Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 1 of 185
Found at i:972 original size:46 final size:46
Alignment explanation
Indices: 874--1125 Score: 393
Period size: 46 Copynumber: 5.5 Consensus size: 46
864 TACGTATGAT
* *
874 CACTTATCAC-TTGTC-CCTAATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
917 CACTTATCACTTTGTCACTTGATCAGGTAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
963 CACTTATCACTTTGTCACTTGATCAAATAAGTGTAGCTAAGGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1009 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* **
1055 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAAACTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
1101 CACTTATCACTTTATCTCTTGATCA
1 CACTTATCACTTTGTCACTTGATCA
1126 AAAGTACTTA
Statistics
Matches: 193, Mismatches: 13, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
43 10 0.05
44 5 0.03
45 18 0.09
46 160 0.83
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
Found at i:3413 original size:23 final size:23
Alignment explanation
Indices: 3383--3491 Score: 146
Period size: 23 Copynumber: 4.7 Consensus size: 23
3373 GATTAGTTCT
**
3383 GCCGAAGCTACCACTGTTATGTA
1 GCCGAAGCTACCACTGAAATGTA
*
3406 GCCGAAGCTACCACTAAAATGTA
1 GCCGAAGCTACCACTGAAATGTA
* **
3429 GCTGAAGCTACCACTGTTATGTA
1 GCCGAAGCTACCACTGAAATGTA
* *
3452 GCCGAAGCTACCACTAAAACGTA
1 GCCGAAGCTACCACTGAAATGTA
3475 GCCGAAGCTACCACTGA
1 GCCGAAGCTACCACTGA
3492 TCAATAACAC
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 73 1.00
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (23 bp):
GCCGAAGCTACCACTGAAATGTA
Found at i:3453 original size:46 final size:46
Alignment explanation
Indices: 3383--3490 Score: 198
Period size: 46 Copynumber: 2.3 Consensus size: 46
3373 GATTAGTTCT
*
3383 GCCGAAGCTACCACTGTTATGTAGCCGAAGCTACCACTAAAATGTA
1 GCCGAAGCTACCACTGTTATGTAGCCGAAGCTACCACTAAAACGTA
*
3429 GCTGAAGCTACCACTGTTATGTAGCCGAAGCTACCACTAAAACGTA
1 GCCGAAGCTACCACTGTTATGTAGCCGAAGCTACCACTAAAACGTA
3475 GCCGAAGCTACCACTG
1 GCCGAAGCTACCACTG
3491 ATCAATAACA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.20
Consensus pattern (46 bp):
GCCGAAGCTACCACTGTTATGTAGCCGAAGCTACCACTAAAACGTA
Found at i:4621 original size:216 final size:216
Alignment explanation
Indices: 4247--4679 Score: 866
Period size: 216 Copynumber: 2.0 Consensus size: 216
4237 AGACAGGGTC
4247 AGAATGGTTTTTGAAGTCCCCTGTTCTGACTTTGGAAAATCATTATAAATTGTAAAAAAATAATT
1 AGAATGGTTTTTGAAGTCCCCTGTTCTGACTTTGGAAAATCATTATAAATTGTAAAAAAATAATT
4312 ACGGGTCATAATTTATATGTATAGATTTCTTAGTGAGTCTATTTTCAAAAGAAACAAACGATAAC
66 ACGGGTCATAATTTATATGTATAGATTTCTTAGTGAGTCTATTTTCAAAAGAAACAAACGATAAC
4377 CTTATATGAATTCTGTACAATGAGATAATTTATTTTTAGTAAAATAGGGGATACTTTAATGAATA
131 CTTATATGAATTCTGTACAATGAGATAATTTATTTTTAGTAAAATAGGGGATACTTTAATGAATA
4442 AACTGTACTAATTGGCTAAGT
196 AACTGTACTAATTGGCTAAGT
4463 AGAATGGTTTTTGAAGTCCCCTGTTCTGACTTTGGAAAATCATTATAAATTGTAAAAAAATAATT
1 AGAATGGTTTTTGAAGTCCCCTGTTCTGACTTTGGAAAATCATTATAAATTGTAAAAAAATAATT
4528 ACGGGTCATAATTTATATGTATAGATTTCTTAGTGAGTCTATTTTCAAAAGAAACAAACGATAAC
66 ACGGGTCATAATTTATATGTATAGATTTCTTAGTGAGTCTATTTTCAAAAGAAACAAACGATAAC
4593 CTTATATGAATTCTGTACAATGAGATAATTTATTTTTAGTAAAATAGGGGATACTTTAATGAATA
131 CTTATATGAATTCTGTACAATGAGATAATTTATTTTTAGTAAAATAGGGGATACTTTAATGAATA
4658 AACTGTACTAATTGGCTAAGT
196 AACTGTACTAATTGGCTAAGT
4679 A
1 A
4680 AAAAATTCTT
Statistics
Matches: 217, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
216 217 1.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (216 bp):
AGAATGGTTTTTGAAGTCCCCTGTTCTGACTTTGGAAAATCATTATAAATTGTAAAAAAATAATT
ACGGGTCATAATTTATATGTATAGATTTCTTAGTGAGTCTATTTTCAAAAGAAACAAACGATAAC
CTTATATGAATTCTGTACAATGAGATAATTTATTTTTAGTAAAATAGGGGATACTTTAATGAATA
AACTGTACTAATTGGCTAAGT
Found at i:13766 original size:21 final size:22
Alignment explanation
Indices: 13728--13771 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
13718 GCTAATGTGG
13728 GATTAAAATTTAAGTTTTAATA
1 GATTAAAATTTAAGTTTTAATA
*
13750 GATTAAAA-TTAATTTTTAATA
1 GATTAAAATTTAAGTTTTAATA
13771 G
1 G
13772 TGAAGAAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (22 bp):
GATTAAAATTTAAGTTTTAATA
Found at i:13867 original size:69 final size:69
Alignment explanation
Indices: 13767--13916 Score: 203
Period size: 69 Copynumber: 2.2 Consensus size: 69
13757 ATTAATTTTT
* * *
13767 AATAGTGAAGAAGTGAGTTATGAAAGTATTCTCTAGTCAATTTGGGATTAAAATTGACTTTTTAA
1 AATAGTGAAGAAGTGAGTTATGAAAGTATTCTCTAGTCAATATAGGATTAAAATTAACTTTTTAA
**
13832 TGGA
66 TAAA
* * * *
13836 TATAGTGAAGAAGTTA-TCTATGAGAGTATTCTCTAGTCAATATAGGATTAAAATTAATTTTTTA
1 AATAGTGAAGAAGTGAGT-TATGAAAGTATTCTCTAGTCAATATAGGATTAAAATTAACTTTTTA
13900 ATAAA
65 ATAAA
13905 AATAGTGAAGAA
1 AATAGTGAAGAA
13917 ATTGTCACTT
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
68 1 0.01
69 69 0.99
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (69 bp):
AATAGTGAAGAAGTGAGTTATGAAAGTATTCTCTAGTCAATATAGGATTAAAATTAACTTTTTAA
TAAA
Found at i:17147 original size:69 final size:68
Alignment explanation
Indices: 17046--17223 Score: 216
Period size: 69 Copynumber: 2.6 Consensus size: 68
17036 GTTGTCTAGC
* * * *
17046 CAATGTG-GAATTAAAATTAATTTTTAATGAAAATTGTGAATACGTGAGCTATGAGAGTATAT-T
1 CAATGTGAG-ATTAAAATTAATTTTTAATGAAAATAGTGAAAAAGTGAACTATGAGAGTAT-TCT
* *
17109 TTAGT
64 CTAAT
* * * *
17114 TAGTGTGAGATTAAAATTAACTTTTTAATGAAAATAGTAAAAAAGTTAACTATGAGAGTATTCTC
1 CAATGTGAGATTAAAATTAA-TTTTTAATGAAAATAGTGAAAAAGTGAACTATGAGAGTATTCTC
17179 TAAT
65 TAAT
17183 CAATGTGAGATTAAAATTAAATTTTTAATGAAAATAGTGAA
1 CAATGTGAGATTAAAATT-AATTTTTAATGAAAATAGTGAA
17224 GAAATTATCA
Statistics
Matches: 93, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
68 17 0.18
69 74 0.80
70 2 0.02
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (68 bp):
CAATGTGAGATTAAAATTAATTTTTAATGAAAATAGTGAAAAAGTGAACTATGAGAGTATTCTCT
AAT
Found at i:19837 original size:68 final size:67
Alignment explanation
Indices: 19727--19853 Score: 166
Period size: 68 Copynumber: 1.9 Consensus size: 67
19717 CAACAAAATT
* ** * *
19727 AATTAATTTTTAATGAAATAGTGAAGAAGTGAGTTATGAGAGTATTCTCTAGTTAATGTGAGATT
1 AATTAATTTTAAATGAAATAGTGAAGAAGTGAGCAATAAGAGTATTCTCTAGTCAATGTGAGATT
19792 AA
66 AA
* *
19794 AATTAACTTTTAAATGAAAATAGTG-ATAAGTGAGCAATAAGAGTATTCTTTAGTCAATGT
1 AATTAA-TTTTAAATG-AAATAGTGAAGAAGTGAGCAATAAGAGTATTCTCTAGTCAATGT
19854 ACTTATTTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
67 6 0.12
68 37 0.73
69 8 0.16
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (67 bp):
AATTAATTTTAAATGAAATAGTGAAGAAGTGAGCAATAAGAGTATTCTCTAGTCAATGTGAGATT
AA
Found at i:20038 original size:21 final size:22
Alignment explanation
Indices: 19998--20039 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
19988 AGCCAATGTA
*
19998 GGATTGAAATTAACTTTTTAAG
1 GGATTAAAATTAACTTTTTAAG
*
20020 GGATTAAAATT-ATTTTTTAA
1 GGATTAAAATTAACTTTTTAA
20040 TGAAATAGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.38, C:0.02, G:0.14, T:0.45
Consensus pattern (22 bp):
GGATTAAAATTAACTTTTTAAG
Found at i:26682 original size:18 final size:19
Alignment explanation
Indices: 26659--26698 Score: 66
Period size: 17 Copynumber: 2.2 Consensus size: 19
26649 ATACTTTTAA
26659 AATTTTTAAA-ATAACA-T
1 AATTTTTAAACATAACATT
26676 AATTTTTAAACATAACATT
1 AATTTTTAAACATAACATT
26695 AATT
1 AATT
26699 CACGTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 10 0.48
18 6 0.29
19 5 0.24
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTTTTAAACATAACATT
Found at i:32737 original size:3 final size:3
Alignment explanation
Indices: 32729--32761 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
32719 GAGCGTGAGG
32729 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
32762 AGAACGGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:35943 original size:24 final size:25
Alignment explanation
Indices: 35905--35953 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
35895 GGCAATACCA
*
35905 TTATTTTTTTAATAAAATTTATTTT
1 TTATATTTTTAATAAAATTTATTTT
35930 TTATATTTTT-ATAAAATTTATTTT
1 TTATATTTTTAATAAAATTTATTTT
35954 ATTTAATGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (25 bp):
TTATATTTTTAATAAAATTTATTTT
Found at i:36396 original size:54 final size:51
Alignment explanation
Indices: 36249--36399 Score: 137
Period size: 54 Copynumber: 2.9 Consensus size: 51
36239 TTTTATGTTG
36249 TTTTTAATTTATTTTAAAGTCATTTTGTTAGTTACTATTATAAA--TTATT
1 TTTTTAATTTATTTTAAAGTCATTTTGTTAGTTACTATTATAAATTTTATT
* * ** * * *
36298 TGTTTAGTTTAATGTTTATTGTGA-TTTGTTAGGTTATTAATATAAATTTTTATT
1 TTTTTAATTT-AT-TTTAAAGTCATTTTGTTA-GTTACTATTATAAA-TTTTATT
* * *
36352 AATTTTTAATTTATTTTAAAGTTATTTTGTTAGTAAGTATTATAAATT
1 --TTTTTAATTTATTTTAAAGTCATTTTGTTAGTTACTATTATAAATT
36400 AATTATTAGT
Statistics
Matches: 78, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
49 8 0.10
50 9 0.12
51 19 0.24
53 2 0.03
54 23 0.29
55 9 0.12
56 8 0.10
ACGTcount: A:0.30, C:0.01, G:0.10, T:0.58
Consensus pattern (51 bp):
TTTTTAATTTATTTTAAAGTCATTTTGTTAGTTACTATTATAAATTTTATT
Found at i:40738 original size:21 final size:21
Alignment explanation
Indices: 40712--40767 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
40702 AACAGCGGTG
*
40712 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
40733 GCGGTGAGATTAGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
40754 GCAGTGAGATTAGA
1 GCGGTGAGATTAGA
40768 AACAATGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:41432 original size:89 final size:89
Alignment explanation
Indices: 41301--41480 Score: 265
Period size: 91 Copynumber: 2.0 Consensus size: 89
41291 GAAATAAATC
* ** *
41301 AAAAATAAATAAAATTACATTATAACAAATCACAATTTACATTAAACT-AA-ACAAATAATTTAT
1 AAAAATAAAAAAAATTACATTATAACAAATCACAATAAACATTAAACTAAACACAAACAATTTAT
41364 AACCTAATCATAAATTACTAACAA
66 AACCTAATCATAAATTACTAACAA
* *
41388 AAAAATACAAAAAAATTACATTTATGACAATTCACAATAAACATTAAACTAAACACAAACAATTT
1 AAAAATA-AAAAAAATTACA-TTATAACAAATCACAATAAACATTAAACTAAACACAAACAATTT
*
41453 ATAACCTAATCATAAATTATTAACAA
64 ATAACCTAATCATAAATTACTAACAA
41479 AA
1 AA
41481 TAACTTTAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
87 7 0.09
88 11 0.13
89 25 0.30
90 2 0.02
91 37 0.45
ACGTcount: A:0.58, C:0.14, G:0.01, T:0.27
Consensus pattern (89 bp):
AAAAATAAAAAAAATTACATTATAACAAATCACAATAAACATTAAACTAAACACAAACAATTTAT
AACCTAATCATAAATTACTAACAA
Found at i:41522 original size:112 final size:111
Alignment explanation
Indices: 41387--41614 Score: 350
Period size: 112 Copynumber: 2.0 Consensus size: 111
41377 ATTACTAACA
* * *
41387 AAAAAATACAAAAAAATTACATTTATGACAATTCACAATAAACATTAAACTAAACACAAACAATT
1 AAAAAATACAAAAAAATTACATTTATAAAAAATCACAATAAACATTAAACTAAACACAAACAATT
* *
41452 TATAACCTAATCATAAATTATTAACAAAATAACTTTAAAATAATTAT
66 TATAACCTAACCATAAATTACTAACAAAATAACTTTAAAATAA-TAT
* * *
41499 AAAAAA-ACAAAAAATTTTACATTTATAAAAAATCACAATAAACATTAAACTAAATACAAATAAT
1 AAAAAATACAAAAAA-ATTACATTTATAAAAAATCACAATAAACATTAAACTAAACACAAACAAT
*
41563 TTATAACCTAACCATAAATTACTAACAAAATGACTTTAAAATAATAT
65 TTATAACCTAACCATAAATTACTAACAAAATAACTTTAAAATAATAT
41610 AAAAA
1 AAAAA
41615 TATATTCATA
Statistics
Matches: 106, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
111 16 0.15
112 90 0.85
ACGTcount: A:0.59, C:0.13, G:0.01, T:0.28
Consensus pattern (111 bp):
AAAAAATACAAAAAAATTACATTTATAAAAAATCACAATAAACATTAAACTAAACACAAACAATT
TATAACCTAACCATAAATTACTAACAAAATAACTTTAAAATAATAT
Found at i:41666 original size:97 final size:95
Alignment explanation
Indices: 41523--41857 Score: 394
Period size: 90 Copynumber: 3.5 Consensus size: 95
41513 TTTTACATTT
* * * *
41523 ATAAAAAATCACAATAAACATTAAACTAAATACAAATAATTTATAACCTAACCATAAATTACTAA
1 ATAAAAAATCAC-A-AAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAA
* *
41588 CAAAATGACTTTAAAATAATATAAAAATATATTC
64 CAAAATAACTTTAAAA-AAT-TAAAAAAATATTC
* * *
41622 ATAACAAATCACAAAACACTAAACTAAACACAAACGATTAATAACCTAATCATAAATTACTAACA
1 ATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACA
*
41687 AAATAACTTTGAAAAAATT----ACAT-TT-
66 AAATAACTTT-AAAAAATTAAAAAAATATTC
* *
41712 ATAAAAAATCACAAAACACTAAACTAAATACAAACAATCTATAACCTAATCATAAATTACTAACA
1 ATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACA
*
41777 AAATAACTATAAAAAAATTAAAAAAATTCAATTC
66 AAATAACT-TTAAAAAATTAAAAAAA-T--ATTC
*
41811 ATAAAAAAAAATCACAAAACACTAAACTAACCACAAACAATTTATAA
1 AT---AAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAA
41858 TAATTAATAA
Statistics
Matches: 203, Mismatches: 19, Indels: 25
0.82 0.08 0.10
Matches are distributed among these distances:
90 76 0.37
91 3 0.01
92 3 0.01
94 2 0.01
95 1 0.00
96 1 0.00
97 58 0.29
98 7 0.03
99 13 0.06
102 39 0.19
ACGTcount: A:0.59, C:0.16, G:0.01, T:0.24
Consensus pattern (95 bp):
ATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACA
AAATAACTTTAAAAAATTAAAAAAATATTC
Found at i:41862 original size:299 final size:293
Alignment explanation
Indices: 41302--41840 Score: 677
Period size: 299 Copynumber: 1.8 Consensus size: 293
41292 AAATAAATCA
* * * *
41302 AAAATAAATAAAATTACATTATAACAAATCACAATTTACATTAAACTAAACAAATAATTTATAAC
1 AAAATAAATAAAAATACATTATAACAAATCACAA-TAACACTAAACTAAACAAATAATTAATAAC
* * * *
41367 CTAATCATAAATTACTAACAAAAAAATACAAAAAAATTACATTTATGACAATTCACAATAAACAT
65 CTAATCATAAATTACTAACAAAAAAATACAAAAAAATTACATTTATAAAAAATCACAATAAACAC
* * * *
41432 TAAACTAAACACAAACAATTTATAACCTAATCATAAATTATTAACAAAATAACTTTAAAATAATT
130 TAAACTAAACACAAACAATCTATAACCTAATCATAAATTACTAACAAAATAACTATAAAAAAATT
* * * *
41497 ATAAAAAAACAAAAAATTTTACATTTATAAAAAATCACAATAAACATTAAACTAAATACAAATAA
195 ATAAAAAAAC---AAA-TTTACATTAAAAAAAAATCACAATAAACACTAAACTAAAAACAAATAA
*
41562 TTTATAACCTAACCATAAATTACTAACAAAATGACTTT
256 TTAATAACCTAACCATAAATTACTAACAAAATGACTTT
*
41600 AAAATAATATAAAAATATATTCATAACAAATCACAA-AACACTAAACTAAACACAA-ACGATTAA
1 AAAATAA-ATAAAAATACATT-ATAACAAATCACAATAACACTAAACTAAACA-AATA--ATTAA
* ***
41663 TAACCTAATCATAAATTACTAACAAAATAACTTTGAAAAAATTACATTTATAAAAAATCAC-A-A
61 TAACCTAATCATAAATTACTAACAAAA-AAATACAAAAAAATTACATTTATAAAAAATCACAATA
*
41726 AACACTAAACTAAATACAAACAATCTATAACCTAATCATAAATTACTAACAAAATAACTATAAAA
125 AACACTAAACTAAACACAAACAATCTATAACCTAATCATAAATTACTAACAAAATAACTATAAAA
*
41791 AAATTA-AAAAAATTC-AA-TT-CA-TAAAAAAAAATCAC-A-AAACACTAAACTAA
190 AAATTATAAAAAA-ACAAATTTACATTAAAAAAAAATCACAATAAACACTAAACTAA
41841 CCACAAACAA
Statistics
Matches: 212, Mismatches: 22, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
289 13 0.06
290 1 0.00
291 12 0.06
292 2 0.01
293 2 0.01
295 2 0.01
298 28 0.13
299 80 0.38
300 46 0.22
301 26 0.12
ACGTcount: A:0.58, C:0.15, G:0.01, T:0.26
Consensus pattern (293 bp):
AAAATAAATAAAAATACATTATAACAAATCACAATAACACTAAACTAAACAAATAATTAATAACC
TAATCATAAATTACTAACAAAAAAATACAAAAAAATTACATTTATAAAAAATCACAATAAACACT
AAACTAAACACAAACAATCTATAACCTAATCATAAATTACTAACAAAATAACTATAAAAAAATTA
TAAAAAAACAAATTTACATTAAAAAAAAATCACAATAAACACTAAACTAAAAACAAATAATTAAT
AACCTAACCATAAATTACTAACAAAATGACTTT
Found at i:44923 original size:14 final size:17
Alignment explanation
Indices: 44891--44928 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
44881 AATTATAAAG
44891 TATATTATTAAATTAAT
1 TATATTATTAAATTAAT
44908 TATATTA-TAAA-T-AT
1 TATATTATTAAATTAAT
44922 TATATTA
1 TATATTA
44929 AGAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 1 0.05
16 4 0.19
17 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTATTAAATTAAT
Found at i:45043 original size:21 final size:22
Alignment explanation
Indices: 45004--45044 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
44994 ATACATTTGT
* *
45004 AATACTTATATTTATTTATTAA
1 AATACTTATATTAAATTATTAA
45026 AATA-TTATATTAAATTATT
1 AATACTTATATTAAATTATT
45045 GTTGTAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
AATACTTATATTAAATTATTAA
Found at i:48510 original size:21 final size:22
Alignment explanation
Indices: 48482--48545 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
48472 GCTTTGCCGA
48482 TCAGGCACTATATGTGTCGTAT
1 TCAGGCACTATATGTGTCGTAT
* **
48504 T-AGGCACCACGTGTGTCGT-T
1 TCAGGCACTATATGTGTCGTAT
* *
48524 TCAGGAACTTTATGTGTCGTAT
1 TCAGGCACTATATGTGTCGTAT
48546 ACTGTTTCTG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (22 bp):
TCAGGCACTATATGTGTCGTAT
Found at i:50818 original size:21 final size:20
Alignment explanation
Indices: 50778--50826 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
50768 ATAAATAAAA
*
50778 TCATTCATGTCAATTCCCTG
1 TCATTCATGACAATTCCCTG
*
50798 TCATTCACTGACAATTTCCTG
1 TCATTCA-TGACAATTCCCTG
50819 TCATTCAT
1 TCATTCAT
50827 AAGTTCTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.22, C:0.29, G:0.08, T:0.41
Consensus pattern (20 bp):
TCATTCATGACAATTCCCTG
Found at i:54165 original size:40 final size:40
Alignment explanation
Indices: 54110--54185 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
54100 ATATGCCAAC
*
54110 AGAAGCTTGAAAGCTTAATAGAAGCTCATAAAAGCTGAAT
1 AGAAGCTCGAAAGCTTAATAGAAGCTCATAAAAGCTGAAT
* *
54150 AGAAGCTCGAAAGCTTAATAGAAGCTCGTAAGAGCT
1 AGAAGCTCGAAAGCTTAATAGAAGCTCATAAAAGCT
54186 AAACAGAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.21
Consensus pattern (40 bp):
AGAAGCTCGAAAGCTTAATAGAAGCTCATAAAAGCTGAAT
Found at i:54176 original size:19 final size:19
Alignment explanation
Indices: 54110--54177 Score: 91
Period size: 19 Copynumber: 3.5 Consensus size: 19
54100 ATATGCCAAC
*
54110 AGAAGCTTGAAAGCTTAAT
1 AGAAGCTCGAAAGCTTAAT
* *
54129 AGAAGCTCATAAAAGCTGAAT
1 AGAAGCTC--GAAAGCTTAAT
54150 AGAAGCTCGAAAGCTTAAT
1 AGAAGCTCGAAAGCTTAAT
54169 AGAAGCTCG
1 AGAAGCTCG
54178 TAAGAGCTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 25 0.60
21 17 0.40
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.21
Consensus pattern (19 bp):
AGAAGCTCGAAAGCTTAAT
Found at i:54230 original size:21 final size:21
Alignment explanation
Indices: 54129--54235 Score: 110
Period size: 21 Copynumber: 5.2 Consensus size: 21
54119 AAAGCTTAAT
* *
54129 AGAAGCTCATAAAAGCTGAAT
1 AGAAGCTCATAAGAGCTGAAC
* * *
54150 AGAAGCTC-GAA-AGCTTAAT
1 AGAAGCTCATAAGAGCTGAAC
* *
54169 AGAAGCTCGTAAGAGCTAAAC
1 AGAAGCTCATAAGAGCTGAAC
* * *
54190 AGAAACTCATTAGAGTTGAAC
1 AGAAGCTCATAAGAGCTGAAC
54211 AGAAGCTCATAAGAGCTGAAC
1 AGAAGCTCATAAGAGCTGAAC
54232 AGAA
1 AGAA
54236 AGTAAAACAC
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
19 15 0.21
20 4 0.06
21 52 0.73
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.18
Consensus pattern (21 bp):
AGAAGCTCATAAGAGCTGAAC
Found at i:58304 original size:25 final size:25
Alignment explanation
Indices: 58267--58322 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
58257 AAAAAGAAAT
* *
58267 GATTATCCTATACATCAAACAATAA
1 GATTATCCAATACATCAAACAACAA
*
58292 GATTATCCAATACATTAAACAACAA
1 GATTATCCAATACATCAAACAACAA
58317 GATTAT
1 GATTAT
58323 TTCATATATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.48, C:0.18, G:0.05, T:0.29
Consensus pattern (25 bp):
GATTATCCAATACATCAAACAACAA
Found at i:61022 original size:16 final size:16
Alignment explanation
Indices: 61001--61032 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
60991 TTTGGATATA
61001 TATATAGTTATATGGT
1 TATATAGTTATATGGT
61017 TATATAGTTATATGGT
1 TATATAGTTATATGGT
61033 ACTTGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (16 bp):
TATATAGTTATATGGT
Found at i:63723 original size:2 final size:2
Alignment explanation
Indices: 63716--63741 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
63706 ACTCCACTAA
63716 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
63742 AGGAGGGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:65447 original size:20 final size:18
Alignment explanation
Indices: 65422--65458 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
65412 AAATAAATCA
65422 TTAAAAATTTCAAAAAAAAT
1 TTAAAAA-TT-AAAAAAAAT
65442 TTAAAAATTAAAAAAAA
1 TTAAAAATTAAAAAAAA
65459 CGGTTCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 2 0.12
20 7 0.41
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (18 bp):
TTAAAAATTAAAAAAAAT
Found at i:65910 original size:15 final size:16
Alignment explanation
Indices: 65890--65919 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
65880 TTATAGAAAG
65890 TTTTTAATAT-TTTTA
1 TTTTTAATATATTTTA
65905 TTTTTAATATATTTT
1 TTTTTAATATATTTT
65920 TTAAAGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTAATATATTTTA
Found at i:65936 original size:18 final size:18
Alignment explanation
Indices: 65915--65949 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
65905 TTTTTAATAT
65915 ATTTTTTAAAGTTTTTTA
1 ATTTTTTAAAGTTTTTTA
*
65933 ATTTTTTATAGTTTTTT
1 ATTTTTTAAAGTTTTTT
65950 TATGAGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (18 bp):
ATTTTTTAAAGTTTTTTA
Found at i:81516 original size:46 final size:46
Alignment explanation
Indices: 81448--81570 Score: 135
Period size: 46 Copynumber: 2.7 Consensus size: 46
81438 CCCAAGTTTG
**
81448 AGCTTCTACATA-TGTTGTGGACTTGAGAATACCA-GTATAGGTTCTG
1 AGCTTCTACA-AGTGTTGTGGACTTGAGAATA-CATGTATAGGTTCCA
* * *
81494 AGC-TCTAGCAAGTGTTGCGGACTCGAGAATACATGTTTAGGTTCCA
1 AGCTTCTA-CAAGTGTTGTGGACTTGAGAATACATGTATAGGTTCCA
* *
81540 AGCTTCTACATGTGTTGTTGACTTGAGAATA
1 AGCTTCTACAAGTGTTGTGGACTTGAGAATA
81571 TAGGAATATT
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
45 7 0.11
46 53 0.83
47 4 0.06
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.33
Consensus pattern (46 bp):
AGCTTCTACAAGTGTTGTGGACTTGAGAATACATGTATAGGTTCCA
Found at i:91959 original size:3 final size:3
Alignment explanation
Indices: 91951--91981 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
91941 AAATTAAGAT
91951 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
91982 AGAAACAGGG
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:92963 original size:3 final size:3
Alignment explanation
Indices: 92955--92985 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
92945 AAATTAAGAT
92955 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
92986 AGAAACAGGG
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:95099 original size:21 final size:20
Alignment explanation
Indices: 95073--95111 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
95063 TTTTTTTAAG
95073 TTTTTTATATATTCTTTAGGT
1 TTTTTTATA-ATTCTTTAGGT
*
95094 TTTTTTATAATTTTTTAG
1 TTTTTTATAATTCTTTAG
95112 ATGTAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.21, C:0.03, G:0.08, T:0.69
Consensus pattern (20 bp):
TTTTTTATAATTCTTTAGGT
Found at i:95110 original size:20 final size:20
Alignment explanation
Indices: 95064--95111 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
95054 TTGAGGTTTT
*
95064 TTTTTTAAGTTTTTTATATA
1 TTTTTTAGGTTTTTTATATA
*
95084 TTCTTTAGGTTTTTT-TATAA
1 TTTTTTAGGTTTTTTATAT-A
95104 TTTTTTAG
1 TTTTTTAG
95112 ATGTAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.21, C:0.02, G:0.08, T:0.69
Consensus pattern (20 bp):
TTTTTTAGGTTTTTTATATA
Found at i:108815 original size:41 final size:41
Alignment explanation
Indices: 108758--108882 Score: 241
Period size: 41 Copynumber: 3.0 Consensus size: 41
108748 CTTTTGTACT
108758 AAAGGTTTTACTCACAAATTGGATGGAATGAATTAAATTTC
1 AAAGGTTTTACTCACAAATTGGATGGAATGAATTAAATTTC
*
108799 AAAGGTTTTACTCACAAATTGGATGAAATGAATTAAATTTC
1 AAAGGTTTTACTCACAAATTGGATGGAATGAATTAAATTTC
108840 AAAGGTTTTACTCACAAATTGGATGGAATGAATTAAATTTC
1 AAAGGTTTTACTCACAAATTGGATGGAATGAATTAAATTTC
108881 AA
1 AA
108883 TTCTCCAAAC
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 82 1.00
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.34
Consensus pattern (41 bp):
AAAGGTTTTACTCACAAATTGGATGGAATGAATTAAATTTC
Found at i:112681 original size:20 final size:19
Alignment explanation
Indices: 112656--112742 Score: 63
Period size: 20 Copynumber: 4.4 Consensus size: 19
112646 TATTTTTTCA
112656 ATAAAAATGAATAAAAAATC
1 ATAAAAAT-AATAAAAAATC
* *
112676 ATAAAAATTATCAAAAATC
1 ATAAAAATAATAAAAAATC
*
112695 AGAAAAA-AATATCAAAAATC
1 ATAAAAATAATA--AAAAATC
*
112715 AGAAAAA-AATTATCAAAAAT-
1 ATAAAAATAA-TA--AAAAATC
112735 ATAAAAAT
1 ATAAAAAT
112743 TATTAAATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
18 2 0.04
19 15 0.26
20 30 0.53
21 10 0.18
ACGTcount: A:0.69, C:0.07, G:0.03, T:0.21
Consensus pattern (19 bp):
ATAAAAATAATAAAAAATC
Found at i:112692 original size:21 final size:19
Alignment explanation
Indices: 112669--112759 Score: 94
Period size: 20 Copynumber: 4.7 Consensus size: 19
112659 AAAATGAATA
*
112669 AAAAATCATAAAAATTATC
1 AAAAATCAAAAAAATTATC
*
112688 AAAAATCAGAAAAAAATATC
1 AAAAATCA-AAAAAATTATC
112708 AAAAATCAGAAAAAAATTATC
1 AAAAATC--AAAAAAATTATC
* *
112729 AAAAAT-ATAAAAATTATT
1 AAAAATCAAAAAAATTATC
* *
112747 AAATATTAAAAAA
1 AAAAATCAAAAAA
112760 GTATGAAAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
18 15 0.25
19 13 0.21
20 16 0.26
21 16 0.26
22 1 0.02
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.23
Consensus pattern (19 bp):
AAAAATCAAAAAAATTATC
Found at i:112874 original size:21 final size:21
Alignment explanation
Indices: 112850--112898 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
112840 TTTAACATAT
**
112850 TTAAAATTTTATAAAAATGTA
1 TTAAAATTCCATAAAAATGTA
*
112871 TTAAAATTCCATAAAAATTTA
1 TTAAAATTCCATAAAAATGTA
112892 TTAAAAT
1 TTAAAAT
112899 AGATATAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (21 bp):
TTAAAATTCCATAAAAATGTA
Found at i:113563 original size:7 final size:7
Alignment explanation
Indices: 113521--113565 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
113511 GTTTATATCC
*
113521 ATTTTTA
1 ATTTTTT
113528 ATTTTTT
1 ATTTTTT
**
113535 ATTTAAT
1 ATTTTTT
113542 ATTTTTT
1 ATTTTTT
113549 AATTTTTT
1 -ATTTTTT
113557 ATTTTTT
1 ATTTTTT
113564 AT
1 AT
113566 GAGAAAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
7 25 0.78
8 7 0.22
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
ATTTTTT
Found at i:123700 original size:26 final size:26
Alignment explanation
Indices: 123640--123694 Score: 89
Period size: 23 Copynumber: 2.2 Consensus size: 26
123630 TACTTATCAC
123640 ATATTTTAATCTAGTATAAAATATGA
1 ATATTTTAATCTAGTATAAAATATGA
123666 ATATTTTAAT-TA-TAT-AAATATGA
1 ATATTTTAATCTAGTATAAAATATGA
123689 ATATTT
1 ATATTT
123695 GTTTAAATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
23 14 0.48
24 3 0.10
25 2 0.07
26 10 0.34
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (26 bp):
ATATTTTAATCTAGTATAAAATATGA
Found at i:124860 original size:3 final size:3
Alignment explanation
Indices: 124852--124886 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
124842 AAAGAAAGCA
124852 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
124887 CAACAACAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:127947 original size:40 final size:40
Alignment explanation
Indices: 127903--127988 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 40
127893 ACCTTATTGT
** * * *
127903 TAAAAATTAATAATTT-AATTATTTATCTGCAATGAATTAA
1 TAAAAATTAAT-ATTTCAACAATTTATATGCAATAAACTAA
127943 TAAAAATTAATATTTCAACAATTTATATGCAATAAACTAA
1 TAAAAATTAATATTTCAACAATTTATATGCAATAAACTAA
127983 TAAAAA
1 TAAAAA
127989 CATTAGTCGT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 4 0.10
40 36 0.90
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.37
Consensus pattern (40 bp):
TAAAAATTAATATTTCAACAATTTATATGCAATAAACTAA
Found at i:129191 original size:18 final size:19
Alignment explanation
Indices: 129170--129210 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
129160 ATTTTGGATT
*
129170 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTTGAA
129188 TTTTAAAAATTATTTTGAA
1 TTTTAAAAATTATTTTGAA
129207 TTTT
1 TTTT
129211 TTTTGTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTTAAAAATTATTTTGAA
Found at i:135795 original size:99 final size:100
Alignment explanation
Indices: 135620--135903 Score: 353
Period size: 99 Copynumber: 2.9 Consensus size: 100
135610 TTGAAAATTT
* ** * *
135620 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCTTTAGCAGTGCAACGAAACAGATGGAAGCTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTA
* *
135685 CGAC-ATTGGATCTGGTCTCCTTGATATT-ACACTTA
66 CGACGA-CGGATCTGGTCTCCCTGATATTGACA-TTA
*
135720 AAAAGATTGAAGCCACAACGGCGGA-CTTACTTCCTTAGCAGTGCAGTGGAATAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTA
* *
135784 CGACGACGGATCTGGTTTCCCTGATATTGGCATTA
66 CGACGACGGATCTGGTCTCCCTGATATTGACATTA
* * * * *
135819 AAAA-NTTAAAGCCACAACGGCGGATCTTACTTCCCT-GACGGTGCGGTGGAACAGATTGAAGCT
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAG-CAGTGCAGTGGAACAGATTGAAGCT
* *
135882 ACGACGGCGGATCTGGTTTCCC
65 ACGACGACGGATCTGGTCTCCC
135904 CAACATTGCA
Statistics
Matches: 163, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
98 19 0.12
99 116 0.71
100 28 0.17
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.24
Consensus pattern (100 bp):
AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTA
CGACGACGGATCTGGTCTCCCTGATATTGACATTA
Found at i:135903 original size:50 final size:49
Alignment explanation
Indices: 135758--135903 Score: 116
Period size: 49 Copynumber: 2.9 Consensus size: 49
135748 ACTTCCTTAG
* *
135758 CAGTGCAGTGGAATAGATTGAAGCTACGACGACGGATCTGGTTTCCCTGA
1 CAGTGCGGTGGAA-AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA
* * * * * * * * ***
135808 TATTG-GCAT-TAAAAANTTAAAGCCACAACGGCGGATCTTACTTCCCTGA
1 CAGTGCG-GTGGAAAGA-TTGAAGCTACGACGGCGGATCTGGTTTCCCTGA
*
135857 CGGTGCGGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCC
1 CAGTGCGGTGGAA-AGATTGAAGCTACGACGGCGGATCTGGTTTCCC
135904 CAACATTGCA
Statistics
Matches: 66, Mismatches: 25, Indels: 10
0.65 0.25 0.10
Matches are distributed among these distances:
48 2 0.03
49 31 0.47
50 31 0.47
51 2 0.03
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (49 bp):
CAGTGCGGTGGAAAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA
Found at i:135921 original size:50 final size:50
Alignment explanation
Indices: 135761--135929 Score: 137
Period size: 50 Copynumber: 3.4 Consensus size: 50
135751 TCCTTAGCAG
* * * *
135761 TGCAGTGGAATAGATTGAAGCTACGACGACGGATCTGGTTTCCCTGATAT
1 TGCAGTGGAACAAATTGAAGCTACGACGGCGGATCTGGTTTCCCTGACAT
* * * * *** **
135811 TGGCA-T-TAA-AAANTTAAAGCCACAACGGCGGATCTTACTTCCCTGACGG
1 T-GCAGTGGAACAAA-TTGAAGCTACGACGGCGGATCTGGTTTCCCTGACAT
* * **
135860 TGCGGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCCAACAT
1 TGCAGTGGAACAAATTGAAGCTACGACGGCGGATCTGGTTTCCCTGACAT
*
135910 TGCAGTTGAACAAATTGAAG
1 TGCAGTGGAACAAATTGAAG
135930 ATTACAGATC
Statistics
Matches: 86, Mismatches: 28, Indels: 10
0.69 0.23 0.08
Matches are distributed among these distances:
48 4 0.05
49 30 0.35
50 47 0.55
51 5 0.06
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.24
Consensus pattern (50 bp):
TGCAGTGGAACAAATTGAAGCTACGACGGCGGATCTGGTTTCCCTGACAT
Found at i:136123 original size:44 final size:43
Alignment explanation
Indices: 136060--136193 Score: 223
Period size: 44 Copynumber: 3.0 Consensus size: 43
136050 GAACAGATTG
*
136060 AAGAAAGCAGATCTTGTCTTCATGCAGTGGCGTGAAGTAGATCA
1 AAGAAAGCAGATCTTGTCTTCATGTA-TGGCGTGAAGTAGATCA
136104 AAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCA
1 AAGAAAGCAGATCTTGTCTTCATGTA-TGGCGTGAAGTAGATCA
*
136148 AAGAAAACAGATCTTGTCTTCATGTATCGGCGTGAAGTAGATCA
1 AAGAAAGCAGATCTTGTCTTCATGTAT-GGCGTGAAGTAGATCA
136192 AA
1 AA
136194 TACAACATAT
Statistics
Matches: 86, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
43 1 0.01
44 85 0.99
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.26
Consensus pattern (43 bp):
AAGAAAGCAGATCTTGTCTTCATGTATGGCGTGAAGTAGATCA
Found at i:136220 original size:88 final size:88
Alignment explanation
Indices: 136060--136232 Score: 199
Period size: 88 Copynumber: 2.0 Consensus size: 88
136050 GAACAGATTG
* * **
136060 AAGAAAGCAGATCTTGTCTTCATGCAGTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTC
1 AAGAAAACAGATCTTGTCTTCATGCAGTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTATCCCC
**
136125 ATGTACTGGCGTG-AAGTAGATCA
66 ACATACTGGCG-GCAAGTAGATCA
* * * *
136148 AAGAAAACAGATCTTGTCTTCATGTA-TCGGCGTGAAGTAGATCAAATACAA-CATATTTTATCC
1 AAGAAAACAGATCTTGTCTTCATGCAGT-GGCGTGAAGTAGATCAAAGA-AAGCAGATCTTATCC
*
136211 CCCCATACTGGCGGCAAGTAGA
64 CCACATACTGGCGGCAAGTAGA
136233 GTGAAGATTA
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
87 2 0.03
88 67 0.94
89 2 0.03
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (88 bp):
AAGAAAACAGATCTTGTCTTCATGCAGTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTATCCCC
ACATACTGGCGGCAAGTAGATCA
Found at i:136450 original size:45 final size:44
Alignment explanation
Indices: 136363--136456 Score: 120
Period size: 44 Copynumber: 2.1 Consensus size: 44
136353 TAGTGGAATC
* * *
136363 GATCGGAAAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTA
1 GATCGGAAAAAACAGATCTTGTCTTCATCTAGTGGCGTGAAGTA
136407 GATCGGAAAAAACAGATCTTGTCTTCCCATACTAGT-G-GTGAAGTA
1 GATCGGAAAAAACAGATCTTGTCTT--CAT-CTAGTGGCGTGAAGTA
136452 GATCG
1 GATCG
136457 AAGATACAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
44 24 0.55
45 13 0.30
46 4 0.09
47 3 0.07
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.28
Consensus pattern (44 bp):
GATCGGAAAAAACAGATCTTGTCTTCATCTAGTGGCGTGAAGTA
Found at i:137523 original size:16 final size:16
Alignment explanation
Indices: 137502--137533 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
137492 CCGAATCACC
137502 TGAGAGGCGGCGCGAG
1 TGAGAGGCGGCGCGAG
137518 TGAGAGGCGGCGCGAG
1 TGAGAGGCGGCGCGAG
137534 GACGCTAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.56, T:0.06
Consensus pattern (16 bp):
TGAGAGGCGGCGCGAG
Found at i:137999 original size:6 final size:6
Alignment explanation
Indices: 137984--138031 Score: 51
Period size: 7 Copynumber: 7.2 Consensus size: 6
137974 ACTGGGTCCA
137984 TTTTAGT TTTTAT TTTTAT TTTTAT TTATTAT TATCTTAT TTATTAT T
1 TTTTA-T TTTTAT TTTTAT TTTTAT TT-TTAT T-T-TTAT TT-TTAT T
138032 ATTGTTACTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
6 15 0.41
7 16 0.43
8 6 0.16
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (6 bp):
TTTTAT
Found at i:138025 original size:15 final size:14
Alignment explanation
Indices: 137992--138034 Score: 63
Period size: 15 Copynumber: 3.1 Consensus size: 14
137982 CATTTTAGTT
137992 TTTATTT-TTATT-
1 TTTATTTATTATTA
138004 TTTATTTATTATTA
1 TTTATTTATTATTA
138018 TCTTATTTATTATTA
1 T-TTATTTATTATTA
138033 TT
1 TT
138035 GTTACTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.25
13 5 0.18
14 2 0.07
15 14 0.50
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTTATTATTA
Found at i:144379 original size:25 final size:24
Alignment explanation
Indices: 144351--144408 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
144341 TGGCTCTCTG
* * *
144351 GAGCTTCTAGTTACATGGCTCACAT
1 GAGCTTCCA-TTACATAGCTCAAAT
144376 GAGCTTCCCATTACATAGCTCAAAT
1 GAGCTT-CCATTACATAGCTCAAAT
144401 GAGCTTCC
1 GAGCTTCC
144409 CGTTATATGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 2 0.07
25 25 0.86
26 2 0.07
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (24 bp):
GAGCTTCCATTACATAGCTCAAAT
Found at i:144409 original size:25 final size:25
Alignment explanation
Indices: 144361--144443 Score: 96
Period size: 25 Copynumber: 3.3 Consensus size: 25
144351 GAGCTTCTAG
*
144361 TTACATGGCTCACATGAGCTTCCCA
1 TTACATGGCTCAAATGAGCTTCCCA
* *
144386 TTACATAGCTCAAATGAGCTTCCCG
1 TTACATGGCTCAAATGAGCTTCCCA
* *
144411 TTATATGGCTTGAAA-GAGCTTCCCGA
1 TTACATGGC-TCAAATGAGCTTCCC-A
144437 TTACATG
1 TTACATG
144444 CTCGTATGGC
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
25 38 0.79
26 10 0.21
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (25 bp):
TTACATGGCTCAAATGAGCTTCCCA
Found at i:144419 original size:50 final size:50
Alignment explanation
Indices: 144351--144446 Score: 115
Period size: 50 Copynumber: 1.9 Consensus size: 50
144341 TGGCTCTCTG
* *
144351 GAGCTTCTAGTTACATGGC-TCACATGAGCTTCCC-ATTACATAGCTCAAAT
1 GAGCTTCCAGTTACATGGCTTCA-AAGAGCTTCCCGATTACAT-GCTCAAAT
* * *
144401 GAGCTTCCCGTTATATGGCTTGAAAGAGCTTCCCGATTACATGCTC
1 GAGCTTCCAGTTACATGGCTTCAAAGAGCTTCCCGATTACATGCTC
144447 GTATGGCATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
50 30 0.77
51 9 0.23
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (50 bp):
GAGCTTCCAGTTACATGGCTTCAAAGAGCTTCCCGATTACATGCTCAAAT
Found at i:148029 original size:30 final size:30
Alignment explanation
Indices: 147995--148053 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
147985 GCCTGAACCG
*
147995 TTTATTTCCTGTACTTTAGAGGAACTTTCT
1 TTTATTTCCAGTACTTTAGAGGAACTTTCT
* *
148025 TTTATTTTCAGTAGTTTAGAGGAACTTTC
1 TTTATTTCCAGTACTTTAGAGGAACTTTC
148054 CTAATGGCGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.22, C:0.14, G:0.15, T:0.49
Consensus pattern (30 bp):
TTTATTTCCAGTACTTTAGAGGAACTTTCT
Found at i:149324 original size:20 final size:20
Alignment explanation
Indices: 149296--149335 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
149286 CATTCTTATC
*
149296 TTACTTAGGTTGCCTGTCGA
1 TTACCTAGGTTGCCTGTCGA
149316 TTACCTAGGTTGCCTGTCGA
1 TTACCTAGGTTGCCTGTCGA
149336 GGTTGCTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.38
Consensus pattern (20 bp):
TTACCTAGGTTGCCTGTCGA
Found at i:158409 original size:21 final size:20
Alignment explanation
Indices: 158368--158412 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
158358 GCACAACAAC
* *
158368 TTTTTTTTTGAAAACACGAA
1 TTTTTTTTTAAAAACAAGAA
158388 TTTTTTTTTAAAATACAAGAA
1 TTTTTTTTTAAAA-ACAAGAA
158409 TTTT
1 TTTT
158413 AGAAACACGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.51
Consensus pattern (20 bp):
TTTTTTTTTAAAAACAAGAA
Found at i:158422 original size:36 final size:36
Alignment explanation
Indices: 158373--158467 Score: 122
Period size: 36 Copynumber: 2.6 Consensus size: 36
158363 ACAACTTTTT
* *
158373 TTTTGAAAACACGAATTTTTTTTTAAAATACA-AGAA
1 TTTTG-AAACACGAATTTTTTTTTAAAAAACACAAAA
158409 TTTTAGAAACACGAA-TTTTTTTTAAAAAACACGAAAA
1 TTTT-GAAACACGAATTTTTTTTTAAAAAACAC-AAAA
158446 TTTTGAAACACGAGATTTTTTT
1 TTTTGAAACACGA-ATTTTTTT
158468 AAGAAGTACC
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
35 15 0.29
36 22 0.42
37 9 0.17
38 6 0.12
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (36 bp):
TTTTGAAACACGAATTTTTTTTTAAAAAACACAAAA
Found at i:158440 original size:20 final size:20
Alignment explanation
Indices: 158368--158443 Score: 63
Period size: 21 Copynumber: 4.0 Consensus size: 20
158358 GCACAACAAC
**
158368 TTTTTTTTTGAAAACACGAA
1 TTTTTTTTAAAAAACACGAA
* *
158388 TTTTTTTTTAAAATACAAGAA
1 -TTTTTTTTAAAAAACACGAA
*
158409 ----TTTT-AGAAACACGAA
1 TTTTTTTTAAAAAACACGAA
158424 TTTTTTTTAAAAAACACGAA
1 TTTTTTTTAAAAAACACGAA
158444 AATTTTGAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
15 8 0.19
16 4 0.10
19 4 0.10
20 10 0.24
21 16 0.38
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTTTTTAAAAAACACGAA
Found at i:158758 original size:27 final size:29
Alignment explanation
Indices: 158728--158785 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
158718 TGCCTTATTT
* *
158728 ATTGAAATT-ATTTAAATTTAAAATA-AA
1 ATTGAAATTAAATTAAATTAAAAATATAA
158755 ATTGAAATTAAATTAAATTAAAAATATAA
1 ATTGAAATTAAATTAAATTAAAAATATAA
158784 AT
1 AT
158786 ACAAAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 9 0.33
28 14 0.52
29 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (29 bp):
ATTGAAATTAAATTAAATTAAAAATATAA
Found at i:158976 original size:9 final size:9
Alignment explanation
Indices: 158951--158998 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
158941 TTTGCTTCAC
158951 TTTTTCTTT
1 TTTTTCTTT
*
158960 TTCGTTCTTT
1 TT-TTTCTTT
158970 TTTTTCTTT
1 TTTTTCTTT
*
158979 TCTTTCTTT
1 TTTTTCTTT
* *
158988 CTCTTCTTT
1 TTTTTCTTT
158997 TT
1 TT
158999 GGCCTGTTGG
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
9 23 0.74
10 8 0.26
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:159240 original size:9 final size:9
Alignment explanation
Indices: 159226--159270 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
159216 CTGTTAATTT
159226 TTTTTCTTC
1 TTTTTCTTC
159235 TTTTTC-TC
1 TTTTTCTTC
*
159243 TCTTTCTTC
1 TTTTTCTTC
159252 TTTTTCTTC
1 TTTTTCTTC
*
159261 TTCTTCTTC
1 TTTTTCTTC
159270 T
1 T
159271 ATCAGCCCCC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
8 7 0.22
9 25 0.78
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:159813 original size:30 final size:30
Alignment explanation
Indices: 159779--159911 Score: 146
Period size: 30 Copynumber: 4.5 Consensus size: 30
159769 GAAAATATCA
**
159779 GGGTCAAAATAAAATTTTAAGAAAGTTTAG
1 GGGTCAAAATGTAATTTTAAGAAAGTTTAG
* *
159809 GGGTCAAAATGTAA-TTTATA-AAAGTTCAA
1 GGGTCAAAATGTAATTTTA-AGAAAGTTTAG
* **
159838 GGGTTAAAATGTAATTTCGAGAAAGTTTAG
1 GGGTCAAAATGTAATTTTAAGAAAGTTTAG
* *
159868 GGGTCAAAAGGTAATTTT-AGAAAAGATTAG
1 GGGTCAAAATGTAATTTTAAG-AAAGTTTAG
159898 GGGTCAAAATGTAA
1 GGGTCAAAATGTAA
159912 AAAAATTTAA
Statistics
Matches: 85, Mismatches: 14, Indels: 8
0.79 0.13 0.07
Matches are distributed among these distances:
29 27 0.32
30 58 0.68
ACGTcount: A:0.43, C:0.05, G:0.23, T:0.29
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTAAGAAAGTTTAG
Found at i:159854 original size:59 final size:60
Alignment explanation
Indices: 159760--159911 Score: 175
Period size: 59 Copynumber: 2.5 Consensus size: 60
159750 GGCTGAAACA
* * ** * *
159760 TAATTTTGAGAAAATA-TCAGGGTCAAAATAAAATTTTAAGAAAGTTTAGGGGTCAAAATG
1 TAATTTT-AGAAAAGATTAAGGGTCAAAATGTAATTTCAAGAAAGTTTAGGGGTCAAAAGG
* * *
159820 TAA-TTTATAAAAG-TTCAAGGGTTAAAATGTAATTTCGAGAAAGTTTAGGGGTCAAAAGG
1 TAATTTTAGAAAAGATT-AAGGGTCAAAATGTAATTTCAAGAAAGTTTAGGGGTCAAAAGG
*
159879 TAATTTTAGAAAAGATTAGGGGTCAAAATGTAA
1 TAATTTTAGAAAAGATTAAGGGTCAAAATGTAA
159912 AAAAATTTAA
Statistics
Matches: 76, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
58 6 0.08
59 42 0.55
60 26 0.34
61 2 0.03
ACGTcount: A:0.43, C:0.05, G:0.22, T:0.30
Consensus pattern (60 bp):
TAATTTTAGAAAAGATTAAGGGTCAAAATGTAATTTCAAGAAAGTTTAGGGGTCAAAAGG
Found at i:165926 original size:30 final size:30
Alignment explanation
Indices: 165859--165930 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
165849 CAGAGACGTA
* * *
165859 AACGGGGTTACCATGTTCGTCAGTCAATTG
1 AACGGGGTTGCCATGCTCGTCAGTCAATGG
165889 AACGGGGTTGCCATGCTCGTCAGT-AAGTGG
1 AACGGGGTTGCCATGCTCGTCAGTCAA-TGG
*
165919 AATGGGGTTGCC
1 AACGGGGTTGCC
165931 GTGCACATCT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 2 0.05
30 35 0.95
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.26
Consensus pattern (30 bp):
AACGGGGTTGCCATGCTCGTCAGTCAATGG
Found at i:167674 original size:27 final size:27
Alignment explanation
Indices: 167624--167676 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
167614 TTAAATTTTT
* *
167624 ATAAAAACGTATTAAAATTTTATAAAA
1 ATAAAAACATATTAAAATTATATAAAA
167651 ATAAAAA-ATATTAAAATTGATATAAA
1 ATAAAAACATATTAAAATT-ATATAAA
167677 CTTATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (27 bp):
ATAAAAACATATTAAAATTATATAAAA
Found at i:167692 original size:9 final size:9
Alignment explanation
Indices: 167643--167696 Score: 51
Period size: 9 Copynumber: 6.1 Consensus size: 9
167633 TATTAAAATT
167643 TTATAAAAA
1 TTATAAAAA
167652 -TA-AAAAA
1 TTATAAAAA
*
167659 -TATTAAAA
1 TTATAAAAA
*
167667 TTGATATAAAC
1 TT-ATA-AAAA
167678 TTATAAAAA
1 TTATAAAAA
167687 TTATAAAAA
1 TTATAAAAA
167696 T
1 T
167697 AAAATAAACT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 7 0.19
8 6 0.16
9 14 0.38
10 5 0.14
11 5 0.14
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (9 bp):
TTATAAAAA
Found at i:168142 original size:10 final size:9
Alignment explanation
Indices: 168127--168184 Score: 53
Period size: 10 Copynumber: 5.8 Consensus size: 9
168117 CCAACTCAAG
168127 TTTTTAAGAT
1 TTTTTAA-AT
168137 TTTTTAAAT
1 TTTTTAAAT
168146 TTTTATAATAAT
1 TTTT-T-A-AAT
168158 TTTTTACAAT
1 TTTTTA-AAT
*
168168 TTTTTATTAT
1 TTTTTA-AAT
168178 TTTTTAA
1 TTTTTAA
168185 GAATTCTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
9 6 0.15
10 26 0.63
11 2 0.05
12 7 0.17
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:168189 original size:21 final size:21
Alignment explanation
Indices: 168135--168184 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
168125 AGTTTTTAAG
168135 ATTTTTTAAATTTTTATAATA
1 ATTTTTTAAATTTTTATAATA
*
168156 ATTTTTTACAATTTTT-T-ATT
1 ATTTTTTA-AATTTTTATAATA
168176 ATTTTTTAA
1 ATTTTTTAA
168185 GAATTCTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 1 0.04
20 10 0.37
21 9 0.33
22 7 0.26
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
ATTTTTTAAATTTTTATAATA
Found at i:168214 original size:19 final size:20
Alignment explanation
Indices: 168192--168230 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
168182 TAAGAATTCT
*
168192 AATATGTTTT-TTAATTTTA
1 AATAAGTTTTATTAATTTTA
168211 AATAAGTTTTATTAATTTTA
1 AATAAGTTTTATTAATTTTA
168231 TATTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
AATAAGTTTTATTAATTTTA
Found at i:168238 original size:9 final size:9
Alignment explanation
Indices: 168226--168287 Score: 54
Period size: 9 Copynumber: 6.3 Consensus size: 9
168216 GTTTTATTAA
168226 TTTTATATT
1 TTTTATATT
168235 TTTTATAATT
1 TTTTAT-ATT
168245 TGTTTGAT-TT
1 T-TTT-ATATT
*
168255 TTTTATAAT
1 TTTTATATT
168264 TTTTATGACTT
1 TTTTAT-A-TT
168275 TTTTAATATT
1 TTTT-ATATT
168285 TTT
1 TTT
168288 ATGAGAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
8 2 0.05
9 16 0.36
10 13 0.30
11 9 0.20
12 4 0.09
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.71
Consensus pattern (9 bp):
TTTTATATT
Found at i:168258 original size:20 final size:20
Alignment explanation
Indices: 168217--168291 Score: 79
Period size: 20 Copynumber: 3.9 Consensus size: 20
168207 TTTAAATAAG
168217 TTTTATTAA-TTTTAT-A-TT
1 TTTTA-TAATTTTTATGACTT
*
168235 TTTTATAATTTGTT-TGATTT
1 TTTTATAATTT-TTATGACTT
168255 TTTTATAATTTTTATGACTT
1 TTTTATAATTTTTATGACTT
168275 TTTTA-ATATTTTTATGA
1 TTTTATA-ATTTTTATGA
168292 GAAAAATATT
Statistics
Matches: 50, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
17 3 0.06
18 8 0.16
19 6 0.12
20 33 0.66
ACGTcount: A:0.25, C:0.01, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTATAATTTTTATGACTT
Found at i:168286 original size:29 final size:29
Alignment explanation
Indices: 168217--168289 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
168207 TTTAAATAAG
* * *
168217 TTTTATTAATTTTATATTTTTTATAA-TT
1 TTTTAATATTTTTATAATTTTTATAACTT
* * *
168245 TGTTTGATTTTTTTATAATTTTTATGACTT
1 T-TTTAATATTTTTATAATTTTTATAACTT
168275 TTTTAATATTTTTAT
1 TTTTAATATTTTTAT
168290 GAGAAAAATA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
28 1 0.03
29 31 0.89
30 3 0.09
ACGTcount: A:0.25, C:0.01, G:0.04, T:0.70
Consensus pattern (29 bp):
TTTTAATATTTTTATAATTTTTATAACTT
Found at i:168773 original size:13 final size:14
Alignment explanation
Indices: 168755--168790 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
168745 AATTTCATTT
168755 AATTTTTA-AATAA
1 AATTTTTAGAATAA
168768 AATTTTTATGAATAA
1 AATTTTTA-GAATAA
168783 AATTTTTA
1 AATTTTTA
168791 CATATTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.38
15 13 0.62
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (14 bp):
AATTTTTAGAATAA
Found at i:169581 original size:27 final size:29
Alignment explanation
Indices: 169540--169594 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
169530 GAAAAGAGTC
* *
169540 AAATTCAAGCATTAAATT-AGATAAAAAG
1 AAATTCAAACATTAAATTAAGAAAAAAAG
169568 AAATT-AAACATTAAATTAAGAAAAAAA
1 AAATTCAAACATTAAATTAAGAAAAAAA
169595 TATAAAGTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.24
Consensus pattern (29 bp):
AAATTCAAACATTAAATTAAGAAAAAAAG
Found at i:170513 original size:43 final size:43
Alignment explanation
Indices: 170452--170538 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
170442 TTTTTATCTG
*
170452 AGCTCAGATACTAAATTATACACAATATCAAAATCCAATCTAA
1 AGCTCAAATACTAAATTATACACAATATCAAAATCCAATCTAA
*
170495 AGCTCAAATACTAAATTATACACAATCTCAAAATCCAATCTAA
1 AGCTCAAATACTAAATTATACACAATATCAAAATCCAATCTAA
170538 A
1 A
170539 ATATTAAAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.49, C:0.22, G:0.03, T:0.25
Consensus pattern (43 bp):
AGCTCAAATACTAAATTATACACAATATCAAAATCCAATCTAA
Found at i:176891 original size:83 final size:83
Alignment explanation
Indices: 176749--176913 Score: 321
Period size: 83 Copynumber: 2.0 Consensus size: 83
176739 AAGCTACTAA
*
176749 ATTCCTGAACTTGTAATCTTGTATGGCAGTAAGCTAAATAAATTATAAAAAAGTTACAGTACAGG
1 ATTCCTGAACTTGTAATCTTGTATGGCAGTAAGCTAAATAAATTATAAAAAAGTAACAGTACAGG
176814 AGAACTTATAAGAAATAC
66 AGAACTTATAAGAAATAC
176832 ATTCCTGAACTTGTAATCTTGTATGGCAGTAAGCTAAATAAATTATAAAAAAGTAACAGTACAGG
1 ATTCCTGAACTTGTAATCTTGTATGGCAGTAAGCTAAATAAATTATAAAAAAGTAACAGTACAGG
176897 AGAACTTATAAGAAATA
66 AGAACTTATAAGAAATA
176914 AACAGTTTTT
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (83 bp):
ATTCCTGAACTTGTAATCTTGTATGGCAGTAAGCTAAATAAATTATAAAAAAGTAACAGTACAGG
AGAACTTATAAGAAATAC
Found at i:180655 original size:89 final size:89
Alignment explanation
Indices: 180512--180710 Score: 265
Period size: 89 Copynumber: 2.2 Consensus size: 89
180502 TTTAAAAAAT
* * ** * *
180512 AAAAAATAAAATTAAGCCCCTACTTTTTTTTTGCACTCCTTTTGGTATTTGAACTTTCAAAATGA
1 AAAAAA-ACAATTAAGCCCCTACATTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGA
* *
180577 ATTAAAAAAGCCCTCAAACCTTTTC
65 ATCAAAAAAACCCTCAAACCTTTTC
* * *
180602 AAGAAAAGCAATTAAGCCCCTA-ATTTTTTTTGCACTCAATTGGGTCCTTGAACTTTCAAAATGC
1 AA-AAAAACAATTAAGCCCCTACATTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGA
*
180666 ATCAAAAAAACCCTCAAACTTTTTC
65 ATCAAAAAAACCCTCAAACCTTTTC
180691 AAAAAAACAATTAAGCCCCT
1 AAAAAAACAATTAAGCCCCT
180711 GCTTTTATTA
Statistics
Matches: 95, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
88 17 0.18
89 59 0.62
90 15 0.16
91 4 0.04
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.32
Consensus pattern (89 bp):
AAAAAAACAATTAAGCCCCTACATTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGAA
TCAAAAAAACCCTCAAACCTTTTC
Found at i:180789 original size:29 final size:27
Alignment explanation
Indices: 180756--180854 Score: 83
Period size: 27 Copynumber: 3.6 Consensus size: 27
180746 AATTAAAATC
* *
180756 AATAAAAGATATAAATATTATTAAATTTT
1 AATAAAAAATATAAATATTA--AAAATTT
**
180785 AATAAAAAATCCAAATATTAAAAATTT
1 AATAAAAAATATAAATATTAAAAATTT
* * *
180812 ATTAAAAAATATAAAAATATAAAAATCGT
1 AATAAAAAATATAAATAT-TAAAAAT-TT
*
180841 AA-AAAATATATAAA
1 AATAAAAAATATAAA
180855 AAATTGTAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
27 20 0.35
28 18 0.32
29 19 0.33
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (27 bp):
AATAAAAAATATAAATATTAAAAATTT
Found at i:180853 original size:20 final size:19
Alignment explanation
Indices: 180824--180895 Score: 72
Period size: 19 Copynumber: 3.6 Consensus size: 19
180814 TAAAAAATAT
180824 AAAAATATAAAAATCGTAA
1 AAAAATATAAAAATCGTAA
*
180843 AAAATATATAAAAAATTGTAA
1 AAAA-ATAT-AAAAATCGTAA
*** *
180864 AATTTTATAAAAATCATAA
1 AAAAATATAAAAATCGTAA
180883 AAAAATTATAAAA
1 AAAAA-TATAAAA
180896 TATAAATAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
19 15 0.37
20 14 0.34
21 12 0.29
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (19 bp):
AAAAATATAAAAATCGTAA
Found at i:180905 original size:31 final size:30
Alignment explanation
Indices: 180842--180936 Score: 86
Period size: 30 Copynumber: 3.1 Consensus size: 30
180832 AAAAATCGTA
* **
180842 AAAAAT-ATATAAAAAATTGTAAAATTTTAT
1 AAAAATCATA-AAAAAATTATAAAATTAAAT
180872 AAAAATCATAAAAAAATTATAAAATATAAAT
1 AAAAATCATAAAAAAATTATAAAAT-TAAAT
* * *
180903 -AAAGTCGTAAAAAAATATACAAAATGTAAAT
1 AAAAATCATAAAAAAAT-TATAAAAT-TAAAT
180934 AAA
1 AAA
180937 TATAAATTTC
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
30 34 0.63
31 18 0.33
32 2 0.04
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.27
Consensus pattern (30 bp):
AAAAATCATAAAAAAATTATAAAATTAAAT
Found at i:181176 original size:10 final size:10
Alignment explanation
Indices: 181158--181205 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
181148 AAAAAAAGTT
*
181158 ATAATTTTTA
1 ATAAATTTTA
181168 ATAAATTTTA
1 ATAAATTTTA
*
181178 A-AATTTTTA
1 ATAAATTTTA
* *
181187 TTAAAATTTA
1 ATAAATTTTA
181197 ATAAATTTT
1 ATAAATTTT
181206 CTAAAATTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
9 7 0.23
10 23 0.77
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
ATAAATTTTA
Found at i:181184 original size:19 final size:19
Alignment explanation
Indices: 181160--181215 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
181150 AAAAAGTTAT
*
181160 AATTTTTAATAAATTTTAA
1 AATTTTTAATAAAATTTAA
*
181179 AATTTTTATTAAAATTTAA
1 AATTTTTAATAAAATTTAA
* *
181198 TAAATTTT-CTAAAATTTA
1 -AATTTTTAATAAAATTTA
181216 TTATTTATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 26 0.81
20 6 0.19
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
AATTTTTAATAAAATTTAA
Found at i:182941 original size:16 final size:16
Alignment explanation
Indices: 182920--182951 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
182910 TTGGGTACAG
182920 AAAAAAGTCAAACGTC
1 AAAAAAGTCAAACGTC
182936 AAAAAAGTCAAACGTC
1 AAAAAAGTCAAACGTC
182952 TAGTGTCACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.19, G:0.12, T:0.12
Consensus pattern (16 bp):
AAAAAAGTCAAACGTC
Found at i:193011 original size:469 final size:469
Alignment explanation
Indices: 192133--193071 Score: 1824
Period size: 469 Copynumber: 2.0 Consensus size: 469
192123 GACATGTGGA
192133 TATACCTCCATTATCGTGTCGGCCCCGAACTCCTTCCTCCATTGGAGCATATCAGCCCACATGAG
1 TATACCTCCATTATCGTGTCGGCCCCGAACTCCTTCCTCCATTGGAGCATATCAGCCCACATGAG
*
192198 CTTTGCTTTATCAAGATCATATTTCCTGGCCCTAAGAAATCTGTATGATCAAAGAATGAGTTAAT
66 CTTTGCTTTATCAAGATCATATTTCCTGGCCCTAAGAAATCTGTATGATCAAAGAAGGAGTTAAT
* *
192263 GGCCTAACCTAATGCCATTCGTATCGAAGCTTAGTATTGTTGAATGGAAGATAGTGACCTTAGCA
131 GGCCTAACCTAATACCATTCCTATCGAAGCTTAGTATTGTTGAATGGAAGATAGTGACCTTAGCA
* *
192328 TCATATGATGATCATCATGTTTAGCAGGCAGTAATTCATCTAAGATGAGTGCTTGGCGGAGTGCA
196 TCATATGATGATCATCATGTTTAGCAGGCAGTAATTCATCTAAGATGAGTGCCTGGCGGAATGCA
192393 TCCACTGCCTGCAGCTCTTCAGAATCAAGGCCATCCTCTATATTAACAACCGACATTACTCTACT
261 TCCACTGCCTGCAGCTCTTCAGAATCAAGGCCATCCTCTATATTAACAACCGACATTACTCTACT
192458 ATGTCTTCTGCTTTTCTTTCTCATTGAATGTCTAAACTTGCTAGAGGCACTCAATGCCTTTTTCT
326 ATGTCTTCTGCTTTTCTTTCTCATTGAATGTCTAAACTTGCTAGAGGCACTCAATGCCTTTTTCT
192523 TAAGAGACCCAAGCTTTTTTTTCTTCTCATCCTCCGAGTTATATATATCAATTTTTTCTGCACCT
391 TAAGAGACCCAAGCTTTTTTTTCTTCTCATCCTCCGAGTTATATATATCAATTTTTTCTGCACCT
192588 GTAAAACAAGCCAC
456 GTAAAACAAGCCAC
192602 TATACCTCCATTATCGTGTCGGCCCCGAACTCCTTCCTCCATTGGAGCATATCAGCCCACATGAG
1 TATACCTCCATTATCGTGTCGGCCCCGAACTCCTTCCTCCATTGGAGCATATCAGCCCACATGAG
192667 CTTTGCTTTATCAAGATCATATTTCCTGGCCCTAAGAAATCTGTATGATCAAAGAAGGAGTTAAT
66 CTTTGCTTTATCAAGATCATATTTCCTGGCCCTAAGAAATCTGTATGATCAAAGAAGGAGTTAAT
192732 GGCCTAACCTAATACCATTCCTATCGAAGCTTAGTATTGTTGAATGGAAGATAGTGACCTTAGCA
131 GGCCTAACCTAATACCATTCCTATCGAAGCTTAGTATTGTTGAATGGAAGATAGTGACCTTAGCA
192797 TCATATGATGATCATCATGTTTAGCAGGCAGTAATTCATCTAAGATGAGTGCCTGGCGGAATGCA
196 TCATATGATGATCATCATGTTTAGCAGGCAGTAATTCATCTAAGATGAGTGCCTGGCGGAATGCA
*
192862 TCCACTGCCTGTAGCTCTTCAGAATCAAGGCCATCCTCTATATTAACAACCGACATTACTCTACT
261 TCCACTGCCTGCAGCTCTTCAGAATCAAGGCCATCCTCTATATTAACAACCGACATTACTCTACT
192927 ATGTCTTCTGCTTTTCTTTCTCATTGAATGTCTAAACTTGCTAGAGGCACTCAATGCCTTTTTCT
326 ATGTCTTCTGCTTTTCTTTCTCATTGAATGTCTAAACTTGCTAGAGGCACTCAATGCCTTTTTCT
192992 TAAGAGACCCAAGCTTTTTTTTCTTCTCATCCTCCGAGTTATATATATCAATTTTTTCTGCACCT
391 TAAGAGACCCAAGCTTTTTTTTCTTCTCATCCTCCGAGTTATATATATCAATTTTTTCTGCACCT
193057 GTAAAACAAGCCAC
456 GTAAAACAAGCCAC
193071 T
1 T
193072 CTCAAACCCC
Statistics
Matches: 464, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
469 464 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (469 bp):
TATACCTCCATTATCGTGTCGGCCCCGAACTCCTTCCTCCATTGGAGCATATCAGCCCACATGAG
CTTTGCTTTATCAAGATCATATTTCCTGGCCCTAAGAAATCTGTATGATCAAAGAAGGAGTTAAT
GGCCTAACCTAATACCATTCCTATCGAAGCTTAGTATTGTTGAATGGAAGATAGTGACCTTAGCA
TCATATGATGATCATCATGTTTAGCAGGCAGTAATTCATCTAAGATGAGTGCCTGGCGGAATGCA
TCCACTGCCTGCAGCTCTTCAGAATCAAGGCCATCCTCTATATTAACAACCGACATTACTCTACT
ATGTCTTCTGCTTTTCTTTCTCATTGAATGTCTAAACTTGCTAGAGGCACTCAATGCCTTTTTCT
TAAGAGACCCAAGCTTTTTTTTCTTCTCATCCTCCGAGTTATATATATCAATTTTTTCTGCACCT
GTAAAACAAGCCAC
Found at i:195777 original size:156 final size:156
Alignment explanation
Indices: 195488--195804 Score: 589
Period size: 156 Copynumber: 2.0 Consensus size: 156
195478 ATGAATGGTT
*
195488 GGAGCTGTCATAAATTGGCTAACAACACCGGTTGCATATGCGATATCTAGACAAGTTAGTGTGAG
1 GGAGTTGTCATAAATTGGCTAACAACACCGGTTGCATATGCGATATCTAGACAAGTTAGTGTGAG
*
195553 ATAGTTCAACTTTTCTACCAATCTTCTATACCTCTTAGGGTTGTCAAATAAACCACCATCTTCTT
66 ATAGTTCAACTTTTCTACCAATCTTCTATACCTCTTAGGGTTCTCAAATAAACCACCATCTTCTT
*
195618 TTGTGAGATGTAGATTAGGAATCATA
131 TTGTGAGATGTAGAGTAGGAATCATA
* *
195644 GGAGTTGTCATAAATTGGCTAACAACACCGGTTGCATGTGCGATATCTAGACAGGTTAGTGTGAG
1 GGAGTTGTCATAAATTGGCTAACAACACCGGTTGCATATGCGATATCTAGACAAGTTAGTGTGAG
195709 ATAGTTCAACTTTTCTACCAATCTTCTATACCTCTTAGGGTTCTCAAATAAACCACCATCTTCTT
66 ATAGTTCAACTTTTCTACCAATCTTCTATACCTCTTAGGGTTCTCAAATAAACCACCATCTTCTT
195774 TTGTGAGATGTAGAGTAGGAATCATA
131 TTGTGAGATGTAGAGTAGGAATCATA
195800 GGAGT
1 GGAGT
195805 GTTGCCCGAT
Statistics
Matches: 156, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
156 156 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Consensus pattern (156 bp):
GGAGTTGTCATAAATTGGCTAACAACACCGGTTGCATATGCGATATCTAGACAAGTTAGTGTGAG
ATAGTTCAACTTTTCTACCAATCTTCTATACCTCTTAGGGTTCTCAAATAAACCACCATCTTCTT
TTGTGAGATGTAGAGTAGGAATCATA
Found at i:198113 original size:31 final size:30
Alignment explanation
Indices: 198049--198113 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
198039 TATAGTTATT
* * *
198049 AAGATAAGTTCTCAATTAAATTAATGTGGG
1 AAGATAAGTTCTCAATCAAATTAATATGAG
*
198079 AAGATTAAGTTCTCAATCAAATTCATATGAG
1 AAGA-TAAGTTCTCAATCAAATTAATATGAG
198110 AAGA
1 AAGA
198114 ATATTACTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.31
Consensus pattern (30 bp):
AAGATAAGTTCTCAATCAAATTAATATGAG
Found at i:199626 original size:18 final size:18
Alignment explanation
Indices: 199603--199641 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
199593 AGTTGACATG
199603 ATCGGTTAGATCATCCCA
1 ATCGGTTAGATCATCCCA
199621 ATCGGTTAGATCATCCCA
1 ATCGGTTAGATCATCCCA
199639 ATC
1 ATC
199642 AACAATGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (18 bp):
ATCGGTTAGATCATCCCA
Found at i:216234 original size:63 final size:63
Alignment explanation
Indices: 216135--216289 Score: 301
Period size: 63 Copynumber: 2.5 Consensus size: 63
216125 GATAAATTAA
216135 TGTAAAAGCAGATTCCTCCTTATCTGCTTGTGTCCTTTATGTATGAGTCATGTCCTTTACGTT
1 TGTAAAAGCAGATTCCTCCTTATCTGCTTGTGTCCTTTATGTATGAGTCATGTCCTTTACGTT
*
216198 TGTAAAAGTAGATTCCTCCTTATCTGCTTGTGTCCTTTATGTATGAGTCATGTCCTTTACGTT
1 TGTAAAAGCAGATTCCTCCTTATCTGCTTGTGTCCTTTATGTATGAGTCATGTCCTTTACGTT
216261 TGTAAAAGCAGATTCCTCCTTATCTGCTT
1 TGTAAAAGCAGATTCCTCCTTATCTGCTT
216290 ACTACTACCT
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 90 1.00
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.43
Consensus pattern (63 bp):
TGTAAAAGCAGATTCCTCCTTATCTGCTTGTGTCCTTTATGTATGAGTCATGTCCTTTACGTT
Found at i:221975 original size:26 final size:27
Alignment explanation
Indices: 221936--221986 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
221926 AATAATTTGT
*
221936 AATATATAACAATTATATAAAAATAAA
1 AATATATAACAATTATAAAAAAATAAA
221963 AATATATAA-AATTATAAAAAAATA
1 AATATATAACAATTATAAAAAAATA
221987 TTTCTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (27 bp):
AATATATAACAATTATAAAAAAATAAA
Found at i:221979 original size:18 final size:16
Alignment explanation
Indices: 221949--221987 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
221939 ATATAACAAT
221949 TATATAAAAATAAAAA
1 TATATAAAAATAAAAA
221965 TATATAAAATTATAAAAA
1 TATATAAAA--ATAAAAA
*
221983 AATAT
1 TATAT
221988 TTCTTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
18 11 0.55
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
TATATAAAAATAAAAA
Found at i:222293 original size:64 final size:65
Alignment explanation
Indices: 222225--222350 Score: 184
Period size: 64 Copynumber: 2.0 Consensus size: 65
222215 TTTCGATATT
* * * *
222225 TTTAAATAATTTTT-ACACATATATTTATAGCCTAA-TTTTAGTTTCTTGATAAATTATATATAC
1 TTTAAAT-ATTTTTCACACATATATTTATAGCCTAATTTTTAATTTCTTAACAAACTATATATAC
222288 A
65 A
*
222289 TTTAAATATTTTTCACACATATATTTATAGTCTAATTTTTAATTTCTTAACAAACTATATAT
1 TTTAAATATTTTTCACACATATATTTATAGCCTAATTTTTAATTTCTTAACAAACTATATAT
222351 TAGTTTGGTA
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
63 6 0.11
64 27 0.49
65 22 0.40
ACGTcount: A:0.37, C:0.10, G:0.03, T:0.49
Consensus pattern (65 bp):
TTTAAATATTTTTCACACATATATTTATAGCCTAATTTTTAATTTCTTAACAAACTATATATACA
Found at i:228187 original size:27 final size:27
Alignment explanation
Indices: 228125--228177 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
228115 ACAACTAATC
**
228125 ATAGCCTTTGTGGTGAACTCTAAAAGA
1 ATAGCCTTTGTGGCAAACTCTAAAAGA
228152 ATAGCCTTTGTGGCAAACTCTAAAAG
1 ATAGCCTTTGTGGCAAACTCTAAAAG
228178 GGATGCCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (27 bp):
ATAGCCTTTGTGGCAAACTCTAAAAGA
Found at i:237951 original size:31 final size:30
Alignment explanation
Indices: 237895--237984 Score: 81
Period size: 31 Copynumber: 2.9 Consensus size: 30
237885 TAATAAGGGT
* *
237895 AATTTTATATTATCAATCATTAAATTATGGACA
1 AATTTTA-ATT-TAAATCACTAAATTATGGA-A
* *** *
237928 AATTTTCATTTTGGTCACTAAATTATTTGAA
1 AATTTTAATTTAAATCACTAAATTA-TGGAA
237959 AATTTTAATTTAAATCACTAAATTAT
1 AATTTTAATTTAAATCACTAAATTAT
237985 TTAAGTTATT
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
30 1 0.02
31 33 0.72
32 6 0.13
33 6 0.13
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.46
Consensus pattern (30 bp):
AATTTTAATTTAAATCACTAAATTATGGAA
Found at i:247508 original size:40 final size:40
Alignment explanation
Indices: 247436--247511 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
247426 TAAACTGATG
*
247436 CCACGTCAGCAAATCGCGTCCTAGAGGGCGCGATTTGTGT
1 CCACGTCAGCAAATCGCGTCCTAGAGGACGCGATTTGTGT
* *
247476 CCACGTCAGCAAATCGCG-CTTACGTGGACGCGATTT
1 CCACGTCAGCAAATCGCGTCCTA-GAGGACGCGATTT
247512 CCTGGCGCGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 3 0.09
40 29 0.91
ACGTcount: A:0.21, C:0.29, G:0.28, T:0.22
Consensus pattern (40 bp):
CCACGTCAGCAAATCGCGTCCTAGAGGACGCGATTTGTGT
Found at i:251099 original size:51 final size:51
Alignment explanation
Indices: 250972--251258 Score: 231
Period size: 51 Copynumber: 5.6 Consensus size: 51
250962 AGTTGCTAGG
* * * * * **
250972 TCACATGTGTAGTACTATGTGCAGGCTATTACGTGTACCGGA-ATGATAAG-
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATA-GCTTCGA
* * * *
251022 TCGCATGTGTAGTACAATGTGCAGGCTACTATGCGTACCGAATAGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
* * * * * *** *
251073 TCACGTGTGTAGTACTATGTGTAGGCTAGTACGTGTATCGGATGAAAAT-GG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAT-AGCTTCGA
* * *
251124 TCACGTGTATAATACTATGTGTAGGCTACTATGCGTACCGGATAGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
* * ** *** *
251175 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATTGGATGAAAAT-GG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAT-AGCTTCGA
*
251226 TCACATGTGTAGTACTATGTGCAGGCTACTATG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATG
251259 TGAACTAGGT
Statistics
Matches: 187, Mismatches: 45, Indels: 9
0.78 0.19 0.04
Matches are distributed among these distances:
50 41 0.22
51 142 0.76
52 4 0.02
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (51 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:251171 original size:102 final size:102
Alignment explanation
Indices: 250972--251258 Score: 425
Period size: 102 Copynumber: 2.8 Consensus size: 102
250962 AGTTGCTAGG
* * * * *
250972 TCACATGTGTAGTACTATGTGCAGGCTATTACGTGTACCGGAATGATAA--GTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGG-ATGAAAATGGTCACATGTGTAGT
*
251035 ACAATGTGCAGGCTACTATGCGTACCGAATAGCTTCGA
65 ACTATGTGCAGGCTACTATGCGTACCGAATAGCTTCGA
* * * * *
251073 TCACGTGTGTAGTACTATGTGTAGGCTAGTACGTGTATCGGATGAAAATGGTCACGTGTATAATA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGGTCACATGTGTAGTA
* *
251138 CTATGTGTAGGCTACTATGCGTACCGGATAGCTTCGA
66 CTATGTGCAGGCTACTATGCGTACCGAATAGCTTCGA
*
251175 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATTGGATGAAAATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGGTCACATGTGTAGTA
251240 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
251259 TGAACTAGGT
Statistics
Matches: 165, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
100 6 0.04
101 37 0.22
102 122 0.74
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCGAATAGCTTCGA
Found at i:261452 original size:25 final size:26
Alignment explanation
Indices: 261424--261474 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
261414 AAAAAACATG
261424 ATTCTTTATTTAAATTTGTAC-AACT
1 ATTCTTTATTTAAATTTGTACTAACT
261449 ATTCTTTATTTAAATTTGTACTAACT
1 ATTCTTTATTTAAATTTGTACTAACT
261475 GATATTTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.53
Consensus pattern (26 bp):
ATTCTTTATTTAAATTTGTACTAACT
Found at i:261482 original size:26 final size:25
Alignment explanation
Indices: 261428--261488 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
261418 AACATGATTC
*
261428 TTTATTTAAATTTGTACAACTATTC
1 TTTATTTAAATTTGTACAACTATTA
261453 TTTATTTAAATTTGTACTAACTGA-TA
1 TTTATTTAAATTTGTAC-AACT-ATTA
*
261479 TTTATCTAAA
1 TTTATTTAAA
261489 AACAAATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 17 0.53
26 14 0.44
27 1 0.03
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (25 bp):
TTTATTTAAATTTGTACAACTATTA
Found at i:262895 original size:16 final size:16
Alignment explanation
Indices: 262828--262899 Score: 72
Period size: 16 Copynumber: 4.5 Consensus size: 16
262818 ACATAAAATT
262828 TTCACTTACCACTTAC
1 TTCACTTACCACTTAC
* * *
262844 ATCACTTACCATTTAT
1 TTCACTTACCACTTAC
* ** *
262860 TTAACTTAGAACTTAT
1 TTCACTTACCACTTAC
*
262876 TTCACTTACCACTTGC
1 TTCACTTACCACTTAC
262892 TTCACTTA
1 TTCACTTA
262900 GCCCTTAGTA
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.28, C:0.28, G:0.03, T:0.42
Consensus pattern (16 bp):
TTCACTTACCACTTAC
Found at i:262997 original size:23 final size:25
Alignment explanation
Indices: 262950--262997 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
262940 ATCACTAAAG
262950 CATCGAAGTGTAGATTACACTTTAA
1 CATCGAAGTGTAGATTACACTTTAA
*
262975 CATCGAAGTGTTG-TT-CACTTTAA
1 CATCGAAGTGTAGATTACACTTTAA
262998 GCACTAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.36
24 2 0.09
25 12 0.55
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (25 bp):
CATCGAAGTGTAGATTACACTTTAA
Found at i:263243 original size:21 final size:22
Alignment explanation
Indices: 263212--263252 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
263202 TTATTTCTCC
*
263212 TCTTGAATTATGTTATTTATGT
1 TCTTGAATTATATTATTTATGT
263234 TCTT-AATTATATTATTTAT
1 TCTTGAATTATATTATTTAT
263253 ACTTATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.61
Consensus pattern (22 bp):
TCTTGAATTATATTATTTATGT
Found at i:263769 original size:18 final size:17
Alignment explanation
Indices: 263742--263776 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
263732 TGAGACTTAA
263742 TTTGTGCTTTAATTCTTC
1 TTTGTGCTTTAA-TCTTC
*
263760 TTTGTTCTTTAATCTTC
1 TTTGTGCTTTAATCTTC
263777 GCACATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.11, C:0.17, G:0.09, T:0.63
Consensus pattern (17 bp):
TTTGTGCTTTAATCTTC
Found at i:268494 original size:4 final size:4
Alignment explanation
Indices: 268476--268560 Score: 62
Period size: 4 Copynumber: 20.5 Consensus size: 4
268466 TATTGTTTAT
* * * * *
268476 TTAA TCAA TTAAA TTAA TTGA TTAA ATAA TTAA CTAAA TTAA TTGA TTAA
1 TTAA TTAA TT-AA TTAA TTAA TTAA TTAA TTAA -TTAA TTAA TTAA TTAA
* * * *
268526 ATAA TTAA CTAAA TTAA TTTA TTAA TTAA ATAA TT
1 TTAA TTAA -TTAA TTAA TTAA TTAA TTAA TTAA TT
268561 TTCTTAACTC
Statistics
Matches: 60, Mismatches: 18, Indels: 6
0.71 0.21 0.07
Matches are distributed among these distances:
4 50 0.83
5 10 0.17
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (4 bp):
TTAA
Found at i:268500 original size:21 final size:21
Alignment explanation
Indices: 268482--268560 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 21
268472 TTATTTAATC
268482 AATTAAATTAATTGATTAAAT
1 AATTAAATTAATTGATTAAAT
268503 AATTAACTAAATTAATTGATTAAAT
1 AA-T---TAAATTAATTGATTAAAT
* * * * *
268528 AATTAACTAAATTAATTTATT
1 AATTAAATTAATTGATTAAAT
268549 AATTAAA-TAATT
1 AATTAAATTAATT
268561 TTCTTAACTC
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
20 4 0.09
21 21 0.45
22 1 0.02
24 1 0.02
25 20 0.43
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.43
Consensus pattern (21 bp):
AATTAAATTAATTGATTAAAT
Found at i:268505 original size:25 final size:25
Alignment explanation
Indices: 268485--268550 Score: 123
Period size: 25 Copynumber: 2.6 Consensus size: 25
268475 TTTAATCAAT
268485 TAAATTAATTGATTAAATAATTAAC
1 TAAATTAATTGATTAAATAATTAAC
268510 TAAATTAATTGATTAAATAATTAAC
1 TAAATTAATTGATTAAATAATTAAC
*
268535 TAAATTAATTTATTAA
1 TAAATTAATTGATTAA
268551 TTAAATAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (25 bp):
TAAATTAATTGATTAAATAATTAAC
Found at i:270526 original size:18 final size:18
Alignment explanation
Indices: 270495--270530 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
270485 TTATTGAAAT
* *
270495 TAAATGCATGAAAAACAC
1 TAAATACATCAAAAACAC
270513 TAAATACATCAAAAACAC
1 TAAATACATCAAAAACAC
270531 ATTACTTACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.19, G:0.06, T:0.17
Consensus pattern (18 bp):
TAAATACATCAAAAACAC
Found at i:274056 original size:21 final size:22
Alignment explanation
Indices: 274027--274073 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
274017 CAGAAGGAGT
*
274027 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
274049 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
274070 GAGT
1 GAGT
274074 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:286849 original size:30 final size:30
Alignment explanation
Indices: 286815--286880 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 30
286805 AAAGGTTGGG
*
286815 CCCTAAAAATTTAACCCTTATGGGAGCAAT
1 CCCTAAAAATTTAACCCATATGGGAGCAAT
* *
286845 CCCT-AAAATTTGACCCATATGTGAGCAAT
1 CCCTAAAAATTTAACCCATATGGGAGCAAT
286874 CCCTAAA
1 CCCTAAA
286881 TACAATATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 26 0.81
30 6 0.19
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.26
Consensus pattern (30 bp):
CCCTAAAAATTTAACCCATATGGGAGCAAT
Found at i:294777 original size:282 final size:285
Alignment explanation
Indices: 294263--294810 Score: 700
Period size: 282 Copynumber: 1.9 Consensus size: 285
294253 ATTGACTCGG
* * * ** *
294263 TGTCACCCTCAATCGGGTCACCAACTAGATTAGGAAGTTACAGGAATGTTCTTCCTTAATTAAAA
1 TGTCACCCTCAATCGGATCACCAACTAGATTAGAAAGTTACAAGAATGCCCTTCCGTAATTAAAA
* *
294328 TAAGTAATATTATTCAAATGTATTTTAATATTTTCATTTTAAAAGAAACCAATAAAAAAATATGC
66 TAAGTAATATTATTCAAAGGTATTTTAATATTTTCACTTTAAAAGAAACCAATAAAAAAATATGC
*
294393 ATATGATGAGATTTGAATCCACACCAATTGCATTAATAAAACATTTAATTTACCATTAAACTAAA
131 ATATGATGAGATTTGAACCCACACCAATTGCATTAATAAAACATTTAATTTACCATTAAACTAAA
* * *
294458 TCTTTTTTTATTATAATTTTATACATTTTAATTTTATTATGCATACTTTATTACATTTATCAGTT
196 GCTTTTTTTATTATAATTTTATACATTTTAATTTTATTATGCAGACTTTATTACATTCATCAGTT
294523 ATATATCTATACTTACTATTATTGA
261 ATATATCTATACTTACTATTATTGA
* * * *
294548 TGTCACGCTCAATCGGATCACCAACTCGGTTAGAAAGTTACAAGAATGCCCTTTCGTAATTAAAA
1 TGTCACCCTCAATCGGATCACCAACTAGATTAGAAAGTTACAAGAATGCCCTTCCGTAATTAAAA
** * * **
294613 TAAGT-ATATT-TTC-GGGGATATTTTAATCTTTTTACTTT-AAA-AAAGTAATAAAAATAATAT
66 TAAGTAATATTATTCAAAGG-TATTTTAATATTTTCACTTTAAAAGAAACCAATAAAAA-AATAT
* * * * *
294673 GCATAT-AGTGCGATTTGAACCCACGCCGATTGCATTAATAAAATC-TTTAATTTATCATTTAAC
129 GCATATGA-TGAGATTTGAACCCACACCAATTGCATTAATAAAA-CATTTAATTTACCATTAAAC
* * *
294736 TAAAGC-TTTTTTA-TATATTTTTATAAACATTTTAATTTTATTATGCAGATTTTATTACATTCG
192 TAAAGCTTTTTTTATTATAATTTTAT--ACATTTTAATTTTATTATGCAGACTTTATTACATTCA
*
294799 TCAGTTGTATAT
255 TCAGTTATATAT
294811 ATTATATTAA
Statistics
Matches: 226, Mismatches: 31, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
280 10 0.04
281 19 0.08
282 111 0.49
283 21 0.09
284 5 0.02
285 60 0.27
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (285 bp):
TGTCACCCTCAATCGGATCACCAACTAGATTAGAAAGTTACAAGAATGCCCTTCCGTAATTAAAA
TAAGTAATATTATTCAAAGGTATTTTAATATTTTCACTTTAAAAGAAACCAATAAAAAAATATGC
ATATGATGAGATTTGAACCCACACCAATTGCATTAATAAAACATTTAATTTACCATTAAACTAAA
GCTTTTTTTATTATAATTTTATACATTTTAATTTTATTATGCAGACTTTATTACATTCATCAGTT
ATATATCTATACTTACTATTATTGA
Found at i:301612 original size:42 final size:42
Alignment explanation
Indices: 301565--301649 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
301555 AGAATATGGG
301565 TTCGAGTGTGCTGAAATGTATTATTCTCCTATTTATTGGGTA
1 TTCGAGTGTGCTGAAATGTATTATTCTCCTATTTATTGGGTA
301607 TTCGAGTGTGCTGAAATGTATTATTCTCCTATTTATTGGGTA
1 TTCGAGTGTGCTGAAATGTATTATTCTCCTATTTATTGGGTA
301649 T
1 T
301650 GGAGGGGCTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.46
Consensus pattern (42 bp):
TTCGAGTGTGCTGAAATGTATTATTCTCCTATTTATTGGGTA
Found at i:302783 original size:22 final size:22
Alignment explanation
Indices: 302757--302825 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
302747 CTTAATAGAT
302757 TTCTGTGCTTAAATTGATTGGA
1 TTCTGTGCTTAAATTGATTGGA
*
302779 TTCTGCT-CCT--A-TGATATAGGA
1 TTCTG-TGCTTAAATTGAT-T-GGA
302800 TT-TGTGCTTAAATTGATTGGA
1 TTCTGTGCTTAAATTGATTGGA
302821 TTCTG
1 TTCTG
302826 CTCCTATGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 16
0.67 0.04 0.29
Matches are distributed among these distances:
19 5 0.14
20 6 0.16
21 10 0.27
22 11 0.30
23 5 0.14
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.45
Consensus pattern (22 bp):
TTCTGTGCTTAAATTGATTGGA
Found at i:302801 original size:21 final size:21
Alignment explanation
Indices: 302776--302843 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
302766 TAAATTGATT
302776 GGATTCTGCTCCTATGATATA
1 GGATTCTGCTCCTATGATATA
* ***
302797 GGATTTGTGCTTAAATTGAT-T-
1 GGA-TTCTGCTCCTA-TGATATA
302818 GGATTCTGCTCCTATGATATA
1 GGATTCTGCTCCTATGATATA
302839 GGATT
1 GGATT
302844 TGAAGTTGAT
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
19 4 0.11
20 8 0.23
21 11 0.31
22 8 0.23
23 4 0.11
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.41
Consensus pattern (21 bp):
GGATTCTGCTCCTATGATATA
Found at i:302815 original size:42 final size:42
Alignment explanation
Indices: 302760--302845 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
302750 AATAGATTTC
302760 TGTGCTTAAATTGATTGGATTCTGCTCCTATGATATAGGATT
1 TGTGCTTAAATTGATTGGATTCTGCTCCTATGATATAGGATT
302802 TGTGCTTAAATTGATTGGATTCTGCTCCTATGATATAGGATT
1 TGTGCTTAAATTGATTGGATTCTGCTCCTATGATATAGGATT
302844 TG
1 TG
302846 AAGTTGATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.23, C:0.12, G:0.22, T:0.43
Consensus pattern (42 bp):
TGTGCTTAAATTGATTGGATTCTGCTCCTATGATATAGGATT
Found at i:307808 original size:11 final size:11
Alignment explanation
Indices: 307788--307817 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
307778 TAAAAAATAA
307788 AAAAAGTATTTT
1 AAAAA-TATTTT
307800 AAAAATATTTT
1 AAAAATATTTT
307811 AAAAATA
1 AAAAATA
307818 AAAAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:310258 original size:14 final size:14
Alignment explanation
Indices: 310222--310263 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
310212 ATAATAGTTG
310222 AATTATAAATGTAAA-
1 AATTA-AAAT-TAAAT
310237 AA-TAAAATTAAAT
1 AATTAAAATTAAAT
310250 AATTAAAATTAAAT
1 AATTAAAATTAAAT
310264 TAGATAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 4 0.16
13 6 0.24
14 13 0.52
15 2 0.08
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (14 bp):
AATTAAAATTAAAT
Found at i:310263 original size:19 final size:19
Alignment explanation
Indices: 310235--310271 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
310225 TATAAATGTA
310235 AAAATAAAATTAAATAATT
1 AAAATAAAATTAAATAATT
* *
310254 AAAATTAAATTAGATAAT
1 AAAATAAAATTAAATAAT
310272 CAAATATGCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
AAAATAAAATTAAATAATT
Done.