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 88 of 193
Found at i:28989030 original size:18 final size:18
Alignment explanation
Indices: 28989007--28989044 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
28988997 GCTATTCATA
*
28989007 AATAATATTAATAATTAT
1 AATAATATTAATAAATAT
28989025 AATAATATTAATAAATAT
1 AATAATATTAATAAATAT
28989043 AA
1 AA
28989045 AAAAAAGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AATAATATTAATAAATAT
Found at i:28990133 original size:29 final size:29
Alignment explanation
Indices: 28990077--28990354 Score: 116
Period size: 29 Copynumber: 9.6 Consensus size: 29
28990067 CTAAATAGTT
*
28990077 CAAAAATTACATTTTTACCC-CGGACTTC
1 CAAAAATTACATTTTTACCCTCGAACTTC
* * *
28990105 TAAATATTCCATTTTTACCCTCGAACTTC
1 CAAAAATTACATTTTTACCCTCGAACTTC
* ** *
28990134 CAAAAATTACTTTTTTACCCTTAAACTTTT
1 CAAAAATTACATTTTTACCCTCGAAC-TTC
* * *
28990164 C-AAAATTCCAATTTTGACCCCCGAAACATT-
1 CAAAAATTAC-ATTTTTACCCTCG-AAC-TTC
*
28990194 CAAAAATTACCA-TTTTACCC-CCATA-TGTC
1 CAAAAATTA-CATTTTTACCCTCGA-ACT-TC
* * * *
28990223 C-AAAACTCCATTTTTTATCC-CGAAACTTT
1 CAAAAATTACA-TTTTTACCCTCG-AACTTC
28990252 CAAAAATTACCA-TTTTACCCTCGAA-TGTC
1 CAAAAATTA-CATTTTTACCCTCGAACT-TC
* * ** *
28990281 CAAAAACTCCATTTTTGAACCC-AAAACTTT
1 CAAAAATTACATTTTT--ACCCTCGAACTTC
*
28990311 C-AAAATTACCA-TTTTACCCTCGGA-TGTC
1 CAAAAATTA-CATTTTTACCCTCGAACT-TC
*
28990339 CAAAAATTTCATTTTT
1 CAAAAATTACATTTTT
28990355 GATCCTGATT
Statistics
Matches: 182, Mismatches: 42, Indels: 51
0.66 0.15 0.19
Matches are distributed among these distances:
27 8 0.04
28 32 0.18
29 88 0.48
30 34 0.19
31 19 0.10
32 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (29 bp):
CAAAAATTACATTTTTACCCTCGAACTTC
Found at i:28990202 original size:60 final size:56
Alignment explanation
Indices: 28990075--28990214 Score: 140
Period size: 60 Copynumber: 2.4 Consensus size: 56
28990065 CCCTAAATAG
** * *
28990075 TTCAAAAATTACATTTTTACCCCGGACTTCTAAATATTCCATTTTTACCCTCGAAC
1 TTCAAAAATTACATTTTTACCCCAAACTTCTAAATATTCCATTTTGACCCCCGAAC
* * *
28990131 TTCCAAAAATTACTTTTTTACCCTTAAACTTTTCAAA-ATTCCAATTTTGACCCCCGAAAC
1 TT-CAAAAATTACATTTTTACCC-CAAACTTCT-AAATATTCC-ATTTTGACCCCCG-AAC
28990191 ATTCAAAAATTACCA-TTTTACCCC
1 -TTCAAAAATTA-CATTTTTACCCC
28990215 CATATGTCCA
Statistics
Matches: 68, Mismatches: 9, Indels: 11
0.77 0.10 0.12
Matches are distributed among these distances:
56 2 0.03
57 19 0.28
58 10 0.15
59 14 0.21
60 20 0.29
61 3 0.04
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (56 bp):
TTCAAAAATTACATTTTTACCCCAAACTTCTAAATATTCCATTTTGACCCCCGAAC
Found at i:28990254 original size:58 final size:57
Alignment explanation
Indices: 28990164--28990442 Score: 224
Period size: 58 Copynumber: 4.8 Consensus size: 57
28990154 TTAAACTTTT
* * * *
28990164 CAAAATTCCAATTTTGACCCCCGAAACATTCAAAAATTACCATTTTACCCCCATATGTC
1 CAAAACTCCATTTTTGA-ACCCGAAACTTTCAAAAATTACCATTTTACCCCCA-ATGTC
* * *
28990223 CAAAACTCCATTTTTTATCCCGAAACTTTCAAAAATTACCATTTTACCCTCGAATGTC
1 CAAAACTCCATTTTTGAACCCGAAACTTTCAAAAATTACCATTTTACCC-CCAATGTC
* **
28990281 CAAAAACTCCATTTTTGAACCCAAAACTTTC-AAAATTACCATTTTACCCTCGGATGTC
1 C-AAAACTCCATTTTTGAACCCGAAACTTTCAAAAATTACCATTTTACCC-CCAATGTC
* * * * ** * * **
28990339 CAAAAATTTCATTTTTGATCCTG-ATTTTTCTAAAAATTATCGTTTTACCCTAAAATGTC
1 C-AAAACTCCATTTTTGAACCCGAAACTTTC-AAAAATTACCATTTTACCC-CCAATGTC
* * * *
28990398 TAAAA-TGCCATTTTT-AACCCCAAATTTTCCCAAAATTACCATTTT
1 CAAAACT-CCATTTTTGAACCCGAAACTTT-CAAAAATTACCATTTT
28990443 TCCCTTGAGA
Statistics
Matches: 182, Mismatches: 31, Indels: 15
0.80 0.14 0.07
Matches are distributed among these distances:
57 9 0.05
58 108 0.59
59 65 0.36
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.35
Consensus pattern (57 bp):
CAAAACTCCATTTTTGAACCCGAAACTTTCAAAAATTACCATTTTACCCCCAATGTC
Found at i:28990469 original size:117 final size:116
Alignment explanation
Indices: 28990079--28990470 Score: 284
Period size: 117 Copynumber: 3.4 Consensus size: 116
28990069 AAATAGTTCA
* * * ** *
28990079 AAAATTA-CATTTTTACCC-CGGACT-TCTAAATATTCCATTTTT-ACCCTCGAACTTCCAAAAA
1 AAAATTACCA-TTTTACCCTCGGA-TGTCCAAAAATTCCATTTTTGATCCT-GATTTTTCAAAAA
** * * * * * * * *
28990140 TTACTTTTTTACCCTTAAACTTTTC-AAAATTCCAATTTTGACCCCCGAAACATTC
63 TTACCATTTTACCC-TAAAATGTCCAAAAACTCCATTTTTGA-ACCCAAAACTTTC
* ** * * * **
28990195 AAAAATTACCATTTTACCCCCATATGTCC-AAAACTCCATTTTTTATCCCGAAACTTTCAAAAAT
1 -AAAATTACCATTTTACCCTCGGATGTCCAAAAATTCCATTTTTGATCCTG-ATTTTTCAAAAAT
**
28990259 TACCATTTTACCCTCGAATGTCCAAAAACTCCATTTTTGAACCCAAAACTTTC
64 TACCATTTTACCCTAAAATGTCCAAAAACTCCATTTTTGAACCCAAAACTTTC
*
28990312 AAAATTACCATTTTACCCTCGGATGTCCAAAAATTTCATTTTTGATCCTGATTTTTCTAAAAATT
1 AAAATTACCATTTTACCCTCGGATGTCCAAAAATTCCATTTTTGATCCTGATTTTTC-AAAAATT
* * * * *
28990377 ATCGTTTTACCCTAAAATGT-CTAAAA-TGCCATTTTT-AACCCCAAATTTTCCC
65 ACCATTTTACCCTAAAATGTCCAAAAACT-CCATTTTTGAACCCAAAACTTT--C
* *
28990429 AAAATTACCATTTTTCCCTTGAGA-GTCC-AAAATTACCATTTT
1 AAAATTACCATTTTACCCTCG-GATGTCCAAAAATT-CCATTTT
28990471 ACCCTCGGGT
Statistics
Matches: 223, Mismatches: 39, Indels: 26
0.77 0.14 0.09
Matches are distributed among these distances:
115 12 0.05
116 49 0.22
117 114 0.51
118 48 0.22
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.36
Consensus pattern (116 bp):
AAAATTACCATTTTACCCTCGGATGTCCAAAAATTCCATTTTTGATCCTGATTTTTCAAAAATTA
CCATTTTACCCTAAAATGTCCAAAAACTCCATTTTTGAACCCAAAACTTTC
Found at i:28996047 original size:19 final size:20
Alignment explanation
Indices: 28996019--28996067 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
28996009 TGAACAAAGG
*
28996019 AAAAGGGGAAAGAAAA-AAA
1 AAAAGAGGAAAGAAAAGAAA
* *
28996038 GAAAGCGGAAAGAAAAGAAA
1 AAAAGAGGAAAGAAAAGAAA
28996058 AAAAGAGGAA
1 AAAAGAGGAA
28996068 CAATAAGAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.69, C:0.02, G:0.29, T:0.00
Consensus pattern (20 bp):
AAAAGAGGAAAGAAAAGAAA
Found at i:28997441 original size:49 final size:48
Alignment explanation
Indices: 28997279--28997471 Score: 167
Period size: 49 Copynumber: 3.9 Consensus size: 48
28997269 CCAAGTTTTA
* *
28997279 AAGGGAAAGG-TTGAGG-TCGCAATGGCGAACTTAGCACCATGAAGAGATG
1 AAGGG-AAGGATTGAGGCT-GCAATGGCGAACCTA-TACCATGAAGAGATG
* * * * * *
28997328 AAGGGAAGGATTGAGGCCGCGATAGCGAATCCAATTCCTAAGAAGATG-TG
1 AAGGGAAGGATTGAGGCTGCAATGGCGAA-CCTATACC-ATGAAGA-GATG
* * *
28997378 ATGGGAAAGTTTGAGGCTGCAATGGCGAACCCTATACCATGAAGAGATG
1 AAGGGAAGGATTGAGGCTGCAATGGCGAA-CCTATACCATGAAGAGATG
* * *
28997427 AAGGGAAGGATTGAGGTTGCAATGGTGAATCTGATACCATGAAGA
1 AAGGGAAGGATTGAGGCTGCAATGGCGAACCT-ATACCATGAAGA
28997472 TGTAAAGGGA
Statistics
Matches: 113, Mismatches: 24, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
48 7 0.06
49 66 0.58
50 39 0.35
51 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.33, T:0.19
Consensus pattern (48 bp):
AAGGGAAGGATTGAGGCTGCAATGGCGAACCTATACCATGAAGAGATG
Found at i:28997799 original size:39 final size:38
Alignment explanation
Indices: 28997756--28997902 Score: 154
Period size: 39 Copynumber: 3.8 Consensus size: 38
28997746 CACAGTCAGT
*
28997756 CAATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATC
1 CAATCTCTTACCCCGAGCCTGGGGCAGATT-CAGCCATC
* * * * *
28997795 CAATCTTTTACCCCGAGCTTGGGGCAGATCACAGTCAGC
1 CAATCTCTTACCCCGAGCCTGGGGCAGAT-TCAGCCATC
*
28997834 CAATCTCTTACCCGGAGCCTGGGGCAGA-TCA-CCATCAGC
1 CAATCTCTTACCCCGAGCCTGGGGCAGATTCAGCCAT---C
* *
28997873 CAATCTCTTACCCCGATCATGGGGCAGATT
1 CAATCTCTTACCCCGAGCCTGGGGCAGATT
28997903 ACAGTTATCA
Statistics
Matches: 88, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
36 2 0.02
37 2 0.02
39 83 0.94
40 1 0.01
ACGTcount: A:0.23, C:0.33, G:0.22, T:0.22
Consensus pattern (38 bp):
CAATCTCTTACCCCGAGCCTGGGGCAGATTCAGCCATC
Found at i:28997804 original size:78 final size:78
Alignment explanation
Indices: 28997719--28997907 Score: 249
Period size: 78 Copynumber: 2.4 Consensus size: 78
28997709 GAAGATTCTG
* * *
28997719 ATCTTTTACCTCGAGCTTGGGGTAGATCACAGTCAGTCAATCTCTTACCCCGAGCCTAGGGCAGA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACAGTCAGCCAATCTCTTACCCCGAGCCTAGGGCAGA
28997784 TTGCAGCCATCCA
66 TTGCAGCCATCCA
* *
28997797 ATCTTTTACCCCGAGCTTGGGGCAGATCACAGTCAGCCAATCTCTTACCCGGAGCCTGGGGCAGA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACAGTCAGCCAATCTCTTACCCCGAGCCTAGGGCAGA
28997862 -T-CA-CCATCAGCCA
66 TTGCAGCCAT---CCA
* * * *
28997875 ATCTCTTACCCCGATCATGGGGCAGATTACAGT
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACAGT
28997908 TATCAAAACA
Statistics
Matches: 99, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
75 4 0.04
76 2 0.02
77 1 0.01
78 92 0.93
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (78 bp):
ATCTTTTACCCCGAGCTTGGGGCAGATCACAGTCAGCCAATCTCTTACCCCGAGCCTAGGGCAGA
TTGCAGCCATCCA
Found at i:28998209 original size:161 final size:161
Alignment explanation
Indices: 28997929--28998351 Score: 659
Period size: 161 Copynumber: 2.6 Consensus size: 161
28997919 ATAAAATGGC
* * * * * **
28997929 CATCTTCCTGATGAGATACTGAGAAGTAGACCAACTCAATGAAACAAAGCTCAATGCAAGCGAAA
1 CATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCAAAGTGAGC-AAA
* * *
28997994 -CTTTGAACCCCAGCTTCCTAATGAGATACTGAGAAGTAGACTAAATTCGTCTTCCTGATGAGAT
65 TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGAT
*
28998058 ACAGAGAAGCGGATTGAAACAAGTGACGCTGT
130 ACAGAGAAGCGGATTGAAACAAGTGACGCGGT
*
28998090 CATCTTCCTGATGAGATACTGAGAAGAAAACCAAATCAATGAAGCCAAGCTCAAAGTGAGCAAAT
1 CATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCAAAGTGAGCAAAT
* * * *
28998155 CTTCGAACCCTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATA
66 CTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATA
*
28998220 CAGAGAAGCGGATTGAAACAAGTGATGCGGT
131 CAGAGAAGCGGATTGAAACAAGTGACGCGGT
28998251 CATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCAAAGTGAGCAAAT
1 CATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCAAAGTGAGCAAAT
* *
28998316 CTTCAAACCCCAACTTCCTGATGAGATACTGAGAAG
66 CTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAG
28998352 CAGGTCGAAG
Statistics
Matches: 239, Mismatches: 22, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
160 3 0.01
161 236 0.99
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.22
Consensus pattern (161 bp):
CATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCAAAGTGAGCAAAT
CTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATA
CAGAGAAGCGGATTGAAACAAGTGACGCGGT
Found at i:28998432 original size:209 final size:209
Alignment explanation
Indices: 28998165--28998708 Score: 788
Period size: 207 Copynumber: 2.6 Consensus size: 209
28998155 CTTCGAACCC
* * * *
28998165 TAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATACAGAGAAGCG
1 TAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCG
28998230 GATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAG
66 GATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAG
28998295 CCAAGCTCAAAGTGAGCAAATCTTCAAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGA
131 CCAAGCTCAAAGTGAGCAAATCTTCAAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGA
*
28998360 AGCAATAAAATGGT
196 AGCAATAAAACGGT
* *
28998374 TAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCTTGATAAGATACAGAGAAGCA
1 TAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCG
* * *
28998439 GATTGAAACAAGTAAT--GGTCATTTTCCTGATGAGGTACTGAGAAGAAGACCAAATCAATGAAG
66 GATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAG
* * * * *
28998502 CCAGGCTCAAAGTGAGCGAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAGGTCGA
131 CCAAGCTCAAAGTGAGCAAATCTTCAAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGA
*
28998567 AGCAATAAAGCGGT
196 AGCAATAAAACGGT
* * * * * * * *
28998581 TACCTTCCTAATGAGATA-TACAGAAGTGAAACATATTCGTCTTCTTGATGAGACACAGAAAAGT
1 TAGCTTCCTGATGAGATACTA-AGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGC
** * * * *
28998645 GGATCAAAACAAGTGATGCAGTTATCTTCCTGATGAGACACTGAGAAGTAGACCAAATCAATGA
65 GGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGA
28998709 CACCAAACCA
Statistics
Matches: 297, Mismatches: 35, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
206 2 0.01
207 182 0.61
209 113 0.38
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (209 bp):
TAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCG
GATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAG
CCAAGCTCAAAGTGAGCAAATCTTCAAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGA
AGCAATAAAACGGT
Found at i:28999038 original size:17 final size:17
Alignment explanation
Indices: 28999007--28999117 Score: 84
Period size: 17 Copynumber: 6.4 Consensus size: 17
28998997 CCAAACCCAT
*
28999007 TTTAAATTTTTTTAAGA
1 TTTAAATTTTTTTAAAA
28999024 -TTAAATTTGTTTTAAAA
1 TTTAAATTT-TTTTAAAA
28999041 TTTAAATTTATTTT-AAA
1 TTTAAATTT-TTTTAAAA
** * *
28999058 TTTAAATCTAATTTAGAG
1 TTTAAAT-TTTTTTAAAA
*
28999076 TTTAAATTTATTTTCAAA
1 TTTAAATTT-TTTTAAAA
* *
28999094 TTTAAA-ATTATTATAAA
1 TTTAAATTTTTTTA-AAA
28999111 TTTAAAT
1 TTTAAAT
28999118 GAATAAATTC
Statistics
Matches: 73, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
16 11 0.15
17 31 0.42
18 31 0.42
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (17 bp):
TTTAAATTTTTTTAAAA
Found at i:28999045 original size:18 final size:18
Alignment explanation
Indices: 28999007--28999117 Score: 113
Period size: 18 Copynumber: 6.4 Consensus size: 18
28998997 CCAAACCCAT
*
28999007 TTTAAATTT-TTTTAAGA
1 TTTAAATTTATTTTAAAA
*
28999024 -TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAAA
28999041 TTTAAATTTATTTT-AAA
1 TTTAAATTTATTTTAAAA
* * * *
28999058 TTTAAATCTAATTTAGAG
1 TTTAAATTTATTTTAAAA
*
28999076 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTTAAAA
* *
28999094 TTTAAAATTATTAT-AAA
1 TTTAAATTTATTTTAAAA
28999111 TTTAAAT
1 TTTAAAT
28999118 GAATAAATTC
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
16 8 0.10
17 31 0.40
18 38 0.49
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (18 bp):
TTTAAATTTATTTTAAAA
Found at i:28999049 original size:6 final size:6
Alignment explanation
Indices: 28999038--28999117 Score: 53
Period size: 6 Copynumber: 13.7 Consensus size: 6
28999028 ATTTGTTTTA
* * *
28999038 AAATTT AAATTT -ATTTT AAATTT AAATCT -AATTT AGAGTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT A-AATTT AAATTT
* *
28999085 -ATTTT CAAATTT AAAATT --ATTAT AAATTT AAAT
1 AAATTT -AAATTT AAATTT AAATT-T AAATTT AAAT
28999118 GAATAAATTC
Statistics
Matches: 56, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
4 2 0.04
5 13 0.23
6 29 0.52
7 12 0.21
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:28999063 original size:35 final size:35
Alignment explanation
Indices: 28999007--28999117 Score: 120
Period size: 35 Copynumber: 3.2 Consensus size: 35
28998997 CCAAACCCAT
*
28999007 TTTAAATTT-TTTTAAGA-TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAA-ATTTAAATTTATTTTAAAA
* * * *
28999041 TTTAAATTTATTTTAAATTTAAATCTAATTTAGAG
1 TTTAAATTTATTTTAAATTTAAATTTATTTTAAAA
* *
28999076 TTTAAATTTATTTTCAAATTTAAAATTATTAT-AAA
1 TTTAAATTTATTTT-AAATTTAAATTTATTTTAAAA
28999111 TTTAAAT
1 TTTAAAT
28999118 GAATAAATTC
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
34 10 0.16
35 40 0.63
36 13 0.21
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (35 bp):
TTTAAATTTATTTTAAATTTAAATTTATTTTAAAA
Found at i:29001099 original size:61 final size:59
Alignment explanation
Indices: 29000995--29001111 Score: 155
Period size: 61 Copynumber: 1.9 Consensus size: 59
29000985 TAAACAGTTC
* * * *
29000995 AAAAATTACATTTTTACCCTCAAACTTCTAAATATTCTATTTTTACCCTTGAACTTCCA
1 AAAAATTACATTTTTACCCTAAAACTTCCAAAAATTCTATTTTTACCCTTAAACTTCCA
*
29001054 AAAAATTCCATTTTTTGACCCTAAAACTTCCAAAAATTACT-TTTTTACCCTTAAACTT
1 AAAAATTACA-TTTTT-ACCCTAAAACTTCCAAAAATT-CTATTTTTACCCTTAAACTT
29001112 TTCAAAATTC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
59 9 0.18
60 5 0.10
61 34 0.68
62 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (59 bp):
AAAAATTACATTTTTACCCTAAAACTTCCAAAAATTCTATTTTTACCCTTAAACTTCCA
Found at i:29001120 original size:29 final size:29
Alignment explanation
Indices: 29000994--29001111 Score: 130
Period size: 29 Copynumber: 4.0 Consensus size: 29
29000984 CTAAACAGTT
* *
29000994 CAAAAATTACATTTTTACCCTCAAACTTC
1 CAAAAATTACTTTTTTACCCTTAAACTTC
* * *
29001023 TAAATATT-CTATTTTTACCCTTGAACTTC
1 CAAAAATTACT-TTTTTACCCTTAAACTTC
* *
29001052 CAAAAAATTCCATTTTTTGACCCTAAAACTTC
1 C-AAAAATTAC-TTTTTT-ACCCTTAAACTTC
29001084 CAAAAATTACTTTTTTACCCTTAAACTT
1 CAAAAATTACTTTTTTACCCTTAAACTT
29001112 TTCAAAATTC
Statistics
Matches: 73, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
28 1 0.01
29 33 0.45
30 12 0.16
31 14 0.19
32 13 0.18
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.40
Consensus pattern (29 bp):
CAAAAATTACTTTTTTACCCTTAAACTTC
Found at i:29001128 original size:61 final size:59
Alignment explanation
Indices: 29000994--29001133 Score: 151
Period size: 61 Copynumber: 2.4 Consensus size: 59
29000984 CTAAACAGTT
* * * * *
29000994 CAAAAATTACA-TTTTTACCCTCAAACTTCTAAATATTCTATTTTTACCCTTGAACTTC
1 CAAAAATTCCATTTTTTACCCTAAAACTTCCAAAAATTCTATTTTTACCCTTAAACTTC
*
29001052 CAAAAAATTCCATTTTTTGACCCTAAAACTTCCAAAAATTACT-TTTTTACCCTTAAACTTTT
1 C-AAAAATTCCATTTTTT-ACCCTAAAACTTCCAAAAATT-CTATTTTTACCCTTAAAC-TTC
* *
29001114 C-AAAATTCCAATTTTGACCC
1 CAAAAATTCCATTTTTTACCC
29001134 CTGAAACATT
Statistics
Matches: 69, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
58 1 0.01
59 13 0.19
60 18 0.26
61 32 0.46
62 5 0.07
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.39
Consensus pattern (59 bp):
CAAAAATTCCATTTTTTACCCTAAAACTTCCAAAAATTCTATTTTTACCCTTAAACTTC
Found at i:29001267 original size:57 final size:58
Alignment explanation
Indices: 29001137--29001305 Score: 207
Period size: 58 Copynumber: 2.9 Consensus size: 58
29001127 TTGACCCCTG
* * * * * * * *
29001137 AAACATTCAAGAATAACCATTTTACCCCCAGATGTCC-AAAACTCCATTTTTGATCTCG
1 AAACTTTCAA-AATTACCATTTTACCCTCGGATGTCCAAAAACTACATTTTTGAACCCA
29001195 AAACTTTCAAAAATTACCATTTTA-CCTCGGATGTCCAAAAACTACATTTTTGAACCCA
1 AAACTTTC-AAAATTACCATTTTACCCTCGGATGTCCAAAAACTACATTTTTGAACCCA
* * *
29001253 AAACTTTCAAAATTACCATTTTACCCTCGAATGTCCAAAAATTTCATTTTTGA
1 AAACTTTCAAAATTACCATTTTACCCTCGGATGTCCAAAAACTACATTTTTGA
29001306 TCTTGTTTTC
Statistics
Matches: 97, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
57 25 0.26
58 70 0.72
59 2 0.02
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (58 bp):
AAACTTTCAAAATTACCATTTTACCCTCGGATGTCCAAAAACTACATTTTTGAACCCA
Found at i:29001815 original size:96 final size:96
Alignment explanation
Indices: 29001650--29001841 Score: 253
Period size: 96 Copynumber: 2.0 Consensus size: 96
29001640 AAAACTTTAA
* * * * *
29001650 AATCGAGGCAATATTCTTTTATTTCGAGTTTCGAAATTTTGTGCCTTAACTTATTAGGAGCATTT
1 AATCGAGGCAATATTCTCTTATTTCGAGTTTCGAAAATTTGTGCCTTAACTTACTAGGAGCAATC
*
29001715 TTTCTTCAAATCGAAATAATCGAATACCCTT
66 TTTCTTCAAATCGAAATAATCAAATACCCTT
* * *
29001746 AATCGAGGCAATGTT-TCCTTATCTTCGA-TTTTGAAAATTTGTGCCTTAACTTACTAGGTGCAA
1 AATCGAGGCAATATTCT-CTTAT-TTCGAGTTTCGAAAATTTGTGCCTTAACTTACTAGGAGCAA
* *
29001809 TCTTTCTTCAAATCGAGATAATCAAATATCCTT
64 TCTTTCTTCAAATCGAAATAATCAAATACCCTT
29001842 TTCCAAAATT
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
95 1 0.01
96 77 0.93
97 5 0.06
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40
Consensus pattern (96 bp):
AATCGAGGCAATATTCTCTTATTTCGAGTTTCGAAAATTTGTGCCTTAACTTACTAGGAGCAATC
TTTCTTCAAATCGAAATAATCAAATACCCTT
Found at i:29003958 original size:3 final size:3
Alignment explanation
Indices: 29003950--29003995 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
29003940 ATCAAAGATT
29003950 TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
29003996 GTTATATTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:29005284 original size:21 final size:21
Alignment explanation
Indices: 29005260--29005299 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29005250 TTCTTTTATT
*
29005260 TTATGTATATATATATATTTG
1 TTATATATATATATATATTTG
*
29005281 TTATATATATATATGTATT
1 TTATATATATATATATATT
29005300 AATTAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TTATATATATATATATATTTG
Found at i:29011734 original size:6 final size:6
Alignment explanation
Indices: 29011719--29011777 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
29011709 AAACTAGCAA
**
29011719 AAAAAG -AAAAG AAAAAG --AAA- AAAAAG AAAAAG AGAAAA- AAAGGG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A-AAAAG AAAAAG
29011763 AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAA
29011778 GGGCCGAGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
4 3 0.07
5 10 0.23
6 26 0.60
7 4 0.09
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:29011780 original size:18 final size:16
Alignment explanation
Indices: 29011719--29011779 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 16
29011709 AAACTAGCAA
*
29011719 AAAAAGAAAAGAAAAAG
1 AAAAA-AAAGGAAAAAG
29011736 AAAAAAAA-GAAAAAG
1 AAAAAAAAGGAAAAAG
29011751 AGAAAAAAAGGGAAAAAG
1 A-AAAAAAA-GGAAAAAG
29011769 AAAAAGAAAGG
1 AAAAA-AAAGG
29011780 GCCGAGATGA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.20
16 10 0.25
17 11 0.28
18 11 0.28
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGGAAAAAG
Found at i:29012849 original size:49 final size:49
Alignment explanation
Indices: 29012773--29013329 Score: 362
Period size: 49 Copynumber: 11.4 Consensus size: 49
29012763 CATAAAGTTT
* * * * *
29012773 GAAGAAGGATAGGTTGAAGCCGCAACGATGGACCTAACATCTTAAAATC
1 GAAGAGGGAAAGGTTGAAGCCGTAACGACGGACCTAACACCTTAAAATC
*
29012822 GAAGAGGGAAAGGTTGAAGCCGTAACGACGGACCTTACACCTTAAAA-C
1 GAAGAGGGAAAGGTTGAAGCCGTAACGACGGACCTAACACCTTAAAATC
* * * * *
29012870 TGAAGAGGGATAGGTTAAAGTCGTAACGGCGGACCTAACACCTAAAAATC
1 -GAAGAGGGAAAGGTTGAAGCCGTAACGACGGACCTAACACCTTAAAATC
* * * * * * *
29012920 -AAAAAGGAAAGATTGAA----AAACGACGGATCTTACACTTTAAAA-C
1 GAAGAGGGAAAGGTTGAAGCCGTAACGACGGACCTAACACCTTAAAATC
* * * * * *
29012963 TGAATAGGGATAGGTTGAAGTCGTAACGACGAACCTAACACCATAAAATAGA
1 -GAAGAGGGAAAGGTTGAAGCCGTAACGACGGACCTAACACCTTAAAAT--C
* * * * * * *
29013015 GAAGAGGGATAGATTGAAGCCGTAATGGCGGATCTAACACCCT-AAACC
1 GAAGAGGGAAAGGTTGAAGCCGTAACGACGGACCTAACACCTTAAAATC
* * * * * *
29013063 AAAGAGGGAAAGGTTAAAGTCATAACAACGGACCTTACACCTTAAAAAT-
1 GAAGAGGGAAAGGTTGAAGCCGTAACGACGGACCTAACACCTT-AAAATC
* ** * * * * *
29013112 AAAGAGGGAAAGGTTGAAGCCACAACAACGAACCTTATACC-TAAAAAC
1 GAAGAGGGAAAGGTTGAAGCCGTAACGACGGACCTAACACCTTAAAATC
* * * * * *
29013160 TGAAGAGGGATAGGTTGAAGCCATAACGGCGAACCTAACACCCTAACAAAC
1 -GAAGAGGGAAAGGTTGAAGCCGTAACGACGGACCTAACACCTTAA-AATC
* * * * * * *
29013211 GACGAGGGAAAGATTGAAGTCGCAACGACGGATCTTACACCTTAAAATA
1 GAAGAGGGAAAGGTTGAAGCCGTAACGACGGACCTAACACCTTAAAATC
* ** * * * *
29013260 GAA-AAGGAATAGGTTGAAGCCGCGATGGCGGACCTAATACCTTAAAATT
1 GAAGAGGGAA-AGGTTGAAGCCGTAACGACGGACCTAACACCTTAAAATC
* *
29013309 GAAGAGGGATAGATTGAAGCC
1 GAAGAGGGAAAGGTTGAAGCC
29013330 ACGACAGCAA
Statistics
Matches: 392, Mismatches: 97, Indels: 38
0.74 0.18 0.07
Matches are distributed among these distances:
43 1 0.00
44 19 0.05
45 13 0.03
47 4 0.01
48 50 0.13
49 218 0.56
50 48 0.12
51 39 0.10
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (49 bp):
GAAGAGGGAAAGGTTGAAGCCGTAACGACGGACCTAACACCTTAAAATC
Found at i:29013143 original size:148 final size:145
Alignment explanation
Indices: 29012823--29013329 Score: 490
Period size: 148 Copynumber: 3.5 Consensus size: 145
29012813 CTTAAAATCG
* * * * * *
29012823 AAGAGGGAAAGGTTGAAGCCGTAACGACGGACCTTACACCTTAAAACTGAAGAGGGATAGGTTAA
1 AAGAGGGAAAGGTTGAAGCCGCAACGACGAACCTAACACCTTAAAATTGAAGAGGGATAGATTGA
* * *
29012888 AGTCGTAACGGCGGACCTAACA-CCTAAAAATCAAA-AAGGAAAGATTGAA---AAACGACGGAT
66 AGCCGTAACGGCGGACCTAACACCCT--AAACCAAAGAGGGAAAGATTGAAGTCAAACGACGGAT
* * *
29012948 CTTACACTTTAAAACTG
129 CTTACACCTTAAAAATA
* * * * * *
29012965 AATAGGGATAGGTTGAAGTCGTAACGACGAACCTAACACCATAAAATAGAGAAGAGGGATAGATT
1 AAGAGGGAAAGGTTGAAGCCGCAACGACGAACCTAACACCTTAAAAT--TGAAGAGGGATAGATT
* * * * *
29013030 GAAGCCGTAATGGCGGATCTAACACCCTAAACCAAAGAGGGAAAGGTTAAAGTCATAACAACGGA
64 GAAGCCGTAACGGCGGACCTAACACCCTAAACCAAAGAGGGAAAGATTGAAGTCA-AACGACGGA
*
29013095 CCTTACACCTTAAAAATA
128 TCTTACACCTTAAAAATA
* * * * * * *
29013113 AAGAGGGAAAGGTTGAAGCCACAACAACGAACCTTATACCTAAAAACTGAAGAGGGATAGGTTGA
1 AAGAGGGAAAGGTTGAAGCCGCAACGACGAACCTAACACCTTAAAATTGAAGAGGGATAGATTGA
* * * *
29013178 AGCCATAACGGCGAACCTAACACCCT-AACAAACGACGAGGGAAAGATTGAAGTCGCAACGACGG
66 AGCCGTAACGGCGGACCTAACACCCTAAACCAA--A-GAGGGAAAGATTGAAGTC-AAACGACGG
29013242 ATCTTACACCTT-AAAATA
127 ATCTTACACCTTAAAAATA
* * * * * *
29013260 GAA-AAGGAATAGGTTGAAGCCGCGATGGCGGACCTAATACCTTAAAATTGAAGAGGGATAGATT
1 -AAGAGGGAA-AGGTTGAAGCCGCAACGACGAACCTAACACCTTAAAATTGAAGAGGGATAGATT
29013324 GAAGCC
64 GAAGCC
29013330 ACGACAGCAA
Statistics
Matches: 295, Mismatches: 56, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
142 40 0.14
143 7 0.02
144 45 0.15
145 8 0.03
146 38 0.13
147 13 0.04
148 144 0.49
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (145 bp):
AAGAGGGAAAGGTTGAAGCCGCAACGACGAACCTAACACCTTAAAATTGAAGAGGGATAGATTGA
AGCCGTAACGGCGGACCTAACACCCTAAACCAAAGAGGGAAAGATTGAAGTCAAACGACGGATCT
TACACCTTAAAAATA
Found at i:29013295 original size:99 final size:98
Alignment explanation
Indices: 29012772--29013331 Score: 271
Period size: 99 Copynumber: 5.7 Consensus size: 98
29012762 TCATAAAGTT
* ** * * * * *
29012772 TGAAGAAGG-ATAGGTTGAAGCCGCAACGATGGACCTAACATCTTAAAATCGAAGAGGGAAAGGT
1 TGAA-AAGGAATAGGTTGAAGCCACAACGGCGAACCTAACACCCTAAAAACGAAGAGGGAAAGAT
** * * *
29012836 TGAAGCCGTAACGACGGACCTTACACCTTAAAAC
65 TGAAGCCACAACAACGAACCTTACACCTAAAAAC
* * * * ** * * *
29012870 TGAAGAGGGATAGGTTAAAGTCGTAACGGCGGACCTAACA-CCTAAAAATC-AAAAAGGAAAGAT
1 TGAAAAGGAATAGGTTGAAGCCACAACGGCGAACCTAACACCCTAAAAA-CGAAGAGGGAAAGAT
* * * * *
29012933 TGAA---A-AACGACGGATCTTACACTTTAAAAC
65 TGAAGCCACAACAACGAACCTTACACCTAAAAAC
* * * ** * * * *
29012963 TGAATAGGGATAGGTTGAAGTCGTAACGACGAACCTAACACCATAAAATAGAGAAGAGGGATAGA
1 TGAAAAGGAATAGGTTGAAGCCACAACGGCGAACCTAACACCCTAAAA-A-CGAAGAGGGAAAGA
** *** * * *
29013028 TTGAAGCCGTAATGGCGGATCTAACACCCT--AAAC
64 TTGAAGCCACAACAACGAACCTTACA-CCTAAAAAC
* * * * ** * * * ** *
29013062 -CAAAGAGGGAA-AGGTTAAAGTCATAACAACGGACCTTACACCTTAAAAATAAAGAGGGAAAGG
1 TGAAA-A-GGAATAGGTTGAAGCCACAACGGCGAACCTAACACCCTAAAAACGAAGAGGGAAAGA
*
29013125 TTGAAGCCACAACAACGAACCTTATACCTAAAAAC
64 TTGAAGCCACAACAACGAACCTTACACCTAAAAAC
* * * *
29013160 TGAAGAGGGATAGGTTGAAGCCATAACGGCGAACCTAACACCCTAACAAACGACGAGGGAAAGAT
1 TGAAAAGGAATAGGTTGAAGCCACAACGGCGAACCTAACACCCTAA-AAACGAAGAGGGAAAGAT
* * * * * *
29013225 TGAAGTCGCAACGACGGATCTTACACCTTAAAA-
65 TGAAGCCACAACAACGAACCTTACACCTAAAAAC
* * * * * * ** *
29013258 TAGAAAAGGAATAGGTTGAAGCCGCGATGGCGGACCTAATACCTTAAAATTGAAGAGGGATAGAT
1 T-GAAAAGGAATAGGTTGAAGCCACAACGGCGAACCTAACACCCTAAAAACGAAGAGGGAAAGAT
29013323 TGAAGCCAC
65 TGAAGCCAC
29013332 GACAGCAAAT
Statistics
Matches: 357, Mismatches: 87, Indels: 36
0.74 0.18 0.08
Matches are distributed among these distances:
93 59 0.17
94 6 0.02
95 1 0.00
96 17 0.05
97 53 0.15
98 89 0.25
99 114 0.32
100 16 0.04
101 2 0.01
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (98 bp):
TGAAAAGGAATAGGTTGAAGCCACAACGGCGAACCTAACACCCTAAAAACGAAGAGGGAAAGATT
GAAGCCACAACAACGAACCTTACACCTAAAAAC
Found at i:29015508 original size:28 final size:28
Alignment explanation
Indices: 29015467--29015529 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
29015457 TGAAAATGAG
* *
29015467 ATTTTCGGATACTTGGGGGCAAAATGGTA
1 ATTTT-GGACACTTGAGGGCAAAATGGTA
*
29015496 ATTTTGGACACTTGAGGGTAAAATGGTA
1 ATTTTGGACACTTGAGGGCAAAATGGTA
29015524 ATTTTG
1 ATTTTG
29015530 CAAAAGTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 26 0.84
29 5 0.16
ACGTcount: A:0.29, C:0.08, G:0.29, T:0.35
Consensus pattern (28 bp):
ATTTTGGACACTTGAGGGCAAAATGGTA
Found at i:29015574 original size:59 final size:58
Alignment explanation
Indices: 29015511--29015910 Score: 327
Period size: 59 Copynumber: 6.8 Consensus size: 58
29015501 GGACACTTGA
* * *
29015511 GGGTAAAATGGTAATTTTGCAAAAGTTTGGTGTTAAAAATGGAATTTTTAGACA-TTTAG
1 GGGTAAAATGGTAATTTTGGAAAAGTTTGG-GTCAAAAATGGAATTTTTGGA-AGTTTAG
* ** * * *
29015570 GGGTAAAATGGTAATTTT-TAGAAAGTTTGGGGTTTAAAATGGGATTTTT--AAATATTCG
1 GGGTAAAATGGTAATTTTGGA-AAAGTTT-GGGTCAAAAATGGAATTTTTGGAAGT-TTAG
* * * * * *
29015628 AGGGTAAAATGGTAATTTTGAAAAAATTAGGGTCAAAAATGAAATTTTTGGAAGTTCAA
1 -GGGTAAAATGGTAATTTTGGAAAAGTTTGGGTCAAAAATGGAATTTTTGGAAGTTTAG
** *
29015687 GGGTAAAATGGTAATTTTGGAAAAAATTGAGGTCAAAAATAGAATTTTTGGAAGTTTAG
1 GGGTAAAATGGTAATTTTGGAAAAGTTTG-GGTCAAAAATGGAATTTTTGGAAGTTTAG
* * * *
29015746 GGGTAAAAAT-GTAATTTT-TAGAAAGTTTAGGGTCAAAAATGGAA-TTTTGGAAATCTCAA
1 GGGT-AAAATGGTAATTTTGGA-AAAGTTT-GGGTCAAAAATGGAATTTTTGGAAGT-TTAG
* * * *
29015805 GGTTAAAAAT-GAAATTTTGGAAAA-TTCGAGGTCAAATATGGAATTTTTGGAAGTTTAG
1 GGGT-AAAATGGTAATTTTGGAAAAGTTTG-GGTCAAAAATGGAATTTTTGGAAGTTTAG
* *
29015863 GGGTAAAAAT-GTAATTTTTGG-AAAGTTTAGAGTTAAAAATGGAATTTT
1 GGGT-AAAATGGTAA-TTTTGGAAAAGTTT-GGGTCAAAAATGGAATTTT
29015911 AGAAAATTTA
Statistics
Matches: 279, Mismatches: 43, Indels: 38
0.77 0.12 0.11
Matches are distributed among these distances:
56 1 0.00
57 3 0.01
58 88 0.32
59 173 0.62
60 14 0.05
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.35
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTGGAAAAGTTTGGGTCAAAAATGGAATTTTTGGAAGTTTAG
Found at i:29015585 original size:29 final size:28
Alignment explanation
Indices: 29015482--29015793 Score: 129
Period size: 29 Copynumber: 10.7 Consensus size: 28
29015472 CGGATACTTG
* * * *
29015482 GGGGCAAAATGGTAA-TTTTGGACACTT
1 GGGGTAAAATGGTAATTTTTAGAAATTT
*
29015509 GAGGGTAAAATGGTAATTTTGCA-AAAGTTT
1 G-GGGTAAAATGGTAATTTT-TAGAAA-TTT
* *
29015539 GGTGTTAAAAATGG-AATTTTTAGACATTT
1 GG-GGT-AAAATGGTAATTTTTAGAAATTT
29015568 AGGGGTAAAATGGTAATTTTTAGAAAGTTT
1 -GGGGTAAAATGGTAATTTTTAGAAA-TTT
* *
29015598 GGGGTTTAAAATGG-GATTTTTA-AATATTC
1 GGGG--TAAAATGGTAATTTTTAGAA-ATTT
* * *
29015627 GAGGGTAAAATGGTAATTTTGAAAAAATT
1 G-GGGTAAAATGGTAATTTTTAGAAATTT
* * * * *
29015656 AGGGTCAAAAAT-GAAATTTTTGGAAGTTCA
1 GGGGT--AAAATGGTAATTTTTAGAAATT-T
* * * *
29015686 AGGGTAAAATGGTAATTTTGGAAAAAATT
1 GGGGTAAAATGGTAATTTT-TAGAAATTT
* * * *
29015715 GAGGTCAAAAATAG-AATTTTTGGAAGTTT
1 GGGGT--AAAATGGTAATTTTTAGAAATTT
29015744 AGGGGTAAAAAT-GTAATTTTTAGAAAGTTT
1 -GGGGT-AAAATGGTAATTTTTAGAAA-TTT
*
29015774 AGGGTCAAAAATGG-AATTTT
1 GGGGT--AAAATGGTAATTTT
29015794 GGAAATCTCA
Statistics
Matches: 214, Mismatches: 43, Indels: 53
0.69 0.14 0.17
Matches are distributed among these distances:
27 1 0.00
28 38 0.18
29 84 0.39
30 69 0.32
31 22 0.10
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (28 bp):
GGGGTAAAATGGTAATTTTTAGAAATTT
Found at i:29015659 original size:28 final size:28
Alignment explanation
Indices: 29015487--29015714 Score: 83
Period size: 28 Copynumber: 7.8 Consensus size: 28
29015477 ACTTGGGGGC
* * *
29015487 AAAATGGTAATTTTG-GACACTTGAGGGT
1 AAAATGGTAATTTTGAAAAAATT-AGGGT
* * *
29015515 AAAATGGTAATTTTGCAAAAGTTTGGTGTT
1 AAAATGGTAATTTTGAAAAAATTAGG-G-T
* * * *
29015545 AAAAATGG-AATTTTTAGACATTTAGGGGT
1 -AAAATGGTAATTTTGAAAAAATTA-GGGT
* ** *
29015574 AAAATGGTAATTTTTAGAAAGTTTGGGGTTT
1 AAAATGGTAATTTTGA-AAAAATTAGGG--T
* * *
29015605 AAAATGG-GATTTT-TAAATATTCGAGGGT
1 AAAATGGTAATTTTGAAAAAATT--AGGGT
29015633 AAAATGGTAATTTTGAAAAAATTAGGGT
1 AAAATGGTAATTTTGAAAAAATTAGGGT
* * *
29015661 CAAAAAT-GAAATTTTTG--GAAGTTCAAGGGT
1 --AAAATGGTAA-TTTTGAAAAAATT--AGGGT
29015691 AAAATGGTAATTTTGGAAAAAATT
1 AAAATGGTAATTTT-GAAAAAATT
29015715 GAGGTCAAAA
Statistics
Matches: 150, Mismatches: 28, Indels: 41
0.68 0.13 0.19
Matches are distributed among these distances:
28 55 0.37
29 29 0.19
30 45 0.30
31 21 0.14
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (28 bp):
AAAATGGTAATTTTGAAAAAATTAGGGT
Found at i:29015858 original size:117 final size:116
Alignment explanation
Indices: 29015629--29015915 Score: 375
Period size: 117 Copynumber: 2.5 Consensus size: 116
29015619 AAATATTCGA
* ** * *
29015629 GGGT-AAAATGGTAATTTTGA-AAAAATTAGGGTCAAAAATGAAATTTTTGGAAGTTCAAGGGTA
1 GGGTAAAAAT-GTAATTTTTAGAAAGTTTAGGGTCAAAAATGGAA-TTTTGGAAATTCAAGGGTA
*
29015692 AAATGGTAATTTTGGAAAAAATTGAGGTCAAAAATAGAATTTTTGGAAGTTTAG
64 AAATGGAAATTTTGG-AAAAATTGAGGTCAAAAATAGAATTTTTGGAAGTTTAG
*
29015746 GGGTAAAAATGTAATTTTTAGAAAGTTTAGGGTCAAAAATGGAATTTTGGAAATCTCAAGGTTAA
1 GGGTAAAAATGTAATTTTTAGAAAGTTTAGGGTCAAAAATGGAATTTTGGAAAT-TCAAGGGT-A
* *
29015811 AAAT-GAAATTTTGG-AAAATTCGAGGTCAAATATGGAATTTTTGGAAGTTTAG
64 AAATGGAAATTTTGGAAAAATT-GAGGTCAAAAATAGAATTTTTGGAAGTTTAG
* * * *
29015863 GGGTAAAAATGTAATTTTTGGAAAGTTTAGAGTTAAAAATGGAATTTTAGAAA
1 GGGTAAAAATGTAATTTTTAGAAAGTTTAGGGTCAAAAATGGAATTTTGGAAA
29015916 ATTTAGGATC
Statistics
Matches: 152, Mismatches: 13, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
116 6 0.04
117 100 0.66
118 41 0.27
119 5 0.03
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.33
Consensus pattern (116 bp):
GGGTAAAAATGTAATTTTTAGAAAGTTTAGGGTCAAAAATGGAATTTTGGAAATTCAAGGGTAAA
ATGGAAATTTTGGAAAAATTGAGGTCAAAAATAGAATTTTTGGAAGTTTAG
Found at i:29015910 original size:176 final size:173
Alignment explanation
Indices: 29015510--29015944 Score: 452
Period size: 176 Copynumber: 2.5 Consensus size: 173
29015500 TGGACACTTG
* * *
29015510 AGGGTAAAATGGTAATTTTGCAAAAGTTTGGTGTTAAAAATGGAATTTTTAGACATTTAGGGGT-
1 AGGGTAAAATGGTAATTTTG-GAAAGTTT-GAGTTAAAAATGGAATTTTTGGA-ATTTAGGGGTA
* ** * * * *
29015574 AAAATGGTAATTTTTAGAAAGTTTGGGGTTTAAAATGGGATTTTTAAATATTCGAGGGTAAAATG
63 AAAAT-GTAATTTTTAGAAAGTTTAGGGTCAAAAATGGAATTTTGAAATACTCAAGGGTAAAATG
*
29015639 GTAATTTTGAAAAAATTAGGGTCAAAAATGAAATTTTTGGAAGTTCA
127 GAAATTTTGAAAAAATTAGGGTCAAAAATGAAATTTTTGGAAGTTCA
** * *
29015686 AGGGTAAAATGGTAATTTTGGAAAAAATTGAGGTCAAAAATAGAATTTTTGGAAGTTTAGGGGTA
1 AGGGTAAAATGGTAATTTTGG-AAAGTTTGA-GTTAAAAATGGAATTTTTGGAA-TTTAGGGGTA
*
29015751 AAAATGTAATTTTTAGAAAGTTTAGGGTCAAAAATGGAATTTTGGAAAT-CTCAAGGTTAAAAAT
63 AAAATGTAATTTTTAGAAAGTTTAGGGTCAAAAATGGAATTTT-GAAATACTCAAGGGT-AAAAT
* * * * *
29015815 -GAAATTTTG-GAAAATTCGAGGTCAAATATGGAATTTTTGGAAGTTTA
126 GGAAATTTTGAAAAAATTAG-GGTCAAAAATGAAATTTTTGGAAGTTCA
* * * *
29015862 GGGGTAAAAAT-GTAATTTTTGGAAAGTTTAGAGTTAAAAATGGAATTTTAGAAAATTTA-GGAT
1 AGGGT-AAAATGGTAA-TTTTGGAAAGTTT-GAGTTAAAAATGGAATTTTTG-GAATTTAGGGGT
*
29015925 CAAAAATGGAA-TTTTAGAAA
62 -AAAAATGTAATTTTTAGAAA
29015945 ATTTTAAATG
Statistics
Matches: 217, Mismatches: 30, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
175 21 0.10
176 167 0.77
177 29 0.13
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (173 bp):
AGGGTAAAATGGTAATTTTGGAAAGTTTGAGTTAAAAATGGAATTTTTGGAATTTAGGGGTAAAA
ATGTAATTTTTAGAAAGTTTAGGGTCAAAAATGGAATTTTGAAATACTCAAGGGTAAAATGGAAA
TTTTGAAAAAATTAGGGTCAAAAATGAAATTTTTGGAAGTTCA
Found at i:29015930 original size:117 final size:116
Alignment explanation
Indices: 29015699--29015947 Score: 349
Period size: 117 Copynumber: 2.1 Consensus size: 116
29015689 GTAAAATGGT
29015699 AATTTTGGAAAAAATTGAGGTCAAAAATAGAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTT
1 AATTTTGG--AAAATTGAGGTCAAAAATAGAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTT
* * *
29015764 TAGAAAGTTTAGGGTCAAAAATGGAATTTTGGAAATCTCAAGGTTAAAAATGA
64 TAGAAAGTTTAGAGTCAAAAATGGAATTTTGAAAATCTCAAGGTCAAAAATGA
* *
29015817 AATTTTGGAAAATTCGAGGTCAAATATGGAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTT
1 AATTTTGGAAAATT-GAGGTCAAAAATAGAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTT
* * * *
29015882 GGAAAGTTTAGAGTTAAAAATGGAATTTTAGAAAAT-T-TAGGATCAAAAATGG
65 AGAAAGTTTAGAGTCAAAAATGGAATTTT-GAAAATCTCAAGG-TCAAAAATGA
*
29015934 AATTTTAGAAAATT
1 AATTTTGGAAAATT
29015948 TTAAATGTCA
Statistics
Matches: 118, Mismatches: 10, Indels: 7
0.87 0.07 0.05
Matches are distributed among these distances:
116 9 0.08
117 96 0.81
118 13 0.11
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.34
Consensus pattern (116 bp):
AATTTTGGAAAATTGAGGTCAAAAATAGAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTA
GAAAGTTTAGAGTCAAAAATGGAATTTTGAAAATCTCAAGGTCAAAAATGA
Found at i:29015945 original size:29 final size:28
Alignment explanation
Indices: 29015691--29015948 Score: 162
Period size: 29 Copynumber: 8.8 Consensus size: 28
29015681 GTTCAAGGGT
* *
29015691 AAAATGGTAATTTTGGAAAAAATTGAGGTCA
1 AAAATGG-AATTTT--AGAAAATTTAGGTCA
* * * *
29015722 AAAATAGAATTTTTGGAAGTTTAGGGGT-A
1 AAAATGGAATTTTAGAAAATTTA--GGTCA
* *
29015751 AAAATGTAATTTTTAGAAAGTTTAGGGTCA
1 AAAATGGAA-TTTTAGAAAATTTA-GGTCA
* * *
29015781 AAAATGGAATTTT-GGAAATCTCAAGGTTA
1 AAAATGGAATTTTAGAAAAT-T-TAGGTCA
* * *
29015810 AAAATGAAATTTTGGAAAATTCGAGGTCA
1 AAAATGGAATTTTAGAAAATT-TAGGTCA
* * * *
29015839 AATATGGAATTTTTGGAAGTTTAGGGGT-A
1 AAAATGGAATTTTAGAAAATTTA--GGTCA
* * * *
29015868 AAAATGTAATTTTTGGAAAGTTTAGAGTTA
1 AAAATGGAA-TTTTAGAAAATTTAG-GTCA
29015898 AAAATGGAATTTTAGAAAATTTAGGATCA
1 AAAATGGAATTTTAGAAAATTTAGG-TCA
29015927 AAAATGGAATTTTAGAAAATTT
1 AAAATGGAATTTTAGAAAATTT
29015949 TAAATGTCAA
Statistics
Matches: 181, Mismatches: 33, Indels: 28
0.75 0.14 0.12
Matches are distributed among these distances:
28 12 0.07
29 103 0.57
30 60 0.33
31 6 0.03
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.34
Consensus pattern (28 bp):
AAAATGGAATTTTAGAAAATTTAGGTCA
Found at i:29018330 original size:16 final size:15
Alignment explanation
Indices: 29018311--29018362 Score: 61
Period size: 14 Copynumber: 3.5 Consensus size: 15
29018301 CACAAAGCAC
*
29018311 GAATAATTATAAGAA
1 GAATAAATATAAGAA
*
29018326 TGAATAAATATACGAA
1 -GAATAAATATAAGAA
29018342 -AATAAATATAAGAA
1 GAATAAATATAAGAA
*
29018356 AAATAAA
1 GAATAAA
29018363 ATACGAATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 13 0.41
15 6 0.19
16 13 0.41
ACGTcount: A:0.65, C:0.02, G:0.10, T:0.23
Consensus pattern (15 bp):
GAATAAATATAAGAA
Found at i:29018346 original size:30 final size:28
Alignment explanation
Indices: 29018312--29018369 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 28
29018302 ACAAAGCACG
* *
29018312 AATAATTATAAGAATGAATAAATATACGAA
1 AATAAATATAAGAA-AAATAAA-ATACGAA
29018342 AATAAATATAAGAAAAATAAAATACGAA
1 AATAAATATAAGAAAAATAAAATACGAA
29018370 TCATGAATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 7 0.27
29 6 0.23
30 13 0.50
ACGTcount: A:0.66, C:0.03, G:0.09, T:0.22
Consensus pattern (28 bp):
AATAAATATAAGAAAAATAAAATACGAA
Found at i:29018347 original size:14 final size:14
Alignment explanation
Indices: 29018328--29018369 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
29018318 TATAAGAATG
29018328 AATAAATATACGAA
1 AATAAATATACGAA
*
29018342 AATAAATATAAGAAA
1 AATAAATATACG-AA
29018357 AATAAA-ATACGAA
1 AATAAATATACGAA
29018370 TCATGAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 2 0.08
14 15 0.60
15 8 0.32
ACGTcount: A:0.69, C:0.05, G:0.07, T:0.19
Consensus pattern (14 bp):
AATAAATATACGAA
Found at i:29018556 original size:29 final size:30
Alignment explanation
Indices: 29018515--29018793 Score: 286
Period size: 29 Copynumber: 9.5 Consensus size: 30
29018505 AAGTTTAGAG
29018515 AAAAATGTAATTTTTGAGAAGTTCGGGGGT
1 AAAAATGTAATTTTTGAGAAGTTCGGGGGT
*
29018545 AAAAATGT-ATTTTTG-GAAGTTCGGGGGC
1 AAAAATGTAATTTTTGAGAAGTTCGGGGGT
*
29018573 AAAAATGTAATTTTTG-GAAGTTCGGGAG-
1 AAAAATGTAATTTTTGAGAAGTTCGGGGGT
* *
29018601 CAAAATGTAATTTTTTAGAGAAGTTCGAGGGT
1 AAAAATGTAA-TTTTT-GAGAAGTTCGGGGGT
*
29018633 AAAAATGTAATTTTTG-GAAGTTCGAGGGT
1 AAAAATGTAATTTTTGAGAAGTTCGGGGGT
*
29018662 AAAAATGTAATTTTTGAGAAGTTCAGGGGT
1 AAAAATGTAATTTTTGAGAAGTTCGGGGGT
* * * *
29018692 AAAAATGTGAGTTTTG-GAAGTTC-GAGAT
1 AAAAATGTAATTTTTGAGAAGTTCGGGGGT
* * * ** * *
29018720 CAAAATATGATTTTAAAAAAGTTTGGGGGGT
1 AAAAATGTAATTTTTGAGAAG-TTCGGGGGT
* * *
29018751 -CAAATGTAATTTTAGAGAAGTTTGGGGGT
1 AAAAATGTAATTTTTGAGAAGTTCGGGGGT
*
29018780 TAAAATGTAATTTT
1 AAAAATGTAATTTT
29018794 GAAAAAGCTT
Statistics
Matches: 211, Mismatches: 28, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
28 43 0.20
29 77 0.36
30 64 0.30
31 18 0.09
32 9 0.04
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (30 bp):
AAAAATGTAATTTTTGAGAAGTTCGGGGGT
Found at i:29018710 original size:59 final size:58
Alignment explanation
Indices: 29018515--29018717 Score: 270
Period size: 60 Copynumber: 3.4 Consensus size: 58
29018505 AAGTTTAGAG
* *
29018515 AAAAATGTAATTTTTGAGAAGTTCGGGGGTAAAAATGT-ATTTTTG-GAAGTTCGGGGGC
1 AAAAATGTAATTTTTG-GAAGTTCGAGGGTAAAAATGTAATTTTTGAGAAGTTC-GGGGT
*
29018573 AAAAATGTAATTTTTGGAAGTTCG-GGAG-CAAAATGTAATTTTTTAGAGAAGTTCGAGGGT
1 AAAAATGTAATTTTTGGAAGTTCGAGG-GTAAAAATGTAA-TTTTT-GAGAAGTTCG-GGGT
29018633 AAAAATGTAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGAGAAGTTCAGGGGT
1 AAAAATGTAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGAGAAGTTC-GGGGT
* *
29018692 AAAAATGTGAGTTTTGGAAGTTCGAG
1 AAAAATGTAATTTTTGGAAGTTCGAG
29018718 ATCAAAATAT
Statistics
Matches: 131, Mismatches: 5, Indels: 17
0.86 0.03 0.11
Matches are distributed among these distances:
56 9 0.07
57 10 0.08
58 21 0.16
59 39 0.30
60 41 0.31
61 11 0.08
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (58 bp):
AAAAATGTAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGAGAAGTTCGGGGT
Found at i:29018750 original size:59 final size:58
Alignment explanation
Indices: 29018515--29018772 Score: 243
Period size: 59 Copynumber: 4.4 Consensus size: 58
29018505 AAGTTTAGAG
* * * * *
29018515 AAAAATGTAATTTTTGAGAAGTTCGGGGGTAAAAATGT-ATTTTTG-GAAGTTCGGGGGC
1 AAAAATGTAATTTTTG-GAAGTTC-GAGATCAAAATGTAATTTTAGAGAAGTTCGGGGGT
* * *
29018573 AAAAATGTAATTTTTGGAAGTTCGGGAGCAAAATGTAATTTTTTAGAGAAGTTCGAGGGT
1 AAAAATGTAATTTTTGGAAGTTCGAGATCAAAATGTAA--TTTTAGAGAAGTTCGGGGGT
* * * *
29018633 AAAAATGTAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGAGAAGTTCAGGGGT
1 AAAAATGTAATTTTTGGAAGTTCGA-GATCAAAATGTAATTTTAGAGAAGTTCGGGGGT
* * * * * * *
29018692 AAAAATGTGAGTTTTGGAAGTTCGAGATCAAAATATGATTTTAAAAAAGTTTGGGGGGT
1 AAAAATGTAATTTTTGGAAGTTCGAGATCAAAATGTAATTTTAGAGAAG-TTCGGGGGT
* *
29018751 -CAAATGTAATTTTAGAGAAGTT
1 AAAAATGTAATTTTTG-GAAGTT
29018773 TGGGGGTTAA
Statistics
Matches: 165, Mismatches: 28, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
56 10 0.06
57 8 0.05
58 44 0.27
59 58 0.35
60 35 0.21
61 10 0.06
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.33
Consensus pattern (58 bp):
AAAAATGTAATTTTTGGAAGTTCGAGATCAAAATGTAATTTTAGAGAAGTTCGGGGGT
Found at i:29018799 original size:60 final size:59
Alignment explanation
Indices: 29018729--29018898 Score: 139
Period size: 60 Copynumber: 2.8 Consensus size: 59
29018719 TCAAAATATG
* * * ** *
29018729 ATTTTAAAAAAGTTTGGGGGGTCAAATGTAATTTTA-GAGAAGTTTGGGGGTTAAAATGTA
1 ATTTTGAAAAAGTTT-GGGGGTCAAATATAATTTTAGGA-AAGTTTAGGGACTAAAATGCA
* * * * *
29018789 ATTTTGAAAAAGCTTAGGGGTTAAAATATGATTTTTGGAAAGTTTAGGGACTAAAATGCA
1 ATTTTGAAAAAG-TTTGGGGGTCAAATATAATTTTAGGAAAGTTTAGGGACTAAAATGCA
* * * *
29018849 ATTTTGGAAAGGTTTGGGGGTCAAAATATGATTTCTA--AAAGTTAAGGGAC
1 ATTTTGAAAAAGTTTGGGGGTC-AAATATAATTT-TAGGAAAGTTTAGGGAC
29018899 CTATCAAATA
Statistics
Matches: 88, Mismatches: 18, Indels: 9
0.77 0.16 0.08
Matches are distributed among these distances:
59 19 0.22
60 64 0.73
61 5 0.06
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (59 bp):
ATTTTGAAAAAGTTTGGGGGTCAAATATAATTTTAGGAAAGTTTAGGGACTAAAATGCA
Found at i:29018809 original size:30 final size:29
Alignment explanation
Indices: 29018729--29018875 Score: 105
Period size: 30 Copynumber: 4.9 Consensus size: 29
29018719 TCAAAATATG
* *
29018729 ATTTTAAAAAAGTTTGGGGGGTCAAATGTA
1 ATTTT-AAAAAGTTTGGGGGTTAAAATGTA
*
29018759 ATTTTAGAGAAGTTTGGGGGTTAAAATGTA
1 ATTTTA-AAAAGTTTGGGGGTTAAAATGTA
* * *
29018789 ATTTTGAAAAAGCTTAGGGGTTAAAATATGA
1 ATTTT-AAAAAGTTTGGGGGTTAAAATGT-A
* ** * ** *
29018820 TTTTTGGAAAGTTTAGGGACTAAAATGCA
1 ATTTTAAAAAGTTTGGGGGTTAAAATGTA
* * *
29018849 ATTTTGGAAAGGTTTGGGGGTCAAAAT
1 ATTTT-AAAAAGTTTGGGGGTTAAAAT
29018876 ATGATTTCTA
Statistics
Matches: 91, Mismatches: 22, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
29 6 0.07
30 79 0.87
31 6 0.07
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.34
Consensus pattern (29 bp):
ATTTTAAAAAGTTTGGGGGTTAAAATGTA
Found at i:29020098 original size:17 final size:16
Alignment explanation
Indices: 29020076--29020126 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
29020066 TGGACATTTT
29020076 TAAATTTAAATTCAAAA
1 TAAATTTAAATT-AAAA
29020093 TAAATTTAAACTTAAAA
1 TAAATTTAAA-TTAAAA
* *
29020110 TAGATTAAAATTTAAAA
1 TAAATTTAAA-TTAAAA
29020127 CTAGGTTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
17 28 0.93
18 2 0.07
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (16 bp):
TAAATTTAAATTAAAA
Found at i:29020792 original size:38 final size:37
Alignment explanation
Indices: 29020734--29021031 Score: 174
Period size: 39 Copynumber: 7.7 Consensus size: 37
29020724 GCTGATGGTG
* * * *
29020734 ATCTACCCTAGGCTCAGGGTAAAATATCGGATTGTTGCA
1 ATCTGCCC-AGGCTCGGGGTAAAAGATCGGATTGCTG-A
* * * * *
29020773 ATCTGCCCATGCTCGGGGTAAGAGATTGGCTGATGGTG-
1 ATCTGCCCAGGCTCGGGGTAAAAGATCGGAT--TGCTGA
* *
29020811 ATCTGCCCTAGGCTCGAGGTAAAAAATCGGA-TGACTGTA
1 ATCTGCCC-AGGCTCGGGGTAAAAGATCGGATTG-CTG-A
* *
29020850 ATCTGCCCCAGGCTCGGGGTAAAAGATTGGATGGCGTG-
1 ATCTG-CCCAGGCTCGGGGTAAAAGATCGGATTGC-TGA
* *
29020888 ATCTGCCTCAGGCTCGGGGTAAAAGATCGGATGGCTACA
1 ATCTGCC-CAGGCTCGGGGTAAAAGATCGGATTGCT-GA
* * * *
29020927 ATCTGCCCCAGGCTTGGGGTAAGAGAT-TGACTGATGGTG-
1 ATCTG-CCCAGGCTCGGGGTAAAAGATCGGA-T--TGCTGA
* ** *
29020966 ATCTACCTCAGGCTTAGGGTAAAAGATCGGATCGCTGCA
1 ATCTGCC-CAGGCTCGGGGTAAAAGATCGGATTGCTG-A
* *
29021005 ATCTGCCCCAGGCTCAGGGTAAGAGAT
1 ATCTG-CCCAGGCTCGGGGTAAAAGAT
29021032 TGGCTAATGG
Statistics
Matches: 202, Mismatches: 36, Indels: 42
0.72 0.13 0.15
Matches are distributed among these distances:
36 2 0.01
37 8 0.04
38 60 0.30
39 114 0.56
40 16 0.08
41 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (37 bp):
ATCTGCCCAGGCTCGGGGTAAAAGATCGGATTGCTGA
Found at i:29020832 original size:39 final size:39
Alignment explanation
Indices: 29020711--29021055 Score: 162
Period size: 39 Copynumber: 8.9 Consensus size: 39
29020701 AATCTGCCCC
* *
29020711 AGGTAAGAGATTGGCTGATGGTGATCTACCCTAGGCTC-
1 AGGTAAAAGATTGGCTGATGGTGATCTGCCCTAGGCTCG
* * * * *
29020749 AGGGTAAAATATCGGAT--TGTTGCAATCTGCCC-ATGCTCG
1 A-GGTAAAAGATTGGCTGATGGTG--ATCTGCCCTAGGCTCG
* *
29020788 GGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCG
1 AGGTAAAAGATTGGCTGATGGTGATCTGCCCTAGGCTCG
* * * * *
29020827 AGGTAAAAAATCGGATGACT-GTAATCTGCCCCAGGCTCG
1 AGGTAAAAGATTGGCTGA-TGGTGATCTGCCCTAGGCTCG
* *
29020866 GGGTAAAAGATTGGATG--GCGTGATCTG-CCTCAGGCTCG
1 AGGTAAAAGATTGGCTGATG-GTGATCTGCCCT-AGGCTCG
* * * * *
29020904 GGGTAAAAGA-T--CGGATGGCTACAATCTGCCCCAGGCTTG
1 AGGTAAAAGATTGGCTGATGG-T--GATCTGCCCTAGGCTCG
* * * * *
29020943 GGGTAAGAGATTGACTGATGGTGATCT-ACCTCAGGCT-T
1 AGGTAAAAGATTGGCTGATGGTGATCTGCCCT-AGGCTCG
* * * ** *
29020981 AGGGTAAAAGATCGGATCGCT-GCAATCTGCCCCAGGCTC-
1 A-GGTAAAAGATTGGCT-GATGGTGATCTGCCCTAGGCTCG
* *
29021020 AGGGTAAGAGATTGGCTAATGGTGATCTGCCCTAGG
1 A-GGTAAAAGATTGGCTGATGGTGATCTGCCCTAGG
29021056 TTTGGGGTAA
Statistics
Matches: 226, Mismatches: 55, Indels: 51
0.68 0.17 0.15
Matches are distributed among these distances:
35 1 0.00
36 1 0.00
37 9 0.04
38 52 0.23
39 144 0.64
40 12 0.05
41 1 0.00
42 6 0.03
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (39 bp):
AGGTAAAAGATTGGCTGATGGTGATCTGCCCTAGGCTCG
Found at i:29020997 original size:78 final size:78
Alignment explanation
Indices: 29020712--29021151 Score: 462
Period size: 78 Copynumber: 5.7 Consensus size: 78
29020702 ATCTGCCCCA
* * *
29020712 GGTAAGAGATTGGCTGATGGTGATCTACCCTAGGCTCAGGGTAAAATATCGGATTGTTGCAATCT
1 GGTAAGAGATTGGCTGATGGTGATCTACCCTAGGCTCAGGGTAAAAGATCGGATGGCTGCAATCT
*
29020777 G-CCCATGCTCGG
66 GCCCCAGGCTCGG
* * * *
29020789 GGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTC-GAGGTAAAAAATCGGATGACTGTAATC
1 GGTAAGAGATTGGCTGATGGTGATCTACCCTAGGCTCAG-GGTAAAAGATCGGATGGCTGCAATC
29020853 TGCCCCAGGCTCGG
65 TGCCCCAGGCTCGG
* * * * *
29020867 GGTAAAAGATTGGATG--GCGTGATCT-GCCTCAGGCTCGGGGTAAAAGATCGGATGGCTACAAT
1 GGTAAGAGATTGGCTGATG-GTGATCTACCCT-AGGCTCAGGGTAAAAGATCGGATGGCTGCAAT
*
29020929 CTGCCCCAGGCTTGG
64 CTGCCCCAGGCTCGG
* * *
29020944 GGTAAGAGATTGACTGATGGTGATCTA-CCTCAGGCTTAGGGTAAAAGATCGGATCGCTGCAATC
1 GGTAAGAGATTGGCTGATGGTGATCTACCCT-AGGCTCAGGGTAAAAGATCGGATGGCTGCAATC
*
29021008 TGCCCCAGGCTCAG
65 TGCCCCAGGCTCGG
* * * ** * ** * *
29021022 GGTAAGAGATTGGCTAATGGTGATCTGCCCTAGGTTTGGGGTAAGAGATCAAATAGCTGTAATCT
1 GGTAAGAGATTGGCTGATGGTGATCTACCCTAGGCTCAGGGTAAAAGATCGGATGGCTGCAATCT
* * **
29021087 GCCCTAAGCTATG
66 GCCCCAGGCTCGG
* * *
29021100 GGTAAGAGATTAGTTGATGGTGATCAACCCTAGGCTC-GGAGTAAAGAGATCG
1 GGTAAGAGATTGGCTGATGGTGATCTACCCTAGGCTCAGG-GTAAA-AGATCG
29021152 AAATATTCAA
Statistics
Matches: 305, Mismatches: 47, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
76 5 0.02
77 120 0.39
78 171 0.56
79 9 0.03
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (78 bp):
GGTAAGAGATTGGCTGATGGTGATCTACCCTAGGCTCAGGGTAAAAGATCGGATGGCTGCAATCT
GCCCCAGGCTCGG
Found at i:29021164 original size:78 final size:78
Alignment explanation
Indices: 29021003--29021169 Score: 171
Period size: 78 Copynumber: 2.1 Consensus size: 78
29020993 CGGATCGCTG
* * * ** * * *
29021003 CAATCTGCCCCAGGCTCAGGGTAAGAGATTGGCTAATGGTGATCTGCCCTAGGTTTGGGGTAAGA
1 CAATCTGCCCTAAGCTCAGGGTAAGAGATTAGCTAATGGTGATCAACCCTAGGCTCGGAGTAAGA
29021068 GATCAAATAGCTGT
66 GATCAAATA-CTGT
* *
29021082 -AATCTGCCCTAAGCT-ATGGGTAAGAGATTAGTTGATGGTGATCAACCCTAGGCTCGGAGTAAA
1 CAATCTGCCCTAAGCTCA-GGGTAAGAGATTAGCTAATGGTGATCAACCCTAGGCTCGGAGT-AA
29021145 GAGATCGAAATA-T-T
64 GAGATC-AAATACTGT
*
29021159 CAATCTACCCT
1 CAATCTGCCCT
29021170 TCTTGATTAA
Statistics
Matches: 73, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
77 2 0.03
78 58 0.79
79 8 0.11
80 5 0.07
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (78 bp):
CAATCTGCCCTAAGCTCAGGGTAAGAGATTAGCTAATGGTGATCAACCCTAGGCTCGGAGTAAGA
GATCAAATACTGT
Found at i:29023397 original size:19 final size:17
Alignment explanation
Indices: 29023358--29023397 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
29023348 GTTTTGCAAT
*
29023358 TCTTAATAGTAAGAATC
1 TCTTAATAGTAAGAATA
29023375 TCTTACATAGTAGAGAATA
1 TCTTA-ATAGTA-AGAATA
29023394 TCTT
1 TCTT
29023398 GGTACCATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 6 0.30
19 9 0.45
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (17 bp):
TCTTAATAGTAAGAATA
Found at i:29032920 original size:14 final size:14
Alignment explanation
Indices: 29032901--29032941 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
29032891 TATACTAATG
29032901 ATAAATATACGAAA
1 ATAAATATACGAAA
*
29032915 ATAAATATAAGAAAA
1 ATAAATATACG-AAA
29032930 ATAAA-ATACGAA
1 ATAAATATACGAA
29032942 TCATGAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 2 0.08
14 14 0.58
15 8 0.33
ACGTcount: A:0.68, C:0.05, G:0.07, T:0.20
Consensus pattern (14 bp):
ATAAATATACGAAA
Found at i:29033080 original size:28 final size:29
Alignment explanation
Indices: 29033048--29033197 Score: 114
Period size: 30 Copynumber: 5.2 Consensus size: 29
29033038 AGTTTCAAAG
* *
29033048 AGTTCGGGATTAAAACATAATTTTTG-GA
1 AGTTCGGGAGTAAAATATAATTTTTGAGA
* *
29033076 AGTTCGGGAGCAAAAATGTAATTTTTGAGA
1 AGTTCGGGAG-TAAAATATAATTTTTGAGA
*
29033106 AGTTCGAGG-GTAAAAATGTAA-TTTTG-GA
1 AGTTCG-GGAGT-AAAATATAATTTTTGAGA
* *
29033134 AGTTCGAGAGTACAAATGTAATTTTTGAGA
1 AGTTCGGGAGTA-AAATATAATTTTTGAGA
* * *
29033164 AGTTTGAGG-GTAAAAATGTGATTTTTG-GA
1 AGTTCG-GGAGT-AAAATATAATTTTTGAGA
29033193 AGTTC
1 AGTTC
29033198 AAAATTAAAA
Statistics
Matches: 102, Mismatches: 10, Indels: 19
0.78 0.08 0.15
Matches are distributed among these distances:
27 2 0.02
28 27 0.26
29 29 0.28
30 40 0.39
31 4 0.04
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (29 bp):
AGTTCGGGAGTAAAATATAATTTTTGAGA
Found at i:29033110 original size:30 final size:29
Alignment explanation
Indices: 29033065--29033197 Score: 180
Period size: 30 Copynumber: 4.6 Consensus size: 29
29033055 GATTAAAACA
*
29033065 TAATTTTTGGAAGTTCG-GGAGCAAAAATG
1 TAATTTTTGGAAGTTCGAGG-GTAAAAATG
29033094 TAATTTTTGAGAAGTTCGAGGGTAAAAATG
1 TAATTTTTG-GAAGTTCGAGGGTAAAAATG
* *
29033124 TAA-TTTTGGAAGTTCGAGAGTACAAATG
1 TAATTTTTGGAAGTTCGAGGGTAAAAATG
*
29033152 TAATTTTTGAGAAGTTTGAGGGTAAAAATG
1 TAATTTTTG-GAAGTTCGAGGGTAAAAATG
*
29033182 TGATTTTTGGAAGTTC
1 TAATTTTTGGAAGTTC
29033198 AAAATTAAAA
Statistics
Matches: 92, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
28 21 0.23
29 25 0.27
30 44 0.48
31 2 0.02
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (29 bp):
TAATTTTTGGAAGTTCGAGGGTAAAAATG
Found at i:29033131 original size:58 final size:59
Alignment explanation
Indices: 29033069--29033197 Score: 206
Period size: 58 Copynumber: 2.2 Consensus size: 59
29033059 AAAACATAAT
*
29033069 TTTTGGAAGTTCGGGAGCAAAAATGTAATTTTTGAGAAGTTCGAGGGTAAAAATGT-AA
1 TTTTGGAAGTTCGAGAGCAAAAATGTAATTTTTGAGAAGTTCGAGGGTAAAAATGTGAA
* * * *
29033127 TTTTGGAAGTTCGAGAGTACAAATGTAATTTTTGAGAAGTTTGAGGGTAAAAATGTGAT
1 TTTTGGAAGTTCGAGAGCAAAAATGTAATTTTTGAGAAGTTCGAGGGTAAAAATGTGAA
29033186 TTTTGGAAGTTC
1 TTTTGGAAGTTC
29033198 AAAATTAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
58 52 0.80
59 13 0.20
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (59 bp):
TTTTGGAAGTTCGAGAGCAAAAATGTAATTTTTGAGAAGTTCGAGGGTAAAAATGTGAA
Found at i:29033209 original size:58 final size:57
Alignment explanation
Indices: 29033088--29033248 Score: 198
Period size: 58 Copynumber: 2.8 Consensus size: 57
29033078 TTCGGGAGCA
* * * *
29033088 AAAATGTAATTTTTGAGAAGTTCGAGGGTAAAAATGTAATTTTGGAAGTTCGAGAGT
1 AAAATGTAATTTTTGAGAAGTTTGAGGGTAAAAATGTATTTTTGGAAGTTCAAAAGT
*
29033145 ACAAATGTAATTTTTGAGAAGTTTGAGGGTAAAAATGTGATTTTTGGAAGTTCAAAATT
1 A-AAATGTAATTTTTGAGAAGTTTGAGGGTAAAAATGT-ATTTTTGGAAGTTCAAAAGT
* * * * * *
29033204 AAAATGTGATTTTAGAAAAGTTTGGGGGT-CAAATGTAATTTTGGA
1 AAAATGTAATTTTTGAGAAGTTTGAGGGTAAAAATGTATTTTTGGA
29033249 GAATGATAAG
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
56 8 0.09
57 7 0.08
58 59 0.65
59 17 0.19
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (57 bp):
AAAATGTAATTTTTGAGAAGTTTGAGGGTAAAAATGTATTTTTGGAAGTTCAAAAGT
Found at i:29045082 original size:30 final size:30
Alignment explanation
Indices: 29045011--29045097 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
29045001 TTAAGGGTTA
29045011 AAAATATGATTTT-GAAAAGTTCAGGGAGC
1 AAAATATGATTTTAGAAAAGTTCAGGGAGC
*** *
29045040 AAAATGCAATTTTAGAAAAGTTCGAGGG-TC
1 AAAATATGATTTTAGAAAAGTTC-AGGGAGC
*
29045070 AAAATATGATTTTTA-AAAAGTTTAGGGA
1 AAAATATGA-TTTTAGAAAAGTTCAGGGA
29045098 CCTATCAGAC
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
29 14 0.30
30 23 0.50
31 9 0.20
ACGTcount: A:0.43, C:0.06, G:0.22, T:0.30
Consensus pattern (30 bp):
AAAATATGATTTTAGAAAAGTTCAGGGAGC
Found at i:29046211 original size:15 final size:15
Alignment explanation
Indices: 29046188--29046217 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29046178 GGCAGAGGCA
*
29046188 AGTGGTGGTGGTGCT
1 AGTGATGGTGGTGCT
29046203 AGTGATGGTGGTGCT
1 AGTGATGGTGGTGCT
29046218 GATGTGGCGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.07, G:0.50, T:0.33
Consensus pattern (15 bp):
AGTGATGGTGGTGCT
Found at i:29046388 original size:17 final size:17
Alignment explanation
Indices: 29046366--29046429 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 17
29046356 CTTTTTTAAA
29046366 TTTAAATTTAAAATAAG
1 TTTAAATTTAAAATAAG
* * *
29046383 TTTAAATTCAAAGTAAA
1 TTTAAATTTAAAATAAG
*
29046400 TTTAAACTTAAAAT-AG
1 TTTAAATTTAAAATAAG
*
29046416 ATTAACATTTAAAA
1 TTTAA-ATTTAAAA
29046430 CTGGGTTCAA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
16 5 0.14
17 32 0.86
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (17 bp):
TTTAAATTTAAAATAAG
Found at i:29051324 original size:23 final size:23
Alignment explanation
Indices: 29051298--29051342 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
29051288 GTTGTTTCGT
*
29051298 TGTCGTTTTTAATATTATTTGGC
1 TGTCATTTTTAATATTATTTGGC
29051321 TGTCATTTTTAATATTATTTGG
1 TGTCATTTTTAATATTATTTGG
29051343 ATATGTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.07, G:0.16, T:0.58
Consensus pattern (23 bp):
TGTCATTTTTAATATTATTTGGC
Found at i:29051384 original size:21 final size:22
Alignment explanation
Indices: 29051360--29051407 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
29051350 AAATTTTTTG
*
29051360 TTTTA-TTATTAATTGTTACTA
1 TTTTAGTTATAAATTGTTACTA
*
29051381 TTTTAGTTGTAAATTGTTACTA
1 TTTTAGTTATAAATTGTTACTA
29051403 TTTTA
1 TTTTA
29051408 ATATAACCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.27, C:0.04, G:0.08, T:0.60
Consensus pattern (22 bp):
TTTTAGTTATAAATTGTTACTA
Found at i:29052128 original size:15 final size:15
Alignment explanation
Indices: 29052108--29052138 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29052098 CGATCAAAGT
29052108 AAGCAATAATTATTC
1 AAGCAATAATTATTC
29052123 AAGCAATAATTATTC
1 AAGCAATAATTATTC
29052138 A
1 A
29052139 TGAATTACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.32
Consensus pattern (15 bp):
AAGCAATAATTATTC
Found at i:29053666 original size:36 final size:36
Alignment explanation
Indices: 29053626--29053700 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 36
29053616 TGTGTGATTT
* *
29053626 AAATTTTAAGAGATTATTTATAATTCAAGTTAAATA
1 AAATTTTAAGAGATTATTTATAAATCAAGTTAAACA
* *
29053662 AAA-TTTAAGAGATTGTTTGTAAATCAAGTTAAACA
1 AAATTTTAAGAGATTATTTATAAATCAAGTTAAACA
29053697 AAAT
1 AAAT
29053701 ATATTATCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 31 0.91
36 3 0.09
ACGTcount: A:0.48, C:0.04, G:0.11, T:0.37
Consensus pattern (36 bp):
AAATTTTAAGAGATTATTTATAAATCAAGTTAAACA
Found at i:29053761 original size:24 final size:24
Alignment explanation
Indices: 29053729--29053775 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
29053719 ATTCAGTTAT
*
29053729 ATAATATATATAACATTTATTAGC
1 ATAATATATATAACATTGATTAGC
* *
29053753 ATAATATATTTTACATTGATTAG
1 ATAATATATATAACATTGATTAG
29053776 AATTCGATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (24 bp):
ATAATATATATAACATTGATTAGC
Found at i:29060642 original size:23 final size:24
Alignment explanation
Indices: 29060617--29060663 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
29060607 GCACCATAAG
29060617 AAATGCTACC-ACAGAGCATACCGAA
1 AAATGCTACCTA-AGAGCATACCG-A
29060642 AAATGCTACCTAAGAGCATACC
1 AAATGCTACCTAAGAGCATACC
29060664 ATTCAATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.43, C:0.28, G:0.15, T:0.15
Consensus pattern (24 bp):
AAATGCTACCTAAGAGCATACCGA
Found at i:29061793 original size:19 final size:20
Alignment explanation
Indices: 29061748--29061810 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
29061738 ATATAATTTT
* *
29061748 ATTTTTTAAATTATTTTTTAGA
1 ATTTTTAAAATTA-TTTTGA-A
29061770 ATTTTTATAAA-TA-TTTGAA
1 ATTTTTA-AAATTATTTTGAA
29061789 ATTTTTAAAATTATTTTGAA
1 ATTTTTAAAATTATTTTGAA
29061809 AT
1 AT
29061811 AGTTTGAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
18 3 0.08
19 10 0.28
20 12 0.33
22 8 0.22
23 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (20 bp):
ATTTTTAAAATTATTTTGAA
Found at i:29072523 original size:131 final size:131
Alignment explanation
Indices: 29072288--29072677 Score: 505
Period size: 130 Copynumber: 3.0 Consensus size: 131
29072278 ACGATATAAG
* * *
29072288 CTGTTCTGATTGTGACTTCTGGAG-A-AGAAGAGGAAGGCTAAATGGTAAATC--TATATAGTGT
1 CTGTTCTGATTGTGACTTGTGGAGAAGAGAAGAGGAAGGCTAAACGCTAAATCTATATATAGTGT
* * *
29072349 CCCAACTAGTGACT-AG-GTATGTCCTAAGCAACTTAAACTCTTTCTAAGATCATCATGGCAGTA
66 CCCGACTAGTGACTGAGTATATGTCCTAAGCAACTTAAACTCTTTCTAAGAACATCATGGCAGTA
29072412 A
131 A
* * * *
29072413 CTGTTCCGATTGTGACTTGTGGAGAAGAGAAGAGTAAGGCTAAACGCTATATCTATATATAGCGT
1 CTGTTCTGATTGTGACTTGTGGAGAAGAGAAGAGGAAGGCTAAACGCTAAATCTATATATAGTGT
* * * * * *
29072478 CCCGACTACTCACTGAGTATATGTCCTAAGCAAATTAAACTCTTTCTAACAACATGATGGTAGTA
66 CCCGACTAGTGACTGAGTATATGTCCTAAGCAACTTAAACTCTTTCTAAGAACATCATGGCAGTA
29072543 GTA
131 --A
* *
29072546 ATGTTCTGGTTGTGACTTGT-GAGAAGA-AA-AGGAAGGCTAAACGCTAAATCTATATATAGTG-
1 CTGTTCTGATTGTGACTTGTGGAGAAGAGAAGAGGAAGGCTAAACGCTAAATCTATATATAGTGT
*
29072607 CCCTGACTGGTGACTGAGTATATGTCCTAAGCAACTTAAACTCTTTCTAAGAACATCATGGCAGT
66 CCC-GACTAGTGACTGAGTATATGTCCTAAGCAACTTAAACTCTTTCTAAGAACATCATGGCAGT
29072672 -A
130 AA
29072673 CTGTT
1 CTGTT
29072678 TGTATATCTT
Statistics
Matches: 226, Mismatches: 30, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
125 22 0.10
126 1 0.00
127 27 0.12
129 23 0.10
130 85 0.38
131 43 0.19
132 7 0.03
133 18 0.08
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (131 bp):
CTGTTCTGATTGTGACTTGTGGAGAAGAGAAGAGGAAGGCTAAACGCTAAATCTATATATAGTGT
CCCGACTAGTGACTGAGTATATGTCCTAAGCAACTTAAACTCTTTCTAAGAACATCATGGCAGTA
A
Found at i:29074767 original size:20 final size:21
Alignment explanation
Indices: 29074744--29074785 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
29074734 AAGTTTGAGA
29074744 TTTGAGTTTA-GATTCAAGGT
1 TTTGAGTTTAGGATTCAAGGT
*
29074764 TTTGAGTTTAGGGTTCAAGGT
1 TTTGAGTTTAGGATTCAAGGT
29074785 T
1 T
29074786 AAAGTTTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.21, C:0.05, G:0.29, T:0.45
Consensus pattern (21 bp):
TTTGAGTTTAGGATTCAAGGT
Found at i:29074834 original size:27 final size:27
Alignment explanation
Indices: 29074753--29074827 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
29074743 ATTTGAGTTT
* *
29074753 AGATTCAAGGTTTTGAGTTTAGGGTTCA
1 AGATTAAAGG-TTTGAGTTCAGGGTTCA
* *
29074781 AGGTTAAA-GTTTAAGCTTCAGGGTTCA
1 AGATTAAAGGTTTGAG-TTCAGGGTTCA
29074808 AGATTAAAGGTTTGAGTTCA
1 AGATTAAAGGTTTGAGTTCA
29074828 AAGTTCAGGG
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
26 5 0.13
27 22 0.56
28 12 0.31
ACGTcount: A:0.29, C:0.08, G:0.27, T:0.36
Consensus pattern (27 bp):
AGATTAAAGGTTTGAGTTCAGGGTTCA
Found at i:29074849 original size:21 final size:20
Alignment explanation
Indices: 29074816--29074855 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
29074806 CAAGATTAAA
*
29074816 GGTTTGAGTTCAAAGTTCAG
1 GGTTTAAGTTCAAAGTTCAG
*
29074836 GGTTTAAGATTCAAGGTTCA
1 GGTTTAAG-TTCAAAGTTCA
29074856 AGTTAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.35
Consensus pattern (20 bp):
GGTTTAAGTTCAAAGTTCAG
Found at i:29077046 original size:250 final size:250
Alignment explanation
Indices: 29076579--29077080 Score: 972
Period size: 250 Copynumber: 2.0 Consensus size: 250
29076569 GGGACAACTT
29076579 TACATTTAGATGGGGAGATAGAGGAGGTGAAAGGTGAATCACCGTAGTCAGGATTGGAGTCTAGA
1 TACATTTAGATGGGGAGATAGAGGAGGTGAAAGGTGAATCACCGTAGTCAGGATTGGAGTCTAGA
29076644 ACTGAAGCGGAGAAATTATCGGAGGAGACTCGAAACGACGAGGAAGAAGCATTAAAGGTAATCAG
66 ACTGAAGCGGAGAAATTATCGGAGGAGACTCGAAACGACGAGGAAGAAGCATTAAAGGTAATCAG
29076709 CTTCGATGAAAGAGACTGAAGACGACTGTCAGGGTGTGTCGAATGTAATGATGGATGAGGAAGTT
131 CTTCGATGAAAGAGACTGAAGACGACTGTCAGGGTGTGTCGAATGTAATGATGGATGAGGAAGTT
29076774 AATACGTTTGGGAGCAAAATGTCAAGTGAGTCTGGAGATGAGGATGTTGGCAAAG
196 AATACGTTTGGGAGCAAAATGTCAAGTGAGTCTGGAGATGAGGATGTTGGCAAAG
29076829 TACATTTAGATGGGGAGATAGAGGAGGTGAAAGGTGAATCACCGTAGTCAGGATTGGAGTCTAGA
1 TACATTTAGATGGGGAGATAGAGGAGGTGAAAGGTGAATCACCGTAGTCAGGATTGGAGTCTAGA
29076894 ACTGAAGCGGAGAAATTATCGGAGGAGACTCGAAACGACGAGGAAGAAGCATTAAAGGTAATCAG
66 ACTGAAGCGGAGAAATTATCGGAGGAGACTCGAAACGACGAGGAAGAAGCATTAAAGGTAATCAG
29076959 CTTCGATGAAAGAGAAACTGAAGACGACTGTCAGGGTGTGTCGAATGTAATGATGGATGAGGAAG
131 CTTCGATGAAAGAG--ACTGAAGACGACTGTCAGGGTGTGTCGAATGTAATGATGGATGAGGAAG
29077024 TTAATACGTTT-GGAGC-AAATGTCAAGTGAGTCTGGAGATGAGGATGTTGGCAAAG
194 TTAATACGTTTGGGAGCAAAATGTCAAGTGAGTCTGGAGATGAGGATGTTGGCAAAG
29077079 TA
1 TA
29077081 TTGGATAGGG
Statistics
Matches: 250, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
250 185 0.74
251 5 0.02
252 60 0.24
ACGTcount: A:0.35, C:0.11, G:0.33, T:0.21
Consensus pattern (250 bp):
TACATTTAGATGGGGAGATAGAGGAGGTGAAAGGTGAATCACCGTAGTCAGGATTGGAGTCTAGA
ACTGAAGCGGAGAAATTATCGGAGGAGACTCGAAACGACGAGGAAGAAGCATTAAAGGTAATCAG
CTTCGATGAAAGAGACTGAAGACGACTGTCAGGGTGTGTCGAATGTAATGATGGATGAGGAAGTT
AATACGTTTGGGAGCAAAATGTCAAGTGAGTCTGGAGATGAGGATGTTGGCAAAG
Found at i:29079545 original size:33 final size:33
Alignment explanation
Indices: 29079502--29079599 Score: 115
Period size: 33 Copynumber: 3.0 Consensus size: 33
29079492 TTGGAAAGTG
*
29079502 CTAGCTGTATAACACAGCCATATTGCAAGTCTA
1 CTAGCTGTATAACACAGCCACATTGCAAGTCTA
* * * *
29079535 TTAGCTGTATAACACAGCCACGTTGCAAGTTTG
1 CTAGCTGTATAACACAGCCACATTGCAAGTCTA
* * * *
29079568 CCAACTGTATAACACAGCCACGTTACAAGTCT
1 CTAGCTGTATAACACAGCCACATTGCAAGTCT
29079600 GCTGCAACCT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.27
Consensus pattern (33 bp):
CTAGCTGTATAACACAGCCACATTGCAAGTCTA
Found at i:29083541 original size:153 final size:153
Alignment explanation
Indices: 29083367--29083648 Score: 449
Period size: 153 Copynumber: 1.8 Consensus size: 153
29083357 GTTTTGAAAG
29083367 CTTTTGAAAAGGATATCCGATT-GACATGAATCACGAAAATCACACTTAACACGTTAAAGCGCGA
1 CTTTTGAAAAGGATATCCGATTCG-CATGAATCACGAAAATCACACTTAACACGTTAAAGCGCGA
* ** * * *
29083431 TTTTTTGAAGTTTTCACACGAAAGGACATTGCCTCGTTTTAAAATTATTTGTGATGTAGATATAT
65 TCTTTCAAAGTTTTCACACGAAAGGACATTGCCTCGCTTTAAAATTATTTGTAATATAGATATAT
29083496 AAAAATTGAAGGATGTTTCGGGGA
130 AAAAATTGAAGGATGTTTCGGGGA
* * * *
29083520 CTTTTGAAGAGGATATTCGATTCGCATGAATTACGAAAATCACACTTAACACGTTAAAGTGCGAT
1 CTTTTGAAAAGGATATCCGATTCGCATGAATCACGAAAATCACACTTAACACGTTAAAGCGCGAT
*
29083585 CTTTCAAAGTTTTCACACGACAGGACATTGCCTCGCTTTAAAATTATTTGTAATATAGATATAT
66 CTTTCAAAGTTTTCACACGAAAGGACATTGCCTCGCTTTAAAATTATTTGTAATATAGATATAT
29083649 GTTTTGAGAA
Statistics
Matches: 117, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
153 116 0.99
154 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (153 bp):
CTTTTGAAAAGGATATCCGATTCGCATGAATCACGAAAATCACACTTAACACGTTAAAGCGCGAT
CTTTCAAAGTTTTCACACGAAAGGACATTGCCTCGCTTTAAAATTATTTGTAATATAGATATATA
AAAATTGAAGGATGTTTCGGGGA
Found at i:29084238 original size:59 final size:59
Alignment explanation
Indices: 29084165--29084520 Score: 406
Period size: 59 Copynumber: 6.1 Consensus size: 59
29084155 TGACTTCCAA
*
29084165 GGGTAAAAAT-GTAATTTTTGGTGAAATCGGGGTCAAAAATGAAATTTTGGAAAGTTTAG
1 GGGT-AAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTAG
* * **
29084224 GGGTAAAATGGTAATTTTTGGTGAAAAT-AGGGTCAAAAATGGAATTTTGGAAGGTTCGG
1 GGGTAAAATGGTAATTTTTGGTG-AAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTAG
* * * *
29084283 GGGTAAAATGGTAATTTTGGGTGAAAAT-GGGGTTAAAAATGGGATTTTGGAAAATTTAG
1 GGGTAAAATGGTAATTTTTGGTG-AAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTAG
* * * * *
29084342 GGGTAAAATAGTAATTTTT-ATGAAACCGCGGGGT-AAAAATGGAATTTTGG-AAGGTTCG
1 GGGTAAAATGGTAATTTTTGGTGAAA--TCGGGGTCAAAAATGGAATTTTGGAAAGTTTAG
*
29084400 AGGGTAAAATGGTAATTTTGGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTAG
1 -GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTAG
* * * *
29084460 GGGTAAAACGGTAATTTTT-G-GAAGTTTCAGGGTCAAAAATAGAATTTTGGAAAGTTT-G
1 GGGTAAAATGGTAATTTTTGGTGAA--ATCGGGGTCAAAAATGGAATTTTGGAAAGTTTAG
29084518 GGG
1 GGG
29084521 ACTAGAGAGC
Statistics
Matches: 254, Mismatches: 32, Indels: 23
0.82 0.10 0.07
Matches are distributed among these distances:
57 6 0.02
58 23 0.09
59 205 0.81
60 20 0.08
ACGTcount: A:0.35, C:0.04, G:0.31, T:0.31
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTAG
Found at i:29084350 original size:118 final size:117
Alignment explanation
Indices: 29084165--29084520 Score: 468
Period size: 118 Copynumber: 3.0 Consensus size: 117
29084155 TGACTTCCAA
* *
29084165 GGGTAAAAAT-GTAATTTTTGGTGAAATCGGGGTCAAAAATGAAATTTTGGAAAGTTTAGGGGTA
1 GGGT-AAAATGGTAATTTTGGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGTA
29084229 AAATGGTAATTTTTGGTGAAAATAGGGTCAAAAATGGAATTTTGGAAGGTTCGG
65 AAATGGTAATTTTT-GTGAAAATAGGGTCAAAAATGGAATTTTGGAAGGTTCGG
* * *
29084283 GGGTAAAATGGTAATTTTGGGTGAAAAT-GGGGTTAAAAATGGGATTTTGGAAAATTTAGGGGTA
1 GGGTAAAATGGTAATTTTGGGTG-AAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGTA
* * *** *
29084347 AAATAGTAATTTTTATGAAACCGCGGGGT-AAAAATGGAATTTTGGAAGGTTCGA
65 AAATGGTAATTTTTGTGAAA--ATAGGGTCAAAAATGGAATTTTGGAAGGTTCGG
29084401 GGGTAAAATGGTAATTTTGGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGTAA
1 GGGTAAAATGGTAATTTTGGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGTAA
* ** * * *
29084466 AACGGTAATTTTTG-GAAGTTTCAGGGTCAAAAATAGAATTTTGGAAAGTTTGG
66 AATGGTAATTTTTGTGAA-AAT-AGGGTCAAAAATGGAATTTTGGAAGGTTCGG
29084519 GG
1 GG
29084521 ACTAGAGAGC
Statistics
Matches: 205, Mismatches: 25, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
117 21 0.10
118 176 0.86
119 8 0.04
ACGTcount: A:0.35, C:0.04, G:0.31, T:0.31
Consensus pattern (117 bp):
GGGTAAAATGGTAATTTTGGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGTAA
AATGGTAATTTTTGTGAAAATAGGGTCAAAAATGGAATTTTGGAAGGTTCGG
Found at i:29084449 original size:30 final size:29
Alignment explanation
Indices: 29084165--29084450 Score: 114
Period size: 30 Copynumber: 9.7 Consensus size: 29
29084155 TGACTTCCAA
* *
29084165 GGGTAAAAATGTAATTTTTGGTGAAATCG
1 GGGTAAAAATGGAATTTTGGGTGAAATCG
* *
29084194 GGGTCAAAAATGAAATTTT--G-GAAAGTTTAG
1 GGGT-AAAAATGGAATTTTGGGTGAAA---TCG
* *
29084224 GGGT-AAAATGGTAATTTTTGGTGAAAAT-A
1 GGGTAAAAATGG-AATTTTGGGTG-AAATCG
** **
29084253 GGGTCAAAAATGGAATTTTGGAAG-GTTCGG
1 GGGT-AAAAATGGAATTTTGGGTGAAATC-G
29084283 GGGT-AAAATGGTAATTTTGGGTGAAAAT-G
1 GGGTAAAAATGG-AATTTTGGGTG-AAATCG
* * *
29084312 GGGTTAAAAATGGGATTTT-GG-AAAATTTAG
1 GGG-TAAAAATGGAATTTTGGGTGAAA--TCG
* ** *
29084342 GGGT-AAAATAGTAATTTT-TATGAAACCGCG
1 GGGTAAAAAT-GGAATTTTGGGTGAAA--TCG
** **
29084372 GGGTAAAAATGGAATTTTGGAAG-GTTCG
1 GGGTAAAAATGGAATTTTGGGTGAAATCG
29084400 AGGGT-AAAATGGTAATTTTGGGTGAAATCG
1 -GGGTAAAAATGG-AATTTTGGGTGAAATCG
29084430 GGGTCAAAAATGGAATTTTGG
1 GGGT-AAAAATGGAATTTTGG
29084451 AAAGTTTAGG
Statistics
Matches: 192, Mismatches: 35, Indels: 59
0.67 0.12 0.21
Matches are distributed among these distances:
27 7 0.04
28 29 0.15
29 54 0.28
30 68 0.35
31 30 0.16
32 1 0.01
33 3 0.02
ACGTcount: A:0.35, C:0.03, G:0.31, T:0.31
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTGGGTGAAATCG
Found at i:29084477 original size:29 final size:29
Alignment explanation
Indices: 29084442--29084520 Score: 76
Period size: 29 Copynumber: 2.7 Consensus size: 29
29084432 GTCAAAAATG
*
29084442 GAATTTTGGAAAGTTTAGGGGT-AAAACG
1 GAATTTTGGAAAGTTTAGGGGTAAAAACA
*
29084470 GTAATTTTTGG-AAGTTTCA-GGGTCAAAAATA
1 G-AA-TTTTGGAAAGTTT-AGGGGT-AAAAACA
29084501 GAATTTTGGAAAGTTT-GGGG
1 GAATTTTGGAAAGTTTAGGGG
29084521 ACTAGAGAGC
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
28 1 0.02
29 21 0.50
30 15 0.36
31 5 0.12
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (29 bp):
GAATTTTGGAAAGTTTAGGGGTAAAAACA
Found at i:29084835 original size:23 final size:24
Alignment explanation
Indices: 29084791--29084835 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
29084781 GGCCAAATTA
**
29084791 AAAATAATTAAAAGTATGAAAAGG
1 AAAATAATTAAAACAATGAAAAGG
*
29084815 AAAA-AATTAAAACAATTAAAA
1 AAAATAATTAAAACAATGAAAA
29084836 ATGCGGAAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.69, C:0.02, G:0.09, T:0.20
Consensus pattern (24 bp):
AAAATAATTAAAACAATGAAAAGG
Found at i:29086147 original size:24 final size:23
Alignment explanation
Indices: 29086097--29086161 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 23
29086087 TCGTAATTAT
*
29086097 ATTTCAAGAACTGGGTTTTTTTGG
1 ATTTCAAGAA-TGGGTTTTGTTGG
29086121 ATTTCAAGAATAGGGTTTGTGTT-G
1 ATTTCAAGAAT-GGGTTT-TGTTGG
29086145 ATTTTC-AGAATTGGGTT
1 A-TTTCAAGAA-TGGGTT
29086162 CATAACCCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
23 1 0.03
24 27 0.75
25 8 0.22
ACGTcount: A:0.23, C:0.06, G:0.26, T:0.45
Consensus pattern (23 bp):
ATTTCAAGAATGGGTTTTGTTGG
Found at i:29093968 original size:47 final size:48
Alignment explanation
Indices: 29093914--29094010 Score: 160
Period size: 47 Copynumber: 2.0 Consensus size: 48
29093904 TCTTTTTTTT
* *
29093914 AAATTCTAATATTTTTGTATATCAGCTGCCTC-TTTAAAGCCAAAATA
1 AAATTCTAATATTTTTGTATATCAGCTACCCCTTTTAAAGCCAAAATA
*
29093961 AAATTCTAATCTTTTTGTATATCAGCTACCCCTTTTAAAGCCAAAATA
1 AAATTCTAATATTTTTGTATATCAGCTACCCCTTTTAAAGCCAAAATA
29094009 AA
1 AA
29094011 TGTTGCCTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 29 0.63
48 17 0.37
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (48 bp):
AAATTCTAATATTTTTGTATATCAGCTACCCCTTTTAAAGCCAAAATA
Found at i:29099691 original size:13 final size:13
Alignment explanation
Indices: 29099675--29099699 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29099665 GGATTCATGT
29099675 TTTGAGTTTGGGG
1 TTTGAGTTTGGGG
29099688 TTTGAGTTTGGG
1 TTTGAGTTTGGG
29099700 TTCAAGGTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.44, T:0.48
Consensus pattern (13 bp):
TTTGAGTTTGGGG
Found at i:29099740 original size:26 final size:26
Alignment explanation
Indices: 29099686--29099741 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 26
29099676 TTGAGTTTGG
*
29099686 GGTTTGAGTTTGGGTTCAAGGTTTAA
1 GGTTTGAGTTCGGGTTCAAGGTTTAA
29099712 GGTTTGAGGTTCGGGTTCAAGGTTT-A
1 GGTTTGA-GTTCGGGTTCAAGGTTTAA
29099738 GGTT
1 GGTT
29099742 AAAAAATTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 12 0.43
27 16 0.57
ACGTcount: A:0.16, C:0.05, G:0.38, T:0.41
Consensus pattern (26 bp):
GGTTTGAGTTCGGGTTCAAGGTTTAA
Found at i:29100333 original size:28 final size:28
Alignment explanation
Indices: 29100274--29100351 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
29100264 AAAACCTTAG
*
29100274 ACCTCAAA-TTCAAACTCTAAATCCTAA
1 ACCTCAAATTTCAAACTCTAAATCATAA
* *
29100301 TCCTCAAATTTTAAA-TCATAAATCATAA
1 ACCTCAAATTTCAAACTC-TAAATCATAA
* * *
29100329 ACCTCAAATGTCACACCCTAAAT
1 ACCTCAAATTTCAAACTCTAAAT
29100352 TTAGGCCTAG
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
27 9 0.22
28 30 0.75
29 1 0.03
ACGTcount: A:0.44, C:0.27, G:0.01, T:0.28
Consensus pattern (28 bp):
ACCTCAAATTTCAAACTCTAAATCATAA
Found at i:29101576 original size:23 final size:23
Alignment explanation
Indices: 29101550--29101782 Score: 322
Period size: 23 Copynumber: 10.1 Consensus size: 23
29101540 TTCTTATACC
*
29101550 TATGCTCAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
29101573 TATGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
* * *
29101596 TGTACTCAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
29101619 TATGCTCAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
29101642 TATACTTAAATATTAACGTGATT
1 TATGCTTAAATATTAATGTGATT
*
29101665 TGTGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
29101688 TATGCTTAAATATTAATATAATT
1 TATGCTTAAATATTAATGTGATT
* *
29101711 TGTGCTTAAATATTAATGTGAAT
1 TATGCTTAAATATTAATGTGATT
* *
29101734 TGTGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
*
29101757 TATGCTCAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
29101780 TAT
1 TAT
29101783 TGTCACACTC
Statistics
Matches: 184, Mismatches: 26, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 184 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (23 bp):
TATGCTTAAATATTAATGTGATT
Found at i:29101664 original size:69 final size:69
Alignment explanation
Indices: 29101550--29101782 Score: 367
Period size: 69 Copynumber: 3.4 Consensus size: 69
29101540 TTCTTATACC
* * *
29101550 TATGCTCAAATATTAATGTGATTTATGCTTAAATATTAATATGATTTGTACTCAAATATTAATGT
1 TATGCTCAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGT
29101615 GATT
66 GATT
* *
29101619 TATGCTCAAATATTAATGTGATTTATACTTAAATATTAACGTGATTTGTGCTTAAATATTAATGT
1 TATGCTCAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGT
29101684 GATT
66 GATT
* * * * * *
29101688 TATGCTTAAATATTAATATAATTTGTGCTTAAATATTAATGTGAATTGTGCTTAAATATTAATAT
1 TATGCTCAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGT
29101753 GATT
66 GATT
29101757 TATGCTCAAATATTAATGTGATTTAT
1 TATGCTCAAATATTAATGTGATTTAT
29101783 TGTCACACTC
Statistics
Matches: 147, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 147 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (69 bp):
TATGCTCAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGT
GATT
Found at i:29103024 original size:23 final size:23
Alignment explanation
Indices: 29102989--29103193 Score: 223
Period size: 23 Copynumber: 9.0 Consensus size: 23
29102979 CTTATACCTA
*
29102989 TGCTCAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
** * *
29103012 TATTTAAATATTAATAT-AATTG
1 TGCTTAAATATTAATGTGATTTG
* *
29103034 TGCTCAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
* *
29103057 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
29103080 TACTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
29103103 TGTTTAAATATTAATTTTATTTG
1 TGCTTAAATATTAATGTGATTTG
** *
29103126 TGCACAAATATTAATGTGAATTG
1 TGCTTAAATATTAATGTGATTTG
* * *
29103149 TGCTCAAAGATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
29103172 TGCCTAAATATTAATGTGATTT
1 TGCTTAAATATTAATGTGATTT
29103194 ATTATCATAC
Statistics
Matches: 147, Mismatches: 34, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
22 17 0.12
23 130 0.88
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.46
Consensus pattern (23 bp):
TGCTTAAATATTAATGTGATTTG
Found at i:29103100 original size:46 final size:46
Alignment explanation
Indices: 29102989--29103193 Score: 261
Period size: 46 Copynumber: 4.5 Consensus size: 46
29102979 CTTATACCTA
** *
29102989 TGCTCAAATATTAATGTGATTTGTATTTAAATATTAATAT-AATTG
1 TGCTCAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTG
* *
29103034 TGCTCAAATATTAATGTGATTTATGCTTAAATATTAATATGATTTA
1 TGCTCAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTG
* * * * *
29103080 TACTTAAATATTAATGTGATTTGTGTTTAAATATTAATTTTATTTG
1 TGCTCAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTG
* * * *
29103126 TGCACAAATATTAATGTGAATTGTGCTCAAAGATTAATATGATTTG
1 TGCTCAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTG
29103172 TGC-CTAAATATTAATGTGATTT
1 TGCTC-AAATATTAATGTGATTT
29103194 ATTATCATAC
Statistics
Matches: 136, Mismatches: 22, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
45 38 0.28
46 98 0.72
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.46
Consensus pattern (46 bp):
TGCTCAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTG
Found at i:29103139 original size:69 final size:69
Alignment explanation
Indices: 29102987--29103195 Score: 249
Period size: 69 Copynumber: 3.0 Consensus size: 69
29102977 TTCTTATACC
* * * *
29102987 TATGCTCAAATATTAATGTGATTTGTATTTAAATATTAATAT-AATTGTGCTCAAATATTAATGT
1 TATGCACAAATATTAATGTGATTTGTACTTAAATATTAATATGATTTGTGCTTAAATATTAATGT
29103051 GATT
66 GATT
** * * * * *
29103055 TATGCTTAAATATTAATATGATTTATACTTAAATATTAATGTGATTTGTGTTTAAATATTAATTT
1 TATGCACAAATATTAATGTGATTTGTACTTAAATATTAATATGATTTGTGCTTAAATATTAATGT
*
29103120 TATT
66 GATT
* * * * * *
29103124 TGTGCACAAATATTAATGTGAATTGTGCTCAAAGATTAATATGATTTGTGCCTAAATATTAATGT
1 TATGCACAAATATTAATGTGATTTGTACTTAAATATTAATATGATTTGTGCTTAAATATTAATGT
29103189 GATT
66 GATT
29103193 TAT
1 TAT
29103196 TATCATACCC
Statistics
Matches: 115, Mismatches: 25, Indels: 1
0.82 0.18 0.01
Matches are distributed among these distances:
68 37 0.32
69 78 0.68
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.46
Consensus pattern (69 bp):
TATGCACAAATATTAATGTGATTTGTACTTAAATATTAATATGATTTGTGCTTAAATATTAATGT
GATT
Found at i:29104434 original size:23 final size:23
Alignment explanation
Indices: 29104408--29104868 Score: 562
Period size: 23 Copynumber: 20.0 Consensus size: 23
29104398 TTCTTATATC
29104408 TATGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATATGATT
* *
29104431 TATGATTAAATATTAATGTGATT
1 TATGCTTAAATATTAATATGATT
* * *
29104454 TGTGCTTAAGTATTAATGTGATT
1 TATGCTTAAATATTAATATGATT
29104477 TATGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATATGATT
* * *
29104500 TGTGCTCAAATATTAATGTGATT
1 TATGCTTAAATATTAATATGATT
* * *
29104523 TGTGCTTAAATATCAATATTATT
1 TATGCTTAAATATTAATATGATT
* * **
29104546 TGTGCTCAAATATTAATATTCTT
1 TATGCTTAAATATTAATATGATT
*
29104569 TATGCTTAGATATTAATATGATT
1 TATGCTTAAATATTAATATGATT
* ** * *
29104592 TGTGCACAAATAATAATGTGATT
1 TATGCTTAAATATTAATATGATT
*
29104615 TATGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATATGATT
*
29104638 TGTGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATATGATT
* * * *
29104661 TGTGCTCAAATGTTAATGTGATT
1 TATGCTTAAATATTAATATGATT
*
29104684 TGTGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATATGATT
29104707 TATGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATATGATT
* *
29104730 TATGATTAAATATTAATGTGATT
1 TATGCTTAAATATTAATATGATT
* * *
29104753 TGTGCTTAAATATTAATGTGATC
1 TATGCTTAAATATTAATATGATT
*
29104776 TATGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATATGATT
29104799 TATGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATATGATT
** *
29104822 TGCGCTTAAATATTAATATAATT
1 TATGCTTAAATATTAATATGATT
* * *
29104845 TAAGATTAAATATTAATGTGATT
1 TATGCTTAAATATTAATATGATT
29104868 T
1 T
29104869 GTGTGCTTAC
Statistics
Matches: 380, Mismatches: 58, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 380 1.00
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.46
Consensus pattern (23 bp):
TATGCTTAAATATTAATATGATT
Found at i:29104519 original size:69 final size:69
Alignment explanation
Indices: 29104410--29104871 Score: 627
Period size: 69 Copynumber: 6.7 Consensus size: 69
29104400 CTTATATCTA
* *
29104410 TGCTTAAATATTAATATGATTTATGATTAAATATTAATGTGATTTGTGCTTAAGTATTAATGTGA
1 TGCTTAAATATTAATATGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGA
*
29104475 TTTA
66 TTTG
* * * * *
29104479 TGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTGTGCTTAAATATCAATATTA
1 TGCTTAAATATTAATATGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGA
29104544 TTTG
66 TTTG
* ** * * ** *
29104548 TGCTCAAATATTAATATTCTTTATGCTTAGATATTAATATGATTTGTGCACAAATAATAATGTGA
1 TGCTTAAATATTAATATGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGA
*
29104613 TTTA
66 TTTG
* * * * *
29104617 TGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTGTGCTCAAATGTTAATGTGA
1 TGCTTAAATATTAATATGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGA
29104682 TTTG
66 TTTG
* * *
29104686 TGCTTAAATATTAATATGATTTATGCTTAAATATTAATATGATTTATGATTAAATATTAATGTGA
1 TGCTTAAATATTAATATGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGA
29104751 TTTG
66 TTTG
* * * *
29104755 TGCTTAAATATTAATGTGATCTATGCTTAAATATTAATGTGATTTATGCTTAAATATTAATATGA
1 TGCTTAAATATTAATATGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGA
29104820 TTTG
66 TTTG
* * * *
29104824 CGCTTAAATATTAATATAATTTAAGATTAAATATTAATGTGATTTGTG
1 TGCTTAAATATTAATATGATTTATGCTTAAATATTAATGTGATTTGTG
29104872 TGCTTACAGA
Statistics
Matches: 343, Mismatches: 50, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 343 1.00
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.46
Consensus pattern (69 bp):
TGCTTAAATATTAATATGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATGTGA
TTTG
Found at i:29105034 original size:3 final size:3
Alignment explanation
Indices: 29105021--29105061 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
29105011 AGTGAACATG
29105021 TAA TGAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
29105062 GTGAATATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:29106215 original size:14 final size:14
Alignment explanation
Indices: 29106192--29106255 Score: 60
Period size: 14 Copynumber: 4.7 Consensus size: 14
29106182 TTTGAGGTGT
* *
29106192 GTTTAGGGTTCAGG
1 GTTTAAGGTTCAAG
* *
29106206 GTTTGAGGTTC-GG
1 GTTTAAGGTTCAAG
* *
29106219 GTTTAAAGTTTAAG
1 GTTTAAGGTTCAAG
29106233 GTTTAAGGTTCAAG
1 GTTTAAGGTTCAAG
29106247 GTTT-AGGTT
1 GTTTAAGGTT
29106256 AAAAAAATTA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
13 15 0.37
14 26 0.63
ACGTcount: A:0.20, C:0.05, G:0.34, T:0.41
Consensus pattern (14 bp):
GTTTAAGGTTCAAG
Found at i:29106239 original size:7 final size:7
Alignment explanation
Indices: 29106218--29106255 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
29106208 TTGAGGTTCG
29106218 GGTTTAA
1 GGTTTAA
*
29106225 AGTTTAA
1 GGTTTAA
29106232 GGTTTAA
1 GGTTTAA
*
29106239 GGTTCAA
1 GGTTTAA
29106246 GGTTT-A
1 GGTTTAA
29106252 GGTT
1 GGTT
29106256 AAAAAAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.26, C:0.03, G:0.29, T:0.42
Consensus pattern (7 bp):
GGTTTAA
Found at i:29106379 original size:16 final size:17
Alignment explanation
Indices: 29106360--29106391 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
29106350 CTTATTGGGG
29106360 AAAAGCGGT-ATTCAAA
1 AAAAGCGGTCATTCAAA
29106376 AAAAGCGGTCATTCAA
1 AAAAGCGGTCATTCAA
29106392 TTGCTCCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.19
Consensus pattern (17 bp):
AAAAGCGGTCATTCAAA
Found at i:29107412 original size:26 final size:27
Alignment explanation
Indices: 29107364--29107427 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
29107354 GAGAAGCAAA
29107364 AAAAGAAAAAAGAAAGTTAAAAAACAT
1 AAAAGAAAAAAGAAAGTTAAAAAACAT
29107391 AAAAGAAAAAAGAAAGTTAAAAAACAT
1 AAAAGAAAAAAGAAAGTTAAAAAACAT
29107418 -AAAGAAAAAA
1 AAAAGAAAAAA
29107428 TATGAAAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 10 0.27
27 27 0.73
ACGTcount: A:0.77, C:0.03, G:0.11, T:0.09
Consensus pattern (27 bp):
AAAAGAAAAAAGAAAGTTAAAAAACAT
Found at i:29116080 original size:103 final size:103
Alignment explanation
Indices: 29115896--29116161 Score: 367
Period size: 103 Copynumber: 2.6 Consensus size: 103
29115886 CAATTCATGA
* * **
29115896 CACCAAGTGCCTAGCAGATAAACCACATTAAGTGAGCCCTGCTCTAGTTGGATTAACCAACAGTT
1 CACCAAGTGCCTAGCAGATAAATCGCATTAAGTGAGCCCAACTCTAGTTGGATTAACCAACAGTT
* * *
29115961 TTGCACTCAGCGCTAATCGGTTAAACTGATGATCTTGG
66 TTGCACCCAACGCTAATCGGTTAAACCGATGATCTTGG
* * *
29115999 CACCCAGTGCTTAGCAGATAAATCGCATTAAGTGAGCCCAACTCTAGTTGGATTAACCAACGGTT
1 CACCAAGTGCCTAGCAGATAAATCGCATTAAGTGAGCCCAACTCTAGTTGGATTAACCAACAGTT
*
29116064 TTGCGCCCAACGCTAATCGGTTAAACCGATGATCTTGG
66 TTGCACCCAACGCTAATCGGTTAAACCGATGATCTTGG
* * * *
29116102 CACCTAGTGCCTAGCGGATAAATCGCA-AAAGTGAG-TCAAGCTCTAG-TGGATTAACCAACA
1 CACCAAGTGCCTAGCAGATAAATCGCATTAAGTGAGCCCAA-CTCTAGTTGGATTAACCAACA
29116162 AATGATCCGT
Statistics
Matches: 145, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
101 16 0.11
102 13 0.09
103 116 0.80
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (103 bp):
CACCAAGTGCCTAGCAGATAAATCGCATTAAGTGAGCCCAACTCTAGTTGGATTAACCAACAGTT
TTGCACCCAACGCTAATCGGTTAAACCGATGATCTTGG
Found at i:29117469 original size:2 final size:2
Alignment explanation
Indices: 29117462--29117494 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
29117452 ATACCTTGAC
29117462 TA TA TA TA TA TA 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 T
29117495 TTCATTCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29118261 original size:21 final size:21
Alignment explanation
Indices: 29118237--29118276 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
29118227 TAAAACGACG
*
29118237 TAGTTTTGCCTTTTAACTTGA
1 TAGTTTTGACTTTTAACTTGA
29118258 TAGTTTTGACTTTTAACTT
1 TAGTTTTGACTTTTAACTT
29118277 TAGAAAAGGT
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:0.20, C:0.12, G:0.12, T:0.55
Consensus pattern (21 bp):
TAGTTTTGACTTTTAACTTGA
Found at i:29118688 original size:19 final size:19
Alignment explanation
Indices: 29118646--29118717 Score: 74
Period size: 18 Copynumber: 3.7 Consensus size: 19
29118636 TAAAAATACA
* *
29118646 TATTTAGAATTTTATAAA-
1 TATTTTGAATTTTAAAAAT
29118664 TATTTTGAATTTTAAAAAT
1 TATTTTGAATTTTAAAAAT
* *
29118683 TATTTTTAATTTTTTGAAAAT
1 TATTTTGAA--TTTTAAAAAT
29118704 TATTTTGATATTTT
1 TATTTTGA-ATTTT
29118718 TTTTAATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
18 16 0.36
19 8 0.18
20 4 0.09
21 16 0.36
22 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (19 bp):
TATTTTGAATTTTAAAAAT
Found at i:29118716 original size:22 final size:21
Alignment explanation
Indices: 29118604--29118719 Score: 75
Period size: 21 Copynumber: 5.6 Consensus size: 21
29118594 TTTATATATT
*
29118604 TTTTGATTTTTTTAAAAAATTA
1 TTTTGAATTTTTT-AAAAATTA
* *
29118626 -TAT-ATTTTTTTAAAAATACATA
1 TTTTGAATTTTTTAAAAAT---TA
* *
29118648 TTTAGAA--TTTTATAAA-TA
1 TTTTGAATTTTTTAAAAATTA
29118666 TTTTGAA--TTTTAAAAATTA
1 TTTTGAATTTTTTAAAAATTA
* *
29118685 TTTTTAATTTTTTGAAAATTA
1 TTTTGAATTTTTTAAAAATTA
29118706 TTTTGATATTTTTT
1 TTTTGA-ATTTTTT
29118720 TTAATTTTTG
Statistics
Matches: 75, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
18 16 0.21
19 14 0.19
20 8 0.11
21 18 0.24
22 17 0.23
23 1 0.01
24 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (21 bp):
TTTTGAATTTTTTAAAAATTA
Found at i:29118717 original size:20 final size:20
Alignment explanation
Indices: 29118654--29118717 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
29118644 CATATTTAGA
*
29118654 ATTTTATAAA-TATTTTGA-
1 ATTTTAAAAATTATTTTGAT
*
29118672 ATTTTAAAAATTATTTTTAAT
1 ATTTTAAAAATTA-TTTTGAT
* *
29118693 TTTTTGAAAATTATTTTGAT
1 ATTTTAAAAATTATTTTGAT
29118713 ATTTT
1 ATTTT
29118718 TTTTAATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
18 9 0.24
19 2 0.05
20 15 0.41
21 11 0.30
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
ATTTTAAAAATTATTTTGAT
Found at i:29118819 original size:9 final size:9
Alignment explanation
Indices: 29118797--29118841 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
29118787 ATACTAATAT
29118797 GTTATTCGA
1 GTTATTCGA
* *
29118806 ATTATTTGA
1 GTTATTCGA
29118815 GTTATTCGA
1 GTTATTCGA
* *
29118824 ATTATTTGA
1 GTTATTCGA
29118833 GTTATTCGA
1 GTTATTCGA
29118842 ATTTTAAAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.49
Consensus pattern (9 bp):
GTTATTCGA
Found at i:29118820 original size:18 final size:18
Alignment explanation
Indices: 29118797--29118844 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
29118787 ATACTAATAT
29118797 GTTATTCGAATTATTTGA
1 GTTATTCGAATTATTTGA
29118815 GTTATTCGAATTATTTGA
1 GTTATTCGAATTATTTGA
29118833 GTTATTCGAATT
1 GTTATTCGAATT
29118845 TTAAAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.27, C:0.06, G:0.17, T:0.50
Consensus pattern (18 bp):
GTTATTCGAATTATTTGA
Found at i:29120300 original size:30 final size:30
Alignment explanation
Indices: 29120260--29120317 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
29120250 AGAAATAAAA
29120260 ATTTTAATTTTAGGCATTGGCGTTAAAACC
1 ATTTTAATTTTAGGCATTGGCGTTAAAACC
* * **
29120290 ATTTTCATTTTAGTCATTGTTGTTAAAA
1 ATTTTAATTTTAGGCATTGGCGTTAAAA
29120318 AATGTTTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (30 bp):
ATTTTAATTTTAGGCATTGGCGTTAAAACC
Found at i:29122003 original size:71 final size:71
Alignment explanation
Indices: 29121916--29122068 Score: 288
Period size: 71 Copynumber: 2.1 Consensus size: 71
29121906 AACCCGTCTC
29121916 AAAGAGATACAAATGAGCAAATAAAGAAAGAATCCTTACAATATCAAAATATTTGCAAATTAAGC
1 AAAGAGA-A-AAATGAGCAAATAAAGAAAGAATCCTTACAATATCAAAATATTTGCAAATTAAGC
29121981 TCAATTGT
64 TCAATTGT
29121989 AAAGAGAAAAATGAGCAAATAAAGAAAGAATCCTTACAATATCAAAATATTTGCAAATTAAGCTC
1 AAAGAGAAAAATGAGCAAATAAAGAAAGAATCCTTACAATATCAAAATATTTGCAAATTAAGCTC
29122054 AATTGT
66 AATTGT
29122060 AAAGAGAAA
1 AAAGAGAAA
29122069 CATTTGAGCT
Statistics
Matches: 80, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
71 72 0.90
72 1 0.01
73 7 0.09
ACGTcount: A:0.53, C:0.11, G:0.13, T:0.23
Consensus pattern (71 bp):
AAAGAGAAAAATGAGCAAATAAAGAAAGAATCCTTACAATATCAAAATATTTGCAAATTAAGCTC
AATTGT
Found at i:29122087 original size:71 final size:69
Alignment explanation
Indices: 29121937--29122087 Score: 234
Period size: 71 Copynumber: 2.1 Consensus size: 69
29121927 AATGAGCAAA
29121937 TAAA-GAAAGAATCCTTACAATATCAAAATATTTGCAAATTAAGCTCAATTGTAAAGAGAAAAAT
1 TAAATGAAAGAATCCTTACAATATCAAAATATTTGCAAATTAAGCTCAATTGTAAAGAGAAAAAT
29122001 GAGC
66 GAGC
29122005 -AAATAAAGAAAGAATCCTTACAATATCAAAATATTTGCAAATTAAGCTCAATTGTAAAGAGAAA
1 TAAAT---GAAAGAATCCTTACAATATCAAAATATTTGCAAATTAAGCTCAATTGTAAAGAGAAA
*
29122069 CATTTGAGC
63 -A-ATGAGC
29122078 TAAATGAAAG
1 TAAATGAAAG
29122088 CTCACAAGTG
Statistics
Matches: 75, Mismatches: 1, Indels: 11
0.86 0.01 0.13
Matches are distributed among these distances:
67 3 0.04
71 62 0.83
72 1 0.01
73 5 0.07
74 4 0.05
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.25
Consensus pattern (69 bp):
TAAATGAAAGAATCCTTACAATATCAAAATATTTGCAAATTAAGCTCAATTGTAAAGAGAAAAAT
GAGC
Found at i:29122155 original size:13 final size:13
Alignment explanation
Indices: 29122137--29122161 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29122127 ACAATGTTGT
29122137 TTTTTTATTGATC
1 TTTTTTATTGATC
29122150 TTTTTTATTGAT
1 TTTTTTATTGAT
29122162 AATCTCTCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.04, G:0.08, T:0.72
Consensus pattern (13 bp):
TTTTTTATTGATC
Found at i:29134489 original size:127 final size:128
Alignment explanation
Indices: 29134238--29134497 Score: 396
Period size: 127 Copynumber: 2.0 Consensus size: 128
29134228 CAAGATATAC
* * *
29134238 AAACAGTACTGCCATGATGTTCTTAGAAAGAGTTTAAGTTGCTTAGGACATATACTCAGTCACCA
1 AAACAGTACTGCCATCATGTTCTTAGAAAGAGTTTAAGTTGCTTAGGACATATAATCAATCACCA
** * * *
29134303 GTCAGGGCACTATATATAGATTTAGAGTTTAGCCTTCCTCTTCTTCTCCACAAGTCACAATCA
66 ACCAGGACACTATATATAGATATAGAGTTTAGCCTTACTCTTCTTCTCCACAAGTCACAATCA
* * *
29134366 GAACATTACTGCCATCATGTTGTTAGAAAGAGTTTAAGTTGCTTAGGACATATAATCAATCA-CA
1 AAACAGTACTGCCATCATGTTCTTAGAAAGAGTTTAAGTTGCTTAGGACATATAATCAATCACCA
* *
29134430 ACCAGGATACTATATATAGATATAGCGTTTAGCCTTACTCTTCTTCTCCACAAGTCACAATCA
66 ACCAGGACACTATATATAGATATAGAGTTTAGCCTTACTCTTCTTCTCCACAAGTCACAATCA
29134493 AAACA
1 AAACA
29134498 ACTTATATTG
Statistics
Matches: 118, Mismatches: 14, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
127 62 0.53
128 56 0.47
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (128 bp):
AAACAGTACTGCCATCATGTTCTTAGAAAGAGTTTAAGTTGCTTAGGACATATAATCAATCACCA
ACCAGGACACTATATATAGATATAGAGTTTAGCCTTACTCTTCTTCTCCACAAGTCACAATCA
Found at i:29135516 original size:16 final size:17
Alignment explanation
Indices: 29135492--29135533 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
29135482 AAATAATATA
29135492 AAATAAAAATTAATTT-T
1 AAAT-AAAATTAATTTAT
*
29135509 AAATAAAATTTATTTAT
1 AAATAAAATTAATTTAT
*
29135526 AATTAAAA
1 AAATAAAA
29135534 ATAAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATAAAATTAATTTAT
Found at i:29141227 original size:24 final size:22
Alignment explanation
Indices: 29141183--29141243 Score: 65
Period size: 24 Copynumber: 2.8 Consensus size: 22
29141173 TTAAAATTAA
29141183 AAATATTT-TTTTTA-AAAAAT
1 AAATATTTATTTTTATAAAAAT
29141203 AAATATTTATTTTTATCAAACAAT
1 AAATATTTATTTTTAT-AAA-AAT
*
29141227 ATAAT-TATATTTTTATA
1 A-AATATTTATTTTTATA
29141244 TTTACTTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
20 8 0.23
21 6 0.17
23 4 0.11
24 14 0.40
25 3 0.09
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATATTTATTTTTATAAAAAT
Found at i:29143674 original size:28 final size:29
Alignment explanation
Indices: 29143633--29143714 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 29
29143623 TGATTCGCAT
* * *
29143633 TTGGACAGTTCGCCAGATGTGCTCGCT-G
1 TTGGACTGTCCGCCACATGTGCTCGCTGG
** *
29143661 TTGGACTGTCCGCCTTATTTGCTCGCTGG
1 TTGGACTGTCCGCCACATGTGCTCGCTGG
* *
29143690 TTTGACTATCCGCCACATGTGCTCG
1 TTGGACTGTCCGCCACATGTGCTCG
29143715 TCGTTGCATG
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
28 22 0.51
29 21 0.49
ACGTcount: A:0.12, C:0.28, G:0.27, T:0.33
Consensus pattern (29 bp):
TTGGACTGTCCGCCACATGTGCTCGCTGG
Found at i:29143712 original size:29 final size:28
Alignment explanation
Indices: 29143643--29143714 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
29143633 TTGGACAGTT
* *
29143643 CGCCAGATGTGCTCGCTGTTGGACTGTC
1 CGCCACATGTGCTCGCTGTTGGACTATC
** * *
29143671 CGCCTTATTTGCTCGCTGGTTTGACTATC
1 CGCCACATGTGCTCGCT-GTTGGACTATC
29143700 CGCCACATGTGCTCG
1 CGCCACATGTGCTCG
29143715 TCGTTGCATG
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
28 14 0.40
29 21 0.60
ACGTcount: A:0.11, C:0.31, G:0.26, T:0.32
Consensus pattern (28 bp):
CGCCACATGTGCTCGCTGTTGGACTATC
Found at i:29153427 original size:210 final size:209
Alignment explanation
Indices: 29153065--29153772 Score: 1004
Period size: 210 Copynumber: 3.4 Consensus size: 209
29153055 AATGGGCTTC
* *
29153065 AAATTAGGACAATGCCATATAACTAATTCTTTTAGACAAGTGGAGGTAGATAATCCGTCTCCAAT
1 AAATTAGGACAAT-CAATATAACTAATTCTTTCAGACAAGTGGAGGTAGATAATCCGTCTCCAAT
** * *
29153130 CTTGCTTAATTTTTCGCAAAAGGAAATGCTAAGCTTTTCAAGAGATGAACATCTTCCGGTCATCG
65 CTTGCTTAATTTTTCGCAAAACAAAATGCAAAGCTTTTCAAGAGATGAACATCTTCCGGTTATCG
*
29153195 GAATAACTTCCAACTTGTCGCACCTTCCAATTAATAGATTTTGAAGAGAGGAAAATCCTTCCAAA
130 GAATAACTTCCAACTCGTCGCACCTTCCAATTAATAGATTTTGAAGAGAGGAAAATCCTTCCAAA
*
29153260 TCTGGAATTGAACTT
195 TCTGGAATCGAACTT
*
29153275 AAATTAGGACAATGCAATATATCTAATTCTTTCAGACAAGTGGAGGTAGATAATCCGTCTCCAAT
1 AAATTAGGACAAT-CAATATAACTAATTCTTTCAGACAAGTGGAGGTAGATAATCCGTCTCCAAT
* ***
29153340 CTTGCTTAATTTTTTGCAGCCCAAAATGCAAAGCTTTTCAAGAGATGAACATCTTCCGGTTATCG
65 CTTGCTTAATTTTTCGCAAAACAAAATGCAAAGCTTTTCAAGAGATGAACATCTTCCGGTTATCG
* * * *
29153405 AAATAACTTCCAACTCGTCGCACCTTCCAATTAATAGATTTTGAATAGAGGAAAACCCTTCCAAC
130 GAATAACTTCCAACTCGTCGCACCTTCCAATTAATAGATTTTGAAGAGAGGAAAATCCTTCCAAA
29153470 TCTGGAATCGAACTT
195 TCTGGAATCGAACTT
* * * * *
29153485 AAATTAGGGCAATC-ATTTAGCTCTAATTTTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCAA
1 AAATTAGGACAATCAATATA--ACTAATTCTTTCAGACAAGTGGAGGTAGATAATCCGTCTCCAA
* *** * * *
29153549 TCTTGCTTAATTTTTCGCAATATTTAATGCGAAGCTTTTCAAGAGATGAACATCTTCCTGTTATG
64 TCTTGCTTAATTTTTCGCAAAACAAAATGCAAAGCTTTTCAAGAGATGAACATCTTCCGGTTATC
* * *
29153614 GGAAGAACTTCCAAGTCATCGCACCTTCCAATTAATAGATTTTGAAGAGAGGAAAATCCTTCCAA
129 GGAATAACTTCCAACTCGTCGCACCTTCCAATTAATAGATTTTGAAGAGAGGAAAATCCTTCCAA
29153679 ATCTGGAATCGAACTT
194 ATCTGGAATCGAACTT
* * * * * * * *
29153695 AAATTAGGACAATCATCTAGAAGTATTTCTTTCAGACAGGTGGGGGTACATAATCCATCTCCAAT
1 AAATTAGGACAATCA-ATATAACTAATTCTTTCAGACAAGTGGAGGTAGATAATCCGTCTCCAAT
29153760 CTTGCTTAATTTT
65 CTTGCTTAATTTT
29153773 CGGCAACTGG
Statistics
Matches: 443, Mismatches: 51, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
208 4 0.01
209 1 0.00
210 436 0.98
212 2 0.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (209 bp):
AAATTAGGACAATCAATATAACTAATTCTTTCAGACAAGTGGAGGTAGATAATCCGTCTCCAATC
TTGCTTAATTTTTCGCAAAACAAAATGCAAAGCTTTTCAAGAGATGAACATCTTCCGGTTATCGG
AATAACTTCCAACTCGTCGCACCTTCCAATTAATAGATTTTGAAGAGAGGAAAATCCTTCCAAAT
CTGGAATCGAACTT
Found at i:29155736 original size:81 final size:81
Alignment explanation
Indices: 29155643--29155813 Score: 297
Period size: 81 Copynumber: 2.1 Consensus size: 81
29155633 GAAGATACTT
*
29155643 GATCTGATCCTTTCCTCCTTTGGCCCCTTCATTCTTCTGCTCGAGTTTCTCAACCATTGCATTCT
1 GATCTGATCCTTTCCTCCTTTGGCCCCTTCAATCTTCTGCTCGAGTTTCTCAACCATTGCATTCT
* *
29155708 TATTTTTAGGAATTAA
66 TATTTTGAAGAATTAA
*
29155724 GATCTGATCCTTTCCTCCTTTGGCCCCTTCAATCTTCTGCTTGAGTTTCTCAACCATTGCATTCT
1 GATCTGATCCTTTCCTCCTTTGGCCCCTTCAATCTTCTGCTCGAGTTTCTCAACCATTGCATTCT
*
29155789 TATTTTGAAGAATTGA
66 TATTTTGAAGAATTAA
29155805 GATCTGATC
1 GATCTGATC
29155814 ATCAGTAAAA
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 85 1.00
ACGTcount: A:0.18, C:0.26, G:0.13, T:0.42
Consensus pattern (81 bp):
GATCTGATCCTTTCCTCCTTTGGCCCCTTCAATCTTCTGCTCGAGTTTCTCAACCATTGCATTCT
TATTTTGAAGAATTAA
Found at i:29158486 original size:21 final size:21
Alignment explanation
Indices: 29158462--29158503 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
29158452 TAAAAAAAGG
29158462 GTAAATATTAACATCTTAATA
1 GTAAATATTAACATCTTAATA
29158483 GTAAATATTAACATCTTAATA
1 GTAAATATTAACATCTTAATA
29158504 CAAATTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.38
Consensus pattern (21 bp):
GTAAATATTAACATCTTAATA
Found at i:29160385 original size:19 final size:20
Alignment explanation
Indices: 29160345--29160385 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
29160335 GATTGGTTGA
* *
29160345 ATAAGAGAAATTTACTGAAC
1 ATAAAAGAAATTTACAGAAC
29160365 ATAAAAGAAATTTA-AGAAC
1 ATAAAAGAAATTTACAGAAC
29160384 AT
1 AT
29160386 TAATAAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.56, C:0.07, G:0.12, T:0.24
Consensus pattern (20 bp):
ATAAAAGAAATTTACAGAAC
Found at i:29172316 original size:10 final size:10
Alignment explanation
Indices: 29172295--29172327 Score: 52
Period size: 9 Copynumber: 3.5 Consensus size: 10
29172285 TTTTGACACG
29172295 TATTTTTT-T
1 TATTTTTTAT
29172304 TATTTTTTAT
1 TATTTTTTAT
29172314 TATTTTTTA-
1 TATTTTTTAT
29172323 TATTT
1 TATTT
29172328 AAAAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.57
10 10 0.43
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (10 bp):
TATTTTTTAT
Found at i:29173131 original size:21 final size:21
Alignment explanation
Indices: 29173105--29173151 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
29173095 ACGAGCCACC
*
29173105 GCAATACTTTACTCCTCCCGG
1 GCAATACTCTACTCCTCCCGG
*
29173126 GCAATACTCTACTCCTCCGGG
1 GCAATACTCTACTCCTCCCGG
29173147 GCAAT
1 GCAAT
29173152 TGGACCCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.36, G:0.17, T:0.26
Consensus pattern (21 bp):
GCAATACTCTACTCCTCCCGG
Found at i:29176443 original size:4 final size:4
Alignment explanation
Indices: 29176417--29176484 Score: 75
Period size: 4 Copynumber: 17.0 Consensus size: 4
29176407 ACACATTACT
* * * *
29176417 TTTC -TTC TCTC TTTC TCTC TTTC TTTC TTTC TTTC TTTCC TCTC ATTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC
*
29176465 TTCC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC
29176485 CGTTTATTTG
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
3 3 0.06
4 46 0.88
5 3 0.06
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.66
Consensus pattern (4 bp):
TTTC
Found at i:29177437 original size:13 final size:13
Alignment explanation
Indices: 29177406--29177431 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29177396 GAATATTGTA
29177406 AAAAATCATTTTT
1 AAAAATCATTTTT
29177419 AAAAATCATTTTT
1 AAAAATCATTTTT
29177432 GGAAATTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAAATCATTTTT
Found at i:29177685 original size:18 final size:18
Alignment explanation
Indices: 29177662--29177704 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
29177652 AGAATAATTT
29177662 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
29177680 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
29177698 TTAATTA
1 TTAATTA
29177705 TAACTGAAAA
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:29184816 original size:17 final size:17
Alignment explanation
Indices: 29184794--29184826 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29184784 ATATAGTTTT
29184794 TATAAA-TATAATAAATA
1 TATAAATTATAA-AAATA
29184811 TATAAATTATAAAAAT
1 TATAAATTATAAAAAT
29184827 GAATACATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TATAAATTATAAAAATA
Done.