGGAGCACGTTGAAGATACCAATATTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTAT
23315982 TAA
131 TAA
*
23315985 TCCTATCTCCCTGAAGTTGCAATGGA
1 TCTTATCTCCCTGAAGTTGCAATGGA
23316011 ACGGATTAAA
Statistics
Matches: 146, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
133 146 1.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.28
Consensus pattern (133 bp):
TCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAACAAACCTTATCTCCCTGAAGTTAC
AGTGGAGCACGTTGAAGATACCAATATTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTAT
TAA
Found at i:23319430 original size:3 final size:3
Alignment explanation
Indices: 23319422--23319457 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
23319412 TGGATTTCTC
23319422 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
23319458 TATTATTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
CCT
Found at i:23319463 original size:3 final size:3
Alignment explanation
Indices: 23319457--23319485 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
23319447 CTCCTCCTCC
23319457 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
23319486 TACTTTAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:23321432 original size:49 final size:48
Alignment explanation
Indices: 23321361--23321628 Score: 452
Period size: 49 Copynumber: 5.6 Consensus size: 48
23321351 CCCTTCGGGA
*
23321361 CTTATCACT-TATATACACTTTCACATTCATCACATCGGCCATTAGAC
1 CTTATCACTATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
23321408 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC-TATATATACACTTTCACATTCATCACATCGGCCATTAGGC
23321457 CTTATCAC-ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACTATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
23321504 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCAC-TATATATACACTTTCACATTCATCACATCGGCCATTAGGC
23321553 CTTATCAC-ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACTATATATACACTTTCACATTCATCACATCGGCCATTAGGC
23321600 CTTATCACATATATATACACTTTCACATT
1 CTTATCAC-TATATATACACTTTCACATT
23321629 TATTCAAATA
Statistics
Matches: 208, Mismatches: 7, Indels: 10
0.92 0.03 0.04
Matches are distributed among these distances:
47 99 0.48
48 1 0.00
49 108 0.52
ACGTcount: A:0.30, C:0.29, G:0.07, T:0.34
Consensus pattern (48 bp):
CTTATCACTATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:23321488 original size:96 final size:96
Alignment explanation
Indices: 23321361--23321628 Score: 509
Period size: 96 Copynumber: 2.8 Consensus size: 96
23321351 CCCTTCGGGA
* *
23321361 CTTATCACTTATATACACTTTCACATTCATCACATCGGCCATTAGACCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
*
23321426 ACTTTCACATTCATCACATTGGCCATTCGGC
66 ACTTTCACATTCATCACATCGGCCATTCGGC
23321457 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
23321522 ACTTTCACATTCATCACATCGGCCATTCGGC
66 ACTTTCACATTCATCACATCGGCCATTCGGC
23321553 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
23321618 ACTTTCACATT
66 ACTTTCACATT
23321629 TATTCAAATA
Statistics
Matches: 169, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 169 1.00
ACGTcount: A:0.30, C:0.29, G:0.07, T:0.34
Consensus pattern (96 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTCGGC
Found at i:23329511 original size:21 final size:22
Alignment explanation
Indices: 23329474--23329516 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
23329464 CCTTATATAA
23329474 TTTTCTTCACATAAAAT-TTAC
1 TTTTCTTCACATAAAATGTTAC
23329495 TTTTCATTCACAT-AAATGTTAC
1 TTTTC-TTCACATAAAATGTTAC
23329517 GCCATATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.33, C:0.19, G:0.02, T:0.47
Consensus pattern (22 bp):
TTTTCTTCACATAAAATGTTAC
Found at i:23330706 original size:3 final size:3
Alignment explanation
Indices: 23330698--23330802 Score: 63
Period size: 3 Copynumber: 33.3 Consensus size: 3
23330688 ATATGCAAGT
* *
23330698 ATA ATA ATA ATA ATAA ATA AT- ATA ATA ATTA TTA GT- ATGA ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA A-TA ATA ATA AT-A ATA ATA
* * *
23330744 ATA ATA ATA ATA ACAA ATA ATGCA ATA ATA ATG ATGCA ATA ACA ATA
1 ATA ATA ATA ATA A-TA ATA AT--A ATA ATA ATA AT--A ATA ATA ATA
*
23330791 TTA ATA A-A ATA A
1 ATA ATA ATA ATA A
23330803 ACTAAAAAAG
Statistics
Matches: 80, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
2 5 0.06
3 61 0.76
4 9 0.11
5 5 0.06
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:23332210 original size:50 final size:51
Alignment explanation
Indices: 23332154--23332628 Score: 263
Period size: 50 Copynumber: 9.5 Consensus size: 51
23332144 GCTAAGGAAG
* * *
23332154 TAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGTAATGTCGGGGAAAC
1 TAAGATCCGCCGTCGTGGCTTCAATCTTTTTAACTGCAATGTCGGGGAAAC
* * ** ** **** * * *
23332205 T-AGATCCACCGTCGTAGCTTCAATCTGCTCCACTGCACCACCAGAG-AAG
1 TAAGATCCGCCGTCGTGGCTTCAATCTTTTTAACTGCAATGTCGGGGAAAC
* * * * * *
23332254 TAAGATCTGACGTTGTGGCTTCAATC-TTTTAATTACAATGTCGAGGAAAC
1 TAAGATCCGCCGTCGTGGCTTCAATCTTTTTAACTGCAATGTCGGGGAAAC
* * * * ** ** ** * * *
23332304 -CAGATCCACCATCGTAGCTTCAATCTGCTCCACTGCACCGCCAGGG-AAG
1 TAAGATCCGCCGTCGTGGCTTCAATCTTTTTAACTGCAATGTCGGGGAAAC
* *
23332353 TAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAAC
1 TAAGATCCGCCGTCGTGGCTTCAATCTTTTTAACTGCAATGTCGGGGAAAC
* * * * ** ** * *
23332404 -CAGATCTGCCGTCGTAGCTTCAATCTATTCCACTGCACCGCCAGGGAAA-
1 TAAGATCCGCCGTCGTGGCTTCAATCTTTTTAACTGCAATGTCGGGGAAAC
** * * *
23332453 TAAGATCCGCCGTTAT-GCTTCAATATTTTTAATTGTAATGTCGGGGAAAC
1 TAAGATCCGCCGTCGTGGCTTCAATCTTTTTAACTGCAATGTCGGGGAAAC
* * ** * * * *
23332503 -AAGATCCGCCGTCGTAGCTTCAATCTGTTCT-ACTGCACCGCCAGAG-AAG
1 TAAGATCCGCCGTCGTGGCTTCAATCT-TTTTAACTGCAATGTCGGGGAAAC
* * *
23332552 TAAGATCCGTCGTTGTGGCTTCAATCTTTTTAACTGCAATGTTGGGGAAA-
1 TAAGATCCGCCGTCGTGGCTTCAATCTTTTTAACTGCAATGTCGGGGAAAC
* **
23332602 TCAGATCCGCCGTCGTGATTTCAATCT
1 TAAGATCCGCCGTCGTGGCTTCAATCT
23332629 GTTCCTCTAC
Statistics
Matches: 290, Mismatches: 122, Indels: 25
0.66 0.28 0.06
Matches are distributed among these distances:
49 71 0.24
50 211 0.73
51 8 0.03
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (51 bp):
TAAGATCCGCCGTCGTGGCTTCAATCTTTTTAACTGCAATGTCGGGGAAAC
Found at i:23332254 original size:100 final size:100
Alignment explanation
Indices: 23332122--23332681 Score: 739
Period size: 100 Copynumber: 5.6 Consensus size: 100
23332112 GCCGTCATGA
* * * * *
23332122 CTTCAATCTATTTCACTACACCGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
1 CTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
* * *
23332187 TTGTAATGTCGGGGAAACTAGATCCACCGTCGTAG
66 TTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAG
* * * * *
23332222 CTTCAATCTGCTCCACTGCACCACCAGAGAAGTAAGATCTGACGTTGTGGCTTCAATC-TTTTAA
1 CTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
* * * *
23332286 TTACAATGTCGAGGAAACCAGATCCACCATCGTAG
66 TTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAG
*
23332321 CTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
1 CTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
*
23332386 TTGCAATGTCGGGGAAACCAGATCTGCCGTCGTAG
66 TTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAG
* * * *
23332421 CTTCAATCTATTCCACTGCACCGCCAGGGAAATAAGATCCGCCGTTAT-GCTTCAATATTTTTAA
1 CTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
* *
23332485 TTGTAATGTCGGGGAAACAAGATCCGCCGTCGTAG
66 TTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAG
* * *
23332520 CTTCAATCTGTTCTACTGCACCGCCAGAGAAGTAAGATCCGTCGTTGTGGCTTCAATCTTTTTAA
1 CTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
* * *
23332585 CTGCAATGTTGGGGAAATCAGATCCGCCGTCGT-G
66 TTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAG
* * * * * * * *
23332619 ATTTCAATCTGTTCCTCTACACCGCTAGGGAAGTATGATTCGCCGTTGTCGTTTCAATCTTTT
1 -CTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTT
23332682 CCACTGTAAT
Statistics
Matches: 402, Mismatches: 55, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
99 180 0.45
100 222 0.55
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (100 bp):
CTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
TTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAG
Found at i:23332485 original size:199 final size:199
Alignment explanation
Indices: 23332135--23332681 Score: 720
Period size: 199 Copynumber: 2.7 Consensus size: 199
23332125 CAATCTATTT
* * * *
23332135 CACTACACCGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGTAATGTCGGG
1 CACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGG
* * * * * * *
23332200 GAAACTAGATCCACCGTCGTAGCTTCAATCTGCTCCACTGCACCACCAGAGAAGTAAGATCTGAC
66 GAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATCCGCC
* *
23332265 GTTGTGGCTTCAATCTTTTAATTACAATGTCGAGGAAACCAGATCCACCATCGTAGCTTCAATCT
131 GTTATGGCTTCAATCTTTTAATTACAATGTCGAGGAAACAAGATCCACCATCGTAGCTTCAATCT
23332330 GCTC
196 GCTC
23332334 CACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGG
1 CACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGG
* * *
23332399 GAAACCAGATCTGCCGTCGTAGCTTCAATCTATTCCACTGCACCGCCAGGGAAATAAGATCCGCC
66 GAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATCCGCC
* ** * * *
23332464 GTTAT-GCTTCAATATTTTTAATTGTAATGTCGGGGAAACAAGATCCGCCGTCGTAGCTTCAATC
131 GTTATGGCTTCAAT-CTTTTAATTACAATGTCGAGGAAACAAGATCCACCATCGTAGCTTCAATC
*
23332528 TGTTC
195 TGCTC
* * * * *
23332533 TACTGCACCGCCAGAGAAGTAAGATCCGTCGTTGTGGCTTCAATCTTTTTAACTGCAATGTTGGG
1 CACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGG
* * * * * * *
23332598 GAAATCAGATCCGCCGTCGT-GATTTCAATCTGTTCCTCTACACCGCTAGGGAAGTATGATTCGC
66 GAAACCAGATCCGCCGTCGTAG-CTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATCCGC
* * *
23332662 CGTTGTCGTTTCAATCTTTT
130 CGTTATGGCTTCAATCTTTT
23332682 CCACTGTAAT
Statistics
Matches: 304, Mismatches: 41, Indels: 6
0.87 0.12 0.02
Matches are distributed among these distances:
198 9 0.03
199 288 0.95
200 7 0.02
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (199 bp):
CACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGG
GAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATCCGCC
GTTATGGCTTCAATCTTTTAATTACAATGTCGAGGAAACAAGATCCACCATCGTAGCTTCAATCT
GCTC
Found at i:23333653 original size:23 final size:23
Alignment explanation
Indices: 23333623--23333668 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
23333613 TCCAAAGAGA
23333623 AAGTCTTAATTTAGACTCTTTCT
1 AAGTCTTAATTTAGACTCTTTCT
23333646 AAGTCTTAATTTAGACTCTTTCT
1 AAGTCTTAATTTAGACTCTTTCT
23333669 TATTAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.48
Consensus pattern (23 bp):
AAGTCTTAATTTAGACTCTTTCT
Found at i:23334331 original size:20 final size:20
Alignment explanation
Indices: 23334306--23334345 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
23334296 TTTTTTCATC
*
23334306 ATTTTTATTTTTTCGATTTTG
1 ATTTTT-TTATTTCGATTTTG
*
23334327 ATTTTTTTATTTTGATTTT
1 ATTTTTTTATTTCGATTTT
23334346 TTTCTGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.15, C:0.03, G:0.07, T:0.75
Consensus pattern (20 bp):
ATTTTTTTATTTCGATTTTG
Found at i:23334348 original size:14 final size:14
Alignment explanation
Indices: 23334306--23334379 Score: 69
Period size: 15 Copynumber: 5.0 Consensus size: 14
23334296 TTTTTTCATC
* *
23334306 ATTTTTATTTTTTCG
1 ATTTTGATTTTTT-T
23334321 ATTTTGATTTTTTT
1 ATTTTGATTTTTTT
23334335 ATTTTGATTTTTTTCT
1 ATTTTGA-TTTTTT-T
*
23334351 GATTTTTTATTTTTTT
1 -A-TTTTGATTTTTTT
23334367 ATTTTG-TTTTTTT
1 ATTTTGATTTTTTT
23334380 TTTCAGATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
13 7 0.14
14 11 0.22
15 19 0.37
16 2 0.04
17 7 0.14
18 5 0.10
ACGTcount: A:0.12, C:0.03, G:0.07, T:0.78
Consensus pattern (14 bp):
ATTTTGATTTTTTT
Found at i:23334363 original size:32 final size:30
Alignment explanation
Indices: 23334313--23334380 Score: 100
Period size: 32 Copynumber: 2.2 Consensus size: 30
23334303 ATCATTTTTA
23334313 TTTTTTCGATTTTGATTTTTTTATTTTGAT
1 TTTTTTCGATTTTGATTTTTTTATTTTGAT
* *
23334343 TTTTTTCTGATTTTTTATTTTTTTATTTTGTT
1 TTTTTTC-GA-TTTTGATTTTTTTATTTTGAT
23334375 TTTTTT
1 TTTTTT
23334381 TTCAGATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 7 0.21
31 2 0.06
32 25 0.74
ACGTcount: A:0.10, C:0.03, G:0.07, T:0.79
Consensus pattern (30 bp):
TTTTTTCGATTTTGATTTTTTTATTTTGAT
Found at i:23334380 original size:14 final size:14
Alignment explanation
Indices: 23334321--23334380 Score: 66
Period size: 14 Copynumber: 4.0 Consensus size: 14
23334311 TATTTTTTCG
*
23334321 ATTTTGATTTTTTT
1 ATTTTGTTTTTTTT
23334335 ATTTTGATTTTTTTCT
1 ATTTTG-TTTTTTT-T
*
23334351 GATTTTTTATTTTTTT
1 -ATTTTGT-TTTTTTT
23334367 ATTTTGTTTTTTTT
1 ATTTTGTTTTTTTT
23334381 TTCAGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 13 0.33
15 12 0.31
16 3 0.08
17 11 0.28
ACGTcount: A:0.12, C:0.02, G:0.07, T:0.80
Consensus pattern (14 bp):
ATTTTGTTTTTTTT
Found at i:23339304 original size:3 final size:3
Alignment explanation
Indices: 23339296--23339367 Score: 58
Period size: 3 Copynumber: 23.3 Consensus size: 3
23339286 ATATGCAAGT
* *
23339296 ATA ATA ATAA ATA AT- ATA GTA ATA ATTA GTA ATA ATA ATA ATA ATA
1 ATA ATA AT-A ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA
* *
23339342 ATGCA ATA ACA ATA TTA ATA A-A ATA A
1 AT--A ATA ATA ATA ATA ATA ATA ATA A
23339368 ACTAAAAAAG
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
2 4 0.07
3 43 0.78
4 5 0.09
5 3 0.05
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:23341580 original size:24 final size:24
Alignment explanation
Indices: 23341553--23341599 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
23341543 TATATGTGTA
23341553 TTTTATTATTGGGATCGAATTATG
1 TTTTATTATTGGGATCGAATTATG
23341577 TTTTATTATTGGGATCGAATTAT
1 TTTTATTATTGGGATCGAATTAT
23341600 TATTGGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.26, C:0.04, G:0.19, T:0.51
Consensus pattern (24 bp):
TTTTATTATTGGGATCGAATTATG
Found at i:23344505 original size:17 final size:17
Alignment explanation
Indices: 23344485--23344520 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
23344475 CATTGTAACT
23344485 TATTTAAGATTGGTTCA
1 TATTTAAGATTGGTTCA
23344502 TATTTAAGATTGGTTCA
1 TATTTAAGATTGGTTCA
23344519 TA
1 TA
23344521 CTTTTGTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.47
Consensus pattern (17 bp):
TATTTAAGATTGGTTCA
Found at i:23345892 original size:29 final size:29
Alignment explanation
Indices: 23345850--23345907 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
23345840 ATCCCAAAAG
23345850 TTAGTTTTTTCAAAAAGGGGAACATTTGT
1 TTAGTTTTTTCAAAAAGGGGAACATTTGT
*
23345879 TTAGTTTTTTCAAAAGGGGGAACATTTGT
1 TTAGTTTTTTCAAAAAGGGGAACATTTGT
23345908 GGGAAGGGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.41
Consensus pattern (29 bp):
TTAGTTTTTTCAAAAAGGGGAACATTTGT
Found at i:23353628 original size:22 final size:22
Alignment explanation
Indices: 23353603--23353645 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
23353593 TATCCAAACA
23353603 ATAACAACAAAATAGTAGCAAT
1 ATAACAACAAAATAGTAGCAAT
* * *
23353625 ATAATAGCGAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
23353646 AACAACATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.14, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAT
Found at i:23354888 original size:17 final size:16
Alignment explanation
Indices: 23354866--23354905 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
23354856 AAGCTTCAGG
23354866 TTAATAAT-ATGTATAT
1 TTAATAATAATGTA-AT
23354882 ATTAATAATAATGTAAT
1 -TTAATAATAATGTAAT
23354899 TTAATAA
1 TTAATAA
23354906 CATAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.32
17 10 0.45
18 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (16 bp):
TTAATAATAATGTAAT
Found at i:23355010 original size:22 final size:22
Alignment explanation
Indices: 23354985--23355035 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
23354975 ATCTTGACTT
* *
23354985 AATAATTACTGAA-TCGAGTTTA
1 AATAATTA-TCAAGTCGAATTTA
*
23355007 AATATTTATCAAGTCGAATTTA
1 AATAATTATCAAGTCGAATTTA
23355029 AATAATT
1 AATAATT
23355036 TGTAAGCATC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (22 bp):
AATAATTATCAAGTCGAATTTA
Found at i:23355114 original size:3 final size:3
Alignment explanation
Indices: 23355108--23355132 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
23355098 TTAATTGAAA
23355108 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
23355133 TTAAAGGATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:23355561 original size:19 final size:18
Alignment explanation
Indices: 23355537--23355587 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
23355527 ATTTTTGTTA
23355537 AAAATTTGAATATATATTT
1 AAAATTTGAA-ATATATTT
**
23355556 AAAA-TTGCAACCATATTT
1 AAAATTTG-AAATATATTT
23355574 AAAATTTGAAATAT
1 AAAATTTGAAATAT
23355588 TAAAATATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
18 17 0.65
19 9 0.35
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (18 bp):
AAAATTTGAAATATATTT
Found at i:23355885 original size:23 final size:24
Alignment explanation
Indices: 23355839--23355882 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
23355829 TTTAATATTC
*
23355839 AAATTTAAACATTAACAGATTTCA
1 AAATTTAAACATTAACAAATTTCA
23355863 AAATTTAAA-ATTAA-AAATTT
1 AAATTTAAACATTAACAAATTT
23355883 TCAGTACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 5 0.26
24 9 0.47
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (24 bp):
AAATTTAAACATTAACAAATTTCA
Found at i:23360690 original size:13 final size:13
Alignment explanation
Indices: 23360674--23360698 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23360664 TTAATTTAGC
23360674 TAATTTAATTGAT
1 TAATTTAATTGAT
23360687 TAATTTAATTGA
1 TAATTTAATTGA
23360699 ATATATAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
TAATTTAATTGAT
Found at i:23362671 original size:23 final size:22
Alignment explanation
Indices: 23362629--23362681 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
23362619 TAGTTCTCTA
*
23362629 TTTAAATTTTTGCTTCTTTATT
1 TTTAAATTTGTGCTTCTTTATT
* *
23362651 CTTTAAATTTGTGTTTTTTTATT
1 -TTTAAATTTGTGCTTCTTTATT
23362674 TATTAAAT
1 T-TTAAAT
23362682 CACCCAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 1 0.04
23 25 0.96
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.66
Consensus pattern (22 bp):
TTTAAATTTGTGCTTCTTTATT
Found at i:23362890 original size:18 final size:18
Alignment explanation
Indices: 23362838--23362890 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
23362828 TAAAATCATT
* *
23362838 AAAATTATTAAAAGTTAT
1 AAAATTATTAAATGTTAA
*
23362856 AAAATTA-TAAATTTTAA
1 AAAATTATTAAATGTTAA
*
23362873 AAAATAATTAAATGTTAA
1 AAAATTATTAAATGTTAA
23362891 TGTGTCATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
17 13 0.45
18 16 0.55
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (18 bp):
AAAATTATTAAATGTTAA
Found at i:23363027 original size:21 final size:22
Alignment explanation
Indices: 23362994--23363034 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
23362984 ATTAAAGGAT
23362994 TAAAAAAGATAAAATAATTAAA
1 TAAAAAAGATAAAATAATTAAA
*
23363016 TAAAAAA-CTAAAATAATTA
1 TAAAAAAGATAAAATAATTA
23363035 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (22 bp):
TAAAAAAGATAAAATAATTAAA
Found at i:23369920 original size:22 final size:21
Alignment explanation
Indices: 23369888--23369934 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
23369878 TATTGATAAA
*
23369888 TTGATGAATTAGGCTT-GAAT
1 TTGATGAATTAAGCTTAGAAT
*
23369908 TTGATAGATATTAAGCTTAGATT
1 TTGAT-GA-ATTAAGCTTAGAAT
23369931 TTGA
1 TTGA
23369935 AAAGGACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 2 0.09
22 8 0.36
23 7 0.32
ACGTcount: A:0.32, C:0.04, G:0.21, T:0.43
Consensus pattern (21 bp):
TTGATGAATTAAGCTTAGAAT
Found at i:23370612 original size:5 final size:5
Alignment explanation
Indices: 23370572--23370600 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
23370562 TATATATATA
23370572 TGAAT TGAAT TGAAT TGAAT TGAAT TGAA
1 TGAAT TGAAT TGAAT TGAAT TGAAT TGAA
23370601 CTAAAATGAA
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:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (5 bp):
TGAAT
Found at i:23370988 original size:204 final size:204
Alignment explanation
Indices: 23370638--23371045 Score: 726
Period size: 204 Copynumber: 2.0 Consensus size: 204
23370628 GACCGAACAC
*
23370638 AGGGTATGACAAATAAATGTAAATGATTATAGGATATGGATATGCAAACAAGAGTAGTTATAAGT
1 AGGGTATGACAAATAAATGTAAATGATTATAGGATATGGATATGCAAACAAGAGTAGTTACAAGT
* *
23370703 ATGATAAAGAAAATATAAATATTTATGCCCATATGAACTTAGTAAAAGGTTAGGATACGATTGAC
66 ATGATAAAGAAAATATAAATATTTATGCCCATATGAACTTAGTAAAAGGTTAGAATACAATTGAC
* *
23370768 ATGCTAATAGGGTTATATGTGCGCTTATATGAGATATGTGATTGCACGAAGATTATTACATGTTA
131 ATGCTAATAAGGTTATATGTGCGCTTATATGAGATATGTGATTGCACGAAGATTATTACAGGTTA
*
23370833 TATCGGGAT
196 TATCAGGAT
*
23370842 AGGGTATGACAAATAAATGTAAATGATTATAGGATATGGATATGCGAACAAGAGTAGTTACAAGT
1 AGGGTATGACAAATAAATGTAAATGATTATAGGATATGGATATGCAAACAAGAGTAGTTACAAGT
*
23370907 ATGATAAAGAAAATATGAATATTTATGCCCATATGAACTTAGTAAAAGGTTAGAATACAATTGAC
66 ATGATAAAGAAAATATAAATATTTATGCCCATATGAACTTAGTAAAAGGTTAGAATACAATTGAC
* *
23370972 ATGCTAATAAGGTTATATGTGCGCTTATATGAGATATGTGGTTGTACGAAGATTATTACAGGTTA
131 ATGCTAATAAGGTTATATGTGCGCTTATATGAGATATGTGATTGCACGAAGATTATTACAGGTTA
23371037 TATCAGGAT
196 TATCAGGAT
23371046 CTAGCATCTA
Statistics
Matches: 194, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
204 194 1.00
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (204 bp):
AGGGTATGACAAATAAATGTAAATGATTATAGGATATGGATATGCAAACAAGAGTAGTTACAAGT
ATGATAAAGAAAATATAAATATTTATGCCCATATGAACTTAGTAAAAGGTTAGAATACAATTGAC
ATGCTAATAAGGTTATATGTGCGCTTATATGAGATATGTGATTGCACGAAGATTATTACAGGTTA
TATCAGGAT
Found at i:23377404 original size:18 final size:18
Alignment explanation
Indices: 23377381--23377416 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
23377371 ACTTTGCATC
23377381 TAATATTGATACCAAAAT
1 TAATATTGATACCAAAAT
*
23377399 TAATATTGATAGCAAAAT
1 TAATATTGATACCAAAAT
23377417 AGCATTCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.33
Consensus pattern (18 bp):
TAATATTGATACCAAAAT
Found at i:23383004 original size:16 final size:16
Alignment explanation
Indices: 23382983--23383015 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
23382973 ATTTTTTGTG
23382983 TTAAATAAATTGTGTT
1 TTAAATAAATTGTGTT
23382999 TTAAATAAATTGTGTT
1 TTAAATAAATTGTGTT
23383015 T
1 T
23383016 ATGTTAAAAT
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:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (16 bp):
TTAAATAAATTGTGTT
Found at i:23384106 original size:20 final size:20
Alignment explanation
Indices: 23384080--23384196 Score: 69
Period size: 20 Copynumber: 5.8 Consensus size: 20
23384070 CTTGTATGAG
23384080 TTTGCACTTTAGTGCCTCTGA
1 TTTGCACTTTAGTGCCTCT-A
* * *
23384101 -TTGCACATCAATGCCTCTA
1 TTTGCACTTTAGTGCCTCTA
* ***
23384120 TTTGGACTACGGTGCCTCTA
1 TTTGCACTTTAGTGCCTCTA
* *
23384140 TTTGCACTTTGGTGCTTCTGA
1 TTTGCACTTTAGTGCCTCT-A
*
23384161 -TTGCACATTT-GTGCCTTTA
1 TTTGCAC-TTTAGTGCCTCTA
* **
23384180 TCTAAACTTTAGTGCCT
1 TTTGCACTTTAGTGCCT
23384197 TTGTTACGCA
Statistics
Matches: 74, Mismatches: 17, Indels: 11
0.73 0.17 0.11
Matches are distributed among these distances:
19 5 0.07
20 65 0.88
21 4 0.05
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (20 bp):
TTTGCACTTTAGTGCCTCTA
Found at i:23387094 original size:13 final size:13
Alignment explanation
Indices: 23387068--23387110 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
23387058 GTATTCTGTT
23387068 AAATGTGTAAATG
1 AAATGTGTAAATG
23387081 AAATG-GTAAGATG
1 AAATGTGTAA-ATG
*
23387094 AAATGTTTAAATG
1 AAATGTGTAAATG
23387107 AAAT
1 AAAT
23387111 TGCTATACGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 4 0.15
13 20 0.74
14 3 0.11
ACGTcount: A:0.49, C:0.00, G:0.21, T:0.30
Consensus pattern (13 bp):
AAATGTGTAAATG
Found at i:23387333 original size:18 final size:18
Alignment explanation
Indices: 23387307--23387345 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
23387297 TCATGTATAT
23387307 GTTTATTAATATGATAAA
1 GTTTATTAATATGATAAA
*
23387325 GTTTGTTAATATGATAAA
1 GTTTATTAATATGATAAA
23387343 GTT
1 GTT
23387346 ACATGTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (18 bp):
GTTTATTAATATGATAAA
Found at i:23397883 original size:21 final size:22
Alignment explanation
Indices: 23397854--23397914 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
23397844 TACATAGCTA
* * *
23397854 GAAAATGAAATGAAATTAGATT
1 GAAATTGAAATGAAATAAGAAT
23397876 G-AATTGAAATGAAATAAGAAT
1 GAAATTGAAATGAAATAAGAAT
*
23397897 GACAATTGATATGAAATA
1 GA-AATTGAAATGAAATA
23397915 GTATAGAGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 18 0.55
22 1 0.03
23 14 0.42
ACGTcount: A:0.54, C:0.02, G:0.18, T:0.26
Consensus pattern (22 bp):
GAAATTGAAATGAAATAAGAAT
Found at i:23417255 original size:12 final size:11
Alignment explanation
Indices: 23417236--23417267 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
23417226 ACCACGTAGG
23417236 TTTTTTGTTTT
1 TTTTTTGTTTT
23417247 TTGTTTTGTTTT
1 TT-TTTTGTTTT
23417259 TTTTTTGTT
1 TTTTTTGTT
23417268 AACCTCATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:23418990 original size:24 final size:24
Alignment explanation
Indices: 23418963--23419014 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
23418953 TTAGTAAGTC
*
23418963 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
23418987 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
23419011 AAAT
1 AAAT
23419015 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:23420957 original size:24 final size:24
Alignment explanation
Indices: 23420930--23420981 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
23420920 TTAGTAAGTC
*
23420930 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
23420954 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
23420978 AAAT
1 AAAT
23420982 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:23421617 original size:15 final size:15
Alignment explanation
Indices: 23421597--23421650 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
23421587 ATACTAAAAA
23421597 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
23421612 ATATTTATAATTATAAT
1 ATATTTATTA-T-TAAT
*
23421629 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
23421646 ATATT
1 ATATT
23421651 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:23421636 original size:19 final size:19
Alignment explanation
Indices: 23421612--23421648 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
23421602 TATTATTAAT
*
23421612 ATATTTATAATTATAATAA
1 ATATTTATAATTAAAATAA
*
23421631 ATATTTATTATTAAAATA
1 ATATTTATAATTAAAATA
23421649 TTAATATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:23423953 original size:2 final size:2
Alignment explanation
Indices: 23423948--23423978 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
23423938 TACACACACA
23423948 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
23423979 ATATATAGCT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:23424117 original size:10 final size:10
Alignment explanation
Indices: 23424102--23424136 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
23424092 GAGAATTTGA
23424102 TCCTTTCTGT
1 TCCTTTCTGT
23424112 TCCTTTCTGT
1 TCCTTTCTGT
*
23424122 TCCTATCT-T
1 TCCTTTCTGT
23424131 TCCTTT
1 TCCTTT
23424137 TTCTTTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 6 0.26
10 17 0.74
ACGTcount: A:0.03, C:0.31, G:0.06, T:0.60
Consensus pattern (10 bp):
TCCTTTCTGT
Found at i:23427345 original size:2 final size:2
Alignment explanation
Indices: 23427338--23427368 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
23427328 GAAAGACACC
23427338 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
23427369 ATGGGCATAA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:23428150 original size:2 final size:2
Alignment explanation
Indices: 23428094--23428130 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
23428084 CAGCTTTAAT
23428094 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
23428131 TTCTTACCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:23429801 original size:30 final size:32
Alignment explanation
Indices: 23429749--23429807 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 32
23429739 AATTAGACAC
23429749 TTTTAAGAAGTTAATGATCAAATTCAACTATT
1 TTTTAAGAAGTTAATGATCAAATTCAACTATT
* *
23429781 TTTTAA-AAGTTTATG-TCAAATTTAACT
1 TTTTAAGAAGTTAATGATCAAATTCAACT
23429808 CTAAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 11 0.44
31 8 0.32
32 6 0.24
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (32 bp):
TTTTAAGAAGTTAATGATCAAATTCAACTATT
Found at i:23432078 original size:27 final size:27
Alignment explanation
Indices: 23432040--23432122 Score: 87
Period size: 27 Copynumber: 3.1 Consensus size: 27
23432030 ATACAAAATA
*
23432040 GTGGCGCCTATCTTAGAGGCGCCAATG
1 GTGGTGCCTATCTTAGAGGCGCCAATG
* * * *
23432067 GTGGTGCCTATCTGACAGGCGCCACTA
1 GTGGTGCCTATCTTAGAGGCGCCAATG
* *
23432094 GTTGTGCC-ATGTTGAGAGGCGCCAATG
1 GTGGTGCCTATCTT-AGAGGCGCCAATG
23432121 GT
1 GT
23432123 CTTATTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
26 3 0.07
27 41 0.93
ACGTcount: A:0.18, C:0.24, G:0.34, T:0.24
Consensus pattern (27 bp):
GTGGTGCCTATCTTAGAGGCGCCAATG
Found at i:23437351 original size:16 final size:16
Alignment explanation
Indices: 23437330--23437368 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
23437320 AAAATAAAAT
23437330 AAAATTACATTATATA
1 AAAATTACATTATATA
23437346 AAAATTACATTATATA
1 AAAATTACATTATATA
23437362 AAAATTA
1 AAAATTA
23437369 AATGAGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATTACATTATATA
Found at i:23437371 original size:21 final size:19
Alignment explanation
Indices: 23437323--23437364 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 19
23437313 AAAATAAAAA
23437323 ATAAAATAAAATTACATTAT
1 ATAAAAT-AAATTACATTAT
23437343 AT--AA-AAATTACATTAT
1 ATAAAATAAATTACATTAT
23437359 ATAAAA
1 ATAAAA
23437365 ATTAAATGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
16 14 0.70
18 4 0.20
20 2 0.10
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAAAATAAATTACATTAT
Found at i:23438530 original size:14 final size:14
Alignment explanation
Indices: 23438507--23438540 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
23438497 TGGTATGAGT
23438507 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
23438520 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
23438534 TTATAGG
1 TTATAGG
23438541 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:23445314 original size:3 final size:3
Alignment explanation
Indices: 23445306--23445337 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
23445296 AACAAATAGG
23445306 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
23445338 GGACTAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:23472412 original size:31 final size:31
Alignment explanation
Indices: 23472352--23472412 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
23472342 ATAATTATTG
* * *
23472352 AACTATTTGAAAGTTTTCATTTAAGTCATTA
1 AACTATTTAAAAGTTTTCATTCAACTCATTA
23472383 AACTATTTAAAAGTTCTT-ATTCAACTCATT
1 AACTATTTAAAAGTT-TTCATTCAACTCATT
23472413 GAGTTGTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (31 bp):
AACTATTTAAAAGTTTTCATTCAACTCATTA
Found at i:23474096 original size:23 final size:23
Alignment explanation
Indices: 23474066--23474112 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
23474056 ATGTTATAAC
*
23474066 TTTTTTTTATTTATCAAAAAATA
1 TTTTTTTTATTTACCAAAAAATA
*
23474089 TTTTTTTTATTTACCAAAATATA
1 TTTTTTTTATTTACCAAAAAATA
23474112 T
1 T
23474113 CAAAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTTTTTATTTACCAAAAAATA
Found at i:23474385 original size:19 final size:21
Alignment explanation
Indices: 23474347--23474385 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
23474337 AATAATTGAT
*
23474347 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
23474368 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
23474386 TTGTTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:23474458 original size:3 final size:3
Alignment explanation
Indices: 23474452--23474480 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
23474442 ATTATTATTA
23474452 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
23474481 AGTATTAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:23478360 original size:22 final size:22
Alignment explanation
Indices: 23478334--23478396 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 22
23478324 CCTTCCTTCC
23478334 CTCTTCTTCTTCTTTTTTTTTT
1 CTCTTCTTCTTCTTTTTTTTTT
*
23478356 CTCTTC-TC--CTTTCCTTTTTT
1 CTCTTCTTCTTCTTT-TTTTTTT
23478376 CTCCTTCTTTCTTTCTTTTTT
1 CT-CTTC-TTC-TTCTTTTTT
23478397 CTTCTCCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
19 4 0.12
20 8 0.25
21 6 0.19
22 6 0.19
23 2 0.06
25 2 0.06
26 4 0.12
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (22 bp):
CTCTTCTTCTTCTTTTTTTTTT
Found at i:23478370 original size:40 final size:38
Alignment explanation
Indices: 23478312--23478504 Score: 183
Period size: 40 Copynumber: 5.2 Consensus size: 38
23478302 TTACCTTTTT
* *
23478312 TTTCTTTTTTT-TCCT-TCC-TTCC-CTCTTCTTCTTC
1 TTTCTTTTTTTCTCTTCTCCTTTCCTTTCTTCTTCTTC
* *
23478346 TTT-TTTTTTTCTCTTCTCCTTTCCTTTTTTCTCCTTC
1 TTTCTTTTTTTCTCTTCTCCTTTCCTTTCTTCTTCTTC
*
23478383 TTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTCTTCTTTC
1 TTTCTTT-TTTTCTCTTCTCCTTTCC-TTTCTTCTTC-TTC
23478424 TTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTT-
1 TTTCTTTTTTTCTCTTCTCCTTTCC-TTTC-TT-CTTCTTC
* *
23478464 GTTCTTTCTTTC-C-TCTCC-TTCCTTTC-T-TTCTTTC
1 TTTCTTTTTTTCTCTTCTCCTTTCCTTTCTTCTTC-TTC
23478498 TTTCTTT
1 TTTCTTT
23478505 CCCTCTCCTT
Statistics
Matches: 136, Mismatches: 11, Indels: 24
0.80 0.06 0.14
Matches are distributed among these distances:
32 3 0.02
33 9 0.07
34 13 0.10
35 3 0.02
36 8 0.06
37 16 0.12
38 8 0.06
39 18 0.13
40 40 0.29
41 14 0.10
42 4 0.03
ACGTcount: A:0.00, C:0.31, G:0.01, T:0.68
Consensus pattern (38 bp):
TTTCTTTTTTTCTCTTCTCCTTTCCTTTCTTCTTCTTC
Found at i:23478375 original size:21 final size:21
Alignment explanation
Indices: 23478349--23478462 Score: 118
Period size: 21 Copynumber: 5.7 Consensus size: 21
23478339 CTTCTTCTTT
23478349 TTTTTTTCTCTTCTCCTTTCC
1 TTTTTTTCTCTTCTCCTTTCC
*
23478370 -TTTTTTCTC--CTTCTTT-C
1 TTTTTTTCTCTTCTCCTTTCC
*
23478387 TTTCTTTTTTCTTCTCCTTTCC
1 TTT-TTTTCTCTTCTCCTTTCC
*
23478409 TTTTCTTCTTCTT-T-CTTT-C
1 TTTTTTTC-TCTTCTCCTTTCC
23478428 TTTTTTTCTCTTCTCCTTTCC
1 TTTTTTTCTCTTCTCCTTTCC
23478449 TTTTCTTTC-CTTCT
1 TTTT-TTTCTCTTCT
23478463 TGTTCTTTCT
Statistics
Matches: 77, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
17 1 0.01
18 12 0.16
19 15 0.19
20 17 0.22
21 20 0.26
22 12 0.16
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTTTTCTCTTCTCCTTTCC
Found at i:23478383 original size:37 final size:39
Alignment explanation
Indices: 23478335--23478504 Score: 203
Period size: 40 Copynumber: 4.5 Consensus size: 39
23478325 CTTCCTTCCC
*
23478335 TCTTCTTCTTCTTT-TTTTTTTCTCTTCTCCTTTCCTTT
1 TCTTCTCCTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTT
*
23478373 T-TTCTCCTTCTTTCTTTCTTTTTTCTTCTCCTTTCCTTT
1 TCTTCTCCTTCTTTCTTT-TTTTCTCTTCTCCTTTCCTTT
*
23478412 TCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTT
1 TCTTC-TCCTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTT
*
23478452 TCTT-TCCTTCTTGTTCTTTCTTTC-C-TCTCC-TTCC-TT
1 TCTTCTCCTTC-T-TTCTTTTTTTCTCTTCTCCTTTCCTTT
*
23478488 TCTT-TCTTTCTTTCTTT
1 TCTTCTCCTTCTTTCTTT
23478505 CCCTCTCCTT
Statistics
Matches: 119, Mismatches: 7, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
34 6 0.05
35 1 0.01
36 11 0.09
37 15 0.13
38 14 0.12
39 23 0.19
40 37 0.31
41 12 0.10
ACGTcount: A:0.00, C:0.31, G:0.01, T:0.69
Consensus pattern (39 bp):
TCTTCTCCTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTT
Found at i:23478389 original size:4 final size:4
Alignment explanation
Indices: 23478380--23478505 Score: 80
Period size: 4 Copynumber: 29.8 Consensus size: 4
23478370 TTTTTTCTCC
23478380 TTCT TTCT TTCT TT-T TTCT TCTCCT TTCCT TT-T CTTC- TTCT TTCT
1 TTCT TTCT TTCT TTCT TTCT T-T-CT TT-CT TTCT -TTCT TTCT TTCT
* * *
23478425 TTCT TTTT TTCT CTTC- TCCT TTCCTT TTCT TTCC TTCTT GTTCT TTCT
1 TTCT TTCT TTCT -TTCT TTCT TT-C-T TTCT TTCT TTC-T -TTCT TTCT
* *
23478473 TTCCT CTCCT TCCT TTCT TTCT TTCT TTCT TTC
1 TT-CT -TTCT TTCT TTCT TTCT TTCT TTCT TTC
23478506 CCTCTCCTTT
Statistics
Matches: 100, Mismatches: 8, Indels: 28
0.74 0.06 0.21
Matches are distributed among these distances:
3 9 0.09
4 64 0.64
5 17 0.17
6 10 0.10
ACGTcount: A:0.00, C:0.31, G:0.01, T:0.68
Consensus pattern (4 bp):
TTCT
Found at i:23478420 original size:58 final size:54
Alignment explanation
Indices: 23478352--23478504 Score: 145
Period size: 54 Copynumber: 2.8 Consensus size: 54
23478342 CTTCTTTTTT
23478352 TTTTC-TCTTCTCCTTTCCTTTTTTCTCCTTCTTTCTTTCTTTTTTCTTCTCCTTTCC
1 TTTTCTTCTTCTCCTTTCCTTTTTTCT-CTTCTTTCTTTCTTTTTTCTT-TCC-TT-C
* * * *
23478409 TTTTCTTCTTCTTTCTTTCTTTTTTTCTCTTC-TCCTTTC-CTTTTCTTTCCTTC
1 TTTTCTTCTTC-TCCTTTCCTTTTTTCTCTTCTTTCTTTCTTTTTTCTTTCCTTC
* *
23478462 TTGTTCTTTCTT-TCCTCTCCTTCCTTTCT-TTCTTTCTTTCTTT
1 TT-TTC-TTCTTCTCCTTTCCTT-TTTTCTCTTCTTTCTTTCTTT
23478505 CCCTCTCCTT
Statistics
Matches: 79, Mismatches: 10, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
53 13 0.16
54 16 0.20
55 9 0.11
56 7 0.09
57 11 0.14
58 9 0.11
59 14 0.18
ACGTcount: A:0.00, C:0.31, G:0.01, T:0.68
Consensus pattern (54 bp):
TTTTCTTCTTCTCCTTTCCTTTTTTCTCTTCTTTCTTTCTTTTTTCTTTCCTTC
Found at i:23478584 original size:27 final size:27
Alignment explanation
Indices: 23478554--23478627 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 27
23478544 TTATGCACTA
*
23478554 GTGCTGCCAATGGTATTGGCACCATTG
1 GTGCTGCCAATGGCATTGGCACCATTG
* * *
23478581 GTGCCGCCAATGGCATGGGCACCTTTG
1 GTGCTGCCAATGGCATTGGCACCATTG
23478608 GTG-TCGCCAATGGCATTGGC
1 GTGCT-GCCAATGGCATTGGC
23478628 GTGACCAGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.16, C:0.26, G:0.32, T:0.26
Consensus pattern (27 bp):
GTGCTGCCAATGGCATTGGCACCATTG
Found at i:23485597 original size:29 final size:30
Alignment explanation
Indices: 23485517--23485598 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 30
23485507 GATTAAATCA
*
23485517 AAATTAAAGTTTCAAGTATACATTTGAACC
1 AAATTAAAGTTTCAAGTATATATTTGAACC
* * * *
23485547 ACAACTAGAGTTTCACGTATATATTTGCACC
1 A-AATTAAAGTTTCAAGTATATATTTGAACC
*
23485578 AAATTAAAG-TTCATGTATATA
1 AAATTAAAGTTTCAAGTATATA
23485599 ATTGTACATT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
29 11 0.26
30 7 0.16
31 25 0.58
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (30 bp):
AAATTAAAGTTTCAAGTATATATTTGAACC
Found at i:23487184 original size:26 final size:27
Alignment explanation
Indices: 23487153--23487213 Score: 90
Period size: 26 Copynumber: 2.3 Consensus size: 27
23487143 TTAGCTCTTA
23487153 TGAGCTTCCCGATT-ATAGGCTCTTCG
1 TGAGCTTCCCGATTAATAGGCTCTTCG
* *
23487179 TGAGCTT-CCTATTAATTGGCTCTTCG
1 TGAGCTTCCCGATTAATAGGCTCTTCG
23487205 TGAGCTTCC
1 TGAGCTTCC
23487214 TGATATGGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 5 0.16
26 25 0.81
27 1 0.03
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.38
Consensus pattern (27 bp):
TGAGCTTCCCGATTAATAGGCTCTTCG
Found at i:23487322 original size:25 final size:24
Alignment explanation
Indices: 23487293--23487339 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
23487283 AGCTACTCGT
*
23487293 TATAGGCTCGCATGAGTTTCCTGAA
1 TATA-GCTCGCATGAGCTTCCTGAA
**
23487318 TATAGCTCTTATGAGCTTCCTG
1 TATAGCTCGCATGAGCTTCCTG
23487340 TTATACAGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (24 bp):
TATAGCTCGCATGAGCTTCCTGAA
Found at i:23489113 original size:21 final size:21
Alignment explanation
Indices: 23489084--23489130 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
23489074 CCCATATATT
*
23489084 TAATGTAAACATACTTTT-TCA
1 TAATATAAACAT-CTTTTCTCA
*
23489105 TAATATAAACATGTTTTCTCA
1 TAATATAAACATCTTTTCTCA
23489126 TAATA
1 TAATA
23489131 CAATTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.43
Consensus pattern (21 bp):
TAATATAAACATCTTTTCTCA
Found at i:23490981 original size:98 final size:98
Alignment explanation
Indices: 23490807--23491003 Score: 322
Period size: 98 Copynumber: 2.0 Consensus size: 98
23490797 TGTACAATAA
* * * *
23490807 ACTTTAAAAGAACATCTACTAATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTAATCCAAGATTTAAGAAATCACACACAATACGTTAAGGCACAATT
*
23490872 CCTCTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
*
23490905 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACACAATACGTTAAGGCACAATT
1 ACTTTAAAAGAACATCCACTAATCCAAGATTTAAGAAATCACACACAATACGTTAAGGCACAATT
* *
23490970 CCTTTAAAATCCCAAACTCGGAATATTTTCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
23491003 A
1 A
23491004 TTATTTTTTA
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTAATCCAAGATTTAAGAAATCACACACAATACGTTAAGGCACAATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:23492341 original size:19 final size:19
Alignment explanation
Indices: 23492307--23492362 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 19
23492297 AATCATATAT
23492307 TCTAAGATTGCACATATCATA
1 TCTAAGATTG--CATATCATA
**
23492328 TCTTGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
23492347 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
23492363 CTCAAAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 23 0.74
21 8 0.26
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:23492631 original size:44 final size:42
Alignment explanation
Indices: 23492582--23493418 Score: 427
Period size: 44 Copynumber: 19.4 Consensus size: 42
23492572 TCTACTCCAT
23492582 TGCAACTTCAGGGAGATAAGACTTGCCATCTTAGTCTGTCTCAC
1 TGCAACTTCAGGGAGATAAGACTTG-CATCTTAGTCTG-CTCAC
*
23492626 TGCAACTTCA-GGAGGATAAGACTTGCTTCCTTAGTCTGCTCCAC
1 TGCAACTTCAGGGA-GATAAGACTTGCAT-CTTAGTCTGCT-CAC
* * *
23492670 TGCAACTTCAGGGAGATAA-ACTAG-ATGC-GA-TCTGCTCTC
1 TGCAACTTCAGGGAGATAAGACTTGCAT-CTTAGTCTGCTCAC
* * * *
23492709 TGCAACTTCAGAGAGATAAGATCTGTG-ATTTTAATCCGCTCTAC
1 TGCAACTTCAGGGAGATAAGA-CT-TGCATCTTAGTCTGCTC-AC
* * *
23492753 TGCAACTTCAGGGAGATAGGATTATCGGC-T-TTATTCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGACT-T--GCATCTTAGTCTGCT-CAC
* *
23492797 TGCAACTTCAGGGAGATAAGATTTGCCAT-TTCAGTCTGCTTCAT
1 TGCAACTTCAGGGAGATAAGACTTG-CATCTT-AGTCTGC-TCAC
* * *
23492841 TGTAACTTCA-GGAGGATAAGGCTTGCTTACTTAGTCTTG-TCCAC
1 TGCAACTTCAGGGA-GATAAGACTTGCAT-CTTAGTC-TGCT-CAC
* * * * *
23492885 CGCAACTTTAGGGAGATAAGACTAG-ATGC-GA-TCTGCTCTC
1 TGCAACTTCAGGGAGATAAGACTTGCAT-CTTAGTCTGCTCAC
* ** * * * *
23492925 TGTAACTTCAAAGAGATAAGA-TCTGTAATTTTAATCCGCTCCAC
1 TGCAACTTCAGGGAGATAAGACT-TG-CATCTTAGTCTGCT-CAC
* * * * ** * *
23492969 TGTAACTTCAGGAAAATAGGAC-TGCCGGCTTTAATCTGCTCTAT
1 TGCAACTTCAGGGAGATAAGACTTG-CATC-TTAGTCTGCTC-AC
* *
23493013 TGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCAC
1 TGCAACTTCAGGGAGATAAGACTTG-CATCTT-AGTCTG-CTCAC
* *
23493058 TGTAACTTCA-GGAGGATAAGACTTGCTTACTTAGTCTG-TCCAC
1 TGCAACTTCAGGGA-GATAAGACTTGCAT-CTTAGTCTGCT-CAC
* * *
23493101 -GCAACTTCAGGGAGATAAGACTAG-ATGC-GA-TCTGCTCTC
1 TGCAACTTCAGGGAGATAAGACTTGCAT-CTTAGTCTGCTCAC
* * * * * *
23493140 TGTAACTTCAGAGAGATAAGA-TCTGTAATTTTAATCCGCTCCAC
1 TGCAACTTCAGGGAGATAAGACT-TG-CATCTTAGTCTGCT-CAC
* ** *
23493184 TGCAACTTCAGGGAGATAGGA-TTGTCGGCTTTAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGACTTG-CATC-TTAGTCTGCT-CAC
* *
23493228 TGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCAC
1 TGCAACTTCAGGGAGATAAGACTTG-CATCTT-AGTCTG-CTCAC
* * * *
23493273 TGTAACTTTA-GAAGGATAAGACTTGCTTACTTAGTCTGCTCCAC
1 TGCAACTTCAGGGA-GATAAGACTTGCAT-CTTAGTCTGCT-CAC
* * *
23493317 TGCAACTTCAGGGAGATAAGACTAG-ATGC-GA-TCTGCTCTC
1 TGCAACTTCAGGGAGATAAGACTTGCAT-CTTAGTCTGCTCAC
* * * *
23493357 TGCAACTTCAGAGAGATAAGATCTGTG-ATTTTAATCCGCTCCAC
1 TGCAACTTCAGGGAGATAAGA-CT-TGCATCTTAGTCTGCT-CAC
23493401 TGCAACTTCAGGGAGATA
1 TGCAACTTCAGGGAGATA
23493419 GGATTGTCGA
Statistics
Matches: 616, Mismatches: 115, Indels: 124
0.72 0.13 0.15
Matches are distributed among these distances:
39 28 0.05
40 71 0.12
41 17 0.03
42 38 0.06
43 62 0.10
44 312 0.51
45 83 0.13
46 5 0.01
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (42 bp):
TGCAACTTCAGGGAGATAAGACTTGCATCTTAGTCTGCTCAC
Found at i:23492755 original size:83 final size:83
Alignment explanation
Indices: 23492576--23492770 Score: 209
Period size: 83 Copynumber: 2.3 Consensus size: 83
23492566 CTTCAATCTA
* * *
23492576 CTCCATTGCAACTTCAGGGAGATAAGACTTGCCAT-CTTAGTCTGTCTCACTGCAACTTCAGGAG
1 CTCCACTGCAACTTCAGGGAGATAA-ACTAG--ATGC-GA-TCTGTCTCACTGCAACTTCAGGAG
* * *
23492640 GATAAGACTTGCTTCCTTAGTCTG
61 GATAAGACTTGATT-CTTAATCCG
*
23492664 CTCCACTGCAACTTCAGGGAGATAAACTAGATGCGATCTG-CTCTCTGCAACTTCA-GAGAGATA
1 CTCCACTGCAACTTCAGGGAGATAAACTAGATGCGATCTGTCTCACTGCAACTTCAGGAG-GATA
23492727 AGATCTGTGATT-TTAATCCG
65 AGA-CT-TGATTCTTAATCCG
*
23492747 CTCTACTGCAACTTCAGGGAGATA
1 CTCCACTGCAACTTCAGGGAGATA
23492771 GGATTATCGG
Statistics
Matches: 95, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
82 3 0.03
83 50 0.53
84 6 0.06
85 7 0.07
86 1 0.01
87 4 0.04
88 24 0.25
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Consensus pattern (83 bp):
CTCCACTGCAACTTCAGGGAGATAAACTAGATGCGATCTGTCTCACTGCAACTTCAGGAGGATAA
GACTTGATTCTTAATCCG
Found at i:23493174 original size:215 final size:217
Alignment explanation
Indices: 23492565--23493440 Score: 1413
Period size: 215 Copynumber: 4.1 Consensus size: 217
23492555 AGGAATTAGT
* * * * * * *
23492565 GCTTCAATCTACTCCATTGCAACTTCAGGGAGATAAGACTTGCCATCTT-AGTCTGTCTCACTGC
1 GCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGT
*
23492629 AACTTCAGGAGGATAAGACTTGCTTCCTTAGTCTGCTCCACTGCAACTTCAGGGAGATAA-ACTA
66 AACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
* *
23492693 GATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCTACTGCAA
131 GATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGCAA
*
23492758 CTTCAGGGAGATAGGATTATCG
196 CTTCAGGGAGATAGGATTGTCG
* * * *
23492780 GCTTTATTCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCAT-TTCAGTCTGCTTCATTGT
1 GCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGT
* * *
23492844 AACTTCAGGAGGATAAGGCTTGCTTACTTAGTCTTG-TCCACCGCAACTTTAGGGAGATAAGACT
66 AACTTCAGGAGGATAAGACTTGCTTACTTAGTC-TGCTCCACTGCAACTTCAGGGAGATAAGACT
* * *
23492908 AGATGCGATCTGCTCTCTGTAACTTCAAAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGTA
130 AGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGCA
* * * *
23492973 ACTTCAGGAAAATAGGACTGCCG
195 ACTTCAGGGAGATAGGATTGTCG
* *
23492996 GCTTTAATCTGCTCTATTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGT
1 GCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGT
23493061 AACTTCAGGAGGATAAGACTTGCTTACTTAGTCTG-TCCAC-GCAACTTCAGGGAGATAAGACTA
66 AACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
*
23493124 GATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGCAA
131 GATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGCAA
23493189 CTTCAGGGAGATAGGATTGTCG
196 CTTCAGGGAGATAGGATTGTCG
23493211 GCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGT
1 GCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGT
* *
23493276 AACTTTAGAAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
66 AACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
*
23493341 GATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCACTGCAA
131 GATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGCAA
23493406 CTTCAGGGAGATAGGATTGTCG
196 CTTCAGGGAGATAGGATTGTCG
*
23493428 ACTTTAATCTGCT
1 GCTTTAATCTGCT
23493441 TCCCACTATC
Statistics
Matches: 611, Mismatches: 44, Indels: 10
0.92 0.07 0.02
Matches are distributed among these distances:
214 2 0.00
215 304 0.50
216 137 0.22
217 168 0.27
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (217 bp):
GCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGT
AACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
GATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGCAA
CTTCAGGGAGATAGGATTGTCG
Found at i:23493401 original size:432 final size:431
Alignment explanation
Indices: 23492565--23493440 Score: 1425
Period size: 432 Copynumber: 2.0 Consensus size: 431
23492555 AGGAATTAGT
* * * *
23492565 GCTTCAATCTACTCCATTGCAACTTCAGGGAGATAAGACTTGCCATCTTAGTCTGTCTCACTGCA
1 GCTTTAATCTGCTCCATTGCAACTTCAGGAAGATAAGACTTGCCATCTTAGTCTGCCTCACTGCA
*
23492630 ACTTCAGGAGGATAAGACTTGCTTCCTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAACTAGA
66 ACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAACTAGA
* *
23492695 TGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCTACTGCAACT
131 TGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGCAACT
* *
23492760 TCAGGGAGATAGGATTATCGGCTTTATTCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCA
196 TCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCA
* * * *
23492825 TTTCAGTCTGCTTCATTGTAACTTCAGGAGGATAAGGCTTGCTTACTTAGTCTTGTCCACCGCAA
261 TTTCAGTCTGCCTCACTGTAACTTCAGAAGGATAAGACTTGCTTACTTAGTCTTGTCCACCGCAA
* *
23492890 CTTTAGGGAGATAAGACTAGATGCGATCTGCTCTCTGTAACTTCAAAGAGATAAGATCTGTAATT
326 CTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAAAGAGATAAGATCTGTAATT
*
23492955 TTAATCCGCTCCACTGTAACTTCAGGAAAATAGGACTGCCG
391 TTAATCCGCTCCACTGCAACTTCAGGAAAATAGGACTGCCG
* * *
23492996 GCTTTAATCTGCTCTATTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGT
1 GCTTTAATCTGCTCCATTGCAACTTCAGGAAGATAAGACTTGCCATCTT-AGTCTGCCTCACTGC
23493061 AACTTCAGGAGGATAAGACTTGCTTACTTAGTCTG-TCCAC-GCAACTTCAGGGAGATAAGACTA
65 AACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAA-ACTA
*
23493124 GATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGCAA
129 GATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGCAA
*
23493189 CTTCAGGGAGATAGGATTGTCGGCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGC
194 CTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGC
* *
23493254 CATCTTCAGTCTGCCTCACTGTAACTTTAGAAGGATAAGACTTGCTTACTTAGTC-TGCTCCACT
259 CAT-TTCAGTCTGCCTCACTGTAACTTCAGAAGGATAAGACTTGCTTACTTAGTCTTG-TCCACC
*
23493318 GCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGT
322 GCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAAAGAGATAAGATCTGT
* * * * *
23493383 GATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGTCG
387 AATTTTAATCCGCTCCACTGCAACTTCAGGAAAATAGGACTGCCG
*
23493428 ACTTTAATCTGCT
1 GCTTTAATCTGCT
23493441 TCCCACTATC
Statistics
Matches: 411, Mismatches: 30, Indels: 7
0.92 0.07 0.02
Matches are distributed among these distances:
430 18 0.04
431 182 0.44
432 211 0.51
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (431 bp):
GCTTTAATCTGCTCCATTGCAACTTCAGGAAGATAAGACTTGCCATCTTAGTCTGCCTCACTGCA
ACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAACTAGA
TGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGCAACT
TCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCA
TTTCAGTCTGCCTCACTGTAACTTCAGAAGGATAAGACTTGCTTACTTAGTCTTGTCCACCGCAA
CTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAAAGAGATAAGATCTGTAATT
TTAATCCGCTCCACTGCAACTTCAGGAAAATAGGACTGCCG
Found at i:23493593 original size:132 final size:132
Alignment explanation
Indices: 23493433--23494048 Score: 1056
Period size: 132 Copynumber: 4.7 Consensus size: 132
23493423 TGTCGACTTT
* * * *
23493433 AATCTGCTTCCCACTATCTTGGAAAGATATGATTTGTTGTCTTCGATCTGCTCCACTATTGCTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTA
* *
23493498 GGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAAACAAGGCTTGGTGGCT
66 GGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCT
23493563 TA
131 TA
*
23493565 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTA
* *
23493630 GGGAGAGAAGATCTACAATTTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCT
66 GGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCT
23493695 TA
131 TA
*
23493697 AATCTGCTTCCCACTATCTTGGAAATATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTA
* *
23493762 GGGAGATAAGATCTACAAT-TTCAACCTTCTCAGCTGCTGCTTAGGGAGACAAGGCTTGGTGGCT
66 GGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCT
23493826 TA
131 TA
*
23493828 AATCTGCTTCCCACTATCTTAGAAAGATAAGATTCG-CTGTCTTCGATCTGCTCCACTACTGCTT
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGTC-GTCTTCGATCTGCTCCACTACTGCTT
*
23493892 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCACAGGGAGACAAGGCTTGGTGGC
65 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
23493957 TTA
130 TTA
* *
23493960 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGTTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTA
*
23494025 GGGAGATAAGATCTACAATTTTCA
66 GGGAGATAAGATCTACAATCTTCA
23494049 CTGATTTGTT
Statistics
Matches: 461, Mismatches: 20, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
130 1 0.00
131 125 0.27
132 334 0.72
133 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (132 bp):
AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTA
GGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCT
TA
Found at i:23493836 original size:263 final size:263
Alignment explanation
Indices: 23493433--23494045 Score: 1057
Period size: 263 Copynumber: 2.3 Consensus size: 263
23493423 TGTCGACTTT
* * * *
23493433 AATCTGCTTCCCACTATCTTGGAAAGATATGATTTGTTGTCTTCGATCTGCTCCACTATTGCTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTA
*
23493498 GGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAAACAAGGCTTGGTGGCT
66 GGGAGATAAGATCTACAAT-TTCAACCTACTCAGCTGCTGCTCAGGGAAACAAGGCTTGGTGGCT
* *
23493563 TAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTG-TCGTCTTCGATCTGCTCCACTACTGC
130 TAAATCTGCTTCCCACTATCTTAGAAAGATAAGATTCGCT-GTCTTCGATCTGCTCCACTACTGC
* *
23493627 TTAGGGAGAGAAGATCTACAATTTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTG
194 TTAGGGAGAGAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCACAGGGAGACAAGGCTTGGTG
23493692 GCTTA
259 GCTTA
*
23493697 AATCTGCTTCCCACTATCTTGGAAATATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTA
* * *
23493762 GGGAGATAAGATCTACAATTTCAACCTTCTCAGCTGCTGCTTAGGGAGACAAGGCTTGGTGGCTT
66 GGGAGATAAGATCTACAATTTCAACCTACTCAGCTGCTGCTCAGGGAAACAAGGCTTGGTGGCTT
23493827 AAATCTGCTTCCCACTATCTTAGAAAGATAAGATTCGCTGTCTTCGATCTGCTCCACTACTGCTT
131 AAATCTGCTTCCCACTATCTTAGAAAGATAAGATTCGCTGTCTTCGATCTGCTCCACTACTGCTT
*
23493892 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCACAGGGAGACAAGGCTTGGTGGC
196 AGGGAGAGAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCACAGGGAGACAAGGCTTGGTGGC
23493957 TTA
261 TTA
* *
23493960 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGTTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTA
23494025 GGGAGATAAGATCTACAATTT
66 GGGAGATAAGATCTACAATTT
23494046 TCACTGATTT
Statistics
Matches: 331, Mismatches: 17, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
263 251 0.76
264 80 0.24
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (263 bp):
AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGTCGTCTTCGATCTGCTCCACTACTGCTTA
GGGAGATAAGATCTACAATTTCAACCTACTCAGCTGCTGCTCAGGGAAACAAGGCTTGGTGGCTT
AAATCTGCTTCCCACTATCTTAGAAAGATAAGATTCGCTGTCTTCGATCTGCTCCACTACTGCTT
AGGGAGAGAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCACAGGGAGACAAGGCTTGGTGGC
TTA
Found at i:23495273 original size:21 final size:21
Alignment explanation
Indices: 23495244--23495289 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
23495234 TGGCCTCTCA
*
23495244 TTTTACTTTTTCTTTTTTC-CT
1 TTTTAC-TTTTCTTTTTCCTCT
*
23495265 TTTTCCTTTTCTTTTTCCTCT
1 TTTTACTTTTCTTTTTCCTCT
23495286 TTTT
1 TTTT
23495290 TTTGAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTACTTTTCTTTTTCCTCT
Found at i:23495287 original size:14 final size:14
Alignment explanation
Indices: 23495239--23495288 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
23495229 CACCTTGGCC
23495239 TCTCATTTTACTTTT
1 TCTC-TTTTACTTTT
* *
23495254 TCTTTTTTCCTTTT
1 TCTCTTTTACTTTT
23495268 TC-CTTTT-CTTTT
1 TCTCTTTTACTTTT
23495280 TCCTCTTTT
1 T-CTCTTTT
23495289 TTTTGAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 6 0.20
13 5 0.17
14 16 0.53
15 3 0.10
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.72
Consensus pattern (14 bp):
TCTCTTTTACTTTT
Found at i:23499559 original size:98 final size:98
Alignment explanation
Indices: 23499380--23499576 Score: 322
Period size: 98 Copynumber: 2.0 Consensus size: 98
23499370 GTACAATAAA
* * *
23499380 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCTAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAAGGCACAATT
*
23499445 CCTCTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
*
23499478 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAAGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAAGGCACAATT
* * *
23499543 CTTTTAAAATCTCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
23499576 A
1 A
23499577 TTATTTAAAA
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.29
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAAGGCACAATT
CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:23500897 original size:19 final size:19
Alignment explanation
Indices: 23500873--23500945 Score: 119
Period size: 19 Copynumber: 3.8 Consensus size: 19
23500863 AATGATATAT
23500873 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
** *
23500892 TCTAAGATTATATATCATC
1 TCTAAGATTGCATATCATA
23500911 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
23500930 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
23500946 CTCAAAAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:23501461 original size:22 final size:22
Alignment explanation
Indices: 23501436--23501481 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
23501426 AAAGTAGTAG
* *
23501436 GCACTGAAGTGCGGAACGATAA
1 GCACCGAAGTGCGAAACGATAA
*
23501458 GCACCGAAGTGCGAAACGGTAA
1 GCACCGAAGTGCGAAACGATAA
23501480 GC
1 GC
23501482 GTTAAAGAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.22, G:0.33, T:0.11
Consensus pattern (22 bp):
GCACCGAAGTGCGAAACGATAA
Found at i:23504116 original size:45 final size:41
Alignment explanation
Indices: 23504024--23504155 Score: 122
Period size: 45 Copynumber: 3.0 Consensus size: 41
23504014 ACAGATACAT
*
23504024 GGTGGATCAGCACATAGC-ACCACCCTTATAGTCAATGATACTC
1 GGTGGATCAGCACATAGCAACCA-CCTTATAATCAATG-TAC-C
23504067 GGTGGATTCAGCACATAGCAACCACCTTCATAATCAATAGTACC
1 GGTGGA-TCAGCACATAGCAACCACCTT-ATAATCAAT-GTACC
* * * *
23504111 AGGTGGAATCAACACACAACAACCACATTTATAATCAATGGTACC
1 -GGTGG-ATCAGCACATAGCAACCAC-CTTATAATCAAT-GTACC
23504156 CGGTACACGT
Statistics
Matches: 76, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
43 6 0.08
44 17 0.22
45 49 0.64
46 4 0.05
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.22
Consensus pattern (41 bp):
GGTGGATCAGCACATAGCAACCACCTTATAATCAATGTACC
Found at i:23504434 original size:17 final size:18
Alignment explanation
Indices: 23504405--23504438 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
23504395 TCAATTTAGT
23504405 CCAAAAATCACATTTTTG
1 CCAAAAATCACATTTTTG
23504423 CCAAAAAT-ACATTTTT
1 CCAAAAATCACATTTTT
23504439 ACCCCTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.41, C:0.21, G:0.03, T:0.35
Consensus pattern (18 bp):
CCAAAAATCACATTTTTG
Found at i:23518686 original size:20 final size:21
Alignment explanation
Indices: 23518641--23518686 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
23518631 GCTCATCTGG
* *
23518641 TTTTGCTGCTGCTCCCTCCCT
1 TTTTCCTGCTGCTCCCGCCCT
*
23518662 GTTTCCTGCTGC-CCCGCCCT
1 TTTTCCTGCTGCTCCCGCCCT
23518682 TTTTC
1 TTTTC
23518687 TAATATTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.00, C:0.43, G:0.15, T:0.41
Consensus pattern (21 bp):
TTTTCCTGCTGCTCCCGCCCT
Found at i:23522730 original size:21 final size:22
Alignment explanation
Indices: 23522701--23522747 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
23522691 CAGAAGGAGT
*
23522701 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
23522723 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
23522744 GAGT
1 GAGT
23522748 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:23527763 original size:28 final size:25
Alignment explanation
Indices: 23527707--23527763 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 25
23527697 TAATTTAGAG
*
23527707 ATCACTTAAACAAAAAAAATTAAAT
1 ATCACTTAAACAAAAAAAAATAAAT
*
23527732 ATCACTTATAACAAAAATAAAAATAAGT
1 ATCACTTA-AAC-AAAA-AAAAATAAAT
23527760 ATCA
1 ATCA
23527764 AAATATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 8 0.30
26 3 0.11
27 4 0.15
28 12 0.44
ACGTcount: A:0.61, C:0.12, G:0.02, T:0.25
Consensus pattern (25 bp):
ATCACTTAAACAAAAAAAAATAAAT
Found at i:23527898 original size:21 final size:21
Alignment explanation
Indices: 23527868--23527910 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
23527858 TTGAAGAAGA
*
23527868 AAGTTCAACCCACCAACTGGC
1 AAGTTCAACCCACCAACCGGC
*
23527889 AAGTTTAACCCACCAACCGGC
1 AAGTTCAACCCACCAACCGGC
23527910 A
1 A
23527911 TAAGCACACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.35, C:0.37, G:0.14, T:0.14
Consensus pattern (21 bp):
AAGTTCAACCCACCAACCGGC
Found at i:23528996 original size:41 final size:41
Alignment explanation
Indices: 23528951--23529124 Score: 233
Period size: 41 Copynumber: 4.2 Consensus size: 41
23528941 CTTATAGACT
* ** *
23528951 TATAGTCTAATTCCGTTCACCGGCACTTAGCCTGCTAGG-CC
1 TATAGTCTGATTCAATTCACCGGCACTTAGCCTGCT-GGACG
* * *
23528992 TATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTGGACA
1 TATAGTCTGATTCAATTCACCGGCACTTAGCCTGCTGGACG
* *
23529033 TATAATCCGATTCAATTCACCGGCACTTAGCCTGCTGGACG
1 TATAGTCTGATTCAATTCACCGGCACTTAGCCTGCTGGACG
* *
23529074 TATAGTCCGATTCAATTCACCGGCACTTAGCCTGCTAGACG
1 TATAGTCTGATTCAATTCACCGGCACTTAGCCTGCTGGACG
23529115 TATAGTCTGA
1 TATAGTCTGA
23529125 ACAATTTCAC
Statistics
Matches: 120, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 2 0.02
41 118 0.98
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (41 bp):
TATAGTCTGATTCAATTCACCGGCACTTAGCCTGCTGGACG
Found at i:23530691 original size:11 final size:11
Alignment explanation
Indices: 23530675--23530733 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
23530665 TAAAAAAATT
23530675 TATTTTAAAAA
1 TATTTTAAAAA
23530686 TATTTT--AAA
1 TATTTTAAAAA
23530695 -A--TTAAAAA
1 TATTTTAAAAA
*
23530703 -A-TTAAAAAA
1 TATTTTAAAAA
23530712 GTATTTTAAAAA
1 -TATTTTAAAAA
23530724 TATTTTAAAA
1 TATTTTAAAA
23530734 TTAAAAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
6 2 0.05
8 5 0.12
9 9 0.22
11 17 0.43
12 7 0.17
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:23530755 original size:44 final size:42
Alignment explanation
Indices: 23530659--23530796 Score: 180
Period size: 44 Copynumber: 3.4 Consensus size: 42
23530649 ATTTTATTTT
**
23530659 AAAAA-TTAAAAAAATTTATTTTAAAAATATTTTAAAATT-A
1 AAAAATTTAAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
23530699 AAAAA-TT--AAAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAATTTAAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
*
23530738 AAAAATTTTAAAAAAAAAGTATTTTAAAAGTATTTTAAAATTAA
1 AAAAA-TTT-AAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
*
23530782 AAAAA-TAAAAAAAAA
1 AAAAATTTAAAAAAAA
23530797 TTTATTATAT
Statistics
Matches: 88, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
38 28 0.32
39 6 0.07
40 7 0.08
41 10 0.11
42 1 0.01
44 36 0.41
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (42 bp):
AAAAATTTAAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
Found at i:23530766 original size:11 final size:11
Alignment explanation
Indices: 23530752--23530777 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
23530742 ATTTTAAAAA
23530752 AAAAGTATTTT
1 AAAAGTATTTT
23530763 AAAAGTATTTT
1 AAAAGTATTTT
23530774 AAAA
1 AAAA
23530778 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:23530783 original size:17 final size:17
Alignment explanation
Indices: 23530653--23530766 Score: 76
Period size: 17 Copynumber: 6.6 Consensus size: 17
23530643 ACCAAAATTT
23530653 TATTTTAAAAATTAAAAA
1 TATTTT-AAAATTAAAAA
* **
23530671 -AATTT-ATTTTAAAAA
1 TATTTTAAAATTAAAAA
23530686 TATTTTAAAATTAAAAA
1 TATTTTAAAATTAAAAA
**
23530703 -ATTAAAAAAGTATTTTAAAAA
1 TATT-TTAAA--A--TTAAAAA
23530724 TATTTTAAAATTAAAAA
1 TATTTTAAAATTAAAAA
*
23530741 AATTTTAAAA--AAAAA
1 TATTTTAAAATTAAAAA
23530756 GTATTTTAAAA
1 -TATTTTAAAA
23530767 GTATTTTAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
15 13 0.17
16 16 0.21
17 31 0.41
19 2 0.03
21 10 0.13
22 3 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
TATTTTAAAATTAAAAA
Found at i:23532155 original size:154 final size:152
Alignment explanation
Indices: 23531877--23532390 Score: 665
Period size: 154 Copynumber: 3.3 Consensus size: 152
23531867 CAATTGTTCG
* **
23531877 TATTTCGACCCTTTGTTCGTATTTTTTTC-GGATTTTATTA-TTTTAAAAAATATAATATTTTCT
1 TATTTCGACCCTTTGTTCGTATTTTTTCCTGGATTTTATTACTTCAAAAAAATATAATATTTTCT
*
23531940 AATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTCATTTAGTATGTTTTTT
66 AATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTCATTAAGTATGTTTTTT
23532005 AAATAAATTTAAAAAAAACCCT
131 AAATAAATTTAAAAAAAACCCT
* *
23532027 TATTTCGGCCCTTTGTTCGTATTTTTTCCTGGATTTTATTACATTCAATAAAAATATATTATTTT
1 TATTTCGACCCTTTGTTCGTATTTTTTCCTGGATTTTATTAC-TTCAA-AAAAATATAATATTTT
* * * * * *
23532092 CGT-ATTTTATTATTTTACATTGTTTTAGTACATTATGTTTGAAATGTATTAACTAATTTTGTTT
64 C-TAATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTCATTAAGTATGTTT
*
23532156 TTTAAATAAATTTAGTAAAAAACCCT
128 TTTAAATAAATTTA-AAAAAAACCCT
* * ** * *
23532182 TATTTTGACCCTTTGTTCGTATTTTTTCCTTAGATTTTATTACTTTTAAAAAATATACTATTTTT
1 TATTTCGACCCTTTGTTCGTATTTTTTCC-TGGATTTTATTACTTCAAAAAAATATAATATTTTC
* * * * *
23532247 TAATTTGATTATTTTACATTATTTTAGTACATTACAATTGAAATGTATTCATTCAGTGTGTTTTT
65 TAATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTCATTAAGTATGTTTTT
*
23532312 TAAATAAATTTTAAAAAAACCCCT
130 TAAATAAA-TTTAAAAAAAACCCT
* * * *
23532336 TATTTCGGCCATTTGTTCATATTTTTTCCCCGGATTTTATTACTTGCAATAAAAA
1 TATTTCGACCCTTTGTTCGTATTTTTT-CCTGGATTTTATTACTT-CAA-AAAAA
23532391 ACACACTAAA
Statistics
Matches: 312, Mismatches: 40, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
150 27 0.09
151 11 0.04
153 4 0.01
154 205 0.66
155 48 0.15
156 17 0.05
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.51
Consensus pattern (152 bp):
TATTTCGACCCTTTGTTCGTATTTTTTCCTGGATTTTATTACTTCAAAAAAATATAATATTTTCT
AATTTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTCATTAAGTATGTTTTTT
AAATAAATTTAAAAAAAACCCT
Found at i:23538248 original size:30 final size:30
Alignment explanation
Indices: 23538212--23538271 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
23538202 ACTCTCAGAT
23538212 AACTTTACCCTTTCAATCATTAAATGGCAC
1 AACTTTACCCTTTCAATCATTAAATGGCAC
23538242 AACTTTACCCTTTCAATCATTAAATGGCAC
1 AACTTTACCCTTTCAATCATTAAATGGCAC
23538272 CTTTCCCTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (30 bp):
AACTTTACCCTTTCAATCATTAAATGGCAC
Found at i:23541693 original size:21 final size:19
Alignment explanation
Indices: 23541669--23541720 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 19
23541659 TAAAATTTAA
23541669 AATTATTAAAAATATAATTTT
1 AATT-TTAAAAA-ATAATTTT
*
23541690 AATTTTAAAAAATAGTTTT
1 AATTTTAAAAAATAATTTT
23541709 ATATTTTTAAAA
1 A-A-TTTTAAAA
23541721 TTTTAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 8 0.29
20 8 0.29
21 12 0.43
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
AATTTTAAAAAATAATTTT
Found at i:23541708 original size:19 final size:20
Alignment explanation
Indices: 23541669--23541721 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
23541659 TAAAATTTAA
23541669 AATTATTAAAAATATAATTTT
1 AATT-TTAAAAATATAATTTT
*
23541690 AATTTTAAAAA-ATAGTTTT
1 AATTTTAAAAATATAATTTT
*
23541709 ATATTTTTAAAAT
1 A-ATTTTAAAAAT
23541722 TTTAAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 8 0.29
20 16 0.57
21 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
AATTTTAAAAATATAATTTT
Found at i:23564083 original size:22 final size:22
Alignment explanation
Indices: 23564058--23564102 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
23564048 ATAAATAATT
*
23564058 ATAAAACAATAATATATGATAA
1 ATAAAACAATAATAAATGATAA
* * *
23564080 ATAATATAATAATAAATGTTAA
1 ATAAAACAATAATAAATGATAA
23564102 A
1 A
23564103 ATATGCTCCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (22 bp):
ATAAAACAATAATAAATGATAA
Found at i:23564505 original size:20 final size:22
Alignment explanation
Indices: 23564471--23564523 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
23564461 AATTTAAAAA
*
23564471 TTTAAAAATTATAAAAGTTATT
1 TTTAAAAATTATAAAAATTATT
23564493 TTTAAAAA-T-TAAAAATTA--
1 TTTAAAAATTATAAAAATTATT
23564511 -TTAAAAATTATAA
1 TTTAAAAATTATAA
23564524 TTTTTTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 7 0.25
18 1 0.04
19 3 0.11
20 8 0.29
21 1 0.04
22 8 0.29
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
TTTAAAAATTATAAAAATTATT
Found at i:23564506 original size:29 final size:31
Alignment explanation
Indices: 23564463--23564521 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
23564453 TTTTTTAAAA
*
23564463 TTTAAAAATTTAAAAATTA-TAAAAGTTATT
1 TTTAAAAATTTAAAAATTATTAAAAATTATT
23564493 TTTAAAAA-TTAAAAATTATTAAAAATTAT
1 TTTAAAAATTTAAAAATTATTAAAAATTAT
23564522 AATTTTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (31 bp):
TTTAAAAATTTAAAAATTATTAAAAATTATT
Found at i:23568187 original size:1 final size:1
Alignment explanation
Indices: 23568181--23568207 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
23568171 ATGCAAAATT
23568181 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
23568208 GGGAACTCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:23575838 original size:6 final size:6
Alignment explanation
Indices: 23575827--23575905 Score: 95
Period size: 6 Copynumber: 13.2 Consensus size: 6
23575817 TCTTTTTATG
* * * ** * *
23575827 TGTGTA TGTGTA TGTGTA TGTTTA TGTGTA TGTGTA TGTGCA TGTGCA
1 TGTGCA TGTGCA TGTGCA TGTGCA TGTGCA TGTGCA TGTGCA TGTGCA
23575875 TGTGCA TGTGCA TGTGCA TGTGCA TGTGCA T
1 TGTGCA TGTGCA TGTGCA TGTGCA TGTGCA T
23575906 TTATAATAAG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 70 1.00
ACGTcount: A:0.16, C:0.09, G:0.32, T:0.43
Consensus pattern (6 bp):
TGTGCA
Found at i:23588682 original size:13 final size:14
Alignment explanation
Indices: 23588666--23588695 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
23588656 ATTTATAAAC
23588666 AATATTATG-ATAT
1 AATATTATGTATAT
23588679 AATATTATGTATAT
1 AATATTATGTATAT
23588693 AAT
1 AAT
23588696 CCCTTAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (14 bp):
AATATTATGTATAT
Found at i:23591541 original size:4 final size:4
Alignment explanation
Indices: 23591525--23591580 Score: 94
Period size: 4 Copynumber: 13.8 Consensus size: 4
23591515 GTAAGGGCAG
*
23591525 CATA CATTA CATA CATA CATA CATA CATA CATG CATA CATA CATA CATA
1 CATA CA-TA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
23591574 CATA CAT
1 CATA CAT
23591581 TCACATATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
4 45 0.92
5 4 0.08
ACGTcount: A:0.46, C:0.25, G:0.02, T:0.27
Consensus pattern (4 bp):
CATA
Found at i:23592157 original size:6 final size:6
Alignment explanation
Indices: 23592137--23592185 Score: 80
Period size: 6 Copynumber: 8.0 Consensus size: 6
23592127 TTTATCAATC
*
23592137 TCTGAT TCATGAT TCTGAT TCTGAT TCTGAT TCTGGT TCTGAT TCTGAT
1 TCTGAT TC-TGAT TCTGAT TCTGAT TCTGAT TCTGAT TCTGAT TCTGAT
23592186 ATGTTTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
6 34 0.85
7 6 0.15
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.49
Consensus pattern (6 bp):
TCTGAT
Found at i:23594978 original size:27 final size:27
Alignment explanation
Indices: 23594948--23595020 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 27
23594938 TGTCTTGAAT
23594948 TTGTTAGATATTGATTATGTTTTAAGC
1 TTGTTAGATATTGATTATGTTTTAAGC
23594975 TTGTTAGATATTGAATTTATTATGTTTTAAGC
1 TTGTTAGATATTG-----ATTATGTTTTAAGC
*
23595007 TTGTTGGATATTGA
1 TTGTTAGATATTGA
23595021 AATGATTGAC
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
27 14 0.35
32 26 0.65
ACGTcount: A:0.26, C:0.03, G:0.19, T:0.52
Consensus pattern (27 bp):
TTGTTAGATATTGATTATGTTTTAAGC
Found at i:23595000 original size:32 final size:32
Alignment explanation
Indices: 23594961--23595021 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
23594951 TTAGATATTG
23594961 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
*
23594993 ATTATGTTTTAAGCTTGTTGGATATTGAA
1 ATTATGTTTTAAGCTTGTTAGATATTGAA
23595022 ATGATTGACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.28, C:0.03, G:0.18, T:0.51
Consensus pattern (32 bp):
ATTATGTTTTAAGCTTGTTAGATATTGAATTT
Found at i:23596251 original size:20 final size:20
Alignment explanation
Indices: 23596226--23596263 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
23596216 ACAATTTAAA
23596226 ATATAAATTTATTAATATGT
1 ATATAAATTTATTAATATGT
23596246 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
23596264 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
ATATAAATTTATTAATATGT
Found at i:23596375 original size:14 final size:14
Alignment explanation
Indices: 23596356--23596393 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
23596346 CCAGAAAAGT
23596356 AAATCATTTTCCAA
1 AAATCATTTTCCAA
*
23596370 AAATCATTTTTCGAA
1 AAATCA-TTTTCCAA
23596385 AAA-CATTTT
1 AAATCATTTT
23596394 ACTGGCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 4 0.18
14 8 0.36
15 10 0.45
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39
Consensus pattern (14 bp):
AAATCATTTTCCAA
Found at i:23596386 original size:15 final size:15
Alignment explanation
Indices: 23596356--23596393 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
23596346 CCAGAAAAGT
23596356 AAATCA-TTTTCCAA
1 AAATCATTTTTCCAA
*
23596370 AAATCATTTTTCGAA
1 AAATCATTTTTCCAA
23596385 AAA-CATTTT
1 AAATCATTTT
23596394 ACTGGCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39
Consensus pattern (15 bp):
AAATCATTTTTCCAA
Found at i:23606475 original size:18 final size:18
Alignment explanation
Indices: 23606452--23606486 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
23606442 TGTTCATATC
*
23606452 TATTGTTGAAAATAAGAT
1 TATTGTTAAAAATAAGAT
23606470 TATTGTTAAAAATAAGA
1 TATTGTTAAAAATAAGA
23606487 AATTGAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (18 bp):
TATTGTTAAAAATAAGAT
Found at i:23606491 original size:17 final size:18
Alignment explanation
Indices: 23606453--23606491 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
23606443 GTTCATATCT
* *
23606453 ATTGTTGAAAATAAGATT
1 ATTGTTAAAAATAAGATA
23606471 ATTGTTAAAAATAAGA-A
1 ATTGTTAAAAATAAGATA
23606488 ATTG
1 ATTG
23606492 AATTAAATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (18 bp):
ATTGTTAAAAATAAGATA
Found at i:23606627 original size:24 final size:25
Alignment explanation
Indices: 23606551--23606634 Score: 134
Period size: 25 Copynumber: 3.4 Consensus size: 25
23606541 GTGGAAAAAT
*
23606551 GATGAATTGATGGTAAAATGCAAAG
1 GATGAATTGACGGTAAAATGCAAAG
23606576 GATGAATTGACGGTAAAATGCAAAG
1 GATGAATTGACGGTAAAATGCAAAG
* *
23606601 GATGAATTGACGGT-ATATGCAAGG
1 GATGAATTGACGGTAAAATGCAAAG
23606625 GATGAATTGA
1 GATGAATTGA
23606635 TGACAAATGT
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
24 18 0.32
25 38 0.68
ACGTcount: A:0.40, C:0.06, G:0.30, T:0.24
Consensus pattern (25 bp):
GATGAATTGACGGTAAAATGCAAAG
Found at i:23608785 original size:22 final size:23
Alignment explanation
Indices: 23608760--23608816 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
23608750 TGCACTAATG
23608760 AACAGAGAGCACTA-AAGTGCTA
1 AACAGAGAGCACTAGAAGTGCTA
* *
23608782 AACAAAGAGCAC-AGATGTGCTA
1 AACAGAGAGCACTAGAAGTGCTA
*
23608804 AACGGAGAGCACT
1 AACAGAGAGCACT
23608817 GTTGTGCTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 1 0.03
22 28 0.97
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACTAGAAGTGCTA
Found at i:23608822 original size:22 final size:22
Alignment explanation
Indices: 23608776--23608825 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
23608766 GAGCACTAAA
23608776 GTGCTAAACAAAGAGCACAGAT
1 GTGCTAAACAAAGAGCACAGAT
** * *
23608798 GTGCTAAACGGAGAGCACTGTT
1 GTGCTAAACAAAGAGCACAGAT
23608820 GTGCTA
1 GTGCTA
23608826 GTAATCAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (22 bp):
GTGCTAAACAAAGAGCACAGAT
Found at i:23609818 original size:5 final size:5
Alignment explanation
Indices: 23609808--23609876 Score: 138
Period size: 5 Copynumber: 13.8 Consensus size: 5
23609798 TGTTTGTTTT
23609808 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
23609858 TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATA
23609877 TACTTAACTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 64 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:23614087 original size:22 final size:23
Alignment explanation
Indices: 23614062--23614109 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 23
23614052 AATTTTATGT
23614062 TTTTTTAA-ATATATTTTTATAA
1 TTTTTTAATATATATTTTTATAA
23614084 -TTTTTAATATATATTTTTATAA
1 TTTTTTAATATATATTTTTATAA
23614106 TTTT
1 TTTT
23614110 ATTATAAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 7 0.29
22 14 0.58
23 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTTTAATATATATTTTTATAA
Found at i:23614110 original size:21 final size:21
Alignment explanation
Indices: 23614064--23614135 Score: 87
Period size: 21 Copynumber: 3.4 Consensus size: 21
23614054 TTTTATGTTT
23614064 TTTTAA-ATATATTTTTATAA
1 TTTTAATATATATTTTTATAA
23614084 TTTTTAATATATATTTTTATAA
1 -TTTTAATATATATTTTTATAA
*
23614106 TTTTATTATA-AGTTTTTGA-AA
1 TTTTAATATATA-TTTTT-ATAA
23614127 TTTTAATAT
1 TTTTAATAT
23614136 TTTTTGTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
20 1 0.02
21 30 0.65
22 15 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (21 bp):
TTTTAATATATATTTTTATAA
Found at i:23619825 original size:43 final size:43
Alignment explanation
Indices: 23619679--23619837 Score: 164
Period size: 43 Copynumber: 3.7 Consensus size: 43
23619669 GATGTGTTTT
* * *
23619679 CGTGTAAGACCAAGTTTGGGACGTTGGCATCGAT-TTGAGATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATT-TGA-TTA
* * * * * *
23619723 CGTGTAAGACCATGTCTGGGACATCGACATCG-TATATGATTT
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTA
23619765 CGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATTTGATTA
1 CGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTTGATTA
*
23619808 CATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
23619838 TGTACGAGCT
Statistics
Matches: 94, Mismatches: 15, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
42 29 0.31
43 36 0.38
44 29 0.31
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.30
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTA
Done.