Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 40 of 120
Found at i:10778164 original size:16 final size:15
Alignment explanation
Indices: 10778139--10778172 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
10778129 AGTTATGATA
*
10778139 ATAATTAATATACATT
1 ATAATAAATATA-ATT
10778155 ATAATAAATATAATT
1 ATAATAAATATAATT
10778170 ATA
1 ATA
10778173 TATTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:10782815 original size:55 final size:55
Alignment explanation
Indices: 10782728--10782845 Score: 200
Period size: 55 Copynumber: 2.1 Consensus size: 55
10782718 AGGGGTCACA
10782728 CGGTCGTGCCCCAAACCATGTACCAGAACGTGTGCATACTCGTAATACCCATACT
1 CGGTCGTGCCCCAAACCATGTACCAGAACGTGTGCATACTCGTAATACCCATACT
* * * *
10782783 CGGTCGTGCCCCAAATCGTGTGCCAGACCGTGTGCATACTCGTAATACCCATACT
1 CGGTCGTGCCCCAAACCATGTACCAGAACGTGTGCATACTCGTAATACCCATACT
10782838 CGGTCGTG
1 CGGTCGTG
10782846 TTACAAACCG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 59 1.00
ACGTcount: A:0.23, C:0.32, G:0.22, T:0.23
Consensus pattern (55 bp):
CGGTCGTGCCCCAAACCATGTACCAGAACGTGTGCATACTCGTAATACCCATACT
Found at i:10782858 original size:55 final size:55
Alignment explanation
Indices: 10782728--10782859 Score: 192
Period size: 55 Copynumber: 2.4 Consensus size: 55
10782718 AGGGGTCACA
* * *
10782728 CGGTCGTGCCCCAAACCATGTACCAGAACGTGTGCATACTCGTAATACCCATACT
1 CGGTCGTGCCACAAACCGTGTGCCAGAACGTGTGCATACTCGTAATACCCATACT
* * *
10782783 CGGTCGTGCCCCAAATCGTGTGCCAGACCGTGTGCATACTCGTAATACCCATACT
1 CGGTCGTGCCACAAACCGTGTGCCAGAACGTGTGCATACTCGTAATACCCATACT
**
10782838 CGGTCGTGTTACAAACCGTGTG
1 CGGTCGTGCCACAAACCGTGTG
10782860 ATAGGTCGCG
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 69 1.00
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.23
Consensus pattern (55 bp):
CGGTCGTGCCACAAACCGTGTGCCAGAACGTGTGCATACTCGTAATACCCATACT
Found at i:10791193 original size:37 final size:37
Alignment explanation
Indices: 10791172--10791517 Score: 412
Period size: 37 Copynumber: 9.4 Consensus size: 37
10791162 TGACTGAGTT
*
10791172 GTAAGCCTTCCATATAACATTACGCTCTAACCGAGAC
1 GTAAGCCTTCCATATAACATTACGCTCTAACTGAGAC
* ** * *
10791209 ATAAGCCTTTTATATAACATTACACTCT-AGTCGAGAC
1 GTAAGCCTTCCATATAACATTACGCTCTAACT-GAGAC
10791246 GTAAGCCTTCCATATAACATCT-CGCTCTAA-TCGAGAC
1 GTAAGCCTTCCATATAACAT-TACGCTCTAACT-GAGAC
* *
10791283 GTAAGCCTTCCATATAACATTACGCTCTAACCGAGAT
1 GTAAGCCTTCCATATAACATTACGCTCTAACTGAGAC
* * * * *
10791320 GTAAGCATTCTATATAACATTATGCTCTAACCGAGAT
1 GTAAGCCTTCCATATAACATTACGCTCTAACTGAGAC
* * * * *
10791357 GTAAACCTTTCATATAACATTATGCTCTAACCGAGAA
1 GTAAGCCTTCCATATAACATTACGCTCTAACTGAGAC
*
10791394 GTAAACCTTCCATATAACATTACGCTCTAACTGAGAC
1 GTAAGCCTTCCATATAACATTACGCTCTAACTGAGAC
*
10791431 ATAAGCCTTCCATATAACATTACGCTCTAA-TCGAGAC
1 GTAAGCCTTCCATATAACATTACGCTCTAACT-GAGAC
* * **
10791468 GTAAGCCTTACATATAACATTACGATCTAACCAAGAC
1 GTAAGCCTTCCATATAACATTACGCTCTAACTGAGAC
10791505 GTAAGCCTTCCAT
1 GTAAGCCTTCCAT
10791518 TGAAGTAGTC
Statistics
Matches: 270, Mismatches: 32, Indels: 14
0.85 0.10 0.04
Matches are distributed among these distances:
36 3 0.01
37 265 0.98
38 2 0.01
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.28
Consensus pattern (37 bp):
GTAAGCCTTCCATATAACATTACGCTCTAACTGAGAC
Found at i:10791250 original size:74 final size:74
Alignment explanation
Indices: 10791172--10791517 Score: 469
Period size: 74 Copynumber: 4.7 Consensus size: 74
10791162 TGACTGAGTT
* ** *
10791172 GTAAGCCTTCCATATAACATTACGCTCTAACCGAGACATAAGCCTTTTATATAACATTACACTCT
1 GTAAGCCTTCCATATAACATTACGCTCTAACCGAGACGTAAGCCTTCCATATAACATTACGCTCT
**
10791237 AGTCGAGAC
66 AACCGAGAC
*
10791246 GTAAGCCTTCCATATAACATCT-CGCTCTAATCGAGACGTAAGCCTTCCATATAACATTACGCTC
1 GTAAGCCTTCCATATAACAT-TACGCTCTAACCGAGACGTAAGCCTTCCATATAACATTACGCTC
*
10791310 TAACCGAGAT
65 TAACCGAGAC
* * * * * * *
10791320 GTAAGCATTCTATATAACATTATGCTCTAACCGAGATGTAAACCTTTCATATAACATTATGCTCT
1 GTAAGCCTTCCATATAACATTACGCTCTAACCGAGACGTAAGCCTTCCATATAACATTACGCTCT
*
10791385 AACCGAGAA
66 AACCGAGAC
* * *
10791394 GTAAACCTTCCATATAACATTACGCTCTAACTGAGACATAAGCCTTCCATATAACATTACGCTCT
1 GTAAGCCTTCCATATAACATTACGCTCTAACCGAGACGTAAGCCTTCCATATAACATTACGCTCT
*
10791459 AATCGAGAC
66 AACCGAGAC
* * *
10791468 GTAAGCCTTACATATAACATTACGATCTAACCAAGACGTAAGCCTTCCAT
1 GTAAGCCTTCCATATAACATTACGCTCTAACCGAGACGTAAGCCTTCCAT
10791518 TGAAGTAGTC
Statistics
Matches: 235, Mismatches: 35, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
73 1 0.00
74 233 0.99
75 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.28
Consensus pattern (74 bp):
GTAAGCCTTCCATATAACATTACGCTCTAACCGAGACGTAAGCCTTCCATATAACATTACGCTCT
AACCGAGAC
Found at i:10791315 original size:111 final size:111
Alignment explanation
Indices: 10791172--10791517 Score: 496
Period size: 111 Copynumber: 3.1 Consensus size: 111
10791162 TGACTGAGTT
* *
10791172 GTAAGCCTTCCATATAACATTACGCTCTAACCGAGACATAAGCCTTTTATATAACATTACACTCT
1 GTAAGCCTTCCATATAACATTACGCTCTAACCGAGACATAAGCCTTCTATATAACATTACGCTCT
* * *
10791237 AGTCGAGACGTAAGCCTTCCATATAACATCT-CGCTCTAATCGAGAC
66 AATCGAGACGTAAGCCTTACATATAACAT-TACGCTCTAACCGAGAC
** * *
10791283 GTAAGCCTTCCATATAACATTACGCTCTAACCGAGATGTAAGCATTCTATATAACATTATGCTCT
1 GTAAGCCTTCCATATAACATTACGCTCTAACCGAGACATAAGCCTTCTATATAACATTACGCTCT
* * * * * *
10791348 AACCGAGATGTAAACCTTTCATATAACATTATGCTCTAACCGAGAA
66 AATCGAGACGTAAGCCTTACATATAACATTACGCTCTAACCGAGAC
* * *
10791394 GTAAACCTTCCATATAACATTACGCTCTAACTGAGACATAAGCCTTCCATATAACATTACGCTCT
1 GTAAGCCTTCCATATAACATTACGCTCTAACCGAGACATAAGCCTTCTATATAACATTACGCTCT
* *
10791459 AATCGAGACGTAAGCCTTACATATAACATTACGATCTAACCAAGAC
66 AATCGAGACGTAAGCCTTACATATAACATTACGCTCTAACCGAGAC
10791505 GTAAGCCTTCCAT
1 GTAAGCCTTCCAT
10791518 TGAAGTAGTC
Statistics
Matches: 204, Mismatches: 30, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
110 1 0.00
111 203 1.00
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.28
Consensus pattern (111 bp):
GTAAGCCTTCCATATAACATTACGCTCTAACCGAGACATAAGCCTTCTATATAACATTACGCTCT
AATCGAGACGTAAGCCTTACATATAACATTACGCTCTAACCGAGAC
Found at i:10795375 original size:20 final size:20
Alignment explanation
Indices: 10795350--10795391 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
10795340 AAACTAAGAA
10795350 AACTAAGAAGGAATGGAATG
1 AACTAAGAAGGAATGGAATG
10795370 AACTAAGAAGGAATGGAATG
1 AACTAAGAAGGAATGGAATG
10795390 AA
1 AA
10795392 ATCCCGAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.05, G:0.29, T:0.14
Consensus pattern (20 bp):
AACTAAGAAGGAATGGAATG
Found at i:10795612 original size:80 final size:80
Alignment explanation
Indices: 10795478--10795638 Score: 286
Period size: 80 Copynumber: 2.0 Consensus size: 80
10795468 AGTCCGGATC
* *
10795478 TCATCTGATAAGGATGCTATCACTTCATGTTGTTGGAGTGAAACACCTGGCAAATGCTTTTCCTT
1 TCATCAGATAAGGATGCTATCACCTCATGTTGTTGGAGTGAAACACCTGGCAAATGCTTTTCCTT
10795543 GTTGATAAGCATTAG
66 GTTGATAAGCATTAG
* *
10795558 TCATCAGATAAGGATGCTATCACCTCATGTTGTTGGAGTGAAACACCTGTCAAATGCTTTTCTTT
1 TCATCAGATAAGGATGCTATCACCTCATGTTGTTGGAGTGAAACACCTGGCAAATGCTTTTCCTT
10795623 GTTGATAAGCATTAG
66 GTTGATAAGCATTAG
10795638 T
1 T
10795639 TCTTCCGGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 77 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35
Consensus pattern (80 bp):
TCATCAGATAAGGATGCTATCACCTCATGTTGTTGGAGTGAAACACCTGGCAAATGCTTTTCCTT
GTTGATAAGCATTAG
Found at i:10804174 original size:80 final size:80
Alignment explanation
Indices: 10804014--10804167 Score: 281
Period size: 80 Copynumber: 1.9 Consensus size: 80
10804004 ATCCGGAAGA
*
10804014 ACTAATGCTTATCAACAAAGAAAAGCATTTGACAGGTGTTTCACTCCAACAACATGAGGTGATAG
1 ACTAATGCTTATCAACAAAGAAAAGCATTTGACAGGTGTTTCACTCCAACAACATGAAGTGATAG
10804079 CATCCTTATCTGATG
66 CATCCTTATCTGATG
* *
10804094 ACTAATGCTTATCAACAAGGAAAAGCATTTGCCAGGTGTTTCACTCCAACAACATGAAGTGATAG
1 ACTAATGCTTATCAACAAAGAAAAGCATTTGACAGGTGTTTCACTCCAACAACATGAAGTGATAG
10804159 CATCCTTAT
66 CATCCTTAT
10804168 TAGATGAGAT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 71 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (80 bp):
ACTAATGCTTATCAACAAAGAAAAGCATTTGACAGGTGTTTCACTCCAACAACATGAAGTGATAG
CATCCTTATCTGATG
Found at i:10805438 original size:80 final size:80
Alignment explanation
Indices: 10805305--10805465 Score: 277
Period size: 80 Copynumber: 2.0 Consensus size: 80
10805295 ATCCGAAAGA
*
10805305 ACTAATGCTTATCAACAAAGAAAAGCATTTGACAGGTGTTTCACTCCAACAACATGAGGTGATAG
1 ACTAATGCTTATCAACAAAGAAAAGCATTTGACAGGTGTTTCACTCCAACAACATGAAGTGATAG
*
10805370 CATCCTTATCTGATG
66 CATCCTTATCAGATG
* **
10805385 ACTAATGCTTATCAACAAGGAAAAGCATTTTCCAGGTGTTTCACTCCAACAACATGAAGTGATAG
1 ACTAATGCTTATCAACAAAGAAAAGCATTTGACAGGTGTTTCACTCCAACAACATGAAGTGATAG
10805450 CATCCTTATCAGATG
66 CATCCTTATCAGATG
10805465 A
1 A
10805466 GATCCGGACT
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.27
Consensus pattern (80 bp):
ACTAATGCTTATCAACAAAGAAAAGCATTTGACAGGTGTTTCACTCCAACAACATGAAGTGATAG
CATCCTTATCAGATG
Found at i:10805579 original size:9 final size:9
Alignment explanation
Indices: 10805565--10805589 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
10805555 ATTCCCTTCC
10805565 TTCTTAGTT
1 TTCTTAGTT
10805574 TTCTTAGTT
1 TTCTTAGTT
10805583 TTCTTAG
1 TTCTTAG
10805590 ACACTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.64
Consensus pattern (9 bp):
TTCTTAGTT
Found at i:10813183 original size:16 final size:16
Alignment explanation
Indices: 10813164--10813203 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
10813154 TAGTACTGTA
*
10813164 GAAACTACGTACTTGT
1 GAAACTACATACTTGT
*
10813180 GAAAACTCCATACTTGT
1 G-AAACTACATACTTGT
10813197 GAAACTA
1 GAAACTA
10813204 GAGATAGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (16 bp):
GAAACTACATACTTGT
Found at i:10819068 original size:28 final size:29
Alignment explanation
Indices: 10819037--10819091 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
10819027 AAGGAGGAAG
10819037 ATGTGACCA-TTT-TGGCAAAATATGTGAT
1 ATGTGACCATTTTATGG-AAAATATGTGAT
*
10819065 ATGTGGCCATTTTATGGAAAATATGTG
1 ATGTGACCATTTTATGGAAAATATGTG
10819092 GTAGTTCATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 8 0.33
29 13 0.54
30 3 0.12
ACGTcount: A:0.31, C:0.09, G:0.24, T:0.36
Consensus pattern (29 bp):
ATGTGACCATTTTATGGAAAATATGTGAT
Found at i:10826785 original size:11 final size:11
Alignment explanation
Indices: 10826758--10826787 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
10826748 AACTTGTGCA
10826758 TCCAAAAACAC
1 TCCAAAAACAC
10826769 TCCCAAAAACAC
1 T-CCAAAAACAC
10826781 TCCAAAA
1 TCCAAAA
10826788 CCTTTATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.53, C:0.37, G:0.00, T:0.10
Consensus pattern (11 bp):
TCCAAAAACAC
Found at i:10837857 original size:3 final size:3
Alignment explanation
Indices: 10837849--10837873 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
10837839 CATGCAAATT
10837849 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
10837874 ATTAATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:10843663 original size:16 final size:17
Alignment explanation
Indices: 10843642--10843674 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
10843632 ATCTCATTTC
*
10843642 CTTTATTTTTAT-TTTA
1 CTTTATGTTTATGTTTA
10843658 CTTTATGTTTATGTTTA
1 CTTTATGTTTATGTTTA
10843675 TTATAAAACT
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:0.18, C:0.06, G:0.06, T:0.70
Consensus pattern (17 bp):
CTTTATGTTTATGTTTA
Found at i:10844084 original size:9 final size:9
Alignment explanation
Indices: 10844052--10844093 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
10844042 GGGTTGAGAA
10844052 AATT-ATTT
1 AATTAATTT
*
10844060 AATTAA-TA
1 AATTAATTT
10844068 AATTAATTT
1 AATTAATTT
*
10844077 AGTTAATTT
1 AATTAATTT
10844086 AATTAATT
1 AATTAATT
10844094 AATATTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
8 11 0.39
9 17 0.61
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (9 bp):
AATTAATTT
Found at i:10851287 original size:30 final size:30
Alignment explanation
Indices: 10851226--10851289 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
10851216 AAAATTTTTT
***
10851226 AAATATTATTTATTATCTTTGTACCTAAAA
1 AAATATTATTTATTATCTACCTACCTAAAA
*
10851256 AAATATTATTTATTATCTCACCT-CCTCAAA
1 AAATATTATTTATTATCT-ACCTACCTAAAA
10851286 AAAT
1 AAAT
10851290 TTTGGCTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.41, C:0.16, G:0.02, T:0.42
Consensus pattern (30 bp):
AAATATTATTTATTATCTACCTACCTAAAA
Found at i:10852318 original size:24 final size:26
Alignment explanation
Indices: 10852282--10852337 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
10852272 TATTTTTTAG
* *
10852282 AATTTTTATAATTTTTTTAAATA-TA
1 AATTTTGATAATTTTTATAAATATTA
10852307 AATTTTGA-AATTTTTATAAATATTA
1 AATTTTGATAATTTTTATAAATATTA
10852332 AATTTT
1 AATTTT
10852338 TTTTTGTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 13 0.46
25 15 0.54
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
AATTTTGATAATTTTTATAAATATTA
Found at i:10852339 original size:18 final size:18
Alignment explanation
Indices: 10852303--10852338 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
10852293 TTTTTTTAAA
*
10852303 TATAAATTTTGAAATTTT
1 TATAAATATTGAAATTTT
10852321 TATAAATATT-AAATTTT
1 TATAAATATTGAAATTTT
10852338 T
1 T
10852339 TTTTGTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
TATAAATATTGAAATTTT
Found at i:10857293 original size:3 final size:3
Alignment explanation
Indices: 10857285--10857311 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
10857275 AGAAAAACTT
10857285 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
10857312 AGTTGAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:10859202 original size:30 final size:29
Alignment explanation
Indices: 10859138--10859208 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 29
10859128 AATATTGAGT
* *
10859138 GTAAAATTTAGTTAAAAAATTAAAGTTATG
1 GTAAAATTTA-ATAAAAAATTAAAGTTATA
*
10859168 GTAAAATTTAAT-AAAATTTAAAGTT-TA
1 GTAAAATTTAATAAAAAATTAAAGTTATA
10859195 GTAGTAAATTTAAT
1 GTA--AAATTTAAT
10859209 CACATAAAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.11
28 12 0.33
29 10 0.28
30 10 0.28
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.39
Consensus pattern (29 bp):
GTAAAATTTAATAAAAAATTAAAGTTATA
Found at i:10874879 original size:11 final size:11
Alignment explanation
Indices: 10874865--10874900 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
10874855 CCAGAACAGT
10874865 AAAAGAAGAAG
1 AAAAGAAGAAG
10874876 AAAAGAAGAAG
1 AAAAGAAGAAG
10874887 AAAA-AGAGAAG
1 AAAAGA-AGAAG
10874898 AAA
1 AAA
10874901 TGGAGATGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 1 0.04
11 23 0.96
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAAG
Found at i:10874884 original size:14 final size:14
Alignment explanation
Indices: 10874867--10874899 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
10874857 AGAACAGTAA
10874867 AAGAAGAAGAAA-AG
1 AAGAAGAA-AAAGAG
10874881 AAGAAGAAAAAGAG
1 AAGAAGAAAAAGAG
10874895 AAGAA
1 AAGAA
10874900 ATGGAGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (14 bp):
AAGAAGAAAAAGAG
Found at i:10875839 original size:15 final size:14
Alignment explanation
Indices: 10875815--10875844 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
10875805 AGATTTAGAA
10875815 TTTTTCTTTTCTTC
1 TTTTTCTTTTCTTC
10875829 TTTTTCTTTTTCTTC
1 TTTTTC-TTTTCTTC
10875844 T
1 T
10875845 CCTACCTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTCTTTTCTTC
Found at i:10877804 original size:47 final size:47
Alignment explanation
Indices: 10877753--10877865 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
10877743 ATAACAGTAA
* **
10877753 TGCAGATAAACTATCACTTAATAATATTGTGGACAAGCCACCACTTT
1 TGCAGATAAACTGTCACTTAATAATATTGTAAACAAGCCACCACTTT
* * * *
10877800 TGCAGATAAATTGTCACTTTATAATATTGTAAACGAGCCATCACTTT
1 TGCAGATAAACTGTCACTTAATAATATTGTAAACAAGCCACCACTTT
*
10877847 TGCAAATAAACTGTCACTT
1 TGCAGATAAACTGTCACTT
10877866 CTTCCTCCTT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33
Consensus pattern (47 bp):
TGCAGATAAACTGTCACTTAATAATATTGTAAACAAGCCACCACTTT
Found at i:10881921 original size:60 final size:59
Alignment explanation
Indices: 10881821--10881959 Score: 197
Period size: 60 Copynumber: 2.3 Consensus size: 59
10881811 TTACATTTTA
* * * * * *
10881821 ACCCCCAAACTATCCAAACATTTAGATTTGACACTTGAACTTCCCAAAATTTTGGATTT
1 ACCCCCAAACTTTCCAAAAATTTAGATTTGACACTCGAACTTACCAAAAATTTGAATTT
*
10881880 GACCCCCAAACTTTCCAAAAATTTAGATTTGACCCTCGAACTTACCAAAAATTTGAATTT
1 -ACCCCCAAACTTTCCAAAAATTTAGATTTGACACTCGAACTTACCAAAAATTTGAATTT
10881940 AGCCCCCAAACTTTCCAAAA
1 A-CCCCCAAACTTTCCAAAA
10881960 TTTCATTTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
59 1 0.01
60 70 0.99
ACGTcount: A:0.36, C:0.27, G:0.08, T:0.29
Consensus pattern (59 bp):
ACCCCCAAACTTTCCAAAAATTTAGATTTGACACTCGAACTTACCAAAAATTTGAATTT
Found at i:10881952 original size:30 final size:30
Alignment explanation
Indices: 10881821--10881959 Score: 122
Period size: 30 Copynumber: 4.6 Consensus size: 30
10881811 TTACATTTTA
* *
10881821 ACCCCCAAACTATCCAAACATTT-AGATTTG
1 ACCCCCAAACTTTCCAAAAATTTGA-ATTTG
* *** * * *
10881851 ACACTTGAACTTCCCAAAATTTTGGATTTG
1 ACCCCCAAACTTTCCAAAAATTTGAATTTG
10881881 ACCCCCAAACTTTCCAAAAATTT-AGATTTG
1 ACCCCCAAACTTTCCAAAAATTTGA-ATTTG
* * *
10881911 ACCCTCGAACTTACCAAAAATTTGAATTT-
1 ACCCCCAAACTTTCCAAAAATTTGAATTTG
10881940 AGCCCCCAAACTTTCCAAAA
1 A-CCCCCAAACTTTCCAAAA
10881960 TTTCATTTTT
Statistics
Matches: 83, Mismatches: 22, Indels: 8
0.73 0.19 0.07
Matches are distributed among these distances:
29 1 0.01
30 81 0.98
31 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.08, T:0.29
Consensus pattern (30 bp):
ACCCCCAAACTTTCCAAAAATTTGAATTTG
Found at i:10883938 original size:18 final size:18
Alignment explanation
Indices: 10883915--10883950 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
10883905 AACTATGCCA
10883915 AACCTTTAGTGGTTACCC
1 AACCTTTAGTGGTTACCC
10883933 AACCTTTAGTGGTTACCC
1 AACCTTTAGTGGTTACCC
10883951 GAATAAGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (18 bp):
AACCTTTAGTGGTTACCC
Found at i:10888203 original size:99 final size:98
Alignment explanation
Indices: 10888025--10888385 Score: 374
Period size: 99 Copynumber: 3.7 Consensus size: 98
10888015 TTTAATAGGG
* * * * *
10888025 AAGATTGAGGCCGCAACGGCGAATCTAATACCCTAGAA-ATACGAAGGAAAAGGTTGAGACCACA
1 AAGATTGAGGCCGCAACGGCGAATCTGATACCAT-GAAGATATGAAGGGAAAGGTTGAGGCCA-A
* *
10888089 ACGACAAGCCTTGTACCTTAGAAGACATGATGGGA
64 ACGGCAAACCTTGTACCTTAGAAGACATGATGGGA
* *
10888124 AAGATCGAGGCCGCAACGGTGAAT-TCGATACCATGAAGATATGAAGGGAAAGGTT-AGGGCCAT
1 AAGATTGAGGCCGCAACGGCGAATCT-GATACCATGAAGATATGAAGGGAAAGGTTGA-GGCCA-
* **
10888187 AACGGCAAACCCTGTACCTTAGAAGATGTGATGGGA
63 AACGGCAAACCTTGTACCTTAGAAGACATGATGGGA
* * * * *
10888223 AGGATTGAGGCTGTAACAGCGAATCTGATACCATGAAGATATGAAAGGAAAGGTTGAGGCCGAAA
1 AAGATTGAGGCCGCAACGGCGAATCTGATACCATGAAGATATGAAGGGAAAGGTTGAGGCC-AAA
** *
10888288 CGGCAAACCTTGTACCTTAGAAGATGTGAT-AGA
65 CGGCAAACCTTGTACCTTAGAAGACATGATGGGA
* * * * *
10888321 AAGGATTGAGGCTGCAACGACGAATC-CAGTACCATGAATATGTGAAGGG-AAGGATTGAGGCCA
1 AA-GATTGAGGCCGCAACGGCGAATCTGA-TACCATGAAGATATGAAGGGAAAGG-TTGAGGCCA
10888384 AA
63 AA
10888386 ATGACGAATC
Statistics
Matches: 223, Mismatches: 30, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
98 16 0.07
99 204 0.91
100 3 0.01
ACGTcount: A:0.37, C:0.17, G:0.29, T:0.18
Consensus pattern (98 bp):
AAGATTGAGGCCGCAACGGCGAATCTGATACCATGAAGATATGAAGGGAAAGGTTGAGGCCAAAC
GGCAAACCTTGTACCTTAGAAGACATGATGGGA
Found at i:10888280 original size:49 final size:50
Alignment explanation
Indices: 10888150--10888332 Score: 128
Period size: 50 Copynumber: 3.7 Consensus size: 50
10888140 CGGTGAATTC
* *
10888150 GATACCATGAAGATATGAAGGGAAAGGTT-AGGGCCATAACGGCAAACCCT
1 GATACCATGAAGATATGAAAGGAAAGGTTGA-GGCCATAACAGCAAACCCT
* * * * ** * *
10888200 G-TACCTTAGAAGATGTG-ATGGGAAGGATTGAGGCTGTAACAGCGAA-TCT
1 GATACCAT-GAAGATATGAAAGGAAAGG-TTGAGGCCATAACAGCAAACCCT
* *
10888249 GATACCATGAAGATATGAAAGGAAAGGTTGAGGCCGA-AACGGCAAACCTT
1 GATACCATGAAGATATGAAAGGAAAGGTTGAGGCC-ATAACAGCAAACCCT
* * *
10888299 G-TACCTTAGAAGATGTGATA-GAAAGGATTGAGGC
1 GATACCAT-GAAGATATGAAAGGAAAGG-TTGAGGC
10888333 TGCAACGACG
Statistics
Matches: 102, Mismatches: 22, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
49 48 0.47
50 53 0.52
51 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.30, T:0.20
Consensus pattern (50 bp):
GATACCATGAAGATATGAAAGGAAAGGTTGAGGCCATAACAGCAAACCCT
Found at i:10888353 original size:50 final size:50
Alignment explanation
Indices: 10888197--10888410 Score: 172
Period size: 49 Copynumber: 4.3 Consensus size: 50
10888187 AACGGCAAAC
* * *
10888197 CCTGTACCTTAGAAGATGTGAT-GGGAAGGATTGAGGCTGTAAC-AGCGAAT
1 CCTGTACCAT-GAAGATGTGATAGGAAAGGATTGAGGCTGAAACGA-CGAAT
* * * * *
10888247 -CTGATACCATGAAGATATGAAAGGAAAGG-TTGAGGCCGAAACGGC-AAA
1 CCTG-TACCATGAAGATGTGATAGGAAAGGATTGAGGCTGAAACGACGAAT
* *
10888295 CCTTGTACCTTAGAAGATGTGATA-GAAAGGATTGAGGCTGCAACGACGAAT
1 CC-TGTACCAT-GAAGATGTGATAGGAAAGGATTGAGGCTGAAACGACGAAT
* * * ** *
10888346 CCAGTACCATGAATATGTGA-AGGGAAGGATTGAGGCCAAAATGACGAAT
1 CCTGTACCATGAAGATGTGATAGGAAAGGATTGAGGCTGAAACGACGAAT
* *
10888395 CTTGTACCATGGAGAT
1 CCTGTACCATGAAGAT
10888411 ATGGAGGGAA
Statistics
Matches: 128, Mismatches: 27, Indels: 19
0.74 0.16 0.11
Matches are distributed among these distances:
48 3 0.02
49 79 0.62
50 42 0.33
51 4 0.03
ACGTcount: A:0.35, C:0.15, G:0.29, T:0.21
Consensus pattern (50 bp):
CCTGTACCATGAAGATGTGATAGGAAAGGATTGAGGCTGAAACGACGAAT
Found at i:10888498 original size:48 final size:49
Alignment explanation
Indices: 10888392--10888545 Score: 120
Period size: 49 Copynumber: 3.2 Consensus size: 49
10888382 CAAAATGACG
* * * * **
10888392 AATCTTGTACCATGGAGATATGGAGGGAAAGGTTGAAGCCGCAACGATG
1 AATCTTATACCATAGAGATATGCAGGGAAAGATTGAAGCCGCAACGACA
* * * *
10888441 AACCTTATACCTTAGAGATATGCAGGGAAAGATT-AAGCCGCAATGGCA
1 AATCTTATACCATAGAGATATGCAGGGAAAGATTGAAGCCGCAACGACA
* * * * *
10888489 AATCTTATACCCT-GA-AGATG-A-GGAGTAGATTGAAGTCGCAACGACG
1 AATCTTATACCATAGAGATATGCAGGGA-AAGATTGAAGCCGCAACGACA
*
10888535 AATCTTCTACC
1 AATCTTATACC
10888546 TCAAAGTTAC
Statistics
Matches: 84, Mismatches: 19, Indels: 7
0.76 0.17 0.06
Matches are distributed among these distances:
44 3 0.04
45 6 0.07
46 24 0.29
47 2 0.02
48 21 0.25
49 28 0.33
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.22
Consensus pattern (49 bp):
AATCTTATACCATAGAGATATGCAGGGAAAGATTGAAGCCGCAACGACA
Found at i:10888747 original size:37 final size:41
Alignment explanation
Indices: 10888578--10889478 Score: 573
Period size: 42 Copynumber: 22.4 Consensus size: 41
10888568 CGAAGCTGCA
* * * *
10888578 CCAATCTCTTACCCCAATCATGGGGCAGATTGAAG-C--AT
1 CCAATCTTTTACCCCGATCATGGGGCAGACTAAAGACATAT
* * * ** **
10888616 CCAAACTCTTACCCCGATCATGGGGCAGATTGTAG-C-CGT
1 CCAATCTTTTACCCCGATCATGGGGCAGACTAAAGACATAT
* * * *
10888655 CCAATCTCTTACCCTGATCATGGGGCAGATTGAAGACATTAT
1 CCAATCTTTTACCCCGATCATGGGGCAGACTAAAGACA-TAT
* *
10888697 CCAATCTCTTACCCCGAT-ATGAGGCAGACTAAAG-CAT-T
1 CCAATCTTTTACCCCGATCATGGGGCAGACTAAAGACATAT
* *
10888735 -CGATCTTTTACCCCGATCATGGGGCAGATTAAAGACATCAT
1 CCAATCTTTTACCCCGATCATGGGGCAGACTAAAGACAT-AT
* *
10888776 CCAATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCAT
1 CCAATCTTTTACCCCGATCATGGGGCAGACTAAAGACAT-AT
* *
10888818 CCAATCTTTTACCCCGACCATGGGGCAGA-T--TGA-ATCAT
1 CCAATCTTTTACCCCGATCATGGGGCAGACTAAAGACAT-AT
*** * * * * *
10888856 CCAATCTTTTACCTTAATCA-GAGGGCAAATTGAAGATATCGT
1 CCAATCTTTTACCCCGATCATG-GGGCAGACTAAAGACAT-AT
* * * * * *
10888898 CCAATCTCTTACCCAGATCATGGGGCAAATTGAAG-C-CAT
1 CCAATCTTTTACCCCGATCATGGGGCAGACTAAAGACATAT
* *
10888937 CCAATCTTTTACCCCGATCATGGGGTAGATTAAAGACATCAT
1 CCAATCTTTTACCCCGATCATGGGGCAGACTAAAGACAT-AT
* * * * * *
10888979 CCAATCTCTTACGCCGATCATGGGGCAAATTGAAGACACA-
1 CCAATCTTTTACCCCGATCATGGGGCAGACTAAAGACATAT
* * *
10889019 CCAATCTTTTACCCCGATCATGGGGCAAATTGAAGACATCAT
1 CCAATCTTTTACCCCGATCATGGGGCAGACTAAAGACAT-AT
* * * *** *
10889061 CCAATCTTTTACTCCGATCATGAGGCAGATTGCTG-C-TGT
1 CCAATCTTTTACCCCGATCATGGGGCAGACTAAAGACATAT
* * *
10889100 CCAATCTCTTACCCCGATCATGGGGCAGAATGAAGACATCAT
1 CCAATCTTTTACCCCGATCATGGGGCAGACTAAAGACAT-AT
* * *
10889142 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAG-CAT-T
1 CCAATCTTTTACCCCGATCATGGGGCAGACTAAAGACATAT
** * * * * *
10889181 -TGATCTTTTGCCCTGATCATGGGGTAGATTGAAGACATCAT
1 CCAATCTTTTACCCCGATCATGGGGCAGACTAAAGACAT-AT
* * *
10889222 CCAATCTTTTACCCCGATCATGGGGTAGATTGAAGACATCAT
1 CCAATCTTTTACCCCGATCATGGGGCAGACTAAAGACAT-AT
* * * * *
10889264 CCAATCTCTTACCCCGACCATGGGGTAGATTGAAG-C--AT
1 CCAATCTTTTACCCCGATCATGGGGCAGACTAAAGACATAT
* * ** * ** * * * *
10889302 CCGATCCTTTACCCTAATTAAAGGGTAGATTGAAGACACA-
1 CCAATCTTTTACCCCGATCATGGGGCAGACTAAAGACATAT
* * * *
10889342 CTAATCTTTTACCCCGATCATGGGGCAGATTGAAGCCAT-T
1 CCAATCTTTTACCCCGATCATGGGGCAGACTAAAGACATAT
* * * * * *
10889382 -CAAACTCTTACCCAG-TAATGGGGTAGATTAAAGACATCAT
1 CCAATCTTTTACCCCGATCATGGGGCAGACTAAAGACAT-AT
* * * *
10889422 CCAATCTTTTACCCCGATCATGGGGCAGATTGAAGCCACCAT
1 CCAATCTTTTACCCCGATCATGGGGCAGACTAAAGACA-TAT
10889464 CCAATCTTTTACCCC
1 CCAATCTTTTACCCC
10889479 TAAATCAAGA
Statistics
Matches: 715, Mismatches: 112, Indels: 68
0.80 0.13 0.08
Matches are distributed among these distances:
37 16 0.02
38 149 0.21
39 117 0.16
40 71 0.10
41 39 0.05
42 322 0.45
43 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (41 bp):
CCAATCTTTTACCCCGATCATGGGGCAGACTAAAGACATAT
Found at i:10888796 original size:42 final size:42
Alignment explanation
Indices: 10888737--10889478 Score: 818
Period size: 42 Copynumber: 18.3 Consensus size: 42
10888727 AAAGCATTCG
*
10888737 ATCTTTTACCCCGATCATGGGGCAGATTAAAGACATCATCCA
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
10888779 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
*
10888821 ATCTTTTACCCCGACCATGGGGCAGATT---GA-ATCATCCA
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
*** * * *
10888859 ATCTTTTACCTTAATCA-GAGGGCAAATTGAAGATATCGTCCA
1 ATCTTTTACCCCGATCATG-GGGCAGATTGAAGACATCATCCA
* * *
10888901 ATCTCTTACCCAGATCATGGGGCAAATTGAAG-C--CATCCA
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
* *
10888940 ATCTTTTACCCCGATCATGGGGTAGATTAAAGACATCATCCA
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
* * *
10888982 ATCTCTTACGCCGATCATGGGGCAAATTGAAGACA-CA-CCA
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
*
10889022 ATCTTTTACCCCGATCATGGGGCAAATTGAAGACATCATCCA
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
* * ** *
10889064 ATCTTTTACTCCGATCATGAGGCAGATTGCTG-C-T-GTCCA
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
* *
10889103 ATCTCTTACCCCGATCATGGGGCAGAATGAAGACATCATCCA
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
* **
10889145 ATCTCTTACCCCGATCATGGGGCAGATTGAAG-CAT--T-TG
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
* * *
10889183 ATCTTTTGCCCTGATCATGGGGTAGATTGAAGACATCATCCA
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
*
10889225 ATCTTTTACCCCGATCATGGGGTAGATTGAAGACATCATCCA
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
* * * *
10889267 ATCTCTTACCCCGACCATGGGGTAGATTGAAG----CATCCG
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
* ** * ** * *
10889305 ATCCTTTACCCTAATTAAAGGGTAGATTGAAGACA-CA-CTA
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
*
10889345 ATCTTTTACCCCGATCATGGGGCAGATTGAAG-C--CATTCA
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
* * * * * *
10889384 AACTCTTACCCAG-TAATGGGGTAGATTAAAGACATCATCCA
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
* *
10889425 ATCTTTTACCCCGATCATGGGGCAGATTGAAGCCACCATCCA
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
10889467 ATCTTTTACCCC
1 ATCTTTTACCCC
10889479 TAAATCAAGA
Statistics
Matches: 587, Mismatches: 87, Indels: 52
0.81 0.12 0.07
Matches are distributed among these distances:
37 1 0.00
38 103 0.18
39 81 0.14
40 65 0.11
41 29 0.05
42 307 0.52
43 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27
Consensus pattern (42 bp):
ATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
Found at i:10889038 original size:243 final size:244
Alignment explanation
Indices: 10888578--10889478 Score: 955
Period size: 243 Copynumber: 3.7 Consensus size: 244
10888568 CGAAGCTGCA
* * * *
10888578 CCAATCTCTTACCCCAATCATGGGGCAGATTGAAGCATCCAAACTCTTACCCCGATCATGGGGCA
1 CCAATCTTTTACCCCGATCATGGGGCAGATTGAATCATCCAATCTCTTACCCCGATCATGGGGCA
* * * * * *
10888643 GATTGTAG--CCGTCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGACATTATCCAATCTCT
66 AATTGAAGAATCGTCCAATCTCTTACCCAGATCATGGGGCAGATTGAAG-C--CATCCAATCTTT
* * * * *
10888706 TACCCCGAT-ATGAGGCAGACTAAAG-CAT--T-CGATCTTTTACCCCGATCATGGGGCAGATTA
128 TACCCCGATCATGGGGTAGATTAAAGACATCATCCAATCTTTTACCCCGATCATGGGGCAGATTG
10888766 AAGACATCATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCAT
193 AAGACATCATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCAT
* * ***
10888818 CCAATCTTTTACCCCGACCATGGGGCAGATTGAATCATCCAATCTTTTACCTTAATCA-GAGGGC
1 CCAATCTTTTACCCCGATCATGGGGCAGATTGAATCATCCAATCTCTTACCCCGATCATG-GGGC
*
10888882 AAATTGAAGATATCGTCCAATCTCTTACCCAGATCATGGGGCAAATTGAAGCCATCCAATCTTTT
65 AAATTGAAGA-ATCGTCCAATCTCTTACCCAGATCATGGGGCAGATTGAAGCCATCCAATCTTTT
* * *
10888947 ACCCCGATCATGGGGTAGATTAAAGACATCATCCAATCTCTTACGCCGATCATGGGGCAAATTGA
129 ACCCCGATCATGGGGTAGATTAAAGACATCATCCAATCTTTTACCCCGATCATGGGGCAGATTGA
*
10889012 AGACA-CA-CCAATCTTTTACCCCGATCATGGGGCAAATTGAAGACATCAT
194 AGACATCATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCAT
* * * *
10889061 CCAATCTTTTACTCCGATCATGAGGCAGATTG-CTGCTGTCCAATCTCTTACCCCGATCATGGGG
1 CCAATCTTTTACCCCGATCATGGGGCAGATTGAAT-C-ATCCAATCTCTTACCCCGATCATGGGG
* * ***
10889125 CAGAA-TGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAG-CATTTGATCTT
64 CA-AATTGAAGA-ATCGTCCAATCTCTTACCCAGATCATGGGGCAGATTGAAGCCATCCAATCTT
* * * *
10889188 TTGCCCTGATCATGGGGTAGATTGAAGACATCATCCAATCTTTTACCCCGATCATGGGGTAGATT
127 TTACCCCGATCATGGGGTAGATTAAAGACATCATCCAATCTTTTACCCCGATCATGGGGCAGATT
* * *
10889253 GAAGACATCATCCAATCTCTTACCCCGACCATGGGGTAGATTGAAG----CAT
192 GAAGACATCATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCAT
* * ** * ** * * *
10889302 CCGATCCTTTACCCTAATTAAAGGGTAGATTGAAGACA-CACTAATCTTTTACCCCGATCATGGG
1 CCAATCTTTTACCCCGATCATGGGGCAGATTGAA-TCATC-C-AATCTCTTACCCCGATCATGGG
* * * * * *
10889366 GCAGATTGAAGCCAT--T-CAAACTCTTACCCAG-TAATGGGGTAGATTAAAGACATCATCCAAT
63 GCAAATTGAAG-AATCGTCCAATCTCTTACCCAGATCATGGGGCAGATTGAAG-C--CATCCAAT
* * * *
10889427 CTTTTACCCCGATCATGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCC
124 CTTTTACCCCGATCATGGGGTAGATTAAAGACATCATCCAATCTTTTACCCC
10889479 TAAATCAAGA
Statistics
Matches: 555, Mismatches: 81, Indels: 48
0.81 0.12 0.07
Matches are distributed among these distances:
238 15 0.03
239 14 0.03
240 81 0.15
241 40 0.07
242 89 0.16
243 180 0.32
244 70 0.13
245 66 0.12
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (244 bp):
CCAATCTTTTACCCCGATCATGGGGCAGATTGAATCATCCAATCTCTTACCCCGATCATGGGGCA
AATTGAAGAATCGTCCAATCTCTTACCCAGATCATGGGGCAGATTGAAGCCATCCAATCTTTTAC
CCCGATCATGGGGTAGATTAAAGACATCATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAG
ACATCATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCAT
Found at i:10889256 original size:80 final size:81
Alignment explanation
Indices: 10888737--10889478 Score: 745
Period size: 80 Copynumber: 9.1 Consensus size: 81
10888727 AAAGCATTCG
*
10888737 ATCTTTTACCCCGATCATGGGGCAGATTAAAGACATCATCCAATCTTTTACCCCGATCATGGGGC
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACAT--T-CAATCTTTTACCCCGATCATGGGGC
10888802 AGATTGAAGACATCATCCA
63 AGATTGAAGACATCATCCA
* * * *** *
10888821 ATCTTTTACCCCGACCATGGGGCAGATTGAA-TCATCCAATCTTTTACCTTAATCA-GAGGGCAA
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACATTCAATCTTTTACCCCGATCATG-GGGCAG
* *
10888884 ATTGAAGATATCGTCCA
65 ATTGAAGACATCATCCA
* * * * * *
10888901 ATCTCTTACCCAGATCATGGGGCAAATTGAAGCCATCCAATCTTTTACCCCGATCATGGGGTAGA
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACATTCAATCTTTTACCCCGATCATGGGGCAGA
*
10888966 TTAAAGACATCATCCA
66 TTGAAGACATCATCCA
* * * ** *
10888982 ATCTCTTACGCCGATCATGGGGCAAATTGAAGACACACCAATCTTTTACCCCGATCATGGGGCAA
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACA-TTCAATCTTTTACCCCGATCATGGGGCAG
10889047 ATTGAAGACATCATCCA
65 ATTGAAGACATCATCCA
* * ** *
10889064 ATCTTTTACTCCGATCATGAGGCAGATTGCTG-C-TGTCCAATCTCTTACCCCGATCATGGGGCA
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACAT-T-CAATCTTTTACCCCGATCATGGGGCA
*
10889127 GAATGAAGACATCATCCA
64 GATTGAAGACATCATCCA
* ** * * *
10889145 ATCTCTTACCCCGATCATGGGGCAGATTGAAG-CATTTGATCTTTTGCCCTGATCATGGGGTAGA
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACATTCAATCTTTTACCCCGATCATGGGGCAGA
10889209 TTGAAGACATCATCCA
66 TTGAAGACATCATCCA
* * * *
10889225 ATCTTTTACCCCGATCATGGGGTAGATTGAAGACATCATCCAATCTCTTACCCCGACCATGGGGT
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACAT--T-CAATCTTTTACCCCGATCATGGGGC
*
10889290 AGATTGAAG----CATCCG
63 AGATTGAAGACATCATCCA
* ** * ** * **
10889305 ATCCTTTACCCTAATTAAAGGGTAGATTGAAGACACACTAATCTTTTACCCCGATCATGGGGCAG
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACATTC-AATCTTTTACCCCGATCATGGGGCAG
*
10889370 ATTGAAG-C--CATTCA
65 ATTGAAGACATCATCCA
* * * * * *
10889384 AACTCTTACCCAG-TAATGGGGTAGATTAAAGACATCATCCAATCTTTTACCCCGATCATGGGGC
1 ATCTTTTACCCCGATCATGGGGCAGATTGAAGACAT--T-CAATCTTTTACCCCGATCATGGGGC
* *
10889448 AGATTGAAGCCACCATCCA
63 AGATTGAAGACATCATCCA
10889467 ATCTTTTACCCC
1 ATCTTTTACCCC
10889479 TAAATCAAGA
Statistics
Matches: 549, Mismatches: 90, Indels: 39
0.81 0.13 0.06
Matches are distributed among these distances:
77 1 0.00
78 47 0.09
79 13 0.02
80 197 0.36
81 146 0.27
82 70 0.13
83 18 0.03
84 57 0.10
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27
Consensus pattern (81 bp):
ATCTTTTACCCCGATCATGGGGCAGATTGAAGACATTCAATCTTTTACCCCGATCATGGGGCAGA
TTGAAGACATCATCCA
Found at i:10889374 original size:78 final size:79
Alignment explanation
Indices: 10888613--10889457 Score: 410
Period size: 80 Copynumber: 10.5 Consensus size: 79
10888603 CAGATTGAAG
* * * * * * * *
10888613 CATCCAAACTCTTACCCCGATCATGGGGCAGATTGTAGCCGTCCAATCTCTTACCCTGATCATGG
1 CATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAG-CATCCAAACTCTTACCCAG-TAATAG
*
10888678 GGCAGATTGAAGACAT
64 GGTAGATTGAAGACAT
* * * * * * * * * * * *
10888694 TATCCAATCTCTTACCCCGAT-ATGAGGCAGACTAAAGCATTCGATCTTTTACCCCGATCATGGG
1 CATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAGCATCCAAACTCTTACCCAG-TAATAGG
* *
10888758 GCAGATTAAAGACAT
65 GTAGATTGAAGACAT
* * *
10888773 CATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTTTTACCCCG-ACC
1 CATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAG----CATCCAAACTCTTACCCAGTA--
* *
10888837 ATGGGGCAGATT---GA-AT
60 ATAGGGTAGATTGAAGACAT
*** * * * *
10888853 CATCCAATCTTTTACCTTAATCA-GAGGGCAAATTGAAGATATCGTCCAATCTCTTACCCAGATC
1 CATCCAATCTTTTACCCCGATCATG-GGGCAGATTGAAG----CATCCAAACTCTTACCCAG-TA
* * *
10888917 ATGGGGCAAATTGAAG-C--
60 ATAGGGTAGATTGAAGACAT
* * * *
10888934 CATCCAATCTTTTACCCCGATCATGGGGTAGATTAAAGACATCATCCAATCTCTTACGCC-GATC
1 CATCCAATCTTTTACCCCGATCATGGGGCAGATT---GA-AGCATCCAAACTCTTAC-CCAG-TA
* * *
10888998 ATGGGGCAAATTGAAGACA-
60 ATAGGGTAGATTGAAGACAT
* * * *
10889017 CA-CCAATCTTTTACCCCGATCATGGGGCAAATTGAAGACATCATCCAATCTTTTACTCC-GATC
1 CATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAG----CATCCAAACTCTTAC-CCAG-TA
* **
10889080 AT-GAGGCAGATTGCTG-C-T
60 ATAG-GGTAGATTGAAGACAT
* * * * * *
10889098 -GTCCAATCTCTTACCCCGATCATGGGGCAGAATGAAGACATCATCCAATCTCTTACCCCGATCA
1 CATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAG----CATCCAAACTCTTACCCAG-TAA
* *
10889162 TGGGGCAGATTGAAG-CAT
61 TAGGGTAGATTGAAGACAT
** * * * * * * *
10889180 --T-TGATCTTTTGCCCTGATCATGGGGTAGATTGAAGACATCATCCAATCTTTTACCCCGATCA
1 CATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAG----CATCCAAACTCTTACCCAG-TAA
*
10889242 TGGGGTAGATTGAAGACAT
61 TAGGGTAGATTGAAGACAT
* * * * * *
10889261 CATCCAATCTCTTACCCCGACCATGGGGTAGATTGAAGCATCCGATC-CTTTACCCTAATTAA-A
1 CATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAGCATCCAAACTC-TTACCC--AGTAATA
10889324 GGGTAGATTGAAGACA-
63 GGGTAGATTGAAGACAT
* * *
10889340 CA-CTAATCTTTTACCCCGATCATGGGGCAGATTGAAGCCATTCAAACTCTTACCCAGTAATGGG
1 CATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAG-CATCCAAACTCTTACCCAGTAATAGG
*
10889404 GTAGATTAAAGACAT
65 GTAGATTGAAGACAT
10889419 CATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAGC
1 CATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAGC
10889458 CACCATCCAA
Statistics
Matches: 636, Mismatches: 84, Indels: 90
0.79 0.10 0.11
Matches are distributed among these distances:
77 4 0.01
78 47 0.07
79 75 0.12
80 223 0.35
81 157 0.25
82 66 0.10
83 4 0.01
84 59 0.09
85 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (79 bp):
CATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAGCATCCAAACTCTTACCCAGTAATAGGG
TAGATTGAAGACAT
Found at i:10891163 original size:30 final size:29
Alignment explanation
Indices: 10891129--10891323 Score: 162
Period size: 30 Copynumber: 6.5 Consensus size: 29
10891119 ATTTTAACCA
*
10891129 CTAAACTATCCAAAAATTTTGATTTGACCC
1 CTAAACT-TCCAAAAATTTAGATTTGACCC
10891159 CTAAACTTTCCAAAAATTTTA-ATTTGACCC
1 CTAAAC-TTCCAAAAA-TTTAGATTTGACCC
* * * *
10891189 CCAAACTTCCTAAAAATTCAAATTTAACCC
1 CTAAACTTCC-AAAAATTTAGATTTGACCC
* * *
10891219 CTGAAGTTCCCAAAAATTTGGATTTGACTCC
1 CTAAACTT-CCAAAAATTTAGATTTGAC-CC
*
10891250 C-AAGCTTTCCAAAAATTTAGATTTGACCC
1 CTAAAC-TTCCAAAAATTTAGATTTGACCC
* * *
10891279 TTAAACTTCCCAAAAATTCAAATTTTG-CCC
1 CTAAACTT-CCAAAAATTTAGA-TTTGACCC
*
10891309 CCAAACTTTCCAAAA
1 CTAAAC-TTCCAAAA
10891324 TTTCATTTTT
Statistics
Matches: 133, Mismatches: 21, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
29 11 0.08
30 105 0.79
31 17 0.13
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (29 bp):
CTAAACTTCCAAAAATTTAGATTTGACCC
Found at i:10891195 original size:60 final size:60
Alignment explanation
Indices: 10891131--10891323 Score: 219
Period size: 60 Copynumber: 3.2 Consensus size: 60
10891121 TTTAACCACT
* * * *
10891131 AAACTATCCAAAAATTTTGATTTGACCCCTAAACTTTCCAAAAATTTTAATTTGACCCCC
1 AAACTTTCCAAAAATTTAGATTTGACCCCTAAACTTCCCAAAAATTTAAATTTGACCCCC
* * * * * ** *
10891191 AAAC-TTCCTAAAAATTCAAATTTAACCCCTGAAGTTCCCAAAAATTTGGATTTGACTCCC
1 AAACTTTCC-AAAAATTTAGATTTGACCCCTAAACTTCCCAAAAATTTAAATTTGACCCCC
* * *
10891251 AAGCTTTCCAAAAATTTAGATTTGACCCTTAAACTTCCCAAAAATTCAAATTTTG-CCCCC
1 AAACTTTCCAAAAATTTAGATTTGACCCCTAAACTTCCCAAAAATTTAAA-TTTGACCCCC
10891311 AAACTTTCCAAAA
1 AAACTTTCCAAAA
10891324 TTTCATTTTT
Statistics
Matches: 107, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
59 3 0.03
60 96 0.90
61 8 0.07
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.31
Consensus pattern (60 bp):
AAACTTTCCAAAAATTTAGATTTGACCCCTAAACTTCCCAAAAATTTAAATTTGACCCCC
Found at i:10891265 original size:90 final size:90
Alignment explanation
Indices: 10891138--10891303 Score: 255
Period size: 90 Copynumber: 1.8 Consensus size: 90
10891128 ACTAAACTAT
* *
10891138 CCAAAAATTTTGATTTGACCCCTAAACTTTCCAAAAATTTTA-ATTTGACCCCCAAACTTCCTAA
1 CCAAAAATTTGGATTTGACCCCTAAACTTTCCAAAAA-TTTAGATTTGACCCCCAAACTTCCCAA
10891202 AAATTCAAATTTAACCCCTGAAGTTC
65 AAATTCAAATTTAACCCCTGAAGTTC
* **
10891228 CCAAAAATTTGGATTTGACTCCC-AAGCTTTCCAAAAATTTAGATTTGACCCTTAAACTTCCCAA
1 CCAAAAATTTGGATTTGAC-CCCTAAACTTTCCAAAAATTTAGATTTGACCCCCAAACTTCCCAA
10891292 AAATTCAAATTT
65 AAATTCAAATTT
10891304 TGCCCCCAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
89 4 0.06
90 62 0.90
91 3 0.04
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.33
Consensus pattern (90 bp):
CCAAAAATTTGGATTTGACCCCTAAACTTTCCAAAAATTTAGATTTGACCCCCAAACTTCCCAAA
AATTCAAATTTAACCCCTGAAGTTC
Found at i:10891322 original size:90 final size:90
Alignment explanation
Indices: 10891121--10891323 Score: 248
Period size: 90 Copynumber: 2.3 Consensus size: 90
10891111 GAAATTACAT
* * * *
10891121 TTTAACCACTAAACTATCCAAAAATTTTGATTTGACCCCTAAACTTTCCAAAAATTTTAATTTGA
1 TTTAACCCCCAAACTTTCCAAAAATTTGGATTTGACCCCTAAACTTTCCAAAAATTTTAATTTGA
*
10891186 CCCCCAAACTTCCTAAAAATTCAAA
66 CCCCCAAACTTCCCAAAAATTCAAA
** * * *
10891211 TTTAACCCCTGAAGTTCCCAAAAATTTGGATTTGACTCCC-AAGCTTTCCAAAAA-TTTAGATTT
1 TTTAACCCCCAAACTTTCCAAAAATTTGGATTTGAC-CCCTAAACTTTCCAAAAATTTTA-ATTT
**
10891274 GACCCTTAAACTTCCCAAAAATTCAAA
64 GACCCCCAAACTTCCCAAAAATTCAAA
**
10891301 TTTTGCCCCCAAACTTTCCAAAA
1 TTTAACCCCCAAACTTTCCAAAA
10891324 TTTCATTTTT
Statistics
Matches: 95, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
89 4 0.04
90 88 0.93
91 3 0.03
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.32
Consensus pattern (90 bp):
TTTAACCCCCAAACTTTCCAAAAATTTGGATTTGACCCCTAAACTTTCCAAAAATTTTAATTTGA
CCCCCAAACTTCCCAAAAATTCAAA
Found at i:10900192 original size:12 final size:12
Alignment explanation
Indices: 10900175--10900205 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
10900165 CTTTGCCCAT
10900175 GCATGGAAACTA
1 GCATGGAAACTA
10900187 GCATGGAAACTA
1 GCATGGAAACTA
10900199 GCATGGA
1 GCATGGA
10900206 TGGTTTTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.39, C:0.16, G:0.29, T:0.16
Consensus pattern (12 bp):
GCATGGAAACTA
Found at i:10904458 original size:7 final size:7
Alignment explanation
Indices: 10904446--10904473 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
10904436 TCAACAAGAA
10904446 TTAATAT
1 TTAATAT
10904453 TTAATAT
1 TTAATAT
10904460 TTAATAT
1 TTAATAT
10904467 TTAATAT
1 TTAATAT
10904474 ATTATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TTAATAT
Found at i:10908314 original size:10 final size:10
Alignment explanation
Indices: 10908285--10908329 Score: 63
Period size: 10 Copynumber: 4.3 Consensus size: 10
10908275 TGGCAATATA
10908285 TTTCTTTCTT
1 TTTCTTTCTT
10908295 TTCTCTTTTCTT
1 TT-TC-TTTCTT
*
10908307 CTTCTTTCTT
1 TTTCTTTCTT
10908317 TTTCTTTCTT
1 TTTCTTTCTT
10908327 TTT
1 TTT
10908330 GTGATTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 20 0.65
11 4 0.13
12 7 0.23
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:10908316 original size:15 final size:16
Alignment explanation
Indices: 10908285--10908328 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
10908275 TGGCAATATA
10908285 TTTCTTTCTTTTCTCT
1 TTTCTTTCTTTTCTCT
10908301 TTTC-TTCTTCTT-TCTT
1 TTTCTTTCTT-TTCTC-T
10908317 TTTCTTTCTTTT
1 TTTCTTTCTTTT
10908329 TGTGATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 7 0.28
16 13 0.52
17 5 0.20
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTTTCTTTTCTCT
Found at i:10909454 original size:3 final size:3
Alignment explanation
Indices: 10909446--10909479 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
10909436 TTCTCATTTC
10909446 CTT CTT CTT -TCT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CT-T CTT CTT CTT CTT CTT CTT CTT C
10909480 CTAAGGCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.03
3 27 0.93
4 1 0.03
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:10909461 original size:12 final size:12
Alignment explanation
Indices: 10909442--10909478 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
10909432 CTCCTTCTCA
10909442 TTTC-CTTCTTC
1 TTTCTCTTCTTC
10909453 TTTCTCTTCTTC
1 TTTCTCTTCTTC
10909465 -TTCTTCTTCTTC
1 TTTC-TCTTCTTC
10909477 TT
1 TT
10909479 CCTAAGGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 7 0.30
12 15 0.65
13 1 0.04
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTCTCTTCTTC
Found at i:10924465 original size:13 final size:13
Alignment explanation
Indices: 10924429--10924477 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
10924419 CTCAAGCTCC
10924429 TTTGTTTTTCTTGT
1 TTTG-TTTTCTTGT
10924443 TTTG--TT-TTGT
1 TTTGTTTTCTTGT
10924453 TTTGTTTTCTTGT
1 TTTGTTTTCTTGT
* *
10924466 TGTGTTTGCTTG
1 TTTGTTTTCTTG
10924478 AGGACAAGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
10 8 0.27
11 2 0.07
12 2 0.07
13 14 0.47
14 4 0.13
ACGTcount: A:0.00, C:0.06, G:0.20, T:0.73
Consensus pattern (13 bp):
TTTGTTTTCTTGT
Found at i:10926686 original size:37 final size:35
Alignment explanation
Indices: 10926636--10926710 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 35
10926626 AAGTGTAGCC
*
10926636 ATTTGTCCCACAATTTTATGGATTTATTTGACTAA
1 ATTTGTCCCACAATTTTAGGGATTTATTTGACTAA
* *
10926671 ATTTGTCTTCCACAATTTTAGGGATTTTTTTGGCTAA
1 ATTTGTC--CCACAATTTTAGGGATTTATTTGACTAA
10926708 ATT
1 ATT
10926711 GTAGGCATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
35 7 0.20
37 28 0.80
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.48
Consensus pattern (35 bp):
ATTTGTCCCACAATTTTAGGGATTTATTTGACTAA
Found at i:10926697 original size:23 final size:23
Alignment explanation
Indices: 10926671--10926745 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
10926661 ATTTGACTAA
*
10926671 ATTTGTCTTCCACAATTTTAGGG
1 ATTTGTCTTCAACAATTTTAGGG
* * * *
10926694 ATTT-TTTTGGCTA-AATTGTAGGC
1 ATTTGTCTT--CAACAATTTTAGGG
*
10926717 ATTTATCTTCAACAATTTTAGGG
1 ATTTGTCTTCAACAATTTTAGGG
10926740 ATTTGT
1 ATTTGT
10926746 TTCTCTTTTA
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
22 5 0.13
23 29 0.74
24 5 0.13
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (23 bp):
ATTTGTCTTCAACAATTTTAGGG
Found at i:10927000 original size:12 final size:12
Alignment explanation
Indices: 10926983--10927011 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
10926973 TTGAAGGGAG
10926983 TTGTTGGATCTC
1 TTGTTGGATCTC
10926995 TTGTTGGATCTC
1 TTGTTGGATCTC
10927007 TTGTT
1 TTGTT
10927012 CCAAAGGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.14, G:0.24, T:0.55
Consensus pattern (12 bp):
TTGTTGGATCTC
Found at i:10936971 original size:17 final size:17
Alignment explanation
Indices: 10936949--10936986 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
10936939 AGTTTTCATA
*
10936949 CATTTTTATTGT-GCCTG
1 CATTTTAATTGTCG-CTG
10936966 CATTTTAATTGTCGCTG
1 CATTTTAATTGTCGCTG
10936983 CATT
1 CATT
10936987 CATTTTAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.16, C:0.18, G:0.16, T:0.50
Consensus pattern (17 bp):
CATTTTAATTGTCGCTG
Found at i:10937601 original size:6 final size:6
Alignment explanation
Indices: 10937570--10937609 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
10937560 TCAGTCACTT
* *
10937570 GAAAAA GTATAA GAAAAA GAAGAAA GAAAAA GAAAAA GAA
1 GAAAAA GAAAAA GAAAAA GAA-AAA GAAAAA GAAAAA GAA
10937610 TTGCTGAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (6 bp):
GAAAAA
Found at i:10954729 original size:18 final size:18
Alignment explanation
Indices: 10954695--10954730 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
10954685 TAATCAGTGT
*
10954695 CTTCTTTCTGTGAGTAGC
1 CTTCTTTCTATGAGTAGC
*
10954713 CTTCTTTCTATGTGTAGC
1 CTTCTTTCTATGAGTAGC
10954731 ATTTCCCTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.22, G:0.19, T:0.47
Consensus pattern (18 bp):
CTTCTTTCTATGAGTAGC
Found at i:10958500 original size:11 final size:11
Alignment explanation
Indices: 10958486--10958561 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
10958476 TATAATCTTT
10958486 TTAATATTAAA
1 TTAATATTAAA
10958497 TTAATA--AAA
1 TTAATATTAAA
*
10958506 -TACTATTAAA
1 TTAATATTAAA
*
10958516 ATAAGTATTAAA
1 TTAA-TATTAAA
10958528 TTTAAT-TTAATA
1 -TTAATATTAA-A
10958540 TTAAATTATTAAA
1 TT-AA-TATTAAA
*
10958553 ATAATATTA
1 TTAATATTA
10958562 TTTTGGAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 3 0.06
11 19 0.37
12 13 0.25
13 6 0.12
14 4 0.08
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:10958538 original size:37 final size:35
Alignment explanation
Indices: 10958492--10958561 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 35
10958482 CTTTTTAATA
10958492 TTAAATTAATA-AAATACTATTAAAATAAGTATTAAAT
1 TTAAATTAATATAAAT--TATTAAAATAA-TATTAAAT
*
10958529 TTAATTTAATATTAAATTATTAAAATAATATTA
1 TTAAATTAATA-TAAATTATTAAAATAATATTA
10958562 TTTTGGAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
36 5 0.17
37 21 0.70
39 4 0.13
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (35 bp):
TTAAATTAATATAAATTATTAAAATAATATTAAAT
Found at i:10961297 original size:150 final size:149
Alignment explanation
Indices: 10961020--10961314 Score: 439
Period size: 150 Copynumber: 2.0 Consensus size: 149
10961010 TCAGGATTTT
* *
10961020 CAGGTTACATGGGTGCTGGTCTTAGATGTCCTATTGATGGCTGAGATCCAGCATTTATTGTGGAA
1 CAGGTTACATGGGTGCTGGTCTTAGATGTCCTACTGATGGCTGAGATCCAGCATTTATTATGGAA
* * * *
10961085 TCTCCATAACTCATGTGAGTAGCATCGTGTAGCCTAACATCTCAACCTACAGCTCATTTGAGCAG
66 TCTCCACAACTCATGTGAGCAGCATCGTGTAGCCTAACATCTCAACCCACAGCTCATGTGAGCAG
*
10961150 GCCCACTTCACAGCTTGTA
131 ACCCACTTCACAGCTTGTA
* *
10961169 CAGGTTACATGGGTGCTGGTCTTAGATGTGCTACTGATGGCTGAGATCCGGGCATTTATTAT-GA
1 CAGGTTACATGGGTGCTGGTCTTAGATGTCCTACTGATGGCTGAGATCC-AGCATTTATTATGGA
* * * *
10961233 ATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCCTAACATCTCGACCCACAGCTCGTGTGAGC
65 A-TCTCCACAACTCATGTGAGCAGCATCGTGTAGCCTAACATCTCAACCCACAGCTCATGTGAGC
*
10961298 AGACCCATTTCACAGCT
129 AGACCCACTTCACAGCT
10961315 CATGTGAGCA
Statistics
Matches: 130, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
149 50 0.38
150 80 0.62
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (149 bp):
CAGGTTACATGGGTGCTGGTCTTAGATGTCCTACTGATGGCTGAGATCCAGCATTTATTATGGAA
TCTCCACAACTCATGTGAGCAGCATCGTGTAGCCTAACATCTCAACCCACAGCTCATGTGAGCAG
ACCCACTTCACAGCTTGTA
Found at i:10963288 original size:24 final size:26
Alignment explanation
Indices: 10963256--10963305 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
10963246 AAGTTGTAAA
10963256 TAAAAAATCTCTT-AGAG-ATTTTCT
1 TAAAAAATCTCTTCAGAGAATTTTCT
*
10963280 TAAATAATCTCTTCAGAGAATTTTCT
1 TAAAAAATCTCTTCAGAGAATTTTCT
10963306 CTCTACAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.52
25 4 0.17
26 7 0.30
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (26 bp):
TAAAAAATCTCTTCAGAGAATTTTCT
Found at i:10963609 original size:31 final size:32
Alignment explanation
Indices: 10963510--10963610 Score: 84
Period size: 31 Copynumber: 3.2 Consensus size: 32
10963500 TATCTACAAG
10963510 ATAAACATTAAATTAAATTTAATATTAAGA-TA
1 ATAAA-ATTAAATTAAATTTAATATTAAGACTA
** ** * *
10963542 ACCATTTTAATATTAAA-TTAATA-AAATACTA
1 ATAAAATTAA-ATTAAATTTAATATTAAGACTA
*
10963573 CTAAAATTAAATTAAATTTAATATTAA-ACTA
1 ATAAAATTAAATTAAATTTAATATTAAGACTA
*
10963604 TTAAAAT
1 ATAAAAT
10963611 AATATTATTT
Statistics
Matches: 52, Mismatches: 13, Indels: 9
0.70 0.18 0.12
Matches are distributed among these distances:
30 9 0.17
31 33 0.63
32 10 0.19
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (32 bp):
ATAAAATTAAATTAAATTTAATATTAAGACTA
Found at i:10963720 original size:9 final size:9
Alignment explanation
Indices: 10963700--10963730 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
10963690 AAAATATCAT
10963700 ATTAATTTTA
1 ATTAA-TTTA
10963710 ATTAATTTA
1 ATTAATTTA
10963719 ATTAATTTA
1 ATTAATTTA
10963728 ATT
1 ATT
10963731 TTACTTGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.76
10 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
ATTAATTTA
Found at i:10970513 original size:22 final size:22
Alignment explanation
Indices: 10970465--10970513 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
10970455 TAAGTAGTCA
*
10970465 AAAAATATATAAATTAATAATT
1 AAAAATATATAAATTAATAAAT
* *
10970487 CAAAATATATAAA-TACTCAAAT
1 AAAAATATATAAATTAAT-AAAT
10970509 AAAAA
1 AAAAA
10970514 GTTAAAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAATATATAAATTAATAAAT
Found at i:10977967 original size:35 final size:36
Alignment explanation
Indices: 10977923--10977999 Score: 129
Period size: 36 Copynumber: 2.2 Consensus size: 36
10977913 TTGTGTGACC
*
10977923 CAAATTCTAAGAG-ATTGCTTGCAAGTCAAGTTAAA
1 CAAAATCTAAGAGAATTGCTTGCAAGTCAAGTTAAA
*
10977958 TAAAATCTAAGAGAATTGCTTGCAAGTCAAGTTAAA
1 CAAAATCTAAGAGAATTGCTTGCAAGTCAAGTTAAA
10977994 CAAAAT
1 CAAAAT
10978000 ATATTATCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
35 11 0.29
36 27 0.71
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (36 bp):
CAAAATCTAAGAGAATTGCTTGCAAGTCAAGTTAAA
Found at i:10979297 original size:24 final size:24
Alignment explanation
Indices: 10979203--10979303 Score: 114
Period size: 24 Copynumber: 4.2 Consensus size: 24
10979193 ACTGAGTCTT
*
10979203 CCAGA-AATTTAGCTCATACGAGC
1 CCAGATAAGTTAGCTCATACGAGC
* *
10979226 CCAGACAAAATTAGCTCATACGAGC
1 CCAGA-TAAGTTAGCTCATACGAGC
* * *
10979251 CCAGATAGGTTAGGTCTTACGAGC
1 CCAGATAAGTTAGCTCATACGAGC
*
10979275 CCAGATAAGTTAGCTCATTCGAGC
1 CCAGATAAGTTAGCTCATACGAGC
*
10979299 TCAGA
1 CCAGA
10979304 CAGAGTTTAA
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
23 5 0.08
24 38 0.58
25 22 0.34
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.22
Consensus pattern (24 bp):
CCAGATAAGTTAGCTCATACGAGC
Found at i:10980956 original size:54 final size:56
Alignment explanation
Indices: 10980848--10980960 Score: 158
Period size: 56 Copynumber: 2.1 Consensus size: 56
10980838 CTCTCTTTCC
* *
10980848 CTCTAATTATTTTTTCAAATTTTATCAAACTTTCTTTCTTTCCAAACACCTATTTT
1 CTCTAATTATTTTTCCAAATTTTATCAAACTTTCTATCTTTCCAAACACCTATTTT
* * * *
10980904 CTCTCATTATTTTTCCAGATTTTTTCAGAC-TT-TATCTTTCCAAACACCTATTTT
1 CTCTAATTATTTTTCCAAATTTTATCAAACTTTCTATCTTTCCAAACACCTATTTT
10980958 CTC
1 CTC
10980961 ATTTTTATAG
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 24 0.47
55 2 0.04
56 25 0.49
ACGTcount: A:0.24, C:0.24, G:0.02, T:0.50
Consensus pattern (56 bp):
CTCTAATTATTTTTCCAAATTTTATCAAACTTTCTATCTTTCCAAACACCTATTTT
Found at i:10982196 original size:55 final size:56
Alignment explanation
Indices: 10982024--10982199 Score: 259
Period size: 56 Copynumber: 3.2 Consensus size: 56
10982014 CAAAAAGAAA
*
10982024 GAAAAA-AATGAGAGAAAATGGGTGTTTGGAAAGAGAGAAAATTTGAGAAAATCTG
1 GAAAAATAATGAGAGAAAATGGGTGTTTGGAAAGAGAGAAAGTTTGAGAAAATCTG
10982079 GAAAAATAATGAGAGAAAATGGGTGTTTGGAAAGAGAGAAAGTTTGAGGAAAA-CTG
1 GAAAAATAATGAGAGAAAATGGGTGTTTGGAAAGAGAGAAAGTTTGA-GAAAATCTG
* * * * *
10982135 GAAAAATAATGAGAGAAAGT-GGTGTTTTGAAAAAGAGAAAGTATGAGAAAATTTG
1 GAAAAATAATGAGAGAAAATGGGTGTTTGGAAAGAGAGAAAGTTTGAGAAAATCTG
*
10982190 GGAAAATAAT
1 GAAAAATAAT
10982200 TAGAAGGGAA
Statistics
Matches: 111, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
54 5 0.05
55 40 0.36
56 61 0.55
57 5 0.05
ACGTcount: A:0.49, C:0.01, G:0.29, T:0.21
Consensus pattern (56 bp):
GAAAAATAATGAGAGAAAATGGGTGTTTGGAAAGAGAGAAAGTTTGAGAAAATCTG
Found at i:10982518 original size:18 final size:18
Alignment explanation
Indices: 10982495--10982531 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
10982485 TAAGTAAATA
*
10982495 TTTACAAGTATGCCTTTT
1 TTTACAAGTATGACTTTT
*
10982513 TTTACAATTATGACTTTT
1 TTTACAAGTATGACTTTT
10982531 T
1 T
10982532 AACCATGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.14, G:0.08, T:0.54
Consensus pattern (18 bp):
TTTACAAGTATGACTTTT
Found at i:10987274 original size:24 final size:24
Alignment explanation
Indices: 10987237--10987293 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
10987227 TTTCTAGAAG
* * *
10987237 ATTTAGTAGTATAATATATTTAGC
1 ATTTATTAGCATAATACATTTAGC
*
10987261 ATTTATTAGCATAATACATTTTGC
1 ATTTATTAGCATAATACATTTAGC
*
10987285 ATTGATTAG
1 ATTTATTAG
10987294 AATTAGGCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (24 bp):
ATTTATTAGCATAATACATTTAGC
Found at i:10993996 original size:34 final size:34
Alignment explanation
Indices: 10993933--10993998 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
10993923 GTGATATATG
* * *
10993933 AAAATGCAATGACAATGTATATGTAGTGACAAGA
1 AAAATGCAATGACAAAGGAAATGTAGTGACAAGA
*
10993967 AAAATGCAATGACAAAGGAAATGTGGTGACAA
1 AAAATGCAATGACAAAGGAAATGTAGTGACAA
10993999 TTACATTACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.48, C:0.09, G:0.23, T:0.20
Consensus pattern (34 bp):
AAAATGCAATGACAAAGGAAATGTAGTGACAAGA
Found at i:11027392 original size:60 final size:60
Alignment explanation
Indices: 11027328--11027462 Score: 270
Period size: 60 Copynumber: 2.2 Consensus size: 60
11027318 AGATTTGAAA
11027328 TCTTGATTTTCTTGATTCTTAAAATTGTTTAGAATGGAAAAATTGGACCAAGATTCGATT
1 TCTTGATTTTCTTGATTCTTAAAATTGTTTAGAATGGAAAAATTGGACCAAGATTCGATT
11027388 TCTTGATTTTCTTGATTCTTAAAATTGTTTAGAATGGAAAAATTGGACCAAGATTCGATT
1 TCTTGATTTTCTTGATTCTTAAAATTGTTTAGAATGGAAAAATTGGACCAAGATTCGATT
11027448 TCTTGATTTTCTTGA
1 TCTTGATTTTCTTGA
11027463 AAATAAGAAA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 75 1.00
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.44
Consensus pattern (60 bp):
TCTTGATTTTCTTGATTCTTAAAATTGTTTAGAATGGAAAAATTGGACCAAGATTCGATT
Found at i:11033925 original size:24 final size:26
Alignment explanation
Indices: 11033892--11033939 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
11033882 ATCCTTGAAG
11033892 TAATCAGAGTTCAACTA-GAAAAAGA
1 TAATCAGAGTTCAACTAGGAAAAAGA
*
11033917 TAAT-AGAGTTTAACTAGGAAAAA
1 TAATCAGAGTTCAACTAGGAAAAA
11033940 AACTCGATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.52, C:0.08, G:0.17, T:0.23
Consensus pattern (26 bp):
TAATCAGAGTTCAACTAGGAAAAAGA
Found at i:11035314 original size:11 final size:10
Alignment explanation
Indices: 11035288--11035334 Score: 60
Period size: 10 Copynumber: 4.6 Consensus size: 10
11035278 TTTTTTATTT
11035288 ATAAAAAATC
1 ATAAAAAATC
11035298 ATAAAAAATC
1 ATAAAAAATC
*
11035308 ATAAAAAATT
1 ATAAAAAATC
11035318 ATTTAAAAAATC
1 A--TAAAAAATC
11035330 -TAAAA
1 ATAAAA
11035335 TTTTCGAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
9 5 0.15
10 20 0.61
12 8 0.24
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (10 bp):
ATAAAAAATC
Found at i:11035423 original size:11 final size:11
Alignment explanation
Indices: 11035409--11035433 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11035399 TTAAAAAGCA
11035409 TAAAATAATTC
1 TAAAATAATTC
11035420 TAAAATAATTC
1 TAAAATAATTC
11035431 TAA
1 TAA
11035434 TTTTCTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (11 bp):
TAAAATAATTC
Found at i:11035491 original size:9 final size:9
Alignment explanation
Indices: 11035456--11035519 Score: 53
Period size: 9 Copynumber: 7.0 Consensus size: 9
11035446 TTTTATAATT
11035456 TATTTTTAAA
1 TATTTTT-AA
*
11035466 TGATTTTCTAT
1 T-ATTTT-TAA
11035477 TATTTTTAA
1 TATTTTTAA
11035486 TA-TTTTAA
1 TATTTTTAA
*
11035494 TATTTTTCA
1 TATTTTTAA
11035503 T-TTTTT-A
1 TATTTTTAA
11035510 TAATTTTTAA
1 T-ATTTTTAA
11035520 AAATTCTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
7 2 0.04
8 13 0.29
9 15 0.33
10 7 0.16
11 7 0.16
12 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.66
Consensus pattern (9 bp):
TATTTTTAA
Found at i:11035497 original size:20 final size:22
Alignment explanation
Indices: 11035451--11035497 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
11035441 ATAATTTTTA
11035451 TAAT-TTATTTTTAAATGATTT
1 TAATATTATTTTTAAATGATTT
*
11035472 T-CTATTATTTTT-AAT-ATTT
1 TAATATTATTTTTAAATGATTT
11035491 TAATATT
1 TAATATT
11035498 TTTCATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
19 5 0.23
20 8 0.36
21 9 0.41
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
TAATATTATTTTTAAATGATTT
Found at i:11035499 original size:17 final size:16
Alignment explanation
Indices: 11035477--11035519 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
11035467 GATTTTCTAT
11035477 TATTTTTAATATTTTAA
1 TATTTTTAAT-TTTTAA
* *
11035494 TATTTTTCATTTTTTA
1 TATTTTTAATTTTTAA
11035510 TAATTTTTAA
1 T-ATTTTTAA
11035520 AAATTCTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTTTAATTTTTAA
Found at i:11038969 original size:20 final size:21
Alignment explanation
Indices: 11038929--11038977 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
11038919 ATGTGCATTC
*
11038929 TTTTTCCTTCACTAGGAAAAT
1 TTTTTCCCTCACTAGGAAAAT
11038950 TTTTTCCCTCACTAGG-AAAT
1 TTTTTCCCTCACTAGGAAAAT
11038970 TTTTTCCC
1 TTTTTCCC
11038978 CACAGGGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.22, C:0.24, G:0.08, T:0.45
Consensus pattern (21 bp):
TTTTTCCCTCACTAGGAAAAT
Found at i:11039330 original size:27 final size:27
Alignment explanation
Indices: 11039288--11039339 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
11039278 AGCATTTTTA
11039288 AATTTTTTAAAATTTTT-TATAAATTCT
1 AATTTTTTAAAATTTTTCTA-AAATTCT
**
11039315 AATTTTTTAATTTTTTTCTAAAATT
1 AATTTTTTAAAATTTTTCTAAAATT
11039340 TTAAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (27 bp):
AATTTTTTAAAATTTTTCTAAAATTCT
Found at i:11040295 original size:13 final size:14
Alignment explanation
Indices: 11040260--11040297 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
11040250 TTTATAACAT
* *
11040260 TATTTTATTTTTCT
1 TATTTTAATTTTCC
11040274 TATTTTAATTTTCC
1 TATTTTAATTTTCC
11040288 TA-TTTAATTT
1 TATTTTAATTT
11040298 GTGTAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTTTAATTTTCC
Found at i:11041443 original size:16 final size:17
Alignment explanation
Indices: 11041401--11041445 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
11041391 AGTAATAATG
11041401 TCAATAAATATTAATTAA
1 TCAATAAATA-TAATTAA
*
11041419 TTAAT-AATATAATTAA
1 TCAATAAATATAATTAA
11041435 -CAATAAATATA
1 TCAATAAATATA
11041446 TAAAATACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 3 0.12
16 13 0.54
17 4 0.17
18 4 0.17
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (17 bp):
TCAATAAATATAATTAA
Found at i:11041610 original size:18 final size:17
Alignment explanation
Indices: 11041589--11041774 Score: 84
Period size: 18 Copynumber: 10.7 Consensus size: 17
11041579 AAATGTAGGC
11041589 AAAAATATAAATAACATA
1 AAAAATATAAATAA-ATA
*
11041607 AAAAATAACAAATAAATA
1 AAAAAT-ATAAATAAATA
* *
11041625 AAATACATAAA-ACAATA
1 AAAAATATAAATA-AATA
*
11041642 AATAAA-ATTAAATAAAAGA
1 AA-AAATA-TAAAT-AAATA
*
11041661 AAAAATGTAAAT-AATA
1 AAAAATATAAATAAATA
* *
11041677 AAGAAA-ATGAAT-AACA
1 AA-AAATATAAATAAATA
*
11041693 AATAA-AT-AATAAATA
1 AAAAATATAAATAAATA
11041708 AATAAATA-ATAATAAATA
1 AA-AAATATA-AATAAATA
*
11041726 AAAATTA-AATACTAAATA
1 AAAAATATAA-A-TAAATA
* **
11041744 AAATCATGCAAATAATATA
1 AAA-AATATAAATAA-ATA
11041763 AAAAATATAAAT
1 AAAAATATAAAT
11041775 GAGACCAAAT
Statistics
Matches: 129, Mismatches: 21, Indels: 36
0.69 0.11 0.19
Matches are distributed among these distances:
14 3 0.02
15 9 0.07
16 18 0.14
17 21 0.16
18 55 0.43
19 20 0.16
20 3 0.02
ACGTcount: A:0.70, C:0.04, G:0.03, T:0.23
Consensus pattern (17 bp):
AAAAATATAAATAAATA
Found at i:11041625 original size:4 final size:4
Alignment explanation
Indices: 11041595--11041745 Score: 72
Period size: 4 Copynumber: 38.2 Consensus size: 4
11041585 AGGCAAAAAT
* *
11041595 ATAA ATAA CATAA A-AA AT-A ACAA ATAA ATAAA ATAC ATAA A-ACA ATAA
1 ATAA ATAA -ATAA ATAA ATAA ATAA ATAA AT-AA ATAA ATAA ATA-A ATAA
* * *
11041643 ATAAA ATTAA ATAA A-AGA AAAA ATGTAA AT-A ATAA AGAAA ATGA AT-A
1 AT-AA A-TAA ATAA ATA-A ATAA A--TAA ATAA ATAA A-TAA ATAA ATAA
* *
11041690 ACAA ATAA AT-A ATAA ATAA ATAA AT-A AT-A ATAA ATAA A-AA TTAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
*
11041734 AT-A CTAA ATAA A
1 ATAA ATAA ATAA A
11041746 ATCATGCAAA
Statistics
Matches: 114, Mismatches: 14, Indels: 38
0.69 0.08 0.23
Matches are distributed among these distances:
3 25 0.22
4 66 0.58
5 19 0.17
6 4 0.04
ACGTcount: A:0.72, C:0.04, G:0.03, T:0.22
Consensus pattern (4 bp):
ATAA
Found at i:11041634 original size:9 final size:9
Alignment explanation
Indices: 11041616--11041728 Score: 67
Period size: 10 Copynumber: 12.3 Consensus size: 9
11041606 AAAAAATAAC
11041616 AAATAAATA
1 AAATAAATA
*
11041625 AAATACATAAA
1 AAATA-A-ATA
11041636 ACAATAAATA
1 A-AATAAATA
11041646 AAATTAAATA
1 AAA-TAAATA
*
11041656 AAAGAAA-A
1 AAATAAATA
*
11041664 AATGTAAAT-
1 AA-ATAAATA
*
11041673 -AATAAAGA
1 AAATAAATA
*
11041681 AAATGAATAA
1 AAATAAAT-A
11041691 CAAATAAAT-
1 -AAATAAATA
11041700 -AATAAAT-
1 AAATAAATA
11041707 AAATAAATA
1 AAATAAATA
11041716 ATAATAAATA
1 A-AATAAATA
11041726 AAA
1 AAA
11041729 ATTAAATACT
Statistics
Matches: 81, Mismatches: 10, Indels: 26
0.69 0.09 0.22
Matches are distributed among these distances:
7 11 0.14
8 11 0.14
9 21 0.26
10 23 0.28
11 11 0.14
12 4 0.05
ACGTcount: A:0.73, C:0.03, G:0.04, T:0.21
Consensus pattern (9 bp):
AAATAAATA
Found at i:11041644 original size:44 final size:44
Alignment explanation
Indices: 11041595--11041719 Score: 116
Period size: 44 Copynumber: 2.9 Consensus size: 44
11041585 AGGCAAAAAT
*
11041595 ATAAATAACATAAAAAATAACAAATAAATAAAATACATAAA-ACA
1 ATAAATAACATAAAAAATAACAAATAAATAAAATA-ATAAAGAAA
* * * *
11041639 ATAAATAAAATTAAATAA-AAGAAA-AAATGTAAATAATAAAGAAA
1 ATAAATAACA-TAAAAAATAACAAATAAAT-AAAATAATAAAGAAA
* * *
11041683 ATGAATAACA-AATAAATAATAAATAAAT-AAATAATAA
1 ATAAATAACATAAAAAATAACAAATAAATAAAATAATAA
11041720 TAAATAAAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
42 13 0.20
43 14 0.21
44 33 0.50
45 6 0.09
ACGTcount: A:0.72, C:0.04, G:0.03, T:0.21
Consensus pattern (44 bp):
ATAAATAACATAAAAAATAACAAATAAATAAAATAATAAAGAAA
Found at i:11041666 original size:22 final size:21
Alignment explanation
Indices: 11041597--11041728 Score: 70
Period size: 22 Copynumber: 5.8 Consensus size: 21
11041587 GCAAAAATAT
* *
11041597 AAATAACATAAAAAATAACAAA
1 AAATAAAATAAATAA-AACAAA
* *
11041619 TAAATAAAATACATAAAACAAT
1 -AAATAAAATAAATAAAACAAA
*
11041641 AAATAAAATTAAATAAAAGAAA
1 AAATAAAA-TAAATAAAACAAA
*
11041663 AAATGTAAAT-AATAAAGA-AAA
1 AAAT-AAAATAAATAAA-ACAAA
* *
11041684 TGAATAACAAATAAATAATAAATAAA
1 -AAAT-A-AAATAAAT-A-AAACAAA
11041710 TAAATAATAATAAATAAAA
1 -AAATAA-AATAAATAAAA
11041729 ATTAAATACT
Statistics
Matches: 87, Mismatches: 12, Indels: 20
0.73 0.10 0.17
Matches are distributed among these distances:
21 17 0.20
22 24 0.28
23 22 0.25
24 5 0.06
25 10 0.11
26 9 0.10
ACGTcount: A:0.73, C:0.04, G:0.03, T:0.20
Consensus pattern (21 bp):
AAATAAAATAAATAAAACAAA
Found at i:11042424 original size:97 final size:97
Alignment explanation
Indices: 11042068--11042448 Score: 293
Period size: 97 Copynumber: 3.8 Consensus size: 97
11042058 CCTTGTGACT
*** * * *
11042068 TCAAGGATATAGGATTTGGGCTTGTAATTTCACTTCATTCCATTGAAACTTCAGTGGAGATTGAG
1 TCAAGGATATAGGATTTGGG---GTGGCTTCACTCCATTCCACTGCAACTTCAGTGGAGATTGAG
* * * * * * **
11042133 GTCCGCTACTGTGAGTTTTAATTCGCCTCTCTAC-ATT
63 ATCTGCTACT-T--GTTTTACTCCACCCCTCTACAACC
* * * * * *
11042170 TTAAGGGTATAGGATTTGGTGTGGCTTCACTCCATTCCACTACAACTTCAGTGGAAATTGAGATA
1 TCAAGGATATAGGATTTGGGGTGGCTTCACTCCATTCCACTGCAACTTCAGTGGAGATTGAGATC
* * * *
11042235 TACTACTTGTTCTACTCCACCCCTCTATAATC
66 TGCTACTTGTTTTACTCCACCCCTCTACAACC
* * * ** ** * *
11042267 TTAAGGGTATATGAGCTGGTGTTGTAACTTCACTTCATTCCA-TCGTAACTTCAGTGGAGATTGA
1 TCAAGGATATAGGATTTGG-G--GTGGCTTCACTCCATTCCACT-GCAACTTCAGTGGAGATTGA
*
11042331 GATCTGCTACTTGTTTTACTCCGA-TCCT-TACAACC
62 GATCTGCTACTTGTTTTACTCC-ACCCCTCTACAACC
* * *
11042366 TCAATGATATAGGATTTGGAGGTGGCTTCACTCCATTCCACTGCAACTTCCGAGGAGATTGAGAT
1 TCAAGGATATAGGATTTGG-GGTGGCTTCACTCCATTCCACTGCAACTTCAGTGGAGATTGAGAT
11042431 CTGCTACTTGTTTTACTC
65 CTGCTACTTGTTTTACTC
11042449 TCCGCCCTTA
Statistics
Matches: 221, Mismatches: 51, Indels: 19
0.76 0.18 0.07
Matches are distributed among these distances:
96 14 0.06
97 72 0.33
98 2 0.01
99 60 0.27
100 55 0.25
101 1 0.00
102 17 0.08
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.35
Consensus pattern (97 bp):
TCAAGGATATAGGATTTGGGGTGGCTTCACTCCATTCCACTGCAACTTCAGTGGAGATTGAGATC
TGCTACTTGTTTTACTCCACCCCTCTACAACC
Found at i:11042476 original size:199 final size:198
Alignment explanation
Indices: 11042089--11042448 Score: 467
Period size: 197 Copynumber: 1.8 Consensus size: 198
11042079 GGATTTGGGC
* * *
11042089 TTGTAATTTCACTTCATTCCATTGAAACTTCAGTGGAGATTGAGGTCCGCTACTGTGAGTTTTAA
1 TTGTAACTTCACTTCATTCCATCGAAACTTCAGTGGAGATTGAGATCCGCTACTGT-AGTTTTAA
* ** * * *
11042154 TTCGCCTCTCTACATTTTAAGGGTATAGGATTTGGTGTGGCTTCACTCCATTCCACTACAACTTC
65 TCCGCCTCTCTACACCTCAAGGATATAGGATTTGGGGTGGCTTCACTCCATTCCACTACAACTTC
*
11042219 AGTGGAAATTGAGATATACTACTTGTTCTACTCCACCCCTCTATAATCTTAAGGGTATATGAGCT
130 AGAGGAAATTGAGATATACTACTTGTTCTACTCCACCCCTCTATAATCTTAAGGGTATATGAGCT
11042284 GGTG
195 GGTG
* * *
11042288 TTGTAACTTCACTTCATTCCATCGTAACTTCAGTGGAGATTGAGATCTGCTACT-T-GTTTTACT
1 TTGTAACTTCACTTCATTCCATCGAAACTTCAGTGGAGATTGAGATCCGCTACTGTAGTTTTAAT
* * *
11042351 CCG-ATC-CTTACAACCTCAATGATATAGGATTTGGAGGTGGCTTCACTCCATTCCACTGCAACT
66 CCGCCTCTC-TAC-ACCTCAAGGATATAGGATTTGG-GGTGGCTTCACTCCATTCCACTACAACT
* * * * *
11042414 TCCGAGGAGATTGAGATCTGCTACTTGTTTTACTC
128 TCAGAGGAAATTGAGATATACTACTTGTTCTACTC
11042449 TCCGCCCTTA
Statistics
Matches: 137, Mismatches: 21, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
194 1 0.01
195 5 0.04
196 26 0.19
197 55 0.40
198 1 0.01
199 49 0.36
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.36
Consensus pattern (198 bp):
TTGTAACTTCACTTCATTCCATCGAAACTTCAGTGGAGATTGAGATCCGCTACTGTAGTTTTAAT
CCGCCTCTCTACACCTCAAGGATATAGGATTTGGGGTGGCTTCACTCCATTCCACTACAACTTCA
GAGGAAATTGAGATATACTACTTGTTCTACTCCACCCCTCTATAATCTTAAGGGTATATGAGCTG
GTG
Found at i:11044051 original size:26 final size:26
Alignment explanation
Indices: 11044012--11044368 Score: 196
Period size: 26 Copynumber: 14.2 Consensus size: 26
11044002 TTAAATTAAA
* *
11044012 TAAACGCGTAATTAAGCTAGA-GAGCG
1 TAAACGCATGATTAAGCT-GACGAGCG
11044038 TAAACGCATGATTAAGCTGACGAGCG
1 TAAACGCATGATTAAGCTGACGAGCG
* * *
11044064 TAAACG--TG-TGCAAGTTGGCGAGCG
1 TAAACGCATGAT-TAAGCTGACGAGCG
** *
11044088 CGAATGCATGATTAAGCTGACGAGCG
1 TAAACGCATGATTAAGCTGACGAGCG
* *
11044114 TAAACG--TG-TGCAAGCTGACGAGTG
1 TAAACGCATGAT-TAAGCTGACGAGCG
* *
11044138 TAAACGCATGATTAAGTTGACGACCG
1 TAAACGCATGATTAAGCTGACGAGCG
* * *
11044164 TAAA--CATG-TGCAAGTTGGCGAGCG
1 TAAACGCATGAT-TAAGCTGACGAGCG
*
11044188 TAAACGCATGATTAAGTTGACGAGCG
1 TAAACGCATGATTAAGCTGACGAGCG
* *
11044214 TAAACG--TG-TCCAAGCTGCCGAGCG
1 TAAACGCATGAT-TAAGCTGACGAGCG
* * * *
11044238 TAAACACATAATTAAGCTAACAAGCG
1 TAAACGCATGATTAAGCTGACGAGCG
* * * *
11044264 TAAA--CTTG-TGCAAGTTGGCGAGCG
1 TAAACGCATGAT-TAAGCTGACGAGCG
* ** *
11044288 CAAACG-ATGATTAAGCTGGTGAGTG
1 TAAACGCATGATTAAGCTGACGAGCG
* **
11044313 TAAACG--TG-TGCAAGCTGGTGAGCG
1 TAAACGCATGAT-TAAGCTGACGAGCG
* *
11044337 TAAACACATAATTAAGCTGACGAGCG
1 TAAACGCATGATTAAGCTGACGAGCG
11044363 TAAACG
1 TAAACG
11044369 TGTGCAAGCT
Statistics
Matches: 250, Mismatches: 56, Indels: 50
0.70 0.16 0.14
Matches are distributed among these distances:
23 6 0.02
24 106 0.42
25 19 0.08
26 114 0.46
27 5 0.02
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (26 bp):
TAAACGCATGATTAAGCTGACGAGCG
Found at i:11044097 original size:50 final size:50
Alignment explanation
Indices: 11044033--11044445 Score: 506
Period size: 50 Copynumber: 8.3 Consensus size: 50
11044023 TTAAGCTAGA
*
11044033 GAGCGTAAACGCATGATTAAGCTGACGAGCGTAAACGTGTGCAAGTTGGC
1 GAGCGTAAACGCATGATTAAGCTGACGAGCGTAAACGTGTGCAAGCTGGC
** * *
11044083 GAGCGCGAATGCATGATTAAGCTGACGAGCGTAAACGTGTGCAAGCTGAC
1 GAGCGTAAACGCATGATTAAGCTGACGAGCGTAAACGTGTGCAAGCTGGC
* * * * *
11044133 GAGTGTAAACGCATGATTAAGTTGACGACCGTAAACATGTGCAAGTTGGC
1 GAGCGTAAACGCATGATTAAGCTGACGAGCGTAAACGTGTGCAAGCTGGC
* * *
11044183 GAGCGTAAACGCATGATTAAGTTGACGAGCGTAAACGTGTCCAAGCTGCC
1 GAGCGTAAACGCATGATTAAGCTGACGAGCGTAAACGTGTGCAAGCTGGC
* * * * * *
11044233 GAGCGTAAACACATAATTAAGCTAACAAGCGTAAACTTGTGCAAGTTGGC
1 GAGCGTAAACGCATGATTAAGCTGACGAGCGTAAACGTGTGCAAGCTGGC
* ** * *
11044283 GAGCGCAAACG-ATGATTAAGCTGGTGAGTGTAAACGTGTGCAAGCTGGT
1 GAGCGTAAACGCATGATTAAGCTGACGAGCGTAAACGTGTGCAAGCTGGC
* * *
11044332 GAGCGTAAACACATAATTAAGCTGACGAGCGTAAACGTGTGCAAGCTGGT
1 GAGCGTAAACGCATGATTAAGCTGACGAGCGTAAACGTGTGCAAGCTGGC
* * * * *
11044382 GAGCGTAAATGCGA-AATTAAGTTGACGAGTGTAAACGTGTGCAAGTTGGC
1 GAGCGTAAACGC-ATGATTAAGCTGACGAGCGTAAACGTGTGCAAGCTGGC
*
11044432 GTGCGTAAACGCAT
1 GAGCGTAAACGCAT
11044446 AAACATGATA
Statistics
Matches: 306, Mismatches: 54, Indels: 6
0.84 0.15 0.02
Matches are distributed among these distances:
49 39 0.13
50 266 0.87
51 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (50 bp):
GAGCGTAAACGCATGATTAAGCTGACGAGCGTAAACGTGTGCAAGCTGGC
Found at i:11044130 original size:24 final size:23
Alignment explanation
Indices: 11044025--11044390 Score: 140
Period size: 24 Copynumber: 14.7 Consensus size: 23
11044015 ACGCGTAATT
*
11044025 AAGCTAGA-GAGCGTAAACGCATGATT
1 AAGCT-GACGAGCGTAAACG--TG-TC
11044051 AAGCTGACGAGCGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTGT-C
* * * * * *
11044075 AAGTTGGCGAGCGCGAATGCATGATT
1 AAGCTGACGAGCG-TAA-ACGTG-TC
11044101 AAGCTGACGAGCGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTGT-C
* *
11044125 AAGCTGACGAGTGTAAACGCATGATT
1 AAGCTGACGAGCGTAAACG--TG-TC
* * *
11044151 AAGTTGACGACCGTAAACATGTGC
1 AAGCTGACGAGCGTAAACGTGT-C
* * *
11044175 AAGTTGGCGAGCGTAAACGCATGATT
1 AAGCTGACGAGCGTAAACG--TG-TC
*
11044201 AAGTTGACGAGCGTAAACGTGTCC
1 AAGCTGACGAGCGTAAACGTGT-C
* * * *
11044225 AAGCTGCCGAGCGTAAACACATAATT
1 AAGCTGACGAGCGT-AA-ACGT-GTC
* * *
11044251 AAGCTAACAAGCGTAAACTTGTGC
1 AAGCTGACGAGCGTAAACGTGT-C
* * * *
11044275 AAGTTGGCGAGCGCAAACGATGATT
1 AAGCTGACGAGCGTAAACG-TG-TC
** *
11044300 AAGCTGGTGAGTGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTGT-C
** * * *
11044324 AAGCTGGTGAGCGTAAACACATAATT
1 AAGCTGACGAGCGT-AA-ACGT-GTC
11044350 AAGCTGACGAGCGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTGT-C
**
11044374 AAGCTGGTGAGCGTAAA
1 AAGCTGACGAGCGTAAA
11044391 TGCGAAATTA
Statistics
Matches: 255, Mismatches: 60, Indels: 52
0.69 0.16 0.14
Matches are distributed among these distances:
23 7 0.03
24 115 0.45
25 31 0.12
26 97 0.38
27 5 0.02
ACGTcount: A:0.33, C:0.18, G:0.29, T:0.20
Consensus pattern (23 bp):
AAGCTGACGAGCGTAAACGTGTC
Found at i:11047465 original size:18 final size:19
Alignment explanation
Indices: 11047430--11047470 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
11047420 ATTAAATAAT
*
11047430 TCGAGTTATTTGAGTTAA-
1 TCGAGTTATTGGAGTTAAC
11047448 TCGAGTTATTCGGA-TTAAC
1 TCGAGTTATT-GGAGTTAAC
11047467 TCGA
1 TCGA
11047471 ATAAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (19 bp):
TCGAGTTATTGGAGTTAAC
Found at i:11047798 original size:20 final size:21
Alignment explanation
Indices: 11047775--11047814 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
11047765 TGAATTTTTA
*
11047775 GCATTTCAT-ACTTAGTGTTT
1 GCATTTCATAACTCAGTGTTT
*
11047795 GCATTTTATAACTCAGTGTT
1 GCATTTCATAACTCAGTGTT
11047815 GTTTGATCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.47
Consensus pattern (21 bp):
GCATTTCATAACTCAGTGTTT
Found at i:11051538 original size:51 final size:51
Alignment explanation
Indices: 11051462--11051632 Score: 263
Period size: 51 Copynumber: 3.4 Consensus size: 51
11051452 TTTCCTTTGA
* *
11051462 TACTCACGATGACATATTA-TCATCGGACCTTTAATCCGTAAAAGATTCATT
1 TACTCACGATGACA-CTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
*
11051513 TACTCACGATAACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* *
11051564 TACTCATGATGACACTTAGTCATCGGACCTTTACTCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* *
11051615 TACTTACTATGACACTTA
1 TACTCACGATGACACTTA
11051633 CTCACCAGAC
Statistics
Matches: 110, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
50 3 0.03
51 107 0.97
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
Found at i:11054727 original size:51 final size:51
Alignment explanation
Indices: 11054669--11054887 Score: 316
Period size: 51 Copynumber: 4.3 Consensus size: 51
11054659 ATGACATATT
* * * *
11054669 GTCATCGGACCTTTAATTCGTCATGAATTCATTTACTCACGATGAAACTTA
1 GTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGAAACTTA
*
11054720 GTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCAAGAT-AACACTTA
1 GTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGAA-ACTTA
**
11054771 GTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGACTCTTA
1 GTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGAAACTTA
*
11054822 GTCATC-GAGCCTTTAATCCGTAAAGGATTCATTTACTCACGATGACACTTA
1 GTCATCGGA-CCTTTAATCCGTAAAGGATTCATTTACTCACGATGAAACTTA
*
11054873 GTCACCGGACTCTTT
1 GTCATCGGAC-CTTT
11054888 CGTTTATAGC
Statistics
Matches: 153, Mismatches: 10, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
50 4 0.03
51 142 0.93
52 7 0.05
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (51 bp):
GTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGAAACTTA
Found at i:11065351 original size:15 final size:15
Alignment explanation
Indices: 11065331--11065389 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
11065321 GTATTGCAGT
*
11065331 AGAAGAAGAAGCAAG
1 AGAAGAAGAAGAAAG
*
11065346 AGAAGAGGAGAGAAAG
1 AGAAGAAGA-AGAAAG
*
11065362 -GAAG-AGAAGGAAG
1 AGAAGAAGAAGAAAG
*
11065375 AAAAAGAAGAAGAAA
1 -AGAAGAAGAAGAAA
11065390 TTGCCCCGAG
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
13 5 0.15
14 2 0.06
15 15 0.44
16 12 0.35
ACGTcount: A:0.63, C:0.02, G:0.36, T:0.00
Consensus pattern (15 bp):
AGAAGAAGAAGAAAG
Found at i:11065826 original size:16 final size:18
Alignment explanation
Indices: 11065793--11065839 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
11065783 AATTGTCATT
*
11065793 GCATTTTTATTATCTCTA
1 GCATTTTAATTATCTCTA
11065811 -CATTTTAATTAT-TCTA
1 GCATTTTAATTATCTCTA
*
11065827 GCATTTTCATTAT
1 GCATTTTAATTAT
11065840 AGTTGCATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 4 0.15
17 22 0.85
ACGTcount: A:0.26, C:0.15, G:0.04, T:0.55
Consensus pattern (18 bp):
GCATTTTAATTATCTCTA
Found at i:11069346 original size:43 final size:43
Alignment explanation
Indices: 11069298--11069380 Score: 157
Period size: 43 Copynumber: 1.9 Consensus size: 43
11069288 CCAAAGAATG
11069298 TTATTGAGGTACGAAGTTTCTTGGGATTAGTAGGGTATTAATA
1 TTATTGAGGTACGAAGTTTCTTGGGATTAGTAGGGTATTAATA
*
11069341 TTATTGAGGTACGAAGTTTCTTGGGATTAGTAGTGTATTA
1 TTATTGAGGTACGAAGTTTCTTGGGATTAGTAGGGTATTA
11069381 TCACTAATGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.27, C:0.05, G:0.28, T:0.41
Consensus pattern (43 bp):
TTATTGAGGTACGAAGTTTCTTGGGATTAGTAGGGTATTAATA
Found at i:11072655 original size:26 final size:26
Alignment explanation
Indices: 11072626--11072705 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 26
11072616 GCAAGCTGGT
11072626 GAGCGTAAACGCATAATTAAGCTGAC
1 GAGCGTAAACGCATAATTAAGCTGAC
* * * **
11072652 GAGCATAAACG--T-GTGGAAGCTGGT
1 GAGCGTAAACGCATAAT-TAAGCTGAC
*
11072676 GAGCGTAAATGCATAATTAAGCTGAC
1 GAGCGTAAACGCATAATTAAGCTGAC
11072702 GAGC
1 GAGC
11072706 TGATGGTATT
Statistics
Matches: 39, Mismatches: 11, Indels: 8
0.67 0.19 0.14
Matches are distributed among these distances:
23 1 0.03
24 16 0.41
26 21 0.54
27 1 0.03
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.20
Consensus pattern (26 bp):
GAGCGTAAACGCATAATTAAGCTGAC
Found at i:11072705 original size:50 final size:50
Alignment explanation
Indices: 11072518--11072701 Score: 235
Period size: 50 Copynumber: 3.7 Consensus size: 50
11072508 ACGCGTAATT
* *
11072518 AAGCTGGTGAGCGTAAATGCATGATTAAGCTGACAAGCATAAACGTGTGCG
1 AAGCTGGTGAGCGTAAACGCATAATTAAGCTGACAAGCATAAACGTGTG-G
* * * * * * * * *
11072569 -AGCTGGCGAGTGTAAACACATGATTAAGTTAACAAGCGTAAATGTGTGC
1 AAGCTGGTGAGCGTAAACGCATAATTAAGCTGACAAGCATAAACGTGTGG
*
11072618 AAGCTGGTGAGCGTAAACGCATAATTAAGCTGACGAGCATAAACGTGTGG
1 AAGCTGGTGAGCGTAAACGCATAATTAAGCTGACAAGCATAAACGTGTGG
*
11072668 AAGCTGGTGAGCGTAAATGCATAATTAAGCTGAC
1 AAGCTGGTGAGCGTAAACGCATAATTAAGCTGAC
11072702 GAGCTGATGG
Statistics
Matches: 112, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
50 112 1.00
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.22
Consensus pattern (50 bp):
AAGCTGGTGAGCGTAAACGCATAATTAAGCTGACAAGCATAAACGTGTGG
Found at i:11075531 original size:32 final size:32
Alignment explanation
Indices: 11075490--11075558 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
11075480 AATGACATAG
11075490 ATTTTCTCCCTAATTTAGTGTCTTAATTATCT
1 ATTTTCTCCCTAATTTAGTGTCTTAATTATCT
11075522 ATTTTCTCCCTAATTTAGTGTCTTAATTATCT
1 ATTTTCTCCCTAATTTAGTGTCTTAATTATCT
*
11075554 CTTTT
1 ATTTT
11075559 GTATTTCATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.20, C:0.19, G:0.06, T:0.55
Consensus pattern (32 bp):
ATTTTCTCCCTAATTTAGTGTCTTAATTATCT
Found at i:11085037 original size:17 final size:18
Alignment explanation
Indices: 11085015--11085055 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
11085005 TTAGTTTTGA
11085015 TGCATTCTT-ATTGT-GCT
1 TGCATTCTTAATTGTCG-T
11085032 TGCATT-TTAATTGTCGT
1 TGCATTCTTAATTGTCGT
11085049 TGCATTC
1 TGCATTC
11085056 ATTTTAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.10
17 18 0.86
18 1 0.05
ACGTcount: A:0.15, C:0.17, G:0.17, T:0.51
Consensus pattern (18 bp):
TGCATTCTTAATTGTCGT
Found at i:11093733 original size:10 final size:10
Alignment explanation
Indices: 11093703--11093754 Score: 63
Period size: 10 Copynumber: 5.4 Consensus size: 10
11093693 TCAGTCTTTT
11093703 GAAAAAGAAA
1 GAAAAAGAAA
* *
11093713 CAAAATG--A
1 GAAAAAGAAA
11093721 GAAAAAGAAA
1 GAAAAAGAAA
11093731 GAAAAAGAAA
1 GAAAAAGAAA
*
11093741 AAAAAAGAAA
1 GAAAAAGAAA
11093751 GAAA
1 GAAA
11093755 TTTTTTATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
8 6 0.18
10 28 0.82
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (10 bp):
GAAAAAGAAA
Found at i:11093743 original size:18 final size:19
Alignment explanation
Indices: 11093704--11093754 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
11093694 CAGTCTTTTG
* * *
11093704 AAAAAGAAACAAAATG-AG
1 AAAAAGAAAGAAAAAGAAA
11093722 AAAAAGAAAGAAAAAGAAAA
1 AAAAAGAAAGAAAAAG-AAA
11093742 AAAAAGAAAGAAA
1 AAAAAGAAAGAAA
11093755 TTTTTTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 14 0.50
20 14 0.50
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (19 bp):
AAAAAGAAAGAAAAAGAAA
Found at i:11095270 original size:24 final size:24
Alignment explanation
Indices: 11095238--11095321 Score: 80
Period size: 24 Copynumber: 3.4 Consensus size: 24
11095228 ACGCGATCAC
*
11095238 GAGCATAAACGTGTGTAAGCTGGT
1 GAGCGTAAACGTGTGTAAGCTGGT
* **
11095262 GAGCGTAAACGCATAAT-TAAGCTGAC
1 GAGCGTAAACG--T-GTGTAAGCTGGT
*
11095288 GAGCGTAAACGTGTGCAAGCTGGT
1 GAGCGTAAACGTGTGTAAGCTGGT
*
11095312 GACCGTAAAC
1 GAGCGTAAAC
11095322 ACGTAATTAA
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
23 1 0.02
24 26 0.55
26 19 0.40
27 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.30, T:0.20
Consensus pattern (24 bp):
GAGCGTAAACGTGTGTAAGCTGGT
Found at i:11095297 original size:50 final size:50
Alignment explanation
Indices: 11095236--11095345 Score: 166
Period size: 50 Copynumber: 2.2 Consensus size: 50
11095226 AGACGCGATC
* * * *
11095236 ACGAGCATAAACGTGTGTAAGCTGGTGAGCGTAAACGCATAATTAAGCTG
1 ACGAGCGTAAACGTGTGCAAGCTGGTGACCGTAAACACATAATTAAGCTG
*
11095286 ACGAGCGTAAACGTGTGCAAGCTGGTGACCGTAAACACGTAATTAAGCTG
1 ACGAGCGTAAACGTGTGCAAGCTGGTGACCGTAAACACATAATTAAGCTG
*
11095336 ACGAACGTAA
1 ACGAGCGTAA
11095346 CTAAATGCGT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (50 bp):
ACGAGCGTAAACGTGTGCAAGCTGGTGACCGTAAACACATAATTAAGCTG
Found at i:11095333 original size:26 final size:26
Alignment explanation
Indices: 11095253--11095335 Score: 73
Period size: 26 Copynumber: 3.3 Consensus size: 26
11095243 TAAACGTGTG
* *
11095253 TAAGCTGGTGAGCGTAAACGCATAAT
1 TAAGCTGGTGAGCGTAAACACGTAAT
** *
11095279 TAAGCTGACGAGCGT-AA-ACGT-GT
1 TAAGCTGGTGAGCGTAAACACGTAAT
* *
11095302 GCAAGCTGGTGACCGTAAACACGTAAT
1 -TAAGCTGGTGAGCGTAAACACGTAAT
11095329 TAAGCTG
1 TAAGCTG
11095336 ACGAACGTAA
Statistics
Matches: 42, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
23 1 0.02
24 13 0.31
25 4 0.10
26 23 0.55
27 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.22
Consensus pattern (26 bp):
TAAGCTGGTGAGCGTAAACACGTAAT
Found at i:11096559 original size:53 final size:52
Alignment explanation
Indices: 11096449--11096547 Score: 137
Period size: 52 Copynumber: 1.9 Consensus size: 52
11096439 ATGAATGATA
* *
11096449 ACAAACATTGGTTAAGAATATCAACATCGATAAAAAAAAGTGGCAAAAAATT
1 ACAAACATTGGTTAAAAATATAAACATCGATAAAAAAAAGTGGCAAAAAATT
** *
11096501 ACAAACATTGGTTAAAAATAATAAATGTTGATAAAAAAAA-TGGCAAA
1 ACAAACATTGGTTAAAAAT-ATAAACATCGATAAAAAAAAGTGGCAAA
11096548 CATCAATCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
52 25 0.61
53 16 0.39
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (52 bp):
ACAAACATTGGTTAAAAATATAAACATCGATAAAAAAAAGTGGCAAAAAATT
Found at i:11102160 original size:25 final size:24
Alignment explanation
Indices: 11102132--11102196 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 24
11102122 ATTTTTGTCT
11102132 TTTTCTTTTCTTTTTTTCAATT-TAC
1 TTTT-TTTTCTTTTTTTC-ATTCTAC
** *
11102157 TTTTTTTTTCAATTTTTCTTTCCTAC
1 -TTTTTTTTCTTTTTTTCATT-CTAC
11102183 TTTTTTTTCTTTTT
1 TTTTTTTTCTTTTT
11102197 AAAAATATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
24 2 0.06
25 23 0.72
26 7 0.22
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTTTTTCTTTTTTTCATTCTAC
Found at i:11104781 original size:22 final size:21
Alignment explanation
Indices: 11104751--11104876 Score: 62
Period size: 22 Copynumber: 5.9 Consensus size: 21
11104741 TAGGAATACT
* *
11104751 AAAAAAAAACT-AATAATATA
1 AAAAAAAAAATAAATAAAATA
11104771 AAAAAAGAAAATAAATAAAAT-
1 AAAAAA-AAAATAAATAAAATA
* ** **
11104792 CAAAAAATGATAACA-ATGATA
1 AAAAAAAAAATAA-ATAAAATA
*
11104813 ATAAAATAAAATAAAATAAAATA
1 A-AAAAAAAAAT-AAATAAAATA
* * *
11104836 AAAAGAAATACT-AAGAAAATA
1 AAAA-AAAAAATAAATAAAATA
*
11104857 AAGAAAATAAATAAATAAAA
1 AA-AAAAAAAATAAATAAAA
11104877 GGAATAAAAT
Statistics
Matches: 75, Mismatches: 21, Indels: 18
0.66 0.18 0.16
Matches are distributed among these distances:
20 14 0.19
21 24 0.32
22 26 0.35
23 11 0.15
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17
Consensus pattern (21 bp):
AAAAAAAAAATAAATAAAATA
Found at i:11104796 original size:6 final size:5
Alignment explanation
Indices: 11104750--11104890 Score: 64
Period size: 5 Copynumber: 28.0 Consensus size: 5
11104740 ATAGGAATAC
* *
11104750 TAAAA AAAAA CTAATAA TATAAA -AAAA GAAAA T-AAA TAAAA TCAAAA
1 TAAAA TAAAA -TAA-AA TA-AAA TAAAA TAAAA TAAAA TAAAA T-AAAA
* *
11104797 -AATGA TAACAA TGATAA TAAAA TAAAA TAAAA TAAAA TAAAA -AGAAA
1 TAA-AA TAA-AA T-AAAA TAAAA TAAAA TAAAA TAAAA TAAAA TA-AAA
* * * **
11104844 TACTAA GAAAA T-AAA GAAAA T-AAA T-AAA TAAAA -GGAA TAAAA TAAAA
1 TA-AAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
11104891 ATTAAAAAGA
Statistics
Matches: 103, Mismatches: 19, Indels: 28
0.69 0.13 0.19
Matches are distributed among these distances:
4 23 0.22
5 55 0.53
6 21 0.20
7 4 0.04
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.18
Consensus pattern (5 bp):
TAAAA
Found at i:11104902 original size:21 final size:22
Alignment explanation
Indices: 11104860--11104902 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
11104850 GAAAATAAAG
*
11104860 AAAATAAATAAATAAAAGGAAT
1 AAAATAAATAAATAAAAAGAAT
*
11104882 AAAATAAA-AATTAAAAAGAAT
1 AAAATAAATAAATAAAAAGAAT
11104903 GAGGGCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (22 bp):
AAAATAAATAAATAAAAAGAAT
Found at i:11116745 original size:22 final size:23
Alignment explanation
Indices: 11116720--11116770 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
11116710 GCATAAAAAT
*
11116720 AACAAATAAATAAAA-TACATAA
1 AACAAATAAATAAAATTAAATAA
11116742 AAC-AATAAATAAAATTAAATAA
1 AACAAATAAATAAAATTAAATAA
11116764 AAGCAAA
1 AA-CAAA
11116771 ATTGTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 11 0.44
22 11 0.44
23 1 0.04
24 2 0.08
ACGTcount: A:0.73, C:0.08, G:0.02, T:0.18
Consensus pattern (23 bp):
AACAAATAAATAAAATTAAATAA
Found at i:11116756 original size:26 final size:28
Alignment explanation
Indices: 11116698--11116762 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 28
11116688 AATGTAGGCA
*
11116698 AAAATATAAATAGCATAAAAATAACAAAT
1 AAAATA-AAATAGCATAAAAACAACAAAT
*
11116727 -AAATAAAATA-CAT-AAAACAATAAAT
1 AAAATAAAATAGCATAAAAACAACAAAT
*
11116752 AAAATTAAATA
1 AAAATAAAATA
11116763 AAAGCAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 10 0.31
26 12 0.38
27 5 0.16
28 5 0.16
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.22
Consensus pattern (28 bp):
AAAATAAAATAGCATAAAAACAACAAAT
Found at i:11116785 original size:7 final size:7
Alignment explanation
Indices: 11116775--11116858 Score: 53
Period size: 7 Copynumber: 13.0 Consensus size: 7
11116765 AGCAAAATTG
11116775 TAAATAA
1 TAAATAA
*
11116782 TAAA-GA
1 TAAATAA
11116788 -AAATGAA
1 TAAAT-AA
11116795 T-AATAAA
1 TAAAT-AA
11116802 TAAAT-A
1 TAAATAA
11116808 -AA-TAA
1 TAAATAA
11116813 TAAATAA
1 TAAATAA
11116820 TAAATAAA
1 TAAAT-AA
11116828 TAAA-AA
1 TAAATAA
11116834 TAAATAA
1 TAAATAA
11116841 -AAAT--
1 TAAATAA
*
11116845 TAAATAC
1 TAAATAA
11116852 TAAATAA
1 TAAATAA
11116859 AATCATGCAA
Statistics
Matches: 61, Mismatches: 4, Indels: 24
0.69 0.04 0.27
Matches are distributed among these distances:
4 1 0.02
5 10 0.16
6 14 0.23
7 27 0.44
8 9 0.15
ACGTcount: A:0.71, C:0.01, G:0.02, T:0.25
Consensus pattern (7 bp):
TAAATAA
Found at i:11116805 original size:4 final size:4
Alignment explanation
Indices: 11116775--11116859 Score: 69
Period size: 4 Copynumber: 23.0 Consensus size: 4
11116765 AGCAAAATTG
* *
11116775 TAAA T-AA TAAA GAAAA TGAA T-AA TAAA TAAA TAAA T-AA TAAA T-AA
1 TAAA TAAA TAAA -TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* *
11116820 TAAA TAAA T-AA -AAA TAAA TAAA -AAT TAAA T-AC TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
11116860 ATCATGCAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
3 20 0.31
4 42 0.65
5 3 0.05
ACGTcount: A:0.72, C:0.01, G:0.02, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:11116855 original size:18 final size:17
Alignment explanation
Indices: 11116646--11116860 Score: 93
Period size: 18 Copynumber: 12.1 Consensus size: 17
11116636 TATGACATAC
*
11116646 AAATAAATAACAAATAA
1 AAATAAATAATAAATAA
11116663 AAATATCAATGAATAAATAA
1 AAATA--AAT-AATAAATAA
* * ***
11116683 AATTAAAT-GTAGGCAA
1 AAATAAATAATAAATAA
* *
11116699 AAATATA-AATAGCATAA
1 AAATAAATAATA-AATAA
11116716 AAATAACA-AATAAATAAA
1 AAATAA-ATAATAAAT-AA
*
11116734 ATACATAAAACAATAAATAA
1 A-A-AT-AAATAATAAATAA
* **
11116754 AATTAAATAA-AAGCAA
1 AAATAAATAATAAATAA
* *
11116770 AATTGTAAATAATAAA-GA
1 AA--ATAAATAATAAATAA
*
11116788 AAATGAATAATAAAT--
1 AAATAAATAATAAATAA
11116803 AAATAAATAATAAATAA
1 AAATAAATAATAAATAA
11116820 TAAATAAATAAAAATAAATAA
1 -AAATAAAT---AATAAATAA
*
11116841 AAATTAAATACTAAATAA
1 AAA-TAAATAATAAATAA
11116859 AA
1 AA
11116861 TCATGCAAAT
Statistics
Matches: 151, Mismatches: 25, Indels: 43
0.69 0.11 0.20
Matches are distributed among these distances:
15 14 0.09
16 27 0.18
17 19 0.13
18 40 0.26
19 7 0.05
20 21 0.14
21 23 0.15
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (17 bp):
AAATAAATAATAAATAA
Found at i:11116859 original size:11 final size:10
Alignment explanation
Indices: 11116716--11116850 Score: 96
Period size: 11 Copynumber: 12.5 Consensus size: 10
11116706 AATAGCATAA
11116716 AAATAACAAAT
1 AAATAA-AAAT
11116727 AAAT-AAAAT
1 AAATAAAAAT
*
11116736 ACATAAAACAAT
1 AAAT-AAA-AAT
*
11116748 AAATAAAATT
1 AAATAAAAAT
11116758 AAATAAAAGCA-
1 AAATAAAA--AT
11116769 AAATTGTAAATAAT
1 AAA---TAAA-AAT
*
11116783 AAA-GAAAAT
1 AAATAAAAAT
*
11116792 GAATAATAAAT
1 AAATAA-AAAT
11116803 AAATAAATAAT
1 AAATAAA-AAT
11116814 AAATAATAAAT
1 AAATAA-AAAT
11116825 AAATAAAAAT
1 AAATAAAAAT
11116835 AAATAAAAATT
1 AAATAAAAA-T
11116846 AAATA
1 AAATA
11116851 CTAAATAAAA
Statistics
Matches: 101, Mismatches: 8, Indels: 30
0.73 0.06 0.22
Matches are distributed among these distances:
9 12 0.12
10 28 0.28
11 45 0.45
12 7 0.07
13 1 0.01
14 7 0.07
15 1 0.01
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:11116916 original size:33 final size:32
Alignment explanation
Indices: 11116879--11116967 Score: 78
Period size: 32 Copynumber: 2.8 Consensus size: 32
11116869 ATAATGTAAA
**
11116879 AAAATATAAATGGGACAAAATTAAATGAAAATT
1 AAAATATAAATGGG-CAAAATTAAATGAAAAAC
*
11116912 AAAATAGT--AGGGGTCAAAATTATAA-GAAAAAC
1 AAAATA-TAAATGGG-CAAAATTA-AATGAAAAAC
*
11116944 ATAA-ATAAATGGGCAAAATTAAAT
1 AAAATATAAATGGGCAAAATTAAAT
11116968 AAAGGACTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
30 3 0.07
31 9 0.20
32 24 0.53
33 8 0.18
34 1 0.02
ACGTcount: A:0.58, C:0.04, G:0.15, T:0.22
Consensus pattern (32 bp):
AAAATATAAATGGGCAAAATTAAATGAAAAAC
Found at i:11119830 original size:25 final size:25
Alignment explanation
Indices: 11119797--11119849 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
11119787 ATATTCTAAT
* * *
11119797 TCTGTCTCGTAAGAGCGTAATTCTG
1 TCTGCCTCGTAAAAACGTAATTCTG
*
11119822 TCTGCCTCGTAAAAACGTAATTTTG
1 TCTGCCTCGTAAAAACGTAATTCTG
11119847 TCT
1 TCT
11119850 AAGCTCATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.38
Consensus pattern (25 bp):
TCTGCCTCGTAAAAACGTAATTCTG
Found at i:11119881 original size:26 final size:26
Alignment explanation
Indices: 11119847--11119945 Score: 126
Period size: 26 Copynumber: 3.8 Consensus size: 26
11119837 CGTAATTTTG
* * * *
11119847 TCTAAGCTCATAAGAGCTAAACTTTT
1 TCTAGGCTCGTAAGAGCTAAACTCTA
11119873 TCTAGGCTCGTAAGAGCTAAACTCTA
1 TCTAGGCTCGTAAGAGCTAAACTCTA
* *
11119899 TCTAGGCTCGTACGAGTTAAACTCTA
1 TCTAGGCTCGTAAGAGCTAAACTCTA
* *
11119925 TCTGGGCTCGTATGAGCTAAA
1 TCTAGGCTCGTAAGAGCTAAA
11119946 TTTCTAGAAG
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 64 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.30
Consensus pattern (26 bp):
TCTAGGCTCGTAAGAGCTAAACTCTA
Done.