Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, whole genome shotgun sequence
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: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 25 of 160
Found at i:6536875 original size:4 final size:5
Alignment explanation
Indices: 6536813--6536887 Score: 73
Period size: 5 Copynumber: 14.4 Consensus size: 5
6536803 TTAATATTCT
*
6536813 TTTTA TCTTTA TTTTA TTTTTA TTTTTA TTTTTG TTTTA CTTTT- TTTTA
1 TTTTA T-TTTA TTTTA -TTTTA -TTTTA -TTTTA TTTTA -TTTTA TTTTA
*
6536862 TTTTA TTTTA -TTTA TTTTG TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
6536888 ATTCAATTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
4 8 0.13
5 28 0.46
6 25 0.41
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:6536885 original size:14 final size:14
Alignment explanation
Indices: 6536755--6536887 Score: 64
Period size: 14 Copynumber: 9.5 Consensus size: 14
6536745 CGTTCCAGAT
* *
6536755 TTTTTTTTATTTGTT
1 TTTTATTTATTT-TA
*
6536770 TTTTATTTATTTGA
1 TTTTATTTATTTTA
*
6536784 -TTTA-TTATATTA
1 TTTTATTTATTTTA
* *
6536796 GGTTTATTTA--ATA
1 -TTTTATTTATTTTA
6536809 TTCTT-TTTATCTTTA
1 TT-TTATTTAT-TTTA
6536824 TTTTATTT-TTATT-
1 TTTTATTTATT-TTA
* *
6536837 TTTATTTTTGTTTTA
1 TTT-TATTTATTTTA
*
6536852 CTTTTTTTTATTTTA
1 -TTTTATTTATTTTA
*
6536867 TTTTATTTATTTTG
1 TTTTATTTATTTTA
6536881 TTTTATT
1 TTTTATT
6536888 ATTCAATTTT
Statistics
Matches: 93, Mismatches: 12, Indels: 27
0.70 0.09 0.20
Matches are distributed among these distances:
12 11 0.12
13 12 0.13
14 34 0.37
15 33 0.35
16 3 0.03
ACGTcount: A:0.17, C:0.02, G:0.05, T:0.76
Consensus pattern (14 bp):
TTTTATTTATTTTA
Found at i:6536984 original size:58 final size:58
Alignment explanation
Indices: 6536914--6537483 Score: 694
Period size: 58 Copynumber: 9.7 Consensus size: 58
6536904 ATAAAAATAA
*
6536914 AAAAAAATCTTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTC
1 AAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTC
** * *
6536972 AAAAAAAGCT-TTTTTTTGAAGAAAGTTGAAAGTATCAATTTTTCTTGAAAATTAAAGTTTC
1 AAAAAAA--TATTTTTGGGAA-AAAGTTGAAAGTATCAATTTTTCTT-AAAAATAAAATTTC
*
6537033 -AAAAAATATTTTTGAGG-AAAAGTTAAAAGTATCAA-TTTTCTTTAAAAATAAAATTTC
1 AAAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTTC-TTAAAAATAAAATTTC
* *
6537090 AAAAAAATATTTTTGGAAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTT
1 AAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTC
* * * *
6537148 AAAAAAAAAATTTTGAGG-AAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTTC
1 AAAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAA-ATTTC
* * * * *
6537208 CAAAAAATATTTTTGAGAAAAATTTGAAAGTATCAATTTTCCTT-AAAA-AAATTTTC
1 AAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTC
* ** *
6537264 AAAAGAATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTT-TTAAAAATAAATTTTC
1 AAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTC
* * *
6537321 AAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTC
*
6537379 AAAAAAAATATTTTTGGAGAAAAA-TTGAAAGTATCAATTTTTCTTGAAAATAAAATTTTC
1 -AAAAAAATATTTTTGG-GAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAA-TTTC
6537439 -AAAAAATCAATTTTT-GGAGAAAAGTTGAAAGTATCAATATTTTCT
1 AAAAAAAT--ATTTTTGGGA-AAAAGTTGAAAGTATCAAT-TTTTCT
6537484 GCACAAGAAC
Statistics
Matches: 451, Mismatches: 36, Indels: 47
0.84 0.07 0.09
Matches are distributed among these distances:
55 2 0.00
56 45 0.10
57 67 0.15
58 141 0.31
59 76 0.17
60 102 0.23
61 18 0.04
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (58 bp):
AAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTC
Found at i:6537151 original size:14 final size:14
Alignment explanation
Indices: 6537132--6537161 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6537122 TCAATTTTTC
*
6537132 TTAAAAATAAAATT
1 TTAAAAAAAAAATT
6537146 TTAAAAAAAAAATT
1 TTAAAAAAAAAATT
6537160 TT
1 TT
6537162 GAGGAAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TTAAAAAAAAAATT
Found at i:6537359 original size:27 final size:27
Alignment explanation
Indices: 6537216--6537304 Score: 83
Period size: 27 Copynumber: 3.2 Consensus size: 27
6537206 TCCAAAAAAT
*
6537216 ATTTTTGAGAAAAATTTGAAAGTATCA
1 ATTTTTGAAAAAAATTTGAAAGTATCA
* * *
6537243 ATTTTCCTTAAAAAAATTTTCAAAAGAAT--
1 ATTTT--TGAAAAAAA-TTT-GAAAGTATCA
*
6537272 ATTTTTGAAAAAAAGTTGAAAGTATCA
1 ATTTTTGAAAAAAATTTGAAAGTATCA
6537299 ATTTTT
1 ATTTTT
6537305 TTAAAAATAA
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
25 6 0.12
26 2 0.04
27 19 0.40
29 12 0.25
30 3 0.06
31 6 0.12
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (27 bp):
ATTTTTGAAAAAAATTTGAAAGTATCA
Found at i:6539773 original size:34 final size:33
Alignment explanation
Indices: 6539696--6539773 Score: 77
Period size: 34 Copynumber: 2.3 Consensus size: 33
6539686 TTTCAAAAAA
* **
6539696 AATTTGAT-AAAATAAAATTTTTTTTATTTATT
1 AATTTCATAAAAATAAAATTTTAGTTATTTATT
* *
6539728 ACTTGACATAAAAATAAAATTTTAGTTATTTTATT
1 AATT-TCATAAAAATAAAATTTTAGTTA-TTTATT
*
6539763 AATTTTATAAA
1 AATTTCATAAA
6539774 TATTAAATAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
32 3 0.09
33 2 0.06
34 21 0.60
35 9 0.26
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.50
Consensus pattern (33 bp):
AATTTCATAAAAATAAAATTTTAGTTATTTATT
Found at i:6550833 original size:20 final size:22
Alignment explanation
Indices: 6550805--6550846 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
6550795 AGAAAATTGG
6550805 TAGTCTTTTTAA-AAAAGAAGT
1 TAGTCTTTTTAAGAAAAGAAGT
*
6550826 TAGT-TTTTTAAGAAAATAAGT
1 TAGTCTTTTTAAGAAAAGAAGT
6550847 ATTGAAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.40
Consensus pattern (22 bp):
TAGTCTTTTTAAGAAAAGAAGT
Found at i:6552223 original size:12 final size:13
Alignment explanation
Indices: 6552200--6552224 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6552190 TACATTTTGC
6552200 TTTTAAATTTTTT
1 TTTTAAATTTTTT
6552213 TTTTAAATTTTT
1 TTTTAAATTTTT
6552225 ATAAATAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTAAATTTTTT
Found at i:6552900 original size:16 final size:17
Alignment explanation
Indices: 6552879--6552920 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
6552869 TTAACTTCTT
*
6552879 TTTATTATTT-GTAAAA
1 TTTATTATTTAATAAAA
*
6552895 TTTATTTTTTAATAAAA
1 TTTATTATTTAATAAAA
*
6552912 TTTTTTATT
1 TTTATTATT
6552921 ATATTAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTATTATTTAATAAAA
Found at i:6552914 original size:13 final size:13
Alignment explanation
Indices: 6552898--6552956 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
6552888 TGTAAAATTT
6552898 ATTTTTTAATAAA
1 ATTTTTTAATAAA
* *
6552911 ATTTTTT-ATTAT
1 ATTTTTTAATAAA
**
6552923 ATTAATTAATAAA
1 ATTTTTTAATAAA
*
6552936 AATTTTTAATAAA
1 ATTTTTTAATAAA
6552949 ATTCTTTT
1 ATT-TTTT
6552957 TTTATAATTT
Statistics
Matches: 34, Mismatches: 10, Indels: 3
0.72 0.21 0.06
Matches are distributed among these distances:
12 8 0.24
13 22 0.65
14 4 0.12
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTTTTTAATAAA
Found at i:6552980 original size:22 final size:22
Alignment explanation
Indices: 6552956--6552996 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
6552946 AAAATTCTTT
6552956 TTTTAT-AATTTTCTTTAAAGA
1 TTTTATAAATTTTCTTTAAAGA
6552977 TTTTATAAATTTTCTTTAAA
1 TTTTATAAATTTTCTTTAAA
6552997 AAAATAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTTATAAATTTTCTTTAAAGA
Found at i:6553341 original size:25 final size:24
Alignment explanation
Indices: 6553311--6553360 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 24
6553301 ATTTTTTAAT
6553311 TATTTATTTAATTATATATATTATA
1 TATTTATTTAATTATATAT-TTATA
*
6553336 TATTTATTTAATTTTATATTTATA
1 TATTTATTTAATTATATATTTATA
6553360 T
1 T
6553361 TAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TATTTATTTAATTATATATTTATA
Found at i:6553381 original size:34 final size:33
Alignment explanation
Indices: 6553287--6553385 Score: 89
Period size: 37 Copynumber: 2.9 Consensus size: 33
6553277 TTTAATTTAA
6553287 TATATATAAAAAT-TATTTT-TTAATTATT-TATT
1 TATAT-TAAAAATATATTTTATTAATT-TTATATT
*
6553319 TA-ATTATATATATTATATATTTATTTAATTTTATATT
1 TATATTA-A-A-AATATAT-TTTA-TTAATTTTATATT
6553356 TATATTAAAAATAATATTTTATTAATTTTA
1 TATATTAAAAAT-ATATTTTATTAATTTTA
6553386 GATTGAATAT
Statistics
Matches: 55, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
30 2 0.04
31 3 0.05
32 3 0.05
33 2 0.04
34 12 0.22
35 9 0.16
36 7 0.13
37 13 0.24
38 4 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (33 bp):
TATATTAAAAATATATTTTATTAATTTTATATT
Found at i:6557004 original size:174 final size:176
Alignment explanation
Indices: 6556713--6557097 Score: 589
Period size: 174 Copynumber: 2.2 Consensus size: 176
6556703 TTTTCTTTTC
* * * * *
6556713 CACTCCAGGTTCTAATATTGCCAGGTCTAGGGATGAGGCATATGAGTGATATACCTACCTGTTCC
1 CACTCCAGGATCTAACATTGCTAGGTCTAGGGA-GAGGCACAAGAGTGATATACCTACCTGTTCC
* * *
6556778 AAATAAAAAGAGTTTGCAGTGTAAAAGGAATGTATGAGGTGTGGAGGAGTTGTTGAGAGATAAGA
65 AAATAAAAAGAGTTTGCAATGTAAAAGGAATGCATGAGGTGTGGAGGAGTTGTTGAAAGATAAGA
*
6556843 GACTG-GGGAGTTTTT-ATTTTCTAGATGATC-TTAAGGGTGGCTCAA
130 GACTGAGGAAGTTTTTCATTTTCTAGATGATCTTTAA-GGTGGCTCAA
*
6556888 CACTCCAGGGTCTAACATTGCTAGGTCTAGGGAGAGGCACAAGAGTGATATACCTACCTGTT-CA
1 CACTCCAGGATCTAACATTGCTAGGTCTAGGGAGAGGCACAAGAGTGATATACCTACCTGTTCCA
*
6556952 AATTAAAAAGAGTTTGCAATGTAAAAGGAATGCATGAGGTGTGGAGGAGTTGTTGAAAGATGAGA
66 AA-TAAAAAGAGTTTGCAATGTAAAAGGAATGCATGAGGTGTGGAGGAGTTGTTGAAAGATAAGA
*
6557017 GACTGAGGAAGTTTTTCTTTTTCTAGATGATCTTTAAGGTGGCTCAA
130 GACTGAGGAAGTTTTTCATTTTCTAGATGATCTTTAAGGTGGCTCAA
* *
6557064 CACTCCAGAATCTAACATAGCTAGGTCTAGGGAG
1 CACTCCAGGATCTAACATTGCTAGGTCTAGGGAG
6557098 TTTCAGATGC
Statistics
Matches: 192, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
173 4 0.02
174 90 0.47
175 39 0.20
176 55 0.29
177 4 0.02
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (176 bp):
CACTCCAGGATCTAACATTGCTAGGTCTAGGGAGAGGCACAAGAGTGATATACCTACCTGTTCCA
AATAAAAAGAGTTTGCAATGTAAAAGGAATGCATGAGGTGTGGAGGAGTTGTTGAAAGATAAGAG
ACTGAGGAAGTTTTTCATTTTCTAGATGATCTTTAAGGTGGCTCAA
Found at i:6562407 original size:2 final size:2
Alignment explanation
Indices: 6562395--6562426 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
6562385 GCATAAGTTA
6562395 TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
6562427 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:6572416 original size:2 final size:2
Alignment explanation
Indices: 6572409--6572435 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6572399 CATATAGTCA
6572409 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
6572436 AAAGCAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6576221 original size:2 final size:2
Alignment explanation
Indices: 6576214--6576242 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
6576204 TAGCAATCAG
6576214 GA GA GA GA -A GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
6576243 AGCTACATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6583563 original size:85 final size:84
Alignment explanation
Indices: 6583421--6583591 Score: 279
Period size: 85 Copynumber: 2.0 Consensus size: 84
6583411 AGATCATAAG
*
6583421 AAAGGTTTTAACTTCTTTATATGTTTCATAGGATAAGCCCATAACCAAATAGAATGGAGAAAATA
1 AAAGGTTTTAACTTCTTTACATGTTTCATAGGATAAGCCCATAACCAAATAGAATGGAGAAAATA
* *
6583486 ATTTCATGTAGCTTGGCCC
66 ATTTCACGTAGCTAGGCCC
* * *
6583505 AAAGGTTTTGACTTCTTTTACATGTTTCTTAGGATAAGCCCCTAACCAAATAGAATGGAGAAAAT
1 AAAGGTTTTAACTTC-TTTACATGTTTCATAGGATAAGCCCATAACCAAATAGAATGGAGAAAAT
6583570 AATTTCACGTAGCTAGGCCC
65 AATTTCACGTAGCTAGGCCC
6583590 AA
1 AA
6583592 CTAGTTTCAT
Statistics
Matches: 80, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
84 14 0.17
85 66 0.82
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (84 bp):
AAAGGTTTTAACTTCTTTACATGTTTCATAGGATAAGCCCATAACCAAATAGAATGGAGAAAATA
ATTTCACGTAGCTAGGCCC
Found at i:6587047 original size:26 final size:26
Alignment explanation
Indices: 6587017--6587067 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
6587007 TCTTTAAAAG
6587017 TTTGTTATCATACTTGAAGGTCATGT
1 TTTGTTATCATACTTGAAGGTCATGT
*
6587043 TTTGTTATCATACTTGAATGTCATG
1 TTTGTTATCATACTTGAAGGTCATG
6587068 ATTACTCTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.47
Consensus pattern (26 bp):
TTTGTTATCATACTTGAAGGTCATGT
Found at i:6592022 original size:9 final size:9
Alignment explanation
Indices: 6592008--6592040 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
6591998 TTTTAAAAAA
6592008 CTTTTTTTT
1 CTTTTTTTT
6592017 CTTTTTTTT
1 CTTTTTTTT
*
6592026 CTTTCTTTT
1 CTTTTTTTT
6592035 -TTTTTT
1 CTTTTTT
6592041 ATTAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 5 0.23
9 17 0.77
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:6592025 original size:13 final size:13
Alignment explanation
Indices: 6592009--6592040 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
6591999 TTTAAAAAAC
6592009 TTTTTTTTCTTTT
1 TTTTTTTTCTTTT
*
6592022 TTTTCTTTCTTTT
1 TTTTTTTTCTTTT
6592035 TTTTTT
1 TTTTTT
6592041 ATTAATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (13 bp):
TTTTTTTTCTTTT
Found at i:6592497 original size:29 final size:30
Alignment explanation
Indices: 6592433--6592507 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 30
6592423 TTTTTTAGTT
*
6592433 AAAAT-AAAACTTATTTAAATATAAATTAA
1 AAAATAAAAATTTATTTAAATATAAATTAA
* *
6592462 AGAATAAAAATTTATTTGAATAT-AA-TAA
1 AAAATAAAAATTTATTTAAATATAAATTAA
6592490 AAATATAAAAATTTATTT
1 AAA-ATAAAAATTTATTT
6592508 TTAAAAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
28 5 0.12
29 20 0.50
30 15 0.38
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (30 bp):
AAAATAAAAATTTATTTAAATATAAATTAA
Found at i:6592521 original size:29 final size:29
Alignment explanation
Indices: 6592438--6592523 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 29
6592428 TAGTTAAAAT
* *
6592438 AAAACTTATTTAAATATAAATTAAAGA-ATA
1 AAAATTTATTTGAATA-AAATTAAA-ATATA
* *
6592468 AAAATTTATTTGAATATAATAAAAATATA
1 AAAATTTATTTGAATAAAATTAAAATATA
*
6592497 AAAATTTATTTTTAA-AAAATTAAAATA
1 AAAATTTA-TTTGAATAAAATTAAAATA
6592524 GTTCAAATAC
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
28 1 0.02
29 27 0.57
30 19 0.40
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.37
Consensus pattern (29 bp):
AAAATTTATTTGAATAAAATTAAAATATA
Found at i:6597539 original size:94 final size:94
Alignment explanation
Indices: 6597383--6597608 Score: 231
Period size: 94 Copynumber: 2.4 Consensus size: 94
6597373 ATCACTTAGC
* * * * *
6597383 AACCAAAATAAGAGATAAGTAAAGCCTACAAATTCCTATGCCATTCCACTATTGCACATCTGTGC
1 AACCAAAATAAGAGATAGGTAAAGCCTACAAATTCCCATCCCATTCCACTATAGCACATCTGTGA
*
6597448 ATAAAT-AAATGAATTCCACATCGATTAAG
66 AT-AATCAAATGAATTCCACATCGATTAAA
* * * ** ** *
6597477 AACCAAAATAAGGGATAGGTAAAGCCTACATATTCCCATCCCCTTCTTCTACTAG-ATTTCTGTT
1 AACCAAAATAAGAGATAGGTAAAGCCTACAAATTCCCATCCCATTCCACTA-TAGCACATCTGTG
* * *
6597541 AATATTCAAATGAATTCCATATCGCTTAAA
65 AATAATCAAATGAATTCCACATCGATTAAA
* * * *
6597571 AACCAAAACAAAAGATGGGTAAAGCCTATAAATTCCCA
1 AACCAAAATAAGAGATAGGTAAAGCCTACAAATTCCCA
6597609 CCCTCTGCTT
Statistics
Matches: 107, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
93 2 0.02
94 103 0.96
95 2 0.02
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.27
Consensus pattern (94 bp):
AACCAAAATAAGAGATAGGTAAAGCCTACAAATTCCCATCCCATTCCACTATAGCACATCTGTGA
ATAATCAAATGAATTCCACATCGATTAAA
Found at i:6598856 original size:21 final size:19
Alignment explanation
Indices: 6598830--6598870 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
6598820 TTTAAATTGT
6598830 TAGAAAAAATAAATGAAGGAA
1 TAGAAAAAATAAA--AAGGAA
*
6598851 TAGAAATAATAAAAAGGAA
1 TAGAAAAAATAAAAAGGAA
6598870 T
1 T
6598871 CTTGGCTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
21 12 0.63
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (19 bp):
TAGAAAAAATAAAAAGGAA
Found at i:6600754 original size:18 final size:18
Alignment explanation
Indices: 6600720--6600754 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6600710 TTTTTGATAT
**
6600720 TTTATTATTAATTATTAG
1 TTTATTATTAAAAATTAG
6600738 TTTATTATTAAAAATTA
1 TTTATTATTAAAAATTA
6600755 TATTAATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TTTATTATTAAAAATTAG
Found at i:6611947 original size:2 final size:2
Alignment explanation
Indices: 6611936--6611969 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
6611926 TAGCGCTGAG
6611936 TA TA -A 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 TA TA TA T
6611970 TAGATGCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6616601 original size:83 final size:83
Alignment explanation
Indices: 6616462--6616628 Score: 307
Period size: 83 Copynumber: 2.0 Consensus size: 83
6616452 TGGCTATATG
*
6616462 TTCTGTTCAAATCATTCTTTACCACTTGAACTCATAATTTTCAAATCTATATGACCAAGTTATCT
1 TTCTGTTCAAATCATTCTTTACCACTTCAACTCATAATTTTCAAATCTATATGACCAAGTTATCT
*
6616527 AAATACTTCCATCACTCT
66 AAATACTTCAATCACTCT
6616545 TTCTGTTCAAATCATTCTTTACCACTTCAACTCATAATTTTCAAATCTATATGACCAAGTTATCT
1 TTCTGTTCAAATCATTCTTTACCACTTCAACTCATAATTTTCAAATCTATATGACCAAGTTATCT
*
6616610 AAATATTTCAATCACTCT
66 AAATACTTCAATCACTCT
6616628 T
1 T
6616629 CCACACTATT
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.41
Consensus pattern (83 bp):
TTCTGTTCAAATCATTCTTTACCACTTCAACTCATAATTTTCAAATCTATATGACCAAGTTATCT
AAATACTTCAATCACTCT
Found at i:6619054 original size:31 final size:31
Alignment explanation
Indices: 6619019--6619078 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
6619009 TCTTTCTACA
6619019 CCAAGATATGACTATAATTTTACCGTGATTG
1 CCAAGATATGACTATAATTTTACCGTGATTG
* *
6619050 CCAAGGTATGACTATAATTTTACCTTGAT
1 CCAAGATATGACTATAATTTTACCGTGAT
6619079 GGCTCTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (31 bp):
CCAAGATATGACTATAATTTTACCGTGATTG
Found at i:6623936 original size:16 final size:16
Alignment explanation
Indices: 6623915--6623949 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
6623905 ATTTGGATTT
6623915 TTAGGTGATTAGGTTG
1 TTAGGTGATTAGGTTG
6623931 TTAGGTGATTAGGTTG
1 TTAGGTGATTAGGTTG
6623947 TTA
1 TTA
6623950 AGTAGATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (16 bp):
TTAGGTGATTAGGTTG
Found at i:6639176 original size:19 final size:18
Alignment explanation
Indices: 6639148--6639188 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
6639138 TTTAAAATTG
*
6639148 AATATTATTACAAATAAT
1 AATATTATTAAAAATAAT
*
6639166 AATATTTATTAAAAATAGT
1 AATA-TTATTAAAAATAAT
6639185 AATA
1 AATA
6639189 ATAATAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (18 bp):
AATATTATTAAAAATAAT
Found at i:6640161 original size:3 final size:3
Alignment explanation
Indices: 6640153--6640186 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
6640143 AATAGAATGT
6640153 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
6640187 CATATTTGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:6641294 original size:13 final size:13
Alignment explanation
Indices: 6641270--6641304 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
6641260 AAAAGAAAAG
*
6641270 AAAGATAAAAATCA
1 AAAGA-AAAAATAA
6641284 AAAGAAAAAATAA
1 AAAGAAAAAATAA
6641297 AAAGAAAA
1 AAAGAAAA
6641305 CACACCCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.80, C:0.03, G:0.09, T:0.09
Consensus pattern (13 bp):
AAAGAAAAAATAA
Found at i:6641950 original size:22 final size:22
Alignment explanation
Indices: 6641924--6641967 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
6641914 TGTATATTTA
* *
6641924 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
6641946 TATTTGTATCCCTAAAATTAAG
1 TATTTGTATCCCTAAAATTAAG
6641968 GAAGATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:6642135 original size:23 final size:23
Alignment explanation
Indices: 6642115--6642199 Score: 107
Period size: 23 Copynumber: 3.6 Consensus size: 23
6642105 AAAATTTTCA
**
6642115 GCCTTCATTGCTGACTTTTTTAG
1 GCCTTCATTGCCAACTTTTTTAG
6642138 GCCTTCATTGCCAACTTTTTTAG
1 GCCTTCATTGCCAACTTTTTTAG
* * *
6642161 GCTTTCATTGCCGAATCCTGTTTAG
1 GCCTTCATTGCC-AA-CTTTTTTAG
6642186 GCCTTCATTGCCAA
1 GCCTTCATTGCCAA
6642200 ACCCTTTCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
23 32 0.59
24 4 0.07
25 18 0.33
ACGTcount: A:0.16, C:0.26, G:0.16, T:0.41
Consensus pattern (23 bp):
GCCTTCATTGCCAACTTTTTTAG
Found at i:6645872 original size:22 final size:22
Alignment explanation
Indices: 6645846--6645889 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
6645836 TGTATATTTA
*
6645846 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
6645868 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
6645890 GAAGATTTAG
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:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:6647396 original size:2 final size:2
Alignment explanation
Indices: 6647389--6647416 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6647379 CCCCTCTCCC
6647389 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
6647417 CATGGAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6649913 original size:6 final size:6
Alignment explanation
Indices: 6649886--6649924 Score: 51
Period size: 6 Copynumber: 6.0 Consensus size: 6
6649876 ATAAAGAAAG
6649886 AAATTAT AAATGTT AGAATTT AAATTT AAATTT AAATTT
1 AAATT-T AAAT-TT A-AATTT AAATTT AAATTT AAATTT
6649925 TATTAATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 17 0.57
7 9 0.30
8 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (6 bp):
AAATTT
Found at i:6653984 original size:31 final size:31
Alignment explanation
Indices: 6653949--6654015 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
6653939 ATTGTACAAA
6653949 TAATCCATATATTTATATAAAATTTGAAAA-T
1 TAATCCATATATTTATATAAAATTT-AAAATT
**
6653980 TAATCTTTATATTTATATAAAATTTAAAATT
1 TAATCCATATATTTATATAAAATTTAAAATT
6654011 TAATC
1 TAATC
6654016 ATTCTAGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.46
Consensus pattern (31 bp):
TAATCCATATATTTATATAAAATTTAAAATT
Found at i:6654191 original size:64 final size:64
Alignment explanation
Indices: 6654071--6654194 Score: 148
Period size: 64 Copynumber: 1.9 Consensus size: 64
6654061 AGATTTTTTT
* * *
6654071 AATATTTTAATTTAATTTTTTGAAATTTTTGTATTTTTCAAATTTAATATTTTTATTTAAACAA
1 AATATTTTAATTTAATTTTTTGAAATTTTTGAATTTTACAAATTTAATATTATTATTTAAACAA
*
6654135 AATA-TTTAATTTTATTATTTTG-AATTTTTAGAATTTTACAAAATTTTAA-A-TATTATTTAA
1 AATATTTTAATTTAATT-TTTTGAAATTTTT-GAATTTTAC-AAA-TTTAATATTATTATTTAA
6654195 TTTTTAATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
63 18 0.35
64 25 0.48
65 4 0.08
66 5 0.10
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.56
Consensus pattern (64 bp):
AATATTTTAATTTAATTTTTTGAAATTTTTGAATTTTACAAATTTAATATTATTATTTAAACAA
Found at i:6654214 original size:18 final size:18
Alignment explanation
Indices: 6654157--6654216 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
6654147 TATTATTTTG
*
6654157 AATTTTTAGAATTTTACAA
1 AATTTTTA-AATTTTATAA
* **
6654176 AA-TTTTAAATATTATTT
1 AATTTTTAAATTTTATAA
*
6654193 AATTTTTAATTTTTATAA
1 AATTTTTAAATTTTATAA
6654211 AATTTT
1 AATTTT
6654217 ATGTTTTTAA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
17 8 0.25
18 22 0.69
19 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
AATTTTTAAATTTTATAA
Found at i:6654214 original size:35 final size:38
Alignment explanation
Indices: 6654147--6654217 Score: 103
Period size: 35 Copynumber: 1.9 Consensus size: 38
6654137 TATTTAATTT
6654147 TATTATTTTGAATTTTTAGAATTTTACAAAATTTTAAA
1 TATTATTTTGAATTTTTAGAATTTTACAAAATTTTAAA
* *
6654185 TATTA-TTT-AATTTTTA-ATTTTTATAAAATTTTA
1 TATTATTTTGAATTTTTAGAATTTTACAAAATTTTA
6654218 TGTTTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
35 15 0.48
36 8 0.26
37 3 0.10
38 5 0.16
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (38 bp):
TATTATTTTGAATTTTTAGAATTTTACAAAATTTTAAA
Found at i:6654704 original size:31 final size:31
Alignment explanation
Indices: 6654645--6654709 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
6654635 CTGAATTCAA
* **
6654645 AAATATAATTTTTTAAAAAAATTTAAAATATT
1 AAATATAATATTTTAAAAAAATAAAAAAT-TT
*
6654677 AAAT-TAATATTTTAAAAATATAAAAAATTT
1 AAATATAATATTTTAAAAAAATAAAAAATTT
6654707 AAA
1 AAA
6654710 AAAAATTTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 5 0.17
31 20 0.69
32 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (31 bp):
AAATATAATATTTTAAAAAAATAAAAAATTT
Found at i:6659817 original size:65 final size:67
Alignment explanation
Indices: 6659730--6659864 Score: 186
Period size: 67 Copynumber: 2.0 Consensus size: 67
6659720 AGTATAAGTT
* *
6659730 TTATAGCTTTTAATTTAGTTTGCGTCCG-TTTTTTTTTTT-TTTTTTTCATTTGAGACTATTTGA
1 TTATAGCTTTTAATTTAATTTGCGTCCGCTTTTTTTTTTTAATTTTTT-ATTTGAGACTATTTGA
6659793 ATC
65 ATC
** *
6659796 TTATAGC-TTTAATTTAATTTGCGTTTGCTTTTTTTTTTTAAATTTTTTATTTGAGATTATTTGA
1 TTATAGCTTTTAATTTAATTTGCGTCCGCTTTTTTTTTTT-AATTTTTTATTTGAGACTATTTGA
6659860 ATC
65 ATC
6659863 TT
1 TT
6659865 CTACCTGAGA
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
65 17 0.28
66 18 0.30
67 20 0.33
68 6 0.10
ACGTcount: A:0.19, C:0.08, G:0.11, T:0.61
Consensus pattern (67 bp):
TTATAGCTTTTAATTTAATTTGCGTCCGCTTTTTTTTTTTAATTTTTTATTTGAGACTATTTGAA
TC
Found at i:6663434 original size:16 final size:15
Alignment explanation
Indices: 6663411--6663467 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
6663401 TTAACTATAT
6663411 AGAAAAAAAAGAAAA
1 AGAAAAAAAAGAAAA
* *
6663426 AGAAAAAAAACTAAAT
1 AGAAAAAAAA-GAAAA
* *
6663442 TGAAAAAAATGAAAA
1 AGAAAAAAAAGAAAA
*
6663457 AGGAAAAAAAG
1 AGAAAAAAAAG
6663468 TTAAAGGGGT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
15 21 0.66
16 11 0.34
ACGTcount: A:0.77, C:0.02, G:0.14, T:0.07
Consensus pattern (15 bp):
AGAAAAAAAAGAAAA
Found at i:6663447 original size:31 final size:31
Alignment explanation
Indices: 6663403--6663466 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
6663393 CTAATTAATT
*
6663403 AACTATATAGAAAAAAAAGAAAAAGAAAAAA
1 AACTAAATAGAAAAAAAAGAAAAAGAAAAAA
* * *
6663434 AACTAAATTGAAAAAAATGAAAAAGGAAAAA
1 AACTAAATAGAAAAAAAAGAAAAAGAAAAAA
6663465 AA
1 AA
6663467 GTTAAAGGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.75, C:0.03, G:0.11, T:0.11
Consensus pattern (31 bp):
AACTAAATAGAAAAAAAAGAAAAAGAAAAAA
Found at i:6664322 original size:31 final size:31
Alignment explanation
Indices: 6664250--6664323 Score: 78
Period size: 32 Copynumber: 2.4 Consensus size: 31
6664240 ACTTTGATGA
* * * *
6664250 TTATTTATTGTTCGATAAAAAGATATATGCTT
1 TTATATATTGTACGATAAAAAAATAAATGC-T
*
6664282 TTATGTATTGTACGATAAATAAAATAAATG-T
1 TTATATATTGTACGATAAA-AAAATAAATGCT
6664313 TTATATATTGT
1 TTATATATTGT
6664324 TATTTTAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
31 11 0.31
32 17 0.47
33 8 0.22
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (31 bp):
TTATATATTGTACGATAAAAAAATAAATGCT
Found at i:6664443 original size:32 final size:32
Alignment explanation
Indices: 6664407--6664468 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
6664397 TGCATAATAT
*
6664407 TATGATAAAATAAAATAATATAATGTTATAAA
1 TATGATAAAATAAAATAATATAATCTTATAAA
* * * *
6664439 TATGATTAAATTAAATTATATCATCTTATA
1 TATGATAAAATAAAATAATATAATCTTATA
6664469 TTATATTTGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (32 bp):
TATGATAAAATAAAATAATATAATCTTATAAA
Found at i:6665237 original size:139 final size:139
Alignment explanation
Indices: 6665073--6665341 Score: 441
Period size: 139 Copynumber: 1.9 Consensus size: 139
6665063 TTAATATAAG
* * *
6665073 ATATCTAATCATTTCAATAATCAAATTCTTTTATTTAAGTGTATAGTAAATATATGAT-AGAATA
1 ATATCTAATCATTACAATAATCAAATTCTTTTATTTAAATGTATAATAAATATATGATAAG-ATA
* *
6665137 ATTAATATCTTATCATTCAACTAATTTTATGTGCCAAACGTATTATTAATATCTTATCATTGTGA
65 ATTAATATCTTATCATTCAACAAATTTTATGTGCCAAACGTATTATTAATATCTTATCATTATGA
6665202 TAATCCAATA
130 TAATCCAATA
* *
6665212 ATATCTTATCATTACGATAATCAAATTCTTTTATTTAAATGTATAATAAATATATGATAAGATAA
1 ATATCTAATCATTACAATAATCAAATTCTTTTATTTAAATGTATAATAAATATATGATAAGATAA
* *
6665277 TTAATATCTTATTATTCAACAAATTTTATGTGCCAAACGTATTCTTAATATCTTATCATTATGAT
66 TTAATATCTTATCATTCAACAAATTTTATGTGCCAAACGTATTATTAATATCTTATCATTATGAT
6665342 TTAAGTTTCA
Statistics
Matches: 120, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
139 118 0.98
140 2 0.02
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (139 bp):
ATATCTAATCATTACAATAATCAAATTCTTTTATTTAAATGTATAATAAATATATGATAAGATAA
TTAATATCTTATCATTCAACAAATTTTATGTGCCAAACGTATTATTAATATCTTATCATTATGAT
AATCCAATA
Found at i:6666185 original size:18 final size:17
Alignment explanation
Indices: 6666164--6666224 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 17
6666154 AATAACATTA
6666164 AAATACTAAAATATTATT
1 AAATA-TAAAATATTATT
* *
6666182 AAATTTATATTTAATATTATG
1 AAA--TATA--AAATATTATT
6666203 AAATATTAAAATATTATT
1 AAATA-TAAAATATTATT
6666221 AAAT
1 AAAT
6666225 TTATATTTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
18 15 0.44
19 4 0.12
20 4 0.12
21 11 0.32
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
AAATATAAAATATTATT
Found at i:6666199 original size:21 final size:21
Alignment explanation
Indices: 6666173--6666239 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
6666163 AAAATACTAA
6666173 AATATTATTAAATTTATATTT
1 AATATTATTAAATTTATATTT
*
6666194 AATATTATGAAATATTA-A---
1 AATATTATTAAAT-TTATATTT
6666212 AATATTATTAAATTTATATTT
1 AATATTATTAAATTTATATTT
*
6666233 AGTATTA
1 AATATTA
6666240 AATTATTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
17 3 0.08
18 13 0.34
21 19 0.50
22 3 0.08
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (21 bp):
AATATTATTAAATTTATATTT
Found at i:6666207 original size:39 final size:39
Alignment explanation
Indices: 6666164--6666239 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
6666154 AATAACATTA
6666164 AAATACTAAAATATTATTAAATTTATATTTAATATTATG
1 AAATACTAAAATATTATTAAATTTATATTTAATATTATG
* *
6666203 AAATATTAAAATATTATTAAATTTATATTTAGTATTA
1 AAATACTAAAATATTATTAAATTTATATTTAATATTA
6666240 AATTATTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (39 bp):
AAATACTAAAATATTATTAAATTTATATTTAATATTATG
Found at i:6666259 original size:16 final size:18
Alignment explanation
Indices: 6666238--6666274 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
6666228 TATTTAGTAT
6666238 TAAATTA-T-TATTAAAA
1 TAAATTACTATATTAAAA
6666254 TAAATTACTATATTAAAA
1 TAAATTACTATATTAAAA
6666272 TAA
1 TAA
6666275 TAAATTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 1 0.05
18 11 0.58
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAATTACTATATTAAAA
Found at i:6666267 original size:29 final size:28
Alignment explanation
Indices: 6666205--6666273 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
6666195 ATATTATGAA
* *
6666205 ATATTAAAATATTATTAAATTTATATTT
1 ATATTAAAATATTATTAAATATAAATTT
*
6666233 AGTATTAAATTATTATTAAA-ATAAATTACT
1 A-TATTAAAATATTATTAAATATAAATT--T
6666263 ATATTAAAATA
1 ATATTAAAATA
6666274 ATAAATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
28 6 0.18
29 26 0.76
30 2 0.06
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (28 bp):
ATATTAAAATATTATTAAATATAAATTT
Found at i:6666330 original size:11 final size:11
Alignment explanation
Indices: 6666314--6666383 Score: 55
Period size: 10 Copynumber: 7.0 Consensus size: 11
6666304 TATAATATAA
*
6666314 TAAATTGTTAT
1 TAAATTATTAT
6666325 TAAATTATTAT
1 TAAATTATTAT
*
6666336 TTAA-TATTA-
1 TAAATTATTAT
*
6666345 -AAA-TGTTAT
1 TAAATTATTAT
*
6666354 TAAATTATCAT
1 TAAATTATTAT
6666365 T-AA-TATTAT
1 TAAATTATTAT
6666374 TAAA-TATTAT
1 TAAATTATTAT
6666384 AACATTGTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
8 6 0.12
9 6 0.12
10 18 0.38
11 18 0.38
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (11 bp):
TAAATTATTAT
Found at i:6666351 original size:29 final size:28
Alignment explanation
Indices: 6666314--6666372 Score: 91
Period size: 29 Copynumber: 2.1 Consensus size: 28
6666304 TATAATATAA
* *
6666314 TAAATTGTTATTAAATTATTATTTAATAT
1 TAAAATGTTATTAAATTATCA-TTAATAT
6666343 TAAAATGTTATTAAATTATCATTAATAT
1 TAAAATGTTATTAAATTATCATTAATAT
6666371 TA
1 TA
6666373 TTAAATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (28 bp):
TAAAATGTTATTAAATTATCATTAATAT
Found at i:6666497 original size:47 final size:46
Alignment explanation
Indices: 6666398--6666500 Score: 129
Period size: 47 Copynumber: 2.2 Consensus size: 46
6666388 TTGTTAAATG
* *
6666398 TTAAAATATTATTCAATATTCAAATACTATTAATTAATATTTAATA
1 TTAAAATATTATTCAATATTCAAATACTATAAATTAATAGTTAATA
* *
6666444 TTAAAATATTA-TCATATATTCAACCATTCT-TAAATTAATAGTTAATC
1 TTAAAATATTATTCA-ATATTCAA--ATACTATAAATTAATAGTTAATA
6666491 TTAAAATATT
1 TTAAAATATT
6666501 TCTAAAATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
45 3 0.06
46 19 0.38
47 24 0.48
48 4 0.08
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.45
Consensus pattern (46 bp):
TTAAAATATTATTCAATATTCAAATACTATAAATTAATAGTTAATA
Found at i:6666708 original size:29 final size:29
Alignment explanation
Indices: 6666635--6666708 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 29
6666625 AATTGTTGTG
* *
6666635 AAATTAATATTTTATA-AAAAATATTATT
1 AAATTAATATTTTATATAAAAACATTACT
* * ** *
6666663 AAAATAGTATTAAATATATAAACATTACT
1 AAATTAATATTTTATATAAAAACATTACT
*
6666692 AAATTATTATTTTATAT
1 AAATTAATATTTTATAT
6666709 TATTAAATAT
Statistics
Matches: 34, Mismatches: 11, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
28 12 0.35
29 22 0.65
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (29 bp):
AAATTAATATTTTATATAAAAACATTACT
Found at i:6666718 original size:10 final size:10
Alignment explanation
Indices: 6666653--6666734 Score: 64
Period size: 10 Copynumber: 8.4 Consensus size: 10
6666643 ATTTTATAAA
6666653 AAATATTATT
1 AAATATTATT
*
6666663 AAAATAGTATT
1 -AAATATTATT
6666674 AAATA-TA-T
1 AAATATTATT
* *
6666682 AAACATTACT
1 AAATATTATT
6666692 AAATTATTATT
1 AAA-TATTATT
**
6666703 TTATATTATT
1 AAATATTATT
6666713 AAATATTA--
1 AAATATTATT
*
6666721 AAATATTATA
1 AAATATTATT
6666731 AAAT
1 AAAT
6666735 TAATAGTTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
8 13 0.22
9 4 0.07
10 26 0.45
11 15 0.26
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (10 bp):
AAATATTATT
Found at i:6666736 original size:23 final size:23
Alignment explanation
Indices: 6666710--6666780 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 23
6666700 ATTTTATATT
6666710 ATTAAATATTAAAATATTATAAA
1 ATTAAATATTAAAATATTATAAA
6666733 ATT-AATAGTT-AAATA--ATAATA
1 ATTAAATA-TTAAAATATTATAA-A
6666754 ATATAAATATATAAAAATATTACTAAA
1 AT-TAAATAT-T-AAAATATTA-TAAA
6666781 TTCTTTATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 16
0.70 0.00 0.30
Matches are distributed among these distances:
20 4 0.11
21 3 0.08
22 11 0.29
23 10 0.26
25 5 0.13
27 2 0.05
28 3 0.08
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (23 bp):
ATTAAATATTAAAATATTATAAA
Found at i:6666903 original size:21 final size:21
Alignment explanation
Indices: 6666877--6667022 Score: 115
Period size: 21 Copynumber: 7.2 Consensus size: 21
6666867 TAATAGTAAA
6666877 AATATTATTAAATTAATATTT
1 AATATTATTAAATTAATATTT
** * **
6666898 AATATTATTAGTTTTATATAA
1 AATATTATTAAATTAATATTT
*
6666919 AATATTGTTAAA-TAATATTT
1 AATATTATTAAATTAATATTT
**
6666939 AATATTATTTAAA--AA-ATAG
1 AATATTA-TTAAATTAATATTT
*
6666958 AATATT-TTAAAATAATATTT
1 AATATTATTAAATTAATATTT
**
6666978 -ATAAAATTAAATTAATATTT
1 AATATTATTAAATTAATATTT
* * *
6666998 AATATTATGAAATAAACATTT
1 AATATTATTAAATTAATATTT
6667019 AATA
1 AATA
6667023 ATGTGAAATT
Statistics
Matches: 95, Mismatches: 24, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
17 5 0.05
19 13 0.14
20 28 0.29
21 49 0.52
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.46
Consensus pattern (21 bp):
AATATTATTAAATTAATATTT
Found at i:6666973 original size:39 final size:41
Alignment explanation
Indices: 6666875--6666978 Score: 115
Period size: 39 Copynumber: 2.6 Consensus size: 41
6666865 AATAATAGTA
* *** *
6666875 AAAATATTATTAAATTAATATTTAATATTATTAGTTTTATAT
1 AAAATATTATTAAAATAATATTTAATATTATTA-TAAAAAAT
*
6666917 AAAATATTGTT-AAATAATATTTAATATTATT-TAAAAAAT
1 AAAATATTATTAAAATAATATTTAATATTATTATAAAAAAT
*
6666956 AGAATATT-TTAAAATAATATTTA
1 AAAATATTATTAAAATAATATTTA
6666979 TAAAATTAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
38 2 0.04
39 23 0.43
41 19 0.35
42 10 0.19
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (41 bp):
AAAATATTATTAAAATAATATTTAATATTATTATAAAAAAT
Found at i:6668318 original size:68 final size:68
Alignment explanation
Indices: 6668208--6668343 Score: 218
Period size: 68 Copynumber: 2.0 Consensus size: 68
6668198 CTTTTGCCAT
* * *
6668208 TTTCTGGTATAGGCCCATCGGGACTACCAATATTTTGAGCTGAACCCGATATTAGTCCGGTCAAA
1 TTTCTGGTATAGGCCCATCGAGACTACCAATATTTTGAGCTGAACCCGACATTAGTCCGGTAAAA
6668273 AAC
66 AAC
* * *
6668276 TTTCTGGTATAGGCCCATCGAGACTTCCAATATTTTGGGCTGAACCCGACATTAGTCCTGTAAAA
1 TTTCTGGTATAGGCCCATCGAGACTACCAATATTTTGAGCTGAACCCGACATTAGTCCGGTAAAA
6668341 AAC
66 AAC
6668344 CGAAGTTATT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 62 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (68 bp):
TTTCTGGTATAGGCCCATCGAGACTACCAATATTTTGAGCTGAACCCGACATTAGTCCGGTAAAA
AAC
Found at i:6674782 original size:4 final size:4
Alignment explanation
Indices: 6674773--6674895 Score: 53
Period size: 4 Copynumber: 30.2 Consensus size: 4
6674763 CCTATAATAT
*
6674773 TTAA TTAA TTATA TTTA TTATGA TTAA TTAA -T-A TTATA TTAA TTTAA
1 TTAA TTAA TTA-A TTAA TTA--A TTAA TTAA TTAA TTA-A TTAA -TTAA
* * * * *
6674820 TTAA TTAA ATAA -T-A TTAA TTATA ATAA TGCAA TTGA -TAA TTAA TTTA
1 TTAA TTAA TTAA TTAA TTAA TTA-A TTAA T-TAA TTAA TTAA TTAA TTAA
*
6674867 TTAA -T-A TTAA TTTAA TATAA TTAA ATAA T
1 TTAA TTAA TTAA -TTAA T-TAA TTAA TTAA T
6674896 ATTAAATACA
Statistics
Matches: 90, Mismatches: 13, Indels: 32
0.67 0.10 0.24
Matches are distributed among these distances:
2 3 0.03
3 8 0.09
4 50 0.56
5 25 0.28
6 4 0.04
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:6674801 original size:23 final size:24
Alignment explanation
Indices: 6674773--6674844 Score: 94
Period size: 23 Copynumber: 3.0 Consensus size: 24
6674763 CCTATAATAT
* *
6674773 TTAATT-AATTATATTTATTATGA
1 TTAATTAAATTATATTAATTATAA
6674796 TTAATTAATATTATATTAATT-TAA
1 TTAATTAA-ATTATATTAATTATAA
*
6674820 TTAATTAAATAATATTAATTATAA
1 TTAATTAAATTATATTAATTATAA
6674844 T
1 T
6674845 AATGCAATTG
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
23 17 0.40
24 15 0.35
25 11 0.26
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (24 bp):
TTAATTAAATTATATTAATTATAA
Found at i:6674847 original size:23 final size:23
Alignment explanation
Indices: 6674774--6674895 Score: 83
Period size: 23 Copynumber: 5.2 Consensus size: 23
6674764 CTATAATATT
* *
6674774 TAATT-AATTATATTTATTATGAT
1 TAATTAAATTATATTAATTAT-AA
6674797 TAATTAATATTATATTAATT-TAA
1 TAATTAA-ATTATATTAATTATAA
*
6674820 TTAATTAAATAATATTAATTATAA
1 -TAATTAAATTATATTAATTATAA
**
6674844 TAATGCAATTGATAATTAATTTATTAA
1 TAATTAAATT-AT-ATTAA-TTA-TAA
*
6674871 T-ATTAATTTA-ATATAATTA-AA
1 TAATTAAATTATAT-TAATTATAA
6674892 TAAT
1 TAAT
6674896 ATTAAATACA
Statistics
Matches: 80, Mismatches: 9, Indels: 21
0.73 0.08 0.19
Matches are distributed among these distances:
21 3 0.04
22 2 0.03
23 29 0.36
24 17 0.21
25 17 0.21
26 8 0.10
27 4 0.05
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (23 bp):
TAATTAAATTATATTAATTATAA
Found at i:6674887 original size:24 final size:23
Alignment explanation
Indices: 6674856--6674900 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
6674846 ATGCAATTGA
* *
6674856 TAATTAATTTATTAATATTAATT
1 TAATTAATTAAATAATATTAATT
6674879 TAATATAATTAAATAATATTAA
1 TAAT-TAATTAAATAATATTAA
6674901 ATACAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATTAATTAAATAATATTAATT
Found at i:6674930 original size:67 final size:64
Alignment explanation
Indices: 6674795--6674965 Score: 156
Period size: 67 Copynumber: 2.7 Consensus size: 64
6674785 ATTTATTATG
* * * *
6674795 ATTAATTAATATT-ATATTAATTTAAT-TAATTAAATAATATTAATTATAATAATGCAATTGATA
1 ATTAA-TATTATTAATATTAATTTAATATAATTAAATAATATTAATCAAAATAATGAAATTGATA
* *
6674858 ATTAAT-TTATTAATATTAATTTAATATAATTAAATAATATTAAATACAAAATAATATTAAATTT
1 ATTAATATTATTAATATTAATTTAATATAATTAAATAATATT-AAT-CAAAAT-A-ATGAAATTG
6674922 ATA
62 ATA
* * *
6674925 TTTAATATTATGAAATATTAA---AATATTATTAAATTAATATT
1 ATTAATATTAT-TAATATTAATTTAATATAATTAAA-TAATATT
6674966 TAGTATTAAA
Statistics
Matches: 90, Mismatches: 9, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
61 4 0.04
62 14 0.16
63 20 0.22
64 3 0.03
65 4 0.04
66 12 0.13
67 21 0.23
68 4 0.04
69 8 0.09
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (64 bp):
ATTAATATTATTAATATTAATTTAATATAATTAAATAATATTAATCAAAATAATGAAATTGATA
Found at i:6674940 original size:21 final size:21
Alignment explanation
Indices: 6674907--6674973 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
6674897 TTAAATACAA
*
6674907 AATAATATTAAATTTATATTT
1 AATATTATTAAATTTATATTT
*
6674928 AATATTATGAAATATTA-A---
1 AATATTATTAAAT-TTATATTT
*
6674946 AATATTATTAAATTAATATTT
1 AATATTATTAAATTTATATTT
*
6674967 AGTATTA
1 AATATTA
6674974 AATTATTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
17 2 0.06
18 13 0.36
21 18 0.50
22 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (21 bp):
AATATTATTAAATTTATATTT
Found at i:6674989 original size:26 final size:29
Alignment explanation
Indices: 6674940--6674994 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
6674930 TATTATGAAA
6674940 TATTAAAATATTATTAAATTAAT-ATTTAG
1 TATTAAAATATTATTAAA-TAATAATTTAG
*
6674969 TATTAAATTATTATT-AA-AATAATTTA
1 TATTAAAATATTATTAAATAATAATTTA
6674995 CTATACTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 3 0.12
27 5 0.21
28 2 0.08
29 14 0.58
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
TATTAAAATATTATTAAATAATAATTTAG
Found at i:6675206 original size:46 final size:46
Alignment explanation
Indices: 6675156--6675306 Score: 137
Period size: 46 Copynumber: 3.2 Consensus size: 46
6675146 AACATTGTTA
6675156 AATATTAAAATTTTATTCAATATTCAAATACTATTAATTAATATTT
1 AATATTAAAATTTTATTCAATATTCAAATACTATTAATTAATATTT
* *
6675202 AATATTAAAATATTA-TCATATATTCAACATTCTCA--AATTAATATTT
1 AATATTAAAATTTTATTCA-ATATTCAA-ATACT-ATTAATTAATATTT
* * * * *
6675248 AATCTTAAAATATTTATAAAACAATAGTAAAATATTATTAATATCAATATTT
1 AATATTAAAAT-TTTAT---TCAATATTCAAATACTATTAAT-T-AATATTT
6675300 AATATTA
1 AATATTA
6675307 TTACACAATA
Statistics
Matches: 83, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
45 3 0.04
46 43 0.52
47 7 0.08
48 2 0.02
49 3 0.04
50 9 0.11
51 3 0.04
52 13 0.16
ACGTcount: A:0.48, C:0.07, G:0.01, T:0.44
Consensus pattern (46 bp):
AATATTAAAATTTTATTCAATATTCAAATACTATTAATTAATATTT
Found at i:6675415 original size:57 final size:55
Alignment explanation
Indices: 6675362--6675494 Score: 135
Period size: 57 Copynumber: 2.3 Consensus size: 55
6675352 ATTAAAATAT
*
6675362 TATTAAAATCATA-TACAATATATTAAATTGTTA-TGAAATTAATATTTTATAAAAAAA
1 TATTAAAATCATATTA-AATATA-TAAA-TATTACT-AAATTAATATTTTATAAAAAAA
* * **
6675419 TATTAAAATCGTATTAAATATATAAATATTACTAAATTATTATTTTATATTATTAAA
1 TATTAAAATCATATTAAATATATAAATATTACTAAATTAATATTTTATA--AAAAAA
* *
6675476 TATTAAAATCTTATAAAAT
1 TATTAAAATCATATTAAAT
6675495 TAATAGTTAA
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
55 19 0.29
56 5 0.08
57 39 0.60
58 2 0.03
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (55 bp):
TATTAAAATCATATTAAATATATAAATATTACTAAATTAATATTTTATAAAAAAA
Found at i:6675454 original size:10 final size:10
Alignment explanation
Indices: 6675430--6675714 Score: 53
Period size: 10 Copynumber: 28.4 Consensus size: 10
6675420 ATTAAAATCG
6675430 TATTAAATA-
1 TATTAAATAT
6675439 TA-TAAATAT
1 TATTAAATAT
*
6675448 TACTAAATTAT
1 TATTAAA-TAT
**
6675459 TATTTTATAT
1 TATTAAATAT
6675469 TATTAAATAT
1 TATTAAATAT
*
6675479 TA--AAATCT
1 TATTAAATAT
* *
6675487 TATAAAATTAA
1 TATTAAA-TAT
6675498 TAGTTAAATAAT
1 TA-TTAAAT-AT
*
6675510 AATATAAATA-
1 TAT-TAAATAT
*
6675520 TATAAAACTAT
1 TATTAAA-TAT
*
6675531 TACT-AAT-T
1 TATTAAATAT
*
6675539 TCTTTATAATAT
1 T-ATTA-AATAT
6675551 TA--AAATAT
1 TATTAAATAT
*
6675559 TA--AAATTAA
1 TATTAAA-TAT
* *
6675568 TGTTAAATAC
1 TATTAAATAT
*
6675578 TA--AAATAA
1 TATTAAATAT
* *
6675586 TATTTAATTT
1 TATTAAATAT
*
6675596 ATATTTAATAT
1 -TATTAAATAT
*
6675607 TA--AAATAA
1 TATTAAATAT
*
6675615 TATGAAAGTAT
1 TATTAAA-TAT
*
6675626 TATTCAAATAA
1 TATT-AAATAT
*
6675637 TAGTAAAAATAT
1 TA-T-TAAATAT
*
6675649 TATTAAATAAA
1 TATTAAAT-AT
*
6675660 TATTTAATAT
1 TATTAAATAT
* *
6675670 TATT-AGTTT
1 TATTAAATAT
6675679 TATATAAAATAT
1 TAT-T-AAATAT
* *
6675691 TGTTAAATAA
1 TATTAAATAT
*
6675701 TATTTAATAT
1 TATTAAATAT
6675711 TATT
1 TATT
6675715 TAAAAAATTT
Statistics
Matches: 198, Mismatches: 47, Indels: 61
0.65 0.15 0.20
Matches are distributed among these distances:
8 38 0.19
9 19 0.10
10 63 0.32
11 49 0.25
12 29 0.15
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (10 bp):
TATTAAATAT
Found at i:6675592 original size:19 final size:19
Alignment explanation
Indices: 6675544--6675592 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
6675534 TAATTTCTTT
* *
6675544 ATAATATTAAAATATTAAA
1 ATAATATTTAAATACTAAA
*
6675563 ATTAAT-GTTAAATACTAAA
1 A-TAATATTTAAATACTAAA
6675582 ATAATATTTAA
1 ATAATATTTAA
6675593 TTTATATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
18 4 0.17
19 16 0.67
20 4 0.17
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (19 bp):
ATAATATTTAAATACTAAA
Found at i:6675629 original size:22 final size:23
Alignment explanation
Indices: 6675604--6675655 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
6675594 TTATATTTAA
* *
6675604 TATTAAAATAATA-TGAAAGTAT
1 TATTAAAATAATAGTAAAAATAT
*
6675626 TATTCAAATAATAGTAAAAATAT
1 TATTAAAATAATAGTAAAAATAT
6675649 TATTAAA
1 TATTAAA
6675656 TAAATATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (23 bp):
TATTAAAATAATAGTAAAAATAT
Found at i:6675670 original size:21 final size:21
Alignment explanation
Indices: 6675644--6675790 Score: 117
Period size: 21 Copynumber: 7.2 Consensus size: 21
6675634 TAATAGTAAA
6675644 AATATTATTAAATAAATATTT
1 AATATTATTAAATAAATATTT
** ** **
6675665 AATATTATTAGTTTTATATAA
1 AATATTATTAAATAAATATTT
*
6675686 AATATTGTTAAAT-AATATTT
1 AATATTATTAAATAAATATTT
6675706 AATATTATTTAAA-AAAT-TTT
1 AATATTA-TTAAATAAATATTT
6675726 AATATT-TTAAA-ATAATATTT
1 AATATTATTAAATA-AATATTT
** *
6675746 -ATAACATTAAATTAATATTT
1 AATATTATTAAATAAATATTT
* * *
6675766 AATATTATGAAATTAACATTT
1 AATATTATTAAATAAATATTT
6675787 AATA
1 AATA
6675791 ATGTGAAATT
Statistics
Matches: 99, Mismatches: 20, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
18 6 0.06
19 6 0.06
20 34 0.34
21 53 0.54
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (21 bp):
AATATTATTAAATAAATATTT
Found at i:6675737 original size:17 final size:18
Alignment explanation
Indices: 6675686--6675737 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 18
6675676 TTTTATATAA
6675686 AATATTGTTAAATAATATTT
1 AATATT-TTAAA-AATATTT
6675706 AATATTATTTAAAAA-ATTTT
1 AATA-T-TTTAAAAATA-TTT
6675726 AATATTTTAAAA
1 AATATTTTAAAA
6675738 TAATATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
18 7 0.24
19 2 0.07
20 13 0.45
21 6 0.21
22 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
AATATTTTAAAAATATTT
Found at i:6675797 original size:21 final size:21
Alignment explanation
Indices: 6675754--6675802 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
6675744 TTATAACATT
* *
6675754 AAATTAATATTTAATATTATG
1 AAATTAACATTTAATAATATG
*
6675775 AAATTAACATTTAATAATGTG
1 AAATTAACATTTAATAATATG
6675796 AAATTAA
1 AAATTAA
6675803 AGTTATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (21 bp):
AAATTAACATTTAATAATATG
Found at i:6682774 original size:34 final size:34
Alignment explanation
Indices: 6682735--6682807 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 34
6682725 GAAAAAGAAT
*
6682735 AAGAGGAATGAAAAATGTGAGGTTGCCAAAAAGC
1 AAGAGGAATGAAAAATGTAAGGTTGCCAAAAAGC
6682769 AAGAGGAATGAAAAATGTAAGGTTGCCAAAAAGC
1 AAGAGGAATGAAAAATGTAAGGTTGCCAAAAAGC
6682803 AAGAG
1 AAGAG
6682808 CTTGAAGTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.49, C:0.08, G:0.29, T:0.14
Consensus pattern (34 bp):
AAGAGGAATGAAAAATGTAAGGTTGCCAAAAAGC
Found at i:6684354 original size:23 final size:24
Alignment explanation
Indices: 6684326--6684397 Score: 94
Period size: 23 Copynumber: 3.0 Consensus size: 24
6684316 CCTCTAATAT
* *
6684326 TTAATT-AATTATATTTATTATGA
1 TTAATTAAATTATATTAATTATAA
6684349 TTAATTAATATTATATTAATT-TAA
1 TTAATTAA-ATTATATTAATTATAA
*
6684373 TTAATTAAATAATATTAATTATAA
1 TTAATTAAATTATATTAATTATAA
6684397 T
1 T
6684398 AATGCAATTG
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
23 17 0.40
24 15 0.35
25 11 0.26
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (24 bp):
TTAATTAAATTATATTAATTATAA
Found at i:6684489 original size:21 final size:21
Alignment explanation
Indices: 6684463--6684527 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
6684453 AAAACAAAAG
6684463 TATTATTAAATTTATATTTAA
1 TATTATTAAATTTATATTTAA
*
6684484 TATTATCAAATATTA-A---AA
1 TATTATTAAAT-TTATATTTAA
* *
6684502 TATTATTAAATTAATATTTAG
1 TATTATTAAATTTATATTTAA
6684523 TATTA
1 TATTA
6684528 AATTATTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
17 2 0.06
18 13 0.37
21 17 0.49
22 3 0.09
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TATTATTAAATTTATATTTAA
Found at i:6684543 original size:26 final size:29
Alignment explanation
Indices: 6684494--6684548 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
6684484 TATTATCAAA
6684494 TATTAAAATATTATTAAATTAAT-ATTTAG
1 TATTAAAATATTATTAAA-TAATAATTTAG
*
6684523 TATTAAATTATTATT-AA-AATAATTTA
1 TATTAAAATATTATTAAATAATAATTTA
6684549 CTATACTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 3 0.12
27 5 0.21
28 2 0.08
29 14 0.58
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
TATTAAAATATTATTAAATAATAATTTAG
Found at i:6684594 original size:19 final size:21
Alignment explanation
Indices: 6684572--6684615 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
6684562 TAATAAATTA
6684572 AATAGTT-AATATTT-AAAAT
1 AATAGTTAAATATTTGAAAAT
* *
6684591 AATATTTAAATATTTGAATAT
1 AATAGTTAAATATTTGAAAAT
6684612 AATA
1 AATA
6684616 TAATGTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 7 0.33
21 8 0.38
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (21 bp):
AATAGTTAAATATTTGAAAAT
Found at i:6684731 original size:18 final size:18
Alignment explanation
Indices: 6684710--6684744 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6684700 AACATTGTTA
*
6684710 AATATTAAAATATTATTC
1 AATATTAAAATACTATTC
*
6684728 AATATTCAAATACTATT
1 AATATTAAAATACTATT
6684745 AATTAGTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (18 bp):
AATATTAAAATACTATTC
Found at i:6687820 original size:14 final size:14
Alignment explanation
Indices: 6687801--6687827 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6687791 GATATCAATT
6687801 AAATATATGTAATG
1 AAATATATGTAATG
6687815 AAATATATGTAAT
1 AAATATATGTAAT
6687828 ATACATAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (14 bp):
AAATATATGTAATG
Found at i:6690692 original size:8 final size:8
Alignment explanation
Indices: 6690679--6690711 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
6690669 ACACAATAGT
6690679 AAATTAAA
1 AAATTAAA
6690687 AAATTAAA
1 AAATTAAA
*
6690695 ACA-TAAA
1 AAATTAAA
6690702 AAATTAAA
1 AAATTAAA
6690710 AA
1 AA
6690712 TAATGTATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (8 bp):
AAATTAAA
Found at i:6690703 original size:15 final size:14
Alignment explanation
Indices: 6690683--6690714 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
6690673 AATAGTAAAT
6690683 TAAAAAATTAAAACA
1 TAAAAAATTAAAA-A
6690698 TAAAAAATTAAAAA
1 TAAAAAATTAAAAA
6690712 TAA
1 TAA
6690715 TGTATACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAAAAATTAAAAA
Found at i:6697912 original size:15 final size:15
Alignment explanation
Indices: 6697865--6697925 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
6697855 AGTAATTTTT
*
6697865 ATTTTGTTA-TAATTA
1 ATTTTATTATTAA-TA
6697880 ATTTTATTATTAATA
1 ATTTTATTATTAATA
6697895 ATTTT-TTATTAATCA
1 ATTTTATTATTAAT-A
* *
6697910 A-TTAATAATTAATA
1 ATTTTATTATTAATA
6697924 AT
1 AT
6697926 AAGAGAGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 12 0.31
15 24 0.62
16 3 0.08
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (15 bp):
ATTTTATTATTAATA
Found at i:6698714 original size:20 final size:20
Alignment explanation
Indices: 6698664--6698714 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
6698654 TATAAGATTA
*
6698664 TAAATAAAATATGATAAAAT
1 TAAATTAAATATGATAAAAT
* *
6698684 TATA-TATAATATGATTAAAT
1 TAAATTA-AATATGATAAAAT
6698704 TAAATTAAATA
1 TAAATTAAATA
6698715 ATATTATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.04
20 22 0.88
21 2 0.08
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (20 bp):
TAAATTAAATATGATAAAAT
Found at i:6699036 original size:33 final size:33
Alignment explanation
Indices: 6698996--6699060 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
6698986 AATATATCAT
* *
6698996 TATATAATTTAGGATCTC-AAAGCTTGCTTATTA
1 TATATAATTCAAGATC-CAAAAGCTTGCTTATTA
6699029 TATATAATTCAAGATCCAAAAGCTTGCTTATT
1 TATATAATTCAAGATCCAAAAGCTTGCTTATT
6699061 GTGTAAGGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.03
33 28 0.97
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (33 bp):
TATATAATTCAAGATCCAAAAGCTTGCTTATTA
Found at i:6699876 original size:2 final size:2
Alignment explanation
Indices: 6699869--6699902 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6699859 CTAAACATGT
6699869 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6699903 AGCCAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6703160 original size:2 final size:2
Alignment explanation
Indices: 6703153--6703196 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
6703143 AACTATACTC
* * *
6703153 TA TA TA TA GA TA AA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6703195 TA
1 TA
6703197 GGTACGCGCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6708525 original size:2 final size:2
Alignment explanation
Indices: 6708513--6708541 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
6708503 TGGGAGCAGG
6708513 AT AT A- 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
6708542 CTGGTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6714133 original size:26 final size:26
Alignment explanation
Indices: 6714083--6714136 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
6714073 TGCAAAAAAT
*
6714083 AAATATTATTTTATTTAAAGTTTATA
1 AAATATTATTTTATTTAAAGCTTATA
*
6714109 AAATTTTATTTTATTTATAA-CTTATA
1 AAATATTATTTTATTTA-AAGCTTATA
6714135 AA
1 AA
6714137 CGTTTGATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (26 bp):
AAATATTATTTTATTTAAAGCTTATA
Found at i:6715010 original size:17 final size:17
Alignment explanation
Indices: 6714982--6715016 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6714972 CTTATTTTTA
6714982 TATTTATTGCATGATATT
1 TATTTATTGCATGA-ATT
6715000 TATTT-TTGCATGAATT
1 TATTTATTGCATGAATT
6715016 T
1 T
6715017 GCATGACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 8 0.47
18 5 0.29
ACGTcount: A:0.26, C:0.06, G:0.11, T:0.57
Consensus pattern (17 bp):
TATTTATTGCATGAATT
Found at i:6715040 original size:30 final size:27
Alignment explanation
Indices: 6714988--6715042 Score: 74
Period size: 30 Copynumber: 1.9 Consensus size: 27
6714978 TTTATATTTA
*
6714988 TTGCATGATATTTATTTTTGCATGAAT
1 TTGCATGATATTTATGTTTGCATGAAT
6715015 TTGCATGACTATTAATATGTTTGCATGA
1 TTGCATGA-TATT--TATGTTTGCATGA
6715043 TTATTAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 8 0.33
28 4 0.17
30 12 0.50
ACGTcount: A:0.27, C:0.09, G:0.16, T:0.47
Consensus pattern (27 bp):
TTGCATGATATTTATGTTTGCATGAAT
Found at i:6715075 original size:21 final size:22
Alignment explanation
Indices: 6715034--6715092 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
6715024 TATTAATATG
*
6715034 TTTGCATGA-TTAT-TAATTTA
1 TTTGCATGATTTATATTATTTA
6715054 TTTGCATGATTTATATTA-TTA
1 TTTGCATGATTTATATTATTTA
6715075 TTTGCATGATTATATATT
1 TTTGCATGATT-TATATT
6715093 TAATTGTATG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
20 9 0.26
21 18 0.51
22 8 0.23
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56
Consensus pattern (22 bp):
TTTGCATGATTTATATTATTTA
Found at i:6715089 original size:20 final size:21
Alignment explanation
Indices: 6715013--6715094 Score: 91
Period size: 20 Copynumber: 4.0 Consensus size: 21
6715003 TTTTGCATGA
* *
6715013 ATTTGCATGACTAT-TAATAT
1 ATTTGCATGATTATATAATTT
*
6715033 GTTTGCATGATTAT-TAATTT
1 ATTTGCATGATTATATAATTT
*
6715053 ATTTGCATGATT-TATATTATT
1 ATTTGCATGATTATATAAT-TT
6715074 ATTTGCATGATTATAT-ATTT
1 ATTTGCATGATTATATAATTT
6715094 A
1 A
6715095 ATTGTATGTG
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.02
20 34 0.64
21 15 0.28
22 3 0.06
ACGTcount: A:0.30, C:0.06, G:0.11, T:0.52
Consensus pattern (21 bp):
ATTTGCATGATTATATAATTT
Found at i:6716681 original size:25 final size:24
Alignment explanation
Indices: 6716635--6716682 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
6716625 TATCATTCAA
* *
6716635 ATATAATATTAATCATGTAATAAC
1 ATATAATATCAATCATGCAATAAC
6716659 ATATAATATCATATCATGCAATAA
1 ATATAATATCA-ATCATGCAATAA
6716683 TAATAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.35
Consensus pattern (24 bp):
ATATAATATCAATCATGCAATAAC
Found at i:6716840 original size:44 final size:44
Alignment explanation
Indices: 6716791--6716958 Score: 150
Period size: 44 Copynumber: 3.8 Consensus size: 44
6716781 TGCAAATAGA
*
6716791 CATGCAATTAAACATATAATCATGCAAATAAAAATATTAATAAT
1 CATGCAATCAAACATATAATCATGCAAATAAAAATATTAATAAT
* * *
6716835 CATGCAATCACACAAATAA--AT--AAATTAATAAGCATA-CAATTAGA-
1 CATGCAATCAAACATATAATCATGCAAA-TAA-AA--ATATTAA-TA-AT
* * *
6716879 CATGCAATCAAATATATAATTATGCAAATAATAATATTAATAAT
1 CATGCAATCAAACATATAATCATGCAAATAAAAATATTAATAAT
* * *
6716923 CATGCAATTAAATATATAATCATGCAAATAATAATA
1 CATGCAATCAAACATATAATCATGCAAATAAAAATA
6716959 CATAAATTAT
Statistics
Matches: 101, Mismatches: 11, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
40 3 0.03
41 3 0.03
42 4 0.04
43 3 0.03
44 76 0.75
45 3 0.03
46 3 0.03
47 3 0.03
48 3 0.03
ACGTcount: A:0.54, C:0.12, G:0.05, T:0.29
Consensus pattern (44 bp):
CATGCAATCAAACATATAATCATGCAAATAAAAATATTAATAAT
Found at i:6716905 original size:20 final size:20
Alignment explanation
Indices: 6716879--6716963 Score: 80
Period size: 22 Copynumber: 4.0 Consensus size: 20
6716869 TACAATTAGA
*
6716879 CATGCAATCAAATATATAAT
1 CATGCAATAAAATATATAAT
*
6716899 TATGCAAATAATAATATTAATAAT
1 CATGC-AATAA-AATA-T-ATAAT
*
6716923 CATGCAATTAAATATATAAT
1 CATGCAATAAAATATATAAT
*
6716943 CATGCAAATAATAATACATAA
1 CATGC-AATAA-AATATATAA
6716964 ATTATTGCAA
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
20 14 0.26
21 9 0.17
22 16 0.30
23 5 0.09
24 9 0.17
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.32
Consensus pattern (20 bp):
CATGCAATAAAATATATAAT
Found at i:6719955 original size:16 final size:17
Alignment explanation
Indices: 6719916--6719949 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
6719906 TGATGAATGC
6719916 TCATTATATAATATATT
1 TCATTATATAATATATT
6719933 TCATTATATAA-ATATT
1 TCATTATATAATATATT
6719949 T
1 T
6719950 TGTTATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
TCATTATATAATATATT
Found at i:6721919 original size:19 final size:19
Alignment explanation
Indices: 6721846--6721952 Score: 61
Period size: 19 Copynumber: 5.5 Consensus size: 19
6721836 GCATTAAAAG
* * *
6721846 AAAATTTAAAAAAATTTCAC
1 AAAATTTTAAAAAATCT-AA
*
6721866 AAAATTTTAAAAAAATATATA
1 AAAATTTT-AAAAAATCTA-A
* * ** *
6721887 TATATTTTTTAAAATCTGA
1 AAAATTTTAAAAAATCTAA
* *
6721906 AATATTTTAAAAAATATAA
1 AAAATTTTAAAAAATCTAA
* * *
6721925 AAAATTTTGAAAAACCTTA
1 AAAATTTTAAAAAATCTAA
6721944 AAAATTTTA
1 AAAATTTTA
6721953 GTGAAAATCC
Statistics
Matches: 65, Mismatches: 20, Indels: 5
0.72 0.22 0.06
Matches are distributed among these distances:
19 37 0.57
20 14 0.22
21 14 0.22
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAATTTTAAAAAATCTAA
Found at i:6722028 original size:21 final size:21
Alignment explanation
Indices: 6722004--6722043 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6721994 AAATAAAATT
**
6722004 TTCATAAAATTTTAAAAAAAA
1 TTCATAAAAACTTAAAAAAAA
6722025 TTCATAAAAACTTAAAAAA
1 TTCATAAAAACTTAAAAAA
6722044 TTGAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (21 bp):
TTCATAAAAACTTAAAAAAAA
Found at i:6722203 original size:19 final size:19
Alignment explanation
Indices: 6722180--6722229 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
6722170 AACTTTTAAT
*
6722180 TTTTTAGAATTTTT-ACAA
1 TTTTTAGAATTTTTGAAAA
6722198 TATTTTAG-ATTTTTGAAAA
1 T-TTTTAGAATTTTTGAAAA
*
6722217 TTTTTAAAATTTT
1 TTTTTAGAATTTT
6722230 AGAGTTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (19 bp):
TTTTTAGAATTTTTGAAAA
Found at i:6722209 original size:28 final size:26
Alignment explanation
Indices: 6722151--6722257 Score: 99
Period size: 28 Copynumber: 3.8 Consensus size: 26
6722141 ACAATTTAAA
6722151 TTTTTAAAATTTTTTATTAAACTTTTA-AT
1 TTTTTAAAA-TTTTTA--AAA-TTTTAGAT
*
6722180 TTTTTAGAATTTTTACAATATTTTAGAT
1 TTTTTAAAATTTTTA-AA-ATTTTAGAT
*
6722208 TTTTGAAAATTTTTAAAATTTTAGAGT
1 TTTTTAAAATTTTTAAAATTTTAGA-T
* *
6722235 TCTTTAAAATTTTAAAGAATTTT
1 TTTTTAAAATTTTTAA-AATTTT
6722258 TAATTTTGCA
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
26 8 0.12
27 23 0.34
28 28 0.42
29 8 0.12
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.56
Consensus pattern (26 bp):
TTTTTAAAATTTTTAAAATTTTAGAT
Found at i:6722229 original size:18 final size:17
Alignment explanation
Indices: 6722145--6722260 Score: 63
Period size: 18 Copynumber: 6.3 Consensus size: 17
6722135 AATCTTACAA
*
6722145 TTTAAATTTTTAAAATTT
1 TTTAAAATTTTAAAA-TT
*
6722163 TTTATTAAACTTTT-AATTT
1 TTTA--AAA-TTTTAAAATT
* *
6722182 TTTAGAATTTTTACAATAT
1 TTTA-AAATTTTAAAAT-T
* *
6722201 TTTAGATTTTTGAAAATT
1 TTTAAAATTTT-AAAATT
* *
6722219 TTTAAAATTTTAGAGTT
1 TTTAAAATTTTAAAATT
6722236 CTTTAAAATTTTAAAGAATT
1 -TTTAAAATTTT-AA-AATT
6722256 TTTAA
1 TTTAA
6722261 TTTTGCAATT
Statistics
Matches: 75, Mismatches: 14, Indels: 17
0.71 0.13 0.16
Matches are distributed among these distances:
17 8 0.11
18 35 0.47
19 21 0.28
20 7 0.09
21 4 0.05
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTAAAATTTTAAAATT
Found at i:6722298 original size:27 final size:27
Alignment explanation
Indices: 6722244--6722300 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
6722234 TTCTTTAAAA
*
6722244 TTTTAAAGAATTTTTAATTTTGCAATT
1 TTTTAAAAAATTTTTAATTTTGCAATT
* *
6722271 TTTTCAAAAAATTTTTTATTTT-TAATT
1 TTTT-AAAAAATTTTTAATTTTGCAATT
6722298 TTT
1 TTT
6722301 CAAGTATTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 11 0.42
28 15 0.58
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (27 bp):
TTTTAAAAAATTTTTAATTTTGCAATT
Found at i:6722488 original size:26 final size:26
Alignment explanation
Indices: 6722423--6722489 Score: 84
Period size: 25 Copynumber: 2.6 Consensus size: 26
6722413 AATTTTTAAA
* *
6722423 ATTTTTTAATTTCTAAAAATATTTGAG
1 ATTTTTTAATTT-TAAAAAAAATTGAG
6722450 ATTTTTTAA-TTTAAAAAAAATT-AG
1 ATTTTTTAATTTTAAAAAAAATTGAG
6722474 ATTTTTTTAATTTTAA
1 A-TTTTTTAATTTTAA
6722490 TTTTTAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
24 3 0.08
25 17 0.47
26 7 0.19
27 9 0.25
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.54
Consensus pattern (26 bp):
ATTTTTTAATTTTAAAAAAAATTGAG
Found at i:6730805 original size:20 final size:20
Alignment explanation
Indices: 6730777--6730822 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
6730767 TTTTTACATG
*
6730777 GTTTCATTTTGGTGTTTTCA
1 GTTTAATTTTGGTGTTTTCA
6730797 GTTTAATTTTGGTGTTTTCA
1 GTTTAATTTTGGTGTTTTCA
6730817 GTTTAA
1 GTTTAA
6730823 GTTATTCGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.15, C:0.07, G:0.20, T:0.59
Consensus pattern (20 bp):
GTTTAATTTTGGTGTTTTCA
Found at i:6738125 original size:93 final size:93
Alignment explanation
Indices: 6737966--6738153 Score: 324
Period size: 93 Copynumber: 2.0 Consensus size: 93
6737956 ATGAATAGCG
* **
6737966 TTCAACTTTTTTTGGATTGGGTACTTCAAATAGGATTTGGTTGTTTTGTCTTTCTATTGATATAT
1 TTCAACTTTATTTGGATTGGGTACTTCAAATAGGATTTGGTCATTTTGTCTTTCTATTGATATAT
6738031 TTTGTTCTAGTTTTATTTTTGGTAAACT
66 TTTGTTCTAGTTTTATTTTTGGTAAACT
*
6738059 TTCAACTTTATTT-GATTTGGGTACTTCAAATAGGATTTGGTCATTTTGTCTTTCTATTGATTTA
1 TTCAACTTTATTTGGA-TTGGGTACTTCAAATAGGATTTGGTCATTTTGTCTTTCTATTGATATA
6738123 TTTTGTTCTAGTTTTATTTTTGGTAAACT
65 TTTTGTTCTAGTTTTATTTTTGGTAAACT
6738152 TT
1 TT
6738154 TTATTTTTTA
Statistics
Matches: 90, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
92 2 0.02
93 88 0.98
ACGTcount: A:0.20, C:0.09, G:0.16, T:0.55
Consensus pattern (93 bp):
TTCAACTTTATTTGGATTGGGTACTTCAAATAGGATTTGGTCATTTTGTCTTTCTATTGATATAT
TTTGTTCTAGTTTTATTTTTGGTAAACT
Found at i:6738442 original size:22 final size:22
Alignment explanation
Indices: 6738417--6738458 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
6738407 TTGTTTATCC
* *
6738417 TAATTTTAGGGATACAAATACT
1 TAATTCTAGAGATACAAATACT
6738439 TAATTCTAGAGATACAAATA
1 TAATTCTAGAGATACAAATA
6738459 TAAATATACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (22 bp):
TAATTCTAGAGATACAAATACT
Found at i:6742135 original size:25 final size:26
Alignment explanation
Indices: 6742101--6742166 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 26
6742091 TTTGAAAGGG
* *
6742101 TTCGGCAATGAAGGCCT-AAATAGGA
1 TTCGACAATGAAGGCCTAAAATAGAA
6742126 TTCGACAATGAAGGCCTAAAATAGAA
1 TTCGACAATGAAGGCCTAAAATAGAA
* *
6742152 GTCAACAATGAAGGC
1 TTCGACAATGAAGGC
6742167 TGAAAATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
25 16 0.44
26 20 0.56
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (26 bp):
TTCGACAATGAAGGCCTAAAATAGAA
Found at i:6742413 original size:22 final size:22
Alignment explanation
Indices: 6742378--6742419 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
6742368 TTGTCTATCC
* *
6742378 TAATTTTAGGGATACAAATACT
1 TAATTCTAGAGATACAAATACT
6742400 TAATTCTAGAGATACAAATA
1 TAATTCTAGAGATACAAATA
6742420 TAAATATACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (22 bp):
TAATTCTAGAGATACAAATACT
Found at i:6746584 original size:29 final size:31
Alignment explanation
Indices: 6746542--6746607 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
6746532 TTTTTGATTT
6746542 TTTTAAATTAATAT-ATTATTTTTATTAAA-A
1 TTTTAAATTAATATCATTATTTTTA-TAAATA
*
6746572 TTTTAAATT-ATATCATTTTTTTTATAAATA
1 TTTTAAATTAATATCATTATTTTTATAAATA
6746602 TTTTAA
1 TTTTAA
6746608 TATCGGTTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 8 0.24
30 25 0.76
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (31 bp):
TTTTAAATTAATATCATTATTTTTATAAATA
Found at i:6746836 original size:22 final size:22
Alignment explanation
Indices: 6746809--6746852 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
6746799 TAATTTTGAG
*
6746809 TTAAATATTTT-TTTATTT-ATA
1 TTAAA-ATTTTATTTTTTTGATA
6746830 TTAAAATTTTATTTTTTTGATA
1 TTAAAATTTTATTTTTTTGATA
6746852 T
1 T
6746853 AATAAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 11 0.55
22 4 0.20
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (22 bp):
TTAAAATTTTATTTTTTTGATA
Found at i:6749555 original size:12 final size:13
Alignment explanation
Indices: 6749520--6749565 Score: 67
Period size: 13 Copynumber: 3.5 Consensus size: 13
6749510 TAAATGTTAA
6749520 TTTTAATAAAATT
1 TTTTAATAAAATT
6749533 TATTTAAT-AAATT
1 T-TTTAATAAAATT
*
6749546 TTTTATTAAAATT
1 TTTTAATAAAATT
6749559 TTTTAAT
1 TTTTAAT
6749566 CACGATCATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 5 0.17
13 18 0.62
14 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTTAATAAAATT
Found at i:6764109 original size:60 final size:59
Alignment explanation
Indices: 6764038--6764152 Score: 133
Period size: 60 Copynumber: 1.9 Consensus size: 59
6764028 AATAAAACTT
* * * *
6764038 AAAATAGATAAAAGAAATA-AAAATAAAAATAAAAAATAAGTAAATACGATAAATAAGATA
1 AAAATAGAT-AAAGAAACACAAAATAAAAACAAAAAATAAATAAATA-AATAAATAAGATA
* * **
6764098 AAAATATATAAATAAACACAAAATAAAAACATGAAATAAATAAATAAATAAATAA
1 AAAATAGATAAAGAAACACAAAATAAAAACAAAAAATAAATAAATAAATAAATAA
6764153 TACATAGAAC
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
59 15 0.33
60 31 0.67
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.19
Consensus pattern (59 bp):
AAAATAGATAAAGAAACACAAAATAAAAACAAAAAATAAATAAATAAATAAATAAGATA
Found at i:6764112 original size:4 final size:4
Alignment explanation
Indices: 6764064--6764152 Score: 62
Period size: 4 Copynumber: 22.5 Consensus size: 4
6764054 ATAAAAATAA
* * *
6764064 AAAT AAA- AAAT AAGT AAAT ACGAT AAAT AAGAT -AA- AAAT ATAT AAAT
1 AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AA-AT AAAT AAAT AAAT AAAT
* *
6764111 AAAC ACA- AAAT AAA- AACAT GAAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AA-AT -AAAT AAAT AAAT AAAT AAAT AA
6764153 TACATAGAAC
Statistics
Matches: 67, Mismatches: 9, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
3 10 0.15
4 48 0.72
5 7 0.10
6 2 0.03
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:6764495 original size:40 final size:40
Alignment explanation
Indices: 6764407--6764579 Score: 163
Period size: 40 Copynumber: 4.2 Consensus size: 40
6764397 AGCATACAAT
* **
6764407 TTTAAAAATTAAAGACTC-TTTCAACATGAAGGAAGGCACATAAC
1 TTTAAAAATTAAAGGCTCATTT-AACAT----GAAGGCACACGAC
* * * *
6764451 TTTAAAAATTAAGGGCTCCTTTAACATAAAGGCACACGAT
1 TTTAAAAATTAAAGGCTCATTTAACATGAAGGCACACGAC
*
6764491 TTTAAAAATTAAAGG-T-ATTTTCAATATGAAGGCACACGAC
1 TTTAAAAATTAAAGGCTCA-TTT-AACATGAAGGCACACGAC
* **
6764531 TTTAAAAATTAAAGGCTCATTCAACATGAAGGCACATAAC
1 TTTAAAAATTAAAGGCTCATTTAACATGAAGGCACACGAC
6764571 TTTAAAAAT
1 TTTAAAAAT
6764580 ATATGTAATG
Statistics
Matches: 109, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
39 4 0.04
40 77 0.71
41 3 0.03
42 1 0.01
44 21 0.19
45 3 0.03
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (40 bp):
TTTAAAAATTAAAGGCTCATTTAACATGAAGGCACACGAC
Done.