Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 8 of 410
Found at i:2082457 original size:18 final size:18
Alignment explanation
Indices: 2082419--2082463 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2082409 ATCGAAATAG
2082419 AAATCGAAAGCAAAATCA
1 AAATCGAAAGCAAAATCA
* * *
2082437 AAATCGAAAGTAAATTTA
1 AAATCGAAAGCAAAATCA
2082455 AAATCGAAA
1 AAATCGAAA
2082464 TATCCCTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.60, C:0.11, G:0.11, T:0.18
Consensus pattern (18 bp):
AAATCGAAAGCAAAATCA
Found at i:2086382 original size:28 final size:28
Alignment explanation
Indices: 2086346--2086432 Score: 113
Period size: 28 Copynumber: 3.1 Consensus size: 28
2086336 ATATCGCTAA
* *
2086346 ATCATATATAACATACATAAAGCGTTGG
1 ATCAAATATAACACACATAAAGCGTTGG
** *
2086374 ATCAAATATAACACACATAAAGCACTGA
1 ATCAAATATAACACACATAAAGCGTTGG
2086402 ATCAAATATAACACGA-ATAAAGCGTTGG
1 ATCAAATATAACAC-ACATAAAGCGTTGG
2086430 ATC
1 ATC
2086433 TTCCACCTAT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
28 49 0.98
29 1 0.02
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (28 bp):
ATCAAATATAACACACATAAAGCGTTGG
Found at i:2088632 original size:2 final size:2
Alignment explanation
Indices: 2088625--2088673 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2088615 ATCTCCATCC
2088625 TA TA TA TA 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 TA TA TA TA
2088667 TA TA TA T
1 TA TA TA T
2088674 GCCTTAATTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2089972 original size:54 final size:55
Alignment explanation
Indices: 2089897--2090016 Score: 161
Period size: 54 Copynumber: 2.1 Consensus size: 55
2089887 AATGATGCTA
* * *
2089897 GAAATTTAAGTGTAAGGATTAAATATCAAATTTAAGCATATT-AGGACTAAAATT
1 GAAATTAAAGTATAAGAATTAAATATCAAATTTAAGCATATTAAGGACTAAAATT
* *
2089951 GAAATTAAAGTATAAGAATTAAATCTCAAATTTAAGCATATTAAAAGGACTAAAGTT
1 GAAATTAAAGTATAAGAATTAAATATCAAATTTAAGCATATT--AAGGACTAAAATT
2090008 GAAAATTAA
1 G-AAATTAA
2090017 CCAATTTATA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
54 38 0.67
57 12 0.21
58 7 0.12
ACGTcount: A:0.50, C:0.06, G:0.13, T:0.31
Consensus pattern (55 bp):
GAAATTAAAGTATAAGAATTAAATATCAAATTTAAGCATATTAAGGACTAAAATT
Found at i:2091871 original size:21 final size:21
Alignment explanation
Indices: 2091845--2091888 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
2091835 ATTATTCTCG
*
2091845 ATATGCTTATACTTGATTTTA
1 ATATGCTTATACTCGATTTTA
2091866 ATATGCTTATACTCGATTTTA
1 ATATGCTTATACTCGATTTTA
2091887 AT
1 AT
2091889 CGTGTGTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (21 bp):
ATATGCTTATACTCGATTTTA
Found at i:2095300 original size:21 final size:21
Alignment explanation
Indices: 2095274--2095313 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2095264 TTCAATTAAG
2095274 TTTTTTAGATTCAT-TTTATGT
1 TTTTTTA-ATTCATGTTTATGT
2095295 TTTTTTAATTCATGTTTAT
1 TTTTTTAATTCATGTTTAT
2095314 TTATTTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (21 bp):
TTTTTTAATTCATGTTTATGT
Found at i:2095528 original size:2 final size:2
Alignment explanation
Indices: 2095516--2095549 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2095506 ATTTATTCAC
*
2095516 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2095550 TTGTTGTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2095853 original size:23 final size:21
Alignment explanation
Indices: 2095827--2095870 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
2095817 TGTTTTGTGA
*
2095827 ATCAATTATGTGTATTATATCTT
1 ATCAAGTATGT-TATTAT-TCTT
*
2095850 ATCACGTATGTTATTATTCTT
1 ATCAAGTATGTTATTATTCTT
2095871 TCATATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 6 0.32
23 9 0.47
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.52
Consensus pattern (21 bp):
ATCAAGTATGTTATTATTCTT
Found at i:2096698 original size:19 final size:19
Alignment explanation
Indices: 2096674--2096732 Score: 118
Period size: 19 Copynumber: 3.1 Consensus size: 19
2096664 TGAACTATTC
2096674 ACACATTTTAAAGAACCAT
1 ACACATTTTAAAGAACCAT
2096693 ACACATTTTAAAGAACCAT
1 ACACATTTTAAAGAACCAT
2096712 ACACATTTTAAAGAACCAT
1 ACACATTTTAAAGAACCAT
2096731 AC
1 AC
2096733 TTTGAAAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.47, C:0.22, G:0.05, T:0.25
Consensus pattern (19 bp):
ACACATTTTAAAGAACCAT
Found at i:2097059 original size:23 final size:23
Alignment explanation
Indices: 2097028--2097075 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2097018 GACTAGTTTT
*
2097028 AACAAATGGAAAACATAGAAAAA
1 AACAAATGGAAAACAAAGAAAAA
* *
2097051 AACAGATGGAAAATAAAGAAAAA
1 AACAAATGGAAAACAAAGAAAAA
2097074 AA
1 AA
2097076 AAAGAAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.71, C:0.06, G:0.15, T:0.08
Consensus pattern (23 bp):
AACAAATGGAAAACAAAGAAAAA
Found at i:2106896 original size:25 final size:24
Alignment explanation
Indices: 2106868--2106929 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
2106858 TTATATTTAG
*
2106868 TTTTATGTTCAATTTGATACTTGAA
1 TTTTAT-TTCAATTTGATACTTAAA
* *
2106893 TTTTTTTTCTAATTTGGTACTTAAA
1 TTTTATTTC-AATTTGATACTTAAA
*
2106918 TTTGATTTCAAT
1 TTTTATTTCAAT
2106930 GTTCAATTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 6 0.19
25 25 0.81
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (24 bp):
TTTTATTTCAATTTGATACTTAAA
Found at i:2107378 original size:18 final size:18
Alignment explanation
Indices: 2107357--2107462 Score: 72
Period size: 18 Copynumber: 5.6 Consensus size: 18
2107347 TTCAAGTACA
2107357 AAATTAAATATTAAATTT
1 AAATTAAATATTAAATTT
*
2107375 AAATTTAAATATT-TATTT
1 AAA-TTAAATATTAAATTT
** *
2107393 GAGATAAAAAAAATTTAAATATT
1 -A-A-ATTAAATA-TTAAAT-TT
* *
2107416 AAATTAAACATTAAAATT
1 AAATTAAATATTAAATTT
2107434 AAATTCAAATATTAAA-TT
1 AAATT-AAATATTAAATTT
2107452 AAATATAAATA
1 AAAT-TAAATA
2107463 CCAGCGTGTT
Statistics
Matches: 69, Mismatches: 10, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
18 25 0.36
19 25 0.36
20 10 0.14
21 4 0.06
22 3 0.04
23 2 0.03
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (18 bp):
AAATTAAATATTAAATTT
Found at i:2107876 original size:31 final size:30
Alignment explanation
Indices: 2107806--2107908 Score: 102
Period size: 31 Copynumber: 3.3 Consensus size: 30
2107796 AAAATATTAA
* ***
2107806 ATTTACATATAAATTTTAA-TTTAATACGT
1 ATTTATATATAAATTTTAATTTTAATTTAT
2107835 AGTTTGATATATAAATTTTAATTTGTAATTTAT
1 A-TTT-ATATATAAATTTTAATTT-TAATTTAT
*
2107868 ATTTATATATGAAATTTTGATTTTAATTTA-
1 ATTTATATAT-AAATTTTAATTTTAATTTAT
2107898 ATTATATATAT
1 ATT-TATATAT
2107909 TTAAATAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
29 1 0.02
30 6 0.10
31 34 0.54
32 16 0.25
33 6 0.10
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (30 bp):
ATTTATATATAAATTTTAATTTTAATTTAT
Found at i:2113272 original size:29 final size:29
Alignment explanation
Indices: 2113220--2113299 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 29
2113210 CACAAATTTT
* *
2113220 ATTTGATTGAATTTTATCACTAAAATTTGA-A
1 ATTT-ATTGAATTTTGT-ATTAAAATTT-ACA
*
2113251 ATTTATTTAATTTTGTATT-AAATTTATCA
1 ATTTATTGAATTTTGTATTAAAATTTA-CA
*
2113280 CTTTATTGAATTTTGTATTA
1 ATTTATTGAATTTTGTATTA
2113300 TAACTTATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
27 1 0.02
28 6 0.15
29 20 0.49
30 10 0.24
31 4 0.10
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (29 bp):
ATTTATTGAATTTTGTATTAAAATTTACA
Found at i:2118836 original size:39 final size:39
Alignment explanation
Indices: 2118659--2118820 Score: 279
Period size: 39 Copynumber: 4.2 Consensus size: 39
2118649 GCTTTGATGA
* * *
2118659 GCTTCAATTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCAGGCTTCCGTTTAACACTTGTGT
2118698 GCTTCAGTTAGCCTTCAGGCTTCCGTTTAACACTTGTGT
1 GCTTCAGTTAGCCTTCAGGCTTCCGTTTAACACTTGTGT
2118737 GCTTCAGTTAGCCTTCAGGCTTCCGTTTAACACTTGTGT
1 GCTTCAGTTAGCCTTCAGGCTTCCGTTTAACACTTGTGT
* *
2118776 GCTTCAGTTAGCCTTCAGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCAGGCTTCCGTTTAACACTTGTGT
2118815 GCTTCA
1 GCTTCA
2118821 ACTAGACTTC
Statistics
Matches: 118, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 118 1.00
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.38
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCAGGCTTCCGTTTAACACTTGTGT
Found at i:2126399 original size:20 final size:20
Alignment explanation
Indices: 2126371--2126411 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2126361 ATTGTTGGTA
* *
2126371 TTTTATTTTGGTCATTAAAT
1 TTTTATTTTAGACATTAAAT
*
2126391 TTTTTTTTTAGACATTAAAT
1 TTTTATTTTAGACATTAAAT
2126411 T
1 T
2126412 ATTTGAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.61
Consensus pattern (20 bp):
TTTTATTTTAGACATTAAAT
Found at i:2128583 original size:43 final size:43
Alignment explanation
Indices: 2128535--2128620 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
2128525 ATTATCGAGA
2128535 AAGCCAATGCCATGGTGAAGGACATACTGAAGGAGGTGCCTAC
1 AAGCCAATGCCATGGTGAAGGACATACTGAAGGAGGTGCCTAC
2128578 AAGCCAATGCCATGGTGAAGGACATACTGAAGGAGGTGCCTAC
1 AAGCCAATGCCATGGTGAAGGACATACTGAAGGAGGTGCCTAC
2128621 CTACTTAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.33, C:0.21, G:0.30, T:0.16
Consensus pattern (43 bp):
AAGCCAATGCCATGGTGAAGGACATACTGAAGGAGGTGCCTAC
Found at i:2137375 original size:31 final size:30
Alignment explanation
Indices: 2137338--2137400 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 30
2137328 ACATATTTCG
*
2137338 TCGTCGATTTAAACTCATC-CTTAACATATAT
1 TCGTCGATCTAAACTCATCTC-TAACATA-AT
2137369 TCGTCGATCTAAACTCATCTCTAACATAAT
1 TCGTCGATCTAAACTCATCTCTAACATAAT
2137399 TC
1 TC
2137401 AACGTCAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 4 0.13
31 25 0.83
32 1 0.03
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (30 bp):
TCGTCGATCTAAACTCATCTCTAACATAAT
Found at i:2138854 original size:2 final size:2
Alignment explanation
Indices: 2138849--2138873 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2138839 TGGAGGAAGA
2138849 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 A
2138874 AAGGCAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2139980 original size:16 final size:16
Alignment explanation
Indices: 2139959--2140000 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
2139949 AATTAAGGGT
2139959 AAAATTTAAATTAAAA
1 AAAATTTAAATTAAAA
**
2139975 AAAA-TTAAATTTTAA
1 AAAATTTAAATTAAAA
*
2139990 AAAATGTAAAT
1 AAAATTTAAAT
2140001 GTTAAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
AAAATTTAAATTAAAA
Found at i:2140005 original size:16 final size:15
Alignment explanation
Indices: 2139973--2140014 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
2139963 TTTAAATTAA
*
2139973 AAAAAATTAAATTTT
1 AAAAAATTAAATGTT
2139988 AAAAAATGTAAATGTT
1 AAAAAAT-TAAATGTT
2140004 -AAAAATTAAAT
1 AAAAAATTAAAT
2140015 TATTTTAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 5 0.20
15 13 0.52
16 7 0.28
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (15 bp):
AAAAAATTAAATGTT
Found at i:2142267 original size:12 final size:12
Alignment explanation
Indices: 2142250--2142282 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
2142240 CAATGTAATC
2142250 TAATTGTTGGTG
1 TAATTGTTGGTG
2142262 TAATTGTTGGTG
1 TAATTGTTGGTG
*
2142274 TAAATGTTG
1 TAATTGTTG
2142283 CGACTGAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.48
Consensus pattern (12 bp):
TAATTGTTGGTG
Found at i:2145206 original size:11 final size:11
Alignment explanation
Indices: 2145176--2145208 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2145166 ATGAGAATAT
*
2145176 AAATATATTTA
1 AAATATATTAA
2145187 AAATA-ATTAA
1 AAATATATTAA
2145197 AAATATATTAA
1 AAATATATTAA
2145208 A
1 A
2145209 TATTAAGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AAATATATTAA
Found at i:2146663 original size:16 final size:17
Alignment explanation
Indices: 2146642--2146674 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2146632 ATAATTTAAC
2146642 TTATTTTATTAT-AGAT
1 TTATTTTATTATGAGAT
*
2146658 TTATTTTTTTATGAGAT
1 TTATTTTATTATGAGAT
2146675 GTAAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (17 bp):
TTATTTTATTATGAGAT
Found at i:2157299 original size:2 final size:2
Alignment explanation
Indices: 2157294--2157340 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2157284 CCATATTCTA
2157294 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2157336 AC AC A
1 AC AC A
2157341 TATATATATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2157345 original size:2 final size:2
Alignment explanation
Indices: 2157340--2157380 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2157330 ACACACACAC
2157340 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
2157381 CATACATTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2158011 original size:18 final size:19
Alignment explanation
Indices: 2157981--2158031 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
2157971 CATTTTCTGT
*
2157981 TATT-TATTAATTATAATA
1 TATTATATTTATTATAATA
*
2157999 T-TTATATTTATTAT-ATT
1 TATTATATTTATTATAATA
*
2158016 TATTGTATTTATTATA
1 TATTATATTTATTATA
2158032 TGTCTTAGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TATTATATTTATTATAATA
Found at i:2158012 original size:9 final size:9
Alignment explanation
Indices: 2158000--2158032 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
2157990 ATTATAATAT
2158000 TTATATTTA
1 TTATATTTA
2158009 TTATATTTA
1 TTATATTTA
*
2158018 TTGTATTTA
1 TTATATTTA
2158027 TTATAT
1 TTATAT
2158033 GTCTTAGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (9 bp):
TTATATTTA
Found at i:2158014 original size:15 final size:16
Alignment explanation
Indices: 2157981--2158032 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
2157971 CATTTTCTGT
* *
2157981 TATTTATTAATTATAA
1 TATTTATTATTTATTA
2157997 TATTTA-TATTTATTA
1 TATTTATTATTTATTA
2158012 TATTTATTGTATTTATTA
1 TATTTA-T-TATTTATTA
2158030 TAT
1 TAT
2158033 GTCTTAGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 13 0.42
16 6 0.19
18 12 0.39
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TATTTATTATTTATTA
Found at i:2158182 original size:34 final size:34
Alignment explanation
Indices: 2158108--2158183 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 34
2158098 ATGATTTTTT
* * *
2158108 TATATATTATATATATGTATTTAATATTATGTTA
1 TATATATTATATACATATATTTAATATTATGTAA
2158142 TATATATTATATACATATATTTTCAATATTAT-TAA
1 TATATATTATATACATATA-TTT-AATATTATGTAA
2158177 T-TATATT
1 TATATATT
2158184 TTCTTATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 23 0.62
35 6 0.16
36 8 0.22
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (34 bp):
TATATATTATATACATATATTTAATATTATGTAA
Found at i:2159064 original size:2 final size:2
Alignment explanation
Indices: 2159057--2159081 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2159047 TATCACTACT
2159057 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 T
2159082 GTTTTGACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2160926 original size:30 final size:33
Alignment explanation
Indices: 2160872--2160937 Score: 84
Period size: 30 Copynumber: 2.1 Consensus size: 33
2160862 ATTTTAAATT
*
2160872 AATAAAAATAAAATTATATATTAATTCTCTAAA
1 AATAAAAATAAAATTATATATTAATCCTCTAAA
* *
2160905 AATAATAA-AAAATTA-AT-TTAATCCTTTAAA
1 AATAAAAATAAAATTATATATTAATCCTCTAAA
2160935 AAT
1 AAT
2160938 TATATAGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 14 0.47
31 2 0.07
32 7 0.23
33 7 0.23
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (33 bp):
AATAAAAATAAAATTATATATTAATCCTCTAAA
Found at i:2162485 original size:18 final size:19
Alignment explanation
Indices: 2162454--2162492 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
2162444 ATATAGTTCC
*
2162454 ATATTATTACATCATTTCAT
1 ATATTATTA-ATCAATTCAT
2162474 ATATTATT-ATCAATTCAT
1 ATATTATTAATCAATTCAT
2162492 A
1 A
2162493 ATTTCATACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTATTAATCAATTCAT
Found at i:2164275 original size:11 final size:11
Alignment explanation
Indices: 2164259--2164285 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2164249 CTTAACTGAA
2164259 CTTCAATAGAT
1 CTTCAATAGAT
2164270 CTTCAATAGAT
1 CTTCAATAGAT
2164281 CTTCA
1 CTTCA
2164286 TAATGTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.37
Consensus pattern (11 bp):
CTTCAATAGAT
Found at i:2173320 original size:105 final size:101
Alignment explanation
Indices: 2173139--2173332 Score: 246
Period size: 105 Copynumber: 1.9 Consensus size: 101
2173129 AATTGACGGA
* * * **
2173139 TAAGACCATGGTTGGACCATGGCAATGTTTGAATGTAAGACCATAGTTGGGCTATGCCATTTTAA
1 TAAGACCATGGTTGGACCATGGCAATATATGAATGTAAGACCATAGCTGGGCTATGCCATCCTAA
*
2173204 TGAAAATACCATAACTGA-GTTATGACACCTTGAACT
66 TGAAAAGACCATAACT-ACGTTATGACACCTTGAACT
* *
2173240 TAAGACCATGGTTGGACCATGGCAGTATATGTATACGTGTAAGACCATAGCTGGGCTATGGCATC
1 TAAGACCATGGTTGGACCATGGCAATATATG-A-A--TGTAAGACCATAGCTGGGCTATGCCATC
* *
2173305 CTGATGATAAGACCATAACTACGTTATG
62 CTAATGAAAAGACCATAACTACGTTATG
2173333 GCATTAAGAG
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
101 28 0.36
102 1 0.01
103 1 0.01
104 1 0.01
105 47 0.60
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGGCAATATATGAATGTAAGACCATAGCTGGGCTATGCCATCCTAA
TGAAAAGACCATAACTACGTTATGACACCTTGAACT
Found at i:2173349 original size:105 final size:100
Alignment explanation
Indices: 2173139--2173370 Score: 236
Period size: 105 Copynumber: 2.3 Consensus size: 100
2173129 AATTGACGGA
* * * **
2173139 TAAGACCATGGTTGGACCATGGCAATGTTTGAATGTAAGACCATAGTTGGGCTATGCCATTTTAA
1 TAAGACCATGGTTGGACCATGGCAATATATGAATGTAAGACCATAGCTGGGCTATGCCATCCTAA
* *
2173204 TGAAAATACCATAACTGAGTTATGACACCTTGAACT
66 TGAAAAGACCATAACTGAGTTATGACA-CTTAAACT
* *
2173240 TAAGACCATGGTTGGACCATGGCAGTATATGTATACGTGTAAGACCATAGCTGGGCTATGGCATC
1 TAAGACCATGGTTGGACCATGGCAATATATG-A-A--TGTAAGACCATAGCTGGGCTATGCCATC
* * * *
2173305 CTGATGATAAGACCATAACT-ACGTTATGGCA-TTAAGAGT
62 CTAATGAAAAGACCATAACTGA-GTTATGACACTTAA-ACT
*
2173344 GTAAGACCATGG-TAGAGCCATGGCAAT
1 -TAAGACCATGGTTGGA-CCATGGCAAT
2173371 TTTGTAAGAC
Statistics
Matches: 108, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
101 28 0.26
102 1 0.01
103 4 0.04
104 6 0.06
105 69 0.64
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (100 bp):
TAAGACCATGGTTGGACCATGGCAATATATGAATGTAAGACCATAGCTGGGCTATGCCATCCTAA
TGAAAAGACCATAACTGAGTTATGACACTTAAACT
Found at i:2173834 original size:2 final size:2
Alignment explanation
Indices: 2173827--2173852 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2173817 TGAATGATAC
2173827 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2173853 TTGTATGCAT
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):
AT
Found at i:2180426 original size:26 final size:26
Alignment explanation
Indices: 2180389--2180439 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
2180379 TGAGAGGATA
*
2180389 GCAAGGGAAGCTCGCAAACCTAGCTT
1 GCAAGGGAAGCTCACAAACCTAGCTT
*
2180415 GCAAGAGG-AGCTCACAGACCTAGCT
1 GCAAG-GGAAGCTCACAAACCTAGCT
2180440 CACAAGGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.31, C:0.27, G:0.27, T:0.14
Consensus pattern (26 bp):
GCAAGGGAAGCTCACAAACCTAGCTT
Found at i:2180445 original size:26 final size:26
Alignment explanation
Indices: 2180397--2180453 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
2180387 TAGCAAGGGA
* **
2180397 AGCTCGCAAACCTAGCTTGCAA-GAGG
1 AGCTCACAAACCTAGCTCACAAGGA-G
*
2180423 AGCTCACAGACCTAGCTCACAAGGAG
1 AGCTCACAAACCTAGCTCACAAGGAG
2180449 AGCTC
1 AGCTC
2180454 GCGTGAACCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.32, C:0.30, G:0.25, T:0.14
Consensus pattern (26 bp):
AGCTCACAAACCTAGCTCACAAGGAG
Found at i:2182412 original size:18 final size:19
Alignment explanation
Indices: 2182355--2182413 Score: 81
Period size: 18 Copynumber: 3.3 Consensus size: 19
2182345 AAATTAGTAT
2182355 ATTATTAATACATAATATA
1 ATTATTAATACATAATATA
2182374 A-TATTAATACAT-ATATA
1 ATTATTAATACATAATATA
2182391 ATTATTAA-A-ATAATATA
1 ATTATTAATACATAATATA
2182408 GATTAT
1 -ATTAT
2182414 AAAAATACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
16 2 0.05
17 12 0.32
18 22 0.59
19 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (19 bp):
ATTATTAATACATAATATA
Found at i:2182425 original size:19 final size:20
Alignment explanation
Indices: 2182379--2182426 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
2182369 ATATAATATT
*
2182379 AATACATATATAATTATTAA
1 AATACATATATAATTATAAA
*
2182399 AATA-ATATA-GATTATAAA
1 AATACATATATAATTATAAA
2182417 AATACATATA
1 AATACATATA
2182427 CTATTATATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 11 0.44
19 10 0.40
20 4 0.16
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.35
Consensus pattern (20 bp):
AATACATATATAATTATAAA
Found at i:2182795 original size:16 final size:16
Alignment explanation
Indices: 2182753--2182795 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2182743 ATAAATTATT
2182753 ATATTTAAAA-TTAAA
1 ATATTTAAAATTTAAA
*
2182768 ATATTTATAATTTATAA
1 ATATTTAAAATTTA-AA
2182785 AT-TTTAAAATT
1 ATATTTAAAATT
2182796 ATCTTAATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 9 0.38
16 11 0.46
17 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATTTAAAATTTAAA
Found at i:2183372 original size:22 final size:22
Alignment explanation
Indices: 2183347--2183392 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2183337 TATTTCAACT
*
2183347 TTAAAAAA-TTATAAAATAATTA
1 TTAAAAAATTTA-AAAAAAATTA
*
2183369 TTAAAATATTTAAAAAAAATTA
1 TTAAAAAATTTAAAAAAAATTA
2183391 TT
1 TT
2183393 TCTTTTATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TTAAAAAATTTAAAAAAAATTA
Found at i:2183767 original size:30 final size:30
Alignment explanation
Indices: 2183698--2183767 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
2183688 AGAACTTAAC
* *
2183698 AATTTATTGACTTAATAAAAACTTTTGAAT
1 AATTTAATGACTTAATAAAAACTTTTAAAT
* * *
2183728 AAGTCAATGACTTAATGAAAA-TTTCTAAAT
1 AATTTAATGACTTAATAAAAACTTT-TAAAT
2183758 AATTTAATGA
1 AATTTAATGA
2183768 TAGTTTTGTA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
29 3 0.09
30 29 0.91
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.39
Consensus pattern (30 bp):
AATTTAATGACTTAATAAAAACTTTTAAAT
Found at i:2189795 original size:38 final size:37
Alignment explanation
Indices: 2189741--2189815 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
2189731 TTCTTTCTTC
*
2189741 TTCTTTTTATATTTTTTTAAGTTTTGTCC-TATCTATTT
1 TTCTTTTTATAATTTTTTAA-TTTT-TCCTTATCTATTT
* *
2189779 TTCTTTTTTTAATTTTTTAATTTTTCCTTATTTATTT
1 TTCTTTTTATAATTTTTTAATTTTTCCTTATCTATTT
2189816 ATTTTATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 3 0.09
37 12 0.36
38 18 0.55
ACGTcount: A:0.16, C:0.09, G:0.03, T:0.72
Consensus pattern (37 bp):
TTCTTTTTATAATTTTTTAATTTTTCCTTATCTATTT
Found at i:2189801 original size:23 final size:23
Alignment explanation
Indices: 2189775--2189826 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
2189765 TGTCCTATCT
* *
2189775 ATTTTTCTTTTTTTAATTT-TTTA
1 ATTTTTCCTTATTT-ATTTATTTA
*
2189798 ATTTTTCCTTATTTATTTATTTT
1 ATTTTTCCTTATTTATTTATTTA
2189821 ATTTTT
1 ATTTTT
2189827 AGGGACAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (23 bp):
ATTTTTCCTTATTTATTTATTTA
Found at i:2191723 original size:20 final size:20
Alignment explanation
Indices: 2191695--2191736 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2191685 AAGATTAAAA
* *
2191695 TTAATAAATAAATAATTGTT
1 TTAAAAAATAAATAATTATT
*
2191715 TTAAAAAATCAATAATTATT
1 TTAAAAAATAAATAATTATT
2191735 TT
1 TT
2191737 TATAAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (20 bp):
TTAAAAAATAAATAATTATT
Found at i:2195470 original size:36 final size:36
Alignment explanation
Indices: 2195430--2195507 Score: 147
Period size: 36 Copynumber: 2.2 Consensus size: 36
2195420 TTTACTCATT
*
2195430 TCAATTTTTGGGGTTTGCTTCAATTGTAATATATAA
1 TCAATTTTTGGGGTTTGCTTCAATTATAATATATAA
2195466 TCAATTTTTGGGGTTTGCTTCAATTATAATATATAA
1 TCAATTTTTGGGGTTTGCTTCAATTATAATATATAA
2195502 TCAATT
1 TCAATT
2195508 GAGTCTTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.47
Consensus pattern (36 bp):
TCAATTTTTGGGGTTTGCTTCAATTATAATATATAA
Found at i:2196108 original size:36 final size:35
Alignment explanation
Indices: 2196044--2196113 Score: 86
Period size: 36 Copynumber: 2.0 Consensus size: 35
2196034 CCCCTAAAAT
* * *
2196044 GTAAAATTACATTTTAACTCCTTTAAATTAGTAAAG
1 GTAAAATTACACTTTAACCCCTTAAAATTA-TAAAG
**
2196080 GTAAAATTACACTTTGGCCCCTTAAAATTATAAA
1 GTAAAATTACACTTTAACCCCTTAAAATTATAAA
2196114 AATTTGATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
35 4 0.14
36 25 0.86
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (35 bp):
GTAAAATTACACTTTAACCCCTTAAAATTATAAAG
Found at i:2197226 original size:21 final size:22
Alignment explanation
Indices: 2197202--2197252 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
2197192 TCATGGATAC
2197202 TTAAAAAAAAATTTT-GAATAG
1 TTAAAAAAAAATTTTCGAATAG
*
2197223 TTAAATAAAAATTTTCGAATAG
1 TTAAAAAAAAATTTTCGAATAG
*
2197245 TTCAAAAA
1 TTAAAAAA
2197253 TTAAATTGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.55, C:0.04, G:0.08, T:0.33
Consensus pattern (22 bp):
TTAAAAAAAAATTTTCGAATAG
Found at i:2201011 original size:15 final size:16
Alignment explanation
Indices: 2200970--2201011 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
2200960 TTAATAAATG
2200970 AAAAATATATAATTATT
1 AAAAATATA-AATTATT
*
2200987 AAATAT-TAAATT-TT
1 AAAAATATAAATTATT
2201001 AAAAATATAAA
1 AAAAATATAAA
2201012 CATTTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 7 0.32
15 8 0.36
16 2 0.09
17 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAAATATAAATTATT
Found at i:2201022 original size:17 final size:16
Alignment explanation
Indices: 2200970--2201027 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 16
2200960 TTAATAAATG
*
2200970 AAAAATATATAATTATT
1 AAAAATATAAAATT-TT
*
2200987 --AAATATTAAATTTT
1 AAAAATATAAAATTTT
2201001 AAAAATATAAACATTTTT
1 AAAAATATAAA-A-TTTT
2201019 AAAAA-ATAA
1 AAAAATATAA
2201028 TATGGGATGG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
14 2 0.06
15 10 0.29
16 8 0.24
17 5 0.15
18 9 0.26
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAAATATAAAATTTT
Found at i:2202680 original size:54 final size:55
Alignment explanation
Indices: 2202610--2202741 Score: 178
Period size: 54 Copynumber: 2.4 Consensus size: 55
2202600 AATATGCTTG
* **
2202610 AGATTTAAT-TCTTATACTTTAATTTCAATTTTAGTCTTAATATGC-TCAAATTTA
1 AGATTTAATCT-TTATACTTTAATTTCAATTTTAGCCACAATATGCTTCAAATTTA
* * *
2202664 ATATTTAATCTTTATACTTTAATTTCAATTTTAGCCACAATATGCTTTATATTTA
1 AGATTTAATCTTTATACTTTAATTTCAATTTTAGCCACAATATGCTTCAAATTTA
*
2202719 AGATTTAATCCTTATACTTTAAT
1 AGATTTAATCTTTATACTTTAAT
2202742 CTTTTAACAT
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
54 39 0.57
55 29 0.43
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (55 bp):
AGATTTAATCTTTATACTTTAATTTCAATTTTAGCCACAATATGCTTCAAATTTA
Found at i:2205947 original size:26 final size:26
Alignment explanation
Indices: 2205917--2206024 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
2205907 TGAAATTCCC
2205917 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
2205943 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
2205969 ATCATGAAACATTTGCCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
2205995 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
2206021 ATCA
1 ATCA
2206025 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.35, C:0.27, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:2208012 original size:40 final size:40
Alignment explanation
Indices: 2207938--2208159 Score: 331
Period size: 40 Copynumber: 5.6 Consensus size: 40
2207928 AACCCAAGTA
* * *
2207938 CCTTCGGGATTTAG-CCGGATAT-AGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAA-TAGCACAAATG
* * *
2207977 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
*
2208017 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
2208057 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
* *
2208097 CCTTCGGGACTTAGCCCGGATATAATCACTAGCATAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
*
2208137 CCTTCGGGACTTAACCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
2208160 CATTCGAATA
Statistics
Matches: 167, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
39 12 0.07
40 152 0.91
41 3 0.02
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
Found at i:2219544 original size:17 final size:18
Alignment explanation
Indices: 2219518--2219552 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2219508 TATTTGGATA
2219518 GATAAATATAAAA-AATG
1 GATAAATATAAAATAATG
*
2219535 GATAAGTATAAAATAATG
1 GATAAATATAAAATAATG
2219553 TTTTTACTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (18 bp):
GATAAATATAAAATAATG
Found at i:2220289 original size:17 final size:17
Alignment explanation
Indices: 2220269--2220305 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
2220259 TTCAATTAAT
2220269 ATTAATAAAAATATTTA
1 ATTAATAAAAATATTTA
2220286 ATT-ATAAAAATATTTA
1 ATTAATAAAAATATTTA
2220302 ATTA
1 ATTA
2220306 TTATTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.84
17 3 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTAATAAAAATATTTA
Found at i:2220294 original size:16 final size:16
Alignment explanation
Indices: 2220273--2220306 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2220263 ATTAATATTA
2220273 ATAAAAATATTTAATT
1 ATAAAAATATTTAATT
2220289 ATAAAAATATTTAATT
1 ATAAAAATATTTAATT
2220305 AT
1 AT
2220307 TATTAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAAAAATATTTAATT
Found at i:2224903 original size:5 final size:6
Alignment explanation
Indices: 2224874--2224909 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
2224864 GTTCTTAAAT
*
2224874 TAAAACA TAAAAG TAAAAA TAAAAA TAAAAA TAAAA
1 TAAAA-A TAAAAA TAAAAA TAAAAA TAAAAA TAAAA
2224910 GAGCCCTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:2231928 original size:18 final size:19
Alignment explanation
Indices: 2231888--2231933 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
2231878 CATTAATTAT
2231888 ATTTTAAATATGTATTTAG
1 ATTTTAAATATGTATTTAG
2231907 ATTTT-AATAGTGTATTTA-
1 ATTTTAAATA-TGTATTTAG
2231925 ATTTATAAA
1 ATTT-TAAA
2231934 AAAATTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 8 0.33
19 14 0.58
20 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (19 bp):
ATTTTAAATATGTATTTAG
Found at i:2232679 original size:31 final size:31
Alignment explanation
Indices: 2232610--2232682 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
2232600 ACCTAAACAT
* *
2232610 AGATATCAAATTAGAACAAAAAAATAAATTT
1 AGATACCAAATTAGAACAAAAAAATAAATTC
* *
2232641 A-AGTACCAAATT-GAACATTAAAATTAAATTC
1 AGA-TACCAAATTAGAACA-AAAAAATAAATTC
2232672 AGATACCAAAT
1 AGATACCAAAT
2232683 AATATATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
30 6 0.17
31 28 0.80
32 1 0.03
ACGTcount: A:0.56, C:0.11, G:0.07, T:0.26
Consensus pattern (31 bp):
AGATACCAAATTAGAACAAAAAAATAAATTC
Found at i:2233970 original size:3 final size:3
Alignment explanation
Indices: 2233962--2233997 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
2233952 ATCTTTATTT
*
2233962 TTC TTC TTC TTC TTC TTC TTC TTT TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2233998 ATTGAAGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:2237290 original size:127 final size:127
Alignment explanation
Indices: 2236927--2237255 Score: 480
Period size: 127 Copynumber: 2.6 Consensus size: 127
2236917 GAAAATTCCT
* ** *
2236927 TAAAACGAAGGCAAAGTTTGATGTTTAGAAATTCGAGGAATCGTGCCCTATCGTGCTGGGTTTCG
1 TAAAAC-AAGGCAATGTTCAATGTTTGGAAATTCGAGGAATCGTGCCCTATCGTGCTGGGTTTCG
* *
2236992 ATTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTCGTGTTTTTCAAATTC
65 ATTTCTCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTCGTATTTTTCAAATTC
* * * **
2237055 TAAAACGAGGCAATGTTCAACGTTTGGAAACTCGAGGAATCGTGCCCTATCGTGCTGGGTTTAAA
1 TAAAACAAGGCAATGTTCAATGTTTGGAAATTCGAGGAATCGTGCCCTATCGTGCTGGGTTTCGA
* *
2237120 TTTCTGGTTTGTTCAAAATAATTGAATATTCCTTTAGAATTTCACTCGTATTTTAT-AAATTC
66 TTTCTCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTCGTATTTT-TCAAATTC
* * *
2237182 TAAAGCAAGGCAATGTTCAATGTTTGGAAATTCGAGGAATCGTGCCCTACCGTGCTGGGTTTCGG
1 TAAAACAAGGCAATGTTCAATGTTTGGAAATTCGAGGAATCGTGCCCTATCGTGCTGGGTTTCGA
*
2237247 TTTTTCGTT
66 TTTCTCGTT
2237256 GGACTAAATA
Statistics
Matches: 177, Mismatches: 23, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
127 170 0.96
128 7 0.04
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (127 bp):
TAAAACAAGGCAATGTTCAATGTTTGGAAATTCGAGGAATCGTGCCCTATCGTGCTGGGTTTCGA
TTTCTCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTCGTATTTTTCAAATTC
Found at i:2245074 original size:21 final size:21
Alignment explanation
Indices: 2245049--2245116 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
2245039 ATAATGATTG
2245049 TTATTATGGTTTTATATTAAA
1 TTATTATGGTTTTATATTAAA
**
2245070 TTATTATAATTATTA-ATT-AA
1 TTATTATGGTT-TTATATTAAA
* *
2245090 -CATTATGGTTTTATATTAGA
1 TTATTATGGTTTTATATTAAA
2245110 TTATTAT
1 TTATTAT
2245117 TATTAGCATT
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
18 3 0.08
19 10 0.28
20 3 0.08
21 17 0.47
22 3 0.08
ACGTcount: A:0.35, C:0.01, G:0.07, T:0.56
Consensus pattern (21 bp):
TTATTATGGTTTTATATTAAA
Found at i:2245129 original size:15 final size:14
Alignment explanation
Indices: 2245103--2245133 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
2245093 TATGGTTTTA
2245103 TATTAGATTATTAT
1 TATTAGATTATTAT
2245117 TATTAGCATTATTAT
1 TATTAG-ATTATTAT
2245132 TA
1 TA
2245134 AATAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (14 bp):
TATTAGATTATTAT
Found at i:2245472 original size:14 final size:14
Alignment explanation
Indices: 2245448--2245480 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2245438 AAGAATTAAG
2245448 GAAACAAAGAAACA
1 GAAACAAAGAAACA
2245462 -AAACAAAAGAAACA
1 GAAAC-AAAGAAACA
2245476 GAAAC
1 GAAAC
2245481 GAATCAGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.24
14 9 0.53
15 4 0.24
ACGTcount: A:0.73, C:0.15, G:0.12, T:0.00
Consensus pattern (14 bp):
GAAACAAAGAAACA
Found at i:2251416 original size:24 final size:22
Alignment explanation
Indices: 2251380--2251430 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 22
2251370 ATTTTAAATG
*
2251380 TTTAATTACTTTTAGTTTAATTAA
1 TTTAATTAATTTTAGTTT--TTAA
2251404 TTTAATTAATTTTAGTTTTTAA
1 TTTAATTAATTTTAGTTTTTAA
2251426 TTTAA
1 TTTAA
2251431 CATAATGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 9 0.35
24 17 0.65
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (22 bp):
TTTAATTAATTTTAGTTTTTAA
Found at i:2253938 original size:30 final size:30
Alignment explanation
Indices: 2253897--2253954 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
2253887 CATGGGCTGC
* *
2253897 CATATGGGCGTGTGGCT-AGCCCGTGTGGCT
1 CATACGGGCGTGT-GCTCAACCCGTGTGGCT
2253927 CATACGGGCGTGTGCTCAACCCGTGTGG
1 CATACGGGCGTGTGCTCAACCCGTGTGG
2253955 AAACTGCCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 22 0.88
ACGTcount: A:0.12, C:0.26, G:0.38, T:0.24
Consensus pattern (30 bp):
CATACGGGCGTGTGCTCAACCCGTGTGGCT
Found at i:2263870 original size:11 final size:11
Alignment explanation
Indices: 2263856--2263882 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2263846 AATATTAAAA
2263856 ATATATAGAAC
1 ATATATAGAAC
2263867 ATATATAGAAC
1 ATATATAGAAC
2263878 ATATA
1 ATATA
2263883 CAATACATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (11 bp):
ATATATAGAAC
Found at i:2264054 original size:16 final size:16
Alignment explanation
Indices: 2264025--2264095 Score: 52
Period size: 19 Copynumber: 4.1 Consensus size: 16
2264015 CAATATTAAA
* *
2264025 ATATATACATGATAAT
1 ATATATAAAAGATAAT
2264041 ATATATAAAAGATATATGT
1 ATATATAAAAGATA-A--T
*
2264060 ATATATAAATATATAAT
1 ATATATAAA-AGATAAT
*
2264077 ATAATATTAAAATATAAT
1 AT-ATA-TAAAAGATAAT
2264095 A
1 A
2264096 ATACAACATA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
16 12 0.26
17 4 0.09
18 11 0.24
19 15 0.33
20 4 0.09
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.38
Consensus pattern (16 bp):
ATATATAAAAGATAAT
Found at i:2264083 original size:18 final size:17
Alignment explanation
Indices: 2264036--2264095 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 17
2264026 TATATACATG
*
2264036 ATAATAT-ATATAAAAG
1 ATAATATAATATAAAAT
*
2264052 ATATATGTATATATAAATAT
1 ATA-ATATA-ATATAAA-AT
2264072 ATAATATAATATTAAAAT
1 ATAATATAATA-TAAAAT
2264090 ATAATA
1 ATAATA
2264096 ATACAACATA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
16 3 0.08
17 3 0.08
18 11 0.31
19 15 0.42
20 4 0.11
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
ATAATATAATATAAAAT
Found at i:2264109 original size:21 final size:20
Alignment explanation
Indices: 2264066--2264109 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
2264056 ATGTATATAT
* * *
2264066 AAATATATAATATAATATTA
1 AAATATATAATACAACATAA
2264086 AAATATAATAATACAACATAA
1 AAATAT-ATAATACAACATAA
2264107 AAA
1 AAA
2264110 AAACATGATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (20 bp):
AAATATATAATACAACATAA
Found at i:2264309 original size:3 final size:3
Alignment explanation
Indices: 2264301--2264330 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2264291 AAGCATAAAG
*
2264301 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2264331 CATTGGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2264452 original size:23 final size:22
Alignment explanation
Indices: 2264426--2264473 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
2264416 TGTATACACG
2264426 TACATAACAAAAATATATACTAA
1 TACATAACAAAAATA-ATACTAA
* * *
2264449 TACATAATAATAATAATAGTAA
1 TACATAACAAAAATAATACTAA
2264471 TAC
1 TAC
2264474 TAATAATACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.29
Consensus pattern (22 bp):
TACATAACAAAAATAATACTAA
Found at i:2264460 original size:3 final size:3
Alignment explanation
Indices: 2264446--2264499 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
2264436 AAATATATAC
* * *
2264446 TAA TACA TAA TAA TAA TAA TAG TAA TAC TAA TAA TAC TAA TAA T-A
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2264491 TAA AAA TAA
1 TAA TAA TAA
2264500 CAAGGATATT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:2265005 original size:23 final size:22
Alignment explanation
Indices: 2264965--2265009 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
2264955 AAAAAAAAGA
2264965 AGAGAGAGGGAAGAGGGAAGGG
1 AGAGAGAGGGAAGAGGGAAGGG
* *
2264987 AGAGAGAAGGGAGGGGGGAAGGG
1 AGAGAG-AGGGAAGAGGGAAGGG
2265010 GAATCCGGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (22 bp):
AGAGAGAGGGAAGAGGGAAGGG
Found at i:2265787 original size:53 final size:53
Alignment explanation
Indices: 2265707--2265817 Score: 222
Period size: 53 Copynumber: 2.1 Consensus size: 53
2265697 GCTGCCCCTC
2265707 TTTGCTCATTATCGTATAACGGGAATAGAGCAAAGACATAAAGAGAGGCCAAT
1 TTTGCTCATTATCGTATAACGGGAATAGAGCAAAGACATAAAGAGAGGCCAAT
2265760 TTTGCTCATTATCGTATAACGGGAATAGAGCAAAGACATAAAGAGAGGCCAAT
1 TTTGCTCATTATCGTATAACGGGAATAGAGCAAAGACATAAAGAGAGGCCAAT
2265813 TTTGC
1 TTTGC
2265818 CTGGTCTTGC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 58 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (53 bp):
TTTGCTCATTATCGTATAACGGGAATAGAGCAAAGACATAAAGAGAGGCCAAT
Found at i:2266253 original size:15 final size:15
Alignment explanation
Indices: 2266229--2266261 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2266219 TTGATATTTG
*
2266229 AAAAATATAAATTGA
1 AAAAACATAAATTGA
2266244 AAAAACATAAATTGA
1 AAAAACATAAATTGA
2266259 AAA
1 AAA
2266262 TACCTCAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.70, C:0.03, G:0.06, T:0.21
Consensus pattern (15 bp):
AAAAACATAAATTGA
Found at i:2266567 original size:88 final size:89
Alignment explanation
Indices: 2266180--2266604 Score: 443
Period size: 89 Copynumber: 4.7 Consensus size: 89
2266170 CTTTATTCGA
** * * * *
2266180 CATGTGGTCCTGA-GCTCAACTCATTTCTCGCAATATGAATTGATATTTGAAAAATATAAATTGA
1 CATGTGG-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTG-
*
2266244 AAAAACATAAATTGAAAATACCTCAG
64 AAAAACAGAAATTGAAAATACCTCAG
** *** *
2266270 CATGTGAGCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTTTTTTTTTTTGTAACTGCGGAAA
1 CATGTG-GCCTGAGGCTCAACTCACCTCTCGCAATATGAG---TTGATTTTTG-AAAAACAGAAA
2266334 TTGAAAAACAGAAATTGAAAATACCTCAG
61 TTGAAAAACAGAAATTGAAAATACCTCAG
* * * * *
2266363 C--GTGCCCTGAGGCTCAACTCACCTCTCACAATATGAGCTGGTTTTTGAAAAACATAAATTGGA
1 CATGTGGCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT-GA
*
2266426 GAAAACAGAAATTGAAATTACCTCAG
65 -AAAACAGAAATTGAAAATACCTCAG
* *
2266452 CATGT--CCTGAGGCTCAACTCACCTCTCGCAGTGTGAGTTGATTTTTGAAAAACAGAAATT-AA
1 CATGTGGCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
* * * *
2266514 AAATAGAGATTGAAAAGACCTCAA
66 AAACAGAAATTGAAAATACCTCAG
* * *
2266538 CATGTGAGCC-GAGGCTCATCTCACCTCTCGCGATATGAGTTGATTTTTTGACAAACAGAAATTG
1 CATGTG-GCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTG
2266602 AAA
64 AAA
2266605 TTATGTCAGC
Statistics
Matches: 279, Mismatches: 40, Indels: 32
0.79 0.11 0.09
Matches are distributed among these distances:
86 25 0.09
87 9 0.03
88 38 0.14
89 96 0.34
90 36 0.13
91 34 0.12
93 33 0.12
94 8 0.03
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (89 bp):
CATGTGGCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
AAACAGAAATTGAAAATACCTCAG
Found at i:2266705 original size:72 final size:73
Alignment explanation
Indices: 2266548--2266746 Score: 283
Period size: 72 Copynumber: 2.7 Consensus size: 73
2266538 CATGTGAGCC
* * ** **
2266548 GAGGCTCATCTCACCTCTCGCGATATGAGTTGATTTTTTGACAAACAGAAATTGAAATTATGTCA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGA-AAACAGAAATCAAAATTACCTCA
2266613 GCGTGTCCT
65 GCGTGTCCT
* *
2266622 GAGGCTCAACTCACCCCTCGCAATATGAGTTGA-TTTTTGAAAACAGAGATCAAAATTACCTCAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATCAAAATTACCTCAG
2266686 CGTGTCCT
66 CGTGTCCT
*
2266694 GAGGCTGAACTCACCTCTCGCAATATGAGTTGATTATTTTGAAAGACAGAAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATT-TTTTGAAA-ACAGAAAT
2266747 TGGAAAGCAG
Statistics
Matches: 111, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
72 58 0.52
73 8 0.07
74 38 0.34
75 7 0.06
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (73 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATCAAAATTACCTCAG
CGTGTCCT
Found at i:2266893 original size:76 final size:76
Alignment explanation
Indices: 2266750--2266972 Score: 320
Period size: 76 Copynumber: 2.9 Consensus size: 76
2266740 CAGAAATTGG
* * * * *
2266750 AAAGCAGAAATCGAAAATACCTCAGCGTGCCCTGGGGCTCAACTCACCTCTTGCAATATGAGTTG
1 AAAGCATAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
*
2266815 ATTTTTTTTTA
66 ATTTTTTTTGA
** * * *
2266826 CCAGCATAAATTGAAATTACCTCAGTGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAAGCATAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
2266891 ATTTTTTTTGA
66 ATTTTTTTTGA
* * *
2266902 AAAGTATAAATTAAAAATACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTG
1 AAAGCATAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
2266967 ATTTTT
66 ATTTTT
2266973 GAAAAATAGA
Statistics
Matches: 128, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
76 128 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (76 bp):
AAAGCATAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTTTTTTGA
Found at i:2266999 original size:16 final size:16
Alignment explanation
Indices: 2266975--2267005 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2266965 TGATTTTTGA
*
2266975 AAAATAGAAATTGAAG
1 AAAACAGAAATTGAAG
2266991 AAAACAGAAATTGAA
1 AAAACAGAAATTGAA
2267006 ATTACCTCAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.03, G:0.16, T:0.16
Consensus pattern (16 bp):
AAAACAGAAATTGAAG
Found at i:2267060 original size:89 final size:89
Alignment explanation
Indices: 2266909--2267074 Score: 264
Period size: 89 Copynumber: 1.9 Consensus size: 89
2266899 TGAAAAGTAT
*
2266909 AAATTAAAAATACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTG
1 AAATTAAAAATACCTCAGCATGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTG
2266974 AAAAATAGAAATTGAAGAAAACAG
66 AAAAATAGAAATTGAAGAAAACAG
* *
2266998 AAATTGAAATTACCTCAGCATGTCC-TGAGGCTCAACTCACCTCTCGCAATATGAG-TCGATTTT
1 AAATTAAAAATACCTCAGCATG-CCTTGAGGCTCAACTCACCTCTCGCAATATGAGCT-GATTTT
*
2267061 TGAAGAATAGAAAT
64 TGAAAAATAGAAAT
2267075 AAAAACATCA
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
88 1 0.01
89 68 0.96
90 2 0.03
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (89 bp):
AAATTAAAAATACCTCAGCATGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTG
AAAAATAGAAATTGAAGAAAACAG
Found at i:2272005 original size:13 final size:13
Alignment explanation
Indices: 2271987--2272020 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
2271977 CTTTTCTGAT
2271987 CTTTCTTCCACTA
1 CTTTCTTCCACTA
2272000 CTTTCTTCCACTA
1 CTTTCTTCCACTA
2272013 CTTTCTTC
1 CTTTCTTC
2272021 TTTGACGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.12, C:0.38, G:0.00, T:0.50
Consensus pattern (13 bp):
CTTTCTTCCACTA
Found at i:2276886 original size:16 final size:16
Alignment explanation
Indices: 2276857--2276927 Score: 52
Period size: 19 Copynumber: 4.1 Consensus size: 16
2276847 CAATATTAAA
* *
2276857 ATATATACATGATAAT
1 ATATATAAAAGATAAT
2276873 ATATATAAAAGATATATGT
1 ATATATAAAAGATA-A--T
*
2276892 ATATATAAATATATAAT
1 ATATATAAA-AGATAAT
*
2276909 ATAATATTAAAATATAAT
1 AT-ATA-TAAAAGATAAT
2276927 A
1 A
2276928 ATACAACATA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
16 12 0.26
17 4 0.09
18 11 0.24
19 15 0.33
20 4 0.09
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.38
Consensus pattern (16 bp):
ATATATAAAAGATAAT
Found at i:2276915 original size:18 final size:17
Alignment explanation
Indices: 2276868--2276927 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 17
2276858 TATATACATG
*
2276868 ATAATAT-ATATAAAAG
1 ATAATATAATATAAAAT
*
2276884 ATATATGTATATATAAATAT
1 ATA-ATATA-ATATAAA-AT
2276904 ATAATATAATATTAAAAT
1 ATAATATAATA-TAAAAT
2276922 ATAATA
1 ATAATA
2276928 ATACAACATA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
16 3 0.08
17 3 0.08
18 11 0.31
19 15 0.42
20 4 0.11
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
ATAATATAATATAAAAT
Found at i:2276941 original size:21 final size:20
Alignment explanation
Indices: 2276898--2276941 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
2276888 ATGTATATAT
* * *
2276898 AAATATATAATATAATATTA
1 AAATATATAATACAACATAA
2276918 AAATATAATAATACAACATAA
1 AAATAT-ATAATACAACATAA
2276939 AAA
1 AAA
2276942 AACATGATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (20 bp):
AAATATATAATACAACATAA
Found at i:2277138 original size:3 final size:3
Alignment explanation
Indices: 2277130--2277162 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
2277120 AAGCATAAAC
*
2277130 TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2277163 CATTGGAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2277293 original size:3 final size:3
Alignment explanation
Indices: 2277262--2277335 Score: 69
Period size: 3 Copynumber: 24.3 Consensus size: 3
2277252 ATACACGTAC
* * *
2277262 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA ATA ATA GTA ATA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* * *
2277309 CTA ATA ATA CTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2277336 CAAGGATATT
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
2 2 0.04
3 48 0.86
4 6 0.11
ACGTcount: A:0.62, C:0.05, G:0.01, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:2277929 original size:11 final size:11
Alignment explanation
Indices: 2277915--2277958 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
2277905 GTAAAAAAAA
2277915 TTATTTTTATT
1 TTATTTTTATT
2277926 TTATTTTTATT
1 TTATTTTTATT
*
2277937 ATTTTTTTGTATT
1 -TTATTTT-TATT
2277950 TT-TTTTTAT
1 TTATTTTTAT
2277959 GTTTTAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 3 0.10
11 15 0.50
12 8 0.27
13 4 0.13
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (11 bp):
TTATTTTTATT
Found at i:2277958 original size:20 final size:20
Alignment explanation
Indices: 2277914--2277952 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
2277904 GGTAAAAAAA
*
2277914 ATTATTTTTATTTTATTTTT
1 ATTATTTTTATTGTATTTTT
2277934 ATTATTTTT-TTGTATTTTT
1 ATTATTTTTATTGTATTTTT
2277953 TTTTATGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (20 bp):
ATTATTTTTATTGTATTTTT
Found at i:2277963 original size:11 final size:10
Alignment explanation
Indices: 2277915--2277963 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
2277905 GTAAAAAAAA
2277915 TTATTTTTATT
1 TTATTTTT-TT
*
2277926 TTA-TTTTTA
1 TTATTTTTTT
2277935 TTATTTTTTT
1 TTATTTTTTT
*
2277945 GTATTTTTTT
1 TTATTTTTTT
*
2277955 TTATGTTTT
1 TTATTTTTT
2277964 AATATATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
9 4 0.12
10 25 0.78
11 3 0.09
ACGTcount: A:0.14, C:0.00, G:0.04, T:0.82
Consensus pattern (10 bp):
TTATTTTTTT
Found at i:2283133 original size:2 final size:2
Alignment explanation
Indices: 2283126--2283151 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2283116 ATAAATTTTC
2283126 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2283152 GTTTTATACA
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):
AT
Found at i:2285659 original size:18 final size:18
Alignment explanation
Indices: 2285636--2285674 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2285626 CAAATTACAA
*
2285636 AAAAAAAAATTAGATTAT
1 AAAAAAAAATTAAATTAT
**
2285654 AAAAAATCATTAAATTAT
1 AAAAAAAAATTAAATTAT
2285672 AAA
1 AAA
2285675 TTTAAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAAAAAAATTAAATTAT
Found at i:2285924 original size:21 final size:21
Alignment explanation
Indices: 2285894--2285933 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2285884 TAATTTCTAA
*
2285894 TTTTTTATAAAATTTTTATGG
1 TTTTTAATAAAATTTTTATGG
**
2285915 TTTTTAATAATTTTTTTAT
1 TTTTTAATAAAATTTTTAT
2285934 AAATTTCACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTTTAATAAAATTTTTATGG
Found at i:2288754 original size:43 final size:43
Alignment explanation
Indices: 2288706--2288792 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
2288696 AAGAGAGTGT
2288706 ATGATATGGTATGTATAGACCCTTGCTAAGAAATCGAAAAAGA
1 ATGATATGGTATGTATAGACCCTTGCTAAGAAATCGAAAAAGA
2288749 ATGATATGGTATGTATAGACCCTTGCTAAGAAATCGAAAAAGA
1 ATGATATGGTATGTATAGACCCTTGCTAAGAAATCGAAAAAGA
2288792 A
1 A
2288793 AATTGTGTGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.25
Consensus pattern (43 bp):
ATGATATGGTATGTATAGACCCTTGCTAAGAAATCGAAAAAGA
Found at i:2293042 original size:18 final size:19
Alignment explanation
Indices: 2293019--2293059 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
2293009 TATGAAAAAA
*
2293019 TTATTTTTT-GAATAATTT
1 TTATTTTTTAAAATAATTT
2293037 TTATTTTTTAAAAATAATTT
1 TTATTTTTT-AAAATAATTT
2293057 TTA
1 TTA
2293060 CATATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
20 11 0.55
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TTATTTTTTAAAATAATTT
Found at i:2294084 original size:22 final size:21
Alignment explanation
Indices: 2294059--2294108 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
2294049 AAATTTAATC
2294059 TTATATTTT-TATTTTCAGAAAT
1 TTATATTTTATATTTT-A-AAAT
2294081 TTAT-TTTTATATTTTAAAAT
1 TTATATTTTATATTTTAAAAT
*
2294101 TTAAATTT
1 TTATATTT
2294109 AACTGATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 7 0.28
21 8 0.32
22 10 0.40
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (21 bp):
TTATATTTTATATTTTAAAAT
Found at i:2294087 original size:20 final size:20
Alignment explanation
Indices: 2294062--2294103 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2294052 TTTAATCTTA
2294062 TATTTTTAT-TTTCAGAAATT
1 TATTTTTATATTTCA-AAATT
*
2294082 TATTTTTATATTTTAAAATT
1 TATTTTTATATTTCAAAATT
2294102 TA
1 TA
2294104 AATTTAACTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TATTTTTATATTTCAAAATT
Found at i:2294109 original size:20 final size:22
Alignment explanation
Indices: 2294063--2294109 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 22
2294053 TTAATCTTAT
* *
2294063 ATTTTTATTTTCAGAAATTTAT
1 ATTTATATTTTCAGAAATTTAA
*
2294085 TTTTATATTTT-A-AAATTTAA
1 ATTTATATTTTCAGAAATTTAA
2294105 ATTTA
1 ATTTA
2294110 ACTGATAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 11 0.52
21 1 0.05
22 9 0.43
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTTATATTTTCAGAAATTTAA
Found at i:2294955 original size:30 final size:29
Alignment explanation
Indices: 2294877--2294965 Score: 79
Period size: 30 Copynumber: 2.9 Consensus size: 29
2294867 ATATTTAGGG
* * *
2294877 TTCTCTCAAAATTTTTAAAAAATTTCGGATTAA
1 TTCTCTTAAAATTTTTAAAAACTTT---ATT-T
* *
2294910 TTCTTTTAAAATTTTTGAAAAATTTTATTT
1 TTCTCTTAAAATTTTT-AAAAACTTTATTT
*
2294940 TTCTCTTAAATTTTTTAAAAACTTTA
1 TTCTCTTAAAATTTTTAAAAACTTTA
2294966 ATTAAGCTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
29 9 0.19
30 14 0.29
31 3 0.06
33 14 0.29
34 8 0.17
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.52
Consensus pattern (29 bp):
TTCTCTTAAAATTTTTAAAAACTTTATTT
Found at i:2296219 original size:3 final size:3
Alignment explanation
Indices: 2296205--2296279 Score: 141
Period size: 3 Copynumber: 25.0 Consensus size: 3
2296195 TGATTTCATA
*
2296205 TCT TCC TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
2296253 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
2296280 AATTTTACAT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:2302868 original size:25 final size:26
Alignment explanation
Indices: 2302828--2302876 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
2302818 AAATAACATA
*
2302828 ATACTACAATATTGTTCATACCAATG
1 ATACTACAATATTGTTCAAACCAATG
2302854 ATACTAC-ATATTGTTCAAACCAA
1 ATACTACAATATTGTTCAAACCAA
2302877 ATAATCATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (26 bp):
ATACTACAATATTGTTCAAACCAATG
Found at i:2314251 original size:152 final size:153
Alignment explanation
Indices: 2313597--2314279 Score: 1015
Period size: 153 Copynumber: 4.5 Consensus size: 153
2313587 AAATTCATCA
*
2313597 GGGTCTATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
1 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
* * ** *
2313662 GGGCCCTGCTTTT--A-CAT-AT-TTTTGCCAAGTCCGTCCAGAACTTTCATAG-TTTATACATG
66 GGGCCCT-TTTTTAAATTATAATGTTTTGCCAAGTCCGT-C----CTCCCAT-GCTTCATACATG
** *
2313721 TAGTA-ACCAAAGT-AAATTGCATCCCAAAG
124 TAG-AGACCAAAGTAAAATCACATCTCAAAG
*
2313750 GGGTCTATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
1 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
* * * * *
2313815 GGGCCCTTTTTAAAATTTTAAAGTTTTGCCAAGTCCGTCCTCTCATGCTTCATACATGTAGAAAC
66 GGGCCCTTTTTTAAATTATAATGTTTTGCCAAGTCCGTCCTCCCATGCTTCATACATGTAGAGAC
2313880 CAAAGTAAAATCACATCTCAAAG
131 CAAAGTAAAATCACATCTCAAAG
*
2313903 GAGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
1 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
* * * *
2313968 GGGCCCTTTTTTAAATTATAATGTTTTGCCAAGTCCGTCCTTCTATGCTTCATACATGAAGCGAC
66 GGGCCCTTTTTTAAATTATAATGTTTTGCCAAGTCCGTCCTCCCATGCTTCATACATGTAGAGAC
2314033 CAAAGTAAAATCACATCTCAAAG
131 CAAAGTAAAATCACATCTCAAAG
2314056 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
1 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
* *
2314121 GGGCCCTTTTTTAAATTATAATGTTTTGCCAAGTCTGTCCTCCCATGCTTTATACATGTAGAGAC
66 GGGCCCTTTTTTAAATTATAATGTTTTGCCAAGTCCGTCCTCCCATGCTTCATACATGTAGAGAC
* *
2314186 GAATGT-AAATCACATCTCAAAG
131 CAAAGTAAAATCACATCTCAAAG
2314208 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
1 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
2314273 GGGCCCT
66 GGGCCCT
2314280 GATTCTAATT
Statistics
Matches: 492, Mismatches: 30, Indels: 17
0.91 0.06 0.03
Matches are distributed among these distances:
151 2 0.00
152 117 0.24
153 354 0.72
154 1 0.00
155 1 0.00
156 2 0.00
157 15 0.03
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (153 bp):
GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
GGGCCCTTTTTTAAATTATAATGTTTTGCCAAGTCCGTCCTCCCATGCTTCATACATGTAGAGAC
CAAAGTAAAATCACATCTCAAAG
Found at i:2314443 original size:77 final size:77
Alignment explanation
Indices: 2314316--2314471 Score: 303
Period size: 77 Copynumber: 2.0 Consensus size: 77
2314306 CATAGCTCAG
2314316 TGGTAAGAGTATACGACGGCATATTTGAAGGTCAACAGTTCGAGCGCTGTTGTGATCTTTTTGTT
1 TGGTAAGAGTATACGACGGCATATTTGAAGGTCAACAGTTCGAGCGCTGTTGTGATCTTTTTGTT
2314381 CCGTTATTTTTT
66 CCGTTATTTTTT
*
2314393 TGGTAAGAGTATACGACGGCATATTTGAAGGTCACCAGTTCGAGCGCTGTTGTGATCTTTTTGTT
1 TGGTAAGAGTATACGACGGCATATTTGAAGGTCAACAGTTCGAGCGCTGTTGTGATCTTTTTGTT
2314458 CCGTTATTTTTT
66 CCGTTATTTTTT
2314470 TG
1 TG
2314472 CCCCGTCCTC
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.20, C:0.15, G:0.25, T:0.40
Consensus pattern (77 bp):
TGGTAAGAGTATACGACGGCATATTTGAAGGTCAACAGTTCGAGCGCTGTTGTGATCTTTTTGTT
CCGTTATTTTTT
Found at i:2323443 original size:33 final size:34
Alignment explanation
Indices: 2323398--2323463 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
2323388 AAAGTTTTAA
* *
2323398 AAATTTTAATTAAAC-CCTCAAATTTTTTAAAAC
1 AAATTTTAATTAAACTCCTAAAATTTTTGAAAAC
*
2323431 AAATTTTTATTAAACTCCTAAAATTTTTGAAAA
1 AAATTTTAATTAAACTCCTAAAATTTTTGAAAA
2323464 TTTTACTTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 14 0.48
34 15 0.52
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (34 bp):
AAATTTTAATTAAACTCCTAAAATTTTTGAAAAC
Found at i:2325066 original size:2 final size:2
Alignment explanation
Indices: 2325059--2325086 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2325049 ACTTAAGGTT
2325059 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
2325087 AACTTTGCCT
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2327645 original size:26 final size:26
Alignment explanation
Indices: 2327603--2327656 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
2327593 AGATATTTTT
*
2327603 AAAAATTAAAATCATTAACATTATTA
1 AAAAATTAAAATAATTAACATTATTA
* *
2327629 AAAAATATAAAA-AATTAATATTTTTA
1 AAAAAT-TAAAATAATTAACATTATTA
2327655 AA
1 AA
2327657 TTTTAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (26 bp):
AAAAATTAAAATAATTAACATTATTA
Found at i:2333137 original size:16 final size:18
Alignment explanation
Indices: 2333116--2333148 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2333106 TTAGGAAAAA
2333116 AATTTT-AT-TATTTTTT
1 AATTTTCATATATTTTTT
2333132 AATTTTCATATATTTTT
1 AATTTTCATATATTTTT
2333149 ATTTTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (18 bp):
AATTTTCATATATTTTTT
Found at i:2338829 original size:15 final size:15
Alignment explanation
Indices: 2338806--2338844 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2338796 TGATAAATTG
**
2338806 AAAATTAAATGTTGA
1 AAAATTAAATACTGA
*
2338821 AAAAATAAATACTGA
1 AAAATTAAATACTGA
2338836 AAAATTAAA
1 AAAATTAAA
2338845 GTTTAAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.64, C:0.03, G:0.08, T:0.26
Consensus pattern (15 bp):
AAAATTAAATACTGA
Found at i:2341815 original size:26 final size:26
Alignment explanation
Indices: 2341786--2341837 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
2341776 TGTTTCTAAA
2341786 AGTTAAGAGATAATTAATATCATAAC
1 AGTTAAGAGATAATTAATATCATAAC
*
2341812 AGTTAAGAGATAGTTAATATCATAAC
1 AGTTAAGAGATAATTAATATCATAAC
2341838 GATGGATACG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.48, C:0.08, G:0.13, T:0.31
Consensus pattern (26 bp):
AGTTAAGAGATAATTAATATCATAAC
Found at i:2351948 original size:42 final size:43
Alignment explanation
Indices: 2351880--2352086 Score: 181
Period size: 42 Copynumber: 4.7 Consensus size: 43
2351870 CTTCGTTTTC
** *
2351880 TCGATGCCATAGTTCAACTATGGTCTTACACATATTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATAA
* * *
2351923 T-GATGCCATAGCCCAGCTATAGTCTTACACCTATTCATAT-A
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATAA
2351964 TCGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACAT-A
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC---AT---AT-TCACATAA
* *
2352013 TCGATGCCATAGCCCAGCTACGGTCTTACACGA-A-TCACATATC
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA-A
* *
2352056 TCACTGATGCCATATCCCAGATATGGTCTTA
1 T--C-GATGCCATAGCCCAGCTATGGTCTTA
2352087 TACAGTAGTA
Statistics
Matches: 136, Mismatches: 15, Indels: 23
0.78 0.09 0.13
Matches are distributed among these distances:
41 8 0.06
42 61 0.45
43 3 0.02
45 2 0.01
46 23 0.17
47 1 0.01
48 2 0.01
49 36 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (43 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATAA
Found at i:2352025 original size:49 final size:48
Alignment explanation
Indices: 2351908--2352086 Score: 196
Period size: 49 Copynumber: 3.9 Consensus size: 48
2351898 TATGGTCTTA
*
2351908 CACATATTCACATAAT-GATGCCATAGCCCAGCTATAGTCTTACAC----
1 CACATA-TCACAT-ATCGATGCCATAGCCCAGCTATGGTCTTACACGAAT
* *
2351953 C-TAT-TCATATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAAT
1 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACG-AAT
*
2352000 CACATATCACATATCGATGCCATAGCCCAGCTACGGTCTTACACGAAT
1 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGAAT
* * * *
2352048 CACATATCTCA-CT-GATGCCATATCCCAGATATGGTCTTA
1 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTA
2352087 TACAGTAGTA
Statistics
Matches: 115, Mismatches: 11, Indels: 15
0.82 0.08 0.11
Matches are distributed among these distances:
41 2 0.02
42 33 0.29
44 2 0.02
45 1 0.01
46 23 0.20
47 2 0.02
48 15 0.13
49 37 0.32
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.28
Consensus pattern (48 bp):
CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGAAT
Found at i:2352084 original size:46 final size:47
Alignment explanation
Indices: 2351965--2352129 Score: 165
Period size: 47 Copynumber: 3.5 Consensus size: 47
2351955 ATTCATATAT
* * *
2351965 CGATGCCATAGCCCAGCTATGGTCTTACAC-GTAATCACATATCACATAT
1 CGATGCCATATCCCAGATATGGTCTTACACAGTAAT-ACATATCAC--AC
* * * *
2352014 CGATGCCATAGCCCAGCTACGGTCTTACAC-G-AATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTACACAGTAAT-ACATATCACAC
* * * *
2352060 TGATGCCATATCCCAGATATGGTCTTATACAGTAGTATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTACACAGTAATACATATCACAC
*
2352107 CGATGCCATATCCCAAATATGGT
1 CGATGCCATATCCCAGATATGGT
2352130 TTTATGCGGA
Statistics
Matches: 101, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
46 26 0.26
47 31 0.31
48 14 0.14
49 30 0.30
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (47 bp):
CGATGCCATATCCCAGATATGGTCTTACACAGTAATACATATCACAC
Found at i:2352115 original size:47 final size:47
Alignment explanation
Indices: 2351924--2352129 Score: 183
Period size: 49 Copynumber: 4.5 Consensus size: 47
2351914 TTCACATAAT
* * * * *
2351924 GATGCCATAGCCCAGCTATAGTCTTACACCT-AT-TCATAT---ATC
1 GATGCCATAGCCCAGATATGGTCTTACACGTAATCACATATCACACC
* *
2351966 GATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATATC
1 GATGCCATAGCCCAGATATGGTCTTACACGTAATCACATATCAC--ACC
* * * *
2352015 GATGCCATAGCCCAGCTACGGTCTTACACG-AATCACATATCTCACT
1 GATGCCATAGCCCAGATATGGTCTTACACGTAATCACATATCACACC
* * * *
2352061 GATGCCATATCCCAGATATGGTCTTATACAGTAGT-ATATATCACACC
1 GATGCCATAGCCCAGATATGGTCTTACAC-GTAATCACATATCACACC
* *
2352108 GATGCCATATCCCAAATATGGT
1 GATGCCATAGCCCAGATATGGT
2352130 TTTATGCGGA
Statistics
Matches: 139, Mismatches: 16, Indels: 13
0.83 0.10 0.08
Matches are distributed among these distances:
42 29 0.21
43 2 0.01
44 5 0.04
46 26 0.19
47 31 0.22
48 14 0.10
49 32 0.23
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (47 bp):
GATGCCATAGCCCAGATATGGTCTTACACGTAATCACATATCACACC
Found at i:2352205 original size:31 final size:31
Alignment explanation
Indices: 2352162--2352310 Score: 244
Period size: 31 Copynumber: 4.8 Consensus size: 31
2352152 CTTGTCACTT
* *
2352162 GTAGTCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
2352193 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
2352224 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
2352255 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
2352286 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
2352311 TGTCATTGAT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 110 1.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:2354800 original size:26 final size:26
Alignment explanation
Indices: 2354771--2354852 Score: 128
Period size: 26 Copynumber: 3.2 Consensus size: 26
2354761 TGATACAAAT
*
2354771 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
2354797 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
* *
2354823 TGATAATGGTTTAGGTAAATGTTTCA
1 TGATAATGGATTAGGTAAATGTTCCA
2354849 TGAT
1 TGAT
2354853 GAGAATTTCA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.38
Consensus pattern (26 bp):
TGATAATGGATTAGGTAAATGTTCCA
Found at i:2361088 original size:26 final size:26
Alignment explanation
Indices: 2361059--2361166 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
2361049 TGATACAAAT
2361059 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
2361085 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
2361111 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
2361137 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
2361163 TGAT
1 TGAT
2361167 GGGAATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:2362608 original size:26 final size:27
Alignment explanation
Indices: 2362579--2362629 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
2362569 GGAATATGCA
2362579 TGAAAAACCCTAAAA-TAGAAAATTAC
1 TGAAAAACCCTAAAAGTAGAAAATTAC
* * *
2362605 TGAAATACTCTAAAAGTGGAAAATT
1 TGAAAAACCCTAAAAGTAGAAAATT
2362630 TACAGTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.24
Consensus pattern (27 bp):
TGAAAAACCCTAAAAGTAGAAAATTAC
Found at i:2376127 original size:9 final size:9
Alignment explanation
Indices: 2376113--2376155 Score: 70
Period size: 9 Copynumber: 4.8 Consensus size: 9
2376103 TTCTAATATT
2376113 TTTTTTTAC
1 TTTTTTTAC
2376122 TTTTTTTTAC
1 -TTTTTTTAC
2376132 TTTTTTTAC
1 TTTTTTTAC
2376141 -TTTTTTAC
1 TTTTTTTAC
2376149 TTTTTTT
1 TTTTTTT
2376156 CTTATATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.25
9 15 0.47
10 9 0.28
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTAC
Done.