Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 109 of 132
Found at i:33077947 original size:12 final size:12
Alignment explanation
Indices: 33077925--33077958 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
33077915 TGTTGGAATA
*
33077925 GTGATTGAACTG
1 GTGATTTAACTG
*
33077937 TTGATTTAACTG
1 GTGATTTAACTG
33077949 GTGATTTAAC
1 GTGATTTAAC
33077959 CATCAATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (12 bp):
GTGATTTAACTG
Found at i:33084513 original size:17 final size:17
Alignment explanation
Indices: 33084491--33084526 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
33084481 TCCCTTGACT
*
33084491 TTTAACCTTCCATCTTC
1 TTTAACCTTCCATATTC
*
33084508 TTTAACCTTTCATATTC
1 TTTAACCTTCCATATTC
33084525 TT
1 TT
33084527 GCAACTATTT
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:0.19, C:0.28, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAACCTTCCATATTC
Found at i:33089848 original size:24 final size:24
Alignment explanation
Indices: 33089816--33089863 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
33089806 ATGGATGTGC
33089816 AACCTTTCATCTCCCTTAACCTTT
1 AACCTTTCATCTCCCTTAACCTTT
* *
33089840 AACCTTTCATCTTCTTTAACCTTT
1 AACCTTTCATCTCCCTTAACCTTT
33089864 CATATTCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.21, C:0.33, G:0.00, T:0.46
Consensus pattern (24 bp):
AACCTTTCATCTCCCTTAACCTTT
Found at i:33089856 original size:17 final size:17
Alignment explanation
Indices: 33089836--33089877 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
33089826 CTCCCTTAAC
*
33089836 CTTTAACCTTTCATCTT
1 CTTTAACCTTTCATATT
33089853 CTTTAACCTTTCATATT
1 CTTTAACCTTTCATATT
33089870 CTTATAAC
1 CTT-TAAC
33089878 TACTTTTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.24, C:0.26, G:0.00, T:0.50
Consensus pattern (17 bp):
CTTTAACCTTTCATATT
Found at i:33094975 original size:16 final size:18
Alignment explanation
Indices: 33094946--33094982 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
33094936 GTATTTATCA
33094946 AATTAAATTAATTTTC-C
1 AATTAAATTAATTTTCTC
33094963 AATTAAA-TAATTTTCTC
1 AATTAAATTAATTTTCTC
33094980 AAT
1 AAT
33094983 CCAGTTCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (18 bp):
AATTAAATTAATTTTCTC
Found at i:33097632 original size:4 final size:4
Alignment explanation
Indices: 33097623--33097648 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
33097613 CGATTAACGA
33097623 TAAT TAAT TAAT TAAT TAAT TAAT TA
1 TAAT TAAT TAAT TAAT TAAT TAAT TA
33097649 TCAATAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:33109632 original size:22 final size:21
Alignment explanation
Indices: 33109571--33109670 Score: 91
Period size: 22 Copynumber: 4.8 Consensus size: 21
33109561 ATTATATTGT
33109571 TGTTTTGGTGCTGTTTTTTGC
1 TGTTTTGGTGCTGTTTTTTGC
*
33109592 TGTTTTGGTTGCTATTTTTTGC
1 TGTTTTGG-TGCTGTTTTTTGC
* * *
33109614 TATTTTGGTGTTGTGTTTTTAC
1 TGTTTTGGTGCTGT-TTTTTGC
*
33109636 TG-TTT--TGAT-TTTTTTGC
1 TGTTTTGGTGCTGTTTTTTGC
*
33109653 TGTTTTGGTTGTTGTTTT
1 TGTTTTGG-TGCTGTTTT
33109671 GATGCTATTT
Statistics
Matches: 63, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
17 8 0.13
18 4 0.06
19 3 0.05
21 18 0.29
22 30 0.48
ACGTcount: A:0.04, C:0.06, G:0.24, T:0.66
Consensus pattern (21 bp):
TGTTTTGGTGCTGTTTTTTGC
Found at i:33109743 original size:40 final size:39
Alignment explanation
Indices: 33109686--33109761 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 39
33109676 TATTTTTTTT
* *
33109686 ATTATTTTGGTGATGTTTTTATTGTTATTTTTGTTGCTA
1 ATTATTTTGCTGATGTTTTTATTGTTATTTTGGTTGCTA
* *
33109725 ATTATTTTTGCTGCTGTTTTTGTTGTTATTTTGGTTG
1 ATTA-TTTTGCTGATGTTTTTATTGTTATTTTGGTTG
33109762 TTTGGATGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
39 4 0.12
40 28 0.88
ACGTcount: A:0.12, C:0.04, G:0.20, T:0.64
Consensus pattern (39 bp):
ATTATTTTGCTGATGTTTTTATTGTTATTTTGGTTGCTA
Found at i:33112288 original size:27 final size:24
Alignment explanation
Indices: 33112215--33112288 Score: 67
Period size: 27 Copynumber: 2.8 Consensus size: 24
33112205 ATTTTAAAAT
33112215 ATAAAAATAAAAAAAATTAAATTC
1 ATAAAAATAAAAAAAATTAAATTC
* * *
33112239 CTACAAATAAAAATAAATTTTAAATTT
1 ATAAAAATAAAAA-AAA--TTAAATTC
33112266 ATAAAAAATACAAAAAAACTTAA
1 AT-AAAAATA-AAAAAAA-TTAA
33112289 CACATATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
24 11 0.28
25 3 0.08
27 12 0.31
28 9 0.23
29 4 0.10
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (24 bp):
ATAAAAATAAAAAAAATTAAATTC
Found at i:33113276 original size:22 final size:21
Alignment explanation
Indices: 33113224--33113283 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 21
33113214 ATCTTCAAAT
* *
33113224 AAAATATAAAA-AATTGAA-A
1 AAAAAATAAAATAATTAAACA
* *
33113243 AAAAAATCAAATATTTAAACA
1 AAAAAATAAAATAATTAAACA
33113264 AAAAAATAAAAATAATTAAA
1 AAAAAAT-AAAATAATTAAA
33113284 AAACTTTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
19 9 0.28
20 5 0.16
21 8 0.25
22 10 0.31
ACGTcount: A:0.73, C:0.03, G:0.02, T:0.22
Consensus pattern (21 bp):
AAAAAATAAAATAATTAAACA
Found at i:33114234 original size:9 final size:9
Alignment explanation
Indices: 33114220--33114275 Score: 51
Period size: 9 Copynumber: 6.1 Consensus size: 9
33114210 AAGAATATGG
*
33114220 TTTTTGAAA
1 TTTTTAAAA
*
33114229 TTTTTGAAA
1 TTTTTAAAA
* *
33114238 TCTTTTTATA
1 T-TTTTAAAA
33114248 TTTTTAATAA
1 TTTTTAA-AA
33114258 -TTTTAAAA
1 TTTTTAAAA
33114266 TTTTTAAAA
1 TTTTTAAAA
33114275 T
1 T
33114276 GATTTTTACT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
8 2 0.05
9 30 0.75
10 8 0.20
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.59
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:33114435 original size:25 final size:25
Alignment explanation
Indices: 33114406--33114453 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
33114396 TGTTTTAAAG
*
33114406 AATAAAGATTAAATTAACAAAAAAT
1 AATAAAGATCAAATTAACAAAAAAT
33114431 AATAAAGATCAAATTAACAAAAA
1 AATAAAGATCAAATTAACAAAAA
33114454 GAATAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.21
Consensus pattern (25 bp):
AATAAAGATCAAATTAACAAAAAAT
Found at i:33119964 original size:16 final size:16
Alignment explanation
Indices: 33119943--33119976 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
33119933 TTGATTTGAG
*
33119943 AAAATTATTTAATTAA
1 AAAATTAATTAATTAA
33119959 AAAATTAATTAATTAA
1 AAAATTAATTAATTAA
33119975 AA
1 AA
33119977 TTAATTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATTAATTAATTAA
Found at i:33119989 original size:14 final size:14
Alignment explanation
Indices: 33119943--33119982 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
33119933 TTGATTTGAG
*
33119943 AAAATTATTTAATT
1 AAAATTAATTAATT
33119957 AAAAAATTAATTAATT
1 --AAAATTAATTAATT
33119973 AAAATTAATT
1 AAAATTAATT
33119983 TGATAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.43
16 13 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAAATTAATTAATT
Found at i:33130020 original size:6 final size:6
Alignment explanation
Indices: 33130002--33130109 Score: 89
Period size: 6 Copynumber: 18.0 Consensus size: 6
33129992 TTAAATTGAT
* *
33130002 TTTAAA TTT--A TTTAAA TTTAGA TTT-AT TTTAAA TTTAAATA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AA-A TTTAAA
* ** *
33130049 TTT-AA TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA TATTAAA TTTAACA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAA-A
*
33130098 TTAAAA TTTAAA
1 TTTAAA TTTAAA
33130110 AGTCCAAATA
Statistics
Matches: 83, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 53 0.64
7 14 0.17
8 4 0.05
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:33130032 original size:17 final size:15
Alignment explanation
Indices: 33130006--33130070 Score: 78
Period size: 17 Copynumber: 4.1 Consensus size: 15
33129996 ATTGATTTTA
33130006 AATTTATTTAAATTT
1 AATTTATTTAAATTT
33130021 AGATTTATTTTAAATTT
1 A-ATTTA-TTTAAATTT
*
33130038 AA-ATATTTAAATTT
1 AATTTATTTAAATTT
33130052 AATTTGAATTTAAATTT
1 AATTT--ATTTAAATTT
33130069 AA
1 AA
33130071 ATAAAAATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
14 11 0.26
15 4 0.09
16 6 0.14
17 22 0.51
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
AATTTATTTAAATTT
Found at i:33130048 original size:31 final size:31
Alignment explanation
Indices: 33130010--33130073 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
33130000 ATTTTAAATT
*
33130010 TATTTAAATTTAGATTT-ATTTTAAATTTAAA
1 TATTTAAATTTA-ATTTGAATTTAAATTTAAA
33130041 TATTTAAATTTAATTTGAATTTAAATTTAAA
1 TATTTAAATTTAATTTGAATTTAAATTTAAA
33130072 TA
1 TA
33130074 AAAATTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (31 bp):
TATTTAAATTTAATTTGAATTTAAATTTAAA
Found at i:33130056 original size:11 final size:11
Alignment explanation
Indices: 33129992--33130072 Score: 64
Period size: 11 Copynumber: 7.5 Consensus size: 11
33129982 GACTTTTGAG
* *
33129992 TTAAATTGATT
1 TTAAATTTAAT
33130003 TTAAATTT-AT
1 TTAAATTTAAT
33130013 TTAAATTTAGAT
1 TTAAATTTA-AT
*
33130025 TT-ATTTTAAAT
1 TTAAATTT-AAT
33130036 TTAAA--T-AT
1 TTAAATTTAAT
33130044 TTAAATTTAAT
1 TTAAATTTAAT
*
33130055 TTGAATTTAAAT
1 TTAAATTT-AAT
33130067 TTAAAT
1 TTAAAT
33130073 AAAAATTAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
8 7 0.12
10 11 0.20
11 24 0.43
12 14 0.25
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:33130069 original size:42 final size:41
Alignment explanation
Indices: 33130002--33130109 Score: 110
Period size: 42 Copynumber: 2.6 Consensus size: 41
33129992 TTAAATTGAT
* ** * *
33130002 TTTAAATTT-ATTTAAATTTAGATTTATTTTAAATTTAAATA
1 TTTAAATTTAATTTAAATTTAAATTTAAATAAAAATTAAA-A
*
33130043 TTTAAATTTAATTTGAATTTAAATTTAAATAAAAATTAAAA
1 TTTAAATTTAATTTAAATTTAAATTTAAATAAAAATTAAAA
*
33130084 TATTAAATTTAACATTAAAATTTAAA
1 T-TTAAATTT-A-ATTTAAATTTAAA
33130110 AGTCCAAATA
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
41 11 0.20
42 32 0.58
43 1 0.02
44 11 0.20
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (41 bp):
TTTAAATTTAATTTAAATTTAAATTTAAATAAAAATTAAAA
Found at i:33130206 original size:14 final size:14
Alignment explanation
Indices: 33130187--33130225 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
33130177 TTTGGCCCAC
33130187 GGCCCAATTACAAA
1 GGCCCAATTACAAA
*
33130201 GGCCCAATT--AAG
1 GGCCCAATTACAAA
33130213 GGCCCAATTACAA
1 GGCCCAATTACAA
33130226 TAGTCTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 11 0.50
14 11 0.50
ACGTcount: A:0.38, C:0.28, G:0.18, T:0.15
Consensus pattern (14 bp):
GGCCCAATTACAAA
Found at i:33132024 original size:30 final size:30
Alignment explanation
Indices: 33131989--33132196 Score: 240
Period size: 30 Copynumber: 6.9 Consensus size: 30
33131979 AAACAATCCA
* * * *
33131989 AAAATTATATTTTGACCTCAAAACTTTTTC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
* *
33132019 GAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
*
33132049 AAAATTACATTTTAACCCTAAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
** * *
33132079 AAAATTGTATTTTGACCCCAAAACTTTTCT
1 AAAATTACATTTTAACCCCAAAACTTTTCC
* *
33132109 GAAATTATATTTTAACCCCAAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
*
33132139 AAAATTACATTTTAACCCTAAAAC-TTT-C
1 AAAATTACATTTTAACCCCAAAACTTTTCC
* *
33132167 AGAAATTACCATTTTACCCCCAAATCTTTT
1 A-AAATTA-CATTTTAACCCCAAAACTTTT
33132197 AAAATTCCGT
Statistics
Matches: 153, Mismatches: 22, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
28 2 0.01
29 9 0.06
30 139 0.91
31 3 0.02
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.38
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCAAAACTTTTCC
Found at i:33132142 original size:90 final size:90
Alignment explanation
Indices: 33131989--33132165 Score: 302
Period size: 90 Copynumber: 2.0 Consensus size: 90
33131979 AAACAATCCA
* *
33131989 AAAATTATATTTTGACCTCAAAACTTTTTCGAAATTACATTTTGACCCCAAAACTTTTCCAAAAT
1 AAAATTATATTTTGACCCCAAAACTTTTTCGAAATTACATTTTAACCCCAAAACTTTTCCAAAAT
33132054 TACATTTTAACCCTAAAACTTTTCC
66 TACATTTTAACCCTAAAACTTTTCC
* *
33132079 AAAATTGTATTTTGACCCCAAAAC-TTTTCTGAAATTATATTTTAACCCCAAAACTTTTCCAAAA
1 AAAATTATATTTTGACCCCAAAACTTTTTC-GAAATTACATTTTAACCCCAAAACTTTTCCAAAA
33132143 TTACATTTTAACCCTAAAACTTT
65 TTACATTTTAACCCTAAAACTTT
33132166 CAGAAATTAC
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
89 5 0.06
90 77 0.94
ACGTcount: A:0.37, C:0.21, G:0.03, T:0.38
Consensus pattern (90 bp):
AAAATTATATTTTGACCCCAAAACTTTTTCGAAATTACATTTTAACCCCAAAACTTTTCCAAAAT
TACATTTTAACCCTAAAACTTTTCC
Found at i:33132181 original size:90 final size:90
Alignment explanation
Indices: 33131997--33132196 Score: 282
Period size: 90 Copynumber: 2.2 Consensus size: 90
33131987 CAAAAATTAT
* *
33131997 ATTTTGACCTCAAAACTTTTTCGAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTT
1 ATTTTGACCCCAAAACTTTTTCGAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTTT
**
33132062 AACCCTAAAACTTTTCCAAAATTGT
66 AACCCTAAAACTTTTCCAAAATTCC
*
33132087 ATTTTGACCCCAAAAC-TTTTCTGAAATTATATTTTAACCCCAAAACTTTTCCAAAATTACATTT
1 ATTTTGACCCCAAAACTTTTTC-GAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTT
33132151 TAACCCTAAAAC-TTT-CAGAAATTACC
65 TAACCCTAAAACTTTTCCA-AAATT-CC
*
33132177 ATTTT-ACCCCCAAATCTTTT
1 ATTTTGA-CCCCAAAACTTTT
33132197 AAAATTCCGT
Statistics
Matches: 99, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
88 2 0.02
89 14 0.14
90 80 0.81
91 3 0.03
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (90 bp):
ATTTTGACCCCAAAACTTTTTCGAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTTT
AACCCTAAAACTTTTCCAAAATTCC
Found at i:33132213 original size:59 final size:57
Alignment explanation
Indices: 33132169--33132770 Score: 738
Period size: 59 Copynumber: 10.2 Consensus size: 57
33132159 AAACTTTCAG
* * **
33132169 AAATTACCATTTTACCCCCAAATCTTTTAAAATTCCGTTTTTAACCTTGATTTCACCAA
1 AAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTT--CCAA
* *
33132228 AAATTACCATTTTACCCCCGAATCTTTTAAAATTCCGTTTTTAACCCCGGTTTCACCAA
1 AAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTT--CCAA
* * ** *
33132287 AAATTACCATTTTACCCTCGAAGCTCCTAAAATTCCATTTTTAACCCCGATTTCATCGA
1 AAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTC--CAA
* * *
33132346 AAATTACCATTTTACCCCCAAATCTTTTAAAATTCCATTTTTAACCCCGATTTTATCGA
1 AAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGA-TTT-CCAA
* *
33132405 AAATTACCATTTTACCCCCGAAGCTTTTAAAATTCCATTTTTAACCCTGATTTCACCAA
1 AAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTT--CCAA
** *
33132464 AAATTACCATTTTACCCCCGAATCTTTTAAAATTCTGTTTTTAACCCCAATTTTACCAA
1 AAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGA-TTT-CCAA
* * *
33132523 AAATTACCATTTTACCCCCAAAGCTTTTAAAATTCCATTTTTAACCCTGATTTCACCAA
1 AAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTT--CCAA
** *
33132582 AAATTACCATTTTACCCCCGAATCTTTTAAAATTCTGTTTTTAACCCCGATTTCACTGA
1 AAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTC-C-AA
* *
33132641 AAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAA
1 AAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTT--CCAA
* * * *
33132700 AAATTACCATTATACCCTCGAATCTTTTAAAATTCCATTTTTAATCCCGA-TTACATCA
1 AAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCCA--A
33132758 AAATTACCATTTT
1 AAATTACCATTTT
33132771 GCCCTCGGGT
Statistics
Matches: 479, Mismatches: 51, Indels: 27
0.86 0.09 0.05
Matches are distributed among these distances:
56 2 0.00
57 2 0.00
58 22 0.05
59 445 0.93
60 7 0.01
61 1 0.00
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.37
Consensus pattern (57 bp):
AAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCCAA
Found at i:33132448 original size:177 final size:177
Alignment explanation
Indices: 33132169--33132770 Score: 918
Period size: 177 Copynumber: 3.4 Consensus size: 177
33132159 AAACTTTCAG
* **
33132169 AAATTACCATTTTACCCCCAAATCTTTTAAAATTCCGTTTTTAACCTTGATTTCACCAAAAATTA
1 AAATTACCATTTTACCCCCAAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTA
*
33132234 CCATTTTACCCCCGAATCTTTTAAAATTCCGTTTTTAACCCCGGTTTCACCAAAAATTACCATTT
66 CCATTTTACCCCCGAATCTTTTAAAATTCCGTTTTTAACCCCGATTTCACCAAAAATTACCATTT
* * * *
33132299 TACCCTCGAAGCTCCTAAAATTCCATTTTTAACCCCGATTTCATCGA
131 TACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAA
* * *
33132346 AAATTACCATTTTACCCCCAAATCTTTTAAAATTCCATTTTTAACCCCGATTTTATCGAAAATTA
1 AAATTACCATTTTACCCCCAAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTA
* * *
33132411 CCATTTTACCCCCGAAGCTTTTAAAATTCCATTTTTAACCCTGATTTCACCAAAAATTACCATTT
66 CCATTTTACCCCCGAATCTTTTAAAATTCCGTTTTTAACCCCGATTTCACCAAAAATTACCATTT
* * ** * *
33132476 TACCCCCGAATCTTTTAAAATTCTGTTTTTAACCCCAATTTTACCAA
131 TACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAA
* *
33132523 AAATTACCATTTTACCCCCAAAGCTTTTAAAATTCCATTTTTAACCCTGATTTCACCAAAAATTA
1 AAATTACCATTTTACCCCCAAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTA
* **
33132588 CCATTTTACCCCCGAATCTTTTAAAATTCTGTTTTTAACCCCGATTTCACTGAAAATTACCATTT
66 CCATTTTACCCCCGAATCTTTTAAAATTCCGTTTTTAACCCCGATTTCACCAAAAATTACCATTT
33132653 TACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAA
131 TACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAA
* * * * * *
33132700 AAATTACCATTATACCCTCGAATCTTTTAAAATTCCATTTTTAATCCCGATTACATC-AAAATTA
1 AAATTACCATTTTACCCCCAAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTA
33132764 CCATTTT
66 CCATTTT
33132771 GCCCTCGGGT
Statistics
Matches: 380, Mismatches: 45, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
176 14 0.04
177 366 0.96
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.37
Consensus pattern (177 bp):
AAATTACCATTTTACCCCCAAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTA
CCATTTTACCCCCGAATCTTTTAAAATTCCGTTTTTAACCCCGATTTCACCAAAAATTACCATTT
TACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAA
Found at i:33132800 original size:118 final size:117
Alignment explanation
Indices: 33132169--33132770 Score: 848
Period size: 118 Copynumber: 5.1 Consensus size: 117
33132159 AAACTTTCAG
* * * * **
33132169 AAATTACCATTTTACCCCCAAATCTTTTAAAATTCCGTTTTTAACCTTGATTTCACCAAAAATTA
1 AAATTACCATTTTACCCCC-GAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTA
* *
33132234 CCATTTTACCCCCGAATCTTTTAAAATTCCGTTTTTAACCCCGGTTTCACCAA
65 CCATTTTACCCCCGAATCTTTTAAAATTCCGTTTTTAACCCCGATTTCATCAA
* * * *
33132287 AAATTACCATTTTACCCTCGAAGCTCCTAAAATTCCATTTTTAACCCCGATTTCATCGAAAATTA
1 AAATTACCATTTTACCCCCG-AGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTA
* * * *
33132352 CCATTTTACCCCCAAATCTTTTAAAATTCCATTTTTAACCCCGATTTTATCGA
65 CCATTTTACCCCCGAATCTTTTAAAATTCCGTTTTTAACCCCGATTTCATCAA
* *
33132405 AAATTACCATTTTACCCCCGAAGCTTTTAAAATTCCATTTTTAACCCTGATTTCACCAAAAATTA
1 AAATTACCATTTTACCCCCG-AGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTA
* * * *
33132470 CCATTTTACCCCCGAATCTTTTAAAATTCTGTTTTTAACCCCAATTTTACCAA
65 CCATTTTACCCCCGAATCTTTTAAAATTCCGTTTTTAACCCCGATTTCATCAA
* * *
33132523 AAATTACCATTTTACCCCCAAAGCTTTTAAAATTCCATTTTTAACCCTGATTTCACCAAAAATTA
1 AAATTACCATTTTACCCCC-GAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTA
* *
33132588 CCATTTTACCCCCGAATCTTTTAAAATTCTGTTTTTAACCCCGATTTCA-CTGA
65 CCATTTTACCCCCGAATCTTTTAAAATTCCGTTTTTAACCCCGATTTCATC-AA
33132641 AAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTA
1 AAATTACCATTTTACCCCCG-AGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTA
* * * * *
33132706 CCATTATACCCTCGAATCTTTTAAAATTCCATTTTTAATCCCGATTACATC-A
65 CCATTTTACCCCCGAATCTTTTAAAATTCCGTTTTTAACCCCGATTTCATCAA
33132758 AAATTACCATTTT
1 AAATTACCATTTT
33132771 GCCCTCGGGT
Statistics
Matches: 438, Mismatches: 41, Indels: 11
0.89 0.08 0.02
Matches are distributed among these distances:
117 15 0.03
118 422 0.96
119 1 0.00
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.37
Consensus pattern (117 bp):
AAATTACCATTTTACCCCCGAGCTTCTAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTAC
CATTTTACCCCCGAATCTTTTAAAATTCCGTTTTTAACCCCGATTTCATCAA
Found at i:33136598 original size:17 final size:17
Alignment explanation
Indices: 33136576--33136647 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
33136566 AATTTAATTT
*
33136576 TTTTTAGTTTATATAAG
1 TTTTTAATTTATATAAG
* * **
33136593 TTTTTAATTTTTTTATT
1 TTTTTAATTTATATAAG
*
33136610 TTTTTAATTT-T-TGAAT
1 TTTTTAATTTATAT-AAG
33136626 TTTTTAAGTTTATATAAG
1 TTTTTAA-TTTATATAAG
33136644 TTTT
1 TTTT
33136648 AAAATAATTG
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
15 1 0.02
16 10 0.23
17 25 0.57
18 7 0.16
19 1 0.02
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (17 bp):
TTTTTAATTTATATAAG
Found at i:33136610 original size:8 final size:8
Alignment explanation
Indices: 33136593--33136632 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
33136583 TTTATATAAG
33136593 TTTTTAATT
1 TTTTTAA-T
*
33136602 TTTTTATT
1 TTTTTAAT
33136610 TTTTTAAT
1 TTTTTAAT
*
33136618 TTTTGAAT
1 TTTTTAAT
33136626 TTTTTAA
1 TTTTTAA
33136633 GTTTATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
8 21 0.78
9 6 0.22
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (8 bp):
TTTTTAAT
Found at i:33136621 original size:25 final size:26
Alignment explanation
Indices: 33136568--33136647 Score: 101
Period size: 25 Copynumber: 3.1 Consensus size: 26
33136558 ACCAAAATAA
33136568 TTTAATTTTTTTTAGTTTATATAAGTT
1 TTTAA-TTTTTTTAGTTTATATAAGTT
* *
33136595 TTTAATTTTTTTA-TTTTTTTAA-TT
1 TTTAATTTTTTTAGTTTATATAAGTT
*
33136619 TTTGAATTTTTTAAGTTTATATAAGTT
1 TTT-AATTTTTTTAGTTTATATAAGTT
33136646 TT
1 TT
33136648 AAAATAATTG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
24 5 0.11
25 16 0.36
26 15 0.33
27 9 0.20
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (26 bp):
TTTAATTTTTTTAGTTTATATAAGTT
Found at i:33136813 original size:41 final size:41
Alignment explanation
Indices: 33136769--33136937 Score: 214
Period size: 41 Copynumber: 4.1 Consensus size: 41
33136759 GAGAAAGTGT
* * *
33136769 CGCTAATGCTCTAATCTTTAGCGGCGCTTTCTCATAAGCGT
1 CGCTAATGCTCTAATCTTTAGCGGCGCTTTCCCGTAAGCGC
* *
33136810 CGCTAATGCTCTGA-CTTTTAGCGGCACTTTCCCGTAAGCGC
1 CGCTAATGCTCTAATC-TTTAGCGGCGCTTTCCCGTAAGCGC
* * * * *
33136851 CTCTAATGCTTTGACCTTTAGCGGCGCTTTCCTGTAAAGCGC
1 CGCTAATGCTCTAATCTTTAGCGGCGCTTTCCCGT-AAGCGC
*
33136893 CGCTAATGCTCTAATCTTTAGCGGTGCTTTCCCGTAAGCGC
1 CGCTAATGCTCTAATCTTTAGCGGCGCTTTCCCGTAAGCGC
33136934 CGCT
1 CGCT
33136938 TTCCCATAAA
Statistics
Matches: 110, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
40 1 0.01
41 73 0.66
42 36 0.33
ACGTcount: A:0.17, C:0.30, G:0.21, T:0.32
Consensus pattern (41 bp):
CGCTAATGCTCTAATCTTTAGCGGCGCTTTCCCGTAAGCGC
Found at i:33138428 original size:50 final size:50
Alignment explanation
Indices: 33138368--33138467 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
33138358 AAAATAGAGG
33138368 CAGATCTTTAGCTGATTACAGGTGGAGGAACATTGATTAGCTGAGATTCA
1 CAGATCTTTAGCTGATTACAGGTGGAGGAACATTGATTAGCTGAGATTCA
33138418 CAGATCTTTAGCTGATTACAGGTGGAGGAACATTGATTAGCTGAGATTCA
1 CAGATCTTTAGCTGATTACAGGTGGAGGAACATTGATTAGCTGAGATTCA
33138468 ATAAATTTAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (50 bp):
CAGATCTTTAGCTGATTACAGGTGGAGGAACATTGATTAGCTGAGATTCA
Found at i:33139502 original size:23 final size:24
Alignment explanation
Indices: 33139472--33139522 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
33139462 TGCTGCAAGT
*
33139472 CAGAGGAAAAGTATGCCACAAA-G
1 CAGAGGAAAAGCATGCCACAAAGG
33139495 CAGAGGAAAAGCATGCCACAAAGG
1 CAGAGGAAAAGCATGCCACAAAGG
33139519 CAGA
1 CAGA
33139523 TAAAAACTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.47, C:0.20, G:0.27, T:0.06
Consensus pattern (24 bp):
CAGAGGAAAAGCATGCCACAAAGG
Found at i:33139528 original size:24 final size:23
Alignment explanation
Indices: 33139472--33139528 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
33139462 TGCTGCAAGT
* *
33139472 CAGAGGAAAAGTATGCCACAAAG
1 CAGAGAAAAAGCATGCCACAAAG
*
33139495 CAGAGGAAAAGCATGCCACAAAGG
1 CAGAGAAAAAGCATGCCACAAA-G
*
33139519 CAGATAAAAA
1 CAGAGAAAAA
33139529 CTATAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 21 0.70
24 9 0.30
ACGTcount: A:0.51, C:0.18, G:0.25, T:0.07
Consensus pattern (23 bp):
CAGAGAAAAAGCATGCCACAAAG
Found at i:33148803 original size:25 final size:25
Alignment explanation
Indices: 33148775--33148823 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
33148765 TAGGGTATTT
**
33148775 TATTTTTATGTAATTTTTTTAAAAA
1 TATTTTTATGTAAAGTTTTTAAAAA
*
33148800 TATTTTTATTTAAAGTTTTTAAAA
1 TATTTTTATGTAAAGTTTTTAAAA
33148824 TTGATCATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (25 bp):
TATTTTTATGTAAAGTTTTTAAAAA
Found at i:33161226 original size:43 final size:45
Alignment explanation
Indices: 33161179--33161268 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 45
33161169 TATAATTTTT
* *
33161179 AAAAAAAATATTTTTA-TTTAATTTA-GAGTTTTTTTTAAGAA-G
1 AAAAAAAAAATTTTGAGTTTAATTTATGAGTTTTTTTTAAGAACG
** *
33161221 AAAAAATTAATTTTGAGTTTAGTTTATGAGTTTTTTTTAAGAACG
1 AAAAAAAAAATTTTGAGTTTAATTTATGAGTTTTTTTTAAGAACG
33161266 AAA
1 AAA
33161269 TTATATTTGG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
42 12 0.30
43 8 0.20
44 16 0.40
45 4 0.10
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.46
Consensus pattern (45 bp):
AAAAAAAAAATTTTGAGTTTAATTTATGAGTTTTTTTTAAGAACG
Found at i:33162867 original size:20 final size:21
Alignment explanation
Indices: 33162830--33162869 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
33162820 AACCAAATAA
* *
33162830 TATTTTAAAATATATTTAAAT
1 TATTTAAAAAAATATTTAAAT
33162851 TATTTAAAAAAAT-TTTAAA
1 TATTTAAAAAAATATTTAAA
33162870 AATATAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TATTTAAAAAAATATTTAAAT
Found at i:33163832 original size:49 final size:51
Alignment explanation
Indices: 33163736--33163843 Score: 134
Period size: 49 Copynumber: 2.2 Consensus size: 51
33163726 TTAAATCTTG
* * *
33163736 TTTATTTAATTTGTTTTCTTCAGATATAGTATTTTGCATAACTATAAATA-
1 TTTATTTAACTTGTTTTCTTCAAATATAGTATTTTACATAACTATAAATAT
*
33163786 TTTATTTAACTTG-TTTGTTCAAATAT-GATATTTTACATAAAC-ATAAATAT
1 TTTATTTAACTTGTTTTCTTCAAATATAG-TATTTTACAT-AACTATAAATAT
33163836 TTTATTTA
1 TTTATTTA
33163844 TATTATTTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
48 1 0.02
49 27 0.53
50 23 0.45
ACGTcount: A:0.34, C:0.07, G:0.06, T:0.52
Consensus pattern (51 bp):
TTTATTTAACTTGTTTTCTTCAAATATAGTATTTTACATAACTATAAATAT
Found at i:33168405 original size:2 final size:2
Alignment explanation
Indices: 33168398--33168437 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
33168388 TCATCAATTC
33168398 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33168438 GCATAATTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33171047 original size:62 final size:62
Alignment explanation
Indices: 33170950--33171098 Score: 214
Period size: 62 Copynumber: 2.4 Consensus size: 62
33170940 GGATTTAGGT
* *
33170950 TTTAAAATTTTAGGGATTTTCGAGATTTTTAGGGTTGTTGGGTTTGGGTAA-TTTGGTTTAGG
1 TTTAAAATTTTGGGGATTTTCGAGATTTTTAGGGTTGTTGGGTTTGGG-AATTTTGGTTTAAG
* *
33171012 TTTAAGGAA-TTTGGGGATTTT-GGGATTTTTGGGGTTGTTGGGTTTGGGAATTTTGGTTTAAG
1 TTTAA--AATTTTGGGGATTTTCGAGATTTTTAGGGTTGTTGGGTTTGGGAATTTTGGTTTAAG
33171074 TTTAAAATTTTGGGGATTTTCGAGA
1 TTTAAAATTTTGGGGATTTTCGAGA
33171099 CTTAGGTTTC
Statistics
Matches: 77, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
60 2 0.03
61 14 0.18
62 48 0.62
63 11 0.14
64 2 0.03
ACGTcount: A:0.19, C:0.01, G:0.32, T:0.47
Consensus pattern (62 bp):
TTTAAAATTTTGGGGATTTTCGAGATTTTTAGGGTTGTTGGGTTTGGGAATTTTGGTTTAAG
Found at i:33173650 original size:52 final size:51
Alignment explanation
Indices: 33173568--33173755 Score: 243
Period size: 52 Copynumber: 3.6 Consensus size: 51
33173558 TGAATGAAAT
*
33173568 AGGTCCGATGACTATGTGTCATCGTAAGTATATGAATCCTTCACGGATTAAG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTT-ACGGATTAAG
*
33173620 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCC-TTACGGATTAAG
* ** * * *
33173672 AGGTCCAATGACTATGCATCATCATGAGTATATGATTCCCAATACGGATTAA-
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAAT-CC-TTACGGATTAAG
* *
33173724 AGGTCTGATGACTCTGTGTCATCGTGAGTATA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATA
33173756 AAAAATGCAT
Statistics
Matches: 118, Mismatches: 16, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
52 105 0.89
53 13 0.11
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (51 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTACGGATTAAG
Found at i:33186101 original size:52 final size:52
Alignment explanation
Indices: 33186023--33186262 Score: 347
Period size: 52 Copynumber: 4.6 Consensus size: 52
33186013 TGAATGAAAT
* * *
33186023 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTAGGGATTAAG
1 AGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTAAG
*
33186075 AGGTCCAATGACTATGTGTCATCGTGATTATATGAATCCTTTACGAATTAAG
1 AGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTAAG
* *
33186127 AGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTAAG
* * * **
33186179 AGGTCCGATGACTATGCGTCATCGTGAGTATATGATTCCCAATACGAATTAA-
1 AGGTCCAATGACTATGTGTCATCGTGAGTATATGAAT-CCTTTACGAATTAAG
* *
33186231 AGGTCTAATGACTCTGTGTCATCGTGAGTATA
1 AGGTCCAATGACTATGTGTCATCGTGAGTATA
33186263 AAAAATGCGT
Statistics
Matches: 169, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
52 159 0.94
53 10 0.06
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (52 bp):
AGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTAAG
Found at i:33186969 original size:21 final size:21
Alignment explanation
Indices: 33186945--33186997 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
33186935 GTGAACCTTA
33186945 TATCGGTAGAA-GAGTCACTTG
1 TATCGGTAGAACGA-TCACTTG
*
33186966 TATCGGTAGAACTATCACTTG
1 TATCGGTAGAACGATCACTTG
33186987 TATCGGTAGAA
1 TATCGGTAGAA
33186998 ATCTGTACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 29 0.97
22 1 0.03
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (21 bp):
TATCGGTAGAACGATCACTTG
Found at i:33189607 original size:37 final size:37
Alignment explanation
Indices: 33189566--33189636 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
33189556 CTTAAAATCA
33189566 TAAAAACC-ATAAACTTATAAAAAATATAA-AAATTAAT
1 TAAAAACCTATAAA-TTATAAAAAA-ATAATAAATTAAT
*
33189603 TAAAATCCTATAAATTATAAAAAAATAATAAATT
1 TAAAAACCTATAAATTATAAAAAAATAATAAATT
33189637 GCATCCTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 4 0.13
37 22 0.71
38 5 0.16
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (37 bp):
TAAAAACCTATAAATTATAAAAAAATAATAAATTAAT
Found at i:33192504 original size:27 final size:27
Alignment explanation
Indices: 33192426--33192491 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
33192416 TATTTTTGGG
*
33192426 TGGTGCCTACCTGGTAGGCGACATCAA
1 TGGTGCCTACCTGGTAGGCGACACCAA
33192453 TGGTGCCTACCTGGTAGGCGACACCAA
1 TGGTGCCTACCTGGTAGGCGACACCAA
33192480 TGGTGCCTACCT
1 TGGTGCCTACCT
33192492 ACCAGGCGGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.20, C:0.29, G:0.29, T:0.23
Consensus pattern (27 bp):
TGGTGCCTACCTGGTAGGCGACACCAA
Found at i:33192837 original size:17 final size:17
Alignment explanation
Indices: 33192815--33192848 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
33192805 AAAAAAATTT
*
33192815 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
33192832 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
33192849 TTATTGTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:33193598 original size:30 final size:31
Alignment explanation
Indices: 33193537--33193599 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
33193527 GAATTGAATC
* *
33193537 TTTCAATTTTAAATTTTCAATTAATAATAAA
1 TTTCAATTTAAAATTTTCAATAAATAATAAA
33193568 TTTCAATTTAAAATTTT-AA-AAATAATTAAA
1 TTTCAATTTAAAATTTTCAATAAATAA-TAAA
33193598 TT
1 TT
33193600 AGTGTGTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 5 0.17
30 8 0.28
31 16 0.55
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (31 bp):
TTTCAATTTAAAATTTTCAATAAATAATAAA
Found at i:33195954 original size:6 final size:6
Alignment explanation
Indices: 33195943--33195983 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
33195933 TAGAATTAAA
*
33195943 TATGTT TATGTT TATGTT TATGTT CT-TATT TATGTT TATGT
1 TATGTT TATGTT TATGTT TATGTT -TATGTT TATGTT TATGT
33195984 ATGCAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 1 0.03
6 29 0.94
7 1 0.03
ACGTcount: A:0.17, C:0.02, G:0.15, T:0.66
Consensus pattern (6 bp):
TATGTT
Found at i:33196112 original size:26 final size:26
Alignment explanation
Indices: 33196057--33196132 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
33196047 GCTAAACCTT
**
33196057 ATTAAATAAATTCAAACATAAAAATT
1 ATTAAATAAATTCAAACATAAAAAGA
** *
33196083 ATTAAATAAATTCAAATTTAAACAGA
1 ATTAAATAAATTCAAACATAAAAAGA
* *
33196109 ATTAATTCCAAATTCAATCATAAA
1 ATTAAAT--AAATTCAAACATAAA
33196133 CTTAATTAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
26 27 0.69
28 12 0.31
ACGTcount: A:0.57, C:0.11, G:0.01, T:0.32
Consensus pattern (26 bp):
ATTAAATAAATTCAAACATAAAAAGA
Found at i:33199128 original size:5 final size:5
Alignment explanation
Indices: 33199118--33199142 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
33199108 CAACTTGTCA
33199118 AATTT AATTT AATTT AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT
33199143 TCTTTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
AATTT
Found at i:33200730 original size:21 final size:21
Alignment explanation
Indices: 33200689--33200730 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
33200679 CATTAGGATG
*
33200689 CCCCTCCTTCCCCATTTTTTC
1 CCCCTCCTTCCCCATTCTTTC
* *
33200710 CCCCTCTTTCCCCCTTCTTTC
1 CCCCTCCTTCCCCATTCTTTC
33200731 ATTTGTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.02, C:0.55, G:0.00, T:0.43
Consensus pattern (21 bp):
CCCCTCCTTCCCCATTCTTTC
Found at i:33200747 original size:18 final size:18
Alignment explanation
Indices: 33200724--33200766 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
33200714 TCTTTCCCCC
*
33200724 TTCTTTCATTTGTTTATT
1 TTCTTTCATTTATTTATT
*
33200742 TTCTTTCGTTTATTTATT
1 TTCTTTCATTTATTTATT
*
33200760 TGCTTTC
1 TTCTTTC
33200767 TTTTTATGCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.09, C:0.14, G:0.07, T:0.70
Consensus pattern (18 bp):
TTCTTTCATTTATTTATT
Found at i:33208918 original size:34 final size:33
Alignment explanation
Indices: 33208860--33208924 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 33
33208850 GATTAGGTAG
33208860 TATTTTTCTTAATGAAAAAATCATACACAAAAT
1 TATTTTTCTTAATGAAAAAATCATACACAAAAT
33208893 TATTTTTCTTAATTTG-AAAAATCATACACAAA
1 TATTTTTCTTAA--TGAAAAAATCATACACAAA
33208925 CATTGTAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
33 12 0.40
34 16 0.53
35 2 0.07
ACGTcount: A:0.46, C:0.12, G:0.03, T:0.38
Consensus pattern (33 bp):
TATTTTTCTTAATGAAAAAATCATACACAAAAT
Found at i:33216757 original size:17 final size:18
Alignment explanation
Indices: 33216737--33216774 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
33216727 ATATATAAAA
33216737 AAATTTAA--ATATAATTT
1 AAATTTAATGATA-AATTT
33216754 AAATTTAATGATAAATTT
1 AAATTTAATGATAAATTT
33216772 AAA
1 AAA
33216775 AATAAATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 8 0.42
19 3 0.16
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
AAATTTAATGATAAATTT
Found at i:33233135 original size:24 final size:24
Alignment explanation
Indices: 33233107--33233157 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
33233097 AGAAATAATC
*
33233107 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
33233131 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
33233155 TTT
1 TTT
33233158 AAGTCAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.12, G:0.10, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:33236831 original size:25 final size:25
Alignment explanation
Indices: 33236802--33236853 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
33236792 AGAAATAATC
* *
33236802 TTTCAGTTAAACTCTGTTTATTTGT
1 TTTCAATTAAACTCTATTTATTTGT
33236827 TTTCAATTAAACTCTATTTATTTGT
1 TTTCAATTAAACTCTATTTATTTGT
33236852 TT
1 TT
33236854 GAGTCAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.23, C:0.12, G:0.08, T:0.58
Consensus pattern (25 bp):
TTTCAATTAAACTCTATTTATTTGT
Found at i:33237352 original size:7 final size:7
Alignment explanation
Indices: 33237342--33237372 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
33237332 TTTTAATAAT
33237342 TAATTTA
1 TAATTTA
33237349 TAATTTA
1 TAATTTA
33237356 TAATTTA
1 TAATTTA
33237363 TAATTT-
1 TAATTTA
33237369 TAAT
1 TAAT
33237373 GATACATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 20 0.83
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TAATTTA
Found at i:33240565 original size:22 final size:22
Alignment explanation
Indices: 33240526--33240567 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
33240516 TCTTGAAAAC
*
33240526 TTAAATTTATTAATATTAATAA
1 TTAAATTTATCAATATTAATAA
33240548 TTAAATTTCATCAA-ATTAAT
1 TTAAATTT-ATCAATATTAAT
33240568 CTTAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (22 bp):
TTAAATTTATCAATATTAATAA
Found at i:33240593 original size:19 final size:18
Alignment explanation
Indices: 33240560--33240596 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
33240550 AAATTTCATC
*
33240560 AAATTAATCTTAAAAATT
1 AAATTAATATTAAAAATT
33240578 AAATTAAATATTAAAAATT
1 AAATT-AATATTAAAAATT
33240597 TAATATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATTAATATTAAAAATT
Found at i:33241140 original size:29 final size:30
Alignment explanation
Indices: 33241084--33241140 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
33241074 TGACATGAAT
* * *
33241084 TTTAAAATTTAAAAATAGAAGAATTAAATA
1 TTTAAAATATAAAAATAGAAAAACTAAATA
*
33241114 TTTAAAA-ATAAAAATATAAAAACTAAA
1 TTTAAAATATAAAAATAGAAAAACTAAA
33241141 CTTCAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 16 0.70
30 7 0.30
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (30 bp):
TTTAAAATATAAAAATAGAAAAACTAAATA
Found at i:33243839 original size:50 final size:50
Alignment explanation
Indices: 33243740--33243839 Score: 134
Period size: 50 Copynumber: 2.0 Consensus size: 50
33243730 TTTTCAAGTC
* *
33243740 ATTTTCATTTTAGATAAACCATATTCATTTCCAAATGATTTCATTTTTCT
1 ATTTTCATTTTAGATAAACCATAATCATTTCCAAATGATTTCATATTTCT
33243790 ATTTTCATTTTGGAGA-AAACCATAATCATTTCCAAAT-ATTTC-TCATTTCT
1 ATTTTCATTTT--AGATAAACCATAATCATTTCCAAATGATTTCAT-ATTTCT
33243840 CCATTTCACC
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
49 1 0.02
50 21 0.47
51 20 0.44
52 3 0.07
ACGTcount: A:0.31, C:0.17, G:0.05, T:0.47
Consensus pattern (50 bp):
ATTTTCATTTTAGATAAACCATAATCATTTCCAAATGATTTCATATTTCT
Found at i:33243847 original size:51 final size:50
Alignment explanation
Indices: 33243739--33243845 Score: 137
Period size: 51 Copynumber: 2.1 Consensus size: 50
33243729 ATTTTCAAGT
* *
33243739 CATTTTCATTTTAGATAAACCATATTCATTTCCAAATGATTTCATTTTTC
1 CATTTTCATTTTAGATAAACCATAATCATTTCCAAATGATTTCATTTCTC
*
33243789 TATTTTCATTTTGGAGA-AAACCATAATCATTTCCAAAT-ATTTCTCATTTCTC
1 CATTTTCATTTT--AGATAAACCATAATCATTTCCAAATGA-TT-TCATTTCTC
33243841 CATTT
1 CATTT
33243846 CACCATTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
50 12 0.24
51 22 0.45
52 15 0.31
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.47
Consensus pattern (50 bp):
CATTTTCATTTTAGATAAACCATAATCATTTCCAAATGATTTCATTTCTC
Found at i:33247746 original size:16 final size:16
Alignment explanation
Indices: 33247717--33247752 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
33247707 TTACTATAAC
33247717 TTTATTTTGTTTTTAA
1 TTTATTTTGTTTTTAA
33247733 TTTATGTTTG-TTTTAA
1 TTTAT-TTTGTTTTTAA
33247749 TTTA
1 TTTA
33247753 CATGATACGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.72
Consensus pattern (16 bp):
TTTATTTTGTTTTTAA
Found at i:33248133 original size:19 final size:19
Alignment explanation
Indices: 33248097--33248134 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
33248087 TAAAGAATTC
*
33248097 TTATTTATTTATTTATTTA
1 TTATTTATTTATTAATTTA
33248116 TTATTTA-TTATTAAATTTA
1 TTATTTATTTATT-AATTTA
33248135 AATTGTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTTATTTATTAATTTA
Found at i:33254928 original size:18 final size:18
Alignment explanation
Indices: 33254907--33254941 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33254897 CAGAATTCAG
*
33254907 CTCTTTTTCATTCTTTTT
1 CTCTCTTTCATTCTTTTT
*
33254925 CTCTCTTTCCTTCTTTT
1 CTCTCTTTCATTCTTTT
33254942 AAAAAGACAC
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:0.03, C:0.29, G:0.00, T:0.69
Consensus pattern (18 bp):
CTCTCTTTCATTCTTTTT
Found at i:33255938 original size:25 final size:25
Alignment explanation
Indices: 33255883--33255929 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
33255873 AAACATTATG
*
33255883 AAAAATAAAACCACTTTAAAATTCA
1 AAAAATAAAAACACTTTAAAATTCA
33255908 AAAAATAAAAACA-TTTAAAATT
1 AAAAATAAAAACACTTTAAAATT
33255930 TCATGAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.64, C:0.11, G:0.00, T:0.26
Consensus pattern (25 bp):
AAAAATAAAAACACTTTAAAATTCA
Found at i:33255954 original size:28 final size:28
Alignment explanation
Indices: 33255880--33255974 Score: 76
Period size: 28 Copynumber: 3.6 Consensus size: 28
33255870 CCAAAACATT
* *
33255880 ATGAAAA-ATAAAACCACTTTAAAAT-TC
1 ATGAAAATATAAAAACA-TATAAAATGTC
* *
33255907 A--AAAA-ATAAAAACATTTAAAATTTC
1 ATGAAAATATAAAAACATATAAAATGTC
* *
33255932 ATGAAATTATAAAAATATATAAAATGTC
1 ATGAAAATATAAAAACATATAAAATGTC
*
33255960 TTGAAAATA-AAAAAC
1 ATGAAAATATAAAAAC
33255975 GTGTTCTTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
24 8 0.14
25 15 0.27
27 9 0.16
28 24 0.43
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.27
Consensus pattern (28 bp):
ATGAAAATATAAAAACATATAAAATGTC
Found at i:33256206 original size:30 final size:30
Alignment explanation
Indices: 33256162--33256238 Score: 75
Period size: 31 Copynumber: 2.6 Consensus size: 30
33256152 GTAATTTGAT
* *
33256162 ACAT-AAATTTTAATTTGGTGCAATTATAC
1 ACATGAAACTTTAATTTGGTGCAAATATAC
* * *
33256191 ACATGAAACTTTAATTGTGGTTCAAATGTAT
1 ACATGAAACTTTAATT-TGGTGCAAATATAC
**
33256222 TTATGAAACTTTAATTT
1 ACATGAAACTTTAATTT
33256239 TGATCCAATC
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
29 4 0.10
30 11 0.28
31 24 0.62
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (30 bp):
ACATGAAACTTTAATTTGGTGCAAATATAC
Found at i:33257115 original size:19 final size:18
Alignment explanation
Indices: 33257093--33257129 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
33257083 ACGTATGAAA
*
33257093 TTTTTTATAATATTTTTAT
1 TTTTTTA-AACATTTTTAT
33257112 TTTTTTAAACATTTTTAT
1 TTTTTTAAACATTTTTAT
33257130 AATATTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTTTAAACATTTTTAT
Found at i:33257409 original size:20 final size:17
Alignment explanation
Indices: 33257393--33257428 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
33257383 CGTTAATATT
*
33257393 AAAATTTTAATAATAATA
1 AAAATATTAAT-ATAATA
33257411 AAAATATTAATATAATA
1 AAAATATTAATATAATA
33257428 A
1 A
33257429 TATATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATATTAATATAATA
Found at i:33258100 original size:1 final size:1
Alignment explanation
Indices: 33258094--33258124 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
33258084 TAGTTGAAGT
33258094 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
33258125 AGTCCACTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:33276081 original size:6 final size:6
Alignment explanation
Indices: 33276072--33276102 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
33276062 ATTTAAATTG
*
33276072 ATTTAA ATTTAA ATTTAA ATTAAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
33276103 CACTAAACGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:33276220 original size:14 final size:14
Alignment explanation
Indices: 33276201--33276250 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
33276191 TCCATTTTTC
33276201 GGCCCAATTACAAA
1 GGCCCAATTACAAA
33276215 GGCCCAATTACAAA
1 GGCCCAATTACAAA
* * * *
33276229 TGTCCAAATAC-AT
1 GGCCCAATTACAAA
33276242 GGCCCAATT
1 GGCCCAATT
33276251 GGCCCAATCC
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
13 7 0.24
14 22 0.76
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.20
Consensus pattern (14 bp):
GGCCCAATTACAAA
Found at i:33277775 original size:162 final size:162
Alignment explanation
Indices: 33277601--33277939 Score: 590
Period size: 162 Copynumber: 2.1 Consensus size: 162
33277591 TCTTTCCAAT
* *
33277601 TTAGTCCTTTGACTGTTTGACTGCACCAAGGGTTGCCACGTGTCATTTTTTTGATTATTTATGTA
1 TTAGTCCTTTGACTGTTTGACTGCACCAAGGGCTGCCACGTGTCATTTTTTGGATTATTTATGTA
33277666 TTTAGTCCTTTCTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTTAATTACGA
66 TTTAGTCCTTTCTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTTAATTACGA
* * *
33277731 AATTAGT-CCAAGAATTTTTCATGGTTTATAAA
131 AATTA-TCCCAAGAATTTTTCAAGATTTACAAA
*
33277763 TTAGTCCTTTGACTGTTTGACTGCACCAGGGGCTGCCACGTGTCATTTTTTGGATTATTTATGTA
1 TTAGTCCTTTGACTGTTTGACTGCACCAAGGGCTGCCACGTGTCATTTTTTGGATTATTTATGTA
33277828 TTTAGTCCTTTCTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTTAATTACGA
66 TTTAGTCCTTTCTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTTAATTACGA
*
33277893 AATTATCCCAAGAATTTTTCAAGATTTACAAC
131 AATTATCCCAAGAATTTTTCAAGATTTACAAA
*
33277925 TTAATCCTTTGACTG
1 TTAGTCCTTTGACTG
33277940 CTGGATGCCT
Statistics
Matches: 168, Mismatches: 8, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
161 1 0.01
162 167 0.99
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (162 bp):
TTAGTCCTTTGACTGTTTGACTGCACCAAGGGCTGCCACGTGTCATTTTTTGGATTATTTATGTA
TTTAGTCCTTTCTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTTAATTACGA
AATTATCCCAAGAATTTTTCAAGATTTACAAA
Found at i:33278220 original size:29 final size:30
Alignment explanation
Indices: 33278040--33278230 Score: 132
Period size: 29 Copynumber: 6.5 Consensus size: 30
33278030 CAAAAGTTTT
33278040 GAAAATTACCATTTT-ACCCCTGAACTTTC--C
1 GAAAATTACCATTTTAACCCC-G-A-TTTCATC
*
33278070 -AAAATT-CCATTTTTAACCCCGATTTCACC
1 GAAAATTACCA-TTTTAACCCCGATTTCATC
* * * * *
33278099 GAAAATTGCCATTTTACCCCCGA-ATCTTT
1 GAAAATTACCATTTTAACCCCGATTTCATC
* *
33278128 TAAAATT-CCATTTTTAACCCCGATTTTATC
1 GAAAATTACCA-TTTTAACCCCGATTTCATC
* * * *
33278158 AAAAATTACCATTTT-ACCCTCGA-ATCTTT
1 GAAAATTACCATTTTAACCC-CGATTTCATC
* *
33278187 TAAAATT-CCATTTTAACCCCGATTTCACC
1 GAAAATTACCATTTTAACCCCGATTTCATC
33278216 GAAAATTACCATTTT
1 GAAAATTACCATTTT
33278231 GCCCTCGAGT
Statistics
Matches: 126, Mismatches: 22, Indels: 26
0.72 0.13 0.15
Matches are distributed among these distances:
27 4 0.03
28 17 0.13
29 55 0.44
30 44 0.35
31 6 0.05
ACGTcount: A:0.31, C:0.27, G:0.05, T:0.37
Consensus pattern (30 bp):
GAAAATTACCATTTTAACCCCGATTTCATC
Found at i:33278229 original size:58 final size:59
Alignment explanation
Indices: 33278040--33278238 Score: 296
Period size: 59 Copynumber: 3.4 Consensus size: 59
33278030 CAAAAGTTTT
*
33278040 GAAAATTACCATTTTACCC-CTGAA-CTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
1 GAAAATTACCATTTTACCCTC-GAATCTTT-TAAAATTCCATTTTTAACCCCGATTTCACC
* * * *
33278099 GAAAATTGCCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTTATC
1 GAAAATTACCATTTTACCCTCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACC
*
33278158 AAAAATTACCATTTTACCCTCGAATCTTTTAAAATTCCA-TTTTAACCCCGATTTCACC
1 GAAAATTACCATTTTACCCTCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACC
*
33278216 GAAAATTACCATTTTGCCCTCGA
1 GAAAATTACCATTTTACCCTCGA
33278239 GTATCCATAA
Statistics
Matches: 127, Mismatches: 11, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
58 38 0.30
59 84 0.66
60 5 0.04
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.36
Consensus pattern (59 bp):
GAAAATTACCATTTTACCCTCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACC
Found at i:33278259 original size:117 final size:118
Alignment explanation
Indices: 33278041--33278275 Score: 300
Period size: 117 Copynumber: 2.0 Consensus size: 118
33278031 AAAAGTTTTG
33278041 AAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCGAAAATT
1 AAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCGAAAATT
* ** * *
33278106 GCCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTTATCA
66 ACCATTTTACCCCCGAATCTCATAAAATCCCATTTTTAACCCCGATTTCATCA
*
33278159 AAAATTACCATTTTA-CCCTCGAATCTTT-TAAAATTCCA-TTTTAACCCCGATTTCACCGAAAA
1 AAAATTACCATTTTACCCCT-GAA-CTTTCCAAAATTCCATTTTTAACCCCGATTTCACCGAAAA
* * * * *
33278221 TTACCATTTTGCCCTCGAGTATC-CAT-AAGTCCCGTTTTTCACCCCGATTTCATCA
64 TTACCATTTTACCCCCGA--ATCTCATAAAATCCCATTTTTAACCCCGATTTCATCA
33278276 TTTATCAATG
Statistics
Matches: 102, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
117 67 0.66
118 28 0.27
119 7 0.07
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.36
Consensus pattern (118 bp):
AAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCGAAAATT
ACCATTTTACCCCCGAATCTCATAAAATCCCATTTTTAACCCCGATTTCATCA
Found at i:33289290 original size:26 final size:28
Alignment explanation
Indices: 33289230--33289290 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 28
33289220 AGTATTACAA
*
33289230 AATTGTAAAATTATAAAAAAATTATATT
1 AATTGTTAAATTATAAAAAAATTATATT
* *
33289258 --TTTTTAAATT-TTAAAAAATTA-ATT
1 AATTGTTAAATTATAAAAAAATTATATT
33289282 AATTGTTAA
1 AATTGTTAA
33289291 TGTGACATAC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
24 3 0.11
25 10 0.37
26 14 0.52
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (28 bp):
AATTGTTAAATTATAAAAAAATTATATT
Found at i:33290615 original size:2 final size:2
Alignment explanation
Indices: 33290608--33290644 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
33290598 CATTGAAGAT
33290608 TC TC TC TC TC 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 TC TC T
33290645 AGACTCTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:33293023 original size:41 final size:41
Alignment explanation
Indices: 33292921--33293108 Score: 200
Period size: 41 Copynumber: 4.5 Consensus size: 41
33292911 TGGTGTATAA
* * * * * *
33292921 AAAGGAAGATTCATGTCTCGGGTTGAGCATGAGAAATTGTAT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGATA-TGAAT
33292963 AAATGGAAGACTCATGTCTCGAGATGAGAATGAGACTATGAAT
1 AAA-GGAAGACTCATGTCTCGAGATGAGAATGAGA-TATGAAT
* *
33293006 -AAGGAAGACTCATGTCTCGAAATGAGAATGAGATTTTG-AT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGA-TATGAAT
* **
33293046 TAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGGTT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAG-ATATGAAT
* *
33293088 AAAGGAAGACTTATGACTCGA
1 AAAGGAAGACTCATGTCTCGA
33293109 TAGAGCATAA
Statistics
Matches: 126, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
40 2 0.02
41 67 0.53
42 25 0.20
43 31 0.25
44 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.27, T:0.26
Consensus pattern (41 bp):
AAAGGAAGACTCATGTCTCGAGATGAGAATGAGATATGAAT
Found at i:33293072 original size:82 final size:85
Alignment explanation
Indices: 33292921--33293108 Score: 238
Period size: 82 Copynumber: 2.2 Consensus size: 85
33292911 TGGTGTATAA
* *** *
33292921 AAAGGAAGATTCATGTCTCGGGTTGAGCATGAGAAATTGTATAAATGGAAGACTCATGTCTCGAG
1 AAAGGAAGACTCATGTCTCGAAATGAGAATGAGAAATTGTATAAATGGAAGACTCATGTCTCGAG
*
33292986 ATGAGAATGAGACTATGAAT
66 ATGAGAATGAGAATATGAAT
** *
33293006 -AAGGAAGACTCATGTCTCGAAATGAGAATGAGATTTTG-ATTAA-GGAAGACTCATGTCTCGAG
1 AAAGGAAGACTCATGTCTCGAAATGAGAATGAGAAATTGTATAAATGGAAGACTCATGTCTCGAG
**
33293068 ATGAGAATGAGAATATGGTT
66 ATGAGAATGAGAATATGAAT
* *
33293088 AAAGGAAGACTTATGACTCGA
1 AAAGGAAGACTCATGTCTCGA
33293109 TAGAGCATAA
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
82 36 0.40
83 22 0.25
84 31 0.35
ACGTcount: A:0.37, C:0.11, G:0.27, T:0.26
Consensus pattern (85 bp):
AAAGGAAGACTCATGTCTCGAAATGAGAATGAGAAATTGTATAAATGGAAGACTCATGTCTCGAG
ATGAGAATGAGAATATGAAT
Found at i:33294997 original size:2 final size:2
Alignment explanation
Indices: 33294990--33295015 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
33294980 ACATTGAAAT
33294990 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
33295016 AGGAACACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33296021 original size:15 final size:15
Alignment explanation
Indices: 33295978--33296023 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 15
33295968 TTTTCGTAAA
33295978 TTTAAGT-TTTAATT
1 TTTAAGTATTTAATT
*
33295992 TTT--GTACTTTTATT
1 TTTAAGTA-TTTAATT
33296006 TTTAAGTATTTAATT
1 TTTAAGTATTTAATT
33296021 TTT
1 TTT
33296024 TTATTTTTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
12 2 0.08
14 12 0.46
15 9 0.35
16 3 0.12
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (15 bp):
TTTAAGTATTTAATT
Found at i:33297269 original size:10 final size:10
Alignment explanation
Indices: 33297254--33297282 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
33297244 TATTTTAAAA
33297254 AAATTATTTT
1 AAATTATTTT
33297264 AAATTATTTT
1 AAATTATTTT
33297274 AAATT-TTTT
1 AAATTATTTT
33297283 GTTGAAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
AAATTATTTT
Found at i:33306909 original size:15 final size:16
Alignment explanation
Indices: 33306872--33306911 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
33306862 GCGAAATTTT
33306872 GAAGAAAA-AAAAGAA
1 GAAGAAAACAAAAGAA
33306887 GAAG-AAACAAAAGAA
1 GAAGAAAACAAAAGAA
33306902 -AAGAAAACAA
1 GAAGAAAACAA
33306912 GGGGTTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.78, C:0.05, G:0.17, T:0.00
Consensus pattern (16 bp):
GAAGAAAACAAAAGAA
Found at i:33309937 original size:23 final size:24
Alignment explanation
Indices: 33309911--33309980 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 24
33309901 TTTATTTAAC
**
33309911 TTAATTGAACATGTTCACGGTCA-
1 TTAATTGAACATGTTCACGAACAT
** * *
33309934 TTAAGCGTACATGTTCATGAACAT
1 TTAATTGAACATGTTCACGAACAT
* *
33309958 TTAATTGAATATGTTCACAAACA
1 TTAATTGAACATGTTCACGAACA
33309981 ATATTAATGA
Statistics
Matches: 34, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
23 17 0.50
24 17 0.50
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (24 bp):
TTAATTGAACATGTTCACGAACAT
Found at i:33330042 original size:60 final size:58
Alignment explanation
Indices: 33329879--33330050 Score: 197
Period size: 59 Copynumber: 2.9 Consensus size: 58
33329869 TTAAATTAGG
* * * * * *
33329879 TTTGACATTTTTT-TTAATTTGGTACTTAAATTTTTTT-ATCCAGTTTGATA-CTTGAA
1 TTTGATATTTTTTCTTAATTTGATACCTAAATTTTTTTGATTCAATTTGGTATC-TGAA
* * * *
33329935 ATAGATATTTTTTCTTAATTTGATATCTAAATTTTTTTGGACTCAATTTGGTATCTGAA
1 TTTGATATTTTTTCTTAATTTGATACCTAAATTTTTTT-GATTCAATTTGGTATCTGAA
33329994 TTTGATATTTTTTCTTAATTTGATACCTAATATTTTTTTAGATTCAATTTGGTATCT
1 TTTGATATTTTTTCTTAATTTGATACCTAA-ATTTTTTT-GATTCAATTTGGTATCT
33330051 AAACTTATTA
Statistics
Matches: 96, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
56 10 0.10
57 21 0.22
59 40 0.42
60 25 0.26
ACGTcount: A:0.26, C:0.09, G:0.10, T:0.55
Consensus pattern (58 bp):
TTTGATATTTTTTCTTAATTTGATACCTAAATTTTTTTGATTCAATTTGGTATCTGAA
Found at i:33330244 original size:31 final size:30
Alignment explanation
Indices: 33330209--33330331 Score: 83
Period size: 31 Copynumber: 4.1 Consensus size: 30
33330199 ATTAAGTACT
33330209 AAATTAGAAAAAAGAGTCAAGTTTAGATACC
1 AAATTAGAAAAAA-AGTCAAGTTTAGATACC
* *** *
33330240 AAATTGGACCTCAAA---AAGTTTAAATACC
1 AAATTAGA-AAAAAAGTCAAGTTTAGATACC
* ** *
33330268 AACTTA-AAAAAGTGTCAAGTTTAGGTACC
1 AAATTAGAAAAAAAGTCAAGTTTAGATACC
* * *
33330297 AAATTAGAAAAAAATATCGAGTTTAGGTACC
1 AAATTAGAAAAAAA-GTCAAGTTTAGATACC
33330328 AAAT
1 AAAT
33330332 ATTATATTAA
Statistics
Matches: 67, Mismatches: 19, Indels: 12
0.68 0.19 0.12
Matches are distributed among these distances:
26 1 0.01
27 1 0.01
28 16 0.24
29 16 0.24
30 5 0.07
31 26 0.39
32 2 0.03
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25
Consensus pattern (30 bp):
AAATTAGAAAAAAAGTCAAGTTTAGATACC
Found at i:33330808 original size:20 final size:20
Alignment explanation
Indices: 33330771--33330809 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
33330761 TGATAGAGAT
* *
33330771 ATTAAAATATGCACAATAAA
1 ATTAAAATATACAAAATAAA
*
33330791 ATTAAAATATATAAAATAA
1 ATTAAAATATACAAAATAA
33330810 TAAAAATAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (20 bp):
ATTAAAATATACAAAATAAA
Found at i:33330829 original size:24 final size:23
Alignment explanation
Indices: 33330785--33330832 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
33330775 AAATATGCAC
* * *
33330785 AATAAAATTAAAATATATAAAAT
1 AATAAAAATAAAAAAGATAAAAT
33330808 AATAAAAATAAAAAAGATTAAAAT
1 AATAAAAATAAAAAAGA-TAAAAT
33330832 A
1 A
33330833 CCTTCAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (23 bp):
AATAAAAATAAAAAAGATAAAAT
Found at i:33331292 original size:31 final size:31
Alignment explanation
Indices: 33331257--33331322 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
33331247 TTTTTAGTTA
*
33331257 AATTTGACCT-TCAACTTTTTCAAAAGAATCG
1 AATTTGA-CTATCAACTTTTTCAAAAAAATCG
* *
33331288 AATTTGACTATTAACTTTTTGAAAAAAATCG
1 AATTTGACTATCAACTTTTTCAAAAAAATCG
33331319 AATT
1 AATT
33331323 GTTTTTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (31 bp):
AATTTGACTATCAACTTTTTCAAAAAAATCG
Found at i:33335088 original size:84 final size:84
Alignment explanation
Indices: 33334937--33335093 Score: 183
Period size: 84 Copynumber: 1.9 Consensus size: 84
33334927 CGAACTTCCG
* * **
33334937 GTTGAGGATTGCACTCCAAGGAGACTTACATTCAAGAAAAGAGAGCTCGTTAACAACAGAAACGA
1 GTTGAGGACTGCACTCCAAGGAGACTCACATTCAAGAAAAGAGAAATCGTTAACAACAGAAACGA
33335002 TGACAACCGGAATGGCAAA
66 TGACAACCGGAATGGCAAA
* * * * * *
33335021 GTTGAGGACTGTACTCCAAGGAGACTCA-AGTTCAAGCAAAGGGTAAAT-GTTAATAACATAAAT
1 GTTGAGGACTGCACTCCAAGGAGACTCACA-TTCAAGAAAAGAG-AAATCGTTAACAACAGAAAC
*
33335084 GATGATAACC
64 GATGACAACC
33335094 AAAACAGTAG
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
83 1 0.02
84 57 0.95
85 2 0.03
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (84 bp):
GTTGAGGACTGCACTCCAAGGAGACTCACATTCAAGAAAAGAGAAATCGTTAACAACAGAAACGA
TGACAACCGGAATGGCAAA
Found at i:33335129 original size:84 final size:82
Alignment explanation
Indices: 33335036--33335349 Score: 301
Period size: 84 Copynumber: 3.7 Consensus size: 82
33335026 GGACTGTACT
* * * *
33335036 CCAAGGAGACTCAAGTTCAAGCAAAGGGTAAATGTTAATAACATAAATGATGATAACCAAAACAG
1 CCAAGGAGACTCAAGTTC-AGCAAAGAGTAAATGTTGACAACA-AAATGGTGATAACCAAAACAG
33335101 TAGAGTCAAGGAGTTTACC
64 TAGAGTCAAGGAGTTTACC
* *
33335120 CCGAA-GAGACTCAAGTTCAGACGAAGAG-AAATTGTTGACAACCGAAATGGTGATAACCAAAAC
1 CC-AAGGAGACTCAAGTTCAG-CAAAGAGTAAA-TGTTGACAA-CAAAATGGTGATAACCAAAAC
* *
33335183 AGTAAAGTCAAGGAGTTTACT
62 AGTAGAGTCAAGGAGTTTACC
* * * *
33335204 CCAAGGAGACTGAAGTTTCAGCAAAGAGTAATTGTTGACAACCAAAATGGTGATATCAAAAACAG
1 CCAAGGAGACTCAAG-TTCAGCAAAGAGTAAATGTTGACAA-CAAAATGGTGATAACCAAAACAG
* * ** *
33335269 TAGAATCGAGGAACTTACT
64 TAGAGTCAAGGAGTTTACC
* * * * * *
33335288 CCAAGGATACTCAAGTTCAGGCGAAA-ATTAATTGTTGACAACATAGATGATCATAACCAAAA
1 CCAAGGAGACTCAAGTTCA-GC-AAAGAGTAAATGTTGACAACA-AAATGGTGATAACCAAAA
33335350 TGCCAAAGTC
Statistics
Matches: 193, Mismatches: 27, Indels: 20
0.80 0.11 0.08
Matches are distributed among these distances:
83 13 0.07
84 167 0.87
85 13 0.07
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.21
Consensus pattern (82 bp):
CCAAGGAGACTCAAGTTCAGCAAAGAGTAAATGTTGACAACAAAATGGTGATAACCAAAACAGTA
GAGTCAAGGAGTTTACC
Found at i:33335323 original size:168 final size:168
Alignment explanation
Indices: 33335032--33335378 Score: 387
Period size: 168 Copynumber: 2.1 Consensus size: 168
33335022 TTGAGGACTG
* * *
33335032 TACTCCAAGGAGACTCAAGTTCAAGCAAAGGGTAAATGTTAATAACATAAATGATGATAACCAAA
1 TACTCCAAGGAGACTCAAGTTCAAGCAAAGAGTAAATGTTAACAACATAAATGATGATAACAAAA
* ** *
33335097 ACAGTAGAGTCAAGGAGTTTACCCCGAAGAGACTCAAGTTCAGACGAAGAGAAATTGTTGACAAC
66 ACAGTAGAATCAAGGAACTTACCCCGAAGAGACTCAAGTTCAGACGAAAAGAAATTGTTGACAAC
* * * *
33335162 CGAAATGGTGATAACCAAAACAG-TAAAGTCAAGGAGTT
131 AGAAATGATCATAACCAAAA-AGCCAAAGTCAAGGAGTT
* * * * *
33335200 TACTCCAAGGAGACTGAAGTTTC-AGCAAAGAGTAATTGTTGACAACCA-AAATGGTGATATCAA
1 TACTCCAAGGAGACTCAAG-TTCAAGCAAAGAGTAAATGTTAACAA-CATAAATGATGATAACAA
* * * * **
33335263 AAACAGTAGAATCGAGGAACTTACTCC-AAGGATACTCAAGTTCAGGCGAAAATTAATTGTTGAC
64 AAACAGTAGAATCAAGGAACTTACCCCGAA-GAGACTCAAGTTCAGACGAAAAGAAATTGTTGAC
* * * *
33335327 AACATAGATGATCATAACCAAAATGCCAAAGTCGAGGAGTT
128 AACAGAAATGATCATAACCAAAAAGCCAAAGTCAAGGAGTT
*
33335368 TAGTCCAAGGA
1 TACTCCAAGGA
33335379 AACTTGAGTC
Statistics
Matches: 148, Mismatches: 27, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
167 3 0.02
168 140 0.95
169 5 0.03
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.21
Consensus pattern (168 bp):
TACTCCAAGGAGACTCAAGTTCAAGCAAAGAGTAAATGTTAACAACATAAATGATGATAACAAAA
ACAGTAGAATCAAGGAACTTACCCCGAAGAGACTCAAGTTCAGACGAAAAGAAATTGTTGACAAC
AGAAATGATCATAACCAAAAAGCCAAAGTCAAGGAGTT
Found at i:33335431 original size:81 final size:81
Alignment explanation
Indices: 33335371--33335707 Score: 550
Period size: 81 Copynumber: 4.2 Consensus size: 81
33335361 AGGAGTTTAG
* * * * **
33335371 TCCAAGGAAACTTGAGTCCCGCCAAAGAAATATTGACAACAGAAATTCCGGCGATCAAAATAGTA
1 TCCAACGAAACTTGAGTCCTGCCAAAGAAATCTTGACAACAGAAATTCTGATGATCAAAATAGTA
33335436 GAGGTGAGGACTCTGC
66 GAGGTGAGGACTCTGC
33335452 TCCAACGAAACTTGAGTCCTGCCAAA-AAACTCTTGACAACAGAAATTCTGATGATCAAAATAGT
1 TCCAACGAAACTTGAGTCCTGCCAAAGAAA-TCTTGACAACAGAAATTCTGATGATCAAAATAGT
*
33335516 AGAGGTGTGGACTCTGC
65 AGAGGTGAGGACTCTGC
*
33335533 TCCAACGAAACTTGAGTCCTGCCAAAGAACTCTTGACAACAGAAATTCTGATGATCAAAATAGTA
1 TCCAACGAAACTTGAGTCCTGCCAAAGAAATCTTGACAACAGAAATTCTGATGATCAAAATAGTA
33335598 GAGGTGAGGACTCTGC
66 GAGGTGAGGACTCTGC
*
33335614 TCCAACGAAACTTGAGTCCTGCCAAAGAACTCTTGACAACAGAAATTCTGATGATCAAAATAGTA
1 TCCAACGAAACTTGAGTCCTGCCAAAGAAATCTTGACAACAGAAATTCTGATGATCAAAATAGTA
* *
33335679 CAGTTGAGGACTCTGC
66 GAGGTGAGGACTCTGC
*
33335695 TCCAAGGAAACTT
1 TCCAACGAAACTT
33335708 ATCTTCAGGC
Statistics
Matches: 242, Mismatches: 12, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
80 3 0.01
81 237 0.98
82 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (81 bp):
TCCAACGAAACTTGAGTCCTGCCAAAGAAATCTTGACAACAGAAATTCTGATGATCAAAATAGTA
GAGGTGAGGACTCTGC
Found at i:33339833 original size:17 final size:17
Alignment explanation
Indices: 33339811--33339843 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
33339801 TGTGAACAAT
*
33339811 TTTTTATTATTTTTTTG
1 TTTTTAATATTTTTTTG
33339828 TTTTTAATATTTTTTT
1 TTTTTAATATTTTTTT
33339844 CTCAAAACAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTTAATATTTTTTTG
Found at i:33340522 original size:30 final size:30
Alignment explanation
Indices: 33340481--33340572 Score: 89
Period size: 30 Copynumber: 3.1 Consensus size: 30
33340471 CCCAAGACTG
*
33340481 AAAGAGGTCCAAAATTTTTTTCTCAACTTTT
1 AAAG-GGTCCAAAATTTTTTTATCAACTTTT
****
33340512 AAAGGGTCCAAAA-AAAATTATCAACTTTT
1 AAAGGGTCCAAAATTTTTTTATCAACTTTT
* *
33340541 -AAGGGTTCAAAAATTTTTTTAACAACTTTT
1 AAAGGG-TCCAAAATTTTTTTATCAACTTTT
33340571 AA
1 AA
33340573 GGAGCCTAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
28 5 0.11
29 17 0.36
30 20 0.43
31 5 0.11
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (30 bp):
AAAGGGTCCAAAATTTTTTTATCAACTTTT
Found at i:33340573 original size:30 final size:29
Alignment explanation
Indices: 33340532--33340614 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 29
33340522 AAAAAAATTA
* *
33340532 TCAACTTTTAAGGGTTCAAAAA-TTTTTT
1 TCAACTTTTAAGGGATCAAAAAGTTTTCT
* *
33340560 TAACAACTTTTAAGGAGCCTAAAAAAGTTTTCT
1 T--CAACTTTTAAGG-G-ATCAAAAAGTTTTCT
33340593 TCAACTTTTAAGGGATCAAAAA
1 TCAACTTTTAAGGGATCAAAAA
33340615 CTCCAATTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
28 1 0.02
29 6 0.13
30 13 0.29
31 13 0.29
32 6 0.13
33 6 0.13
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (29 bp):
TCAACTTTTAAGGGATCAAAAAGTTTTCT
Found at i:33344191 original size:31 final size:31
Alignment explanation
Indices: 33344123--33344349 Score: 163
Period size: 30 Copynumber: 7.6 Consensus size: 31
33344113 AAAAAGTCTG
* * *
33344123 GGGTCAAAATGAAATTTTTAGAAAATTTAG-
1 GGGTTAAAATGTAATTTTTAGAAAGTTTAGA
* * *
33344153 GGGTTAAAATGTGATTTTTAGAAGGTTTGGA
1 GGGTTAAAATGTAATTTTTAGAAAGTTTAGA
*
33344184 GGGTTAAAATGCAATTTTTAGAAAGTTTAGA
1 GGGTTAAAATGTAATTTTTAGAAAGTTTAGA
* *
33344215 -GGTTAAAATATAATTTTT-GAAAATTTTA-A
1 GGGTTAAAATGTAATTTTTAG-AAAGTTTAGA
* * *
33344244 GGGTCAAAA-G-ATAGTTTTGGAAAG-TTAG-
1 GGGTTAAAATGTA-ATTTTTAGAAAGTTTAGA
* * * * *
33344272 GGGTTTAAAATATAAATTTTGGAAAG-TAAAA
1 GGG-TTAAAATGTAATTTTTAGAAAGTTTAGA
*
33344303 GGGTTAAAATATAATTTTTGAGAAA-TTT--A
1 GGGTTAAAATGTAATTTTT-AGAAAGTTTAGA
*
33344332 GGGTTAAAATATAATTTT
1 GGGTTAAAATGTAATTTT
33344350 GAAATAGAAT
Statistics
Matches: 160, Mismatches: 25, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
28 7 0.04
29 34 0.21
30 83 0.52
31 36 0.22
ACGTcount: A:0.40, C:0.01, G:0.22, T:0.37
Consensus pattern (31 bp):
GGGTTAAAATGTAATTTTTAGAAAGTTTAGA
Found at i:33344283 original size:59 final size:58
Alignment explanation
Indices: 33344199--33344353 Score: 161
Period size: 59 Copynumber: 2.6 Consensus size: 58
33344189 AAAATGCAAT
* * * **
33344199 TTTTAGAAAGTTTAGAGGTTAAAATATAATTTTTGAAAATTTTAAGGGTCAAAAGAT-AG
1 TTTTGGAAAG-TTAGGGGTTAAAATATAA-TTTTGAAAAGTAAAAGGGTCAAAAGATAAG
* * * *
33344258 TTTTGGAAAGTTAGGGGTTTAAAATATAAATTTTGGAAAGTAAAAGGGTTAAAATATAAT
1 TTTTGGAAAGTTAGGGG-TTAAAATAT-AATTTTGAAAAGTAAAAGGGTCAAAAGATAAG
*
33344318 TTTTGAGAAATTTA-GGGTTAAAATATAATTTTGAAA
1 TTTTG-GAAAGTTAGGGGTTAAAATATAATTTTGAAA
33344354 TAGAATAGGG
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
58 15 0.19
59 48 0.59
60 11 0.14
61 7 0.09
ACGTcount: A:0.43, C:0.01, G:0.19, T:0.37
Consensus pattern (58 bp):
TTTTGGAAAGTTAGGGGTTAAAATATAATTTTGAAAAGTAAAAGGGTCAAAAGATAAG
Found at i:33344362 original size:29 final size:28
Alignment explanation
Indices: 33344276--33344363 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 28
33344266 AGTTAGGGGT
33344276 TTAAAATATAAATTTTGGAAAGTAAA-AGGG
1 TTAAAATAT-AATTTT-GAAA-TAAATAGGG
**
33344306 TTAAAATATAATTTTTGAGAA-ATTTAGGG
1 TTAAAATATAA-TTTTGA-AATAAATAGGG
33344335 TTAAAATATAATTTTGAAATAGAATAGGG
1 TTAAAATATAATTTTGAAATA-AATAGGG
33344364 GCTTATTGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
27 2 0.04
28 8 0.16
29 24 0.49
30 15 0.31
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (28 bp):
TTAAAATATAATTTTGAAATAAATAGGG
Found at i:33344728 original size:14 final size:13
Alignment explanation
Indices: 33344702--33344726 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33344692 ATTTCAAAAA
33344702 AAAAAAAACTTTC
1 AAAAAAAACTTTC
33344715 AAAAAAAACTTT
1 AAAAAAAACTTT
33344727 TCTCTCTCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAAAAACTTTC
Found at i:33346074 original size:23 final size:23
Alignment explanation
Indices: 33346000--33346213 Score: 142
Period size: 23 Copynumber: 9.5 Consensus size: 23
33345990 TAAACGGAAC
* * *
33346000 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
33346022 GAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
33346044 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
33346070 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
33346090 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
33346109 AATCAGAGAGAACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
33346132 AATCGGAGAGCACACACAGTGCTT
1 AAACAGAGAGCACACAAAGTGC-T
* *
33346156 ATAACAGAGAGCACGA-GACGTGCT
1 A-AACAGAGAGCAC-ACAAAGTGCT
*
33346180 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
33346203 AATCAGAGAGC
1 AAACAGAGAGC
33346214 GCGCTAGTGT
Statistics
Matches: 149, Mismatches: 27, Indels: 31
0.72 0.13 0.15
Matches are distributed among these distances:
16 10 0.07
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.01
22 18 0.12
23 75 0.50
24 4 0.03
25 27 0.18
26 8 0.05
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:33346108 original size:39 final size:39
Alignment explanation
Indices: 33346054--33346128 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
33346044 GGGCAACAGA
*
33346054 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGAACACAAAGTACT
* *
33346093 GAGCACACAAAGTGCTAATCAGAGAGAACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGAACACAAAGT
33346129 GCTAATCGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGAACACAAAGTACT
Found at i:33346210 original size:46 final size:44
Alignment explanation
Indices: 33346093--33346213 Score: 152
Period size: 48 Copynumber: 2.6 Consensus size: 44
33346083 ACAAAGTACT
* * *
33346093 GAGCACACAAAGTGCTAATCAGAGAGAACACGAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATCAGAGAG--CACGAAGTGCTAAACAGA
*
33346139 GAGCACACACAGTGCTTATAACAGAGAGCACGAGACGTGCTAAACAGA
1 GAGCACACACAGTGC-TA-ATCAGAGAGCACGA-A-GTGCTAAACAGA
33346187 GAGCACACACAGTGCTAATCAGAGAGC
1 GAGCACACACAGTGCTAATCAGAGAGC
33346214 GCGCTAGTGT
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
46 28 0.42
47 5 0.08
48 33 0.50
ACGTcount: A:0.40, C:0.22, G:0.26, T:0.12
Consensus pattern (44 bp):
GAGCACACACAGTGCTAATCAGAGAGCACGAAGTGCTAAACAGA
Found at i:33349347 original size:10 final size:9
Alignment explanation
Indices: 33349316--33349340 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
33349306 TTCTGACACG
33349316 TATTTTTTT
1 TATTTTTTT
33349325 TATTTTTTT
1 TATTTTTTT
33349334 TATTTTT
1 TATTTTT
33349341 ATATATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TATTTTTTT
Found at i:33349783 original size:74 final size:74
Alignment explanation
Indices: 33349699--33349849 Score: 302
Period size: 74 Copynumber: 2.0 Consensus size: 74
33349689 AAAATAAATA
33349699 TTTATTTTGTACCATTTTAGTAAATAATATGATGGGGATATTATTTTGATAATTAATTATTTTTT
1 TTTATTTTGTACCATTTTAGTAAATAATATGATGGGGATATTATTTTGATAATTAATTATTTTTT
33349764 ATATTATAT
66 ATATTATAT
33349773 TTTATTTTGTACCATTTTAGTAAATAATATGATGGGGATATTATTTTGATAATTAATTATTTTTT
1 TTTATTTTGTACCATTTTAGTAAATAATATGATGGGGATATTATTTTGATAATTAATTATTTTTT
33349838 ATATTATAT
66 ATATTATAT
33349847 TTT
1 TTT
33349850 GGTAATTAAT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 77 1.00
ACGTcount: A:0.32, C:0.03, G:0.11, T:0.55
Consensus pattern (74 bp):
TTTATTTTGTACCATTTTAGTAAATAATATGATGGGGATATTATTTTGATAATTAATTATTTTTT
ATATTATAT
Found at i:33349833 original size:16 final size:16
Alignment explanation
Indices: 33349812--33349861 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
33349802 TGATGGGGAT
33349812 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
33349828 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
33349843 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
33349858 ATTA
1 ATTA
33349862 GCTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:33350114 original size:30 final size:25
Alignment explanation
Indices: 33350037--33350105 Score: 111
Period size: 25 Copynumber: 2.7 Consensus size: 25
33350027 AAAAATATTT
33350037 AAAATTTTATATTAATTTTTTATAACA
1 AAAATTTTAT-TTAA-TTTTTATAACA
33350064 AAAATTTTATTTAATTTTTATAACA
1 AAAATTTTATTTAATTTTTATAACA
*
33350089 AAAATTTTATTTTATTT
1 AAAATTTTATTTAATTT
33350106 AATTTTTATC
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 27 0.66
26 4 0.10
27 10 0.24
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (25 bp):
AAAATTTTATTTAATTTTTATAACA
Found at i:33350128 original size:35 final size:30
Alignment explanation
Indices: 33350040--33350114 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
33350030 AATATTTAAA
33350040 ATTTTATATTAATTTTTTATAAC-AAAA----
1 ATTTTAT-TTAA-TTTTTATAACAAAAATTTT
33350067 ATTTTATTTAATTTTTATAACAAAAATTTT
1 ATTTTATTTAATTTTTATAACAAAAATTTT
33350097 ATTTTATTTAATTTTTAT
1 ATTTTATTTAATTTTTAT
33350115 CACTTATCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
25 10 0.23
26 8 0.19
27 7 0.16
30 18 0.42
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (30 bp):
ATTTTATTTAATTTTTATAACAAAAATTTT
Found at i:33354618 original size:36 final size:36
Alignment explanation
Indices: 33354576--33354650 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
33354566 ATTTCCTTGA
33354576 ATCCCAATTCAAGCAATTAGAGGATGGGACATTCCT
1 ATCCCAATTCAAGCAATTAGAGGATGGGACATTCCT
33354612 ATCCCAATTCAAGCAATTAGAGGATGGGACATTCCT
1 ATCCCAATTCAAGCAATTAGAGGATGGGACATTCCT
33354648 ATC
1 ATC
33354651 TCAAAAGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (36 bp):
ATCCCAATTCAAGCAATTAGAGGATGGGACATTCCT
Found at i:33358911 original size:19 final size:19
Alignment explanation
Indices: 33358884--33358920 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
33358874 TTTAACCACG
* *
33358884 TTAATAATTAATATAATTT
1 TTAAAAATTAAAATAATTT
33358903 TTAAAAATTAAAATAATT
1 TTAAAAATTAAAATAATT
33358921 ATTTTAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAAAAATTAAAATAATTT
Found at i:33359599 original size:28 final size:27
Alignment explanation
Indices: 33359554--33359631 Score: 88
Period size: 29 Copynumber: 2.9 Consensus size: 27
33359544 TAAGGTGTCC
*
33359554 AATTTTGTTTT-TAATTTTTAAAGG-TT
1 AATTTT-TTTTATAACTTTTAAAGGATT
*
33359580 AATTTTTTTTATCAACTTTTAAGGGACTT
1 AATTTTTTTTAT-AACTTTTAAAGGA-TT
*
33359609 AATTTTTTTTCTAACTTTTAAAG
1 AATTTTTTTTATAACTTTTAAAG
33359632 AACTTAAAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
25 4 0.09
26 7 0.16
27 10 0.23
28 10 0.23
29 13 0.30
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.56
Consensus pattern (27 bp):
AATTTTTTTTATAACTTTTAAAGGATT
Found at i:33359611 original size:29 final size:28
Alignment explanation
Indices: 33359554--33359638 Score: 86
Period size: 28 Copynumber: 3.1 Consensus size: 28
33359544 TAAGGTGTCC
* *
33359554 AATTTTGTTTT-TAATTTTTAAAG--GTT
1 AATTTT-TTTTATAACTTTTAAAGAACTT
* *
33359580 AATTTTTTTTATCAACTTTTAAGGGACTT
1 AATTTTTTTTAT-AACTTTTAAAGAACTT
*
33359609 AATTTTTTTTCTAACTTTTAAAGAACTT
1 AATTTTTTTTATAACTTTTAAAGAACTT
33359637 AA
1 AA
33359639 AACCTCATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
25 4 0.08
26 7 0.14
27 9 0.18
28 16 0.33
29 13 0.27
ACGTcount: A:0.31, C:0.07, G:0.08, T:0.54
Consensus pattern (28 bp):
AATTTTTTTTATAACTTTTAAAGAACTT
Found at i:33360359 original size:30 final size:30
Alignment explanation
Indices: 33360296--33360366 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
33360286 AATCATTTAT
* * *
33360296 ATTTTATAATTTTTAAAAGATTAAATCAAA
1 ATTTTATCATTTTTAAAAAATAAAATCAAA
*
33360326 ATTTTATCATTTTTAAAAAATCAAAAT-ATA
1 ATTTTATCATTTTTAAAAAAT-AAAATCAAA
33360356 ATTTTATCATT
1 ATTTTATCATT
33360367 ACAAATTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
30 32 0.89
31 4 0.11
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.46
Consensus pattern (30 bp):
ATTTTATCATTTTTAAAAAATAAAATCAAA
Found at i:33365849 original size:41 final size:41
Alignment explanation
Indices: 33365690--33365849 Score: 216
Period size: 41 Copynumber: 3.9 Consensus size: 41
33365680 ACAAAAGGTT
* *
33365690 AAGCAATAGTGACGTTTATGAGGAAGCGCCGCTAAA-AGTCA
1 AAGCATTAGTGGCGTTTATGAGGAAGCGCCGCTAAAGA-TCA
*
33365731 AAGCATTAGTGGCGTTTATGAGGAAGCGCCGCTAAAGGTCA
1 AAGCATTAGTGGCGTTTATGAGGAAGCGCCGCTAAAGATCA
* *
33365772 AACCATTAGTGGCATTTATG-GGAAAGCGCCGCTAAAGATCA
1 AAGCATTAGTGGCGTTTATGAGG-AAGCGCCGCTAAAGATCA
* * *
33365813 GAGCATTAGCGGCGTTTATGAGTAAGCGCCGCTAAAG
1 AAGCATTAGTGGCGTTTATGAGGAAGCGCCGCTAAAG
33365850 GTTAGAGCTG
Statistics
Matches: 105, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
40 2 0.02
41 102 0.97
42 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
AAGCATTAGTGGCGTTTATGAGGAAGCGCCGCTAAAGATCA
Found at i:33365857 original size:41 final size:41
Alignment explanation
Indices: 33365683--33365905 Score: 210
Period size: 41 Copynumber: 5.6 Consensus size: 41
33365673 AAACGCCACA
* * * *
33365683 AAAGGTTA-AGCAATAGTGACGTTTATGAGGAAGCGCCGCT
1 AAAGGTCAGAGCATTAGTGGCGTTTATGAGAAAGCGCCGCT
* * *
33365723 AAAAGTCAAAGCATTAGTGGCGTTTATGAGGAAGCGCCGCT
1 AAAGGTCAGAGCATTAGTGGCGTTTATGAGAAAGCGCCGCT
* * * *
33365764 AAAGGTCAAACCATTAGTGGCATTTATGGGAAAGCGCCGCT
1 AAAGGTCAGAGCATTAGTGGCGTTTATGAGAAAGCGCCGCT
* * *
33365805 AAAGATCAGAGCATTAGCGGCGTTTATGAGTAAGCGCCGCT
1 AAAGGTCAGAGCATTAGTGGCGTTTATGAGAAAGCGCCGCT
* * *
33365846 AAAGGTTAGAGC-----T-GCGTTTATTAAAAAGCGCCGCT
1 AAAGGTCAGAGCATTAGTGGCGTTTATGAGAAAGCGCCGCT
* *
33365881 AAAAGT-AGGAGCATTAGCGGCGTTT
1 AAAGGTCA-GAGCATTAGTGGCGTTT
33365906 TTGATAAAAG
Statistics
Matches: 151, Mismatches: 24, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
34 1 0.01
35 28 0.19
40 6 0.04
41 116 0.77
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (41 bp):
AAAGGTCAGAGCATTAGTGGCGTTTATGAGAAAGCGCCGCT
Found at i:33375578 original size:63 final size:63
Alignment explanation
Indices: 33375479--33375604 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
33375469 TAAATACATA
*
33375479 CTTTTGCTTGTTCAAATTTGATTAGTTGCCTTACTTCCCCTTCCATACTTGTCTTTTAAAGGC
1 CTTTTGCTTGTTCAAATTTGATCAGTTGCCTTACTTCCCCTTCCATACTTGTCTTTTAAAGGC
33375542 CTTTTGCTTGTTCAAATTTGATCAGTTGCCTTACTTCCCCTTCCATACTTGTCTTTTAAAGGC
1 CTTTTGCTTGTTCAAATTTGATCAGTTGCCTTACTTCCCCTTCCATACTTGTCTTTTAAAGGC
33375605 TGAGGATAGA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.17, C:0.25, G:0.13, T:0.45
Consensus pattern (63 bp):
CTTTTGCTTGTTCAAATTTGATCAGTTGCCTTACTTCCCCTTCCATACTTGTCTTTTAAAGGC
Found at i:33381478 original size:19 final size:18
Alignment explanation
Indices: 33381454--33381524 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 18
33381444 AAAAATATAA
33381454 ATTTTGAATTTTTATAAAT
1 ATTTTGAATTTTTA-AAAT
* *
33381473 ATTTTGAAATTTAAAAATT
1 ATTTTGAATTTTTAAAA-T
* *
33381492 ATCTTGATTTTTTAAAGAT
1 ATTTTGAATTTTTAAA-AT
33381511 CATTTTGAATTTTT
1 -ATTTTGAATTTTT
33381525 TTTTTGTAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
18 3 0.07
19 26 0.63
20 12 0.29
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (18 bp):
ATTTTGAATTTTTAAAAT
Found at i:33381656 original size:7 final size:7
Alignment explanation
Indices: 33381644--33381684 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
33381634 AGCTCGACTT
33381644 AAACTCG
1 AAACTCG
33381651 AAACTCG
1 AAACTCG
33381658 AAACTCG
1 AAACTCG
33381665 AAACTCG
1 AAACTCG
33381672 AAACTCG
1 AAACTCG
33381679 AAACTC
1 AAACTC
33381685 AAATAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.44, C:0.29, G:0.12, T:0.15
Consensus pattern (7 bp):
AAACTCG
Found at i:33388119 original size:24 final size:24
Alignment explanation
Indices: 33388066--33388120 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
33388056 ATAATCTTTT
33388066 AGTTAAACCATGTTTAATTGTTTC
1 AGTTAAACCATGTTTAATTGTTTC
* * *
33388090 AATTAAACTC-TGTTTATTTGTTTG
1 AGTTAAAC-CATGTTTAATTGTTTC
33388114 AGTTAAA
1 AGTTAAA
33388121 TTTCTATTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.47
Consensus pattern (24 bp):
AGTTAAACCATGTTTAATTGTTTC
Done.