Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 94 of 356
Found at i:29603794 original size:222 final size:221
Alignment explanation
Indices: 29603260--29604227 Score: 1172
Period size: 222 Copynumber: 4.4 Consensus size: 221
29603250 ATCTGTTATT
* * * * * *
29603260 TTCGATCTGCTCTTTGAC-AATACAGAGACGCCAAATCTGCTACCTTCGATCTGCTCTCTAACAA
1 TTCGATCTGCTCTCTGTCGAATATAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAA
* * * *
29603324 TACAGAGACGCCAAATTTACTATCTTTGATCTGCTCTCTGACAATACAGAGACGCCAAATCTACT
66 TACAGAGACGCCAAATCTGCTATCTTTGATCTGCTCTCTGACAATACAGAGACGCCAAACCTGCT
* ** * * * ** **
29603389 ACCTTCGATCTGC-CCTCTG-ACAATAC-AGAGACGTCAAATCTGCTATCTTTGAT-TTGTTCTC
131 ATCTTCGATCTGCTCCT-TGTA-AACGCAAG-GATGCCAAA--T-C-ATCTTGGATCTACTTCGA
* * ** * *
29603450 TGACAATACA---GAGGCGCCA-AA-T-CTGTTATC
189 TGA-AAAACATCCGAAG-GTTAGAACTACT-ATGTC
* * * * * * *
29603480 TTTGATCTGCTCTCTGAC-AATACAGAGACGCCAAATCTGCTATCGTCGATCTACACTCTGACAA
1 TTCGATCTGCTCTCTGTCGAATATAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAA
* ** * * *
29603544 TATAGAGACAACAAGTCTGCTATCTTTGATCAGCTCTCTGACAATACAAAGACGCCAAACCTGCT
66 TACAGAGACGCCAAATCTGCTATCTTTGATCTGCTCTCTGACAATACAGAGACGCCAAACCTGCT
29603609 ATCTTCGATCTGCTCCTTGTAAACGCAAGGATGCCAAATCATCTTGGATCTACTTCGATGCAAAA
131 ATCTTCGATCTGCTCCTTGTAAACGCAAGGATGCCAAATCATCTTGGATCTACTTCGATG-AAAA
29603674 ACATCCGAAGGTTAGAACTACTATGTC
195 ACATCCGAAGGTTAGAACTACTATGTC
*
29603701 TTCGATCTGCTCTCTGTCGAATATAGAGATGCCAAATCTGCTATCTTCGATCTACTCTCTGACAA
1 TTCGATCTGCTCTCTGTCGAATATAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAA
* *
29603766 TACAGAGACGCCAAATTTGCTATCTTTGATCTGCTCCCTGACAATACAGAGACGCCAAACCTGCT
66 TACAGAGACGCCAAATCTGCTATCTTTGATCTGCTCTCTGACAATACAGAGACGCCAAACCTGCT
* *
29603831 ATCTTCAATCTGCTCATTGTAAACGCAAGGATGCCAAATCATCTTGGATCTACTTCGATGCAAAA
131 ATCTTCGATCTGCTCCTTGTAAACGCAAGGATGCCAAATCATCTTGGATCTACTTCGATG-AAAA
* *
29603896 ACATCCGAAGGTTAGATCTGCTATGTC
195 ACATCCGAAGGTTAGAACTACTATGTC
* * *
29603923 TTTGATCTGCTCTCTGTCGAATATAGAGATGCCAAATCTACTATCTTCGATCTGCTTTCTGACAA
1 TTCGATCTGCTCTCTGTCGAATATAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAA
* *
29603988 TATAGAGACGCTAAATCTGCTATCTTTGATCTGCT-TCCTGACAATACAGAGACGCCAAACCTGC
66 TACAGAGACGCCAAATCTGCTATCTTTGATCTGCTCT-CTGACAATACAGAGACGCCAAACCTGC
*
29604052 TATCTTCGACCTGCTCCTTGTAAACGCAAGGATGCCAAATCATCTTGGATCTACTTCGATGAAAA
130 TATCTTCGATCTGCTCCTTGTAAACGCAAGGATGCCAAATCATCTTGGATCTACTTCGATGAAAA
*
29604117 ACCATCCGAAGGTTAGATCTGA-TATGTC
195 A-CATCCGAAGGTTAGAACT-ACTATGTC
* * * *
29604145 TTCGATCTGCTCTCTGTCGAATATAGAGATGCCAAATCTGTTTTTTTTCGATCTGTTCTCTGACA
1 TTCGATCTGCTCTCTGTCGAATATAGAGATGCCAAATCTG-CTATCTTCGATCTGCTCTCTGACA
*
29604210 ATACAGAGATGCCAAATC
65 ATACAGAGACGCCAAATC
29604228 ATCTTAGATC
Statistics
Matches: 659, Mismatches: 73, Indels: 29
0.87 0.10 0.04
Matches are distributed among these distances:
216 8 0.01
217 12 0.02
218 2 0.00
219 2 0.00
220 141 0.21
221 31 0.05
222 429 0.65
223 34 0.05
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (221 bp):
TTCGATCTGCTCTCTGTCGAATATAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCTGACAA
TACAGAGACGCCAAATCTGCTATCTTTGATCTGCTCTCTGACAATACAGAGACGCCAAACCTGCT
ATCTTCGATCTGCTCCTTGTAAACGCAAGGATGCCAAATCATCTTGGATCTACTTCGATGAAAAA
CATCCGAAGGTTAGAACTACTATGTC
Found at i:29616333 original size:9 final size:9
Alignment explanation
Indices: 29616319--29616406 Score: 51
Period size: 9 Copynumber: 9.3 Consensus size: 9
29616309 AAACTATGTG
29616319 ATAAATAAT
1 ATAAATAAT
29616328 ATAAATAAT
1 ATAAATAAT
*
29616337 ATAAAAAAT
1 ATAAATAAT
29616346 AATAAA-AAT
1 -ATAAATAAT
29616355 AATAGAATAAGT
1 -ATA-AATAA-T
29616367 GA-AATATAAT
1 -ATAA-ATAAT
29616377 A-AAATAA-
1 ATAAATAAT
29616384 ATAATATATAT
1 ATAA-ATA-AT
29616395 AGTAAA-AAT
1 A-TAAATAAT
29616404 ATA
1 ATA
29616407 TAACATATAA
Statistics
Matches: 67, Mismatches: 2, Indels: 21
0.74 0.02 0.23
Matches are distributed among these distances:
7 1 0.01
8 8 0.12
9 33 0.49
10 11 0.16
11 9 0.13
12 5 0.07
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (9 bp):
ATAAATAAT
Found at i:29616386 original size:31 final size:30
Alignment explanation
Indices: 29616343--29616446 Score: 85
Period size: 31 Copynumber: 3.5 Consensus size: 30
29616333 TAATATAAAA
29616343 AATAATAA-AAATAATAGAATAAGTGAAATAT
1 AATAA-AATAAATAATA-AATAAGTGAAATAT
* *
29616374 AATAAAATAAATAATATATATAGT-AAAAAT
1 AATAAAATAAATAATAAATA-AGTGAAATAT
* *
29616404 ATATAACAT--ATAATAAA-ATGTG-AATAT
1 A-ATAAAATAAATAATAAATAAGTGAAATAT
*
29616431 AATAGAATAAATAATA
1 AATAAAATAAATAATA
29616447 TATATAATAA
Statistics
Matches: 59, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
26 5 0.08
27 7 0.12
28 7 0.12
29 7 0.12
30 11 0.19
31 22 0.37
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.29
Consensus pattern (30 bp):
AATAAAATAAATAATAAATAAGTGAAATAT
Found at i:29616431 original size:57 final size:57
Alignment explanation
Indices: 29616319--29616477 Score: 180
Period size: 57 Copynumber: 2.7 Consensus size: 57
29616309 AAACTATGTG
* * *
29616319 ATAAATAATATAAATAATATAAAAAATAATAA-AAATAATAGAATAAGTGAAATATAATAAA
1 ATAAATAATATATAT-A-ATAAAAAAT-ATAACATATAATA-AA-ATGTGAAATATAATAAA
* *
29616380 ATAAATAATATATATAGTAAAAATATATAACATATAATAAAATGTG-AATATAATAGA
1 ATAAATAATATATATAATAAAAA-ATATAACATATAATAAAATGTGAAATATAATAAA
* *
29616437 ATAAATAATATATATAAT-AAAAACATAACATATAGTAAAAT
1 ATAAATAATATATATAATAAAAAATATAACATATAATAAAAT
29616478 TTATAAAAAT
Statistics
Matches: 88, Mismatches: 8, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
55 17 0.19
56 4 0.05
57 27 0.31
58 4 0.05
59 12 0.14
60 10 0.11
61 14 0.16
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (57 bp):
ATAAATAATATATATAATAAAAAATATAACATATAATAAAATGTGAAATATAATAAA
Found at i:29622676 original size:11 final size:11
Alignment explanation
Indices: 29622660--29622695 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
29622650 CCACCCCAAA
29622660 CATATACATAT
1 CATATACATAT
29622671 CATATACATAT
1 CATATACATAT
* *
29622682 CTTATACTTAT
1 CATATACATAT
29622693 CAT
1 CAT
29622696 GATCATAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.42
Consensus pattern (11 bp):
CATATACATAT
Found at i:29631645 original size:23 final size:24
Alignment explanation
Indices: 29631619--29631764 Score: 86
Period size: 24 Copynumber: 6.2 Consensus size: 24
29631609 GCAAACCCCC
29631619 ATATGTTTTAATTTGTGAA-CCTT
1 ATATGTTTTAATTTGTGAACCCTT
* * * **
29631642 ATATGATTTAGTATGTGAACCCCC
1 ATATGTTTTAATTTGTGAACCCTT
29631666 ATATGTTTT-ATTATGTGAACCCTT
1 ATATGTTTTAATT-TGTGAACCCTT
* * * *
29631690 AT-GGATTTAATATGTGCACCCTT
1 ATATGTTTTAATTTGTGAACCCTT
* * * *
29631713 ATGTGATTT-ATTATGCGAACCCTC
1 ATATGTTTTAATT-TGTGAACCCTT
* * * *
29631737 ATGTGATTTAGTATGTGAA-CCTT
1 ATATGTTTTAATTTGTGAACCCTT
29631760 ATATG
1 ATATG
29631765 CGAACCATGT
Statistics
Matches: 93, Mismatches: 24, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
23 42 0.45
24 50 0.54
25 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.42
Consensus pattern (24 bp):
ATATGTTTTAATTTGTGAACCCTT
Found at i:29631650 original size:47 final size:48
Alignment explanation
Indices: 29631599--29631751 Score: 141
Period size: 47 Copynumber: 3.2 Consensus size: 48
29631589 AACACTTATG
*
29631599 GATTTGGTATGCAAACCCCCATATGTTTTAATT-TGTGAA-CCTTATAT
1 GATTTAGTATGCAAACCCCCATATGTTTT-ATTATGTGAACCCTTATAT
** *
29631646 GATTTAGTATGTGAACCCCCATATGTTTTATTATGTGAACCCTTAT-G
1 GATTTAGTATGCAAACCCCCATATGTTTTATTATGTGAACCCTTATAT
* *** ** * * * * *
29631693 GATTTAATATGTGCACCCTTATGTGATTTATTATGCGAACCCTCATGT
1 GATTTAGTATGCAAACCCCCATATGTTTTATTATGTGAACCCTTATAT
29631741 GATTTAGTATG
1 GATTTAGTATG
29631752 TGAACCTTAT
Statistics
Matches: 89, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
46 3 0.03
47 70 0.79
48 16 0.18
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (48 bp):
GATTTAGTATGCAAACCCCCATATGTTTTATTATGTGAACCCTTATAT
Found at i:29631727 original size:24 final size:24
Alignment explanation
Indices: 29631632--29631761 Score: 140
Period size: 24 Copynumber: 5.5 Consensus size: 24
29631622 TGTTTTAATT
*
29631632 TGTGAA-CCTTATATGATTTAGTA
1 TGTGAACCCTTATGTGATTTAGTA
** * * *
29631655 TGTGAACCCCCATATGTTTTATTA
1 TGTGAACCCTTATGTGATTTAGTA
*
29631679 TGTGAACCCTTATG-GATTTAATA
1 TGTGAACCCTTATGTGATTTAGTA
* *
29631702 TGTGCACCCTTATGTGATTTATTA
1 TGTGAACCCTTATGTGATTTAGTA
* *
29631726 TGCGAACCCTCATGTGATTTAGTA
1 TGTGAACCCTTATGTGATTTAGTA
29631750 TGTGAA-CCTTAT
1 TGTGAACCCTTAT
29631762 ATGCGAACCA
Statistics
Matches: 88, Mismatches: 17, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
23 31 0.35
24 57 0.65
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (24 bp):
TGTGAACCCTTATGTGATTTAGTA
Found at i:29631733 original size:71 final size:69
Alignment explanation
Indices: 29631625--29631761 Score: 175
Period size: 71 Copynumber: 2.0 Consensus size: 69
29631615 CCCCATATGT
* * * *
29631625 TTTAATTTGTGAACCTTATATGATTTAGTATGTGAACCCCCATATGTTTTATTATGTGAACCCTT
1 TTTAATATGTGAACCTTATATGATTTAGTATGCGAACCCCCATATGATTTAGTATGTGAA-CCTT
29631690 ATGGA
65 ATGGA
* * * * *
29631695 TTTAATATGTGCACCCTTATGTGATTTATTATGCGAACCCTCATGTGATTTAGTATGTGAACCTT
1 TTTAATATGTG-AACCTTATATGATTTAGTATGCGAACCCCCATATGATTTAGTATGTGAACCTT
29631760 AT
65 AT
29631762 ATGCGAACCA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
70 16 0.28
71 41 0.72
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.42
Consensus pattern (69 bp):
TTTAATATGTGAACCTTATATGATTTAGTATGCGAACCCCCATATGATTTAGTATGTGAACCTTA
TGGA
Found at i:29631760 original size:47 final size:47
Alignment explanation
Indices: 29631645--29631764 Score: 143
Period size: 47 Copynumber: 2.5 Consensus size: 47
29631635 GAACCTTATA
** * * *
29631645 TGATTTAGTATGTGAACCCCCATATGTTTTATTATGTGAACCCTTATG
1 TGATTTAGTATGTGAA-CCTTATATGATTTATTATGCGAACCCTCATG
* * *
29631693 -GATTTAATATGTGCACCCTTATGTGATTTATTATGCGAACCCTCATG
1 TGATTTAGTATGTG-AACCTTATATGATTTATTATGCGAACCCTCATG
29631740 TGATTTAGTATGTGAACCTTATATG
1 TGATTTAGTATGTGAACCTTATATG
29631765 CGAACCATGT
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
47 46 0.78
48 13 0.22
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (47 bp):
TGATTTAGTATGTGAACCTTATATGATTTATTATGCGAACCCTCATG
Found at i:29631821 original size:28 final size:26
Alignment explanation
Indices: 29631747--29631834 Score: 70
Period size: 28 Copynumber: 3.2 Consensus size: 26
29631737 ATGTGATTTA
* *
29631747 GTATGTGAACCTTATATGCGAACCAT
1 GTATGTGAACCCTATATGCAAACCAT
* * **
29631773 GTATGTGTGAACTCTACATGCAAACTTT
1 GTA--TGTGAACCCTATATGCAAACCAT
29631801 GTATGTGCAAACCCTATATGCAAACC-T
1 GTATGTG--AACCCTATATGCAAACCAT
29631828 GTTATGT
1 G-TATGT
29631835 AAGTGTTAGT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
26 7 0.15
27 2 0.04
28 39 0.81
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (26 bp):
GTATGTGAACCCTATATGCAAACCAT
Found at i:29632599 original size:3 final size:3
Alignment explanation
Indices: 29632591--29632632 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
29632581 AGCATATCAT
*
29632591 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TCTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
29632633 GAATTTTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:29634484 original size:33 final size:31
Alignment explanation
Indices: 29634442--29634502 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 31
29634432 ATGAAATAAT
*
29634442 TATTTCAAATAATTATTATTTTTATATCTAAAA
1 TATTTCAAAT-ATCATTATTTTT-TATCTAAAA
29634475 TATTTCAAATATCATTATTTTTTATCTA
1 TATTTCAAATATCATTATTTTTTATCTA
29634503 CATTGTGGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 6 0.22
32 11 0.41
33 10 0.37
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (31 bp):
TATTTCAAATATCATTATTTTTTATCTAAAA
Found at i:29634782 original size:18 final size:18
Alignment explanation
Indices: 29634756--29634793 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
29634746 AAAATGAATT
29634756 AAAATTTTA-AAATTAAA
1 AAAATTTTATAAATTAAA
*
29634773 AAAATATTTATTAATTAAA
1 AAAAT-TTTATAAATTAAA
29634792 AA
1 AA
29634794 TTAAAAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 4 0.22
19 9 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATTTTATAAATTAAA
Found at i:29637598 original size:17 final size:17
Alignment explanation
Indices: 29637568--29637613 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
29637558 CTCTTCTCCC
29637568 TCTTCTTTCATTTT-TATT
1 TCTT-TTTCATTTTCT-TT
*
29637586 TCTTTTTCTTTTTCTTT
1 TCTTTTTCATTTTCTTT
29637603 TCTTTTT-ATTT
1 TCTTTTTCATTT
29637614 GTGCTTCTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 3 0.12
17 17 0.68
18 5 0.20
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (17 bp):
TCTTTTTCATTTTCTTT
Found at i:29645032 original size:21 final size:22
Alignment explanation
Indices: 29645006--29645052 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
29644996 CTCTGCTCAA
*
29645006 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
29645027 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
29645049 ACTC
1 ACTC
29645053 ACTCCTTCTG
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:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:29649022 original size:13 final size:13
Alignment explanation
Indices: 29649004--29649033 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
29648994 TATTGGTACA
29649004 TTATTTTTTATAT
1 TTATTTTTTATAT
29649017 TTA-TTTTTATAT
1 TTATTTTTTATAT
29649029 TTATT
1 TTATT
29649034 ATATTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTATTTTTTATAT
Found at i:29652768 original size:13 final size:13
Alignment explanation
Indices: 29652750--29652777 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29652740 ATTATTTTAA
29652750 TAGTTTTACTATT
1 TAGTTTTACTATT
29652763 TAGTTTTACTATT
1 TAGTTTTACTATT
29652776 TA
1 TA
29652778 ATTTAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.07, G:0.07, T:0.61
Consensus pattern (13 bp):
TAGTTTTACTATT
Found at i:29653896 original size:68 final size:69
Alignment explanation
Indices: 29653787--29653986 Score: 278
Period size: 68 Copynumber: 2.9 Consensus size: 69
29653777 AATAGTCCGT
29653787 CAGGACAATAAACATGGGATTATATTGTGTAAGACCACAACTAGGCTATGGCAACATATGAAGTT
1 CAGGACAATAAACATGGGATTATATTGTGTAAGACCACAACTAGGCTATGGCAACATATGAAGTT
29653852 C-GC
66 CTGC
* * * * *
29653855 CAGGACAACAAAAAAGGGTTTATATTGTGTAAGACCACAACTAGGCTATGGCAACATATAAAG-T
1 CAGGACAATAAACATGGGATTATATTGTGTAAGACCACAACTAGGCTATGGCAACATATGAAGTT
29653919 CTGC
66 CTGC
* * * * * **
29653923 CAGAACAATAAACATGGGATCATATTGTGTAAGACTACAACTAAGCTATAGTGACATATGAAGT
1 CAGGACAATAAACATGGGATTATATTGTGTAAGACCACAACTAGGCTATGGCAACATATGAAGT
29653987 CCGACATGAT
Statistics
Matches: 113, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
67 2 0.02
68 111 0.98
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (69 bp):
CAGGACAATAAACATGGGATTATATTGTGTAAGACCACAACTAGGCTATGGCAACATATGAAGTT
CTGC
Found at i:29656621 original size:21 final size:21
Alignment explanation
Indices: 29656595--29656634 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29656585 AATAGAAGTT
29656595 GTGAATGACAGGAAATTGACG
1 GTGAATGACAGGAAATTGACG
* *
29656616 GTGAATGATAGGGAATTGA
1 GTGAATGACAGGAAATTGA
29656635 AATGAATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.35, T:0.23
Consensus pattern (21 bp):
GTGAATGACAGGAAATTGACG
Found at i:29659660 original size:17 final size:18
Alignment explanation
Indices: 29659612--29659666 Score: 103
Period size: 18 Copynumber: 3.1 Consensus size: 18
29659602 TGAATTTTAT
29659612 CAAGTTTTATTTCAAAAA
1 CAAGTTTTATTTCAAAAA
29659630 CAAGTTTTATTTCAAAAA
1 CAAGTTTTATTTCAAAAA
29659648 CAAGTTTTA-TTCAAAAA
1 CAAGTTTTATTTCAAAAA
29659665 CA
1 CA
29659667 TTATATTTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 10 0.27
18 27 0.73
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.36
Consensus pattern (18 bp):
CAAGTTTTATTTCAAAAA
Found at i:29660535 original size:20 final size:19
Alignment explanation
Indices: 29660500--29660540 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
29660490 GATTTTTATG
29660500 TAATATTTTAATTATATAAT
1 TAATATTTTAATTATA-AAT
29660520 TAATATTTTAGA-TATAAAT
1 TAATATTTTA-ATTATAAAT
29660539 TA
1 TA
29660541 TGATAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 14 0.70
21 1 0.05
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATATTTTAATTATAAAT
Found at i:29662806 original size:8 final size:8
Alignment explanation
Indices: 29662795--29662827 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
29662785 CTAGATCGGC
29662795 AAAAGCCG
1 AAAAGCCG
29662803 AAAAGCCG
1 AAAAGCCG
29662811 AAATA-CCG
1 AAA-AGCCG
29662819 AAAAGCCG
1 AAAAGCCG
29662827 A
1 A
29662828 CATTTTGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 1 0.04
8 21 0.91
9 1 0.04
ACGTcount: A:0.52, C:0.24, G:0.21, T:0.03
Consensus pattern (8 bp):
AAAAGCCG
Found at i:29663477 original size:20 final size:21
Alignment explanation
Indices: 29663434--29663479 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
29663424 ACTGTTTTGT
29663434 TATGGG-CCAACTGTATTGAA
1 TATGGGCCCAACTGTATTGAA
*
29663454 -ATGGGCCCAACTGTGTT-AA
1 TATGGGCCCAACTGTATTGAA
29663473 TATGGGC
1 TATGGGC
29663480 AAGGCCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGGGCCCAACTGTATTGAA
Found at i:29669176 original size:32 final size:29
Alignment explanation
Indices: 29669105--29669176 Score: 85
Period size: 28 Copynumber: 2.4 Consensus size: 29
29669095 TATAAAATGA
*
29669105 AATTTATTATATATTTTTTCATAATTATTT
1 AATTTATTA-ATATTTTTTAATAATTATTT
29669135 -A-TTATTAATATTTTATTAATTCAATTATTT
1 AATTTATTAATATTTT-TTAA-T-AATTATTT
29669165 AATTTATTAATA
1 AATTTATTAATA
29669177 AAATATATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
27 7 0.19
28 9 0.25
29 2 0.06
30 8 0.22
31 1 0.03
32 9 0.25
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (29 bp):
AATTTATTAATATTTTTTAATAATTATTT
Found at i:29673492 original size:25 final size:27
Alignment explanation
Indices: 29673455--29673504 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
29673445 TCAAACATGC
29673455 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
29673481 ATTTCGGT-AATTTATCTCCTAGGG
1 ATTTAGGTCAATTTAACTCCTAGGG
29673505 TAAAACTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:29675029 original size:26 final size:26
Alignment explanation
Indices: 29674993--29675076 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
29674983 CATGAAAGTC
29674993 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
29675019 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
29675045 TTATCATGGAACATTTACCTAAACTA
1 TTATCATGAAACATTTACCTAACCCA
29675071 TTATCA
1 TTATCA
29675077 ATTTGTATCA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:29683129 original size:26 final size:26
Alignment explanation
Indices: 29683093--29683176 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
29683083 CATGAAATTC
29683093 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
29683119 TTATCATGAAACATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
29683145 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
29683171 TTATCA
1 TTATCA
29683177 ATTTGTATCA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:29683520 original size:45 final size:45
Alignment explanation
Indices: 29683467--29683641 Score: 242
Period size: 45 Copynumber: 3.8 Consensus size: 45
29683457 GACAATGTTA
*
29683467 TGAGAGCCAGTGTAAGACCATGTTGGACATGGCATCGGCATTGAT
1 TGAGAGCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTTGAT
29683512 TGAGAGCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTTGAT
1 TGAGAGCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTTGAT
* * * * *
29683557 TGTGAGCCAGTGTAAGACCATGTTGGACACGGCATCTGCGTGGAGA
1 TGAGAGCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTTGA-T
* * *
29683603 CGAGAGCTAGCGTAAGACCATGTCTGGGACATGGCATCG
1 TGAGAGCCAGTGTAAGACCATGT-T-GGACATGGCATCG
29683642 ACCTCGACAT
Statistics
Matches: 115, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
45 84 0.73
46 19 0.17
47 1 0.01
48 11 0.10
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (45 bp):
TGAGAGCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTTGAT
Found at i:29687173 original size:14 final size:15
Alignment explanation
Indices: 29687135--29687179 Score: 65
Period size: 14 Copynumber: 3.0 Consensus size: 15
29687125 TATAGTATCG
*
29687135 TATCTTGGAATTTCTC
1 TATCTTGG-ATTTCTT
29687151 TATCTTGGATTTCTT
1 TATCTTGGATTTCTT
29687166 TA-CTTGGATTTCTT
1 TATCTTGGATTTCTT
29687180 GTTATCTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 12 0.43
15 8 0.29
16 8 0.29
ACGTcount: A:0.16, C:0.16, G:0.13, T:0.56
Consensus pattern (15 bp):
TATCTTGGATTTCTT
Found at i:29691631 original size:48 final size:45
Alignment explanation
Indices: 29691579--29691843 Score: 177
Period size: 45 Copynumber: 5.8 Consensus size: 45
29691569 GGGCGATATG
* *
29691579 TGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACAT-TTCA
1 TGTGCCAGTGTAAGACCATGT-TGGGACATGGCATCA-ACA-ATGTT-A
*
29691627 TGTGCCAGTGTAAGACCATGTTTGGAACATGGCATCAACAATGTTA
1 TGTGCCAGTGTAAGACCATG-TTGGGACATGGCATCAACAATGTTA
* ** **
29691673 TGAGAGCCAGTGTAAGACCATGTT-GGACATGGCATCGGCGTTGATTGA
1 T--GTGCCAGTGTAAGACCATGTTGGGACATGGCATCAACAATG-TT-A
* * * **
29691721 -GAGCCAGTGTAAAACCATGTT-GGACATGGCATCAGCGTTGATTGA
1 TGTGCCAGTGTAAGACCATGTTGGGACATGGCATCAACAATG-TT-A
* * * ** *
29691766 -GAGCCAGTGTAAAACCATGTT-GGACAAGGCATCGGCATTGATTGA
1 TGTGCCAGTGTAAGACCATGTTGGGACATGGCATCAACAATG-TT-A
*
29691811 -GAGCCAGTGTAAGACCATGTT-GGACATGGCATC
1 TGTGCCAGTGTAAGACCATGTTGGGACATGGCATC
29691844 GGCGTTGATT
Statistics
Matches: 195, Mismatches: 16, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
45 116 0.59
46 18 0.09
47 8 0.04
48 52 0.27
49 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (45 bp):
TGTGCCAGTGTAAGACCATGTTGGGACATGGCATCAACAATGTTA
Found at i:29691938 original size:48 final size:45
Alignment explanation
Indices: 29691630--29691989 Score: 398
Period size: 45 Copynumber: 7.8 Consensus size: 45
29691620 CATTTCATGT
** * *
29691630 GCCAGTGTAAGACCATGTTTGGAACATGGCATCAACAATGTTATGAGA
1 GCCAGTGTAAGACCATG-TTGG-ACATGGCATCGGCATTGAT-TGAGA
*
29691678 GCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTTGATTGAGA
1 GCCAGTGTAAGACCATGTTGGACATGGCATCGGCATTGATTGAGA
* * *
29691723 GCCAGTGTAAAACCATGTTGGACATGGCATCAGCGTTGATTGAGA
1 GCCAGTGTAAGACCATGTTGGACATGGCATCGGCATTGATTGAGA
* *
29691768 GCCAGTGTAAAACCATGTTGGACAAGGCATCGGCATTGATTGAGA
1 GCCAGTGTAAGACCATGTTGGACATGGCATCGGCATTGATTGAGA
* *
29691813 GCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTTGATTGTGA
1 GCCAGTGTAAGACCATGTTGGACATGGCATCGGCATTGATTGAGA
* * * * **
29691858 GCCAATGGAAGACCATGTTGGACATGGTATCGGCATGGAGACGAGA
1 GCCAGTGTAAGACCATGTTGGACATGGCATCGGCATTGA-TTGAGA
* * * *
29691904 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGACAT-ATGA
1 GCCAGTGTAAGACCATGT-T-GGACATGGCATCGGCATTGA-TTGA-GA
* * *
29691952 GCTAGTGTAAGACCATGTCCGGGACATGGCATCAGCAT
1 GCCAGTGTAAGACCATGT--TGGACATGGCATCGGCAT
29691990 CTTACCCTAT
Statistics
Matches: 274, Mismatches: 33, Indels: 10
0.86 0.10 0.03
Matches are distributed among these distances:
45 165 0.60
46 32 0.12
47 6 0.02
48 70 0.26
49 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (45 bp):
GCCAGTGTAAGACCATGTTGGACATGGCATCGGCATTGATTGAGA
Found at i:29694151 original size:21 final size:21
Alignment explanation
Indices: 29694104--29694154 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
29694094 CTTGCACAAA
*
29694104 GTATCAATATCTTTGTAATAG
1 GTATCGATATCTTTGTAATAG
*
29694125 GTATCGATAT-TTTGTTATTAG
1 GTATCGATATCTTTG-TAATAG
29694146 GTATCGATA
1 GTATCGATA
29694155 CCAAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (21 bp):
GTATCGATATCTTTGTAATAG
Found at i:29696770 original size:17 final size:17
Alignment explanation
Indices: 29696744--29696779 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
29696734 AAAATTAAAT
* *
29696744 ATTTTGATATGACACTA
1 ATTTTAATATAACACTA
29696761 ATTTTAATATAACACTA
1 ATTTTAATATAACACTA
29696778 AT
1 AT
29696780 GACCTCGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.42
Consensus pattern (17 bp):
ATTTTAATATAACACTA
Found at i:29705676 original size:43 final size:43
Alignment explanation
Indices: 29705629--29705780 Score: 150
Period size: 43 Copynumber: 3.6 Consensus size: 43
29705619 TGTGTTCTCA
*
29705629 TGTAAGACCACGTCTGGGACTTTGGCATCGATATGTGATTAAG
1 TGTAAGACCACGTCTGGGACATTGGCATCGATATGTGATTAAG
* * ** * *
29705672 TGTAAGACCATGTCGGGGACATCAGCATCG-TATTTGATT-CG
1 TGTAAGACCACGTCTGGGACATTGGCATCGATATGTGATTAAG
* * * *
29705713 TGTAAGACC-CTATCTGGGGCAGTGACATCGATATGTGATTACA-
1 TGTAAGACCAC-GTCTGGGACATTGGCATCGATATGTGATTA-AG
*
29705756 TGTAAGACCACGTCTGGGACGTTGG
1 TGTAAGACCACGTCTGGGACATTGG
29705781 AATTGTACGA
Statistics
Matches: 82, Mismatches: 22, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
41 22 0.27
42 16 0.20
43 43 0.52
44 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.28
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACATTGGCATCGATATGTGATTAAG
Found at i:29723398 original size:41 final size:41
Alignment explanation
Indices: 29723352--29723434 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
29723342 TTTATTTTAA
29723352 TAGTTTCAATTTTTTTCCTACTTATTTAATTGACTCAATGT
1 TAGTTTCAATTTTTTTCCTACTTATTTAATTGACTCAATGT
29723393 TAGTTTCAATTTTTTTCCTACTTATTTAATTGACTCAATGT
1 TAGTTTCAATTTTTTTCCTACTTATTTAATTGACTCAATGT
29723434 T
1 T
29723435 TAGACTTTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.24, C:0.14, G:0.07, T:0.54
Consensus pattern (41 bp):
TAGTTTCAATTTTTTTCCTACTTATTTAATTGACTCAATGT
Found at i:29725626 original size:18 final size:18
Alignment explanation
Indices: 29725603--29725643 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
29725593 TACTTTTCTC
29725603 TTTCTA-TCACAATTCCAA
1 TTTCTATTCACAATT-CAA
*
29725621 TTTCTATTCATAATTCAA
1 TTTCTATTCACAATTCAA
29725639 TTTCT
1 TTTCT
29725644 TTTTTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.29, C:0.22, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTCTATTCACAATTCAA
Found at i:29725819 original size:39 final size:40
Alignment explanation
Indices: 29725776--29725887 Score: 106
Period size: 39 Copynumber: 2.8 Consensus size: 40
29725766 TTGGATCGTT
*
29725776 CGAAGTAATAGTTGACACCCAGTGTCTCATCG-GCCTAGC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGC
* ** * *
29725815 CGAAGTAA-AGTTCG-TACCCAGTACCTCATCGAATCTATC
1 CGAAGTAATAGTT-GACACCCAGTGTCTCATCGAACCTAGC
*
29725854 CGAAGAAATTTAG-TGACACCCAGTGTCTCATCGA
1 CGAAGTAA--TAGTTGACACCCAGTGTCTCATCGA
29725888 CTCGAGGTCG
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
38 18 0.32
39 20 0.35
40 1 0.02
41 16 0.28
42 2 0.04
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (40 bp):
CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGC
Found at i:29727650 original size:46 final size:46
Alignment explanation
Indices: 29727601--29727770 Score: 163
Period size: 46 Copynumber: 3.7 Consensus size: 46
29727591 GGCATCTGAG
*
29727601 CTCGTTGAGTTGAGT-TCGAGTTCACTTATGGATGCGAATGTCCGAG
1 CTCGTTGAGTTGAGTCT-GAGTTCACTTATGGATGCGAATGTCCGAA
* * * * *
29727647 CTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATCTGAA
1 CTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAA-T--G--TCCGAA
**
29727694 CTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAA-CACCTGAA
1 CTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATGTCC-GAA
29727740 CTCGTTGAGTTGAGTCTGAGTTCACTTATGG
1 CTCGTTGAGTTGAGTCTGAGTTCACTTATGG
29727771 GTAGGTTACA
Statistics
Matches: 100, Mismatches: 13, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 4 0.04
46 55 0.55
47 26 0.26
48 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (46 bp):
CTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATGTCCGAA
Found at i:29727750 original size:93 final size:93
Alignment explanation
Indices: 29727591--29727762 Score: 267
Period size: 93 Copynumber: 1.8 Consensus size: 93
29727581 AGGATATTTG
* ** *
29727591 GGCATCTGAGCTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATGTCCGAGCTCGTTGAG
1 GGCATCTGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATCACCGAACTCGTTGAG
29727656 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
29727684 GGCATCTGAACTCGTTGAGTTGAG-TCTGAGTTCACTTATGGATGCGAA-CACCTGAACTCGTTG
1 GGCATCTGAACTCGTTGAGTTGAGTTC-GAGTTCACTTATGGATGCGAATCACC-GAACTCGTTG
*
29727747 AGTTGAGTCTGAGTTC
64 AGTTGAGTCCGAGTTC
29727763 ACTTATGGGT
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
92 4 0.06
93 68 0.94
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (93 bp):
GGCATCTGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATCACCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:29729287 original size:9 final size:9
Alignment explanation
Indices: 29729269--29729299 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
29729259 GTAGTGATTC
*
29729269 AATTCAGGT
1 AATTCGGGT
29729278 AATTCGGGT
1 AATTCGGGT
29729287 AATTCGGGT
1 AATTCGGGT
29729296 AATT
1 AATT
29729300 TGGTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.35
Consensus pattern (9 bp):
AATTCGGGT
Found at i:29729326 original size:17 final size:17
Alignment explanation
Indices: 29729284--29729326 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
29729274 AGGTAATTCG
*
29729284 GGTAATTCGGGTAATTT
1 GGTAATTTGGGTAATTT
* *
29729301 GGTTAATTTGGTTACTTT
1 GG-TAATTTGGGTAATTT
29729319 GGTAATTT
1 GGTAATTT
29729327 TTAACCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.21, C:0.05, G:0.26, T:0.49
Consensus pattern (17 bp):
GGTAATTTGGGTAATTT
Found at i:29731937 original size:40 final size:40
Alignment explanation
Indices: 29731863--29732087 Score: 303
Period size: 40 Copynumber: 5.6 Consensus size: 40
29731853 AACCCAAGTA
* * * *
29731863 CCTTCGGGATTTAG-CTGGATATAG-CAACTCGCACACATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
*
29731902 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
29731942 CCTTCGGGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATG
* *
29731985 CCTTCGGGACTTCGTCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
29732025 CCTTCGGGACTTAGCCCGGATATGGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
29732065 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
29732088 CATCCGAATA
Statistics
Matches: 166, Mismatches: 13, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
39 13 0.08
40 116 0.70
41 1 0.01
43 35 0.21
44 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:29731986 original size:83 final size:83
Alignment explanation
Indices: 29731863--29732087 Score: 313
Period size: 83 Copynumber: 2.8 Consensus size: 83
29731853 AACCCAAGTA
* * * *
29731863 CCTTCGGGATTTAG-CTGGATATAG-CA--ACTCGCACACATGCCTTCGGGTCTTAGCCCGGATA
1 CCTTCGGGACTTAGCCCGGATATAGTCACTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA
29731924 TAGTCACTAGCACAAATG
66 TAGTCACTAGCACAAATG
* * *
29731942 CCTTCGGGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATGCCTTCGGGACTTCGTCCGGAT
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTACTCGCACAAATGCCTTCGGGACTTAGCCCGGAT
29732006 ATAGTCACTAGCACAAATG
65 ATAGTCACTAGCACAAATG
*
29732025 CCTTCGGGACTTAGCCCGGATATGGTCACTA---GCACAAATGCCTTCGGGACTTAGCCCGGATA
1 CCTTCGGGACTTAGCCCGGATATAGTCACTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA
29732087 T
66 T
29732088 CATCCGAATA
Statistics
Matches: 130, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
79 13 0.10
80 39 0.30
81 1 0.01
83 76 0.58
84 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (83 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA
TAGTCACTAGCACAAATG
Found at i:29739758 original size:40 final size:40
Alignment explanation
Indices: 29739684--29739868 Score: 241
Period size: 40 Copynumber: 4.6 Consensus size: 40
29739674 AACCCAAGTA
* * *
29739684 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACACATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATG
*
29739723 CCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATG
* *
29739763 CCTTCGGGACTTAGCCCGGGTATAGCAACTACTCGCACAAATA
1 CCTTCGGGACTTAGCCCGGATATAGCAACTA---GCACAAATG
*
29739806 CCTTCGGGACTTCGCCCGGATATAGTC-ACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATG
29739846 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
29739869 CATCCGAATA
Statistics
Matches: 128, Mismatches: 11, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
39 13 0.10
40 78 0.61
41 1 0.01
43 35 0.27
44 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATG
Found at i:29739810 original size:83 final size:80
Alignment explanation
Indices: 29739684--29739868 Score: 282
Period size: 83 Copynumber: 2.3 Consensus size: 80
29739674 AACCCAAGTA
* * * *
29739684 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACACATGCCTTCGGGTCTTAGCCCGGATATAG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATACCTTCGGGACTTAGCCCGGATATAG
29739748 TCACTAGCACAAATG
66 TCACTAGCACAAATG
* *
29739763 CCTTCGGGACTTAGCCCGGGTATAGCAACTACTCGCACAAATACCTTCGGGACTTCGCCCGGATA
1 CCTTCGGGACTTAGCCCGGATATAGC-A--ACTCGCACAAATACCTTCGGGACTTAGCCCGGATA
29739828 TAGTCACTAGCACAAATG
63 TAGTCACTAGCACAAATG
29739846 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
29739869 CATCCGAATA
Statistics
Matches: 95, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
79 13 0.14
80 10 0.11
81 1 0.01
83 71 0.75
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATACCTTCGGGACTTAGCCCGGATATAG
TCACTAGCACAAATG
Found at i:29748055 original size:19 final size:19
Alignment explanation
Indices: 29748009--29748056 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
29747999 GTATATATTT
29748009 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
29748027 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
29748046 TAAATTTTATT
1 TAAATTTTATT
29748057 CATATTCTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:29748117 original size:43 final size:43
Alignment explanation
Indices: 29748070--29748159 Score: 128
Period size: 42 Copynumber: 2.1 Consensus size: 43
29748060 ATTCTAGGAA
**
29748070 TATTTTTATTTTATATTTTAGTAGTTTATTAGAATAAGGAAAC
1 TATTTTTACCTTATATTTTAGTAGTTTATTAGAATAAGGAAAC
* * *
29748113 TA-TTTTCCCTTATGTTTTAGTAGTTTATTAGAATAAGGGAAC
1 TATTTTTACCTTATATTTTAGTAGTTTATTAGAATAAGGAAAC
29748155 TATTT
1 TATTT
29748160 CCCCAATTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
42 37 0.90
43 4 0.10
ACGTcount: A:0.31, C:0.06, G:0.13, T:0.50
Consensus pattern (43 bp):
TATTTTTACCTTATATTTTAGTAGTTTATTAGAATAAGGAAAC
Found at i:29748138 original size:42 final size:42
Alignment explanation
Indices: 29748080--29748159 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
29748070 TATTTTTATT
29748080 TTATATTTTAGTAGTTTATTAGAATAAGGAAACTATTTTCCC
1 TTATATTTTAGTAGTTTATTAGAATAAGGAAACTATTTTCCC
* *
29748122 TTATGTTTTAGTAGTTTATTAGAATAAGGGAACTATTT
1 TTATATTTTAGTAGTTTATTAGAATAAGGAAACTATTT
29748160 CCCCAATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.46
Consensus pattern (42 bp):
TTATATTTTAGTAGTTTATTAGAATAAGGAAACTATTTTCCC
Found at i:29751984 original size:19 final size:19
Alignment explanation
Indices: 29751942--29751985 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
29751932 ATATTTTAAA
*
29751942 TTTATTTAGATAGATAAAT
1 TTTATTTAGATAGAAAAAT
*
29751961 CTTATTTAGATAGAAAAAT
1 TTTATTTAGATAGAAAAAT
29751980 TTTATT
1 TTTATT
29751986 CATATTCTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (19 bp):
TTTATTTAGATAGAAAAAT
Found at i:29752045 original size:42 final size:42
Alignment explanation
Indices: 29751995--29752088 Score: 136
Period size: 42 Copynumber: 2.3 Consensus size: 42
29751985 TCATATTCTA
**
29751995 GGAA-TATTTTATTTTATCTTTTAGTAGTTTATTAAAATAAG
1 GGAACTATTTTACCTTATCTTTTAGTAGTTTATTAAAATAAG
* * *
29752036 GGAACTATTTTCCCTTATGTTTTAGTAGTTTATTAGAATAAG
1 GGAACTATTTTACCTTATCTTTTAGTAGTTTATTAAAATAAG
29752078 GGAACTATTTT
1 GGAACTATTTT
29752089 CCCAATTAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 4 0.09
42 43 0.91
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (42 bp):
GGAACTATTTTACCTTATCTTTTAGTAGTTTATTAAAATAAG
Found at i:29752089 original size:42 final size:42
Alignment explanation
Indices: 29752008--29752091 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
29751998 ATATTTTATT
29752008 TTATCTTTTAGTAGTTTATTAAAATAAGGGAACTATTTTCCC
1 TTATCTTTTAGTAGTTTATTAAAATAAGGGAACTATTTTCCC
* *
29752050 TTATGTTTTAGTAGTTTATTAGAATAAGGGAACTATTTTCCC
1 TTATCTTTTAGTAGTTTATTAAAATAAGGGAACTATTTTCCC
29752092 AATTAAGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (42 bp):
TTATCTTTTAGTAGTTTATTAAAATAAGGGAACTATTTTCCC
Found at i:29754153 original size:52 final size:52
Alignment explanation
Indices: 29754075--29754179 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
29754065 CGCTATACTT
29754075 ATATACTTAAGCTCAGAGACAAGGATTAGTGAAAAATTAGATAATTCCACTA
1 ATATACTTAAGCTCAGAGACAAGGATTAGTGAAAAATTAGATAATTCCACTA
**
29754127 ATATACTTAAGCTTGGAGACAAGGATTAGTGAAAAATTAGATAATTCCACTA
1 ATATACTTAAGCTCAGAGACAAGGATTAGTGAAAAATTAGATAATTCCACTA
29754179 A
1 A
29754180 CTCTCTTGAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (52 bp):
ATATACTTAAGCTCAGAGACAAGGATTAGTGAAAAATTAGATAATTCCACTA
Found at i:29758089 original size:21 final size:21
Alignment explanation
Indices: 29758044--29758092 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
29758034 ATTAAAAATT
*
29758044 TTAAAAATAATTTTTAGAAAA
1 TTAAAAAAAATTTTTAGAAAA
29758065 -TAAAAAAAATTGTTT-GAAAA
1 TTAAAAAAAATT-TTTAGAAAA
29758085 TTAAAAAA
1 TTAAAAAA
29758093 TAATAAGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (21 bp):
TTAAAAAAAATTTTTAGAAAA
Found at i:29758462 original size:31 final size:31
Alignment explanation
Indices: 29758422--29758482 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
29758412 AGTTGGTCAC
* *
29758422 CCAACTTTTAAGG-TGTTTTCATTTTGGTTAT
1 CCAACTTTT-AGGATGCTTTCATTTTAGTTAT
*
29758453 CCAATTTTTAGGATGCTTTCATTTTAGTTA
1 CCAACTTTTAGGATGCTTTCATTTTAGTTA
29758483 CCTAAACGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 3 0.12
31 23 0.88
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.51
Consensus pattern (31 bp):
CCAACTTTTAGGATGCTTTCATTTTAGTTAT
Found at i:29762863 original size:3 final size:3
Alignment explanation
Indices: 29762844--29762889 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
29762834 TATTTGAGAA
* *
29762844 TAT TTT TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
29762890 TGGTAGCCCA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TAT
Found at i:29764829 original size:22 final size:22
Alignment explanation
Indices: 29764788--29764829 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
29764778 AGAAAACAAC
* *
29764788 GGTGAAGCTACTGTTGAATGGT
1 GGTGAAGCTACTGCTAAATGGT
*
29764810 GGTGAAGCTATTGCTAAATG
1 GGTGAAGCTACTGCTAAATG
29764830 TCAATGAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.10, G:0.33, T:0.31
Consensus pattern (22 bp):
GGTGAAGCTACTGCTAAATGGT
Found at i:29785275 original size:24 final size:25
Alignment explanation
Indices: 29785248--29785296 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
29785238 CTTTTTTTAT
*
29785248 TAAATAAAAAAC-TTTAAAATATAA
1 TAAATAAAAAACATTTAAAACATAA
* *
29785272 TAAATCAAATACATTTAAAACATAA
1 TAAATAAAAAACATTTAAAACATAA
29785297 AAACAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (25 bp):
TAAATAAAAAACATTTAAAACATAA
Found at i:29785289 original size:25 final size:23
Alignment explanation
Indices: 29785260--29785324 Score: 66
Period size: 25 Copynumber: 2.9 Consensus size: 23
29785250 AATAAAAAAC
*
29785260 TTTAAAATATAATAAATCAAATACA
1 TTTAAAACATAA-AAA-CAAATACA
29785285 TTTAAAACATAAAAACAAAT--A
1 TTTAAAACATAAAAACAAATACA
*
29785306 -TTAAAACA-AAAAATAAATA
1 TTTAAAACATAAAAACAAATA
29785325 AATAATGGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
19 9 0.24
20 8 0.22
21 1 0.03
23 5 0.14
24 3 0.08
25 11 0.30
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (23 bp):
TTTAAAACATAAAAACAAATACA
Found at i:29785323 original size:19 final size:20
Alignment explanation
Indices: 29785286--29785324 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
29785276 TCAAATACAT
29785286 TTAAAACATAAAAACAAATA
1 TTAAAACATAAAAACAAATA
*
29785306 TTAAAACA-AAAAATAAATA
1 TTAAAACATAAAAACAAATA
29785325 AATAATGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
TTAAAACATAAAAACAAATA
Found at i:29785545 original size:15 final size:16
Alignment explanation
Indices: 29785520--29785553 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
29785510 AAAGTTATTT
*
29785520 AAAATTAAAAATTAAA
1 AAAATTAAAAAATAAA
29785536 AAAATT-AAAAATAAA
1 AAAATTAAAAAATAAA
29785551 AAA
1 AAA
29785554 TAAAATAATT
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:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAATTAAAAAATAAA
Found at i:29785570 original size:22 final size:22
Alignment explanation
Indices: 29785516--29785571 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
29785506 TACTAAAGTT
*
29785516 ATTTAAAATTAAAAATTAAAAAA
1 ATTTAAAA-TAAAAAATAAAAAA
* *
29785539 ATTAAAAATAAAAAATAAAATA
1 ATTTAAAATAAAAAATAAAAAA
29785561 ATTTAAAATAA
1 ATTTAAAATAA
29785572 TTTAATATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 22 0.76
23 7 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
ATTTAAAATAAAAAATAAAAAA
Found at i:29787794 original size:45 final size:45
Alignment explanation
Indices: 29787730--29787821 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
29787720 TTTAAGAGAA
29787730 TAATTGTTCAAACTTAAAAAGGAATAAATGCAATAGGGTTTCTGC
1 TAATTGTTCAAACTTAAAAAGGAATAAATGCAATAGGGTTTCTGC
29787775 TAATTGTTCAAACTTAAAAAGGAATAAATGCAATAGGGTTTCTGC
1 TAATTGTTCAAACTTAAAAAGGAATAAATGCAATAGGGTTTCTGC
29787820 TA
1 TA
29787822 TGATCCTCGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (45 bp):
TAATTGTTCAAACTTAAAAAGGAATAAATGCAATAGGGTTTCTGC
Found at i:29791348 original size:3 final size:3
Alignment explanation
Indices: 29791328--29791375 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
29791318 TTCATTATGG
* *
29791328 GAA GAAA GAA GGA GAA GAA GAA -AA GAA G-A GAA GAA GAA GAA GGA
1 GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
29791372 GAA G
1 GAA G
29791376 GAGGCGGCAC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 4 0.11
3 31 0.82
4 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:29791349 original size:16 final size:16
Alignment explanation
Indices: 29791328--29791375 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
29791318 TTCATTATGG
29791328 GAAGAAAGAAGGAGAA
1 GAAGAAAGAAGGAGAA
29791344 GAAGAAAAGAA-GAGAA
1 GAAG-AAAGAAGGAGAA
29791360 GAAG-AAGAAGGAGAA
1 GAAGAAAGAAGGAGAA
29791375 G
1 G
29791376 GAGGCGGCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.17
15 6 0.20
16 13 0.43
17 6 0.20
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
GAAGAAAGAAGGAGAA
Found at i:29791360 original size:22 final size:21
Alignment explanation
Indices: 29791329--29791369 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
29791319 TCATTATGGG
*
29791329 AAGAAAGAAGGAGAAGAAGAA
1 AAGAAAGAAGAAGAAGAAGAA
29791350 AAGAAGAGAAGAAGAAGAAG
1 AAGAA-AGAAGAAGAAGAAG
29791370 GAGAAGGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (21 bp):
AAGAAAGAAGAAGAAGAAGAA
Found at i:29791362 original size:25 final size:24
Alignment explanation
Indices: 29791328--29791374 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
29791318 TTCATTATGG
*
29791328 GAAGAAAGAAGGAGAAGAAGAAAA
1 GAAGAAAGAAGAAGAAGAAGAAAA
*
29791352 GAAGAGAAGAAGAAGAAGGAGAA
1 GAAGA-AAGAAGAAGAAGAAGAA
29791375 GGAGGCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (24 bp):
GAAGAAAGAAGAAGAAGAAGAAAA
Found at i:29791900 original size:17 final size:17
Alignment explanation
Indices: 29791878--29791911 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
29791868 ACCTTTTACA
* *
29791878 AAAATAGTATAAAAAAT
1 AAAATACTAAAAAAAAT
29791895 AAAATACTAAAAAAAAT
1 AAAATACTAAAAAAAAT
29791912 CTTAATCAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (17 bp):
AAAATACTAAAAAAAAT
Found at i:29792428 original size:153 final size:147
Alignment explanation
Indices: 29792017--29792465 Score: 661
Period size: 152 Copynumber: 3.0 Consensus size: 147
29792007 AAATTTAAAA
*
29792017 AAGGTTATTTACTAAATTAATATAAAAAACACTAAAATAATACATTTGAAACATTATGTACTAAA
1 AAGGTTATTTACTAAATTAATATAAAAAACACTAAAATAATACATTTGAAACATTATGTATTAAA
* *
29792082 ATAATATAAAAATTAATTACGAAAATTGTATATTTTAAAAAATAAAATCTAAAAATTTAAAAAAT
66 ATAATATAAAAA--AA-TACGAAAATAGTATATTTTAAAAAATAAAATCTAAAAATTTAAAAAAA
* *
29792147 ACAAATAAATGGTCAAAATC
128 ACAAACAAATGGCCAAAATC
* * *
29792167 AGGGTTATTTACTAAATTAATATAAAAAA-ATTAAAATAATACATTTGAAACAATATGTATTAAA
1 AAGGTTATTTACTAAATTAATATAAAAAACACTAAAATAATACATTTGAAACATTATGTATTAAA
29792231 ATAATATAAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAAT-TCAAAAATTTTAAA
66 ATAATAT----AAA-AAAATACGAAAATAGTATATTTTAAAAAATAAAATCT-AAAAA-TTTAAA
29792295 AAAAACAAACAAATGGCCAAAATC
124 AAAAACAAACAAATGGCCAAAATC
*
29792319 AAGGTTATTTATTAAATTAATATAAAAAACACTAAAATAATACATTTGAAACATTATGTATTAAA
1 AAGGTTATTTACTAAATTAATATAAAAAACACTAAAATAATACATTTGAAACATTATGTATTAAA
** * *
29792384 ATAATATAAAAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAA-TTAAAAAATACC
66 ATAATATAAAAAAATACGAAAATAGTATATTTTAAAAAATAAAATCTAAAAATTTAAAAAAAACA
*
29792448 AACAAATGGCAAAAATC
131 AACAAATGGCCAAAATC
29792465 A
1 A
29792466 TCGAAAAAAA
Statistics
Matches: 273, Mismatches: 17, Indels: 22
0.88 0.05 0.07
Matches are distributed among these distances:
146 27 0.10
148 39 0.14
149 42 0.15
150 29 0.11
151 35 0.13
152 56 0.21
153 43 0.16
154 2 0.01
ACGTcount: A:0.58, C:0.07, G:0.06, T:0.29
Consensus pattern (147 bp):
AAGGTTATTTACTAAATTAATATAAAAAACACTAAAATAATACATTTGAAACATTATGTATTAAA
ATAATATAAAAAAATACGAAAATAGTATATTTTAAAAAATAAAATCTAAAAATTTAAAAAAAACA
AACAAATGGCCAAAATC
Found at i:29793652 original size:22 final size:23
Alignment explanation
Indices: 29793618--29793679 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 23
29793608 CAATAACAAC
* *
29793618 AAAATAGTTGCAACATAAT-AGT
1 AAAATAGTAGCAAAATAATGAGT
* *
29793640 AAAATGGTAGCAAAATAGTGAGT
1 AAAATAGTAGCAAAATAATGAGT
* *
29793663 AAAA-AATAGAAAAATAA
1 AAAATAGTAGCAAAATAA
29793680 CATTTAAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
22 24 0.77
23 7 0.23
ACGTcount: A:0.58, C:0.05, G:0.16, T:0.21
Consensus pattern (23 bp):
AAAATAGTAGCAAAATAATGAGT
Found at i:29795240 original size:18 final size:18
Alignment explanation
Indices: 29795193--29795246 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
29795183 GTAGCCAATA
*
29795193 TAGAGCCTGAGCCAGAGC
1 TAGAGCCAGAGCCAGAGC
** * *
29795211 TAGCTCCCGAGCCCGAGC
1 TAGAGCCAGAGCCAGAGC
*
29795229 TAGAGCCAGAGCCTGAGC
1 TAGAGCCAGAGCCAGAGC
29795247 CACAGCTAGA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.24, C:0.33, G:0.31, T:0.11
Consensus pattern (18 bp):
TAGAGCCAGAGCCAGAGC
Found at i:29799951 original size:19 final size:19
Alignment explanation
Indices: 29799914--29799953 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
29799904 TTTTCAAACA
*
29799914 GTTTTTTTATACAATTTAT
1 GTTTTTTTAAACAATTTAT
29799933 GTTTTTTTAAACTAA-TTAT
1 GTTTTTTTAAAC-AATTTAT
29799952 GT
1 GT
29799954 CAGAAAAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (19 bp):
GTTTTTTTAAACAATTTAT
Found at i:29805765 original size:42 final size:42
Alignment explanation
Indices: 29805706--29805789 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
29805696 ACAGAAAGCA
29805706 AGTGGTCCTCATTCTCACCACTCCTATCATAAATATTGTAGC
1 AGTGGTCCTCATTCTCACCACTCCTATCATAAATATTGTAGC
29805748 AGTGGTCCTCATTCTCACCACTCCTATCATAAATATTGTAGC
1 AGTGGTCCTCATTCTCACCACTCCTATCATAAATATTGTAGC
29805790 TTTGGGTTGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.33
Consensus pattern (42 bp):
AGTGGTCCTCATTCTCACCACTCCTATCATAAATATTGTAGC
Found at i:29808408 original size:26 final size:26
Alignment explanation
Indices: 29808379--29808435 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
29808369 TGATAAAAAT
29808379 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29808405 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29808431 TGATA
1 TGATA
29808436 GGCATTTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.32, C:0.07, G:0.26, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:29809930 original size:26 final size:26
Alignment explanation
Indices: 29809901--29809953 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
29809891 TTTACAGTTT
29809901 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTA-GAGATAAATTGACCGAAA
* *
29809927 TACCCCTAGAGTTAAATTGACCTAAA
1 TACCCCTAGAGATAAATTGACCGAAA
29809953 T
1 T
29809954 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.25
Consensus pattern (26 bp):
TACCCCTAGAGATAAATTGACCGAAA
Found at i:29811587 original size:12 final size:12
Alignment explanation
Indices: 29811560--29811602 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
29811550 ACTCGGGGAA
*
29811560 GAGGCCGTCGTC
1 GAGGCCGTGGTC
* *
29811572 GAGGCTGTGGTT
1 GAGGCCGTGGTC
29811584 GAGGCCGTGGTC
1 GAGGCCGTGGTC
29811596 GAGGCCG
1 GAGGCCG
29811603 AGGTAGTACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (12 bp):
GAGGCCGTGGTC
Found at i:29817839 original size:49 final size:48
Alignment explanation
Indices: 29817786--29817882 Score: 142
Period size: 48 Copynumber: 2.0 Consensus size: 48
29817776 ATAAAGAGGG
* *
29817786 TTTAAAATAAATAATATATAAAATAGTTT-AACTACATAATGTATATAAA
1 TTTAAAATAAATAATATAT-AAA-AGTTTAAAATAAATAATGTATATAAA
*
29817835 TTTAAAATAAATAATATGTAAAAGTTTAAAATAAATAATGTATATAAA
1 TTTAAAATAAATAATATATAAAAGTTTAAAATAAATAATGTATATAAA
29817883 AAGAAAATCA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
47 5 0.11
48 21 0.48
49 18 0.41
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (48 bp):
TTTAAAATAAATAATATATAAAAGTTTAAAATAAATAATGTATATAAA
Found at i:29817862 original size:24 final size:24
Alignment explanation
Indices: 29817785--29817883 Score: 103
Period size: 24 Copynumber: 4.0 Consensus size: 24
29817775 AATAAAGAGG
29817785 GTTTAAAATAAATAATATATAAAATA
1 GTTTAAAATAAATAATATAT-AAA-A
* * *
29817811 GTTT-AACTACATAATGTATATAAA
1 GTTTAAAATAAATAATATATA-AAA
*
29817835 -TTTAAAATAAATAATATGTAAAA
1 GTTTAAAATAAATAATATATAAAA
29817858 GTTTAAAATAAATAATGTATATAAAA
1 GTTTAAAATAAATAA--TATATAAAA
29817884 AGAAAATCAT
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
23 6 0.10
24 28 0.47
25 14 0.23
26 12 0.20
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (24 bp):
GTTTAAAATAAATAATATATAAAA
Found at i:29820591 original size:26 final size:26
Alignment explanation
Indices: 29820561--29820613 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
29820551 TTTAGAGTTT
29820561 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* * *
29820587 TACCCTTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
29820613 T
1 T
29820614 GCATATTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:29823487 original size:39 final size:39
Alignment explanation
Indices: 29823441--29823580 Score: 199
Period size: 39 Copynumber: 3.6 Consensus size: 39
29823431 GTTCTGATGA
* *
29823441 GCTTCAGTTAGCCTCCGGCCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* *
29823480 GCTTCAGTTAACCTTCGGGCTTCCGTTTAACACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* *
29823519 GCTTTAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
** *
29823558 GCTTCAACTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
29823581 AAATCACGAT
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 89 1.00
ACGTcount: A:0.14, C:0.27, G:0.22, T:0.37
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
Found at i:29827967 original size:18 final size:17
Alignment explanation
Indices: 29827938--29827985 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
29827928 GAAGTGAATG
29827938 AAAAAAAG-AAAAAGAA
1 AAAAAAAGTAAAAAGAA
29827954 AAAAAAAGTTAAAAAGAA
1 AAAAAAAG-TAAAAAGAA
* *
29827972 CATAAAAGTAAAAA
1 AAAAAAAGTAAAAA
29827986 ATTAAATTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 8 0.29
17 6 0.21
18 14 0.50
ACGTcount: A:0.79, C:0.02, G:0.10, T:0.08
Consensus pattern (17 bp):
AAAAAAAGTAAAAAGAA
Found at i:29832698 original size:13 final size:13
Alignment explanation
Indices: 29832680--29832705 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29832670 CTTAAGTTTT
29832680 TACAGAGAATTAA
1 TACAGAGAATTAA
29832693 TACAGAGAATTAA
1 TACAGAGAATTAA
29832706 GTTATTTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (13 bp):
TACAGAGAATTAA
Found at i:29841090 original size:20 final size:20
Alignment explanation
Indices: 29841067--29841116 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 20
29841057 AACTATTCAA
*
29841067 ATAATATTATTTGAATAGTT
1 ATAATATTATTTGAATAATT
* **
29841087 ATAAAATTAAATGAATAATT
1 ATAATATTATTTGAATAATT
29841107 AT--TATTATTT
1 ATAATATTATTT
29841117 ATTTATTAAT
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
18 5 0.22
20 18 0.78
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (20 bp):
ATAATATTATTTGAATAATT
Found at i:29845117 original size:7 final size:7
Alignment explanation
Indices: 29845105--29845142 Score: 55
Period size: 6 Copynumber: 5.9 Consensus size: 7
29845095 TCCAAATGAA
29845105 TCATTTC
1 TCATTTC
29845112 TCATTTC
1 TCATTTC
29845119 TCATTT-
1 TCATTTC
29845125 TCATTTC
1 TCATTTC
29845132 -CATTTC
1 TCATTTC
29845138 -CATTT
1 TCATTT
29845143 TGAGAACACC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 17 0.57
7 13 0.43
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.58
Consensus pattern (7 bp):
TCATTTC
Found at i:29852464 original size:26 final size:26
Alignment explanation
Indices: 29852435--29852542 Score: 207
Period size: 26 Copynumber: 4.2 Consensus size: 26
29852425 TGATACAAAT
29852435 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
29852461 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29852487 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29852513 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29852539 TGAT
1 TGAT
29852543 GGAAATTTCA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:29857908 original size:26 final size:26
Alignment explanation
Indices: 29857879--29857960 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
29857869 TGATACAAAT
*
29857879 TGATAATGGGTTATGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
29857905 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29857931 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29857957 TGAT
1 TGAT
29857961 GGGAATTTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.30, C:0.06, G:0.26, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:29859635 original size:54 final size:54
Alignment explanation
Indices: 29859553--29859696 Score: 227
Period size: 54 Copynumber: 2.7 Consensus size: 54
29859543 TGGAGGAAAC
*
29859553 GTCCTGGTGGCTATGCCACAATTATCTGATTTGGTGGCTCTACCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTACCACATATATCT
*
29859607 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTACCACATATATCT
* * *
29859661 GTTCTGGTGGCTCTGCCACAA-TATCTGTGTCTGGTG
1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTG
29859697 ACTTCGTCAC
Statistics
Matches: 84, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
53 6 0.07
54 78 0.93
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTACCACATATATCT
Found at i:29859693 original size:27 final size:26
Alignment explanation
Indices: 29859556--29859713 Score: 176
Period size: 27 Copynumber: 5.9 Consensus size: 26
29859546 AGGAAACGTC
*
29859556 CTGGTGGCTATGCCACAATTATCTGATT
1 CTGGTGGCTCTGCCACAA-TATCTG-TT
* *
29859584 -TGGTGGCTCTACCACATATATCTGTC
1 CTGGTGGCTCTGCCACA-ATATCTGTT
* *
29859610 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAA-TATCTGTT
29859637 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACA-ATATCTGTT
29859664 CTGGTGGCTCTGCCACAATATCTGTGT
1 CTGGTGGCTCTGCCACAATATCTGT-T
* *
29859691 CTGGTGACT-TCGTCACAATATCT
1 CTGGTGGCTCT-GCCACAATATCT
29859714 AGCAGCCTTG
Statistics
Matches: 113, Mismatches: 11, Indels: 13
0.82 0.08 0.09
Matches are distributed among these distances:
26 11 0.10
27 100 0.88
28 2 0.02
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.35
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACAATATCTGTT
Found at i:29859708 original size:81 final size:80
Alignment explanation
Indices: 29859556--29859713 Score: 198
Period size: 81 Copynumber: 2.0 Consensus size: 80
29859546 AGGAAACGTC
*
29859556 CTGGTGGCTATGCCACAATTATCTGATTTGGTGGCTCTACCACATATATCTGTCCTGGTGGCTAT
1 CTGGTGGCTATGCCACAATTATCTGATTTGGTGGCTCTACCACATATATCTGTCCTGGTGACTAT
29859621 GCCACAATTATCTGAT
66 GCCACAA-TATCTGAT
* * *
29859637 CTGGTGGCTCTGCCAC-ATATATCTG-TTCTGGTGGCTCTGCCACA-ATATCTGTGTCTGGTGAC
1 CTGGTGGCTATGCCACAAT-TATCTGATT-TGGTGGCTCTACCACATATATCTGT-CCTGGTGAC
*
29859699 T-TCGTCACAATATCT
63 TAT-GCCACAATATCT
29859714 AGCAGCCTTG
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
80 18 0.26
81 50 0.74
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.35
Consensus pattern (80 bp):
CTGGTGGCTATGCCACAATTATCTGATTTGGTGGCTCTACCACATATATCTGTCCTGGTGACTAT
GCCACAATATCTGAT
Found at i:29863320 original size:43 final size:43
Alignment explanation
Indices: 29863271--29863378 Score: 164
Period size: 43 Copynumber: 2.5 Consensus size: 43
29863261 GATTACTGAG
* *
29863271 ATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATTG-T
1 ATGTGATTACGTGTAAGACCATGTCTGGGACAGTGGCATCGAT
29863313 ATTGTGATTACGTGTAAGACCATGTCTGGGACAGTGGCATCGAT
1 A-TGTGATTACGTGTAAGACCATGTCTGGGACAGTGGCATCGAT
* *
29863357 ATGTGATAACATGTAAGACCAT
1 ATGTGATTACGTGTAAGACCAT
29863379 ATCTAGGATA
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
42 1 0.02
43 57 0.95
44 2 0.03
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.31
Consensus pattern (43 bp):
ATGTGATTACGTGTAAGACCATGTCTGGGACAGTGGCATCGAT
Found at i:29866708 original size:14 final size:14
Alignment explanation
Indices: 29866689--29866716 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29866679 ACCTATGTAA
29866689 TCATTTATATCATC
1 TCATTTATATCATC
29866703 TCATTTATATCATC
1 TCATTTATATCATC
29866717 ACATAAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (14 bp):
TCATTTATATCATC
Found at i:29869169 original size:3 final size:3
Alignment explanation
Indices: 29869146--29869195 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
29869136 ATAAAAAAAA
* * *
29869146 TAT TTT TAT TTT TATT TAT TAT TAT TAT TAT TAT TAG TAT TAT TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29869192 TAT T
1 TAT T
29869196 TTTGACTCAG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:29872102 original size:47 final size:47
Alignment explanation
Indices: 29871972--29872102 Score: 217
Period size: 47 Copynumber: 2.8 Consensus size: 47
29871962 TTCGAGTAAA
* * * * *
29871972 TACCTTGATTTGGTTACGAGCCATGGTATAGGTACTCCGGGATATGT
1 TACCTTGATTTGGCTATGGGCCATGGTATAGGTACTTCGGGATAAGT
29872019 TACCTTGATTTGGCTATGGGCCATGGTATAGGTACTTCGGGATAAGT
1 TACCTTGATTTGGCTATGGGCCATGGTATAGGTACTTCGGGATAAGT
29872066 TACCTTGATTTGGCTATGGGCCATGGTATAGGTACTT
1 TACCTTGATTTGGCTATGGGCCATGGTATAGGTACTT
29872103 ATCGATTGTG
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 79 1.00
ACGTcount: A:0.21, C:0.16, G:0.28, T:0.35
Consensus pattern (47 bp):
TACCTTGATTTGGCTATGGGCCATGGTATAGGTACTTCGGGATAAGT
Found at i:29876700 original size:26 final size:26
Alignment explanation
Indices: 29876586--29876713 Score: 87
Period size: 26 Copynumber: 4.9 Consensus size: 26
29876576 AATGCAAGCA
* * * * *
29876586 TTGAGCTGGTGGTTATTTGGTAGGCT
1 TTGAGCTAGTGTTTATTTAGCAGGCC
* * *
29876612 TTGAGCT-GATGTTTTTTTAGTAGGAC
1 TTGAGCTAG-TGTTTATTTAGCAGGCC
** * *
29876638 TTGAGCCGGTGATTATTTAGCAGACC
1 TTGAGCTAGTGTTTATTTAGCAGGCC
* * **
29876664 TTAAGCCAGTGTTTATTTAGCAGGTT
1 TTGAGCTAGTGTTTATTTAGCAGGCC
*
29876690 TTGAGCTAGTGTATATTTAGCAGG
1 TTGAGCTAGTGTTTATTTAGCAGG
29876714 TACTATGTAG
Statistics
Matches: 80, Mismatches: 20, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
25 1 0.01
26 78 0.98
27 1 0.01
ACGTcount: A:0.20, C:0.11, G:0.29, T:0.40
Consensus pattern (26 bp):
TTGAGCTAGTGTTTATTTAGCAGGCC
Found at i:29888224 original size:43 final size:43
Alignment explanation
Indices: 29888160--29888242 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
29888150 ACATGAATCC
* *
29888160 CATCCATTATGAACTCGGACCTCTCAACGAGCTCGGATGCTCG
1 CATCCATAATGAACTCAGACCTCTCAACGAGCTCGGATGCTCG
*
29888203 CATCCATAATGAACTCAGACCTCTCAATGAGCTCGGATGC
1 CATCCATAATGAACTCAGACCTCTCAACGAGCTCGGATGC
29888243 CACATATCTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (43 bp):
CATCCATAATGAACTCAGACCTCTCAACGAGCTCGGATGCTCG
Found at i:29895189 original size:26 final size:26
Alignment explanation
Indices: 29895136--29895252 Score: 128
Period size: 26 Copynumber: 4.5 Consensus size: 26
29895126 ATACAAGAAA
* *
29895136 AGCAGGCCTTGACCT-GTGGTTATTT
1 AGCAGGCCTTGAGCTGGTGTTTATTT
* * *
29895161 AGCATGACTTGAGCTGGTGTTGATTT
1 AGCAGGCCTTGAGCTGGTGTTTATTT
* **
29895187 AGCAGGCCTTAAGCCAGTGTTTATTT
1 AGCAGGCCTTGAGCTGGTGTTTATTT
* *
29895213 AGTAGGCCTTGAGCTGGTCTTTATTT
1 AGCAGGCCTTGAGCTGGTGTTTATTT
*
29895239 AGCAAGCCTTGAGC
1 AGCAGGCCTTGAGC
29895253 CAGTGGTTAT
Statistics
Matches: 73, Mismatches: 18, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
25 12 0.16
26 61 0.84
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (26 bp):
AGCAGGCCTTGAGCTGGTGTTTATTT
Found at i:29895224 original size:52 final size:52
Alignment explanation
Indices: 29895136--29895271 Score: 175
Period size: 52 Copynumber: 2.6 Consensus size: 52
29895126 ATACAAGAAA
* * * * *
29895136 AGCAGGCCTTGA-CCTGTGGTTATTTAGCATGACTTGAGCTGGTGTTGATTT
1 AGCAGGCCTTGAGCCAGTGGTTATTTAGTAGGCCTTGAGCTGGTCTTGATTT
* * *
29895187 AGCAGGCCTTAAGCCAGTGTTTATTTAGTAGGCCTTGAGCTGGTCTTTATTT
1 AGCAGGCCTTGAGCCAGTGGTTATTTAGTAGGCCTTGAGCTGGTCTTGATTT
* *
29895239 AGCAAGCCTTGAGCCAGTGGTTATCTAGTAGGC
1 AGCAGGCCTTGAGCCAGTGGTTATTTAGTAGGC
29895272 TTTAAGCCAG
Statistics
Matches: 72, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
51 11 0.15
52 61 0.85
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.35
Consensus pattern (52 bp):
AGCAGGCCTTGAGCCAGTGGTTATTTAGTAGGCCTTGAGCTGGTCTTGATTT
Found at i:29895262 original size:26 final size:26
Alignment explanation
Indices: 29895136--29895283 Score: 120
Period size: 26 Copynumber: 5.7 Consensus size: 26
29895126 ATACAAGAAA
*
29895136 AGCAGGCCTTGA-CCTGTGGTTATTT
1 AGCAGGCCTTGAGCCAGTGGTTATTT
* * **
29895161 AGCATGACTTGAGCTGGT-GTTGATTT
1 AGCAGGCCTTGAGCCAGTGGTT-ATTT
* *
29895187 AGCAGGCCTTAAGCCAGTGTTTATTT
1 AGCAGGCCTTGAGCCAGTGGTTATTT
* ** **
29895213 AGTAGGCCTTGAGCTGGTCTTTATTT
1 AGCAGGCCTTGAGCCAGTGGTTATTT
* *
29895239 AGCAAGCCTTGAGCCAGTGGTTATCT
1 AGCAGGCCTTGAGCCAGTGGTTATTT
* * *
29895265 AGTAGGCTTTAAGCCAGTG
1 AGCAGGCCTTGAGCCAGTG
29895284 TATGTTTAAT
Statistics
Matches: 94, Mismatches: 26, Indels: 5
0.75 0.21 0.04
Matches are distributed among these distances:
25 13 0.14
26 79 0.84
27 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (26 bp):
AGCAGGCCTTGAGCCAGTGGTTATTT
Found at i:29897573 original size:12 final size:13
Alignment explanation
Indices: 29897551--29897579 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
29897541 AAAATCTTTC
29897551 TTGTGTTTTTTTT
1 TTGTGTTTTTTTT
29897564 TTGT-TTTTTTTT
1 TTGTGTTTTTTTT
29897576 TTGT
1 TTGT
29897580 ACTTTGACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (13 bp):
TTGTGTTTTTTTT
Found at i:29902135 original size:13 final size:13
Alignment explanation
Indices: 29902117--29902143 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29902107 GGTATACTGA
29902117 CTTATCAATACAG
1 CTTATCAATACAG
29902130 CTTATCAATACAG
1 CTTATCAATACAG
29902143 C
1 C
29902144 CAAGTCACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.26, G:0.07, T:0.30
Consensus pattern (13 bp):
CTTATCAATACAG
Found at i:29904504 original size:47 final size:47
Alignment explanation
Indices: 29904433--29904745 Score: 177
Period size: 47 Copynumber: 6.7 Consensus size: 47
29904423 AGGGTATATT
* * *
29904433 GCCGATGCCATGTCTCAGACATGGTCTTACACTGGCTCATCTATTAA
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTGACTCATCTATTAA
* * * * *
29904480 GTCGATGCCATGTCCTAAACATGGTCTTACACTGACT-ATCGAAATCGAG
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTGACTCATC--TAT-TAA
* * **
29904529 GCCGACGCCATGTCCCAAACATGGTCTTACACTGACACATCTCGT-A
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTGACTCATCTATTAA
* * * *
29904575 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACATCT-TGAG
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTGAC-T-CATCTATTAA
** * * * *
29904621 GTTGACG-CATGTCCCAAACAT-GTC-TAAAATTAGCTC-TC-ATCTCAA
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTGA-CTCATCTAT-T-AA
* * * *
29904666 TGCCGATGCCATGTCCCAGACATGTTCTTACACTGTCTC-TCATAATGT-G
1 -GCCGATGCCATGTCCCAAACATGGTCTTACACTGACTCATC-T-AT-TAA
*
29904715 GCCAATG-CATGTCCCAAACAT-GTCTTACACT
1 GCCGATGCCATGTCCCAAACATGGTCTTACACT
29904746 AGCACACAAT
Statistics
Matches: 200, Mismatches: 48, Indels: 37
0.70 0.17 0.13
Matches are distributed among these distances:
43 3 0.01
44 13 0.06
45 19 0.09
46 48 0.24
47 58 0.29
48 15 0.08
49 38 0.19
50 3 0.01
51 3 0.01
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.28
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAAACATGGTCTTACACTGACTCATCTATTAA
Found at i:29906228 original size:23 final size:23
Alignment explanation
Indices: 29906202--29906294 Score: 73
Period size: 23 Copynumber: 3.9 Consensus size: 23
29906192 TGAACTAAAA
29906202 CAGTAAGCTC-TGACGAGCTGAAT
1 CAGTAAGCTCAT-ACGAGCTGAAT
29906225 CAGTAAGCTCATACGAGCTGAGAAT
1 CAGTAAGCTCATACGAGCT--GAAT
* * * *
29906250 -AGTAAGGTCTTACAAGGTGTTATAT
1 CAGTAAGCTCATACGAGCTG--A-AT
*
29906275 CAGTAATCTCATACGAGCTG
1 CAGTAAGCTCATACGAGCTG
29906295 TGGTGAGTCT
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
22 1 0.02
23 17 0.31
24 16 0.30
25 6 0.11
26 14 0.26
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (23 bp):
CAGTAAGCTCATACGAGCTGAAT
Found at i:29909082 original size:40 final size:40
Alignment explanation
Indices: 29908883--29909089 Score: 159
Period size: 40 Copynumber: 5.2 Consensus size: 40
29908873 GATTATTGTT
** * * ** *
29908883 TGATTGCACATATGTACCTCTATTTGTACTTTGGTACCTC
1 TGATTGCACATACATGCCCCTATTTGTACTTCAGTACCCC
* * ** *
29908923 TAATTGCATATATGTGCCTCTATTTGTACTTC-GATACCCC
1 TGATTGCACATACATGCCCCTATTTGTACTTCAG-TACCCC
* * * *
29908963 TGTTTGCACATACGTGTCCC-ATTTTGTACTTCGGTACCCC
1 TGATTGCACATACATGCCCCTA-TTTGTACTTCAGTACCCC
* * * * * *
29909003 TAACTACACATACATGCCCTTGTTTGTACTTCAGTACCCT
1 TGATTGCACATACATGCCCCTATTTGTACTTCAGTACCCC
*
29909043 TGATTGCACATACATGCCCCTATTTGTAATTCAGTA-CCC
1 TGATTGCACATACATGCCCCTATTTGTACTTCAGTACCCC
*
29909082 TGAATGCA
1 TGATTGCA
29909090 TATTTTGTGC
Statistics
Matches: 134, Mismatches: 29, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
39 11 0.08
40 122 0.91
41 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.37
Consensus pattern (40 bp):
TGATTGCACATACATGCCCCTATTTGTACTTCAGTACCCC
Found at i:29915390 original size:42 final size:42
Alignment explanation
Indices: 29915331--29915417 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
29915321 ATATACCAAA
29915331 AACTTACCAATTTGACCAATTCATTTGGCCATTCAAGAACCT
1 AACTTACCAATTTGACCAATTCATTTGGCCATTCAAGAACCT
29915373 AACTTACCAATTTGACCAATTCATTTGGCCATTCAAGAACCT
1 AACTTACCAATTTGACCAATTCATTTGGCCATTCAAGAACCT
29915415 AAC
1 AAC
29915418 ACATAGGCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.30
Consensus pattern (42 bp):
AACTTACCAATTTGACCAATTCATTTGGCCATTCAAGAACCT
Found at i:29916576 original size:43 final size:43
Alignment explanation
Indices: 29916529--29916649 Score: 147
Period size: 43 Copynumber: 2.8 Consensus size: 43
29916519 TCAAATATCA
* * *
29916529 ATGCCACTGTCCCAGACAGGGCCTTACACG-TAATCTCTAA-TCG
1 ATGCCAATGTCCCAGACAAGGTCTTACACGAT-ATCTC-AAGTCG
* * *
29916572 ATGCCAATGTCTCAGACACGGTCTTACATGATATCTCAAGTCG
1 ATGCCAATGTCCCAGACAAGGTCTTACACGATATCTCAAGTCG
*
29916615 ATGCCAAAGTCCCAGACAAGGTCTTACACGATATC
1 ATGCCAATGTCCCAGACAAGGTCTTACACGATATC
29916650 ACATATCGGA
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 2 0.03
43 64 0.96
44 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAAGGTCTTACACGATATCTCAAGTCG
Found at i:29916951 original size:34 final size:34
Alignment explanation
Indices: 29916908--29916975 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
29916898 TACTCGACGA
* *
29916908 CTTTCGACTTTTCCCGGTCTAATTCCATTTTCTT
1 CTTTCGACTTTCCCCAGTCTAATTCCATTTTCTT
29916942 CTTTCGACTTTCCCCAGTCTAATTCCATTTTCTT
1 CTTTCGACTTTCCCCAGTCTAATTCCATTTTCTT
29916976 TGGTTCTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.13, C:0.31, G:0.07, T:0.49
Consensus pattern (34 bp):
CTTTCGACTTTCCCCAGTCTAATTCCATTTTCTT
Found at i:29941294 original size:40 final size:40
Alignment explanation
Indices: 29941227--29941403 Score: 234
Period size: 40 Copynumber: 4.5 Consensus size: 40
29941217 ACCCAAGTAT
*
29941227 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
*
29941266 CCTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * *
29941306 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* *
29941346 CTTCGGGACATAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* *
29941386 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAGCCCGG
29941404 TTATCATCCG
Statistics
Matches: 119, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.01
39 12 0.10
40 104 0.87
41 2 0.02
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:29949688 original size:40 final size:40
Alignment explanation
Indices: 29949621--29949876 Score: 324
Period size: 40 Copynumber: 6.5 Consensus size: 40
29949611 ACCCAAGTAT
*
29949621 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
*
29949660 CCTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * *
29949700 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* *
29949740 CTTCGGGACATAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * *
29949780 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* *
29949820 CTTCGGGACATAG-CCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* *
29949859 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAGCCCGG
29949877 TTATCATCCG
Statistics
Matches: 186, Mismatches: 24, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
38 3 0.02
39 42 0.23
40 137 0.74
41 4 0.02
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:29949754 original size:80 final size:80
Alignment explanation
Indices: 29949621--29949876 Score: 403
Period size: 80 Copynumber: 3.2 Consensus size: 80
29949611 ACCCAAGTAT
* * * * *
29949621 CTTCGGGAT-TTAG-CCGGATATAA-CAACTCGCACAAATGCCCTCGGGTCTTAGCCCGGATATA
1 CTTCGGG-TCTTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCGGGACATAGCCCGGATATA
29949683 GCAACTCGCACAAATGC
64 GCAACTCGCACAAATGC
29949700 CTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACATAGCCCGGATATAGC
1 CTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACATAGCCCGGATATAGC
29949765 AACTCGCACAAATGC
66 AACTCGCACAAATGC
29949780 CTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACATAG-CCGGATATAGC
1 CTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACATAGCCCGGATATAGC
29949844 AACTCGCACAAATGC
66 AACTCGCACAAATGC
* *
29949859 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAGCCCGG
29949877 TTATCATCCG
Statistics
Matches: 167, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
78 1 0.01
79 53 0.32
80 112 0.67
81 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (80 bp):
CTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACATAGCCCGGATATAGC
AACTCGCACAAATGC
Found at i:29955001 original size:40 final size:40
Alignment explanation
Indices: 29954946--29955167 Score: 295
Period size: 40 Copynumber: 5.6 Consensus size: 40
29954936 TATTCGAATG
*
29954946 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCGAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGTGACT
* * *
29954986 ATATCTGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGTGACT
29955026 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGTGACT
* * * *
29955066 ATATCGGGGCGAAGTCCCGAAGGCTTTTGTGCTATTAACT
1 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGTGACT
* * * *
29955106 ATATTCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAG-TGACT
* *
29955146 ATATCC-GGCTAAATCCTGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
29955168 TACTTGGGTT
Statistics
Matches: 158, Mismatches: 23, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
39 13 0.08
40 144 0.91
41 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGTGACT
Found at i:29956065 original size:17 final size:17
Alignment explanation
Indices: 29956043--29956079 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
29956033 TGAGCCGTAT
29956043 TTTATGAGATGTTTAAG
1 TTTATGAGATGTTTAAG
29956060 TTTATGAGATGTTTAAG
1 TTTATGAGATGTTTAAG
29956077 TTT
1 TTT
29956080 TCGTGAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.22, T:0.51
Consensus pattern (17 bp):
TTTATGAGATGTTTAAG
Found at i:29960872 original size:40 final size:40
Alignment explanation
Indices: 29960803--29960907 Score: 185
Period size: 40 Copynumber: 2.6 Consensus size: 40
29960793 AACCCAAGTA
* *
29960803 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
29960842 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
29960882 CCTTCGGGACTTAGCCCGGATATAGT
1 CCTTCGGGACTTAGCCCGGATATAGT
29960908 CACTAGCATC
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
39 13 0.21
40 50 0.79
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:29968199 original size:17 final size:17
Alignment explanation
Indices: 29968177--29968212 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
29968167 CGATTAGTGA
29968177 TTCTACCTAGTTTTATC
1 TTCTACCTAGTTTTATC
29968194 TTCTACCTAGTTTTATC
1 TTCTACCTAGTTTTATC
29968211 TT
1 TT
29968213 TTATTTATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.22, G:0.06, T:0.56
Consensus pattern (17 bp):
TTCTACCTAGTTTTATC
Found at i:29976221 original size:15 final size:15
Alignment explanation
Indices: 29976201--29976231 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29976191 TTCAAAACTT
29976201 AATTAAATCATTTCA
1 AATTAAATCATTTCA
*
29976216 AATTAAATCGTTTCA
1 AATTAAATCATTTCA
29976231 A
1 A
29976232 CCACGCCTCG
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:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (15 bp):
AATTAAATCATTTCA
Found at i:29978823 original size:11 final size:11
Alignment explanation
Indices: 29978809--29978833 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29978799 GTGAATAAAT
29978809 TGTGAAATTTA
1 TGTGAAATTTA
29978820 TGTGAAATTTA
1 TGTGAAATTTA
29978831 TGT
1 TGT
29978834 AATAATAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (11 bp):
TGTGAAATTTA
Found at i:29980158 original size:25 final size:24
Alignment explanation
Indices: 29980121--29980168 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
29980111 ATGGCCCTCT
*
29980121 CGAGCTTCCCGTTATATGGTTCTTG
1 CGAGCTTCCCGTTA-ATAGTTCTTG
**
29980146 CGAGCTTTTCGTTAATAGTTCTT
1 CGAGCTTCCCGTTAATAGTTCTT
29980169 CGGAGCATCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.44
Consensus pattern (24 bp):
CGAGCTTCCCGTTAATAGTTCTTG
Found at i:29980382 original size:24 final size:24
Alignment explanation
Indices: 29980324--29980410 Score: 79
Period size: 24 Copynumber: 3.6 Consensus size: 24
29980314 ATGGTTATCT
* * *
29980324 AGAGCTTCCCGTTAATAGCTCTTC
1 AGAGCTTCCCGTTATTGGCTCTTA
* * *
29980348 GGAACTACCCGTTATTGGCT-TGTA
1 AGAGCTTCCCGTTATTGGCTCT-TA
29980372 AGAGCTTCCCGATTA-TGGCTCTTA
1 AGAGCTTCCCG-TTATTGGCTCTTA
*
29980396 TGAGCTTCCCGTTAT
1 AGAGCTTCCCGTTAT
29980411 ATAGCCCGAA
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
23 4 0.08
24 41 0.84
25 4 0.08
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (24 bp):
AGAGCTTCCCGTTATTGGCTCTTA
Found at i:29980464 original size:25 final size:25
Alignment explanation
Indices: 29980374--29980470 Score: 90
Period size: 25 Copynumber: 3.9 Consensus size: 25
29980364 GGCTTGTAAG
* ** *
29980374 AGCTTCCCGAT-TATGGCTCTTATG
1 AGCTTCCCGTTATATGGCTCGAATA
* *
29980398 AGCTTCCCGTTATATAGCCCGAATA
1 AGCTTCCCGTTATATGGCTCGAATA
* *
29980423 AGCTTCCCATTACATGGCTC-ACATA
1 AGCTTCCCGTTATATGGCTCGA-ATA
*
29980448 AGCTTCCTGTTATATGGCTCGAA
1 AGCTTCCCGTTATATGGCTCGAA
29980471 AGAGGGCTTC
Statistics
Matches: 57, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
24 11 0.19
25 45 0.79
26 1 0.02
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.32
Consensus pattern (25 bp):
AGCTTCCCGTTATATGGCTCGAATA
Found at i:29983559 original size:89 final size:89
Alignment explanation
Indices: 29983422--29983584 Score: 308
Period size: 89 Copynumber: 1.8 Consensus size: 89
29983412 TTTCAAATAA
29983422 CCAATTCCAATTACAATCACAATATACAATATCAAATAAATTAATTTATTTTAACTTTAACCATT
1 CCAATTCCAATTACAATCACAATATACAATATCAAATAAATTAATTTATTTTAACTTTAACCATT
29983487 TAGCCTCATTTCAAATAACCAATT
66 TAGCCTCATTTCAAATAACCAATT
* *
29983511 CCAATTCCAATTCCAATCACAATATACAATATCAAATAAATTAGTTTATTTTAACTTTAACCATT
1 CCAATTCCAATTACAATCACAATATACAATATCAAATAAATTAATTTATTTTAACTTTAACCATT
29983576 TAGCCTCAT
66 TAGCCTCAT
29983585 GAACTATAAT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 72 1.00
ACGTcount: A:0.41, C:0.21, G:0.02, T:0.36
Consensus pattern (89 bp):
CCAATTCCAATTACAATCACAATATACAATATCAAATAAATTAATTTATTTTAACTTTAACCATT
TAGCCTCATTTCAAATAACCAATT
Found at i:29994151 original size:17 final size:17
Alignment explanation
Indices: 29994129--29994164 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
29994119 ATAGTGCCAA
*
29994129 ATGCTTCATTTATATGC
1 ATGCTTCATTTATACGC
29994146 ATGCTTCATTTATACGC
1 ATGCTTCATTTATACGC
29994163 AT
1 AT
29994165 ACTTATATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.44
Consensus pattern (17 bp):
ATGCTTCATTTATACGC
Done.