Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 89 of 193
Found at i:29184912 original size:19 final size:19
Alignment explanation
Indices: 29184870--29184931 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
29184860 AAATTTTTTA
* **
29184870 AAAAATAATATAAAAGTTGA
1 AAAAATAATTTAAAA-TTCT
29184890 AAAAATAATTTAAAATTCT
1 AAAAATAATTTAAAATTCT
*
29184909 AAAACAT-ATTTAAAATTTT
1 AAAA-ATAATTTAAAATTCT
29184928 AAAA
1 AAAA
29184932 TTTAAAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 21 0.57
20 16 0.43
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (19 bp):
AAAAATAATTTAAAATTCT
Found at i:29184912 original size:20 final size:19
Alignment explanation
Indices: 29184866--29184931 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
29184856 CATTAAATTT
*
29184866 TTTAAAAAATAATATAAAA
1 TTTAAAAAATAATTTAAAA
*
29184885 GTTGAAAAAATAATTTAAAA
1 -TTTAAAAAATAATTTAAAA
*
29184905 TTCTAAAACAT-ATTTAAAA
1 TT-TAAAAAATAATTTAAAA
*
29184924 TTTTAAAA
1 TTTAAAAA
29184932 TTTAAAATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
18 4 0.10
19 12 0.31
20 23 0.59
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (19 bp):
TTTAAAAAATAATTTAAAA
Found at i:29184935 original size:7 final size:7
Alignment explanation
Indices: 29184916--29184948 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
29184906 TCTAAAACAT
29184916 ATTTAAA
1 ATTTAAA
29184923 ATTTTAAA
1 A-TTTAAA
29184931 ATTTAAA
1 ATTTAAA
29184938 ATTTAAA
1 ATTTAAA
29184945 ATTT
1 ATTT
29184949 TAGAAAGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
ATTTAAA
Found at i:29184950 original size:8 final size:8
Alignment explanation
Indices: 29184898--29184950 Score: 56
Period size: 7 Copynumber: 6.5 Consensus size: 8
29184888 GAAAAAATAA
29184898 TTTAAAAT
1 TTTAAAAT
*
29184906 TCTAAAACAT
1 T-TTAAA-AT
29184916 ATTTAAAAT
1 -TTTAAAAT
29184925 TTTAAAA-
1 TTTAAAAT
29184932 TTTAAAA-
1 TTTAAAAT
29184939 TTTAAAAT
1 TTTAAAAT
29184947 TTTA
1 TTTA
29184951 GAAAGTTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
7 14 0.36
8 12 0.31
9 6 0.15
10 6 0.15
11 1 0.03
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (8 bp):
TTTAAAAT
Found at i:29185166 original size:2 final size:2
Alignment explanation
Indices: 29185159--29185188 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29185149 ACTTTTTCAA
29185159 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29185189 TATTTTTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29185322 original size:17 final size:18
Alignment explanation
Indices: 29185281--29185327 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
29185271 TAAAATTGTT
*
29185281 TATTAATTTTTAATGTATA
1 TATTAA-TTTTAAAGTATA
29185300 TATTAATTTTAAAG-ATA
1 TATTAATTTTAAAGTATA
*
29185317 TTTTAAATTTT
1 TATT-AATTTT
29185328 TAGAATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.24
18 13 0.52
19 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (18 bp):
TATTAATTTTAAAGTATA
Found at i:29185328 original size:19 final size:19
Alignment explanation
Indices: 29185281--29185329 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
29185271 TAAAATTGTT
*
29185281 TATTAATTTTTAATGTATA
1 TATTAATTTTTAAAGTATA
29185300 TATTAA-TTTTAAAG-ATA
1 TATTAATTTTTAAAGTATA
*
29185317 TTTTAAATTTTTA
1 TATT-AATTTTTA
29185330 GAATAATTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 6 0.23
18 9 0.35
19 11 0.42
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (19 bp):
TATTAATTTTTAAAGTATA
Found at i:29190010 original size:62 final size:62
Alignment explanation
Indices: 29189939--29190064 Score: 162
Period size: 62 Copynumber: 2.0 Consensus size: 62
29189929 TAAATTTTTA
* *** * * *
29189939 TTTAGGTACTCAAAATAAAAAAGGTTTATAATTTAAGCACTTAAGTTATATAGTTTGATCAT
1 TTTAAGTACTCAAAATAAAAAAAAATTACAATTTAAGCACTTAAGTTACATAGTTCGATCAT
* * *
29190001 TTTAAGTACTCAAAATAAAAAAAAATTGCAATTTAAGCACTTATGTTACATAGTTCGGTCAT
1 TTTAAGTACTCAAAATAAAAAAAAATTACAATTTAAGCACTTAAGTTACATAGTTCGATCAT
29190063 TT
1 TT
29190065 GGGTCACTCA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
62 54 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.37
Consensus pattern (62 bp):
TTTAAGTACTCAAAATAAAAAAAAATTACAATTTAAGCACTTAAGTTACATAGTTCGATCAT
Found at i:29191298 original size:13 final size:14
Alignment explanation
Indices: 29191278--29191315 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
29191268 AAAATATATA
29191278 TATATAAAAAAATT
1 TATATAAAAAAATT
*
29191292 T-TATAAAAACATT
1 TATATAAAAAAATT
*
29191305 TATGTAAAAAA
1 TATATAAAAAA
29191316 TTATAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (14 bp):
TATATAAAAAAATT
Found at i:29201933 original size:11 final size:11
Alignment explanation
Indices: 29201917--29201958 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
29201907 TGCTCTGAAA
29201917 TTAAATTTAAT
1 TTAAATTTAAT
29201928 TTAAATTTAAAT
1 TTAAATTT-AAT
29201940 TTAAATTTAAT
1 TTAAATTTAAT
*
29201951 TTTAATTT
1 TTAAATTT
29201959 TTAATTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 18 0.62
12 11 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:29201934 original size:6 final size:6
Alignment explanation
Indices: 29201917--29201967 Score: 68
Period size: 6 Copynumber: 8.7 Consensus size: 6
29201907 TGCTCTGAAA
* * *
29201917 TTAAAT TT-AAT TTAAAT TTAAAT TTAAAT TTAATT TTAATT TTTAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
29201964 TTAA
1 TTAA
29201968 TATTATTGCA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
5 5 0.12
6 35 0.88
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (6 bp):
TTAAAT
Found at i:29203958 original size:29 final size:28
Alignment explanation
Indices: 29203926--29204067 Score: 136
Period size: 29 Copynumber: 5.0 Consensus size: 28
29203916 TTGACCCCTG
29203926 AACTTTATCAAAATTACCA-TTTACCCTC
1 AACTTTATCAAAATTACCATTTTACCC-C
* *
29203954 AAACTTTTTTAAAATT-CCATTTTACCCC
1 -AACTTTATCAAAATTACCATTTTACCCC
29203982 AA-TTTCA-CTAAAATTACCATTTTACCCCC
1 AACTTT-ATC-AAAATTACCATTTTA-CCCC
*
29204011 AAACTTT-CCAAAATT-CCATTTTGACCCC
1 -AACTTTATCAAAATTACCATTTT-ACCCC
29204039 AA-TTTCATCAAAATTACCATTTTACCCC
1 AACTTT-ATCAAAATTACCATTTTACCCC
29204067 A
1 A
29204068 GAGTATATAA
Statistics
Matches: 96, Mismatches: 5, Indels: 25
0.76 0.04 0.20
Matches are distributed among these distances:
26 6 0.06
27 10 0.10
28 36 0.38
29 38 0.40
30 3 0.03
31 3 0.03
ACGTcount: A:0.35, C:0.29, G:0.01, T:0.36
Consensus pattern (28 bp):
AACTTTATCAAAATTACCATTTTACCCC
Found at i:29204015 original size:57 final size:57
Alignment explanation
Indices: 29203914--29204066 Score: 206
Period size: 57 Copynumber: 2.7 Consensus size: 57
29203904 AAAAATAATG
* **
29203914 TTTTGACCCCTGAACTTT-ATCAAAATTACCA-TTTACCCTCAAACTTTTTTAAAATTCCA
1 TTTTGACCCC--AA-TTTCATCAAAATTACCATTTTACCCCCAAAC-TTTCCAAAATTCCA
29203973 TTTT-ACCCCAATTTCA-CTAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCA
1 TTTTGACCCCAATTTCATC-AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCA
29204029 TTTTGACCCCAATTTCATCAAAATTACCATTTTACCCC
1 TTTTGACCCCAATTTCATCAAAATTACCATTTTACCCC
29204067 AGAGTATATA
Statistics
Matches: 86, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
55 4 0.05
56 29 0.34
57 43 0.50
58 6 0.07
59 4 0.05
ACGTcount: A:0.32, C:0.29, G:0.02, T:0.37
Consensus pattern (57 bp):
TTTTGACCCCAATTTCATCAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCA
Found at i:29204079 original size:28 final size:26
Alignment explanation
Indices: 29203963--29204067 Score: 122
Period size: 28 Copynumber: 3.8 Consensus size: 26
29203953 CAAACTTTTT
29203963 TAAAATTCCATTTTACCCCAATTTCA
1 TAAAATTCCATTTTACCCCAATTTCA
29203989 CTAAAATTACCATTTTACCCCCAAACTTTC-
1 -TAAAATT-CCATTTTA-CCCC-AA-TTTCA
*
29204019 CAAAATTCCATTTTGACCCCAATTTCA
1 TAAAATTCCATTTT-ACCCCAATTTCA
29204046 TCAAAATTACCATTTTACCCCA
1 T-AAAATT-CCATTTTACCCCA
29204068 GAGTATATAA
Statistics
Matches: 68, Mismatches: 2, Indels: 15
0.80 0.02 0.18
Matches are distributed among these distances:
26 4 0.06
27 9 0.13
28 31 0.46
29 18 0.26
30 2 0.03
31 4 0.06
ACGTcount: A:0.34, C:0.30, G:0.01, T:0.34
Consensus pattern (26 bp):
TAAAATTCCATTTTACCCCAATTTCA
Found at i:29210838 original size:49 final size:49
Alignment explanation
Indices: 29210793--29210938 Score: 204
Period size: 49 Copynumber: 3.0 Consensus size: 49
29210783 GTGTACCTCA
*
29210793 GAAGACA-GAAGGGAAAGATTTAAGCCGCAACGACGGATCCAGTACCAT
1 GAAGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCAT
* * **
29210841 GAAGACATCAAAGGAAAGATCTAAGCCGCAACGGTGGATCCAGTACCAT
1 GAAGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCAT
* * *
29210890 GAAGATATGAAGAGAAAGATCTAAGACCGCGACGACGGATCCAGTACCA
1 GAAGACATGAAGGGAAAGATCTAAG-CCGCAACGACGGATCCAGTACCA
29210939 CAATGAGGCA
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
48 7 0.08
49 57 0.68
50 20 0.24
ACGTcount: A:0.40, C:0.21, G:0.26, T:0.13
Consensus pattern (49 bp):
GAAGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCCAGTACCAT
Found at i:29211637 original size:200 final size:200
Alignment explanation
Indices: 29211290--29211932 Score: 968
Period size: 200 Copynumber: 3.2 Consensus size: 200
29211280 GATTATACAC
29211290 AAAC-AGCGAGGCGATCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACAC
1 AAACAAGCGAGGCGATCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACAC
* *
29211354 GAGTAAATCTTCGAACCCAGCTTCCTGATGAGACACTAAGAAGCAGGTCGAAGCAATAAAATGGT
66 GAGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGT
* * * *
29211419 TAGCTTCCTGAAGAGATACAAAGAAGCGGACCAAATTCGTCTTCCTGATGAGACACAGAGAAGCG
131 TAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAGAAACG
29211484 AATTG
196 AATTG
* *
29211489 AAACAAGCGAGGCGGTCATCTTCCTGATGAGATATAGAGAAGAATACCAACTCAACGCTCAACAC
1 AAACAAGCGAGGCGATCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACAC
*
29211554 GAGCAAATCTTCGAACCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGT
66 GAGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGT
* * *
29211619 TAGCTTCCTGATGAGATACAGAGAAGTGGACCGAATTCGTCTTCCTGATGGGACACAGAGAAACA
131 TAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAGAAACG
29211684 AATTG
196 AATTG
* *
29211689 AAACAAGCGAGGCGATCATCTTCCTGATAAGATACAGAGAAGAATACCAACTCAACGCTCAACGC
1 AAACAAGCGAGGCGATCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACAC
* **
29211754 GAGCAAATCTTTGAACTTAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGT
66 GAGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGT
* * * * *
29211819 TAGCTTCTTGAT-ATGATACAGAGAAGTGAACCAAATCCGTCTTCCTG-TGAAAACCCAGAGAAA
131 TAGCTTCCTGATGA-GATACAGAGAAGTGGACCAAATTCGTCTTCCTGATG-AGACACAGAGAAA
* * **
29211882 TGGATCA
194 CGAATTG
* * * * *
29211889 AAACAAACGACGCGGTCATCTTCCTGATGAGACACTGAGAAGAA
1 AAACAAGCGAGGCGATCATCTTCCTGATGAGATACAGAGAAGAA
29211933 GGCCAAATAA
Statistics
Matches: 403, Mismatches: 38, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
199 7 0.02
200 396 0.98
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (200 bp):
AAACAAGCGAGGCGATCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACAC
GAGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGT
TAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAGAAACG
AATTG
Found at i:29212274 original size:11 final size:11
Alignment explanation
Indices: 29212272--29212330 Score: 75
Period size: 11 Copynumber: 5.3 Consensus size: 11
29212262 ATTTATTTTA
29212272 AATTTAAATTT
1 AATTTAAATTT
*
29212283 ATTTTAAATTT
1 AATTTAAATTT
29212294 AAATTT-AATTT
1 -AATTTAAATTT
*
29212305 AAGTTTGAATTT
1 AA-TTTAAATTT
29212317 AATTTAAATTT
1 AATTTAAATTT
29212328 AAT
1 AAT
29212331 ATTATTGCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
10 2 0.05
11 29 0.69
12 11 0.26
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:29212278 original size:17 final size:17
Alignment explanation
Indices: 29212258--29212329 Score: 108
Period size: 17 Copynumber: 4.2 Consensus size: 17
29212248 TGCTCTGAAA
*
29212258 TTAAATTTATTTTAAAT
1 TTAAATTTAATTTAAAT
*
29212275 TTAAATTTATTTTAAAT
1 TTAAATTTAATTTAAAT
*
29212292 TTAAATTTAATTTAAGT
1 TTAAATTTAATTTAAAT
*
29212309 TTGAATTTAATTTAAAT
1 TTAAATTTAATTTAAAT
29212326 TTAA
1 TTAA
29212330 TATTATTGCA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 50 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TTAAATTTAATTTAAAT
Found at i:29212298 original size:23 final size:23
Alignment explanation
Indices: 29212268--29212328 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
29212258 TTAAATTTAT
*
29212268 TTTAAATTTAAATTTATTTTAAA
1 TTTAAATTTAAATTTAGTTTAAA
*
29212291 TTTAAATTT-AATTTAAGTTTGAA
1 TTTAAATTTAAATTT-AGTTTAAA
29212314 TTT-AATTTAAATTTA
1 TTTAAATTTAAATTTA
29212329 ATATTATTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 11 0.32
23 23 0.68
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (23 bp):
TTTAAATTTAAATTTAGTTTAAA
Found at i:29212303 original size:28 final size:29
Alignment explanation
Indices: 29212253--29212330 Score: 90
Period size: 28 Copynumber: 2.8 Consensus size: 29
29212243 GAATTTGCTC
* *
29212253 TGAAATTAAATTT-ATTTTAAATTTAAATT
1 TGAATTTAAATTTAAATTT-AATTTAAATT
* *
29212282 T-ATTTTAAATTTAAATTTAATTTAAGTT
1 TGAATTTAAATTTAAATTTAATTTAAATT
29212310 TGAATTT-AATTTAAATTTAAT
1 TGAATTTAAATTTAAATTTAAT
29212331 ATTATTGCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
28 33 0.79
29 9 0.21
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (29 bp):
TGAATTTAAATTTAAATTTAATTTAAATT
Found at i:29214339 original size:29 final size:28
Alignment explanation
Indices: 29214302--29214420 Score: 102
Period size: 29 Copynumber: 4.1 Consensus size: 28
29214292 AAAAATAATG
29214302 TTTTAACCCTGAACTTTATCAAAATTACCA
1 TTTT-ACCCTGAACTTTATCAAAATT-CCA
*
29214332 TTTTACCCTCGAACTTTCT-AAAATTCCA
1 TTTTACCCT-GAACTTTATCAAAATTCCA
* *
29214360 TTTTTGCCCTG-A-TTTCACCAAAATTGCCA
1 -TTTTACCCTGAACTTT-ATCAAAATT-CCA
* *
29214389 TTTTACCCCTAAACTTT-CCAAAATTCCA
1 TTTTA-CCCTGAACTTTATCAAAATTCCA
29214417 TTTT
1 TTTT
29214421 TCCCCAATGT
Statistics
Matches: 75, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
26 3 0.04
27 1 0.01
28 21 0.28
29 34 0.45
30 13 0.17
31 3 0.04
ACGTcount: A:0.29, C:0.27, G:0.04, T:0.39
Consensus pattern (28 bp):
TTTTACCCTGAACTTTATCAAAATTCCA
Found at i:29214382 original size:28 final size:29
Alignment explanation
Indices: 29214351--29214453 Score: 83
Period size: 28 Copynumber: 3.7 Consensus size: 29
29214341 CGAACTTTCT
*
29214351 AAAATT-CCATTTTTGCCCTGATTTCACC
1 AAAATTACCATTTTTGCCCTAATTTCACC
* **
29214379 AAAATTGCCATTTTACCCCTAAACTTT--CC
1 AAAATTACCATTTTTGCCCT-AA-TTTCACC
* * *
29214408 AAAATT-CCATTTTT-CCCCAATGTCATC
1 AAAATTACCATTTTTGCCCTAATTTCACC
29214435 AAAATTACCA-TTTTGCCCT
1 AAAATTACCATTTTTGCCCT
29214454 CGAGTATCAA
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
25 2 0.03
26 2 0.03
27 14 0.23
28 19 0.32
29 19 0.32
30 1 0.02
31 3 0.05
ACGTcount: A:0.29, C:0.29, G:0.05, T:0.37
Consensus pattern (29 bp):
AAAATTACCATTTTTGCCCTAATTTCACC
Found at i:29214390 original size:57 final size:56
Alignment explanation
Indices: 29214321--29214456 Score: 175
Period size: 57 Copynumber: 2.4 Consensus size: 56
29214311 TGAACTTTAT
* ** *
29214321 CAAAATTACCATTTTACCCTCGAACTTTCTAAAATTCCATTTTTGCCCTGATTTCAC
1 CAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTT-CCCCAATGTCAC
* * *
29214378 CAAAATTGCCATTTTACCC-CTAAACTTTCCAAAATTCCATTTTTCCCCAATGTCAT
1 CAAAATTACCATTTTACCCTC-GAACTTTCCAAAATTCCATTTTTCCCCAATGTCAC
*
29214434 CAAAATTACCATTTTGCCCTCGA
1 CAAAATTACCATTTTACCCTCGA
29214457 GTATCAAAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
56 27 0.40
57 40 0.60
ACGTcount: A:0.29, C:0.29, G:0.05, T:0.36
Consensus pattern (56 bp):
CAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTCCCCAATGTCAC
Found at i:29214421 original size:29 final size:29
Alignment explanation
Indices: 29214279--29214425 Score: 85
Period size: 29 Copynumber: 5.1 Consensus size: 29
29214269 CCCTAAGAGT
* * * *
29214279 CCCTAAACTATCCAAAAAT-AATGTTTTAA
1 CCCTAAACTTTCCAAAATTCCAT-TTTTAC
* *
29214308 CCCTGAACTTTATCAAAATTACCA-TTTTA-
1 CCCTAAACTTT-CCAAAATT-CCATTTTTAC
* * *
29214337 CCCTCGAACTTTCTAAAATTCCATTTTT-G
1 CCCT-AAACTTTCCAAAATTCCATTTTTAC
*
29214366 CCCT-GA-TTTCACCAAAATTGCCA-TTTTAC
1 CCCTAAACTTT--CCAAAATT-CCATTTTTAC
29214395 CCCTAAACTTTCCAAAATTCCATTTTT-C
1 CCCTAAACTTTCCAAAATTCCATTTTTAC
29214423 CCC
1 CCC
29214426 AATGTCATCA
Statistics
Matches: 94, Mismatches: 11, Indels: 27
0.71 0.08 0.20
Matches are distributed among these distances:
26 3 0.03
27 1 0.01
28 21 0.22
29 46 0.49
30 19 0.20
31 3 0.03
32 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.36
Consensus pattern (29 bp):
CCCTAAACTTTCCAAAATTCCATTTTTAC
Found at i:29222621 original size:24 final size:24
Alignment explanation
Indices: 29222582--29222644 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
29222572 TAAACTAATA
* * *
29222582 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
* *
29222606 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
29222630 AGGGTTTAACTGAAA
1 AGAGTTTAACTGAAA
29222645 GATTATTTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:29228185 original size:2 final size:2
Alignment explanation
Indices: 29228178--29228204 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29228168 AGCTGTCTAT
29228178 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
29228205 AAAAAATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:29230948 original size:15 final size:16
Alignment explanation
Indices: 29230916--29230948 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
29230906 TTTGATTTCA
29230916 AACCAATCAAGTACAC
1 AACCAATCAAGTACAC
29230932 AACCAATCAAG-ACAC
1 AACCAATCAAGTACAC
29230947 AA
1 AA
29230949 GTAGACACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.55, C:0.30, G:0.06, T:0.09
Consensus pattern (16 bp):
AACCAATCAAGTACAC
Found at i:29232694 original size:14 final size:15
Alignment explanation
Indices: 29232661--29232701 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
29232651 TTCCAAATAG
29232661 AATTAGAATAAATCTT
1 AATTA-AATAAATCTT
29232677 AATTAAATAAAT-TT
1 AATTAAATAAATCTT
*
29232691 AATTAATTAAA
1 AATTAAATAAA
29232702 ATTTTTATCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 12 0.50
15 7 0.29
16 5 0.21
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (15 bp):
AATTAAATAAATCTT
Found at i:29232911 original size:23 final size:23
Alignment explanation
Indices: 29232856--29232899 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
29232846 TAATGGAAAA
29232856 AAGATATTGGAATCAAAGATAAG
1 AAGATATTGGAATCAAAGATAAG
29232879 AAGATATTGGAATCAAAGATA
1 AAGATATTGGAATCAAAGATA
29232900 TTGAATCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.52, C:0.05, G:0.20, T:0.23
Consensus pattern (23 bp):
AAGATATTGGAATCAAAGATAAG
Found at i:29232954 original size:68 final size:68
Alignment explanation
Indices: 29232877--29233009 Score: 212
Period size: 68 Copynumber: 2.0 Consensus size: 68
29232867 ATCAAAGATA
* * *
29232877 AGAAGATATTGGAATCAAAGATATTGAATCTTTGGGTTAATGGGTTTTAAAAATTCAAGCTTTGA
1 AGAAGATATTGGAATCAAAGATATTGAATCTTTGGGTTAATAGATTTCAAAAATTCAAGCTTTGA
29232942 GGC
66 GGC
* * *
29232945 AGAAGATATTGGAATCAAAGATATTGAATTTTTGGGTTAATAGATTTCAAATATTCAAGTTTTGA
1 AGAAGATATTGGAATCAAAGATATTGAATCTTTGGGTTAATAGATTTCAAAAATTCAAGCTTTGA
29233010 AACAGATTTG
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 59 1.00
ACGTcount: A:0.37, C:0.06, G:0.21, T:0.36
Consensus pattern (68 bp):
AGAAGATATTGGAATCAAAGATATTGAATCTTTGGGTTAATAGATTTCAAAAATTCAAGCTTTGA
GGC
Found at i:29236053 original size:29 final size:28
Alignment explanation
Indices: 29236020--29236079 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
29236010 TTAAATTAGT
29236020 AATAAAAAAATTACAGTTTAATCTTTTAA
1 AATAAAAAAATTACA-TTTAATCTTTTAA
* **
29236049 AATAATAAAATTTGATTTAATCTTTTAA
1 AATAAAAAAATTACATTTAATCTTTTAA
29236077 AAT
1 AAT
29236080 TTATAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 16 0.57
29 12 0.43
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (28 bp):
AATAAAAAAATTACATTTAATCTTTTAA
Found at i:29236113 original size:17 final size:17
Alignment explanation
Indices: 29236074--29236113 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
29236064 TTTAATCTTT
29236074 TAAAATT-TATAAAAAA
1 TAAAATTATATAAAAAA
29236090 T-AAATTAT-TAAAATAA
1 TAAAATTATATAAAA-AA
29236106 TAAAATTA
1 TAAAATTA
29236114 CATTTTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 10 0.48
16 5 0.24
17 6 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAATTATATAAAAAA
Found at i:29237673 original size:21 final size:21
Alignment explanation
Indices: 29237647--29237687 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
29237637 TAACGGAACC
29237647 GCTTATGTGGCAAGTTAACTA
1 GCTTATGTGGCAAGTTAACTA
*
29237668 GCTTATGTGGCCAGTTAACT
1 GCTTATGTGGCAAGTTAACT
29237688 TGACTTGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
GCTTATGTGGCAAGTTAACTA
Found at i:29238738 original size:15 final size:17
Alignment explanation
Indices: 29238718--29238750 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
29238708 TAAGCCTTGC
29238718 AAAAAAC-TAAAA-AAA
1 AAAAAACATAAAAGAAA
29238733 AAAAAACATAAAAGAAA
1 AAAAAACATAAAAGAAA
29238750 A
1 A
29238751 CAACAAGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 5 0.31
17 4 0.25
ACGTcount: A:0.85, C:0.06, G:0.03, T:0.06
Consensus pattern (17 bp):
AAAAAACATAAAAGAAA
Found at i:29238908 original size:3 final size:3
Alignment explanation
Indices: 29238900--29238944 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
29238890 TTTTTCTCAG
*
29238900 CTT CTT CTT CTT CTT CTT CTT CTT CTT TTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
29238945 AAACCTTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
CTT
Found at i:29278591 original size:73 final size:74
Alignment explanation
Indices: 29278482--29278625 Score: 238
Period size: 73 Copynumber: 2.0 Consensus size: 74
29278472 GTCCTATTTA
*
29278482 AATGCTTTGTTGCCTTATTATTTGTCAAATAAAACTGCCTATATTGCTAACAATTCC-CCTTTCT
1 AATGCTTTGTTGCCTTATTATTTGTCAAATAAAACTGCCAATATTGCTAACAA-TCCTCCTTTCT
29278546 TTCTTTCTTC
65 TTCTTTCTTC
* *
29278556 AATGCTTTGTTGCCTTA-TATTTGTCAGATAAAACTGCCAATATTGTTAACAATCCTCCTTTCTT
1 AATGCTTTGTTGCCTTATTATTTGTCAAATAAAACTGCCAATATTGCTAACAATCCTCCTTTCTT
29278620 TCTTTC
66 TCTTTC
29278626 AGCTGTGCTA
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
72 3 0.05
73 46 0.70
74 17 0.26
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.45
Consensus pattern (74 bp):
AATGCTTTGTTGCCTTATTATTTGTCAAATAAAACTGCCAATATTGCTAACAATCCTCCTTTCTT
TCTTTCTTC
Found at i:29279375 original size:42 final size:42
Alignment explanation
Indices: 29279328--29279524 Score: 238
Period size: 42 Copynumber: 4.8 Consensus size: 42
29279318 TTCCCCCGTG
* *
29279328 ACAAGCACAAGCAATGGTATCTTCGGTGGTACATCTGCAAAT
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAAAT
* *
29279370 ACAAGCGCAGGCAATGGTATCTTTGGTGGTACATCTGCAACT
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAAAT
* * * * *
29279412 ACAAGCACGGGCACTGGTTTATTTGGTGCTACATCTGCAAAT
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAAAT
* *
29279454 ACAAGCACTGGCAATGGCATCTTTGGTGGTACATCTGC--A-
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAAAT
* * * *
29279493 ACAAGCACAGGTAGTAGTATTTTTGGTGGTAC
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTAC
29279525 TTCTTTGCCA
Statistics
Matches: 132, Mismatches: 23, Indels: 3
0.84 0.15 0.02
Matches are distributed among these distances:
39 26 0.20
40 1 0.01
42 105 0.80
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (42 bp):
ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAAAT
Found at i:29284263 original size:28 final size:28
Alignment explanation
Indices: 29284232--29284294 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
29284222 AAAACGGGAC
*
29284232 TTTTGGA-TACCCGGGGGCAAAATGGTAA
1 TTTTGGACT-CCCAGGGGCAAAATGGTAA
** *
29284260 TTTTGGACTTTCAGGGGCAAAATTGTAA
1 TTTTGGACTCCCAGGGGCAAAATGGTAA
29284288 TTTTGGA
1 TTTTGGA
29284295 GAAATCGGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.27, C:0.11, G:0.29, T:0.33
Consensus pattern (28 bp):
TTTTGGACTCCCAGGGGCAAAATGGTAA
Found at i:29284322 original size:57 final size:56
Alignment explanation
Indices: 29284245--29284406 Score: 157
Period size: 57 Copynumber: 2.8 Consensus size: 56
29284235 TGGATACCCG
* ** * *
29284245 GGGGCAAAATGGTAATTTTGGACTTTCAGGGGCAAAATTGTAATTTTGG-AGAAATC
1 GGGGCAAAATGGTAACTTTGGAAGTTCAGGGGCAAAATGGTAAATTTGGTA-AAATC
* *
29284301 GGGGCTAAAATTGTAACTTTGGAAGTTCAGGGGTAAAATGGTAAATTTGGTAAAATC
1 GGGGC-AAAATGGTAACTTTGGAAGTTCAGGGGCAAAATGGTAAATTTGGTAAAATC
* * * * *
29284358 GAGGTCAAAAAT-GAAATTTTGGAAAGTTTAGGGGTAAAATGGTAAATTT
1 G-GGGC-AAAATGGTAACTTTGG-AAGTTCAGGGGCAAAATGGTAAATTT
29284407 TTTGGTGAAA
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
56 5 0.06
57 51 0.57
58 34 0.38
ACGTcount: A:0.36, C:0.06, G:0.28, T:0.30
Consensus pattern (56 bp):
GGGGCAAAATGGTAACTTTGGAAGTTCAGGGGCAAAATGGTAAATTTGGTAAAATC
Found at i:29284333 original size:29 final size:28
Alignment explanation
Indices: 29284245--29284563 Score: 123
Period size: 28 Copynumber: 10.9 Consensus size: 28
29284235 TGGATACCCG
**
29284245 GGGGCAAAATGGTAATTTTGGACTTTCA
1 GGGGCAAAATGGTAATTTTGGAAATTCA
* *
29284273 GGGGCAAAATTGTAATTTTGGAGAAATC-
1 GGGGCAAAATGGTAATTTTGGA-AATTCA
* * *
29284301 GGGGCTAAAATTGTAACTTTGGAAGTTCA
1 GGGGC-AAAATGGTAATTTTGGAAATTCA
* * *
29284330 GGGGTAAAATGGTAAATTTGGTAAAATC-
1 GGGGCAAAATGGTAATTTTGG-AAATTCA
* * *
29284358 GAGGTCAAAAAT-GAAATTTTGGAAAGTTTA
1 G-GGGC-AAAATGGTAATTTTGGAAA-TTCA
*
29284388 GGGGTAAAATGGTAAATTTTTTGGTGAAATT--
1 GGGGCAAAATGGT-AA--TTTT-G-GAAATTCA
* * *
29284419 GGGGATAAAAATGG-AATTTTGGAAGGTTCG
1 GGGG--CAAAATGGTAATTTTGGAA-ATTCA
* * *
29284449 GGGGTAAAATGGTAATTTTTAGTGAAACTGA
1 GGGGCAAAATGGTAA-TTTT-G-GAAATTCA
* **** *
29284480 -GGTCAAAAACAAAATTTTGGAAAGTTCG
1 GGGGCAAAATGGTAATTTTGGAAA-TTCA
* * *
29284508 GGGGTAAAATGGTAAATTATGGAAAAGTTTA
1 GGGGCAAAATGGT-AATTTTGG-AAA-TTCA
29284539 GGGGTCAAAAT-GTAATTTTGGAAAT
1 GGGG-CAAAATGGTAATTTTGGAAAT
29284564 GTTTTAGGGT
Statistics
Matches: 215, Mismatches: 48, Indels: 56
0.67 0.15 0.18
Matches are distributed among these distances:
27 7 0.03
28 65 0.30
29 59 0.27
30 38 0.18
31 20 0.09
32 12 0.06
33 10 0.05
34 4 0.02
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.30
Consensus pattern (28 bp):
GGGGCAAAATGGTAATTTTGGAAATTCA
Found at i:29284407 original size:30 final size:30
Alignment explanation
Indices: 29284301--29284621 Score: 115
Period size: 30 Copynumber: 10.8 Consensus size: 30
29284291 TGGAGAAATC
* * *
29284301 GGGGCTAAAATTGT-AACTTTGG-AAGTTCA
1 GGGG-TAAAATGGTAAATTTTGGAAAGTTTA
* **
29284330 GGGGTAAAATGGTAAA-TTTGGTAAAATCGA
1 GGGGTAAAATGGTAAATTTTGG-AAAGTTTA
***
29284360 GGTCAAAAAT-G-AAATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAAATTTTGGAAAGTTTA
29284388 GGGGTAAAATGGTAAATTTTTTGGTGAAA--TT-
1 GGGGTAAAATGGTAAA--TTTT-G-GAAAGTTTA
* **
29284419 GGGGATAAAAATGG--AATTTTGGAAGGTTCG
1 GGGG-T-AAAATGGTAAATTTTGGAAAGTTTA
* *
29284449 GGGGTAAAATGGTAATTTTTAGTGAAA--CT-
1 GGGGTAAAATGGTAAATTTT-G-GAAAGTTTA
* *** **
29284478 GAGGTCAAAA-ACAAAATTTTGGAAAGTTCG
1 GGGGT-AAAATGGTAAATTTTGGAAAGTTTA
*
29284508 GGGGTAAAATGGTAAATTATGGAAAAGTTTA
1 GGGGTAAAATGGTAAATTTTGG-AAAGTTTA
29284539 GGGGTCAAAAT-GT-AATTTTGGAAATGTTTTA
1 GGGGT-AAAATGGTAAATTTTGGAAA-G-TTTA
* * *
29284570 -GGGTTAAA--GTATAATTTTAGAAAAGTTTT
1 GGGGTAAAATGGTA-AATTTT-GGAAAGTTTA
*
29284599 GGGGTCAAAAT-GTAATTTTTGGA
1 GGGGT-AAAATGGTAAATTTTGGA
29284622 TTGTTTGGGG
Statistics
Matches: 218, Mismatches: 40, Indels: 67
0.67 0.12 0.21
Matches are distributed among these distances:
27 7 0.03
28 39 0.18
29 42 0.19
30 64 0.29
31 36 0.17
32 18 0.08
33 8 0.04
34 4 0.02
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.32
Consensus pattern (30 bp):
GGGGTAAAATGGTAAATTTTGGAAAGTTTA
Found at i:29284497 original size:59 final size:59
Alignment explanation
Indices: 29284318--29284522 Score: 238
Period size: 59 Copynumber: 3.5 Consensus size: 59
29284308 AAATTGTAAC
*
29284318 TTTGG-AAGTTCAGGGGTAAAATGGTAA-ATTTGGT-AAAATCGAGGTCAAAAATGAAAT
1 TTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTGAAAAT-GAGGTCAAAAATGAAAT
* * * *
29284375 TTTGGAAAGTTTAGGGGTAAAATGGTAAATTTTTTGGTGAAATTGGGGAT-AAAAATGGAAT
1 TTTGGAAAGTTCAGGGGTAAAATGGT-AA-TTTTTGGTGAAAATGAGG-TCAAAAATGAAAT
* * * * **
29284436 TTTGGAAGGTTCGGGGGTAAAATGGTAATTTTTAGTGAAACTGAGGTCAAAAACAAAAT
1 TTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTGAAAATGAGGTCAAAAATGAAAT
*
29284495 TTTGGAAAGTTCGGGGGTAAAATGGTAA
1 TTTGGAAAGTTCAGGGGTAAAATGGTAA
29284523 ATTATGGAAA
Statistics
Matches: 126, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
57 5 0.04
58 20 0.16
59 52 0.41
60 2 0.02
61 42 0.33
62 5 0.04
ACGTcount: A:0.37, C:0.04, G:0.29, T:0.30
Consensus pattern (59 bp):
TTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTGAAAATGAGGTCAAAAATGAAAT
Found at i:29284512 original size:120 final size:118
Alignment explanation
Indices: 29284288--29284525 Score: 316
Period size: 120 Copynumber: 2.0 Consensus size: 118
29284278 AAAATTGTAA
* * * *
29284288 TTTTGGAGAAATCGGGGCTAAAATTGTAACTTTGGAAGTTCAGGGGTAAAATGGTAAATTTGGTA
1 TTTTGGAGAAATCGGGGATAAAAATGGAACTTTGGAAGTTCAGGGGTAAAATGGTAAATTTAGTA
** *
29284353 AAATCGAGGTCAAAAATGAAATTTTGGAAAGTTTAGGGGTAAAATGGTAAATT
66 AAATCGAGGTCAAAAACAAAATTTTGGAAAGTTCAGGGGTAAAATGGTAAATT
* * * * *
29284406 TTTTGGTGAAATTGGGGATAAAAATGGAATTTTGGAAGGTTCGGGGGTAAAATGGTAATTTTTAG
1 TTTTGGAGAAATCGGGGATAAAAATGGAACTTTGGAA-GTTCAGGGGTAAAATGGTAA-ATTTAG
* *
29284471 TGAAA-CTGAGGTCAAAAACAAAATTTTGGAAAGTTCGGGGGTAAAATGGTAAATT
64 TAAAATC-GAGGTCAAAAACAAAATTTTGGAAAGTTCAGGGGTAAAATGGTAAATT
29284526 ATGGAAAAGT
Statistics
Matches: 103, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
118 31 0.30
119 20 0.19
120 52 0.50
ACGTcount: A:0.37, C:0.05, G:0.28, T:0.31
Consensus pattern (118 bp):
TTTTGGAGAAATCGGGGATAAAAATGGAACTTTGGAAGTTCAGGGGTAAAATGGTAAATTTAGTA
AAATCGAGGTCAAAAACAAAATTTTGGAAAGTTCAGGGGTAAAATGGTAAATT
Found at i:29284543 original size:31 final size:31
Alignment explanation
Indices: 29284491--29284621 Score: 121
Period size: 30 Copynumber: 4.3 Consensus size: 31
29284481 GTCAAAAACA
**
29284491 AAATTTTGG-AAAGTTCGGGGGT-AAAATGGT
1 AAATTTTGGAAAAGTTTAGGGGTCAAAAT-GT
*
29284521 AAATTATGGAAAAGTTTAGGGGTCAAAATGT
1 AAATTTTGGAAAAGTTTAGGGGTCAAAATGT
* *
29284552 -AATTTTGGAAATGTTTTA-GGGT-TAAA-GT
1 AAATTTTGGAAAAG-TTTAGGGGTCAAAATGT
* *
29284580 ATAATTTTAGAAAAGTTTTGGGGTCAAAATGT
1 A-AATTTTGGAAAAGTTTAGGGGTCAAAATGT
*
29284612 AATTTTTGGA
1 AAATTTTGGA
29284622 TTGTTTGGGG
Statistics
Matches: 81, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
28 2 0.02
29 6 0.07
30 38 0.47
31 27 0.33
32 8 0.10
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (31 bp):
AAATTTTGGAAAAGTTTAGGGGTCAAAATGT
Found at i:29284587 original size:120 final size:119
Alignment explanation
Indices: 29284269--29284561 Score: 280
Period size: 120 Copynumber: 2.5 Consensus size: 119
29284259 ATTTTGGACT
* * * * * * *
29284269 TTCAGGGGCAAAATTGT-AATTT-TGG-AGAAATCGGGGCTAAAATTGTAACTTTGGAA-GTTCA
1 TTCAGGGGTAAAATGGTAAATTTATGGTA-AAATTGGGGATAAAAATGGAATTTTGGAAGGTTCA
* * * * **
29284330 GGGGTAAAATGGTAA-ATTTGGT-AAAATCGAGGTCAAAAATGAAATTTTGGAAAG
65 GGGGTAAAATGATAATTTTTAGTGAAACT-GAGGTCAAAAACAAAATTTTGGAAAG
* * * *
29284384 TTTAGGGGTAAAATGGTAAATTTTTTGGTGAAATTGGGGATAAAAATGGAATTTTGGAAGGTTCG
1 TTCAGGGGTAAAATGGTAAA-TTTATGGTAAAATTGGGGATAAAAATGGAATTTTGGAAGGTTCA
*
29284449 GGGGTAAAATGGTAATTTTTAGTGAAACTGAGGTCAAAAACAAAATTTTGGAAAG
65 GGGGTAAAATGATAATTTTTAGTGAAACTGAGGTCAAAAACAAAATTTTGGAAAG
* * *
29284504 TTCGGGGGTAAAATGGTAAA-TTATGG-AAAAGTTTAGGGG-TCAAAATGTAATTTTGGAA
1 TTCAGGGGTAAAATGGTAAATTTATGGTAAAA--TT-GGGGATAAAAATGGAATTTTGGAA
29284562 ATGTTTTAGG
Statistics
Matches: 147, Mismatches: 21, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
115 14 0.10
116 2 0.01
117 6 0.04
118 32 0.22
119 38 0.26
120 51 0.35
121 4 0.03
ACGTcount: A:0.37, C:0.05, G:0.28, T:0.30
Consensus pattern (119 bp):
TTCAGGGGTAAAATGGTAAATTTATGGTAAAATTGGGGATAAAAATGGAATTTTGGAAGGTTCAG
GGGTAAAATGATAATTTTTAGTGAAACTGAGGTCAAAAACAAAATTTTGGAAAG
Found at i:29286541 original size:12 final size:12
Alignment explanation
Indices: 29286519--29286562 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
29286509 AGTTAAATTC
29286519 AAATTCAAATTTA
1 AAATT-AAATTTA
*
29286532 AAATTGAATTTA
1 AAATTAAATTTA
29286544 AAA-TAAATTTA
1 AAATTAAATTTA
29286555 AAATTAAA
1 AAATTAAA
29286563 ATAATTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 10 0.36
12 13 0.46
13 5 0.18
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (12 bp):
AAATTAAATTTA
Found at i:29286554 original size:11 final size:11
Alignment explanation
Indices: 29286525--29286558 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
29286515 ATTCAAATTC
29286525 AAATTTAAAATT
1 AAATTTAAAA-T
*
29286537 GAATTTAAAAT
1 AAATTTAAAAT
29286548 AAATTTAAAAT
1 AAATTTAAAAT
29286559 TAAAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (11 bp):
AAATTTAAAAT
Found at i:29288942 original size:158 final size:157
Alignment explanation
Indices: 29288651--29288971 Score: 444
Period size: 158 Copynumber: 2.0 Consensus size: 157
29288641 CTTTATATCA
29288651 TGTAATGCTCACACGAGCTATGAAATGGATCTGCTCACACGAGCTTGGGTCGAGATGTTGAGCTA
1 TGTAATGCTCACACGAGCTATGAAATGGATCTGCTCACACGAGCTTGGGTCGAGATGTTGAGCTA
* ** * * * * * *
29288716 CATGATGCTACTCACACGAGTTGTGGAGAATCCAGAATGATTACTGGATCTCAGCCATCAGTAGG
66 CACGATGCTACTCACACGAACTATGGAGAATCCACAATGATTACCGAATCTCAACCATCAGTAAG
* *
29288781 ACATCTAAGACTAGCACTTATGTAACC
131 ACATCTAAGACCAGCACTCATGTAACC
* * * * *
29288808 TGTAATGCTCACATGAGTTGTGAAATGGGTCTGCTCACATGAGCTGTGGGTCGAGATGTTGAGCT
1 TGTAATGCTCACACGAGCTATGAAATGGATCTGCTCACACGAGCT-TGGGTCGAGATGTTGAGCT
* ** * *
29288873 ACACGATGCTGCTCACACGAACTATGGAGAATTTACAATGATTGCCGAATCTCAACCATCGGTAA
65 ACACGATGCTACTCACACGAACTATGGAGAATCCACAATGATTACCGAATCTCAACCATCAGTAA
29288938 GACATCTAAGACCAGCACTCATGTAACC
130 GACATCTAAGACCAGCACTCATGTAACC
29288966 TGTAAT
1 TGTAAT
29288972 CCCAATAATG
Statistics
Matches: 142, Mismatches: 21, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
157 40 0.28
158 102 0.72
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (157 bp):
TGTAATGCTCACACGAGCTATGAAATGGATCTGCTCACACGAGCTTGGGTCGAGATGTTGAGCTA
CACGATGCTACTCACACGAACTATGGAGAATCCACAATGATTACCGAATCTCAACCATCAGTAAG
ACATCTAAGACCAGCACTCATGTAACC
Found at i:29300289 original size:50 final size:50
Alignment explanation
Indices: 29300229--29300578 Score: 395
Period size: 50 Copynumber: 7.0 Consensus size: 50
29300219 TGTAAATAGA
* *
29300229 TATACATGCTGACGAGCGTAAACATAGATATATGCTGGTGAGCATAAACG
1 TATACATGCTGACGAGCGTAAACATAGATATATGCTGGCGAGCGTAAACG
* *
29300279 TATACATGCTGACGAGTGTAAACATAGATATATGCTGGTGAGCGTAAACG
1 TATACATGCTGACGAGCGTAAACATAGATATATGCTGGCGAGCGTAAACG
* * * *
29300329 TATACATGCTGACGAGCATAAACGTAGGTACATGCTGGCGAGCGTAAACG
1 TATACATGCTGACGAGCGTAAACATAGATATATGCTGGCGAGCGTAAACG
* * * * *
29300379 TATACATGCTGGCGCGCATAAACAT--ATACATGCTGACGAGCGTAAACG
1 TATACATGCTGACGAGCGTAAACATAGATATATGCTGGCGAGCGTAAACG
* * *
29300427 TATATACATGCTGACGAGCATAAACGTAGATATATGTTGGCGAGCGTAAACG
1 --TATACATGCTGACGAGCGTAAACATAGATATATGCTGGCGAGCGTAAACG
* * * * ** * *
29300479 TATACATGCTGGCGAGTGTAAACAT--ATACATGTTGATGGGCGTAAATG
1 TATACATGCTGACGAGCGTAAACATAGATATATGCTGGCGAGCGTAAACG
*
29300527 TATATACATGCTGACGAGCGTAAACATAGATATATGTTGGCGAG-GATAAACG
1 --TATACATGCTGACGAGCGTAAACATAGATATATGCTGGCGAGCG-TAAACG
29300579 CATATTAGCT
Statistics
Matches: 256, Mismatches: 35, Indels: 16
0.83 0.11 0.05
Matches are distributed among these distances:
48 39 0.15
50 180 0.70
51 1 0.00
52 36 0.14
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.24
Consensus pattern (50 bp):
TATACATGCTGACGAGCGTAAACATAGATATATGCTGGCGAGCGTAAACG
Found at i:29300402 original size:100 final size:99
Alignment explanation
Indices: 29300227--29300578 Score: 465
Period size: 100 Copynumber: 3.5 Consensus size: 99
29300217 AATGTAAATA
* * * *
29300227 GATATACATGCTGACGAGCGTAAACATAGATATATGCTGGTGAGCATAAACGTATACATGCTGAC
1 GATATACATGCTGACGAGCATAAACATAGATATATGCTGGCGAGCGTAAACGTATACATGCTGGC
* *
29300292 GAGTGTAAACATAGATATATGCTGGTGAGCGTAAAC
66 GAGTGTAAACAT--ATACATGCTGATGAGCGTAAAC
* * *
29300328 G-TATACATGCTGACGAGCATAAACGTAGGTACATGCTGGCGAGCGTAAACGTATACATGCTGGC
1 GATATACATGCTGACGAGCATAAACATAGATATATGCTGGCGAGCGTAAACGTATACATGCTGGC
* ** *
29300392 GCGCATAAACATATACATGCTGACGAGCGTAAAC
66 GAGTGTAAACATATACATGCTGATGAGCGTAAAC
* *
29300426 GTATATACATGCTGACGAGCATAAACGTAGATATATGTTGGCGAGCGTAAACGTATACATGCTGG
1 G-ATATACATGCTGACGAGCATAAACATAGATATATGCTGGCGAGCGTAAACGTATACATGCTGG
* * *
29300491 CGAGTGTAAACATATACATGTTGATGGGCGTAAAT
65 CGAGTGTAAACATATACATGCTGATGAGCGTAAAC
* *
29300526 GTATATACATGCTGACGAGCGTAAACATAGATATATGTTGGCGAG-GATAAACG
1 G-ATATACATGCTGACGAGCATAAACATAGATATATGCTGGCGAGCG-TAAACG
29300579 CATATTAGCT
Statistics
Matches: 223, Mismatches: 25, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
98 20 0.09
99 1 0.00
100 201 0.90
101 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (99 bp):
GATATACATGCTGACGAGCATAAACATAGATATATGCTGGCGAGCGTAAACGTATACATGCTGGC
GAGTGTAAACATATACATGCTGATGAGCGTAAAC
Found at i:29300506 original size:74 final size:74
Alignment explanation
Indices: 29300230--29300554 Score: 330
Period size: 74 Copynumber: 4.3 Consensus size: 74
29300220 GTAAATAGAT
* * ** *
29300230 ATACATGCTGACGAGCGTAAACATAGATATATGCTGGTGAGCATAAACGTATACATGCTGACGAG
1 ATACATGCTGGCGAGCGTAAACAT--ATACATGCTGACGAGCATAAACATATACATGCTGACGAG
* *
29300295 TGTAAACATAG
64 CGTAAACGTAG
* * * * *
29300306 ATATATGCTGGTGAGCGTAAACGTATACATGCTGACGAGCATAAACGTAGGTACATGCTGGCGAG
1 ATACATGCTGGCGAGCGTAAACATATACATGCTGACGAGCATAAACATA--TACATGCTGACGAG
29300371 CGTAAACGT--
64 CGTAAACGTAG
* * *
29300380 ATACATGCTGGCGCGCATAAACATATACATGCTGACGAGCGTAAACGTATATACATGCTGACGAG
1 ATACATGCTGGCGAGCGTAAACATATACATGCTGACGAGCATAAAC--ATATACATGCTGACGAG
*
29300445 CATAAACGTAG
64 CGTAAACGTAG
* * * * ** * * *
29300456 ATATATGTTGGCGAGCGTAAACGTATACATGCTGGCGAGTGTAAACATATACATGTTGATGGGCG
1 ATACATGCTGGCGAGCGTAAACATATACATGCTGACGAGCATAAACATATACATGCTGACGAGCG
* *
29300521 TAAATGTAT
66 TAAACGTAG
*
29300530 ATACATGCTGACGAGCGTAAACATA
1 ATACATGCTGGCGAGCGTAAACATA
29300555 GATATATGTT
Statistics
Matches: 207, Mismatches: 36, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
74 126 0.61
76 81 0.39
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (74 bp):
ATACATGCTGGCGAGCGTAAACATATACATGCTGACGAGCATAAACATATACATGCTGACGAGCG
TAAACGTAG
Found at i:29300570 original size:26 final size:25
Alignment explanation
Indices: 29300230--29300578 Score: 289
Period size: 26 Copynumber: 13.9 Consensus size: 25
29300220 GTAAATAGAT
* *
29300230 ATACATGCTGACGAGCGTAAACATA
1 ATACATGCTGGCGAGCGTAAACGTA
* * *
29300255 GATATATGCTGGTGAGCATAAACGT-
1 -ATACATGCTGGCGAGCGTAAACGTA
* * *
29300280 ATACATGCTGACGAGTGTAAACATA
1 ATACATGCTGGCGAGCGTAAACGTA
* *
29300305 GATATATGCTGGTGAGCGTAAACGT-
1 -ATACATGCTGGCGAGCGTAAACGTA
* *
29300330 ATACATGCTGACGAGCATAAACGTA
1 ATACATGCTGGCGAGCGTAAACGTA
*
29300355 GGTACATGCTGGCGAGCGTAAACGT-
1 -ATACATGCTGGCGAGCGTAAACGTA
* * *
29300380 ATACATGCTGGCGCGCATAAACAT-
1 ATACATGCTGGCGAGCGTAAACGTA
*
29300404 ATACATGCTGACGAGCGTAAACGTA
1 ATACATGCTGGCGAGCGTAAACGTA
* *
29300429 TATACATGCTGACGAGCATAAACGTA
1 -ATACATGCTGGCGAGCGTAAACGTA
* *
29300455 GATATATGTTGGCGAGCGTAAACGT-
1 -ATACATGCTGGCGAGCGTAAACGTA
* *
29300480 ATACATGCTGGCGAGTGTAAACAT-
1 ATACATGCTGGCGAGCGTAAACGTA
* ** * *
29300504 ATACATGTTGATGGGCGTAAATGTA
1 ATACATGCTGGCGAGCGTAAACGTA
* *
29300529 TATACATGCTGACGAGCGTAAACATA
1 -ATACATGCTGGCGAGCGTAAACGTA
* *
29300555 GATATATGTTGGCGAG-GATAAACG
1 -ATACATGCTGGCGAGCG-TAAACG
29300579 CATATTAGCT
Statistics
Matches: 256, Mismatches: 58, Indels: 18
0.77 0.17 0.05
Matches are distributed among these distances:
24 115 0.45
25 1 0.00
26 140 0.55
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (25 bp):
ATACATGCTGGCGAGCGTAAACGTA
Found at i:29300620 original size:24 final size:24
Alignment explanation
Indices: 29300566--29300624 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
29300556 ATATATGTTG
*
29300566 GCGAGGATAAACGCATATTAGCTA
1 GCGAGCATAAACGCATATTAGCTA
*
29300590 GCAAGCATAAACGCATATTAGCTTA
1 GCGAGCATAAACGCATATTAGC-TA
29300615 -CGAGCATAAA
1 GCGAGCATAAA
29300625 TGTACTGAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 29 0.94
25 2 0.06
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20
Consensus pattern (24 bp):
GCGAGCATAAACGCATATTAGCTA
Found at i:29302552 original size:20 final size:21
Alignment explanation
Indices: 29302513--29302552 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
29302503 TGTGATCATT
* *
29302513 TCTTGTTGTATGGTTAAATGG
1 TCTTGTAGTATGGCTAAATGG
29302534 TCTTGTAGT-TGGCTAAATG
1 TCTTGTAGTATGGCTAAATG
29302553 CATGTATTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.20, C:0.07, G:0.28, T:0.45
Consensus pattern (21 bp):
TCTTGTAGTATGGCTAAATGG
Found at i:29304195 original size:32 final size:32
Alignment explanation
Indices: 29304130--29304197 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 32
29304120 TTCATTTGAA
*
29304130 TTCTTCCTCTTCTTTTCTCTCTGAAACTCTTC
1 TTCTTCCTCTTCTTTTCTCTCTCAAACTCTTC
*
29304162 TTCTTCTTCTTCTTTT-TCTTCTCAAA-TCTTTC
1 TTCTTCCTCTTCTTTTCTC-TCTCAAACTC-TTC
29304194 TTCT
1 TTCT
29304198 CTTGAGTTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 4 0.12
32 28 0.88
ACGTcount: A:0.09, C:0.31, G:0.01, T:0.59
Consensus pattern (32 bp):
TTCTTCCTCTTCTTTTCTCTCTCAAACTCTTC
Found at i:29304856 original size:42 final size:42
Alignment explanation
Indices: 29304809--29305005 Score: 238
Period size: 42 Copynumber: 4.8 Consensus size: 42
29304799 TTCCCCAGTG
* * *
29304809 ACAAGCACAAGCAATGGTATCTTCGGTGGTACATCTGCAAAT
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAACT
29304851 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAACT
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAACT
* ** * * *
29304893 ACAAGCACGGGCCCTGGTTTATTTGGTGCTACATCTGCAACT
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAACT
* *
29304935 ACAAGCACTGGCAATGGCATCTTTGGTGGTACATCTGC-A--
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAACT
* * * *
29304974 ACAAGCACAGGTAGTAGTATTTTTGGTGGTAC
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTAC
29305006 TTCTTTGCCA
Statistics
Matches: 133, Mismatches: 22, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
39 26 0.20
41 1 0.01
42 106 0.80
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (42 bp):
ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAACT
Found at i:29310103 original size:27 final size:29
Alignment explanation
Indices: 29310036--29310131 Score: 92
Period size: 27 Copynumber: 3.4 Consensus size: 29
29310026 GTCAAACTTG
*
29310036 AATTAAAATTTTGATTTTTGAATTTATATTA
1 AATTTAAA-TTTGA-TTTTGAATTTATATTA
* * *
29310067 AGTTTGAA-TTGATTTTAAATTTAT-TTA
1 AATTTAAATTTGATTTTGAATTTATATTA
* *
29310094 AATTTAAATTTG-TTTTGAATTTAAATTT
1 AATTTAAATTTGATTTTGAATTTATATTA
29310122 AA-TTAAATTT
1 AATTTAAATTT
29310132 AAAATGGTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
27 27 0.50
28 18 0.33
29 4 0.07
31 5 0.09
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (29 bp):
AATTTAAATTTGATTTTGAATTTATATTA
Found at i:29310136 original size:17 final size:16
Alignment explanation
Indices: 29310080--29310134 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
29310070 TTGAATTGAT
29310080 TTTAAATTTATTTAAA
1 TTTAAATTTATTTAAA
* *
29310096 TTTAAATTTGTTTTGAA
1 TTTAAATTT-ATTTAAA
*
29310113 TTTAAATTTAATTAAA
1 TTTAAATTTATTTAAA
29310129 TTTAAA
1 TTTAAA
29310135 ATGGTTTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
16 19 0.58
17 14 0.42
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:29310142 original size:33 final size:33
Alignment explanation
Indices: 29310075--29310142 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
29310065 TAAGTTTGAA
* * * *
29310075 TTGATTTTAAATTTATTTAAATTTAAATTTGTT
1 TTGAATTTAAATTTAATTAAATTTAAAATGGTT
29310108 TTGAATTTAAATTTAATTAAATTTAAAATGGTT
1 TTGAATTTAAATTTAATTAAATTTAAAATGGTT
29310141 TT
1 TT
29310143 AAACTTAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (33 bp):
TTGAATTTAAATTTAATTAAATTTAAAATGGTT
Found at i:29313724 original size:158 final size:158
Alignment explanation
Indices: 29313436--29313757 Score: 455
Period size: 158 Copynumber: 2.0 Consensus size: 158
29313426 CTTTATATCA
*
29313436 TGTAATGCTCACACGAGCTATGAAATGGGTCTGCTCACACGAGCTATGGGTTGAGATGCTGAGCT
1 TGTAATGCTCACACGAGCTATGAAATGGGTCTGCTCACACGAGCTATGAGTTGAGATGCTGAGCT
* * * * * * *
29313501 ACATGATGTTGCCCACACGAACTGTGGAGAATCCGTAATGATTGCTGAATCTCAGCCATCGGTAG
66 ACACGATGCTACCCACACGAACTATGGAGAATCCGCAATGATTGCCGAATCTCAACCATCGGTAG
*
29313566 GACATCTAAGACCAGCACCCATGTAATC
131 GACATCTAAGACCAGCACCCATGTAACC
* * * * * *
29313594 TGTAATGCTCACATGAGCTGTGAAATGGGTTTGCTCACATGAGCTGTGAGTTGAGATGTTGAGCT
1 TGTAATGCTCACACGAGCTATGAAATGGGTCTGCTCACACGAGCTATGAGTTGAGATGCTGAGCT
* * * * *
29313659 ACACGATGCTACTCACACGAGCTATGGAGAATCTGCAATGATTGCCGGATCTCAACCATTGGTAG
66 ACACGATGCTACCCACACGAACTATGGAGAATCCGCAATGATTGCCGAATCTCAACCATCGGTAG
*
29313724 GACATCTAAGACCAGCACCCATTTAACC
131 GACATCTAAGACCAGCACCCATGTAACC
29313752 TGTAAT
1 TGTAAT
29313758 CCCAATAACG
Statistics
Matches: 143, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
158 143 1.00
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.25
Consensus pattern (158 bp):
TGTAATGCTCACACGAGCTATGAAATGGGTCTGCTCACACGAGCTATGAGTTGAGATGCTGAGCT
ACACGATGCTACCCACACGAACTATGGAGAATCCGCAATGATTGCCGAATCTCAACCATCGGTAG
GACATCTAAGACCAGCACCCATGTAACC
Found at i:29317139 original size:2 final size:2
Alignment explanation
Indices: 29317132--29317173 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
29317122 ATTTAATTGA
29317132 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29317173 A
1 A
29317174 ATTGTTTATG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29320223 original size:18 final size:18
Alignment explanation
Indices: 29320200--29320236 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29320190 ACAATTCATA
29320200 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
29320218 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
29320236 T
1 T
29320237 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:29323363 original size:52 final size:52
Alignment explanation
Indices: 29323285--29323390 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
29323275 CTTATAATCG
29323285 GACCTCATAACCCATAAAGGATTCATATACTCACGATGACACATAGTCACCA
1 GACCTCATAACCCATAAAGGATTCATATACTCACGATGACACATAGTCACCA
** *
29323337 GACCTCATAACCTGTAAAGGATTCATATACTCACGATGACACATAGTCATCA
1 GACCTCATAACCCATAAAGGATTCATATACTCACGATGACACATAGTCACCA
29323389 GA
1 GA
29323391 TCTTTTCATT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (52 bp):
GACCTCATAACCCATAAAGGATTCATATACTCACGATGACACATAGTCACCA
Found at i:29327178 original size:46 final size:46
Alignment explanation
Indices: 29327103--29327268 Score: 239
Period size: 46 Copynumber: 3.6 Consensus size: 46
29327093 GATAAAAGAG
* *
29327103 AAACAAATCCCTGAAATTGAGGAAAACAAATGCCTACAATTTAG-C
1 AAACAAATCCCTGAAATTGTGGAAGACAAATGCCTACAATTTAGTC
*
29327148 TAAACAAATCTCTGAAATTGTGGAAGACAAATGCCTACAATTTAGTC
1 -AAACAAATCCCTGAAATTGTGGAAGACAAATGCCTACAATTTAGTC
* *
29327195 AAACAAAT-CCTTAGAATTGTGGAAGACAAATGCCTACACTTTAGTC
1 AAACAAATCCCTGA-AATTGTGGAAGACAAATGCCTACAATTTAGTC
*
29327241 AAACAAATCCCTAAAATTGT-GAAGACAA
1 AAACAAATCCCTGAAATTGTGGAAGACAA
29327269 CTTGACTTGA
Statistics
Matches: 110, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
45 11 0.10
46 94 0.85
47 5 0.05
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.23
Consensus pattern (46 bp):
AAACAAATCCCTGAAATTGTGGAAGACAAATGCCTACAATTTAGTC
Found at i:29327189 original size:23 final size:22
Alignment explanation
Indices: 29327102--29327232 Score: 76
Period size: 23 Copynumber: 5.7 Consensus size: 22
29327092 GGATAAAAGA
* *
29327102 GAAACAAATCCCTGA-AATTGAG
1 GAAACAAATGCCT-ACAATTGTG
29327124 GAAAACAAATGCCTACAATT-TAG
1 G-AAACAAATGCCTACAATTGT-G
*
29327147 CTAAACAAAT-CTCTGA-AATTGTG
1 -GAAACAAATGC-CT-ACAATTGTG
29327170 GAAGACAAATGCCTACAATT-TAG
1 GAA-ACAAATGCCTACAATTGT-G
* *
29327193 TCAAACAAAT-CCTTAGAATTGTG
1 -GAAACAAATGCC-TACAATTGTG
29327216 GAAGACAAATGCCTACA
1 GAA-ACAAATGCCTACA
29327233 CTTTAGTCAA
Statistics
Matches: 85, Mismatches: 8, Indels: 31
0.69 0.06 0.25
Matches are distributed among these distances:
22 11 0.13
23 66 0.78
24 8 0.09
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.23
Consensus pattern (22 bp):
GAAACAAATGCCTACAATTGTG
Found at i:29327246 original size:23 final size:22
Alignment explanation
Indices: 29327174--29327253 Score: 65
Period size: 23 Copynumber: 3.5 Consensus size: 22
29327164 ATTGTGGAAG
29327174 ACAAATGCCTACAATTTAGTCAA
1 ACAAATGCCTAC-ATTTAGTCAA
* * *
29327197 ACAAAT-CCTTAGAATT-GTGGAA
1 ACAAATGCC-TACATTTAGT-CAA
29327219 GACAAATGCCTACACTTTAGTCAA
1 -ACAAATGCCTACA-TTTAGTCAA
*
29327243 ACAAATCCCTA
1 ACAAATGCCTA
29327254 AAATTGTGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
21 2 0.05
22 7 0.16
23 27 0.61
24 6 0.14
25 2 0.05
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.25
Consensus pattern (22 bp):
ACAAATGCCTACATTTAGTCAA
Found at i:29330004 original size:28 final size:28
Alignment explanation
Indices: 29329955--29330010 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
29329945 GATATCCAAT
29329955 TTACTCCTTGTTAACCCAAAGGTCATGC
1 TTACTCCTTGTTAACCCAAAGGTCATGC
* * *
29329983 TTACTCCTTGTTGATCCGAAGGTCATGC
1 TTACTCCTTGTTAACCCAAAGGTCATGC
29330011 CTGTTACCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (28 bp):
TTACTCCTTGTTAACCCAAAGGTCATGC
Found at i:29335696 original size:26 final size:26
Alignment explanation
Indices: 29335667--29335923 Score: 98
Period size: 26 Copynumber: 10.2 Consensus size: 26
29335657 TTGGTGAATG
29335667 TAAATAGATATACATGCTGACGAGCA
1 TAAATAGATATACATGCTGACGAGCA
* * *
29335693 TAAA-CG-TATACATGCTTACGAGCCT
1 TAAATAGATATACATGCTGACGAG-CA
* * *
29335718 TAACGTAG--GTACATGCTGGCGAGCA
1 TAA-ATAGATATACATGCTGACGAGCA
* * *
29335743 TAAA-CG-TATACATGCTGATGAGCG
1 TAAATAGATATACATGCTGACGAGCA
* *
29335767 TAAA-CGTATATACATGTTGACGAG-A
1 TAAATAG-ATATACATGCTGACGAGCA
* * *
29335792 GTAAACGTAGATAT--ATACTGTCGAGCT
1 -TAAA--TAGATATACATGCTGACGAGCA
* * *
29335819 TAAA-CG-TATACATGCTGGCGAGCG
1 TAAATAGATATACATGCTGACGAGCA
* * * *
29335843 T-AA-ACATATACATGTTGATGAGCG
1 TAAATAGATATACATGCTGACGAGCA
*
29335867 TAAAT-GTATATACATGCTGACGAGCG
1 TAAATAG-ATATACATGCTGACGAGCA
* *
29335893 TAAACATAGATAT--ATGTTGGCGAGCA
1 T-AA-ATAGATATACATGCTGACGAGCA
29335919 TAAAT
1 TAAAT
29335924 GCATATTAGC
Statistics
Matches: 173, Mismatches: 38, Indels: 42
0.68 0.15 0.17
Matches are distributed among these distances:
22 3 0.02
23 4 0.02
24 63 0.36
25 13 0.08
26 75 0.43
27 3 0.02
28 10 0.06
29 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (26 bp):
TAAATAGATATACATGCTGACGAGCA
Found at i:29335703 original size:24 final size:24
Alignment explanation
Indices: 29335675--29335897 Score: 212
Period size: 24 Copynumber: 9.0 Consensus size: 24
29335665 TGTAAATAGA
*
29335675 TATACATGCTGACGAGCATAAACG
1 TATACATGCTGACGAGCGTAAACG
* * *
29335699 TATACATGCTTACGAGCCTTAACG
1 TATACATGCTGACGAGCGTAAACG
* *
29335723 TAGGTACATGCTGGCGAGCATAAACG
1 TA--TACATGCTGACGAGCGTAAACG
*
29335749 TATACATGCTGATGAGCGTAAACG
1 TATACATGCTGACGAGCGTAAACG
* *
29335773 TATATACATGTTGACGAGAGTAAACG
1 --TATACATGCTGACGAGCGTAAACG
* * * *
29335799 TAGATATATACTGTCGAGCTTAAACG
1 T--ATACATGCTGACGAGCGTAAACG
* *
29335825 TATACATGCTGGCGAGCGTAAACA
1 TATACATGCTGACGAGCGTAAACG
* * *
29335849 TATACATGTTGATGAGCGTAAATG
1 TATACATGCTGACGAGCGTAAACG
29335873 TATATACATGCTGACGAGCGTAAAC
1 --TATACATGCTGACGAGCGTAAAC
29335898 ATAGATATAT
Statistics
Matches: 159, Mismatches: 32, Indels: 14
0.78 0.16 0.07
Matches are distributed among these distances:
24 80 0.50
26 79 0.50
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (24 bp):
TATACATGCTGACGAGCGTAAACG
Found at i:29335898 original size:50 final size:50
Alignment explanation
Indices: 29335674--29335900 Score: 226
Period size: 50 Copynumber: 4.5 Consensus size: 50
29335664 ATGTAAATAG
* * * * * *
29335674 ATATACATGCTGACGAGCATAAACGTATACATGCTTACGAGCCTTAACGT
1 ATATACATGCTGACGAGCGTAAACATATACATGCTGATGAGCGTAAACGT
** * * *
29335724 AGGTACATGCTGGCGAGCATAAACGTATACATGCTGATGAGCGTAAACGT
1 ATATACATGCTGACGAGCGTAAACATATACATGCTGATGAGCGTAAACGT
* * * * * *
29335774 ATATACATGTTGACGAGAGTAAACGTAGATATATACTG-TCGAGCTTAAACG-
1 ATATACATGCTGACGAGCGTAAAC--ATATACATGCTGAT-GAGCGTAAACGT
* * *
29335825 -TATACATGCTGGCGAGCGTAAACATATACATGTTGATGAGCGTAAATGT
1 ATATACATGCTGACGAGCGTAAACATATACATGCTGATGAGCGTAAACGT
29335874 ATATACATGCTGACGAGCGTAAACATA
1 ATATACATGCTGACGAGCGTAAACATA
29335901 GATATATGTT
Statistics
Matches: 143, Mismatches: 28, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
48 17 0.12
49 1 0.01
50 106 0.74
51 1 0.01
52 18 0.13
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (50 bp):
ATATACATGCTGACGAGCGTAAACATATACATGCTGATGAGCGTAAACGT
Found at i:29335917 original size:100 final size:101
Alignment explanation
Indices: 29335666--29335922 Score: 310
Period size: 100 Copynumber: 2.6 Consensus size: 101
29335656 GTTGGTGAAT
* *
29335666 GTAAATAG-ATATACATGCTGACGAGCATAAACGT--ATACATGCTT-ACGAGCCTT-AACGTAG
1 GTAAAT-GTATATACATGCTGACGAGCGTAAACGTAGATATATG-TTGACGAG-CTTAAACGTA-
*
29335726 GTACATGCTGGCGAGCATAAACGTATACATGCTGATGAGC
62 GTACATGCTGGCGAGCATAAACATATACATGCTGATGAGC
* * * ** *
29335766 GTAAACGTATATACATGTTGACGAGAGTAAACGTAGATATATACTGTCGAGCTTAAACGTA-TAC
1 GTAAATGTATATACATGCTGACGAGCGTAAACGTAGATATATGTTGACGAGCTTAAACGTAGTAC
* *
29335830 ATGCTGGCGAGCGTAAACATATACATGTTGATGAGC
66 ATGCTGGCGAGCATAAACATATACATGCTGATGAGC
* * *
29335866 GTAAATGTATATACATGCTGACGAGCGTAAACATAGATATATGTTGGCGAGCATAAA
1 GTAAATGTATATACATGCTGACGAGCGTAAACGTAGATATATGTTGACGAGCTTAAA
29335923 TGCATATTAG
Statistics
Matches: 133, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
99 1 0.01
100 113 0.85
101 4 0.03
102 15 0.11
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (101 bp):
GTAAATGTATATACATGCTGACGAGCGTAAACGTAGATATATGTTGACGAGCTTAAACGTAGTAC
ATGCTGGCGAGCATAAACATATACATGCTGATGAGC
Found at i:29335936 original size:100 final size:100
Alignment explanation
Indices: 29335727--29335948 Score: 293
Period size: 100 Copynumber: 2.2 Consensus size: 100
29335717 TTAACGTAGG
* *
29335727 TACATGCTGGCGAGCATAAACGTATACATGCTGATGAGCGTAAACGTATATACATGTTGACGAGA
1 TACATGCTGGCGAGCATAAACATATACATGCTGATGAGCGTAAACGTATATACATGCTGACGAGA
* * * *
29335792 GTAAACGTAGATATATACTGTCGAGCTTAAACGTA
66 GTAAACATAGATATATACTGGCGAGCATAAACGCA
* * * *
29335827 TACATGCTGGCGAGCGTAAACATATACATGTTGATGAGCGTAAATGTATATACATGCTGACGAGC
1 TACATGCTGGCGAGCATAAACATATACATGCTGATGAGCGTAAACGTATATACATGCTGACGAGA
** *
29335892 GTAAACATAGATATATGTTGGCGAGCATAAATGCA
66 GTAAACATAGATATATACTGGCGAGCATAAACGCA
* *
29335927 TA-TTAGCTGGCAAGCATAAACA
1 TACAT-GCTGGCGAGCATAAACA
29335949 CATATTAGAT
Statistics
Matches: 105, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
99 1 0.01
100 104 0.99
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.26
Consensus pattern (100 bp):
TACATGCTGGCGAGCATAAACATATACATGCTGATGAGCGTAAACGTATATACATGCTGACGAGA
GTAAACATAGATATATACTGGCGAGCATAAACGCA
Found at i:29335937 original size:24 final size:24
Alignment explanation
Indices: 29335910--29335972 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
29335900 AGATATATGT
*
29335910 TGGCGAGCATAAATGCATATTAGC
1 TGGCGAGCATAAATGCATATTAGA
* **
29335934 TGGCAAGCATAAACACATATTAGA
1 TGGCGAGCATAAATGCATATTAGA
*
29335958 TGACGAGCATAAATG
1 TGGCGAGCATAAATG
29335973 TACTGAACTT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (24 bp):
TGGCGAGCATAAATGCATATTAGA
Found at i:29335971 original size:100 final size:100
Alignment explanation
Indices: 29335727--29335974 Score: 257
Period size: 100 Copynumber: 2.5 Consensus size: 100
29335717 TTAACGTAGG
* ** * * * *
29335727 TACATGCTGGCGAGCATAAACGTATACATGCTGATGAGCGTAAACGTATATACATGTTGACGAGA
1 TACATGCTGGCAAGCATAAACACATACATGATGACGAGCGTAAATGTATATACATGCTGACGAGA
* * * *
29335792 GTAAACGTAGATATATACTGTCGAGCTTAAACGTA
66 GTAAACATAGATATATACTGGCGAGCATAAACGCA
* * * * * *
29335827 TACATGCTGGCGAGCGTAAACATATACATGTTGATGAGCGTAAATGTATATACATGCTGACGAGC
1 TACATGCTGGCAAGCATAAACACATACATGATGACGAGCGTAAATGTATATACATGCTGACGAGA
** *
29335892 GTAAACATAGATATATGTTGGCGAGCATAAATGCA
66 GTAAACATAGATATATACTGGCGAGCATAAACGCA
* * *
29335927 TA-TTAGCTGGCAAGCATAAACACATA-TTAGATGACGAGCATAAATGTA
1 TACAT-GCTGGCAAGCATAAACACATACAT-GATGACGAGCGTAAATGTA
29335975 CTGAACTTGC
Statistics
Matches: 125, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
99 2 0.02
100 123 0.98
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (100 bp):
TACATGCTGGCAAGCATAAACACATACATGATGACGAGCGTAAATGTATATACATGCTGACGAGA
GTAAACATAGATATATACTGGCGAGCATAAACGCA
Found at i:29339342 original size:23 final size:22
Alignment explanation
Indices: 29339278--29339356 Score: 95
Period size: 23 Copynumber: 3.5 Consensus size: 22
29339268 TTCGCACCTC
* *
29339278 GTGTGCCTACTGATTTTCGCTAT
1 GTGTGCCTACTGA-TTGCACTAT
* *
29339301 GTGCGCCTACTGATTGCACTGT
1 GTGTGCCTACTGATTGCACTAT
29339323 GTGTGCCTACTGGATTGCACTAT
1 GTGTGCCTACT-GATTGCACTAT
*
29339346 GTGTGCTTACT
1 GTGTGCCTACT
29339357 ATTTCCCCAG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.33
23 32 0.67
ACGTcount: A:0.14, C:0.23, G:0.25, T:0.38
Consensus pattern (22 bp):
GTGTGCCTACTGATTGCACTAT
Found at i:29344287 original size:23 final size:23
Alignment explanation
Indices: 29344257--29344309 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
29344247 GTTATTAGTC
29344257 AAGCATTCAAATGACGCCTTATG
1 AAGCATTCAAATGACGCCTTATG
*
29344280 AAGCATTCAAATGGCGCCTTATG
1 AAGCATTCAAATGACGCCTTATG
29344303 AAGCATT
1 AAGCATT
29344310 ATATGGAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (23 bp):
AAGCATTCAAATGACGCCTTATG
Found at i:29346634 original size:23 final size:23
Alignment explanation
Indices: 29346608--29346661 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
29346598 TTCGTGTGCT
29346608 TACTGATTTGCGCTATGTGCGCC
1 TACTGATTTGCGCTATGTGCGCC
29346631 TACTGATTTGCGCTATGTGCGCC
1 TACTGATTTGCGCTATGTGCGCC
29346654 TACTGATT
1 TACTGATT
29346662 GCACAGTGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (23 bp):
TACTGATTTGCGCTATGTGCGCC
Found at i:29346671 original size:22 final size:22
Alignment explanation
Indices: 29346608--29346687 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 22
29346598 TTCGTGTGCT
*
29346608 TACTGATTTGCGCTATGTGCGCC
1 TACTGA-TTGCACTATGTGCGCC
*
29346631 TACTGATTTGCGCTATGTGCGCC
1 TACTGA-TTGCACTATGTGCGCC
*
29346654 TACTGATTGCAC-AGTGTGTGCC
1 TACTGATTGCACTA-TGTGCGCC
29346676 TACTGGATTGCA
1 TACT-GATTGCA
29346688 TTGTGTGTGC
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
21 1 0.02
22 16 0.30
23 36 0.68
ACGTcount: A:0.16, C:0.24, G:0.26, T:0.34
Consensus pattern (22 bp):
TACTGATTGCACTATGTGCGCC
Found at i:29346693 original size:23 final size:23
Alignment explanation
Indices: 29346646--29346703 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
29346636 ATTTGCGCTA
*
29346646 TGTGCGCCTACT-GATTGCACAG
1 TGTGTGCCTACTGGATTGCACAG
**
29346668 TGTGTGCCTACTGGATTGCATTG
1 TGTGTGCCTACTGGATTGCACAG
*
29346691 TGTGTGCTTACTG
1 TGTGTGCCTACTG
29346704 TTTCCCCAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 11 0.35
23 20 0.65
ACGTcount: A:0.14, C:0.21, G:0.29, T:0.36
Consensus pattern (23 bp):
TGTGTGCCTACTGGATTGCACAG
Found at i:29346703 original size:45 final size:46
Alignment explanation
Indices: 29346585--29346703 Score: 104
Period size: 45 Copynumber: 2.6 Consensus size: 46
29346575 CTAGCGCACT
*
29346585 TACTG-TTTCGCACT-TCGTGTGCTTACTGATTTGCGCTATGTGCGCC
1 TACTGATTT-GCACTAT-GTGTGCTTACTGATTTGCACTATGTGCGCC
* * * *
29346631 TACTGATTTGCGCTATGTGCGCCTACTGA-TTGCAC-AGTGTGTGCC
1 TACTGATTTGCACTATGTGTGCTTACTGATTTGCACTA-TGTGCGCC
* *
29346676 TACTGGA-TTGCATTGTGTGTGCTTACTG
1 TACT-GATTTGCACTATGTGTGCTTACTG
29346704 TTTCCCCAGC
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
44 1 0.02
45 32 0.54
46 22 0.37
47 4 0.07
ACGTcount: A:0.13, C:0.23, G:0.26, T:0.38
Consensus pattern (46 bp):
TACTGATTTGCACTATGTGTGCTTACTGATTTGCACTATGTGCGCC
Found at i:29348228 original size:29 final size:28
Alignment explanation
Indices: 29348196--29348295 Score: 85
Period size: 29 Copynumber: 3.5 Consensus size: 28
29348186 TGATAAGATC
29348196 GGGGTTTAAATGGGATTTTAGGAAGTTT
1 GGGGTTTAAATGGGATTTTAGGAAGTTT
* * * **
29348224 AGGGG-TAAAATGGTAAATTTTAGTAAAATT
1 -GGGGTTTAAATGG--GATTTTAGGAAGTTT
*
29348254 GGGGTTTAAAATGGGATTTTGGGAAGTTT
1 GGGGTTT-AAATGGGATTTTAGGAAGTTT
* *
29348283 GGGGATGAAATGG
1 GGGGTTTAAATGG
29348296 TAATTTTTGG
Statistics
Matches: 54, Mismatches: 13, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
28 13 0.24
29 23 0.43
30 12 0.22
31 6 0.11
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.34
Consensus pattern (28 bp):
GGGGTTTAAATGGGATTTTAGGAAGTTT
Found at i:29348279 original size:59 final size:59
Alignment explanation
Indices: 29348167--29348656 Score: 623
Period size: 59 Copynumber: 8.4 Consensus size: 59
29348157 AATGCTCGGG
* * * * *
29348167 GGGGCAAAATGGTAATTTTTGAT-AAGATCGGGGTT-TAAATGGGATTTTAGGAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAA-ATCGGGGTTAAAAATGGAATTTTGGGAAGTTTA
* * * * * *
29348225 GGGGTAAAATGGTAAATTTTAGTAAAATTGGGGTTTAAAATGGGATTTTGGGAAGTTT-
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTTA
* * * *
29348283 GGGGATGAAATGGTAATTTTTGGTGAAATTGGGGTTTAAAATGAAATTTTGGGAAGTTT-
1 GGGG-TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTTA
* * *
29348342 GTGGGTGAAATGGTAATTTTTGGTGAAATCGAGGTAAAAAATGGAATTTTGGGAAGTTTA
1 G-GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTTA
* * *
29348402 GGGGTAAAATGGTAA-TTTTGGTGAAATTGGGGTTAAAAATGGGATTTTAGGAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTTA
* * * * *
29348460 GGGGTAAAATGGTAATTTTTGGTAAAATGGGGGTT-AAAGTGGAATTTTAGGAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTTA
*
29348518 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGGAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTTA
* * * * *
29348577 GGGGTAAAATGGTAATTTTTAGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTTA
29348636 GGGGTAAAATGGTAATTTTTG
1 GGGGTAAAATGGTAATTTTTG
29348657 AACAGTCCAG
Statistics
Matches: 383, Mismatches: 42, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
58 137 0.36
59 242 0.63
60 4 0.01
ACGTcount: A:0.32, C:0.01, G:0.32, T:0.35
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTTA
Found at i:29348470 original size:117 final size:118
Alignment explanation
Indices: 29348166--29348656 Score: 641
Period size: 117 Copynumber: 4.2 Consensus size: 118
29348156 GAATGCTCGG
* * * *
29348166 GGGGGCAAAATGGTAATTTTTGAT-AAGATCGGGGTT-TAAATGGGATTTTAGGAAGTTTAGGGG
1 GGGGGTAAAATGGTAATTTTTGGTGAA-ATCGGGGTTAAAAATGGAATTTTAGGAAGTTTAGGGG
* * * * *
29348229 TAAAATGGTAAATTTTAGTAAAATTGGGGTTTAAAATGGGATTTTGGGAAGTTT
65 TAAAATGGTAATTTTTAGTAAAATCGAGGTTAAAAATGGAATTTTGGGAAGTTT
* * * * * *
29348283 GGGGATGAAATGGTAATTTTTGGTGAAATTGGGGTTTAAAATGAAATTTTGGGAAGTTT-GTGGG
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGGAAGTTTAG-GGG
* * * *
29348347 TGAAATGGTAATTTTTGGTGAAATCGAGGTAAAAAATGGAATTTTGGGAAGTTT
65 TAAAATGGTAATTTTTAGTAAAATCGAGGTTAAAAATGGAATTTTGGGAAGTTT
* * *
29348401 AGGGGTAAAATGGTAA-TTTTGGTGAAATTGGGGTTAAAAATGGGATTTTAGGAAGTTTAGGGGT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGGAAGTTTAGGGGT
* * * * *
29348465 AAAATGGTAATTTTTGGTAAAATGGGGGTT-AAAGTGGAATTTTAGGAAGTTT
66 AAAATGGTAATTTTTAGTAAAATCGAGGTTAAAAATGGAATTTTGGGAAGTTT
* *
29348517 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGGAAGTTTAGGGGT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGGAAGTTTAGGGGT
* * *
29348582 AAAATGGTAATTTTTAGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTT
66 AAAATGGTAATTTTTAGTAAAATCGAGGTTAAAAATGGAATTTTGGGAAGTTT
29348635 GGGGGTAAAATGGTAATTTTTG
1 GGGGGTAAAATGGTAATTTTTG
29348657 AACAGTCCAG
Statistics
Matches: 323, Mismatches: 45, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
116 35 0.11
117 166 0.51
118 122 0.38
ACGTcount: A:0.32, C:0.01, G:0.32, T:0.35
Consensus pattern (118 bp):
GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGGAAGTTTAGGGGT
AAAATGGTAATTTTTAGTAAAATCGAGGTTAAAAATGGAATTTTGGGAAGTTT
Found at i:29350511 original size:6 final size:6
Alignment explanation
Indices: 29350500--29350558 Score: 59
Period size: 6 Copynumber: 9.8 Consensus size: 6
29350490 TGAAATTTGA
* *
29350500 TTAAAT TTAAAT TTAAA- GTAAAT TTAAAT AGGTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT
*
29350548 GTAAAT TTAAA
1 TTAAAT TTAAA
29350559 ATCAATTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 8 0.19
6 30 0.70
8 5 0.12
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.41
Consensus pattern (6 bp):
TTAAAT
Found at i:29350521 original size:17 final size:17
Alignment explanation
Indices: 29350501--29350558 Score: 86
Period size: 17 Copynumber: 3.6 Consensus size: 17
29350491 GAAATTTGAT
29350501 TAAATTTAAATTTAAAG
1 TAAATTTAAATTTAAAG
*
29350518 TAAATTTAAA--T-AGG
1 TAAATTTAAATTTAAAG
29350532 TAAATTTAAATTTAAAG
1 TAAATTTAAATTTAAAG
29350549 TAAATTTAAA
1 TAAATTTAAA
29350559 ATCAATTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
14 12 0.33
15 1 0.03
16 1 0.03
17 22 0.61
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAG
Found at i:29350523 original size:11 final size:11
Alignment explanation
Indices: 29350507--29350569 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
29350497 TGATTAAATT
29350507 TAAATTTAAAG
1 TAAATTTAAAG
29350518 TAAATTTAAA-
1 TAAATTTAAAG
** *
29350528 T--AGGTAAATT
1 TAAATTTAAA-G
29350538 TAAATTTAAAG
1 TAAATTTAAAG
*
29350549 TAAATTTAAAA
1 TAAATTTAAAG
*
29350560 TCAATTTAAA
1 TAAATTTAAA
29350570 CTTTTAATTA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
8 5 0.12
10 2 0.05
11 29 0.71
12 5 0.12
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAG
Found at i:29351423 original size:16 final size:17
Alignment explanation
Indices: 29351382--29351424 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
29351372 TAAATGGTCT
29351382 TGTAGTTGGCTAAATGCA
1 TGTAGTTGG-TAAATGCA
*
29351400 TGTA-TTGGTATATGCA
1 TGTAGTTGGTAAATGCA
29351416 T-TAGTTGGT
1 TGTAGTTGGT
29351425 TTTGTGCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 2 0.09
16 13 0.57
17 4 0.17
18 4 0.17
ACGTcount: A:0.23, C:0.07, G:0.28, T:0.42
Consensus pattern (17 bp):
TGTAGTTGGTAAATGCA
Found at i:29356323 original size:4 final size:4
Alignment explanation
Indices: 29356314--29356353 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
29356304 TAACAATCCC
*
29356314 CTTT CTTT CTTT CTTT CTTT CTTT CTTT TTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
29356354 TAACGCTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78
Consensus pattern (4 bp):
CTTT
Found at i:29357189 original size:42 final size:42
Alignment explanation
Indices: 29357130--29357326 Score: 233
Period size: 42 Copynumber: 4.8 Consensus size: 42
29357120 TTCCCCAGTG
* *
29357130 ACAAGCACAAGCAATGGTATCTTCGGTGGTACATCTGCAAG-T
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGC-AGCT
29357172 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAGCT
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAGCT
* * * * *
29357214 ACAAGCAC-GGACACTGGTTTATTTGGTGGTAAATCAGCAGCT
1 ACAAGCACAGG-CAATGGTATCTTTGGTGGTACATCTGCAGCT
*
29357256 ACAAGCACAGGCAATGGCATCTTTGGTGGTACATCTGCA---
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAGCT
* * * *
29357295 ACAAGCACAGGTAGTAGTATTTTTGGTGGTAC
1 ACAAGCACAGGCAATGGTATCTTTGGTGGTAC
29357327 GTCTTTGCCA
Statistics
Matches: 134, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
39 27 0.20
41 4 0.03
42 101 0.75
43 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (42 bp):
ACAAGCACAGGCAATGGTATCTTTGGTGGTACATCTGCAGCT
Found at i:29360766 original size:42 final size:41
Alignment explanation
Indices: 29360698--29360878 Score: 224
Period size: 42 Copynumber: 4.4 Consensus size: 41
29360688 ACTACTACTA
*
29360698 CCTGTGCTTGT--TGCAGATGTACCACCAAAGATGCCATTG
1 CCTGTGCTTGTACTGCAGATGTACCACCAAAGATACCATTG
* * * * *
29360737 CCTGTGCTTGTAGCTGCTGATGTAACACCAAATAAACCAGTG
1 CCTGTGCTTGTA-CTGCAGATGTACCACCAAAGATACCATTG
29360779 ACC-GTGCTTGTAGCTGCAGATGTACCACCAAAGATACCATTG
1 -CCTGTGCTTGTA-CTGCAGATGTACCACCAAAGATACCATTG
*
29360821 CCTGTGCTTGTACTTGCAGATGTACCACCGAAGATACCATTG
1 CCTGTGCTTGTAC-TGCAGATGTACCACCAAAGATACCATTG
*
29360863 CTTGTGCTTGTCACTG
1 CCTGTGCTTGT-ACTG
29360879 GAGAAAATGT
Statistics
Matches: 122, Mismatches: 13, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
39 11 0.09
41 3 0.02
42 104 0.85
43 4 0.03
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.28
Consensus pattern (41 bp):
CCTGTGCTTGTACTGCAGATGTACCACCAAAGATACCATTG
Found at i:29362857 original size:3 final size:3
Alignment explanation
Indices: 29362849--29362877 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
29362839 ATTTCTCCTT
29362849 CTG CTG CTG CTG CTG CTG CTG CTG CTG CT
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CT
29362878 TTTTTACACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.31, T:0.34
Consensus pattern (3 bp):
CTG
Found at i:29363699 original size:14 final size:14
Alignment explanation
Indices: 29363667--29363721 Score: 60
Period size: 13 Copynumber: 4.1 Consensus size: 14
29363657 TAACCCAAAC
* *
29363667 TTTTCAAAAGTA-A
1 TTTTCAAAAGCACT
*
29363680 TTTTCAAAATCACT
1 TTTTCAAAAGCACT
29363694 TTTTC-AAAGCACT
1 TTTTCAAAAGCACT
*
29363707 TTTTTAAAAGCACT
1 TTTTCAAAAGCACT
29363721 T
1 T
29363722 CCAAAAACAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
13 21 0.60
14 14 0.40
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.42
Consensus pattern (14 bp):
TTTTCAAAAGCACT
Found at i:29375485 original size:42 final size:42
Alignment explanation
Indices: 29375415--29375581 Score: 192
Period size: 42 Copynumber: 4.0 Consensus size: 42
29375405 TTCCCCAGTG
* * * * *
29375415 ACAAGCACAAGCAATGGTATCTTCGGTGGTGCATCTGCAAGT
1 ACAAGCACAGGCAATGGTAACTTTGGTGGTACATCTGCAACT
* * *
29375457 ACAAGAAAAGGCAGTGGTAACTTTGGTGGTACATCTGCAACT
1 ACAAGCACAGGCAATGGTAACTTTGGTGGTACATCTGCAACT
* * *
29375499 ACAAGCACGGGCACTGGTTTA-TTTGGTGGTACATCTGCAACT
1 ACAAGCACAGGCAATGG-TAACTTTGGTGGTACATCTGCAACT
* * *
29375541 ACAAGCACAGGCAATGGCATCTTTGCTGGTACATCTGCAAC
1 ACAAGCACAGGCAATGGTAACTTTGGTGGTACATCTGCAAC
29375582 AAGCACAGGT
Statistics
Matches: 104, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
42 102 0.98
43 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.25
Consensus pattern (42 bp):
ACAAGCACAGGCAATGGTAACTTTGGTGGTACATCTGCAACT
Found at i:29375610 original size:39 final size:41
Alignment explanation
Indices: 29375415--29375611 Score: 175
Period size: 42 Copynumber: 4.8 Consensus size: 41
29375405 TTCCCCAGTG
* * * * *
29375415 ACAAGCACAAGCAATGGTATCTTCGGTGGTGCATCTGCAAGT
1 ACAAGCACAGGCAATGGTATTTTTGGTGGTACATCTGCAA-C
* * * **
29375457 ACAAGAAAAGGCAGTGGTAACTTTGGTGGTACATCTGCAAC
1 ACAAGCACAGGCAATGGTATTTTTGGTGGTACATCTGCAAC
* *
29375498 TACAAGCACGGGCACTGGT-TTATTTGGTGGTACATCTGCAAC
1 -ACAAGCACAGGCAATGGTATT-TTTGGTGGTACATCTGCAAC
* * *
29375540 TACAAGCACAGGCAATGGCATCTTTGCTGGTACATCTGC-A-
1 -ACAAGCACAGGCAATGGTATTTTTGGTGGTACATCTGCAAC
* * *
29375580 ACAAGCACAGGTAGTAGTATTTTTGGTGGTAC
1 ACAAGCACAGGCAATGGTATTTTTGGTGGTAC
29375612 GTCTTTGCCA
Statistics
Matches: 127, Mismatches: 25, Indels: 9
0.79 0.16 0.06
Matches are distributed among these distances:
39 26 0.20
41 1 0.01
42 99 0.78
43 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (41 bp):
ACAAGCACAGGCAATGGTATTTTTGGTGGTACATCTGCAAC
Found at i:29379521 original size:42 final size:42
Alignment explanation
Indices: 29379462--29379626 Score: 224
Period size: 42 Copynumber: 3.9 Consensus size: 42
29379452 CTTTGCTTGT
**
29379462 TGCAGATGTACCACCAAAGACGCCATTGCCTGTGCTTGTAGC
1 TGCAGATGTACCACCAAAGATACCATTGCCTGTGCTTGTAGC
* * * * * *
29379504 TGCTGATGTACCTCCAAATAAACCAGTGCCCGTGCTTGTAGC
1 TGCAGATGTACCACCAAAGATACCATTGCCTGTGCTTGTAGC
29379546 TGCAGATGTACCACCAAAGATACCATTGCCTGTGCTTGTA-C
1 TGCAGATGTACCACCAAAGATACCATTGCCTGTGCTTGTAGC
* *
29379587 TTGCAGATGTACCACCGAAGATACCATTGCTTGTGCTTGT
1 -TGCAGATGTACCACCAAAGATACCATTGCCTGTGCTTGT
29379627 CACTGGGGAA
Statistics
Matches: 107, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
41 1 0.01
42 106 0.99
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (42 bp):
TGCAGATGTACCACCAAAGATACCATTGCCTGTGCTTGTAGC
Found at i:29382504 original size:123 final size:123
Alignment explanation
Indices: 29382280--29382526 Score: 350
Period size: 123 Copynumber: 2.0 Consensus size: 123
29382270 AAAAGCTGTA
* * * *
29382280 GATATTGATGGAAGTGATGAAGATGATGTTAAAGATTTGGAGTCTCCTGTAAAGTCAGGTGGAAA
1 GATATTGACGAAAGTGATGAAGAGGATATTAAAGATTTGGAGTCTCCTGTAAAGTCAGGTGGAAA
* * * * *
29382345 GGTTCATGGTGGCAGGGGTGCATCAAAAGGCCCAGCTGGTGGAAGAGGCAGAGGTGGT
66 GGGTCATGGTGGCAGAGGTACATCAAAAGGACCAGCTAGTGGAAGAGGCAGAGGTGGT
* * *
29382403 GATATTGACGAAAGTGATGAAGAGGATATTAAAGATTTGGAGTCTCCTGTGAAGTCTGGTGGAAG
1 GATATTGACGAAAGTGATGAAGAGGATATTAAAGATTTGGAGTCTCCTGTAAAGTCAGGTGGAAA
* * * *
29382468 GGGTCGTGGTGGTAGAGGTACATCAACAGGATCAGCTAGTGGAAGAGGCAGAGGTGGT
66 GGGTCATGGTGGCAGAGGTACATCAAAAGGACCAGCTAGTGGAAGAGGCAGAGGTGGT
29382526 G
1 G
29382527 GACGGGGTGG
Statistics
Matches: 108, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
123 108 1.00
ACGTcount: A:0.29, C:0.10, G:0.38, T:0.23
Consensus pattern (123 bp):
GATATTGACGAAAGTGATGAAGAGGATATTAAAGATTTGGAGTCTCCTGTAAAGTCAGGTGGAAA
GGGTCATGGTGGCAGAGGTACATCAAAAGGACCAGCTAGTGGAAGAGGCAGAGGTGGT
Found at i:29393704 original size:55 final size:55
Alignment explanation
Indices: 29393620--29393735 Score: 214
Period size: 55 Copynumber: 2.1 Consensus size: 55
29393610 TTATCTCATC
29393620 CTTTTGTTCTTGATTGATAAGTGATTATTATATTACCCCAACCTCACTAATTAAT
1 CTTTTGTTCTTGATTGATAAGTGATTATTATATTACCCCAACCTCACTAATTAAT
*
29393675 CTTTTGTTCTTGATTGATAAGTGATTATTATATTACCCCAACCTCCCTAATTAAT
1 CTTTTGTTCTTGATTGATAAGTGATTATTATATTACCCCAACCTCACTAATTAAT
29393730 CATTTT
1 C-TTTT
29393736 TTTAATATTT
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
55 55 0.93
56 4 0.07
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.45
Consensus pattern (55 bp):
CTTTTGTTCTTGATTGATAAGTGATTATTATATTACCCCAACCTCACTAATTAAT
Found at i:29405294 original size:17 final size:17
Alignment explanation
Indices: 29405272--29405308 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
29405262 GGTGGAGAAC
* *
29405272 TGTTCGTTGAGAGTTCT
1 TGTTCGTAGAGAATTCT
29405289 TGTTCGTAGAGAATTCT
1 TGTTCGTAGAGAATTCT
29405306 TGT
1 TGT
29405309 CAAGGTGGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.16, C:0.11, G:0.27, T:0.46
Consensus pattern (17 bp):
TGTTCGTAGAGAATTCT
Found at i:29409719 original size:12 final size:12
Alignment explanation
Indices: 29409704--29409731 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
29409694 AATTTAGTAG
29409704 ACAGATTAGGAT
1 ACAGATTAGGAT
29409716 ACAGATTAGGAT
1 ACAGATTAGGAT
29409728 ACAG
1 ACAG
29409732 TTGGCATACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.11, G:0.25, T:0.21
Consensus pattern (12 bp):
ACAGATTAGGAT
Found at i:29418338 original size:16 final size:17
Alignment explanation
Indices: 29418306--29418339 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29418296 TTGCCTTTTT
29418306 TTTTTTTTTTTGCTTGGG
1 TTTTTTTTTTT-CTTGGG
29418324 TTTTTTTTTTT-TTGGG
1 TTTTTTTTTTTCTTGGG
29418340 GGGGGGGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
18 11 0.69
ACGTcount: A:0.00, C:0.03, G:0.21, T:0.76
Consensus pattern (17 bp):
TTTTTTTTTTTCTTGGG
Found at i:29419806 original size:56 final size:54
Alignment explanation
Indices: 29419714--29419854 Score: 174
Period size: 56 Copynumber: 2.5 Consensus size: 54
29419704 CCTTTTATGT
* * * * *
29419714 GTATACTATGTACATGTGTATCTATCATAAACTTTTGTCTATGTCACTTGTTGG
1 GTATACTATGTACATGTGTATCTATTATAAAATTTTGGCTATGTCAATTGTTGC
* *
29419768 GTATACTCTGTATATGTGTACCTCTATTATAAAATTTTGGCTATGTCAATTGTTGC
1 GTATACTATGTACATGTGTA--TCTATTATAAAATTTTGGCTATGTCAATTGTTGC
*
29419824 ATATACTATGTACATGTGTAGTTCTATTATA
1 GTATACTATGTACATGTGTA--TCTATTATA
29419855 CTCTGTAGAG
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
54 18 0.25
56 55 0.75
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (54 bp):
GTATACTATGTACATGTGTATCTATTATAAAATTTTGGCTATGTCAATTGTTGC
Found at i:29419884 original size:15 final size:14
Alignment explanation
Indices: 29419851--29419884 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
29419841 GTAGTTCTAT
*
29419851 TATACTCTGTAGAG
1 TATACTCTGTACAG
29419865 TATACTCTGTACATG
1 TATACTCTGTACA-G
29419880 TATAC
1 TATAC
29419885 CTCTATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (14 bp):
TATACTCTGTACAG
Found at i:29424225 original size:25 final size:25
Alignment explanation
Indices: 29424197--29424256 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
29424187 TTCTGTTAAG
**
29424197 TCAATTTTCTACAACATAACAGTTA
1 TCAATTTGATACAACATAACAGTTA
*
29424222 TCAATTTGATACAAGATAACAGTTA
1 TCAATTTGATACAACATAACAGTTA
29424247 TCAATTTGAT
1 TCAATTTGAT
29424257 CTTTTGACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (25 bp):
TCAATTTGATACAACATAACAGTTA
Found at i:29429291 original size:18 final size:18
Alignment explanation
Indices: 29429268--29429310 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
29429258 ATGTTCAACT
29429268 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
29429286 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
29429304 TTAATTA
1 TTAATTA
29429311 CAACTGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:29431661 original size:26 final size:26
Alignment explanation
Indices: 29431632--29431685 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
29431622 TTTTTAAATT
*
29431632 TTTTTATAA-ACTTTATATAATTTTTA
1 TTTTTAGAATACTTTA-ATAATTTTTA
* *
29431658 TTTTTAGAATATTTTAATATTTTTTA
1 TTTTTAGAATACTTTAATAATTTTTA
29431684 TT
1 TT
29431686 ATTTTTTGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTTTAGAATACTTTAATAATTTTTA
Found at i:29432199 original size:19 final size:18
Alignment explanation
Indices: 29432167--29432213 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
29432157 TTTTAATTAA
**
29432167 ATAAATATTATTTTTATAT
1 ATAAATATGGTTTTTAT-T
29432186 ATAAATATGG-TTTTATT
1 ATAAATATGGTTTTTATT
*
29432203 TTAAATATGGT
1 ATAAATATGGT
29432214 AATATTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 10 0.42
18 6 0.25
19 8 0.33
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
ATAAATATGGTTTTTATT
Found at i:29432219 original size:17 final size:17
Alignment explanation
Indices: 29432187--29432220 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
29432177 TTTTTATATA
**
29432187 TAAATATGGTTTTATTT
1 TAAATATGGTAATATTT
29432204 TAAATATGGTAATATTT
1 TAAATATGGTAATATTT
29432221 AATCATGTTA
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:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (17 bp):
TAAATATGGTAATATTT
Found at i:29434288 original size:29 final size:31
Alignment explanation
Indices: 29434238--29434301 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
29434228 TTAATAAAAG
* *
29434238 TAAAAATACACTTTACTCTC-TTAAAAATAA
1 TAAAAATACAATTTAATCTCTTTAAAAATAA
* *
29434268 TAAAAATTCAATTTAAT-TCTTTAAAAATTA
1 TAAAAATACAATTTAATCTCTTTAAAAATAA
29434298 TAAA
1 TAAA
29434302 GATATAGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAATACAATTTAATCTCTTTAAAAATAA
Found at i:29434471 original size:2 final size:2
Alignment explanation
Indices: 29434464--29434497 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
29434454 TTCTATATTC
29434464 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29434498 GCTTATTCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29437587 original size:120 final size:120
Alignment explanation
Indices: 29437374--29437616 Score: 468
Period size: 120 Copynumber: 2.0 Consensus size: 120
29437364 CTGCTCGTTC
29437374 CAAATCTTTGGGAGGGAGTTCGAATAGGGAAGTGAATGTTAGTGGTGTGGGACCAAAGCCTGTGA
1 CAAATCTTTGGGAGGGAGTTCGAATAGGGAAGTGAATGTTAGTGGTGTGGGACCAAAGCCTGTGA
29437439 GATATGGATCTCAAGGTGCTGAGTCAGAGACACATAGCATGTCACAGAAAGAGAT
66 GATATGGATCTCAAGGTGCTGAGTCAGAGACACATAGCATGTCACAGAAAGAGAT
29437494 CAAATCTTTGGGAGGGAGTTCGAATAGGGAAGTGAATGTTAGTGGTGTGGGACCAAAGCCTGTGA
1 CAAATCTTTGGGAGGGAGTTCGAATAGGGAAGTGAATGTTAGTGGTGTGGGACCAAAGCCTGTGA
* *
29437559 GATATGGATCTCAAGGTGCTGAGTCAGAGACATATAGCGTGTCACAGAAAGAGAT
66 GATATGGATCTCAAGGTGCTGAGTCAGAGACACATAGCATGTCACAGAAAGAGAT
29437614 CAA
1 CAA
29437617 TGATGAAGAT
Statistics
Matches: 121, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 121 1.00
ACGTcount: A:0.32, C:0.13, G:0.33, T:0.23
Consensus pattern (120 bp):
CAAATCTTTGGGAGGGAGTTCGAATAGGGAAGTGAATGTTAGTGGTGTGGGACCAAAGCCTGTGA
GATATGGATCTCAAGGTGCTGAGTCAGAGACACATAGCATGTCACAGAAAGAGAT
Found at i:29457186 original size:24 final size:24
Alignment explanation
Indices: 29457149--29457223 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
29457139 GATTACTGGT
*
29457149 TAACTATTCTGGGCTCGTAAGAGC
1 TAACCATTCTGGGCTCGTAAGAGC
*
29457173 TCACCATTCTGGGCTCGTAAGAGC
1 TAACCATTCTGGGCTCGTAAGAGC
* * * *
29457197 TAACCTTTTTAGGCTCGTGAGAGC
1 TAACCATTCTGGGCTCGTAAGAGC
29457221 TAA
1 TAA
29457224 TTTGGTCTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (24 bp):
TAACCATTCTGGGCTCGTAAGAGC
Found at i:29457978 original size:21 final size:21
Alignment explanation
Indices: 29457954--29457993 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
29457944 CGGTATAAGA
29457954 GTCACTTGTATCGATAGAACT
1 GTCACTTGTATCGATAGAACT
*
29457975 GTCACTTGTATCGGTAGAA
1 GTCACTTGTATCGATAGAA
29457994 GTCTGTACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (21 bp):
GTCACTTGTATCGATAGAACT
Found at i:29459373 original size:35 final size:35
Alignment explanation
Indices: 29459334--29459403 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
29459324 GTGTTTTGGG
29459334 ACAAAGTGTAAAGTTGGAAGGCCCAGGGACTAAAA
1 ACAAAGTGTAAAGTTGGAAGGCCCAGGGACTAAAA
29459369 ACAAAGTGTAAAGTTGGAAGGCCCAGGGACTAAAA
1 ACAAAGTGTAAAGTTGGAAGGCCCAGGGACTAAAA
29459404 GTACAATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.43, C:0.14, G:0.29, T:0.14
Consensus pattern (35 bp):
ACAAAGTGTAAAGTTGGAAGGCCCAGGGACTAAAA
Found at i:29460938 original size:22 final size:23
Alignment explanation
Indices: 29460879--29460959 Score: 101
Period size: 23 Copynumber: 3.6 Consensus size: 23
29460869 TATTCAGCAC
* * *
29460879 TGTGTGCTTACTGATTCGTACTA
1 TGTGTGCTTACTGATTTGCACTG
* * *
29460902 TATATGCTTACTGATTTGCATTG
1 TGTGTGCTTACTGATTTGCACTG
29460925 TGTGTGC-TACTGATTTGCACTG
1 TGTGTGCTTACTGATTTGCACTG
29460947 TGTGTGCTTACTG
1 TGTGTGCTTACTG
29460960 TTTCCCCAGC
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
22 21 0.44
23 27 0.56
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.44
Consensus pattern (23 bp):
TGTGTGCTTACTGATTTGCACTG
Found at i:29460950 original size:20 final size:21
Alignment explanation
Indices: 29460910--29460950 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
29460900 TATATATGCT
*
29460910 TACTGATTTGCATTGTGTGTGC
1 TACTGATTTGCA-TCTGTGTGC
29460932 TACTGATTTGCA-CTGTGTG
1 TACTGATTTGCATCTGTGTG
29460951 TGCTTACTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
22 12 0.67
ACGTcount: A:0.15, C:0.15, G:0.27, T:0.44
Consensus pattern (21 bp):
TACTGATTTGCATCTGTGTGC
Found at i:29465354 original size:26 final size:26
Alignment explanation
Indices: 29465325--29465409 Score: 72
Period size: 26 Copynumber: 3.3 Consensus size: 26
29465315 AGCTCAAACA
* *
29465325 AGCCCAGACAGAGTT-TAGCTCTTAAG
1 AGCCCAAACAAAGTTCT-GCTCTTAAG
*
29465351 AGCCCAAACAAAGTTCTGCTCTTACG
1 AGCCCAAACAAAGTTCTGCTCTTAAG
*
29465377 AG-CCAAACAGAA-TATC-GCTCTTACG
1 AGCCCAAACA-AAGT-TCTGCTCTTAAG
29465402 AG-CCAAAC
1 AGCCCAAAC
29465410 CGAATATCGC
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
25 25 0.47
26 27 0.51
27 1 0.02
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (26 bp):
AGCCCAAACAAAGTTCTGCTCTTAAG
Found at i:29465396 original size:25 final size:25
Alignment explanation
Indices: 29465342--29465467 Score: 157
Period size: 25 Copynumber: 5.0 Consensus size: 25
29465332 ACAGAGTTTA
*
29465342 GCTCTTAAGAGCCCAAACA-AAGT-TC
1 GCTCTTACGAG-CCAAACAGAA-TATC
29465367 TGCTCTTACGAGCCAAACAGAATATC
1 -GCTCTTACGAGCCAAACAGAATATC
*
29465393 GCTCTTACGAGCCAAACCGAATATC
1 GCTCTTACGAGCCAAACAGAATATC
* * *
29465418 GCTCTTATGAGCCAGATAGAATATC
1 GCTCTTACGAGCCAAACAGAATATC
*
29465443 GCTCTTACGAGCGAAACAGAATATC
1 GCTCTTACGAGCCAAACAGAATATC
29465468 TTCATCATCT
Statistics
Matches: 88, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
25 74 0.84
26 14 0.16
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.22
Consensus pattern (25 bp):
GCTCTTACGAGCCAAACAGAATATC
Found at i:29466800 original size:16 final size:18
Alignment explanation
Indices: 29466779--29466816 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29466769 GGATTTTCAA
29466779 TTCAATT-C-ATATCACT
1 TTCAATTCCAATATCACT
*
29466795 TTCAATTCCAATTTCACT
1 TTCAATTCCAATATCACT
29466813 TTCA
1 TTCA
29466817 CTTTAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 1 0.05
18 11 0.58
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.45
Consensus pattern (18 bp):
TTCAATTCCAATATCACT
Found at i:29473118 original size:41 final size:38
Alignment explanation
Indices: 29473018--29473121 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
29473008 TTCGAAGCAA
* *
29473018 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
29473055 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
29473093 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
29473122 CACAAGGTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:29473247 original size:18 final size:18
Alignment explanation
Indices: 29473224--29473260 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29473214 ATAATTCATA
29473224 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
29473242 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
29473260 T
1 T
29473261 TGATCAAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Done.