Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008048.1 Hibiscus syriacus cultivar Beakdansim tig00110540_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: 541079
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:62 original size:21 final size:20
Alignment explanation
Indices: 23--63 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
13 ACTTCAAGTT
* *
23 CGATAATTGAAACAAGTTTA
1 CGATAATTAAAAAAAGTTTA
43 CGATAATTAAAATAAAGTTTA
1 CGATAATTAAAA-AAAGTTTA
64 AAAATAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (20 bp):
CGATAATTAAAAAAAGTTTA
Found at i:3607 original size:28 final size:28
Alignment explanation
Indices: 3574--3673 Score: 94
Period size: 28 Copynumber: 3.5 Consensus size: 28
3564 TTCATTTGAA
*
3574 TACCTAAAATATTTTTAGTTAAAATAAG
1 TACCTAAAATATTTTTAGTCAAAATAAG
* * *
3602 TACCTAAAGTTATTTTTTGGTCAGAATAAG
1 TACCTAAA-ATA-TTTTTAGTCAAAATAAG
* * *
3632 TACTTCAAATATTTTATA-TCAAAATAGG
1 TACCTAAAATATTTT-TAGTCAAAATAAG
*
3660 TACCTAAACTATTT
1 TACCTAAAATATTT
3674 AAACTTTTTC
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
28 31 0.55
29 5 0.09
30 20 0.36
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (28 bp):
TACCTAAAATATTTTTAGTCAAAATAAG
Found at i:8110 original size:16 final size:16
Alignment explanation
Indices: 8070--8119 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
8060 CGTTCATTTA
8070 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
*
8084 AT-AACGAACACGAAC
1 ATAAATGAACACGAAC
8099 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
8115 ATAAA
1 ATAAA
8120 CGTTGGAGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 2 0.06
14 4 0.13
15 8 0.26
16 17 0.55
ACGTcount: A:0.60, C:0.18, G:0.10, T:0.12
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:9208 original size:14 final size:14
Alignment explanation
Indices: 9191--9232 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
9181 GATTGGGTTA
*
9191 AACATAAATGAACG
1 AACATAAACGAACG
*
9205 AACATAACCGAACG
1 AACATAAACGAACG
9219 AACATAAACGAACG
1 AACATAAACGAACG
9233 TTCACGAACG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.55, C:0.21, G:0.14, T:0.10
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:10825 original size:32 final size:32
Alignment explanation
Indices: 10784--10861 Score: 147
Period size: 32 Copynumber: 2.4 Consensus size: 32
10774 ATCAAATAAG
*
10784 GGTGGAGGAAATATATTTATCTAGTTAAGTCA
1 GGTGAAGGAAATATATTTATCTAGTTAAGTCA
10816 GGTGAAGGAAATATATTTATCTAGTTAAGTCA
1 GGTGAAGGAAATATATTTATCTAGTTAAGTCA
10848 GGTGAAGGAAATAT
1 GGTGAAGGAAATAT
10862 GTTTTTAAGG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (32 bp):
GGTGAAGGAAATATATTTATCTAGTTAAGTCA
Found at i:20171 original size:527 final size:528
Alignment explanation
Indices: 19178--20234 Score: 2017
Period size: 527 Copynumber: 2.0 Consensus size: 528
19168 GTAGAGCTAT
*
19178 GACTCTGTTGAATGGCCAATTTTAATCAGAGCAACGTCAGAGATGGGTTTTGGCAATATATGGTC
1 GACTCTGTTGAATGGCCAATTTTAATCAGAGCAACGTCAGAGATGGGTTTTGGCAATAGATGGTC
19243 CTCGTGGATTTCTCAGTGCCTTTCTACAGCTTCAATTTCGGTACTTGTAAATGGGTCACCTTCGG
66 CTCGTGGATTTCTCAGTGCCTTTCTACAGCTTCAATTTCGGTACTTGTAAATGGGTCACCTTCGG
19308 AAGAGTTTCCTATGGCCAAAGGTTTAAGACAAGGGTGTAGCCTCTCTTCGCTCCTGTTTAACATT
131 AAGAGTTTCCTATGGCCAAAGGTTTAAGACAAGGGTGTAGCCTCTCTTCGCTCCTGTTTAACATT
*
19373 GTAGGCTAGCTGCTTCATTTGATGCTGTCTAAAGCAGTAGACATGGGTTTGTTCCAAGGTTTTGT
196 GTAGGCTAGCTGCTTCATTTGATGCTGTCTAAAGCAATAGACATGGGTTTGTTCCAAGGTTTTGT
*
19438 TATTGGGAAATCTGAAAATTATGCTAAGTTGTCTCATTTTCAGTTTGCCAATGACCTAATCATTT
261 TATTGGGAAATCTGAAAATTATGCTAAGTTGTCTCATTTTCAGTTTGCCAATGACCTAATCAGTT
19503 TTTGCCAAGCCTCTCTTACTCAGATCAAGAATGTTAAAAGAGTGTTGAGGATTTTTAGTATTATG
326 TTTGCCAAGCCTCTCTTACTCAGATCAAGAATGTTAAAAGAGTGTTGAGGATTTTTAGTATTATG
19568 GCAGGGCTGCATCTAAACCTGGCGAAGAGCAAACTGTTTGGAATTAATGTGGATGATGAAGTTTT
391 GCAGGGCTGCATCTAAACCTGGCGAAGAGCAAACTGTTTGGAATTAATGTGGATGATGAAGTTTT
*
19633 AACAGATTGGGCATTTCCCACAGATTATTT-GGATTTCCCCTGGGTGCTAAGAAAAATTCAGAGG
456 AACAGATTGGGCATTTCCCACAGATTATTTGGGACTTCCCCTGGGTGCTAAGAAAAATTCAGAGG
19697 TCTTATGG
521 TCTTATGG
*
19705 GACTCTGTTGAATGGCCAATTTTAATCAGAGCAATGTCAGAGATGGGTTTTGGCAATAGATGGTC
1 GACTCTGTTGAATGGCCAATTTTAATCAGAGCAACGTCAGAGATGGGTTTTGGCAATAGATGGTC
19770 CTCGTGGATTTCTCAGTGCCTTTCTACAGCTTCAATTTCGGTACTTGTAAATGGGTCACCTTCGG
66 CTCGTGGATTTCTCAGTGCCTTTCTACAGCTTCAATTTCGGTACTTGTAAATGGGTCACCTTCGG
19835 AAGAGTTTCCTATGGCCAAAGGTTTAAGACAAGGGTGTAGCCTCTCTTCGCTCCTGTTTAACATT
131 AAGAGTTTCCTATGGCCAAAGGTTTAAGACAAGGGTGTAGCCTCTCTTCGCTCCTGTTTAACATT
*
19900 GTAGGCTAGCTGTTTCATTTGATGCTGTCTAAAGCAATAGACATGGGTTTGTTCCAAGGTTTTGT
196 GTAGGCTAGCTGCTTCATTTGATGCTGTCTAAAGCAATAGACATGGGTTTGTTCCAAGGTTTTGT
* * *
19965 TATTGGGAAATCTGAAAATTCTGCTAGGTTGTCTCATTTTCAGTTTGCCGATGACCTAATCAGTT
261 TATTGGGAAATCTGAAAATTATGCTAAGTTGTCTCATTTTCAGTTTGCCAATGACCTAATCAGTT
*
20030 TTTGCCAGGCCTCTCTTACTCAGATCAAGAATGTTAAAAGAGTGTTGAGGATTTTTAGTATTATG
326 TTTGCCAAGCCTCTCTTACTCAGATCAAGAATGTTAAAAGAGTGTTGAGGATTTTTAGTATTATG
20095 GCAGGGCTGCATCTAAACCTGGCGAAGAGCAAACTGTTTGGAATTAATGTGGATGATGAAGTTTT
391 GCAGGGCTGCATCTAAACCTGGCGAAGAGCAAACTGTTTGGAATTAATGTGGATGATGAAGTTTT
20160 AACAGATTGGGCATTTCCCACAGATTATTTGGGACTTCCCCTGGGTGCTAAGAAAAATTCAGAGG
456 AACAGATTGGGCATTTCCCACAGATTATTTGGGACTTCCCCTGGGTGCTAAGAAAAATTCAGAGG
20225 TCTTATGG
521 TCTTATGG
20233 GA
1 GA
20235 TCCAGTTTTT
Statistics
Matches: 519, Mismatches: 10, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
527 476 0.92
528 43 0.08
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (528 bp):
GACTCTGTTGAATGGCCAATTTTAATCAGAGCAACGTCAGAGATGGGTTTTGGCAATAGATGGTC
CTCGTGGATTTCTCAGTGCCTTTCTACAGCTTCAATTTCGGTACTTGTAAATGGGTCACCTTCGG
AAGAGTTTCCTATGGCCAAAGGTTTAAGACAAGGGTGTAGCCTCTCTTCGCTCCTGTTTAACATT
GTAGGCTAGCTGCTTCATTTGATGCTGTCTAAAGCAATAGACATGGGTTTGTTCCAAGGTTTTGT
TATTGGGAAATCTGAAAATTATGCTAAGTTGTCTCATTTTCAGTTTGCCAATGACCTAATCAGTT
TTTGCCAAGCCTCTCTTACTCAGATCAAGAATGTTAAAAGAGTGTTGAGGATTTTTAGTATTATG
GCAGGGCTGCATCTAAACCTGGCGAAGAGCAAACTGTTTGGAATTAATGTGGATGATGAAGTTTT
AACAGATTGGGCATTTCCCACAGATTATTTGGGACTTCCCCTGGGTGCTAAGAAAAATTCAGAGG
TCTTATGG
Found at i:28021 original size:98 final size:98
Alignment explanation
Indices: 27905--28782 Score: 1345
Period size: 98 Copynumber: 9.0 Consensus size: 98
27895 ATTCTTCGTG
* * * * * *
27905 AAAGAAAGAAAAAGATAGTGTGAAAGAAAAGATTGTTCTTCGTGAGAATGAAAAGATAGAAACTA
1 AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGATTGTTCTTGGTGAGAGTGAGAAGATAGAAACCA
* *
27970 TACCCGAATCAACTCAAAAGCTACACCCGAACT
66 TACCCGAATCAGCTCAAAAACTACACCCGAACT
* * *
28003 AAAGAAAGAAAAAAATAGTGTGGAAGAGAAGATTGCTCTTGGTGAGAGTGAGAAGATAGAAATCA
1 AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGATTGTTCTTGGTGAGAGTGAGAAGATAGAAACCA
* * * *
28068 TATCCAAATCAGCTAAAAAACTAAACCCG----
66 TACCCGAATCAGCTCAAAAACTACACCCGAACT
* * *
28097 -AAGAAAGAAAAAAATAGTGTGGAAGAGAAGATTGTTCTTGGTGAGAGTGATAAGATATAAACCA
1 AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGATTGTTCTTGGTGAGAGTGAGAAGATAGAAACCA
* * *
28161 TACTCGAATCAACTCAAAAACTACACCCGAATT
66 TACCCGAATCAGCTCAAAAACTACACCCGAACT
*
28194 AAAGAAAGAAAAAGATAGTGCGGAAGAGAAGATTGTTCTTGGTGAGAGTGAGAAGATAGAAACCA
1 AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGATTGTTCTTGGTGAGAGTGAGAAGATAGAAACCA
* *
28259 TATCCGAATCAGCTTAAAAACTACACCCGAACT
66 TACCCGAATCAGCTCAAAAACTACACCCGAACT
* * *
28292 AAAGAAAGAAAAATATAGTGCGGAAGAGAAGATTGTTCTTGGTGACAGTGAGAAGATAGAAACCA
1 AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGATTGTTCTTGGTGAGAGTGAGAAGATAGAAACCA
28357 TACCCGAATCAGCTCAAAAACTAC-CCCTGAACT
66 TACCCGAATCAGCTCAAAAACTACACCC-GAACT
*
28390 AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGATTGTTCTTGGTGAGAGTGAGAAGATAAAAACCA
1 AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGATTGTTCTTGGTGAGAGTGAGAAGATAGAAACCA
* *
28455 TACCCGAATCAACTCAAAAACTACACCTGAACT
66 TACCCGAATCAGCTCAAAAACTACACCCGAACT
*
28488 AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGTTTGTTCTTGGTGAGAGTGAGAAGATAGAAACCA
1 AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGATTGTTCTTGGTGAGAGTGAGAAGATAGAAACCA
28553 TACCCGAATCAGCTCAAAAACTACACCCGAACT
66 TACCCGAATCAGCTCAAAAACTACACCCGAACT
* * * *
28586 AAAGAAAGAAAAATATAGTGCGGAAGAGAATATTGTCCTTGGTGAGAGTGAGAAGATAGAAACCA
1 AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGATTGTTCTTGGTGAGAGTGAGAAGATAGAAACCA
*
28651 TACCCGAATCAACTCAAAAACTACACCCGAACT
66 TACCCGAATCAGCTCAAAAACTACACCCGAACT
* *
28684 AAAGAAAGAAAAAGATAGCGTGGAAGAGAAGATTGTTTTTGGTGAGAAGTGAGAAGATAGAAACC
1 AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGATTGTTCTTGGTGAG-AGTGAGAAGATAGAAACC
*
28749 ATACCCGAATCAGCTCAAAAAATACACCCGAACT
65 ATACCCGAATCAGCTCAAAAACTACACCCGAACT
28783 GATCTAACCT
Statistics
Matches: 710, Mismatches: 62, Indels: 15
0.90 0.08 0.02
Matches are distributed among these distances:
93 83 0.12
97 3 0.00
98 572 0.81
99 52 0.07
ACGTcount: A:0.45, C:0.15, G:0.22, T:0.18
Consensus pattern (98 bp):
AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGATTGTTCTTGGTGAGAGTGAGAAGATAGAAACCA
TACCCGAATCAGCTCAAAAACTACACCCGAACT
Found at i:35087 original size:12 final size:12
Alignment explanation
Indices: 35070--35107 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
35060 TAAAATTCAT
35070 GTCCAAACTCGA
1 GTCCAAACTCGA
35082 GTCCAAACTCGA
1 GTCCAAACTCGA
* *
35094 GTTCAAACTTGA
1 GTCCAAACTCGA
35106 GT
1 GT
35108 TTGAATTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (12 bp):
GTCCAAACTCGA
Found at i:38411 original size:29 final size:30
Alignment explanation
Indices: 38378--38466 Score: 90
Period size: 35 Copynumber: 2.8 Consensus size: 30
38368 GTATTTTATC
*
38378 AAAGTAGAAGTGTCATATTGTACATGTTAAA
1 AAAGTAGAAGTATCATATTGTACATGTT-AA
38409 AGTACATGTAGAAGTATCATATTGTACATGTT-A
1 A--A-A-GTAGAAGTATCATATTGTACATGTTAA
* * *
38442 AAAGTACAAGTATCACATTGAACAT
1 AAAGTAGAAGTATCATATTGTACAT
38467 TGTATCAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
29 19 0.38
30 1 0.02
31 2 0.04
33 3 0.06
34 1 0.02
35 24 0.48
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (30 bp):
AAAGTAGAAGTATCATATTGTACATGTTAA
Found at i:38429 original size:35 final size:35
Alignment explanation
Indices: 38381--38449 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
38371 TTTTATCAAA
*
38381 GTAGAAGTGTCATATTGTACATGTTAAAAGTACAT
1 GTAGAAGTATCATATTGTACATGTTAAAAGTACAT
38416 GTAGAAGTATCATATTGTACATGTTAAAAGTACA
1 GTAGAAGTATCATATTGTACATGTTAAAAGTACA
38450 AGTATCACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (35 bp):
GTAGAAGTATCATATTGTACATGTTAAAAGTACAT
Found at i:42213 original size:28 final size:30
Alignment explanation
Indices: 42173--42228 Score: 89
Period size: 28 Copynumber: 1.9 Consensus size: 30
42163 ATGTTGAGAG
*
42173 ATTTTCATAA-CCCTCT-CTTTATTTCTAA
1 ATTTTCATAACCCCTCTGCTATATTTCTAA
42201 ATTTTCATAACCCCTCTGCTATATTTCT
1 ATTTTCATAACCCCTCTGCTATATTTCT
42229 TTCACTGGCG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 10 0.40
29 6 0.24
30 9 0.36
ACGTcount: A:0.23, C:0.27, G:0.02, T:0.48
Consensus pattern (30 bp):
ATTTTCATAACCCCTCTGCTATATTTCTAA
Found at i:45276 original size:60 final size:60
Alignment explanation
Indices: 45162--45300 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 60
45152 AATAGTCAAC
* * * **
45162 TGACCATTTTGTAACTTTTAATAGTTAGAGGAAACAATAAAACACCACCCTATAGTCGGA
1 TGACTATTTTGTAACTTTTAATAGTCAGAGGAAACAACAAAACAAAACCCTATAGTCGGA
* ** * * *
45222 TGACTATTTTGTAACTTTTAATAGTCGGAGGACTCAACAAAATAAAACCTTATAGTCGGG
1 TGACTATTTTGTAACTTTTAATAGTCAGAGGAAACAACAAAACAAAACCCTATAGTCGGA
*
45282 GGACTATTTT-TATACTTTT
1 TGACTATTTTGTA-ACTTTT
45301 CCCAATAAGT
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 2 0.03
60 64 0.97
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Consensus pattern (60 bp):
TGACTATTTTGTAACTTTTAATAGTCAGAGGAAACAACAAAACAAAACCCTATAGTCGGA
Found at i:48017 original size:21 final size:22
Alignment explanation
Indices: 47984--48028 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
47974 TAGAGATTTT
47984 TATTTTTATATTAAT-AAAATA
1 TATTTTTATATTAATAAAAATA
*
48005 TATTCTTTA-ATTATTAAAAATA
1 TATT-TTTATATTAATAAAAATA
48027 TA
1 TA
48029 AAATTTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TATTTTTATATTAATAAAAATA
Found at i:48797 original size:183 final size:184
Alignment explanation
Indices: 48489--48821 Score: 625
Period size: 183 Copynumber: 1.8 Consensus size: 184
48479 ATAAAATTTT
*
48489 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAGAAA
1 AAATATTAAATATATAATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAGAAA
*
48554 TTTAAGATTCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATAT-AAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
48618 TTATTTTATAATTATATATTTAAATTAATTGTAAATTATTTTTCTGAATTAAAA
131 TTATTTTATAATTATATATTTAAATTAATTGTAAATTATTTTTCTGAATTAAAA
48672 AAATATTAAATATATAATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTA-ATA
1 AAATATTAAATATATAATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAGA-A
48736 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATT
65 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATT
48801 TTTATTTTATAATTATATATT
130 TTTATTTTATAATTATATATT
48822 ATTTAAATTA
Statistics
Matches: 146, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
182 1 0.01
183 119 0.82
184 26 0.18
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.39
Consensus pattern (184 bp):
AAATATTAAATATATAATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAGAAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
TTATTTTATAATTATATATTTAAATTAATTGTAAATTATTTTTCTGAATTAAAA
Found at i:48823 original size:18 final size:19
Alignment explanation
Indices: 48802--48854 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
48792 TATAAAATTT
48802 TTATTTTATAATTATA-TA
1 TTATTTTATAATTATACTA
*
48820 TTATTTAAATTAATTATACTA
1 TTATTT-TA-TAATTATACTA
48841 TT-TTTT-TAATTATA
1 TTATTTTATAATTATA
48855 AAATATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
17 8 0.27
18 6 0.20
19 1 0.03
20 11 0.37
21 4 0.13
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATTTTATAATTATACTA
Found at i:48835 original size:20 final size:21
Alignment explanation
Indices: 48810--48852 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
48800 TTTTATTTTA
48810 TAATTATA-TATTATTTAAAT
1 TAATTATACTATTATTTAAAT
* *
48830 TAATTATACTATTTTTTTAAT
1 TAATTATACTATTATTTAAAT
48851 TA
1 TA
48853 TAAAATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TAATTATACTATTATTTAAAT
Found at i:48860 original size:183 final size:183
Alignment explanation
Indices: 48489--48865 Score: 620
Period size: 183 Copynumber: 2.1 Consensus size: 183
48479 ATAAAATTTT
*
48489 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAGAAA
1 AAATATTAAATATATAATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAGAAA
*
48554 TTTAAGATTCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAATTTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAATTTT
*
48619 TATTTTATAATTATATATTTAAATTAATTGTAAATTATTTTTCTGAATTAAAA
131 TATTTTATAATTATATATTTAAATTAATTGTAAACTATTTTTCTGAATTAAAA
48672 AAATATTAAATATATAATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTA-ATA
1 AAATATTAAATATATAATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAGA-A
48736 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATT
65 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATAT-AAATT
* * *
48801 TTTATTTTATAATTATATATTATTTAAATTAA-T-TATACTATTTTT-TTAATT-ATA
129 TTTATTTTATAA-T-TATA-TATTTAAATTAATTGTAAACTATTTTTCTGAATTAAAA
48855 AAATATTAAAT
1 AAATATTAAAT
48866 TTTTATATAA
Statistics
Matches: 183, Mismatches: 6, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
182 1 0.01
183 132 0.72
184 22 0.12
185 11 0.06
186 5 0.03
187 12 0.07
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.41
Consensus pattern (183 bp):
AAATATTAAATATATAATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAGAAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAATTTT
TATTTTATAATTATATATTTAAATTAATTGTAAACTATTTTTCTGAATTAAAA
Found at i:49943 original size:62 final size:65
Alignment explanation
Indices: 49784--49943 Score: 150
Period size: 62 Copynumber: 2.5 Consensus size: 65
49774 CTCCAACTAG
* *
49784 ATATCTTTTAATATCTAAATTTAAACAAATAATAATATCTTTAAATTTAAAATATTAAAAAATAA
1 ATATCTTTAAATAT-TAAACTTAAACAAA-AAT-ATATCTTTAAATTTAAAATATTAAAAAATAA
49849 ACA
63 ACA
* * * * * * *
49852 AT-TCTTTCATTATTCAAACTTAAATAAAAAT-TAT-TTT-AATTTGAAATATTGAAAAATATAT
1 ATATCTTTAAATATT-AAACTTAAACAAAAATATATCTTTAAATTTAAAATATTAAAAAATAAAC
49913 A
65 A
*
49914 ATTATCTTTAAATATTAAAGTTAAA-AAAAA
1 A-TATCTTTAAATATTAAACTTAAACAAAAA
49944 GTAATTTATC
Statistics
Matches: 78, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
62 27 0.35
63 12 0.15
64 13 0.17
66 4 0.05
67 20 0.26
68 2 0.03
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (65 bp):
ATATCTTTAAATATTAAACTTAAACAAAAATATATCTTTAAATTTAAAATATTAAAAAATAAACA
Found at i:50615 original size:15 final size:15
Alignment explanation
Indices: 50566--50616 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
50556 ATTTTTTTAA
50566 TTTAATTACT-TAAC
1 TTTAATTACTCTAAC
50580 TTTCAAATTACTCGTAA-
1 TTT--AATTACTC-TAAC
*
50597 TTTAATCACTCTAAC
1 TTTAATTACTCTAAC
50612 TTTAA
1 TTTAA
50617 AATTTATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
14 6 0.19
15 12 0.39
16 7 0.23
17 3 0.10
18 3 0.10
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.45
Consensus pattern (15 bp):
TTTAATTACTCTAAC
Found at i:50924 original size:21 final size:21
Alignment explanation
Indices: 50898--50942 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
50888 GATTTTGAAA
50898 AAAATTAAAAGTTTAAATACT
1 AAAATTAAAAGTTTAAATACT
* * *
50919 AAAATTGATAGTTTAGATACT
1 AAAATTAAAAGTTTAAATACT
50940 AAA
1 AAA
50943 TGCATAATTT
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:0.53, C:0.04, G:0.09, T:0.33
Consensus pattern (21 bp):
AAAATTAAAAGTTTAAATACT
Found at i:51968 original size:5 final size:5
Alignment explanation
Indices: 51958--51991 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
51948 TACTTATAGT
*
51958 TAAAA TAAAA TAAAG TAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
51992 TCGACGAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:55365 original size:28 final size:29
Alignment explanation
Indices: 55315--55372 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
55305 TGATTTCGCC
* * *
55315 CTCCTAAAATTTTATAAGTTTAAGTTTGT
1 CTCCTAAAATTTTAAAAATTTAAATTTGT
*
55344 CTCCTGAAA-TTTAAAAATTTAAATTTGT
1 CTCCTAAAATTTTAAAAATTTAAATTTGT
55372 C
1 C
55373 CACTTAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (29 bp):
CTCCTAAAATTTTAAAAATTTAAATTTGT
Found at i:56382 original size:27 final size:27
Alignment explanation
Indices: 56344--56405 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
56334 AATCCGACCC
* *
56344 GATCCGAAAAATATATACTCTCCATCT
1 GATCCGAAAAATATATACCCTCCACCT
56371 GATCCGAAAAATATATACCCTCCACCT
1 GATCCGAAAAATATATACCCTCCACCT
56398 GAGTCCGA
1 GA-TCCGA
56406 CCCGACCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 27 0.84
28 5 0.16
ACGTcount: A:0.35, C:0.29, G:0.11, T:0.24
Consensus pattern (27 bp):
GATCCGAAAAATATATACCCTCCACCT
Found at i:58645 original size:15 final size:15
Alignment explanation
Indices: 58625--58662 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
58615 ATATTTAGCT
*
58625 GGGCGGGTGGATGTG
1 GGGCGGGTGGATGCG
*
58640 GGGCGGGCGGATGCG
1 GGGCGGGTGGATGCG
58655 GGGCGGGT
1 GGGCGGGT
58663 AATGTCTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.05, C:0.13, G:0.68, T:0.13
Consensus pattern (15 bp):
GGGCGGGTGGATGCG
Found at i:58847 original size:2 final size:2
Alignment explanation
Indices: 58840--58867 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
58830 ATTGAATTTA
58840 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
58868 CTGTTGGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63663 original size:21 final size:21
Alignment explanation
Indices: 63639--63694 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
63629 CGGAAATATT
*
63639 CATTTTAGGTAGCGAAATTAA
1 CATTTTAGGTAGCGAAAATAA
* ***
63660 CATTTTCGGTATAAAAAATAA
1 CATTTTAGGTAGCGAAAATAA
*
63681 CATTTAAGGTAGCG
1 CATTTTAGGTAGCG
63695 CTCTACTGAA
Statistics
Matches: 25, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (21 bp):
CATTTTAGGTAGCGAAAATAA
Found at i:69370 original size:14 final size:14
Alignment explanation
Indices: 69351--69402 Score: 81
Period size: 14 Copynumber: 3.9 Consensus size: 14
69341 TGTTTTATTC
69351 TCTTCATTTCTTCT
1 TCTTCATTTCTTCT
69365 TCTTCATTTCTTCT
1 TCTTCATTTCTTCT
*
69379 TCTTCCTTTC-TCT
1 TCTTCATTTCTTCT
69392 TCTT-ATTTCTT
1 TCTTCATTTCTT
69403 TCTCCAAGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
12 4 0.11
13 8 0.23
14 23 0.66
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.65
Consensus pattern (14 bp):
TCTTCATTTCTTCT
Found at i:72757 original size:163 final size:163
Alignment explanation
Indices: 72487--72826 Score: 545
Period size: 163 Copynumber: 2.1 Consensus size: 163
72477 AACCGGATTC
* * *
72487 AATATGACAAAATCGATAAAGATCTACCGGATATGTTGAAGGTATCGATACCATTAAAATAAGTA
1 AATATGACAAAACCAATAAAGAGCTACCGGATATGTTGAAGGTATCGATACCATTAAAATAAGTA
* * * *
72552 TCGGTACTTTTGGAATTTAAAAGAAAAACAATAATAGCGCCTATACAGTATCGATACTTTATAAA
66 TCGATACTTTTGGAATTAAAAAGAAAAACAATAATAGCGCCTATAAAGTATCAATACTTTATAAA
72617 CACGTATCGATACATAACAATATAACAAGTAAA
131 CACGTATCGATACATAACAATATAACAAGTAAA
* *
72650 AATATGAAAAAACCAATAAAGAGCTACCGGATATGTTGAAGGTATCGATACCATTAAAATAAGTG
1 AATATGACAAAACCAATAAAGAGCTACCGGATATGTTGAAGGTATCGATACCATTAAAATAAGTA
* * *
72715 TCGATGCTTTTGGAATTAAAAAGAAAAGCAATACTAGCGCCTATAAAGTATCAATACTTTATAAA
66 TCGATACTTTTGGAATTAAAAAGAAAAACAATAATAGCGCCTATAAAGTATCAATACTTTATAAA
* * *
72780 CATGTATCGATACATAATAATATAACATGTAAA
131 CACGTATCGATACATAACAATATAACAAGTAAA
72813 AATATGACAAAACC
1 AATATGACAAAACC
72827 GGTTTCATTA
Statistics
Matches: 161, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
163 161 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (163 bp):
AATATGACAAAACCAATAAAGAGCTACCGGATATGTTGAAGGTATCGATACCATTAAAATAAGTA
TCGATACTTTTGGAATTAAAAAGAAAAACAATAATAGCGCCTATAAAGTATCAATACTTTATAAA
CACGTATCGATACATAACAATATAACAAGTAAA
Found at i:73049 original size:183 final size:183
Alignment explanation
Indices: 72652--73066 Score: 634
Period size: 183 Copynumber: 2.3 Consensus size: 183
72642 CAAGTAAAAA
* * * *
72652 TATGAAAAAACCAATAAAGAGCTACCGGATATGTTGAAGGTATCGATACCATTAAAATAAGTGTC
1 TATGACAAAACCAGTAAAGAGCTACCAGATATGTTGAAGGTATCGATACCATTAAAATAAGTATC
* * * *
72717 GATGCTTTTGGAATTAAAAAGAAAAGCAATACTAGCGCCTATAAAGTATCAATACTTTATAAACA
66 GATACTTTTGGAATTAAAAAGAAAAACAATAATAGCGCCTATAAAGCATCAATACTTTATAAACA
* *
72782 TGTATCGATACATAATAATATAACATGTAAAAATATGACAAAACCGGTTTCAT
131 TGTATCGATACATAACAATATAACAGGTAAAAATATGACAAAACCGGTTTCAT
* * *
72835 TATGACAAAACCAGTAAAGAG-AAGTCAGATATGTTGAAGGTATCGATACCATTCAAATAAGTAT
1 TATGACAAAACCAGTAAAGAGCTA-CCAGATATGTTGAAGGTATCGATACCATTAAAATAAGTAT
*
72899 CGATACTTTTGGAATTTAAAAGAAAAACAATAATAGCGCCTATAAAGCATCAATACTTTATAAAC
65 CGATACTTTTGGAATTAAAAAGAAAAACAATAATAGCGCCTATAAAGCATCAATACTTTATAAAC
* *
72964 ATGTATCGATACATAACAATATAACAGGTCAAAATATGACAAAATCGGTTTCAT
130 ATGTATCGATACATAACAATATAACAGGTAAAAATATGACAAAACCGGTTTCAT
* * * *
73018 TATGACAAAACCGGTAAAGTGCTACCAGATATGTTAAACGTATCGATAC
1 TATGACAAAACCAGTAAAGAGCTACCAGATATGTTGAAGGTATCGATAC
73067 TTTAATAAGT
Statistics
Matches: 208, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
182 1 0.00
183 206 0.99
184 1 0.00
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (183 bp):
TATGACAAAACCAGTAAAGAGCTACCAGATATGTTGAAGGTATCGATACCATTAAAATAAGTATC
GATACTTTTGGAATTAAAAAGAAAAACAATAATAGCGCCTATAAAGCATCAATACTTTATAAACA
TGTATCGATACATAACAATATAACAGGTAAAAATATGACAAAACCGGTTTCAT
Found at i:75256 original size:21 final size:21
Alignment explanation
Indices: 75230--75273 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
75220 ACTAAAACGA
* *
75230 ACCAAAACTTATGGTTTAAGT
1 ACCAAAACTGATAGTTTAAGT
*
75251 ACCAAATCTGATAGTTTAAGT
1 ACCAAAACTGATAGTTTAAGT
75272 AC
1 AC
75274 TAAATGCATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.32
Consensus pattern (21 bp):
ACCAAAACTGATAGTTTAAGT
Found at i:75286 original size:20 final size:20
Alignment explanation
Indices: 75243--75288 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
75233 AAAACTTATG
75243 GTTTAAGTACCAAATCTGATA
1 GTTTAAGTACCAAATC-GATA
*
75264 GTTTAAGTACTAAAT-GCATA
1 GTTTAAGTACCAAATCG-ATA
75284 GTTTA
1 GTTTA
75289 CCCGTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 8 0.35
21 14 0.61
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (20 bp):
GTTTAAGTACCAAATCGATA
Found at i:77690 original size:2 final size:2
Alignment explanation
Indices: 77685--77712 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
77675 TTTTATTCTA
77685 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
77713 TAGATCATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:77894 original size:2 final size:2
Alignment explanation
Indices: 77887--77942 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
77877 CTCGATATTG
77887 AT AT AT 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
77929 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
77943 GTTTGAGATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78698 original size:16 final size:16
Alignment explanation
Indices: 78677--78719 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
78667 ATAAATAAAC
78677 GAACATAAACGAACAA
1 GAACATAAACGAACAA
*
78693 GAACATAAACGAACAC
1 GAACATAAACGAACAA
78709 GAACATAAACG
1 GAACATAAACG
78720 TTGGAGACCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.58, C:0.21, G:0.14, T:0.07
Consensus pattern (16 bp):
GAACATAAACGAACAA
Found at i:79481 original size:24 final size:24
Alignment explanation
Indices: 79444--79519 Score: 98
Period size: 24 Copynumber: 3.2 Consensus size: 24
79434 AGGTTGGGTT
**
79444 AAACATAAATGAATGAACATAAAC
1 AAACATAACCGAATGAACATAAAC
* *
79468 GAACATTACCGAATGAACATAAAC
1 AAACATAACCGAATGAACATAAAC
* *
79492 AAACATAACCGAACGAACATAACC
1 AAACATAACCGAATGAACATAAAC
79516 AAAC
1 AAAC
79520 GTTCATGAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.57, C:0.21, G:0.09, T:0.13
Consensus pattern (24 bp):
AAACATAACCGAATGAACATAAAC
Found at i:82988 original size:60 final size:60
Alignment explanation
Indices: 82879--83012 Score: 144
Period size: 60 Copynumber: 2.2 Consensus size: 60
82869 GTCGGATGAT
* *
82879 CATTTTATAAGTTTTAAAAGTCGAAGGACTTAACAAAGCAACATCCTATAGTCGAAGGAC
1 CATTTTGTAACTTTTAAAAGTCGAAGGACTTAACAAAGCAACATCCTATAGTCGAAGGAC
* * * * * ** * * *
82939 CATTTTGTAACTTTTAATAGTCGGATGACTTAATAAAGCTATGTTCTATAGTCGGAGGAT
1 CATTTTGTAACTTTTAAAAGTCGAAGGACTTAACAAAGCAACATCCTATAGTCGAAGGAC
82999 CATTTGTGT-ACTTT
1 CATTT-TGTAACTTT
83013 ACCCTAAATA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 58 0.95
61 3 0.05
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (60 bp):
CATTTTGTAACTTTTAAAAGTCGAAGGACTTAACAAAGCAACATCCTATAGTCGAAGGAC
Found at i:83536 original size:103 final size:102
Alignment explanation
Indices: 83320--83554 Score: 274
Period size: 103 Copynumber: 2.3 Consensus size: 102
83310 CTAATTATAT
*
83320 CAATTAGGCTCAATGCCTCTCTTTATCATTGACTCAACAATATCCTCAGTTTTACAAATCACCCC
1 CAATTAGGCTCAATGCCTCGCTTTATCATTGACTCAACAATATCCTCAG-TTTACAAATCACCCC
** * *
83385 GTTCTTGCAATGTGCATCAACCAATGTATTATATGTGA
65 GTTCTCACAACGTGCATCAACCAATGTATTATACGTGA
* * * ***
83423 CAATTAGGCTCAATGCCTCGCTTTATCATTGTCTCCACAATATCCTCA-TTTAGAAATCATTTCG
1 CAATTAGGCTCAATGCCTCGCTTTATCATTGACTCAACAATATCCTCAGTTTACAAATCACCCCG
* ** *
83487 TTCTCACGACGTTTATCAACCGATGTATTATACGTGA
66 TTCTCACAACGTGCATCAACCAATGTATTATACGTGA
* * *
83524 CAACATTCGGCTCGATGCCTCGTTTTATCAT
1 C-A-ATTAGGCTCAATGCCTCGCTTTATCAT
83555 CGTGTGATGT
Statistics
Matches: 112, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
101 42 0.38
102 1 0.01
103 69 0.62
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.35
Consensus pattern (102 bp):
CAATTAGGCTCAATGCCTCGCTTTATCATTGACTCAACAATATCCTCAGTTTACAAATCACCCCG
TTCTCACAACGTGCATCAACCAATGTATTATACGTGA
Found at i:84803 original size:105 final size:104
Alignment explanation
Indices: 84675--84992 Score: 404
Period size: 105 Copynumber: 3.0 Consensus size: 104
84665 ATTAATGCAC
* * *
84675 TATAAATAACAACGTTAGGCTCAATGCCTCTCTTTATCATTGACTCAACAATATCCTCAGCTTTA
1 TATAAGTAACAACATTAGGCTCAATGCCTCGCTTTATCATTGACTCAACAATATCCTCAGCTTTA
84740 GAAATCATCACGTTCTTGCAATGTGCATCAACCAATGTAT
66 G-AATCATCACGTTCTTGCAATGTGCATCAACCAATGTAT
* *
84780 TATATGTAACAACATTAGGCTCAATGCCTCGCTTTATCATTGTCTCAACAATATCCTCAGCTTTA
1 TATAAGTAACAACATTAGGCTCAATGCCTCGCTTTATCATTGACTCAACAATATCCTCAGCTTTA
** **
84845 CGAATCATTTCGTTCTTGCAATGTGTGTCAACCAATGTAT
66 -GAATCATCACGTTCTTGCAATGTGCATCAACCAATGTAT
* * * * * * * *
84885 TACAAGTGACAACATTAGGCTCAACGCCTCGCTTTATCATCGAGTCAACAGTGT-CTACAGCTTC
1 TATAAGTAACAACATTAGGCTCAATGCCTCGCTTTATCATTGACTCAACAATATCCT-CAGCTTT
* * * *
84949 AGCAATCATCCCCTTCTTGCAATGTGCATCGACCAATATAT
65 AG-AATCATCACGTTCTTGCAATGTGCATCAACCAATGTAT
84990 TAT
1 TAT
84993 TGGTGATAGC
Statistics
Matches: 183, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
104 3 0.02
105 179 0.98
106 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (104 bp):
TATAAGTAACAACATTAGGCTCAATGCCTCGCTTTATCATTGACTCAACAATATCCTCAGCTTTA
GAATCATCACGTTCTTGCAATGTGCATCAACCAATGTAT
Found at i:90123 original size:17 final size:17
Alignment explanation
Indices: 90101--90174 Score: 73
Period size: 17 Copynumber: 4.5 Consensus size: 17
90091 CCGTGTCCCG
90101 ACCCGGATGTTTCGGGT
1 ACCCGGATGTTTCGGGT
*
90118 ACCCGGATATTTCGGGT
1 ACCCGGATGTTTCGGGT
*
90135 ACCCGTAT-TTTGCGGGT
1 ACCCGGATGTTT-CGGGT
* *
90152 ACTCGTATG--TCGGGT
1 ACCCGGATGTTTCGGGT
*
90167 ACTCGGAT
1 ACCCGGAT
90175 ACCCGGATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
15 12 0.24
16 4 0.08
17 35 0.69
ACGTcount: A:0.15, C:0.23, G:0.31, T:0.31
Consensus pattern (17 bp):
ACCCGGATGTTTCGGGT
Found at i:90482 original size:2 final size:2
Alignment explanation
Indices: 90475--90502 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
90465 TTAAAAATTT
90475 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
90503 AATTAATCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:92875 original size:20 final size:21
Alignment explanation
Indices: 92839--92877 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
92829 AATATCACAC
92839 TAAAAAAACCCGAACCCGAAT
1 TAAAAAAACCCGAACCCGAAT
*
92860 TAAAAAAAGCCG-ACCCGA
1 TAAAAAAACCCGAACCCGA
92878 TCGGGTTAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.51, C:0.28, G:0.13, T:0.08
Consensus pattern (21 bp):
TAAAAAAACCCGAACCCGAAT
Found at i:95353 original size:3 final size:3
Alignment explanation
Indices: 95345--95370 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
95335 CCATGAAAAC
95345 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
95371 CATTATCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:98191 original size:21 final size:20
Alignment explanation
Indices: 98167--98205 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
98157 ATTATTTTAC
98167 TATGAGTTAAAAATATTTATT
1 TATGAGTTAAAAAT-TTTATT
*
98188 TATGAGTTATAAATTTTA
1 TATGAGTTAAAAATTTTA
98206 ATTAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (20 bp):
TATGAGTTAAAAATTTTATT
Found at i:98638 original size:30 final size:30
Alignment explanation
Indices: 98598--98657 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
98588 AGCCTTTTAG
98598 GGTTACTGTATTTATCGATTATAACAATCA
1 GGTTACTGTATTTATCGATTATAACAATCA
* *
98628 GGTTATTGTATTTATTGATTATAACAATCA
1 GGTTACTGTATTTATCGATTATAACAATCA
98658 AGTCATGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.43
Consensus pattern (30 bp):
GGTTACTGTATTTATCGATTATAACAATCA
Found at i:101044 original size:20 final size:20
Alignment explanation
Indices: 101019--101057 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
101009 TTAGTAAATG
101019 AACATAAACGAACGTCATAT
1 AACATAAACGAACGTCATAT
101039 AACATAAACGAACGTCATA
1 AACATAAACGAACGTCATA
101058 CGAACAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.21, G:0.10, T:0.18
Consensus pattern (20 bp):
AACATAAACGAACGTCATAT
Found at i:103015 original size:30 final size:28
Alignment explanation
Indices: 102980--103079 Score: 94
Period size: 30 Copynumber: 3.4 Consensus size: 28
102970 ATAAAAAATG
102980 AATACTTTAGATATTAATTTTGACAAAAAA
1 AATACTTTAGATATT-ATTTTGAC-AAAAA
* *
103010 AATACTTTAGGTACCTATTTTGACCAAAAA
1 AATACTTTAGATA-TTATTTTGA-CAAAAA
* *
103040 AATAAATTTATATATTTATTTTGATC-AAAA
1 AAT-ACTTTAGATA-TTATTTTGA-CAAAAA
103070 AATACTTTAG
1 AATACTTTAG
103080 GTACTGAAAT
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
29 5 0.09
30 34 0.60
31 18 0.32
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (28 bp):
AATACTTTAGATATTATTTTGACAAAAA
Found at i:107262 original size:2 final size:2
Alignment explanation
Indices: 107255--107283 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
107245 AGTAATATTA
107255 AT 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 AT A
107284 ACACTTTTTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:108631 original size:222 final size:227
Alignment explanation
Indices: 108252--108674 Score: 572
Period size: 222 Copynumber: 1.9 Consensus size: 227
108242 AAAAATACCC
* *
108252 GACCCAAATATATATATAATTTTACCTTATATATTTAAGAATAATGACAATAATACTCATATATA
1 GACCCAAATAAATATATAATTTTACCTTATATATTTAAGAATAATGACAATAATACCCATATATA
*
108317 TATAATTTTTTCAATTAAGTTACTATTTTTATTGAATAAAAATAATTTTTTTATTATTTCAGGTC
66 TATAATTTTTTCAATTAAGTCACTATTTTTATTG-----AAATAATTTTTTTATTATTTCA-GT-
* * *
108382 GGGTCGGGTCGGGTTTATAATTCATATATTCAGGTCCGGTCGGGTGAAACTTTATTTTGGTTGGG
124 -GGTCGGGTCGGGTTTATAATTCATATATTCAGGTCAGGTCGGGTGAAACTTTATTTTAGTCGGG
108447 TCGGGTTCAGGTTTAGGGTGAAAAATACCCGACTCGACCT
188 TCGGGTTCAGGTTTAGGGTGAAAAATACCCGACTCGACCT
* * * *
108487 GACCCAAA-AAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATA
1 GACCCAAATAAATATATAATTTTACCTTATATATTTAAGAATAATGACAATAATACCCATATATA
*
108551 TATAACTTTTTTTCAATTAAGTCACTATTTTTATTG-AATAATTTTTTT-TTA-TT-A-T-TTCG
66 TATAA--TTTTTTCAATTAAGTCACTATTTTTATTGAAATAATTTTTTTATTATTTCAGTGGTCG
* * * *
108610 GGTCGGGTTTCTAATTCATATATTCGGGTTAGGTTGGGTGAAACTTTATTTTAGTCGGGTCGGGT
129 GGTCGGGTTTATAATTCATATATTCAGGTCAGGTCGGGTGAAACTTTATTTTAGTCGGGTCGGGT
108675 CTCGGATGGA
Statistics
Matches: 171, Mismatches: 15, Indels: 17
0.84 0.07 0.08
Matches are distributed among these distances:
222 61 0.36
225 1 0.01
227 1 0.01
228 2 0.01
229 3 0.02
230 12 0.07
234 55 0.32
235 8 0.05
236 28 0.16
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (227 bp):
GACCCAAATAAATATATAATTTTACCTTATATATTTAAGAATAATGACAATAATACCCATATATA
TATAATTTTTTCAATTAAGTCACTATTTTTATTGAAATAATTTTTTTATTATTTCAGTGGTCGGG
TCGGGTTTATAATTCATATATTCAGGTCAGGTCGGGTGAAACTTTATTTTAGTCGGGTCGGGTTC
AGGTTTAGGGTGAAAAATACCCGACTCGACCT
Found at i:109298 original size:27 final size:27
Alignment explanation
Indices: 109258--109324 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 27
109248 TTTGGGCACA
** * *
109258 ATTCTCGTCTTTTTACATCATAAGGGT
1 ATTCTCGTAATTTTACATAATAAGAGT
*
109285 ATTCTCGTAATTTTACCTAATAAGAGT
1 ATTCTCGTAATTTTACATAATAAGAGT
* *
109312 ATTTTCATAATTT
1 ATTCTCGTAATTT
109325 CTTTTCCAAG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.46
Consensus pattern (27 bp):
ATTCTCGTAATTTTACATAATAAGAGT
Found at i:109893 original size:17 final size:17
Alignment explanation
Indices: 109871--109907 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
109861 TTTGGGTCAA
* *
109871 AGTCAACGCGTTGGCTC
1 AGTCAACGAGTTGACTC
109888 AGTCAACGAGTTGACTC
1 AGTCAACGAGTTGACTC
109905 AGT
1 AGT
109908 TTACACAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (17 bp):
AGTCAACGAGTTGACTC
Found at i:111963 original size:35 final size:35
Alignment explanation
Indices: 111879--111951 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
111869 TACCCGACCC
111879 GATACCCGTTTAAATAACCATTTATGCTAAATGAG
1 GATACCCGTTTAAATAACCATTTATGCTAAATGAG
*
111914 GATACCCGTTTAAATAACCATTTATGCTAAATGGG
1 GATACCCGTTTAAATAACCATTTATGCTAAATGAG
111949 GAT
1 GAT
111952 CCATGTTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (35 bp):
GATACCCGTTTAAATAACCATTTATGCTAAATGAG
Found at i:121658 original size:341 final size:338
Alignment explanation
Indices: 121038--121716 Score: 1258
Period size: 341 Copynumber: 2.0 Consensus size: 338
121028 GGTGGAACAG
121038 GCAAGACCGTTCCACCCCGGATACCATCTGAATCTGTCATGTCAAGTGTCTTCTGAGCTTCGATA
1 GCAAGACCGTTCCACCCCGGATACCATCTGAATCTGTCATGTCAAGTGTCTTCTGAGCTTCGATA
121103 TAGACCTTGAGATCGCGTATCTGTCGCAATAAATTACATTAAAGCCGGGAAATCTCGAGCATTGC
66 TAGACCTTGAGATCGCGTATCTGTCGCAATAAATTACATTAAAGCCGGGAAATCTCGAGCATTGC
121168 ATAGAAATTATAACTCGGGTCATTAAGATACCTGCTCTTCCAGATCAAGTATCTTCTCATCCATC
131 ATAGAAATTATAACTCGGGTCATTAAGATACCTGCTCTTCCAGATCAAGTATCTTCTCATCCATC
121233 AACCTCGACTCAGAGGCTTCCCTAAAAGAAAAACAAAGGCACCGTGTAAGGTCTGGAACCCGAAA
196 AACCTCGACTCAGAGGCTTCCCTAAAAGAAAAACAAAGGCACCGTGTAAGGTCTGGAACCCGAAA
121298 AACATGAGAAAAAAGCCAAATGTTAATAC-AAGAAGTG-GTTGCATGTGCACCGTAGTAGTAAGT
261 AACATGAGAAAAAAGCCAAATGTTAATACAAAGAAGTGAGTTGCATGTGCACCG--GTAGTAAGT
121361 TTCCCCTTTTCGGGC
324 TTCCCCTTTTCGGGC
121376 GCAAGACCGTT-CACCCCGGATACCATCTGAATCTGTCATGTCAAGTGTCTTCTGAGCTTCGATA
1 GCAAGACCGTTCCACCCCGGATACCATCTGAATCTGTCATGTCAAGTGTCTTCTGAGCTTCGATA
121440 TAGACCTTGAGATCGCGTATCTGTCGCAATAAATTACGATTAAAGCCGGGAAATCTCGAGCAATT
66 TAGACCTTGAGATCGCGTATCTGTCGCAATAAATTAC-ATTAAAGCCGGGAAATCTCGAGC-ATT
121505 GCATAGAAAATTATAAACTCGGGTCATTAAGATACCTGCTCTTCCAGATCAAGTATCTTCTCATC
129 GCATAG-AAATTAT-AACTCGGGTCATTAAGATACCTGCTCTTCCAGATCAAGTATCTTCTCATC
*
121570 CATCAACCTCGACTCAGAGGCTTCCCTAAAAGGGAAAACAAAGGCACCGTGTAAGGTCTGGAACC
192 CATCAACCTCGACTCAGAGGCTTCCCTAAAA-GAAAAACAAAGGCACCGTGTAAGGTCTGGAACC
121635 CGAAAAACATGAG-AAAAAGCCAAATGTTAATACAAAGAAGTGAGTTGCATGTGCACCGGTAGTA
256 CGAAAAACATGAGAAAAAAGCCAAATGTTAATACAAAGAAGTGAGTTGCATGTGCACCGGTAGTA
121699 AGTTTCCCCTTTTCGGGC
321 AGTTTCCCCTTTTCGGGC
121717 AAGAAGATGA
Statistics
Matches: 333, Mismatches: 1, Indels: 11
0.97 0.00 0.03
Matches are distributed among these distances:
337 90 0.27
338 34 0.10
339 9 0.03
340 7 0.02
341 125 0.38
342 53 0.16
343 15 0.05
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (338 bp):
GCAAGACCGTTCCACCCCGGATACCATCTGAATCTGTCATGTCAAGTGTCTTCTGAGCTTCGATA
TAGACCTTGAGATCGCGTATCTGTCGCAATAAATTACATTAAAGCCGGGAAATCTCGAGCATTGC
ATAGAAATTATAACTCGGGTCATTAAGATACCTGCTCTTCCAGATCAAGTATCTTCTCATCCATC
AACCTCGACTCAGAGGCTTCCCTAAAAGAAAAACAAAGGCACCGTGTAAGGTCTGGAACCCGAAA
AACATGAGAAAAAAGCCAAATGTTAATACAAAGAAGTGAGTTGCATGTGCACCGGTAGTAAGTTT
CCCCTTTTCGGGC
Found at i:124700 original size:50 final size:50
Alignment explanation
Indices: 124622--124722 Score: 132
Period size: 50 Copynumber: 2.0 Consensus size: 50
124612 TGAAAAAGAG
* * * *
124622 ACCATAATCACGATAAATGAAAAACAACTGAAAAAGCGACTGCAACCGCA
1 ACCATAATCACAATAAATCAAAAACAACTGAAAAAACGACGGCAACCGCA
* *
124672 ACCATAATCACAATAAA-CACAAAGCAACTGAAAAAACGACGGCATCCGCA
1 ACCATAATCACAATAAATCA-AAAACAACTGAAAAAACGACGGCAACCGCA
124722 A
1 A
124723 TTTAAATTTC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
49 1 0.02
50 43 0.98
ACGTcount: A:0.50, C:0.26, G:0.13, T:0.11
Consensus pattern (50 bp):
ACCATAATCACAATAAATCAAAAACAACTGAAAAAACGACGGCAACCGCA
Found at i:125062 original size:21 final size:21
Alignment explanation
Indices: 125025--125064 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
125015 TTGGATGAAA
*
125025 AATTAGGGATTGAGGGTCAAG
1 AATTAGGAATTGAGGGTCAAG
125046 AATTAGGAATT-ACGGGTCA
1 AATTAGGAATTGA-GGGTCA
125065 GAAAATTGGG
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:0.07, G:0.33, T:0.25
Consensus pattern (21 bp):
AATTAGGAATTGAGGGTCAAG
Found at i:130806 original size:16 final size:17
Alignment explanation
Indices: 130785--130820 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
130775 TATGCAGATA
130785 TTAAAA-AAATATTATT
1 TTAAAATAAATATTATT
130801 TTAAAATAAATATTATT
1 TTAAAATAAATATTATT
130818 TTA
1 TTA
130821 TATATTTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAAATAAATATTATT
Found at i:132412 original size:10 final size:10
Alignment explanation
Indices: 132361--132458 Score: 79
Period size: 10 Copynumber: 9.1 Consensus size: 10
132351 GTATTTGTGT
132361 TGTTCGTTTA
1 TGTTCGTTTA
132371 TGTTCAGTTATTA
1 TGTTC-G-T-TTA
*
132384 TGTTTGTTTATA
1 TGTTCG-TT-TA
*
132396 TTCGTTCGTTTG
1 -T-GTTCGTTTA
132408 TGTTCGTTTA
1 TGTTCGTTTA
* *
132418 CGTTCATTTA
1 TGTTCGTTTA
132428 TGTTCGTTTA
1 TGTTCGTTTA
* *
132438 CGTTCATTTA
1 TGTTCGTTTA
132448 TGTTCGTTTA
1 TGTTCGTTTA
132458 T
1 T
132459 CATTTAAATG
Statistics
Matches: 70, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
10 46 0.66
11 3 0.04
12 7 0.10
13 10 0.14
14 4 0.06
ACGTcount: A:0.13, C:0.11, G:0.17, T:0.58
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:132421 original size:20 final size:20
Alignment explanation
Indices: 132398--132457 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
132388 TGTTTATATT
* *
132398 CGTTCGTTTGTGTTCGTTTA
1 CGTTCATTTATGTTCGTTTA
132418 CGTTCATTTATGTTCGTTTA
1 CGTTCATTTATGTTCGTTTA
132438 CGTTCATTTATGTTCGTTTA
1 CGTTCATTTATGTTCGTTTA
132458 TCATTTAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.12, C:0.15, G:0.18, T:0.55
Consensus pattern (20 bp):
CGTTCATTTATGTTCGTTTA
Found at i:132515 original size:16 final size:16
Alignment explanation
Indices: 132494--132526 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
132484 AAAAAAAATT
132494 TGTTCGCTTATGTTCG
1 TGTTCGCTTATGTTCG
*
132510 TGTTCGTTTATGTTCG
1 TGTTCGCTTATGTTCG
132526 T
1 T
132527 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.15, G:0.24, T:0.55
Consensus pattern (16 bp):
TGTTCGCTTATGTTCG
Found at i:137610 original size:68 final size:68
Alignment explanation
Indices: 137532--137659 Score: 186
Period size: 68 Copynumber: 1.9 Consensus size: 68
137522 TGATGAGTGA
* * *
137532 TACATTTCATATATCCAAAGCGATGATGTGACACT-GTCATGTGTCTAAAGTGATGACTCATGAC
1 TACATATCATATATCCAAAGCGATGATGTGACACTAAT-ATGTGTCTAAAATGATGACTCATGAC
137596 TTGG
65 TTGG
* * *
137600 TACATATCATATATCTAAAGTGATGATGTGACATTAATATGTGTCTAAAATGATGACTCA
1 TACATATCATATATCCAAAGCGATGATGTGACACTAATATGTGTCTAAAATGATGACTCA
137660 ATACATGCCA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
68 52 0.98
69 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Consensus pattern (68 bp):
TACATATCATATATCCAAAGCGATGATGTGACACTAATATGTGTCTAAAATGATGACTCATGACT
TGG
Found at i:138262 original size:4 final size:4
Alignment explanation
Indices: 138250--138279 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
138240 TACATACATA
*
138250 CATG GATG CATG CATG CATG CATG CATG CA
1 CATG CATG CATG CATG CATG CATG CATG CA
138280 CGTGCTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (4 bp):
CATG
Found at i:140117 original size:7 final size:7
Alignment explanation
Indices: 140105--140131 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
140095 TTGTTGAACG
140105 ACCGAGA
1 ACCGAGA
140112 ACCGAGA
1 ACCGAGA
140119 ACCGAGA
1 ACCGAGA
140126 ACCGAG
1 ACCGAG
140132 CTTTCATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.30, G:0.30, T:0.00
Consensus pattern (7 bp):
ACCGAGA
Found at i:143674 original size:21 final size:19
Alignment explanation
Indices: 143635--143681 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
143625 TTTAAATTTC
* *
143635 TATTTAAATTTAATTATAT
1 TATTTAAATATAATGATAT
143654 ATATTTATAATATAATGATAT
1 -TATTTA-AATATAATGATAT
143675 TATTTAA
1 TATTTAA
143682 TTTTAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 12 0.50
21 11 0.46
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TATTTAAATATAATGATAT
Found at i:146413 original size:201 final size:199
Alignment explanation
Indices: 146068--146611 Score: 815
Period size: 199 Copynumber: 2.7 Consensus size: 199
146058 TAAAACCTGA
*
146068 AGCTGAATTAACTCATGTCACATTGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCT
1 AGCTGAATTAACTCATGTCACACTGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCT
* * * *
146133 GGAGCTGAATTAGCTCATGTTACACCGAGCAAGGCCTTCATA-AGATAGAAAGCAACAATGAAAG
66 GGAGTTGAATTAGCTCATGTCACACCGAGCAAGGCCTTTATACA-ATAGAAAGCAACAACGAAAG
146197 GCTGAAGTTGAATTAGCTCATGTCACACCAAGCAAGGCCTTTATATGATAGAAAGCAACAAC-AT
130 GCTGAAGTTGAATTAGCTCATGTCACACCAAGCAAGGCC-TT-TATGATAGAAAGCAACAACGA-
*
146261 AAGGCTGC
192 AAGACTGC
* * *
146269 AGCTGAATTAGCTCATGCCACACTGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAATGGCT
1 AGCTGAATTAACTCATGTCACACTGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCT
* * *
146334 GGAGTTGAATTAGCTCATGTCACACTGAGCAAGGCCTTTATACAATAGAGAGCAACAACGAGAGG
66 GGAGTTGAATTAGCTCATGTCACACCGAGCAAGGCCTTTATACAATAGAAAGCAACAACGAAAGG
* * *
146399 CTGCAGTTGAATTAGCTCATGTCACACCGAGCAAGTCCTTTATGATAGAAAGCAACAACGAAAGA
131 CTGAAGTTGAATTAGCTCATGTCACACCAAGCAAGGCCTTTATGATAGAAAGCAACAACGAAAGA
146464 CTGC
196 CTGC
* *
146468 AGCTGAATTAACTCATGTCACACCGAACAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCT
1 AGCTGAATTAACTCATGTCACACTGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCT
* * * *
146533 GCA-TCTGAATTAGCTCATGTCACACCGAACAAGACCTTTATACAATAGAAAGCAACAACTAAAG
66 GGAGT-TGAATTAGCTCATGTCACACCGAGCAAGGCCTTTATACAATAGAAAGCAACAACGAAAG
* *
146597 GCTGGAGTTAAATTA
130 GCTGAAGTTGAATTA
146612 ATTTAGGTCA
Statistics
Matches: 311, Mismatches: 29, Indels: 8
0.89 0.08 0.02
Matches are distributed among these distances:
198 1 0.00
199 154 0.50
200 3 0.01
201 152 0.49
202 1 0.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (199 bp):
AGCTGAATTAACTCATGTCACACTGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCT
GGAGTTGAATTAGCTCATGTCACACCGAGCAAGGCCTTTATACAATAGAAAGCAACAACGAAAGG
CTGAAGTTGAATTAGCTCATGTCACACCAAGCAAGGCCTTTATGATAGAAAGCAACAACGAAAGA
CTGC
Found at i:146624 original size:67 final size:67
Alignment explanation
Indices: 146071--146611 Score: 748
Period size: 67 Copynumber: 8.1 Consensus size: 67
146061 AACCTGAAGC
* ** *
146071 TGAATTAACTCATGTCACATTGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCTGGA
1 TGAATTAGCTCATGTCACACCGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCTGCA
*
146136 GC
66 GT
* * * * *
146138 TGAATTAGCTCATGTTACACCGAGCAAGGCCTTCATAAGATAGAAAGCAACAATGAAAGGCTGAA
1 TGAATTAGCTCATGTCACACCGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCTGCA
146203 GT
66 GT
* *
146205 TGAATTAGCTCATGTCACACCAAGCAAGGCCTTTATATGATAGAAAGCAACAAC-ATAAGGCTGC
1 TGAATTAGCTCATGTCACACCGAGCAAGGCCTTTATACGATAGAAAGCAACAACGA-AAGGCTGC
*
146269 AGC
65 AGT
* * * *
146272 TGAATTAGCTCATGCCACACTGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAATGGCTGGA
1 TGAATTAGCTCATGTCACACCGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCTGCA
146337 GT
66 GT
* * * *
146339 TGAATTAGCTCATGTCACACTGAGCAAGGCCTTTATACAATAGAGAGCAACAACGAGAGGCTGCA
1 TGAATTAGCTCATGTCACACCGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCTGCA
146404 GT
66 GT
* *
146406 TGAATTAGCTCATGTCACACCGAGCAAGTCCTTTAT--GATAGAAAGCAACAACGAAAGACTGCA
1 TGAATTAGCTCATGTCACACCGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCTGCA
*
146469 GC
66 GT
* *
146471 TGAATTAACTCATGTCACACCGAACAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCTGCA
1 TGAATTAGCTCATGTCACACCGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCTGCA
146536 -T
66 GT
* * * * *
146537 CTGAATTAGCTCATGTCACACCGAACAAGACCTTTATACAATAGAAAGCAACAACTAAAGGCTGG
1 -TGAATTAGCTCATGTCACACCGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCTGC
146602 AGT
65 AGT
*
146605 TAAATTA
1 TGAATTA
146612 ATTTAGGTCA
Statistics
Matches: 421, Mismatches: 47, Indels: 12
0.88 0.10 0.03
Matches are distributed among these distances:
65 57 0.14
66 1 0.00
67 361 0.86
68 2 0.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (67 bp):
TGAATTAGCTCATGTCACACCGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCTGCA
GT
Found at i:146624 original size:266 final size:267
Alignment explanation
Indices: 146073--146628 Score: 803
Period size: 266 Copynumber: 2.1 Consensus size: 267
146063 CCTGAAGCTG
* * * *
146073 AATTAACTCATGTCACATTGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAAAGGCTGGAGC
1 AATTAACTCAGGTCACACTGAGCAAGGCCTTTATACAATAGAAAGCAACAACGAAAGGCTGCAGC
* * *
146138 TGAATTAGCTCATGTTACACCGAGCAAGGCCTTCATAAGATAGAAAGCAACAATGAAAGGCTGAA
66 TGAATTAGCTCATGTCACACCGAGCAAGGCCTT-ATAAGATAGAAAGCAACAACGAAAGACTGAA
* * *
146203 GTTGAATTAGCTCATGTCACACCAAGCAAGGCCTTTATATGATAGAAAGCAACAACATAAGGCTG
130 GCTGAATTAACTCATGTCACACCAAGCAAGGCCTTTATACGATAGAAAGCAACAACATAAGGCTG
* * * * *
146268 CAGCTGAATTAGCTCATGCCACACTGAGCAAGGCCTTTATACGATAGAAAGCAACAACGAATGGC
195 CAGCTGAATTAGCTCATGCCACACCGAACAAGACCTTTATACAATAGAAAGCAACAACGAAAGGC
*
146333 TGGAGTTG
260 TGGAGTTA
* * * * *
146341 AATTAGCTCATGTCACACTGAGCAAGGCCTTTATACAATAGAGAGCAACAACGAGAGGCTGCAGT
1 AATTAACTCAGGTCACACTGAGCAAGGCCTTTATACAATAGAAAGCAACAACGAAAGGCTGCAGC
* * *
146406 TGAATTAGCTCATGTCACACCGAGCAAGTCCTT-TATGATAGAAAGCAACAACGAAAGACTGCAG
66 TGAATTAGCTCATGTCACACCGAGCAAGGCCTTATAAGATAGAAAGCAACAACGAAAGACTGAAG
146470 CTGAATTAACTCATGTCACACCGAA-CAAGGCCTTTATACGATAGAAAGCAACAACGA-AAGGCT
131 CTGAATTAACTCATGTCACACC-AAGCAAGGCCTTTATACGATAGAAAGCAACAAC-ATAAGGCT
* * *
146533 GCATCTGAATTAGCTCATGTCACACCGAACAAGACCTTTATACAATAGAAAGCAACAACTAAAGG
194 GCAGCTGAATTAGCTCATGCCACACCGAACAAGACCTTTATACAATAGAAAGCAACAACGAAAGG
146598 CTGGAGTTA
259 CTGGAGTTA
* *
146607 AATTAATTTAGGTCACACTGAG
1 AATTAACTCAGGTCACACTGAG
146629 AATTTCTTCG
Statistics
Matches: 257, Mismatches: 29, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
266 165 0.64
267 3 0.01
268 89 0.35
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (267 bp):
AATTAACTCAGGTCACACTGAGCAAGGCCTTTATACAATAGAAAGCAACAACGAAAGGCTGCAGC
TGAATTAGCTCATGTCACACCGAGCAAGGCCTTATAAGATAGAAAGCAACAACGAAAGACTGAAG
CTGAATTAACTCATGTCACACCAAGCAAGGCCTTTATACGATAGAAAGCAACAACATAAGGCTGC
AGCTGAATTAGCTCATGCCACACCGAACAAGACCTTTATACAATAGAAAGCAACAACGAAAGGCT
GGAGTTA
Found at i:150707 original size:16 final size:17
Alignment explanation
Indices: 150688--150723 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
150678 CTTTTCCTCC
150688 TCTG-TTTTTTTTTCGT
1 TCTGTTTTTTTTTTCGT
150704 TCTGTTTTTTTTTTCGT
1 TCTGTTTTTTTTTTCGT
150721 TCT
1 TCT
150724 CTGCCGTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.00, C:0.14, G:0.11, T:0.75
Consensus pattern (17 bp):
TCTGTTTTTTTTTTCGT
Found at i:151149 original size:3 final size:3
Alignment explanation
Indices: 151141--151253 Score: 138
Period size: 3 Copynumber: 37.0 Consensus size: 3
151131 TTATTTATTA
*
151141 AAT AAT AAT AAT ATAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
* * *
151188 AAT AAAT AAT TAT AAT TAT AAT -AT AAT AAT AAT ACT AAT AAT AAT
1 AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
151233 AAT AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT
151254 TTAAATGAAA
Statistics
Matches: 94, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
2 2 0.02
3 83 0.88
4 9 0.10
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:151227 original size:48 final size:51
Alignment explanation
Indices: 151139--151253 Score: 164
Period size: 48 Copynumber: 2.3 Consensus size: 51
151129 AATTATTTAT
*
151139 TAAATAATAATAATATATAATAATAATATATAATATTAATAATAATAATAA
1 TAAATAATAATAATATATAATAATAATATATAATACTAATAATAATAATAA
*
151190 TAAATAATTATAAT-TATAAT-ATAATA-ATAATACTAATAATAATAATAA
1 TAAATAATAATAATATATAATAATAATATATAATACTAATAATAATAATAA
*
151238 TTTTAATAATAATAAT
1 --TAAATAATAATAAT
151254 TTAAATGAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
48 21 0.36
49 6 0.10
50 18 0.31
51 13 0.22
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (51 bp):
TAAATAATAATAATATATAATAATAATATATAATACTAATAATAATAATAA
Found at i:151509 original size:76 final size:76
Alignment explanation
Indices: 151378--152551 Score: 2161
Period size: 76 Copynumber: 15.5 Consensus size: 76
151368 GATGGAAATG
* * *
151378 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
*
151443 CCTGAAGGCTT
66 CCCGAAGGCTT
151454 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
151519 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
151530 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
151595 CCCGAAGGCTT
66 CCCGAAGGCTT
151606 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
*
151671 CTCGAAGGCTT
66 CCCGAAGGCTT
* *
151682 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
151747 CCCGAAGGCTT
66 CCCGAAGGCTT
151758 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
*
151823 CTCGAAGGCTT
66 CCCGAAGGCTT
* *
151834 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
151899 CCCGAAGGCTT
66 CCCGAAGGCTT
151910 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
*
151975 CTCGAAGGCTT
66 CCCGAAGGCTT
* *
151986 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
152051 CCCGAAGGCTT
66 CCCGAAGGCTT
152062 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
*
152127 CTCGAAGGCTT
66 CCCGAAGGCTT
* *
152138 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
*
152203 CCCGAAGGTTT
66 CCCGAAGGCTT
152214 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
152279 CCCGAAGGCTT
66 CCCGAAGGCTT
152290 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
152355 CCCGAAGGC-T
66 CCCGAAGGCTT
152365 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
152430 CCCGAAGGCTT
66 CCCGAAGGCTT
152441 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
152506 CCCGAAGGCTT
66 CCCGAAGGCTT
*
152517 TTTGGAAACATCATGTACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
152552 TGAGAAATAG
Statistics
Matches: 1062, Mismatches: 35, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
75 75 0.07
76 987 0.93
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:156131 original size:83 final size:83
Alignment explanation
Indices: 155991--156255 Score: 444
Period size: 83 Copynumber: 3.2 Consensus size: 83
155981 CTTATTTCTA
* * *
155991 CTATGAGCAAATTCATCTT-TCAAATTCAATGATTGGTTCTGTCC-AACCAGATTAGATAACTCA
1 CTATGAACAAATTCATCTTCT-AAATTCAATGATTGGTTTTG-CCAAACCAGATCAGATAACTCA
156054 AAGAACACTTCCAGAAGATG
64 AAGAACACTTCCAGAAGATG
*
156074 CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAC
1 CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
156139 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
156157 CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
156222 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
156240 CTATGAGCACATTCAT
1 CTATGAACAAATTCAT
156256 TTGTTCCATT
Statistics
Matches: 173, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
82 2 0.01
83 170 0.98
84 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (83 bp):
CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:158248 original size:14 final size:14
Alignment explanation
Indices: 158228--158261 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
158218 TCAATTTTCC
158228 TCTT-TTTTTTTTT
1 TCTTCTTTTTTTTT
158241 T-TTCTTTTTTTTT
1 TCTTCTTTTTTTTT
158254 TCTTCTTT
1 TCTTCTTT
158262 CTTTGCTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 11 0.58
14 6 0.32
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (14 bp):
TCTTCTTTTTTTTT
Found at i:163744 original size:53 final size:53
Alignment explanation
Indices: 163629--163747 Score: 123
Period size: 53 Copynumber: 2.2 Consensus size: 53
163619 TATAATATAG
* * * * * *
163629 TAAAACAATAATTAAAGTAATGATTGAAAATATATTAAAATAATAAAAATTAAGT
1 TAAAAC-ATAACTAAA-CAATGATTAAAAATATAATAAAATAATAAAAATAAAAT
**
163684 TAAAACATAACTAAACAATGATTAAAAATA-AATAAAATAATAAATGTAAAAT
1 TAAAACATAACTAAACAATGATTAAAAATATAATAAAATAATAAAAATAAAAT
*
163736 TATGAACATAAC
1 TA-AAACATAAC
163748 CTGAATCATC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
52 19 0.35
53 21 0.39
54 8 0.15
55 6 0.11
ACGTcount: A:0.61, C:0.05, G:0.06, T:0.28
Consensus pattern (53 bp):
TAAAACATAACTAAACAATGATTAAAAATATAATAAAATAATAAAAATAAAAT
Found at i:164313 original size:13 final size:13
Alignment explanation
Indices: 164295--164323 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
164285 CCACCGTATT
164295 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
164308 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
164321 CCG
1 CCG
164324 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:164606 original size:16 final size:17
Alignment explanation
Indices: 164585--164620 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
164575 TCTTTCCTCC
164585 TCTG-TTTTTTTTTCGT
1 TCTGTTTTTTTTTTCGT
164601 TCTGTTTTTTTTTTCGT
1 TCTGTTTTTTTTTTCGT
164618 TCT
1 TCT
164621 CTGCCGTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.00, C:0.14, G:0.11, T:0.75
Consensus pattern (17 bp):
TCTGTTTTTTTTTTCGT
Found at i:165046 original size:3 final size:3
Alignment explanation
Indices: 165038--165164 Score: 166
Period size: 3 Copynumber: 41.7 Consensus size: 3
165028 TTATTTATTA
*
165038 AAT AAT AAT AAT ATAT AAT AAT AAT AAT -AT ATAT AAT ATT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT
* *
165084 AAT AAT AAT AAT AAT AAAT AAT TAT AAT TAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* **
165130 ACT AAT AAT AAT AAT AAT AAT TTT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
165165 ATTTAAATGA
Statistics
Matches: 108, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
2 2 0.02
3 97 0.90
4 9 0.08
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:169676 original size:2 final size:2
Alignment explanation
Indices: 169669--169765 Score: 194
Period size: 2 Copynumber: 48.5 Consensus size: 2
169659 ACATTTGGTT
169669 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
169711 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
169753 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
169766 CCAGGGACGG
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 95 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:172113 original size:2 final size:2
Alignment explanation
Indices: 172106--172137 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
172096 CACTGAATCT
172106 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
172138 AAAAAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:174622 original size:25 final size:23
Alignment explanation
Indices: 174574--174618 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
174564 AATGTCATGG
*
174574 GGGAACCGATACCCCCCACAGAA
1 GGGAACCGATACCCCCCAAAGAA
*
174597 GGGAACCGATTCCCCCCTAAAG
1 GGGAACCGATACCCCCC-AAAG
174619 GAAGAAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.31, C:0.38, G:0.22, T:0.09
Consensus pattern (23 bp):
GGGAACCGATACCCCCCAAAGAA
Found at i:176185 original size:23 final size:23
Alignment explanation
Indices: 176159--176214 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
176149 TATGGCATTA
176159 CGGTGCAATTCTACGCGGCACTC
1 CGGTGCAATTCTACGCGGCACTC
* *
176182 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCAATTCTACGCGGCACTC
*
176205 CGGTGTAATT
1 CGGTGCAATT
176215 ATATGAGCTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.29
Consensus pattern (23 bp):
CGGTGCAATTCTACGCGGCACTC
Found at i:179285 original size:18 final size:18
Alignment explanation
Indices: 179262--179350 Score: 124
Period size: 18 Copynumber: 4.9 Consensus size: 18
179252 AGGGATTATC
*
179262 AGTGGTCTTTCGGGACAT
1 AGTGGTCATTCGGGACAT
179280 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGGGACAT
*
179298 AGTGGTCATTCGGGATAT
1 AGTGGTCATTCGGGACAT
* *
179316 AGTGGTCCTTCAGGACAT
1 AGTGGTCATTCGGGACAT
* *
179334 AGTGGCCATACGGGACA
1 AGTGGTCATTCGGGACA
179351 AATTCTATGC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.27
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:180607 original size:2 final size:2
Alignment explanation
Indices: 180600--180628 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
180590 AGCGTATAAG
180600 AT 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 AT A
180629 AAGTCAGAGC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:182484 original size:18 final size:17
Alignment explanation
Indices: 182445--182487 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
182435 AAATGGTAAC
*
182445 AAAATAAATAACATAAG
1 AAAATAAATAAAATAAG
* *
182462 GAAATCAAATAAAATAAT
1 AAAAT-AAATAAAATAAG
182480 AAAATAAA
1 AAAATAAA
182488 CAAACATGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.19
Consensus pattern (17 bp):
AAAATAAATAAAATAAG
Found at i:182801 original size:29 final size:28
Alignment explanation
Indices: 182693--182803 Score: 82
Period size: 29 Copynumber: 3.8 Consensus size: 28
182683 ATACAACAGT
* *
182693 TAAGTAAAATAATAAAAATAT-TATGTAA
1 TAAG-AAAATAATAATAATATATATATAA
* *
182721 TAA-AAAATAATATATACATATGTAGATAAACA
1 TAAGAAAATAATA-ATA-ATA--TATATATA-A
* *
182753 CTAAAAAAATAATAACAATATATATATATA
1 -TAAGAAAATAATAATAATATATATATA-A
182783 TAAGAAAATAATAATAATATA
1 TAAGAAAATAATAATAATATA
182804 ATGGTAGTAA
Statistics
Matches: 65, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
26 9 0.14
27 2 0.03
28 6 0.09
29 19 0.29
30 8 0.12
31 3 0.05
32 4 0.06
33 5 0.08
34 9 0.14
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.30
Consensus pattern (28 bp):
TAAGAAAATAATAATAATATATATATAA
Found at i:185501 original size:18 final size:18
Alignment explanation
Indices: 185475--185509 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
185465 AGGGATTATC
185475 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
185493 AGTGTTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
185510 AATTCTACGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:187499 original size:23 final size:23
Alignment explanation
Indices: 187464--187536 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
187454 ATACTTTACA
*
187464 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
187487 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
187510 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
187533 ATAT
1 ATAT
187537 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:189078 original size:31 final size:31
Alignment explanation
Indices: 189011--189078 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
189001 ACAATGATAG
* * **
189011 AGTGACCATTTTGTTACAAATCGATAACGTT
1 AGTGACCATTTTATTACAAACCGATAAAATT
189042 AGTGACCATTTTATTACAAACCGATAAAATT
1 AGTGACCATTTTATTACAAACCGATAAAATT
*
189073 GGTGAC
1 AGTGAC
189079 TAATTTGTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (31 bp):
AGTGACCATTTTATTACAAACCGATAAAATT
Found at i:190031 original size:199 final size:199
Alignment explanation
Indices: 189691--190067 Score: 745
Period size: 199 Copynumber: 1.9 Consensus size: 199
189681 TTATTAATAA
189691 TTATAGATGCTCTCTCATATAATATTACCCTAATATTTATCTCTATTAAGAAATTTCTCTTATAC
1 TTATAGATGCTCTCTCATATAATATTACCCTAATATTTATCTCTATTAAGAAATTTCTCTTATAC
189756 TTGATTCAACAAGGTGATTTGAATTTTGATATTACGAATAAAATAAATTTAGTTGGGAGAACGGA
66 TTGATTCAACAAGGTGATTTGAATTTTGATATTACGAATAAAATAAATTTAGTTGGGAGAACGGA
189821 TCTTATAATAAATTTTAACTATGATTTATTCATATTAGTCGACTAATATGAATAAATCATAGTTA
131 TCTTATAATAAATTTTAACTATGATTTATTCATATTAGTCGACTAATATGAATAAATCATAGTTA
189886 AAAT
196 AAAT
189890 TTATAGATGCTCTCTCATATAATATTACCCTAATATTTATCTCTATTAAGAAATTTCTCTTATAC
1 TTATAGATGCTCTCTCATATAATATTACCCTAATATTTATCTCTATTAAGAAATTTCTCTTATAC
189955 TTGATTCAACAAGGTGATTTGAATTTTGATATTACGAATAAAATAAATTTAGTTGGGAGAACGGA
66 TTGATTCAACAAGGTGATTTGAATTTTGATATTACGAATAAAATAAATTTAGTTGGGAGAACGGA
*
190020 TCTTATAATAAATTTTAACTATGATTTATTCATATTAGTCGATTAATA
131 TCTTATAATAAATTTTAACTATGATTTATTCATATTAGTCGACTAATA
190068 AATCAACTAT
Statistics
Matches: 177, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
199 177 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (199 bp):
TTATAGATGCTCTCTCATATAATATTACCCTAATATTTATCTCTATTAAGAAATTTCTCTTATAC
TTGATTCAACAAGGTGATTTGAATTTTGATATTACGAATAAAATAAATTTAGTTGGGAGAACGGA
TCTTATAATAAATTTTAACTATGATTTATTCATATTAGTCGACTAATATGAATAAATCATAGTTA
AAAT
Found at i:190081 original size:7 final size:7
Alignment explanation
Indices: 190069--190113 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
190059 CGATTAATAA
190069 ATCAACT
1 ATCAACT
190076 ATCAACTT
1 ATCAAC-T
190084 AT-AA--
1 ATCAACT
190088 ATCAACT
1 ATCAACT
190095 ATCAACT
1 ATCAACT
190102 ATCAACTT
1 ATCAAC-T
190110 ATCA
1 ATCA
190114 TATTTCGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
4 2 0.06
5 2 0.06
7 21 0.64
8 8 0.24
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.31
Consensus pattern (7 bp):
ATCAACT
Found at i:190089 original size:19 final size:19
Alignment explanation
Indices: 190065--190101 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
190055 TAGTCGATTA
190065 ATAAATCAACTATCAACTT
1 ATAAATCAACTATCAACTT
190084 ATAAATCAACTATCAACT
1 ATAAATCAACTATCAACT
190102 ATCAACTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (19 bp):
ATAAATCAACTATCAACTT
Found at i:190559 original size:20 final size:22
Alignment explanation
Indices: 190534--190580 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
190524 GACTAATGTT
*
190534 TTTTTTAAATG-AAA-TTCAAA
1 TTTTTTAAAAGAAAAGTTCAAA
190554 TTTTTTAAAAGAAAAGTTCAAA
1 TTTTTTAAAAGAAAAGTTCAAA
190576 TTTTT
1 TTTTT
190581 CCTACCCGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 10 0.42
21 3 0.12
22 11 0.46
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (22 bp):
TTTTTTAAAAGAAAAGTTCAAA
Found at i:190559 original size:21 final size:23
Alignment explanation
Indices: 190533--190580 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 23
190523 GGACTAATGT
*
190533 TTTTTTTAAATG-AAA-TTCAAA
1 TTTTTTTAAAAGAAAAGTTCAAA
190554 -TTTTTTAAAAGAAAAGTTCAAA
1 TTTTTTTAAAAGAAAAGTTCAAA
190576 TTTTT
1 TTTTT
190581 CCTACCCGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 10 0.43
21 3 0.13
22 6 0.26
23 4 0.17
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (23 bp):
TTTTTTTAAAAGAAAAGTTCAAA
Found at i:190754 original size:3 final size:3
Alignment explanation
Indices: 190740--190771 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
190730 TGCAAAGGGG
*
190740 AGA AGA ATA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
190772 GGCGGTGGCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:191673 original size:37 final size:37
Alignment explanation
Indices: 191597--191673 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
191587 TTTTTATATT
*
191597 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
191634 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
191671 TTT
1 TTT
191674 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:195851 original size:15 final size:16
Alignment explanation
Indices: 195815--195852 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
195805 TTTAATTAAA
*
195815 ATAAAATAAAAATGATT
1 ATAAAATAAAAA-GAAT
195832 ATAAAATAAAAA-AAT
1 ATAAAATAAAAAGAAT
195847 ATAAAA
1 ATAAAA
195853 AATCCCGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
17 12 0.60
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
ATAAAATAAAAAGAAT
Found at i:196585 original size:19 final size:20
Alignment explanation
Indices: 196560--196650 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 20
196550 CTTATTTTGG
196560 ATTTTTCACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
196580 -TTTTTCACTATCGCAACAAC
1 ATTTTTCACTATCGCAAC-AC
*
196600 ACGTTTTTCAAACTCTCGCAACAC
1 A--TTTTTC--ACTATCGCAACAC
*
196624 A-TTTTAACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
196643 ATTTTTCA
1 ATTTTTCA
196651 AAATCGCGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
19 30 0.50
20 7 0.12
21 4 0.07
23 6 0.10
24 3 0.05
25 10 0.17
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (20 bp):
ATTTTTCACTATCGCAACAC
Found at i:196622 original size:44 final size:41
Alignment explanation
Indices: 196571--196652 Score: 119
Period size: 44 Copynumber: 1.9 Consensus size: 41
196561 TTTTTCACTA
* *
196571 TCGCAACACTTTTTCACTATCGCAACAACACGTTTTTCAAACTC
1 TCGCAACACATTTTAACTATCGCAAC-ACA--TTTTTCAAACTC
196615 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
1 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
196653 ATCGCGTTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 9 0.25
43 3 0.08
44 24 0.67
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.32
Consensus pattern (41 bp):
TCGCAACACATTTTAACTATCGCAACACATTTTTCAAACTC
Found at i:202261 original size:84 final size:83
Alignment explanation
Indices: 202116--202277 Score: 292
Period size: 84 Copynumber: 2.0 Consensus size: 83
202106 TCTCTTACGG
202116 AAGCTGCTCTCAATCTGGTGTTGGGGGTAGCCTACTATCTTACCTCCCCCTTACCCCATATATAT
1 AAGCTGCTCTCAATCTGGTGTTGGGGGTAGCCTACTATCTTACCTCCCCCTTA-CCCATATATAT
202181 GGGAAAAAGGGACAGCCAT
65 GGGAAAAAGGGACAGCCAT
202200 AAGCTGCTCTCAA-CTTGGTGTTGGGGGTAGCCTACTATCTTACCT-CCCCTTACCCATATATAT
1 AAGCTGCTCTCAATC-TGGTGTTGGGGGTAGCCTACTATCTTACCTCCCCCTTACCCATATATAT
202263 GGGAAAAAGGGACAG
65 GGGAAAAAGGGACAG
202278 TCATTTATAT
Statistics
Matches: 77, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
82 26 0.34
83 8 0.10
84 43 0.56
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (83 bp):
AAGCTGCTCTCAATCTGGTGTTGGGGGTAGCCTACTATCTTACCTCCCCCTTACCCATATATATG
GGAAAAAGGGACAGCCAT
Found at i:205484 original size:16 final size:16
Alignment explanation
Indices: 205456--205492 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
205446 ACAATGATAT
*
205456 ATAT-AAGTTAGGTAA
1 ATATCAAGTCAGGTAA
205471 ATATCAAGTCAGGTAA
1 ATATCAAGTCAGGTAA
205487 ATATCA
1 ATATCA
205493 TATCAAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.46, C:0.08, G:0.16, T:0.30
Consensus pattern (16 bp):
ATATCAAGTCAGGTAA
Found at i:207375 original size:21 final size:21
Alignment explanation
Indices: 207351--207414 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
207341 TTGATAAAAA
*
207351 TTTATATAAAATATGATTATT
1 TTTATATAAAATATTATTATT
*
207372 TTTATTTAAAATATTATTATT
1 TTTATATAAAATATTATTATT
*
207393 TTTACATAAAATATTATT-TT
1 TTTATATAAAATATTATTATT
207413 TT
1 TT
207415 AACATTTCTG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 4 0.10
21 35 0.90
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTATATAAAATATTATTATT
Found at i:212782 original size:6 final size:7
Alignment explanation
Indices: 212773--212828 Score: 55
Period size: 8 Copynumber: 7.9 Consensus size: 7
212763 AAATTAAATT
212773 TATTA-A
1 TATTATA
212779 TATTATA
1 TATTATA
212786 TA-TATA
1 TATTATA
212792 TA-TATA
1 TATTATA
212798 TATATATA
1 TAT-TATA
212806 TATATATA
1 TAT-TATA
212814 TATATATA
1 TAT-TATA
212822 TAATTAT
1 T-ATTAT
212829 TTTAATATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
6 17 0.37
7 3 0.07
8 24 0.52
9 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TATTATA
Found at i:212789 original size:2 final size:2
Alignment explanation
Indices: 212778--212823 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
212768 AAATTTATTA
212778 AT AT -T 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
212819 AT AT A
1 AT AT A
212824 ATTATTTTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:213652 original size:21 final size:21
Alignment explanation
Indices: 213623--213662 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
213613 TTGATCTTAT
213623 AATTAAATGAT-TGAAAAAAAA
1 AATTAAATG-TCTGAAAAAAAA
*
213644 AATTCAATGTCTGAAAAAA
1 AATTAAATGTCTGAAAAAA
213663 GACACGTGTA
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:0.60, C:0.05, G:0.10, T:0.25
Consensus pattern (21 bp):
AATTAAATGTCTGAAAAAAAA
Found at i:214913 original size:36 final size:36
Alignment explanation
Indices: 214842--214914 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 36
214832 GTTGAAAAAT
* *
214842 ATTTATATATTTTCTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTAAAAATCATAAA
214878 ATTTATATAATTTT-TTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAAATTAAAAATCATAAA
214914 A
1 A
214915 ATGGGTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 18 0.55
37 15 0.45
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTAAAAATCATAAA
Found at i:214916 original size:37 final size:37
Alignment explanation
Indices: 214837--214916 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
214827 AATAAGTTGA
* *
214837 AAAATATTTATATATTTTCTTTAAAAATTTAAATTCAT
1 AAAA-ATTTATATATTTTCTTTAAAAATTAAAAATCAT
214875 -AAAATTTATATAATTTT-TTTACAAAATTAAAAAT-AT
1 AAAAATTTATAT-ATTTTCTTTA-AAAATTAAAAATCAT
214911 AAAAAT
1 AAAAAT
214917 GGGTAATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
36 14 0.38
37 23 0.62
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (37 bp):
AAAAATTTATATATTTTCTTTAAAAATTAAAAATCAT
Found at i:220989 original size:2 final size:2
Alignment explanation
Indices: 220982--221017 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
220972 GAATTTAAGA
220982 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
221018 TTTCCCGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:225388 original size:35 final size:36
Alignment explanation
Indices: 225340--225420 Score: 87
Period size: 36 Copynumber: 2.3 Consensus size: 36
225330 AACTTAATGT
* *
225340 TAAATTTCAAAC-G-GATACTATAATGAAACA-AAAAC
1 TAAATTTTAAACGGTGATACTAAAAT-AAA-ATAAAAC
* *
225375 TAAATTTTTAACGGTGGTACTAAAATAAAATAAAAC
1 TAAATTTTAAACGGTGATACTAAAATAAAATAAAAC
225411 TAAATTTTAA
1 TAAATTTTAA
225421 GGATGATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
35 11 0.29
36 18 0.47
37 9 0.24
ACGTcount: A:0.52, C:0.10, G:0.09, T:0.30
Consensus pattern (36 bp):
TAAATTTTAAACGGTGATACTAAAATAAAATAAAAC
Found at i:226291 original size:23 final size:23
Alignment explanation
Indices: 226258--226309 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
226248 TTAAAGATTT
*
226258 CGGGTTAACCCAAACTATTAACA
1 CGGGTTAACCCAAACTACTAACA
*
226281 CGGGTTGACCCAAACTACTAACA
1 CGGGTTAACCCAAACTACTAACA
226304 CGGGTT
1 CGGGTT
226310 TCAGGGTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (23 bp):
CGGGTTAACCCAAACTACTAACA
Found at i:233636 original size:33 final size:33
Alignment explanation
Indices: 233599--233661 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
233589 TGCAGAGGAT
*
233599 GCATCCACCGCATCTGATGCAGCAGACCTTGGA
1 GCATCCACCACATCTGATGCAGCAGACCTTGGA
* *
233632 GCATCCACCACGTCTGTTGCAGCAGACCTT
1 GCATCCACCACATCTGATGCAGCAGACCTT
233662 CGATGTCGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.22, C:0.35, G:0.22, T:0.21
Consensus pattern (33 bp):
GCATCCACCACATCTGATGCAGCAGACCTTGGA
Found at i:239795 original size:31 final size:31
Alignment explanation
Indices: 239759--239859 Score: 93
Period size: 31 Copynumber: 3.3 Consensus size: 31
239749 TATGCCTATA
239759 CAAATTGGTAACTAAACTTGGAAACTTTTCT
1 CAAATTGGTAACTAAACTTGGAAACTTTTCT
* * * *
239790 CAAATTGATATCTGAACTTTG---CTTTGTCT
1 CAAATTGGTAACTAAACTTGGAAACTTT-TCT
* *
239819 CAAATTGGT-ACTTTAACTTGGAAAATTTTCT
1 CAAATTGGTAAC-TAAACTTGGAAACTTTTCT
*
239850 CACATTGGTA
1 CAAATTGGTA
239860 CTCTTTTTAC
Statistics
Matches: 54, Mismatches: 10, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
28 5 0.09
29 18 0.33
31 28 0.52
32 3 0.06
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.40
Consensus pattern (31 bp):
CAAATTGGTAACTAAACTTGGAAACTTTTCT
Found at i:241602 original size:13 final size:13
Alignment explanation
Indices: 241584--241610 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
241574 TTACAAACGC
241584 GCATATGAAGACT
1 GCATATGAAGACT
241597 GCATATGAAGACT
1 GCATATGAAGACT
241610 G
1 G
241611 TTCAACTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:241662 original size:24 final size:24
Alignment explanation
Indices: 241618--241664 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
241608 CTGTTCAACT
*
241618 ATGTATTTATTTATTTATTTATTC
1 ATGTATTTATTTATATATTTATTC
*
241642 ATGTATTGTATTT-TATCTTTATT
1 ATGTATT-TATTTATATATTTATT
241665 TTTAATTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.23, C:0.04, G:0.06, T:0.66
Consensus pattern (24 bp):
ATGTATTTATTTATATATTTATTC
Found at i:250676 original size:21 final size:22
Alignment explanation
Indices: 250650--250698 Score: 91
Period size: 21 Copynumber: 2.3 Consensus size: 22
250640 CTTAAATACA
250650 TTAAAATCTTATTGTA-TTTTT
1 TTAAAATCTTATTGTATTTTTT
250671 TTAAAATCTTATTGTATTTTTT
1 TTAAAATCTTATTGTATTTTTT
250693 TTAAAA
1 TTAAAA
250699 ATCAATACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (22 bp):
TTAAAATCTTATTGTATTTTTT
Found at i:251370 original size:7 final size:7
Alignment explanation
Indices: 251355--251400 Score: 74
Period size: 7 Copynumber: 6.6 Consensus size: 7
251345 TACTAACTTA
251355 AAACCCT
1 AAACCCT
*
251362 AAACTCT
1 AAACCCT
251369 AAACCCT
1 AAACCCT
251376 AAACCCT
1 AAACCCT
*
251383 AAACCTT
1 AAACCCT
251390 AAACCCT
1 AAACCCT
251397 AAAC
1 AAAC
251401 TATAATCCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.46, C:0.37, G:0.00, T:0.17
Consensus pattern (7 bp):
AAACCCT
Found at i:253883 original size:31 final size:32
Alignment explanation
Indices: 253845--253909 Score: 114
Period size: 31 Copynumber: 2.0 Consensus size: 32
253835 TTCTTCAATC
253845 TCTTATTTTAGTTATTAAAGATTA-ATTTTTT
1 TCTTATTTTAGTTATTAAAGATTATATTTTTT
253876 TCTTATTTTAGTTATTAAAGATTATTATTTTTT
1 TCTTATTTTAGTTATTAAAGATTA-TATTTTTT
253909 T
1 T
253910 AATTTACCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 24 0.75
33 8 0.25
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.63
Consensus pattern (32 bp):
TCTTATTTTAGTTATTAAAGATTATATTTTTT
Found at i:259692 original size:24 final size:24
Alignment explanation
Indices: 259660--259708 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
259650 TCAAAATTAA
259660 TAATATTTTATATATCTTAAATTT
1 TAATATTTTATATATCTTAAATTT
* * * *
259684 TAATTTTTTTTATTTTTTAAATTT
1 TAATATTTTATATATCTTAAATTT
259708 T
1 T
259709 TTTAAATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (24 bp):
TAATATTTTATATATCTTAAATTT
Found at i:261769 original size:21 final size:21
Alignment explanation
Indices: 261745--261788 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
261735 CCGAAGGAGG
*
261745 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
* *
261766 AGGAGCAGCTCGTGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
261787 AG
1 AG
261789 CTCCCGGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.16, G:0.41, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAGCT
Found at i:262616 original size:12 final size:12
Alignment explanation
Indices: 262599--262626 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
262589 TAGGTGGAGG
262599 AGGAACGGGATT
1 AGGAACGGGATT
262611 AGGAACGGGATT
1 AGGAACGGGATT
262623 AGGA
1 AGGA
262627 GGTTGGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.07, G:0.43, T:0.14
Consensus pattern (12 bp):
AGGAACGGGATT
Found at i:268662 original size:17 final size:18
Alignment explanation
Indices: 268622--268664 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
268612 CAAGTAGTGT
*
268622 TCTTGAAAGCAAAATGAA
1 TCTTGAAAGAAAAATGAA
* *
268640 TATTGAATGAAAAAT-AA
1 TCTTGAAAGAAAAATGAA
268657 TCTTGAAA
1 TCTTGAAA
268665 TGCTCAAACT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.51, C:0.07, G:0.14, T:0.28
Consensus pattern (18 bp):
TCTTGAAAGAAAAATGAA
Found at i:268988 original size:18 final size:17
Alignment explanation
Indices: 268934--268982 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
268924 TTGGACCCTC
* *
268934 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
268952 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
268970 AGTGCATTCGATG
1 AGTGCA-TCGATG
268983 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:269087 original size:65 final size:64
Alignment explanation
Indices: 268954--269098 Score: 204
Period size: 65 Copynumber: 2.2 Consensus size: 64
268944 TGCACTAAGA
* *
268954 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAACCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAACCACAGTGCATCGATGCATGGCTG
* *
269018 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGATGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAACCACAGTGCATCGATGCATGGCT
269081 G
64 G
*
269082 TGTGCATCGGTGCATCA
1 -GTGCATCGATGCATCA
269099 CTTTGAAAAA
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
64 30 0.41
65 40 0.55
66 3 0.04
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAACCACAGTGCATCGATGCATGGCTG
Done.