Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1213
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1372454
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.28
Warning! 222767 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:402764 original size:12 final size:12
Alignment explanation
Indices: 402744--402775 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
402734 TACCCTTGTG
*
402744 TGTCTGTCTGTC
1 TGTCCGTCTGTC
402756 TGTCCGTCTGTC
1 TGTCCGTCTGTC
402768 TGTCCGTC
1 TGTCCGTC
402776 CGTAACAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.31, G:0.25, T:0.44
Consensus pattern (12 bp):
TGTCCGTCTGTC
Found at i:403184 original size:166 final size:166
Alignment explanation
Indices: 402802--403761 Score: 1336
Period size: 166 Copynumber: 5.8 Consensus size: 166
402792 GTCGCATTTA
* * * * *
402802 TCTCAGCAACTATGTATTGCAGATGCTTGAAATTTTAACACAGTGTTTGTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
* * *
402867 CGTGGGATATATTTTTGTACCAATCAGACATCAACTTCCTGTTAAATGACAACTTTGCTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTA-TTT
*
402932 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
130 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * * *
402969 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
* * *
403034 CGTGGGATATATTTTTGTACCAATCAGATGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
* * *
403099 TAGCAAAAATTTTCAAACAAATTTCCGTCAAAGAAT
131 TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
*
403135 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
* * *
403200 TGTGGGATATATTTTTGTATCAATCGGACGTCAACTTCCTGTTAAATGATGACTTTGCTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTA-TTT
*
403265 TTAACC-AAATTTTCAAACAAATTTTCGTCAAAGATT
130 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* *
403301 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAAC-ATTTGTATAGGCATGCCATA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACAC-ACTATTTGTTTAGGCATGCCATA
* * ** * *
403365 TTGTGGGATATATTTCTGTACCAATCGGGTGTCAACTTCCTGTTAAATGACCACTTTGTTTATTT
65 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTT
*
403430 TTAGCCAACATTTTCAAACAAATTTTCGTCAAAGATT
130 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * * * * * *
403467 TCTCAGCAGCTATTTATCGGAGATGCTTGAAATTTTTACCCAGTGTTT-TTTAAGGCATCCCATA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTT-AGGCATGCCATA
* *
403531 TCGTGGGATATATTTTTGTACCAATCGGACGTCATCTTCCTGTTAAATGA-GTACTTTGTTTA-T
65 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACG-ACTTTGCTTATT
* *
403594 TTTAGCCAAAATTTTCAAATAAATTTTCCTCAAAGATT
129 TTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * * *
403632 TCTCAGCAGCTATTTATCACAGATGCTTGAAATTTTAACTCACTATTTATTTAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
* * * * * * * *
403697 TGTGGAATATATTTCTGTACCAATCGGATGCCAGCTTTCTGTTAAATGTCGACTTTGCTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
403762 GCATATTCAC
Statistics
Matches: 712, Mismatches: 72, Indels: 19
0.89 0.09 0.02
Matches are distributed among these distances:
165 151 0.21
166 437 0.61
167 124 0.17
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.39
Consensus pattern (166 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
Found at i:409297 original size:18 final size:17
Alignment explanation
Indices: 409265--409309 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
409255 ATATGAAGTG
409265 TTACACTTTTTAAAAAC
1 TTACACTTTTTAAAAAC
409282 TTACACTTTTTAAAAAC
1 TTACACTTTTTAAAAAC
409299 TTACCACTTTT
1 TTA-CACTTTT
409310 CCTAGGTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 20 0.74
18 7 0.26
ACGTcount: A:0.36, C:0.20, G:0.00, T:0.44
Consensus pattern (17 bp):
TTACACTTTTTAAAAAC
Found at i:409588 original size:31 final size:31
Alignment explanation
Indices: 409551--409612 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
409541 TCCATGACAC
409551 ACACAAAGAGTACATGTTTGGGGGGGGGGGG
1 ACACAAAGAGTACATGTTTGGGGGGGGGGGG
409582 ACACAAAGAGTACATGTTTGGGGGGGGGGGG
1 ACACAAAGAGTACATGTTTGGGGGGGGGGGG
409613 TGGCTTTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.10, G:0.48, T:0.16
Consensus pattern (31 bp):
ACACAAAGAGTACATGTTTGGGGGGGGGGGG
Found at i:409697 original size:21 final size:21
Alignment explanation
Indices: 409673--410256 Score: 406
Period size: 21 Copynumber: 27.7 Consensus size: 21
409663 CTCTCAAATA
* *
409673 TTAGTTACATACTCCGGGAGG
1 TTAGTTACATACTCTGTGAGG
* **
409694 TTAGATACATACTCCATGAGG
1 TTAGTTACATACTCTGTGAGG
* *
409715 TTAGTTACACACTCTATGAGG
1 TTAGTTACATACTCTGTGAGG
*
409736 -TAGGTTACATACTTTGTGAGG
1 TTA-GTTACATACTCTGTGAGG
* *
409757 TAAGTTACACAACTCTGTGAGG
1 TTAGTTACA-TACTCTGTGAGG
* ** *
409779 TTAGTTACGTACAATGTGATG
1 TTAGTTACATACTCTGTGAGG
*
409800 TTAGTAACATACTCTGTGAGG
1 TTAGTTACATACTCTGTGAGG
* * *
409821 TAAGGT---TACTCTATGAGG
1 TTAGTTACATACTCTGTGAGG
* * * *
409839 TAAGTTAAATACTCTGTAATG
1 TTAGTTACATACTCTGTGAGG
* * *
409860 TTAGTTACATATTCTATGAGA
1 TTAGTTACATACTCTGTGAGG
* * * *
409881 TTAGTCACATACTATGAGATG
1 TTAGTTACATACTCTGTGAGG
409902 TTAGTTACATAACTC--TGAGG
1 TTAGTTACAT-ACTCTGTGAGG
* * * * *
409922 TAAGTTATATACACTATCAGG
1 TTAGTTACATACTCTGTGAGG
* * * * * *
409943 TAAGTCATATACACTATAAGG
1 TTAGTTACATACTCTGTGAGG
*
409964 TTAGTTACATACTCTATGAGG
1 TTAGTTACATACTCTGTGAGG
* *
409985 TTAGTTACATACTCTATGGGG
1 TTAGTTACATACTCTGTGAGG
* * * *
410006 TAAATTACAAACTCTATGAGG
1 TTAGTTACATACTCTGTGAGG
* * *
410027 TAAGTTACATACTCTATGGGG
1 TTAGTTACATACTCTGTGAGG
* *
410048 TAAGTTACATATCTCTATGAGG
1 TTAGTTACATA-CTCTGTGAGG
* *
410070 TAAGTTACATACTCTATGAGG
1 TTAGTTACATACTCTGTGAGG
* *
410091 TAAGTTACATATCTCTATGAGG
1 TTAGTTACATA-CTCTGTGAGG
* *
410113 TAAGTTACATACTCTATGAGG
1 TTAGTTACATACTCTGTGAGG
* * *
410134 TAAGTTACATACTCTATTAGG
1 TTAGTTACATACTCTGTGAGG
* *
410155 TAAGTTACATACTCTATGAGG
1 TTAGTTACATACTCTGTGAGG
* * *
410176 TAAGTTACATACTCTATTAGG
1 TTAGTTACATACTCTGTGAGG
* * *
410197 TAAGTTACATATTTCTATGAGG
1 TTAGTTACATA-CTCTGTGAGG
* *
410219 TAAGTTACATACTCTGTGATG
1 TTAGTTACATACTCTGTGAGG
*
410240 TTTGATATACATACTCT
1 TTAG-T-TACATACTCT
410257 ACGACAAATG
Statistics
Matches: 470, Mismatches: 79, Indels: 26
0.82 0.14 0.05
Matches are distributed among these distances:
18 16 0.03
19 3 0.01
20 13 0.03
21 346 0.74
22 82 0.17
23 10 0.02
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (21 bp):
TTAGTTACATACTCTGTGAGG
Found at i:409720 original size:42 final size:42
Alignment explanation
Indices: 409675--410233 Score: 565
Period size: 42 Copynumber: 13.3 Consensus size: 42
409665 CTCAAATATT
*** * * * *
409675 AGTTACATACTCCGGGAGGTTAGATACATACTCCATGAGGTT
1 AGTTACATACTCTATGAGGTAAGTTACATACTCTATGAGGTA
* * * *
409717 AGTTACACACTCTATGAGGTAGGTTACATACTTTGTGAGGTA
1 AGTTACATACTCTATGAGGTAAGTTACATACTCTATGAGGTA
* * * * ** * * *
409759 AGTTACACAACTCTGTGAGGTTAGTTACGTACAATGTGATGTT
1 AGTTACA-TACTCTATGAGGTAAGTTACATACTCTATGAGGTA
* * *
409802 AGTAACATACTCTGTGAGGTAAGGT---TACTCTATGAGGTA
1 AGTTACATACTCTATGAGGTAAGTTACATACTCTATGAGGTA
* * * * * * * *
409841 AGTTAAATACTCTGTAATGTTAGTTACATATTCTATGAGATT
1 AGTTACATACTCTATGAGGTAAGTTACATACTCTATGAGGTA
* *
409883 AGTCACATA--CTATGAGATGTTAGTTACATAACTC--TGAGGTA
1 AGTTACATACTCTATGAG--GTAAGTTACAT-ACTCTATGAGGTA
* * * * * * * *
409924 AGTTATATACACTATCAGGTAAGTCATATACACTATAAGGTT
1 AGTTACATACTCTATGAGGTAAGTTACATACTCTATGAGGTA
* *
409966 AGTTACATACTCTATGAGGTTAGTTACATACTCTATGGGGTA
1 AGTTACATACTCTATGAGGTAAGTTACATACTCTATGAGGTA
* * *
410008 AATTACAAACTCTATGAGGTAAGTTACATACTCTATGGGGTA
1 AGTTACATACTCTATGAGGTAAGTTACATACTCTATGAGGTA
410050 AGTTACATATCTCTATGAGGTAAGTTACATACTCTATGAGGTA
1 AGTTACATA-CTCTATGAGGTAAGTTACATACTCTATGAGGTA
410093 AGTTACATATCTCTATGAGGTAAGTTACATACTCTATGAGGTA
1 AGTTACATA-CTCTATGAGGTAAGTTACATACTCTATGAGGTA
*
410136 AGTTACATACTCTATTAGGTAAGTTACATACTCTATGAGGTA
1 AGTTACATACTCTATGAGGTAAGTTACATACTCTATGAGGTA
* *
410178 AGTTACATACTCTATTAGGTAAGTTACATATTTCTATGAGGTA
1 AGTTACATACTCTATGAGGTAAGTTACATA-CTCTATGAGGTA
410221 AGTTACATACTCT
1 AGTTACATACTCT
410234 GTGATGTTTG
Statistics
Matches: 431, Mismatches: 73, Indels: 25
0.81 0.14 0.05
Matches are distributed among these distances:
39 28 0.06
40 7 0.02
41 20 0.05
42 227 0.53
43 149 0.35
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (42 bp):
AGTTACATACTCTATGAGGTAAGTTACATACTCTATGAGGTA
Found at i:410220 original size:64 final size:63
Alignment explanation
Indices: 409675--410233 Score: 565
Period size: 64 Copynumber: 8.9 Consensus size: 63
409665 CTCAAATATT
*** * * * * *
409675 AGTTACATACTCCGGGAGGTTAGATACATACTCCATGAGGTTAGTTACACACTCTATGAGGTA
1 AGTTACATACTCTATGAGGTAAGTTACATACTCTATGAGGTAAGTTACATACTCTATGAGGTA
* * * * * * * ** * * *
409738 GGTTACATACTTTGTGAGGTAAGTTACACAACTCTGTGAGGTTAGTTACGTACAATGTGATGTT
1 AGTTACATACTCTATGAGGTAAGTTACA-TACTCTATGAGGTAAGTTACATACTCTATGAGGTA
* * * * * * * *
409802 AGTAACATACTCTGTGAGGTAAGGT---TACTCTATGAGGTAAGTTAAATACTCTGTAATGTT
1 AGTTACATACTCTATGAGGTAAGTTACATACTCTATGAGGTAAGTTACATACTCTATGAGGTA
* * * * *
409862 AGTTACATATTCTATGAGATTAGTCACATA--CTATGAGATGTTAGTTACATAACTC--TGAGGT
1 AGTTACATACTCTATGAGGTAAGTTACATACTCTATGAG--GTAAGTTACAT-ACTCTATGAGGT
409923 A
63 A
* * * * * * * * *
409924 AGTTATATACACTATCAGGTAAGTCATATACACTATAAGGTTAGTTACATACTCTATGAGGTT
1 AGTTACATACTCTATGAGGTAAGTTACATACTCTATGAGGTAAGTTACATACTCTATGAGGTA
* * * *
409987 AGTTACATACTCTATGGGGTAAATTACAAACTCTATGAGGTAAGTTACATACTCTATGGGGTA
1 AGTTACATACTCTATGAGGTAAGTTACATACTCTATGAGGTAAGTTACATACTCTATGAGGTA
410050 AGTTACATATCTCTATGAGGTAAGTTACATACTCTATGAGGTAAGTTACATATCTCTATGAGGTA
1 AGTTACATA-CTCTATGAGGTAAGTTACATACTCTATGAGGTAAGTTACATA-CTCTATGAGGTA
*
410115 AGTTACATACTCTATGAGGTAAGTTACATACTCTATTAGGTAAGTTACATACTCTATGAGGTA
1 AGTTACATACTCTATGAGGTAAGTTACATACTCTATGAGGTAAGTTACATACTCTATGAGGTA
* *
410178 AGTTACATACTCTATTAGGTAAGTTACATATTTCTATGAGGTAAGTTACATACTCT
1 AGTTACATACTCTATGAGGTAAGTTACATA-CTCTATGAGGTAAGTTACATACTCT
410234 GTGATGTTTG
Statistics
Matches: 412, Mismatches: 70, Indels: 27
0.81 0.14 0.05
Matches are distributed among these distances:
60 45 0.11
61 11 0.03
62 38 0.09
63 139 0.34
64 159 0.39
65 20 0.05
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (63 bp):
AGTTACATACTCTATGAGGTAAGTTACATACTCTATGAGGTAAGTTACATACTCTATGAGGTA
Found at i:410798 original size:145 final size:146
Alignment explanation
Indices: 410524--410847 Score: 404
Period size: 145 Copynumber: 2.2 Consensus size: 146
410514 TGGGGAGTGG
* *
410524 ATGTTTCTCCATAAGATAGATATGGACCGGACACAAATTTTGCACTCTTCCTTCCAATGACCTTG
1 ATGTTTCTCCATAAGAAAGATATGGACCGGACACAAATTTTGCACTCTTCCTCCCAATGACCTTG
* * * *
410589 AATTTGCAAGAATGACCTTGGGTCAAAATCATGACACACCTTCAGGTCATAAGCAACTTTTGTGT
66 AACTTGCAAGAATGACCTTGAGTCAAAATCATGAAACACCTTCAGGTCATAAGCAACTTCTGTGT
* *
410654 GAAGTAATAACTTCAA
131 GAAATAAGAACTTCAA
* * * *
410670 ATGTTTCTCCGTAAGAAAGATATGGACCGGACACAAATTTTGCATTTTTCCTCCCAGTGA-CTTG
1 ATGTTTCTCCATAAGAAAGATATGGACCGGACACAAATTTTGCACTCTTCCTCCCAATGACCTTG
* *
410734 AACTTGCACA-AATGACCTTGAGTCAAAATCATGAAACAGCC-TCAGGTCATGAGCTA-TCTCTG
66 AACTTGCA-AGAATGACCTTGAGTCAAAATCATGAAACA-CCTTCAGGTCATAAGCAACT-TCTG
* **
410796 TGTGAAATAAGATCTTCTT
128 TGTGAAATAAGAACTTCAA
* ** *
410815 ACGTACCTCCATAAGAAAGATATGGACCAGACA
1 ATGTTTCTCCATAAGAAAGATATGGACCGGACA
410848 TGATTGCTGA
Statistics
Matches: 153, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
144 1 0.01
145 95 0.62
146 57 0.37
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (146 bp):
ATGTTTCTCCATAAGAAAGATATGGACCGGACACAAATTTTGCACTCTTCCTCCCAATGACCTTG
AACTTGCAAGAATGACCTTGAGTCAAAATCATGAAACACCTTCAGGTCATAAGCAACTTCTGTGT
GAAATAAGAACTTCAA
Found at i:411148 original size:11 final size:11
Alignment explanation
Indices: 411132--411171 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
411122 AAAAGCAATT
411132 TCCAAGTAAAC
1 TCCAAGTAAAC
411143 TCCAAGTAAAC
1 TCCAAGTAAAC
411154 -CCAAAGTAAAC
1 TCC-AAGTAAAC
*
411165 CCCAAGT
1 TCCAAGT
411172 GGACCCAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 2 0.07
11 23 0.85
12 2 0.07
ACGTcount: A:0.45, C:0.30, G:0.10, T:0.15
Consensus pattern (11 bp):
TCCAAGTAAAC
Found at i:411160 original size:22 final size:22
Alignment explanation
Indices: 411135--411180 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
411125 AGCAATTTCC
*
411135 AAGTAAACTCCAAGTAAACCCA
1 AAGTAAACCCCAAGTAAACCCA
**
411157 AAGTAAACCCCAAGTGGACCCA
1 AAGTAAACCCCAAGTAAACCCA
411179 AA
1 AA
411181 TTTTCAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.28, G:0.13, T:0.11
Consensus pattern (22 bp):
AAGTAAACCCCAAGTAAACCCA
Found at i:412272 original size:17 final size:17
Alignment explanation
Indices: 412250--412283 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
412240 CTTTGAAAAA
412250 ATTTTTCAAAGTGCGTT
1 ATTTTTCAAAGTGCGTT
412267 ATTTTTCAAAGTGCGTT
1 ATTTTTCAAAGTGCGTT
412284 GTAACAGGCC
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:0.24, C:0.12, G:0.18, T:0.47
Consensus pattern (17 bp):
ATTTTTCAAAGTGCGTT
Found at i:412575 original size:168 final size:167
Alignment explanation
Indices: 412325--413227 Score: 1108
Period size: 168 Copynumber: 5.4 Consensus size: 167
412315 AAGGAGATTG
* * ** ** * * *
412325 TGGATATCATAACCATGTATTCAGTTTTTTGCCCACATGTGTGGGAGTAGAGAAGAAGATTTTTT
1 TGGACATCATAACCATGCATTCAGTTTTTAACAAACATATATGGGAGTAGAGAAGAAGATTTTCT
* *
412390 AAGATTTAAAACATTTTTACTATATGGCCATATTAGCCCCACCCTAGAGCCTGAACACCTAACAA
66 AAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACACCTAACAA
* * *
412455 AGGGGTCATAAATTTCACAATTTTAGTAAAGGCCCTCA
131 AGGGGTCATGAATTTCACAATTTT-GTAGAGGGCCTCA
* * ** ** * * *
412493 TGAACATCATAACCATGTATTCAGTTTTTTGCTCACATGTGTGGGAGTAGAGAAGAAGATTTTTT
1 TGGACATCATAACCATGCATTCAGTTTTTAACAAACATATATGGGAGTAGAGAAGAAGATTTTCT
* * * *
412558 AAGATTTAAAACATTTTTACTGTATGGCCATATTGGCCCCACCCTAGAGCTTGAACACCAAACAA
66 AAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACACCTAACAA
412623 AGGGGTCATGAATTTCACAATTTTGATAGAGGGCCTCA
131 AGGGGTCATGAATTTCACAATTTTG-TAGAGGGCCTCA
* *
412661 TGGACATCATAACCATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCT
1 TGGACATCATAACCATGCATTCAGTTTTTAACAAACATATATGGGAGTAGAGAAGAAGATTTTCT
* * * *
412726 AAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCACCCTAGAGCCTGAACCCCTCACTG
66 AAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACACCTAAC-A
** *
412791 AA-GGGTCATGAATTTCACAATTAAGGTAGAGGGCTTCA
130 AAGGGGTCATGAATTTCACAATT-TTGTAGAGGGCCTCA
* * * * *
412829 TGGACATCATAACCATGCATTTAATTTTTAACAAATATATATGGTAGTTGAGAAGAAGATTTTCT
1 TGGACATCATAACCATGCATTCAGTTTTTAACAAACATATATGGGAGTAGAGAAGAAGATTTTCT
* * *
412894 AAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCACCCTAGAGCCTGAAC-CTCTGACC
66 AAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACAC-CTAACA
* *
412958 CAGGGGTCATGAATTTCACAATTTTGATAAAGGGCCTCA
130 AAGGGGTCATGAATTTCACAATTTTG-TAGAGGGCCTCA
* * * * *
412997 TGGACATCATAATCATGCATTTAGTTTTTAAAAAATATATATGGGAGTTGAGAAGAAGATTTTCT
1 TGGACATCATAACCATGCATTCAGTTTTTAACAAACATATATGGGAGTAGAGAAGAAGATTTTCT
* * * * **
413062 AAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCACCCTAAAGCCAGAACCCCTGACCC
66 AAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACACCTAACAA
* * *
413127 AGGGGCCATAAATTTCACAATTTTGGTAGAGGGCTTCA
131 AGGGGTCATGAATTTCACAATTTT-GTAGAGGGCCTCA
** ** ** ***
413165 TGGACATCATAACCATGCAACCAGTTTTTTCCTCACATGCGTGGGAGTAGAGAAGAAGATTTT
1 TGGACATCATAACCATGCATTCAGTTTTTAACAAACATATATGGGAGTAGAGAAGAAGATTTT
413228 TGAAAATTTG
Statistics
Matches: 660, Mismatches: 67, Indels: 16
0.89 0.09 0.02
Matches are distributed among these distances:
167 4 0.01
168 651 0.99
169 5 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (167 bp):
TGGACATCATAACCATGCATTCAGTTTTTAACAAACATATATGGGAGTAGAGAAGAAGATTTTCT
AAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACACCTAACAA
AGGGGTCATGAATTTCACAATTTTGTAGAGGGCCTCA
Found at i:413220 original size:336 final size:336
Alignment explanation
Indices: 412366--413227 Score: 1242
Period size: 336 Copynumber: 2.6 Consensus size: 336
412356 CCCACATGTG
* * *
412366 TGGGAGTAGAGAAGAAGATTTTTTAAGATTTAAAACATTTTTACTATATGGCCATATTAGCCCCA
1 TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA
* * * * * *
412431 CCCTAGAGCCTGAACACCTAACAAAGGGGTCATAAATTTCACAATTTTAGTAAAGGCCCTCATGA
66 CCCTAGAGCCTGAACCCCTAACAAAGGGGTCATAAATTTCACAATTTTGGTAGAGGGCTTCATGG
* * *
412496 ACATCATAACCATGTATTCAGTTTTTTGCTCACATGTGTGGGAGTAGAGAAGAAGATTTTTTAAG
131 ACATCATAACCATGCATTCAGTTTTTTACTCACATGTGTGGGAGTAGAGAAGAAGATTTTCTAAG
* *
412561 ATTTAAAACATTTTTACTGTATGGCCATATTGGCCCCACCCTAGAGCTTGAACACCAAACAAAGG
196 ATTTAAAACATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACACCAAACAAAGG
*
412626 GGTCATGAATTTCACAATTTTGATAGAGGGCCTCATGGACATCATAACCATGCATTTAGTTTTTA
261 GGTCATGAATTTCACAATTTTGATAAAGGGCCTCATGGACATCATAACCATGCATTTAGTTTTTA
*
412691 ACAAATATATA
326 AAAAATATATA
*
412702 TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCA
1 TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA
* * * **
412767 CCCTAGAGCCTGAACCCCTCACTGAA-GGGTCATGAATTTCACAATTAAGGTAGAGGGCTTCATG
66 CCCTAGAGCCTGAACCCCTAAC-AAAGGGGTCATAAATTTCACAATTTTGGTAGAGGGCTTCATG
* * * ** * * * * *
412831 GACATCATAACCATGCATTTAATTTTTAACAAATATATATGGTAGTTGAGAAGAAGATTTTCTAA
130 GACATCATAACCATGCATTCAGTTTTTTACTCACATGTGTGGGAGTAGAGAAGAAGATTTTCTAA
* * ** **
412896 GATTTAATACATTTTTACTATTTGGCCATATTGGCCCCACCCTAGAGCCTGAAC-CTCTGACCCA
195 GATTTAAAACATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACAC-CAAACAAA
*
412960 GGGGTCATGAATTTCACAATTTTGATAAAGGGCCTCATGGACATCATAATCATGCATTTAGTTTT
259 GGGGTCATGAATTTCACAATTTTGATAAAGGGCCTCATGGACATCATAACCATGCATTTAGTTTT
413025 TAAAAAATATATA
324 TAAAAAATATATA
*
413038 TGGGAGTTGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA
1 TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA
* * * ** *
413103 CCCTAAAGCCAGAACCCCTGACCCAGGGGCCATAAATTTCACAATTTTGGTAGAGGGCTTCATGG
66 CCCTAGAGCCTGAACCCCTAACAAAGGGGTCATAAATTTCACAATTTTGGTAGAGGGCTTCATGG
** * *
413168 ACATCATAACCATGCAACCAGTTTTTTCCTCACATGCGTGGGAGTAGAGAAGAAGATTTT
131 ACATCATAACCATGCATTCAGTTTTTTACTCACATGTGTGGGAGTAGAGAAGAAGATTTT
413228 TGAAAATTTG
Statistics
Matches: 459, Mismatches: 64, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
335 2 0.00
336 455 0.99
337 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (336 bp):
TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA
CCCTAGAGCCTGAACCCCTAACAAAGGGGTCATAAATTTCACAATTTTGGTAGAGGGCTTCATGG
ACATCATAACCATGCATTCAGTTTTTTACTCACATGTGTGGGAGTAGAGAAGAAGATTTTCTAAG
ATTTAAAACATTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACACCAAACAAAGG
GGTCATGAATTTCACAATTTTGATAAAGGGCCTCATGGACATCATAACCATGCATTTAGTTTTTA
AAAAATATATA
Found at i:415766 original size:168 final size:167
Alignment explanation
Indices: 415568--416358 Score: 938
Period size: 168 Copynumber: 4.7 Consensus size: 167
415558 CCTCATGTCA
* * * * * *
415568 TGAACCCCTGACCCAGGGGCCATAAATTTCACAATTCAGGTAAAGGAGATTGTGGATATCATAAC
1 TGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGG-GATTATGGACATCATAAC
* ** ** * * * * *
415633 CATGTATTCAGTTTTTTGCCCACATGTGTGGGAGTAGAGAAGAAGATTTTTTGAGATTTAAAACA
65 CATGCATTCAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAAAACA
* * * *
415698 TTTTCACTATTTGGTCATATTGGTCCCACCCTAGAGCC
130 TTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCC
* * *
415736 TGAACCCCTGACCGAGGGGTCATGAATTTCACAATTTAAGTAGAGGGCTTCATGGACATCATAAC
1 TGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGGGATT-ATGGACATCATAAC
* * * *
415801 CATGCATTTAGTTTTCAAAAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACA
65 CATGCATTCAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAAAACA
*
415866 ATTTTACTATATGGCCATATTGGCCCCACCCTAGAGCC
130 TTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCC
* * * *
415904 TGAAACCCTGACCAAGGGGTCATGAATTTCACAATTTAGGTTGAGAGATTCATGGACATCATAAC
1 TGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGGGATT-ATGGACATCATAAC
* **
415969 CATGCATTTAGTTTTTAACAAATATATATGATAGTAGAGAAGAAGATTTTCTAAGATTTAAAACA
65 CATGCATTCAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAAAACA
*
416034 TTTTTACTATTTGGCCATATTGGCCCCACCCTAGAGCC
130 TTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCC
* ** *
416072 TAAACCTTTGACGACCTAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCTTTATGGACATCAT
1 TGAACCCCTGAC--CC-AGGGGTCATGAATTTCACAATTTAGGTAGAGGG-ATTATGGACATCAT
* * ** *
416137 AATCATGCA-TCTAGTTTTCCAA-AAATATATATGATAGTAGAGAAGAAGATTTTCCAAGATTTA
62 AACCATGCATTC-AGTTTT-TAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTA
416200 AAACATTTTTACTATATGGCCATATTGGTCCCCACCCTAGAGCC
125 AAACATTTTTACTATATGGCCATATTGG-CCCCACCCTAGAGCC
* * * * *
416244 AGAACCCCTGACCCAGGGGCCATAAATTTCACAATTTTGGTAGAGGGCTTTATGGACATCATAAC
1 TGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGGG-ATTATGGACATCATAAC
** ** ** * **
416309 CATGCAACCAGTTTTTTCCTCACATGCATGGGAGTAGAGAAGAAGATTTT
65 CATGCATTCAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTT
416359 TGAAAATTTG
Statistics
Matches: 540, Mismatches: 73, Indels: 19
0.85 0.12 0.03
Matches are distributed among these distances:
167 3 0.01
168 299 0.55
169 83 0.15
170 5 0.01
171 123 0.23
172 27 0.05
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (167 bp):
TGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGGGATTATGGACATCATAACC
ATGCATTCAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAAAACAT
TTTTACTATATGGCCATATTGGCCCCACCCTAGAGCC
Found at i:425728 original size:13 final size:13
Alignment explanation
Indices: 425710--425734 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
425700 GAAAATACAG
425710 AAATACATGATAC
1 AAATACATGATAC
425723 AAATACATGATA
1 AAATACATGATA
425735 ATGATGAACG
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:0.56, C:0.12, G:0.08, T:0.24
Consensus pattern (13 bp):
AAATACATGATAC
Found at i:441764 original size:11 final size:11
Alignment explanation
Indices: 441748--441774 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
441738 AGTATGTAAA
441748 AAATGGAATAG
1 AAATGGAATAG
441759 AAATGGAATAG
1 AAATGGAATAG
441770 AAATG
1 AAATG
441775 AGAGTAATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.26, T:0.19
Consensus pattern (11 bp):
AAATGGAATAG
Found at i:454385 original size:16 final size:16
Alignment explanation
Indices: 454354--454400 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 16
454344 TCGTCAATAG
454354 TGTTGATTTTTT-GTT
1 TGTTGATTTTTTAGTT
*
454369 TGTTGTTTTTTTAGTT
1 TGTTGATTTTTTAGTT
*
454385 TGTT-CTTTTTTAGTT
1 TGTTGATTTTTTAGTT
454400 T
1 T
454401 TCTTATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 22 0.76
16 7 0.24
ACGTcount: A:0.06, C:0.02, G:0.17, T:0.74
Consensus pattern (16 bp):
TGTTGATTTTTTAGTT
Found at i:454647 original size:2 final size:2
Alignment explanation
Indices: 454640--454707 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
454630 TAAAAGCATA
454640 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
454682 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
454708 TCTTTACTAC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:455023 original size:11 final size:11
Alignment explanation
Indices: 455007--455040 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
454997 ATTTTTAGAT
455007 TTGTACACGAA
1 TTGTACACGAA
455018 TTGTACACGAA
1 TTGTACACGAA
455029 TTGTACACGAA
1 TTGTACACGAA
455040 T
1 T
455041 ATTGGAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (11 bp):
TTGTACACGAA
Found at i:457022 original size:146 final size:146
Alignment explanation
Indices: 456806--457506 Score: 826
Period size: 146 Copynumber: 4.9 Consensus size: 146
456796 TTTTAAACAA
* * * *
456806 TGACCTTGAACTT-CCTCAATTGACCTTGAG-TCAAGGTTATGACACA-CTTTAGGTCATAAGCA
1 TGACCTTGACCTTGCC-CAAATGACCTTG-GTTCAAGGTCATGACACACCCTTAGGTCATAAGCA
* * * * * **
456868 ATCTTTGTGTGAACTGAGAACTTCCAATGTTTATCCATAAGTAAGATATAAACTGGACACGAATT
64 ATCTCTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACTGGACACGAATT
456933 TTGCACTTTTTCTACCAG
129 TTGCACTTTTTCTACCAG
* * * * **
456951 TGATCTTGACCTTGTCCAAATGGCAC-TGGATCAAGGTCATGACA-ACCCCGAAGGTCATAAGCA
1 TGACCTTGACCTTGCCCAAATGAC-CTTGGTTCAAGGTCATGACACA-CCCTTAGGTCATAAGCA
* * * *
457014 ATCTTTGTGTGAAGTAAGAACTTCAAATGTTTCTCCATAAGAAAGATATGGACAGGACACAAATT
64 ATCTCTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACTGGACACGAATT
**
457079 TTGCACTTTTTCTGTCAG
129 TTGCACTTTTTCTACCAG
* *
457097 TGACCTTG-CCATTGCCCAAATGACCTTGGTTCAAGGTCATGACATATCCTTAGGTCATAAGCAA
1 TGACCTTGACC-TTGCCCAAATGACCTTGGTTCAAGGTCATGACACACCCTTAGGTCATAAGCAA
* * * * *
457161 TCTCTGTGTAAAGTAAGAAATTCCAATGTTTCTCCATAAAAAAAGATATAGACCGGACACGAATT
65 TCTCTGTGTGAAGTAAGAACTTCCAATGTTTCTCCAT-AAGAAAGATATGGACTGGACACGAATT
457226 TTGCACTTTTTCTACCAG
129 TTGCACTTTTTCTACCAG
** **
457244 TGACCTTGA---TGCCCAAATGACCTTGGTTCAAGGTCATGACACATTCTTAGGTCATATCCAAT
1 TGACCTTGACCTTGCCCAAATGACCTTGGTTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
* * *
457306 ATCTGTG-GAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAAATATGGAC-CGACACGAATTTT
66 CTCTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACTGGACACGAATTTT
457369 GCACTTTTTCT----G
131 GCACTTTTTCTACCAG
** * * *
457381 T--CAGTGACCTTGCCCAAATGACCTGGGTTCAAGGTCATGACACACCCTTAGATCATATGCAAT
1 TGACCTTGACCTTGCCCAAATGACCTTGGTTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
* *
457444 CTCTGTGTGAAGAAAGAACTT-CAATGTTTTTCCATAAGAAAGATATGGACTGGACACGAATTT
66 CTCTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACTGGACACGAATTT
457507 AACAGACAGA
Statistics
Matches: 481, Mismatches: 60, Indels: 36
0.83 0.10 0.06
Matches are distributed among these distances:
135 4 0.01
137 2 0.00
138 81 0.17
139 23 0.05
141 23 0.05
142 12 0.02
143 26 0.05
144 57 0.12
145 35 0.07
146 170 0.35
147 48 0.10
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (146 bp):
TGACCTTGACCTTGCCCAAATGACCTTGGTTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
CTCTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACTGGACACGAATTTT
GCACTTTTTCTACCAG
Found at i:461830 original size:2 final size:2
Alignment explanation
Indices: 461743--461816 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
461733 AAGAGTTCTC
461743 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
461785 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
461817 AATTTGTTGT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:462918 original size:21 final size:21
Alignment explanation
Indices: 462894--462946 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
462884 CTGTAAAATT
*
462894 AAATTCACACTTTA-ATCTGTA
1 AAATTTACACTTTACA-CTGTA
*
462915 AAATTTATACTTTACACTGTA
1 AAATTTACACTTTACACTGTA
462936 AAATTTACACT
1 AAATTTACACT
462947 GTAAAATTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.40
Consensus pattern (21 bp):
AAATTTACACTTTACACTGTA
Found at i:462944 original size:14 final size:14
Alignment explanation
Indices: 462925--462954 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
462915 AAATTTATAC
462925 TTTACACTGTAAAA
1 TTTACACTGTAAAA
462939 TTTACACTGTAAAA
1 TTTACACTGTAAAA
462953 TT
1 TT
462955 CGCTGATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (14 bp):
TTTACACTGTAAAA
Found at i:463040 original size:21 final size:20
Alignment explanation
Indices: 462989--463045 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
462979 ACTTTCATCT
462989 GTAAAATTCACACTTTAAAC
1 GTAAAATTCACACTTTAAAC
* *
463009 -TAAAAAGTTCACGCTTTAATCC
1 GT-AAAA-TTCACACTTTAA-AC
463031 GTAAAATTCACACTT
1 GTAAAATTCACACTT
463046 AAAAGTGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
19 1 0.03
20 4 0.13
21 19 0.63
22 5 0.17
23 1 0.03
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.32
Consensus pattern (20 bp):
GTAAAATTCACACTTTAAAC
Found at i:463235 original size:21 final size:21
Alignment explanation
Indices: 463211--463621 Score: 174
Period size: 21 Copynumber: 20.0 Consensus size: 21
463201 CAATTTTATG
463211 CTTTAATCTGTAAAATTTACA
1 CTTTAATCTGTAAAATTTACA
* **
463232 CTTTTATCTG-----TGCACA
1 CTTTAATCTGTAAAATTTACA
* * *
463248 -TT-AATCTCTAAAAATCACA
1 CTTTAATCTGTAAAATTTACA
* * * *
463267 CATTAATCTCTAAAATTCAAA
1 CTTTAATCTGTAAAATTTACA
* *
463288 CATTAATCTGTAAAATTCACA
1 CTTTAATCTGTAAAATTTACA
* *
463309 CTTTGATCTGTAAAATTCACA
1 CTTTAATCTGTAAAATTTACA
* *
463330 C-TTAGATCTGTAAAATTAAGA
1 CTTTA-ATCTGTAAAATTTACA
* **
463351 CTTGAATCTGTAAAATAAACA
1 CTTTAATCTGTAAAATTTACA
* * *
463372 CTTTAATGTG-AAAAATCACA
1 CTTTAATCTGTAAAATTTACA
* * *
463392 CTTTAA-ATGTAAAAATTACT
1 CTTTAATCTGTAAAATTTACA
*
463412 CTTTAATCTGTAAAGTTTATCA
1 CTTTAATCTGTAAAATTTA-CA
* ** *
463434 -TTGAATGGGT-AAACTTACA
1 CTTTAATCTGTAAAATTTACA
** *
463453 CTTTAATCTGTTTAATGTAC-
1 CTTTAATCTGTAAAATTTACA
463473 CGTTTATAT-TGTAAAATTTACA
1 C-TTTA-ATCTGTAAAATTTACA
* * * * *
463495 ATTTTATCTGTGAAGTTCA-A
1 CTTTAATCTGTAAAATTTACA
* * *
463515 TTTTAAACGTGTAACATTTACA
1 CTTTAATC-TGTAAAATTTACA
** *
463537 CTTTAAAAGTGTAAAAATTCACA
1 CTTT-AATCTGT-AAAATTTACA
** *
463560 CTTTGAA-GAGTAAAAATTACA
1 CTTT-AATCTGTAAAATTTACA
463581 CTTTAATCT-TAAAAATTTACA
1 CTTTAATCTGT-AAAATTTACA
* *
463602 -ATTAATCTGTAAATTTTACA
1 CTTTAATCTGTAAAATTTACA
463622 GATATGTCTA
Statistics
Matches: 294, Mismatches: 71, Indels: 51
0.71 0.17 0.12
Matches are distributed among these distances:
14 4 0.01
15 2 0.01
16 4 0.01
19 8 0.03
20 70 0.24
21 174 0.59
22 15 0.05
23 17 0.06
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (21 bp):
CTTTAATCTGTAAAATTTACA
Found at i:463392 original size:20 final size:19
Alignment explanation
Indices: 463369--463418 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
463359 TGTAAAATAA
463369 ACACTTTAATGTGAAAAATC
1 ACACTTTAATGT-AAAAATC
*
463389 ACACTTTAAATGTAAAAATT
1 ACACTTT-AATGTAAAAATC
*
463409 ACTCTTTAAT
1 ACACTTTAAT
463419 CTGTAAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 3 0.11
20 19 0.70
21 5 0.19
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (19 bp):
ACACTTTAATGTAAAAATC
Found at i:463548 original size:22 final size:22
Alignment explanation
Indices: 463516--463586 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
463506 GAAGTTCAAT
* *
463516 TTTAAACGTGTAACATTTACAC
1 TTTAAAAGTGTAAAATTTACAC
*
463538 TTTAAAAGTGTAAAAATTCACAC
1 TTTAAAAGTGT-AAAATTTACAC
* * *
463561 TTT-GAAGAGTAAAAATTACAC
1 TTTAAAAGTGTAAAATTTACAC
463582 TTTAA
1 TTTAA
463587 TCTTAAAAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
21 12 0.31
22 15 0.38
23 12 0.31
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.34
Consensus pattern (22 bp):
TTTAAAAGTGTAAAATTTACAC
Found at i:463606 original size:20 final size:21
Alignment explanation
Indices: 463569--463614 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
463559 ACTTTGAAGA
*
463569 GTAAAAATTACACTTTAATCT
1 GTAAAAATTACACATTAATCT
463590 -TAAAAATTTACA-ATTAATCT
1 GTAAAAA-TTACACATTAATCT
463610 GTAAA
1 GTAAA
463615 TTTTACAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37
Consensus pattern (21 bp):
GTAAAAATTACACATTAATCT
Found at i:463619 original size:20 final size:21
Alignment explanation
Indices: 463583--463667 Score: 72
Period size: 20 Copynumber: 4.2 Consensus size: 21
463573 AAATTACACT
*
463583 TTAATCT-TAAAAATTTACA-A
1 TTAATCTGT-AAATTTTACAGA
463603 TTAATCTGTAAATTTTACAGA
1 TTAATCTGTAAATTTTACAGA
* *
463624 -T-ATGTCTAAATTTTACACG-
1 TTAATCTGTAAATTTTACA-GA
* *
463643 TTTATGTGTAAATTTTACAGA
1 TTAATCTGTAAATTTTACAGA
463664 TTAA
1 TTAA
463668 AGTAAAACGT
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
19 14 0.26
20 20 0.37
21 20 0.37
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.44
Consensus pattern (21 bp):
TTAATCTGTAAATTTTACAGA
Found at i:463654 original size:21 final size:19
Alignment explanation
Indices: 463609--463664 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 19
463599 ACAATTAATC
463609 TGTAAATTTTACAGATATG
1 TGTAAATTTTACAGATATG
* *
463628 TCTAAATTTTACACGTTTATG
1 TGTAAATTTTACA-G-ATATG
463649 TGTAAATTTTACAGAT
1 TGTAAATTTTACAGAT
463665 TAAAGTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 13 0.42
20 2 0.06
21 16 0.52
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (19 bp):
TGTAAATTTTACAGATATG
Found at i:463891 original size:21 final size:21
Alignment explanation
Indices: 463859--463975 Score: 69
Period size: 21 Copynumber: 5.7 Consensus size: 21
463849 CGATATAATG
*
463859 TACATTTTAATCTGTACAATT
1 TACACTTTAATCTGTACAATT
* * * *
463880 TACACTTAAATCTTTAAAAAT
1 TACACTTTAATCTGTACAATT
*
463901 T--ACTTTATTCTGT-CAATTT
1 TACACTTTAATCTGTACAA-TT
* * *
463920 TATACTTTTATTTGTACAATT
1 TACACTTTAATCTGTACAATT
* * * *
463941 TATACCTAAATCTGTAAAATT
1 TACACTTTAATCTGTACAATT
* *
463962 CACTCTTTAATCTG
1 TACACTTTAATCTG
463976 AAAATTTCAA
Statistics
Matches: 69, Mismatches: 23, Indels: 8
0.69 0.23 0.08
Matches are distributed among these distances:
18 2 0.03
19 11 0.16
21 53 0.77
22 3 0.04
ACGTcount: A:0.33, C:0.15, G:0.04, T:0.47
Consensus pattern (21 bp):
TACACTTTAATCTGTACAATT
Found at i:496420 original size:430 final size:432
Alignment explanation
Indices: 495666--497601 Score: 1649
Period size: 430 Copynumber: 4.3 Consensus size: 432
495656 TTTACAAACT
* * * * * * *
495666 GATATTGCTGCGATCAACAACTTT-ATTCTATAGTGCATTACAAAATCTTGATCATTTTTTACG-
1 GATATTGGTACGATCAACAACTTTGCTTCTATAATGCATTACAAAATCTTTATC-GTTTTTAAGT
** * * *** * *
495729 TATGAGTAATAGAGTTTAGGAGTTTATTGACCCCTAATTTAAGGGGCCAGCCCC-TTTTTCTTGA
65 TATTTGTAATAGAGTTAACGAGTACCTTGGCCCCTAA--AAAGGGGCCAGCCCCTTTTTTCTTGA
* * * * * * * * ** *
495793 TTT-TAT-ACGAAAGGTCTCATGTATACTAACATGTTTTGTTGTTACATCCATCTAAAATTGATG
128 TTTCTTTGA--AAAGGTCTTAAGAATACAAACATTTTTTGTTCTTACACCCATGAAAAATTGTTG
*
495856 ATCACTTTTGAGATACAAATGATGGAATATTTTAGGGGCCAGCCCTCTAGATCCTTAATGGGGAC
191 ATCATTTTTGAGATACAAATGATGGAATATTTTAGGGGCCAGCCCTCTAGATCCTTAATGGGGAC
*
495921 AGAAATTCGTGTTTTGATAAGTAGAATCAATTCAAATCATTTAATCAAACATTTTCTCTTCTTTG
256 AGAAATTCGTGTTTTGATAAGTAGAATCAATTCAAATCATTTAATCAAACATTTTCTCTTCTATG
495986 ATGTCTAACAAAATATGTATACTTCTCTAGTTATTTTTCGTC-A-AAGTACTTTGGCCCCTAAAA
321 ATGTCTAACAAAATATGTATACTTCTCTAGTTATTTTTCGTCAATAAGTACTTTGGCCCCTAAAA
496049 ATCCCTAATTACGTAATAAATGGACGTGGCAATGATTTTTTCTAATA
386 ATCCCTAATTACGTAATAAATGGACGTGGCAATGATTTTTTCTAATA
496096 GATATTGGTACGATCAACAACTTTGCTTCTATAATGCATTACAAAATCTTTATCGTTTTTAAGTT
1 GATATTGGTACGATCAACAACTTTGCTTCTATAATGCATTACAAAATCTTTATCGTTTTTAAGTT
496161 ATTTGTAATAGAGTTAACGAGTACCTTGGCCCCTAAAAAGGGGCCAGCCCCTTTTTTCTTGATTT
66 ATTTGTAATAGAGTTAACGAGTACCTTGGCCCCTAAAAAGGGGCCAGCCCCTTTTTTCTTGATTT
496226 CTTTGAAAAGGTCTTAAGAATACAAACATTTTTTGTTCTTACACCCATGAAAAATTGTTGATCAT
131 CTTTGAAAAGGTCTTAAGAATACAAACATTTTTTGTTCTTACACCCATGAAAAATTGTTGATCAT
496291 TTTTGAGATACAAATGATGGAATATTTTAGGGGCCAGCCCTCTAGATCCTTAATGGGGACAGAAA
196 TTTTGAGATACAAATGATGGAATATTTTAGGGGCCAGCCCTCTAGATCCTTAATGGGGACAGAAA
* * * * *
496356 TTCGTGTTTTGATAAGTGGAATTAATTTAAATCATTTATTCAAACATTTTCTTTTCTATGATGTC
261 TTCGTGTTTTGATAAGTAGAATCAATTCAAATCATTTAATCAAACATTTTCTCTTCTATGATGTC
496421 TAACAAAATATGTATACTTCTCTAGTTATTTTTCGTCAAAGTTTAAGTACTTTGGCCCCTAAAAN
326 TAACAAAATATGTATACTTCTCTAGTTATTTTTCGTC-AA---TAAGTACTTTGGCCCCTAAAA-
* * ** ** ** * * *** *
496486 TTAACAAAGAGTTTTGCTCTTTAACATACAGAACATTAAAAGATTTAAGATTTTAGTCCCCTAA-
386 AT-CCCTA-A-TTACG-T-AATAA-AT---GGAC-GTGGCA-A--T--GATTTT--T--TCTAAT
496550 A
432 A
* ** * ** * ** * **
496551 -ATCTCTAAATACG-TCATCAA-TAAGTTTGGA-AATG-AGTTTTTACAAACTGATATTGCTGCG
1 GATAT-T-GGTACGATCAACAACTTTGCTTCTATAATGCA----TTACAAA---ATCTTTAT-CG
**** * * * ** * ** ** **** * **** ***
496611 ATCAACAACTT-TATTCT-ATAGTGCATT-AC-AAAATCTTGATCATTTTTTACGTATGAG-TAA
56 -TTTTTAAGTTAT-TTGTAATAGAG--TTAACGAGTACCTTGGCCCCTAAAAAGGGGCCAGCCCC
** ** * * **** ** * *
496671 TAGAGTTT-AGGAGTTT-ATTGACCCCTAA--T-TTAAGGGGCCAGCCCCTTTTTCTTGATTTTA
117 T--TTTTTCTTGA-TTTCTTTGA----AAAGGTCTTAAGAATACA--AACATTTT-TTG-TTCT-
* * * * * * ** * * *
496731 TACGAAAGGTCTCATGTATACTAACATGTTTTGTTGTTACATCCATCTAAAATTGATGATCACTT
170 TAC---A---CCCATG-A-A--AA-A----TTGTTGAT-CAT--TTTTGAGATACA-AATGA-TG
**
496796 TTGAGATACAAATGATGGAATATTTTAGGGGCCAGCCCTCTAGATCCTTAATGGGGACAGAAATT
215 GA-----------------ATATTTTAGGGGCCAGCCCTCTAGATCCTTAATGGGGACAGAAATT
*
496861 CGTGTTTTGATAAGTAGAATCAATTCAAATCATTTAATCAAACATTTTCTCTTCTTTGATGTCTA
263 CGTGTTTTGATAAGTAGAATCAATTCAAATCATTTAATCAAACATTTTCTCTTCTATGATGTCTA
496926 ACAAAATATGTATACTTCTCTAGTTATTTTTCGTC-A-AAGTACTTTGGCCCCTAAAAATCCCTA
328 ACAAAATATGTATACTTCTCTAGTTATTTTTCGTCAATAAGTACTTTGGCCCCTAAAAATCCCTA
496989 ATTACGTAATAAATGGACGTGGCAATGATTTTTTCTAATA
393 ATTACGTAATAAATGGACGTGGCAATGATTTTTTCTAATA
497029 GATATTGGTACGATCAACAACTTTGCTTCTATAATGCATTACAAAATCTTTATCGTTTTTAAGTT
1 GATATTGGTACGATCAACAACTTTGCTTCTATAATGCATTACAAAATCTTTATCGTTTTTAAGTT
497094 ATTTGTAATAGAGTTAACGAGTACCTTGGCCCCTAAAAAGGGGCCAGCCCCTTTTTTCTTGATTT
66 ATTTGTAATAGAGTTAACGAGTACCTTGGCCCCTAAAAAGGGGCCAGCCCCTTTTTTCTTGATTT
497159 CTTTGAAAAGGTCTTAAGAATACAAACATTTTTTGTTCTTACACCCATGAAAAATTGTTGATCAT
131 CTTTGAAAAGGTCTTAAGAATACAAACATTTTTTGTTCTTACACCCATGAAAAATTGTTGATCAT
497224 TTTTGAGATACAAATGATGGAATATTTTAGGGGCCAGCCCTCTAGATCCTTAATGGGGACAGAAA
196 TTTTGAGATACAAATGATGGAATATTTTAGGGGCCAGCCCTCTAGATCCTTAATGGGGACAGAAA
* * * * *
497289 TTCGTGTTTTGATAAGTGGAATTAATTTAAATCATTTATTCAAACATTTTCTTTTCTATGATGTC
261 TTCGTGTTTTGATAAGTAGAATCAATTCAAATCATTTAATCAAACATTTTCTCTTCTATGATGTC
497354 TAACAAAATATGTATACTTCTCTAGTTATTTTTCGTCAAAGTTTAAGTACTTTGGCCCCT-AAAA
326 TAACAAAATATGTATACTTCTCTAGTTATTTTTCGTC-AA---TAAGTACTTTGGCCCCTAAAAA
*
497418 TCCCTAATTACGTAATAAATGGGCGTGGCAATGATTTTTTCTAATA
387 TCCCTAATTACGTAATAAATGGACGTGGCAATGATTTTTTCTAATA
*
497464 TATATTGGTACGATCAACAACTTTGCTTCTATAATGCATTACAAAATCTTTATCGTTTTTAAGTT
1 GATATTGGTACGATCAACAACTTTGCTTCTATAATGCATTACAAAATCTTTATCGTTTTTAAGTT
* * * * * *
497529 ATTCGTAATAGAGTTTACGAGTGCATTGGCCCCTAAATAAAGGGGTCAACCCC-TTTTTCTTGAT
66 ATTTGTAATAGAGTTAACGAGTACCTTGGCCCCT-AA-AAAGGGGCCAGCCCCTTTTTTCTTGAT
*
497593 TTCGTTGAA
129 TTCTTTGAA
497602 TAGAACTTTT
Statistics
Matches: 1175, Mismatches: 213, Indels: 230
0.73 0.13 0.14
Matches are distributed among these distances:
429 14 0.01
430 391 0.33
431 57 0.05
432 3 0.00
435 143 0.12
436 57 0.05
437 14 0.01
438 2 0.00
439 1 0.00
440 3 0.00
441 1 0.00
442 3 0.00
443 2 0.00
446 3 0.00
447 3 0.00
448 4 0.00
449 6 0.01
450 1 0.00
451 3 0.00
452 14 0.01
453 4 0.00
454 9 0.01
455 8 0.01
456 16 0.01
457 2 0.00
459 7 0.01
460 27 0.02
461 28 0.02
462 3 0.00
463 5 0.00
464 6 0.01
465 3 0.00
466 3 0.00
467 3 0.00
468 3 0.00
469 6 0.01
470 5 0.00
471 3 0.00
472 28 0.02
473 27 0.02
474 7 0.01
476 2 0.00
477 16 0.01
478 8 0.01
479 9 0.01
480 4 0.00
481 14 0.01
482 3 0.00
483 1 0.00
484 6 0.01
485 4 0.00
486 3 0.00
487 3 0.00
490 2 0.00
491 3 0.00
492 1 0.00
493 3 0.00
494 1 0.00
495 2 0.00
496 1 0.00
497 20 0.02
501 1 0.00
503 140 0.12
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (432 bp):
GATATTGGTACGATCAACAACTTTGCTTCTATAATGCATTACAAAATCTTTATCGTTTTTAAGTT
ATTTGTAATAGAGTTAACGAGTACCTTGGCCCCTAAAAAGGGGCCAGCCCCTTTTTTCTTGATTT
CTTTGAAAAGGTCTTAAGAATACAAACATTTTTTGTTCTTACACCCATGAAAAATTGTTGATCAT
TTTTGAGATACAAATGATGGAATATTTTAGGGGCCAGCCCTCTAGATCCTTAATGGGGACAGAAA
TTCGTGTTTTGATAAGTAGAATCAATTCAAATCATTTAATCAAACATTTTCTCTTCTATGATGTC
TAACAAAATATGTATACTTCTCTAGTTATTTTTCGTCAATAAGTACTTTGGCCCCTAAAAATCCC
TAATTACGTAATAAATGGACGTGGCAATGATTTTTTCTAATA
Found at i:500769 original size:5 final size:5
Alignment explanation
Indices: 500750--500818 Score: 79
Period size: 5 Copynumber: 14.0 Consensus size: 5
500740 GTAAAGTGTT
* * *
500750 AAACG AAATCG AAACG AAACG AAACC AATCG AAACG AAACG AAACC AAA--
1 AAACG AAA-CG AAACG AAACG AAACG AAACG AAACG AAACG AAACG AAACG
*
500799 AATCG AAACG AAACG AAACG
1 AAACG AAACG AAACG AAACG
500819 GAATCAAAAC
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
3 2 0.04
5 47 0.87
6 5 0.09
ACGTcount: A:0.58, C:0.22, G:0.16, T:0.04
Consensus pattern (5 bp):
AAACG
Found at i:501025 original size:1 final size:1
Alignment explanation
Indices: 500977--501012 Score: 63
Period size: 1 Copynumber: 36.0 Consensus size: 1
500967 CGGAATTTGT
*
500977 AAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
501013 CACAACAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:501102 original size:2 final size:2
Alignment explanation
Indices: 501095--501137 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
501085 CTCAAGTTTG
* *
501095 GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
501137 G
1 G
501138 GATGATTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:510930 original size:2 final size:2
Alignment explanation
Indices: 510923--510951 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
510913 TAATAGAATG
510923 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
510952 CTAAAATAAA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:512183 original size:2 final size:2
Alignment explanation
Indices: 512170--512205 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
512160 GACTTGATAG
* *
512170 AT AT AT AG AT AT AT AT AT NT 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
512206 TCTCTCTCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:515451 original size:17 final size:17
Alignment explanation
Indices: 515431--515463 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
515421 AACCCTCAGT
515431 TTAGCCGATAACTGGTC
1 TTAGCCGATAACTGGTC
515448 TTAGCCGATAACTGGT
1 TTAGCCGATAACTGGT
515464 ACAGTACCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (17 bp):
TTAGCCGATAACTGGTC
Found at i:523927 original size:12 final size:12
Alignment explanation
Indices: 523910--523934 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
523900 CAATGTCGTA
523910 CTGTTATATCAT
1 CTGTTATATCAT
523922 CTGTTATATCAT
1 CTGTTATATCAT
523934 C
1 C
523935 GCATATGCGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.20, G:0.08, T:0.48
Consensus pattern (12 bp):
CTGTTATATCAT
Found at i:532727 original size:18 final size:18
Alignment explanation
Indices: 532673--532728 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
532663 TTTAACGCGA
*
532673 TTTG-TTTG-TTTTATGT
1 TTTGTTTTGTTTTTGTGT
* *
532689 TTTGTTTTGTTTTTTTCT
1 TTTGTTTTGTTTTTGTGT
532707 TTTGTTTT-TTATTTGTGT
1 TTTGTTTTGTT-TTTGTGT
532725 TTTG
1 TTTG
532729 CTCTTCACCT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 4 0.12
17 6 0.18
18 23 0.70
ACGTcount: A:0.04, C:0.02, G:0.16, T:0.79
Consensus pattern (18 bp):
TTTGTTTTGTTTTTGTGT
Found at i:534833 original size:21 final size:21
Alignment explanation
Indices: 534803--534879 Score: 127
Period size: 21 Copynumber: 3.7 Consensus size: 21
534793 AAAATTAATC
* *
534803 TTATTCGTTCGGACGAATAAG
1 TTATTTGTTCGGACAAATAAG
*
534824 CTATTTGTTCGGACAAATAAG
1 TTATTTGTTCGGACAAATAAG
534845 TTATTTGTTCGGACAAATAAG
1 TTATTTGTTCGGACAAATAAG
534866 TTATTTGTTCGGAC
1 TTATTTGTTCGGAC
534880 GAACAAGGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.38
Consensus pattern (21 bp):
TTATTTGTTCGGACAAATAAG
Found at i:535469 original size:41 final size:41
Alignment explanation
Indices: 535398--536032 Score: 669
Period size: 41 Copynumber: 15.6 Consensus size: 41
535388 TTATTCGTTT
* *
535398 GGACGAATAAGCTATTTGTTCGGACGAATAAGTTATTTGTTC
1 GGACGAATTAGTTATTTGTTCGGACGAATAAG-TATTTGTTC
* *
535440 GGACGAATTAG-GATTTGTTCGGACAAATAAGTTATTTGTTC
1 GGACGAATTAGTTATTTGTTCGGACGAATAAG-TATTTGTTC
* * **
535481 GGACGAACTAG-GATTTGTTCGGAAAAATAAGTTATTTGTTC
1 GGACGAATTAGTTATTTGTTCGGACGAATAAG-TATTTGTTC
*
535522 GGACGAATTAG-GATTTGTTCGGACGAATAAGTTATTTGTTC
1 GGACGAATTAGTTATTTGTTCGGACGAATAAG-TATTTGTTC
* * *
535563 GGACGAATTAGCTATTTGTTCGGACGAATTAGGATTTGTTC
1 GGACGAATTAGTTATTTGTTCGGACGAATAAGTATTTGTTC
* * *
535604 GGACGAATTAG-GATTTGTTCGGACGAATTAGGATTTGTTC
1 GGACGAATTAGTTATTTGTTCGGACGAATAAGTATTTGTTC
* *
535644 GGAC------G--A-TTGTTCGGACGAAATAACG-AATTGGTC
1 GGACGAATTAGTTATTTGTTCGGACG-AATAA-GTATTTGTTC
* * *
535677 CGACAAAAATA-TTATTTGTTCGGACGAATAAGTTATTTGTTC
1 GGAC-GAATTAGTTATTTGTTCGGACGAATAAG-TATTTGTTC
* * *
535719 GGACGAATTAGCTATTTGTTCGGACGAATTAGGATTTGTTC
1 GGACGAATTAGTTATTTGTTCGGACGAATAAGTATTTGTTC
* *
535760 GGACAAATTAG-GATTTGTTCGGACGAA-ATAGCTATTTGTTC
1 GGACGAATTAGTTATTTGTTCGGACGAATA-AG-TATTTGTTC
* * * *
535801 GGACAAATAAGTTATTTGTTCGGACGAATTAGGATTTGTTC
1 GGACGAATTAGTTATTTGTTCGGACGAATAAGTATTTGTTC
*
535842 GGACGAATTAG-GATTTGTTCGGACGAA-ATAGCTATTTGTTC
1 GGACGAATTAGTTATTTGTTCGGACGAATA-AG-TATTTGTTC
* * * *
535883 GGACAAATAAGTTATTTGTTCGGACGAATTAGGATTTGTTC
1 GGACGAATTAGTTATTTGTTCGGACGAATAAGTATTTGTTC
*
535924 GGACGAATTAGTTATTTGTTCGGACAAATAAGTTATTTGTTC
1 GGACGAATTAGTTATTTGTTCGGACGAATAAG-TATTTGTTC
* * * *
535966 GGACAAATAAGTTATTTGTTCGGACGAATTAGGATTTGTTC
1 GGACGAATTAGTTATTTGTTCGGACGAATAAGTATTTGTTC
536007 GGACGAATTAGTTATTTGTTCGGACG
1 GGACGAATTAGTTATTTGTTCGGACG
536033 GATTGGCTTT
Statistics
Matches: 514, Mismatches: 54, Indels: 51
0.83 0.09 0.08
Matches are distributed among these distances:
32 11 0.02
33 14 0.03
34 2 0.00
40 67 0.13
41 283 0.55
42 137 0.27
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (41 bp):
GGACGAATTAGTTATTTGTTCGGACGAATAAGTATTTGTTC
Found at i:535526 original size:82 final size:82
Alignment explanation
Indices: 535388--536031 Score: 755
Period size: 82 Copynumber: 7.9 Consensus size: 82
535378 AAAAATTATC
* * * * *
535388 TTATTCGTTTGGACG-AATAAGCTATTTGTTCGGACGAATAAGTTATTTGTTCGGACGAATTAGG
1 TTATTTGTTCGGACGAAAT-AGTTATTTGTTCGGACGAATTAG-GATTTGTTCGGACGAATTAGG
535452 ATTTGTTCGGACAAATAAG
64 ATTTGTTCGGACAAATAAG
* * ** * *
535471 TTATTTGTTCGGACGAACTAG-GATTTGTTCGGAAAAATAAGTTATTTGTTCGGACGAATTAGGA
1 TTATTTGTTCGGACGAAATAGTTATTTGTTCGGACGAATTAG-GATTTGTTCGGACGAATTAGGA
*
535535 TTTGTTCGGACGAATAAG
65 TTTGTTCGGACAAATAAG
* *
535553 TTATTTGTTCGGACGAATTAGCTATTTGTTCGGACGAATTAGGATTTGTTCGGACGAATTAGGAT
1 TTATTTGTTCGGACGAAATAGTTATTTGTTCGGACGAATTAGGATTTGTTCGGACGAATTAGGAT
* *
535618 TTGTTCGGACGAATTAG
66 TTGTTCGGACAAATAAG
* * * * * * * * **
535635 -GATTTGTTCGGAC------G--A-TTGTTCGGACGAAATAACGAATTGGTCCGACAAAAATATT
1 TTATTTGTTCGGACGAAATAGTTATTTGTTCGGACG-AATTAGGATTTGTTCGGAC-GAATTAGG
*
535690 ATTTGTTCGGACGAATAAG
64 ATTTGTTCGGACAAATAAG
* * *
535709 TTATTTGTTCGGACGAATTAGCTATTTGTTCGGACGAATTAGGATTTGTTCGGACAAATTAGGAT
1 TTATTTGTTCGGACGAAATAGTTATTTGTTCGGACGAATTAGGATTTGTTCGGACGAATTAGGAT
535774 TTGTTCGGACGAAAT-AG
66 TTGTTCGGAC-AAATAAG
*
535791 CTATTTGTTCGGAC-AAATAAGTTATTTGTTCGGACGAATTAGGATTTGTTCGGACGAATTAGGA
1 TTATTTGTTCGGACGAAAT-AGTTATTTGTTCGGACGAATTAGGATTTGTTCGGACGAATTAGGA
535855 TTTGTTCGGACGAAAT-AG
65 TTTGTTCGGAC-AAATAAG
* *
535873 CTATTTGTTCGGAC-AAATAAGTTATTTGTTCGGACGAATTAGGATTTGTTCGGACGAATTAGTT
1 TTATTTGTTCGGACGAAAT-AGTTATTTGTTCGGACGAATTAGGATTTGTTCGGACGAATTAG-G
535937 ATTTGTTCGGACAAATAAG
64 ATTTGTTCGGACAAATAAG
*
535956 TTATTTGTTCGGAC-AAATAAGTTATTTGTTCGGACGAATTAGGATTTGTTCGGACGAATTAGTT
1 TTATTTGTTCGGACGAAAT-AGTTATTTGTTCGGACGAATTAGGATTTGTTCGGACGAATTAG-G
536020 ATTTGTTCGGAC
64 ATTTGTTCGGAC
536032 GGATTGGCTT
Statistics
Matches: 502, Mismatches: 41, Indels: 36
0.87 0.07 0.06
Matches are distributed among these distances:
72 11 0.02
73 15 0.03
74 22 0.04
75 13 0.03
81 16 0.03
82 274 0.55
83 138 0.27
84 13 0.03
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (82 bp):
TTATTTGTTCGGACGAAATAGTTATTTGTTCGGACGAATTAGGATTTGTTCGGACGAATTAGGAT
TTGTTCGGACAAATAAG
Found at i:535673 original size:21 final size:21
Alignment explanation
Indices: 535650--536032 Score: 314
Period size: 21 Copynumber: 18.5 Consensus size: 21
535640 GTTCGGACGA
* *
535650 TTGTTCGGACGAAATAACGAA
1 TTGTTCGGACGAAATAAGGAT
* * * **
535671 TTGGTCCGAC-AAAAATATTAT
1 TTGTTCGGACGAAATA-AGGAT
*
535692 TTGTTCGGACG-AATAAGTTAT
1 TTGTTCGGACGAAATAAG-GAT
* *
535713 TTGTTCGGACG-AATTAGCTAT
1 TTGTTCGGACGAAATAAG-GAT
*
535734 TTGTTCGGACG-AATTAGGAT
1 TTGTTCGGACGAAATAAGGAT
*
535754 TTGTTCGGAC-AAATTAGGAT
1 TTGTTCGGACGAAATAAGGAT
*
535774 TTGTTCGGACGAAAT-AGCTAT
1 TTGTTCGGACGAAATAAG-GAT
*
535795 TTGTTCGGAC-AAATAAGTTAT
1 TTGTTCGGACGAAATAAG-GAT
*
535816 TTGTTCGGACG-AATTAGGAT
1 TTGTTCGGACGAAATAAGGAT
*
535836 TTGTTCGGACG-AATTAGGAT
1 TTGTTCGGACGAAATAAGGAT
*
535856 TTGTTCGGACGAAAT-AGCTAT
1 TTGTTCGGACGAAATAAG-GAT
*
535877 TTGTTCGGAC-AAATAAGTTAT
1 TTGTTCGGACGAAATAAG-GAT
*
535898 TTGTTCGGACG-AATTAGGAT
1 TTGTTCGGACGAAATAAGGAT
* *
535918 TTGTTCGGACG-AATTAGTTAT
1 TTGTTCGGACGAAATAAG-GAT
*
535939 TTGTTCGGAC-AAATAAGTTAT
1 TTGTTCGGACGAAATAAG-GAT
*
535960 TTGTTCGGAC-AAATAAGTTAT
1 TTGTTCGGACGAAATAAG-GAT
*
535981 TTGTTCGGACG-AATTAGGAT
1 TTGTTCGGACGAAATAAGGAT
* *
536001 TTGTTCGGACG-AATTAGTTAT
1 TTGTTCGGACGAAATAAG-GAT
536022 TTGTTCGGACG
1 TTGTTCGGACG
536033 GATTGGCTTT
Statistics
Matches: 320, Mismatches: 26, Indels: 32
0.85 0.07 0.08
Matches are distributed among these distances:
20 119 0.37
21 201 0.63
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.36
Consensus pattern (21 bp):
TTGTTCGGACGAAATAAGGAT
Found at i:551717 original size:2 final size:2
Alignment explanation
Indices: 551710--551734 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
551700 TGAATGAATG
551710 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
551735 GTACTAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:554127 original size:22 final size:22
Alignment explanation
Indices: 554099--554386 Score: 576
Period size: 22 Copynumber: 13.1 Consensus size: 22
554089 CATTAGAGAC
554099 ATATGATAGGTTATACACCTCA
1 ATATGATAGGTTATACACCTCA
554121 ATATGATAGGTTATACACCTCA
1 ATATGATAGGTTATACACCTCA
554143 ATATGATAGGTTATACACCTCA
1 ATATGATAGGTTATACACCTCA
554165 ATATGATAGGTTATACACCTCA
1 ATATGATAGGTTATACACCTCA
554187 ATATGATAGGTTATACACCTCA
1 ATATGATAGGTTATACACCTCA
554209 ATATGATAGGTTATACACCTCA
1 ATATGATAGGTTATACACCTCA
554231 ATATGATAGGTTATACACCTCA
1 ATATGATAGGTTATACACCTCA
554253 ATATGATAGGTTATACACCTCA
1 ATATGATAGGTTATACACCTCA
554275 ATATGATAGGTTATACACCTCA
1 ATATGATAGGTTATACACCTCA
554297 ATATGATAGGTTATACACCTCA
1 ATATGATAGGTTATACACCTCA
554319 ATATGATAGGTTATACACCTCA
1 ATATGATAGGTTATACACCTCA
554341 ATATGATAGGTTATACACCTCA
1 ATATGATAGGTTATACACCTCA
554363 ATATGATAGGTTATACACCTCA
1 ATATGATAGGTTATACACCTCA
554385 AT
1 AT
554387 TTGCATTTCT
Statistics
Matches: 266, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 266 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (22 bp):
ATATGATAGGTTATACACCTCA
Found at i:555757 original size:50 final size:50
Alignment explanation
Indices: 555693--555789 Score: 158
Period size: 50 Copynumber: 1.9 Consensus size: 50
555683 TTCTATCAAT
*
555693 AGCCGCTAAATGTAGGGGAATAACAAAATGTGTACCCTATCTATATAACA
1 AGCCGCTAAATGTAGGGGAATAACAAAATGTATACCCTATCTATATAACA
** *
555743 AGCCGCTAAATGTAGGGGAATAAGGAGATGTATACCCTATCTATATA
1 AGCCGCTAAATGTAGGGGAATAACAAAATGTATACCCTATCTATATA
555790 TTATATTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (50 bp):
AGCCGCTAAATGTAGGGGAATAACAAAATGTATACCCTATCTATATAACA
Found at i:557744 original size:34 final size:34
Alignment explanation
Indices: 557706--557774 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
557696 CTGTGCATGC
*
557706 AATTAAAAATGTATGCTATAAAATTGGAAACCAA
1 AATTAAAAATGTATGCTATAAAATCGGAAACCAA
* *
557740 AATTAAATATTTATGCTATAAAATCGGAAACCAA
1 AATTAAAAATGTATGCTATAAAATCGGAAACCAA
557774 A
1 A
557775 TAAGTATGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (34 bp):
AATTAAAAATGTATGCTATAAAATCGGAAACCAA
Found at i:568029 original size:2 final size:2
Alignment explanation
Indices: 568022--568064 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
568012 ACATAGCATC
568022 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
568064 A
1 A
568065 TTCTTTATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:586819 original size:14 final size:14
Alignment explanation
Indices: 586800--586827 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
586790 CAAAATGTAA
586800 ACAAAAGCTTTGTT
1 ACAAAAGCTTTGTT
586814 ACAAAAGCTTTGTT
1 ACAAAAGCTTTGTT
586828 TACATAGCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
ACAAAAGCTTTGTT
Found at i:615027 original size:20 final size:21
Alignment explanation
Indices: 614993--615039 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
614983 TAATAAACTC
614993 TCCCAGCATTCTCAGCC-ACTA
1 TCCCAGCATTCTCAGCCGA-TA
615014 TCCCAGCA-TCTCAGCCGATA
1 TCCCAGCATTCTCAGCCGATA
615034 TCCCAG
1 TCCCAG
615040 AATTTTCCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.23, C:0.43, G:0.13, T:0.21
Consensus pattern (21 bp):
TCCCAGCATTCTCAGCCGATA
Found at i:619516 original size:2 final size:2
Alignment explanation
Indices: 619506--619536 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
619496 TGAGTTTTTT
*
619506 TG TG CG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
619537 TTTTTTTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.48, T:0.48
Consensus pattern (2 bp):
TG
Found at i:624441 original size:177 final size:176
Alignment explanation
Indices: 624070--624534 Score: 657
Period size: 177 Copynumber: 2.6 Consensus size: 176
624060 TGGTCCTTAA
* *
624070 TAACTTCACCAAACTTGCATAGATGATGCGTCTTATGATACTGATGCACCTGACAGGCTTGAATG
1 TAACTTCACCAAACTTGCATGGATGATGCATCTTATGATACTGATGCACCTGACAGGCTTGAATG
* * * * * ** *
624135 CTGAATCTGAGGCATAGGTTTTGTATGATGGCGGAGGTTAAGGTTTTTGAGTTGGTTAAAGTTTT
66 CTGAATCTGAGCCAAAGGTTTCGGATGCTGGATGAGGTTAAAGTTTTTGAGTTGGTTAAAGTTTT
* *
624200 TGGATCAGGTGCCCTCTGACGATTTTATCTTAGTTATAACTGGTCC
131 TGGAGCAGGTGCCCTCTGACGATTTTATCTTAGTTATAACTAGTCC
* * * * * *
624246 TAACTTCACCAAACTTGCATGGATGATGCTTCATATAATACTGATGCATCTGACAGGCATGATTG
1 TAACTTCACCAAACTTGCATGGATGATGCATCTTATGATACTGATGCACCTGACAGGCTTGAATG
624311 CTGAATCTGAGCCAAAGGTTTCGGATGCTGGATGAGGTTAAAGTTTTTAGAAG-TGGTTAAAGTT
66 CTGAATCTGAGCCAAAGGTTTCGGATGCTGGATGAGGTTAAAGTTTTT-G-AGTTGGTTAAAGTT
* * * *
624375 TTTGGAGCATGTGCCCTCTGATGGTTTTATCTTAGTTATTACTAGTCC
129 TTTGGAGCAGGTGCCCTCTGACGATTTTATCTTAGTTATAACTAGTCC
*
624423 TAACTTCACCAAACTTGCATGGATGATGCATCTTATGATACTGATGCACCCT-ACAGGCTTAAAT
1 TAACTTCACCAAACTTGCATGGATGATGCATCTTATGATACTGATGCA-CCTGACAGGCTTGAAT
* *
624487 GCTGAATCTGAGCCACAGGTTTCGGATGCTGGATGAGGTT-TAGTTTTT
65 GCTGAATCTGAGCCAAAGGTTTCGGATGCTGGATGAGGTTAAAGTTTTT
624535 TTGGAACAAG
Statistics
Matches: 256, Mismatches: 30, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
176 105 0.41
177 147 0.57
178 4 0.02
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (176 bp):
TAACTTCACCAAACTTGCATGGATGATGCATCTTATGATACTGATGCACCTGACAGGCTTGAATG
CTGAATCTGAGCCAAAGGTTTCGGATGCTGGATGAGGTTAAAGTTTTTGAGTTGGTTAAAGTTTT
TGGAGCAGGTGCCCTCTGACGATTTTATCTTAGTTATAACTAGTCC
Found at i:626619 original size:20 final size:20
Alignment explanation
Indices: 626566--626621 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
626556 AATGATGTAT
*
626566 TATGATATTGTATCATATAA
1 TATGATATTGTATTATATAA
*
626586 TACGATATTGTATTATAT-A
1 TATGATATTGTATTATATAA
626605 TAATGATATTGTATTAT
1 T-ATGATATTGTATTAT
626622 GTGATCAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.48
Consensus pattern (20 bp):
TATGATATTGTATTATATAA
Found at i:626924 original size:16 final size:16
Alignment explanation
Indices: 626894--626935 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
626884 ATATAATATG
626894 ATAAAGGTG--GTCTC
1 ATAAAGGTGATGTCTC
626908 ATAAAGGTGATGTCTC
1 ATAAAGGTGATGTCTC
*
626924 ATAAGGGTGATG
1 ATAAAGGTGATG
626936 CCTCGTCTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 9 0.36
16 16 0.64
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.29
Consensus pattern (16 bp):
ATAAAGGTGATGTCTC
Found at i:634159 original size:32 final size:31
Alignment explanation
Indices: 634114--634196 Score: 96
Period size: 35 Copynumber: 2.5 Consensus size: 31
634104 GTTTCCCCCC
*
634114 ATAGTAGCTTTTCCCCAC-GGAAAACCTACTAT
1 ATAGTAGC-TTTCCCC-CGGGAAAAACTACTAT
634146 ATAGTAGCATTTCCCCCTGGGGGAAAAACTACTAT
1 ATAGTAGC-TTTCCCCC---GGGAAAAACTACTAT
634181 ATAGTAGCTTTCCCCC
1 ATAGTAGCTTTCCCCC
634197 ATAGTAGGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
31 1 0.02
32 15 0.33
34 8 0.18
35 21 0.47
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28
Consensus pattern (31 bp):
ATAGTAGCTTTCCCCCGGGAAAAACTACTAT
Found at i:641941 original size:12 final size:12
Alignment explanation
Indices: 641924--641977 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 12
641914 TAAGATTTTT
641924 ATTTCAAAATAA
1 ATTTCAAAATAA
*
641936 ATTTCAAAATTA
1 ATTTCAAAATAA
641948 A-TT-AAAATAA
1 ATTTCAAAATAA
* *
641958 ATTTGAAAAAAA
1 ATTTCAAAATAA
*
641970 ACTTCAAA
1 ATTTCAAA
641978 CAGCACAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 7 0.20
11 4 0.11
12 24 0.69
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.31
Consensus pattern (12 bp):
ATTTCAAAATAA
Found at i:642844 original size:2 final size:2
Alignment explanation
Indices: 642839--642890 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
642829 CCCTCCCCCC
642839 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
642881 CT CT CT CT CT
1 CT CT CT CT CT
642891 ATTATATTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:648858 original size:18 final size:18
Alignment explanation
Indices: 648835--648870 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
648825 AAATGATGTA
*
648835 ATTTGAACAATAAACTCT
1 ATTTGAACAACAAACTCT
648853 ATTTGAACAACAAACTCT
1 ATTTGAACAACAAACTCT
648871 TTTACATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (18 bp):
ATTTGAACAACAAACTCT
Found at i:678333 original size:2 final size:2
Alignment explanation
Indices: 678326--678389 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
678316 CCCATACATA
678326 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
678368 TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC
678390 CGTGTGTGTA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:678814 original size:2 final size:2
Alignment explanation
Indices: 678807--678841 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
678797 GTAGTACTAG
*
678807 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
678842 CGTCAAATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:680136 original size:365 final size:366
Alignment explanation
Indices: 679441--680165 Score: 1040
Period size: 365 Copynumber: 2.0 Consensus size: 366
679431 TAATACTATA
* *
679441 TAAATGGTGCCTGTTTGGGAGGGTAACAGTTGAAATTGACACCCCGAGAAAACCATTGTCAACCG
1 TAAATGGTGCCTGTTTGGGAGGGTAACAGTTGAAATCGACACCCCAAGAAAACCATTGTCAACCG
*
679506 ACGCGAAGCGGAGGTTGACAATGGTTTTCGAGGGGTATCAATTTCAACTGTTATCCTCCCAACCA
66 ACGCGAAGCGGAGGTTGACAATGGTTTTCGAGGGGTATCAATTTCAACTGTTATCCTCCCAAACA
* * * *
679571 GGCTCTATTTATTTTGTTATACTGAATGTCTTAATTTTAAAGAAAACATCACTGCTTTTAGATAG
131 GGCACTATTTATTTTATTATACTGAATGTC-TAATTTTAAAGAAAACATAAATGCTTTTAGATAG
* * * *
679636 GAATAACCTGAATTCTAAGGCGAACCGTACGCGCATGATTTTCGCGCATGTAAGAATTCGTAATG
195 GAATAACCTGAATTCTAAGGCCAACCGTACGCGCATCATTTACGCGCATGTAACAATTCGTAATG
*
679701 TTACCCGTTGCTAAGTGCGTTGCTAACGCTGAGGGTAATAGAACAGATTATGAACTGCGTCTAAA
260 TTACCCGTTGCTAAGTGCGTTGCTAACGCTGAGGGTAATAGAACAGATTATCAACTGCGTCTAAA
679766 CCAATCAGA-TTTCAGTATTTAACATGAAAGTATAACAATATG
325 CCAATCAGAGTTT-AGTATTTAACATGAAAGTATAACAATATG
* * *
679808 TAAATGGTGCCTGTTTTGGAGGGTACCAGTTGAAATCGACACCCCAAGAAAACCATTGTCAACCT
1 TAAATGGTGCCTGTTTGGGAGGGTAACAGTTGAAATCGACACCCCAAGAAAACCATTGTCAACCG
* *** ** ** * **
679873 CCGCTTCGCGTCGGTTGACAATGGTTTTCTTGGGGTGTTGATTTCAACTGTTATCCTCCCAAACA
66 ACGCGAAGCGGAGGTTGACAATGGTTTTCGAGGGGTATCAATTTCAACTGTTATCCTCCCAAACA
* * **
679938 GGCACTGTTTATTTTATTATACTGAATGTC-AATTTTAAAGAAAACTTAAATGCTTTTCTATAGG
131 GGCACTATTTATTTTATTATACTGAATGTCTAATTTTAAAGAAAACATAAATGCTTTTAGATAGG
* * ** * * * *
680002 AATGACTTGAATTCTACTGCCAACCGTACGCGCATCATTTACGTGTATGTAACAATTCGTTATTT
196 AATAACCTGAATTCTAAGGCCAACCGTACGCGCATCATTTACGCGCATGTAACAATTCGTAATGT
* * *
680067 TACCCGTTGCTAAGTGTGTTGCTAATGCTGAGGGTAATAGAACGGATTATCAACTGCGTCTAAAC
261 TACCCGTTGCTAAGTGCGTTGCTAACGCTGAGGGTAATAGAACAGATTATCAACTGCGTCTAAAC
*
680132 CAATCAGAGTTTAGTTTTTAACATGAAAGTATAA
326 CAATCAGAGTTTAGTATTTAACATGAAAGTATAA
680166 TAATTTACAA
Statistics
Matches: 315, Mismatches: 42, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
365 172 0.55
366 3 0.01
367 140 0.44
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Consensus pattern (366 bp):
TAAATGGTGCCTGTTTGGGAGGGTAACAGTTGAAATCGACACCCCAAGAAAACCATTGTCAACCG
ACGCGAAGCGGAGGTTGACAATGGTTTTCGAGGGGTATCAATTTCAACTGTTATCCTCCCAAACA
GGCACTATTTATTTTATTATACTGAATGTCTAATTTTAAAGAAAACATAAATGCTTTTAGATAGG
AATAACCTGAATTCTAAGGCCAACCGTACGCGCATCATTTACGCGCATGTAACAATTCGTAATGT
TACCCGTTGCTAAGTGCGTTGCTAACGCTGAGGGTAATAGAACAGATTATCAACTGCGTCTAAAC
CAATCAGAGTTTAGTATTTAACATGAAAGTATAACAATATG
Found at i:681268 original size:2 final size:2
Alignment explanation
Indices: 681261--681317 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
681251 CCAACAATCA
681261 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
681303 CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT C
681318 ATTAGAAACG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:682008 original size:9 final size:9
Alignment explanation
Indices: 681996--682028 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
681986 TGAAAGCTGT
*
681996 AACAATAAC
1 AACAATGAC
682005 AACAATGAC
1 AACAATGAC
682014 AACAATGAC
1 AACAATGAC
682023 AACAAT
1 AACAAT
682029 CTTTATTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.61, C:0.21, G:0.06, T:0.12
Consensus pattern (9 bp):
AACAATGAC
Found at i:682970 original size:89 final size:89
Alignment explanation
Indices: 682819--682999 Score: 353
Period size: 89 Copynumber: 2.0 Consensus size: 89
682809 GAAGTTTCCT
682819 ACTGTGGATTTGACCATTTAAATCTGACTTGCTCCTTCAGGTATCAAATATATGTACAGATCAAC
1 ACTGTGGATTTGACCATTTAAATCTGACTTGCTCCTTCAGGTATCAAATATATGTACAGATCAAC
*
682884 ACAAATTTCACAAGGCAAAACTAC
66 ACAAATTTCACAAAGCAAAACTAC
682908 ACTGTGGATTTGACCATTTAAATCTGACTTGCTCCTTCAGGTATCAAATATATGTACAGATCAAC
1 ACTGTGGATTTGACCATTTAAATCTGACTTGCTCCTTCAGGTATCAAATATATGTACAGATCAAC
682973 ACAAATTTCACAAAGCAAAACTAC
66 ACAAATTTCACAAAGCAAAACTAC
682997 ACT
1 ACT
683000 CAACAGTCAG
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 91 1.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (89 bp):
ACTGTGGATTTGACCATTTAAATCTGACTTGCTCCTTCAGGTATCAAATATATGTACAGATCAAC
ACAAATTTCACAAAGCAAAACTAC
Found at i:685025 original size:21 final size:21
Alignment explanation
Indices: 685000--685052 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
684990 CAAATCCTTT
*
685000 ATGTTGAATATATTGTAATGT
1 ATGTTGAATATATTGTAATGA
* *
685021 GTGTTTAATATATTGTAATGA
1 ATGTTGAATATATTGTAATGA
685042 ATGTTGAATAT
1 ATGTTGAATAT
685053 CATGTTCAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (21 bp):
ATGTTGAATATATTGTAATGA
Found at i:689922 original size:43 final size:43
Alignment explanation
Indices: 689873--689971 Score: 162
Period size: 43 Copynumber: 2.3 Consensus size: 43
689863 AATCTCCAAA
*** *
689873 CATATAGCTACTAGATTGATATTCTTAATTACCAATCTGCTAT
1 CATATAGCTACTAGATTGATATTAAAAATTACCAATCTACTAT
689916 CATATAGCTACTAGATTGATATTAAAAATTACCAATCTACTAT
1 CATATAGCTACTAGATTGATATTAAAAATTACCAATCTACTAT
689959 CATATAGCTACTA
1 CATATAGCTACTA
689972 ATGTGGTTTC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.36
Consensus pattern (43 bp):
CATATAGCTACTAGATTGATATTAAAAATTACCAATCTACTAT
Found at i:690643 original size:22 final size:22
Alignment explanation
Indices: 690606--690652 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
690596 TCTAATCATT
690606 TTTTTAAAATAAAAAATCCGCGA
1 TTTTTAAAATAAAAAATCCGC-A
*
690629 TTTTTAAAAT-CAAAATCCGCA
1 TTTTTAAAATAAAAAATCCGCA
690650 TTT
1 TTT
690653 AATTTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.17
22 9 0.39
23 10 0.43
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.36
Consensus pattern (22 bp):
TTTTTAAAATAAAAAATCCGCA
Found at i:696595 original size:18 final size:19
Alignment explanation
Indices: 696558--696595 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
696548 TAATAAGTCT
696558 AAATCTACTAATAGATCTCG
1 AAATCTAC-AATAGATCTCG
*
696578 AAATCTAC-ATATATCTCG
1 AAATCTACAATAGATCTCG
696596 GTCTCTAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (19 bp):
AAATCTACAATAGATCTCG
Found at i:697191 original size:2 final size:2
Alignment explanation
Indices: 697184--697236 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
697174 TGAAAAGTCA
697184 CT CT CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
697225 CT CT CT CT CT CT
1 CT CT CT CT CT CT
697237 GTTCAAAACA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:707410 original size:33 final size:33
Alignment explanation
Indices: 707373--707445 Score: 139
Period size: 33 Copynumber: 2.2 Consensus size: 33
707363 TACTTATCAT
707373 ACTTAACATGAAATTTCATTTAAAAATTGTGAA
1 ACTTAACATGAAATTTCATTTAAAAATTGTGAA
707406 ACTTAACATGAAATTTCATTTAAAAATTGTGAA
1 ACTTAACATGAAATTTCATTTAAAAATTGTGAA
707439 AC-TAACA
1 ACTTAACA
707446 GAATATGAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 5 0.12
33 35 0.88
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (33 bp):
ACTTAACATGAAATTTCATTTAAAAATTGTGAA
Found at i:712891 original size:12 final size:11
Alignment explanation
Indices: 712847--712894 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
712837 GGAATTCTCG
712847 AGTAAACCCAA
1 AGTAAACCCAA
**
712858 AGTAAACTCCCG
1 AGTAAAC-CCAA
712870 AGTAAACCCAA
1 AGTAAACCCAA
*
712881 AGTAAACCCCA
1 AGTAAACCCAA
712892 AGT
1 AGT
712895 GGACCCATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
11 22 0.71
12 9 0.29
ACGTcount: A:0.46, C:0.29, G:0.12, T:0.12
Consensus pattern (11 bp):
AGTAAACCCAA
Found at i:723361 original size:21 final size:21
Alignment explanation
Indices: 723337--723654 Score: 297
Period size: 21 Copynumber: 15.3 Consensus size: 21
723327 TCTGATATAT
*
723337 ACTTAACTATACTGACATTCA
1 ACTTAACTATACTGACATACA
*
723358 ACTTAACTATACTGACATTCA
1 ACTTAACTATACTGACATACA
*
723379 ATTTAACTATACTGACATACA
1 ACTTAACTATACTGACATACA
*
723400 ACTATAACTATACTGACACACA
1 ACT-TAACTATACTGACATACA
* * *
723422 ACATAACTTTACTGGCATACA
1 ACTTAACTATACTGACATACA
*
723443 ACTTAACTTTACTGACATACA
1 ACTTAACTATACTGACATACA
* **
723464 ACTCAACTATGTTGACATACA
1 ACTTAACTATACTGACATACA
* * *
723485 ACTTAATTATACCGACATAAA
1 ACTTAACTATACTGACATACA
* * * *
723506 AATTAACTATGCTTATAATACA
1 ACTTAACTATACTGA-CATACA
** *
723528 TGTGT-ACTA-AC--A-A-AAA
1 ACT-TAACTATACTGACATACA
* *
723544 ACTTCATTATACTGACATACA
1 ACTTAACTATACTGACATACA
* *
723565 ACTCAACTATACTGGCATACA
1 ACTTAACTATACTGACATACA
*
723586 ACTTAACTATACTGGCATACA
1 ACTTAACTATACTGACATACA
* *
723607 AATTAACTATACTGGCATACA
1 ACTTAACTATACTGACATACA
* *
723628 ACTTAACTATACCGACATAAA
1 ACTTAACTATACTGACATACA
723649 ACTTAA
1 ACTTAA
723655 ATATGCTTAT
Statistics
Matches: 243, Mismatches: 45, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
15 1 0.00
16 6 0.02
17 3 0.01
19 2 0.01
20 1 0.00
21 201 0.83
22 28 0.12
23 1 0.00
ACGTcount: A:0.42, C:0.22, G:0.07, T:0.30
Consensus pattern (21 bp):
ACTTAACTATACTGACATACA
Found at i:723483 original size:85 final size:84
Alignment explanation
Indices: 723340--723654 Score: 250
Period size: 85 Copynumber: 3.8 Consensus size: 84
723330 GATATATACT
* * * *
723340 TAACTATACTGACATTCAACTTAACTATACTGACATTCAATTTAACTATACTGACATACAACTAT
1 TAACTATACTGACATACAACTTAACTATACTGACATACAACTCAACTATACTGACATACAACT-T
*
723405 AACTATACTGACACACAACA
65 AACTATACCGACACACAACA
* * * **
723425 TAACTTTACTGGCATACAACTTAACTTTACTGACATACAACTCAACTATGTTGACATACAACTTA
1 TAACTATACTGACATACAACTTAACTATACTGACATACAACTCAACTATACTGACATACAACTTA
* * *
723490 ATTATACCGACATA-AAAA
66 ACTATACCGACACACAACA
* * * ** * *
723508 TTAACTATGCTTATAATACATGTGT-ACTA-AC--A-A-AAAACTTC-ATTATACTGACATACAA
1 -TAACTATACTGA-CATACAACT-TAACTATACTGACATACAAC-TCAACTATACTGACATACAA
* * * * *
723566 CTCAACTATACTGGCATACAACT
62 CTTAACTATACCGACACACAACA
* * * * * *
723589 TAACTATACTGGCATACAAATTAACTATACTGGCATACAACTTAACTATACCGACATAAAACTTA
1 TAACTATACTGACATACAACTTAACTATACTGACATACAACTCAACTATACTGACATACAACTTA
723654 A
66 A
723655 ATATGCTTAT
Statistics
Matches: 174, Mismatches: 44, Indels: 25
0.72 0.18 0.10
Matches are distributed among these distances:
78 1 0.01
79 10 0.06
80 43 0.25
81 5 0.03
82 1 0.01
83 5 0.03
84 45 0.26
85 63 0.36
86 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.07, T:0.30
Consensus pattern (84 bp):
TAACTATACTGACATACAACTTAACTATACTGACATACAACTCAACTATACTGACATACAACTTA
ACTATACCGACACACAACA
Found at i:725942 original size:2 final size:2
Alignment explanation
Indices: 725935--725974 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
725925 TAATGACGGG
725935 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
725975 ATTAACAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:727051 original size:2 final size:2
Alignment explanation
Indices: 727044--727086 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
727034 TGAAAAGACA
727044 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
727086 T
1 T
727087 GTAGAGTGTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:740344 original size:31 final size:31
Alignment explanation
Indices: 740306--740394 Score: 169
Period size: 31 Copynumber: 2.9 Consensus size: 31
740296 GCACACTATG
740306 TATCAATTTTGTACTATACAGTCCAATTATA
1 TATCAATTTTGTACTATACAGTCCAATTATA
*
740337 TATCAATTTTGTACTATACAGTCCAATTATG
1 TATCAATTTTGTACTATACAGTCCAATTATA
740368 TATCAATTTTGTACTATACAGTCCAAT
1 TATCAATTTTGTACTATACAGTCCAAT
740395 AAATTCAAAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.42
Consensus pattern (31 bp):
TATCAATTTTGTACTATACAGTCCAATTATA
Found at i:746425 original size:52 final size:52
Alignment explanation
Indices: 746347--746450 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
746337 NNNNNNNNNN
746347 AATTTGAATGTTGAAATTGATCATTATGTCTTTAAAATAATATCAAGGGTTT
1 AATTTGAATGTTGAAATTGATCATTATGTCTTTAAAATAATATCAAGGGTTT
746399 AATTTGAATGTTGAAATTGATCATTATGTCTTTAAAATAATATCAAGGGTTT
1 AATTTGAATGTTGAAATTGATCATTATGTCTTTAAAATAATATCAAGGGTTT
746451 CTCTTTAACA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.42
Consensus pattern (52 bp):
AATTTGAATGTTGAAATTGATCATTATGTCTTTAAAATAATATCAAGGGTTT
Found at i:749360 original size:10 final size:10
Alignment explanation
Indices: 749345--749373 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
749335 GACGTCATAT
749345 TGACCTTGTA
1 TGACCTTGTA
749355 TGACCTTGTA
1 TGACCTTGTA
749365 TGACCTTGT
1 TGACCTTGT
749374 CTTTATGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41
Consensus pattern (10 bp):
TGACCTTGTA
Found at i:757346 original size:2 final size:2
Alignment explanation
Indices: 757339--757375 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
757329 ACAATGATCT
*
757339 GA GA GA GA GA GA GA AA GA GA GA GA G- GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
757376 CACACACACA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:766239 original size:23 final size:23
Alignment explanation
Indices: 766209--766273 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 23
766199 GAATAACACC
766209 GGAAACAGTTATATTGCCCTCCA
1 GGAAACAGTTATATTGCCCTCCA
766232 GGAAACAGTTATATT----TCACA
1 GGAAACAGTTATATTGCCCTC-CA
*
766252 GGAAATAGTTATATTGCCCTCC
1 GGAAACAGTTATATTGCCCTCC
766274 CGAAACTGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
19 2 0.06
20 16 0.44
23 16 0.44
24 2 0.06
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (23 bp):
GGAAACAGTTATATTGCCCTCCA
Found at i:768965 original size:20 final size:20
Alignment explanation
Indices: 768928--768965 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
768918 TGTGTAAAAC
*
768928 ATTTTTTTACAGAGATGTCA
1 ATTTTTTAACAGAGATGTCA
768948 ATTTTTTAATCAGA-ATGT
1 ATTTTTTAA-CAGAGATGT
768966 GAATCTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.47
Consensus pattern (20 bp):
ATTTTTTAACAGAGATGTCA
Found at i:778900 original size:17 final size:17
Alignment explanation
Indices: 778878--778913 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
778868 CGAAAGAACA
*
778878 CACCTTTGTTCTTAATT
1 CACCTTTGTTCTGAATT
778895 CACCTTTGTTCTGAATT
1 CACCTTTGTTCTGAATT
778912 CA
1 CA
778914 TTTTCCGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.25, G:0.08, T:0.47
Consensus pattern (17 bp):
CACCTTTGTTCTGAATT
Found at i:779336 original size:2 final size:2
Alignment explanation
Indices: 779329--779388 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
779319 ATAGTGTCTG
779329 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
779371 GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA
779389 TTTTAAAAAG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:796607 original size:2 final size:2
Alignment explanation
Indices: 796594--796669 Score: 111
Period size: 2 Copynumber: 39.0 Consensus size: 2
796584 ATTGAAAAAT
* * *
796594 AG AG AG AA AG AG AG GG AG -G A- AG AC AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
796634 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
796670 TGTTTTAGAA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
1 2 0.03
2 64 0.97
ACGTcount: A:0.50, C:0.01, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:805825 original size:2 final size:2
Alignment explanation
Indices: 805744--805808 Score: 96
Period size: 2 Copynumber: 33.0 Consensus size: 2
805734 CTCGTAACTT
* * *
805744 AG AG AG AG GG AG AG GG AG A- AA AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
805785 AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG
805809 GGGGGGGTGA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:812582 original size:1 final size:1
Alignment explanation
Indices: 812576--812600 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
812566 GGAACCCGAG
812576 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
812601 ACACACACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:827194 original size:2 final size:2
Alignment explanation
Indices: 827187--827247 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
827177 TAATCATATA
827187 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
827229 CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT C
827248 CTAAATTATA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:829407 original size:129 final size:129
Alignment explanation
Indices: 829172--829407 Score: 357
Period size: 129 Copynumber: 1.8 Consensus size: 129
829162 ACGACATCAG
** * * * *
829172 CGACATCGCAATGTGGATCGACATCGTGTAGACATTGTGTCTACATCGTACCTCTTATATCCTGT
1 CGACATCGCAATGTGGATAAACATCGAGTAGACATCGTGTCTACATCGTACCGCTTATATCATGT
*
829237 TTACATCGTCGACATTGTCGATATCGCAATGTTGACCAACATTGAGCCGACATGTTTACATCGT
66 TTACATCGTCGACATTGTCGATATCGCAATGTTGAACAACATTGAGCCGACATGTTTACATCGT
* *
829301 CGACATCGCAATGTTGATAAACATCGAGTCA-ACATCGTGTCTACATCGTATCGCTTATATCATG
1 CGACATCGCAATGTGGATAAACATCGAGT-AGACATCGTGTCTACATCGTACCGCTTATATCATG
* *
829365 TTTACATCGTCGACATTGTCGATATTGCAATGTTGAATAACAT
65 TTTACATCGTCGACATTGTCGATATCGCAATGTTGAACAACAT
829408 CGAGTCAATA
Statistics
Matches: 95, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
129 94 0.99
130 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Consensus pattern (129 bp):
CGACATCGCAATGTGGATAAACATCGAGTAGACATCGTGTCTACATCGTACCGCTTATATCATGT
TTACATCGTCGACATTGTCGATATCGCAATGTTGAACAACATTGAGCCGACATGTTTACATCGT
Found at i:829500 original size:101 final size:102
Alignment explanation
Indices: 829383--829584 Score: 316
Period size: 101 Copynumber: 2.0 Consensus size: 102
829373 GTCGACATTG
* * * *
829383 TCGATATTGCAATGTTGAATAACATCGAGTCAATATCGCAATGTTGATCGAC-TCGAGTTAACAT
1 TCGATATCGCAATGTTGAATAACATCGAGTCAACATCGCAATGTTGATCGACATCGAATCAACAT
*
829447 CGTGTCTACATCGTACCTCTTATATTCTGTTTACATA
66 CGTGTCTACATCGTACCTCTTATATCCTGTTTACATA
**
829484 TCGATATCGCAATGTTGAATAACATCGAGTTGACATCGCAATGTTGATCGACATCGAATCAACAT
1 TCGATATCGCAATGTTGAATAACATCGAGTCAACATCGCAATGTTGATCGACATCGAATCAACAT
* *
829549 CTTGTCTACATTGTACCTCTTATATCCTGTTTACAT
66 CGTGTCTACATCGTACCTCTTATATCCTGTTTACAT
829585 CGTCGACATC
Statistics
Matches: 91, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
101 48 0.53
102 43 0.47
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (102 bp):
TCGATATCGCAATGTTGAATAACATCGAGTCAACATCGCAATGTTGATCGACATCGAATCAACAT
CGTGTCTACATCGTACCTCTTATATCCTGTTTACATA
Found at i:829548 original size:29 final size:29
Alignment explanation
Indices: 829489--829549 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
829479 ACATATCGAT
* **
829489 ATCGCAATGTTGAATAACATCGAGTTGAC
1 ATCGCAATGTTGAATAACATCGAATCAAC
*
829518 ATCGCAATGTTG-ATCGACATCGAATCAAC
1 ATCGCAATGTTGAAT-AACATCGAATCAAC
829547 ATC
1 ATC
829550 TTGTCTACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 2 0.07
29 25 0.93
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.26
Consensus pattern (29 bp):
ATCGCAATGTTGAATAACATCGAATCAAC
Found at i:829702 original size:25 final size:24
Alignment explanation
Indices: 829674--829751 Score: 74
Period size: 25 Copynumber: 3.3 Consensus size: 24
829664 ACATCGTGTC
829674 TACATCGTACCTCATATATCCTGTT
1 TACATCGTACCTC-TATATCCTGTT
* * * *
829699 TACATCG----TCGACATCGTGTC
1 TACATCGTACCTCTATATCCTGTT
829719 TACATCGTACCTCTTATATCCTGTT
1 TACATCGTACCTC-TATATCCTGTT
829744 TACATCGT
1 TACATCGT
829752 CGACATCGTG
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
20 14 0.35
21 2 0.05
24 2 0.05
25 22 0.55
ACGTcount: A:0.22, C:0.28, G:0.12, T:0.38
Consensus pattern (24 bp):
TACATCGTACCTCTATATCCTGTT
Found at i:829716 original size:45 final size:44
Alignment explanation
Indices: 829664--829804 Score: 205
Period size: 45 Copynumber: 3.1 Consensus size: 44
829654 CAATGAGTCA
829664 ACATCGTGTCTACATCGTACCTCATATATCCTGTTTACATCGTCG
1 ACATCGTGTCTACATCGTACCTC-TATATCCTGTTTACATCGTCG
829709 ACATCGTGTCTACATCGTACCTCTTATATCCTGTTTACATCGTCG
1 ACATCGTGTCTACATCGTACCTC-TATATCCTGTTTACATCGTCG
* *
829754 ACATCGTGTCTACTTCGCGTGCCTTCT-T-TCCTGTTTACATCGTCG
1 ACATCGTGTCTACAT--CGTACC-TCTATATCCTGTTTACATCGTCG
829799 ACATCG
1 ACATCG
829805 CAATGTTAAT
Statistics
Matches: 90, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
45 81 0.90
46 1 0.01
47 6 0.07
48 2 0.02
ACGTcount: A:0.18, C:0.30, G:0.15, T:0.37
Consensus pattern (44 bp):
ACATCGTGTCTACATCGTACCTCTATATCCTGTTTACATCGTCG
Found at i:829731 original size:164 final size:164
Alignment explanation
Indices: 829545--829876 Score: 522
Period size: 164 Copynumber: 2.0 Consensus size: 164
829535 CATCGAATCA
* * * *
829545 ACATCTTGTCTACATTGTACCTCTTATATCCTGTTTACATCGTCGACATCTTGTCTACAACGTGT
1 ACATCGTGTCTACATCGTACCTCTTATATCCTGTTTACATCGTCGACATCGTGTCTACAACGCGT
* *
829610 GCCTTCTTTCCTGTTTACATCGTCGACATTGCAACGTTGATCGACAAT-GAGTCAACATCGTGTC
66 GCCTTCTTTCCTGTTTACATCGTCGACATCGCAACGTTAATCGAC-ATCGAGTCAACATCGTGTC
*
829674 TACATCGTACCTCATATATCCTGTTTACATCGTCG
130 TACATCGTACCTCATATATCCTGTTTACATCATCG
**
829709 ACATCGTGTCTACATCGTACCTCTTATATCCTGTTTACATCGTCGACATCGTGTCTACTTCGCGT
1 ACATCGTGTCTACATCGTACCTCTTATATCCTGTTTACATCGTCGACATCGTGTCTACAACGCGT
* * * *
829774 GCCTTCTTTCCTGTTTACATCGTCGACATCGCAATGTTAATCGGCATCGAGTTAAGATCGTGTCT
66 GCCTTCTTTCCTGTTTACATCGTCGACATCGCAACGTTAATCGACATCGAGTCAACATCGTGTCT
*
829839 ACATCGTACCTCTTATATCCTGTTTACATCATCG
131 ACATCGTACCTCATATATCCTGTTTACATCATCG
829873 ACAT
1 ACAT
829877 TGTCAATATC
Statistics
Matches: 153, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
163 2 0.01
164 151 0.99
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.36
Consensus pattern (164 bp):
ACATCGTGTCTACATCGTACCTCTTATATCCTGTTTACATCGTCGACATCGTGTCTACAACGCGT
GCCTTCTTTCCTGTTTACATCGTCGACATCGCAACGTTAATCGACATCGAGTCAACATCGTGTCT
ACATCGTACCTCATATATCCTGTTTACATCATCG
Found at i:829741 original size:119 final size:119
Alignment explanation
Indices: 829515--829759 Score: 350
Period size: 119 Copynumber: 2.1 Consensus size: 119
829505 ACATCGAGTT
* * * *
829515 GACATCGCAATGTTGATCGACATCGAATCAACATCTTGTCTACATTGTACCTCTTATATCCTGTT
1 GACATCGCAACGTTGATCGACATCGAATCAACATCGTGTCTACATCGTACCTCATATATCCTGTT
* ** * *
829580 TACATCGTCGACATCTTGTCTACAACGTGTGCCTTCTTTCCTGTTTACATCGTC
66 TACATCGTCGACATCGTGTCTACAACGTGACCCTTATATCCTGTTTACATCGTC
* *
829634 GACATTGCAACGTTGATCGACAAT-GAGTCAACATCGTGTCTACATCGTACCTCATATATCCTGT
1 GACATCGCAACGTTGATCGAC-ATCGAATCAACATCGTGTCTACATCGTACCTCATATATCCTGT
*
829698 TTACATCGTCGACATCGTGTCTACATCGT-ACCTCTTATATCCTGTTTACATCGTC
65 TTACATCGTCGACATCGTGTCTACAACGTGACC-CTTATATCCTGTTTACATCGTC
829753 GACATCG
1 GACATCG
829760 TGTCTACTTC
Statistics
Matches: 111, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
118 1 0.01
119 108 0.97
120 2 0.02
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (119 bp):
GACATCGCAACGTTGATCGACATCGAATCAACATCGTGTCTACATCGTACCTCATATATCCTGTT
TACATCGTCGACATCGTGTCTACAACGTGACCCTTATATCCTGTTTACATCGTC
Found at i:830017 original size:57 final size:57
Alignment explanation
Indices: 829955--830072 Score: 157
Period size: 57 Copynumber: 2.1 Consensus size: 57
829945 GATGTAGACA
* *
829955 ATGTAAATTCGATATTAG-TTCAACATCGTCGACATTGCGATGTCGACAATGTTAACG
1 ATGTAAATTCGATA-TAGATTCAACATCGTCGACATTGCGATGTCGAAAATGTCAACG
* * * * *
830012 ATGTAAATTCGATATCGATTCATCATTGTCGACGTTGCGATGTCGAAAATGTCGACG
1 ATGTAAATTCGATATAGATTCAACATCGTCGACATTGCGATGTCGAAAATGTCAACG
830069 ATGT
1 ATGT
830073 TAACTGCAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
56 2 0.04
57 51 0.96
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (57 bp):
ATGTAAATTCGATATAGATTCAACATCGTCGACATTGCGATGTCGAAAATGTCAACG
Found at i:846494 original size:16 final size:16
Alignment explanation
Indices: 846473--846507 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
846463 TTTCCTCTGC
846473 GTCCGTCAGTCCGTCT
1 GTCCGTCAGTCCGTCT
*
846489 GTCCGTCAGTCCTTCT
1 GTCCGTCAGTCCGTCT
846505 GTC
1 GTC
846508 TGTCCCACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.37, G:0.23, T:0.34
Consensus pattern (16 bp):
GTCCGTCAGTCCGTCT
Found at i:852489 original size:13 final size:13
Alignment explanation
Indices: 852471--852496 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
852461 TGTATGCATT
852471 CAAGAAAGAAATA
1 CAAGAAAGAAATA
852484 CAAGAAAGAAATA
1 CAAGAAAGAAATA
852497 TAGTTAGTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (13 bp):
CAAGAAAGAAATA
Found at i:854757 original size:25 final size:25
Alignment explanation
Indices: 854723--854772 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
854713 TCAGAACAAA
854723 ACAATGACATCATAATCAACGACTG
1 ACAATGACATCATAATCAACGACTG
* *
854748 ACAATGACATCATTATCAATGACTG
1 ACAATGACATCATAATCAACGACTG
854773 CAAATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.24
Consensus pattern (25 bp):
ACAATGACATCATAATCAACGACTG
Found at i:863689 original size:31 final size:31
Alignment explanation
Indices: 863646--863866 Score: 117
Period size: 31 Copynumber: 7.5 Consensus size: 31
863636 TTTTCATCGG
*
863646 CAATGTACTGTTGTCTGTCTAGTAACAGTGA
1 CAATGTACTGTTGTCTATCTAGTAACAGTGA
* * * * *
863677 CAATATACTGTTGTCTTTCTAG-AAGTAATGG
1 CAATGTACTGTTGTCTATCTAGTAA-CAGTGA
*
863708 CGATGTACTGTTGTCTATCTAGTAACAGTGA
1 CAATGTACTGTTGTCTATCTAGTAACAGTGA
* *
863739 CAA--T-C---TG----TCTAGTAACAGCGG
1 CAATGTACTGTTGTCTATCTAGTAACAGTGA
* *
863760 CAATGCACTGTT-TCTGTCTAGTAACAGT-A
1 CAATGTACTGTTGTCTATCTAGTAACAGTGA
* * * * *
863789 TCGATGTACCGCTGTCTGTCTAGTAACAATGA
1 -CAATGTACTGTTGTCTATCTAGTAACAGTGA
* * * * * * *
863821 CAAAGTCCTGCTGTCTGTTTAGTAACGGTGG
1 CAATGTACTGTTGTCTATCTAGTAACAGTGA
*
863852 CGATGTACTGTTGTC
1 CAATGTACTGTTGTC
863867 GGTATAATAA
Statistics
Matches: 141, Mismatches: 34, Indels: 30
0.69 0.17 0.15
Matches are distributed among these distances:
21 15 0.11
24 1 0.01
25 2 0.01
27 1 0.01
28 1 0.01
29 1 0.01
30 21 0.15
31 96 0.68
32 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (31 bp):
CAATGTACTGTTGTCTATCTAGTAACAGTGA
Found at i:864787 original size:31 final size:31
Alignment explanation
Indices: 864749--866377 Score: 1724
Period size: 31 Copynumber: 52.9 Consensus size: 31
864739 TTTATCACAA
864749 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
*
864780 TAGTAACAGTGACGATGTACTGTTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
*
864811 TAGTAACAGTGGCGATGTTCTGTTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
***
864842 TAGTAACAGTATTGATGTACTGTTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
*
864873 TAGTAACAGAGGCGATGTACTGTTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
*** *
864904 TAGTAACAGTATTGATGTACTGTTGTCTGTA
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* *** * *
864935 TAG--GCAGTATTGATGTACCGGTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
*
864964 TAGTAACAGTGGCGATGTACTTTTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* ***
864995 GAGTAACAGTATTGATGTACTGTTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* * * *
865026 GAGTAACAGTGGCAATGTCCTGCTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* *
865057 TTGTAACAGTGGCGATGTACTGCTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* *
865088 TAGTAACAGAGGTGATGTACTGTTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
** *
865119 TAGTAACAGTATCGATGTTCTGTTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
** *
865150 TAGTAACAGTATCGATGTACTGTTGACTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
**
865181 TAGTAACAGTATCGATGTACTGTTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* * *
865212 GAGTAACAGTGGCGATGTCCTGCTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* *
865243 TAGTAACAGTGGCGATGTACTGCTGTCTATC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
*
865274 TAGTAACAGTGGCGATGTTCTGTTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* *
865305 TAGTAACGGTGGCGATGTACTGTTGTCTGTT
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
** *
865336 TAGTAACAGTATCGATGTACTGTTATCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* ** *
865367 CAGTAACAGTATCGATTTACTGTTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* **
865398 GAGTAACAGTATCGATGTACTGTTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
*
865429 TAGTAACGGTGGCGATGTACTGTTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* * *
865460 TAGTAACAGTAGCGATGTTCTGTTGTGTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
*
865491 TAGTAACGGTGGCGATGTACTGTTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* ** *
865522 TTA-TACCAGTATCGATGTACTGTTGTCTGTG
1 -TAGTAACAGTGGCGATGTACTGTTGTCTGTC
** *
865553 TAGTAACAGTATCGATTTACTGTTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* * * *
865584 GAGTAACACTGGCGATGTCCTGCTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
*
865615 TAGTAACAGTGGCGATGTTCTGTTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
*
865646 TAGTAACGGTGGCGATGTACTGTTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* *
865677 TTGTAACAGTGGCGATGTACTGTTGTCTGCC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
*
865708 TTGTAACAGTGGCGATGTACTGTTGTCTGAT-
1 TAGTAACAGTGGCGATGTACTGTTGTCTG-TC
** * * *
865739 TAAAAAAAGTGACGATGTACTGTAGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* * * * *
865770 TAG-ATATAGCGTCGATGTAATGTTGTCTGCC
1 TAGTA-ACAGTGGCGATGTACTGTTGTCTGTC
* *
865801 TTGTAACAGTGGCGATGTACTGTTGTCGGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
** * * *
865832 TAGTAACAGTATCAATGTACTATTGTCTGCC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* *
865863 TTA-TAACAGTGGGGATGTACTGTTCTCTGTC
1 -TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* * * * *
865894 TAGAAAAAGTGACGATGTACTGTAGTGTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* * * * *
865925 TAGAAATAGCGTCGATGTACTGTTGTCTGCC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* *
865956 TTGTTACAGTGGCGATGTACTGTTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* * * *
865987 TAGAAAAAGTGACGATGTACTGTTGTCTGAC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
*
866018 TAGT-A-A----C-A-GTACTATTGTCTG-C
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* *
866040 CATGTAACAGTGGCGATGTACTGTTCTCTGTC
1 TA-GTAACAGTGGCGATGTACTGTTGTCTGTC
* * * * *
866072 TAGAAAAAGTGACGATGTACTGTAGTGTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* * * * *
866103 TAGAAATAGCGTCGATGTACTGTTGTCTGCC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* * *
866134 TTGTTACAGTGGCGATGTACTGTTGTCTGTA
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* * * * *
866165 TAGAAAAAGTGACGGTGTACTGTTGTATGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* * * * *
866196 TAGAAATAGCGTCGATGGACTGTTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* * * *
866227 TAGCAAAAGTTGCGATGTACTGTTGTCGGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
**
866258 TAGTAACAGTTTCGATGT-CTGTTGTCTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
** *
866288 TAGTAACAGTATCGATGTACTGTTGTCTTTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* * *
866319 TAGTAACAGTGGCAATGGACTGTTGTTTGTC
1 TAGTAACAGTGGCGATGTACTGTTGTCTGTC
* * * *
866350 TAGTAACAGAGGCGTTGAACTGCTGTCT
1 TAGTAACAGTGGCGATGTACTGTTGTCT
866378 TATGAATTTG
Statistics
Matches: 1337, Mismatches: 240, Indels: 42
0.83 0.15 0.03
Matches are distributed among these distances:
22 2 0.00
23 14 0.01
24 2 0.00
25 2 0.00
29 27 0.02
30 36 0.03
31 1247 0.93
32 7 0.01
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.36
Consensus pattern (31 bp):
TAGTAACAGTGGCGATGTACTGTTGTCTGTC
Found at i:866661 original size:33 final size:33
Alignment explanation
Indices: 866588--866775 Score: 129
Period size: 32 Copynumber: 5.8 Consensus size: 33
866578 AGATCAAATA
*
866588 GTCATTGTAGAATGTAAAGTGTGAGATT-AAGG
1 GTCATTGTAGAATGTAAAGGGTGAGATTAAAGG
* *
866620 GTCATTGTAGGATGTAAAGGGTAAGATTAAAGG
1 GTCATTGTAGAATGTAAAGGGTGAGATTAAAGG
* ** *
866653 GTCGTTGTAGTTTCTAAAGGGTGAGA-TAAAGG
1 GTCATTGTAGAATGTAAAGGGTGAGATTAAAGG
* * * *
866685 TTGC-TCG-AGGAA-GAAAAGGGTGAGA-TAAAAG
1 GT-CATTGTA-GAATGTAAAGGGTGAGATTAAAGG
* * * **
866716 GTTACTGTAGGATGTAAAGGGTGAGAGCAAAGG
1 GTCATTGTAGAATGTAAAGGGTGAGATTAAAGG
* * *
866749 ATCAATGTAG-TTGCTAAAGGGTGAGAT
1 GTCATTGTAGAATG-TAAAGGGTGAGAT
866776 CAAGGTTGTA
Statistics
Matches: 120, Mismatches: 28, Indels: 15
0.74 0.17 0.09
Matches are distributed among these distances:
31 21 0.17
32 50 0.42
33 49 0.41
ACGTcount: A:0.35, C:0.05, G:0.34, T:0.26
Consensus pattern (33 bp):
GTCATTGTAGAATGTAAAGGGTGAGATTAAAGG
Found at i:866748 original size:32 final size:32
Alignment explanation
Indices: 866593--867181 Score: 205
Period size: 33 Copynumber: 18.2 Consensus size: 32
866583 AAATAGTCAT
* * * * * *
866593 TGTAGAATGTAAAGTGTGAGATTAAGGGTCAT
1 TGTAGGATGTAAAGGGTGAGATCAAAGGTTAC
* * *
866625 TGTAGGATGTAAAGGGTAAGATTAAAGGGT-C
1 TGTAGGATGTAAAGGGTGAGATCAAAGGTTAC
** * *
866656 GTTGTAGTTTCTAAAGGGTGAGAT-AAAGGTTGC
1 --TGTAGGATGTAAAGGGTGAGATCAAAGGTTAC
* * *
866689 TCG-AGGAAGAAAAGGGTGAGATAAAAGGTTAC
1 T-GTAGGATGTAAAGGGTGAGATCAAAGGTTAC
* * *
866721 TGTAGGATGTAAAGGGTGAGAGCAAAGGATCAA
1 TGTAGGATGTAAAGGGTGAGATCAAAGG-TTAC
*
866754 TGTA-GTTGCTAAAGGGTGAGATC-AAGG-T--
1 TGTAGGATG-TAAAGGGTGAGATCAAAGGTTAC
* * *
866782 TGTAAAGAT-T----GG-GAG--CAAAACGTTAT
1 TGT-AGGATGTAAAGGGTGAGATC-AAAGGTTAC
* * * *
866808 TATAGGATGTATAA-GTTGAGATCAAAGGATCAA
1 TGTAGGATGTA-AAGGGTGAGATCAAAGG-TTAC
* * *
866841 TATAGGATGTAAAAGGTGAGATCAAAGGTTAT
1 TGTAGGATGTAAAGGGTGAGATCAAAGGTTAC
* * * *
866873 TGTAAG-TAGTAAAGGGTGCGATCAAAGGCTCAA
1 TGTAGGAT-GTAAAGGGTGAGATCAAAGG-TTAC
* ** * * * *
866906 TATAGTTTCTAAAGGATGACATC-AAGGTT-G
1 TGTAGGATGTAAAGGGTGAGATCAAAGGTTAC
** * * *
866936 TAAAGGTTGCTGGAGGATATGAGTGAGATCAAAAGGTTAT
1 TGTAGGATG-T--A--A-A-GGGTGAGATC-AAAGGTTAC
*
866976 TGTA-GATTTGTAAAGGGTGAGATCAAAAGGTTAT
1 TGTAGGA--TGTAAAGGGTGAGATC-AAAGGTTAC
* *
867010 TGTAGGATGTTAAGGGTGAGATCAAAAGGTTAT
1 TGTAGGATGTAAAGGGTGAGATC-AAAGGTTAC
* * *
867043 TGTAGGATGTAAAGGTTGAGATTAAAAAGGTTAT
1 TGTAGGATGTAAAGGGTGAGA-T-CAAAGGTTAC
* *
867077 TGTAGGATGTAAAGGGTGAGATTAAAAAGGTTAT
1 TGTAGGATGTAAAGGGTGAGA-T-CAAAGGTTAC
* * * * *
867111 TGAAGAATGTAAAAGGTGAAATCAAAGGGCTAC
1 TGTAGGATGTAAAGGGTGAGATCAAA-GGTTAC
* *
867144 TGTAGGATGTGAAA-GGTGGGATCAAAGGGTCAC
1 TGTAGGATGT-AAAGGGTGAGATCAAA-GGTTAC
867177 TGTAG
1 TGTAG
867182 TATAAAAAGT
Statistics
Matches: 430, Mismatches: 82, Indels: 89
0.72 0.14 0.15
Matches are distributed among these distances:
21 1 0.00
23 6 0.01
24 3 0.01
25 4 0.01
26 3 0.01
28 4 0.01
29 1 0.00
30 9 0.02
31 22 0.05
32 105 0.24
33 159 0.37
34 87 0.20
35 4 0.01
36 2 0.00
37 7 0.02
38 1 0.00
39 7 0.02
40 3 0.01
41 2 0.00
ACGTcount: A:0.36, C:0.05, G:0.31, T:0.27
Consensus pattern (32 bp):
TGTAGGATGTAAAGGGTGAGATCAAAGGTTAC
Found at i:867030 original size:33 final size:33
Alignment explanation
Indices: 866958--867169 Score: 257
Period size: 34 Copynumber: 6.3 Consensus size: 33
866948 GAGGATATGA
866958 GTGAGATCAAAAGGTTATTGTA-GATTTGTAAAGG
1 GTGAGATCAAAAGGTTATTGTAGGA--TGTAAAGG
*
866992 GTGAGATCAAAAGGTTATTGTAGGATGTTAAGG
1 GTGAGATCAAAAGGTTATTGTAGGATGTAAAGG
867025 GTGAGATCAAAAGGTTATTGTAGGATGTAAAGG
1 GTGAGATCAAAAGGTTATTGTAGGATGTAAAGG
* *
867058 TTGAGATTAAAAAGGTTATTGTAGGATGTAAAGG
1 GTGAGA-TCAAAAGGTTATTGTAGGATGTAAAGG
* * * *
867092 GTGAGATTAAAAAGGTTATTGAAGAATGTAAAAG
1 GTGAGA-TCAAAAGGTTATTGTAGGATGTAAAGG
* * * *
867126 GTGAAATCAAAGGGCTACTGTAGGATGTGAAA-G
1 GTGAGATCAAAAGGTTATTGTAGGATGT-AAAGG
*
867159 GTGGGATCAAA
1 GTGAGATCAAA
867170 GGGTCACTGT
Statistics
Matches: 158, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
33 70 0.44
34 86 0.54
35 2 0.01
ACGTcount: A:0.38, C:0.03, G:0.31, T:0.28
Consensus pattern (33 bp):
GTGAGATCAAAAGGTTATTGTAGGATGTAAAGG
Found at i:867040 original size:67 final size:65
Alignment explanation
Indices: 866958--867169 Score: 255
Period size: 67 Copynumber: 3.2 Consensus size: 65
866948 GAGGATATGA
*
866958 GTGAGATCAAAAGGTTATTGTAGATTTGTAAAGGGTGAGATCAAAAGGTTATTGTAGGATGTTAA
1 GTGAGATCAAAAGGTTATTGTAGA--TGTAAAGGGTGAGATCAAAAGGTTATTGTAGGATGTAAA
867023 GG
64 GG
* *
867025 GTGAGATCAAAAGGTTATTGTAGGATGTAAAGGTTGAGATTAAAAAGGTTATTGTAGGATGTAAA
1 GTGAGATCAAAAGGTTATTGTA-GATGTAAAGGGTGAGA-TCAAAAGGTTATTGTAGGATGTAAA
867090 GG
64 GG
* * * * * * *
867092 GTGAGATTAAAAAGGTTATTGAAGAATGTAAAAGGTGAAATCAAAGGGCTACTGTAGGATGTGAA
1 GTGAGA-TCAAAAGGTTATTGTAG-ATGTAAAGGGTGAGATCAAAAGGTTATTGTAGGATGT-AA
867157 A-G
63 AGG
*
867159 GTGGGATCAAA
1 GTGAGATCAAA
867170 GGGTCACTGT
Statistics
Matches: 126, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
66 17 0.13
67 78 0.62
68 31 0.25
ACGTcount: A:0.38, C:0.03, G:0.31, T:0.28
Consensus pattern (65 bp):
GTGAGATCAAAAGGTTATTGTAGATGTAAAGGGTGAGATCAAAAGGTTATTGTAGGATGTAAAGG
Found at i:867058 original size:19 final size:19
Alignment explanation
Indices: 867034--867091 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
867024 GGTGAGATCA
867034 AAAGGTTATTGTAGGATGT
1 AAAGGTTATTGTAGGATGT
867053 AAAGG---TTG-A-GAT-T
1 AAAGGTTATTGTAGGATGT
867066 AAAAAGGTTATTGTAGGATGT
1 --AAAGGTTATTGTAGGATGT
867087 AAAGG
1 AAAGG
867092 GTGAGATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 16
0.66 0.00 0.34
Matches are distributed among these distances:
13 1 0.03
14 3 0.10
15 6 0.19
16 3 0.10
18 3 0.10
19 11 0.35
20 3 0.10
21 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (19 bp):
AAAGGTTATTGTAGGATGT
Found at i:867626 original size:21 final size:21
Alignment explanation
Indices: 867600--867712 Score: 154
Period size: 21 Copynumber: 5.4 Consensus size: 21
867590 CCCATCTAAA
* * *
867600 CTACACGCGATCAATCTAATG
1 CTACACGTGATCCATCTACTG
867621 CTACACGTGATCCATCTACTG
1 CTACACGTGATCCATCTACTG
* * *
867642 CTACACATGATCAATCTAATG
1 CTACACGTGATCCATCTACTG
867663 CTACACGTGATCCATCTACTG
1 CTACACGTGATCCATCTACTG
**
867684 CTACACAAGATCCATCTACTG
1 CTACACGTGATCCATCTACTG
867705 CTACACGT
1 CTACACGT
867713 AAAAAATCAT
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 79 1.00
ACGTcount: A:0.30, C:0.31, G:0.12, T:0.27
Consensus pattern (21 bp):
CTACACGTGATCCATCTACTG
Found at i:867659 original size:42 final size:42
Alignment explanation
Indices: 867608--867712 Score: 183
Period size: 42 Copynumber: 2.5 Consensus size: 42
867598 AACTACACGC
*
867608 GATCAATCTAATGCTACACGTGATCCATCTACTGCTACACAT
1 GATCAATCTAATGCTACACGTGATCCATCTACTGCTACACAA
867650 GATCAATCTAATGCTACACGTGATCCATCTACTGCTACACAA
1 GATCAATCTAATGCTACACGTGATCCATCTACTGCTACACAA
* *
867692 GATCCATCTACTGCTACACGT
1 GATCAATCTAATGCTACACGT
867713 AAAAAATCAT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.28
Consensus pattern (42 bp):
GATCAATCTAATGCTACACGTGATCCATCTACTGCTACACAA
Found at i:867686 original size:63 final size:62
Alignment explanation
Indices: 867578--867710 Score: 178
Period size: 63 Copynumber: 2.1 Consensus size: 62
867568 ATGCTTCTTA
* **
867578 TGCTACACATGTCCCATCTAAACTACACGCGATCAATCTAATGCTACACGTGATCCATCTAC
1 TGCTACACATGTCCAATCTAAACTACACGCGATCAATCTAATGCTACACAAGATCCATCTAC
* * * *
867640 TGCTACACATGAT-CAATCTAATGCTACACGTGATCCATCTACTGCTACACAAGATCCATCTAC
1 TGCTACACATG-TCCAATCTAA-ACTACACGCGATCAATCTAATGCTACACAAGATCCATCTAC
867703 TGCTACAC
1 TGCTACAC
867711 GTAAAAAATC
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
62 18 0.29
63 44 0.71
ACGTcount: A:0.31, C:0.32, G:0.11, T:0.26
Consensus pattern (62 bp):
TGCTACACATGTCCAATCTAAACTACACGCGATCAATCTAATGCTACACAAGATCCATCTAC
Found at i:867803 original size:19 final size:20
Alignment explanation
Indices: 867754--867803 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
867744 ATTTTCCATC
*
867754 TAACTTATATAATGCTACAT
1 TAACTTATCTAATGCTACAT
* *
867774 TAAC-AAACTAATGCTACAT
1 TAACTTATCTAATGCTACAT
867793 T-ACTTATCTAA
1 TAACTTATCTAA
867804 AGCTTTACAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
18 2 0.08
19 18 0.75
20 4 0.17
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.36
Consensus pattern (20 bp):
TAACTTATCTAATGCTACAT
Found at i:871365 original size:2 final size:2
Alignment explanation
Indices: 871358--871394 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
871348 CGGCGGTCAA
871358 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
871395 ACACACACAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:871399 original size:2 final size:2
Alignment explanation
Indices: 871394--871421 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
871384 CTCTCTCTCT
871394 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
871422 TTAACTTGAT
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:875645 original size:2 final size:2
Alignment explanation
Indices: 875638--875706 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
875628 ATGTACTCAC
875638 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
875680 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
875707 ATTTTTAAAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:877661 original size:30 final size:30
Alignment explanation
Indices: 877620--877676 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
877610 CGCCCATAAT
*
877620 GTTCATGGTGCGCACACTCATGAACAGTTA
1 GTTCATAGTGCGCACACTCATGAACAGTTA
877650 GTTCATAGTGCGCACACTCATGAACAG
1 GTTCATAGTGCGCACACTCATGAACAG
877677 ACACAAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (30 bp):
GTTCATAGTGCGCACACTCATGAACAGTTA
Found at i:885971 original size:156 final size:157
Alignment explanation
Indices: 885771--886053 Score: 410
Period size: 156 Copynumber: 1.8 Consensus size: 157
885761 AATATTTTGG
* *
885771 TATATCTTATCAATAACACACACTAAGAAAACTAACTCTTTCTTTAGTTTATTTTAG-CTGTCCT
1 TATATCTTATCAATAACACACACTAAGAAAACTAACTCTTTCTTTAGTATATTCTAGTCT-TCCT
* ** * * *
885835 CCATATGTTGTCTAATTTTTTTAAGTGCCATTTTAAGGCAATTTGTAATTCAAGAGGAAAATTTA
65 CCATATGTTGTCAAATCCTTTAAAGTGCCATTTTAACGCAATTCGTAATTCAAGAGGAAAATTTA
885900 CATTTGTGTCAATAATTTATTATATTAA
130 CATTTGTGTCAATAATTTATTATATTAA
* *
885928 TATATCTTATCAATGAACA-A-ACTAAGAAAACTAACTCTTTCTTTCGTATGTTCTAGTCTTCCT
1 TATATCTTATCAAT-AACACACACTAAGAAAACTAACTCTTTCTTTAGTATATTCTAGTCTTCCT
* * *
885991 CCATATGTTGTCAAATCCTTTAAAGTGCCATTTTATCGCAATTCGTATTTCACGAGGAAAATT
65 CCATATGTTGTCAAATCCTTTAAAGTGCCATTTTAACGCAATTCGTAATTCAAGAGGAAAATT
886054 ATACCTTTTT
Statistics
Matches: 111, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
156 90 0.81
157 17 0.15
158 4 0.04
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.41
Consensus pattern (157 bp):
TATATCTTATCAATAACACACACTAAGAAAACTAACTCTTTCTTTAGTATATTCTAGTCTTCCTC
CATATGTTGTCAAATCCTTTAAAGTGCCATTTTAACGCAATTCGTAATTCAAGAGGAAAATTTAC
ATTTGTGTCAATAATTTATTATATTAA
Found at i:889297 original size:172 final size:172
Alignment explanation
Indices: 888904--889701 Score: 1317
Period size: 172 Copynumber: 4.6 Consensus size: 172
888894 GTATCGAGTC
* ** * * *
888904 TATCGACCAAGGCTGATTTAGGAACTTGACTAAGGTATTAGTGGTAAAAACATTTGGTATAAATT
1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTAATAGTGGTATAAACATTTGGTATAAATT
* * *
888969 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGCGCGCTTACAAGGTCAATTTTTGGAAAAAAAT
66 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGG-ATAAAAC
* *
889034 GGAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG
130 GGAGTCATGATTGTGGTCAAAGTCCCATAACGCCAACAAAAAG
* *
889077 TATCGACCAATGCTGATTTTCGAACTTGACCAAAGTATTAGTGGTATAAACATTTGGTATAAATT
1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTAATAGTGGTATAAACATTTGGTATAAATT
* * * *
889142 TAATAAAAATCTGTCAAAATGTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACT
66 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
* *
889207 GAGTCATTATTGTGGTCAAAGTCCCATAAAGCCAACAAAAAG
131 GAGTCATGATTGTGGTCAAAGTCCCATAACGCCAACAAAAAG
* * *
889249 TATCGACTAACGCTGATTTTCGAACTTGACCAAGGTAATAGCGGTATAAACATTTGGTATAAATT
1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTAATAGTGGTATAAACATTTGGTATAAATT
*
889314 TAATGAAAATCCGTCAAAAATTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
66 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
*
889379 GAGTCATGATTGTGGTCAAAGTCCCATAACGCCATCAAAAAG
131 GAGTCATGATTGTGGTCAAAGTCCCATAACGCCAACAAAAAG
* *
889421 TATCGACTAATGCTGATTTTCAAACTTGACCAAGGTAATAGTGGTATAAACATTTGGTATAAATT
1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTAATAGTGGTATAAACATTTGGTATAAATT
*
889486 TAATGAAAATCTGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
66 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
* *
889551 GAGTCATGATTGTAGTCAAAGTCCCATAACTCCAACAAAAAG
131 GAGTCATGATTGTGGTCAAAGTCCCATAACGCCAACAAAAAG
*
889593 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTAATAGTGCTATAAACATTTGGTATAAATT
1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTAATAGTGGTATAAACATTTGGTATAAATT
889658 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAA
66 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAA
889702 AAAAGTGTGA
Statistics
Matches: 585, Mismatches: 40, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
172 473 0.81
173 112 0.19
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (172 bp):
TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTAATAGTGGTATAAACATTTGGTATAAATT
TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
GAGTCATGATTGTGGTCAAAGTCCCATAACGCCAACAAAAAG
Found at i:889726 original size:8 final size:8
Alignment explanation
Indices: 889710--889778 Score: 84
Period size: 8 Copynumber: 8.6 Consensus size: 8
889700 AAAAAAGTGT
*
889710 GACGGACG
1 GACGCACG
889718 GACGCACG
1 GACGCACG
*
889726 GACACACG
1 GACGCACG
889734 GACGCACG
1 GACGCACG
*
889742 GACCCACG
1 GACGCACG
*
889750 GACACACG
1 GACGCACG
*
889758 GACCCACG
1 GACGCACG
*
889766 GACCCACG
1 GACGCACG
889774 GACGC
1 GACGC
889779 CCGGCATTTC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 54 1.00
ACGTcount: A:0.28, C:0.41, G:0.32, T:0.00
Consensus pattern (8 bp):
GACGCACG
Found at i:889736 original size:16 final size:16
Alignment explanation
Indices: 889715--889776 Score: 97
Period size: 16 Copynumber: 3.9 Consensus size: 16
889705 AGTGTGACGG
*
889715 ACGGACGCACGGACAC
1 ACGGACGCACGGACCC
889731 ACGGACGCACGGACCC
1 ACGGACGCACGGACCC
*
889747 ACGGACACACGGACCC
1 ACGGACGCACGGACCC
*
889763 ACGGACCCACGGAC
1 ACGGACGCACGGAC
889777 GCCCGGCATT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.29, C:0.42, G:0.29, T:0.00
Consensus pattern (16 bp):
ACGGACGCACGGACCC
Found at i:889742 original size:24 final size:24
Alignment explanation
Indices: 889710--889776 Score: 107
Period size: 24 Copynumber: 2.8 Consensus size: 24
889700 AAAAAAGTGT
* *
889710 GACGGACGGACGCACGGACACACG
1 GACGCACGGACCCACGGACACACG
889734 GACGCACGGACCCACGGACACACG
1 GACGCACGGACCCACGGACACACG
*
889758 GACCCACGGACCCACGGAC
1 GACGCACGGACCCACGGAC
889777 GCCCGGCATT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.28, C:0.40, G:0.31, T:0.00
Consensus pattern (24 bp):
GACGCACGGACCCACGGACACACG
Found at i:896713 original size:7 final size:7
Alignment explanation
Indices: 896701--896725 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
896691 GTTTTTAGAA
896701 CGCAGTT
1 CGCAGTT
896708 CGCAGTT
1 CGCAGTT
896715 CGCAGTT
1 CGCAGTT
896722 CGCA
1 CGCA
896726 ATTGAATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.32, G:0.28, T:0.24
Consensus pattern (7 bp):
CGCAGTT
Done.