Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 201 of 208
Found at i:62182267 original size:181 final size:175
Alignment explanation
Indices: 62181970--62182348 Score: 498
Period size: 181 Copynumber: 2.1 Consensus size: 175
62181960 TAGGGCTAGA
62181970 TTTAGGGTTT-GGGATTTTGGATCTCCAAGCCAAAACAAGGTCCGTCACGACCAGGTTTTTTACA
1 TTTAGGGTTTAGGG-TTTTGGATCTCCAAGCCAAAACAAGGTCCGTCACGACCAGGTTTTTTACA
62182034 TTACCGCTCTTGTTAACCACTGTGTTTTAGAGTTTAAGGTTCTGGATCTCCATGCCGGAACAAGG
65 TTACCGCTCTTGTTAACCACTGTGTTTTAGAGTTTAAGGTTCTGGATCTCCATGCCGGAACAAGG
62182099 TCACCACCGTGCTTTTCGACA-TATC-TCTGGCATTAACTACTGTAT
130 TCACCACCGTGCTTTTCGACATTATCTTC-GGCATTAACTACTGTAT
* * * * * *
62182144 TTTAGGGTTTAGGGTTTTGGATTTTCAGGCCAAAACAAGGTCCTTCACGACCAGTTTTTTTATAT
1 TTTAGGGTTTAGGGTTTTGGATCTCCAAGCCAAAACAAGGTCCGTCACGACCAGGTTTTTTACAT
* * * *
62182209 TATCTCATG-TGTTAAGTGTTAACCACTGTGTTTTAGAGTTTAGGGTTTTGGATCTCCATGCTGG
66 TA-C-C--GCT-CT---TGTTAACCACTGTGTTTTAGAGTTTAAGGTTCTGGATCTCCATGCCGG
* * * *
62182273 AACAAGGTCGCCACCGTGCTTTTTGACATTATCTTCGGCATTAACTATTGTGT
123 AACAAGGTCACCACCGTGCTTTTCGACATTATCTTCGGCATTAACTACTGTAT
*
62182326 TTTA-GGTTTAGGGTTTTGAATCT
1 TTTAGGGTTTAGGGTTTTGGATCT
62182349 AATGCTTACA
Statistics
Matches: 178, Mismatches: 16, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
174 57 0.32
175 4 0.02
176 1 0.01
177 1 0.01
178 2 0.01
181 88 0.49
182 23 0.13
183 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (175 bp):
TTTAGGGTTTAGGGTTTTGGATCTCCAAGCCAAAACAAGGTCCGTCACGACCAGGTTTTTTACAT
TACCGCTCTTGTTAACCACTGTGTTTTAGAGTTTAAGGTTCTGGATCTCCATGCCGGAACAAGGT
CACCACCGTGCTTTTCGACATTATCTTCGGCATTAACTACTGTAT
Found at i:62184149 original size:18 final size:18
Alignment explanation
Indices: 62184122--62184162 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
62184112 TAATCAAATG
62184122 ATAT-AAAAAAAATCTTA
1 ATATGAAAAAAAATCTTA
*
62184139 ATATGAAAAAAATTCTTA
1 ATATGAAAAAAAATCTTA
*
62184157 GTATGA
1 ATATGA
62184163 TTCAAATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (18 bp):
ATATGAAAAAAAATCTTA
Found at i:62184703 original size:5 final size:5
Alignment explanation
Indices: 62184670--62184700 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
62184660 CATGGGGTAT
62184670 AATAA AATAA AATAA AATAA AATAA ATATAA
1 AATAA AATAA AATAA AATAA AATAA A-ATAA
62184701 TATTGGACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.84
6 4 0.16
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
AATAA
Found at i:62194888 original size:28 final size:26
Alignment explanation
Indices: 62194843--62194906 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 26
62194833 TAAGATAATT
62194843 ATATATAAAATTTTAATAAATAAAA-A
1 ATATATAAAATTTTAAT-AATAAAATA
*
62194869 ATATATAAAATTATTAAATATTAAAATA
1 ATATATAAAATT-TT-AATAATAAAATA
62194897 ATAATATAAA
1 AT-ATATAAA
62194907 TATATATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
26 12 0.36
27 8 0.24
28 6 0.18
29 7 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
ATATATAAAATTTTAATAATAAAATA
Found at i:62194907 original size:28 final size:28
Alignment explanation
Indices: 62194827--62194906 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 28
62194817 AAACATTAAA
*
62194827 AAATATTAAGATAATTATATATAAAATTTT
1 AAATATTAAAATAA-TA-ATATAAAATTTT
*
62194857 -AATAAATAAAA-AAT-ATATAAAATTATT
1 AAAT-ATTAAAATAATAATATAAAATT-TT
62194884 AAATATTAAAATAATAATATAAA
1 AAATATTAAAATAATAATATAAA
62194907 TATATATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
26 10 0.24
27 8 0.19
28 7 0.17
29 12 0.29
30 5 0.12
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (28 bp):
AAATATTAAAATAATAATATAAAATTTT
Found at i:62198486 original size:24 final size:23
Alignment explanation
Indices: 62198458--62198505 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
62198448 TTTATCTATG
62198458 ATTTTATATGTATTTTT-TTATAAA
1 ATTTT-TATGTATTTTTATTA-AAA
62198482 A-TTTTATGTATTTTTATTAAAA
1 ATTTTTATGTATTTTTATTAAAA
62198504 AT
1 AT
62198506 GAACTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
22 15 0.68
23 6 0.27
24 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
ATTTTTATGTATTTTTATTAAAA
Found at i:62198489 original size:22 final size:22
Alignment explanation
Indices: 62198464--62198505 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
62198454 TATGATTTTA
62198464 TATGTATTTTT-TTATAAAATTT
1 TATGTATTTTTATTA-AAAATTT
62198486 TATGTATTTTTATTAAAAAT
1 TATGTATTTTTATTAAAAAT
62198506 GAACTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
TATGTATTTTTATTAAAAATTT
Found at i:62198929 original size:21 final size:22
Alignment explanation
Indices: 62198905--62198952 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
62198895 GAAAATGTGC
*
62198905 AATTTAAACCCTTTA-AAAAAT
1 AATTTAAAACCTTTATAAAAAT
* **
62198926 AATTCAAAATGTTTATAAAAAT
1 AATTTAAAACCTTTATAAAAAT
62198948 AATTT
1 AATTT
62198953 TCCAAAATTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (22 bp):
AATTTAAAACCTTTATAAAAAT
Found at i:62208124 original size:25 final size:25
Alignment explanation
Indices: 62208092--62208144 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
62208082 GATATCACAG
62208092 ATATTACAAATGTGACTTAGTGCAT
1 ATATTACAAATGTGACTTAGTGCAT
62208117 ATATTACAAATGTGACTTAGTGCAT
1 ATATTACAAATGTGACTTAGTGCAT
62208142 ATA
1 ATA
62208145 GATAGTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (25 bp):
ATATTACAAATGTGACTTAGTGCAT
Found at i:62208943 original size:18 final size:18
Alignment explanation
Indices: 62208920--62208955 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
62208910 AATTTAGTCA
62208920 TTATAATTTTATTTTCAG
1 TTATAATTTTATTTTCAG
62208938 TTATAATTTTATTTTCAG
1 TTATAATTTTATTTTCAG
62208956 GATTTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.61
Consensus pattern (18 bp):
TTATAATTTTATTTTCAG
Found at i:62209092 original size:36 final size:37
Alignment explanation
Indices: 62209037--62209115 Score: 151
Period size: 36 Copynumber: 2.2 Consensus size: 37
62209027 ACTAAATTCT
62209037 TGAAAATAAAAAATTCAAGGATTAAATTTCAAATATA
1 TGAAAATAAAAAATTCAAGGATTAAATTTCAAATATA
62209074 TGAAAAT-AAAAATTCAAGGATTAAATTTCAAATATA
1 TGAAAATAAAAAATTCAAGGATTAAATTTCAAATATA
62209110 TGAAAA
1 TGAAAA
62209116 GTACAGGGAC
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 35 0.83
37 7 0.17
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.29
Consensus pattern (37 bp):
TGAAAATAAAAAATTCAAGGATTAAATTTCAAATATA
Found at i:62209360 original size:25 final size:25
Alignment explanation
Indices: 62209305--62209362 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
62209295 TCAAGTAAAA
**
62209305 TAAAAAAATATAATAATTAAAATTT
1 TAAAAAAATATAATAATTAAAAGAT
* * *
62209330 TCAAAAAATATAATAATTGATAGAT
1 TAAAAAAATATAATAATTAAAAGAT
62209355 TAAAAAAA
1 TAAAAAAA
62209363 ATATTGAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (25 bp):
TAAAAAAATATAATAATTAAAAGAT
Found at i:62209721 original size:7 final size:7
Alignment explanation
Indices: 62209709--62209742 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
62209699 TCAGCTATTG
62209709 TTTTTCT
1 TTTTTCT
62209716 TTTTTCT
1 TTTTTCT
*
62209723 TTTTCCT
1 TTTTTCT
*
62209730 TTTTCCT
1 TTTTTCT
62209737 TTTTTC
1 TTTTTC
62209743 GCTTGGCTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTCT
Found at i:62212278 original size:52 final size:51
Alignment explanation
Indices: 62212207--62212461 Score: 341
Period size: 52 Copynumber: 5.1 Consensus size: 51
62212197 ATCAAGTGAT
62212207 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAGT-G
*
62212259 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTG---A-T-
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAGTG
62212305 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAGTG
*
62212356 AAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC-----
1 -AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAGTG
** * * *
62212403 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGACCAAGAGACAAAGTG
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC-AAGTG
62212455 ATAAGTG
1 A-AAGTG
62212462 GCTGCACTTA
Statistics
Matches: 183, Mismatches: 7, Indels: 25
0.85 0.03 0.12
Matches are distributed among these distances:
46 85 0.46
48 1 0.01
49 2 0.01
50 1 0.01
52 89 0.49
53 5 0.03
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAGTG
Found at i:62212312 original size:98 final size:98
Alignment explanation
Indices: 62212193--62212461 Score: 439
Period size: 98 Copynumber: 2.7 Consensus size: 98
62212183 TTTGAGTACT
62212193 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAGTG
*
62212258 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
62212291 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAGTG
*
62212356 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* * ** * * *
62212389 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGACCAAGAGACAAAGT
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC-AAGT
*
62212454 GATAAGTG
65 GAAAAGTG
62212462 GCTGCACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (98 bp):
TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:62212322 original size:46 final size:46
Alignment explanation
Indices: 62212259--62212498 Score: 282
Period size: 46 Copynumber: 5.3 Consensus size: 46
62212249 TGACAAGTGG
* * *
62212259 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAT
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
*
62212305 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
62212351 AAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 ------AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
** * *
62212403 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGACCAAGAGAC
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
*
62212449 AAAGTGATAAGTG---GC-T--GC---ACTTATCTGATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
62212486 AAAGTGATAAGTG
1 AAAGTGATAAGTG
62212499 GCTACACTTA
Statistics
Matches: 179, Mismatches: 9, Indels: 21
0.86 0.04 0.10
Matches are distributed among these distances:
37 30 0.17
40 2 0.01
42 1 0.01
43 2 0.01
46 99 0.55
52 45 0.25
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
Found at i:62212473 original size:37 final size:37
Alignment explanation
Indices: 62212425--62212570 Score: 224
Period size: 37 Copynumber: 4.0 Consensus size: 37
62212415 GATAGCTTTA
* *
62212425 GCTACACTTATCTGACCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
62212462 GCTGCACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
62212499 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
62212536 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
62212571 ATCATACGTA
Statistics
Matches: 101, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 86 0.85
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:62213886 original size:49 final size:49
Alignment explanation
Indices: 62213825--62213968 Score: 207
Period size: 49 Copynumber: 2.9 Consensus size: 49
62213815 ATGTGAACAT
* *
62213825 GTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTGTGGCATCGGTAA
1 GTGA-TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* * *
62213875 GTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCAGTAT
1 GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* * *
62213924 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCG
62213969 AGAAAACGAA
Statistics
Matches: 85, Mismatches: 9, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
49 81 0.95
50 4 0.05
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.32
Consensus pattern (49 bp):
GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
Found at i:62217179 original size:52 final size:49
Alignment explanation
Indices: 62217094--62217362 Score: 346
Period size: 46 Copynumber: 5.6 Consensus size: 49
62217084 TTTGAGTACT
62217094 TCTGATCAAGTG---ATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
*
62217140 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTATACTTA
62217192 TCTGATCAAGTG---ATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
62217238 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTATACTTA
* ** *
62217290 TCTGATCAAGAGAC---AAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
*
62217336 TCTGATCAAGAGAC---AAAGTGATAAGTG
1 TCTGATCAAGTGACAATAAAGTGATAAGTG
62217363 GCTGCACTTA
Statistics
Matches: 205, Mismatches: 6, Indels: 24
0.87 0.03 0.10
Matches are distributed among these distances:
46 111 0.54
48 1 0.00
49 3 0.01
50 2 0.01
52 88 0.43
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.29
Consensus pattern (49 bp):
TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
Found at i:62217213 original size:98 final size:98
Alignment explanation
Indices: 62217094--62217362 Score: 448
Period size: 98 Copynumber: 2.7 Consensus size: 98
62217084 TTTGAGTACT
62217094 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAGTG
*
62217159 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
62217192 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAGTG
*
62217257 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* * ** * *
62217290 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC-AAGT
*
62217355 GATAAGTG
65 GAAAAGTG
62217363 GCTGCACTTA
Statistics
Matches: 161, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
98 150 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.29
Consensus pattern (98 bp):
TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:62217223 original size:46 final size:46
Alignment explanation
Indices: 62217160--62217399 Score: 291
Period size: 46 Copynumber: 5.3 Consensus size: 46
62217150 TGACAAGTGG
* * *
62217160 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAT
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
*
62217206 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
62217252 AAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 ------AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
** *
62217304 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
*
62217350 AAAGTGATAAGTG---GC-T--GC---ACTTATCTGATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
62217387 AAAGTGATAAGTG
1 AAAGTGATAAGTG
62217400 GCTACACTTA
Statistics
Matches: 181, Mismatches: 7, Indels: 21
0.87 0.03 0.10
Matches are distributed among these distances:
37 31 0.17
40 2 0.01
42 1 0.01
43 2 0.01
46 100 0.55
52 45 0.25
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
Found at i:62217374 original size:37 final size:37
Alignment explanation
Indices: 62217326--62217471 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
62217316 GATAGCTTTA
*
62217326 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
62217363 GCTGCACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
62217400 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
62217437 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
62217472 ATCATACGTA
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 87 0.85
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:62218463 original size:9 final size:9
Alignment explanation
Indices: 62218449--62218524 Score: 98
Period size: 9 Copynumber: 8.4 Consensus size: 9
62218439 GTAGTGATTC
62218449 AATTCGGTT
1 AATTCGGTT
*
62218458 AATTCGGGT
1 AATTCGGTT
62218467 AATTCGGTT
1 AATTCGGTT
*
62218476 AATTCGGGT
1 AATTCGGTT
*
62218485 AATCCGGTT
1 AATTCGGTT
*
62218494 AATTCGGGT
1 AATTCGGTT
*
62218503 AATTTGGTT
1 AATTCGGTT
*
62218512 AATTCAGTT
1 AATTCGGTT
62218521 AATT
1 AATT
62218525 TTTAACTAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 56 1.00
ACGTcount: A:0.25, C:0.11, G:0.24, T:0.41
Consensus pattern (9 bp):
AATTCGGTT
Found at i:62218525 original size:18 final size:18
Alignment explanation
Indices: 62218449--62218516 Score: 118
Period size: 18 Copynumber: 3.8 Consensus size: 18
62218439 GTAGTGATTC
62218449 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
62218467 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
62218485 AATCCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
62218503 AATTTGGTTAATTC
1 AATTCGGTTAATTC
62218517 AGTTAATTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.24, C:0.12, G:0.25, T:0.40
Consensus pattern (18 bp):
AATTCGGTTAATTCGGGT
Found at i:62218965 original size:43 final size:39
Alignment explanation
Indices: 62218890--62219011 Score: 131
Period size: 43 Copynumber: 3.0 Consensus size: 39
62218880 TGGCCTGAAT
*
62218890 TATATATTGAATATATATATTTTTTATTTTTAATCAAATA
1 TATATATTAAATATATAT-TTTTTTATTTTTAATCAAATA
* ** *
62218930 TACTTTTTATTAAATATATATTTTTTTGAACTTTAATCCGAAT-
1 TA---TATATTAAATATATATTTTTTT-ATTTTTAAT-CAAATA
62218973 TATATATTAAATATATA-TTTTTTATTTTTAATCAAATA
1 TATATATTAAATATATATTTTTTTATTTTTAATCAAATA
62219011 T
1 T
62219012 GACCCGAGCC
Statistics
Matches: 67, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
37 4 0.06
38 8 0.12
39 6 0.09
40 16 0.24
42 6 0.09
43 23 0.34
44 4 0.06
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (39 bp):
TATATATTAAATATATATTTTTTTATTTTTAATCAAATA
Found at i:62228695 original size:40 final size:40
Alignment explanation
Indices: 62228640--62228720 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
62228630 TAGGGAAGAC
62228640 AACTTTTTATACTATGCTTAGCTTTTATTTAAGTTATTTA
1 AACTTTTTATACTATGCTTAGCTTTTATTTAAGTTATTTA
62228680 AACTTTTTATACTATGCTTAGCTTTTATTTAAGTTATTTA
1 AACTTTTTATACTATGCTTAGCTTTTATTTAAGTTATTTA
62228720 A
1 A
62228721 TTATTGAAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.54
Consensus pattern (40 bp):
AACTTTTTATACTATGCTTAGCTTTTATTTAAGTTATTTA
Found at i:62230408 original size:17 final size:16
Alignment explanation
Indices: 62230382--62230413 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
62230372 GACATACTTC
62230382 AAATTCATTTTTTAAT
1 AAATTCATTTTTTAAT
62230398 AAATGTCATTTTTTAA
1 AAAT-TCATTTTTTAA
62230414 AATATTACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (16 bp):
AAATTCATTTTTTAAT
Found at i:62232372 original size:23 final size:23
Alignment explanation
Indices: 62232346--62232409 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
62232336 AATGGAACAA
* *
62232346 TAAACAAGCTTTGAATGATTTAT
1 TAAACAAGCTTTAAATGATCTAT
*
62232369 TAAACGAGCTTTAAATGATCTAT
1 TAAACAAGCTTTAAATGATCTAT
62232392 TAAACAAG-TTTCAAATGA
1 TAAACAAGCTTT-AAATGA
62232410 ACATAAATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 3 0.08
23 33 0.92
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.34
Consensus pattern (23 bp):
TAAACAAGCTTTAAATGATCTAT
Found at i:62235286 original size:6 final size:6
Alignment explanation
Indices: 62235275--62235309 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
62235265 TTTATTCTCG
*
62235275 TTGATA TTGATA TTGATA TTGATA TAGATA TTGAT
1 TTGATA TTGATA TTGATA TTGATA TTGATA TTGAT
62235310 CTTCACGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (6 bp):
TTGATA
Found at i:62236081 original size:32 final size:31
Alignment explanation
Indices: 62236037--62236100 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 31
62236027 GACAGGCGCG
62236037 ACCCTTTTTACCCGTATTTTGACCCGTTGAC
1 ACCCTTTTTACCCGTATTTTGACCCGTTGAC
62236068 ACCCTTTTTTACCCGTATTTTGACCCGTTGAC
1 ACCC-TTTTTACCCGTATTTTGACCCGTTGAC
62236100 A
1 A
62236101 ATATTTTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 4 0.12
32 28 0.88
ACGTcount: A:0.17, C:0.31, G:0.12, T:0.39
Consensus pattern (31 bp):
ACCCTTTTTACCCGTATTTTGACCCGTTGAC
Found at i:62236111 original size:31 final size:31
Alignment explanation
Indices: 62236041--62236116 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 31
62236031 GGCGCGACCC
*
62236041 TTTTTACCCGTATTTTGACCCGTTGACACCCT
1 TTTTTACCCGTATTTTGACCCGTTGACA-CAT
62236073 TTTTTACCCGTATTTTGACCCGTTGACA-AT
1 TTTTTACCCGTATTTTGACCCGTTGACACAT
*
62236103 ATTTTTACCTGTAT
1 -TTTTTACCCGTAT
62236117 ATATATTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
30 1 0.02
31 12 0.29
32 28 0.68
ACGTcount: A:0.18, C:0.25, G:0.12, T:0.45
Consensus pattern (31 bp):
TTTTTACCCGTATTTTGACCCGTTGACACAT
Found at i:62236217 original size:52 final size:50
Alignment explanation
Indices: 62236155--62236311 Score: 149
Period size: 52 Copynumber: 3.0 Consensus size: 50
62236145 AAAAAATAAT
*
62236155 ATTTTATTTAA-ACAAAAAAATTGATTCACGCCTGTCAGATAGGTGCGATTAAA
1 ATTTT-TTTAATA-AAAAAAATTGATT-A-GCCTGTCAGATAGGAGCGATTAAA
* * *
62236208 ATTTTTTTAATATAAAAAATTGATTAGAGCCTATCAGATAGGCGCGATT-AA
1 ATTTTTTTAATAAAAAAAATTGATT--AGCCTGTCAGATAGGAGCGATTAAA
* * *
62236259 ATTTTTTTAATATAAAAAAGTT-ATTTGAGCCTGTCAAATAAGAGCGATTAAA
1 ATTTTTTTAATA-AAAAAAATTGA-TT-AGCCTGTCAGATAGGAGCGATTAAA
62236311 A
1 A
62236312 AAAACATACC
Statistics
Matches: 89, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
51 34 0.38
52 48 0.54
53 7 0.08
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (50 bp):
ATTTTTTTAATAAAAAAAATTGATTAGCCTGTCAGATAGGAGCGATTAAA
Found at i:62236266 original size:51 final size:51
Alignment explanation
Indices: 62236169--62236310 Score: 180
Period size: 51 Copynumber: 2.8 Consensus size: 51
62236159 TATTTAAACA
* *
62236169 AAAAAATTGATTCA-CGCCTGTCAGATAGGTGCGATTAAAATTTTTTTAATAT
1 AAAAAATTGATT-AGAGCCTGTCAGATAGGAGCGATT-AAATTTTTTTAATAT
* *
62236221 AAAAAATTGATTAGAGCCTATCAGATAGGCGCGATTAAATTTTTTTAATAT
1 AAAAAATTGATTAGAGCCTGTCAGATAGGAGCGATTAAATTTTTTTAATAT
* * *
62236272 AAAAAAGTT-ATTTGAGCCTGTCAAATAAGAGCGATTAAA
1 AAAAAA-TTGATTAGAGCCTGTCAGATAGGAGCGATTAAA
62236311 AAAAACATAC
Statistics
Matches: 80, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
51 47 0.59
52 33 0.41
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (51 bp):
AAAAAATTGATTAGAGCCTGTCAGATAGGAGCGATTAAATTTTTTTAATAT
Found at i:62237646 original size:3 final size:3
Alignment explanation
Indices: 62237638--62237668 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
62237628 TAATATTTTC
62237638 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
62237669 GTTTTTTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:62242718 original size:35 final size:35
Alignment explanation
Indices: 62242673--62242754 Score: 107
Period size: 35 Copynumber: 2.4 Consensus size: 35
62242663 ATTTATTTAA
* *
62242673 TAATATAATAT-CATTATAATTTAATTATCATAAAT
1 TAATATAATATAAATTATAATTCAA-TATCATAAAT
*
62242708 TAATATAATATAAATTATAATTCAATATCATTAAT
1 TAATATAATATAAATTATAATTCAATATCATAAAT
62242743 T-ATATAAT-TAAA
1 TAATATAATATAAA
62242755 AAAATAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
33 4 0.09
34 7 0.16
35 21 0.49
36 11 0.26
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (35 bp):
TAATATAATATAAATTATAATTCAATATCATAAAT
Found at i:62242748 original size:22 final size:22
Alignment explanation
Indices: 62242669--62242751 Score: 71
Period size: 24 Copynumber: 3.6 Consensus size: 22
62242659 TTTGATTTAT
* *
62242669 TTAATAATATAATATCATTATAA
1 TTAATTATATAAT-TCAATATAA
62242692 TTTAATTATCATAAATT-AATATAA
1 -TTAATTAT-AT-AATTCAATATAA
* *
62242716 TATAAAT-TATAATTCAATATCA
1 T-TAATTATATAATTCAATATAA
62242738 TTAATTATATAATT
1 TTAATTATATAATT
62242752 AAAAAAATAA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
21 8 0.16
22 16 0.33
23 2 0.04
24 17 0.35
25 3 0.06
26 3 0.06
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAATTATATAATTCAATATAA
Found at i:62245044 original size:25 final size:26
Alignment explanation
Indices: 62244989--62245143 Score: 93
Period size: 25 Copynumber: 5.9 Consensus size: 26
62244979 TTTTAAACTT
* *
62244989 TATATTATTTATTCTAAATTGTTCTA
1 TATATTATTTATTTTAAATTGTTATA
*
62245015 T-TATTATTTATTTTAAGTT-TTATA
1 TATATTATTTATTTTAAATTGTTATA
**
62245039 TATATTATGCATTTTAAACTATGTTA-A
1 TATATTATTTATTTTAAA-T-TGTTATA
* * *
62245066 TCTATAATTCATTTTAAATT-TATATA
1 TATATTATTTATTTTAAATTGT-TATA
* *** *
62245092 TGTATATTATTTATGTTAAACTACATATG
1 --TATATTATTTATTTTAAA-TTGTTATA
**
62245121 TATATTATTTATTTGGAATTGTT
1 TATATTATTTATTTTAAATTGTT
62245144 TTTATGCACA
Statistics
Matches: 97, Mismatches: 22, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
24 6 0.06
25 32 0.33
26 6 0.06
27 32 0.33
28 17 0.18
29 4 0.04
ACGTcount: A:0.33, C:0.05, G:0.06, T:0.55
Consensus pattern (26 bp):
TATATTATTTATTTTAAATTGTTATA
Found at i:62245252 original size:21 final size:22
Alignment explanation
Indices: 62245227--62245275 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
62245217 GACATATTAT
62245227 TTATTTTAAACT-TTTTACATA
1 TTATTTTAAACTGTTTTACATA
* * *
62245248 TTATTTTAAATTGTTTTATATG
1 TTATTTTAAACTGTTTTACATA
62245270 TTATTT
1 TTATTT
62245276 AATTTTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (22 bp):
TTATTTTAAACTGTTTTACATA
Found at i:62245323 original size:26 final size:26
Alignment explanation
Indices: 62245184--62245344 Score: 113
Period size: 26 Copynumber: 6.3 Consensus size: 26
62245174 AAAATAAAAT
62245184 TTGTTTT-CATATTATTCA-TTTAAGA
1 TTGTTTTACATATTATTCATTTTAA-A
* *
62245209 TTCCTTTTGACATATTATTTATTTTAAA
1 TT-GTTTT-ACATATTATTCATTTTAAA
*
62245237 CT-TTTTAC--A-TATT-ATTTTAAA
1 TTGTTTTACATATTATTCATTTTAAA
* * *
62245258 TTGTTTTATATGTTATTTAATTTTAAA
1 TTGTTTTACATATTA-TTCATTTTAAA
* * *
62245285 TTGCTTTGA-ATATTATTCCTTTTAAT
1 TTG-TTTTACATATTATTCATTTTAAA
***
62245311 TTGTTTTACATATTATTTGCTTTAAA
1 TTGTTTTACATATTATTCATTTTAAA
62245337 TTGTTTTA
1 TTGTTTTA
62245345 TGCTATCACT
Statistics
Matches: 108, Mismatches: 16, Indels: 23
0.73 0.11 0.16
Matches are distributed among these distances:
21 9 0.08
22 9 0.08
23 1 0.01
25 10 0.09
26 42 0.39
27 16 0.15
28 16 0.15
29 5 0.05
ACGTcount: A:0.27, C:0.07, G:0.06, T:0.59
Consensus pattern (26 bp):
TTGTTTTACATATTATTCATTTTAAA
Found at i:62250683 original size:31 final size:30
Alignment explanation
Indices: 62250643--62250788 Score: 131
Period size: 30 Copynumber: 4.9 Consensus size: 30
62250633 TATTTATTTC
* *
62250643 TTTT-AATTTTAAAATATTTTTTACATACTT
1 TTTTAAATTTTAAAATA-TTTTAAAATACTT
***
62250673 TTTTAAATTTTTTTA-ATTTTAAAATACTTT
1 TTTTAAATTTTAAAATATTTTAAAATAC-TT
62250703 TTTTAAATTTTAAAATATTTTAAAATACTT
1 TTTTAAATTTTAAAATATTTTAAAATACTT
* ***
62250733 TTTTTAATTTTTTTA-ATTTTAAAATA-TT
1 TTTTAAATTTTAAAATATTTTAAAATACTT
*
62250761 TTTTAAATATTTTATAAT-TTTTAAAATA
1 TTTT-AA-ATTTTAAAATATTTTAAAATA
62250789 AAATGGGCGG
Statistics
Matches: 95, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
28 6 0.06
29 21 0.22
30 49 0.52
31 19 0.20
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTTAAATTTTAAAATATTTTAAAATACTT
Found at i:62250699 original size:29 final size:29
Alignment explanation
Indices: 62250667--62250788 Score: 156
Period size: 30 Copynumber: 4.1 Consensus size: 29
62250657 TATTTTTTAC
*
62250667 ATACTTTTTTAAATTTTTTTAATTTTAAA
1 ATACTTTTTTAAATTTTTATAATTTTAAA
* *
62250696 ATACTTTTTTTAAATTTTAAAATATTTTAAA
1 ATAC-TTTTTTAAATTTTTATA-ATTTTAAA
* *
62250727 ATACTTTTTTTAATTTTTTTAATTTTAAA
1 ATACTTTTTTAAATTTTTATAATTTTAAA
62250756 ATA-TTTTTTAAATATTTTATAATTTTTAAA
1 ATACTTTTTTAAAT-TTTTATAA-TTTTAAA
62250786 ATA
1 ATA
62250789 AAATGGGCGG
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
28 9 0.11
29 22 0.28
30 37 0.46
31 12 0.15
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (29 bp):
ATACTTTTTTAAATTTTTATAATTTTAAA
Found at i:62250707 original size:60 final size:59
Alignment explanation
Indices: 62250637--62250788 Score: 209
Period size: 60 Copynumber: 2.5 Consensus size: 59
62250627 TAAATATATT
* *
62250637 TATTTCTTTT-AATTTTAAAATATTTTTTACATACTTTTTTAAATTTTTTTAATTTTAAAA
1 TATTT-TTTTAAATTTTAAAATA-TTTTAAAATACTTTTTTAAATTTTTTTAATTTTAAAA
*
62250697 TACTTTTTTTAAATTTTAAAATATTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAA
1 TA-TTTTTTTAAATTTTAAAATATTTTAAAATACTTTTTTAAATTTTTTTAATTTTAAAA
* *
62250757 TATTTTTTAAATATTTTATAAT-TTTTAAAATA
1 TATTTTTTTAA-ATTTTAAAATATTTTAAAATA
62250789 AAATGGGCGG
Statistics
Matches: 84, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
59 18 0.21
60 51 0.61
61 15 0.18
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (59 bp):
TATTTTTTTAAATTTTAAAATATTTTAAAATACTTTTTTAAATTTTTTTAATTTTAAAA
Found at i:62250723 original size:40 final size:41
Alignment explanation
Indices: 62250637--62250723 Score: 101
Period size: 40 Copynumber: 2.1 Consensus size: 41
62250627 TAAATATATT
**
62250637 TATTTCTTTTAATTTTAAAATATTTTTTACATACTTTTTTAA
1 TATTT-TTTTAATTTTAAAATATTTTTTACATACTTTTAAAA
62250679 -ATTTTTTTAATTTTAAAATACTTTTTTTA-A-A-TTTTAAAA
1 TATTTTTTTAATTTTAAAATA--TTTTTTACATACTTTTAAAA
62250718 TATTTT
1 TATTTT
62250724 AAAATACTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
39 6 0.15
40 22 0.55
41 5 0.12
42 7 0.17
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (41 bp):
TATTTTTTTAATTTTAAAATATTTTTTACATACTTTTAAAA
Found at i:62250742 original size:20 final size:20
Alignment explanation
Indices: 62250637--62250723 Score: 83
Period size: 20 Copynumber: 4.3 Consensus size: 20
62250627 TAAATATATT
62250637 TATTTCTTTT-AATTTTAAAA
1 TATTT-TTTTAAATTTTAAAA
**
62250657 TA-TTTTTTACATACTTTTTTAA
1 TATTTTTTTA-A-A-TTTTAAAA
62250679 -ATTTTTTT-AATTTTAAAA
1 TATTTTTTTAAATTTTAAAA
62250697 TACTTTTTTTAAATTTTAAAA
1 TA-TTTTTTTAAATTTTAAAA
62250718 TATTTT
1 TATTTT
62250724 AAAATACTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
18 10 0.18
19 4 0.07
20 15 0.27
21 14 0.25
22 12 0.22
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTTTTAAATTTTAAAA
Found at i:62250764 original size:12 final size:11
Alignment explanation
Indices: 62250649--62250773 Score: 60
Period size: 10 Copynumber: 12.3 Consensus size: 11
62250639 TTTCTTTTAA
*
62250649 TTTTAAAATAT
1 TTTTTAAATAT
*
62250660 TTTTTACATACT
1 TTTTTAAATA-T
62250672 TTTTTAAAT-T
1 TTTTTAAATAT
62250682 TTTTT--A-A-
1 TTTTTAAATAT
*
62250689 TTTTAAAATACT
1 TTTTTAAATA-T
*
62250701 TTTTTTAA-A-
1 TTTTTAAATAT
*
62250710 TTTTAAAATA-
1 TTTTTAAATAT
*
62250720 TTTTAAAATACT
1 TTTTTAAATA-T
*
62250732 TTTTTTAAT-T
1 TTTTTAAATAT
62250742 TTTTT--A-A-
1 TTTTTAAATAT
*
62250749 TTTTAAAATAT
1 TTTTTAAATAT
62250760 TTTTTAAATAT
1 TTTTTAAATAT
62250771 TTT
1 TTT
62250774 ATAATTTTTA
Statistics
Matches: 87, Mismatches: 12, Indels: 30
0.67 0.09 0.23
Matches are distributed among these distances:
7 8 0.09
8 2 0.02
9 8 0.09
10 25 0.29
11 22 0.25
12 22 0.25
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTTAAATAT
Found at i:62252583 original size:24 final size:23
Alignment explanation
Indices: 62252541--62252588 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
62252531 ATTTTTTAAT
* *
62252541 ATATAAAGAAATACTAAAATGAAA
1 ATATAAAGAAAAAC-AAAAAGAAA
*
62252565 ATATAAAGAAAAAGAAAAAGAAA
1 ATATAAAGAAAAACAAAAAGAAA
62252588 A
1 A
62252589 AATCATTACC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (23 bp):
ATATAAAGAAAAACAAAAAGAAA
Found at i:62255548 original size:23 final size:23
Alignment explanation
Indices: 62255518--62255595 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
62255508 AATAGAACAA
* * *
62255518 TAAACAAGCTTTGAATGGTTTAT
1 TAAACAAGCTTTAAATGATCTAT
62255541 TAAACAAGCTTTAAATGATCTAT
1 TAAACAAGCTTTAAATGATCTAT
*
62255564 TAAACAAG-TTTCAAATGAAC-A-
1 TAAACAAGCTTT-AAATGATCTAT
62255585 TAAACAAGCTT
1 TAAACAAGCTT
62255596 GTTTATGAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
21 8 0.16
22 6 0.12
23 35 0.71
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.32
Consensus pattern (23 bp):
TAAACAAGCTTTAAATGATCTAT
Found at i:62259771 original size:29 final size:31
Alignment explanation
Indices: 62259738--62259814 Score: 104
Period size: 29 Copynumber: 2.5 Consensus size: 31
62259728 TTTGGCTCAG
*
62259738 GTTACATTTTAGTCACTTATGTT-TGA-AAT
1 GTTACATTTTAGTCACTTATGTTATCACAAT
* *
62259767 GTTACGTTTTAGTCACTTATGTTATCACATT
1 GTTACATTTTAGTCACTTATGTTATCACAAT
*
62259798 GTAACATTTTAGTCACT
1 GTTACATTTTAGTCACT
62259815 AAGCCGTTAG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
29 22 0.54
30 2 0.05
31 17 0.41
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.47
Consensus pattern (31 bp):
GTTACATTTTAGTCACTTATGTTATCACAAT
Found at i:62260736 original size:60 final size:60
Alignment explanation
Indices: 62260650--62260768 Score: 202
Period size: 60 Copynumber: 2.0 Consensus size: 60
62260640 TTTCTTTTTA
* ** *
62260650 TAATTATTTTAAAATTAATTTGTTAGTAATTTAGGATTTTGTTATAAATTTTTGTGTTTG
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGTTTG
62260710 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGTTT
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGTTT
62260769 AGTTTAGTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.55
Consensus pattern (60 bp):
TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGTTTG
Found at i:62260895 original size:19 final size:19
Alignment explanation
Indices: 62260873--62260950 Score: 60
Period size: 19 Copynumber: 4.3 Consensus size: 19
62260863 ATTTGTTAGT
*
62260873 AATTTAGGATTATGTTATA
1 AATTTAGAATTATGTTATA
*
62260892 AATTTTTATAATTAT-TT-TA
1 AA--TTTAGAATTATGTTATA
*
62260911 AAATT--AATT-TGTTAGT-
1 AATTTAGAATTATGTTA-TA
62260927 AATTTAGAATTATGTTATA
1 AATTTAGAATTATGTTATA
62260946 AATTT
1 AATTT
62260951 TTGTGTTTGT
Statistics
Matches: 46, Mismatches: 4, Indels: 18
0.68 0.06 0.26
Matches are distributed among these distances:
14 1 0.02
15 6 0.13
16 4 0.09
17 3 0.07
18 5 0.11
19 16 0.35
20 2 0.04
21 9 0.20
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (19 bp):
AATTTAGAATTATGTTATA
Found at i:62260970 original size:60 final size:59
Alignment explanation
Indices: 62260858--62261019 Score: 217
Period size: 60 Copynumber: 2.8 Consensus size: 59
62260848 GACTCTTTGT
62260858 AATTAATTTGTTAGTAATTTAGGATTATGTTATAAA---T-T-TTTATAATTATTTTAA
1 AATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTGTGTTTATAATTATTTTAA
* *
62260912 AATTAATTTGTTAGTAATTTAGAATTATGTTATAAATTTTTGTGTTTGTAATTATTTTAA
1 AATTAATTTGTTAGTAATTTAGGATTATGTTATAAA-TTTTGTGTTTATAATTATTTTAA
* * **
62260972 AATTAATTTATTAATAATTTAGGATTAAATTATAAATTGTTGTGTTTA
1 AATTAATTTGTTAGTAATTTAGGATTATGTTATAAATT-TTGTGTTTA
62261020 GTTTAGTATT
Statistics
Matches: 93, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
54 35 0.38
58 1 0.01
59 3 0.03
60 54 0.58
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.53
Consensus pattern (59 bp):
AATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTGTGTTTATAATTATTTTAA
Found at i:62267616 original size:24 final size:23
Alignment explanation
Indices: 62267575--62267621 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
62267565 TTTTTTTATT
* *
62267575 TATAAAGAAATACTAAAATGAAAA
1 TATAAAGAAAAAC-AAAAAGAAAA
*
62267599 TATAAAGAAAAAGAAAAAGAAAA
1 TATAAAGAAAAACAAAAAGAAAA
62267622 AAAAACATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (23 bp):
TATAAAGAAAAACAAAAAGAAAA
Found at i:62269912 original size:35 final size:34
Alignment explanation
Indices: 62269860--62269968 Score: 130
Period size: 35 Copynumber: 3.1 Consensus size: 34
62269850 TTTTTTCTTT
*
62269860 TTTTGAAAACACGAAATTTTTTTAAAATAC-AAGAA
1 TTTTG-AAACACGAAATTTTTTTAAAACACGAA-AA
*
62269895 TTTTATAAACACGAAATTTTTTTTTAAAACACGAAAA
1 TTTT-GAAACACGAAA--TTTTTTTAAAACACGAAAA
*
62269932 TTTTGAAACACGATAATTTTTTTGAAACACGAAAA
1 TTTTGAAACACGA-AATTTTTTTAAAACACGAAAA
62269967 TT
1 TT
62269969 CTTTTTGAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
35 34 0.52
36 8 0.12
37 21 0.32
38 2 0.03
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (34 bp):
TTTTGAAACACGAAATTTTTTTAAAACACGAAAA
Found at i:62269986 original size:20 final size:19
Alignment explanation
Indices: 62269857--62269991 Score: 122
Period size: 19 Copynumber: 7.2 Consensus size: 19
62269847 AACTTTTTTC
62269857 TTTTTTTGAAAACACG-AAA
1 TTTTTTTG-AAACACGAAAA
* *
62269876 TTTTTTTAAAATAC-AAGAA
1 TTTTTTTGAAACACGAA-AA
* *
62269895 -TTTTAT-AAACACGAAATT
1 TTTTTTTGAAACACGAAA-A
*
62269913 TTTTTTTAAAACACGAAAA
1 TTTTTTTGAAACACGAAAA
*
62269932 ---TTTTGAAACACGATAA
1 TTTTTTTGAAACACGAAAA
62269948 TTTTTTTGAAACACGAAAA
1 TTTTTTTGAAACACGAAAA
62269967 TTCTTTTTGAAACACGAAAAA
1 TT-TTTTTGAAACACG-AAAA
62269988 TTTT
1 TTTT
62269992 CAAAATACAT
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
16 14 0.15
17 6 0.06
18 13 0.14
19 31 0.33
20 25 0.26
21 6 0.06
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (19 bp):
TTTTTTTGAAACACGAAAA
Found at i:62270007 original size:55 final size:55
Alignment explanation
Indices: 62269901--62270013 Score: 140
Period size: 55 Copynumber: 2.1 Consensus size: 55
62269891 AGAATTTTAT
* * *
62269901 AAACACGAAATTTTTTTTTAAAACACGAAAATTTTGAAACACGATAATTTTTTTG
1 AAACACGAAAATTCTTTTTAAAACACGAAAATTTTAAAACACGATAATTTTTTTG
* * *
62269956 AAACACGAAAATTCTTTTTGAAACACGAAAAATTTTCAAAATAC-AT-TTTTTTTTG
1 AAACACGAAAATTCTTTTTAAAACACG-AAAATTTT-AAAACACGATAATTTTTTTG
62270011 AAA
1 AAA
62270014 ACATAATATT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
55 35 0.70
56 10 0.20
57 5 0.10
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (55 bp):
AAACACGAAAATTCTTTTTAAAACACGAAAATTTTAAAACACGATAATTTTTTTG
Found at i:62270711 original size:24 final size:24
Alignment explanation
Indices: 62270684--62270736 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
62270674 TTTTATAGCC
*
62270684 TTTTTTACATGAATTTTTAATCTG
1 TTTTTTACATGAATTTTTAATCTA
*
62270708 TTTTTTATATGAATTTTTAATCTA
1 TTTTTTACATGAATTTTTAATCTA
62270732 TTTTT
1 TTTTT
62270737 GAAGCCCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.64
Consensus pattern (24 bp):
TTTTTTACATGAATTTTTAATCTA
Found at i:62272115 original size:36 final size:36
Alignment explanation
Indices: 62272058--62272127 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
62272048 GAGATTAGTC
* *
62272058 GATTTCTTGTGAGAAGATAGGAGATTGAGTTTGGCA
1 GATTACTTGTGAGAAGATAGGAGATTAAGTTTGGCA
* *
62272094 GATTACTTGTTAGAAGTTAGGAGATTAAGTTTGG
1 GATTACTTGTGAGAAGATAGGAGATTAAGTTTGG
62272128 ATTAAATGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.36
Consensus pattern (36 bp):
GATTACTTGTGAGAAGATAGGAGATTAAGTTTGGCA
Found at i:62273561 original size:29 final size:29
Alignment explanation
Indices: 62273529--62273620 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 29
62273519 ATTTTTACCA
62273529 CAAACTCCCAAACCTTTTTACTTTTCCCT
1 CAAACTCCCAAACCTTTTTACTTTTCCCT
*** ** *** *
62273558 CAAAACTTTTACTCCTTCCCACTTTTCCCC
1 C-AAACTCCCAAACCTTTTTACTTTTCCCT
62273588 CAAACTCCCAAACCTTTTTACTTTTCCCT
1 CAAACTCCCAAACCTTTTTACTTTTCCCT
62273617 CAAA
1 CAAA
62273621 ACTTTTACTC
Statistics
Matches: 44, Mismatches: 18, Indels: 2
0.69 0.28 0.03
Matches are distributed among these distances:
29 24 0.55
30 20 0.45
ACGTcount: A:0.25, C:0.39, G:0.00, T:0.36
Consensus pattern (29 bp):
CAAACTCCCAAACCTTTTTACTTTTCCCT
Found at i:62273582 original size:30 final size:30
Alignment explanation
Indices: 62273548--62273661 Score: 131
Period size: 30 Copynumber: 3.8 Consensus size: 30
62273538 AAACCTTTTT
62273548 ACTTTTCCCTCAAAACTTTTACTCCTTCCC
1 ACTTTTCCCTCAAAACTTTTACTCCTTCCC
* *** ** ***
62273578 ACTTTTCCC-CCAAACTCCCAAACCTTTTT
1 ACTTTTCCCTCAAAACTTTTACTCCTTCCC
62273607 ACTTTTCCCTCAAAACTTTTACTCCTTCCC
1 ACTTTTCCCTCAAAACTTTTACTCCTTCCC
*
62273637 ACTTTTCCCCCAAAACTTTTACTCC
1 ACTTTTCCCTCAAAACTTTTACTCC
62273662 CCTCCCCTCC
Statistics
Matches: 64, Mismatches: 19, Indels: 2
0.75 0.22 0.02
Matches are distributed among these distances:
29 20 0.31
30 44 0.69
ACGTcount: A:0.22, C:0.40, G:0.00, T:0.38
Consensus pattern (30 bp):
ACTTTTCCCTCAAAACTTTTACTCCTTCCC
Found at i:62273596 original size:59 final size:59
Alignment explanation
Indices: 62273529--62273650 Score: 244
Period size: 59 Copynumber: 2.1 Consensus size: 59
62273519 ATTTTTACCA
62273529 CAAACTCCCAAACCTTTTTACTTTTCCCTCAAAACTTTTACTCCTTCCCACTTTTCCCC
1 CAAACTCCCAAACCTTTTTACTTTTCCCTCAAAACTTTTACTCCTTCCCACTTTTCCCC
62273588 CAAACTCCCAAACCTTTTTACTTTTCCCTCAAAACTTTTACTCCTTCCCACTTTTCCCC
1 CAAACTCCCAAACCTTTTTACTTTTCCCTCAAAACTTTTACTCCTTCCCACTTTTCCCC
62273647 CAAA
1 CAAA
62273651 ACTTTTACTC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.24, C:0.40, G:0.00, T:0.36
Consensus pattern (59 bp):
CAAACTCCCAAACCTTTTTACTTTTCCCTCAAAACTTTTACTCCTTCCCACTTTTCCCC
Found at i:62273935 original size:17 final size:17
Alignment explanation
Indices: 62273908--62273969 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
62273898 ACACCCCCTA
*
62273908 TTTACTTCCCCTCAAACT
1 TTTACTTCCCC-AAAACT
62273926 TTTA-TTCCCCAAAACTT
1 TTTACTTCCCCAAAAC-T
* *
62273943 TTTATTTTTCCCCTAAACT
1 TTTA--CTTCCCCAAAACT
62273962 TTTACTTC
1 TTTACTTC
62273970 TCACCCTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
16 4 0.11
17 14 0.38
18 4 0.11
19 5 0.14
20 10 0.27
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTACTTCCCCAAAACT
Found at i:62275199 original size:43 final size:42
Alignment explanation
Indices: 62275138--62275272 Score: 148
Period size: 43 Copynumber: 3.2 Consensus size: 42
62275128 ATAATTTTTT
* *
62275138 TAAAGGTTATGTT-TTTAGCGACGTTTTTCGAGAAAAACGCCGC
1 TAAAGGTT-TGTTCTTTAGCGGCGTTTGT-GAGAAAAACGCCGC
* *
62275181 TAAAGGTTTGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGC
1 TAAAGGTTTGTTCTTTAGCGGCGTTTGTGAGAAAAACGCCGC
* ** *
62275223 TAAAGGTCATGACCTTTAGCGGCATTTGTG-GAAAAAGCGCCGC
1 TAAAGGT-TTGTTCTTTAGCGGCGTTTGTGAGAAAAA-CGCCGC
62275266 TAAAGGT
1 TAAAGGT
62275273 CATGGTCTAT
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
42 27 0.34
43 52 0.66
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (42 bp):
TAAAGGTTTGTTCTTTAGCGGCGTTTGTGAGAAAAACGCCGC
Found at i:62275302 original size:43 final size:43
Alignment explanation
Indices: 62275170--62275409 Score: 184
Period size: 43 Copynumber: 5.9 Consensus size: 43
62275160 GTTTTTCGAG
* * * *
62275170 AAAAACGCCGCTAAAGGT-TTGTTCTTTAGCGGCGTTTGTGAT
1 AAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGGT
* * *
62275212 AAAAGCGCCGCTAAAGGTCATGACCTTTAGCGGCATTTGTGGA
1 AAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGGT
* * * *
62275255 AAAAGCGCCGCTAAAGGTCATGGTCTATAACGGCGTTTATGGT
1 AAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGGT
* * *
62275298 ---A--------AAA-GTCATGACCTTTAGCGGCTTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGGT
* * * * * *
62275329 AAAGGCGCCGCTAAAGGTCATGGTCTATAGCGGCTTTTTTGGG
1 AAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGGT
*
62275372 AAAAACGCCGCTAAAGGTCATGA-CTTTTAGCGGCGTTT
1 AAAAGCGCCGCTAAAGGTCATGATC-TTTAGCGGCGTTT
62275410 ATTTCTAAAA
Statistics
Matches: 153, Mismatches: 31, Indels: 27
0.73 0.15 0.13
Matches are distributed among these distances:
31 20 0.13
32 3 0.02
40 1 0.01
42 21 0.14
43 108 0.71
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGGT
Found at i:62275349 original size:74 final size:74
Alignment explanation
Indices: 62275223--62275362 Score: 235
Period size: 74 Copynumber: 1.9 Consensus size: 74
62275213 AAAGCGCCGC
*
62275223 TAAAGGTCATGACCTTTAGCGGCATTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAACGG
1 TAAAAGTCATGACCTTTAGCGGCATTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAACGG
62275288 CGTTTATGG
66 CGTTTATGG
* * * *
62275297 TAAAAGTCATGACCTTTAGCGGCTTTTGTGGGAAAGGCGCCGCTAAAGGTCATGGTCTATAGCGG
1 TAAAAGTCATGACCTTTAGCGGCATTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAACGG
62275362 C
66 C
62275363 TTTTTTGGGA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 61 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (74 bp):
TAAAAGTCATGACCTTTAGCGGCATTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAACGG
CGTTTATGG
Found at i:62275406 original size:117 final size:117
Alignment explanation
Indices: 62275193--62275411 Score: 298
Period size: 117 Copynumber: 1.9 Consensus size: 117
62275183 AAGGTTTGTT
* *
62275193 CTTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGACCTTTAGCGGCATTTGTGGAAAA
1 CTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGACCTATAGCGGCATTTGTGGAAAA
*
62275258 AGCGCCGCTAAAGGTCATGGTCTATAACGGCGTTTATGGTAAAAGTCATGAC
66 AGCGCCGCTAAAGGTCATGCTCTATAACGGCGTTTATGGTAAAAGTCATGAC
* * * ** * *
62275310 CTTTAGCGGCTTTTGTGGGAAAGGCGCCGCTAAAGGTCATGGTCTATAGCGGCTTTTTTGGGAAA
1 CTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGACCTATAGCGGCATTTGT-GGAAA
* *
62275375 AA-CGCCGCTAAAGGTCATGACT-TTTAGCGGCGTTTAT
65 AAGCGCCGCTAAAGGTCATG-CTCTATAACGGCGTTTAT
62275412 TTCTAAAAAC
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
117 80 0.91
118 8 0.09
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (117 bp):
CTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGACCTATAGCGGCATTTGTGGAAAA
AGCGCCGCTAAAGGTCATGCTCTATAACGGCGTTTATGGTAAAAGTCATGAC
Found at i:62275548 original size:23 final size:23
Alignment explanation
Indices: 62275514--62275572 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
62275504 TGGTGTAGTG
* *
62275514 AAGCTTTGAATGATTTATTAAAC
1 AAGCTTTAAATGATCTATTAAAC
*
62275537 GAGCTTTAAATGATCTATTAAAC
1 AAGCTTTAAATGATCTATTAAAC
62275560 AAG-TTTCAAATGA
1 AAGCTTT-AAATGA
62275573 ACATAAACGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 3 0.10
23 28 0.90
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.36
Consensus pattern (23 bp):
AAGCTTTAAATGATCTATTAAAC
Found at i:62277784 original size:3 final size:3
Alignment explanation
Indices: 62277776--62277807 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
62277766 TAAATAAATA
62277776 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
62277808 ACAAAAAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:62280249 original size:23 final size:23
Alignment explanation
Indices: 62280217--62280260 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
62280207 TTGTTTAAGT
*
62280217 TAAACAAACAAGTTCGTGAATGC
1 TAAACAAACAAGTTCATGAATGC
* *
62280240 TAAACGAACATGTTCATGAAT
1 TAAACAAACAAGTTCATGAAT
62280261 ATATAATGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (23 bp):
TAAACAAACAAGTTCATGAATGC
Found at i:62282041 original size:2 final size:2
Alignment explanation
Indices: 62282034--62282071 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
62282024 ATCAAAAGAG
62282034 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
62282072 TATATATATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:62286561 original size:17 final size:17
Alignment explanation
Indices: 62286539--62286575 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
62286529 TTGTAATTTG
62286539 AACACATTAAAAAAATA
1 AACACATTAAAAAAATA
62286556 AACACATTAAAAAAATA
1 AACACATTAAAAAAATA
62286573 AAC
1 AAC
62286576 CTATACTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.70, C:0.14, G:0.00, T:0.16
Consensus pattern (17 bp):
AACACATTAAAAAAATA
Found at i:62296723 original size:31 final size:31
Alignment explanation
Indices: 62296575--62296731 Score: 88
Period size: 31 Copynumber: 4.9 Consensus size: 31
62296565 TGAGGGGATA
*
62296575 ATGTCACATTTGGTACATGTACTTTCATAAAAT
1 ATGTCA-ATGTGGTACATGTACTTTCA-AAAAT
* * * *
62296608 AT-CCAATGTGATACTTATACTTT-AAAAAT
1 ATGTCAATGTGGTACATGTACTTTCAAAAAT
* * *
62296637 GAATGTCCAATGTGATACATGAACTATC-AAAAT
1 --ATGT-CAATGTGGTACATGTACTTTCAAAAAT
* * * * *
62296670 GTGTTCTATTATGGTGCTTGTACTTTCATAAAAT
1 ATG-TC-AATGTGGTACATGTACTTTCA-AAAAT
*
62296704 -TGTCAATGTGGTACATGTACTTTGAAAA
1 ATGTCAATGTGGTACATGTACTTTCAAAA
62296732 TATCTAATAT
Statistics
Matches: 92, Mismatches: 23, Indels: 21
0.68 0.17 0.15
Matches are distributed among these distances:
29 5 0.05
30 4 0.04
31 35 0.38
32 18 0.20
33 25 0.27
34 5 0.05
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (31 bp):
ATGTCAATGTGGTACATGTACTTTCAAAAAT
Found at i:62302335 original size:21 final size:21
Alignment explanation
Indices: 62302311--62302352 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
62302301 ACTATTAGTT
62302311 TTAATCTCACTACTATAGTAA
1 TTAATCTCACTACTATAGTAA
* * *
62302332 TTAATTTCACTGCTATTGTAA
1 TTAATCTCACTACTATAGTAA
62302353 CTTCTCCAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (21 bp):
TTAATCTCACTACTATAGTAA
Found at i:62302510 original size:19 final size:19
Alignment explanation
Indices: 62302486--62302523 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
62302476 AGAAAAAGTT
62302486 AGCGTGTTTTCGAAAGATA
1 AGCGTGTTTTCGAAAGATA
62302505 AGCGTGTTTTCGAAAGATA
1 AGCGTGTTTTCGAAAGATA
62302524 CAATTTAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (19 bp):
AGCGTGTTTTCGAAAGATA
Found at i:62310283 original size:16 final size:16
Alignment explanation
Indices: 62310262--62310296 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
62310252 GAAATACATT
*
62310262 AAACTTGGAATGATTC
1 AAACTTGGAATGACTC
*
62310278 AAACTTGTAATGACTC
1 AAACTTGGAATGACTC
62310294 AAA
1 AAA
62310297 GAATTTAAAC
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:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (16 bp):
AAACTTGGAATGACTC
Found at i:62315991 original size:16 final size:16
Alignment explanation
Indices: 62315970--62316000 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
62315960 CAAAATAATA
*
62315970 TTAAATCATTGGTATC
1 TTAAATCATTAGTATC
62315986 TTAAATCATTAGTAT
1 TTAAATCATTAGTAT
62316001 TTGATTTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (16 bp):
TTAAATCATTAGTATC
Found at i:62316139 original size:49 final size:49
Alignment explanation
Indices: 62316076--62316172 Score: 160
Period size: 49 Copynumber: 2.0 Consensus size: 49
62316066 TGAATTTAAC
62316076 TAATCAATCTAATCCCTTATTCAAATCAGTACTCAGATTGGACCAAGTT
1 TAATCAATCTAATCCCTTATTCAAATCAGTACTCAGATTGGACCAAGTT
* *
62316125 TAATCAAT-TCAATCCTTTATTCAAATCAGTACTCAGATTGTACCAAGT
1 TAATCAATCT-AATCCCTTATTCAAATCAGTACTCAGATTGGACCAAGT
62316173 GTAAAAACAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
48 1 0.02
49 44 0.98
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (49 bp):
TAATCAATCTAATCCCTTATTCAAATCAGTACTCAGATTGGACCAAGTT
Found at i:62322167 original size:14 final size:14
Alignment explanation
Indices: 62322148--62322176 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
62322138 TCAAAGATGG
62322148 AGGTTTGATAGTGA
1 AGGTTTGATAGTGA
62322162 AGGTTTGATAGTGA
1 AGGTTTGATAGTGA
62322176 A
1 A
62322177 TAAAATTCGT
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:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (14 bp):
AGGTTTGATAGTGA
Found at i:62326907 original size:22 final size:22
Alignment explanation
Indices: 62326877--62326919 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
62326867 CTAGTACCGA
*
62326877 GGCTTATAGTTTAGGAAACTTG
1 GGCTCATAGTTTAGGAAACTTG
*
62326899 GGCTCATAGTTTAGGGAACTT
1 GGCTCATAGTTTAGGAAACTT
62326920 TAAGTAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.35
Consensus pattern (22 bp):
GGCTCATAGTTTAGGAAACTTG
Found at i:62326938 original size:82 final size:82
Alignment explanation
Indices: 62326801--62326962 Score: 245
Period size: 82 Copynumber: 2.0 Consensus size: 82
62326791 CTTGGGCTCG
*
62326801 TAGTTTAGGAATCTCAGGGTCATAGTTTAGGAAACTCTAAGCAATAAGTTAAATCCAAACTATGC
1 TAGTTTAGGAAACTCAGGGTCATAGTTTAGGAAACTCTAAGCAATAAGTTAAATCCAAACTATGC
62326866 ACTAGTACCGAGGCTTA
66 ACTAGTACCGAGGCTTA
* * * * *
62326883 TAGTTTAGGAAACT-TGGGCTCATAGTTTAGGGAACTTTAAGTAATAAGTTAAATCCAAATTATG
1 TAGTTTAGGAAACTCAGGG-TCATAGTTTAGGAAACTCTAAGCAATAAGTTAAATCCAAACTATG
*
62326947 CACTAGTACTGAGGCT
65 CACTAGTACCGAGGCT
62326963 CCAAGTCACT
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
81 3 0.04
82 69 0.96
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (82 bp):
TAGTTTAGGAAACTCAGGGTCATAGTTTAGGAAACTCTAAGCAATAAGTTAAATCCAAACTATGC
ACTAGTACCGAGGCTTA
Found at i:62328533 original size:63 final size:63
Alignment explanation
Indices: 62328456--62328585 Score: 251
Period size: 63 Copynumber: 2.1 Consensus size: 63
62328446 AGTTTACCTG
62328456 CAGCCCCGTCTCACTATCCATCATCCTATCAAGGTTCCGAGACTCCTTACAATCCTCCACAGT
1 CAGCCCCGTCTCACTATCCATCATCCTATCAAGGTTCCGAGACTCCTTACAATCCTCCACAGT
*
62328519 CAGCCCCGTCTCACTATCCATCATCCTATCAAGGTTCCGAGACTCCTTACAATCCTCCCCAGT
1 CAGCCCCGTCTCACTATCCATCATCCTATCAAGGTTCCGAGACTCCTTACAATCCTCCACAGT
62328582 CAGC
1 CAGC
62328586 TCCTCCGACA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.23, C:0.41, G:0.12, T:0.25
Consensus pattern (63 bp):
CAGCCCCGTCTCACTATCCATCATCCTATCAAGGTTCCGAGACTCCTTACAATCCTCCACAGT
Found at i:62329102 original size:5 final size:5
Alignment explanation
Indices: 62329092--62329118 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
62329082 TTTAGACTTG
62329092 TTAAT TTAAT TTAAT TTAAT TTAAT TT
1 TTAAT TTAAT TTAAT TTAAT TTAAT TT
62329119 TTCCTCCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TTAAT
Found at i:62330507 original size:4 final size:4
Alignment explanation
Indices: 62330498--62330532 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
62330488 GTAGAAGAAG
*
62330498 ATAC ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
62330533 TATGAAGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:62330523 original size:16 final size:16
Alignment explanation
Indices: 62330502--62330535 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
62330492 AAGAAGATAC
62330502 ATACATACATACATAT
1 ATACATACATACATAT
62330518 ATACATACATACATAT
1 ATACATACATACATAT
62330534 AT
1 AT
62330536 GAAGTGATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (16 bp):
ATACATACATACATAT
Found at i:62330808 original size:29 final size:30
Alignment explanation
Indices: 62330770--62330828 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
62330760 CTTTGTTTTG
62330770 TTAATGCACTTCAATGCCACTCTGTTCTGA
1 TTAATGCACTTCAATGCCACTCTGTTCTGA
* * *
62330800 TTAA-GCACTTCAGTGCTATTCTGTTCTGA
1 TTAATGCACTTCAATGCCACTCTGTTCTGA
62330829 CATTCCACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (30 bp):
TTAATGCACTTCAATGCCACTCTGTTCTGA
Found at i:62333924 original size:33 final size:33
Alignment explanation
Indices: 62333887--62333952 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
62333877 CAACATTCTC
62333887 GTAAATAATTCTTAACTCAACCTATTTTAGTAA
1 GTAAATAATTCTTAACTCAACCTATTTTAGTAA
* * * * *
62333920 GTAAATAATTTTTATCTTAATCTATTTTCGTAA
1 GTAAATAATTCTTAACTCAACCTATTTTAGTAA
62333953 ATATATTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (33 bp):
GTAAATAATTCTTAACTCAACCTATTTTAGTAA
Found at i:62334784 original size:18 final size:20
Alignment explanation
Indices: 62334741--62334784 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
62334731 ATATCATACT
*
62334741 TAATTTTTTGTATTTGTTAA
1 TAATTTTTTATATTTGTTAA
62334761 -AA-TTTTTATA-TT-TTAA
1 TAATTTTTTATATTTGTTAA
62334777 TAATTTTT
1 TAATTTTT
62334785 CGGTGTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
16 4 0.19
17 4 0.19
18 11 0.52
19 2 0.10
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (20 bp):
TAATTTTTTATATTTGTTAA
Found at i:62340122 original size:162 final size:162
Alignment explanation
Indices: 62339645--62340602 Score: 1265
Period size: 155 Copynumber: 6.0 Consensus size: 162
62339635 TTTTTGTGCT
* ** * *
62339645 ATGGTTGTTTACTCTGAACTGGAATGAACCTTATCTTTTTGGTTAGGAGATCGGTGTTCCTCGG-
1 ATGGTTGTTTACTCTGAACTTGAATGAACCTTATCGATTTGGATAGGAGATCGGTGATCCTCGGA
* * * * *
62339709 AACCTATATTCTCGGATTTTCATCGTGATTTAGTATAGCTTGGTTTTTCATCTTGAGACTAAGGA
66 AACCGATATTCCCGGATTTTCATCGTGATTTAGTATAGCTTGGTTTGTCATCTAGAGACTAGGGA
*
62339774 AGTTCACTTTTGTTTGATTGTCATCTCCTCCC
131 AGTTCACTTTTGTTTGATTGTCATCTCCTGCC
*
62339806 ATGGTTGTTTACTCTGAACTTGAATGAACCTTATCGATTTGGAT------T-GGTGATCCTCAGA
1 ATGGTTGTTTACTCTGAACTTGAATGAACCTTATCGATTTGGATAGGAGATCGGTGATCCTCGGA
* * * * * *
62339864 AACCAATATTCCCAGATTTTCATCTTGAGTTAGTATATAGCTTGGTTTATCATCTAGAGACCAGG
66 AACCGATATTCCCGGATTTTCATCGTGATTTAG--TATAGCTTGGTTTGTCATCTAGAGACTAGG
* *
62339929 GAAGTTCACTTTTGTTTGCTTGTCGTCTCCTGCC
129 GAAGTTCACTTTTGTTTGATTGTCATCTCCTGCC
* * * *
62339963 ATGGTTGTTTACACTGAACTTGAATAAACCTTATCGATTTTGATAGGAGATTGGTGATCCTCGGA
1 ATGGTTGTTTACTCTGAACTTGAATGAACCTTATCGATTTGGATAGGAGATCGGTGATCCTCGGA
* *
62340028 AACCGATATTCCCGGATTTTTATTGTGATTTAGTATAGCTTGGTTTGTCATCTAGAGACTAGGGA
66 AACCGATATTCCCGGATTTTCATCGTGATTTAGTATAGCTTGGTTTGTCATCTAGAGACTAGGGA
62340093 AGTTCACTTTTGTTTGATTGTCATCTCCTGCC
131 AGTTCACTTTTGTTTGATTGTCATCTCCTGCC
* * * * *
62340125 ATGTTTGTTTACTCTAAAC-TGAATGAACCTT-TCAATTTGGATAGGAGATCAGTGATCCTTGGA
1 ATGGTTGTTTACTCTGAACTTGAATGAACCTTATCGATTTGGATAGGAGATCGGTGATCCTCGGA
* * * * *
62340188 AACAGATATT-CCTGATTTCTCATCGTGATTTAGTGTAGCTTCGTTTGGCATCTAG-GACTA-GG
66 AACCGATATTCCCGGATTT-TCATCGTGATTTAGTATAGCTTGGTTTGTCATCTAGAGACTAGGG
*
62340250 AAGTTCACTTTTGTTTGATTGTCGTCTCCTGCC
130 AAGTTCACTTTTGTTTGATTGTCATCTCCTGCC
* * * *
62340283 ATTGTTGTGTACTCTGAACTTGAATGAACCTTATC-AGTTTGGATAGGAGAACGGTGATCTTC--
1 ATGGTTGTTTACTCTGAACTTGAATGAACCTTATCGA-TTTGGATAGGAGATCGGTGATCCTCGG
* *
62340345 --A--GATATTCCTGGATTTTCATCGTGATTTAGTATAGTTTGGTTTGTCATCTAGAGACTAGGG
65 AAACCGATATTCCCGGATTTTCATCGTGATTTAGTATAGCTTGGTTTGTCATCTAGAGACTAGGG
* *
62340406 AAGTT-ACTTTTGTTTGATTATCATGTCCTGCC
130 AAGTTCACTTTTGTTTGATTGTCATCTCCTGCC
* * * *
62340438 ATGGTTGTATACTCTGAACTTGAATGAACCTTATTGATTTGGATAGGAGATTGGTGGTCCTCGGA
1 ATGGTTGTTTACTCTGAACTTGAATGAACCTTATCGATTTGGATAGGAGATCGGTGATCCTCGGA
* *
62340503 AACCGATATTCCCGGATTTTCATCATGATTTAGTATAGCTTGGTTTGTTATCTAGAGACTAGGGA
66 AACCGATATTCCCGGATTTTCATCGTGATTTAGTATAGCTTGGTTTGTCATCTAGAGACTAGGGA
*
62340568 AGTTCACTTTTGTTTGATTATCATCTCCTGCC
131 AGTTCACTTTTGTTTGATTGTCATCTCCTGCC
62340600 ATG
1 ATG
62340603 ATTCCCTATA
Statistics
Matches: 694, Mismatches: 78, Indels: 49
0.85 0.10 0.06
Matches are distributed among these distances:
154 48 0.07
155 117 0.17
156 9 0.01
157 98 0.14
158 49 0.07
159 26 0.04
160 90 0.13
161 112 0.16
162 105 0.15
163 1 0.00
164 39 0.06
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (162 bp):
ATGGTTGTTTACTCTGAACTTGAATGAACCTTATCGATTTGGATAGGAGATCGGTGATCCTCGGA
AACCGATATTCCCGGATTTTCATCGTGATTTAGTATAGCTTGGTTTGTCATCTAGAGACTAGGGA
AGTTCACTTTTGTTTGATTGTCATCTCCTGCC
Found at i:62346600 original size:61 final size:61
Alignment explanation
Indices: 62346502--62346628 Score: 146
Period size: 61 Copynumber: 2.1 Consensus size: 61
62346492 CCTAGATATA
* * * ** *
62346502 AAAAAAATCAACAAATTTAGCCCTGAATGTTAACAAAACTTGTCATTTTAGTTCAAATTCT
1 AAAAAAATCAACAAATTTAACCCTGAATATTAACAAAAATTAACAATTTAGTTCAAATTCT
* * * ** *
62346563 AAAAAAATTAATAAATTTAACCCTTAATATTTTCAAAAATTAACAATTTAGTTCTAATTCT
1 AAAAAAATCAACAAATTTAACCCTGAATATTAACAAAAATTAACAATTTAGTTCAAATTCT
62346624 AAAAA
1 AAAAA
62346629 TGTTAATATA
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.35
Consensus pattern (61 bp):
AAAAAAATCAACAAATTTAACCCTGAATATTAACAAAAATTAACAATTTAGTTCAAATTCT
Found at i:62351239 original size:68 final size:68
Alignment explanation
Indices: 62351115--62351257 Score: 180
Period size: 68 Copynumber: 2.1 Consensus size: 68
62351105 TTTGAGTGTC
* * **
62351115 TTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAGAAGAAAGTAGGGGCTTAATTG
1 TTTTTGATGCATTTTGAAAGTTCAAGTACCCAAATGAGTGCAAGAAAAAAACAGGGGCTTAATTG
*
62351180 CTT
66 CTA
* * * * *
62351183 TTTTTGATGTATTTTGAACGTTCATGTACCCAAATGAGTGCATA-AAAAAAACAGGGGTTTAGTT
1 TTTTTGATGCATTTTGAAAGTTCAAGTACCCAAATGAGTGCA-AGAAAAAAACAGGGGCTTAATT
62351247 GCTA
65 GCTA
62351251 TTTTTGA
1 TTTTTGA
62351258 AAAGGGTTTG
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
68 63 0.98
69 1 0.02
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (68 bp):
TTTTTGATGCATTTTGAAAGTTCAAGTACCCAAATGAGTGCAAGAAAAAAACAGGGGCTTAATTG
CTA
Found at i:62351609 original size:2 final size:2
Alignment explanation
Indices: 62351604--62351634 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
62351594 CTTAGGGACC
62351604 AT AT AT AT AT AT AT CAT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT
62351635 TCCATTCTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:62351623 original size:15 final size:15
Alignment explanation
Indices: 62351603--62351632 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
62351593 ACTTAGGGAC
62351603 CATATATATATATAT
1 CATATATATATATAT
62351618 CATATATATATATAT
1 CATATATATATATAT
62351633 ATTCCATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (15 bp):
CATATATATATATAT
Found at i:62352605 original size:233 final size:236
Alignment explanation
Indices: 62352182--62352660 Score: 793
Period size: 233 Copynumber: 2.0 Consensus size: 236
62352172 AAATTTTTGG
*
62352182 TAAATCAACTCTTCATTTTTATGAATAAAAATTATATGGTAGAAAGGAAGTGGTGTTAATAATAA
1 TAAATCAACTCTTCATTTTTATGAATAAAAATTATATGGTAAAAAGGAAGTGGTG---AT-ATAA
* *
62352247 TAATAATAATAAAAAGATTAACAATAGAACACTAATAAAGCAATTTAGTCTATGATCTGCACAAT
62 TAATAATAAT-AAAAGATCAACAATAGAAAACTAATAAAGCAATTTAGTCTATGATCTGCACAAT
* *
62352312 ATATTACTACAAATGTACCGTACAGAATATTGAAAGAAAACTAATAAAGAAGTTCGAAATTTAAA
126 ATATTACTACAAATGTACCGTACAGAATATTGAAAGAAAACTAATAAAGAAATCCGAAATTTAAA
* * *
62352377 CAATGTTCCGCAAATTATGTTTATGATCTGCTGTAAATTGATATGT
191 CAAGGTTCCGCAAATTATGTTTATGATATGATGTAAATTGATATGT
62352423 TAAATCAACTCTTCATTTTTATGAATAAAAATTATATGGTAAAAAGGAAGTGGTG-T-TAATAAT
1 TAAATCAACTCTTCATTTTTATGAATAAAAATTATATGGTAAAAAGGAAGTGGTGATATAATAAT
*
62352486 AATAAT-AAAGATCAACAATAGAAAACTAATAAAGCAATTTAGTCTATGATCTGCATAATATATT
66 AATAATAAAAGATCAACAATAGAAAACTAATAAAGCAATTTAGTCTATGATCTGCACAATATATT
*
62352550 ACTACAAATGTACCGTACAGAATATTGAAAGAAAACTAATAAAGAAATCCGAAATTTTAACAAGG
131 ACTACAAATGTACCGTACAGAATATTGAAAGAAAACTAATAAAGAAATCCGAAATTTAAACAAGG
62352615 TTCCGCAAATTATGTTTATGATATGATGTAAATTGATATGT
196 TTCCGCAAATTATGTTTATGATATGATGTAAATTGATATGT
*
62352656 CAAAT
1 TAAAT
62352661 TTTGTGGCAA
Statistics
Matches: 227, Mismatches: 11, Indels: 8
0.92 0.04 0.03
Matches are distributed among these distances:
233 159 0.70
235 13 0.06
237 1 0.00
241 54 0.24
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (236 bp):
TAAATCAACTCTTCATTTTTATGAATAAAAATTATATGGTAAAAAGGAAGTGGTGATATAATAAT
AATAATAAAAGATCAACAATAGAAAACTAATAAAGCAATTTAGTCTATGATCTGCACAATATATT
ACTACAAATGTACCGTACAGAATATTGAAAGAAAACTAATAAAGAAATCCGAAATTTAAACAAGG
TTCCGCAAATTATGTTTATGATATGATGTAAATTGATATGT
Found at i:62352975 original size:14 final size:14
Alignment explanation
Indices: 62352936--62352975 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
62352926 TTCAGAAACC
*
62352936 AAAATTATTTTCTA
1 AAAATTATTTTTTA
62352950 AAAATTATTTTTTA
1 AAAATTATTTTTTA
*
62352964 AAAACTATTTTT
1 AAAATTATTTTT
62352976 AGTGAAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (14 bp):
AAAATTATTTTTTA
Found at i:62356476 original size:29 final size:29
Alignment explanation
Indices: 62356434--62356490 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
62356424 GGCGGTAGTA
*
62356434 ACTTGGGAAAAAAAAGT-AGTTTATGTACC
1 ACTTGGGAAAAAAAA-TAAGTTTAGGTACC
* *
62356463 ACTTGTGACAAAAAATAAGTTTAGGTAC
1 ACTTGGGAAAAAAAATAAGTTTAGGTAC
62356491 TATCATGGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (29 bp):
ACTTGGGAAAAAAAATAAGTTTAGGTACC
Found at i:62357540 original size:61 final size:61
Alignment explanation
Indices: 62357473--62357595 Score: 140
Period size: 61 Copynumber: 2.0 Consensus size: 61
62357463 AAAAATCAAC
* * * *
62357473 AAATTTAGCCCTGAATGTTAACAAAACTT-GTCATTTTAGTTCAAACTCTAAAAAATTTAAT
1 AAATTTAACCCTGAATATTAACAAAAATTAG-CAATTTAGTTCAAACTCTAAAAAATTTAAT
* ** * * *
62357534 AAATTTAACCCTTAATATTTTCAAAAATTAGCAATTTAGTTCTAATTCTAAAAATTTTAAT
1 AAATTTAACCCTGAATATTAACAAAAATTAGCAATTTAGTTCAAACTCTAAAAAATTTAAT
62357595 A
1 A
62357596 TATATATTTA
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 50 0.98
62 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (61 bp):
AAATTTAACCCTGAATATTAACAAAAATTAGCAATTTAGTTCAAACTCTAAAAAATTTAAT
Found at i:62359277 original size:84 final size:84
Alignment explanation
Indices: 62359128--62359308 Score: 314
Period size: 84 Copynumber: 2.2 Consensus size: 84
62359118 TATCAAAGAA
*
62359128 TTCC-AATC-CAAATCACTAGAATATTTATATCTAAACAATAATAATCTTAGTGGTGTGATAGAG
1 TTCCAAATCTCAAATCACTAGAATATTTATATCTAAACAATAATAATCTTAGTGGTGTCATAGAG
62359191 TTTAGCATGTTCTCAAACC
66 TTTAGCATGTTCTCAAACC
*
62359210 TTCCAAATCTCAAATCACTAGAATATTTATTTCTAAACAATAATAATCTTAGTGGTGTCATAGAG
1 TTCCAAATCTCAAATCACTAGAATATTTATATCTAAACAATAATAATCTTAGTGGTGTCATAGAG
*
62359275 TTTCGCATGTTCTCAAACC
66 TTTAGCATGTTCTCAAACC
62359294 TTCCAAATCT-AAATC
1 TTCCAAATCTCAAATC
62359309 TTCTCGACCT
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
82 4 0.04
83 9 0.10
84 81 0.86
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (84 bp):
TTCCAAATCTCAAATCACTAGAATATTTATATCTAAACAATAATAATCTTAGTGGTGTCATAGAG
TTTAGCATGTTCTCAAACC
Found at i:62359828 original size:17 final size:17
Alignment explanation
Indices: 62359806--62359839 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
62359796 ATCCACTAAT
*
62359806 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
62359823 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
62359840 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:62364467 original size:17 final size:17
Alignment explanation
Indices: 62364445--62364478 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
62364435 ATCCACTAAT
*
62364445 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
62364462 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
62364479 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:62367174 original size:50 final size:52
Alignment explanation
Indices: 62367060--62367181 Score: 133
Period size: 56 Copynumber: 2.3 Consensus size: 52
62367050 TTAAGTTTGA
* *
62367060 AGTCAATAGACAATTGATAGTCTTAGTCTTAGTCTTTTGTTGTCGAGTTAAAGTGT
1 AGTCAATAGACAATTGATAGTCTTAGTC----TCCTTTGTTGTCGAGTTAAAGTAT
* * *
62367116 AGTTAATAGACAATTGATAGTCTTAG-C-CCTTT-TTGTGGAGTTAAATTTAT
1 AGTCAATAGACAATTGATAGTCTTAGTCTCCTTTGTTGTCGAGTTAAA-GTAT
62367166 AGTCAATAGACAATTG
1 AGTCAATAGACAATTG
62367182 GGACCAAACT
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
49 12 0.20
50 21 0.36
55 1 0.02
56 25 0.42
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (52 bp):
AGTCAATAGACAATTGATAGTCTTAGTCTCCTTTGTTGTCGAGTTAAAGTAT
Found at i:62367733 original size:20 final size:20
Alignment explanation
Indices: 62367708--62367748 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
62367698 AAAAAGGGTT
*
62367708 AAAAATGATTTTTTTTAAAA
1 AAAAATGATTTTTATTAAAA
*
62367728 AAAAATTATTTTTATTAAAA
1 AAAAATGATTTTTATTAAAA
62367748 A
1 A
62367749 TTTAGAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
AAAAATGATTTTTATTAAAA
Found at i:62374880 original size:61 final size:61
Alignment explanation
Indices: 62374782--62374916 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
62374772 CCTAAATATA
* * * * * *
62374782 AAAAAAATCAATAAATTTAGCCCTGAATGTTAACAAAACTT-GTCATTTTAGTTCAAATTCT
1 AAAAAATTTAATAAATTTAACCCTGAATATTAACAAAAATTAG-CAATTTAGTTCAAATTCT
* ** *
62374843 AAAAAATTTAATAAATTTAACCCTTAATATTTTCAAAAATTAGCAATTTAGTTCTAATTCT
1 AAAAAATTTAATAAATTTAACCCTGAATATTAACAAAAATTAGCAATTTAGTTCAAATTCT
*
62374904 AAAAATTTTAATA
1 AAAAAATTTAATA
62374917 TATATATTTA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
61 61 0.98
62 1 0.02
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (61 bp):
AAAAAATTTAATAAATTTAACCCTGAATATTAACAAAAATTAGCAATTTAGTTCAAATTCT
Found at i:62379492 original size:88 final size:87
Alignment explanation
Indices: 62379356--62379616 Score: 249
Period size: 86 Copynumber: 3.0 Consensus size: 87
62379346 ATTTAAGTAC
* * * * * * * * *
62379356 TTTTTTTTCTACTCAATTGAGCACTTAAACTTTTAAAATGTATCAAAAATATCTTTA-CACTTCT
1 TTTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAA-ACCTTAATCACTTCT
62379420 TCAAAAAAAGCAATTAAACCCCTA
65 TCAAAAAAA-CAATTAAACCCCTA
* * *** *
62379444 TTTTTTTTCCGCTCAATTGGGTACTTGAACTTTCATAATGCATAAAAAAACCTTAATTTTTTTTT
1 TTTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAAACCTTAATCACTTCTT
* * *
62379509 CAAAGAAACAATTAAGCCTCTA
66 CAAAAAAACAATTAAACCCCTA
* * ** *
62379531 -TTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAAGGCCTTAAT-TTTTTT
1 TTTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAA-ACCTTAATCACTTCT
* *
62379594 TCAAAAAAGCAATTAAGCCCCTA
65 TCAAAAAAACAATTAAACCCCTA
62379617 CTCTTATTAA
Statistics
Matches: 146, Mismatches: 25, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
86 71 0.49
87 24 0.16
88 51 0.35
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (87 bp):
TTTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAAACCTTAATCACTTCTT
CAAAAAAACAATTAAACCCCTA
Found at i:62379556 original size:86 final size:87
Alignment explanation
Indices: 62379423--62379616 Score: 295
Period size: 86 Copynumber: 2.2 Consensus size: 87
62379413 CACTTCTTCA
* * *
62379423 AAAAAAGCAATTAAACCCCTATTTTTTTTCCGCTCAATTGGGTACTTGAACTTTCATAATGCAT-
1 AAAAAAGCAATTAAGCCCCTATTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCATC
62379487 AAAAAAACCTTAATTTTTTTTTC
66 AAAAAAACCTTAA-TTTTTTTTC
*
62379510 AAAGAAA-CAATTAAGCCTCTA-TTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCAT
1 AAA-AAAGCAATTAAGCCCCTATTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCAT
**
62379573 CAAAAAGGCCTTAATTTTTTTTC
65 CAAAAAAACCTTAATTTTTTTTC
62379596 AAAAAAGCAATTAAGCCCCTA
1 AAAAAAGCAATTAAGCCCCTA
62379617 CTCTTATTAA
Statistics
Matches: 97, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
85 3 0.03
86 65 0.67
87 26 0.27
88 3 0.03
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.36
Consensus pattern (87 bp):
AAAAAAGCAATTAAGCCCCTATTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCATC
AAAAAAACCTTAATTTTTTTTC
Found at i:62379687 original size:19 final size:20
Alignment explanation
Indices: 62379643--62379687 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
62379633 GAAAAAAATC
62379643 ATAAAAATAATAAATTTTAG
1 ATAAAAATAATAAATTTTAG
* *
62379663 AAAAAAATATTAAATTTTA-
1 ATAAAAATAATAAATTTTAG
62379682 ATAAAA
1 ATAAAA
62379688 TTTAAAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
ATAAAAATAATAAATTTTAG
Found at i:62379747 original size:27 final size:28
Alignment explanation
Indices: 62379717--62379772 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
62379707 TTTAAATTTT
*
62379717 TTTTAGAAAAAT-AGT-CAAAAAATAAAA
1 TTTTAGAAAAATCA-TAAAAAAAATAAAA
*
62379744 TTTTATAAAAATCATAAAAAAAATAAAA
1 TTTTAGAAAAATCATAAAAAAAATAAAA
62379772 T
1 T
62379773 CCATCAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.29
Consensus pattern (28 bp):
TTTTAGAAAAATCATAAAAAAAATAAAA
Found at i:62380007 original size:90 final size:92
Alignment explanation
Indices: 62379894--62380067 Score: 298
Period size: 92 Copynumber: 1.9 Consensus size: 92
62379884 AAAACAGATA
* *
62379894 AAAGTAGGGGCTTAATTGCTTTTTTT-AAAA-GTTTGAGGGTCTTTTTGATGCATTTTGAAAGTT
1 AAAGTAGGGGCCTAATTGCTTTTTTTGAAAATGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTT
*
62379957 CAAGTACCCAATTGAGTGCCAAAAAAT
66 CAAGTACCCAAATGAGTGCCAAAAAAT
*
62379984 AAAGTAGGGGCCTAATTGCTTTTTTTGAAAATGTTTGAGGGCCTTTTTGATGTATTTTGAAAGTT
1 AAAGTAGGGGCCTAATTGCTTTTTTTGAAAATGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTT
62380049 CAAGTACCCAAATGAGTGC
66 CAAGTACCCAAATGAGTGC
62380068 ATAAAAAGAA
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
90 25 0.32
91 4 0.05
92 49 0.63
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.37
Consensus pattern (92 bp):
AAAGTAGGGGCCTAATTGCTTTTTTTGAAAATGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTT
CAAGTACCCAAATGAGTGCCAAAAAAT
Found at i:62380433 original size:27 final size:30
Alignment explanation
Indices: 62380403--62380474 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 30
62380393 CTCAATTGGG
62380403 TATTTAAATTTTTAATATT-T-GATTTT-T
1 TATTTAAATTTTTAATATTATAGATTTTAT
* *
62380430 TATTAAAATTTAATAATATTATAGATTTTAT
1 TATTTAAATTT-TTAATATTATAGATTTTAT
*
62380461 TGATTTTAATTTTT
1 T-ATTTAAATTTTT
62380475 TTTCTAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
27 10 0.29
28 7 0.20
29 1 0.03
30 6 0.17
31 3 0.09
32 8 0.23
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (30 bp):
TATTTAAATTTTTAATATTATAGATTTTAT
Found at i:62382088 original size:10 final size:10
Alignment explanation
Indices: 62382068--62382156 Score: 53
Period size: 9 Copynumber: 9.2 Consensus size: 10
62382058 TTCTTATGAC
*
62382068 TATAAAATTT
1 TATAAATTTT
62382078 TAT-AATTTT
1 TATAAATTTT
* *
62382087 T-TATATTTC
1 TATAAATTTT
*
62382096 TATATA-TTT
1 TATAAATTTT
62382105 TA-AAATTTT
1 TATAAATTTT
*
62382114 TATAAAATTT
1 TATAAATTTT
* *
62382124 CA-CAATTTT
1 TATAAATTTT
*
62382133 TATATATTTTT
1 TATA-AATTTT
62382144 TAATAAATTTT
1 T-ATAAATTTT
62382155 TA
1 TA
62382157 AGATTTGAAT
Statistics
Matches: 59, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
8 3 0.05
9 26 0.44
10 15 0.25
11 12 0.20
12 3 0.05
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.58
Consensus pattern (10 bp):
TATAAATTTT
Found at i:62382104 original size:27 final size:27
Alignment explanation
Indices: 62382030--62382145 Score: 74
Period size: 28 Copynumber: 4.1 Consensus size: 27
62382020 TTTTACAAAA
* *
62382030 TTTATATTTCTTTACATTTTGTATAATTT
1 TTTATATTTCTATA-AATTT-TATAATTT
* **
62382059 TCT-TATGACTATAAAATTTTATAATTT
1 TTTATATTTCTAT-AAATTTTATAATTT
* *
62382086 TTTATATTTCTATATATTTTAAAATTT
1 TTTATATTTCTATAAATTTTATAATTT
* * *
62382113 TTATAAAATTTC-ACAATTTTTATATATTT
1 TT-T-ATATTTCTATAAATTTTATA-ATTT
62382142 TTTA
1 TTTA
62382146 ATAAATTTTT
Statistics
Matches: 67, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
27 25 0.37
28 27 0.40
29 15 0.22
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (27 bp):
TTTATATTTCTATAAATTTTATAATTT
Found at i:62382392 original size:89 final size:89
Alignment explanation
Indices: 62382221--62382443 Score: 232
Period size: 89 Copynumber: 2.5 Consensus size: 89
62382211 AATTTTTAAT
* * * * * **
62382221 AAAAGTAGGGACTTAATTGGTTTTTTTTATTAAGTTTGAGGGTGTTTTTGATGCATTTTGAAAGT
1 AAAAGCAGGGGCTTAATTGCTTTTTTTGA-AAAGTTTGAGGGCCTTTTTGATGCATTTTGAAAGT
* *
62382286 TTAAGTACCCAATTGAG-TGCAAAA
65 TCAAGTACCCAAATGAGTTGCAAAA
* *
62382310 AAAAGGAGGGGCTTAATTGCTTTTTTTGAAAATGTTTGAGGGCCTTTTTGATGTATTTTGAAAGT
1 AAAAGCAGGGGCTTAATTGCTTTTTTTGAAAA-GTTTGAGGGCCTTTTTGATGCATTTTGAAAGT
* * **
62382375 TCAAGTTCTCAAATGAGTTTTAAAA
65 TCAAGTACCCAAATGAGTTGCAAAA
* * *
62382400 AAAAGAACAGGGGTTTAGTTGCTATTTTTGAAAAAGTTTGAGGG
1 AAAAG--CAGGGGCTTAATTGCTTTTTTTG-AAAAGTTTGAGGG
62382444 TTTTTTGCAC
Statistics
Matches: 111, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
88 2 0.02
89 67 0.60
90 10 0.09
92 28 0.25
93 4 0.04
ACGTcount: A:0.31, C:0.07, G:0.24, T:0.39
Consensus pattern (89 bp):
AAAAGCAGGGGCTTAATTGCTTTTTTTGAAAAGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTT
CAAGTACCCAAATGAGTTGCAAAA
Found at i:62383706 original size:13 final size:13
Alignment explanation
Indices: 62383688--62383765 Score: 59
Period size: 13 Copynumber: 6.0 Consensus size: 13
62383678 TTGGAAAGTG
*
62383688 AAAAAAAAAAACA
1 AAAAAAAAAAATA
* **
62383701 AAAAAAAGAAGGA
1 AAAAAAAAAAATA
*
62383714 AAAAAAGAAAA-A
1 AAAAAAAAAAATA
* *
62383726 AAAAGAAGAAATA
1 AAAAAAAAAAATA
*
62383739 AAAAAAGAAAATA
1 AAAAAAAAAAATA
*
62383752 AAAGAAAAATAATA
1 AAA-AAAAAAAATA
62383766 CTTCTCTGAT
Statistics
Matches: 49, Mismatches: 14, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
12 9 0.18
13 32 0.65
14 8 0.16
ACGTcount: A:0.83, C:0.01, G:0.10, T:0.05
Consensus pattern (13 bp):
AAAAAAAAAAATA
Found at i:62383716 original size:22 final size:22
Alignment explanation
Indices: 62383689--62383757 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 22
62383679 TGGAAAGTGA
62383689 AAAAAAAAAACAAAAAAAAGAAG
1 AAAAAAAAAA-AAAAAAAAGAAG
* *
62383712 GAAAAAAAGAAAAAAAAAGAAG
1 AAAAAAAAAAAAAAAAAAGAAG
62383734 AAATAAAAAAAGAAAATAAAAGAA
1 AAA-AAAAAAA-AAAA-AAAAGAA
62383758 AAATAATACT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.36
23 14 0.36
24 4 0.10
25 7 0.18
ACGTcount: A:0.84, C:0.01, G:0.12, T:0.03
Consensus pattern (22 bp):
AAAAAAAAAAAAAAAAAAGAAG
Found at i:62383758 original size:22 final size:21
Alignment explanation
Indices: 62383687--62383760 Score: 76
Period size: 23 Copynumber: 3.3 Consensus size: 21
62383677 CTTGGAAAGT
*
62383687 GAAAAAAAAAAACAAAAAAAA
1 GAAAAAAAAAAAGAAAAAAAA
*
62383708 GAAGGAAAAAAAGAAAAAAAAAGAA
1 GAA--AAAAAAA-AAGAAAAAA-AA
*
62383733 GAAATAAAAAAAGAAAATAAAA
1 GAAAAAAAAAAAGAAAA-AAAA
62383755 GAAAAA
1 GAAAAA
62383761 TAATACTTCT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
21 3 0.07
22 13 0.30
23 15 0.34
24 8 0.18
25 5 0.11
ACGTcount: A:0.84, C:0.01, G:0.12, T:0.03
Consensus pattern (21 bp):
GAAAAAAAAAAAGAAAAAAAA
Found at i:62397584 original size:91 final size:87
Alignment explanation
Indices: 62397455--62397653 Score: 283
Period size: 91 Copynumber: 2.2 Consensus size: 87
62397445 CACTTCTTCA
* * *
62397455 AAAAAAGCAATTAAACCCCTTTTTTTTTCCCGCTCAATTGGGTACTTGAACTTTCATAATGCATA
1 AAAAAAGCAATTAAGCCCCTATTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCATA
62397520 AAAAAAACCTTTAAATTTTTTTTTTC
66 AAAAAAACC-TT-AA--TTTTTTTTC
*
62397546 AAAGAAA-CAATTAAGCCTCTATTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCAT
1 AAA-AAAGCAATTAAGCCCCTATTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCAT
* **
62397610 CAAAAAGGCCTTAATTTTTTTTC
65 AAAAAAAACCTTAATTTTTTTTC
62397633 AAAAAAGCAATTAAGCCCCTA
1 AAAAAAGCAATTAAGCCCCTA
62397654 CTCTTATTAA
Statistics
Matches: 98, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
86 3 0.03
87 25 0.26
89 2 0.02
90 2 0.02
91 63 0.64
92 3 0.03
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.36
Consensus pattern (87 bp):
AAAAAAGCAATTAAGCCCCTATTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCATA
AAAAAAACCTTAATTTTTTTTC
Found at i:62397724 original size:19 final size:20
Alignment explanation
Indices: 62397680--62397724 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
62397670 GAAAAAAATC
62397680 ATAAAAATAATAAATTTTAG
1 ATAAAAATAATAAATTTTAG
* *
62397700 AAAAAAATATTAAATTTTA-
1 ATAAAAATAATAAATTTTAG
62397719 ATAAAA
1 ATAAAA
62397725 TTTAAAACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
ATAAAAATAATAAATTTTAG
Found at i:62397809 original size:9 final size:10
Alignment explanation
Indices: 62397774--62397801 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
62397764 TAGTCAAAAA
62397774 ATAAAAATTT
1 ATAAAAATTT
62397784 ATAAAAATTT
1 ATAAAAATTT
62397794 ATAAAAAT
1 ATAAAAAT
62397802 CATAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
ATAAAAATTT
Found at i:62398084 original size:10 final size:10
Alignment explanation
Indices: 62398062--62398141 Score: 71
Period size: 9 Copynumber: 8.4 Consensus size: 10
62398052 TTCTTATGAC
*
62398062 TTTATAAAAT
1 TTTATAAATT
62398072 TTTAT-AATT
1 TTTATAAATT
*
62398081 TTT-TATATT
1 TTTATAAATT
** *
62398090 TCAATATATT
1 TTTATAAATT
62398100 TTTA-AAATT
1 TTTATAAATT
62398109 TTTA-AAATT
1 TTTATAAATT
62398118 TTTA-AAATT
1 TTTATAAATT
62398127 TTTAATAAATT
1 TTT-ATAAATT
62398138 TTTA
1 TTTA
62398142 ATATTTGATT
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
8 1 0.02
9 35 0.59
10 15 0.25
11 8 0.14
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTATAAATT
Found at i:62398147 original size:9 final size:9
Alignment explanation
Indices: 62398097--62398147 Score: 75
Period size: 9 Copynumber: 5.4 Consensus size: 9
62398087 ATTTCAATAT
62398097 ATTTTTAAA
1 ATTTTTAAA
62398106 ATTTTTAAA
1 ATTTTTAAA
62398115 ATTTTTAAA
1 ATTTTTAAA
62398124 ATTTTTAATAA
1 ATTTTT-A-AA
*
62398135 ATTTTTAAT
1 ATTTTTAAA
62398144 ATTT
1 ATTT
62398148 GATTTTTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
9 29 0.74
10 2 0.05
11 8 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:62398322 original size:90 final size:92
Alignment explanation
Indices: 62398216--62398389 Score: 280
Period size: 92 Copynumber: 1.9 Consensus size: 92
62398206 ATTTTTAATA
* * *
62398216 AAAGTAGGGGCTTAATTGCTTTTTTT-TAAA-GTTTGAGGGTCTTTTTGATGCATTTTGAAAGTT
1 AAAGTAGGGGCCTAATTGCTTTTTTTGAAAATGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTT
* *
62398279 TAAGTACCCAATTGAGTGCCAAAAAAT
66 CAAGTACCCAAATGAGTGCCAAAAAAT
*
62398306 AAAGTAGGGGCCTAATTGCTTTTTTTGAAAATGTTTGAGGGCCTTTTTGATGTATTTTGAAAGTT
1 AAAGTAGGGGCCTAATTGCTTTTTTTGAAAATGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTT
62398371 CAAGTACCCAAATGAGTGC
66 CAAGTACCCAAATGAGTGC
62398390 ATAAAAAGAA
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
90 25 0.33
91 3 0.04
92 48 0.63
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (92 bp):
AAAGTAGGGGCCTAATTGCTTTTTTTGAAAATGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTT
CAAGTACCCAAATGAGTGCCAAAAAAT
Found at i:62403434 original size:72 final size:72
Alignment explanation
Indices: 62403346--62403494 Score: 253
Period size: 72 Copynumber: 2.1 Consensus size: 72
62403336 TCAGGAACGG
* **
62403346 TTCCAAGATCACTGGGGAACCTCTTGCAACTCACTCATTTAGACTTGTCGGGGAACCAATTGAGT
1 TTCCAAGATCACTGGGGAACCACTTGCAACTCACTCATTTAGACTTGTCGCAGAACCAATTGAGT
62403411 GGACAAA
66 GGACAAA
* *
62403418 TTCCAAGATCATTGGGGAACCACTTGCAACTCACTCTTTTAGACTTGTCGCAGAACCAATTGAGT
1 TTCCAAGATCACTGGGGAACCACTTGCAACTCACTCATTTAGACTTGTCGCAGAACCAATTGAGT
62403483 GGACAAA
66 GGACAAA
62403490 TTCCA
1 TTCCA
62403495 TCGTCAATTC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (72 bp):
TTCCAAGATCACTGGGGAACCACTTGCAACTCACTCATTTAGACTTGTCGCAGAACCAATTGAGT
GGACAAA
Done.