Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 22 of 126
Found at i:6458320 original size:16 final size:16
Alignment explanation
Indices: 6458301--6458371 Score: 70
Period size: 16 Copynumber: 4.4 Consensus size: 16
6458291 TATACATATC
6458301 TATACATATATATCTA
1 TATACATATATATCTA
* * * *
6458317 TATACATTTTTTTCCA
1 TATACATATATATCTA
* * *
6458333 TATACATTTTTTTCTA
1 TATACATATATATCTA
*
6458349 TATAGATATATATCTA
1 TATACATATATATCTA
6458365 TATACAT
1 TATACAT
6458372 TTTTTTCTTC
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.35, C:0.13, G:0.01, T:0.51
Consensus pattern (16 bp):
TATACATATATATCTA
Found at i:6458349 original size:32 final size:32
Alignment explanation
Indices: 6458313--6458379 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
6458303 TACATATATA
* * *
6458313 TCTATATACATTTTTTTCCATATACATTTTTT
1 TCTATATACATATATATCCATATACATTTTTT
* *
6458345 TCTATATAGATATATATCTATATACATTTTTT
1 TCTATATACATATATATCCATATACATTTTTT
6458377 TCT
1 TCT
6458380 TCCTGTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.28, C:0.13, G:0.01, T:0.57
Consensus pattern (32 bp):
TCTATATACATATATATCCATATACATTTTTT
Found at i:6458350 original size:14 final size:16
Alignment explanation
Indices: 6458316--6458378 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
6458306 ATATATATCT
6458316 ATATACATTTTTTTCC
1 ATATACATTTTTTTCC
*
6458332 ATATACATTTTTTTCT
1 ATATACATTTTTTTCC
* * * * *
6458348 ATATAGATATATATCT
1 ATATACATTTTTTTCC
6458364 ATATACATTTTTTTC
1 ATATACATTTTTTTC
6458379 TTCCTGTTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.30, C:0.13, G:0.02, T:0.56
Consensus pattern (16 bp):
ATATACATTTTTTTCC
Found at i:6458476 original size:20 final size:19
Alignment explanation
Indices: 6458453--6458497 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
6458443 AATACCTTCA
6458453 TATATATATATTATATATTT
1 TATATATA-ATTATATATTT
* *
6458473 TATATGTACTTATATATTT
1 TATATATAATTATATATTT
6458492 TCATAT
1 T-ATAT
6458498 TTTATAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (19 bp):
TATATATAATTATATATTT
Found at i:6458532 original size:12 final size:12
Alignment explanation
Indices: 6458517--6458550 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6458507 TTTTTATCTA
6458517 TTTTATTTATTT
1 TTTTATTTATTT
6458529 TTTTATTTATTT
1 TTTTATTTATTT
**
6458541 AATTATTTAT
1 TTTTATTTAT
6458551 ATGTCCATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTATTTATTT
Found at i:6464878 original size:30 final size:28
Alignment explanation
Indices: 6464834--6464935 Score: 114
Period size: 30 Copynumber: 3.4 Consensus size: 28
6464824 GGTCAATCTA
6464834 TAATTTTAAGAAAGTTTAGGGTTTAAAAATG
1 TAATTTTAA-AAAGTTTAGGG-TT-AAAATG
* * * *
6464865 AAATTTTGAAAAGTTGAGGGGTCAAAATG
1 TAATTTTAAAAAGTTTA-GGGTTAAAATG
6464894 TAATTTTAGAAAAGTTTAGAGGTTAAAATG
1 TAATTTTA-AAAAGTTTAG-GGTTAAAATG
6464924 TAATTTTAAAAA
1 TAATTTTAAAAA
6464936 AATAAAATTT
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
29 17 0.28
30 33 0.55
31 10 0.17
ACGTcount: A:0.44, C:0.01, G:0.20, T:0.35
Consensus pattern (28 bp):
TAATTTTAAAAAGTTTAGGGTTAAAATG
Found at i:6464923 original size:59 final size:60
Alignment explanation
Indices: 6464800--6464935 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 60
6464790 TTTAGGTGTC
* * **
6464800 AAATGAAAATTTTG-GAAGTTTAGGGGTCAATCTATAATTTTAAGAAAGTTTAGGGTTTAA
1 AAATG-AAATTTTGAAAAGTTGAGGGGTCAAAATATAATTTTAAGAAAGTTTAGGGTTTAA
*
6464860 AAATGAAATTTTGAAAAGTTGAGGGGTCAAAATGTAATTTT-AGAAAAGTTTAGAGG-TT-A
1 AAATGAAATTTTGAAAAGTTGAGGGGTCAAAATATAATTTTAAG-AAAGTTTAG-GGTTTAA
* *
6464919 AAATGTAATTTTAAAAA
1 AAATGAAATTTTGAAAA
6464936 AATAAAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
59 26 0.39
60 38 0.58
61 2 0.03
ACGTcount: A:0.43, C:0.02, G:0.21, T:0.35
Consensus pattern (60 bp):
AAATGAAATTTTGAAAAGTTGAGGGGTCAAAATATAATTTTAAGAAAGTTTAGGGTTTAA
Found at i:6468669 original size:18 final size:18
Alignment explanation
Indices: 6468642--6468694 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
6468632 TGCATGCATC
* *
6468642 ATGCATGCTCTTTGTTTG
1 ATGCATGCTCCTTGTTTA
* *
6468660 ATGCACGCTCCGTGTTTA
1 ATGCATGCTCCTTGTTTA
6468678 ATGCATGCTCCTTGTTT
1 ATGCATGCTCCTTGTTT
6468695 CTTACAATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.43
Consensus pattern (18 bp):
ATGCATGCTCCTTGTTTA
Found at i:6473357 original size:16 final size:16
Alignment explanation
Indices: 6473326--6473364 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
6473316 TGTTGTTTAG
*
6473326 TAGAATAACTCATGTT
1 TAGAACAACTCATGTT
* *
6473342 TGGAACAACTCGTGTT
1 TAGAACAACTCATGTT
6473358 TAGAACA
1 TAGAACA
6473365 CTCTTTGTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (16 bp):
TAGAACAACTCATGTT
Found at i:6489327 original size:23 final size:23
Alignment explanation
Indices: 6489283--6489327 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
6489273 TTTTAAAAAA
* *
6489283 ATATGTTTTTTAATTGATATTTT
1 ATATATTTTTTAATTGAAATTTT
6489306 ATATATTTTTATAATT-AAATTT
1 ATATATTTTT-TAATTGAAATTT
6489328 ACATAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (23 bp):
ATATATTTTTTAATTGAAATTTT
Found at i:6490716 original size:11 final size:11
Alignment explanation
Indices: 6490700--6490754 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
6490690 ATAATTATAC
6490700 AAAATTATTTA
1 AAAATTATTTA
6490711 AAAATTA--TA
1 AAAATTATTTA
6490720 AAAA-TATATT-
1 AAAATTAT-TTA
*
6490730 AACATTATTTA
1 AAAATTATTTA
6490741 AAAATTA-TTA
1 AAAATTATTTA
6490751 AAAA
1 AAAA
6490755 GAATATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
8 2 0.05
9 6 0.16
10 12 0.32
11 17 0.46
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAATTATTTA
Found at i:6490716 original size:21 final size:21
Alignment explanation
Indices: 6490686--6490729 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
6490676 CCGCTGGTTT
*
6490686 TTTAATAATTATACAAAAT-TA
1 TTTAAAAATTATA-AAAATATA
6490707 TTTAAAAATTATAAAAATATA
1 TTTAAAAATTATAAAAATATA
6490728 TT
1 TT
6490730 AACATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTAAAAATTATAAAAATATA
Found at i:6490928 original size:20 final size:20
Alignment explanation
Indices: 6490903--6490944 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
6490893 TATCTATTTG
*
6490903 AATTAT-AAGAAATTGTAAAA
1 AATTATCAAG-AATTATAAAA
6490923 AATTATCAAGAATTATAAAA
1 AATTATCAAGAATTATAAAA
6490943 AA
1 AA
6490945 AAAAGTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (20 bp):
AATTATCAAGAATTATAAAA
Found at i:6492804 original size:25 final size:24
Alignment explanation
Indices: 6492767--6492818 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
6492757 AATGGAAAAG
*
6492767 AAAAAAGACAAAA-AAAAGAAAGTT
1 AAAAAAGACAAAAGAAAA-AAAATT
*
6492791 AAAAAAGCATAAAAGAAAAAAAATT
1 AAAAAAG-ACAAAAGAAAAAAAATT
6492816 AAA
1 AAA
6492819 TTGCTCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
25 13 0.54
26 4 0.17
ACGTcount: A:0.77, C:0.04, G:0.10, T:0.10
Consensus pattern (24 bp):
AAAAAAGACAAAAGAAAAAAAATT
Found at i:6514904 original size:21 final size:21
Alignment explanation
Indices: 6514878--6514918 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6514868 ATCTGCTCAA
* *
6514878 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
6514899 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
6514919 TTACTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:6517875 original size:15 final size:15
Alignment explanation
Indices: 6517857--6517899 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
6517847 ATAATATTTT
*
6517857 AAATATAAGTGAATA
1 AAATATAAGTGAAAA
*
6517872 AAATATAATCTGAAAA
1 AAATATAA-GTGAAAA
*
6517888 AAATAAAAGTGA
1 AAATATAAGTGA
6517900 CTTTTTGGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.23
Consensus pattern (15 bp):
AAATATAAGTGAAAA
Found at i:6525474 original size:43 final size:42
Alignment explanation
Indices: 6525407--6525563 Score: 145
Period size: 43 Copynumber: 3.7 Consensus size: 42
6525397 CTCGTACAAT
* ** * *
6525407 GCCAACATCCCAGATGTGGTCTTACATGTAATCAAATAACGAT
1 GCCAATATCCCAGACATGGTCTTACACGTAATCAAAT-ACGAC
* * *
6525450 GTCACTATCCCAGACATGGTCTTACACGTAATCATATACGAC
1 GCCAATATCCCAGACATGGTCTTACACGTAATCAAATACGAC
* * *
6525492 GCCAATGTCCCAGACATGGTATTACACGTAAATCTCAAAT-CGAT
1 GCCAATATCCCAGACATGGTCTTACACGT-AA--TCAAATACGAC
** *
6525536 GCCAACGTCCCAGACGTGGTCTTACACG
1 GCCAATATCCCAGACATGGTCTTACACG
6525564 ATATCACATT
Statistics
Matches: 94, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
42 29 0.31
43 32 0.34
44 28 0.30
45 5 0.05
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (42 bp):
GCCAATATCCCAGACATGGTCTTACACGTAATCAAATACGAC
Found at i:6525517 original size:42 final size:44
Alignment explanation
Indices: 6525457--6525563 Score: 139
Period size: 44 Copynumber: 2.5 Consensus size: 44
6525447 GATGTCACTA
* *
6525457 TCCCAGACATGGTCTTACACGT-AA--TCATATACGACGCCAATG
1 TCCCAGACATGGTCTTACACGTAAATCTCAAAT-CGACGCCAACG
* *
6525499 TCCCAGACATGGTATTACACGTAAATCTCAAATCGATGCCAACG
1 TCCCAGACATGGTCTTACACGTAAATCTCAAATCGACGCCAACG
*
6525543 TCCCAGACGTGGTCTTACACG
1 TCCCAGACATGGTCTTACACG
6525564 ATATCACATT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
42 21 0.38
43 2 0.04
44 28 0.50
45 5 0.09
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (44 bp):
TCCCAGACATGGTCTTACACGTAAATCTCAAATCGACGCCAACG
Found at i:6527901 original size:215 final size:215
Alignment explanation
Indices: 6527530--6527961 Score: 756
Period size: 215 Copynumber: 2.0 Consensus size: 215
6527520 TGGTCCTTCC
* *
6527530 ATACTGGCTCATGCATCTATGCCCTTAACCTACTGGAATGATGCCTTTAGTAGTGCAGTATACTT
1 ATACTGGCTCATGCATCTATGCCCTTAACCTACTGGAATGATACCTTCAGTAGTGCAGTATACTT
*
6527595 CATAAACAGGTTACCTTATTTTCCTTTAGGCAACATCTCACCGTATGAAAAACTCTTTCAGCTTC
66 CATAAACAGGTTACCTTATTTTCCCTTAGGCAACATCTCACCGTATGAAAAACTCTTTCAGCTTC
*
6527660 AACCAAGCTATTCATCTCTTCGAGTTTTTGGCTACTTGTGCTTTCCCAATCTTAGACCCTACAAC
131 AACCAAGCTATTCATATCTTCGAGTTTTTGGCTACTTGTGCTTTCCCAATCTTAGACCCTACAAC
*
6527725 ACCCATAAGCTACAGTTTCG
196 ACCCATAAACTACAGTTTCG
6527745 ATACTGGCTCATGCATCTATGCCCTTAACCTACTGGAATGATACCTTCAGTAGTGCAGTATACTT
1 ATACTGGCTCATGCATCTATGCCCTTAACCTACTGGAATGATACCTTCAGTAGTGCAGTATACTT
* * * * * *
6527810 GATAAACAGTTTGCCTTATTTTCCCTTAGGCAACATCTCACCGTATGAAAAGCTCTTTTAGGTTC
66 CATAAACAGGTTACCTTATTTTCCCTTAGGCAACATCTCACCGTATGAAAAACTCTTTCAGCTTC
6527875 AACCAAGCTATTCATATCTTCGAGTTTTTGGCTACTTGTGCTTTCCCAATCTTAGACCCTACAAC
131 AACCAAGCTATTCATATCTTCGAGTTTTTGGCTACTTGTGCTTTCCCAATCTTAGACCCTACAAC
*
6527940 ACCCATAAACTATAGTTTCG
196 ACCCATAAACTACAGTTTCG
6527960 AT
1 AT
6527962 CAACTCCATG
Statistics
Matches: 205, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
215 205 1.00
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (215 bp):
ATACTGGCTCATGCATCTATGCCCTTAACCTACTGGAATGATACCTTCAGTAGTGCAGTATACTT
CATAAACAGGTTACCTTATTTTCCCTTAGGCAACATCTCACCGTATGAAAAACTCTTTCAGCTTC
AACCAAGCTATTCATATCTTCGAGTTTTTGGCTACTTGTGCTTTCCCAATCTTAGACCCTACAAC
ACCCATAAACTACAGTTTCG
Found at i:6531678 original size:19 final size:19
Alignment explanation
Indices: 6531654--6531707 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
6531644 ATTAAAAATA
* *
6531654 TATTTTTATATTTTTTAAT
1 TATTTTAATAGTTTTTAAT
6531673 TATTTTAATAGTTTTTAAT
1 TATTTTAATAGTTTTTAAT
* *
6531692 T-TTTAAATAATTTTTA
1 TATTTTAATAGTTTTTA
6531708 CAACTTTCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 13 0.42
19 18 0.58
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TATTTTAATAGTTTTTAAT
Found at i:6531687 original size:18 final size:18
Alignment explanation
Indices: 6531665--6531707 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
6531655 ATTTTTATAT
* *
6531665 TTTTTAATTATTTTAATAG
1 TTTTTAATT-TTTAAATAA
6531684 TTTTTAATTTTTAAATAA
1 TTTTTAATTTTTAAATAA
6531702 TTTTTA
1 TTTTTA
6531708 CAACTTTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTTAATTTTTAAATAA
Found at i:6532099 original size:21 final size:21
Alignment explanation
Indices: 6532075--6532116 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6532065 TAATGGATCT
*
6532075 CATGGACCTCACAGTATACTC
1 CATGGACCTCACAGTAAACTC
* *
6532096 CATGGATCTTACAGTAAACTC
1 CATGGACCTCACAGTAAACTC
6532117 ATAGAGAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (21 bp):
CATGGACCTCACAGTAAACTC
Found at i:6540981 original size:29 final size:27
Alignment explanation
Indices: 6540949--6541002 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 27
6540939 AATGGAGAAT
6540949 AATTAAATTCCTTAAATA-AATAAAAAAGA
1 AATTAAATT--TTAAATATAA-AAAAAAGA
6540978 AATTAAATTTTAAATATAAAAAAAA
1 AATTAAATTTTAAATATAAAAAAAA
6541003 TACAGGGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 13 0.54
28 2 0.08
29 9 0.38
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.30
Consensus pattern (27 bp):
AATTAAATTTTAAATATAAAAAAAAGA
Found at i:6541380 original size:4 final size:4
Alignment explanation
Indices: 6541371--6541400 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
6541361 GATACTACAG
6541371 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
6541401 TGTGTACCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:6542223 original size:26 final size:26
Alignment explanation
Indices: 6542167--6542217 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
6542157 AATTTTTTTT
*
6542167 ATAA-TTTTTGAAATTTAATTTTTAA
1 ATAATTTTTTGAAATTTAAATTTTAA
*
6542192 ATAATTTTTTGAATTTTTAAATTTTA
1 ATAATTTTTTGAA-ATTTAAATTTTA
6542218 GAAATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.18
26 8 0.36
27 10 0.45
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (26 bp):
ATAATTTTTTGAAATTTAAATTTTAA
Found at i:6547700 original size:19 final size:19
Alignment explanation
Indices: 6547676--6547713 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
6547666 TCTTTTTGTC
6547676 TTGTTAGAATTTAGAATAG
1 TTGTTAGAATTTAGAATAG
6547695 TTGTTAGAATTTAGAATAG
1 TTGTTAGAATTTAGAATAG
6547714 CTGAAGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.21, T:0.42
Consensus pattern (19 bp):
TTGTTAGAATTTAGAATAG
Found at i:6555339 original size:23 final size:23
Alignment explanation
Indices: 6555309--6555355 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
6555299 AAAGGCTTAC
*
6555309 TAAATATATCGATTAGTTGTTTT
1 TAAATATATCAATTAGTTGTTTT
6555332 TAAATATATCAATTAGTTGTTTT
1 TAAATATATCAATTAGTTGTTTT
6555355 T
1 T
6555356 CTATCTAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.53
Consensus pattern (23 bp):
TAAATATATCAATTAGTTGTTTT
Found at i:6556309 original size:20 final size:22
Alignment explanation
Indices: 6556268--6556310 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
6556258 TCGATGTCTA
6556268 CATGTCTCAAGACAATAAAGTT
1 CATGTCTCAAGACAATAAAGTT
*
6556290 CATGTCTCGAGA-AA-AAAGTT
1 CATGTCTCAAGACAATAAAGTT
6556310 C
1 C
6556311 TCAAGTCTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 2 0.10
22 11 0.55
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.26
Consensus pattern (22 bp):
CATGTCTCAAGACAATAAAGTT
Found at i:6559919 original size:13 final size:14
Alignment explanation
Indices: 6559871--6559933 Score: 74
Period size: 14 Copynumber: 4.5 Consensus size: 14
6559861 GAGTTGATTT
* *
6559871 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
6559885 TTGGAAAAACAGAAA
1 TT-GAAAAACAGAAA
*
6559900 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
*
6559914 TT-AAAAACAGAAT
1 TTGAAAAACAGAAA
6559927 TTGAAAA
1 TTGAAAA
6559934 GACCTCAGCG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
13 11 0.26
14 19 0.45
15 12 0.29
ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:6559989 original size:117 final size:117
Alignment explanation
Indices: 6559798--6560022 Score: 317
Period size: 117 Copynumber: 1.9 Consensus size: 117
6559788 ACTTAATTTG
* * *
6559798 AAAAACAGATTTTGAAAATACCTCAACATGTGAACCCAAGGCTCAACTCACATCTCGCAATATGA
1 AAAAACAGAATTTGAAAAGACCTCAACATGTGAACCCAAGACTCAACTCACATCTCGCAATATGA
* * *
6559863 GTTGATTTTTGAAAAATATAAATTGGAAAAACAGAAATTGAAAAGCAGAAATT
66 GTTGATTTTTGAAAAACAGAAATT-GAAAAACAGAAATGGAAAAGCAGAAATT
* * * * *
6559916 AAAAACAGAATTTGAAAAGACCTCAGCGTGTG-GCCCGAGACTCAACTCACCTCTCGCAATATGA
1 AAAAACAGAATTTGAAAAGACCTCAACATGTGAACCCAAGACTCAACTCACATCTCGCAATATGA
* *
6559980 GTTGATTTTTGAAAAGCAGAAATTGAAAAACATAAATGGAAAA
66 GTTGATTTTTGAAAAACAGAAATTGAAAAACAGAAATGGAAAA
6560023 CACCTCAGCG
Statistics
Matches: 94, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
116 17 0.18
117 49 0.52
118 28 0.30
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.23
Consensus pattern (117 bp):
AAAAACAGAATTTGAAAAGACCTCAACATGTGAACCCAAGACTCAACTCACATCTCGCAATATGA
GTTGATTTTTGAAAAACAGAAATTGAAAAACAGAAATGGAAAAGCAGAAATT
Found at i:6560064 original size:85 final size:84
Alignment explanation
Indices: 6559900--6560177 Score: 285
Period size: 83 Copynumber: 3.2 Consensus size: 84
6559890 AAAACAGAAA
* * * * * *
6559900 TTGAAAAGCAGAAATTAAAAACAGAATTTGAAAAGACCTCAGCGTGTGGCCCGAGACTCAACTCA
1 TTGAAAA-CAGAAATTAAAAACAAAAATGGAAAACACCTCAGC--GT-CCCCGAGGCTCAACTCA
6559965 CCTCTCGCAATATGAGTTGATTT
62 CCTCTCGCAATATGAGTTGATTT
* ** *
6559988 TTGAAAAGCAGAAATTGAAAAACATAAATGGAAAACACCTCAGCGT-CTTGAGGTTCAACTCACC
1 TTGAAAA-CAGAAATT-AAAAACAAAAATGGAAAACACCTCAGCGTCCCCGAGGCTCAACTCACC
*
6560052 TCTTGCAATATGAGTT--TTT
64 TCTCGCAATATGAGTTGATTT
* * * * * *
6560071 TTGAAAA-ATAAATTAAAACACAAAAATTGACAATACCTCAGCGTGCCCCGATGCTCATCTCACC
1 TTGAAAACAGAAATTAAAA-ACAAAAATGGAAAACACCTCAGCGT-CCCCGAGGCTCAACTCACC
6560135 TCTCGCAATATGAGTTGATTT
64 TCTCGCAATATGAGTTGATTT
6560156 TTGAAAAACAGAAATTTAAAAA
1 TTG-AAAACAGAAA-TTAAAAA
6560178 TACCTCAGGG
Statistics
Matches: 160, Mismatches: 21, Indels: 19
0.80 0.10 0.09
Matches are distributed among these distances:
80 4 0.03
81 27 0.17
83 38 0.24
85 35 0.22
86 4 0.03
87 7 0.04
88 22 0.14
89 23 0.14
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (84 bp):
TTGAAAACAGAAATTAAAAACAAAAATGGAAAACACCTCAGCGTCCCCGAGGCTCAACTCACCTC
TCGCAATATGAGTTGATTT
Found at i:6560294 original size:78 final size:77
Alignment explanation
Indices: 6560094--6560865 Score: 965
Period size: 78 Copynumber: 10.1 Consensus size: 77
6560084 TAAAACACAA
* * * * *
6560094 AAATTGACAATACCTCAGC--GTGCCCCGATGCTCATCTCACCTCTCGCAATATGAGTTGA--TT
1 AAATTGAAAAGACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
*
6560155 TTTGAAAAACAG
66 TTTGACAAACAG
* * * * *
6560167 AAATTTAAAAATACCTCAG--GGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 AAA-TTGAAAAGACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TT
* *
6560230 TTTTTTACGAACAG
64 TTTTTGACAAACAG
*
6560244 AAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 AAATTGAAAAGACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTT
* *
6560309 TTTTTACGAACAG
65 TTTTGACAAACAG
* * *
6560322 AAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCACAATATGAGTT-A-ATT
1 AAATTGAAAAGACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
6560385 TTTGACAAACAG
66 TTTGACAAACAG
** *
6560397 AAATTGAAATTACCTCAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 AAATTGAAAAGACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTT
* *
6560460 TTTTTACGAACAG
65 TTTTGACAAACAG
* *
6560473 AAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATAAGTTGA--TT
1 AAATTGAAAAGACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
6560536 TTTGA-AAAGCAG
66 TTTGACAAA-CAG
*
6560548 AAATTGAAAATG-CCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 AAATTGAAAA-GACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TT
* *
6560612 TTTTTTACGAACAG
64 TTTTTGACAAACAG
* *
6560626 AAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATAAGTTGA--TT
1 AAATTGAAAAGACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
6560689 TTTGA-AAAGCAG
66 TTTGACAAA-CAG
* *
6560701 AAATTGAAAATG-CCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTC
1 AAATTGAAAA-GACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
6560765 TTTTGA-AAAGCAG
65 TTTTGACAAA-CAG
* *
6560778 AAATTGAAAACG-CCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTC
1 AAATTGAAAA-GACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
*
6560842 TTTTGA-AAAGTAG
65 TTTTGACAAA-CAG
6560855 AAATTGAAAAG
1 AAATTGAAAAG
6560866 CAGAAATTGA
Statistics
Matches: 626, Mismatches: 50, Indels: 43
0.87 0.07 0.06
Matches are distributed among these distances:
73 38 0.06
74 54 0.09
75 159 0.25
76 45 0.07
77 114 0.18
78 214 0.34
79 2 0.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (77 bp):
AAATTGAAAAGACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
TTTGACAAACAG
Found at i:6560863 original size:14 final size:14
Alignment explanation
Indices: 6560844--6560878 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
6560834 GTTGATTCTT
*
6560844 TTGAAAAGTAGAAA
1 TTGAAAAGCAGAAA
6560858 TTGAAAAGCAGAAA
1 TTGAAAAGCAGAAA
6560872 TTGAAAA
1 TTGAAAA
6560879 TACCTCAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.57, C:0.03, G:0.20, T:0.20
Consensus pattern (14 bp):
TTGAAAAGCAGAAA
Found at i:6560922 original size:91 final size:91
Alignment explanation
Indices: 6560767--6560938 Score: 290
Period size: 91 Copynumber: 1.9 Consensus size: 91
6560757 GTTGATTCTT
* * **
6560767 TTGAAAAGCAGAAATTGAAAACGCCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAGCAGAAATTGAAAACACCTCAACGTGTGAAACGAGGCTCAACTCACCTCTCGCAATAT
6560832 GAGTTGATTCTTTTGAAAAGTAGAAA
66 GAGTTGATTCTTTTGAAAAGTAGAAA
*
6560858 TTGAAAAGCAGAAATTGAAAATACCTCAACGTGTGAAACGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAGCAGAAATTGAAAACACCTCAACGTGTGAAACGAGGCTCAACTCACCTCTCGCAATAT
*
6560923 GAGTTGATTTTTTTGA
66 GAGTTGATTCTTTTGA
6560939 TGATAAATTG
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 75 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (91 bp):
TTGAAAAGCAGAAATTGAAAACACCTCAACGTGTGAAACGAGGCTCAACTCACCTCTCGCAATAT
GAGTTGATTCTTTTGAAAAGTAGAAA
Found at i:6560988 original size:72 final size:73
Alignment explanation
Indices: 6560869--6561010 Score: 223
Period size: 72 Copynumber: 1.9 Consensus size: 73
6560859 TGAAAAGCAG
*
6560869 AAATTGAAAATACCTCAACGTGTGAAACGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 AAATTGAAAATACCTCAAC-TGTGAAACGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCT
6560934 TTTGATGAT
65 TTTGATGAT
****
6560943 AAATTGAAAATACCTCAA-TGTGGCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTT
1 AAATTGAAAATACCTCAACTGTGAAACGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTT
6561007 TTGA
66 TTGA
6561011 AAAGTAGAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
72 45 0.71
74 18 0.29
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Consensus pattern (73 bp):
AAATTGAAAATACCTCAACTGTGAAACGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTT
TTGATGAT
Found at i:6561026 original size:14 final size:14
Alignment explanation
Indices: 6561007--6561041 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
6560997 GTTGATTCTT
*
6561007 TTGAAAAGTAGAAA
1 TTGAAAAGCAGAAA
6561021 TTGAAAAGCAGAAA
1 TTGAAAAGCAGAAA
6561035 TTGAAAA
1 TTGAAAA
6561042 CGCCTCAGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.57, C:0.03, G:0.20, T:0.20
Consensus pattern (14 bp):
TTGAAAAGCAGAAA
Found at i:6561033 original size:163 final size:165
Alignment explanation
Indices: 6560690--6561516 Score: 863
Period size: 163 Copynumber: 4.9 Consensus size: 165
6560680 AAGTTGATTT
* *
6560690 TTGAAAAGCAGAAATTGAAAATGCCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAGCAGAAATTGAAAATACCTCAACGTGTGACCCGAGGCTCAACTCACCTCTCGCAATAT
* * **
6560755 GAGTTGATTCTTTTGAAAAGCAGAAATTGAAAACGCCTCAGCGTGTGACCCGAGGCTCAACTCAC
66 GAGTTGATT-TTTTTAGAAG-AGAAATTGAAAATACCTCA-CGTGTGACCCGAGGCTCAACTCAC
6560820 CTCTCGCAATATGAGTTGATTCTTTTGAAAAGTAGAAA
128 CTCTCGCAATATGAGTTGATTCTTTTGAAAAGTAGAAA
**
6560858 TTGAAAAGCAGAAATTGAAAATACCTCAACGTGTGAAACGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAGCAGAAATTGAAAATACCTCAACGTGTGACCCGAGGCTCAACTCACCTCTCGCAATAT
* * * * **
6560923 GAGTTGATTTTTTT-GATGATAAATTGAAAATACCTCA-ATGTGGCTTGAGGCTCAACTCACCTC
66 GAGTTGATTTTTTTAGAAGAGAAATTGAAAATACCTCACGTGTGACCCGAGGCTCAACTCACCTC
6560986 TCGCAATATGAGTTGATTCTTTTGAAAAGTAGAAA
131 TCGCAATATGAGTTGATTCTTTTGAAAAGTAGAAA
** * *
6561021 TTGAAAAGCAGAAATTGAAAACGCCTCAGCGTGTGACCCGAGGCTTAACTCACCTCTCGCAATAT
1 TTGAAAAGCAGAAATTGAAAATACCTCAACGTGTGACCCGAGGCTCAACTCACCTCTCGCAATAT
**
6561086 GAGTTGATTCTTTTGAAAAGTAGAAATTGAAAAGCAGAAATTGAAAACGCCTCAGCGTGTGACCC
66 GAGTTGATT-TTTT------T----A--G--AAG-AGAAATTGAAAATACCTCA-CGTGTGACCC
*
6561151 GAGGCTTAACTCACCTCTCGCAATATGAGTTGATTCTTTTGAAAAGTAGAAA
114 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTTGAAAAGTAGAAA
* **
6561203 TTGAAAAGCAGAAATTGAAAATACCTCAA--TGTGGCTTGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAGCAGAAATTGAAAATACCTCAACGTGTGACCCGAGGCTCAACTCACCTCTCGCAATAT
* * * * * *
6561266 GAGTTGATTTTTGAAAAATAAATTAAAACACAAAAATTGACAATACCTCA-GCGTGCCCCGAGGC
66 GAGTTGA-TTTT------T---TT-AGA-AGAGAAATTGAAAATACCTCACGTGTGACCCGAGGC
*
6561330 TCAACTCACCTCTCGCAATATGAGTTGA-T-TTTTGAAAA--ATAAA
119 TCAACTCACCTCTCGCAATATGAGTTGATTCTTTTGAAAAGTAGAAA
* * * * *
6561373 TT-AAAACACAAAAATTGACAATACCTC-A-GCGTGCCCCGAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAA-GCAGAAATTGAAAATACCTCAACGTGTGACCCGAGGCTCAACTCACCTCTCGCAATA
* * * *
6561435 TGAGTTGATTTTTTTTTACGAACAGAAATTGAAAATACCTCAGCATGTGAGCTGAGGCTCAACTC
65 TGAGTTGA--TTTTTTTA-GAAGAGAAATTGAAAATACCTCA-CGTGTGACCCGAGGCTCAACTC
6561500 ACCTCT--CAATATGAGTT
126 ACCTCTCGCAATATGAGTT
6561517 AATTTTTGAC
Statistics
Matches: 562, Mismatches: 61, Indels: 79
0.80 0.09 0.11
Matches are distributed among these distances:
161 31 0.06
162 3 0.01
163 147 0.26
164 4 0.01
165 17 0.03
166 2 0.00
167 4 0.01
168 70 0.12
169 5 0.01
170 61 0.11
171 5 0.01
172 9 0.02
173 1 0.00
174 39 0.07
176 16 0.03
177 2 0.00
179 2 0.00
180 57 0.10
181 2 0.00
182 82 0.15
183 1 0.00
186 1 0.00
189 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (165 bp):
TTGAAAAGCAGAAATTGAAAATACCTCAACGTGTGACCCGAGGCTCAACTCACCTCTCGCAATAT
GAGTTGATTTTTTTAGAAGAGAAATTGAAAATACCTCACGTGTGACCCGAGGCTCAACTCACCTC
TCGCAATATGAGTTGATTCTTTTGAAAAGTAGAAA
Found at i:6561073 original size:254 final size:251
Alignment explanation
Indices: 6560623--6561966 Score: 1026
Period size: 254 Copynumber: 5.6 Consensus size: 251
6560613 TTTTTACGAA
* * * * *
6560623 CAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATAAGTTGA-
1 CAGAAATTGAAAATACCTCAACGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
* * * * * * **
6560687 TTTTTGAAAAGCAGAAATTGAAAATGCCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAA
66 TTTTTTAGATG-AGAAATTGAAAATACCTCA--ATGTGGCTTGAGGCTCAACTCACCTCTCGCAA
*
6560752 TATGAGTTGATTCTT----------TTGAAAAGCAGAAATTGAAAACGCCTCAGCGTGTGACCCG
128 TATGAGTTGATTTTTGAAAAAGAAATTGAAAAGCAGAAATTGAAAACGCCTCAGCGTGTGACCCG
6560807 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTTGAAAAGTAGAAATTGAAAAG
193 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTTGAAAAGTAGAAATTGAAAAG
**
6560866 CAGAAATTGAAAATACCTCAACGTGTGAAACGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 CAGAAATTGAAAATACCTCAACGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
6560931 TTTTTT-GATGATAAATTGAAAATACCTCAATGTGGCTTGAGGCTCAACTCACCTCTCGCAATAT
66 TTTTTTAGATGAGAAATTGAAAATACCTCAATGTGGCTTGAGGCTCAACTCACCTCTCGCAATAT
6560995 GAGTTGATTCTTTTGAAAAGTAGAAATTGAAAAGCAGAAATTGAAAACGCCTCAGCGTGTGACCC
131 GAGTTGA-T-TTTTGAAAA--AGAAATTGAAAAGCAGAAATTGAAAACGCCTCAGCGTGTGACCC
*
6561060 GAGGCTTAACTCACCTCTCGCAATATGAGTTGATTCTTTTGAAAAGTAGAAATTGAAAAG
192 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTTGAAAAGTAGAAATTGAAAAG
** * *
6561120 CAGAAATTGAAAACGCCTCAGCGTGTGACCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGAT
1 CAGAAATTGAAAATACCTCAACGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
6561185 TCTTTTGAAAAGTAGAAATTGAAAAGCAGAAATTGAAAATACCTCAATGTGGCTTGAGGCTCAAC
66 T-TTTT------TAG--A-T-----G-AGAAATTGAAAATACCTCAATGTGGCTTGAGGCTCAAC
* * * * **
6561250 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAAATT-AAAACACAAAAATTGACAATACCT
115 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAAGAAATTGAAAA-GCAGAAATTGAAAACGCCT
* *
6561314 CAGC--GTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-T-TTTTGAAAA--ATAAA
179 CAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTTGAAAAGTAGAAA
*
6561373 TT-AAAACA
244 TTGAAAA-G
* * * *
6561381 CAAAAATTGACAATACCTC-A-GCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 CAGAAATTGAAAATACCTCAACGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
**
6561444 TTTTTTTTACGAACAGAAATTGAAAATACCTCAGCATGTGAGC-TGAGGCTCAACTCACCTCT--
65 -TTTTTTTA-GATGAGAAATTGAAAATACCTCA--ATGTG-GCTTGAGGCTCAACTCACCTCTCG
* * * **
6561506 CAATATGAGTTAATTTTTG-ACAA-ACA---AAAA-TTGAAATT----A--CCTCAGCGTGT--C
125 CAATATGAGTTGATTTTTGAAAAAGAAATTGAAAAGCAGAAATTGAAAACGCCTCAGCGTGTGAC
*
6561557 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT-TTTT------T-----TT-ACGAA-
190 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTTGAAAAGTAGAAATTGA-AAAG
* * * * *
6561606 CAGAAATTGAAAATACCTCAGCATGTGAGCTGAGGCTCAACTCACCTCT--CAATATGAGTT-AA
1 CAGAAATTGAAAATACCTCAACGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
* * ** * * ** * **
6561668 TTTTTGACAAACAAAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATA
66 TTTTTTA-GATGAGAAATTGAAAATACCTCAATGTGGCTTGAGGCTCAACTCACCTCTCGCAATA
* * * ** * * *
6561733 TGAGTTGATTTTT---------TTTTACGAA-CAGAAATTGAAAATACCTCAGCATGTGAGCTGA
130 TGAGTTGATTTTTGAAAAAGAAATTGA-AAAGCAGAAATTGAAAACGCCTCAGCGTGTGACCCGA
* *
6561788 GGCTCAACTCACCTCT--CAATATGAGTT-A--ATTTT------T-G--A---CAAA-
194 GGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTTGAAAAGTAGAAATTGAAAAG
* * *
6561828 CAAAAATTGAAATTACCTCAGCGTGT--CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
1 CAGAAATTGAAAATACCTCAACGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
* * ** * * ** * *
6561890 TTTTTGACAAACAGAAATTGAAATTACCTTAGCGTGTCTTGAGGCTCAACTCATCTCTCGCAATA
66 TTTTTTA-GATGAGAAATTGAAAATACCTCAATGTGGCTTGAGGCTCAACTCACCTCTCGCAATA
6561955 TGAGTTGATTTT
130 TGAGTTGATTTT
6561967 CCTTGAAAAG
Statistics
Matches: 945, Mismatches: 88, Indels: 157
0.79 0.07 0.13
Matches are distributed among these distances:
218 1 0.00
219 9 0.01
220 40 0.04
222 152 0.16
223 7 0.01
224 2 0.00
225 49 0.05
226 3 0.00
227 43 0.05
234 43 0.05
235 5 0.01
236 3 0.00
240 43 0.05
241 1 0.00
242 24 0.03
243 60 0.06
244 7 0.01
245 3 0.00
246 37 0.04
248 24 0.03
249 2 0.00
253 1 0.00
254 160 0.17
255 5 0.01
259 39 0.04
260 8 0.01
261 24 0.03
262 1 0.00
263 9 0.01
264 2 0.00
265 39 0.04
266 4 0.00
267 24 0.03
269 9 0.01
270 2 0.00
271 60 0.06
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (251 bp):
CAGAAATTGAAAATACCTCAACGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTTTAGATGAGAAATTGAAAATACCTCAATGTGGCTTGAGGCTCAACTCACCTCTCGCAATAT
GAGTTGATTTTTGAAAAAGAAATTGAAAAGCAGAAATTGAAAACGCCTCAGCGTGTGACCCGAGG
CTCAACTCACCTCTCGCAATATGAGTTGATTCTTTTGAAAAGTAGAAATTGAAAAG
Found at i:6561096 original size:91 final size:90
Alignment explanation
Indices: 6560943--6561449 Score: 655
Period size: 91 Copynumber: 5.7 Consensus size: 90
6560933 TTTTGATGAT
* * **
6560943 AAATTGAAAATACCTCA-ATGTGGCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTT
1 AAATTGAAAATACCTCAGCTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTT
6561007 TTGAAAAGTAGAAATTGAAAAGCAG
66 TTGAAAAGTAGAAATTGAAAAGCAG
** *
6561032 AAATTGAAAACGCCTCAGCGTGTGACCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTCT
1 AAATTGAAAATACCTCAGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCT
6561097 TTTGAAAAGTAGAAATTGAAAAGCAG
65 TTTGAAAAGTAGAAATTGAAAAGCAG
** *
6561123 AAATTGAAAACGCCTCAGCGTGTGACCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTCT
1 AAATTGAAAATACCTCAGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCT
6561188 TTTGAAAAGTAGAAATTGAAAAGCAG
65 TTTGAAAAGTAGAAATTGAAAAGCAG
* * **
6561214 AAATTGAAAATACCTCA-ATGTGGCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-T-TT
1 AAATTGAAAATACCTCAGCTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTT
* * *
6561276 TTGAAAA--ATAAATT-AAAACACAA
66 TTGAAAAGTAGAAATTGAAAA-GCAG
* *
6561299 AAATTGACAATACCTCAGC-GTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-T-TT
1 AAATTGAAAATACCTCAGCTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTT
* * *
6561361 TTGAAAA--ATAAATT-AAAACACAA
66 TTGAAAAGTAGAAATTGAAAA-GCAG
* * *
6561384 AAATTGACAATACCTCAGC-GTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AAATTGAAAATACCTCAGCTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTT
6561448 TT
66 TT
6561450 TTACGAACAG
Statistics
Matches: 390, Mismatches: 22, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
84 4 0.01
85 146 0.37
86 1 0.00
87 13 0.03
88 1 0.00
89 52 0.13
91 173 0.44
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27
Consensus pattern (90 bp):
AAATTGAAAATACCTCAGCTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTT
TTGAAAAGTAGAAATTGAAAAGCAG
Found at i:6561117 original size:14 final size:14
Alignment explanation
Indices: 6561098--6561132 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
6561088 GTTGATTCTT
*
6561098 TTGAAAAGTAGAAA
1 TTGAAAAGCAGAAA
6561112 TTGAAAAGCAGAAA
1 TTGAAAAGCAGAAA
6561126 TTGAAAA
1 TTGAAAA
6561133 CGCCTCAGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.57, C:0.03, G:0.20, T:0.20
Consensus pattern (14 bp):
TTGAAAAGCAGAAA
Found at i:6561208 original size:14 final size:14
Alignment explanation
Indices: 6561189--6561223 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
6561179 GTTGATTCTT
*
6561189 TTGAAAAGTAGAAA
1 TTGAAAAGCAGAAA
6561203 TTGAAAAGCAGAAA
1 TTGAAAAGCAGAAA
6561217 TTGAAAA
1 TTGAAAA
6561224 TACCTCAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.57, C:0.03, G:0.20, T:0.20
Consensus pattern (14 bp):
TTGAAAAGCAGAAA
Found at i:6561583 original size:73 final size:73
Alignment explanation
Indices: 6561380--6561966 Score: 693
Period size: 73 Copynumber: 7.9 Consensus size: 73
6561370 AAATTAAAAC
*
6561380 ACAAAAATTGACAA-TACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 ACAAAAATTGA-AATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT-A-
* * *
6561444 TTTTTTTTACGA
63 -ATTTTTGACAA
* * ** *
6561456 ACAGAAATTGAAAATACCTCAGCATGTGAGCTGAGGCTCAACTCACCTCT--CAATATGAGTTAA
1 ACAAAAATTGAAATTACCTCAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAA
6561519 TTTTTGACAA
64 TTTTTGACAA
6561529 ACAAAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
1 ACAAAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT-A--
* * *
6561594 TTTTTTTACGA
63 ATTTTTGACAA
* * ** *
6561605 ACAGAAATTGAAAATACCTCAGCATGTGAGCTGAGGCTCAACTCACCTCT--CAATATGAGTTAA
1 ACAAAAATTGAAATTACCTCAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAA
6561668 TTTTTGACAA
64 TTTTTGACAA
6561678 ACAAAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
1 ACAAAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTT-A--
* * *
6561743 TTTTTTTACGA
63 ATTTTTGACAA
* * ** *
6561754 ACAGAAATTGAAAATACCTCAGCATGTGAGCTGAGGCTCAACTCACCTCT--CAATATGAGTTAA
1 ACAAAAATTGAAATTACCTCAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAA
6561817 TTTTTGACAA
64 TTTTTGACAA
*
6561827 ACAAAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
1 ACAAAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAATT
6561892 TTTGACAA
66 TTTGACAA
* * ** * *
6561900 ACAGAAATTGAAATTACCTTAGCGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAGTTGATT
1 ACAAAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAATT
6561965 TT
66 TT
6561967 CCTTGAAAAG
Statistics
Matches: 442, Mismatches: 50, Indels: 41
0.83 0.09 0.08
Matches are distributed among these distances:
71 66 0.15
73 193 0.44
74 2 0.00
75 5 0.01
76 110 0.25
78 66 0.15
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.29
Consensus pattern (73 bp):
ACAAAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAATT
TTTGACAA
Found at i:6561650 original size:149 final size:149
Alignment explanation
Indices: 6561380--6561966 Score: 1017
Period size: 149 Copynumber: 4.0 Consensus size: 149
6561370 AAATTAAAAC
*
6561380 ACAAAAATTGACAA-TACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 ACAAAAATTGA-AATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
6561444 TTTTTTTTACGAACAGAAATTGAAAATACCTCAGCATGTGAGCTGAGGCTCAACTCACCTCTCAA
65 TTTTTTTTACGAACAGAAATTGAAAATACCTCAGCATGTGAGCTGAGGCTCAACTCACCTCTCAA
6561509 TATGAGTTAATTTTTGACAA
130 TATGAGTTAATTTTTGACAA
6561529 ACAAAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
1 ACAAAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
6561594 TTTTTTTACGAACAGAAATTGAAAATACCTCAGCATGTGAGCTGAGGCTCAACTCACCTCTCAAT
66 TTTTTTTACGAACAGAAATTGAAAATACCTCAGCATGTGAGCTGAGGCTCAACTCACCTCTCAAT
6561659 ATGAGTTAATTTTTGACAA
131 ATGAGTTAATTTTTGACAA
6561678 ACAAAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
1 ACAAAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
6561743 TTTTTTTACGAACAGAAATTGAAAATACCTCAGCATGTGAGCTGAGGCTCAACTCACCTCTCAAT
66 TTTTTTTACGAACAGAAATTGAAAATACCTCAGCATGTGAGCTGAGGCTCAACTCACCTCTCAAT
6561808 ATGAGTTAATTTTTGACAA
131 ATGAGTTAATTTTTGACAA
6561827 ACAAAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--
1 ACAAAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
* * * * * *
6561890 -TTTTTGACAAACAGAAATTGAAATTACCTTAGC--GTG-TCTTGAGGCTCAACTCATCTCTCGC
66 TTTTTTTACGAACAGAAATTGAAAATACCTCAGCATGTGAGC-TGAGGCTCAACTCA-C-CTCTC
*
6561951 AATATGAGTTGATTTT
128 AATATGAGTTAATTTT
6561967 CCTTGAAAAG
Statistics
Matches: 426, Mismatches: 8, Indels: 11
0.96 0.02 0.02
Matches are distributed among these distances:
143 1 0.00
144 17 0.04
145 1 0.00
146 48 0.11
148 2 0.00
149 357 0.84
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.29
Consensus pattern (149 bp):
ACAAAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
TTTTTTTACGAACAGAAATTGAAAATACCTCAGCATGTGAGCTGAGGCTCAACTCACCTCTCAAT
ATGAGTTAATTTTTGACAA
Found at i:6570989 original size:30 final size:30
Alignment explanation
Indices: 6570911--6571028 Score: 132
Period size: 30 Copynumber: 3.9 Consensus size: 30
6570901 TAGGTACAAG
* *
6570911 TGGTGGTGGAGCAA-GTGTGGTTAGTGGAGT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
* ** * *
6570941 AGGTAATGGAGCAA-GTGTGGCTAGTGGATT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
6570971 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
*
6571001 TGGTGGTGGAAAAGGAGTGGCTAGTGGA
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGA
6571029 AAGGAGTGGC
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
29 2 0.03
30 74 0.97
ACGTcount: A:0.22, C:0.04, G:0.47, T:0.26
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:6571017 original size:18 final size:18
Alignment explanation
Indices: 6570996--6571045 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
6570986 TGTGGCTAGT
*
6570996 GGAGTTGG-TGGTGGAAAA
1 GGAGTTGGCTAGTGG-AAA
6571014 GGAG-TGGCTAGTGGAAA
1 GGAGTTGGCTAGTGGAAA
6571031 GGAG-TGGCTAGTGGA
1 GGAGTTGGCTAGTGGA
6571046 GTTGGTGGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 21 0.70
18 9 0.30
ACGTcount: A:0.26, C:0.04, G:0.50, T:0.20
Consensus pattern (18 bp):
GGAGTTGGCTAGTGGAAA
Found at i:6571033 original size:17 final size:17
Alignment explanation
Indices: 6571006--6571045 Score: 71
Period size: 17 Copynumber: 2.3 Consensus size: 17
6570996 GGAGTTGGTG
6571006 GTGGAAAAGGAGTGGCTA
1 GTGG-AAAGGAGTGGCTA
6571024 GTGGAAAGGAGTGGCTA
1 GTGGAAAGGAGTGGCTA
6571041 GTGGA
1 GTGGA
6571046 GTTGGTGGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.30, C:0.05, G:0.47, T:0.17
Consensus pattern (17 bp):
GTGGAAAGGAGTGGCTA
Found at i:6571040 original size:47 final size:47
Alignment explanation
Indices: 6570976--6571075 Score: 173
Period size: 47 Copynumber: 2.1 Consensus size: 47
6570966 GGATTTGGTG
*
6570976 GTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAGGAGTGGCTA
1 GTGG-AAAGGAGTGGCTAGTGGAGTTGGTGGTGGAAAAGGAGTGGCTA
*
6571024 GTGGAAAGGAGTGGCTAGTGGAGTTGGTGGTGGAAAAGGTGTGGCTA
1 GTGGAAAGGAGTGGCTAGTGGAGTTGGTGGTGGAAAAGGAGTGGCTA
6571071 GTGGA
1 GTGGA
6571076 GTTGGTGGTG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 46 0.92
48 4 0.08
ACGTcount: A:0.24, C:0.04, G:0.49, T:0.23
Consensus pattern (47 bp):
GTGGAAAGGAGTGGCTAGTGGAGTTGGTGGTGGAAAAGGAGTGGCTA
Found at i:6571068 original size:30 final size:30
Alignment explanation
Indices: 6571024--6571090 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
6571014 GGAGTGGCTA
6571024 GTGG-AAAGGAGTGGCTAGTGGAGTTGGTG
1 GTGGAAAAGGAGTGGCTAGTGGAGTTGGTG
*
6571053 GTGGAAAAGGTGTGGCTAGTGGAGTTGGTG
1 GTGGAAAAGGAGTGGCTAGTGGAGTTGGTG
6571083 GTGGAAAA
1 GTGGAAAA
6571091 AGCTAAGATT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 4 0.11
30 32 0.89
ACGTcount: A:0.24, C:0.03, G:0.49, T:0.24
Consensus pattern (30 bp):
GTGGAAAAGGAGTGGCTAGTGGAGTTGGTG
Found at i:6571591 original size:100 final size:100
Alignment explanation
Indices: 6571456--6571655 Score: 400
Period size: 100 Copynumber: 2.0 Consensus size: 100
6571446 TTGTTTTGTA
6571456 TTCATTTAGATTTTATGTTAGCTAGCCATAATTGATATATGCTATCAAAGCTTGTCTAGGTTATG
1 TTCATTTAGATTTTATGTTAGCTAGCCATAATTGATATATGCTATCAAAGCTTGTCTAGGTTATG
6571521 TATGATACCATATTGAGAGCACTTTTAATTTGTTC
66 TATGATACCATATTGAGAGCACTTTTAATTTGTTC
6571556 TTCATTTAGATTTTATGTTAGCTAGCCATAATTGATATATGCTATCAAAGCTTGTCTAGGTTATG
1 TTCATTTAGATTTTATGTTAGCTAGCCATAATTGATATATGCTATCAAAGCTTGTCTAGGTTATG
6571621 TATGATACCATATTGAGAGCACTTTTAATTTGTTC
66 TATGATACCATATTGAGAGCACTTTTAATTTGTTC
6571656 GTTGAAGAAC
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (100 bp):
TTCATTTAGATTTTATGTTAGCTAGCCATAATTGATATATGCTATCAAAGCTTGTCTAGGTTATG
TATGATACCATATTGAGAGCACTTTTAATTTGTTC
Found at i:6574441 original size:5 final size:5
Alignment explanation
Indices: 6574431--6574455 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6574421 AGAAGAAAAC
6574431 AAAGA AAAGA AAAGA AAAGA AAAGA
1 AAAGA AAAGA AAAGA AAAGA AAAGA
6574456 GTCGAATCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:6575280 original size:15 final size:17
Alignment explanation
Indices: 6575254--6575288 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
6575244 TTATTATTGT
6575254 TTTTGTTTGTTTT-TTA
1 TTTTGTTTGTTTTATTA
6575270 TTTTG-TTGTTTTATTA
1 TTTTGTTTGTTTTATTA
6575286 TTT
1 TTT
6575289 CTATTAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.09, C:0.00, G:0.11, T:0.80
Consensus pattern (17 bp):
TTTTGTTTGTTTTATTA
Found at i:6577864 original size:49 final size:49
Alignment explanation
Indices: 6577774--6577868 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 49
6577764 CAGTTCACCA
* * *
6577774 TGGTTATATGGTCAGAAGTTGAAGTATAACTAGGGCTCCCAGTTGATGG
1 TGGTTATATGGTCACAAGTTGAAGTATAACTAGAGCCCCCAGTTGATGG
* * * *
6577823 TGGTTATGTGGTCACAGGTTGAGGTATAACTTGAGCCCCCAGTTGA
1 TGGTTATATGGTCACAAGTTGAAGTATAACTAGAGCCCCCAGTTGA
6577869 CGTTGATTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 39 1.00
ACGTcount: A:0.24, C:0.15, G:0.31, T:0.31
Consensus pattern (49 bp):
TGGTTATATGGTCACAAGTTGAAGTATAACTAGAGCCCCCAGTTGATGG
Found at i:6577879 original size:49 final size:49
Alignment explanation
Indices: 6577777--6577879 Score: 116
Period size: 49 Copynumber: 2.1 Consensus size: 49
6577767 TTCACCATGG
* * * * * *
6577777 TTATATGGTCAGAAGTTGAAGTATAACTAGGGCTCCCAGTTGATGGTGG
1 TTATGTGGTCACAAGTTGAAGTATAACTAGAGCCCCCAGTTGACGGTGA
* * * *
6577826 TTATGTGGTCACAGGTTGAGGTATAACTTGAGCCCCCAGTTGACGTTGA
1 TTATGTGGTCACAAGTTGAAGTATAACTAGAGCCCCCAGTTGACGGTGA
6577875 TTATG
1 TTATG
6577880 CAGTCATGGG
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.32
Consensus pattern (49 bp):
TTATGTGGTCACAAGTTGAAGTATAACTAGAGCCCCCAGTTGACGGTGA
Found at i:6580074 original size:25 final size:25
Alignment explanation
Indices: 6580040--6580091 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
6580030 GATATTGAAC
6580040 TATGTTATCTACTTGTGGAACAATT
1 TATGTTATCTACTTGTGGAACAATT
6580065 TATGTTATCTACTTGTGGAACAATT
1 TATGTTATCTACTTGTGGAACAATT
6580090 TA
1 TA
6580092 GAATAACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (25 bp):
TATGTTATCTACTTGTGGAACAATT
Found at i:6588460 original size:21 final size:21
Alignment explanation
Indices: 6588428--6588468 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
6588418 GAACATTTGG
6588428 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
6588449 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
6588469 CCTCGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:6590567 original size:20 final size:20
Alignment explanation
Indices: 6590520--6590569 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
6590510 TTAATATTTT
6590520 TTTCATAAATTTTAGTATGCC
1 TTTCA-AAATTTTAGTATGCC
*
6590541 ATT-AAAATTTTAGGTATG-C
1 TTTCAAAATTTTA-GTATGCC
6590560 TTTCAAAATT
1 TTTCAAAATT
6590570 AAATTTTGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 11 0.44
20 12 0.48
21 2 0.08
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (20 bp):
TTTCAAAATTTTAGTATGCC
Found at i:6590605 original size:19 final size:20
Alignment explanation
Indices: 6590564--6590607 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
6590554 GTATGCTTTC
6590564 AAAATTAAATTTTGACATGA
1 AAAATTAAATTTTGACATGA
* *
6590584 AAAATTAATTTTTGATAT-A
1 AAAATTAAATTTTGACATGA
6590603 AAAAT
1 AAAAT
6590608 ATTTTTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (20 bp):
AAAATTAAATTTTGACATGA
Found at i:6590620 original size:9 final size:9
Alignment explanation
Indices: 6590606--6590636 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
6590596 TGATATAAAA
6590606 ATATTTTTT
1 ATATTTTTT
*
6590615 ATATTTTTA
1 ATATTTTTT
6590624 ATATTTTTT
1 ATATTTTTT
6590633 ATAT
1 ATAT
6590637 ATACTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
ATATTTTTT
Found at i:6591131 original size:20 final size:20
Alignment explanation
Indices: 6591097--6591165 Score: 86
Period size: 20 Copynumber: 3.4 Consensus size: 20
6591087 TCCTCCTTTT
6591097 AAAATTATGAGGGAA-CATCAA
1 AAAATTATGA-GGAAGCAT-AA
* *
6591118 AAAAATATGAGGAAGTATAA
1 AAAATTATGAGGAAGCATAA
*
6591138 AAAATTATGAGGATGCATAA
1 AAAATTATGAGGAAGCATAA
6591158 AAAATTAT
1 AAAATTAT
6591166 AAAGGGATAC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
20 31 0.74
21 11 0.26
ACGTcount: A:0.55, C:0.04, G:0.17, T:0.23
Consensus pattern (20 bp):
AAAATTATGAGGAAGCATAA
Found at i:6591173 original size:22 final size:21
Alignment explanation
Indices: 6591116--6591182 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 21
6591106 AGGGAACATC
* * *
6591116 AAAAAAATATGAGGA-AGTAT
1 AAAAAATTATAAGGATACTAT
* *
6591136 AAAAAATTATGAGGATGC-AT
1 AAAAAATTATAAGGATACTAT
6591156 AAAAAATTATAAAGGGATACTAT
1 AAAAAATTAT-AA-GGATACTAT
6591179 AAAA
1 AAAA
6591183 TATGAGGATG
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
20 26 0.68
21 1 0.03
22 5 0.13
23 6 0.16
ACGTcount: A:0.58, C:0.03, G:0.16, T:0.22
Consensus pattern (21 bp):
AAAAAATTATAAGGATACTAT
Found at i:6592300 original size:20 final size:20
Alignment explanation
Indices: 6592266--6592334 Score: 86
Period size: 20 Copynumber: 3.4 Consensus size: 20
6592256 TCCTCCTTTT
6592266 AAAATTATGAGGGAA-CATCAA
1 AAAATTATGA-GGAAGCAT-AA
* *
6592287 AAAAATATGAGGAAGTATAA
1 AAAATTATGAGGAAGCATAA
*
6592307 AAAATTATGAGGATGCATAA
1 AAAATTATGAGGAAGCATAA
6592327 AAAATTAT
1 AAAATTAT
6592335 AAAGGGATAC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
20 31 0.74
21 11 0.26
ACGTcount: A:0.55, C:0.04, G:0.17, T:0.23
Consensus pattern (20 bp):
AAAATTATGAGGAAGCATAA
Found at i:6592342 original size:22 final size:21
Alignment explanation
Indices: 6592285--6592351 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 21
6592275 AGGGAACATC
* * *
6592285 AAAAAAATATGAGGA-AGTAT
1 AAAAAATTATAAGGATACTAT
* *
6592305 AAAAAATTATGAGGATGC-AT
1 AAAAAATTATAAGGATACTAT
6592325 AAAAAATTATAAAGGGATACTAT
1 AAAAAATTAT-AA-GGATACTAT
6592348 AAAA
1 AAAA
6592352 TATGAGGATG
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
20 26 0.68
21 1 0.03
22 5 0.13
23 6 0.16
ACGTcount: A:0.58, C:0.03, G:0.16, T:0.22
Consensus pattern (21 bp):
AAAAAATTATAAGGATACTAT
Found at i:6593525 original size:13 final size:13
Alignment explanation
Indices: 6593507--6593534 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6593497 TTATATTATT
6593507 TCCATTTTTGTTA
1 TCCATTTTTGTTA
6593520 TCCATTTTTGTTA
1 TCCATTTTTGTTA
6593533 TC
1 TC
6593535 ACTTCTATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.18, G:0.07, T:0.61
Consensus pattern (13 bp):
TCCATTTTTGTTA
Found at i:6594022 original size:618 final size:618
Alignment explanation
Indices: 6592577--6594385 Score: 2533
Period size: 618 Copynumber: 2.9 Consensus size: 618
6592567 AATGAAGAGG
* ** * *
6592577 AAAAATATGTATCAATGCTTTTGTATGATAGCATTGCATTGCAATCGTTGAATTTAATTTTTTTT
1 AAAAAAATGTATCAATTTTTTTGTATGATTG-ATTGCATTTCAATCGTTGAATTT-ATTTTTTTT
* * *
6592642 TAAAGGGGGAAGGAATAGAACGATTACATAGTAACTAATCTAGGCAAAACCATGCTACAATCATC
64 AAAAAGGGGAA--AATAGAACAATTACATAGTAACTAATCTAGGCAAAACCATGCTACAATCATC
* *
6592707 ATATAGAGCCTTTTAAAATAAAGTCATAGAGAGATGCATAAACATGAAGGCATAAAAGGAGATTT
127 ATATAGAGCCTTTTAAAATAAAGTCATAGAGAGATGCATAAACATGAAGGCGTAAAGGGAGATTT
* * *
6592772 CCAACACAA-GCAGCCATGCTATTAGCTACTTGGTTCCCC-TCCTAATACCTATGGAATAGTAAA
192 CC-ACA-AAGGCAACCATGATATTAGCTACTTGGTTCCCCTTCCTAA-ACCTATGGAATAGTAGA
*
6592835 GGAAG-AAC----T--G--CTGTAAGTTAGGCTCAACTAAATCTAGTTATGAGTAGTTTCCATTT
254 GGAAGTAACTAGATAAGTTCTGTAAGTTAGGCTCAACTAAATCTAGTTAT-ATTAGTTTCCATTT
* * * *
6592891 CTATTATCCATTTTTGTTATCACTTCTGTTAAGCCTCC-AGTGTATAAATACACAAGGCCCTTGT
318 ATGTTATCCATTTTTGTTATCACTTCTGTTAAGCC-CCTAGTGTATAAATACACAAGGCCCCTAT
* * * * **
6592955 ATTTTATGAGTACGATTAATCAATTACTCTTCTTAC-TCTATATTTCTAGTATATTATCAAAGCT
382 ATTCTAAGAGTATGATTAATGAATTACTCTTCTT-CTTCTATATTTCTAGTATGGTATCAAAGCT
* * *
6593019 ATTTTTTTTGTTGATCGTTGCTTCAATCATGGATTCTGCAATCTCGACAGAATCGAA-AAATGGG
446 A-TTTTTTTGTTGATCATTGCTTCAATCATGGATTCTGCAGTCTCAACAGAATC-AACAAATGGG
*
6593083 AAGTTCTTCAATCCCCTTACATTTGCTTTTCAAAAAGTGGCAATTCTTGTAAATGATAGTAACTT
509 AAGTTCTTCAATCCCCTTAC-TTTGCTTTTCAAAAAGTGGCAATTCTTGTAGATGATAGTAACTT
*
6593148 GCGTCTCAAGTGGAATGTAACTTCCAAACATCTTGAATTTACACCA
573 GCGTCTCAAGTGAAATGTAACTTCCAAACATCTTGAATTTACACCA
* *
6593194 AAAGAAAATGTATCAATTTTTTTGTATGACTGAATGCATTTCAATCGTTGAATTTATTTTTTTTA
1 AAA-AAAATGTATCAATTTTTTTGTATGATTGATTGCATTTCAATCGTTGAATTTATTTTTTTT-
* *
6593259 AAAAAGAAGGAAAATAGAACAATTACATAGTAACTAATCTAGGCAAAGCCATGCTACAATCATCA
64 AAAAAG-GGGAAAATAGAACAATTACATAGTAACTAATCTAGGCAAAACCATGCTACAATCATCA
* *
6593324 TATAGAGCCTTTTAAAATAAATTCATAGAGAGATGAATAAACATGAAGGCGTAAAGGGAGATTTC
128 TATAGAGCCTTTTAAAATAAAGTCATAGAGAGATGCATAAACATGAAGGCGTAAAGGGAGATTTC
* *
6593389 CATCAAAGACAACCATGATATTAGCTACTTGGTTCCCCTTCTTAAACCTATGGAATAGTAGAGGA
193 CA-CAAAGGCAACCATGATATTAGCTACTTGGTTCCCCTTCCTAAACCTATGGAATAGTAGAGGA
* * *
6593454 AGTAACTAGATAAGTTCTATAAGTTAGGCTCAAGTAAATCTAGTTATATTA-TTTCCATTTTTGT
257 AGTAACTAGATAAGTTCTGTAAGTTAGGCTCAACTAAATCTAGTTATATTAGTTTCCATTTATGT
* *
6593518 TATCCATTTTTGTTATCACTTCTATTCAGCCCCTAGTGTATAAATACACAAGGCCCCTATATTCT
322 TATCCATTTTTGTTATCACTTCTGTTAAGCCCCTAGTGTATAAATACACAAGGCCCCTATATTCT
*
6593583 AAGAGTATTATTAATGAATTACTCTTCTTCTTCTATATTTCTAGTATGGTATCAAAGCTATTTTT
387 AAGAGTATGATTAATGAATTACTCTTCTTCTTCTATATTTCTAGTATGGTATCAAAGCTATTTTT
* * * * *
6593648 TTGTCGATCATTGCTTCAATCATGGATTCTACAGTCTCAAAAAAATCAACAAATGGGAAGTTCTC
452 TTGTTGATCATTGCTTCAATCATGGATTCTGCAGTCTCAACAGAATCAACAAATGGGAAGTTCTT
* *
6593713 CAATCCCCTTATCTTTGCTTCTCAAAAAGCGGCAATTCTTGTAGATGATAGTAACTT-CGTCTCA
517 CAATCCCCTTA-CTTTGCTTTTCAAAAAGTGGCAATTCTTGTAGATGATAGTAACTTGCGTCTCA
*
6593777 AGTTAAATGTAACTTCCAAACATCTTGAATTTACACCCA
581 AGTGAAATGTAACTTCCAAACATCTTGAATTTACA-CCA
* **
6593816 AAAAAAAT-TATCAATTTTTTTTTATGATTGATTGCATTTCAATAATTGAATTTATTTTTTTTAA
1 AAAAAAATGTATCAATTTTTTTGTATGATTGATTGCATTTCAATCGTTGAATTTATTTTTTTTAA
* * * *
6593880 AATGGGGAAAATAAAACAATGACATAGTAACTAATCTAGGCAAAACCATGCTACAAACATCATAT
66 AAAGGGGAAAATAGAACAATTACATAGTAACTAATCTAGGCAAAACCATGCTACAATCATCATAT
* *
6593945 AGAGCCTTTTAAAATAAAGTCATAGGGAGATGCACAAACATGAAGGCGTAAAGGGAGATTTCCGA
131 AGAGCCTTTTAAAATAAAGTCATAGAGAGATGCATAAACATGAAGGCGTAAAGGGAGATTTCC-A
* ** * *
6594010 CAAAGGCAACCAT-ACTATTAGCTACTTGGTTCCCCTCCCTGTACCAATGGAATATTAGAGGAAG
195 CAAAGGCAACCATGA-TATTAGCTACTTGGTTCCCCTTCCTAAACCTATGGAATAGTAGAGGAAG
* *
6594074 TAACTAGATAA-TTGTTGTAAGTTAGGCTCAACTAAATCTAGTTATGTGTAGTTTCCATTTATGT
259 TAACTAGATAAGTT-CTGTAAGTTAGGCTCAACTAAATCTAGTTATAT-TAGTTTCCATTTATGT
* *
6594138 TATCCATTTTTGTTATAACTTCTGTTAAGCCTCTAGTGTATAAATACAC-AGGCCCCTATATTCT
322 TATCCATTTTTGTTATCACTTCTGTTAAGCCCCTAGTGTATAAATACACAAGGCCCCTATATTCT
* * *
6594202 AAGAGTATGATTAATGAATTACTCTTTTTCTTTTATATTTCTAGTATGGTATCAAAGTTATTTTT
387 AAGAGTATGATTAATGAATTACTCTTCTTCTTCTATATTTCTAGTATGGTATCAAAGCTATTTTT
* * * ** *
6594267 TTGTTGATCATTACTTCAATCATGGGTTCTGCAGTCTCAGCAGAATTGACAAATTGGAAGTTCTT
452 TTGTTGATCATTGCTTCAATCATGGATTCTGCAGTCTCAACAGAATCAACAAATGGGAAGTTCTT
* * *
6594332 CAAACCCCTTGCCTTTGCTTTTCAAAAAGTGGCAATTCTTATAGATGATAGTAA
517 CAATCCCCTT-ACTTTGCTTTTCAAAAAGTGGCAATTCTTGTAGATGATAGTAA
6594386 GTTTTTTTTG
Statistics
Matches: 1065, Mismatches: 101, Indels: 50
0.88 0.08 0.04
Matches are distributed among these distances:
615 3 0.00
616 172 0.16
617 39 0.04
618 237 0.22
619 186 0.17
620 106 0.10
621 48 0.05
622 120 0.11
623 122 0.11
624 3 0.00
625 29 0.03
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (618 bp):
AAAAAAATGTATCAATTTTTTTGTATGATTGATTGCATTTCAATCGTTGAATTTATTTTTTTTAA
AAAGGGGAAAATAGAACAATTACATAGTAACTAATCTAGGCAAAACCATGCTACAATCATCATAT
AGAGCCTTTTAAAATAAAGTCATAGAGAGATGCATAAACATGAAGGCGTAAAGGGAGATTTCCAC
AAAGGCAACCATGATATTAGCTACTTGGTTCCCCTTCCTAAACCTATGGAATAGTAGAGGAAGTA
ACTAGATAAGTTCTGTAAGTTAGGCTCAACTAAATCTAGTTATATTAGTTTCCATTTATGTTATC
CATTTTTGTTATCACTTCTGTTAAGCCCCTAGTGTATAAATACACAAGGCCCCTATATTCTAAGA
GTATGATTAATGAATTACTCTTCTTCTTCTATATTTCTAGTATGGTATCAAAGCTATTTTTTTGT
TGATCATTGCTTCAATCATGGATTCTGCAGTCTCAACAGAATCAACAAATGGGAAGTTCTTCAAT
CCCCTTACTTTGCTTTTCAAAAAGTGGCAATTCTTGTAGATGATAGTAACTTGCGTCTCAAGTGA
AATGTAACTTCCAAACATCTTGAATTTACACCA
Found at i:6599180 original size:21 final size:21
Alignment explanation
Indices: 6599156--6599195 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
6599146 AAAATGGATA
6599156 AATTAGGACCAAATTACAAAT
1 AATTAGGACCAAATTACAAAT
*
6599177 AATTAGGACTAAATTACAA
1 AATTAGGACCAAATTACAA
6599196 TTTTACTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.12, G:0.10, T:0.25
Consensus pattern (21 bp):
AATTAGGACCAAATTACAAAT
Found at i:6601284 original size:20 final size:20
Alignment explanation
Indices: 6601259--6601296 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6601249 TGTGCCCCAA
*
6601259 CCGTGTGGAGGTTTACACGC
1 CCGTGTGGAGGTCTACACGC
*
6601279 CCGTGTGGTGGTCTACAC
1 CCGTGTGGAGGTCTACAC
6601297 ATCCATGTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.34, T:0.26
Consensus pattern (20 bp):
CCGTGTGGAGGTCTACACGC
Found at i:6604146 original size:18 final size:18
Alignment explanation
Indices: 6604123--6604158 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
6604113 TAAAGTTAAT
6604123 CATATATA-AAAACAAATA
1 CATATATACAAAA-AAATA
6604141 CATATATACAAAAAAATA
1 CATATATACAAAAAAATA
6604159 AAATAACAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (18 bp):
CATATATACAAAAAAATA
Found at i:6604978 original size:13 final size:14
Alignment explanation
Indices: 6604960--6604993 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
6604950 CCCTTTTTAC
6604960 AGAAAAAAT-GAAA
1 AGAAAAAATCGAAA
6604973 AGAAAAAATCGAAA
1 AGAAAAAATCGAAA
6604987 AGAAAAA
1 AGAAAAA
6604994 TAAAATCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.76, C:0.03, G:0.15, T:0.06
Consensus pattern (14 bp):
AGAAAAAATCGAAA
Found at i:6605692 original size:87 final size:87
Alignment explanation
Indices: 6605538--6605952 Score: 490
Period size: 87 Copynumber: 4.8 Consensus size: 87
6605528 GGTAGTATTT
* * * * *
6605538 ATGGCTTAAATCTGTTTCCCTATTCTTAGGGAAGATAAGGTTCGCCGTCTTGGATCTGCTCCACT
1 ATGGCTTAAATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTTCGATCCGCTCCACT
6605603 ATTGCTTAGGGAGATAGAACCA
66 ATTGCTTAGGGAGATAGAACCA
* * * ** * * * * *
6605625 GTGGCTTAAATCTGTTTCCCTACTCCTGGGGAAAATGGGATTTGCCATCTTTGGTCCGCTCAACT
1 ATGGCTTAAATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTTCGATCCGCTCCACT
* **
6605690 ATTGATTAGGGAGATAGAATTA
66 ATTGCTTAGGGAGATAGAACCA
* * * * * **
6605712 ATGGCTTAGATCTATTTCCCTACTCTTGGGGAAGATAAGATTCACTGTCTTCGATCTGCTTTACT
1 ATGGCTTAAATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTTCGATCCGCTCCACT
* *
6605777 ATTGCTTAGAGAGATAAAACCA
66 ATTGCTTAGGGAGATAGAACCA
* * * *
6605799 GTGGCTTAAATTTGTTTCCCTACTCCTGGGGAAGATGAGATTCGCCGTCTTCGATCCGCTCCACT
1 ATGGCTTAAATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTTCGATCCGCTCCACT
**
6605864 A-TGACTTAGGGAGATAGAATTA
66 ATTG-CTTAGGGAGATAGAACCA
* * *
6605886 ATGGCTTGAATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCTACT
1 ATGGCTTAAATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTTCGATCCGCTCCACT
6605951 AT
66 AT
6605953 AGACACATGA
Statistics
Matches: 266, Mismatches: 60, Indels: 3
0.81 0.18 0.01
Matches are distributed among these distances:
86 2 0.01
87 264 0.99
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (87 bp):
ATGGCTTAAATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTTCGATCCGCTCCACT
ATTGCTTAGGGAGATAGAACCA
Found at i:6605828 original size:174 final size:174
Alignment explanation
Indices: 6605538--6605952 Score: 618
Period size: 174 Copynumber: 2.4 Consensus size: 174
6605528 GGTAGTATTT
* * * * * *
6605538 ATGGCTTAAATCTGTTTCCCTATTCTTAGGGAAGATAAGGTTCGCCGTCTTGGATCTGCTCCACT
1 ATGGCTTAGATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCTACT
* * * *
6605603 ATTGCTTAGGGAGATAGAACCAGTGGCTTAAATCTGTTTCCCTACTCCTGGGGAAAATGGGATTT
66 ATTGCTTAGAGAGATAAAACCAGTGGCTTAAATCTGTTTCCCTACTCCTGGGGAAAATGAGATTC
* *
6605668 GCCATCTTTGGTCCGCTCAACTATTGA-TTAGGGAGATAGAATTA
131 GCCATCTTCGATCCGCTCAACTA-TGACTTAGGGAGATAGAATTA
* * * *
6605712 ATGGCTTAGATCTATTTCCCTACTCTTGGGGAAGATAAGATTCACTGTCTTCGATCTGCTTTACT
1 ATGGCTTAGATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCTACT
* *
6605777 ATTGCTTAGAGAGATAAAACCAGTGGCTTAAATTTGTTTCCCTACTCCTGGGGAAGATGAGATTC
66 ATTGCTTAGAGAGATAAAACCAGTGGCTTAAATCTGTTTCCCTACTCCTGGGGAAAATGAGATTC
* *
6605842 GCCGTCTTCGATCCGCTCCACTATGACTTAGGGAGATAGAATTA
131 GCCATCTTCGATCCGCTCAACTATGACTTAGGGAGATAGAATTA
6605886 ATGGCTT-GAATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCTAC
1 ATGGCTTAG-ATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCTAC
6605950 TAT
65 TAT
6605953 AGACACATGA
Statistics
Matches: 215, Mismatches: 24, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
173 4 0.02
174 211 0.98
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (174 bp):
ATGGCTTAGATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCTACT
ATTGCTTAGAGAGATAAAACCAGTGGCTTAAATCTGTTTCCCTACTCCTGGGGAAAATGAGATTC
GCCATCTTCGATCCGCTCAACTATGACTTAGGGAGATAGAATTA
Found at i:6610418 original size:11 final size:11
Alignment explanation
Indices: 6610402--6610432 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
6610392 GGGCATATCA
6610402 AAGAATATACC
1 AAGAATATACC
6610413 AAGAATATACC
1 AAGAATATACC
6610424 AAGAATATA
1 AAGAATATA
6610433 TAAATTTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.58, C:0.13, G:0.10, T:0.19
Consensus pattern (11 bp):
AAGAATATACC
Found at i:6618273 original size:18 final size:17
Alignment explanation
Indices: 6618250--6618284 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
6618240 TAAAGTTAAT
6618250 CATATATAAAAACAAATA
1 CATATATAAAAA-AAATA
*
6618268 CATATATACAAAAAATA
1 CATATATAAAAAAAATA
6618285 AAATAAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (17 bp):
CATATATAAAAAAAATA
Found at i:6619105 original size:13 final size:15
Alignment explanation
Indices: 6619073--6619104 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
6619063 ATTTTTACAG
6619073 AAAATATGAAAAGAA
1 AAAATATGAAAAGAA
6619088 AAAAT-TGAAAAGAA
1 AAAATATGAAAAGAA
6619102 AAA
1 AAA
6619105 TAAAATCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (15 bp):
AAAATATGAAAAGAA
Found at i:6620314 original size:24 final size:24
Alignment explanation
Indices: 6620258--6620308 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
6620248 ATAATAAGAA
*
6620258 ATTGGGAATTAAGGAATTTAATAT
1 ATTGGGAATTAAAGAATTTAATAT
6620282 ATTGGGAATTAAAGAATTTAATAT
1 ATTGGGAATTAAAGAATTTAATAT
6620306 ATT
1 ATT
6620309 TTGAATATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.18, T:0.39
Consensus pattern (24 bp):
ATTGGGAATTAAAGAATTTAATAT
Found at i:6621247 original size:37 final size:37
Alignment explanation
Indices: 6621197--6621280 Score: 123
Period size: 37 Copynumber: 2.3 Consensus size: 37
6621187 TAGCCATCTG
**
6621197 AGCTAAACTTATAAAATGACATCAAGTTACTCGTCCA
1 AGCTAAACTTATAAAACAACATCAAGTTACTCGTCCA
* **
6621234 AGCTAAACTTATAAAACAACATTAAGTTACTCGTCTG
1 AGCTAAACTTATAAAACAACATCAAGTTACTCGTCCA
6621271 AGCTAAACTT
1 AGCTAAACTT
6621281 GTGTCACATA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (37 bp):
AGCTAAACTTATAAAACAACATCAAGTTACTCGTCCA
Found at i:6625187 original size:16 final size:16
Alignment explanation
Indices: 6625166--6625204 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
6625156 ATCTTCGCCA
6625166 AGCTTCCAACCCAACG
1 AGCTTCCAACCCAACG
*
6625182 AGCTTCCAACCCAATG
1 AGCTTCCAACCCAACG
6625198 AGCTTCC
1 AGCTTCC
6625205 GAAGTACTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.41, G:0.13, T:0.18
Consensus pattern (16 bp):
AGCTTCCAACCCAACG
Found at i:6631636 original size:38 final size:38
Alignment explanation
Indices: 6631579--6631668 Score: 99
Period size: 38 Copynumber: 2.4 Consensus size: 38
6631569 CAAGTTTGAG
** * * *
6631579 CGTGTGGGCCACATGGGCGTATGGATAATGGGTCAGGC
1 CGTGTGGGCCACACAGGCGTATGGACAATGGGCCAAGC
* *
6631617 CGTGTGGGCCACACAGGCGTGTGGGCAATGGGCCAAGC
1 CGTGTGGGCCACACAGGCGTATGGACAATGGGCCAAGC
* *
6631655 CATGTGAGCCACAC
1 CGTGTGGGCCACAC
6631669 GAGTGAGACC
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.20, C:0.24, G:0.39, T:0.17
Consensus pattern (38 bp):
CGTGTGGGCCACACAGGCGTATGGACAATGGGCCAAGC
Found at i:6640339 original size:13 final size:13
Alignment explanation
Indices: 6640321--6640345 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6640311 TTCAGCTGGA
6640321 GAGAAGAAAGAAG
1 GAGAAGAAAGAAG
6640334 GAGAAGAAAGAA
1 GAGAAGAAAGAA
6640346 AAAGAAAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (13 bp):
GAGAAGAAAGAAG
Found at i:6640350 original size:10 final size:10
Alignment explanation
Indices: 6640337--6640478 Score: 83
Period size: 10 Copynumber: 14.1 Consensus size: 10
6640327 AAAGAAGGAG
6640337 AAGAAAGAAA
1 AAGAAAGAAA
6640347 AAGAAAGAAA
1 AAGAAAGAAA
* *
6640357 AGGAAAGGAA
1 AAGAAAGAAA
* * *
6640367 AGGAAAGGAG
1 AAGAAAGAAA
*
6640377 AATAAAGAAA
1 AAGAAAGAAA
6640387 AAGAAAGAAA
1 AAGAAAGAAA
* * *
6640397 AGGAAAGGAG
1 AAGAAAGAAA
6640407 AAG-AAGAAA
1 AAGAAAGAAA
* **
6640416 AGGGAGGGAAGGA
1 A-AGAAAGAA--A
*
6640429 AGGAAA-AAGA
1 AAGAAAGAA-A
6640439 AAGAAAGAAA
1 AAGAAAGAAA
6640449 AAGAAAGAAA
1 AAGAAAGAAA
* * *
6640459 AGGAAAGGAG
1 AAGAAAGAAA
6640469 AAG-AAGAAA
1 AAGAAAGAAA
6640478 A
1 A
6640479 GGGAGGGAAG
Statistics
Matches: 101, Mismatches: 26, Indels: 11
0.73 0.19 0.08
Matches are distributed among these distances:
9 10 0.10
10 79 0.78
11 7 0.07
12 3 0.03
13 2 0.02
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.01
Consensus pattern (10 bp):
AAGAAAGAAA
Found at i:6640363 original size:5 final size:5
Alignment explanation
Indices: 6640339--6640467 Score: 63
Period size: 5 Copynumber: 26.4 Consensus size: 5
6640329 AGAAGGAGAA
* * * * * *
6640339 GAAAG AAAAA GAAAG AAAAG GAAAG GAAAG GAAAG GAGAA- TAAAG AAAAA
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GA-AAG GAAAG GAAAG
* * * * *
6640389 GAAAG AAAAG GAAAG GAGAA- G-AAG AAAAG G-GAG GGAAG G-AAG GAAAAA
1 GAAAG GAAAG GAAAG GA-AAG GAAAG GAAAG GAAAG GAAAG GAAAG G-AAAG
* * *
6640437 GAAA- GAAAG AAAAA GAAAG AAAAG GAAAG GA
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG GA
6640468 GAAGAAGAAA
Statistics
Matches: 91, Mismatches: 24, Indels: 18
0.68 0.18 0.14
Matches are distributed among these distances:
3 2 0.02
4 13 0.14
5 69 0.76
6 7 0.08
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.01
Consensus pattern (5 bp):
GAAAG
Found at i:6640455 original size:62 final size:62
Alignment explanation
Indices: 6640380--6640512 Score: 257
Period size: 62 Copynumber: 2.1 Consensus size: 62
6640370 AAAGGAGAAT
6640380 AAAGAAAAAGAAAGAAAAGGAAAGGAGAAGAAGAAAAGGGAGGGAAGGAAGGAAAAAGAAAG
1 AAAGAAAAAGAAAGAAAAGGAAAGGAGAAGAAGAAAAGGGAGGGAAGGAAGGAAAAAGAAAG
*
6640442 AAAGAAAAAGAAAGAAAAGGAAAGGAGAAGAAGAAAAGGGAGGGAAGGAATGAAAAAGAAAG
1 AAAGAAAAAGAAAGAAAAGGAAAGGAGAAGAAGAAAAGGGAGGGAAGGAAGGAAAAAGAAAG
6640504 AAAGAAAAA
1 AAAGAAAAA
6640513 AAATAAGTAA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 70 1.00
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (62 bp):
AAAGAAAAAGAAAGAAAAGGAAAGGAGAAGAAGAAAAGGGAGGGAAGGAAGGAAAAAGAAAG
Found at i:6641163 original size:158 final size:157
Alignment explanation
Indices: 6640707--6642039 Score: 2011
Period size: 156 Copynumber: 8.6 Consensus size: 157
6640697 ATAAAATATG
* * *
6640707 AAAAGAATGTAAAATAATAAAA-TACGAAAATAA-ACTA-TTTT-TTAAAAGTAATAAAA-TC-T
1 AAAATAATGTAAAATAATAAAATTA-GAAAATAATA-TATTTTTATTGAAAGTAATAAAATTCGG
* *
6640766 G-AAAAAATACAAATAAAGGGCCGAAATAAGGGTT--TTTTACT-AAATTTATTTAAAAAACACA
64 GAAAAAAATACGAACAAAGGGCCGAAATAAGGGTTAATTTT--TGAAATTTATTTAAAAAACACA
6640827 CTAAATTAATACA-TTCAAACATAATGTACT
127 CTAAATTAATACATTTCAAACATAATGTACT
*
6640857 AAAATAATGTAAAATAATAAAA-TACGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGAG
1 AAAATAATGTAAAATAATAAAATTA-GAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGG
*
6640921 AAAAAAATACGAACAAAGGGCCAAAATAAGGGTTAATTTTTGAAATTTATTTAAAAAACACACTA
65 AAAAAAATACGAACAAAGGGCCGAAATAAGGGTTAATTTTTGAAATTTATTTAAAAAACACACTA
*
6640986 AATTAATACATTTCAAACATAATTTACT
130 AATTAATACATTTCAAACATAATGTACT
*
6641014 AAAATAATGTAAAATAATAAAATTAGAAAATAATATAGTTTTATTGAAAGTAATAAAATTCGGGA
1 AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGA
* *
6641079 AGAAAAATACGAATAAAGGGCCGAAATAATGGTTAATTTTTGAAATTTATTTAAAAAACACACTA
66 A-AAAAATACGAACAAAGGGCCGAAATAAGGGTTAATTTTTGAAATTTATTTAAAAAACACACTA
6641144 AATTAATACATTTCAAACATAATGTACT
130 AATTAATACATTTCAAACATAATGTACT
* * * *
6641172 AAAACAATGTAAAATAATAAAATTAAAAAATAATATGTTTTTATTGAAAGTAATAAAATTTGGGA
1 AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGA
* * * *
6641237 AGAAACATACGAACAAATGGCTGAAATAAGGGTTAATTATTGAAATTTATTTAAAAAACACACTA
66 A-AAAAATACGAACAAAGGGCCGAAATAAGGGTTAATTTTTGAAATTTATTTAAAAAACACACTA
6641302 AATTAATACATTTCAAACATAATGTACT
130 AATTAATACATTTCAAACATAATGTACT
6641330 AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAA-TCTGGG
1 AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATTC-GGG
*
6641394 -AAAAAATACGAACAAAGGGCCGAAATAAGGGTTAACTTTTGAAATTTATTTAAAAAACACACTA
65 AAAAAAATACGAACAAAGGGCCGAAATAAGGGTTAATTTTTGAAATTTATTTAAAAAACACACTA
6641458 AATTAATACATTTCAAACATAATGTACT
130 AATTAATACATTTCAAACATAATGTACT
*
6641486 AAAATAATGTAAAATAATAAAATTA-AAAATAATATATTTTTATTGAAAGTAATAAAATTCGAGA
1 AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGA
* * *
6641550 AGAAAAATACGAACAAAGGGCTGAAATAAGGGTTAATTTTTGAAATTTATTT-AAAAACGCAATA
66 A-AAAAATACGAACAAAGGGCCGAAATAAGGGTTAATTTTTGAAATTTATTTAAAAAACACACTA
6641614 AATTAATACATTTCAAACATAATGTACT
130 AATTAATACATTTCAAACATAATGTACT
*
6641642 AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAA-TCGGGG
1 AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGA
* *
6641706 AAAAAATACGAACAAAGGGCCGAAATAAGGGTTAATTATTAAAATTTATTTAAAAAACACACTAA
66 AAAAAATACGAACAAAGGGCCGAAATAAGGGTTAATTTTTGAAATTTATTTAAAAAACACACTAA
* *
6641771 GTTAATGCATTTCAAACATAATGTACT
131 ATTAATACATTTCAAACATAATGTACT
* *
6641798 AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTACTGAAAGTAATAAAATTCAGGA
1 AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGA
* * *
6641863 AAAAAATACAAACAAAGGGCCGAAATAAGGG----TTTTTGTAATTTATTTAAGAAACACACTAA
66 AAAAAATACGAACAAAGGGCCGAAATAAGGGTTAATTTTTGAAATTTATTTAAAAAACACACTAA
*
6641924 ATTAATACATTTCAAACATAATGAACT
131 ATTAATACATTTCAAACATAATGTACT
* * * *
6641951 AAAAATAATGTAAAATTAGAAAATTAGAAAAT-A-GTATTTTT-TT--AAGTAATAAAA-TCAAG
1 -AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATTC-GG
*
6642010 G-AAAAAATACGAACAAATGGCCGAAATAAG
64 GAAAAAAATACGAACAAAGGGCCGAAATAAG
6642040 AGTTTTTTAC
Statistics
Matches: 1098, Mismatches: 64, Indels: 44
0.91 0.05 0.04
Matches are distributed among these distances:
148 29 0.03
149 14 0.01
150 34 0.03
151 6 0.01
152 21 0.02
153 53 0.05
154 30 0.03
155 112 0.10
156 308 0.28
157 197 0.18
158 294 0.27
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.29
Consensus pattern (157 bp):
AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGA
AAAAAATACGAACAAAGGGCCGAAATAAGGGTTAATTTTTGAAATTTATTTAAAAAACACACTAA
ATTAATACATTTCAAACATAATGTACT
Found at i:6646340 original size:23 final size:22
Alignment explanation
Indices: 6646313--6646359 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 22
6646303 TTCTAAGTCG
6646313 ATATTCA-ATTCAATTCCACACCT
1 ATATTCATATTCAATT--ACACCT
6646336 ATATTCATTATTCAATTACACCT
1 ATATTCA-TATTCAATTACACCT
6646359 A
1 A
6646360 GTCAATTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 14 0.64
25 8 0.36
ACGTcount: A:0.36, C:0.26, G:0.00, T:0.38
Consensus pattern (22 bp):
ATATTCATATTCAATTACACCT
Found at i:6646473 original size:45 final size:45
Alignment explanation
Indices: 6646409--6646494 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
6646399 CTCGGTGGAT
* *
6646409 TCAGCATATAGCAACCACCTTATTAATCAATGATGTCCGGTAGAA
1 TCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGTAGAA
*
6646454 TCAGCACATAGCAACCACCTTACTAATCAATGATGTTCGGT
1 TCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGT
6646495 TCACATAGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (45 bp):
TCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGTAGAA
Found at i:6646559 original size:51 final size:50
Alignment explanation
Indices: 6646500--6646686 Score: 218
Period size: 51 Copynumber: 3.7 Consensus size: 50
6646490 TCGGTTCACA
* *
6646500 TAGTAGCCTGTACATAGTACTACACATGTGACCATTACCATCTGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATTA-CATCTGATACACG
* * * *
6646551 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAATTA-TTC-GATACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-C--CATTACATCTGATACACG
* * * *
6646602 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-ATCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATTACATCTGATACACG
6646652 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
6646687 CACTTTCACT
Statistics
Matches: 115, Mismatches: 16, Indels: 12
0.80 0.11 0.08
Matches are distributed among these distances:
49 7 0.06
50 37 0.32
51 64 0.56
52 3 0.03
54 4 0.03
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATTACATCTGATACACG
Found at i:6646674 original size:101 final size:102
Alignment explanation
Indices: 6646498--6646682 Score: 311
Period size: 101 Copynumber: 1.8 Consensus size: 102
6646488 GTTCGGTTCA
* * *
6646498 CATAGTAGCCTGTACATAGTACTACACATGTGACCATTACCATCTGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATTACAATCTGATACACGTAGTAGCCTGCA
6646563 CATAGTACTACACACGTGATCGAAATTATTCGATACG
66 CATAGTACTACACACGTGATCGAAATTATTCGATACG
*
6646600 CATAGTAGCCTGCACATAGTACTACACATGCGACC--TATCAATCTGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATTA-CAATCTGATACACGTAGTAGCCTGC
6646663 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
6646683 CCATCACTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
100 2 0.03
101 43 0.55
102 33 0.42
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATTACAATCTGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCGAAATTATTCGATACG
Found at i:6650192 original size:14 final size:14
Alignment explanation
Indices: 6650175--6650202 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6650165 ACTTAAATAA
6650175 AAAAATTAATGTTT
1 AAAAATTAATGTTT
6650189 AAAAATTAATGTTT
1 AAAAATTAATGTTT
6650203 CAATATGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
AAAAATTAATGTTT
Found at i:6650383 original size:37 final size:38
Alignment explanation
Indices: 6650298--6650504 Score: 116
Period size: 39 Copynumber: 5.3 Consensus size: 38
6650288 ACTAACACAA
** *
6650298 TAACAATAATAATAGTTTTTTACTCAAAATAATACTAAC
1 TAACAATAATAATAGGGTTTTACT-AAAATAATAATAAC
6650337 TAACAATAATAATTAGGGTTTTACT-AAA-AATAATAAC
1 TAACAATAATAA-TAGGGTTTTACTAAAATAATAATAAC
** *** * *
6650374 TAACAATAAT-ATAATGTAAAAACTAACAATCATACTAAC
1 TAACAATAATAATAGGGT-TTTACTAA-AATAATAATAAC
**
6650413 TAA-AATAATAATTAGGGTTTTTACTAATCCTAATAACTAACC
1 TAACAATAATAA-TAGGG-TTTTACTAA-AATAATAA-TAA-C
* * * ** * *
6650455 ATAATAAAAATATTAGTTTTTTACTAACAATAATACTAAG
1 -TAACAATAATAATAGGGTTTTACTAA-AATAATAATAAC
6650495 TAACAATAAT
1 TAACAATAAT
6650505 TATTAATAAC
Statistics
Matches: 125, Mismatches: 31, Indels: 24
0.69 0.17 0.13
Matches are distributed among these distances:
35 4 0.03
36 4 0.03
37 19 0.15
38 11 0.09
39 31 0.25
40 22 0.18
41 7 0.06
42 15 0.12
43 6 0.05
44 6 0.05
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (38 bp):
TAACAATAATAATAGGGTTTTACTAAAATAATAATAAC
Found at i:6650416 original size:23 final size:23
Alignment explanation
Indices: 6650371--6650417 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
6650361 TAAAAATAAT
*
6650371 AACTAACAATAATATAATGTAAA
1 AACTAACAATAATATAATCTAAA
*
6650394 AACTAACAATCATACTAA-CTAAA
1 AACTAACAATAATA-TAATCTAAA
6650417 A
1 A
6650418 TAATAATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.60, C:0.15, G:0.02, T:0.23
Consensus pattern (23 bp):
AACTAACAATAATATAATCTAAA
Found at i:6650493 original size:41 final size:40
Alignment explanation
Indices: 6650314--6650493 Score: 110
Period size: 40 Copynumber: 4.5 Consensus size: 40
6650304 TAATAATAGT
*
6650314 TTTTTACTCAA-AATAATACTAACTAACAATAATAATTAGGG
1 TTTTTACT-AACAATAATACTAACTAA-AAAAATAATTAGGG
* * *
6650355 -TTTTACTAAAAATAATAACTAAC-AATAATATAA-T---G
1 TTTTTACTAACAATAAT-ACTAACTAAAAAAATAATTAGGG
**** * *
6650390 TAAAAACTAACAATCATACTAACTAAAATAATAATTAGGG
1 TTTTTACTAACAATAATACTAACTAAAAAAATAATTAGGG
* *
6650430 TTTTTACTAATC-CTAATAACTAACCATAATAAAAAT-ATTA-GT
1 TTTTTACTAA-CAATAAT-ACTAA-C-TAA-AAAAATAATTAGGG
6650472 TTTTTACTAACAATAATACTAA
1 TTTTTACTAACAATAATACTAA
6650494 GTAACAATAA
Statistics
Matches: 104, Mismatches: 21, Indels: 28
0.68 0.14 0.18
Matches are distributed among these distances:
35 7 0.07
36 17 0.16
37 1 0.01
38 1 0.01
39 7 0.07
40 25 0.24
41 18 0.17
42 16 0.15
43 7 0.07
44 5 0.05
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.34
Consensus pattern (40 bp):
TTTTTACTAACAATAATACTAACTAAAAAAATAATTAGGG
Found at i:6650597 original size:13 final size:12
Alignment explanation
Indices: 6650579--6650624 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 12
6650569 TTATTAATCT
6650579 TAATAACTAACAA
1 TAATAACTAA-AA
*
6650592 TAATAACTAAAC
1 TAATAACTAAAA
6650604 TAATAAC-AAAA
1 TAATAACTAAAA
6650615 -AATAA-TAAAA
1 TAATAACTAAAA
6650625 ATTATACAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
10 9 0.30
11 3 0.10
12 8 0.27
13 10 0.33
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (12 bp):
TAATAACTAAAA
Found at i:6650761 original size:25 final size:25
Alignment explanation
Indices: 6650733--6650781 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
6650723 GGCACCACCT
6650733 TCTTCTTCTTCTTCTCCTTCAGCTC
1 TCTTCTTCTTCTTCTCCTTCAGCTC
6650758 TCTTCTTCTTCTTCTCCTTCAGCT
1 TCTTCTTCTTCTTCTCCTTCAGCT
6650782 GGGCTGAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.04, C:0.39, G:0.04, T:0.53
Consensus pattern (25 bp):
TCTTCTTCTTCTTCTCCTTCAGCTC
Found at i:6651068 original size:27 final size:27
Alignment explanation
Indices: 6651038--6651137 Score: 82
Period size: 27 Copynumber: 3.7 Consensus size: 27
6651028 AATTTAACAT
6651038 ATATTTATTATTAAAATATTAATATAA
1 ATATTTATTATTAAAATATTAATATAA
* *
6651065 ATATTT-TTCAATAATATATTAATA-ATA
1 ATATTTATT-ATTAAAATATTAATATA-A
* * *
6651092 TTATTAAAATT-TTAAAATATTATTGATAA
1 ATATT--TATTATTAAAATATTAAT-ATAA
6651121 AT-TTTATTATTAAAATA
1 ATATTTATTATTAAAATA
6651138 AAATTTTAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
26 6 0.11
27 32 0.57
28 12 0.21
29 3 0.05
30 3 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (27 bp):
ATATTTATTATTAAAATATTAATATAA
Found at i:6651112 original size:19 final size:22
Alignment explanation
Indices: 6651083--6651126 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 22
6651073 CAATAATATA
6651083 TTAATAATATTATT-A-AAATT
1 TTAATAATATTATTGATAAATT
6651103 TTAA-AATATTATTGATAAATT
1 TTAATAATATTATTGATAAATT
6651124 TTA
1 TTA
6651127 TTATTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.41
20 5 0.23
21 8 0.36
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TTAATAATATTATTGATAAATT
Found at i:6651213 original size:20 final size:19
Alignment explanation
Indices: 6651145--6651213 Score: 54
Period size: 20 Copynumber: 3.6 Consensus size: 19
6651135 ATAAAATTTT
*
6651145 AATATTAAATAATTTATTAA
1 AATATTAAATAATATATT-A
* *
6651165 AATAATAAAT--TATTTTA
1 AATATTAAATAATATATTA
6651182 ATCATATT-AATAATATATTA
1 A--ATATTAAATAATATATTA
6651202 AAGTATTAAATA
1 AA-TATTAAATA
6651214 TAAACAATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
17 2 0.05
18 8 0.21
19 8 0.21
20 20 0.53
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (19 bp):
AATATTAAATAATATATTA
Found at i:6655495 original size:88 final size:88
Alignment explanation
Indices: 6655350--6656091 Score: 1119
Period size: 88 Copynumber: 8.4 Consensus size: 88
6655340 GACTTGTTGC
** * * * * *
6655350 TTCAACCTACTCC-CTTGCAACTTCAGGGAGATAAGACTTGT-TGCTTCAACCTACTTCGTTGCC
1 TTCAACCTACTCCAC-TGCTGC-TCAGGGAGATAAGGCTGGTGT-CTTCGATCTACTTCGCTGCC
6655413 AATACAGGAAGACAAGATCTGCTATT
63 AATACAGGAAGACAAGATCTGCTATT
* *
6655439 TTCAACCTACTCCACTGCTGCTCAAGGAGATAGGGCTGGTGTCTTCGATCTACTTCGCTGCCAAT
1 TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTGGTGTCTTCGATCTACTTCGCTGCCAAT
* *
6655504 ATAGGAAGACAATATCTGCTATT
66 ACAGGAAGACAAGATCTGCTATT
*
6655527 TTCAACCAACTCCACTGCTGCTCAGGGAGATAAGGCTGGTGTCTTCGATCTACTTCGCTGCCAAT
1 TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTGGTGTCTTCGATCTACTTCGCTGCCAAT
6655592 ACAGGAAGACAAGATCTGCTATT
66 ACAGGAAGACAAGATCTGCTATT
* * **
6655615 TTCAACCTACTCCACTGCTGCTTAGGGAGATAAGTCTGGTGTCTTCGATCTACTTCGCTGTTAAT
1 TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTGGTGTCTTCGATCTACTTCGCTGCCAAT
* * *
6655680 ACAAGAAAACAAGATTTGCTATT
66 ACAGGAAGACAAGATCTGCTATT
* * * * **
6655703 TTTAACCTACTCCACAGCTGCTCAGGGAGATAAGGTTGGTATCTTCGATCTACTTCGCTGTTAAT
1 TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTGGTGTCTTCGATCTACTTCGCTGCCAAT
6655768 ACAGGAAGACAAGATCTGCTATT
66 ACAGGAAGACAAGATCTGCTATT
* *
6655791 TTCAACCAACTCCACTGCTGCTCAGGGAGATAAGGCTGGTGTCTTCGATCTACGTCGCTGCCAAT
1 TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTGGTGTCTTCGATCTACTTCGCTGCCAAT
*
6655856 ACAGGAAGACAAGATCTGTTATT
66 ACAGGAAGACAAGATCTGCTATT
* * *
6655879 TTCAACCTACTCCATTGCTACTTAGGGAGATAAGGCTGGTGTCTTCGATCTACTTCGCTGCCAAT
1 TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTGGTGTCTTCGATCTACTTCGCTGCCAAT
*
6655944 ACAGGAAGACAAGATTTGCTATT
66 ACAGGAAGACAAGATCTGCTATT
* * *
6655967 TTCAACCTACTCTACTGCTGCTCAGGGAAATAAGGCTGGTATCTTCGATCTACTTCGCTGCCAAT
1 TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTGGTGTCTTCGATCTACTTCGCTGCCAAT
*
6656032 ACCGGAAGACAAGATCTGCTATT
66 ACAGGAAGACAAGATCTGCTATT
6656055 TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCT
1 TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCT
6656092 TGCGGTTCCA
Statistics
Matches: 592, Mismatches: 59, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
88 573 0.97
89 18 0.03
90 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (88 bp):
TTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTGGTGTCTTCGATCTACTTCGCTGCCAAT
ACAGGAAGACAAGATCTGCTATT
Found at i:6657751 original size:41 final size:40
Alignment explanation
Indices: 6657706--6657807 Score: 132
Period size: 41 Copynumber: 2.5 Consensus size: 40
6657696 TGATTCAGTA
6657706 CACCGGCACTTAGCCTGCTAGACATATAGTCTGAAATATTT
1 CACCGGCA-TTAGCCTGCTAGACATATAGTCTGAAATATTT
* * * *
6657747 CACCGGCATTAAGCCTGCTAGACATTTTGTCTGAAGTGTTT
1 CACCGGCATT-AGCCTGCTAGACATATAGTCTGAAATATTT
*
6657788 CACCGGCAATAAGCCTGCTA
1 CACCGGC-ATTAGCCTGCTA
6657808 AGCTCTAAGC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
40 2 0.04
41 50 0.93
42 2 0.04
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.28
Consensus pattern (40 bp):
CACCGGCATTAGCCTGCTAGACATATAGTCTGAAATATTT
Found at i:6664002 original size:67 final size:66
Alignment explanation
Indices: 6663883--6664007 Score: 223
Period size: 67 Copynumber: 1.9 Consensus size: 66
6663873 TTTCCATTTC
*
6663883 AGAGAGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTATCAGTCCAGGCTAAATCCCCTGC
1 AGAGAGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGC
6663948 A
66 A
*
6663949 AGAGAGCACACTCCCGCGAACCTCATTCCTTACAGTGGGATTACCAGTCCAGGCTAAAT
1 AGAGAGCACACTCCCGCGAACCTCA-TCCTTACAGCGGGATTACCAGTCCAGGCTAAAT
6664008 ACCTTGTAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
66 25 0.45
67 31 0.55
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.19
Consensus pattern (66 bp):
AGAGAGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGC
A
Found at i:6664233 original size:57 final size:60
Alignment explanation
Indices: 6664135--6664282 Score: 187
Period size: 57 Copynumber: 2.5 Consensus size: 60
6664125 ACCCTAATTC
* * * *
6664135 GGATTACCCGTCCGGGCTAAATCCATTTTCCACATATTCTTCGGGAGGCCTATATC-A-A
1 GGATCACCCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGAGAGGCCTATATCGATA
* *
6664193 -GATCACCCATCCGGGCTAGAT-CTTTTTCACACATATTCTTCGAGAGGGCTATATCAGGATA
1 GGATCACCCGTCCGGGCTAGATCCTTTTTC-CACATATTCTTCGAGAGGCCTATATC--GATA
6664254 GGATCACCCGTCCGGGCTAGATCCTTTTT
1 GGATCACCCGTCCGGGCTAGATCCTTTTT
6664283 TACTGTCAAT
Statistics
Matches: 76, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
56 6 0.08
57 42 0.55
60 1 0.01
61 1 0.01
62 20 0.26
63 6 0.08
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (60 bp):
GGATCACCCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGAGAGGCCTATATCGATA
Found at i:6666976 original size:41 final size:41
Alignment explanation
Indices: 6666919--6667116 Score: 288
Period size: 41 Copynumber: 4.8 Consensus size: 41
6666909 TTTTGTAAGT
*
6666919 TCAGGCTTTATGCCTAGAAGGCTCTGTGCCGGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAATTATA
6666960 TCAGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAATTATA
* *
6667001 ACAGGCTTTATGCCTAGCAGGCTCTATGCCGGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAATTATA
* * * * *
6667042 TCAGACTTTATGTCTAGCAGGCTTTGTGCCGGTGAAATGTA
1 TCAGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAATTATA
* * * *
6667083 TCGGGCTTTGTGCCTAGCAGGCTTTATGCCGGTG
1 TCAGGCTTTATGCCTAGCAGGCTCTGTGCCGGTG
6667117 TTTTATACAA
Statistics
Matches: 142, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 142 1.00
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.32
Consensus pattern (41 bp):
TCAGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAATTATA
Found at i:6668020 original size:69 final size:69
Alignment explanation
Indices: 6667924--6668200 Score: 401
Period size: 69 Copynumber: 4.0 Consensus size: 69
6667914 TATGATGTAT
* * *
6667924 TATGTATATGTTGCCTATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTACTCAAT
1 TATGTATATGCTGCCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTCAAT
6667989 TTGG
66 TTGG
* * *
6667993 TACGTATATGATGCCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATACTGCTCAAT
1 TATGTATATGCTGCCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTCAAT
6668058 TTGG
66 TTGG
* * * * *
6668062 TATGTACATGCTACCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAGTGCTGTTAAAT
1 TATGTATATGCTGCCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTCAAT
6668127 TTGG
66 TTGG
* * * * *
6668131 TATGTATATGCTGCCCATTTGTTGTATATAAGCTGTCCAAATTTTGGTGTATAAATGCTGTTTAA
1 TATGTATATGCTGCCCATTTGTTGTATATATGCTGT-TAAATTTTGGTGTAAAAATGCTGCTCAA
6668196 TTTGG
65 TTTGG
6668201 CATATAAATG
Statistics
Matches: 187, Mismatches: 20, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
69 158 0.84
70 29 0.16
ACGTcount: A:0.26, C:0.10, G:0.19, T:0.44
Consensus pattern (69 bp):
TATGTATATGCTGCCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTCAAT
TTGG
Found at i:6668142 original size:23 final size:22
Alignment explanation
Indices: 6668088--6668143 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 22
6668078 ATTTGTTGTA
6668088 TATATGCTGTTAAATTTTGGTG
1 TATATGCTGTTAAATTTTGGTG
*
6668110 TAAAAGTGCTGTTAAA-TTTGGTATG
1 T-ATA-TGCTGTTAAATTTTGG--TG
6668135 TATATGCTG
1 TATATGCTG
6668144 CCCATTTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
22 1 0.04
23 12 0.43
24 12 0.43
25 3 0.11
ACGTcount: A:0.27, C:0.05, G:0.23, T:0.45
Consensus pattern (22 bp):
TATATGCTGTTAAATTTTGGTG
Found at i:6668199 original size:23 final size:23
Alignment explanation
Indices: 6667940--6668210 Score: 88
Period size: 24 Copynumber: 11.7 Consensus size: 23
6667930 TATGTTGCCT
* *
6667940 ATTTGTTGTATATATGCTGTTAA
1 ATTTGGTGTATAAATGCTGTTAA
* ** *
6667963 ATTTTGGTGTAAAAATGCTACTCA
1 A-TTTGGTGTATAAATGCTGTTAA
* ***
6667987 ATTTGGTACGTAT--ATGATG-CCC
1 ATTTGGT--GTATAAATGCTGTTAA
* *
6668009 ATTTGTTGTATATATGCTGTTAA
1 ATTTGGTGTATAAATGCTGTTAA
* * * *
6668032 ATTTTGGTGTAAAAATACTGCTCA
1 A-TTTGGTGTATAAATGCTGTTAA
* * * ****
6668056 ATTTGGTATGTACATGCT-ACCC
1 ATTTGGTGTATAAATGCTGTTAA
* *
6668078 ATTTGTTGTATATATGCTGTTAA
1 ATTTGGTGTATAAATGCTGTTAA
6668101 ATTTTGGTGTA-AAAGTGCTGTTAA
1 A-TTTGGTGTATAAA-TGCTGTTAA
* * * ***
6668125 ATTTGGTATGTATATGCTG-CCC
1 ATTTGGTGTATAAATGCTGTTAA
* *
6668147 ATTTGTTGTATATAA-GCTGTCCAA
1 ATTTGGTGTATA-AATGCTGT-TAA
*
6668171 ATTTTGGTGTATAAATGCTGTTTA
1 A-TTTGGTGTATAAATGCTGTTAA
**
6668195 ATTTGGCATATAAATG
1 ATTTGGTGTATAAATG
6668211 ATGTCCAAAT
Statistics
Matches: 175, Mismatches: 57, Indels: 32
0.66 0.22 0.12
Matches are distributed among these distances:
20 4 0.02
22 40 0.23
23 53 0.30
24 60 0.34
25 18 0.10
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.43
Consensus pattern (23 bp):
ATTTGGTGTATAAATGCTGTTAA
Found at i:6674692 original size:41 final size:41
Alignment explanation
Indices: 6674643--6674840 Score: 279
Period size: 41 Copynumber: 4.8 Consensus size: 41
6674633 TTTTGTAAGT
*
6674643 TCAGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGATTTATA
1 TCAGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAATTATA
6674684 TCAGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAATTATA
* *
6674725 TCAGGCTTTATGCCTAGCAGGCTCTATGCAGGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAATTATA
* * * * *
6674766 TCAGACTTTATGTCTAGCAGGCTTTGTGCCGGTGAAATGTA
1 TCAGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAATTATA
* * * * *
6674807 TCGGGCTTTGTACCTAGCAGGCTTTATGCCGGTG
1 TCAGGCTTTATGCCTAGCAGGCTCTGTGCCGGTG
6674841 TTTTATACAA
Statistics
Matches: 141, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 141 1.00
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (41 bp):
TCAGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAATTATA
Found at i:6675479 original size:24 final size:23
Alignment explanation
Indices: 6675446--6675646 Score: 95
Period size: 24 Copynumber: 8.6 Consensus size: 23
6675436 TATGCTGCCC
*
6675446 ATTTGTTGTATATATGCTGTTAA
1 ATTTGGTGTATATATGCTGTTAA
* * ** *
6675469 ATTTTGGTGTAAAAATGCTACTCA
1 A-TTTGGTGTATATATGCTGTTAA
*** ***
6675493 ATTTGGTACGTATATGCTG-CCC
1 ATTTGGTGTATATATGCTGTTAA
6675515 ATTT-GTAGTATATATGCTGTTAA
1 ATTTGGT-GTATATATGCTGTTAA
* * * * *
6675538 ATTTTGGCGTAAAAATGCTGCTCA
1 A-TTTGGTGTATATATGCTGTTAA
* * * *
6675562 ATTTGGTATGTATATGCTG-CAC
1 ATTTGGTGTATATATGCTGTTAA
* *
6675584 ATTTGTTGTATATATGCTATTAA
1 ATTTGGTGTATATATGCTGTTAA
*
6675607 ATTTTGGTGTA-AAAGTGCTGTTAA
1 A-TTTGGTGTATATA-TGCTGTTAA
6675631 ATTTGGTATGTATATA
1 ATTTGG--TGTATATA
6675647 CTACCCAGTT
Statistics
Matches: 124, Mismatches: 43, Indels: 19
0.67 0.23 0.10
Matches are distributed among these distances:
21 2 0.02
22 29 0.23
23 36 0.29
24 50 0.40
25 5 0.04
26 2 0.02
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.43
Consensus pattern (23 bp):
ATTTGGTGTATATATGCTGTTAA
Found at i:6675520 original size:69 final size:69
Alignment explanation
Indices: 6675430--6675719 Score: 391
Period size: 69 Copynumber: 4.2 Consensus size: 69
6675420 TATGATGTAT
*
6675430 TATGTATATGCTGCCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTACTCAAT
1 TATGTATATGCTGCCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTCAAT
6675495 TTGG
66 TTGG
* * *
6675499 TACGTATATGCTGCCCATTTGTAGTATATATGCTGTTAAATTTTGGCGTAAAAATGCTGCTCAAT
1 TATGTATATGCTGCCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTCAAT
6675564 TTGG
66 TTGG
* * * * *
6675568 TATGTATATGCTGCACATTTGTTGTATATATGCTATTAAATTTTGGTGTAAAAGTGCTGTTAAAT
1 TATGTATATGCTGCCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTCAAT
6675633 TTGG
66 TTGG
* * * * * ** * *
6675637 TATGTATATACTACCCAGTTGTTGTATATAAGCTGTCCAAATTTTGGTGTGTAAATGCTGTTTAA
1 TATGTATATGCTGCCCATTTGTTGTATATATGCTGT-TAAATTTTGGTGTAAAAATGCTGCTCAA
6675702 TTTGG
65 TTTGG
* *
6675707 TATATAAATGCTG
1 TATGTATATGCTG
6675720 TCCAAACAAG
Statistics
Matches: 193, Mismatches: 27, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
69 156 0.81
70 37 0.19
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.42
Consensus pattern (69 bp):
TATGTATATGCTGCCCATTTGTTGTATATATGCTGTTAAATTTTGGTGTAAAAATGCTGCTCAAT
TTGG
Found at i:6675597 original size:22 final size:22
Alignment explanation
Indices: 6675434--6675601 Score: 77
Period size: 22 Copynumber: 7.4 Consensus size: 22
6675424 ATGTATTATG
* *
6675434 TATATGCTGCCCATTTGTTGTA
1 TATATGCTGCACATTTGGTGTA
* *
6675456 TATATGCTGTTAAATTTTGGTGTA
1 TATATGCTG-CACA-TTTGGTGTA
* * * * ***
6675480 AAAATGCTACTCAATTTGGTACG
1 TATATGCTGCAC-ATTTGGTGTA
*
6675503 TATATGCTGCCCATTT-GTAGTA
1 TATATGCTGCACATTTGGT-GTA
* * *
6675525 TATATGCTGTTAAATTTTGGCGTA
1 TATATGCTG-CACA-TTTGGTGTA
* * * * *
6675549 AAAATGCTGCTCAATTTGGTATG
1 TATATGCTGCAC-ATTTGGTGTA
*
6675572 TATATGCTGCACATTTGTTGTA
1 TATATGCTGCACATTTGGTGTA
6675594 TATATGCT
1 TATATGCT
6675602 ATTAAATTTT
Statistics
Matches: 100, Mismatches: 38, Indels: 16
0.65 0.25 0.10
Matches are distributed among these distances:
21 2 0.02
22 37 0.37
23 31 0.31
24 29 0.29
25 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (22 bp):
TATATGCTGCACATTTGGTGTA
Found at i:6680423 original size:24 final size:25
Alignment explanation
Indices: 6680396--6680454 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 25
6680386 AATATATATT
*
6680396 TATAATA-ATTTTAAAAAATGTACG
1 TATAATATATTATAAAAAATGTACG
* * *
6680420 TATATGTATATTATAGAAAATGTATG
1 TATA-ATATATTATAAAAAATGTACG
6680446 TATAA-ATAT
1 TATAATATAT
6680455 GGTTATAATG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
24 8 0.29
25 2 0.07
26 18 0.64
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (25 bp):
TATAATATATTATAAAAAATGTACG
Found at i:6681815 original size:8 final size:8
Alignment explanation
Indices: 6681802--6681826 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
6681792 ACACATCAAT
6681802 ATTTTAAA
1 ATTTTAAA
6681810 ATTTTAAA
1 ATTTTAAA
6681818 ATTTTAAA
1 ATTTTAAA
6681826 A
1 A
6681827 AATAATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTTTAAA
Found at i:6682838 original size:14 final size:15
Alignment explanation
Indices: 6682806--6682861 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
6682796 TTTGATAAAA
* *
6682806 TGAAGAATTAAGTGT
1 TGAAAAATTAAGTAT
*
6682821 TGAAAATTTAAGTA-
1 TGAAAAATTAAGTAT
6682835 TGAAAAATTAAGTAT
1 TGAAAAATTAAGTAT
*
6682850 TGAAAAACTAAG
1 TGAAAAATTAAG
6682862 GGTGTGTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 13 0.37
15 22 0.63
ACGTcount: A:0.50, C:0.02, G:0.18, T:0.30
Consensus pattern (15 bp):
TGAAAAATTAAGTAT
Found at i:6682861 original size:29 final size:29
Alignment explanation
Indices: 6682805--6682861 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
6682795 GTTTGATAAA
* * **
6682805 ATGAAGAATTAAGTGTTGAAAATTTAAGT
1 ATGAAAAATTAAGTATTGAAAAACTAAGT
6682834 ATGAAAAATTAAGTATTGAAAAACTAAG
1 ATGAAAAATTAAGTATTGAAAAACTAAG
6682862 GGTGTGTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.18, T:0.30
Consensus pattern (29 bp):
ATGAAAAATTAAGTATTGAAAAACTAAGT
Found at i:6685975 original size:24 final size:23
Alignment explanation
Indices: 6685939--6685983 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
6685929 GAATATATTT
6685939 TAAAACAACAATTTTACTCATTGG
1 TAAAACAACAATTTT-CTCATTGG
* *
6685963 TAAAATAATAATTTTCTCATT
1 TAAAACAACAATTTTCTCATT
6685984 ATTAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.40
Consensus pattern (23 bp):
TAAAACAACAATTTTCTCATTGG
Found at i:6685989 original size:23 final size:24
Alignment explanation
Indices: 6685938--6685989 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
6685928 GGAATATATT
*
6685938 TTAAAACAACAATTTTACTCATTG
1 TTAAAACAACAATTTTACTCATTA
* * *
6685962 GTAAAATAATAATTTT-CTCATTA
1 TTAAAACAACAATTTTACTCATTA
6685985 TTAAA
1 TTAAA
6685990 TTTTTATCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (24 bp):
TTAAAACAACAATTTTACTCATTA
Found at i:6686290 original size:26 final size:26
Alignment explanation
Indices: 6686261--6686313 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
6686251 CAGTTATATA
*
6686261 TAATATAAT-TTATTTATTTATTTATT
1 TAATATAATATAATTTA-TTATTTATT
*
6686287 TAATATTATATAATTTATTATTTATT
1 TAATATAATATAATTTATTATTTATT
6686313 T
1 T
6686314 CATCATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
TAATATAATATAATTTATTATTTATT
Found at i:6692397 original size:20 final size:20
Alignment explanation
Indices: 6692364--6692412 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
6692354 CAAAATTAAA
* * *
6692364 TTTTGACATGAAAAACTAAT
1 TTTTGATATAAAAAAATAAT
*
6692384 TTTTGATATAAAAAAATATT
1 TTTTGATATAAAAAAATAAT
*
6692404 TTTTTATAT
1 TTTTGATAT
6692413 TTTTAATATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (20 bp):
TTTTGATATAAAAAAATAAT
Found at i:6692904 original size:21 final size:20
Alignment explanation
Indices: 6692880--6692947 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
6692870 TTGAAATTAC
6692880 GAGGGAACATCAAAAAAATAT
1 GAGGGAACAT-AAAAAAATAT
*
6692901 GA-GGAAGTATAAAAAAATAT
1 GAGGGAA-CATAAAAAAATAT
** *
6692921 GAGGGTGCATAAAAAATTAT
1 GAGGGAACATAAAAAAATAT
*
6692941 AAGGGAA
1 GAGGGAA
6692948 TACTATAATA
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
20 31 0.84
21 6 0.16
ACGTcount: A:0.54, C:0.04, G:0.24, T:0.18
Consensus pattern (20 bp):
GAGGGAACATAAAAAAATAT
Found at i:6705974 original size:30 final size:31
Alignment explanation
Indices: 6705929--6705988 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
6705919 GGAGGTGGGA
*
6705929 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
6705960 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
6705989 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:6706298 original size:9 final size:9
Alignment explanation
Indices: 6706281--6706329 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
6706271 TCGAGTTGAT
6706281 TCGAATAAC
1 TCGAATAAC
*
6706290 TCGATTAAC
1 TCGAATAAC
6706299 TCGAATAAC
1 TCGAATAAC
* *
6706308 TTGATTAAC
1 TCGAATAAC
6706317 TCGAATAAC
1 TCGAATAAC
6706326 TCGA
1 TCGA
6706330 TTCGTTTAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (9 bp):
TCGAATAAC
Found at i:6706302 original size:18 final size:18
Alignment explanation
Indices: 6706281--6706331 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
6706271 TCGAGTTGAT
6706281 TCGAATAACTCGATTAAC
1 TCGAATAACTCGATTAAC
*
6706299 TCGAATAACTTGATTAAC
1 TCGAATAACTCGATTAAC
6706317 TCGAATAACTCGATT
1 TCGAATAACTCGATT
6706332 CGTTTAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (18 bp):
TCGAATAACTCGATTAAC
Found at i:6707173 original size:50 final size:50
Alignment explanation
Indices: 6707105--6707292 Score: 146
Period size: 50 Copynumber: 3.7 Consensus size: 50
6707095 AAAAAAAAAA
* *
6707105 TTTT-GGTGGTGGCTTGTCAATGGCTGGCACCACCTTTACGAGAAATTTT
1 TTTTGGGTGGTGGCCTGTCAATGGCCGGCACCACCTTTACGAGAAATTTT
* * * ****
6707154 TTTTGGGTGGTGGCCTGTCAATGGCCGGCACTACCTTTATGGGAAAAAAAAACAA
1 TTTTGGGTGGTGGCCTGTCAATGGCCGGCACCACCTTTA--CG---AGAAATTTT
* * * * *
6707209 TTTCGGGTGCTGGCCTGTTAAAGGCTGGCACCACCTTTACG-GAAAATTTT
1 TTTTGGGTGGTGGCCTGTCAATGGCCGGCACCACCTTTACGAG-AAATTTT
* * *
6707259 TTTTCAGGTGTTGGCCTGTTAATGGCCGGCACCA
1 TTTT-GGGTGGTGGCCTGTCAATGGCCGGCACCA
6707293 TCTATACGGG
Statistics
Matches: 105, Mismatches: 26, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
49 4 0.04
50 37 0.35
51 25 0.24
52 1 0.01
53 1 0.01
55 37 0.35
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.31
Consensus pattern (50 bp):
TTTTGGGTGGTGGCCTGTCAATGGCCGGCACCACCTTTACGAGAAATTTT
Done.