Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 2 of 126
Found at i:339207 original size:40 final size:40
Alignment explanation
Indices: 339163--339244 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
339153 GAAATACTAG
*
339163 ATTAATGTAAACCCAATAAGTGTGAATCTCTCAAGAGAAA
1 ATTAATGTAAACCCAATAAATGTGAATCTCTCAAGAGAAA
*
339203 ATTAATGTAAACCCAATAAATGTGAGTCTCTCAAGAGAAA
1 ATTAATGTAAACCCAATAAATGTGAATCTCTCAAGAGAAA
339243 AT
1 AT
339245 CACTAACTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.26
Consensus pattern (40 bp):
ATTAATGTAAACCCAATAAATGTGAATCTCTCAAGAGAAA
Found at i:344732 original size:21 final size:20
Alignment explanation
Indices: 344706--344752 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
344696 TTTTTAACCA
* *
344706 AGGTAACGATTATAGTTATTT
1 AGGTAACGAATATA-TAATTT
*
344727 AGGTAATGAATATATAATTT
1 AGGTAACGAATATATAATTT
344747 AGGTAA
1 AGGTAA
344753 GCACTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.38
Consensus pattern (20 bp):
AGGTAACGAATATATAATTT
Found at i:347911 original size:2 final size:2
Alignment explanation
Indices: 347906--347930 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
347896 TAAATAAAAA
347906 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
347931 AAATAATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:349410 original size:15 final size:14
Alignment explanation
Indices: 349379--349422 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
349369 TGCAACTAAA
349379 AAATGACATTGTAATG
1 AAATGA-ATT-TAATG
349395 AATATGAATTTAATG
1 AA-ATGAATTTAATG
*
349410 AAATGATTTTAAT
1 AAATGAATTTAAT
349423 AATGTTAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 10 0.38
15 7 0.27
16 5 0.19
17 4 0.15
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.39
Consensus pattern (14 bp):
AAATGAATTTAATG
Found at i:349781 original size:29 final size:28
Alignment explanation
Indices: 349732--349789 Score: 64
Period size: 29 Copynumber: 2.0 Consensus size: 28
349722 TAATTTTCAA
* *
349732 AAAATAAAAAAAATCATTTTA-ATCTTTT
1 AAAATAAAAAAAATAAATTTATAT-TTTT
*
349760 AAAATAATAAATAATAAATTTATATTTTT
1 AAAATAA-AAAAAATAAATTTATATTTTT
349789 A
1 A
349790 CTTCTCAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
28 7 0.28
29 16 0.64
30 2 0.08
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (28 bp):
AAAATAAAAAAAATAAATTTATATTTTT
Found at i:364709 original size:2 final size:2
Alignment explanation
Indices: 364702--364730 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
364692 CTGATCAGGT
364702 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
364731 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:366974 original size:22 final size:22
Alignment explanation
Indices: 366949--366999 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
366939 TAAACTAACT
366949 TTAAAATATTACAAAATTGTTA
1 TTAAAATATTACAAAATTGTTA
* ** *
366971 TTAAATTATTTGAAAATTTTTA
1 TTAAAATATTACAAAATTGTTA
*
366993 TTTAAAT
1 TTAAAAT
367000 CATAAGGGTG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (22 bp):
TTAAAATATTACAAAATTGTTA
Found at i:367709 original size:29 final size:28
Alignment explanation
Indices: 367676--367738 Score: 81
Period size: 30 Copynumber: 2.2 Consensus size: 28
367666 AAAAATTATG
* * *
367676 AAAATAGATCAAATCAAAATTTGATGTAT
1 AAAATACATAAAATCAAAATTT-ATGCAT
367705 AAAATTACATAAAATCAAAATTTATGCAT
1 AAAA-TACATAAAATCAAAATTTATGCAT
367734 AAAAT
1 AAAAT
367739 TACACATCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 1 0.03
29 13 0.43
30 16 0.53
ACGTcount: A:0.56, C:0.08, G:0.06, T:0.30
Consensus pattern (28 bp):
AAAATACATAAAATCAAAATTTATGCAT
Found at i:367720 original size:30 final size:29
Alignment explanation
Indices: 367686--367742 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
367676 AAAATAGATC
*
367686 AAATCAAAATTTGATGTATAAAATTACATA
1 AAATCAAAATTT-ATGCATAAAATTACATA
367716 AAATCAAAATTTATGCATAAAATTACA
1 AAATCAAAATTTATGCATAAAATTACA
367743 CATCAAACCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.54, C:0.09, G:0.05, T:0.32
Consensus pattern (29 bp):
AAATCAAAATTTATGCATAAAATTACATA
Found at i:369736 original size:33 final size:33
Alignment explanation
Indices: 369692--369757 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
369682 GTATATTAAA
* *
369692 TGGATTTAATATTTTCGGCCAAATTACACTTTC
1 TGGATTCAATATTTTCGGCCAAATCACACTTTC
*
369725 TGGATTCAATATTTTCGTCCAAATCACACTTTC
1 TGGATTCAATATTTTCGGCCAAATCACACTTTC
369758 CAAGCCCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.41
Consensus pattern (33 bp):
TGGATTCAATATTTTCGGCCAAATCACACTTTC
Found at i:380100 original size:2 final size:2
Alignment explanation
Indices: 380044--380085 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
380034 CCAAAAATTA
380044 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
380086 GAACCTTGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:380710 original size:16 final size:16
Alignment explanation
Indices: 380689--380723 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
380679 TTGAATCGTG
*
380689 TTTGAATCATTTCAAA
1 TTTGAATCATTTAAAA
*
380705 TTTGAATTATTTAAAA
1 TTTGAATCATTTAAAA
380721 TTT
1 TTT
380724 TAAAAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (16 bp):
TTTGAATCATTTAAAA
Found at i:394983 original size:212 final size:212
Alignment explanation
Indices: 394343--395111 Score: 832
Period size: 212 Copynumber: 3.6 Consensus size: 212
394333 TATTTGTTTT
** * * * * * *
394343 GTATGTTTATCATTTGTGCTTTCTCTGCGGAAGCCCCGACCTTGTTCAGACTTTGGGTAGAATTC
1 GTATGTTGGTCATTTTTGCTTCCTCCGCGGAAGCCCCGACCTTGTTCGGACTTTGAGTAGAATTT
* * * *
394408 CTTCCCGGCACTTAG-ACAGGCATATGTTTGTAGACTAGATAGATAGTTCGAGAATGGAACTTTT
66 TTTCCCGGCACTTAGAACAAGCAAATG--TCT-G--TAGATAGATAGTTCGAGAATGGAACTTTT
** * * * *
394472 CGCGCTAATATAAACACGAATAACGCACGCCGCTGCTAGATATCGTGTTAATGGTATATCTCCAT
126 CATGCTAATATAAACACGAATAACGTAGGCCGCTGCTAGATTTCGTGTTAATGG--TATCT-CGT
*
394537 TTGTTCAAAAGTATGTTTTCATGGC
188 TTGTTCAAAAGTATGTTTTCATTGC
*
394562 GTATGTTGGTCATTTTTGCTTCCTCCGCGGAAGCCTCGACCTTGTTTCGGACTTTGAGTAGAATT
1 GTATGTTGGTCATTTTTGCTTCCTCCGCGGAAGCCCCGACCTTG-TTCGGACTTTGAGTAGAATT
*
394627 TTTCCCCGGCACTTAGAACAAGCAAATGTCTGTAGATAG-T--TT-GAGAATGGAACTTTTCATG
65 TTTTCCCGGCACTTAGAACAAGCAAATGTCTGTAGATAGATAGTTCGAGAATGGAACTTTTCATG
* * * * *
394688 CTAATATAAACATGAATTACGTAGGCCGCCGATAGATTTCATGTTAATGGTGTATCTCCGTTTGT
130 CTAATATAAACACGAATAACGTAGGCCGCTGCTAGATTTCGTGTTAAT-G-GTATCT-CGTTTGT
*
394753 TCAAATGTATGTTTTCATTGC
192 TCAAAAGTATGTTTTCATTGC
*
394774 GTATGTTGGTCATTTTTGCTTCCTCCGCGGAAGCCCCGACCTTGTTCGGACTTTGAGTGGAATTT
1 GTATGTTGGTCATTTTTGCTTCCTCCGCGGAAGCCCCGACCTTGTTCGGACTTTGAGTAGAATTT
* * *
394839 TTTCCCAGCATTTAGAACACGCAAATGTCTGTAGATAGATAGTTCGAGAATGGAACTTTTCATGC
66 TTTCCCGGCACTTAGAACAAGCAAATGTCTGTAGATAGATAGTTCGAGAATGGAACTTTTCATGC
* *
394904 TAATATGAACACCAAATAACGTAGGCCGCTGCTAGATTTCGTGTTAATGGTATCT-GTTTGTTCA
131 TAATATAAACA-CGAATAACGTAGGCCGCTGCTAGATTTCGTGTTAATGGTATCTCGTTTGTTCA
394968 AAAGTATGTTTTCATTGC
195 AAAGTATGTTTTCATTGC
* * * ** * ** * ** *
394986 ATTATATATTTGTTTTGTATGTTGGTTGTTTCCGCAGAAGCCCCGATATTGTTCAGACTTTGAGT
1 ---GTATGTTGGTCAT-T-T-TTGCTT-CCTCCGCGGAAGCCCCGACCTTGTTCGGACTTTGAGT
* ** * * * * *
395051 AGAAATTTTTCTTGGTACGTAGAACACGCAAAAG-CCGTAGATAGATAGTTCGAGAATGGAA
59 AGAATTTTTTCCCGGCACTTAGAACAAGCAAATGTCTGTAGATAGATAGTTCGAGAATGGAA
395112 ATTTCCGTGT
Statistics
Matches: 471, Mismatches: 63, Indels: 33
0.83 0.11 0.06
Matches are distributed among these distances:
211 54 0.11
212 158 0.34
213 3 0.01
214 9 0.02
215 40 0.08
216 38 0.08
217 1 0.00
218 32 0.07
219 96 0.20
220 31 0.07
221 9 0.02
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (212 bp):
GTATGTTGGTCATTTTTGCTTCCTCCGCGGAAGCCCCGACCTTGTTCGGACTTTGAGTAGAATTT
TTTCCCGGCACTTAGAACAAGCAAATGTCTGTAGATAGATAGTTCGAGAATGGAACTTTTCATGC
TAATATAAACACGAATAACGTAGGCCGCTGCTAGATTTCGTGTTAATGGTATCTCGTTTGTTCAA
AAGTATGTTTTCATTGC
Found at i:399103 original size:43 final size:43
Alignment explanation
Indices: 399054--399151 Score: 187
Period size: 43 Copynumber: 2.3 Consensus size: 43
399044 ACTGTCCATG
*
399054 TTCAATGTATGTAAAAAACTTTGATTTCATATGTATGTCTATC
1 TTCAATGTATGTAAAAAACTGTGATTTCATATGTATGTCTATC
399097 TTCAATGTATGTAAAAAACTGTGATTTCATATGTATGTCTATC
1 TTCAATGTATGTAAAAAACTGTGATTTCATATGTATGTCTATC
399140 TTCAATGTATGT
1 TTCAATGTATGT
399152 TTGATATATT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (43 bp):
TTCAATGTATGTAAAAAACTGTGATTTCATATGTATGTCTATC
Found at i:399766 original size:29 final size:28
Alignment explanation
Indices: 399710--399767 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
399700 TCGCCATACT
* *
399710 ATTTAAAGTTTTTGAAGTTCAATGATCA
1 ATTTAAAGTTTTTGAAGATCAATAATCA
* *
399738 ATTTATAATTTTTTGAAGATGAATAATCA
1 ATTTA-AAGTTTTTGAAGATCAATAATCA
399767 A
1 A
399768 AACTTAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (28 bp):
ATTTAAAGTTTTTGAAGATCAATAATCA
Found at i:402464 original size:2 final size:2
Alignment explanation
Indices: 402457--402497 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
402447 ATGAAACTTC
402457 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
402498 TGCAATATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:402969 original size:31 final size:31
Alignment explanation
Indices: 402921--402996 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
402911 ACAAATTAAT
* * *
402921 TTAACAAT-ATATATATATAACTTGTAAGATA
1 TTAATAATAATAT-TATATAAATTATAAGATA
* *
402952 TTATTAATAATATTATATAAATTATAATATA
1 TTAATAATAATATTATATAAATTATAAGATA
*
402983 TTAATATTAATATT
1 TTAATAATAATATT
402997 TAAATCATCA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
31 33 0.89
32 4 0.11
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (31 bp):
TTAATAATAATATTATATAAATTATAAGATA
Found at i:403009 original size:28 final size:28
Alignment explanation
Indices: 402953--403009 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
402943 TGTAAGATAT
* *
402953 TATTAATAATATTATATAAATTATAATA
1 TATTAATAATAATATATAAATCATAATA
* * *
402981 TATTAATATTAATATTTAAATCATCATA
1 TATTAATAATAATATATAAATCATAATA
403009 T
1 T
403010 TTTTGTATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (28 bp):
TATTAATAATAATATATAAATCATAATA
Found at i:410782 original size:21 final size:21
Alignment explanation
Indices: 410758--410797 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
410748 GAAAATCAAT
410758 TTCAATTTCAAGCTCAACAAA
1 TTCAATTTCAAGCTCAACAAA
410779 TTCAATTTCAAGCTCAACA
1 TTCAATTTCAAGCTCAACA
410798 CCATTAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.25, G:0.05, T:0.30
Consensus pattern (21 bp):
TTCAATTTCAAGCTCAACAAA
Found at i:415131 original size:208 final size:207
Alignment explanation
Indices: 414720--415328 Score: 727
Period size: 194 Copynumber: 3.0 Consensus size: 207
414710 CAAGTTGTAA
* * *
414720 CTCGCAAGTAACTTCTCGAAAAAAAACCCGATTTTACGACATTTCCAAAGCTATGAAA-CTTTGA
1 CTCGCAAGTAACTTCTCG--ACAAAACCCGGTTTTACGACATTTCCGAAGCTATGAAATC-TTGA
* *
414784 TTCCTTACTGATTCTGCTATGTCGTGTTTATGATTGTTGATATATGCTGTTTGTTGCTGTATATT
63 TTCCTTACTGATTCTGCTAAGTTGTGTTTATGATTGTTGATATATGCTGTTTGTTGCTGTATATT
* * * *
414849 GCTTTTGAGTTTTTCAAAAATCGAAGAGAAA-TGTCTTTGAAGAAAGGGAATT-TGGTTTTTGTT
128 GCTTTTGAGTTTTTCAAAAGTCGAAGAGAAACT-T-TTTTAAGAAAGGGAATTCAGG-TGTTGTT
*
414912 TAACTGTCTGAATTGCTT
190 TAACCGTCTGAATTGCTT
* * *
414930 CTCGCAAGTAACTTCTCGACAAAACCCGGTTTTACAACATTTCCGAAGTTATAAAATCTTGATTC
1 CTCGCAAGTAACTTCTCGACAAAACCCGGTTTTACGACATTTCCGAAGCTATGAAATCTTGATTC
*
414995 CTTGCTGATTCTGCTAAAGTTGTGTTTATGATTGTTGATATATGCTGTTTGTTGCTGTATATTGC
66 CTTACTGATTCTGCT-AAGTTGTGTTTATGATTGTTGATATATGCTGTTTGTTGCTGTATATTGC
*
415060 TTTTGAGTTTTTCAAAAGTCGAAGAGAAACTTTTTTAAGAATGGGAATTCAGGTGTTGTTTAACC
130 TTTTGAGTTTTTCAAAAGTCGAAGAGAAACTTTTTTAAGAAAGGGAATTCAGGTGTTGTTTAACC
415125 GTCTGAATTGCTT
195 GTCTGAATTGCTT
* *
415138 CT--C-----A-------ACAAAACCCGGTTTTATGACATATCCGAAGCTATGAAATCTTGATTC
1 CTCGCAAGTAACTTCTCGACAAAACCCGGTTTTACGACATTTCCGAAGCTATGAAATCTTGATTC
* * * *
415189 CTTATTGATTCTGCTGAATTTGTGTTTAGGATTGTTGATATATGCTGTTTGTTGCTATATATTGC
66 CTTACTGATTCTGCT-AAGTTGTGTTTATGATTGTTGATATATGCTGTTTGTTGCTGTATATTGC
* * *** * * *
415254 --TTGAGTTTTTCAAGAGTCGAAGAAAAACGACTTTAAGAACGGGAA-TCCGTGTGTCGTTTAAC
130 TTTTGAGTTTTTCAAAAGTCGAAGAGAAACTTTTTTAAGAAAGGGAATTCAG-GTGTTGTTTAAC
*
415316 CATCTGAATTGCT
194 CGTCTGAATTGCT
415329 GCTCTGGTCG
Statistics
Matches: 359, Mismatches: 35, Indels: 28
0.85 0.08 0.07
Matches are distributed among these distances:
191 3 0.01
192 62 0.17
194 101 0.28
201 1 0.00
206 1 0.00
208 93 0.26
209 79 0.22
210 19 0.05
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (207 bp):
CTCGCAAGTAACTTCTCGACAAAACCCGGTTTTACGACATTTCCGAAGCTATGAAATCTTGATTC
CTTACTGATTCTGCTAAGTTGTGTTTATGATTGTTGATATATGCTGTTTGTTGCTGTATATTGCT
TTTGAGTTTTTCAAAAGTCGAAGAGAAACTTTTTTAAGAAAGGGAATTCAGGTGTTGTTTAACCG
TCTGAATTGCTT
Found at i:419581 original size:20 final size:19
Alignment explanation
Indices: 419556--419626 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
419546 CATGCTCTCT
419556 CTTTTTTAAATTTTTATGAA
1 CTTTTTTAAATTTTT-TGAA
*
419576 CTTTTTTCAATTTTTTGAA
1 CTTTTTTAAATTTTTTGAA
* *
419595 -TTTTTT-ATTTTTTTAAA
1 CTTTTTTAAATTTTTTGAA
*
419612 TATTTTTTAAATTTT
1 -CTTTTTTAAATTTT
419627 AAATTATTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
17 9 0.20
18 6 0.14
19 10 0.23
20 19 0.43
ACGTcount: A:0.25, C:0.04, G:0.03, T:0.68
Consensus pattern (19 bp):
CTTTTTTAAATTTTTTGAA
Found at i:419589 original size:9 final size:9
Alignment explanation
Indices: 419557--419626 Score: 61
Period size: 9 Copynumber: 7.4 Consensus size: 9
419547 ATGCTCTCTC
419557 TTTTTTAAA
1 TTTTTTAAA
*
419566 TTTTTATGAAC
1 TTTTT-T-AAA
*
419577 TTTTTTCAA
1 TTTTTTAAA
*
419586 TTTTTTGAA
1 TTTTTTAAA
*
419595 TTTTTT-AT
1 TTTTTTAAA
419603 TTTTTTAAATA
1 TTTTTT-AA-A
419614 TTTTTTAAA
1 TTTTTTAAA
419623 TTTT
1 TTTT
419627 AAATTATTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
8 7 0.14
9 25 0.50
10 5 0.10
11 13 0.26
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:419626 original size:18 final size:19
Alignment explanation
Indices: 419605--419640 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
419595 TTTTTTATTT
*
419605 TTTTAAA-TATTTTTTAAA
1 TTTTAAATTATTTGTTAAA
419623 TTTTAAATTATTTGTTAA
1 TTTTAAATTATTTGTTAA
419641 TGCGTCCATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTTAAATTATTTGTTAAA
Found at i:423777 original size:8 final size:7
Alignment explanation
Indices: 423750--423776 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
423740 TTCCCCTCCT
423750 TTTTTTC
1 TTTTTTC
423757 TTTTTTC
1 TTTTTTC
423764 TTTTTTC
1 TTTTTTC
423771 TTTTTT
1 TTTTTT
423777 TGAAATATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:427695 original size:75 final size:75
Alignment explanation
Indices: 427612--427757 Score: 274
Period size: 75 Copynumber: 1.9 Consensus size: 75
427602 TAAACTTTAA
* *
427612 AGTTTTTAAGAATTAACTTGAACAAAAAATGTGCCTAAACTTTAAAATTTTTAATAACTAACTTG
1 AGTTTTTAAGAATTAACTTGAACAAAAAATGTGCCAAAACTTTAAAATTTTTAATAACTAACTTA
427677 AACAAACTAT
66 AACAAACTAT
427687 AGTTTTTAAGAATTAACTTGAACAAAAAATGTGCCAAAACTTTAAAATTTTTAATAACTAACTTA
1 AGTTTTTAAGAATTAACTTGAACAAAAAATGTGCCAAAACTTTAAAATTTTTAATAACTAACTTA
427752 AACAAA
66 AACAAA
427758 AAAAAAATAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.34
Consensus pattern (75 bp):
AGTTTTTAAGAATTAACTTGAACAAAAAATGTGCCAAAACTTTAAAATTTTTAATAACTAACTTA
AACAAACTAT
Found at i:436549 original size:16 final size:18
Alignment explanation
Indices: 436512--436549 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
436502 TAATTTTTTA
436512 AATATATTAAAAAAATTT
1 AATATATTAAAAAAATTT
*
436530 AATA-ATTAAACAAA-TT
1 AATATATTAAAAAAATTT
436546 AATA
1 AATA
436550 CTGAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 9 0.47
18 4 0.21
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
AATATATTAAAAAAATTT
Found at i:438515 original size:18 final size:20
Alignment explanation
Indices: 438480--438521 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
438470 TCATTTATGT
438480 ATTTTTCAAAAATATAAAGA
1 ATTTTTCAAAAATATAAAGA
*
438500 ATTTTT-AAAAAT-TAAATA
1 ATTTTTCAAAAATATAAAGA
438518 ATTT
1 ATTT
438522 ATGTCTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 6 0.29
20 6 0.29
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
ATTTTTCAAAAATATAAAGA
Found at i:441648 original size:25 final size:25
Alignment explanation
Indices: 441619--441686 Score: 102
Period size: 25 Copynumber: 2.7 Consensus size: 25
441609 TGAATTGGTG
441619 TGAACCAATTATTTGACTAGGCCGA
1 TGAACCAATTATTTGACTAGGCCGA
* *
441644 TGAACCAATTATTTGGCTAGGTCGA
1 TGAACCAATTATTTGACTAGGCCGA
441669 TGAA-CAAGTTATTTGACT
1 TGAACCAA-TTATTTGACT
441687 GATTTGATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
24 3 0.08
25 36 0.92
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (25 bp):
TGAACCAATTATTTGACTAGGCCGA
Found at i:446305 original size:18 final size:18
Alignment explanation
Indices: 446267--446302 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
446257 ATTTTTTTGT
446267 TTTAATTTAATATTTAAA
1 TTTAATTTAATATTTAAA
*
446285 TTTAATTTTAATGTTTAA
1 TTTAA-TTTAATATTTAA
446303 TTTGATACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
TTTAATTTAATATTTAAA
Found at i:450916 original size:30 final size:30
Alignment explanation
Indices: 450870--450941 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 30
450860 TTAATGTATC
450870 TTTA-TATTTT-AAAAGATT-AAATCAAAAT
1 TTTATTATTTTAAAAAGATTAAAAT-AAAAT
*
450898 TTTATTATTTTAAAAAGATTAAAATATAAT
1 TTTATTATTTTAAAAAGATTAAAATAAAAT
450928 TTTATTATTATTAA
1 TTTATTATT-TTAA
450942 TTTAAATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
28 4 0.10
29 6 0.15
30 21 0.54
31 8 0.21
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (30 bp):
TTTATTATTTTAAAAAGATTAAAATAAAAT
Found at i:452691 original size:6 final size:6
Alignment explanation
Indices: 452680--452707 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
452670 TTCCTTTCCA
452680 ATTTTG ATTTTG ATTTTG ATTTTG ATTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTT
452708 ATTTATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.14, T:0.68
Consensus pattern (6 bp):
ATTTTG
Found at i:454300 original size:30 final size:30
Alignment explanation
Indices: 454260--454318 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
454250 TAAGAATAGG
454260 AAAAATATATAATATATTTTT-AATATATA
1 AAAAATATATAATATATTTTTAAATATATA
454289 AAAAGATATATAATATATTTTTAAATATAT
1 AAAA-ATATATAATATATTTTTAAATATAT
454319 GTCTAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 4 0.14
30 17 0.61
31 7 0.25
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (30 bp):
AAAAATATATAATATATTTTTAAATATATA
Found at i:455456 original size:26 final size:24
Alignment explanation
Indices: 455428--455491 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 24
455418 TCTTTATGGA
*
455428 TTTAAAATTTAGTACCTATATTTTTAT
1 TTTAAAATTTAGTA-CT-T-TTTATAT
455455 TTTAAAAAATTTAGTACTTTTTATAT
1 TTT--AAAATTTAGTACTTTTTATAT
455481 TTTAAAATTTA
1 TTTAAAATTTA
455492 AGTTCAATTC
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
24 8 0.24
26 9 0.26
27 4 0.12
28 2 0.06
29 11 0.32
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (24 bp):
TTTAAAATTTAGTACTTTTTATAT
Found at i:455466 original size:29 final size:26
Alignment explanation
Indices: 455431--455487 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 26
455421 TTATGGATTT
*
455431 AAAATTTAGTACCTATATTTTTATTTTAA
1 AAAATTTAGTA-CT-T-TTTATATTTTAA
455460 AAAATTTAGTACTTTTTATATTTTAA
1 AAAATTTAGTACTTTTTATATTTTAA
455486 AA
1 AA
455488 TTTAAGTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 13 0.48
27 1 0.04
28 2 0.07
29 11 0.41
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (26 bp):
AAAATTTAGTACTTTTTATATTTTAA
Found at i:456646 original size:29 final size:30
Alignment explanation
Indices: 456603--456662 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
456593 ATTTTGATTT
* * *
456603 TTTTGAAAATAATAAAATTTTAATTTAATA
1 TTTTGAAAATAATAAAAATATAAATTAATA
*
456633 TTTT-AAAATTATAAAAATATAAATTAATA
1 TTTTGAAAATAATAAAAATATAAATTAATA
456662 T
1 T
456663 AATGATAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (30 bp):
TTTTGAAAATAATAAAAATATAAATTAATA
Found at i:457634 original size:135 final size:137
Alignment explanation
Indices: 457306--458801 Score: 1292
Period size: 146 Copynumber: 10.8 Consensus size: 137
457296 GAAAAAAAAA
457306 ATATTTTGTTGTTTGGTT--TTAGAAAGTAAATTGA-AGTGGATTAAGCTTAATTTAGCTACTTT
1 ATATTTTGTTGTTTGGTTACTTAGAAAGTAAATT-ATAGTGGATTAAGCTTAATTTAGCTACTTT
* * * *
457368 AATTGTCTAAATTTGGTCATTTAGGTGAAAATTTTAGTGTTCTTTTGTTATTAATAAGTTTCTTT
65 AATTGTCTAAATTTCGTCATTTAGGTGAAAAATTTAGTGTTC--TT-TT-TTAGT--GGTTCTTT
* *
457433 ACGAATATATGCAT
124 ATGAATATATGTAT
* *
457447 ATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTGA-AGTGGATTAAGTTTAATTTAGCTA-TAT
1 ATATTTTGTTGTTTGGTTACTTAGAAAGTAAATT-ATAGTGGATTAAGCTTAATTTAGCTACT-T
* * * *
457510 TAATTGTCTCAATTTCG-AATTTAGGTGAAAAAATTAGTGTTC-TTTTTGGTGGTTCTTTATGAA
64 TAATTGTCTAAATTTCGTCATTTAGGTGAAAAATTTAGTGTTCTTTTTTAGTGGTTCTTTATGAA
*
457573 TATAAGTAT
129 TATATGTAT
*
457582 ATATTTTGTTCTTTGGTTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATTTAGCTACTTTA
1 ATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATTTAGCTACTTTA
* * ** ** * * ** *
457647 ATCGTCGTGAA--TAAT--TTTA-GTG--TTATTT-TTG-GCGGTTCT--T--T-----ATGAAT
66 ATTGTC-TAAATTTCGTCATTTAGGTGAAAAATTTAGTGTTCTTTTTTAGTGGTTCTTTATGAAT
*
457694 ATAAGTAT
130 ATATGTAT
* *
457702 ATATTTTGTTGTTTGGTTACTTGGAAAGTAAATTTTAGTGGATTAAGCTTAATTTAGCTACTTTA
1 ATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATTTAGCTACTTTA
* * *
457767 ATTGTCTCAATTTCGTCATTTAGGTGAAAAATTTTAGTGTTC-ATTTTGGTGG-T-TTTATGAAT
66 ATTGTCTAAATTTCGTCATTTAGGTGAAAAA-TTTAGTGTTCTTTTTTAGTGGTTCTTTATGAAT
*
457829 ATAAGTAT
130 ATATGTAT
* * * * * *
457837 ATATTTTGTTGTTGGGTTACTGAGAAAGTAAATTATAGTGGAATAAGCTTGAGTTAGCTACTTTT
1 ATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATTTAGCTACTTTA
* * * *
457902 ATTGTCTAAATATGGTCATTTAGGCGAAAAACATTAGTGTTCTTTTGCTATTTTTTTA-TGGTTC
66 ATTGTCTAAATTTCGTCATTTAGGTGAAAAA-TTTAGTG-----TT-C---TTTTTTAGTGGTTC
457966 TTTATGAATATATGTAT
121 TTTATGAATATATGTAT
* *
457983 ATAATTTGTTGTTTGTTTACTTAGAAAGTAAATTATAGTGGGA-TAAGCTTAATTTAGCTACTTT
1 ATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGT-GGATTAAGCTTAATTTAGCTACTTT
* * * ** * *
458047 AATTGTCTAAATTCCGTCATTTAGGTGAAAAA---ATTGTTATTAGTAAGT--TACTTTATGAAT
65 AATTGTCTAAATTTCGTCATTTAGGTGAAAAATTTAGTGTTCTTTTTTAGTGGTTCTTTATGAAT
458107 ATATGTAT
130 ATATGTAT
* ** **
458115 ATGTTTTGTTGTTTGGTTACTTAGAAAGTAAATGGTAGTGGGA-TAAGCTTAA-GAATGCTACTT
1 ATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGT-GGATTAAGCTTAATTTA-GCTACTT
* * * * *
458178 TAGTTTTCTCAATTTCGTCACTTT-GGTGAAAACCTTTTGTGTTCTTTTGCCATTTTTTTA-TGG
64 TAATTGTCTAAATTTCGTCA-TTTAGGTGAAAA-ATTTAGTG-----TT--C--TTTTTTAGTGG
*
458241 TTCATTATGAATATATGTAT
118 TTCTTTATGAATATATGTAT
* * * * *
458261 ATAATTTATTGTTTGGTTACTTAGAAAGTAAATTACAGTGGGA-TAACCTTAATTTGGCTACTTT
1 ATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGT-GGATTAAGCTTAATTTAGCTACTTT
* *
458325 AATTGTCTAAATTTCTTCATTTAGGTGAAAAACTTTAGTGTTCTATTGCTATTTTTTTGATGGTT
65 AATTGTCTAAATTTCGTCATTTAGGTGAAAAA-TTTAGTG-----TT-C--TTTTTTAG-TGGTT
* *
458390 CTTTATGAATATCTTTAT
120 CTTTATGAATATATGTAT
* * *
458408 ATATTATGTTGTTTGGTTAC-TAGAAAGTAAATTATAGTGGATTGAGCTTAATTTAGCTACTTTC
1 ATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATTTAGCTACTTTA
* *
458472 ATTGTCTAAATTTCGTCATTTAGGTGAAAATATTTTGTGTTCTTTTGTTATTAGCAAGTTCCTTT
66 ATTGTCTAAATTTCGTCATTTAGGTGAAAA-ATTTAGTGTTCTTTT-TTAGT-G---GTT-CTTT
*
458537 ATGAATATTTGTAT
124 ATGAATATATGTAT
* * * **
458551 ATATTTTGTTGTTTGGTTTCTTAGAAAGTAGATTGTAGTGGGGTAAGCTTAATTTAGCTACTTTA
1 ATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATTTAGCTACTTTA
* * ** * *
458616 ATTGTCTAAATTTTGCCATTTAGGTGAAAAACTTTTCTGTTCTTTTGTTATTAGTAAGTTTCTTC
66 ATTGTCTAAATTTCGTCATTTAGGTGAAAAA-TTTAGTGTTC--TT-TT-TTAGT--GGTTCTTT
*
458681 ATAAATATATGTAT
124 ATGAATATATGTAT
* * * * *
458695 ATATATTGTTTTTTGGTTGCTTAGAAAGTAAATTATGGTGGAATAAGCTTAAATTTAGCTACTTT
1 ATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGATTAAGCTT-AATTTAGCTACTTT
*
458760 AATTGTCCAAATTTCGTCATTTAGGTGAAAAATTTTAGTGTT
65 AATTGTCTAAATTTCGTCATTTAGGTGAAAAA-TTTAGTGTT
458802 TTGTTTTTTT
Statistics
Matches: 1115, Mismatches: 163, Indels: 150
0.78 0.11 0.11
Matches are distributed among these distances:
119 3 0.00
120 81 0.07
121 2 0.00
123 4 0.00
124 3 0.00
125 1 0.00
126 1 0.00
127 4 0.00
128 6 0.01
129 6 0.01
130 4 0.00
131 1 0.00
132 100 0.09
133 11 0.01
134 3 0.00
135 185 0.17
136 6 0.01
137 5 0.00
138 7 0.01
139 4 0.00
140 3 0.00
141 23 0.02
142 29 0.03
143 89 0.08
144 136 0.12
145 74 0.07
146 275 0.25
147 47 0.04
148 2 0.00
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (137 bp):
ATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATTTAGCTACTTTA
ATTGTCTAAATTTCGTCATTTAGGTGAAAAATTTAGTGTTCTTTTTTAGTGGTTCTTTATGAATA
TATGTAT
Found at i:457756 original size:120 final size:120
Alignment explanation
Indices: 457543--457768 Score: 407
Period size: 120 Copynumber: 1.9 Consensus size: 120
457533 GGTGAAAAAA
* *
457543 TTAGTGTTCTTTTTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTCTTTGGTTACTTAGAA
1 TTAGTGTTATTTTTGGCGGTTCTTTATGAATATAAGTATATATTTTGTTCTTTGGTTACTTAGAA
457608 AGTAAATTATAGTGGATTAAGCTTAATTTAGCTACTTTAATCGTCGTGAATAATT
66 AGTAAATTATAGTGGATTAAGCTTAATTTAGCTACTTTAATCGTCGTGAATAATT
* *
457663 TTAGTGTTATTTTTGGCGGTTCTTTATGAATATAAGTATATATTTTGTTGTTTGGTTACTTGGAA
1 TTAGTGTTATTTTTGGCGGTTCTTTATGAATATAAGTATATATTTTGTTCTTTGGTTACTTAGAA
*
457728 AGTAAATTTTAGTGGATTAAGCTTAATTTAGCTACTTTAAT
66 AGTAAATTATAGTGGATTAAGCTTAATTTAGCTACTTTAAT
457769 TGTCTCAATT
Statistics
Matches: 101, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 101 1.00
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.48
Consensus pattern (120 bp):
TTAGTGTTATTTTTGGCGGTTCTTTATGAATATAAGTATATATTTTGTTCTTTGGTTACTTAGAA
AGTAAATTATAGTGGATTAAGCTTAATTTAGCTACTTTAATCGTCGTGAATAATT
Found at i:457878 original size:255 final size:255
Alignment explanation
Indices: 457427--457900 Score: 747
Period size: 255 Copynumber: 1.9 Consensus size: 255
457417 ATTAATAAGT
*
457427 TTCTTTACGAATATATGCATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTGAAGTGGATTA
1 TTCTTTACGAATATAAGCATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTGAAGTGGATTA
* *
457492 AGTTTAATTTAGCTATATTAATTGTCTCAATTTCGAATTTAGGTGAAAAAATTAGTGTTCTTTTT
66 AGCTTAATTTAGCTATATTAATTGTCTCAATTTCGAATTTAGGTGAAAAAATTAGTGTTCATTTT
* *
457557 GGTGGTTCTTTATGAATATAAGTATATATTTTGTTCTTTGGTTACTTAGAAAGTAAATTATAGTG
131 GGTGGTTCTTTATGAATATAAGTATATATTTTGTTCTTGGGTTACTGAGAAAGTAAATTATAGTG
* *
457622 GATTAAGCTTAATTTAGCTACTTTAATCGTCGTGAATAATTTTAGTGTTATTTTTGGCGG
196 GAATAAGCTTAAGTTAGCTACTTTAATCGTCGTGAATAATTTTAGTGTTATTTTTGGCGG
* * * * **
457682 TTCTTTATGAATATAAGTATATATTTTGTTGTTTGGTTACTTGGAAAGTAAATTTTAGTGGATTA
1 TTCTTTACGAATATAAGCATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTGAAGTGGATTA
* *
457747 AGCTTAATTTAGCTACT-TTAATTGTCTCAATTTCGTCATTTAGGTGAAAAATTTTAGTGTTCAT
66 AGCTTAATTTAGCTA-TATTAATTGTCTCAATTTCG-AATTTAGGTGAAAAA-ATTAGTGTTCAT
*
457811 TTTGGTGG-T-TTTATGAATATAAGTATATATTTTGTTGTTGGGTTACTGAGAAAGTAAATTATA
128 TTTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTCTTGGGTTACTGAGAAAGTAAATTATA
*
457874 GTGGAATAAGCTTGAGTTAGCTACTTT
193 GTGGAATAAGCTTAAGTTAGCTACTTT
457901 TATTGTCTAA
Statistics
Matches: 199, Mismatches: 17, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
255 165 0.83
256 16 0.08
257 18 0.09
ACGTcount: A:0.29, C:0.07, G:0.19, T:0.46
Consensus pattern (255 bp):
TTCTTTACGAATATAAGCATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTGAAGTGGATTA
AGCTTAATTTAGCTATATTAATTGTCTCAATTTCGAATTTAGGTGAAAAAATTAGTGTTCATTTT
GGTGGTTCTTTATGAATATAAGTATATATTTTGTTCTTGGGTTACTGAGAAAGTAAATTATAGTG
GAATAAGCTTAAGTTAGCTACTTTAATCGTCGTGAATAATTTTAGTGTTATTTTTGGCGG
Found at i:458254 original size:278 final size:276
Alignment explanation
Indices: 457680--458801 Score: 1131
Period size: 278 Copynumber: 3.9 Consensus size: 276
457670 TATTTTTGGC
* * * *
457680 GGTTCTTTATGAATATAAGTATATATTTTGTTGTTTGGTTACTTGGAAAGTAAATTTTAGT-GGA
1 GGTTCTTTATGAATATATGTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGGA
* *
457744 TTAAGCTTAATTTAGCTACTTTAATTGTCTCAATTTCGTCATTTAGGTGAAAAATTTTAGTGTTC
66 -TAAGCTTAATTTAGCTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAA----ATTGTT-
* * * * *
457809 ATTTTGGT--GGT-TTTATGAATATAAGTATATATTTTGTTGTTGGGTTACTGAGAAAGTAAATT
125 ATTAT-GTAAGTTCTTTATGAATATATGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATT
* * * * * *
457871 ATAGTGGAATAAGCTTGAGTTAGCTACTTTTATTGTCTAAATATGGTCATTTAGGCGAAAAACAT
189 ATAGTGGGATAAGCTTAAGTTAGCTAC-TTTATTGTCTAAATTTCGTCATTTAGGTGAAAAACTT
*
457936 TAGTGTTCTTTTGCTATTTTTTTAT
253 TTGTGTTCTTTTGC-ATTTTTTTAT
*
457961 GGTTCTTTATGAATATATGTATATAATTTGTTGTTTGTTTACTTAGAAAGTAAATTATAGTGGGA
1 GGTTCTTTATGAATATATGTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGGA
*
458026 TAAGCTTAATTTAGCTACTTTAATTGTCTAAATTCCGTCATTTAGGTGAAAAAATTGTTATTA-G
66 TAAGCTTAATTTAGCTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAATTGTTATTATG
* **
458090 TAAGTTACTTTATGAATATATGTATATGTTTTGTTGTTTGGTTACTTAGAAAGTAAATGGTAGTG
131 TAAGTT-CTTTATGAATATATGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTG
* * * *
458155 GGATAAGCTTAAG-AATGCTACTTTAGTTTTCTCAATTTCGTCACTTT-GGTGAAAACCTTTTGT
195 GGATAAGCTTAAGTTA-GCTACTTTA-TTGTCTAAATTTCGTCA-TTTAGGTGAAAAACTTTTGT
458218 GTTCTTTTGCCATTTTTTTAT
257 GTTCTTTTG-CATTTTTTTAT
* * *
458239 GGTTCATTATGAATATATGTATATAATTTATTGTTTGGTTACTTAGAAAGTAAATTACAGTGGGA
1 GGTTCTTTATGAATATATGTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGGA
* * * *
458304 TAACCTTAATTTGGCTACTTTAATTGTCTAAATTTCTTCATTTAGGTGAAAAACTTTAGTGT-TC
66 TAAGCTTAATTTAGCTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAA-ATT-GT-TAT-
* * *
458368 TATTGCTATTTTTTTGATGGTTCTTTATGAATATCTTTATATATTATGTTGTTTGGTTAC-TAGA
127 TA-TG-TA--------A--GTTCTTTATGAATATATGTATATATTTTGTTGTTTGGTTACTTAGA
* *
458432 AAGTAAATTATAGT-GGATTGAGCTTAATTTAGCTACTTTCATTGTCTAAATTTCGTCATTTAGG
180 AAGTAAATTATAGTGGGA-TAAGCTTAAGTTAGCTACTTT-ATTGTCTAAATTTCGTCATTTAGG
***
458496 TGAAAATA-TTTTGTGTTCTTTTG--TTATTAGCA-
243 TGAAAA-ACTTTTGTGTTCTTTTGCATT-TTTTTAT
* * * * * *
458528 AGTTCCTTTATGAATATTTGTATATATTTTGTTGTTTGGTTTCTTAGAAAGTAGATTGTAGTGGG
1 GGTT-CTTTATGAATATATGTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGG
* * * *
458593 GTAAGCTTAATTTAGCTACTTTAATTGTCTAAATTTTGCCATTTAGGTGAAAAACTTTTCTGTTC
65 ATAAGCTTAATTTAGCTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAA---AT-TG---
* * * * * *
458658 TTTTGTTATTAGTAAGTTTCTTCATAAATATATGTATATATATTGTTTTTTGGTTGCTTAGAAAG
123 --TTATTA-T-GTAAG-TTCTTTATGAATATATGTATATATTTTGTTGTTTGGTTACTTAGAAAG
* * * *
458723 TAAATTATGGTGGAATAAGCTTAAATTTAGCTACTTTAATTGTCCAAATTTCGTCATTTAGGTGA
183 TAAATTATAGTGGGATAAGCTT-AAGTTAGCTACTTT-ATTGTCTAAATTTCGTCATTTAGGTGA
458788 AAAA-TTTTAGTGTT
246 AAAACTTTT-GTGTT
458802 TTGTTTTTTT
Statistics
Matches: 713, Mismatches: 80, Indels: 88
0.81 0.09 0.10
Matches are distributed among these distances:
274 2 0.00
276 5 0.01
277 10 0.01
278 221 0.31
279 6 0.01
280 3 0.00
281 110 0.15
282 3 0.00
283 1 0.00
284 2 0.00
286 1 0.00
287 32 0.04
288 29 0.04
289 55 0.08
290 103 0.14
291 6 0.01
292 74 0.10
293 37 0.05
294 3 0.00
296 7 0.01
297 3 0.00
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.46
Consensus pattern (276 bp):
GGTTCTTTATGAATATATGTATATAATTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGGGA
TAAGCTTAATTTAGCTACTTTAATTGTCTAAATTTCGTCATTTAGGTGAAAAAATTGTTATTATG
TAAGTTCTTTATGAATATATGTATATATTTTGTTGTTTGGTTACTTAGAAAGTAAATTATAGTGG
GATAAGCTTAAGTTAGCTACTTTATTGTCTAAATTTCGTCATTTAGGTGAAAAACTTTTGTGTTC
TTTTGCATTTTTTTAT
Found at i:463210 original size:28 final size:28
Alignment explanation
Indices: 463175--463240 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 28
463165 AGTGTTTTTA
463175 ATTA-ATAAATGTAAAATATTTA-T-GTTT
1 ATTATATAAAT-T-AAATATTTATTAGTTT
*
463202 ATTATAT-AATTACATATTTATTAGTTT
1 ATTATATAAATTAAATATTTATTAGTTT
463229 ATTTATATAAAT
1 A-TTATATAAAT
463241 AATGAGTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
25 8 0.24
26 2 0.06
27 12 0.36
28 8 0.24
29 3 0.09
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (28 bp):
ATTATATAAATTAAATATTTATTAGTTT
Found at i:463250 original size:28 final size:27
Alignment explanation
Indices: 463198--463252 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
463188 AAATATTTAT
* *
463198 GTTTATTATATAATTACATATTTATTA
1 GTTTATTATATAAATACATAGTTATTA
463225 GTTTATTTATATAAATA-ATGAGTTATTA
1 GTTTA-TTATATAAATACAT-AGTTATTA
463253 ATTAAAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (27 bp):
GTTTATTATATAAATACATAGTTATTA
Found at i:464869 original size:15 final size:15
Alignment explanation
Indices: 464849--464898 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
464839 TCTTTTTTCC
464849 TATATACATTCATCA
1 TATATACATTCATCA
*
464864 TATATACATACAT-A
1 TATATACATTCATCA
464878 TATATACA-TCA-CA
1 TATATACATTCATCA
464891 TA-ATACAT
1 TATATACAT
464899 AAGCATCATC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 5 0.16
13 5 0.16
14 9 0.29
15 12 0.39
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (15 bp):
TATATACATTCATCA
Found at i:464887 original size:25 final size:26
Alignment explanation
Indices: 464850--464899 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
464840 CTTTTTTCCT
* *
464850 ATATACATTCATCATAT-ATACATAC
1 ATATACATACATCACATAATACATAC
*
464875 ATATATATACATCACATAATACATA
1 ATATACATACATCACATAATACATA
464900 AGCATCATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (26 bp):
ATATACATACATCACATAATACATAC
Found at i:474896 original size:28 final size:29
Alignment explanation
Indices: 474865--474926 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
474855 ATAATTAATT
* *
474865 TTAAAATTTGGAATATAAAAACA-AAAAA
1 TTAAAATTTGAAAAATAAAAACATAAAAA
* *
474893 TTAAAATTTTAAAAATAAAAATATAAAAA
1 TTAAAATTTGAAAAATAAAAACATAAAAA
474922 TTAAA
1 TTAAA
474927 TTTCAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 19 0.66
29 10 0.34
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (29 bp):
TTAAAATTTGAAAAATAAAAACATAAAAA
Found at i:474908 original size:15 final size:15
Alignment explanation
Indices: 474888--474926 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
474878 TATAAAAACA
* *
474888 AAAAATTAAAATTTT
1 AAAAATTAAAAATAT
474903 AAAAA-TAAAAATAT
1 AAAAATTAAAAATAT
474917 AAAAATTAAA
1 AAAAATTAAA
474927 TTTCAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAAATTAAAAATAT
Found at i:490859 original size:51 final size:51
Alignment explanation
Indices: 490783--490885 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
490773 TTTTTCTATG
490783 TTTTTATTTTTGTTTATTTAAAGGGTTTTTAAAAGAATATATCTTATTGAA
1 TTTTTATTTTTGTTTATTTAAAGGGTTTTTAAAAGAATATATCTTATTGAA
490834 TTTTTATTTTTGTTTATTTAAAGGGTTTTTAAAAGAATATATCTTATTGAA
1 TTTTTATTTTTGTTTATTTAAAGGGTTTTTAAAAGAATATATCTTATTGAA
490885 T
1 T
490886 ATACATTAGC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (51 bp):
TTTTTATTTTTGTTTATTTAAAGGGTTTTTAAAAGAATATATCTTATTGAA
Found at i:510539 original size:117 final size:112
Alignment explanation
Indices: 510335--510613 Score: 285
Period size: 117 Copynumber: 2.4 Consensus size: 112
510325 AAATATAGAA
* *
510335 AATGTCAAGGATAAACTTATATATATAGGAAACCACTAGGATTAGTATATATATATATATATATA
1 AATGTC-A-GATAAACTTATATATATAGGAAACCTCTAGG---A-T-TATATATATAGATATATA
* *
510400 TGACTTCCAAGATAGTTCCACTAACACATACTATGAAGACATATATTTATATAGGC
59 TGACTTCCAAGACAGTTCCACTAACACATACTATGAAG--ATATATATATATAGGC
*
510456 AATG-C-GATAAACTTATATATATAGGAAACCTCTAGGATTA-ATATATAGATGTATATGACTTC
1 AATGTCAGATAAACTTATATATATAGGAAACCTCTAGGATTATATATATAGATATATATGACTTC
* *
510518 CAAGACAGTTCTTCTAGCACTAACAGATGCTATGAAGATATATATATATAGGC
66 CAAGACAG---TTC---CACTAACACATACTATGAAGATATATATATATAGGC
* * * *
510571 AATGTCTAGGATAAACATGTATATATAAGAAATCTCTAGGATT
1 AATGTC-A-GATAAACTTATATATATAGGAAACCTCTAGGATT
510614 GACCTATATA
Statistics
Matches: 137, Mismatches: 11, Indels: 22
0.81 0.06 0.13
Matches are distributed among these distances:
111 27 0.20
112 2 0.01
113 1 0.01
114 4 0.03
115 19 0.14
116 1 0.01
117 48 0.35
119 30 0.22
120 1 0.01
121 4 0.03
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (112 bp):
AATGTCAGATAAACTTATATATATAGGAAACCTCTAGGATTATATATATAGATATATATGACTTC
CAAGACAGTTCCACTAACACATACTATGAAGATATATATATATAGGC
Found at i:510624 original size:30 final size:30
Alignment explanation
Indices: 510557--510627 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 30
510547 CTATGAAGAT
* * *
510557 ATATATATATAGGCAATGTCTAGGATAAAC
1 ATATATATATAAGAAATCTCTAGGATAAAC
* **
510587 ATGTATATATAAGAAATCTCTAGGATTGAC
1 ATATATATATAAGAAATCTCTAGGATAAAC
*
510617 CTATATATATA
1 ATATATATATA
510628 TGCATGTAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (30 bp):
ATATATATATAAGAAATCTCTAGGATAAAC
Found at i:510777 original size:4 final size:4
Alignment explanation
Indices: 510770--510817 Score: 53
Period size: 4 Copynumber: 12.2 Consensus size: 4
510760 CGGGCAAGCA
* * * *
510770 CATG CATG CATA CATA CATA CATA CATG -ATG CATG CATG CATG CATG
1 CATG CATG CATG CATG CATG CATG CATG CATG CATG CATG CATG CATG
510817 C
1 C
510818 CTGCCTGCCA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 3 0.07
4 38 0.93
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (4 bp):
CATG
Found at i:510817 original size:12 final size:12
Alignment explanation
Indices: 510769--510815 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
510759 ACGGGCAAGC
510769 ACATGCATGCAT
1 ACATGCATGCAT
* *
510781 ACATACATACAT
1 ACATGCATGCAT
510793 ACATG-ATGCAT
1 ACATGCATGCAT
*
510804 GCATGCATGCAT
1 ACATGCATGCAT
510816 GCCTGCCTGC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
11 9 0.31
12 20 0.69
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (12 bp):
ACATGCATGCAT
Found at i:512046 original size:22 final size:23
Alignment explanation
Indices: 512020--512066 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
512010 ATAGTTTTAA
*
512020 TATTTTTA-ATTTTTTTAAATTT
1 TATTTTTATATTTTTTAAAATTT
512042 TA-TTTTATATTTTTTAAAATTT
1 TATTTTTATATTTTTTAAAATTT
512064 TAT
1 TAT
512067 ACATTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TATTTTTATATTTTTTAAAATTT
Found at i:512075 original size:18 final size:17
Alignment explanation
Indices: 512043--512081 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
512033 TTTAAATTTT
*
512043 ATTTTATATTTTTTAAA
1 ATTTTATAATTTTTAAA
*
512060 ATTTTATACATTTTTAAT
1 ATTTTATA-ATTTTTAAA
512078 ATTT
1 ATTT
512082 GTAGTGATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTATAATTTTTAAA
Found at i:512566 original size:185 final size:184
Alignment explanation
Indices: 512240--512595 Score: 426
Period size: 185 Copynumber: 1.9 Consensus size: 184
512230 GAACATCTTC
* *
512240 AAACGATGATTCAAAATTACAAAATCATCCTTTAACTTCAAAACATTTTTAATTGAGCTTCGAAG
1 AAACGATGATTCAAAATTACAAAATCACCCTTTAACTTCAAAACATTTTTAATTGAACTTCGAAG
* * * ** ** * * * * *
512305 TATCACCATCTCATCCATCAGACTGTTTTATAGCTTAAAATTAGTTTGAACGTTAAACGTCAATT
66 TATCAACATCTCATCAATCAAACCATTCCATAGCTTAAAATCAGTATGAACATCAAACGTCAAAT
* * * *
512370 TAGATTTGATTTGGAGTAAATTTAAAATATGTACATTAAATTTTAAACTTTCCT
131 TAGACTTGATTTGCAATAAATTTAAAATATATACATTAAATTTTAAACTTTCCT
* * *
512424 AAACTATGATTC-AAATTTCAAAATGACCCTTTAACTTCAAAACATTTTTCAATTGAACTTTCGA
1 AAACGATGATTCAAAATTACAAAATCACCCTTTAACTTCAAAACATTTTT-AATTGAAC-TTCGA
* * * * *
512488 AGTATCAACATCTTATCAATCAAACCATTCCATAGCTTAACATCGGTATGGACATCAAATGTCAA
64 AGTATCAACATCTCATCAATCAAACCATTCCATAGCTTAAAATCAGTATGAACATCAAACGTCAA
* * *
512553 ATTGGACTTGATTTGCAATATATTTAAAATATATAGATTAAAT
129 ATTAGACTTGATTTGCAATAAATTTAAAATATATACATTAAAT
512596 CTCAAACATT
Statistics
Matches: 141, Mismatches: 29, Indels: 3
0.82 0.17 0.02
Matches are distributed among these distances:
183 34 0.24
184 18 0.13
185 89 0.63
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (184 bp):
AAACGATGATTCAAAATTACAAAATCACCCTTTAACTTCAAAACATTTTTAATTGAACTTCGAAG
TATCAACATCTCATCAATCAAACCATTCCATAGCTTAAAATCAGTATGAACATCAAACGTCAAAT
TAGACTTGATTTGCAATAAATTTAAAATATATACATTAAATTTTAAACTTTCCT
Found at i:525441 original size:96 final size:96
Alignment explanation
Indices: 525322--525531 Score: 321
Period size: 96 Copynumber: 2.2 Consensus size: 96
525312 GGTTTCACCT
* * *
525322 CCTTCAAAAGCGGTGGCATCGATGTTCAGAGCAACTGTGGAACTTAGAAAGCTGTTTTGATTATA
1 CCTTCAAAAGCGGTGGCGTCGATGTTCAGAGCAACTCTGGAACTTAGAAAGCTATTTTGATTATA
525387 AATATTTCCCGCCTGCGTGAAGAATTGACCA
66 AATATTTCCCGCCTGCGTGAAGAATTGACCA
* * * * *
525418 CCTTCAAAAGCTGTGGCGTCGATGTTCGGAGCAACTCTGGAATTTAGAACGCTATTTTTATTATA
1 CCTTCAAAAGCGGTGGCGTCGATGTTCAGAGCAACTCTGGAACTTAGAAAGCTATTTTGATTATA
* *
525483 AATATTTTCCTCCTGCGTGAAGAATTGACCA
66 AATATTTCCCGCCTGCGTGAAGAATTGACCA
*
525514 CCTTCATAAGCGGTGGCG
1 CCTTCAAAAGCGGTGGCG
525532 CCACTGTCCG
Statistics
Matches: 102, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
96 102 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.30
Consensus pattern (96 bp):
CCTTCAAAAGCGGTGGCGTCGATGTTCAGAGCAACTCTGGAACTTAGAAAGCTATTTTGATTATA
AATATTTCCCGCCTGCGTGAAGAATTGACCA
Found at i:525577 original size:96 final size:96
Alignment explanation
Indices: 525322--525588 Score: 288
Period size: 96 Copynumber: 2.8 Consensus size: 96
525312 GGTTTCACCT
* * * ** *
525322 CCTTCAAAAGCGGTGGCATCGATGTTCAG-AGCAACTGTGGAACTTAGAAAGCTGTTTTGATTAT
1 CCTTCAAAAGCGGTGGCGTCCATG-TCCGCAGCAACTAAGGAACTTAGAACGCTGTTTTGATTAT
*
525386 AAATATTTCCCGCCTGCGTGAAGAATTGACCA
65 AAATATTTTCCGCCTGCGTGAAGAATTGACCA
* * * * ** * * *
525418 CCTTCAAAAGCTGTGGCGTCGATGTTCGGAGCAACTCTGGAATTTAGAACGCTATTTTTATTATA
1 CCTTCAAAAGCGGTGGCGTCCATGTCCGCAGCAACTAAGGAACTTAGAACGCTGTTTTGATTATA
*
525483 AATATTTTCCTCCTGCGTGAAGAATTGACCA
66 AATATTTTCCGCCTGCGTGAAGAATTGACCA
* * * *
525514 CCTTCATAAGCGGTGGCG-CCACTGTCCGCAGCAGCTAAGTAACTTAGCATC-CTGTTTTGATTA
1 CCTTCAAAAGCGGTGGCGTCCA-TGTCCGCAGCAACTAAGGAACTTAG-AACGCTGTTTTGATTA
525577 TAAATATCTTTC
64 TAAATAT-TTTC
525589 ATCTTTGTCG
Statistics
Matches: 143, Mismatches: 24, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
95 4 0.03
96 133 0.93
97 6 0.04
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (96 bp):
CCTTCAAAAGCGGTGGCGTCCATGTCCGCAGCAACTAAGGAACTTAGAACGCTGTTTTGATTATA
AATATTTTCCGCCTGCGTGAAGAATTGACCA
Found at i:525813 original size:96 final size:95
Alignment explanation
Indices: 525713--526194 Score: 369
Period size: 96 Copynumber: 5.1 Consensus size: 95
525703 CCTTCAAGAC
*
525713 CGGTGG-TGTTGATGTTCGAAGCAGTTGAGGAATTTGGAATGTTGTCTTGATTATCAATATTCGC
1 CGGTGGCT-TTGATGTTCGAAGCAGCTGAGGAATTTGGAATGTTGT-TTGATTATCAATATTCGC
525777 CGCCATTGTGACAAGTTGACAGCCTTCATAAG
64 CGCCATTGTGACAAGTTGACAGCCTTCATAAG
* ** ** * * * * * * * *
525809 CGGTGGCTTCGCCGTAAGGAGCAGCTGAGTAAATTAGTATGTTG-TT-ATAATC-CTCATTCTCC
1 CGGTGGCTTTGATGTTCGAAGCAGCTGAGGAATTTGGAATGTTGTTTGATTATCAAT-ATTCGCC
* * * * *
525871 GCCGTCGTGAC-GGTT-TCATCTCCTTCA-AGAG
65 GCCATTGTGACAAGTTGACA--GCCTTCATA-AG
* * *
525902 CGGTGGCTTTGATGCTCGAAGCAGTTGAGGAATTTGGAATGTTGTTTTGATTATCAATACTCGCC
1 CGGTGGCTTTGATGTTCGAAGCAGCTGAGGAATTTGGAATGTTG-TTTGATTATCAATATTCGCC
525967 GCCATTGTGACAAGTTGACAGCCTTCATAAG
65 GCCATTGTGACAAGTTGACAGCCTTCATAAG
** ** ** * * * * * * * * *
525998 CGGTGGCTCCGCCGTAAGCAGCAGCTGAGTAAATTAGTATGTTG-TT-ATAATC-CTCATTCTCG
1 CGGTGGCTTTGATGTTCGAAGCAGCTGAGGAATTTGGAATGTTGTTTGATTATCAAT-ATTCGCC
* * * **
526060 GCCGTTGTGAC-GGTTTCACCTCCTTCA-AGAG
65 GCCATTGTGACAAG-TTGACAGCCTTCATA-AG
*
526091 CGGTGG-TGTTGATGTTCGAAGCAGATGAGGAATTTGGAATGTTGTTTTGATTATCAATATTCGC
1 CGGTGGCT-TTGATGTTCGAAGCAGCTGAGGAATTTGGAATGTTG-TTTGATTATCAATATTCGC
*
526155 CGCCATTGTGACAAATTGACAGCCTTCATAAG
64 CGCCATTGTGACAAGTTGACAGCCTTCATAAG
526187 CGGTGGCT
1 CGGTGGCT
526195 CCGCCGTAAA
Statistics
Matches: 278, Mismatches: 85, Indels: 45
0.68 0.21 0.11
Matches are distributed among these distances:
91 2 0.01
92 9 0.03
93 121 0.44
94 4 0.01
95 4 0.01
96 127 0.46
97 9 0.03
98 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (95 bp):
CGGTGGCTTTGATGTTCGAAGCAGCTGAGGAATTTGGAATGTTGTTTGATTATCAATATTCGCCG
CCATTGTGACAAGTTGACAGCCTTCATAAG
Found at i:525896 original size:189 final size:189
Alignment explanation
Indices: 525639--526406 Score: 1217
Period size: 189 Copynumber: 4.1 Consensus size: 189
525629 GGCCATCGGT
* *
525639 AGCAGCTGAGTAAAATAGTATGTT-TTCATAATCCTCATTCTCCGCCGTTGTGACGGTTTCACCT
1 AGCAGCTGAGTAAATTAGTATGTTGTT-ATAATCCTCATTCTCCGCCGTCGTGACGGTTTCACCT
* *
525703 CCTTCAAGACCGGTGGTGTTGATGTTCGAAGCAGTTGAGGAATTTGGAATGTTGTCTTGATTATC
65 CCTTCAAGAGCGGTGGTGTTGATGTTCGAAGCAGTTGAGGAATTTGGAATGTTGTTTTGATTATC
* *
525768 AATATTCGCCGCCATTGTGACAAGTTGACAGCCTTCATAAGCGGTGGCTTCGCCGTAAGG
130 AATATTCGCCGCCATTGTGACAAGTTGACAGCCTTCATAAGCGGTGGCTCCGCCGTAAGC
*
525828 AGCAGCTGAGTAAATTAGTATGTTGTTATAATCCTCATTCTCCGCCGTCGTGACGGTTTCATCTC
1 AGCAGCTGAGTAAATTAGTATGTTGTTATAATCCTCATTCTCCGCCGTCGTGACGGTTTCACCTC
*
525893 CTTCAAGAGCGGTGGCT-TTGATGCTCGAAGCAGTTGAGGAATTTGGAATGTTGTTTTGATTATC
66 CTTCAAGAGCGGTGG-TGTTGATGTTCGAAGCAGTTGAGGAATTTGGAATGTTGTTTTGATTATC
*
525957 AATACTCGCCGCCATTGTGACAAGTTGACAGCCTTCATAAGCGGTGGCTCCGCCGTAAGC
130 AATATTCGCCGCCATTGTGACAAGTTGACAGCCTTCATAAGCGGTGGCTCCGCCGTAAGC
* *
526017 AGCAGCTGAGTAAATTAGTATGTTGTTATAATCCTCATTCTCGGCCGTTGTGACGGTTTCACCTC
1 AGCAGCTGAGTAAATTAGTATGTTGTTATAATCCTCATTCTCCGCCGTCGTGACGGTTTCACCTC
*
526082 CTTCAAGAGCGGTGGTGTTGATGTTCGAAGCAGATGAGGAATTTGGAATGTTGTTTTGATTATCA
66 CTTCAAGAGCGGTGGTGTTGATGTTCGAAGCAGTTGAGGAATTTGGAATGTTGTTTTGATTATCA
*
526147 ATATTCGCCGCCATTGTGACAAATTGACAGCCTTCATAAGCGGTGGCTCCGCCGTAAAG-
131 ATATTCGCCGCCATTGTGACAAGTTGACAGCCTTCATAAGCGGTGGCTCCGCCGT-AAGC
* * * *
526206 AGCAGTTGAGTAAATTAGTA---TGTTATAATCCTCATTCTCCACAGTCGTGACGGTTTCACCTA
1 AGCAGCTGAGTAAATTAGTATGTTGTTATAATCCTCATTCTCCGCCGTCGTGACGGTTTCACCTC
* ** *
526268 CTTCAAGAGCGGCGACGTTGATGTTCGAAGCAATTGAGGAATTTGGAATGTTGTTTTGATTATCA
66 CTTCAAGAGCGGTGGTGTTGATGTTCGAAGCAGTTGAGGAATTTGGAATGTTGTTTTGATTATCA
* ** * * *
526333 ATATTCGCCGCCATTGTGACAACTTGATGGCCTTCAGAAGCGGTGGCGCCGCCGTTAGC
131 ATATTCGCCGCCATTGTGACAAGTTGACAGCCTTCATAAGCGGTGGCTCCGCCGTAAGC
526392 AGCAGCTGAG-AAATT
1 AGCAGCTGAGTAAATT
526407 TTGCTCTTCG
Statistics
Matches: 540, Mismatches: 34, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
185 7 0.01
186 156 0.29
188 1 0.00
189 370 0.69
190 6 0.01
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (189 bp):
AGCAGCTGAGTAAATTAGTATGTTGTTATAATCCTCATTCTCCGCCGTCGTGACGGTTTCACCTC
CTTCAAGAGCGGTGGTGTTGATGTTCGAAGCAGTTGAGGAATTTGGAATGTTGTTTTGATTATCA
ATATTCGCCGCCATTGTGACAAGTTGACAGCCTTCATAAGCGGTGGCTCCGCCGTAAGC
Found at i:528522 original size:15 final size:15
Alignment explanation
Indices: 528502--528568 Score: 64
Period size: 15 Copynumber: 4.5 Consensus size: 15
528492 ATGTCGACGG
528502 TGGTGGTTTTGGAGT
1 TGGTGGTTTTGGAGT
*
528517 TGGTGGTCTTGGAGT
1 TGGTGGTTTTGGAGT
* ** *
528532 TAGTGGTGGT-GATTT
1 TGGTGGTTTTGGA-GT
*
528547 TGGTGGTTTTGGAGC
1 TGGTGGTTTTGGAGT
528562 TGGTGGT
1 TGGTGGT
528569 GGTGGACATT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
14 2 0.05
15 36 0.90
16 2 0.05
ACGTcount: A:0.07, C:0.03, G:0.46, T:0.43
Consensus pattern (15 bp):
TGGTGGTTTTGGAGT
Found at i:528550 original size:30 final size:30
Alignment explanation
Indices: 528516--528572 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
528506 GGTTTTGGAG
*
528516 TTGGTGGTCTTGGAGTTAGTGGTGGTGATT
1 TTGGTGGTCTTGGAGCTAGTGGTGGTGATT
* *
528546 TTGGTGGTTTTGGAGCTGGTGGTGGTG
1 TTGGTGGTCTTGGAGCTAGTGGTGGTG
528573 GACATTCAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.07, C:0.04, G:0.47, T:0.42
Consensus pattern (30 bp):
TTGGTGGTCTTGGAGCTAGTGGTGGTGATT
Found at i:529334 original size:130 final size:130
Alignment explanation
Indices: 529151--529412 Score: 409
Period size: 130 Copynumber: 2.0 Consensus size: 130
529141 ATATTCTATT
* * *
529151 AATTTAATCTTAATCTTAAAAAAATAATTTAACCCTCATTTACATCTACTGTCAATTAATTTTTA
1 AATTTAATCTTAATCTTAAAAAAATAATTCAACCCTCATTAACACCTACTGTCAATTAATTTTTA
*
529216 ATTTTAAAATTTTAAAAATAATTTTTTTAATAATATGTCAACTGAATTTATTAAAAATTAAAGTA
66 ATTTTAAAATTTTAAAAAT-ATTTTTTTAATAATATGTCAACTGAATTTATTAAAAATTAAAATA
529281 G
130 G
* * *
529282 AATTTAGTTTTAATCTT-AAAAAATAATTCAACCCTCATTAACACCTATTGTCAATTAATTTTTA
1 AATTTAATCTTAATCTTAAAAAAATAATTCAACCCTCATTAACACCTACTGTCAATTAATTTTTA
* ** *
529346 CTTTTAAAATTTTAAAAATATTTTTTTAATAATATGTCGGCTGAATTTATTAGAAATTAAAATAG
66 ATTTTAAAATTTTAAAAATATTTTTTTAATAATATGTCAACTGAATTTATTAAAAATTAAAATAG
529411 AA
1 AA
529413 AAATATGAAA
Statistics
Matches: 120, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
129 44 0.37
130 61 0.51
131 15 0.12
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.43
Consensus pattern (130 bp):
AATTTAATCTTAATCTTAAAAAAATAATTCAACCCTCATTAACACCTACTGTCAATTAATTTTTA
ATTTTAAAATTTTAAAAATATTTTTTTAATAATATGTCAACTGAATTTATTAAAAATTAAAATAG
Found at i:529844 original size:26 final size:25
Alignment explanation
Indices: 529796--529849 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
529786 GTACAATAAT
*
529796 AAAAAAGCGTGCCACAAGATAGAAA
1 AAAAAAGCGTGCCACAAAATAGAAA
*
529821 AAAAAAGCGTGCCACAAAAGTAGATA
1 AAAAAAGCGTGCCACAAAA-TAGAAA
529847 AAA
1 AAA
529850 GCAAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 18 0.69
26 8 0.31
ACGTcount: A:0.57, C:0.15, G:0.19, T:0.09
Consensus pattern (25 bp):
AAAAAAGCGTGCCACAAAATAGAAA
Found at i:530617 original size:26 final size:25
Alignment explanation
Indices: 530576--530624 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 25
530566 TAACATTGCT
530576 TTTGAAAAACGTTTTTAAAAAGTAC
1 TTTGAAAAACGTTTTTAAAAAGTAC
530601 TTTGAAAAA-GTAATTTTAAAAAGT
1 TTTGAAAAACGT--TTTTAAAAAGT
530625 TTGAATTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 2 0.09
25 9 0.41
26 11 0.50
ACGTcount: A:0.47, C:0.04, G:0.12, T:0.37
Consensus pattern (25 bp):
TTTGAAAAACGTTTTTAAAAAGTAC
Found at i:531185 original size:20 final size:20
Alignment explanation
Indices: 531160--531206 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
531150 TTCTCCTTAA
*
531160 ATTATTTTATTAACAATATT
1 ATTATTTTATTAACAAAATT
* * *
531180 ATTATTGTATTTATAAAATT
1 ATTATTTTATTAACAAAATT
531200 ATTATTT
1 ATTATTT
531207 AATAAATAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTATTTTATTAACAAAATT
Found at i:534735 original size:31 final size:31
Alignment explanation
Indices: 534699--534757 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
534689 TAGTCCAATA
*
534699 ACTTAAATAAAAACTTTCGAATAATTTAATG
1 ACTTAAATAAAAACTTTCAAATAATTTAATG
* *
534730 ACTTAAATAAAAAGTTTTAAATAATTTA
1 ACTTAAATAAAAACTTTCAAATAATTTA
534758 TTAACTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTCAAATAATTTAATG
Found at i:535429 original size:7 final size:7
Alignment explanation
Indices: 535417--535442 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
535407 AAAATTTTAA
535417 TAAATAT
1 TAAATAT
535424 TAAATAT
1 TAAATAT
535431 TAAATAT
1 TAAATAT
535438 TAAAT
1 TAAAT
535443 TAAAATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TAAATAT
Found at i:545751 original size:30 final size:29
Alignment explanation
Indices: 545704--545904 Score: 188
Period size: 30 Copynumber: 6.7 Consensus size: 29
545694 TTATTTTTTG
* * *
545704 ACCCCAAACTATCCAAAAATTTAAATTTA
1 ACCCCAAATTTTCCAAAAATTTGAATTTA
* * *
545733 ACCCTTAAATTTTCCAAAAATTTGAGTTCA
1 ACCC-CAAATTTTCCAAAAATTTGAATTTA
* *
545763 ACCCTTAAATTTTCCAAAAATTTGAATTCA
1 ACCC-CAAATTTTCCAAAAATTTGAATTTA
545793 ACCCCCAAATTTTCCAAAAATTTGAATTTGA
1 A-CCCCAAATTTTCCAAAAATTTGAATTT-A
* * **
545824 TCCCTAAATTTTCCAAAAATTCCAATTTGA
1 ACCCCAAATTTTCCAAAAATTTGAATTT-A
* * *
545854 TCCCCAAAATTTCC-AAAATTTCCAATTTA
1 ACCCCAAATTTTCCAAAAATTT-GAATTTA
*
545883 ATCCCCAATTTTTCCAAAAATT
1 A-CCCCAAATTTTCCAAAAATT
545905 CCGATTTGAC
Statistics
Matches: 147, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
29 11 0.07
30 126 0.86
31 10 0.07
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.34
Consensus pattern (29 bp):
ACCCCAAATTTTCCAAAAATTTGAATTTA
Found at i:545867 original size:90 final size:90
Alignment explanation
Indices: 545705--545904 Score: 217
Period size: 90 Copynumber: 2.2 Consensus size: 90
545695 TATTTTTTGA
* * ** *
545705 CCCCAAACTATCCAAAAATTTAAATTTAACCCTTAAATTTTCCAAAAATTTGAGTTCAACCCTTA
1 CCCCAAATTTTCCAAAAATTTAAATTTAACCCTTAAATTTTCCAAAAATTCAAGTTCAACCCTCA
* *
545770 AATTTTCCAAAAATTT-GAATTCAAC
66 AAATTTCC-AAAATTTCCAATTCAAC
* * * * *
545795 CCCCAAATTTTCCAAAAATTTGAATTTGATCCC-TAAATTTTCCAAAAATTCCAATTTGATCCC-
1 CCCCAAATTTTCCAAAAATTTAAATTT-AACCCTTAAATTTTCCAAAAATT-CAAGTTCAACCCT
* *
545858 CAAAATTTCCAAAATTTCCAATTTAAT
64 CAAAATTTCCAAAATTTCCAATTCAAC
*
545885 CCCCAATTTTTCCAAAAATT
1 CCCCAAATTTTCCAAAAATT
545905 CCGATTTGAC
Statistics
Matches: 92, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
89 7 0.08
90 74 0.80
91 11 0.12
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.34
Consensus pattern (90 bp):
CCCCAAATTTTCCAAAAATTTAAATTTAACCCTTAAATTTTCCAAAAATTCAAGTTCAACCCTCA
AAATTTCCAAAATTTCCAATTCAAC
Found at i:548838 original size:15 final size:15
Alignment explanation
Indices: 548814--548852 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
548804 AATAAAAAAG
548814 GAAGAAGAAAATGAT
1 GAAGAAGAAAATGAT
* *
548829 GAAGATGAAAATGAA
1 GAAGAAGAAAATGAT
*
548844 GATGAAGAA
1 GAAGAAGAA
548853 GAGAGGTGTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.13
Consensus pattern (15 bp):
GAAGAAGAAAATGAT
Found at i:552025 original size:24 final size:24
Alignment explanation
Indices: 551995--552047 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
551985 CACAACATAT
551995 GCTCCGACAGCACCACAATATACA
1 GCTCCGACAGCACCACAATATACA
552019 GCTCCGACAGCACCACAATATACA
1 GCTCCGACAGCACCACAATATACA
552043 GCTCC
1 GCTCC
552048 TCCTCCACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.34, C:0.40, G:0.13, T:0.13
Consensus pattern (24 bp):
GCTCCGACAGCACCACAATATACA
Found at i:552208 original size:21 final size:21
Alignment explanation
Indices: 552161--552212 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
552151 CCTTCATCCG
* **
552161 CATACCCTCCTCCACCTTCGG
1 CATACCCTCCGCCACCTTCCA
*
552182 CTTACCCTCCGCCACCTTCCA
1 CATACCCTCCGCCACCTTCCA
552203 CATACCCTCC
1 CATACCCTCC
552213 ACCTCCACCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.15, C:0.56, G:0.06, T:0.23
Consensus pattern (21 bp):
CATACCCTCCGCCACCTTCCA
Found at i:553366 original size:73 final size:73
Alignment explanation
Indices: 553276--553423 Score: 287
Period size: 73 Copynumber: 2.0 Consensus size: 73
553266 TGGACAAAAA
553276 TATTAAAAGTCCAAGCAATATTAGTTGTGATGAAATCCCTAGCATAAGAACAGTGAAGGAGTTAC
1 TATTAAAAGTCCAAGCAATATTAGTTGTGATGAAATCCCTAGCATAAGAACAGTGAAGGAGTTAC
553341 ATTACATG
66 ATTACATG
*
553349 TATTAAAAGTCCAAGCAATATTAGTTGTGATGAAATCTCTAGCATAAGAACAGTGAAGGAGTTAC
1 TATTAAAAGTCCAAGCAATATTAGTTGTGATGAAATCCCTAGCATAAGAACAGTGAAGGAGTTAC
553414 ATTACATG
66 ATTACATG
553422 TA
1 TA
553424 GGATCATTTG
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (73 bp):
TATTAAAAGTCCAAGCAATATTAGTTGTGATGAAATCCCTAGCATAAGAACAGTGAAGGAGTTAC
ATTACATG
Found at i:555860 original size:18 final size:17
Alignment explanation
Indices: 555833--555885 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
555823 TAAAAATAAA
*
555833 AAATAAATAAATATTATT
1 AAATACATAAATATT-TT
* *
555851 GAATACATAAAAATTTT
1 AAATACATAAATATTTT
555868 AAATACA-AAATTATTTT
1 AAATACATAAA-TATTTT
555885 A
1 A
555886 TGTAAATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 3 0.10
17 14 0.48
18 12 0.41
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (17 bp):
AAATACATAAATATTTT
Found at i:563859 original size:16 final size:17
Alignment explanation
Indices: 563828--563860 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
563818 TGTAAAACAA
563828 CATTCATCCCTTCATCT
1 CATTCATCCCTTCATCT
*
563845 CATTC-TCCGTTCATCT
1 CATTCATCCCTTCATCT
563861 TTAAGCCTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.15, C:0.39, G:0.03, T:0.42
Consensus pattern (17 bp):
CATTCATCCCTTCATCT
Found at i:565094 original size:31 final size:31
Alignment explanation
Indices: 565058--565123 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
565048 ATCATTTGAT
*
565058 TTAAGTACCATATTAAATATCAAAA-TCAAAC
1 TTAAGTACCAAATTAAATATCAAAACT-AAAC
* * *
565089 TTAAGTATCAAATTGAATATTAAAACTAAAC
1 TTAAGTACCAAATTAAATATCAAAACTAAAC
565120 TTAA
1 TTAA
565124 TTATGATATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 29 0.97
32 1 0.03
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.32
Consensus pattern (31 bp):
TTAAGTACCAAATTAAATATCAAAACTAAAC
Found at i:565819 original size:21 final size:21
Alignment explanation
Indices: 565767--565817 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
565757 ATTCACATGT
*
565767 ATTCAAAATATATGAAAATAA
1 ATTCAAAAAATATGAAAATAA
565788 ATTCAAAAAATAT-AAAA-AA
1 ATTCAAAAAATATGAAAATAA
565807 ATTCCAAAAAA
1 ATT-CAAAAAA
565818 ATTAGCATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 5 0.18
20 11 0.39
21 12 0.43
ACGTcount: A:0.67, C:0.08, G:0.02, T:0.24
Consensus pattern (21 bp):
ATTCAAAAAATATGAAAATAA
Found at i:568363 original size:31 final size:31
Alignment explanation
Indices: 568328--568395 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
568318 TTGCATAATG
* *
568328 GTCATTAAACTGTT-TAAAAATTTTCATTTAA
1 GTCATTAAACTATTCAAAAAATTTT-ATTTAA
*
568359 GTCATTGAACTATTCAAAAAATTTTATTTAA
1 GTCATTAAACTATTCAAAAAATTTTATTTAA
568390 GTCATT
1 GTCATT
568396 GAGCTGCTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 24 0.73
32 9 0.27
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.44
Consensus pattern (31 bp):
GTCATTAAACTATTCAAAAAATTTTATTTAA
Found at i:570983 original size:21 final size:20
Alignment explanation
Indices: 570959--571011 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
570949 TAACTCAATT
*
570959 AATTTAAATTATTTAATTCAA
1 AATTTAAATT-TTTAATTAAA
* *
570980 AATTAAAATTTTTTATTAAA
1 AATTTAAATTTTTAATTAAA
571000 AATTTTAAATTT
1 AA-TTTAAATTT
571012 ATCAGATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTTAAATTTTTAATTAAA
Found at i:571001 original size:20 final size:21
Alignment explanation
Indices: 570959--571003 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
570949 TAACTCAATT
* *
570959 AATTTAAATTATTTAATTCAA
1 AATTAAAATTATTTAATTAAA
*
570980 AATTAAAATT-TTTTATTAAA
1 AATTAAAATTATTTAATTAAA
571000 AATT
1 AATT
571004 TTAAATTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
AATTAAAATTATTTAATTAAA
Found at i:573611 original size:182 final size:180
Alignment explanation
Indices: 573194--573885 Score: 608
Period size: 190 Copynumber: 3.7 Consensus size: 180
573184 GCAAGCACCA
** * * * * ** *
573194 AATATGGCAAACATAATAAAATCCAGTGGACCAAATCGAAGCTAAAATGTCAACATCGACTTGAG
1 AATATGGCAAACATAATAAAGGCCA-TGGA-CAAATTGAAGCTAAAAGGTCAACATCAAATCAAA
*
573259 GAAGCAAATGGAACAGCAACAACAACGATGGCAATGACAACATAATGAAGCCTTGGGATTTAGGT
64 GAAGC-AA---AA-AG-AACAACAACGA---CAACGACAACATAATGAAGCCTTGGGATTTAGGT
* * * * * *
573324 AGTTTTCAGAGA-TTACCTTGTTTTCAGG-TTCAAG-AAAGCACCATAACCAAAAGATGGGAATA
120 A-CTTT-A-AGATTTACCTGGTTTT-AGGATTCAAGCAAAGCACCATAGCCAAAACAAGGGAATG
* * * * *
573386 AATATGGCAAACATAATCAAGTCCAATGGACCAAATTGAAGCTAAAAGCTCAATATTAAATCAAA
1 AATATGGCAAACATAATAAAGGCC-ATGGA-CAAATTGAAGCTAAAAGGTCAACATCAAATCAAA
** *
573451 GAAG-AAAAAGGAACAACAACGACCGCGACAACATAATGAAGCCTTGGGATTTGGGTACTTTAAG
64 GAAGCAAAAA-GAACAACAACGACAACGACAACATAATGAAGCCTTGGGATTTAGGTACTTTAAG
* * *
573515 ATTTACCCGGTTTTAGGATTCAAGCAAAGCACCATAGCCAGAACAAGGGAAGG
128 ATTTACCTGGTTTTAGGATTCAAGCAAAGCACCATAGCCAAAACAAGGGAATG
* * *
573568 AATATAGAAAACATAATAAAGGCCAGTGGACAAATTCGAAGCTAAAAGGTCAACATCAAACCAAA
1 AATATGGCAAACATAATAAAGGCCA-TGGACAAATT-GAAGCTAAAAGGTCAACATCAAATCAAA
* * * * *
573633 GAAGCAAACACAAAATAAAAATGGCGTTGACAACTACAATATAATGAAGCCTTGGGATTT-GAGT
64 GAAGCAAA-A-AGAACAACAA---C---GACAACGACAACATAATGAAGCCTTGGGATTTAG-GT
** * * * *
573697 ACTTTCGGATTTACCTGGGTTTCGGATTCAAGCAGAGCACCATAGCCAAAACAAGGAAATG
120 ACTTTAAGATTTACCTGGTTTTAGGATTCAAGCAAAGCACCATAGCCAAAACAAGGGAATG
* *
573758 AATATGGCAAACATAATAAATG-C--GGACAAATTTGAAGCTACAAGGTCAACATCAAATCAAAG
1 AATATGGCAAACATAATAAAGGCCATGGACAAA-TTGAAGCTAAAAGGTCAACATCAAATCAAAG
* * ** * * *
573820 AAGCAAATAGAACAACAACGACAACTATGACTTAATGAAGCCTTGGGATTTAGTTACTTTGAGAT
65 AAGCAAAAAGAACAACAACGACAACGACAACATAATGAAGCCTTGGGATTTAGGTACTTTAAGAT
573885 T
130 T
573886 GATATTACCC
Statistics
Matches: 416, Mismatches: 65, Indels: 52
0.78 0.12 0.10
Matches are distributed among these distances:
178 38 0.09
179 1 0.00
180 6 0.01
181 25 0.06
182 77 0.19
183 34 0.08
184 14 0.03
185 1 0.00
186 53 0.13
187 6 0.01
189 2 0.00
190 103 0.25
192 55 0.13
193 1 0.00
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.21
Consensus pattern (180 bp):
AATATGGCAAACATAATAAAGGCCATGGACAAATTGAAGCTAAAAGGTCAACATCAAATCAAAGA
AGCAAAAAGAACAACAACGACAACGACAACATAATGAAGCCTTGGGATTTAGGTACTTTAAGATT
TACCTGGTTTTAGGATTCAAGCAAAGCACCATAGCCAAAACAAGGGAATG
Found at i:579053 original size:25 final size:25
Alignment explanation
Indices: 579006--579054 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
578996 TTATATGTTT
**
579006 TAAAATTATTTTATTTTTTATAAAG
1 TAAAATTATTTTATTTTAAATAAAG
579031 TAAAA-TATTTTATTTTAAAATAAA
1 TAAAATTATTTTATTTT-AAATAAA
579055 CGATAAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TAAAATTATTTTATTTTAAATAAAG
Found at i:579145 original size:30 final size:30
Alignment explanation
Indices: 579076--579146 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
579066 ATTGATCTGG
* * * *
579076 ATATAAGAAAATCTGGTTTTGATTAAAGAT
1 ATATAATAAAATCTGATTTTGATGAAAAAT
579106 ATATAATAAAATCTGATTTTGATGAAATAAT
1 ATATAATAAAATCTGATTTTGATGAAA-AAT
*
579137 TTAT-ATAAAA
1 ATATAATAAAA
579147 ATTATTTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 30 0.86
31 5 0.14
ACGTcount: A:0.48, C:0.03, G:0.11, T:0.38
Consensus pattern (30 bp):
ATATAATAAAATCTGATTTTGATGAAAAAT
Found at i:586572 original size:29 final size:29
Alignment explanation
Indices: 586529--586585 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
586519 TTTAATTGAA
586529 ACAAAAAAATAACTTAAGTACTAAATTAAG
1 ACAAAAAAATAACTTAA-TACTAAATTAAG
* *
586559 ACAAAAAAA-AACTTGATATTAAATTAA
1 ACAAAAAAATAACTTAATACTAAATTAA
586586 ATATTGAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 10 0.40
29 6 0.24
30 9 0.36
ACGTcount: A:0.61, C:0.09, G:0.05, T:0.25
Consensus pattern (29 bp):
ACAAAAAAATAACTTAATACTAAATTAAG
Found at i:586581 original size:28 final size:28
Alignment explanation
Indices: 586515--586586 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 28
586505 TAAAAATATA
*
586515 AATATTTAATTGAAACAAAAAAATAACTT
1 AATATTAAATT-AAACAAAAAAATAACTT
*
586544 AAGTACTAAATTAAGACAAAAAAA-AACTT
1 AA-TATTAAATTAA-ACAAAAAAATAACTT
*
586573 GATATTAAATTAAA
1 AATATTAAATTAAA
586587 TATTGAAGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
27 1 0.03
28 10 0.27
29 10 0.27
30 16 0.43
ACGTcount: A:0.60, C:0.07, G:0.06, T:0.28
Consensus pattern (28 bp):
AATATTAAATTAAACAAAAAAATAACTT
Found at i:588474 original size:13 final size:12
Alignment explanation
Indices: 588456--588489 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
588446 ATATAAATTC
588456 AAACAAATAAGGA
1 AAACAAAT-AGGA
588469 AAACAAATAGGA
1 AAACAAATAGGA
588481 ACAACAAAT
1 A-AACAAAT
588490 TAAAAAAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.68, C:0.12, G:0.12, T:0.09
Consensus pattern (12 bp):
AAACAAATAGGA
Found at i:589362 original size:86 final size:86
Alignment explanation
Indices: 589248--589426 Score: 232
Period size: 86 Copynumber: 2.1 Consensus size: 86
589238 GAGCTATTCG
* * * *
589248 AGCTCAAGCTTGATTAAGCTTGTTTATCAATTTTTGTACTCAAGTTTGAACTTCAGCTCAATTAA
1 AGCTCGAGCTTGATTAAGCTTATTTATCAATTTTTATACTCAAGCTTGAACTTCAGCTCAATTAA
* *
589313 GCTCATATGTATTAAAGCTCA
66 GCTCATACGCATTAAAGCTCA
* * * * *
589334 AGCTCGAGCTTGATTCAGCTTATTTATCAATTTTTATATTCAAGCTTGAATTTTAGCTCGATTAA
1 AGCTCGAGCTTGATTAAGCTTATTTATCAATTTTTATACTCAAGCTTGAACTTCAGCTCAATTAA
* **
589399 GCTCGTACGCATTAAAGCTTG
66 GCTCATACGCATTAAAGCTCA
589420 AGCTCGA
1 AGCTCGA
589427 ACTCAGCTTG
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
86 79 1.00
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (86 bp):
AGCTCGAGCTTGATTAAGCTTATTTATCAATTTTTATACTCAAGCTTGAACTTCAGCTCAATTAA
GCTCATACGCATTAAAGCTCA
Found at i:593579 original size:16 final size:16
Alignment explanation
Indices: 593558--593588 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
593548 AACTTCGAAT
593558 TTATTTATTATTTTTA
1 TTATTTATTATTTTTA
*
593574 TTATTTTTTATTTTT
1 TTATTTATTATTTTT
593589 TTCCATAATT
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:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (16 bp):
TTATTTATTATTTTTA
Found at i:594381 original size:12 final size:13
Alignment explanation
Indices: 594341--594383 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
594331 CTGGACATAT
594341 AATAAAATA-AATA
1 AATAAAATAGAA-A
594354 AATAAAATAGAAA
1 AATAAAATAGAAA
*
594367 AATAAAA-ATAAA
1 AATAAAATAGAAA
594379 AATAA
1 AATAA
594384 CCGGGTTGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 9 0.32
13 17 0.61
14 2 0.07
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (13 bp):
AATAAAATAGAAA
Found at i:604308 original size:31 final size:31
Alignment explanation
Indices: 604273--604339 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
604263 CAAAAATATC
*
604273 ATTGAACTATTAGAAAATTTTCATTTAAGTT
1 ATTGAACTATTAGAAAATTTTCATTTAAATT
* * *
604304 ATTGAACTATTAGAGAGTTTTTATTTAAATT
1 ATTGAACTATTAGAAAATTTTCATTTAAATT
604335 ATTGA
1 ATTGA
604340 GCTGTTAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.46
Consensus pattern (31 bp):
ATTGAACTATTAGAAAATTTTCATTTAAATT
Found at i:611480 original size:15 final size:15
Alignment explanation
Indices: 611460--611490 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
611450 ACGTTCAAGC
611460 TGTTCATGCAGTAGT
1 TGTTCATGCAGTAGT
611475 TGTTCATGCAGTAGT
1 TGTTCATGCAGTAGT
611490 T
1 T
611491 AAACATGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.13, G:0.26, T:0.42
Consensus pattern (15 bp):
TGTTCATGCAGTAGT
Found at i:625696 original size:23 final size:23
Alignment explanation
Indices: 625669--625738 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
625659 TTAGATATCT
*
625669 TTTTGGTTTACAAGGACTTAGAA
1 TTTTGGTTTACAAGGACTTAAAA
** ***
625692 TTTT-GTTT-TTA-GA-TTATCT
1 TTTTGGTTTACAAGGACTTAAAA
625711 TTTTGGTTTACAAGGACTTAAAA
1 TTTTGGTTTACAAGGACTTAAAA
625734 TTTTG
1 TTTTG
625739 TTTTTCTTTG
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
19 7 0.21
20 6 0.18
21 2 0.06
22 6 0.18
23 12 0.36
ACGTcount: A:0.26, C:0.07, G:0.17, T:0.50
Consensus pattern (23 bp):
TTTTGGTTTACAAGGACTTAAAA
Found at i:625716 original size:42 final size:41
Alignment explanation
Indices: 625654--625743 Score: 162
Period size: 42 Copynumber: 2.2 Consensus size: 41
625644 TTGGGTTTTG
*
625654 TGTTTTTAGATATCTTTTTGGTTTACAAGGACTTAGAATTT
1 TGTTTTTAGATATCTTTTTGGTTTACAAGGACTTAAAATTT
625695 TGTTTTTAGATTATCTTTTTGGTTTACAAGGACTTAAAATTT
1 TGTTTTTAGA-TATCTTTTTGGTTTACAAGGACTTAAAATTT
625737 TGTTTTT
1 TGTTTTT
625744 CTTTGTTTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 10 0.21
42 37 0.79
ACGTcount: A:0.23, C:0.07, G:0.16, T:0.54
Consensus pattern (41 bp):
TGTTTTTAGATATCTTTTTGGTTTACAAGGACTTAAAATTT
Found at i:626407 original size:135 final size:137
Alignment explanation
Indices: 626221--626465 Score: 431
Period size: 135 Copynumber: 1.8 Consensus size: 137
626211 GCATCTATCA
* *
626221 TCTTAGAAAAAGGGGTGTTCAAGGGCAACTAGGTGTGTGCCTAATTGAATGCATCTTGCCCGAAA
1 TCTTAGAAAAAGGGGTGTTCAAGGGAAACTAGGTGTGTGCCTAATTGAATGCATCTTGCCCAAAA
*
626286 GGGT-TAAGGCGCTTTTGTTGTTTGATGTTAAGCCGC-ATGGCTTAAGAACACTTCTCGTCTGGT
66 GGGTCTAAGGCGCTATTGTTGTTTGATGTTAAGCCGCAATGGCTTAAGAACACTTCTCGTCTGGT
626349 CCGGTTG
131 CCGGTTG
* *
626356 TCTTAGAAAAAGGGGTGTTCAATGGAAACTCGGTGTGTGCCTAATTGAATGCATCTTGCCCAAAA
1 TCTTAGAAAAAGGGGTGTTCAAGGGAAACTAGGTGTGTGCCTAATTGAATGCATCTTGCCCAAAA
626421 GGGTCTAAGGCGCTATTGTTGTTTGATGTTAAGCCGCAATGGCTT
66 GGGTCTAAGGCGCTATTGTTGTTTGATGTTAAGCCGCAATGGCTT
626466 GCAAACACTG
Statistics
Matches: 103, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
135 65 0.63
136 31 0.30
137 7 0.07
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (137 bp):
TCTTAGAAAAAGGGGTGTTCAAGGGAAACTAGGTGTGTGCCTAATTGAATGCATCTTGCCCAAAA
GGGTCTAAGGCGCTATTGTTGTTTGATGTTAAGCCGCAATGGCTTAAGAACACTTCTCGTCTGGT
CCGGTTG
Found at i:627726 original size:2 final size:2
Alignment explanation
Indices: 627719--627770 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
627709 ATGTTAAAAG
627719 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
627761 CT TT AT AT AT
1 AT AT AT AT AT
627771 TTTTTAGATT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:632563 original size:133 final size:132
Alignment explanation
Indices: 632304--632682 Score: 460
Period size: 132 Copynumber: 2.9 Consensus size: 132
632294 AGCTGCTTTC
* * * *
632304 CCTGTATGTCACGAATTTGGGTTTTATGTG-TTCTTTTACCTGACTGCTATCTCGTATCATTTTG
1 CCTGTATGTCACAAATCTGGG-TTTATGTGTTTCTTTTACCTGACTGCTAACTAGTATCATTTTG
* *
632368 CTCATCCCATCTCGTATCAAGAATCATAGACCACTGATGTCTTTGTACTGCTTATATCGGTTAAT
65 CTCATCCCATCTCGTATCAAGAATCATAGACCACGGATGTCTTTGTACTGCTCATATCGGTTAAT
632433 ATA
130 ATA
*
632436 CCTGTATGTCAC-AATCTGGGTTTGATGTGTTTCTTTTACCTGACTGATAACTAGTATCATTTTG
1 CCTGTATGTCACAAATCTGGGTTT-ATGTGTTTCTTTTACCTGACTGCTAACTAGTATCATTTTG
* * * **
632500 CTCATGCCACTCTTGTATCAAGATTCATAGACTGCGGATGTCTTTGTACTGCTCATATCGGTTAA
65 CTCATCCCA-TCTCGTATCAAGAATCATAGACCACGGATGTCTTTGTACTGCTCATATCGGTTAA
632565 TATA
129 TATA
* * *
632569 CCTGTATGTCACAAATCTTGGTTT-TATGTTTATTTTACCTGACTGCTAACTCA-TATCATTTTG
1 CCTGTATGTCACAAATCTGGGTTTATGTGTTTCTTTTACCTGACTGCTAACT-AGTATCATTTTG
* ** * * * ** ** *
632632 GTTGTCCCGTTTCATATTGAGAATCATAGACTGCAGATGTCTTTGTACTGC
65 CTCATCCCATCTCGTATCAAGAATCATAGACCACGGATGTCTTTGTACTGC
632683 ATATATCTGT
Statistics
Matches: 215, Mismatches: 27, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
130 3 0.01
131 47 0.22
132 89 0.41
133 66 0.31
134 10 0.05
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (132 bp):
CCTGTATGTCACAAATCTGGGTTTATGTGTTTCTTTTACCTGACTGCTAACTAGTATCATTTTGC
TCATCCCATCTCGTATCAAGAATCATAGACCACGGATGTCTTTGTACTGCTCATATCGGTTAATA
TA
Found at i:633314 original size:27 final size:27
Alignment explanation
Indices: 633261--633314 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
633251 TTGTTCTAAT
* * * **
633261 TTATTTAATTTAATTTAATTTTTATTA
1 TTATTTAAGTTAACTTAAATTACATTA
633288 TTATTTAAGTTAACTTAAATTACATTA
1 TTATTTAAGTTAACTTAAATTACATTA
633315 GTAGCCATTC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (27 bp):
TTATTTAAGTTAACTTAAATTACATTA
Found at i:634373 original size:44 final size:41
Alignment explanation
Indices: 634325--634415 Score: 102
Period size: 37 Copynumber: 2.2 Consensus size: 41
634315 TAAACCTAAA
*
634325 ACAATCCAAACATAAAATTGACC-AAGCTTGAAATGATAATATAT
1 ACAATCCAAAC---AAATTG-CCTAAGCTCGAAATGATAATATAT
634369 ACAAT-C---CAAATTGCCTAAGCTCGAAATGATAATATAT
1 ACAATCCAAACAAATTGCCTAAGCTCGAAATGATAATATAT
634406 ACAATCCAAA
1 ACAATCCAAA
634416 TTGCCTGAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 13
0.75 0.02 0.24
Matches are distributed among these distances:
36 2 0.05
37 31 0.76
38 1 0.02
40 1 0.02
43 1 0.02
44 5 0.12
ACGTcount: A:0.48, C:0.19, G:0.09, T:0.24
Consensus pattern (41 bp):
ACAATCCAAACAAATTGCCTAAGCTCGAAATGATAATATAT
Found at i:634389 original size:37 final size:37
Alignment explanation
Indices: 634339--634421 Score: 141
Period size: 37 Copynumber: 2.2 Consensus size: 37
634329 TCCAAACATA
*
634339 AAATTGACC-AAGCTTGAAATGATAATATATACAATCC
1 AAATTG-CCTAAGCTCGAAATGATAATATATACAATCC
634376 AAATTGCCTAAGCTCGAAATGATAATATATACAATCC
1 AAATTGCCTAAGCTCGAAATGATAATATATACAATCC
634413 AAATTGCCT
1 AAATTGCCT
634422 GAATTAGGTT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
36 2 0.05
37 42 0.95
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.28
Consensus pattern (37 bp):
AAATTGCCTAAGCTCGAAATGATAATATATACAATCC
Found at i:639916 original size:316 final size:315
Alignment explanation
Indices: 639337--640282 Score: 1344
Period size: 316 Copynumber: 3.0 Consensus size: 315
639327 TGTAACTGAA
*
639337 TTATCTAATCCGGAGGTAACTATAAGCCATTACTACAAAATGCTTAGATCACCAGCATTTTGAAA
1 TTATCCAATCCGGAGGTAACTATAAGCCATTACTACAAAATGCTTAGATCACCAGCATTTTGAAA
*
639402 CTCATTTTTATTATCATATATCTGTTTAAGAACCGACCAAACTCAAATCAAACACTCTAAATCTA
66 CTCATTTTTATTATCATACATCTGTTTAAGAACCGACCAAACTCAAATCAAACACTCTAAATCTA
* * * *
639467 TGTTCACTCAGACTCGGGTAAGAGTTTCAAATAAAGCCAAGTGTTTGACACATATATATTCACAT
131 TGTTCACTCAGACTCGGGTAAGAGTTTCAAATAAAGGCATGTGTTTGACACAGATATATTCAAAT
* * *
639532 TTTTTTCAAGTACCTAGAGGATCTTTGAAAAGACATAT-AGCCACAAACATGTTAAGATATTAGT
196 TTTTTTCATGTACCTAGAGGATCTTTG-AAAGACATATCA-CCGCAAACATGTTCAGATATTAGT
*
639596 CTAAAACGGGTACTTCAAGAAAAACTGAGAGTCAGAGAAACTTAGCTCTAAACCACT
259 CTAAAACGGGTACTTCAAGCAAAACTGAGAGTCAGAGAAACTTAGCTCTAAACCACT
639653 TTATCCAATCCGGAGGTAACTATAAGCCATTACTACAAAATGCTTAGATCACCAGCATTTTGAAA
1 TTATCCAATCCGGAGGTAACTATAAGCCATTACTACAAAATGCTTAGATCACCAGCATTTTGAAA
639718 CTCATTTTTATTATCATACATCTGTTTAAGAACCGACCAAACTCAAATCAAACACTCTAAATCTA
66 CTCATTTTTATTATCATACATCTGTTTAAGAACCGACCAAACTCAAATCAAACACTCTAAATCTA
639783 TGTTCACTCAGACTCGGGTAAGAGTTTCAAATAAAGGCATGTGTTTGACACAGATATATTCAAAT
131 TGTTCACTCAGACTCGGGTAAGAGTTTCAAATAAAGGCATGTGTTTGACACAGATATATTCAAAT
639848 TTTTTTCATGTACCTAGAGGATCTTTGAGAAGACATATCACCGCAAACATGTTCAGATATTAGTC
196 TTTTTTCATGTACCTAGAGGATCTTTGA-AAGACATATCACCGCAAACATGTTCAGATATTAGTC
* * *
639913 TAAAATGGGTACTTCAAGCAAAACTGAGAGTCACAGAAACTTAGCTCTGAACCACT
260 TAAAACGGGTACTTCAAGCAAAACTGAGAGTCAGAGAAACTTAGCTCTAAACCACT
** * * * *
639969 TTATCCAATCCGGAGAAAACTATAAGCCATTACCACGAAATTCTTAGATAAATAACCAGCATTTT
1 TTATCCAATCCGGAGGTAACTATAAGCCATTACTACAAAATGCTTAG----ATCACCAGCATTTT
* * * * * ** *
640034 G-AATTCTTTTTTAATATCATACATCTGATTTCAGAACCAACCAAACTCAGCTC--ACACCCTAA
62 GAAACTCATTTTTATTATCATACATCTG-TTTAAGAACCGACCAAACTCAAATCAAACACTCTAA
* * * ** *
640096 ATCTATGTTCACTCGGACTCGGGTATGAGTTTCAAATACA-GCTATGTGTTTGACATGGATGTAT
126 ATCTATGTTCACTCAGACTCGGGTAAGAGTTTCAAATAAAGGC-ATGTGTTTGACACAGATATAT
* * *** * *
640160 TCAATTTTTTTTCATGTACCTAGAAGGATCTTTGAAAAACCATATCACCGTGCACATGCTCGGAT
190 TCAAATTTTTTTCATGTACCTAG-AGGATCTTTGAAAGA-CATATCACCGCAAACATGTTCAGAT
* * ** *
640225 ATTGAGTCTAAAACCGGTACTTAAAGCAAAACCAAGAATCAGAGAAACTTAGCTCTAA
253 ATT-AGTCTAAAACGGGTACTTCAAGCAAAACTGAGAGTCAGAGAAACTTAGCTCTAA
640283 TTTTGCAGAC
Statistics
Matches: 571, Mismatches: 48, Indels: 18
0.90 0.08 0.03
Matches are distributed among these distances:
315 1 0.00
316 341 0.60
317 3 0.01
318 88 0.15
319 57 0.10
320 81 0.14
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (315 bp):
TTATCCAATCCGGAGGTAACTATAAGCCATTACTACAAAATGCTTAGATCACCAGCATTTTGAAA
CTCATTTTTATTATCATACATCTGTTTAAGAACCGACCAAACTCAAATCAAACACTCTAAATCTA
TGTTCACTCAGACTCGGGTAAGAGTTTCAAATAAAGGCATGTGTTTGACACAGATATATTCAAAT
TTTTTTCATGTACCTAGAGGATCTTTGAAAGACATATCACCGCAAACATGTTCAGATATTAGTCT
AAAACGGGTACTTCAAGCAAAACTGAGAGTCAGAGAAACTTAGCTCTAAACCACT
Found at i:646529 original size:18 final size:18
Alignment explanation
Indices: 646506--646543 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
646496 AATTACCCTG
646506 CCAAACTGCCCTGCCAAA
1 CCAAACTGCCCTGCCAAA
646524 CCAAACTGCCCTGCCAAA
1 CCAAACTGCCCTGCCAAA
646542 CC
1 CC
646544 GATACATGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.47, G:0.11, T:0.11
Consensus pattern (18 bp):
CCAAACTGCCCTGCCAAA
Found at i:653849 original size:18 final size:18
Alignment explanation
Indices: 653826--653863 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
653816 AATTACCCTG
653826 CCAAACTGCCCTGCCAAA
1 CCAAACTGCCCTGCCAAA
653844 CCAAACTGCCCTGCCAAA
1 CCAAACTGCCCTGCCAAA
653862 CC
1 CC
653864 GATACATGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.47, G:0.11, T:0.11
Consensus pattern (18 bp):
CCAAACTGCCCTGCCAAA
Found at i:662420 original size:2 final size:2
Alignment explanation
Indices: 662413--662466 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
662403 ATTGAAAATA
662413 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
662455 AT AT AT AT AT AT
1 AT AT AT AT AT AT
662467 TTGGATAAAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:666341 original size:22 final size:22
Alignment explanation
Indices: 666290--666369 Score: 106
Period size: 23 Copynumber: 3.5 Consensus size: 22
666280 GCTGGGGAAA
*
666290 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
666312 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
* * *
666335 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
666358 CAGTAGGCACAC
1 CAGTAGGCACAC
666370 GAAGTGCGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
22 16 0.31
23 35 0.69
ACGTcount: A:0.36, C:0.29, G:0.23, T:0.12
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:666410 original size:23 final size:23
Alignment explanation
Indices: 666262--666411 Score: 89
Period size: 23 Copynumber: 6.4 Consensus size: 23
666252 CGAAGTACTT
666262 AACAGTAAGCACAC-AAGTGCTGGGGA
1 AACAGTAAGCACACGAAGTGC----GA
666288 AACAGTAAGCACAC-ACAGTGC-A
1 AACAGTAAGCACACGA-AGTGCGA
* *
666310 ATCCAGTAGGCACAC-ACAGTGC-A
1 A-ACAGTAAGCACACGA-AGTGCGA
* * * *
666333 ATCAGTAGGCGCAC-ATAGCGC-A
1 AACAGTAAGCACACGA-AGTGCGA
*
666355 AATCAGTAGGCACACGAAGTGCGA
1 AA-CAGTAAGCACACGAAGTGCGA
*
666379 AACAATAAGCACACGAAGTGCGA
1 AACAGTAAGCACACGAAGTGCGA
*
666402 AAGAGTAAGC
1 AACAGTAAGC
666412 GCGCTAGCAT
Statistics
Matches: 106, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
22 20 0.19
23 62 0.58
24 4 0.04
26 15 0.14
27 5 0.05
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.11
Consensus pattern (23 bp):
AACAGTAAGCACACGAAGTGCGA
Found at i:669016 original size:83 final size:83
Alignment explanation
Indices: 668917--669120 Score: 214
Period size: 84 Copynumber: 2.4 Consensus size: 83
668907 ATAGAATATG
* * * * **
668917 ATATGTTAATCAGCGGGAATTAATCCCGAAATAGATTTATTCAACTTATTTTTTTTTTGG-AAAC
1 ATATGTTAAACGGCGGGAATAAATCCCGAAATAGATTTATT-AACTTAATTAATTTTTGGAAAAC
*
668981 AAAATCAAAGTAGAAT-ACA
65 AAAATCAAAATAGAATCA-A
* * * * *
669000 ATCTGTTAAACGGCGGGAATAAATCTCAAAACAGAATTATTAACTTAATTAATTTTTGGAAAAAC
1 ATATGTTAAACGGCGGGAATAAATCCCGAAATAGATTTATTAACTTAATTAATTTTTGG-AAAAC
*
669065 AAAGTCAAAATAGAATCAA
65 AAAATCAAAATAGAATCAA
* * **
669084 ATATGTTGAACGACAAGAATAAATCCCGAAATAGATT
1 ATATGTTAAACGGCGGGAATAAATCCCGAAATAGATT
669121 ATTTTAAAAC
Statistics
Matches: 96, Mismatches: 22, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
82 15 0.16
83 33 0.34
84 47 0.49
85 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (83 bp):
ATATGTTAAACGGCGGGAATAAATCCCGAAATAGATTTATTAACTTAATTAATTTTTGGAAAACA
AAATCAAAATAGAATCAA
Found at i:670961 original size:366 final size:366
Alignment explanation
Indices: 670289--671026 Score: 1467
Period size: 366 Copynumber: 2.0 Consensus size: 366
670279 TCTCTTGATT
670289 GTTTGAGATGTCCTTATTTGTCAAAATCAAGTTTTTAGGGTCATGCATTCAAGGGTAAAGTCAGA
1 GTTTGAGATGTCCTTATTTGTCAAAATCAAGTTTTTAGGGTCATGCATTCAAGGGTAAAGTCAGA
*
670354 ATATATTATTTTTGGAGGAGTCGAATTTGAATTATAAATTGTTAACATTGTTCTTGTTTATTCCC
66 ATATATTATTTTTGGAGGAGTCGAATTTGAATTATAAATTGTTAACATTGTTCTAGTTTATTCCC
670419 CACTATTAACCCTCCCCACTAAATTTTGGGGAGTTACATTTTTAATGCTTATTTCTAATCCATGG
131 CACTATTAACCCTCCCCACTAAATTTTGGGGAGTTACATTTTTAATGCTTATTTCTAATCCATGG
670484 GATGGGTTGTAGTTAAAGGTTTCCAAGTAGAATAAAGTTTACTCAAAAGGGTCTCCTTCAAAGCA
196 GATGGGTTGTAGTTAAAGGTTTCCAAGTAGAATAAAGTTTACTCAAAAGGGTCTCCTTCAAAGCA
670549 ATTTAATTATAACCCATACTTCTATGCAACAATGAGTGAATTTTCTCAGAGAATTTGACTCAAGG
261 ATTTAATTATAACCCATACTTCTATGCAACAATGAGTGAATTTTCTCAGAGAATTTGACTCAAGG
670614 GATTCGATCAATGGCTTCAGTCAAAACATCACCCTCTAAGA
326 GATTCGATCAATGGCTTCAGTCAAAACATCACCCTCTAAGA
670655 GTTTGAGATGTCCTTATTTGTCAAAATCAAGTTTTTAGGGTCATGCATTCAAGGGTAAAGTCAGA
1 GTTTGAGATGTCCTTATTTGTCAAAATCAAGTTTTTAGGGTCATGCATTCAAGGGTAAAGTCAGA
670720 ATATATTATTTTTGGAGGAGTCGAATTTGAATTATAAATTGTTAACATTGTTCTAGTTTATTCCC
66 ATATATTATTTTTGGAGGAGTCGAATTTGAATTATAAATTGTTAACATTGTTCTAGTTTATTCCC
670785 CACTATTAACCCTCCCCACTAAATTTTGGGGAGTTACATTTTTAATGCTTATTTCTAATCCATGG
131 CACTATTAACCCTCCCCACTAAATTTTGGGGAGTTACATTTTTAATGCTTATTTCTAATCCATGG
670850 GATGGGTTGTAGTTAAAGGTTTCCAAGTAGAATAAAGTTTACTCAAAAGGGTCTCCTTCAAAGCA
196 GATGGGTTGTAGTTAAAGGTTTCCAAGTAGAATAAAGTTTACTCAAAAGGGTCTCCTTCAAAGCA
670915 ATTTAATTATAACCCATACTTCTATGCAACAATGAGTGAATTTTCTCAGAGAATTTGACTCAAGG
261 ATTTAATTATAACCCATACTTCTATGCAACAATGAGTGAATTTTCTCAGAGAATTTGACTCAAGG
670980 GATTCGATCAATGGCTTCAGTCAAAACATCACCCTCTAAGA
326 GATTCGATCAATGGCTTCAGTCAAAACATCACCCTCTAAGA
671021 GTTTGA
1 GTTTGA
671027 TATCTTACTC
Statistics
Matches: 371, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
366 371 1.00
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (366 bp):
GTTTGAGATGTCCTTATTTGTCAAAATCAAGTTTTTAGGGTCATGCATTCAAGGGTAAAGTCAGA
ATATATTATTTTTGGAGGAGTCGAATTTGAATTATAAATTGTTAACATTGTTCTAGTTTATTCCC
CACTATTAACCCTCCCCACTAAATTTTGGGGAGTTACATTTTTAATGCTTATTTCTAATCCATGG
GATGGGTTGTAGTTAAAGGTTTCCAAGTAGAATAAAGTTTACTCAAAAGGGTCTCCTTCAAAGCA
ATTTAATTATAACCCATACTTCTATGCAACAATGAGTGAATTTTCTCAGAGAATTTGACTCAAGG
GATTCGATCAATGGCTTCAGTCAAAACATCACCCTCTAAGA
Found at i:672378 original size:211 final size:213
Alignment explanation
Indices: 671951--672391 Score: 566
Period size: 211 Copynumber: 2.1 Consensus size: 213
671941 CTTCGGTCTT
* * * *
671951 GCTTTTAAACTTTTAAACTAATTTATTCACCCCCGATAGAAAGTGAGGGTTTGTTATTATCTTGT
1 GCTTTTAAACTTTTCAACCAATTTATCCACCCCCGATAGAAAGTGAGGGTCTGTTATTATCTTGT
* * * * *
672016 TCAAATGCCCCCCTTGTATTCCACCCTTTTGTAATCCAAGGATAATGGCAGACATAACTGAAGCC
66 TCAAACGCCCCCCTTGTATTCCACCATCTTGCAATCCAAAGATAATGGCAGACATAACTGAAGCC
* * * * * * * *
672081 GAAAATAAGTGCATTGATTCTGGGGATGCTGCAACCTCTTTAGCTACGGTAGAAGTTGTCCCATC
131 GAAAATAACTGCATCGATTCTGGGAACGCTACAACCTCATAAACTACGGTAGAAGTTGTCCCATC
672146 CACACTCTCTCTAATAGA
196 CACACTCTCTCTAATAGA
* *** * * * *
672164 GCTTTTAAACTTTTCATCCAATTTATCCACCGTTGATGGAAATTTAGGGTCTGTTATTATTTTGT
1 GCTTTTAAACTTTTCAACCAATTTATCCACCCCCGATAGAAAGTGAGGGTCTGTTATTATCTTGT
* *
672229 TCAAACGCTCCCCTTGTATT-CACCATCTTGCAATCCAAAGATAATGGCGGACATAACTGAAGCC
66 TCAAACGCCCCCCTTGTATTCCACCATCTTGCAATCCAAAGATAATGGCAGACATAACTGAAGCC
*
672293 GAAAA-ACCCT-CATCGATTCTGGGAACGCTACAACCTCATAAACTACGGTAGAAGTTGTCCCAT
131 GAAAATA-ACTGCATCGATTCTGGGAACGCTACAACCTCATAAACTACGGTAGAAGTTGTCCCAT
*
672356 CCACACTCTCTC-CATCAGA
195 CCACACTCTCTCTAAT-AGA
*
672375 GCTTTTAAACGTTTCAA
1 GCTTTTAAACTTTTCAA
672392 TGAGTTCAGC
Statistics
Matches: 195, Mismatches: 31, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
210 2 0.01
211 77 0.39
212 45 0.23
213 71 0.36
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (213 bp):
GCTTTTAAACTTTTCAACCAATTTATCCACCCCCGATAGAAAGTGAGGGTCTGTTATTATCTTGT
TCAAACGCCCCCCTTGTATTCCACCATCTTGCAATCCAAAGATAATGGCAGACATAACTGAAGCC
GAAAATAACTGCATCGATTCTGGGAACGCTACAACCTCATAAACTACGGTAGAAGTTGTCCCATC
CACACTCTCTCTAATAGA
Found at i:672425 original size:211 final size:213
Alignment explanation
Indices: 671978--672451 Score: 519
Period size: 211 Copynumber: 2.2 Consensus size: 213
671968 CTAATTTATT
* * * * *
671978 CACCCCCGATAGAAA-GTGAGGGTTTGTTATTATCTTGTTCAAATGCCCCCCTTGTATTCCACCC
1 CACCCCCGACAGAAAGGT-AGGGTCTGTTATTATTTTGTTCAAATGCTCCCCTTGTATTCCACCA
* * * * * *
672042 TTTTGTAATCCAAGGATAATGGCAGACATAACTGAAGCCGAAAATAAGTGCATTGATTCTGGGGA
65 TCTTGCAATCCAAAGATAATGGCAGACATAACTGAAGCCGAAAATAACTGCATCGATTCTGGGAA
* * * * *
672107 TGCTGCAACCTCTTTAGCTACGGTAGAAGTTGTCCCATCCACACTCTCTCTAATAGAGCTTTTAA
130 CGCTACAACCTCATAAACTACGGTAGAAGTTGTCCCATCCACACTCTCTCTAATAGAGCTTTTAA
* * *
672172 ACTTTTCATCCAATTTATC
195 ACGTTTCATCCAATTCAGC
*** ** ** *
672191 CACCGTTGATGGAAATTTAGGGTCTGTTATTATTTTGTTCAAACGCTCCCCTTGTATT-CACCAT
1 CACCCCCGACAGAAAGGTAGGGTCTGTTATTATTTTGTTCAAATGCTCCCCTTGTATTCCACCAT
* *
672255 CTTGCAATCCAAAGATAATGGCGGACATAACTGAAGCCGAAAA-ACCCT-CATCGATTCTGGGAA
66 CTTGCAATCCAAAGATAATGGCAGACATAACTGAAGCCGAAAATA-ACTGCATCGATTCTGGGAA
*
672318 CGCTACAACCTCATAAACTACGGTAGAAGTTGTCCCATCCACACTCTCTC-CATCAGAGCTTTTA
130 CGCTACAACCTCATAAACTACGGTAGAAGTTGTCCCATCCACACTCTCTCTAAT-AGAGCTTTTA
* *
672382 AACGTTTCAAT-GAGTTCAGC
194 AACGTTTC-ATCCAATTCAGC
* ** * * * *
672402 CGCCCCCGACATTAAGGTAGGGTCTATTAGTATTTTTTTGAAATGCTCCC
1 CACCCCCGACAGAAAGGTAGGGTCTGTTATTATTTTGTTCAAATGCTCCC
672452 TAAAGTCTGT
Statistics
Matches: 213, Mismatches: 44, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
210 2 0.01
211 116 0.54
212 47 0.22
213 47 0.22
214 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (213 bp):
CACCCCCGACAGAAAGGTAGGGTCTGTTATTATTTTGTTCAAATGCTCCCCTTGTATTCCACCAT
CTTGCAATCCAAAGATAATGGCAGACATAACTGAAGCCGAAAATAACTGCATCGATTCTGGGAAC
GCTACAACCTCATAAACTACGGTAGAAGTTGTCCCATCCACACTCTCTCTAATAGAGCTTTTAAA
CGTTTCATCCAATTCAGC
Found at i:678064 original size:22 final size:22
Alignment explanation
Indices: 678038--678104 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
678028 TTTTAAAACA
678038 TTAAAACATGCCATTGATGAAT
1 TTAAAACATGCCATTGATGAAT
* * * *
678060 TTAAAACATG--TTTAACAGATT
1 TTAAAACATGCCATTGA-TGAAT
678081 TTAAAACATGCCATTGATGAAT
1 TTAAAACATGCCATTGATGAAT
678103 TT
1 TT
678105 GTTATGTTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
20 3 0.09
21 13 0.38
22 15 0.44
23 3 0.09
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (22 bp):
TTAAAACATGCCATTGATGAAT
Found at i:678432 original size:23 final size:22
Alignment explanation
Indices: 678390--678433 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
678380 AAAATCTTGA
*
678390 TAAGTGTTTATATATGTGAATT
1 TAAGTGTTTAAATATGTGAATT
678412 TAAGTGTTTTAAAGTAT-TGAAT
1 TAAGTG-TTTAAA-TATGTGAAT
678434 AGGTTAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.32
23 10 0.53
24 3 0.16
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (22 bp):
TAAGTGTTTAAATATGTGAATT
Found at i:678577 original size:15 final size:16
Alignment explanation
Indices: 678559--678588 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
678549 TTTAATGTTT
678559 AAAAA-TTTGTAAAAA
1 AAAAAGTTTGTAAAAA
678574 AAAAAGTTTGTAAAA
1 AAAAAGTTTGTAAAA
678589 GTTCAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (16 bp):
AAAAAGTTTGTAAAAA
Found at i:680675 original size:97 final size:97
Alignment explanation
Indices: 680500--680675 Score: 255
Period size: 97 Copynumber: 1.8 Consensus size: 97
680490 AATTTTGGAA
*
680500 AAGGATATTCAATTATCTCGATTTGAAGAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGATATTCAATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
* *
680565 GTATCAGAGATAAAGAAACGTTGCCTAGATTT
66 GAATCAGAAATAAAGAAACGTTGCCTAGATTT
* * * * * *
680597 AAGGGTATTCGATTATTTCGATTTGAGGAAAAATTGCACTTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGATATTCAATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
680662 GAACTCA-AAATAAA
66 GAA-TCAGAAATAAA
680676 AGAATATTGC
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
97 66 0.96
98 3 0.04
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (97 bp):
AAGGATATTCAATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
GAATCAGAAATAAAGAAACGTTGCCTAGATTT
Found at i:681037 original size:28 final size:28
Alignment explanation
Indices: 681006--681155 Score: 85
Period size: 27 Copynumber: 5.3 Consensus size: 28
680996 AAACATTCAG
* *
681006 GGGGAAAATGGTACTTTTTGGAAGAATC
1 GGGGAAAATGGTAATTTTTGGAAGAATA
**
681034 GGGGTTAAAAATGG-AATTTTTGGAAGTTTA
1 GGGG---AAAATGGTAATTTTTGGAAGAATA
* * *
681064 GGGTAAAATGGTAAATTTTGGAA-AAAA
1 GGGGAAAATGGTAATTTTTGGAAGAATA
** **
681091 GGTTAAAAATGG-AATTTTTGGAAGTTTGA
1 GG-GGAAAATGGTAATTTTTGGAAGAAT-A
* *
681120 GGGTAAAAAT-GTAATTTTT-GAAAAATA
1 GGG-GAAAATGGTAATTTTTGGAAGAATA
681147 GGGGTAAAA
1 GGGG-AAAA
681156 ATGTATTTTT
Statistics
Matches: 92, Mismatches: 20, Indels: 21
0.69 0.15 0.16
Matches are distributed among these distances:
27 28 0.30
28 26 0.28
29 16 0.17
30 15 0.16
31 7 0.08
ACGTcount: A:0.39, C:0.01, G:0.28, T:0.31
Consensus pattern (28 bp):
GGGGAAAATGGTAATTTTTGGAAGAATA
Found at i:681080 original size:29 final size:28
Alignment explanation
Indices: 681039--681296 Score: 164
Period size: 29 Copynumber: 9.0 Consensus size: 28
681029 GAATCGGGGT
681039 TAAAAATGGAATTTTTGGAAGTTTAGGG
1 TAAAAATGGAATTTTTGGAAGTTTAGGG
* *** *
681067 T-AAAATGGTAAATTTTGGAA-AAAAGGT
1 TAAAAATGG-AATTTTTGGAAGTTTAGGG
681094 TAAAAATGGAATTTTTGGAAGTTTGAGGG
1 TAAAAATGGAATTTTTGGAAGTTT-AGGG
* ***
681123 TAAAAATGTAATTTTT-GAAAAATAGGGG
1 TAAAAATGGAATTTTTGGAAGTTTA-GGG
* * * *
681151 TAAAAATGTATTTTTTGCAAAATTTAGGG
1 TAAAAATGGAATTTTTG-GAAGTTTAGGG
681180 TTAAAAATGGAA-TTTTGGAAAGTTTAGGGG
1 -TAAAAATGGAATTTTTGG-AAGTTTA-GGG
* * * *
681210 TAAAAATGTAATTTTTGTAAAATTAAGGG
1 TAAAAATGGAATTTTTG-GAAGTTTAGGG
** * * *
681239 TTAAAAATATAATTTTAGAAAGTTTGGGGG
1 -TAAAAATGGAATTTTTGGAAGTTT-AGGG
* * *
681269 TAAATATGTAATTTTTGAACAGTTTAGG
1 TAAAAATGGAATTTTTGGA-AGTTTAGG
681297 AACCTTCTAA
Statistics
Matches: 180, Mismatches: 35, Indels: 29
0.74 0.14 0.12
Matches are distributed among these distances:
27 22 0.12
28 40 0.22
29 68 0.38
30 50 0.28
ACGTcount: A:0.40, C:0.01, G:0.23, T:0.36
Consensus pattern (28 bp):
TAAAAATGGAATTTTTGGAAGTTTAGGG
Found at i:681107 original size:55 final size:57
Alignment explanation
Indices: 681010--681226 Score: 219
Period size: 58 Copynumber: 3.8 Consensus size: 57
681000 ATTCAGGGGG
* * *
681010 AAAATGGTACTTTTTGGAAGAATCGGGGTTAAAAATGGAATTTTTGGAAGTTTAGGGT-
1 AAAATGGTA-ATTTTGGAAAAAT-AGGGTTAAAAATGGAATTTTTGGAAGTTTAGGGTA
681068 AAAATGGTAAATTTTGGAAAAA-A-GGTTAAAAATGGAATTTTTGGAAGTTTGAGGGTA
1 AAAATGGT-AATTTTGGAAAAATAGGGTTAAAAATGGAATTTTTGGAAGTTT-AGGGTA
* * * * * *
681125 AAAAT-GTAATTTTTGAAAAATAGGGGTAAAAATGTATTTTTTGCAAAATTTAGGGTTA
1 AAAATGGTAATTTTGGAAAAATAGGGTTAAAAATGGAATTTTTG-GAAGTTTAGGG-TA
** * *
681183 AAAATGG-AATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTG
1 AAAATGGTAATTTTGGAAA-AATAGGGTTAAAAATGGAATTTTTG
681227 TAAAATTAAG
Statistics
Matches: 137, Mismatches: 13, Indels: 17
0.82 0.08 0.10
Matches are distributed among these distances:
55 39 0.28
56 8 0.06
57 26 0.19
58 40 0.29
59 24 0.18
ACGTcount: A:0.39, C:0.01, G:0.25, T:0.35
Consensus pattern (57 bp):
AAAATGGTAATTTTGGAAAAATAGGGTTAAAAATGGAATTTTTGGAAGTTTAGGGTA
Found at i:681219 original size:59 final size:59
Alignment explanation
Indices: 681094--681285 Score: 226
Period size: 59 Copynumber: 3.3 Consensus size: 59
681084 GAAAAAAGGT
* * ** * * **
681094 TAAAAATGGAATTTTTGGAAGTTTGAGGG-TAAAAATGTAATTTTTGAAA-AATAGGGG
1 TAAAAATGTAATTTTTGCAAAATTAAGGGTTAAAAATGTAATTTTAGAAAGTTTAGGGG
* * * *
681151 TAAAAATGTATTTTTTGCAAAATTTAGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGG
1 TAAAAATGTAATTTTTGCAAAATTAAGGGTTAAAAATGTAATTTTAGAAAGTTTAGGGG
* * *
681210 TAAAAATGTAATTTTTGTAAAATTAAGGGTTAAAAATATAATTTTAGAAAGTTTGGGGG
1 TAAAAATGTAATTTTTGCAAAATTAAGGGTTAAAAATGTAATTTTAGAAAGTTTAGGGG
*
681269 TAAATATGTAATTTTTG
1 TAAAAATGTAATTTTTG
681286 AACAGTTTAG
Statistics
Matches: 115, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
57 23 0.20
58 18 0.16
59 74 0.64
ACGTcount: A:0.40, C:0.01, G:0.22, T:0.38
Consensus pattern (59 bp):
TAAAAATGTAATTTTTGCAAAATTAAGGGTTAAAAATGTAATTTTAGAAAGTTTAGGGG
Found at i:682870 original size:6 final size:6
Alignment explanation
Indices: 682859--682949 Score: 64
Period size: 6 Copynumber: 15.7 Consensus size: 6
682849 TAATCTAAAC
* * *
682859 TAAATT TAAATT TAAATT TAAATT TAAA-A CAAGTT TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* * * * * *
682906 CAGAA-A TAAATT TAAA-A TCAATT TAAACT T-AATA TAAATT TAAA
1 TA-AATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
682950 AGTTTGATCC
Statistics
Matches: 62, Mismatches: 18, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
5 10 0.16
6 50 0.81
7 2 0.03
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (6 bp):
TAAATT
Found at i:682874 original size:17 final size:17
Alignment explanation
Indices: 682859--682949 Score: 69
Period size: 17 Copynumber: 5.2 Consensus size: 17
682849 TAATCTAAAC
682859 TAAATTTAAATTTAAATT
1 TAAATTTAAA-TTAAATT
** *
682877 TAAATTTAAAACAAGTT
1 TAAATTTAAATTAAATT
*
682894 TAAATTTAAATTCAGAA-A
1 TAAATTTAAATT-A-AATT
* *
682912 TAAATTTAAAATCAATT
1 TAAATTTAAATTAAATT
*
682929 TAAACTT-AATATAAATT
1 TAAATTTAAAT-TAAATT
682946 TAAA
1 TAAA
682950 AGTTTGATCC
Statistics
Matches: 56, Mismatches: 13, Indels: 9
0.72 0.17 0.12
Matches are distributed among these distances:
16 4 0.07
17 29 0.52
18 22 0.39
19 1 0.02
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTAAATT
Found at i:682905 original size:35 final size:35
Alignment explanation
Indices: 682859--682949 Score: 107
Period size: 35 Copynumber: 2.6 Consensus size: 35
682849 TAATCTAAAC
682859 TAAATTTAAATTTAAATTTAAATTTAAAA-CAAGTT
1 TAAATTTAAATTTAAATTTAAATTTAAAATCAA-TT
* *
682894 TAAATTTAAATTCAGAA-ATAAATTTAAAATCAATT
1 TAAATTTAAATTTA-AATTTAAATTTAAAATCAATT
* *
682929 TAAACTT-AATATAAATTTAAA
1 TAAATTTAAATTTAAATTTAAA
682950 AGTTTGATCC
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
33 2 0.04
34 8 0.17
35 32 0.68
36 5 0.11
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (35 bp):
TAAATTTAAATTTAAATTTAAATTTAAAATCAATT
Found at i:684620 original size:23 final size:23
Alignment explanation
Indices: 684562--684620 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
684552 TCGTCCATCC
**
684562 TTGCTGACTAAACCTTCTAGAAG
1 TTGCTGACTGGACCTTCTAGAAG
*
684585 CTGCTGA-TCGGACCTTCTAGAAG
1 TTGCTGACT-GGACCTTCTAGAAG
684608 TTGCTGACTGGAC
1 TTGCTGACTGGAC
684621 GCCACGTCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 1 0.03
23 28 0.93
24 1 0.03
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (23 bp):
TTGCTGACTGGACCTTCTAGAAG
Found at i:690256 original size:25 final size:23
Alignment explanation
Indices: 690228--690273 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
690218 GTTGGATCCA
690228 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
690253 AATTAAATCTAAATAATAATT
1 AATTAAATCTAAAAAATAATT
690274 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Done.