Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 128 of 182
Found at i:40624264 original size:4 final size:4
Alignment explanation
Indices: 40624257--40624283 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
40624247 TGACAAAAAA
40624257 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
40624284 AAGAGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:40625179 original size:40 final size:41
Alignment explanation
Indices: 40625124--40625405 Score: 208
Period size: 40 Copynumber: 7.0 Consensus size: 41
40625114 AAATTACATC
* *
40625124 ACCATCCAACCTTTTACCCTAAT-TAAAGGGCAGATTGAAG
1 ACCATCCAATCTTTTACCCTAATCCAAAGGGCAGATTGAAG
*
40625164 ACCATCCAATCTTTTACCTTAA-CCAGAA-GGCAGATTGAAG
1 ACCATCCAATCTTTTACCCTAATCCA-AAGGGCAGATTGAAG
* *** *
40625204 ACCATCCAATCTTTTACTCT-ATCCACTTGGCAAATTGAAG
1 ACCATCCAATCTTTTACCCTAATCCAAAGGGCAGATTGAAG
* * ** * *
40625244 TCAACATCTAATCTTTTACCCT-ATTTAGAGGGCAGATTAAAG
1 --ACCATCCAATCTTTTACCCTAATCCAAAGGGCAGATTGAAG
* * * * **
40625286 TCACTATCTAATCTTTTACCC-CATCCAATGGGTTGATTGAAG
1 --ACCATCCAATCTTTTACCCTAATCCAAAGGGCAGATTGAAG
* * *
40625328 -CCATCCAATCTTTTA-CCTCATCTAGAGGGCAGATTGAAG
1 ACCATCCAATCTTTTACCCTAATCCAAAGGGCAGATTGAAG
* *
40625367 -CCATTCAATCTCTTATCCC--ATCCAAAGGGCAGATTGAAG
1 ACCATCCAATCTTTTA-CCCTAATCCAAAGGGCAGATTGAAG
40625406 TATGAAAGCG
Statistics
Matches: 194, Mismatches: 38, Indels: 21
0.77 0.15 0.08
Matches are distributed among these distances:
38 2 0.01
39 61 0.31
40 65 0.34
41 4 0.02
42 62 0.32
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (41 bp):
ACCATCCAATCTTTTACCCTAATCCAAAGGGCAGATTGAAG
Found at i:40625363 original size:39 final size:40
Alignment explanation
Indices: 40625124--40625405 Score: 209
Period size: 39 Copynumber: 7.0 Consensus size: 40
40625114 AAATTACATC
* * * *
40625124 ACCATCCAACCTTTTACCCTAAT-TAAAGGGCAGATTGAAG
1 ACCATCCAATCTTTTA-CCTCATCCAGAGGGCAGATTGAAG
* * *
40625164 ACCATCCAATCTTTTACCTTAACCAGAAGGCAGATTGAAG
1 ACCATCCAATCTTTTACCTCATCCAGAGGGCAGATTGAAG
*** *
40625204 ACCATCCAATCTTTTA-CTCTATCCACTTGGCAAATTGAAG
1 ACCATCCAATCTTTTACCTC-ATCCAGAGGGCAGATTGAAG
* * ** *
40625244 TCAACATCTAATCTTTTACC-CTATTTAGAGGGCAGATTAAAG
1 --ACCATCCAATCTTTTACCTC-ATCCAGAGGGCAGATTGAAG
* * * **
40625286 TCACTATCTAATCTTTTACCCCATCCA-ATGGGTTGATTGAAG
1 --ACCATCCAATCTTTTACCTCATCCAGA-GGGCAGATTGAAG
*
40625328 -CCATCCAATCTTTTACCTCATCTAGAGGGCAGATTGAAG
1 ACCATCCAATCTTTTACCTCATCCAGAGGGCAGATTGAAG
* * *
40625367 -CCATTCAATCTCTTATCC-CATCCAAAGGGCAGATTGAAG
1 ACCATCCAATCTTTTA-CCTCATCCAGAGGGCAGATTGAAG
40625406 TATGAAAGCG
Statistics
Matches: 195, Mismatches: 38, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
39 69 0.35
40 63 0.32
41 1 0.01
42 60 0.31
43 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (40 bp):
ACCATCCAATCTTTTACCTCATCCAGAGGGCAGATTGAAG
Found at i:40630851 original size:4 final size:4
Alignment explanation
Indices: 40630842--40630877 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
40630832 ATAAATGAAA
* *
40630842 ATTT ATTT ATTT ATTT ATTT ATAT ATTT ATAT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
40630878 TAGAGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (4 bp):
ATTT
Found at i:40633396 original size:18 final size:18
Alignment explanation
Indices: 40633373--40633411 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
40633363 TGTTTCCTCA
*
40633373 ATTTTTT-TTATTTTTATG
1 ATTTTTTATAATTTTT-TG
40633391 ATTTTTTATAATTTTTTG
1 ATTTTTTATAATTTTTTG
40633409 ATT
1 ATT
40633412 GAATCAGACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (18 bp):
ATTTTTTATAATTTTTTG
Found at i:40647864 original size:27 final size:27
Alignment explanation
Indices: 40647819--40647891 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
40647809 GGTAAAAAAA
* *
40647819 GTCAAC-GGTCAACGATCAAAGTTAACA-
1 GTCAACGGGTCAAAG-TCAAAGGTAA-AG
* *
40647846 GTCAATGGGTCAAAGTCAACGGTAAAG
1 GTCAACGGGTCAAAGTCAAAGGTAAAG
*
40647873 GTCAACGAGTCAAAGTCAA
1 GTCAACGGGTCAAAGTCAA
40647892 TAGTCAACGG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
26 1 0.03
27 30 0.79
28 7 0.18
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18
Consensus pattern (27 bp):
GTCAACGGGTCAAAGTCAAAGGTAAAG
Found at i:40647910 original size:20 final size:21
Alignment explanation
Indices: 40647873--40647914 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
40647863 AACGGTAAAG
40647873 GTCAACGAGTCAAAGTCAATA
1 GTCAACGAGTCAAAGTCAATA
*
40647894 GTCAACG-GTCTAAGTCAATA
1 GTCAACGAGTCAAAGTCAATA
40647914 G
1 G
40647915 GTTAATGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.21
Consensus pattern (21 bp):
GTCAACGAGTCAAAGTCAATA
Found at i:40651636 original size:11 final size:11
Alignment explanation
Indices: 40651613--40651643 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
40651603 GGTTTTTCTT
40651613 TTTCTTTTA-A
1 TTTCTTTTAGA
40651623 TTTCTTTTAGA
1 TTTCTTTTAGA
40651634 TTTCTTTTAG
1 TTTCTTTTAG
40651644 GACGTTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.16, C:0.10, G:0.06, T:0.68
Consensus pattern (11 bp):
TTTCTTTTAGA
Found at i:40652288 original size:14 final size:14
Alignment explanation
Indices: 40652271--40652322 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
40652261 CAACTTACTG
*
40652271 TTCTCGATTTTTTA
1 TTCTCAATTTTTTA
* **
40652285 TTCTCAATTGTGAA
1 TTCTCAATTTTTTA
40652299 TTCTCAATTTTTTA
1 TTCTCAATTTTTTA
*
40652313 TTCTAAATTT
1 TTCTCAATTT
40652323 CCAATTCCAT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.23, C:0.13, G:0.06, T:0.58
Consensus pattern (14 bp):
TTCTCAATTTTTTA
Found at i:40652328 original size:28 final size:27
Alignment explanation
Indices: 40652271--40652338 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 27
40652261 CAACTTACTG
* *
40652271 TTCTCGATTTTTTATTCTCAATTGTGAA
1 TTCTC-ATTTTTTATTCTAAATTGTCAA
40652299 TTCTCAATTTTTTATTCTAAATT-TCCAA
1 TTCTC-ATTTTTTATTCTAAATTGT-CAA
40652327 TTC-CATTTTTTA
1 TTCTCATTTTTTA
40652339 AAAAAATTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 8 0.22
27 2 0.06
28 26 0.72
ACGTcount: A:0.24, C:0.16, G:0.04, T:0.56
Consensus pattern (27 bp):
TTCTCATTTTTTATTCTAAATTGTCAA
Found at i:40654386 original size:8 final size:8
Alignment explanation
Indices: 40654373--40654416 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
40654363 ATATCAGCTT
40654373 ATTATTTA
1 ATTATTTA
40654381 ATTATTTA
1 ATTATTTA
40654389 ATTATTTA
1 ATTATTTA
40654397 A-T-TTTA
1 ATTATTTA
* *
40654403 ATCAGTTA
1 ATTATTTA
40654411 ATTATT
1 ATTATT
40654417 ATGATGTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
6 5 0.17
7 1 0.03
8 24 0.80
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (8 bp):
ATTATTTA
Found at i:40658533 original size:19 final size:19
Alignment explanation
Indices: 40658475--40658534 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 19
40658465 TTCTATTGAA
40658475 ATTTATTTTAAATATTTAAT
1 ATTTATTTT-AATATTTAAT
* *
40658495 ATTATATATTTACATTTTTATT
1 ATT-TAT-TTTA-ATATTTAAT
40658517 ATTTATTTTAATATTTAA
1 ATTTATTTTAATATTTAA
40658535 AATATAGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
19 6 0.18
20 7 0.21
21 7 0.21
22 13 0.39
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTATTTTAATATTTAAT
Found at i:40668237 original size:21 final size:21
Alignment explanation
Indices: 40668213--40668262 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
40668203 TTTTCCCAAT
40668213 TTTCCCTCCTAAACCAAAATA
1 TTTCCCTCCTAAACCAAAATA
*
40668234 TTTCCCTCCTAAACCGAAATA
1 TTTCCCTCCTAAACCAAAATA
40668255 TTTCCCTC
1 TTTCCCTC
40668263 TTTCTTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.36, G:0.02, T:0.32
Consensus pattern (21 bp):
TTTCCCTCCTAAACCAAAATA
Found at i:40671717 original size:31 final size:31
Alignment explanation
Indices: 40671650--40671710 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
40671640 TTAACAATTG
* *
40671650 AGTGACTTGAATAAAAACTTTTGAATAGTTC
1 AGTGACTTAAATAAAAACTTTCGAATAGTTC
*
40671681 AGTGACTTAAATGAAAACTTTCGAATAGTT
1 AGTGACTTAAATAAAAACTTTCGAATAGTT
40671711 TGGTGACCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.34
Consensus pattern (31 bp):
AGTGACTTAAATAAAAACTTTCGAATAGTTC
Found at i:40681680 original size:41 final size:41
Alignment explanation
Indices: 40681622--40681706 Score: 127
Period size: 41 Copynumber: 2.1 Consensus size: 41
40681612 GTGAAACCAA
* * *
40681622 AAACAAACATCATTGTATGTTAAAAATCCGAAAGA-AAATTG
1 AAACAAAAATCAATGTATGTT-AAAATCCGAAAAAGAAATTG
40681663 AAACAAAAATCAATGTATGTTAAAATCCGAAAAAGAAATTG
1 AAACAAAAATCAATGTATGTTAAAATCCGAAAAAGAAATTG
40681704 AAA
1 AAA
40681707 TTATGGATTG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 12 0.30
41 28 0.70
ACGTcount: A:0.55, C:0.11, G:0.12, T:0.22
Consensus pattern (41 bp):
AAACAAAAATCAATGTATGTTAAAATCCGAAAAAGAAATTG
Found at i:40682817 original size:26 final size:27
Alignment explanation
Indices: 40682788--40682842 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
40682778 AATCATGTAA
*
40682788 TTTAGTAACTAAAATTTAATT-TTTAT
1 TTTAATAACTAAAATTTAATTATTTAT
** *
40682814 TTTAATTTCTAAAATTTTATTATTTAT
1 TTTAATAACTAAAATTTAATTATTTAT
40682841 TT
1 TT
40682843 ATGAATTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTAATAACTAAAATTTAATTATTTAT
Found at i:40683110 original size:2 final size:2
Alignment explanation
Indices: 40683103--40683145 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
40683093 CCCAATCCAA
* *
40683103 AC AC AC AC AC AC AC AC AC AC AC AC AC TC AC AC TC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
40683145 A
1 A
40683146 GGGTAAAGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.47, C:0.49, G:0.00, T:0.05
Consensus pattern (2 bp):
AC
Found at i:40687750 original size:27 final size:26
Alignment explanation
Indices: 40687723--40687775 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
40687713 ATTGTAATTA
40687723 TAAAAAATAATTGAATAAAATGATTTAT
1 TAAAAAAT-ATTGAA-AAAATGATTTAT
* *
40687751 TACAAAATATTGAAAAAATTATTTA
1 TAAAAAATATTGAAAAAATGATTTA
40687776 ATAACTATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 10 0.43
27 6 0.26
28 7 0.30
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.36
Consensus pattern (26 bp):
TAAAAAATATTGAAAAAATGATTTAT
Found at i:40688910 original size:17 final size:18
Alignment explanation
Indices: 40688888--40688927 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
40688878 AAATAATTTC
40688888 TTTTAGATTAATT-AAAA
1 TTTTAGATTAATTGAAAA
* *
40688905 TTTTAGTTTACTTGAAAA
1 TTTTAGATTAATTGAAAA
40688923 TTTTA
1 TTTTA
40688928 TTTAGATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (18 bp):
TTTTAGATTAATTGAAAA
Found at i:40689878 original size:17 final size:18
Alignment explanation
Indices: 40689858--40689892 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
40689848 TTAATTCTTA
40689858 ATTTTATG-TTTTCATTT
1 ATTTTATGCTTTTCATTT
*
40689875 ATTTTATGCTTTTTATTT
1 ATTTTATGCTTTTCATTT
40689893 TTTCTTTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (18 bp):
ATTTTATGCTTTTCATTT
Found at i:40702362 original size:23 final size:24
Alignment explanation
Indices: 40702307--40702362 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
40702297 ATTGATATAT
* *
40702307 ATTTTTTAAAATGATTGTTTTTTA
1 ATTTATTAAAATGATTGTTTTTAA
*
40702331 ATATATTAAAATGATTG-TTTTAA
1 ATTTATTAAAATGATTGTTTTTAA
*
40702354 ATTTCTTAA
1 ATTTATTAA
40702363 TCAATAAAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 12 0.44
24 15 0.56
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (24 bp):
ATTTATTAAAATGATTGTTTTTAA
Found at i:40709756 original size:25 final size:26
Alignment explanation
Indices: 40709721--40709783 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 26
40709711 AGATGATAAA
*
40709721 GATATTATGTCTAG-CTCGTAAGAGC
1 GATATTCTGTCTAGACTCGTAAGAGC
*
40709746 GATATTCTGTCT-GACTCGTAAGATC
1 GATATTCTGTCTAGACTCGTAAGAGC
* *
40709771 GTTAATCTGTCTA
1 GATATTCTGTCTA
40709784 AGCTTGAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 1 0.03
25 31 0.97
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (26 bp):
GATATTCTGTCTAGACTCGTAAGAGC
Found at i:40714823 original size:24 final size:25
Alignment explanation
Indices: 40714778--40714824 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
40714768 TTTACCCATT
**
40714778 TAAAAATTAAAAAAATTTAAATTTC
1 TAAAAATTAAAAAAATAAAAATTTC
*
40714803 TAAAAA-TAAAAATATAAAAATT
1 TAAAAATTAAAAAAATAAAAATT
40714825 AAATTCTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (25 bp):
TAAAAATTAAAAAAATAAAAATTTC
Found at i:40727471 original size:18 final size:18
Alignment explanation
Indices: 40727438--40727475 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
40727428 GAAAATTATG
40727438 TATTTAAAATATAAAACTA
1 TATTTAAAATATAAAA-TA
40727457 TATTTAAAA-ATAAAATA
1 TATTTAAAATATAAAATA
40727474 TA
1 TA
40727476 ATAACAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.21
18 6 0.32
19 9 0.47
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
TATTTAAAATATAAAATA
Found at i:40736889 original size:18 final size:18
Alignment explanation
Indices: 40736839--40736891 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
40736829 ATATTTTTGA
40736839 AATTTTATTATATTT-TAT
1 AATTTT-TTATATTTATAT
* *
40736857 -ATTTGTAATAGTTTATAT
1 AATTTTTTATA-TTTATAT
40736875 AATTTTTTATATTTATA
1 AATTTTTTATATTTATA
40736892 ATTATTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
16 4 0.14
17 7 0.25
18 9 0.32
19 8 0.29
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (18 bp):
AATTTTTTATATTTATAT
Found at i:40736899 original size:28 final size:27
Alignment explanation
Indices: 40736851--40736903 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
40736841 TTTTATTATA
*
40736851 TTTTATATTTGTAATAGTTTATATAATT
1 TTTTATATTTATAATAGTTTA-ATAATT
40736879 TTTTATATTTATAATTA-TTTAATAA
1 TTTTATATTTATAA-TAGTTTAATAA
40736904 CTTCTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 17 0.74
29 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (27 bp):
TTTTATATTTATAATAGTTTAATAATT
Found at i:40737505 original size:28 final size:28
Alignment explanation
Indices: 40737473--40737526 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
40737463 AACAATGTAA
*
40737473 CCTCATAAAATAATTAAAATAATTAAAT
1 CCTCATAAAATAATTAAAAAAATTAAAT
*
40737501 CCTCATAACATAATTAAAAAAATTAA
1 CCTCATAAAATAATTAAAAAAATTAA
40737527 TTAATCTCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
CCTCATAAAATAATTAAAAAAATTAAAT
Found at i:40738428 original size:11 final size:11
Alignment explanation
Indices: 40738412--40738437 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
40738402 TCTTATCCAT
40738412 CAAAAAATAAA
1 CAAAAAATAAA
40738423 CAAAAAATAAA
1 CAAAAAATAAA
40738434 CAAA
1 CAAA
40738438 CCCAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.81, C:0.12, G:0.00, T:0.08
Consensus pattern (11 bp):
CAAAAAATAAA
Found at i:40740029 original size:16 final size:16
Alignment explanation
Indices: 40740005--40740035 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40739995 TCCCTTTTAT
*
40740005 TATTTTTATTTATTTG
1 TATTATTATTTATTTG
40740021 TATTATTATTTATTT
1 TATTATTATTTATTT
40740036 TAGGTATTTA
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:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (16 bp):
TATTATTATTTATTTG
Found at i:40740042 original size:19 final size:19
Alignment explanation
Indices: 40740002--40740043 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
40739992 TAATCCCTTT
**
40740002 TATTATTTTTATTTATTTG
1 TATTATTTTTATTTATAGG
40740021 TATTATTATTTATTT-TAGG
1 TATTATT-TTTATTTATAGG
40740040 TATT
1 TATT
40740044 TAATTTGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (19 bp):
TATTATTTTTATTTATAGG
Found at i:40740249 original size:11 final size:11
Alignment explanation
Indices: 40740231--40740290 Score: 61
Period size: 11 Copynumber: 5.5 Consensus size: 11
40740221 AACTAAACCT
40740231 ATTT-TTTTAA
1 ATTTATTTTAA
40740241 ATTTATTTTAA
1 ATTTATTTTAA
*
40740252 ATTTAAATTT-A
1 ATTT-ATTTTAA
*
40740263 ATTTAAGTTTAA
1 ATTT-ATTTTAA
*
40740275 ATTTATTTTTA
1 ATTTATTTTAA
40740286 ATTTA
1 ATTTA
40740291 AAAATATTCT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
10 4 0.09
11 30 0.70
12 9 0.21
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
ATTTATTTTAA
Found at i:40740256 original size:6 final size:6
Alignment explanation
Indices: 40740236--40740292 Score: 57
Period size: 6 Copynumber: 10.0 Consensus size: 6
40740226 AACCTATTTT
* * *
40740236 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AA TTTAAG TTTAAA TTT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
40740281 TTTTAA TTTAAA
1 TTTAAA TTTAAA
40740293 AATATTCTGA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
5 13 0.32
6 28 0.68
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:40740258 original size:17 final size:17
Alignment explanation
Indices: 40740236--40740311 Score: 89
Period size: 17 Copynumber: 4.5 Consensus size: 17
40740226 AACCTATTTT
40740236 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
40740253 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
*
40740270 TTTAAATTTATTTTTAA
1 TTTAAATTTATTTTAAA
** * *
40740287 TTTAAAAATATTCTGAA
1 TTTAAATTTATTTTAAA
40740304 TTTAAATT
1 TTTAAATT
40740312 AAAAAAGTCT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 48 1.00
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:40740973 original size:3 final size:3
Alignment explanation
Indices: 40740965--40741013 Score: 53
Period size: 3 Copynumber: 15.3 Consensus size: 3
40740955 ATAATGACTT
* *
40740965 TAA TAA TAA TAA TAA TAAA TAAA TAA TAT TAA TAAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA T-AA TAA TAA TAA T-AA TAA TAA TAA TAA
40741013 T
1 T
40741014 CAAAAAGGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
3 30 0.75
4 10 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:40740998 original size:13 final size:13
Alignment explanation
Indices: 40740965--40741012 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
40740955 ATAATGACTT
40740965 TAATAAT-AATAA
1 TAATAATAAATAA
40740977 TAATAAATAAATAA
1 TAAT-AATAAATAA
* *
40740991 TATTAATAAATAT
1 TAATAATAAATAA
40741004 TAATAATAA
1 TAATAATAA
40741013 TCAAAAAGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 4 0.13
13 19 0.61
14 8 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TAATAATAAATAA
Found at i:40742257 original size:27 final size:27
Alignment explanation
Indices: 40742198--40742274 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 27
40742188 TTTGCTCTCG
* * * *
40742198 AACTTCTAAAAATTCTATATTTGCCCTCG
1 AACTTCTAAAAA-TC-ACATTTTCCCCCA
40742227 AACTTCTAAAAATCACATTTTCCCCCA
1 AACTTCTAAAAATCACATTTTCCCCCA
*
40742254 AACTT-TCAAAAATTACATTTT
1 AACTTCT-AAAAATCACATTTT
40742275 TTACCCTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.02
27 27 0.64
28 2 0.05
29 12 0.29
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (27 bp):
AACTTCTAAAAATCACATTTTCCCCCA
Found at i:40742286 original size:29 final size:28
Alignment explanation
Indices: 40742108--40742337 Score: 134
Period size: 29 Copynumber: 8.0 Consensus size: 28
40742098 TTTGACTGTC
* *
40742108 AAACTTTCCAAAAATTACATTTTAACCACC
1 AAACTTT-CAAAAATTACATTTTTACC-CT
40742138 AAACTTTTCAAAAATT-CTATTTTTACCCTT
1 AAAC-TTTCAAAAATTAC-ATTTTTACCC-T
* * * *
40742168 GAACTTTCAAAAATCACATTTTTGCTCT
1 AAACTTTCAAAAATTACATTTTTACCCT
* * *
40742196 CGAAC-TTCTAAAAATT-CTATATTTGCCCT
1 -AAACTTTC-AAAAATTAC-ATTTTTACCCT
* * * *
40742225 CGAAC-TTCTAAAAATCACA-TTTTCCCCC
1 -AAACTTTC-AAAAATTACATTTTTACCCT
40742253 AAACTTTCAAAAATTACATTTTTTACCCT
1 AAACTTTCAAAAATTACA-TTTTTACCCT
40742282 AAACTTTTC-AAAATTACCA-TTTTACCCT
1 AAAC-TTTCAAAAATTA-CATTTTTACCCT
* *
40742310 CAAA-TATCCAAAAATTACATTTTGACCC
1 -AAACT-TTCAAAAATTACATTTTTACCC
40742338 ATTTTACCCC
Statistics
Matches: 164, Mismatches: 19, Indels: 35
0.75 0.09 0.16
Matches are distributed among these distances:
27 13 0.08
28 27 0.16
29 90 0.55
30 31 0.19
31 3 0.02
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.37
Consensus pattern (28 bp):
AAACTTTCAAAAATTACATTTTTACCCT
Found at i:40742310 original size:85 final size:85
Alignment explanation
Indices: 40742169--40742332 Score: 181
Period size: 85 Copynumber: 1.9 Consensus size: 85
40742159 TTTACCCTTG
* * * * * *
40742169 AACTTTCAAAAATCACATTTTTGCTCTCGAACTTCTAAAAATTCTATATTTGCCCTCGAACT-TC
1 AACTTTCAAAAATCACATTTTTACCCTCAAACTTCTAAAAATTCCATATTTACCCTC-AAATATC
*
40742233 TAAAAATCACATTTTCCCCCA
65 CAAAAATCACATTTTCCCCCA
* * *
40742254 AACTTTCAAAAATTACATTTTTTACCCT-AAACTTTTCAAAATTACCAT-TTTACCCTCAAATAT
1 AACTTTCAAAAATCACA-TTTTTACCCTCAAACTTCTAAAAATT-CCATATTTACCCTCAAATAT
*
40742317 CCAAAAATTACATTTT
64 CCAAAAATCACATTTT
40742333 GACCCATTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
84 3 0.05
85 51 0.78
86 11 0.17
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.37
Consensus pattern (85 bp):
AACTTTCAAAAATCACATTTTTACCCTCAAACTTCTAAAAATTCCATATTTACCCTCAAATATCC
AAAAATCACATTTTCCCCCA
Found at i:40742352 original size:38 final size:39
Alignment explanation
Indices: 40742298--40742377 Score: 135
Period size: 38 Copynumber: 2.1 Consensus size: 39
40742288 TTCAAAATTA
*
40742298 CCATTTTACCCTCAAATATCCAAAAATTACA-TTTTGAC
1 CCATTTTACCCCCAAATATCCAAAAATTACATTTTTGAC
*
40742336 CCATTTTACCCCCAAATGTCCAAAAATTACATTTTTGAC
1 CCATTTTACCCCCAAATATCCAAAAATTACATTTTTGAC
40742375 CCA
1 CCA
40742378 AACTTCTCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 29 0.74
39 10 0.26
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.33
Consensus pattern (39 bp):
CCATTTTACCCCCAAATATCCAAAAATTACATTTTTGAC
Found at i:40742417 original size:95 final size:95
Alignment explanation
Indices: 40742242--40742422 Score: 242
Period size: 96 Copynumber: 1.9 Consensus size: 95
40742232 CTAAAAATCA
* * *
40742242 CATTTTCCCCCAAACTTTCAAAAATTACATTTTTTACCCTAAACTTTTCAAAATTACCATTTTAC
1 CATTTTCCCCCAAACTTCCAAAAATTACATTTTTGACCCTAAACTTCTCAAAATTACCATTTTAC
40742307 CCTCAAATATCCAAAAATTACATTTTGACC
66 CCTCAAATATCCAAAAATTACATTTTGACC
*
40742337 CATTTTACCCCCAAA-TGTCCAAAAATTACATTTTTGACCC-AAACTTCTCAAAAGTTATCATTT
1 CATTTT-CCCCCAAACT-TCCAAAAATTACATTTTTGACCCTAAACTTCTCAAAA-TTACCATTT
* * * *
40742400 T-GCCTCTAGTGTCCAAAAATTAC
63 TACCCTCAAATATCCAAAAATTAC
40742423 CGTTTTACCC
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
95 37 0.49
96 38 0.51
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (95 bp):
CATTTTCCCCCAAACTTCCAAAAATTACATTTTTGACCCTAAACTTCTCAAAATTACCATTTTAC
CCTCAAATATCCAAAAATTACATTTTGACC
Found at i:40742418 original size:29 final size:28
Alignment explanation
Indices: 40742385--40742623 Score: 185
Period size: 29 Copynumber: 8.3 Consensus size: 28
40742375 CCAAACTTCT
* * * *
40742385 CAAAAGTTATCATTTTGCCTCTAGTGTC
1 CAAAAATTACCATTTTCCCTCGAGTGTC
* * *
40742413 CAAAAATTACCGTTTTACCCCTGGA-TGGC
1 CAAAAATTACCATTTT--CCCTCGAGTGTC
40742442 CAAAAATTACCATTTTACCCTCGAGTGTC
1 CAAAAATTACCATTTT-CCCTCGAGTGTC
***
40742471 CAAAAATTACCATTTTACCCTCGAACATC
1 CAAAAATTACCATTTT-CCCTCGAGTGTC
* *
40742500 CAAAAATTACCGTTTTGTCCTCGAGTGTC
1 CAAAAATTACCATTTT-CCCTCGAGTGTC
* * *
40742529 CAAAAATTAACATTTTACCCCCGAATGTC
1 CAAAAATTACCATTTT-CCCTCGAGTGTC
* * *
40742558 TAAAAATTACTATTTTGCCCCCGAAGTGTC
1 CAAAAATTACCATTTT-CCCTCG-AGTGTC
** * *
40742588 C-AAAATTACTGTTTTACCCTCGGGTATC
1 CAAAAATTACCATTTT-CCCTCGAGTGTC
40742616 CAAAAATT
1 CAAAAATT
40742624 GCATTTTTAA
Statistics
Matches: 169, Mismatches: 37, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
28 24 0.14
29 136 0.80
30 9 0.05
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.32
Consensus pattern (28 bp):
CAAAAATTACCATTTTCCCTCGAGTGTC
Found at i:40742621 original size:58 final size:58
Alignment explanation
Indices: 40742385--40742623 Score: 250
Period size: 58 Copynumber: 4.1 Consensus size: 58
40742375 CCAAACTTCT
* * * * * **
40742385 CAAAAGTTATCATTTTG-CCTCTAGTGTCCAAAAATTACCGTTTTACCC-CTGGATGGC
1 CAAAAATTACCATTTTGCCCTCGAGTGTCCAAAAATTACCATTTTACCCTC-GAATATC
* *
40742442 CAAAAATTACCATTTTACCCTCGAGTGTCCAAAAATTACCATTTTACCCTCGAACATC
1 CAAAAATTACCATTTTGCCCTCGAGTGTCCAAAAATTACCATTTTACCCTCGAATATC
* * * * *
40742500 CAAAAATTACCGTTTTGTCCTCGAGTGTCCAAAAATTAACATTTTACCCCCGAATGTC
1 CAAAAATTACCATTTTGCCCTCGAGTGTCCAAAAATTACCATTTTACCCTCGAATATC
* * * ** **
40742558 TAAAAATTACTATTTTGCCCCCGAAGTGTCC-AAAATTACTGTTTTACCCTCGGGTATC
1 CAAAAATTACCATTTTGCCCTCG-AGTGTCCAAAAATTACCATTTTACCCTCGAATATC
40742616 CAAAAATT
1 CAAAAATT
40742624 GCATTTTTAA
Statistics
Matches: 150, Mismatches: 29, Indels: 5
0.82 0.16 0.03
Matches are distributed among these distances:
57 14 0.09
58 128 0.85
59 8 0.05
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.32
Consensus pattern (58 bp):
CAAAAATTACCATTTTGCCCTCGAGTGTCCAAAAATTACCATTTTACCCTCGAATATC
Found at i:40742632 original size:87 final size:88
Alignment explanation
Indices: 40742407--40742623 Score: 253
Period size: 87 Copynumber: 2.5 Consensus size: 88
40742397 TTTTGCCTCT
* * * *
40742407 AGTGTCCAAAAATTACCGTTTTACCC-CTGG-ATGGCCAAAAATTACCATTTTACCCTCGAGTGT
1 AGTGTCCAAAAATTACCGTTTTACCCTCGGGTAT--CCAAAAATTAACATTTTACCCCCGAATGT
*
40742470 CCAAAAATTACCATTTTACCCTCGA
64 CCAAAAATTACCATTTTACCCCCGA
** ** * * *
40742495 A-CATCCAAAAATTACCGTTTTGTCCTCGAGTGTCCAAAAATTAACATTTTACCCCCGAATGTCT
1 AGTGTCCAAAAATTACCGTTTTACCCTCGGGTATCCAAAAATTAACATTTTACCCCCGAATGTCC
* *
40742559 AAAAATTACTATTTTGCCCCCGA
66 AAAAATTACCATTTTACCCCCGA
*
40742582 AGTGTCC-AAAATTACTGTTTTACCCTCGGGTATCCAAAAATT
1 AGTGTCCAAAAATTACCGTTTTACCCTCGGGTATCCAAAAATT
40742624 GCATTTTTAA
Statistics
Matches: 105, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
87 98 0.93
88 6 0.06
89 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (88 bp):
AGTGTCCAAAAATTACCGTTTTACCCTCGGGTATCCAAAAATTAACATTTTACCCCCGAATGTCC
AAAAATTACCATTTTACCCCCGA
Found at i:40755160 original size:209 final size:209
Alignment explanation
Indices: 40754795--40755233 Score: 551
Period size: 209 Copynumber: 2.1 Consensus size: 209
40754785 GGTCGAAGCA
* * * * *
40754795 ATACAGAGAAGTGAACCAGATTCGTTTTCCTGATGAGACACAAAGAAGTGGATCAAAACAAGTGA
1 ATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAAAGAAGCGGATCAAAACAAGTGA
**
40754860 TGTGGTCATCTTCCTGATGAAATACTGAGAAGTAGGCCAAATCAATGAAACCAAGCTCAATATAA
66 TGTGGTCATCTTCCTGATGAAATACTGAGAAGTAAACCAAATCAATGAAACCAAGCTCAATATAA
* * *
40754925 GCAAAACTTCGAACCCTAGCTTCCTGATGAGATATTGAAAAGCAAGTCGAAGCAATAAAATGGTC
131 GCAAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAAAAGCAAGTCGAAGCAATAAAACGGTC
*
40754990 AGCTTCCTGATGAG
196 ACCTTCCTGATGAG
* * * * ** *
40755004 ATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATATAGAGAAGCGGATTGAAATAAGTGA
1 ATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAAAGAAGCGGATCAAAACAAGTGA
* * *
40755069 TGCT-GTCATCTTCTTGATGAGATACTGAGAAGTAAACCAAATCAATGAAACCAGGCTCAA-AGT
66 TG-TGGTCATCTTCCTGATGAAATACTGAGAAGTAAACCAAATCAATGAAACCAAGCTCAATA-T
* * * * * * *
40755132 GAGCAAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGTAGGTCGAAGCCATAAAACGG
129 AAGCAAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAAAAGCAAGTCGAAGCAATAAAACGG
* *
40755197 TTACCTTCTTGATGAG
194 TCACCTTCCTGATGAG
*
40755213 ATACTGATG-AGTAGACCAAAT
1 ATACTGA-GAAGTGGACCAAAT
40755234 CAATGACACC
Statistics
Matches: 196, Mismatches: 31, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
208 1 0.01
209 193 0.98
210 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.24
Consensus pattern (209 bp):
ATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAAAGAAGCGGATCAAAACAAGTGA
TGTGGTCATCTTCCTGATGAAATACTGAGAAGTAAACCAAATCAATGAAACCAAGCTCAATATAA
GCAAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAAAAGCAAGTCGAAGCAATAAAACGGTC
ACCTTCCTGATGAG
Found at i:40755555 original size:11 final size:11
Alignment explanation
Indices: 40755539--40755628 Score: 74
Period size: 11 Copynumber: 8.0 Consensus size: 11
40755529 AAACCCACTC
40755539 TTTTAAATTTA
1 TTTTAAATTTA
*
40755550 TTTTAAGATTAA
1 TTTTAA-ATTTA
* *
40755562 ATTT-ATTTTAA
1 TTTTAAATTT-A
* *
40755573 ATTTAAATTTG
1 TTTTAAATTTA
40755584 TTTTAAATTTAA
1 TTTTAAATTT-A
* *
40755596 ATTTAAATTAA
1 TTTTAAATTTA
40755607 TTTTAAATTTA
1 TTTTAAATTTA
*
40755618 TCTTAAATTTA
1 TTTTAAATTTA
40755629 AAATTATTCT
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
10 2 0.03
11 41 0.66
12 19 0.31
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:40755563 original size:17 final size:17
Alignment explanation
Indices: 40755540--40755649 Score: 132
Period size: 17 Copynumber: 6.5 Consensus size: 17
40755530 AACCCACTCT
40755540 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
40755558 -TTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
40755574 TTTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
** *
40755591 TTTAAATTTAAATTAAT
1 TTTAAATTTATTTTAAA
*
40755608 TTTAAATTTATCTTAAA
1 TTTAAATTTATTTTAAA
* * *
40755625 TTTAAAATTATTCTGAA
1 TTTAAATTTATTTTAAA
40755642 TTTAAATT
1 TTTAAATT
40755650 AAAAAAGTCC
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
16 1 0.01
17 77 0.99
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:40755577 original size:23 final size:22
Alignment explanation
Indices: 40755568--40755628 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
40755558 TTAAATTTAT
*
40755568 TTTAAATTTAAATTTGTTTTAAA
1 TTTAAA-TTAAATTTATTTTAAA
*
40755591 TTTAAATTTAAATTAATTTTAAA
1 TTTAAA-TTAAATTTATTTTAAA
**
40755614 TTTATCTTAAATTTA
1 TTTAAATTAAATTTA
40755629 AAATTATTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
22 8 0.24
23 25 0.76
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAAATTAAATTTATTTTAAA
Found at i:40755643 original size:28 final size:28
Alignment explanation
Indices: 40755592--40755645 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
40755582 TGTTTTAAAT
*
40755592 TTAAATTTAAATTAATTTTAAATTTATC
1 TTAAATTTAAATTAATTCTAAATTTATC
*
40755620 TTAAATTTAAAATT-ATTCTGAATTTA
1 TTAAATTT-AAATTAATTCTAAATTTA
40755646 AATTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (28 bp):
TTAAATTTAAATTAATTCTAAATTTATC
Found at i:40756326 original size:3 final size:3
Alignment explanation
Indices: 40756318--40756362 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
40756308 ATAATGACTT
* *
40756318 TAA TAA TAA TAA TAA TAAA TAA TAT TAA TAAA TAT TAA TAA TAA T
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA T-AA TAA TAA TAA TAA T
40756363 CAAAAAGGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
3 30 0.83
4 6 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:40756340 original size:13 final size:13
Alignment explanation
Indices: 40756318--40756361 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
40756308 ATAATGACTT
40756318 TAAT-AATAATAA
1 TAATAAATAATAA
*
40756330 TAATAAATAATAT
1 TAATAAATAATAA
*
40756343 TAATAAATATTAA
1 TAATAAATAATAA
40756356 TAATAA
1 TAATAA
40756362 TCAAAAAGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 4 0.14
13 24 0.86
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATAAATAATAA
Found at i:40757606 original size:56 final size:57
Alignment explanation
Indices: 40757520--40757711 Score: 205
Period size: 56 Copynumber: 3.4 Consensus size: 57
40757510 AAACTTTTTG
* *
40757520 AAAATTCCATTTTTACCCTCAAACTTCTAAAAATCACATTTT-TCCCTCGAACTTCCA
1 AAAATTCCATTTTTACCCTCAAACTTCTAAAAATCACATTTTACCCCT-AAACTTCCA
** *
40757577 AAAATTCCATTTTT-CCCTCGGACTTCTAAAAATCACATTTTACCCCTAAATTTCCA
1 AAAATTCCATTTTTACCCTCAAACTTCTAAAAATCACATTTTACCCCTAAACTTCCA
* * * * *
40757633 AAAATTACATTTTTAACCC-CAAACTTTCCAAAAATTACCATTTTATCCCCTGAACATCC-
1 AAAATTCCATTTTT-ACCCTCAAAC-TTCTAAAAATCA-CATTTTA-CCCCTAAACTTCCA
40757692 AAAATTACCA-TTTTACCCTC
1 AAAATT-CCATTTTTACCCTC
40757712 GATGTCAAAA
Statistics
Matches: 113, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
56 45 0.40
57 21 0.19
58 17 0.15
59 18 0.16
60 12 0.11
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.34
Consensus pattern (57 bp):
AAAATTCCATTTTTACCCTCAAACTTCTAAAAATCACATTTTACCCCTAAACTTCCA
Found at i:40757677 original size:30 final size:28
Alignment explanation
Indices: 40757485--40757732 Score: 166
Period size: 28 Copynumber: 8.6 Consensus size: 28
40757475 TACCCTTACT
*
40757485 TTCCAAAAATTACAATTTGACCCTCAAAC
1 TTCCAAAAATTAC-ATTTTACCCTCAAAC
*** *
40757514 TTTTTGAAAATTCCATTTTTACCCTCAAAC
1 -TTCCAAAAATTACA-TTTTACCCTCAAAC
* * * *
40757544 TTCTAAAAATCACATTTTTCCCTCGAAC
1 TTCCAAAAATTACATTTTACCCTCAAAC
* * **
40757572 TTCCAAAAATTCCATTTTTCCCTCGGAC
1 TTCCAAAAATTACATTTTACCCTCAAAC
* * *
40757600 TTCTAAAAATCACATTTTACCC-CTAAAT
1 TTCCAAAAATTACATTTTACCCTC-AAAC
40757628 TTCCAAAAATTACATTTTTAACCC-CAAAC
1 TTCCAAAAATTACA-TTTT-ACCCTCAAAC
*
40757657 TTTCCAAAAATTACCATTTTATCCC-CTGAAC
1 -TTCCAAAAATTA-CATTTTA-CCCTC-AAAC
* *
40757688 ATCC-AAAATTACCATTTTACCCTC-GA-
1 TTCCAAAAATTA-CATTTTACCCTCAAAC
*
40757714 TGTCAAAAAATTACATTTT
1 T-TCCAAAAATTACATTTT
40757733 TTACCCTGAA
Statistics
Matches: 177, Mismatches: 30, Indels: 25
0.76 0.13 0.11
Matches are distributed among these distances:
27 10 0.06
28 77 0.44
29 35 0.20
30 50 0.28
31 5 0.03
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (28 bp):
TTCCAAAAATTACATTTTACCCTCAAAC
Found at i:40757752 original size:29 final size:29
Alignment explanation
Indices: 40757440--40757752 Score: 152
Period size: 28 Copynumber: 10.9 Consensus size: 29
40757430 CAGTAACCAA
* *
40757440 ATTTTGACCCTCGAACTTTTCAAAATTGC
1 ATTTTTACCCTCGAACTTTTCAAAATTAC
* *
40757469 ATTTTTTACCCT--TACTTTCCAAAAATTAC
1 A-TTTTTACCCTCGAACTTTTC-AAAATTAC
* * * * *
40757498 AATTTGACCCTCAAACTTTTTGAAAATTCC
1 ATTTTTACCCTCGAAC-TTTTCAAAATTAC
* * * *
40757528 ATTTTTACCCTCAAACTTCTAAAAATCAC
1 ATTTTTACCCTCGAACTTTTCAAAATTAC
* *
40757557 ATTTTT-CCCTCGAAC-TTCCAAAAATTCC
1 ATTTTTACCCTCGAACTTTTC-AAAATTAC
* * * *
40757585 ATTTTT-CCCTCGGACTTCTAAAAATCAC
1 ATTTTTACCCTCGAACTTTTCAAAATTAC
* * *
40757613 A-TTTTACCC-CTAAATTTCCAAAAATTAC
1 ATTTTTACCCTCGAACTTTTC-AAAATTAC
* *
40757641 ATTTTTAACCC-CAAACTTTCCAAAAATTACC
1 ATTTTT-ACCCTCGAACTTTTC-AAAATTA-C
* * *
40757672 ATTTTATCCCCT-GAAC-ATCCAAAATTACC
1 ATTTT-TACCCTCGAACTTTTCAAAATTA-C
*
40757701 A-TTTTACCCTCG-A--TGTCAAAAAATTAC
1 ATTTTTACCCTCGAACTTTTC--AAAATTAC
40757728 ATTTTTTACCCT-GAACTTTTCAAAA
1 A-TTTTTACCCTCGAACTTTTCAAAA
40757753 GTGACCATTT
Statistics
Matches: 217, Mismatches: 45, Indels: 44
0.71 0.15 0.14
Matches are distributed among these distances:
26 1 0.00
27 17 0.08
28 72 0.33
29 53 0.24
30 55 0.25
31 18 0.08
32 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (29 bp):
ATTTTTACCCTCGAACTTTTCAAAATTAC
Found at i:40757939 original size:29 final size:29
Alignment explanation
Indices: 40757520--40757940 Score: 190
Period size: 29 Copynumber: 14.6 Consensus size: 29
40757510 AAACTTTTTG
* *
40757520 AAAATT-CCATTTTTACCCTCAAACT-TCTA
1 AAAATTACC-TTTTTACCCTCGAA-TGTCCA
* *
40757549 AAAATCACATTTTT-CCCTCGAACT-TCCA
1 AAAATTACCTTTTTACCCTCGAA-TGTCCA
* *
40757577 AAAATT-CCATTTTT-CCCTCGGACT-TCTA
1 AAAATTACC-TTTTTACCCTC-GAATGTCCA
* * * *
40757605 AAAATCA-CATTTTACCC-CTAAATTTCCA
1 AAAATTACCTTTTTACCCTC-GAATGTCCA
* * *
40757633 AAAATTACATTTTTAACCC-CAAACTTTCCA
1 AAAATTACCTTTTT-ACCCTCGAA-TGTCCA
* **
40757663 AAAATTACCATTTTATCCC-CTGAACATCC-
1 AAAATTACCTTTTTA-CCCTC-GAATGTCCA
* *
40757692 AAAATTACCATTTTACCCTCG-ATGTCAA
1 AAAATTACCTTTTTACCCTCGAATGTCCA
* * *
40757720 AAAATTACATTTTTTACCCT-GAACTTTTCA
1 AAAATTAC-CTTTTTACCCTCGAA-TGTCCA
* * * * * *
40757750 AAAGTGACCATTTTGCCCT-GAGTGTTCA
1 AAAATTACCTTTTTACCCTCGAATGTCCA
* * * * * *
40757778 AAAATTATCGTTTTACCTTTGGATGGCCA
1 AAAATTACCTTTTTACCCTCGAATGTCCA
* * * *
40757807 GAAATTACCATTTTGCTCTCGAATGTCCA
1 AAAATTACCTTTTTACCCTCGAATGTCCA
* * *
40757836 AAAATTACCTTTTTACTCTC-AGACGTCTA
1 AAAATTACCTTTTTACCCTCGA-ATGTCCA
* * * * *
40757865 AAAATTACCGTTTTGCCTTTGAGTGTCCA
1 AAAATTACCTTTTTACCCTCGAATGTCCA
* *
40757894 AAAATTACCATTTTACCCTCGAATATCCA
1 AAAATTACCTTTTTACCCTCGAATGTCCA
40757923 AAAATTACCTTTTTACCC
1 AAAATTACCTTTTTACCC
40757941 CTGAACATCC
Statistics
Matches: 297, Mismatches: 76, Indels: 38
0.72 0.18 0.09
Matches are distributed among these distances:
27 11 0.04
28 81 0.27
29 162 0.55
30 41 0.14
31 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.35
Consensus pattern (29 bp):
AAAATTACCTTTTTACCCTCGAATGTCCA
Found at i:40757955 original size:87 final size:88
Alignment explanation
Indices: 40757548--40757956 Score: 283
Period size: 87 Copynumber: 4.7 Consensus size: 88
40757538 TCAAACTTCT
* * * * *
40757548 AAAAATCACATTTTT-CCCTCGAAC-TTCCAAAAATT-CCATTTT-TCCCTCGGACTTCTAAAAA
1 AAAAATTACATTTTTACCCTCGAACTTTCCAAAAATTACCATTTTACCCCT-GAACATCCAAAAA
* * ** * * *
40757609 TCA-CATTTTACCCCTAAATTTCC
65 TTACCGTTTTACCTTTGAGTGTCC
*
40757632 AAAAATTACATTTTTAACCC-CAAACTTTCCAAAAATTACCATTTTATCCCCTGAACATCC-AAA
1 AAAAATTACATTTTT-ACCCTCGAACTTTCCAAAAATTACCATTTTA-CCCCTGAACATCCAAAA
* * * *
40757695 ATTACCATTTTACCCTCGA-TGTCA
64 ATTACCGTTTTACCTTTGAGTGTCC
* * * * *** *
40757719 AAAAATTACATTTTTTACCCT-GAACTTTTCAAAAGTGACCATTTT-GCCCTGAGTGTTCAAAAA
1 AAAAATTACA-TTTTTACCCTCGAACTTTCCAAAAATTACCATTTTACCCCTGAACATCCAAAAA
* *
40757782 TTATCGTTTTACCTTTG-GATGGCC
65 TTACCGTTTTACCTTTGAG-TGTCC
* * * * * * * * *
40757806 AGAAATTACCA-TTTTGCTCTCGAA-TGTCCAAAAATTACCTTTTTA-CTCTCAGACGTCTAAAA
1 AAAAATTA-CATTTTTACCCTCGAACTTTCCAAAAATTACCATTTTACCCCTGA-ACATCCAAAA
*
40757868 ATTACCGTTTTGCCTTTGAGTGTCC
64 ATTACCGTTTTACCTTTGAGTGTCC
* *
40757893 AAAAATTACCA-TTTTACCCTCGAA-TATCCAAAAATTACCTTTTTACCCCTGAACATCCAAAAA
1 AAAAATTA-CATTTTTACCCTCGAACTTTCCAAAAATTACCATTTTACCCCTGAACATCCAAAAA
40757956 T
65 T
40757957 CATATTTTTA
Statistics
Matches: 255, Mismatches: 52, Indels: 33
0.75 0.15 0.10
Matches are distributed among these distances:
84 14 0.05
85 12 0.05
86 57 0.22
87 140 0.55
88 28 0.11
89 4 0.02
ACGTcount: A:0.33, C:0.25, G:0.08, T:0.34
Consensus pattern (88 bp):
AAAAATTACATTTTTACCCTCGAACTTTCCAAAAATTACCATTTTACCCCTGAACATCCAAAAAT
TACCGTTTTACCTTTGAGTGTCC
Found at i:40757964 original size:29 final size:29
Alignment explanation
Indices: 40757890--40757966 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
40757880 CCTTTGAGTG
* *
40757890 TCCAAAAATTACCA-TTTTACCCTCGAATA
1 TCCAAAAATCA-CATTTTTACCCTCGAACA
* *
40757919 TCCAAAAATTACCTTTTTACCC-CTGAACA
1 TCCAAAAATCACATTTTTACCCTC-GAACA
*
40757948 TCCAAAAATCATATTTTTA
1 TCCAAAAATCACATTTTTA
40757967 ACTCTATTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 2 0.05
29 39 0.95
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.34
Consensus pattern (29 bp):
TCCAAAAATCACATTTTTACCCTCGAACA
Found at i:40770052 original size:21 final size:21
Alignment explanation
Indices: 40770026--40770066 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40770016 ATTGAGTTCT
* *
40770026 TCATGCTTGTTTCGGTAGAAC
1 TCATGCATGTATCGGTAGAAC
*
40770047 TCATGCATGTATCGTTAGAA
1 TCATGCATGTATCGGTAGAA
40770067 GTACAAGGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (21 bp):
TCATGCATGTATCGGTAGAAC
Found at i:40780059 original size:99 final size:99
Alignment explanation
Indices: 40779888--40780078 Score: 346
Period size: 99 Copynumber: 1.9 Consensus size: 99
40779878 ATATGGTGAC
* *
40779888 TGAAACCAATAATTTATGGACAACAGATTGCTTAGATCAAATATGCGATGAGCTTGAGCTGTCTT
1 TGAAACCAATAATTTATAGACAACAGATTGCTTAGATCAAATATGCGATGAGCCTGAGCTGTCTT
*
40779953 TCAATACCAAATTTGGACCAAATGACCGTGACTG
66 CCAATACCAAATTTGGACCAAATGACCGTGACTG
*
40779987 TGAAACCAATAATTTATAGACAAGAGATTGCTTAGATCAAATATGCGATGAGCCTGAGCTGTCTT
1 TGAAACCAATAATTTATAGACAACAGATTGCTTAGATCAAATATGCGATGAGCCTGAGCTGTCTT
40780052 CCAATACCAAATTTGGACCAAATGACC
66 CCAATACCAAATTTGGACCAAATGACC
40780079 ATTGTGTTAT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
99 88 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (99 bp):
TGAAACCAATAATTTATAGACAACAGATTGCTTAGATCAAATATGCGATGAGCCTGAGCTGTCTT
CCAATACCAAATTTGGACCAAATGACCGTGACTG
Found at i:40781222 original size:21 final size:21
Alignment explanation
Indices: 40781189--40781242 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
40781179 GGACTTTTTA
* *
40781189 GTATCGGTAGAAGCGTGACTT
1 GTATCGATAGAAGCGTCACTT
* *
40781210 GTTTCGATAGAAGCTTCACTT
1 GTATCGATAGAAGCGTCACTT
*
40781231 GTATCGGTAGAA
1 GTATCGATAGAA
40781243 CTGTCATAGG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (21 bp):
GTATCGATAGAAGCGTCACTT
Found at i:40782215 original size:25 final size:24
Alignment explanation
Indices: 40782181--40782237 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 24
40782171 AGGTATTTTG
40782181 TTTATTATCTGT-TTATATTTATTA
1 TTTATTATCTGTATT-TATTTATTA
40782205 TTTATCTATCTGTATTTATTTATTA
1 TTTAT-TATCTGTATTTATTTATTA
*
40782230 TTTTTTAT
1 TTTATTAT
40782238 TTTCAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 8 0.27
25 20 0.67
26 2 0.07
ACGTcount: A:0.23, C:0.05, G:0.04, T:0.68
Consensus pattern (24 bp):
TTTATTATCTGTATTTATTTATTA
Found at i:40782230 original size:21 final size:21
Alignment explanation
Indices: 40782181--40782230 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
40782171 AGGTATTTTG
* *
40782181 TTTATTATCTGTTTATATTTA
1 TTTATTATCTATCTATATTTA
*
40782202 -TTATTTATCTATCTGTATTTA
1 TTTA-TTATCTATCTATATTTA
40782223 TTTATTAT
1 TTTATTAT
40782231 TTTTTATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 3 0.12
21 18 0.75
22 3 0.12
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.66
Consensus pattern (21 bp):
TTTATTATCTATCTATATTTA
Found at i:40783508 original size:19 final size:19
Alignment explanation
Indices: 40783473--40783513 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
40783463 TATATTTCTT
*
40783473 TTTTTATTTTGTGTTTCATA
1 TTTTTATTTTGTATTTCA-A
40783493 TTTTTATTTTG-ATTTCAA
1 TTTTTATTTTGTATTTCAA
40783511 TTT
1 TTT
40783514 AATCCTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 5 0.25
20 11 0.55
ACGTcount: A:0.17, C:0.05, G:0.07, T:0.71
Consensus pattern (19 bp):
TTTTTATTTTGTATTTCAA
Found at i:40783912 original size:104 final size:105
Alignment explanation
Indices: 40783732--40783968 Score: 344
Period size: 104 Copynumber: 2.3 Consensus size: 105
40783722 ATAAATTATG
* *
40783732 TTTAAAAATCT-AGGCAATGTTCTTTTA-TTGAGGGAATTCGAGAAATTGTGCCCCTAATCTGTT
1 TTTAAAAAT-TGAGGTAATGTTCTTTTATTTTAGGGAATTCGAGAAATTGTGCCCCTAATCTGTT
** *
40783795 GGGTATGGTTTTTCTTTGAACCTAAGTAATTGAACATCCTA
65 GGGTATAATTTTTCTTCGAACCTAAGTAATTGAACATCCTA
40783836 TTTAAAAATTGAGGTAATGTTCTTTTATTTTAGGGAATTCGAGAAATTGTG-CCCTAA-CGTGTT
1 TTTAAAAATTGAGGTAATGTTCTTTTATTTTAGGGAATTCGAGAAATTGTGCCCCTAATC-TGTT
40783899 GGGTATAATTTTTCTTCGAACCTAAGTAATTGAACATCCTA
65 GGGTATAATTTTTCTTCGAACCTAAGTAATTGAACATCCTA
*
40783940 TTTTAAAATTGA--TAAGTGTTC-TTTATTTT
1 TTTAAAAATTGAGGTAA-TGTTCTTTTATTTT
40783969 CGAAAATTCA
Statistics
Matches: 123, Mismatches: 6, Indels: 10
0.88 0.04 0.07
Matches are distributed among these distances:
102 11 0.09
103 7 0.06
104 83 0.67
105 22 0.18
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (105 bp):
TTTAAAAATTGAGGTAATGTTCTTTTATTTTAGGGAATTCGAGAAATTGTGCCCCTAATCTGTTG
GGTATAATTTTTCTTCGAACCTAAGTAATTGAACATCCTA
Found at i:40788174 original size:13 final size:13
Alignment explanation
Indices: 40788156--40788191 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
40788146 TTCTACAAAT
40788156 ACTTCATATAAAC
1 ACTTCATATAAAC
*
40788169 ACTTCATATAATC
1 ACTTCATATAAAC
*
40788182 ATTTCATATA
1 ACTTCATATA
40788192 TCTATTTCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (13 bp):
ACTTCATATAAAC
Found at i:40788229 original size:13 final size:13
Alignment explanation
Indices: 40788175--40788251 Score: 50
Period size: 13 Copynumber: 5.8 Consensus size: 13
40788165 AAACACTTCA
*
40788175 TATAATCATTTCA
1 TATAATCATTTCG
*
40788188 TAT-ATCTATTTCCA
1 TATAATC-ATTT-CG
*
40788202 TATAA-GATTTCG
1 TATAATCATTTCG
* *
40788214 TATAGTCATTTTG
1 TATAATCATTTCG
*
40788227 TATAATCATTTAACA
1 TATAATCATTT--CG
40788242 TATAATCATT
1 TATAATCATT
40788252 ATGTATAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
12 8 0.16
13 26 0.52
14 5 0.10
15 11 0.22
ACGTcount: A:0.35, C:0.13, G:0.05, T:0.47
Consensus pattern (13 bp):
TATAATCATTTCG
Found at i:40788722 original size:45 final size:45
Alignment explanation
Indices: 40788670--40789047 Score: 355
Period size: 45 Copynumber: 8.4 Consensus size: 45
40788660 TGCCGTAGTT
* * *
40788670 TCTTTCAACTGTGGTGTTACTCGTTTGATTAGTGATGCGATAATG
1 TCTTTCAACTATGGTCTTACTCGTTTGATTAGTGATGCCATAATG
* * * * * * * **
40788715 TCTTTCAACCATGGTTTTACTCGATAGAATAGTGATGCTAAAACA
1 TCTTTCAACTATGGTCTTACTCGTTTGATTAGTGATGCCATAATG
* ** * * *
40788760 TCCTTCAGTTATGGTCTTACTCGTTTGATTTGTGATGTCATAGTG
1 TCTTTCAACTATGGTCTTACTCGTTTGATTAGTGATGCCATAATG
* * *
40788805 TCTTTCAACTATGGCCTTACTCGTTTGATTTGTGATGCCATAGTG
1 TCTTTCAACTATGGTCTTACTCGTTTGATTAGTGATGCCATAATG
* * * *
40788850 TCTTTCAACTATGGTCTTACTCGATAGAATAATGATGCCATAATG
1 TCTTTCAACTATGGTCTTACTCGTTTGATTAGTGATGCCATAATG
* * * *
40788895 TCTTTCAGCTATGATCTTACTCGTTTGATTTGTGATGCCATAGTG
1 TCTTTCAACTATGGTCTTACTCGTTTGATTAGTGATGCCATAATG
* * * * * *
40788940 TCTTTCAGC-ATGGTCTTACTTGATAGAATAGTGATGCCATAACG
1 TCTTTCAACTATGGTCTTACTCGTTTGATTAGTGATGCCATAATG
* * * ** * *
40788984 TCTTTCAGCTATGGTCTTATTCGTTT-CTGGGGTGGTGCCATAGTG
1 TCTTTCAACTATGGTCTTACTCGTTTGAT-TAGTGATGCCATAATG
40789029 TCTTTCAACTATGGTCTTA
1 TCTTTCAACTATGGTCTTA
40789048 ATCATTTCTT
Statistics
Matches: 266, Mismatches: 65, Indels: 4
0.79 0.19 0.01
Matches are distributed among these distances:
44 36 0.14
45 230 0.86
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.40
Consensus pattern (45 bp):
TCTTTCAACTATGGTCTTACTCGTTTGATTAGTGATGCCATAATG
Found at i:40788840 original size:135 final size:135
Alignment explanation
Indices: 40788653--40789002 Score: 441
Period size: 135 Copynumber: 2.6 Consensus size: 135
40788643 TTCATTTTCC
* * * * * *
40788653 TTTGTGTTGCCGTAGTTTCTTTCAACTGTGGTGTTACTCGTTTGATTAGTGATGCGATAATGTCT
1 TTTGTGATGCCATAGTGTCTTTCAACTATGGTCTTACTCGTTTGATTAGTGATGCCATAATGTCT
* * * * *
40788718 TTCAACCATGGTTTTACTCGATAGAATAGTGATGCTAAAACATCCTTCAGTTATGGTCTTACTCG
66 TTCAACCATGGTCTTACTCGATAGAATAATGATGCCAAAACATCCTTCAGCTATGATCTTACTCG
40788783 TTTGA
131 TTTGA
* * * *
40788788 TTTGTGATGTCATAGTGTCTTTCAACTATGGCCTTACTCGTTTGATTTGTGATGCCATAGTGTCT
1 TTTGTGATGCCATAGTGTCTTTCAACTATGGTCTTACTCGTTTGATTAGTGATGCCATAATGTCT
* * ** *
40788853 TTCAACTATGGTCTTACTCGATAGAATAATGATGCCATAATGTCTTTCAGCTATGATCTTACTCG
66 TTCAACCATGGTCTTACTCGATAGAATAATGATGCCAAAACATCCTTCAGCTATGATCTTACTCG
40788918 TTTGA
131 TTTGA
* * * * * *
40788923 TTTGTGATGCCATAGTGTCTTTCAGC-ATGGTCTTACTTGATAGAATAGTGATGCCATAACGTCT
1 TTTGTGATGCCATAGTGTCTTTCAACTATGGTCTTACTCGTTTGATTAGTGATGCCATAATGTCT
* *
40788987 TTCAGCTATGGTCTTA
66 TTCAACCATGGTCTTA
40789003 TTCGTTTCTG
Statistics
Matches: 184, Mismatches: 31, Indels: 1
0.85 0.14 0.00
Matches are distributed among these distances:
134 45 0.24
135 139 0.76
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (135 bp):
TTTGTGATGCCATAGTGTCTTTCAACTATGGTCTTACTCGTTTGATTAGTGATGCCATAATGTCT
TTCAACCATGGTCTTACTCGATAGAATAATGATGCCAAAACATCCTTCAGCTATGATCTTACTCG
TTTGA
Found at i:40788993 original size:89 final size:90
Alignment explanation
Indices: 40788804--40789047 Score: 357
Period size: 89 Copynumber: 2.7 Consensus size: 90
40788794 ATGTCATAGT
* *
40788804 GTCTTTCAACTATGGCCTTACTCGTTTGATTTGTGATGCCATAGTGTCTTTCAACTATGGTCTTA
1 GTCTTTCAGCTATGGTCTTACTCGTTTGATTTGTGATGCCATAGTGTCTTTCAACTATGGTCTTA
*
40788869 CTCGATAGAATAATGATGCCATAAT
66 CTCGATAGAATAATGATGCCATAAC
* *
40788894 GTCTTTCAGCTATGATCTTACTCGTTTGATTTGTGATGCCATAGTGTCTTTCAGC-ATGGTCTTA
1 GTCTTTCAGCTATGGTCTTACTCGTTTGATTTGTGATGCCATAGTGTCTTTCAACTATGGTCTTA
* *
40788958 CTTGATAGAATAGTGATGCCATAAC
66 CTCGATAGAATAATGATGCCATAAC
* * ** *
40788983 GTCTTTCAGCTATGGTCTTATTCGTTT-CTGGGGTGGTGCCATAGTGTCTTTCAACTATGGTCTT
1 GTCTTTCAGCTATGGTCTTACTCGTTTGAT-TTGTGATGCCATAGTGTCTTTCAACTATGGTCTT
40789047 A
65 A
40789048 ATCATTTCTT
Statistics
Matches: 138, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
88 1 0.01
89 77 0.56
90 60 0.43
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.40
Consensus pattern (90 bp):
GTCTTTCAGCTATGGTCTTACTCGTTTGATTTGTGATGCCATAGTGTCTTTCAACTATGGTCTTA
CTCGATAGAATAATGATGCCATAAC
Found at i:40790396 original size:24 final size:24
Alignment explanation
Indices: 40790369--40790419 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
40790359 TTGATAATGC
40790369 TTAAATATGACATACTTTTAGA-TA
1 TTAAATAT-ACATACTTTTAGAGTA
* *
40790393 TTAAATATATATATTTTTAGAGTA
1 TTAAATATACATACTTTTAGAGTA
40790417 TTA
1 TTA
40790420 TCCTATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (24 bp):
TTAAATATACATACTTTTAGAGTA
Found at i:40790642 original size:19 final size:19
Alignment explanation
Indices: 40790620--40790664 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
40790610 TTATATTAGG
40790620 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
40790639 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
40790658 ATTTAAT
1 ATTTAAT
40790665 TTATATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:40792312 original size:8 final size:8
Alignment explanation
Indices: 40792288--40792349 Score: 54
Period size: 8 Copynumber: 7.6 Consensus size: 8
40792278 ATTATTTTTA
40792288 TTTTTATT
1 TTTTTATT
*
40792296 TTTAT-TT
1 TTTTTATT
40792303 TTTTTATT
1 TTTTTATT
*
40792311 TTTCTATCT
1 TTTTTAT-T
40792320 TATTTTATT
1 T-TTTTATT
*
40792329 TATTTATT
1 TTTTTATT
**
40792337 CATTTATT
1 TTTTTATT
40792345 TTTTT
1 TTTTT
40792350 TCTTGGAAAC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
7 6 0.14
8 28 0.65
9 4 0.09
10 5 0.12
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTATT
Found at i:40792313 original size:6 final size:6
Alignment explanation
Indices: 40792279--40792304 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
40792269 GGCAACCCAA
40792279 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
40792305 TTTATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:40793807 original size:19 final size:19
Alignment explanation
Indices: 40793785--40793829 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
40793775 TTATATTAGG
40793785 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
40793804 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
40793823 ATTTAAT
1 ATTTAAT
40793830 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:40794653 original size:15 final size:16
Alignment explanation
Indices: 40794633--40794662 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40794623 CTTCCCTATT
40794633 TTCTA-TTTCTTTTAG
1 TTCTATTTTCTTTTAG
40794648 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
40794663 TTTGTAATTC
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:0.13, C:0.13, G:0.03, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAG
Found at i:40794673 original size:22 final size:21
Alignment explanation
Indices: 40794628--40794687 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
40794618 TTCGACTTCC
* *
40794628 CTATTTTCTATTTCTTTTAGTT
1 CTATTTTCT-TTTATTTTAATT
40794650 CTATTTTCTTTTATTTGTAATT
1 CTATTTTCTTTTATTT-TAATT
*
40794672 CT-GTTTCTTTTATTTT
1 CTATTTTCTTTTATTTT
40794688 TCCTTAGATC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.03
21 18 0.53
22 15 0.44
ACGTcount: A:0.13, C:0.12, G:0.05, T:0.70
Consensus pattern (21 bp):
CTATTTTCTTTTATTTTAATT
Found at i:40798476 original size:5 final size:5
Alignment explanation
Indices: 40798466--40798500 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
40798456 CCTTATTTCT
*
40798466 TTTTA TTTTA TTTTA TTTTA TTTTG TTTTAA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A TTTT
40798501 TATGATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:40807037 original size:143 final size:143
Alignment explanation
Indices: 40806810--40807098 Score: 578
Period size: 143 Copynumber: 2.0 Consensus size: 143
40806800 TTTTGTCTAA
40806810 TTAAATTTGCATTTATTATTTGTATTACAATTGTAATTGCAAACTCCTTAAAAAACAAAATTAAT
1 TTAAATTTGCATTTATTATTTGTATTACAATTGTAATTGCAAACTCCTTAAAAAACAAAATTAAT
40806875 GGAATTCAAGTTTTTACCTCTTGTTTAGAGGCTGTTCTGTTGGTATGTAACTTGCTTCTATGAAA
66 GGAATTCAAGTTTTTACCTCTTGTTTAGAGGCTGTTCTGTTGGTATGTAACTTGCTTCTATGAAA
40806940 TAAAGTATTTTGC
131 TAAAGTATTTTGC
40806953 TTAAATTTGCATTTATTATTTGTATTACAATTGTAATTGCAAACTCCTTAAAAAACAAAATTAAT
1 TTAAATTTGCATTTATTATTTGTATTACAATTGTAATTGCAAACTCCTTAAAAAACAAAATTAAT
40807018 GGAATTCAAGTTTTTACCTCTTGTTTAGAGGCTGTTCTGTTGGTATGTAACTTGCTTCTATGAAA
66 GGAATTCAAGTTTTTACCTCTTGTTTAGAGGCTGTTCTGTTGGTATGTAACTTGCTTCTATGAAA
40807083 TAAAGTATTTTGC
131 TAAAGTATTTTGC
40807096 TTA
1 TTA
40807099 CTTTTCAGAG
Statistics
Matches: 146, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
143 146 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (143 bp):
TTAAATTTGCATTTATTATTTGTATTACAATTGTAATTGCAAACTCCTTAAAAAACAAAATTAAT
GGAATTCAAGTTTTTACCTCTTGTTTAGAGGCTGTTCTGTTGGTATGTAACTTGCTTCTATGAAA
TAAAGTATTTTGC
Found at i:40815145 original size:21 final size:20
Alignment explanation
Indices: 40815099--40815145 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
40815089 GTATCGATCT
* *
40815099 GGTATCGATACTTTTTATAA
1 GGTATCGATAATTTTTACAA
*
40815119 GGTATCGATAATTTTGTACAG
1 GGTATCGATAATTTT-TACAA
40815140 GGTATC
1 GGTATC
40815146 AATTTTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (20 bp):
GGTATCGATAATTTTTACAA
Found at i:40823916 original size:27 final size:26
Alignment explanation
Indices: 40823872--40823929 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
40823862 AAACTAAACT
*
40823872 AAATTTTATAAAAATTAAAAACAAAA
1 AAATTTTAAAAAAATTAAAAACAAAA
* *
40823898 TAATTTTAAAATAAATTAAAAAGAAAA
1 AAATTTTAAAA-AAATTAAAAACAAAA
40823925 AAATT
1 AAATT
40823930 ACTCTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 9 0.33
27 18 0.67
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (26 bp):
AAATTTTAAAAAAATTAAAAACAAAA
Found at i:40825132 original size:17 final size:16
Alignment explanation
Indices: 40825087--40825145 Score: 55
Period size: 17 Copynumber: 3.6 Consensus size: 16
40825077 TTGATCAAAT
*
40825087 AATTATTATTTTTAAA
1 AATTTTTATTTTTAAA
*
40825103 AATTTCTATTTTTTAAA
1 AATTTTTA-TTTTTAAA
* *
40825120 AGTTTTTTATTTTTAAT
1 A-ATTTTTATTTTTAAA
*
40825137 TATTTTTAT
1 AATTTTTAT
40825146 GACACCTGTC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
16 13 0.38
17 16 0.47
18 5 0.15
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (16 bp):
AATTTTTATTTTTAAA
Found at i:40830900 original size:16 final size:17
Alignment explanation
Indices: 40830876--40830910 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
40830866 AATAGAGGAG
*
40830876 TTTACTTTTTTTTA-AT
1 TTTAATTTTTTTTATAT
40830892 TTTAATTTTTTTTATAT
1 TTTAATTTTTTTTATAT
40830909 TT
1 TT
40830911 GAAATTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTAATTTTTTTTATAT
Found at i:40831049 original size:14 final size:15
Alignment explanation
Indices: 40831030--40831062 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
40831020 AAAATAAATC
40831030 TTATTTTTA-ATTTT
1 TTATTTTTAGATTTT
40831044 TTA-TTTTAGATTTT
1 TTATTTTTAGATTTT
40831058 TTATT
1 TTATT
40831063 GTTTTATGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 5 0.29
14 11 0.65
15 1 0.06
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (15 bp):
TTATTTTTAGATTTT
Found at i:40832135 original size:19 final size:20
Alignment explanation
Indices: 40832108--40832154 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
40832098 TGTTCAATTG
**
40832108 AATAAATTAGTAA-AAATAA
1 AATAAATTAAAAATAAATAA
*
40832127 AATATATTAAAAATAAATAA
1 AATAAATTAAAAATAAATAA
*
40832147 AATCAATT
1 AATAAATT
40832155 CAACTGATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (20 bp):
AATAAATTAAAAATAAATAA
Found at i:40832144 original size:15 final size:15
Alignment explanation
Indices: 40832108--40832145 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
40832098 TGTTCAATTG
40832108 AATAAAT-TAGTAAA
1 AATAAATATAGTAAA
*
40832122 AATAAAATATATTAAA
1 AAT-AAATATAGTAAA
40832138 AATAAATA
1 AATAAATA
40832146 AAATCAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 3 0.14
15 9 0.43
16 9 0.43
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (15 bp):
AATAAATATAGTAAA
Found at i:40833456 original size:32 final size:32
Alignment explanation
Indices: 40833415--40833476 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
40833405 AAATATTCAG
* *
40833415 AATGAATTTGGTCAAATAATTGTCCAAATTTA
1 AATGAATTTGGACAAACAATTGTCCAAATTTA
*
40833447 AATGAATTTGGACAACCAATTGTCCAAATT
1 AATGAATTTGGACAAACAATTGTCCAAATT
40833477 CATTTTGCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (32 bp):
AATGAATTTGGACAAACAATTGTCCAAATTTA
Found at i:40834982 original size:25 final size:25
Alignment explanation
Indices: 40834944--40834991 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
40834934 TACCCACAGC
40834944 ACAAATAACTTTGATATTCCTATCA
1 ACAAATAACTTTGATATTCCTATCA
40834969 ACAAAT-ACTCTTGATATTCCTAT
1 ACAAATAACT-TTGATATTCCTAT
40834992 GAGCTACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 3 0.14
25 19 0.86
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.38
Consensus pattern (25 bp):
ACAAATAACTTTGATATTCCTATCA
Found at i:40840051 original size:3 final size:3
Alignment explanation
Indices: 40840043--40840069 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
40840033 CACCTACTAA
40840043 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
40840070 CCTCCATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:40844790 original size:16 final size:16
Alignment explanation
Indices: 40844762--40844826 Score: 57
Period size: 14 Copynumber: 4.0 Consensus size: 16
40844752 TTCATGGAAG
40844762 CTTTTT-TTT-TTTCT
1 CTTTTTCTTTCTTTCT
40844776 CTTTTT-TTTCCTTTCTT
1 CTTTTTCTTT-CTTTC-T
40844793 CCTTCTTTCTTTTCTTTCT
1 -CTT-TTTC-TTTCTTTCT
40844812 -TTTTTCTTTCTTTCT
1 CTTTTTCTTTCTTTCT
40844827 TCTCTCTCCT
Statistics
Matches: 44, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
14 9 0.20
15 9 0.20
16 8 0.18
17 3 0.07
18 3 0.07
19 4 0.09
20 5 0.11
21 3 0.07
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
CTTTTTCTTTCTTTCT
Found at i:40844800 original size:11 final size:11
Alignment explanation
Indices: 40844786--40844844 Score: 61
Period size: 11 Copynumber: 5.6 Consensus size: 11
40844776 CTTTTTTTTC
40844786 CTTTCTTCCTT
1 CTTTCTTCCTT
40844797 CTTTCTT--TT
1 CTTTCTTCCTT
**
40844806 CTTTCTTTTTT
1 CTTTCTTCCTT
*
40844817 CTTTCTTTCTT
1 CTTTCTTCCTT
*
40844828 CTCTC-TCCTT
1 CTTTCTTCCTT
40844838 CTTTCTT
1 CTTTCTT
40844845 TCCTCTGCTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
9 9 0.22
10 8 0.20
11 24 0.59
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (11 bp):
CTTTCTTCCTT
Found at i:40844802 original size:4 final size:4
Alignment explanation
Indices: 40844786--40844846 Score: 63
Period size: 4 Copynumber: 15.2 Consensus size: 4
40844776 CTTTTTTTTC
* *
40844786 CTTT C-TT CCTT CTTT CTTTT CTTT CTTT -TTT CTTT CTTT CTTCT CTCT
1 CTTT CTTT CTTT CTTT C-TTT CTTT CTTT CTTT CTTT CTTT CTT-T CTTT
*
40844834 CCTT CTTT CTTT C
1 CTTT CTTT CTTT C
40844847 CTCTGCTTCC
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
3 6 0.12
4 35 0.73
5 7 0.15
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
CTTT
Found at i:40844805 original size:24 final size:24
Alignment explanation
Indices: 40844775--40844827 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
40844765 TTTTTTTTTC
*
40844775 TCTTTTTTTTCCTTTCTTCCTTCTT
1 TCTTTTCTTT-CTTTCTTCCTTCTT
* *
40844800 TCTTTTCTTTCTTTTTTCTTTCTT
1 TCTTTTCTTTCTTTCTTCCTTCTT
40844824 TCTT
1 TCTT
40844828 CTCTCTCCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (24 bp):
TCTTTTCTTTCTTTCTTCCTTCTT
Found at i:40844815 original size:32 final size:31
Alignment explanation
Indices: 40844770--40844845 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 31
40844760 AGCTTTTTTT
*
40844770 TTTTCTCTT-TTTTTTCCTTTCTTCCTTCTTTC
1 TTTTCT-TTCTTTTTT-CTTTCTTCCTTCTCTC
*
40844802 TTTTCTTTCTTTTTTCTTTCTTTCTTCTCTC
1 TTTTCTTTCTTTTTTCTTTCTTCCTTCTCTC
*
40844833 TCCTTCTTTCTTT
1 T-TTTCTTTCTTT
40844846 CCTCTGCTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
31 17 0.44
32 22 0.56
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (31 bp):
TTTTCTTTCTTTTTTCTTTCTTCCTTCTCTC
Found at i:40845872 original size:33 final size:33
Alignment explanation
Indices: 40845830--40845897 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
40845820 AACAAATACC
40845830 TATATTTGGAGTTCTCCAAAGGATGATGTGATG
1 TATATTTGGAGTTCTCCAAAGGATGATGTGATG
40845863 TATATTTGGAGTTCTCCAAAGGATGATGTGATG
1 TATATTTGGAGTTCTCCAAAGGATGATGTGATG
40845896 TA
1 TA
40845898 ATGAGAGGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.28, C:0.09, G:0.26, T:0.37
Consensus pattern (33 bp):
TATATTTGGAGTTCTCCAAAGGATGATGTGATG
Found at i:40850710 original size:37 final size:37
Alignment explanation
Indices: 40850643--40850756 Score: 104
Period size: 40 Copynumber: 3.0 Consensus size: 37
40850633 GTGTCATTAT
* * *
40850643 TTTACTTCGGATAGATTCGATGAGGTACTGGGTACCAC
1 TTTACTTCGGCTAGA-CCGATGAGGCACTGGGTACCAC
* **
40850681 TTTACTTCGGCTAGACCGATGAGACACTGGGTGTCAC
1 TTTACTTCGGCTAGACCGATGAGGCACTGGGTACCAC
* *
40850718 TTTATTGCTTCGAACTA-TCCGATGAGGCACTGGGTACCA
1 TTTA---CTTCG-GCTAGACCGATGAGGCACTGGGTACCA
40850757 TTCTGGTGTG
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
37 21 0.34
38 14 0.23
40 23 0.38
41 3 0.05
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (37 bp):
TTTACTTCGGCTAGACCGATGAGGCACTGGGTACCAC
Found at i:40852583 original size:24 final size:24
Alignment explanation
Indices: 40852554--40852604 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
40852544 AGAAATAATC
40852554 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
40852578 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
40852602 TTT
1 TTT
40852605 GAGTCAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:40852613 original size:24 final size:24
Alignment explanation
Indices: 40852554--40852616 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
40852544 AGAAATAATC
*
40852554 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATCAAACTCTGTTTATTTG
*
40852578 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATCAAACTCTGTTTATTTG
* *
40852602 TTTGAGTCAAACTCT
1 TTTCAATCAAACTCT
40852617 TATTAGTCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (24 bp):
TTTCAATCAAACTCTGTTTATTTG
Found at i:40853014 original size:22 final size:22
Alignment explanation
Indices: 40852971--40853018 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
40852961 GGTATCAGAG
*
40852971 TAAAATAAAATACAGTGATAAA
1 TAAAATAAAATAAAGTGATAAA
*
40852993 TAAAATAAAAGTAAAGT-CTAAA
1 TAAAATAAAA-TAAAGTGATAAA
40853015 TAAA
1 TAAA
40853019 CTAGAGTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.65, C:0.04, G:0.08, T:0.23
Consensus pattern (22 bp):
TAAAATAAAATAAAGTGATAAA
Found at i:40853720 original size:30 final size:30
Alignment explanation
Indices: 40853685--40853743 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
40853675 CAATAAGTTA
40853685 TTAATTGAAAAATTA-CAATCAATTGAGCTC
1 TTAATT-AAAAATTAGCAATCAATTGAGCTC
*
40853715 TTAATTAAAAGTTAGCAATCAATTGAGCT
1 TTAATTAAAAATTAGCAATCAATTGAGCT
40853744 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (30 bp):
TTAATTAAAAATTAGCAATCAATTGAGCTC
Found at i:40858019 original size:29 final size:29
Alignment explanation
Indices: 40857953--40858025 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
40857943 GGGCTTTTTT
* * *
40857953 TATAAAATTAATCTATTTTTTTAATTAAT
1 TATAAAAATAATCTATTTCTTTAATTAAA
* * * *
40857982 TACATAAATAATTTATTTCTTTGATTAAA
1 TATAAAAATAATCTATTTCTTTAATTAAA
40858011 TATAAAAATAATCTA
1 TATAAAAATAATCTA
40858026 AAATCTACAG
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.48
Consensus pattern (29 bp):
TATAAAAATAATCTATTTCTTTAATTAAA
Found at i:40858896 original size:28 final size:28
Alignment explanation
Indices: 40858864--40858920 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
40858854 CTGTAAATTT
* * *
40858864 TAAATTATTTTCGTATTTAATAAAAAAA
1 TAAATTATTTACCTAATTAATAAAAAAA
*
40858892 TAAATTATTTACCTAATTAATTAAAAAA
1 TAAATTATTTACCTAATTAATAAAAAAA
40858920 T
1 T
40858921 GGGTTAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (28 bp):
TAAATTATTTACCTAATTAATAAAAAAA
Found at i:40863867 original size:18 final size:18
Alignment explanation
Indices: 40863834--40863871 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
40863824 GAAAATTATG
40863834 TATTTAAAATATAAAACTA
1 TATTTAAAATATAAAA-TA
40863853 TATTTAAAA-ATAAAATA
1 TATTTAAAATATAAAATA
40863870 TA
1 TA
40863872 ATAACAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.21
18 6 0.32
19 9 0.47
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
TATTTAAAATATAAAATA
Found at i:40870426 original size:25 final size:25
Alignment explanation
Indices: 40870392--40870442 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
40870382 TAAATAAAGT
40870392 TAGTCACTAAATTTGACATATTTAC
1 TAGTCACTAAATTTGACATATTTAC
40870417 TAGTCACTAAATTTGACATATTTAC
1 TAGTCACTAAATTTGACATATTTAC
40870442 T
1 T
40870443 TTTAATACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (25 bp):
TAGTCACTAAATTTGACATATTTAC
Found at i:40871621 original size:9 final size:9
Alignment explanation
Indices: 40871607--40871633 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
40871597 GAAACATTTA
40871607 TTTTAATAT
1 TTTTAATAT
40871616 TTTTAATAT
1 TTTTAATAT
40871625 TTTTAATAT
1 TTTTAATAT
40871634 AGTATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTAATAT
Found at i:40871651 original size:25 final size:26
Alignment explanation
Indices: 40871612--40871660 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
40871602 ATTTATTTTA
* * *
40871612 ATATTTTTAATATTTTTA-ATATAGT
1 ATATTTTCAAAATTTATATATATAGT
40871637 ATATTTTCAAAATTTATATATATA
1 ATATTTTCAAAATTTATATATATA
40871661 TAGAAATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (26 bp):
ATATTTTCAAAATTTATATATATAGT
Found at i:40881096 original size:24 final size:24
Alignment explanation
Indices: 40881069--40881158 Score: 126
Period size: 24 Copynumber: 3.8 Consensus size: 24
40881059 CAGACAATAT
* *
40881069 TTAGCTCTTACGAGCCTAGAACGG
1 TTAGCTCCTACGAGCCCAGAACGG
*
40881093 TTAGCTCCTACGAGCCCAAAACGG
1 TTAGCTCCTACGAGCCCAGAACGG
*
40881117 TTAGCTCCTACGAGCCCAGAATGG
1 TTAGCTCCTACGAGCCCAGAACGG
* *
40881141 TTAGCTCTTACAAGCCCA
1 TTAGCTCCTACGAGCCCA
40881159 AAATTAGAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.22
Consensus pattern (24 bp):
TTAGCTCCTACGAGCCCAGAACGG
Found at i:40881143 original size:48 final size:48
Alignment explanation
Indices: 40881069--40881161 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
40881059 CAGACAATAT
* * *
40881069 TTAGCTCTTACGAGCCTAGAACGGTTAGCTCCTACGAGCCCAAAACGG
1 TTAGCTCCTACGAGCCCAGAACGGTTAGCTCCTACAAGCCCAAAACGG
* *
40881117 TTAGCTCCTACGAGCCCAGAATGGTTAGCTCTTACAAGCCCAAAA
1 TTAGCTCCTACGAGCCCAGAACGGTTAGCTCCTACAAGCCCAAAA
40881162 TTAGAATAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (48 bp):
TTAGCTCCTACGAGCCCAGAACGGTTAGCTCCTACAAGCCCAAAACGG
Found at i:40881176 original size:28 final size:26
Alignment explanation
Indices: 40881144--40881247 Score: 82
Period size: 27 Copynumber: 3.8 Consensus size: 26
40881134 AGAATGGTTA
*
40881144 GCTCTTACAAGCCCAAAATTAGAATAAC
1 GCTCTT-CAAG-CCAAAATCAGAATAAC
* *
40881172 GCTCTTTAAGCCAGAATCAGAATAAC
1 GCTCTTCAAGCCAAAATCAGAATAAC
** * *
40881198 GCTCTTTTGAGCCAGAATCAAAATAAC
1 GCTC-TTCAAGCCAAAATCAGAATAAC
**
40881225 GCTCTCTTTGAGCCAAAATCAGA
1 G--CTCTTCAAGCCAAAATCAGA
40881248 TTACTCCTCA
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
26 18 0.27
27 24 0.36
28 21 0.32
29 3 0.05
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (26 bp):
GCTCTTCAAGCCAAAATCAGAATAAC
Found at i:40881222 original size:27 final size:27
Alignment explanation
Indices: 40881166--40881245 Score: 117
Period size: 27 Copynumber: 3.0 Consensus size: 27
40881156 CCAAAATTAG
* *
40881166 AATAACGCTC-TTTAAGCCAGAATCAG
1 AATAACGCTCTTTTGAGCCAGAATCAA
40881192 AATAACGCTCTTTTGAGCCAGAATCAA
1 AATAACGCTCTTTTGAGCCAGAATCAA
*
40881219 AATAACGCTCTCTTTGAGCCAAAATCA
1 AATAACGCTCT-TTTGAGCCAGAATCA
40881246 GATTACTCCT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
26 10 0.20
27 25 0.51
28 14 0.29
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.25
Consensus pattern (27 bp):
AATAACGCTCTTTTGAGCCAGAATCAA
Found at i:40885307 original size:24 final size:24
Alignment explanation
Indices: 40885288--40885445 Score: 217
Period size: 24 Copynumber: 6.6 Consensus size: 24
40885278 ATTTAGCCCA
40885288 TACGAGCCCAGAATGGTTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCT
* *
40885312 TACGAGCCCAGAATAGTTAGCTCC
1 TACGAGCCCAGAATGGTTAGCTCT
* * * *
40885336 TATGAGCCTAGAACGGTTAGCTCC
1 TACGAGCCCAGAATGGTTAGCTCT
*
40885360 TACGAGCCCAGAACGGTTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCT
*
40885384 TACGAGCCCAAAATGGTTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCT
* *
40885408 TACGAGCCTAAAATGGTTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCT
*
40885432 TACGAGCCTAGAAT
1 TACGAGCCCAGAAT
40885446 CAGAATAATG
Statistics
Matches: 121, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 121 1.00
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.24
Consensus pattern (24 bp):
TACGAGCCCAGAATGGTTAGCTCT
Found at i:40885489 original size:27 final size:27
Alignment explanation
Indices: 40885439--40885530 Score: 107
Period size: 27 Copynumber: 3.4 Consensus size: 27
40885429 TCTTACGAGC
*
40885439 CTAGAATCAGAATAATGCTC-TTTGAG
1 CTAGAATCAGAATAACGCTCTTTTGAG
40885465 CTAGAATCAGAATAACGCTCTTTTGAG
1 CTAGAATCAGAATAACGCTCTTTTGAG
** * *
40885492 CCGGAATCAAAATAACGCTCTCTTTAAG
1 CTAGAATCAGAATAACGCTCT-TTTGAG
40885520 -TCAGAATCAGA
1 CT-AGAATCAGA
40885531 TTACTCCTCA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
26 19 0.35
27 24 0.44
28 12 0.22
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (27 bp):
CTAGAATCAGAATAACGCTCTTTTGAG
Found at i:40888938 original size:107 final size:107
Alignment explanation
Indices: 40888743--40888982 Score: 410
Period size: 107 Copynumber: 2.2 Consensus size: 107
40888733 TTGCGAGTCC
*
40888743 TCGACAGCTCGTGTGAGCAACATCGTGAGTCAGAAAAATGAGAAATAAATCCAAGAATGGATTAT
1 TCGACAGCTCGTGTGAGCAACATCGTGAGTAAGAAAAATGAGAAATAAATCCAAGAATGGATTAT
*
40888808 GAGCCCTACGATGGTTGGAAAATTATGCATAAGTGCATATTA
66 GAGCCCTACGATGGCTGGAAAATTATGCATAAGTGCATATTA
*
40888850 TC-AGCAGCTCGTGTGAGCAACATCGTGAGTAAGAAAAATGAGAAATAAATCCAAGAATGTATTA
1 TCGA-CAGCTCGTGTGAGCAACATCGTGAGTAAGAAAAATGAGAAATAAATCCAAGAATGGATTA
*
40888914 TGAGCCCTACGATGGCTGGGAAATTATGCATAAGTGCATATTA
65 TGAGCCCTACGATGGCTGGAAAATTATGCATAAGTGCATATTA
* *
40888957 TCGACAGCTCGTGTAAGCAGCATCGT
1 TCGACAGCTCGTGTGAGCAACATCGT
40888983 TAGAGAACAA
Statistics
Matches: 125, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
106 1 0.01
107 123 0.98
108 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (107 bp):
TCGACAGCTCGTGTGAGCAACATCGTGAGTAAGAAAAATGAGAAATAAATCCAAGAATGGATTAT
GAGCCCTACGATGGCTGGAAAATTATGCATAAGTGCATATTA
Found at i:40890131 original size:21 final size:21
Alignment explanation
Indices: 40890105--40890151 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
40890095 CATAACTATT
40890105 GATACTTGCAATTCAACCACC
1 GATACTTGCAATTCAACCACC
*
40890126 GATACTTGCAATTCAACTACC
1 GATACTTGCAATTCAACCACC
40890147 GATAC
1 GATAC
40890152 AACCCAAGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.30, G:0.11, T:0.26
Consensus pattern (21 bp):
GATACTTGCAATTCAACCACC
Found at i:40897216 original size:29 final size:29
Alignment explanation
Indices: 40897097--40897209 Score: 136
Period size: 29 Copynumber: 3.9 Consensus size: 29
40897087 AGTGACTGGG
* * *
40897097 GTATCGTGTCTGCATCTGTAACTGTATTT
1 GTATCATGTTTGCATCTGTAACTGTATCT
* *
40897126 GTATCATATTTGTATCTGTAACTGTATCT
1 GTATCATGTTTGCATCTGTAACTGTATCT
* * * *
40897155 ATATCATGTTTGCATTTGTAATTATATCT
1 GTATCATGTTTGCATCTGTAACTGTATCT
*
40897184 GTATCATGTTCGCATCTGTAACTGTA
1 GTATCATGTTTGCATCTGTAACTGTA
40897210 CCCGTATTAT
Statistics
Matches: 68, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 68 1.00
ACGTcount: A:0.23, C:0.15, G:0.16, T:0.46
Consensus pattern (29 bp):
GTATCATGTTTGCATCTGTAACTGTATCT
Found at i:40901119 original size:33 final size:32
Alignment explanation
Indices: 40901071--40901246 Score: 165
Period size: 33 Copynumber: 5.3 Consensus size: 32
40901061 AGTGTATATA
*
40901071 GATGTAAGACCATAGCTGGGGTATGGCATTTT
1 GATGTAAGACCATAGCTGGGCTATGGCATTTT
*
40901103 GATGTTAAGACTATAGCT-GGCTATGGCATTTT
1 GATG-TAAGACCATAGCTGGGCTATGGCATTTT
* * * * * *
40901135 GACGTAAGACCATGGTTGGACCATGACAGTGTATTT
1 GATGTAAGACCATAGCTGGGCTATGGCA---T-TTT
40901171 AGATGTAAGACCATAGCTGGGCTATGGCATTTT
1 -GATGTAAGACCATAGCTGGGCTATGGCATTTT
* * * *
40901204 GATGTTAAGACCATAACTGGGTTTTGGCATTAT
1 GATG-TAAGACCATAGCTGGGCTATGGCATTTT
40901237 GAATGTAAGA
1 G-ATGTAAGA
40901247 TCACGGTTAA
Statistics
Matches: 116, Mismatches: 19, Indels: 17
0.76 0.12 0.11
Matches are distributed among these distances:
31 10 0.09
32 31 0.27
33 45 0.39
34 4 0.03
35 1 0.01
36 3 0.03
37 22 0.19
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.32
Consensus pattern (32 bp):
GATGTAAGACCATAGCTGGGCTATGGCATTTT
Found at i:40901202 original size:101 final size:101
Alignment explanation
Indices: 40901027--40901223 Score: 331
Period size: 101 Copynumber: 2.0 Consensus size: 101
40901017 GAGACAGGCT
* * *
40901027 GCATTCTGACGTAAGACCGTGGTTGGACCATGGCAGTGTATATAGATGTAAGACCATAGCTGGGG
1 GCATTCTGACGTAAGACCATGGTTGGACCATGACAGTGTATATAGATGTAAGACCATAGCTGGGC
* *
40901092 TATGGCATTTTGATGTTAAGACTATAGCTGGCTATG
66 TATGGCATTTTGATGTTAAGACCATAACTGGCTATG
* *
40901128 GCATTTTGACGTAAGACCATGGTTGGACCATGACAGTGTATTTAGATGTAAGACCATAGCTGGGC
1 GCATTCTGACGTAAGACCATGGTTGGACCATGACAGTGTATATAGATGTAAGACCATAGCTGGGC
40901193 TATGGCATTTTGATGTTAAGACCATAACTGG
66 TATGGCATTTTGATGTTAAGACCATAACTGG
40901224 GTTTTGGCAT
Statistics
Matches: 89, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 89 1.00
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (101 bp):
GCATTCTGACGTAAGACCATGGTTGGACCATGACAGTGTATATAGATGTAAGACCATAGCTGGGC
TATGGCATTTTGATGTTAAGACCATAACTGGCTATG
Found at i:40902126 original size:46 final size:46
Alignment explanation
Indices: 40902059--40902153 Score: 174
Period size: 46 Copynumber: 2.1 Consensus size: 46
40902049 TATAAGTTTT
40902059 TAAGGTATCAGTATTCTGAACACTTGTAT-AGGTAGAAGCTACAGGG
1 TAAGGTATCAGTATTCTGAACACTTGTATCA-GTAGAAGCTACAGGG
40902105 TAAGGTATCAGTATTCTGAACACTTGTATCAGTAGAAGCTACAGGG
1 TAAGGTATCAGTATTCTGAACACTTGTATCAGTAGAAGCTACAGGG
40902151 TAA
1 TAA
40902154 AACGTCTGAG
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 47 0.98
47 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (46 bp):
TAAGGTATCAGTATTCTGAACACTTGTATCAGTAGAAGCTACAGGG
Found at i:40902202 original size:21 final size:21
Alignment explanation
Indices: 40902178--40902233 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
40902168 CTAAAGTTTG
40902178 TTGTTTCGGTAGAAGTAACAA
1 TTGTTTCGGTAGAAGTAACAA
* * * *
40902199 TTGTATT-GGTAGTAGTGATAC
1 TTGT-TTCGGTAGAAGTAACAA
*
40902220 TTGTATCGGTAGAA
1 TTGTTTCGGTAGAA
40902234 CCTTCCCAAC
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
20 1 0.04
21 24 0.89
22 2 0.07
ACGTcount: A:0.29, C:0.07, G:0.27, T:0.38
Consensus pattern (21 bp):
TTGTTTCGGTAGAAGTAACAA
Found at i:40905388 original size:24 final size:25
Alignment explanation
Indices: 40905275--40905379 Score: 185
Period size: 25 Copynumber: 4.2 Consensus size: 25
40905265 CTCTGTTTGA
*
40905275 GCTCGTAAGAGCTAACCAATTATGG
1 GCTCGTAAGAGCTAACCAATTCTGG
40905300 GCTCGTAAGAGCTAACCAATTCTGG
1 GCTCGTAAGAGCTAACCAATTCTGG
40905325 GCTCGTAAGAGCTAACCAATTCTGG
1 GCTCGTAAGAGCTAACCAATTCTGG
*
40905350 GCTCGTAAGAGCTAACC-ATTCTAG
1 GCTCGTAAGAGCTAACCAATTCTGG
40905374 GCTCGT
1 GCTCGT
40905380 GTGGGCTAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
24 12 0.15
25 66 0.85
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.25
Consensus pattern (25 bp):
GCTCGTAAGAGCTAACCAATTCTGG
Found at i:40907320 original size:19 final size:20
Alignment explanation
Indices: 40907293--40907339 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
40907283 TCTTCAATTG
**
40907293 AATAAATTATTAA-AAATAA
1 AATAAATTAAAAATAAATAA
*
40907312 AATACATTAAAAATAAATAA
1 AATAAATTAAAAATAAATAA
*
40907332 AATTAATT
1 AATAAATT
40907340 CAACCAATCT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
AATAAATTAAAAATAAATAA
Found at i:40907378 original size:16 final size:16
Alignment explanation
Indices: 40907353--40907385 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
40907343 CCAATCTGAT
*
40907353 TGATCGATCAATTTAA
1 TGATCAATCAATTTAA
40907369 TGATCAATCAATTTAA
1 TGATCAATCAATTTAA
40907385 T
1 T
40907386 CCCTTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (16 bp):
TGATCAATCAATTTAA
Done.