Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 168 of 378
Found at i:49053888 original size:47 final size:46
Alignment explanation
Indices: 49053767--49053892 Score: 164
Period size: 46 Copynumber: 2.7 Consensus size: 46
49053757 ATAATCTCAC
* * * *
49053767 CCATAATGAACTCGGTACGCAACTCAACGAGCTCGGGTGTTCGCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCAGATGTTCGCAT
*
49053813 CCATAATGAACTCGGAACACAACTCAACGAGTTCAGATGCTT-GCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCAGATG-TTCGCAT
* *
49053859 CCATAGGTGAACTCAGAACGCAACTCAACGAGTT
1 CCATA-ATGAACTCGGAACGCAACTCAACGAGTT
49053893 TGGATTCCTC
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
46 43 0.61
47 27 0.39
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAATGAACTCGGAACGCAACTCAACGAGTTCAGATGTTCGCAT
Found at i:49055735 original size:27 final size:27
Alignment explanation
Indices: 49055686--49055910 Score: 186
Period size: 27 Copynumber: 8.4 Consensus size: 27
49055676 TTAGTTTACC
* *
49055686 AAATCACC-AAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
* **
49055712 AAATTACCAAAATACCCTTAGTTTACA
1 AAATTACCAAAATACCCCTAGTTTGTA
* *
49055739 AAATTATCAAAATACCCCTAGTTTATA
1 AAATTACCAAAATACCCCTAGTTTGTA
* * *
49055766 AAATCACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
* * *
49055793 AAATTACCAAAATACCCCTAATTTTTG
1 AAATTACCAAAATACCCCTAGTTTGTA
* * *
49055820 AAATTACCGAAATA-CCATAGTTTGAA
1 AAATTACCAAAATACCCCTAGTTTGTA
*** *
49055846 AAATTATTGAAATA-CCCTCGATTTGTA
1 AAATTACCAAAATACCCCTAG-TTTGTA
** * **
49055873 AAATTACTGAAATACCCTTAACTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
*
49055900 AAATTATCAAA
1 AAATTACCAAA
49055911 GCACCCTCGA
Statistics
Matches: 158, Mismatches: 38, Indels: 5
0.79 0.19 0.02
Matches are distributed among these distances:
26 30 0.19
27 125 0.79
28 3 0.02
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTAGTTTGTA
Found at i:49055985 original size:27 final size:26
Alignment explanation
Indices: 49055962--49056267 Score: 317
Period size: 27 Copynumber: 11.4 Consensus size: 26
49055952 CAAAATTATT
49055962 GAAATACACCTGTAGGGTAGAATTACC
1 GAAATAC-CCTGTAGGGTAGAATTACC
* * **
49055989 GAAATACCCCTATATGGTAGAATTATT
1 GAAATA-CCCTGTAGGGTAGAATTACC
* * *
49056016 GCAATACCCCTGTAGGGTAAAAATACC
1 GAAATA-CCCTGTAGGGTAGAATTACC
* *
49056043 GAAATACCCTTGTAGGGTAGAAATACT
1 GAAATACCC-TGTAGGGTAGAATTACC
* *
49056070 GAAATACCCTTCTAGGGTAGAAATACC
1 GAAATACCC-TGTAGGGTAGAATTACC
*
49056097 TAAATACCACTGTAGGGTAGAATTACC
1 GAAATACC-CTGTAGGGTAGAATTACC
*
49056124 GAAATACCCCTGTAGGGTAGAATTACT
1 GAAATA-CCCTGTAGGGTAGAATTACC
* *
49056151 AAAATACCCTTGTAGGGTAGAAATACC
1 GAAATACCC-TGTAGGGTAGAATTACC
**
49056178 GAAATACCCTTGTAGGGTAGAAACACC
1 GAAATACCC-TGTAGGGTAGAATTACC
* *
49056205 GAAATACCCCTATA-GGTAGAATTATC
1 GAAATA-CCCTGTAGGGTAGAATTACC
* *
49056231 GAAATACCCCTGTAAGGTAGAAATACC
1 GAAATA-CCCTGTAGGGTAGAATTACC
49056258 GAAATACCCT
1 GAAATACCCT
49056268 TATTTAGAAT
Statistics
Matches: 239, Mismatches: 33, Indels: 15
0.83 0.11 0.05
Matches are distributed among these distances:
26 32 0.13
27 200 0.84
28 7 0.03
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.24
Consensus pattern (26 bp):
GAAATACCCTGTAGGGTAGAATTACC
Found at i:49056047 original size:81 final size:81
Alignment explanation
Indices: 49055962--49057029 Score: 676
Period size: 81 Copynumber: 13.4 Consensus size: 81
49055952 CAAAATTATT
* * * * * *
49055962 GAAATACACCTGTAGGGTAGAATTACCGAAATACCCCTATATGGTAGAATTATTGCAATACCCCT
1 GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAAATACTGAAATACCCCT
*
49056027 GTAGGGTAAAAATACC
66 GTAGGGTAGAAATACC
* * * * * *
49056043 GAAATACCCTTGTAGGGTAGAAATACTGAAATACCCTTCTAGGGTAGAAATACCT-AAATACCAC
1 GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAAATA-CTGAAATACCCC
*
49056107 TGTAGGGTAGAATTACC
65 TGTAGGGTAGAAATACC
** * * *
49056124 GAAATACCCCTGTAGGGTAGAATTACTAAAATACCCTTGTAGGGTAGAAATACCGAAATACCCTT
1 GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAAATACTGAAATACCCCT
*
49056189 GTAGGGTAGAAACACC
66 GTAGGGTAGAAATACC
* * * *
49056205 GAAATACCCCTATA-GGTAGAATTATCGAAATACCCCTGTAAGGTAGAAATACCGAAATA-CCCT
1 GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAAATACTGAAATACCCCT
**
49056268 -TA-TTTAG-AATA-C
66 GTAGGGTAGAAATACC
** * * ** * * ** **
49056280 --TTTA---GTTTA--CCA-AATCACCAAAATACCCCTAGT-TTGTA-AAATTACCAAAATACCC
1 GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCT-GTAGGGTAGAAA-TACTGAAATACCC
* **
49056335 TTGGT-TTGTA-AAATCACC
64 CT-GTAGGGTAGAAAT-ACC
* * ** ** * ** *
49056353 AAAATACCCATG-ATTTGT-GAAATTACTAAAATACCCCCAGT-TTGCA-AAATTACTGAAATA-
1 GAAATACCCCTGTA-GGGTAG-AATTACCGAAATA-CCCCTGTAGGGTAGAAA-TACTGAAATAC
** *
49056413 CCCTCG-ATTTGTA-AAATTACT
62 CCCT-GTA-GGGTAGAAA-TACC
* *** * * ** * * ***
49056434 GAAATACCCTTG-ACTTATAAAATTACC-AAAGTACCCCCG-A-TTTACAGAATTACCGTTTTA-
1 GAAATACCCCTGTA-GGGTAGAATTACCGAAA-TACCCCTGTAGGGT--AGAAATACTGAAATAC
* ** * **
49056494 TCCTCG-A-TTTACAAAATTATT
62 CCCT-GTAGGGTA-GAAA-TACC
* * * *
49056515 GAAATACCCCTATAGGGTAGAATTACCAAAATACCCCTGTAGGGTAGAATTA-TCGAAATACCCT
1 GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAAATACT-GAAATACCCC
* * *
49056579 TATAGGATAGAAATATC
65 TGTAGGGTAGAAATACC
* * *
49056596 GAAATACCCCTGTAGGGTAGAATTACTGAAATACCCCTGTAGGGTAGAATTA-TCGAAATACCCT
1 GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAAATACT-GAAATACCCC
*
49056660 TATAGGGTAGAAATACC
65 TGTAGGGTAGAAATACC
* * * * *
49056677 GAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAGAATTACTAAAATACCCTT
1 GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAAATACTGAAATACCCCT
49056742 GTAGGGTAGAAATACC
66 GTAGGGTAGAAATACC
* * * * * * *
49056758 GAACTACCCTTGTAGGGTAGAAATACCGAAATACCCTTATAGGGTAGAATTACCGAAATACCCCT
1 GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAAATACTGAAATACCCCT
* * **
49056823 CTAGGGTAGAATTATT
66 GTAGGGTAGAAATACC
* * * * * *
49056839 GAAATACCCTTGTAGGGTAGAAATACCGAAATACCCTTGTAGGATAGAAATACCGAAATACCCTT
1 GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAAATACTGAAATACCCCT
* *
49056904 GTAGGGTAAAAATATC
66 GTAGGGTAGAAATACC
* * * *
49056920 GAAATACCCCTGTAGGGTAAAAATACCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCT
1 GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAAATACTGAAATACCCCT
* *
49056985 GTAGGGTAGAATTACT
66 GTAGGGTAGAAATACC
49057001 GAAATACCCCTGTAGGGTAGAATTACCGA
1 GAAATACCCCTGTAGGGTAGAATTACCGA
49057030 GATATCCTTG
Statistics
Matches: 806, Mismatches: 139, Indels: 84
0.78 0.14 0.08
Matches are distributed among these distances:
67 3 0.00
68 27 0.03
69 6 0.01
70 3 0.00
71 7 0.01
72 1 0.00
73 3 0.00
75 3 0.00
76 3 0.00
77 4 0.00
78 3 0.00
79 7 0.01
80 53 0.07
81 660 0.82
82 20 0.02
83 3 0.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (81 bp):
GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAAATACTGAAATACCCCT
GTAGGGTAGAAATACC
Found at i:49056351 original size:54 final size:54
Alignment explanation
Indices: 49056291--49056476 Score: 187
Period size: 54 Copynumber: 3.4 Consensus size: 54
49056281 TTAGTTTACC
*
49056291 AAATCACCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCCTTGGTTTGTA
1 AAATCACCAAAATACCCCTGA-TTTGTAAAATTACTAAAATACCCTTGGTTTGTA
* * *** *
49056345 AAATCACCAAAATACCCATGATTTGTGAAATTACTAAAATACCCCCAGTTTGCA
1 AAATCACCAAAATACCCCTGATTTGTAAAATTACTAAAATACCCTTGGTTTGTA
* ** * ** *
49056399 AAATTACTGAAATA-CCCTCGATTTGTAAAATTACTGAAATACCCTTGACTTATA
1 AAATCACCAAAATACCCCT-GATTTGTAAAATTACTAAAATACCCTTGGTTTGTA
* * *
49056453 AAATTACCAAAGTACCCCCGATTT
1 AAATCACCAAAATACCCCTGATTT
49056477 ACAGAATTAC
Statistics
Matches: 105, Mismatches: 24, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
53 3 0.03
54 98 0.93
55 4 0.04
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.29
Consensus pattern (54 bp):
AAATCACCAAAATACCCCTGATTTGTAAAATTACTAAAATACCCTTGGTTTGTA
Found at i:49056430 original size:27 final size:27
Alignment explanation
Indices: 49056299--49056476 Score: 155
Period size: 27 Copynumber: 6.6 Consensus size: 27
49056289 CCAAATCACC
* *
49056299 AAAATACCC-CTAGTTTGTAAAATTACC
1 AAAATACCCTCGA-TTTGTAAAATTACT
* * * *
49056326 AAAATACCCTTGGTTTGTAAAATCACC
1 AAAATACCCTCGATTTGTAAAATTACT
*
49056353 AAAATACCCAT-GATTTGTGAAATTACT
1 AAAATACCC-TCGATTTGTAAAATTACT
* *
49056380 AAAATACCC-CCAGTTTGCAAAATTACT
1 AAAATACCCTCGA-TTTGTAAAATTACT
*
49056407 GAAATACCCTCGATTTGTAAAATTACT
1 AAAATACCCTCGATTTGTAAAATTACT
* * * * *
49056434 GAAATACCCTTGACTTATAAAATTACC
1 AAAATACCCTCGATTTGTAAAATTACT
* *
49056461 AAAGTACCCCCGATTT
1 AAAATACCCTCGATTT
49056477 ACAGAATTAC
Statistics
Matches: 123, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
26 1 0.01
27 119 0.97
28 3 0.02
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.30
Consensus pattern (27 bp):
AAAATACCCTCGATTTGTAAAATTACT
Found at i:49056538 original size:27 final size:27
Alignment explanation
Indices: 49056515--49057054 Score: 684
Period size: 27 Copynumber: 20.0 Consensus size: 27
49056505 CAAAATTATT
*
49056515 GAAATACCCCTATAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
49056542 AAAATACCCCTGTAGGGTAGAATTATC
1 GAAATACCCCTGTAGGGTAGAATTACC
* * * * *
49056569 GAAATACCCTTATAGGATAGAAATATC
1 GAAATACCCCTGTAGGGTAGAATTACC
*
49056596 GAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACC
*
49056623 GAAATACCCCTGTAGGGTAGAATTATC
1 GAAATACCCCTGTAGGGTAGAATTACC
* * *
49056650 GAAATACCCTTATAGGGTAGAAATACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
49056677 GAAATACCCTTGTAGGGTAGAAATACC
1 GAAATACCCCTGTAGGGTAGAATTACC
*
49056704 GAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACC
* * *
49056731 AAAATACCCTTGTAGGGTAGAAATACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* * *
49056758 GAACTACCCTTGTAGGGTAGAAATACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
49056785 GAAATACCCTTATAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* **
49056812 GAAATACCCCTCTAGGGTAGAATTATT
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
49056839 GAAATACCCTTGTAGGGTAGAAATACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* * *
49056866 GAAATACCCTTGTAGGATAGAAATACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* * * *
49056893 GAAATACCCTTGTAGGGTAAAAATATC
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
49056920 GAAATACCCCTGTAGGGTAAAAATACC
1 GAAATACCCCTGTAGGGTAGAATTACC
49056947 GAAATACCCCTGTAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
*
49056974 GAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACC
49057001 GAAATACCCCTGTAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* * * * *
49057028 GAGATATCCTTGTGGGGTAAAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
49057055 ATTTTGCCCC
Statistics
Matches: 456, Mismatches: 57, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 456 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.24
Consensus pattern (27 bp):
GAAATACCCCTGTAGGGTAGAATTACC
Found at i:49057619 original size:22 final size:22
Alignment explanation
Indices: 49057567--49057627 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
49057557 GCCAATTATT
* *
49057567 CTGATTATGGCTTTGCGCCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
49057589 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
*
49057611 CTGATTATGGCTGTGTG
1 CTGATTATGGCTCTGTG
49057628 GCAAACGTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 1 0.03
22 30 0.94
23 1 0.03
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.33
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:49057826 original size:26 final size:26
Alignment explanation
Indices: 49057790--49057869 Score: 106
Period size: 26 Copynumber: 3.0 Consensus size: 26
49057780 ATTCTATTAA
* *
49057790 GTGGCTTTGCCACATTATCTGTTCTG
1 GTGGCTCTGCCACAATATCTGTTCTG
*
49057816 GTGGCTCTGCCACAATATCTGTATTTG
1 GTGGCTCTGCCACAATATCTGT-TCTG
* *
49057843 GTGACTCTGTCACAATATCTGTTCTG
1 GTGGCTCTGCCACAATATCTGTTCTG
49057869 G
1 G
49057870 CAGCCAAGCT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 24 0.51
27 23 0.49
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.39
Consensus pattern (26 bp):
GTGGCTCTGCCACAATATCTGTTCTG
Found at i:49057856 original size:27 final size:26
Alignment explanation
Indices: 49057797--49057869 Score: 101
Period size: 27 Copynumber: 2.8 Consensus size: 26
49057787 TAAGTGGCTT
* *
49057797 TGCCACATTATCTGTTCTGGTGGCTC
1 TGCCACAATATCTGTTCTGGTGACTC
*
49057823 TGCCACAATATCTGTATTTGGTGACTC
1 TGCCACAATATCTGT-TCTGGTGACTC
*
49057850 TGTCACAATATCTGTTCTGG
1 TGCCACAATATCTGTTCTGG
49057870 CAGCCAAGCT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
26 18 0.44
27 23 0.56
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.38
Consensus pattern (26 bp):
TGCCACAATATCTGTTCTGGTGACTC
Found at i:49057996 original size:6 final size:6
Alignment explanation
Indices: 49057987--49058055 Score: 59
Period size: 6 Copynumber: 11.3 Consensus size: 6
49057977 TTGCATTCAC
* * * * *
49057987 ATTCTG ATTCTG ATTCTG TTATCTA ATGCTG ATTTTG ATTCTG ATTCTC
1 ATTCTG ATTCTG ATTCTG AT-TCTG ATTCTG ATTCTG ATTCTG ATTCTG
*
49058036 ATTTTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG A-TTCTG AT
49058056 AATGTTTCTT
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
5 1 0.02
6 42 0.88
7 5 0.10
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.52
Consensus pattern (6 bp):
ATTCTG
Found at i:49058494 original size:21 final size:21
Alignment explanation
Indices: 49058468--49058509 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
49058458 TATTGTTGTT
49058468 CAAAACATCACTTATCCGTAA
1 CAAAACATCACTTATCCGTAA
49058489 CAAAACATCACTTATCCGTAA
1 CAAAACATCACTTATCCGTAA
49058510 TTGTTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.29, G:0.05, T:0.24
Consensus pattern (21 bp):
CAAAACATCACTTATCCGTAA
Found at i:49059519 original size:15 final size:15
Alignment explanation
Indices: 49059480--49059511 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
49059470 ATGATATGAT
49059480 TAAGAATGTATGGTA
1 TAAGAATGTATGGTA
49059495 TAAGAATGTATGGTA
1 TAAGAATGTATGGTA
49059510 TA
1 TA
49059512 GTTATGTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.25, T:0.34
Consensus pattern (15 bp):
TAAGAATGTATGGTA
Found at i:49069598 original size:28 final size:29
Alignment explanation
Indices: 49069532--49069602 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
49069522 AGTGATTAAG
* *
49069532 CCTAGTGGGCCATATAGATGTGATTTGGG
1 CCTAGTGGGCCATATAGATGAGATTTGGA
*
49069561 CCTAATGGGCCATAT-GAATGAGA-TTGGA
1 CCTAGTGGGCCATATAG-ATGAGATTTGGA
*
49069589 CTTAGTGGGCCATA
1 CCTAGTGGGCCATA
49069603 AGCATGTATG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 17 0.47
29 19 0.53
ACGTcount: A:0.25, C:0.15, G:0.31, T:0.28
Consensus pattern (29 bp):
CCTAGTGGGCCATATAGATGAGATTTGGA
Found at i:49076253 original size:40 final size:39
Alignment explanation
Indices: 49076209--49076390 Score: 247
Period size: 39 Copynumber: 4.6 Consensus size: 39
49076199 GTTCAAAACA
* * ** * *
49076209 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
49076249 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
49076289 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
49076328 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
49076367 CCTTCGGGCTTAGCCCGGATATCA
1 CCTTCGGGCTTAGCCCGGATATCA
49076391 CTCGAACATT
Statistics
Matches: 128, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
39 88 0.69
40 40 0.31
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:49076320 original size:39 final size:39
Alignment explanation
Indices: 49076239--49076391 Score: 252
Period size: 39 Copynumber: 3.9 Consensus size: 39
49076229 TATGGTAACC
* *
49076239 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
49076279 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
49076318 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
49076357 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
49076392 TCGAACATTC
Statistics
Matches: 106, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 89 0.84
40 17 0.16
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:49079852 original size:47 final size:47
Alignment explanation
Indices: 49079789--49079906 Score: 218
Period size: 47 Copynumber: 2.5 Consensus size: 47
49079779 CGAACGTCCA
*
49079789 AACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATCCG
*
49079836 AACTCATTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATCCG
49079883 AACTCGTTGAGTTGAGTCCGAGTT
1 AACTCGTTGAGTTGAGTCCGAGTT
49079907 TACTTATGGA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 68 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.29
Consensus pattern (47 bp):
AACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATCCG
Found at i:49082102 original size:19 final size:21
Alignment explanation
Indices: 49082078--49082118 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
49082068 CGAATAAGTC
49082078 AACAGAAGCTCG-AA-AGCTA
1 AACAGAAGCTCGTAAGAGCTA
49082097 AACAGAAGCTCGTAAGAGCTA
1 AACAGAAGCTCGTAAGAGCTA
49082118 A
1 A
49082119 TTCACCCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 12 0.60
20 2 0.10
21 6 0.30
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAGCTA
Found at i:49082766 original size:13 final size:13
Alignment explanation
Indices: 49082748--49082782 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
49082738 TTAATATTTA
*
49082748 ATAAAATCACTTT
1 ATAAAATCACTTC
49082761 ATAAAATCACTTC
1 ATAAAATCACTTC
49082774 ATAAAATCA
1 ATAAAATCA
49082783 TTATACAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAAAATCACTTC
Found at i:49088430 original size:2 final size:2
Alignment explanation
Indices: 49088417--49088458 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
49088407 GAGAAGGAAA
*
49088417 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49088459 GAATTACTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49088985 original size:39 final size:39
Alignment explanation
Indices: 49088941--49089112 Score: 272
Period size: 39 Copynumber: 4.4 Consensus size: 39
49088931 TGAGCTCCAA
* *
49088941 TTAGCCTTTGGGCTTCTGTTTAGCACTTTTGTGCTTCAG
1 TTAGCCTTCGGGCTTCCGTTTAGCACTTTTGTGCTTCAG
49088980 TTAGCCTTCGGGCTTCCGTTTAGCACTTTTGTGCTTCAG
1 TTAGCCTTCGGGCTTCCGTTTAGCACTTTTGTGCTTCAG
* *
49089019 TTAGCCTTCGGGCTTCCGTTTAGCACTTGTGTGTTTCAG
1 TTAGCCTTCGGGCTTCCGTTTAGCACTTTTGTGCTTCAG
*
49089058 TTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGCTTCAG
1 TTAGCCTTCGGGCTTCCGTTTAGCACTTTTGTGCTTCAG
* * *
49089097 CTAGACTTTGGGCTTC
1 TTAGCCTTCGGGCTTC
49089113 AGATCACTAT
Statistics
Matches: 124, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 124 1.00
ACGTcount: A:0.11, C:0.24, G:0.24, T:0.41
Consensus pattern (39 bp):
TTAGCCTTCGGGCTTCCGTTTAGCACTTTTGTGCTTCAG
Found at i:49090028 original size:28 final size:29
Alignment explanation
Indices: 49089966--49090029 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
49089956 GTGACGAGAT
** *
49089966 CGGCACTAAGTGTGCGTGCTGGAAATATA
1 CGGCACTAAGTGTGCAAGCTGGAAAAATA
*
49089995 TGGCACTAAGTGTGCAAGCT-GAAAAATA
1 CGGCACTAAGTGTGCAAGCTGGAAAAATA
49090023 CGGCACT
1 CGGCACT
49090030 GGGTGTGCGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 13 0.43
29 17 0.57
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (29 bp):
CGGCACTAAGTGTGCAAGCTGGAAAAATA
Found at i:49099589 original size:48 final size:48
Alignment explanation
Indices: 49099518--49099788 Score: 276
Period size: 48 Copynumber: 5.6 Consensus size: 48
49099508 TGTGAGCCAA
*
49099518 TGTAAGACCATGTTTGGAACATGGCATCGACATTTATATGAGAGCTAG
1 TGTAAGACCATGTCTGGAACATGGCATCGACATTTATATGAGAGCTAG
* * * * ** * *
49099566 TGTAAGATCATGTCTGGGACATGGCATCGGCCTCGATATGTGAGCCAG
1 TGTAAGACCATGTCTGGAACATGGCATCGACATTTATATGAGAGCTAG
* * *
49099614 TGTAAGACCATGTTTGGAACATGGCATCAATATTTATATGAGAGCTAG
1 TGTAAGACCATGTCTGGAACATGGCATCGACATTTATATGAGAGCTAG
* * ** * *
49099662 TGTAAGACCATGTCTAGG-ACATGGCGTCGGTC-TCGATATGTGAGGTAG
1 TGTAAGACCATGTCT-GGAACATGGCATC-GACATTTATATGAGAGCTAG
* * * * *
49099710 AGTAAGACCATGTTTGGAACATGGAATCGGCATTGATATATGAGAGCAAG
1 TGTAAGACCATGTCTGGAACATGGCATCGACATT--TATATGAGAGCTAG
*
49099760 TGTAAGACCATGTCTGGGACATGGCATCG
1 TGTAAGACCATGTCTGGAACATGGCATCG
49099789 GCATCTTACC
Statistics
Matches: 174, Mismatches: 43, Indels: 10
0.77 0.19 0.04
Matches are distributed among these distances:
47 4 0.02
48 133 0.76
49 2 0.01
50 35 0.20
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (48 bp):
TGTAAGACCATGTCTGGAACATGGCATCGACATTTATATGAGAGCTAG
Found at i:49099674 original size:96 final size:96
Alignment explanation
Indices: 49099506--49099790 Score: 435
Period size: 96 Copynumber: 2.9 Consensus size: 96
49099496 ATACTAGGGT
*
49099506 TATGTGAGCCAATGTAAGACCATGTTTGGAACATGGCATCGACATTTATATGAGAGCTAGTGTAA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTTATATGAGAGCTAGTGTAA
*
49099571 GATCATGTCTGGGACATGGCATCGGCCTCGA
66 GACCATGTCTGGGACATGGCATCGGCCTCGA
* *
49099602 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCAATATTTATATGAGAGCTAGTGTAA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTTATATGAGAGCTAGTGTAA
* * *
49099667 GACCATGTCTAGGACATGGCGTCGGTCTCGA
66 GACCATGTCTGGGACATGGCATCGGCCTCGA
** * * * *
49099698 TATGTGAGGTAGAGTAAGACCATGTTTGGAACATGGAATCGGCATTGATATATGAGAGCAAGTGT
1 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATT--TATATGAGAGCTAGTGT
49099763 AAGACCATGTCTGGGACATGGCATCGGC
64 AAGACCATGTCTGGGACATGGCATCGGC
49099791 ATCTTACCCT
Statistics
Matches: 169, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
96 128 0.76
98 41 0.24
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (96 bp):
TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTTATATGAGAGCTAGTGTAA
GACCATGTCTGGGACATGGCATCGGCCTCGA
Found at i:49102356 original size:20 final size:21
Alignment explanation
Indices: 49102334--49102378 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 21
49102324 ATTGATGCCT
*
49102334 ATTTTATTGTTGTTG-T-ATTT
1 ATTTTATT-TTATTGTTCATTT
49102354 A-TTTATTTTATTGTTCATTT
1 ATTTTATTTTATTGTTCATTT
49102374 ATTTT
1 ATTTT
49102379 TCTCTAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
18 5 0.24
19 7 0.33
20 6 0.29
21 3 0.14
ACGTcount: A:0.18, C:0.02, G:0.09, T:0.71
Consensus pattern (21 bp):
ATTTTATTTTATTGTTCATTT
Found at i:49102832 original size:12 final size:12
Alignment explanation
Indices: 49102815--49102839 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49102805 GCATATTCTT
49102815 CATAAAAATCAA
1 CATAAAAATCAA
49102827 CATAAAAATCAA
1 CATAAAAATCAA
49102839 C
1 C
49102840 CGTGTGGAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.20, G:0.00, T:0.16
Consensus pattern (12 bp):
CATAAAAATCAA
Found at i:49106688 original size:50 final size:50
Alignment explanation
Indices: 49106629--49106729 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
49106619 AATTCAAAAA
*
49106629 CAAAGGGCCGAGGAATTTAGACCGACTCTAGAAAATACCATTAGGGTATT
1 CAAAGGGCCGAGGAATTTAGACCGACTCAAGAAAATACCATTAGGGTATT
*
49106679 CAAAGGGCCGAGGAATTTAGACTGACTCAAGAAAATACCATTAGGGTATT
1 CAAAGGGCCGAGGAATTTAGACCGACTCAAGAAAATACCATTAGGGTATT
49106729 C
1 C
49106730 GATGAATTGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.22
Consensus pattern (50 bp):
CAAAGGGCCGAGGAATTTAGACCGACTCAAGAAAATACCATTAGGGTATT
Found at i:49108480 original size:40 final size:40
Alignment explanation
Indices: 49108435--49108515 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
49108425 ACAAGGTGAC
*
49108435 TGTGAAGACCAAGTATCCTTTGCCGAGGATCGATGATCTG
1 TGTGAAGACCAAGTATCCTTTGCCAAGGATCGATGATCTG
*
49108475 TGTGAAGAGCAAGTATCCTTTGCCAAGGATCGATGATCTG
1 TGTGAAGACCAAGTATCCTTTGCCAAGGATCGATGATCTG
49108515 T
1 T
49108516 TTGACCAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (40 bp):
TGTGAAGACCAAGTATCCTTTGCCAAGGATCGATGATCTG
Found at i:49112297 original size:48 final size:48
Alignment explanation
Indices: 49112233--49112710 Score: 431
Period size: 48 Copynumber: 9.9 Consensus size: 48
49112223 ATACTAGGGT
* * * *
49112233 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGACATTGGCATTTA
1 TATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGA
* * * *
49112281 TATGAGAGCTAGTGTAAGACCAT-TTCTGGGACATGGCATCGGCCTCGA
1 TATGTGAGCTAGTGTAAGACCATGTT-TGGAACATGGCATCGGCATTGA
* * * *
49112329 TATGTGAGCCAGTGTAAGACCATGTTTGAAACATGGCATCGGAATTTA
1 TATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGA
* ** * * * *
49112377 TATGAGAGCTAGTGTAAGACCATGTCCGGGACATGGCATCGACCTCGA
1 TATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGA
* * * * *
49112425 TATGTGAGCTAATGTAAGACCATGTTTGAAACATGACATCGACATTTA
1 TATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGA
** * * *
49112473 TATAAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGA
1 TATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGA
* * * * * *
49112521 TATGTGAGCCAATATAAGACCATGTTTGAAACATGGCATCGGTATTTA
1 TATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGA
* * * * *
49112569 TATGAGAGTTAGTGTAAGACCATGTTTAG-ACATGGCATCGGCCTCGA
1 TATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGA
* * * * ** * **
49112616 TATGTGAGCTAGAGTAATACCATATTTAGAACATAACATCTGCACCGA
1 TATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGA
* * *
49112664 TATCTGAGAACCAGTGTAAGACCATGTCT-GAGACATGGCATCGGCAT
1 TATGTGAG--CTAGTGTAAGACCATGTTTGGA-ACATGGCATCGGCAT
49112711 CTTACCCTTT
Statistics
Matches: 335, Mismatches: 89, Indels: 10
0.77 0.21 0.02
Matches are distributed among these distances:
47 40 0.12
48 266 0.79
49 4 0.01
50 25 0.07
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (48 bp):
TATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTGA
Found at i:49112397 original size:96 final size:96
Alignment explanation
Indices: 49112233--49112708 Score: 616
Period size: 96 Copynumber: 4.9 Consensus size: 96
49112223 ATACTAGGGT
* * *
49112233 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGACATTGGCATTTATATGAGAGCTAGTGTAA
1 TATGTGAGCCAGTGTAAGACCATGTTTGAAACATGACATCGGAATTTATATGAGAGCTAGTGTAA
*
49112298 GACCATTTCTGGGACATGGCATCGGCCTCGA
66 GACCATGTCTGGGACATGGCATCGGCCTCGA
*
49112329 TATGTGAGCCAGTGTAAGACCATGTTTGAAACATGGCATCGGAATTTATATGAGAGCTAGTGTAA
1 TATGTGAGCCAGTGTAAGACCATGTTTGAAACATGACATCGGAATTTATATGAGAGCTAGTGTAA
* *
49112394 GACCATGTCCGGGACATGGCATCGACCTCGA
66 GACCATGTCTGGGACATGGCATCGGCCTCGA
* * *
49112425 TATGTGAGCTAATGTAAGACCATGTTTGAAACATGACATC-GACATTTATATAAGAGCTAGTGTA
1 TATGTGAGCCAGTGTAAGACCATGTTTGAAACATGACATCGGA-ATTTATATGAGAGCTAGTGTA
*
49112489 AGACCATGTCTGGGACATGGCATCGGCCTTGA
65 AGACCATGTCTGGGACATGGCATCGGCCTCGA
* * * * *
49112521 TATGTGAGCCAATATAAGACCATGTTTGAAACATGGCATCGGTATTTATATGAGAGTTAGTGTAA
1 TATGTGAGCCAGTGTAAGACCATGTTTGAAACATGACATCGGAATTTATATGAGAGCTAGTGTAA
**
49112586 GACCATGT-TTAGACATGGCATCGGCCTCGA
66 GACCATGTCTGGGACATGGCATCGGCCTCGA
* * * * * * *** * * *
49112616 TATGTGAGCTAGAGTAATACCATATTT-AGAACATAACATCTGCACCGATATCTGAGAACCAGTG
1 TATGTGAGCCAGTGTAAGACCATGTTTGA-AACATGACATC-GGA-ATTTATATGAGAGCTAGTG
*
49112680 TAAGACCATGTCTGAGACATGGCATCGGC
63 TAAGACCATGTCTGGGACATGGCATCGGC
49112709 ATCTTACCCT
Statistics
Matches: 333, Mismatches: 41, Indels: 10
0.87 0.11 0.03
Matches are distributed among these distances:
94 1 0.00
95 51 0.15
96 241 0.72
97 24 0.07
98 16 0.05
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (96 bp):
TATGTGAGCCAGTGTAAGACCATGTTTGAAACATGACATCGGAATTTATATGAGAGCTAGTGTAA
GACCATGTCTGGGACATGGCATCGGCCTCGA
Found at i:49116535 original size:38 final size:38
Alignment explanation
Indices: 49116448--49116575 Score: 175
Period size: 38 Copynumber: 3.3 Consensus size: 38
49116438 AAACCCAAAC
* *
49116448 ATAACACCAGCACGAAGCCTACGGGACTTTAAACTCAGAT
1 ATAATACCAGCACGAAGCCTACGGGA-TTT-AACTCGGAT
* * * *
49116488 ATAATACCAGCACTAGGCCTGCGGGATTTAACCCGGAT
1 ATAATACCAGCACGAAGCCTACGGGATTTAACTCGGAT
49116526 ATAATACCAGCACGAAGCCTACGGGATTTAACTCGGAT
1 ATAATACCAGCACGAAGCCTACGGGATTTAACTCGGAT
*
49116564 ATAATTCCAGCA
1 ATAATACCAGCA
49116576 TATAGCCTGT
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
38 52 0.68
39 3 0.04
40 22 0.29
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (38 bp):
ATAATACCAGCACGAAGCCTACGGGATTTAACTCGGAT
Found at i:49116601 original size:78 final size:78
Alignment explanation
Indices: 49116448--49116604 Score: 203
Period size: 78 Copynumber: 2.0 Consensus size: 78
49116438 AAACCCAAAC
* *
49116448 ATAACACCAGCACGAAGCCTACGGGACTTTAAACTCAGATATAATACCAGCACTAGGCCTGCGGG
1 ATAACACCAGCACGAAGCCTACGGGACTTTAAACTCAGATATAATACCAGCACTAAGCCTGAGGG
49116513 ATTTAACCCGGAT
66 ATTTAACCCGGAT
* * *
49116526 ATAATACCAGCACGAAGCCTACGGGA-TTT-AACTCGGATATAATTCCAGCA-TATAGCCTGTAG
1 ATAACACCAGCACGAAGCCTACGGGACTTTAAACTCAGATATAATACCAGCACTA-AGCCTG-AG
**
49116588 GTCTTTAAGCCCGGAT
64 GGATTTAA-CCCGGAT
49116604 A
1 A
49116605 CAATCTCAGC
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
75 2 0.03
76 24 0.35
77 10 0.14
78 33 0.48
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.22
Consensus pattern (78 bp):
ATAACACCAGCACGAAGCCTACGGGACTTTAAACTCAGATATAATACCAGCACTAAGCCTGAGGG
ATTTAACCCGGAT
Found at i:49119698 original size:19 final size:19
Alignment explanation
Indices: 49119674--49119714 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
49119664 GGGCTGTCAC
*
49119674 ACAGTACTTCATCCATATA
1 ACAGTAATTCATCCATATA
49119693 ACAGTAATTCATCCATATA
1 ACAGTAATTCATCCATATA
49119712 ACA
1 ACA
49119715 CATAGTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.29
Consensus pattern (19 bp):
ACAGTAATTCATCCATATA
Found at i:49119830 original size:23 final size:24
Alignment explanation
Indices: 49119800--49119891 Score: 91
Period size: 24 Copynumber: 3.8 Consensus size: 24
49119790 GCTGATGGAT
49119800 AGTAAGCTCT-ATTGAGCTGA-AAC
1 AGTAAGCTCTGA-TGAGCTGAGAAC
*
49119823 AGTAAGCTCTGATGAGCTGAGAGC
1 AGTAAGCTCTGATGAGCTGAGAAC
* * *
49119847 AGTAAGCTCTTACGAGCTGATATATC
1 AGTAAGCTCTGATGAGCTGAGA-A-C
49119873 AGTAAGCT-TGTATGAGCTG
1 AGTAAGCTCTG-ATGAGCTG
49119892 CAGTGAGTCT
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
23 18 0.32
24 22 0.39
25 1 0.02
26 16 0.28
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.27
Consensus pattern (24 bp):
AGTAAGCTCTGATGAGCTGAGAAC
Found at i:49126353 original size:19 final size:19
Alignment explanation
Indices: 49126279--49126364 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 19
49126269 CATTCTCAAT
*
49126279 CATATTAACAGTAATTCATT
1 CATA-TAACAGTAATTCATC
* * *
49126299 C-GATAATAGTAACTCATC
1 CATATAACAGTAATTCATC
** * *
49126317 TGTATAAACAGCACTTCATC
1 CATAT-AACAGTAATTCATC
49126337 CATATAACAGTAATTCATC
1 CATATAACAGTAATTCATC
*
49126356 CGTATAACA
1 CATATAACA
49126365 CATTGCTTTT
Statistics
Matches: 49, Mismatches: 15, Indels: 5
0.71 0.22 0.07
Matches are distributed among these distances:
18 12 0.24
19 23 0.47
20 14 0.29
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (19 bp):
CATATAACAGTAATTCATC
Found at i:49126729 original size:19 final size:19
Alignment explanation
Indices: 49126705--49126743 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
49126695 GATCAATTCC
*
49126705 TCAATT-ATATACAATTATT
1 TCAATTAAT-TACAAGTATT
49126724 TCAATTAATTACAAGTATT
1 TCAATTAATTACAAGTATT
49126743 T
1 T
49126744 AAAAGTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (19 bp):
TCAATTAATTACAAGTATT
Found at i:49131575 original size:46 final size:45
Alignment explanation
Indices: 49131483--49131605 Score: 146
Period size: 46 Copynumber: 2.7 Consensus size: 45
49131473 GGTATGTGAA
49131483 CCAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGAG-
1 CCAGTGTAAGACATGTCTGGGACATGCATC-G-CACATTATGAGAGC
* *
49131529 CCAGTGTAAGACATGTCTAGAACATGCATCG-ACATT-TAGACAAGAGC
1 CCAGTGTAAGACATGTCTGGGACATGCATCGCACATTAT-G---AGAGC
49131576 CCA-TGTAAGACATGTCTGGGACATGCATCG
1 CCAGTGTAAGACATGTCTGGGACATGCATCG
49131606 GCCTCAAGAT
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
42 1 0.01
43 6 0.09
45 1 0.01
46 57 0.84
47 3 0.04
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (45 bp):
CCAGTGTAAGACATGTCTGGGACATGCATCGCACATTATGAGAGC
Found at i:49131735 original size:49 final size:49
Alignment explanation
Indices: 49131483--49131840 Score: 225
Period size: 49 Copynumber: 7.6 Consensus size: 49
49131473 GGTATGTGAA
* ** *
49131483 CCAGTGTAAGACATGTCTGGGACAT-GCATC-AGCC-ACAT-TATGAGAG
1 CCAGTGTAAGACCTGTCTGGGACATGGCATCGA-CCTTGATATATGAAAG
* * * * * *
49131529 CCAGTGTAAGACATGTCTAGAACAT-GCATCGACATT--TAGA-CAAGAG
1 CCAGTGTAAGACCTGTCTGGGACATGGCATCGACCTTGATATATGAA-AG
* * ** *
49131575 CCCA-TGTAAGACATGTCTGGGACAT-GCATCGGCCTCAAGATAT-ACAAG
1 -CCAGTGTAAGACCTGTCTGGGACATGGCATCGACCTTGATATATGA-AAG
* * * * *
49131623 CTAGTGTAAGACCTGTATGGGACATGGCATC-AGCTTG-T-TGTG--TG
1 CCAGTGTAAGACCTGTCTGGGACATGGCATCGACCTTGATATATGAAAG
* *
49131667 TCAGTGTAAGACCTGTCTGGGACATGGCATCGACAC-TGATAGT-TGAGAG
1 CCAGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTTGATA-TATGAAAG
* *
49131716 CCAGTTTAAGACCTGTCTGGGACATGGCATCGGCCTTGATATATGAAAG
1 CCAGTGTAAGACCTGTCTGGGACATGGCATCGACCTTGATATATGAAAG
* * * * **
49131765 TCAGTGTAAGACCTGTCTGGGACACGGCATCGA-CTTTA-ATGTGCTAG
1 CCAGTGTAAGACCTGTCTGGGACATGGCATCGACCTTGATATATGAAAG
* *
49131812 CCAGTGGAAGACCATGTCTAGGACATGGC
1 CCAGTGTAAGACC-TGTCTGGGACATGGC
49131841 GTCAACATTT
Statistics
Matches: 245, Mismatches: 45, Indels: 42
0.74 0.14 0.13
Matches are distributed among these distances:
44 29 0.12
45 5 0.02
46 63 0.26
47 25 0.10
48 46 0.19
49 77 0.31
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (49 bp):
CCAGTGTAAGACCTGTCTGGGACATGGCATCGACCTTGATATATGAAAG
Found at i:49132890 original size:28 final size:28
Alignment explanation
Indices: 49132858--49132978 Score: 170
Period size: 28 Copynumber: 4.3 Consensus size: 28
49132848 CATGGGATAT
* * * *
49132858 GACACGGGTGTTTCATGGTCGTGTGAGG
1 GACACGGGCGTGTCATGGCCGTGTGAGA
*
49132886 GACACGGGCGTGTCATGGCCATGTGAGA
1 GACACGGGCGTGTCATGGCCGTGTGAGA
* *
49132914 GACACGGACGTGTCATGGCCGTGTGAGG
1 GACACGGGCGTGTCATGGCCGTGTGAGA
*
49132942 GACACGGGCGTGTCATAGCCGTGTGAGA
1 GACACGGGCGTGTCATGGCCGTGTGAGA
49132970 GACACGGGC
1 GACACGGGC
49132979 CATGGACACG
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 82 1.00
ACGTcount: A:0.19, C:0.21, G:0.41, T:0.19
Consensus pattern (28 bp):
GACACGGGCGTGTCATGGCCGTGTGAGA
Found at i:49135180 original size:22 final size:22
Alignment explanation
Indices: 49135155--49135198 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
49135145 AACTTATTAA
49135155 ATTGAAGTGTGAAAGCGGGGAT
1 ATTGAAGTGTGAAAGCGGGGAT
*
49135177 ATTGAAGTGTGAAAGTGGGGAT
1 ATTGAAGTGTGAAAGCGGGGAT
49135199 GTTCTTCGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.02, G:0.41, T:0.25
Consensus pattern (22 bp):
ATTGAAGTGTGAAAGCGGGGAT
Found at i:49139594 original size:48 final size:49
Alignment explanation
Indices: 49139470--49139599 Score: 174
Period size: 49 Copynumber: 2.7 Consensus size: 49
49139460 TATACAAGCT
*
49139470 AGTGTAAGACCTGTCTGGGACATGGCATCGACACTGATAGATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACACTAATAGATGAGAGCC
* * ** **
49139519 AGTGTATGACCTGTCTGGGACACGGCATCGACTTTAAT-G-TGCTAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACACTAATAGATGAGAGCC
49139566 AGTGTAAGACCATGTCTGGGACATGGCATCGACA
1 AGTGTAAGACC-TGTCTGGGACATGGCATCGACA
49139600 TTTTATCCCA
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
47 16 0.23
48 21 0.30
49 33 0.47
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCGACACTAATAGATGAGAGCC
Found at i:49141567 original size:31 final size:32
Alignment explanation
Indices: 49141532--49141608 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 32
49141522 ATGATGCTAG
* *
49141532 AGATATTTTAATATTTTA-TAATTA-TTTAATT
1 AGATATTTTATTATTTTATTAA-TACTTTAATA
**
49141563 AGATA-AATATTATTTTATTAATACTTTAATA
1 AGATATTTTATTATTTTATTAATACTTTAATA
49141594 AGATATTTTATTATT
1 AGATATTTTATTATT
49141609 ATTTTATTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
30 11 0.30
31 19 0.51
32 7 0.19
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (32 bp):
AGATATTTTATTATTTTATTAATACTTTAATA
Found at i:49143791 original size:46 final size:46
Alignment explanation
Indices: 49143739--49144040 Score: 415
Period size: 46 Copynumber: 6.7 Consensus size: 46
49143729 AGTGTGCTCT
49143739 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
49143785 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
49143831 C-----TG---TGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
49143869 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCGTGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
49143915 CTGATATGAGATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * ** *
49143961 GTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGACAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
49144007 ATGACA-GAAAATGAGTAAAACCATAGTTGAAAGA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGA
49144041 CATTATGGCA
Statistics
Matches: 232, Mismatches: 15, Indels: 18
0.88 0.06 0.07
Matches are distributed among these distances:
38 36 0.16
41 2 0.01
43 2 0.01
45 1 0.00
46 191 0.82
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:49143891 original size:84 final size:87
Alignment explanation
Indices: 49143749--49144006 Score: 387
Period size: 84 Copynumber: 2.9 Consensus size: 87
49143739 CTGATATGAA
49143749 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTG
49143814 AAAGATACCATGGCAACC-T-G
66 AAAGATACCATGGCAACCATAG
49143834 -TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTG
*
49143898 AAAGATACCGTGGCAACCTGATATGAG
66 AAAGATACCATGGCAACC----AT-AG
* * * **
49143925 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTTG
1 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTG
*
49143990 AAAGATACCATGACAAC
66 AAAGATACCATGGCAAC
49144007 ATGACAGAAA
Statistics
Matches: 157, Mismatches: 8, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
84 81 0.52
89 1 0.01
91 1 0.01
92 74 0.47
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (87 bp):
ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTG
AAAGATACCATGGCAACCATAG
Found at i:49144356 original size:23 final size:25
Alignment explanation
Indices: 49144311--49144357 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
49144301 AATGAATATA
*
49144311 CATAAAATATATGGAAATGATGAAG
1 CATAAAATATATGGAAATAATGAAG
*
49144336 CATAAAATAT-T-GATATAATGAA
1 CATAAAATATATGGAAATAATGAA
49144358 ATGAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (25 bp):
CATAAAATATATGGAAATAATGAAG
Found at i:49145982 original size:21 final size:21
Alignment explanation
Indices: 49145956--49145996 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
49145946 TCAAAATCTA
*
49145956 AACAGAAGCTTGTAAGAGCTT
1 AACAGAAGCTAGTAAGAGCTT
49145977 AACAGAAGCTAGTAAGAGCT
1 AACAGAAGCTAGTAAGAGCT
49145997 AATTCACCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (21 bp):
AACAGAAGCTAGTAAGAGCTT
Found at i:49146731 original size:23 final size:22
Alignment explanation
Indices: 49146688--49146740 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
49146678 TATTTTATTC
* *
49146688 ATCAA-AAAAATTCTAATATTT
1 ATCAATAAAAATTCCAAAATTT
49146709 ATCAATAAAAACTTCCAAAATTT
1 ATCAATAAAAA-TTCCAAAATTT
*
49146732 -TTAATAAAA
1 ATCAATAAAA
49146741 TCAAAAACGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.19
22 13 0.48
23 9 0.33
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (22 bp):
ATCAATAAAAATTCCAAAATTT
Found at i:49147834 original size:20 final size:20
Alignment explanation
Indices: 49147784--49147834 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
49147774 AAATTAATAC
49147784 AATATTAAA-AATAAAAATT
1 AATATTAAATAATAAAAATT
**
49147803 AATA-TAATATAATTCAAATT
1 AATATTAA-ATAATAAAAATT
*
49147823 CATATTAAATAA
1 AATATTAAATAA
49147835 ATGTCATTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 3 0.12
19 5 0.19
20 15 0.58
21 3 0.12
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (20 bp):
AATATTAAATAATAAAAATT
Found at i:49148353 original size:20 final size:20
Alignment explanation
Indices: 49148328--49148560 Score: 92
Period size: 20 Copynumber: 12.2 Consensus size: 20
49148318 TTATTAGATA
49148328 AAAAATTGTAAAAAATTATT
1 AAAAATTGTAAAAAATTATT
*
49148348 AAAAATCG--AAAAATTATT
1 AAAAATTGTAAAAAATTATT
* *
49148366 TAAAA--GT---ATATTA--
1 AAAAATTGTAAAAAATTATT
*
49148379 AAAAATTGTAAAAGAA-AATT
1 AAAAATTGTAAAA-AATTATT
** *
49148399 -TTAGTTGTTAAAAAAATT-TT
1 AAAAATTGT-AAA-AAATTATT
* *
49148419 AAAATTTTTAAAAAA-TA--
1 AAAAATTGTAAAAAATTATT
*
49148436 AAATATTGTTAAAAATATT-TT
1 AAAAATTG-TAAAAA-ATTATT
*
49148457 -AAAATTGTAACAAAGTTATT
1 AAAAATTGTAA-AAAATTATT
* *
49148477 AAAAATTATAAAACATTAATT
1 AAAAATTGTAAAAAATT-ATT
* * *
49148498 AAAATTTGTAAAAAAATA-A
1 AAAAATTGTAAAAAATTATT
**
49148517 AAAAATT-TGGAAAATTATT
1 AAAAATTGTAAAAAATTATT
49148536 AAATAATTGTAAAAAATTA-T
1 AAA-AATTGTAAAAAATTATT
49148556 AAAAA
1 AAAAA
49148561 AAACTATGAA
Statistics
Matches: 153, Mismatches: 34, Indels: 53
0.64 0.14 0.22
Matches are distributed among these distances:
13 4 0.03
15 7 0.05
16 1 0.01
17 5 0.03
18 30 0.20
19 26 0.17
20 42 0.27
21 38 0.25
ACGTcount: A:0.58, C:0.01, G:0.06, T:0.35
Consensus pattern (20 bp):
AAAAATTGTAAAAAATTATT
Found at i:49148439 original size:16 final size:18
Alignment explanation
Indices: 49148418--49148450 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
49148408 AAAAAAATTT
49148418 TAAAAT-TT-TTAAAAAA
1 TAAAATATTGTTAAAAAA
49148434 TAAAATATTGTTAAAAA
1 TAAAATATTGTTAAAAA
49148451 TATTTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
TAAAATATTGTTAAAAAA
Found at i:49148483 original size:21 final size:21
Alignment explanation
Indices: 49148457--49148510 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
49148447 AAAATATTTT
49148457 AAAATTGTAACAA-AGTT-ATTA
1 AAAATTGTAA-AACA-TTAATTA
*
49148478 AAAATTATAAAACATTAATTA
1 AAAATTGTAAAACATTAATTA
*
49148499 AAATTTGTAAAA
1 AAAATTGTAAAA
49148511 AAATAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (21 bp):
AAAATTGTAAAACATTAATTA
Found at i:49148562 original size:11 final size:10
Alignment explanation
Indices: 49148457--49148561 Score: 61
Period size: 10 Copynumber: 10.4 Consensus size: 10
49148447 AAAATATTTT
*
49148457 AAAATTGTAA
1 AAAATTATAA
* *
49148467 CAAAGTTATTA
1 -AAAATTATAA
49148478 AAAATTATAA
1 AAAATTATAA
* *
49148488 AACATTAATTA
1 AAAATT-ATAA
* *
49148499 AAATTTGTAA
1 AAAATTATAA
*
49148509 AAAAATA-AA
1 AAAATTATAA
**
49148518 AAAATT-TGG
1 AAAATTATAA
49148527 AAAATTATTAA
1 AAAATTA-TAA
* *
49148538 ATAATTGTAA
1 AAAATTATAA
49148548 AAAATTATAA
1 AAAATTATAA
49148558 AAAA
1 AAAA
49148562 AACTATGAAT
Statistics
Matches: 67, Mismatches: 23, Indels: 9
0.68 0.23 0.09
Matches are distributed among these distances:
9 13 0.19
10 34 0.51
11 20 0.30
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (10 bp):
AAAATTATAA
Found at i:49148896 original size:18 final size:18
Alignment explanation
Indices: 49148873--49148907 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
49148863 ATTTACAATT
*
49148873 TTTAAATATTTTTTATAA
1 TTTAAATACTTTTTATAA
49148891 TTTAAATACTTTTTATA
1 TTTAAATACTTTTTATA
49148908 CTTTTTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTAAATACTTTTTATAA
Found at i:49148939 original size:9 final size:9
Alignment explanation
Indices: 49148882--49148949 Score: 73
Period size: 9 Copynumber: 7.3 Consensus size: 9
49148872 TTTTAAATAT
49148882 TTTTTATAA
1 TTTTTATAA
** *
49148891 TTTAAATAC
1 TTTTTATAA
*
49148900 TTTTTATAC
1 TTTTTATAA
49148909 TTTTTATAA
1 TTTTTATAA
*
49148918 TTTTTAAATA
1 TTTTTATA-A
49148928 TTTTTATAA
1 TTTTTATAA
49148937 TTTTTAATAA
1 TTTTT-ATAA
49148947 TTT
1 TTT
49148950 ATTTACAACT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
9 34 0.69
10 15 0.31
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:49148946 original size:10 final size:10
Alignment explanation
Indices: 49148813--49148949 Score: 72
Period size: 10 Copynumber: 13.8 Consensus size: 10
49148803 TTTTAAATTA
49148813 AATAATATTTT
1 AATAAT-TTTT
* *
49148824 ATTATTTTTAT
1 AATAATTTT-T
*
49148835 AAAAATATTTT
1 AATAAT-TTTT
* *
49148846 AACAATATTT
1 AATAATTTTT
*
49148856 AATAATCATTT
1 AATAAT-TTTT
*
49148867 -ACAATTTTT
1 AATAATTTTT
49148876 AA-ATATTTTT
1 AATA-ATTTTT
* *
49148886 TATAA-TTTA
1 AATAATTTTT
*
49148895 AATACTTTTT
1 AATAATTTTT
*
49148905 -ATACTTTTT
1 AATAATTTTT
49148914 -ATAATTTTT
1 AATAATTTTT
49148923 AA-ATATTTTT
1 AATA-ATTTTT
49148933 -ATAATTTTT
1 AATAATTTTT
49148942 AATAATTT
1 AATAATTT
49148950 ATTTACAACT
Statistics
Matches: 99, Mismatches: 16, Indels: 23
0.72 0.12 0.17
Matches are distributed among these distances:
9 35 0.35
10 42 0.42
11 19 0.19
12 3 0.03
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (10 bp):
AATAATTTTT
Found at i:49151978 original size:21 final size:21
Alignment explanation
Indices: 49151954--49151993 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
49151944 AAATTCTATA
49151954 TTTGTATGATTTGAATTGATG
1 TTTGTATGATTTGAATTGATG
49151975 TTTGTATGATTTGAATTGA
1 TTTGTATGATTTGAATTGA
49151994 ATATTGTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.53
Consensus pattern (21 bp):
TTTGTATGATTTGAATTGATG
Found at i:49152204 original size:25 final size:24
Alignment explanation
Indices: 49152176--49152254 Score: 86
Period size: 25 Copynumber: 3.2 Consensus size: 24
49152166 ATAAGTATCC
*
49152176 CGATATTTGGCTCTTACGAGCTTCT
1 CGAT-TTTGGCTCTCACGAGCTTCT
* *
49152201 CGATTAATGGCTCTCACGAGCTTCC
1 CGATT-TTGGCTCTCACGAGCTTCT
* *
49152226 CGATTTATGGCTCGCATGAGCTTCT
1 CGATTT-TGGCTCTCACGAGCTTCT
49152251 CGAT
1 CGAT
49152255 ATACAACTCG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
24 1 0.02
25 44 0.98
ACGTcount: A:0.18, C:0.27, G:0.22, T:0.34
Consensus pattern (24 bp):
CGATTTTGGCTCTCACGAGCTTCT
Found at i:49154124 original size:21 final size:21
Alignment explanation
Indices: 49154098--49154139 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
49154088 ATACCTGGTA
*
49154098 AAAAGTATCGGTACTTTTTGT
1 AAAAGTATCGATACTTTTTGT
49154119 AAAAGTATCGATACTTTTTGT
1 AAAAGTATCGATACTTTTTGT
49154140 GTTGATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.43
Consensus pattern (21 bp):
AAAAGTATCGATACTTTTTGT
Found at i:49166003 original size:30 final size:30
Alignment explanation
Indices: 49165969--49166028 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
49165959 TTCAAGTGTA
49165969 ATGATATATATAAGTGAAGTGAATACTAAG
1 ATGATATATATAAGTGAAGTGAATACTAAG
49165999 ATGATATATATAAGTGAAGTGAATACTAAG
1 ATGATATATATAAGTGAAGTGAATACTAAG
49166029 TAAGAGGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.30
Consensus pattern (30 bp):
ATGATATATATAAGTGAAGTGAATACTAAG
Found at i:49169245 original size:20 final size:20
Alignment explanation
Indices: 49169210--49169252 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
49169200 ACCTTCTTAT
49169210 AATTATTAATTACAAATAAAA
1 AATTATTAATTACAAA-AAAA
*
49169231 AATTATTGA-TACAAAAAAA
1 AATTATTAATTACAAAAAAA
49169250 AAT
1 AAT
49169253 ATAATAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 6 0.29
21 8 0.38
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (20 bp):
AATTATTAATTACAAAAAAA
Found at i:49172115 original size:30 final size:30
Alignment explanation
Indices: 49172081--49172142 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
49172071 ACTTATTTTA
49172081 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
49172111 TTGTTAATTTTGTTATTATTTTAGAGTCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
49172141 TT
1 TT
49172143 ACTTGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.26, C:0.03, G:0.11, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:49175744 original size:31 final size:31
Alignment explanation
Indices: 49175679--49175736 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
49175669 TGCGTTACCT
*
49175679 TATTTATTGAAATAAAAAAAAAGAATAAAAA
1 TATTTATTGAAATAAAAAAAAAAAATAAAAA
49175710 TATTT-TT-AAATAAAAAATAAAAAATAA
1 TATTTATTGAAATAAAAAA-AAAAAATAA
49175737 TTAATATTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 10 0.40
30 10 0.40
31 5 0.20
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.29
Consensus pattern (31 bp):
TATTTATTGAAATAAAAAAAAAAAATAAAAA
Found at i:49176012 original size:27 final size:27
Alignment explanation
Indices: 49175951--49176012 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
49175941 TATATAAAAC
49175951 ATATAATACTAGATTAAAAAAATATAT
1 ATATAATACTAGATTAAAAAAATATAT
* * *
49175978 ATACAATA-TATATTGAAAACAATA-AT
1 ATATAATACTAGATT-AAAAAAATATAT
49176004 AATATAATA
1 -ATATAATA
49176013 ACTAATAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (27 bp):
ATATAATACTAGATTAAAAAAATATAT
Found at i:49176263 original size:23 final size:23
Alignment explanation
Indices: 49176232--49176275 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
49176222 ATCGAGTATT
* *
49176232 AAAAGTATATATATAATATAGAC
1 AAAAATATATACATAATATAGAC
*
49176255 AAAAATATATGCATAATATAG
1 AAAAATATATACATAATATAG
49176276 TATTGAAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.30
Consensus pattern (23 bp):
AAAAATATATACATAATATAGAC
Found at i:49176347 original size:25 final size:24
Alignment explanation
Indices: 49176302--49176360 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 24
49176292 ATGGGGGATA
* * **
49176302 ATATAAAAAATGTATGAATAATGT
1 ATATTAAAAATATATGAATAACAT
49176326 GATATTAAAAATATAT-ACATAACAT
1 -ATATTAAAAATATATGA-ATAACAT
49176351 ATATTAAAAA
1 ATATTAAAAA
49176361 AATAATATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 11 0.38
25 18 0.62
ACGTcount: A:0.58, C:0.03, G:0.07, T:0.32
Consensus pattern (24 bp):
ATATTAAAAATATATGAATAACAT
Found at i:49176354 original size:13 final size:13
Alignment explanation
Indices: 49176336--49176454 Score: 65
Period size: 13 Copynumber: 9.4 Consensus size: 13
49176326 GATATTAAAA
49176336 ATATATACATAAC
1 ATATATACATAAC
* *
49176349 ATATATTA-AAAAA
1 ATATA-TACATAAC
* *
49176362 ATAATATTA-AAAAT
1 AT-ATA-TACATAAC
*
49176376 ATATATACATAAT
1 ATATATACATAAC
*
49176389 ATATATATATAGA-
1 ATATATACATA-AC
49176402 ATATATACAT-A-
1 ATATATACATAAC
* *
49176413 ATATAGTA-TTAAA
1 ATATA-TACATAAC
49176426 ATATATACATAAC
1 ATATATACATAAC
49176439 --ATATACATAAC
1 ATATATACATAAC
49176450 ATATA
1 ATATA
49176455 CATATTAGAA
Statistics
Matches: 87, Mismatches: 9, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
11 18 0.21
12 7 0.08
13 47 0.54
14 15 0.17
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (13 bp):
ATATATACATAAC
Found at i:49176375 original size:12 final size:13
Alignment explanation
Indices: 49176327--49176408 Score: 53
Period size: 13 Copynumber: 6.2 Consensus size: 13
49176317 GAATAATGTG
49176327 ATATTAAAAATAT
1 ATATTAAAAATAT
* * *
49176340 ATA--CATAACAT
1 ATATTAAAAATAT
*
49176351 ATATTAAAAAAAT
1 ATATTAAAAATAT
49176364 AATATTAAAAATAT
1 -ATATTAAAAATAT
*
49176378 ATA-TACATAATAT
1 ATATTA-AAAATAT
*
49176391 ATATATATAGAATAT
1 ATAT-TA-AAAATAT
49176406 ATA
1 ATA
49176409 CATAATATAG
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
11 8 0.15
12 2 0.04
13 20 0.38
14 12 0.23
15 11 0.21
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (13 bp):
ATATTAAAAATAT
Found at i:49176390 original size:11 final size:11
Alignment explanation
Indices: 49176376--49176458 Score: 67
Period size: 11 Copynumber: 7.0 Consensus size: 11
49176366 TATTAAAAAT
49176376 ATATATACATAA
1 ATATATACAT-A
*
49176388 TATATATATATAGA
1 -ATATATACAT--A
49176402 ATATATACATA
1 ATATATACATA
* *
49176413 ATATAGTATTAAA
1 ATATA-TA-CATA
49176426 ATATATACATA
1 ATATATACATA
*
49176437 ACATATACATA
1 ATATATACATA
*
49176448 ACATATACATA
1 ATATATACATA
49176459 TTAGAAATGA
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
11 29 0.49
12 4 0.07
13 25 0.42
14 1 0.02
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.35
Consensus pattern (11 bp):
ATATATACATA
Found at i:49176392 original size:15 final size:15
Alignment explanation
Indices: 49176374--49176408 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
49176364 AATATTAAAA
*
49176374 ATATATATACATAAT
1 ATATATATACAGAAT
*
49176389 ATATATATATAGAAT
1 ATATATATACAGAAT
49176404 ATATA
1 ATATA
49176409 CATAATATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (15 bp):
ATATATATACAGAAT
Found at i:49176405 original size:24 final size:24
Alignment explanation
Indices: 49176361--49176443 Score: 89
Period size: 26 Copynumber: 3.3 Consensus size: 24
49176351 ATATTAAAAA
49176361 AATA-ATATTAAAAATATATATACAT
1 AATATATATT-AAAA-ATATATACAT
*
49176386 AATATATATATATAGAATATATACAT
1 AATATATAT-TA-AAAATATATACAT
49176412 AATATAGTATT-AAAATATATACAT
1 AATATA-TATTAAAAATATATACAT
*
49176436 AACATATA
1 AATATATA
49176444 CATAACATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
23 2 0.04
24 17 0.33
25 4 0.08
26 22 0.43
27 6 0.12
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (24 bp):
AATATATATTAAAAATATATACAT
Found at i:49176405 original size:26 final size:23
Alignment explanation
Indices: 49176376--49176443 Score: 91
Period size: 26 Copynumber: 2.8 Consensus size: 23
49176366 TATTAAAAAT
49176376 ATATATACATAATATATATATATAGA
1 ATATATACATAATATATAT-TA-A-A
49176402 ATATATACATAATATAGTATTAAA
1 ATATATACATAATATA-TATTAAA
*
49176426 ATATATACATAACATATA
1 ATATATACATAATATATA
49176444 CATAACATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
23 2 0.05
24 16 0.40
25 1 0.03
26 18 0.45
27 3 0.08
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (23 bp):
ATATATACATAATATATATTAAA
Found at i:49176457 original size:6 final size:6
Alignment explanation
Indices: 49176428--49176459 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
49176418 GTATTAAAAT
49176428 ATATAC ATA-AC ATATAC ATA-AC ATATAC ATAT
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATAT
49176460 TAGAAATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.42
6 14 0.58
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (6 bp):
ATATAC
Found at i:49176946 original size:25 final size:25
Alignment explanation
Indices: 49176917--49176981 Score: 80
Period size: 24 Copynumber: 2.6 Consensus size: 25
49176907 AACTAATACT
*
49176917 AATAATAGTAAAACTAATAATATA-A
1 AATAATAGTAAAA-TAAAAATATAGA
*
49176942 CATAATA-TAAAATAAAAATATAGA
1 AATAATAGTAAAATAAAAATATAGA
49176966 AATAATAGTAATAATA
1 AATAATAGTAA-AATA
49176982 CGAAGATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 9 0.26
24 12 0.35
25 9 0.26
26 4 0.12
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (25 bp):
AATAATAGTAAAATAAAAATATAGA
Found at i:49178552 original size:21 final size:21
Alignment explanation
Indices: 49178527--49178575 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
49178517 TAAAATCTGC
**
49178527 AACTTCAATGTGCTCCACTGT
1 AACTTCAATCAGCTCCACTGT
**
49178548 AACTTTGATCAGCTCCACTGT
1 AACTTCAATCAGCTCCACTGT
49178569 AACTTCA
1 AACTTCA
49178576 GGGCTCTGCT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.33
Consensus pattern (21 bp):
AACTTCAATCAGCTCCACTGT
Found at i:49178875 original size:85 final size:86
Alignment explanation
Indices: 49178693--49179012 Score: 419
Period size: 85 Copynumber: 3.7 Consensus size: 86
49178683 CAGCATGTGA
* * * * * * *
49178693 CCCGAGGCTCTACTCACCTCTCGCAATATGATTTGACTTTTGATAAAAACAGAATTTGAAAAATA
1 CCCGAGGCTCAACTCACCTCTCACAATATGAGTTGACTTTT--T-GAAACATAAATTGAAAAATG
*
49178758 GAAACTGAAAATACCTCAGCGTGT
63 GAAATTGAAAATACCTCAGCGTGT
49178782 CCCGAGGCTCAACTCACCTCTCACAATATGAGTTGA-TTTTTGAAACATAAATTGAAAAATGGAA
1 CCCGAGGCTCAACTCACCTCTCACAATATGAGTTGACTTTTTGAAACATAAATTGAAAAATGGAA
*
49178846 ATTGAAAATACCTCAGCTTGT
66 ATTGAAAATACCTCAGCGTGT
** * *
49178867 CTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAACATAAATTGAAAAACGGAA
1 CCCGAGGCTCAACTCACCTCTCACAATATGAGTTGACTTTTTGAAACATAAATTGAAAAATGGAA
*
49178931 ATTAAAAATACCTCAGCGTGT
66 ATTGAAAATACCTCAGCGTGT
* * * *
49178952 CCCGACGCTTAACTCACCTCTCACAATATGAGTTGATTTTTTGAAAGACAAAAATTGAAAA
1 CCCGAGGCTCAACTCACCTCTCACAATATGAGTTGACTTTTTG-AA-ACATAAATTGAAAA
49179013 TTACCTCAGC
Statistics
Matches: 207, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
85 148 0.71
86 7 0.03
87 2 0.01
88 17 0.08
89 33 0.16
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (86 bp):
CCCGAGGCTCAACTCACCTCTCACAATATGAGTTGACTTTTTGAAACATAAATTGAAAAATGGAA
ATTGAAAATACCTCAGCGTGT
Found at i:49179041 original size:75 final size:74
Alignment explanation
Indices: 49178929--49179149 Score: 300
Period size: 75 Copynumber: 2.9 Consensus size: 74
49178919 TGAAAAACGG
* * * *
49178929 AAATTAAAAATACCTCAGCGTGTCCCGACGCTTAACTCACCTCTCACAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
49178994 GAAAGACAA
66 GAAAGACAA
*
49179003 AAATTGAAAATTACCTCAGCGTGTCCCGAGGCTCAACTCAACTCTCGCAATATGAGTTGATTTTT
1 AAATTGAAAA-TACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----T
*
49179068 TTTTTGAAAGACAG
61 TTTTTGAAAGACAA
* * **
49179082 AAATTGAAAACACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTT
1 AAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
49179146 GAAA
66 GAAA
49179150 CAGAAATAAA
Statistics
Matches: 131, Mismatches: 11, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
73 9 0.07
74 9 0.07
75 45 0.34
78 44 0.34
79 24 0.18
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.30
Consensus pattern (74 bp):
AAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
GAAAGACAA
Found at i:49179117 original size:78 final size:78
Alignment explanation
Indices: 49178918--49179145 Score: 311
Period size: 78 Copynumber: 3.0 Consensus size: 78
49178908 GAAACATAAA
* * * * * *
49178918 TTGAAAAACGGAAATTAAAAATACCTCAGCGTGTCCCGACGCTTAACTCACCTCTCACAATATGA
1 TTGAAAGACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
49178983 GTTGA----TTTT
66 GTTGATTTTTTTT
* *
49178992 TTGAAAGACAAAAATTGAAAATTACCTCAGCGTGTCCCGAGGCTCAACTCAACTCTCGCAATATG
1 TTGAAAGACAGAAATTGAAAA-TACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATG
49179057 AGTTGATTTTTTTT
65 AGTTGATTTTTTTT
* * **
49179071 TTGAAAGACAGAAATTGAAAACACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAGACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
49179136 GTTGATTTTT
66 GTTGATTTTT
49179146 GAAACAGAAA
Statistics
Matches: 135, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
74 17 0.13
75 45 0.33
78 49 0.36
79 24 0.18
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (78 bp):
TTGAAAGACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTTTTT
Found at i:49179137 original size:153 final size:153
Alignment explanation
Indices: 49178844--49179149 Score: 391
Period size: 153 Copynumber: 2.0 Consensus size: 153
49178834 TGAAAAATGG
* ** *
49178844 AAATTGAAAATACCTCAGCTTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
1 AAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCAACTCTCGCAATATGAGTTGATTTTT-
* * * *
49178909 AAACATAAATTGAAAAACGGAAATTAAAAATACCTCAGCGTGTCCCGACGCTTAACTCACCTCTC
65 ----ATAAATTGAAAAACAGAAATTAAAAACACCTCAACGTGTCCCGACGCTCAACTCACCTCTC
49178974 ACAATATGAGTTGATTTTTTGAAAGACAA
126 ACAATATGAGTTGA-TTTTTGAAAGACAA
49179003 AAATTGAAAATTACCTCAGCGTGTCCCGAGGCTCAACTCAACTCTCGCAATATGAGTTGATTTTT
1 AAATTGAAAA-TACCTCAGCGTGTCCCGAGGCTCAACTCAACTCTCGCAATATGAGTTGATTTTT
** * * ** * *
49179068 -T-TTTTGAAAGACAGAAATTGAAAACACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAA
65 ATAAATTGAAAAACAGAAATTAAAAACACCTCAACGTGTCCCGACGCTCAACTCACCTCTCACAA
49179131 TATGAGTTGATTTTTGAAA
130 TATGAGTTGATTTTTGAAA
49179150 CAGAAATAAA
Statistics
Matches: 130, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
152 9 0.07
153 60 0.46
154 1 0.01
159 10 0.08
160 50 0.38
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (153 bp):
AAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCAACTCTCGCAATATGAGTTGATTTTTA
TAAATTGAAAAACAGAAATTAAAAACACCTCAACGTGTCCCGACGCTCAACTCACCTCTCACAAT
ATGAGTTGATTTTTGAAAGACAA
Found at i:49187478 original size:22 final size:22
Alignment explanation
Indices: 49187451--49187495 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
49187441 AATGGGTGAA
*
49187451 TGAATAAATGACAAATGAATGT
1 TGAATAAATAACAAATGAATGT
*
49187473 TGAATAAATAACGAATGAATGT
1 TGAATAAATAACAAATGAATGT
49187495 T
1 T
49187496 AGTCATGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.04, G:0.18, T:0.29
Consensus pattern (22 bp):
TGAATAAATAACAAATGAATGT
Found at i:49191133 original size:27 final size:27
Alignment explanation
Indices: 49191072--49191133 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
49191062 TATATAAAAC
49191072 ATATAATACTAGATTAAAAAAATATAT
1 ATATAATACTAGATTAAAAAAATATAT
* * *
49191099 ATACAATA-TATATTGAAAACAATA-AT
1 ATATAATACTAGATT-AAAAAAATATAT
49191125 AATATAATA
1 -ATATAATA
49191134 ACTAATAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (27 bp):
ATATAATACTAGATTAAAAAAATATAT
Found at i:49191372 original size:23 final size:23
Alignment explanation
Indices: 49191341--49191384 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
49191331 ATTGAGTATT
* *
49191341 AAAAGTATATATATAATATAGAC
1 AAAAATATATACATAATATAGAC
*
49191364 AAAAATATATGCATAATATAG
1 AAAAATATATACATAATATAG
49191385 TATTGAAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.30
Consensus pattern (23 bp):
AAAAATATATACATAATATAGAC
Found at i:49191452 original size:50 final size:49
Alignment explanation
Indices: 49191335--49191483 Score: 124
Period size: 50 Copynumber: 3.0 Consensus size: 49
49191325 AATAGTATTG
* * * *
49191335 AGTATTAAAAGTATATATAT-A-ATATAGACAAAAATATATGCATAATAT
1 AGTATTAAAAATATATACATAACATATATA-AAAAATATATGAATAATAT
* * * *** *
49191383 AGTATTGAAAGTATTTACATGGGATAATATAAAAAATATATGAATAATGT
1 AGTATTAAAAATATATACATAACAT-ATATAAAAAATATATGAATAATAT
* *
49191433 -GATATTAAAAATATATACATAACATATATAAAAAATAATATTAAAAATAT
1 AG-TATTAAAAATATATACATAACATATATAAAAAAT-ATATGAATAATAT
49191483 A
1 A
49191484 TATACATAAT
Statistics
Matches: 79, Mismatches: 16, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
48 17 0.22
49 12 0.15
50 46 0.58
51 4 0.05
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.33
Consensus pattern (49 bp):
AGTATTAAAAATATATACATAACATATATAAAAAATATATGAATAATAT
Found at i:49191461 original size:13 final size:13
Alignment explanation
Indices: 49191443--49191559 Score: 72
Period size: 13 Copynumber: 9.4 Consensus size: 13
49191433 GATATTAAAA
49191443 ATATATACATAAC
1 ATATATACATAAC
*
49191456 ATATATA-A-AAA
1 ATATATACATAAC
* *
49191467 ATAATATTA-AAAAT
1 AT-ATA-TACATAAC
*
49191481 ATATATACATAAT
1 ATATATACATAAC
*
49191494 ATATATATATAGA-
1 ATATATACATA-AC
49191507 ATATATACAT-A-
1 ATATATACATAAC
* *
49191518 ATATAGTA-TTAAA
1 ATATA-TACATAAC
49191531 ATATATACATAAC
1 ATATATACATAAC
49191544 --ATATACATAAC
1 ATATATACATAAC
49191555 ATATA
1 ATATA
49191560 CATATTAGAA
Statistics
Matches: 85, Mismatches: 8, Indels: 22
0.74 0.07 0.19
Matches are distributed among these distances:
11 22 0.26
12 11 0.13
13 47 0.55
14 5 0.06
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (13 bp):
ATATATACATAAC
Found at i:49191473 original size:25 final size:25
Alignment explanation
Indices: 49191409--49191469 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
49191399 ACATGGGATA
**
49191409 ATATAAAAAATATATGAATAATGTG
1 ATATAAAAAATATATGAATAACATG
*
49191434 ATATTAAAAATATAT-ACATAACAT-
1 ATATAAAAAATATATGA-ATAACATG
49191458 ATATAAAAAATA
1 ATATAAAAAATA
49191470 ATATTAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 12 0.39
25 19 0.61
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (25 bp):
ATATAAAAAATATATGAATAACATG
Found at i:49191484 original size:11 final size:11
Alignment explanation
Indices: 49191434--49191484 Score: 50
Period size: 12 Copynumber: 4.4 Consensus size: 11
49191424 GAATAATGTG
49191434 ATATTAAAAAT
1 ATATTAAAAAT
49191445 ATA-TACATAACAT
1 ATATTA-A-AA-AT
*
49191458 ATATAAAAAAT
1 ATATTAAAAAT
49191469 AATATTAAAAAT
1 -ATATTAAAAAT
49191481 ATAT
1 ATAT
49191485 ATACATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
10 2 0.06
11 10 0.30
12 14 0.42
13 6 0.18
14 1 0.03
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
ATATTAAAAAT
Found at i:49191495 original size:11 final size:11
Alignment explanation
Indices: 49191481--49191563 Score: 67
Period size: 11 Copynumber: 7.0 Consensus size: 11
49191471 TATTAAAAAT
49191481 ATATATACATAA
1 ATATATACAT-A
*
49191493 TATATATATATAGA
1 -ATATATACAT--A
49191507 ATATATACATA
1 ATATATACATA
* *
49191518 ATATAGTATTAAA
1 ATATA-TA-CATA
49191531 ATATATACATA
1 ATATATACATA
*
49191542 ACATATACATA
1 ATATATACATA
*
49191553 ACATATACATA
1 ATATATACATA
49191564 TTAGAAATGA
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
11 29 0.49
12 4 0.07
13 25 0.42
14 1 0.02
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.35
Consensus pattern (11 bp):
ATATATACATA
Found at i:49191510 original size:24 final size:24
Alignment explanation
Indices: 49191456--49191548 Score: 91
Period size: 26 Copynumber: 3.8 Consensus size: 24
49191446 TATACATAAC
* *
49191456 ATATATAAAAAATA-ATATTAAAAA
1 ATATATACATAATATATATT-AAAA
*
49191480 TATATATACATAATATATATATATAGA
1 -ATATATACATAATATATAT-TA-AAA
49191507 ATATATACATAATATAGTATT-AAA
1 ATATATACATAATATA-TATTAAAA
*
49191531 ATATATACATAACATATA
1 ATATATACATAATATATA
49191549 CATAACATAT
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
23 2 0.03
24 17 0.29
25 12 0.20
26 22 0.37
27 6 0.10
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.35
Consensus pattern (24 bp):
ATATATACATAATATATATTAAAA
Found at i:49191562 original size:6 final size:6
Alignment explanation
Indices: 49191533--49191564 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
49191523 GTATTAAAAT
49191533 ATATAC ATA-AC ATATAC ATA-AC ATATAC ATAT
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATAT
49191565 TAGAAATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.42
6 14 0.58
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (6 bp):
ATATAC
Found at i:49191619 original size:11 final size:11
Alignment explanation
Indices: 49191603--49191628 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
49191593 TACTATTAAT
49191603 AATACTACATA
1 AATACTACATA
49191614 AATACTACATA
1 AATACTACATA
49191625 AATA
1 AATA
49191629 TGTACATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (11 bp):
AATACTACATA
Found at i:49191881 original size:15 final size:15
Alignment explanation
Indices: 49191861--49191899 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
49191851 TGTACATAAT
*
49191861 ATAATATTAAGAAAA
1 ATAATATTAACAAAA
*
49191876 ATAATAATAACAAAA
1 ATAATATTAACAAAA
49191891 A-AATATTAA
1 ATAATATTAA
49191900 TAATACTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (15 bp):
ATAATATTAACAAAA
Found at i:49195258 original size:24 final size:22
Alignment explanation
Indices: 49195216--49195259 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
49195206 TTAAAGTGTA
49195216 AATATGAAAAATTTGAAGGGCT
1 AATATGAAAAATTTGAAGGGCT
*
49195238 AATAGTGAAAATATTTTAAGGG
1 AATA-TGAAAA-ATTTGAAGGG
49195260 TGGAATGATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 6 0.32
24 9 0.47
ACGTcount: A:0.45, C:0.02, G:0.23, T:0.30
Consensus pattern (22 bp):
AATATGAAAAATTTGAAGGGCT
Found at i:49197473 original size:16 final size:17
Alignment explanation
Indices: 49197436--49197476 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
49197426 AATTGGTTCC
49197436 AAATATAAATATTAGATG
1 AAATA-AAATATTAGATG
49197454 AAATAAAATATCT-GAT-
1 AAATAAAATAT-TAGATG
49197470 AAATAAA
1 AAATAAA
49197477 TCGATAACGC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 7 0.32
17 9 0.41
18 6 0.27
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (17 bp):
AAATAAAATATTAGATG
Found at i:49197855 original size:43 final size:41
Alignment explanation
Indices: 49197802--49197935 Score: 142
Period size: 43 Copynumber: 3.1 Consensus size: 41
49197792 CATAAATGCT
*
49197802 GCTAAAGAACATAACCTTTAGCGGCACTTTTTTTACAAACGCC
1 GCTAAAGAACAT-ACCTTTAGCGGC-CTTTTTTTACAAACACC
* * *
49197845 GCTATAGAACATGTCCTTTAGCGGCTTTTTTTTACAAACACC
1 GCTAAAGAACAT-ACCTTTAGCGGCCTTTTTTTACAAACACC
* * * **
49197887 ACTAAAGAACAGTACCTTTAGCGGCGCTTTTATCACAAATTCC
1 GCTAAAGAACA-TACCTTTAGCGGC-CTTTTTTTACAAACACC
49197930 GCTAAA
1 GCTAAA
49197936 AGTATCGTTC
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
42 35 0.47
43 40 0.53
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (41 bp):
GCTAAAGAACATACCTTTAGCGGCCTTTTTTTACAAACACC
Found at i:49197896 original size:42 final size:43
Alignment explanation
Indices: 49197803--49197917 Score: 144
Period size: 42 Copynumber: 2.7 Consensus size: 43
49197793 ATAAATGCTG
** * *
49197803 CTAAAGAACATAACCTTTAGCGGCACTTTTTTTACAAACGCCG
1 CTAAAGAACATGTCCTTTAGCGGCACTTTTTTTACAAACACCA
* *
49197846 CTATAGAACATGTCCTTTAGCGGC-TTTTTTTTACAAACACCA
1 CTAAAGAACATGTCCTTTAGCGGCACTTTTTTTACAAACACCA
*
49197888 CTAAAGAACA-GTACCTTTAGCGGCGCTTTT
1 CTAAAGAACATGT-CCTTTAGCGGCACTTTT
49197918 ATCACAAATT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 2 0.03
42 35 0.56
43 25 0.40
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (43 bp):
CTAAAGAACATGTCCTTTAGCGGCACTTTTTTTACAAACACCA
Found at i:49197925 original size:85 final size:84
Alignment explanation
Indices: 49197710--49197925 Score: 213
Period size: 85 Copynumber: 2.5 Consensus size: 84
49197700 TTATGTGAAA
* * * *
49197710 AAACACCGCTAAAAAACAAG-ACCTTTAGCGGTGCTTTTTCCACAATCGGCACTATAGAACATGA
1 AAACACCGCTAAAGAAC-AGTACCTTTAGCGGCGCTTTTT-CACAAACGCCACTATAGAACATGA
* *
49197774 CCTTTAGCATGCTTTTATCAT
64 CCTTTAGCAGGCTTTTATCAC
** * * * * *
49197795 AAATGCTGCTAAAGAACA-TAACCTTTAGCGGCACTTTTTTTACAAACGCCGCTATAGAACATGT
1 AAACACCGCTAAAGAACAGT-ACCTTTAGCGGCGC-TTTTTCACAAACGCCACTATAGAACATGA
* *
49197859 CCTTTAGC-GGCTTTTTTTTAC
64 CCTTTAGCAGGC-TTTTATCAC
*
49197880 AAACACCACTAAAGAACAGTACCTTTAGCGGCGCTTTTATCACAAA
1 AAACACCGCTAAAGAACAGTACCTTTAGCGGCGCTTTT-TCACAAA
49197926 TTCCGCTAAA
Statistics
Matches: 104, Mismatches: 21, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
84 7 0.07
85 91 0.88
86 6 0.06
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.29
Consensus pattern (84 bp):
AAACACCGCTAAAGAACAGTACCTTTAGCGGCGCTTTTTCACAAACGCCACTATAGAACATGACC
TTTAGCAGGCTTTTATCAC
Found at i:49198286 original size:21 final size:21
Alignment explanation
Indices: 49198261--49198310 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
49198251 TTCTGCTCTG
49198261 CTCTGCTTCCCTCGCTGCTAC
1 CTCTGCTTCCCTCGCTGCTAC
*
49198282 CTCTGCTTCCCTCGCTGCTGC
1 CTCTGCTTCCCTCGCTGCTAC
*
49198303 CTCCGCTT
1 CTCTGCTT
49198311 TAAGCTATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.02, C:0.48, G:0.16, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCTAC
Found at i:49198774 original size:13 final size:14
Alignment explanation
Indices: 49198748--49198776 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
49198738 ACTAACAAAA
49198748 AATTAAACCATTAT
1 AATTAAACCATTAT
49198762 AATTAAA-CATTAT
1 AATTAAACCATTAT
49198775 AA
1 AA
49198777 ATATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:49203777 original size:9 final size:9
Alignment explanation
Indices: 49203763--49203932 Score: 93
Period size: 9 Copynumber: 18.8 Consensus size: 9
49203753 TAAGTATAAT
49203763 TAAGTTATG
1 TAAGTTATG
49203772 TAAGTTATG
1 TAAGTTATG
* * *
49203781 ATATGATATA
1 -TAAGTTATG
* *
49203791 T-ATTTATA
1 TAAGTTATG
49203799 T-A-TTATG
1 TAAGTTATG
49203806 TAAGTTATG
1 TAAGTTATG
*
49203815 TAAGTAATG
1 TAAGTTATG
*
49203824 TGAGTTATG
1 TAAGTTATG
49203833 TAAGTTATG
1 TAAGTTATG
* * *
49203842 ATATGATATA
1 -TAAGTTATG
*
49203852 TATA-TATATA
1 TA-AGT-TATG
49203862 TAAGTTAT-
1 TAAGTTATG
49203870 TAAGTTATG
1 TAAGTTATG
*
49203879 TATGTTATG
1 TAAGTTATG
49203888 -AGAGTTATG
1 TA-AGTTATG
49203897 TAAGTTATG
1 TAAGTTATG
* *
49203906 ATATGATATATA
1 -TAAG-T-TATG
49203918 TAAGTTAT-
1 TAAGTTATG
49203926 TAAGTTA
1 TAAGTTA
49203933 AGATCCAAAG
Statistics
Matches: 127, Mismatches: 21, Indels: 27
0.73 0.12 0.15
Matches are distributed among these distances:
7 5 0.04
8 23 0.18
9 68 0.54
10 24 0.19
11 4 0.03
12 3 0.02
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:49203907 original size:64 final size:62
Alignment explanation
Indices: 49203765--49203919 Score: 242
Period size: 64 Copynumber: 2.5 Consensus size: 62
49203755 AGTATAATTA
*
49203765 AGTTATGTAAGTTATGATATGATATATAT-TTATATATTATGTAAGTTATGTAAGTAATGTG
1 AGTTATGTAAGTTATGATATGATATATATATTATATATTATGTAAGTTATGTAAGTAATGAG
* *
49203826 AGTTATGTAAGTTATGATATGATATATATATATATATAAGTTAT-TAAGTTATGTATGTTATGAG
1 AGTTATGTAAGTTATGATATGATATATATAT-TATAT-A-TTATGTAAGTTATGTAAGTAATGAG
49203890 AGTTATGTAAGTTATGATATGATATATATA
1 AGTTATGTAAGTTATGATATGATATATATA
49203920 AGTTATTAAG
Statistics
Matches: 87, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
61 29 0.33
62 1 0.01
63 5 0.06
64 48 0.55
65 4 0.05
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.45
Consensus pattern (62 bp):
AGTTATGTAAGTTATGATATGATATATATATTATATATTATGTAAGTTATGTAAGTAATGAG
Found at i:49203919 original size:56 final size:55
Alignment explanation
Indices: 49203765--49203932 Score: 189
Period size: 56 Copynumber: 2.9 Consensus size: 55
49203755 AGTATAATTA
* *
49203765 AGTTATGTAAGTTATGATATGATATATATTTATATATTATGTAAGTTATGTAAGTAATGTG
1 AGTTATGTAAGTTATGATAAGATATATA--TATATA-TA--TAAGTTAT-TAAGTTATGTG
*
49203826 AGTTATGTAAGTTATGATATGATATATATATATATATAAGTTATTAAGTTATGT-
1 AGTTATGTAAGTTATGATAAGATATATATATATATATAAGTTATTAAGTTATGTG
*
49203880 ATGTTATG-AGAGTTATG-TAAGTTATGATATGATATATATAAGTTATTAAGTTA
1 A-GTTATGTA-AGTTATGATAAGATAT-ATAT-ATATATATAAGTTATTAAGTTA
49203933 AGATCCAAAG
Statistics
Matches: 100, Mismatches: 3, Indels: 13
0.86 0.03 0.11
Matches are distributed among these distances:
54 8 0.08
55 26 0.26
56 30 0.30
58 2 0.02
59 6 0.06
61 28 0.28
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (55 bp):
AGTTATGTAAGTTATGATAAGATATATATATATATATAAGTTATTAAGTTATGTG
Found at i:49204106 original size:18 final size:18
Alignment explanation
Indices: 49204085--49204120 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
49204075 TCATTTATAG
49204085 CAAAGTTATCTTTTATTC
1 CAAAGTTATCTTTTATTC
49204103 CAAAGTTATCTTTTATTC
1 CAAAGTTATCTTTTATTC
49204121 TTTAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.50
Consensus pattern (18 bp):
CAAAGTTATCTTTTATTC
Found at i:49204371 original size:10 final size:10
Alignment explanation
Indices: 49204340--49204377 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
49204330 TATATTGATA
49204340 AAAAATATTT
1 AAAAATATTT
* *
49204350 ATAAGT-TTT
1 AAAAATATTT
49204359 AAAAATATTT
1 AAAAATATTT
49204369 AAAAATATT
1 AAAAATATT
49204378 AAATATTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
9 7 0.30
10 16 0.70
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (10 bp):
AAAAATATTT
Found at i:49204379 original size:19 final size:19
Alignment explanation
Indices: 49204340--49204380 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
49204330 TATATTGATA
* * *
49204340 AAAAATATTTATAAGTTTT
1 AAAAATATTTAAAAATATT
49204359 AAAAATATTTAAAAATATT
1 AAAAATATTTAAAAATATT
49204378 AAA
1 AAA
49204381 TATTAAAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
AAAAATATTTAAAAATATT
Found at i:49205134 original size:22 final size:21
Alignment explanation
Indices: 49205105--49205147 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
49205095 GAAGCTAAGT
*
49205105 AAATTGGATGGCAGATAATAG
1 AAATTGGATGGCAGAAAATAG
49205126 AAATCTGGATGGCAGAAAATAG
1 AAAT-TGGATGGCAGAAAATAG
49205148 GAGAAGCAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.44, C:0.07, G:0.28, T:0.21
Consensus pattern (21 bp):
AAATTGGATGGCAGAAAATAG
Found at i:49205175 original size:25 final size:25
Alignment explanation
Indices: 49205147--49205195 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
49205137 GCAGAAAATA
*
49205147 GGAGAAGCAGCAGAGGGATGCCGAC
1 GGAGAAGCAGCAAAGGGATGCCGAC
* * *
49205172 GGAGATGTAGCAAAGGGCTGCCGA
1 GGAGAAGCAGCAAAGGGATGCCGA
49205196 TGATGATGCG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.18, G:0.43, T:0.08
Consensus pattern (25 bp):
GGAGAAGCAGCAAAGGGATGCCGAC
Found at i:49206762 original size:14 final size:14
Alignment explanation
Indices: 49206743--49206773 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
49206733 GAAAATAAAA
*
49206743 GGGATTTTGATTTG
1 GGGATTTTGAATTG
49206757 GGGATTTTGAATTG
1 GGGATTTTGAATTG
49206771 GGG
1 GGG
49206774 GAAATTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.42, T:0.42
Consensus pattern (14 bp):
GGGATTTTGAATTG
Found at i:49207646 original size:21 final size:21
Alignment explanation
Indices: 49207622--49207661 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
49207612 CTATAAAACA
49207622 CTAAACCAT-AAACCCTAAATC
1 CTAAA-CATAAAACCCTAAATC
*
49207643 CTAAACTTAAAACCCTAAA
1 CTAAACATAAAACCCTAAA
49207662 CCCAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (21 bp):
CTAAACATAAAACCCTAAATC
Found at i:49207731 original size:28 final size:28
Alignment explanation
Indices: 49207623--49207724 Score: 102
Period size: 28 Copynumber: 3.6 Consensus size: 28
49207613 TATAAAACAC
* *
49207623 TAAACCATAAACCCTAAA-TCCTAAACT
1 TAAACCCTAAACCCTAAATTACTAAACT
* *
49207650 TAAAACCCTAAACCCAAAATAAC-AAATCT
1 T-AAACCCTAAACCCTAAATTACTAAA-CT
*
49207679 TAACCCCTAAA-CCTAAATTACTAAACAT
1 TAAACCCTAAACCCTAAATTACTAAAC-T
*
49207707 TAAACCCTAAACTCTAAA
1 TAAACCCTAAACCCTAAA
49207725 GCCTAAAATC
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
27 10 0.17
28 41 0.68
29 9 0.15
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (28 bp):
TAAACCCTAAACCCTAAATTACTAAACT
Found at i:49208371 original size:40 final size:41
Alignment explanation
Indices: 49208281--49208373 Score: 109
Period size: 40 Copynumber: 2.3 Consensus size: 41
49208271 ATACATATTC
* *
49208281 GCGGCGTTTGAATAAAAAACGTCACTATAGTTCAACCTTTT
1 GCGGCGTTTGAATAAAAAACGCCACTATAGCTCAACCTTTT
* * * *
49208322 GCGGTGTTTGGAT-AAAAACGCCACTATTGCTC-AGCTTTT
1 GCGGCGTTTGAATAAAAAACGCCACTATAGCTCAACCTTTT
49208361 AGCGGCGTTTGAA
1 -GCGGCGTTTGAA
49208374 ACAAAAGCAC
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
39 6 0.14
40 26 0.60
41 11 0.26
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (41 bp):
GCGGCGTTTGAATAAAAAACGCCACTATAGCTCAACCTTTT
Found at i:49220110 original size:19 final size:20
Alignment explanation
Indices: 49220075--49220114 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
49220065 TTCAAAAAAA
49220075 TTATTACATTCAATTTTATTT
1 TTATTACATTCAATTTT-TTT
49220096 TTATTAC-TT-AATTTTTTT
1 TTATTACATTCAATTTTTTT
49220114 T
1 T
49220115 AAAAACATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 6 0.32
20 2 0.11
21 7 0.37
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTACATTCAATTTTTTT
Found at i:49221910 original size:50 final size:48
Alignment explanation
Indices: 49221791--49221970 Score: 154
Period size: 50 Copynumber: 3.7 Consensus size: 48
49221781 TGGGTAATGT
* * * * *
49221791 GCCGATGCCATGTCCCAAACATGGTATTAAACT-GACTATCATCATCGA-G
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAG-CTCTCATAAT--ATG
* * *
49221840 GCTGATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCGCATATTCAT-
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT--CATAAT-ATG
* * * *
49221890 GCCGATGCCATTTCCCAGACATGGTCTTACAATGGCTCTCATAATGTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATATG
*
49221938 GCCAATG-CATGTCCCAGACAT-GTCTTACACTAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAG
49221971 TTCACACAAG
Statistics
Matches: 106, Mismatches: 20, Indels: 13
0.76 0.14 0.09
Matches are distributed among these distances:
46 10 0.09
47 14 0.13
48 11 0.10
49 31 0.29
50 36 0.34
51 4 0.04
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATATG
Found at i:49229449 original size:46 final size:46
Alignment explanation
Indices: 49229395--49229509 Score: 151
Period size: 46 Copynumber: 2.5 Consensus size: 46
49229385 CGTAGCCGTC
* *
49229395 GCATGTCCCAGACATGTCTTATACTGGC-TTACGTCCCGAGGCCGAT
1 GCATGTCCCAGACATGTCTTATACTGGCACT-CGTCCCAAGGCCGAT
* *
49229441 GCATGTCCCAGACATGTCTTATACTGGCACTCGTCTCAATGCCGAT
1 GCATGTCCCAGACATGTCTTATACTGGCACTCGTCCCAAGGCCGAT
*
49229487 GCCATGTCCTAGACATGGTCTTA
1 G-CATGTCCCAGACAT-GTCTTA
49229510 CATTGGCTCT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
46 41 0.67
47 14 0.23
48 6 0.10
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.28
Consensus pattern (46 bp):
GCATGTCCCAGACATGTCTTATACTGGCACTCGTCCCAAGGCCGAT
Found at i:49235039 original size:80 final size:80
Alignment explanation
Indices: 49234955--49235103 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
49234945 TATGGTAACC
* * * *
49234955 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
49235019 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
49235035 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
49235100 CCGG
66 CCGG
49235104 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:49235045 original size:40 final size:38
Alignment explanation
Indices: 49234996--49235103 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
49234986 ATCACGATTT
*
49234996 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
49235036 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
49235076 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
49235104 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:49239141 original size:45 final size:45
Alignment explanation
Indices: 49239038--49239257 Score: 153
Period size: 45 Copynumber: 4.9 Consensus size: 45
49239028 TTGGCTTGAA
* * * * **
49239038 GGAAACGAATAAGACCATGGTTGAAAGATATTATGGCAGT-ATACC
1 GGAAACGTATAAGACCATAGTTGAAAGACACTATGGCA-TCATAAT
*
49239083 GG-AACTGAATAAGACCATAGTTGAAAGACACTATGGCATCATAAT
1 GGAAAC-GTATAAGACCATAGTTGAAAGACACTATGGCATCATAAT
* ** ** * *
49239128 GGAAACGTGTAAGACCATAGCAGAAAGACGTTGTGGCATCATGACT
1 GGAAACGTATAAGACCATAGTTGAAAGACACTATGGCATCAT-AAT
* * * * * * *
49239174 -CAGACGAACAAGACCATGGTTGAAAGACATTATGGCATC--AAG
1 GGAAACGTATAAGACCATAGTTGAAAGACACTATGGCATCATAAT
* *
49239216 GCGAGAATGTATAAGACCATGGTTGAAAGACACTATGGCATC
1 G-GA-AACGTATAAGACCATAGTTGAAAGACACTATGGCATC
49239258 CTTCAATCAT
Statistics
Matches: 137, Mismatches: 31, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
42 1 0.01
44 5 0.04
45 126 0.92
46 5 0.04
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (45 bp):
GGAAACGTATAAGACCATAGTTGAAAGACACTATGGCATCATAAT
Found at i:49239256 original size:90 final size:89
Alignment explanation
Indices: 49239038--49239257 Score: 223
Period size: 90 Copynumber: 2.4 Consensus size: 89
49239028 TTGGCTTGAA
* * * *
49239038 GGAAACGAATAAGACCATGGTTGAAAGATATTATGGCAGT-ATACCGGAACTGAATAAGACCATA
1 GGAAACGTATAAGACCATGGTTGAAAGACATTATGGCA-TCATACCAGAACTGAACAAGACCATA
*
49239102 GTTGAAAGACACTATGGCATCATAAT
65 GTTGAAAGACACTATGGCATCA-AAG
* * ** * *
49239128 GGAAACGTGTAAGACCATAGCAGAAAGACGTTGTGGCATCATGACTCAG-AC-GAACAAGACCAT
1 GGAAACGTATAAGACCATGGTTGAAAGACATTATGGCATCAT-AC-CAGAACTGAACAAGACCAT
* *
49239191 GGTTGAAAGACATTATGGCATC-AAG
64 AGTTGAAAGACACTATGGCATCAAAG
* *
49239216 GCGAGAATGTATAAGACCATGGTTGAAAGACACTATGGCATC
1 G-GA-AACGTATAAGACCATGGTTGAAAGACATTATGGCATC
49239258 CTTCAATCAT
Statistics
Matches: 104, Mismatches: 21, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
88 3 0.03
89 3 0.03
90 92 0.88
91 4 0.04
92 2 0.02
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (89 bp):
GGAAACGTATAAGACCATGGTTGAAAGACATTATGGCATCATACCAGAACTGAACAAGACCATAG
TTGAAAGACACTATGGCATCAAAG
Found at i:49239380 original size:12 final size:12
Alignment explanation
Indices: 49239363--49239387 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49239353 TGAATATGTG
49239363 AAAATAAAATAA
1 AAAATAAAATAA
49239375 AAAATAAAATAA
1 AAAATAAAATAA
49239387 A
1 A
49239388 GAACACACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:49246258 original size:44 final size:44
Alignment explanation
Indices: 49246195--49246283 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
49246185 AGTTAAGTTC
49246195 CTTAGTACGAACTTACTAAGCACTAATTGCTTATGTAGTTGTTT
1 CTTAGTACGAACTTACTAAGCACTAATTGCTTATGTAGTTGTTT
49246239 CTTAGTACGAACTTACTAAGCACTAATTGCTTATGTAGTTGTTT
1 CTTAGTACGAACTTACTAAGCACTAATTGCTTATGTAGTTGTTT
49246283 C
1 C
49246284 CTCTGTTTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (44 bp):
CTTAGTACGAACTTACTAAGCACTAATTGCTTATGTAGTTGTTT
Found at i:49248123 original size:43 final size:43
Alignment explanation
Indices: 49248073--49248161 Score: 106
Period size: 43 Copynumber: 2.1 Consensus size: 43
49248063 ATATGTGATT
** * **
49248073 TTGATATGTGTTTACGGGTAAGACCTTGTCTGGGACAGTGGCA
1 TTGATATGTGACTACAGGTAAGACCACGTCTGGGACAGTGGCA
* * *
49248116 TTGATATGTGACTACATGTAAGACCACGTCTGGGACATTTGCA
1 TTGATATGTGACTACAGGTAAGACCACGTCTGGGACAGTGGCA
49248159 TTG
1 TTG
49248162 TACGACTTGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.33
Consensus pattern (43 bp):
TTGATATGTGACTACAGGTAAGACCACGTCTGGGACAGTGGCA
Found at i:49249585 original size:26 final size:26
Alignment explanation
Indices: 49249556--49249608 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
49249546 TCAAACATGC
49249556 ATTTAGGTTAATTTAAC-CCTAGGGGT
1 ATTTAGG-TAATTTAACTCCTAGGGGT
* *
49249582 ATTTCGGTAATTTATCTCCTAGGGGT
1 ATTTAGGTAATTTAACTCCTAGGGGT
49249608 A
1 A
49249609 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.40
Consensus pattern (26 bp):
ATTTAGGTAATTTAACTCCTAGGGGT
Done.