Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 123 of 135
Found at i:40712751 original size:30 final size:30
Alignment explanation
Indices: 40712659--40712929 Score: 92
Period size: 30 Copynumber: 9.2 Consensus size: 30
40712649 CTGGATGGTA
*
40712659 CAAAAATTACCATTTTACCCCTAAACTTT-
1 CAAAAATTACAATTTTACCCCTAAACTTTC
* *
40712688 CTAAAATT-CAATTTTCAACCCC--GA-TTTCAC
1 CAAAAATTACAATTTT--ACCCCTAAACTTT--C
*
40712718 CAAAAATTACTATTTTACCCCTAAACTTTC
1 CAAAAATTACAATTTTACCCCTAAACTTTC
* * * **
40712748 C-AAAATTCCATTTTTA-ACCTCGA-TTTC
1 CAAAAATTACAATTTTACCCCTAAACTTTC
*
40712775 ATCAAAAATTACCATTTTACCCCTAAAAC-TT-
1 --CAAAAATTACAATTTTACCCCT-AAACTTTC
* * * *
40712806 CTAAAATTCCATTTTTAACCCC---AGTTTCAC
1 CAAAAATTACAATTTT-ACCCCTAAACTTT--C
* *
40712836 CAAAAATTACCATTTTACCCTTAAAC-TTC
1 CAAAAATTACAATTTTACCCCTAAACTTTC
* * * *
40712865 CTAAAATTTCATTTTTAACCCC--GA-TTTAAC
1 CAAAAATTACAATTTT-ACCCCTAAACTTT--C
* *
40712895 CAAAAATTACTATTTTA-CCCTCAAATTTTC
1 CAAAAATTACAATTTTACCCCT-AAACTTTC
40712925 CAAAA
1 CAAAA
40712930 TTCTCTTTTT
Statistics
Matches: 171, Mismatches: 40, Indels: 61
0.63 0.15 0.22
Matches are distributed among these distances:
26 1 0.01
27 9 0.05
28 17 0.10
29 55 0.32
30 66 0.39
31 13 0.08
32 10 0.06
ACGTcount: A:0.36, C:0.27, G:0.01, T:0.36
Consensus pattern (30 bp):
CAAAAATTACAATTTTACCCCTAAACTTTC
Found at i:40712753 original size:59 final size:59
Alignment explanation
Indices: 40712659--40712974 Score: 408
Period size: 59 Copynumber: 5.4 Consensus size: 59
40712649 CTGGATGGTA
* * *
40712659 CAAAAATTACCATTTTACCCCTAAACTTTCTAAAATTCAATTTTCAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
* * *
40712718 CAAAAATTACTATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCAT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
*
40712777 CAAAAATTACCATTTTACCCCTAAAAC-TTCTAAAATTCCATTTTTAACCCC-AGTTTCAC
1 CAAAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCCCGA-TTTCAC
* * *
40712836 CAAAAATTACCATTTTACCCTTAAAC-TTCCTAAAATTTCATTTTTAACCCCGATTTAAC
1 CAAAAATTACCATTTTACCCCTAAACTTTCC-AAAATTCCATTTTTAACCCCGATTTCAC
* * * * *
40712895 CAAAAATTACTATTTTA-CCCTCAAATTTTCCAAAATTCTC-TTTTTGACCTCGATTTCAT
1 CAAAAATTACCATTTTACCCCT-AAACTTTCCAAAATTC-CATTTTTAACCCCGATTTCAC
*
40712954 CAAAAATTACCATTTTGCCCC
1 CAAAAATTACCATTTTACCCC
40712975 GCGAGTCCAA
Statistics
Matches: 225, Mismatches: 24, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
58 11 0.05
59 201 0.89
60 13 0.06
ACGTcount: A:0.34, C:0.27, G:0.02, T:0.37
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
Found at i:40713011 original size:28 final size:27
Alignment explanation
Indices: 40712956--40713014 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 27
40712946 GATTTCATCA
*
40712956 AAAATTACCATTTTGCCCCGCGAGTCC
1 AAAATTACCATTTTGCCCCGCGAATCC
40712983 AAAATTACCATTTTGCCCC-CGGATATCC
1 AAAATTACCATTTTGCCCCGC-GA-ATCC
40713011 AAAA
1 AAAA
40713015 GTCTCATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 1 0.03
27 21 0.72
28 7 0.24
ACGTcount: A:0.32, C:0.31, G:0.12, T:0.25
Consensus pattern (27 bp):
AAAATTACCATTTTGCCCCGCGAATCC
Found at i:40717291 original size:59 final size:59
Alignment explanation
Indices: 40717210--40717384 Score: 208
Period size: 61 Copynumber: 2.9 Consensus size: 59
40717200 AAGAAACGAC
* * *
40717210 GAAATCGGGGTTGAAAACAGAATTTTGGAAAGTTTAGGGGTAAAATAGTAAATTTTAGT
1 GAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTTAGGGGTAAAATGGTAAATTTTAGT
* * * *
40717269 GAGATCGGGGTTAAAAATAGAATTTTGGAAAGTTTTAAGGGTAAAAATGGTAATTTTTGGT
1 GAAATCGGGGTTAAAAATAGAATTTTGGAAAG-TTTAGGGGT-AAAATGGTAAATTTTAGT
* * * * **
40717330 GAAACCGAGGTTAAAAATGGAGTTTTGGAAAGTTCGGGGGTAAAATGGT-AATTTT
1 GAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTTAGGGGTAAAATGGTAAATTTT
40717385 CGGACAGTCC
Statistics
Matches: 98, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
58 5 0.05
59 37 0.38
60 14 0.14
61 42 0.43
ACGTcount: A:0.37, C:0.03, G:0.29, T:0.31
Consensus pattern (59 bp):
GAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTTAGGGGTAAAATGGTAAATTTTAGT
Found at i:40719349 original size:6 final size:6
Alignment explanation
Indices: 40719338--40719388 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
40719328 TCATAATTTG
* * *
40719338 ATTTAA ATTTAA ATAGTTGA ATATAA ATTTAA A-ATAA ATTTAA ATTTAA
1 ATTTAA ATTTAA AT--TTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
40719387 AT
1 AT
40719389 AAATCAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
5 4 0.11
6 27 0.75
8 5 0.14
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (6 bp):
ATTTAA
Found at i:40719390 original size:27 final size:29
Alignment explanation
Indices: 40719341--40719410 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 29
40719331 TAATTTGATT
**
40719341 TAAATTTAAATAGTTGAATATAAATTTAAAA
1 TAAATTTAAAT--TTGAATATAAATCAAAAA
40719372 TAAATTTAAATTT-AA-ATAAATCAAAAA
1 TAAATTTAAATTTGAATATAAATCAAAAA
*
40719399 TTAATTTAAATT
1 TAAATTTAAATT
40719411 CAAAATTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 21 0.58
28 2 0.06
29 2 0.06
31 11 0.31
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (29 bp):
TAAATTTAAATTTGAATATAAATCAAAAA
Found at i:40721069 original size:17 final size:17
Alignment explanation
Indices: 40721034--40721079 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
40721024 GTTTGTTGGT
*
40721034 TTAAAATAAATAAATTA
1 TTAAAATAAATAAAATA
40721051 TTAAACATAAA-AAAATA
1 TTAAA-ATAAATAAAATA
40721068 TTTAAAA-AAATA
1 -TTAAAATAAATA
40721080 TATAATTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 3 0.12
17 12 0.48
18 10 0.40
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
TTAAAATAAATAAAATA
Found at i:40721446 original size:63 final size:63
Alignment explanation
Indices: 40721362--40721483 Score: 190
Period size: 63 Copynumber: 1.9 Consensus size: 63
40721352 GTTTTCATTA
* * ** *
40721362 TTAAAATTATTGTGTTGAATTTAGGTTCATTACACTGTTCTTTTTTAGTTCATAGTTATATTG
1 TTAAAATTATTGTATTAAATTTAGGTTCATTACACCATTATTTTTTAGTTCATAGTTATATTG
*
40721425 TTAAAATTATTTTATTAAATTTAGGTTCATTACACCATTATTTTTTAGTTCATAGTTAT
1 TTAAAATTATTGTATTAAATTTAGGTTCATTACACCATTATTTTTTAGTTCATAGTTAT
40721484 CAGGAGCATA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 53 1.00
ACGTcount: A:0.29, C:0.08, G:0.11, T:0.52
Consensus pattern (63 bp):
TTAAAATTATTGTATTAAATTTAGGTTCATTACACCATTATTTTTTAGTTCATAGTTATATTG
Found at i:40724135 original size:16 final size:17
Alignment explanation
Indices: 40724103--40724135 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40724093 TGTTGAGGTC
*
40724103 AAAATAAATAAATTTTA
1 AAAATAAATAAAATTTA
40724120 AAAATAAA-AAAATTTA
1 AAAATAAATAAAATTTA
40724136 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAATAAATAAAATTTA
Found at i:40728508 original size:30 final size:30
Alignment explanation
Indices: 40728467--40728700 Score: 196
Period size: 30 Copynumber: 7.8 Consensus size: 30
40728457 TGTTTTGTTT
*
40728467 AAAAATTACATTTTAACCTTCGAACTTCTC
1 AAAAATTACATTTTAACCCTCGAACTTCTC
* * * *
40728497 AAAAATCACATTTTGACCCACGAACTTCCC
1 AAAAATTACATTTTAACCCTCGAACTTCTC
* * *
40728527 AAAAATCATATTTTAACCCTCAAACTTCAT-
1 AAAAATTACATTTTAACCCTCGAACTTC-TC
*
40728557 AAAAATTACATTTTAACCCTCTAACTTCTC
1 AAAAATTACATTTTAACCCTCGAACTTCTC
* *
40728587 AAAAATTACATTTTGACTCCT-AAACTT-TGC
1 AAAAATTACATTTTAAC-CCTCGAACTTCT-C
* *
40728617 AAAAGTTACATTTTGACTCC-CGAACTTCTTC
1 AAAAATTACATTTTAAC-CCTCGAACTTC-TC
* *
40728648 ATAAATTACCATTTT-GCCCTCGAA-TATC-C
1 AAAAATTA-CATTTTAACCCTCGAACT-TCTC
*
40728677 AAAAATTACCATTTT-ACCCCCGAA
1 AAAAATTA-CATTTTAACCCTCGAA
40728701 TATCTGAGAA
Statistics
Matches: 171, Mismatches: 23, Indels: 21
0.80 0.11 0.10
Matches are distributed among these distances:
29 24 0.14
30 123 0.72
31 17 0.10
32 7 0.04
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (30 bp):
AAAAATTACATTTTAACCCTCGAACTTCTC
Found at i:40728739 original size:29 final size:29
Alignment explanation
Indices: 40728651--40728747 Score: 108
Period size: 29 Copynumber: 3.4 Consensus size: 29
40728641 CTTCTTCATA
* * *
40728651 AATTACCATTTTGCCCTCGAATATCCAAA
1 AATTACCATTTTACCCCCGAATATCCAAG
**
40728680 AATTACCATTTTACCCCCGAATATCTGAG
1 AATTACCATTTTACCCCCGAATATCCAAG
* * *
40728709 AATTACCGTTTTACCCCCAAATTTCCAAG
1 AATTACCATTTTACCCCCGAATATCCAAG
40728738 AA-TA-CATTTT
1 AATTACCATTTT
40728748 CGACCTCAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
27 5 0.09
28 2 0.04
29 50 0.88
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (29 bp):
AATTACCATTTTACCCCCGAATATCCAAG
Found at i:40729248 original size:30 final size:31
Alignment explanation
Indices: 40729206--40729349 Score: 108
Period size: 30 Copynumber: 4.7 Consensus size: 31
40729196 AAACTTTTCA
*
40729206 AACTTCGT-AAAAATTACATTTTAAC-CCTCT
1 AACTTC-TCAAAAATTACATTTTAACTCCTCG
* *
40729236 AACTTCTCAAAAATTACATTTTGACTCCT-A
1 AACTTCTCAAAAATTACATTTTAACTCCTCG
* *
40729266 AACTT-TGCAAAAGTTACATTTTGACTCC-CG
1 AACTTCT-CAAAAATTACATTTTAACTCCTCG
* *
40729296 AACTTCTTCATAAATTACCATTTT-GC-CCTCG
1 AACTTC-TCAAAAATTA-CATTTTAACTCCTCG
40729327 AA-TATC-CAAAAATTACCATTTTA
1 AACT-TCTCAAAAATTA-CATTTTA
40729350 CCCCCGAATA
Statistics
Matches: 96, Mismatches: 8, Indels: 20
0.77 0.06 0.16
Matches are distributed among these distances:
29 17 0.18
30 55 0.57
31 17 0.18
32 7 0.07
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.36
Consensus pattern (31 bp):
AACTTCTCAAAAATTACATTTTAACTCCTCG
Found at i:40729286 original size:60 final size:62
Alignment explanation
Indices: 40729205--40729320 Score: 148
Period size: 60 Copynumber: 1.9 Consensus size: 62
40729195 CAAACTTTTC
* *
40729205 AAACTTCGTAAAAATTACATTTTAAC-CCTCTAACTTC-TCAAAAATTA-CATTTTGACTCCT
1 AAACTTCGCAAAAATTACATTTTAACTCC-CGAACTTCTTCAAAAATTACCATTTTGACTCCT
* * * *
40729265 AAACTTTGCAAAAGTTACATTTTGACTCCCGAACTTCTTCATAAATTACCATTTTG
1 AAACTTCGCAAAAATTACATTTTAACTCCCGAACTTCTTCAAAAATTACCATTTTG
40729321 CCCTCGAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
60 29 0.62
61 11 0.23
62 7 0.15
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.37
Consensus pattern (62 bp):
AAACTTCGCAAAAATTACATTTTAACTCCCGAACTTCTTCAAAAATTACCATTTTGACTCCT
Found at i:40729369 original size:29 final size:29
Alignment explanation
Indices: 40729307--40729393 Score: 93
Period size: 29 Copynumber: 3.0 Consensus size: 29
40729297 ACTTCTTCAT
* *
40729307 AAATTACCATTTTGCCCTCGAATATCCAA
1 AAATTACCATTTTACCCCCGAATATCCAA
**
40729336 AAATTACCATTTTACCCCCGAATATCTGA
1 AAATTACCATTTTACCCCCGAATATCCAA
* * * * *
40729365 GAATTATCGTTTTACCCCCAAATTTCCAA
1 AAATTACCATTTTACCCCCGAATATCCAA
40729394 GAATACATTT
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.33, C:0.28, G:0.07, T:0.32
Consensus pattern (29 bp):
AAATTACCATTTTACCCCCGAATATCCAA
Found at i:40729396 original size:29 final size:29
Alignment explanation
Indices: 40729308--40729404 Score: 90
Period size: 29 Copynumber: 3.4 Consensus size: 29
40729298 CTTCTTCATA
* * * *
40729308 AATTACCATTTTGCCCTCGAATATCCAAA
1 AATTACCATTTTACCCCCAAATATCCAAG
* **
40729337 AATTACCATTTTACCCCCGAATATCTGAG
1 AATTACCATTTTACCCCCAAATATCCAAG
* * *
40729366 AATTATCGTTTTACCCCCAAATTTCCAAG
1 AATTACCATTTTACCCCCAAATATCCAAG
40729395 AA-TA-CATTTT
1 AATTACCATTTT
40729405 CGACCTCAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
27 5 0.09
28 2 0.04
29 49 0.88
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.34
Consensus pattern (29 bp):
AATTACCATTTTACCCCCAAATATCCAAG
Found at i:40729800 original size:657 final size:657
Alignment explanation
Indices: 40728546--40729864 Score: 2620
Period size: 657 Copynumber: 2.0 Consensus size: 657
40728536 ATTTTAACCC
40728546 TCAAACTTCATAAAAATTACATTTTAACCCTCTAACTTCTCAAAAATTACATTTTGACTCCTAAA
1 TCAAACTTCATAAAAATTACATTTTAACCCTCTAACTTCTCAAAAATTACATTTTGACTCCTAAA
40728611 CTTTGCAAAAGTTACATTTTGACTCCCGAACTTCTTCATAAATTACCATTTTGCCCTCGAATATC
66 CTTTGCAAAAGTTACATTTTGACTCCCGAACTTCTTCATAAATTACCATTTTGCCCTCGAATATC
40728676 CAAAAATTACCATTTTACCCCCGAATATCTGAGAATTACCGTTTTACCCCCAAATTTCCAAGAAT
131 CAAAAATTACCATTTTACCCCCGAATATCTGAGAATTACCGTTTTACCCCCAAATTTCCAAGAAT
40728741 ACATTTTCGACCTCAAATTTTCCAAAAGTTCGATTTTAGTCTCAAAGTTTTCAAAAATTTCAATT
196 ACATTTTCGACCTCAAATTTTCCAAAAGTTCGATTTTAGTCTCAAAGTTTTCAAAAATTTCAATT
40728806 TTGATCCCTAAATTCCTCGAAAATTATGTTTTCATCCCGAATTCTTTGAAACTCTGTTTTTGACC
261 TTGATCCCTAAATTCCTCGAAAATTATGTTTTCATCCCGAATTCTTTGAAACTCTGTTTTTGACC
40728871 CCGTTTGTTTTTTTTTCTTTTTTTTTCGATGTTCATACACAAAATTTAATTATTATTCTTTCTTA
326 CCGTTTGTTTTTTTTTCTTTTTTTTTCGATGTTCATACACAAAATTTAATTATTATTCTTTCTTA
40728936 TTTTGTATTCTATTAATTTTATGTTTAATTTTTGTGCATTTATTTATCTACTTAATTATTTTGTT
391 TTTTGTATTCTATTAATTTTATGTTTAATTTTTGTGCATTTATTTATCTACTTAATTATTTTGTT
40729001 TCATGTTATTTAATTTTTGCTATAAACTGCCTATTCATATTTAATTTACACATTCGTTTTCAAAA
456 TCATGTTATTTAATTTTTGCTATAAACTGCCTATTCATATTTAATTTACACATTCGTTTTCAAAA
40729066 TTACTTTCACATACAAATAAACCTTTAAAACCGACGCAATATCCTTGTCATGTGGAAATCTCAAA
521 TTACTTTCACATACAAATAAACCTTTAAAACCGACGCAATATCCTTGTCATGTGGAAATCTCAAA
40729131 AAATTATGCCCTAACGTGCTGGGTGTGATTTTTCGTATAATCTGCACGAATTGATATCCTCTTCC
586 AAATTATGCCCTAACGTGCTGGGTGTGATTTTTCGTATAATCTGCACGAATTGATATCCTCTTCC
40729196 AAACTTT
651 AAACTTT
*
40729203 TCAAACTTCGTAAAAATTACATTTTAACCCTCTAACTTCTCAAAAATTACATTTTGACTCCTAAA
1 TCAAACTTCATAAAAATTACATTTTAACCCTCTAACTTCTCAAAAATTACATTTTGACTCCTAAA
40729268 CTTTGCAAAAGTTACATTTTGACTCCCGAACTTCTTCATAAATTACCATTTTGCCCTCGAATATC
66 CTTTGCAAAAGTTACATTTTGACTCCCGAACTTCTTCATAAATTACCATTTTGCCCTCGAATATC
*
40729333 CAAAAATTACCATTTTACCCCCGAATATCTGAGAATTATCGTTTTACCCCCAAATTTCCAAGAAT
131 CAAAAATTACCATTTTACCCCCGAATATCTGAGAATTACCGTTTTACCCCCAAATTTCCAAGAAT
40729398 ACATTTTCGACCTCAAATTTTCCAAAAGTTCGATTTTAGTCTCAAAGTTTTCAAAAATTTCAATT
196 ACATTTTCGACCTCAAATTTTCCAAAAGTTCGATTTTAGTCTCAAAGTTTTCAAAAATTTCAATT
40729463 TTGATCCCTAAATTCCTCGAAAATTATGTTTTCATCCCGAATTCTTTGAAACTCTGTTTTTGACC
261 TTGATCCCTAAATTCCTCGAAAATTATGTTTTCATCCCGAATTCTTTGAAACTCTGTTTTTGACC
40729528 CCGTTTGTTTTTTTTTCTTTTTTTTTCGATGTTCATACACAAAATTTAATTATTATTCTTTCTTA
326 CCGTTTGTTTTTTTTTCTTTTTTTTTCGATGTTCATACACAAAATTTAATTATTATTCTTTCTTA
40729593 TTTTGTATTCTATTAATTTTATGTTTAATTTTTGTGCATTTATTTATCTACTTAATTATTTTGTT
391 TTTTGTATTCTATTAATTTTATGTTTAATTTTTGTGCATTTATTTATCTACTTAATTATTTTGTT
40729658 TCATGTTATTTAATTTTTGCTATAAACTGCCTATTCATATTTAATTTACACATTCGTTTTCAAAA
456 TCATGTTATTTAATTTTTGCTATAAACTGCCTATTCATATTTAATTTACACATTCGTTTTCAAAA
40729723 TTACTTTCACATACAAATAAACCTTTAAAACCGACGCAATATCCTTGTCATGTGGAAATCTCAAA
521 TTACTTTCACATACAAATAAACCTTTAAAACCGACGCAATATCCTTGTCATGTGGAAATCTCAAA
40729788 AAATTATGCCCTAACGTGCTGGGTGTGATTTTTCGTATAATCTGCACGAATTGATATCCTCTTCC
586 AAATTATGCCCTAACGTGCTGGGTGTGATTTTTCGTATAATCTGCACGAATTGATATCCTCTTCC
40729853 AAACTTT
651 AAACTTT
40729860 TCAAA
1 TCAAA
40729865 TGCCCTTTAA
Statistics
Matches: 660, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
657 660 1.00
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (657 bp):
TCAAACTTCATAAAAATTACATTTTAACCCTCTAACTTCTCAAAAATTACATTTTGACTCCTAAA
CTTTGCAAAAGTTACATTTTGACTCCCGAACTTCTTCATAAATTACCATTTTGCCCTCGAATATC
CAAAAATTACCATTTTACCCCCGAATATCTGAGAATTACCGTTTTACCCCCAAATTTCCAAGAAT
ACATTTTCGACCTCAAATTTTCCAAAAGTTCGATTTTAGTCTCAAAGTTTTCAAAAATTTCAATT
TTGATCCCTAAATTCCTCGAAAATTATGTTTTCATCCCGAATTCTTTGAAACTCTGTTTTTGACC
CCGTTTGTTTTTTTTTCTTTTTTTTTCGATGTTCATACACAAAATTTAATTATTATTCTTTCTTA
TTTTGTATTCTATTAATTTTATGTTTAATTTTTGTGCATTTATTTATCTACTTAATTATTTTGTT
TCATGTTATTTAATTTTTGCTATAAACTGCCTATTCATATTTAATTTACACATTCGTTTTCAAAA
TTACTTTCACATACAAATAAACCTTTAAAACCGACGCAATATCCTTGTCATGTGGAAATCTCAAA
AAATTATGCCCTAACGTGCTGGGTGTGATTTTTCGTATAATCTGCACGAATTGATATCCTCTTCC
AAACTTT
Found at i:40744356 original size:209 final size:208
Alignment explanation
Indices: 40743996--40744662 Score: 996
Period size: 209 Copynumber: 3.2 Consensus size: 208
40743986 GAGAAAGAGT
* * *
40743996 GAAACTTCGAATCCCAACTTCCTGATGAGAGACAGAGAAGCAAGTCGAAGCAATAAAGCGGTCAT
1 GAAACTTCGAATCCCAACTTCCTGATGAGATACAGAGAAGCAGGTCGAAGCAATAAAGCGGTCGT
* * *
40744061 CTTCCTGATGAGATACAGAGAAGTGGACCAAAT-TCGTCTTCCTGTTGAGATACAGAGAAGTAGA
66 CTTCTTGATGAGATACAGAGAAGTGGACCAAATCT-GTCTTCCTGATGAGATACAGAGAAGTGGA
40744125 TTAAAACAAATGATGCGGTCATCTTTCCGATGAGATACAAAGAAGTATACCAAATCAATGAAACA
130 TTAAAACAAATGATGCGGTCATC-TTCCGATGAGATACAAAGAAGTATACCAAATCAATGAAACA
*
40744190 AAGCTCAATGTAAGC
194 AAGCTCAATGTGAGC
* * * *
40744205 GAAACTTCGAATCCCAACTTCCTGATGAGATACAAAGAAGTAGGTTGAAGCAATAAAGCGATCGT
1 GAAACTTCGAATCCCAACTTCCTGATGAGATACAGAGAAGCAGGTCGAAGCAATAAAGCGGTCGT
* * * *
40744270 C-TCTTTGATGAGATACAGAGAAGTGGACAAAATCTGTCTTTCTGATGAGATATAAAGAAGTGGA
66 CTTC-TTGATGAGATACAGAGAAGTGGACCAAATCTGTCTTCCTGATGAGATACAGAGAAGTGGA
* ** *
40744334 TTAAAAAAAACAATGCGGTCATCTTCCTGATAAGATACAAAGAAGTATACCAAATCAATGAAACA
130 TTAAAACAAATGATGCGGTCATCTTCC-GATGAGATACAAAGAAGTATACCAAATCAATGAAACA
*
40744399 AAGCTCAATGTGAGT
194 AAGCTCAATGTGAGC
* *
40744414 GAAACTTCGAATCCCAGCTTCCTGATGAGATACAGAGAAGCAGGTCGAAGCAATAAAGCGGTTGT
1 GAAACTTCGAATCCCAACTTCCTGATGAGATACAGAGAAGCAGGTCGAAGCAATAAAGCGGTCGT
* *
40744479 CTTCTTGATGAGATACAAAGAAGTGGACCAAGTCTGTCTTCCTGATGAGATACAGAGAAGTGGAT
66 CTTCTTGATGAGATACAGAGAAGTGGACCAAATCTGTCTTCCTGATGAGATACAGAGAAGTGGAT
* * **
40744544 TAAAACAAATGAGGCGGTCATCTTCTTGATGAGATACGGAGAAGTATACCAAATCAATGAAACAA
131 TAAAACAAATGATGCGGTCATCTTC-CGATGAGATACAAAGAAGTATACCAAATCAATGAAACAA
40744609 AGCTCAATGTGAGC
195 AGCTCAATGTGAGC
* * *
40744623 GAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAG
1 GAAACTTCGAATCCCAACTTCCTGATGAGATACAGAGAAG
40744663 TGGACCTAAT
Statistics
Matches: 410, Mismatches: 43, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
208 6 0.01
209 401 0.98
210 3 0.01
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (208 bp):
GAAACTTCGAATCCCAACTTCCTGATGAGATACAGAGAAGCAGGTCGAAGCAATAAAGCGGTCGT
CTTCTTGATGAGATACAGAGAAGTGGACCAAATCTGTCTTCCTGATGAGATACAGAGAAGTGGAT
TAAAACAAATGATGCGGTCATCTTCCGATGAGATACAAAGAAGTATACCAAATCAATGAAACAAA
GCTCAATGTGAGC
Found at i:40744741 original size:78 final size:74
Alignment explanation
Indices: 40744562--40744743 Score: 193
Period size: 75 Copynumber: 2.4 Consensus size: 74
40744552 ATGAGGCGGT
* * *
40744562 CATCTTCTTGATGAGATACGGAGAAGTATACCAAATCAATGAAACAAAGCTCAATGTGAGCGAAA
1 CATCTTCATGATGAGATACGG-GAAGTAGACCAAATCAATGAAACAAAGCTCAATGCGAGCGAAA
*
40744627 CTTCGAACCC
65 CTTCAAACCC
* * * * * * * *
40744637 CAGCTTCCTGATGAGATACTGAGAAGTGGACCTAATCAAATGAAGCAAAGTTCAAATGCGAGTGA
1 CATCTTCATGATGAGATAC-GGGAAGTAGACCAAATC-AATGAAACAAAGCTC-AATGCGAGCGA
*
40744702 AGCTTCAAACCC
63 AACTTCAAACCC
40744714 CTATCTTCATGATGAGATACAGGGAAGTAG
1 C-ATCTTCATGATGAGATAC-GGGAAGTAG
40744744 GTCGAAGCAA
Statistics
Matches: 86, Mismatches: 17, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
75 29 0.34
76 14 0.16
77 20 0.23
78 23 0.27
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (74 bp):
CATCTTCATGATGAGATACGGGAAGTAGACCAAATCAATGAAACAAAGCTCAATGCGAGCGAAAC
TTCAAACCC
Found at i:40746888 original size:30 final size:30
Alignment explanation
Indices: 40746842--40747143 Score: 180
Period size: 30 Copynumber: 10.2 Consensus size: 30
40746832 TATTTTATTT
* *
40746842 AAAAATTACA-TTTGACCCTCAAACTTCTC
1 AAAAATCACATTTTGACCCTCGAACTTCTC
* * * *
40746871 AAAACTCACATTTTGACCCACGAACTTTTT
1 AAAAATCACATTTTGACCCTCGAACTTCTC
*
40746901 AAAAATCATATTTTGACCCTCGAACTTCGT-
1 AAAAATCACATTTTGACCCTCGAACTTC-TC
* *
40746931 AAAAATTACATTTTGACTCCT-GAACTTCAC
1 AAAAATCACATTTTGAC-CCTCGAACTTCTC
* * *
40746961 AAAAATTACATTTTGACCCTCTAACTT-TGA
1 AAAAATCACATTTTGACCCTCGAACTTCT-C
* * *
40746991 AAAAATTATATTTTGACTCTCGAACTTCTC
1 AAAAATCACATTTTGACCCTCGAACTTCTC
* * * *
40747021 GACAAATTACCATTTTG-CCC-CTAAATATC-C
1 -AAAAATCA-CATTTTGACCCTCGAACT-TCTC
* *
40747051 AAAAATTACCATTTTG-CCCTCGAACATC-C
1 AAAAATCA-CATTTTGACCCTCGAACTTCTC
* * * *
40747080 AAAAATTACTATTTT-ACCCCCAAATTTCT-
1 AAAAATCAC-ATTTTGACCCTCGAACTTCTC
* *
40747109 AAGAATCACATTTTCGA-CCTC-AAATTCTC
1 AAAAATCACATTTT-GACCCTCGAACTTCTC
*
40747138 CAAAAT
1 AAAAAT
40747144 TTCGATTTTA
Statistics
Matches: 217, Mismatches: 39, Indels: 34
0.75 0.13 0.12
Matches are distributed among these distances:
28 12 0.06
29 67 0.31
30 116 0.53
31 16 0.07
32 6 0.03
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (30 bp):
AAAAATCACATTTTGACCCTCGAACTTCTC
Found at i:40747018 original size:60 final size:60
Alignment explanation
Indices: 40746842--40747098 Score: 224
Period size: 60 Copynumber: 4.3 Consensus size: 60
40746832 TATTTTATTT
* * * * * *
40746842 AAAAATTACA-TTTGACCCTCAAACTTCT-CAAAACTCACATTTTGACCCACGAACTTTTT
1 AAAAATTACATTTTGACCCTCTAACTT-TGCAAAAATTACATTTTGACCCTCGAACTTCTC
* * * * * *
40746901 AAAAATCATATTTTGACCCTCGAACTTCGTAAAAATTACATTTTGACTCCT-GAACTTCAC
1 AAAAATTACATTTTGACCCTCTAACTTTGCAAAAATTACATTTTGAC-CCTCGAACTTCTC
* * *
40746961 AAAAATTACATTTTGACCCTCTAACTTTGAAAAAATTATATTTTGACTCTCGAACTTCTC
1 AAAAATTACATTTTGACCCTCTAACTTTGCAAAAATTACATTTTGACCCTCGAACTTCTC
* * * * *
40747021 GACAAATTACCATTTTG-CCC-CTAAATATCCAAAAATTACCATTTTG-CCCTCGAACATC-C
1 -AAAAATTA-CATTTTGACCCTCTAACTTTGCAAAAATTA-CATTTTGACCCTCGAACTTCTC
40747080 AAAAATTACTATTTT-ACCC
1 AAAAATTAC-ATTTTGACCC
40747099 CCAAATTTCT
Statistics
Matches: 161, Mismatches: 28, Indels: 19
0.77 0.13 0.09
Matches are distributed among these distances:
57 1 0.01
58 15 0.09
59 11 0.07
60 109 0.68
61 18 0.11
62 7 0.04
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.33
Consensus pattern (60 bp):
AAAAATTACATTTTGACCCTCTAACTTTGCAAAAATTACATTTTGACCCTCGAACTTCTC
Found at i:40747054 original size:90 final size:90
Alignment explanation
Indices: 40746841--40747075 Score: 250
Period size: 90 Copynumber: 2.6 Consensus size: 90
40746831 CTATTTTATT
* * * * * **
40746841 TAAAAATTACA-TTTGA-CCCTCAAACTTCTCAAAACTCACATTTTGACCCACGAACTTTTTAAA
1 TAAAAATTACATTTTGACCCCTGAAA-TTCACAAAAATTACATTTTGACCCTCGAACTTTGAAAA
40746904 AATCATATTTTGACCCTCGAACTTCG
65 AATCATATTTTGACCCTCGAACTTCG
* * *
40746930 TAAAAATTACATTTTGACTCCTGAACTTCACAAAAATTACATTTTGACCCTCTAACTTTGAAAAA
1 TAAAAATTACATTTTGACCCCTGAAATTCACAAAAATTACATTTTGACCCTCGAACTTTGAAAAA
* *
40746995 ATTATATTTTGACTCTCGAACTTC-
66 ATCATATTTTGACCCTCGAACTTCG
*
40747019 TCGACAAATTACCATTTTG-CCCCT-AAATATC-CAAAAATTACCATTTTG-CCCTCGAAC
1 T--AAAAATTA-CATTTTGACCCCTGAAAT-TCACAAAAATTA-CATTTTGACCCTCGAAC
40747076 ATCCAAAAAT
Statistics
Matches: 123, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
89 12 0.10
90 79 0.64
91 25 0.20
92 7 0.06
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.34
Consensus pattern (90 bp):
TAAAAATTACATTTTGACCCCTGAAATTCACAAAAATTACATTTTGACCCTCGAACTTTGAAAAA
ATCATATTTTGACCCTCGAACTTCG
Found at i:40747152 original size:30 final size:30
Alignment explanation
Indices: 40747118--40747195 Score: 70
Period size: 29 Copynumber: 2.6 Consensus size: 30
40747108 TAAGAATCAC
*
40747118 ATTTTCGACCTCAAATTCTCC-AAAATTTCG
1 ATTTTAGACCTCAAATTCTCCAAAAATTT-G
* * * *
40747148 ATTTTAG-TCTTAAATTTTCCAAAAATTTT
1 ATTTTAGACCTCAAATTCTCCAAAAATTTG
*
40747177 ATTTTTGATCCTCAAATTC
1 ATTTTAGA-CCTCAAATTC
40747196 CTTGAAAATT
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
29 16 0.44
30 13 0.36
31 7 0.19
ACGTcount: A:0.31, C:0.19, G:0.05, T:0.45
Consensus pattern (30 bp):
ATTTTAGACCTCAAATTCTCCAAAAATTTG
Found at i:40747207 original size:29 final size:29
Alignment explanation
Indices: 40747175--40747247 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
40747165 TCCAAAAATT
40747175 TTATTTTTGATCCTCAAATTCCTTGAAAA
1 TTATTTTTGATCCTCAAATTCCTTGAAAA
* * * *
40747204 TTATGTTTTTATCC-CGAATTCTTTGAAAC
1 TTAT-TTTTGATCCTCAAATTCCTTGAAAA
40747233 TCTATTTTTGA-CCTC
1 T-TATTTTTGATCCTC
40747248 GTTTGTTTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
28 2 0.06
29 23 0.64
30 11 0.31
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.48
Consensus pattern (29 bp):
TTATTTTTGATCCTCAAATTCCTTGAAAA
Found at i:40750401 original size:30 final size:30
Alignment explanation
Indices: 40750365--40750425 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
40750355 AATACGAAGC
*
40750365 AATATAATAAGCAGA-TAAATAATATGCGAA
1 AATATAAGAAGCAGAGTAAATAA-ATGCGAA
*
40750395 AATATAAGATGCAGATGTAAATAAATGCGAA
1 AATATAAGAAGCAGA-GTAAATAAATGCGAA
40750426 TATTGGTGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 13 0.48
31 7 0.26
32 7 0.26
ACGTcount: A:0.54, C:0.07, G:0.16, T:0.23
Consensus pattern (30 bp):
AATATAAGAAGCAGAGTAAATAAATGCGAA
Found at i:40750925 original size:60 final size:60
Alignment explanation
Indices: 40750604--40750925 Score: 396
Period size: 60 Copynumber: 5.3 Consensus size: 60
40750594 TTTGGCAAAA
* * *
40750604 TTAGGGTCAAAAATGTAATATTAGAAAAGTTTTAGGGTCAAAATGTAATTTTTAGAAAGTT
1 TTAGGGTC-AAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTTAGAAAGTT
* * * * * ** *
40750665 TTAGGGTCAAAATGTGATTTCGGAAAAGCTTTGGTGTCAAAATGTGA-TTTCGGAAAAGCT
1 TTAGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTTAG-AAAGTT
* * **
40750725 TTAGGGTTAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAACTAAAATTTTTAGAAAGTT
1 TTAGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTTAGAAAGTT
* * *
40750785 TTGAGGGT-AATATGTAATTATGGAAAAGTTTTGGGGTTAAAATGTAATTTTTAGAAAGTT
1 TT-AGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTTAGAAAGTT
* * *
40750845 TTATGGTCAAAATGTAATTTTAGAAAAGTTTTGGGGTCGAAATGTAATTTTTAGAAAGTT
1 TTAGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTTAGAAAGTT
* *
40750905 TTGGGGTCAAAATATAATTTT
1 TTAGGGTCAAAATGTAATTTT
40750926 TGGGTTGTTT
Statistics
Matches: 219, Mismatches: 38, Indels: 9
0.82 0.14 0.03
Matches are distributed among these distances:
59 8 0.04
60 194 0.89
61 17 0.08
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.38
Consensus pattern (60 bp):
TTAGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTTAGAAAGTT
Found at i:40750926 original size:30 final size:30
Alignment explanation
Indices: 40750607--40750925 Score: 315
Period size: 30 Copynumber: 10.6 Consensus size: 30
40750597 GGCAAAATTA
* *
40750607 GGGTCAAAAATGTAATATTAGAAAAGTTTTA
1 GGGTC-AAAATGTAATTTTAGAAAAGTTTTG
*
40750638 GGGTCAAAATGTAATTTTTAG-AAAGTTTTA
1 GGGTCAAAATGTAA-TTTTAGAAAAGTTTTG
* ** *
40750668 GGGTCAAAATGTGATTTCGGAAAAGCTTTG
1 GGGTCAAAATGTAATTTTAGAAAAGTTTTG
* * ** * *
40750698 GTGTCAAAATGTGATTTCGGAAAAGCTTTA
1 GGGTCAAAATGTAATTTTAGAAAAGTTTTG
* *
40750728 GGGTTAAAATGTAATTTTGGAAAAGTTTTG
1 GGGTCAAAATGTAATTTTAGAAAAGTTTTG
* **
40750758 GGGTCAAACTAAAATTTTTAG-AAAGTTTTG
1 GGGTCAAAATGTAA-TTTTAGAAAAGTTTTG
* * *
40750788 AGGGT-AATATGTAATTATGGAAAAGTTTTG
1 -GGGTCAAAATGTAATTTTAGAAAAGTTTTG
* *
40750818 GGGTTAAAATGTAATTTTTAG-AAAGTTTTA
1 GGGTCAAAATGTAA-TTTTAGAAAAGTTTTG
*
40750848 TGGTCAAAATGTAATTTTAGAAAAGTTTTG
1 GGGTCAAAATGTAATTTTAGAAAAGTTTTG
*
40750878 GGGTCGAAATGTAATTTTTAG-AAAGTTTTG
1 GGGTCAAAATGTAA-TTTTAGAAAAGTTTTG
*
40750908 GGGTCAAAATATAATTTT
1 GGGTCAAAATGTAATTTT
40750926 TGGGTTGTTT
Statistics
Matches: 243, Mismatches: 36, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
29 22 0.09
30 192 0.79
31 29 0.12
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.37
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTAGAAAAGTTTTG
Found at i:40752777 original size:11 final size:11
Alignment explanation
Indices: 40752769--40752830 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
40752759 TCATAATTTG
40752769 ATTTAAATTTAA
1 ATTT-AATTTAA
**
40752781 ATTTAAAATAA
1 ATTTAATTTAA
40752792 ATTTAAATTTAA
1 ATTT-AATTTAA
* *
40752804 A-TAAATTAAA
1 ATTTAATTTAA
*
40752814 AATTAATTTAA
1 ATTTAATTTAA
40752825 ATTTAA
1 ATTTAA
40752831 AATTAAAACA
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
10 7 0.18
11 22 0.56
12 10 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATTTAATTTAA
Found at i:40752780 original size:6 final size:6
Alignment explanation
Indices: 40752769--40752837 Score: 74
Period size: 6 Copynumber: 12.2 Consensus size: 6
40752759 TCATAATTTG
* *
40752769 ATTTAA ATTTAA ATTTAA A-ATAA ATTTAA ATTTAA A--TAA ATTAAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* *
40752814 AATT-A ATTTAA ATTTAA AATTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA A
40752838 ACATAAAGTC
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
4 4 0.08
5 8 0.15
6 40 0.77
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:40752791 original size:27 final size:26
Alignment explanation
Indices: 40752743--40752837 Score: 83
Period size: 27 Copynumber: 3.7 Consensus size: 26
40752733 AATTTTAATG
** *
40752743 TTTAAATTTAATATTTTCATAATTTGA
1 TTTAAATTTAA-ATTTAAATAATTTAA
40752770 TTTAAATTTAAATTTAAAATAAATTTAAA
1 TTTAAATTTAAATTT-AAAT-AATTT-AA
40752799 TTTAAA--TAAA-TTAAA-AA-TTAA
1 TTTAAATTTAAATTTAAATAATTTAA
*
40752820 TTTAAATTTAAAATTAAA
1 TTTAAATTTAAATTTAAA
40752838 ACATAAAGTC
Statistics
Matches: 59, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
21 8 0.14
22 2 0.03
23 6 0.10
24 5 0.08
25 3 0.05
26 6 0.10
27 17 0.29
28 5 0.08
29 7 0.12
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (26 bp):
TTTAAATTTAAATTTAAATAATTTAA
Found at i:40752792 original size:17 final size:17
Alignment explanation
Indices: 40752772--40752838 Score: 82
Period size: 17 Copynumber: 4.0 Consensus size: 17
40752762 TAATTTGATT
*
40752772 TAAATTTAAATTTAAAA
1 TAAATTTAAAATTAAAA
*
40752789 TAAATTT-AAATTTAAA
1 TAAATTTAAAATTAAAA
* **
40752805 TAAATTAAAAATTAATT
1 TAAATTTAAAATTAAAA
40752822 TAAATTTAAAATTAAAA
1 TAAATTTAAAATTAAAA
40752839 CATAAAGTCC
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
16 13 0.32
17 27 0.68
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATTTAAAATTAAAA
Found at i:40752809 original size:33 final size:33
Alignment explanation
Indices: 40752772--40752837 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
40752762 TAATTTGATT
* * *
40752772 TAAATTTAAATTTAAAATAAATTTAAATTTAAA
1 TAAATTAAAAATTAAAATAAATTTAAAATTAAA
**
40752805 TAAATTAAAAATTAATTTAAATTTAAAATTAAA
1 TAAATTAAAAATTAAAATAAATTTAAAATTAAA
40752838 ACATAAAGTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (33 bp):
TAAATTAAAAATTAAAATAAATTTAAAATTAAA
Found at i:40759787 original size:18 final size:18
Alignment explanation
Indices: 40759759--40759802 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
40759749 AGGTTTGCGC
*
40759759 GTATGTCTAAGTTTATATGT
1 GTATGT-TAAG-TAATATGT
40759779 -TATGTTAAGTAATATGT
1 GTATGTTAAGTAATATGT
40759796 GTATGTT
1 GTATGTT
40759803 TGTGTGTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 10 0.45
19 5 0.23
ACGTcount: A:0.27, C:0.02, G:0.20, T:0.50
Consensus pattern (18 bp):
GTATGTTAAGTAATATGT
Found at i:40763993 original size:6 final size:6
Alignment explanation
Indices: 40763984--40764008 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40763974 ACATCATCTT
40763984 CCACTC CCACTC CCACTC CCACTC C
1 CCACTC CCACTC CCACTC CCACTC C
40764009 TTATGCCGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.68, G:0.00, T:0.16
Consensus pattern (6 bp):
CCACTC
Found at i:40767677 original size:41 final size:39
Alignment explanation
Indices: 40767608--40767693 Score: 97
Period size: 41 Copynumber: 2.2 Consensus size: 39
40767598 ACCCATTGTT
40767608 TTATTTATTTAATTTTATACTTCATTATTAATTTA-TTTTGG
1 TTATTTATTTAATTTTATA-TTCATTATT--TTTATTTTTGG
*
40767649 TTATTTATTTTATTTTAT-TTCTATTTATTTTTATTTTTGG
1 TTATTTATTTAATTTTATATTC-A-TTATTTTTATTTTTGG
40767689 -TATTT
1 TTATTT
40767694 TAAATTTTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
39 12 0.29
40 7 0.17
41 22 0.54
ACGTcount: A:0.22, C:0.03, G:0.05, T:0.70
Consensus pattern (39 bp):
TTATTTATTTAATTTTATATTCATTATTTTTATTTTTGG
Found at i:40769452 original size:23 final size:23
Alignment explanation
Indices: 40769422--40769479 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
40769412 CTGAAGTGAC
*
40769422 GTCCAGTCAGCAGCCTCTTGAAG
1 GTCCAGTCAGCAGCCTCTAGAAG
*
40769445 GTCCAGTCAGCAGCTTCTAGAAG
1 GTCCAGTCAGCAGCCTCTAGAAG
*
40769468 GTCTAGTCAGCA
1 GTCCAGTCAGCA
40769480 AGGATGGACG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.24, C:0.28, G:0.26, T:0.22
Consensus pattern (23 bp):
GTCCAGTCAGCAGCCTCTAGAAG
Found at i:40776259 original size:34 final size:34
Alignment explanation
Indices: 40776221--40776334 Score: 106
Period size: 34 Copynumber: 3.2 Consensus size: 34
40776211 ATATCTGTTT
40776221 AAGTCCATGAAGATGAAACCATCGTAAATATAAG
1 AAGTCCATGAAGATGAAACCATCGTAAATATAAG
* * * **
40776255 AAGTCCAATGAGACATTAAA-CA-CGAGATAATATCTG
1 AAGTCC-ATGA-AGATGAAACCATCG-TA-AATATAAG
40776291 TTTAAGTCCATGAAGATGAAACCATCGTAAATATAAG
1 ---AAGTCCATGAAGATGAAACCATCGTAAATATAAG
40776328 AAGTCCA
1 AAGTCCA
40776335 ATGACACATT
Statistics
Matches: 61, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
34 15 0.25
35 7 0.11
36 12 0.20
37 12 0.20
38 7 0.11
39 8 0.13
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.23
Consensus pattern (34 bp):
AAGTCCATGAAGATGAAACCATCGTAAATATAAG
Found at i:40776329 original size:73 final size:73
Alignment explanation
Indices: 40776210--40776355 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 73
40776200 ACAATACATG
*
40776210 AATATCTGTTTAAGTCCATGAAGATGAAACCATCGTAAATATAAGAAGTCCAATGAGACATTAAA
1 AATATCTGTTTAAGTCCATGAAGATGAAACCATCGTAAATATAAGAAGTCCAATGACACATTAAA
40776275 CACGAGAT
66 CACGAGAT
40776283 AATATCTGTTTAAGTCCATGAAGATGAAACCATCGTAAATATAAGAAGTCCAATGACACATTAAA
1 AATATCTGTTTAAGTCCATGAAGATGAAACCATCGTAAATATAAGAAGTCCAATGACACATTAAA
40776348 CACGAGAT
66 CACGAGAT
40776356 TTTGTATGTA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.25
Consensus pattern (73 bp):
AATATCTGTTTAAGTCCATGAAGATGAAACCATCGTAAATATAAGAAGTCCAATGACACATTAAA
CACGAGAT
Found at i:40776416 original size:24 final size:24
Alignment explanation
Indices: 40776356--40776430 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
40776346 AACACGAGAT
40776356 TTTGTATGTAGCCTTTGTGGCGTA
1 TTTGTATGTAGCCTTTGTGGCGTA
* * *
40776380 TTGCGTATGTAGCATTTGTGGTGTA
1 TT-TGTATGTAGCCTTTGTGGCGTA
40776405 TTTGTATGTAGCCTTTGTGGCGTA
1 TTTGTATGTAGCCTTTGTGGCGTA
40776429 TT
1 TT
40776431 CTGTTTGGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
24 23 0.52
25 21 0.48
ACGTcount: A:0.13, C:0.11, G:0.29, T:0.47
Consensus pattern (24 bp):
TTTGTATGTAGCCTTTGTGGCGTA
Found at i:40781777 original size:10 final size:10
Alignment explanation
Indices: 40781762--40781789 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
40781752 GTACATATAT
40781762 GTGTGTGTGG
1 GTGTGTGTGG
40781772 GTGTGTGTGG
1 GTGTGTGTGG
40781782 GTGTGTGT
1 GTGTGTGT
40781790 AGTACCATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.57, T:0.43
Consensus pattern (10 bp):
GTGTGTGTGG
Found at i:40789007 original size:18 final size:18
Alignment explanation
Indices: 40788984--40789018 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
40788974 AGTGTTTTTT
*
40788984 ATTAAATTGAAAACTAAA
1 ATTAAATTAAAAACTAAA
40789002 ATTAAATTAAAAACTAA
1 ATTAAATTAAAAACTAA
40789019 TTTAAGTTGA
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:0.63, C:0.06, G:0.03, T:0.29
Consensus pattern (18 bp):
ATTAAATTAAAAACTAAA
Found at i:40790434 original size:22 final size:22
Alignment explanation
Indices: 40790409--40790450 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
40790399 TATCCAAAAA
40790409 ATAACAATAAAATAATAACAGT
1 ATAACAATAAAATAATAACAGT
* * *
40790431 ATAATAATGAAATGATAACA
1 ATAACAATAAAATAATAACA
40790451 AAACAACGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.24
Consensus pattern (22 bp):
ATAACAATAAAATAATAACAGT
Found at i:40793208 original size:30 final size:32
Alignment explanation
Indices: 40793149--40793208 Score: 79
Period size: 30 Copynumber: 1.9 Consensus size: 32
40793139 GAAGAAACAT
*
40793149 TTTTTTTCCTCAAAAATAGATTGTTTAAAAATG
1 TTTTTGTCCTCAAAAATA-ATTGTTTAAAAATG
*
40793182 TTTTTGTCC-CAAAAAT-ATTTTTTAAAA
1 TTTTTGTCCTCAAAAATAATTGTTTAAAA
40793209 GCCATACTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 10 0.40
32 7 0.28
33 8 0.32
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.47
Consensus pattern (32 bp):
TTTTTGTCCTCAAAAATAATTGTTTAAAAATG
Found at i:40795457 original size:23 final size:23
Alignment explanation
Indices: 40795430--40795479 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
40795420 TTAATATTAA
40795430 TATTTAATTTATCCACAATTTGG
1 TATTTAATTTATCCACAATTTGG
40795453 TATTTAATTTATCCACAATTTGG
1 TATTTAATTTATCCACAATTTGG
40795476 TATT
1 TATT
40795480 CAACAGCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (23 bp):
TATTTAATTTATCCACAATTTGG
Found at i:40796356 original size:58 final size:58
Alignment explanation
Indices: 40796258--40796372 Score: 178
Period size: 58 Copynumber: 2.0 Consensus size: 58
40796248 TATTAAAAAT
* *
40796258 ATAATTATATTAAAAATGTTATTAAATTATATATTATTTTATTAAATTATATTTAATA
1 ATAATTATATTAAAAATATAATTAAATTATATATTATTTTATTAAATTATATTTAATA
* *
40796316 ATAATTATGTT-AAAATATAATTAAATTATTTATTATTTTTATTAAATTATATTTAAT
1 ATAATTATATTAAAAATATAATTAAATTATATATTA-TTTTATTAAATTATATTTAAT
40796373 TAAATCTTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
57 21 0.40
58 31 0.60
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (58 bp):
ATAATTATATTAAAAATATAATTAAATTATATATTATTTTATTAAATTATATTTAATA
Found at i:40796386 original size:57 final size:57
Alignment explanation
Indices: 40796258--40796393 Score: 177
Period size: 57 Copynumber: 2.4 Consensus size: 57
40796248 TATTAAAAAT
* *
40796258 ATAATTATATTAAAAATGTTATTAAATTATATATTATTTTATTAAATTATATTTAATA
1 ATAATTATATT-AAAATATAATTAAATTATATATTATTTTATTAAATTATATTTAATA
* * *
40796316 ATAATTATGTTAAAATATAATTAAATTATTTATTATTTTTATTAAATTATATTTAATT
1 ATAATTATATTAAAATATAATTAAATTATATATTA-TTTTATTAAATTATATTTAATA
*
40796374 A-AATCT-TATTAAAATTTAAT
1 ATAAT-TATATTAAAATATAAT
40796394 AACAATAATC
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
57 36 0.52
58 33 0.48
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (57 bp):
ATAATTATATTAAAATATAATTAAATTATATATTATTTTATTAAATTATATTTAATA
Found at i:40796572 original size:16 final size:15
Alignment explanation
Indices: 40796551--40796586 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
40796541 TGAATTACTG
40796551 ATTACAACCCTATTC
1 ATTACAACCCTATTC
*
40796566 TATTACAACTCTATTC
1 -ATTACAACCCTATTC
40796582 ATTAC
1 ATTAC
40796587 GGCGAACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTACAACCCTATTC
Found at i:40801236 original size:7 final size:7
Alignment explanation
Indices: 40801226--40801254 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
40801216 TTAGAGATAG
40801226 GGCAGGA
1 GGCAGGA
40801233 GGCAGGA
1 GGCAGGA
40801240 GGCAGGA
1 GGCAGGA
40801247 GGCAGGA
1 GGCAGGA
40801254 G
1 G
40801255 AGATGCTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.14, G:0.59, T:0.00
Consensus pattern (7 bp):
GGCAGGA
Found at i:40802258 original size:29 final size:31
Alignment explanation
Indices: 40802211--40802278 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
40802201 TTAAATTAGT
**
40802211 AATGAT-AAAATTATAATTTGGTCC-CTAAA
1 AATGATAAAAATTATAATTTACTCCTCTAAA
* *
40802240 AATGATAAAAATT-TGATTTACTCCTTTAAA
1 AATGATAAAAATTATAATTTACTCCTCTAAA
40802270 AATGATAAA
1 AATGATAAA
40802279 GATATAGACT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 14 0.42
30 19 0.58
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (31 bp):
AATGATAAAAATTATAATTTACTCCTCTAAA
Found at i:40813115 original size:44 final size:44
Alignment explanation
Indices: 40813058--40813154 Score: 149
Period size: 44 Copynumber: 2.2 Consensus size: 44
40813048 TGCCTAAATA
* * *
40813058 AAAAAAAGAAGAAATTGAGATAAAAACCTGCAAAGGGCGTCTCG
1 AAAAAAAGAAGAAATCGAGATAAAAACCTACAAAGGGCATCTCG
*
40813102 AAAAAAAGAAGAAATCGAGATAAAAACCTACAAAGGGCATCTTG
1 AAAAAAAGAAGAAATCGAGATAAAAACCTACAAAGGGCATCTCG
40813146 AAAATAAAG
1 AAAA-AAAG
40813155 GAATTTTGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
44 44 0.92
45 4 0.08
ACGTcount: A:0.55, C:0.12, G:0.20, T:0.13
Consensus pattern (44 bp):
AAAAAAAGAAGAAATCGAGATAAAAACCTACAAAGGGCATCTCG
Found at i:40813823 original size:30 final size:30
Alignment explanation
Indices: 40813778--40813922 Score: 154
Period size: 30 Copynumber: 4.9 Consensus size: 30
40813768 GTAAATCCCT
*
40813778 AAACTTTCTCAAAATCACATTTTAACCCCC
1 AAACCTTCTCAAAATCACATTTTAACCCCC
* * *
40813808 AAACCTTCTCGAAATCACATTTTGA-CCTC
1 AAACCTTCTCAAAATCACATTTTAACCCCC
40813837 AAA-CTTCTCCAAAATCACATTTTAACCCCC
1 AAACCTTCT-CAAAATCACATTTTAACCCCC
* * * **
40813867 AAACCTTCTCGAAATCACATGTTGA-CCTT
1 AAACCTTCTCAAAATCACATTTTAACCCCC
*
40813896 AAA-CTTCTCCAAAATTACATTTTAACC
1 AAACCTTCT-CAAAATCACATTTTAACC
40813923 TCAAACTTCC
Statistics
Matches: 94, Mismatches: 16, Indels: 10
0.78 0.13 0.08
Matches are distributed among these distances:
28 10 0.11
29 37 0.39
30 42 0.45
31 5 0.05
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.30
Consensus pattern (30 bp):
AAACCTTCTCAAAATCACATTTTAACCCCC
Found at i:40813851 original size:29 final size:29
Alignment explanation
Indices: 40813778--40813985 Score: 174
Period size: 29 Copynumber: 7.1 Consensus size: 29
40813768 GTAAATCCCT
*
40813778 AAACTT-TCTCAAAATCACATTTTAACCCCC
1 AAACTTCTC-CAAAATCACATTTTAA-CCTC
* *
40813808 AAACCTTCT-CGAAATCACATTTTGACCTC
1 AAA-CTTCTCCAAAATCACATTTTAACCTC
*
40813837 AAACTTCTCCAAAATCACATTTTAACCCCC
1 AAACTTCTCCAAAATCACATTTTAA-CCTC
* * * *
40813867 AAACCTTCT-CGAAATCACATGTTGACCTT
1 AAA-CTTCTCCAAAATCACATTTTAACCTC
*
40813896 AAACTTCTCCAAAATTACATTTTAACCTC
1 AAACTTCTCCAAAATCACATTTTAACCTC
* * * *
40813925 AAACTTC-CTAAAATTACATTACT-ACCCC
1 AAACTTCTCCAAAATCACATT-TTAACCTC
* * *
40813953 TAAACTTTTCCAAAATTATATTTTAACCTC
1 -AAACTTCTCCAAAATCACATTTTAACCTC
40813983 AAA
1 AAA
40813986 TTTTTTGAAA
Statistics
Matches: 144, Mismatches: 24, Indels: 21
0.76 0.13 0.11
Matches are distributed among these distances:
28 26 0.18
29 58 0.40
30 51 0.35
31 8 0.06
32 1 0.01
ACGTcount: A:0.37, C:0.29, G:0.02, T:0.32
Consensus pattern (29 bp):
AAACTTCTCCAAAATCACATTTTAACCTC
Found at i:40813870 original size:59 final size:59
Alignment explanation
Indices: 40813778--40813922 Score: 247
Period size: 59 Copynumber: 2.5 Consensus size: 59
40813768 GTAAATCCCT
*
40813778 AAACTT-TCTCAAAATCACATTTTAACCCCCAAACCTTCTCGAAATCACATTTTGACCTC
1 AAACTTCTC-CAAAATCACATTTTAACCCCCAAACCTTCTCGAAATCACATGTTGACCTC
*
40813837 AAACTTCTCCAAAATCACATTTTAACCCCCAAACCTTCTCGAAATCACATGTTGACCTT
1 AAACTTCTCCAAAATCACATTTTAACCCCCAAACCTTCTCGAAATCACATGTTGACCTC
*
40813896 AAACTTCTCCAAAATTACATTTTAACC
1 AAACTTCTCCAAAATCACATTTTAACC
40813923 TCAAACTTCC
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
59 80 0.98
60 2 0.02
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.30
Consensus pattern (59 bp):
AAACTTCTCCAAAATCACATTTTAACCCCCAAACCTTCTCGAAATCACATGTTGACCTC
Found at i:40815351 original size:53 final size:53
Alignment explanation
Indices: 40815270--40815376 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
40815260 CGCGACTCAA
* *
40815270 ACCCAAGCCACACATGAGATAATGAACACCCTTGACCATCAGGCCAACACACG
1 ACCCAAGCCACACATGAGATAATAAACACCCTTGACCATCAGACCAACACACG
*
40815323 ACCCAAGCCACACCTGAGATAATAAACACCCTTGACCATCAGACCAACACACG
1 ACCCAAGCCACACATGAGATAATAAACACCCTTGACCATCAGACCAACACACG
40815376 A
1 A
40815377 GGTTCTTGCT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.39, C:0.36, G:0.13, T:0.11
Consensus pattern (53 bp):
ACCCAAGCCACACATGAGATAATAAACACCCTTGACCATCAGACCAACACACG
Found at i:40817361 original size:25 final size:25
Alignment explanation
Indices: 40817318--40817367 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
40817308 ATTTTTATAG
* *
40817318 TTAATTTTATATAATTTTAATAATA
1 TTAATTTTATACAATTTTAAAAATA
40817343 TTAATATTTATACAA-TTTAAAAATA
1 TTAAT-TTTATACAATTTTAAAAATA
40817368 AATATCTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
TTAATTTTATACAATTTTAAAAATA
Found at i:40820494 original size:29 final size:29
Alignment explanation
Indices: 40820452--40820527 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
40820442 TTTAATTATT
* *
40820452 TTTTTAAAATTTAAAAATTATAAAAATAA
1 TTTTTAAAAATTAAAAATCATAAAAATAA
* *
40820481 TTTTTAAAAATTAAAAATCATTAAAATTA
1 TTTTTAAAAATTAAAAATCATAAAAATAA
**
40820510 TTTAAAAAAATTATAAAA
1 TTTTTAAAAATTA-AAAA
40820528 ATATTTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 36 0.90
30 4 0.10
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (29 bp):
TTTTTAAAAATTAAAAATCATAAAAATAA
Found at i:40820526 original size:21 final size:22
Alignment explanation
Indices: 40820493--40820533 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
40820483 TTTAAAAATT
*
40820493 AAAAATCATTAAAATTATTTAA
1 AAAAATCATTAAAAATATTTAA
*
40820515 AAAAATTA-TAAAAATATTT
1 AAAAATCATTAAAAATATTT
40820534 TTTTAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAAATCATTAAAAATATTTAA
Found at i:40821989 original size:30 final size:30
Alignment explanation
Indices: 40821955--40822011 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
40821945 CGCGGTCTGG
*
40821955 CACATGACCGTGTGCCTAGCCCATGTGGCT
1 CACATGACCGTGTGCCCAGCCCATGTGGCT
** *
40821985 CACATGGTCGTGTGCCCAGCCCGTGTG
1 CACATGACCGTGTGCCCAGCCCATGTG
40822012 AGAGAGTCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.14, C:0.33, G:0.30, T:0.23
Consensus pattern (30 bp):
CACATGACCGTGTGCCCAGCCCATGTGGCT
Found at i:40823222 original size:27 final size:27
Alignment explanation
Indices: 40823192--40823243 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
40823182 ATTTTTTTAG
* * * *
40823192 AAATTTAAAAATTATTTAAAGTATTAA
1 AAATATAAAAAATATTCAAAATATTAA
40823219 AAATATAAAAAATATTCAAAATATT
1 AAATATAAAAAATATTCAAAATATT
40823244 TTTTATGCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (27 bp):
AAATATAAAAAATATTCAAAATATTAA
Found at i:40823239 original size:9 final size:9
Alignment explanation
Indices: 40823192--40823243 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
40823182 ATTTTTTTAG
40823192 AAAT-TTAA
1 AAATATTAA
*
40823200 AAATTATTTA
1 AAA-TATTAA
*
40823210 AAGTATTAA
1 AAATATTAA
*
40823219 AAATATAAA
1 AAATATTAA
*
40823228 AAATATTCA
1 AAATATTAA
40823237 AAATATT
1 AAATATT
40823244 TTTTATGCTT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
8 3 0.09
9 27 0.77
10 5 0.14
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (9 bp):
AAATATTAA
Found at i:40826747 original size:5 final size:6
Alignment explanation
Indices: 40826732--40826761 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
40826722 GCTAAATGTC
40826732 AAAAAG AAAAAG AAAAAG AAAAACG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAA-G AAAAA
40826762 AGTTTTGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:40832945 original size:12 final size:12
Alignment explanation
Indices: 40832928--40832953 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40832918 TCCCCATCCT
40832928 TATTATCCGTCG
1 TATTATCCGTCG
40832940 TATTATCCGTCG
1 TATTATCCGTCG
40832952 TA
1 TA
40832954 AAACCCGCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.42
Consensus pattern (12 bp):
TATTATCCGTCG
Found at i:40834824 original size:32 final size:33
Alignment explanation
Indices: 40834764--40834826 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
40834754 TATCTAACAA
*
40834764 TTTTATAAATTATTTTTTCTAACTATTTTATGGT
1 TTTTATAAATTATTTTTTATAAC-ATTTTATGGT
40834798 TTTTAATAAATT-TTTTTTATAA-ATTTTAT
1 TTTT-ATAAATTATTTTTTATAACATTTTAT
40834827 AAAATTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 7 0.26
34 13 0.48
35 7 0.26
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (33 bp):
TTTTATAAATTATTTTTTATAACATTTTATGGT
Found at i:40836770 original size:3 final size:3
Alignment explanation
Indices: 40836755--40836801 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
40836745 GATAGAGAAT
* *
40836755 TCA TCA GCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCG TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
40836802 TTCTTCTCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.30, C:0.34, G:0.04, T:0.32
Consensus pattern (3 bp):
TCA
Found at i:40837813 original size:20 final size:20
Alignment explanation
Indices: 40837776--40837814 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40837766 TGCAAAATGA
* * *
40837776 AATTCATAGGATATATATAT
1 AATTCAAAGGAGAAATATAT
40837796 AATTCAAAGGAGAAATATA
1 AATTCAAAGGAGAAATATA
40837815 AATATTTGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.05, G:0.13, T:0.31
Consensus pattern (20 bp):
AATTCAAAGGAGAAATATAT
Found at i:40839769 original size:17 final size:16
Alignment explanation
Indices: 40839743--40839788 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
40839733 TGATTACCTG
*
40839743 CAAAATAAAAAAGAAGA
1 CAAAACAAAAAAG-AGA
40839760 CAAAACAAAAATAGAGA
1 CAAAACAAAAA-AGAGA
*
40839777 AAAAACAAAAAA
1 CAAAACAAAAAA
40839789 CACATTGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 1 0.04
17 23 0.88
18 2 0.08
ACGTcount: A:0.78, C:0.09, G:0.09, T:0.04
Consensus pattern (16 bp):
CAAAACAAAAAAGAGA
Found at i:40840780 original size:30 final size:30
Alignment explanation
Indices: 40840729--40840931 Score: 111
Period size: 30 Copynumber: 6.8 Consensus size: 30
40840719 TGAAGGTCCT
* *
40840729 TAAACTTC-CAAAAATCT-CATTTTAGATCC
1 TAAACTTCTCTAAAAT-TACATTTTAGACCC
* *
40840758 TTAACTTCTCTAAAATTACATTTCA-ACCC
1 TAAACTTCTCTAAAATTACATTTTAGACCC
* * *
40840787 TTAAACTTTTCCAAAATCACATTTT-GACCAC
1 -TAAACTTCTCTAAAATTACATTTTAGACC-C
* *
40840818 CAAACCTTCTC-AAAATCACATTTT-GA-CC
1 TAAA-CTTCTCTAAAATTACATTTTAGACCC
* * *
40840846 TCAAACTCCTTTAAAATTAAATTTTTA-ACCC
1 T-AAACTTCTCTAAAATTACA-TTTTAGACCC
* *
40840877 TAAACTT-TCTCAAAATTACATTTT-TACCTT
1 TAAACTTCTCT-AAAATTACATTTTAGACC-C
* * *
40840907 TAAACTTTTTTAAAATTACGTTTTA
1 TAAACTTCTCTAAAATTACATTTTA
40840932 ATCCCAAACT
Statistics
Matches: 136, Mismatches: 22, Indels: 30
0.72 0.12 0.16
Matches are distributed among these distances:
28 5 0.04
29 31 0.23
30 89 0.65
31 11 0.08
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.39
Consensus pattern (30 bp):
TAAACTTCTCTAAAATTACATTTTAGACCC
Found at i:40840931 original size:59 final size:57
Alignment explanation
Indices: 40840763--40840941 Score: 160
Period size: 59 Copynumber: 3.0 Consensus size: 57
40840753 GATCCTTAAC
* ** * * *
40840763 TTCTCTAAAATTACATTTCAACCCTTAAACTTTTCCAAAATCACATTTTGACCACCAAACC
1 TTCTC-AAAATTACATTTTAA-CCTTAAACTTTTTTAAAATTACATTTT-AAC-CCAAACT
* * * ** *
40840824 TTCTCAAAATCACATTTTGACCTCAAACTCCTTTAAAATTAAATTTTTAACCCTAAACT
1 TTCTCAAAATTACATTTTAACCTTAAACTTTTTTAAAATTACA-TTTTAACCC-AAACT
* *
40840883 TTCTCAAAATTACATTTTTACCTTTAAACTTTTTTAAAATTACGTTTTAATCCCAAACT
1 TTCTCAAAATTACATTTTAACC-TTAAACTTTTTTAAAATTACATTTTAA-CCCAAACT
40840942 CTCCGAAACT
Statistics
Matches: 95, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
58 2 0.02
59 53 0.56
60 35 0.37
61 5 0.05
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.39
Consensus pattern (57 bp):
TTCTCAAAATTACATTTTAACCTTAAACTTTTTTAAAATTACATTTTAACCCAAACT
Found at i:40844909 original size:22 final size:22
Alignment explanation
Indices: 40844880--40844923 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
40844870 AGAACCCAAT
40844880 AAAAAAAGAGAA-AAAAGAAAG
1 AAAAAAAGAGAAGAAAAGAAAG
*
40844901 AAAAGAAAGAGAAGAAAGGAAAG
1 AAAA-AAAGAGAAGAAAAGAAAG
40844924 TCAAGACGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 8 0.40
23 8 0.40
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (22 bp):
AAAAAAAGAGAAGAAAAGAAAG
Found at i:40845790 original size:7 final size:7
Alignment explanation
Indices: 40845773--40845851 Score: 76
Period size: 7 Copynumber: 11.3 Consensus size: 7
40845763 ATAAATAAAT
40845773 AAAAGAA
1 AAAAGAA
40845780 AGAAA-AA
1 A-AAAGAA
40845787 AGAAAG-A
1 A-AAAGAA
40845794 AAAAGAA
1 AAAAGAA
40845801 AAAAGAA
1 AAAAGAA
40845808 AAAAGAAA
1 AAAAG-AA
40845816 AAAAGAA
1 AAAAGAA
40845823 AAAA-AA
1 AAAAGAA
40845829 GAAAA-AA
1 -AAAAGAA
* *
40845836 AAGAGGA
1 AAAAGAA
40845843 AAAAGAA
1 AAAAGAA
40845850 AA
1 AA
40845852 GAGAGGTCGA
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
6 9 0.15
7 43 0.69
8 10 0.16
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:40845800 original size:17 final size:16
Alignment explanation
Indices: 40845759--40845835 Score: 93
Period size: 17 Copynumber: 4.8 Consensus size: 16
40845749 TTCGATGAAG
* *
40845759 AAAAATAAATAAATAAA
1 AAAAAGAAA-AAAGAAA
*
40845776 AGAAAGAAAAAAGAAA
1 AAAAAGAAAAAAGAAA
40845792 GAAAAAGAAAAAAGAAA
1 -AAAAAGAAAAAAGAAA
*
40845809 AAAGA-AAAAAAGAAA
1 AAAAAGAAAAAAGAAA
40845824 AAAAAGAAAAAA
1 AAAAAGAAAAAA
40845836 AAGAGGAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
15 14 0.27
16 16 0.31
17 22 0.42
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (16 bp):
AAAAAGAAAAAAGAAA
Found at i:40845805 original size:24 final size:24
Alignment explanation
Indices: 40845778--40845851 Score: 98
Period size: 24 Copynumber: 3.0 Consensus size: 24
40845768 TAAATAAAAG
40845778 AAAGAAAAAAGAAAGAAAAAGAAA
1 AAAGAAAAAAGAAAGAAAAAGAAA
*
40845802 AAAGAAAAAAGAAA-AAAAGAAAAA
1 AAAGAAAAAAGAAAGAAAA-AGAAA
40845826 AAAGAAAAAA-AAGAGGAAAAAGAAA
1 AAAGAAAAAAGAA-A-GAAAAAGAAA
40845851 A
1 A
40845852 GAGAGGTCGA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
23 6 0.14
24 29 0.66
25 5 0.11
26 4 0.09
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (24 bp):
AAAGAAAAAAGAAAGAAAAAGAAA
Found at i:40845806 original size:28 final size:27
Alignment explanation
Indices: 40845773--40845851 Score: 88
Period size: 31 Copynumber: 2.7 Consensus size: 27
40845763 ATAAATAAAT
40845773 AAAAGAAAGAAAAAAGAAAGAAAAAGAA
1 AAAAGAAAGAAAAAAGAAA-AAAAAGAA
40845801 AAAAGAAAAAAGAAAAAAAGAAAAAAAAGAA
1 AAAAG---AAAG-AAAAAAGAAAAAAAAGAA
*
40845832 AAAA-AAGAGGAAAAAGAAAA
1 AAAAGAA-AGAAAAAAGAAAA
40845852 GAGAGGTCGA
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
27 12 0.27
28 7 0.16
31 16 0.36
32 10 0.22
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (27 bp):
AAAAGAAAGAAAAAAGAAAAAAAAGAA
Found at i:40845830 original size:48 final size:49
Alignment explanation
Indices: 40845759--40845851 Score: 127
Period size: 48 Copynumber: 1.9 Consensus size: 49
40845749 TTCGATGAAG
* * * *
40845759 AAAAATAAATAAATAAAAGAAAGAAAAAAGAA-A-GAAAAAGAAAAAAGA
1 AAAAAGAAAAAAAGAAAAAAAAGAAAAAA-AAGAGGAAAAAGAAAAAAGA
40845807 AAAAAGAAAAAAAGAAAAAAAAGAAAAAAAAGAGGAAAAAGAAAA
1 AAAAAGAAAAAAAGAAAAAAAAGAAAAAAAAGAGGAAAAAGAAAA
40845852 GAGAGGTCGA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
47 2 0.05
48 26 0.67
49 11 0.28
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (49 bp):
AAAAAGAAAAAAAGAAAAAAAAGAAAAAAAAGAGGAAAAAGAAAAAAGA
Found at i:40845836 original size:17 final size:17
Alignment explanation
Indices: 40845759--40845851 Score: 86
Period size: 17 Copynumber: 5.6 Consensus size: 17
40845749 TTCGATGAAG
* * *
40845759 AAAAATAAATAAATAAA
1 AAAAAGAAAAAAAGAAA
*
40845776 AGAAAG-AAAAAAGAAA
1 AAAAAGAAAAAAAGAAA
40845792 GAAAAAG-AAAAAAG--A
1 -AAAAAGAAAAAAAGAAA
40845807 AAAAAGAAAAAAAGAAA
1 AAAAAGAAAAAAAGAAA
**
40845824 AAAAAGAAAAAAAAGAGG
1 AAAAAG-AAAAAAAGAAA
40845842 AAAAAGAAAA
1 AAAAAGAAAA
40845852 GAGAGGTCGA
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
14 6 0.09
15 8 0.12
16 8 0.12
17 27 0.42
18 15 0.23
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (17 bp):
AAAAAGAAAAAAAGAAA
Found at i:40845846 original size:1 final size:1
Alignment explanation
Indices: 40845759--40845837 Score: 50
Period size: 1 Copynumber: 79.0 Consensus size: 1
40845749 TTCGATGAAG
* * * * * * * * * * *
40845759 AAAAATAAATAAATAAAAGAAAGAAAAAAGAAAGAAAAAGAAAAAAGAAAAAAGAAAAAAAGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
40845824 AAAAAGAAAAAAAA
1 AAAAAAAAAAAAAA
40845838 GAGGAAAAAG
Statistics
Matches: 54, Mismatches: 24, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.85, C:0.00, G:0.11, T:0.04
Consensus pattern (1 bp):
A
Found at i:40847013 original size:48 final size:48
Alignment explanation
Indices: 40846925--40847060 Score: 128
Period size: 48 Copynumber: 2.8 Consensus size: 48
40846915 TGAGGCCACG
* * * *
40846925 ACGGTGAATTCGATACCTCAAAATATTTGAGGGGAAAGGTTGAGCCGT
1 ACGGTGAATTCGATACCTCAAAAGATGTAACGGGAAAGGTTGAGCCGT
* * * *
40846973 ACGGTGAATTCGGTACCTTAAAAGATGTAACGGGAGAGGTTGAGGCCGCA
1 ACGGTGAATTCGATACCTCAAAAGATGTAACGGGAAAGGTTGA-GCCG-T
* * ** * *
40847023 ACAGCGAACCCGATACCTCAAAAGATGTGATGGGAAAG
1 ACGGTGAATTCGATACCTCAAAAGATGTAACGGGAAAG
40847061 ATTGTGGCCG
Statistics
Matches: 69, Mismatches: 17, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
48 36 0.52
49 4 0.06
50 29 0.42
ACGTcount: A:0.33, C:0.17, G:0.30, T:0.20
Consensus pattern (48 bp):
ACGGTGAATTCGATACCTCAAAAGATGTAACGGGAAAGGTTGAGCCGT
Found at i:40847231 original size:99 final size:100
Alignment explanation
Indices: 40846796--40847587 Score: 538
Period size: 99 Copynumber: 8.0 Consensus size: 100
40846786 AGAAAAACAT
* ** * * * * *
40846796 GAAGATTTGAAGAAAAATGTTGAGGCCGCAACGACGAACCCGATACCTTAAATGATGTGAAGGGA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACTCGATACCATAAAAGATGTGAAGGGA
** ** * *
40846861 AAGGTTGAGGCTACAACGACGAACCCGATACCAT-
66 AAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
* * * * * * * * *
40846895 GAAGATTTAAAGGG-AAGGATTGAGGCCACGACGGTGAATTCGATACC-TCAAAATATTTGAGGG
1 GAAGATGTGAAGGGAAAGG-TTGAGGCCGCAACGGCGAACTCGATACCAT-AAAAGATGTGAAGG
* **
40846958 GAAAGGTTGA-GCCG-TACGGTGAATTCGGTACCTTA
64 GAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
* * * * *
40846993 AAAGATGT-AACGGGAGAGGTTGAGGCCGCAACAGCGAACCCGATACC-TCAAAAGATGTGATGG
1 GAAGATGTGAA-GGGAAAGGTTGAGGCCGCAACGGCGAACTCGATACCAT-AAAAGATGTGAAGG
* * ** * *
40847056 GAAAGATTGTGGCCGCAACAATAAATCCGGTACC--A
64 GAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
* * * * * * * * *
40847091 TAA-ATGTGATGGAAAAGGTTGAGGCTGCAATGGTGAACTCGGTACCAT-GAAGATTTGAAGGGA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACTCGATACCATAAAAGATGTGAAGGGA
* *
40847154 AAGGTTGAGGCCGCAACGGCGAACCCAGTACCTTA
66 AAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
* * * * *
40847189 GAAGATGTGAAGGGAAAGGTTGAGGCCGTAACGGCGAACTCGGTACCAT-GAAGATTTGAACGG-
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACTCGATACCATAAAAGATGTGAAGGGA
* * * * * *
40847252 AAGGATTGAGGCCGCGATGGCGAATCCGATACCTCA
66 AAGG-TTGAGGCCGCAACGGTGAACCCGGTACCTTA
* ** * * * * *
40847288 AAAGACT-TGAAGGGAAAGGTTGAGGCCGCAACGATGAACCCGGTACCTTAAAAGGTGTGACGGG
1 GAAGA-TGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACTCGATACCATAAAAGATGTGAAGGG
*** * * *
40847352 AAAGGTTGAGGCTATAACGATGAACCCAGTACCTCA
65 AAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
* * * * ** * * *
40847388 GAAGATGTGATGAGAAAGATTGAGGTCGCAACGATGAATTCGATACCAT-GAA-ATGTGATGGGA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACTCGATACCATAAAAGATGTGAAGGGA
* * * *
40847451 AAGGTTGAGGCCGCAATGGAGAACTCGGTACCAT-
66 AAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
* * * * * * * * *
40847485 GAAGATTTTAAGGGAAAGGTTGAGGTCGCAACGGCGAACTTGGTACCTTAGAAGATATGAGGGGA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACTCGATACCATAAAAGATGTGAAGGGA
* *
40847550 AAGGTTAAGGCCACAACGGTGAACCCGGTACCTTA
66 AAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
40847585 GAA
1 GAA
40847588 AATAAGATCG
Statistics
Matches: 534, Mismatches: 139, Indels: 39
0.75 0.20 0.05
Matches are distributed among these distances:
96 36 0.07
97 85 0.16
98 106 0.20
99 218 0.41
100 85 0.16
101 4 0.01
ACGTcount: A:0.33, C:0.17, G:0.31, T:0.19
Consensus pattern (100 bp):
GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACTCGATACCATAAAAGATGTGAAGGGA
AAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
Found at i:40847334 original size:149 final size:148
Alignment explanation
Indices: 40846815--40847567 Score: 421
Period size: 147 Copynumber: 5.1 Consensus size: 148
40846805 AAGAAAAATG
* * * **
40846815 TTGAGGCCGCAACGACGAACCCGATACC-TTAAATGATGTGAAGGGAAAGGTTGAGGCTACAACG
1 TTGAGGCCGCAACGACGAATCCGATACCATCAAAAGAT-TGAAGGGAAAGGTTGAGGCCGCAACG
* * * * *** * * *
40846879 ACGAACCCGATACCAT-GAAGATTTAAAGGG-AAGGATTGAGGCCACGACGGTGAATTCGATACC
65 A-GAACCCGGTACCTTAGAAGATGTGAAGGGAAAGG-TTGAGGCCGTAACGGCGAACTCGGTACC
* * * * * *
40846942 TCAAAATATTTGAGGGGAAAGG
128 T-AGAAGATGTGACGAGAAAGA
* ** * * * *
40846964 TTGA-GCCG-TACGGTGAATTCGGTACC-TTAAAAGA-TGTAACGGGAGAGGTTGAGGCCGCAAC
1 TTGAGGCCGCAACGACGAATCCGATACCATCAAAAGATTG-AA-GGGAAAGGTTGAGGCCGCAAC
* * * * * * * * *** *
40847025 AGCGAACCCGATACCTCAAAAGATGTGATGGGAAAGATTGTGGCCGCAAC-AATAAATCCGGTAC
64 -GAGAACCCGGTACCTTAGAAGATGTGAAGGGAAAGGTTGAGGCCGTAACGGCGAACT-CGGTAC
* * *
40847089 C-ATAA-ATGTGATG-GAAAAGG
127 CTAGAAGATGTGACGAG-AAAGA
* * ** * *
40847109 TTGAGGCTGCAATGGTGAA-CTCGGTACCAT--GAAGATTTGAAGGGAAAGGTTGAGGCCGCAAC
1 TTGAGGCCGCAACGACGAATC-CGATACCATCAAAAGA-TTGAAGGGAAAGGTTGAGGCCGCAAC
* *
40847171 GGCGAACCCAGTACCTTAGAAGATGTGAAGGGAAAGGTTGAGGCCGTAACGGCGAACTCGGTACC
64 -GAGAACCCGGTACCTTAGAAGATGTGAAGGGAAAGGTTGAGGCCGTAACGGCGAACTCGGTACC
* *
40847236 -ATGAAGATTTGAACG-GAAGGA
128 TA-GAAGATGTG-ACGAGAAAGA
* * *
40847257 TTGAGGCCGCGATGGCGAATCCGATACC-TCAAAAGACTTGAAGGGAAAGGTTGAGGCCGCAACG
1 TTGAGGCCGCAACGACGAATCCGATACCATCAAAAGA-TTGAAGGGAAAGGTTGAGGCCGCAACG
* * * ** ** * *
40847321 ATGAACCCGGTACCTTAAAAGGTGTGACGGGAAAGGTTGAGGCTATAACGATGAACCCAGTACCT
65 A-GAACCCGGTACCTTAGAAGATGTGAAGGGAAAGGTTGAGGCCGTAACGGCGAACTCGGTACCT
*
40847386 CAGAAGATGTGATGAGAAAGA
129 -AGAAGATGTGACGAGAAAGA
* * * * * * *
40847407 TTGAGGTCGCAACGATGAATTCGATACCATGAAATG--TGATGGGAAAGGTTGAGGCCGCAATGG
1 TTGAGGCCGCAACGACGAATCCGATACCATCAAAAGATTGAAGGGAAAGGTTGAGGCCGCAA-CG
* * * * * * *
40847470 AGAACTCGGTACCAT-GAAGATTTTAAGGGAAAGGTTGAGGTCGCAACGGCGAACTTGGTACCTT
65 AGAACCCGGTACCTTAGAAGATGTGAAGGGAAAGGTTGAGGCCGTAACGGCGAACTCGGTACC-T
* * * *
40847534 AGAAGATATGAGGGGAAAGG
129 AGAAGATGTGACGAGAAAGA
* *
40847554 TTAAGGCCACAACG
1 TTGAGGCCGCAACG
40847568 GTGAACCCGG
Statistics
Matches: 471, Mismatches: 106, Indels: 56
0.74 0.17 0.09
Matches are distributed among these distances:
144 1 0.00
145 17 0.04
146 81 0.17
147 134 0.28
148 100 0.21
149 97 0.21
150 35 0.07
151 6 0.01
ACGTcount: A:0.33, C:0.17, G:0.31, T:0.19
Consensus pattern (148 bp):
TTGAGGCCGCAACGACGAATCCGATACCATCAAAAGATTGAAGGGAAAGGTTGAGGCCGCAACGA
GAACCCGGTACCTTAGAAGATGTGAAGGGAAAGGTTGAGGCCGTAACGGCGAACTCGGTACCTAG
AAGATGTGACGAGAAAGA
Found at i:40847585 original size:50 final size:50
Alignment explanation
Indices: 40846796--40847587 Score: 536
Period size: 50 Copynumber: 16.1 Consensus size: 50
40846786 AGAAAAACAT
* ** * ** *
40846796 GAAGATTTGAAGAAAAATGTTGAGGCCGCAACGACGAACCCGATACCTTA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
** ** * *
40846846 -AATGATGTGAAGGGAAAGGTTGAGGCTACAACGACGAACCCGATACCAT-
1 GAA-GATGTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
* * * * ** * *
40846895 GAAGATTTAAAGGG-AAGGATTGAGGCCACGACGGTGAATTCGATACCTCA
1 GAAGATGTGAAGGGAAAGG-TTGAGGCCGCAACGGTGAACCCGGTACCTTA
* * * * * **
40846945 AAATATTTGAGGGGAAAGGTTGA-GCCG-TACGGTGAATTCGGTACCTTA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
* * * * * *
40846993 AAAGATGT-AACGGGAGAGGTTGAGGCCGCAACAGCGAACCCGATACCTCA
1 GAAGATGTGAA-GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
* * * * ** * *
40847043 AAAGATGTGATGGGAAAGATTGTGGCCGCAACAATAAATCCGGTACC--A
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
* * * * * * *
40847091 TAA-ATGTGATGGAAAAGGTTGAGGCTGCAATGGTGAACTCGGTACCAT-
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
* * *
40847139 GAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACCTTA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
* * * *
40847189 GAAGATGTGAAGGGAAAGGTTGAGGCCGTAACGGCGAACTCGGTACCAT-
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
* * * * * * * *
40847238 GAAGATTTGAACGG-AAGGATTGAGGCCGCGATGGCGAATCCGATACCTCA
1 GAAGATGTGAAGGGAAAGG-TTGAGGCCGCAACGGTGAACCCGGTACCTTA
* *
40847288 AAAGACT-TGAAGGGAAAGGTTGAGGCCGCAACGATGAACCCGGTACCTTA
1 GAAGA-TGTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
* * * *** * * *
40847338 AAAGGTGTGACGGGAAAGGTTGAGGCTATAACGATGAACCCAGTACCTCA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
* * * * * ** * *
40847388 GAAGATGTGATGAGAAAGATTGAGGTCGCAACGATGAATTCGATACCAT-
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
* * * * *
40847437 GAA-ATGTGATGGGAAAGGTTGAGGCCGCAATGGAGAACTCGGTACCAT-
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
* * * * **
40847485 GAAGATTTTAAGGGAAAGGTTGAGGTCGCAACGGCGAACTTGGTACCTTA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
* * * *
40847535 GAAGATATGAGGGGAAAGGTTAAGGCCACAACGGTGAACCCGGTACCTTA
1 GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
40847585 GAA
1 GAA
40847588 AATAAGATCG
Statistics
Matches: 585, Mismatches: 137, Indels: 40
0.77 0.18 0.05
Matches are distributed among these distances:
47 34 0.06
48 88 0.15
49 151 0.26
50 302 0.52
51 10 0.02
ACGTcount: A:0.33, C:0.17, G:0.31, T:0.19
Consensus pattern (50 bp):
GAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA
Found at i:40847881 original size:41 final size:41
Alignment explanation
Indices: 40847821--40847903 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
40847811 TACATCATCA
* * *
40847821 TTCAGTCTTTTACCTTTAATTAAGAAGGGCAGATTGAAGAT
1 TTCAGGCTTTTACCCTTAATTAAGAAGGGCAGAATGAAGAT
40847862 TTCAGGCTTTTACCCTTAATTAAGAAGGGCAGAATGAAGAT
1 TTCAGGCTTTTACCCTTAATTAAGAAGGGCAGAATGAAGAT
40847903 T
1 T
40847904 CTGATATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (41 bp):
TTCAGGCTTTTACCCTTAATTAAGAAGGGCAGAATGAAGAT
Found at i:40848027 original size:78 final size:78
Alignment explanation
Indices: 40847945--40848485 Score: 450
Period size: 78 Copynumber: 7.0 Consensus size: 78
40847935 CTATCAGTCA
* * * * *
40847945 ATCTTTTACCCCGACCCTAGGGCATATCATCATCAACCAATCTCTTACCCCGAGCTTGAGGCAGA
1 ATCTTTTACCCCGAACCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGGCAGA
*
40848010 TTACAGCCATTCG
66 TTGCAGCCATTCG
* * * ** * * * * *
40848023 ATCTTTTACCCCG-AGCTTGAGGAAGATCACTTTTAGTCAATCTCTTACTCCGAGCTTGGGGCAG
1 ATCTTTTACCCCGAACCTAG-GGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGGCAG
*
40848087 ATTGCAGCCATCCG
65 ATTGCAGCCATTCG
* * * * *
40848101 ATCTTTTACCCCGAGCTTAGGGCAGATTACCATCAGCCAATCTCTTGCCCCGAGCCT-AGGGTAG
1 ATCTTTTACCCCGAACCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGA-GGCAG
*
40848165 ATTGCAGCCATTTG
65 ATTGCAGCCATTCG
* * * * * * * *
40848179 ATCTTTTACTCTGAGCTTGGGGCAAATCACCATCAGCCAATCTCTTACACCGAGCCTGGGGCAGA
1 ATCTTTTACCCCGAACCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGGCAGA
*
40848244 TTGCAGCCATCCG
66 TTGCAGCCATTCG
* * * * * * *
40848257 ATCTTTTACCTCAAACCT-GGGCAAATCACCATTAGTCAATCTCTTACCCCGAGCCT-AGGGTAA
1 ATCTTTTACCCCGAACCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGA-GGCAG
* *
40848320 ATTGTAACCA-TCTG
65 ATTGCAGCCATTC-G
* * * *
40848334 ATCTTTTA-CCCTAAGCTTGAGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTG-GGATA
1 ATCTTTTACCCCGAACCTAG-GGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGG-CA
*
40848397 GATTGCAACCATTCG
64 GATTGCAGCCATTCG
* *** * * * * * * *
40848412 ATCTTTTACCTCGATTATGGGGCTGATCA-CGTCAGCTAATCTCTTACCCCGCGACAGAGGCAGA
1 ATCTTTTACCCCGAACCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGGCAGA
*
40848476 TTGCAACCAT
66 TTGCAGCCAT
40848486 CCAATATCTT
Statistics
Matches: 371, Mismatches: 79, Indels: 27
0.78 0.17 0.06
Matches are distributed among these distances:
76 7 0.02
77 97 0.26
78 258 0.70
79 9 0.02
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (78 bp):
ATCTTTTACCCCGAACCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAGGCAGA
TTGCAGCCATTCG
Found at i:40848114 original size:156 final size:156
Alignment explanation
Indices: 40847945--40848421 Score: 575
Period size: 156 Copynumber: 3.1 Consensus size: 156
40847935 CTATCAGTCA
* * * * * *
40847945 ATCTTTTACCCCGACCCTAGGGCATATCATCATCAACCAATCTCTTACCCCGAG-CTTGAGGCAG
1 ATCTTTTACCCCGAACCTAGGGCAAATCACCATCAGCCAATCTCTTACCCCGAGCCTAG-GGTAG
* * ** * * *
40848009 ATTACAGCCATTCGATCTTTTACCCCGAGCTTGAGGAAGATCACTTTTAGTCAATCTCTTACTCC
65 ATTGCAGCCATTCGATCTTTTACCCTGAGCTTGAGGAAGATCACCATCAGCCAATCTCTTACACC
*
40848074 GAGCTTGGGGCAGATTGCAGCCATCCG
130 GAGCCTGGGGCAGATTGCAGCCATCCG
* * * * *
40848101 ATCTTTTACCCCGAGCTTAGGGCAGATTACCATCAGCCAATCTCTTGCCCCGAGCCTAGGGTAGA
1 ATCTTTTACCCCGAACCTAGGGCAAATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGTAGA
* * *
40848166 TTGCAGCCATTTGATCTTTTACTCTGAGCTTGGGGCAA-ATCACCATCAGCCAATCTCTTACACC
66 TTGCAGCCATTCGATCTTTTACCCTGAGCTTGAGG-AAGATCACCATCAGCCAATCTCTTACACC
40848230 GAGCCTGGGGCAGATTGCAGCCATCCG
130 GAGCCTGGGGCAGATTGCAGCCATCCG
* * * * *
40848257 ATCTTTTACCTCAAACCT-GGGCAAATCACCATTAGTCAATCTCTTACCCCGAGCCTAGGGTAAA
1 ATCTTTTACCCCGAACCTAGGGCAAATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGTAGA
* * * * *
40848321 TTGTAACCA-TCTGATCTTTTACCCTAAGCTTGAGGCAGATCACCATCAGCCAATCTCTTACCCC
66 TTGCAGCCATTC-GATCTTTTACCCTGAGCTTGAGGAAGATCACCATCAGCCAATCTCTTACACC
** * *
40848385 GAGCCTGGGATAGATTGCAACCATTCG
130 GAGCCTGGGGCAGATTGCAGCCATCCG
40848412 ATCTTTTACC
1 ATCTTTTACC
40848422 TCGATTATGG
Statistics
Matches: 275, Mismatches: 42, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
154 2 0.01
155 125 0.45
156 143 0.52
157 5 0.02
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.27
Consensus pattern (156 bp):
ATCTTTTACCCCGAACCTAGGGCAAATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGTAGA
TTGCAGCCATTCGATCTTTTACCCTGAGCTTGAGGAAGATCACCATCAGCCAATCTCTTACACCG
AGCCTGGGGCAGATTGCAGCCATCCG
Found at i:40848152 original size:39 final size:39
Alignment explanation
Indices: 40847937--40848388 Score: 156
Period size: 39 Copynumber: 11.6 Consensus size: 39
40847927 GCAGATCGCT
* * * * * * *
40847937 ATCAGTCAATCTTTTACCCCGACCCTAGGGCATATCATC
1 ATCAGCCAATCTCTTACCCCGAGCTTAGGGCAGATTACC
*
40847976 ATCAACCAATCTCTTACCCCGAGCTT-GAGGCAGATTA-C
1 ATCAGCCAATCTCTTACCCCGAGCTTAG-GGCAGATTACC
* ** * * * * *
40848014 AGCCATTCGATCTTTTACCCCGAGCTT-GAGGAAGATCACT
1 A-TCAGCCAATCTCTTACCCCGAGCTTAG-GGCAGATTACC
* * * * * *
40848054 TTTAGTCAATCTCTTACTCCGAGCTTGGGGCAGATT-GC
1 ATCAGCCAATCTCTTACCCCGAGCTTAGGGCAGATTACC
* * * *
40848092 AGCCATCCGATCTTTTACCCCGAGCTTAGGGCAGATTACC
1 A-TCAGCCAATCTCTTACCCCGAGCTTAGGGCAGATTACC
* * *
40848132 ATCAGCCAATCTCTTGCCCCGAGCCTAGGGTAGATTGCAGCC
1 ATCAGCCAATCTCTTACCCCGAGCTTAGGGCAGATT--A-CC
** * * * * * *
40848174 ATTTG---ATCTTTTACTCTGAGCTTGGGGCAAATCACC
1 ATCAGCCAATCTCTTACCCCGAGCTTAGGGCAGATTACC
* * * *
40848210 ATCAGCCAATCTCTTACACCGAGCCTGGGGCAGATT-GC
1 ATCAGCCAATCTCTTACCCCGAGCTTAGGGCAGATTACC
* * * * * * * * * *
40848248 AGCCATCCGATCTTTTACCTCAAACCT-GGGCAAATCACC
1 A-TCAGCCAATCTCTTACCCCGAGCTTAGGGCAGATTACC
* * * * *
40848287 ATTAGTCAATCTCTTACCCCGAGCCTAGGGTAAATTGTAACC
1 ATCAGCCAATCTCTTACCCCGAGCTTAGGGCAGA-T-T-ACC
* * ** *
40848329 ATCTG---ATCTTTTACCCTAAGCTT-GAGGCAGATCACC
1 ATCAGCCAATCTCTTACCCCGAGCTTAG-GGCAGATTACC
40848365 ATCAGCCAATCTCTTACCCCGAGC
1 ATCAGCCAATCTCTTACCCCGAGC
40848389 CTGGGATAGA
Statistics
Matches: 293, Mismatches: 98, Indels: 44
0.67 0.23 0.10
Matches are distributed among these distances:
36 12 0.04
37 1 0.00
38 30 0.10
39 234 0.80
40 4 0.01
41 1 0.00
42 11 0.04
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (39 bp):
ATCAGCCAATCTCTTACCCCGAGCTTAGGGCAGATTACC
Found at i:40848484 original size:155 final size:155
Alignment explanation
Indices: 40847964--40848486 Score: 545
Period size: 155 Copynumber: 3.4 Consensus size: 155
40847954 CCCGACCCTA
* * * * * * *
40847964 GGGCATATCATCATCAACCAATCTCTTACCCCGAG-CTTGAGGCAGATTACAGCCAT-TCGATCT
1 GGGCAGATCACCATCAGCTAATCTCTTACCCCGAGCCTAG-GGCAGATTGCAACCATCT-GATCT
* * ** * * * *
40848027 TTTACCCCGAGCTTGAGGAAGATCACTTTTAGTCAATCTCTTACTCCGAGCTTGGGGCAGATTGC
64 TTTACCCTGAGCTTGAGGCAGATCACCATCAGCCAATCTCTTACACCGAGCCTGGGGCAGATTGC
*
40848092 AGCCATCCGATCTTTTACCCCGAGCTTA-
129 AGCCATCCGATCTTTTACCTCGA--TTAT
* * * * * *
40848120 GGGCAGATTACCATCAGCCAATCTCTTGCCCCGAGCCTAGGGTAGATTGCAGCCATTTGATCTTT
1 GGGCAGATCACCATCAGCTAATCTCTTACCCCGAGCCTAGGGCAGATTGCAACCATCTGATCTTT
* * *
40848185 TACTCTGAGCTTGGGGCAAATCACCATCAGCCAATCTCTTACACCGAGCCTGGGGCAGATTGCAG
66 TACCCTGAGCTTGAGGCAGATCACCATCAGCCAATCTCTTACACCGAGCCTGGGGCAGATTGCAG
* ***
40848250 CCATCCGATCTTTTACCTCAAACCT
131 CCATCCGATCTTTTACCTCGATTAT
* * * * *
40848275 GGGCAAATCACCATTAG-TCAATCTCTTACCCCGAGCCTAGGGTAAATTGTAACCATCTGATCTT
1 GGGCAGATCACCATCAGCT-AATCTCTTACCCCGAGCCTAGGGCAGATTGCAACCATCTGATCTT
* * **
40848339 TTACCCTAAGCTTGAGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGATAGATTGCA
65 TTACCCTGAGCTTGAGGCAGATCACCATCAGCCAATCTCTTACACCGAGCCTGGGGCAGATTGCA
* *
40848404 ACCATTCGATCTTTTACCTCGATTAT
130 GCCATCCGATCTTTTACCTCGATTAT
* * * *
40848430 GGGGCTGATCA-CGTCAGCTAATCTCTTACCCCGCGAC-AGAGGCAGATTGCAACCATC
1 -GGGCAGATCACCATCAGCTAATCTCTTACCCCGAGCCTAG-GGCAGATTGCAACCATC
40848487 CAATATCTTA
Statistics
Matches: 305, Mismatches: 55, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
154 2 0.01
155 166 0.54
156 133 0.44
157 4 0.01
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (155 bp):
GGGCAGATCACCATCAGCTAATCTCTTACCCCGAGCCTAGGGCAGATTGCAACCATCTGATCTTT
TACCCTGAGCTTGAGGCAGATCACCATCAGCCAATCTCTTACACCGAGCCTGGGGCAGATTGCAG
CCATCCGATCTTTTACCTCGATTAT
Found at i:40849588 original size:2 final size:2
Alignment explanation
Indices: 40849583--40849618 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
40849573 ACGTAAGTAC
*
40849583 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40849619 CATTTTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:40850711 original size:3 final size:3
Alignment explanation
Indices: 40850703--40850771 Score: 129
Period size: 3 Copynumber: 23.0 Consensus size: 3
40850693 AGTTTTAGGG
*
40850703 AAT AAT AAT AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40850751 AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT
40850772 TCAAGATTCG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:40852326 original size:15 final size:15
Alignment explanation
Indices: 40852306--40852339 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
40852296 AGAGGTCAAA
40852306 GTGATGACATGGCAT
1 GTGATGACATGGCAT
*
40852321 GTGATGACGTGGCAT
1 GTGATGACATGGCAT
40852336 GTGA
1 GTGA
40852340 GGATGTGGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.12, G:0.38, T:0.26
Consensus pattern (15 bp):
GTGATGACATGGCAT
Found at i:40852347 original size:15 final size:15
Alignment explanation
Indices: 40852315--40852349 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
40852305 AGTGATGACA
*
40852315 TGGCATGTGATGACG
1 TGGCATGTGAGGACG
*
40852330 TGGCATGTGAGGATG
1 TGGCATGTGAGGACG
40852345 TGGCA
1 TGGCA
40852350 ACTGATGTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.20, C:0.11, G:0.43, T:0.26
Consensus pattern (15 bp):
TGGCATGTGAGGACG
Found at i:40853295 original size:49 final size:49
Alignment explanation
Indices: 40853168--40853555 Score: 219
Period size: 49 Copynumber: 7.9 Consensus size: 49
40853158 TTTTATTTTT
* * * *
40853168 TGAGGTACAAGGTTCGCTGTTGCGGCTTAAACCTTTCACTTTGTAT-CTTC
1 TGAGGTACAAGGTTCGCCGTTGCGACTTAAATCTTTC-CTTT-CATGCTTC
** * * * *
40853218 --ATGGTA-TTGGATTCGCCGTTGTGGCTTAAATCTTTCCTTTTACGCTTC
1 TGA-GGTACAAGG-TTCGCCGTTGCGACTTAAATCTTTCCTTTCATGCTTC
** * *
40853266 TGAGGTACAAGGTTCGTTGTTGCGACTTAAACCTTTCCCTTCAAAT-CTTC
1 TGAGGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCTTTC--ATGCTTC
* * *
40853316 -GTGGTAC-TGGATTCGCCGTTGCGACTTAAATCCTTCCTTTCATGTCTT-
1 TGAGGTACAAGG-TTCGCCGTTGCGACTTAAATCTTTCCTTTCATG-CTTC
* * * *
40853364 TGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTT-GTGTCTTC
1 TGAGGTACAAGGTTCGCCGTTGCGACTTAAATCTTT-CCTTTCATG-CTTC
* * * * * *
40853414 -GTGGTACTAGATTCGCCGTTACGGCTTAAATCTTTCCCTTCATGCTTC
1 TGAGGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCTTTCATGCTTC
* * * * * *
40853462 TGAGGTATAAGGTTCGCCATTGTGACTTAGACCTTTTCCTTT-GTGTCTTC
1 TGAGGTACAAGGTTCGCCGTTGCGACTTAAATC-TTTCCTTTCATG-CTTC
* * * *
40853512 -GTGGTAC-TGGATTCACCGTTGC-AGCTTAAATCTTTCCCTTCATG
1 TGAGGTACAAGG-TTCGCCGTTGCGA-CTTAAATCTTTCCTTTCATG
40853556 GTCATGAAAC
Statistics
Matches: 254, Mismatches: 62, Indels: 45
0.70 0.17 0.12
Matches are distributed among these distances:
47 4 0.02
48 31 0.12
49 193 0.76
50 25 0.10
51 1 0.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.39
Consensus pattern (49 bp):
TGAGGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCTTTCATGCTTC
Found at i:40853298 original size:98 final size:98
Alignment explanation
Indices: 40853026--40853555 Score: 562
Period size: 98 Copynumber: 5.4 Consensus size: 98
40853016 TGTCTTCGCA
* * * * * * *
40853026 GTACTGGATTCACCATTACGGCTTAAATCTTTCCCTTCGTGCTT-TCGAAGTACAAGGTTCGCCG
1 GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCTTTCATGCTTCT-GAGGTACAAGGTTCGCCA
* * * **
40853090 TTACTACTTAAACATTTCCCTTTGCGTCTTCGTG
65 TTGCGACTTAAACCTTTCCCTTTGTATCTTCGTG
** * * * * * * * **
40853124 GTACTGGATTCATCATTGCGGTTTAGATCATTCCTTTTAT-TTTTTGAGGTACAAGGTTCGCTGT
1 GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCTTTCATGCTTCTGAGGTACAAGGTTCGCCAT
* * *
40853188 TGCGGCTTAAACCTTTCACTTTGTATCTTCATG
66 TGCGACTTAAACCTTTCCCTTTGTATCTTCGTG
* * * * ***
40853221 GTATTGGATTCGCCGTTGTGGCTTAAATCTTTCCTTTTACGCTTCTGAGGTACAAGGTTCGTTGT
1 GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCTTTCATGCTTCTGAGGTACAAGGTTCGCCAT
***
40853286 TGCGACTTAAACCTTTCCCTTCAAATCTTCGTG
66 TGCGACTTAAACCTTTCCCTTTGTATCTTCGTG
* * *
40853319 GTACTGGATTCGCCGTTGCGACTTAAATCCTTCCTTTCATGTCTT-TGAGGTATAAGGTTCGCCA
1 GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCTTTCATG-CTTCTGAGGTACAAGGTTCGCCA
*
40853383 TTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTG
65 TTGCGACTTAAACCTTTCCCTTTGTATCTTCGTG
* * * *
40853417 GTACTAGATTCGCCGTTACGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGGTTCGCCAT
1 GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCTTTCATGCTTCTGAGGTACAAGGTTCGCCAT
* * * *
40853482 TGTGACTTAGACCTTTTCCTTTGTGTCTTCGTG
66 TGCGACTTAAACCTTTCCCTTTGTATCTTCGTG
* * *
40853515 GTACTGGATTCACCGTTGCAGCTTAAATCTTTCCCTTCATG
1 GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCTTTCATG
40853556 GTCATGAAAC
Statistics
Matches: 365, Mismatches: 63, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
97 78 0.21
98 284 0.78
99 3 0.01
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.39
Consensus pattern (98 bp):
GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCTTTCATGCTTCTGAGGTACAAGGTTCGCCAT
TGCGACTTAAACCTTTCCCTTTGTATCTTCGTG
Found at i:40853449 original size:196 final size:196
Alignment explanation
Indices: 40853016--40853555 Score: 627
Period size: 196 Copynumber: 2.8 Consensus size: 196
40853006 GTGGTTATAA
** * * * *
40853016 TGTCTTCGCAGTACTGGATTCACCATTACGGCTTAAATCTTTCCCTTCGTGCTT-TCGAAGTACA
1 TGTCTTCGTGGTACTGGATTCGCCGTTACGGCTTAAATCTTTCCCTTCATGCTTCT-GAGGTACA
* * * * * * *
40853080 AGGTTCGCCGTTACTACTTAAACATTTCCCTTTGCGTCTTCGTGGTACTGGATTCATCATTGCGG
65 AGGTTCGCCGTTGCGACTTAAACCTTTCCCTTTGAGTCTTCGTGGTACTGGATTCACCGTTGCGA
* * * * ** *
40853145 TTTAGATCATTCCTTTTAT-TTTTTGAGGTACAAGGTTCGCTGTTGCGGCTTAAACCTTTCACTT
130 CTTAAATCATTCCTTTCATGTCTTTGAGGTACAAGGTTCGCCATTGCGACTTAAACCTTTCACTT
40853209 TG
195 TG
* * * ** * * *
40853211 TATCTTCATGGTATTGGATTCGCCGTTGTGGCTTAAATCTTTCCTTTTACGCTTCTGAGGTACAA
1 TGTCTTCGTGGTACTGGATTCGCCGTTACGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
** ** * *
40853276 GGTTCGTTGTTGCGACTTAAACCTTTCCCTTCAAATCTTCGTGGTACTGGATTCGCCGTTGCGAC
66 GGTTCGCCGTTGCGACTTAAACCTTTCCCTTTGAGTCTTCGTGGTACTGGATTCACCGTTGCGAC
* * *
40853341 TTAAATCCTTCCTTTCATGTCTTTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTT
131 TTAAATCATTCCTTTCATGTCTTTGAGGTACAAGGTTCGCCATTGCGACTTAAACCTTTCACTTT
40853406 G
196 G
* *
40853407 TGTCTTCGTGGTACTAGATTCGCCGTTACGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAA
1 TGTCTTCGTGGTACTGGATTCGCCGTTACGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
* * * * *
40853472 GGTTCGCCATTGTGACTTAGACCTTTTCCTTTGTGTCTTCGTGGTACTGGATTCACCGTTGC-AG
66 GGTTCGCCGTTGCGACTTAAACCTTTCCCTTTGAGTCTTCGTGGTACTGGATTCACCGTTGCGA-
* *
40853536 CTTAAATCTTTCCCTTCATG
130 CTTAAATCATTCCTTTCATG
40853556 GTCATGAAAC
Statistics
Matches: 282, Mismatches: 60, Indels: 5
0.81 0.17 0.01
Matches are distributed among these distances:
195 116 0.41
196 166 0.59
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (196 bp):
TGTCTTCGTGGTACTGGATTCGCCGTTACGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
GGTTCGCCGTTGCGACTTAAACCTTTCCCTTTGAGTCTTCGTGGTACTGGATTCACCGTTGCGAC
TTAAATCATTCCTTTCATGTCTTTGAGGTACAAGGTTCGCCATTGCGACTTAAACCTTTCACTTT
G
Found at i:40854007 original size:18 final size:18
Alignment explanation
Indices: 40853980--40854016 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
40853970 AGAAATTGCC
*
40853980 AAATATTTACAAGGAACA
1 AAATAATTACAAGGAACA
*
40853998 AAATAATTACAAGTAACA
1 AAATAATTACAAGGAACA
40854016 A
1 A
40854017 TATCAGATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.59, C:0.11, G:0.08, T:0.22
Consensus pattern (18 bp):
AAATAATTACAAGGAACA
Found at i:40864927 original size:3 final size:3
Alignment explanation
Indices: 40864919--40864948 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
40864909 TTTAGGGAAA
40864919 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40864949 TCAAGATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:40867596 original size:29 final size:30
Alignment explanation
Indices: 40867439--40867708 Score: 216
Period size: 30 Copynumber: 9.1 Consensus size: 30
40867429 GTCCTTAAAC
40867439 TTCCTAAAATTACATTTTGACCCCTAAACTT
1 TTCC-AAAATTACATTTTGACCCCTAAACTT
*
40867470 CTT-TAAAATTACATTTTGACCCCTAAACTT
1 -TTCCAAAATTACATTTTGACCCCTAAACTT
* * *
40867500 CTCTAAAATTACATTTCGACCCCTAAACTT
1 TTCCAAAATTACATTTTGACCCCTAAACTT
* * *
40867530 CTCCAAAATCATATTTTGA-CCCTCAAACTT
1 TTCCAAAATTACATTTTGACCCCT-AAACTT
* **
40867560 TTTC-AAATTGTATTTTGA-CCCTAAACTT
1 TTCCAAAATTACATTTTGACCCCTAAACTT
* * * *
40867588 TTCCAAAATCATATTTTAACCACC-AAAC-C
1 TTCCAAAATTACATTTTGACC-CCTAAACTT
* * *
40867617 TTCTCGAAATGACATTTTGACCCC-AAACTC
1 TTC-CAAAATTACATTTTGACCCCTAAACTT
* * *
40867647 CTCCAAAATCACATTTTTGACCTC-AAA-TT
1 TTCCAAAATTACA-TTTTGACCCCTAAACTT
* *
40867676 TTCCCAAAATTACATTTTTACCCTTAAACTT
1 TT-CCAAAATTACATTTTGACCCCTAAACTT
40867707 TT
1 TT
40867709 TTGAAATTAC
Statistics
Matches: 197, Mismatches: 30, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
28 9 0.05
29 58 0.29
30 122 0.62
31 6 0.03
32 2 0.01
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.37
Consensus pattern (30 bp):
TTCCAAAATTACATTTTGACCCCTAAACTT
Found at i:40871851 original size:21 final size:19
Alignment explanation
Indices: 40871806--40871843 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
40871796 CATTAATTAA
40871806 AAATAAAAAAGTATTTTTT
1 AAATAAAAAAGTATTTTTT
*
40871825 AGATAAAAAAGTATTTTTT
1 AAATAAAAAAGTATTTTTT
40871844 TTAAATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (19 bp):
AAATAAAAAAGTATTTTTT
Found at i:40871967 original size:24 final size:24
Alignment explanation
Indices: 40871935--40871980 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
40871925 TTAATTAAAT
* *
40871935 TTTATAAATAATTAATATTTATTG
1 TTTAAAAATAATTAAAATTTATTG
*
40871959 TTTAAAAATATTTAAAATTTAT
1 TTTAAAAATAATTAAAATTTAT
40871981 ATTTCATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTAAAAATAATTAAAATTTATTG
Found at i:40881875 original size:42 final size:44
Alignment explanation
Indices: 40881821--40881911 Score: 118
Period size: 42 Copynumber: 2.1 Consensus size: 44
40881811 TTTTAAAAAA
* *
40881821 ATATTTT-TATTTAGTTTAGGA-TTTTTT-TAAGAAGAGAAAATT
1 ATATTTTGGATTTAGTTTAGGAGTTTTTTGTAAGAACAG-AAATT
*
40881863 A-ATTTTGGATTTAGTTTATGAGTTTTTTGTAAGAACAGAAATT
1 ATATTTTGGATTTAGTTTAGGAGTTTTTTGTAAGAACAGAAATT
40881906 ATATTT
1 ATATTT
40881912 GGGTAAGGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
41 5 0.12
42 13 0.31
43 12 0.29
44 12 0.29
ACGTcount: A:0.34, C:0.01, G:0.15, T:0.49
Consensus pattern (44 bp):
ATATTTTGGATTTAGTTTAGGAGTTTTTTGTAAGAACAGAAATT
Found at i:40882105 original size:18 final size:18
Alignment explanation
Indices: 40882082--40882119 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
40882072 TAATATAGTT
40882082 TTATTC-AGTTTATTCGAA
1 TTATTCGAG-TTATTCGAA
40882100 TTATTCGAGTTATTCGAA
1 TTATTCGAGTTATTCGAA
40882118 TT
1 TT
40882120 CAAAAATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.50
Consensus pattern (18 bp):
TTATTCGAGTTATTCGAA
Found at i:40885054 original size:24 final size:25
Alignment explanation
Indices: 40885010--40885056 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
40885000 GTTGGATCCA
40885010 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAATTCTAAAAAGATAATTAG
40885035 AATTAAA-TCTAAACAA-ATAATT
1 AATTAAATTCTAAA-AAGATAATT
40885057 CCCTAATTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.32
Consensus pattern (25 bp):
AATTAAATTCTAAAAAGATAATTAG
Found at i:40887060 original size:5 final size:5
Alignment explanation
Indices: 40887050--40887110 Score: 59
Period size: 5 Copynumber: 10.8 Consensus size: 5
40887040 AATGTATAAT
40887050 TAAAA TAAAA TTAAAAA TAAAA TAAAA TAAAA CTAAAAA TGAAAA TGAAAA
1 TAAAA TAAAA -T-AAAA TAAAA TAAAA TAAAA -T-AAAA T-AAAA T-AAAA
40887101 TGAAAA TAAA
1 T-AAAA TAAA
40887111 TATACTAATT
Statistics
Matches: 51, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
5 22 0.43
6 21 0.41
7 8 0.16
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:40887070 original size:6 final size:6
Alignment explanation
Indices: 40887051--40887110 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
40887041 ATGTATAATT
* * * *
40887051 AAAATA AAATTA AAAAT- AAAAT- AAAATA AAACTA AAAATG AAAATG
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
*
40887097 AAAATG AAAATA AA
1 AAAATA AAAATA AA
40887111 TATACTAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
5 10 0.21
6 37 0.79
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:40891124 original size:24 final size:25
Alignment explanation
Indices: 40891079--40891125 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
40891069 GTTGGATCCA
*
40891079 AATTAAATTCTAAAAAGTTAATTAG
1 AATTAAATTCTAAAAAGATAATTAG
40891104 AATTAAA-TCTAAACAA-ATAATT
1 AATTAAATTCTAAA-AAGATAATT
40891126 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.34
Consensus pattern (25 bp):
AATTAAATTCTAAAAAGATAATTAG
Found at i:40894390 original size:28 final size:29
Alignment explanation
Indices: 40894341--40894400 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
40894331 GTTATCTCTT
40894341 TTATTATTATTTATTTAATTTG-TATTTA
1 TTATTATTATTTATTTAATTTGTTATTTA
* *
40894369 TTATTATTATCTTGTTT-GTTTGTTTATTTA
1 TTATTATTAT-TTATTTAATTTG-TTATTTA
40894399 TT
1 TT
40894401 TATCATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 14 0.52
29 5 0.19
30 8 0.30
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.70
Consensus pattern (29 bp):
TTATTATTATTTATTTAATTTGTTATTTA
Found at i:40896239 original size:13 final size:13
Alignment explanation
Indices: 40896223--40896281 Score: 50
Period size: 14 Copynumber: 4.5 Consensus size: 13
40896213 ACAACAAGGT
40896223 AAATAAACAATAA
1 AAATAAACAATAA
* *
40896236 AAATTAAATACT-A
1 AAA-TAAACAATAA
*
40896249 AAATAAATAA-ACA
1 AAATAAACAATA-A
40896262 AATATAAACAATAA
1 AA-ATAAACAATAA
40896276 AAATAA
1 AAATAA
40896282 TTGGGATTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
12 6 0.16
13 14 0.38
14 16 0.43
15 1 0.03
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAACAATAA
Found at i:40896295 original size:94 final size:97
Alignment explanation
Indices: 40896197--40896374 Score: 229
Period size: 100 Copynumber: 1.8 Consensus size: 97
40896187 ACAATAAAAT
** *
40896197 GGCATGAAAATAAATAACAACA-AGGTAAATAAAC-AA-TAA-AAATTAAATACTAAAATAAATA
1 GGCATGAAAATAAATAACAA-ATAAATAAATAAACAAATTAATAAATTAAATACTAAAATAAACA
40896258 AACAAATATAAACAATAAAAATAATTGGGATTA
65 AACAAATATAAACAATAAAAATAATTGGGATTA
*
40896291 GGCATGAAAATAAATGACAAATAAATAAATAAACAAAAAATTAATAAATTAAATACTAAAATAAA
1 GGCATGAAAATAAATAACAAATAAATAAATAAAC---AAATTAATAAATTAAATACTAAAATAAA
** *
40896356 CAATTAAATATAAATAATA
63 CAAACAAATATAAACAATA
40896375 GTAAAAAAGA
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
93 1 0.01
94 29 0.41
98 2 0.03
99 3 0.04
100 35 0.50
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.22
Consensus pattern (97 bp):
GGCATGAAAATAAATAACAAATAAATAAATAAACAAATTAATAAATTAAATACTAAAATAAACAA
ACAAATATAAACAATAAAAATAATTGGGATTA
Found at i:40896331 original size:15 final size:15
Alignment explanation
Indices: 40896297--40896338 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
40896287 ATTAGGCATG
*
40896297 AAAATAAAT-GACAA
1 AAAATAAATAAACAA
40896311 ATAAATAAATAAACAA
1 A-AAATAAATAAACAA
*
40896327 AAAATTAATAAA
1 AAAATAAATAAA
40896339 TTAAATACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 1 0.04
15 18 0.75
16 5 0.21
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (15 bp):
AAAATAAATAAACAA
Found at i:40899547 original size:29 final size:29
Alignment explanation
Indices: 40899516--40899650 Score: 139
Period size: 29 Copynumber: 4.6 Consensus size: 29
40899506 AAAATCAAAA
* *
40899516 TTTTGGAAAGTTTGGGGGTTAAAATGCAAT
1 TTTTAGAAAGTTTAGGGGTTAAAATG-AAT
* * *
40899546 TTTCAAAAAG-TTAGGGGTTAAAACGTAAT
1 TTTTAGAAAGTTTAGGGGTTAAAATG-AAT
40899575 TTTTAGAAAGTTTA-GGGTTAAAATGAAAT
1 TTTTAGAAAGTTTAGGGGTTAAAATG-AAT
* * *
40899604 TTTTAAAAAGTTTAGGGGTCAAATTTGAAT
1 TTTTAGAAAGTTTAGGGGTTAAA-ATGAAT
*
40899634 TTTTGGAAAGTTTAGGG
1 TTTTAGAAAGTTTAGGG
40899651 TTGAATATAA
Statistics
Matches: 87, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
29 50 0.57
30 35 0.40
31 2 0.02
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (29 bp):
TTTTAGAAAGTTTAGGGGTTAAAATGAAT
Found at i:40899635 original size:59 final size:58
Alignment explanation
Indices: 40899516--40899652 Score: 177
Period size: 59 Copynumber: 2.3 Consensus size: 58
40899506 AAAATCAAAA
* * *
40899516 TTTTGGAAAGTTTGGGGGTTAAAATGCAATTTTCAAAAAGTTAGGGGTTAAAACGTAAT
1 TTTTGGAAAGTTT-AGGGTTAAAATGAAATTTTCAAAAAGTTAGGGGTCAAAACGTAAT
* * **
40899575 TTTTAGAAAGTTTAGGGTTAAAATGAAATTTTTAAAAAGTTTAGGGGTC-AAATTTGAAT
1 TTTTGGAAAGTTTAGGGTTAAAATGAAATTTTCAAAAAG-TTAGGGGTCAAAACGT-AAT
40899634 TTTTGGAAAGTTTAGGGTT
1 TTTTGGAAAGTTTAGGGTT
40899653 GAATATAATT
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
58 27 0.40
59 41 0.60
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (58 bp):
TTTTGGAAAGTTTAGGGTTAAAATGAAATTTTCAAAAAGTTAGGGGTCAAAACGTAAT
Found at i:40899651 original size:29 final size:29
Alignment explanation
Indices: 40899501--40899651 Score: 117
Period size: 29 Copynumber: 5.1 Consensus size: 29
40899491 TAAGGAAAAT
* * * *
40899501 GGGTCAAAATCAAAATTTTGGAAAGTTTGG
1 GGGTCAAAATGAAATTTTTAGAAAGTTT-A
* * * *
40899531 GGGTTAAAATGCAATTTTCAAAAAG-TTA
1 GGGTCAAAATGAAATTTTTAGAAAGTTTA
* * *
40899559 GGGGTTAAAACGTAATTTTTAGAAAGTTTA
1 -GGGTCAAAATGAAATTTTTAGAAAGTTTA
* *
40899589 GGGTTAAAATGAAATTTTTAAAAAGTTTA
1 GGGTCAAAATGAAATTTTTAGAAAGTTTA
* *
40899618 GGGGTCAAATTTG-AATTTTTGGAAAGTTTA
1 -GGGTCAAA-ATGAAATTTTTAGAAAGTTTA
40899648 GGGT
1 GGGT
40899652 TGAATATAAT
Statistics
Matches: 98, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
29 53 0.54
30 43 0.44
31 2 0.02
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (29 bp):
GGGTCAAAATGAAATTTTTAGAAAGTTTA
Found at i:40901617 original size:42 final size:42
Alignment explanation
Indices: 40901460--40901999 Score: 450
Period size: 42 Copynumber: 13.4 Consensus size: 42
40901450 TTTTGACTTA
* * ** *
40901460 GGGGTAAAATATTGGATG--GTCTTCAATCTGCCCTTTGATT
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* * * *
40901500 AGGGTAAAACATTGGATGA---CTTTAATCTGCCCCATGATC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* *
40901539 GGGGTAAGAGATTGGATG--G-CTTCAATCTGCCTCATGGTC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* * *
40901578 GGGGTAAGAGATTGGATGATGCCTTCAATCTGCCTCATGGTC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
*
40901620 GAGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* * *
40901662 AGGGTAAGAGATTGGATGGTAG-CTTCAATCTGCCCCATGGTC
1 GGGGTAAGAGATTGGATGAT-GTCTTCAATCTGCCCCATGATC
* * **
40901704 GGGGTAAGAGATTGGATGGTTTCTTCAATCTATCCCATGATC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* *
40901746 GGGGTAAGAGATTAGATGATGTCTTCAATCTTCCCCATGATC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* *
40901788 GAGGTAAGAGATTGGATG--G-CTTCAA-CATGCCCCGTGATC
1 GGGGTAAGAGATTGGATGATGTCTTCAATC-TGCCCCATGATC
* * * * *
40901827 GGGGTAA-AAAATCGATG-TCTCTTCAATCTGCCCTC-TGATT
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCC-CATGATC
* * * * * *
40901867 AGGGTAAAAGA-T-CA-AATG-CTTCGATCTGCCTCATGATC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* * *
40901905 -GGATAAGAGATTGG-TG-TGTCTTCAATCTGCCCTATGATT
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* * * *
40901944 AGGGTAAAAGA-TCG--GATG-CTTCAATCTGCCTCATGATC
1 GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
* *
40901982 GGGGTATGAGATTAGATG
1 GGGGTAAGAGATTGGATG
40902000 GTAGCTTCAC
Statistics
Matches: 410, Mismatches: 66, Indels: 47
0.78 0.13 0.09
Matches are distributed among these distances:
37 9 0.02
38 52 0.13
39 112 0.27
40 47 0.11
41 6 0.01
42 183 0.45
43 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (42 bp):
GGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATC
Found at i:40902270 original size:49 final size:49
Alignment explanation
Indices: 40902217--40902755 Score: 429
Period size: 49 Copynumber: 11.0 Consensus size: 49
40902207 TACTTTTCCT
* * * *
40902217 CATCTTTAGGGTATAAGATTCGCCGTTGCAGCCTCAATCTTTCCCTTCA
1 CATCTCTAAGGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCTTCA
* * * *
40902266 CATCTCTAAGGTATAAGGTTCACCGTTGCGGCTTCAACCTTTCCCTCCA
1 CATCTCTAAGGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCTTCA
* * * * *
40902315 TATCTCCATGGTACT-AGATTCGCCATTGCGGCTTCAATCTTT-CCATCA
1 CATCTCTAAGGTA-TAAGATTCGCCGTTGCGGCTTCAATCTTTCCCTTCA
* * * * * *
40902363 CATCTCTAAGGTATAAGGTTTGCCGTTACGACTTCAACCTTTCCCTCCA
1 CATCTCTAAGGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCTTCA
* * * * * ** *
40902412 TATCTCCATGGTACAAAATTCGTTGTTGCGGCTTCAATATTTCCCATT-A
1 CATCTCTAAGGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCC-TTCA
** * * * * * *
40902461 TTTTTCTAAGGTATAAGGTTTGTCGTTGCGGCTTCAACCTTTCCCTCCA
1 CATCTCTAAGGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCTTCA
* * * * * * *
40902510 TATCTCCATGGTACAAGATTCGCCATTGCGGCTTCAGTCTTTCCCATCA
1 CATCTCTAAGGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCTTCA
* * * *
40902559 CATCCCTAAGGTACAACG-TTCGCCTGTTGCGACTTCAATCTTTCCCTCCA
1 CATCTCTAAGGTATAA-GATTCGCC-GTTGCGGCTTCAATCTTTCCCTTCA
* * * * * *
40902609 TATCTCCATGGTACAAGATTCGCCATTGCGGCTTCAATCTTTCCCGTCA
1 CATCTCTAAGGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCTTCA
* * * * * * *
40902658 CATCTCTAAGGTACAAGGTTCGTCATTGCGGCTTTAACCTTTCCCTCCA
1 CATCTCTAAGGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCTTCA
* * * * * *
40902707 TATCTCTAGGGTGTTAGATTTGCCGTTGCGTCTTCAATCTTTCCCTTCA
1 CATCTCTAAGGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCTTCA
40902756 GACCTATAGA
Statistics
Matches: 376, Mismatches: 106, Indels: 16
0.76 0.21 0.03
Matches are distributed among these distances:
47 1 0.00
48 36 0.10
49 298 0.79
50 41 0.11
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (49 bp):
CATCTCTAAGGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCTTCA
Found at i:40902522 original size:98 final size:98
Alignment explanation
Indices: 40902226--40902751 Score: 676
Period size: 98 Copynumber: 5.4 Consensus size: 98
40902216 TCATCTTTAG
* * * * * *
40902226 GGTATAAGATTCGCCGTTGCAGCCTCAATCTTTCCCTTCACATCTCTAAGGTATAAGGTTCACCG
1 GGTACAAGATTCGCCATTGCGGCTTCAATCTTTCCCATCACATCTCTAAGGTATAAGGTTCGCCG
40902291 TTGCGGCTTCAACCTTTCCCTCCATATCTCCAT
66 TTGCGGCTTCAACCTTTCCCTCCATATCTCCAT
* *
40902324 GGTACTAGATTCGCCATTGCGGCTTCAATCTTT-CCATCACATCTCTAAGGTATAAGGTTTGCCG
1 GGTACAAGATTCGCCATTGCGGCTTCAATCTTTCCCATCACATCTCTAAGGTATAAGGTTCGCCG
* *
40902388 TTACGACTTCAACCTTTCCCTCCATATCTCCAT
66 TTGCGGCTTCAACCTTTCCCTCCATATCTCCAT
* *** * * ** * * *
40902421 GGTACAAAATTCGTTGTTGCGGCTTCAATATTTCCCATTATTTTTCTAAGGTATAAGGTTTGTCG
1 GGTACAAGATTCGCCATTGCGGCTTCAATCTTTCCCATCACATCTCTAAGGTATAAGGTTCGCCG
40902486 TTGCGGCTTCAACCTTTCCCTCCATATCTCCAT
66 TTGCGGCTTCAACCTTTCCCTCCATATCTCCAT
* * * *
40902519 GGTACAAGATTCGCCATTGCGGCTTCAGTCTTTCCCATCACATCCCTAAGGTACAACGTTCGCCT
1 GGTACAAGATTCGCCATTGCGGCTTCAATCTTTCCCATCACATCTCTAAGGTATAAGGTTCGCC-
* *
40902584 GTTGCGACTTCAATCTTTCCCTCCATATCTCCAT
65 GTTGCGGCTTCAACCTTTCCCTCCATATCTCCAT
* * * *
40902618 GGTACAAGATTCGCCATTGCGGCTTCAATCTTTCCCGTCACATCTCTAAGGTACAAGGTTCGTCA
1 GGTACAAGATTCGCCATTGCGGCTTCAATCTTTCCCATCACATCTCTAAGGTATAAGGTTCGCCG
* * *
40902683 TTGCGGCTTTAACCTTTCCCTCCATATCTCTAG
66 TTGCGGCTTCAACCTTTCCCTCCATATCTCCAT
*** * * *
40902716 GGTGTTAGATTTGCCGTTGCGTCTTCAATCTTTCCC
1 GGTACAAGATTCGCCATTGCGGCTTCAATCTTTCCC
40902752 TTCAGACCTA
Statistics
Matches: 369, Mismatches: 57, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
97 86 0.23
98 192 0.52
99 91 0.25
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (98 bp):
GGTACAAGATTCGCCATTGCGGCTTCAATCTTTCCCATCACATCTCTAAGGTATAAGGTTCGCCG
TTGCGGCTTCAACCTTTCCCTCCATATCTCCAT
Found at i:40902750 original size:197 final size:196
Alignment explanation
Indices: 40902226--40902751 Score: 721
Period size: 197 Copynumber: 2.7 Consensus size: 196
40902216 TCATCTTTAG
* * * * **
40902226 GGTATAAGATTCGCCGTTGCAGCCTCAATCTTTCCCTTCACATCTCTAAGGTATAAGGTTCACCG
1 GGTACAAGATTCGCCGTTGCGGCTTCAATCTTTCCCATCACATCTCTAAGGTATAAGGTTCGTCG
40902291 TTGCGGCTTCAACCTTTCCCTCCATATCTCCATGGTACTAGATTCGCCATTGCGGCTTCAATCTT
66 TTGCGGCTTCAACCTTTCCCTCCATATCTCCATGGTACTAGATTCGCCATTGCGGCTTCAATCTT
* * * *
40902356 T-CCATCACATCTCTAAGGTATAAGGTTTGCCGTTACGACTTCAACCTTTCCCTCCATATCTCCA
131 TCCCATCACATCCCTAAGGTACAACGTTCGCCGTTACGACTTCAACCTTTCCCTCCATATCTCCA
40902420 T
196 T
* ** * * ** * *
40902421 GGTACAAAATTCGTTGTTGCGGCTTCAATATTTCCCATTATTTTTCTAAGGTATAAGGTTTGTCG
1 GGTACAAGATTCGCCGTTGCGGCTTCAATCTTTCCCATCACATCTCTAAGGTATAAGGTTCGTCG
* *
40902486 TTGCGGCTTCAACCTTTCCCTCCATATCTCCATGGTACAAGATTCGCCATTGCGGCTTCAGTCTT
66 TTGCGGCTTCAACCTTTCCCTCCATATCTCCATGGTACTAGATTCGCCATTGCGGCTTCAATCTT
* *
40902551 TCCCATCACATCCCTAAGGTACAACGTTCGCCTGTTGCGACTTCAATCTTTCCCTCCATATCTCC
131 TCCCATCACATCCCTAAGGTACAACGTTCGCC-GTTACGACTTCAACCTTTCCCTCCATATCTCC
40902616 AT
195 AT
* * * *
40902618 GGTACAAGATTCGCCATTGCGGCTTCAATCTTTCCCGTCACATCTCTAAGGTACAAGGTTCGTCA
1 GGTACAAGATTCGCCGTTGCGGCTTCAATCTTTCCCATCACATCTCTAAGGTATAAGGTTCGTCG
* * * ** * * *
40902683 TTGCGGCTTTAACCTTTCCCTCCATATCTCTAGGGTGTTAGATTTGCCGTTGCGTCTTCAATCTT
66 TTGCGGCTTCAACCTTTCCCTCCATATCTCCATGGTACTAGATTCGCCATTGCGGCTTCAATCTT
40902748 TCCC
131 TCCC
40902752 TTCAGACCTA
Statistics
Matches: 283, Mismatches: 46, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
195 114 0.40
196 26 0.09
197 143 0.51
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (196 bp):
GGTACAAGATTCGCCGTTGCGGCTTCAATCTTTCCCATCACATCTCTAAGGTATAAGGTTCGTCG
TTGCGGCTTCAACCTTTCCCTCCATATCTCCATGGTACTAGATTCGCCATTGCGGCTTCAATCTT
TCCCATCACATCCCTAAGGTACAACGTTCGCCGTTACGACTTCAACCTTTCCCTCCATATCTCCA
T
Found at i:40904105 original size:24 final size:24
Alignment explanation
Indices: 40904078--40904128 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
40904068 TTTCAGAAAT
*
40904078 TTAGCTCATACGAGCCTAAAATGG
1 TTAGCTCATACAAGCCTAAAATGG
* * *
40904102 TTAGGTCTTACAAGCCTAGAATGG
1 TTAGCTCATACAAGCCTAAAATGG
40904126 TTA
1 TTA
40904129 ACCAGTATAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (24 bp):
TTAGCTCATACAAGCCTAAAATGG
Found at i:40906461 original size:112 final size:115
Alignment explanation
Indices: 40906261--40906475 Score: 346
Period size: 112 Copynumber: 1.9 Consensus size: 115
40906251 TATCGCTATA
* *
40906261 CCACTAACCGTTATTTAAAATGCCAAAAATGCTTGAATCAAGGTTGTAAGGTGGATGAAATTGAG
1 CCACTAACCGTTATTTAAAATGCCAAAAATGCTTGAATCAAGGTTGTAAGGTGGATAAAATTGAA
* *
40906326 TTTTATTGGAGACAAAGCTCGTATGAATGAAAAGATTACGAATCATTGGT
66 TTTTATTAGAGACAAAACTCGTATGAATGAAAAGATTACGAATCATTGGT
**
40906376 CCACTAACCGTTATTT-CGATG-CAAAAATGCTTG-ATCAAGGTTGTAAGGTGGATAAAATTGAA
1 CCACTAACCGTTATTTAAAATGCCAAAAATGCTTGAATCAAGGTTGTAAGGTGGATAAAATTGAA
*
40906438 TTTTATTAGAGGCAAAACTCGTATGAATGAAAAGATTA
66 TTTTATTAGAGACAAAACTCGTATGAATGAAAAGATTA
40906476 AAAATGACAA
Statistics
Matches: 93, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
112 62 0.67
113 12 0.13
114 3 0.03
115 16 0.17
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (115 bp):
CCACTAACCGTTATTTAAAATGCCAAAAATGCTTGAATCAAGGTTGTAAGGTGGATAAAATTGAA
TTTTATTAGAGACAAAACTCGTATGAATGAAAAGATTACGAATCATTGGT
Found at i:40906816 original size:10 final size:10
Alignment explanation
Indices: 40906797--40906852 Score: 62
Period size: 10 Copynumber: 5.6 Consensus size: 10
40906787 TCTCTTTTTA
*
40906797 TTTTTCCTTC
1 TTTTTTCTTC
40906807 TTTTTTCTTC
1 TTTTTTCTTC
40906817 TTCTTTT-TTC
1 TT-TTTTCTTC
40906827 TTTTTAT-TTC
1 TTTTT-TCTTC
*
40906837 TTTCTTCTTC
1 TTTTTTCTTC
40906847 TTTTTT
1 TTTTTT
40906853 TCCTTTTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
9 4 0.10
10 32 0.80
11 4 0.10
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTCTTC
Found at i:40906831 original size:30 final size:29
Alignment explanation
Indices: 40906791--40906861 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 29
40906781 TCGACCTCTC
* * *
40906791 TTTTTATTTTTCCTTCTTTTTTCTTCTTCT
1 TTTTTCTTTTTACTTCTTTCTTCTTCTT-T
*
40906821 TTTTTCTTTTTATTTCTTTCTTCTTCTTT
1 TTTTTCTTTTTACTTCTTTCTTCTTCTTT
*
40906850 TTTTCCTTTTTA
1 TTTTTCTTTTTA
40906862 ATTTTTTTGG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 12 0.33
30 24 0.67
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.77
Consensus pattern (29 bp):
TTTTTCTTTTTACTTCTTTCTTCTTCTTT
Found at i:40906860 original size:10 final size:9
Alignment explanation
Indices: 40906804--40906860 Score: 60
Period size: 10 Copynumber: 5.9 Consensus size: 9
40906794 TTATTTTTCC
40906804 TTCTTTTTT
1 TTCTTTTTT
40906813 CTTCTTCTTTT
1 -TTCTT-TTTT
40906824 TTCTTTTTAT
1 TTCTTTTT-T
*
40906834 TTCTTTCTTC
1 TTCTTT-TTT
40906844 TTCTTTTTT
1 TTCTTTTTT
*
40906853 TCCTTTTT
1 TTCTTTTT
40906861 AATTTTTTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
9 12 0.29
10 23 0.56
11 6 0.15
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:40907735 original size:15 final size:15
Alignment explanation
Indices: 40907712--40907753 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40907702 TTCATCTTGA
40907712 CTTTT-TTTTCTTC-
1 CTTTTCTTTTCTTCT
*
40907725 CTTTTTCTTTTCTTTT
1 C-TTTTCTTTTCTTCT
40907741 CTTTTCTTTTCTT
1 CTTTTCTTTTCTT
40907754 TTTTCTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 1 0.04
14 4 0.16
15 19 0.76
16 1 0.04
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
CTTTTCTTTTCTTCT
Found at i:40907737 original size:5 final size:5
Alignment explanation
Indices: 40907727--40907765 Score: 60
Period size: 5 Copynumber: 7.6 Consensus size: 5
40907717 TTTTCTTCCT
*
40907727 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTT TCTTTC TTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T-TTTC TTT
40907766 GGGTTTCGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Done.