Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008217.1 Hibiscus syriacus cultivar Beakdansim tig00110847_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: 2417150
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 14
Found at i:239315 original size:65 final size:65
Alignment explanation
Indices: 239182--239340 Score: 220
Period size: 64 Copynumber: 2.5 Consensus size: 65
239172 TGCACTAAGA
*
239182 GTGCATCGATGCATAAAATGCATTCGATG-TTTCAAAATAGCCTGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATAGCTG
*
239246 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-A-CTCTGAGTGCATCGATGCATAG-
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAGC-CTGAGTGCATCGATGCATAGC
*
239308 TAT
64 T-G
*
239311 GTGCATCG-TGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
239341 CGATTTTTTC
Statistics
Matches: 87, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
64 51 0.59
65 33 0.38
66 3 0.03
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATAGCTG
Found at i:239896 original size:19 final size:19
Alignment explanation
Indices: 239872--239915 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
239862 TCACTCATTG
*
239872 CTCCCTTGCATATGAGCAT
1 CTCCCTTGCATATGAGCAA
239891 CTCCCTTGCATATGAGCAA
1 CTCCCTTGCATATGAGCAA
239910 CTCCCT
1 CTCCCT
239916 CTTAAGCTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.20, C:0.36, G:0.14, T:0.30
Consensus pattern (19 bp):
CTCCCTTGCATATGAGCAA
Found at i:240069 original size:14 final size:14
Alignment explanation
Indices: 240047--240076 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
240037 TATCGCCGAC
*
240047 CAAATTTCACTATT
1 CAAAATTCACTATT
240061 CAAAATTCACTATT
1 CAAAATTCACTATT
240075 CA
1 CA
240077 CATGAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (14 bp):
CAAAATTCACTATT
Found at i:242051 original size:205 final size:208
Alignment explanation
Indices: 241711--242098 Score: 597
Period size: 205 Copynumber: 1.9 Consensus size: 208
241701 AACAGATTAG
*
241711 ATTTTCAGACACAAGTTTTGATCTTTTTTCCCTTTGATTTCTTTTGCCTACCAACCCTCTCAAAC
1 ATTTTCAGACACAAGTTTTGATCTTTTTTCCCTTTGATGTCTTTTGCCTACCAACCCTCTCAAA-
* *
241776 CTTGTCAAAGTTGAGTGACAAAACAGTTAATCAGTGAAGACAAGGGAAGGACCGGTACAGGTTTT
65 CTTGTCAAAGTTGAGTGACAAAACACTTAACCAGTGAAGACAAGGGAAGGACCGGTACAGGTTTT
* * *
241841 GATCTCTTTCACTAAATCTATTTCAGGATTTATATCTGTTTATGCTTGTAGAAGAACACAGACAC
130 GATCTCTTCCACTAAATCTATTTCAGGATGTATATCTGTTTATGCTAGTAGAAGAACACAGACAC
241906 ATAAACATATAATC
195 ATAAACATATAATC
* * *
241920 ATTTTCA-A-ACAAGTTTTGATATTTTTTTCCCTTTGATGTCTTTTGCCTACCAACGCTCTC-GA
1 ATTTTCAGACACAAGTTTTGAT-CTTTTTTCCCTTTGATGTCTTTTGCCTACCAACCCTCTCAAA
* *
241982 -TTGTCAAAGTTGAGTGACAAAGCACTTAACCATTGAAGACAAGGGAA-GAGCCGGTACAGGTTT
65 CTTGTCAAAGTTGAGTGACAAAACACTTAACCAGTGAAGACAAGGGAAGGA-CCGGTACAGGTTT
* *
242045 TGATCTCTTCCACTAAATCTATTTCGGGATGTGTATCTGTTTATGCTAGTAGAA
129 TGATCTCTTCCACTAAATCTATTTCAGGATGTATATCTGTTTATGCTAGTAGAA
242099 CACACACACA
Statistics
Matches: 164, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
204 2 0.01
205 105 0.64
207 13 0.08
208 37 0.23
209 7 0.04
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (208 bp):
ATTTTCAGACACAAGTTTTGATCTTTTTTCCCTTTGATGTCTTTTGCCTACCAACCCTCTCAAAC
TTGTCAAAGTTGAGTGACAAAACACTTAACCAGTGAAGACAAGGGAAGGACCGGTACAGGTTTTG
ATCTCTTCCACTAAATCTATTTCAGGATGTATATCTGTTTATGCTAGTAGAAGAACACAGACACA
TAAACATATAATC
Found at i:244056 original size:23 final size:23
Alignment explanation
Indices: 244030--244178 Score: 244
Period size: 23 Copynumber: 6.5 Consensus size: 23
244020 GAGTCGAGGG
244030 ATTCTATGTGGTCCTTCGGGACA
1 ATTCTATGTGGTCCTTCGGGACA
* *
244053 ATTCTATGTGGTCCTTCAGGATA
1 ATTCTATGTGGTCCTTCGGGACA
* *
244076 ATTCTACGTGGTCATTCGGGACA
1 ATTCTATGTGGTCCTTCGGGACA
244099 ATTCTATGTGGTCCTTCGGGACA
1 ATTCTATGTGGTCCTTCGGGACA
244122 ATTCTATGTGGTCCTTCGGGACA
1 ATTCTATGTGGTCCTTCGGGACA
244145 ATTCTATGTGGTCCTTCGGGACA
1 ATTCTATGTGGTCCTTCGGGACA
* *
244168 AATCTACGTGG
1 ATTCTATGTGG
244179 CACTTTGGTG
Statistics
Matches: 116, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 116 1.00
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (23 bp):
ATTCTATGTGGTCCTTCGGGACA
Found at i:251825 original size:13 final size:13
Alignment explanation
Indices: 251784--251818 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
251774 TGCGTCATAA
*
251784 ATTTATGACGTGC
1 ATTTATGACATGC
*
251797 ATTTATGACACGC
1 ATTTATGACATGC
251810 ATTTATGAC
1 ATTTATGAC
251819 TTACATTGCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (13 bp):
ATTTATGACATGC
Found at i:251940 original size:85 final size:85
Alignment explanation
Indices: 251797--251962 Score: 296
Period size: 85 Copynumber: 2.0 Consensus size: 85
251787 TATGACGTGC
*
251797 ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCATCATAAATGAAGATGA
1 ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCATCATAAATGAAAATGA
*
251862 CACACATTTGTGTGTCATAA
66 CACACATTCGTGTGTCATAA
* *
251882 ATTTATGACACGCATTTATGACTTACATTGCGTGTCATTGAAGCCCCCGTCATAAATGAAAATGA
1 ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCATCATAAATGAAAATGA
251947 CACACATTCGTGTGTC
66 CACACATTCGTGTGTC
251963 GTGATTGTAT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 77 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (85 bp):
ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCATCATAAATGAAAATGA
CACACATTCGTGTGTCATAA
Found at i:256193 original size:580 final size:580
Alignment explanation
Indices: 255093--256251 Score: 2156
Period size: 580 Copynumber: 2.0 Consensus size: 580
255083 GAATGTGAAA
255093 CTACGCGCCCTATTGCCTTTGGAGCCATGTCCCTGATCATTTCCTTTCTTATGCTCTATTAACAA
1 CTACGCGCCCTATTGCCTTTGGAGCCATGTCCCTGATCATTTCCTTTCTTATGCTCTATTAACAA
255158 AATTTCGAACAAACTAATAATCAAAACCACTGGGAAAGAAGAAAGTTTCCCGAGAAATTTGGTGT
66 AATTTCGAACAAACTAATAATCAAAACCACTGGGAAAGAAGAAAGTTTCCCGAGAAATTTGGTGT
255223 TAGAATACTTAGCATTACCTTCTAGAAATGCCTTTCTTCTCGTAGCGTAGGAAACTGGTTACAAA
131 TAGAATACTTAGCATTACCTTCTAGAAATGCCTTTCTTCTCGTAGCGTAGGAAACTGGTTACAAA
*
255288 AATGAAGAAAGATTTTATAGATAAGCAAGATTGTACGGAAAAGTAATGAGAAAAAGGGAAATGAA
196 AATGAAGAAAGATTTTATAGATAAGCAAGATTGTACGAAAAAGTAATGAGAAAAAGGGAAATGAA
* *
255353 AAGGAAACCTGAGGAATCAGCGGAATGGCGATAAGTGGTTCGACTTCCATTGTCAATGTCGATCC
261 AAGGAAACCTGAGGAATCAGCGAAATGGCGAAAAGTGGTTCGACTTCCATTGTCAATGTCGATCC
**
255418 TTGAATCTTTAGAAGGAGGATTAAAGCAAGGGAAACAACTCATCTTCTTTTTGTTTATCTCCACA
326 TTGAATCTTTAGAAGGAGGATTAAAGCAAGGGAAACAACTCATCTTCTTTTTACTTATCTCCACA
*
255483 ATGTTGCAGTTTTCTCCAAGCAAAGTCAGGACACCAAAGAATTTCCAGTATTTCATTGAAATATC
391 ATGTTGCAGTTTTCTCCAAGCAAAGTCAGGACACCAAAGAATTTCCAGTATTTCATTGAAATACC
* *
255548 ATCAAATTAAAAAGACGAGAAAGAGTATTGACCCCTTTGAAGCGAGCCAATTGGTCCTCCTTAGA
456 ATCAAATTAAAAAGACAAGAAAGAGTACTGACCCCTTTGAAGCGAGCCAATTGGTCCTCCTTAGA
255613 TGATTTTGGGTGTTTTCGATTGGATTTTGGAGGGGTAGGGTTTGGAGAAGAAGCATTCTT
521 TGATTTTGGGTGTTTTCGATTGGATTTTGGAGGGGTAGGGTTTGGAGAAGAAGCATTCTT
* * *
255673 CTACGCGCCCTATTGTCTTTGGAGCCATGTCCCTGATCATTTCCTTTCTTATGCTCTGTTACCAA
1 CTACGCGCCCTATTGCCTTTGGAGCCATGTCCCTGATCATTTCCTTTCTTATGCTCTATTAACAA
255738 AATTTCGAACAAACTAATAATCAAAACCACTGGGAAAGAAGAAAGTTTCCCGAGAAATTTGGTGT
66 AATTTCGAACAAACTAATAATCAAAACCACTGGGAAAGAAGAAAGTTTCCCGAGAAATTTGGTGT
* *
255803 TAGAATACTTAGCATTACCTTCTAGAATTGCCTTTCTTCTCTTAGCGTAGGAAACTGGTTACAAA
131 TAGAATACTTAGCATTACCTTCTAGAAATGCCTTTCTTCTCGTAGCGTAGGAAACTGGTTACAAA
255868 AATGAAGAAAGATTTTATAGATAAGCAAGATTGTACGAAAAAGTAATGAGAAAAAGGGAAATGAA
196 AATGAAGAAAGATTTTATAGATAAGCAAGATTGTACGAAAAAGTAATGAGAAAAAGGGAAATGAA
255933 AAGGAAACCTGAGGAATCAGCGAAATGGCGAAAAGTGGTTCGACTTCCATTGTCAATGTCGATCC
261 AAGGAAACCTGAGGAATCAGCGAAATGGCGAAAAGTGGTTCGACTTCCATTGTCAATGTCGATCC
**
255998 TTGAATCTTTAGAATTAGGATTAAAGCAAGGGAAACAACTCATCTTCTTTTTACTTATCTCCACA
326 TTGAATCTTTAGAAGGAGGATTAAAGCAAGGGAAACAACTCATCTTCTTTTTACTTATCTCCACA
* *
256063 ATGTTGCGGTTTTCTCCAAGCAAAGTCAGGACACCAAAGAATTTCCAGTATTTCGTTGAAATACC
391 ATGTTGCAGTTTTCTCCAAGCAAAGTCAGGACACCAAAGAATTTCCAGTATTTCATTGAAATACC
256128 ATCAAATTAAAAAGACAAGAAAGAGTACTGACCCCTTTGAAGCGAGCCAATTGGTCCTCCTTAGA
456 ATCAAATTAAAAAGACAAGAAAGAGTACTGACCCCTTTGAAGCGAGCCAATTGGTCCTCCTTAGA
*
256193 TGATTTTGGGTGTTTTCGATTGGATTTTGGAGGGGTAGGGTTTGGGGAAGAAGCATTCT
521 TGATTTTGGGTGTTTTCGATTGGATTTTGGAGGGGTAGGGTTTGGAGAAGAAGCATTCT
256252 CCATCTGATC
Statistics
Matches: 561, Mismatches: 18, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
580 561 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (580 bp):
CTACGCGCCCTATTGCCTTTGGAGCCATGTCCCTGATCATTTCCTTTCTTATGCTCTATTAACAA
AATTTCGAACAAACTAATAATCAAAACCACTGGGAAAGAAGAAAGTTTCCCGAGAAATTTGGTGT
TAGAATACTTAGCATTACCTTCTAGAAATGCCTTTCTTCTCGTAGCGTAGGAAACTGGTTACAAA
AATGAAGAAAGATTTTATAGATAAGCAAGATTGTACGAAAAAGTAATGAGAAAAAGGGAAATGAA
AAGGAAACCTGAGGAATCAGCGAAATGGCGAAAAGTGGTTCGACTTCCATTGTCAATGTCGATCC
TTGAATCTTTAGAAGGAGGATTAAAGCAAGGGAAACAACTCATCTTCTTTTTACTTATCTCCACA
ATGTTGCAGTTTTCTCCAAGCAAAGTCAGGACACCAAAGAATTTCCAGTATTTCATTGAAATACC
ATCAAATTAAAAAGACAAGAAAGAGTACTGACCCCTTTGAAGCGAGCCAATTGGTCCTCCTTAGA
TGATTTTGGGTGTTTTCGATTGGATTTTGGAGGGGTAGGGTTTGGAGAAGAAGCATTCTT
Found at i:256786 original size:17 final size:17
Alignment explanation
Indices: 256751--256782 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
256741 GGTCTTAAAA
256751 AAATTCTTAAATCCTTC
1 AAATTCTTAAATCCTTC
256768 AAATT-TTAAATCCTT
1 AAATTCTTAAATCCTT
256783 TCAATACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTCTTAAATCCTTC
Found at i:262336 original size:49 final size:50
Alignment explanation
Indices: 262244--262345 Score: 134
Period size: 49 Copynumber: 2.1 Consensus size: 50
262234 AAATACCATG
* * ** *
262244 AGTGGTACCTTTTATGCCGAAAATGCACTGTTATGCAGCTAACTTTCATT
1 AGTGGCACCTTTAATGCCGAAAATGCACAATTATGCAGCTAACTATCATT
**
262294 AGTGGCACCTTTAATGCCG-AAATGCACAATTATGCATTTAACTATCATT
1 AGTGGCACCTTTAATGCCGAAAATGCACAATTATGCAGCTAACTATCATT
262343 AGT
1 AGT
262346 TTATTTTAGA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
49 28 0.62
50 17 0.38
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (50 bp):
AGTGGCACCTTTAATGCCGAAAATGCACAATTATGCAGCTAACTATCATT
Found at i:262513 original size:22 final size:22
Alignment explanation
Indices: 262485--262526 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
262475 CCTCATTTTA
262485 TATATTATGGTA-TCGATACTTC
1 TATATTATGGTACT-GATACTTC
262507 TATATTATGGTACTGATACT
1 TATATTATGGTACTGATACT
262527 CCCTTTCAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (22 bp):
TATATTATGGTACTGATACTTC
Found at i:269132 original size:31 final size:31
Alignment explanation
Indices: 269097--269157 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
269087 CTGCATCAAC
*
269097 TACTCATCATTTGTTCTTTTGTGTGATGGTA
1 TACTCATCATGTGTTCTTTTGTGTGATGGTA
269128 TACTCATCATGTGTTCTTTTGTGTGATGGT
1 TACTCATCATGTGTTCTTTTGTGTGATGGT
269158 TGAGATCTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (31 bp):
TACTCATCATGTGTTCTTTTGTGTGATGGTA
Found at i:269828 original size:20 final size:20
Alignment explanation
Indices: 269786--269856 Score: 108
Period size: 20 Copynumber: 3.5 Consensus size: 20
269776 TTTAAACAAG
*
269786 TTTTGACAAGAAGTTTTGAAAC
1 TTTT-ACAAGAA-TTTCGAAAC
269808 TTTTACAAGAATTTCGAAAC
1 TTTTACAAGAATTTCGAAAC
269828 TTTTACAAGAATTTCGAAAC
1 TTTTACAAGAATTTCGAAAC
269848 TTTT-CAAGA
1 TTTTACAAGA
269857 CAGTAGTAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
19 5 0.10
20 32 0.67
21 7 0.15
22 4 0.08
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.37
Consensus pattern (20 bp):
TTTTACAAGAATTTCGAAAC
Found at i:269921 original size:20 final size:19
Alignment explanation
Indices: 269868--269922 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
269858 AGTAGTAAAA
269868 AAAGTTTCGATAC-TTTTC
1 AAAGTTTCGATACTTTTTC
* *
269886 AAGAGTCTCGAAACTTTTTC
1 AA-AGTTTCGATACTTTTTC
*
269906 TAAAGTTTTGATACTTT
1 -AAAGTTTCGATACTTT
269923 GGCTCCAACG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
18 2 0.07
19 9 0.31
20 16 0.55
21 2 0.07
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.44
Consensus pattern (19 bp):
AAAGTTTCGATACTTTTTC
Found at i:272673 original size:20 final size:19
Alignment explanation
Indices: 272628--272682 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
272618 CAATAATCCA
* *
272628 AAAAGTTTCGATACTTTTC
1 AAAAGTTTCGAAACTTATC
*
272647 AAGAGTTTCGAAACTATATC
1 AAAAGTTTCGAAACT-TATC
*
272667 AAAAGTTTCTAAACTT
1 AAAAGTTTCGAAACTT
272683 TCCCTAAAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (19 bp):
AAAAGTTTCGAAACTTATC
Found at i:272691 original size:20 final size:20
Alignment explanation
Indices: 272668--272710 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
272658 AACTATATCA
272668 AAAGTTTCTAAACTTTCCCT
1 AAAGTTTCTAAACTTTCCCT
272688 AAAGTTTCTAAACTTTCCCT
1 AAAGTTTCTAAACTTTCCCT
272708 AAA
1 AAA
272711 ATTCCGATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (20 bp):
AAAGTTTCTAAACTTTCCCT
Found at i:272722 original size:20 final size:20
Alignment explanation
Indices: 272677--272723 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
272667 AAAAGTTTCT
* * *
272677 AAACTTTCCCTAAAGTTTCT
1 AAACTTTCCCTAAAATTCCG
272697 AAACTTTCCCTAAAATTCCG
1 AAACTTTCCCTAAAATTCCG
*
272717 ATACTTT
1 AAACTTT
272724 GGCTCTAACG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (20 bp):
AAACTTTCCCTAAAATTCCG
Found at i:274609 original size:17 final size:17
Alignment explanation
Indices: 274584--274650 Score: 62
Period size: 17 Copynumber: 3.9 Consensus size: 17
274574 ATAAAATAAA
*
274584 AGTAAAAGATATAGTAT
1 AGTAAAAGATACAGTAT
* ** *
274601 AGGAAAAGAGGCAATAT
1 AGTAAAAGATACAGTAT
* * *
274618 AATAAAAGATATAGAAT
1 AGTAAAAGATACAGTAT
274635 AGTAAAAGATACAGTA
1 AGTAAAAGATACAGTA
274651 CAATAAGAGA
Statistics
Matches: 35, Mismatches: 15, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.57, C:0.03, G:0.19, T:0.21
Consensus pattern (17 bp):
AGTAAAAGATACAGTAT
Found at i:274656 original size:34 final size:34
Alignment explanation
Indices: 274586--274656 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
274576 AAAATAAAAG
* * *
274586 TAAAAGATATAGTATAGGAAAAGAGGCAATATAA
1 TAAAAGATATAGAATAGGAAAAGAGACAATACAA
* * *
274620 TAAAAGATATAGAATAGTAAAAGATACAGTACAA
1 TAAAAGATATAGAATAGGAAAAGAGACAATACAA
274654 TAA
1 TAA
274657 GAGAAATAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.58, C:0.04, G:0.17, T:0.21
Consensus pattern (34 bp):
TAAAAGATATAGAATAGGAAAAGAGACAATACAA
Found at i:274678 original size:17 final size:17
Alignment explanation
Indices: 274613--274747 Score: 103
Period size: 17 Copynumber: 8.0 Consensus size: 17
274603 GAAAAGAGGC
*
274613 AATATAATAAAAGATAT
1 AATATAATAAAAGAAAT
* * *
274630 AGA-ATAGTAAAAGATAC
1 A-ATATAATAAAAGAAAT
* * *
274647 AGTACAATAAGAGAAAT
1 AATATAATAAAAGAAAT
274664 AATATAATAAAAGAAAT
1 AATATAATAAAAGAAAT
* * * *
274681 GATACAGTAAGAGAAAT
1 AATATAATAAAAGAAAT
*
274698 AGTATAATAAAAGAAAT
1 AATATAATAAAAGAAAT
* * *
274715 GATACAAT-AGAGAAAT
1 AATATAATAAAAGAAAT
*
274731 AGTATAATAAAAGAAAT
1 AATATAATAAAAGAAAT
274748 GATACAGTAG
Statistics
Matches: 87, Mismatches: 28, Indels: 6
0.72 0.23 0.05
Matches are distributed among these distances:
16 12 0.14
17 74 0.85
18 1 0.01
ACGTcount: A:0.61, C:0.03, G:0.14, T:0.21
Consensus pattern (17 bp):
AATATAATAAAAGAAAT
Found at i:274690 original size:51 final size:51
Alignment explanation
Indices: 274613--274746 Score: 128
Period size: 51 Copynumber: 2.6 Consensus size: 51
274603 GAAAAGAGGC
* * * *
274613 AATATAATAAAAGATATAGAATAGTAAAAGATACAGTACAATAAGAGAAAT
1 AATATAATAAAAGAAATAGAACAGTAAAAGAAACAGTACAATAAAAGAAAT
* * *
274664 AATATAATAAAAGAAAT-GATACAGTAAGAGAAATAGTATAATAAAAGAAAT
1 AATATAATAAAAGAAATAGA-ACAGTAAAAGAAACAGTACAATAAAAGAAAT
* * * * * *
274715 GATACAAT-AGAGAAATAGTATAATAAAAGAAA
1 AATATAATAAAAGAAATAGAACAGTAAAAGAAA
274747 TGATACAGTA
Statistics
Matches: 67, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
50 19 0.28
51 48 0.72
ACGTcount: A:0.62, C:0.03, G:0.14, T:0.21
Consensus pattern (51 bp):
AATATAATAAAAGAAATAGAACAGTAAAAGAAACAGTACAATAAAAGAAAT
Found at i:274732 original size:33 final size:34
Alignment explanation
Indices: 274649--274775 Score: 204
Period size: 33 Copynumber: 3.8 Consensus size: 34
274639 AAAGATACAG
*
274649 TACAATAAGAGAAATAATATAATAAAAGAAATGA
1 TACAATAAGAGAAATAGTATAATAAAAGAAATGA
*
274683 TACAGTAAGAGAAATAGTATAATAAAAGAAATGA
1 TACAATAAGAGAAATAGTATAATAAAAGAAATGA
274717 TACAAT-AGAGAAATAGTATAATAAAAGAAATGA
1 TACAATAAGAGAAATAGTATAATAAAAGAAATGA
* *
274750 TACAGT-AGAGAAACAGTATAATAAAA
1 TACAATAAGAGAAATAGTATAATAAAA
274776 TAACAGTACA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
33 51 0.58
34 37 0.42
ACGTcount: A:0.61, C:0.04, G:0.15, T:0.20
Consensus pattern (34 bp):
TACAATAAGAGAAATAGTATAATAAAAGAAATGA
Found at i:274743 original size:67 final size:67
Alignment explanation
Indices: 274649--274775 Score: 220
Period size: 67 Copynumber: 1.9 Consensus size: 67
274639 AAAGATACAG
*
274649 TACAATAAGAGAAATAATATAATAAAAGAAATGATACAGTAAGAGAAATAGTATAATAAAAGAAA
1 TACAATAAGAGAAATAATATAATAAAAGAAATGATACAGT-AGAGAAACAGTATAATAAAAGAAA
274714 TGA
65 TGA
*
274717 TACAAT-AGAGAAATAGTATAATAAAAGAAATGATACAGTAGAGAAACAGTATAATAAAA
1 TACAATAAGAGAAATAATATAATAAAAGAAATGATACAGTAGAGAAACAGTATAATAAAA
274776 TAACAGTACA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
66 19 0.33
67 32 0.56
68 6 0.11
ACGTcount: A:0.61, C:0.04, G:0.15, T:0.20
Consensus pattern (67 bp):
TACAATAAGAGAAATAATATAATAAAAGAAATGATACAGTAGAGAAACAGTATAATAAAAGAAAT
GA
Found at i:276073 original size:20 final size:21
Alignment explanation
Indices: 276031--276073 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
276021 TAGAACCCCA
*
276031 GGGGGTATCGATTCCCCTGTGG
1 GGGGGAATCGATTCCCC-GTGG
*
276053 GGGGGAATCGGTTCCCC-TGG
1 GGGGGAATCGATTCCCCGTGG
276073 G
1 G
276074 ACCAGGATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
22 15 0.79
ACGTcount: A:0.09, C:0.23, G:0.44, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGATTCCCCGTGG
Found at i:276893 original size:21 final size:22
Alignment explanation
Indices: 276867--276947 Score: 69
Period size: 21 Copynumber: 3.8 Consensus size: 22
276857 TAGAACCCCA
*
276867 GGGGGGTATCGATTCCCCT-AT
1 GGGGGGAATCGATTCCCCTCAT
* * *
276888 GGGGGGAATTGGTTCCCCTTCAA
1 GGGGGGAATCGATTCCCC-TCAT
* *
276911 AGGGGGAATCGGTT-CCCTCAT
1 GGGGGGAATCGATTCCCCTCAT
*
276932 -GGGGGTATCGATTCCC
1 GGGGGGAATCGATTCCC
276948 TCTGCACCAA
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
20 11 0.23
21 20 0.42
22 4 0.08
23 13 0.27
ACGTcount: A:0.16, C:0.23, G:0.35, T:0.26
Consensus pattern (22 bp):
GGGGGGAATCGATTCCCCTCAT
Found at i:276941 original size:20 final size:20
Alignment explanation
Indices: 276912--276949 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
276902 CCCCTTCAAA
*
276912 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
276932 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
276950 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.34, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:280789 original size:22 final size:21
Alignment explanation
Indices: 280747--280786 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
280737 GAGTTTATTT
*
280747 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
280768 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
280787 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:282689 original size:20 final size:20
Alignment explanation
Indices: 282638--282692 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
282628 TGGAGCGTGG
*
282638 GGGGAATCGGTACCCCTTAA
1 GGGGAATCGGTTCCCCTTAA
282658 GGGGAATCGGTTCCCCTTAA
1 GGGGAATCGGTTCCCCTTAA
282678 GGGGAATCGGTTCCC
1 GGGGAATCGGTTCCC
282693 TAAGTGTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.20, C:0.25, G:0.33, T:0.22
Consensus pattern (20 bp):
GGGGAATCGGTTCCCCTTAA
Found at i:283458 original size:31 final size:31
Alignment explanation
Indices: 283423--283494 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
283413 ATGGACTAGA
*
283423 CTAAGTAAATGTTTTGGATTAATTAAGGAAT
1 CTAAGTAAATGTTTTAGATTAATTAAGGAAT
283454 CTAAGTAAATGTTTTAGATTAATTAAGGAAT
1 CTAAGTAAATGTTTTAGATTAATTAAGGAAT
* *
283485 CCAAATAAAT
1 CTAAGTAAAT
283495 ATGGATGTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.36
Consensus pattern (31 bp):
CTAAGTAAATGTTTTAGATTAATTAAGGAAT
Found at i:284383 original size:12 final size:12
Alignment explanation
Indices: 284366--284413 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
284356 CGAATGTTTT
284366 ATTTGATTTCTG
1 ATTTGATTTCTG
*
284378 ATTTGAATTCTG
1 ATTTGATTTCTG
284390 -TTCTGATTTCTG
1 ATT-TGATTTCTG
* *
284402 ATCTGAGTTCTG
1 ATTTGATTTCTG
284414 TTCTGGTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
11 2 0.07
12 27 0.90
13 1 0.03
ACGTcount: A:0.17, C:0.12, G:0.19, T:0.52
Consensus pattern (12 bp):
ATTTGATTTCTG
Found at i:284396 original size:24 final size:24
Alignment explanation
Indices: 284369--284470 Score: 123
Period size: 24 Copynumber: 4.2 Consensus size: 24
284359 ATGTTTTATT
*
284369 TGATTTCTGATTTGAATTCTGTTC
1 TGATTTCTGATCTGAATTCTGTTC
*
284393 TGATTTCTGATCTGAGTTCTGTTC
1 TGATTTCTGATCTGAATTCTGTTC
* * * *
284417 TGGTTTTTTATCTGAATTCTGTTA
1 TGATTTCTGATCTGAATTCTGTTC
* * *
284441 TGATATCTGATCTGAATTATGTTT
1 TGATTTCTGATCTGAATTCTGTTC
284465 TGATTT
1 TGATTT
284471 TCAATATCTC
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 64 1.00
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.54
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTCTGTTC
Found at i:284418 original size:12 final size:12
Alignment explanation
Indices: 284385--284418 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
284375 CTGATTTGAA
*
284385 TTCTGTTCTGAT
1 TTCTGTTCTGAG
*
284397 TTCTGATCTGAG
1 TTCTGTTCTGAG
284409 TTCTGTTCTG
1 TTCTGTTCTG
284419 GTTTTTTATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.09, C:0.18, G:0.21, T:0.53
Consensus pattern (12 bp):
TTCTGTTCTGAG
Found at i:290755 original size:15 final size:17
Alignment explanation
Indices: 290725--290763 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
290715 CGAAAGGAAA
290725 ATTATTTAATATTAAAT
1 ATTATTTAATATTAAAT
290742 ATTATTTAA-A-TAAAT
1 ATTATTTAATATTAAAT
290757 ATT-TTTA
1 ATTATTTA
290764 TAGAATCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.18
15 8 0.36
16 1 0.05
17 9 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTATTTAATATTAAAT
Found at i:294567 original size:21 final size:21
Alignment explanation
Indices: 294528--294567 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
294518 ATTATTCAGA
* *
294528 AGAAAAAGAAAATTTACATAC
1 AGAAAAAGAAAAATCACATAC
*
294549 AGAAAATGAAAAATCACAT
1 AGAAAAAGAAAAATCACAT
294568 TATGCAGAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.17
Consensus pattern (21 bp):
AGAAAAAGAAAAATCACATAC
Found at i:301955 original size:13 final size:13
Alignment explanation
Indices: 301937--301961 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
301927 TGCTTCATAG
301937 ACATCGTAGGTAA
1 ACATCGTAGGTAA
301950 ACATCGTAGGTA
1 ACATCGTAGGTA
301962 TTGCAATTCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (13 bp):
ACATCGTAGGTAA
Found at i:305264 original size:14 final size:14
Alignment explanation
Indices: 305242--305300 Score: 56
Period size: 14 Copynumber: 4.6 Consensus size: 14
305232 TAAAATGATA
*
305242 AACGAACACAAATG
1 AACGAACACAAACG
*
305256 AATGAACACAAACG
1 AACGAACACAAACG
*
305270 AACG-A-AC--A-T
1 AACGAACACAAACG
305279 AACGAACACAAACG
1 AACGAACACAAACG
305293 AACGAACA
1 AACGAACA
305301 TAACGAACAT
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
9 4 0.11
10 2 0.06
11 2 0.06
12 2 0.06
13 2 0.06
14 23 0.66
ACGTcount: A:0.58, C:0.24, G:0.14, T:0.05
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:305289 original size:23 final size:23
Alignment explanation
Indices: 305259--305319 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
305249 ACAAATGAAT
305259 GAACACAAACGAACGAACATAAC
1 GAACACAAACGAACGAACATAAC
305282 GAACACAAACGAACGAACATAAC
1 GAACACAAACGAACGAACATAAC
* *
305305 GAACATAAACAAACG
1 GAACACAAACGAACG
305320 TAAATGAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.57, C:0.25, G:0.13, T:0.05
Consensus pattern (23 bp):
GAACACAAACGAACGAACATAAC
Found at i:305333 original size:10 final size:10
Alignment explanation
Indices: 305270--305336 Score: 55
Period size: 10 Copynumber: 6.5 Consensus size: 10
305260 AACACAAACG
305270 AACGAACAT-
1 AACGAACATA
*
305279 AACGAACACA
1 AACGAACATA
*
305289 AACGAACGAACA
1 AACGAAC--ATA
305301 TAACGAACATA
1 -AACGAACATA
* *
305312 AACAAACGTA
1 AACGAACATA
*
305322 AATGAACATA
1 AACGAACATA
305332 AACGA
1 AACGA
305337 GCGAACATAA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
9 8 0.17
10 26 0.57
11 2 0.04
12 3 0.07
13 7 0.15
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
AACGAACATA
Found at i:305504 original size:23 final size:23
Alignment explanation
Indices: 305461--305504 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
305451 TAATTGGATT
*
305461 TTAAAATATTAATGAGTTTAAGA
1 TTAAAATATTAATAAGTTTAAGA
*
305484 TTAAAAT-TTATTAAGTCTTAA
1 TTAAAATATTAATAAGT-TTAA
305505 TATTTCAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (23 bp):
TTAAAATATTAATAAGTTTAAGA
Found at i:307180 original size:23 final size:22
Alignment explanation
Indices: 307150--307197 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
307140 TTGTTACTTG
*
307150 AAATAATA-TATATAAATAAATA
1 AAATAATAGTACATAAA-AAATA
*
307172 AAATCAATAGTACATTAAAAATA
1 AAAT-AATAGTACATAAAAAATA
307195 AAA
1 AAA
307198 ATAAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 4 0.18
23 12 0.55
24 6 0.27
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (22 bp):
AAATAATAGTACATAAAAAATA
Found at i:315053 original size:17 final size:17
Alignment explanation
Indices: 315031--315099 Score: 58
Period size: 15 Copynumber: 4.3 Consensus size: 17
315021 CCGTGTCCCG
*
315031 ACCCGGATGTTACGGGT
1 ACCCGGATATTACGGGT
*
315048 ACCCGG-TAAT-CGGGT
1 ACCCGGATATTACGGGT
*
315063 ACCCGGATTTTGA-GGGT
1 ACCCGGATATT-ACGGGT
*
315080 ACCCGG-TAAT-CGGGT
1 ACCCGGATATTACGGGT
315095 ACCCG
1 ACCCG
315100 ATACCCGGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
15 20 0.48
16 6 0.14
17 16 0.38
ACGTcount: A:0.19, C:0.26, G:0.33, T:0.22
Consensus pattern (17 bp):
ACCCGGATATTACGGGT
Found at i:315063 original size:15 final size:15
Alignment explanation
Indices: 315043--315099 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
315033 CCGGATGTTA
315043 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
**
315058 CGGGTACCCGGATTTT
1 CGGGTACCCGG-TAAT
*
315074 GAGGGTACCCGGTAAT
1 -CGGGTACCCGGTAAT
315090 CGGGTACCCG
1 CGGGTACCCG
315100 ATACCCGGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 20 0.59
16 4 0.12
17 10 0.29
ACGTcount: A:0.18, C:0.26, G:0.35, T:0.21
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:315067 original size:32 final size:32
Alignment explanation
Indices: 315031--315099 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
315021 CCGTGTCCCG
315031 ACCCGGATGTT-ACGGGTACCCGGTAATCGGGT
1 ACCCGGATGTTGA-GGGTACCCGGTAATCGGGT
*
315063 ACCCGGATTTTGAGGGTACCCGGTAATCGGGT
1 ACCCGGATGTTGAGGGTACCCGGTAATCGGGT
315095 ACCCG
1 ACCCG
315100 ATACCCGGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 34 0.97
33 1 0.03
ACGTcount: A:0.19, C:0.26, G:0.33, T:0.22
Consensus pattern (32 bp):
ACCCGGATGTTGAGGGTACCCGGTAATCGGGT
Found at i:318388 original size:64 final size:64
Alignment explanation
Indices: 318314--318539 Score: 273
Period size: 64 Copynumber: 3.5 Consensus size: 64
318304 TTGAAGGTGT
* * *
318314 ATCGATGCATAGGTAGTGCATCGATGCA-CTCTTTTAAATAGAAAACATCGAATAGGATTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCTTTTAAATAGAAAACATCGAAT-GAATTTATGC
* ** **
318378 ATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-AAAACATCGAATGTAATTCGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCTTTTAAATAGAAAACATCGAATG-AATTTATGC
*
318442 ATCGATGCATAAGTAGTGCATCGATGCATCCCGTTATT-AAT-G-AAACATCGAATGCATTTTAT
1 ATCGATGCATAAGTAGTGCATCGATGCATCCC-TT-TTAAATAGAAAACATCGAATG-AATTTAT
318504 GC
63 GC
* *
318506 ATCGATGCACAAGTAGTGCATCGATGCATACCTT
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCTT
318540 CATTAAAAGA
Statistics
Matches: 140, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
63 3 0.02
64 123 0.88
65 12 0.09
66 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCTTTTAAATAGAAAACATCGAATGAATTTATGC
Found at i:319262 original size:12 final size:12
Alignment explanation
Indices: 319245--319279 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
319235 ATATATGTTC
*
319245 ATGTGATATGCT
1 ATGTGATATGAT
319257 ATGTGATATGAT
1 ATGTGATATGAT
319269 ATGTGATATGA
1 ATGTGATATGA
319280 CCTGTAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.31, C:0.03, G:0.26, T:0.40
Consensus pattern (12 bp):
ATGTGATATGAT
Found at i:319289 original size:24 final size:24
Alignment explanation
Indices: 319245--319291 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
319235 ATATATGTTC
*
319245 ATGTGATATGCTATGTGATATGAT
1 ATGTGATATGCTATGTAATATGAT
*
319269 ATGTGATATGAC-CTGTAATATGA
1 ATGTGATATG-CTATGTAATATGA
319292 GAACATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.38
Consensus pattern (24 bp):
ATGTGATATGCTATGTAATATGAT
Found at i:319349 original size:29 final size:29
Alignment explanation
Indices: 319307--319380 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
319297 TGATATGAAG
319307 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
319336 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
319365 TGACATGAG-TACATGA
1 TGACATGAGCTACATGA
319381 ACATATGAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (29 bp):
TGACATGAGCTACATGATCACAAGAGAAA
Found at i:319483 original size:15 final size:15
Alignment explanation
Indices: 319465--319572 Score: 171
Period size: 15 Copynumber: 7.2 Consensus size: 15
319455 GAGGGTATAA
319465 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
**
319480 TAGTCCTTCGGGACA
1 TAGTCCTTCGGGATG
319495 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
* *
319510 TAGTCATTCGGGACG
1 TAGTCCTTCGGGATG
319525 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
*
319540 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGATG
319555 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
319570 TAG
1 TAG
319573 GAGTCCTACG
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 83 1.00
ACGTcount: A:0.16, C:0.21, G:0.32, T:0.31
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:319500 original size:30 final size:30
Alignment explanation
Indices: 319464--319572 Score: 191
Period size: 30 Copynumber: 3.6 Consensus size: 30
319454 CGAGGGTATA
319464 ATAGTCCTTCGGGATGTAGTCCTTCGGGAC
1 ATAGTCCTTCGGGATGTAGTCCTTCGGGAC
*
319494 ATAGTCCTTCGGGATGTAGTCATTCGGGAC
1 ATAGTCCTTCGGGATGTAGTCCTTCGGGAC
*
319524 GTAGTCCTTCGGGATGTAGTCCTTCGGGAC
1 ATAGTCCTTCGGGATGTAGTCCTTCGGGAC
*
319554 GTAGTCCTTCGGGATGTAG
1 ATAGTCCTTCGGGATGTAG
319573 GAGTCCTACG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 76 1.00
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (30 bp):
ATAGTCCTTCGGGATGTAGTCCTTCGGGAC
Found at i:323036 original size:64 final size:64
Alignment explanation
Indices: 322958--323179 Score: 249
Period size: 64 Copynumber: 3.5 Consensus size: 64
322948 AGGTGTATCA
* *
322958 ATGCAT-AGGTAGTGCATCGATGCA-CTCTTTTAAATAGAAAACATCGAATAGGATTTATGCATC
1 ATGCATAAGG-AGTGCATCGATGCATCCCTTTTAAATAGAAAACATCGAAT-GAATTTATGCATC
323021 G
64 G
** **
323022 ATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-AAAACATCGAATGTAATTCGTGCATCG
1 ATGCATAAGGAGTGCATCGATGCATCCCTTTTAAATAGAAAACATCGAATG-AATTTATGCATCG
* *
323086 ATGCATAAGTAGTGCATCGATGCATCCCGTTATT-AAT-G-AAACATCGAATGCATTTTATGCAT
1 ATGCATAAGGAGTGCATCGATGCATCCC-TT-TTAAATAGAAAACATCGAATG-AATTTATGCAT
323148 CG
63 CG
* * *
323150 ATGCACAAGTAGTGCATCGATGCATACCTT
1 ATGCATAAGGAGTGCATCGATGCATCCCTT
323180 CATTAAAAGA
Statistics
Matches: 137, Mismatches: 15, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
63 3 0.02
64 117 0.85
65 15 0.11
66 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (64 bp):
ATGCATAAGGAGTGCATCGATGCATCCCTTTTAAATAGAAAACATCGAATGAATTTATGCATCG
Found at i:323902 original size:12 final size:12
Alignment explanation
Indices: 323885--323919 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
323875 ATATATGTTC
*
323885 ATGTGATATGCT
1 ATGTGATATGAT
323897 ATGTGATATGAT
1 ATGTGATATGAT
323909 ATGTGATATGA
1 ATGTGATATGA
323920 CCTGTAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.31, C:0.03, G:0.26, T:0.40
Consensus pattern (12 bp):
ATGTGATATGAT
Found at i:323929 original size:24 final size:24
Alignment explanation
Indices: 323885--323931 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
323875 ATATATGTTC
*
323885 ATGTGATATGCTATGTGATATGAT
1 ATGTGATATGCTATGTAATATGAT
*
323909 ATGTGATATGAC-CTGTAATATGA
1 ATGTGATATG-CTATGTAATATGA
323932 GAACATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.38
Consensus pattern (24 bp):
ATGTGATATGCTATGTAATATGAT
Found at i:323989 original size:29 final size:29
Alignment explanation
Indices: 323947--324049 Score: 199
Period size: 29 Copynumber: 3.6 Consensus size: 29
323937 TGATATGAAG
323947 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
323976 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
324005 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
324034 TGACATGAG-TACATGA
1 TGACATGAGCTACATGA
324050 ACATATGAAA
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
28 7 0.09
29 67 0.91
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.18
Consensus pattern (29 bp):
TGACATGAGCTACATGATCACAAGAGAAA
Found at i:324152 original size:15 final size:15
Alignment explanation
Indices: 324134--324241 Score: 171
Period size: 15 Copynumber: 7.2 Consensus size: 15
324124 GAGGGTATAA
324134 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
**
324149 TAGTCCTTCGGGACA
1 TAGTCCTTCGGGATG
324164 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
* *
324179 TAGTCATTCGGGACG
1 TAGTCCTTCGGGATG
324194 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
*
324209 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGATG
324224 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
324239 TAG
1 TAG
324242 GAGTCCTACC
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 83 1.00
ACGTcount: A:0.16, C:0.21, G:0.32, T:0.31
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:324169 original size:30 final size:30
Alignment explanation
Indices: 324133--324241 Score: 191
Period size: 30 Copynumber: 3.6 Consensus size: 30
324123 CGAGGGTATA
324133 ATAGTCCTTCGGGATGTAGTCCTTCGGGAC
1 ATAGTCCTTCGGGATGTAGTCCTTCGGGAC
*
324163 ATAGTCCTTCGGGATGTAGTCATTCGGGAC
1 ATAGTCCTTCGGGATGTAGTCCTTCGGGAC
*
324193 GTAGTCCTTCGGGATGTAGTCCTTCGGGAC
1 ATAGTCCTTCGGGATGTAGTCCTTCGGGAC
*
324223 GTAGTCCTTCGGGATGTAG
1 ATAGTCCTTCGGGATGTAG
324242 GAGTCCTACC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 76 1.00
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (30 bp):
ATAGTCCTTCGGGATGTAGTCCTTCGGGAC
Found at i:326544 original size:22 final size:23
Alignment explanation
Indices: 326513--326565 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
326503 TAAATGAAAA
*
326513 AATATAAAGAATATACATATAAT
1 AATATAAAGAAAATACATATAAT
*
326536 AATA-AAAGAAAATATATATATAT
1 AATATAAAGAAAATACATATA-AT
326559 ATATATA
1 A-ATATA
326566 TGTTTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 14 0.56
23 7 0.28
24 3 0.12
25 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (23 bp):
AATATAAAGAAAATACATATAAT
Found at i:328221 original size:43 final size:43
Alignment explanation
Indices: 328160--328500 Score: 172
Period size: 43 Copynumber: 7.4 Consensus size: 43
328150 ATCAGCGGTC
*
328160 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATAT
1 CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * *
328203 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGT-T-GATTGACAACCAGCGGT
1 CCTTCGTTGTGAAGTTGAACTTGCG---TTGTCTGGAGT-CCAA-TA----T
*
328253 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * *
328297 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGT-T-GATTGACAACCAGCGGT
1 CCTTCGTTGTGAAGTTGAACTTGCG---TTGTCTGGAGT-CCAA-TA----T
** *
328347 CCCTTCGTCATGAAGTTGAACTTGCATTGTCTGGAGTCCAATAT
1 -CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * *
328391 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGT-T-GATTGACAACCAGCGGT
1 CCTTCGTTGTGAAGTTGAACTTGCG---TTGTCTGGAGT-CCAA-TA----T
* *
328441 CCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATAT
1 -CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
328485 CCTTCGTTGTGAAGTT
1 CCTTCGTTGTGAAGTT
328501 AAAATTGGCT
Statistics
Matches: 221, Mismatches: 41, Indels: 72
0.66 0.12 0.22
Matches are distributed among these distances:
43 80 0.36
44 12 0.05
45 12 0.05
46 15 0.07
48 15 0.07
49 12 0.05
50 12 0.05
51 63 0.29
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (43 bp):
CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:328266 original size:51 final size:51
Alignment explanation
Indices: 328203--328460 Score: 214
Period size: 51 Copynumber: 5.4 Consensus size: 51
328193 AGTCCAATAT
*
328203 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAGCGGTC
1 CCTTCGTCGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAGCGGTC
* * * * *
328254 CCTTCGTCGTGAAGTTGAACTTGCG---TTGTCTGGAGT-CCAA-TA----T-
1 CCTTCGTCGTGAAGTTGAAATTGGGAAATTGT-T-GATTGACAACCAGCGGTC
*
328297 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAGCGGTC
1 CCTTCGTCGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAGCGGTC
* * * * * *
328348 CCTTCGTCATGAAGTTGAACTT--G-CATTGTCTGGAGT-CCAA-TA----T-
1 CCTTCGTCGTGAAGTTGAAATTGGGAAATTGT-T-GATTGACAACCAGCGGTC
*
328391 CCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAGCGGTC
1 CCTTCGTCGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAGCGGTC
328442 CCTTCGTCGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
328461 CTTGCATTGT
Statistics
Matches: 156, Mismatches: 27, Indels: 48
0.68 0.12 0.21
Matches are distributed among these distances:
43 41 0.26
44 8 0.05
45 9 0.06
46 11 0.07
48 11 0.07
49 9 0.06
50 8 0.05
51 59 0.38
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.33
Consensus pattern (51 bp):
CCTTCGTCGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAGCGGTC
Found at i:328295 original size:94 final size:95
Alignment explanation
Indices: 328134--328822 Score: 920
Period size: 94 Copynumber: 7.0 Consensus size: 95
328124 TGGAACTGGA
* * * **
328134 AAATTGTTTATTGACAATCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGGAGTCCA
1 AAATTGTTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
328199 ATATCCTTCGTTGTGAAGTTGAAATTGG-G
66 ATATCCTTCGTTGTGAAGTTGAAATTGGTG
*
328228 AAATTGTTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAATTGTTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
328293 ATATCCTTCGTTGTGAAGTTGAAATTGG-G
66 ATATCCTTCGTTGTGAAGTTGAAATTGGTG
*
328322 AAATTGTTGATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCATTGTCTGGAGTCCA
1 AAATTGTTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
328387 ATATCCTTCGTTGTGAAGTTGAAATTGG-G
66 ATATCCTTCGTTGTGAAGTTGAAATTGGTG
328416 AAATTGTTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
1 AAATTGTTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
*
328481 ATATCCTTCGTTGTGAAGTTAAAATTGGCTCTAAAATTG
66 ATATCCTTCGTTGTGAAGTTGAAATTGG---------TG
* *
328520 AGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCC
1 A-AATTGTTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCC
*
328585 AATGTCCTTCGTTGTGAAGTTGAAATTGGCTCTG
65 AATATCCTTCGTTGTGAAGTTGAAATTGG---TG
328619 AAATTGAGAAATGTTTG-TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
1 AAA-T------TG-TTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
**
328683 GGAGTCCAACGTCCTTCGTTGTGAAGTTGAAATTGGCTCTG
58 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG---TG
*
328724 AAATTGAGAAATATTTG-TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
1 AAATT--G------TTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
*
328788 GGAGTCCAATATCCTTCGTTGAGAAGTTGAAATTG
58 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
328823 ACTCTGGGTA
Statistics
Matches: 547, Mismatches: 22, Indels: 41
0.90 0.04 0.07
Matches are distributed among these distances:
94 273 0.50
98 3 0.01
99 3 0.01
100 1 0.00
104 3 0.01
105 262 0.48
106 2 0.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (95 bp):
AAATTGTTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
ATATCCTTCGTTGTGAAGTTGAAATTGGTG
Found at i:328611 original size:105 final size:105
Alignment explanation
Indices: 328406--328828 Score: 720
Period size: 105 Copynumber: 4.0 Consensus size: 105
328396 GTTGTGAAGT
* *
328406 TGAAATTGGGAAATTGTTGATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGT
1 TGAAATTGAGAAA-TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGT
*
328471 CTGGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
328512 TAAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTC
1 TGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTC
*
328577 TGGAGTCCAATGTCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
328617 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTC
1 TGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTC
**
328682 TGGAGTCCAACGTCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * *
328722 TGAAATTGAGAAATATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTC
* *
328787 TGGAGTCCAATATCCTTCGTTGAGAAGTTGAAATTGACTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
328827 TG
1 TG
328829 GGTAAAACCT
Statistics
Matches: 303, Mismatches: 14, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
105 292 0.96
106 11 0.04
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (105 bp):
TGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTC
TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
Found at i:329591 original size:21 final size:21
Alignment explanation
Indices: 329567--329608 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
329557 ACCTTATTTT
329567 CTCTTCTT-TTGTTCTTTTCTC
1 CTCTT-TTCTTGTTCTTTTCTC
*
329588 CTCTTTTCTTTTTCTTTTCTC
1 CTCTTTTCTTGTTCTTTTCTC
329609 AATTTAGGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (21 bp):
CTCTTTTCTTGTTCTTTTCTC
Found at i:329674 original size:17 final size:15
Alignment explanation
Indices: 329648--329694 Score: 62
Period size: 14 Copynumber: 3.1 Consensus size: 15
329638 CTAAACGTTC
329648 TTTTCTTCTTCTTTTT
1 TTTTCTTCTT-TTTTT
329664 TTTTC--CTTCTTTTT
1 TTTTCTTCTT-TTTTT
329678 TTTTCTTCTTTTTTT
1 TTTTCTTCTTTTTTT
329693 TT
1 TT
329695 CACCTTAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 14 0.48
15 7 0.24
16 8 0.28
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTCTTCTTTTTTT
Found at i:329694 original size:13 final size:13
Alignment explanation
Indices: 329648--329695 Score: 78
Period size: 13 Copynumber: 3.6 Consensus size: 13
329638 CTAAACGTTC
*
329648 TTTTCTTCTTCTT
1 TTTTTTTCTTCTT
329661 TTTTTTTCCTTCTT
1 TTTTTTT-CTTCTT
329675 TTTTTTTCTTCTT
1 TTTTTTTCTTCTT
329688 TTTTTTTC
1 TTTTTTTC
329696 ACCTTAGGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
13 20 0.61
14 13 0.39
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTTCTTCTT
Found at i:339141 original size:20 final size:20
Alignment explanation
Indices: 339103--339146 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
339093 ATAGTTAGTA
*
339103 AAATAAAAATAAATGGAAAT
1 AAATAAAAATAAATAGAAAT
339123 AAATAAAAATAACA-AGAAAT
1 AAATAAAAATAA-ATAGAAAT
339143 AAAT
1 AAAT
339147 GGCAAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (20 bp):
AAATAAAAATAAATAGAAAT
Found at i:340362 original size:22 final size:23
Alignment explanation
Indices: 340331--340383 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
340321 TAAATGAAAA
*
340331 AATATAAAGAATATACATATAAT
1 AATATAAAGAAAATACATATAAT
*
340354 AATA-AAAGAAAATATATATATAT
1 AATATAAAGAAAATACATATA-AT
340377 ATATATA
1 A-ATATA
340384 TGTTTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 14 0.56
23 7 0.28
24 3 0.12
25 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (23 bp):
AATATAAAGAAAATACATATAAT
Found at i:340441 original size:2 final size:2
Alignment explanation
Indices: 340434--340465 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
340424 TAATGATGGT
*
340434 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
340466 AAATAAAATA
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:340544 original size:49 final size:47
Alignment explanation
Indices: 340439--340545 Score: 121
Period size: 49 Copynumber: 2.3 Consensus size: 47
340429 ATGGTTATAT
* *
340439 ATATA-TATATATATATATATAAATATAAAATAAAATAAAAATGTAC
1 ATATAGTATATATATATATATAAATATAAAATAAAATAAAAATGAAA
* *
340485 ATA-AGATATATATATATATATAAGGGA-ATAAAATATAATAATAATGAAA
1 ATATAG-TATATATATATATATAA---ATATAAAATAAAATAAAAATGAAA
340534 ATATAGTATATA
1 ATATAGTATATA
340546 ATAATAGTAG
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
45 1 0.02
46 3 0.06
47 17 0.33
49 27 0.53
50 3 0.06
ACGTcount: A:0.59, C:0.01, G:0.07, T:0.34
Consensus pattern (47 bp):
ATATAGTATATATATATATATAAATATAAAATAAAATAAAAATGAAA
Found at i:348273 original size:23 final size:24
Alignment explanation
Indices: 348245--348294 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
348235 ACGAATGAAT
*
348245 ATAAATAAACGAACATTAAC-AAC
1 ATAAATAAACGAACATAAACAAAC
*
348268 ATAAATAAATGAACATAAACAAAC
1 ATAAATAAACGAACATAAACAAAC
348292 ATA
1 ATA
348295 TTATCGGACG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.64, C:0.14, G:0.04, T:0.18
Consensus pattern (24 bp):
ATAAATAAACGAACATAAACAAAC
Found at i:348540 original size:2 final size:2
Alignment explanation
Indices: 348533--348603 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
348523 TATGATGGTT
348533 TA TA TA TA TA 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
348575 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
348604 TTTTTTAAAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:355045 original size:16 final size:16
Alignment explanation
Indices: 355024--355057 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
355014 AAATAGTGGG
355024 AGCTATCCGTATTAGA
1 AGCTATCCGTATTAGA
355040 AGCTATCCGTATTAGA
1 AGCTATCCGTATTAGA
355056 AG
1 AG
355058 TTATTGCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (16 bp):
AGCTATCCGTATTAGA
Found at i:365532 original size:22 final size:22
Alignment explanation
Indices: 365497--365551 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
365487 ATTCAGCTGT
*
365497 TATAACTCCC-GGAATTATATCA
1 TATAAC-CCCTGGAATTAAATCA
365519 TATAACCCCTGGAATTAAATCA
1 TATAACCCCTGGAATTAAATCA
* *
365541 AATAACTCCTG
1 TATAACCCCTG
365552 TAACTCCTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 3 0.10
22 26 0.90
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.29
Consensus pattern (22 bp):
TATAACCCCTGGAATTAAATCA
Found at i:366716 original size:2 final size:2
Alignment explanation
Indices: 366709--366735 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
366699 AACCAAAATA
366709 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
366736 AATTTAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:366925 original size:18 final size:16
Alignment explanation
Indices: 366882--366923 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
366872 ATTTGAAAGA
366882 TTTA-ATATATTTCTG
1 TTTATATATATTTCTG
366897 TTTATATATATTTCTG
1 TTTATATATATTTCTG
366913 TTTATATATAT
1 TTTATATATAT
366924 ATATATTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.15
16 22 0.85
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (16 bp):
TTTATATATATTTCTG
Found at i:369986 original size:17 final size:17
Alignment explanation
Indices: 369964--369997 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
369954 TACCACTGGC
369964 AGTCCACTTCGATTTCG
1 AGTCCACTTCGATTTCG
369981 AGTCCACTTCGATTTCG
1 AGTCCACTTCGATTTCG
369998 GGTGTACGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.35
Consensus pattern (17 bp):
AGTCCACTTCGATTTCG
Found at i:371459 original size:30 final size:30
Alignment explanation
Indices: 371423--371488 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
371413 AGTGAACTGG
* *
371423 CGGTTCAAATCGGTTTTCCCGGTTTTCAGC
1 CGGTTCAAACCGGCTTTCCCGGTTTTCAGC
**
371453 CGGTTCACCCCGGCTTTCCCGGTTTTCAGC
1 CGGTTCAAACCGGCTTTCCCGGTTTTCAGC
371483 CGGTTC
1 CGGTTC
371489 TTTATCGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.09, C:0.33, G:0.24, T:0.33
Consensus pattern (30 bp):
CGGTTCAAACCGGCTTTCCCGGTTTTCAGC
Found at i:372168 original size:16 final size:16
Alignment explanation
Indices: 372147--372208 Score: 88
Period size: 16 Copynumber: 3.9 Consensus size: 16
372137 TAAATAAACG
*
372147 AACATAAACAAACACA
1 AACATAAACGAACACA
*
372163 AACATAAACGAACACG
1 AACATAAACGAACACA
**
372179 AACATAAATTAACACA
1 AACATAAACGAACACA
372195 AACATAAACGAACA
1 AACATAAACGAACA
372209 TAATATTGAG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.63, C:0.23, G:0.05, T:0.10
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:372180 original size:32 final size:32
Alignment explanation
Indices: 372144--372208 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
372134 TAATAAATAA
372144 ACGAACATAAACAAACACAAACATAAACGAAC
1 ACGAACATAAACAAACACAAACATAAACGAAC
**
372176 ACGAACATAAATTAACACAAACATAAACGAAC
1 ACGAACATAAACAAACACAAACATAAACGAAC
372208 A
1 A
372209 TAATATTGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.62, C:0.23, G:0.06, T:0.09
Consensus pattern (32 bp):
ACGAACATAAACAAACACAAACATAAACGAAC
Found at i:372318 original size:36 final size:36
Alignment explanation
Indices: 372272--372380 Score: 87
Period size: 31 Copynumber: 3.3 Consensus size: 36
372262 GTCAGCTCGA
*
372272 CTCGATTCGAAAACTCGCGAGATTAAAATTATCAAG
1 CTCGACTCGAAAACTCGCGAGATTAAAATTATCAAG
* * *
372308 CTCGACTCG--AACT--CGA-AATATAA-TATTGAA-
1 CTCGACTCGAAAACTCGCGAGATTAAAATTA-TCAAG
*
372338 ----ACTCGAAAACTCGCGAGCTTAAAATTATCAAG
1 CTCGACTCGAAAACTCGCGAGATTAAAATTATCAAG
372370 CTCGACTCGAA
1 CTCGACTCGAA
372381 CTCAAAATAT
Statistics
Matches: 53, Mismatches: 8, Indels: 24
0.62 0.09 0.28
Matches are distributed among these distances:
26 5 0.09
28 4 0.08
30 5 0.09
31 15 0.28
32 5 0.09
34 4 0.08
36 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.24
Consensus pattern (36 bp):
CTCGACTCGAAAACTCGCGAGATTAAAATTATCAAG
Found at i:372347 original size:62 final size:62
Alignment explanation
Indices: 372278--372405 Score: 229
Period size: 62 Copynumber: 2.1 Consensus size: 62
372268 TCGACTCGAT
* *
372278 TCGAAAACTCGCGAGATTAAAATTATCAAGCTCGACTCGAACTCGAAATATAATATTGAAAC
1 TCGAAAACTCGCGAGATTAAAATTATCAAGCTCGACTCGAACTCAAAATATAATATTAAAAC
*
372340 TCGAAAACTCGCGAGCTTAAAATTATCAAGCTCGACTCGAACTCAAAATATAATATTAAAAC
1 TCGAAAACTCGCGAGATTAAAATTATCAAGCTCGACTCGAACTCAAAATATAATATTAAAAC
372402 TCGA
1 TCGA
372406 CTTGAACTCG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.24
Consensus pattern (62 bp):
TCGAAAACTCGCGAGATTAAAATTATCAAGCTCGACTCGAACTCAAAATATAATATTAAAAC
Found at i:372461 original size:47 final size:47
Alignment explanation
Indices: 372373--372463 Score: 114
Period size: 47 Copynumber: 1.9 Consensus size: 47
372363 TATCAAGCTC
* * *
372373 GACTCGAACTCAAAATATAATATTAAAACTCGACTTGAACTCGAAAA
1 GACTCGAACTCAAAATAAAAAATTAAAACTCGACTTAAACTCGAAAA
*
372420 GACTCGAACTCAAAA-AAAAAATTAAGAGCTCGA-TTAAAACTCGA
1 GACTCGAACTCAAAATAAAAAATTAA-AACTCGACTT-AAACTCGA
372464 GACTCGAGCG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
46 10 0.26
47 28 0.74
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (47 bp):
GACTCGAACTCAAAATAAAAAATTAAAACTCGACTTAAACTCGAAAA
Found at i:373394 original size:10 final size:10
Alignment explanation
Indices: 373379--373426 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
373369 ATAATTGAAT
373379 GAACATAAAC
1 GAACATAAAC
373389 GAACATAACCGAAC
1 GAACAT-A---AAC
373403 GAACATAAAC
1 GAACATAAAC
*
373413 GAACATAACC
1 GAACATAAAC
373423 GAAC
1 GAAC
373427 GTTCACGAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.08
Consensus pattern (10 bp):
GAACATAAAC
Found at i:373403 original size:14 final size:14
Alignment explanation
Indices: 373386--373427 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
373376 AATGAACATA
373386 AACGAACATAACCG
1 AACGAACATAACCG
373400 AACGAACAT-A---
1 AACGAACATAACCG
373410 AACGAACATAACCG
1 AACGAACATAACCG
373424 AACG
1 AACG
373428 TTCACGAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 9 0.38
11 1 0.04
13 1 0.04
14 13 0.54
ACGTcount: A:0.52, C:0.26, G:0.14, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:373406 original size:24 final size:24
Alignment explanation
Indices: 373379--373427 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
373369 ATAATTGAAT
373379 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
373403 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
373427 G
1 G
373428 TTCACGAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.53, C:0.24, G:0.14, T:0.08
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:373939 original size:114 final size:113
Alignment explanation
Indices: 373733--373950 Score: 346
Period size: 114 Copynumber: 1.9 Consensus size: 113
373723 TTTACCGCAA
* *
373733 TAACAAACCATTATTCCCGCTACTCTTCTATTATTCTATTTGTTTTAAAAAAATCAACTTCTTTT
1 TAACAAACCATTATTCCCACTACTATTCTATTATTCTATTTGTTTTAAAAAAATCAACTTCTTTT
*
373798 TTAGAAAAAATAATAGGGTTTTATATTATGATCAAACTTTTAGATATT
66 TTAGAAAAAATAATAGGATTTTATATTATGATCAAACTTTTAGATATT
* * * * *
373846 TAACAGACCATTATTCCCACTATTATTTTATTATTCTATTTATTTTTTAAAAAATCAACTTCTTT
1 TAACAAACCATTATTCCCACTACTATTCTATTATTCTATTT-GTTTTAAAAAAATCAACTTCTTT
*
373911 TTTAGAAAAAATAATAGGATTTTATATTATGATCCAACTT
65 TTTAGAAAAAATAATAGGATTTTATATTATGATCAAACTT
373951 CTAGGTTAGC
Statistics
Matches: 95, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
113 36 0.38
114 59 0.62
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (113 bp):
TAACAAACCATTATTCCCACTACTATTCTATTATTCTATTTGTTTTAAAAAAATCAACTTCTTTT
TTAGAAAAAATAATAGGATTTTATATTATGATCAAACTTTTAGATATT
Found at i:380998 original size:21 final size:21
Alignment explanation
Indices: 380956--381000 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
380946 CTACACCAGT
*
380956 AATAGCGCCCGCTACGGTCGC
1 AATAGCGCCCGCTACGGCCGC
* *
380977 AATAGCGCCCGTTATGGCCGC
1 AATAGCGCCCGCTACGGCCGC
380998 AAT
1 AAT
381001 CGCAGTAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.33, G:0.27, T:0.18
Consensus pattern (21 bp):
AATAGCGCCCGCTACGGCCGC
Found at i:382639 original size:44 final size:44
Alignment explanation
Indices: 382589--382681 Score: 159
Period size: 44 Copynumber: 2.1 Consensus size: 44
382579 TACTCCTGTT
*
382589 TTGATCACTGATCTTTTCTTTTGTTTTAATAATGATCTCTTCCA
1 TTGATCACTGATATTTTCTTTTGTTTTAATAATGATCTCTTCCA
* *
382633 TTGATCACTGATATTTTCTTTTGTTTTGATAATGATCTTTTCCA
1 TTGATCACTGATATTTTCTTTTGTTTTAATAATGATCTCTTCCA
382677 TTGAT
1 TTGAT
382682 TATTAGCTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.20, C:0.15, G:0.11, T:0.54
Consensus pattern (44 bp):
TTGATCACTGATATTTTCTTTTGTTTTAATAATGATCTCTTCCA
Found at i:382673 original size:24 final size:25
Alignment explanation
Indices: 382585--382674 Score: 68
Period size: 24 Copynumber: 3.9 Consensus size: 25
382575 ACATTACTCC
*
382585 TGTTTTGATCACTGATCTTTTCTTT
1 TGTTTTGATCAATGATCTTTTCTTT
*
382610 TGTTTTAAT-AATGATC---TC--T
1 TGTTTTGATCAATGATCTTTTCTTT
*** * *
382629 TCCATTGATCACTGATATTTTCTTT
1 TGTTTTGATCAATGATCTTTTCTTT
382654 TGTTTTGAT-AATGATCTTTTC
1 TGTTTTGATCAATGATCTTTTC
382675 CATTGATTAT
Statistics
Matches: 46, Mismatches: 13, Indels: 13
0.64 0.18 0.18
Matches are distributed among these distances:
19 6 0.13
20 5 0.11
21 2 0.04
23 2 0.04
24 16 0.35
25 15 0.33
ACGTcount: A:0.19, C:0.14, G:0.11, T:0.56
Consensus pattern (25 bp):
TGTTTTGATCAATGATCTTTTCTTT
Found at i:382726 original size:68 final size:68
Alignment explanation
Indices: 382654--382790 Score: 211
Period size: 68 Copynumber: 2.0 Consensus size: 68
382644 TATTTTCTTT
* **
382654 TGTTTTGATAATGATCTTTTCCATTGATTATTAGCTAAGGTACACTCTTTTTCTTCCCCTTTTAG
1 TGTTTTGATAATGATCTTTTCCATTGATCATTAGCTAAGGTACACTCTTTTTCTTCAACTTTTAG
382719 GAA
66 GAA
* * * *
382722 TGTTTTGATAATGGTCTTTTCCATTGATCATTGGCTAGGGTATACTCTTTTTCTTCAACTTTTAG
1 TGTTTTGATAATGATCTTTTCCATTGATCATTAGCTAAGGTACACTCTTTTTCTTCAACTTTTAG
382787 GAA
66 GAA
382790 T
1 T
382791 AGAGGTTTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 62 1.00
ACGTcount: A:0.21, C:0.16, G:0.15, T:0.47
Consensus pattern (68 bp):
TGTTTTGATAATGATCTTTTCCATTGATCATTAGCTAAGGTACACTCTTTTTCTTCAACTTTTAG
GAA
Found at i:383955 original size:2 final size:2
Alignment explanation
Indices: 383950--383978 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
383940 TTTTTGACTT
383950 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
383979 TATTCTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:384460 original size:159 final size:160
Alignment explanation
Indices: 384261--384605 Score: 525
Period size: 159 Copynumber: 2.2 Consensus size: 160
384251 TGTAGTATAT
* * *
384261 GAGCATGTGGTTCAAATTTGGT--AAAAAAGTAACTTAAAATAAATCACAAATTGAAGGAATAAG
1 GAGCATATGGCTCAAATTTGGTAAAAAAAAGTAACTTAAAATAAATCACAAATTGAAGAAATAAG
* * *
384324 GAGATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAAATTGTTATCAAAAAGAGGAATTG
66 AAGATTATGAAAAATTGAAAGACTAAATTGAAAAATAAAAAAATTGTCATCAAAAAGAGGAATTG
384389 AAAGTACACATGTAATCTACTATAGTTTAG
131 AAAGTACACATGTAATCTACTATAGTTTAG
* * *
384419 GAGCTTATGGCTCAAATTTGGTAAAAAAAAG-AACTTAAAATAAATGACGAATTGAAGAAATAAG
1 GAGCATATGGCTCAAATTTGGTAAAAAAAAGTAACTTAAAATAAATCACAAATTGAAGAAATAAG
* * *
384483 AAGATTATGAAAAATTGAAAGACTAAATTGAAAAATATAAAATTTGTCATCAAAAAGTGGAATTG
66 AAGATTATGAAAAATTGAAAGACTAAATTGAAAAATAAAAAAATTGTCATCAAAAAGAGGAATTG
* *
384548 AAAGTACACATGTATTCTACTATTGTTTAG
131 AAAGTACACATGTAATCTACTATAGTTTAG
* *
384578 GAGCATGTGGTTCAAATTTGGTAAAAAA
1 GAGCATATGGCTCAAATTTGGTAAAAAA
384606 TGGACTTAAA
Statistics
Matches: 168, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
158 19 0.11
159 142 0.85
160 7 0.04
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.28
Consensus pattern (160 bp):
GAGCATATGGCTCAAATTTGGTAAAAAAAAGTAACTTAAAATAAATCACAAATTGAAGAAATAAG
AAGATTATGAAAAATTGAAAGACTAAATTGAAAAATAAAAAAATTGTCATCAAAAAGAGGAATTG
AAAGTACACATGTAATCTACTATAGTTTAG
Found at i:384686 original size:159 final size:158
Alignment explanation
Indices: 384261--384647 Score: 438
Period size: 159 Copynumber: 2.4 Consensus size: 158
384251 TGTAGTATAT
* * ** * *
384261 GAGCATGTGGTTCAAATTTGGT--AAAAAAGTAACTTAAAATAAATCACAAATTGAAGGAATAAG
1 GAGCATATGGCTCAAATTTGGTAAAAAAAAG-AACTTAAAATAAAGGACGAATTGAAGAAATAAG
* * * * * * * * *
384324 GAGATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAAATTGTTATCAAAAAGAGGAATTG
65 AAAATCATGAAAAATCGAAAGACT-AATTCAAAAATATAAAATTTGTCATCAAAAAGAGGAATTG
384389 AAAGTACACATGTAATCTACTATAGTTTAG
129 AAAGTACACATGTAATCTACTATAGTTTAG
* *
384419 GAGCTTATGGCTCAAATTTGGTAAAAAAAAGAACTTAAAATAAATGACGAATTGAAGAAATAAGA
1 GAGCATATGGCTCAAATTTGGTAAAAAAAAGAACTTAAAATAAAGGACGAATTGAAGAAATAAGA
* * * * *
384484 AGATTATGAAAAATTGAAAGACTAAATTGAAAAATATAAAATTTGTCATCAAAAAGTGGAATTGA
66 AAATCATGAAAAATCGAAAGACT-AATTCAAAAATATAAAATTTGTCATCAAAAAGAGGAATTGA
* *
384549 AAGTACACATGTATTCTACTATTGTTTAG
130 AAGTACACATGTAATCTACTATAGTTTAG
* * * * ** * *
384578 GAGCATGTGGTTCAAATTTGGT-AAAAAATGGACTTAAAATGGAGGAGGAATTGAAGAAATAATA
1 GAGCATATGGCTCAAATTTGGTAAAAAAAAGAACTTAAAATAAAGGACGAATTGAAGAAATAAGA
384642 AAATCA
66 AAATCA
384648 GACTAAATCG
Statistics
Matches: 201, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
158 58 0.29
159 136 0.68
160 7 0.03
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27
Consensus pattern (158 bp):
GAGCATATGGCTCAAATTTGGTAAAAAAAAGAACTTAAAATAAAGGACGAATTGAAGAAATAAGA
AAATCATGAAAAATCGAAAGACTAATTCAAAAATATAAAATTTGTCATCAAAAAGAGGAATTGAA
AGTACACATGTAATCTACTATAGTTTAG
Found at i:385580 original size:18 final size:19
Alignment explanation
Indices: 385558--385621 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
385548 AATAGAAAAA
385558 ATATAAAAATATTATATATT
1 ATAT-AAAATATTATATATT
* * * *
385578 ATATATAATTAATATAAAAT
1 ATATA-AAATATTATATATT
385598 ATATAAAATATTATATA-T
1 ATATAAAATATTATATATT
385616 ATATAA
1 ATATAA
385622 TTAATATAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
18 7 0.19
19 10 0.28
20 19 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATAAAATATTATATATT
Found at i:385624 original size:36 final size:36
Alignment explanation
Indices: 385555--385692 Score: 165
Period size: 36 Copynumber: 3.8 Consensus size: 36
385545 AAAAATAGAA
385555 AAAATATA-AAAATATTATATATTATATATAATTAATAT
1 AAAATATATAAAATA-T-TATA-TATATATAATTAATAT
385593 AAAATATATAAAATATTATATATATATAATTAATAT
1 AAAATATATAAAATATTATATATATATAATTAATAT
* *
385629 AAAAAATAT-AAA-GTTATATATATATAATTAATAT
1 AAAATATATAAAATATTATATATATATAATTAATAT
* * *
385663 AAAAAATAAAAAAAATATTTTATATATATA
1 --AAAATATATAAAATATTATATATATATA
385693 TATAATTGGG
Statistics
Matches: 88, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
34 21 0.24
35 3 0.03
36 30 0.34
37 7 0.08
38 21 0.24
39 6 0.07
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (36 bp):
AAAATATATAAAATATTATATATATATAATTAATAT
Found at i:385646 original size:34 final size:36
Alignment explanation
Indices: 385548--385692 Score: 177
Period size: 34 Copynumber: 3.9 Consensus size: 36
385538 TCATTAAAAA
*
385548 AATAGAAAAAATATAAAAATATTATATATTATATATAATT
1 AATATAAAAAATAT-AAAATA-T-TATA-TATATATAATT
*
385588 AATATAAAATATATAAAATATTATATATATATAATT
1 AATATAAAAAATATAAAATATTATATATATATAATT
*
385624 AATATAAAAAATAT-AAA-GTTATATATATATAATT
1 AATATAAAAAATATAAAATATTATATATATATAATT
* *
385658 AATATAAAAAATAAAAAAAATATTTTATATATATA
1 AATATAAAAAAT--ATAAAATATTATATATATATA
385693 TATAATTGGG
Statistics
Matches: 94, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
34 28 0.30
35 3 0.03
36 25 0.27
37 7 0.07
38 13 0.14
39 6 0.06
40 12 0.13
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (36 bp):
AATATAAAAAATATAAAATATTATATATATATAATT
Found at i:387113 original size:39 final size:40
Alignment explanation
Indices: 387070--387182 Score: 131
Period size: 39 Copynumber: 2.9 Consensus size: 40
387060 TGGCCCTGGT
*
387070 AAATTACAGGAATCTTCAGATATTCTCTTTGTCCCC-GAG
1 AAATTACAGGAATCTTCAGATTTTCTCTTTGTCCCCAGAG
* *
387109 AAATTACAGGAATTTTCATATTTTCTCTTTG-CCCCAGAG
1 AAATTACAGGAATCTTCAGATTTTCTCTTTGTCCCCAGAG
* * * * * *
387148 ACATCAGAAGAATCTTCGGATTTTCTTTTTGTCCC
1 AAATTACAGGAATCTTCAGATTTTCTCTTTGTCCC
387183 TAAAATATCA
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
38 4 0.07
39 54 0.89
40 3 0.05
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (40 bp):
AAATTACAGGAATCTTCAGATTTTCTCTTTGTCCCCAGAG
Found at i:387228 original size:39 final size:39
Alignment explanation
Indices: 387150--387228 Score: 88
Period size: 39 Copynumber: 2.0 Consensus size: 39
387140 CCCCAGAGAC
* * *
387150 ATCAGAAGAATCTTCGGATTTTCTTTTTGTCCCTAAAAT
1 ATCAGAAGAATCATCGGATTTTCTTTTGGTCACTAAAAT
* * *
387189 ATCATAAGAATCATCTGATTTTCTCTTTGGT-ACTGAAAT
1 ATCAGAAGAATCATCGGATTTTCT-TTTGGTCACTAAAAT
387228 A
1 A
387229 GCACAAGAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
39 28 0.85
40 5 0.15
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (39 bp):
ATCAGAAGAATCATCGGATTTTCTTTTGGTCACTAAAAT
Found at i:394424 original size:66 final size:65
Alignment explanation
Indices: 394341--394584 Score: 317
Period size: 66 Copynumber: 3.7 Consensus size: 65
394331 TATTGTACAG
* * *
394341 ATCACTCAATGAGACTCATGTACTTTTTTGGTGCATGAGGTGGAGTGATAATTGAGTACTGCACA
1 ATCACTCAATGAGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTGCAC-
394406 T
65 T
*
394407 ATCACCCAATGAGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTGCACG
1 ATCACTCAATGAGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTGCAC-
*
394472 G
65 T
* * * * * * **
394473 ATCACTCAATGAGACTCATGTACCTTTGTAGTGTATGAGGAGGAATAATAATTGAATATTATACT
1 ATCACTCAATGAGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTGCACT
** *
394538 GATCACTCAATGAGACTTGTGTACCTTTGTGGTGCATAAGGTGGAGT
1 -ATCACTCAATGAGACTCATGTACCTTTGTGGTGCATGAGGTGGAGT
394585 CACTATATGA
Statistics
Matches: 154, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
66 154 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.32
Consensus pattern (65 bp):
ATCACTCAATGAGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTGCACT
Found at i:394864 original size:17 final size:19
Alignment explanation
Indices: 394832--394867 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
394822 GGAACAAGAC
394832 AGAAAAGAGAAACATTATA
1 AGAAAAGAGAAACATTATA
394851 AGAAAA-AG-AACATTATA
1 AGAAAAGAGAAACATTATA
394868 GGAAGAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 2 0.12
19 6 0.35
ACGTcount: A:0.64, C:0.06, G:0.14, T:0.17
Consensus pattern (19 bp):
AGAAAAGAGAAACATTATA
Found at i:396980 original size:60 final size:59
Alignment explanation
Indices: 396886--396999 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 59
396876 ACAAGGGTCA
* * * * * **
396886 TAGTTTGAGGATGAATTTGGAATGTTCAACAATTTAGAGGTTAATTTAGAATGAGAACCG
1 TAGTTTAAAGATGAAATTAGAATGTTCAAAAATTT-GAGACTAATTTAGAATGAGAACCG
*
396946 TAGTTTAAAGATGAAATTAGAATGTTTAAAAATTTGAGACTAATTTAGAATGAG
1 TAGTTTAAAGATGAAATTAGAATGTTCAAAAATTTGAGACTAATTTAGAATGAG
397000 GACCATAATT
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
59 17 0.37
60 29 0.63
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.34
Consensus pattern (59 bp):
TAGTTTAAAGATGAAATTAGAATGTTCAAAAATTTGAGACTAATTTAGAATGAGAACCG
Found at i:397618 original size:102 final size:102
Alignment explanation
Indices: 397501--397704 Score: 399
Period size: 102 Copynumber: 2.0 Consensus size: 102
397491 TATTTCATTT
*
397501 TAAAATTTAAAAAAATAATTTAAAAAACTCTAATTTTTTCTAAAACAATAAAAAAATCAAGACAT
1 TAAAATTTAAAAAAATAATTTAAAAAACTCTAATTTTATCTAAAACAATAAAAAAATCAAGACAT
397566 TAAAATCTCTAATTCAAACTCATTACATCAACCACTA
66 TAAAATCTCTAATTCAAACTCATTACATCAACCACTA
397603 TAAAATTTAAAAAAATAATTTAAAAAACTCTAATTTTATCTAAAACAATAAAAAAATCAAGACAT
1 TAAAATTTAAAAAAATAATTTAAAAAACTCTAATTTTATCTAAAACAATAAAAAAATCAAGACAT
397668 TAAAATCTCTAATTCAAACTCATTACATCAACCACTA
66 TAAAATCTCTAATTCAAACTCATTACATCAACCACTA
397705 CTTCCTCTGA
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.30
Consensus pattern (102 bp):
TAAAATTTAAAAAAATAATTTAAAAAACTCTAATTTTATCTAAAACAATAAAAAAATCAAGACAT
TAAAATCTCTAATTCAAACTCATTACATCAACCACTA
Found at i:398183 original size:60 final size:60
Alignment explanation
Indices: 398115--398275 Score: 232
Period size: 60 Copynumber: 2.7 Consensus size: 60
398105 ACGGAATATC
* * * *
398115 TAAAAGTTTAGGGACCAATTTAGAATGAGATTCATAATTTAAGGATAAAATTGGAATGTT
1 TAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAATTTAAGGATAAAATTAGAATGTT
* *
398175 TAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTAAGGATGAAATTAGAATGTT
1 TAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAATTTAAGGATAAAATTAGAATGTT
* * * *
398235 TAAAAATTTAAAGACTTATTTAGAATGAGAGACATAATTTA
1 TAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAATTTA
398276 GAAACATATG
Statistics
Matches: 90, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 90 1.00
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (60 bp):
TAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAATTTAAGGATAAAATTAGAATGTT
Found at i:398217 original size:31 final size:31
Alignment explanation
Indices: 398134--398232 Score: 96
Period size: 31 Copynumber: 3.3 Consensus size: 31
398124 AGGGACCAAT
*
398134 TTAGAATGAGATTCATAATTTAAGGATAAAA
1 TTAGAATGAGATTCATAGTTTAAGGATAAAA
* * * * *
398165 TTGGAAT--GTTTAAAAGTTTAAGGACT-AAT
1 TTAGAATGAGATTCATAGTTTAAGGA-TAAAA
* *
398194 TTAGAATGAGAGTCATAGTTTAAGGATGAAA
1 TTAGAATGAGATTCATAGTTTAAGGATAAAA
398225 TTAGAATG
1 TTAGAATG
398233 TTTAAAAATT
Statistics
Matches: 52, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
29 21 0.40
30 2 0.04
31 29 0.56
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.33
Consensus pattern (31 bp):
TTAGAATGAGATTCATAGTTTAAGGATAAAA
Found at i:399558 original size:32 final size:32
Alignment explanation
Indices: 399522--399582 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
399512 ATATAGACCC
* * *
399522 GAACATATTGTGCATTATCTGAATGCAAAAAT
1 GAACATACTGCGCATTATCTGAATACAAAAAT
*
399554 GAACATACTGCGTATTATCTGAATACAAA
1 GAACATACTGCGCATTATCTGAATACAAA
399583 CCTGACTAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (32 bp):
GAACATACTGCGCATTATCTGAATACAAAAAT
Found at i:400487 original size:40 final size:41
Alignment explanation
Indices: 400443--400529 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 41
400433 TGGTTTGGAT
*
400443 ACCAGTCT-TTTGATATGGAGACTAGTTCTTCAGTATAGAG
1 ACCAGTCTCTTTGATATAGAGACTAGTTCTTCAGTATAGAG
* * * *
400483 ACCAGT-TCTTTGGTATAGATACTAGTTCTTCGGTATTGAG
1 ACCAGTCTCTTTGATATAGAGACTAGTTCTTCAGTATAGAG
*
400523 ACTAGTC
1 ACCAGTC
400530 GATCTCGAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
39 1 0.03
40 38 0.97
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (41 bp):
ACCAGTCTCTTTGATATAGAGACTAGTTCTTCAGTATAGAG
Found at i:400489 original size:20 final size:20
Alignment explanation
Indices: 400460--400528 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
400450 TTTTGATATG
*
400460 GAGACTAGTTCTTCAGTATA
1 GAGACTAGTTCTTCGGTATA
* *
400480 GAGACCAGTTCTTTGGTATA
1 GAGACTAGTTCTTCGGTATA
* *
400500 GATACTAGTTCTTCGGTATT
1 GAGACTAGTTCTTCGGTATA
400520 GAGACTAGT
1 GAGACTAGT
400529 CGATCTCGAG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.36
Consensus pattern (20 bp):
GAGACTAGTTCTTCGGTATA
Found at i:404211 original size:85 final size:86
Alignment explanation
Indices: 404067--404243 Score: 218
Period size: 85 Copynumber: 2.1 Consensus size: 86
404057 TATTTTACAG
* *
404067 AAATAGCACATTTTTTAAAATAATTACCAAACTAGAACCTTTTCGAATTAAATTTCCAAAATAGC
1 AAATAGCACATTTTTTAAAATAATTACCAAAATAGAACCTTTTCGAATTAAATTCCCAAAATAGC
404132 A-C-TTTCAAATTAAATTCCCA
66 ACCATTTCAAATT-AATTCCCA
* * * * *
404152 AAATAGCATATTTTTT-GAATAAATTCCCAAAATAGCACCCTTTTTGAATT-AATTCCCAAAATA
1 AAATAGCACATTTTTTAAAAT-AATTACCAAAATAG-AACCTTTTCGAATTAAATTCCCAAAATA
*
404215 GCACCCATTTCGAATTAATTCCCA
64 GCA-CCATTTCAAATTAATTCCCA
404239 AAATA
1 AAATA
404244 TCACCCGGTC
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
84 3 0.04
85 42 0.53
86 12 0.15
87 14 0.18
88 8 0.10
ACGTcount: A:0.42, C:0.20, G:0.06, T:0.33
Consensus pattern (86 bp):
AAATAGCACATTTTTTAAAATAATTACCAAAATAGAACCTTTTCGAATTAAATTCCCAAAATAGC
ACCATTTCAAATTAATTCCCA
Found at i:404235 original size:58 final size:58
Alignment explanation
Indices: 404067--404249 Score: 178
Period size: 58 Copynumber: 3.2 Consensus size: 58
404057 TATTTTACAG
** * * * *
404067 AAATAGCACATTTTTTAAAATAATTACCAAACTAG-AACCTTTTCGAATTAAATTTCCA
1 AAATAGCACCCTTTTTAAATTAATTCCCAAAATAGCAACCTTTTCGAATT-AATTCCCA
* * * *
404125 AAATAGCA--C-TTTCAAATTAAATTCCCAAAATAGCATA-TTTTTTGAATAAATTCCCA
1 AAATAGCACCCTTTTTAAATT-AATTCCCAAAATAGCA-ACCTTTTCGAATTAATTCCCA
* * *
404181 AAATAGCACCCTTTTTGAATTAATTCCCAAAATAGCACCCATTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTTAAATTAATTCCCAAAATAGCAACCTTTTCGAATTAATTCCCA
*
404239 AAATATCACCC
1 AAATAGCACCC
404250 GGTCAACGGT
Statistics
Matches: 101, Mismatches: 17, Indels: 14
0.77 0.13 0.11
Matches are distributed among these distances:
55 7 0.07
56 27 0.27
57 9 0.09
58 51 0.50
59 7 0.07
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.32
Consensus pattern (58 bp):
AAATAGCACCCTTTTTAAATTAATTCCCAAAATAGCAACCTTTTCGAATTAATTCCCA
Found at i:404248 original size:29 final size:29
Alignment explanation
Indices: 404087--404249 Score: 163
Period size: 29 Copynumber: 5.7 Consensus size: 29
404077 TTTTTTAAAA
* * *
404087 TAATTACCAAACTAG-AACCTTTTCGAAT
1 TAATTCCCAAAATAGCACCCTTTTCGAAT
* *
404115 TAAATTTCCAAAATAGCA--C-TTTCAAAT
1 T-AATTCCCAAAATAGCACCCTTTTCGAAT
*** *
404142 TAAATTCCCAAAATAGCATATTTTTTGAAT
1 T-AATTCCCAAAATAGCACCCTTTTCGAAT
* *
404172 AAATTCCCAAAATAGCACCCTTTTTGAAT
1 TAATTCCCAAAATAGCACCCTTTTCGAAT
*
404201 TAATTCCCAAAATAGCACCCATTTCGAAT
1 TAATTCCCAAAATAGCACCCTTTTCGAAT
*
404230 TAATTCCCAAAATATCACCC
1 TAATTCCCAAAATAGCACCC
404250 GGTCAACGGT
Statistics
Matches: 115, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
27 24 0.21
28 2 0.02
29 82 0.71
30 7 0.06
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.32
Consensus pattern (29 bp):
TAATTCCCAAAATAGCACCCTTTTCGAAT
Found at i:404283 original size:18 final size:18
Alignment explanation
Indices: 404262--404331 Score: 113
Period size: 18 Copynumber: 3.9 Consensus size: 18
404252 TCAACGGTCG
*
404262 GGTCGGGTCGGGTCAACG
1 GGTCGGGTCGGGTCAACA
*
404280 GGTCGAGTCGGGTCAACA
1 GGTCGGGTCGGGTCAACA
*
404298 GGTTGGGTCGGGTCAACA
1 GGTCGGGTCGGGTCAACA
404316 GGTCGGGTCGGGTCAA
1 GGTCGGGTCGGGTCAA
404332 AACCGGTCAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.16, C:0.20, G:0.46, T:0.19
Consensus pattern (18 bp):
GGTCGGGTCGGGTCAACA
Found at i:411435 original size:28 final size:28
Alignment explanation
Indices: 411381--411512 Score: 149
Period size: 28 Copynumber: 4.7 Consensus size: 28
411371 ATTTTAAAAA
* * *
411381 TAATTACCAAACTAACACCTTTTCGAAT
1 TAATTCCCAAAATAGCACCTTTTCGAAT
411409 TAAATTCCCAAAATAGCA-CTTTTCGAAT
1 T-AATTCCCAAAATAGCACCTTTTCGAAT
* * *
411437 AAATTCCCAAAATATCACCTTTTTGAAT
1 TAATTCCCAAAATAGCACCTTTTCGAAT
* *
411465 TAATTCGCAAAATAGCATCTATTTCGAAT
1 TAATTCCCAAAATAGCACCT-TTTCGAAT
* *
411494 TAATTCTCAAAATATCACC
1 TAATTCCCAAAATAGCACC
411513 CGGTCAACGG
Statistics
Matches: 87, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
27 15 0.17
28 36 0.41
29 36 0.41
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.33
Consensus pattern (28 bp):
TAATTCCCAAAATAGCACCTTTTCGAAT
Found at i:411445 original size:27 final size:28
Alignment explanation
Indices: 411382--411512 Score: 138
Period size: 29 Copynumber: 4.6 Consensus size: 28
411372 TTTTAAAAAT
* * *
411382 AATTACCAAACTAACACCTTTTCGAATTA
1 AATTCCCAAAATAGCACCTTTTCGAA-TA
411411 AATTCCCAAAATAGCA-CTTTTCGAATA
1 AATTCCCAAAATAGCACCTTTTCGAATA
* * *
411438 AATTCCCAAAATATCACCTTTTTGAATT
1 AATTCCCAAAATAGCACCTTTTCGAATA
* * *
411466 AATTCGCAAAATAGCATCTATTTCGAATT
1 AATTCCCAAAATAGCACCT-TTTCGAATA
* *
411495 AATTCTCAAAATATCACC
1 AATTCCCAAAATAGCACC
411513 CGGTCAACGG
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
27 17 0.20
28 34 0.39
29 36 0.41
ACGTcount: A:0.40, C:0.22, G:0.05, T:0.33
Consensus pattern (28 bp):
AATTCCCAAAATAGCACCTTTTCGAATA
Found at i:411505 original size:57 final size:56
Alignment explanation
Indices: 411382--411512 Score: 174
Period size: 56 Copynumber: 2.3 Consensus size: 56
411372 TTTTAAAAAT
* * *
411382 AATTACCAAACTAACACCTTTTCGAATTAAATTCCCAAAATAGCACTTTTCGAATA
1 AATTCCCAAAATATCACCTTTTCGAATTAAATTCCCAAAATAGCACTTTTCGAATA
* * *
411438 AATTCCCAAAATATCACCTTTTTGAATT-AATTCGCAAAATAGCATCTATTTCGAATT
1 AATTCCCAAAATATCACCTTTTCGAATTAAATTCCCAAAATAGCA-CT-TTTCGAATA
*
411495 AATTCTCAAAATATCACC
1 AATTCCCAAAATATCACC
411513 CGGTCAACGG
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
55 15 0.23
56 26 0.39
57 25 0.38
ACGTcount: A:0.40, C:0.22, G:0.05, T:0.33
Consensus pattern (56 bp):
AATTCCCAAAATATCACCTTTTCGAATTAAATTCCCAAAATAGCACTTTTCGAATA
Found at i:415229 original size:612 final size:612
Alignment explanation
Indices: 414066--415289 Score: 2376
Period size: 612 Copynumber: 2.0 Consensus size: 612
414056 ACCAGTCATG
*
414066 CCGTAAAAATCCCCCCAAATTGTCCAGTGGCAAGACTACGGCCTGCAGGGAAATGCCTGCCTGGA
1 CCGTAAAAATCCCCCCAAATTGTCCAGTGGCAAGACTACGGCCTGCAGGGAAATACCTGCCTGGA
414131 GAGGTTGTTGCTGTTCGTGTCCCACTCCTGCATCTTTCGAATTTTCATATAAATGATTGACCTGA
66 GAGGTTGTTGCTGTTCGTGTCCCACTCCTGCATCTTTCGAATTTTCATATAAATGATTGACCTGA
414196 ACTTTCAACGAAAAGATATGCTTTGATGGTTTTGATGCTCCCTTCAGATAGTGCAAGGCAATGGC
131 ACTTTCAACGAAAAGATATGCTTTGATGGTTTTGATGCTCCCTTCAGATAGTGCAAGGCAATGGC
414261 ATGTTCACGAGTTGGAGCTCGTTGAAGCGGTTGCTGATCAGGTAAAAATTGCCTTGTTTTGCTTC
196 ATGTTCACGAGTTGGAGCTCGTTGAAGCGGTTGCTGATCAGGTAAAAATTGCCTTGTTTTGCTTC
414326 TTAACCATGTGTTAATTATTTCCTACTGCCCTTTCCTATCTTTTATGTTTTTAAATACTTCATTG
261 TTAACCATGTGTTAATTATTTCCTACTGCCCTTTCCTATCTTTTATGTTTTTAAATACTTCATTG
414391 TCCAGTAAACATTTCTAATATTTTATGTTTCTTAAATACATACATTGTTTGTGCATGTACAATAA
326 TCCAGTAAACATTTCTAATATTTTATGTTTCTTAAATACATACATTGTTTGTGCATGTACAATAA
414456 TAGTATCACAATGTCATTTCTGTATATAAATACATATTTCGATGGCCTATAGTAATTGATTTGAG
391 TAGTATCACAATGTCATTTCTGTATATAAATACATATTTCGATGGCCTATAGTAATTGATTTGAG
*
414521 CTATTGATAAATGGCTACTTGAGTAGTTACAAGAATATTTTGTAGTCGACTTATTTTGTTAGGCT
456 CTATTGATAAATAGCTACTTGAGTAGTTACAAGAATATTTTGTAGTCGACTTATTTTGTTAGGCT
414586 AATATGTATAATTTGCTATTAATTCTTCGATATTGACGCCTTCAAGTTATTTATGGAAATTGGAG
521 AATATGTATAATTTGCTATTAATTCTTCGATATTGACGCCTTCAAGTTATTTATGGAAATTGGAG
414651 AGCTTTTGACTCTTCTTTAATTGAGTA
586 AGCTTTTGACTCTTCTTTAATTGAGTA
*
414678 CCGTAAAAATCCCCCCAAATTGTCCAGTGGCAAGACTACGGCCTGCAGGGAAGTACCTGCCTGGA
1 CCGTAAAAATCCCCCCAAATTGTCCAGTGGCAAGACTACGGCCTGCAGGGAAATACCTGCCTGGA
*
414743 GAGGTTGTTGCTGTTCGTGTCCCACTCCTGCATCTTTCGAATTTTCATATAAATGATTGGCCTGA
66 GAGGTTGTTGCTGTTCGTGTCCCACTCCTGCATCTTTCGAATTTTCATATAAATGATTGACCTGA
*
414808 ACTTTCAACGAAAAGATATGCTTTGATGGTTTTGATGCTCCCTTCATATAGTGCAAGGCAATGGC
131 ACTTTCAACGAAAAGATATGCTTTGATGGTTTTGATGCTCCCTTCAGATAGTGCAAGGCAATGGC
414873 ATGTTCACGAGTTGGAGCTCGTTGAAGCGGTTGCTGATCAGGTAAAAATTGCCTTGTTTTGCTTC
196 ATGTTCACGAGTTGGAGCTCGTTGAAGCGGTTGCTGATCAGGTAAAAATTGCCTTGTTTTGCTTC
*
414938 TTCACCATGTGTTAATTATTTCCTACTGCCCTTTCCTATCTTTTATGTTTTTAAATACTTCATTG
261 TTAACCATGTGTTAATTATTTCCTACTGCCCTTTCCTATCTTTTATGTTTTTAAATACTTCATTG
415003 TCCAGTAAACATTTCTAATATTTTATGTTTCTTAAATACATACATTGTTTGTGCATGTACAATAA
326 TCCAGTAAACATTTCTAATATTTTATGTTTCTTAAATACATACATTGTTTGTGCATGTACAATAA
* *
415068 TAGTATCGCAATGTCATTTTTGTATATAAATACATATTTCGATGGCCTATAGTAATTGATTTGAG
391 TAGTATCACAATGTCATTTCTGTATATAAATACATATTTCGATGGCCTATAGTAATTGATTTGAG
415133 CTATTGATAAATAGCTACTTGAGTAGTTACAAGAATATTTTGTAGTCGACTTATTTTGTTAGGCT
456 CTATTGATAAATAGCTACTTGAGTAGTTACAAGAATATTTTGTAGTCGACTTATTTTGTTAGGCT
415198 AATATGTATAATTTGCTATTAATTCTTCGATATTGACGCCTTCAAGTTATTTATGGAAATTGGAG
521 AATATGTATAATTTGCTATTAATTCTTCGATATTGACGCCTTCAAGTTATTTATGGAAATTGGAG
415263 AGCTTTTGACTCTTCTTTAATTGAGTA
586 AGCTTTTGACTCTTCTTTAATTGAGTA
415290 ATCATGTCCG
Statistics
Matches: 604, Mismatches: 8, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
612 604 1.00
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.38
Consensus pattern (612 bp):
CCGTAAAAATCCCCCCAAATTGTCCAGTGGCAAGACTACGGCCTGCAGGGAAATACCTGCCTGGA
GAGGTTGTTGCTGTTCGTGTCCCACTCCTGCATCTTTCGAATTTTCATATAAATGATTGACCTGA
ACTTTCAACGAAAAGATATGCTTTGATGGTTTTGATGCTCCCTTCAGATAGTGCAAGGCAATGGC
ATGTTCACGAGTTGGAGCTCGTTGAAGCGGTTGCTGATCAGGTAAAAATTGCCTTGTTTTGCTTC
TTAACCATGTGTTAATTATTTCCTACTGCCCTTTCCTATCTTTTATGTTTTTAAATACTTCATTG
TCCAGTAAACATTTCTAATATTTTATGTTTCTTAAATACATACATTGTTTGTGCATGTACAATAA
TAGTATCACAATGTCATTTCTGTATATAAATACATATTTCGATGGCCTATAGTAATTGATTTGAG
CTATTGATAAATAGCTACTTGAGTAGTTACAAGAATATTTTGTAGTCGACTTATTTTGTTAGGCT
AATATGTATAATTTGCTATTAATTCTTCGATATTGACGCCTTCAAGTTATTTATGGAAATTGGAG
AGCTTTTGACTCTTCTTTAATTGAGTA
Found at i:415676 original size:201 final size:201
Alignment explanation
Indices: 415332--415740 Score: 626
Period size: 201 Copynumber: 2.0 Consensus size: 201
415322 ATGCTAATGA
* *
415332 CCCTCCAAAGACATGGAAAAACTTGGGAAAATTTATCATATTTGTGTAAATCACATACTCATATT
1 CCCTCCAAAGACATGGAAAAACGTGGGAAAATTTATCATATTTGTGTAAATAACATACTCATATT
* * * * *
415397 CAATACTCACAACCAAGTTTGAGTAACATTTTCTACTACAATAAATACATACATTATTGTGATTA
66 AAATACTCACAACCAAGTTTGAGTAACATTTGCTACAACAATAAATACAAACATTATTGTGATCA
* *
415462 TTGGATTTTAGATTTAGTTTTGTAATTAAAAATCGGGACTCTTGCTACATA-TTTTC-TCTGTTT
131 TTGGATTTTAGATTTAGTTTTGTAATTAAAAATCAGGACTCTTGCTACATATTTTTCTTC-ATTT
415525 GCGAGCT
195 GCGAGCT
* *
415532 CCCTCCAAAGAC-TAGGAAGAACGTGGGAAAAATTTATCATATTTGTGTTAATAACATACTCATA
1 CCCTCCAAAGACAT-GGAAAAACGTGGG-AAAATTTATCATATTTGTGTAAATAACATACTCATA
* *
415596 TTAAATACTGACAACCAAGTTTGAGTAACATTTGCTGCAACAATAAATACAAACATTATTGTGAT
64 TTAAATACTCACAACCAAGTTTGAGTAACATTTGCTACAACAATAAATACAAACATTATTGTGAT
* *
415661 CATTGGATTTTAGATTTAGTTTTGTAATTCAAAATCAGGATTCTTGCTACATATTTTTCTTCATT
129 CATTGGATTTTAGATTTAGTTTTGTAATTAAAAATCAGGACTCTTGCTACATATTTTTCTTCATT
*
415726 TGGGAGCT
194 TGCGAGCT
415734 CCCTCCA
1 CCCTCCA
415741 TTCTCTCCTA
Statistics
Matches: 189, Mismatches: 16, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
199 1 0.01
200 23 0.12
201 142 0.75
202 21 0.11
203 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.36
Consensus pattern (201 bp):
CCCTCCAAAGACATGGAAAAACGTGGGAAAATTTATCATATTTGTGTAAATAACATACTCATATT
AAATACTCACAACCAAGTTTGAGTAACATTTGCTACAACAATAAATACAAACATTATTGTGATCA
TTGGATTTTAGATTTAGTTTTGTAATTAAAAATCAGGACTCTTGCTACATATTTTTCTTCATTTG
CGAGCT
Found at i:418011 original size:56 final size:56
Alignment explanation
Indices: 417925--418040 Score: 223
Period size: 56 Copynumber: 2.1 Consensus size: 56
417915 GATCCTGAAA
417925 CATGTATTAAGGTCGAGTTGCTTTCCGATTCAAATTTCGAGATATTTTGACGTTTT
1 CATGTATTAAGGTCGAGTTGCTTTCCGATTCAAATTTCGAGATATTTTGACGTTTT
*
417981 CATGTATTAAGGTCGAGTTGCTTTCCGATTCAAATTTCGAGATGTTTTGACGTTTT
1 CATGTATTAAGGTCGAGTTGCTTTCCGATTCAAATTTCGAGATATTTTGACGTTTT
418037 CATG
1 CATG
418041 GAATTAAAAG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.22, C:0.15, G:0.21, T:0.42
Consensus pattern (56 bp):
CATGTATTAAGGTCGAGTTGCTTTCCGATTCAAATTTCGAGATATTTTGACGTTTT
Found at i:418252 original size:23 final size:21
Alignment explanation
Indices: 418225--418272 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
418215 ATTAATTATT
*
418225 TTTAATTTTATATCATTTATATA
1 TTTAA-TTTATAT-ATTTAAATA
*
418248 TTTAATTTATATTTTTAAATA
1 TTTAATTTATATATTTAAATA
418269 TTTA
1 TTTA
418273 TCAATTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 7 0.30
23 5 0.22
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTAATTTATATATTTAAATA
Found at i:418257 original size:13 final size:13
Alignment explanation
Indices: 418239--418316 Score: 58
Period size: 13 Copynumber: 6.2 Consensus size: 13
418229 ATTTTATATC
418239 ATTTATATATTTA
1 ATTTATATATTTA
*
418252 ATTTATATTTTTA
1 ATTTATATATTTA
* * *
418265 A-ATATTTA-TCA
1 ATTTATATATTTA
418276 ATTTA-AT-TTTA
1 ATTTATATATTTA
*
418287 ATTTAATATATTAA
1 ATTT-ATATATTTA
418301 ATTTA-ATTATTTA
1 ATTTATA-TATTTA
418314 ATT
1 ATT
418317 AGATTGTGAA
Statistics
Matches: 49, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
11 10 0.20
12 8 0.16
13 24 0.49
14 7 0.14
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTATATATTTA
Found at i:418262 original size:36 final size:35
Alignment explanation
Indices: 418221--418291 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 35
418211 GATTATTAAT
*
418221 TATTTTT-AATTTTATATC-ATTTATATATTTAATTTA
1 TATTTTTAAATATT-TATCAATTTA-AT-TTTAATTTA
418257 TATTTTTAAATATTTATCAATTTAATTTTAATTTA
1 TATTTTTAAATATTTATCAATTTAATTTTAATTTA
418292 ATATATTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
35 9 0.28
36 13 0.41
37 10 0.31
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (35 bp):
TATTTTTAAATATTTATCAATTTAATTTTAATTTA
Found at i:418290 original size:29 final size:30
Alignment explanation
Indices: 418224--418290 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
418214 TATTAATTAT
*
418224 TTTTAA-TTTTATATCATTTATATATTTAA
1 TTTTAATTTTTAAATCATTTATATATTTAA
418253 -TTTATATTTTTAAAT-ATTTATCA-ATTTAA
1 TTTTA-ATTTTTAAATCATTTAT-ATATTTAA
418282 TTTTAATTT
1 TTTTAATTT
418291 AATATATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
28 4 0.12
29 17 0.52
30 12 0.36
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (30 bp):
TTTTAATTTTTAAATCATTTATATATTTAA
Found at i:418301 original size:35 final size:36
Alignment explanation
Indices: 418235--418302 Score: 88
Period size: 35 Copynumber: 1.9 Consensus size: 36
418225 TTTAATTTTA
*
418235 TATCATTTATATATTTAATTTATATTTTTAAATATT
1 TATCATTTATATATTTAATTTATATTATTAAATATT
418271 TATCAATTTA-AT-TTTAATTTA-ATATATTAAAT
1 TATC-ATTTATATATTTAATTTATAT-TATTAAAT
418303 TTAATTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 2 0.07
35 16 0.55
36 6 0.21
37 5 0.17
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (36 bp):
TATCATTTATATATTTAATTTATATTATTAAATATT
Done.