Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 6 of 216
Found at i:1927523 original size:86 final size:86
Alignment explanation
Indices: 1927375--1928172 Score: 842
Period size: 86 Copynumber: 9.2 Consensus size: 86
1927365 CGCTAGTTCT
* * *
1927375 TAGGAAGGAAATATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
1 TAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTT
* * *
1927440 TGGTCTGCTTCGCTGTTAATG
66 CGATCTGCTTCGCTGTCAATG
* * *
1927461 TAAGAAGGCAAGATCTGCTTCTTTAACCAGCTCCATTGCAACCGATGGAGGCAAGGCTTTGTTTT
1 TAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTT
* *
1927526 CGATTTGCTTCGCTATCAATG
66 CGATCTGCTTCGCTGTCAATG
* * * *
1927547 CAAGAAGGCAAGACCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
1 TAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTT
* * *
1927612 TGGTCTGCTTCGCTGTTAATG
66 CGATCTGCTTCGCTGTCAATG
*
1927633 TAGGAAGGCAAGACCTGCTTCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTT
1 TAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTT
* * * *
1927698 TGGTCTGCTTCGCTATTAATG
66 CGATCTGCTTCGCTGTCAATG
* * * *
1927719 TAGGAAGGCAAGATGTGCTTCTTTAACCAGCTCCACTGCAACCGGTGGAGGTAAGGCTTTGTTTT
1 TAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTT
* * * *
1927784 TGGTCTGCTTCGCTATTAATG
66 CGATCTGCTTCGCTGTCAATG
** * * *
1927805 TAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCA-TCACAACTGA-GAGAAGCAAGG-TTTGT
1 TAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACT-ACAACCGATG-GAGGCAAGGCTTTGT
* *
1927867 GTCTTCGACCTGCTTCGCTGTCAATA
63 -T-TTCGATCTGCTTCGCTGTCAATG
* * * * * *
1927893 CAGGAAGGCAAGATCTGTTGTCTTCAACCAACTCCGCTACAACCGA-GAGAGGGAAGG-TTTGTG
1 TAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTACAACCGATG-GAGGCAAGGCTTTGT-
* *
1927956 TCTTCGACCTGCTTCGCTGTCAATA
63 T-TTCGATCTGCTTCGCTGTCAATG
* * * * *
1927981 CAGGAAGACAAGATCTGTTGTCTTCAACCAGCTCCGCTACAACCGA-GAGAGGCAAGG-TTTGTG
1 TAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTACAACCGATG-GAGGCAAGGCTTTGT-
* *
1928044 TCTTCGACCTGCTTCGCTGTCAATA
63 T-TTCGATCTGCTTCGCTGTCAATG
* ** * *
1928069 CAGGAAGGCAAGA-CTATTGTCTTCAACCAGCTCCACCACAACCGA-GAGAGGCAAGG-TTTGTG
1 TAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTACAACCGATG-GAGGCAAGGCTTTGT-
*
1928131 TCTTCGATCTGCTTCGCTGTCAATT
63 T-TTCGATCTGCTTCGCTGTCAATG
1928156 TAGGAAGGCAAGATCTG
1 TAGGAAGGCAAGATCTG
1928173 TTGTCTTCAT
Statistics
Matches: 646, Mismatches: 59, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
86 341 0.53
87 109 0.17
88 195 0.30
89 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (86 bp):
TAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTTT
CGATCTGCTTCGCTGTCAATG
Found at i:1927599 original size:43 final size:43
Alignment explanation
Indices: 1927552--1927687 Score: 109
Period size: 43 Copynumber: 3.2 Consensus size: 43
1927542 CAATGCAAGA
1927552 AGGCAAGACCTGCTTCTTTAACCAGCTCCACTGCAACCGATGG
1 AGGCAAGACCTGCTTCTTTAACCAGCTCCACTGCAACCGATGG
* * *** * * * * *
1927595 AGGCAAGGCTTTG-TT-TTTGGTCTGCTTCGCTGTTAA-TG-TAGG
1 AGGCAAGAC-CTGCTTCTTTAACCAGCTCCACTG-CAACCGAT-GG
*
1927637 AAGGCAAGACCTGCTTCTTTAACCAGCTCCACTACAACCGATGG
1 -AGGCAAGACCTGCTTCTTTAACCAGCTCCACTGCAACCGATGG
1927681 AGGCAAG
1 AGGCAAG
1927688 GCTTTGTTTT
Statistics
Matches: 64, Mismatches: 21, Indels: 16
0.63 0.21 0.16
Matches are distributed among these distances:
41 1 0.02
42 16 0.25
43 31 0.48
44 15 0.23
45 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (43 bp):
AGGCAAGACCTGCTTCTTTAACCAGCTCCACTGCAACCGATGG
Found at i:1927728 original size:43 final size:43
Alignment explanation
Indices: 1927595--1927816 Score: 109
Period size: 43 Copynumber: 5.2 Consensus size: 43
1927585 CAACCGATGG
*
1927595 AGGCAAGGCTTTGTTTTTGGTCTGCTTCGCTGTTAATGTAGGA
1 AGGCAAGGCTTTGTTTTTGGTCTGCTTCGCTATTAATGTAGGA
* * *** * * * * *
1927638 AGGCAAGAC-CTGCTTCTTTAACCAGCTCCACTA-CAACCG-ATGG-
1 AGGCAAGGCTTTG-TT-TTTGGTCTGCTTCGCTATTAA-TGTA-GGA
1927681 AGGCAAGGCTTTGTTTTTGGTCTGCTTCGCTATTAATGTAGGA
1 AGGCAAGGCTTTGTTTTTGGTCTGCTTCGCTATTAATGTAGGA
* * *** * * * ** *
1927724 AGGCAA-GATGTGCTTCTTTAACCAGCTCCACT-GCAACCGGT-GG-
1 AGGCAAGGCTTTG-TT-TTTGGTCTGCTTCGCTATTAA--TGTAGGA
*
1927767 AGGTAAGGCTTTGTTTTTGGTCTGCTTCGCTATTAATGTAGGA
1 AGGCAAGGCTTTGTTTTTGGTCTGCTTCGCTATTAATGTAGGA
1927810 AGGCAAG
1 AGGCAAG
1927817 ATCTTTTGTC
Statistics
Matches: 118, Mismatches: 45, Indels: 32
0.61 0.23 0.16
Matches are distributed among these distances:
41 2 0.02
42 32 0.27
43 51 0.43
44 31 0.26
45 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.32
Consensus pattern (43 bp):
AGGCAAGGCTTTGTTTTTGGTCTGCTTCGCTATTAATGTAGGA
Found at i:1930804 original size:13 final size:13
Alignment explanation
Indices: 1930786--1930811 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1930776 CCTGCATGAT
1930786 ATTCGCATTGTGC
1 ATTCGCATTGTGC
1930799 ATTCGCATTGTGC
1 ATTCGCATTGTGC
1930812 CATTTGGGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (13 bp):
ATTCGCATTGTGC
Found at i:1936799 original size:30 final size:30
Alignment explanation
Indices: 1936765--1936823 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
1936755 GTAATGATGT
*
1936765 TATGGTCATAGTTTGGACCACATTTAATGC
1 TATGGTCATAGCTTGGACCACATTTAATGC
1936795 TATGGTCATAGCTTGGACCACATTTAATG
1 TATGGTCATAGCTTGGACCACATTTAATG
1936824 TTATAATGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (30 bp):
TATGGTCATAGCTTGGACCACATTTAATGC
Found at i:1938684 original size:51 final size:51
Alignment explanation
Indices: 1938624--1938846 Score: 200
Period size: 51 Copynumber: 4.4 Consensus size: 51
1938614 CGGTGGTTTG
* * * *
1938624 CACATAGTACCACCCATGTGACCATTGTCATCCGATACACTTAGTAGCCTA
1 CACATAGTACTACACACGTGACCATTGTCATCCGATACACGTAGTAGCCTA
* * ** * * *
1938675 CACATAGTACTACACACGTGATCA-AGTTTTCCGGTTCACGTAGTAGCCTT
1 CACATAGTACTACACACGTGACCATTGTCATCCGATACACGTAGTAGCCTA
* ** * * * *
1938725 CACATAGTACTACACACGTGGCCAAGGCCATTCTG-TACACATAGTAGCCTG
1 CACATAGTACTACACACGTGACCATTGTCA-TCCGATACACGTAGTAGCCTA
* * *
1938776 CACATAGTACTACACATGTGACCATTATCTAT-CGATACACGTAGTAGCCTG
1 CACATAGTACTACACACGTGACCATTGTC-ATCCGATACACGTAGTAGCCTA
**
1938827 CAGTTAGTACTACACACGTG
1 CACATAGTACTACACACGTG
1938847 TTCATAGGTA
Statistics
Matches: 136, Mismatches: 32, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
50 42 0.31
51 90 0.66
52 4 0.03
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (51 bp):
CACATAGTACTACACACGTGACCATTGTCATCCGATACACGTAGTAGCCTA
Found at i:1940673 original size:18 final size:20
Alignment explanation
Indices: 1940647--1940684 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
1940637 ATCAATTATC
1940647 AACAATAAAA-AAAA-GAAA
1 AACAATAAAATAAAATGAAA
*
1940665 AACATTAAAATAAAATGAAA
1 AACAATAAAATAAAATGAAA
1940685 CTTCGAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 4 0.24
20 4 0.24
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.13
Consensus pattern (20 bp):
AACAATAAAATAAAATGAAA
Found at i:1942558 original size:27 final size:28
Alignment explanation
Indices: 1942524--1942577 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
1942514 AAACTATTCT
* *
1942524 AAAAGAAACTCA-AGAGAAATTATTAAA
1 AAAAGAAACCCAGAAAGAAATTATTAAA
*
1942551 AAAAGAAACCCAGAAAGAATTTATTAA
1 AAAAGAAACCCAGAAAGAAATTATTAA
1942578 CTCAAGAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.19
Consensus pattern (28 bp):
AAAAGAAACCCAGAAAGAAATTATTAAA
Found at i:1943766 original size:23 final size:24
Alignment explanation
Indices: 1943734--1943778 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
1943724 AAATCAACAA
1943734 TTTTTAAAATATCA-ATAACAAAAC
1 TTTTTAAAATAT-ATATAACAAAAC
1943758 TTTTT-AAATATATATAACAAA
1 TTTTTAAAATATATATAACAAA
1943779 GATCACGTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 1 0.05
23 14 0.70
24 5 0.25
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (24 bp):
TTTTTAAAATATATATAACAAAAC
Found at i:1944429 original size:14 final size:14
Alignment explanation
Indices: 1944410--1944437 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1944400 TGTCCCCATT
1944410 TATGCATGCATTGC
1 TATGCATGCATTGC
1944424 TATGCATGCATTGC
1 TATGCATGCATTGC
1944438 CTAACATCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (14 bp):
TATGCATGCATTGC
Found at i:1946072 original size:17 final size:17
Alignment explanation
Indices: 1946047--1946080 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1946037 AAATTTATTT
* *
1946047 TTTTTAAATTTTTTTAA
1 TTTTAAAATATTTTTAA
1946064 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
1946081 AATACTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:1949120 original size:3 final size:3
Alignment explanation
Indices: 1949107--1949138 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1949097 ATTCATACGG
1949107 TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1949139 CTTATATATC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:1950937 original size:4 final size:4
Alignment explanation
Indices: 1950930--1950954 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1950920 TTTCAATCAA
1950930 ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A
1950955 GGTGAAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:1965069 original size:10 final size:10
Alignment explanation
Indices: 1965054--1965103 Score: 64
Period size: 10 Copynumber: 5.0 Consensus size: 10
1965044 GAGAAAACAC
1965054 GAGAAAGTGA
1 GAGAAAGTGA
* *
1965064 GGGAAAGTGC
1 GAGAAAGTGA
1965074 GAGAAAGTGA
1 GAGAAAGTGA
* *
1965084 GGGAAAGTGC
1 GAGAAAGTGA
1965094 GAGAAAGTGA
1 GAGAAAGTGA
1965104 AAACCTCGAG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.42, C:0.04, G:0.44, T:0.10
Consensus pattern (10 bp):
GAGAAAGTGA
Found at i:1965076 original size:20 final size:20
Alignment explanation
Indices: 1965053--1965103 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1965043 TGAGAAAACA
1965053 CGAGAAAGTGAGGGAAAGTG
1 CGAGAAAGTGAGGGAAAGTG
1965073 CGAGAAAGTGAGGGAAAGTG
1 CGAGAAAGTGAGGGAAAGTG
1965093 CGAGAAAGTGA
1 CGAGAAAGTGA
1965104 AAACCTCGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.41, C:0.06, G:0.43, T:0.10
Consensus pattern (20 bp):
CGAGAAAGTGAGGGAAAGTG
Found at i:1966100 original size:71 final size:71
Alignment explanation
Indices: 1966010--1966141 Score: 194
Period size: 71 Copynumber: 1.9 Consensus size: 71
1966000 TTGGTACAAA
* *
1966010 TATTCAGAATATTGACTTATTTAAAAGAAAATCTATTTTATTAAAAATATTAAAGTAAATTACAA
1 TATTCAGAATATTGACTTATTTAAAAGAAAATCTATTATATTAAAAATATAAAAGTAAATTACAA
1966075 TTACTT
66 TTACTT
* ** *
1966081 TATTCA-ACATATTGTCTTATTTAAAAGAATTTCTATTATATTAAAAATGTAAAAGTAAATT
1 TATTCAGA-ATATTGACTTATTTAAAAGAAAATCTATTATATTAAAAATATAAAAGTAAATT
1966142 TCTATTTTAG
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
70 1 0.02
71 53 0.98
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (71 bp):
TATTCAGAATATTGACTTATTTAAAAGAAAATCTATTATATTAAAAATATAAAAGTAAATTACAA
TTACTT
Found at i:1968477 original size:12 final size:12
Alignment explanation
Indices: 1968460--1968487 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1968450 AGAGGAAATT
1968460 GAGAGAATATTA
1 GAGAGAATATTA
1968472 GAGAGAATATTA
1 GAGAGAATATTA
1968484 GAGA
1 GAGA
1968488 AATGATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (12 bp):
GAGAGAATATTA
Found at i:1969548 original size:5 final size:5
Alignment explanation
Indices: 1969517--1969547 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1969507 CTCGCCCTTA
*
1969517 ACTTT ACTTT ACTTT ACTTT ACTTT AATTT A
1 ACTTT ACTTT ACTTT ACTTT ACTTT ACTTT A
1969548 AGGCTATGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.26, C:0.16, G:0.00, T:0.58
Consensus pattern (5 bp):
ACTTT
Found at i:1979398 original size:21 final size:22
Alignment explanation
Indices: 1979374--1979414 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1979364 ATAATAAGCT
1979374 AGTTT-TAAATGAATATAAACG
1 AGTTTGTAAATGAATATAAACG
**
1979395 AGTTTGTTCATGAATATAAA
1 AGTTTGTAAATGAATATAAA
1979415 TGAACTAAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.37
Consensus pattern (22 bp):
AGTTTGTAAATGAATATAAACG
Found at i:1979818 original size:44 final size:44
Alignment explanation
Indices: 1979755--1979846 Score: 175
Period size: 44 Copynumber: 2.1 Consensus size: 44
1979745 CACTAGTTTC
*
1979755 GCCCCTGTTCATAAGTTCTTCATCGAACATTCTATTCATTTATA
1 GCCCCTGTTCATAAGTTCTTCATCGAACATTCTATACATTTATA
1979799 GCCCCTGTTCATAAGTTCTTCATCGAACATTCTATACATTTATA
1 GCCCCTGTTCATAAGTTCTTCATCGAACATTCTATACATTTATA
1979843 GCCC
1 GCCC
1979847 TACTCACAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.25, C:0.27, G:0.10, T:0.38
Consensus pattern (44 bp):
GCCCCTGTTCATAAGTTCTTCATCGAACATTCTATACATTTATA
Found at i:1980439 original size:12 final size:13
Alignment explanation
Indices: 1980416--1980444 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1980406 TTTGCACGAG
1980416 TTAAATTTTAAAT
1 TTAAATTTTAAAT
1980429 TTAAA-TTTAAAT
1 TTAAATTTTAAAT
1980441 TTAA
1 TTAA
1980445 TTGAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTAAATTTTAAAT
Found at i:1982188 original size:24 final size:22
Alignment explanation
Indices: 1982161--1982218 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
1982151 GGCCTGGCCC
*
1982161 ATTTTATACATTTGTGATATATAT
1 ATTTTATA-ATTT-TAATATATAT
* *
1982185 ATTTTTTAATTTTAATTTATAT
1 ATTTTATAATTTTAATATATAT
*
1982207 ATTATATAATTT
1 ATTTTATAATTT
1982219 ATATCACATA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 18 0.62
23 4 0.14
24 7 0.24
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.60
Consensus pattern (22 bp):
ATTTTATAATTTTAATATATAT
Found at i:1987819 original size:22 final size:22
Alignment explanation
Indices: 1987794--1987835 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1987784 TCTTTATACA
*
1987794 CTTTGTACATTTAGAATTTAGT
1 CTTTCTACATTTAGAATTTAGT
* *
1987816 CTTTCTACTTTTTGAATTTA
1 CTTTCTACATTTAGAATTTA
1987836 AAATTTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.55
Consensus pattern (22 bp):
CTTTCTACATTTAGAATTTAGT
Found at i:2006295 original size:13 final size:13
Alignment explanation
Indices: 2006277--2006309 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2006267 GTAACTATTT
2006277 TATTAAAAAAATA
1 TATTAAAAAAATA
*
2006290 TATTAAATAAATA
1 TATTAAAAAAATA
2006303 -ATTAAAA
1 TATTAAAA
2006310 TGATTATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TATTAAAAAAATA
Found at i:2006469 original size:20 final size:18
Alignment explanation
Indices: 2006428--2006469 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2006418 TTTTTATATT
2006428 TTAA-AAAAAATTGTTAA
1 TTAATAAAAAATTGTTAA
*
2006445 ATAATAAAAAATATGTTACA
1 TTAATAAAAAAT-TGTTA-A
2006465 TTAAT
1 TTAAT
2006470 CATCCAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 3 0.15
18 7 0.35
19 5 0.25
20 5 0.25
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (18 bp):
TTAATAAAAAATTGTTAA
Found at i:2006487 original size:7 final size:7
Alignment explanation
Indices: 2006475--2006500 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2006465 TTAATCATCC
2006475 AATAGGA
1 AATAGGA
2006482 AATAGGA
1 AATAGGA
2006489 AATAGGA
1 AATAGGA
2006496 AATAG
1 AATAG
2006501 TTGATAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.27, T:0.15
Consensus pattern (7 bp):
AATAGGA
Found at i:2008195 original size:11 final size:11
Alignment explanation
Indices: 2008179--2008206 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2008169 TATTAATTTA
2008179 TAATAATAAAG
1 TAATAATAAAG
2008190 TAATAATAAAG
1 TAATAATAAAG
2008201 TAATAA
1 TAATAA
2008207 AACCATCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (11 bp):
TAATAATAAAG
Found at i:2008366 original size:3 final size:3
Alignment explanation
Indices: 2008358--2008387 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2008348 GTGTCGAAAG
2008358 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2008388 AAGTGGTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2012178 original size:8 final size:8
Alignment explanation
Indices: 2012165--2012194 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
2012155 AAAGAACCTG
2012165 TTTGATGT
1 TTTGATGT
2012173 TTTGATGT
1 TTTGATGT
2012181 TTTGATGT
1 TTTGATGT
2012189 TTTGAT
1 TTTGAT
2012195 ATTTGGTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.13, C:0.00, G:0.23, T:0.63
Consensus pattern (8 bp):
TTTGATGT
Found at i:2012367 original size:6 final size:6
Alignment explanation
Indices: 2012357--2012390 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
2012347 TAACATGGGG
*
2012357 TTTTTG TTTTTA TTTTTA TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
2012391 GTTTGCATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:2013984 original size:20 final size:20
Alignment explanation
Indices: 2013959--2014000 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2013949 AAATTCTGAT
2013959 CATATCTACTTTTTAAGATA
1 CATATCTACTTTTTAAGATA
2013979 CATATCTACTTTTTAAGATA
1 CATATCTACTTTTTAAGATA
2013999 CA
1 CA
2014001 ATGCTTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.43
Consensus pattern (20 bp):
CATATCTACTTTTTAAGATA
Found at i:2015440 original size:26 final size:26
Alignment explanation
Indices: 2015383--2015441 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
2015373 ACCTTTTTTT
* *
2015383 TAAAAAGATTGATGGTCAAATTCGAC
1 TAAAAAGATTGATGATCAAATTAGAC
* *
2015409 TAAAAAGATTGATGATTAAATTTAGCC
1 TAAAAAGATTGATGATCAAA-TTAGAC
2015436 TAAAAA
1 TAAAAA
2015442 AGGCCAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 18 0.64
27 10 0.36
ACGTcount: A:0.47, C:0.08, G:0.15, T:0.29
Consensus pattern (26 bp):
TAAAAAGATTGATGATCAAATTAGAC
Found at i:2019470 original size:20 final size:20
Alignment explanation
Indices: 2019445--2019483 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2019435 AAAAAAAATT
2019445 TAAAGTTAAAATATATTATC
1 TAAAGTTAAAATATATTATC
2019465 TAAAGTTAAAATATATTAT
1 TAAAGTTAAAATATATTAT
2019484 AATATTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (20 bp):
TAAAGTTAAAATATATTATC
Found at i:2020532 original size:25 final size:25
Alignment explanation
Indices: 2020504--2020605 Score: 92
Period size: 22 Copynumber: 4.3 Consensus size: 25
2020494 GCGCTCTCTA
2020504 ATTATTAGCACGTCAGTGCTATCTG
1 ATTATTAGCACGTCAGTGCTATCTG
*
2020529 ATTATTAGCACGTCAATGCTATCTG
1 ATTATTAGCACGTCAGTGCTATCTG
* * *
2020554 --T-TTAGCACATCTGTGCTCTCTG
1 ATTATTAGCACGTCAGTGCTATCTG
* *
2020576 --TA-TAGCACTTCAGTGCTCTCT-
1 ATTATTAGCACGTCAGTGCTATCTG
2020597 ATTCATTAG
1 ATT-ATTAG
2020606 TGCATAATAA
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
22 35 0.54
23 2 0.03
24 1 0.02
25 27 0.42
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (25 bp):
ATTATTAGCACGTCAGTGCTATCTG
Found at i:2020561 original size:22 final size:24
Alignment explanation
Indices: 2020506--2020561 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
2020496 GCTCTCTAAT
*
2020506 TATTAGCACGTCAGTGCTATCTGA
1 TATTAGCACGTCAATGCTATCTGA
2020530 TTATTAGCACGTCAATGCTATCTG-
1 -TATTAGCACGTCAATGCTATCTGA
2020554 T-TTAGCAC
1 TATTAGCAC
2020562 ATCTGTGCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 7 0.23
23 1 0.03
25 22 0.73
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (24 bp):
TATTAGCACGTCAATGCTATCTGA
Found at i:2020725 original size:31 final size:31
Alignment explanation
Indices: 2020689--2020747 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
2020679 AAGAATATGA
2020689 GATAGTGAATTGAAAATAGAATGTGAAAAAC
1 GATAGTGAATTGAAAATAGAATGTGAAAAAC
*
2020720 GATAGTGAATTGAAAATAGGATGTGAAA
1 GATAGTGAATTGAAAATAGAATGTGAAA
2020748 TATGTTGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.49, C:0.02, G:0.25, T:0.24
Consensus pattern (31 bp):
GATAGTGAATTGAAAATAGAATGTGAAAAAC
Found at i:2026115 original size:24 final size:22
Alignment explanation
Indices: 2026088--2026146 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 22
2026078 TGATATATAA
2026088 AAATTAATTTTTAATAGTAAAAAT
1 AAATTAATTTTT-ATAG-AAAAAT
* *
2026112 AAATGAAATTTTTATAGAAAATT
1 AAAT-TAATTTTTATAGAAAAAT
* *
2026135 AATTTACTTTTT
1 AAATTAATTTTT
2026147 GATCTAATAG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
22 6 0.21
23 8 0.28
24 8 0.28
25 7 0.24
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (22 bp):
AAATTAATTTTTATAGAAAAAT
Found at i:2028462 original size:9 final size:10
Alignment explanation
Indices: 2028450--2028500 Score: 54
Period size: 9 Copynumber: 5.2 Consensus size: 10
2028440 CAAAAAAATT
2028450 AAAATATT-A
1 AAAATATTAA
*
2028459 AAAAT-TTGA
1 AAAATATTAA
2028468 AAAAT-TTAAA
1 AAAATATT-AA
2028478 AAAATATTACA
1 AAAATATTA-A
2028489 AAAATATTAA
1 AAAATATTAA
2028499 AA
1 AA
2028501 TTATGGAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
8 2 0.05
9 13 0.35
10 10 0.27
11 12 0.32
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (10 bp):
AAAATATTAA
Found at i:2028491 original size:11 final size:11
Alignment explanation
Indices: 2028467--2028500 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2028457 TAAAAATTTG
2028467 AAAAAT-TTAA
1 AAAAATATTAA
*
2028477 AAAAATATTAC
1 AAAAATATTAA
2028488 AAAAATATTAA
1 AAAAATATTAA
2028499 AA
1 AA
2028501 TTATGGAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAAATATTAA
Found at i:2028572 original size:18 final size:18
Alignment explanation
Indices: 2028551--2028586 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2028541 TTTAAAAATT
*
2028551 TATTAAAAAATGAATAAA
1 TATTAAAAAATAAATAAA
2028569 TATTAAAAAATAAATAAA
1 TATTAAAAAATAAATAAA
2028587 ATCATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
TATTAAAAAATAAATAAA
Found at i:2037685 original size:15 final size:15
Alignment explanation
Indices: 2037665--2037703 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2037655 GATCAAGAAA
* *
2037665 TTTGGATTAGATTGG
1 TTTGGATCAGATCGG
2037680 TTTGGATCAGATCGG
1 TTTGGATCAGATCGG
*
2037695 ATTGGATCA
1 TTTGGATCA
2037704 TTGAAGACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.23, C:0.08, G:0.31, T:0.38
Consensus pattern (15 bp):
TTTGGATCAGATCGG
Found at i:2053167 original size:11 final size:11
Alignment explanation
Indices: 2053153--2053187 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
2053143 TATTTTAAAA
2053153 AATATTTTTAT
1 AATATTTTTAT
2053164 AATATTTTTAT
1 AATATTTTTAT
*
2053175 AAT-TTTTAAT
1 AATATTTTTAT
2053185 AAT
1 AAT
2053188 TTTAATGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
AATATTTTTAT
Found at i:2053181 original size:10 final size:10
Alignment explanation
Indices: 2053157--2053190 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
2053147 TTAAAAAATA
2053157 TTTTTATAAT
1 TTTTTATAAT
2053167 ATTTTTATAAT
1 -TTTTTATAAT
*
2053178 TTTTAATAAT
1 TTTTTATAAT
2053188 TTT
1 TTT
2053191 AATGATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:2053189 original size:19 final size:18
Alignment explanation
Indices: 2053153--2053207 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 18
2053143 TATTTTAAAA
*
2053153 AATATTTTTATAATATTTT
1 AATAATTTT-TAATATTTT
*
2053172 TATAATTTTTAATAATTTT
1 AATAATTTTTAAT-ATTTT
*
2053191 AATGATTTTTAAT-TTTT
1 AATAATTTTTAATATTTT
2053208 CAATTTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 4 0.13
18 4 0.13
19 23 0.74
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
AATAATTTTTAATATTTT
Found at i:2053200 original size:10 final size:9
Alignment explanation
Indices: 2053153--2053207 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
2053143 TATTTTAAAA
2053153 AATATTTTTAT
1 AATA-TTTT-T
2053164 AATATTTTT
1 AATATTTTT
2053173 -ATAATTTTT
1 AAT-ATTTTT
*
2053182 AATAATTTT
1 AATATTTTT
2053191 AATGATTTTT
1 AAT-ATTTTT
2053201 AAT-TTTT
1 AATATTTT
2053208 CAATTTTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
8 6 0.15
9 15 0.38
10 14 0.36
11 4 0.10
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (9 bp):
AATATTTTT
Found at i:2069541 original size:11 final size:11
Alignment explanation
Indices: 2069527--2069553 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2069517 AATAAATATT
2069527 ATTTTATTAAG
1 ATTTTATTAAG
2069538 ATTTTATTAAG
1 ATTTTATTAAG
2069549 ATTTT
1 ATTTT
2069554 TAGTATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (11 bp):
ATTTTATTAAG
Found at i:2071125 original size:5 final size:5
Alignment explanation
Indices: 2071115--2071146 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
2071105 AAATGATAAT
*
2071115 ATTGA ATTGA ATTGA ATTAA ATTGA ATTGA AT
1 ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA AT
2071147 GAAGAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.41
Consensus pattern (5 bp):
ATTGA
Found at i:2081480 original size:69 final size:69
Alignment explanation
Indices: 2081363--2081491 Score: 177
Period size: 69 Copynumber: 1.9 Consensus size: 69
2081353 ATTCGCAAAT
* * * *
2081363 ATTTGGACAGCAGTAAAAACATTTGGACAGCATTGACTTGTACCAAAAATGGACAGCATTTAAGC
1 ATTTGGACAACAGTAAAAACATTCGGACAACATAGACTTGTACCAAAAATGGACAGCATTTAAGC
2081428 ACTA
66 ACTA
* * * **
2081432 ATTTGGACAACATTAATAACATTCGGACAACATAGATTTGTATGAAAAATGGACAGCATT
1 ATTTGGACAACAGTAAAAACATTCGGACAACATAGACTTGTACCAAAAATGGACAGCATT
2081492 AATATGCTCA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
69 51 1.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (69 bp):
ATTTGGACAACAGTAAAAACATTCGGACAACATAGACTTGTACCAAAAATGGACAGCATTTAAGC
ACTA
Found at i:2082324 original size:41 final size:41
Alignment explanation
Indices: 2082254--2082430 Score: 211
Period size: 40 Copynumber: 4.3 Consensus size: 41
2082244 ACTCAATGTT
* *
2082254 TCGCACACTAAATGCCATTGCATAGCCGAAGCTAT-T-ATAA
1 TCGCACACTAAGTGCCA-TACATAGCCGAAGCTATCTCATAA
* *
2082294 TCCCGCACACTAAGTGCCTTACATAGCCGAAGCTATCTCAGT-C
1 T--CGCACACTAAGTGCCATACATAGCCGAAGCTATCTCA-TAA
* *
2082337 TCGCACACTAAGTGCCATATATAGCCGAAGCTAT-TCCTAA
1 TCGCACACTAAGTGCCATACATAGCCGAAGCTATCTCATAA
* *
2082377 TCGCACACTAAGTGCCATAAATAGCCGAATCTATCTCA-AA
1 TCGCACACTAAGTGCCATACATAGCCGAAGCTATCTCATAA
2082417 TCGCACACTAAGTG
1 TCGCACACTAAGTG
2082431 ATAAACATAG
Statistics
Matches: 119, Mismatches: 11, Indels: 14
0.83 0.08 0.10
Matches are distributed among these distances:
39 1 0.01
40 51 0.43
41 49 0.41
42 15 0.13
43 2 0.02
44 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (41 bp):
TCGCACACTAAGTGCCATACATAGCCGAAGCTATCTCATAA
Found at i:2082403 original size:81 final size:80
Alignment explanation
Indices: 2082254--2082430 Score: 232
Period size: 81 Copynumber: 2.2 Consensus size: 80
2082244 ACTCAATGTT
* * *
2082254 TCGCACACTAAATGCCATTGCATAGCCGAAGCTATTATAATCCCGCACACTAAGTGCCTTACATA
1 TCGCACACTAAGTGCCATT-CATAGCCGAAGCTATTATAAT-CCGCACACTAAGTGCCATAAATA
**
2082319 GCCGAAGCTATCTCAGTC
64 GCCGAAGCTATCTCA-AA
*
2082337 TCGCACACTAAGTGCCATAT-ATAGCCGAAGCTATTCCTAAT-CGCACACTAAGTGCCATAAATA
1 TCGCACACTAAGTGCCAT-TCATAGCCGAAGCTATT-ATAATCCGCACACTAAGTGCCATAAATA
*
2082400 GCCGAATCTATCTCAAA
64 GCCGAAGCTATCTCAAA
2082417 TCGCACACTAAGTG
1 TCGCACACTAAGTG
2082431 ATAAACATAG
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
80 14 0.16
81 34 0.40
82 15 0.18
83 21 0.25
84 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (80 bp):
TCGCACACTAAGTGCCATTCATAGCCGAAGCTATTATAATCCGCACACTAAGTGCCATAAATAGC
CGAAGCTATCTCAAA
Found at i:2084977 original size:61 final size:61
Alignment explanation
Indices: 2084854--2084979 Score: 139
Period size: 61 Copynumber: 2.1 Consensus size: 61
2084844 TTTGATCCTA
* * * **
2084854 AATTTTAAAAAAATCAAAAAATTTAACTATCAATATTTATAAAATTTATCATTTTAGTTTT
1 AATTCTAAAAAAATCAAAAAATTTAACCATCAATATTTATAAAATTTATCAATTTAAATTT
* * * *
2084915 AATTCTAAAAAAATCAACAAATTTAACCCTTAGTATTTACT-AAATGTT-TCAATTTAAATTT
1 AATTCTAAAAAAATCAAAAAATTTAACCATCAATATTTA-TAAAAT-TTATCAATTTAAATTT
2084976 AATT
1 AATT
2084980 TTAATTCTAA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
61 51 0.94
62 3 0.06
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (61 bp):
AATTCTAAAAAAATCAAAAAATTTAACCATCAATATTTATAAAATTTATCAATTTAAATTT
Found at i:2086901 original size:61 final size:61
Alignment explanation
Indices: 2086806--2086927 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
2086796 TGTTGATGGG
2086806 CCGCATTTATGATGGTTTGTACCAGTTTGATCTATTAGACACTCAGAGTTTCAAAACTTCT
1 CCGCATTTATGATGGTTTGTACCAGTTTGATCTATTAGACACTCAGAGTTTCAAAACTTCT
2086867 CCGCATTTATGATGGTTTGTACCAGTTTGATCTATTAGACACTCAGAGTTTCAAAACTTCT
1 CCGCATTTATGATGGTTTGTACCAGTTTGATCTATTAGACACTCAGAGTTTCAAAACTTCT
2086928 TCTTCTTCTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (61 bp):
CCGCATTTATGATGGTTTGTACCAGTTTGATCTATTAGACACTCAGAGTTTCAAAACTTCT
Found at i:2088834 original size:12 final size:12
Alignment explanation
Indices: 2088817--2088843 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2088807 AAGTTAAGAG
2088817 TGTGCTTCTGTA
1 TGTGCTTCTGTA
2088829 TGTGCTTCTGTA
1 TGTGCTTCTGTA
2088841 TGT
1 TGT
2088844 CCTAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.15, G:0.26, T:0.52
Consensus pattern (12 bp):
TGTGCTTCTGTA
Found at i:2102883 original size:17 final size:17
Alignment explanation
Indices: 2102861--2102896 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2102851 GATATTAAAA
2102861 AATAATGAATTAAATGT
1 AATAATGAATTAAATGT
* *
2102878 AATAATGAGTTAGATGT
1 AATAATGAATTAAATGT
2102895 AA
1 AA
2102897 AAATTGTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (17 bp):
AATAATGAATTAAATGT
Found at i:2110609 original size:136 final size:135
Alignment explanation
Indices: 2110365--2110638 Score: 521
Period size: 136 Copynumber: 2.0 Consensus size: 135
2110355 CTGAACTAGA
2110365 ACAAATTTAAGGTTGGAAGCGATTTCTGGGCTCTTGGCTGTCTAGGCTTTGTTTTTGACTACTTA
1 ACAAATTTAAGGTTGGAAGCGATTTCTGGGCTCTTGGCTGTCTAGGCTTTGTTTTTGACTACTTA
2110430 ATTTTCAACGACTTTTAGCCCTTGAGTAGGCCCAGAGTCGATTTTGGAAGAAAAAAAAAAGGATT
66 ATTTTCAACGACTTTTAGCCCTTGAGTAGGCCCAGAGTCGATTTTGGAAGAAAAAAAAAA-GATT
2110495 CAAGGT
130 CAAGGT
* *
2110501 ACAAATTTAAGGTTGGAAGCGATTTCTGGGCTCTTGGCTGTCTAGGCTTTGTTTTTTACTATTTA
1 ACAAATTTAAGGTTGGAAGCGATTTCTGGGCTCTTGGCTGTCTAGGCTTTGTTTTTGACTACTTA
2110566 ATTTTCAACGACTTTTAGCCCTTGAGTAGGCCCAGAGTCGATTTTGGAAGAAAAAAAAAAGATTC
66 ATTTTCAACGACTTTTAGCCCTTGAGTAGGCCCAGAGTCGATTTTGGAAGAAAAAAAAAAGATTC
2110631 AAGGT
131 AAGGT
2110636 ACA
1 ACA
2110639 TTAGACCAAA
Statistics
Matches: 136, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
135 13 0.10
136 123 0.90
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (135 bp):
ACAAATTTAAGGTTGGAAGCGATTTCTGGGCTCTTGGCTGTCTAGGCTTTGTTTTTGACTACTTA
ATTTTCAACGACTTTTAGCCCTTGAGTAGGCCCAGAGTCGATTTTGGAAGAAAAAAAAAAGATTC
AAGGT
Found at i:2110792 original size:34 final size:34
Alignment explanation
Indices: 2110749--2110818 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
2110739 ATATATTAAG
2110749 TTAGTCTCCCCCTCCCGTTATCACCTACATTTCC
1 TTAGTCTCCCCCTCCCGTTATCACCTACATTTCC
2110783 TTAGTCTCCCCCTCCCGTTATCACCTACATTTCC
1 TTAGTCTCCCCCTCCCGTTATCACCTACATTTCC
2110817 TT
1 TT
2110819 CAAGGCTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.14, C:0.43, G:0.06, T:0.37
Consensus pattern (34 bp):
TTAGTCTCCCCCTCCCGTTATCACCTACATTTCC
Found at i:2116198 original size:29 final size:30
Alignment explanation
Indices: 2116165--2116221 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2116155 GTTTCGTGAT
* **
2116165 CACATAGGTGG-CCACACGGGCGTGTGCCG
1 CACATAGGCGGTCCACACGACCGTGTGCCG
2116194 CACATAGGCGGTCCACACGACCGTGTGC
1 CACATAGGCGGTCCACACGACCGTGTGC
2116222 AATTGGGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.19, C:0.33, G:0.33, T:0.14
Consensus pattern (30 bp):
CACATAGGCGGTCCACACGACCGTGTGCCG
Found at i:2139526 original size:6 final size:6
Alignment explanation
Indices: 2139481--2139509 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2139471 AGAATGTTCT
2139481 TTTACA TTTACA TTTACA TTTACA TTTAC
1 TTTACA TTTACA TTTACA TTTACA TTTAC
2139510 TTGACTCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTACA
Found at i:2157642 original size:22 final size:23
Alignment explanation
Indices: 2157614--2157658 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2157604 AAGTTTGAGA
* *
2157614 TTTAAAA-TTATATTTTAATTTT
1 TTTAAAATTTATAATTCAATTTT
2157636 TTTAAAATTTATAATTCAATTTT
1 TTTAAAATTTATAATTCAATTTT
2157659 GATTCAGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTAAAATTTATAATTCAATTTT
Found at i:2160469 original size:18 final size:18
Alignment explanation
Indices: 2160442--2160478 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2160432 TGAAAGGATC
* *
2160442 ACAAATAAAAACAAAACT
1 ACAAAAAAAAAAAAAACT
2160460 ACAAAAAAAAAAAAAACT
1 ACAAAAAAAAAAAAAACT
2160478 A
1 A
2160479 AATTACACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.78, C:0.14, G:0.00, T:0.08
Consensus pattern (18 bp):
ACAAAAAAAAAAAAAACT
Found at i:2162805 original size:23 final size:22
Alignment explanation
Indices: 2162776--2162830 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
2162766 TCTCTTAACA
2162776 AAAATTACAAAAA-AAAATTAAAT
1 AAAATTACAAAAATAAAA--AAAT
*
2162799 AATATTA-AAAAATAAAAAAAT
1 AAAATTACAAAAATAAAAAAAT
2162820 AAAATT-CAAAA
1 AAAATTACAAAA
2162831 TATTTATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 13 0.46
22 5 0.18
23 10 0.36
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.22
Consensus pattern (22 bp):
AAAATTACAAAAATAAAAAAAT
Found at i:2162824 original size:31 final size:30
Alignment explanation
Indices: 2162775--2162843 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 30
2162765 CTCTCTTAAC
* *
2162775 AAAAATTACAAAAAAAAATTAAATAATA-TT
1 AAAAAATAAAAAAAAAAATTAAA-AATATTT
*
2162805 AAAAAATAAAAAAATAAAATTCAAAATATTT
1 AAAAAATAAAAAAA-AAAATTAAAAATATTT
2162836 ATAAAAAT
1 A-AAAAAT
2162844 TCTAAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 16 0.48
31 11 0.33
32 6 0.18
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (30 bp):
AAAAAATAAAAAAAAAAATTAAAAATATTT
Found at i:2162844 original size:19 final size:18
Alignment explanation
Indices: 2162820--2162855 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2162810 ATAAAAAAAT
2162820 AAAATTCAAAATATTTATA
1 AAAATTCAAAAT-TTTATA
*
2162839 AAAATTCTAAATTTTAT
1 AAAATTCAAAATTTTAT
2162856 TTTTTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAATTCAAAATTTTATA
Found at i:2163542 original size:26 final size:26
Alignment explanation
Indices: 2163509--2163562 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
2163499 TAACTAGAAC
*
2163509 AATTTCACTCAATTCAACTCGATTCG
1 AATTTCACTCAACTCAACTCGATTCG
* *
2163535 AATTTCACTCCACTCGACTCGATTCG
1 AATTTCACTCAACTCAACTCGATTCG
2163561 AA
1 AA
2163563 AAATTTCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31
Consensus pattern (26 bp):
AATTTCACTCAACTCAACTCGATTCG
Found at i:2166073 original size:27 final size:27
Alignment explanation
Indices: 2166043--2166095 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
2166033 GGTAATGGAA
*
2166043 GGTGATTTTTGCAGATATTTGATTTAT
1 GGTGATTTTAGCAGATATTTGATTTAT
2166070 GGTGATTTTAGCAGATATTTGATTTA
1 GGTGATTTTAGCAGATATTTGATTTA
2166096 CTTTATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.04, G:0.23, T:0.49
Consensus pattern (27 bp):
GGTGATTTTAGCAGATATTTGATTTAT
Found at i:2167280 original size:10 final size:10
Alignment explanation
Indices: 2167265--2167291 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2167255 TACACTCATA
2167265 TAAAAGAAAG
1 TAAAAGAAAG
2167275 TAAAAGAAAG
1 TAAAAGAAAG
2167285 TAAAAGA
1 TAAAAGA
2167292 TACACACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.19, T:0.11
Consensus pattern (10 bp):
TAAAAGAAAG
Found at i:2169067 original size:22 final size:21
Alignment explanation
Indices: 2169042--2169082 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
2169032 AGTTACTTTC
2169042 ATTAATT-TTACAAATAATATAT
1 ATTAATTATTA-AAA-AATATAT
2169064 ATTAATTATTAAAAAATAT
1 ATTAATTATTAAAAAATAT
2169083 TTAAAATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 10 0.56
23 3 0.17
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTAATTATTAAAAAATATAT
Found at i:2173611 original size:31 final size:31
Alignment explanation
Indices: 2173576--2173639 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
2173566 AAAGTACTCC
2173576 TGTCTATGAGGCTATTACATCCAGAGATCGG
1 TGTCTATGAGGCTATTACATCCAGAGATCGG
2173607 TGTCTATGAGGCTATTACATCCAGAGATCGG
1 TGTCTATGAGGCTATTACATCCAGAGATCGG
2173638 TG
1 TG
2173640 AAAGTATCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (31 bp):
TGTCTATGAGGCTATTACATCCAGAGATCGG
Found at i:2174060 original size:33 final size:33
Alignment explanation
Indices: 2174018--2174086 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
2174008 ATGAAAAAAA
2174018 ACAAAGAAATAACTAAGCATAGTCATGTTGGGC
1 ACAAAGAAATAACTAAGCATAGTCATGTTGGGC
2174051 ACAAAGAAATAACTAAGCATAGTCATGTTGGGC
1 ACAAAGAAATAACTAAGCATAGTCATGTTGGGC
2174084 ACA
1 ACA
2174087 TACACACTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.20
Consensus pattern (33 bp):
ACAAAGAAATAACTAAGCATAGTCATGTTGGGC
Found at i:2174386 original size:133 final size:133
Alignment explanation
Indices: 2174148--2174415 Score: 527
Period size: 133 Copynumber: 2.0 Consensus size: 133
2174138 CCTTCACAAA
2174148 TGAGACCAACTCAACCTCATAATACACAGTTGAGTATTCAGATGAACCGAAAGCGTATTCGGGCT
1 TGAGACCAACTCAACCTCATAATACACAGTTGAGTATTCAGATGAACCGAAAGCGTATTCGGGCT
2174213 GGATAGTGGTAAGTGCATGTTCTCCTTTCTTCATGGTCTTCACAGTTTTTTCAAGACCATCAACT
66 GGATAGTGGTAAGTGCATGTTCTCCTTTCTTCATGGTCTTCACAGTTTTTTCAAGACCATCAACT
2174278 ACT
131 ACT
2174281 TGAGACCAACTCAACCTCATAATACACAGTTGAGTATTCAGATGAACCGAAAGCGTATTCGGGCT
1 TGAGACCAACTCAACCTCATAATACACAGTTGAGTATTCAGATGAACCGAAAGCGTATTCGGGCT
*
2174346 GGATAGTGGTAAGTGCATGTTCTCCTTTCTTCATGGTCTTCACAGTTTTTTCAAGACCATCAATT
66 GGATAGTGGTAAGTGCATGTTCTCCTTTCTTCATGGTCTTCACAGTTTTTTCAAGACCATCAACT
2174411 ACT
131 ACT
2174414 TG
1 TG
2174416 TCCTGCCACA
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 134 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (133 bp):
TGAGACCAACTCAACCTCATAATACACAGTTGAGTATTCAGATGAACCGAAAGCGTATTCGGGCT
GGATAGTGGTAAGTGCATGTTCTCCTTTCTTCATGGTCTTCACAGTTTTTTCAAGACCATCAACT
ACT
Found at i:2184549 original size:72 final size:73
Alignment explanation
Indices: 2184462--2184607 Score: 276
Period size: 72 Copynumber: 2.0 Consensus size: 73
2184452 AATGTTTGGT
2184462 AAAATTTACATTTAATCAATAAATTTTTAAAAGTAACATCTAAAAATAAAGTAAAATTG-AAAAA
1 AAAATTTACATTTAATCAATAAATTTTTAAAAGTAACATCTAAAAATAAAGTAAAATTGAAAAAA
2184526 AAAAATAA
66 AAAAATAA
*
2184534 AAAATTTACATTTAATCAATAATTTTTTAAAAGTAACATCTAAAAATAAAGTAAAATTGAAAAAA
1 AAAATTTACATTTAATCAATAAATTTTTAAAAGTAACATCTAAAAATAAAGTAAAATTGAAAAAA
2184599 AAAAATAA
66 AAAAATAA
2184607 A
1 A
2184608 GAGTGGACGA
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
72 58 0.81
73 14 0.19
ACGTcount: A:0.61, C:0.05, G:0.04, T:0.29
Consensus pattern (73 bp):
AAAATTTACATTTAATCAATAAATTTTTAAAAGTAACATCTAAAAATAAAGTAAAATTGAAAAAA
AAAAATAA
Found at i:2195435 original size:3 final size:3
Alignment explanation
Indices: 2195427--2195496 Score: 140
Period size: 3 Copynumber: 23.3 Consensus size: 3
2195417 ATCTATAGGT
2195427 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2195475 ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
2195497 AATGACAGAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2197932 original size:23 final size:23
Alignment explanation
Indices: 2197906--2197980 Score: 132
Period size: 23 Copynumber: 3.3 Consensus size: 23
2197896 GTGTTATTGA
*
2197906 TCAGTGGTAGCTTCGGCTACGTT
1 TCAGTGGTAGCTTCGGCTACATT
2197929 TCAGTGGTAGCTTCGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
*
2197952 TCAGTGGTAGCTTCGGCTACATA
1 TCAGTGGTAGCTTCGGCTACATT
2197975 TCAGTG
1 TCAGTG
2197981 TTGCACTTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.17, C:0.21, G:0.28, T:0.33
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACATT
Found at i:2205331 original size:22 final size:22
Alignment explanation
Indices: 2205281--2205354 Score: 121
Period size: 23 Copynumber: 3.3 Consensus size: 22
2205271 GTGTTATTGA
*
2205281 TCAGTGGTAGCTTCGGCTACGTT
1 TCAGTGGTAGCTTCGGCTAC-AT
2205304 TCAGTGGTAGCTTCGGCTACAT
1 TCAGTGGTAGCTTCGGCTACAT
2205326 TCAGTGGTAGCTTCGGCTACAT
1 TCAGTGGTAGCTTCGGCTACAT
2205348 ATCAGTG
1 -TCAGTG
2205355 TTGCACTTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
22 23 0.47
23 26 0.53
ACGTcount: A:0.18, C:0.22, G:0.28, T:0.32
Consensus pattern (22 bp):
TCAGTGGTAGCTTCGGCTACAT
Found at i:2216282 original size:33 final size:33
Alignment explanation
Indices: 2216237--2216467 Score: 150
Period size: 33 Copynumber: 6.6 Consensus size: 33
2216227 AAAATACGGT
*
2216237 GGAATCAACACTTAGCAACCACCAATGAATCGG
1 GGAATCAGCACTTAGCAACCACCAATGAATCGG
* * *
2216270 GGAATCATCACTTAGCAATCCCCCTTCACATTTAAAATACGG
1 GGAATCAGCACTTAGCAA--CCAC--CA-A--T-GAAT-CGG
*
2216312 TGGAATCAGCGCTTAGCAACCACCAATGAATCGG
1 -GGAATCAGCACTTAGCAACCACCAATGAATCGG
* *
2216346 GGAATCAGCGCTTAGCAACC-CC--T---TGGG
1 GGAATCAGCACTTAGCAACCACCAATGAATCGG
* * *
2216373 GGAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGG
1 GGAATCAGCACTTAGCAA-CCAC--CA-A--T-GAAT-CGG
*
2216414 TGGAATCAGCACTTAGCAACCACCAATGAATAGG
1 -GGAATCAGCACTTAGCAACCACCAATGAATCGG
2216448 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
2216468 CTTAGGGGGA
Statistics
Matches: 158, Mismatches: 15, Indels: 50
0.71 0.07 0.22
Matches are distributed among these distances:
27 19 0.12
28 2 0.01
29 1 0.01
30 1 0.01
31 1 0.01
32 2 0.01
33 57 0.36
34 5 0.03
35 9 0.06
36 3 0.02
37 2 0.01
38 3 0.02
39 4 0.03
40 2 0.01
41 11 0.07
42 20 0.13
43 16 0.10
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATGAATCGG
Found at i:2216327 original size:76 final size:76
Alignment explanation
Indices: 2216158--2216367 Score: 300
Period size: 76 Copynumber: 2.8 Consensus size: 76
2216148 TATCCGTTGT
* * * * *
2216158 CGGTGGATTCAGCAATTAGCAACCACCAGT-AATTCGGGGAATCAGCACTTAACAA-CCCTTGTC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAA-TCGGGGAATCAGCACTTAGCAACCCCCTGTC
2216221 ACATTTAAAATA
65 ACATTTAAAATA
* *
2216233 CGGTGGAATCAACACTTAGCAACCACCAATGAATCGGGGAATCATCACTTAGCAATCCCCCT-TC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAA-CCCCCTGTC
2216297 ACATTTAAAATA
65 ACATTTAAAATA
* *
2216309 CGGTGGAATCAGCGCTTAGCAACCACCAATGAATCGGGGAATCAGCGCTTAGCAACCCC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCC
2216368 TTGGGGGAAT
Statistics
Matches: 121, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
75 50 0.41
76 67 0.55
77 4 0.03
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (76 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTGTCA
CATTTAAAATA
Found at i:2216420 original size:102 final size:102
Alignment explanation
Indices: 2216268--2216499 Score: 385
Period size: 102 Copynumber: 2.3 Consensus size: 102
2216258 CCAATGAATC
* *
2216268 GGGGAATCATCACTTAGCAATCCCCCTTCACATTTAAAATACGGTGGAATCAGCGCTTAGCAACC
1 GGGGAATCAACACTTAGCAA-CCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACC
* *
2216333 ACCAATGAATCGGGGAATCAGCGCTTAGCAACCCCTT-G
65 ACCAATGAATAGGGGAATCAGCACTTAGCAA-CCCTTAG
2216371 GGGGAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
2216436 CCAATGAATAGGGGAATCAGCACTTAGCAACCCTTAG
66 CCAATGAATAGGGGAATCAGCACTTAGCAACCCTTAG
* *
2216473 GGGGAATCAGCACGTAGCAACCCCCTT
1 GGGGAATCAACACTTAGCAACCCCCTT
2216500 TTTATTCAAT
Statistics
Matches: 122, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
101 5 0.04
102 98 0.80
103 19 0.16
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (102 bp):
GGGGAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
CCAATGAATAGGGGAATCAGCACTTAGCAACCCTTAG
Found at i:2219573 original size:45 final size:45
Alignment explanation
Indices: 2219500--2219648 Score: 183
Period size: 45 Copynumber: 3.3 Consensus size: 45
2219490 ATATACCGAG
*
2219500 TACTGTTACTGTTACCGATTCGATACTTTGTGTGTTAAATACTGT
1 TACTGTTACTGTTACCGATTCGACACTTTGTGTGTTAAATACTGT
* **
2219545 TACTATTACTGTTACCGATTCGACACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGATTCGACACTTTGTGTGTTAAATACTGT
* * * **
2219590 TACCGTTAATGTTACAGATTC-AGCACTTTGTGTACTAAATACTGT
1 TACTGTTACTGTTACCGATTCGA-CACTTTGTGTGTTAAATACTGT
* *
2219635 TACTGCTACCGTTA
1 TACTGTTACTGTTA
2219649 TTGATTACTG
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
44 1 0.01
45 86 0.99
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (45 bp):
TACTGTTACTGTTACCGATTCGACACTTTGTGTGTTAAATACTGT
Found at i:2219843 original size:19 final size:20
Alignment explanation
Indices: 2219821--2219863 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
2219811 CGTGATTGTA
* *
2219821 GAATAT-AATTTGAAAATGT
1 GAATATGAATATGAAAATAT
2219840 GAAT-TGAATATGAAAATAT
1 GAATATGAATATGAAAATAT
2219859 GAATA
1 GAATA
2219864 GAAAGCATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.33
Consensus pattern (20 bp):
GAATATGAATATGAAAATAT
Found at i:2222254 original size:25 final size:26
Alignment explanation
Indices: 2222190--2222275 Score: 83
Period size: 25 Copynumber: 3.4 Consensus size: 26
2222180 CAGACACACC
*
2222190 ACAGCTCGTATGAGCTT-CTTGATTT
1 ACAGCTCGTATGAGCTTACTCGATTT
*
2222215 ACAGCTCATGA-GAGCTTAC-CGATTCT
1 ACAGCTCGT-ATGAGCTTACTCGATT-T
*
2222241 -CAGCTCGTATGAGCTTA-TTGATTT
1 ACAGCTCGTATGAGCTTACTCGATTT
*
2222265 ATAGCTCGTAT
1 ACAGCTCGTAT
2222276 AAGCATTTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
24 2 0.04
25 45 0.90
26 3 0.06
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (26 bp):
ACAGCTCGTATGAGCTTACTCGATTT
Found at i:2225546 original size:14 final size:13
Alignment explanation
Indices: 2225520--2225570 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
2225510 GTTTATTTGA
2225520 AATATAATAATAT
1 AATATAATAATAT
2225533 AATATAATTAATAT
1 AATATAA-TAATAT
* *
2225547 AAT-TTACAATAT
1 AATATAATAATAT
*
2225559 AATAAAATAATA
1 AATATAATAATA
2225571 ATATACTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 8 0.26
13 14 0.45
14 9 0.29
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATAATAATAT
Found at i:2230026 original size:263 final size:263
Alignment explanation
Indices: 2229559--2230875 Score: 2591
Period size: 263 Copynumber: 5.0 Consensus size: 263
2229549 ATGGAGGAGT
2229559 CTAACAATTATGGCCACCAACATCCCCTGCTTCTTATCTTGAATCACGACCAGCTGATCCACAAT
1 CTAACAATTATGGCCACCAACATCCCCTGCTTCTTATCTTGAATCACGACCAGCTGATCCACAAT
2229624 CAAAGTGATATAACTGATTGCTCCAGGTATGCGGAGAAGGTGTCTTCAGCATGCACAATAGTTAA
66 CAAAGTGATATAACTGATTGCTCCAGGTATGCGGAGAAGGTGTCTTCAGCATGCACAATAGTTAA
2229689 CTTTTGGTATTTCGACAGTTCTGTCCCTTTACGAGTTCAACATGCAGCCCGTTGGGGAACCACCT
131 CTTTTGGTATTTCGACAGTTCTGTCCCTTTACGAGTTCAACATGCAGCCCGTTGGGGAACCACCT
2229754 AGATGGTCTTGACATAGGACACTTTATAACTTACCTCTCGAATAGGGAGCAATCGTTATACACCT
196 AGATGGTCTTGACATAGGACACTTTATAACTTACCTCTCGAATAGGGAGCAATCGTTATACACCT
2229819 ACC
261 ACC
2229822 CTAACAATTATGGCCACCAACATCCCCTGCTTCTTATCTTGAATCACGACCAGCTGATCCACAAT
1 CTAACAATTATGGCCACCAACATCCCCTGCTTCTTATCTTGAATCACGACCAGCTGATCCACAAT
2229887 CAAAGTGATATAACTGATTGCTCCAGGTATGCGGAGAAGGTGTCTTCAGCATGCACAATAGTTAA
66 CAAAGTGATATAACTGATTGCTCCAGGTATGCGGAGAAGGTGTCTTCAGCATGCACAATAGTTAA
2229952 CTTTTGGTATTTCGACAGTTCTGTCCCTTTACGAGTTCAACATGCAGCCCGTTGGGGAACCACCT
131 CTTTTGGTATTTCGACAGTTCTGTCCCTTTACGAGTTCAACATGCAGCCCGTTGGGGAACCACCT
2230017 AGATGGTCTTGACATAGGACACTTTATAACTTACCTCTCGAATAGGGAGCAATCGTTATACACCT
196 AGATGGTCTTGACATAGGACACTTTATAACTTACCTCTCGAATAGGGAGCAATCGTTATACACCT
2230082 ACC
261 ACC
2230085 CTAACAATTATGGCCACCAACATCCCCTGCTTCTTATCTTGAATCACGACCAGCTGATCCACAAT
1 CTAACAATTATGGCCACCAACATCCCCTGCTTCTTATCTTGAATCACGACCAGCTGATCCACAAT
2230150 CAAAGTGATATAACTGATTGCTCCAGGTATGCGGAGAAGGTGTCTTCAGCATGCACAATAGTTAA
66 CAAAGTGATATAACTGATTGCTCCAGGTATGCGGAGAAGGTGTCTTCAGCATGCACAATAGTTAA
2230215 CTTTTGGTATTTCGACAGTTCTGTCCCTTTACGAGTTCAACATGCAGCCCGTTGGGGAACCACCT
131 CTTTTGGTATTTCGACAGTTCTGTCCCTTTACGAGTTCAACATGCAGCCCGTTGGGGAACCACCT
2230280 AGATGGTCTTGACATAGGACACTTTATAACTTACCTCTCGAATAGGGAGCAATCGTTATACACCT
196 AGATGGTCTTGACATAGGACACTTTATAACTTACCTCTCGAATAGGGAGCAATCGTTATACACCT
2230345 ACC
261 ACC
2230348 CTAACAATTATGGCCACCAACATCCCCTGCTTCTTATCTTGAATCACGACCAGCTGATCCACAAT
1 CTAACAATTATGGCCACCAACATCCCCTGCTTCTTATCTTGAATCACGACCAGCTGATCCACAAT
2230413 CAAAGTGATATAACTGATTGCTCCAGGTATGCGGAGAAGGTGTCTTCAGCATGCACAATAGTTAA
66 CAAAGTGATATAACTGATTGCTCCAGGTATGCGGAGAAGGTGTCTTCAGCATGCACAATAGTTAA
2230478 CTTTTGGTATTTCGACAGTTCTGTCCCTTTACGAGTTCAACATGCAGCCCGTTGGGGAACCACCT
131 CTTTTGGTATTTCGACAGTTCTGTCCCTTTACGAGTTCAACATGCAGCCCGTTGGGGAACCACCT
2230543 AGATGGTCTTGACATAGGACACTTTATAACTTACCTCTCGAATAGGGAGCAATCGTTATACACCT
196 AGATGGTCTTGACATAGGACACTTTATAACTTACCTCTCGAATAGGGAGCAATCGTTATACACCT
2230608 ACC
261 ACC
2230611 CTAACAATTATGGCCACCAACATCCCCTGCTTCTTATCTTGAATCACGACCAGCTGATCCACAAT
1 CTAACAATTATGGCCACCAACATCCCCTGCTTCTTATCTTGAATCACGACCAGCTGATCCACAAT
2230676 CAAAGTGATATAACTGATTGCTCCAGGTATGCGGAGAAGGTGTCTTCAGCATGCACAATAGTTAA
66 CAAAGTGATATAACTGATTGCTCCAGGTATGCGGAGAAGGTGTCTTCAGCATGCACAATAGTTAA
**
2230741 CTTTTGGTATTTCGACAGTTCTGTCCCTTTACGAGTTCAACATGCAGCCCGCGGGGGAACCACCT
131 CTTTTGGTATTTCGACAGTTCTGTCCCTTTACGAGTTCAACATGCAGCCCGTTGGGGAACCACCT
* *
2230806 AGATGGTCTTGACATAGGAC-GTTTATAACTTACCTCTGGAATAGGGAGCAATCGTTATACACCT
196 AGATGGTCTTGACATAGGACACTTTATAACTTACCTCTCGAATAGGGAGCAATCGTTATACACCT
2230870 ACC
261 ACC
2230873 CTA
1 CTA
2230876 GCTTAGTATT
Statistics
Matches: 1050, Mismatches: 4, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
262 48 0.05
263 1002 0.95
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (263 bp):
CTAACAATTATGGCCACCAACATCCCCTGCTTCTTATCTTGAATCACGACCAGCTGATCCACAAT
CAAAGTGATATAACTGATTGCTCCAGGTATGCGGAGAAGGTGTCTTCAGCATGCACAATAGTTAA
CTTTTGGTATTTCGACAGTTCTGTCCCTTTACGAGTTCAACATGCAGCCCGTTGGGGAACCACCT
AGATGGTCTTGACATAGGACACTTTATAACTTACCTCTCGAATAGGGAGCAATCGTTATACACCT
ACC
Found at i:2236103 original size:2 final size:2
Alignment explanation
Indices: 2236096--2236124 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2236086 ACATACCTTT
2236096 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2236125 TTATCTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2240168 original size:29 final size:29
Alignment explanation
Indices: 2240134--2240197 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 29
2240124 TAAATATATT
2240134 TATTTTTTT-AA-TTTTTTAATTTTAAAA
1 TATTTTTTTAAATTTTTTTAATTTTAAAA
2240161 TACTTTTTTTAAATTTTTTTAATTTTAAAA
1 TA-TTTTTTTAAATTTTTTTAATTTTAAAA
2240191 TATTTTT
1 TATTTTT
2240198 AAAATATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
27 2 0.06
28 7 0.21
29 7 0.21
30 18 0.53
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (29 bp):
TATTTTTTTAAATTTTTTTAATTTTAAAA
Found at i:2240227 original size:42 final size:43
Alignment explanation
Indices: 2240153--2240241 Score: 121
Period size: 42 Copynumber: 2.1 Consensus size: 43
2240143 AATTTTTTAA
*
2240153 TTTTAAAATACTTTTTTTAAATTTTTTTAA-TTTTAAAAT-AT
1 TTTTAAAATACTTTTTTTAAATTTTTTAAATTTTTAAAATAAT
*
2240194 TTTTAAAATA-TATATTTTTTAATTTTTTAAATTTTTAAAATAAT
1 TTTTAAAATACT-T-TTTTTAAATTTTTTAAATTTTTAAAATAAT
2240238 TTTT
1 TTTT
2240242 TGGTATTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
40 1 0.02
41 11 0.26
42 15 0.36
43 9 0.21
44 6 0.14
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (43 bp):
TTTTAAAATACTTTTTTTAAATTTTTTAAATTTTTAAAATAAT
Found at i:2240228 original size:32 final size:31
Alignment explanation
Indices: 2240145--2240242 Score: 112
Period size: 30 Copynumber: 3.2 Consensus size: 31
2240135 ATTTTTTTAA
**
2240145 TTTTTTAATTTTAAAATACTTTTT-TTA-AAT
1 TTTTTTAATTTTAAAATA-TTTTTAAAATAAT
2240175 TTTTTTAATTTTAAAATATTTTTAAAATATAT
1 TTTTTTAATTTTAAAATATTTTTAAAATA-AT
**
2240207 ATTTTTTAATTTTTTAA-ATTTTTAAAATAAT
1 -TTTTTTAATTTTAAAATATTTTTAAAATAAT
2240238 TTTTT
1 TTTTT
2240243 GGTATTTATT
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
29 5 0.08
30 24 0.40
31 3 0.05
32 14 0.23
33 14 0.23
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (31 bp):
TTTTTTAATTTTAAAATATTTTTAAAATAAT
Found at i:2241367 original size:29 final size:30
Alignment explanation
Indices: 2241320--2241376 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
2241310 TTGATATAAT
*
2241320 ATACAATTATACATATG-AACTTTAATTTG
1 ATACAATTATACACATGAAACTTTAATTTG
* * *
2241349 ATACAATTATATACGTGAAATTTTAATT
1 ATACAATTATACACATGAAACTTTAATT
2241377 GTTATACTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 14 0.61
30 9 0.39
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (30 bp):
ATACAATTATACACATGAAACTTTAATTTG
Found at i:2241383 original size:21 final size:21
Alignment explanation
Indices: 2241358--2241397 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2241348 GATACAATTA
* *
2241358 TATACGTGAAATTTTAATTGT
1 TATACGTAAAACTTTAATTGT
*
2241379 TATACTTAAAACTTTAATT
1 TATACGTAAAACTTTAATT
2241398 TTGATTTAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.47
Consensus pattern (21 bp):
TATACGTAAAACTTTAATTGT
Found at i:2242170 original size:105 final size:105
Alignment explanation
Indices: 2241830--2242338 Score: 686
Period size: 106 Copynumber: 4.8 Consensus size: 105
2241820 GAAATTTATG
* * *
2241830 AGGATATTTGGCTATTTGGTCGAACGAGAAATTGAAACCCAGCACATTAGGGCACGTTCTCTCGA
1 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGTT-TCTCGA
* * * *
2241895 ATTTCCAAACGC-AAGTATTGCCTCACTTTGAAA-TTTCGAA
65 TTTTCCAAACGCGAAATATTGCCTTACTTTGAAAGTTT-AAA
* * * * *
2241935 AGGATATTCGGCTATTCGGTCAAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTCTCTTGA
1 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGTT-TCTCGA
** *
2242000 AATTACAAACGCGAAATATTGCCTTACTTTGAAAGTTTAAA
65 TTTTCCAAACGCGAAATATTGCCTTACTTTGAAAGTTTAAA
* *
2242041 AGGATATTTGACTATTTGGTCGAACGATAAATCGAAACCCAACACGTTAGGGCACGTATTCTCGA
1 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGT-TTCTCGA
* *
2242106 TTTTCTAAACGCG-AATATTGTCTTA-TTTGGAAAGTTTAAA
65 TTTTCCAAACGCGAAATATTGCCTTACTTT-GAAAGTTTAAA
*
2242146 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACATTAGGGCACGTATTCTCGA
1 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGT-TTCTCGA
2242211 TTTTCCAAACGCGAAATATTGCCTTA-TTTGGAAAGTTTAAA
65 TTTTCCAAACGCGAAATATTGCCTTACTTT-GAAAGTTTAAA
*
2242252 AGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGTTTTCTCGA
1 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACG-TTTCTCGA
* * * *
2242317 TTTTTCGAACTCAAAATATTGC
65 TTTTCCAAACGCGAAATATTGC
2242339 TTTATTTAGA
Statistics
Matches: 364, Mismatches: 34, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
104 3 0.01
105 165 0.45
106 191 0.52
107 5 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (105 bp):
AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGTTTCTCGAT
TTTCCAAACGCGAAATATTGCCTTACTTTGAAAGTTTAAA
Found at i:2242198 original size:211 final size:210
Alignment explanation
Indices: 2241830--2242320 Score: 695
Period size: 211 Copynumber: 2.3 Consensus size: 210
2241820 GAAATTTATG
* * *
2241830 AGGATATTTGGCTATTTGGTCGAACGAGAAATTGAAACCCAGCACATTAGGGCACGTTCTCTCGA
1 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGTT-TCTCGA
* *
2241895 ATTTCCAAACGCAAGTATTGCCTCACTTTGAAATTTCGAAAGGATATTCGGCTATTCGGTCAAAC
65 TTTTCCAAACGCAAGTATTGCCTCACTTTGAAATTTCAAAAGGATATTCGGCTATTCGGTCAAAC
* * *
2241960 GAGAAATCGAAACCCAGCACGTTAGGGCACGT-TCTCTTGAAATTACAAACGCGAAATATTGCCT
130 GAGAAATCGAAACCCAACACATTAGGGCACGTAT-TCTCGAAATTACAAACGCGAAATATTGCCT
2242024 TACTTT-GAAAGTTTAAA
194 TA-TTTGGAAAGTTTAAA
* *
2242041 AGGATATTTGACTATTTGGTCGAACGATAAATCGAAACCCAACACGTTAGGGCACGTATTCTCGA
1 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGT-TTCTCGA
* * * * * *
2242106 TTTTCTAAACGCGAA-TATTGTCTTA-TTTGGAAAGTTT-AAAAGGATATTTGGCTATTTGGTCG
65 TTTTCCAAACGC-AAGTATTGCCTCACTTT-GAAA-TTTCAAAAGGATATTCGGCTATTCGGTCA
** *
2242168 AACGAGAAATCGAAACCCAACACATTAGGGCACGTATTCTCGATTTTCCAAACGCGAAATATTGC
127 AACGAGAAATCGAAACCCAACACATTAGGGCACGTATTCTCGAAATTACAAACGCGAAATATTGC
2242233 CTTATTTGGAAAGTTTAAA
192 CTTATTTGGAAAGTTTAAA
*
2242252 AGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGTTTTCTCGA
1 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACG-TTTCTCGA
2242317 TTTT
65 TTTT
2242321 TCGAACTCAA
Statistics
Matches: 251, Mismatches: 22, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
210 6 0.02
211 237 0.94
212 8 0.03
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (210 bp):
AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACGTTAGGGCACGTTTCTCGAT
TTTCCAAACGCAAGTATTGCCTCACTTTGAAATTTCAAAAGGATATTCGGCTATTCGGTCAAACG
AGAAATCGAAACCCAACACATTAGGGCACGTATTCTCGAAATTACAAACGCGAAATATTGCCTTA
TTTGGAAAGTTTAAA
Found at i:2243069 original size:2 final size:2
Alignment explanation
Indices: 2243057--2243091 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2243047 GCAAAAAGGA
* *
2243057 AT AT AT GT AT AT AT AT AT AT AT AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2243092 GGAGTTATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2248141 original size:18 final size:17
Alignment explanation
Indices: 2248116--2248153 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
2248106 AACATTAATA
*
2248116 AATAAATTTAATAAAAT
1 AATAAATTCAATAAAAT
2248133 AATACAATTCAATAAAAT
1 AATA-AATTCAATAAAAT
2248151 AAT
1 AAT
2248154 TAATATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (17 bp):
AATAAATTCAATAAAAT
Found at i:2249771 original size:12 final size:12
Alignment explanation
Indices: 2249750--2249780 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2249740 AAACATAAAA
2249750 TAAT-ATTATAT
1 TAATAATTATAT
2249761 TAATAATTATAT
1 TAATAATTATAT
2249773 TAATAATT
1 TAATAATT
2249781 TACAAGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAATAATTATAT
Found at i:2249819 original size:29 final size:31
Alignment explanation
Indices: 2249787--2249846 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
2249777 AATTTACAAG
*
2249787 AATTAAAT-AAATTAAAATTT-TATGTATAA
1 AATTAAATAAAATTAAAATTTATATATATAA
*
2249816 AATTACATAAAATTAAAATTTATATATATAA
1 AATTAAATAAAATTAAAATTTATATATATAA
2249847 TTACACATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 7 0.26
30 12 0.44
31 8 0.30
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (31 bp):
AATTAAATAAAATTAAAATTTATATATATAA
Found at i:2249848 original size:29 final size:29
Alignment explanation
Indices: 2249787--2249851 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
2249777 AATTTACAAG
* *
2249787 AATTAAATAAATTAAAATTTTATGTATAA
1 AATTACATAAATTAAAATTTTATATATAA
*
2249816 AATTACATAAAATTAAAA-TTTATATATAT
1 AATTACAT-AAATTAAAATTTTATATATAA
2249845 AATTACA
1 AATTACA
2249852 CATTAAACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 23 0.72
30 9 0.28
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (29 bp):
AATTACATAAATTAAAATTTTATATATAA
Found at i:2252769 original size:331 final size:324
Alignment explanation
Indices: 2252124--2252785 Score: 732
Period size: 329 Copynumber: 2.0 Consensus size: 324
2252114 CCTGATTGTG
*
2252124 ATAAATGCGATAAGCCTTGTGAAGATTTGACTCTTGAATGCTCAAAGTCAGAGTGTAAATATATT
1 ATAAATGCGATAAGCCTTGTGAAGATTTGACTCTTGAATGCTCAAAGTCA-AGTGCAAATATATT
* * *
2252189 GTCCACTGGAATTGTGCAGCACCTAAATTTCTACGGAGTGTGATCTATTGGCCCATGTAGTAATT
65 ATCCACTGGAATTGTGCAGCACCTAAATTTCTACGAAGTGT-ATCTATTGGCCCATGTAGCAATT
* * * * *
2252254 TAGACGTAATCATATTTAAAACCTACCGCTTCATTTATAGGAAAACTCAAGATTGAAGAACAGAG
129 TAGACCTAATCATATTTAAAACCTACCACTTCATTTACAGGAAAACTCAAGACTGAAGAACAAAG
*
2252319 TGTGATCTTTGTCTTGTTACTTGTAATGCTAGTTGTTGTCATAATAATTTGGTTTTTTTAAGTTT
194 TGTGATCATTGTC----T-CTTGTAATGCTAGTTGTTGTCATAATAATTTGGTTTTTTTAAGTTT
* * * * *
2252384 TAACATAATAATTTGAAGCCAAAACTGATGAGATTTACATTGGTGTTTGATTGTTGATTTTAAAA
254 TAACACAATAATCTGAAGCCAAAACTGACGAGATTTACATTGGTGTTCGATTGTTGAATTTAAAA
2252449 TTTCTT
319 TTTCTT
* * **
2252455 ATAAATGCTG-TAAGCCTTGTGAAGATTTGGCTTTTGAATGCTTGAAGTC-AGTGCAAATATATT
1 ATAAATGC-GATAAGCCTTGTGAAGATTTGACTCTTGAATGCTCAAAGTCAAGTGCAAATATATT
* * * * *
2252518 ATTCACTGGAATTGTGTAGCACC-CAGTTCTCTAC-AACGT-T-TCTGGGATTGGTCCATGTAGC
65 ATCCACTGGAATTGTGCAGCACCTAAATT-TCTACGAA-GTGTATCT---ATTGGCCCATGTAGC
* *
2252579 AATTTAGACCTAATCATATTTGAAACCTACCACTAT-ATTTGCAGGAAAACTCAAGACTGAAGAA
125 AATTTAGACCTAATCATATTTAAAACCTACCACT-TCATTTACAGGAAAACTCAAGACTGAAGAA
* *
2252643 CAAAGTTTGATCATTG-C-CTTGTAATGCTAGTTGTTATTGTCATAGT-ATTTGGTTTTTTTGAC
189 CAAAGTGTGATCATTGTCTCTTGTAATGCTAGTTG---TTGTCATAATAATTTGG----TTT---
** * * *
2252705 TTTTAAGTTTTAATGCAATAATCTGAAGCCAAAACTTACGAGGTTTGCATTGGTGTTCGATTGTT
244 TTTTAAGTTTTAACACAATAATCTGAAGCCAAAACTGACGAGATTTACATTGGTGTTCGATTGTT
*
2252770 GAATTTAGAATTTCTT
309 GAATTTAAAATTTCTT
2252786 GTAATTGGTC
Statistics
Matches: 280, Mismatches: 34, Indels: 34
0.80 0.10 0.10
Matches are distributed among these distances:
322 16 0.06
324 6 0.02
325 9 0.03
326 3 0.01
328 9 0.03
329 122 0.44
330 1 0.00
331 113 0.40
332 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.38
Consensus pattern (324 bp):
ATAAATGCGATAAGCCTTGTGAAGATTTGACTCTTGAATGCTCAAAGTCAAGTGCAAATATATTA
TCCACTGGAATTGTGCAGCACCTAAATTTCTACGAAGTGTATCTATTGGCCCATGTAGCAATTTA
GACCTAATCATATTTAAAACCTACCACTTCATTTACAGGAAAACTCAAGACTGAAGAACAAAGTG
TGATCATTGTCTCTTGTAATGCTAGTTGTTGTCATAATAATTTGGTTTTTTTAAGTTTTAACACA
ATAATCTGAAGCCAAAACTGACGAGATTTACATTGGTGTTCGATTGTTGAATTTAAAATTTCTT
Found at i:2261148 original size:16 final size:16
Alignment explanation
Indices: 2261127--2261159 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2261117 AACCATTAAC
2261127 AAAATATACATGTTGG
1 AAAATATACATGTTGG
2261143 AAAATATACATGTTGG
1 AAAATATACATGTTGG
2261159 A
1 A
2261160 TAAAACAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.30
Consensus pattern (16 bp):
AAAATATACATGTTGG
Found at i:2270781 original size:21 final size:22
Alignment explanation
Indices: 2270757--2270812 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
2270747 ATTATAATTT
2270757 TATAAAAATTATC-TAAAAAAA
1 TATAAAAATTATCTTAAAAAAA
*
2270778 TATAAAATTTCA-CTTAAAAAAA
1 TATAAAAATT-ATCTTAAAAAAA
2270800 TATAAAAAATTAT
1 TAT-AAAAATTAT
2270813 AGCATCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 10 0.34
22 13 0.45
23 6 0.21
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (22 bp):
TATAAAAATTATCTTAAAAAAA
Found at i:2274189 original size:30 final size:30
Alignment explanation
Indices: 2274148--2274287 Score: 114
Period size: 30 Copynumber: 4.8 Consensus size: 30
2274138 AAATTTAGTA
* *
2274148 TTTTTTTAAATTATATTTTGGCCTCTAAAC
1 TTTTTTAAAATTATATTTTGACCTCTAAAC
*
2274178 TTTTTTAAAATTACATTTTGACAC-CT-AAC
1 TTTTTTAAAATTATATTTTGAC-CTCTAAAC
*
2274207 TTTCTTAAAATTATATTTTGAACCT-TAAAC
1 TTTTTTAAAATTATATTTTG-ACCTCTAAAC
* * * *
2274237 TTTTCT--ATTTACATTTTCACC-CTTAAA-
1 TTTTTTAAAATTATATTTTGACCTC-TAAAC
*
2274264 TTTTCCTAAAATTATATTTTGACC
1 TTTT-TTAAAATTATATTTTGACC
2274288 CAAAATTTTT
Statistics
Matches: 88, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
27 7 0.08
28 15 0.17
29 23 0.26
30 42 0.48
31 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.04, T:0.49
Consensus pattern (30 bp):
TTTTTTAAAATTATATTTTGACCTCTAAAC
Found at i:2274285 original size:58 final size:59
Alignment explanation
Indices: 2274155--2274285 Score: 153
Period size: 59 Copynumber: 2.2 Consensus size: 59
2274145 GTATTTTTTT
* * * *
2274155 AAATTATATTTTG-GCCTCTAAACTTTTTTAAAATTACATTTTGACACCTAACTTTCTTA
1 AAATTATATTTTGAACCTCTAAACTTTTCT-AAATTACATTTTCACACCTAACTTTCCTA
* *
2274214 AAATTATATTTTGAACCT-TAAACTTTTCT-ATTTACATTTTCAC-CCTTAAATTTTCCTA
1 AAATTATATTTTGAACCTCTAAACTTTTCTAAATTACATTTTCACACC-T-AACTTTCCTA
2274272 AAATTATATTTTGA
1 AAATTATATTTTGA
2274286 CCCAAAATTT
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
56 2 0.03
57 13 0.21
58 22 0.35
59 23 0.37
60 3 0.05
ACGTcount: A:0.33, C:0.16, G:0.04, T:0.47
Consensus pattern (59 bp):
AAATTATATTTTGAACCTCTAAACTTTTCTAAATTACATTTTCACACCTAACTTTCCTA
Found at i:2274747 original size:11 final size:11
Alignment explanation
Indices: 2274727--2274776 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
2274717 TAGGGTGAAC
2274727 GAAAGAAAGAA
1 GAAAGAAAGAA
*
2274738 GAAAGGAAGAA
1 GAAAGAAAGAA
*
2274749 AAATAGAAA-AA
1 GAA-AGAAAGAA
2274760 -AAAGAAAGAA
1 GAAAGAAAGAA
*
2274770 AAAAGAA
1 GAAAGAA
2274777 GAAAAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 5 0.15
10 4 0.12
11 20 0.61
12 4 0.12
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (11 bp):
GAAAGAAAGAA
Found at i:2274771 original size:13 final size:13
Alignment explanation
Indices: 2274753--2274792 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
2274743 GAAGAAAAAT
2274753 AGAAAAAAAAGAA
1 AGAAAAAAAAGAA
2274766 AGAAAAAAGAAGAA
1 AGAAAAAA-AAGAA
2274780 A-AAAATAAAAGAA
1 AGAAAA-AAAAGAA
2274793 CAGTCGGGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (13 bp):
AGAAAAAAAAGAA
Found at i:2283868 original size:75 final size:75
Alignment explanation
Indices: 2283685--2284331 Score: 764
Period size: 77 Copynumber: 8.5 Consensus size: 75
2283675 ATTTTGATTT
* * * *
2283685 TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGTG-CGCACACTGAGGTATTT
1 TTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTT
* *
2283749 TTAATTTATG
66 TCAATTTCTG
* * * * *
2283759 TTTTTAAAAAAAAATCAACTCATAATCTGAGAGGTGAGTTTAGCCTCGGGTCACGCGCTGAGGCA
1 TTTTT---CAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTA
2283824 TTTTCAATTTCTG
63 TTTTCAATTTCTG
* * * * *
2283837 TTCTTCAAAGATCAACTCATAACCCGAGAGGTGGGTTGAGCCTCCGGTCACACGCTGAGGTATTT
1 TTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTT
2283902 TCAA-TT-T-
66 TCAATTTCTG
** * ** *
2283909 TTTTTCAAAAATCAACTCATAATTTGAGAGGTGAGTTTGAGCCTCGGGTCGCACGCCAAGGTGTT
1 TTTTTCAAAAATCAACTCATAATCCGAGAGGTGAG-TTGAGCCTCGGGTCACACGCTGAGGTATT
2283974 TTCAATTTCTG
65 TTCAATTTCTG
* *
2283985 TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACAGGCTGAGGTATTT
1 TTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTA-TT
*
2284050 TTCAATTTCTAT
65 TTCAATTTCT-G
* * *
2284062 TTTTTCAAAAATCAACTCATAATACGAGAAGTGAGTTGAGCCTCGGGTCACACGTTGAGGTATCT
1 TTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTAT-T
2284127 TTCAATTTCTG
65 TTCAATTTCTG
* * **** *
2284138 TTTTTTCAAAAATCAACTCATAGTGCGAGAGGTGAGTTGAGCCTTATTTCA-AGCGCCGAGGTAT
1 -TTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCACA-CGCTGAGGTA-
*
2284202 TTTTCAATTTCTATT
63 TTTTCAATTTC--TG
* * *
2284217 TTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCACGCACTGAGGCATTT
1 TTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTT
*
2284282 TCAATTTCTA
66 TCAATTTCTG
* * *
2284292 TTTTTCAAAGATCAACTCATAATTCGAGAGGTGAGCTGAG
1 TTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAG
2284332 ATCCAGGTCG
Statistics
Matches: 487, Mismatches: 69, Indels: 33
0.83 0.12 0.06
Matches are distributed among these distances:
72 29 0.06
73 30 0.06
74 9 0.02
75 116 0.24
76 47 0.10
77 178 0.37
78 77 0.16
79 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (75 bp):
TTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTT
TCAATTTCTG
Found at i:2284580 original size:30 final size:30
Alignment explanation
Indices: 2284490--2284631 Score: 130
Period size: 29 Copynumber: 4.8 Consensus size: 30
2284480 AAATTTTATA
*
2284490 TTTTTTAAAATTACATCTTGAACCC-TAAAC
1 TTTTTTAAAATTACATTTTG-ACCCTTAAAC
* *
2284520 TTTTTTAAAATTACATTTT-AACCTTTAAC
1 TTTTTTAAAATTACATTTTGACCCTTAAAC
**
2284549 TTTTTTAAAATTAGTTTTTGACCCTTAAAC
1 TTTTTTAAAATTACATTTTGACCCTTAAAC
* ** * *
2284579 TTTTCTT--ATTTACATTTTGGGCCTTTAAT
1 TTTT-TTAAAATTACATTTTGACCCTTAAAC
*
2284608 TTTTTCTAAAATTACACTTTGACC
1 TTTTT-TAAAATTACATTTTGACC
2284632 GTAGAAGTTT
Statistics
Matches: 88, Mismatches: 18, Indels: 11
0.75 0.15 0.09
Matches are distributed among these distances:
28 4 0.05
29 41 0.47
30 30 0.34
31 13 0.15
ACGTcount: A:0.30, C:0.16, G:0.05, T:0.49
Consensus pattern (30 bp):
TTTTTTAAAATTACATTTTGACCCTTAAAC
Found at i:2284582 original size:59 final size:59
Alignment explanation
Indices: 2284490--2284623 Score: 148
Period size: 59 Copynumber: 2.3 Consensus size: 59
2284480 AAATTTTATA
2284490 TTTTTTAAAATTACATCTTGAACCCTAAACTTTT-TTAAAATTACATTTT-AACCTTTAAC
1 TTTTTTAAAATTACATCTTGAACCCTAAACTTTTCTT--AATTACATTTTGAACCTTTAAC
** * * ** *
2284549 TTTTTTAAAATTAGTTTTTG-ACCCTTAAACTTTTCTTATTTACATTTTGGGCCTTTAAT
1 TTTTTTAAAATTACATCTTGAACCC-TAAACTTTTCTTAATTACATTTTGAACCTTTAAC
2284608 TTTTTCTAAAATTACA
1 TTTTT-TAAAATTACA
2284624 CTTTGACCGT
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
58 14 0.23
59 38 0.61
60 10 0.16
ACGTcount: A:0.31, C:0.15, G:0.04, T:0.50
Consensus pattern (59 bp):
TTTTTTAAAATTACATCTTGAACCCTAAACTTTTCTTAATTACATTTTGAACCTTTAAC
Found at i:2284802 original size:13 final size:13
Alignment explanation
Indices: 2284784--2284831 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
2284774 ACAATAAAAG
2284784 CAAAAAAATCAAC
1 CAAAAAAATCAAC
* * *
2284797 CAAAAAGGAGCAGC
1 CAAAAA-AATCAAC
*
2284811 CAAAAAAATCAAG
1 CAAAAAAATCAAC
2284824 CAAAAAAA
1 CAAAAAAA
2284832 GGAAAAGTAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
13 17 0.63
14 10 0.37
ACGTcount: A:0.67, C:0.19, G:0.10, T:0.04
Consensus pattern (13 bp):
CAAAAAAATCAAC
Found at i:2285174 original size:15 final size:15
Alignment explanation
Indices: 2285124--2285168 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
2285114 GGGCTAAGGT
* *
2285124 GAAAGAAAGAAAGAA
1 GAAAAAAAGAAAAAA
**
2285139 GAAATGAAGAAAAAA
1 GAAAAAAAGAAAAAA
2285154 GAAAAAAAGAAAAAA
1 GAAAAAAAGAAAAAA
2285169 ATAAAAGAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (15 bp):
GAAAAAAAGAAAAAA
Found at i:2295188 original size:18 final size:19
Alignment explanation
Indices: 2295165--2295202 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
2295155 GGAAGCAAGC
*
2295165 AATGATTGAAGA-AATCAG
1 AATGATTGAAAAGAATCAG
2295183 AATGATTGAAAAGAATCAG
1 AATGATTGAAAAGAATCAG
2295202 A
1 A
2295203 CCTGGAGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (19 bp):
AATGATTGAAAAGAATCAG
Found at i:2298439 original size:50 final size:50
Alignment explanation
Indices: 2298383--2298481 Score: 162
Period size: 50 Copynumber: 2.0 Consensus size: 50
2298373 CACTATGGTT
*
2298383 AATTAAATTGACCAAATTGATCACTCCACCATTAAATTCACTATTTCATC
1 AATTAAATTGACCAAATCGATCACTCCACCATTAAATTCACTATTTCATC
* * *
2298433 AATTAAATTGATCAAATCGATCCCTCCTCCATTAAATTCACTATTTCAT
1 AATTAAATTGACCAAATCGATCACTCCACCATTAAATTCACTATTTCAT
2298482 TGTTAAATTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.35
Consensus pattern (50 bp):
AATTAAATTGACCAAATCGATCACTCCACCATTAAATTCACTATTTCATC
Found at i:2307793 original size:50 final size:50
Alignment explanation
Indices: 2307737--2307836 Score: 166
Period size: 50 Copynumber: 2.0 Consensus size: 50
2307727 CACTATGGTT
* *
2307737 AATTAAATTGATCAAATTGATCAT-TCCACCATTACATTCACTATTTCATC
1 AATTAAATTGATCAAATCGATC-TCTCCACCATTAAATTCACTATTTCATC
2307787 AATTAAATTGATCAAATCGATCTCTCCACCATTAAATTCACTATTTCATC
1 AATTAAATTGATCAAATCGATCTCTCCACCATTAAATTCACTATTTCATC
2307837 GTTAAATCCA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
49 1 0.02
50 46 0.98
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (50 bp):
AATTAAATTGATCAAATCGATCTCTCCACCATTAAATTCACTATTTCATC
Found at i:2310322 original size:14 final size:14
Alignment explanation
Indices: 2310305--2310341 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2310295 AGGTATGAGG
**
2310305 ATGTATATATGTAT
1 ATGTATATATAAAT
2310319 ATGTATATATAAAT
1 ATGTATATATAAAT
2310333 ATGTATATA
1 ATGTATATA
2310342 ATGCTCGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (14 bp):
ATGTATATATAAAT
Found at i:2310730 original size:75 final size:75
Alignment explanation
Indices: 2310593--2310733 Score: 169
Period size: 75 Copynumber: 1.9 Consensus size: 75
2310583 ACTTACATAT
* * * * * *
2310593 ATGTATATATTCTTTTATTGAATTTAGGAAGGACATTTATATAAGTTTATATGAGATTCGATTAT
1 ATGTATATATTCTTGTAATGAATTTAAGAAGGAAATTTATATAAGTGTATATGAGATCCGATTAT
2310658 GCAGGTATAC
66 GCAGGTATAC
* * *
2310668 ATGTATATGTTCTTGTAATGAATTTAAGTATGAAATTTATAT-A-TGTATATGGAAGATCCGATT
1 ATGTATATATTCTTGTAATGAATTTAAGAAGGAAATTTATATAAGTGTATAT-G-AGATCCGATT
2310731 ATG
64 ATG
2310734 TATATATATT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
73 6 0.11
74 2 0.04
75 47 0.85
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.43
Consensus pattern (75 bp):
ATGTATATATTCTTGTAATGAATTTAAGAAGGAAATTTATATAAGTGTATATGAGATCCGATTAT
GCAGGTATAC
Found at i:2310895 original size:41 final size:41
Alignment explanation
Indices: 2310845--2310924 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 41
2310835 AGCAAGTTTG
* * * * * *
2310845 ATGCTGGTGAAATATTTCAGACTTTATGTCTAGTAGGCTTA
1 ATGCCGGTGAAACAATTCAGACTATAAGTCTAGCAGGCTTA
*
2310886 ATGCCGGTGAAACAATTCGGACTATAAGTCTAGCAGGCT
1 ATGCCGGTGAAACAATTCAGACTATAAGTCTAGCAGGCT
2310925 AAAAGCCAGT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (41 bp):
ATGCCGGTGAAACAATTCAGACTATAAGTCTAGCAGGCTTA
Found at i:2311126 original size:71 final size:68
Alignment explanation
Indices: 2311059--2311259 Score: 216
Period size: 63 Copynumber: 2.9 Consensus size: 68
2311049 TGTATATCCT
* * *
2311059 TTCGGTGATAATACTTGTTAGGCATATGTATATATGCATTCAGCTATTCAAGTTTAAAGTGTATA
1 TTCGGTGATAATATTTGTTA-GCATATGTATATA-GCATTCGGCTATTCATGTTTAAAGTGTATA
2311124 TAT-A
64 TATCA
* *
2311128 TTCGGTGATAATATTTGTT---ATGTGTATA-AGCATTCGGTTATTCATGTTTAAAGTGTATATA
1 TTCGGTGATAATATTTGTTAGCATATGTATATAGCATTCGGCTATTCATGTTTAAAGTGTATATA
2311189 -CA
66 TCA
* * * *
2311191 TTCGATGATAATATTTTTTAAGCATATATGTATATACACATTCGGCTATTCATGTTTTAAACTGT
1 TTCGGTGATAATATTTGTT-AGC--ATATGTATATA-GCATTCGGCTATTCATG-TTTAAAGTGT
2311256 ATAT
61 ATAT
2311260 GCATTTGGTT
Statistics
Matches: 111, Mismatches: 11, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
63 47 0.42
64 1 0.01
65 8 0.07
69 26 0.23
70 1 0.01
71 15 0.14
72 13 0.12
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (68 bp):
TTCGGTGATAATATTTGTTAGCATATGTATATAGCATTCGGCTATTCATGTTTAAAGTGTATATA
TCA
Found at i:2311193 original size:31 final size:31
Alignment explanation
Indices: 2311089--2311194 Score: 83
Period size: 31 Copynumber: 3.4 Consensus size: 31
2311079 GGCATATGTA
* * * *
2311089 TATATGCATTCAGCTATTCAAGTTTAAAGTG
1 TATATACATTCGGTTATTCATGTTTAAAGTG
* * * *
2311120 TATATATATTCGGTGATAAT-AT-TTGTTATGTG
1 TATATACATTCGGT--TATTCATGTT-TAAAGTG
2311152 TATA-AGCATTCGGTTATTCATGTTTAAAGTG
1 TATATA-CATTCGGTTATTCATGTTTAAAGTG
2311183 TATATACATTCG
1 TATATACATTCG
2311195 ATGATAATAT
Statistics
Matches: 56, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
30 3 0.05
31 30 0.54
32 20 0.36
33 3 0.05
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.43
Consensus pattern (31 bp):
TATATACATTCGGTTATTCATGTTTAAAGTG
Found at i:2313358 original size:64 final size:67
Alignment explanation
Indices: 2313281--2313419 Score: 167
Period size: 73 Copynumber: 2.0 Consensus size: 67
2313271 TTATTGTACA
* * *
2313281 TAAACAACGGTGATGA-G-T-AATTATTAAGTATTAAATTTAACTCATAATATAGTCTTCTTTTT
1 TAAACAACAGTGATGACGATAAATTATTAAGTACTAAATTTAACTCATAATATAATCTTCTTTTT
2313343 TC
66 TC
*
2313345 TAAACAACAGTGATGACGAATTATTAGAATTATTAGGTACTAAATTTAACTCATAATATAATCTT
1 TAAACAACAGTGATGACG----A-TA-AATTATTAAGTACTAAATTTAACTCATAATATAATCTT
2313410 CTTTTTTC
60 CTTTTTTC
2313418 TA
1 TA
2313420 TCAATGAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
64 15 0.24
65 1 0.02
71 1 0.02
73 45 0.73
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (67 bp):
TAAACAACAGTGATGACGATAAATTATTAAGTACTAAATTTAACTCATAATATAATCTTCTTTTT
TC
Found at i:2317124 original size:26 final size:27
Alignment explanation
Indices: 2317095--2317152 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
2317085 AATATTAAAC
*
2317095 TATTTTTATAATTT-TATTATATATTA
1 TATTTTTAAAATTTGTATTATATATTA
* *
2317121 TATTTTTAAAATTTGTATTTTCTATTA
1 TATTTTTAAAATTTGTATTATATATTA
2317148 T-TTTT
1 TATTTT
2317153 AATGGTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 17 0.61
27 11 0.39
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (27 bp):
TATTTTTAAAATTTGTATTATATATTA
Found at i:2320265 original size:9 final size:9
Alignment explanation
Indices: 2320247--2320320 Score: 61
Period size: 9 Copynumber: 8.6 Consensus size: 9
2320237 ATTAGATTTT
*
2320247 TATATTTTA
1 TATATATTA
2320256 TATATATTA
1 TATATATTA
*
2320265 T-TTTATTA
1 TATATATTA
2320273 TATA-A-TA
1 TATATATTA
2320280 TAATATATTA
1 T-ATATATTA
2320290 TAT-TAATTA
1 TATAT-ATTA
2320299 TAT-TAATTA
1 TATAT-ATTA
2320308 TAT-TATTA
1 TATATATTA
2320316 TATAT
1 TATAT
2320321 TAAATAAACC
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
7 3 0.05
8 19 0.34
9 31 0.55
10 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TATATATTA
Found at i:2320292 original size:5 final size:5
Alignment explanation
Indices: 2320246--2320322 Score: 65
Period size: 5 Copynumber: 15.6 Consensus size: 5
2320236 TATTAGATTT
* *
2320246 TTATA TTTTA TATATA TTAT- TT-TA TTATA TAATATA ATATA TTATA
1 TTATA TTATA T-TATA TTATA TTATA TTATA T--TATA TTATA TTATA
2320292 TTA-A TTATA TTA-A TTATA TTAT- TATATA TTA
1 TTATA TTATA TTATA TTATA TTATA T-TATA TTA
2320323 AATAAACCAA
Statistics
Matches: 59, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
3 1 0.02
4 13 0.22
5 36 0.61
6 5 0.08
7 4 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:2320552 original size:22 final size:22
Alignment explanation
Indices: 2320513--2320560 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
2320503 AAACAAAAGA
2320513 AAAAGAAACAAAAGAAGA-ACAG
1 AAAAGAAACAAAAGAAGAGAC-G
*
2320535 AAAAGAAAC-AGAGAAAGAGACG
1 AAAAGAAACAAAAG-AAGAGACG
2320557 AAAA
1 AAAA
2320561 CAGGGGAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 3 0.13
22 18 0.78
23 2 0.09
ACGTcount: A:0.71, C:0.08, G:0.21, T:0.00
Consensus pattern (22 bp):
AAAAGAAACAAAAGAAGAGACG
Done.