Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 22 of 163
Found at i:6022213 original size:11 final size:10
Alignment explanation
Indices: 6022125--6022218 Score: 57
Period size: 11 Copynumber: 8.7 Consensus size: 10
6022115 ACTTTTGATT
*
6022125 TTTAATTAAA
1 TTTAAATAAA
*
6022135 GTTTAAATTAAT
1 -TTTAAA-TAAA
* *
6022147 TTTAAATTTAT
1 TTTAAA-TAAA
6022158 TTTAAATTTAAA
1 TTTAAA--TAAA
6022170 TTTAAAATAAA
1 TTT-AAATAAA
6022181 TTTAAATAAA
1 TTTAAATAAA
6022191 --TAAATTTAAA
1 TTTAAA--TAAA
6022201 TTTAAGATAAA
1 TTTAA-ATAAA
6022212 TTTAAAT
1 TTTAAAT
6022219 TTAATTAAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 17
0.76 0.05 0.18
Matches are distributed among these distances:
8 4 0.06
10 13 0.19
11 37 0.53
12 12 0.17
13 4 0.06
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (10 bp):
TTTAAATAAA
Found at i:6022224 original size:11 final size:11
Alignment explanation
Indices: 6022136--6022250 Score: 74
Period size: 11 Copynumber: 10.1 Consensus size: 11
6022126 TTAATTAAAG
6022136 TTTAAA-TTAA
1 TTTAAATTTAA
*
6022146 TTTTAAATTTAT
1 -TTTAAATTTAA
6022158 TTTAAATTTAAA
1 TTTAAATTT-AA
* *
6022170 TTTAAAATAAA
1 TTTAAATTTAA
*
6022181 TTTAAATAAATAAA
1 TTTAAAT---TTAA
6022195 TTTAAATTTAA
1 TTTAAATTTAA
**
6022206 GATAAATTTAAA
1 TTTAAATTT-AA
*
6022218 TTT-AATTAAA
1 TTTAAATTTAA
*
6022228 TTTAAA-ATAA
1 TTTAAATTTAA
6022238 TATTAAATTTAA
1 T-TTAAATTTAA
6022250 T
1 T
6022251 ACAAAATTAA
Statistics
Matches: 81, Mismatches: 14, Indels: 17
0.72 0.12 0.15
Matches are distributed among these distances:
10 8 0.10
11 44 0.54
12 18 0.22
14 11 0.14
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:6022235 original size:17 final size:16
Alignment explanation
Indices: 6022130--6022249 Score: 109
Period size: 17 Copynumber: 7.2 Consensus size: 16
6022120 TGATTTTTAA
*
6022130 TTAAAGTTTAAATTAATT
1 TTAAA-TTT-AATTAAAT
*
6022148 TTAAATTTATTTTAAAT
1 TTAAATTTA-ATTAAAT
*
6022165 TTAAATTTAAAATAAAT
1 TTAAATTT-AATTAAAT
*
6022182 TTAAA--TAAATAAAT
1 TTAAATTTAATTAAAT
*
6022196 TTAAATTTAAGATAAAT
1 TTAAATTTAA-TTAAAT
6022213 TTAAATTTAATTAAAT
1 TTAAATTTAATTAAAT
* *
6022229 TTAAAATAATATTAAAT
1 TTAAATTTA-ATTAAAT
6022246 TTAA
1 TTAA
6022250 TACAAAATTA
Statistics
Matches: 89, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
14 13 0.15
15 1 0.01
16 16 0.18
17 53 0.60
18 6 0.07
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
TTAAATTTAATTAAAT
Found at i:6022249 original size:6 final size:6
Alignment explanation
Indices: 6022130--6022233 Score: 87
Period size: 6 Copynumber: 17.8 Consensus size: 6
6022120 TGATTTTTAA
* *
6022130 TTAAAGT TTAAA- TTAATT TTAAAT TT-ATT TTAAAT TTAAAT TTAAA-
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
6022176 ATAAAT TTAAAT AAATAAAT TTAAAT TTAAGA- -TAAAT TTAAAT TT-AA-
1 TTAAAT TTAAAT --TTAAAT TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT
6022223 TTAAAT TTAAA
1 TTAAAT TTAAA
6022234 ATAATATTAA
Statistics
Matches: 79, Mismatches: 8, Indels: 21
0.73 0.07 0.19
Matches are distributed among these distances:
4 3 0.04
5 19 0.24
6 46 0.58
7 6 0.08
8 5 0.06
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (6 bp):
TTAAAT
Found at i:6022259 original size:17 final size:17
Alignment explanation
Indices: 6022221--6022261 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
6022211 ATTTAAATTT
*
6022221 AATTAAATTTAAAATAA
1 AATTAAATTTAAAACAA
* *
6022238 TATTAAATTTAATACAA
1 AATTAAATTTAAAACAA
6022255 AATTAAA
1 AATTAAA
6022262 ATTCATTTAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
AATTAAATTTAAAACAA
Found at i:6024111 original size:30 final size:29
Alignment explanation
Indices: 6024071--6024189 Score: 113
Period size: 30 Copynumber: 4.1 Consensus size: 29
6024061 AAAGGTCTCT
6024071 AAACTATCCAAAAATTACATTTTTGACCC
1 AAACTATCCAAAAATTACATTTTTGACCC
*
6024100 TAAAACT-TCCAAAAAATACATTTTTGACCC
1 --AAACTATCCAAAAATTACATTTTTGACCC
* *
6024130 --CCTCTCCAAAAATTACATTTTT-ACCCCC
1 AAACTATCCAAAAATTACATTTTTGA--CCC
* *
6024158 AAACT-TTCAAAAATTCCATTTTTGACCTC
1 AAACTATCCAAAAATTACATTTTTGACC-C
6024187 AAA
1 AAA
6024190 ATTCCATTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 16
0.77 0.06 0.16
Matches are distributed among these distances:
26 3 0.04
27 17 0.23
28 5 0.07
29 20 0.27
30 25 0.33
31 5 0.07
ACGTcount: A:0.39, C:0.27, G:0.03, T:0.32
Consensus pattern (29 bp):
AAACTATCCAAAAATTACATTTTTGACCC
Found at i:6024150 original size:26 final size:27
Alignment explanation
Indices: 6024107--6024157 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
6024097 CCCTAAAACT
6024107 TCCAAAAAATACATTTTTGACCCCCTC
1 TCCAAAAAATACATTTTTGACCCCCTC
*
6024134 TCCAAAAATTACATTTTT-ACCCCC
1 TCCAAAAAATACATTTTTGACCCCC
6024158 AAACTTTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.33, C:0.33, G:0.02, T:0.31
Consensus pattern (27 bp):
TCCAAAAAATACATTTTTGACCCCCTC
Found at i:6024179 original size:56 final size:57
Alignment explanation
Indices: 6024077--6024184 Score: 164
Period size: 56 Copynumber: 1.9 Consensus size: 57
6024067 CTCTAAACTA
*
6024077 TCCAAAAATTACATTTTTGACCCTAAAACTTCCAAAAAATACATTTTTGACCCCCTC
1 TCCAAAAATTACATTTTTGACCCCAAAACTTCCAAAAAATACATTTTTGACCCCCTC
* * * *
6024134 TCCAAAAATTACATTTTT-ACCCCCAAACTTTCAAAAATTCCATTTTTGACC
1 TCCAAAAATTACATTTTTGACCCCAAAACTTCCAAAAAATACATTTTTGACC
6024185 TCAAAATTCC
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
56 28 0.61
57 18 0.39
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (57 bp):
TCCAAAAATTACATTTTTGACCCCAAAACTTCCAAAAAATACATTTTTGACCCCCTC
Found at i:6024192 original size:20 final size:20
Alignment explanation
Indices: 6024167--6024210 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
6024157 CAAACTTTCA
*
6024167 AAAATTCCATTTTTGACCTC
1 AAAATTCCATTTTTAACCTC
6024187 AAAATTCCATTTTTAACCTC
1 AAAATTCCATTTTTAACCTC
6024207 AAAA
1 AAAA
6024211 CTTTCAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.39, C:0.23, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAATTCCATTTTTAACCTC
Found at i:6025305 original size:35 final size:34
Alignment explanation
Indices: 6025276--6025343 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
6025266 ACCGACTCTC
6025276 GAACTTATTTTTCTGGATTTCGAAGACCGACATT
1 GAACTTATTTTTCTGGATTTCGAAGACCGACATT
*** *
6025310 TTTCTTGTTTTTCTGGATTTCGAAGACCGACATT
1 GAACTTATTTTTCTGGATTTCGAAGACCGACATT
6025344 TTTTTAACGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.43
Consensus pattern (34 bp):
GAACTTATTTTTCTGGATTTCGAAGACCGACATT
Found at i:6025834 original size:20 final size:20
Alignment explanation
Indices: 6025811--6025888 Score: 54
Period size: 19 Copynumber: 3.9 Consensus size: 20
6025801 TGCTTTTTAC
6025811 AATTTTTAAATAATTTTAAT
1 AATTTTTAAATAATTTTAAT
* *
6025831 AA-TTTCAAATATATATATATAT
1 AATTTTTAAATA-AT-TTTA-AT
**
6025853 AATTTCTT--ATAAACTTAAT
1 AATTT-TTAAATAATTTTAAT
*
6025872 AGTTTTTAAATAATTTT
1 AATTTTTAAATAATTTT
6025889 CTATAATGTT
Statistics
Matches: 42, Mismatches: 9, Indels: 14
0.65 0.14 0.22
Matches are distributed among these distances:
18 2 0.05
19 14 0.33
20 12 0.29
21 4 0.10
22 7 0.17
23 2 0.05
24 1 0.02
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (20 bp):
AATTTTTAAATAATTTTAAT
Found at i:6026965 original size:18 final size:18
Alignment explanation
Indices: 6026944--6027001 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 18
6026934 GCAACCGCTG
6026944 CCACCCCCACAACCTCCT
1 CCACCCCCACAACCTCCT
*
6026962 CCA---CCAC--CAT-CT
1 CCACCCCCACAACCTCCT
6026974 CCACCCCCACAACCTCCT
1 CCACCCCCACAACCTCCT
*
6026992 CCACCTCCAC
1 CCACCCCCAC
6027002 CTCCACCTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 12
0.67 0.07 0.26
Matches are distributed among these distances:
12 5 0.16
13 2 0.06
15 8 0.26
17 2 0.06
18 14 0.45
ACGTcount: A:0.22, C:0.66, G:0.00, T:0.12
Consensus pattern (18 bp):
CCACCCCCACAACCTCCT
Found at i:6026980 original size:30 final size:30
Alignment explanation
Indices: 6026944--6027008 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
6026934 GCAACCGCTG
*
6026944 CCACCCCCACAACCTCCTCCACCACCATCT
1 CCACCCCCACAACCTCCTCCACCACCACCT
*
6026974 CCACCCCCACAACCTCCTCCACCTCCACCT
1 CCACCCCCACAACCTCCTCCACCACCACCT
6027004 CCACC
1 CCACC
6027009 TCCGGTTCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.22, C:0.66, G:0.00, T:0.12
Consensus pattern (30 bp):
CCACCCCCACAACCTCCTCCACCACCACCT
Found at i:6026998 original size:6 final size:6
Alignment explanation
Indices: 6026959--6027011 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
6026949 CCCACAACCT
* * * ** *
6026959 CCTCCA CCACCA TCTCCA CCCCCA CAACCT CCTCCA CCTCCA CCTCCA
1 CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA
6027007 CCTCC
1 CCTCC
6027012 GGTTCTTCTG
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.19, C:0.66, G:0.00, T:0.15
Consensus pattern (6 bp):
CCTCCA
Found at i:6027010 original size:18 final size:18
Alignment explanation
Indices: 6026959--6027011 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
6026949 CCCACAACCT
*
6026959 CCTCCACCACCATCTCCA
1 CCTCCACCACCACCTCCA
* * *
6026977 CCCCCACAACCTCCTCCA
1 CCTCCACCACCACCTCCA
*
6026995 CCTCCACCTCCACCTCC
1 CCTCCACCACCACCTCC
6027012 GGTTCTTCTG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.19, C:0.66, G:0.00, T:0.15
Consensus pattern (18 bp):
CCTCCACCACCACCTCCA
Found at i:6027739 original size:2 final size:2
Alignment explanation
Indices: 6027732--6027834 Score: 190
Period size: 2 Copynumber: 52.0 Consensus size: 2
6027722 TTACAATTTA
6027732 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6027774 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
6027816 AT AT AT AT AA AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT
6027835 TTTAAAATAT
Statistics
Matches: 98, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 97 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6032079 original size:2 final size:2
Alignment explanation
Indices: 6032074--6032100 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6032064 GAGACTTTTT
6032074 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6032101 TGGTTTCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6034138 original size:30 final size:28
Alignment explanation
Indices: 6034072--6034154 Score: 85
Period size: 30 Copynumber: 2.8 Consensus size: 28
6034062 ATTTTTGAAG
* *
6034072 TTGTTCATGTTCGTTAAGAATTTCAAATTTT
1 TTGTTCATGTTCGTT---TATTTAAAATTTT
6034103 TTGTTCATGTTCGTTTATTTAAAATTATGT
1 TTGTTCATGTTCGTTTATTTAAAATT-T-T
* *
6034133 TTGTTCATATTCGTTTGTTTAA
1 TTGTTCATGTTCGTTTATTTAA
6034155 TGTTCACGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
28 9 0.20
29 1 0.02
30 21 0.46
31 15 0.33
ACGTcount: A:0.23, C:0.08, G:0.13, T:0.55
Consensus pattern (28 bp):
TTGTTCATGTTCGTTTATTTAAAATTTT
Found at i:6034200 original size:25 final size:24
Alignment explanation
Indices: 6034154--6034201 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6034144 CGTTTGTTTA
*
6034154 ATGTTCACGAACATGTTTATGAAC
1 ATGTTCACGAACATGTTAATGAAC
*
6034178 ATGTTCACGAATTATGTTAATGAA
1 ATGTTCACGAA-CATGTTAATGAA
6034202 TAACATACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (24 bp):
ATGTTCACGAACATGTTAATGAAC
Found at i:6037519 original size:23 final size:23
Alignment explanation
Indices: 6037493--6037544 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
6037483 GTTTAACAAG
*
6037493 TGTCAATATAAGAGAATGATAGA
1 TGTCAATATAAGAAAATGATAGA
*
6037516 TGTCAATATAAGAAAATGATAGG
1 TGTCAATATAAGAAAATGATAGA
6037539 TGTCAA
1 TGTCAA
6037545 CCCTTGAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.46, C:0.06, G:0.21, T:0.27
Consensus pattern (23 bp):
TGTCAATATAAGAAAATGATAGA
Found at i:6037903 original size:33 final size:33
Alignment explanation
Indices: 6037866--6037930 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
6037856 AATTTGGTAA
* *
6037866 AAGATAGTTTGTAGAGTGTTAAAATTATGAGAT
1 AAGATAATTTGTAGAGAGTTAAAATTATGAGAT
* *
6037899 AAGATAATTTGTAGAGAGTTAAATTTGTGAGA
1 AAGATAATTTGTAGAGAGTTAAAATTATGAGA
6037931 ATAAAAGGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.40, C:0.00, G:0.25, T:0.35
Consensus pattern (33 bp):
AAGATAATTTGTAGAGAGTTAAAATTATGAGAT
Found at i:6038514 original size:23 final size:25
Alignment explanation
Indices: 6038469--6038519 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
6038459 TAATTCTATT
*
6038469 TAGGGGAATTTACATATAAATAACTAA
1 TAGGGGAATTTA-ATAT-AATAAATAA
6038496 TAGGGGAATTT-ATAT-ATAAATAA
1 TAGGGGAATTTAATATAATAAATAA
6038519 T
1 T
6038520 TCATTTGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 8 0.35
25 4 0.17
27 11 0.48
ACGTcount: A:0.47, C:0.04, G:0.16, T:0.33
Consensus pattern (25 bp):
TAGGGGAATTTAATATAATAAATAA
Found at i:6056557 original size:15 final size:15
Alignment explanation
Indices: 6056537--6056570 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
6056527 TACAAATGAA
6056537 ATTGGTCAATCCAGC
1 ATTGGTCAATCCAGC
6056552 ATTGGTCAATCCAGC
1 ATTGGTCAATCCAGC
6056567 ATTG
1 ATTG
6056571 ATCTTAGCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (15 bp):
ATTGGTCAATCCAGC
Found at i:6061375 original size:25 final size:26
Alignment explanation
Indices: 6061338--6061387 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
6061328 TTGTAAATAA
6061338 AAAAAAATATCTTTAGA-AATTTTCT
1 AAAAAAATATCTTTAGATAATTTTCT
* *
6061363 AAAATAATTTCTTTAGATAATTTTC
1 AAAAAAATATCTTTAGATAATTTTC
6061388 ATTCTACAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (26 bp):
AAAAAAATATCTTTAGATAATTTTCT
Found at i:6067278 original size:20 final size:20
Alignment explanation
Indices: 6067249--6067288 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
6067239 ATGGCCGTGG
*
6067249 CTGTCTAAAAT-ATTTGGTCA
1 CTGTCCAAAATCA-TTGGTCA
6067269 CTGTCCAAAATCATTGGTCA
1 CTGTCCAAAATCATTGGTCA
6067289 AAAATTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (20 bp):
CTGTCCAAAATCATTGGTCA
Found at i:6071986 original size:26 final size:25
Alignment explanation
Indices: 6071953--6072003 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
6071943 ATTTTTAAAT
*
6071953 AAATAATTAATAAAATTAATTGATC
1 AAATAATTAATAAAATCAATTGATC
*
6071978 AAATCAATTAATAAAATCAGTTGATC
1 AAAT-AATTAATAAAATCAATTGATC
6072004 TCATATAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.33
Consensus pattern (25 bp):
AAATAATTAATAAAATCAATTGATC
Found at i:6071994 original size:13 final size:13
Alignment explanation
Indices: 6071953--6071996 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
6071943 ATTTTTAAAT
6071953 AAAT-AATTAATA
1 AAATCAATTAATA
* * *
6071965 AAATTAATTGATC
1 AAATCAATTAATA
6071978 AAATCAATTAATA
1 AAATCAATTAATA
6071991 AAATCA
1 AAATCA
6071997 GTTGATCTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 4 0.15
13 22 0.85
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32
Consensus pattern (13 bp):
AAATCAATTAATA
Found at i:6079447 original size:16 final size:16
Alignment explanation
Indices: 6079409--6079450 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
6079399 AAAACACCGA
*
6079409 CACAAAGCCTACTAGG
1 CACAAATCCTACTAGG
6079425 CACAAATCCTACTAGG
1 CACAAATCCTACTAGG
6079441 CACAAATCCT
1 CACAAATCCT
6079451 GAAAACACCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.38, C:0.33, G:0.12, T:0.17
Consensus pattern (16 bp):
CACAAATCCTACTAGG
Found at i:6079482 original size:37 final size:37
Alignment explanation
Indices: 6079423--6079508 Score: 136
Period size: 37 Copynumber: 2.3 Consensus size: 37
6079413 AAGCCTACTA
* *
6079423 GGCACAAATCCTACTAGGCACAAATCCTGAAAACACC
1 GGCACAAAGCCTACTAGGCACAAAACCTGAAAACACC
* *
6079460 TGCACGAAGCCTACTAGGCACAAAACCTGAAAACACC
1 GGCACAAAGCCTACTAGGCACAAAACCTGAAAACACC
6079497 GGCACAAAGCCT
1 GGCACAAAGCCT
6079509 GAAAATTGTG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.40, C:0.33, G:0.16, T:0.12
Consensus pattern (37 bp):
GGCACAAAGCCTACTAGGCACAAAACCTGAAAACACC
Found at i:6080359 original size:2 final size:2
Alignment explanation
Indices: 6080352--6080379 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6080342 AACTTATAAT
6080352 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
6080380 AAATAACCTT
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:6081409 original size:24 final size:24
Alignment explanation
Indices: 6081347--6081400 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
6081337 CTCTGTCTGA
*
6081347 GCTCGTAAGAGCTAATCATTCTAG
1 GCTCGTAAAAGCTAATCATTCTAG
*
6081371 GCTCGTAAAAGCTAATCATTCTGG
1 GCTCGTAAAAGCTAATCATTCTAG
6081395 GCTCGT
1 GCTCGT
6081401 GTTGGCTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (24 bp):
GCTCGTAAAAGCTAATCATTCTAG
Found at i:6083805 original size:73 final size:74
Alignment explanation
Indices: 6083682--6083898 Score: 233
Period size: 73 Copynumber: 3.0 Consensus size: 74
6083672 GTTGGATCAT
* * * * * * * * *
6083682 CAGCACAAAACCTGCTAGGCAAATAGCCGAATACACCGACACGAAGCCTACTAAG-TACATAGCC
1 CAGCACAAAGCCTACTAGGCACATAGCCTAAAACACCGGCACAAAGCCTACTAAGACACAAAGCC
*
6083746 TGAAACCAC
66 TGAAAACAC
** *
6083755 TGGTACAAAGCCTACTAGGCACATAGCCTAAAACACCGGCACAAAGCCTACT-AGACACAAAGCC
1 CAGCACAAAGCCTACTAGGCACATAGCCTAAAACACCGGCACAAAGCCTACTAAGACACAAAGCC
6083819 TGAAAACAC
66 TGAAAACAC
* * * * * *
6083828 CAGCACGAAGCCTACTAGGCACAAAACCTGAAAACACCGGCACAAAACCTACT-AGGCAAAAAGC
1 CAGCACAAAGCCTACTAGGCACATAGCCT-AAAACACCGGCACAAAGCCTACTAAGACACAAAGC
6083892 CTGAAAA
65 CTGAAAA
6083899 TTGTGTAAGC
Statistics
Matches: 120, Mismatches: 22, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
72 2 0.02
73 80 0.67
74 38 0.32
ACGTcount: A:0.42, C:0.30, G:0.17, T:0.11
Consensus pattern (74 bp):
CAGCACAAAGCCTACTAGGCACATAGCCTAAAACACCGGCACAAAGCCTACTAAGACACAAAGCC
TGAAAACAC
Found at i:6083882 original size:37 final size:37
Alignment explanation
Indices: 6083684--6083898 Score: 238
Period size: 37 Copynumber: 5.9 Consensus size: 37
6083674 TGGATCATCA
* * *
6083684 GCACAAAACCTGCTAGGCA-AATAGCC-GAATACACCG
1 GCACAAAGCCTACTAGGCACAA-AGCCTGAAAACACCG
* * * * * * *
6083720 ACACGAAGCCTACTAAGTACATAGCCTGAAACCACTG
1 GCACAAAGCCTACTAGGCACAAAGCCTGAAAACACCG
* *
6083757 GTACAAAGCCTACTAGGCACATAGCCT-AAAACACCG
1 GCACAAAGCCTACTAGGCACAAAGCCTGAAAACACCG
* *
6083793 GCACAAAGCCTACTAGACACAAAGCCTGAAAACACCA
1 GCACAAAGCCTACTAGGCACAAAGCCTGAAAACACCG
* *
6083830 GCACGAAGCCTACTAGGCACAAAACCTGAAAACACCG
1 GCACAAAGCCTACTAGGCACAAAGCCTGAAAACACCG
* *
6083867 GCACAAAACCTACTAGGCAAAAAGCCTGAAAA
1 GCACAAAGCCTACTAGGCACAAAGCCTGAAAA
6083899 TTGTGTAAGC
Statistics
Matches: 147, Mismatches: 29, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
36 48 0.33
37 99 0.67
ACGTcount: A:0.42, C:0.30, G:0.17, T:0.11
Consensus pattern (37 bp):
GCACAAAGCCTACTAGGCACAAAGCCTGAAAACACCG
Found at i:6086789 original size:19 final size:19
Alignment explanation
Indices: 6086745--6086792 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
6086735 GTATTAAATG
*
6086745 GAAAAAGGAAAACATTCAT
1 GAAAAAAGAAAACATTCAT
**
6086764 GCGAAAAGAAAACATTCAT
1 GAAAAAAGAAAACATTCAT
6086783 GAAAAAAGAA
1 GAAAAAAGAA
6086793 CAGACAGGAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.60, C:0.10, G:0.17, T:0.12
Consensus pattern (19 bp):
GAAAAAAGAAAACATTCAT
Found at i:6091730 original size:39 final size:40
Alignment explanation
Indices: 6091667--6091800 Score: 155
Period size: 39 Copynumber: 3.3 Consensus size: 40
6091657 GTTTTGGTGA
*
6091667 TTTTTTACTGTTTTGGTTACTTTTTTTGCTGTTTTGATGGT
1 TTTTTTACTGTTTTGG-TACTTTTTTTACTGTTTTGATGGT
* * *
6091708 TTTTTTACTATTTTGGTA-TTTTTTTACTGTTTTGGTGTT
1 TTTTTTACTGTTTTGGTACTTTTTTTACTGTTTTGATGGT
* *
6091747 TTTTTTACTGTTTTGGTGCTTTCTTTTTACTGTTTTG-TTGT
1 TTTTTTACTGTTTTGGTAC-TT-TTTTTACTGTTTTGATGGT
*
6091788 TGTTTTTGCTGTT
1 T-TTTTTACTGTT
6091801 ATTTTTGCTG
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
39 34 0.43
40 2 0.03
41 20 0.25
42 24 0.30
ACGTcount: A:0.07, C:0.07, G:0.18, T:0.68
Consensus pattern (40 bp):
TTTTTTACTGTTTTGGTACTTTTTTTACTGTTTTGATGGT
Found at i:6091799 original size:20 final size:19
Alignment explanation
Indices: 6091656--6091800 Score: 146
Period size: 20 Copynumber: 7.2 Consensus size: 19
6091646 AATATATTGT
*
6091656 TGTTTTGGTGATTTTTTAC
1 TGTTTTGGTGTTTTTTTAC
* *
6091675 TGTTTTGGTTACTTTTTTTGC
1 TGTTTTGG-T-GTTTTTTTAC
*
6091696 TGTTTTGATGGTTTTTTTAC
1 TGTTTTGGT-GTTTTTTTAC
* *
6091716 TATTTTGGTATTTTTTTAC
1 TGTTTTGGTGTTTTTTTAC
6091735 TGTTTTGGTGTTTTTTTTAC
1 TGTTTTGGTG-TTTTTTTAC
6091755 TGTTTTGGTGCTTTCTTTTTAC
1 TGTTTTGGTG--TT-TTTTTAC
* *
6091777 TGTTTTGTTGTTGTTTTTGC
1 TGTTTTGGTGTT-TTTTTAC
6091797 TGTT
1 TGTT
6091801 ATTTTTGCTG
Statistics
Matches: 106, Mismatches: 15, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
19 25 0.24
20 48 0.45
21 17 0.16
22 16 0.15
ACGTcount: A:0.07, C:0.07, G:0.19, T:0.67
Consensus pattern (19 bp):
TGTTTTGGTGTTTTTTTAC
Found at i:6091806 original size:24 final size:24
Alignment explanation
Indices: 6091779--6091879 Score: 107
Period size: 24 Copynumber: 4.3 Consensus size: 24
6091769 CTTTTTACTG
*
6091779 TTTTGTTGTTGTTTTTGCTGTTAT
1 TTTTGTTGTTGTTTTTGCTGCTAT
* * *
6091803 TTTTGCTGTTATTTTTGTTGCTAT
1 TTTTGTTGTTGTTTTTGCTGCTAT
* * * *
6091827 TTTTATTGAT-ATTTTGCTGTTA-
1 TTTTGTTGTTGTTTTTGCTGCTAT
*
6091849 TTTTGTTGTTGTTTTTGTTGCTAT
1 TTTTGTTGTTGTTTTTGCTGCTAT
6091873 TTTTGTT
1 TTTTGTT
6091880 ATTTTTGGGA
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
22 8 0.13
23 18 0.30
24 34 0.57
ACGTcount: A:0.08, C:0.05, G:0.18, T:0.69
Consensus pattern (24 bp):
TTTTGTTGTTGTTTTTGCTGCTAT
Found at i:6091818 original size:13 final size:12
Alignment explanation
Indices: 6091779--6091930 Score: 93
Period size: 12 Copynumber: 13.2 Consensus size: 12
6091769 CTTTTTACTG
* *
6091779 TTTTGTTGTTGT
1 TTTTGCTGTTAT
6091791 TTTTGCTGTTAT
1 TTTTGCTGTTAT
6091803 TTTTGCTGTTAT
1 TTTTGCTGTTAT
* *
6091815 TTTTGTTGCTAT
1 TTTTGCTGTTAT
** *
6091827 TTTTATTGATA-
1 TTTTGCTGTTAT
6091838 TTTTGCTGTTA-
1 TTTTGCTGTTAT
* *
6091849 TTTTGTTGTTGT
1 TTTTGCTGTTAT
* *
6091861 TTTTGTTGCTA-
1 TTTTGCTGTTAT
6091872 TTTT--TGTTAT
1 TTTTGCTGTTAT
* * *
6091882 TTTTG-GGATAG
1 TTTTGCTGTTAT
*
6091893 TTTTGCTGTTAC
1 TTTTGCTGTTAT
*
6091905 TTTTACTGTT-T
1 TTTTGCTGTTAT
**
6091916 TTTTATTGTTAT
1 TTTTGCTGTTAT
6091928 TTT
1 TTT
6091931 GGTTGTTTGG
Statistics
Matches: 112, Mismatches: 23, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
9 4 0.04
10 4 0.04
11 38 0.34
12 66 0.59
ACGTcount: A:0.10, C:0.05, G:0.17, T:0.68
Consensus pattern (12 bp):
TTTTGCTGTTAT
Found at i:6091849 original size:35 final size:35
Alignment explanation
Indices: 6091803--6091886 Score: 111
Period size: 34 Copynumber: 2.5 Consensus size: 35
6091793 TTGCTGTTAT
6091803 TTTTGCTGTTATTTTTGTTGCTATTTTTATTGATA
1 TTTTGCTGTTATTTTTGTTGCTATTTTTATTGATA
* * * *
6091838 TTTTGCTGTTA-TTTTGTTGTTGTTTTTGTTGCTA
1 TTTTGCTGTTATTTTTGTTGCTATTTTTATTGATA
6091872 TTTT--TGTTATTTTTG
1 TTTTGCTGTTATTTTTG
6091887 GGATAGTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
32 5 0.11
33 5 0.11
34 23 0.52
35 11 0.25
ACGTcount: A:0.10, C:0.05, G:0.17, T:0.69
Consensus pattern (35 bp):
TTTTGCTGTTATTTTTGTTGCTATTTTTATTGATA
Found at i:6091914 original size:67 final size:69
Alignment explanation
Indices: 6091779--6091935 Score: 158
Period size: 67 Copynumber: 2.3 Consensus size: 69
6091769 CTTTTTACTG
* * * * * * *
6091779 TTTTGTTGTTGTTTTTGCTGTTATTTTTGCTGTTATTTTTGTTGCTATTTTTATTGATATTTTGC
1 TTTTGTTGTTGTTTTTGTTGCTATTTTT-CTGTTATTTTTGTGGATAGTTTTACTGATATTTTAC
6091844 TGTTA
65 TGTTA
* *
6091849 TTTTGTTGTTGTTTTTGTTGCTA-TTTT-TGTTATTTTTG-GGATAGTTTTGCTGTTACTTTTAC
1 TTTTGTTGTTGTTTTTGTTGCTATTTTTCTGTTATTTTTGTGGATAGTTTTACTGATA-TTTTAC
*
6091911 TGTTT
65 TGTTA
* * *
6091916 TTTTATTGTTATTTTGGTTG
1 TTTTGTTGTTGTTTTTGTTG
6091936 TTTGGATGTT
Statistics
Matches: 73, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
66 11 0.15
67 37 0.51
69 4 0.05
70 21 0.29
ACGTcount: A:0.10, C:0.05, G:0.18, T:0.67
Consensus pattern (69 bp):
TTTTGTTGTTGTTTTTGTTGCTATTTTTCTGTTATTTTTGTGGATAGTTTTACTGATATTTTACT
GTTA
Found at i:6093928 original size:18 final size:17
Alignment explanation
Indices: 6093902--6093935 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
6093892 CGAGTACAAA
6093902 ATTTAAATTTTCTGCTTT
1 ATTTAAA-TTTCTGCTTT
*
6093920 ATTTCAATTTCTGCTT
1 ATTTAAATTTCTGCTT
6093936 ATCAAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.21, C:0.15, G:0.06, T:0.59
Consensus pattern (17 bp):
ATTTAAATTTCTGCTTT
Found at i:6096004 original size:13 final size:14
Alignment explanation
Indices: 6095984--6096027 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 14
6095974 TCAAAACTTA
6095984 TAATAAAATAATTT
1 TAATAAAATAATTT
*
6095998 TAA-AAAAGAA-TT
1 TAATAAAATAATTT
*
6096010 CAATAAAATAATTT
1 TAATAAAATAATTT
6096024 TAAT
1 TAAT
6096028 GTAGAGCTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 4 0.17
13 12 0.50
14 8 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (14 bp):
TAATAAAATAATTT
Found at i:6100328 original size:15 final size:15
Alignment explanation
Indices: 6100284--6100329 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
6100274 TCATTTTATA
*
6100284 TTTTAATCACTTATG
1 TTTTAATCACTTACG
*
6100299 TTTGAAAT-A-TTACG
1 TTT-TAATCACTTACG
6100313 TTTTAATCACTTACG
1 TTTTAATCACTTACG
6100328 TT
1 TT
6100330 ATCGTGTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
13 3 0.12
14 8 0.32
15 11 0.44
16 3 0.12
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.50
Consensus pattern (15 bp):
TTTTAATCACTTACG
Found at i:6102791 original size:3 final size:3
Alignment explanation
Indices: 6102783--6102822 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
6102773 TCTAATTGTT
6102783 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
6102823 CATGTAGTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:6102949 original size:12 final size:13
Alignment explanation
Indices: 6102929--6102964 Score: 65
Period size: 12 Copynumber: 2.8 Consensus size: 13
6102919 GAGAGAGAGA
6102929 GAGGGGGAGGGGG
1 GAGGGGGAGGGGG
6102942 GA-GGGGAGGGGG
1 GAGGGGGAGGGGG
6102954 GAGGGGGAGGG
1 GAGGGGGAGGG
6102965 AGATAAGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.17, C:0.00, G:0.83, T:0.00
Consensus pattern (13 bp):
GAGGGGGAGGGGG
Found at i:6107703 original size:520 final size:517
Alignment explanation
Indices: 6106725--6107764 Score: 1954
Period size: 520 Copynumber: 2.0 Consensus size: 517
6106715 TAATTCTTAC
*
6106725 AATTTGTACTTAATAATTAATATTTCATCTTTAAGCTTAAAAATTTTCCAGTGTTTTAGGCTTTT
1 AATTTGTACTTAATAATTAATATTTCATCTTTAAGCTTAAAAAATTTCCAGTGTTTTAGGCTTTT
6106790 AGCATGGCAGTAAATGGTTAGACATTACATGTTGCTGTATGCACTACATTACCAGTGCTAGACAT
66 AGCATGGCAGTAAATGGTTAGACATTACATGTTGCTGTATGCACTACATTACCAGTGCTAGACAT
6106855 TTAATAGTTAGACACAAACACAAAAAAAAAAGACTAGTCACACTTGCACGAGCACAGATTAAACA
131 TTAATAGTTAGACACAAACACAAAAAAAAAAGACTAGTCACACTTGCACGAGCACAGATTAAACA
6106920 TTTTACTAGCTTGAAGCCTATAAGAGGGTTGTAATAATCCCTTTGAGATAATGGCTGATTGTCAA
196 TTTTACTAGCTTGAAGCCTATAAGAGGGTTGTAATAATCCCTTTGAGATAATGGCTGATTGTCAA
6106985 GCCTATATTTACAACATGAATCTTCCTACAATTTTTGACACCAATTCAGATTCTGATTTTCTTGA
261 GCCTATATTTACAACATGAATCTTCCTACAATTTTTGACACCAATTCAGATTCTGATTTTCTTGA
*
6107050 TTGTGGGCCTATATAGCTGGGCTTTTTCCAAGTTCCTACATGGAGAATTTATGGTCTTTACTTTC
326 TTGTGGGCCTATATAGCTGGGCTTTTTCCAAGTTCCTACATGGAGAATTTATGGTCCTTACTTTC
*
6107115 TAATTTAGTTATAACTTATAATATATGGTTTAATTTAGTCTATATTCAAAGGTTGATTTCATTAT
391 TAATTTAGTTATAACTTATAATATATCGTTTAATTTAGTCTATATTCAAAGGTTGATTTCATTAT
6107180 TTGAGCATTAAGATACTAAAGAAGTCCTCAAAAGCATTCCTTGTGCTAAAGGAATATTATGA
456 TTGAGCATTAAGATACTAAAGAAGTCCTCAAAAGCATTCCTTGTGCTAAAGGAATATTATGA
6107242 AATTTGTACTTAATAATTAATATTTCATCTTTAAGCTTAAAAAATTTCCAGTGTTTTAGGCTTTT
1 AATTTGTACTTAATAATTAATATTTCATCTTTAAGCTTAAAAAATTTCCAGTGTTTTAGGCTTTT
* *
6107307 AGCATGGCAGTAAATGGTTAGATATTATATGTTGCTGTATGCACTACATTACCAGTGCTAGACAT
66 AGCATGGCAGTAAATGGTTAGACATTACATGTTGCTGTATGCACTACATTACCAGTGCTAGACAT
* *
6107372 TTAATAGTTAGAGACACACACACAAAAAAAAAGACTAGTCACACTTGCACGAGCACAGATTAAAC
131 TTAATAGTTAGACACAAACACA-AAAAAAAAAGACTAGTCACACTTGCACGAGCACAGATTAAAC
6107437 ATTTTACTAGCTTGAAGCCTATAAGAGGGTTGTAATAATCCCTTTGAGATAATGGCTGATTGTCA
195 ATTTTACTAGCTTGAAGCCTATAAGAGGGTTGTAATAATCCCTTTGAGATAATGGCTGATTGTCA
*
6107502 AGCCTATATTTACAACATGAATCTTCCTACAATTTTTTTGACACCAATTCAGATTTTGATTTTCT
260 AGCCTATATTTACAACATGAATCTTCCTACAA--TTTTTGACACCAATTCAGATTCTGATTTTCT
6107567 TGATTGTGGGCCTATATAGCTGGGCTTTTTCCAAGTTCCTACATGGAGAATTTATGGTCCTTACT
323 TGATTGTGGGCCTATATAGCTGGGCTTTTTCCAAGTTCCTACATGGAGAATTTATGGTCCTTACT
6107632 TTCTAATTTAGTTATAACTTATAATATATCGTTTAATTTAGTCTATATTCAAAGGTTGATTTCAT
388 TTCTAATTTAGTTATAACTTATAATATATCGTTTAATTTAGTCTATATTCAAAGGTTGATTTCAT
* * *
6107697 TATTTGAGCATTACGATACTAAAGAAGTCCTCATAAGCATTCCTTGTGCTAAAGGAGTATTATGA
453 TATTTGAGCATTAAGATACTAAAGAAGTCCTCAAAAGCATTCCTTGTGCTAAAGGAATATTATGA
6107762 AAT
1 AAT
6107765 ATGTGCAGAT
Statistics
Matches: 509, Mismatches: 11, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
517 147 0.29
518 139 0.27
520 223 0.44
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (517 bp):
AATTTGTACTTAATAATTAATATTTCATCTTTAAGCTTAAAAAATTTCCAGTGTTTTAGGCTTTT
AGCATGGCAGTAAATGGTTAGACATTACATGTTGCTGTATGCACTACATTACCAGTGCTAGACAT
TTAATAGTTAGACACAAACACAAAAAAAAAAGACTAGTCACACTTGCACGAGCACAGATTAAACA
TTTTACTAGCTTGAAGCCTATAAGAGGGTTGTAATAATCCCTTTGAGATAATGGCTGATTGTCAA
GCCTATATTTACAACATGAATCTTCCTACAATTTTTGACACCAATTCAGATTCTGATTTTCTTGA
TTGTGGGCCTATATAGCTGGGCTTTTTCCAAGTTCCTACATGGAGAATTTATGGTCCTTACTTTC
TAATTTAGTTATAACTTATAATATATCGTTTAATTTAGTCTATATTCAAAGGTTGATTTCATTAT
TTGAGCATTAAGATACTAAAGAAGTCCTCAAAAGCATTCCTTGTGCTAAAGGAATATTATGA
Found at i:6113005 original size:15 final size:16
Alignment explanation
Indices: 6112981--6113021 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
6112971 GCTATTCCCA
* *
6112981 TCTTCGTTTCTT-TGT
1 TCTTCTTTTCTTCTGC
6112996 TCTTCTTTTCTTCTGC
1 TCTTCTTTTCTTCTGC
6113012 T-TTCTTTTCT
1 TCTTCTTTTCT
6113022 CTTTGTTCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 20 0.87
16 3 0.13
ACGTcount: A:0.00, C:0.24, G:0.07, T:0.68
Consensus pattern (16 bp):
TCTTCTTTTCTTCTGC
Found at i:6116505 original size:5 final size:5
Alignment explanation
Indices: 6116495--6116532 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
6116485 GTCCGTTGGT
6116495 CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTC
1 CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTC
6116533 CTCACCTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (5 bp):
CTCTC
Found at i:6139368 original size:72 final size:70
Alignment explanation
Indices: 6139241--6139372 Score: 192
Period size: 72 Copynumber: 1.9 Consensus size: 70
6139231 GATTAGGGTC
* * * **
6139241 AAATTTTTTTAAAAAAAATAATTAAATTTTTATTATTTTGCATTCAATTGGATACTTGAAAAAAC
1 AAATTTTTTTAAAAAAAATAATTAAAGTTATATTATTTTGCACTCAATTAAATACTTGAAAAAAC
6139306 CCTTA
66 CCTTA
*
6139311 AAATTTTTTTAAAAAAAATAATTAAACCGTTATATTTTTTTGCACTCAATTAAATACTTGAA
1 AAATTTTTTTAAAAAAAATAATTAAA--GTTATATTATTTTGCACTCAATTAAATACTTGAA
6139373 TTTTCAAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
70 26 0.48
72 28 0.52
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.42
Consensus pattern (70 bp):
AAATTTTTTTAAAAAAAATAATTAAAGTTATATTATTTTGCACTCAATTAAATACTTGAAAAAAC
CCTTA
Found at i:6139615 original size:30 final size:29
Alignment explanation
Indices: 6139538--6139613 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 29
6139528 TAAAAAATTA
*
6139538 TAAAAATTATAAAAATATTTAATTTTAAT
1 TAAAAATTATAAAAAAATTTAATTTTAAT
*
6139567 TAAAAAACTATAAAAAAATTTAAATTTT-AT
1 T-AAAAATTATAAAAAAATTT-AATTTTAAT
*
6139597 TAAAAATTAGAAAAAAA
1 TAAAAATTATAAAAAAA
6139614 ATAAAATATA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 15 0.37
30 20 0.49
31 6 0.15
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (29 bp):
TAAAAATTATAAAAAAATTTAATTTTAAT
Found at i:6139903 original size:11 final size:11
Alignment explanation
Indices: 6139887--6139920 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
6139877 TTTAATGCAA
6139887 TTTATAATTTT
1 TTTATAATTTT
6139898 TTTATAA-TTT
1 TTTATAATTTT
6139908 TTTATAATTTT
1 TTTATAATTTT
6139919 TT
1 TT
6139921 ACGATTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTATAATTTT
Found at i:6139908 original size:10 final size:10
Alignment explanation
Indices: 6139887--6139921 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
6139877 TTTAATGCAA
6139887 TTTATAATTTT
1 TTTATAA-TTT
6139898 TTTATAATTT
1 TTTATAATTT
6139908 TTTATAATTT
1 TTTATAATTT
6139918 TTTA
1 TTTA
6139922 CGATTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 17 0.71
11 7 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTATAATTT
Found at i:6139987 original size:28 final size:27
Alignment explanation
Indices: 6139947--6140023 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 27
6139937 AATCCTAATT
*
6139947 TTTAATAAATTTTATATTTTTATTAAAA
1 TTTAATAATTTTTATATTTTTATT-AAA
*
6139975 TTTAATAATTTTTATAAATTTTA-TAAA
1 TTTAATAATTTTTAT-ATTTTTATTAAA
*
6140002 TTT--TATTTATTTATATTTTTAT
1 TTTAATAATT-TTTATATTTTTAT
6140024 AGTTTTTTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
25 10 0.24
26 5 0.12
27 6 0.14
28 15 0.36
29 6 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
TTTAATAATTTTTATATTTTTATTAAA
Found at i:6139996 original size:9 final size:9
Alignment explanation
Indices: 6139946--6140007 Score: 63
Period size: 9 Copynumber: 6.7 Consensus size: 9
6139936 AAATCCTAAT
6139946 TTTTAATAAA
1 TTTT-ATAAA
*
6139956 TTTTAT-AT
1 TTTTATAAA
6139964 TTTTATTAAAA
1 TTTTA-T-AAA
* *
6139975 TTTAATAAT
1 TTTTATAAA
6139984 TTTTATAAA
1 TTTTATAAA
6139993 TTTTATAAA
1 TTTTATAAA
6140002 TTTTAT
1 TTTTAT
6140008 TTATTTATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
8 6 0.14
9 27 0.63
10 5 0.12
11 5 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTTATAAA
Found at i:6140000 original size:18 final size:18
Alignment explanation
Indices: 6139942--6140024 Score: 82
Period size: 18 Copynumber: 4.6 Consensus size: 18
6139932 AAAAAAATCC
6139942 TAATTTTTAATAAATTTTA
1 TAATTTTT-ATAAATTTTA
*
6139961 T-ATTTTTATTAAAATTTAA
1 TAATTTTTA-T-AAATTTTA
6139980 TAATTTTTATAAATTTTA
1 TAATTTTTATAAATTTTA
* **
6139998 TAAATTTTATTTA-TTTA
1 TAATTTTTATAAATTTTA
6140015 T-ATTTTTATA
1 TAATTTTTATA
6140025 GTTTTTTGTC
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
16 7 0.13
17 6 0.11
18 24 0.44
19 10 0.19
20 7 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TAATTTTTATAAATTTTA
Found at i:6140922 original size:28 final size:27
Alignment explanation
Indices: 6140890--6140947 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
6140880 TAAAACCTTG
6140890 AATCTT-AAACATTAAATCTCAAACCCCA
1 AATCTTGAAACA-TAAAT-TCAAACCCCA
* *
6140918 AATCTTGAACCATAAATTCAAACCCTA
1 AATCTTGAAACATAAATTCAAACCCCA
6140945 AAT
1 AAT
6140948 TTAGAGTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 12 0.44
28 11 0.41
29 4 0.15
ACGTcount: A:0.47, C:0.26, G:0.02, T:0.26
Consensus pattern (27 bp):
AATCTTGAAACATAAATTCAAACCCCA
Found at i:6142326 original size:24 final size:24
Alignment explanation
Indices: 6142265--6142327 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
6142255 TAGAGTAATA
* * * *
6142265 AGAGTTTGACTCAAATAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
*
6142289 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
6142313 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
6142328 GATTATTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.51, C:0.08, G:0.14, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:6142765 original size:22 final size:22
Alignment explanation
Indices: 6142720--6142764 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
6142710 AATTTTTTTT
6142720 AATAAATATTAAAATAAAATAA
1 AATAAATATTAAAATAAAATAA
*
6142742 AATAAATATTAAAA-AAATTAA
1 AATAAATATTAAAATAAAATAA
6142763 AA
1 AA
6142765 AATATGAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (22 bp):
AATAAATATTAAAATAAAATAA
Found at i:6143523 original size:6 final size:6
Alignment explanation
Indices: 6143485--6143578 Score: 63
Period size: 6 Copynumber: 15.8 Consensus size: 6
6143475 GGCTTGGGCT
* **
6143485 TTTAAA GTTTAAA -TTAAT TTTAAA TTT-GT TTTAAA TTTAAA TTT--A
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
6143530 TCTTAAA TTTAAA TTTACTTA TTTAAA TTT-AT TTTAGA TTTAAA TTTAA
1 T-TTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
6143579 TCAAATTCAA
Statistics
Matches: 67, Mismatches: 12, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
4 2 0.03
5 13 0.19
6 39 0.58
7 8 0.12
8 5 0.07
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:6143523 original size:17 final size:17
Alignment explanation
Indices: 6143498--6143577 Score: 94
Period size: 17 Copynumber: 4.9 Consensus size: 17
6143488 AAAGTTTAAA
* * *
6143498 TTAATTTTAAATTTGTT
1 TTAAATTTAAATTTATC
6143515 TTAAATTTAAATTTATC
1 TTAAATTTAAATTTATC
6143532 TTAAATTTAAATTTA-C
1 TTAAATTTAAATTTATC
*
6143548 TT--ATTTAAATTTATT
1 TTAAATTTAAATTTATC
*
6143563 TTAGATTTAAATTTA
1 TTAAATTTAAATTTA
6143578 ATCAAATTCA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
14 11 0.20
15 2 0.04
16 3 0.05
17 40 0.71
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (17 bp):
TTAAATTTAAATTTATC
Found at i:6143526 original size:28 final size:29
Alignment explanation
Indices: 6143484--6143539 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
6143474 GGGCTTGGGC
*
6143484 TTTTAAAGTTTAAATTAATTTTAAATTTG
1 TTTTAAAGTTTAAATTAATCTTAAATTTG
*
6143513 TTTTAAA-TTTAAATTTATCTTAAATTT
1 TTTTAAAGTTTAAATTAATCTTAAATTT
6143540 AAATTTACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (29 bp):
TTTTAAAGTTTAAATTAATCTTAAATTTG
Found at i:6143557 original size:31 final size:31
Alignment explanation
Indices: 6143519--6143577 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
6143509 TTTGTTTTAA
6143519 ATTTAAATTTATCTTAAATTTAAATTTACTT
1 ATTTAAATTTATCTTAAATTTAAATTTACTT
* *
6143550 ATTTAAATTTATTTTAGATTTAAATTTA
1 ATTTAAATTTATCTTAAATTTAAATTTA
6143578 ATCAAATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (31 bp):
ATTTAAATTTATCTTAAATTTAAATTTACTT
Found at i:6143570 original size:11 final size:11
Alignment explanation
Indices: 6143492--6143571 Score: 52
Period size: 11 Copynumber: 6.9 Consensus size: 11
6143482 GCTTTTAAAG
*
6143492 TTTAAATTAAT
1 TTTAAATTTAT
*
6143503 TTTAAATTTGT
1 TTTAAATTTAT
*
6143514 TTTAAATTTAAA
1 TTTAAATTT-AT
** * *
6143526 TTTATCTTAAA
1 TTTAAATTTAT
6143537 TTTAAATTTACTT
1 TTTAAATTTA--T
6143550 ATTTAAATTTAT
1 -TTTAAATTTAT
*
6143562 TTTAGATTTA
1 TTTAAATTTA
6143572 AATTTAATCA
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
11 36 0.68
12 7 0.13
14 10 0.19
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:6144430 original size:12 final size:12
Alignment explanation
Indices: 6144415--6144445 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
6144405 AATATAGTAT
*
6144415 TAATATTTTTAA
1 TAATAATTTTAA
6144427 TAATAATTTTAA
1 TAATAATTTTAA
6144439 TAATAAT
1 TAATAAT
6144446 AATTAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAATAATTTTAA
Found at i:6144447 original size:15 final size:15
Alignment explanation
Indices: 6144386--6144449 Score: 53
Period size: 15 Copynumber: 4.4 Consensus size: 15
6144376 AATAACAGTT
*
6144386 ATAAGTTTTAATAGTA
1 ATAA-TTTTAATAATA
* * * *
6144402 ATAAATATAGTATTA
1 ATAATTTTAATAATA
6144417 AT-ATTTT--TAATA
1 ATAATTTTAATAATA
6144429 ATAATTTTAATAATA
1 ATAATTTTAATAATA
6144444 ATAATT
1 ATAATT
6144450 AATAAATAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
12 6 0.16
13 5 0.13
14 3 0.08
15 20 0.53
16 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (15 bp):
ATAATTTTAATAATA
Found at i:6145589 original size:29 final size:28
Alignment explanation
Indices: 6145548--6145743 Score: 137
Period size: 29 Copynumber: 6.8 Consensus size: 28
6145538 AAAATTTTAG
* * *
6145548 AAAATTACGTTTTAACCCCGAACTTCCA
1 AAAATTACATTTTTACCCCGAACTTCCT
* *
6145576 AAAATTACATTTTTACCCCTAAACTTTCT
1 AAAATTACATTTTTACCCC-GAACTTCCT
* * * *
6145605 AAAATTCCATTTTAACCCCG-ATTTCACCA
1 AAAATTACATTTTTACCCCGAACTT--CCT
*
6145634 AAAATTACCATTTTTACCCCTGAACTTTCT
1 AAAATTA-CATTTTTACCCC-GAACTTCCT
* * *
6145664 AAAATTCCATTTTTAACCCCG-ATTTCACC
1 AAAATTACATTTTT-ACCCCGAACTTC-CT
* *
6145693 AAAATTACCA-TTTTACCCCAAATTTCTCT
1 AAAATTA-CATTTTTACCCCGAACTTC-CT
*
6145722 AAAATTCCATTTTTGACCCCGA
1 AAAATTACATTTTT-ACCCCGA
6145744 TTTCACCAAA
Statistics
Matches: 130, Mismatches: 26, Indels: 22
0.73 0.15 0.12
Matches are distributed among these distances:
27 3 0.02
28 27 0.21
29 65 0.50
30 31 0.24
31 1 0.01
32 3 0.02
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (28 bp):
AAAATTACATTTTTACCCCGAACTTCCT
Found at i:6145597 original size:58 final size:57
Alignment explanation
Indices: 6145520--6145770 Score: 210
Period size: 58 Copynumber: 4.3 Consensus size: 57
6145510 AACAGTCTAG
* * *
6145520 AAATTGCA-TTTTAACCCTAAAATTT-TAGAAAATTACGTTTTAACCCCGAACTT-CCAA
1 AAATTACATTTTTACCCCTAAAATTTCT--AAAATTACATTTTAACCCCG-ACTTACCAA
* * *
6145577 AAATTACATTTTTACCCCTAAACTTTCTAAAATTCCATTTTAACCCCGATTTCACCAA
1 AAATTACATTTTTACCCCTAAAATTTCTAAAATTACATTTTAACCCCGACTT-ACCAA
* * * *
6145635 AAATTACCATTTTTACCCCTGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACC-A
1 AAATTA-CATTTTTACCCCTAAAATTTCTAAAATTACA-TTTTAACCCCGACTT-ACCAA
* * * *
6145694 AAATTACCA-TTTTACCCC-AAATTTCTCTAAAATTCCATTTTTGACCCCGATTTCACCAA
1 AAATTA-CATTTTTACCCCTAAAATT-TCTAAAATTACA-TTTTAACCCCGACTT-ACCAA
*
6145753 AAAATACCA-TTTTACCCC
1 AAATTA-CATTTTTACCCC
6145771 CGCGAGTCCA
Statistics
Matches: 175, Mismatches: 11, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
56 3 0.02
57 29 0.17
58 65 0.37
59 59 0.34
60 19 0.11
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (57 bp):
AAATTACATTTTTACCCCTAAAATTTCTAAAATTACATTTTAACCCCGACTTACCAA
Found at i:6145660 original size:59 final size:59
Alignment explanation
Indices: 6145557--6145770 Score: 305
Period size: 59 Copynumber: 3.7 Consensus size: 59
6145547 GAAAATTACG
*
6145557 TTTTAACCCCGAACTT--CCAAAAATTA-CATTTTTACCCCTAAACTTTCTAAAATTCCA-
1 TTTTAACCCCG-ATTTCACCAAAAATTACCA-TTTTACCCCTAAACTTTCTAAAATTCCAT
*
6145614 TTTTAACCCCGATTTCACCAAAAATTACCATTTTTACCCCTGAACTTTCTAAAATTCCAT
1 TTTTAACCCCGATTTCACCAAAAATTACCA-TTTTACCCCTAAACTTTCTAAAATTCCAT
*
6145674 TTTTAACCCCGATTTCACC-AAAATTACCATTTTACCCC-AAATTTCTCTAAAATTCCAT
1 TTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTAAACTT-TCTAAAATTCCAT
* *
6145732 TTTTGACCCCGATTTCACCAAAAAATACCATTTTACCCC
1 TTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCC
6145771 CGCGAGTCCA
Statistics
Matches: 145, Mismatches: 6, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
56 3 0.02
57 15 0.10
58 50 0.34
59 58 0.40
60 19 0.13
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (59 bp):
TTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTAAACTTTCTAAAATTCCAT
Found at i:6145746 original size:29 final size:28
Alignment explanation
Indices: 6145576--6145747 Score: 143
Period size: 29 Copynumber: 5.9 Consensus size: 28
6145566 CGAACTTCCA
* * *
6145576 AAAATTACATTTTTACCCCTAAACTT-TCT
1 AAAATTCCATTTTTACCCC--GATTTCTCT
* * *
6145605 AAAATTCCATTTTAACCCCGATTTCACCA
1 AAAATTCCATTTTTACCCCGATTTC-TCT
*
6145634 AAAATTACCATTTTTACCCCTGAACTT-TCT
1 AAAATT-CCATTTTTACCCC-G-ATTTCTCT
* *
6145664 AAAATTCCATTTTTAACCCCGATTTCACC
1 AAAATTCCATTTTT-ACCCCGATTTCTCT
*
6145693 AAAATTACCA-TTTTACCCCAAATTTCTCT
1 AAAATT-CCATTTTTACCCC-GATTTCTCT
6145722 AAAATTCCATTTTTGACCCCGATTTC
1 AAAATTCCATTTTT-ACCCCGATTTC
6145748 ACCAAAAAAT
Statistics
Matches: 115, Mismatches: 17, Indels: 22
0.75 0.11 0.14
Matches are distributed among these distances:
27 3 0.03
28 11 0.10
29 65 0.57
30 32 0.28
31 1 0.01
32 3 0.03
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.37
Consensus pattern (28 bp):
AAAATTCCATTTTTACCCCGATTTCTCT
Found at i:6145754 original size:29 final size:28
Alignment explanation
Indices: 6145605--6145754 Score: 153
Period size: 29 Copynumber: 5.1 Consensus size: 28
6145595 TAAACTTTCT
*
6145605 AAAATTCCATTTTAACCCCGATTTCACC
1 AAAATTCCATTTTTACCCCGATTTCACC
*
6145633 AAAAATTACCATTTTTACCCCTGAACTTT--CT
1 -AAAATT-CCATTTTTACCCC-G-A-TTTCACC
6145664 AAAATTCCATTTTTAACCCCGATTTCACC
1 AAAATTCCATTTTT-ACCCCGATTTCACC
* * *
6145693 AAAATTACCA-TTTTACCCCAAATTTCTCT
1 AAAATT-CCATTTTTACCCC-GATTTCACC
6145722 AAAATTCCATTTTTGACCCCGATTTCACC
1 AAAATTCCATTTTT-ACCCCGATTTCACC
6145751 AAAA
1 AAAA
6145755 AATACCATTT
Statistics
Matches: 101, Mismatches: 9, Indels: 22
0.77 0.07 0.17
Matches are distributed among these distances:
27 3 0.03
28 9 0.09
29 52 0.51
30 31 0.31
31 2 0.02
32 1 0.01
33 3 0.03
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (28 bp):
AAAATTCCATTTTTACCCCGATTTCACC
Found at i:6145770 original size:29 final size:30
Alignment explanation
Indices: 6145605--6145765 Score: 131
Period size: 30 Copynumber: 5.4 Consensus size: 30
6145595 TAAACTTTCT
*
6145605 AAAATTCCA-TTTTAACCCCGATTTCACCA
1 AAAATACCATTTTTAACCCCGATTTCACCA
*
6145634 AAAATTACCATTTTT-ACCCCTGAACTTT---CT
1 AAAA-TACCATTTTTAACCCC-G-A-TTTCACCA
*
6145664 AAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATACCATTTTTAACCCCGATTTCACCA
* * * *
6145694 AAATTACCA-TTTT-ACCCCAAATTTC-TCT
1 AAAATACCATTTTTAACCCC-GATTTCACCA
* *
6145722 AAAATTCCATTTTTGACCCCGATTTCACCAA
1 AAAATACCATTTTTAACCCCGATTTCACC-A
6145753 AAAATACCATTTT
1 AAAATACCATTTT
6145766 ACCCCCGCGA
Statistics
Matches: 103, Mismatches: 15, Indels: 26
0.72 0.10 0.18
Matches are distributed among these distances:
27 3 0.03
28 14 0.14
29 32 0.31
30 33 0.32
31 17 0.17
32 1 0.01
33 3 0.03
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATACCATTTTTAACCCCGATTTCACCA
Found at i:6145800 original size:58 final size:57
Alignment explanation
Indices: 6145605--6145793 Score: 213
Period size: 59 Copynumber: 3.2 Consensus size: 57
6145595 TAAACTTTCT
* * *
6145605 AAAATTCCA-TTTTAACCCCGATTTCACCAAAAATTACCATTTTTACCCCTGAACTTTCT
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCA-TTTTACCCCCG--CATTCC
**
6145664 AAAATTCCATTTTTAACCCCGATTTCACC-AAAATTACCATTTTA-CCCCAAATTTCTC
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGCA-TTC-C
* * *
6145721 TAAAATTCCATTTTTGACCCCGATTTCACCAAAAAATACCATTTTACCCCCGCGAGTCC
1 -AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGC-ATTCC
6145780 AAAATTACCATTTT
1 AAAATT-CCATTTT
6145794 ACCCCCGGGT
Statistics
Matches: 112, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
56 3 0.03
57 3 0.03
58 39 0.35
59 41 0.37
60 25 0.22
61 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (57 bp):
AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGCATTCC
Found at i:6145821 original size:28 final size:28
Alignment explanation
Indices: 6145752--6145813 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
6145742 GATTTCACCA
*
6145752 AAAAATACCATTTTACCCCCGCGAGTCC
1 AAAAGTACCATTTTACCCCCGCGAGTCC
* *
6145780 AAAATTACCATTTTACCCCCGGGTA-TCC
1 AAAAGTACCATTTTACCCCCGCG-AGTCC
6145808 AAAAGT
1 AAAAGT
6145814 CCCGTTTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.34, C:0.31, G:0.11, T:0.24
Consensus pattern (28 bp):
AAAAGTACCATTTTACCCCCGCGAGTCC
Found at i:6158316 original size:76 final size:76
Alignment explanation
Indices: 6157936--6158526 Score: 936
Period size: 76 Copynumber: 7.8 Consensus size: 76
6157926 ATCAGACCGC
* * * *
6157936 AGCAAGATCATTCCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACACGTCTTTATCTCTGAA
1 AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
6158001 ATTGAAGTAAG
66 ATTGAAGTAAG
*
6158012 AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAA
1 AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
6158076 ATTGAAGTAAG
66 ATTGAAGTAAG
* * *
6158087 AGCAAGATCTTTTCCTATCTGCTTGAAATTGAAGTAGAG-TGGATAACACGTATTTATCTCTGAA
1 AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
*
6158151 ATTGAAGTAAA
66 ATTGAAGTAAG
*
6158162 AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAA
1 AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
6158226 ATTGAAGTAAG
66 ATTGAAGTAAG
*
6158237 AGCAAGATCTTTTCCTATCCGCTTGAAGTTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
1 AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
6158302 ATTGAAGTAAG
66 ATTGAAGTAAG
* * * * * *
6158313 AGCAAGATCGTTTCCCATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAA
1 AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
6158378 ATTGAAGTAAG
66 ATTGAAGTAAG
* * *
6158389 AGCAAGATCATTTCATATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
1 AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
6158454 ATTGAAGTAAG
66 ATTGAAGTAAG
* * * * *
6158465 AGCAAGATCGTTTCCCATCCTCTTGAAATTGAAGTAAAGTTGGATAGCAAGTCTTTATCTCT
1 AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCT
6158527 CTGAAGAGCA
Statistics
Matches: 485, Mismatches: 29, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
75 218 0.45
76 267 0.55
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (76 bp):
AGCAAGATCTTTTCCTATCCGCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
ATTGAAGTAAG
Found at i:6158833 original size:6 final size:6
Alignment explanation
Indices: 6158795--6158888 Score: 63
Period size: 6 Copynumber: 15.8 Consensus size: 6
6158785 GGCTTGGGCT
* **
6158795 TTTAAA GTTTAAA -TTAAT TTTAAA TTT-GT TTTAAA TTTAAA TTT--A
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
6158840 TCTTAAA TTTAAA TTTACTTA TTTAAA TTT-AT TTTAGA TTTAAA TTTAA
1 T-TTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
6158889 TCAAATTCAA
Statistics
Matches: 67, Mismatches: 12, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
4 2 0.03
5 13 0.19
6 39 0.58
7 8 0.12
8 5 0.07
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:6158833 original size:17 final size:17
Alignment explanation
Indices: 6158808--6158887 Score: 94
Period size: 17 Copynumber: 4.9 Consensus size: 17
6158798 AAAGTTTAAA
* * *
6158808 TTAATTTTAAATTTGTT
1 TTAAATTTAAATTTATC
6158825 TTAAATTTAAATTTATC
1 TTAAATTTAAATTTATC
6158842 TTAAATTTAAATTTA-C
1 TTAAATTTAAATTTATC
*
6158858 TT--ATTTAAATTTATT
1 TTAAATTTAAATTTATC
*
6158873 TTAGATTTAAATTTA
1 TTAAATTTAAATTTA
6158888 ATCAAATTCA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
14 11 0.20
15 2 0.04
16 3 0.05
17 40 0.71
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (17 bp):
TTAAATTTAAATTTATC
Found at i:6158836 original size:28 final size:29
Alignment explanation
Indices: 6158794--6158849 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
6158784 GGGCTTGGGC
*
6158794 TTTTAAAGTTTAAATTAATTTTAAATTTG
1 TTTTAAAGTTTAAATTAATCTTAAATTTG
*
6158823 TTTTAAA-TTTAAATTTATCTTAAATTT
1 TTTTAAAGTTTAAATTAATCTTAAATTT
6158850 AAATTTACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (29 bp):
TTTTAAAGTTTAAATTAATCTTAAATTTG
Found at i:6158867 original size:31 final size:31
Alignment explanation
Indices: 6158829--6158887 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
6158819 TTTGTTTTAA
6158829 ATTTAAATTTATCTTAAATTTAAATTTACTT
1 ATTTAAATTTATCTTAAATTTAAATTTACTT
* *
6158860 ATTTAAATTTATTTTAGATTTAAATTTA
1 ATTTAAATTTATCTTAAATTTAAATTTA
6158888 ATCAAATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (31 bp):
ATTTAAATTTATCTTAAATTTAAATTTACTT
Found at i:6158880 original size:11 final size:11
Alignment explanation
Indices: 6158802--6158881 Score: 52
Period size: 11 Copynumber: 6.9 Consensus size: 11
6158792 GCTTTTAAAG
*
6158802 TTTAAATTAAT
1 TTTAAATTTAT
*
6158813 TTTAAATTTGT
1 TTTAAATTTAT
*
6158824 TTTAAATTTAAA
1 TTTAAATTT-AT
** * *
6158836 TTTATCTTAAA
1 TTTAAATTTAT
6158847 TTTAAATTTACTT
1 TTTAAATTTA--T
6158860 ATTTAAATTTAT
1 -TTTAAATTTAT
*
6158872 TTTAGATTTA
1 TTTAAATTTA
6158882 AATTTAATCA
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
11 36 0.68
12 7 0.13
14 10 0.19
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:6159740 original size:12 final size:12
Alignment explanation
Indices: 6159725--6159755 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
6159715 AATATAGTAT
*
6159725 TAATATTTTTAA
1 TAATAATTTTAA
6159737 TAATAATTTTAA
1 TAATAATTTTAA
6159749 TAATAAT
1 TAATAAT
6159756 AAAAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAATAATTTTAA
Found at i:6160900 original size:29 final size:29
Alignment explanation
Indices: 6160822--6160924 Score: 115
Period size: 28 Copynumber: 3.6 Consensus size: 29
6160812 CCCCAAACAA
6160822 TCCAAAAATTACATTTTGACCCTAAAA-T
1 TCCAAAAATTACATTTTGACCCTAAAACT
**
6160850 TTAAAAAATTACATTTTGACCCTAAAACT
1 TCCAAAAATTACATTTTGACCCTAAAACT
*
6160879 TCCAAAAATTATCGTTTT-ACCCCT-AAACTT
1 TCCAAAAATTA-CATTTTGA-CCCTAAAAC-T
*
6160909 TCC-AAAATTCCATTTT
1 TCCAAAAATTACATTTT
6160925 TAACCTCGAT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
28 30 0.47
29 21 0.33
30 13 0.20
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (29 bp):
TCCAAAAATTACATTTTGACCCTAAAACT
Found at i:6160925 original size:29 final size:28
Alignment explanation
Indices: 6160826--6160990 Score: 88
Period size: 29 Copynumber: 5.7 Consensus size: 28
6160816 AAACAATCCA
* * * **
6160826 AAAATTACATTTTGACCCTAAAATTTAA
1 AAAATTCCATTTTTACCCTAAACTTTCC
* *
6160854 AAAATTACATTTTGACCCTAAAAC-TTCC
1 AAAATTCCATTTTTACCCT-AAACTTTCC
6160882 AAAAATT--ATCGTTTTACCCCTAAACTTTCC
1 -AAAATTCCAT--TTTTA-CCCTAAACTTTCC
* **
6160912 AAAATTCCATTTTTAACCTCGA-TTTCACC
1 AAAATTCCATTTTTACCCTAAACTTT--CC
* *
6160941 AAAAATTTCCA-TTTTACCCCTAAACTCTCT
1 -AAAA-TTCCATTTTTA-CCCTAAACTTTCC
*
6160971 AAAATTCCATTTTAACCCTA
1 AAAATTCCATTTTTACCCTA
6160991 TTTCACCAAA
Statistics
Matches: 109, Mismatches: 13, Indels: 30
0.72 0.09 0.20
Matches are distributed among these distances:
27 5 0.05
28 35 0.32
29 38 0.35
30 18 0.17
31 11 0.10
32 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36
Consensus pattern (28 bp):
AAAATTCCATTTTTACCCTAAACTTTCC
Found at i:6160961 original size:59 final size:58
Alignment explanation
Indices: 6160880--6161075 Score: 222
Period size: 59 Copynumber: 3.4 Consensus size: 58
6160870 CCTAAAACTT
* *
6160880 CCAAAAATTATCGTTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACC-CGATTTCA
* * * *
6160939 CCAAAAATTTCCATTTTACCCCTAAACTCTCTAAAATTCCA-TTTTAACCCTATTTCA
1 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCGATTTCA
* * *
6160996 CC-AAAATTACCATTTCA-CCCTCGAA-TTCTCCAAAATTCC-TTTTTCGACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCT-AAACTT-TCCAAAATTCCATTTTT--AACCCGATTTCA
*
6161054 TCAAAAATTACCATTTTACCCC
1 CCAAAAATTACCATTTTACCCC
6161076 CGTGAGTCCA
Statistics
Matches: 115, Mismatches: 15, Indels: 13
0.80 0.10 0.09
Matches are distributed among these distances:
55 5 0.04
56 29 0.25
57 9 0.08
58 19 0.17
59 50 0.43
60 3 0.03
ACGTcount: A:0.32, C:0.31, G:0.03, T:0.35
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCGATTTCA
Found at i:6161030 original size:29 final size:29
Alignment explanation
Indices: 6160992--6161075 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 29
6160982 TTAACCCTAT
6160992 TTCA-CCAAAATTACCATTTCACCCTCGAA
1 TTCATCCAAAATTACCATTTCACCC-CGAA
* *
6161021 TTC-TCCAAAATT-CCTTTTTCGACCCCGAT
1 TTCATCCAAAATTACC-ATTTC-ACCCCGAA
* *
6161050 TTCATCAAAAATTACCATTTTACCCC
1 TTCATCCAAAATTACCATTTCACCCC
6161076 CGTGAGTCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
28 2 0.04
29 26 0.58
30 15 0.33
31 2 0.04
ACGTcount: A:0.30, C:0.33, G:0.04, T:0.33
Consensus pattern (29 bp):
TTCATCCAAAATTACCATTTCACCCCGAA
Found at i:6161113 original size:28 final size:28
Alignment explanation
Indices: 6160996--6161116 Score: 86
Period size: 28 Copynumber: 4.2 Consensus size: 28
6160986 CCCTATTTCA
* * *
6160996 CCAAAATTACCATTTCACCCTCGAATTCT
1 CCAAAATTACCATTTTACCCTCG-AGTAT
* *
6161025 CCAAAATT-CCTTTTTCGACCC-CGATTTCAT
1 CCAAAATTACCATTTT--ACCCTCGA-GT-AT
* * *
6161055 CAAAAATTACCATTTTACCCCCGTG-AGT
1 CCAAAATTACCATTTTACCCTCGAGTA-T
*
6161083 CCAAAATTACCATTTTGCCCTCGAGTAT
1 CCAAAATTACCATTTTACCCTCGAGTAT
6161111 CCAAAA
1 CCAAAA
6161117 GTCCTGTTTT
Statistics
Matches: 73, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
27 1 0.01
28 35 0.48
29 17 0.23
30 14 0.19
31 6 0.08
ACGTcount: A:0.31, C:0.31, G:0.07, T:0.31
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCCTCGAGTAT
Found at i:6162183 original size:8 final size:9
Alignment explanation
Indices: 6162166--6162199 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
6162156 TCGTAGACCG
*
6162166 ACGTTTTTA
1 ACGTTTTAA
6162175 ACGTTTTAA
1 ACGTTTTAA
6162184 ACGTTTTAA
1 ACGTTTTAA
6162193 ACGTTTT
1 ACGTTTT
6162200 GTGGTGATCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.50
Consensus pattern (9 bp):
ACGTTTTAA
Found at i:6166948 original size:34 final size:34
Alignment explanation
Indices: 6166894--6166986 Score: 152
Period size: 34 Copynumber: 2.8 Consensus size: 34
6166884 GTCTCATTTT
*
6166894 TACATACTAA-TTCTTCAGTTTGAAAACTTACAA
1 TACATACTAATTTCTTGAGTTTGAAAACTTACAA
6166927 TACATACTAATTTCTTGAGTTTGAAAACTTACAA
1 TACATACTAATTTCTTGAGTTTGAAAACTTACAA
* *
6166961 TACATACTGATTTCTTGAGCTTGAAA
1 TACATACTAATTTCTTGAGTTTGAAA
6166987 GTGAGTTGTG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 10 0.18
34 46 0.82
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.38
Consensus pattern (34 bp):
TACATACTAATTTCTTGAGTTTGAAAACTTACAA
Found at i:6169738 original size:2 final size:2
Alignment explanation
Indices: 6169731--6169772 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
6169721 AAAATTAATA
6169731 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6169773 TTAGAACTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6171382 original size:26 final size:26
Alignment explanation
Indices: 6171338--6171389 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
6171328 AATTGTAGTG
* *
6171338 ATTGGTTTGATCAACTGATTCTATTA
1 ATTGATTTGACCAACTGATTCTATTA
*
6171364 ATTGATTTGACCAATTGATTCTATTA
1 ATTGATTTGACCAACTGATTCTATTA
6171390 TATGTTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (26 bp):
ATTGATTTGACCAACTGATTCTATTA
Found at i:6173655 original size:15 final size:15
Alignment explanation
Indices: 6173619--6173684 Score: 53
Period size: 15 Copynumber: 4.4 Consensus size: 15
6173609 CATGTAAATT
6173619 ATTTTTT-ATAATAA
1 ATTTTTTAATAATAA
* * *
6173633 ACTATTTAATTATAA
1 ATTTTTTAATAATAA
* *
6173648 ATTTTTTAAAAATTA
1 ATTTTTTAATAATAA
* *
6173663 ATATTTAAATAATATA
1 ATTTTTTAATAATA-A
6173679 ATTTTT
1 ATTTTT
6173685 GTTATAATTT
Statistics
Matches: 37, Mismatches: 13, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
14 5 0.14
15 26 0.70
16 6 0.16
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTTTTAATAATAA
Found at i:6176063 original size:12 final size:12
Alignment explanation
Indices: 6176027--6176063 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
6176017 ATTCCTAAAT
6176027 CAGAGACCAAAC
1 CAGAGACCAAAC
* *
6176039 AAGAGGCCAAAC
1 CAGAGACCAAAC
6176051 CAGAGACCAAAC
1 CAGAGACCAAAC
6176063 C
1 C
6176064 GGAAACTGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.49, C:0.32, G:0.19, T:0.00
Consensus pattern (12 bp):
CAGAGACCAAAC
Found at i:6180994 original size:21 final size:20
Alignment explanation
Indices: 6180968--6181027 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 20
6180958 GGTGTTTAAA
6180968 TATAAAGATTGATATATTTTT
1 TATAAAGATT-ATATATTTTT
*
6180989 TATAAA-AGTTAATATTAATTTT
1 TATAAAGA-TT-ATA-TATTTTT
*
6181011 TA-AAAGATTATTTATTT
1 TATAAAGATTATATATTT
6181028 CTAATTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
19 4 0.12
20 3 0.09
21 16 0.50
22 9 0.28
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.52
Consensus pattern (20 bp):
TATAAAGATTATATATTTTT
Found at i:6192369 original size:10 final size:11
Alignment explanation
Indices: 6192346--6192371 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6192336 TTCTTCCTTC
6192346 TTTTGTTTCTT
1 TTTTGTTTCTT
6192357 TTTTGTTTCTT
1 TTTTGTTTCTT
6192368 TTTT
1 TTTT
6192372 CTTTTATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (11 bp):
TTTTGTTTCTT
Found at i:6196330 original size:15 final size:15
Alignment explanation
Indices: 6196310--6196339 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6196300 TGATGTGCAA
6196310 GTCGAAAACAATGGT
1 GTCGAAAACAATGGT
*
6196325 GTCGAAAATAATGGT
1 GTCGAAAACAATGGT
6196340 TTCAAGAGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.27, T:0.23
Consensus pattern (15 bp):
GTCGAAAACAATGGT
Found at i:6196599 original size:20 final size:20
Alignment explanation
Indices: 6196567--6196612 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
6196557 ACATTGTTTA
*
6196567 AATTAAGTATAAATA-GATTT
1 AATTAAGTATAAAAATGA-TT
6196587 AATTAAG-ATTAAAAATGATT
1 AATTAAGTA-TAAAAATGATT
6196607 AATTAA
1 AATTAA
6196613 ATCTTAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 1 0.04
20 20 0.87
21 2 0.09
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (20 bp):
AATTAAGTATAAAAATGATT
Found at i:6199156 original size:23 final size:23
Alignment explanation
Indices: 6198984--6199144 Score: 166
Period size: 23 Copynumber: 6.9 Consensus size: 23
6198974 CGAAGTACTT
6198984 AACAGTAAGCACAC-AAGTGCTGGGGA
1 AACAGTAAGCACACAAAGTGC----GA
*
6199010 AACAGTAAGCACACACAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * * *
6199032 ATCAGTAGGCGCACATAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * *
6199054 AATCAGTAGGCACACGAAGTGCGG
1 AA-CAGTAAGCACACAAAGTGCGA
*
6199078 AACAGTAGGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
6199101 AACAGTAAGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
*
6199124 AACAGTAAGCACACACAGTGC
1 AACAGTAAGCACACAAAGTGC
6199145 TGAACGGTAA
Statistics
Matches: 118, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
22 20 0.17
23 77 0.65
24 2 0.02
26 14 0.12
27 5 0.04
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.11
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:6203892 original size:3 final size:3
Alignment explanation
Indices: 6203884--6203921 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
6203874 ACACGCACAT
6203884 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
6203922 TTAATTTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:6209853 original size:43 final size:43
Alignment explanation
Indices: 6209806--6209891 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
6209796 TTAATTTTTT
6209806 TTTGTGAAAATCCTAAAAAAATTCTCTCTTTTTCCCTCTCACC
1 TTTGTGAAAATCCTAAAAAAATTCTCTCTTTTTCCCTCTCACC
* *
6209849 TTTGTGAAAATCTTAAAAAAATTCTCTCTTTTTCCCTTTCACC
1 TTTGTGAAAATCCTAAAAAAATTCTCTCTTTTTCCCTCTCACC
6209892 AACTTGTTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.28, C:0.26, G:0.05, T:0.42
Consensus pattern (43 bp):
TTTGTGAAAATCCTAAAAAAATTCTCTCTTTTTCCCTCTCACC
Found at i:6210814 original size:50 final size:51
Alignment explanation
Indices: 6210722--6210819 Score: 135
Period size: 50 Copynumber: 1.9 Consensus size: 51
6210712 AAATAATATT
*
6210722 TGATTATATTTTTTTTCTCTTTTAATACCAGCAAACTCAATCT-AAAACAA
1 TGATTATATTTTTTTTATCTTTTAATACCAGCAAACTCAATCTGAAAACAA
* * ** *
6210772 TGATTATATTTTTTTTATTTTTTAATACCGGGTAACTTAATCTGAAAA
1 TGATTATATTTTTTTTATCTTTTAATACCAGCAAACTCAATCTGAAAA
6210820 TATTATTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
50 37 0.90
51 4 0.10
ACGTcount: A:0.34, C:0.13, G:0.07, T:0.46
Consensus pattern (51 bp):
TGATTATATTTTTTTTATCTTTTAATACCAGCAAACTCAATCTGAAAACAA
Found at i:6214054 original size:25 final size:25
Alignment explanation
Indices: 6214020--6214078 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
6214010 AATATTCATA
6214020 TTATATTATTTTAATATTTAAT-AAAT
1 TTATA-TATTTT-ATATTTAATGAAAT
* *
6214046 TTATATATTTTTTATTTATTGAAAT
1 TTATATATTTTATATTTAATGAAAT
*
6214071 TTTTATAT
1 TTATATAT
6214079 AGTTATCTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 7 0.24
25 17 0.59
26 5 0.17
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (25 bp):
TTATATATTTTATATTTAATGAAAT
Found at i:6215013 original size:166 final size:166
Alignment explanation
Indices: 6214739--6215076 Score: 599
Period size: 166 Copynumber: 2.0 Consensus size: 166
6214729 AAGCATACAG
*
6214739 GAAAATGACTGTCAGTTTTCAATCATTTGATATGAAAAATGATTTAATTCAATTAGTTTGTTCCC
1 GAAAATGAATGTCAGTTTTCAATCATTTGATATGAAAAATGATTTAATTCAATTAGTTTGTTCCC
* *
6214804 TAAGTGTAAAATTGTCTACTACAAGATACTAGAAGATTGGAACAAGTCCATGCATACAGGAAAAG
66 CAAGTGTAAAATTGTCTACTACAAAATACTAGAAGATTGGAACAAGTCCATGCATACAGGAAAAG
6214869 TAGCAGGAAATCACCCTAAGAAATTACAAGCATGGA
131 TAGCAGGAAATCACCCTAAGAAATTACAAGCATGGA
6214905 GAAAATGAATGTCAGTTTTCGAA-CATTTGATATGAAAAATGATTTAATTCAATTAGTTTGTTCC
1 GAAAATGAATGTCAGTTTTC-AATCATTTGATATGAAAAATGATTTAATTCAATTAGTTTGTTCC
* *
6214969 CCAAGTGTAAAATTGTCTACTACAAAA-ATCTAGAAGATTGGAACAATTCCATGCATACAGGAAG
65 CCAAGTGTAAAATTGTCTACTACAAAATA-CTAGAAGATTGGAACAAGTCCATGCATACAGGAAA
6215033 AGTAGCAGGAAATCACCCTAAGAAATTACAAGCATGGA
129 AGTAGCAGGAAATCACCCTAAGAAATTACAAGCATGGA
6215071 GAAAAT
1 GAAAAT
6215077 TCCAAGTAAA
Statistics
Matches: 165, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
165 1 0.01
166 162 0.98
167 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (166 bp):
GAAAATGAATGTCAGTTTTCAATCATTTGATATGAAAAATGATTTAATTCAATTAGTTTGTTCCC
CAAGTGTAAAATTGTCTACTACAAAATACTAGAAGATTGGAACAAGTCCATGCATACAGGAAAAG
TAGCAGGAAATCACCCTAAGAAATTACAAGCATGGA
Found at i:6220941 original size:36 final size:36
Alignment explanation
Indices: 6220888--6220961 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
6220878 GACGCCTATT
6220888 GATCAATACAACACCTAAGTAAGTCTGAAATCGATC
1 GATCAATACAACACCTAAGTAAGTCTGAAATCGATC
* * *
6220924 GATCAATGCAACGCCTAATTAAGTCTGAAATCGATC
1 GATCAATACAACACCTAAGTAAGTCTGAAATCGATC
6220960 GA
1 GA
6220962 AGCTAGAGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (36 bp):
GATCAATACAACACCTAAGTAAGTCTGAAATCGATC
Found at i:6234045 original size:25 final size:25
Alignment explanation
Indices: 6233976--6234048 Score: 103
Period size: 25 Copynumber: 2.9 Consensus size: 25
6233966 CCAGTGTGAC
* *
6233976 CTCCAAACTGCCCTGCCACAACTGG
1 CTCCAAACTGCCCTGCCACCACCGG
*
6234001 CTCCAAATTGCCCTGCCACCACCGG
1 CTCCAAACTGCCCTGCCACCACCGG
6234026 CTCCAAACT-CCTCTGCCACCACC
1 CTCCAAACTGCC-CTGCCACCACC
6234049 ACCGCTACAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 2 0.05
25 41 0.95
ACGTcount: A:0.22, C:0.49, G:0.12, T:0.16
Consensus pattern (25 bp):
CTCCAAACTGCCCTGCCACCACCGG
Found at i:6235807 original size:30 final size:29
Alignment explanation
Indices: 6235772--6235996 Score: 111
Period size: 30 Copynumber: 7.6 Consensus size: 29
6235762 TAAACTATCC
* *
6235772 AAAAATTATATTTTAACCTTAAAACATTTT
1 AAAAATTACATTTTAACCTCAAAAC-TTTT
* * *
6235802 GAAAATTACACTTTGACC-CACAAACTTCTT
1 AAAAATTACATTTTAACCTCA-AAACTT-TT
* *
6235832 TAAAATT-CTATTTTGACCTCAAAACTTTCT
1 AAAAATTAC-ATTTTAACCTCAAAACTTT-T
* * **
6235862 AAAAAATACACTTTAACC-CTTGAACTTCTT
1 AAAAATTACATTTTAACCTC-AAAACTT-TT
* * *
6235892 TAAAATTATATTTTAACCCCAAAACTTTTT
1 AAAAATTACATTTTAACCTCAAAAC-TTTT
* * * *
6235922 AAAAATTACATTTTGACCCCTAAA-TTTCCC
1 AAAAATTACATTTTAACCTCAAAACTTT--T
* *
6235952 AAAAATTACTATTTTACCCTC-GAACTTTCT
1 AAAAATTAC-ATTTTAACCTCAAAACTTT-T
*
6235982 -AAAATTCCATTTTAA
1 AAAAATTACATTTTAA
6235997 ACCCTAATTT
Statistics
Matches: 150, Mismatches: 31, Indels: 30
0.71 0.15 0.14
Matches are distributed among these distances:
28 9 0.06
29 13 0.09
30 110 0.73
31 18 0.12
ACGTcount: A:0.39, C:0.20, G:0.03, T:0.38
Consensus pattern (29 bp):
AAAAATTACATTTTAACCTCAAAACTTTT
Found at i:6235957 original size:60 final size:59
Alignment explanation
Indices: 6235759--6236057 Score: 214
Period size: 60 Copynumber: 5.0 Consensus size: 59
6235749 CTCTATAGGT
** * *
6235759 CCCTAAACTAT-CCAAAAATTATATTTTAACCTTAAAACATTT-TGAAAATTACACTTTGAC
1 CCCTAAACT-TCCCAAAAATTATATTTTAACCCCAAAAC-TTTCT-AAAATTACATTTTAAC
*** * * * * *
6235819 CCAC-AAACTTCTTTAAAATTCTATTTTGACCTCAAAACTTTCTAAAAAATACACTTTAAC
1 CC-CTAAACTTCCCAAAAATTATATTTTAACCCCAAAACTTTCT-AAAATTACATTTTAAC
* * *** * *
6235879 CCTTGAACTTCTTTAAAATTATATTTTAACCCCAAAACTTTTTAAAAATTACATTTTGAC
1 CCCTAAACTTCCCAAAAATTATATTTTAACCCCAAAACTTTCT-AAAATTACATTTTAAC
* * * *
6235939 CCCTAAATTTCCCAAAAATTACTATTTT-ACCCTC-GAACTTTCTAAAATTCCATTTTAAA
1 CCCTAAACTTCCCAAAAATTA-TATTTTAACCC-CAAAACTTTCTAAAATTACATTTTAAC
* * ** * *
6235998 CCCT-AATTTCACCAAAAATTACATTTTTGCCCCCAAACTTTCTAAAATTCCATTTTAAC
1 CCCTAAACTTC-CCAAAAATTATATTTTAACCCCAAAACTTTCTAAAATTACATTTTAAC
6236057 C
1 C
6236058 TCGATTTCAC
Statistics
Matches: 197, Mismatches: 33, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
58 12 0.06
59 58 0.29
60 119 0.60
61 8 0.04
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.37
Consensus pattern (59 bp):
CCCTAAACTTCCCAAAAATTATATTTTAACCCCAAAACTTTCTAAAATTACATTTTAAC
Found at i:6236000 original size:90 final size:91
Alignment explanation
Indices: 6235803--6235996 Score: 204
Period size: 90 Copynumber: 2.2 Consensus size: 91
6235793 AAACATTTTG
* * * *
6235803 AAAATTACACTTTGA-CCCACAAACTTCTTTAAAATTCTATTTTGACCTCAAAACTTTCTAAAAA
1 AAAATTACATTTTAACCCCACAAACTTCTTTAAAATTCTATTTTGACCCCAAAACTTTCCAAAAA
* *
6235867 ATACACTTTAACCCTTGAACTTCTTT
66 ATACACTTTAACCCTCGAACTTCTCT
* *
6235893 AAAATTATATTTTAACCCCA-AAACTT-TTTAAAAATTAC-ATTTTGACCCCTAAA-TTTCCCAA
1 AAAATTACATTTTAACCCCACAAACTTCTTT-AAAATT-CTATTTTGACCCCAAAACTTT-CCAA
* *
6235954 AAATTACTA-TTTTACCCTCGAACTT-TCT
63 AAAATAC-ACTTTAACCCTCGAACTTCTCT
*
6235982 AAAATTCCATTTTAA
1 AAAATTACATTTTAA
6235997 ACCCTAATTT
Statistics
Matches: 87, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
89 21 0.24
90 60 0.69
91 6 0.07
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.38
Consensus pattern (91 bp):
AAAATTACATTTTAACCCCACAAACTTCTTTAAAATTCTATTTTGACCCCAAAACTTTCCAAAAA
ATACACTTTAACCCTCGAACTTCTCT
Found at i:6236073 original size:58 final size:58
Alignment explanation
Indices: 6235893--6236207 Score: 307
Period size: 58 Copynumber: 5.4 Consensus size: 58
6235883 GAACTTCTTT
* * * * * * **
6235893 AAAATTATATTTTAACCCCAAAACTTTTTAAAAATTACATTTTGACCCCTAAATTTC-CCA
1 AAAATTACATTTT-ACCCCCAAACTTTCT-AAAATTCCATTTTTA-ACCTCGATTTCACCA
* * * *
6235953 AAAATTACTATTTTACCCTCGAACTTTCTAAAATTCCATTTTAAACC-CTAATTTCACCA
1 AAAATTAC-ATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCTC-GATTTCACCA
*
6236012 AAAATTACATTTTTGCCCCCAAACTTTCTAAAATTCCA-TTTTAACCTCGATTTCACCA
1 AAAATTACA-TTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCTCGATTTCACCA
* * * * *
6236070 AAAATTACCATTTTACCTCCTAACTTTCCAAAATTCCATTTTTGACCTCGATTTCACTA
1 AAAATTA-CATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCTCGATTTCACCA
* * * *
6236129 AAAATTGCATTTTACCCCCGAACTTTCTAAAATTTCATTTTTAACCCCGAATTTTC-CC-
1 AAAATTACATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCTCG-A-TTTCACCA
*
6236187 AAAATTACATTTTGCCCCCAA
1 AAAATTACATTTTACCCCCAA
6236208 GAGTAAAAAA
Statistics
Matches: 215, Mismatches: 31, Indels: 20
0.81 0.12 0.08
Matches are distributed among these distances:
58 110 0.51
59 78 0.36
60 22 0.10
61 5 0.02
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (58 bp):
AAAATTACATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCTCGATTTCACCA
Found at i:6236103 original size:117 final size:117
Alignment explanation
Indices: 6235893--6236199 Score: 331
Period size: 117 Copynumber: 2.6 Consensus size: 117
6235883 GAACTTCTTT
* * * * * *
6235893 AAAATTATATTTTAACCCCAAAACTTTTTAAAAATTACA-TTTTGACCCCTAAATTTCCCAAAAA
1 AAAATTACATTTT-ACCCCCAAACTTTCT-AAAATTCCATTTTTAACCCC-GAATTTCCCAAAAA
* *
6235957 TTACTATTTTACCCTCGAACTTTCTAAAATTCCATTTTAAACC-CTAATTTCACCA
63 TTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTAAACCTC-AATTTCACCA
* *
6236012 AAAATTACATTTTTGCCCCCAAACTTTCTAAAATTCCA-TTTTAACCTCG-ATTTCACCAAAAAT
1 AAAATTACA-TTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCCCGAATTTC-CCAAAAAT
* ** * *
6236075 TACCATTTTA-CCTCCTAACTTTCCAAAATTCCATTTTTGACCTCGATTTCACTA
64 TACCATTTTACCCT-CGAACTTTCCAAAATTCCATTTTAAACCTCAATTTCACCA
* * *
6236129 AAAATTGCATTTTACCCCCGAACTTTCTAAAATTTCATTTTTAACCCCGAATTTTCCC-AAAATT
1 AAAATTACATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCCCGAA-TTTCCCAAAAATT
6236193 A-CATTTT
65 ACCATTTT
6236200 GCCCCCAAGA
Statistics
Matches: 161, Mismatches: 20, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
116 39 0.24
117 74 0.46
118 20 0.12
119 24 0.15
120 4 0.02
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (117 bp):
AAAATTACATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCCCGAATTTCCCAAAAATTA
CCATTTTACCCTCGAACTTTCCAAAATTCCATTTTAAACCTCAATTTCACCA
Found at i:6236191 original size:30 final size:29
Alignment explanation
Indices: 6235923--6236199 Score: 121
Period size: 29 Copynumber: 9.4 Consensus size: 29
6235913 AAACTTTTTA
* * *
6235923 AAAATTACA-TTTTGACCCCTAAATTTCCC
1 AAAATTACATTTTTAACCCCGAACTTT-CC
*
6235952 AAAAATTAC-TATTTT-ACCCTCGAACTTTCT
1 -AAAATTACAT-TTTTAACCC-CGAACTTTCC
* * *
6235982 AAAATTCCA-TTTTAAACCCTAA-TTTCACC
1 AAAATTACATTTTTAACCCCGAACTTT--CC
** * *
6236011 AAAAATTACATTTTTGCCCCCAAACTTTCT
1 -AAAATTACATTTTTAACCCCGAACTTTCC
* *
6236041 AAAATTCCA-TTTTAACCTCG-A-TTTCACC
1 AAAATTACATTTTTAACCCCGAACTTT--CC
*
6236069 AAAAATTACCA-TTTT-ACCTCCTAACTTTCC
1 -AAAATTA-CATTTTTAACC-CCGAACTTTCC
* * *
6236099 AAAATTCCATTTTTGACCTCG-A-TTTCAC
1 AAAATTACATTTTTAACCCCGAACTTTC-C
* * *
6236127 TAAAAATTGCA-TTTTACCCCCGAACTTTCT
1 --AAAATTACATTTTTAACCCCGAACTTTCC
* *
6236157 AAAATTTCATTTTTAACCCCGAATTTTCCC
1 AAAATTACATTTTTAACCCCGAACTTT-CC
6236187 AAAATTACATTTT
1 AAAATTACATTTT
6236200 GCCCCCAAGA
Statistics
Matches: 186, Mismatches: 35, Indels: 52
0.68 0.13 0.19
Matches are distributed among these distances:
26 3 0.02
27 8 0.04
28 27 0.15
29 62 0.33
30 56 0.30
31 24 0.13
32 6 0.03
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (29 bp):
AAAATTACATTTTTAACCCCGAACTTTCC
Found at i:6250557 original size:200 final size:200
Alignment explanation
Indices: 6250208--6250667 Score: 740
Period size: 200 Copynumber: 2.3 Consensus size: 200
6250198 TTCATGACGG
* *
6250208 ATCCAGAGAAGCGAATTAAAACAAGCGAGGTGGTCATCTTCCTGATGAGATACAGAGAAGAATAC
1 ATCCAGAGAAACGAATTAAAACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATAC
*
6250273 CGACTCAACACTCAACACGAACCAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGG
66 CAACTCAACACTCAACACGAACCAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGG
* * * *
6250338 TCGAAGCAATAAAATGGTTAGCTTCCTGATAAGATACAGAGAAGTGGACCAGATTCGTCTTCCTG
131 TCGAAGCAATAAAATGGTTAGCTTCCTAATAAGACACAGAGAAGTGAACCAAATTCGTCTTCCTG
6250403 AGGAA
196 AGGAA
* * *
6250408 ATCCAGAGAAATGAATCAAAACAAGCGAGGCAGTCATCTTCCTGATGAGATACAGAGAAGAATAC
1 ATCCAGAGAAACGAATTAAAACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATAC
* * * *
6250473 CAACTCAACGCTCAACACGAGCCAATCTTCGAACCCAGCTTCCTGATGAGACACTGGGAAGTAGG
66 CAACTCAACACTCAACACGAACCAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGG
* * *
6250538 TCGAAGCAATAACATGGTTAGCTTCCTAATGAGACACAGAGAAGTGAACTAAATTCGTCTTCCTG
131 TCGAAGCAATAAAATGGTTAGCTTCCTAATAAGACACAGAGAAGTGAACCAAATTCGTCTTCCTG
*
6250603 AGGAG
196 AGGAA
* *
6250608 ATCCAGAGAAACGAATTGAAACAAGCAAGGCGGTCATCTTCCTGATGAGATACAGAGAAG
1 ATCCAGAGAAACGAATTAAAACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAG
6250668 TGAACTAAAT
Statistics
Matches: 237, Mismatches: 23, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
200 237 1.00
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.19
Consensus pattern (200 bp):
ATCCAGAGAAACGAATTAAAACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATAC
CAACTCAACACTCAACACGAACCAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGG
TCGAAGCAATAAAATGGTTAGCTTCCTAATAAGACACAGAGAAGTGAACCAAATTCGTCTTCCTG
AGGAA
Found at i:6250615 original size:37 final size:37
Alignment explanation
Indices: 6250574--6250704 Score: 91
Period size: 37 Copynumber: 3.2 Consensus size: 37
6250564 TAATGAGACA
6250574 CAGAGAAGTGAACTAAATTCGTCTTCCTGAGGAGATC
1 CAGAGAAGTGAACTAAATTCGTCTTCCTGAGGAGATC
* * * * *
6250611 CAGAGAAACGAATTGAAACAAGCAAGGCGGTCATCTTCCTGATGAGATA
1 CAGAG-AA-G---TG-AACTA--AA----TTCGTCTTCCTGAGGAGATC
* *
6250660 CAGAGAAGTGAACTAAATTTGTCTTCCGGAGGAGATC
1 CAGAGAAGTGAACTAAATTCGTCTTCCTGAGGAGATC
6250697 CAGAGAAG
1 CAGAGAAG
6250705 CAAATTAAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 24
0.66 0.11 0.23
Matches are distributed among these distances:
37 27 0.39
38 2 0.03
39 1 0.01
41 2 0.03
42 2 0.03
43 8 0.11
44 2 0.03
45 2 0.03
47 1 0.01
48 2 0.03
49 21 0.30
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.21
Consensus pattern (37 bp):
CAGAGAAGTGAACTAAATTCGTCTTCCTGAGGAGATC
Found at i:6250664 original size:86 final size:86
Alignment explanation
Indices: 6250559--6250753 Score: 293
Period size: 86 Copynumber: 2.3 Consensus size: 86
6250549 ACATGGTTAG
* * * *
6250559 CTTCCTAATGAGACACAGAGAAGTGAACTAAATTCGTCTTCCTGAGGAGATCCAGAGAAACGAAT
1 CTTCCTGATGAGATACAGAGAAGTGAACTAAATTCGTCTTCCGGAGGAGATCCAGAGAAACAAAT
*
6250624 TGAAACAAGCA-AGGCGGTCAT
66 TAAAACAA-CAGAGGCGGTCAT
* *
6250645 CTTCCTGATGAGATACAGAGAAGTGAACTAAATTTGTCTTCCGGAGGAGATCCAGAGAAGCAAAT
1 CTTCCTGATGAGATACAGAGAAGTGAACTAAATTCGTCTTCCGGAGGAGATCCAGAGAAACAAAT
6250710 TAAAACAACAGAGGCGGTCAT
66 TAAAACAACAGAGGCGGTCAT
* *
6250731 CTTTCTGATGAGATATAGAGAAG
1 CTTCCTGATGAGATACAGAGAAG
6250754 AATACTAACT
Statistics
Matches: 99, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
85 2 0.02
86 97 0.98
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (86 bp):
CTTCCTGATGAGATACAGAGAAGTGAACTAAATTCGTCTTCCGGAGGAGATCCAGAGAAACAAAT
TAAAACAACAGAGGCGGTCAT
Found at i:6250880 original size:286 final size:286
Alignment explanation
Indices: 6250359--6250953 Score: 832
Period size: 286 Copynumber: 2.1 Consensus size: 286
6250349 AAATGGTTAG
* * * * **
6250359 CTTCCTGATAAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAAATCCAGAGAAATGAAT
1 CTTCCTGATGAGATACAGAGAAGTGAACCAAATTCGTCTTCCGGAGGAAATCCAGAGAAACAAAT
6250424 CAAAACAAGCGAGGCAGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAAC
66 CAAAACAAGCGAGGCAGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAAC
* * * * * *
6250489 ACGAGCCAATCTTCGAACCCAGCTTCCTGATGAGACACTGGGAAGTAGGTCGAAGCAATAACATG
131 ACGAGCAAATCTTCGAACCCAGCTCCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAAG
* * * * *
6250554 GTTAGCTTCCTAATGAGACACAGAGAAGTGAACTAAATTCGTCTTCCTGAGGAGATCCAGAGAAA
196 GTTAGCTTCCGAATGAGACACAAAGAAGTGAACCAAATTCGTCTTCCTGAGAAAATCCAGAGAAA
*
6250619 CGAATTGAAACAAGCAAGGCGGTCAT
261 CGAATTGAAACAAACAAGGCGGTCAT
* * * *
6250645 CTTCCTGATGAGATACAGAGAAGTGAACTAAATTTGTCTTCCGGAGGAGATCCAGAGAAGCAAAT
1 CTTCCTGATGAGATACAGAGAAGTGAACCAAATTCGTCTTCCGGAGGAAATCCAGAGAAACAAAT
* * * * * *
6250710 TAAAACAA-CAGAGGCGGTCATCTTTCTGATGAGATATAGAGAAGAATACTAACTCAACGCTCCA
66 CAAAACAAGC-GAGGCAGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAA
* * * *
6250774 CGCGAGCAAATCTTTGAGCCCAGCTCCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAA
130 CACGAGCAAATCTTCGAACCCAGCTCCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAA
* * *
6250839 GGTTAGCTTTCGGATGAGACACAAAGAAGTGGACCAAATTCGTCTTCCTGAGAAAATCCAGAGAA
195 GGTTAGCTTCCGAATGAGACACAAAGAAGTGAACCAAATTCGTCTTCCTGAGAAAATCCAGAGAA
*
6250904 ACGAATTGAAACAAACGAGGCGGTCAT
260 ACGAATTGAAACAAACAAGGCGGTCAT
* *
6250931 CTTCCTGATGAGACATAGAGAAG
1 CTTCCTGATGAGATACAGAGAAG
6250954 AAGACCAGGT
Statistics
Matches: 270, Mismatches: 38, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
285 1 0.00
286 269 1.00
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (286 bp):
CTTCCTGATGAGATACAGAGAAGTGAACCAAATTCGTCTTCCGGAGGAAATCCAGAGAAACAAAT
CAAAACAAGCGAGGCAGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAAC
ACGAGCAAATCTTCGAACCCAGCTCCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAAG
GTTAGCTTCCGAATGAGACACAAAGAAGTGAACCAAATTCGTCTTCCTGAGAAAATCCAGAGAAA
CGAATTGAAACAAACAAGGCGGTCAT
Found at i:6251344 original size:17 final size:18
Alignment explanation
Indices: 6251308--6251348 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
6251298 CATTTCAAAG
6251308 ATTTATTTTAAAGATTAA
1 ATTTATTTTAAAGATTAA
* *
6251326 ATTTATTTTGAA-TTTAA
1 ATTTATTTTAAAGATTAA
6251343 ATTTAT
1 ATTTAT
6251349 CTGAATTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
ATTTATTTTAAAGATTAA
Found at i:6251355 original size:16 final size:17
Alignment explanation
Indices: 6251322--6251355 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
6251312 ATTTTAAAGA
*
6251322 TTAAATTTATTTTGAAT
1 TTAAATTTATTCTGAAT
6251339 TTAAATTTA-TCTGAAT
1 TTAAATTTATTCTGAAT
6251355 T
1 T
6251356 CATATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (17 bp):
TTAAATTTATTCTGAAT
Found at i:6259792 original size:200 final size:200
Alignment explanation
Indices: 6259444--6259942 Score: 696
Period size: 200 Copynumber: 2.5 Consensus size: 200
6259434 ACAAAACATT
* *
6259444 GAGGTGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACGCGAGCAAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACGAGAGCAAAT
* *
6259509 CTTCGAACCCAGCTTCCTGATGAGACACTAAAAAGCAGGTCGAAGCAATAAAATTGTTAGCTTCC
66 CTTCGAACCCAACTTCCTGATGAGACACTAAAAAGCAGGTCAAAGCAATAAAATTGTTAGCTTCC
* *
6259574 TGATGAGATACAGAGAAGTGGACCAAATTCATCTTCCTGAGGAGATCCAGAGAAGCGAATTAAAA
131 TGATGAGATACAGAGAAGTAGACCAAATTCATCTTCCTGAGGAAATCCAGAGAAGCGAATTAAAA
6259639 CAAAC
196 CAAAC
* *
6259644 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAATGCTCAACGAGAGCCAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACGAGAGCAAAT
* * * *
6259709 CTTCGAACCCAACTTCCTGATGAGACATTGAGAAGTAGGTCAAAGCAATAAAA-TGATTAGCTTC
66 CTTCGAACCCAACTTCCTGATGAGACACTAAAAAGCAGGTCAAAGCAATAAAATTG-TTAGCTTC
* * *
6259773 CTGATGAGATACGGAGAAGTAGACCAGATTCGTCTTCCTGAGGAAATCCAGAGAAGCGAATTAAA
130 CTGATGAGATACAGAGAAGTAGACCAAATTCATCTTCCTGAGGAAATCCAGAGAAGCGAATTAAA
*
6259838 ACAATC
195 ACAAAC
* * * * * * *
6259844 GAGGCGATCATCTTCTTGATGAGACACTGAGAAGAAGACTAAATCAAAC-CAACGCTCAATGCGA
1 GAGGCGGTCATCTTCCTGATGAGATAC--AG-AGAAGA--ATA-CCAACTCAACGCTCAACGAGA
* *
6259908 GCAAATCTTCGAATCCAGCTTCCTGATGAGACACT
60 GCAAATCTTCGAACCCAACTTCCTGATGAGACACT
6259943 TAGAAGGTCG
Statistics
Matches: 264, Mismatches: 28, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
199 2 0.01
200 205 0.78
202 2 0.01
203 6 0.02
205 45 0.17
206 4 0.02
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (200 bp):
GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACGAGAGCAAAT
CTTCGAACCCAACTTCCTGATGAGACACTAAAAAGCAGGTCAAAGCAATAAAATTGTTAGCTTCC
TGATGAGATACAGAGAAGTAGACCAAATTCATCTTCCTGAGGAAATCCAGAGAAGCGAATTAAAA
CAAAC
Found at i:6260319 original size:17 final size:17
Alignment explanation
Indices: 6260297--6260337 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
6260287 CAATGGGATA
* *
6260297 AAATTTATTTTTAAATT
1 AAATTTATTATGAAATT
*
6260314 AAATTTATTATGAATTT
1 AAATTTATTATGAAATT
6260331 AAATTTA
1 AAATTTA
6260338 CATAAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
AAATTTATTATGAAATT
Found at i:6260366 original size:17 final size:17
Alignment explanation
Indices: 6260307--6260366 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
6260297 AAATTTATTT
**
6260307 TTAAATTAAATTTATTA
1 TTAAATTAAATTTAAAA
* * *
6260324 TGAATTTAAATTT-ACA
1 TTAAATTAAATTTAAAA
*
6260340 TAAAATTTAAATTTAAAA
1 TTAAA-TTAAATTTAAAA
6260358 TTAAATTAA
1 TTAAATTAA
6260367 TGTCCAAAGT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
16 4 0.12
17 23 0.70
18 6 0.18
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TTAAATTAAATTTAAAA
Found at i:6260561 original size:25 final size:25
Alignment explanation
Indices: 6260533--6260580 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
6260523 CCAGTGTCAC
* *
6260533 CTCCATACTGCCCTGCCACCACCGA
1 CTCCAAACTGCCCTACCACCACCGA
*
6260558 CTCCAAACTGCTCTACCACCACC
1 CTCCAAACTGCCCTACCACCACC
6260581 ATTGCTACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.23, C:0.52, G:0.08, T:0.17
Consensus pattern (25 bp):
CTCCAAACTGCCCTACCACCACCGA
Found at i:6262376 original size:30 final size:31
Alignment explanation
Indices: 6262291--6262428 Score: 119
Period size: 30 Copynumber: 4.6 Consensus size: 31
6262281 TAAACTATCC
*
6262291 AAAAATTATATTTTGA-CC-CAAAACTTTTT
1 AAAAATTACATTTTGACCCTCAAAACTTTTT
* * * * *
6262320 GAAAATTACACTTTGACCCTC-TAACTTCTC
1 AAAAATTACATTTTGACCCTCAAAACTTTTT
* *
6262350 CAAAATTATATTTTGA-CCTCAAAACTTTTT
1 AAAAATTACATTTTGACCCTCAAAACTTTTT
* *
6262380 AAAAATTACATTTTAACCCTC-AAA-TTTCCT
1 AAAAATTACATTTTGACCCTCAAAACTTT-TT
6262410 AAAAATTACTATTTT-ACCC
1 AAAAATTAC-ATTTTGACCC
6262429 CCGAACTTTC
Statistics
Matches: 87, Mismatches: 16, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
29 20 0.23
30 57 0.66
31 10 0.11
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (31 bp):
AAAAATTACATTTTGACCCTCAAAACTTTTT
Done.