Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000073.1 Hibiscus syriacus cultivar Beakdansim tig00000132_pilon, whole genome shotgun sequence
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: 1402814
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 7
Found at i:204016 original size:21 final size:21
Alignment explanation
Indices: 203990--204029 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
203980 CCCCTTTTGA
*
203990 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
204011 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
204030 TGGGGTTCTG
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:204742 original size:21 final size:21
Alignment explanation
Indices: 204717--204756 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
204707 ACCGTCAACC
*
204717 AAATCCACTTCCAAATCCTCA
1 AAATCCAATTCCAAATCCTCA
*
204738 AAATCCAATTCCTAATCCT
1 AAATCCAATTCCAAATCCT
204757 AATCCCATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATCCAATTCCAAATCCTCA
Found at i:206006 original size:24 final size:23
Alignment explanation
Indices: 205956--206029 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
205946 GCTTCAACTT
* *
205956 TTTGGATTGTTTGATTTTGTGAC
1 TTTGGATTGTTTGATGTTGTGAA
205979 TTTGGATTTGTTTGGATGTT-TGAA
1 TTTGGA-TTGTTT-GATGTTGTGAA
*
206003 TTTGTGGATTGATTGAT-TT-TGAA
1 -TT-TGGATTGTTTGATGTTGTGAA
206026 TTTG
1 TTTG
206030 TTTGGATTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
21 2 0.05
22 2 0.05
23 12 0.27
24 12 0.27
25 12 0.27
26 4 0.09
ACGTcount: A:0.16, C:0.01, G:0.27, T:0.55
Consensus pattern (23 bp):
TTTGGATTGTTTGATGTTGTGAA
Found at i:208806 original size:20 final size:20
Alignment explanation
Indices: 208781--208828 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
208771 GCGTAAAAAT
208781 ATTTGACTATCGCATTGCAA
1 ATTTGACTATCGCATTGCAA
** *
208801 ATTTGACTATCGTGTTGCGA
1 ATTTGACTATCGCATTGCAA
208821 ATTTGACT
1 ATTTGACT
208829 TCTATGTTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTTGACTATCGCATTGCAA
Found at i:208836 original size:20 final size:20
Alignment explanation
Indices: 208781--208840 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
208771 GCGTAAAAAT
*** *
208781 ATTTGACTATCGCATTGCAA
1 ATTTGACTATCATGTTGCGA
*
208801 ATTTGACTATCGTGTTGCGA
1 ATTTGACTATCATGTTGCGA
208821 ATTTGACT-TCTATGTTGCGA
1 ATTTGACTATC-ATGTTGCGA
208841 TTTACAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 2 0.06
20 33 0.94
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (20 bp):
ATTTGACTATCATGTTGCGA
Found at i:208857 original size:20 final size:20
Alignment explanation
Indices: 208834--208919 Score: 86
Period size: 20 Copynumber: 4.2 Consensus size: 20
208824 TGACTTCTAT
208834 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
* *
208854 GTTGCGATTTACAGATTTGC
1 GTTGCGATTTACAAATTCGC
208874 GTTGCGAATTTGGA-AAATT-GC
1 GTTGCG-ATTT--ACAAATTCGC
** *
208895 AATGCGATTTACATATTCGC
1 GTTGCGATTTACAAATTCGC
208915 GTTGC
1 GTTGC
208920 AAAATTGGAA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
18 1 0.02
19 4 0.08
20 33 0.62
21 10 0.19
22 4 0.08
23 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:208958 original size:20 final size:20
Alignment explanation
Indices: 208911--208981 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
208901 ATTTACATAT
* *
208911 TCGCGTTGCAAAATTGGAAAA
1 TCGCGTTGCGAAATTGG-AGA
* *
208932 T-GGGTTGCGAAATTGGAGT
1 TCGCGTTGCGAAATTGGAGA
* *
208951 TCGCGTTGTG-AATTTGAGA
1 TCGCGTTGCGAAATTGGAGA
208970 TCGCGTTGCGAA
1 TCGCGTTGCGAA
208982 TTTGTTGGTC
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
19 18 0.46
20 20 0.51
21 1 0.03
ACGTcount: A:0.25, C:0.13, G:0.32, T:0.30
Consensus pattern (20 bp):
TCGCGTTGCGAAATTGGAGA
Found at i:210195 original size:21 final size:22
Alignment explanation
Indices: 210155--210207 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
210145 TGTTCCCCAT
*
210155 GTATCGATACCCTCCACATA-G
1 GTATCGATACCCTACACATAGG
210176 GTATCGATACCTCTAC-CATAGG
1 GTATCGATACC-CTACACATAGG
*
210198 GTATCAATAC
1 GTATCGATAC
210208 TGTTTATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (22 bp):
GTATCGATACCCTACACATAGG
Found at i:211174 original size:21 final size:20
Alignment explanation
Indices: 211136--211186 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 20
211126 ATTACTTTAT
211136 ATATTTTT-TTCAATTAAATCA
1 ATATTTTTATTCAATTAAA--A
* *
211157 CTATTTTTATTGAA-TAAAA
1 ATATTTTTATTCAATTAAAA
211176 ATATTTTTATT
1 ATATTTTTATT
211187 ATTTCGGGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 11 0.42
21 11 0.42
22 4 0.15
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (20 bp):
ATATTTTTATTCAATTAAAA
Found at i:212780 original size:17 final size:17
Alignment explanation
Indices: 212754--212787 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
212744 TTTAGGTCCC
212754 CATTTTGCCA-TGTTTA
1 CATTTTGCCACTGTTTA
212770 CATTATTGCCACTGTTTA
1 CATT-TTGCCACTGTTTA
212788 GGTTTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 6 0.38
18 6 0.38
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.47
Consensus pattern (17 bp):
CATTTTGCCACTGTTTA
Found at i:215186 original size:19 final size:19
Alignment explanation
Indices: 215162--215199 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
215152 TCCAACACCT
215162 TCAATTGCAACAAGTATCC
1 TCAATTGCAACAAGTATCC
215181 TCAATTGCAACAAGTATCC
1 TCAATTGCAACAAGTATCC
215200 CTACCTCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (19 bp):
TCAATTGCAACAAGTATCC
Found at i:219174 original size:171 final size:171
Alignment explanation
Indices: 218875--219219 Score: 514
Period size: 171 Copynumber: 2.0 Consensus size: 171
218865 AGATAGATAC
* * *
218875 AAACAAATCTGATCGCATCGACAAACGAACCACAAAAAGGGATCAAGCTATTGAAAGACCACCGG
1 AAACAAATCTGATCACATCGACAAACGAACCACAAAAAGGGATCAAGCGATTGAAAGACCACCGA
* *
218940 CAAATCGTAAATCAGACTTGAGCGACGTGAAAAACTATCAATGAACGAATAAAGGAGATCCAAAT
66 CAAACCGTAAATCAAACTTGAGCGACGTGAAAAACTATCAATGAACGAATAAAGGAGATCCAAAT
** * *
219005 CCAATCCGATTGTCCAAAGCATGGAAGATCACTAATATAAT
131 CCAATCCGAAGGTCCAAAGCAGGGAAGATCACCAATATAAT
219046 AAACAAATCTGATCACATCGACAAACGAACCAC-AAAAGAGGATCAAGCGATTGAAAGACCACCG
1 AAACAAATCTGATCACATCGACAAACGAACCACAAAAAG-GGATCAAGCGATTGAAAGACCACCG
* * * * *
219110 ACAAACCGTAAATCAAACTTGAGTGACTTGAAAAACTATCTATGAATGCATAAA-GAGTATCCAA
65 ACAAACCGTAAATCAAACTTGAGCGACGTGAAAAACTATCAATGAACGAATAAAGGAG-ATCCAA
* *
219174 ATCCAATCTGAAGGTCCAAAGCAGGGAATATCACCAATATAAT
129 ATCCAATCCGAAGGTCCAAAGCAGGGAAGATCACCAATATAAT
219217 AAA
1 AAA
219220 TAAGAGTCAT
Statistics
Matches: 156, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
170 8 0.05
171 148 0.95
ACGTcount: A:0.45, C:0.21, G:0.17, T:0.18
Consensus pattern (171 bp):
AAACAAATCTGATCACATCGACAAACGAACCACAAAAAGGGATCAAGCGATTGAAAGACCACCGA
CAAACCGTAAATCAAACTTGAGCGACGTGAAAAACTATCAATGAACGAATAAAGGAGATCCAAAT
CCAATCCGAAGGTCCAAAGCAGGGAAGATCACCAATATAAT
Found at i:228846 original size:20 final size:21
Alignment explanation
Indices: 228821--228862 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
228811 CCAACTTACA
228821 ATGCATTATG-AACCATTATT
1 ATGCATTATGTAACCATTATT
*
228841 ATGCATTATGTAACTATTATT
1 ATGCATTATGTAACCATTATT
228862 A
1 A
228863 GTTGCATGAC
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:0.36, C:0.12, G:0.10, T:0.43
Consensus pattern (21 bp):
ATGCATTATGTAACCATTATT
Found at i:233385 original size:23 final size:23
Alignment explanation
Indices: 233355--233399 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
233345 ATGTCACTTT
*
233355 TGAACCATTATTAG-TGCCAACTA
1 TGAACCATAATT-GTTGCCAACTA
233378 TGAACCATAATTGTTGCCAACT
1 TGAACCATAATTGTTGCCAACT
233400 TACAATGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.31
Consensus pattern (23 bp):
TGAACCATAATTGTTGCCAACTA
Found at i:233445 original size:19 final size:18
Alignment explanation
Indices: 233420--233462 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 18
233410 TATGAACCAT
233420 TATTATGCATTATGCAAC
1 TATTATGCATTATGCAAC
233438 TAATTATGCATTATGCAAC
1 T-ATTATGCATTATGCAAC
233457 TATTAT
1 TATTAT
233463 TAGTTGCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (18 bp):
TATTATGCATTATGCAAC
Found at i:233478 original size:40 final size:38
Alignment explanation
Indices: 233404--233481 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 38
233394 CCAACTTACA
233404 ATGCATTATGAACCATTATTATGCATTATGCAACTAATT
1 ATGCATTATGAACCATTATTATGCATTA-GCAACTAATT
*
233443 ATGCATTATGCAACTATTATTAGTTGCATTA-CAACTAAT
1 ATGCATTATG-AACCATTATTA--TGCATTAGCAACTAAT
233482 AGATTGGCTG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
39 10 0.29
40 18 0.51
42 7 0.20
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.38
Consensus pattern (38 bp):
ATGCATTATGAACCATTATTATGCATTAGCAACTAATT
Found at i:237158 original size:20 final size:21
Alignment explanation
Indices: 237119--237158 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
237109 CACGCTGAAT
237119 GCTGAACGGTTCAGCATTCAAC
1 GCTGAACGGTTCA-CATTCAAC
*
237141 GCTGAATGGTTC-CATTCA
1 GCTGAACGGTTCACATTCA
237159 GAGCCAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (21 bp):
GCTGAACGGTTCACATTCAAC
Found at i:241415 original size:35 final size:35
Alignment explanation
Indices: 241352--241451 Score: 119
Period size: 35 Copynumber: 2.7 Consensus size: 35
241342 TTTCGTCCTA
*
241352 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTCTG
*
241389 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
** *
241424 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAA-ATAGGAT
241452 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 22 0.39
36 18 0.32
37 16 0.29
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (35 bp):
CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
Found at i:242035 original size:16 final size:16
Alignment explanation
Indices: 242014--242044 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
242004 ATATGTATAT
242014 TTTTTATTGTATTTTA
1 TTTTTATTGTATTTTA
*
242030 TTTTTATTTTATTTT
1 TTTTTATTGTATTTT
242045 TACTTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTTTATTGTATTTTA
Found at i:242037 original size:11 final size:11
Alignment explanation
Indices: 242023--242056 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
242013 TTTTTTATTG
242023 TATTTTATTTT
1 TATTTTATTTT
242034 TATTTTATTTT
1 TATTTTATTTT
*
242045 TACTTT-TTTT
1 TATTTTATTTT
242055 TA
1 TA
242057 AACATATGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 6 0.27
11 16 0.73
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (11 bp):
TATTTTATTTT
Found at i:242175 original size:16 final size:16
Alignment explanation
Indices: 242135--242168 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
242125 AATGTATTTA
*
242135 TATTATATTACATTAT
1 TATTATTTTACATTAT
*
242151 TATTATTTTACTTTAT
1 TATTATTTTACATTAT
242167 TA
1 TA
242169 ATTTTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATTTTACATTAT
Found at i:246758 original size:183 final size:183
Alignment explanation
Indices: 246450--246799 Score: 637
Period size: 183 Copynumber: 1.9 Consensus size: 183
246440 ATTAAACCCG
246450 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTAGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTAGCTTTATGA
** *
246515 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
246580 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
* *
246633 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGTTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTAGCTTTATGA
*
246698 ATAGATTACATTCAAACCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
246763 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTT
131 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTT
246800 TAGTTAAACC
Statistics
Matches: 160, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 160 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTAGCTTTATGA
ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
Found at i:248007 original size:37 final size:37
Alignment explanation
Indices: 247940--248026 Score: 113
Period size: 37 Copynumber: 2.4 Consensus size: 37
247930 ATTGAAAACA
** * *
247940 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
247976 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGATACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
248013 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
248027 TAAACATTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 12 0.27
37 32 0.73
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:248032 original size:102 final size:103
Alignment explanation
Indices: 247896--248092 Score: 290
Period size: 102 Copynumber: 1.9 Consensus size: 103
247886 CAGATGATTA
* * *
247896 TCTCACTTGAGACAGTTTCTTTTTAAACATAAACATTGAAAACATTTCCCTT-GAA-ATGAATTT
1 TCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGGAACA-AAATTT
* *
247959 TGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTG
65 TGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATTTTG
* *
247998 TCTCCCTTGATACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGGAACAAAATTTT
1 TCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGGAACAAAATTTT
* *
248063 TTCTCCCTTGAGACAGTTTCTCTTGAAACA
66 GTCTCCCTTGAGACAGTTTCCCTTGAAACA
248093 TAAACATTGA
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
102 48 0.57
103 35 0.42
104 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (103 bp):
TCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGGAACAAAATTTT
GTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATTTTG
Found at i:248082 original size:66 final size:66
Alignment explanation
Indices: 247976--248157 Score: 269
Period size: 66 Copynumber: 2.8 Consensus size: 66
247966 CTTGAGATAG
* *
247976 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGATACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
248041 A
66 A
*
248042 TTTCCCTTGGAACAAAATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
248107 A
66 A
* * * * *
248108 TTTCCCTT-GAA-ATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1 TTTCCCTTGGAACA-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
248158 AAATTCCGTC
Statistics
Matches: 106, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
64 1 0.01
65 34 0.32
66 71 0.67
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (66 bp):
TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
A
Found at i:248148 original size:102 final size:102
Alignment explanation
Indices: 248042--248499 Score: 810
Period size: 102 Copynumber: 4.5 Consensus size: 102
248032 ATTGAAAACA
* *
248042 TTTCCCTTGGAACAAAATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
*
248107 ATTTCCCTTGAAATGAGTTTTGTCTCTCTTGAGATAG
66 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
** * *
248144 TTTCCCTTGAAACAAAATTCCGTCTCCATTGAGACAGTTTCTCTTGAAACATAAACATTGGAAAC
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
248209 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
66 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
*
248246 TTTCCCTTGAAACAAAATTTTGTCTCCATTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
248311 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
66 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
*
248348 TTTCCCTCGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
*
248413 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAG
66 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
*
248450 TTTTCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
248500 CAAAACCTTT
Statistics
Matches: 341, Mismatches: 15, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
101 37 0.11
102 304 0.89
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (102 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
Found at i:248183 original size:37 final size:37
Alignment explanation
Indices: 248124--248499 Score: 180
Period size: 37 Copynumber: 10.9 Consensus size: 37
248114 TTGAAATGAG
*
248124 TTTTGTCTCTC-TTGAGATAGTTTCCCTTGAAACAAAA
1 TTTTGTCTC-CATTGAGACAGTTTCCCTTGAAACAAAA
** *
248161 TTCCGTCTCCATTGAGACAGTTTCTCTTGAAACATAAA
1 TTTTGTCTCCATTGAGACAGTTTCCCTTGAAACA-AAA
* **
248199 ---------CATTGGAAACA-TTTCCCTTGAAA-TGAA
1 TTTTGTCTCCATT-GAGACAGTTTCCCTTGAAACAAAA
*
248226 TTTTGTCTCTC-TTGAGATAGTTTCCCTTGAAACAAAA
1 TTTTGTCTC-CATTGAGACAGTTTCCCTTGAAACAAAA
*
248263 TTTTGTCTCCATTGAGACAGTTTCTCTTGAAACATAAA
1 TTTTGTCTCCATTGAGACAGTTTCCCTTGAAACA-AAA
* **
248301 ---------CATTGAAAACA-TTTCCCTTGAAA-TGAA
1 TTTTGTCTCCATTG-AGACAGTTTCCCTTGAAACAAAA
* *
248328 TTTTGTCTCTC-TTGAGATAGTTTCCCTCGAAACAAAA
1 TTTTGTCTC-CATTGAGACAGTTTCCCTTGAAACAAAA
* *
248365 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
1 TTTTGTCTCCATTGAGACAGTTTCCCTTGAAACA-AAA
* **
248403 ---------CATTGAAAACA-TTTCCCTTGAAA-TGAA
1 TTTTGTCTCCATTG-AGACAGTTTCCCTTGAAACAAAA
* * *
248430 TTTCGTCTCTC-TTGAGATAGTTTTCCTTGAAAC-AAA
1 TTTTGTCTC-CATTGAGACAGTTTCCCTTGAAACAAAA
* *
248466 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTTTGTCTCCATTGAGACAGTTTCCCTTGAAACA
248500 CAAAACCTTT
Statistics
Matches: 253, Mismatches: 39, Indels: 94
0.66 0.10 0.24
Matches are distributed among these distances:
27 6 0.02
29 46 0.18
30 13 0.05
35 11 0.04
36 74 0.29
37 94 0.37
38 9 0.04
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.37
Consensus pattern (37 bp):
TTTTGTCTCCATTGAGACAGTTTCCCTTGAAACAAAA
Found at i:248183 original size:168 final size:167
Alignment explanation
Indices: 247896--248259 Score: 577
Period size: 168 Copynumber: 2.2 Consensus size: 167
247886 CAGATGATTA
* *
247896 TCTCACTTGAGACAGTTTCTTTTTAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTG
1 TCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTG
** * *
247961 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGATACAGTTTCTCTTGAAAC
66 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTCCGTCTCCATTGAGACAGTTTCTCTTGAAAC
*
248026 ATAAACATTGAAAACATTTCCCTTGGAACA-AAATTTTT
131 ATAAACATTGAAAACATTTCCCTT-GAA-ATAAATTTTG
* *
248064 TCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAGTTTTG
1 TCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTG
248129 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTCCGTCTCCATTGAGACAGTTTCTCTTGAAAC
66 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTCCGTCTCCATTGAGACAGTTTCTCTTGAAAC
* *
248194 ATAAACATTGGAAACATTTCCCTTGAAATGAATTTTG
131 ATAAACATTGAAAACATTTCCCTTGAAATAAATTTTG
* * *
248231 TCTCTCTTGAGATAGTTTCCCTTGAAACA
1 TCTCACTTGAGACAGTTTCTCTTGAAACA
248260 AAATTTTGTC
Statistics
Matches: 181, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
166 1 0.01
167 35 0.19
168 145 0.80
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (167 bp):
TCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTG
TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTCCGTCTCCATTGAGACAGTTTCTCTTGAAAC
ATAAACATTGAAAACATTTCCCTTGAAATAAATTTTG
Found at i:248257 original size:36 final size:37
Alignment explanation
Indices: 248210--248499 Score: 157
Period size: 36 Copynumber: 8.4 Consensus size: 37
248200 ATTGGAAACA
** *
248210 TTTCCCTTGAAA-TGAATTTTGTCTCTC-TTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTC-CATTGAGACAG
248246 TTTCCCTTGAAACAAAATTTTGTCTCCATTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCATTGAGACAG
* *
248283 TTTCTCTTGAAACATAAA---------CATTGAAAACA-
1 TTTCCCTTGAAACA-AAATTTTGTCTCCATTG-AGACAG
** *
248312 TTTCCCTTGAAA-TGAATTTTGTCTCTC-TTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTC-CATTGAGACAG
* *
248348 TTTCCCTCGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCATTGAGACAG
* *
248385 TTTCTCTTGAAACATAAA---------CATTGAAAACA-
1 TTTCCCTTGAAACA-AAATTTTGTCTCCATTG-AGACAG
** * *
248414 TTTCCCTTGAAA-TGAATTTCGTCTCTC-TTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTC-CATTGAGACAG
* *
248450 TTTTCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCATTGAGACAG
*
248486 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
248500 CAAAACCTTT
Statistics
Matches: 192, Mismatches: 29, Indels: 65
0.67 0.10 0.23
Matches are distributed among these distances:
27 4 0.02
29 31 0.16
30 8 0.04
35 7 0.04
36 71 0.37
37 65 0.34
38 6 0.03
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCATTGAGACAG
Found at i:248597 original size:67 final size:67
Alignment explanation
Indices: 248441--248599 Score: 232
Period size: 67 Copynumber: 2.4 Consensus size: 67
248431 TTCGTCTCTC
* * *
248441 TTGAGATAGTTTTCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAAC
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAC
248506 CT
66 CT
* *
248508 TTGAGATTGTTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAT
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAC
248573 CT
66 CT
*
248575 TTGA-ATT-TATCTCCCTTAAAACAAA
1 TTGAGATTGT-T-TCCCTTGAAACAAA
248600 ATTTCGTTTC
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 78 0.94
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.35
Consensus pattern (67 bp):
TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAC
CT
Found at i:248774 original size:37 final size:36
Alignment explanation
Indices: 248733--248861 Score: 100
Period size: 37 Copynumber: 3.5 Consensus size: 36
248723 CATCTCCCCG
*
248733 TGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TGAGACAATTTCTTTTGAAAC-AAGTTTTGTCTCTCT
* * * *
248770 TGAGACAGTTT-TTCTTAAAACAAAATTTTGTCTCCCT
1 TGAGACAATTTCTT-TTGAAAC-AAGTTTTGTCTCTCT
* * * * * *
248807 TAAGATC-GTTTCTCTTGAAACGAGTTCTGTCTCTTT
1 TGAGA-CAATTTCTTTTGAAACAAGTTTTGTCTCTCT
*
248843 TGAGACAATTTCTCTTGAA
1 TGAGACAATTTCTTTTGAA
248862 GCATCATCTG
Statistics
Matches: 72, Mismatches: 16, Indels: 9
0.74 0.16 0.09
Matches are distributed among these distances:
35 1 0.01
36 27 0.38
37 42 0.58
38 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.43
Consensus pattern (36 bp):
TGAGACAATTTCTTTTGAAACAAGTTTTGTCTCTCT
Found at i:249506 original size:106 final size:105
Alignment explanation
Indices: 249147--249667 Score: 484
Period size: 109 Copynumber: 4.9 Consensus size: 105
249137 TAGCTATAGT
* * * * *
249147 CAAGTTCAACTTCACAACAAAGGGACGGCTGGTTGCCAAC-AACAATTTCCCAATTTCGGAACCG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT-TCAATTTCAGAACCA
* * *
249211 ATTTCAACTCCAC-GACGGAGGATATCGTGCTACCCGAGACAACA
65 ATTTCAACTTCACAG-CGGAGGATAT--TG-GACTCGAGACAACA
* * * **
249255 CAAGATCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTTTCAGTTTCA-TCCGC
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTTCAATTTCAGAAC-C
* * * *
249319 GATTTTAACTCCAC-GACGGAGGATATCGTGCCACTCGAGACAACA
64 AATTTCAACTTCACAG-CGGAGGATAT--TG-GACTCGAGACAACA
* * *
249364 CAAGTTCAACTTCACAACGAAGGGACAGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTC-AATTTCAGAACCA
* *
249429 ATTTCAACTTCACAGCGAATGATATTGGACTCGAGACAACA
65 ATTTCAACTTCACAGCGGAGGATATTGGACTCGAGACAACA
* * ** * * **
249470 CAAGTTCAACTTCACAACGAAGGGACGGTTGATTGTC-AGTAA-GA-TTTC--GTTCAGAGTCAA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTCAATTTCAGAACCAA
* * *
249530 TTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAGCA
66 TTTCAACTTCACAGCGGAGGATATTGGACTCGAGACAACA
* * * ** * ** *
249570 CAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCGGTTCCAGAACCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT-TCAATTTCAGAACCA
249635 ATTTCAACTTCACAGCGGAGGATATTGGACTCG
65 ATTTCAACTTCACAGCGGAGGATATTGGACTCG
249668 GAACAATATT
Statistics
Matches: 350, Mismatches: 51, Indels: 26
0.82 0.12 0.06
Matches are distributed among these distances:
100 79 0.23
101 3 0.01
102 1 0.00
103 6 0.02
104 1 0.00
105 3 0.01
106 85 0.24
107 2 0.01
108 43 0.12
109 122 0.35
110 5 0.01
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.22
Consensus pattern (105 bp):
CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTCAATTTCAGAACCAA
TTTCAACTTCACAGCGGAGGATATTGGACTCGAGACAACA
Found at i:250191 original size:35 final size:35
Alignment explanation
Indices: 250128--250227 Score: 119
Period size: 35 Copynumber: 2.7 Consensus size: 35
250118 TTTCGTCCTA
*
250128 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTCTG
*
250165 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
** *
250200 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAA-ATAGGAT
250228 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 22 0.39
36 18 0.32
37 16 0.29
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (35 bp):
CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
Found at i:250678 original size:2 final size:2
Alignment explanation
Indices: 250673--250704 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
250663 TTAAAGTTAT
*
250673 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
250705 ACTATTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:250941 original size:16 final size:16
Alignment explanation
Indices: 250901--250934 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
250891 AATGTATTTA
*
250901 TATTATATTACATTAT
1 TATTATTTTACATTAT
*
250917 TATTATTTTACTTTAT
1 TATTATTTTACATTAT
250933 TA
1 TA
250935 ATTTTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATTTTACATTAT
Found at i:250968 original size:2 final size:2
Alignment explanation
Indices: 250952--250995 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
250942 TTTTCGTTAT
*
250952 TA TA TT TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
250993 TA T
1 TA T
250996 CATAATGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:253001 original size:19 final size:20
Alignment explanation
Indices: 252979--253019 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
252969 TTTAAATAGT
**
252979 AATAAAAATGATTAAA-TAA
1 AATAAAAACAATTAAAGTAA
252998 AATAAAAACAATTAAAGTAA
1 AATAAAAACAATTAAAGTAA
253018 AA
1 AA
253020 ATAAGAGGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (20 bp):
AATAAAAACAATTAAAGTAA
Found at i:254811 original size:6 final size:6
Alignment explanation
Indices: 254790--254832 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
254780 CTTGATCAAA
* *
254790 AAAAAT -AAATT AAAAAT AAAAAT AAAAAA ATAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT A-AAAAT AAAAAT A
254833 TAACAGAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
5 4 0.13
6 22 0.71
7 5 0.16
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAAAT
Found at i:254835 original size:13 final size:13
Alignment explanation
Indices: 254788--254835 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
254778 CGCTTGATCA
*
254788 AAAAAAATAAATT
1 AAAAAAATAAAAT
*
254801 AAAAATA-AAAAT
1 AAAAAAATAAAAT
254813 AAAAAAATAAAAT
1 AAAAAAATAAAAT
*
254826 AAAAATATAA
1 AAAAAAATAA
254836 CAGAATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (13 bp):
AAAAAAATAAAAT
Found at i:265612 original size:18 final size:17
Alignment explanation
Indices: 265589--265634 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
265579 TGTTTACGAG
265589 GGAATTGAAATATGTGAA
1 GGAATTGAAATATGT-AA
* * *
265607 GGAATTGGAATCTGTCA
1 GGAATTGAAATATGTAA
265624 GGAATTGAAAT
1 GGAATTGAAAT
265635 CCAATTCCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.39, C:0.04, G:0.28, T:0.28
Consensus pattern (17 bp):
GGAATTGAAATATGTAA
Found at i:266273 original size:34 final size:34
Alignment explanation
Indices: 266205--266278 Score: 125
Period size: 33 Copynumber: 2.2 Consensus size: 34
266195 TTTTCACCCT
*
266205 AAACCCGAAACCGACCCGAATATCACACTTAAAA
1 AAACCCGAAACCGAACCGAATATCACACTTAAAA
266239 AAACCCG-AACCGAACCGAATATCACACTT-AAA
1 AAACCCGAAACCGAACCGAATATCACACTTAAAA
266271 AAACCCGA
1 AAACCCGA
266279 CCTGACCCCA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
32 10 0.26
33 21 0.55
34 7 0.18
ACGTcount: A:0.47, C:0.32, G:0.09, T:0.11
Consensus pattern (34 bp):
AAACCCGAAACCGAACCGAATATCACACTTAAAA
Found at i:267270 original size:51 final size:51
Alignment explanation
Indices: 267207--267321 Score: 142
Period size: 51 Copynumber: 2.3 Consensus size: 51
267197 AGTATTTGAT
* *
267207 TTATTATTTTATTAGAAATTAAAATA-GAGTTAAAACATTATATTTAGTTAA
1 TTATTATTTTATTAGAAACTAAAATAGGA-TCAAAACATTATATTTAGTTAA
* ** * *
267258 TTATTATTTTATTAGGAACTAGGATAGGATCAAAACATTATTTTTAGTTTA
1 TTATTATTTTATTAGAAACTAAAATAGGATCAAAACATTATATTTAGTTAA
*
267309 TTGTTATTTTATT
1 TTATTATTTTATT
267322 CATTTGTTGC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
51 53 0.96
52 2 0.04
ACGTcount: A:0.37, C:0.03, G:0.10, T:0.49
Consensus pattern (51 bp):
TTATTATTTTATTAGAAACTAAAATAGGATCAAAACATTATATTTAGTTAA
Found at i:268860 original size:16 final size:16
Alignment explanation
Indices: 268835--268870 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
268825 TTTAGATATG
*
268835 AAAA-TTTGGATATCT
1 AAAATTTTGGATACCT
268850 AAAATTTTGGATACCT
1 AAAATTTTGGATACCT
268866 AAAAT
1 AAAAT
268871 AATAATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (16 bp):
AAAATTTTGGATACCT
Found at i:269930 original size:16 final size:17
Alignment explanation
Indices: 269911--269942 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
269901 TACTACCATA
269911 ATATTAT-TTTTATATT
1 ATATTATATTTTATATT
269927 ATATTATATTTTATAT
1 ATATTATATTTTATAT
269943 AAATAATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:273619 original size:35 final size:35
Alignment explanation
Indices: 273571--273648 Score: 122
Period size: 35 Copynumber: 2.2 Consensus size: 35
273561 CATAATTATT
*
273571 AATTACATTCTAAACCCT-AAATTCTAAAATACTTC
1 AATTACATTCTAAA-CCTAAAATTCCAAAATACTTC
*
273606 AGTTACATTCTAAACCTAAAATTCCAAAATACTTC
1 AATTACATTCTAAACCTAAAATTCCAAAATACTTC
273641 AATTACAT
1 AATTACAT
273649 ACCCAACCAC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
34 3 0.08
35 36 0.92
ACGTcount: A:0.44, C:0.22, G:0.01, T:0.33
Consensus pattern (35 bp):
AATTACATTCTAAACCTAAAATTCCAAAATACTTC
Found at i:273663 original size:35 final size:35
Alignment explanation
Indices: 273571--273664 Score: 93
Period size: 35 Copynumber: 2.7 Consensus size: 35
273561 CATAATTATT
* * *
273571 AATTACATTCTAAACCCT-AAATTCTAAAATACTTC
1 AATTACATACCAAA-CCTAAAATTCCAAAATACTTC
* * *
273606 AGTTACATTCTAAACCTAAAATTCCAAAATACTTC
1 AATTACATACCAAACCTAAAATTCCAAAATACTTC
*
273641 AATTACATACCCAACC-ACAAATTC
1 AATTACATACCAAACCTA-AAATTC
273665 ATAATTCATT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
34 4 0.08
35 47 0.92
ACGTcount: A:0.44, C:0.26, G:0.01, T:0.30
Consensus pattern (35 bp):
AATTACATACCAAACCTAAAATTCCAAAATACTTC
Found at i:274139 original size:141 final size:141
Alignment explanation
Indices: 273833--274244 Score: 662
Period size: 141 Copynumber: 2.9 Consensus size: 141
273823 CAATTCAGTT
*
273833 TAAAATAGTTAACTTGAAATTTTTTCGATTGAGTTTATAAAATTTAAATCAAGTTGAATTGAATT
1 TAAAATAGTTAACTTGAAATTTTTTCAATTGAGTTTATAAAATTTAAATCAAGTTGAATTGAATT
273898 TTTGAGTTTCTGTTTAAATTTAATTATAAATATTATCATATTATAATATTATTTGATTCTAATTC
66 TTTGAGTTTCTGTTTAAATTTAATTATAAATATTATCATATTATAATATTATTTGATTCTAATTC
*
273963 AATTTAGTTTA
131 AATTTAATTTA
*
273974 TAAAATAGTTAACTTGAAATTTTTTCAATTGATTTTATAAAATTTAAATCAAGTTGAATTGAATT
1 TAAAATAGTTAACTTGAAATTTTTTCAATTGAGTTTATAAAATTTAAATCAAGTTGAATTGAATT
274039 TTTGAGTTTCTGTTTAAATTTTAATTATAAATATTATCATATTATAATATTATTTGATTCTAATT
66 TTTGAGTTTCTGTTTAAA-TTTAATTATAAATATTATCATATTATAATATTATTTGATTCTAATT
274104 CAATTTAATTTA
130 CAATTTAATTTA
** * *
274116 TAAAATAGTTGCCTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGACTTGAAT
1 TAAAATAGTTAACTTGAAATTTTTTC-AATTGAGTTTATAAAATTTAAATCAA---G--TTGAAT
* * *
274181 TGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATTTGAT
60 TGAATTTTTGAGTTTCTGTTTAAATTTAATTATAAATA-TTATCATATTATAATATTATTTGAT
274245 CATATACAAT
Statistics
Matches: 252, Mismatches: 11, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
141 81 0.32
142 80 0.32
143 24 0.10
146 1 0.00
147 14 0.06
148 52 0.21
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.48
Consensus pattern (141 bp):
TAAAATAGTTAACTTGAAATTTTTTCAATTGAGTTTATAAAATTTAAATCAAGTTGAATTGAATT
TTTGAGTTTCTGTTTAAATTTAATTATAAATATTATCATATTATAATATTATTTGATTCTAATTC
AATTTAATTTA
Found at i:275087 original size:19 final size:20
Alignment explanation
Indices: 275061--275136 Score: 102
Period size: 20 Copynumber: 3.8 Consensus size: 20
275051 GAATGCTCGA
275061 ATGGTATCGATACCCCCCAT
1 ATGGTATCGATACCCCCCAT
275081 A-GGTATCGATA-CCCCCAT
1 ATGGTATCGATACCCCCCAT
*
275099 GAAATGGTATCGATACCCCTCAT
1 ---ATGGTATCGATACCCCCCAT
275122 ATGGTATCGATACCC
1 ATGGTATCGATACCC
275137 TAAGACATAT
Statistics
Matches: 50, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
18 7 0.14
19 10 0.20
20 16 0.32
21 1 0.02
22 10 0.20
23 6 0.12
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (20 bp):
ATGGTATCGATACCCCCCAT
Found at i:276603 original size:3 final size:3
Alignment explanation
Indices: 276561--276619 Score: 50
Period size: 3 Copynumber: 20.0 Consensus size: 3
276551 GATGATGAAG
* * * *
276561 GAA GAT GAA GAA -AGA GAA G-A GAA GAA AAA CAA GAA AAA GAA GAA
1 GAA GAA GAA GAA GA-A GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
276605 GAA GGA GAA GAA GAA
1 GAA GAA GAA GAA GAA
276620 TGAGGATCTA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
2 3 0.07
3 40 0.91
4 1 0.02
ACGTcount: A:0.66, C:0.02, G:0.31, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:280537 original size:23 final size:23
Alignment explanation
Indices: 280509--280590 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 23
280499 CCCTAAGACT
*
280509 GGTATCGATTCCCCCTTTGAATA
1 GGTATCGATACCCCCTTTGAATA
*
280532 GGTATCGATA-CCCCTGT-AATA
1 GGTATCGATACCCCCTTTGAATA
* *
280553 GGTATCGATACCATCC-TTGAATG
1 GGTATCGATACC-CCCTTTGAATA
280576 GGTATCGATACCCCC
1 GGTATCGATACCCCC
280591 ATGATAGTAC
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
21 14 0.28
22 10 0.20
23 26 0.52
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (23 bp):
GGTATCGATACCCCCTTTGAATA
Found at i:281351 original size:12 final size:12
Alignment explanation
Indices: 281334--281358 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
281324 CAAATCCAAT
281334 TCCTCAAATTCC
1 TCCTCAAATTCC
281346 TCCTCAAATTCC
1 TCCTCAAATTCC
281358 T
1 T
281359 GATTCCCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.40, G:0.00, T:0.36
Consensus pattern (12 bp):
TCCTCAAATTCC
Found at i:283337 original size:20 final size:20
Alignment explanation
Indices: 283273--283346 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
283263 TAATGCTCGA
*
283273 ATGGTACCGATACCCC-CAT
1 ATGGTATCGATACCCCTCAT
*
283292 AT-GTAT-GATATCTCCATGCA-
1 ATGGTATCGATA-C-CCCT-CAT
283312 ATGGTATCGATACCCCTCAT
1 ATGGTATCGATACCCCTCAT
283332 ATGGTATCGATACCC
1 ATGGTATCGATACCC
283347 TAAGGTAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
17 4 0.09
18 4 0.09
19 6 0.13
20 20 0.44
21 7 0.16
22 4 0.09
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.28
Consensus pattern (20 bp):
ATGGTATCGATACCCCTCAT
Found at i:285951 original size:17 final size:17
Alignment explanation
Indices: 285929--285980 Score: 104
Period size: 17 Copynumber: 3.1 Consensus size: 17
285919 AAATGATAAG
285929 AAAACCTACTATTCCAA
1 AAAACCTACTATTCCAA
285946 AAAACCTACTATTCCAA
1 AAAACCTACTATTCCAA
285963 AAAACCTACTATTCCAA
1 AAAACCTACTATTCCAA
285980 A
1 A
285981 TGGTTATGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAACCTACTATTCCAA
Found at i:286352 original size:24 final size:24
Alignment explanation
Indices: 286323--286415 Score: 109
Period size: 23 Copynumber: 4.0 Consensus size: 24
286313 ACCAAAGTGC
*
286323 CACGTAGAATTTGTCCCGAAGGAT
1 CACGTAGAATTTGTCCCGAAGGAA
* * *
286347 CGCGTAAAATTTGTCCCGAAGGAC
1 CACGTAGAATTTGTCCCGAAGGAA
*
286371 CACGTAGAA-TTGTCCCGAATGAA
1 CACGTAGAATTTGTCCCGAAGGAA
* *
286394 AACATAG-ATTTGTCCCGAAGGA
1 CACGTAGAATTTGTCCCGAAGGA
286416 CAACATAGAT
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
22 1 0.02
23 29 0.50
24 28 0.48
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.23
Consensus pattern (24 bp):
CACGTAGAATTTGTCCCGAAGGAA
Found at i:286387 original size:23 final size:23
Alignment explanation
Indices: 286322--286439 Score: 101
Period size: 23 Copynumber: 5.0 Consensus size: 23
286312 CACCAAAGTG
286322 CCACGTAGAATTTGTCCCGAAGGA
1 CCACGTAGAA-TTGTCCCGAAGGA
* * *
286346 TCGCGTAAAATTTGTCCCGAAGGA
1 CCACGTAGAA-TTGTCCCGAAGGA
*
286370 CCACGTAGAATTGTCCCGAATGA
1 CCACGTAGAATTGTCCCGAAGGA
** * *
286393 AAACATAGATTTGTCCCGAAGGA
1 CCACGTAGAATTGTCCCGAAGGA
* * * * *
286416 CAACATAGATTTATTCCGAAGGA
1 CCACGTAGAATTGTCCCGAAGGA
286439 C
1 C
286440 TGTGTAGAAC
Statistics
Matches: 79, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
23 51 0.65
24 28 0.35
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (23 bp):
CCACGTAGAATTGTCCCGAAGGA
Found at i:287797 original size:29 final size:30
Alignment explanation
Indices: 287742--287801 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
287732 GTTTAAAAAT
287742 GAATTTTAAATTCATGTCCTGCAAAAAAGA
1 GAATTTTAAATTCATGTCCTGCAAAAAAGA
287772 GAATTTTAAATTCATGTCCTGCAAAAAAGA
1 GAATTTTAAATTCATGTCCTGCAAAAAAGA
287802 TTAATATACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (30 bp):
GAATTTTAAATTCATGTCCTGCAAAAAAGA
Found at i:289195 original size:28 final size:28
Alignment explanation
Indices: 289155--289211 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
289145 CCAAAGACTG
289155 GAGAACTTCATGAGCTTTAGACATGCAA
1 GAGAACTTCATGAGCTTTAGACATGCAA
289183 GAGAACTTCATGAGCTTTAGACATGCAA
1 GAGAACTTCATGAGCTTTAGACATGCAA
289211 G
1 G
289212 GGTTCATACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.25
Consensus pattern (28 bp):
GAGAACTTCATGAGCTTTAGACATGCAA
Found at i:289564 original size:20 final size:21
Alignment explanation
Indices: 289518--289564 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
289508 GATGACATTG
289518 TTAATTTTAAGATTAAATAAA
1 TTAATTTTAAGATTAAATAAA
*
289539 TT-ATTTTAA-AGTTCAA-AAA
1 TTAATTTTAAGA-TTAAATAAA
289558 TTAATTT
1 TTAATTT
289565 AAAATGAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 6 0.26
20 15 0.65
21 2 0.09
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (21 bp):
TTAATTTTAAGATTAAATAAA
Found at i:290213 original size:32 final size:32
Alignment explanation
Indices: 290172--290249 Score: 156
Period size: 32 Copynumber: 2.4 Consensus size: 32
290162 AATAATTACC
290172 ATCTTAATGTTACTTTTTCTTTTTATATAGAG
1 ATCTTAATGTTACTTTTTCTTTTTATATAGAG
290204 ATCTTAATGTTACTTTTTCTTTTTATATAGAG
1 ATCTTAATGTTACTTTTTCTTTTTATATAGAG
290236 ATCTTAATGTTACT
1 ATCTTAATGTTACT
290250 CTTATATCTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.26, C:0.10, G:0.09, T:0.55
Consensus pattern (32 bp):
ATCTTAATGTTACTTTTTCTTTTTATATAGAG
Found at i:290497 original size:17 final size:17
Alignment explanation
Indices: 290475--290511 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
290465 CGATTTTGAG
290475 CTCGATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
290492 CTCGATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
290509 CTC
1 CTC
290512 AAACTCGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.24
Consensus pattern (17 bp):
CTCGATTCAAGCTCGAA
Found at i:290766 original size:37 final size:37
Alignment explanation
Indices: 290718--290829 Score: 190
Period size: 37 Copynumber: 3.1 Consensus size: 37
290708 AAAGTTTACA
290718 AAATATGACAACACATCTAAATTTATAAAAAGATGAC
1 AAATATGACAACACATCTAAATTTATAAAAAGATGAC
290755 AAATATGACAACACATCTAAATTTATAAAAAGATGAC
1 AAATATGACAACACATCTAAATTTATAAAAAGATGAC
* * *
290792 AAATATGACAACATATCCAAATTTAT-ACAAGATGAC
1 AAATATGACAACACATCTAAATTTATAAAAAGATGAC
290828 AA
1 AA
290830 TATTTTCCTT
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 11 0.15
37 61 0.85
ACGTcount: A:0.54, C:0.14, G:0.08, T:0.24
Consensus pattern (37 bp):
AAATATGACAACACATCTAAATTTATAAAAAGATGAC
Found at i:290981 original size:30 final size:32
Alignment explanation
Indices: 290924--290991 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 32
290914 CCAGTTAAGC
290924 TTACTTACAAAAGATGGCAGTAACATGT-CAAGT
1 TTACTTACAAAAGATGGCA--AACATGTCCAAGT
*
290957 TTACTTACAAAAGATTGC-AACATGTCCAAGT
1 TTACTTACAAAAGATGGCAAACATGTCCAAGT
290988 TTAC
1 TTAC
290992 AAAAGATGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
30 7 0.21
31 9 0.27
33 17 0.52
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (32 bp):
TTACTTACAAAAGATGGCAAACATGTCCAAGT
Found at i:301372 original size:25 final size:25
Alignment explanation
Indices: 301341--301460 Score: 231
Period size: 25 Copynumber: 4.8 Consensus size: 25
301331 CAGTTGGGGA
301341 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
301366 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
301391 TTAGGGTTTGAAACCCTAAACTGATT
1 TTAGGGTTTGAAACCCTAAACTGA-T
301417 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
301442 TTAGGGTTTGAAACCCTAA
1 TTAGGGTTTGAAACCCTAA
301461 TCTGGTGGGT
Statistics
Matches: 94, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
25 69 0.73
26 25 0.27
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAACTGAT
Found at i:301441 original size:51 final size:50
Alignment explanation
Indices: 301341--301460 Score: 231
Period size: 51 Copynumber: 2.4 Consensus size: 50
301331 CAGTTGGGGA
301341 TTAGGGTTTGAAACCCTAAACTGATTTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGATTTAGGGTTTGAAACCCTAAACTGAT
301391 TTAGGGTTTGAAACCCTAAACTGATTTTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGA-TTTAGGGTTTGAAACCCTAAACTGAT
301442 TTAGGGTTTGAAACCCTAA
1 TTAGGGTTTGAAACCCTAA
301461 TCTGGTGGGT
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
50 24 0.35
51 45 0.65
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Consensus pattern (50 bp):
TTAGGGTTTGAAACCCTAAACTGATTTAGGGTTTGAAACCCTAAACTGAT
Found at i:301557 original size:3 final size:3
Alignment explanation
Indices: 301543--301583 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
301533 TAATATGTAA
301543 AAT AATT AAT AAT AAT AATT AAT AAT AAT AA- AAT AA- AAT AA
1 AAT AA-T AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AA
301584 ATAAAAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 4 0.12
3 24 0.71
4 6 0.18
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:301561 original size:13 final size:13
Alignment explanation
Indices: 301543--301573 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
301533 TAATATGTAA
301543 AATAATTAATAAT
1 AATAATTAATAAT
301556 AATAATTAATAAT
1 AATAATTAATAAT
301569 AATAA
1 AATAA
301574 AATAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AATAATTAATAAT
Found at i:301582 original size:13 final size:14
Alignment explanation
Indices: 301540--301594 Score: 60
Period size: 14 Copynumber: 3.8 Consensus size: 14
301530 ATGTAATATG
301540 TAAAATAATTAATAA
1 TAAAATAA-TAATAA
301555 TAATAATTAATAATAA
1 TAA-AA-TAATAATAA
301571 TAAAATAA-AATAAA
1 TAAAATAATAAT-AA
301585 TAAAA-AATAA
1 TAAAATAATAA
301595 ATATAAAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
13 5 0.14
14 12 0.33
15 5 0.14
16 11 0.31
17 3 0.08
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAAATAATAATAA
Found at i:301600 original size:17 final size:17
Alignment explanation
Indices: 301540--301601 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 17
301530 ATGTAATATG
*
301540 TAAAATAATTAATAATAA
1 TAAAATAAATAATAA-AA
301558 TAATTAAT-AATAATAAAA
1 TAA--AATAAATAATAAAA
301576 TAAAATAAATAA-AAAA
1 TAAAATAAATAATAAAA
301592 TAAATATAAA
1 TAAA-ATAAA
301602 AGACCCGGAC
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
16 11 0.28
17 10 0.26
18 8 0.21
19 7 0.18
20 3 0.08
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAATAAATAATAAAA
Found at i:302126 original size:94 final size:91
Alignment explanation
Indices: 301831--302137 Score: 374
Period size: 94 Copynumber: 3.3 Consensus size: 91
301821 GGTCAAGGGA
* * * *
301831 TGACACGACTCATACGCGATGAAGAGTTCTGGTCATCTTTAAGAAGGGTGATAACTCGGTTCCTA
1 TGACACGGCTCATACGTGATGAAGA-ATCTGGCCATC-TT-AGAAGGGTGATAACTCGGTTCCTA
*
301896 CGTGATGAGGACGGCTGATTATC--AGGT
63 CGTGATGAGGACGGCTGGTTATCTAAGGT
* *
301923 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATC-TA-AA-GGTGATAACACGGTTCCTACG
1 TGACACGGCTCATACGTGATGAAGA-ATCTGGCCATCTTAGAAGGGTGATAACTCGGTTCCTACG
*
301985 TGATGAGGACGGCTGGTTATCTACGGT
65 TGATGAGGACGGCTGGTTATCTAAGGT
*
302012 TGACACGGCTCATACATGATGAAGAACTCTGGCCATCGTTAGGAAGGGTGATAACTCGGTTCCTA
1 TGACACGGCTCATACGTGATGAAGAA-TCTGGCCATC-TTA-GAAGGGTGATAACTCGGTTCCTA
*
302077 CGTGATGAGGACGGCTGGTTATCCTAATGT
63 CGTGATGAGGACGGCTGGTTAT-CTAAGGT
* * *
302107 TGACAC-TCTCCTACGTGATGAGGAGATCTGG
1 TGACACGGCTCATACGTGATGAAGA-ATCTGG
302138 TCAGTTGATG
Statistics
Matches: 188, Mismatches: 17, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
87 40 0.21
88 3 0.02
89 37 0.20
90 1 0.01
91 2 0.01
92 32 0.17
93 2 0.01
94 59 0.31
95 12 0.06
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (91 bp):
TGACACGGCTCATACGTGATGAAGAATCTGGCCATCTTAGAAGGGTGATAACTCGGTTCCTACGT
GATGAGGACGGCTGGTTATCTAAGGT
Found at i:316565 original size:25 final size:25
Alignment explanation
Indices: 316534--316653 Score: 231
Period size: 25 Copynumber: 4.8 Consensus size: 25
316524 CAGTTGGGGA
316534 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
316559 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
316584 TTAGGGTTTGAAACCCTAAACTGATT
1 TTAGGGTTTGAAACCCTAAACTGA-T
316610 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
316635 TTAGGGTTTGAAACCCTAA
1 TTAGGGTTTGAAACCCTAA
316654 TCTGGTGGGT
Statistics
Matches: 94, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
25 69 0.73
26 25 0.27
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAACTGAT
Found at i:316634 original size:51 final size:50
Alignment explanation
Indices: 316534--316653 Score: 231
Period size: 51 Copynumber: 2.4 Consensus size: 50
316524 CAGTTGGGGA
316534 TTAGGGTTTGAAACCCTAAACTGATTTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGATTTAGGGTTTGAAACCCTAAACTGAT
316584 TTAGGGTTTGAAACCCTAAACTGATTTTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGA-TTTAGGGTTTGAAACCCTAAACTGAT
316635 TTAGGGTTTGAAACCCTAA
1 TTAGGGTTTGAAACCCTAA
316654 TCTGGTGGGT
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
50 24 0.35
51 45 0.65
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Consensus pattern (50 bp):
TTAGGGTTTGAAACCCTAAACTGATTTAGGGTTTGAAACCCTAAACTGAT
Found at i:316750 original size:3 final size:3
Alignment explanation
Indices: 316736--316776 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
316726 TAATATGTAA
316736 AAT AATT AAT AAT AAT AATT AAT AAT AAT AA- AAT AA- AAT AA
1 AAT AA-T AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AA
316777 ATAAAAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 4 0.12
3 24 0.71
4 6 0.18
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:316754 original size:13 final size:13
Alignment explanation
Indices: 316736--316766 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
316726 TAATATGTAA
316736 AATAATTAATAAT
1 AATAATTAATAAT
316749 AATAATTAATAAT
1 AATAATTAATAAT
316762 AATAA
1 AATAA
316767 AATAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AATAATTAATAAT
Found at i:316775 original size:13 final size:14
Alignment explanation
Indices: 316733--316787 Score: 60
Period size: 14 Copynumber: 3.8 Consensus size: 14
316723 ATGTAATATG
316733 TAAAATAATTAATAA
1 TAAAATAA-TAATAA
316748 TAATAATTAATAATAA
1 TAA-AA-TAATAATAA
316764 TAAAATAA-AATAAA
1 TAAAATAATAAT-AA
316778 TAAAA-AATAA
1 TAAAATAATAA
316788 ATATAAAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
13 5 0.14
14 12 0.33
15 5 0.14
16 11 0.31
17 3 0.08
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAAATAATAATAA
Found at i:316793 original size:17 final size:17
Alignment explanation
Indices: 316733--316794 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 17
316723 ATGTAATATG
*
316733 TAAAATAATTAATAATAA
1 TAAAATAAATAATAA-AA
316751 TAATTAAT-AATAATAAAA
1 TAA--AATAAATAATAAAA
316769 TAAAATAAATAA-AAAA
1 TAAAATAAATAATAAAA
316785 TAAATATAAA
1 TAAA-ATAAA
316795 AGACCCGGAC
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
16 11 0.28
17 10 0.26
18 8 0.21
19 7 0.18
20 3 0.08
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAATAAATAATAAAA
Found at i:318542 original size:21 final size:21
Alignment explanation
Indices: 318516--318557 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
318506 ATGCTCCACA
318516 TCTAGTT-CTTGAACATCTATT
1 TCTAGTTGCTTGAACAT-TATT
*
318537 TCTAGTTGCTTGGACATTATT
1 TCTAGTTGCTTGAACATTATT
318558 GTGATTGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.48
Consensus pattern (21 bp):
TCTAGTTGCTTGAACATTATT
Found at i:320880 original size:2 final size:2
Alignment explanation
Indices: 320867--320912 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
320857 CCATGGGTTA
*
320867 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
320909 AT AT
1 AT AT
320913 TAAAATGTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:328818 original size:23 final size:23
Alignment explanation
Indices: 328792--328841 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
328782 ATCATGACTA
328792 TTCATGAAAAATAATTAAGTCAT
1 TTCATGAAAAATAATTAAGTCAT
* **
328815 TTCATGAAAAATAGTTATTTCAT
1 TTCATGAAAAATAATTAAGTCAT
328838 TTCA
1 TTCA
328842 CCCCAAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (23 bp):
TTCATGAAAAATAATTAAGTCAT
Found at i:328901 original size:21 final size:22
Alignment explanation
Indices: 328867--328909 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
328857 CTTTTCATGT
*
328867 TAATCTTTTGATCAAAAGGTTA
1 TAATCTTTTAATCAAAAGGTTA
*
328889 TAAT-TTTTAATCAAATGGTTA
1 TAATCTTTTAATCAAAAGGTTA
328910 AGTCATTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (22 bp):
TAATCTTTTAATCAAAAGGTTA
Found at i:333171 original size:11 final size:11
Alignment explanation
Indices: 333151--333216 Score: 78
Period size: 11 Copynumber: 6.0 Consensus size: 11
333141 GTTCACAAAC
*
333151 ATGTTTGTTTA
1 ATGTTCGTTTA
*
333162 GTGTTCGTTTA
1 ATGTTCGTTTA
333173 ATGTTCGTTTA
1 ATGTTCGTTTA
* *
333184 ATGTTTGCTTA
1 ATGTTCGTTTA
*
333195 ATGTTCATTTA
1 ATGTTCGTTTA
*
333206 GTGTTCGTTTA
1 ATGTTCGTTTA
333217 TTTTTTGTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 45 1.00
ACGTcount: A:0.17, C:0.08, G:0.20, T:0.56
Consensus pattern (11 bp):
ATGTTCGTTTA
Found at i:333189 original size:33 final size:33
Alignment explanation
Indices: 333151--333227 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
333141 GTTCACAAAC
* *
333151 ATGTTTGTTTAGTGTTCGTTTAATGTTCGTTTA
1 ATGTTTGTTTAATGTTCATTTAATGTTCGTTTA
* *
333184 ATGTTTGCTTAATGTTCATTTAGTGTTCGTTTA
1 ATGTTTGTTTAATGTTCATTTAATGTTCGTTTA
* *
333217 TTTTTTGTTTA
1 ATGTTTGTTTA
333228 TCATATATTC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.16, C:0.06, G:0.18, T:0.60
Consensus pattern (33 bp):
ATGTTTGTTTAATGTTCATTTAATGTTCGTTTA
Found at i:333227 original size:22 final size:22
Alignment explanation
Indices: 333151--333216 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
333141 GTTCACAAAC
*
333151 ATGTTTGTTTAGTGTTCGTTTA
1 ATGTTCGTTTAGTGTTCGTTTA
* * *
333173 ATGTTCGTTTAATGTTTGCTTA
1 ATGTTCGTTTAGTGTTCGTTTA
*
333195 ATGTTCATTTAGTGTTCGTTTA
1 ATGTTCGTTTAGTGTTCGTTTA
333217 TTTTTTGTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.17, C:0.08, G:0.20, T:0.56
Consensus pattern (22 bp):
ATGTTCGTTTAGTGTTCGTTTA
Found at i:334435 original size:20 final size:20
Alignment explanation
Indices: 334412--334558 Score: 231
Period size: 20 Copynumber: 7.3 Consensus size: 20
334402 GAATACGTAA
*
334412 ATCGCAACGCGAATCTGACT
1 ATCGCAACGCGATTCTGACT
334432 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
334452 ATCGCAACGAGATTCTAACT
1 ATCGCAACGCGATTCTGACT
* *
334472 ATCGCAACGAGATTATGACT
1 ATCGCAACGCGATTCTGACT
* *
334492 ATCGCAATGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
334512 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
334532 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
334552 ATCGCAA
1 ATCGCAA
334559 TACTGAATTT
Statistics
Matches: 118, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 118 1.00
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:334559 original size:60 final size:60
Alignment explanation
Indices: 334352--334559 Score: 242
Period size: 60 Copynumber: 3.5 Consensus size: 60
334342 GTTTCCAGAT
* ** * * *
334352 TCGCAACGCGATTCTGACTATCGCATTGCGATT-TTCCTAATTCGCAATGCGAATAC-GTA-AA
1 TCGCAACGCGATTCTGACTATCGCAATGCGATTCTGACT-A-TCGCAACGCG-ATTCTG-ACTA
* * * *
334413 TCGCAACGCGAATCTGACTATCGCAACGCGATTCTGACTATCGCAACGAGATTCTAACTA
1 TCGCAACGCGATTCTGACTATCGCAATGCGATTCTGACTATCGCAACGCGATTCTGACTA
* * *
334473 TCGCAACGAGATTATGACTATCGCAATGAGATTCTGACTATCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTATCGCAATGCGATTCTGACTATCGCAACGCGATTCTGACTA
334533 TCGCAACGCGATTCTGACTATCGCAAT
1 TCGCAACGCGATTCTGACTATCGCAAT
334560 ACTGAATTTC
Statistics
Matches: 125, Mismatches: 19, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
59 4 0.03
60 87 0.70
61 31 0.25
62 3 0.02
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (60 bp):
TCGCAACGCGATTCTGACTATCGCAATGCGATTCTGACTATCGCAACGCGATTCTGACTA
Found at i:335427 original size:24 final size:24
Alignment explanation
Indices: 335400--335453 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
335390 GTATTCGAAA
335400 TTTGATATTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* * *
335424 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
335448 TTTGAT
1 TTTGAT
335454 GATTTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:337892 original size:20 final size:20
Alignment explanation
Indices: 337867--337960 Score: 145
Period size: 20 Copynumber: 4.7 Consensus size: 20
337857 GACATTCATT
337867 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
* *
337887 TGACTATCTCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
337907 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
*
337927 TGACTATCGCAACGCGAAAA
1 TGACTATCGCAACGCGGAAA
337947 TGACTATCGCAACG
1 TGACTATCGCAACG
337961 AGAGAATCGC
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
20 65 0.96
21 3 0.04
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:337971 original size:14 final size:14
Alignment explanation
Indices: 337952--338005 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
337942 GAAAATGACT
337952 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
337966 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
337985 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
337999 ATCGCAA
1 ATCGCAA
338006 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:337989 original size:33 final size:34
Alignment explanation
Indices: 337932--338026 Score: 156
Period size: 33 Copynumber: 2.8 Consensus size: 34
337922 GGAAATGACT
* **
337932 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
337966 ATCGCAATGCG-AAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
337999 ATCGCAATGCGAAAATGAAAATCGCAAC
1 ATCGCAATGCGAAAATGAAAATCGCAAC
338027 ACGAATTTAG
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
Found at i:338083 original size:14 final size:14
Alignment explanation
Indices: 338064--338117 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
338054 CATATTCGCA
338064 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
338078 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
338095 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
338111 TTGCGAT
1 TTGCGAT
338118 AGTCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:338100 original size:33 final size:33
Alignment explanation
Indices: 338042--338137 Score: 147
Period size: 33 Copynumber: 2.8 Consensus size: 33
338032 TTTAGTTTTG
338042 CGTTGCGATTTTCATATTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCAT-TTCGCATTGCGATTCTCT
338076 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
** *
338109 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
338138 AATCTGTTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 33 0.57
34 25 0.43
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.42
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:339762 original size:42 final size:42
Alignment explanation
Indices: 339683--339775 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
339673 CCTCTTCAAC
* * *
339683 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
339725 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAT
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
339767 GATGACAGG
1 GATGACAGG
339776 TGAGTCGGGA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.16, G:0.40, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:340282 original size:20 final size:20
Alignment explanation
Indices: 340259--340327 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
340249 CTTAAAATCA
340259 CAACGCGAAAATGACTATCG
1 CAACGCGAAAATGACTATCG
*
340279 CAACGCGAAAATGACTATAG
1 CAACGCGAAAATGACTATCG
* **
340299 CAATGCGAATTTGACTATCG
1 CAACGCGAAAATGACTATCG
*
340319 CAATGCGAA
1 CAACGCGAA
340328 TTTGACTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (20 bp):
CAACGCGAAAATGACTATCG
Found at i:340328 original size:20 final size:20
Alignment explanation
Indices: 340270--340336 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
340260 AACGCGAAAA
* **
340270 TGACTATCGCAACGCGAAAA
1 TGACTATCGCAATGCGAATT
*
340290 TGACTATAGCAATGCGAATT
1 TGACTATCGCAATGCGAATT
340310 TGACTATCGCAATGCGAATT
1 TGACTATCGCAATGCGAATT
340330 TGACTAT
1 TGACTAT
340337 TGTAATAAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (20 bp):
TGACTATCGCAATGCGAATT
Found at i:340394 original size:20 final size:20
Alignment explanation
Indices: 340369--340525 Score: 135
Period size: 20 Copynumber: 8.5 Consensus size: 20
340359 GATTCTTTCG
* **
340369 TTGCGATAATCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
340389 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
340409 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
340429 TTGCGATAGTCATTTTTGCG
1 TTGCGATAGTCATTTTCGCA
340449 TTGCGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
**
340463 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
340482 TTGCGAT--TC----TCTCA
1 TTGCGATAGTCATTTTCGCA
340496 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
340516 TTGCGATAGT
1 TTGCGATAGT
340526 AAACTATTCT
Statistics
Matches: 116, Mismatches: 7, Indels: 28
0.77 0.05 0.19
Matches are distributed among these distances:
14 18 0.16
16 8 0.07
17 6 0.05
18 1 0.01
19 7 0.06
20 76 0.66
ACGTcount: A:0.19, C:0.18, G:0.20, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:342443 original size:20 final size:20
Alignment explanation
Indices: 342420--342475 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
342410 TCTGAAACTT
342420 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
*
342440 AAAATCGCAACACAAAAATG
1 AAAATCGCAACACGAAAATG
** *
342460 ACTATCGCAACGCGAA
1 AAAATCGCAACACGAA
342476 TTTGACTATC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.52, C:0.23, G:0.14, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:342531 original size:33 final size:34
Alignment explanation
Indices: 342422--342535 Score: 97
Period size: 40 Copynumber: 3.2 Consensus size: 34
342412 TGAAACTTAA
* *
342422 AATCGCAACACGAAAATGAAAATCGCAACACAAAAATG
1 AATCGCAACGCGAATATGAAAATCGCAACAC---AA-G
* ** *
342460 ACTATCGCAACGCGAATTTGACTATCGCAACGCAAG
1 A--ATCGCAACGCGAATATGAAAATCGCAACACAAG
342496 AATCGCAACGCGAA-ATGAAAATCGCAACTAC-AG
1 AATCGCAACGCGAATATGAAAATCGCAAC-ACAAG
342529 AATCGCA
1 AATCGCA
342536 TTGCGATAGT
Statistics
Matches: 63, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
33 20 0.32
34 14 0.22
36 2 0.03
37 2 0.03
38 1 0.02
40 24 0.38
ACGTcount: A:0.45, C:0.25, G:0.17, T:0.14
Consensus pattern (34 bp):
AATCGCAACGCGAATATGAAAATCGCAACACAAG
Found at i:343121 original size:20 final size:20
Alignment explanation
Indices: 343105--343190 Score: 163
Period size: 20 Copynumber: 4.3 Consensus size: 20
343095 CAGATTCACG
343105 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
343125 TTGCGATTTACGTATTCGTA
1 TTGCGATTTACGTATTCGCA
343145 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
343165 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
343185 TTGCGA
1 TTGCGA
343191 ATTAGGAAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.41
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:343212 original size:21 final size:21
Alignment explanation
Indices: 343188--343232 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
343178 ATTCGCATTG
343188 CGAATTAGGAAAATCGCAACA
1 CGAATTAGGAAAATCGCAACA
* *
343209 CGAATTTGGAAAATCGCAATA
1 CGAATTAGGAAAATCGCAACA
343230 CGA
1 CGA
343233 TAGTAGAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (21 bp):
CGAATTAGGAAAATCGCAACA
Found at i:346550 original size:93 final size:93
Alignment explanation
Indices: 346391--346564 Score: 285
Period size: 93 Copynumber: 1.9 Consensus size: 93
346381 ATCTTTCCCT
* * * *
346391 TGGAAATGTTGATCCCTCGAGTGAGGCGTCGCTGATTCGAAATGTCGTGAATCGAACAAATATTG
1 TGGAAATGTTAATCCCTCAAGTAAGGCGTCGCTGATTCGAAATGTCGTGAATCGAACAAAGATTG
346456 AACAAGTTCTTCATTATGAGTTCTCTAC
66 AACAAGTTCTTCATTATGAGTTCTCTAC
* * *
346484 TGGAAATGTTAATCCCTCAAGTAAGGCGTTGCTGATTCGAAATGTCGTGAATCGAGCAAAGGTTG
1 TGGAAATGTTAATCCCTCAAGTAAGGCGTCGCTGATTCGAAATGTCGTGAATCGAACAAAGATTG
346549 AACAAGTTCTTCATTA
66 AACAAGTTCTTCATTA
346565 CGAACTTCTT
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.30
Consensus pattern (93 bp):
TGGAAATGTTAATCCCTCAAGTAAGGCGTCGCTGATTCGAAATGTCGTGAATCGAACAAAGATTG
AACAAGTTCTTCATTATGAGTTCTCTAC
Found at i:346834 original size:36 final size:36
Alignment explanation
Indices: 346794--346903 Score: 85
Period size: 39 Copynumber: 3.0 Consensus size: 36
346784 AAGCAAGATT
346794 AAATTTGTTTTAAGAAAAACAATCTTGAGTGAAATA
1 AAATTTGTTTTAAGAAAAACAATCTTGAGTGAAATA
** *** * ** * * *
346830 AAATTTATTGTTTCGAGTGGAACTATCTCAAGCGAGATG
1 AAA--T-TTGTTTTAAGAAAAACAATCTTGAGTGAAATA
*
346869 AAATTTGTTTTAAGAAAAACAATCTTGTGTGAAAT
1 AAATTTGTTTTAAGAAAAACAATCTTGAGTGAAAT
346904 GATATTTCTT
Statistics
Matches: 49, Mismatches: 22, Indels: 6
0.64 0.29 0.08
Matches are distributed among these distances:
36 23 0.47
37 1 0.02
38 1 0.02
39 24 0.49
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (36 bp):
AAATTTGTTTTAAGAAAAACAATCTTGAGTGAAATA
Found at i:346969 original size:36 final size:36
Alignment explanation
Indices: 346924--348309 Score: 481
Period size: 36 Copynumber: 37.7 Consensus size: 36
346914 GTTTCGATTT
* * *
346924 AAACTATCTCAAGCGAGATGAATCTTGCTTTAAGAA
1 AAACAATCTCAAGTGAGATAAATCTTGCTTTAAGAA
* * * *
346960 AAACAATCTCAAGTCAGATAAAATTTCTG-TTTCGAGTGA
1 AAACAATCTCAAGTGAGAT-AAATCT-TGCTTT-AAG-AA
* ** * * *
346999 AATCTGTCTCAAGCGAGACGAAA-CTTGTTTTAAGAA
1 AAACAATCTCAAGTGAGA-TAAATCTTGCTTTAAGAA
* *
347035 AAACAATCTCAAGTGTGATAAAAT-TT-CAATTTCAAGAG
1 AAACAATCTCAAGTGAGAT-AAATCTTGC--TTT-AAGAA
* * * *
347073 AAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAA
1 AAACAATCTCAAGTGAGATAAATCTTGCTTTAAGAA
* ** * **
347109 AAACAATCTCAAGTGAGATAAAATTTCTATTTTGAGTG
1 AAACAATCTCAAGTGAGAT-AAATCT-TGCTTTAAGAA
* * * * ** **
347147 AACCTATTTAAAGTGAGATAAAATCTTTGCTTCGAGTG
1 AAACAATCTCAAGTGAGAT-AAATC-TTGCTTTAAGAA
* * * *
347185 AAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAA
1 AAACAATCTCAAGTGAGATAAATCTTGCTTTAAGAA
* **
347221 AAACAATCTCAAGTGAGATAAATCTT-CTGTTTCGAGTG
1 AAACAATCTCAAGTGAGATAAATCTTGC--TTT-AAGAA
* * * *
347259 AAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAA
1 AAACAATCTCAAGTGAGATAAATCTTGCTTTAAGAA
**
347295 AAACAATCTCAAGTGAGATAAATCTT-CTGTTTCAAGTG
1 AAACAATCTCAAGTGAGATAAATCTTGC--TTT-AAGAA
* * * * ** * *
347333 AAATACTTTCAAAT--TTTATAT-TT-C---AATG-G
1 AAACAATCTCAAGTGAGATAAATCTTGCTTTAA-GAA
** *
347362 AAACTTTCTCAAGCT-AGATGAAAT-TTGTTTTAAGAA
1 AAACAATCTCAAG-TGAGAT-AAATCTTGCTTTAAGAA
** * *
347398 AAACAATCTTGAGTGAAATGAAATTTCTTG-TTTCGAGTAA
1 AAACAATCTCAAGTGAGAT-AAA--TCTTGCTTT-AAG-AA
** * * *
347438 AAACTGTCTCAAGCGAGACAAAGT-TTGTTTTAAGAA
1 AAACAATCTCAAGTGAGATAAA-TCTTGCTTTAAGAA
* * **
347474 AAA-AATCTCAAGTGAGATAAAAT-TTTCTGTTTCGAGTG
1 AAACAATCTCAAGTGAGAT-AAATCTTGC--TTT-AAGAA
* * * *
347512 AAACTATCTCAAGAGAGATTAATCTTGTTTTAAGAA
1 AAACAATCTCAAGTGAGATAAATCTTGCTTTAAGAA
* * **
347548 AAACAATATCAAGTGAGATAAATCTT-CTGTTTCGAGTG
1 AAACAATCTCAAGTGAGATAAATCTTGC--TTT-AAGAA
* * * *
347586 AAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAA
1 AAACAATCTCAAGTGAGATAAATCTTGCTTTAAGAA
* *
347622 AAACAATCTCAAGTGAGATAAATCTT-CTGTTTCGAGTA
1 AAACAATCTCAAGTGAGATAAATCTTGC--TTT-AAGAA
* * * ** **
347660 AAACTATTTAAAGTGAGATAAAATCTTTGCTTCGAGTG
1 AAACAATCTCAAGTGAGAT-AAATC-TTGCTTTAAGAA
* * * *
347698 AAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAA
1 AAACAATCTCAAGTGAGATAAATCTTGCTTTAAGAA
* * **
347734 AAATAATCTCAAGTGAGATAAATCTT-CTGTTTCGAGTG
1 AAACAATCTCAAGTGAGATAAATCTTGC--TTT-AAGAA
* * * *
347772 AAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAA
1 AAACAATCTCAAGTGAGATAAATCTTGCTTTAAGAA
* **
347808 AAACAATATCAAGTGAGATAAATCTT-CTATTTCAAGTG
1 AAACAATCTCAAGTGAGATAAATCTTGC--TTT-AAGAA
* * ** * **
347846 AAACAATTTCAAAT--TTTATAT-TT-C---AAGGG
1 AAACAATCTCAAGTGAGATAAATCTTGCTTTAAGAA
** *
347875 AAACTTTCTCAAGCT-AGATGAAAT-TTGTTTTAAGAA
1 AAACAATCTCAAG-TGAGAT-AAATCTTGCTTTAAGAA
** * *
347911 AAACAATCTTGAGTGAAATGAAATTTCTTG-TTTCTAGTAA
1 AAACAATCTCAAGTGAGAT-AAA--TCTTGCTTT-AAG-AA
** * * *
347951 AAACTGTCTCAAGCGAGACAAAGT-TTGTTTTAAGAA
1 AAACAATCTCAAGTGAGATAAA-TCTTGCTTTAAGAA
* * * * * **
347987 AAACAATCTTAAGTGAAATAAAATTTTCCGTTTCGAGTG
1 AAACAATCTCAAGTGAGAT-AAATCTTGC-TTT-AAGAA
* * * *
348026 AAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAA
1 AAACAATCTCAAGTGAGATAAATCTTGCTTTAAGAA
* **
348062 AAACAATCTCAAGTGAGATAAATCTT-CTGTTTCGAGTG
1 AAACAATCTCAAGTGAGATAAATCTTGC--TTT-AAGAA
* * * *
348100 AAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAA
1 AAACAATCTCAAGTGAGATAAATCTTGCTTTAAGAA
* *
348136 AAACAATCTCAAGTGAGATAAATCTT-CTGTTTCGAGTA
1 AAACAATCTCAAGTGAGATAAATCTTGC--TTT-AAGAA
* * *
348174 AAACTATCTCAAGTGAGATTAATCTTGTTTTAAGAA
1 AAACAATCTCAAGTGAGATAAATCTTGCTTTAAGAA
* * * **
348210 AAACAATCTCTAGTGAGATAAATATT-CTGTTTCGAGTG
1 AAACAATCTCAAGTGAGATAAATCTTGC--TTT-AAGAA
* * * * * *
348248 AAGCTATCTCAAGCGAGATGAATTTTGTTTTAAGAA
1 AAACAATCTCAAGTGAGATAAATCTTGCTTTAAGAA
348284 AAACAATCTCAAGTGAGATAAATCTT
1 AAACAATCTCAAGTGAGATAAATCTT
348310 CTGTTTCGAG
Statistics
Matches: 973, Mismatches: 285, Indels: 184
0.67 0.20 0.13
Matches are distributed among these distances:
29 24 0.02
30 3 0.00
31 2 0.00
32 10 0.01
35 23 0.02
36 380 0.39
37 101 0.10
38 326 0.34
39 73 0.08
40 30 0.03
41 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.32
Consensus pattern (36 bp):
AAACAATCTCAAGTGAGATAAATCTTGCTTTAAGAA
Found at i:347116 original size:74 final size:73
Alignment explanation
Indices: 346762--348340 Score: 1218
Period size: 74 Copynumber: 21.4 Consensus size: 73
346752 ACATTAAATT
* * * * **
346762 TGTTTCGAGGGAAAACTGTCTCAAGCAAGATTAAAT-TTGTTTTAAGAAAAACAATCTTGAGTGA
1 TGTTTCGAGTG-AAACTATCTCAAGCGAGA-TGAATCTTGTTTTAAGAAAAACAATCTCAAGTGA
* *
346826 AATAAAATTTAT
64 GAT-AAATTT-C
* *** *
346838 TGTTTCGAGTGGAACTATCTCAAGCGAGATGAAAT-TTGTTTTAAGAAAAACAATCTTGTGTGAA
1 TGTTTCGAGTGAAACTATCTCAAGCGAGATG-AATCTTGTTTTAAGAAAAACAATCTCAAGTGAG
*
346902 ATGATATTTC
65 AT-AAATTTC
* * * *
346912 TTGTTTCGATTTAAACTATCTCAAGCGAGATGAATCTTGCTTTAAGAAAAACAATCTCAAGTCAG
1 -TGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAG
346977 ATAAAATTTC
65 AT-AAATTTC
* * * *
346987 TGTTTCGAGTGAAATCTGTCTCAAGCGAGACGAAACTTGTTTTAAGAAAAACAATCTCAAGTGTG
1 TGTTTCGAGTGAAA-CTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAG
347052 ATAAAATTTC
65 AT-AAATTTC
** * *
347062 AATTTCAAGAGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGA
347127 TAAAATTTC
66 T-AAATTTC
* * * * * * * * ** ** * *
347136 TATTTTGAGTGAACCTATTTAAAGTGAGATAAAATCTTTGCTTCGAGTGAAACTATCTCAAGCGA
1 TGTTTCGAGTGAAACTATCTCAAGCGAGAT-GAATC-TTGTTTTAAGAAAAACAATCTCAAGTGA
* *
347201 GATGAATCT-
64 GATAAATTTC
** ** * * * ** ** * *
347210 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGA
1 TGTTTCGAGTGAAACTATCTCAAGCGAGATGAATC-T-TGTTTTAAGAAAAACAATCTCAAGTGA
* *
347275 GATGAATCT-
64 GATAAATTTC
** ** * * * * ** * * *
347284 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAATACTTTC-A---A
1 TGTTTCGAGTGAAACTATCTCAAGCGAGATGAATC-T-TGTTTTAAGAAAAACAATCTCAAGTGA
*
347345 -AT---TTTA
64 GATAAATTTC
* * * * **
347351 TATTTC-AATGGAAACTTTCTCAAGCTAGATGAAAT-TTGTTTTAAGAAAAACAATCTTGAGTGA
1 TGTTTCGAGT-GAAACTATCTCAAGCGAGATG-AATCTTGTTTTAAGAAAAACAATCTCAAGTGA
*
347414 AATGAAATTTC
64 GAT-AAATTTC
* * **
347425 TTGTTTCGAGTAAAAACTGTCTCAAGCGAGACAAAGT-TTGTTTTAAGAAAAA-AATCTCAAGTG
1 -TGTTTCGAGT-GAAACTATCTCAAGCGAGATGAA-TCTTGTTTTAAGAAAAACAATCTCAAGTG
347488 AGATAAAATTTTC
63 AGAT-AAA-TTTC
* * *
347501 TGTTTCGAGTGAAACTATCTCAAGAGAGATTAATCTTGTTTTAAGAAAAACAATATCAAGTGAGA
1 TGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGA
347566 TAAATCTTC
66 TAAAT-TTC
347575 TGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGA
347640 TAAATCTTC
66 TAAAT-TTC
* * * * * * ** ** * *
347649 TGTTTCGAGTAAAACTATTTAAAGTGAGATAAAATCTTTGCTTCGAGTGAAACTATCTCAAGCGA
1 TGTTTCGAGTGAAACTATCTCAAGCGAGAT-GAATC-TTGTTTTAAGAAAAACAATCTCAAGTGA
* *
347714 GATGAATCT-
64 GATAAATTTC
** * * * * ** ** * *
347723 TGTTTTAAG-AAAAATAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCG
1 TGTTTCGAGTGAAACT-ATCTCAAGCGAGATGAATC-T-TGTTTTAAGAAAAACAATCTCAAGTG
* *
347787 AGATGAATCT-
63 AGATAAATTTC
** ** * * * * * ** *
347797 TGTTTTAAGAAAAACAATATCAAGTGAGATAAATCTTCTATTTCAAGTGAAACAATTTC-A---A
1 TGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGT-TTT-AAGAAAAACAATCTCAAGTGA
*
347858 -AT---TTTA
64 GATAAATTTC
* * * * * ** *
347864 TATTTCAAGGGAAACTTTCTCAAGCTAGATGAAAT-TTGTTTTAAGAAAAACAATCTTGAGTGAA
1 TGTTTCGAGTGAAACTATCTCAAGCGAGATG-AATCTTGTTTTAAGAAAAACAATCTCAAGTGAG
347928 ATGAAATTTC
65 AT-AAATTTC
* * * ** *
347938 TTGTTTCTAGTAAAAACTGTCTCAAGCGAGACAAAGT-TTGTTTTAAGAAAAACAATCTTAAGTG
1 -TGTTTCGAGT-GAAACTATCTCAAGCGAGATGAA-TCTTGTTTTAAGAAAAACAATCTCAAGTG
*
348002 AAATAAAATTTTC
63 AGAT-AAA-TTTC
*
348015 CGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGA
348080 TAAATCTTC
66 TAAAT-TTC
348089 TGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGA
348154 TAAATCTTC
66 TAAAT-TTC
* * * *
348163 TGTTTCGAGTAAAACTATCTCAAGTGAGATTAATCTTGTTTTAAGAAAAACAATCTCTAGTGAGA
1 TGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGA
348228 TAAATATTC
66 TAAAT-TTC
* *
348237 TGTTTCGAGTGAAGCTATCTCAAGCGAGATGAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGA
348302 TAAATCTTC
66 TAAAT-TTC
348311 TGTTTCGAGTGAAACTATCTCAAGCGAGAT
1 TGTTTCGAGTGAAACTATCTCAAGCGAGAT
348341 AAAATTTTTG
Statistics
Matches: 1268, Mismatches: 185, Indels: 102
0.82 0.12 0.07
Matches are distributed among these distances:
65 25 0.02
66 11 0.01
67 43 0.03
68 6 0.00
69 6 0.00
70 6 0.00
72 2 0.00
73 27 0.02
74 685 0.54
75 296 0.23
76 157 0.12
77 4 0.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.33
Consensus pattern (73 bp):
TGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGA
TAAATTTC
Found at i:347184 original size:38 final size:38
Alignment explanation
Indices: 347119--347191 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
347109 AAACAATCTC
* * *
347119 AAGTGAGATAAAATTTCTATTTTGAGTGAACCTATTTA
1 AAGTGAGATAAAATTTCTACTTCGAGTGAAACTATTTA
*
347157 AAGTGAGATAAAATCTT-TGCTTCGAGTGAAACTAT
1 AAGTGAGATAAAAT-TTCTACTTCGAGTGAAACTAT
347192 CTCAAGCGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
38 28 0.93
39 2 0.07
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.36
Consensus pattern (38 bp):
AAGTGAGATAAAATTTCTACTTCGAGTGAAACTATTTA
Found at i:347202 original size:186 final size:187
Alignment explanation
Indices: 346970--347316 Score: 565
Period size: 186 Copynumber: 1.9 Consensus size: 187
346960 AAACAATCTC
* *
346970 AAGTCAGATAAAATTTCTGTTTCGAGTGAAATCTGTCTCAAGCGAGACGAAACTTGTTTTAAGAA
1 AAGTCAGATAAAATTTCTGCTTCGAGTGAAATCTATCTCAAGCGAGACGAAACTTGTTTTAAGAA
*
347035 AAACAATCTCAAGTGTGATAAAAT-TTCAATTTCAAGAGAAACTATCTCAAGCGAGATGAATCTT
66 AAACAATCTCAAGTGAGAT-AAATCTTCAATTTCAAGAGAAACTATCTCAAGCGAGATGAATCTT
347099 GTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCTATTTTGAGTGAACCTATTTA
130 GTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCTATTTTGAGTGAACCTATTTA
* * *
347157 AAGTGAGATAAAATCTT-TGCTTCGAGTGAAA-CTATCTCAAGCGAGATGAATCTTGTTTTAAGA
1 AAGTCAGATAAAAT-TTCTGCTTCGAGTGAAATCTATCTCAAGCGAGACGAAACTTGTTTTAAGA
** * *
347220 AAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTT
65 AAAACAATCTCAAGTGAGATAAATCTTCAATTTCAAGAGAAACTATCTCAAGCGAGATGAATCTT
347285 GTTTTAAGAAAAACAATCTCAAGTGAGATAAA
130 GTTTTAAGAAAAACAATCTCAAGTGAGATAAA
347317 TCTTCTGTTT
Statistics
Matches: 148, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
185 4 0.03
186 116 0.78
187 26 0.18
188 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.31
Consensus pattern (187 bp):
AAGTCAGATAAAATTTCTGCTTCGAGTGAAATCTATCTCAAGCGAGACGAAACTTGTTTTAAGAA
AAACAATCTCAAGTGAGATAAATCTTCAATTTCAAGAGAAACTATCTCAAGCGAGATGAATCTTG
TTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCTATTTTGAGTGAACCTATTTA
Found at i:347277 original size:112 final size:110
Alignment explanation
Indices: 346850--348309 Score: 713
Period size: 112 Copynumber: 13.2 Consensus size: 110
346840 TTTCGAGTGG
* *** * * *
346850 AACTATCTCAAGCGAGATGAAAT-TTGTTTTAAGAAAAACAATCTTGTGTGAAATGATATTTCTT
1 AACTATCTCAAGTGAGAT-AAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGAT-AAATCT-TT
* * * *
346914 GTTTCGATTTAAACTATCTCAAGCGAGATGAATC-TTGCTTT-AAGAAA
63 GTTTCGAGTGAAACTATCTCAAGCGAGATAAATCTTTG-TTTCAAGTAA
* * * ** * * ** * *
346961 AACAATCTCAAGTCAGATAAAATTTCTGTTTCGAGTGAAATCTGTCTCAAGCGAGACGAAA-C-T
1 AACTATCTCAAGTGAGAT-AAATCT-TGTTTTAAG-AAAAACAATCTCAAGTGAGA-TAAATCTT
** ** * * * **
347024 TGTTTTAAGAAAAACAATCTCAAGTGTGATAAAAT-TTCAATTTCAAG-AGA
62 TGTTTCGAGTGAAACTATCTCAAGCGAGAT-AAATCTT-TGTTTCAAGTA-A
* * *
347074 AACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAAT-TTCTA
1 AACTATCTCAAGTGAGATAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGAT-AAATCTT-TG
* * * * * * * *
347138 TTTTGAGTGAACCTATTTAAAGTGAGATAAAATCTTTGCTTCGAGTGA
64 TTTCGAGTGAAACTATCTCAAGCGAGAT-AAATCTTTGTTTCAAGTAA
* *
347186 AACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGT
1 AACTATCTCAAGTGAGATAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTT-TGT
* * *
347251 TTCGAGTGAAACTATCTCAAGCGAGATGAATC-TTGTTTTAAGAAA
65 TTCGAGTGAAACTATCTCAAGCGAGATAAATCTTTGTTTCAAGTAA
* * ** * * *
347296 AACAATCTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAATACTTTC-A---A-AT---T-TTAT
1 AACTATCTCAAGTGAGATAAATC-T-TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTT-T
* * * * * *
347352 ATTTC-AATGGAAACTTTCTCAAGCTAGATGAAA--TTTGTTTTAAGAAA
63 GTTTCGAGT-GAAACTATCTCAAGCGAGAT-AAATCTTTGTTTCAAGTAA
* ** * ** ** * * *
347399 AACAATCTTGAGTGAAATGAAATTTCTTGTTTCGAGTAAAAACTGTCTCAAGCGAGACAAA-GTT
1 AACTATCTCAAGTGAGAT-AAA--TCTTGTTTTAAG-AAAAACAATCTCAAGTGAGATAAATCTT
** * ** * * * *
347463 TGTTTTAAG-AAAAAAATCTCAAGTGAGATAAAATTTTCTGTTTCGAGTGA
62 TGTTTCGAGTGAAACTATCTCAAGCGAGAT-AAATCTT-TGTTTCAAGTAA
* * *
347513 AACTATCTCAAGAGAGATTAATCTTGTTTTAAGAAAAACAATATCAAGTGAGATAAATCTTCTGT
1 AACTATCTCAAGTGAGATAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTT-TGT
* * *
347578 TTCGAGTGAAACTATCTCAAGCGAGATGAATC-TTGTTTTAAGAAA
65 TTCGAGTGAAACTATCTCAAGCGAGATAAATCTTTGTTTCAAGTAA
* ** * * * *
347623 AACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTAAAACTATTTAAAGTGAGATAAAATCTTT
1 AACTATCTCAAGTGAGATAAATC-T-TGTTTTAAGAAAAACAATCTCAAGTGAGAT-AAATCTTT
* * *
347688 GCTTCGAGTGAAACTATCTCAAGCGAGATGAATC-TTGTTTTAAG-AA
63 GTTTCGAGTGAAACTATCTCAAGCGAGATAAATCTTTGTTTCAAGTAA
* ** ** * * *
347734 AAATAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATC-TT
1 AACT-ATCTCAAGTGAGATAAATC-T-TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTT
** ** * * * * *
347798 GTTTTAAGAAAAACAATATCAAGTGAGATAAATCTTCTATTTCAAGTGA
63 GTTTCGAGTGAAACTATCTCAAGCGAGATAAATCTT-TGTTTCAAGTAA
* * * ** **
347847 AACAATTTC-A---A-AT---T-TTATATTTCAAGGGAAACTTTCTCAAGCT-AGATGAAA--TT
1 AACTATCTCAAGTGAGATAAATCTTGT-TTT-AAGAAAAACAATCTCAAG-TGAGAT-AAATCTT
** ** * ** * * * *
347900 TGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATTTCTTGTTTCTAGTAAA
62 TGTTTCGAGTGAAACTATCTCAAGCGAGAT-AAATCT-TTGTTTCAAGT-AA
* * * * *
347952 AACTGTCTCAAGCGAGACAAAGT-TTGTTTTAAGAAAAACAATCTTAAGTGAAATAAAAT-TTTC
1 AACTATCTCAAGTGAGATAAA-TCTTGTTTTAAGAAAAACAATCTCAAGTGAGAT-AAATCTTT-
* * *
348015 CGTTTCGAGTGAAACTATCTCAAGCGAGATGAATC-TTGTTTTAAGAAA
63 -GTTTCGAGTGAAACTATCTCAAGCGAGATAAATCTTTGTTTCAAGTAA
* ** ** * * *
348063 AACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATC-TTG
1 AACTATCTCAAGTGAGATAAATC-T-TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTTG
** ** * * *
348127 TTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTAA
64 TTTCGAGTGAAACTATCTCAAGCGAGATAAATCTT-TGTTTCAAGTAA
* * *
348175 AACTATCTCAAGTGAGATTAATCTTGTTTTAAGAAAAACAATCTCTAGTGAGATAAATATTCTGT
1 AACTATCTCAAGTGAGATAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTT-TGT
* * * *
348240 TTCGAGTGAAGCTATCTCAAGCGAGATGAAT-TTTGTTTTAAGAAA
65 TTCGAGTGAAACTATCTCAAGCGAGATAAATCTTTGTTTCAAGTAA
*
348285 AACAATCTCAAGTGAGATAAATCTT
1 AACTATCTCAAGTGAGATAAATCTT
348310 CTGTTTCGAG
Statistics
Matches: 1018, Mismatches: 254, Indels: 155
0.71 0.18 0.11
Matches are distributed among these distances:
101 2 0.00
102 5 0.00
103 99 0.10
104 30 0.03
105 15 0.01
106 4 0.00
107 4 0.00
108 2 0.00
109 2 0.00
110 208 0.20
111 126 0.12
112 371 0.36
113 89 0.09
114 41 0.04
115 20 0.02
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (110 bp):
AACTATCTCAAGTGAGATAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTTGTT
TCGAGTGAAACTATCTCAAGCGAGATAAATCTTTGTTTCAAGTAA
Found at i:347822 original size:513 final size:514
Alignment explanation
Indices: 346850--348192 Score: 2266
Period size: 513 Copynumber: 2.6 Consensus size: 514
346840 TTTCGAGTGG
* * * *
346850 AACTATCTCAAGCGAGATGAAATTTGTTTTAAGAAAAACAATCTTGTGTGAAATGATATTTCTTG
1 AACTTTCTCAAGCTAGATGAAATTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATTTCTTG
** * ** * *
346915 TTTCGA-TTTAAACTATCTCAAGCGAGATGAA-TCTTGCTTTAAGAAAAACAATCTCAAGTCAGA
66 TTTCGAGTAAAAACTGTCTCAAGCGAGACAAAGT-TTGTTTTAAGAAAAACAATCTCAAGTGAGA
* * *
346978 TAAAA-TTTCTGTTTCGAGTGAAATCTGTCTCAAGCGAGACGAAACTTGTTTTAAGAAAAACAAT
130 TAAAATTTTCTGTTTCGAGTGAAA-CTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAAT
* ** * *
347042 CTCAAGTGTGATAAAAT-TTCAATTTCAAGAGAAACTATCTCAAGCGAGATGAATCTTGTTTTAA
194 CTCAAGTGAGAT-AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAA
* * * *
347106 GAAAAACAATCTCAAGTGAGATAAAAT-TTCTATTTTGAGTGAACCTATTTAAAGTGAGATAAAA
258 GAAAAACAATCTCAAGTGAGAT-AAATCTTCTGTTTCGAGTAAAACTATTTAAAGTGAGATAAAA
347170 TCTTTGCTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGT
322 TCTTTGCTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGT
347235 GAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACA
387 GAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACA
* * * * *
347300 ATCTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAATACTTTCAAATTTTATATTTCAATGGA
452 ATATCAAGTGAGATAAATCTTCTATTTCAAGTGAAACAATTTCAAATTTTATATTTCAAGGGA
347363 AACTTTCTCAAGCTAGATGAAATTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATTTCTTG
1 AACTTTCTCAAGCTAGATGAAATTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATTTCTTG
347428 TTTCGAGTAAAAACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAA-AATCTCAAGTGAGAT
66 TTTCGAGTAAAAACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGAT
* * *
347492 AAAATTTTCTGTTTCGAGTGAAACTATCTCAAGAGAGATTAATCTTGTTTTAAGAAAAACAATAT
131 AAAATTTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCT
347557 CAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAA
196 CAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAA
347622 AAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTAAAACTATTTAAAGTGAGATAAAATCTT
261 AAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTAAAACTATTTAAAGTGAGATAAAATCTT
*
347687 TGCTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAATAATCTCAAGTGAGA
326 TGCTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGA
347752 TAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATAT
391 TAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATAT
347817 CAAGTGAGATAAATCTTCTATTTCAAGTGAAACAATTTCAAATTTTATATTTCAAGGGA
456 CAAGTGAGATAAATCTTCTATTTCAAGTGAAACAATTTCAAATTTTATATTTCAAGGGA
347876 AACTTTCTCAAGCTAGATGAAATTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATTTCTTG
1 AACTTTCTCAAGCTAGATGAAATTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATTTCTTG
* * *
347941 TTTCTAGTAAAAACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATCTTAAGTGAAAT
66 TTTCGAGTAAAAACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGAT
*
348006 AAAATTTTCCGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCT
131 AAAATTTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCT
348071 CAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAA
196 CAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAA
* *
348136 AAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTAAAACTATCTCAAGTGAGAT
261 AAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTAAAACTATTTAAAGTGAGAT
348193 TAATCTTGTT
Statistics
Matches: 783, Mismatches: 41, Indels: 11
0.94 0.05 0.01
Matches are distributed among these distances:
512 8 0.01
513 528 0.67
514 246 0.31
515 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (514 bp):
AACTTTCTCAAGCTAGATGAAATTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATTTCTTG
TTTCGAGTAAAAACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGAT
AAAATTTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCT
CAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAA
AAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTAAAACTATTTAAAGTGAGATAAAATCTT
TGCTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGA
TAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATAT
CAAGTGAGATAAATCTTCTATTTCAAGTGAAACAATTTCAAATTTTATATTTCAAGGGA
Found at i:348200 original size:588 final size:580
Alignment explanation
Indices: 346773--348356 Score: 1808
Period size: 588 Copynumber: 2.7 Consensus size: 580
346763 GTTTCGAGGG
*
346773 AAAACTGTCTCAAGCAAGATTAAATTTGTTTTAAGAAAAACAATCTTGAGTGAAATAAAATTTAT
1 AAAACTGTCTCAAGCAAGATCAAATTTGTTTTAAGAAAAACAATCTTGAGTGAAATAAAATTT-T
* *** *
346838 -TGTTTCGAGTGGAACTATCTCAAGCGAGATGAAATTTGTTTTAAGAAAAACAATCTTGTGTGAA
65 CTGTTTCGAGTGAAACTATCTCAAGCGAGATG-AATTTGTTTTAAGAAAAACAATCTCAAGTGAG
* * * * *
346902 ATGATATTTCTTGTTTCGATTTAAACTATCTCAAGCGAGATGAATCTTGCTTTAAGAAAAACAAT
129 ATAAAATTTC-TGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAAT
* * * * *
346967 CTCAAGTCAGATAAAAT-TTCTGTTTCGAGTGAAATCTGTCTCAAGCGAGACGAAACTTGTTTTA
193 CTCAAGTGAGAT-AAATCTTCTGTTTCGAGT-AAAACTATCTCAAGCGAGATGAATCTTGTTTTA
* ** * * *
347031 AGAAAAACAATCTCAAGTGTGATAAAATTTCAATTTCAAG-AGAAACTATCTCAAGCGAGATGAA
256 AGAAAAACAATCTCAAGTGAGAT-AAATTTCTGTTTCGAGTAGAAACTATCTAAAGCGAGATAAA
* * * * * * ** *
347095 TCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCTATTTTGAGTGAACCTATTTAAAG
320 TCTTGCTTCAAGAAAAACAATCTCAAGCGAGATAAAATCTCTATTTTAAGTAAAAATATCTAAAG
347160 TGAGATAAAATCTTTGCTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAAC
385 TGAGATAAAATCTTTGCTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAAC
* * * * *
347225 AATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTT
450 AATATCAAGTGAGATAAATCTTCTATTTCAAGTGAAACAATCTCAA--GAGAT--ATCTTATTTT
** *
347290 AAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAATACTTTCAAATTTTATATT
511 AAGAAAAACAATCTCAAGTGAGATAAA-CTTCTGTTTCAAGAAAAAAACTTTCAAATTTTATATT
*
347355 TCAATG
575 TCAATA
* * * * *
347361 GAAACTTTCTCAAGCTAGATGAAATTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAA-TTTC
1 AAAACTGTCTCAAGCAAGATCAAATTTGTTTTAAGAAAAACAATCTTGAGTGAAATAAAATTTTC
* * **
347425 TTGTTTCGAGTAAAAACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAA-AATCTCAAGTGA
66 -TGTTTCGAGT-GAAACTATCTCAAGCGAGATGAA-TTTGTTTTAAGAAAAACAATCTCAAGTGA
* *
347489 GATAAAATTTTCTGTTTCGAGTGAAACTATCTCAAGAGAGATTAATCTTGTTTTAAGAAAAACAA
128 GATAAAA-TTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAA
* *
347554 TATCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAA
192 TCTCAAGTGAGATAAATCTTCTGTTTCGAGTAAAACTATCTCAAGCGAGATGAATCTTGTTTTAA
* *
347619 GAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTA-AAACTATTTAAAGTGAGATAAAA
257 GAAAAACAATCTCAAGTGAGATAAAT-TTCTGTTTCGAGTAGAAACTATCTAAAGCGAGAT-AAA
* ** * * * *
347683 TCTTTGCTTCGAGTGAAACTATCTCAAGCGAGAT-GAATCT-TGTTTTAAG-AAAAATAATCTCA
320 TC-TTGCTTCAAGAAAAACAATCTCAAGCGAGATAAAATCTCTATTTTAAGTAAAAAT-ATCTAA
*
347745 AGTGAGAT-AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAA
383 AGTGAGATAAAATCTT-TGCTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAA
*
347809 AACAATATCAAGTGAGATAAATCTTCTATTTCAAGTGAAACAATTTC-A-A-AT-T-TTATATTT
447 AACAATATCAAGTGAGATAAATCTTCTATTTCAAGTGAAACAATCTCAAGAGATATCTTAT-TTT
** ** * *
347869 CAAGGGAAACTTTCTCAAGCT-AGATGAAA-TT-TGTTTTAAGAAAAACAATCTTGAGTGAAATG
511 -AAGAAAAACAATCTCAAG-TGAGAT-AAACTTCTGTTTCAAGAAAAA-AA-CTT---TCAAAT-
* * *
347931 AAATTTCTTGTTTCTAGTA
567 ---TTT-ATATTTC-AATA
* *
347950 AAAACTGTCTCAAGCGAGA-CAAAGTTTGTTTTAAGAAAAACAATCTTAAGTGAAATAAAATTTT
1 AAAACTGTCTCAAGCAAGATCAAA-TTTGTTTTAAGAAAAACAATCTTGAGTGAAATAAAATTTT
*
348014 CCGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAG
65 CTGTTTCGAGTGAAACTATCTCAAGCGAGATGAAT-TTGTTTTAAGAAAAACAATCTCAAGTGAG
348079 AT-AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAAT
129 ATAAAAT-TTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAAT
* *
348143 CTCAAGTGAGATAAATCTTCTGTTTCGAGTAAAACTATCTCAAGTGAGATTAATCTTGTTTTAAG
193 CTCAAGTGAGATAAATCTTCTGTTTCGAGTAAAACTATCTCAAGCGAGATGAATCTTGTTTTAAG
* * * * *
348208 AAAAACAATCTCTAGTGAGATAAATATTCTGTTTCGAGT-GAAGCTATCTCAAGCGAGATGAATT
258 AAAAACAATCTCAAGTGAGATAAAT-TTCTGTTTCGAGTAGAAACTATCTAAAGCGAGATAAATC
* * * * ** * * * *
348272 TTGTTTTAAGAAAAACAATCTCAAGTGAGAT-AAATCTTCTGTTTCGAGTGAAACTATCTCAAGC
322 TTGCTTCAAGAAAAACAATCTCAAGCGAGATAAAATC-TCTATTTTAAGTAAAAATATCTAAAGT
*
348336 GAGATAAAATTTTTGCTTCGA
386 GAGATAAAATCTTTGCTTCGA
348357 AAATGTTGAA
Statistics
Matches: 847, Mismatches: 112, Indels: 74
0.82 0.11 0.07
Matches are distributed among these distances:
578 14 0.02
579 7 0.01
580 21 0.02
581 4 0.00
582 2 0.00
583 6 0.01
586 44 0.05
587 198 0.23
588 401 0.47
589 146 0.17
590 4 0.00
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (580 bp):
AAAACTGTCTCAAGCAAGATCAAATTTGTTTTAAGAAAAACAATCTTGAGTGAAATAAAATTTTC
TGTTTCGAGTGAAACTATCTCAAGCGAGATGAATTTGTTTTAAGAAAAACAATCTCAAGTGAGAT
AAAATTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTC
AAGTGAGATAAATCTTCTGTTTCGAGTAAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAA
AACAATCTCAAGTGAGATAAATTTCTGTTTCGAGTAGAAACTATCTAAAGCGAGATAAATCTTGC
TTCAAGAAAAACAATCTCAAGCGAGATAAAATCTCTATTTTAAGTAAAAATATCTAAAGTGAGAT
AAAATCTTTGCTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATATC
AAGTGAGATAAATCTTCTATTTCAAGTGAAACAATCTCAAGAGATATCTTATTTTAAGAAAAACA
ATCTCAAGTGAGATAAACTTCTGTTTCAAGAAAAAAACTTTCAAATTTTATATTTCAATA
Found at i:349629 original size:3 final size:3
Alignment explanation
Indices: 349617--349664 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
349607 TTTTATTGTG
349617 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
349664 T
1 T
349665 TTATTAACCT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:354364 original size:5 final size:5
Alignment explanation
Indices: 354354--354387 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
354344 GAATATATTA
354354 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
354388 TTTAGCGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:355595 original size:20 final size:22
Alignment explanation
Indices: 355570--355612 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
355560 TTCTTAGAAT
355570 TTGTTTTC-AAA-TTTAAAAAA
1 TTGTTTTCAAAATTTTAAAAAA
355590 TTGTTTTCAAAATTTTAAAAAA
1 TTGTTTTCAAAATTTTAAAAAA
355612 T
1 T
355613 AAAAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 8 0.38
21 3 0.14
22 10 0.48
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (22 bp):
TTGTTTTCAAAATTTTAAAAAA
Found at i:356498 original size:3 final size:3
Alignment explanation
Indices: 356487--356533 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
356477 TTTTTTATCG
356487 TTA TT- TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
356531 TTA
1 TTA
356534 ATATCAAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:356648 original size:25 final size:25
Alignment explanation
Indices: 356615--356691 Score: 129
Period size: 25 Copynumber: 3.1 Consensus size: 25
356605 CAATCAACCC
*
356615 ATCATATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
356640 ATCAGATTAGGGTTTCAAACCCTAAA
1 ATCAGATTAGGGTTTCAAACCCT-AA
356666 AT-AGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
356690 AT
1 AT
356692 GTTCCAGCCG
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
24 4 0.08
25 42 0.84
26 4 0.08
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:360213 original size:31 final size:32
Alignment explanation
Indices: 360177--360238 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
360167 ATTTTACATG
360177 TACTAACTTATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
360208 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
360239 CATTTTGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.61
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
Found at i:360784 original size:210 final size:210
Alignment explanation
Indices: 360416--360831 Score: 564
Period size: 210 Copynumber: 2.0 Consensus size: 210
360406 ATGAGATTTT
* *
360416 CTCGAAGATCGTGCATCATTCGAGACTGATATGATAATCCACTGATCTAAGGAGTAATCCAGCAG
1 CTCGAAGATCGTGCATCATTCGAGACTGATATGATAATCCACTGATCGAAGGAGTAATCCAACAG
* * * *
360481 TAGATTCTCATCCACAATTATTCCATCGTTAACCATCAGGGAGTGAAGCACAAACTTCAGCATAG
66 TAGATTCTCATCCACAATTATTCCATCGCTAACCATCAAGGAGCGAAGCACAAACTTCAGCACAG
* * * * *
360546 CCGAGGTATTAATGGAGTTAGTTTACAGAGCATAGAGGGGCATCGGTTCCAAGTACAAAGATCCG
131 CCGAGGCATTAATGGAGTCAGATTACAGAGCATAGAGGGGCATCAGTTCCAAGGACAAAGATCCG
360611 AGACGAAGCAGTGAG
196 AGACGAAGCAGTGAG
*
360626 CTCGAAGATCGTGCATCATTCGAGACTGATATGATAATCCATTGATCCGAA-GAGTAATCCAACA
1 CTCGAAGATCGTGCATCATTCGAGACTGATATGATAATCCACTGAT-CGAAGGAGTAATCCAACA
* * * * ** *
360690 GTAGATTCTCATCTACAATTATTTCATCGCTATCCATCAAGGAGCGACGCACTGACTTCAGCACC
65 GTAGATTCTCATCCACAATTATTCCATCGCTAACCATCAAGGAGCGAAGCACAAACTTCAGCACA
* * * * * * * * *
360755 GCCGGGGCATTAATGGTGTCAGATTACAGATCATTGAGGGGCATTATTTTCAAGGACGAAGATCT
130 GCCGAGGCATTAATGGAGTCAGATTACAGAGCATAGAGGGGCATCAGTTCCAAGGACAAAGATCC
360820 GAGACGAAGCAG
195 GAGACGAAGCAG
360832 CGATCTATTT
Statistics
Matches: 177, Mismatches: 28, Indels: 2
0.86 0.14 0.01
Matches are distributed among these distances:
210 174 0.98
211 3 0.02
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (210 bp):
CTCGAAGATCGTGCATCATTCGAGACTGATATGATAATCCACTGATCGAAGGAGTAATCCAACAG
TAGATTCTCATCCACAATTATTCCATCGCTAACCATCAAGGAGCGAAGCACAAACTTCAGCACAG
CCGAGGCATTAATGGAGTCAGATTACAGAGCATAGAGGGGCATCAGTTCCAAGGACAAAGATCCG
AGACGAAGCAGTGAG
Found at i:362703 original size:26 final size:25
Alignment explanation
Indices: 362674--362751 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
362664 AATTTTTGAC
362674 ATTCTATCTCTTTGAGACCTTGAAAT
1 ATTCT-TCTCTTTGAGACCTTGAAAT
* *
362700 A---TTCT-TTT-CGACCTTGAAAC
1 ATTCTTCTCTTTGAGACCTTGAAAT
*
362720 ATTCCCTCTCTTTGAGACCTTGAAAT
1 ATT-CTTCTCTTTGAGACCTTGAAAT
362746 ATTCTT
1 ATTCTT
362752 TCCACCTTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
20 11 0.28
21 3 0.08
22 3 0.08
23 1 0.03
24 3 0.08
25 5 0.12
26 14 0.35
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.42
Consensus pattern (25 bp):
ATTCTTCTCTTTGAGACCTTGAAAT
Found at i:362712 original size:20 final size:20
Alignment explanation
Indices: 362689--362763 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
362679 ATCTCTTTGA
362689 GACCTTGAAATATTCTTTTC
1 GACCTTGAAATATTCTTTTC
* *
362709 GACCTTGAAACATTCCCTCTCTTTGA
1 GACCTTGAAATA-T---TCT-TTT-C
362735 GACCTTGAAATATTC-TTTC
1 GACCTTGAAATATTCTTTTC
*
362754 CACCTTGAAA
1 GACCTTGAAA
362764 CACTGTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 9 0.20
20 14 0.32
21 1 0.02
22 2 0.05
24 3 0.07
25 4 0.09
26 11 0.25
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (20 bp):
GACCTTGAAATATTCTTTTC
Found at i:365274 original size:105 final size:102
Alignment explanation
Indices: 365087--365325 Score: 286
Period size: 105 Copynumber: 2.3 Consensus size: 102
365077 TGAGAATTTT
** * *
365087 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACT
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
*
365152 TAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC-
66 TAAAACAAAATTAATCTCA-CTTGAGATCG-T-TTTC--TCA
* * * *
365192 AAAACAAATTTTGTCTCGCTTGAGACCTTTTCCCTTTGGGATCCAAATTTCGAATTTGTTTCACA
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCAC-
* *
365257 TT-AAACAAAGTTGATCTCACTTGAGATCGTTTTCTCA
65 TTAAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
* *
365294 AAAACAAACTTTGTCTCGCTTGAGACAATTTC
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTC
365326 TCTAAAAACA
Statistics
Matches: 117, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
101 2 0.02
102 29 0.25
103 4 0.03
104 4 0.03
105 76 0.65
106 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (102 bp):
AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
TAAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
Found at i:365316 original size:36 final size:36
Alignment explanation
Indices: 365271--365355 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
365261 ACAAAGTTGA
**
365271 TCTCACTTGAGATCGTTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGA-CAATTTCTCTAAAAACAAACTTTG
* *
365307 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
*
365343 TCTCATTTGAGAC
1 TCTCACTTGAGAC
365356 TATATCTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
35 7 0.17
36 35 0.83
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (36 bp):
TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
Found at i:365387 original size:34 final size:36
Alignment explanation
Indices: 365289--365390 Score: 95
Period size: 36 Copynumber: 2.9 Consensus size: 36
365279 GAGATCGTTT
* *
365289 TCTC-AAAAACAAACTTT-GTCTCGCTTGAGACAATT
1 TCTCTAAAAACAAA-TTTCATCTCGCTTGAGACAATA
** ** *
365324 TCTCTAAAAACAAATTTTGTCTCATTTGAGACTATA
1 TCTCTAAAAACAAATTTCATCTCGCTTGAGACAATA
*
365360 TCT-T-AAAGCAAATTTCATCTCGCTTGAGACA
1 TCTCTAAAAACAAATTTCATCTCGCTTGAGACA
365391 TCATTTTTTC
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
34 21 0.38
35 8 0.15
36 26 0.47
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (36 bp):
TCTCTAAAAACAAATTTCATCTCGCTTGAGACAATA
Found at i:365668 original size:29 final size:29
Alignment explanation
Indices: 365636--365729 Score: 127
Period size: 29 Copynumber: 3.3 Consensus size: 29
365626 ACAGTTTCTC
365636 TTGAAAAAAAATCTTTGAGTTTGTTCCTT
1 TTGAAAAAAAATCTTTGAGTTTGTTCCTT
* *
365665 TTGAATAAAAATCTTGGAGTTTGTTCCTT
1 TTGAAAAAAAATCTTTGAGTTTGTTCCTT
* * * *
365694 TTGAATAAATATCTTTGAG-TCGTTTCTT
1 TTGAAAAAAAATCTTTGAGTTTGTTCCTT
365722 TTGAAAAA
1 TTGAAAAA
365730 TCTTTGAGTC
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
28 14 0.24
29 44 0.76
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.45
Consensus pattern (29 bp):
TTGAAAAAAAATCTTTGAGTTTGTTCCTT
Done.