Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 2 of 333
Found at i:229226 original size:98 final size:92
Alignment explanation
Indices: 229019--229414 Score: 358
Period size: 98 Copynumber: 4.3 Consensus size: 92
229009 TTTGAGTACT
* * * **
229019 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-----
* * *
229084 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
61 -AAAGTGATAAGTGATAGCTTCAGCTACACTTA
* *
229117 TCTGAT-------C-AAGTGATAAGTTATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAAGT
229174 GATAAGTGATAGCTTCAGCTACACTTA
66 GATAAGTGATAGCTTCAGCTACACTTA
*
229201 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 TCTGATCAAGAGAC------AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
* *
229266 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
60 C------AAAGTGATAAGTGATAGCTTCAGCTACACTTA
** *
229305 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAAGT
229370 GATAA--G-T-G-----GCTACACTTA
66 GATAAGTGATAGCTTCAGCTACACTTA
*
229388 TCTGATCAAGAAACAAAGTGATAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTG
229415 GCTACACTTA
Statistics
Matches: 259, Mismatches: 19, Indels: 55
0.78 0.06 0.17
Matches are distributed among these distances:
83 35 0.14
84 35 0.14
88 1 0.00
89 1 0.00
90 41 0.16
91 1 0.00
92 10 0.04
98 92 0.36
104 43 0.17
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (92 bp):
TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAAGT
GATAAGTGATAGCTTCAGCTACACTTA
Found at i:229234 original size:52 final size:51
Alignment explanation
Indices: 229169--229377 Score: 293
Period size: 52 Copynumber: 4.1 Consensus size: 51
229159 ATCAAGTGAC
*
229169 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGT-G
* *
229221 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
* *
229272 AAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC-----
1 -AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
*
229319 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGAC-AAGTG
229371 ATAAGTG
1 A-AAGTG
229378 GCTACACTTA
Statistics
Matches: 143, Mismatches: 6, Indels: 15
0.87 0.04 0.09
Matches are distributed among these distances:
46 43 0.30
51 1 0.01
52 94 0.66
53 5 0.03
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.27
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
Found at i:229385 original size:37 final size:37
Alignment explanation
Indices: 229341--229450 Score: 195
Period size: 37 Copynumber: 3.0 Consensus size: 37
229331 GATAGCTTTA
229341 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
229378 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
229415 GCTACACTTATCTGATCAAGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
229451 ATCATACGTA
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 12 0.17
37 58 0.83
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:230808 original size:49 final size:49
Alignment explanation
Indices: 230705--230939 Score: 358
Period size: 49 Copynumber: 4.9 Consensus size: 49
230695 ATGTGAACAT
230705 GTGATTATGTGATT-CGTGT-A-A-CATAGCT-GGCTATGGCATC-GT-A
1 GTGA-TATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
230748 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
230797 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* *
230846 GTGATATGTGACTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* * * *
230895 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCG
230940 AGAAAACGAA
Statistics
Matches: 178, Mismatches: 7, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
42 9 0.05
43 9 0.05
44 1 0.01
45 1 0.01
46 7 0.04
47 12 0.07
48 2 0.01
49 137 0.77
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.31
Consensus pattern (49 bp):
GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
Found at i:247128 original size:127 final size:130
Alignment explanation
Indices: 246827--247110 Score: 364
Period size: 131 Copynumber: 2.2 Consensus size: 130
246817 ACCTTTATCA
* * * *
246827 CCTACCGTGCTGGGTTGCGATTTTCTGTTTGTTCAAAATAATCGAATATTCTTTTGGAATTTCAC
1 CCTACTGTGCTGGGTTTCGATTTTCTGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCAC
* * * * * * * *
246892 TCATGTCTTTAAAAATTCTTCAAAACGAAGGTAATGTTCTATGTTTGGCAATTCGGGGAATCGTG
66 TCATGTCTCT-AAAATTCTTCAAAACGAAGGCAATGTCCGATGTCTAGAAATTCGAGGAATCGTG
246957 C
130 C
*
246958 CCTA-TCGTGCTGGGTTGT-GATTTCCTGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTC
1 CCTACT-GTGCTGGGTT-TCGATTTTCTGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTC
*
247021 ACTCATGTTCTCT-AAATTC-T-AAAAC-AAGGCAATGTCCGATGTCTAGAAATTCGAGGAGTCG
64 ACTCATG-TCTCTAAAATTCTTCAAAACGAAGGCAATGTCCGATGTCTAGAAATTCGAGGAATCG
247082 TGC
128 TGC
247085 CCTACTGTGCTGGGTTTCGATTTTCT
1 CCTACTGTGCTGGGTTTCGATTTTCT
247111 CGTCGGACTA
Statistics
Matches: 133, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
126 1 0.01
127 52 0.39
128 6 0.05
129 1 0.01
130 6 0.05
131 63 0.47
132 4 0.03
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (130 bp):
CCTACTGTGCTGGGTTTCGATTTTCTGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCAC
TCATGTCTCTAAAATTCTTCAAAACGAAGGCAATGTCCGATGTCTAGAAATTCGAGGAATCGTGC
Found at i:249384 original size:19 final size:18
Alignment explanation
Indices: 249362--249401 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
249352 TATAAATAAA
* *
249362 ATAATAAATATGTAATTAT
1 ATAATAAAAATAT-ATTAT
249381 ATAATAAAAATATATTAT
1 ATAATAAAAATATATTAT
249399 ATA
1 ATA
249402 TATCATTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
ATAATAAAAATATATTAT
Found at i:249927 original size:3 final size:3
Alignment explanation
Indices: 249919--249952 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
249909 AATAAGAAAA
249919 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
249953 GAATGTTACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:258033 original size:24 final size:24
Alignment explanation
Indices: 257970--258020 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
257960 TTTCTAGAAG
* * *
257970 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
257994 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
258018 ATT
1 ATT
258021 ACACTTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:259722 original size:7 final size:6
Alignment explanation
Indices: 259686--259719 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
259676 TACTATGACT
* *
259686 AAAATG AAAATG AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
259720 ATATTGTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:261206 original size:76 final size:76
Alignment explanation
Indices: 261107--261257 Score: 275
Period size: 76 Copynumber: 2.0 Consensus size: 76
261097 TTGTAATTTA
* * *
261107 ATTTTTTAAAATTATAAATTTTTAAACTTACAATAAAATTTTTATATTTTAACTCTCATAAAAAT
1 ATTTTTTAAAATTATAAAATTTTAAACTTACAATAAAATTTTTACATTTTAACCCTCATAAAAAT
261172 TATAAATTTTT
66 TATAAATTTTT
261183 ATTTTTTAAAATTATAAAATTTTAAACTTACAATAAAATTTTTACATTTTAACCCTCATAAAAAT
1 ATTTTTTAAAATTATAAAATTTTAAACTTACAATAAAATTTTTACATTTTAACCCTCATAAAAAT
261248 TATAAATTTT
66 TATAAATTTT
261258 AAAATAAATT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (76 bp):
ATTTTTTAAAATTATAAAATTTTAAACTTACAATAAAATTTTTACATTTTAACCCTCATAAAAAT
TATAAATTTTT
Found at i:267431 original size:4 final size:4
Alignment explanation
Indices: 267422--267450 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
267412 AAATTTGTTC
267422 TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
267451 TGAGTTCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:267684 original size:42 final size:42
Alignment explanation
Indices: 267637--267719 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
267627 ATTACATAGG
* *
267637 TATTCATTGATGTTGAGACTTTAACTGTTTAAGATGTCATTA
1 TATTCATTGATGTTGAGACCTTAACTATTTAAGATGTCATTA
*
267679 TATTCATTGATGTTGAGACCTTATCTATTTAAGATGTCATT
1 TATTCATTGATGTTGAGACCTTAACTATTTAAGATGTCATT
267720 GTTCGAACAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.46
Consensus pattern (42 bp):
TATTCATTGATGTTGAGACCTTAACTATTTAAGATGTCATTA
Found at i:270096 original size:12 final size:12
Alignment explanation
Indices: 270076--270112 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
270066 GAAGAAGATG
*
270076 ACGGTGGTGGAA
1 ACGGCGGTGGAA
*
270088 ACGGCGGTGCAA
1 ACGGCGGTGGAA
270100 ACGGCGGTGGAA
1 ACGGCGGTGGAA
270112 A
1 A
270113 TGGAAATAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.27, C:0.16, G:0.46, T:0.11
Consensus pattern (12 bp):
ACGGCGGTGGAA
Found at i:270710 original size:2 final size:2
Alignment explanation
Indices: 270705--270733 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
270695 TCAGGAGAGA
270705 AT 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 AT A
270734 AGAAAACAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:271235 original size:43 final size:43
Alignment explanation
Indices: 271187--271272 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
271177 CCTTTTAAAA
**
271187 ATTTAATGAATCTTACCACTAATTCTTAGGAAAAACTAAACAC
1 ATTTAATGAATCTTACCACTAATTCTTAAAAAAAACTAAACAC
271230 ATTTAATGAATCTTACCACTAATTCTTAAAAAAAACTAAACAC
1 ATTTAATGAATCTTACCACTAATTCTTAAAAAAAACTAAACAC
271273 GTAATAGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.47, C:0.19, G:0.05, T:0.30
Consensus pattern (43 bp):
ATTTAATGAATCTTACCACTAATTCTTAAAAAAAACTAAACAC
Found at i:271935 original size:34 final size:33
Alignment explanation
Indices: 271892--271988 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 33
271882 CTGAAAGGTT
271892 TAATTAAAATTTTCAAAATTTTTGAAAGAGGGTC
1 TAATTAAAATTTT-AAAATTTTTGAAAGAGGGTC
* *
271926 TAATTAAAATTTTAAAACTTTTGAAAAAGGGTC
1 TAATTAAAATTTTAAAATTTTTGAAAGAGGGTC
* *
271959 TAATTAAAATTTTAAAATCTTTAAAAGAGG
1 TAATTAAAATTTTAAAATTTTTGAAAGAGG
271989 TACTCAAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 44 0.77
34 13 0.23
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.37
Consensus pattern (33 bp):
TAATTAAAATTTTAAAATTTTTGAAAGAGGGTC
Found at i:287984 original size:3 final size:3
Alignment explanation
Indices: 287976--288019 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
287966 GTTCACAAAC
*
287976 TAT TAT TAT TAT T-T TA- CAT TAT TAT T-T TA- TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
288020 ATCTTACTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
2 7 0.20
3 28 0.80
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:287998 original size:13 final size:13
Alignment explanation
Indices: 287980--288014 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
287970 ACAAACTATT
287980 ATTATTATTTTAC
1 ATTATTATTTTAC
*
287993 ATTATTATTTTAT
1 ATTATTATTTTAC
288006 ATTATTATT
1 ATTATTATT
288015 ATTATATCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (13 bp):
ATTATTATTTTAC
Found at i:287998 original size:16 final size:16
Alignment explanation
Indices: 287977--288017 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 16
287967 TTCACAAACT
287977 ATTATTATTATTTTAC
1 ATTATTATTATTTTAC
*
287993 ---ATTATTATTTTAT
1 ATTATTATTATTTTAC
288006 ATTATTATTATT
1 ATTATTATTATT
288018 ATATCTTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
13 12 0.57
16 9 0.43
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTATTATTATTTTAC
Found at i:288686 original size:29 final size:29
Alignment explanation
Indices: 288643--288713 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
288633 TGTAGTACTC
* *
288643 TTTTTTGTATGTCATGCATTATTTTATTA
1 TTTTTTGTATATCATGCATTATTTAATTA
288672 TTTTTTGTATATCATGCATTATTTAATTA
1 TTTTTTGTATATCATGCATTATTTAATTA
*
288701 TTACTTTGTATAT
1 TT-TTTTGTATAT
288714 ATATATATCT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 29 0.76
30 9 0.24
ACGTcount: A:0.24, C:0.07, G:0.08, T:0.61
Consensus pattern (29 bp):
TTTTTTGTATATCATGCATTATTTAATTA
Found at i:296020 original size:16 final size:17
Alignment explanation
Indices: 295999--296032 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
295989 AAATAAATTT
*
295999 ATAAAAATTTA-TAAAA
1 ATAAAAATATATTAAAA
296015 ATAAAAATATATTAAAA
1 ATAAAAATATATTAAAA
296032 A
1 A
296033 ATTAGTTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAAATATATTAAAA
Found at i:296861 original size:33 final size:33
Alignment explanation
Indices: 296821--296886 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
296811 ACCACCTCCT
296821 TCATCAGACAGAGTGAACTGACCATCGTCACCA
1 TCATCAGACAGAGTGAACTGACCATCGTCACCA
296854 TCATCAGACAGAGTGAACTGACCATCGTCACCA
1 TCATCAGACAGAGTGAACTGACCATCGTCACCA
296887 CCCTCTCTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.30, G:0.18, T:0.18
Consensus pattern (33 bp):
TCATCAGACAGAGTGAACTGACCATCGTCACCA
Found at i:297749 original size:22 final size:22
Alignment explanation
Indices: 297724--297771 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
297714 TCACTTGATT
297724 TAAATTGATTTTATGTAAAACA
1 TAAATTGATTTTATGTAAAACA
*
297746 TAAATTGATTTTATGTAAAAGA
1 TAAATTGATTTTATGTAAAACA
297768 TAAA
1 TAAA
297772 AAATAGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (22 bp):
TAAATTGATTTTATGTAAAACA
Found at i:298744 original size:104 final size:105
Alignment explanation
Indices: 298564--298823 Score: 320
Period size: 104 Copynumber: 2.5 Consensus size: 105
298554 TTCATATGCC
* * *
298564 ACACGGCCT-GG-ACATGCCCATGTCCTTGCCTGTGTGGCTCACACGGCCT-GACACACGCACAT
1 ACACGGCCTGGGCACACGCCCATATCCTTGCCTGTGTGGCTCACACGGCCTGGGCACACGCACAT
* *
298626 GTTGTCTGCTCGTGTGGTTCTAAATCGTAAACAGTGAGTT
66 GTTGTCTGCTCGTGTGGTTCTAAAGCGTAAACAATGAGTT
* * *
298666 ACACGGCCTGGGCACACGCCAATATCCTTACCCGTGTGGCTCACACGGCCTGGGCACACGTC-CA
1 ACACGGCCTGGGCACACGCCCATATCCTTGCCTGTGTGGCTCACACGGCCTGGGCACACG-CACA
298730 TGTCT-T-TGGC-CGTGTGGTTCTAAAGCGTAAACAATGAGTT
65 TGT-TGTCT-GCTCGTGTGGTTCTAAAGCGTAAACAATGAGTT
* * * *
298770 ACACGGCCTGGACACACACCCATTTCCTTGCCTGTGTGGCAT-ACACTGCCTGGG
1 ACACGGCCTGGGCACACGCCCATATCCTTGCCTGTGTGGC-TCACACGGCCTGGG
298824 TGCCCATTTC
Statistics
Matches: 136, Mismatches: 15, Indels: 12
0.83 0.09 0.07
Matches are distributed among these distances:
102 9 0.07
103 2 0.01
104 107 0.79
105 16 0.12
106 2 0.01
ACGTcount: A:0.20, C:0.30, G:0.25, T:0.24
Consensus pattern (105 bp):
ACACGGCCTGGGCACACGCCCATATCCTTGCCTGTGTGGCTCACACGGCCTGGGCACACGCACAT
GTTGTCTGCTCGTGTGGTTCTAAAGCGTAAACAATGAGTT
Found at i:298836 original size:38 final size:38
Alignment explanation
Indices: 298788--298862 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
298778 TGGACACACA
* *
298788 CCCATTTCCTTGCCTGTGTGGCAT-ACACTGCCTGGGTG
1 CCCATTTCCTTGCCCGTGTGGC-TCACACGGCCTGGGTG
298826 CCCATTTCCTTGCCCGTGTGGCTCACACGGCCTGGGT
1 CCCATTTCCTTGCCCGTGTGGCTCACACGGCCTGGGT
298863 ACACGCCCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 1 0.03
38 33 0.97
ACGTcount: A:0.09, C:0.35, G:0.27, T:0.29
Consensus pattern (38 bp):
CCCATTTCCTTGCCCGTGTGGCTCACACGGCCTGGGTG
Found at i:298857 original size:142 final size:142
Alignment explanation
Indices: 298690--298948 Score: 374
Period size: 142 Copynumber: 1.8 Consensus size: 142
298680 CACGCCAATA
* ** *
298690 TCCTTACCCGTGTGGCTCACACGGCCTGGGCACACGTCCATGTCTTTGGCCGTGTGGTTCTAAAG
1 TCCTTACCCGTGTGGCTCACACGGCCTGGGCACACGCCCATGTCCCTGACCGTGTGGTTCTAAAG
* * * *
298755 CGTAAACAATGAGTTACACGGCCTGGACACACACCCATTTCCTTGCCTGTGTGGCATACACTGCC
66 CGTAAACAATGAGTTACACGACCTAGACACACACCCATGTCCTTGCCCGTGTGGCATACACTGCC
298820 TGGGTGCCCATT
131 TGGGTGCCCATT
* * *
298832 TCCTTGCCCGTGTGGCTCACACGGCCTGGGTACACGCCCATGTCCCTGATCGTGTGGTTCTAAAG
1 TCCTTACCCGTGTGGCTCACACGGCCTGGGCACACGCCCATGTCCCTGACCGTGTGGTTCTAAAG
* * * **
298897 TGTAAACAGTGAGTTACACGACTTAGACACACGTCCATGTCCTTGCCCGTGT
66 CGTAAACAATGAGTTACACGACCTAGACACACACCCATGTCCTTGCCCGTGT
298949 AGGTCACACA
Statistics
Matches: 101, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
142 101 1.00
ACGTcount: A:0.19, C:0.31, G:0.25, T:0.26
Consensus pattern (142 bp):
TCCTTACCCGTGTGGCTCACACGGCCTGGGCACACGCCCATGTCCCTGACCGTGTGGTTCTAAAG
CGTAAACAATGAGTTACACGACCTAGACACACACCCATGTCCTTGCCCGTGTGGCATACACTGCC
TGGGTGCCCATT
Found at i:308803 original size:14 final size:14
Alignment explanation
Indices: 308784--308812 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
308774 AAAGTTTAAT
308784 AATCTAAGCTTGAA
1 AATCTAAGCTTGAA
308798 AATCTAAGCTTGAA
1 AATCTAAGCTTGAA
308812 A
1 A
308813 TAACCAAACT
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:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (14 bp):
AATCTAAGCTTGAA
Found at i:310041 original size:30 final size:33
Alignment explanation
Indices: 310005--310078 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 33
309995 CACTTATAAA
310005 AATTGAAAGTTCCATTTTTTT-GT-T-TTCTAC
1 AATTGAAAGTTCCATTTTTTTCGTCTCTTCTAC
*
310035 AATTGAAAGTTCCATTTTTTTCTTCTCTTCTAC
1 AATTGAAAGTTCCATTTTTTTCGTCTCTTCTAC
310068 AATTGAAAGTT
1 AATTGAAAGTT
310079 TTTTTTAAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
30 21 0.52
31 1 0.03
32 1 0.03
33 17 0.43
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (33 bp):
AATTGAAAGTTCCATTTTTTTCGTCTCTTCTAC
Found at i:312319 original size:16 final size:16
Alignment explanation
Indices: 312298--312330 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
312288 AACAGGTGGA
312298 GATTAATTGTGATAAT
1 GATTAATTGTGATAAT
312314 GATTAATTGTGATAAT
1 GATTAATTGTGATAAT
312330 G
1 G
312331 CGATGCTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.42
Consensus pattern (16 bp):
GATTAATTGTGATAAT
Found at i:314218 original size:15 final size:15
Alignment explanation
Indices: 314198--314228 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
314188 ATCAAATTAT
314198 TATTTCTTAGAAAGA
1 TATTTCTTAGAAAGA
314213 TATTTCTTAGAAAGA
1 TATTTCTTAGAAAGA
314228 T
1 T
314229 GAAAACGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (15 bp):
TATTTCTTAGAAAGA
Found at i:316315 original size:31 final size:31
Alignment explanation
Indices: 316280--316343 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
316270 CACCCTAGTA
* *
316280 ACTTAAATAAAAACTTTCAAATAGTTCAGTG
1 ACTTAAATAAAAACTTTCAAATAATTCAATG
* *
316311 ACTTAAATGAAAACTTTCGAATAATTCAATG
1 ACTTAAATAAAAACTTTCAAATAATTCAATG
316342 AC
1 AC
316344 CATTTTGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.31
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTCAAATAATTCAATG
Found at i:317177 original size:18 final size:18
Alignment explanation
Indices: 317161--317193 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
317151 TTTTTATATT
317161 TTTTA-AATT-TTAAATA
1 TTTTATAATTATTAAATA
317177 TTTTATAATTATTAAAT
1 TTTTATAATTATTAAAT
317194 TGTTTGTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 4 0.27
18 6 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTATAATTATTAAATA
Found at i:317842 original size:24 final size:24
Alignment explanation
Indices: 317810--317859 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
317800 CGAAAATACT
317810 TGATTTGGTTTATAATTTAATGTG
1 TGATTTGGTTTATAATTTAATGTG
317834 TGATTTGGTTTATAATTTAATGTG
1 TGATTTGGTTTATAATTTAATGTG
317858 TG
1 TG
317860 TATGTTTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (24 bp):
TGATTTGGTTTATAATTTAATGTG
Found at i:317866 original size:22 final size:24
Alignment explanation
Indices: 317810--317868 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
317800 CGAAAATACT
*
317810 TGATTTGGTTTATAATTTAATGTG
1 TGATATGGTTTATAATTTAATGTG
*
317834 TGATTTGGTTTATAATTTAATGTG
1 TGATATGGTTTATAATTTAATGTG
317858 TG-TAT-GTTTAT
1 TGATATGGTTTAT
317869 CTAAGATGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 6 0.18
23 2 0.06
24 26 0.76
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (24 bp):
TGATATGGTTTATAATTTAATGTG
Found at i:321583 original size:19 final size:19
Alignment explanation
Indices: 321555--321598 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
321545 GTACTTTACA
*
321555 ACATATAAAATCTAAAAAC
1 ACATAAAAAATCTAAAAAC
* *
321574 ACATAAAAAATTTTAAAAC
1 ACATAAAAAATCTAAAAAC
321593 -CATAAA
1 ACATAAA
321599 TAAAAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.23
Consensus pattern (19 bp):
ACATAAAAAATCTAAAAAC
Found at i:321651 original size:18 final size:18
Alignment explanation
Indices: 321617--321651 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
321607 ATAATTCCAA
321617 AAATTATAAAATATAAAT
1 AAATTATAAAATATAAAT
321635 AAATCTATAAAAT-TAAA
1 AAAT-TATAAAATATAAA
321652 ACGAACAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATTATAAAATATAAAT
Found at i:324066 original size:16 final size:16
Alignment explanation
Indices: 324047--324077 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
324037 ATTATTCTGA
324047 ATTTGAATTATTTTTT
1 ATTTGAATTATTTTTT
*
324063 ATTTGGATTATTTTT
1 ATTTGAATTATTTTT
324078 AAACTCGAAT
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:0.23, C:0.00, G:0.10, T:0.68
Consensus pattern (16 bp):
ATTTGAATTATTTTTT
Found at i:326706 original size:29 final size:30
Alignment explanation
Indices: 326658--326723 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
326648 AATATAATTG
* * * *
326658 ATCAAATTAGTCTCTCTACTA-TTAAAAGA
1 ATCAATTTAGTCCCTATACTACTAAAAAGA
326687 ATCAATTTAGTCCCTATACTACTAAAAAGA
1 ATCAATTTAGTCCCTATACTACTAAAAAGA
326717 ATCAATT
1 ATCAATT
326724 AAAACTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 18 0.56
30 14 0.44
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.33
Consensus pattern (30 bp):
ATCAATTTAGTCCCTATACTACTAAAAAGA
Found at i:327504 original size:34 final size:34
Alignment explanation
Indices: 327451--327515 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
327441 GCCTATTTGC
*
327451 AGGTTTTAACTTTTTAGAAATCTTCTCATGTCGT
1 AGGTTTTAACTTTTCAGAAATCTTCTCATGTCGT
327485 AGGTTTTAA-TTTCTCAGAAATCTTCTCATGT
1 AGGTTTTAACTTT-TCAGAAATCTTCTCATGT
327516 TTTAAGTAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 3 0.10
34 26 0.90
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (34 bp):
AGGTTTTAACTTTTCAGAAATCTTCTCATGTCGT
Found at i:329951 original size:34 final size:33
Alignment explanation
Indices: 329908--330003 Score: 118
Period size: 34 Copynumber: 3.1 Consensus size: 33
329898 AATAAAGTTT
329908 GTACATGGCTATAATGGCCATCCTAGAACCGATA
1 GTACATGGCTATAATGGCCAT-CTAGAACCGATA
329942 GTACATGGCTATAAT-G-------GAACCGATA
1 GTACATGGCTATAATGGCCATCTAGAACCGATA
329967 GTACATGGCTATAATGGCCATACTAGAACCGATA
1 GTACATGGCTATAATGGCCAT-CTAGAACCGATA
330001 GTA
1 GTA
330004 GGGGGGATCG
Statistics
Matches: 53, Mismatches: 0, Indels: 18
0.75 0.00 0.25
Matches are distributed among these distances:
25 24 0.45
26 1 0.02
33 1 0.02
34 27 0.51
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (33 bp):
GTACATGGCTATAATGGCCATCTAGAACCGATA
Found at i:329961 original size:25 final size:25
Alignment explanation
Indices: 329933--329983 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
329923 GGCCATCCTA
329933 GAACCGATAGTACATGGCTATAATG
1 GAACCGATAGTACATGGCTATAATG
329958 GAACCGATAGTACATGGCTATAATG
1 GAACCGATAGTACATGGCTATAATG
329983 G
1 G
329984 CCATACTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (25 bp):
GAACCGATAGTACATGGCTATAATG
Found at i:330712 original size:40 final size:39
Alignment explanation
Indices: 330666--330781 Score: 171
Period size: 40 Copynumber: 3.0 Consensus size: 39
330656 AAAATAAAGT
*
330666 ATGGTTTTAATTAATAATAAAAATAAAATAGTATGGGGGA
1 ATGGTTTTAATTAATAATAAAAACAAAATAGTAT-GGGGA
*
330706 ATGGTTTTAATTAATAATGAAAACAAAATAGTATGGGGA
1 ATGGTTTTAATTAATAATAAAAACAAAATAGTATGGGGA
* * *
330745 ATAGTTTTAATTAATAAT-AAAACAAAGTAGCATGGGG
1 ATGGTTTTAATTAATAATAAAAACAAAATAGTATGGGG
330782 GGAGTGGAAT
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
38 17 0.24
39 22 0.31
40 32 0.45
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.31
Consensus pattern (39 bp):
ATGGTTTTAATTAATAATAAAAACAAAATAGTATGGGGA
Found at i:333870 original size:16 final size:16
Alignment explanation
Indices: 333844--333882 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
333834 AATTTGAATT
333844 TTTGG-TTGTTT-TAA
1 TTTGGATTGTTTCTAA
333858 GTTTGGATTGTTTCTAA
1 -TTTGGATTGTTTCTAA
333875 TTTGGATT
1 TTTGGATT
333883 ATTTGAAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.23
16 14 0.64
17 3 0.14
ACGTcount: A:0.15, C:0.03, G:0.23, T:0.59
Consensus pattern (16 bp):
TTTGGATTGTTTCTAA
Found at i:334174 original size:17 final size:16
Alignment explanation
Indices: 334149--334192 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
334139 ATTTCAAATT
*
334149 ATTTTAAATTTTGATC
1 ATTTTAAATTTCGATC
334165 ATTTTAAAATTTCGATC
1 ATTTT-AAATTTCGATC
* *
334182 AATTCAAATTT
1 ATTTTAAATTT
334193 AAATTAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (16 bp):
ATTTTAAATTTCGATC
Found at i:345641 original size:2 final size:2
Alignment explanation
Indices: 345634--345666 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
345624 ATACTTCTAT
345634 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
345667 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:347672 original size:15 final size:16
Alignment explanation
Indices: 347654--347687 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
347644 AATTTGGATT
347654 TTTCAAATTGAG-TCA
1 TTTCAAATTGAGATCA
*
347669 TTTCAAATTTAGATCA
1 TTTCAAATTGAGATCA
347685 TTT
1 TTT
347688 GTATTTGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47
Consensus pattern (16 bp):
TTTCAAATTGAGATCA
Found at i:352358 original size:21 final size:20
Alignment explanation
Indices: 352320--352358 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
352310 ATTGACCCTT
352320 AAATTATACCTTAATTTTTC
1 AAATTATACCTTAATTTTTC
*
352340 AAATTCAT-CCTTAAATTTT
1 AAATT-ATACCTTAATTTTT
352359 GTCTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATTATACCTTAATTTTTC
Found at i:361826 original size:58 final size:58
Alignment explanation
Indices: 361731--361860 Score: 158
Period size: 58 Copynumber: 2.2 Consensus size: 58
361721 AACCCCTTTT
* *
361731 TTATTTTTGTTATTTTACTGTTAAATTAATTAATTTGAGCTTTAT-TCTCATTATTTTTATA
1 TTATTTTT-TTATTTTACTATTAAATTAATTAATTTGAG--TTATGTCTCA-TATTATTATA
* *
361792 -TATTTTTTTATTTT-CTATTAATTTAATTAATTTGAGTTATGTTTCATATTATTATA
1 TTATTTTTTTATTTTACTATTAAATTAATTAATTTGAGTTATGTCTCATATTATTATA
*
361848 TTATTTATTTATT
1 TTATTTTTTTATT
361861 ATATATTTAT
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
56 13 0.21
57 15 0.24
58 20 0.32
59 7 0.11
60 7 0.11
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.63
Consensus pattern (58 bp):
TTATTTTTTTATTTTACTATTAAATTAATTAATTTGAGTTATGTCTCATATTATTATA
Found at i:361860 original size:11 final size:11
Alignment explanation
Indices: 361840--361873 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
361830 ATGTTTCATA
361840 TTATTATATTAT
1 TTATT-TATTAT
361852 TTATTTATTAT
1 TTATTTATTAT
*
361863 ATATTTATTAT
1 TTATTTATTAT
361874 GTAAATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATTTATTAT
Found at i:361861 original size:16 final size:15
Alignment explanation
Indices: 361840--361871 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
361830 ATGTTTCATA
361840 TTATTATATTATTTAT
1 TTATTATA-TATTTAT
361856 TTATTATATATTTAT
1 TTATTATATATTTAT
361871 T
1 T
361872 ATGTAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTATTATATATTTAT
Found at i:366104 original size:21 final size:21
Alignment explanation
Indices: 366078--366122 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
366068 GAGGGATCAA
*
366078 ATGCTGGAGTCCCAGAAAAAC
1 ATGCTGGAGTCACAGAAAAAC
*
366099 ATGCTGGAGTCACAGAACAAC
1 ATGCTGGAGTCACAGAAAAAC
366120 ATG
1 ATG
366123 ATGAACCAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (21 bp):
ATGCTGGAGTCACAGAAAAAC
Found at i:368704 original size:17 final size:17
Alignment explanation
Indices: 368668--368710 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
368658 GAAAAAATGA
*
368668 AAAATAAAAAGAAGAGAG
1 AAAA-AAAAAGAAGAAAG
368686 AAACAAAAAAG-AGAAAG
1 AAA-AAAAAAGAAGAAAG
368703 AAAAAAAA
1 AAAAAAAA
368711 GCAAAGGAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 5 0.22
17 8 0.35
18 9 0.39
19 1 0.04
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.02
Consensus pattern (17 bp):
AAAAAAAAAGAAGAAAG
Found at i:368708 original size:15 final size:15
Alignment explanation
Indices: 368646--368711 Score: 55
Period size: 15 Copynumber: 4.4 Consensus size: 15
368636 AAAAAAAGAG
368646 AAAAAG-GAAAGAGAA
1 AAAAAGAGAAAGA-AA
* * *
368661 AAAATGAAAAATAAA
1 AAAAAGAGAAAGAAA
* *
368676 AAGAAGAGAGAA-ACA
1 AAAAAGAGA-AAGAAA
368691 AAAAAGAGAAAGAAA
1 AAAAAGAGAAAGAAA
368706 AAAAAG
1 AAAAAG
368712 CAAAGGAGGG
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
14 2 0.05
15 31 0.79
16 6 0.15
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.03
Consensus pattern (15 bp):
AAAAAGAGAAAGAAA
Found at i:370042 original size:44 final size:44
Alignment explanation
Indices: 369955--370080 Score: 139
Period size: 44 Copynumber: 2.8 Consensus size: 44
369945 TTTGGCAAGC
* * * * *
369955 CTTATCCCACTGACCAGGAGTGGAACAGGTTAAATATAGCAGAT
1 CTTATCCCACTGAGCAGGAGTGGAACAGATCAAATTTAACAGAT
*
369999 CTTATCCCACT-AGCAGGAGTGGAATAGATCAAATTTCAACAGAT
1 CTTATCCCACTGAGCAGGAGTGGAACAGATCAAATTT-AACAGAT
* *
370043 CTTATCTTCACTGAGCAGGAG-CGAAGCAGATCAAATTT
1 CTTATC-CCACTGAGCAGGAGTGGAA-CAGATCAAATTT
370081 TGGCGAATTT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
43 20 0.29
44 23 0.33
45 7 0.10
46 19 0.28
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (44 bp):
CTTATCCCACTGAGCAGGAGTGGAACAGATCAAATTTAACAGAT
Found at i:370192 original size:135 final size:134
Alignment explanation
Indices: 370039--370883 Score: 1180
Period size: 133 Copynumber: 6.3 Consensus size: 134
370029 AAATTTCAAC
* * * *
370039 AGATCTTATCTTCACTGAGCAGGAGCGAAGCAGATCAAATTTTGGCGAATTTTATCTCCACGTAC
1 AGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGCGAATCTTATCTCCATGTAT
* * * *
370104 CGGCGATGGAGCAGATTCCAATCACCAGCCTTATCTTCATTGAGCAGGAGTGGAGCAGGCTAAAC
66 CGGCAATGGAGCAGATTTCAACCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-AAC
370169 ATACT
130 ATACT
*
370174 AGATCTTATCTTCACTGAGCAGAAGTGAAGCAGATCAAATTTTGGC-AAGTCTTATCTCCATGTA
1 AGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGCGAA-TCTTATCTCCATGTA
** * * *
370238 TCGGCAATGGAGCAGATTTCTGCCACCAGCCTTATCTTTACTGAGTAGGAGTGAAGCAGGCTAAA
65 TCGGCAATGGAGCAGATTTCAACCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-AA
370303 CATACT
129 CATACT
* * *
370309 AGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATTAAATTTTGGCAAATCTTATTTCCATGTAT
1 AGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGCGAATCTTATCTCCATGTAT
* *
370374 CGGCAATGGAGCAGATTTCAACCACCAGCCTTATCTTCAGTGAGCAGGAGTGGAGCAGGCTAA-G
66 CGGCAATGGAGCAGATTTCAACCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAACA
370438 TACT
131 TACT
* * *
370442 AGATCTTATCTTCGCTGAGCATGAGTGAAGCAGATCAAATTTTGGC-AAGTCTTATTTCCATGTA
1 AGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGCGAA-TCTTATCTCCATGTA
* * *
370506 TCGGCAATGGAGCAGATTTCAGCCACCAGCCTTATCTTCACTGAGTAAGAGTGGAGCAGGCTAA-
65 TCGGCAATGGAGCAGATTTCAACCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAC
370570 ATACT
130 ATACT
* * * * * *
370575 AGTTCTTATATTCGCTGAGCAGGAG-CAGAGCAGATCAAGTTTTGGTGAATCTTATCTCCATGTA
1 AGATCTTATCTTCACTGAGCAGGAGTGA-AGCAGATCAAATTTTGGCGAATCTTATCTCCATGTA
* * *
370639 TCGGCAATGGAGCAGATTTCAGCCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGG-TTAT
65 TCGGCAATGGAGCAGATTTCAACCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAC
370703 ATACT
130 ATACT
* * **
370708 AGATCTTATCTTCGCTGAGCAGGAGTAAAGCAGATCAAATTTTGATGAATCTTATCTCCATGTAT
1 AGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGCGAATCTTATCTCCATGTAT
* * * *
370773 CGGCAATGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGTAGGCTAAAC
66 CGGCAATGGAGCAGATTTCAACCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-AAC
*
370838 ATACC
130 ATACT
* * *
370843 AGATCTTATCTTTACTGAGCAGGAGTAAAACAGATCAAATT
1 AGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATT
370884 ACAGCAGATC
Statistics
Matches: 643, Mismatches: 58, Indels: 18
0.89 0.08 0.03
Matches are distributed among these distances:
132 5 0.01
133 353 0.55
134 8 0.01
135 275 0.43
136 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28
Consensus pattern (134 bp):
AGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGCGAATCTTATCTCCATGTAT
CGGCAATGGAGCAGATTTCAACCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAACA
TACT
Found at i:371129 original size:29 final size:29
Alignment explanation
Indices: 371096--371159 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
371086 CCAAATTAAA
371096 CACCCCACTAAACCGA-CCACTAACTCCAT
1 CACCCCACTAAACC-ATCCACTAACTCCAT
* *
371125 CACCCTACTAAACCATCCACTACCTCCAT
1 CACCCCACTAAACCATCCACTAACTCCAT
371154 CACCCC
1 CACCCC
371160 CACACCCTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.31, C:0.52, G:0.02, T:0.16
Consensus pattern (29 bp):
CACCCCACTAAACCATCCACTAACTCCAT
Found at i:371172 original size:37 final size:37
Alignment explanation
Indices: 371125--371199 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
371115 CTAACTCCAT
371125 CACCCTACTAAACCATCCACTACCTCCATCACCCCCA
1 CACCCTACTAAACCATCCACTACCTCCATCACCCCCA
371162 CACCCTACTAAACCATCCACTACCTCCATCACCCCCA
1 CACCCTACTAAACCATCCACTACCTCCATCACCCCCA
371199 C
1 C
371200 TAACTCCATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.29, C:0.55, G:0.00, T:0.16
Consensus pattern (37 bp):
CACCCTACTAAACCATCCACTACCTCCATCACCCCCA
Found at i:371201 original size:18 final size:18
Alignment explanation
Indices: 371141--371213 Score: 69
Period size: 18 Copynumber: 4.0 Consensus size: 18
371131 ACTAAACCAT
371141 CCACTACCTCCATCACCC
1 CCACTACCTCCATCACCC
* * *
371159 CCAC-ACC-CTACTAAACCAT
1 CCACTACCTCCA-T-CACC-C
371178 CCACTACCTCCATCACCC
1 CCACTACCTCCATCACCC
*
371196 CCACTAACTCCATCACCC
1 CCACTACCTCCATCACCC
371214 TACTTGTTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
16 2 0.05
17 4 0.09
18 24 0.56
19 7 0.16
20 4 0.09
21 2 0.05
ACGTcount: A:0.27, C:0.56, G:0.00, T:0.16
Consensus pattern (18 bp):
CCACTACCTCCATCACCC
Found at i:371588 original size:59 final size:57
Alignment explanation
Indices: 371496--371622 Score: 150
Period size: 57 Copynumber: 2.2 Consensus size: 57
371486 CTTTTTTTAT
* *
371496 TTTTGTTATTTTACTGTTAAATTAATTAATTTGAGCTTTAT-TCTCATTATTTTTATATATA
1 TTTT-TTATTTTACTATTAAATTAATTAATTTGAG--TTATGTCTCA-TATTATTATAT-TA
* *
371557 TTTTTTATTTT-CTATTAATTTAATTAATTTGAGTTATGTTTCATATTATTATATTA
1 TTTTTTATTTTACTATTAAATTAATTAATTTGAGTTATGTCTCATATTATTATATTA
371613 TTTATTTATT
1 TTT-TTTATT
371623 ATTATATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
56 5 0.08
57 20 0.33
58 4 0.07
59 20 0.33
60 7 0.12
61 4 0.07
ACGTcount: A:0.28, C:0.05, G:0.06, T:0.62
Consensus pattern (57 bp):
TTTTTTATTTTACTATTAAATTAATTAATTTGAGTTATGTCTCATATTATTATATTA
Found at i:371619 original size:60 final size:59
Alignment explanation
Indices: 371491--371622 Score: 146
Period size: 59 Copynumber: 2.2 Consensus size: 59
371481 TAACCCTTTT
*
371491 TTTATTTTTGTTATTTTACTGTTAAATTAATTAATTTGAGCTTTATTCTCATTATTTTTATA
1 TTTA-TTTT-TTATTTTACTATTAAATTAATTAATTTGAGC-TTATTCTCATTATTTTTATA
* * * *
371553 TATATTTTTTATTTT-CTATTAATTTAATTAATTTGAG-TTATGTTTCA-TATTATTATA
1 TTTATTTTTTATTTTACTATTAAATTAATTAATTTGAGCTTAT-TCTCATTATTTTTATA
371610 -TTATTTATTTATT
1 TTTATTT-TTTATT
371623 ATTATATATT
Statistics
Matches: 62, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
56 5 0.08
57 19 0.31
58 4 0.06
59 20 0.32
60 7 0.11
61 4 0.06
62 3 0.05
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.63
Consensus pattern (59 bp):
TTTATTTTTTATTTTACTATTAAATTAATTAATTTGAGCTTATTCTCATTATTTTTATA
Found at i:371624 original size:19 final size:18
Alignment explanation
Indices: 371600--371636 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
371590 TTATGTTTCA
371600 TATTATTATATTATTTATT
1 TATTATTATA-TATTTATT
371619 TATTATTATATATTTATT
1 TATTATTATATATTTATT
371637 ATGTAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TATTATTATATATTTATT
Found at i:371648 original size:17 final size:14
Alignment explanation
Indices: 371608--371638 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
371598 CATATTATTA
*
371608 TATTATTTATTTAT
1 TATTATATATTTAT
371622 TATTATATATTTAT
1 TATTATATATTTAT
371636 TAT
1 TAT
371639 GTAAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTATATATTTAT
Found at i:372325 original size:126 final size:126
Alignment explanation
Indices: 372100--372332 Score: 439
Period size: 126 Copynumber: 1.8 Consensus size: 126
372090 TCTCAAAATT
372100 TTTCAAAATAAAGGCAATGTTCGGTATTTAAAGAATTCGAAGAATCGTGCCCTAACGTACTGGGT
1 TTTCAAAATAAAGGCAATGTTCGGTATTTAAAGAATTCGAAGAATCGTGCCCTAACGTACTGGGT
*
372165 TTCGCTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTACCAGTTCACTATAAAAAAA
66 TTCACTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTACCAGTTCACTATAAAAAAA
*
372226 TTTCAAAATAAAGGCAATGTTCGGTATTTAAAGAATTCGAATAATCGTGCCCTAACGTACTGGGT
1 TTTCAAAATAAAGGCAATGTTCGGTATTTAAAGAATTCGAAGAATCGTGCCCTAACGTACTGGGT
*
372291 TTCACTTTCTTTGTTTGTTTTGAATATTCGAATATCCTCTTA
66 TTCACTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTA
372333 AGGCTAAAAC
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
126 104 1.00
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.38
Consensus pattern (126 bp):
TTTCAAAATAAAGGCAATGTTCGGTATTTAAAGAATTCGAAGAATCGTGCCCTAACGTACTGGGT
TTCACTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTACCAGTTCACTATAAAAAAA
Found at i:375707 original size:14 final size:13
Alignment explanation
Indices: 375677--375709 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
375667 TATCATAATA
*
375677 TTTTTCATATTCG
1 TTTTTCATACTCG
375690 TTTTTCATACTCG
1 TTTTTCATACTCG
375703 TTTTTCA
1 TTTTTCA
375710 GCTTCTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.18, G:0.06, T:0.61
Consensus pattern (13 bp):
TTTTTCATACTCG
Found at i:375777 original size:35 final size:35
Alignment explanation
Indices: 375731--375801 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
375721 AGGTTTATAA
375731 TTACCTTCTCAATAATATCATCTTCAAAATTTGAG
1 TTACCTTCTCAATAATATCATCTTCAAAATTTGAG
375766 TTACCTTCTCAATAATATCATCTTCAAAATTTGAG
1 TTACCTTCTCAATAATATCATCTTCAAAATTTGAG
375801 T
1 T
375802 GTTATATTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.41
Consensus pattern (35 bp):
TTACCTTCTCAATAATATCATCTTCAAAATTTGAG
Found at i:383318 original size:15 final size:15
Alignment explanation
Indices: 383298--383328 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
383288 TATATATGAT
383298 TTTATTATTTCATTA
1 TTTATTATTTCATTA
*
383313 TTTATTATTTTATTA
1 TTTATTATTTCATTA
383328 T
1 T
383329 AATTTGATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTATTATTTCATTA
Found at i:386485 original size:23 final size:23
Alignment explanation
Indices: 386455--386502 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
386445 AATGATGATG
386455 ATTACAGTTTCTTCTGAAAAATC
1 ATTACAGTTTCTTCTGAAAAATC
386478 ATTACAGTTTCTTCTGAAAAATC
1 ATTACAGTTTCTTCTGAAAAATC
386501 AT
1 AT
386503 GTTGAAAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (23 bp):
ATTACAGTTTCTTCTGAAAAATC
Found at i:389679 original size:20 final size:20
Alignment explanation
Indices: 389654--389698 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
389644 ATAAATAGAT
389654 TAAATTATATCAAATTA-AAA
1 TAAATT-TATCAAATTATAAA
**
389674 TAAATTTATTTAATTATAAA
1 TAAATTTATCAAATTATAAA
389694 TAAAT
1 TAAAT
389699 CAAGATGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAATTTATCAAATTATAAA
Found at i:396817 original size:22 final size:23
Alignment explanation
Indices: 396790--396841 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 23
396780 TTTTATTTAA
396790 AAATTTTATATAAAAT-AAT-TAT
1 AAATTTTATA-AAAATAAATGTAT
396812 AAATTTT-TAAAAATAAATGTAT
1 AAATTTTATAAAAATAAATGTAT
396834 -AATTTTAT
1 AAATTTTAT
396842 CATGTATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.19
21 11 0.41
22 11 0.41
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
AAATTTTATAAAAATAAATGTAT
Found at i:405505 original size:17 final size:14
Alignment explanation
Indices: 405471--405500 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
405461 ATAAAACATT
405471 TATTATATTGAAGG
1 TATTATATTGAAGG
405485 TATTATATTGAAGG
1 TATTATATTGAAGG
405499 TA
1 TA
405501 GTATTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (14 bp):
TATTATATTGAAGG
Found at i:417844 original size:40 final size:40
Alignment explanation
Indices: 417789--417869 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
417779 CTTTTGTTTT
*
417789 CTTTGGTTTTCTAAGTGTCTTGATTAGATAATACCTTTAA
1 CTTTGGTTTTCTAAGTGTCTTGATTAGATAATACCTATAA
417829 CTTTGGTTTTCTAAGTGTCTTGATTAGATAATACCTATAA
1 CTTTGGTTTTCTAAGTGTCTTGATTAGATAATACCTATAA
417869 C
1 C
417870 ATCTTGTTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.46
Consensus pattern (40 bp):
CTTTGGTTTTCTAAGTGTCTTGATTAGATAATACCTATAA
Found at i:418462 original size:16 final size:18
Alignment explanation
Indices: 418443--418479 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
418433 AAATTGAAAA
*
418443 AGAAAAAGAA-AA-AATG
1 AGAAAAAAAATAATAATG
418459 AGAAAAAAAATAATAATG
1 AGAAAAAAAATAATAATG
418477 AGA
1 AGA
418480 CAATCAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 2 0.11
18 7 0.39
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (18 bp):
AGAAAAAAAATAATAATG
Found at i:423336 original size:11 final size:11
Alignment explanation
Indices: 423320--423345 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
423310 TATATATATG
423320 TAAAATAAAAA
1 TAAAATAAAAA
423331 TAAAATAAAAA
1 TAAAATAAAAA
423342 TAAA
1 TAAA
423346 TGTTGAAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
TAAAATAAAAA
Found at i:424874 original size:22 final size:21
Alignment explanation
Indices: 424837--424877 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
424827 AATTTTCTTC
424837 TTAATTGTTTTAAAGGTTTAA
1 TTAATTGTTTTAAAGGTTTAA
424858 TTAAGTTGTGTTT-AAGGTTT
1 TTAA-TTGT-TTTAAAGGTTT
424878 CTAGTTAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 11 0.61
23 3 0.17
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.54
Consensus pattern (21 bp):
TTAATTGTTTTAAAGGTTTAA
Found at i:425572 original size:11 final size:11
Alignment explanation
Indices: 425558--425598 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
425548 ATTAATTTTA
425558 ATATAATGTGT
1 ATATAATGTGT
425569 ATATAATGTGT
1 ATATAATGTGT
*
425580 ATATAATGTAT
1 ATATAATGTGT
425591 AATATAAT
1 -ATATAAT
425599 ATCAAACATG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
11 21 0.75
12 7 0.25
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (11 bp):
ATATAATGTGT
Found at i:462577 original size:5 final size:5
Alignment explanation
Indices: 462563--462606 Score: 63
Period size: 5 Copynumber: 9.0 Consensus size: 5
462553 TGTGAAATAT
* *
462563 TTTTA ATTTA TTTTA ATTTA TTTTA TTTTA TTTTA -TTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
462607 ATCGTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
4 4 0.12
5 30 0.88
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:462578 original size:10 final size:10
Alignment explanation
Indices: 462563--462608 Score: 76
Period size: 10 Copynumber: 4.7 Consensus size: 10
462553 TGTGAAATAT
462563 TTTTAATTTA
1 TTTTAATTTA
462573 TTTTAATTTA
1 TTTTAATTTA
*
462583 TTTTATTTTA
1 TTTTAATTTA
462593 TTTT-ATTTA
1 TTTTAATTTA
462602 TTTTAAT
1 TTTTAAT
462609 CGTATAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
9 8 0.24
10 25 0.76
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTAATTTA
Found at i:463855 original size:72 final size:71
Alignment explanation
Indices: 463765--463992 Score: 377
Period size: 72 Copynumber: 3.2 Consensus size: 71
463755 CCCATGATGT
* *
463765 AATCTCAACCG-TTATATTTGACCATCGATCATGTTAATTTTCAGATCATTAAAGGCAAATATCC
1 AATCTCAACCGTTTATATTTGACCATTG-TCATGTTAATTTTCAGATCATAAAAGGCAAATATCC
463829 TTGTTGC
65 TTGTTGC
*
463836 AATCTCAACCGTTTATATTTCACCATTTGTCATGTTAATTTTCAGATCATAAAAGGCAAATATCC
1 AATCTCAACCGTTTATATTTGACCA-TTGTCATGTTAATTTTCAGATCATAAAAGGCAAATATCC
*
463901 TTGATGC
65 TTGTTGC
463908 AATCTCAACCGTTTATATTTGACCATTGGTCATGTTAATTTTCAGATCATAAAAGGCAAATATCC
1 AATCTCAACCGTTTATATTTGACCATT-GTCATGTTAATTTTCAGATCATAAAAGGCAAATATCC
*
463973 TCGTTGC
65 TTGTTGC
463980 AATCTCAACCGTT
1 AATCTCAACCGTT
463993 AATTCTTGGA
Statistics
Matches: 147, Mismatches: 7, Indels: 5
0.92 0.04 0.03
Matches are distributed among these distances:
71 13 0.09
72 132 0.90
73 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.36
Consensus pattern (71 bp):
AATCTCAACCGTTTATATTTGACCATTGTCATGTTAATTTTCAGATCATAAAAGGCAAATATCCT
TGTTGC
Found at i:467566 original size:23 final size:23
Alignment explanation
Indices: 467540--467615 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
467530 ATAAGTGCCA
467540 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
467563 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
467586 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
467609 CACTGAT
1 CACTGAT
467616 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:470257 original size:12 final size:12
Alignment explanation
Indices: 470242--470266 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
470232 GATTAAAAAA
470242 TAATAATATTAT
1 TAATAATATTAT
470254 TAATAATATTAT
1 TAATAATATTAT
470266 T
1 T
470267 GAAATTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAATAATATTAT
Found at i:472325 original size:3 final size:3
Alignment explanation
Indices: 472317--472341 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
472307 AAGGAACATG
472317 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
472342 TTTCATGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:482601 original size:42 final size:42
Alignment explanation
Indices: 482546--482626 Score: 121
Period size: 42 Copynumber: 1.9 Consensus size: 42
482536 AAAAGACTTT
*
482546 TATCATTATGAGTTTATGACT-TTAAAATATTGTAGAATAGTA
1 TATCATTATGAGTTTATGACTACT-AAATATTGTAGAATAGTA
482588 TATCATT-TCGAGTTTATGACTACTAAATATTGTAGAATA
1 TATCATTAT-GAGTTTATGACTACTAAATATTGTAGAATA
482627 TTTAATTCTG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
41 1 0.03
42 34 0.94
43 1 0.03
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (42 bp):
TATCATTATGAGTTTATGACTACTAAATATTGTAGAATAGTA
Found at i:484842 original size:19 final size:19
Alignment explanation
Indices: 484797--484843 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
484787 TATATATTTT
484797 AATTTTATTTAAGTAGATA
1 AATTTTATTTAAGTAGATA
* * *
484816 AATCTTATTTAGGTATATA
1 AATTTTATTTAAGTAGATA
*
484835 AGTTTTATT
1 AATTTTATT
484844 CATATTCTAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (19 bp):
AATTTTATTTAAGTAGATA
Found at i:488774 original size:19 final size:19
Alignment explanation
Indices: 488728--488775 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
488718 GTATATATTT
488728 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
488746 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
488765 TAAGTTTTATT
1 TAAATTTTATT
488776 CATATTCTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:488850 original size:42 final size:42
Alignment explanation
Indices: 488797--488878 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
488787 AATATTTTTA
* *
488797 TTTTATCTTTTAGTAGTTTATTAGGACAAGGGAACTATTTCC
1 TTTTATATTTTAGTAGTTTATTAGAACAAGGGAACTATTTCC
*
488839 TTTTATATTTTAGTAGTTTATTAGAATAAGGGAACTATTT
1 TTTTATATTTTAGTAGTTTATTAGAACAAGGGAACTATTT
488879 TCCCAATTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.29, C:0.07, G:0.16, T:0.48
Consensus pattern (42 bp):
TTTTATATTTTAGTAGTTTATTAGAACAAGGGAACTATTTCC
Found at i:501091 original size:5 final size:5
Alignment explanation
Indices: 501081--501113 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
501071 TTTTTATCTT
*
501081 CTTCA CTTCA CTTCA CTTCA CTTCA CCTCA CTT
1 CTTCA CTTCA CTTCA CTTCA CTTCA CTTCA CTT
501114 TTCTTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.18, C:0.42, G:0.00, T:0.39
Consensus pattern (5 bp):
CTTCA
Found at i:501225 original size:18 final size:18
Alignment explanation
Indices: 501202--501240 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
501192 CTTATATTAA
*
501202 AGTTGGGGTTCTCCACTT
1 AGTTGGGGCTCTCCACTT
501220 AGTTGGGGCTCTCCACTT
1 AGTTGGGGCTCTCCACTT
501238 AGT
1 AGT
501241 GCCAAACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.13, C:0.23, G:0.28, T:0.36
Consensus pattern (18 bp):
AGTTGGGGCTCTCCACTT
Found at i:516795 original size:54 final size:54
Alignment explanation
Indices: 516734--516839 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 54
516724 TTAATATATT
* ** *
516734 ATTTGGTACTTAAGTTTGGTTTTAATATTTAATTTTGA-ACTTT-AGTTTTTTTCA
1 ATTTGGTACTTAAATTTAATTATAATATTTAA-TTTGATA-TTTGAGTTTTTTTCA
*
516788 ATTTGGTACTTAAATTTAATTATAATGTTTAATTTGATATTTGAGTTTTTTT
1 ATTTGGTACTTAAATTTAATTATAATATTTAATTTGATATTTGAGTTTTTTT
516840 TTTGGCTGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
53 8 0.18
54 37 0.82
ACGTcount: A:0.26, C:0.04, G:0.12, T:0.58
Consensus pattern (54 bp):
ATTTGGTACTTAAATTTAATTATAATATTTAATTTGATATTTGAGTTTTTTTCA
Found at i:519235 original size:20 final size:18
Alignment explanation
Indices: 519212--519252 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
519202 ATAAATTATG
519212 AATAATATAATTAAAATGTA
1 AATAATAT-ATTAAAATG-A
*
519232 AATATTATATTAAAATGA
1 AATAATATATTAAAATGA
519250 AAT
1 AAT
519253 TTTGATTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 9 0.45
20 7 0.35
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (18 bp):
AATAATATATTAAAATGA
Found at i:519410 original size:24 final size:23
Alignment explanation
Indices: 519382--519429 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
519372 AAAATTATTT
*
519382 AAAAATATAAAACTAAAAAATAAAC
1 AAAAA-ATAAAAATAAAAAA-AAAC
519407 AAAAAATAAAAATAAAAAAAAAC
1 AAAAAATAAAAATAAAAAAAAAC
519430 TAGTAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.18
24 13 0.59
25 5 0.23
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.12
Consensus pattern (23 bp):
AAAAAATAAAAATAAAAAAAAAC
Found at i:519412 original size:11 final size:12
Alignment explanation
Indices: 519381--519431 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 12
519371 TAAAATTATT
519381 TAAAAATATAAAAC
1 TAAAAA-AT-AAAC
519395 TAAAAAATAAAC
1 TAAAAAATAAAC
*
519407 -AAAAAATAAAAA
1 TAAAAAAT-AAAC
519419 TAAAAAA-AAAC
1 TAAAAAATAAAC
519430 TA
1 TA
519432 GTAAAAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
11 12 0.36
12 7 0.21
13 8 0.24
14 6 0.18
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.16
Consensus pattern (12 bp):
TAAAAAATAAAC
Found at i:519417 original size:17 final size:16
Alignment explanation
Indices: 519397--519428 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
519387 TATAAAACTA
519397 AAAAATAAACAAAAAAT
1 AAAAATAAA-AAAAAAT
519414 AAAAATAAAAAAAAA
1 AAAAATAAAAAAAAA
519429 CTAGTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.09
Consensus pattern (16 bp):
AAAAATAAAAAAAAAT
Found at i:520210 original size:26 final size:26
Alignment explanation
Indices: 520176--520231 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
520166 ATAATGTGTT
520176 CATATTCTTTTATTTAAGTTAAATGA
1 CATATTCTTTTATTTAAGTTAAATGA
520202 CATATTCTTTTATTTAAGTTAAATGA
1 CATATTCTTTTATTTAAGTTAAATGA
520228 -ATAT
1 CATAT
520232 GTTTATAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 4 0.13
26 26 0.87
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (26 bp):
CATATTCTTTTATTTAAGTTAAATGA
Found at i:520689 original size:119 final size:119
Alignment explanation
Indices: 520461--520694 Score: 310
Period size: 119 Copynumber: 2.0 Consensus size: 119
520451 ACAAGCTTTG
* * *
520461 TTCATGTTAGATTCGTTTAATAAATGAATTGTAAAATTTTGTTCAAATATGTTTATTCAACTTGA
1 TTCATGTTAGATTCGTTTAATAAATGAATTGTAAAATATTATTAAAATATGTTTATTCAACTTGA
* *
520526 TAAACAAACAAATACCTAAAGGTTGATGAACTATAAATTAAATTTTCTATTCAT
66 TAAACAAACAAACACCTAAAGGTTGATGAACAATAAATTAAATTTTCTATTCAT
* *
520580 TTCATGTTGGATTCGTTTAATAAATGAATCT-TAAAATATTATTAAAATTTGTTTATTCAACTTG
1 TTCATGTTAGATTCGTTTAATAAATGAAT-TGTAAAATATTATTAAAATATGTTTATTCAACTTG
* ** * * * *
520644 TTAAATGAACAAACATCTAAATGTTGATGAAGAATTAA-TAGAATTTTCTAT
65 ATAAACAAACAAACACCTAAAGGTTGATGAACAATAAATTA-AATTTTCTAT
520695 CCAAGTACAA
Statistics
Matches: 99, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
118 2 0.02
119 96 0.97
120 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (119 bp):
TTCATGTTAGATTCGTTTAATAAATGAATTGTAAAATATTATTAAAATATGTTTATTCAACTTGA
TAAACAAACAAACACCTAAAGGTTGATGAACAATAAATTAAATTTTCTATTCAT
Found at i:528694 original size:14 final size:15
Alignment explanation
Indices: 528675--528705 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
528665 TAACCCATTA
528675 TTATTTA-TTTATAT
1 TTATTTATTTTATAT
528689 TTATTTATTTTATAT
1 TTATTTATTTTATAT
528704 TT
1 TT
528706 GGATTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATTTATTTTATAT
Found at i:529343 original size:17 final size:19
Alignment explanation
Indices: 529304--529347 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
529294 TTCAACCTAT
* *
529304 TCAATTTTTTATTTTTGTC
1 TCAATTTTCTATTTTTGTA
529323 TCAATTTTCTA-TTTT-TA
1 TCAATTTTCTATTTTTGTA
529340 TCAATTTT
1 TCAATTTT
529348 AAGCAGCTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 9 0.39
18 4 0.17
19 10 0.43
ACGTcount: A:0.20, C:0.11, G:0.02, T:0.66
Consensus pattern (19 bp):
TCAATTTTCTATTTTTGTA
Found at i:530469 original size:8 final size:8
Alignment explanation
Indices: 530456--530483 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
530446 AATAATTATA
530456 TATATATT
1 TATATATT
530464 TATATATT
1 TATATATT
530472 TATATATT
1 TATATATT
530480 TATA
1 TATA
530484 CTTATATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TATATATT
Found at i:530890 original size:38 final size:38
Alignment explanation
Indices: 530846--530924 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
530836 AACTTAAACT
530846 TAAAAAATTAATCTAAATACTTTATCTAGCTTAGTTCA
1 TAAAAAATTAATCTAAATACTTTATCTAGCTTAGTTCA
530884 TAAAAAATTAATCTAAATACTTTATCTAGCTTAGTTCA
1 TAAAAAATTAATCTAAATACTTTATCTAGCTTAGTTCA
530922 TAA
1 TAA
530925 GCACCTCTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.43, C:0.13, G:0.05, T:0.39
Consensus pattern (38 bp):
TAAAAAATTAATCTAAATACTTTATCTAGCTTAGTTCA
Found at i:536489 original size:13 final size:13
Alignment explanation
Indices: 536471--536495 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
536461 CTGGGAAACC
536471 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
536484 TTTTTCTTTTTT
1 TTTTTCTTTTTT
536496 AAGGAAAGAA
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Found at i:539371 original size:14 final size:14
Alignment explanation
Indices: 539352--539404 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 14
539342 GGACAAAAAT
539352 TTTAATTAAATAAA
1 TTTAATTAAATAAA
*
539366 TTTAATTAATTAAAAAA
1 TTTAATT-A--AATAAA
539383 TTTTAATTAAATAAA
1 -TTTAATTAAATAAA
539398 -TTAATTA
1 TTTAATTA
539405 CATCTTGAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
13 7 0.21
14 7 0.21
15 6 0.18
17 6 0.18
18 7 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:539376 original size:18 final size:17
Alignment explanation
Indices: 539353--539404 Score: 74
Period size: 14 Copynumber: 3.2 Consensus size: 17
539343 GACAAAAATT
539353 TTAATTAAATAAATTTAA
1 TTAATTAAATAAA-TTAA
539371 TTAATTAAA-AAATT--
1 TTAATTAAATAAATTAA
539385 TTAATTAAATAAATTAA
1 TTAATTAAATAAATTAA
539402 TTA
1 TTA
539405 CATCTTGAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
14 9 0.29
15 5 0.16
16 2 0.06
17 6 0.19
18 9 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAATTAAATAAATTAA
Found at i:541782 original size:19 final size:20
Alignment explanation
Indices: 541760--541822 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 20
541750 TTTAATATTT
*
541760 TTTTATAATTTTTTACA-AA
1 TTTTATAATTTTTTAAAGAA
541779 TTTTAT--TTTTTTAAAAGAA
1 TTTTATAATTTTTT-AAAGAA
*
541798 TTTTAATGAATTTTTTAAAAAA
1 TTTT-AT-AATTTTTTAAAGAA
541820 TTT
1 TTT
541823 AACTATTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
17 6 0.17
18 2 0.06
19 12 0.33
20 2 0.06
22 8 0.22
23 6 0.17
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTTATAATTTTTTAAAGAA
Found at i:541857 original size:27 final size:26
Alignment explanation
Indices: 541818--541906 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 26
541808 TTTTTTAAAA
* *
541818 AATTTAACTATTTTAAATAAGTTTATT
1 AATTTTACAATTTT-AATAAGTTTATT
541845 AATTTTACAATTTTTTTAATAA-TTT-TT
1 AATTTTACAA---TTTTAATAAGTTTATT
*
541872 AATTTTATAATTTTAATAAGTTTATAT
1 AATTTTACAATTTTAATAAGTTTAT-T
541899 CAATTTTA
1 -AATTTTA
541907 ATATTTTTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
24 9 0.17
25 3 0.06
26 1 0.02
27 20 0.38
28 10 0.19
29 5 0.10
30 4 0.08
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.56
Consensus pattern (26 bp):
AATTTTACAATTTTAATAAGTTTATT
Found at i:541914 original size:53 final size:51
Alignment explanation
Indices: 541827--541928 Score: 129
Period size: 53 Copynumber: 1.9 Consensus size: 51
541817 AAATTTAACT
541827 ATTTTAAATAAGTTTATTAATTTTACAAT-TTTTTTAATAATTTTTAATTTTATA
1 ATTTTAAATAAGTTTATTAATTTTA-AATATTTTTTAAT-A--TTTAATTTTATA
541881 ATTTT-AATAAGTTTATATCAATTTT-AATATTTTTTAATATTTAATTTT
1 ATTTTAAATAAGTTTAT-T-AATTTTAAATATTTTTTAATATTTAATTTT
541929 TTTTATTGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
51 9 0.20
53 15 0.33
54 15 0.33
55 6 0.13
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (51 bp):
ATTTTAAATAAGTTTATTAATTTTAAATATTTTTTAATATTTAATTTTATA
Found at i:544331 original size:28 final size:30
Alignment explanation
Indices: 544285--544341 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 30
544275 TTCTTCGTAA
544285 ATTTAAAATTTAATTTTTA-TA-TTTTTAT
1 ATTTAAAATTTAATTTTTATTACTTTTTAT
544313 ATTTAAGAATTTAA-TTTTATTACTTTTTA
1 ATTTAA-AATTTAATTTTTATTACTTTTTA
544342 AATGTTCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 11 0.42
29 9 0.35
30 6 0.23
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (30 bp):
ATTTAAAATTTAATTTTTATTACTTTTTAT
Found at i:544339 original size:29 final size:28
Alignment explanation
Indices: 544285--544339 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
544275 TTCTTCGTAA
*
544285 ATTTAAAATTTAATTTTTATATTTTTAT
1 ATTTAAAATTTAATTTTTATACTTTTAT
544313 ATTTAAGAATTTAA-TTTTATTACTTTT
1 ATTTAA-AATTTAATTTTTA-TACTTTT
544340 TAAATGTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (28 bp):
ATTTAAAATTTAATTTTTATACTTTTAT
Found at i:544393 original size:15 final size:14
Alignment explanation
Indices: 544360--544394 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
544350 ACTATTAATA
*
544360 TTATTAAAATTATT
1 TTATTAAAATTAGT
544374 TTATTAAAATTAGGT
1 TTATTAAAATTA-GT
544389 TTATTA
1 TTATTA
544395 TAATGCCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (14 bp):
TTATTAAAATTAGT
Found at i:546484 original size:21 final size:20
Alignment explanation
Indices: 546459--546500 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
546449 TATTTAATTA
546459 TTAATGATTTTAAATTATAAT
1 TTAATGATTTT-AATTATAAT
* *
546480 TTAATTATTTTTATTATAAT
1 TTAATGATTTTAATTATAAT
546500 T
1 T
546501 CTAAAACATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTAATGATTTTAATTATAAT
Found at i:547360 original size:4 final size:4
Alignment explanation
Indices: 547353--547385 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
547343 GAAGCAATGG
*
547353 GTAT GTAT GTAT GTAT GTAT GTAT GCAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
547386 CATATGAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.24, C:0.03, G:0.27, T:0.45
Consensus pattern (4 bp):
GTAT
Found at i:547511 original size:4 final size:4
Alignment explanation
Indices: 547504--547534 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
547494 AAGCAATGGA
547504 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
547535 TAACCTCCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:550865 original size:27 final size:27
Alignment explanation
Indices: 550827--550880 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
550817 AATTATGTAA
550827 GTATATTACATCACTTTTTTTTGTTGC
1 GTATATTACATCACTTTTTTTTGTTGC
550854 GTATATTACATCACTTTTTTTTGTTGC
1 GTATATTACATCACTTTTTTTTGTTGC
550881 TTTCCAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.11, T:0.56
Consensus pattern (27 bp):
GTATATTACATCACTTTTTTTTGTTGC
Found at i:551534 original size:16 final size:18
Alignment explanation
Indices: 551513--551547 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
551503 TTTGCACATC
551513 TATATA-TTC-GTTCAAA
1 TATATACTTCTGTTCAAA
551529 TATATACTTCTGTTCAAA
1 TATATACTTCTGTTCAAA
551547 T
1 T
551548 TCTGCTGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 3 0.18
18 8 0.47
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.46
Consensus pattern (18 bp):
TATATACTTCTGTTCAAA
Found at i:553805 original size:30 final size:31
Alignment explanation
Indices: 553771--553854 Score: 152
Period size: 30 Copynumber: 2.7 Consensus size: 31
553761 GAGACCCAAG
553771 GACCCAATCTACCCAAACAGCCCCGTTAC-A
1 GACCCAATCTACCCAAACAGCCCCGTTACAA
553801 GACCCAATCTACCCAAACAGCCCCGTTACAA
1 GACCCAATCTACCCAAACAGCCCCGTTACAA
*
553832 GCCCCAATCTACCCAAACAGCCC
1 GACCCAATCTACCCAAACAGCCC
553855 ACTACAGCAA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 29 0.56
31 23 0.44
ACGTcount: A:0.33, C:0.45, G:0.10, T:0.12
Consensus pattern (31 bp):
GACCCAATCTACCCAAACAGCCCCGTTACAA
Found at i:554986 original size:15 final size:15
Alignment explanation
Indices: 554966--554996 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
554956 GTTTTATTGC
554966 TATTATTATTAATGT
1 TATTATTATTAATGT
*
554981 TATTATTATTATTGT
1 TATTATTATTAATGT
554996 T
1 T
554997 TCTATACTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (15 bp):
TATTATTATTAATGT
Found at i:565813 original size:30 final size:31
Alignment explanation
Indices: 565779--565862 Score: 152
Period size: 30 Copynumber: 2.7 Consensus size: 31
565769 GAGACCCAAG
565779 GACCCAATCTACCCAAACAGCCCCGTTAC-A
1 GACCCAATCTACCCAAACAGCCCCGTTACAA
565809 GACCCAATCTACCCAAACAGCCCCGTTACAA
1 GACCCAATCTACCCAAACAGCCCCGTTACAA
*
565840 GCCCCAATCTACCCAAACAGCCC
1 GACCCAATCTACCCAAACAGCCC
565863 ACTACAGCAA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 29 0.56
31 23 0.44
ACGTcount: A:0.33, C:0.45, G:0.10, T:0.12
Consensus pattern (31 bp):
GACCCAATCTACCCAAACAGCCCCGTTACAA
Found at i:566996 original size:15 final size:15
Alignment explanation
Indices: 566976--567006 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
566966 GTTTTATTGC
566976 TATTATTATTAATGT
1 TATTATTATTAATGT
*
566991 TATTATTATTATTGT
1 TATTATTATTAATGT
567006 T
1 T
567007 TCTATACTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (15 bp):
TATTATTATTAATGT
Found at i:571651 original size:26 final size:26
Alignment explanation
Indices: 571622--571676 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
571612 ATAAATTGAT
**
571622 TTTTTTAAAT-TTAATATATTTATATA
1 TTTTTTAAATATT-ATATATACATATA
*
571648 TTTTTTAGATATTATATATACATATA
1 TTTTTTAAATATTATATATACATATA
571674 TTT
1 TTT
571677 GTATTTTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTTTTAAATATTATATATACATATA
Found at i:588579 original size:18 final size:18
Alignment explanation
Indices: 588514--588580 Score: 80
Period size: 18 Copynumber: 3.7 Consensus size: 18
588504 TTCATGGCTA
* * *
588514 TGGTCAAAGTTATACTGT
1 TGGTCAAAATTGTAATGT
* *
588532 TGGTCAAAATTATAATGC
1 TGGTCAAAATTGTAATGT
588550 TGGTCAAAATTGTAATGT
1 TGGTCAAAATTGTAATGT
*
588568 TTGTCAAAATTGT
1 TGGTCAAAATTGT
588581 TCTCTGCCTT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (18 bp):
TGGTCAAAATTGTAATGT
Found at i:599261 original size:131 final size:132
Alignment explanation
Indices: 599027--599286 Score: 353
Period size: 131 Copynumber: 2.0 Consensus size: 132
599017 ATTATTCCTT
* ** *
599027 TAAAAATTCTTTAAAACGAAAGCGATGTCCGATATTTGGCAATCGGCGAAATCGTGCCCTAACGT
1 TAAAAACTCTTTAAAACGAAAGAAATGTCCGATATTTGGCAATCGGCGAAATAGTGCCCTAACGT
* *
599092 GCTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAAT-GTCCTTTAGAATTTCATTCATGTTT
66 GCTAGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAATAGTCCTTTAGAATTTCACTCATGTTT
599156 TC
131 TC
* * * * * *
599158 TAAAAACTCTTTAAAATGAAGGAAATGTTCGATGTTTGGCAATTCGG-GGAATAGTGCCCTATCG
1 TAAAAACTCTTTAAAACGAAAGAAATGTCCGATATTTGGCAA-TCGGCGAAATAGTGCCCTAACG
* * * *
599222 TGCTAGGTTGCGATTTCTTGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTCATGTT
65 TGCTAGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAATAGTCCTTTAGAATTTCACTCATGTT
599287 CTCCAAATTC
Statistics
Matches: 111, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
131 85 0.77
132 26 0.23
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (132 bp):
TAAAAACTCTTTAAAACGAAAGAAATGTCCGATATTTGGCAATCGGCGAAATAGTGCCCTAACGT
GCTAGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAATAGTCCTTTAGAATTTCACTCATGTTT
TC
Found at i:604955 original size:18 final size:19
Alignment explanation
Indices: 604928--604968 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
604918 AGATTTATAA
604928 TTTTCTTGTTT-TCTT-TG
1 TTTTCTTGTTTATCTTCTG
604945 TTTTGCTTGTTTATCTTCTG
1 TTTT-CTTGTTTATCTTCTG
604965 TTTT
1 TTTT
604969 ATATATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.19
18 7 0.33
19 4 0.19
20 6 0.29
ACGTcount: A:0.02, C:0.12, G:0.12, T:0.73
Consensus pattern (19 bp):
TTTTCTTGTTTATCTTCTG
Done.