Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 131 of 182
Found at i:41280035 original size:60 final size:60
Alignment explanation
Indices: 41279966--41280422 Score: 346
Period size: 60 Copynumber: 7.7 Consensus size: 60
41279956 CACTTTTCAT
* * * * * * * *
41279966 AAATCATATTTTGGTCCTTAAACTTTT-TAAGATTCACATTTTGACTCTCGAACTTTTTTC-
1 AAATTATATTTTGATCCTTAAACTTTTCTAAAATT-ACATTTTAACCCTCAAAC-CTTTCCA
* *
41280026 AAATTATATTTTGATCCCTAAACTTTTCTAAAATTACATTTTAACCCTTAAACCTTTCCA
1 AAATTATATTTTGATCCTTAAACTTTTCTAAAATTACATTTTAACCCTCAAACCTTTCCA
* * * * *
41280086 AAATTATATTTTGACCCTTAAACTTTTCCAAAATTACATTGTAATGCCT-AAA-CTTTCATA
1 AAATTATATTTTGATCCTTAAACTTTTCTAAAATTACATTTTAA-CCCTCAAACCTTTC-CA
* * * * * * *
41280146 AAATTACATTTTTACTCC-TAAACTTTTCAAAAATCAAATTTTTA-CC-CAAACCTTTTCA
1 AAATTATATTTTGA-TCCTTAAACTTTTCTAAAATTACATTTTAACCCTCAAACCTTTCCA
* * * *
41280204 AAATTACATTTTGACCCTTAAACTTTTCTAAAATTACATTTTAAACCCT-AACCCTTTCTA
1 AAATTATATTTTGATCCTTAAACTTTTCTAAAATTACATTTT-AACCCTCAAACCTTTCCA
* * * * * * * * * **
41280264 AAATTACATTTTAACCCTTAAACTTCTCTAAAATCACATTTTGACTCTTAAGCCTTT-TT
1 AAATTATATTTTGATCCTTAAACTTTTCTAAAATTACATTTTAACCCTCAAACCTTTCCA
* * * *
41280323 AAATTACATTTT-AACCCTAAACTTTTCCAAAATTACATTTTAACCCT-AAA-CTTTCCTA
1 AAATTATATTTTGATCCTTAAACTTTTCTAAAATTACATTTTAACCCTCAAACCTTTCC-A
* * * *
41280381 AAATTATATATTT-ACCCCTAAACTTTTCCAAAATTATATTTT
1 AAATTATAT-TTTGATCCTTAAACTTTTCTAAAATTACATTTT
41280423 GACCTCGTAT
Statistics
Matches: 327, Mismatches: 55, Indels: 31
0.79 0.13 0.08
Matches are distributed among these distances:
56 4 0.01
57 4 0.01
58 76 0.23
59 61 0.19
60 171 0.52
61 11 0.03
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.42
Consensus pattern (60 bp):
AAATTATATTTTGATCCTTAAACTTTTCTAAAATTACATTTTAACCCTCAAACCTTTCCA
Found at i:41280050 original size:30 final size:28
Alignment explanation
Indices: 41279984--41280422 Score: 263
Period size: 30 Copynumber: 14.9 Consensus size: 28
41279974 TTTTGGTCCT
* *
41279984 TAAAC-TTTTTAAGATTCACATTTTGACTC
1 TAAACTTTTTTAAAATT-ACATTTT-ACCC
* * *
41280013 TCGAACTTTTTTCAAATTATATTTTGATCCC
1 T-AAACTTTTTTAAAATTACATTTT-A-CCC
*
41280044 TAAACTTTTCTAAAATTACATTTTAACCC
1 TAAACTTTTTTAAAATTACATTTT-ACCC
* ** *
41280073 TTAAACCTTTCCAAAATTATATTTTGACCC
1 -TAAACTTTTTTAAAATTACATTTT-ACCC
** * *
41280103 TTAAACTTTTCCAAAATTACATTGTAATGCC
1 -TAAACTTTTTTAAAATTACATT-TTA-CCC
**
41280134 TAAACTTTCATAAAATTACATTTTTACTCC
1 TAAACTTTTTTAAAATTACA-TTTTAC-CC
** * *
41280164 TAAACTTTTCAAAAATCAAATTTTTACCC
1 TAAACTTTTTTAAAATTACA-TTTTACCC
* *
41280193 -AAACCTTTTCAAAATTACATTTTGACCC
1 TAAACTTTTTTAAAATTACATTTT-ACCC
*
41280221 TTAAACTTTTCTAAAATTACATTTTAAACCC
1 -TAAACTTTTTTAAAATTACATTTT--ACCC
* * *
41280252 TAACCCTTTCTAAAATTACATTTTAACCC
1 TAAACTTTTTTAAAATTACATTTT-ACCC
* * * *
41280281 TTAAACTTCTCTAAAATCACATTTTGACTCT
1 -TAAACTTTTTTAAAATTACATTTT-AC-CC
* *
41280312 TAAGCCTTTTT-AAATTACATTTTAACCC
1 TAAACTTTTTTAAAATTACATTTT-ACCC
**
41280340 TAAACTTTTCCAAAATTACATTTTAACCC
1 TAAACTTTTTTAAAATTACATTTT-ACCC
** *
41280369 TAAACTTTCCTAAAATTATATATTTACCCC
1 TAAACTTTTTTAAAATTACAT-TTTA-CCC
** *
41280399 TAAACTTTTCCAAAATTATATTTT
1 TAAACTTTTTTAAAATTACATTTT
41280423 GACCTCGTAT
Statistics
Matches: 332, Mismatches: 61, Indels: 34
0.78 0.14 0.08
Matches are distributed among these distances:
27 4 0.01
28 26 0.08
29 63 0.19
30 217 0.65
31 22 0.07
ACGTcount: A:0.35, C:0.21, G:0.02, T:0.41
Consensus pattern (28 bp):
TAAACTTTTTTAAAATTACATTTTACCC
Found at i:41280239 original size:118 final size:115
Alignment explanation
Indices: 41280026--41280414 Score: 449
Period size: 118 Copynumber: 3.3 Consensus size: 115
41280016 AACTTTTTTC
* * * *
41280026 AAATTATATTTTGATCCCTAAACTTTTCTAAAATTACATTTTAACCCTTAAACCTTTCCAAAATT
1 AAATTACATTTTTA-CCCTAAACTTTTCTAAAATCACATTTTAACCC--AAACCTTTTCAAAATT
* * *
41280091 ATATTTTGACCCTTAAACTTTTCCAAAATTACATTGTAATGCCTAAACTTTCATA
63 ACATTTTGACCCTTAAACTTTTCCAAAATTACATTTTAA-CCCTAAACTTTC-TA
* * *
41280146 AAATTACATTTTTACTCCTAAACTTTTCAAAAATCAAATTTTTACCCAAACCTTTTCAAAATTAC
1 AAATTACATTTTTAC-CCTAAACTTTTCTAAAATCACATTTTAACCCAAACCTTTTCAAAATTAC
* *
41280211 ATTTTGACCCTTAAACTTTTCTAAAATTACATTTTAAACCCTAACCCTTTCTA
65 ATTTTGACCCTTAAACTTTTCCAAAATTACATTTT-AACCCTAA-ACTTTCTA
* * * * * *
41280264 AAATTACATTTTAACCCTTAAACTTCTCTAAAATCACATTTTGACTCTTAAGCCTTTT-TAAATT
1 AAATTACATTTTTACCC-TAAACTTTTCTAAAATCACATTTTAAC-C-CAAACCTTTTCAAAATT
*
41280328 ACATTTTAACCC-TAAACTTTTCCAAAATTACATTTTAACCCTAAACTTTCCTA
63 ACATTTTGACCCTTAAACTTTTCCAAAATTACATTTTAACCCTAAACTTT-CTA
* * *
41280381 AAATTATATATTTACCCCTAAACTTTTCCAAAAT
1 AAATTACATTTTTA-CCCTAAACTTTTCTAAAAT
41280415 TATATTTTGA
Statistics
Matches: 233, Mismatches: 28, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
116 4 0.02
117 38 0.16
118 119 0.51
119 25 0.11
120 47 0.20
ACGTcount: A:0.36, C:0.22, G:0.02, T:0.40
Consensus pattern (115 bp):
AAATTACATTTTTACCCTAAACTTTTCTAAAATCACATTTTAACCCAAACCTTTTCAAAATTACA
TTTTGACCCTTAAACTTTTCCAAAATTACATTTTAACCCTAAACTTTCTA
Found at i:41292938 original size:125 final size:125
Alignment explanation
Indices: 41292657--41292941 Score: 355
Period size: 125 Copynumber: 2.3 Consensus size: 125
41292647 AGTGATGTGG
* *
41292657 TCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATAAAGCGAAACTCAATGTCAGTGAA
1 TCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATAAAGCGAAACTCAATGACAGTGAA
* * * * **
41292722 ACTTCGAACCCCCATCTTCCTGATGAGATACAAAGAAGGGGATTAAAACAAGTGATACGG
66 ACTCCAAACCCCCATCTTCCTGATGAGATACAAAGAAGGGGATCAAAACAAGTGAAACAA
* * *
41292782 TCATCTTCCTGATAAGATACAGAGAAGTAGACCAAATCAAATGAAGC-AAAGTTCAAT-ACGAGT
1 TCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATC-AATAAAGCGAAA-CTCAATGAC-AGT
** *
41292845 GAAACTCCAAACCCTTATCTTCCTGATGAGATACAAAGAAGTGGG-TCGAAACAA-T-AAAGCAA
63 GAAACTCCAAACCCCCATCTTCCTGATGAGATACAAAGAAG-GGGATCAAAACAAGTGAAA-CAA
*
41292907 TCATCTTCTTGATGAGATACAGAGAAGTAGACCAA
1 TCATCTTCCTGATGAGATACAGAGAAGTAGACCAA
41292942 GAGATGAAGC
Statistics
Matches: 139, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
124 2 0.01
125 76 0.55
126 58 0.42
127 3 0.02
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (125 bp):
TCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATAAAGCGAAACTCAATGACAGTGAA
ACTCCAAACCCCCATCTTCCTGATGAGATACAAAGAAGGGGATCAAAACAAGTGAAACAA
Found at i:41294985 original size:30 final size:29
Alignment explanation
Indices: 41294944--41295015 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 29
41294934 TTTCTAGTAG
*
41294944 GTCCCTGAACTTTCTAGAAAA-CATATTTT
1 GTCCCTAAACTTTCTA-AAAATCATATTTT
41294973 AGTCCCTAAACTTTCTAAAAATCATATTTT
1 -GTCCCTAAACTTTCTAAAAATCATATTTT
*
41295003 GACCCCTAAACTT
1 G-TCCCTAAACTT
41295016 GTCCAAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 5 0.13
30 33 0.87
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (29 bp):
GTCCCTAAACTTTCTAAAAATCATATTTT
Found at i:41295045 original size:60 final size:58
Alignment explanation
Indices: 41294980--41295319 Score: 301
Period size: 60 Copynumber: 5.8 Consensus size: 58
41294970 TTTAGTCCCT
* * * * *
41294980 AAACTTTCTAAAAATCATATTTTGACCCCTAAACTTGTCCAAAATTACATTTTGACCCTC
1 AAACTTTCTCAAAATTACATTTT-ACCCCTAAACTTTTCCAAAATCACATTTTGACCC-C
* ** * * *
41295040 GAACTTT-TCCAAAATTGTATTCTAACCCTTAAACTTTTCCAAAATCACATTTTTACCCTC
1 AAACTTTCT-CAAAATTACATT-TTACCCCTAAACTTTTCCAAAATCACATTTTGACCC-C
* * *
41295100 AAACCTTTCT-AAAAGTACATTTTAACCTCTAAACTTTTCCAAAATCACATTTTAAACCCC
1 AAA-CTTTCTCAAAATTACATTTT-ACCCCTAAACTTTTCCAAAATCACATTTT-GACCCC
* * * *
41295160 AAGCCTT-TCAAAATTACATTTTGACCCCCAAACTTCTCCAAAATCACATTTTGACCCCC
1 AAACTTTCTCAAAATTACATTTT-ACCCCTAAACTTTTCCAAAATCACATTTTGA-CCCC
* * * * * * * * *
41295219 AAACCTTCTCGAAATCACATTTTAACCCTAGACTTCTCAAAAATTACATTTT-AACCC
1 AAACTTTCTCAAAATTACATTTTACCCCTAAACTTTTCCAAAATCACATTTTGACCCC
* *
41295276 AAACTTTCCCAAAATTACATTTTACCCCTAAACTTTTCTAAAAT
1 AAACTTTCTCAAAATTACATTTTACCCCTAAACTTTTCCAAAAT
41295320 TATGTTTTGA
Statistics
Matches: 229, Mismatches: 42, Indels: 21
0.78 0.14 0.07
Matches are distributed among these distances:
57 39 0.17
58 3 0.01
59 77 0.34
60 100 0.44
61 9 0.04
62 1 0.00
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (58 bp):
AAACTTTCTCAAAATTACATTTTACCCCTAAACTTTTCCAAAATCACATTTTGACCCC
Found at i:41295319 original size:29 final size:30
Alignment explanation
Indices: 41294976--41295331 Score: 264
Period size: 30 Copynumber: 12.0 Consensus size: 30
41294966 ATATTTTAGT
* * *
41294976 CCCTAAAC-TTTCTAAAAATCATATTTTGAC
1 CCCTAAACTTTTC-CAAAATTACATTTTGAC
*
41295006 CCCTAAACTTGTCCAAAATTACATTTTGA-
1 CCCTAAACTTTTCCAAAATTACATTTTGAC
* ** * *
41295035 CCCTCGAACTTTTCCAAAATTGTATTCTAAC
1 CCCT-AAACTTTTCCAAAATTACATTTTGAC
* * *
41295066 CCTTAAACTTTTCCAAAATCACATTTTTA-
1 CCCTAAACTTTTCCAAAATTACATTTTGAC
* * * *
41295095 CCCTCAAACCTTTCTAAAAGTACATTTTAAC
1 CCCT-AAACTTTTCCAAAATTACATTTTGAC
* * *
41295126 CTCTAAACTTTTCCAAAATCACATTTTAAAC
1 CCCTAAACTTTTCCAAAATTACATTTT-GAC
* *
41295157 CCC-AAGCCTTT-CAAAATTACATTTTGAC
1 CCCTAAACTTTTCCAAAATTACATTTTGAC
* * *
41295185 CCCCAAACTTCTCCAAAATCACATTTTGAC
1 CCCTAAACTTTTCCAAAATTACATTTTGAC
* * * * *
41295215 CCCCAAAC-CTTCTCGAAATCACATTTT-AA
1 CCCTAAACTTTTC-CAAAATTACATTTTGAC
* * * *
41295244 CCCTAGACTTCTCAAAAATTACATTTT-AA
1 CCCTAAACTTTTCCAAAATTACATTTTGAC
*
41295273 CCC-AAACTTTCCCAAAATTACATTTT-AC
1 CCCTAAACTTTTCCAAAATTACATTTTGAC
* **
41295301 CCCTAAACTTTTCTAAAATTATGTTTTGAC
1 CCCTAAACTTTTCCAAAATTACATTTTGAC
41295331 C
1 C
41295332 TTGTATTCTT
Statistics
Matches: 257, Mismatches: 57, Indels: 24
0.76 0.17 0.07
Matches are distributed among these distances:
28 28 0.11
29 69 0.27
30 146 0.57
31 14 0.05
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (30 bp):
CCCTAAACTTTTCCAAAATTACATTTTGAC
Found at i:41300533 original size:3 final size:3
Alignment explanation
Indices: 41300527--41300592 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
41300517 GGTTTATGAC
41300527 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41300575 ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT
41300593 TATGTCAATT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:41301334 original size:18 final size:18
Alignment explanation
Indices: 41301295--41301330 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
41301285 TTTTTAATTG
41301295 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
41301313 TAATTAA-TTAAAATTTT
1 TAATTAATTTAAAATTTT
41301330 T
1 T
41301331 TAATCTGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:41303540 original size:14 final size:14
Alignment explanation
Indices: 41303521--41303549 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41303511 CGAATTGAAT
41303521 AATAAAAAAAAAAA
1 AATAAAAAAAAAAA
41303535 AATAAAAAAAAAAA
1 AATAAAAAAAAAAA
41303549 A
1 A
41303550 GAACATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (14 bp):
AATAAAAAAAAAAA
Found at i:41303543 original size:13 final size:13
Alignment explanation
Indices: 41303525--41303549 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41303515 TTGAATAATA
41303525 AAAAAAAAAAAAT
1 AAAAAAAAAAAAT
41303538 AAAAAAAAAAAA
1 AAAAAAAAAAAA
41303550 GAACATATTT
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:0.96, C:0.00, G:0.00, T:0.04
Consensus pattern (13 bp):
AAAAAAAAAAAAT
Found at i:41304399 original size:30 final size:30
Alignment explanation
Indices: 41304365--41304693 Score: 376
Period size: 30 Copynumber: 10.9 Consensus size: 30
41304355 AGAGGTCCTC
* * *
41304365 AAACTTTTCCAAAACTACAGTTTGACCCCT
1 AAACTTTTCCAAAATTACATTTTAACCCCT
* * *
41304395 AAACTTTTCTAAAATCATATTTTAACCCCT
1 AAACTTTTCCAAAATTACATTTTAACCCCT
*
41304425 AAACTTTTCCAAAATTACATTTTAACCCTT
1 AAACTTTTCCAAAATTACATTTTAACCCCT
*
41304455 AAAGTTTTCCAAAATTACATTTTAAGCCCC-
1 AAACTTTTCCAAAATTACATTTTAA-CCCCT
*
41304485 AAACTTTTCCAAAATTATATTTTAACCCCT
1 AAACTTTTCCAAAATTACATTTTAACCCCT
* * *
41304515 AAAGTTTTCTAAAATTACATTTTAACCTCT
1 AAACTTTTCCAAAATTACATTTTAACCCCT
* * *
41304545 AAACTTTTCTAAAATTATATTTTGACCCCT
1 AAACTTTTCCAAAATTACATTTTAACCCCT
* *
41304575 AAACTTTTCCAAAATTATATTTTAACCTCT
1 AAACTTTTCCAAAATTACATTTTAACCCCT
*
41304605 AAACTTTTTCCAAAATTACATTTTCACCTCC-
1 AAAC-TTTTCCAAAATTACATTTTAACC-CCT
* * * *
41304636 AAACTTCTCCAAAATCATATTTTGACCTCC-
1 AAACTTTTCCAAAATTACATTTTAACC-CCT
* * *
41304666 AAACTTTTCTAAAATCACATTTTGACCC
1 AAACTTTTCCAAAATTACATTTTAACCC
41304694 TCGAGCTTCT
Statistics
Matches: 260, Mismatches: 35, Indels: 9
0.86 0.12 0.03
Matches are distributed among these distances:
29 5 0.02
30 226 0.87
31 28 0.11
32 1 0.00
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.38
Consensus pattern (30 bp):
AAACTTTTCCAAAATTACATTTTAACCCCT
Found at i:41304523 original size:90 final size:90
Alignment explanation
Indices: 41304361--41304680 Score: 423
Period size: 90 Copynumber: 3.6 Consensus size: 90
41304351 CTCAAGAGGT
* * * *
41304361 CCTC-AAACTTTTCCAAAACTACAGTTTGACCCCTAAACTTTTCTAAAATCATATTTTAACCCCT
1 CCTCTAAACTTTTCCAAAATTACATTTTGACCCCTAAACTTTTCCAAAATTATATTTTAACCCCT
41304425 AAACTTTTCCAAAATTACATTTTAA
66 AAACTTTTCCAAAATTACATTTTAA
* *
41304450 CC-CTTAAAGTTTTCCAAAATTACATTTTAAGCCCC-AAACTTTTCCAAAATTATATTTTAACCC
1 CCTC-TAAACTTTTCCAAAATTACATTTTGA-CCCCTAAACTTTTCCAAAATTATATTTTAACCC
* *
41304513 CTAAAGTTTTCTAAAATTACATTTTAA
64 CTAAACTTTTCCAAAATTACATTTTAA
* * *
41304540 CCTCTAAACTTTTCTAAAATTATATTTTGACCCCTAAACTTTTCCAAAATTATATTTTAACCTCT
1 CCTCTAAACTTTTCCAAAATTACATTTTGACCCCTAAACTTTTCCAAAATTATATTTTAACCCCT
*
41304605 AAACTTTTTCCAAAATTACATTTTCA
66 AAAC-TTTTCCAAAATTACATTTTAA
* * * * *
41304631 CCTCCAAACTTCTCCAAAATCATATTTTGACCTCC-AAACTTTTCTAAAAT
1 CCTCTAAACTTTTCCAAAATTACATTTTGACC-CCTAAACTTTTCCAAAAT
41304681 CACATTTTGA
Statistics
Matches: 203, Mismatches: 21, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
88 1 0.00
89 6 0.03
90 128 0.63
91 66 0.33
92 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.38
Consensus pattern (90 bp):
CCTCTAAACTTTTCCAAAATTACATTTTGACCCCTAAACTTTTCCAAAATTATATTTTAACCCCT
AAACTTTTCCAAAATTACATTTTAA
Found at i:41310788 original size:49 final size:49
Alignment explanation
Indices: 41310716--41311092 Score: 326
Period size: 49 Copynumber: 7.7 Consensus size: 49
41310706 CAGGTTTCAT
* * **
41310716 TACCATGAAGATTTGAAGGGAAAGATTTAAGTCGCAACGGTAAATCTAG
1 TACCACGAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAG
* * * * * *
41310765 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGTAATGGCGAACCTTG
1 TACCACGAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAG
* * *
41310814 TACCTCAGAAGACATGAAGGGAAAGATTTAAGTCGCAACGGTGAATCTAG
1 TACCAC-GAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAG
** * * * * * * *
41310864 TACTGCAAAGATATGGAGGGAAAGGTTTAAGCCGTAACGGCGAACCTTG
1 TACCACGAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAG
* * * * * * *
41310913 TACCTCAGAAGACATAAAGGGAAAGATTTAAGCCACAATGGCAAATCTAG
1 TACCAC-GAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAG
* * * * *
41310963 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGTGAACCTTG
1 TACCACGAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAG
* * * * *
41311012 TAGCTCA-GAAG-CATGAAGGGAAGGATTTAAGCCGCAACGGCAAATCCAG
1 TA-C-CACGAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAG
* * *
41311061 TACCACAAAGATATGGAGGGAAAGGTTTAAGT
1 TACCACGAAGATATGAAGGGAAAGATTTAAGT
41311093 TACAATGACG
Statistics
Matches: 251, Mismatches: 71, Indels: 12
0.75 0.21 0.04
Matches are distributed among these distances:
47 2 0.01
48 4 0.02
49 162 0.65
50 81 0.32
51 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (49 bp):
TACCACGAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAG
Found at i:41310893 original size:99 final size:99
Alignment explanation
Indices: 41310729--41311092 Score: 550
Period size: 99 Copynumber: 3.7 Consensus size: 99
41310719 CATGAAGATT
* * *
41310729 TGAAGGGAAAGATTTAAGTCGCAACGGTAAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTA
1 TGAAGGGAAAGATTTAAGCCGCAACGGCAAATCTAGTACCACAAAGATATGGAGGGAAAGGTTTA
*
41310794 AGTCGTAATGGCGAACCTTGTACCTCAGAAGACA
66 AGTCGTAACGGCGAACCTTGTACCTCAGAAGACA
* ** **
41310828 TGAAGGGAAAGATTTAAGTCGCAACGGTGAATCTAGTACTGCAAAGATATGGAGGGAAAGGTTTA
1 TGAAGGGAAAGATTTAAGCCGCAACGGCAAATCTAGTACCACAAAGATATGGAGGGAAAGGTTTA
*
41310893 AGCCGTAACGGCGAACCTTGTACCTCAGAAGACA
66 AGTCGTAACGGCGAACCTTGTACCTCAGAAGACA
* * * *
41310927 TAAAGGGAAAGATTTAAGCCACAATGGCAAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTA
1 TGAAGGGAAAGATTTAAGCCGCAACGGCAAATCTAGTACCACAAAGATATGGAGGGAAAGGTTTA
* * *
41310992 AGTCGCAACGGTGAACCTTGTAGCTCAGAAG-CA
66 AGTCGTAACGGCGAACCTTGTACCTCAGAAGACA
* *
41311025 TGAAGGGAAGGATTTAAGCCGCAACGGCAAATCCAGTACCACAAAGATATGGAGGGAAAGGTTTA
1 TGAAGGGAAAGATTTAAGCCGCAACGGCAAATCTAGTACCACAAAGATATGGAGGGAAAGGTTTA
41311090 AGT
66 AGT
41311093 TACAATGACG
Statistics
Matches: 240, Mismatches: 25, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
98 64 0.27
99 176 0.73
ACGTcount: A:0.37, C:0.16, G:0.28, T:0.20
Consensus pattern (99 bp):
TGAAGGGAAAGATTTAAGCCGCAACGGCAAATCTAGTACCACAAAGATATGGAGGGAAAGGTTTA
AGTCGTAACGGCGAACCTTGTACCTCAGAAGACA
Found at i:41311064 original size:148 final size:149
Alignment explanation
Indices: 41310729--41311091 Score: 407
Period size: 148 Copynumber: 2.5 Consensus size: 149
41310719 CATGAAGATT
* * * *
41310729 TGAAGGGAAAGATTTAAGTCGCAACGGTAAATCTAGTACCAC-GAAGATATGGAGGGAAAGGTTT
1 TGAAGGGAAGGATTTAAGCCGCAACGGCAAATCCAGTACCACAGAAGATATGGAGGGAAAGGTTT
* ** * * *
41310793 AAGTCGTAATGGCGAACCTTGTACCTCAGAAGACATGAAGGGAAAGATTTAAGTCGCAACGGTGA
66 AAGCCACAATGGCAAACCTAGTACCACAGAAGACATGAAGGGAAAGATTTAAGTCGCAACGGTGA
* *
41310858 ATCTAGTACTGCAAAGATA
131 ACCTAGTACTGCAAAGACA
* * * * * * ** *
41310877 TGGAGGGAAAGG-TTTAAGCCGTAACGGCGAA-CCTTGTACCTCAGAAGACATAAAGGGAAAGAT
1 TGAAGGG-AAGGATTTAAGCCGCAACGGCAAATCC-AGTACCACAGAAGATATGGAGGGAAAGGT
* * * *
41310940 TTAAGCCACAATGGCAAATCTAGTACCAC-GAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGT
64 TTAAGCCACAATGGCAAACCTAGTACCACAGAAGACATGAAGGGAAAGATTTAAGTCGCAACGGT
*
41311004 GAACCTTGTAGCT-CAGAAG-CA
129 GAACCTAGTA-CTGCA-AAGACA
41311025 TGAAGGGAAGGATTTAAGCCGCAACGGCAAATCCAGTACCACA-AAGATATGGAGGGAAAGGTTT
1 TGAAGGGAAGGATTTAAGCCGCAACGGCAAATCCAGTACCACAGAAGATATGGAGGGAAAGGTTT
41311089 AAG
66 AAG
41311092 TTACAATGAC
Statistics
Matches: 173, Mismatches: 35, Indels: 15
0.78 0.16 0.07
Matches are distributed among these distances:
147 25 0.14
148 100 0.58
149 48 0.28
ACGTcount: A:0.37, C:0.16, G:0.28, T:0.20
Consensus pattern (149 bp):
TGAAGGGAAGGATTTAAGCCGCAACGGCAAATCCAGTACCACAGAAGATATGGAGGGAAAGGTTT
AAGCCACAATGGCAAACCTAGTACCACAGAAGACATGAAGGGAAAGATTTAAGTCGCAACGGTGA
ACCTAGTACTGCAAAGACA
Found at i:41311218 original size:49 final size:49
Alignment explanation
Indices: 41311165--41311268 Score: 136
Period size: 49 Copynumber: 2.1 Consensus size: 49
41311155 CAACGACTCT
* ** *
41311165 GATACCATGAATATACGATGGGAAAGGTTGAGGCCGCAACGGTAAACCC
1 GATACCATGAAAATACGAAAGGAAAGGTTGAGGCCGCAACGGCAAACCC
** *
41311214 GATACCATGAAAATTTGAAAGGAAAGGTTGAGGCCGCAATGGCAAACCC
1 GATACCATGAAAATACGAAAGGAAAGGTTGAGGCCGCAACGGCAAACCC
*
41311263 AATACC
1 GATACC
41311269 TTAGGAAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.38, C:0.20, G:0.26, T:0.16
Consensus pattern (49 bp):
GATACCATGAAAATACGAAAGGAAAGGTTGAGGCCGCAACGGCAAACCC
Found at i:41311622 original size:102 final size:102
Alignment explanation
Indices: 41311340--41311658 Score: 439
Period size: 102 Copynumber: 3.1 Consensus size: 102
41311330 AGATCATATC
* *
41311340 AAAAAT-AATAGCAAGTCTTTATCTCTCTGAAATTGCAGT---AGCAAGATGAAGCTTCAACATC
1 AAAAATAAATAGCAAGTCTTTATCTCTCTGAAGTTACAGTAAGAGCAAGATGAAGCTTCAACATC
*
41311401 AAATCCTATCCTCTTGAAGTTGTAGTGAAGTTGGATT
66 AAATCCTATCCTCTTGAAGTTGCAGTGAAGTTGGATT
*
41311438 AAAAACTACAATAGCAAGTCTTTATCTCTCTGAAGTTACAGTAAGAGCAAGATGAGGCTTCAACA
1 AAAAA-TA-AATAGCAAGTCTTTATCTCTCTGAAGTTACAGTAAGAGCAAGATGAAGCTTCAACA
* *
41311503 TCAAATCTTATCCTCTTGAAGTTGCAGTAAAGTTGGATT
64 TCAAATCCTATCCTCTTGAAGTTGCAGTGAAGTTGGATT
* * * **
41311542 AAAAATAAATAACAGGTCTTTATCTCTCTGAAGTTACAGTAAGAGCAATATGAAGCTTCAATGTC
1 AAAAATAAATAGCAAGTCTTTATCTCTCTGAAGTTACAGTAAGAGCAAGATGAAGCTTCAACATC
** *
41311607 AAATCCTATATTCTTGTAGTTGCAGTGAAGTTGGATT
66 AAATCCTATCCTCTTGAAGTTGCAGTGAAGTTGGATT
* * *
41311644 AGAAACAATTAGCAA
1 AAAAATAAATAGCAA
41311659 ATCTCGATTT
Statistics
Matches: 193, Mismatches: 22, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
98 5 0.03
99 1 0.01
101 31 0.16
102 94 0.49
103 2 0.01
104 60 0.31
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (102 bp):
AAAAATAAATAGCAAGTCTTTATCTCTCTGAAGTTACAGTAAGAGCAAGATGAAGCTTCAACATC
AAATCCTATCCTCTTGAAGTTGCAGTGAAGTTGGATT
Found at i:41313366 original size:30 final size:30
Alignment explanation
Indices: 41313332--41313628 Score: 216
Period size: 30 Copynumber: 10.0 Consensus size: 30
41313322 AAGAGGTACC
* * *
41313332 TAAACTTTTTAAAAACTATATTTTGACCCT
1 TAAACTTTTTCAAAATTACATTTTGACCCT
* *
41313362 TAAACTTTTCCAAAATTATATTTTGACCC-
1 TAAACTTTTTCAAAATTACATTTTGACCCT
* *
41313391 TAAAC-TTTTCTAAAATTACATTTTAACCCC
1 TAAACTTTTTC-AAAATTACATTTTGACCCT
* * *
41313421 TAAA-GTTTTCTAAAATTACATTTTAACCCC
1 TAAACTTTTTC-AAAATTACATTTTGACCCT
* * *
41313451 TAAA-GTTTTCTAAAATTACATTTTAACCCC
1 TAAACTTTTTC-AAAATTACATTTTGACCCT
* * * *
41313481 TAAACTTTTCCAAAATCATATTTTAACCCT
1 TAAACTTTTTCAAAATTACATTTTGACCCT
* * *
41313511 TAAAATTTTCCAAAATTACATTTTGACCCC
1 TAAACTTTTTCAAAATTACATTTTGACCCT
* * *
41313541 T-AA-TTTTCCAAAATCATATTTTGA-CCT
1 TAAACTTTTTCAAAATTACATTTTGACCCT
* * *
41313568 CCAAAC-TTTTCTAAAATCACATTTT-AACCT
1 -TAAACTTTTTC-AAAATTACATTTTGACCCT
* * *
41313598 ACAAACTTTTTCAAAATCATATTTTGACCCT
1 -TAAACTTTTTCAAAATTACATTTTGACCCT
41313629 CGAGCTTCTC
Statistics
Matches: 231, Mismatches: 25, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
27 2 0.01
28 23 0.10
29 30 0.13
30 163 0.71
31 13 0.06
ACGTcount: A:0.36, C:0.22, G:0.02, T:0.40
Consensus pattern (30 bp):
TAAACTTTTTCAAAATTACATTTTGACCCT
Found at i:41313504 original size:90 final size:89
Alignment explanation
Indices: 41313351--41313627 Score: 339
Period size: 88 Copynumber: 3.1 Consensus size: 89
41313341 TAAAAACTAT
* *
41313351 ATTTTGACCCTTAAACTTTTCCAAAATTATATTTTGA-CCCTAAACTTTTCTAAAATTACATTTT
1 ATTTTGACCCCTAAA-TTTTCCAAAATTATATTTTGACCCCTAAACTTTTCTAAAATCACATTTT
* *
41313415 AACCCCTAAAGTTTTCTAAAATTAC
65 AACCCCTAAAATTTTCCAAAATTAC
* * * * * *
41313440 ATTTTAACCCCTAAAGTTTTCTAAAATTACATTTTAACCCCTAAACTTTTCCAAAATCATATTTT
1 ATTTTGACCCCTAAA-TTTTCCAAAATTATATTTTGACCCCTAAACTTTTCTAAAATCACATTTT
*
41313505 AACCCTTAAAATTTTCCAAAATTAC
65 AACCCCTAAAATTTTCCAAAATTAC
*
41313530 ATTTTGACCCCT-AATTTTCCAAAATCATATTTTGACCTCC-AAACTTTTCTAAAATCACATTTT
1 ATTTTGACCCCTAAATTTTCCAAAATTATATTTTGACC-CCTAAACTTTTCTAAAATCACATTTT
* * *
41313593 AA--CCTACAAACTTTTTCAAAATCAT
65 AACCCCTA-AAA-TTTTCCAAAATTAC
41313618 ATTTTGACCC
1 ATTTTGACCC
41313628 TCGAGCTTCT
Statistics
Matches: 161, Mismatches: 23, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
86 3 0.02
87 3 0.02
88 63 0.39
89 35 0.22
90 57 0.35
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (89 bp):
ATTTTGACCCCTAAATTTTCCAAAATTATATTTTGACCCCTAAACTTTTCTAAAATCACATTTTA
ACCCCTAAAATTTTCCAAAATTAC
Found at i:41313641 original size:60 final size:60
Alignment explanation
Indices: 41313333--41313652 Score: 348
Period size: 60 Copynumber: 5.4 Consensus size: 60
41313323 AGAGGTACCT
* * * * *
41313333 AAACTTTT-TAAAAACTATATTTTGACCCTTAAACTTTTCCAAAATTATATTTTGACCCT-
1 AAACTTTTCT-AAAATTACATTTTAACCCCTAAACTTTTCCAAAATCATATTTTGACCCTC
* * * * *
41313392 AAACTTTTCTAAAATTACATTTTAACCCCTAAAGTTTTCTAAAATTACATTTTAACCC-C
1 AAACTTTTCTAAAATTACATTTTAACCCCTAAACTTTTCCAAAATCATATTTTGACCCTC
* * *
41313451 TAAAGTTTTCTAAAATTACATTTTAACCCCTAAACTTTTCCAAAATCATATTTTAACCCTT
1 -AAACTTTTCTAAAATTACATTTTAACCCCTAAACTTTTCCAAAATCATATTTTGACCCTC
* * *
41313512 AAAATTTTCCAAAATTACATTTTGACCCCT-AA-TTTTCCAAAATCATATTTTGA-CCTCC
1 AAACTTTTCTAAAATTACATTTTAACCCCTAAACTTTTCCAAAATCATATTTTGACCCT-C
* * *
41313570 AAACTTTTCTAAAATCACATTTTAACCTAC-AAACTTTTTCAAAATCATATTTTGACCCTC
1 AAACTTTTCTAAAATTACATTTTAACC-CCTAAACTTTTCCAAAATCATATTTTGACCCTC
* * * *
41313630 GAGCTTCTCTAAAATTTCATTTT
1 AAACTTTTCTAAAATTACATTTT
41313653 CATCTCGAGT
Statistics
Matches: 222, Mismatches: 30, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
57 3 0.01
58 43 0.19
59 53 0.24
60 120 0.54
61 3 0.01
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (60 bp):
AAACTTTTCTAAAATTACATTTTAACCCCTAAACTTTTCCAAAATCATATTTTGACCCTC
Found at i:41313644 original size:118 final size:119
Alignment explanation
Indices: 41313330--41313652 Score: 370
Period size: 118 Copynumber: 2.7 Consensus size: 119
41313320 TCAAGAGGTA
* * * *
41313330 CCTAAACTTTT-TAAAAACTATATTTTGACC-CTTAAACTTTTCCAAAATTATATTTTGACCCTA
1 CCTAAACTTTTCTAAAATC-ACATTTTAACCAC-TAAACTTTTCCAAAATCATATTTTGACCCTA
* *
41313393 AACTTTTCTAAAATTACATTTTAACCCCTAAAGTTTTCTAAAATTACATTTTAACC
64 AACTTTTCTAAAATTACATTTTAACCCCTAAAGTTTTCCAAAATCACATTTTAACC
* * * *
41313449 CCTAAAGTTTTCTAAAATTACATTTTAACCCCTAAACTTTTCCAAAATCATATTTTAACCCTTAA
1 CCTAAACTTTTCTAAAATCACATTTTAACCACTAAACTTTTCCAAAATCATATTTTGACCC-TAA
* * * * *
41313514 AATTTTCCAAAATTACATTTTGACCCCT-AA-TTTTCCAAAATCATATTTTGACC
65 ACTTTTCTAAAATTACATTTTAACCCCTAAAGTTTTCCAAAATCACATTTTAACC
*
41313567 TCC-AAACTTTTCTAAAATCACATTTTAACCTAC-AAACTTTTTCAAAATCATATTTTGACCCTC
1 -CCTAAACTTTTCTAAAATCACATTTTAACC-ACTAAACTTTTCCAAAATCATATTTTGACCCT-
* * * *
41313630 GAGCTTCTCTAAAATTTCATTTT
63 AAACTTTTCTAAAATTACATTTT
41313653 CATCTCGAGT
Statistics
Matches: 173, Mismatches: 25, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
117 1 0.01
118 87 0.50
119 51 0.29
120 34 0.20
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (119 bp):
CCTAAACTTTTCTAAAATCACATTTTAACCACTAAACTTTTCCAAAATCATATTTTGACCCTAAA
CTTTTCTAAAATTACATTTTAACCCCTAAAGTTTTCCAAAATCACATTTTAACC
Found at i:41315355 original size:62 final size:62
Alignment explanation
Indices: 41315258--41315383 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 62
41315248 TTTCTATGTA
*
41315258 AAAATTTTCAAAGATTGTAACTTTCCTTTTAAAGTTATCAATAAACTTAAATCCAAATTTTC
1 AAAATATTCAAAGATTGTAACTTTCCTTTTAAAGTTATCAATAAACTTAAATCCAAATTTTC
41315320 AAAATATTCAAAGATTGTAACTTTCCTTTTAAAGTTATCAATAAACTTAAATCCAAATTTTC
1 AAAATATTCAAAGATTGTAACTTTCCTTTTAAAGTTATCAATAAACTTAAATCCAAATTTTC
41315382 AA
1 AA
41315384 GTCTAACTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.39
Consensus pattern (62 bp):
AAAATATTCAAAGATTGTAACTTTCCTTTTAAAGTTATCAATAAACTTAAATCCAAATTTTC
Found at i:41316301 original size:22 final size:22
Alignment explanation
Indices: 41316248--41316301 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
41316238 CATCAAGTTC
**
41316248 AATTTTAATTCTATTCTAAAAT
1 AATTTTAAAACTATTCTAAAAT
41316270 -ATTTTAAAAACTATT-TAAATAT
1 AATTTT-AAAACTATTCTAAA-AT
41316292 AATTTTAAAA
1 AATTTTAAAA
41316302 GAAGATAGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 9 0.33
22 13 0.48
23 5 0.19
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (22 bp):
AATTTTAAAACTATTCTAAAAT
Found at i:41318362 original size:16 final size:16
Alignment explanation
Indices: 41318341--41318372 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41318331 TAAATTATAT
*
41318341 TTAAAAAATATATAAA
1 TTAAAAAACATATAAA
41318357 TTAAAAAACATATAAA
1 TTAAAAAACATATAAA
41318373 AATAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
TTAAAAAACATATAAA
Found at i:41318369 original size:18 final size:16
Alignment explanation
Indices: 41318343--41318382 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
41318333 AATTATATTT
*
41318343 AAAAAATATATAAATTA
1 AAAAAATATA-AAAATA
41318360 AAAAACATATAAAAATA
1 AAAAA-ATATAAAAATA
41318377 AAAAAA
1 AAAAAA
41318383 ATTAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 15 0.71
18 5 0.24
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (16 bp):
AAAAAATATAAAAATA
Found at i:41318379 original size:16 final size:16
Alignment explanation
Indices: 41318342--41318381 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
41318332 AAATTATATT
*
41318342 TAAAAAATATATAAAT
1 TAAAAAATATATAAAA
*
41318358 TAAAAAACATATAAAAA
1 TAAAAAATATAT-AAAA
41318375 TAAAAAA
1 TAAAAAA
41318382 AATTAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
TAAAAAATATATAAAA
Found at i:41319752 original size:14 final size:16
Alignment explanation
Indices: 41319729--41319760 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
41319719 TATTGTTTGA
41319729 TTTGATTTTAAA-AAT
1 TTTGATTTTAAAGAAT
41319744 TTTGA-TTTAAAGAAT
1 TTTGATTTTAAAGAAT
41319759 TT
1 TT
41319761 AAACCAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (16 bp):
TTTGATTTTAAAGAAT
Found at i:41339746 original size:39 final size:39
Alignment explanation
Indices: 41339659--41339757 Score: 119
Period size: 39 Copynumber: 2.5 Consensus size: 39
41339649 ATTATTCTAA
* *
41339659 TGCAGTGTTTACAGTGTCACTGCCAGTTTAGCATTGAGT
1 TGCAGTGTTTATAGTGTCACTGCCAGTTTAGCATTGAAT
* * *
41339698 TGTAGTGTTTATAGTGTCACTGGCAGTTTAGTATT-ATAT
1 TGCAGTGTTTATAGTGTCACTGCCAGTTTAGCATTGA-AT
*
41339737 TGCAATGTTTTATAGTGTCAC
1 TGCAGTG-TTTATAGTGTCAC
41339758 GCTGTTGAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.02
39 37 0.73
40 13 0.25
ACGTcount: A:0.22, C:0.13, G:0.23, T:0.41
Consensus pattern (39 bp):
TGCAGTGTTTATAGTGTCACTGCCAGTTTAGCATTGAAT
Found at i:41340898 original size:13 final size:13
Alignment explanation
Indices: 41340864--41340913 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 13
41340854 AAATGGCATG
41340864 AAAATAAATAACAAC
1 AAAATAAAT-A-AAC
*
41340879 AAGATAAATAAAC
1 AAAATAAATAAAC
*
41340892 AAAATAAATAAATA
1 AAAATAAATAAA-C
41340906 AAAATAAA
1 AAAATAAA
41340914 AATTAAATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 14 0.45
14 9 0.29
15 8 0.26
ACGTcount: A:0.76, C:0.06, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAATAAATAAAC
Found at i:41340921 original size:17 final size:17
Alignment explanation
Indices: 41340865--41340907 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
41340855 AATGGCATGA
*
41340865 AAATAAAT-AACAACA-
1 AAATAAATAAACAAAAT
*
41340880 AGATAAATAAACAAAAT
1 AAATAAATAAACAAAAT
41340897 AAATAAATAAA
1 AAATAAATAAA
41340908 AATAAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 7 0.30
16 6 0.26
17 10 0.43
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.16
Consensus pattern (17 bp):
AAATAAATAAACAAAAT
Found at i:41341027 original size:20 final size:20
Alignment explanation
Indices: 41341003--41341055 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
41340993 AAGTAAAAAA
*
41341003 AAAAATAATAAATTAAATAT
1 AAAAATAATAAACTAAATAT
*
41341023 CAAAATAA-ACAACTAAATAT
1 AAAAATAATA-AACTAAATAT
41341043 AAATAATAATAAA
1 AAA-AATAATAAA
41341056 AAGGAAGACG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 1 0.04
20 18 0.67
21 7 0.26
22 1 0.04
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.25
Consensus pattern (20 bp):
AAAAATAATAAACTAAATAT
Found at i:41341323 original size:22 final size:23
Alignment explanation
Indices: 41341292--41341344 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
41341282 AATCTTATTT
41341292 AAAAAAA-T-TCCTCTCTAAACA
1 AAAAAAATTCTCCTCTCTAAACA
41341313 AAAATAAATTCTCCTCTCTAAACA
1 AAAA-AAATTCTCCTCTCTAAACA
41341337 AAACAAAA
1 AAA-AAAA
41341345 AAAATCCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.14
22 3 0.11
23 1 0.04
24 19 0.68
25 1 0.04
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.23
Consensus pattern (23 bp):
AAAAAAATTCTCCTCTCTAAACA
Found at i:41342060 original size:14 final size:14
Alignment explanation
Indices: 41342041--41342067 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41342031 AGGCAAAATT
41342041 GGAAAATTGCAGAG
1 GGAAAATTGCAGAG
41342055 GGAAAATTGCAGA
1 GGAAAATTGCAGA
41342068 AAACGAGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.33, T:0.15
Consensus pattern (14 bp):
GGAAAATTGCAGAG
Found at i:41343709 original size:21 final size:21
Alignment explanation
Indices: 41343672--41343722 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
41343662 TTATTGCTTT
*
41343672 TTTCATTATGTTTTCA-TTTAA
1 TTTCATT-TGGTTTCATTTTAA
41343693 CTTTCATTTGGTTTCATTTTAA
1 -TTTCATTTGGTTTCATTTTAA
41343715 TTTCATTT
1 TTTCATTT
41343723 CGTGACACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.20, C:0.12, G:0.06, T:0.63
Consensus pattern (21 bp):
TTTCATTTGGTTTCATTTTAA
Found at i:41344585 original size:32 final size:32
Alignment explanation
Indices: 41344548--41344643 Score: 165
Period size: 32 Copynumber: 3.0 Consensus size: 32
41344538 GTAGATGATA
* *
41344548 GAGTAGTGAATCTATCGTTATCTGACTCAGAT
1 GAGTAGTGAATCTATCGTTTTTTGACTCAGAT
41344580 GAGTAGTGAATCTATCGTTTTTTGACTCAGAT
1 GAGTAGTGAATCTATCGTTTTTTGACTCAGAT
*
41344612 GAGTAGTGAATCTGTCGTTTTTTGACTCAGAT
1 GAGTAGTGAATCTATCGTTTTTTGACTCAGAT
41344644 ATCAATAATA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.39
Consensus pattern (32 bp):
GAGTAGTGAATCTATCGTTTTTTGACTCAGAT
Found at i:41348895 original size:78 final size:79
Alignment explanation
Indices: 41348760--41348957 Score: 239
Period size: 78 Copynumber: 2.5 Consensus size: 79
41348750 TAAAATTTAA
* * * * *
41348760 AATCTCGAACC-TTAAATCCTAAGCTTAGAACCTCAAA-TCTTAAAATCATGGATACTAAAC-CC
1 AATCTCAAACCTTTAAATCCTAAACATA-AACCTCAAACTCTTAAAACCATGGATACTAAACTAC
*
41348822 TAAACTCGTAAACTAT
65 -AAACTCATAAACTAT
* *
41348838 AATCTCAAACCTTTAAATCATAAACATAAACCCCAAACTC-TAAAACCAT-GATCACTAAACTAC
1 AATCTCAAACCTTTAAATCCTAAACATAAACCTCAAACTCTTAAAACCATGGAT-ACTAAACTAC
41348901 AAACTCATAAACTAT
65 AAACTCATAAACTAT
41348916 AATCTCAAA-CTCTTAAATCCTAAACATAAACCTCAAAC-CTTA
1 AATCTCAAACCT-TTAAATCCTAAACATAAACCTCAAACTCTTA
41348958 GACCTTATAT
Statistics
Matches: 104, Mismatches: 10, Indels: 12
0.83 0.08 0.10
Matches are distributed among these distances:
77 6 0.06
78 82 0.79
79 16 0.15
ACGTcount: A:0.45, C:0.26, G:0.04, T:0.25
Consensus pattern (79 bp):
AATCTCAAACCTTTAAATCCTAAACATAAACCTCAAACTCTTAAAACCATGGATACTAAACTACA
AACTCATAAACTAT
Found at i:41349813 original size:18 final size:18
Alignment explanation
Indices: 41349726--41349813 Score: 67
Period size: 18 Copynumber: 5.1 Consensus size: 18
41349716 TTTTTGAGCC
* *
41349726 TATTTTTTATTTAAAAAA
1 TATTTTTTATCTCAAAAA
* *
41349744 TATTTTTTCTCTCAAAAG
1 TATTTTTTATCTCAAAAA
* * *
41349762 TA--ATTTAT-TGAATAA
1 TATTTTTTATCTCAAAAA
*
41349777 TA-TTTTTATCCCAAAAA
1 TATTTTTTATCTCAAAAA
*
41349794 TATTTTTTATCTCAATAA
1 TATTTTTTATCTCAAAAA
41349812 TA
1 TA
41349814 CTTCTTAAAA
Statistics
Matches: 52, Mismatches: 15, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
15 6 0.12
16 9 0.17
17 6 0.12
18 31 0.60
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (18 bp):
TATTTTTTATCTCAAAAA
Found at i:41350155 original size:16 final size:16
Alignment explanation
Indices: 41350123--41350157 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
41350113 TATTTTTATT
* *
41350123 AATTTAAAAATTTTAA
1 AATTTAAAAAGTCTAA
41350139 AATTTAAAAAGTCTAA
1 AATTTAAAAAGTCTAA
41350155 AAT
1 AAT
41350158 GGAAAATTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (16 bp):
AATTTAAAAAGTCTAA
Found at i:41352760 original size:20 final size:20
Alignment explanation
Indices: 41352737--41352775 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41352727 AAATAGTTTT
*
41352737 AATATTTTTATATTTTTAAA
1 AATATTTTTATAATTTTAAA
*
41352757 AATATTTTTTTAATTTTAA
1 AATATTTTTATAATTTTAA
41352776 GAATTCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
AATATTTTTATAATTTTAAA
Found at i:41355123 original size:11 final size:12
Alignment explanation
Indices: 41355090--41355125 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
41355080 CATGCATAAA
41355090 ATGGTTTATTTT
1 ATGGTTTATTTT
41355102 ATGGTTTATTTT
1 ATGGTTTATTTT
41355114 ATGG-TTATTTT
1 ATGGTTTATTTT
41355125 A
1 A
41355126 ACATAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.19, C:0.00, G:0.17, T:0.64
Consensus pattern (12 bp):
ATGGTTTATTTT
Found at i:41355241 original size:22 final size:22
Alignment explanation
Indices: 41355216--41355268 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
41355206 TAATATAAAA
*
41355216 TATTTCATTA-ATAATTTGGGTT
1 TATTTAATTATATAA-TTGGGTT
*
41355238 TATTTAATTATTTAATTGGGTT
1 TATTTAATTATATAATTGGGTT
*
41355260 AATTTAATT
1 TATTTAATT
41355269 CTTTGGTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 24 0.89
23 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (22 bp):
TATTTAATTATATAATTGGGTT
Found at i:41358430 original size:18 final size:18
Alignment explanation
Indices: 41358407--41358453 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
41358397 TTAAATTGAT
41358407 TTTAAATTAATTTTTAAA
1 TTTAAATTAATTTTTAAA
41358425 TTTAAATT--TGTTTTAAA
1 TTTAAATTAAT-TTTTAAA
41358442 TTTGAAA-TAATT
1 TTT-AAATTAATT
41358454 CTAAACTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 1 0.04
17 11 0.44
18 12 0.48
19 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (18 bp):
TTTAAATTAATTTTTAAA
Found at i:41360339 original size:29 final size:29
Alignment explanation
Indices: 41360293--41360618 Score: 311
Period size: 29 Copynumber: 11.2 Consensus size: 29
41360283 TTTTGGTTTT
*
41360293 ATTTTTGACCC-CAAAACTTCCAAAAAATAC
1 ATTTTT-ACCCTC-AAACTTCCAAAAATTAC
* *
41360323 ATTTTTACCCTCGAACTTCCAAAAATTCC
1 ATTTTTACCCTCAAACTTCCAAAAATTAC
*
41360352 ATTTTTAACCTCGAAACTTCCAAAAATTAC
1 ATTTTTACCCTC-AAACTTCCAAAAATTAC
*
41360382 ATTTTTACCCTTAAACTTCCAAAAATTAC
1 ATTTTTACCCTCAAACTTCCAAAAATTAC
* * *
41360411 ATTTTTATCCTCAAACTTCTAAAAATTTC
1 ATTTTTACCCTCAAACTTCCAAAAATTAC
* *
41360440 ATTTTAACCC-CAAAACTTTC-AAAATTAC
1 ATTTTTACCCTC-AAACTTCCAAAAATTAC
** *
41360468 ATTTTTACCCTTGAACTTCCAAAAATTCC
1 ATTTTTACCCTCAAACTTCCAAAAATTAC
* * * *
41360497 ACTTTGACCTTAAAACTTCCAAAAATTAC
1 ATTTTTACCCTCAAACTTCCAAAAATTAC
* * *
41360526 ATTTTTACCCCCAAAATTCCAAAAATTCC
1 ATTTTTACCCTCAAACTTCCAAAAATTAC
* * *
41360555 ATTTTTTACCATGAAACTTGC-AAAATTAC
1 A-TTTTTACCCTCAAACTTCCAAAAATTAC
** * * *
41360584 CCTTTTACCCTCGAA-TGTTCAAAAATTTC
1 ATTTTTACCCTCAAACT-TCCAAAAATTAC
41360613 ATTTTT
1 ATTTTT
41360619 GATCCCGATT
Statistics
Matches: 238, Mismatches: 50, Indels: 17
0.78 0.16 0.06
Matches are distributed among these distances:
27 1 0.00
28 35 0.15
29 156 0.66
30 46 0.19
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.36
Consensus pattern (29 bp):
ATTTTTACCCTCAAACTTCCAAAAATTAC
Found at i:41360637 original size:29 final size:29
Alignment explanation
Indices: 41360605--41360707 Score: 75
Period size: 29 Copynumber: 3.5 Consensus size: 29
41360595 CGAATGTTCA
*
41360605 AAAATTTCATTTTTGATCCCGATTTTTCT
1 AAAATTTCATTTTTGATCCCAATTTTTCT
* * * *
41360634 AAAAATT-ATTGTTTGACCCCCAA-ATGTCT
1 AAAATTTCATT-TTTGA-TCCCAATTTTTCT
* * *
41360663 AAAATGTCATTTTTGACTCCAAATTTTTCC
1 AAAATTTCATTTTTGA-TCCCAATTTTTCT
* *
41360693 AAAATTACAATTTTG
1 AAAATTTCATTTTTG
41360708 CTCTCTAGTA
Statistics
Matches: 55, Mismatches: 15, Indels: 7
0.71 0.19 0.09
Matches are distributed among these distances:
28 3 0.05
29 30 0.55
30 22 0.40
ACGTcount: A:0.32, C:0.17, G:0.08, T:0.43
Consensus pattern (29 bp):
AAAATTTCATTTTTGATCCCAATTTTTCT
Found at i:41362798 original size:51 final size:51
Alignment explanation
Indices: 41362687--41362919 Score: 249
Period size: 51 Copynumber: 4.6 Consensus size: 51
41362677 TTTCATTTAA
* * ** *
41362687 TACTCACGATGACA-TATAGTCATCGGACCTCTTGTTCCGTATAGGAATTCA--
1 TACTCACGATGACACT-TAGTCATCAGA-CTTTTAATCCGTAAAGG-ATTCATT
* * * * *
41362738 TACTCACGATGACACTGAGTCATC-GAACCTTTAATCCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCAG-ACTTTTAATCCGTAAAGGATTCATT
* * * * *
41362789 TGCTTACGATCACACTTAGTCGTCAGATTTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCAGACTTTTAATCCGTAAAGGATTCATT
*
41362840 TACTCACGATGACACTTAGTCATCAGACTTTTAATCTGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCAGACTTTTAATCCGTAAAGGATTCATT
*
41362891 TACTCACGATGACACTTAGTCATCGGACT
1 TACTCACGATGACACTTAGTCATCAGACT
41362920 CTTTCGTTTA
Statistics
Matches: 151, Mismatches: 26, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
49 5 0.03
50 10 0.07
51 134 0.89
52 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCAGACTTTTAATCCGTAAAGGATTCATT
Found at i:41370045 original size:51 final size:51
Alignment explanation
Indices: 41369939--41370117 Score: 157
Period size: 51 Copynumber: 3.5 Consensus size: 51
41369929 TTTCATTTAA
* ** * * *
41369939 TACTCACGATGACA-TATAGTCATTGGACCTCTTGTTCCGTATAGAAATTCA--
1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCATAAAG-GATTCATT
* * *
41369990 TACTCATGATGACACTAAGTCATCGGACCTTTAATCCATAATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
** * *** *
41370041 TACTCACGATGACACTTAGTCATCAAACTTTTAATTTGTAAAGGATTTATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
*
41370092 TACTCACGATGACACTTAGTTATCGG
1 TACTCACGATGACACTTAGTCATCGG
41370118 GCTTTTTCAT
Statistics
Matches: 103, Mismatches: 22, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
49 5 0.05
50 8 0.08
51 89 0.86
52 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.35
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
Found at i:41370123 original size:51 final size:51
Alignment explanation
Indices: 41369990--41370123 Score: 160
Period size: 51 Copynumber: 2.6 Consensus size: 51
41369980 TAGAAATTCA
* * * *
41369990 TACTCATGATGACACTAAGTCATCGGACCTTTAATCCATAATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACTTTTAATCCATAAAGGATTCATT
** *** *
41370041 TACTCACGATGACACTTAGTCATCAAACTTTTAATTTGTAAAGGATTTATT
1 TACTCACGATGACACTTAGTCATCGGACTTTTAATCCATAAAGGATTCATT
* *
41370092 TACTCACGATGACACTTAGTTATCGGGCTTTT
1 TACTCACGATGACACTTAGTCATCGGACTTTT
41370124 TCATTTATAG
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 69 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACTTTTAATCCATAAAGGATTCATT
Found at i:41377702 original size:39 final size:39
Alignment explanation
Indices: 41377635--41377742 Score: 128
Period size: 39 Copynumber: 2.8 Consensus size: 39
41377625 ACGTCGAAAG
* * * *
41377635 TATACCGAACTGGCAGTGACATTATAAACACTGTAAT-C
1 TATACTGAACTGGCAGTGACACTGTAAACACTGCAATGC
*
41377673 TTATATTGAACTGGCAGTGACACTGTAAACACTGCAATGC
1 -TATACTGAACTGGCAGTGACACTGTAAACACTGCAATGC
* **
41377713 TATACTAAACTGGTGGTGACACTGTAAACA
1 TATACTGAACTGGCAGTGACACTGTAAACA
41377743 TCGTAATATA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
39 58 0.98
40 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (39 bp):
TATACTGAACTGGCAGTGACACTGTAAACACTGCAATGC
Found at i:41383994 original size:18 final size:18
Alignment explanation
Indices: 41383971--41384007 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
41383961 TTGGATAATG
41383971 AATGAACTACTATGATGA
1 AATGAACTACTATGATGA
**
41383989 AATGAACTGTTATGATGA
1 AATGAACTACTATGATGA
41384007 A
1 A
41384008 CCTTCCACCT
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:0.43, C:0.08, G:0.19, T:0.30
Consensus pattern (18 bp):
AATGAACTACTATGATGA
Found at i:41384216 original size:39 final size:39
Alignment explanation
Indices: 41384024--41384209 Score: 212
Period size: 39 Copynumber: 4.8 Consensus size: 39
41384014 ACCTTGAAAG
* * * *
41384024 TATACTGAATTAGCAGTGACACTGTAAACACTGTAAAGC
1 TATACTGAACTGGCAGTGACACTGTAAACACTGCAATGC
* * *
41384063 TATACTGAACTGGCAATGCCACTGTAAACACTTCAATGC
1 TATACTGAACTGGCAGTGACACTGTAAACACTGCAATGC
* ** *
41384102 TATACTGAACTGACAAAGACACTGTAAACACTGCAATGT
1 TATACTGAACTGGCAGTGACACTGTAAACACTGCAATGC
* * * *
41384141 TATAATGAACTGGCAGTGACACTATAAATAATGCAATGC
1 TATACTGAACTGGCAGTGACACTGTAAACACTGCAATGC
*
41384180 TATACTGAACT-GCTGGTGACACTGTAAACA
1 TATACTGAACTGGC-AGTGACACTGTAAACA
41384210 TCGCAATACA
Statistics
Matches: 122, Mismatches: 24, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
38 2 0.02
39 120 0.98
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (39 bp):
TATACTGAACTGGCAGTGACACTGTAAACACTGCAATGC
Found at i:41390934 original size:39 final size:39
Alignment explanation
Indices: 41390891--41390977 Score: 129
Period size: 39 Copynumber: 2.2 Consensus size: 39
41390881 ACCTCGGAAG
* * * * *
41390891 TATACTGAACTGGTAGTGACATTGTAAACACTGCAATGT
1 TATACTGAACTGGCAATGACACTATAAACACTGCAATGC
41390930 TATACTGAACTGGCAATGACACTATAAACACTGCAATGC
1 TATACTGAACTGGCAATGACACTATAAACACTGCAATGC
41390969 TATACTGAA
1 TATACTGAA
41390978 TTACCGATCT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (39 bp):
TATACTGAACTGGCAATGACACTATAAACACTGCAATGC
Found at i:41395326 original size:94 final size:94
Alignment explanation
Indices: 41395146--41395458 Score: 362
Period size: 94 Copynumber: 3.4 Consensus size: 94
41395136 ATTGTCTCTA
* * *
41395146 TTACCAGTATACGATGCTGCTCACGCTAAGCTGATGAGGACTCGTAACATATGTGGTACCTTAGC
1 TTACCAGAATACGATGCTGCTCACACTAAGCTGATGAGGACTCGTAACATATGAGGTACCTTAGC
* * *
41395211 CATCGATACAGTATATGTACATGTAATTG
66 CATCGATACGGTATATATACATATAATTG
* * * * * * *
41395240 TTACTAGAATACGATGCTACTCACACTAAGCTGACGAGAACTCGTAACATATGCGATACCTCAGC
1 TTACCAGAATACGATGCTGCTCACACTAAGCTGATGAGGACTCGTAACATATGAGGTACCTTAGC
*
41395305 CATCGATACGGTATCTATACATATAATTG
66 CATCGATACGGTATATATACATATAATTG
* * * * *
41395334 TTACCAGTATACGATGTTGCTCATACTAAGCTGATGAGGACTCGCAACATATGAGGTACCTTAAC
1 TTACCAGAATACGATGCTGCTCACACTAAGCTGATGAGGACTCGTAACATATGAGGTACCTTAGC
* * * * *
41395399 CATCGATATGGTATTTGTACATATAACTA
66 CATCGATACGGTATATATACATATAATTG
** *
41395428 TT-CC-CTA-ACGATGTTGCTCACACTAAGCTGA
1 TTACCAGAATACGATGCTGCTCACACTAAGCTGA
41395459 CGGGAATATG
Statistics
Matches: 187, Mismatches: 32, Indels: 3
0.84 0.14 0.01
Matches are distributed among these distances:
91 23 0.12
92 2 0.01
93 2 0.01
94 160 0.86
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (94 bp):
TTACCAGAATACGATGCTGCTCACACTAAGCTGATGAGGACTCGTAACATATGAGGTACCTTAGC
CATCGATACGGTATATATACATATAATTG
Found at i:41399313 original size:29 final size:30
Alignment explanation
Indices: 41399262--41399326 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
41399252 AGTTTATATT
*
41399262 TTTTATAATTTTTAAAAGATTAAATTATAA
1 TTTTATAATTTTTAAAAGATTAAAGTATAA
* * *
41399292 TTTTATAA-TTTTAAGAGGTTAAAGTGTAA
1 TTTTATAATTTTTAAAAGATTAAAGTATAA
41399321 TTTTAT
1 TTTTAT
41399327 TTTTATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (30 bp):
TTTTATAATTTTTAAAAGATTAAAGTATAA
Found at i:41400434 original size:12 final size:12
Alignment explanation
Indices: 41400426--41400460 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
41400416 TTATTCCTCG
41400426 TTCTATTCCTTA
1 TTCTATTCCTTA
*
41400438 TTCTATTACTTA
1 TTCTATTCCTTA
41400450 TTCTATTCCTT
1 TTCTATTCCTT
41400461 GTAACAAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.17, C:0.23, G:0.00, T:0.60
Consensus pattern (12 bp):
TTCTATTCCTTA
Found at i:41401563 original size:42 final size:43
Alignment explanation
Indices: 41401471--41401870 Score: 448
Period size: 43 Copynumber: 9.2 Consensus size: 43
41401461 AAAGATAACT
* *
41401471 CCGCTATAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAATG
1 CCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACG
*
41401514 CCGCTAAAGAACATGGTCTTTAGCGACGC-TTTCCCACAAACG
1 CCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACG
* * * *
41401556 CCACTAAAGAACAT-GTCTTTAGCGGCACTTTTCCTACAAATG
1 CCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACG
* *
41401598 CCGCTAAAGAACATGATCTTTAGCGGCGC-TTTCTCCACAAAGG
1 CCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTC-CCACAAACG
* *
41401641 CCGCAAAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAACG
1 CCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACG
* * * *
41401684 CCGCTAAAGAACATGGTCTTTAGCGACTCTTTTCTCACAAATG
1 CCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACG
* * * * *
41401727 CCGGTAAAGAACATGATCTTTAGCAGCGCTTTTGCCACAAACA
1 CCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACG
* *
41401770 CCGCTAAAGATCATGGTCTTTAGATCTTTAGCGGCGC-TTTCCCATAAACG
1 CCGCTAAAGAACAT-G------G-TCTTTAGCGGCGCTTTTCCCACAAACG
* * * * *
41401820 CCGCTAAAGAACACGATCTTTAGCGACGCTTTTCCTAAAAACG
1 CCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACG
41401863 CCGCTAAA
1 CCGCTAAA
41401871 TTAACAAATT
Statistics
Matches: 299, Mismatches: 45, Indels: 26
0.81 0.12 0.07
Matches are distributed among these distances:
41 12 0.04
42 65 0.22
43 183 0.61
44 4 0.01
49 1 0.00
50 22 0.07
51 12 0.04
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.25
Consensus pattern (43 bp):
CCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACG
Found at i:41401842 original size:50 final size:51
Alignment explanation
Indices: 41401741--41401842 Score: 134
Period size: 50 Copynumber: 2.0 Consensus size: 51
41401731 TAAAGAACAT
* * * *
41401741 GATCTTTAGCAGCGCTTTTGCCACAAACACCGCTAAAGATCATGGTCTTTA
1 GATCTTTAGCAGCGCTTTTCCCACAAACACCGCTAAAGAACACGATCTTTA
* * *
41401792 GATCTTTAGCGGCGC-TTTCCCATAAACGCCGCTAAAGAACACGATCTTTA
1 GATCTTTAGCAGCGCTTTTCCCACAAACACCGCTAAAGAACACGATCTTTA
41401842 G
1 G
41401843 CGACGCTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
50 30 0.68
51 14 0.32
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.27
Consensus pattern (51 bp):
GATCTTTAGCAGCGCTTTTCCCACAAACACCGCTAAAGAACACGATCTTTA
Found at i:41409839 original size:168 final size:168
Alignment explanation
Indices: 41409573--41409894 Score: 545
Period size: 168 Copynumber: 1.9 Consensus size: 168
41409563 AGACATTTAT
* * * * **
41409573 GGGAATTAGCTTATCCATCCTCGGAATAATACTATAAGAATCAGTACTGAACATCCCTCCTGTAA
1 GGGAATTAGCTTATCCACCCCCCGAATAATACTATAAGAATCAGTACTAAACATCCCTCCTACAA
*
41409638 TTGTACACGCGCCCATAGCAATAACATATTTAGGTTCGGGTATTTGTTCATATAATCTCACTAAA
66 TTGTACACGCGCCCATAGCAATAACATATTTAGGTTCGGGCATTTGTTCATATAATCTCACTAAA
*
41409703 GAGGGCGCCATTTTCATTGTTACTGTATAGACATCCAC
131 GAGGGCACCATTTTCATTGTTACTGTATAGACATCCAC
* *
41409741 GGGAATTAGCTTATCGACCCCCCGAATAGTACTATAAGAATCAGTACTAAACATCCCTCCTACAA
1 GGGAATTAGCTTATCCACCCCCCGAATAATACTATAAGAATCAGTACTAAACATCCCTCCTACAA
41409806 TTGTACACGCGCCCATAGCAATAACATATTTAGGTTCGGGCATTTGTTCATATAATCTCACTAAA
66 TTGTACACGCGCCCATAGCAATAACATATTTAGGTTCGGGCATTTGTTCATATAATCTCACTAAA
*
41409871 GAGGGTACCATTTTCATTGTTACT
131 GAGGGCACCATTTTCATTGTTACT
41409895 ATTCCAGCTG
Statistics
Matches: 143, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
168 143 1.00
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (168 bp):
GGGAATTAGCTTATCCACCCCCCGAATAATACTATAAGAATCAGTACTAAACATCCCTCCTACAA
TTGTACACGCGCCCATAGCAATAACATATTTAGGTTCGGGCATTTGTTCATATAATCTCACTAAA
GAGGGCACCATTTTCATTGTTACTGTATAGACATCCAC
Found at i:41410582 original size:41 final size:40
Alignment explanation
Indices: 41410537--41410787 Score: 295
Period size: 41 Copynumber: 6.1 Consensus size: 40
41410527 AGCCAGAGCA
* * * *
41410537 TTAGCGGCGTTTATGAGAAAGCGCAGCTAATGCCCTAACCT
1 TTAGCGGCGCTTGTG-GAAAGCGCCGCTAATGCCCTGACCT
*
41410578 TTAGCGGCGCTTGTGGGAAAGCGCTGCTAATGCCCTGACCT
1 TTAGCGGCGCTTGT-GGAAAGCGCCGCTAATGCCCTGACCT
* * *
41410619 TTAGCGGCGTTTGTGGGAAAGCACCGCTAATACCCTGACCTT
1 TTAGCGGCGCTTGT-GGAAAGCGCCGCTAATGCCCTGACC-T
* *
41410661 TTAGCGGCGCTTGTGAAAAAGCGCCGCTAATACCCTGACCT
1 TTAGCGGCGCTTGTG-GAAAGCGCCGCTAATGCCCTGACCT
* * *
41410702 TTAGCGGCGTTTGTGGAAAAGAGCCGCTAATGCCCTGATCT
1 TTAGCGGCGCTTGTGG-AAAGCGCCGCTAATGCCCTGACCT
* * *
41410743 TTAGCGGTGCTTAGTGTAAAGCGCCGCTAATGCCCTGACCA
1 TTAGCGGCGCTT-GTGGAAAGCGCCGCTAATGCCCTGACCT
41410784 TTAG
1 TTAG
41410788 AGGTACTTCG
Statistics
Matches: 183, Mismatches: 22, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
41 143 0.78
42 40 0.22
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.25
Consensus pattern (40 bp):
TTAGCGGCGCTTGTGGAAAGCGCCGCTAATGCCCTGACCT
Found at i:41410690 original size:124 final size:124
Alignment explanation
Indices: 41410537--41410782 Score: 332
Period size: 124 Copynumber: 2.0 Consensus size: 124
41410527 AGCCAGAGCA
* * * * *
41410537 TTAGCGGCGTTTATGAGAAAGCGCAGCTAATGCCCTAACCTTTAGCGGCGCTTGTGGGAAAGCGC
1 TTAGCGGCGCTTATGAAAAAGCGCAGCTAATACCCTAACCTTTAGCGGCGCTTGTGGAAAAGAGC
* *
41410602 TGCTAATGCCCTGACCTTTAGCGGCG-TTTGTGGGAAAGCACCGCTAATACCCTGACCTT
66 CGCTAATGCCCTGACCTTTAGCGGCGCTTAGT-GGAAAGCACCGCTAATACCCTGACCTT
* * * *
41410661 TTAGCGGCGCTTGTGAAAAAGCGCCGCTAATACCCTGACCTTTAGCGGCGTTTGTGGAAAAGAGC
1 TTAGCGGCGCTTATGAAAAAGCGCAGCTAATACCCTAACCTTTAGCGGCGCTTGTGGAAAAGAGC
* * * * *
41410726 CGCTAATGCCCTGATCTTTAGCGGTGCTTAGTGTAAAGCGCCGCTAATGCCCTGACC
66 CGCTAATGCCCTGACCTTTAGCGGCGCTTAGTGGAAAGCACCGCTAATACCCTGACC
41410783 ATTAGAGGTA
Statistics
Matches: 105, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
124 101 0.96
125 4 0.04
ACGTcount: A:0.22, C:0.26, G:0.27, T:0.25
Consensus pattern (124 bp):
TTAGCGGCGCTTATGAAAAAGCGCAGCTAATACCCTAACCTTTAGCGGCGCTTGTGGAAAAGAGC
CGCTAATGCCCTGACCTTTAGCGGCGCTTAGTGGAAAGCACCGCTAATACCCTGACCTT
Found at i:41410697 original size:83 final size:81
Alignment explanation
Indices: 41410537--41410787 Score: 324
Period size: 83 Copynumber: 3.0 Consensus size: 81
41410527 AGCCAGAGCA
* * * * * *
41410537 TTAGCGGCGTTTATGAGAAAGCGCAGCTAATGCCCTAACCTTTAGCGGCGCTTGTGGGAAAGCGC
1 TTAGCGGCGTTTGTGGGAAAGCACCGCTAATGCCCTGACCTTTAGCGGCGCTTGT-GAAAAGCGC
*
41410602 TGCTAATGCCCTGACCT
65 CGCTAATGCCCTGACCT
*
41410619 TTAGCGGCGTTTGTGGGAAAGCACCGCTAATACCCTGACCTTTTAGCGGCGCTTGTGAAAAAGCG
1 TTAGCGGCGTTTGTGGGAAAGCACCGCTAATGCCCTGACC-TTTAGCGGCGCTTGTG-AAAAGCG
*
41410684 CCGCTAATACCCTGACCT
64 CCGCTAATGCCCTGACCT
* * * *
41410702 TTAGCGGCGTTTGTGGAAAAG-AGCCGCTAATGCCCTGATCTTTAGCGGTGCTTAGTGTAAAGCG
1 TTAGCGGCGTTTGTGGGAAAGCA-CCGCTAATGCCCTGACCTTTAGCGGCGCTT-GTGAAAAGCG
*
41410766 CCGCTAATGCCCTGACCA
64 CCGCTAATGCCCTGACCT
41410784 TTAG
1 TTAG
41410788 AGGTACTTCG
Statistics
Matches: 149, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
82 74 0.50
83 75 0.50
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.25
Consensus pattern (81 bp):
TTAGCGGCGTTTGTGGGAAAGCACCGCTAATGCCCTGACCTTTAGCGGCGCTTGTGAAAAGCGCC
GCTAATGCCCTGACCT
Found at i:41410809 original size:41 final size:41
Alignment explanation
Indices: 41410719--41410813 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 41
41410709 CGTTTGTGGA
* * * * * *
41410719 AAAGAGCCGCTAATGCCCTGATCTTTAGCGGTGCTTAGTGT
1 AAAGCGCCGCTAATGCCCTGACCATTAGAGGTACTTAGTAT
*
41410760 AAAGCGCCGCTAATGCCCTGACCATTAGAGGTACTTCGTCAT
1 AAAGCGCCGCTAATGCCCTGACCATTAGAGGTACTTAGT-AT
41410802 AAA-CGCCGCTAA
1 AAAGCGCCGCTAA
41410814 AGGTCAGAGC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
41 42 0.91
42 4 0.09
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.24
Consensus pattern (41 bp):
AAAGCGCCGCTAATGCCCTGACCATTAGAGGTACTTAGTAT
Found at i:41410844 original size:41 final size:42
Alignment explanation
Indices: 41410799--41410895 Score: 126
Period size: 41 Copynumber: 2.3 Consensus size: 42
41410789 GGTACTTCGT
*
41410799 CATAAACGCCGCTAAAGGTCAGAGCATTAGCGGCGC-TTTTC
1 CATAAACGCCGCTAAAGGTCAGAGCATTAGCAGCGCTTTTTC
* *
41410840 CATAAGA-GCCGCTAAAGGTTAGGGCATTAGCAGCGCTTTTTC
1 CATAA-ACGCCGCTAAAGGTCAGAGCATTAGCAGCGCTTTTTC
* *
41410882 TATAAACACCGCTA
1 CATAAACGCCGCTA
41410896 TTGCTTTACC
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
41 32 0.67
42 16 0.33
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.24
Consensus pattern (42 bp):
CATAAACGCCGCTAAAGGTCAGAGCATTAGCAGCGCTTTTTC
Found at i:41413064 original size:2 final size:2
Alignment explanation
Indices: 41413021--41413047 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41413011 TAGATTAATA
41413021 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
41413048 ATTAAAGCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41419654 original size:18 final size:17
Alignment explanation
Indices: 41419622--41419657 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
41419612 TAAATGAGTT
*
41419622 AATTAGGATTAAATTGG
1 AATTAAGATTAAATTGG
41419639 AATTAAGATATAAATTGG
1 AATTAAGAT-TAAATTGG
41419657 A
1 A
41419658 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.33
Consensus pattern (17 bp):
AATTAAGATTAAATTGG
Found at i:41422703 original size:23 final size:23
Alignment explanation
Indices: 41422634--41422805 Score: 145
Period size: 23 Copynumber: 7.4 Consensus size: 23
41422624 TGGAACAAAT
* *
41422634 AGAGAGTAC-CAAAGTACT-AAC
1 AGAGAGCACACAAAGTGCTAAAC
* *
41422655 AGAGAGCACA-TAAGTGCTGGGCAAC
1 AGAGAGCACACAAAGTGCT---AAAC
*
41422680 AGAGAGCACACACAGTGCTAAAC
1 AGAGAGCACACAAAGTGCTAAAC
* * * *
41422703 AGAAAGTACACAAAGTACTAATC
1 AGAGAGCACACAAAGTGCTAAAC
*
41422726 AGAGAGCACACAAAGTGCTAATC
1 AGAGAGCACACAAAGTGCTAAAC
*
41422749 AGAGAGCACACACAGTGCTAATAAC
1 AGAGAGCACACAAAGTGCT-A-AAC
* *
41422774 AGAGAGCACGA-GAGGTGCTAAAC
1 AGAGAGCAC-ACAAAGTGCTAAAC
41422797 AGAGAGCAC
1 AGAGAGCAC
41422806 TATAGTGTTC
Statistics
Matches: 123, Mismatches: 19, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
21 14 0.11
23 71 0.58
24 2 0.02
25 29 0.24
26 7 0.06
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.12
Consensus pattern (23 bp):
AGAGAGCACACAAAGTGCTAAAC
Found at i:41422753 original size:69 final size:66
Alignment explanation
Indices: 41422638--41422769 Score: 185
Period size: 69 Copynumber: 1.9 Consensus size: 66
41422628 ACAAATAGAG
*
41422638 AGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACACAGTGCTAAAC
1 AGTACCAAAGTACTAACAGAGAGCACAAAAGTGCT--G-AACAGAGAGCACACACAGTGCTAAAC
41422703 AGAA
63 AGAA
41422707 AGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACACAGTGCTAA
1 AGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGAA-CAGAGAGCACACACAGTGCTAA
41422770 TAACAGAGAG
Statistics
Matches: 58, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
68 2 0.03
69 27 0.47
70 11 0.19
71 11 0.19
72 7 0.12
ACGTcount: A:0.44, C:0.22, G:0.21, T:0.13
Consensus pattern (66 bp):
AGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAACAGAGAGCACACACAGTGCTAAACAGA
A
Found at i:41429915 original size:23 final size:23
Alignment explanation
Indices: 41429886--41429987 Score: 102
Period size: 23 Copynumber: 4.4 Consensus size: 23
41429876 AGTGCTAGGC
41429886 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* * *
41429909 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACACAGTGCTA
* *
41429932 ATCAGATAG--CACACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
*
41429954 TAACAGAGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
41429978 AACAGAGAGC
1 AACAGAGAGC
41429988 GCACTAGTGT
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
21 9 0.14
22 1 0.02
23 44 0.69
24 1 0.02
25 6 0.09
26 3 0.05
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:41429960 original size:69 final size:69
Alignment explanation
Indices: 41429839--41429986 Score: 203
Period size: 69 Copynumber: 2.1 Consensus size: 69
41429829 TATACGGATC
* *
41429839 AAACAGAGAGTACCAAAGTACTAATAGATGGCACATAAGTGCTAGGCAACAGAGAGCAC-ACACA
1 AAACAGAGAGTACCAAAGTACTAATAGATAGCACATAAGTGCTAGACAACAGAGAGCACGACAC-
41429903 GTGCT
65 GTGCT
* * *
41429908 AAACAGAGAGTACACAAAGTACTAATCAGATAGCACA-CAGTGCTA-ATAACAGAGAGCACGAGA
1 AAACAGAGAGTAC-CAAAGTACTAAT-AGATAGCACATAAGTGCTAGACAACAGAGAGCACGACA
41429971 CGTGCT
64 CGTGCT
41429977 AAACAGAGAG
1 AAACAGAGAG
41429987 CGCACTAGTG
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
69 40 0.56
70 22 0.31
71 9 0.13
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.14
Consensus pattern (69 bp):
AAACAGAGAGTACCAAAGTACTAATAGATAGCACATAAGTGCTAGACAACAGAGAGCACGACACG
TGCT
Found at i:41438297 original size:16 final size:17
Alignment explanation
Indices: 41438262--41438312 Score: 68
Period size: 16 Copynumber: 2.9 Consensus size: 17
41438252 GGTAAAAGAC
41438262 AAAAGAGAAAAGGCAGAAAG
1 AAAAGAGAAAA---AGAAAG
41438282 AAAAGA-AAAAAGAAAG
1 AAAAGAGAAAAAGAAAG
41438298 AAAAGAGAAAAAGAA
1 AAAAGAGAAAAAGAA
41438313 TCGTGCTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 12 0.40
17 8 0.27
19 4 0.13
20 6 0.20
ACGTcount: A:0.75, C:0.02, G:0.24, T:0.00
Consensus pattern (17 bp):
AAAAGAGAAAAAGAAAG
Found at i:41439003 original size:78 final size:78
Alignment explanation
Indices: 41438902--41439057 Score: 285
Period size: 78 Copynumber: 2.0 Consensus size: 78
41438892 CATTATCAAT
* * *
41438902 TTAACGGCTAGTGACAAAAACAAGAACGAATTCAAACATTAGTATCTAAGTTAAAAACTTTTAAA
1 TTAACGACGAGTGACAAAAACAAGAACAAATTCAAACATTAGTATCTAAGTTAAAAACTTTTAAA
41438967 ATTGGGTAACCAA
66 ATTGGGTAACCAA
41438980 TTAACGACGAGTGACAAAAACAAGAACAAATTCAAACATTAGTATCTAAGTTAAAAACTTTTAAA
1 TTAACGACGAGTGACAAAAACAAGAACAAATTCAAACATTAGTATCTAAGTTAAAAACTTTTAAA
41439045 ATTGGGTAACCAA
66 ATTGGGTAACCAA
41439058 AATAGTAACA
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.25
Consensus pattern (78 bp):
TTAACGACGAGTGACAAAAACAAGAACAAATTCAAACATTAGTATCTAAGTTAAAAACTTTTAAA
ATTGGGTAACCAA
Found at i:41449724 original size:30 final size:29
Alignment explanation
Indices: 41449682--41449790 Score: 114
Period size: 30 Copynumber: 3.7 Consensus size: 29
41449672 TTTGGATACC
*
41449682 CGAGGG-AAAATGGTAATTTTGGAAACTCT
1 CGAGGGCAAAATGGTAATTTTGGAAAGT-T
*
41449711 CGAGGGCAAAATGGTATTTTTGGGAAAGTT
1 CGAGGGCAAAATGGTAATTTT-GGAAAGTT
* * *
41449741 CGAGGTCAAAAAT-GAAATTTTTGAAAGTT
1 CGAGGGC-AAAATGGTAATTTTGGAAAGTT
* *
41449770 CGACGGTAAAATGGTAATTTT
1 CGAGGGCAAAATGGTAATTTT
41449791 TGGGAAAATT
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
28 5 0.08
29 24 0.36
30 26 0.39
31 11 0.17
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.30
Consensus pattern (29 bp):
CGAGGGCAAAATGGTAATTTTGGAAAGTT
Found at i:41449793 original size:60 final size:58
Alignment explanation
Indices: 41449712--41449961 Score: 222
Period size: 60 Copynumber: 4.2 Consensus size: 58
41449702 GGAAACTCTC
* * *
41449712 GAGGGCAAAATGGT-ATTTTTGGGAAAGTTCGAGGTCAAAAATGAAATTTTTGAAAGTT
1 GAGGGTAAAATGGTAATTTTTGGGAAAATT-GAGGTCAAAAATGAAATTTTTGGAAGTT
* * * **
41449770 CGACGGTAAAATGGTAATTTTTGGGAAAATTGAGGTAAAAAAATGGAATAGTTGGAAGTTT
1 -GAGGGTAAAATGGTAATTTTTGGGAAAATTGAGGT-CAAAAATGAAATTTTTGGAAG-TT
* * *
41449831 GAGGGTACAATGGTAATTTTTGGAAAAATT-AGGGTCAAAAATGGAATTTTTTGGAAGTT
1 GAGGGTAAAATGGTAATTTTTGGGAAAATTGA-GGTCAAAAAT-GAAATTTTTGGAAGTT
* * * *
41449890 TAGGGGTAAAATGGTAATTTTT--GAAAAGTTTAGGGGTC-GAAATGTAATTTTTGGAAGTTT
1 GA-GGGTAAAATGGTAATTTTTGGGAAAA--TT-GAGGTCAAAAATGAAATTTTTGGAAG-TT
41449950 GAGGGTTAAAAT
1 GAGGG-TAAAAT
41449962 ATGATTTTTG
Statistics
Matches: 155, Mismatches: 24, Indels: 23
0.77 0.12 0.11
Matches are distributed among these distances:
58 4 0.03
59 42 0.27
60 103 0.66
61 6 0.04
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (58 bp):
GAGGGTAAAATGGTAATTTTTGGGAAAATTGAGGTCAAAAATGAAATTTTTGGAAGTT
Found at i:41449879 original size:30 final size:31
Alignment explanation
Indices: 41449688--41449983 Score: 119
Period size: 29 Copynumber: 9.9 Consensus size: 31
41449678 TACCCGAGGG
* * *
41449688 AAAATGGTAA-TTTTGGAAACTCTCGAGGG-C
1 AAAATGGTAATTTTTGGAAAATTTAG-GGGTC
* * * *
41449718 AAAATGGT-ATTTTTGGGAAAGTTCGAGGTC
1 AAAATGGTAATTTTTGGAAAATTTAGGGGTC
* * * *
41449748 AAAAAT-GAAATTTTT-G-AAAGTTCGACGGT-
1 -AAAATGGTAATTTTTGGAAAATTTAG-GGGTC
* ****
41449777 AAAATGGTAATTTTTGGGAAAATTGAGGTAAA
1 AAAATGGTAATTTTT-GGAAAATTTAGGGGTC
** *
41449809 AAAATGG-AATAGTTGG-AAGTTT-GAGGGT-
1 AAAATGGTAATTTTTGGAAAATTTAG-GGGTC
* *
41449837 ACAATGGTAATTTTTGGAAAAATTA-GGGTC
1 AAAATGGTAATTTTTGGAAAATTTAGGGGTC
*
41449867 AAAAATGG-AATTTTTTGG-AAGTTTAGGGGT-
1 -AAAATGGTAA-TTTTTGGAAAATTTAGGGGTC
41449897 AAAATGGTAATTTTT-GAAAAGTTTAGGGGTC
1 AAAATGGTAATTTTTGGAAAA-TTTAGGGGTC
* * *
41449928 GAAAT-GTAATTTTTGG-AAGTTT-GAGGGTT
1 AAAATGGTAATTTTTGGAAAATTTAG-GGGTC
* * *
41449957 AAAAT-ATGATTTTTGGACAATTTAGGG
1 AAAATGGTAATTTTTGGAAAATTTAGGG
41449984 ACTTTAGGGC
Statistics
Matches: 201, Mismatches: 39, Indels: 52
0.69 0.13 0.18
Matches are distributed among these distances:
28 14 0.07
29 69 0.34
30 66 0.33
31 40 0.20
32 12 0.06
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.33
Consensus pattern (31 bp):
AAAATGGTAATTTTTGGAAAATTTAGGGGTC
Found at i:41451102 original size:9 final size:9
Alignment explanation
Indices: 41451088--41451171 Score: 66
Period size: 9 Copynumber: 9.4 Consensus size: 9
41451078 ATTATTAGCA
41451088 ATTATTAAT
1 ATTATTAAT
41451097 ATTATT-A-
1 ATTATTAAT
41451104 ATTATTAAT
1 ATTATTAAT
*
41451113 ATTTATTACT
1 A-TTATTAAT
* * **
41451123 ACTACTGTT
1 ATTATTAAT
41451132 ATTATTAAT
1 ATTATTAAT
*
41451141 ACTATTAAT
1 ATTATTAAT
41451150 ATTA-TAACT
1 ATTATTAA-T
*
41451159 AATATTAAT
1 ATTATTAAT
41451168 ATTA
1 ATTA
41451172 ATGATATTCA
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
7 6 0.11
8 5 0.09
9 35 0.61
10 11 0.19
ACGTcount: A:0.42, C:0.06, G:0.01, T:0.51
Consensus pattern (9 bp):
ATTATTAAT
Found at i:41451106 original size:16 final size:17
Alignment explanation
Indices: 41451087--41451120 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
41451077 TATTATTAGC
41451087 AATTATTAATA-TTATT
1 AATTATTAATATTTATT
41451103 AATTATTAATATTTATT
1 AATTATTAATATTTATT
41451120 A
1 A
41451121 CTACTACTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTATTAATATTTATT
Found at i:41451152 original size:18 final size:18
Alignment explanation
Indices: 41451090--41451171 Score: 80
Period size: 18 Copynumber: 4.6 Consensus size: 18
41451080 TATTAGCAAT
41451090 TATTAATATTATTAAT--
1 TATTAATATTATTAATAC
*
41451106 TATTAATATTTATTACTAC
1 TATTAATA-TTATTAATAC
* **
41451125 TACTGTTATTATTAATAC
1 TATTAATATTATTAATAC
*
41451143 TATTAATATTA-TAACTAA
1 TATTAATATTATTAA-TAC
41451161 TATTAATATTA
1 TATTAATATTA
41451172 ATGATATTCA
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
16 8 0.15
17 10 0.19
18 30 0.57
19 5 0.09
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.51
Consensus pattern (18 bp):
TATTAATATTATTAATAC
Found at i:41451922 original size:6 final size:6
Alignment explanation
Indices: 41451913--41451974 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
41451903 AATTGAAAGC
** *
41451913 AAATTT AAATTT AAAGAT AAATTT AAATTT GAGA--T AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT -AAATTT AAATTT AAATTT
**
41451960 AAAAAT AAATTT AAA
1 AAATTT AAATTT AAA
41451975 CCAATCTAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
4 2 0.05
5 1 0.02
6 38 0.88
7 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (6 bp):
AAATTT
Found at i:41451941 original size:35 final size:35
Alignment explanation
Indices: 41451895--41451974 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
41451885 CAAATTTAAT
* *
41451895 TAAATTCAAA-TTGAAAGCAAATTTAAATTTAAAGA
1 TAAATTTAAATTTGAAA-CAAATTTAAATTTAAAAA
* *
41451930 TAAATTTAAATTTGAGATAAATTTAAATTTAAAAA
1 TAAATTTAAATTTGAAACAAATTTAAATTTAAAAA
41451965 TAAATTTAAA
1 TAAATTTAAA
41451975 CCAATCTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 35 0.88
36 5 0.12
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (35 bp):
TAAATTTAAATTTGAAACAAATTTAAATTTAAAAA
Found at i:41452697 original size:164 final size:164
Alignment explanation
Indices: 41452418--41452756 Score: 556
Period size: 164 Copynumber: 2.1 Consensus size: 164
41452408 TCTCAATATT
* * *
41452418 TCATCAAGAAGCTAACTATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGA
1 TCATCAGGAAGCTAACTATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGA
*
41452483 TTCGAAGATTTGCTCACATCGAGCCCTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATAA
66 TTCGAAGATTTGCTCACATCGAGCCCTGAGTTGGTATACTTCTCTGTATCTCATCAAGAAGATAA
41452548 CCGTCCC-GTTTGTTTCAATCCGCTTCTCTGTACC
131 CCG-CCCTGTTTGTTTCAATCCGCTTCTCTGTACC
41452582 TCATCAGGAAGCTAAAC-ATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGG
1 TCATCAGGAAGCT-AACTATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGG
** * *
41452646 ATTCGAAGATTTGCTCTTATTGAGCCCTGAGTTGGTATACTTCTTTGTATCTCATCAAGAAGATA
65 ATTCGAAGATTTGCTCACATCGAGCCCTGAGTTGGTATACTTCTCTGTATCTCATCAAGAAGATA
* *
41452711 ACCGCCCTGTTTGTTTTAATCCGCTTCTCTGTATC
130 ACCGCCCTGTTTGTTTCAATCCGCTTCTCTGTACC
41452746 TCATCAGGAAG
1 TCATCAGGAAG
41452757 ATGAATTTGG
Statistics
Matches: 163, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
163 3 0.02
164 157 0.96
165 3 0.02
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (164 bp):
TCATCAGGAAGCTAACTATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGA
TTCGAAGATTTGCTCACATCGAGCCCTGAGTTGGTATACTTCTCTGTATCTCATCAAGAAGATAA
CCGCCCTGTTTGTTTCAATCCGCTTCTCTGTACC
Found at i:41452965 original size:194 final size:194
Alignment explanation
Indices: 41452570--41453114 Score: 626
Period size: 194 Copynumber: 2.7 Consensus size: 194
41452560 TTTCAATCCG
* * *
41452570 CTTCTCTGTACCTCATCAGGAAGCTAAACATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCT-AACCTTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
* * * * *
41452635 AAGAAGCTGGGATTCGAAGATTTGCTCTTATTGAGCCCTGAGTTGGTATACTTCTTTGTATCTCA
65 AGGAAGCTGGGGTTCGAAGATTTGCTC---GT-A--CTTGAGTTGGTATACTTCTCTGTATCTCA
* * ** * * **
41452700 TCAAGAAGATAACCGCC-CTGTTTGTTTTAATCCGCTTCTCTGTATCTCATCAGGAAGATGAATT
124 TCAGGAAGATGACCGCCTC-ACTTGTTTCAATCCGCTTCTCTGTACCTCATCAGGAAGACAAATT
41452764 TGGTCCA
188 TGGTCCA
* * * * * *
41452771 CTTCTTAGTGTCTCATCAGAAAGCTAACCTTTTTATTGCTTTGCCCTGCTTCTCAATATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCTAACC-TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
* **
41452836 AGGAAGTTGGGGTTCGAAGATTTATTCGTA-TTGAGTTGGTATACTTCTCTGTATCTCATCAGGA
65 AGGAAGCTGGGGTTCGAAGATTTGCTCGTACTTGAGTTGGTATACTTCTCTGTATCTCATCAGGA
*
41452900 AGATGACCGCCTCACTTGTTTCAATCTGCTTCTCTGTACCTCATCAGGAAGACAAATTTGGTCCA
130 AGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTGTACCTCATCAGGAAGACAAATTTGGTCCA
* * * * *
41452965 CTTGTCAGTATCTCATTAGGAAGCTAACCATTTGTTGCTTCGACCTGCTTCTCAGTATCTTATCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCA
* *
41453030 GAAAGCTGGGGTTCGAAGATTTGCTCGTATTAAACCTTGAGTTGGTATACTTCTCTATATCTCAT
66 GGAAGCTGGGGTTCGAAGATTTGCTCG---T--A-CTTGAGTTGGTATACTTCTCTGTATCTCAT
* *
41453095 CAGAAAGATGATCGCCTCAC
125 CAGGAAGATGACCGCCTCAC
41453115 AGTTTGTGGA
Statistics
Matches: 291, Mismatches: 44, Indels: 19
0.82 0.12 0.05
Matches are distributed among these distances:
193 53 0.18
194 110 0.38
195 1 0.00
196 1 0.00
197 1 0.00
198 2 0.01
200 49 0.17
201 74 0.25
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (194 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCA
GGAAGCTGGGGTTCGAAGATTTGCTCGTACTTGAGTTGGTATACTTCTCTGTATCTCATCAGGAA
GATGACCGCCTCACTTGTTTCAATCCGCTTCTCTGTACCTCATCAGGAAGACAAATTTGGTCCA
Found at i:41465172 original size:60 final size:59
Alignment explanation
Indices: 41465079--41465400 Score: 345
Period size: 60 Copynumber: 5.4 Consensus size: 59
41465069 AGGAAAGTTT
* *
41465079 GGGTCAAAAATGGAATTTTTAGATA-TTTGGGGGTAAAATGGTAATTTTTGGAAAAAATCA
1 GGGTC-AAAATGGAATTTTTGGA-AGTTTAGGGGTAAAATGGTAATTTTTGGAAAAAATCA
* **
41465139 GGGTCAAAATGGAATTTTTTTGAAGTTTAGGGGTAAAATGGTAATTTTAAG-AAAAATCAA
1 GGGTCAAAATGGAA-TTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGGAAAAAATC-A
* * *
41465199 GGTTAAAAATGGAATTTTTGGAAGTTT-GGAGG-AAAATGGTAATTTTAGG-AAAAATCGA
1 GGGTCAAAATGGAATTTTTGGAAGTTTAGG-GGTAAAATGGTAATTTTTGGAAAAAATC-A
* *
41465257 GGTTAAAAATGGAATTTTTGGAAGTTTAAGGGGTAAAATGGTAA-TTTTGGAAAAAATC-
1 GGGTCAAAATGGAATTTTTGGAAGTTT-AGGGGTAAAATGGTAATTTTTGGAAAAAATCA
* * * ** **
41465315 GAGGTCAAAAATGGAATTTTTGGAAGTTTAAGGATAAAATGATAATTTTT-GAAAAGTTTG
1 G-GGTC-AAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGGAAAAAATCA
*
41465375 GGGTCAAAATGTAATTTTTGGAAGTT
1 GGGTCAAAATGGAATTTTTGGAAGTT
41465401 CGGGGGTTAA
Statistics
Matches: 231, Mismatches: 19, Indels: 26
0.84 0.07 0.09
Matches are distributed among these distances:
58 74 0.32
59 63 0.27
60 94 0.41
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.34
Consensus pattern (59 bp):
GGGTCAAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGGAAAAAATCA
Found at i:41465235 original size:118 final size:119
Alignment explanation
Indices: 41465080--41465400 Score: 388
Period size: 118 Copynumber: 2.7 Consensus size: 119
41465070 GGAAAGTTTG
* *
41465080 GGTCAAAAATGGAATTTTTAGATA-TTTGGGGGTAAAATGGTAATTTTTGGAAAAAATCAGGGTC
1 GGTCAAAAATGGAATTTTTGGA-AGTTTGGAGG-AAAATGGTAATTTTTGGAAAAAATCAGGGTC
*
41465144 AAAATGGAATTTTTTTGAAGTTT-AGGGGTAAAATGGTAATTTTA-AGAAAAATCAA
64 AAAATGGAATTTTTTGGAAGTTTAAGGGGTAAAATGGTAATTTTAGA-AAAAATCAA
* * * *
41465199 GGTTAAAAATGGAATTTTTGGAAGTTTGGAGGAAAATGGTAATTTTAGG-AAAAATCGAGGTTAA
1 GGTCAAAAATGGAATTTTTGGAAGTTTGGAGGAAAATGGTAATTTTTGGAAAAAATC-AGGGTCA
* *
41465263 AAATGGAA-TTTTTGGAAGTTTAAGGGGTAAAATGGTAATTTTGGAAAAAATCGA
65 AAATGGAATTTTTTGGAAGTTTAAGGGGTAAAATGGTAATTTTAGAAAAAATCAA
* * ** **
41465317 GGTCAAAAATGGAATTTTTGGAAGTTTAAGGA-TAAAATGATAATTTTT-GAAAAGTTTGGGGTC
1 GGTCAAAAATGGAATTTTTGGAAGTTT--GGAGGAAAATGGTAATTTTTGGAAAAAATCAGGGTC
*
41465380 AAAATGTAA-TTTTTGGAAGTT
64 AAAATGGAATTTTTTGGAAGTT
41465401 CGGGGGTTAA
Statistics
Matches: 175, Mismatches: 20, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
117 19 0.11
118 108 0.62
119 45 0.26
120 3 0.02
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.34
Consensus pattern (119 bp):
GGTCAAAAATGGAATTTTTGGAAGTTTGGAGGAAAATGGTAATTTTTGGAAAAAATCAGGGTCAA
AATGGAATTTTTTGGAAGTTTAAGGGGTAAAATGGTAATTTTAGAAAAAATCAA
Found at i:41465406 original size:29 final size:28
Alignment explanation
Indices: 41465204--41465423 Score: 88
Period size: 29 Copynumber: 7.5 Consensus size: 28
41465194 ATCAAGGTTA
* * *
41465204 AAAATGGAATTTTTGGAAGTTTGGAGG-
1 AAAATGTAATTTTTGGAAGTTCGGGGGT
* ** * *
41465231 AAAATGGTAATTTTAGGAAAAATCGAGGTT
1 AAAAT-GTAATTTTTGG-AAGTTCGGGGGT
* **
41465261 AAAAATGGAATTTTTGGAAGTTTAAGGGGT
1 -AAAATGTAATTTTTGGAAG-TTCGGGGGT
** *
41465291 AAAATGGTAA-TTTTGGAAAAAATC-GAGGT
1 AAAAT-GTAATTTTTGG--AAGTTCGGGGGT
* *** *
41465320 CAAAAATGGAATTTTTGGAAGTTTAAGGAT
1 --AAAATGTAATTTTTGGAAGTTCGGGGGT
* *
41465350 AAAATGATAATTTTTGAAAAGTT-TGGGGT
1 AAAATG-TAATTTTTG-GAAGTTCGGGGGT
41465379 CAAAATGTAATTTTTGGAAGTTCGGGGGTT
1 -AAAATGTAATTTTTGGAAGTTCGGGGG-T
* *
41465409 AAAATATGATTTTTG
1 AAAATGTAATTTTTG
41465424 AACAGTTTAG
Statistics
Matches: 139, Mismatches: 37, Indels: 32
0.67 0.18 0.15
Matches are distributed among these distances:
27 5 0.04
28 20 0.14
29 62 0.45
30 34 0.24
31 18 0.13
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.34
Consensus pattern (28 bp):
AAAATGTAATTTTTGGAAGTTCGGGGGT
Found at i:41465421 original size:58 final size:59
Alignment explanation
Indices: 41465055--41465431 Score: 214
Period size: 58 Copynumber: 6.4 Consensus size: 59
41465045 CCCGGGGGGC
* * * * * * *
41465055 AAAATGGTAATTTTAGGAAAGTTT-GGGTCAAAAATGGAATTTTTAGATATTTG-GGGGT
1 AAAATGATAATTTTTGAAAAGTTTGGGGTCAAAAATGGAATTTTTGGA-AGTTGAAGGAT
* ** ** * * * *
41465113 AAAATGGTAATTTTTGGAAAAAATCAGGGTC-AAAATGGAATTTTTTTGAAGTTTAGGGGT
1 AAAATGATAATTTTT-GAAAAGTTTGGGGTCAAAAATGGAA-TTTTTGGAAGTTGAAGGAT
* * * *** * *
41465173 AAAATGGTAATTTTAAGAAAA-ATCAAGGTTAAAAATGGAATTTTTGGAAGTTTGGAGG--
1 AAAATGATAATTTT-TGAAAAGTTTGGGGTCAAAAATGGAATTTTTGGAAG-TTGAAGGAT
* * * * * * * *
41465231 AAAATGGTAATTTTAGGAAAA-ATCGAGGTTAAAAATGGAATTTTTGGAAGTTTAAGGGGT
1 AAAATGATAATTTT-TGAAAAGTTTGGGGTCAAAAATGGAATTTTTGGAAGTTGAA-GGAT
* * ** * * *
41465291 AAAATGGTAATTTTGGAAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTTAAGGAT
1 AAAATGATAATTTTTGAAAAGTTTGGGGTCAAAAATGGAATTTTTGGAAGTTGAAGGAT
* ** *
41465350 AAAATGATAATTTTTGAAAAGTTTGGGGTC-AAAATGTAATTTTTGGAAGTTCGGGGGTT
1 AAAATGATAATTTTTGAAAAGTTTGGGGTCAAAAATGGAATTTTTGGAAGTT-GAAGGAT
* *
41465409 AAAAT-ATGATTTTTGAACAGTTT
1 AAAATGATAATTTTTGAAAAGTTT
41465432 AGGGACCTCT
Statistics
Matches: 273, Mismatches: 34, Indels: 24
0.82 0.10 0.07
Matches are distributed among these distances:
57 3 0.01
58 100 0.37
59 74 0.27
60 96 0.35
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (59 bp):
AAAATGATAATTTTTGAAAAGTTTGGGGTCAAAAATGGAATTTTTGGAAGTTGAAGGAT
Found at i:41466545 original size:9 final size:9
Alignment explanation
Indices: 41466533--41466626 Score: 68
Period size: 9 Copynumber: 10.2 Consensus size: 9
41466523 TTATTAGCAA
41466533 TATTAATAT
1 TATTAATAT
41466542 TATT-A-AT
1 TATTAATAT
41466549 TATTAATATT
1 TATTAATA-T
* *
41466559 TATTACTAC
1 TATTAATAT
* *
41466568 TGTTATTAT
1 TATTAATAT
41466577 TATTAATGTTAT
1 TATTAA---TAT
*
41466589 TATTAATAC
1 TATTAATAT
41466598 TATTAATAT
1 TATTAATAT
*
41466607 TA-TAACTAA
1 TATTAA-TAT
41466616 TATTAATAT
1 TATTAATAT
41466625 TA
1 TA
41466627 ATGATATTCA
Statistics
Matches: 66, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
7 6 0.09
8 5 0.08
9 35 0.53
10 11 0.17
12 9 0.14
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (9 bp):
TATTAATAT
Found at i:41466578 original size:15 final size:15
Alignment explanation
Indices: 41466558--41466608 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
41466548 TTATTAATAT
*
41466558 TTATTACTACTGTTA
1 TTATTAATACTGTTA
* *
41466573 TTATTATTAATGTTA
1 TTATTAATACTGTTA
*
41466588 TTATTAATACTATTA
1 TTATTAATACTGTTA
*
41466603 ATATTA
1 TTATTA
41466609 TAACTAATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (15 bp):
TTATTAATACTGTTA
Found at i:41466616 original size:21 final size:21
Alignment explanation
Indices: 41466577--41466617 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
41466567 CTGTTATTAT
* * *
41466577 TATTAATGTTATTATTAATAC
1 TATTAATATTATAACTAATAC
41466598 TATTAATATTATAACTAATA
1 TATTAATATTATAACTAATA
41466618 TTAATATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (21 bp):
TATTAATATTATAACTAATAC
Found at i:41467372 original size:18 final size:17
Alignment explanation
Indices: 41467330--41467390 Score: 70
Period size: 18 Copynumber: 3.5 Consensus size: 17
41467320 ATTAAGTTTT
*
41467330 AAATCAATTCAAATTT-
1 AAATAAATTCAAATTTA
*
41467346 AATTAAATTCAAATTTA
1 AAATAAATTCAAATTTA
*
41467363 AAGATAAATTTAAATTTAA
1 AA-ATAAATTCAAATTT-A
41467382 AAATAAATT
1 AAATAAATT
41467391 TAAACCAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
16 14 0.37
17 2 0.05
18 19 0.50
19 3 0.08
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (17 bp):
AAATAAATTCAAATTTA
Found at i:41467376 original size:6 final size:6
Alignment explanation
Indices: 41467335--41467394 Score: 52
Period size: 6 Copynumber: 10.3 Consensus size: 6
41467325 GTTTTAAATC
* * **
41467335 AATTCA AATTT- AA-TTA AATTCA AATTTA AAGATA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
**
41467381 AAAATA AATTTA AA
1 AATTTA AATTTA AA
41467395 CCAATTTAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
4 2 0.05
5 4 0.10
6 35 0.85
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (6 bp):
AATTTA
Found at i:41467391 original size:18 final size:18
Alignment explanation
Indices: 41467349--41467394 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
41467339 CAAATTTAAT
* *
41467349 TAAATTCAAATTTAAAGA
1 TAAATTTAAATTTAAAAA
41467367 TAAATTTAAATTTAAAAA
1 TAAATTTAAATTTAAAAA
41467385 TAAATTTAAA
1 TAAATTTAAA
41467395 CCAATTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (18 bp):
TAAATTTAAATTTAAAAA
Found at i:41467413 original size:11 final size:10
Alignment explanation
Indices: 41467387--41467420 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
41467377 TTTAAAAATA
41467387 AATTTAAACC
1 AATTTAAACC
41467397 AATTTAAACC
1 AATTTAAACC
41467407 TAATTTAAAACC
1 -AATTT-AAACC
41467419 AA
1 AA
41467421 AAGCTTGATC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 7 0.32
12 5 0.23
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (10 bp):
AATTTAAACC
Found at i:41471131 original size:82 final size:82
Alignment explanation
Indices: 41470994--41471145 Score: 232
Period size: 82 Copynumber: 1.9 Consensus size: 82
41470984 TTTAACAATC
* ** * * * *
41470994 CAGGTTCTAGTGGTGTCGGAAATGGCAGTTTCAGAACACCGTTCTTCGATGGTCGAGTTTGTAAA
1 CAGGTTCCAGTGGTGTCAAAAATGGCAGTTTCAGAACACCGTTCTCCAATGGTCGAGTCTATAAA
41471059 TATTAATTGAAACGACT
66 TATTAATTGAAACGACT
*
41471076 CAGGTTCCAGTGGTGTCAAAAATGGCGGTTTCAGAACACCGTTCTCCAATGGTCGAGTCTATAAA
1 CAGGTTCCAGTGGTGTCAAAAATGGCAGTTTCAGAACACCGTTCTCCAATGGTCGAGTCTATAAA
41471141 TATTA
66 TATTA
41471146 TTTAATAATA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 62 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (82 bp):
CAGGTTCCAGTGGTGTCAAAAATGGCAGTTTCAGAACACCGTTCTCCAATGGTCGAGTCTATAAA
TATTAATTGAAACGACT
Found at i:41473442 original size:21 final size:19
Alignment explanation
Indices: 41473417--41473456 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
41473407 TTAACTTGGG
41473417 CATTTCAAATGTATTATATTA
1 CATTT-AAATGT-TTATATTA
*
41473438 CATTTTAATGTTTATATTA
1 CATTTAAATGTTTATATTA
41473457 TAAAAATACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 5 0.28
21 5 0.28
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (19 bp):
CATTTAAATGTTTATATTA
Found at i:41478238 original size:16 final size:16
Alignment explanation
Indices: 41478217--41478247 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
41478207 AAGGATATAA
41478217 TTCAAAATAAAAATAG
1 TTCAAAATAAAAATAG
41478233 TTCAAAATAAAAATA
1 TTCAAAATAAAAATA
41478248 ACTTTTAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (16 bp):
TTCAAAATAAAAATAG
Found at i:41479724 original size:30 final size:30
Alignment explanation
Indices: 41479678--41479968 Score: 306
Period size: 29 Copynumber: 9.7 Consensus size: 30
41479668 CTTTGACCCT
*
41479678 AAACTTCTCCAAAATTACATTTTTAACCCCA
1 AAACTTC-CAAAAATTACATTTTTAACCCCA
41479709 AAACTTCCAAAAATTACATTTTT-ACCCTC-
1 AAACTTCCAAAAATTACATTTTTAACCC-CA
* * *
41479738 AAACTTCCAAAAATTCCA-TTTTAACCTCG
1 AAACTTCCAAAAATTACATTTTTAACCCCA
* *
41479767 AAACTTCCAAAAATTCCATTTTTAACCCTA
1 AAACTTCCAAAAATTACATTTTTAACCCCA
* *
41479797 AAACTTCCAAAAATTGCATTTTT-ACCCCT
1 AAACTTCCAAAAATTACATTTTTAACCCCA
* * *
41479826 AAACTTCTAAAAATTCCATTTTTAACCCTA
1 AAACTTCCAAAAATTACATTTTTAACCCCA
* *
41479856 AAACTTCTCCAAAATTACATTTTTGACCCCA
1 AAACTTC-CAAAAATTACATTTTTAACCCCA
*
41479887 AAACTTCCAAAAATTACATTTTT-GCCCTC-
1 AAACTTCCAAAAATTACATTTTTAACCC-CA
* * * *
41479916 GAACTTCCAAAAATTCCATTTTTGACCTCA
1 AAACTTCCAAAAATTACATTTTTAACCCCA
* **
41479946 AAAATTTTAAAAATTACCATTTT
1 AAACTTCCAAAAATTA-CATTTT
41479969 ACCCTCGAAT
Statistics
Matches: 221, Mismatches: 29, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
28 5 0.02
29 92 0.42
30 86 0.39
31 38 0.17
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (30 bp):
AAACTTCCAAAAATTACATTTTTAACCCCA
Found at i:41479752 original size:59 final size:59
Alignment explanation
Indices: 41479655--41479997 Score: 354
Period size: 59 Copynumber: 5.8 Consensus size: 59
41479645 CCCTAAATTA
* * * * * *
41479655 TCCATAAATTATACTTTGACCCT-AAACTTCTCCAAAATTACATTTTTAACCCCAAAACT
1 TCCAAAAATTACATTTTTACCCTCAAACTTC-CAAAAATTCCATTTTTAACCCCAAAACT
* *
41479714 TCCAAAAATTACATTTTTACCCTCAAACTTCCAAAAATTCCA-TTTTAACCTCGAAACT
1 TCCAAAAATTACATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCCCAAAACT
* * * *
41479772 TCCAAAAATTCCATTTTTAACCCTAAAACTTCCAAAAATTGCATTTTT-ACCCCTAAACT
1 TCCAAAAATTACATTTTT-ACCCTCAAACTTCCAAAAATTCCATTTTTAACCCCAAAACT
* * * * * *
41479831 TCTAAAAATTCCATTTTTAACCCTAAAACTTCTCCAAAATTACATTTTTGACCCCAAAACT
1 TCCAAAAATTACATTTTT-ACCCTCAAACTTC-CAAAAATTCCATTTTTAACCCCAAAACT
* * * * *
41479892 TCCAAAAATTACATTTTTGCCCTCGAACTTCCAAAAATTCCATTTTTGACCTCAAAAAT
1 TCCAAAAATTACATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCCCAAAACT
** * *
41479951 TTTAAAAATTACCA-TTTTACCCTCGAA-TATCCAAAAACTCCATTTTT
1 TCCAAAAATTA-CATTTTTACCCTCAAACT-TCCAAAAATTCCATTTTT
41479998 TATTTCGATC
Statistics
Matches: 247, Mismatches: 30, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
58 32 0.13
59 152 0.62
60 37 0.15
61 26 0.11
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.34
Consensus pattern (59 bp):
TCCAAAAATTACATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCCCAAAACT
Found at i:41485626 original size:8 final size:7
Alignment explanation
Indices: 41485591--41485640 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 7
41485581 TGAATAAAAG
41485591 AAAAGAA
1 AAAAGAA
41485598 AAAAG-A
1 AAAAGAA
*
41485604 AGAAGAA
1 AAAAGAA
41485611 AAATAGAA
1 AAA-AGAA
41485619 ACAAAG-A
1 A-AAAGAA
41485626 AAAAG-A
1 AAAAGAA
41485632 AAAAGAA
1 AAAAGAA
41485639 AA
1 AA
41485641 GGAGAGGTCG
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
6 15 0.41
7 13 0.35
8 7 0.19
9 2 0.05
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (7 bp):
AAAAGAA
Found at i:41485631 original size:22 final size:21
Alignment explanation
Indices: 41485594--41485635 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
41485584 ATAAAAGAAA
*
41485594 AGAAAAAAGAAGAAGAAAAAT
1 AGAAAAAAGAAAAAGAAAAAT
41485615 AGAAACAAAGAAAAAGAAAAA
1 AGAAA-AAAGAAAAAGAAAAA
41485636 GAAAAGGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (21 bp):
AGAAAAAAGAAAAAGAAAAAT
Found at i:41486648 original size:50 final size:50
Alignment explanation
Indices: 41486592--41486958 Score: 154
Period size: 50 Copynumber: 7.3 Consensus size: 50
41486582 AGATACAATA
*
41486592 GGGAAAGGTCTAAGTCACAACGACAGACCGTGTACCACAAAAGACACGAC
1 GGGAAAGATCTAAGTCACAACGACAGACCGTGTACCACAAAAGACACGAC
* * * * * * *
41486642 GAGAAAGATCTAAGGC-CGTAACGACGGATCCAGTATAGCA-AAAAGACA-AAA
1 GGGAAAGATCTAAGTCAC--AACGACAGA-CC-GTGTACCACAAAAGACACGAC
* ** * * * * *
41486693 GGGAAAGGTCTAAGTCGTAACGGCAGACTGTGTACCTCAGAAGACCCGAC
1 GGGAAAGATCTAAGTCACAACGACAGACCGTGTACCACAAAAGACACGAC
* *** ** * * *
41486743 GGGAAAGATCTAAGACCACAACGGTGGATCC-AATACCGCAAAAAGACA-AAA
1 GGGAAAGATCTAAG-TCACAACGACAGA-CCGTGTACCAC-AAAAGACACGAC
* ** * * * * * *
41486794 GGGAAAGGTCTAAGTCGTAACGGCACACTGTGTACCTCAGAAGACCCGAC
1 GGGAAAGATCTAAGTCACAACGACAGACCGTGTACCACAAAAGACACGAC
* *** ** * * *
41486844 GGGAAAGATCTAAGACCACAACGGTGGATCC-AATACCGCAAAAAGACA-AAA
1 GGGAAAGATCTAAG-TCACAACGACAGA-CCGTGTACCAC-AAAAGACACGAC
* * * ** *
41486895 GGGAAAGGTCTAAGTTACAACGGCAGACCGTGTACCTTAGAAGACACGAC
1 GGGAAAGATCTAAGTCACAACGACAGACCGTGTACCACAAAAGACACGAC
41486945 GGGAAAGATCTAAG
1 GGGAAAGATCTAAG
41486959 ACTGCAACGG
Statistics
Matches: 221, Mismatches: 79, Indels: 34
0.66 0.24 0.10
Matches are distributed among these distances:
48 5 0.02
49 24 0.11
50 87 0.39
51 75 0.34
52 24 0.11
53 6 0.03
ACGTcount: A:0.40, C:0.22, G:0.26, T:0.13
Consensus pattern (50 bp):
GGGAAAGATCTAAGTCACAACGACAGACCGTGTACCACAAAAGACACGAC
Found at i:41486753 original size:101 final size:101
Alignment explanation
Indices: 41486571--41487097 Score: 591
Period size: 101 Copynumber: 5.3 Consensus size: 101
41486561 GGGAGAGATT
* * * * * * *
41486571 CAATACCGCAAAGATACAATAGGGAAAGGTCTAAGTCACAACGACAGACCGTGTACCACAAAAGA
1 CAATACCGCAAAAAGACAAAAGGGAAAGGTCTAAGTCGCAACGGCAGACCGTGTACCTCAGAAGA
* * ** *
41486636 CACGACGAGAAAGATCTAAGGCCGTAACGACGGATC
66 CACGACGGGAAAGATCTAAGACCACAACGGCGGATC
* ** * *
41486672 CAGTATAGCAAAAAGACAAAAGGGAAAGGTCTAAGTCGTAACGGCAGACTGTGTACCTCAGAAGA
1 CAATACCGCAAAAAGACAAAAGGGAAAGGTCTAAGTCGCAACGGCAGACCGTGTACCTCAGAAGA
* *
41486737 CCCGACGGGAAAGATCTAAGACCACAACGGTGGATC
66 CACGACGGGAAAGATCTAAGACCACAACGGCGGATC
* * *
41486773 CAATACCGCAAAAAGACAAAAGGGAAAGGTCTAAGTCGTAACGGCACACTGTGTACCTCAGAAGA
1 CAATACCGCAAAAAGACAAAAGGGAAAGGTCTAAGTCGCAACGGCAGACCGTGTACCTCAGAAGA
* *
41486838 CCCGACGGGAAAGATCTAAGACCACAACGGTGGATC
66 CACGACGGGAAAGATCTAAGACCACAACGGCGGATC
** *
41486874 CAATACCGCAAAAAGACAAAAGGGAAAGGTCTAAGTTACAACGGCAGACCGTGTACCTTAGAAGA
1 CAATACCGCAAAAAGACAAAAGGGAAAGGTCTAAGTCGCAACGGCAGACCGTGTACCTCAGAAGA
**
41486939 CACGACGGGAAAGATCTAAGACTGCAACGGCGGATC
66 CACGACGGGAAAGATCTAAGACCACAACGGCGGATC
* * * * * *
41486975 CAATACTGCAAAAA-A-ACAAGGGAAAGATCTAAGATCGCAACGGCGGATC-TAGTACCAC-GAA
1 CAATACCGCAAAAAGACAAAAGGGAAAGGTCTAAG-TCGCAACGGCAGACCGT-GTACCTCAGAA
* * * * * *
41487036 GACATGAAGAGAAAGATTTAAG-CCGCAACAGCGGATC
64 GACACGACGGGAAAGATCTAAGACCACAACGGCGGATC
* * *
41487073 CAGTACCGC--GAAGACACAAGGGAAA
1 CAATACCGCAAAAAGACAAAAGGGAAA
41487098 AATCTAAACT
Statistics
Matches: 371, Mismatches: 51, Indels: 11
0.86 0.12 0.03
Matches are distributed among these distances:
96 2 0.01
97 1 0.00
98 30 0.08
99 38 0.10
100 17 0.05
101 283 0.76
ACGTcount: A:0.40, C:0.22, G:0.25, T:0.13
Consensus pattern (101 bp):
CAATACCGCAAAAAGACAAAAGGGAAAGGTCTAAGTCGCAACGGCAGACCGTGTACCTCAGAAGA
CACGACGGGAAAGATCTAAGACCACAACGGCGGATC
Found at i:41487200 original size:97 final size:97
Alignment explanation
Indices: 41486990--41487231 Score: 283
Period size: 97 Copynumber: 2.5 Consensus size: 97
41486980 CTGCAAAAAA
* * * * *
41486990 ACAAGGGAAAGATCTAAGATCGCAACGGCGGATCTAGTACCACGAAGACATGAAGAGAAAGATTT
1 ACAAGAGAAAGATCTAA-ATCGCAACGGCGGATCCAATACCACGAAGACATGAAGAGAAAAATCT
* *
41487055 AAGCCGCAACAGCGGATCCAGTACCGCGAAGAC
65 AAGCCGCAACAGCAGATCCAGTACCACGAAGAC
* * * *
41487088 ACAAGGGAAAAATCTAAA-CTGCAACGGCGGATCCAATACCTCGAAGACAT-AAGGGAAAAATCT
1 ACAAGAGAAAGATCTAAATC-GCAACGGCGGATCCAATACCACGAAGACATGAAGAGAAAAATCT
*
41487151 AAGCCGCAA-AGGCAGATCCAGTACCACTAAGAC
65 AAGCCGCAACA-GCAGATCCAGTACCACGAAGAC
* * * *
41487184 ATGAAGAGAAAGATCTAAGTCGCGACGGTGGATCCAATACCACGAAGA
1 A-CAAGAGAAAGATCTAAATCGCAACGGCGGATCCAATACCACGAAGA
41487232 TTTAAAGGGA
Statistics
Matches: 123, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
95 1 0.01
96 40 0.33
97 65 0.53
98 17 0.14
ACGTcount: A:0.40, C:0.22, G:0.24, T:0.13
Consensus pattern (97 bp):
ACAAGAGAAAGATCTAAATCGCAACGGCGGATCCAATACCACGAAGACATGAAGAGAAAAATCTA
AGCCGCAACAGCAGATCCAGTACCACGAAGAC
Found at i:41487217 original size:145 final size:148
Alignment explanation
Indices: 41486934--41487231 Score: 388
Period size: 145 Copynumber: 2.0 Consensus size: 148
41486924 GTGTACCTTA
* *
41486934 GAAGACACGACGGGAAAGATCTAAGACTGCAACGGCGGATCCAATACTGCAAAAAAACAAGGGAA
1 GAAGACACGAAGGGAAAAATCTAAGACTGCAACGGCGGATCCAATACTGCAAAAAAACAAGGGAA
* * * * * *
41486999 AGATCTAAGATCGCAACGGCGGATCTAGTACCACGAAGACATGAAGAGAAAGATTTAAGCCGCAA
66 AAATCTAAGACCGCAAAGGCAGATCCAGTACCACGAAGACATGAAGAGAAAGATCTAAGCCGCAA
* *
41487064 CAGCGGATCCAGTACCGC
131 CAGCGGATCCAATACCAC
* * * *
41487082 GAAGACAC-AAGGGAAAAATCTAA-ACTGCAACGGCGGATCCAATACCT-CGAAGACATAAGGGA
1 GAAGACACGAAGGGAAAAATCTAAGACTGCAACGGCGGATCCAATA-CTGCAAAAAAACAAGGGA
* * *
41487144 AAAATCTAAG-CCGCAAAGGCAGATCCAGTACCACTAAGACATGAAGAGAAAGATCTAAGTCGCG
65 AAAATCTAAGACCGCAAAGGCAGATCCAGTACCACGAAGACATGAAGAGAAAGATCTAAGCCGCA
* *
41487208 ACGGTGGATCCAATACCAC
130 ACAGCGGATCCAATACCAC
41487227 GAAGA
1 GAAGA
41487232 TTTAAAGGGA
Statistics
Matches: 130, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
145 66 0.51
146 41 0.32
147 15 0.12
148 8 0.06
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.12
Consensus pattern (148 bp):
GAAGACACGAAGGGAAAAATCTAAGACTGCAACGGCGGATCCAATACTGCAAAAAAACAAGGGAA
AAATCTAAGACCGCAAAGGCAGATCCAGTACCACGAAGACATGAAGAGAAAGATCTAAGCCGCAA
CAGCGGATCCAATACCAC
Found at i:41487244 original size:49 final size:49
Alignment explanation
Indices: 41486844--41487262 Score: 269
Period size: 49 Copynumber: 8.5 Consensus size: 49
41486834 AAGACCCGAC
* * * * **
41486844 GGGAAAGATCTAAGACCACAACGGTGGATCCAATACCGCAAAAAGACA-AAA
1 GGGAAAGATCTAAG-TCGCAACGGCGGATCCAGTA-C-CACGAAGACATAAA
* ** * * ** *
41486895 GGGAAAGGTCTAAGTTACAACGGCAGA-CCGTGTACCTTA-GAAGACACGAC
1 GGGAAAGATCTAAGTCGCAACGGCGGATCC-AGTACC--ACGAAGACATAAA
* * ** * *
41486945 GGGAAAGATCTAAGACTGCAACGGCGGATCCAATACTGC-AA-AAAAACAA
1 GGGAAAGATCTAAGTC-GCAACGGCGGATCCAGTACCACGAAGACATA-AA
* *
41486994 GGGAAAGATCTAAGATCGCAACGGCGGATCTAGTACCACGAAGACATGAA
1 GGGAAAGATCTAAG-TCGCAACGGCGGATCCAGTACCACGAAGACATAAA
* * * * * *
41487044 GAGAAAGATTTAAGCCGCAACAGCGGATCCAGTACCGCGAAGACA-CAA
1 GGGAAAGATCTAAGTCGCAACGGCGGATCCAGTACCACGAAGACATAAA
* * * *
41487092 GGGAAAAATCTAA-ACTGCAACGGCGGATCCAATACCTCGAAGACAT-AA
1 GGGAAAGATCTAAGTC-GCAACGGCGGATCCAGTACCACGAAGACATAAA
* * * * * *
41487140 GGGAAAAATCTAAGCCGCAAAGGCAGATCCAGTACCACTAAGACATGAA
1 GGGAAAGATCTAAGTCGCAACGGCGGATCCAGTACCACGAAGACATAAA
* * * * **
41487189 GAGAAAGATCTAAGTCGCGACGGTGGATCCAATACCACGAAGATTTAAA
1 GGGAAAGATCTAAGTCGCAACGGCGGATCCAGTACCACGAAGACATAAA
* * *
41487238 GGGAAAGGTTTAAGTCGCAATGGCG
1 GGGAAAGATCTAAGTCGCAACGGCG
41487263 AACCTGGTAC
Statistics
Matches: 284, Mismatches: 69, Indels: 32
0.74 0.18 0.08
Matches are distributed among these distances:
47 1 0.00
48 81 0.29
49 130 0.46
50 43 0.15
51 27 0.10
52 2 0.01
ACGTcount: A:0.40, C:0.21, G:0.25, T:0.14
Consensus pattern (49 bp):
GGGAAAGATCTAAGTCGCAACGGCGGATCCAGTACCACGAAGACATAAA
Found at i:41487551 original size:39 final size:39
Alignment explanation
Indices: 41487507--41487713 Score: 143
Period size: 39 Copynumber: 5.3 Consensus size: 39
41487497 GAAGATTCTG
41487507 ATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAATCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAATCA
* * * **
41487546 ATCTCTTACCTCGAGCTAGGGGCAGAT--TGCAGTCATTTG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCAT-CA-TCAATCA
* * * * *
41487585 ATCTTTTACCCCAAGCCTGGGACAGATCATCATCAACCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAATCA
* * * * * *
41487624 ATTTCTTACCCTGAGCTAGGGGCAGAT--TGCAACCATCTG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCAT-CATCAATC-A
* * * ** *
41487663 ACCTTTTACTCCGAGCTTGCAGCAGATCATCATCAACCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAATCA
*
41487702 ATCTTTTACCCC
1 ATCTCTTACCCC
41487714 AATCACGGGG
Statistics
Matches: 120, Mismatches: 40, Indels: 16
0.68 0.23 0.09
Matches are distributed among these distances:
37 2 0.02
38 7 0.06
39 102 0.85
40 7 0.06
41 2 0.02
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAATCA
Found at i:41487595 original size:78 final size:78
Alignment explanation
Indices: 41487503--41487712 Score: 278
Period size: 78 Copynumber: 2.7 Consensus size: 78
41487493 AAATGAAGAT
* *
41487503 TCTGATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAATCAATCTCTTA-CCTCGAGCTAGGG
1 TCTGATCTTTTACCCCGAGCTTGGGGCAGATCATCATCAACCAATCTCTTACCCT-GAGCTAGGG
**
41487567 GCAGATTGCAGTCA
65 GCAGATTGCAACCA
* * * * *
41487581 TTTGATCTTTTACCCCAAGCCTGGGACAGATCATCATCAACCAATTTCTTACCCTGAGCTAGGGG
1 TCTGATCTTTTACCCCGAGCTTGGGGCAGATCATCATCAACCAATCTCTTACCCTGAGCTAGGGG
41487646 CAGATTGCAACCA
66 CAGATTGCAACCA
* * ** *
41487659 TCTGACCTTTTACTCCGAGCTTGCAGCAGATCATCATCAACCAATCTTTTACCC
1 TCTGATCTTTTACCCCGAGCTTGGGGCAGATCATCATCAACCAATCTCTTACCC
41487713 CAATCACGGG
Statistics
Matches: 112, Mismatches: 19, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
78 109 0.97
79 3 0.03
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.28
Consensus pattern (78 bp):
TCTGATCTTTTACCCCGAGCTTGGGGCAGATCATCATCAACCAATCTCTTACCCTGAGCTAGGGG
CAGATTGCAACCA
Found at i:41488196 original size:204 final size:204
Alignment explanation
Indices: 41487752--41488794 Score: 1255
Period size: 204 Copynumber: 5.1 Consensus size: 204
41487742 ACAAACGATA
* * * ** ** ** *
41487752 CGGTCATCTTTCTGATGAGATACTGAGAAGAAGACAAAATCAAACCCACACTTGATATGAGCATA
1 CGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCAGGCTCAATGCGAGCAAA
* *
41487817 TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCAAT-AAATGGTTAGCTT
66 TCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTT
* * *
41487881 CCTGATGAGACACTGAGAAGTGGACCAAATTCGTCTTCTTGAGGAGATCTACAGAAGCGAATTAA
131 CCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGA-C-ACAGAAGCGAATTAA
*
41487946 AACAAGTGATG
194 AACAAGTGAGG
*
41487957 CAGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCAGGCTCAATGCGAGCAAA
1 CGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCAGGCTCAATGCGAGCAAA
* * * *
41488022 TCTTCGAACTCC-AACCTCTTGATGAGATATTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCT
66 TCTTCGAAC-CCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCT
*
41488086 TCCTGATGAGATACTGAGAAGCGGACCAAATTCGTCTTCCTGATGAGACACAGAAGCGAATTAAA
130 TCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAAGCGAATTAAA
*
41488151 ACAAGTGATG
195 ACAAGTGAGG
41488161 CGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCAGGCTCAATGCGAGCAAA
1 CGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCAGGCTCAATGCGAGCAAA
* * *
41488226 ACTTCGAACCCTAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTT
66 TCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTT
* * * * *
41488291 CCTGATGAGATACTAAGAAGTGAACCAAATTCAG-CTTCCTGATGAGATATAGAGAAGCGAATTG
131 CCTGATGAGATACTGAGAAGTGGACCAAATTC-GTCTTCCTGATGAG--ACACAGAAGCGAATTA
**
41488355 AAACAAACGAGG
193 AAACAAGTGAGG
* * * ** * *
41488367 CGGTCATCTTCCTGATGAGATAC--AGAA-AAG----TATGCCAACTCGGGGCTCGATGTGAGCA
1 CGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAAT-CAAAC-CCAGGCTCAATGCGAGCA
41488425 AATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT-AAATGGTTAGC
64 AATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGC
* * * *
41488489 TTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTC-TCTTGATTGAGATACAGAGAAGCGGAT
129 TTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGA-TGAG--ACACAGAAGCGAAT
*
41488553 TGAAACAAGTGAGG
191 TAAAACAAGTGAGG
* * * * * * *
41488567 TGGTCATCTTCTTGATGAGATCACAGAG-AGTA-ACC-AA-C---TCGAGTCTCAATGCGAGCAA
1 CGGTCATCTTCCTGATGAGA-CACTGAGAAGAAGACCAAATCAAACCCAGGCTCAATGCGAGCAA
41488625 ATCTTCGAACCCTAGCTTCCTGATGAGATACT-AGAAGCAGGTCGAAGCAATAAAATGGTTAGCT
65 ATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCT
* * * * * * *
41488689 TCCCGATGAGATACGGAGAAGTGAACCAAATCCGTCTTCCTGATGAAACATAGAGAGTCG-ATCA
130 TCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGA-AG-CGAATTA
41488753 AAACAAGTGAGG
193 AAACAAGTGAGG
* * *
41488765 CGGTCATCTTCCTTATGAGATACAGAGAAG
1 CGGTCATCTTCCTGATGAGACACTGAGAAG
41488795 TATACCAACT
Statistics
Matches: 739, Mismatches: 77, Indels: 51
0.85 0.09 0.06
Matches are distributed among these distances:
197 12 0.02
198 54 0.07
199 103 0.14
200 100 0.14
201 66 0.09
202 1 0.00
203 9 0.01
204 192 0.26
205 100 0.14
206 102 0.14
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (204 bp):
CGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCAGGCTCAATGCGAGCAAA
TCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTT
CCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAAGCGAATTAAAA
CAAGTGAGG
Found at i:41489208 original size:34 final size:34
Alignment explanation
Indices: 41489170--41489236 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
41489160 TTTTTAAATA
*
41489170 AGTTTGAATTTATTTTAAATTCAAATTCATTTTG
1 AGTTTGAATTTACTTTAAATTCAAATTCATTTTG
* * *
41489204 AGTTTGGATTTACTTTAAATTTAAATTTATTTT
1 AGTTTGAATTTACTTTAAATTCAAATTCATTTT
41489237 TAAAAATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.31, C:0.04, G:0.09, T:0.55
Consensus pattern (34 bp):
AGTTTGAATTTACTTTAAATTCAAATTCATTTTG
Found at i:41489269 original size:12 final size:12
Alignment explanation
Indices: 41489252--41489291 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
41489242 ATTAAAATTA
*
41489252 AATTAAAGGTCC
1 AATTAAAAGTCC
41489264 AATTAAAAAGTCC
1 AATT-AAAAGTCC
41489277 AATTAAAAAGTCC
1 AATT-AAAAGTCC
41489290 AA
1 AA
41489292 ATACAAATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 4 0.15
13 22 0.85
ACGTcount: A:0.53, C:0.15, G:0.10, T:0.23
Consensus pattern (12 bp):
AATTAAAAGTCC
Found at i:41489278 original size:13 final size:13
Alignment explanation
Indices: 41489260--41489291 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
41489250 TAAATTAAAG
41489260 GTCCAATTAAAAA
1 GTCCAATTAAAAA
41489273 GTCCAATTAAAAA
1 GTCCAATTAAAAA
41489286 GTCCAA
1 GTCCAA
41489292 ATACAAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.50, C:0.19, G:0.09, T:0.22
Consensus pattern (13 bp):
GTCCAATTAAAAA
Found at i:41489341 original size:16 final size:16
Alignment explanation
Indices: 41489320--41489351 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41489310 ATAGGCTCAT
*
41489320 TTTCAATTGACCCAAA
1 TTTCAATCGACCCAAA
41489336 TTTCAATCGACCCAAA
1 TTTCAATCGACCCAAA
41489352 CAATAACCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.28, G:0.06, T:0.28
Consensus pattern (16 bp):
TTTCAATCGACCCAAA
Found at i:41491025 original size:29 final size:29
Alignment explanation
Indices: 41490943--41491263 Score: 256
Period size: 29 Copynumber: 10.9 Consensus size: 29
41490933 AAAGGTCCCT
* * * *
41490943 AAACTATCCATAAATTATATTTTAACCCCC
1 AAACT-TCCAAAAATTACATTTTGACCCCA
* * **
41490973 GAACTTCTCCAAAATTACATTTTTGACCTTA
1 AAACTTC-CAAAAATTACA-TTTTGACCCCA
*
41491004 AAACTTCCAAAAATTACATTTTTA-CCC-
1 AAACTTCCAAAAATTACATTTTGACCCCA
* * * *
41491031 AAACTTCTAAAAATTCCATTTTGACCTCG
1 AAACTTCCAAAAATTACATTTTGACCCCA
* * ***
41491060 AAACTTCCAAAAATTCCATTTTTAACCTTG
1 AAACTTCCAAAAATTACA-TTTTGACCCCA
* * *
41491090 AAACTTCCAAAAAATACATTTTTACCCCC
1 AAACTTCCAAAAATTACATTTTGACCCCA
* *
41491119 AAACTTCCAAAAATTCCATTTTAACCCCA
1 AAACTTCCAAAAATTACATTTTGACCCCA
* *
41491148 AAACTTCTCCAAAATTACATTTTTTGACCCTA
1 AAACTTC-CAAAAATTACA--TTTTGACCCCA
*
41491180 AAACTTCCAAAAATTACATTTTG-CCCCC
1 AAACTTCCAAAAATTACATTTTGACCCCA
* * *
41491208 AAACTTCC-AAAATTCCATTTTTAACCTCA
1 AAACTTCCAAAAATTACA-TTTTGACCCCA
*
41491237 AAAGTTCCAAAAATTACCATTTT-ACCC
1 AAACTTCCAAAAATTA-CATTTTGACCC
41491264 TCGAATGTCC
Statistics
Matches: 235, Mismatches: 44, Indels: 25
0.77 0.14 0.08
Matches are distributed among these distances:
27 29 0.12
28 18 0.08
29 81 0.34
30 66 0.28
31 25 0.11
32 16 0.07
ACGTcount: A:0.38, C:0.27, G:0.02, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTGACCCCA
Found at i:41491123 original size:59 final size:57
Alignment explanation
Indices: 41490974--41491259 Score: 245
Period size: 59 Copynumber: 4.9 Consensus size: 57
41490964 TTAACCCCCG
* ** *
41490974 AACTTCTCCAAAATTACATTTTTGACCTTAAAACTTCCAAAAATTACATTTTT-ACCCA
1 AACTTC-CAAAAATTACATTTTT-ACCCCAAAACTTCCAAAAATTACATTTTTAACCAA
* * * * * * *
41491032 AACTTCTAAAAATTCCATTTTGACCTCGAAACTTCCAAAAATTCCATTTTTAACCTTGA
1 AACTTCCAAAAATTACATTTTTACCCCAAAACTTCCAAAAATTACATTTTTAACC--AA
* * *
41491091 AACTTCCAAAAAATACATTTTTACCCCCAAACTTCCAAAAATTCCA-TTTTAACCCCAA
1 AACTTCCAAAAATTACATTTTTACCCCAAAACTTCCAAAAATTACATTTTTAA--CCAA
* * *** *
41491149 AACTTCTCCAAAATTACATTTTTTGACCCTAAAACTTCCAAAAATTACATTTTGCCCCCA
1 AACTTC-CAAAAATTACA-TTTTT-ACCCCAAAACTTCCAAAAATTACATTTTTAACCAA
* * *
41491209 AACTTCC-AAAATTCCATTTTTAACCTCAAAAGTTCCAAAAATTACCATTTT
1 AACTTCCAAAAATTACATTTTT-ACCCCAAAACTTCCAAAAATTA-CATTTT
41491260 ACCCTCGAAT
Statistics
Matches: 189, Mismatches: 29, Indels: 20
0.79 0.12 0.08
Matches are distributed among these distances:
56 26 0.14
57 39 0.21
58 33 0.17
59 51 0.27
60 16 0.08
61 21 0.11
62 3 0.02
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (57 bp):
AACTTCCAAAAATTACATTTTTACCCCAAAACTTCCAAAAATTACATTTTTAACCAA
Found at i:41491227 original size:88 final size:85
Alignment explanation
Indices: 41490943--41491259 Score: 355
Period size: 88 Copynumber: 3.6 Consensus size: 85
41490933 AAAGGTCCCT
** ** *
41490943 AAACTATCCATAAATTATATTTTAACCCCCGAACTTCTCCAAAATTACATTTTTGACCTTAAAAC
1 AAACT-TCCA-AAATTCCATTTTAACCCCAAAACTTC-CAAAAATTACATTTTTGACCTTAAAAC
**
41491008 TTCCAAAAATTACATTTTTACCC
63 TTCCAAAAATTACATTTTCCCCC
* * * * * * *
41491031 AAACTTCTAAAAATTCCATTTTGACCTCGAAACTTCCAAAAATTCCATTTTTAACCTTGAAACTT
1 AAACTTC-CAAAATTCCATTTTAACCCCAAAACTTCCAAAAATTACATTTTTGACCTTAAAACTT
*
41491096 CCAAAAAATACATTTTTACCCCC
65 CCAAAAATTACA-TTTT-CCCCC
* *
41491119 AAACTTCCAAAAATTCCATTTTAACCCCAAAACTTCTCCAAAATTACATTTTTTGACCCTAAAAC
1 AAACTTCC-AAAATTCCATTTTAACCCCAAAACTTC-CAAAAATTACA-TTTTTGACCTTAAAAC
41491184 TTCCAAAAATTACATTTTGCCCCC
63 TTCCAAAAATTACATTTT-CCCCC
* *
41491208 AAACTTCCAAAATTCCATTTTTAACCTCAAAAGTTCCAAAAATTACCATTTT
1 AAACTTCCAAAATTCCA-TTTTAACCCCAAAACTTCCAAAAATTA-CATTTT
41491260 ACCCTCGAAT
Statistics
Matches: 193, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
86 36 0.19
87 26 0.13
88 61 0.32
89 44 0.23
90 26 0.13
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (85 bp):
AAACTTCCAAAATTCCATTTTAACCCCAAAACTTCCAAAAATTACATTTTTGACCTTAAAACTTC
CAAAAATTACATTTTCCCCC
Found at i:41491277 original size:176 final size:176
Alignment explanation
Indices: 41490943--41491289 Score: 470
Period size: 176 Copynumber: 2.0 Consensus size: 176
41490933 AAAGGTCCCT
* * ** *
41490943 AAACTATCCATAAATTATATTTTAACCCCCGAACTTCTCCAAAATTACATTTTTGACCTTAAAAC
1 AAACTATCCAAAAATTACATTTTAACCCCAAAACTTCTCCAAAATTACATTTTTGACCCTAAAAC
* * *
41491008 TTCCAAAAATTACATTTTTACCCAAACTTCTAAAAATTCCATTTTGACCTCGAAACTTCCAAAAA
66 TTCCAAAAATTACATTTTCACCCAAACTTCTAAAAATTCCATTTTAACCTCAAAACTTCCAAAAA
*
41491073 TTCCATTTTTAACCTTGAAACTTCCAAAAAATACATTTTTACCCCC
131 TTCCATTTTTAACCTCGAAACTTCCAAAAAATACATTTTTACCCCC
*
41491119 AAACT-TCCAAAAATTCCATTTTAACCCCAAAACTTCTCCAAAATTACATTTTTTGACCCTAAAA
1 AAACTATCCAAAAATTACATTTTAACCCCAAAACTTCTCCAAAATTACA-TTTTTGACCCTAAAA
* * *
41491183 CTTCCAAAAATTACATTTTGCCCCCAAACTTC-CAAAATTCCATTTTTAACCTCAAAAGTTCCAA
65 CTTCCAAAAATTACATTTT-CACCCAAACTTCTAAAAATTCCA-TTTTAACCTCAAAACTTCCAA
* * *
41491247 AAATTACCA-TTTTACCCTCG-AA-TGTCCAAAAACTCCATTTTTA
128 AAATT-CCATTTTTAACCTCGAAACT-TCCAAAAAATACATTTTTA
41491290 ATCCCTATTT
Statistics
Matches: 150, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
175 39 0.26
176 66 0.44
177 42 0.28
178 3 0.02
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.33
Consensus pattern (176 bp):
AAACTATCCAAAAATTACATTTTAACCCCAAAACTTCTCCAAAATTACATTTTTGACCCTAAAAC
TTCCAAAAATTACATTTTCACCCAAACTTCTAAAAATTCCATTTTAACCTCAAAACTTCCAAAAA
TTCCATTTTTAACCTCGAAACTTCCAAAAAATACATTTTTACCCCC
Found at i:41492684 original size:26 final size:26
Alignment explanation
Indices: 41492637--41492691 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
41492627 ATACATATTA
* * *
41492637 TATTTTTTGAACTTTAGGAAAGTTTT
1 TATTTTTTAAACTTTAGAAAAGCTTT
* *
41492663 TATTTTTTAAATTTTTGAAAAGCTTT
1 TATTTTTTAAACTTTAGAAAAGCTTT
41492689 TAT
1 TAT
41492692 ATAGTTTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.04, G:0.11, T:0.56
Consensus pattern (26 bp):
TATTTTTTAAACTTTAGAAAAGCTTT
Found at i:41492731 original size:15 final size:15
Alignment explanation
Indices: 41492703--41492738 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
41492693 TAGTTTTTGG
*
41492703 AATTATAATTTTTTT
1 AATTATAATTTTTTA
*
41492718 AATTTTAATTTTTTA
1 AATTATAATTTTTTA
41492733 AATTAT
1 AATTAT
41492739 TTATTGATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
AATTATAATTTTTTA
Found at i:41494686 original size:10 final size:10
Alignment explanation
Indices: 41494671--41494700 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
41494661 GTATTTATTA
41494671 TATCCAAAAT
1 TATCCAAAAT
*
41494681 TATCCAAAAG
1 TATCCAAAAT
41494691 TATCCAAAAT
1 TATCCAAAAT
41494701 AATTTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.50, C:0.20, G:0.03, T:0.27
Consensus pattern (10 bp):
TATCCAAAAT
Found at i:41496212 original size:15 final size:17
Alignment explanation
Indices: 41496182--41496215 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
41496172 TAAAATTAAA
41496182 TTATAATTTTTAATAAT
1 TTATAATTTTTAATAAT
41496199 TTAT-ATTTTT-ATAAT
1 TTATAATTTTTAATAAT
41496214 TT
1 TT
41496216 TTAAAAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 6 0.35
17 4 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATAATTTTTAATAAT
Found at i:41496461 original size:2 final size:2
Alignment explanation
Indices: 41496456--41496514 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
41496446 TTTTTTCTTA
41496456 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41496498 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
41496515 CTTGTATGAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.