Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007992.1 Hibiscus syriacus cultivar Beakdansim tig00110442_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1314873
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:268209 original size:361 final size:359
Alignment explanation
Indices: 267582--268668 Score: 1529
Period size: 361 Copynumber: 3.0 Consensus size: 359
267572 AATGCACTAT
* * * * * * *
267582 TTTTCATCCAACTTGCATTAATGGCACCTTTCGGCCAAAATGCACCGTTAGACATTTAAATTTTC
1 TTTTCATCTAACTTGCAATAGTGGCACCTTTCTGCCAAAATGCATCGTTAGGCATTTAACTTTTC
* * * * * * *
267647 ATCTAACTTGCATTATTGGA-ACATTTCTACCAAAATGCATCATTAGGCATTTAGCTTATCATCT
66 ATCTAACTTGCAATAGT-GACACCTTTTTACAAAAATGCATCATTAGGCATTTAACTTTTCATCT
* *** *
267711 AACTTGCAATAGTGGCACCTTTAAACCAAAATGTATCGTTAGGCATTTAAC-TTTCATCTAACTT
130 AACTTGCAATAGTGGCAACTTTCTGCCAAAATGCATCGTTAGGCATTTAACTTTTCATCTAACTT
* * * *
267775 GCAATAGTGGCACCTTTCTTCCAAAATACATTGTTACGCAATAAATTTTTCATCTAACTTGCAAT
195 GCAATAGTGGCACCTTTCTTCCAAAATGCATTGTTACGCATTAAACTTTTCATTTAACTTGCAAT
267840 AGTGTCATCTTTCTACCAAAATGCATCATTAGGCATTTAATTTTTCATCTGACTTGCAATAGTGC
260 AGTGTCATCTTTCTACCAAAATGCATCATTAGGCATTTAATTTTTCATCTGACTTGCAATAGTGC
*
267905 CACCTTTCTACCGAAATGCATCATTAGGCATTTAAC
325 CACCTTTCTACC-AAATGCATCGTTAGGCATTTAAC
267941 TTTTCATCTAACTTGCAATAGTGGCACCTTTCTGCCAAAATGCATCGTTAGGCATTTAACTTTTC
1 TTTTCATCTAACTTGCAATAGTGGCACCTTTCTGCCAAAATGCATCGTTAGGCATTTAACTTTTC
* *
268006 ATCTAACATGCAATAGTGACACCTTTTTACAAAAAATGCATCTTTAGGCATTTAACTTTTCATCT
66 ATCTAACTTGCAATAGTGACACCTTTTTAC-AAAAATGCATCATTAGGCATTTAACTTTTCATCT
*
268071 AACTTGCAATAGTGGCAACTTTCTGCCAAAATGCATCGTTACGCATTTAACTTTTCATCTAACTT
130 AACTTGCAATAGTGGCAACTTTCTGCCAAAATGCATCGTTAGGCATTTAACTTTTCATCTAACTT
*
268136 GCAATAGTGGCACATTTCTTCCAAAATGCATTGTTACGCATTAAACTTTTCATTTAACTTGCAAT
195 GCAATAGTGGCACCTTTCTTCCAAAATGCATTGTTACGCATTAAACTTTTCATTTAACTTGCAAT
*
268201 AGTGTCATCTTTCTACCAAAATGCATCATTAGGCATTTAATTTTTCATCTGACTAGCAATAGTGC
260 AGTGTCATCTTTCTACCAAAATGCATCATTAGGCATTTAATTTTTCATCTGACTTGCAATAGTGC
* *
268266 CACCTTTCTACCAAATTACATCGTTAGACATTTAAC
325 CACCTTTCTACCAAA-TGCATCGTTAGGCATTTAAC
*
268302 TTTTCATCTAACTTGCAATAGTAGCACCTTTCTGCCAAAATGCATCGTTAGGCATTTAACTTTTC
1 TTTTCATCTAACTTGCAATAGTGGCACCTTTCTGCCAAAATGCATCGTTAGGCATTTAACTTTTC
* *
268367 ATCTAACTTGCAATAGTGACACCTTTTTACCGAAAATGCATCGTTAGGCATTTAACTTTTCATCT
66 ATCTAACTTGCAATAGTGACACCTTTTTA-CAAAAATGCATCATTAGGCATTTAACTTTTCATCT
* * *
268432 AACTTGCAATAGTGGCAACTTTCTGCCAAAATGCATCATT-GGGATTTTAACTTTTCATCTATCT
130 AACTTGCAATAGTGGCAACTTTCTGCCAAAATGCATCGTTAGGCA-TTTAACTTTTCATCTAACT
* * * * * * * * *
268496 TGTAATATTTGCACCTTTATGCCAAAATGCATCGTTA-GACATTTAACTTTTCATCTAAAC-TAC
194 TGCAATAGTGGCACCTTTCTTCCAAAATGCATTGTTACG-CATTAAACTTTTCAT-TTAACTTGC
* * * * * * * * *
268559 AATAGTGACACCTTTATGCCAAAATGTATCGTTAGGCATTTAACTTTACATCTAACTTGCAATAG
257 AATAGTGTCATCTTTCTACCAAAATGCATCATTAGGCATTTAATTTTTCATCTGACTTGCAATAG
* * *
268624 TGTCA-CTTTCTACTAAAATGCATCGTTAGGCATTTACC
322 TGCCACCTTTCTAC-CAAATGCATCGTTAGGCATTTAAC
268662 TTTTCAT
1 TTTTCAT
268669 TTTAGAGCAG
Statistics
Matches: 655, Mismatches: 64, Indels: 17
0.89 0.09 0.02
Matches are distributed among these distances:
358 2 0.00
359 80 0.12
360 113 0.17
361 455 0.69
362 5 0.01
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.37
Consensus pattern (359 bp):
TTTTCATCTAACTTGCAATAGTGGCACCTTTCTGCCAAAATGCATCGTTAGGCATTTAACTTTTC
ATCTAACTTGCAATAGTGACACCTTTTTACAAAAATGCATCATTAGGCATTTAACTTTTCATCTA
ACTTGCAATAGTGGCAACTTTCTGCCAAAATGCATCGTTAGGCATTTAACTTTTCATCTAACTTG
CAATAGTGGCACCTTTCTTCCAAAATGCATTGTTACGCATTAAACTTTTCATTTAACTTGCAATA
GTGTCATCTTTCTACCAAAATGCATCATTAGGCATTTAATTTTTCATCTGACTTGCAATAGTGCC
ACCTTTCTACCAAATGCATCGTTAGGCATTTAAC
Found at i:280716 original size:13 final size:13
Alignment explanation
Indices: 280698--280758 Score: 104
Period size: 13 Copynumber: 4.7 Consensus size: 13
280688 TGCGTCATAA
280698 ATTTATGACGCGC
1 ATTTATGACGCGC
*
280711 ATTTATGACACGC
1 ATTTATGACGCGC
280724 ATTTATGACGCGC
1 ATTTATGACGCGC
*
280737 ATTTATGACGCAC
1 ATTTATGACGCGC
280750 ATTTATGAC
1 ATTTATGAC
280759 TTACATTGCT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 45 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:286792 original size:138 final size:138
Alignment explanation
Indices: 286544--286800 Score: 376
Period size: 138 Copynumber: 1.9 Consensus size: 138
286534 GAGTATGATG
* * *
286544 GTTATCGATCGATTTTGTTTAATGCATAACTGTGCATTTTCGTAATAGTATTATGTGTACTATTG
1 GTTATCGATCGATTTTGTTTAATGCATAACGGTGCATATTCGTAATAGTACTATGTGTACTATTG
*
286609 GAACTAGATATGCAATCATGGTATTCATAATAAGTTTATGAATTACCATTTCGATAAACAATTAT
66 GAACTAGATATGCAACCATGGTATTCATAATAAGTTTATGAATTACCATTTCGATAAACAATTAT
286674 GTATAAAA
131 GTATAAAA
* *
286682 GTTATCGATCGATTTTGTTTAATGCATAACGGT-CTATATTCGT-ATCAGTACTATGTTTACTTT
1 GTTATCGATCGATTTTGTTTAATGCATAACGGTGC-ATATTCGTAAT-AGTACTATGTGTACTAT
* * * *
286745 TGGCACTACG-TGTGCACCCATGGTATTCATAATAAGTTTGTGAATTACCATTTCGA
64 TGGAACTA-GATATGCAACCATGGTATTCATAATAAGTTTATGAATTACCATTTCGA
286801 CACTATGTGT
Statistics
Matches: 106, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
137 3 0.03
138 102 0.96
139 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (138 bp):
GTTATCGATCGATTTTGTTTAATGCATAACGGTGCATATTCGTAATAGTACTATGTGTACTATTG
GAACTAGATATGCAACCATGGTATTCATAATAAGTTTATGAATTACCATTTCGATAAACAATTAT
GTATAAAA
Found at i:286812 original size:53 final size:53
Alignment explanation
Indices: 286748--286851 Score: 154
Period size: 53 Copynumber: 2.0 Consensus size: 53
286738 TTACTTTTGG
* * *
286748 CACTACGTGTGCACCCATGGTATTCATAATAAGTTTGTGAATTACCATTTCGA
1 CACTACGTGTGCACCCATAGAATTCATAATAAGTTCGTGAATTACCATTTCGA
* * *
286801 CACTATGTGTGCATCCATAGAATTCATAATAAGTTCGTGAATTTCCATTTC
1 CACTACGTGTGCACCCATAGAATTCATAATAAGTTCGTGAATTACCATTTC
286852 AGCACTTTGG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (53 bp):
CACTACGTGTGCACCCATAGAATTCATAATAAGTTCGTGAATTACCATTTCGA
Found at i:288865 original size:2 final size:2
Alignment explanation
Indices: 288858--288888 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
288848 GATGTCAGAA
288858 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
288889 GCTTTTCTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:294824 original size:11 final size:11
Alignment explanation
Indices: 294810--294869 Score: 68
Period size: 11 Copynumber: 5.5 Consensus size: 11
294800 AAATTTTGGC
294810 TTTTTTTTGTT
1 TTTTTTTTGTT
**
294821 TTTTTTTTGCC
1 TTTTTTTTGTT
*
294832 TTTTTTTTG-C
1 TTTTTTTTGTT
*
294842 CTTTTTTTGTTT
1 TTTTTTTTG-TT
294854 TTTTTTTTGTT
1 TTTTTTTTGTT
294865 TTTTT
1 TTTTT
294870 GAAAAAATAG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
10 9 0.21
11 25 0.60
12 8 0.19
ACGTcount: A:0.00, C:0.07, G:0.08, T:0.85
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:294828 original size:22 final size:21
Alignment explanation
Indices: 294803--294869 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 21
294793 TTTTTTGAAA
*
294803 TTTTGGCTTTTTTTTGTTTTT
1 TTTTTGCTTTTTTTTGTTTTT
294824 TTTTTGCCTTTTTTTTGCCTTTTT
1 TTTTTG-CTTTTTTTTG--TTTTT
294848 TTGTTT--TTTTTTTTGTTTTT
1 TT-TTTGCTTTTTTTTGTTTTT
294868 TT
1 TT
294870 GAAAAAATAG
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
20 7 0.17
21 5 0.12
22 19 0.46
24 7 0.17
25 3 0.07
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.82
Consensus pattern (21 bp):
TTTTTGCTTTTTTTTGTTTTT
Found at i:294850 original size:10 final size:11
Alignment explanation
Indices: 294803--294849 Score: 67
Period size: 11 Copynumber: 4.3 Consensus size: 11
294793 TTTTTTGAAA
*
294803 TTTTGGCTTTT
1 TTTTGCCTTTT
**
294814 TTTTGTTTTTT
1 TTTTGCCTTTT
294825 TTTTGCCTTTT
1 TTTTGCCTTTT
294836 TTTTGCCTTTT
1 TTTTGCCTTTT
294847 TTT
1 TTT
294850 GTTTTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.79
Consensus pattern (11 bp):
TTTTGCCTTTT
Found at i:306921 original size:10 final size:10
Alignment explanation
Indices: 306906--306936 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
306896 TCATTTTAGG
306906 TGCATGTAGT
1 TGCATGTAGT
*
306916 TGCATGTAGA
1 TGCATGTAGT
306926 TGCATGTAGT
1 TGCATGTAGT
306936 T
1 T
306937 ATATTTGGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.10, G:0.29, T:0.39
Consensus pattern (10 bp):
TGCATGTAGT
Found at i:323479 original size:23 final size:23
Alignment explanation
Indices: 323431--323480 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
323421 ATAATGACTA
* *
323431 TTCATGAAAAATAATTAAGTCTT
1 TTCATAAAAAATAATTAAGTCAT
**
323454 TTCATAAAAAATAATTATTTCAT
1 TTCATAAAAAATAATTAAGTCAT
323477 TTCA
1 TTCA
323481 CCCCAATAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (23 bp):
TTCATAAAAAATAATTAAGTCAT
Found at i:334348 original size:136 final size:137
Alignment explanation
Indices: 334134--334385 Score: 321
Period size: 136 Copynumber: 1.8 Consensus size: 137
334124 GTATGTAATG
* * * * * *
334134 GTTATTGATCGATTTTGTGTAATGCATAATGGTGCATTTTTGTATCAGTACTATGTGTACTTTCG
1 GTTATCGATCAATTTTGTGTAATGCATAACGGTGCATTTTCGTATCAGTACAATATGTACTTTCG
* * * *
334199 GCACTAGATGTGCAAACATTGTATTCATAATGATTTTATGAATTACCATTTCTACATATAATTAT
66 ACACTAGAGGTGCAAACA-TGGATTCATAATGAGTTTATGAATTACCATTTCTACATATAATTAT
334264 GTATAAAA
130 GTATAAAA
*
334272 GTTATCGATCAATTTT-T-TAATGCATAACGTTGCATTTTCGTATCAGTACAATATGTACTTTCG
1 GTTATCGATCAATTTTGTGTAATGCATAACGGTGCATTTTCGTATCAGTACAATATGTACTTTCG
** * * *
334335 ACACTATG-GGTGCATCCATGGATTCATAATGAGTTTGTTAATTTCCATTTC
66 ACACTA-GAGGTGCAAACATGGATTCATAATGAGTTTATGAATTACCATTTC
334386 GAAACTTAGG
Statistics
Matches: 97, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
135 28 0.29
136 53 0.55
137 2 0.02
138 14 0.14
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.42
Consensus pattern (137 bp):
GTTATCGATCAATTTTGTGTAATGCATAACGGTGCATTTTCGTATCAGTACAATATGTACTTTCG
ACACTAGAGGTGCAAACATGGATTCATAATGAGTTTATGAATTACCATTTCTACATATAATTATG
TATAAAA
Found at i:342470 original size:18 final size:18
Alignment explanation
Indices: 342449--342486 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
342439 CTTTAATCTT
342449 ACAACACTTACCACGACA
1 ACAACACTTACCACGACA
* *
342467 ACAACATTTCCCACGACA
1 ACAACACTTACCACGACA
342485 AC
1 AC
342487 GCCATTCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.39, G:0.05, T:0.13
Consensus pattern (18 bp):
ACAACACTTACCACGACA
Found at i:342806 original size:9 final size:9
Alignment explanation
Indices: 342792--342823 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
342782 CCTAGTTAGT
342792 AAAAAAATC
1 AAAAAAATC
342801 AAAAAAATC
1 AAAAAAATC
342810 AAAAAAAATC
1 -AAAAAAATC
342820 AAAA
1 AAAA
342824 CAAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.81, C:0.09, G:0.00, T:0.09
Consensus pattern (9 bp):
AAAAAAATC
Found at i:342832 original size:19 final size:19
Alignment explanation
Indices: 342792--342834 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
342782 CCTAGTTAGT
*
342792 AAAAAAATCAAAAAAATCA
1 AAAAAAATCAAAAAAATAA
342811 AAAAAAATCAAAACAAA-AA
1 AAAAAAATCAAAA-AAATAA
342830 AAAAA
1 AAAAA
342835 GAAAAAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.84, C:0.09, G:0.00, T:0.07
Consensus pattern (19 bp):
AAAAAAATCAAAAAAATAA
Found at i:342833 original size:10 final size:10
Alignment explanation
Indices: 342792--342828 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
342782 CCTAGTTAGT
342792 AAAAAAATC-
1 AAAAAAATCA
342801 AAAAAAATCA
1 AAAAAAATCA
342811 AAAAAAATCA
1 AAAAAAATCA
342821 AAACAAAA
1 AAA-AAAA
342829 AAAAAAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.35
10 13 0.50
11 4 0.15
ACGTcount: A:0.81, C:0.11, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAATCA
Found at i:348491 original size:21 final size:21
Alignment explanation
Indices: 348467--348509 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
348457 TTAAGGCCAA
*
348467 ATTCAGCTTCAAAATG-TCTAG
1 ATTCAGC-CCAAAATGATCTAG
*
348488 ATTCATCCCAAAATGATCTAG
1 ATTCAGCCCAAAATGATCTAG
348509 A
1 A
348510 ATATTCATCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (21 bp):
ATTCAGCCCAAAATGATCTAG
Found at i:349073 original size:21 final size:22
Alignment explanation
Indices: 349027--349075 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
349017 TTCTTTTTCA
*
349027 TTATATCATTTCAATTATTATT
1 TTATATCATTTCAATTATTATG
* *
349049 TTATATCATTTC-CTTCTTATG
1 TTATATCATTTCAATTATTATG
349070 TTATAT
1 TTATAT
349076 TGATGCAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.27, C:0.12, G:0.02, T:0.59
Consensus pattern (22 bp):
TTATATCATTTCAATTATTATG
Found at i:359604 original size:48 final size:48
Alignment explanation
Indices: 359533--359665 Score: 221
Period size: 48 Copynumber: 2.8 Consensus size: 48
359523 TAAACCAGGA
*
359533 GTGGCACCTTTCTGCCAAAATGCATCGTTATGCATTTAAGTCTCATTT
1 GTGGCACCTTTATGCCAAAATGCATCGTTATGCATTTAAGTCTCATTT
* *
359581 GTGGCACCTTTTTGCCAAAATGCATCGCTATGCATTTAAGTCTCATTT
1 GTGGCACCTTTATGCCAAAATGCATCGTTATGCATTTAAGTCTCATTT
* *
359629 GTGGCACCTTTATGCCAAAATGCACCATTATGCATTT
1 GTGGCACCTTTATGCCAAAATGCATCGTTATGCATTT
359666 TCTTTTATGC
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 79 1.00
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (48 bp):
GTGGCACCTTTATGCCAAAATGCATCGTTATGCATTTAAGTCTCATTT
Found at i:359747 original size:44 final size:43
Alignment explanation
Indices: 359623--359760 Score: 188
Period size: 44 Copynumber: 3.2 Consensus size: 43
359613 CATTTAAGTC
* *
359623 TCATTTGTGGCACCTTTATGCCAA-AATGCACCATTATGCATTT
1 TCATTTAT-GCACCTTTCTGCCAATAATGCACCATTATGCATTT
* * * *
359666 TCTTTTATGCACCCTTCTTCCAATAATGCACCATTATGAATTT
1 TCATTTATGCACCTTTCTGCCAATAATGCACCATTATGCATTT
*
359709 TCATTTATGCCACCTTTCTGCCAATAATGCACCGTTATGCATTT
1 TCATTTATG-CACCTTTCTGCCAATAATGCACCATTATGCATTT
359753 TCATTTAT
1 TCATTTAT
359761 CCATTCATTT
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
42 12 0.15
43 32 0.39
44 38 0.46
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.41
Consensus pattern (43 bp):
TCATTTATGCACCTTTCTGCCAATAATGCACCATTATGCATTT
Found at i:364111 original size:42 final size:41
Alignment explanation
Indices: 364028--364148 Score: 109
Period size: 42 Copynumber: 2.9 Consensus size: 41
364018 AAGGGTTTTT
* * * *
364028 TGATGAGTAAGTTCTTTGGGCCA-TCAGTAAGTCTTTCGAGCA
1 TGATG-GTAAGTCCTTCGGGCCATTCA-TAAGACTTTTGAGCA
*
364070 TGATGCGTAAGTCCTTCGGGCCATTTATAAGACTTTTGAGCA
1 TGATG-GTAAGTCCTTCGGGCCATTCATAAGACTTTTGAGCA
** * * * *
364112 AAATGATAAGGCCTTCGGGCCATCCATAAGACCTTTG
1 TGATGGTAAGTCCTTCGGGCCATTCATAAGACTTTTG
364149 GGCAGGAAGT
Statistics
Matches: 65, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
41 27 0.42
42 36 0.55
43 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (41 bp):
TGATGGTAAGTCCTTCGGGCCATTCATAAGACTTTTGAGCA
Found at i:364163 original size:263 final size:264
Alignment explanation
Indices: 363695--364224 Score: 765
Period size: 263 Copynumber: 2.0 Consensus size: 264
363685 TAAGCTTGAT
* * * *
363695 GGACCAACGTGATATGTAGGGGTTCCTTGATGATAACTAAGAAATTGAGCATGATTTTCAAGGGT
1 GGACCAACGTGATATGTAGGGGTTCCTTAATGACAACTAAGAAACTAAGCATGATTTTCAAGGGT
* * *
363760 TTCTTGATTGAGTTAGTCCTTCGGTCAATCAGTAAGTCTTTTGAGCATGATGCGTAAATCCTTCG
66 TTCTTGATTGAGTAAGTCCTTCGGGCAATCAGTAAGTCTTTCGAGCATGATGCGTAAATCCTTCG
* * * * **
363825 GGCCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCATTCGGACCATCCATAAGACCTTTGCGTT
131 GGCCATCTATAAGACTTTCGAGCAAAATGATAAGGCATTCGGACCATCCATAAGACCTTTGCGCA
* * * *
363890 GGATGTTTTCAACATTTATAGCACTTGATTCATCACATATGGAGTTAAATCAGCACCACCTCACT
196 GGAAGTTTTCAACATTTACAACACTTGATTCATCACATATGGAGTTAAATCAGCAACACCTCACT
363955 CAAG
261 CAAG
*
363959 GGACCAACGTGATATGTAGGGGTTCCTTAATGACAACTAAGAAACTAAGCTTGATTTTCAAGGGT
1 GGACCAACGTGATATGTAGGGGTTCCTTAATGACAACTAAGAAACTAAGCATGATTTTCAAGGGT
* * * * *
364024 TTTTTGA-TGAGTAAGTTCTTTGGGCCATCAGTAAGTCTTTCGAGCATGATGCGTAAGTCCTTCG
66 TTCTTGATTGAGTAAGTCCTTCGGGCAATCAGTAAGTCTTTCGAGCATGATGCGTAAATCCTTCG
* * * * *
364088 GGCCATTTATAAGACTTTTGAGCAAAATGATAAGGCCTTCGGGCCATCCATAAGACCTTTGGGCA
131 GGCCATCTATAAGACTTTCGAGCAAAATGATAAGGCATTCGGACCATCCATAAGACCTTTGCGCA
* * *
364153 GGAAGTTTTCAACATTTCCAATACTTGATTCATCACATATGGAGTTGAATCAGCAACACCTCACT
196 GGAAGTTTTCAACATTTACAACACTTGATTCATCACATATGGAGTTAAATCAGCAACACCTCACT
*
364218 CGAG
261 CAAG
364222 GGA
1 GGA
364225 TAAACGTTGC
Statistics
Matches: 234, Mismatches: 32, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
263 168 0.72
264 66 0.28
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (264 bp):
GGACCAACGTGATATGTAGGGGTTCCTTAATGACAACTAAGAAACTAAGCATGATTTTCAAGGGT
TTCTTGATTGAGTAAGTCCTTCGGGCAATCAGTAAGTCTTTCGAGCATGATGCGTAAATCCTTCG
GGCCATCTATAAGACTTTCGAGCAAAATGATAAGGCATTCGGACCATCCATAAGACCTTTGCGCA
GGAAGTTTTCAACATTTACAACACTTGATTCATCACATATGGAGTTAAATCAGCAACACCTCACT
CAAG
Found at i:372878 original size:48 final size:47
Alignment explanation
Indices: 372818--372942 Score: 189
Period size: 48 Copynumber: 2.6 Consensus size: 47
372808 GAATAAATGA
*
372818 AAATGCATAACGGTGCATTTTCGCAGAAAGCTGCCACAAATGAGACTT
1 AAATGCATAACGGTGCATTTTGGCAGAAAG-TGCCACAAATGAGACTT
372866 AAATGCATAACGGTGCATTTTGGCAGAAATGTGCCACAAATGAGACTT
1 AAATGCATAACGGTGCATTTTGGCAGAAA-GTGCCACAAATGAGACTT
* * *
372914 -AATTCACAACGGTGCATTTTGGTAGAAAG
1 AAATGCATAACGGTGCATTTTGGCAGAAAG
372943 GTGCAACTTC
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
46 1 0.01
47 25 0.35
48 45 0.62
49 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (47 bp):
AAATGCATAACGGTGCATTTTGGCAGAAAGTGCCACAAATGAGACTT
Found at i:379953 original size:21 final size:21
Alignment explanation
Indices: 379904--379962 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
379894 ATTATCCAAT
*
379904 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
*
379925 AAACTTGAAATCCATAACTAC
1 AAACTTGAAATCCATAACAAC
* * *
379946 TAAGTTGAACTCCATAA
1 AAACTTGAAATCCATAA
379963 TAATAAATCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.24
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:387610 original size:10 final size:11
Alignment explanation
Indices: 387583--387612 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
387573 AGGTAAAACA
387583 AAAATAAAATG
1 AAAATAAAATG
387594 AAAATAAAATG
1 AAAATAAAATG
387605 -AAATAAAA
1 AAAATAAAA
387613 CAAAAAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.17
Consensus pattern (11 bp):
AAAATAAAATG
Found at i:387612 original size:32 final size:32
Alignment explanation
Indices: 387550--387618 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
387540 AAAGTTTTCT
** **
387550 AAAAATAAAATGAAAATTTAACGAGGTAAAAC
1 AAAAATAAAATGAAAATAAAACGAAATAAAAC
*
387582 AAAAATAAAATGAAAATAAAATGAAATAAAAC
1 AAAAATAAAATGAAAATAAAACGAAATAAAAC
387614 AAAAA
1 AAAAA
387619 AAAGAACAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.71, C:0.04, G:0.09, T:0.16
Consensus pattern (32 bp):
AAAAATAAAATGAAAATAAAACGAAATAAAAC
Found at i:392243 original size:48 final size:48
Alignment explanation
Indices: 392163--392295 Score: 203
Period size: 48 Copynumber: 2.8 Consensus size: 48
392153 TAAACCATGA
* *
392163 GTGGCACCTTTCTGCCAAAATGCACTGTTATGCATTTAAGTCTCATTT
1 GTGGCACCTTTCTGCCAAAATGCACCGTTATGCATTTAAGTCTCATTC
* * *
392211 GTGGAACCTTTTTGCCAAAATGCACCGCTATGCATTTAAGTCTCATTC
1 GTGGCACCTTTCTGCCAAAATGCACCGTTATGCATTTAAGTCTCATTC
* *
392259 GTGGCACCTTTCTACCAAAATGCACCATTATGCATTT
1 GTGGCACCTTTCTGCCAAAATGCACCGTTATGCATTT
392296 TCTTTTATGC
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 75 1.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.35
Consensus pattern (48 bp):
GTGGCACCTTTCTGCCAAAATGCACCGTTATGCATTTAAGTCTCATTC
Found at i:392377 original size:44 final size:44
Alignment explanation
Indices: 392260--392390 Score: 185
Period size: 44 Copynumber: 3.0 Consensus size: 44
392250 GTCTCATTCG
*
392260 TGGCACCTTTCTACCAA-AATGCACCATTATGCATTTTCTTTTA
1 TGGCACCTTTCTACCAATAATGCACCATTATGCATTTTCATTTA
* * * *
392303 T-GCACCTTTCTTCCAATATTGCATCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTACCAATAATGCACCATTATGCATTTTCATTTA
* *
392346 TGGCACATTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
1 TGGCACCTTTCTACCAATAATGCACCATTATGCATTTTCATTTA
392390 T
1 T
392391 CCATTCATTT
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
42 14 0.18
43 24 0.32
44 38 0.50
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.42
Consensus pattern (44 bp):
TGGCACCTTTCTACCAATAATGCACCATTATGCATTTTCATTTA
Found at i:395305 original size:40 final size:40
Alignment explanation
Indices: 395250--395371 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
395240 TGGAGGTTTA
*
395250 TAATACACTTCGGTGTATTTGGTGGGCATGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCATGACCTTATGTG
395290 TAATACACTTCGGTGTATATGGTGGGCATGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCATGACCTTATGTG
395330 TAATACACTTCGGTGTATATGGTGGGCATGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCATGACCTTATGTG
395370 TA
1 TA
395372 GCACTACGGT
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.22, C:0.15, G:0.27, T:0.36
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCATGACCTTATGTG
Found at i:395569 original size:47 final size:45
Alignment explanation
Indices: 395487--395600 Score: 149
Period size: 47 Copynumber: 2.5 Consensus size: 45
395477 AATAAACTAT
* *
395487 GAGCTTACGGAAT-AATGGCAAGTATATAGGAAAAATAAGCTTAC
1 GAGCTTATGGAATAAATGGTAAGTATATAGGAAAAATAAGCTTAC
* * *
395531 GAGCTTATGGAATTTAAATGGTAAGTATTTTGGTAAAATAAGCTTAC
1 GAGCTTATGGAA--TAAATGGTAAGTATATAGGAAAAATAAGCTTAC
*
395578 GAGCTTATGGGATAAATGGTAAG
1 GAGCTTATGGAATAAATGGTAAG
395601 AGAGTTTATA
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
44 11 0.18
45 11 0.18
46 1 0.02
47 38 0.62
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.29
Consensus pattern (45 bp):
GAGCTTATGGAATAAATGGTAAGTATATAGGAAAAATAAGCTTAC
Found at i:402297 original size:40 final size:40
Alignment explanation
Indices: 402242--402363 Score: 208
Period size: 40 Copynumber: 3.0 Consensus size: 40
402232 TGCAGGTTTA
402242 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
402282 TAATACACTTCGGTGTATATGGTGGGAACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* * *
402322 TAACACACTTCGGTGTATATGGTGGCCACGACCTTATTTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
402362 TA
1 TA
402364 GCACTACGGT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 77 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:402567 original size:47 final size:44
Alignment explanation
Indices: 402468--402592 Score: 144
Period size: 47 Copynumber: 2.8 Consensus size: 44
402458 GTAACCATAC
* * ** *
402468 AAATAAACTTATGAGCTTACAGAAT-AATGGCAAGTATATAGGA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGA
* *
402511 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAGG-A
*
402558 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
402593 AGATTTTATA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
43 20 0.29
45 12 0.17
46 14 0.20
47 24 0.34
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGA
Found at i:411081 original size:21 final size:21
Alignment explanation
Indices: 411032--411090 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
411022 ATTATCCAGT
*
411032 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
*
411053 AAACTTGAAATCCATAACTAC
1 AAACTTGAAATCCATAACAAC
* * *
411074 TAAGTTGAACTCCATAA
1 AAACTTGAAATCCATAA
411091 TAATAAATCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.24
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:413248 original size:4 final size:4
Alignment explanation
Indices: 413228--413261 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
413218 TACTCTCTCC
*
413228 GAAT AGAAT GGAT GAAT GAAT GAAT GAAT GAAT G
1 GAAT -GAAT GAAT GAAT GAAT GAAT GAAT GAAT G
413262 CAAATGAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.29, T:0.24
Consensus pattern (4 bp):
GAAT
Found at i:415865 original size:48 final size:48
Alignment explanation
Indices: 415737--415956 Score: 203
Period size: 48 Copynumber: 4.8 Consensus size: 48
415727 TAAACCATGA
* * *
415737 GTGGCACCTTTCTGCCAAAATGCACTGTTAAGCATTTAAGTCTCATTT
1 GTGGCACCTTTTTGCCAAAATGCACCGTTATGCATTTAAGTCTCATTT
* * *
415785 GTGGAACCTTTTTGCCAAAATGCATCGCTATGCATTTAAGTCTCATTT
1 GTGGCACCTTTTTGCCAAAATGCACCGTTATGCATTTAAGTCTCATTT
* *
415833 GTGGCACCTTTTTGCCAAAATACACCATTATGCATTT---TCT--TTT
1 GTGGCACCTTTTTGCCAAAATGCACCGTTATGCATTTAAGTCTCATTT
* * *
415876 AT-GCACCTTTCTT-CCAATATTGCATCGTTATGCA-TT---T-TCATTT
1 GTGGCACCTTT-TTGCCAA-AATGCACCGTTATGCATTTAAGTCTCATTT
* * *
415919 ATGGCACATTTCTGCCAATAATGCACCGTTATGCATTT
1 GTGGCACCTTTTTGCCAA-AATGCACCGTTATGCATTT
415957 TCATTTATCC
Statistics
Matches: 145, Mismatches: 20, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
41 1 0.01
42 15 0.10
43 24 0.17
44 26 0.18
45 5 0.03
48 74 0.51
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.39
Consensus pattern (48 bp):
GTGGCACCTTTTTGCCAAAATGCACCGTTATGCATTTAAGTCTCATTT
Found at i:415910 original size:43 final size:44
Alignment explanation
Indices: 415827--415964 Score: 172
Period size: 44 Copynumber: 3.2 Consensus size: 44
415817 CATTTAAGTC
* * * * *
415827 TCATTTGTGGCACCTTTTTGCCAA-AATACACCATTATGCATTT
1 TCATTTATGGCACATTTCTGCCAATAATGCACCGTTATGCATTT
* * * * *
415870 TCTTTTAT-GCACCTTTCTTCCAATATTGCATCGTTATGCATTT
1 TCATTTATGGCACATTTCTGCCAATAATGCACCGTTATGCATTT
415913 TCATTTATGGCACATTTCTGCCAATAATGCACCGTTATGCATTT
1 TCATTTATGGCACATTTCTGCCAATAATGCACCGTTATGCATTT
415957 TCATTTAT
1 TCATTTAT
415965 CCATTCATTT
Statistics
Matches: 80, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
42 13 0.16
43 28 0.35
44 39 0.49
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.43
Consensus pattern (44 bp):
TCATTTATGGCACATTTCTGCCAATAATGCACCGTTATGCATTT
Found at i:418879 original size:40 final size:40
Alignment explanation
Indices: 418824--418945 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
418814 TGCAGGTTTA
* *
418824 TAATACACTTCGGTGTATTTGGTGGGAACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
418864 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
418904 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
418944 TA
1 TA
418946 GCACTACGGT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:419144 original size:47 final size:45
Alignment explanation
Indices: 419050--419175 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
419040 GTAACCATGC
* * * *
419050 AAATAAACTTATGAGCTTACGGAAT-AATGGCAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
* * *
419094 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAGGAA
*
419141 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
419176 AGATTTTATA
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 21 0.30
45 11 0.15
46 1 0.01
47 38 0.54
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
Found at i:425826 original size:40 final size:40
Alignment explanation
Indices: 425768--425849 Score: 139
Period size: 40 Copynumber: 2.0 Consensus size: 40
425758 TGCAGGTTTA
425768 TAATACACTTCGATGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGATGTATATGGTGGGCACGACCTTATGTG
*
425808 TAATACACTTCGGA-GTATATGGTGGGCACGACCTTATTTG
1 TAATACACTTC-GATGTATATGGTGGGCACGACCTTATGTG
425848 TA
1 TA
425850 GCACTACGGT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 38 0.95
41 2 0.05
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGATGTATATGGTGGGCACGACCTTATGTG
Found at i:426036 original size:47 final size:45
Alignment explanation
Indices: 425979--426079 Score: 139
Period size: 47 Copynumber: 2.2 Consensus size: 45
425969 CGTACAAAAT
*
425979 AATGGCAAGTATATAGGAAAAATAAGCTTACGAGCTTATGGAATTTA
1 AATGGTAAGTATATAGGAAAAATAAGCTTACGAGCTTATGGAA--TA
* * * *
426026 AATGGTAAGTATTTTGGTAAAATAAGCTTACGAGCTTATGGGATA
1 AATGGTAAGTATATAGGAAAAATAAGCTTACGAGCTTATGGAATA
426071 AATGGTAAG
1 AATGGTAAG
426080 AGATTTTATA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
45 11 0.22
47 38 0.78
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.30
Consensus pattern (45 bp):
AATGGTAAGTATATAGGAAAAATAAGCTTACGAGCTTATGGAATA
Found at i:435421 original size:13 final size:13
Alignment explanation
Indices: 435403--435432 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
435393 TAAAACTCAT
*
435403 AAAATTTTGAAAC
1 AAAATTTTAAAAC
435416 AAAATTTTAAAAC
1 AAAATTTTAAAAC
435429 AAAA
1 AAAA
435433 CATTTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.63, C:0.07, G:0.03, T:0.27
Consensus pattern (13 bp):
AAAATTTTAAAAC
Found at i:435886 original size:48 final size:44
Alignment explanation
Indices: 435815--436027 Score: 216
Period size: 44 Copynumber: 4.7 Consensus size: 44
435805 CCTTTCTACT
* *
435815 AAAATGCACCGTTGTGCATTTAAGTCTCATTTGTGGCACATTTATGCC
1 AAAATGCACCGTTATGCATTT---T-TCATTTATGGCACATTTATGCC
* * *
435863 AAAATGCACCGTTATGCATTTAAGTCTCATTTGTGGCACCTTTCTGCC
1 AAAATGCACCGTTATGCATTT---T-TCATTTATGGCACATTTATGCC
** * *
435911 AAAATGCATTGTTTTGCA-TTTTCATTTATGGCACAATTATGCC
1 AAAATGCACCGTTATGCATTTTTCATTTATGGCACATTTATGCC
* *
435954 AATAATGCACCGTTATGCA-TTTTCATTTATGGCACCTTTCTGCC
1 AA-AATGCACCGTTATGCATTTTTCATTTATGGCACATTTATGCC
435998 AATAATGCACCGTTATGCA-TTTTCATTTAT
1 AA-AATGCACCGTTATGCATTTTTCATTTAT
436028 TCATTCATTT
Statistics
Matches: 148, Mismatches: 16, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
43 20 0.14
44 66 0.45
47 2 0.01
48 60 0.41
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.38
Consensus pattern (44 bp):
AAAATGCACCGTTATGCATTTTTCATTTATGGCACATTTATGCC
Found at i:435976 original size:44 final size:43
Alignment explanation
Indices: 435841--436027 Score: 221
Period size: 44 Copynumber: 4.2 Consensus size: 43
435831 CATTTAAGTC
*
435841 TCATTTGTGGCACATTTATGCCAAAATGCACCGTTATGCATTTAAGT
1 TCATTTATGGCACATTTATGCCAAAATGCACCGTTATGCA-TT---T
* * * ** *
435888 CTCATTTGTGGCACCTTTCTGCCAAAATGCATTGTTTTGCATTT
1 -TCATTTATGGCACATTTATGCCAAAATGCACCGTTATGCATTT
*
435932 TCATTTATGGCACAATTATGCCAATAATGCACCGTTATGCATTT
1 TCATTTATGGCACATTTATGCCAA-AATGCACCGTTATGCATTT
* *
435976 TCATTTATGGCACCTTTCTGCCAATAATGCACCGTTATGCATTT
1 TCATTTATGGCACATTTATGCCAA-AATGCACCGTTATGCATTT
436020 TCATTTAT
1 TCATTTAT
436028 TCATTCATTT
Statistics
Matches: 123, Mismatches: 15, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
43 20 0.16
44 66 0.54
47 2 0.02
48 35 0.28
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (43 bp):
TCATTTATGGCACATTTATGCCAAAATGCACCGTTATGCATTT
Found at i:435998 original size:87 final size:90
Alignment explanation
Indices: 435841--436027 Score: 265
Period size: 88 Copynumber: 2.1 Consensus size: 90
435831 CATTTAAGTC
* * *
435841 TCATTTGTGGCACATTTATGCCAAAATGCACCGTTATGCATTTAAGTCTCATTTGTGGCACCTTT
1 TCATTTATGGCACAATTATGCCAAAATGCACCGTTATGCATTT-A-TCTCATTTATGGCACCTTT
** *
435906 CTGCCAA-AATGCATTGTTTTGCATTT
64 CTGCCAATAATGCACCGTTATGCATTT
435932 TCATTTATGGCACAATTATGCCAATAATGCACCGTTATGCA-TT-T-TCATTTATGGCACCTTTC
1 TCATTTATGGCACAATTATGCCAA-AATGCACCGTTATGCATTTATCTCATTTATGGCACCTTTC
435994 TGCCAATAATGCACCGTTATGCATTT
65 TGCCAATAATGCACCGTTATGCATTT
436020 TCATTTAT
1 TCATTTAT
436028 TCATTCATTT
Statistics
Matches: 88, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
87 23 0.26
88 25 0.28
91 24 0.27
92 16 0.18
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (90 bp):
TCATTTATGGCACAATTATGCCAAAATGCACCGTTATGCATTTATCTCATTTATGGCACCTTTCT
GCCAATAATGCACCGTTATGCATTT
Found at i:451210 original size:13 final size:13
Alignment explanation
Indices: 451192--451216 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
451182 ATCTTAAAGA
451192 TAATGTCAACTTC
1 TAATGTCAACTTC
451205 TAATGTCAACTT
1 TAATGTCAACTT
451217 GCATGCCCAC
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:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (13 bp):
TAATGTCAACTTC
Found at i:454739 original size:55 final size:55
Alignment explanation
Indices: 454670--454843 Score: 285
Period size: 55 Copynumber: 3.2 Consensus size: 55
454660 AATTTTTTTT
454670 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* * *
454725 ATGAATTTCTGTATGGTCACTTTATGTGTAAACTTAAGCAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* * * *
454780 ATGAATTTCCGTATTGGCACTTTATATGTAAATTTAAGAAATTCATACGAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
454835 ATGAATTTC
1 ATGAATTTC
454844 ATACGAAGTG
Statistics
Matches: 109, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 109 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (55 bp):
ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
Found at i:454846 original size:20 final size:20
Alignment explanation
Indices: 454821--454862 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
454811 ATTTAAGAAA
454821 TTCATACGAAGTGGATGAAT
1 TTCATACGAAGTGGATGAAT
454841 TTCATACGAAGTGGATGAAT
1 TTCATACGAAGTGGATGAAT
454861 TT
1 TT
454863 TCGTATGGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (20 bp):
TTCATACGAAGTGGATGAAT
Found at i:454892 original size:75 final size:75
Alignment explanation
Indices: 454766--454909 Score: 218
Period size: 75 Copynumber: 1.9 Consensus size: 75
454756 ACTTAAGCAA
* *
454766 TTCATACTAAGTGGATGAATTTCCGTATTGGCACTTTATATGTAAATTTAAGAAATTCATACGAA
1 TTCATACGAAGTGGATGAATTTCCGTATTGGCACTTTATATGTAAACTTAAGAAATTCATACGAA
454831 GTGGATGAAT
66 GTGGATGAAT
* * * *
454841 TTCATACGAAGTGGATGAATTTTCGTA-TGGACATTTTATGTGTAAACTTAAGAAATTCATACTA
1 TTCATACGAAGTGGATGAATTTCCGTATTGG-CACTTTATATGTAAACTTAAGAAATTCATACGA
454905 AGTGG
65 AGTGG
454910 TCAAATTTCC
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
74 3 0.05
75 59 0.95
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.36
Consensus pattern (75 bp):
TTCATACGAAGTGGATGAATTTCCGTATTGGCACTTTATATGTAAACTTAAGAAATTCATACGAA
GTGGATGAAT
Found at i:454925 original size:55 final size:56
Alignment explanation
Indices: 454841--455031 Score: 194
Period size: 55 Copynumber: 3.5 Consensus size: 56
454831 GTGGATGAAT
* * * * *
454841 TTCATACGAAGTGGATGAATTTTCGTATGGACATTTTATGTGTAAACTTA-AGAAA
1 TTCATACTAAGTGGATAAATTTCCGTATGGACACTTTATGTGCAAACTTATAGAAA
* *
454896 TTCATACTAAGTGG-TCAAATTTCCGTATGGGCACTTTATGTGCAAACTTATGGAAA
1 TTCATACTAAGTGGAT-AAATTTCCGTATGGACACTTTATGTGCAAACTTATAGAAA
* ** * * * *
454952 -TCATACTAAGTGGATGAATTTCTATATGGGCACTTTTTATGCAAAAC-TA-GGAAA
1 TTCATACTAAGTGGATAAATTTCCGTATGGACACTTTATGTGC-AAACTTATAGAAA
*
455006 TTCATACTAAGTGTATAAATTTCCGT
1 TTCATACTAAGTGGATAAATTTCCGT
455032 TTTGATAGTG
Statistics
Matches: 115, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
54 6 0.05
55 100 0.87
56 9 0.08
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (56 bp):
TTCATACTAAGTGGATAAATTTCCGTATGGACACTTTATGTGCAAACTTATAGAAA
Found at i:454956 original size:130 final size:130
Alignment explanation
Indices: 454711--454973 Score: 379
Period size: 130 Copynumber: 2.0 Consensus size: 130
454701 ACTTAAGAAA
* * *
454711 TTCATACTAAGTGGATGAATTTCTGTATGGTCACTTTATGTGTAAACTTAAGCAATTCATACTAA
1 TTCATACGAAGTGGATGAATTTCTGTATGGACACTTTATGTGTAAACTTAAGAAATTCATACTAA
* * * *
454776 GTGGATGAATTTCCGTATTGGCACTTTATATGTAAATTTAAGAAATTCATACGAAGTGGATGAAT
66 GTGGATAAATTTCCGTATGGGCACTTTATATGCAAACTTAAGAAATTCATACGAAGTGGATGAAT
*
454841 TTCATACGAAGTGGATGAATTT-TCGTATGGACATTTTATGTGTAAACTTAAGAAATTCATACTA
1 TTCATACGAAGTGGATGAATTTCT-GTATGGACACTTTATGTGTAAACTTAAGAAATTCATACTA
* * *
454905 AGTGG-TCAAATTTCCGTATGGGCACTTTATGTGCAAACTTATGGAAA-TCATACTAAGTGGATG
65 AGTGGAT-AAATTTCCGTATGGGCACTTTATATGCAAACTTA-AGAAATTCATACGAAGTGGATG
454968 AAT
128 AAT
454971 TTC
1 TTC
454974 TATATGGGCA
Statistics
Matches: 119, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
129 2 0.02
130 113 0.95
131 4 0.03
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (130 bp):
TTCATACGAAGTGGATGAATTTCTGTATGGACACTTTATGTGTAAACTTAAGAAATTCATACTAA
GTGGATAAATTTCCGTATGGGCACTTTATATGCAAACTTAAGAAATTCATACGAAGTGGATGAAT
Found at i:454986 original size:185 final size:185
Alignment explanation
Indices: 454670--455028 Score: 513
Period size: 185 Copynumber: 1.9 Consensus size: 185
454660 AATTTTTTTT
* * *
454670 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTCT
1 ATGAATTTCCGTATGGACACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATAAATTTCC
* * * * *
454735 GTATGGTCACTTTATGTGTAAACTTAAGCAATTCATACTAAGTGGATGAATTTCCGTATTGGCAC
66 GTATGGGCACTTTATGTGCAAACTTAAGCAAATCATACTAAGTGGATGAATTTCCATATGGGCAC
* ** *
454800 TTTATATGTAAATTTAAGAAATTCATACGAAGTGGATGAATTTCATACGAAGTGG
131 TTTATATGCAAAACTAAGAAATTCATACGAAGTGGATAAATTTCATACGAAGTGG
* *
454855 ATGAATTTTCGTATGGACATTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG-TCAAATTTC
1 ATGAATTTCCGTATGGACACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGAT-AAATTTC
* * *
454919 CGTATGGGCACTTTATGTGCAAACTTATGGAAATCATACTAAGTGGATGAATTTCTATATGGGCA
65 CGTATGGGCACTTTATGTGCAAACTTAAGCAAATCATACTAAGTGGATGAATTTCCATATGGGCA
* * * *
454984 CTTTTTATGCAAAACTAGGAAATTCATACTAAGTGTATAAATTTC
130 CTTTATATGCAAAACTAAGAAATTCATACGAAGTGGATAAATTTC
455029 CGTTTTGATA
Statistics
Matches: 152, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
184 1 0.01
185 151 0.99
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (185 bp):
ATGAATTTCCGTATGGACACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATAAATTTCC
GTATGGGCACTTTATGTGCAAACTTAAGCAAATCATACTAAGTGGATGAATTTCCATATGGGCAC
TTTATATGCAAAACTAAGAAATTCATACGAAGTGGATAAATTTCATACGAAGTGG
Found at i:464234 original size:44 final size:43
Alignment explanation
Indices: 464170--464326 Score: 126
Period size: 43 Copynumber: 3.7 Consensus size: 43
464160 TATTTCAGAC
* * * * * * *
464170 TCCTCTGCTATGTGCGAGGGTAAGTTCTTACCGTTACCGCATGT
1 TCCTTTGCTGTGTGCAAGGGTAAG-CCTTACAGTTACCCCAGGT
* *
464214 TTCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGT
1 TCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTACCCCAGGT
* * *
464257 TCCTTTGTTGTGTGC-AGGG--GGCCTTACAGTT-TCCCAGGCT
1 TCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTACCCCAGG-T
* *
464297 T-TTTTGCTATGTGCAAGGGTAAGACCTTAC
1 TCCTTTGCTGTGTGCAAGGGTAAG-CCTTAC
464327 CATTTTTGCA
Statistics
Matches: 91, Mismatches: 17, Indels: 11
0.76 0.14 0.09
Matches are distributed among these distances:
39 16 0.18
40 17 0.19
42 5 0.05
43 33 0.36
44 20 0.22
ACGTcount: A:0.16, C:0.23, G:0.26, T:0.35
Consensus pattern (43 bp):
TCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTACCCCAGGT
Found at i:464269 original size:43 final size:43
Alignment explanation
Indices: 464214--464326 Score: 130
Period size: 43 Copynumber: 2.7 Consensus size: 43
464204 TACCGCATGT
464214 TTCTTTGCTGTGTGCAAGGGTAAG-CCTTACAGTTTCCCCAGG
1 TTCTTTGCTGTGTGCAAGGGTAAGACCTTACAGTTTCCCCAGG
* *
464256 TTCCTTTGTTGTGTGC-AGGG---GGCCTTACAGTTT-CCCAGG
1 TT-CTTTGCTGTGTGCAAGGGTAAGACCTTACAGTTTCCCCAGG
* *
464295 CTTTTTTGCTATGTGCAAGGGTAAGACCTTAC
1 -TTCTTTGCTGTGTGCAAGGGTAAGACCTTAC
464327 CATTTTTGCA
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
39 17 0.29
40 17 0.29
42 6 0.10
43 19 0.32
ACGTcount: A:0.16, C:0.22, G:0.27, T:0.35
Consensus pattern (43 bp):
TTCTTTGCTGTGTGCAAGGGTAAGACCTTACAGTTTCCCCAGG
Found at i:465722 original size:55 final size:55
Alignment explanation
Indices: 465658--465896 Score: 304
Period size: 55 Copynumber: 4.3 Consensus size: 55
465648 TAATTGTGTA
* ** * *
465658 TAAAGTTAAGAAATTCATAATTTGCT-TATGAATTTTCGTATGGGCACTTTATGTG
1 TAAACTTAAGAAATTCATAATAAG-TGGATGAATTTCCGTATGGGCACTTTATGTG
*
465713 TAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTTTATGTG
1 TAAACTTAAGAAATTCATAATAAGTGGATGAATTTCCGTATGGGCACTTTATGTG
* * * *
465768 TAAACTTAAGAAATTCATACTAAGTGAACGAATTTCCGTATGGGCACCTTATGTG
1 TAAACTTAAGAAATTCATAATAAGTGGATGAATTTCCGTATGGGCACTTTATGTG
* * *
465823 TAAACTTAAGGAATTCATACA-AAGTGGATGAATTTCTGTATGGGTACTTTATGTG
1 TAAACTTAAGAAATTCATA-ATAAGTGGATGAATTTCCGTATGGGCACTTTATGTG
*
465878 TAAAAC-TAGGAAATTCATA
1 T-AAACTTAAGAAATTCATA
465897 CTAGGTGTAT
Statistics
Matches: 163, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
54 1 0.01
55 158 0.97
56 4 0.02
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (55 bp):
TAAACTTAAGAAATTCATAATAAGTGGATGAATTTCCGTATGGGCACTTTATGTG
Found at i:465897 original size:55 final size:55
Alignment explanation
Indices: 465685--465918 Score: 335
Period size: 55 Copynumber: 4.3 Consensus size: 55
465675 TAATTTGCTT
*
465685 ATGAATTTTCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
*
465740 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGA
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* * * *
465795 ACGAATTTCCGTATGGGCACCTTATGTGTAAACTTAAGGAATTCATACAAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* * * * *
465850 ATGAATTTCTGTATGGGTACTTTATGTGTAAAAC-TAGGAAATTCATACTAGGTGT
1 ATGAATTTCCGTATGGGCACTTTATGTGT-AAACTTAAGAAATTCATACTAAGTGG
* *
465905 ATAAATTTACGTAT
1 ATGAATTTCCGTAT
465919 TGATAGTGGG
Statistics
Matches: 159, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
55 155 0.97
56 4 0.03
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (55 bp):
ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
Found at i:468307 original size:17 final size:19
Alignment explanation
Indices: 468265--468302 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
468255 TTGGACCCTT
468265 AGTGCATCAGTGCACTAAG
1 AGTGCATCAGTGCACTAAG
*
468284 AGTGCATCGGTGCACTAAG
1 AGTGCATCAGTGCACTAAG
468303 TGCATTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (19 bp):
AGTGCATCAGTGCACTAAG
Found at i:468414 original size:45 final size:46
Alignment explanation
Indices: 468328--468416 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 46
468318 AAAATAGTCA
*
468328 GAGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCACT
1 GAGTGCATCGATGCATGGTCGTGTGCATCGATGCATCAAATGCACT
*
468374 GAGTGCATCGATGCATGGT-GTGTGCATCGATGCATTAAATGCA
1 GAGTGCATCGATGCATGGTCGTGTGCATCGATGCATCAAATGCA
468417 TTCGATGTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 22 0.54
46 19 0.46
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (46 bp):
GAGTGCATCGATGCATGGTCGTGTGCATCGATGCATCAAATGCACT
Found at i:468445 original size:37 final size:33
Alignment explanation
Indices: 468404--468471 Score: 82
Period size: 33 Copynumber: 1.9 Consensus size: 33
468394 TGTGCATCGA
468404 TGCATTAAATGCATTCGATGTTTAAAAAAATAATTGG
1 TGCA-TAAATGCA-TC-A-GTTTAAAAAAATAATTGG
* *
468441 TGCATCAATGCATCAGTTTGAAAAAATAATT
1 TGCATAAATGCATCAGTTTAAAAAAATAATT
468472 TTAGGCTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 15 0.52
34 1 0.03
35 2 0.07
36 7 0.24
37 4 0.14
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (33 bp):
TGCATAAATGCATCAGTTTAAAAAAATAATTGG
Found at i:478988 original size:23 final size:22
Alignment explanation
Indices: 478951--478993 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
478941 TCAATTCCTT
478951 ATCTTTTCTTTATCTTGTTTTG
1 ATCTTTTCTTTATCTTGTTTTG
*
478973 ATCTTATTTTTTATCTTGTTT
1 ATCTT-TTCTTTATCTTGTTT
478994 CCAGTACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.12, C:0.12, G:0.07, T:0.70
Consensus pattern (22 bp):
ATCTTTTCTTTATCTTGTTTTG
Found at i:479333 original size:10 final size:10
Alignment explanation
Indices: 479318--479342 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
479308 TTGCTATTTT
479318 AAAAAAAACA
1 AAAAAAAACA
479328 AAAAAAAACA
1 AAAAAAAACA
479338 AAAAA
1 AAAAA
479343 GCCAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:485896 original size:23 final size:22
Alignment explanation
Indices: 485859--485901 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
485849 GCAATTCCTT
485859 ATCTTTTCTTTATCTTGTTTTA
1 ATCTTTTCTTTATCTTGTTTTA
*
485881 ATCTTATTTTTTATCTTGTTT
1 ATCTT-TTCTTTATCTTGTTT
485902 CCAGTACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (22 bp):
ATCTTTTCTTTATCTTGTTTTA
Found at i:486415 original size:21 final size:21
Alignment explanation
Indices: 486347--486416 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
486337 GCTTTGGAAT
* * **
486347 TTTTCTTGGGATGCAATTAGC
1 TTTTCTTAGGATGTAACCAGC
* *
486368 TTTTCCTAGGATGTAACCAAC
1 TTTTCTTAGGATGTAACCAGC
486389 TTTTCTTAGGATGTAACCAGC
1 TTTTCTTAGGATGTAACCAGC
*
486410 TGTTCTT
1 TTTTCTT
486417 GTGAAATTCC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (21 bp):
TTTTCTTAGGATGTAACCAGC
Found at i:493825 original size:54 final size:54
Alignment explanation
Indices: 493634--493810 Score: 282
Period size: 54 Copynumber: 3.3 Consensus size: 54
493624 ACCGAATGGG
*
493634 CACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCATATTGA
1 CACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGA
* * * *
493688 CACTATGTGTGCAACCCACGTAATTCATAATGAGTTTATGAATTACCGTATTGA
1 CACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGA
** *
493742 CACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTTTGTATTGG
1 CACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGA
493796 CACTATGTGTGCAAC
1 CACTATGTGTGCAAC
493811 ACACGTAATT
Statistics
Matches: 111, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 111 1.00
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (54 bp):
CACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGA
Found at i:493891 original size:70 final size:70
Alignment explanation
Indices: 493763--493895 Score: 196
Period size: 70 Copynumber: 1.9 Consensus size: 70
493753 CAACCTAAGA
*** * * *
493763 AATTCATAATGAGTTTATGAATTTTTGTATTGGCACTATGTGTGCAACACACGTAATTCATAACC
1 AATTCATAATGAGTTTATGAATTACCGTATTGGCACTATGTGTACAACACAAGAAATTCATAACC
493828 CACAT
66 CACAT
493833 AATTCATAATGAGTTTATGAATTACCGTATTGGCACTATGTGTACAAC-CTAAGAAATTCATAA
1 AATTCATAATGAGTTTATGAATTACCGTATTGGCACTATGTGTACAACAC-AAGAAATTCATAA
493896 TGAGTTTATG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
69 1 0.02
70 55 0.98
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (70 bp):
AATTCATAATGAGTTTATGAATTACCGTATTGGCACTATGTGTACAACACAAGAAATTCATAACC
CACAT
Found at i:493917 original size:54 final size:54
Alignment explanation
Indices: 493833--493982 Score: 225
Period size: 54 Copynumber: 2.8 Consensus size: 54
493823 TAACCCACAT
493833 AATTCATAATGAGTTTATGAATTACCGTATTGGCACTATGTGTACAAC-CTAAGA
1 AATTCATAATGAGTTTATGAATTACCGTATTGGCACTATGTGTACAACTC-AAGA
*** * *
493887 AATTCATAATGAGTTTATGAATTTTTGTATTGGCACTATGTGTACAACTCACGT
1 AATTCATAATGAGTTTATGAATTACCGTATTGGCACTATGTGTACAACTCAAGA
493941 AATTCATAATGAG--TATGAATTACCGTATTGGCACTATGTGTA
1 AATTCATAATGAGTTTATGAATTACCGTATTGGCACTATGTGTA
493983 TTGGCACTAC
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
52 26 0.30
54 60 0.69
55 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (54 bp):
AATTCATAATGAGTTTATGAATTACCGTATTGGCACTATGTGTACAACTCAAGA
Found at i:493920 original size:124 final size:124
Alignment explanation
Indices: 493700--493949 Score: 455
Period size: 124 Copynumber: 2.0 Consensus size: 124
493690 CTATGTGTGC
* *
493700 AACCCACGTAATTCATAATGAGTTTATGAATTACCGTATTGACACTATGTGTGCAACCTAAGAAA
1 AACCCACATAATTCATAATGAGTTTATGAATTACCGTATTGACACTATGTGTACAACCTAAGAAA
*
493765 TTCATAATGAGTTTATGAATTTTTGTATTGGCACTATGTGTGCAACACACGTAATTCAT
66 TTCATAATGAGTTTATGAATTTTTGTATTGGCACTATGTGTACAACACACGTAATTCAT
*
493824 AACCCACATAATTCATAATGAGTTTATGAATTACCGTATTGGCACTATGTGTACAACCTAAGAAA
1 AACCCACATAATTCATAATGAGTTTATGAATTACCGTATTGACACTATGTGTACAACCTAAGAAA
*
493889 TTCATAATGAGTTTATGAATTTTTGTATTGGCACTATGTGTACAACTCACGTAATTCAT
66 TTCATAATGAGTTTATGAATTTTTGTATTGGCACTATGTGTACAACACACGTAATTCAT
493948 AA
1 AA
493950 TGAGTATGAA
Statistics
Matches: 121, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
124 121 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (124 bp):
AACCCACATAATTCATAATGAGTTTATGAATTACCGTATTGACACTATGTGTACAACCTAAGAAA
TTCATAATGAGTTTATGAATTTTTGTATTGGCACTATGTGTACAACACACGTAATTCAT
Found at i:493954 original size:178 final size:176
Alignment explanation
Indices: 493655--494085 Score: 476
Period size: 178 Copynumber: 2.4 Consensus size: 176
493645 CAACCTAAGA
* * * *
493655 AATTCATAATGAGTTTATGAATTTCCATATTGACACTATGTGTGCAACCCACGTAATTCATAATG
1 AATTCATAATGAGTTTATGAATTACCATATTGACACTATGTGTACAACCCAAGAAATTCATAATG
*
493720 AGTTTATGAATTACCGTATTGACACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAAT
66 AGTTTATGAATTACCGTATTGACACTATGTGTACAACCTAAGAAATTCATAATGAG--TATGAAT
***
493785 TTTTGTATTGGCACTATGTGTGCAACACACGTAATTCATAACCCACAT
129 TACCGTATTGGCACTATGTGTGCAACACACGTAATTCATAACCCACAT
* * *
493833 AATTCATAATGAGTTTATGAATTACCGTATTGGCACTATGTGTACAACCTAAGAAATTCATAATG
1 AATTCATAATGAGTTTATGAATTACCATATTGACACTATGTGTACAACCCAAGAAATTCATAATG
*** * * *
493898 AGTTTATGAATTTTTGTATTGGCACTATGTGTACAA-CTCACGTAATTCATAATGAGTATGAATT
66 AGTTTATGAATTACCGTATTGACACTATGTGTACAACCT-AAGAAATTCATAATGAGTATGAATT
**** * * *
493962 ACCGTATTGGCACTATGTGTATTGGCACTACGT-GTGC--AACCCACGT
130 ACCGTATTGGCACTATGTGT-GCAACAC-ACGTAATTCATAACCCACAT
* * * ** ** * *
494008 AATTCACAAT-AGTTTGTGAATTACCATATTGGCACTATGTGCGCAATGCACGTAATTCATAATG
1 AATTCATAATGAGTTTATGAATTACCATATTGACACTATGTGTACAACCCAAGAAATTCATAATG
*
494072 AGTTTGTGAATTAC
66 AGTTTATGAATTAC
494086 AATATCGGCA
Statistics
Matches: 213, Mismatches: 37, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
174 56 0.26
175 17 0.08
176 25 0.12
177 7 0.03
178 108 0.51
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (176 bp):
AATTCATAATGAGTTTATGAATTACCATATTGACACTATGTGTACAACCCAAGAAATTCATAATG
AGTTTATGAATTACCGTATTGACACTATGTGTACAACCTAAGAAATTCATAATGAGTATGAATTA
CCGTATTGGCACTATGTGTGCAACACACGTAATTCATAACCCACAT
Found at i:493985 original size:15 final size:15
Alignment explanation
Indices: 493965--493996 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
493955 ATGAATTACC
*
493965 GTATTGGCACTATGT
1 GTATTGGCACTACGT
493980 GTATTGGCACTACGT
1 GTATTGGCACTACGT
493995 GT
1 GT
493997 GCAACCCACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.16, G:0.28, T:0.38
Consensus pattern (15 bp):
GTATTGGCACTACGT
Found at i:494048 original size:68 final size:67
Alignment explanation
Indices: 493912--494048 Score: 195
Period size: 67 Copynumber: 2.0 Consensus size: 67
493902 TATGAATTTT
* * * *
493912 TGTATTGGCACTATGTGTACAACTCACGTAATTCATAATGAGTATGAATTACCGTATTGGCACTA
1 TGTATTGGCACTACGTGTACAACCCACGTAATTCACAATGAGTATGAATTACCATATTGGCACTA
493977 TG
66 TG
* *
493979 TGTATTGGCACTACGTGTGCAACCCACGTAATTCACAAT-AGTTTGTGAATTACCATATTGGCAC
1 TGTATTGGCACTACGTGTACAACCCACGTAATTCACAATGAG--TATGAATTACCATATTGGCAC
494043 TATG
64 TATG
494047 TG
1 TG
494049 CGCAATGCAC
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
66 2 0.03
67 35 0.56
68 25 0.40
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (67 bp):
TGTATTGGCACTACGTGTACAACCCACGTAATTCACAATGAGTATGAATTACCATATTGGCACTA
TG
Found at i:494060 original size:120 final size:122
Alignment explanation
Indices: 493859--494101 Score: 294
Period size: 120 Copynumber: 2.0 Consensus size: 122
493849 ATGAATTACC
* * * ****
493859 GTATTGGCACTATGTGTACAACCTAAGAAATTCATAATGAGTTTATGAATTTTTGTATTGGCACT
1 GTATTGGCACTACGTGTACAACCCAAGAAATTCACAATGAGTTTATGAATTACCATATTGGCACT
* ** *
493924 ATGTGTACAACTCACGTAATTCATAATGAG-TATGAATTACCGTATTGGCACTATGT
66 ATGTGCACAACTCACGTAATTCATAATGAGTTATGAATTACAATATCGGCACTATGT
* * * *
493980 GTATTGGCACTACGTGTGCAACCCACGTAATTCACAAT-AGTTTGTGAATTACCATATTGGCACT
1 GTATTGGCACTACGTGTACAACCCAAGAAATTCACAATGAGTTTATGAATTACCATATTGGCACT
* *
494044 ATGTGCGCAA-TGCACGTAATTCATAATGAGTTTGTGAATTACAATATCGGCACTATGT
66 ATGTGCACAACT-CACGTAATTCATAATGAG-TTATGAATTACAATATCGGCACTATGT
494102 ATGCAAAACC
Statistics
Matches: 102, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
119 1 0.01
120 47 0.46
121 32 0.31
122 22 0.22
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (122 bp):
GTATTGGCACTACGTGTACAACCCAAGAAATTCACAATGAGTTTATGAATTACCATATTGGCACT
ATGTGCACAACTCACGTAATTCATAATGAGTTATGAATTACAATATCGGCACTATGT
Found at i:494061 original size:53 final size:54
Alignment explanation
Indices: 493981--494101 Score: 172
Period size: 53 Copynumber: 2.3 Consensus size: 54
493971 GCACTATGTG
* * *
493981 TATTGGCACTACGTGTGCAACCCACGTAATTCACAAT-AGTTTGTGAATTACCA
1 TATTGGCACTATGTGCGCAACCCACGTAATTCACAATGAGTTTGTGAATTACAA
** *
494034 TATTGGCACTATGTGCGCAATGCACGTAATTCATAATGAGTTTGTGAATTACAA
1 TATTGGCACTATGTGCGCAACCCACGTAATTCACAATGAGTTTGTGAATTACAA
*
494088 TATCGGCACTATGT
1 TATTGGCACTATGT
494102 ATGCAAAACC
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
53 32 0.53
54 28 0.47
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (54 bp):
TATTGGCACTATGTGCGCAACCCACGTAATTCACAATGAGTTTGTGAATTACAA
Found at i:494825 original size:17 final size:17
Alignment explanation
Indices: 494803--494836 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
494793 TAGTTGAGAA
494803 ATATTTAAGTTAAGCAT
1 ATATTTAAGTTAAGCAT
494820 ATATTTAAGTTAAGCAT
1 ATATTTAAGTTAAGCAT
494837 TAAATTGTGT
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:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (17 bp):
ATATTTAAGTTAAGCAT
Found at i:496146 original size:46 final size:46
Alignment explanation
Indices: 496055--496147 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
496045 CACTTTAAAC
*
496055 TTCGACTTCGTTATTGATTCTCAAACTGTCAACAAGCCTCCTTTAT
1 TTCGACTTCGTTATTGATTCTCAAACTGTCAACAAGCCTACTTTAT
*
496101 TTCGACTTCGTTATTGATTCTCAAACTGTCAACAAGCCTATTTTAT
1 TTCGACTTCGTTATTGATTCTCAAACTGTCAACAAGCCTACTTTAT
496147 T
1 T
496148 CAATGGAGCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.25, C:0.24, G:0.11, T:0.41
Consensus pattern (46 bp):
TTCGACTTCGTTATTGATTCTCAAACTGTCAACAAGCCTACTTTAT
Found at i:496695 original size:21 final size:21
Alignment explanation
Indices: 496643--496688 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
496633 AAACAATAAT
496643 ATGAGAGTGATTCTGATGATG
1 ATGAGAGTGATTCTGATGATG
496664 ATGAGAGTGATTCTGATGATG
1 ATGAGAGTGATTCTGATGATG
496685 ATGA
1 ATGA
496689 CGATGATGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.04, G:0.33, T:0.33
Consensus pattern (21 bp):
ATGAGAGTGATTCTGATGATG
Found at i:498937 original size:12 final size:12
Alignment explanation
Indices: 498920--498944 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
498910 TTGAAAACGC
498920 ACATGACGTTGG
1 ACATGACGTTGG
498932 ACATGACGTTGG
1 ACATGACGTTGG
498944 A
1 A
498945 GAACCATCAT
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:0.28, C:0.16, G:0.32, T:0.24
Consensus pattern (12 bp):
ACATGACGTTGG
Found at i:501692 original size:12 final size:12
Alignment explanation
Indices: 501675--501699 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
501665 TCTAGTTGGT
501675 CAAACCGACCTC
1 CAAACCGACCTC
501687 CAAACCGACCTC
1 CAAACCGACCTC
501699 C
1 C
501700 TATTCCACCT
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:0.32, C:0.52, G:0.08, T:0.08
Consensus pattern (12 bp):
CAAACCGACCTC
Found at i:503300 original size:13 final size:13
Alignment explanation
Indices: 503271--503305 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
503261 GGGGAGTAAT
*
503271 TTTTCAAAATTGA
1 TTTTCAAAAATGA
503284 -TTTCAAAAATGA
1 TTTTCAAAAATGA
503296 TTTTCAAAAA
1 TTTTCAAAAA
503306 GAAAATCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:508722 original size:54 final size:54
Alignment explanation
Indices: 508641--509151 Score: 576
Period size: 54 Copynumber: 9.5 Consensus size: 54
508631 TGTATTGCAT
* * * *
508641 TTACCGAATGGGCACTATGTGTGCAACCTAAGAAATTCAAAATGAGTTTATGAA
1 TTACCGTATTGGCACTATGTGTGCAACCCAAGAAATTCATAATGAGTTTATGAA
* * * * *
508695 TTTA-TGTATTGGAACTATGTGTGCAACCCAGGTAATTAATAATGAGTTTATGAA
1 -TTACCGTATTGGCACTATGTGTGCAACCCAAGAAATTCATAATGAGTTTATGAA
*
508749 TTACCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAA
1 TTACCGTATTGGCACTATGTGTGCAACCCAAGAAATTCATAATGAGTTTATGAA
*** * * * * * *
508803 TTTTTGTATTGGAACTATGTGTGTAACCCACGTAATTTATAACGAGTTTATGAA
1 TTACCGTATTGGCACTATGTGTGCAACCCAAGAAATTCATAATGAGTTTATGAA
** ** * *
508857 TTATTGTATTGGCACTATGTGCACAACCTAAGAAAATCATAATGAGTTTATGAA
1 TTACCGTATTGGCACTATGTGTGCAACCCAAGAAATTCATAATGAGTTTATGAA
* *
508911 TTACCGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAACGAGTTTATGAA
1 TTACCGTATTGGCACTATGTGTGCAACCCAAGAAATTCATAATGAGTTTATGAA
* * *
508965 TTTCCATATTGGCACTATGTGTGCAACCCAAGTAATTCATAATGAGTTTATGAA
1 TTACCGTATTGGCACTATGTGTGCAACCCAAGAAATTCATAATGAGTTTATGAA
* * * * * *
509019 TTACCGTATTGGCACTGTGTGTACAACCCACGTAATTTATAATGAGTTTTTGAA
1 TTACCGTATTGGCACTATGTGTGCAACCCAAGAAATTCATAATGAGTTTATGAA
* * * * * * *
509073 TTACCATATTGGCACTATATGTGCAA-TCACGTAATTCATAATAAGTTTGTGAA
1 TTACCGTATTGGCACTATGTGTGCAACCCAAGAAATTCATAATGAGTTTATGAA
* * * *
509126 TTACAGTATCGACACTATATGTGCAA
1 TTACCGTATTGGCACTATGTGTGCAA
509152 AACCACAGAA
Statistics
Matches: 389, Mismatches: 66, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
53 48 0.12
54 338 0.87
55 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.34
Consensus pattern (54 bp):
TTACCGTATTGGCACTATGTGTGCAACCCAAGAAATTCATAATGAGTTTATGAA
Found at i:511479 original size:45 final size:45
Alignment explanation
Indices: 511415--511549 Score: 225
Period size: 45 Copynumber: 3.0 Consensus size: 45
511405 GTAAAATTTC
* *
511415 TTACCAGTATACTTGCCATTTATTCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
511460 TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
* *
511505 TTACCAATATACTTACCATTTAATCTCATAAGCTCATAAGCTTAT
1 TTACCAATATACTTACCATTTATTC-CATAAGCTCGTAAGCTTAT
511550 CTGTGTGTTT
Statistics
Matches: 85, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
45 67 0.79
46 18 0.21
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.39
Consensus pattern (45 bp):
TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
Found at i:513817 original size:24 final size:26
Alignment explanation
Indices: 513764--513816 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
513754 ACTAATGACT
513764 AAATCTACATATAATTAACTAATAAA
1 AAATCTACATATAATTAACTAATAAA
* *
513790 AAATCTAAATAATAA-TAAGTAATAAA
1 AAATCTACAT-ATAATTAACTAATAAA
513816 A
1 A
513817 TAAAAGTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.28
Consensus pattern (26 bp):
AAATCTACATATAATTAACTAATAAA
Found at i:513845 original size:43 final size:42
Alignment explanation
Indices: 513783--513863 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 42
513773 TATAATTAAC
*
513783 TAATAAAAAATCTAAATAATAATAA-GTAATAAAATAAAAGTGG
1 TAATAAAAAATCTAAATAAT-ATAATATAAT-AAATAAAAGTGG
*
513826 TAATAATAAAT-TAATATAATATAATATAATAAATAAAA
1 TAATAAAAAATCTAA-ATAATATAATATAATAAATAAAA
513864 TTTGAGATGG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
42 15 0.44
43 19 0.56
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.30
Consensus pattern (42 bp):
TAATAAAAAATCTAAATAATATAATATAATAAATAAAAGTGG
Found at i:516235 original size:18 final size:18
Alignment explanation
Indices: 516202--516236 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
516192 AATTAACTAA
516202 TAATAGAAATATAAATAT
1 TAATAGAAATATAAATAT
516220 TAATAAGAAATA-AAATA
1 TAAT-AGAAATATAAATA
516237 AAAATGGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
TAATAGAAATATAAATAT
Found at i:518244 original size:90 final size:88
Alignment explanation
Indices: 518130--518299 Score: 277
Period size: 90 Copynumber: 1.9 Consensus size: 88
518120 TCCCGAATAT
*
518130 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTCAAATAATAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTCAAATAATAAAA-CCCTAATATGATTAG
518195 GGTAACTTGGATATAAGAGGATTA
65 GGTAACTTGGATATAAGAGGATTA
* *
518219 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATTTGATTAG
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTCAAATAATAAAACCCTAATATGATTAG
* *
518284 GGTAAGTTGGCTATAA
65 GGTAACTTGGATATAA
518300 AAGGGTGTGT
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
89 35 0.47
90 40 0.53
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (88 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTCAAATAATAAAACCCTAATATGATTAGG
GTAACTTGGATATAAGAGGATTA
Found at i:518773 original size:8 final size:8
Alignment explanation
Indices: 518760--518785 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
518750 CCCGCAACGA
518760 TTAATATG
1 TTAATATG
518768 TTAATATG
1 TTAATATG
518776 TTAATATG
1 TTAATATG
518784 TT
1 TT
518786 TTTCAATCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (8 bp):
TTAATATG
Found at i:523534 original size:31 final size:30
Alignment explanation
Indices: 523432--523535 Score: 91
Period size: 31 Copynumber: 3.3 Consensus size: 30
523422 ATTGGAGTTG
* ** *
523432 CTTTTATTTAGCATGCATCCATGTAAGATGA
1 CTTTTATTTAACATGCATCCAAAT-TGATGA
* *
523463 CTTTTATTTAACATGCACCCAAAATTGAGCGA
1 CTTTTATTTAACATGCATCC-AAATTGA-TGA
* *
523495 CTTTTATTTATCATGCATCCACATTGGATGA
1 CTTTTATTTAACATGCATCCAAATT-GATGA
*
523526 GTTTTATTTA
1 CTTTTATTTA
523536 GCATAGTATA
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
31 35 0.59
32 24 0.41
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.40
Consensus pattern (30 bp):
CTTTTATTTAACATGCATCCAAATTGATGA
Found at i:536968 original size:8 final size:8
Alignment explanation
Indices: 536955--536980 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
536945 CCCGCAATGA
536955 TTAATATG
1 TTAATATG
536963 TTAATATG
1 TTAATATG
536971 TTAATATG
1 TTAATATG
536979 TT
1 TT
536981 TTTCAATCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (8 bp):
TTAATATG
Found at i:539678 original size:3 final size:3
Alignment explanation
Indices: 539670--539708 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
539660 CTCATAAGCC
539670 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
539709 GGAACAACTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:541770 original size:31 final size:30
Alignment explanation
Indices: 541668--541771 Score: 91
Period size: 31 Copynumber: 3.3 Consensus size: 30
541658 ATTGGAGTTG
* ** *
541668 CTTTTATTTAGCATGCATCCATGTAAGATGA
1 CTTTTATTTAACATGCATCCAAAT-TGATGA
* *
541699 CTTTTATTTAACATGCACCCAAAATTGAGCGA
1 CTTTTATTTAACATGCATCC-AAATTGA-TGA
* *
541731 CTTTTATTTATCATGCATCCACATTGGATGA
1 CTTTTATTTAACATGCATCCAAATT-GATGA
*
541762 GTTTTATTTA
1 CTTTTATTTA
541772 GCATAGTATA
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
31 35 0.59
32 24 0.41
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.40
Consensus pattern (30 bp):
CTTTTATTTAACATGCATCCAAATTGATGA
Found at i:554441 original size:59 final size:59
Alignment explanation
Indices: 554374--554519 Score: 193
Period size: 59 Copynumber: 2.5 Consensus size: 59
554364 ATTCTCTACT
* *
554374 GGAAATGTTAATCCCTCGAGTGAGGTGTCGCTAATTCGAAATGATGTGAATCAAGAAAA
1 GGAAATGTTAATCCCTCGAGTAAGGCGTCGCTAATTCGAAATGATGTGAATCAAGAAAA
* * * * * * *
554433 GGAAATGTTAATCCCTCGAGTAAGGCGTTGCTGATTCGAAGTGTTGTGAATCGAGCAAT
1 GGAAATGTTAATCCCTCGAGTAAGGCGTCGCTAATTCGAAATGATGTGAATCAAGAAAA
* *
554492 GGAAATGTTAATCCCTCAAGTCAGGCGT
1 GGAAATGTTAATCCCTCGAGTAAGGCGT
554520 AGTTTATTTT
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 76 1.00
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.27
Consensus pattern (59 bp):
GGAAATGTTAATCCCTCGAGTAAGGCGTCGCTAATTCGAAATGATGTGAATCAAGAAAA
Found at i:554657 original size:38 final size:37
Alignment explanation
Indices: 554560--554749 Score: 143
Period size: 38 Copynumber: 5.1 Consensus size: 37
554550 GTGATAAGCT
* *
554560 TTTTGTTTCAAGTGAAACTATCTTAAGCGAGATAAAAT-
1 TTTTG-TTCGAGTGAAACTATCTCAAGCGAGAT-AAATC
* ** *
554598 TTGTT-TT-AAGAAAAACAATCTCAAGCGAGATAAATC
1 TT-TTGTTCGAGTGAAACTATCTCAAGCGAGATAAATC
* * *
554634 TTTTGTTACGAGTGACACTATCTCAAGTGAGATAACTC
1 TTTTGTT-CGAGTGAAACTATCTCAAGCGAGATAAATC
* * * **
554672 TTCTGTTTTGAGTGAAACTATCTCATGCGAGATAAAAAA
1 TTTTG-TTCGAGTGAAACTATCTCAAGCGAGAT-AAATC
* * * *
554711 ATTTCTTCGAGTGAAACTATCTCAAGTGAGATGAATC
1 TTTTGTTCGAGTGAAACTATCTCAAGCGAGATAAATC
554748 TT
1 TT
554750 GTTTTAAGAA
Statistics
Matches: 116, Mismatches: 29, Indels: 15
0.73 0.18 0.09
Matches are distributed among these distances:
35 6 0.05
36 24 0.21
37 5 0.04
38 73 0.63
39 8 0.07
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (37 bp):
TTTTGTTCGAGTGAAACTATCTCAAGCGAGATAAATC
Found at i:556825 original size:23 final size:23
Alignment explanation
Indices: 556798--556847 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
556788 AATATCAAAT
*
556798 ATAAA-CATAAATCCACCATTAAA
1 ATAAAGCATAAA-CAACCATTAAA
**
556821 ATAAAGTTTAAACAACCATTAAA
1 ATAAAGCATAAACAACCATTAAA
556844 ATAA
1 ATAA
556848 CTCACACCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.58, C:0.16, G:0.02, T:0.24
Consensus pattern (23 bp):
ATAAAGCATAAACAACCATTAAA
Found at i:557484 original size:18 final size:18
Alignment explanation
Indices: 557461--557508 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
557451 ACCACCAACA
*
557461 ACAACACCTTTCTCTCAT
1 ACAACACCTTTATCTCAT
557479 ACAACACCTTTATCTCAT
1 ACAACACCTTTATCTCAT
557497 ACAACACCTTTA
1 ACAACACCTTTA
557509 AGATATAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.31
Consensus pattern (18 bp):
ACAACACCTTTATCTCAT
Found at i:559564 original size:37 final size:37
Alignment explanation
Indices: 559472--559574 Score: 125
Period size: 37 Copynumber: 2.8 Consensus size: 37
559462 TTTTCGTCCT
**
559472 ACTAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 ACTAGGATTCAAACTCCTAAAAATAGGATAAAATTCA
* * *
559509 GCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTCA
1 ACTAGGATTCAAACTCCTAAAAATAGGATAAAATTCA
* * * *
559546 ACTAAGATTTAAATTCCTAAAGATAGGAT
1 ACTAGGATTCAAACTCCTAAAAATAGGAT
559575 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.28
Consensus pattern (37 bp):
ACTAGGATTCAAACTCCTAAAAATAGGATAAAATTCA
Found at i:559973 original size:18 final size:17
Alignment explanation
Indices: 559934--559976 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
559924 ATTATATGGA
559934 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
559950 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
559968 TATTATTAT
1 TATTATTAT
559977 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:560287 original size:11 final size:10
Alignment explanation
Indices: 560223--560284 Score: 58
Period size: 10 Copynumber: 6.1 Consensus size: 10
560213 ATCTTATAAC
560223 TTTATA-TA-
1 TTTATATTAT
560231 TTTATATTAT
1 TTTATATTAT
*
560241 TTTTTATTAT
1 TTTATATTAT
560251 TTTCATATT-T
1 TTT-ATATTAT
560261 TTTATTCATTAT
1 TTTA-T-ATTAT
560273 TATTATATTAT
1 T-TTATATTAT
560284 T
1 T
560285 ATTTTTTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
8 6 0.13
9 3 0.07
10 17 0.38
11 13 0.29
12 3 0.07
13 3 0.07
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTATATTAT
Found at i:564930 original size:192 final size:191
Alignment explanation
Indices: 564601--565005 Score: 675
Period size: 192 Copynumber: 2.1 Consensus size: 191
564591 TATAAAGATG
564601 AGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCAAAAGCCCTGGCTTTATGAATAGATCG
1 AGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCAAAAGCCCTGGCTTTATGAATAGATCG
*
564666 CATTCAAACCATGACATTGCTCGGACACTTGGCGATTCGGTGTTTGCTCCACTGCTTTTGTCAGG
66 CATTCAAACCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTTTTGTCAGG
* * **
564731 TTGAAGACTTTGTGATGAGATGAACCCTTCAGTTAAGCCTAATAAAGGTGATTATAATATTA
131 CTGAAGACTTTGTGATGAGATGAACCCTTCAGTTAAACCTAATAAAAAT-ATTATAATATTA
* *
564793 AGCTATTCCACTAAGGCAATTGGTTATATAGGAAACTCAAAAGCCCTGGCTTTATGAATAGATTG
1 AGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCAAAAGCCCTGGCTTTATGAATAGATCG
* *
564858 CATTCAATCCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTTTTTTCAGG
66 CATTCAAACCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTTTTGTCAGG
*
564923 CTGAAGACTTTGTGATGAGATGAACCCTTCAGTTAAACCTGATAAAAATATTATAATATTA
131 CTGAAGACTTTGTGATGAGATGAACCCTTCAGTTAAACCTAATAAAAATATTATAATATTA
* * * *
564984 AGCTGTCCCTCTAAAGCAATTG
1 AGCTATTCCACTAAGGCAATTG
565006 ATTTAATGCC
Statistics
Matches: 199, Mismatches: 14, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
191 30 0.15
192 169 0.85
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (191 bp):
AGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCAAAAGCCCTGGCTTTATGAATAGATCG
CATTCAAACCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTTTTGTCAGG
CTGAAGACTTTGTGATGAGATGAACCCTTCAGTTAAACCTAATAAAAATATTATAATATTA
Found at i:566168 original size:73 final size:76
Alignment explanation
Indices: 566073--566235 Score: 221
Period size: 73 Copynumber: 2.2 Consensus size: 76
566063 ATGCAGATGA
* **
566073 TTATCTCACTCAA-ATTTGTTTTTCTTAAAAC-ATACTTTGTCTCACTTGAG-TCTGTTTTTTCT
1 TTATTTCACTCAAGATTTGTTTTTCTTAAAACAATA-TTTGTCTCACTTGAGATC-GTTTTCACT
566135 CGAAAGAA-G-AT
64 CGAAAGAAGGCAT
*
566146 TTATTTCACTCAAGATTT-TTTTTCTTAAAACAATATTTGTCTCGCTTGAGATCGTTTTCACTCG
1 TTATTTCACTCAAGATTTGTTTTTCTTAAAACAATATTTGTCTCACTTGAGATCGTTTTCACTCG
566210 AAAGAAGGCAT
66 AAAGAAGGCAT
566221 TTCATTTCACTCAAG
1 TT-ATTTCACTCAAG
566236 GCTGTTTTTT
Statistics
Matches: 80, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
73 54 0.68
74 10 0.12
75 4 0.05
76 12 0.15
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (76 bp):
TTATTTCACTCAAGATTTGTTTTTCTTAAAACAATATTTGTCTCACTTGAGATCGTTTTCACTCG
AAAGAAGGCAT
Found at i:566308 original size:39 final size:39
Alignment explanation
Indices: 566265--566413 Score: 115
Period size: 39 Copynumber: 3.6 Consensus size: 39
566255 TTTTATCTTG
*
566265 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
* * *
566304 CTTGAGACAGTTTCTCTTGAAAACATTTCCCTTG-AAATTAAT-TCTCTC
1 CTTGAGACAGTTTCCCTCG-AAACA--------GAAAATT-TTGTCTC-C
*
566352 C-TGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
* *
566390 CTTGAGACAGTTTCTCTTGAAACA
1 CTTGAGACAGTTTCCCTCGAAACA
566414 TAATTGAAAA
Statistics
Matches: 85, Mismatches: 11, Indels: 28
0.69 0.09 0.23
Matches are distributed among these distances:
38 4 0.05
39 44 0.52
40 5 0.06
46 5 0.06
47 23 0.27
48 4 0.05
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (39 bp):
CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
Found at i:566493 original size:104 final size:101
Alignment explanation
Indices: 566320--566621 Score: 404
Period size: 104 Copynumber: 3.0 Consensus size: 101
566310 ACAGTTTCTC
* *
566320 TTGAAAACATTTCCCTTGAAATTAA---T-TCTCTCCTGAGATAGTTTCCCTCGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
566381 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAA
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAA
* * *
566417 TTGAAAACATTTCCCTTGAAATGATTTTTTCTCTCTCTCTTGAGATAGTTTCCCTCAAAACAGAA
1 TTGAAAACATTTCCCTTGAAATGA--ATTT-TATCTCTCTTGAGATAGTTTCCCTCGAAACAGAA
*
566482 AATTTTGTCTCCCTTGAGACATTTTCTCTTGAAACATAAACA
63 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAT--A-A
*
566524 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAGTTTCCCAT-GAAAC-G--AA
1 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCTCTTGAGATAGTTTCCC-TCGAAACAGAAAA
**
566585 TTTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAA
65 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAA
566622 ACTTTGAAAA
Statistics
Matches: 182, Mismatches: 12, Indels: 21
0.85 0.06 0.10
Matches are distributed among these distances:
97 23 0.13
98 1 0.01
99 1 0.01
101 34 0.19
103 2 0.01
104 91 0.50
105 4 0.02
106 1 0.01
107 25 0.14
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (101 bp):
TTGAAAACATTTCCCTTGAAATGAATTTTATCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAA
Found at i:566580 original size:36 final size:36
Alignment explanation
Indices: 566533--566608 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
566523 ATTGAAAACA
* * * *
566533 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCATGAAACGAATTTTATCTCCCTTGAGACAG
*
566569 TTTCCCATGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCATGAAACGAATTTTATCTCCCTTGAGACAG
566605 TTTC
1 TTTC
566609 TCTCCAAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (36 bp):
TTTCCCATGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:567005 original size:105 final size:105
Alignment explanation
Indices: 566808--567433 Score: 867
Period size: 105 Copynumber: 6.0 Consensus size: 105
566798 ATATCGTGAC
* * * * *
566808 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTTAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTC
*
566873 AATTTCAGAGCCAATTTCAATTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
566914 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
* *
566979 ATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTAG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
567019 ACTTCAGACAACGCAAGTTCAACTTCACGACGAATGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
*
567084 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
567124 ACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
* *
567185 A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
567224 ACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
* *
567285 A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * * *
567324 AGTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTC
** * * *
567389 GGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
567430 ACTC
1 ACTC
567434 GGAACAATGC
Statistics
Matches: 477, Mismatches: 37, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
100 181 0.38
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 199 0.42
106 84 0.18
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:568029 original size:37 final size:37
Alignment explanation
Indices: 567976--568080 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
567966 CATTTTCGTC
567976 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
568013 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
568050 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
568081 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:568463 original size:17 final size:18
Alignment explanation
Indices: 568441--568479 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
568431 TATGGATATT
568441 TTATTCAT-TTATTTTTA
1 TTATTCATGTTATTTTTA
568458 TTATTCATGTTATTTTTA
1 TTATTCATGTTATTTTTA
568476 TTAT
1 TTAT
568480 ATGTATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (18 bp):
TTATTCATGTTATTTTTA
Found at i:568572 original size:23 final size:23
Alignment explanation
Indices: 568503--568572 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
568493 TATATTAAAT
*
568503 TATTTTCATTTATTTTTTTAC-TA
1 TATTTTC-TTTATTATTTTACTTA
* *
568526 TATTTT-ATTATTATTATA-TATA
1 TATTTTCTTTATTATTTTACT-TA
*
568548 TATTTTCTTTAATATTTTACTTA
1 TATTTTCTTTATTATTTTACTTA
568571 TA
1 TA
568573 AGTCTAATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
21 9 0.24
22 8 0.22
23 19 0.51
24 1 0.03
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.66
Consensus pattern (23 bp):
TATTTTCTTTATTATTTTACTTA
Found at i:568752 original size:16 final size:16
Alignment explanation
Indices: 568733--568783 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
568723 TAACTTTATA
568733 TATTTATATTATTTTT
1 TATTTATATTATTTTT
*
568749 TA-TTATTTTCATTTTT
1 TATTTATATT-ATTTTT
*
568765 TATTCATTATTATTTTT
1 TATTTA-TATTATTTTT
568782 TA
1 TA
568784 AAAAAAAACC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.21
16 10 0.34
17 10 0.34
18 3 0.10
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.73
Consensus pattern (16 bp):
TATTTATATTATTTTT
Found at i:568979 original size:2 final size:2
Alignment explanation
Indices: 568972--568999 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
568962 TAATACTTTG
568972 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
569000 TTTTTTCCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:570210 original size:27 final size:26
Alignment explanation
Indices: 570119--570219 Score: 107
Period size: 27 Copynumber: 3.8 Consensus size: 26
570109 AAATGAGAGG
*
570119 GAGAAA-GTAAAAGTTACAAATGAAA
1 GAGAAATGTAAAAGTTAAAAATGAAA
570144 GAGAAATAAG-AAAAGTTAAAAATGAAA
1 GAGAAAT--GTAAAAGTTAAAAATGAAA
* *
570171 GAGACATGGAAAAGGTTAAAAATGAAA
1 GAGAAATGTAAAA-GTTAAAAATGAAA
* *
570198 TAGAAATGTAAAAATTTAAAAA
1 GAGAAATGT-AAAAGTTAAAAA
570220 AATTGAGAGG
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
25 7 0.11
26 4 0.06
27 48 0.75
28 5 0.08
ACGTcount: A:0.61, C:0.02, G:0.19, T:0.18
Consensus pattern (26 bp):
GAGAAATGTAAAAGTTAAAAATGAAA
Found at i:570385 original size:26 final size:24
Alignment explanation
Indices: 570330--570379 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
570320 ATGATAGGAC
570330 AAAACAATGGAGAGAGAAAAGTAA
1 AAAACAATGGAGAGAGAAAAGTAA
*
570354 AAAACAGTGGAGAGAGAAAAGTAA
1 AAAACAATGGAGAGAGAAAAGTAA
570378 AA
1 AA
570380 GAAACAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.62, C:0.04, G:0.26, T:0.08
Consensus pattern (24 bp):
AAAACAATGGAGAGAGAAAAGTAA
Found at i:579155 original size:16 final size:16
Alignment explanation
Indices: 579134--579164 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
579124 TTATTATTAT
579134 TATTTTAATGAATGAA
1 TATTTTAATGAATGAA
*
579150 TATTTTAATGTATGA
1 TATTTTAATGAATGA
579165 TTTGGAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (16 bp):
TATTTTAATGAATGAA
Found at i:587608 original size:2 final size:2
Alignment explanation
Indices: 587601--587648 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
587591 TATGCACATT
587601 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
587643 T- TA TA T
1 TA TA TA T
587649 TCATTTATGG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:588037 original size:81 final size:81
Alignment explanation
Indices: 587901--588793 Score: 1140
Period size: 81 Copynumber: 11.1 Consensus size: 81
587891 AGACATTTAG
* * * * *
587901 TCTTTTACCCAAAGGTATTTAACTTTTCATCTAACT-AGCATGATTAACACCTTTCT-TCCAAAG
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGA-CATAATTGACACCTTTCTAT-CAAAT
* ** *
587964 GCACAATTAGGCTTTTAG
64 GCACAACTAGGCCATTAA
* * * *
587982 TCTTTTACTCAAAGTTATTTAACCTTTCATCTAATTGAAATAATTGACACATTTCTATCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACCTTTCTATCAAATGC
* *
588047 ACAGCTAGACCATTAA
66 ACAACTAGGCCATTAA
* *
588063 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAA-TTAGCATAATTGACACCATTCTATCAAATG
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGA-CATAATTGACACCTTTCTATCAAATG
*
588127 CACAGCTAGGCCATTAA
65 CACAACTAGGCCATTAA
* * * * *
588144 TATTTTACTCAAAGGTATTTAACATTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACCTTTCTATCAAATGC
588209 ACAACTAGGCCATTAA
66 ACAACTAGGCCATTAA
* * * * *
588225 TCTTTTAATCAAAGGTATTTAATCTTTCATCTAATTGGCATAATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACCTTTCTATCAAATGC
* *
588290 ACAGCTAGGCAATTAA
66 ACAACTAGGCCATTAA
* * * * *
588306 TATTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTTTGTCAAATAC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACCTTTCTATCAAATGC
588371 ACAACTAGGCCATTAA
66 ACAACTAGGCCATTAA
*
588387 TCTTTTACTCAAAGGTATTTAACATTTCATCTAACTG-CATAATTGACACCTTTCTATCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACCTTTCTATCAAATGC
* *
588451 ACAGCTAGGCCGTTAA
66 ACAACTAGGCCATTAA
* * *
588467 TATTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGA-AAAAATGACACCTTTC-AGTCAAAT
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACT-GACATAATTGACACCTTTCTA-TCAAAT
*
588530 GCACAGCTAGGCCATTAA
64 GCACAACTAGGCCATTAA
* * * * *
588548 TCTTTTACTCAAAGGTATCTAGCCTTTCATCTAACT-AGCATAATTGACTCCTTTATGTCAAATG
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGA-CATAATTGACACCTTTCTATCAAATG
* *
588612 CACAACCATGCCATTAA
65 CACAACTAGGCCATTAA
* *
588629 TCTTTTACTCAAATGTATTTAACCTTTCATCTAACTG-CATAATTGACACCTTTCTATCAAACGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACCTTTCTATCAAATGC
588693 ACAGA-TAGGCCATTAA
66 ACA-ACTAGGCCATTAA
* * * *
588709 TCTTTTACTTAAAAGTATTTAACCTTTCATATAACTG-CATAATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACCTTTCTATCAAATGC
* *
588773 ATAACAAGGCCATTAA
66 ACAACTAGGCCATTAA
588789 TCTTT
1 TCTTT
588794 ATTTTAGAAC
Statistics
Matches: 715, Mismatches: 84, Indels: 27
0.87 0.10 0.03
Matches are distributed among these distances:
79 2 0.00
80 186 0.26
81 524 0.73
82 3 0.00
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.35
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACCTTTCTATCAAATGC
ACAACTAGGCCATTAA
Found at i:588557 original size:242 final size:243
Alignment explanation
Indices: 587870--588793 Score: 1216
Period size: 242 Copynumber: 3.8 Consensus size: 243
587860 CCAGTGGCAT
* * * * * * *
587870 CTTTATGTAAAATGCACCATTA-GACATTTAGTCTTTTACCCAAAGGTATTTAACTTTTCATCTA
1 CTTTATGTCAAATGCACAACTAGGCCA-TTAATCTTTTACTCAAAGGTATTTAACATTTCATCTA
* * * * ** * *
587934 ACTAGCATGATTAACACCTTTCT-TCCAAAGGCACAATTAGGCTTTTAGTCTTTTACTCAAAGTT
65 ACTAGCATAATTGACACCTTTCTAT-CAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGT
* * *
587998 ATTTAACCTTTCATCTAA-TTGAAATAATTGACACATTTCTA-TCAAATGCACAGCTAGACCATT
129 ATTTAACCTTTCATCTAACTGGAAA-AATTGACACCTTTC-AGTCAAATGCACAGCTAGGCCATT
*
588061 AATCTTTTACTCAAAGGTATTTAACCTTTCATCTAATTAGCATAATTGACAC
192 AATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATAATTGACAC
* * * * *
588113 CATTCTATCAAATGCACAGCTAGGCCATTAATATTTTACTCAAAGGTATTTAACATTTCATCTAA
1 CTTTATGTCAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTAA
* * * *
588178 CTGGCATAATTGACACATTTCTGTCAAATGCACAACTAGGCCATTAATCTTTTAATCAAAGGTAT
66 CTAGCATAATTGACACCTTTCTATCAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTAT
* * * * * * *
588243 TTAATCTTTCATCTAATTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATA
131 TTAACCTTTCATCTAACTGGAAAAATTGACACCTTTCAGTCAAATGCACAGCTAGGCCATTAATC
*
588308 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACAC
196 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATAATTGACAC
* *
588356 CTTTTTGTCAAATACACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTAA
1 CTTTATGTCAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTAA
* * *
588421 CT-GCATAATTGACACCTTTCTATCAAATGCACAGCTAGGCCGTTAATATTTTACTCAAAGGTAT
66 CTAGCATAATTGACACCTTTCTATCAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTAT
*
588485 TTAACCTTTCATCTAACTGGAAAAAATGACACCTTTCAGTCAAATGCACAGCTAGGCCATTAATC
131 TTAACCTTTCATCTAACTGGAAAAATTGACACCTTTCAGTCAAATGCACAGCTAGGCCATTAATC
* * *
588550 TTTTACTCAAAGGTATCTAGCCTTTCATCTAACTAGCATAATTGACTC
196 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATAATTGACAC
* * * *
588598 CTTTATGTCAAATGCACAACCATGCCATTAATCTTTTACTCAAATGTATTTAACCTTTCATCTAA
1 CTTTATGTCAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTAA
* * *
588663 CT-GCATAATTGACACCTTTCTATCAAACGCACAGA-TAGGCCATTAATCTTTTACTTAAAAGTA
66 CTAGCATAATTGACACCTTTCTATCAAATGCACA-ACTAGGCCATTAATCTTTTACTCAAAGGTA
* * * * * * *
588726 TTTAACCTTTCATATAACT-GCATAATTGACACCTTTCTGTCAAATGCATAACAAGGCCATTAAT
130 TTTAACCTTTCATCTAACTGGAAAAATTGACACCTTTCAGTCAAATGCACAGCTAGGCCATTAAT
588790 CTTT
195 CTTT
588794 ATTTTAGAAC
Statistics
Matches: 598, Mismatches: 78, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
241 42 0.07
242 290 0.48
243 259 0.43
244 7 0.01
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.35
Consensus pattern (243 bp):
CTTTATGTCAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTAA
CTAGCATAATTGACACCTTTCTATCAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTAT
TTAACCTTTCATCTAACTGGAAAAATTGACACCTTTCAGTCAAATGCACAGCTAGGCCATTAATC
TTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATAATTGACAC
Found at i:588962 original size:55 final size:55
Alignment explanation
Indices: 588872--589060 Score: 297
Period size: 55 Copynumber: 3.4 Consensus size: 55
588862 TACAATAATA
* * * *
588872 CATAAACTTTTTATGAATTTCTTAGTTTTGTACACACAATGCCCATTCAGAAATT
1 CATAAACTTATTATGAATTTCTTAGTTTTGCACACACAATGCCCATACTGAAATT
* *
588927 CATTAACTTATTATGAATTTCTTAGTTTTGCACACACAATTCCCATACTGAAATT
1 CATAAACTTATTATGAATTTCTTAGTTTTGCACACACAATGCCCATACTGAAATT
* *
588982 CATAAACTTATTATGAATTTCTTAGTTTTGCACGCACAGTGCCCATACTGAAATT
1 CATAAACTTATTATGAATTTCTTAGTTTTGCACACACAATGCCCATACTGAAATT
*
589037 CATAAACTTATTATGCATTTCTTA
1 CATAAACTTATTATGAATTTCTTA
589061 TTCTACACGC
Statistics
Matches: 123, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 123 1.00
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (55 bp):
CATAAACTTATTATGAATTTCTTAGTTTTGCACACACAATGCCCATACTGAAATT
Found at i:593727 original size:81 final size:81
Alignment explanation
Indices: 593561--594210 Score: 887
Period size: 81 Copynumber: 8.1 Consensus size: 81
593551 AGACATTTAG
* * * * * * *
593561 TCTTTTACCCAAAAGTATTTAACCTTTCATTTAACTGCCAT-GTTGACACCTTTCTGCCAAAGGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGC
* ** **
593625 ACAGTTAGGCTTTTTG
66 ACAGCTAGGCCATTAA
* * *
593641 TCTTTTACTCAAAGGTATATAACCATTCATCTAACTGACATAATTGACACCTTTCTGTCAAATTC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGC
*
593706 ACAACTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* *
593722 TCTTTTACTGAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGC
*
593787 ATAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * *
593803 TCTTTTACTCAAAAGTATTTAATCTTTCATCTAACT-AGCATAATTGACACCTTTCTGTCAAATA
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGA-CATAATTGACACCTTTCTGTCAAATG
* *
593867 CACAACTAGCCCATTAA
65 CACAGCTAGGCCATTAA
* * *
593884 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACT-AGTATAATTAACACATTTCTGTCAAATG
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGA-CATAATTGACACCTTTCTGTCAAATG
*
593948 CACAGTTAGGCCATTAA
65 CACAGCTAGGCCATTAA
* * * * *
593965 TATTTTACTTAAAGGTATTTAACATTTCATCTAACTGGCATAATTGACAACTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGC
594030 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* *
594046 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTTACATAATTGACACCTTTCTGTTAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGC
* *
594111 ATAGCTAGACCATTAA
66 ACAGCTAGGCCATTAA
* *
594127 TCTTTTACT--AAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGC
*
594190 ACAACTAGGCCATTAA
66 ACAGCTAGGCCATTAA
594206 TCTTT
1 TCTTT
594211 ATTTTAGAAC
Statistics
Matches: 502, Mismatches: 65, Indels: 7
0.87 0.11 0.01
Matches are distributed among these distances:
79 68 0.14
80 35 0.07
81 399 0.79
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.36
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGC
ACAGCTAGGCCATTAA
Found at i:594351 original size:55 final size:55
Alignment explanation
Indices: 594292--594494 Score: 284
Period size: 55 Copynumber: 3.7 Consensus size: 55
594282 GATAATACAG
*
594292 AAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATTCAAAAATTAAT
1 AAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACAAAAATTAAT
* * * *
594347 AAACTTATTATGAATTTTTTAGTTTTGCACACACAATACCCATACAAAAATTGAT
1 AAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACAAAAATTAAT
* ** **
594402 AAACTTATTATGAATTTCTTAGTTTTGCACACACATTGCCCATACTGAAATTCTT
1 AAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACAAAAATTAAT
* *
594457 AAACTTA-TATGAATTTCTTA-TTTTGCACGCATAGTGCC
1 AAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCC
594495 ATTTGGTAAT
Statistics
Matches: 133, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
53 15 0.11
54 13 0.10
55 105 0.79
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.38
Consensus pattern (55 bp):
AAACTTATTATGAATTTCTTAGTTTTGCACACACAGTGCCCATACAAAAATTAAT
Found at i:594896 original size:42 final size:41
Alignment explanation
Indices: 594832--594923 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 41
594822 CCATAACATT
* *
594832 GTATCGATACTTCTATACTATGGTACCAATACCTTCCTCTCA
1 GTATCGATACTACTATACTATGGTACCAATA-CTCCCTCTCA
* * * *
594874 GTATCGATACTACTATATTATGGTACCGATACTCCCTTTCG
1 GTATCGATACTACTATACTATGGTACCAATACTCCCTCTCA
594915 GTATCGATA
1 GTATCGATA
594924 ACATTTTGGC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 16 0.36
42 28 0.64
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (41 bp):
GTATCGATACTACTATACTATGGTACCAATACTCCCTCTCA
Found at i:597593 original size:17 final size:17
Alignment explanation
Indices: 597563--597596 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
597553 TAATGAATTT
*
597563 GGTATGTTATAATATAA
1 GGTATGTTAGAATATAA
*
597580 GGTATGTTGGAATATAA
1 GGTATGTTAGAATATAA
597597 TATTGGCGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (17 bp):
GGTATGTTAGAATATAA
Found at i:600585 original size:20 final size:20
Alignment explanation
Indices: 600560--600597 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
600550 AATGAGCTTA
600560 AAATCT-AAGGTTTTAATTAC
1 AAATCTAAAGG-TTTAATTAC
600580 AAATCTAAAGGTTTAATT
1 AAATCTAAAGGTTTAATT
600598 TTAACATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (20 bp):
AAATCTAAAGGTTTAATTAC
Found at i:603175 original size:11 final size:11
Alignment explanation
Indices: 603168--603300 Score: 75
Period size: 11 Copynumber: 12.6 Consensus size: 11
603158 CTGTTTTTTC
*
603168 TTTCTTTTTATT
1 TTTCTTTCT-TT
*
603180 TTTCCTTCTTT
1 TTTCTTTCTTT
*
603191 TTTCCTTCTTT
1 TTTCTTTCTTT
*
603202 TTTCCTTCTTT
1 TTTCTTTCTTT
*
603213 TTTCCTT-TTT
1 TTTCTTTCTTT
*
603223 TTCCTTT-TTT
1 TTTCTTTCTTT
*
603233 TCTT-TTTCCTT
1 T-TTCTTTCTTT
*
603244 TATCTTTC-TT
1 TTTCTTTCTTT
* *
603254 CTTCTTTCTTA
1 TTTCTTTCTTT
*
603265 CTT-TTTC-TT
1 TTTCTTTCTTT
*
603274 TTTCTTTCTTA
1 TTTCTTTCTTT
*
603285 TTT-TTTC-CT
1 TTTCTTTCTTT
603294 TTTCTTT
1 TTTCTTT
603301 TTAGTAACAG
Statistics
Matches: 99, Mismatches: 15, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
9 6 0.06
10 39 0.39
11 47 0.47
12 7 0.07
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTCTTTCTTT
Found at i:603188 original size:20 final size:21
Alignment explanation
Indices: 603165--603294 Score: 87
Period size: 20 Copynumber: 6.1 Consensus size: 21
603155 TTCCTGTTTT
603165 TTCTTTCTTT-TTATTTTTCC
1 TTCTTTCTTTCTTATTTTTCC
*
603185 TTCTTT-TTTCCTTCTTTTTTCC
1 TTCTTTCTTT-CTT-ATTTTTCC
603207 TTCTTT-TTTCCTT-TTTTTCC
1 TTCTTTCTTT-CTTATTTTTCC
* *
603227 TTTTTTTCTTTTTCCTTTATCTTT-C
1 -TTCTTTC--TTT-C-TTATTTTTCC
603252 TTC-TTCTTTCTTACTTTTT-C
1 TTCTTTCTTTCTTA-TTTTTCC
603272 TT-TTTCTTTCTTATTTTTTCC
1 TTCTTTCTTTCTTA-TTTTTCC
603293 TT
1 TT
603295 TTCTTTTTAG
Statistics
Matches: 92, Mismatches: 6, Indels: 23
0.76 0.05 0.19
Matches are distributed among these distances:
19 6 0.07
20 36 0.39
21 13 0.14
22 20 0.22
23 3 0.03
24 7 0.08
25 3 0.03
26 4 0.04
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (21 bp):
TTCTTTCTTTCTTATTTTTCC
Found at i:603191 original size:27 final size:26
Alignment explanation
Indices: 603152--603203 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
603142 TCACTTTGGT
* *
603152 TTTTTCCTGTTTTTTCTTTCTTTTTA
1 TTTTTCCTCTTTTTTCCTTCTTTTTA
603178 TTTTTCCTTCTTTTTTCCTTCTTTTT
1 TTTTTCC-TCTTTTTTCCTTCTTTTT
603204 TCCTTCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (26 bp):
TTTTTCCTCTTTTTTCCTTCTTTTTA
Done.