Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 81 of 163
Found at i:21912787 original size:26 final size:29
Alignment explanation
Indices: 21912695--21912827 Score: 114
Period size: 30 Copynumber: 4.5 Consensus size: 29
21912685 ACAGTATCAA
*
21912695 TTAATTATTTAATTATATTAAATTAAATAT
1 TTAATTATTTAATTATA-TAAATTAATTAT
** * *
21912725 TTAATT-TAAAATATTTTCGTAAA-TAATTAT
1 TTAATTAT-TTA-ATTAT-ATAAATTAATTAT
21912755 ATATAATTATTTAATT-T-T-AATTAATTAT
1 -T-TAATTATTTAATTATATAAATTAATTAT
*
21912783 TTAATTATTTAATTATACTAAATTAAATAT
1 TTAATTATTTAATTATA-TAAATTAATTAT
21912813 TTAATTATTTAATTA
1 TTAATTATTTAATTA
21912828 ATGAAAACAA
Statistics
Matches: 84, Mismatches: 8, Indels: 22
0.74 0.07 0.19
Matches are distributed among these distances:
26 13 0.15
27 4 0.05
28 8 0.10
29 2 0.02
30 38 0.45
31 12 0.14
32 6 0.07
33 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (29 bp):
TTAATTATTTAATTATATAAATTAATTAT
Found at i:21918423 original size:65 final size:66
Alignment explanation
Indices: 21918315--21918469 Score: 224
Period size: 65 Copynumber: 2.4 Consensus size: 66
21918305 CAAATTGCTC
* *
21918315 AACTTAAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTTAAAAAA-ATATGATGAACTCCATCTA
1 AACTTAAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAATATATGAAGAACTCCATCTA
21918379 A
66 A
* *
21918380 AACTTAAAGAGGAGGCTGCAGTGAGAGAAGCAGAGTCTCAAAAAATATATGAAGAACTCCATCTA
1 AACTTAAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAATATATGAAGAACTCCATCTA
*
21918445 C
66 A
* * *
21918446 AAC-TAAAGTGGAGGCAGCAACGAG
1 AACTTAAAGAGGAGGCTGCAGCGAG
21918470 GCAAGCCGAG
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
65 59 0.74
66 21 0.26
ACGTcount: A:0.43, C:0.16, G:0.25, T:0.16
Consensus pattern (66 bp):
AACTTAAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAATATATGAAGAACTCCATCTA
A
Found at i:21918480 original size:21 final size:21
Alignment explanation
Indices: 21918456--21918496 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
21918446 AACTAAAGTG
21918456 GAGGCAGCAACGAGGCAAGCC
1 GAGGCAGCAACGAGGCAAGCC
*
21918477 GAGGCAGCAGCGAGGCAAGC
1 GAGGCAGCAACGAGGCAAGC
21918497 GAAGGAAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.27, G:0.41, T:0.00
Consensus pattern (21 bp):
GAGGCAGCAACGAGGCAAGCC
Found at i:21918506 original size:21 final size:21
Alignment explanation
Indices: 21918456--21918507 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
21918446 AACTAAAGTG
* *
21918456 GAGGCAGCAACGAGGCAAGCC
1 GAGGAAGCAGCGAGGCAAGCC
*
21918477 GAGGCAGCAGCGAGGCAAG-C
1 GAGGAAGCAGCGAGGCAAGCC
21918497 GAAGGAAGCAG
1 G-AGGAAGCAG
21918508 AGGCTACAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.35, C:0.23, G:0.42, T:0.00
Consensus pattern (21 bp):
GAGGAAGCAGCGAGGCAAGCC
Found at i:21918887 original size:42 final size:42
Alignment explanation
Indices: 21918808--21918929 Score: 181
Period size: 42 Copynumber: 2.9 Consensus size: 42
21918798 GCTTTCTCCA
* *
21918808 AAAGCGCCGCTAAAGAACACGGGCTTTAGCGGCGCTTGTGGAG
1 AAAGCGCCGCTAAAGAACA-TGCCTTTAGCGGCGCTTGTGGAG
*
21918851 AAAGCGCCGCTAAAAAACATGCCTTTAGCGGCGCTTGTGGAG
1 AAAGCGCCGCTAAAGAACATGCCTTTAGCGGCGCTTGTGGAG
* *
21918893 AAAGCACCGCTAAAGAACATGGCCTTTAGCGACGCTT
1 AAAGCGCCGCTAAAGAACAT-GCCTTTAGCGGCGCTT
21918930 TTTCGCATAA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 39 0.54
43 33 0.46
ACGTcount: A:0.29, C:0.25, G:0.29, T:0.18
Consensus pattern (42 bp):
AAAGCGCCGCTAAAGAACATGCCTTTAGCGGCGCTTGTGGAG
Found at i:21923850 original size:50 final size:49
Alignment explanation
Indices: 21923796--21923949 Score: 109
Period size: 50 Copynumber: 3.1 Consensus size: 49
21923786 CCATAAATAA
21923796 AGTATGTTTCTTTATCATATTGTCTTCTTTTTCTCACTGTTTATTCTTTT
1 AGTATGTTTCTTTATCATATTGTCTT-TTTTTCTCACTGTTTATTCTTTT
* ** ** ** * *** **
21923846 AGTA--TTTATAAACTCATAATTGT-TTTCCTAATCGCT-TTTCCATAAATAA
1 AGTATGTTTCTTTA-TCAT-ATTGTCTTTTTTTCTCACTGTTT--ATTCTTTT
21923895 AGTATGTTTCTTTATCATATTGTCTTTTTTTTCTCACTGTTTATTCTTTT
1 AGTATGTTTCTTTATCATATTGTC-TTTTTTTCTCACTGTTTATTCTTTT
21923945 AGTAT
1 AGTAT
21923950 TTCCTCTCCA
Statistics
Matches: 69, Mismatches: 26, Indels: 18
0.61 0.23 0.16
Matches are distributed among these distances:
47 3 0.04
48 11 0.16
49 18 0.26
50 21 0.30
51 13 0.19
52 3 0.04
ACGTcount: A:0.21, C:0.15, G:0.08, T:0.56
Consensus pattern (49 bp):
AGTATGTTTCTTTATCATATTGTCTTTTTTTCTCACTGTTTATTCTTTT
Found at i:21923927 original size:99 final size:99
Alignment explanation
Indices: 21923751--21923951 Score: 384
Period size: 99 Copynumber: 2.0 Consensus size: 99
21923741 GGAAAAACAT
21923751 TTTACAAACTCATAATTGTTTTCCTAATCGCTTTTCCATAAATAAAGTATGTTTCTTTATCATAT
1 TTTACAAACTCATAATTGTTTTCCTAATCGCTTTTCCATAAATAAAGTATGTTTCTTTATCATAT
21923816 TGTCTTCTTTTTCTCACTGTTTATTCTTTTAGTA
66 TGTCTTCTTTTTCTCACTGTTTATTCTTTTAGTA
*
21923850 TTTATAAACTCATAATTGTTTTCCTAATCGCTTTTCCATAAATAAAGTATGTTTCTTTATCATAT
1 TTTACAAACTCATAATTGTTTTCCTAATCGCTTTTCCATAAATAAAGTATGTTTCTTTATCATAT
*
21923915 TGTCTTTTTTTTCTCACTGTTTATTCTTTTAGTA
66 TGTCTTCTTTTTCTCACTGTTTATTCTTTTAGTA
21923949 TTT
1 TTT
21923952 CCTCTCCAAA
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 100 1.00
ACGTcount: A:0.24, C:0.16, G:0.07, T:0.53
Consensus pattern (99 bp):
TTTACAAACTCATAATTGTTTTCCTAATCGCTTTTCCATAAATAAAGTATGTTTCTTTATCATAT
TGTCTTCTTTTTCTCACTGTTTATTCTTTTAGTA
Found at i:21928179 original size:24 final size:24
Alignment explanation
Indices: 21928152--21928201 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
21928142 TTTCACTTAG
21928152 AAAATTATAGGTGCTTCCTAGATT
1 AAAATTATAGGTGCTTCCTAGATT
21928176 AAAATTATAGGTGCTTCCTAGATT
1 AAAATTATAGGTGCTTCCTAGATT
21928200 AA
1 AA
21928202 CTATAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (24 bp):
AAAATTATAGGTGCTTCCTAGATT
Found at i:21932172 original size:8 final size:8
Alignment explanation
Indices: 21932153--21932195 Score: 77
Period size: 8 Copynumber: 5.2 Consensus size: 8
21932143 GATCTATTAC
21932153 TTATATAAA
1 TTATA-AAA
21932162 TTATAAAA
1 TTATAAAA
21932170 TTATAAAA
1 TTATAAAA
21932178 TTATAAAA
1 TTATAAAA
21932186 TTATAAAA
1 TTATAAAA
21932194 TT
1 TT
21932196 GATCAATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 29 0.85
9 5 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
TTATAAAA
Found at i:21932203 original size:24 final size:25
Alignment explanation
Indices: 21932153--21932211 Score: 86
Period size: 24 Copynumber: 2.4 Consensus size: 25
21932143 GATCTATTAC
21932153 TTATATAAATTATAAAATTATAAAA
1 TTATATAAATTATAAAATTATAAAA
*
21932178 TTATA-AAATTATAAAATTGAT-CAA
1 TTATATAAATTATAAAATT-ATAAAA
21932202 TTATATAAAT
1 TTATATAAAT
21932212 ATTGATTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 20 0.65
25 11 0.35
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (25 bp):
TTATATAAATTATAAAATTATAAAA
Found at i:21932728 original size:14 final size:14
Alignment explanation
Indices: 21932709--21932739 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
21932699 TTGTTAGATA
*
21932709 AGTGATTCTTATTT
1 AGTGATTCTTATAT
21932723 AGTGATTCTTATAT
1 AGTGATTCTTATAT
21932737 AGT
1 AGT
21932740 TTGTGGAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.16, T:0.52
Consensus pattern (14 bp):
AGTGATTCTTATAT
Found at i:21935420 original size:16 final size:18
Alignment explanation
Indices: 21935387--21935423 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
21935377 AAAAATATTT
21935387 TAAAAAAATTACATAAAAA
1 TAAAAAAA-TACATAAAAA
21935406 TAAAAAAA-ACA-AAAAA
1 TAAAAAAATACATAAAAA
21935422 TA
1 TA
21935424 TTTTTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
19 8 0.44
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.16
Consensus pattern (18 bp):
TAAAAAAATACATAAAAA
Found at i:21941017 original size:5 final size:5
Alignment explanation
Indices: 21941001--21941054 Score: 63
Period size: 5 Copynumber: 10.6 Consensus size: 5
21940991 TAATCAATAT
* * * *
21941001 AAACC TAAACC AAACC AAACC AAACC AAACC AAGCC ATACC ATACC ATACC
1 AAACC -AAACC AAACC AAACC AAACC AAACC AAACC AAACC AAACC AAACC
21941052 AAA
1 AAA
21941055 ATAAAAAAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
5 39 0.89
6 5 0.11
ACGTcount: A:0.54, C:0.37, G:0.02, T:0.07
Consensus pattern (5 bp):
AAACC
Found at i:21941626 original size:396 final size:394
Alignment explanation
Indices: 21941075--21941875 Score: 1388
Period size: 396 Copynumber: 2.0 Consensus size: 394
21941065 TTACTACCCT
* * * * *
21941075 TTAATCTATGTTCTCCTTGCTCGTTTGCCTCAATTTTATTTAAAGAGATAAGCTATTACATCTTC
1 TTAATCTATATTCCCCTTGCTCATTTGCCTCAAATTTATTTAAAGAGATAAGCTACTACATCTTC
* *
21941140 AATAATAGGAGTGTGGCTCATGGAACAACAAGTACTTTTTTCCATGAAATGGAGTGTGCTTGATA
66 AATAATAGGAGTGTAGCTCATGGAACAACAAGTACTTTTTTCCACGAAATGGAGTGTGCTTGATA
21941205 TTTGAAATAGCCTCAATAGGGTCAACATGAGTTGCAACCTCATGTTTCACTTAAACATCAATAAC
131 TTTGAAATAGCCTCAATAGGGTCAACATGAGTTGCAACCTCATGTTTCACTTAAACATCAATAAC
*
21941270 TTGTTGATCTTCATAACTTAGATGTGGTTGATCTTTTCTCACCCAAATTTGCCTTCGTCACATTC
196 TTGTTGATCTTCATAACTTAGATGTGGTTGATC-TTTCTCACCCAAATTTACCTTCGTCACATTC
* *
21941335 TACCCAATGCACTTGCTATTGGAACAGGTTTTGCAACAAACATGAACTTCTTCTAATCTTTTATC
260 TACCCAATGCACTTACTATTGGAACAGGTTTAGCAACAAACATGAACTTCTTCTAATCTTTTATC
21941400 ATATTAAAACAATAAGGTCTAAAGTGCCTTTTTTTTCCCAAAATTAATGGAATGCAAATTTTATT
325 ATATTAAAACAATAAGGTCTAAAGTGCCTTTTTTTT-CCAAAATTAATGGAATGCAAATTTTATT
21941465 TTCTCC
389 TTCTCC
21941471 TTAATCTATATTCCCCTTGCTCATTTGCCTCAAATTTATTTAAAGAGATAAGCTACTACATCTTC
1 TTAATCTATATTCCCCTTGCTCATTTGCCTCAAATTTATTTAAAGAGATAAGCTACTACATCTTC
*
21941536 AATAATAGGAGTGTAGCTCATGGAACAAGAAGTACTTTTTTCCACGAAAATGGAGTGTGCTTGAT
66 AATAATAGGAGTGTAGCTCATGGAACAACAAGTACTTTTTTCCACG-AAATGGAGTGTGCTTGAT
* *
21941601 ATTTGAAATAGCCTTAATA-GGTCAACATGATTTGCAACCTCATGTTTCACTTAAACATCAATAA
130 ATTTGAAATAGCCTCAATAGGGTCAACATGAGTTGCAACCTCATGTTTCACTTAAACATCAATAA
*
21941665 CTTGTTGATCTTCATAGCTTAGATGTGGTTGATCTTTCTCACCCAAATTTACCTTCGTCACATTC
195 CTTGTTGATCTTCATAACTTAGATGTGGTTGATCTTTCTCACCCAAATTTACCTTCGTCACATTC
* * * *
21941730 TATCCAATGCACTTACTGTTGGAACAGGTTTAGCAACATACATGAACTTCTTCTGATCTTTTATC
260 TACCCAATGCACTTACTATTGGAACAGGTTTAGCAACAAACATGAACTTCTTCTAATCTTTTATC
*
21941795 GTATTAAAACAATAAGGTCTAAAGTGCCTTTTTTTTCCAAAATTAATGGAATGCAAATTTTATTT
325 ATATTAAAACAATAAGGTCTAAAGTGCCTTTTTTTTCCAAAATTAATGGAATGCAAATTTTATTT
21941860 TCTCC
390 TCTCC
*
21941865 TTATTCTATAT
1 TTAATCTATAT
21941876 GTTACTGTTT
Statistics
Matches: 384, Mismatches: 20, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
394 44 0.11
395 124 0.32
396 180 0.47
397 36 0.09
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (394 bp):
TTAATCTATATTCCCCTTGCTCATTTGCCTCAAATTTATTTAAAGAGATAAGCTACTACATCTTC
AATAATAGGAGTGTAGCTCATGGAACAACAAGTACTTTTTTCCACGAAATGGAGTGTGCTTGATA
TTTGAAATAGCCTCAATAGGGTCAACATGAGTTGCAACCTCATGTTTCACTTAAACATCAATAAC
TTGTTGATCTTCATAACTTAGATGTGGTTGATCTTTCTCACCCAAATTTACCTTCGTCACATTCT
ACCCAATGCACTTACTATTGGAACAGGTTTAGCAACAAACATGAACTTCTTCTAATCTTTTATCA
TATTAAAACAATAAGGTCTAAAGTGCCTTTTTTTTCCAAAATTAATGGAATGCAAATTTTATTTT
CTCC
Found at i:21946036 original size:16 final size:15
Alignment explanation
Indices: 21946010--21946040 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
21946000 AATTTTGATG
21946010 AATAGAATAGAATTT
1 AATAGAATAGAATTT
21946025 AATAGTAATAGAATTT
1 AATAG-AATAGAATTT
21946041 TCTAATTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (15 bp):
AATAGAATAGAATTT
Found at i:21950592 original size:22 final size:22
Alignment explanation
Indices: 21950548--21950593 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
21950538 TAGTTAAACT
*
21950548 CTGTTTATTTGTTTCAATTAAA
1 CTGTTTATTTGTTTCAATCAAA
* *
21950570 CTGTTTATTTGTTTGAGTCAAA
1 CTGTTTATTTGTTTCAATCAAA
21950592 CT
1 CT
21950594 CTTATTAGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.11, G:0.13, T:0.52
Consensus pattern (22 bp):
CTGTTTATTTGTTTCAATCAAA
Found at i:21952837 original size:22 final size:22
Alignment explanation
Indices: 21952796--21952837 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
21952786 TTTCACTCGT
* *
21952796 CAAACTTCAATGTTGTGACACC
1 CAAACTTCAATGTCGCGACACC
*
21952818 CAAACTTCAGTGTCGCGACA
1 CAAACTTCAATGTCGCGACA
21952838 TCCATGGTAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (22 bp):
CAAACTTCAATGTCGCGACACC
Found at i:21971528 original size:21 final size:20
Alignment explanation
Indices: 21971498--21971536 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
21971488 GAGTATGAAA
21971498 ATATAATTAAAATTGTGATTC
1 ATATAATTAAAATT-TGATTC
*
21971519 ATATACTTAAAATTTGAT
1 ATATAATTAAAATTTGAT
21971537 ACATGATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (20 bp):
ATATAATTAAAATTTGATTC
Found at i:21984261 original size:16 final size:16
Alignment explanation
Indices: 21984242--21984284 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
21984232 AAAGACGAAA
21984242 AGAAAAAGAAAAAGAG
1 AGAAAAAGAAAAAGAG
*
21984258 AGAAAAAGGAAAAAGGG
1 AGAAAAA-GAAAAAGAG
*
21984275 AAAAAAAGAA
1 AGAAAAAGAA
21984285 GAAAACAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (16 bp):
AGAAAAAGAAAAAGAG
Found at i:21984264 original size:22 final size:22
Alignment explanation
Indices: 21984224--21984272 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
21984214 TCAAACTAGC
21984224 AAAAA-AAAAAAGACGAAAA-G
1 AAAAAGAAAAAAGACGAAAAGG
21984244 AAAAAGAAAAAGAGA-GAAAAAGG
1 AAAAAGAAAAA-AGACG-AAAAGG
21984267 AAAAAG
1 AAAAAG
21984273 GGAAAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 5 0.20
21 6 0.24
22 7 0.28
23 7 0.28
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAGACGAAAAGG
Found at i:21985424 original size:49 final size:49
Alignment explanation
Indices: 21985339--21985689 Score: 260
Period size: 49 Copynumber: 7.2 Consensus size: 49
21985329 GAAAAAGGAT
* * * * *
21985339 AGGTTGAAGCTGCAAAGGCAGACATAACATCCTAAAATTGAAGGGGGAA
1 AGGTTGAAGCTGCAACGGCGGACCTAACACCCTAAAATTGAAGAGGGAA
* ** * * *
21985388 AGGTTGAAACTATAACGGCGGACCTTACACCTTAAAACTGAAGA-GGAA
1 AGGTTGAAGCTGCAACGGCGGACCTAACACCCTAAAATTGAAGAGGGAA
* * *
21985436 TAGGTTGAAGTTGCAATGGCGGACCTAACACCCTAAAATAGAAGAGGGAA
1 -AGGTTGAAGCTGCAACGGCGGACCTAACACCCTAAAATTGAAGAGGGAA
** * * ** * ** * * *
21985486 ATATCGAAGCCGCAACGGCGGATTTTATGCCTTAAAACTGAAGAGGGAT
1 AGGTTGAAGCTGCAACGGCGGACCTAACACCCTAAAATTGAAGAGGGAA
* ** *
21985535 AGGTTGAAG-TCGTAACGATGGACCTAACACCCTAAAATTGAATAGGGATTA
1 AGGTTGAAGCT-GCAACGGCGGACCTAACACCCTAAAATTGAAGAGGGA--A
** * * *
21985586 A--TTGAAGCCACAATGGCGGATCTAACACCCTAAAATCGAAGAGGGAA
1 AGGTTGAAGCTGCAACGGCGGACCTAACACCCTAAAATTGAAGAGGGAA
* * ** * * *
21985633 AGGTTGAAGCTGTAACAGAAGACCTTACACCTTAAAATTGAAGAGGGAT
1 AGGTTGAAGCTGCAACGGCGGACCTAACACCCTAAAATTGAAGAGGGAA
21985682 AGGTTGAA
1 AGGTTGAA
21985690 TGTAACAACC
Statistics
Matches: 222, Mismatches: 72, Indels: 16
0.72 0.23 0.05
Matches are distributed among these distances:
47 2 0.01
48 4 0.02
49 211 0.95
50 4 0.02
51 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.20
Consensus pattern (49 bp):
AGGTTGAAGCTGCAACGGCGGACCTAACACCCTAAAATTGAAGAGGGAA
Found at i:21985506 original size:98 final size:96
Alignment explanation
Indices: 21985337--21985680 Score: 307
Period size: 98 Copynumber: 3.5 Consensus size: 96
21985327 TTGAAAAAGG
* * * * * * * *
21985337 ATAGGTTGAAGCTGCAAAGGCAGACATAACATCCTAAAATTGAAGGGGGAAAGGTTGAAACTATA
1 ATAGGTTGAAGTTGCAAAGGCGGACCTAACACCCTAAAATTGAAGAGGGAAA--TTGAAGCCACA
*
21985402 ACGGCGGACCTTACACCTTAAAACTGAAGAGGA
64 ACGGCGGATCTTACACCTTAAAACTGAAGAGGA
* * *
21985435 ATAGGTTGAAGTTGCAATGGCGGACCTAACACCCTAAAATAGAAGAGGGAAATATCGAAGCCGCA
1 ATAGGTTGAAGTTGCAAAGGCGGACCTAACACCCTAAAATTGAAGAGGGAAAT-T-GAAGCCACA
* ** *
21985500 ACGGCGGATTTTATGCCTTAAAACTGAAGAGGG
64 ACGGCGGATCTTACACCTTAAAACTGAAGAGGA
* * * ** *
21985533 ATAGGTTGAAGTCGTAACGATGGACCTAACACCCTAAAATTGAATAGGGATTAATTGAAGCCACA
1 ATAGGTTGAAGTTGCAAAGGCGGACCTAACACCCTAAAATTGAAGAGGGA--AATTGAAGCCACA
* * *
21985598 ATGGCGGATCTAACACCCTAAAA-TCGAAGAGGGA
64 ACGGCGGATCTTACACCTTAAAACT-GAAGA-GGA
* * ** * *
21985632 A-AGGTTGAAGCTGTAACA-GAAGACCTTACACCTTAAAATTGAAGAGGGA
1 ATAGGTTGAAGTTGCAA-AGGCGGACCTAACACCCTAAAATTGAAGAGGGA
21985681 TAGGTTGAAT
Statistics
Matches: 199, Mismatches: 40, Indels: 14
0.79 0.16 0.06
Matches are distributed among these distances:
96 1 0.01
97 2 0.01
98 189 0.95
99 4 0.02
100 3 0.02
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.19
Consensus pattern (96 bp):
ATAGGTTGAAGTTGCAAAGGCGGACCTAACACCCTAAAATTGAAGAGGGAAATTGAAGCCACAAC
GGCGGATCTTACACCTTAAAACTGAAGAGGA
Found at i:21987788 original size:36 final size:36
Alignment explanation
Indices: 21987735--21987828 Score: 163
Period size: 36 Copynumber: 2.6 Consensus size: 36
21987725 GTAACAGGCC
*
21987735 TGACCTTTAGGTCAACAGGGAGTAAAATGAGCATCA
1 TGACCTTTGGGTCAACAGGGAGTAAAATGAGCATCA
21987771 TGACCTTTGGG-CTAACAGGGAGTAAAATGAGCATCA
1 TGACCTTTGGGTC-AACAGGGAGTAAAATGAGCATCA
21987807 TGACCTTTGGGTCAACAGGGAG
1 TGACCTTTGGGTCAACAGGGAG
21987829 CAAGCATGAC
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
35 1 0.02
36 53 0.96
37 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (36 bp):
TGACCTTTGGGTCAACAGGGAGTAAAATGAGCATCA
Found at i:21989107 original size:49 final size:49
Alignment explanation
Indices: 21989005--21989313 Score: 255
Period size: 49 Copynumber: 6.3 Consensus size: 49
21988995 GGATGCTACA
* * * * * *
21989005 TTGAAGCCGCAATGATGGACCTAACACCTTAAAATCGAAGGGGGGA-AGA
1 TTGAAGCCGCAACGACGAACCTAACACCTTAAAATTGAA-GAGGGATAGG
* ** * * *
21989054 TTGAAGCCGTAACGGTGAATCTTACACCTTAAAATCGAAGAGGGATAGG
1 TTGAAGCCGCAACGACGAACCTAACACCTTAAAATTGAAGAGGGATAGG
* * * * **
21989103 TTGAAGTCGCAACGACAAACCTAACACCCTAAAATTAAAGAGGGATAAA
1 TTGAAGCCGCAACGACGAACCTAACACCTTAAAATTGAAGAGGGATAGG
* * * *
21989152 TTGAAGCCGCAACGGCGGATCTAACA-CTCTAAAATTGAAGAGGGAAAGG
1 TTGAAGCCGCAACGACGAACCTAACACCT-TAAAATTGAAGAGGGATAGG
* **
21989201 TTGAAGCCGCAAAGACGAACCTTTCACCTTAAAATTGAAGAGGGATAGG
1 TTGAAGCCGCAACGACGAACCTAACACCTTAAAATTGAAGAGGGATAGG
** * * * * * * * *
21989250 TTGAAG-CAAAATGGCGGACCTAACACCCTAAAACTGAAGAGGCAAAGA
1 TTGAAGCCGCAACGACGAACCTAACACCTTAAAATTGAAGAGGGATAGG
*
21989298 TTGAAGTCGCAACGAC
1 TTGAAGCCGCAACGAC
21989314 ATATCTTACA
Statistics
Matches: 203, Mismatches: 53, Indels: 8
0.77 0.20 0.03
Matches are distributed among these distances:
48 42 0.21
49 159 0.78
50 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (49 bp):
TTGAAGCCGCAACGACGAACCTAACACCTTAAAATTGAAGAGGGATAGG
Found at i:21989185 original size:98 final size:97
Alignment explanation
Indices: 21989053--21989314 Score: 285
Period size: 98 Copynumber: 2.7 Consensus size: 97
21989043 AGGGGGGAAG
* * * * *
21989053 ATTGAAGCCGTAACGGTGAATCTTACACCTTAAAATCGAAGAGGGATAGGTTGAAGTCGCAACGA
1 ATTGAAGCCGAAACGGCGGATCTAACACC-TAAAATCGAAGAGGGAAAGGTTGAAGTCGCAACGA
21989118 CAAACCTAACACCCTAAAATTAAAGAGGGATAA
65 CAAACCTAACACCCTAAAATTAAAGAGGGATAA
* * * *
21989151 ATTGAAGCCGCAACGGCGGATCTAACACTCTAAAATTGAAGAGGGAAAGGTTGAAGCCGCAAAGA
1 ATTGAAGCCGAAACGGCGGATCTAACAC-CTAAAATCGAAGAGGGAAAGGTTGAAGTCGCAACGA
* ** * * *
21989216 CGAACCTTTCACCTTAAAATTGAAGAGGGATAG
65 CAAACCTAACACCCTAAAATTAAAGAGGGATAA
* * * * * *
21989249 GTTGAAG-CAAAATGGCGGACCTAACACCCTAAAA-CTGAAGAGGCAAAGATTGAAGTCGCAACG
1 ATTGAAGCCGAAACGGCGGATCTAACA-CCTAAAATC-GAAGAGGGAAAGGTTGAAGTCGCAACG
21989312 ACA
64 ACA
21989315 TATCTTACAC
Statistics
Matches: 136, Mismatches: 25, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
97 46 0.34
98 89 0.65
99 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.18
Consensus pattern (97 bp):
ATTGAAGCCGAAACGGCGGATCTAACACCTAAAATCGAAGAGGGAAAGGTTGAAGTCGCAACGAC
AAACCTAACACCCTAAAATTAAAGAGGGATAA
Found at i:21989995 original size:24 final size:24
Alignment explanation
Indices: 21989950--21990002 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
21989940 AGAGTTTGAC
*
21989950 TGAAACAAATAAACAAAGTTTAAT
1 TGAAACAAATAAACAAAATTTAAT
21989974 TGAAACAAATAAA-AAGAATTTAAT
1 TGAAACAAATAAACAA-AATTTAAT
21989998 TGAAA
1 TGAAA
21990003 GATTATTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 2 0.07
24 25 0.93
ACGTcount: A:0.60, C:0.06, G:0.09, T:0.25
Consensus pattern (24 bp):
TGAAACAAATAAACAAAATTTAAT
Found at i:21991206 original size:97 final size:97
Alignment explanation
Indices: 21991074--21991270 Score: 333
Period size: 97 Copynumber: 2.0 Consensus size: 97
21991064 AGTAAAAATT
* *
21991074 AAATTTGATGTGAGGAAAGATGTTGAATAATTGATACAAAATGGTAGGGAGATAGGGAAAGGATA
1 AAATTTGATGTGAAGAAAGATGTTGAATAAGTGATACAAAATGGTAGGGAGATAGGGAAAGGATA
21991139 TAAGGTATGAAGAAAGGGATTAGAAGATGGTG
66 TAAGGTATGAAGAAAGGGATTAGAAGATGGTG
* * *
21991171 AAATTTGATGAT-AAGAAAGATGTTGAATACGTGATACAAAATGGTAGGGAGGTAGGTAAAGGAT
1 AAATTTGATG-TGAAGAAAGATGTTGAATAAGTGATACAAAATGGTAGGGAGATAGGGAAAGGAT
21991235 ATAAGGTATGAAGAAAGGGATTAGAAGATGGTG
65 ATAAGGTATGAAGAAAGGGATTAGAAGATGGTG
21991268 AAA
1 AAA
21991271 GATAAGAAAA
Statistics
Matches: 94, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
97 93 0.99
98 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.32, T:0.23
Consensus pattern (97 bp):
AAATTTGATGTGAAGAAAGATGTTGAATAAGTGATACAAAATGGTAGGGAGATAGGGAAAGGATA
TAAGGTATGAAGAAAGGGATTAGAAGATGGTG
Found at i:22001282 original size:33 final size:32
Alignment explanation
Indices: 22001240--22001304 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
22001230 TGGTAAGTGG
22001240 CAGTGATAATATTGTG-CTAATAATGCAAATATT
1 CAGTGATAATATTGTGTCTAATAAT--AAATATT
*
22001273 CAGTGATAATATTGTGTTTAATAATAAATATT
1 CAGTGATAATATTGTGTCTAATAATAAATATT
22001305 TTGGCCTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 7 0.23
33 16 0.53
34 7 0.23
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (32 bp):
CAGTGATAATATTGTGTCTAATAATAAATATT
Found at i:22006574 original size:26 final size:25
Alignment explanation
Indices: 22006523--22006584 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
22006513 TTAATTACTA
*
22006523 TAAAATATTAACAATTAAAAATAAAT
1 TAAAA-ATTAACAATTAAAAACAAAT
*
22006549 TGAAAAGTTAACTAATT-AAAACAAAT
1 T-AAAAATTAAC-AATTAAAAACAAAT
22006575 TAAAAATTAA
1 TAAAAATTAA
22006585 GGAGAAGACT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 8 0.26
26 15 0.48
27 8 0.26
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (25 bp):
TAAAAATTAACAATTAAAAACAAAT
Found at i:22012541 original size:21 final size:21
Alignment explanation
Indices: 22012517--22012566 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
22012507 TTTTTAATAC
* *
22012517 CGGTAGAAGCATGATTTGTTT
1 CGGTAGAAGCATGACTTGTAT
* * *
22012538 CGGTAAAAGCTTTACTTGTAT
1 CGGTAGAAGCATGACTTGTAT
22012559 CGGTAGAA
1 CGGTAGAA
22012567 CTGTCATAAG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (21 bp):
CGGTAGAAGCATGACTTGTAT
Found at i:22016775 original size:195 final size:195
Alignment explanation
Indices: 22016384--22016830 Score: 510
Period size: 195 Copynumber: 2.3 Consensus size: 195
22016374 GAAACTGACG
* * * **
22016384 CGATGGCTGAGGTATCGGATATGTTGCGAGTCCTCTACAGCTCATGTGAGCAGCATCGTGAGTTG
1 CGATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCATGTGAGCAGCATCGTGACCTG
* * *
22016449 GGAAATGAGAAAAGAATTCAAGAATGGTTTATAGGCCCTACGATGGCTGAGATTTATGCATAAGC
66 AGAAATGAGAAAAGAATTCAAGAATGGATTATAGGCCCTACGATGGCTGAGATCTATGCATAAGC
* ** * * * * * *
22016514 GCATATTCTCGACCGCTCGTGTGAGCAGCATCGTTAGGGAACAGTTATATGCACAGATATCGTAT
131 GCATACTCTCGACAACTCGTGTAAGCAGCATCATTAGGGAACAGTTATATACACAAACACCGTAT
* * *
22016579 CGATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAGCATCGTGACCTG
1 CGATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCATGTGAGCAGCATCGTGACCTG
* * * * * *
22016644 AGAAA-GTGATATGGATCTC-A-AATGGATTATAGGCCCTACGATGGCT-AGGA-CTATGCTTTA
66 AGAAATGAGAAAAGAAT-TCAAGAATGGATTATAGGCCCTACGATGGCTGA-GATCTATGCATAA
* *
22016704 -CGTATACTCTCGACAACTCGTGTAAGCAGCATTATTAGGGAACAGTTTATAGTACAGACAAACA
129 GCGCATACTCTCGACAACTCGTGTAAGCAGCATCATTAGGGAACAG-TTATA-TAC--ACAAACA
22016768 CCGTAT
190 CCGTAT
* * * *
22016774 CGATGGCTGGGGTACCGCATACGTTGCGAGTCCTCGACAGGTCATGTGAGCGGCATC
1 CGATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCATGTGAGCAGCATC
22016831 AAGCACTGGT
Statistics
Matches: 211, Mismatches: 35, Indels: 12
0.82 0.14 0.05
Matches are distributed among these distances:
191 38 0.18
192 13 0.06
193 29 0.14
194 8 0.04
195 123 0.58
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.26
Consensus pattern (195 bp):
CGATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCATGTGAGCAGCATCGTGACCTG
AGAAATGAGAAAAGAATTCAAGAATGGATTATAGGCCCTACGATGGCTGAGATCTATGCATAAGC
GCATACTCTCGACAACTCGTGTAAGCAGCATCATTAGGGAACAGTTATATACACAAACACCGTAT
Found at i:22022043 original size:14 final size:14
Alignment explanation
Indices: 22022024--22022059 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
22022014 TTGTTTGACT
*
22022024 GAAAATGGTTTCTG
1 GAAAATGATTTCTG
22022038 GAAAATGATTTCTG
1 GAAAATGATTTCTG
22022052 GAAAATGA
1 GAAAATGA
22022060 ATTACTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.39, C:0.06, G:0.25, T:0.31
Consensus pattern (14 bp):
GAAAATGATTTCTG
Found at i:22026081 original size:6 final size:6
Alignment explanation
Indices: 22026070--22026094 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
22026060 CGCAATGAAT
22026070 GGGGAA GGGGAA GGGGAA GGGGAA G
1 GGGGAA GGGGAA GGGGAA GGGGAA G
22026095 AACGTTTAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GGGGAA
Found at i:22026285 original size:14 final size:14
Alignment explanation
Indices: 22026266--22026292 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22026256 AGAAAATGTT
22026266 GAAAAGCTTTTACG
1 GAAAAGCTTTTACG
22026280 GAAAAGCTTTTAC
1 GAAAAGCTTTTAC
22026293 AACTAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (14 bp):
GAAAAGCTTTTACG
Found at i:22033936 original size:23 final size:22
Alignment explanation
Indices: 22033905--22033948 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
22033895 AAAGAAATAA
*
22033905 AATTAACCCAATTTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
22033927 AATTCAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
22033949 GAAATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:22045320 original size:26 final size:26
Alignment explanation
Indices: 22045291--22045371 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
22045281 GTCATTGGAC
22045291 CTCATAATCCGTAAAGGATTCATATA
1 CTCATAATCCGTAAAGGATTCATATA
* * ** *
22045317 CTCACAAT--G-ACACTAGTCAT-TGGA
1 CTCATAATCCGTAAAGGATTCATAT--A
22045341 CCTCATAATCCGTAAAGGATTCATATA
1 -CTCATAATCCGTAAAGGATTCATATA
22045368 CTCA
1 CTCA
22045372 CGATAACACA
Statistics
Matches: 38, Mismatches: 10, Indels: 14
0.61 0.16 0.23
Matches are distributed among these distances:
22 1 0.03
23 7 0.18
24 2 0.05
25 7 0.18
26 11 0.29
27 2 0.05
28 7 0.18
29 1 0.03
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.28
Consensus pattern (26 bp):
CTCATAATCCGTAAAGGATTCATATA
Found at i:22045352 original size:51 final size:52
Alignment explanation
Indices: 22045210--22045388 Score: 245
Period size: 52 Copynumber: 3.5 Consensus size: 52
22045200 ATTTCTTTTA
* * ** *
22045210 ATACTCATGATAACACATAGTCATCAG-CCTTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATTGGACC-TCATAATCCGTAAAGGATTCAT
* * *
22045262 ACACTCATGATGAAACATAGTCATTGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATTGGACCTCATAATCCGTAAAGGATTCAT
*
22045314 ATACTCACAATGACAC-TAGTCATTGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATTGGACCTCATAATCCGTAAAGGATTCAT
*
22045365 ATACTCACGATAACACATAGTCAT
1 ATACTCACGATGACACATAGTCAT
22045389 CGAACCTTTT
Statistics
Matches: 113, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
51 49 0.43
52 62 0.55
53 2 0.02
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATTGGACCTCATAATCCGTAAAGGATTCAT
Found at i:22060432 original size:7 final size:7
Alignment explanation
Indices: 22060404--22060457 Score: 65
Period size: 7 Copynumber: 7.6 Consensus size: 7
22060394 TCAGTCGCAT
22060404 AAAAAGA
1 AAAAAGA
22060411 AAGAAA-A
1 AA-AAAGA
22060418 AGAAAAGA
1 A-AAAAGA
22060426 AAAAAGA
1 AAAAAGA
*
22060433 GAAAAGA
1 AAAAAGA
22060440 AAAAAGA
1 AAAAAGA
*
22060447 AAAAGGA
1 AAAAAGA
22060454 AAAA
1 AAAA
22060458 TAATATTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
7 35 0.85
8 6 0.15
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:22060437 original size:14 final size:14
Alignment explanation
Indices: 22060405--22060457 Score: 72
Period size: 14 Copynumber: 3.7 Consensus size: 14
22060395 CAGTCGCATA
*
22060405 AAAAGAAAGAAAAAG
1 AAAAGAAA-AAAGAG
22060420 AAAAGAAAAAAGAG
1 AAAAGAAAAAAGAG
22060434 AAAAGAAAAAAGA-
1 AAAAGAAAAAAGAG
22060447 AAAAGGAAAAA
1 AAAA-GAAAAA
22060458 TAATATTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
13 4 0.11
14 24 0.67
15 8 0.22
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAGAG
Found at i:22065073 original size:51 final size:50
Alignment explanation
Indices: 22064981--22065173 Score: 237
Period size: 50 Copynumber: 3.8 Consensus size: 50
22064971 TTAATAAAAT
*
22064981 CATGCATTATGTAACTTTCATGTTAGTTAAGTATGCATCATAAATAATGA
1 CATGCATTATGTAACTCTCATGTTAGTTAAGTATGCATCATAAATAATGA
* * *
22065031 CTTGCATTATGAAACTCTCATGATTAGTTAAGTTTGCATCATAAATAATGA
1 CATGCATTATGTAACTCTCATG-TTAGTTAAGTATGCATCATAAATAATGA
* * * *
22065082 CATGCATTAAGTAACT-TACATGTTAGTTAAATATGCATAATAAATTAT-A
1 CATGCATTATGTAACTCT-CATGTTAGTTAAGTATGCATCATAAATAATGA
* * *
22065131 TCATGCATTATGTAACTCCCATATTAGTTAAAGTTTGCATCAT
1 -CATGCATTATGTAACTCTCATGTTAGTT-AAGTATGCATCAT
22065174 TAAAACAAGT
Statistics
Matches: 121, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
49 1 0.01
50 66 0.55
51 54 0.45
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.38
Consensus pattern (50 bp):
CATGCATTATGTAACTCTCATGTTAGTTAAGTATGCATCATAAATAATGA
Found at i:22065104 original size:101 final size:101
Alignment explanation
Indices: 22064981--22065173 Score: 282
Period size: 101 Copynumber: 1.9 Consensus size: 101
22064971 TTAATAAAAT
* * * * *
22064981 CATGCATTATGTAACTTTCATGTTAGTTAAGTATGCATCATAAATAATGA-CTTGCATTATGAAA
1 CATGCATTAAGTAACTTACATGTTAGTTAAATATGCATAATAAATAAT-ATCATGCATTATGAAA
*
22065045 CTCTCATGATTAGTT-AAGTTTGCATCATAAATAATGA
65 CTCCCAT-ATTAGTTAAAGTTTGCATCATAAATAATGA
* *
22065082 CATGCATTAAGTAACTTACATGTTAGTTAAATATGCATAATAAATTATATCATGCATTATGTAAC
1 CATGCATTAAGTAACTTACATGTTAGTTAAATATGCATAATAAATAATATCATGCATTATGAAAC
22065147 TCCCATATTAGTTAAAGTTTGCATCAT
66 TCCCATATTAGTTAAAGTTTGCATCAT
22065174 TAAAACAAGT
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
100 8 0.10
101 74 0.90
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.38
Consensus pattern (101 bp):
CATGCATTAAGTAACTTACATGTTAGTTAAATATGCATAATAAATAATATCATGCATTATGAAAC
TCCCATATTAGTTAAAGTTTGCATCATAAATAATGA
Found at i:22065541 original size:78 final size:77
Alignment explanation
Indices: 22065391--22065542 Score: 200
Period size: 78 Copynumber: 2.0 Consensus size: 77
22065381 CATACTTGAT
* **
22065391 CAAGTGAATCTTCAAAAACCAAGGGAAGACTCTTCAAATGCTGATCGGTTTCGATGCACTTAAAG
1 CAAGTGAATCTTCAAAAACCAAGGGAAGACTATTCAAATGCTGATCAATTTCGATGCACTTAAAG
*
22065456 GATAATTCAAGA
66 GACAATTCAAGA
* *
22065468 CAAGCTGACTCTTCAAAAGACCAAGGG-AGACTATTCAAATGCTGATCAATTT-GGTGCACTTAA
1 CAAG-TGAATCTTCAAAA-ACCAAGGGAAGACTATTCAAATGCTGATCAATTTCGATGCACTT-A
*
22065531 AAGGCCAATTCA
63 AAGGACAATTCA
22065543 TGGCACCAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
77 12 0.18
78 45 0.69
79 8 0.12
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (77 bp):
CAAGTGAATCTTCAAAAACCAAGGGAAGACTATTCAAATGCTGATCAATTTCGATGCACTTAAAG
GACAATTCAAGA
Found at i:22066328 original size:28 final size:26
Alignment explanation
Indices: 22066297--22066380 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
22066287 CGAAATCTTG
22066297 AAAAAAAGAGAAAAATCAAAATTAGAAA
1 AAAAAAAGAGAAAAATC-AAATT-GAAA
** * *
22066325 AAAAAACTAGCAAAATTCGAATTGAAA
1 AAAAAAAGAG-AAAAATCAAATTGAAA
* * *
22066352 TAAAAAAGAGAAAATTCGAATT-AAA
1 AAAAAAAGAGAAAAATCAAATTGAAA
22066377 AAAA
1 AAAA
22066381 GAAAAAATTA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
25 6 0.13
26 12 0.26
27 11 0.23
28 12 0.26
29 6 0.13
ACGTcount: A:0.68, C:0.06, G:0.11, T:0.15
Consensus pattern (26 bp):
AAAAAAAGAGAAAAATCAAATTGAAA
Found at i:22066365 original size:26 final size:25
Alignment explanation
Indices: 22066297--22066401 Score: 90
Period size: 22 Copynumber: 4.1 Consensus size: 25
22066287 CGAAATCTTG
* *
22066297 AAAAAAAGAGAAAAATCAAAATTAGAA
1 AAAAAAAGAGAAAATTC-GAATT-GAA
*
22066324 AAAAAAACTAGCAAAATTCGAATTGAA
1 AAAAAAA-GAG-AAAATTCGAATTGAA
22066351 ATAAAAAAGAGAAAATTCGAATT---
1 A-AAAAAAGAGAAAATTCGAATTGAA
* *
22066374 AAAAAAAGAAAAAATTACGAAGTGAA
1 AAAAAAAGAGAAAATT-CGAATTGAA
22066400 AA
1 AA
22066402 TTTGAAAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
22 14 0.22
23 6 0.09
26 14 0.22
27 13 0.20
28 12 0.18
29 6 0.09
ACGTcount: A:0.67, C:0.06, G:0.12, T:0.15
Consensus pattern (25 bp):
AAAAAAAGAGAAAATTCGAATTGAA
Found at i:22066376 original size:21 final size:19
Alignment explanation
Indices: 22066344--22066385 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
22066334 GCAAAATTCG
22066344 AATTGAAATAAAAAAGAGAA
1 AATTGAAATAAAAAA-AGAA
*
22066364 AATTCGAATTAAAAAAAGAA
1 AATT-GAAATAAAAAAAGAA
22066384 AA
1 AA
22066386 AATTACGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.69, C:0.02, G:0.12, T:0.17
Consensus pattern (19 bp):
AATTGAAATAAAAAAAGAA
Found at i:22071799 original size:50 final size:51
Alignment explanation
Indices: 22071745--22071844 Score: 123
Period size: 50 Copynumber: 2.0 Consensus size: 51
22071735 ATCTGCAATT
* *
22071745 AATAA-AATCATGCATTATGTAACTTTCATG-TTAGTTAAATATGCATCATA
1 AATAATAA-CATGCATTATGAAACTCTCATGATTAGTTAAATATGCATCATA
* * * *
22071795 AATAATGACTTGCATTATGAAACTCTCATGATTAGTTAAGTTTGCATCAT
1 AATAATAACATGCATTATGAAACTCTCATGATTAGTTAAATATGCATCAT
22071845 TAAAATAGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
50 24 0.57
51 18 0.43
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (51 bp):
AATAATAACATGCATTATGAAACTCTCATGATTAGTTAAATATGCATCATA
Found at i:22079647 original size:34 final size:34
Alignment explanation
Indices: 22079602--22079667 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
22079592 CTGTAGTATA
*
22079602 ATTGTCCCTGCA-CTATTAATGTCATTGCATTTTT
1 ATTGTCCCTGCATCTA-CAATGTCATTGCATTTTT
* *
22079636 ATTGTCGCTGCATCTACATTGTCATTGCATTT
1 ATTGTCCCTGCATCTACAATGTCATTGCATTT
22079668 CCATAAACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 25 0.89
35 3 0.11
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.45
Consensus pattern (34 bp):
ATTGTCCCTGCATCTACAATGTCATTGCATTTTT
Found at i:22084014 original size:21 final size:21
Alignment explanation
Indices: 22083985--22084027 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
22083975 GGGAAAATTT
*
22083985 AAGACAA-GGTGACTCTTCAA
1 AAGACAAGGGAGACTCTTCAA
22084005 AAGACCAAGGGAGACTCTTCAA
1 AAGA-CAAGGGAGACTCTTCAA
22084027 A
1 A
22084028 TGCTGATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 3 0.15
22 13 0.65
ACGTcount: A:0.42, C:0.21, G:0.21, T:0.16
Consensus pattern (21 bp):
AAGACAAGGGAGACTCTTCAA
Found at i:22089050 original size:14 final size:14
Alignment explanation
Indices: 22089027--22089061 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
22089017 TTATTTAGCT
*
22089027 GAAAACAACTTTTA
1 GAAAATAACTTTTA
22089041 GAAAATAACTTTTA
1 GAAAATAACTTTTA
*
22089055 GAGAATA
1 GAAAATA
22089062 GATTGATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.29
Consensus pattern (14 bp):
GAAAATAACTTTTA
Found at i:22106270 original size:38 final size:36
Alignment explanation
Indices: 22106186--22106270 Score: 89
Period size: 38 Copynumber: 2.3 Consensus size: 36
22106176 CACACTATAA
* *
22106186 TCACTGTCACATGGCATGAAAAATATACCCACATAT
1 TCACTATCACATGGCATGAAAAACATACCCACATAT
* ** *
22106222 TTACTATCACATGGCATGAATATAACATATTCGCATAT
1 TCACTATCACATGGCATGAA-A-AACATACCCACATAT
*
22106260 TCACTTTCACA
1 TCACTATCACA
22106271 ACAGTCATCA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
36 18 0.46
37 1 0.03
38 20 0.51
ACGTcount: A:0.36, C:0.24, G:0.09, T:0.31
Consensus pattern (36 bp):
TCACTATCACATGGCATGAAAAACATACCCACATAT
Found at i:22106759 original size:20 final size:21
Alignment explanation
Indices: 22106737--22106817 Score: 82
Period size: 20 Copynumber: 4.0 Consensus size: 21
22106727 AAATCAAGTT
22106737 AAAATGATTTTAAACAAGGT-
1 AAAATGATTTTAAACAAGGTC
* *
22106757 AAAATGATTTCAATCAA-GTC
1 AAAATGATTTTAAACAAGGTC
* *
22106777 AAAATCATTTT-AAC-ACGTC
1 AAAATGATTTTAAACAAGGTC
22106796 AAAATGATTTTGAAAC-AGGTC
1 AAAATGATTTT-AAACAAGGTC
22106817 A
1 A
22106818 GAATAGCTCT
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
18 1 0.02
19 17 0.34
20 24 0.48
21 8 0.16
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (21 bp):
AAAATGATTTTAAACAAGGTC
Found at i:22106772 original size:40 final size:39
Alignment explanation
Indices: 22106728--22106805 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 39
22106718 ACAATTTTAA
* * *
22106728 AATCAAGTTAAAATGATTTTAAACAAGGT-AAAATGATTTC
1 AATCAAGTCAAAATCATTTT-AAC-ACGTCAAAATGATTTC
22106768 AATCAAGTCAAAATCATTTTAACACGTCAAAATGATTT
1 AATCAAGTCAAAATCATTTTAACACGTCAAAATGATTT
22106806 TGAAACAGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
38 3 0.09
39 13 0.38
40 18 0.53
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (39 bp):
AATCAAGTCAAAATCATTTTAACACGTCAAAATGATTTC
Found at i:22127107 original size:27 final size:28
Alignment explanation
Indices: 22127076--22127140 Score: 78
Period size: 30 Copynumber: 2.3 Consensus size: 28
22127066 CAATATATCT
* *
22127076 AAATAATTGACATGATGTG-TTCTGAAA
1 AAATAATTGACAAGATGGGTTTCTGAAA
*
22127103 AAATAATTTTGAGAAGATGGGTTTCTGAAA
1 AAATAA--TTGACAAGATGGGTTTCTGAAA
22127133 AAATAATT
1 AAATAATT
22127141 TTAAGAAGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 6 0.19
28 2 0.06
29 10 0.31
30 14 0.44
ACGTcount: A:0.43, C:0.05, G:0.18, T:0.34
Consensus pattern (28 bp):
AAATAATTGACAAGATGGGTTTCTGAAA
Found at i:22127131 original size:30 final size:29
Alignment explanation
Indices: 22127089--22127233 Score: 155
Period size: 30 Copynumber: 5.2 Consensus size: 29
22127079 TAATTGACAT
*
22127089 GATGTGTTCTGAAAAAATAATTTTGAGAA
1 GATGGGTTCTGAAAAAATAATTTTGAGAA
*
22127118 GATGGGTTTCTGAAAAAATAATTTTAAGAA
1 GATGGG-TTCTGAAAAAATAATTTTGAGAA
22127148 GATGGG-T-T------ATAATTTTGAGAA
1 GATGGGTTCTGAAAAAATAATTTTGAGAA
* *
22127169 GATGAGTTTCTGAAAAAATAATTTTAAGAA
1 GATG-GGTTCTGAAAAAATAATTTTGAGAA
*
22127199 GATGGGTTCTGAAAAAATTATTTTGATG-A
1 GATGGGTTCTGAAAAAATAATTTTGA-GAA
22127228 GATGGG
1 GATGGG
22127234 GGTTGAAATT
Statistics
Matches: 97, Mismatches: 8, Indels: 22
0.76 0.06 0.17
Matches are distributed among these distances:
21 16 0.16
22 1 0.01
23 1 0.01
24 1 0.01
27 1 0.01
28 1 0.01
29 31 0.32
30 45 0.46
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.34
Consensus pattern (29 bp):
GATGGGTTCTGAAAAAATAATTTTGAGAA
Found at i:22127181 original size:51 final size:51
Alignment explanation
Indices: 22127105--22127206 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
22127095 TTCTGAAAAA
*
22127105 ATAATTTTGAGAAGATGGGTTTCTGAAAAAATAATTTTAAGAAGATGGGTT
1 ATAATTTTGAGAAGATGAGTTTCTGAAAAAATAATTTTAAGAAGATGGGTT
22127156 ATAATTTTGAGAAGATGAGTTTCTGAAAAAATAATTTTAAGAAGATGGGTT
1 ATAATTTTGAGAAGATGAGTTTCTGAAAAAATAATTTTAAGAAGATGGGTT
22127207 CTGAAAAAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (51 bp):
ATAATTTTGAGAAGATGAGTTTCTGAAAAAATAATTTTAAGAAGATGGGTT
Found at i:22127230 original size:29 final size:29
Alignment explanation
Indices: 22127156--22127233 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
22127146 AAGATGGGTT
*
22127156 ATAATTTTGAGAAGATGAGTTTCTGAAAAA
1 ATAATTTTGAGAAGATG-GGTTCTGAAAAA
*
22127186 ATAATTTTAAGAAGATGGGTTCTGAAAAA
1 ATAATTTTGAGAAGATGGGTTCTGAAAAA
*
22127215 ATTATTTTGATG-AGATGGG
1 ATAATTTTGA-GAAGATGGG
22127234 GGTTGAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 26 0.60
30 17 0.40
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.35
Consensus pattern (29 bp):
ATAATTTTGAGAAGATGGGTTCTGAAAAA
Found at i:22128160 original size:156 final size:156
Alignment explanation
Indices: 22127876--22128187 Score: 624
Period size: 156 Copynumber: 2.0 Consensus size: 156
22127866 GGAACGACGC
22127876 TAGTGAGAGTCTCAACTATTAAATTGATTTTGTGCTTTGTTGATCCTGTGACATATGACTCATTT
1 TAGTGAGAGTCTCAACTATTAAATTGATTTTGTGCTTTGTTGATCCTGTGACATATGACTCATTT
22127941 GATATCAAAGGTCCTCGTGGCTTGGAGGCGATTGTGCAGACGCACCTCGTTAGTGAATCTCCCTA
66 GATATCAAAGGTCCTCGTGGCTTGGAGGCGATTGTGCAGACGCACCTCGTTAGTGAATCTCCCTA
22128006 TCTTGAGTTGTATGTGGAATTTTTAA
131 TCTTGAGTTGTATGTGGAATTTTTAA
22128032 TAGTGAGAGTCTCAACTATTAAATTGATTTTGTGCTTTGTTGATCCTGTGACATATGACTCATTT
1 TAGTGAGAGTCTCAACTATTAAATTGATTTTGTGCTTTGTTGATCCTGTGACATATGACTCATTT
22128097 GATATCAAAGGTCCTCGTGGCTTGGAGGCGATTGTGCAGACGCACCTCGTTAGTGAATCTCCCTA
66 GATATCAAAGGTCCTCGTGGCTTGGAGGCGATTGTGCAGACGCACCTCGTTAGTGAATCTCCCTA
22128162 TCTTGAGTTGTATGTGGAATTTTTAA
131 TCTTGAGTTGTATGTGGAATTTTTAA
22128188 GGCCAGATGA
Statistics
Matches: 156, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
156 156 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (156 bp):
TAGTGAGAGTCTCAACTATTAAATTGATTTTGTGCTTTGTTGATCCTGTGACATATGACTCATTT
GATATCAAAGGTCCTCGTGGCTTGGAGGCGATTGTGCAGACGCACCTCGTTAGTGAATCTCCCTA
TCTTGAGTTGTATGTGGAATTTTTAA
Found at i:22131423 original size:21 final size:22
Alignment explanation
Indices: 22131381--22131433 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
22131371 CTATAACTAT
*
22131381 TAATTTAAAATACCGTAAACCC
1 TAATTTAAAATACCGAAAACCC
*
22131403 TTATTTAAAATACC-AAAACCC
1 TAATTTAAAATACCGAAAACCC
22131424 TAATTTAAAA
1 TAATTTAAAA
22131434 ATCCCCAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.49, C:0.19, G:0.02, T:0.30
Consensus pattern (22 bp):
TAATTTAAAATACCGAAAACCC
Found at i:22131687 original size:39 final size:38
Alignment explanation
Indices: 22131597--22131691 Score: 127
Period size: 38 Copynumber: 2.4 Consensus size: 38
22131587 ATTTTCCTGA
* *
22131597 ATATAATACTGTTTAAAAGTTAAATATTTCTTTAATTTTT
1 ATATAATA-T-TTTAAAAGTCAAATACTTCTTTAATTTTT
* *
22131637 ATATAAAATTTTAAAAGTCATATACTTCTTTAATTTTTT
1 ATATAATATTTTAAAAGTCAAATACTTCTTTAA-TTTTT
22131676 ATATAATATTTTAAAA
1 ATATAATATTTTAAAA
22131692 TCTTTAATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
38 21 0.43
39 21 0.43
40 7 0.14
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (38 bp):
ATATAATATTTTAAAAGTCAAATACTTCTTTAATTTTT
Found at i:22134547 original size:16 final size:17
Alignment explanation
Indices: 22134514--22134547 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
22134504 ATGAGTTAGA
*
22134514 ATAATGTTTAGATATTT
1 ATAATGGTTAGATATTT
22134531 ATAATGGTTAG-TATTT
1 ATAATGGTTAGATATTT
22134547 A
1 A
22134548 GGGTTTCAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (17 bp):
ATAATGGTTAGATATTT
Found at i:22134653 original size:17 final size:17
Alignment explanation
Indices: 22134631--22134667 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
22134621 GTAAAAAATT
22134631 ATAGTTGATGTCGTGAC
1 ATAGTTGATGTCGTGAC
*
22134648 ATAGTTGATGTTGTGAC
1 ATAGTTGATGTCGTGAC
22134665 ATA
1 ATA
22134668 TGTAATGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.38
Consensus pattern (17 bp):
ATAGTTGATGTCGTGAC
Found at i:22137500 original size:17 final size:15
Alignment explanation
Indices: 22137449--22137501 Score: 54
Period size: 17 Copynumber: 3.3 Consensus size: 15
22137439 GTCATAAACT
22137449 AAAAATAAATACAAAG
1 AAAAATAAATA-AAAG
*
22137465 AAATAATAAA-AAATG
1 AAA-AATAAATAAAAG
22137480 AAAAATAAAATAAAAG
1 AAAAAT-AAATAAAAG
22137496 TAAAAA
1 -AAAAA
22137502 CTTGTATCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 3 0.10
15 9 0.29
16 8 0.26
17 11 0.35
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (15 bp):
AAAAATAAATAAAAG
Found at i:22143245 original size:3 final size:3
Alignment explanation
Indices: 22143237--22143278 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
22143227 CCCGCAAGTT
*
22143237 TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
22143279 AATTATTTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:22154155 original size:12 final size:12
Alignment explanation
Indices: 22154127--22154158 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
22154117 TTAAACCTTG
22154127 CTTTTA-TTTCT
1 CTTTTATTTTCT
22154138 -TTTTATTTTCT
1 CTTTTATTTTCT
22154149 CTTTTATTTT
1 CTTTTATTTT
22154159 ATGCATTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.26
11 5 0.26
12 9 0.47
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.78
Consensus pattern (12 bp):
CTTTTATTTTCT
Found at i:22158230 original size:28 final size:28
Alignment explanation
Indices: 22158185--22158266 Score: 119
Period size: 28 Copynumber: 2.9 Consensus size: 28
22158175 GATAAACTGC
* *
22158185 CACATAATTGTCATAAATGGTCACATAT
1 CACATAATTGCCAAAAATGGTCACATAT
* *
22158213 CACATAATTGCCAAAAATGATCACAAAT
1 CACATAATTGCCAAAAATGGTCACATAT
*
22158241 CACATAATTGCCAAAAATGGCCACAT
1 CACATAATTGCCAAAAATGGTCACAT
22158267 CTTCCACCTT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.44, C:0.22, G:0.10, T:0.24
Consensus pattern (28 bp):
CACATAATTGCCAAAAATGGTCACATAT
Found at i:22162751 original size:34 final size:34
Alignment explanation
Indices: 22162713--22162778 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
22162703 CTGTAGTATA
*
22162713 ATTGTCCCTGCAT-TATTAATGTCATTGCATTTTT
1 ATTGTCCCTGCATCTA-CAATGTCATTGCATTTTT
* *
22162747 ATTGTCGCTGCATCTACATTGTCATTGCATTT
1 ATTGTCCCTGCATCTACAATGTCATTGCATTT
22162779 CCATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 26 0.93
35 2 0.07
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.47
Consensus pattern (34 bp):
ATTGTCCCTGCATCTACAATGTCATTGCATTTTT
Found at i:22162752 original size:17 final size:17
Alignment explanation
Indices: 22162721--22162778 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
22162711 TAATTGTCCC
* *
22162721 TGCATTATTAATGTCAT
1 TGCATTTTTATTGTCAT
**
22162738 TGCATTTTTATTGTCGC
1 TGCATTTTTATTGTCAT
* **
22162755 TGCATCTACATTGTCAT
1 TGCATTTTTATTGTCAT
22162772 TGCATTT
1 TGCATTT
22162779 CCATATATAT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.48
Consensus pattern (17 bp):
TGCATTTTTATTGTCAT
Found at i:22167135 original size:21 final size:20
Alignment explanation
Indices: 22167106--22167148 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 20
22167096 AGGAAAATTC
22167106 AAGACAAGGTG-ACTCTTCAA
1 AAGACAAGG-GAACTCTTCAA
22167126 AAGACCAAGGGATACTCTTCAA
1 AAGA-CAAGGGA-ACTCTTCAA
22167148 A
1 A
22167149 TGCTGATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 5 0.25
21 5 0.25
22 10 0.50
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.19
Consensus pattern (20 bp):
AAGACAAGGGAACTCTTCAA
Found at i:22194856 original size:16 final size:17
Alignment explanation
Indices: 22194835--22194872 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
22194825 TACTATTACA
22194835 TTTATATTC-ATATATT
1 TTTATATTCTATATATT
*
22194851 TTTATATTCTATTTATT
1 TTTATATTCTATATATT
22194868 TTTAT
1 TTTAT
22194873 CTTATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTATATTCTATATATT
Found at i:22206658 original size:29 final size:26
Alignment explanation
Indices: 22206604--22206658 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
22206594 TTCTTGGACA
*
22206604 AATGTTTGTAATTTTGACCATTGTTT
1 AATGTTTGTAATTTTGACCAATGTTT
*
22206630 AATGTTTGTCATTCTTTGAACCAATGTTT
1 AATGTTTGT-AAT-TTTG-ACCAATGTTT
22206659 GATATTGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 9 0.38
27 2 0.08
28 4 0.17
29 9 0.38
ACGTcount: A:0.24, C:0.11, G:0.15, T:0.51
Consensus pattern (26 bp):
AATGTTTGTAATTTTGACCAATGTTT
Found at i:22207057 original size:10 final size:11
Alignment explanation
Indices: 22207012--22207059 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
22207002 TATTAAACTC
22207012 TTAAAA-AATT
1 TTAAAATAATT
*
22207022 TTGAAATAATT
1 TTAAAATAATT
22207033 TTAAAATCAATT
1 TTAAAAT-AATT
*
22207045 TT-AAATGATT
1 TTAAAATAATT
22207055 TTAAA
1 TTAAA
22207060 CAAGTCAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
10 10 0.31
11 16 0.50
12 6 0.19
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (11 bp):
TTAAAATAATT
Found at i:22207072 original size:20 final size:20
Alignment explanation
Indices: 22207047--22207126 Score: 92
Period size: 20 Copynumber: 4.0 Consensus size: 20
22207037 AATCAATTTT
*
22207047 AAATGATTTTAAACAAGTCA
1 AAATCATTTTAAACAAGTCA
* * *
22207067 AAATGATTTCAATCAAGTCA
1 AAATCATTTTAAACAAGTCA
22207087 AAATCATTTT-AACACA-TCA
1 AAATCATTTTAAACA-AGTCA
22207106 AAATCATTTTCAAACAAGTCA
1 AAATCATTTT-AAACAAGTCA
22207127 GAATTGGTCC
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
19 16 0.31
20 28 0.55
21 7 0.14
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.30
Consensus pattern (20 bp):
AAATCATTTTAAACAAGTCA
Found at i:22209823 original size:497 final size:497
Alignment explanation
Indices: 22208828--22210312 Score: 2219
Period size: 497 Copynumber: 3.0 Consensus size: 497
22208818 TTGTGGCCTG
* * * * * *
22208828 CATTTCTTATTGTCGCAACATGACTTATGGTTTAGCCATTCTTGCATTTTGTTCTTCCATTTCTT
1 CATTTCTCAATGTCGCAACATGACTTCTGTTTTAGCCATTCTTGCATTTTGGTCTTTCATTTCTT
* * *
22208893 ACCAATGATTCATGAGAGCTTTCTAAGCTTACTTAAAACTCGAGTTTGAATTAATAATGCTTATA
66 ACCAATGATTCATGAGAGCTTTCTAAGCTTACTTAAAACCCAAGTTTGAATTAATAATGCTTTTA
* * * * *
22208958 GAAATTGTAAAACTTATTTATTTATGTGAATGCATGGTTAAACTTAATTGTTTACATGATTCATC
131 GAAGTTGTAAAACTTATTTATTTCTGTGAATGCATGATTAAACTTAATTGTTCACATGATTCGTC
* *
22209023 TATTAGATACTGAATTGCGTTTATAGTTGTTTCGATAACGAATGTGGCATCTCACATCTCAAATC
196 TATTAGATATTGAATTGCGTTTATAGTTGTTTCGATAACAAATGTGGCATCTCACATCTCAAATC
* * * *
22209088 TGACAACCGGGTCAAGAGTGAGATGTTATATAAGGGCACTTCTAGTGCTTTCACATACTTATGAT
261 TGACAACCGGGTCGAGAGTGGGGTGTTATATAAGGG-ACTTCCAGTGCTTTCACATACTTATGAT
* * *
22209153 AAAATCTGTATTAATGAAAGCCTTATAAGCATGTTCATTTTTCACATGTAAGCACCGTAGGCACT
325 CAAATCTGTATTAATGAAAGCCTTATAAGCATGTTCATTTTTCGCATGTAAGCACCGTAGGTACT
*
22209218 CTACATTTACAAACACATTTTCACTGTTCTTTAAGTCCTATAAATATGTCCATTTCATATAATAG
390 CTACATTTACAAACACATTTTCACTTTTCTTTAAGTCCTATAAATATGTCCATTTCATATAATAG
*
22209283 TTCTTCATAGTGGAAAATCATATTTTCATTTTTCTTTATCCTA
455 TTCTTCATAGTGGAAAATCATATTTTCATTGTTCTTTATCCTA
*
22209326 CATTTCTCAATGTCGCATCATGACTTCTGTTTTAGCCATTCTTGCATTTTGGTCTTTCATTTCTT
1 CATTTCTCAATGTCGCAACATGACTTCTGTTTTAGCCATTCTTGCATTTTGGTCTTTCATTTCTT
*
22209391 ACCGATGATTCATGAGAGCTTTCTAAGCTTACTTAAAACCCAAGTTTGAATTAATAATGCTTTTA
66 ACCAATGATTCATGAGAGCTTTCTAAGCTTACTTAAAACCCAAGTTTGAATTAATAATGCTTTTA
*
22209456 GAAGTTATAAAACTTATTTATTTCTGTGAATGCATGATTAAACTTAATTGTTCACATGATTCGTC
131 GAAGTTGTAAAACTTATTTATTTCTGTGAATGCATGATTAAACTTAATTGTTCACATGATTCGTC
* * *
22209521 TATTAGATATTGCATTGCATTTATAGTTGTTTTC-ATAACAAAAGTGGCATC-CACATCTCAAAT
196 TATTAGATATTGAATTGCGTTTATAGTTG-TTTCGATAACAAATGTGGCATCTCACATCTCAAAT
* * *
22209584 CTAACAACCAGGTCGAGAGTGGGGTGTTATATAAGGGTACTTCCAGTGCTTTCACATACTTAAGA
260 CTGACAACCGGGTCGAGAGTGGGGTGTTATATAAGGG-ACTTCCAGTGCTTTCACATACTTATGA
* *
22209649 TCAAATTTGTATTAATGAAAGCCTTATAAGCATGTTCATTTTTCGCATGTAAGCACCATAGGTAC
324 TCAAATCTGTATTAATGAAAGCCTTATAAGCATGTTCATTTTTCGCATGTAAGCACCGTAGGTAC
*
22209714 TCTGCATTTACAAACACATTTTCACTTTTCTTTAAGTCCTATAAATATGTCCATTTCATATAATA
389 TCTACATTTACAAACACATTTTCACTTTTCTTTAAGTCCTATAAATATGTCCATTTCATATAATA
*
22209779 GTTCTTCATAGTGGAAAATCATATTTCCATTGTTCTTTATCCTA
454 GTTCTTCATAGTGGAAAATCATATTTTCATTGTTCTTTATCCTA
*
22209823 CATTTCTCAATGTCGCAACATGACTTCTATTTTAGCCATTCTTGCATTTTGGTCTTTCATTTCTT
1 CATTTCTCAATGTCGCAACATGACTTCTGTTTTAGCCATTCTTGCATTTTGGTCTTTCATTTCTT
** *
22209888 ATTAGTGATTCATGAGAGCTTTCTAAGC-TACTTAAAACCCAAGTTTGAATTAATAATGCTTTTA
66 ACCAATGATTCATGAGAGCTTTCTAAGCTTACTTAAAACCCAAGTTTGAATTAATAATGCTTTTA
* * *
22209952 GAAGTTGTAAAACTTATTTATTTCTGTGTATGCATAATTAAACTTAATTGTTCACATGATTTGTC
131 GAAGTTGTAAAACTTATTTATTTCTGTGAATGCATGATTAAACTTAATTGTTCACATGATTCGTC
* * * * * *
22210017 TATTAGATATTGAATTTCGTTTATAGCTGTTTCGGTAACAAATGTGGCATCTCACATCTCGATTT
196 TATTAGATATTGAATTGCGTTTATAGTTGTTTCGATAACAAATGTGGCATCTCACATCTCAAATC
* * * ** * *
22210082 TGACAAGCGGGTCGAGAGTGGGGTGTTACATAA-AGACTCTTGAGTGCTTTCATATACTTATGGT
261 TGACAACCGGGTCGAGAGTGGGGTGTTATATAAGGGACT-TCCAGTGCTTTCACATACTTATGAT
* * * * * *
22210146 CAAATCTGCATTAATGAAAG-CTTGATAAGCATTTTCAATTTTCGTATGTAAGCACCGTATGTGC
325 CAAATCTGTATTAATGAAAGCCTT-ATAAGCATGTTCATTTTTCGCATGTAAGCACCGTAGGTAC
* * * * * *
22210210 TATATATTTACAAACACATTTTCACATTTCTTT-AGGCCTAATACATATGCCCATTTCATATAAT
389 TCTACATTTACAAACACATTTTCACTTTTCTTTAAGTCCT-ATAAATATGTCCATTTCATATAAT
*
22210274 AGTTCTTAATTA-TGGAAAATCATATTTTCATTGTTCTTT
453 AGTTCTTCA-TAGTGGAAAATCATATTTTCATTGTTCTTT
22210313 TATCTTTTAC
Statistics
Matches: 895, Mismatches: 85, Indels: 16
0.90 0.09 0.02
Matches are distributed among these distances:
495 15 0.02
496 295 0.33
497 362 0.40
498 219 0.24
499 4 0.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (497 bp):
CATTTCTCAATGTCGCAACATGACTTCTGTTTTAGCCATTCTTGCATTTTGGTCTTTCATTTCTT
ACCAATGATTCATGAGAGCTTTCTAAGCTTACTTAAAACCCAAGTTTGAATTAATAATGCTTTTA
GAAGTTGTAAAACTTATTTATTTCTGTGAATGCATGATTAAACTTAATTGTTCACATGATTCGTC
TATTAGATATTGAATTGCGTTTATAGTTGTTTCGATAACAAATGTGGCATCTCACATCTCAAATC
TGACAACCGGGTCGAGAGTGGGGTGTTATATAAGGGACTTCCAGTGCTTTCACATACTTATGATC
AAATCTGTATTAATGAAAGCCTTATAAGCATGTTCATTTTTCGCATGTAAGCACCGTAGGTACTC
TACATTTACAAACACATTTTCACTTTTCTTTAAGTCCTATAAATATGTCCATTTCATATAATAGT
TCTTCATAGTGGAAAATCATATTTTCATTGTTCTTTATCCTA
Found at i:22211095 original size:17 final size:17
Alignment explanation
Indices: 22211073--22211106 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
22211063 TGTTAAATTC
22211073 AGTTGTAACTAAACTTT
1 AGTTGTAACTAAACTTT
22211090 AGTTGTAACTAAACTTT
1 AGTTGTAACTAAACTTT
22211107 TGTTAAGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (17 bp):
AGTTGTAACTAAACTTT
Found at i:22219039 original size:14 final size:14
Alignment explanation
Indices: 22219005--22219039 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
22218995 AAACTAAAAG
22219005 TTTTTTATTTTATC
1 TTTTTTATTTTATC
* *
22219019 TTATTTATTTTATT
1 TTTTTTATTTTATC
22219033 TTTTTTA
1 TTTTTTA
22219040 ATAAATTGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTTATTTTATC
Found at i:22219871 original size:16 final size:17
Alignment explanation
Indices: 22219827--22219872 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
22219817 AAGAAAATTA
*
22219827 TATTCTAATTT-TTAATT
1 TATT-TAATTTATTAACT
*
22219844 TATTTAAATTATTAACT
1 TATTTAATTTATTAACT
22219861 T-TTTAATTTATT
1 TATTTAATTTATT
22219873 TTAAATTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (17 bp):
TATTTAATTTATTAACT
Found at i:22219890 original size:26 final size:24
Alignment explanation
Indices: 22219832--22219891 Score: 84
Period size: 26 Copynumber: 2.4 Consensus size: 24
22219822 AATTATATTC
22219832 TAATTTTTAATTTATTTAAATTAT
1 TAATTTTTAATTTATTTAAATTAT
*
22219856 TAACTTTTTAATTTATTTTAAATTGT
1 TAA-TTTTTAATTTA-TTTAAATTAT
22219882 TAATATTTTA
1 TAAT-TTTTA
22219892 GACTAATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 3 0.09
25 12 0.38
26 17 0.53
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (24 bp):
TAATTTTTAATTTATTTAAATTAT
Found at i:22223731 original size:8 final size:8
Alignment explanation
Indices: 22223716--22223747 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
22223706 AGCTTTATTT
22223716 ATTAGTTA
1 ATTAGTTA
*
22223724 ACTAGTTA
1 ATTAGTTA
22223732 ATTAGTTA
1 ATTAGTTA
22223740 ATTAGTTA
1 ATTAGTTA
22223748 TTTGATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (8 bp):
ATTAGTTA
Found at i:22224155 original size:114 final size:114
Alignment explanation
Indices: 22224018--22224241 Score: 412
Period size: 114 Copynumber: 2.0 Consensus size: 114
22224008 TCTTGGAGGA
* * *
22224018 GAAAATTAGAGCCGTTAGTAGGTGGTTGTGGATCTCATTATGGATTCAAGGCTGTCGAGTACATC
1 GAAAATTAGAGCCGTGAGCAGGTGGTTGTGGATCTCATTATGGATTCAAGGCTGCCGAGTACATC
22224083 TTTCAATCACCATCTTCATCTTTCCATCTTTCATTCTTCTTTAATAGGG
66 TTTCAATCACCATCTTCATCTTTCCATCTTTCATTCTTCTTTAATAGGG
*
22224132 GAAAATTAGAGCCGTGAGCAGGTGGTTGTGGATCTCATTGTGGATTCAAGGCTGCCGAGTACATC
1 GAAAATTAGAGCCGTGAGCAGGTGGTTGTGGATCTCATTATGGATTCAAGGCTGCCGAGTACATC
22224197 TTTCAATCACCATCTTCATCTTTCCATCTTTCATTCTTCTTTAAT
66 TTTCAATCACCATCTTCATCTTTCCATCTTTCATTCTTCTTTAAT
22224242 TTCTGTTTTG
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 106 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (114 bp):
GAAAATTAGAGCCGTGAGCAGGTGGTTGTGGATCTCATTATGGATTCAAGGCTGCCGAGTACATC
TTTCAATCACCATCTTCATCTTTCCATCTTTCATTCTTCTTTAATAGGG
Found at i:22231307 original size:18 final size:18
Alignment explanation
Indices: 22231284--22231318 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
22231274 ATTCGAGTTG
*
22231284 ACTCGAATAACTTGATTA
1 ACTCGAATAACTCGATTA
22231302 ACTCGAATAACTCGATT
1 ACTCGAATAACTCGATT
22231319 TGTTTAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (18 bp):
ACTCGAATAACTCGATTA
Found at i:22232486 original size:15 final size:16
Alignment explanation
Indices: 22232466--22232498 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
22232456 TATAATTGAA
22232466 TAAAATTAG-TTTAAT
1 TAAAATTAGTTTTAAT
22232481 TAAAATTAGTTTTAAT
1 TAAAATTAGTTTTAAT
22232497 TA
1 TA
22232499 TATTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (16 bp):
TAAAATTAGTTTTAAT
Found at i:22232518 original size:22 final size:21
Alignment explanation
Indices: 22232479--22232521 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
22232469 AATTAGTTTA
*
22232479 ATTAAAATTAGTTTTAATTAT
1 ATTAAAATTAATTTTAATTAT
22232500 ATTAAAATTAAATTTTAATTAT
1 ATTAAAATT-AATTTTAATTAT
22232522 TTCTAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
ATTAAAATTAATTTTAATTAT
Found at i:22232529 original size:16 final size:15
Alignment explanation
Indices: 22232510--22232544 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
22232500 ATTAAAATTA
22232510 AATTTTAATTATTTCT
1 AATTTTAATTATTT-T
*
22232526 AATTTTATTTATTTT
1 AATTTTAATTATTTT
22232541 AATT
1 AATT
22232545 CGTTGAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
AATTTTAATTATTTT
Found at i:22239890 original size:27 final size:28
Alignment explanation
Indices: 22239859--22239923 Score: 78
Period size: 30 Copynumber: 2.3 Consensus size: 28
22239849 CAATATATCT
* *
22239859 AAATAATTGACATGATGTG-TTCTGAAA
1 AAATAATTGACAAGATGGGTTTCTGAAA
*
22239886 AAATAATTTTGAGAAGATGGGTTTCTGAAA
1 AAATAA--TTGACAAGATGGGTTTCTGAAA
22239916 AAATAATT
1 AAATAATT
22239924 TTAAGAAGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 6 0.19
28 2 0.06
29 10 0.31
30 14 0.44
ACGTcount: A:0.43, C:0.05, G:0.18, T:0.34
Consensus pattern (28 bp):
AAATAATTGACAAGATGGGTTTCTGAAA
Found at i:22239914 original size:30 final size:29
Alignment explanation
Indices: 22239872--22240016 Score: 146
Period size: 30 Copynumber: 5.2 Consensus size: 29
22239862 TAATTGACAT
*
22239872 GATGTGTTCTGAAAAAATAATTTTGAGAA
1 GATGGGTTCTGAAAAAATAATTTTGAGAA
*
22239901 GATGGGTTTCTGAAAAAATAATTTTAAGAA
1 GATGGG-TTCTGAAAAAATAATTTTGAGAA
22239931 GATGGG-T-T------ATAATTTTGAGAA
1 GATGGGTTCTGAAAAAATAATTTTGAGAA
* *
22239952 GATGAGTTTCTGAAAAAATAATTTTAAGAA
1 GATG-GGTTCTGAAAAAATAATTTTGAGAA
* *
22239982 GATGGGTTCTGAAAAATTTATTTTGATG-A
1 GATGGGTTCTGAAAAAATAATTTTGA-GAA
22240011 GATGGG
1 GATGGG
22240017 GGTTGAAATT
Statistics
Matches: 96, Mismatches: 9, Indels: 22
0.76 0.07 0.17
Matches are distributed among these distances:
21 16 0.17
22 1 0.01
23 1 0.01
24 1 0.01
27 1 0.01
28 1 0.01
29 30 0.31
30 45 0.47
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (29 bp):
GATGGGTTCTGAAAAAATAATTTTGAGAA
Found at i:22239964 original size:51 final size:51
Alignment explanation
Indices: 22239888--22239989 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
22239878 TTCTGAAAAA
*
22239888 ATAATTTTGAGAAGATGGGTTTCTGAAAAAATAATTTTAAGAAGATGGGTT
1 ATAATTTTGAGAAGATGAGTTTCTGAAAAAATAATTTTAAGAAGATGGGTT
22239939 ATAATTTTGAGAAGATGAGTTTCTGAAAAAATAATTTTAAGAAGATGGGTT
1 ATAATTTTGAGAAGATGAGTTTCTGAAAAAATAATTTTAAGAAGATGGGTT
22239990 CTGAAAAATT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (51 bp):
ATAATTTTGAGAAGATGAGTTTCTGAAAAAATAATTTTAAGAAGATGGGTT
Found at i:22240013 original size:29 final size:29
Alignment explanation
Indices: 22239939--22240016 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
22239929 AAGATGGGTT
*
22239939 ATAATTTTGAGAAGATGAGTTTCTGAAAAA
1 ATAATTTTGAGAAGATG-GGTTCTGAAAAA
*
22239969 ATAATTTTAAGAAGATGGGTTCTGAAAAA
1 ATAATTTTGAGAAGATGGGTTCTGAAAAA
* *
22239998 TTTATTTTGATG-AGATGGG
1 ATAATTTTGA-GAAGATGGG
22240017 GGTTGAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 25 0.60
30 17 0.40
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (29 bp):
ATAATTTTGAGAAGATGGGTTCTGAAAAA
Found at i:22245617 original size:14 final size:14
Alignment explanation
Indices: 22245600--22245641 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
22245590 AATTTTATTA
22245600 AAAAATAATTAAAT
1 AAAAATAATTAAAT
*
22245614 AAAAA-AA-TAAAA
1 AAAAATAATTAAAT
22245626 ATAAAATAATTAAAT
1 A-AAAATAATTAAAT
22245641 A
1 A
22245642 TTTTCTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
12 5 0.22
13 6 0.26
14 7 0.30
15 5 0.22
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAAATAATTAAAT
Found at i:22245640 original size:19 final size:20
Alignment explanation
Indices: 22245596--22245641 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
22245586 ATTAAATTTT
*
22245596 ATTAAA-AAATAATTAAATA
1 ATTAAATAAATAATAAAATA
**
22245615 AAAAAATAAA-AATAAAATA
1 ATTAAATAAATAATAAAATA
22245634 ATTAAATA
1 ATTAAATA
22245642 TTTTCTATAA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
ATTAAATAAATAATAAAATA
Found at i:22245709 original size:22 final size:22
Alignment explanation
Indices: 22245656--22245708 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
22245646 CTATAACTAT
*
22245656 TAATTTAAAATATCATAAACCC
1 TAATTTAAAATAGCATAAACCC
*
22245678 TTATTTAAAATAGCA-AAACCC
1 TAATTTAAAATAGCATAAACCC
22245699 TAATTTAAAA
1 TAATTTAAAA
22245709 AACCCCAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.51, C:0.15, G:0.02, T:0.32
Consensus pattern (22 bp):
TAATTTAAAATAGCATAAACCC
Found at i:22245792 original size:30 final size:31
Alignment explanation
Indices: 22245758--22245816 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
22245748 AATAGTAAAA
*
22245758 TTTAGATATCTT-GTTTTGAATTTTTAGATT
1 TTTAGATATCTTAGTTTTGAAATTTTAGATT
*
22245788 TTTAGATATGTTAGTTTTGAAATTTTAGA
1 TTTAGATATCTTAGTTTTGAAATTTTAGA
22245817 CTTTAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.27, C:0.02, G:0.15, T:0.56
Consensus pattern (31 bp):
TTTAGATATCTTAGTTTTGAAATTTTAGATT
Found at i:22246918 original size:22 final size:22
Alignment explanation
Indices: 22246889--22246942 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
22246879 CACAAATATC
22246889 AATT-TCATCTCATAATTTCAA
1 AATTATCATCTCATAATTTCAA
22246910 AATTATCATCTCATAATTTCAA
1 AATTATCATCTCATAATTTCAA
22246932 AATTATCATCT
1 AATTATCATCT
22246943 ATCATCTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 4 0.12
22 28 0.88
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTATCATCTCATAATTTCAA
Found at i:22255003 original size:12 final size:12
Alignment explanation
Indices: 22254975--22255006 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
22254965 TTAAACCTTG
22254975 CTTTTA-TTTCT
1 CTTTTATTTTCT
22254986 -TTTTATTTTCT
1 CTTTTATTTTCT
22254997 CTTTTATTTT
1 CTTTTATTTT
22255007 ATGCTTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.26
11 5 0.26
12 9 0.47
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.78
Consensus pattern (12 bp):
CTTTTATTTTCT
Found at i:22259054 original size:28 final size:28
Alignment explanation
Indices: 22259014--22259095 Score: 128
Period size: 28 Copynumber: 2.9 Consensus size: 28
22259004 GATAAATTGC
*
22259014 CACATAATTGTCATAAATGGTCACATAT
1 CACATAATTGTCAAAAATGGTCACATAT
*
22259042 CACATAATTGTCAAAAATGATCACATAT
1 CACATAATTGTCAAAAATGGTCACATAT
* *
22259070 CACATAATTGCCAAAAATGGCCACAT
1 CACATAATTGTCAAAAATGGTCACAT
22259096 CTTCAACCTT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.27
Consensus pattern (28 bp):
CACATAATTGTCAAAAATGGTCACATAT
Found at i:22268618 original size:84 final size:84
Alignment explanation
Indices: 22268477--22268645 Score: 338
Period size: 84 Copynumber: 2.0 Consensus size: 84
22268467 CTTCTATCCA
22268477 TGTAGGAGGGAAAGAAACGTCTGTACTCGACTACGAAATTTATTTTGTACACTGCAGGGAGTTTT
1 TGTAGGAGGGAAAGAAACGTCTGTACTCGACTACGAAATTTATTTTGTACACTGCAGGGAGTTTT
22268542 GTTTTTCTATTAATAGGAG
66 GTTTTTCTATTAATAGGAG
22268561 TGTAGGAGGGAAAGAAACGTCTGTACTCGACTACGAAATTTATTTTGTACACTGCAGGGAGTTTT
1 TGTAGGAGGGAAAGAAACGTCTGTACTCGACTACGAAATTTATTTTGTACACTGCAGGGAGTTTT
22268626 GTTTTTCTATTAATAGGAG
66 GTTTTTCTATTAATAGGAG
22268645 T
1 T
22268646 TTTGGGTCTC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.35
Consensus pattern (84 bp):
TGTAGGAGGGAAAGAAACGTCTGTACTCGACTACGAAATTTATTTTGTACACTGCAGGGAGTTTT
GTTTTTCTATTAATAGGAG
Found at i:22273573 original size:17 final size:17
Alignment explanation
Indices: 22273534--22273582 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
22273524 ATATATATGG
* **
22273534 AAATGCAATGACAATGT
1 AAATGCAGTGACAATAA
*
22273551 AGATGCAGTGACAATAA
1 AAATGCAGTGACAATAA
*
22273568 AAATGCAGGGACAAT
1 AAATGCAGTGACAAT
22273583 TATACTACAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.18
Consensus pattern (17 bp):
AAATGCAGTGACAATAA
Found at i:22274038 original size:12 final size:12
Alignment explanation
Indices: 22274023--22274047 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22274013 TCTCTTCTCT
22274023 TTGTTCCTCTTC
1 TTGTTCCTCTTC
22274035 TTGTTCCTCTTC
1 TTGTTCCTCTTC
22274047 T
1 T
22274048 ATCTCCACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.32, G:0.08, T:0.60
Consensus pattern (12 bp):
TTGTTCCTCTTC
Found at i:22280609 original size:5 final size:5
Alignment explanation
Indices: 22280599--22280645 Score: 67
Period size: 5 Copynumber: 9.4 Consensus size: 5
22280589 TGTGAGGATA
* * *
22280599 TTCTT TTCTT TTCTT TTCTT TTCTT TGCTA TTCTG TTCTT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TT
22280646 TCAAGACTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.74
Consensus pattern (5 bp):
TTCTT
Found at i:22285975 original size:100 final size:100
Alignment explanation
Indices: 22285802--22286004 Score: 397
Period size: 100 Copynumber: 2.0 Consensus size: 100
22285792 CAAGAGCTCG
22285802 AAATTATGTATTTTCTTTATGTTTTCATAGGATTTAACTTATATTTTTCTTTTGAATAAATTGTG
1 AAATTATGTATTTTCTTTATGTTTTCATAGGATTTAACTTATATTTTTCTTTTGAATAAATTGTG
22285867 TAACCTAAGTGCTTAAAGGTTATTTTATTGTCTTT
66 TAACCTAAGTGCTTAAAGGTTATTTTATTGTCTTT
*
22285902 AAATTATGTATTTTCTTTTTGTTTTCATAGGATTTAACTTATATTTTTCTTTTGAATAAATTGTG
1 AAATTATGTATTTTCTTTATGTTTTCATAGGATTTAACTTATATTTTTCTTTTGAATAAATTGTG
22285967 TAACCTAAGTGCTTAAAGGTTATTTTATTGTCTTT
66 TAACCTAAGTGCTTAAAGGTTATTTTATTGTCTTT
22286002 AAA
1 AAA
22286005 GGCCAATTGA
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 102 1.00
ACGTcount: A:0.28, C:0.08, G:0.12, T:0.53
Consensus pattern (100 bp):
AAATTATGTATTTTCTTTATGTTTTCATAGGATTTAACTTATATTTTTCTTTTGAATAAATTGTG
TAACCTAAGTGCTTAAAGGTTATTTTATTGTCTTT
Found at i:22295557 original size:25 final size:25
Alignment explanation
Indices: 22295504--22295558 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
22295494 CACACACTAA
*
22295504 AGTTT-CTATCGTTTTCTCATATAT
1 AGTTTCCTATAGTTTTCTCATATAT
* *
22295528 CGTTTCCTATAGTTTTGCT-ATGTAT
1 AGTTTCCTATAGTTTT-CTCATATAT
22295553 AGTTTC
1 AGTTTC
22295559 ACAAGTATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 4 0.16
25 19 0.76
26 2 0.08
ACGTcount: A:0.18, C:0.16, G:0.13, T:0.53
Consensus pattern (25 bp):
AGTTTCCTATAGTTTTCTCATATAT
Found at i:22297712 original size:48 final size:48
Alignment explanation
Indices: 22297641--22297737 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
22297631 ATAAACAAAA
*
22297641 AATCACTTTACAGATAAACTACCACATAATTGCCAATAATGGCCACAT
1 AATCACTTTACAGATAAACTACCACATAATTGCCAAAAATGGCCACAT
*
22297689 AATCACTTTGCAGATAAACTACCACATAATTGCCAAAAATGGCCACAT
1 AATCACTTTACAGATAAACTACCACATAATTGCCAAAAATGGCCACAT
22297737 A
1 A
22297738 TCTTTGACCT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.42, C:0.25, G:0.09, T:0.24
Consensus pattern (48 bp):
AATCACTTTACAGATAAACTACCACATAATTGCCAAAAATGGCCACAT
Found at i:22300808 original size:17 final size:17
Alignment explanation
Indices: 22300768--22300836 Score: 75
Period size: 17 Copynumber: 4.0 Consensus size: 17
22300758 CATTAACTTA
* *
22300768 CAATGACACATGGAAATA
1 CAATGACA-ATGAAAATG
* *
22300786 CAATGACAATGCAGATG
1 CAATGACAATGAAAATG
*
22300803 CAATGACAATTAAAATG
1 CAATGACAATGAAAATG
*
22300820 CAATGACAAAGAAAATG
1 CAATGACAATGAAAATG
22300837 TGGTGACAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 35 0.81
18 8 0.19
ACGTcount: A:0.51, C:0.14, G:0.17, T:0.17
Consensus pattern (17 bp):
CAATGACAATGAAAATG
Found at i:22303101 original size:20 final size:20
Alignment explanation
Indices: 22303064--22303102 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
22303054 AAGACTAAGA
*
22303064 AAAATAACTGAAATATAAAC
1 AAAATAACTGAAAAATAAAC
22303084 AAAATAAACT-AAAAATAAA
1 AAAAT-AACTGAAAAATAAA
22303103 TGATAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.72, C:0.08, G:0.03, T:0.18
Consensus pattern (20 bp):
AAAATAACTGAAAAATAAAC
Found at i:22328001 original size:133 final size:133
Alignment explanation
Indices: 22327805--22328070 Score: 514
Period size: 133 Copynumber: 2.0 Consensus size: 133
22327795 ATTGTCAACG
*
22327805 CATCCATCGATGCAACTTAGGAAGATATGCTCATTGCCATTTTGAAAGAGCGATAGCCTAGAGCA
1 CATCCATCGATGCAACTTAGGAAGATAAGCTCATTGCCATTTTGAAAGAGCGATAGCCTAGAGCA
22327870 TTGATTATATCAAAGGCATTAGTCCCTCTTTTGTATGCACAAAATTAGGCTAGAAGATGAAAAGA
66 TTGATTATATCAAAGGCATTAGTCCCTCTTTTGTATGCACAAAATTAGGCTAGAAGATGAAAAGA
22327935 AGC
131 AGC
22327938 CATCCATCGATGCAACTTAGGAAGATAAGCTCATTGCCATTTTGAAAGAGCGATAGCCTAGAGCA
1 CATCCATCGATGCAACTTAGGAAGATAAGCTCATTGCCATTTTGAAAGAGCGATAGCCTAGAGCA
*
22328003 TTGCTTATATCAAAGGCATTAGTCCCTCTTTTGTATGCACAAAATTAGGCTAGAAGATGAAAAGA
66 TTGATTATATCAAAGGCATTAGTCCCTCTTTTGTATGCACAAAATTAGGCTAGAAGATGAAAAGA
22328068 AGC
131 AGC
22328071 AATCAATTGA
Statistics
Matches: 131, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
133 131 1.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (133 bp):
CATCCATCGATGCAACTTAGGAAGATAAGCTCATTGCCATTTTGAAAGAGCGATAGCCTAGAGCA
TTGATTATATCAAAGGCATTAGTCCCTCTTTTGTATGCACAAAATTAGGCTAGAAGATGAAAAGA
AGC
Found at i:22329357 original size:468 final size:467
Alignment explanation
Indices: 22328466--22329399 Score: 1474
Period size: 468 Copynumber: 2.0 Consensus size: 467
22328456 GATTTTGCTG
* *
22328466 TGGGAGCTGTACTAGGCCAAAGAAAAGATAAGGTATTTCACTCTACCTATTATGCTAGTAAAACT
1 TGGGAGCTGTACTAAGCCAAAGAAAAGATAAAGTATTTCACTCTACCTATTATGCTAGTAAAACT
* *
22328531 CTAACTGAAGCGCAGGTTAATTACACTACCACTAAGAAGGAGTTACTAGCAGTAGTCTTTACATT
66 CTAACTGAAGCGCAAGTTAATTACACTACCACTAAGAAGGAGTTACTAGCAGTAGTCTTCACATT
* * *
22328596 GACAAGTTTCGCCCCTATCTTGTCGGTGCAAAGACAACAGTTTACATGGACCACTCCGCATTGAA
131 GACAAATTTCGCCCCTATCTTGTCGGTGCAAAGACAACAATTTACACGGACCACTCCGCATTGAA
*
22328661 ATATCTTCTTACAAAATAAGATGCCAAACCTAGACTTATCAGATGGATCCTACTCCTTCAAGAGT
196 ATATCTTCTTACAAAAAAAGATGCCAAACCTAGACTTATCAGATGGATCCTACTCCTTCAAGAGT
* * * * *
22328726 TTGACATAGAAATCACAAATAGGCAAGGATTTGAAAATCAAGTAGCTGATCACTTGTCTTGACTA
261 TTGACATAGAAATCACAAATAGGAAAGGATCTGAAAATCAAGTAGCTGACCACCTGTCTCGACTA
* *
22328791 GAAGTTGAAAGTGAAGATGGGAAAACGTCTCAAATTATCGAAGCATTTCCAGACGAGCAATTATT
326 GAAGTTGAAAGTGAAGATGGGAAAACGTCCCAAATTATCGAAGCATTTCCAGACAAGCAATTATT
* * * * * *
22328856 TTTTGTCGACGCATCGCCCTGGTATGTCGATGTTGTCAATTACCTTGTGTGTGGAAAGCTACCCA
391 TTTTGTCGACACATCACCATAGTATGCCGATGTTGTCAATTACCTTGAGTGTGGAAAGCTACCCA
22328921 TGAGTTATACTA
456 TGAGTTATACTA
*
22328933 TGGGAGCTGTACTAAGCCAAAGAAAAGATAAAGTATTTCACTCTATCTATTATGCTAGTAAAACT
1 TGGGAGCTGTACTAAGCCAAAGAAAAGATAAAGTATTTCACTCTACCTATTATGCTAGTAAAACT
* * * * *
22328998 CTAACTGAAGCGCAAGTTGATTACACTACCATTGAGAAGGAGTTGCTAGCAGTAGTCTTCGCATT
66 CTAACTGAAGCGCAAGTTAATTACACTACCACTAAGAAGGAGTTACTAGCAGTAGTCTTCACA-T
** *
22329063 TGACAAATTTCGTTCCTATCTTGTCGGTGCAAAGACTACAATTTACACGGACCACTCCGCATTGA
130 TGACAAATTTCGCCCCTATCTTGTCGGTGCAAAGACAACAATTTACACGGACCACTCCGCATTGA
* ** * *
22329128 AATATCTT-TTCACAAAAAAAGATGCCAAACTTAGGGTTCTCAGATGGATTCTACTCCTTCAAGA
195 AATATCTTCTT-ACAAAAAAAGATGCCAAACCTAGACTTATCAGATGGATCCTACTCCTTCAAGA
* *
22329192 GTTTGACATAGAAATCAGAGATAGGAAAGGATCTGAAAATCAAGTAGCTGACCACCTGTCTCGAC
259 GTTTGACATAGAAATCACAAATAGGAAAGGATCTGAAAATCAAGTAGCTGACCACCTGTCTCGAC
* * * *
22329257 TGGAAGTTGAAAGTGAAGATGGGCAGATGTCCCAAATTATCGAAGCATTTCCAGACAAGCAATTA
324 TAGAAGTTGAAAGTGAAGATGGGAAAACGTCCCAAATTATCGAAGCATTTCCAGACAAGCAATTA
22329322 TTTTTTGTCGACACATCACCATAGTATGCCGATGTTGTCAATTACCTTGAGTGTGGAAAGCTACC
389 TTTTTTGTCGACACATCACCATAGTATGCCGATGTTGTCAATTACCTTGAGTGTGGAAAGCTACC
22329387 CATGAGTTATACT
454 CATGAGTTATACT
22329400 GGTCACAAGA
Statistics
Matches: 424, Mismatches: 41, Indels: 3
0.91 0.09 0.01
Matches are distributed among these distances:
467 120 0.28
468 304 0.72
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (467 bp):
TGGGAGCTGTACTAAGCCAAAGAAAAGATAAAGTATTTCACTCTACCTATTATGCTAGTAAAACT
CTAACTGAAGCGCAAGTTAATTACACTACCACTAAGAAGGAGTTACTAGCAGTAGTCTTCACATT
GACAAATTTCGCCCCTATCTTGTCGGTGCAAAGACAACAATTTACACGGACCACTCCGCATTGAA
ATATCTTCTTACAAAAAAAGATGCCAAACCTAGACTTATCAGATGGATCCTACTCCTTCAAGAGT
TTGACATAGAAATCACAAATAGGAAAGGATCTGAAAATCAAGTAGCTGACCACCTGTCTCGACTA
GAAGTTGAAAGTGAAGATGGGAAAACGTCCCAAATTATCGAAGCATTTCCAGACAAGCAATTATT
TTTTGTCGACACATCACCATAGTATGCCGATGTTGTCAATTACCTTGAGTGTGGAAAGCTACCCA
TGAGTTATACTA
Found at i:22352928 original size:3 final size:3
Alignment explanation
Indices: 22352920--22352952 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
22352910 AGGAGTGTAA
22352920 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
22352953 TAAGAAGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:22353688 original size:20 final size:20
Alignment explanation
Indices: 22353651--22353688 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
22353641 AAGTGGTGAA
*
22353651 GAAGAGAAATGCATGAAAAT
1 GAAGAGAAATGCAAGAAAAT
22353671 GAAGAAGAAATG-AAGAAA
1 GAAG-AGAAATGCAAGAAA
22353689 TTCTTGACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.61, C:0.03, G:0.26, T:0.11
Consensus pattern (20 bp):
GAAGAGAAATGCAAGAAAAT
Found at i:22355864 original size:20 final size:21
Alignment explanation
Indices: 22355826--22355864 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
22355816 TTTATGGTTT
*
22355826 TAAATAATTTTTGGGTAAAAA
1 TAAATAATTTTCGGGTAAAAA
*
22355847 TAAAT-ATTTTCGGTTAAA
1 TAAATAATTTTCGGGTAAA
22355865 TTGGAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.41
Consensus pattern (21 bp):
TAAATAATTTTCGGGTAAAAA
Found at i:22359660 original size:40 final size:40
Alignment explanation
Indices: 22359590--22359927 Score: 387
Period size: 40 Copynumber: 8.4 Consensus size: 40
22359580 GATGTGGTAA
22359590 AAAAGATTGGATGTTGTCTTCAATCTGCCCTCTGGTTAGGGT
1 AAAAGATTGGATG--GTCTTCAATCTGCCCTCTGGTTAGGGT
* * *
22359632 AAAAGATTTGATGGTCTTCAATATGCCCTCTTGTTAGGGT
1 AAAAGATTGGATGGTCTTCAATCTGCCCTCTGGTTAGGGT
* * *
22359672 AAAAGATTGGATGGTCTTCAATCTACCCTCTGATTAAGGT
1 AAAAGATTGGATGGTCTTCAATCTGCCCTCTGGTTAGGGT
* * **
22359712 AAAAGAATGGATGGTCTTCAATCTGCCTTCTAATTAGGGT
1 AAAAGATTGGATGGTCTTCAATCTGCCCTCTGGTTAGGGT
* * *
22359752 AAAAGATTGGATGGTCTTTAATCTGCCCTCTGATTATGGT
1 AAAAGATTGGATGGTCTTCAATCTGCCCTCTGGTTAGGGT
* *
22359792 AAAAGATTGGATGGTCTTCAATCTGCTCC-ATGG-TCGAGGT
1 AAAAGATTGGATGGTCTTCAATCTGC-CCTCTGGTTAG-GGT
* * * *
22359832 AAGAGATTGGATGGTGTCTTCAATCTGCTCTCTAGTTACGGT
1 AAAAGATTGGAT-G-GTCTTCAATCTGCCCTCTGGTTAGGGT
* *
22359874 AAAAGATTGGATAG-CTTCAATCAGCCC-CATGGTTAGGGT
1 AAAAGATTGGATGGTCTTCAATCTGCCCTC-TGGTTAGGGT
*
22359913 AAGAGATTGGATGGT
1 AAAAGATTGGATGGT
22359928 AGCTTTCCCT
Statistics
Matches: 250, Mismatches: 38, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
38 1 0.00
39 32 0.13
40 171 0.68
41 4 0.02
42 41 0.16
43 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (40 bp):
AAAAGATTGGATGGTCTTCAATCTGCCCTCTGGTTAGGGT
Found at i:22402500 original size:15 final size:14
Alignment explanation
Indices: 22402475--22402510 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 14
22402465 GGACTTTATA
22402475 TTTATTTTTATTTGGT
1 TTTA-TTTTATTT-GT
22402491 TTTATTTTATTTGT
1 TTTATTTTATTTGT
22402505 TTTATT
1 TTTATT
22402511 CTAATTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.40
15 8 0.40
16 4 0.20
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (14 bp):
TTTATTTTATTTGT
Found at i:22406730 original size:32 final size:32
Alignment explanation
Indices: 22406689--22406753 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
22406679 AGTTCTAGCC
22406689 ATAACTGTATGAAAGAAAGAGATTAAAAATTT
1 ATAACTGTATGAAAGAAAGAGATTAAAAATTT
22406721 ATAACTGTATGAAAGAAAGAGATTAAAAATTT
1 ATAACTGTATGAAAGAAAGAGATTAAAAATTT
22406753 A
1 A
22406754 AAGAAATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.54, C:0.03, G:0.15, T:0.28
Consensus pattern (32 bp):
ATAACTGTATGAAAGAAAGAGATTAAAAATTT
Found at i:22419472 original size:14 final size:14
Alignment explanation
Indices: 22419453--22419482 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
22419443 AAATACCTTC
22419453 ATTCTATGCACTTG
1 ATTCTATGCACTTG
*
22419467 ATTCTATGCATTTG
1 ATTCTATGCACTTG
22419481 AT
1 AT
22419483 CTCTCTAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.17, G:0.13, T:0.47
Consensus pattern (14 bp):
ATTCTATGCACTTG
Found at i:22421171 original size:16 final size:15
Alignment explanation
Indices: 22421150--22421183 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
22421140 CTTCAACCCA
22421150 AAATAAATTAATAAAC
1 AAATAAATTAA-AAAC
*
22421166 AAATAAATTTAAAAC
1 AAATAAATTAAAAAC
22421181 AAA
1 AAA
22421184 CATGAATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATAAATTAAAAAC
Found at i:22423736 original size:15 final size:14
Alignment explanation
Indices: 22423711--22423746 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 14
22423701 GGACTTTATA
22423711 TTTATTTTTATTTGGT
1 TTTA-TTTTATTT-GT
22423727 TTTATTTTATTTGT
1 TTTATTTTATTTGT
22423741 TTTATT
1 TTTATT
22423747 CTAATTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.40
15 8 0.40
16 4 0.20
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (14 bp):
TTTATTTTATTTGT
Found at i:22432594 original size:52 final size:52
Alignment explanation
Indices: 22432531--22432629 Score: 144
Period size: 52 Copynumber: 1.9 Consensus size: 52
22432521 CTCATTGCGT
* * *
22432531 TTTACACTCACCAGCTTTCATACGTTTACGCTCGTCAGCATATATATGTGTG
1 TTTACACTCACCAGCTTGCACACGTTTACACTCGTCAGCATATATATGTGTG
* **
22432583 TTTACGCTCACCAGCTTGCACACGTTTACACTCGTCAGTTTATATAT
1 TTTACACTCACCAGCTTGCACACGTTTACACTCGTCAGCATATATAT
22432630 ATATATATGC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 41 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.36
Consensus pattern (52 bp):
TTTACACTCACCAGCTTGCACACGTTTACACTCGTCAGCATATATATGTGTG
Found at i:22432689 original size:28 final size:27
Alignment explanation
Indices: 22432658--22432741 Score: 75
Period size: 28 Copynumber: 3.1 Consensus size: 27
22432648 TTGCCAACTT
22432658 GCTTATATATATGTGTTTACGCTCGTCA
1 GCTTATATATATG-GTTTACGCTCGTCA
** * * *
22432686 GCTTGCACACA---TTTATGCTCGTCA
1 GCTTATATATATGGTTTACGCTCGTCA
*
22432710 GCTTATATATATGCGTTTACGCTCGCCA
1 GCTTATATATATG-GTTTACGCTCGTCA
22432738 GCTT
1 GCTT
22432742 GCACACGTTT
Statistics
Matches: 41, Mismatches: 11, Indels: 8
0.68 0.18 0.13
Matches are distributed among these distances:
24 19 0.46
28 22 0.54
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (27 bp):
GCTTATATATATGGTTTACGCTCGTCA
Found at i:22432705 original size:24 final size:24
Alignment explanation
Indices: 22432672--22432764 Score: 87
Period size: 24 Copynumber: 3.7 Consensus size: 24
22432662 ATATATATGT
22432672 GTTTACGCTCGTCAGCTTGCACAC
1 GTTTACGCTCGTCAGCTTGCACAC
* * ** *
22432696 ATTTATGCTCGTCAGCTTATATATATGC
1 GTTTACGCTCGTCAGC-T-TGCACA--C
*
22432724 GTTTACGCTCGCCAGCTTGCACAC
1 GTTTACGCTCGTCAGCTTGCACAC
*
22432748 GTTTATGCTCGTCAGCT
1 GTTTACGCTCGTCAGCT
22432765 ATATATATAT
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
24 30 0.58
25 1 0.02
26 6 0.12
27 1 0.02
28 14 0.27
ACGTcount: A:0.18, C:0.28, G:0.19, T:0.34
Consensus pattern (24 bp):
GTTTACGCTCGTCAGCTTGCACAC
Found at i:22432717 original size:52 final size:52
Alignment explanation
Indices: 22432658--22432774 Score: 198
Period size: 52 Copynumber: 2.2 Consensus size: 52
22432648 TTGCCAACTT
* *
22432658 GCTTATATATATGTGTTTACGCTCGTCAGCTTGCACACATTTATGCTCGTCA
1 GCTTATATATATGCGTTTACGCTCGCCAGCTTGCACACATTTATGCTCGTCA
*
22432710 GCTTATATATATGCGTTTACGCTCGCCAGCTTGCACACGTTTATGCTCGTCA
1 GCTTATATATATGCGTTTACGCTCGCCAGCTTGCACACATTTATGCTCGTCA
22432762 GCTATATATATAT
1 GCT-TATATATAT
22432775 ATATATATGT
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
52 52 0.85
53 9 0.15
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (52 bp):
GCTTATATATATGCGTTTACGCTCGCCAGCTTGCACACATTTATGCTCGTCA
Found at i:22443793 original size:14 final size:14
Alignment explanation
Indices: 22443774--22443802 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
22443764 ACTAAACAAA
22443774 AGTTTAGTCATAGG
1 AGTTTAGTCATAGG
22443788 AGTTTAGTCATAGG
1 AGTTTAGTCATAGG
22443802 A
1 A
22443803 TCTCTTCTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.07, G:0.28, T:0.34
Consensus pattern (14 bp):
AGTTTAGTCATAGG
Found at i:22445660 original size:11 final size:12
Alignment explanation
Indices: 22445643--22445671 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
22445633 TAAATTGATT
22445643 CTAGAAGCTAAA
1 CTAGAAGCTAAA
22445655 -TAGAAGCTAAA
1 CTAGAAGCTAAA
22445666 CTAGAA
1 CTAGAA
22445672 AAAAAGGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.52, C:0.14, G:0.17, T:0.17
Consensus pattern (12 bp):
CTAGAAGCTAAA
Done.