Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 164 of 167
Found at i:54392930 original size:50 final size:50
Alignment explanation
Indices: 54392824--54393200 Score: 585
Period size: 50 Copynumber: 7.5 Consensus size: 50
54392814 GACTGATCAG
* * * *
54392824 GTAGCTGAAGCTACCACTTTTCAGTTGTCATTTG-CCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCC-TTGATCAGATAAGT
* *
54392875 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTAATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
* *
54392925 GTAGCCGAAGTTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
* *
54392975 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTAATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
* *
54393025 GTAGCCGAAGTTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
* *
54393075 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTAATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
* *
54393125 GTAGCCGAAGTTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
54393175 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
54393201 GTTTCCATGG
Statistics
Matches: 297, Mismatches: 28, Indels: 3
0.91 0.09 0.01
Matches are distributed among these distances:
50 273 0.92
51 24 0.08
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:54392971 original size:100 final size:100
Alignment explanation
Indices: 54392851--54393200 Score: 684
Period size: 100 Copynumber: 3.5 Consensus size: 100
54392841 TTTTCAGTTG
54392851 TCATTTG-CCATTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTAA
1 TCATTTGTCC-TTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTAA
54392915 TCAGATAAGTGTAGCCGAAGTTATTACTTATCACTT
65 TCAGATAAGTGTAGCCGAAGTTATTACTTATCACTT
54392951 TCATTTGTCCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTAAT
1 TCATTTGTCCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTAAT
54393016 CAGATAAGTGTAGCCGAAGTTATTACTTATCACTT
66 CAGATAAGTGTAGCCGAAGTTATTACTTATCACTT
54393051 TCATTTGTCCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTAAT
1 TCATTTGTCCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTAAT
54393116 CAGATAAGTGTAGCCGAAGTTATTACTTATCACTT
66 CAGATAAGTGTAGCCGAAGTTATTACTTATCACTT
54393151 TCATTTGTCCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTT
1 TCATTTGTCCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTT
54393201 GTTTCCATGG
Statistics
Matches: 249, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
100 247 0.99
101 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (100 bp):
TCATTTGTCCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTAAT
CAGATAAGTGTAGCCGAAGTTATTACTTATCACTT
Found at i:54395452 original size:93 final size:93
Alignment explanation
Indices: 54395345--54395515 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
54395335 ACCCCTAAGT
* *
54395345 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
54395410 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* *
54395438 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
*
54395503 TGAGTTCGGATGC
66 CGAGTTCGGATGC
54395516 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:54395512 original size:46 final size:46
Alignment explanation
Indices: 54395340--54395512 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
54395330 AACCCACCCC
* * *
54395340 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACATCCA
*
54395386 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCACATCCA
* * *
54395434 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACATCCA
*
54395479 TAAGTGAACTCGGACTCAACTCAATGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
54395513 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 60 0.56
47 29 0.27
48 2 0.02
49 1 0.01
50 4 0.04
51 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACATCCA
Found at i:54398339 original size:6 final size:6
Alignment explanation
Indices: 54398321--54398414 Score: 68
Period size: 6 Copynumber: 15.3 Consensus size: 6
54398311 AAGAAACATT
* *
54398321 ATCAGA A-CTAGA ATCAGA ATCATA ATCAGA ACCAGA ATCAGGTA A-CAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA
* * * *
54398370 ATCAAA ATCAGA ATCAGT ACCAGGTA A-CAGA ATCAAA ATCAGA AT
1 ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
54398415 GTGAATGCAA
Statistics
Matches: 69, Mismatches: 11, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
5 5 0.07
6 54 0.78
7 7 0.10
8 3 0.04
ACGTcount: A:0.50, C:0.18, G:0.15, T:0.17
Consensus pattern (6 bp):
ATCAGA
Found at i:54398339 original size:24 final size:24
Alignment explanation
Indices: 54398305--54398361 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
54398295 TAACCCATTA
* *
54398305 TAGAATAAGAAACATTATCAGAAC
1 TAGAATCAGAAACATAATCAGAAC
*
54398329 TAGAATCAGAATCATAATCAGAAC
1 TAGAATCAGAAACATAATCAGAAC
*
54398353 CAGAATCAG
1 TAGAATCAG
54398362 GTAACAGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.51, C:0.16, G:0.14, T:0.19
Consensus pattern (24 bp):
TAGAATCAGAAACATAATCAGAAC
Found at i:54398414 original size:31 final size:31
Alignment explanation
Indices: 54398335--54398414 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
54398325 GAACTAGAAT
* * *
54398335 CAGAATCATAATCAGAACCAGAATCAGGTAA
1 CAGAATCAAAATCAGAATCAGAACCAGGTAA
*
54398366 CAGAATCAAAATCAGAATCAGTACCAGGTAA
1 CAGAATCAAAATCAGAATCAGAACCAGGTAA
54398397 CAGAATCAAAATCAGAAT
1 CAGAATCAAAATCAGAAT
54398415 GTGAATGCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.50, C:0.19, G:0.15, T:0.16
Consensus pattern (31 bp):
CAGAATCAAAATCAGAATCAGAACCAGGTAA
Found at i:54398575 original size:27 final size:26
Alignment explanation
Indices: 54398534--54398626 Score: 123
Period size: 27 Copynumber: 3.5 Consensus size: 26
54398524 AGCATGGCTG
* *
54398534 CCAGAACAGATATTGTGACAGAGTCA
1 CCAGAACAGATATTGTGGCAGAGCCA
*
54398560 CCAGATACAAATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATTGTGGCAGAGCCA
*
54398587 CCAGAACAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-TTGTGGCAGAGCCA
54398614 CCAGAAACAGATA
1 CCAG-AACAGATA
54398627 AAGTGGTAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
26 11 0.19
27 40 0.68
28 8 0.14
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.18
Consensus pattern (26 bp):
CCAGAACAGATATTGTGGCAGAGCCA
Found at i:54398632 original size:27 final size:27
Alignment explanation
Indices: 54398534--54398641 Score: 78
Period size: 27 Copynumber: 4.0 Consensus size: 27
54398524 AGCATGGCTG
* * * *
54398534 CCAGAACAGATAT-TGTGACAGAGTCA
1 CCAGAACAGATATAAGTGGCAAAGCCA
* * *
54398560 CCAGATACAAATAT-TGTGGCAGAGCCA
1 CCAGA-ACAGATATAAGTGGCAAAGCCA
** *
54398587 CCAGAACAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATAAGTGGCAAAGCCA
*
54398614 CCAGAAACAGATA-AAGTGGTAAAGCCA
1 CCAG-AACAGATATAAGTGGCAAAGCCA
54398641 C
1 C
54398642 TTAACAGAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
26 12 0.17
27 50 0.71
28 8 0.11
ACGTcount: A:0.39, C:0.21, G:0.22, T:0.18
Consensus pattern (27 bp):
CCAGAACAGATATAAGTGGCAAAGCCA
Found at i:54398640 original size:54 final size:53
Alignment explanation
Indices: 54398534--54398641 Score: 126
Period size: 54 Copynumber: 2.0 Consensus size: 53
54398524 AGCATGGCTG
* * ** *
54398534 CCAGAACAGATATTGTGACAGAGTCACCAGATACAAATATTGTGGCAGAGCCA
1 CCAGAACAGATATTGTGACAGAGCCACCAGAAACAAATAAAGTGGCAAAGCCA
* * * *
54398587 CCAGAACAGATATTTGTGGCATAGCCACCAGAAACAGATAAAGTGGTAAAGCCA
1 CCAGAACAGATA-TTGTGACAGAGCCACCAGAAACAAATAAAGTGGCAAAGCCA
54398641 C
1 C
54398642 TTAACAGAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
53 12 0.27
54 33 0.73
ACGTcount: A:0.39, C:0.21, G:0.22, T:0.18
Consensus pattern (53 bp):
CCAGAACAGATATTGTGACAGAGCCACCAGAAACAAATAAAGTGGCAAAGCCA
Found at i:54399241 original size:27 final size:27
Alignment explanation
Indices: 54399179--54399241 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
54399169 CAGTCACTTG
*
54399179 CCCACAA-GGGCAAAACAGTCATTTAA
1 CCCACAAGGGGCAAAACAGTAATTTAA
* * *
54399205 CACC-CTAGGGGCAAAATAGTAATTTTA
1 C-CCACAAGGGGCAAAACAGTAATTTAA
54399232 CCCACAAGGG
1 CCCACAAGGG
54399242 TATCTCAGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
26 5 0.17
27 24 0.83
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.17
Consensus pattern (27 bp):
CCCACAAGGGGCAAAACAGTAATTTAA
Found at i:54399550 original size:27 final size:27
Alignment explanation
Indices: 54399223--54399542 Score: 484
Period size: 27 Copynumber: 11.9 Consensus size: 27
54399213 GGGCAAAATA
* * * *
54399223 GTAATTTTACCC-ACAAGGGTATCTCA
1 GTAATTCTACCCTACAGGGGTATTTCG
54399249 GTAATTCTACCCT-CAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCG
54399275 GTAATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCG
*
54399302 GTAATTCTACCCTATAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCG
54399329 GTAATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCG
*
54399356 GTAATTCTACCCTATAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCG
54399383 GTAATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCG
*
54399410 GTAATTCTACCCTACAGGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCG
54399437 GTAATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAGGGGTATTTCG
* * * *
54399464 GTAATTCTATCCTATAAGGGTATTTCA
1 GTAATTCTACCCTACAGGGGTATTTCG
* *
54399491 GT-ATTTTGACCCTACAAGGGTATTTCG
1 GTAATTCT-ACCCTACAGGGGTATTTCG
*
54399518 ATAATTCTACCCTACAGGGGTATTT
1 GTAATTCTACCCTACAGGGGTATTT
54399543 TAATAATTTT
Statistics
Matches: 269, Mismatches: 21, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
26 38 0.14
27 227 0.84
28 4 0.01
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (27 bp):
GTAATTCTACCCTACAGGGGTATTTCG
Found at i:54399565 original size:27 final size:27
Alignment explanation
Indices: 54399535--54399703 Score: 130
Period size: 27 Copynumber: 6.3 Consensus size: 27
54399525 TACCCTACAG
* * *
54399535 GGGTATTTTAATAATTTTGTAAATCGA
1 GGGTATTTCAGTAATTTTGCAAATCGA
*** * * *
54399562 GGGTAAAAC-GATAATTCTGTAAATCGG
1 GGGTATTTCAG-TAATTTTGCAAATCGA
* * *
54399589 GGGTACTTT-GGTAATTTTACAAGTCGA
1 GGGTA-TTTCAGTAATTTTGCAAATCGA
* *
54399616 GGGTATTTCAGTAATTTTACAAATTGA
1 GGGTATTTCAGTAATTTTGCAAATCGA
*
54399643 GGGTATTTCAGTAATTTTGCAAA-CTAA
1 GGGTATTTCAGTAATTTTGCAAATC-GA
* *
54399670 GGGTATTTCAGTAATTTTACAAATTG-
1 GGGTATTTCAGTAATTTTGCAAATCGA
54399696 GGGTATTT
1 GGGTATTT
54399704 GGGTGATTTA
Statistics
Matches: 112, Mismatches: 24, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
26 11 0.10
27 100 0.89
28 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.38
Consensus pattern (27 bp):
GGGTATTTCAGTAATTTTGCAAATCGA
Found at i:54399729 original size:27 final size:27
Alignment explanation
Indices: 54399696--54399819 Score: 133
Period size: 27 Copynumber: 4.6 Consensus size: 27
54399686 TTACAAATTG
* *
54399696 GGGTATTTGGGTGATTTAATAAACCAA
1 GGGTATTTTGGTAATTTAATAAACCAA
* * * *
54399723 GGGTATTCTAGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTAATAAACCAA
* **
54399750 AGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTAATAAACCAA
* * *
54399777 GGGTATTTTGGTAATTT-ACAAATCAG
1 GGGTATTTTGGTAATTTAATAAACCAA
54399803 GGGTATTTTGGTAATTT
1 GGGTATTTTGGTAATTT
54399820 GGTAAACTAA
Statistics
Matches: 81, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
26 22 0.27
27 59 0.73
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTAATAAACCAA
Found at i:54399825 original size:53 final size:53
Alignment explanation
Indices: 54399588--54399826 Score: 230
Period size: 54 Copynumber: 4.5 Consensus size: 53
54399578 CTGTAAATCG
* ** ** * *
54399588 GGGGTACTTTGGTAATTTTACAAGTCGAGGGTATTTCAGTAATTTTACAAATT
1 GGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCAGTAATTTTACAAATA
** * * *
54399641 GAGGGTATTTCAGTAATTTTGCAAACTAAGGGTATTTCAGTAATTTTACAAATT
1 G-GGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCAGTAATTTTACAAATA
* * ** *
54399695 GGGGTATTTGGGTGATTTAATAAACCAAGGGTA-TTCTAGTAATTTTACAAACCA
1 GGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTC-AGTAATTTTACAAA-TA
** **
54399749 AAGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGGTAA-TTTACAAATCA
1 GGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCAGTAATTTTACAAAT-A
*
54399802 GGGGTATTTTGGTAATTTGGTAAAC
1 GGGGTATTTTGGTAATTTTGTAAAC
54399827 TAAAGTATTC
Statistics
Matches: 152, Mismatches: 29, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
52 3 0.02
53 71 0.47
54 76 0.50
55 2 0.01
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (53 bp):
GGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCAGTAATTTTACAAATA
Found at i:54399826 original size:107 final size:107
Alignment explanation
Indices: 54399615--54399819 Score: 261
Period size: 107 Copynumber: 1.9 Consensus size: 107
54399605 TTACAAGTCG
*** * *
54399615 AGGGTATTTCAGTAATTTTACAAATTGAGGGTATTTCAGTAATTTTGCAAACTAAGGGTATTTCA
1 AGGGTATTTCAGTAATTTTACAAACCAAAGGTATTTCAGTAATTTTGCAAACCAAGGGTATTTCA
* *
54399680 GTAATTTTACAAATTGGGGTATTTGGGTGATTTAATAAACCA
66 GTAATTTTACAAATAGGGGTATTTGGGTAATTTAATAAACCA
** * *
54399722 AGGGTA-TTCTAGTAATTTTACAAACCAAAGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTT
1 AGGGTATTTC-AGTAATTTTACAAACCAAAGGTATTTCAGTAATTTTGCAAACCAAGGGTATTTC
* *
54399786 GGTAA-TTTACAAATCAGGGGTATTTTGGTAATTT
65 AGTAATTTTACAAAT-AGGGGTATTTGGGTAATTT
54399820 GGTAAACTAA
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
106 12 0.14
107 71 0.86
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.39
Consensus pattern (107 bp):
AGGGTATTTCAGTAATTTTACAAACCAAAGGTATTTCAGTAATTTTGCAAACCAAGGGTATTTCA
GTAATTTTACAAATAGGGGTATTTGGGTAATTTAATAAACCA
Found at i:54399834 original size:26 final size:25
Alignment explanation
Indices: 54399743--54399835 Score: 78
Period size: 26 Copynumber: 3.5 Consensus size: 25
54399733 GTAATTTTAC
54399743 AAACCAAAGGTATTTTGGTAATTTTGT
1 AAACCAAA-GTATTTTGGTAA-TTTGT
* **
54399770 AAACCAAGGGTATTTTGGTAATTTAC
1 AAACCAA-AGTATTTTGGTAATTTGT
* **
54399796 AAATCAGGGGTATTTTGGTAATTTGGT
1 AAACCA-AAGTATTTTGGTAATTT-GT
*
54399823 AAACTAAAGTATT
1 AAACCAAAGTATT
54399836 CTAAACAGGG
Statistics
Matches: 52, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
26 29 0.56
27 23 0.44
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (25 bp):
AAACCAAAGTATTTTGGTAATTTGT
Found at i:54402878 original size:3 final size:3
Alignment explanation
Indices: 54402866--54403333 Score: 191
Period size: 3 Copynumber: 157.3 Consensus size: 3
54402856 ATAAAACATG
*
54402866 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
54402913 AGA ATA TTA ATA TTA GTA ATA ATA ATA ATA ATA ATA ATA ATA GTA CATTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -A-TA
* * * * *
54402963 ATA ATG ATA GTA TATG TTA ATA ATA ATA ATA ATA TATA AAA ATA GGA-A
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA --ATA
* * * * * *
54403011 ATA ATA TATG GTA A-A AAA ATA ATA ATA ATA ATA ACA AAA ATA GTA
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
54403056 ATA ATA GTA TGTG A-A ATA ATA ATT GTA A-A A-A ACTA ATA GTA ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA
* * * * * *
54403100 ATT ATA TTG ATA ATA CTA ATA ATA ATA GTA GTA A-A A-A ATA A-A A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
54403144 AT- ATA AAA ATA ATA ATA ATA GTA AAA ATG ACA ATA A-A ATA A-G ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
54403189 ATA ATA ATG ATA ATA AAA ATA A-A A-A ATA A-A A-A AGTA ATA ATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA
** * * * * * *
54403231 GCA ATA CTA ATA CCATA ATA A-A AGA AAA AGAA ATA ATA ACA TGTAA
1 ATA ATA ATA ATA --ATA ATA ATA ATA ATA A-TA ATA ATA ATA -AT-A
* * * * * *
54403277 ATA ATA ATA ACA ATA ATA AAA ATA AT- ATA TTT ATA ATA ATA GTA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
54403324 AAA ATA ATA A
1 ATA ATA ATA A
54403334 AATTAACTAA
Statistics
Matches: 343, Mismatches: 93, Indels: 58
0.69 0.19 0.12
Matches are distributed among these distances:
2 35 0.10
3 283 0.83
4 18 0.05
5 7 0.02
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:54403165 original size:37 final size:36
Alignment explanation
Indices: 54403116--54403229 Score: 105
Period size: 34 Copynumber: 3.2 Consensus size: 36
54403106 TTGATAATAC
54403116 TAATAATAATAGTAGTAAAAAATAAAAAATATAAAAA
1 TAATAATAATAGTA-TAAAAAATAAAAAATATAAAAA
* * * *
54403153 TAATAATAATAGTA-AAAATGACAATAAA-AT-AAGA
1 TAATAATAATAGTATAAAA-AATAAAAAATATAAAAA
54403187 TAATAATAAT-G-ATAATAAAAATAAAAAATA-AAAAA
1 TAATAATAATAGTAT-A-AAAAATAAAAAATATAAAAA
54403222 GTAATAAT
1 -TAATAAT
54403230 GGCAATACTA
Statistics
Matches: 62, Mismatches: 8, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
32 1 0.02
33 1 0.02
34 20 0.32
35 13 0.21
36 13 0.21
37 14 0.23
ACGTcount: A:0.68, C:0.01, G:0.06, T:0.25
Consensus pattern (36 bp):
TAATAATAATAGTATAAAAAATAAAAAATATAAAAA
Found at i:54403216 original size:25 final size:25
Alignment explanation
Indices: 54403169--54403217 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
54403159 TAATAGTAAA
*
54403169 AATGACAATAAAATAAGATAATAAT
1 AATGACAATAAAATAAGAAAATAAT
*
54403194 AATGATAATAAAAATAA-AAAATAA
1 AATGACAAT-AAAATAAGAAAATAA
54403218 AAAAGTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.22
Consensus pattern (25 bp):
AATGACAATAAAATAAGAAAATAAT
Found at i:54413861 original size:30 final size:30
Alignment explanation
Indices: 54413825--54413889 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
54413815 ACTTATTTTA
54413825 TTGTTAATTTTGCTATTATTTTAAAGACAT
1 TTGTTAATTTTGCTATTATTTTAAAGACAT
* * *
54413855 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGCTATTATTTTAAAGACAT
54413885 TTGTT
1 TTGTT
54413890 TGTTAAGTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.25, C:0.05, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGCTATTATTTTAAAGACAT
Found at i:54417554 original size:13 final size:16
Alignment explanation
Indices: 54417521--54417566 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 16
54417511 AAATGGACTC
54417521 TTTGGACTTATTTATT
1 TTTGGACTTATTTATT
54417537 TTTGGA-TT-TTTATT
1 TTTGGACTTATTTATT
* *
54417551 TTGGGTC-TATTTATT
1 TTTGGACTTATTTATT
54417566 T
1 T
54417567 ACAAATGAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 11 0.42
15 9 0.35
16 6 0.23
ACGTcount: A:0.15, C:0.04, G:0.15, T:0.65
Consensus pattern (16 bp):
TTTGGACTTATTTATT
Found at i:54418713 original size:23 final size:22
Alignment explanation
Indices: 54418687--54418731 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
54418677 ATTAACCTTA
54418687 AATTACATGTATTT-AGATCAGTG
1 AATTACATG-ATTTGA-ATCAGTG
*
54418710 AATTAGATGATTTGAATCAGTG
1 AATTACATGATTTGAATCAGTG
54418732 GATTTGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.38
Consensus pattern (22 bp):
AATTACATGATTTGAATCAGTG
Found at i:54432481 original size:45 final size:45
Alignment explanation
Indices: 54432393--54432485 Score: 114
Period size: 45 Copynumber: 2.1 Consensus size: 45
54432383 CAGTGTGGTA
* * * *
54432393 GGCCATGTGCGAGGCCGTCTGTGACACACGGTCTAGGCCATTTTG
1 GGCCATGTGCGAGGCCGTCTGGGACACACGGGCAAGGACATTTTG
* * * *
54432438 GGCCATGTGCTAGGCCGTGTGGGCCACACGGGCAAGGATATTTTG
1 GGCCATGTGCGAGGCCGTCTGGGACACACGGGCAAGGACATTTTG
54432483 GGC
1 GGC
54432486 GTATGGGCCC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.16, C:0.25, G:0.37, T:0.23
Consensus pattern (45 bp):
GGCCATGTGCGAGGCCGTCTGGGACACACGGGCAAGGACATTTTG
Found at i:54433355 original size:19 final size:20
Alignment explanation
Indices: 54433314--54433355 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
54433304 GATGGAACGA
54433314 TTTTTATGAAAACAACTATT
1 TTTTTATGAAAACAACTATT
* *
54433334 TTTTTCTGAAATCAACTATT
1 TTTTTATGAAAACAACTATT
54433354 TT
1 TT
54433356 ATAGAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (20 bp):
TTTTTATGAAAACAACTATT
Found at i:54440409 original size:20 final size:19
Alignment explanation
Indices: 54440373--54440426 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
54440363 TTATCAAATA
*
54440373 AAAAATATATAATTATATTTT
1 AAAAATA-A-AATTATATCTT
54440394 AAAAATAAAATATATATCTT
1 AAAAATAAAAT-TATATCTT
*
54440414 -AAAATTAAATTAT
1 AAAAATAAAATTAT
54440427 GTTATTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 3 0.10
19 12 0.40
20 8 0.27
21 7 0.23
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAAATAAAATTATATCTT
Found at i:54457921 original size:6 final size:6
Alignment explanation
Indices: 54457903--54457958 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
54457893 CTTTGAGTAC
* **
54457903 TTTTA- TTTTAT TATTAT TACTAT TTTTAT TTTTAT TTTTAT TTTT-T
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
*
54457949 ATTTAT TTTT
1 TTTTAT TTTT
54457959 GAAGACTTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
5 9 0.21
6 34 0.79
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:54458216 original size:16 final size:16
Alignment explanation
Indices: 54458168--54458208 Score: 73
Period size: 16 Copynumber: 2.5 Consensus size: 16
54458158 TTTCTTATGA
54458168 TATTATGCTTCTATTGT
1 TATTAT-CTTCTATTGT
54458185 TATTATCTTCTATTGT
1 TATTATCTTCTATTGT
54458201 TATTATCT
1 TATTATCT
54458209 ATCTTTGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.20, C:0.12, G:0.07, T:0.61
Consensus pattern (16 bp):
TATTATCTTCTATTGT
Found at i:54459837 original size:30 final size:30
Alignment explanation
Indices: 54459802--54459871 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
54459792 TAAGCATTTT
* **
54459802 CACACGGGTAAACCACATGCCCGTGTGTGA
1 CACACGGGCAAACCACACACCCGTGTGTGA
* ** *
54459832 CACACGAGCAGGCCACGCACCCGTGTGTGA
1 CACACGGGCAAACCACACACCCGTGTGTGA
54459862 CACACGGGCA
1 CACACGGGCA
54459872 GGCCACGCGC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.34, G:0.29, T:0.11
Consensus pattern (30 bp):
CACACGGGCAAACCACACACCCGTGTGTGA
Found at i:54459873 original size:30 final size:30
Alignment explanation
Indices: 54459821--54459889 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
54459811 AAACCACATG
54459821 CCCGTGTGTGACACACGAGCAGGCCACGCA
1 CCCGTGTGTGACACACGAGCAGGCCACGCA
* *
54459851 CCCGTGTGTGACACACGGGCAGGCCACGCG
1 CCCGTGTGTGACACACGAGCAGGCCACGCA
*
54459881 CCCATGTGT
1 CCCGTGTGT
54459890 CATGGCCGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.19, C:0.36, G:0.32, T:0.13
Consensus pattern (30 bp):
CCCGTGTGTGACACACGAGCAGGCCACGCA
Found at i:54463077 original size:29 final size:29
Alignment explanation
Indices: 54463032--54463147 Score: 112
Period size: 29 Copynumber: 4.0 Consensus size: 29
54463022 TACTTGTATC
* *
54463032 TGGCCCATTATGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* *
54463060 TGGCCCCTTTAGGCCCAAATCACCTGT-ATA
1 TGG-CCCATTAGGCCCAAATCACAT-TCATA
* * *
54463090 TGGCCCATTAGTCCCAAATCAGATTTATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* *
54463119 TGGGCCATTAGGCCC-AGTCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
54463147 T
1 T
54463148 TCATGCTCAC
Statistics
Matches: 71, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
28 15 0.21
29 43 0.61
30 12 0.17
31 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTCATA
Found at i:54469600 original size:19 final size:19
Alignment explanation
Indices: 54469576--54469613 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
54469566 TAGATAAAAC
54469576 TTCTAAGTCACAATGAGCG
1 TTCTAAGTCACAATGAGCG
*
54469595 TTCTAAGTCATAATGAGCG
1 TTCTAAGTCACAATGAGCG
54469614 CACAAGGTAT
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:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (19 bp):
TTCTAAGTCACAATGAGCG
Found at i:54475129 original size:12 final size:12
Alignment explanation
Indices: 54475114--54475146 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
54475104 GACGTCACAC
54475114 GGCCGTGTGGTA
1 GGCCGTGTGGTA
*
54475126 GGCCGTATGGTA
1 GGCCGTGTGGTA
54475138 GGCCGTGTG
1 GGCCGTGTG
54475147 CGATGACATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.09, C:0.18, G:0.48, T:0.24
Consensus pattern (12 bp):
GGCCGTGTGGTA
Found at i:54476722 original size:13 final size:13
Alignment explanation
Indices: 54476704--54476728 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54476694 TTGTCATGTT
54476704 ATTTAGTTAATTA
1 ATTTAGTTAATTA
54476717 ATTTAGTTAATT
1 ATTTAGTTAATT
54476729 TTAGTTTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (13 bp):
ATTTAGTTAATTA
Found at i:54478217 original size:21 final size:21
Alignment explanation
Indices: 54478190--54478253 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
54478180 TAAAAAACAT
54478190 ACACCCATGTGAGGGGGAGAC
1 ACACCCATGTGAGGGGGAGAC
** ** *
54478211 ATGCCCATGTGA-GGAAACAC
1 ACACCCATGTGAGGGGGAGAC
54478231 ACACCCATGTGAGGGGGAGAC
1 ACACCCATGTGAGGGGGAGAC
54478252 AC
1 AC
54478254 GCTAGTGTGA
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.31, C:0.25, G:0.33, T:0.11
Consensus pattern (21 bp):
ACACCCATGTGAGGGGGAGAC
Found at i:54478284 original size:41 final size:41
Alignment explanation
Indices: 54478184--54478272 Score: 135
Period size: 41 Copynumber: 2.2 Consensus size: 41
54478174 TTCAGATAAA
* *
54478184 AAACATACACCCATGTGAGGGGGAGACATGCCCATGTGAGG
1 AAACACACACCCATGTGAGGGGGAGACACGCCCATGTGAGG
*
54478225 AAACACACACCCATGTGAGGGGGAGACACG-CTAGTGTGAGG
1 AAACACACACCCATGTGAGGGGGAGACACGCCCA-TGTGAGG
54478266 AAACACA
1 AAACACA
54478273 TGTCCCTGTG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 2 0.05
41 42 0.95
ACGTcount: A:0.35, C:0.22, G:0.30, T:0.12
Consensus pattern (41 bp):
AAACACACACCCATGTGAGGGGGAGACACGCCCATGTGAGG
Found at i:54478724 original size:31 final size:30
Alignment explanation
Indices: 54478684--54478744 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 30
54478674 ACAGCTGTTT
54478684 GAACAGCTCATGTGTGGGCACACGCCCTTG
1 GAACAGCTCATGTGTGGGCACACGCCCTTG
*
54478714 NGAACCGCTCATGTGTGGGCACACGCCCTTG
1 -GAACAGCTCATGTGTGGGCACACGCCCTTG
54478745 TGGTCACCTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.18, C:0.31, G:0.30, T:0.20
Consensus pattern (30 bp):
GAACAGCTCATGTGTGGGCACACGCCCTTG
Found at i:54478777 original size:43 final size:43
Alignment explanation
Indices: 54478725--54478837 Score: 163
Period size: 43 Copynumber: 2.6 Consensus size: 43
54478715 GAACCGCTCA
* * * *
54478725 TGTGTGGGCACACGCCCTTGTGGTCACCTGTGTGAACCATCCG
1 TGTGCGGGCACACGCCCGTGTGGTCACCTATGTGAACCACCCG
* *
54478768 TGTGCGGGCACATGCCCGTGTGGTCACTTATGTGAACCACCCG
1 TGTGCGGGCACACGCCCGTGTGGTCACCTATGTGAACCACCCG
*
54478811 TGTGCGAGCACACGCCCGTGTGGTCAC
1 TGTGCGGGCACACGCCCGTGTGGTCAC
54478838 AAAACCACCT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 62 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (43 bp):
TGTGCGGGCACACGCCCGTGTGGTCACCTATGTGAACCACCCG
Found at i:54479597 original size:20 final size:20
Alignment explanation
Indices: 54479568--54479612 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
54479558 CTATTTTTCA
*
54479568 ATAAATATACATACAAAATT
1 ATAAAAATACATACAAAATT
*
54479588 ATAAAAATACATATAAAATT
1 ATAAAAATACATACAAAATT
54479608 ATAAA
1 ATAAA
54479613 TAAATGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (20 bp):
ATAAAAATACATACAAAATT
Found at i:54482706 original size:18 final size:18
Alignment explanation
Indices: 54482683--54482717 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54482673 CAATATGAGA
54482683 AATAATATAAAATAAAAT
1 AATAATATAAAATAAAAT
* *
54482701 AATAATTTTAAATAAAA
1 AATAATATAAAATAAAA
54482718 AGTTATTCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AATAATATAAAATAAAAT
Found at i:54484376 original size:11 final size:11
Alignment explanation
Indices: 54484354--54484396 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
54484344 AGGTTATGTT
54484354 TTTCTGTTTTTC
1 TTTCT-TTTTTC
54484366 TTTCTTTTTTC
1 TTTCTTTTTTC
*
54484377 TTT-TTCATTTC
1 TTTCTT-TTTTC
54484388 TTTCTTTTT
1 TTTCTTTTT
54484397 ACTCTTTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 2 0.07
11 18 0.67
12 7 0.26
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:54484381 original size:18 final size:19
Alignment explanation
Indices: 54484352--54484390 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
54484342 TTAGGTTATG
54484352 TTTTTCTGTTTTTC-TTTCT
1 TTTTTC-GTTTTTCATTTCT
54484371 TTTTTC-TTTTTCATTTCT
1 TTTTTCGTTTTTCATTTCT
54484389 TT
1 TT
54484391 CTTTTTACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 7 0.37
19 6 0.32
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (19 bp):
TTTTTCGTTTTTCATTTCT
Found at i:54484390 original size:22 final size:23
Alignment explanation
Indices: 54484362--54484405 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
54484352 TTTTTCTGTT
*
54484362 TTTCTTTCTTTTTTCT-TTTTCA
1 TTTCTTTCTTTTTACTCTTTTCA
54484384 TTTCTTTCTTTTTACTCTTTTC
1 TTTCTTTCTTTTTACTCTTTTC
54484406 CTTCTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (23 bp):
TTTCTTTCTTTTTACTCTTTTCA
Found at i:54484410 original size:22 final size:22
Alignment explanation
Indices: 54484363--54484412 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
54484353 TTTTCTGTTT
* *
54484363 TTCTTTCTTTTTTCTTTTTCAT
1 TTCTTTCTTTTTACTTTTTCAC
54484385 TTCTTTCTTTTTACTCTTTTC-C
1 TTCTTTCTTTTTACT-TTTTCAC
54484407 TTCTTT
1 TTCTTT
54484413 ATTGTCCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (22 bp):
TTCTTTCTTTTTACTTTTTCAC
Found at i:54491402 original size:26 final size:26
Alignment explanation
Indices: 54491373--54491480 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
54491363 TGATACAAAT
54491373 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
54491399 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
54491425 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
54491451 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
54491477 TGAT
1 TGAT
54491481 GGGAATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:54494506 original size:26 final size:26
Alignment explanation
Indices: 54494475--54494526 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
54494465 CACATTATCT
54494475 CCTTCCATCCCATTACACCATCTGGG
1 CCTTCCATCCCATTACACCATCTGGG
54494501 CCTTCCATCCCATTACACCATCTGGG
1 CCTTCCATCCCATTACACCATCTGGG
54494527 GTTAAAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.42, G:0.12, T:0.27
Consensus pattern (26 bp):
CCTTCCATCCCATTACACCATCTGGG
Found at i:54499120 original size:10 final size:9
Alignment explanation
Indices: 54499106--54499345 Score: 82
Period size: 10 Copynumber: 25.4 Consensus size: 9
54499096 AAAATAACTT
54499106 TAAAAATTA
1 TAAAAATTA
* *
54499115 TTAAAAGTA
1 TAAAAATTA
54499124 -AAAAA-TA
1 TAAAAATTA
*
54499131 TAAAGAAATA
1 TAAA-AATTA
54499141 T-AAAATTA
1 TAAAAATTA
54499149 TTAAAAATTA
1 -TAAAAATTA
54499159 TAAAAAACTTA
1 T-AAAAA-TTA
*
54499170 TAAATA-T-
1 TAAAAATTA
54499177 TAAAAATTA
1 TAAAAATTA
54499186 TAAAAATACTTA
1 T-AAAA-A-TTA
*
54499198 TAAAAAATTC
1 T-AAAAATTA
*
54499208 TAATTAATTA
1 TAA-AAATTA
*
54499218 TAAAAATAA
1 TAAAAATTA
*
54499227 CAAAAA-TA
1 TAAAAATTA
*
54499235 -AAACATATA
1 TAAAAAT-TA
54499244 TAAAATATT-
1 TAAAA-ATTA
* *
54499253 TAAAACCTTT
1 TAAAA-ATTA
*
54499263 TATAAACTTA
1 TA-AAAATTA
* *
54499273 AAAAAATCA
1 TAAAAATTA
54499282 TAAAAACTTA
1 TAAAAA-TTA
* *
54499292 TAAATACTA
1 TAAAAATTA
* *
54499301 AAATAAATTTC
1 TAA-AAA-TTA
*
54499312 TAAAAAAGTA
1 T-AAAAATTA
54499322 TAATAAATTA
1 TAA-AAATTA
54499332 TAAAAACTTA
1 TAAAAA-TTA
54499342 TAAA
1 TAAA
54499346 GTTTCCTAAA
Statistics
Matches: 173, Mismatches: 33, Indels: 49
0.68 0.13 0.19
Matches are distributed among these distances:
7 11 0.06
8 14 0.08
9 53 0.31
10 69 0.40
11 15 0.09
12 11 0.06
ACGTcount: A:0.62, C:0.05, G:0.01, T:0.31
Consensus pattern (9 bp):
TAAAAATTA
Found at i:54499145 original size:18 final size:18
Alignment explanation
Indices: 54499106--54499193 Score: 53
Period size: 18 Copynumber: 5.0 Consensus size: 18
54499096 AAAATAACTT
*
54499106 TAAAAATTATT-AAAAGTA
1 TAAAAA-TATTAAAAAATA
54499124 -AAAAATA-TAAAGAAATA
1 TAAAAATATTAAA-AAATA
* *
54499141 TAAAATTATTAAAAATTA
1 TAAAAATATTAAAAAATA
*
54499159 TAAAAA-ACTT-ATAAATA
1 TAAAAATA-TTAAAAAATA
*
54499176 TTAAAA-ATTATAAAAATA
1 TAAAAATATTA-AAAAATA
54499194 CTTATAAAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 14
0.71 0.10 0.18
Matches are distributed among these distances:
15 1 0.02
16 6 0.11
17 21 0.38
18 23 0.42
19 4 0.07
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (18 bp):
TAAAAATATTAAAAAATA
Found at i:54499191 original size:28 final size:29
Alignment explanation
Indices: 54499122--54499201 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 29
54499112 TTATTAAAAG
* *
54499122 TAAAAAATATAAAGAAA--TATAAAATTAT
1 TAAAAATTATAAAAAAACTTAT-AAATTAT
54499150 TAAAAATTAT-AAAAAACTTATAAA-TAT
1 TAAAAATTATAAAAAAACTTATAAATTAT
*
54499177 TAAAAATTATAAAAATACTTATAAA
1 TAAAAATTATAAAAAAACTTATAAA
54499202 AAATTCTAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
27 18 0.39
28 25 0.54
29 3 0.07
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (29 bp):
TAAAAATTATAAAAAAACTTATAAATTAT
Found at i:54499213 original size:28 final size:27
Alignment explanation
Indices: 54499107--54499203 Score: 101
Period size: 27 Copynumber: 3.6 Consensus size: 27
54499097 AAATAACTTT
* * *
54499107 AAAAA-TTATTAAAAGTAAAAAATATA
1 AAAAACTTATAAAAATTAAAAATTATA
54499133 AAGAAA--TATAAAATTATTAAAAATTATA
1 AA-AAACTTATAAAA--ATTAAAAATTATA
*
54499161 AAAAACTTATAAATATTAAAAATTATA
1 AAAAACTTATAAAAATTAAAAATTATA
54499188 AAAATACTTATAAAAA
1 AAAA-ACTTATAAAAA
54499204 ATTCTAATTA
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
26 8 0.13
27 23 0.38
28 23 0.38
29 6 0.10
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (27 bp):
AAAAACTTATAAAAATTAAAAATTATA
Found at i:54499885 original size:24 final size:24
Alignment explanation
Indices: 54499858--54499917 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
54499848 TAAATGATTT
* *
54499858 TTTTATAATTTCTAATTTTTTTAG-
1 TTTTATAATTTATAA-TTTATTAGA
54499882 TTTTATAATATTATAATTTATTAGA
1 TTTTATAAT-TTATAATTTATTAGA
*
54499907 TTTTAAAATTT
1 TTTTATAATTT
54499918 TTTATATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 18 0.58
25 13 0.42
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (24 bp):
TTTTATAATTTATAATTTATTAGA
Found at i:54500338 original size:17 final size:17
Alignment explanation
Indices: 54500316--54500350 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
54500306 TCTTTGGTTG
54500316 ATTGACCTTATCAAATC
1 ATTGACCTTATCAAATC
*
54500333 ATTGACCTTATTAAATC
1 ATTGACCTTATCAAATC
54500350 A
1 A
54500351 ATAATAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (17 bp):
ATTGACCTTATCAAATC
Found at i:54506132 original size:22 final size:22
Alignment explanation
Indices: 54506100--54506141 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
54506090 TATACAAGCA
*
54506100 ATATTACTTGAATAGTTATGAG
1 ATATTACTTGAATAATTATGAG
*
54506122 ATATTAGTTGAATAATTATG
1 ATATTACTTGAATAATTATG
54506142 TCTCTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.43
Consensus pattern (22 bp):
ATATTACTTGAATAATTATGAG
Found at i:54513083 original size:5 final size:5
Alignment explanation
Indices: 54513067--54513114 Score: 51
Period size: 5 Copynumber: 9.0 Consensus size: 5
54513057 ATAGAAGATA
* *
54513067 TTATT TTCTT TTATT TTTTT TTATTAT TTATTT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTA-T-T TTA-TT TTATT TTATT TTATT
54513115 AATTTAGGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
5 26 0.70
6 5 0.14
7 6 0.16
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:54513092 original size:23 final size:23
Alignment explanation
Indices: 54513065--54513120 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
54513055 AAATAGAAGA
*
54513065 TATTATTT-TCTTTTATTTTTTTT
1 TATTATTTAT-TTTTATTTTATTT
54513088 TATTATTTATTTTTATTTTATTT
1 TATTATTTATTTTTATTTTATTT
54513111 TATTAATTTA
1 TATT-ATTTA
54513121 GGATTAAGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 24 0.80
24 6 0.20
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (23 bp):
TATTATTTATTTTTATTTTATTT
Found at i:54513100 original size:15 final size:15
Alignment explanation
Indices: 54513070--54513110 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
54513060 GAAGATATTA
*
54513070 TTTTCTTTTATTT-T
1 TTTTATTTTATTTAT
*
54513084 TTTT-TATTATTTAT
1 TTTTATTTTATTTAT
54513098 TTTTATTTTATTT
1 TTTTATTTTATTT
54513111 TATTAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 7 0.30
14 9 0.39
15 7 0.30
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTATTTTATTTAT
Found at i:54513106 original size:18 final size:17
Alignment explanation
Indices: 54513076--54513109 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
54513066 ATTATTTTCT
54513076 TTTATTTTTTTTTATTA
1 TTTATTTTTTTTTATTA
54513093 TTTATTTTTATTTTATT
1 TTTATTTTT-TTTTATT
54513110 TTATTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTATTTTTTTTTATTA
Found at i:54515984 original size:18 final size:17
Alignment explanation
Indices: 54515960--54515999 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
54515950 CTGGCCCATA
54515960 GCCCACACACCTGTGTG
1 GCCCACACACCTGTGTG
* *
54515977 GTCCCACACGCTTGTGTG
1 G-CCCACACACCTGTGTG
54515995 GCCCA
1 GCCCA
54516000 TATGTCCCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.15, C:0.40, G:0.25, T:0.20
Consensus pattern (17 bp):
GCCCACACACCTGTGTG
Found at i:54516701 original size:26 final size:26
Alignment explanation
Indices: 54516672--54516781 Score: 193
Period size: 26 Copynumber: 4.2 Consensus size: 26
54516662 TGATACAAAT
54516672 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
54516698 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
54516724 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
54516750 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
54516776 TGATAA
1 TGATAA
54516782 GAATTTCATG
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:54523286 original size:15 final size:16
Alignment explanation
Indices: 54523268--54523301 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
54523258 AGATTAAATT
54523268 AATTAA-CTAAATGCA
1 AATTAATCTAAATGCA
*
54523283 AATTAATTTAAATGCA
1 AATTAATCTAAATGCA
54523299 AAT
1 AAT
54523302 GAGATGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (16 bp):
AATTAATCTAAATGCA
Found at i:54531332 original size:41 final size:41
Alignment explanation
Indices: 54531287--54531369 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
54531277 ACATAGTCCC
54531287 TTGGATTAGCTTTCATCAAAGCCATACTTTCATTACCTTTT
1 TTGGATTAGCTTTCATCAAAGCCATACTTTCATTACCTTTT
54531328 TTGGATTAGCTTTCATCAAAGCCATACTTTCATTACCTTTT
1 TTGGATTAGCTTTCATCAAAGCCATACTTTCATTACCTTTT
54531369 T
1 T
54531370 CATCTTCCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.45
Consensus pattern (41 bp):
TTGGATTAGCTTTCATCAAAGCCATACTTTCATTACCTTTT
Found at i:54537137 original size:34 final size:35
Alignment explanation
Indices: 54537094--54537163 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
54537084 TGGCAATGAC
*
54537094 ACCAAAAAG-TTGTAACAAGTAGGTTTGTGCTATT
1 ACCAAAAAGTTTGTAACAAGTAGGTTTGTGCAATT
**
54537128 ACCAAAAAGTTTGTAACGCGTAGGTTTGTGCAATT
1 ACCAAAAAGTTTGTAACAAGTAGGTTTGTGCAATT
54537163 A
1 A
54537164 TATACAGTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 9 0.28
35 23 0.72
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.31
Consensus pattern (35 bp):
ACCAAAAAGTTTGTAACAAGTAGGTTTGTGCAATT
Found at i:54542438 original size:28 final size:28
Alignment explanation
Indices: 54542399--54542455 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
54542389 TCTTGGTAAG
54542399 TTTTAAGGTTTTTATTGATAGATAATAT
1 TTTTAAGGTTTTTATTGATAGATAATAT
54542427 TTTTAAGGTTTTTATTGATAGATAATAT
1 TTTTAAGGTTTTTATTGATAGATAATAT
54542455 T
1 T
54542456 ACGTTAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (28 bp):
TTTTAAGGTTTTTATTGATAGATAATAT
Found at i:54543796 original size:36 final size:36
Alignment explanation
Indices: 54543706--54543982 Score: 295
Period size: 36 Copynumber: 7.7 Consensus size: 36
54543696 TTACTAAGGG
* * * * * *
54543706 ATCACATACT-AATCACATAAGGGTTAGCATATTTA
1 ATCACATACTAAATTACATGAAGGTTCGCATACTAA
* * * * * *
54543741 ATCACATTCTCAATAACATGATGGTTCACATGCTAA
1 ATCACATACTAAATTACATGAAGGTTCGCATACTAA
* * *
54543777 ATCATACACTAAATTACATGAAGGTTTGCATACTAA
1 ATCACATACTAAATTACATGAAGGTTCGCATACTAA
* * *
54543813 ATCACATATTGAATTACATAAAGGTTCGCATACTAA
1 ATCACATACTAAATTACATGAAGGTTCGCATACTAA
* *
54543849 ATCACATATTAAATTACATGAGGGTTCGCATACTAA
1 ATCACATACTAAATTACATGAAGGTTCGCATACTAA
* * * *
54543885 ATCATATACTAAATTACATGAGGGTTTGCATAGTAA
1 ATCACATACTAAATTACATGAAGGTTCGCATACTAA
*
54543921 ATCACATACTAAATTACATGAAGGTTCGCTTACTAA
1 ATCACATACTAAATTACATGAAGGTTCGCATACTAA
** *
54543957 ATCATTTACTAAATTACATGAGGGTT
1 ATCACATACTAAATTACATGAAGGTT
54543983 TACATATTGG
Statistics
Matches: 202, Mismatches: 39, Indels: 1
0.83 0.16 0.00
Matches are distributed among these distances:
35 9 0.04
36 193 0.96
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.32
Consensus pattern (36 bp):
ATCACATACTAAATTACATGAAGGTTCGCATACTAA
Found at i:54543911 original size:108 final size:107
Alignment explanation
Indices: 54543706--54543988 Score: 352
Period size: 108 Copynumber: 2.6 Consensus size: 107
54543696 TTACTAAGGG
* * * * * * * *
54543706 ATCACATACTAATCACATAAGGGTTAGCATATTTAATCACAT-TCTCAATAACATGATGGTTCAC
1 ATCACATACTAATTACATAAAGGTTCGCATACTAAATCACATAT-TAAATTACATGAGGGTTCAC
*
54543770 ATGCTAAATCATACACTAAATTACATGAAGGTTTGCATACTAA
65 ATACTAAATCATACACTAAATTACATGAAGGTTTGCATACTAA
* *
54543813 ATCACATATTGAATTACATAAAGGTTCGCATACTAAATCACATATTAAATTACATGAGGGTTCGC
1 ATCACATACT-AATTACATAAAGGTTCGCATACTAAATCACATATTAAATTACATGAGGGTTCAC
* * *
54543878 ATACTAAATCATATACTAAATTACATGAGGGTTTGCATAGTAA
65 ATACTAAATCATACACTAAATTACATGAAGGTTTGCATACTAA
* * ** * *
54543921 ATCACATACTAAATTACATGAAGGTTCGCTTACTAAATCATTTACTAAATTACATGAGGGTTTAC
1 ATCACATACT-AATTACATAAAGGTTCGCATACTAAATCACATATTAAATTACATGAGGGTTCAC
54543986 ATA
65 ATA
54543989 TTGGCTACAA
Statistics
Matches: 151, Mismatches: 23, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
107 9 0.06
108 141 0.93
109 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (107 bp):
ATCACATACTAATTACATAAAGGTTCGCATACTAAATCACATATTAAATTACATGAGGGTTCACA
TACTAAATCATACACTAAATTACATGAAGGTTTGCATACTAA
Found at i:54544909 original size:14 final size:14
Alignment explanation
Indices: 54544890--54544920 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
54544880 TTAGCTTGCC
*
54544890 TAATACTTAGCTAT
1 TAATACTTAACTAT
54544904 TAATACTTAACTAT
1 TAATACTTAACTAT
54544918 TAA
1 TAA
54544921 GCCTAGTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (14 bp):
TAATACTTAACTAT
Found at i:54545390 original size:9 final size:10
Alignment explanation
Indices: 54545371--54545418 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 10
54545361 TTTTTATTTC
54545371 TATATATATT
1 TATATATATT
54545381 TATA-ATATT
1 TATATATATT
54545390 T-TATAT-TT
1 TATATATATT
54545398 TATATAGTATT
1 TATATA-TATT
*
54545409 TTTATA-ATT
1 TATATATATT
54545418 T
1 T
54545419 TTATTTTATG
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
8 5 0.15
9 16 0.48
10 5 0.15
11 7 0.21
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (10 bp):
TATATATATT
Found at i:54545391 original size:27 final size:27
Alignment explanation
Indices: 54545361--54545427 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 27
54545351 TTTTTACATG
54545361 TTTTTATTTCTATATA-TATTTATAAT-A
1 TTTTTATTT-TATATAGTATTT-TAATAA
*
54545388 TTTTATATTTTATATAGTATTTTTATAA
1 TTTT-TATTTTATATAGTATTTTAATAA
54545416 TTTTTATTTTAT
1 TTTTTATTTTAT
54545428 GTAATTGATT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
27 21 0.58
28 15 0.42
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (27 bp):
TTTTTATTTTATATAGTATTTTAATAA
Found at i:54545397 original size:28 final size:28
Alignment explanation
Indices: 54545361--54545509 Score: 76
Period size: 30 Copynumber: 5.2 Consensus size: 28
54545351 TTTTTACATG
*
54545361 TTTTTAT-TTCTATATA-TA-TTTATAA
1 TTTTTATATTTTATATAGTATTTTATAA
54545386 TATTTTATATTTTATATAGTATTTTTATAA
1 T-TTTTATATTTTATATAGTA-TTTTATAA
* * * *
54545416 -TTTT-TATTTTATGTAATTGATTTTTTTTA
1 TTTTTATATTTTATAT-AGT-A-TTTTATAA
* * * * *
54545445 TTTTTTTATTTTAATTTAATAATTTTACAT
1 TTTTTATATTTT-ATATAGT-ATTTTATAA
*
54545475 TTTTTATA-TTTATATAATATTTATATAA
1 TTTTTATATTTTATATAGTATTT-TATAA
54545503 GTTTTTA
1 -TTTTTA
54545510 ATATATTTTA
Statistics
Matches: 96, Mismatches: 16, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
25 1 0.01
26 6 0.06
27 21 0.22
28 17 0.18
29 17 0.18
30 22 0.23
31 9 0.09
32 3 0.03
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (28 bp):
TTTTTATATTTTATATAGTATTTTATAA
Found at i:54545470 original size:31 final size:32
Alignment explanation
Indices: 54545407--54545470 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 32
54545397 TTATATAGTA
*
54545407 TTTTTATAATTTTTATTTTATGTAATTGATTT
1 TTTTTATAATTTTTATTTTATGTAATTAATTT
* *
54545439 TTTTTAT-TTTTTTATTTTAATTTAA-TAATTT
1 TTTTTATAATTTTTATTTT-ATGTAATTAATTT
54545470 T
1 T
54545471 ACATTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (32 bp):
TTTTTATAATTTTTATTTTATGTAATTAATTT
Found at i:54545496 original size:27 final size:27
Alignment explanation
Indices: 54545346--54545496 Score: 80
Period size: 29 Copynumber: 5.4 Consensus size: 27
54545336 AATAAATCTT
54545346 TATAAT-TTTTACATGTTTTTAT-TTCTA
1 TATAATATTTTACAT-TTTTTATATT-TA
*
54545373 TAT-ATATTTATA-ATATTTTATATTTTA
1 TATAATATTT-TACATTTTTTATA-TTTA
* * *
54545400 TATAGTATTTTTATAATTTTTAT-TTTA
1 TATAATA-TTTTACATTTTTTATATTTA
* **
54545427 TGTAATTGATTTTTTTTATTTTTT-TATTTTAA
1 TATAA-T-A--TTTTACATTTTTTATA-TTT-A
*
54545459 TTTAATAATTTTACATTTTTTATATTTA
1 TATAAT-ATTTTACATTTTTTATATTTA
54545487 TATAATATTT
1 TATAATATTT
54545497 ATATAAGTTT
Statistics
Matches: 97, Mismatches: 13, Indels: 28
0.70 0.09 0.20
Matches are distributed among these distances:
26 8 0.08
27 24 0.25
28 15 0.15
29 26 0.27
30 14 0.14
31 5 0.05
32 5 0.05
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.66
Consensus pattern (27 bp):
TATAATATTTTACATTTTTTATATTTA
Found at i:54545546 original size:27 final size:25
Alignment explanation
Indices: 54545504--54545553 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 25
54545494 TTTATATAAG
54545504 TTTTTAATATATTTTATATTATAATTT
1 TTTTTAATATATTTTA-ATT-TAATTT
54545531 TTTTTAATAT-TCTTTAATTTAAT
1 TTTTTAATATAT-TTTAATTTAAT
54545554 AATATATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 4 0.18
26 4 0.18
27 14 0.64
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (25 bp):
TTTTTAATATATTTTAATTTAATTT
Found at i:54547503 original size:3 final size:3
Alignment explanation
Indices: 54547495--54547531 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
54547485 AATGTAGAAA
54547495 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
54547532 TTACGTTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:54569855 original size:37 final size:37
Alignment explanation
Indices: 54569794--54570023 Score: 293
Period size: 37 Copynumber: 6.0 Consensus size: 37
54569784 TACGTATGAT
*
54569794 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
* *
54569829 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
* * *
54569866 CACTTATCACTTTGTTTCTTGATCAGATAAGTGCAAC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
*
54569903 CACTTATCACTTTGTCTCTTGATCAGATAAGTGCAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
54569940 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--AGC
*
54569983 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
1 ---CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
54570023 C
1 C
54570024 GAAGCTATCA
Statistics
Matches: 174, Mismatches: 10, Indels: 20
0.85 0.05 0.10
Matches are distributed among these distances:
35 9 0.05
36 4 0.02
37 119 0.68
39 2 0.01
40 4 0.02
42 1 0.01
43 3 0.02
44 2 0.01
46 30 0.17
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (37 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
Found at i:54569993 original size:46 final size:46
Alignment explanation
Indices: 54569940--54570208 Score: 322
Period size: 46 Copynumber: 5.6 Consensus size: 46
54569930 TAAGTGCAGC
* * **
54569940 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
54569986 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
54570032 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
54570084 CACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* * ** *
54570130 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
54570182 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
54570209 AGTACTCAAA
Statistics
Matches: 198, Mismatches: 13, Indels: 24
0.84 0.06 0.10
Matches are distributed among these distances:
46 111 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
Found at i:54570059 original size:52 final size:52
Alignment explanation
Indices: 54569983--54570202 Score: 308
Period size: 52 Copynumber: 4.3 Consensus size: 52
54569973 TAGCTAAAGC
* *
54569983 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
54570036 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
54570088 TATCAC-TTT-A----TCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
54570134 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
54570186 TATCACTTTATCACTTG
1 TATCACTTT-TCACTTG
54570203 ATCAGAAGTA
Statistics
Matches: 150, Mismatches: 10, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
46 41 0.27
47 2 0.01
48 1 0.01
50 1 0.01
51 3 0.02
52 84 0.56
53 18 0.12
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:54570105 original size:98 final size:98
Alignment explanation
Indices: 54569940--54570208 Score: 439
Period size: 98 Copynumber: 2.7 Consensus size: 98
54569930 TAAGTGCAGC
* * * *
54569940 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTATCACT
54570005 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
* **
54570039 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTATCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTATCACTT
*
54570104 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
54570137 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTATCACTT
54570202 GATCAGA
66 GATCAGA
54570209 AGTACTCAAA
Statistics
Matches: 157, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
98 148 0.94
99 9 0.06
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTATCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:54585519 original size:48 final size:48
Alignment explanation
Indices: 54585462--54585685 Score: 185
Period size: 48 Copynumber: 4.7 Consensus size: 48
54585452 CATATTATGA
*
54585462 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATTAAGACGAT
1 GAGCTAGTGTAAGACC-TGTCTGGGACATGGCATCGACATTAAGACGAT
* * * ** *
54585511 -AGCTAGTGTAAGACATGTCTGGGACAT-GCATCGGCCTCGAGA-TAT
1 GAGCTAGTGTAAGACCTGTCTGGGACATGGCATCGACATTAAGACGAT
* *
54585556 GCAAGCTAGTGTAAGACCTGTCTAGGACATGGCATCGGC-TT--GAC-AT
1 G--AGCTAGTGTAAGACCTGTCTGGGACATGGCATCGACATTAAGACGAT
* * * * * *
54585602 GTGTTAGTGTAAGACCTGTTTGGGACATGGCATCGACACTGATAC-AT
1 GAGCTAGTGTAAGACCTGTCTGGGACATGGCATCGACATTAAGACGAT
* * *
54585649 GAGAGCCAGAGTAAAACCTGTCTGGGACATGGCATCG
1 --GAGCTAGTGTAAGACCTGTCTGGGACATGGCATCG
54585686 GCTCGATATA
Statistics
Matches: 142, Mismatches: 23, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
44 31 0.22
45 3 0.02
46 16 0.11
47 16 0.11
48 39 0.27
49 37 0.26
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (48 bp):
GAGCTAGTGTAAGACCTGTCTGGGACATGGCATCGACATTAAGACGAT
Found at i:54585708 original size:141 final size:140
Alignment explanation
Indices: 54585467--54585781 Score: 370
Period size: 141 Copynumber: 2.2 Consensus size: 140
54585457 TATGAGAGCC
* * * * * * *
54585467 AGTGTAAGACCATGTCTGGGACATGGCATCGACATTAAGACGATAGCTAGTGTAAGACATGTCTG
1 AGTGTAAGACCATGTTTGGGACATGGCATCGACATGAACACGAGAGCCAGAGTAAAACATGTCTG
*
54585532 GGACATGCATCGGCCTCGAGATATGCAAGCTAGTGTAAGACCTGTCTA-GGACATGGCATCGGCT
66 GGACATGCATCGGCCTCGAGATATGCAAGCTAGTGTAAGACCTGT-TAGGGACATGGCATCGACT
54585596 TGACATGTGT-T
130 T-ACATGTGTGT
* *
54585607 AGTGTAAGACC-TGTTTGGGACATGGCATCGACACTGATACATGAGAGCCAGAGTAAAACCTGTC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGACA-TGA-ACACGAGAGCCAGAGTAAAACATGTC
* * *
54585671 TGGGACATGGCATCGG-CTCGATATATGGAAG-TCAGTGTAAGACTTGTTAGGGACATGGCATCG
64 TGGGACAT-GCATCGGCCTCGAGATATGCAAGCT-AGTGTAAGACCTGTTAGGGACATGGCATCG
*
54585734 ACTTAGATGTGTGAGCT
127 ACTTACATGTGT--G-T
* *
54585751 AGTGTAAGACCATGTTTGGAACATAGCATCG
1 AGTGTAAGACCATGTTTGGGACATGGCATCG
54585782 GCATCGTACC
Statistics
Matches: 149, Mismatches: 16, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
139 21 0.14
140 23 0.15
141 69 0.46
142 7 0.05
144 12 0.08
145 17 0.11
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (140 bp):
AGTGTAAGACCATGTTTGGGACATGGCATCGACATGAACACGAGAGCCAGAGTAAAACATGTCTG
GGACATGCATCGGCCTCGAGATATGCAAGCTAGTGTAAGACCTGTTAGGGACATGGCATCGACTT
ACATGTGTGT
Found at i:54586097 original size:19 final size:19
Alignment explanation
Indices: 54586073--54586118 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
54586063 GCCTATGAGA
* *
54586073 ATGATTTTGTGATGGCCTT
1 ATGATTATGTGATGACCTT
54586092 ATGATTATGTGATGACCTT
1 ATGATTATGTGATGACCTT
*
54586111 GTGATTAT
1 ATGATTAT
54586119 AGGTCTATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.22, C:0.09, G:0.24, T:0.46
Consensus pattern (19 bp):
ATGATTATGTGATGACCTT
Found at i:54590565 original size:44 final size:44
Alignment explanation
Indices: 54590504--54590588 Score: 143
Period size: 44 Copynumber: 1.9 Consensus size: 44
54590494 CCTAAACCTA
* * *
54590504 ATGATCTGATTGTTTGATATACTGATCTAATTAGGATACTGATG
1 ATGATCTAATTGCTTGATATACTGATCTAATTAGAATACTGATG
54590548 ATGATCTAATTGCTTGATATACTGATCTAATTAGAATACTG
1 ATGATCTAATTGCTTGATATACTGATCTAATTAGAATACTG
54590589 GTATACGTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.40
Consensus pattern (44 bp):
ATGATCTAATTGCTTGATATACTGATCTAATTAGAATACTGATG
Found at i:54590575 original size:21 final size:21
Alignment explanation
Indices: 54590505--54590579 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
54590495 CTAAACCTAA
* *
54590505 TGATCTGATTGTTTGATATAC
1 TGATCTAATTGATTGATATAC
*
54590526 TGATCTAATTAGGATACTGAT-GA-
1 TGATCTAATT--GAT--TGATATAC
*
54590549 TGATCTAATTGCTTGATATAC
1 TGATCTAATTGATTGATATAC
54590570 TGATCTAATT
1 TGATCTAATT
54590580 AGAATACTGG
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
19 4 0.09
20 1 0.02
21 21 0.49
23 12 0.28
24 1 0.02
25 4 0.09
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (21 bp):
TGATCTAATTGATTGATATAC
Found at i:54592219 original size:21 final size:21
Alignment explanation
Indices: 54592195--54592250 Score: 94
Period size: 21 Copynumber: 2.6 Consensus size: 21
54592185 TGATATGACT
*
54592195 GACTAGACTAATAGTACATTG
1 GACTAGACCAATAGTACATTG
54592216 GACTAGACCAATAGTACATTG
1 GACTAGACCAATAGTACATTG
54592237 GACTAGACCCAATA
1 GACTAGA-CCAATA
54592251 AGAATAGATC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 27 0.82
22 6 0.18
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (21 bp):
GACTAGACCAATAGTACATTG
Found at i:54593214 original size:16 final size:18
Alignment explanation
Indices: 54593188--54593221 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
54593178 TGGAATTGAG
54593188 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
54593205 TTGA-AAAATTAATTTAA
1 TTGAGAAAATTAATTTAA
54593222 GATGTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:54594791 original size:29 final size:29
Alignment explanation
Indices: 54594755--54594821 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
54594745 TTGACAAATA
54594755 AAAAGGGATAGCTTCTG-CTATCGAATACG
1 AAAAGGGATAGCTTC-GACTATCGAATACG
* *
54594784 AAAAGGGATAGCTTCGACTATCGATTATG
1 AAAAGGGATAGCTTCGACTATCGAATACG
54594813 AAAAGGGAT
1 AAAAGGGAT
54594822 GGTGACGAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 1 0.03
29 34 0.97
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.24
Consensus pattern (29 bp):
AAAAGGGATAGCTTCGACTATCGAATACG
Found at i:54594933 original size:60 final size:61
Alignment explanation
Indices: 54594755--54595060 Score: 210
Period size: 60 Copynumber: 5.1 Consensus size: 61
54594745 TTGACAAATA
* ** * *
54594755 AAAAGGGATAGCTTCTGCTATCGAA-TACGAAAAGGGATAGCTTC-GACTATC-GATTATG
1 AAAAGGGATGGCTTCAACTATCGAACTATGAAAAGGGATAGCTTCAGACTATCAAATTATG
* * * * * * *
54594813 AAAAGGGATGG-TGACGAAC-ATC-AACAATGAAAAGGAAT-G-TTGATGACCATCGAACTATG
1 AAAAGGGATGGCT-TC-AACTATCGAACTATGAAAAGGGATAGCTTCA-GACTATCAAATTATG
54594872 AAAAGGGATGGCTTCAACTATCGAACTATGAAAAGGGATAGCTTCAG-CTATCAAATTATG
1 AAAAGGGATGGCTTCAACTATCGAACTATGAAAAGGGATAGCTTCAGACTATCAAATTATG
* * * * * * *
54594932 AAAAGGGATGG-TGAT-GACCATCGAACAATGAAAAGGGAT-G-GTGACGACCATAAAATTATG
1 AAAAGGGATGGCT--TCAACTATCGAACTATGAAAAGGGATAGCTTCA-GACTATCAAATTATG
* * * * * * *
54594992 AAAAGGGATAGCTT-AGGCTGTCGAACTATGAAAAGGGATAACTTCAG-TTATCGAATAATG
1 AAAAGGGATGGCTTCA-ACTATCGAACTATGAAAAGGGATAGCTTCAGACTATCAAATTATG
54595052 AAAAGGGAT
1 AAAAGGGAT
54595061 AGGTCAACCA
Statistics
Matches: 190, Mismatches: 39, Indels: 36
0.72 0.15 0.14
Matches are distributed among these distances:
56 2 0.01
57 4 0.02
58 35 0.18
59 25 0.13
60 114 0.60
61 5 0.03
62 5 0.03
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.22
Consensus pattern (61 bp):
AAAAGGGATGGCTTCAACTATCGAACTATGAAAAGGGATAGCTTCAGACTATCAAATTATG
Found at i:54594956 original size:90 final size:90
Alignment explanation
Indices: 54594839--54595030 Score: 244
Period size: 90 Copynumber: 2.1 Consensus size: 90
54594829 AACATCAACA
* * * * * **
54594839 ATGAAAAGGAATGTTGATGACCATCGAACTATGAAAAGGGATGGCT-TCAACTATCGAACTATGA
1 ATGAAAAGGGATGGTGATGACCATCGAACAATGAAAAGGGATGG-TGACAACCATAAAACTATGA
*
54594903 AAAGGGATAGCTTCA-GCTATCAAATT
65 AAAGGGATAGCTT-AGGCTATCAAACT
* *
54594929 ATGAAAAGGGATGGTGATGACCATCGAACAATGAAAAGGGATGGTGACGACCATAAAATTATGAA
1 ATGAAAAGGGATGGTGATGACCATCGAACAATGAAAAGGGATGGTGACAACCATAAAACTATGAA
* *
54594994 AAGGGATAGCTTAGGCTGTCGAACT
66 AAGGGATAGCTTAGGCTATCAAACT
54595019 ATGAAAAGGGAT
1 ATGAAAAGGGAT
54595031 AACTTCAGTT
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
89 2 0.02
90 86 0.98
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.22
Consensus pattern (90 bp):
ATGAAAAGGGATGGTGATGACCATCGAACAATGAAAAGGGATGGTGACAACCATAAAACTATGAA
AAGGGATAGCTTAGGCTATCAAACT
Found at i:54595031 original size:30 final size:30
Alignment explanation
Indices: 54594755--54595062 Score: 172
Period size: 30 Copynumber: 10.4 Consensus size: 30
54594745 TTGACAAATA
** *
54594755 AAAAGGGATAGCTTCTGCTATCGAA-TACG
1 AAAAGGGATAGCTTCAACTATCGAACTATG
* *
54594784 AAAAGGGATAGCTTCGACTATCG-ATTATG
1 AAAAGGGATAGCTTCAACTATCGAACTATG
* * *
54594813 AAAAGGGAT-GGTGACGAAC-ATC-AACAATG
1 AAAAGGGATAGCT-TC-AACTATCGAACTATG
* * *
54594842 AAAAGGAAT-G-TTGATGACCATCGAACTATG
1 AAAAGGGATAGCTTCA--ACTATCGAACTATG
*
54594872 AAAAGGGATGGCTTCAACTATCGAACTATG
1 AAAAGGGATAGCTTCAACTATCGAACTATG
* * *
54594902 AAAAGGGATAGCTTCAGCTATCAAATTATG
1 AAAAGGGATAGCTTCAACTATCGAACTATG
* * * *
54594932 AAAAGGGAT-GGTGAT-GACCATCGAACAATG
1 AAAAGGGATAGCT--TCAACTATCGAACTATG
* * * * ** *
54594962 AAAAGGGAT-GGTGACGACCATAAAATTATG
1 AAAAGGGATAGCT-TCAACTATCGAACTATG
* *
54594992 AAAAGGGATAGCTT-AGGCTGTCGAACTATG
1 AAAAGGGATAGCTTCA-ACTATCGAACTATG
* **
54595022 AAAAGGGATAACTTCAGTTATCGAA-TAATG
1 AAAAGGGATAGCTTCAACTATCGAACT-ATG
54595052 AAAAGGGATAG
1 AAAAGGGATAG
54595063 GTCAACCATC
Statistics
Matches: 217, Mismatches: 45, Indels: 33
0.74 0.15 0.11
Matches are distributed among these distances:
26 1 0.00
28 6 0.03
29 56 0.26
30 146 0.67
31 5 0.02
32 3 0.01
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.22
Consensus pattern (30 bp):
AAAAGGGATAGCTTCAACTATCGAACTATG
Found at i:54599376 original size:40 final size:40
Alignment explanation
Indices: 54599332--54599436 Score: 183
Period size: 40 Copynumber: 2.6 Consensus size: 40
54599322 AGACTAAGAT
*
54599332 CCGAAGGCATTCGTTCGGGTTATTATAACCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGGGTTATTATAACCGGGTTAAGTC
*
54599372 CCGAAGGTATTCGTGCGGGTTATTATAACCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGGGTTATTATAACCGGGTTAAGTC
*
54599412 CCGAAGGCATTCGTGCTGGTTATTA
1 CCGAAGGCATTCGTGCGGGTTATTA
54599437 CATCCGAGCC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGGGTTATTATAACCGGGTTAAGTC
Found at i:54599456 original size:40 final size:40
Alignment explanation
Indices: 54599291--54599456 Score: 129
Period size: 40 Copynumber: 4.2 Consensus size: 40
54599281 CGGACTAAGA
* ** * *
54599291 TCCGAAGGCATTTGTGCTAGTTACTATATCC-AGACTAAGA-
1 TCCGAAGGCATTCGTGCGGGTTATTATAACCGAG-CTAA-AT
* * * *
54599331 TCCGAAGGCATTCGTTCGGGTTATTATAACCGGGTTAAGT
1 TCCGAAGGCATTCGTGCGGGTTATTATAACCGAGCTAAAT
* * * * *
54599371 CCCGAAGGTATTCGTGCGGGTTATTATAACCGGGTTAAGT
1 TCCGAAGGCATTCGTGCGGGTTATTATAACCGAGCTAAAT
* * * * *
54599411 CCCGAAGGCATTCGTGCTGGTTATTACATCCGAGCCAAAT
1 TCCGAAGGCATTCGTGCGGGTTATTATAACCGAGCTAAAT
54599451 TCCGAA
1 TCCGAA
54599457 AGTAATTATG
Statistics
Matches: 103, Mismatches: 21, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
40 102 0.99
41 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (40 bp):
TCCGAAGGCATTCGTGCGGGTTATTATAACCGAGCTAAAT
Found at i:54601005 original size:40 final size:40
Alignment explanation
Indices: 54600929--54601187 Score: 389
Period size: 40 Copynumber: 6.5 Consensus size: 40
54600919 AACCCAAGTA
* * *
54600929 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGTACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAA-TAGCACAAATG
* *
54600968 CCTTTGGTACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
54601008 CCTTCGGGACTTAGCTCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
* *
54601048 CCTTCGGGACTTAGCCCGGATATAGTCAATAGTACAAATT
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
* *
54601088 CCTTCGGGGCTTAGCCCGGATATAGTCACTAGCAC-AATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
54601127 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
54601167 CCTTCGGGACTTAGCCCGGAT
1 CCTTCGGGACTTAGCCCGGAT
54601188 GTCATCCGAA
Statistics
Matches: 201, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
39 48 0.24
40 150 0.75
41 3 0.01
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
Found at i:54601153 original size:119 final size:120
Alignment explanation
Indices: 54600929--54601187 Score: 407
Period size: 119 Copynumber: 2.2 Consensus size: 120
54600919 AACCCAAGTA
* * * *
54600929 CCTTCGGGATTTAG-CCGGATATAGCAACTCGTACAAATGCCTTTGGTACTTAGCCCGGATATAG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTAGTACAAATGCCTTCGGGACTTAGCCCGGATATAG
*
54600993 TCAATAGCACAAATGCCTTCGGGACTTAGCTCGGATATAGTCAATAGCACAAATG
66 TCAATAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
* *
54601048 CCTTCGGGACTTAGCCCGGATATAGTCAA-TAGTACAAATTCCTTCGGGGCTTAGCCCGGATATA
1 CCTTCGGGACTTAGCCCGGATATAG-CAACTAGTACAAATGCCTTCGGGACTTAGCCCGGATATA
* *
54601112 GTCACTAGCAC-AATGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
65 GTCAATAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
54601167 CCTTCGGGACTTAGCCCGGAT
1 CCTTCGGGACTTAGCCCGGAT
54601188 GTCATCCGAA
Statistics
Matches: 129, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
119 76 0.59
120 50 0.39
121 3 0.02
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (120 bp):
CCTTCGGGACTTAGCCCGGATATAGCAACTAGTACAAATGCCTTCGGGACTTAGCCCGGATATAG
TCAATAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
Found at i:54604866 original size:18 final size:18
Alignment explanation
Indices: 54604845--54604908 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 18
54604835 ATCCAAGTGT
54604845 TATTTTATTTTATTAAAG
1 TATTTTATTTTATTAAAG
* *
54604863 TATTTCAGTTTATTTCCAAGAG
1 TATTTTATTTTA-TT--AA-AG
*
54604885 TTATTTTATCTTATTAAAG
1 -TATTTTATTTTATTAAAG
54604904 TATTT
1 TATTT
54604909 CACTTTATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
18 15 0.42
19 4 0.11
20 2 0.06
21 2 0.06
22 4 0.11
23 9 0.25
ACGTcount: A:0.30, C:0.06, G:0.08, T:0.56
Consensus pattern (18 bp):
TATTTTATTTTATTAAAG
Found at i:54604931 original size:41 final size:41
Alignment explanation
Indices: 54604836--54604919 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
54604826 TCAATTTAGA
* * *
54604836 TCCAAGTGTTATTTTATTTTATTAAAGTATTTCAGTTTATT
1 TCCAAGAGTTATTTTATCTTATTAAAGTATTTCACTTTATT
54604877 TCCAAGAGTTATTTTATCTTATTAAAGTATTTCACTTTATT
1 TCCAAGAGTTATTTTATCTTATTAAAGTATTTCACTTTATT
54604918 TC
1 TC
54604920 TTATTTGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.27, C:0.11, G:0.08, T:0.54
Consensus pattern (41 bp):
TCCAAGAGTTATTTTATCTTATTAAAGTATTTCACTTTATT
Found at i:54605109 original size:62 final size:62
Alignment explanation
Indices: 54605012--54605136 Score: 241
Period size: 62 Copynumber: 2.0 Consensus size: 62
54605002 TCTAATCTCG
*
54605012 TTTCTCTTCCCATTCAATCGAATTGTTTACATGATTTATTCAATTGAGTTAAAGATTATGAA
1 TTTCTCTTCCCATTCAATCAAATTGTTTACATGATTTATTCAATTGAGTTAAAGATTATGAA
54605074 TTTCTCTTCCCATTCAATCAAATTGTTTACATGATTTATTCAATTGAGTTAAAGATTATGAA
1 TTTCTCTTCCCATTCAATCAAATTGTTTACATGATTTATTCAATTGAGTTAAAGATTATGAA
54605136 T
1 T
54605137 AACAGGAGTG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.44
Consensus pattern (62 bp):
TTTCTCTTCCCATTCAATCAAATTGTTTACATGATTTATTCAATTGAGTTAAAGATTATGAA
Found at i:54612889 original size:25 final size:24
Alignment explanation
Indices: 54612861--54612923 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 24
54612851 CCAGGTAAAA
54612861 TGCCACAAAGGCTCTTCAGATAAT
1 TGCCACAAAGGCTCTTCAGATAAT
*
54612885 CTGCCACAAAGGCTCTTCAGGTAAT
1 -TGCCACAAAGGCTCTTCAGATAAT
*
54612910 TCACCACAAAGGCT
1 T-GCCACAAAGGCT
54612924 TGGTTTAGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 1 0.03
25 34 0.97
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (24 bp):
TGCCACAAAGGCTCTTCAGATAAT
Found at i:54613438 original size:43 final size:43
Alignment explanation
Indices: 54613340--54613440 Score: 177
Period size: 43 Copynumber: 2.4 Consensus size: 43
54613330 CAGACATATA
* *
54613340 TACACA-AATTTCACTAATAATCTTAACAGAATCAAACTTCTC
1 TACACATAATTTCCCAAATAATCTTAACAGAATCAAACTTCTC
54613382 TACACATAATTTCCCAAATAATCTTAACAGAATCAAACTTCTC
1 TACACATAATTTCCCAAATAATCTTAACAGAATCAAACTTCTC
54613425 TACACATAATTTCCCA
1 TACACATAATTTCCCA
54613441 TGCTTACCAT
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
42 6 0.11
43 50 0.89
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.31
Consensus pattern (43 bp):
TACACATAATTTCCCAAATAATCTTAACAGAATCAAACTTCTC
Found at i:54616778 original size:80 final size:79
Alignment explanation
Indices: 54616694--54616862 Score: 205
Period size: 79 Copynumber: 2.1 Consensus size: 79
54616684 CTAAGATCCG
*
54616694 AAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 AAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* *
54616758 TCCGGGTTAAGTCCCA
64 ACCGGGCTAAGTCCCA
* * * * * * *
54616774 AAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAAC
1 AAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAAAC
* *
54616839 CGGGCTATGTCCCG
66 CGGGCTAAGTCCCA
54616853 AAGGCATTTG
1 AAGGCATTTG
54616863 AACGAGGAGC
Statistics
Matches: 75, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
79 37 0.49
80 35 0.47
81 3 0.04
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
AAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAAAC
CGGGCTAAGTCCCA
Found at i:54616842 original size:39 final size:39
Alignment explanation
Indices: 54616638--54616860 Score: 200
Period size: 40 Copynumber: 5.6 Consensus size: 39
54616628 TTGAATGCTG
* * * * *
54616638 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
54616678 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
54616717 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* * *
54616758 TCCGGGTTAAGTCCCAAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
54616798 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
54616837 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
54616861 TGAACGAGGA
Statistics
Matches: 155, Mismatches: 20, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
39 40 0.26
40 101 0.65
41 13 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:54623631 original size:13 final size:13
Alignment explanation
Indices: 54623610--54623646 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
54623600 AGAGAATAAG
54623610 GAAAG-GAAAAAT
1 GAAAGTGAAAAAT
*
54623622 GAAATTGAAAAA-
1 GAAAGTGAAAAAT
54623634 GAAAGTGAAAAAT
1 GAAAGTGAAAAAT
54623647 AAAAAGAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.14
Consensus pattern (13 bp):
GAAAGTGAAAAAT
Found at i:54625770 original size:40 final size:40
Alignment explanation
Indices: 54625705--54625783 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 40
54625695 AAGCTGATCC
*
54625705 TAGCTCATTTCCAGCTTTTCGAGCTCTGTCT-AGCTCAACT
1 TAGCTCATTTCAAGCTTTTCGAGCTC-GTCTGAGCTCAACT
*
54625745 TAGCTCATTT-AAGCTCGTTTC-AGCTCGTTTGAGCTCAAC
1 TAGCTCATTTCAAGCT--TTTCGAGCTCGTCTGAGCTCAAC
54625784 CGAACTTACT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
39 7 0.21
40 23 0.68
41 4 0.12
ACGTcount: A:0.19, C:0.28, G:0.16, T:0.37
Consensus pattern (40 bp):
TAGCTCATTTCAAGCTTTTCGAGCTCGTCTGAGCTCAACT
Found at i:54631315 original size:23 final size:23
Alignment explanation
Indices: 54631277--54631331 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
54631267 GTTATACAAG
*
54631277 TAAAAAAAATTCGAAAAAAATTC
1 TAAAAAAAATTCGAAAAAAAATC
*
54631300 -AAAAAAAATTTTGAAAAAAAATC
1 TAAAAAAAA-TTCGAAAAAAAATC
54631323 TAAAAAAAA
1 TAAAAAAAA
54631332 GTGTTTAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 8 0.29
23 12 0.43
24 8 0.29
ACGTcount: A:0.71, C:0.05, G:0.04, T:0.20
Consensus pattern (23 bp):
TAAAAAAAATTCGAAAAAAAATC
Found at i:54631331 original size:11 final size:12
Alignment explanation
Indices: 54631277--54631331 Score: 62
Period size: 11 Copynumber: 4.8 Consensus size: 12
54631267 GTTATACAAG
54631277 TAAAAAAAATTC
1 TAAAAAAAATTC
*
54631289 -GAAAAAAATTC
1 TAAAAAAAATTC
*
54631300 -AAAAAAAATTT
1 TAAAAAAAATTC
54631311 TGAAAAAAAA-TC
1 T-AAAAAAAATTC
54631323 TAAAAAAAA
1 TAAAAAAAA
54631332 GTGTTTAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
11 27 0.73
12 2 0.05
13 8 0.22
ACGTcount: A:0.71, C:0.05, G:0.04, T:0.20
Consensus pattern (12 bp):
TAAAAAAAATTC
Found at i:54632268 original size:21 final size:20
Alignment explanation
Indices: 54632234--54632303 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 20
54632224 ACATTATTGT
54632234 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
54632255 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
*
54632276 AAAGAAAAAGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
54632297 AAAGAAA
1 AAAGAAA
54632304 GGCAAGAGGC
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
20 8 0.19
21 30 0.70
22 5 0.12
ACGTcount: A:0.79, C:0.03, G:0.17, T:0.01
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:54632269 original size:6 final size:5
Alignment explanation
Indices: 54632245--54632303 Score: 59
Period size: 5 Copynumber: 11.4 Consensus size: 5
54632235 AAGAGAAAAC
*
54632245 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGAA AAAGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAG-A AAAGA AA-AGA
54632292 AAAGA AAAGA AA
1 AAAGA AAAGA AA
54632304 GGCAAGAGGC
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
4 4 0.09
5 26 0.57
6 16 0.35
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:54632294 original size:25 final size:25
Alignment explanation
Indices: 54632249--54632297 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
54632239 GAAAACAAAG
54632249 AAAAGAAAAGAAAAAGCAAAAGAAGA
1 AAAAGAAAAGAAAAA-CAAAAGAAGA
*
54632275 AAAAGAAAAAGAAATA-AAAAGAA
1 AAAAG-AAAAGAAAAACAAAAGAA
54632298 AAGAAAGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 5 0.24
27 9 0.43
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (25 bp):
AAAAGAAAAGAAAAACAAAAGAAGA
Found at i:54632303 original size:15 final size:16
Alignment explanation
Indices: 54632245--54632304 Score: 72
Period size: 15 Copynumber: 3.9 Consensus size: 16
54632235 AAGAGAAAAC
54632245 AAAG-AAAAGAAAAGAA
1 AAAGAAAAAG-AAAGAA
*
54632261 AAAGCAAAAG-AAGAA
1 AAAGAAAAAGAAAGAA
*
54632276 AAAGAAAAAGAAATAA
1 AAAGAAAAAGAAAGAA
54632292 AAAG-AAAAGAAAG
1 AAAGAAAAAGAAAG
54632305 GCAAGAGGCA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
15 22 0.56
16 12 0.31
17 5 0.13
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (16 bp):
AAAGAAAAAGAAAGAA
Found at i:54632381 original size:11 final size:12
Alignment explanation
Indices: 54632349--54632379 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
54632339 TTGAGAGAAC
54632349 TTGAAAAAGCCT
1 TTGAAAAAGCCT
54632361 TTGAAAAAGCCT
1 TTGAAAAAGCCT
54632373 TTGAAAA
1 TTGAAAA
54632380 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:54632416 original size:30 final size:31
Alignment explanation
Indices: 54632382--54632463 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
54632372 TTTGAAAAGC
* *
54632382 AAAAAGAAAATGTAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
54632412 AAAAAGAGAA-CAAAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
54632442 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
54632464 TGAAACAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 8 0.19
30 24 0.57
31 10 0.24
ACGTcount: A:0.65, C:0.01, G:0.21, T:0.13
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:54635320 original size:88 final size:88
Alignment explanation
Indices: 54635216--54635391 Score: 325
Period size: 88 Copynumber: 2.0 Consensus size: 88
54635206 TGGGTTCAAC
*
54635216 AACGTCCAAAGGAAGGAATTAACTCAATAATTCAACACATTGATTGAATTAAGTGTATGCACAAA
1 AACGTCCAAAGGAAGGAATTAACTCAATAATTCAACACATTGATTGAATTAAGTGCATGCACAAA
54635281 GGGGACAACCAATTTACTAGGTT
66 GGGGACAACCAATTTACTAGGTT
54635304 AACGTCCAAAGGAAGGAATTAACTCAATAATTCAACACATTGATTGAATTAAGTGCATGCACAAA
1 AACGTCCAAAGGAAGGAATTAACTCAATAATTCAACACATTGATTGAATTAAGTGCATGCACAAA
* *
54635369 GGGGAGAACGAATTTACTAGGTT
66 GGGGACAACCAATTTACTAGGTT
54635392 CATGCTGCCA
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 85 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.24
Consensus pattern (88 bp):
AACGTCCAAAGGAAGGAATTAACTCAATAATTCAACACATTGATTGAATTAAGTGCATGCACAAA
GGGGACAACCAATTTACTAGGTT
Found at i:54637179 original size:21 final size:21
Alignment explanation
Indices: 54637155--54637198 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
54637145 ACGACCTAAT
*
54637155 TAAATAGAAAGGATA-ATTAAA
1 TAAATA-AAAGGATACAATAAA
*
54637176 TAAATAAAATGATACAATAAA
1 TAAATAAAAGGATACAATAAA
54637197 TA
1 TA
54637199 CTAAAGATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25
Consensus pattern (21 bp):
TAAATAAAAGGATACAATAAA
Found at i:54644959 original size:5 final size:5
Alignment explanation
Indices: 54644949--54645073 Score: 75
Period size: 5 Copynumber: 24.0 Consensus size: 5
54644939 CTCTTGCCTC
54644949 TCTTT TCTTT T-TATT TCGTTT TCCTTT TC--T TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT T-CTTT TCTTT TCTTT T-C-TTT TCTTT
* *
54644996 TCTTT TCTTT GTTTTCT TCTTT TGCTTT T-TCT T-TTT TCGTTT TCCTTT
1 TCTTT TCTTT -TCTT-T TCTTT T-CTTT TCTTT TCTTT TC-TTT T-CTTT
54645044 TC--T TCTTT TGCTTTT TCTTT TCTTT TCTTT
1 TCTTT TCTTT T-C-TTT TCTTT TCTTT TCTTT
54645074 GTTTTCTCTT
Statistics
Matches: 98, Mismatches: 4, Indels: 36
0.71 0.03 0.26
Matches are distributed among these distances:
3 6 0.06
4 7 0.07
5 43 0.44
6 30 0.31
7 12 0.12
ACGTcount: A:0.01, C:0.19, G:0.05, T:0.75
Consensus pattern (5 bp):
TCTTT
Found at i:54644995 original size:20 final size:20
Alignment explanation
Indices: 54644967--54645067 Score: 91
Period size: 20 Copynumber: 5.7 Consensus size: 20
54644957 TTTTATTTCG
*
54644967 TTTTCCTTTTCTTCTTTTGC
1 TTTTTCTTTTCTTCTTTTGC
54644987 TTTTTC--TT-TTCTTTT-C
1 TTTTTCTTTTCTTCTTTTGC
*
54645003 --TTTGTTTTCTTCTTTTGC
1 TTTTTCTTTTCTTCTTTTGC
54645021 TTTTTCTTTT-TTC----G-
1 TTTTTCTTTTCTTCTTTTGC
*
54645035 TTTTCCTTTTCTTCTTTTGC
1 TTTTTCTTTTCTTCTTTTGC
54645055 TTTTTCTTTTCTT
1 TTTTTCTTTTCTT
54645068 TTCTTTGTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 24
0.69 0.05 0.26
Matches are distributed among these distances:
14 12 0.19
15 4 0.06
16 3 0.05
17 14 0.22
18 3 0.05
19 4 0.06
20 24 0.38
ACGTcount: A:0.00, C:0.20, G:0.05, T:0.75
Consensus pattern (20 bp):
TTTTTCTTTTCTTCTTTTGC
Found at i:54645016 original size:34 final size:34
Alignment explanation
Indices: 54644973--54645084 Score: 167
Period size: 34 Copynumber: 3.3 Consensus size: 34
54644963 TTCGTTTTCC
54644973 TTTTCTTCTTTTGCTTTTTCTTTTCTTTTCTTTG
1 TTTTCTTCTTTTGCTTTTTCTTTTCTTTTCTTTG
**
54645007 TTTTCTTCTTTTGCTTTTTCTTTT-TTCGTT-TTCC
1 TTTTCTTCTTTTGCTTTTTCTTTTCTT--TTCTTTG
54645041 TTTTCTTCTTTTGCTTTTTCTTTTCTTTTCTTTG
1 TTTTCTTCTTTTGCTTTTTCTTTTCTTTTCTTTG
54645075 TTTTC-TCTTT
1 TTTTCTTCTTT
54645085 ACAAGAATGT
Statistics
Matches: 70, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
33 9 0.13
34 57 0.81
35 4 0.06
ACGTcount: A:0.00, C:0.19, G:0.05, T:0.76
Consensus pattern (34 bp):
TTTTCTTCTTTTGCTTTTTCTTTTCTTTTCTTTG
Found at i:54646000 original size:11 final size:11
Alignment explanation
Indices: 54645984--54646036 Score: 79
Period size: 11 Copynumber: 4.7 Consensus size: 11
54645974 ATAAATCACT
54645984 TTTTTTTTGAA
1 TTTTTTTTGAA
54645995 TTTTTTTTGAA
1 TTTTTTTTGAA
**
54646006 TTTTTTTCAAA
1 TTTTTTTTGAA
54646017 TTTTTTTTAGAA
1 TTTTTTTT-GAA
54646029 TTTTTTTT
1 TTTTTTTT
54646037 CGGTTTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
11 27 0.73
12 10 0.27
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.74
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:54648525 original size:14 final size:14
Alignment explanation
Indices: 54648506--54648550 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
54648496 AACTCATCTT
*
54648506 AGTTTAATTAAATG
1 AGTTTAATTTAATG
54648520 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
54648533 AATTTAATTTAATG
1 AGTTTAATTTAATG
54648547 AGTT
1 AGTT
54648551 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:54649731 original size:10 final size:11
Alignment explanation
Indices: 54649715--54649758 Score: 63
Period size: 10 Copynumber: 4.0 Consensus size: 11
54649705 TCAAGTAAGT
54649715 TTCAAAAAAAA
1 TTCAAAAAAAA
54649726 -TCAAAAAAAA
1 TTCAAAAAAAA
54649736 TTCAAAAAAAAA
1 TTC-AAAAAAAA
*
54649748 TTGAAAAAAAA
1 TTCAAAAAAAA
54649759 ACAAAATCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 10 0.33
11 10 0.33
12 10 0.33
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.16
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:54649732 original size:11 final size:11
Alignment explanation
Indices: 54649718--54649764 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
54649708 AGTAAGTTTC
54649718 AAAAAAAATCA
1 AAAAAAAATCA
*
54649729 AAAAAAATTCA
1 AAAAAAAATCA
*
54649740 AAAAAAAATTGA
1 AAAAAAAA-TCA
54649752 AAAAAAAA-CA
1 AAAAAAAATCA
54649762 AAA
1 AAA
54649765 TCTGAAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
10 4 0.13
11 17 0.55
12 10 0.32
ACGTcount: A:0.81, C:0.06, G:0.02, T:0.11
Consensus pattern (11 bp):
AAAAAAAATCA
Found at i:54649735 original size:12 final size:12
Alignment explanation
Indices: 54649718--54649759 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
54649708 AGTAAGTTTC
54649718 AAAAAAAA-TC-
1 AAAAAAAATTCA
54649728 AAAAAAAATTCA
1 AAAAAAAATTCA
*
54649740 AAAAAAAATTGA
1 AAAAAAAATTCA
54649752 AAAAAAAA
1 AAAAAAAA
54649760 CAAAATCTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 8 0.28
11 2 0.07
12 19 0.66
ACGTcount: A:0.81, C:0.05, G:0.02, T:0.12
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:54649759 original size:17 final size:18
Alignment explanation
Indices: 54649739--54649772 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
54649729 AAAAAAATTC
54649739 AAAAAAAAAT-TGAAAAA
1 AAAAAAAAATCTGAAAAA
*
54649756 AAAACAAAATCTGAAAA
1 AAAAAAAAATCTGAAAA
54649773 TTTGAACATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (18 bp):
AAAAAAAAATCTGAAAAA
Done.