Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 18 of 160
Found at i:5112519 original size:15 final size:14
Alignment explanation
Indices: 5112380--5112601 Score: 52
Period size: 14 Copynumber: 15.7 Consensus size: 14
5112370 ATATTAACAG
5112380 ATAAATAAAAATAA
1 ATAAATAAAAATAA
*
5112394 AT-AATAGATAAAT-T
1 ATAAATA-A-AAATAA
* * *
5112408 ATATTATATAAATAG
1 ATA-AATAAAAATAA
*
5112423 ATAAATAATAATAA
1 ATAAATAAAAATAA
* * *
5112437 ATACATATATAT-A
1 ATAAATAAAAATAA
* *
5112450 ATAATATATAAATAG
1 ATAA-ATAAAAATAA
* * *
5112465 CTAAGTAATAATAA
1 ATAAATAAAAATAA
* *
5112479 ATATATATTAACATAA
1 ATA-A-ATAAAAATAA
5112495 A-AAA-AATAAATAA
1 ATAAATAA-AAATAA
* *
5112508 ATAAACAATAAATAC
1 ATAAATAA-AAATAA
**
5112523 ATAAGATACAAAGGAA
1 ATAA-ATA-AAAATAA
*
5112539 A-AAATATAAAATAT
1 ATAAATA-AAAATAA
*
5112553 A-AAATAAAACAAAA
1 ATAAATAAAA-ATAA
*
5112567 AT-AAT-AAAATAC
1 ATAAATAAAAATAA
5112579 A-AAATACAAAATAA
1 ATAAATA-AAAATAA
5112593 A-AAATAAAA
1 ATAAATAAAA
5112602 TGGGCTTAAC
Statistics
Matches: 148, Mismatches: 41, Indels: 39
0.65 0.18 0.17
Matches are distributed among these distances:
12 7 0.05
13 24 0.16
14 74 0.50
15 26 0.18
16 16 0.11
17 1 0.01
ACGTcount: A:0.68, C:0.04, G:0.03, T:0.25
Consensus pattern (14 bp):
ATAAATAAAAATAA
Found at i:5112551 original size:7 final size:7
Alignment explanation
Indices: 5112539--5112602 Score: 57
Period size: 7 Copynumber: 9.7 Consensus size: 7
5112529 TACAAAGGAA
5112539 AAAATAT
1 AAAATAT
5112546 AAAATAT
1 AAAATAT
5112553 -AAA-AT
1 AAAATAT
*
5112558 AAAACA-
1 AAAATAT
5112564 AAAATAAT
1 AAAAT-AT
*
5112572 AAAATAC
1 AAAATAT
*
5112579 AAAATAC
1 AAAATAT
5112586 AAAATA-
1 AAAATAT
5112592 AAAA-AT
1 AAAATAT
5112598 AAAAT
1 AAAAT
5112603 GGGCTTAACC
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
5 3 0.06
6 18 0.37
7 23 0.47
8 5 0.10
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.19
Consensus pattern (7 bp):
AAAATAT
Found at i:5112567 original size:26 final size:26
Alignment explanation
Indices: 5112517--5112602 Score: 86
Period size: 26 Copynumber: 3.2 Consensus size: 26
5112507 AATAAACAAT
5112517 AAATACATAAGATACAAAGGAAAAAATATA
1 AAATACA-AA-ATACAAA--AAAAAATATA
* *
5112547 AAATATAAAATA-AAACAAAAATAATA
1 AAATACAAAATACAAAAAAAAAT-ATA
5112573 AAATACAAAATACAAAATAAAAA-ATA
1 AAATACAAAATACAAAA-AAAAATATA
5112599 AAAT
1 AAAT
5112603 GGGCTTAACC
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
25 6 0.12
26 21 0.43
27 6 0.12
28 8 0.16
29 2 0.04
30 6 0.12
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.17
Consensus pattern (26 bp):
AAATACAAAATACAAAAAAAAATATA
Found at i:5112829 original size:35 final size:35
Alignment explanation
Indices: 5112790--5112860 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
5112780 AAAATGATAA
*
5112790 ACTACTAAAAATTAAAGAATAAAATAATAATGTAT
1 ACTACTAAAAATTAAAAAATAAAATAATAATGTAT
5112825 ACTACTAAAAATTAAAAAATAAAATAATAATGTAT
1 ACTACTAAAAATTAAAAAATAAAATAATAATGTAT
5112860 A
1 A
5112861 AGACTAGAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.28
Consensus pattern (35 bp):
ACTACTAAAAATTAAAAAATAAAATAATAATGTAT
Found at i:5115756 original size:12 final size:12
Alignment explanation
Indices: 5115741--5115822 Score: 58
Period size: 12 Copynumber: 6.5 Consensus size: 12
5115731 AAATTATTTT
5115741 AATAATAATAAA
1 AATAATAATAAA
*
5115753 AATAAAAATAAGTA
1 AATAATAATAA--A
5115767 AGATAATAATTAAA
1 A-ATAATAA-TAAA
*
5115781 AATATATATTAAA
1 AATA-ATAATAAA
**
5115794 AATGCTAA-AAA
1 AATAATAATAAA
* *
5115805 AATGATAATAAT
1 AATAATAATAAA
5115817 AATAAT
1 AATAAT
5115823 TATTTTCCCT
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
11 10 0.18
12 19 0.35
13 10 0.18
14 7 0.13
15 6 0.11
16 3 0.05
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.28
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:5116098 original size:16 final size:16
Alignment explanation
Indices: 5116079--5116173 Score: 104
Period size: 16 Copynumber: 6.0 Consensus size: 16
5116069 CTAGGTTTCT
5116079 AAAACCCCTAAAATCC
1 AAAACCCCTAAAATCC
*
5116095 AAAATCTCCTAAAATCC
1 AAAA-CCCCTAAAATCC
* *
5116112 AAAA-TCTTAAAATCC
1 AAAACCCCTAAAATCC
* *
5116127 AAAA-TCCTAAAATTC
1 AAAACCCCTAAAATCC
*
5116142 GAAACCCCTAAAATCC
1 AAAACCCCTAAAATCC
*
5116158 AAAACCCTTAAAATCC
1 AAAACCCCTAAAATCC
5116174 GAATCTTTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
15 26 0.38
16 27 0.40
17 15 0.22
ACGTcount: A:0.49, C:0.29, G:0.01, T:0.20
Consensus pattern (16 bp):
AAAACCCCTAAAATCC
Found at i:5116100 original size:7 final size:7
Alignment explanation
Indices: 5116088--5116139 Score: 50
Period size: 7 Copynumber: 6.7 Consensus size: 7
5116078 TAAAACCCCT
5116088 AAAATCC
1 AAAATCC
5116095 AAAATCTCC
1 AAAA--TCC
5116104 TAAAATCC
1 -AAAATCC
*
5116112 AAAATCTT
1 AAAATC-C
5116120 AAAATCC
1 AAAATCC
5116127 AAAATCC
1 AAAATCC
5116134 TAAAAT
1 -AAAAT
5116140 TCGAAACCCC
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
7 17 0.45
8 14 0.37
9 3 0.08
10 4 0.11
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAATCC
Found at i:5116124 original size:15 final size:15
Alignment explanation
Indices: 5116087--5116187 Score: 87
Period size: 15 Copynumber: 6.5 Consensus size: 15
5116077 CTAAAACCCC
5116087 TAAAATCCAAAATCT
1 TAAAATCCAAAATCT
5116102 CCTAAAATCCAAAATCT
1 --TAAAATCCAAAATCT
*
5116119 TAAAATCCAAAATCC
1 TAAAATCCAAAATCT
* ** *
5116134 TAAAATTCGAAACCCC
1 TAAAA-TCCAAAATCT
*
5116150 TAAAATCCAAAACCCT
1 TAAAATCCAAAA-TCT
*
5116166 TAAAATCC-GAATCTT
1 TAAAATCCAAAATC-T
5116181 TAAAATC
1 TAAAATC
5116188 TTGAAACCTT
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
14 1 0.01
15 34 0.47
16 22 0.31
17 15 0.21
ACGTcount: A:0.49, C:0.26, G:0.02, T:0.24
Consensus pattern (15 bp):
TAAAATCCAAAATCT
Found at i:5116185 original size:31 final size:29
Alignment explanation
Indices: 5116087--5116187 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 29
5116077 CTAAAACCCC
*
5116087 TAAAATCCAAAATCTCCTAAAATCCAAAATCT
1 TAAAATCCAAAA-C-CCTAAAATCC-GAATCT
* * * *
5116119 TAAAATCCAAAATCCTAAAATTCGAAACCCC
1 TAAAATCCAAAACCCTAAAATCCG-AA-TCT
5116150 TAAAATCCAAAACCCTTAAAATCCGAATCTT
1 TAAAATCCAAAACCC-TAAAATCCGAATC-T
5116181 TAAAATC
1 TAAAATC
5116188 TTGAAACCTT
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
30 12 0.21
31 24 0.43
32 20 0.36
ACGTcount: A:0.49, C:0.26, G:0.02, T:0.24
Consensus pattern (29 bp):
TAAAATCCAAAACCCTAAAATCCGAATCT
Found at i:5118031 original size:20 final size:19
Alignment explanation
Indices: 5118001--5118053 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 19
5117991 GTCCTAGTTC
5118001 TTTTGTTTTTCATTTTCAAAA
1 TTTT-TTTTTCATTTTC-AAA
*
5118022 TTTTTTTTTCCTTTTCAAA
1 TTTTTTTTTCATTTTCAAA
5118041 TCTTTTTTTTCAT
1 T-TTTTTTTTCAT
5118054 ATTTTGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 4 0.14
20 21 0.72
21 4 0.14
ACGTcount: A:0.17, C:0.13, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTTTTTTCATTTTCAAA
Found at i:5122144 original size:10 final size:9
Alignment explanation
Indices: 5122126--5122170 Score: 63
Period size: 10 Copynumber: 4.8 Consensus size: 9
5122116 TCAAGATTTC
5122126 AAAAAAATA
1 AAAAAAATA
5122135 AAACAAAATA
1 AAA-AAAATA
*
5122145 AAACAAAACA
1 AAA-AAAATA
5122155 AAAAAAATA
1 AAAAAAATA
5122164 AAAAAAA
1 AAAAAAA
5122171 AAGAAGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
9 15 0.45
10 18 0.55
ACGTcount: A:0.87, C:0.07, G:0.00, T:0.07
Consensus pattern (9 bp):
AAAAAAATA
Found at i:5122152 original size:15 final size:14
Alignment explanation
Indices: 5122126--5122172 Score: 69
Period size: 15 Copynumber: 3.4 Consensus size: 14
5122116 TCAAGATTTC
5122126 AAAAAAATAAAACA
1 AAAAAAATAAAACA
*
5122140 AAATAAAACAAAACA
1 AAA-AAAATAAAACA
5122155 AAAAAAATAAAA-A
1 AAAAAAATAAAACA
5122168 AAAAA
1 AAAAA
5122173 GAAGTTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
13 6 0.20
14 11 0.37
15 13 0.43
ACGTcount: A:0.87, C:0.06, G:0.00, T:0.06
Consensus pattern (14 bp):
AAAAAAATAAAACA
Found at i:5124695 original size:22 final size:22
Alignment explanation
Indices: 5124661--5124746 Score: 75
Period size: 22 Copynumber: 3.9 Consensus size: 22
5124651 AGATTTTAAG
* *
5124661 ATTTGTAAGACCTTCGGGCATA
1 ATTTCTAAAACCTTCGGGCATA
*
5124683 ATTTCTAAAACCTTCGGGCTTA
1 ATTTCTAAAACCTTCGGGCATA
* * *
5124705 ACTTT-TAAGATCTCCGGGCATA
1 A-TTTCTAAAACCTTCGGGCATA
* * *
5124727 ATCTCTAAAGCCTTTGGGCA
1 ATTTCTAAAACCTTCGGGCA
5124747 CAACTTTCAA
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
21 2 0.04
22 44 0.90
23 3 0.06
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (22 bp):
ATTTCTAAAACCTTCGGGCATA
Found at i:5124734 original size:44 final size:44
Alignment explanation
Indices: 5124666--5124759 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
5124656 TTAAGATTTG
* * * **
5124666 TAAGACCTTCGGGCATAATTTCTAAAACCTTCGGGCTTAACTTT
1 TAAGATCTCCGGGCATAATCTCTAAAACCTTCGGGCACAACTTT
* *
5124710 TAAGATCTCCGGGCATAATCTCTAAAGCCTTTGGGCACAACTTT
1 TAAGATCTCCGGGCATAATCTCTAAAACCTTCGGGCACAACTTT
*
5124754 CAAGAT
1 TAAGAT
5124760 TTTTGGATAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (44 bp):
TAAGATCTCCGGGCATAATCTCTAAAACCTTCGGGCACAACTTT
Found at i:5125054 original size:109 final size:109
Alignment explanation
Indices: 5124833--5125149 Score: 363
Period size: 109 Copynumber: 2.9 Consensus size: 109
5124823 AGATTTTGAT
* * ** * * **
5124833 ATTTGTAAGACCTCCGAGTATAATTTTGATTCATGATGTTATCTTGATTGATTCTTTATTTTTTA
1 ATTTCTAAGACCTCAGAACATAATTTTGATTCACGGTGTTATCTTGATTGATTCTTTATTTTTCG
* * * *
5124898 ACTTACGATGTTGTCTCAGTTGATTCTGTAAGACCTCCGGGCATG
66 AC-TATGATGTTATCTCAGTCGATTCTGTAAGACCTCCGAGCATG
* * * * *
5124943 ATTTTTAAGACTTCTAG-GCATAATTTTGATTCACGGTGTTATCTCGATCGATTCTTTATTTTTC
1 ATTTCTAAGACCTC-AGAACATAATTTTGATTCACGGTGTTATCTTGATTGATTCTTTATTTTTC
*
5125007 GACTATGATGTTATCTCAGTCGATTCTGTAAGACCTCTGAGCATG
65 GACTATGATGTTATCTCAGTCGATTCTGTAAGACCTCCGAGCATG
* *
5125052 ATTTCTAAGACCTCCGAACATAATTTCT-ATTCACGGTGTTATCTTGATTGATT-TCTTATCTTT
1 ATTTCTAAGACCTCAGAACATAATTT-TGATTCACGGTGTTATCTTGATTGATTCT-TTATTTTT
*
5125115 CGACT-TGCGATGTTATTTCAGTCGATTCTGTAAGA
64 CGACTAT--GATGTTATCTCAGTCGATTCTGTAAGA
5125150 TCTTCGGGGC
Statistics
Matches: 178, Mismatches: 23, Indels: 12
0.84 0.11 0.06
Matches are distributed among these distances:
108 3 0.02
109 92 0.52
110 82 0.46
111 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (109 bp):
ATTTCTAAGACCTCAGAACATAATTTTGATTCACGGTGTTATCTTGATTGATTCTTTATTTTTCG
ACTATGATGTTATCTCAGTCGATTCTGTAAGACCTCCGAGCATG
Found at i:5125060 original size:22 final size:22
Alignment explanation
Indices: 5125035--5125080 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
5125025 GTCGATTCTG
* * *
5125035 TAAGACCTCTGAGCATGATTTC
1 TAAGACCTCCGAACATAATTTC
5125057 TAAGACCTCCGAACATAATTTC
1 TAAGACCTCCGAACATAATTTC
5125079 TA
1 TA
5125081 TTCACGGTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (22 bp):
TAAGACCTCCGAACATAATTTC
Found at i:5125258 original size:22 final size:22
Alignment explanation
Indices: 5125233--5125275 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5125223 GTCGATTCTG
*
5125233 TAAGACC-TCCGGACATGATTTT
1 TAAGACCTTCAGG-CATGATTTT
5125255 TAAGACCTTCAGGCATGATTT
1 TAAGACCTTCAGGCATGATTT
5125276 CGATTCGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (22 bp):
TAAGACCTTCAGGCATGATTTT
Found at i:5125311 original size:198 final size:196
Alignment explanation
Indices: 5124959--5125363 Score: 518
Period size: 198 Copynumber: 2.1 Consensus size: 196
5124949 AAGACTTCTA
* * *
5124959 GGCATAATTTTGATTCACGGTGTTATCTCGATCGATTCTTTATTTTTCGACTATGATGTTATCTC
1 GGCATAATTTTGATTCACGGTGTTATCTCGATCGATTCCTTATCTTTCGACTATAATGTTATCTC
* * * *
5125024 AGTCGATTCTGTAAGACCTCTGAGCATGATTTCTAAGACCTCCGAACATAATTTCTATTCACGGT
66 AGTCGATTCTGTAAGACCTCGGAGCATGATTTCTAAGACCTCAGAACATAATTTCGATTCACGAT
* ** *
5125089 GTTATCTTGATTGATTTCTTATCTTTCGACTTGCGATGTTAT-TTCAGTCGATTCTGTAAGATCT
131 ATTATCTCCATTGATTTCTTATCTTTCGAC-TGCGATGTTATCTT-AGTCGATTCAGTAAGATC-
*
5125153 TCGG
193 TCCG
*
5125157 GGCATAATTTTGATTCA-GGATGTTATC-CAGATCGATTCCTTATCTTTCGACTGTAATGTTATC
1 GGCATAATTTTGATTCACGG-TGTTATCTC-GATCGATTCCTTATCTTTCGACTATAATGTTATC
* * * *
5125220 TCAGTCGATTCTGTAAGACCTCCGGA-CATGATTTTTAAGACCTTCAG-GCATGATTTCGATTCG
64 TCAGTCGATTCTGTAAGACCT-CGGAGCATGATTTCTAAGACC-TCAGAACATAATTTCGATTCA
5125283 CGATATTATC-CCATTCGA-TTCTTTATCTTTCGACTGCGATGTTATCTTAGTCGATTCAGTAAG
127 CGATATTATCTCCATT-GATTTC-TTATCTTTCGACTGCGATGTTATCTTAGTCGATTCAGTAAG
5125346 ATCTCCG
190 ATCTCCG
*
5125353 GGCATGATTTT
1 GGCATAATTTT
5125364 TAAGACCTCA
Statistics
Matches: 182, Mismatches: 18, Indels: 16
0.84 0.08 0.07
Matches are distributed among these distances:
196 13 0.07
197 37 0.20
198 126 0.69
199 6 0.03
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (196 bp):
GGCATAATTTTGATTCACGGTGTTATCTCGATCGATTCCTTATCTTTCGACTATAATGTTATCTC
AGTCGATTCTGTAAGACCTCGGAGCATGATTTCTAAGACCTCAGAACATAATTTCGATTCACGAT
ATTATCTCCATTGATTTCTTATCTTTCGACTGCGATGTTATCTTAGTCGATTCAGTAAGATCTCC
G
Found at i:5125443 original size:108 final size:109
Alignment explanation
Indices: 5125159--5125676 Score: 584
Period size: 109 Copynumber: 4.9 Consensus size: 109
5125149 ATCTTCGGGG
* * * * ***
5125159 CATAATTTTGATTCAGGATGTTATCCAGATCGATTCCTTATCTTTCGACTGTAATGTTATCTCAG
1 CATAATTTTGATTCACGATATTATCCCGATCGATTCTTTATCTTTCGACTACGATGTTATCTCAG
* *
5125224 TCGATTCTGTAAGACCTCCGGACATGATTTTTAAGACCTTCAGG
66 TCGATTCTGTAAGACCTCCGGGCATGATTTTTAAGACCTTCAGA
* * * * *
5125268 CATGATTTCGATTCGCGATATTATCCC-ATTCGATTCTTTATCTTTCGACTGCGATGTTATCTTA
1 CATAATTTTGATTCACGATATTATCCCGA-TCGATTCTTTATCTTTCGACTACGATGTTATCTCA
* *
5125332 GTCGATTCAGTAAGATCTCCGGGCATGATTTTTAAGACC-TCAGA
65 GTCGATTCTGTAAGACCTCCGGGCATGATTTTTAAGACCTTCAGA
* * * *
5125376 CATAATTTTGATTCACGATATTATCCCGATCGATTTTTTATCTTTTGACTATGATGTTATCCCAG
1 CATAATTTTGATTCACGATATTATCCCGATCGATTCTTTATCTTTCGACTACGATGTTATCTCAG
* *
5125441 TCGATTCTGTAAGACCTCCGGGCATGATTTCTAAGACCTTCGGA
66 TCGATTCTGTAAGACCTCCGGGCATGATTTTTAAGACCTTCAGA
** * **
5125485 CATAATTTTGATTCGTGATGTTATCCCGATCGATT-TTT-T-TTT----TA--A--TTAT-GGA-
1 CATAATTTTGATTCACGATATTATCCCGATCGATTCTTTATCTTTCGACTACGATGTTATCTCAG
* *
5125537 T-GATTCTGTAAGACCTCCAGGCATGATTTTTAAGACCTCCA-A
66 TCGATTCTGTAAGACCTCCGGGCATGATTTTTAAGACCTTCAGA
* *
5125579 GCATAATTTTGATTCACGGTATTATCCCGATCGATTCCTTATCTTTCGACTTACGATGTTATCTC
1 -CATAATTTTGATTCACGATATTATCCCGATCGATTCTTTATCTTTCGAC-TACGATGTTATCTC
* * *
5125644 AGTTGATTCTGTAAGACCTCTGGGCATAATTTT
64 AGTCGATTCTGTAAGACCTCCGGGCATGATTTT
5125677 GATTCACGGT
Statistics
Matches: 344, Mismatches: 46, Indels: 37
0.81 0.11 0.09
Matches are distributed among these distances:
94 1 0.00
95 67 0.19
96 3 0.01
97 2 0.01
98 7 0.02
100 1 0.00
102 2 0.01
103 2 0.01
105 1 0.00
106 3 0.01
107 5 0.01
108 98 0.28
109 126 0.37
110 26 0.08
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (109 bp):
CATAATTTTGATTCACGATATTATCCCGATCGATTCTTTATCTTTCGACTACGATGTTATCTCAG
TCGATTCTGTAAGACCTCCGGGCATGATTTTTAAGACCTTCAGA
Found at i:5125492 original size:22 final size:22
Alignment explanation
Indices: 5125450--5125492 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5125440 GTCGATTCTG
* *
5125450 TAAGACCTCCGGGCATGATTTC
1 TAAGACCTCCGGACATAATTTC
*
5125472 TAAGACCTTCGGACATAATTT
1 TAAGACCTCCGGACATAATTT
5125493 TGATTCGTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (22 bp):
TAAGACCTCCGGACATAATTTC
Found at i:5125572 original size:22 final size:22
Alignment explanation
Indices: 5125536--5125588 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
5125526 TTAATTATGG
* *
5125536 ATGATTCTGTAAGACCTCCAGGC
1 ATGATT-TTTAAGACCTCCAAGC
5125559 ATGATTTTTAAGACCTCCAAGC
1 ATGATTTTTAAGACCTCCAAGC
*
5125581 ATAATTTT
1 ATGATTTT
5125589 GATTCACGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 21 0.78
23 6 0.22
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (22 bp):
ATGATTTTTAAGACCTCCAAGC
Found at i:5125762 original size:22 final size:22
Alignment explanation
Indices: 5125737--5125779 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5125727 ATCTCGATCA
*
5125737 ATTTTTAAGACCTCCGGGCATG
1 ATTTTTAAGACCTCCGAGCATG
5125759 ATTTTTAAGACCTCCGAGCAT
1 ATTTTTAAGACCTCCGAGCAT
5125780 AAATTTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.33
Consensus pattern (22 bp):
ATTTTTAAGACCTCCGAGCATG
Found at i:5125877 original size:22 final size:23
Alignment explanation
Indices: 5125845--5125892 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
5125835 ATCTTGATCA
5125845 ATTCTGTAAGACCTCC-GAGCATG
1 ATTCTGTAAGACCTCCAGA-CATG
5125868 ATTCT-TAAGACCTCCAGACATG
1 ATTCTGTAAGACCTCCAGACATG
5125890 ATT
1 ATT
5125893 TCTAAGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (23 bp):
ATTCTGTAAGACCTCCAGACATG
Found at i:5126535 original size:14 final size:14
Alignment explanation
Indices: 5126495--5126527 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5126485 ACCCATACCC
*
5126495 AAATAGAAACACAA
1 AAATAGAAACAAAA
5126509 AAATAGAAACAAAA
1 AAATAGAAACAAAA
5126523 AAATA
1 AAATA
5126528 AAGACAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.76, C:0.09, G:0.06, T:0.09
Consensus pattern (14 bp):
AAATAGAAACAAAA
Found at i:5127642 original size:17 final size:16
Alignment explanation
Indices: 5127618--5127695 Score: 95
Period size: 16 Copynumber: 4.9 Consensus size: 16
5127608 CTAGGTTTCT
*
5127618 AAAACCCCTAAAATTC
1 AAAACCCCTAAAATCC
5127634 AAAATCCCCTAAAATCC
1 AAAA-CCCCTAAAATCC
*
5127651 AAAA-TCCTAAAATCC
1 AAAACCCCTAAAATCC
* *
5127666 GAAACCCTTAAAATCC
1 AAAACCCCTAAAATCC
*
5127682 AAAACCCTTAAAAT
1 AAAACCCCTAAAAT
5127696 TCGAATCTTC
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
15 13 0.24
16 26 0.48
17 15 0.28
ACGTcount: A:0.50, C:0.29, G:0.01, T:0.19
Consensus pattern (16 bp):
AAAACCCCTAAAATCC
Found at i:5127681 original size:31 final size:32
Alignment explanation
Indices: 5127618--5127700 Score: 105
Period size: 32 Copynumber: 2.6 Consensus size: 32
5127608 CTAGGTTTCT
*
5127618 AAAACCCCTAAAATTCAAAATCCCCTAAAATCC
1 AAAA-CCCTAAAATTCGAAATCCCCTAAAATCC
* * *
5127651 AAAATCCTAAAATCCGAAA-CCCTTAAAATCC
1 AAAACCCTAAAATTCGAAATCCCCTAAAATCC
5127682 AAAACCCTTAAAATTCGAA
1 AAAACCC-TAAAATTCGAA
5127701 TCTTCAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
31 17 0.40
32 22 0.51
33 4 0.09
ACGTcount: A:0.49, C:0.29, G:0.02, T:0.19
Consensus pattern (32 bp):
AAAACCCTAAAATTCGAAATCCCCTAAAATCC
Found at i:5128176 original size:19 final size:20
Alignment explanation
Indices: 5128137--5128175 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5128127 TATTGTATAA
*
5128137 TAAAAAAGAATAATACTTTT
1 TAAAAAAGAATAAAACTTTT
5128157 TAAAAAA-AATAAAA-TTTT
1 TAAAAAAGAATAAAACTTTT
5128175 T
1 T
5128176 TGTGATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 6 0.33
20 7 0.39
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (20 bp):
TAAAAAAGAATAAAACTTTT
Found at i:5129291 original size:9 final size:9
Alignment explanation
Indices: 5129277--5129303 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
5129267 ATACTCCACT
5129277 GTTTAAATC
1 GTTTAAATC
5129286 GTTTAAATC
1 GTTTAAATC
5129295 GTTTAAATC
1 GTTTAAATC
5129304 ATTGAGGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (9 bp):
GTTTAAATC
Found at i:5142401 original size:6 final size:6
Alignment explanation
Indices: 5142387--5142427 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
5142377 TAAAATAAAT
*
5142387 AAATCA AAATTAA AAATTAA AAATTA AAATTA AAATTA AAA
1 AAATTA AAATT-A AAATT-A AAATTA AAATTA AAATTA AAA
5142428 AATAAAAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
6 20 0.61
7 13 0.39
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (6 bp):
AAATTA
Found at i:5142402 original size:26 final size:27
Alignment explanation
Indices: 5142373--5142435 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
5142363 AAAAAGGGTC
5142373 AAAATAAAATAAAT-AAATCAAAATT-A
1 AAAATAAAA-AAATAAAATCAAAATTAA
* * *
5142399 AAAATTAAAAATTAAAATTAAAATTAA
1 AAAATAAAAAAATAAAATCAAAATTAA
5142426 AAAATAAAAA
1 AAAATAAAAA
5142436 CCTGCGATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 3 0.10
26 18 0.58
27 10 0.32
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (27 bp):
AAAATAAAAAAATAAAATCAAAATTAA
Found at i:5142404 original size:7 final size:7
Alignment explanation
Indices: 5142392--5142435 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
5142382 TAAATAAATC
5142392 AAAATTA
1 AAAATTA
5142399 AAAATTA
1 AAAATTA
5142406 AAAATT-
1 AAAATTA
5142412 AAAATT-
1 AAAATTA
5142418 AAAATTA
1 AAAATTA
*
5142425 AAAAATA
1 AAAATTA
5142432 AAAA
1 AAAA
5142436 CCTGCGATTG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
6 12 0.34
7 23 0.66
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (7 bp):
AAAATTA
Found at i:5142435 original size:20 final size:20
Alignment explanation
Indices: 5142373--5142435 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
5142363 AAAAAGGGTC
*
5142373 AAAA-TAAAA-TAAATAAATC
1 AAAATTAAAATTAAA-AAATA
*
5142392 AAAATTAAAAATT-AAAAATT
1 AAAATT-AAAATTAAAAAATA
5142412 AAAATTAAAATTAAAAAATA
1 AAAATTAAAATTAAAAAATA
5142432 AAAA
1 AAAA
5142436 CCTGCGATTG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
19 10 0.26
20 21 0.55
21 6 0.16
22 1 0.03
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAATTAAAATTAAAAAATA
Found at i:5142748 original size:12 final size:12
Alignment explanation
Indices: 5142731--5142760 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
5142721 CTATCGAATT
5142731 TTGGAAATCTCA
1 TTGGAAATCTCA
5142743 TTGG-AATCTCA
1 TTGGAAATCTCA
5142754 TTGGAAA
1 TTGGAAA
5142761 CATCAATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (12 bp):
TTGGAAATCTCA
Found at i:5146038 original size:9 final size:9
Alignment explanation
Indices: 5146013--5146076 Score: 76
Period size: 9 Copynumber: 6.9 Consensus size: 9
5146003 CTTTCCACAT
5146013 ATTTTTTTC
1 ATTTTTTTC
*
5146022 TTTCTTTTTC
1 ATT-TTTTTC
5146032 ATTTTTTTTTC
1 A--TTTTTTTC
5146043 A-TTTTTTC
1 ATTTTTTTC
5146051 ATTTTTTTC
1 ATTTTTTTC
*
5146060 ATTTTTTTA
1 ATTTTTTTC
5146069 ATTTTTTT
1 ATTTTTTT
5146077 TTCTTTCATA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
8 8 0.17
9 25 0.52
10 6 0.12
11 7 0.15
12 2 0.04
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (9 bp):
ATTTTTTTC
Found at i:5146047 original size:8 final size:8
Alignment explanation
Indices: 5146036--5146098 Score: 58
Period size: 8 Copynumber: 7.8 Consensus size: 8
5146026 TTTTTCATTT
5146036 TTTTTTCA
1 TTTTTTCA
5146044 TTTTTTCA
1 TTTTTTCA
5146052 TTTTTTTCA
1 -TTTTTTCA
*
5146061 TTTTTTTAA
1 -TTTTTTCA
5146070 TTTTTT--
1 TTTTTTCA
5146076 TTTCTTTCA
1 TTT-TTTCA
* *
5146085 TATTTCCA
1 TTTTTTCA
5146093 TTTTTT
1 TTTTTT
5146099 GAGAAATTGA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
6 3 0.07
7 3 0.07
8 22 0.48
9 18 0.39
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTTCA
Found at i:5146077 original size:19 final size:19
Alignment explanation
Indices: 5146014--5146077 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
5146004 TTTCCACATA
* *
5146014 TTTTTTTCTTTCTTTTTCATT
1 TTTTTTTCATT-TTTTT-AAT
*
5146035 TTTTTTTCA-TTTTTTCA-
1 TTTTTTTCATTTTTTTAAT
5146052 TTTTTTTCATTTTTTTAAT
1 TTTTTTTCATTTTTTTAAT
5146071 TTTTTTT
1 TTTTTTT
5146078 TCTTTCATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
17 9 0.24
18 7 0.19
19 12 0.32
20 1 0.03
21 8 0.22
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTTTCATTTTTTTAAT
Found at i:5148851 original size:12 final size:12
Alignment explanation
Indices: 5148834--5148859 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5148824 TATCTTACCT
5148834 AAATCTTAATCA
1 AAATCTTAATCA
5148846 AAATCTTAATCA
1 AAATCTTAATCA
5148858 AA
1 AA
5148860 GATTATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (12 bp):
AAATCTTAATCA
Found at i:5148896 original size:23 final size:23
Alignment explanation
Indices: 5148870--5148936 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
5148860 GATTATTTTT
*
5148870 ATCATACAAATAATGTAAAATAA
1 ATCATACAAATCATGTAAAATAA
* **
5148893 ATCATGCAAATCATACCAAAATAA
1 ATCATACAAATCAT-GTAAAATAA
5148917 AT-ATACAAATCATGTCAAAA
1 ATCATACAAATCATGT-AAAA
5148937 ATCATGCAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
23 26 0.74
24 9 0.26
ACGTcount: A:0.57, C:0.15, G:0.04, T:0.24
Consensus pattern (23 bp):
ATCATACAAATCATGTAAAATAA
Found at i:5154998 original size:59 final size:58
Alignment explanation
Indices: 5154897--5155110 Score: 184
Period size: 61 Copynumber: 3.6 Consensus size: 58
5154887 AAACAAAATT
* * * *
5154897 ACCTTTCAATATTTTGGTAAGACTTTA-TTTTA-TTAAATAATTTATTTTAAAAATCTGA
1 ACCTCTCAATATGTTGGTAA-AATTCATTTTTATTTAAA-AATTTATTTTAAAAATCTGA
* *
5154955 ACCTTTCAATATGTTGGTAAAATTCAATTTTTATTTAAAAATTTATTTTTTAGAAA-CTTGA
1 ACCTCTCAATATGTTGGTAAAATTC-ATTTTTATTTAAAAATTTA--TTTTAAAAATC-TGA
* * * * * * *
5155016 ACCTCACAATATGTTGATAAGATTCATTTTATTTTTAAAAAATTATTTTAAAAATTTTAA
1 ACCTCTCAATATGTTGGTAAAATTCATTTT-TATTTAAAAATTTATTTTAAAAA-TCTGA
* *
5155076 ACC-CTCTAATATGTTAGTAAATTTCATTTTTATTT
1 ACCTCTC-AATATGTTGGTAAAATTCATTTTTATTT
5155111 GTTTAAAAAT
Statistics
Matches: 127, Mismatches: 19, Indels: 19
0.77 0.12 0.12
Matches are distributed among these distances:
57 3 0.02
58 20 0.16
59 25 0.20
60 35 0.28
61 44 0.35
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.48
Consensus pattern (58 bp):
ACCTCTCAATATGTTGGTAAAATTCATTTTTATTTAAAAATTTATTTTAAAAATCTGA
Found at i:5155140 original size:21 final size:20
Alignment explanation
Indices: 5155101--5155139 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
5155091 AGTAAATTTC
5155101 ATTTTTATTTGTTTAAAAAT
1 ATTTTTATTTGTTTAAAAAT
5155121 ATTTTTATTT-TTTCAAAAA
1 ATTTTTATTTGTTT-AAAAA
5155140 AAATATTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (20 bp):
ATTTTTATTTGTTTAAAAAT
Found at i:5156814 original size:8 final size:7
Alignment explanation
Indices: 5156796--5156829 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
5156786 TAATATGATA
5156796 GAAAAAT
1 GAAAAAT
5156803 GAAAAAT
1 GAAAAAT
*
5156810 GGAAAAT
1 GAAAAAT
*
5156817 AAAAAAT
1 GAAAAAT
5156824 GAAAAA
1 GAAAAA
5156830 AAGAATGGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (7 bp):
GAAAAAT
Found at i:5164375 original size:23 final size:23
Alignment explanation
Indices: 5164345--5164391 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
5164335 AAAGCAAGTA
5164345 AAAATAAGGCCACAAAATCAAAC
1 AAAATAAGGCCACAAAATCAAAC
*
5164368 AAAATAAGGCCACAGAATCAAAC
1 AAAATAAGGCCACAAAATCAAAC
5164391 A
1 A
5164392 TAGGAAAGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.60, C:0.21, G:0.11, T:0.09
Consensus pattern (23 bp):
AAAATAAGGCCACAAAATCAAAC
Found at i:5169634 original size:12 final size:12
Alignment explanation
Indices: 5169617--5169654 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
5169607 AGATAAAATG
*
5169617 TATATATATATA
1 TATATATGTATA
5169629 TATATATGTATA
1 TATATATGTATA
*
5169641 TGTATATGTATA
1 TATATATGTATA
5169653 TA
1 TA
5169655 CTAATAAGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATATATGTATA
Found at i:5173457 original size:19 final size:20
Alignment explanation
Indices: 5173430--5173468 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5173420 TCGATGAATT
*
5173430 TTTCAATGA-GATTTTCAGA
1 TTTCAATGAGGAATTTCAGA
*
5173449 TTTCGATGAGGAATTTCAGA
1 TTTCAATGAGGAATTTCAGA
5173469 ACACAACGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (20 bp):
TTTCAATGAGGAATTTCAGA
Found at i:5173848 original size:27 final size:28
Alignment explanation
Indices: 5173811--5173866 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 28
5173801 ATTTTTTTAA
*
5173811 TTTGTTTTATGGTT-TTA-TTTATTTATT
1 TTTGTTATAT-GTTATTATTTTATTTATT
5173838 TTTGTTATATGTTATTATTTTATTTATT
1 TTTGTTATATGTTATTATTTTATTTATT
5173866 T
1 T
5173867 ATATGTTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 3 0.12
27 12 0.46
28 11 0.42
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.73
Consensus pattern (28 bp):
TTTGTTATATGTTATTATTTTATTTATT
Found at i:5175769 original size:18 final size:17
Alignment explanation
Indices: 5175739--5175772 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
5175729 TTTTTTAAAA
5175739 TTTTATATTATATTTAT
1 TTTTATATTATATTTAT
5175756 TTTTATATTTATATTTA
1 TTTTATA-TTATATTTA
5175773 ATGAGTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTATATTATATTTAT
Found at i:5175772 original size:12 final size:12
Alignment explanation
Indices: 5175740--5175772 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5175730 TTTTTAAAAT
5175740 TTTATA-TTATA
1 TTTATATTTATA
*
5175751 TTTATTTTTATA
1 TTTATATTTATA
5175763 TTTATATTTA
1 TTTATATTTA
5175773 ATGAGTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTATATTTATA
Found at i:5177140 original size:12 final size:12
Alignment explanation
Indices: 5177103--5177145 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
5177093 ATATTATTTT
5177103 AAATATAAATATA
1 AAAT-TAAATATA
*
5177116 AAA--ATATATA
1 AAATTAAATATA
5177126 AAATTAAATATA
1 AAATTAAATATA
5177138 AAATTAAA
1 AAATTAAA
5177146 AAATAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 9 0.35
12 14 0.54
13 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATTAAATATA
Found at i:5180091 original size:31 final size:30
Alignment explanation
Indices: 5180056--5180136 Score: 74
Period size: 30 Copynumber: 2.7 Consensus size: 30
5180046 TGATTTAGGG
*
5180056 TTTTGGCTTTGAGGGTTTT-AAGATTTTTGGA
1 TTTTGGATTTGAGGGTTTTGAA-A-TTTTGGA
* * *
5180087 TTTTGGATTTTAGAGTTTTGAAATTTTGGG
1 TTTTGGATTTGAGGGTTTTGAAATTTTGGA
* * *
5180117 TTTAGGTTTTGAAGGTTTTG
1 TTTTGGATTTGAGGGTTTTG
5180137 GGGATTGGAT
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
30 21 0.52
31 17 0.43
32 2 0.05
ACGTcount: A:0.17, C:0.01, G:0.28, T:0.53
Consensus pattern (30 bp):
TTTTGGATTTGAGGGTTTTGAAATTTTGGA
Found at i:5180097 original size:23 final size:23
Alignment explanation
Indices: 5180086--5180129 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
5180076 AGATTTTTGG
5180086 ATTTTGGATTTTAGAGTTTTGAA
1 ATTTTGGATTTTAGAGTTTTGAA
*
5180109 ATTTTGG-GTTTAG-GTTTTGAA
1 ATTTTGGATTTTAGAGTTTTGAA
5180130 GGTTTTGGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 5 0.25
23 7 0.35
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.52
Consensus pattern (23 bp):
ATTTTGGATTTTAGAGTTTTGAA
Found at i:5180120 original size:22 final size:22
Alignment explanation
Indices: 5180085--5180138 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
5180075 AAGATTTTTG
*
5180085 GATTTTGGATTTTAGAGTTTTGAA
1 GATTTTGG-GTTTAG-GTTTTGAA
5180109 -ATTTTGGGTTTAGGTTTTGAA
1 GATTTTGGGTTTAGGTTTTGAA
*
5180130 GGTTTTGGG
1 GATTTTGGG
5180139 GATTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 8 0.30
22 12 0.44
23 7 0.26
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (22 bp):
GATTTTGGGTTTAGGTTTTGAA
Found at i:5180159 original size:44 final size:43
Alignment explanation
Indices: 5180109--5180208 Score: 103
Period size: 44 Copynumber: 2.3 Consensus size: 43
5180099 GAGTTTTGAA
* * *
5180109 ATTTTGGGTTTA-GGTTTTGAAGGTTTTGGGGATTGGATTTTAGG
1 ATTTTGGATTTAGGGTTTGGAA-GTTTT-GAGATTGGATTTTAGG
* * *
5180153 GTTTTGGATTTAAGGGTTTGGAAGTTTTGAGTTTTGATTTTAGG
1 ATTTTGGATTT-AGGGTTTGGAAGTTTTGAGATTGGATTTTAGG
*
5180197 ATTTTGGTTTTA
1 ATTTTGGATTTA
5180209 AAGTTTAGAG
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
43 1 0.02
44 31 0.67
45 6 0.13
46 8 0.17
ACGTcount: A:0.17, C:0.00, G:0.32, T:0.51
Consensus pattern (43 bp):
ATTTTGGATTTAGGGTTTGGAAGTTTTGAGATTGGATTTTAGG
Found at i:5180161 original size:15 final size:15
Alignment explanation
Indices: 5180141--5180208 Score: 63
Period size: 15 Copynumber: 4.7 Consensus size: 15
5180131 GTTTTGGGGA
5180141 TTGGATTTTAGGGTT
1 TTGGATTTTAGGGTT
*
5180156 TTGGATTTAAGGG-T
1 TTGGATTTTAGGGTT
*
5180170 TTGGAAGTTTT-GAGTT
1 TTGG-A-TTTTAGGGTT
*
5180186 TT-GATTTTAGGATT
1 TTGGATTTTAGGGTT
5180200 TTGG-TTTTA
1 TTGGATTTTA
5180209 AAGTTTAGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
13 4 0.09
14 16 0.37
15 17 0.40
16 6 0.14
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.53
Consensus pattern (15 bp):
TTGGATTTTAGGGTT
Found at i:5180780 original size:24 final size:20
Alignment explanation
Indices: 5180739--5180789 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
5180729 TTATTACTCA
5180739 TTATTTATTACTTTTTTTGT
1 TTATTTATTACTTTTTTTGT
*
5180759 TTATTTATTTAGCTTTTATT-T
1 TTATTTA-TTA-CTTTTTTTGT
*
5180780 TTATTAATTA
1 TTATTTATTA
5180790 TTATTATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 10 0.37
21 10 0.37
22 7 0.26
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.71
Consensus pattern (20 bp):
TTATTTATTACTTTTTTTGT
Found at i:5180854 original size:24 final size:24
Alignment explanation
Indices: 5180827--5180873 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5180817 AACAAATTTA
*
5180827 AAAATTTAAACAAG-CATAAATAAC
1 AAAACTTAAA-AAGACATAAATAAC
*
5180851 AAAACTTAAAATGACATAAATAA
1 AAAACTTAAAAAGACATAAATAA
5180874 TATATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.64, C:0.11, G:0.04, T:0.21
Consensus pattern (24 bp):
AAAACTTAAAAAGACATAAATAAC
Found at i:5180916 original size:21 final size:22
Alignment explanation
Indices: 5180883--5180929 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
5180873 ATATATAAAT
5180883 AAAATAAATAAAAGC-AAATCCA
1 AAAATAAATAAAA-CAAAATCCA
*
5180905 AAAATTAA-AAAACAAAATCCA
1 AAAATAAATAAAACAAAATCCA
5180926 AAAA
1 AAAA
5180930 AAAAAATACC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 1 0.04
21 15 0.65
22 7 0.30
ACGTcount: A:0.72, C:0.13, G:0.02, T:0.13
Consensus pattern (22 bp):
AAAATAAATAAAACAAAATCCA
Found at i:5183934 original size:22 final size:21
Alignment explanation
Indices: 5183909--5183949 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5183899 TAATTTTCTT
*
5183909 TTAACAGAAAAAGAGGGAAAAG
1 TTAACA-AAAAAAAGGGAAAAG
*
5183931 TTAATAAAAAAAAGGGAAA
1 TTAACAAAAAAAAGGGAAA
5183950 CAAGACCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.63, C:0.02, G:0.22, T:0.12
Consensus pattern (21 bp):
TTAACAAAAAAAAGGGAAAAG
Found at i:5185663 original size:2 final size:2
Alignment explanation
Indices: 5185656--5185680 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5185646 ATGATAGTAT
5185656 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5185681 GCAAAGGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5187873 original size:2 final size:2
Alignment explanation
Indices: 5187815--5187860 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
5187805 TCAAGATTCA
*
5187815 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5187857 AT AT
1 AT AT
5187861 GTGTGTGTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5192363 original size:13 final size:13
Alignment explanation
Indices: 5192345--5192386 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
5192335 AATCTTTTTA
5192345 TTAAATTAATATT
1 TTAAATTAATATT
* *
5192358 TTAAATTAAAATA
1 TTAAATTAATATT
5192371 TTAAA-TAATAATT
1 TTAAATTAAT-ATT
5192384 TTA
1 TTA
5192387 TTAATATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 3 0.12
13 21 0.88
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAAATTAATATT
Found at i:5192391 original size:37 final size:38
Alignment explanation
Indices: 5192349--5192425 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 38
5192339 TTTTTATTAA
** *
5192349 ATTAATATTTTAAAT-TAAAATATTAAATAATA-ATTTT
1 ATTAATATAATAAATAT-AAATATAAAATAATATATTTT
*
5192386 ATTAATATAATATATATAAATATAAAATAATATATTTT
1 ATTAATATAATAAATATAAATATAAAATAATATATTTT
5192424 AT
1 AT
5192426 ATTTTATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 26 0.76
38 8 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (38 bp):
ATTAATATAATAAATATAAATATAAAATAATATATTTT
Found at i:5192407 original size:15 final size:15
Alignment explanation
Indices: 5192346--5192410 Score: 50
Period size: 15 Copynumber: 4.6 Consensus size: 15
5192336 ATCTTTTTAT
*
5192346 TAAAT-TAATAT-TT
1 TAAATATAATATATA
*
5192359 TAAAT-TAAAATAT-
1 TAAATATAATATATA
*
5192372 TAAATAATAAT-TTTA
1 TAAAT-ATAATATATA
*
5192387 TTAATATAATATATA
1 TAAATATAATATATA
5192402 TAAATATAA
1 TAAATATAA
5192411 AATAATATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
13 15 0.37
14 8 0.20
15 18 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAATATAATATATA
Found at i:5192434 original size:34 final size:34
Alignment explanation
Indices: 5192353--5192435 Score: 87
Period size: 37 Copynumber: 2.4 Consensus size: 34
5192343 TATTAAATTA
* *
5192353 ATATTTTAAAT-TAAAATATTAAATAATAATTTT
1 ATATTTTATATATAAAATATAAAATAATAATTTT
* *
5192386 ATTAATATAATATATATAAATATAAAATAATATATTTT
1 A-T-ATTTTATATATA-AAATATAAAATAATA-ATTTT
5192424 ATATTTTATATA
1 ATATTTTATATA
5192436 CACCTCAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
33 1 0.03
34 1 0.03
35 6 0.15
36 10 0.26
37 15 0.38
38 6 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (34 bp):
ATATTTTATATATAAAATATAAAATAATAATTTT
Found at i:5194541 original size:6 final size:6
Alignment explanation
Indices: 5194530--5194559 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
5194520 TATTTTACGT
5194530 CAAGGG CAAGGG CAAGGG CAAGGG CAAGGG
1 CAAGGG CAAGGG CAAGGG CAAGGG CAAGGG
5194560 AGGGCAGCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.50, T:0.00
Consensus pattern (6 bp):
CAAGGG
Found at i:5196195 original size:2 final size:2
Alignment explanation
Indices: 5196188--5196231 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
5196178 ACTTTAATTA
5196188 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5196230 CT
1 CT
5196232 TCAATCAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5198188 original size:7 final size:7
Alignment explanation
Indices: 5198176--5198202 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
5198166 CAGTGCAGTT
5198176 TGCTGAC
1 TGCTGAC
5198183 TGCTGAC
1 TGCTGAC
5198190 TGCTGAC
1 TGCTGAC
5198197 TGCTGA
1 TGCTGA
5198203 GGAAAGGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.26, G:0.30, T:0.30
Consensus pattern (7 bp):
TGCTGAC
Found at i:5199258 original size:18 final size:18
Alignment explanation
Indices: 5199228--5199264 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
5199218 TTGCTACCAC
5199228 AAAAATTACAAGACAAAAA
1 AAAAATTACAAGA-AAAAA
5199247 AAAAATTA-AAGAAAAAA
1 AAAAATTACAAGAAAAAA
5199264 A
1 A
5199265 CGATCATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 4 0.22
19 8 0.44
ACGTcount: A:0.78, C:0.05, G:0.05, T:0.11
Consensus pattern (18 bp):
AAAAATTACAAGAAAAAA
Found at i:5202988 original size:17 final size:18
Alignment explanation
Indices: 5202955--5202988 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5202945 TGTTTCTAAT
*
5202955 TTCTTTGATCATTATAGA
1 TTCTTTGATCATCATAGA
5202973 TTCTTT-ATCATCATAG
1 TTCTTTGATCATCATAG
5202989 GGAGGGAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (18 bp):
TTCTTTGATCATCATAGA
Found at i:5204331 original size:2 final size:2
Alignment explanation
Indices: 5204319--5204350 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5204309 TTCTAGTAGT
*
5204319 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5204351 GAAAGTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5205084 original size:10 final size:10
Alignment explanation
Indices: 5205069--5205098 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
5205059 ATCGAGCTTT
5205069 TATATTTTAA
1 TATATTTTAA
5205079 TATATTTTAA
1 TATATTTTAA
5205089 T-TATTTTAA
1 TATATTTTAA
5205098 T
1 T
5205099 TAATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:5205095 original size:9 final size:9
Alignment explanation
Indices: 5205071--5205100 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
5205061 CGAGCTTTTA
5205071 TATTTTAAT
1 TATTTTAAT
5205080 ATATTTTAAT
1 -TATTTTAAT
5205090 TATTTTAAT
1 TATTTTAAT
5205099 TA
1 TA
5205101 ATAAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTTTAAT
Found at i:5214342 original size:15 final size:15
Alignment explanation
Indices: 5214318--5214347 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5214308 ACAAATATGC
5214318 CCTGAATACTCTCAA
1 CCTGAATACTCTCAA
*
5214333 CCTGAGTACTCTCAA
1 CCTGAATACTCTCAA
5214348 GGCTATCATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.33, G:0.10, T:0.27
Consensus pattern (15 bp):
CCTGAATACTCTCAA
Found at i:5224794 original size:2 final size:2
Alignment explanation
Indices: 5224787--5224817 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5224777 GTGGATCTTC
5224787 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5224818 TATTTGTTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5226473 original size:29 final size:28
Alignment explanation
Indices: 5226398--5226486 Score: 117
Period size: 29 Copynumber: 3.1 Consensus size: 28
5226388 CTTTCGTTTG
*
5226398 AATATAATAACTTATTTAAATACAAATCAA
1 AATATAAAAACTTATTTAAATA-AAAT-AA
* *
5226428 AAGATAAAAACTTATTTAAATATAATAA
1 AATATAAAAACTTATTTAAATAAAATAA
5226456 ATATATAAAAACTTATTTAAA-AAAATAA
1 A-ATATAAAAACTTATTTAAATAAAATAA
5226484 AAT
1 AAT
5226487 TATTCAAAGG
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
27 2 0.04
28 10 0.19
29 21 0.40
30 20 0.38
ACGTcount: A:0.61, C:0.06, G:0.01, T:0.33
Consensus pattern (28 bp):
AATATAAAAACTTATTTAAATAAAATAA
Found at i:5227549 original size:2 final size:2
Alignment explanation
Indices: 5227542--5227577 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5227532 AATATGGAAT
5227542 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5227578 GGAACCTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5229355 original size:19 final size:18
Alignment explanation
Indices: 5229309--5229355 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
5229299 TATCTGGCAA
5229309 TTTTGTTCTTG-TTTTTAT
1 TTTTGTT-TTGCTTTTTAT
*
5229327 TTTTGTTTTGCTTTTTTT
1 TTTTGTTTTGCTTTTTAT
5229345 TTTTGTCTTTG
1 TTTTGT-TTTG
5229356 TGCCACCACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 3 0.12
18 19 0.73
19 4 0.15
ACGTcount: A:0.02, C:0.06, G:0.13, T:0.79
Consensus pattern (18 bp):
TTTTGTTTTGCTTTTTAT
Found at i:5229534 original size:7 final size:7
Alignment explanation
Indices: 5229508--5229575 Score: 57
Period size: 7 Copynumber: 9.1 Consensus size: 7
5229498 CAAATTAAAT
5229508 AAATT-A
1 AAATTAA
*
5229514 AAATATAT
1 AAAT-TAA
5229522 AAATTAA
1 AAATTAA
5229529 AAATTAA
1 AAATTAA
5229536 AAATTAAA
1 AAATT-AA
5229544 AAATTAA
1 AAATTAA
**
5229551 ACTTTTAAAA
1 A-AATT--AA
5229561 AAATTAA
1 AAATTAA
5229568 AAATTAA
1 AAATTAA
5229575 A
1 A
5229576 CTTAAAAACA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
6 4 0.08
7 28 0.56
8 13 0.26
9 2 0.04
10 3 0.06
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (7 bp):
AAATTAA
Found at i:5238160 original size:18 final size:18
Alignment explanation
Indices: 5238133--5238168 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5238123 GATCTTTTAA
5238133 AAAATATATAGAAAATTT
1 AAAATATATAGAAAATTT
*
5238151 AAAATGTATAGAAAATTT
1 AAAATATATAGAAAATTT
5238169 TTGGTCGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (18 bp):
AAAATATATAGAAAATTT
Found at i:5238558 original size:24 final size:26
Alignment explanation
Indices: 5238495--5238565 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 26
5238485 AAAATATAAA
*
5238495 TTATATTTTTAAATTTATATATAATTT
1 TTATATTTTTAAA-TTATATACAATTT
*
5238522 TTATTAAAATTTTAAATTATAT-CAA-TT
1 TTA-T--ATTTTTAAATTATATACAATTT
*
5238549 TTATATTTTTATATTAT
1 TTATATTTTTAAATTAT
5238566 TTTAACATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
24 11 0.30
26 1 0.03
27 8 0.22
28 3 0.08
29 6 0.16
30 8 0.22
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (26 bp):
TTATATTTTTAAATTATATACAATTT
Found at i:5258305 original size:30 final size:30
Alignment explanation
Indices: 5258265--5258324 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
5258255 CAACAACCCT
* *
5258265 GAAGTACAATTTATAGTCATATCAATAAAC
1 GAAGTACAATTTAAAGTCATATCAAGAAAC
*
5258295 GAAGTGCAATTTAAAGTCATATCAAGAAAC
1 GAAGTACAATTTAAAGTCATATCAAGAAAC
5258325 CAATCTTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (30 bp):
GAAGTACAATTTAAAGTCATATCAAGAAAC
Found at i:5261185 original size:5 final size:5
Alignment explanation
Indices: 5261172--5261209 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
5261162 TTTGGAAGCT
* *
5261172 TTTTT TTTTC TTTTT TTTTC TTTTC TTTTC -TTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
5261210 ATCTCTCTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (5 bp):
TTTTC
Found at i:5261187 original size:10 final size:10
Alignment explanation
Indices: 5261172--5261209 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
5261162 TTTGGAAGCT
5261172 TTTTTTTTTC
1 TTTTTTTTTC
5261182 TTTTTTTTTC
1 TTTTTTTTTC
*
5261192 TTTTCTTTTC
1 TTTTTTTTTC
5261202 TTTCTTTT
1 TTT-TTTT
5261210 ATCTCTCTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 22 0.88
11 3 0.12
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:5265844 original size:28 final size:28
Alignment explanation
Indices: 5265781--5265854 Score: 67
Period size: 28 Copynumber: 2.6 Consensus size: 28
5265771 AAATTTTCAT
* * * * * *
5265781 TAAAATTTTCTTTCAATCATAATTATAT
1 TAAATTTTTTTTTTAATTATAATTACAA
*
5265809 TAACTTTTTTTTTTAATTATAATTACAA
1 TAAATTTTTTTTTTAATTATAATTACAA
* *
5265837 TAAATTTTATTATTAATT
1 TAAATTTTTTTTTTAATT
5265855 TCAATCTCAT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (28 bp):
TAAATTTTTTTTTTAATTATAATTACAA
Found at i:5273467 original size:19 final size:19
Alignment explanation
Indices: 5273439--5273477 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
5273429 TGTACAGAGC
*
5273439 TTATTGCAGTCATAATCAT
1 TTATTACAGTCATAATCAT
* *
5273458 TTATTACAGTTATACTCAT
1 TTATTACAGTCATAATCAT
5273477 T
1 T
5273478 AGTACCTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (19 bp):
TTATTACAGTCATAATCAT
Found at i:5280785 original size:22 final size:24
Alignment explanation
Indices: 5280755--5280806 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
5280745 TTCTATGTTC
* *
5280755 AATTTATATAT-AAAAAAT-ATAT
1 AATTAATATATCAAAAAATAATAA
*
5280777 AATTAATATATCAAATAATAATAA
1 AATTAATATATCAAAAAATAATAA
5280801 AATTAA
1 AATTAA
5280807 AGTTTATGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 10 0.40
23 6 0.24
24 9 0.36
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
AATTAATATATCAAAAAATAATAA
Found at i:5281230 original size:27 final size:27
Alignment explanation
Indices: 5281177--5281230 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
5281167 TAAAATTGAA
* * *
5281177 TTAATCAAATTATATTTATTTTATTTT
1 TTAATCAAATTAAAATTATTTAATTTT
5281204 TTAATCAAATTAAAATT-TTTAATTTT
1 TTAATCAAATTAAAATTATTTAATTTT
5281230 T
1 T
5281231 AAAATTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (27 bp):
TTAATCAAATTAAAATTATTTAATTTT
Found at i:5281238 original size:13 final size:13
Alignment explanation
Indices: 5281230--5281254 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5281220 TTTTAATTTT
5281230 TAAAATTAATTCA
1 TAAAATTAATTCA
5281243 TAAAATTAATTC
1 TAAAATTAATTC
5281255 GATCGATTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAAATTAATTCA
Found at i:5286291 original size:3 final size:3
Alignment explanation
Indices: 5286283--5286309 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5286273 GAAAATATGG
5286283 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
5286310 ATGTTGAAAG
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:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5286576 original size:2 final size:2
Alignment explanation
Indices: 5286569--5286610 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
5286559 GGGCAGTGAC
*
5286569 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG TG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5286611 GCGTTGCCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.50, T:0.02
Consensus pattern (2 bp):
AG
Found at i:5297071 original size:26 final size:27
Alignment explanation
Indices: 5297035--5297085 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
5297025 GTACCTAGGA
*
5297035 ATGTTTGCACTCGTATC-TTAAGGCCT
1 ATGTTTACACTCGTATCTTTAAGGCCT
*
5297061 ATGTTTACACTTGTATCTTTAAGGC
1 ATGTTTACACTCGTATCTTTAAGGC
5297086 TTTCTTCTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.41
Consensus pattern (27 bp):
ATGTTTACACTCGTATCTTTAAGGCCT
Found at i:5297638 original size:76 final size:75
Alignment explanation
Indices: 5297512--5297665 Score: 211
Period size: 76 Copynumber: 2.0 Consensus size: 75
5297502 CTTAGAACTA
* * *
5297512 TGGAAGCTAATCTCCATAGTAGTTATGTAGAACTGTGAGTGTATGGTTGTTGCAAGACGATGTCT
1 TGGAAGCTAATCTACATAGTACTTATGTAGAACTGGGAGTGTATGGTTGTTGCAAGAC-ATGTCT
*
5297577 -TGCATTGGTGG
65 CT-CATTGCTGG
* * * *
5297588 TGGAAGCTAATCTACATGGTACTTATTTAGAATTGGGAGTGTATGGTTGTTGTAAGACATGTCTC
1 TGGAAGCTAATCTACATAGTACTTATGTAGAACTGGGAGTGTATGGTTGTTGCAAGACATGTCTC
5297653 TCATTGCTGG
66 TCATTGCTGG
5297663 TGG
1 TGG
5297666 GTGAGTGGTG
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
75 17 0.25
76 52 0.75
ACGTcount: A:0.23, C:0.12, G:0.29, T:0.36
Consensus pattern (75 bp):
TGGAAGCTAATCTACATAGTACTTATGTAGAACTGGGAGTGTATGGTTGTTGCAAGACATGTCTC
TCATTGCTGG
Found at i:5303194 original size:21 final size:21
Alignment explanation
Indices: 5303162--5303203 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5303152 AAAATATGAC
*
5303162 ATTTTGAAGAAAGATTTTAAA
1 ATTTTGAAGAAAGATTCTAAA
*
5303183 ATTTT-AAGGAAATATTCTAAA
1 ATTTTGAA-GAAAGATTCTAAA
5303204 GCATGTAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (21 bp):
ATTTTGAAGAAAGATTCTAAA
Found at i:5304024 original size:2 final size:2
Alignment explanation
Indices: 5304017--5304056 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5304007 GTTATTTCTA
5304017 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5304057 TTTTTTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5310510 original size:148 final size:149
Alignment explanation
Indices: 5310241--5310511 Score: 352
Period size: 148 Copynumber: 1.8 Consensus size: 149
5310231 AGGGGACTCA
* *
5310241 GGTGGACTGCCTCAGCTGCAGCACACCAGCTGCCCGACTGGCCACTGGGGCCTAGCAACGTGCCT
1 GGTGGACTGCCTCAGCTGCAGCACACCA-C-GCCCGACTGGCCACAGGGGCCTAGCAACATGCCT
* *
5310306 GCCTGCTAGCCCGCGCATCCTCTCGGCTCGATGGCATCCCTCCTACATGAATACCATCGCGTGGT
64 GCCTGCTAGCCCGCGCATCCTCTCGGCTCGATGGCATCCCTCCTACATAAACACCATCGCGTGGT
5310371 CCAGTCCCGCAAGGGTCTTTG
129 CCAGTCCCGCAAGGGTCTTTG
* * * *
5310392 GGTGGACTGCCTTAGCTGCAGCCCACCA-GCCCGACTGGCCACAGGGGTCTAGCAGCATGTCC-G
1 GGTGGACTGCCTCAGCTGCAGCACACCACGCCCGACTGGCCACAGGGGCCTAGCAACATG-CCTG
* * ** *
5310455 -CTAGCTAGCCCGCGCATCC-CTTTGGCTCGATGGTATCCCTTTTACGTAAACACCATC
65 CCT-GCTAGCCCGCGCATCCTC-TCGGCTCGATGGCATCCCTCCTACATAAACACCATC
5310512 ACCTGATCCT
Statistics
Matches: 104, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
147 3 0.03
148 73 0.70
149 2 0.02
151 26 0.25
ACGTcount: A:0.17, C:0.36, G:0.26, T:0.21
Consensus pattern (149 bp):
GGTGGACTGCCTCAGCTGCAGCACACCACGCCCGACTGGCCACAGGGGCCTAGCAACATGCCTGC
CTGCTAGCCCGCGCATCCTCTCGGCTCGATGGCATCCCTCCTACATAAACACCATCGCGTGGTCC
AGTCCCGCAAGGGTCTTTG
Found at i:5318958 original size:20 final size:21
Alignment explanation
Indices: 5318919--5318965 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
5318909 ATTCAATAAA
*
5318919 ATATA-ATATAATATTTATTT
1 ATATATATATAATATTAATTT
5318939 ATATATATATAA-ATTAATTT
1 ATATATATATAATATTAATTT
5318959 ATATATA
1 ATATATA
5318966 ATTCACAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATATATATAATATTAATTT
Found at i:5323845 original size:21 final size:19
Alignment explanation
Indices: 5323820--5323865 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
5323810 TTATTCAGTG
5323820 ATATAATAATTAATTATATGA
1 ATATAATAATTAA-T-TATGA
* *
5323841 ATATAATACTTGATTATGA
1 ATATAATAATTAATTATGA
5323860 ATATAA
1 ATATAA
5323866 CTTAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 11 0.48
20 1 0.04
21 11 0.48
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (19 bp):
ATATAATAATTAATTATGA
Found at i:5324823 original size:25 final size:25
Alignment explanation
Indices: 5324768--5324824 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
5324758 ATATATATAT
* * *
5324768 AGTAAAATGAAAATAAAATAAGAAA
1 AGTAAAATCAAAACAAAACAAGAAA
*
5324793 AATAAAATCAAAACAAAACAA-AAA
1 AGTAAAATCAAAACAAAACAAGAAA
5324817 ATGTAAAA
1 A-GTAAAA
5324825 AAAAATACCT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 4 0.15
25 22 0.85
ACGTcount: A:0.74, C:0.05, G:0.07, T:0.14
Consensus pattern (25 bp):
AGTAAAATCAAAACAAAACAAGAAA
Found at i:5328213 original size:15 final size:15
Alignment explanation
Indices: 5328190--5328225 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
5328180 AGCGACGTGA
5328190 TTTTT-TTTTTTTTG
1 TTTTTGTTTTTTTTG
5328204 TTTTTGTTTTTTTTG
1 TTTTTGTTTTTTTTG
5328219 TTTTTGT
1 TTTTTGT
5328226 GATGGATGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (15 bp):
TTTTTGTTTTTTTTG
Found at i:5337443 original size:235 final size:233
Alignment explanation
Indices: 5337026--5337455 Score: 594
Period size: 234 Copynumber: 1.8 Consensus size: 233
5337016 AAAAATAACC
* * *
5337026 TATTTGCTCAACTTCTATATATCAACATGAGTTCCATTCTACTACTTTTCTCCCCTGGATTTCAC
1 TATTTGCTCAACTTCTATATATCAACATAAGTTCCATTCTACTACTTTTCTCCCCTGAAGTTCAC
* * ** **
5337091 TTTTATTGAGGAACCATTGACCACACTGGTAATGTTTGAACAGTACTGTAAGTCTTATGTTTTGA
66 TTTTATTGAGGAACCATTAACCACACTGGTAATGTTTGAACAGTACTGTAAGACACATGTACTGA
5337156 TTTTTCTTCCCTGAAAAATAAAAGTAAAATTAGTAAATGTTAATTTAGGAAATTTCAAGCAGCAA
131 TTTTTCTTCCCTGAAAAATAAAAGTAAAATTAGTAAATGTTAATTTAGGAAATTTCAAGCAGCAA
5337221 ACATAATCTCCTGCAACCAATAATGTTATTTTTAAAGA
196 ACATAATCTCCTGCAACCAATAATGTTATTTTTAAAGA
* * * * * * *
5337259 TATTTGCTCAACTTCTATTTATCAGCCTAAGTTTCATTCTACTTCTTTTTCTCCGCTGAAGTTCC
1 TATTTGCTCAACTTCTATATATCAACATAAGTTCCATTCTACTAC-TTTTCTCCCCTGAAGTTCA
* * **
5337324 CTTTTATTGAGGAACCATTAACCACGCTGGTAATGTTTGAATAGTGTTGTAA-ACACACTGCTAC
65 CTTTTATTGAGGAACCATTAACCACACTGGTAATGTTTGAACAGTACTGTAAGACACA-TG-TAC
* * * *
5337388 TGCTTTTTCTTCCCTGAAAAA-ATAAGGTAAACTTAGTAAATGTTAATTTAGGAAATTTTAAGCA
128 TGATTTTTCTTCCCTGAAAAATA-AAAGTAAAATTAGTAAATGTTAATTTAGGAAATTTCAAGCA
5337452 GCAA
192 GCAA
5337456 GCACAGTCTT
Statistics
Matches: 169, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
233 41 0.24
234 65 0.38
235 63 0.37
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (233 bp):
TATTTGCTCAACTTCTATATATCAACATAAGTTCCATTCTACTACTTTTCTCCCCTGAAGTTCAC
TTTTATTGAGGAACCATTAACCACACTGGTAATGTTTGAACAGTACTGTAAGACACATGTACTGA
TTTTTCTTCCCTGAAAAATAAAAGTAAAATTAGTAAATGTTAATTTAGGAAATTTCAAGCAGCAA
ACATAATCTCCTGCAACCAATAATGTTATTTTTAAAGA
Found at i:5341340 original size:33 final size:33
Alignment explanation
Indices: 5341298--5341364 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
5341288 CAACTAGATA
5341298 CCACTACTGCAAAGCTGTCAGAATATTTAAATT
1 CCACTACTGCAAAGCTGTCAGAATATTTAAATT
5341331 CCACTACTGCAAAGCTGTCAGAATATTTAAATT
1 CCACTACTGCAAAGCTGTCAGAATATTTAAATT
5341364 C
1 C
5341365 TGCCAGAGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (33 bp):
CCACTACTGCAAAGCTGTCAGAATATTTAAATT
Found at i:5349536 original size:24 final size:22
Alignment explanation
Indices: 5349485--5349560 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 22
5349475 AATACATTAC
* * *
5349485 TATTTATTATATAACAGTAAAATA
1 TATTTA-TATATAATAAT-AAATT
5349509 TATTTATCATATAATAATAATATT
1 TATTTAT-ATATAATAATAA-ATT
5349533 TATTTATAT-TAAATTAATAAATT
1 TATTTATATAT-AA-TAATAAATT
5349556 TATTT
1 TATTT
5349561 TAAAATTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
22 1 0.02
23 15 0.33
24 29 0.64
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (22 bp):
TATTTATATATAATAATAAATT
Found at i:5350653 original size:15 final size:17
Alignment explanation
Indices: 5350623--5350655 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
5350613 TTCAATTAAG
5350623 TTTATAATTGATTTTTA
1 TTTATAATTGATTTTTA
5350640 TTTA-AATT-ATTTTTA
1 TTTATAATTGATTTTTA
5350655 T
1 T
5350656 CTTTTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTATAATTGATTTTTA
Found at i:5351188 original size:15 final size:16
Alignment explanation
Indices: 5351170--5351199 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5351160 GAGTGCAAAT
5351170 TAAAAA-AAAAAAAAC
1 TAAAAACAAAAAAAAC
5351185 TAAAAACAAAAAAAA
1 TAAAAACAAAAAAAA
5351200 TAGCGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.87, C:0.07, G:0.00, T:0.07
Consensus pattern (16 bp):
TAAAAACAAAAAAAAC
Found at i:5352058 original size:14 final size:15
Alignment explanation
Indices: 5352029--5352060 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5352019 CAGTAGGGAT
5352029 ATAAATGAATTGAAC
1 ATAAATGAATTGAAC
5352044 ATAAATGAA-TGAAC
1 ATAAATGAATTGAAC
5352058 ATA
1 ATA
5352061 TGTTTATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.25
Consensus pattern (15 bp):
ATAAATGAATTGAAC
Found at i:5356257 original size:2 final size:2
Alignment explanation
Indices: 5356250--5356295 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
5356240 GCAAATAAAG
* * * *
5356250 TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TG TA TG TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5356292 TA TA
1 TA TA
5356296 AACAACAACA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5359578 original size:41 final size:41
Alignment explanation
Indices: 5359477--5359580 Score: 156
Period size: 41 Copynumber: 2.5 Consensus size: 41
5359467 AAATGATTTC
* *
5359477 TAAACAGAGGCTTTAAAATCTTGATTGAAATTGGTTCCTCT
1 TAAACAGAGGCTTTAAAATTTTGATTGAAATCGGTTCCTCT
*
5359518 TAAACAGAGGCTTTAAAATTTTGATTGAGAA-CGGTTTCTCT
1 TAAACAGAGGCTTTAAAATTTTGATTGA-AATCGGTTCCTCT
*
5359559 TAAACAGAGACTTTAAAATTTT
1 TAAACAGAGGCTTTAAAATTTT
5359581 AAAAACATGC
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
41 56 0.97
42 2 0.03
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (41 bp):
TAAACAGAGGCTTTAAAATTTTGATTGAAATCGGTTCCTCT
Found at i:5361042 original size:57 final size:57
Alignment explanation
Indices: 5360961--5361418 Score: 580
Period size: 59 Copynumber: 7.7 Consensus size: 57
5360951 AAATTCCAAA
*
5360961 AAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 AAAAA-ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
* *
5361019 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTCAAA
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC--C
* * *
5361078 AAAAAACATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAATTCC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
* *
5361135 AAAAACTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
*
5361192 AAAAAA-AGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATCGAAATTTCC
1 AAAAAATA---TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT--AAATTTCC
*
5361253 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAA
1 --AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA-TTTC-C
* * *
5361314 AAAAAAAAGGGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATCGAAATTTTC
1 AAAAAATA-----TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT--AAATTTCC
*
5361378 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
5361419 CTACAAAAAA
Statistics
Matches: 353, Mismatches: 25, Indels: 43
0.84 0.06 0.10
Matches are distributed among these distances:
56 1 0.00
57 106 0.30
58 6 0.02
59 131 0.37
60 4 0.01
61 45 0.13
62 1 0.00
63 7 0.02
64 46 0.13
65 3 0.01
66 3 0.01
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (57 bp):
AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
Found at i:5361096 original size:116 final size:117
Alignment explanation
Indices: 5360957--5361418 Score: 659
Period size: 116 Copynumber: 3.9 Consensus size: 117
5360947 AAAAAAATTC
5360957 CAAAAAAAATATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCTT-AGAAAT-AAATTTCC
1 CAAAAAAAA-A-ATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTGA-AAATCAAATTTCC
*
5361019 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAA-TTT
62 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTT
*
5361074 CAAAAAAAAACATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCTT-AGAAAT-AAAATTCCA
1 CAAAAAAAAA-ATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTGA-AAATCAAATTTCCA
*
5361136 AAAACTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTT
63 AAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTT
***
5361191 CAAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCGAAATTTCCAAA
1 CAAAAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC-AAATTTCC--A
5361256 AAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTT
63 AAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTT
5361311 CAAAAAAAAAAGGGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCGAAATTT
1 CAAAAAAAAAA-----TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC-AAATTT
* *
5361376 TCAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
60 CCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
5361419 CTACAAAAAA
Statistics
Matches: 319, Mismatches: 14, Indels: 18
0.91 0.04 0.05
Matches are distributed among these distances:
116 137 0.43
117 22 0.07
118 7 0.02
120 63 0.20
123 40 0.13
125 50 0.16
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.33
Consensus pattern (117 bp):
CAAAAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAATTTCCAAAA
AATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTT
Found at i:5368324 original size:194 final size:192
Alignment explanation
Indices: 5367959--5368343 Score: 662
Period size: 193 Copynumber: 2.0 Consensus size: 192
5367949 TAGTTATTAG
* *
5367959 AAAAAAAAATTATTCTCAAGAAAAATAAATTAAAACTTTTTTATTGAAATAATTCTTAAAATGTT
1 AAAAAAAAATTATTCTCAAGAAAAATAAATTAAAACCTTTTTATTGAAATAATTCTTAAAATATT
* * *
5368024 CCAGTATGTTGGTAACATTAAAAGAACTTTTTCTCACCTAGATATTTCTTAAACATCTCTACTCG
66 CCAGTACGTTGGTAACATTAAAAGAACTCTTTCTCACCTAGAGATTTCTTAAACATCTCTACTCG
* * *
5368089 GAATACTTTTAGAATCTTATCTTTGGGGGCTCGAATTTATTTTTCATAAGAAAATGTCATGT
131 AAATACTTTTAGAATCTCATCTTTGGAGGCTCGAATTTATTTTTCATAAGAAAATGTCATGT
5368151 AAAAAAAAATTTATTCTCAAGAAAAATAAATTAAAACCTTTTTATTGAAATAATTCTTAAAATAT
1 AAAAAAAAA-TTATTCTCAAGAAAAATAAATTAAAACCTTTTTATTGAAATAATTCTTAAAATAT
5368216 TCCAGTACGTTGGTAACATTAAAAGAACTCTTTCTCACCTAGAGATTTCTTAAAGCATCTCTACT
65 TCCAGTACGTTGGTAACATTAAAAGAACTCTTTCTCACCTAGAGATTTCTTAAA-CATCTCTACT
* *
5368281 CGAAATACTTTTAGAATCTCATCTTTGGAGGTTCGAATTTATTTTTCGTAAGAAAATGTCATG
129 CGAAATACTTTTAGAATCTCATCTTTGGAGGCTCGAATTTATTTTTCATAAGAAAATGTCATG
5368344 CATGTAATGC
Statistics
Matches: 181, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
192 9 0.05
193 104 0.57
194 68 0.38
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (192 bp):
AAAAAAAAATTATTCTCAAGAAAAATAAATTAAAACCTTTTTATTGAAATAATTCTTAAAATATT
CCAGTACGTTGGTAACATTAAAAGAACTCTTTCTCACCTAGAGATTTCTTAAACATCTCTACTCG
AAATACTTTTAGAATCTCATCTTTGGAGGCTCGAATTTATTTTTCATAAGAAAATGTCATGT
Found at i:5370368 original size:22 final size:21
Alignment explanation
Indices: 5370332--5370377 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
5370322 CTACTATATC
* *
5370332 ATAATCAAATTACAATCATTGA
1 ATAATCAAATAACAAACATT-A
*
5370354 ATAATCAACTAACAAACATTA
1 ATAATCAAATAACAAACATTA
5370375 ATA
1 ATA
5370378 TAATTAAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.54, C:0.15, G:0.02, T:0.28
Consensus pattern (21 bp):
ATAATCAAATAACAAACATTA
Found at i:5371561 original size:2 final size:2
Alignment explanation
Indices: 5371554--5371592 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
5371544 ATCTATTCTA
5371554 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5371593 TAATACATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5371596 original size:6 final size:7
Alignment explanation
Indices: 5371552--5371602 Score: 54
Period size: 6 Copynumber: 7.4 Consensus size: 7
5371542 ATATCTATTC
5371552 TAATATA
1 TAATATA
5371559 T-ATATA
1 TAATATA
5371565 T-ATATA
1 TAATATA
5371571 TATATATA
1 TA-ATATA
5371579 TATATATA
1 TA-ATATA
5371587 TAATAT-
1 TAATATA
*
5371593 TAATACA
1 TAATATA
5371600 TAA
1 TAA
5371603 ACAAGTTTGC
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
6 17 0.43
7 8 0.20
8 15 0.38
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (7 bp):
TAATATA
Found at i:5372740 original size:269 final size:267
Alignment explanation
Indices: 5372232--5372770 Score: 816
Period size: 269 Copynumber: 2.0 Consensus size: 267
5372222 TCTTTTATAA
* * * *
5372232 ATTTAAGACTACAAATGTAATGTGTTATACATCAATTTTTTTATTTTTTCAGTAACTTTTTTTAA
1 ATTTAAAACCACAAATGTAATGTGTTACACATCAATTTTTTAATTTTTTCAGTAACTTTTTTTAA
* * *
5372297 TGTATATTTTATTACTATTGTAATTTTTTTGTTTATAAATTTTTTCTAAGATATATTTGATCGTT
66 GGTATATTCTATTACTATTGTAATTTTTTTGTTTATAAATTTTTTCTAAGATATATTTAATCGTT
*
5372362 ATTATAGTTTTATTATTATGAAAAATAATTTTTTTCAATTTAGTTTTTCTTTTTTCACATATTTT
131 ATTATAGTTTCATTATTATGAAAAATAATTTTTTTCAATTTAGTTTTTCTTTTTTCACATATTTT
* * *
5372427 CTAACATTTTTCATATTTTGTATAATAATTTAATCAAGATTACTAAAGTGAAAGTATGTTAATAC
196 CTAACATTTTTCATATTTTGTATAACAATCTAATCAAAATTACTAAAGTGAAAGTATGTTAATAC
5372492 TTCTTTT
261 TTCTTTT
5372499 ATTTAAAACCACAAATGTAATGTGTGTTACACATCAATTTTTTAATTTTTTCAGTAA-TTTTTTT
1 ATTTAAAACCACAAATGTAA--TGTGTTACACATCAATTTTTTAATTTTTTCAGTAACTTTTTTT
* *
5372563 AAGGTATATTCTATTACTATTGTAGTTGTTTATATGTTTATTAA-TTTTTCTAAGATATATTTTA
64 AAGGTATATTCTATTACTATTGTAATT-TTT-T-TGTTTATAAATTTTTTCTAAGATATA-TTTA
* *
5372627 AT-GTTATTATAGTTTCATTCTTATGAAAAATAA-TTTTTTCAATTTATTTTTTCTTTTTTCACA
125 ATCGTTATTATAGTTTCATTATTATGAAAAATAATTTTTTTCAATTTAGTTTTTCTTTTTTCACA
* * * * *
5372690 TTTTTTCTAATATTTTTCATATTTTGTATAACAATCTAGTCAAAATTACTAGAGTGAAAGTGTGT
190 TATTTTCTAACATTTTTCATATTTTGTATAACAATCTAATCAAAATTACTAAAGTGAAAGTATGT
5372755 TAATACTTCTTTT
255 TAATACTTCTTTT
5372768 ATT
1 ATT
5372771 ATTTAATTTA
Statistics
Matches: 246, Mismatches: 20, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
267 18 0.07
268 31 0.13
269 138 0.56
270 45 0.18
271 14 0.06
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (267 bp):
ATTTAAAACCACAAATGTAATGTGTTACACATCAATTTTTTAATTTTTTCAGTAACTTTTTTTAA
GGTATATTCTATTACTATTGTAATTTTTTTGTTTATAAATTTTTTCTAAGATATATTTAATCGTT
ATTATAGTTTCATTATTATGAAAAATAATTTTTTTCAATTTAGTTTTTCTTTTTTCACATATTTT
CTAACATTTTTCATATTTTGTATAACAATCTAATCAAAATTACTAAAGTGAAAGTATGTTAATAC
TTCTTTT
Found at i:5373176 original size:2 final size:2
Alignment explanation
Indices: 5373169--5373224 Score: 76
Period size: 2 Copynumber: 28.0 Consensus size: 2
5373159 GCAAATAAAG
* * * *
5373169 TA TA TA TA TA CA TA CA AA TA CA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5373211 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
5373225 AACAACAACA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:5377129 original size:60 final size:57
Alignment explanation
Indices: 5377047--5377512 Score: 598
Period size: 57 Copynumber: 7.8 Consensus size: 57
5377037 TTTTGTAGGA
*
5377047 AAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTTGGCAATTTCGATTT-TCAAGG
1 AAAATTGATACTTTCAACTTTTC-CCAAAAATATTTTTTTGGAAATTT--ATTTCT-AAGG
** *
5377107 AAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTTATTTCTAAGG
1 AAAATTGATACTTTCAACTTTTCC-CAAAAA-TATTTTTTTGGAAATTTATTTCTAAGG
*
5377166 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTTGATTT-TCAAGG
1 AAAATTGATACTTTCAACTTTT-CCCAAAAATATTTTTTTGGAAA-TTT-ATTTCT-AAGG
* *
5377226 AAAATTGATACTTTCAACTTTTCCCTAAAAATATATATTTTTTGAAATTTATTTCTGAGG
1 AAAATTGATACTTTCAACTTTTCCC-AAAAATAT-T-TTTTTGGAAATTTATTTCTAAGG
*
5377286 AAAATTGATACTTTCAACTCTTCCCCAAAAATA-TTTTTTGGAAATTTATTTCTAAGG
1 AAAATTGATACTTTCAACT-TTTCCCAAAAATATTTTTTTGGAAATTTATTTCTAAGG
*
5377343 AAAATTGATACTTTCAACTCTTCCCCAAAAATA-TTTTTTGGAAATTTATTTCTAAGG
1 AAAATTGATACTTTCAACT-TTTCCCAAAAATATTTTTTTGGAAATTTATTTCTAAGG
5377400 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTATTTTTCTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCC-AAAAATA-TTTTTTTGGAAATTTA--TTTC---TAAGG
*
5377464 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGAAATTT
1 AAAATTGATACTTTCAACTTTTCCC-AAAAATA-TTTTTTTGGAAATTT
5377513 TTTATTTTTA
Statistics
Matches: 372, Mismatches: 14, Indels: 36
0.88 0.03 0.09
Matches are distributed among these distances:
56 5 0.01
57 104 0.28
58 11 0.03
59 59 0.16
60 103 0.28
61 27 0.07
62 10 0.03
64 53 0.14
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTGGAAATTTATTTCTAAGG
Found at i:5377198 original size:119 final size:114
Alignment explanation
Indices: 5377047--5377502 Score: 616
Period size: 119 Copynumber: 3.9 Consensus size: 114
5377037 TTTTGTAGGA
* *
5377047 AAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTTGGCAATTTCGATTTTC-AAGGAAAA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTT--ATTTTCTAAGGAAAA
5377111 TTGATACTTTCAACTTTTCCTCAAAAACCCT-TTTTTTGAAAATTTATTTCTAAGG
64 TTGATACTTTCAACTTTTCC-CAAAAA---TATTTTTTG-AAATTTATTTCTAAGG
*
5377166 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTTGATTTTC-AAGGAAAA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAA-TTT-ATTTTCTAAGGAAAA
*
5377230 TTGATACTTTCAACTTTTCCCTAAAAATATATATTTTTTGAAATTTATTTCTGAGG
64 TTGATACTTTCAACTTTTCCC---AAA-A-ATATTTTTTGAAATTTATTTCTAAGG
*
5377286 AAAATTGATACTTTCAACTCTTCCCCAAAAATA-TTTTTTGGAAATTTA-TTTCTAAGGAAAATT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTTCTAAGGAAAATT
*
5377349 GATACTTTCAACTCTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAAGG
66 GATACTTTCAACT-TTTCCCAAAAATATTTTTT-GAAATTTATTTCTAAGG
*
5377400 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTATTTTTCTTTTAAGGA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTGGAAATTTA-TTTTC---TAAGGA
5377465 AAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTT
61 AAATTGATACTTTCAACTTTTCCC-AAAAATATTTTTT
5377503 TTTGAAATTT
Statistics
Matches: 308, Mismatches: 11, Indels: 34
0.87 0.03 0.10
Matches are distributed among these distances:
113 9 0.03
114 48 0.16
115 3 0.01
116 19 0.06
117 24 0.08
118 13 0.04
119 87 0.28
120 56 0.18
121 47 0.15
122 1 0.00
123 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (114 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTTCTAAGGAAAATT
GATACTTTCAACTTTTCCCAAAAATATTTTTTGAAATTTATTTCTAAGG
Found at i:5377602 original size:13 final size:13
Alignment explanation
Indices: 5377584--5377611 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5377574 CTAATCTAAT
5377584 AAATAAACAAATA
1 AAATAAACAAATA
5377597 AAATAAACAAATA
1 AAATAAACAAATA
5377610 AA
1 AA
5377612 CAAAGAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (13 bp):
AAATAAACAAATA
Found at i:5378731 original size:76 final size:78
Alignment explanation
Indices: 5378545--5378731 Score: 179
Period size: 82 Copynumber: 2.3 Consensus size: 78
5378535 TAGATAAGTA
* *
5378545 AAAATACAAAAATGAATAAATAAAAAAGATAAAAATATATATATACATATTAGTAATAATACATA
1 AAAATACAAAAAAGAA-AAA-AAAAAATATAAAAATATATATATACATA-TAGTAATAATACATA
5378610 AATAATAAAATACACAT
63 AATAATAAAATA-ACAT
* * * *
5378627 AAATATTAACAAAAAA-AAATAAATAAATATATACATATAT-TAATACATA-A-TAATAATA-AT
1 AAA-A-T-ACAAAAAAGAAAAAAAAAAATATAAAAATATATAT-ATACATATAGTAATAATACAT
*
5378687 AAATAATACAAT-ACAT
62 AAATAATAAAATAACAT
5378703 AAAATACAAAAGAAGAAGAAAAAAAAATA
1 AAAATACAAAA-AAGAA-AAAAAAAAATA
5378732 CAAGATAAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
73 6 0.07
74 3 0.03
75 3 0.03
76 16 0.18
78 13 0.15
79 8 0.09
80 1 0.01
81 1 0.01
82 25 0.28
83 3 0.03
84 3 0.03
85 7 0.08
ACGTcount: A:0.67, C:0.06, G:0.03, T:0.24
Consensus pattern (78 bp):
AAAATACAAAAAAGAAAAAAAAAAATATAAAAATATATATATACATATAGTAATAATACATAAAT
AATAAAATAACAT
Found at i:5378899 original size:1 final size:1
Alignment explanation
Indices: 5378895--5378987 Score: 87
Period size: 1 Copynumber: 93.0 Consensus size: 1
5378885 CATTTTTTGG
* * * * * * * *
5378895 TTTTTTTGTTTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
5378960 TTTTTTATTTTTATTTTTATTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
5378988 ACCAAAGCTC
Statistics
Matches: 70, Mismatches: 22, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.03, C:0.00, G:0.09, T:0.88
Consensus pattern (1 bp):
T
Found at i:5378916 original size:24 final size:25
Alignment explanation
Indices: 5378887--5378986 Score: 125
Period size: 26 Copynumber: 4.0 Consensus size: 25
5378877 CAACTCAACA
*
5378887 TTTTTTGGTTTTTTTGTTTTTTTTTG
1 TTTTTTTGTTTTTTTG-TTTTTTTTG
5378913 TTTTTTTGTTTTTTTG-TTTTTTTG
1 TTTTTTTGTTTTTTTGTTTTTTTTG
5378937 TTTTTTTGTTTTTTTGTTTTTTGTT-
1 TTTTTTTGTTTTTTTGTTTTTT-TTG
*
5378962 TTTTATTT-TTATTTTTATTTTTTTT
1 TTTT-TTTGTT-TTTTTGTTTTTTTT
5378987 TACCAAAGCT
Statistics
Matches: 68, Mismatches: 2, Indels: 9
0.86 0.03 0.11
Matches are distributed among these distances:
24 24 0.35
25 13 0.19
26 31 0.46
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.87
Consensus pattern (25 bp):
TTTTTTTGTTTTTTTGTTTTTTTTG
Done.