Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 317 of 362
Found at i:105849214 original size:27 final size:27
Alignment explanation
Indices: 105849176--105849231 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
105849166 GGGATTTATC
*
105849176 TATTTTTATAATTTAATGAATTTTTAA
1 TATTTTTATAATTTAATGAATTTTAAA
* **
105849203 TATTTTTCTAATTTTTTGAATTTTAAA
1 TATTTTTATAATTTAATGAATTTTAAA
105849230 TA
1 TA
105849232 AAATTTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.61
Consensus pattern (27 bp):
TATTTTTATAATTTAATGAATTTTAAA
Found at i:105850851 original size:31 final size:31
Alignment explanation
Indices: 105850793--105850851 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
105850783 ATGACCAAAT
* * *
105850793 TAAAGTACAATGACTAAAATCATAACTTTTG
1 TAAACTACAATGACTAAAAGCAGAACTTTTG
*
105850824 TAAACTACAATGACTAATAGCAGAACTT
1 TAAACTACAATGACTAAAAGCAGAACTT
105850852 AACCTAGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (31 bp):
TAAACTACAATGACTAAAAGCAGAACTTTTG
Found at i:105853366 original size:29 final size:29
Alignment explanation
Indices: 105853333--105853391 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
105853323 GGTATGATAG
105853333 ATCAATATCCATCGATCAGTCAAAAACAT
1 ATCAATATCCATCGATCAGTCAAAAACAT
105853362 ATCAATATCCATCGATCAGTCAAAAACAT
1 ATCAATATCCATCGATCAGTCAAAAACAT
105853391 A
1 A
105853392 CTTTAGATCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.24
Consensus pattern (29 bp):
ATCAATATCCATCGATCAGTCAAAAACAT
Found at i:105853622 original size:22 final size:22
Alignment explanation
Indices: 105853596--105853641 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
105853586 CGATAACTTA
*
105853596 AATAA-AATTTTTTAAATATTTT
1 AATAATAATTTTATAAA-ATTTT
*
105853618 AATAATTATTTTATAAAATTTT
1 AATAATAATTTTATAAAATTTT
105853640 AA
1 AA
105853642 AATTAAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AATAATAATTTTATAAAATTTT
Found at i:105853628 original size:23 final size:21
Alignment explanation
Indices: 105853598--105853646 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
105853588 ATAACTTAAA
*
105853598 TAAAATT-TTTTA-AATATTT
1 TAAAATTATTTTATAAAATTT
105853617 TAATAATTATTTTATAAAATTT
1 TAA-AATTATTTTATAAAATTT
105853639 TAAAATTA
1 TAAAATTA
105853647 AACAATCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 3 0.12
20 4 0.15
21 10 0.38
22 9 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TAAAATTATTTTATAAAATTT
Found at i:105856388 original size:22 final size:22
Alignment explanation
Indices: 105856355--105856396 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
105856345 TAAATACGTT
105856355 ATTTAGGAGCCTTTGTGGCTGA
1 ATTTAGGAGCCTTTGTGGCTGA
105856377 ATTT-GGATGCCTTTGTGGCT
1 ATTTAGGA-GCCTTTGTGGCT
105856397 ATCTTGCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.14, C:0.14, G:0.31, T:0.40
Consensus pattern (22 bp):
ATTTAGGAGCCTTTGTGGCTGA
Found at i:105867190 original size:24 final size:24
Alignment explanation
Indices: 105867158--105867229 Score: 135
Period size: 24 Copynumber: 3.0 Consensus size: 24
105867148 TTGGATGGGA
105867158 AATGATTAGAAGATGAATTCTAAC
1 AATGATTAGAAGATGAATTCTAAC
*
105867182 AATGATTAGAGGATGAATTCTAAC
1 AATGATTAGAAGATGAATTCTAAC
105867206 AATGATTAGAAGATGAATTCTAAC
1 AATGATTAGAAGATGAATTCTAAC
105867230 TTATTAGAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.29
Consensus pattern (24 bp):
AATGATTAGAAGATGAATTCTAAC
Found at i:105870615 original size:20 final size:20
Alignment explanation
Indices: 105870544--105870615 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
105870534 AAATTCATGG
* *
105870544 TTATGATTAGGATATGAGTA
1 TTATGATTTGGATTTGAGTA
* *
105870564 TTATGATTTTAGATGATTGAGTT
1 TTATGA-TTTGGAT--TTGAGTA
105870587 TTATGATTTGGATTTGAGTA
1 TTATGATTTGGATTTGAGTA
105870607 TTATGATTT
1 TTATGATTT
105870616 TAGATTCGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
20 21 0.49
21 5 0.12
22 6 0.14
23 11 0.26
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (20 bp):
TTATGATTTGGATTTGAGTA
Found at i:105872437 original size:13 final size:13
Alignment explanation
Indices: 105872412--105872443 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
105872402 ATAGCACATT
105872412 TCAAAAC-ATGCA
1 TCAAAACTATGCA
105872424 TCAAAACTATGCA
1 TCAAAACTATGCA
105872437 T-AAAACT
1 TCAAAACT
105872444 TAACATTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.50, C:0.22, G:0.06, T:0.22
Consensus pattern (13 bp):
TCAAAACTATGCA
Found at i:105882890 original size:16 final size:17
Alignment explanation
Indices: 105882869--105882904 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
105882859 TTATTTTAAA
105882869 AAATTTATAAAAAT-AT
1 AAATTTATAAAAATAAT
105882885 AAATTTATAAAAATAAT
1 AAATTTATAAAAATAAT
105882902 AAA
1 AAA
105882905 AAGCATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATTTATAAAAATAAT
Found at i:105882997 original size:33 final size:33
Alignment explanation
Indices: 105882955--105883021 Score: 100
Period size: 32 Copynumber: 2.0 Consensus size: 33
105882945 TATAATATAT
* *
105882955 ATATATAAATTTAAAATTTATAAATATATA-GAA
1 ATATATAAATAT-AAATTTATAAAAATATATGAA
105882988 ATATATAAATATAAATTTATAAAAATATATGAA
1 ATATATAAATATAAATTTATAAAAATATATGAA
105883021 A
1 A
105883022 GAATTAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 16 0.52
33 15 0.48
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (33 bp):
ATATATAAATATAAATTTATAAAAATATATGAA
Found at i:105885094 original size:21 final size:21
Alignment explanation
Indices: 105885069--105885108 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
105885059 TTTATTATTT
*
105885069 ATTAATCATATTTACTTAATG
1 ATTAATCATATTTAATTAATG
*
105885090 ATTAATCTTATTTAATTAA
1 ATTAATCATATTTAATTAA
105885109 AGGTAAGTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (21 bp):
ATTAATCATATTTAATTAATG
Found at i:105888101 original size:27 final size:27
Alignment explanation
Indices: 105888051--105888105 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
105888041 GTAAACCAAC
*
105888051 TAATTATCTAAAAAAAGACTAAAAAAA
1 TAATTATCTAAAAAAAGACAAAAAAAA
* *
105888078 TAATTATCTAAGAAAAGGAAAAAAAAAA
1 TAATTATCTAA-AAAAAGACAAAAAAAA
105888106 CACTAACAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.20
Consensus pattern (27 bp):
TAATTATCTAAAAAAAGACAAAAAAAA
Found at i:105896185 original size:49 final size:49
Alignment explanation
Indices: 105896103--105896261 Score: 221
Period size: 49 Copynumber: 3.3 Consensus size: 49
105896093 ATAAATTATG
* * ** *
105896103 TTATGCATTTCTAAACTGGGTCTTCCATTGTCTACACTCTCATCACTAT
1 TTATACATTGCTAAACTTAGTCTTCCATTGTCTACACTCTTATCACTAT
* *
105896152 TTATACATTGCTAAACTTCGTCTTCCATTGTCTATACTCTTATCACTAT
1 TTATACATTGCTAAACTTAGTCTTCCATTGTCTACACTCTTATCACTAT
* *
105896201 TTATACATTGCTAAACTTAGTCTTCCACTATCTACACTCTTATCACTAT
1 TTATACATTGCTAAACTTAGTCTTCCATTGTCTACACTCTTATCACTAT
*
105896250 TTATCCA-TGCTA
1 TTATACATTGCTA
105896262 GAATGTCAAA
Statistics
Matches: 99, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
48 5 0.05
49 94 0.95
ACGTcount: A:0.25, C:0.26, G:0.07, T:0.42
Consensus pattern (49 bp):
TTATACATTGCTAAACTTAGTCTTCCATTGTCTACACTCTTATCACTAT
Found at i:105898505 original size:3 final size:3
Alignment explanation
Indices: 105898499--105898536 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
105898489 TTTAATGCAC
*
105898499 TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
105898537 CTACTTATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:105901514 original size:3 final size:3
Alignment explanation
Indices: 105901506--105901535 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
105901496 AAGCATAAAC
*
105901506 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
105901536 CATTGGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:105901666 original size:3 final size:3
Alignment explanation
Indices: 105901635--105901716 Score: 78
Period size: 3 Copynumber: 27.3 Consensus size: 3
105901625 ATACACGTAC
* *
105901635 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
105901682 ATA GTA ATA TTA ATA ACA CTA ATA AT- ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
105901717 CAAGGATATT
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
2 4 0.06
3 53 0.84
4 6 0.10
ACGTcount: A:0.62, C:0.05, G:0.01, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:105903616 original size:55 final size:55
Alignment explanation
Indices: 105903533--105903706 Score: 287
Period size: 57 Copynumber: 3.1 Consensus size: 55
105903523 TAAAAGCAGA
*
105903533 TTTTGAAAAACA-GAAATTAAAGGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 TTTTGAAAAACATGAATTTAAAGGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
105903587 TTTTGAAAAACATGAATTTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 TTTTGAAAAACATGAATTTAAAGGGCTCAACTCACCTCTCGCAATATGAGTTGA--T
* *
105903644 TTTTGAAAAACATAAATTGAAAGGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 TTTTGAAAAACATGAATTTAAAGGGCTCAACTCACCTCTCGCAATATGAGTTGAT
105903699 TTTTGAAA
1 TTTTGAAA
105903707 GGTAGAAATT
Statistics
Matches: 112, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
54 12 0.11
55 48 0.43
57 52 0.46
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (55 bp):
TTTTGAAAAACATGAATTTAAAGGGCTCAACTCACCTCTCGCAATATGAGTTGAT
Found at i:105903896 original size:13 final size:13
Alignment explanation
Indices: 105903878--105903907 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
105903868 TGATTTTTGA
105903878 AAAACAGAAACTG
1 AAAACAGAAACTG
*
105903891 AAAACAGAAATTG
1 AAAACAGAAACTG
105903904 AAAA
1 AAAA
105903908 TACCTCTGCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.10, G:0.13, T:0.10
Consensus pattern (13 bp):
AAAACAGAAACTG
Found at i:105903952 original size:168 final size:171
Alignment explanation
Indices: 105903644--105904136 Score: 596
Period size: 177 Copynumber: 2.8 Consensus size: 171
105903634 GAGTTGATTT
* * *
105903644 TTTTGAAAAACATAAATTGAAAGGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAGG
1 TTTTGAAAAACACAAATTCAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAGG
*
105903709 TAGAAATTGAAAAAAAAATAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATCTCT
66 TAGAAATTG----AAAAA-AAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCT
* * * *
105903774 CGCAATATGAGTTGATTTTTTTG-AAACTTGATTTGA-AAAGTAGG
126 CGCAATATGAGTTGATTTTTTTGAAAACATGAATTGAGAAAATAGA
* * **
105903818 TTTTGAAAAACAGAAATT-AAAAGACTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
1 TTTTGAAAAACACAAATTCAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAGG
* * * * * * *
105903882 CAGAAACTGAAAACAGAAATTGAAAATACCTCTGCGTGCCCTGAGGCTCAACTCACCTCTCGCAA
66 TAGAAATTGAAAAAAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAA
105903947 TATGAGTTGATTTTTTTGAAAACATGAATTGAGAAAATAGA
131 TATGAGTTGATTTTTTTGAAAACATGAATTGAGAAAATAGA
** * * * * ** *
105903988 AATTGCAATTACCTCAACGTGTCATGAGGCTCAACTTACCTCTCGCAATATGAGTTGACTTTTTG
1 TTTTG-AA-AAACACAA-AT-TCAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG
* *
105904053 AAAGGTAGAATTTTGAAAAAAAAAATTGAAATTACCTCAGCGTGTCGTGAGGCTCAACTCACCTC
61 AAAGGTAGAA-ATTGAAAAAAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTC
105904118 TCGCAATATGAGTTGATTT
125 TCGCAATATGAGTTGATTT
105904137 CTGATAACAG
Statistics
Matches: 271, Mismatches: 39, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
168 64 0.24
169 15 0.06
170 9 0.03
171 2 0.01
172 4 0.01
173 50 0.18
174 18 0.07
175 31 0.11
176 13 0.05
177 65 0.24
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (171 bp):
TTTTGAAAAACACAAATTCAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAGG
TAGAAATTGAAAAAAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAA
TATGAGTTGATTTTTTTGAAAACATGAATTGAGAAAATAGA
Found at i:105910941 original size:21 final size:22
Alignment explanation
Indices: 105910898--105910941 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
105910888 AGATATATGT
* * *
105910898 ATATATATAATATAATATTAAA
1 ATATATATAATACAACATAAAA
105910920 ATATA-ATAATACAACATAAAA
1 ATATATATAATACAACATAAAA
105910941 A
1 A
105910942 AAATACATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (22 bp):
ATATATATAATACAACATAAAA
Found at i:105911289 original size:3 final size:3
Alignment explanation
Indices: 105911258--105911331 Score: 69
Period size: 3 Copynumber: 24.3 Consensus size: 3
105911248 ATACACGTAC
* * *
105911258 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA ATA ATA GTA ATA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* * *
105911305 CTA ATA ATA CTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
105911332 CAAGGATATT
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
2 2 0.04
3 48 0.86
4 6 0.11
ACGTcount: A:0.62, C:0.05, G:0.01, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:105917312 original size:5 final size:5
Alignment explanation
Indices: 105917300--105917337 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
105917290 ATGTTGGTTA
* *
105917300 ATATT AAATT AAATT ATATT ATATT ATATT ATATT ATA
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATA
105917338 ATGAAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (5 bp):
ATATT
Found at i:105917677 original size:9 final size:9
Alignment explanation
Indices: 105917663--105917696 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
105917653 AAATAGATAT
105917663 TTATTATAA
1 TTATTATAA
105917672 TTATTATAA
1 TTATTATAA
*
105917681 TGTATTATTA
1 T-TATTATAA
105917691 TTATTA
1 TTATTA
105917697 ACAAATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (9 bp):
TTATTATAA
Found at i:105917785 original size:4 final size:4
Alignment explanation
Indices: 105917776--105917810 Score: 52
Period size: 4 Copynumber: 8.2 Consensus size: 4
105917766 AAAACAGGGG
105917776 AGAA AGAA AGAA AGGAAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA A-G-AA AGAA AGAA AGAA AGAA A
105917811 AGGGAGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 24 0.83
5 2 0.07
6 3 0.10
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:105917797 original size:18 final size:17
Alignment explanation
Indices: 105917718--105917812 Score: 66
Period size: 18 Copynumber: 5.2 Consensus size: 17
105917708 TATAAGATAT
105917718 AAAGTAAAGAAAGAAATGAA
1 AAAG-AAAGAAAGAAA-G-A
* *
105917738 AAAGAAGGAAAAAACAGA
1 AAAGAAAGAAAGAA-AGA
* *
105917756 ATAGAAACGAAA-AACAGG
1 AAAGAAA-GAAAGAA-AGA
**
105917774 GGAGAAAGAAAGAAAGGA
1 AAAGAAAGAAAGAAA-GA
105917792 AAAGAAAGAAAGAAAGA
1 AAAGAAAGAAAGAAAGA
105917809 AAAG
1 AAAG
105917813 GGAGAAATAG
Statistics
Matches: 61, Mismatches: 10, Indels: 11
0.74 0.12 0.13
Matches are distributed among these distances:
17 11 0.18
18 32 0.52
19 13 0.21
20 5 0.08
ACGTcount: A:0.68, C:0.03, G:0.25, T:0.03
Consensus pattern (17 bp):
AAAGAAAGAAAGAAAGA
Found at i:105918219 original size:12 final size:11
Alignment explanation
Indices: 105918199--105918250 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
105918189 GTTAAGATTA
*
105918199 AAATTGAAATT
1 AAATAGAAATT
105918210 AAAGTAGAAATT
1 AAA-TAGAAATT
*
105918222 GAATAGAAATT
1 AAATAGAAATT
*
105918233 GAATAAGAAATTT
1 AAAT-AGAAA-TT
105918246 AAATA
1 AAATA
105918251 TTAAATGTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
11 15 0.43
12 15 0.43
13 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (11 bp):
AAATAGAAATT
Found at i:105918230 original size:11 final size:11
Alignment explanation
Indices: 105918204--105918244 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
105918194 GATTAAAATT
*
105918204 GAAATTAAAGTA
1 GAAATTGAA-TA
105918216 GAAATTGAATA
1 GAAATTGAATA
105918227 GAAATTGAATAA
1 GAAATTGAAT-A
105918239 GAAATT
1 GAAATT
105918245 TAAATATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 12 0.44
12 15 0.56
ACGTcount: A:0.56, C:0.00, G:0.17, T:0.27
Consensus pattern (11 bp):
GAAATTGAATA
Found at i:105919104 original size:47 final size:46
Alignment explanation
Indices: 105918984--105919104 Score: 109
Period size: 47 Copynumber: 2.5 Consensus size: 46
105918974 AACTTTAAGT
* *
105918984 CGATGAGGCACCTTGTGTGTCGTACTGTTACTATTACTTCGGATTTATC
1 CGATGAGGCA-C-TGAGTGTCGTACTGTTACTATTACTTCGGA-TTAGC
* ** ** * *
105919033 CAATGAGATACTGAGTACCATACTGTTACTGTTTACTTCGGCA-TAGC
1 CGATGAGGCACTGAGTGTCGTACTGTTACT-ATTACTTCGG-ATTAGC
105919080 CGATGAGGCACTGAGTGTCGTACTG
1 CGATGAGGCACTGAGTGTCGTACTG
105919105 GTGTGTTGGT
Statistics
Matches: 55, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
47 37 0.67
48 10 0.18
49 8 0.15
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (46 bp):
CGATGAGGCACTGAGTGTCGTACTGTTACTATTACTTCGGATTAGC
Found at i:105921351 original size:24 final size:25
Alignment explanation
Indices: 105921324--105921370 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
105921314 AAACATTAAT
*
105921324 TATAATATTAAA-ATAAATATAAGG
1 TATAAGATTAAATATAAATATAAGG
*
105921348 TATAAGATTAAATATAGATATAA
1 TATAAGATTAAATATAAATATAA
105921371 TTTCTCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (25 bp):
TATAAGATTAAATATAAATATAAGG
Found at i:105921848 original size:30 final size:30
Alignment explanation
Indices: 105921812--105921874 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
105921802 TTTGTGACTA
*
105921812 GCCCTTCTAAATGGCCTCACACGCCCGTGT
1 GCCCTTCGAAATGGCCTCACACGCCCGTGT
105921842 GCCCTTCGAAATGGCCTCACACGCCCGTGT
1 GCCCTTCGAAATGGCCTCACACGCCCGTGT
105921872 GCC
1 GCC
105921875 GGGTCGTGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.16, C:0.41, G:0.22, T:0.21
Consensus pattern (30 bp):
GCCCTTCGAAATGGCCTCACACGCCCGTGT
Found at i:105928992 original size:3 final size:3
Alignment explanation
Indices: 105928984--105929014 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
105928974 TAAAGTGTGC
105928984 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
105929015 AAGTGAAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:105944638 original size:14 final size:14
Alignment explanation
Indices: 105944619--105944648 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
105944609 CATAAATATT
*
105944619 TATTTTAATTGTTA
1 TATTTTAATTCTTA
105944633 TATTTTAATTCTTA
1 TATTTTAATTCTTA
105944647 TA
1 TA
105944649 CTTGACTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (14 bp):
TATTTTAATTCTTA
Found at i:105947850 original size:33 final size:33
Alignment explanation
Indices: 105947813--105947877 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
105947803 TATATCAATG
*
105947813 TGCGAGTCGTAATGATGTCTGAGCTGTGTAATT
1 TGCGAGTCATAATGATGTCTGAGCTGTGTAATT
* *
105947846 TGCGAGTCATAGTGATGTGTGAGCTGTGTAAT
1 TGCGAGTCATAATGATGTCTGAGCTGTGTAAT
105947878 GTGTGAGCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.22, C:0.11, G:0.32, T:0.35
Consensus pattern (33 bp):
TGCGAGTCATAATGATGTCTGAGCTGTGTAATT
Found at i:105947881 original size:16 final size:16
Alignment explanation
Indices: 105947860--105947953 Score: 75
Period size: 16 Copynumber: 5.8 Consensus size: 16
105947850 AGTCATAGTG
105947860 ATGTGTGAGCTGTGTA
1 ATGTGTGAGCTGTGTA
**
105947876 ATGTGTGAGC--TACA
1 ATGTGTGAGCTGTGTA
*
105947890 ATGATGTACGAGTTGTGTA
1 ATG-TGT--GAGCTGTGTA
** *
105947909 ATGTGCAAGCTATGTA
1 ATGTGTGAGCTGTGTA
105947925 ATGTGTGAGCTGTAGTA
1 ATGTGTGAGCTGT-GTA
*
105947942 GTGTGTGAGCTG
1 ATGTGTGAGCTG
105947954 AGAAAATATG
Statistics
Matches: 59, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
14 5 0.08
15 3 0.05
16 27 0.46
17 17 0.29
18 2 0.03
19 5 0.08
ACGTcount: A:0.23, C:0.09, G:0.34, T:0.34
Consensus pattern (16 bp):
ATGTGTGAGCTGTGTA
Found at i:105947895 original size:33 final size:33
Alignment explanation
Indices: 105947823--105947952 Score: 104
Period size: 33 Copynumber: 3.9 Consensus size: 33
105947813 TGCGAGTCGT
* *
105947823 AATGATGTCTGAGCTGTGTAATTTGCGAG-T-C
1 AATGATGTGTGAGCTGTGTAATGTGCGAGCTAC
*
105947854 ATAGTGATGTGTGAGCTGTGTAATGTGTGAGCTAC
1 A-A-TGATGTGTGAGCTGTGTAATGTGCGAGCTAC
** * *
105947889 AATGATGTACGAGTTGTGTAATGTGCAAGCTA-
1 AATGATGTGTGAGCTGTGTAATGTGCGAGCTAC
** * * *
105947921 TGTAATGTGTGAGCTGTAGTAGTGTGTGAGCT
1 AATGATGTGTGAGCTGT-GTAATGTGCGAGCT
105947953 GAGAAAATAT
Statistics
Matches: 77, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
31 1 0.01
32 12 0.16
33 60 0.78
34 2 0.03
35 2 0.03
ACGTcount: A:0.24, C:0.09, G:0.32, T:0.35
Consensus pattern (33 bp):
AATGATGTGTGAGCTGTGTAATGTGCGAGCTAC
Found at i:105951854 original size:22 final size:20
Alignment explanation
Indices: 105951814--105951862 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
105951804 CAATTTAAAA
105951814 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
* *
105951834 TATATAAATTTATTAATATA
1 TATAAAAATTTATTAATATG
*
105951854 TGTAAAAAT
1 TATAAAAAT
105951863 AATTTTTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:105951992 original size:14 final size:15
Alignment explanation
Indices: 105951973--105952010 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
105951963 CCAGAAAAAT
*
105951973 AAATTATTTTT-TAA
1 AAATTATTTTTCGAA
105951987 AAATTATTTTTCGAA
1 AAATTATTTTTCGAA
105952002 AAA-TATTTT
1 AAATTATTTT
105952011 ACTGGCAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (15 bp):
AAATTATTTTTCGAA
Found at i:105955984 original size:8 final size:8
Alignment explanation
Indices: 105955968--105956009 Score: 52
Period size: 7 Copynumber: 5.2 Consensus size: 8
105955958 TACCTTTATT
105955968 AATTT-AA
1 AATTTAAA
105955975 AATTTAAAAA
1 AATTT--AAA
105955985 AATTTAAA
1 AATTTAAA
105955993 AATTT-AA
1 AATTTAAA
105956000 AATTTAAA
1 AATTTAAA
105956008 AA
1 AA
105956010 AATTTAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
7 12 0.39
8 12 0.39
10 7 0.23
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AATTTAAA
Found at i:105955988 original size:10 final size:10
Alignment explanation
Indices: 105955973--105956017 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
105955963 TTATTAATTT
105955973 AAAATTTAAA
1 AAAATTTAAA
105955983 AAAATTT--A
1 AAAATTTAAA
105955991 AAAATTT---
1 AAAATTTAAA
105955998 AAAATTTAAA
1 AAAATTTAAA
105956008 AAAATTTAAA
1 AAAATTTAAA
105956018 GAGTCTACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 7 0.22
8 8 0.25
10 17 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:105955996 original size:25 final size:25
Alignment explanation
Indices: 105955968--105956017 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
105955958 TACCTTTATT
105955968 AATTTAAAATTTAAAAAAATTTAAA
1 AATTTAAAATTTAAAAAAATTTAAA
105955993 AATTTAAAATTTAAAAAAATTTAAA
1 AATTTAAAATTTAAAAAAATTTAAA
105956018 GAGTCTACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
AATTTAAAATTTAAAAAAATTTAAA
Found at i:105956017 original size:17 final size:18
Alignment explanation
Indices: 105955968--105956001 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
105955958 TACCTTTATT
105955968 AATTT-AAAATTTAAAAA
1 AATTTAAAAATTTAAAAA
105955985 AATTTAAAAATTTAAAA
1 AATTTAAAAATTTAAAA
105956002 TTTAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AATTTAAAAATTTAAAAA
Found at i:105956986 original size:21 final size:22
Alignment explanation
Indices: 105956939--105956986 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
105956929 GAATTTTAAC
* *
105956939 AAATTCTTTTAAAATAAGAATT
1 AAATTCTTTAAAAATAAGAAAT
105956961 AAATTC-TTAAAAATAA-AAAT
1 AAATTCTTTAAAAATAAGAAAT
105956981 AGAATT
1 A-AATT
105956987 AAATTATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.17
21 13 0.57
22 6 0.26
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (22 bp):
AAATTCTTTAAAAATAAGAAAT
Found at i:105957365 original size:14 final size:15
Alignment explanation
Indices: 105957341--105957373 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
105957331 GTTTTTAAGG
*
105957341 TTTATTAATTAGGGT
1 TTTATTAATTACGGT
105957356 TTTATT-ATTACGGT
1 TTTATTAATTACGGT
105957370 TTTA
1 TTTA
105957374 AATTGATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.58
Consensus pattern (15 bp):
TTTATTAATTACGGT
Found at i:105957515 original size:29 final size:28
Alignment explanation
Indices: 105957466--105957541 Score: 107
Period size: 29 Copynumber: 2.7 Consensus size: 28
105957456 TTGGAACTCA
* * *
105957466 GAGTACTGAAAAATATTTTTGATGAGAT
1 GAGTTCTGAAAAATATCTTTGACGAGAT
105957494 GAGTTCTGAAAAAATATCTTTGACGAGAT
1 GAGTTCTG-AAAAATATCTTTGACGAGAT
*
105957523 GAGCTCTGAAAAATATCTT
1 GAGTTCTGAAAAATATCTT
105957542 GGGAATCTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 18 0.42
29 25 0.58
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (28 bp):
GAGTTCTGAAAAATATCTTTGACGAGAT
Found at i:105964023 original size:49 final size:50
Alignment explanation
Indices: 105963963--105964088 Score: 148
Period size: 50 Copynumber: 2.5 Consensus size: 50
105963953 CTGGTACGCA
* * ** * *
105963963 TAGTAGCCTGCACTTAGTACTACACATGCGACC-AATTATCCGGTATACG
1 TAGTAGTCTGCACTTAGTACTACACACGCGACCTAACCATCCGATACACG
* *
105964012 TAGTAGTCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGTCTGCACTTAGTACTACACACGCGACCTAACCATCCGATACACG
*
105964062 TAGTA-TCCTACACTTAGTACTACACAC
1 TAGTAGT-CTGCACTTAGTACTACACAC
105964089 ATGATCGAAG
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
49 31 0.47
50 35 0.53
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (50 bp):
TAGTAGTCTGCACTTAGTACTACACACGCGACCTAACCATCCGATACACG
Found at i:105966692 original size:44 final size:42
Alignment explanation
Indices: 105966546--105966718 Score: 127
Period size: 43 Copynumber: 4.0 Consensus size: 42
105966536 GGAAAGCTCG
*** * * *
105966546 TACGATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAA
1 TACGATGCCAACGTCCCAGATACGGTCTTACACGAAACCAAA
* * * * * *
105966588 TATCAATGAC-ACTATCACAGATAGGGTCTTACATGAAACCAAA
1 TA-CGATGCCAAC-GTCCCAGATACGGTCTTACACGAAACCAAA
*
105966631 TACGATGCCAATGTCCCAGATACGGTCTTACACGTAAATCTCAAA
1 TACGATGCCAACGTCCCAGATACGGTCTTACACG-AAA-C-CAAA
* * *
105966676 T-CGATGCCAACGTCCCAGACT-TGGCCTTACACGAAATCAAA
1 TACGATGCCAACGTCCCAGA-TACGGTCTTACACGAAACCAAA
105966717 TA
1 TA
105966719 TCAGAAATCC
Statistics
Matches: 103, Mismatches: 20, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
41 5 0.05
42 27 0.26
43 37 0.36
44 28 0.27
45 6 0.06
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (42 bp):
TACGATGCCAACGTCCCAGATACGGTCTTACACGAAACCAAA
Found at i:105967278 original size:18 final size:20
Alignment explanation
Indices: 105967241--105967279 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
105967231 TCATTTTTAC
*
105967241 AATTCAGTCCAAAATACTCA
1 AATTCAGTCAAAAATACTCA
105967261 AATTCA-TCAAAAAT-CTCA
1 AATTCAGTCAAAAATACTCA
105967279 A
1 A
105967280 TACAAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 7 0.39
20 6 0.33
ACGTcount: A:0.49, C:0.23, G:0.03, T:0.26
Consensus pattern (20 bp):
AATTCAGTCAAAAATACTCA
Found at i:105968379 original size:11 final size:11
Alignment explanation
Indices: 105968358--105968390 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
105968348 ATATTTCTTG
105968358 AAAATATTAATA
1 AAAATA-TAATA
105968370 AAAATATAATA
1 AAAATATAATA
105968381 AAAATATAAT
1 AAAATATAAT
105968391 TTAGATAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAAATATAATA
Found at i:105970487 original size:39 final size:38
Alignment explanation
Indices: 105970440--105970518 Score: 140
Period size: 39 Copynumber: 2.1 Consensus size: 38
105970430 TTCAGCACCT
105970440 ACAACTCCTCCTTCAGCCATGACCCCTAGGGAGGGCCC
1 ACAACTCCTCCTTCAGCCATGACCCCTAGGGAGGGCCC
*
105970478 ACAAGCTCCTCCTTCAGCCATGACCCCTGGGGAGGGCCC
1 ACAA-CTCCTCCTTCAGCCATGACCCCTAGGGAGGGCCC
105970517 AC
1 AC
105970519 CAGGTTCCGC
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 4 0.10
39 35 0.90
ACGTcount: A:0.20, C:0.42, G:0.23, T:0.15
Consensus pattern (38 bp):
ACAACTCCTCCTTCAGCCATGACCCCTAGGGAGGGCCC
Found at i:105973233 original size:27 final size:27
Alignment explanation
Indices: 105973203--105973255 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
105973193 AGCCAAATTC
*
105973203 TATATGAATAATTTTA-AAGAAAATATA
1 TATAT-AATAAATTTAGAAGAAAATATA
105973230 TATATAATAAATTTAGAAGAAAATAT
1 TATATAATAAATTTAGAAGAAAATAT
105973256 TTACATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.36
Consensus pattern (27 bp):
TATATAATAAATTTAGAAGAAAATATA
Found at i:105973263 original size:27 final size:26
Alignment explanation
Indices: 105973209--105973263 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
105973199 ATTCTATATG
* *
105973209 AATAATTTTAAAGAAAATATATATAT
1 AATAAATTTAAAGAAAATATATACAT
*
105973235 AATAAATTTAGAAGAAAATATTTACAT
1 AATAAATTTA-AAGAAAATATATACAT
105973262 AA
1 AA
105973264 AAGGAAGTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (26 bp):
AATAAATTTAAAGAAAATATATACAT
Found at i:105978550 original size:11 final size:11
Alignment explanation
Indices: 105978464--105978550 Score: 52
Period size: 11 Copynumber: 7.9 Consensus size: 11
105978454 CTCATAATTC
*
105978464 TCAACATTCTT
1 TCAAAATTCTT
* *
105978475 TCAATATTCCCT
1 TCAAAATT-CTT
* * *
105978487 TAAAAAATCTA
1 TCAAAATTCTT
* *
105978498 TCAAATTTCAT
1 TCAAAATTCTT
105978509 T-AAAATT-TT
1 TCAAAATTCTT
*
105978518 CTCAAAATTCTA
1 -TCAAAATTCTT
*
105978530 TCAAATTTCTT
1 TCAAAATTCTT
105978541 TCAAAATTCT
1 TCAAAATTCT
105978551 GTTTAAATTT
Statistics
Matches: 54, Mismatches: 18, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
9 1 0.02
10 6 0.11
11 39 0.72
12 8 0.15
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.43
Consensus pattern (11 bp):
TCAAAATTCTT
Found at i:105978786 original size:26 final size:26
Alignment explanation
Indices: 105978754--105978807 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
105978744 ATTTTATTAC
105978754 TGCTTGATTTTTTATTTCATTTATGA
1 TGCTTGATTTTTTATTTCATTTATGA
105978780 TGCTTGATTTTTTATTTCATTTATGA
1 TGCTTGATTTTTTATTTCATTTATGA
105978806 TG
1 TG
105978808 TTTGCATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.19, C:0.07, G:0.13, T:0.61
Consensus pattern (26 bp):
TGCTTGATTTTTTATTTCATTTATGA
Found at i:105980417 original size:18 final size:18
Alignment explanation
Indices: 105980394--105980435 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
105980384 GCCATGTGCA
*
105980394 TATCCTAGCCCTTATATG
1 TATCCTAACCCTTATATG
105980412 TATCCTAACCCTTATATG
1 TATCCTAACCCTTATATG
*
105980430 TTTCCT
1 TATCCT
105980436 TTTCCTAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.29, G:0.07, T:0.43
Consensus pattern (18 bp):
TATCCTAACCCTTATATG
Found at i:105982998 original size:27 final size:26
Alignment explanation
Indices: 105982961--105983055 Score: 136
Period size: 27 Copynumber: 3.5 Consensus size: 26
105982951 AGCATGACTG
105982961 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGACAGAGTCA
**
105982987 CCAGATACAGATAATCGTGGTAGAGTCA
1 CCAGA-ACAGATAAT-GTGACAGAGTCA
105983015 CCAGAACAGATATATGTGACAGAGTCA
1 CCAGAACAGATA-ATGTGACAGAGTCA
*
105983042 CCAGATCAGATAAT
1 CCAGAACAGATAAT
105983056 TGTGGCATAG
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
26 7 0.11
27 37 0.61
28 17 0.28
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (26 bp):
CCAGAACAGATAATGTGACAGAGTCA
Found at i:105983071 original size:54 final size:54
Alignment explanation
Indices: 105982961--105983072 Score: 172
Period size: 54 Copynumber: 2.1 Consensus size: 54
105982951 AGCATGACTG
* *
105982961 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGTAGAGTCA
1 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
* *
105983015 CCAGAACAGATATATGTGACAGAGTCACCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
105983069 CCAG
1 CCAG
105983073 GACGCTTCCT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
54 33 0.62
55 20 0.38
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.19
Consensus pattern (54 bp):
CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
Found at i:105983240 original size:27 final size:26
Alignment explanation
Indices: 105983179--105983240 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
105983169 AAGTAATTCC
* ** *
105983179 TAGGGGTATAATGGTAATTTTGTACC
1 TAGGGGTATAATAGTAATTTCATACA
*
105983205 TAGGGGTATATTAGTAATTTCCATACA
1 TAGGGGTATAATAGTAATTT-CATACA
105983232 TAGGGGTAT
1 TAGGGGTAT
105983241 TCAAGTAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 18 0.60
27 12 0.40
ACGTcount: A:0.29, C:0.08, G:0.26, T:0.37
Consensus pattern (26 bp):
TAGGGGTATAATAGTAATTTCATACA
Found at i:105984510 original size:25 final size:26
Alignment explanation
Indices: 105984477--105984526 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
105984467 ATCTCTTGCT
105984477 CCTTGATCAGCTCCTAAATCTTCTCC
1 CCTTGATCAGCTCCTAAATCTTCTCC
105984503 CCTT-ATCAGCTCCTAAATCTTCTC
1 CCTTGATCAGCTCCTAAATCTTCTC
105984527 TCTTATCCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.20, C:0.38, G:0.06, T:0.36
Consensus pattern (26 bp):
CCTTGATCAGCTCCTAAATCTTCTCC
Found at i:105984539 original size:24 final size:25
Alignment explanation
Indices: 105984477--105984540 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
105984467 ATCTCTTGCT
*
105984477 CCTTGATCAGCTCCTAAATCTTCTCC
1 CCTT-ATCACCTCCTAAATCTTCTCC
*
105984503 CCTTATCAGCTCCTAAATCTTCT-C
1 CCTTATCACCTCCTAAATCTTCTCC
* *
105984527 TCTTATCCCCTCCT
1 CCTTATCACCTCCT
105984541 TACTCAATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
24 12 0.34
25 19 0.54
26 4 0.11
ACGTcount: A:0.17, C:0.41, G:0.05, T:0.38
Consensus pattern (25 bp):
CCTTATCACCTCCTAAATCTTCTCC
Found at i:105987045 original size:126 final size:126
Alignment explanation
Indices: 105986820--105987052 Score: 405
Period size: 126 Copynumber: 1.8 Consensus size: 126
105986810 ATTTATAACC
* * *
105986820 TTATTTTTCTACGAACTACTGTAGCAAAAGAGCATCCACGTGGGAGCTTTTTTCAGAAATTTTGT
1 TTATTTTTCTACGAACTACTATAGCAAAAGAGCATCCACGTGGGAGCTTTTTCCAGAAATTTTGC
105986885 TAACAGTGCATCCTGCTTGAAGCGTTTTCGGCACTATTTGTTCAGAAACGTCTACTCAGAA
66 TAACAGTGCATCCTGCTTGAAGCGTTTTCGGCACTATTTGTTCAGAAACGTCTACTCAGAA
*
105986946 TTATTTTTGC-ACGAACTACTATAGCAAAAGAGCGTCCACGTGGGAGCTTTTTCCAGAAATTTTG
1 TTATTTTT-CTACGAACTACTATAGCAAAAGAGCATCCACGTGGGAGCTTTTTCCAGAAATTTTG
*
105987010 CTGACAGTGCATCCTGCTTGAAGCGTTTTCGGCACTATTTGTT
65 CTAACAGTGCATCCTGCTTGAAGCGTTTTCGGCACTATTTGTT
105987053 AGCGTCCATG
Statistics
Matches: 101, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
126 100 0.99
127 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (126 bp):
TTATTTTTCTACGAACTACTATAGCAAAAGAGCATCCACGTGGGAGCTTTTTCCAGAAATTTTGC
TAACAGTGCATCCTGCTTGAAGCGTTTTCGGCACTATTTGTTCAGAAACGTCTACTCAGAA
Found at i:105987108 original size:77 final size:78
Alignment explanation
Indices: 105986976--105987127 Score: 252
Period size: 77 Copynumber: 2.0 Consensus size: 78
105986966 ATAGCAAAAG
*
105986976 AGCGTCCACGTGGGAGCTTTTTCCAGAAATTTTGCTGACAGTGCATCCTGCTTGAAGCG-TTTTC
1 AGCGTCCACGTGAGAGCTTTTTCCAGAAATTTTGCTGACAGTGCATCCTGCTTGAAGCGTTTTTC
*
105987040 GGCACTATTTGTT
66 GACACTATTTGTT
* * *
105987053 AGCGTCCATGTGAGAGTTTTTTCCAGAAATTTTGCTGACAGTGCATCCTGTTTGAAGCGTTTTTC
1 AGCGTCCACGTGAGAGCTTTTTCCAGAAATTTTGCTGACAGTGCATCCTGCTTGAAGCGTTTTTC
105987118 GACACTATTT
66 GACACTATTT
105987128 TTCCAGAAAC
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
77 55 0.80
78 14 0.20
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (78 bp):
AGCGTCCACGTGAGAGCTTTTTCCAGAAATTTTGCTGACAGTGCATCCTGCTTGAAGCGTTTTTC
GACACTATTTGTT
Found at i:105987664 original size:21 final size:23
Alignment explanation
Indices: 105987629--105987674 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
105987619 TAAATCCTTA
*
105987629 AACCTTTACAAAACCCTAACCCT
1 AACCTTTACAAAACCATAACCCT
105987652 AACC-TTA-AAAACCATAACCCT
1 AACCTTTACAAAACCATAACCCT
105987673 AA
1 AA
105987675 ATCAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 15 0.68
22 3 0.14
23 4 0.18
ACGTcount: A:0.46, C:0.35, G:0.00, T:0.20
Consensus pattern (23 bp):
AACCTTTACAAAACCATAACCCT
Found at i:105988621 original size:18 final size:17
Alignment explanation
Indices: 105988589--105988622 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
105988579 GTTTGTTATA
*
105988589 TATCAAATTAGATTAGT
1 TATCAAATTACATTAGT
105988606 TATCAATATTACATTAG
1 TATCAA-ATTACATTAG
105988623 CATAAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (17 bp):
TATCAAATTACATTAGT
Found at i:105994564 original size:3 final size:3
Alignment explanation
Indices: 105994552--105994602 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
105994542 GTTTGAAAAA
*
105994552 AAG AAA AAG AAG AAG AAG AAG -AG AAG AAGG AAG -AG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG AAG AAG AAG
*
105994596 GAG AAG A
1 AAG AAG A
105994603 GGAAAAATGG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:105995243 original size:59 final size:59
Alignment explanation
Indices: 105995151--105995289 Score: 233
Period size: 59 Copynumber: 2.4 Consensus size: 59
105995141 TGTTGTTGTT
* *
105995151 TACAAATTGCTTAACACTTGGTATACATGGCTGCTGGTTAGAAAAGATAACAATTGATA
1 TACAAATTGCTTAACAGTTGGTATACATGGCTGCTAGTTAGAAAAGATAACAATTGATA
* * *
105995210 TACAAATTGCTGAACAGTTGGTATACATGGCTGCTAGTTAGAAAAGATAACAGTTGGTA
1 TACAAATTGCTTAACAGTTGGTATACATGGCTGCTAGTTAGAAAAGATAACAATTGATA
105995269 TACAAATTGCTTAACAGTTGG
1 TACAAATTGCTTAACAGTTGG
105995290 ATAACAAATA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
59 74 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (59 bp):
TACAAATTGCTTAACAGTTGGTATACATGGCTGCTAGTTAGAAAAGATAACAATTGATA
Found at i:105995749 original size:21 final size:21
Alignment explanation
Indices: 105995725--105995764 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
105995715 CCTTGTTGAG
105995725 TTGGGGTACCCTCTTGCTAAC
1 TTGGGGTACCCTCTTGCTAAC
* *
105995746 TTGGGGTAGCCTGTTGCTA
1 TTGGGGTACCCTCTTGCTA
105995765 GGTTCGGACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.23, G:0.30, T:0.35
Consensus pattern (21 bp):
TTGGGGTACCCTCTTGCTAAC
Found at i:105996524 original size:43 final size:43
Alignment explanation
Indices: 105996428--105996605 Score: 229
Period size: 43 Copynumber: 4.2 Consensus size: 43
105996418 TAAAAAAAAC
* *
105996428 TCATTGCATGCATATTAAAAAATAGGCAAC-ACATT--AACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAACTTTCCAACAA
* *
105996468 TTATTACATGCATATTAAAAAATAGTCAACAACTTTCCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAACTTTCCAACAA
* *
105996511 TTATTGCATGCATATTACAAAATAGTCAACAACTTTCCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAACTTTCCAACAA
* * * *
105996554 TCATTACATACATATTAAAAAA-AGTCAATAGCTTTCCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAACTTTCCAACAA
*
105996596 TCAGTGCATG
1 TCATTGCATG
105996606 TGGTCAGCAA
Statistics
Matches: 120, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
40 27 0.22
41 4 0.03
42 25 0.21
43 64 0.53
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.29
Consensus pattern (43 bp):
TCATTGCATGCATATTAAAAAATAGTCAACAACTTTCCAACAA
Found at i:105998404 original size:47 final size:48
Alignment explanation
Indices: 105998333--105998453 Score: 199
Period size: 47 Copynumber: 2.5 Consensus size: 48
105998323 AATAAACATC
105998333 ATGGCAGATATACACAATAAACATCAATTTGATAAT-GCATTCATACA
1 ATGGCAGATATACACAATAAACATCAATTTGATAATCGCATTCATACA
*
105998380 ATGGCAGATATACACAATACACATCAATTTGATAATCGCATTCATACA
1 ATGGCAGATATACACAATAAACATCAATTTGATAATCGCATTCATACA
* * *
105998428 ATGGTAGAAATAAACAATAAACATCA
1 ATGGCAGATATACACAATAAACATCA
105998454 TGCACATGGC
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
47 35 0.51
48 33 0.49
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (48 bp):
ATGGCAGATATACACAATAAACATCAATTTGATAATCGCATTCATACA
Found at i:105998513 original size:6 final size:6
Alignment explanation
Indices: 105998490--105998585 Score: 84
Period size: 6 Copynumber: 16.0 Consensus size: 6
105998480 AAATAACCCT
* * * * * * *
105998490 AAATCG AAATCT AGATCA AAATCA AAATCA AATTCT AAATCT AAATCG
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
* ** * *
105998538 AGATCA AAATTG GAATCA AAATTA AAATCA AAATCA AAATCA AAATCA
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
105998586 GTGAGTGTTT
Statistics
Matches: 71, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.56, C:0.15, G:0.06, T:0.23
Consensus pattern (6 bp):
AAATCA
Found at i:105998555 original size:36 final size:37
Alignment explanation
Indices: 105998488--105998585 Score: 101
Period size: 36 Copynumber: 2.7 Consensus size: 37
105998478 TGAAATAACC
* *
105998488 CTAAATCGAAATCTAGATCAAAATCAAAATC-AAATT
1 CTAAATCAAAATCAAGATCAAAATCAAAATCAAAATT
* * ***
105998524 CTAAATCTAAATCGAGATCAAAATTGGAATCAAAATT
1 CTAAATCAAAATCAAGATCAAAATCAAAATCAAAATT
* *
105998561 -AAAATCAAAATCAAAATCAAAATCA
1 CTAAATCAAAATCAAGATCAAAATCA
105998586 GTGAGTGTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
36 45 0.90
37 5 0.10
ACGTcount: A:0.55, C:0.15, G:0.06, T:0.23
Consensus pattern (37 bp):
CTAAATCAAAATCAAGATCAAAATCAAAATCAAAATT
Found at i:105998618 original size:12 final size:12
Alignment explanation
Indices: 105998597--105998643 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
105998587 TGAGTGTTTT
*
105998597 AAAATTGAAATC
1 AAAATCGAAATC
105998609 AAAATCGAAATC
1 AAAATCGAAATC
* *
105998621 AGAATCGAAATT
1 AAAATCGAAATC
*
105998633 AAAATTGAAAT
1 AAAATCGAAAT
105998644 AGAAACAACC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.57, C:0.09, G:0.11, T:0.23
Consensus pattern (12 bp):
AAAATCGAAATC
Found at i:105999119 original size:21 final size:21
Alignment explanation
Indices: 105999093--105999132 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
105999083 AACGTGGCAA
105999093 GTTAACTTGCCACATCAACTG
1 GTTAACTTGCCACATCAACTG
*
105999114 GTTAACTTGCCACGTCAAC
1 GTTAACTTGCCACATCAAC
105999133 AATCCCGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.28
Consensus pattern (21 bp):
GTTAACTTGCCACATCAACTG
Found at i:106006035 original size:13 final size:14
Alignment explanation
Indices: 106006019--106006054 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
106006009 CAATCTCATA
106006019 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
106006032 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
106006045 TCTC-ATTTCA
1 TCTCAATTTCA
106006055 TTCCAATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:106006044 original size:18 final size:19
Alignment explanation
Indices: 106006006--106006046 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
106005996 TGGTTCATGT
106006006 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
106006025 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
106006043 TTTC
1 TTTC
106006047 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:106006235 original size:21 final size:21
Alignment explanation
Indices: 106006210--106006294 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
106006200 TGATCAGTAT
*
106006210 ACGACACATAAAGTGCCTAAA
1 ACGACACACAAAGTGCCTAAA
* * * * *
106006231 ACGACATACGAGGTGCCTGAT
1 ACGACACACAAAGTGCCTAAA
*
106006252 ACGACACACAAGGTGCCTGAAA
1 ACGACACACAAAGTGCCT-AAA
*
106006274 TACGACACATAAAGTGCCTAA
1 -ACGACACACAAAGTGCCTAA
106006295 TCGGTAAAGC
Statistics
Matches: 50, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
21 31 0.62
22 3 0.06
23 16 0.32
ACGTcount: A:0.40, C:0.25, G:0.20, T:0.15
Consensus pattern (21 bp):
ACGACACACAAAGTGCCTAAA
Found at i:106006690 original size:15 final size:15
Alignment explanation
Indices: 106006665--106006736 Score: 90
Period size: 15 Copynumber: 4.7 Consensus size: 15
106006655 TCATATATAT
106006665 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
106006681 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
106006696 AATAATTTCAATCAA
1 TATAAATTCAATCAA
*
106006711 TATAAATTCAATAAAA
1 TATAAATTCAAT-CAA
*
106006727 TATATATTCA
1 TATAAATTCA
106006737 TAAATCAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
15 34 0.69
16 15 0.31
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:106006707 original size:30 final size:28
Alignment explanation
Indices: 106006668--106006728 Score: 104
Period size: 30 Copynumber: 2.1 Consensus size: 28
106006658 TATATATTAT
106006668 ATAATTCAATCAATATAAATTCAATCAAA
1 ATAATTCAATCAATATAAATTCAAT-AAA
106006697 ATAATTTCAATCAATATAAATTCAATAAA
1 ATAA-TTCAATCAATATAAATTCAATAAA
106006726 ATA
1 ATA
106006729 TATATTCATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 10 0.32
30 21 0.68
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATTCAATCAATATAAATTCAATAAA
Found at i:106006892 original size:2 final size:2
Alignment explanation
Indices: 106006887--106006920 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
106006877 TCACACACGC
*
106006887 AT AT AT AT AT AT AT AT AT AT AT TT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
106006921 ATTCAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:106006950 original size:15 final size:17
Alignment explanation
Indices: 106006930--106006968 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
106006920 AATTCAATTT
106006930 AATTCAATCA-ATA-TA
1 AATTCAATCACATACTA
106006945 AATTC-ATCACATACTA
1 AATTCAATCACATACTA
106006961 AATT-AATC
1 AATTCAATC
106006969 CATTTCCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 4 0.19
15 8 0.38
16 9 0.43
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (17 bp):
AATTCAATCACATACTA
Found at i:106008447 original size:40 final size:40
Alignment explanation
Indices: 106008402--106008520 Score: 125
Period size: 40 Copynumber: 3.0 Consensus size: 40
106008392 GAAAAAATCA
* *
106008402 AATAGATGGAGTTTTAGCGGCGTTTTTAAAAAAACGCCGC
1 AATAGATCGAGCTTTAGCGGCGTTTTTAAAAAAACGCCGC
* * *
106008442 AATAGATCGAGCTTTCGCGGCGTTTTTGAAAAAGCGCCGC
1 AATAGATCGAGCTTTAGCGGCGTTTTTAAAAAAACGCCGC
* * * **
106008482 TAA-AGGTCGACCTTTTGCGGCG-TTTTACTAAAACGCCGC
1 -AATAGATCGAGCTTTAGCGGCGTTTTTAAAAAAACGCCGC
106008521 TAAAAGTTTA
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
39 13 0.20
40 51 0.77
41 2 0.03
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (40 bp):
AATAGATCGAGCTTTAGCGGCGTTTTTAAAAAAACGCCGC
Found at i:106009713 original size:25 final size:24
Alignment explanation
Indices: 106009663--106009714 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
106009653 TAACTTATTT
**
106009663 TTTAAATGAATTTAAAATTTTCTA
1 TTTAAATGAATTTAAAATTTAATA
* *
106009687 TTTAAACTGATTTTTAAATTTAATA
1 TTTAAA-TGAATTTAAAATTTAATA
106009712 TTT
1 TTT
106009715 TTATAGGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (24 bp):
TTTAAATGAATTTAAAATTTAATA
Found at i:106012110 original size:46 final size:45
Alignment explanation
Indices: 106012057--106012228 Score: 170
Period size: 46 Copynumber: 3.7 Consensus size: 45
106012047 TGAGCATCCA
*
106012057 AACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT-TCCG
* * * * *
106012103 AACTCGTTGAGTTGAGTCCGAGTTC-GTGAAATGTAACTAG-GCATT-CA
1 AACTCGTTGAGTTGAGTCCGAGTTCACT--TATG-GA-T-GCGAATTCCG
* **
106012150 AACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAACACCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-TTCCG
*
106012196 AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
106012229 GCGGGTTACA
Statistics
Matches: 101, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 59 0.58
47 29 0.29
48 3 0.03
49 4 0.04
50 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (45 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATTCCG
Found at i:106012214 original size:93 final size:93
Alignment explanation
Indices: 106012050--106012220 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
106012040 GGATGGTTGA
* ***
106012050 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACCTATAGATGCGAACACCCGAACTCGTTGAGT
106012115 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* * *
106012143 GCATTCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAACACCCGAGCTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACCTATAGATGCGAACACCCGAACTCGTTGAGT
106012208 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
106012221 ACTTATGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACCTATAGATGCGAACACCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:106014023 original size:21 final size:21
Alignment explanation
Indices: 106013975--106014026 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
106013965 TAAGGGTTAA
* *
106013975 TTAGGGTTTAGGGTCTAGAGT
1 TTAGGGTTTAAGGTCTAGAAT
* * *
106013996 TTGGGGTTTAAGGTTTATAAT
1 TTAGGGTTTAAGGTCTAGAAT
106014017 TTAGGGTTTA
1 TTAGGGTTTA
106014027 TGGTATAGGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.02, G:0.33, T:0.44
Consensus pattern (21 bp):
TTAGGGTTTAAGGTCTAGAAT
Found at i:106014172 original size:19 final size:20
Alignment explanation
Indices: 106014148--106014185 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
106014138 GGATTTTAGG
106014148 GTTTAGGGTTT-AGGGTTAT
1 GTTTAGGGTTTAAGGGTTAT
*
106014167 GTTTAGTGTTTAAGGGTTA
1 GTTTAGGGTTTAAGGGTTA
106014186 GCAGGTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.47
Consensus pattern (20 bp):
GTTTAGGGTTTAAGGGTTAT
Found at i:106016043 original size:24 final size:24
Alignment explanation
Indices: 106015980--106016048 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
106015970 TTTGTGACTG
*
106015980 TGAAAATCGTATTATAATAATGTTA
1 TGAAAATTGTATTATAAT-ATGTTA
**
106016005 T-ACTATCT-TATTTATAATATGTTA
1 TGAAAAT-TGTA-TTATAATATGTTA
106016029 TGAAAATTGTATTATAATAT
1 TGAAAATTGTATTATAATAT
106016049 ACTTTGGTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
24 22 0.63
25 13 0.37
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (24 bp):
TGAAAATTGTATTATAATATGTTA
Found at i:106017742 original size:70 final size:70
Alignment explanation
Indices: 106017624--106017758 Score: 209
Period size: 70 Copynumber: 1.9 Consensus size: 70
106017614 GACTCAGATC
* *
106017624 CATGGTTCAAATAAGTCACTTACCTTTTAAGTACTAAATTGGACAAAAATCTAAATTCATGTGTT
1 CATGGTTCAAATAAGTCACTTACCTTTTAAGTACTAAATTGGAAAAAAATCTAAATTCAAGTGTT
106017689 AGGTT
66 AGGTT
* * *
106017694 CATGGTTCAAATAAGTCATTTACC-TTTAAGTACTTATTTGGAAAAAAAATCTAAATTCAAGTGT
1 CATGGTTCAAATAAGTCACTTACCTTTTAAGTACTAAATTGG-AAAAAAATCTAAATTCAAGTGT
106017758 T
65 T
106017759 GATTACTTAA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
69 15 0.25
70 44 0.75
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Consensus pattern (70 bp):
CATGGTTCAAATAAGTCACTTACCTTTTAAGTACTAAATTGGAAAAAAATCTAAATTCAAGTGTT
AGGTT
Found at i:106018925 original size:9 final size:9
Alignment explanation
Indices: 106018911--106019027 Score: 117
Period size: 9 Copynumber: 12.3 Consensus size: 9
106018901 CCTTAAAAAA
106018911 TTACATAAC
1 TTACATAAC
106018920 TTACATAAC
1 TTACATAAC
* *
106018929 TCATATAAC
1 TTACATAAC
*
106018938 TTACATAAT
1 TTACATAAC
106018947 TTACATAACAAC
1 TTACAT---AAC
106018959 TTACATAAC
1 TTACATAAC
*
106018968 TCACATAAC
1 TTACATAAC
*
106018977 TTACATAAT
1 TTACATAAC
106018986 TTACATAAC
1 TTACATAAC
*
106018995 TCACATAAC
1 TTACATAAC
*
106019004 GTACATAACAAC
1 TTACAT---AAC
106019016 TTACATAAC
1 TTACATAAC
106019025 TTA
1 TTA
106019028 ACTAATACAT
Statistics
Matches: 88, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
9 72 0.82
12 16 0.18
ACGTcount: A:0.45, C:0.22, G:0.01, T:0.32
Consensus pattern (9 bp):
TTACATAAC
Found at i:106018964 original size:39 final size:39
Alignment explanation
Indices: 106018917--106018994 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
106018907 AAAATTACAT
*
106018917 AACTTACATAACTCATATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
106018956 AACTTACATAACTCACATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
106018995 TCACATAACG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (39 bp):
AACTTACATAACTCACATAACTTACATAATTTACATAAC
Found at i:106019001 original size:57 final size:57
Alignment explanation
Indices: 106018913--106019025 Score: 172
Period size: 57 Copynumber: 2.0 Consensus size: 57
106018903 TTAAAAAATT
* * **
106018913 ACATAACTTACATAACTCATATAACTTACATAATTTACATAACAACTTACATAACTC
1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC
* *
106018970 ACATAACTTACATAATTTACATAACTCACATAACGTACATAACAACTTACATAACT
1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACT
106019026 TAACTAATAC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.46, C:0.23, G:0.01, T:0.30
Consensus pattern (57 bp):
ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC
Found at i:106019017 original size:39 final size:36
Alignment explanation
Indices: 106018912--106019023 Score: 129
Period size: 39 Copynumber: 2.9 Consensus size: 36
106018902 CTTAAAAAAT
106018912 TACATAACTTACATAACT-CATATAACTTACATAATT
1 TACATAACTTACATAACTACATA-AACTTACATAATT
106018948 TACATAACAACTTACATAACTCACAT-AACTTACATAATT
1 TACAT---AACTTACATAACT-ACATAAACTTACATAATT
*
106018987 TACATAACTCACATAACGTACATAACAACTTACATAA
1 TACATAACTTACATAAC-TACAT-A-AACTTACATAA
106019024 CTTAACTAAT
Statistics
Matches: 66, Mismatches: 1, Indels: 15
0.80 0.01 0.18
Matches are distributed among these distances:
36 20 0.30
37 1 0.02
39 42 0.64
41 3 0.05
ACGTcount: A:0.46, C:0.22, G:0.01, T:0.30
Consensus pattern (36 bp):
TACATAACTTACATAACTACATAAACTTACATAATT
Found at i:106019528 original size:20 final size:20
Alignment explanation
Indices: 106019482--106019519 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
106019472 AGCTCGTTTC
* *
106019482 CAGCTTACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
106019502 CAGCTCACTCAAGCTCAA
1 CAGCTCACTCAAGCTCAA
106019520 TTTAGCTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.34, G:0.16, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:106025318 original size:21 final size:21
Alignment explanation
Indices: 106025292--106025336 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
106025282 ACTTAGAGCG
* *
106025292 GAGGCAGCAGCGCGGGAGGCA
1 GAGGCAGCAGCGAGGAAGGCA
106025313 GAGGCAGCAGCGAGGAAGGCA
1 GAGGCAGCAGCGAGGAAGGCA
106025334 GAG
1 GAG
106025337 CAGAACAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.29, C:0.20, G:0.51, T:0.00
Consensus pattern (21 bp):
GAGGCAGCAGCGAGGAAGGCA
Found at i:106025719 original size:41 final size:42
Alignment explanation
Indices: 106025647--106025790 Score: 121
Period size: 41 Copynumber: 3.4 Consensus size: 42
106025637 CGTTTCTTAA
* ****
106025647 AAAAAGCACCGCTAAAAGTACTGCAAATTAGCGGCATTTTTT
1 AAAAAGCGCCGCTAAAAGTACTGGTCTTTAGCGGCATTTTTT
* *
106025689 -AAAAGCGCCGCTAAAAGTACTGGTCTTTAGCGTCGTTTTTT
1 AAAAAGCGCCGCTAAAAGTACTGGTCTTTAGCGGCATTTTTT
* * * *
106025730 AAAAAAGAGCCGCGAAAAGT-CTTTGTCTTTAGCGGCGCTTTTTT
1 -AAAAAGCGCCGCTAAAAGTAC-TGGTCTTTAGCGGC-ATTTTTT
*
106025774 CAAAAAAACGCCGCTAA
1 --AAAAAGCGCCGCTAA
106025791 TTTTACCGGC
Statistics
Matches: 82, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
41 34 0.41
42 1 0.01
43 28 0.34
44 6 0.07
45 13 0.16
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (42 bp):
AAAAAGCGCCGCTAAAAGTACTGGTCTTTAGCGGCATTTTTT
Found at i:106025758 original size:43 final size:45
Alignment explanation
Indices: 106025689--106025780 Score: 118
Period size: 43 Copynumber: 2.1 Consensus size: 45
106025679 GGCATTTTTT
* * *
106025689 AAAAGCGCCGCTAAAAGTACTGGTCTTTAGCGTCG-TTTTTT-AA
1 AAAAGAGCCGCGAAAAGTACTGGTCTTTAGCGGCGCTTTTTTCAA
*
106025732 AAAAGAGCCGCGAAAAGT-CTTTGTCTTTAGCGGCGCTTTTTTCAA
1 AAAAGAGCCGCGAAAAGTAC-TGGTCTTTAGCGGCGCTTTTTTCAA
106025777 AAAA
1 AAAA
106025781 ACGCCGCTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
42 1 0.02
43 29 0.69
44 6 0.14
45 6 0.14
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (45 bp):
AAAAGAGCCGCGAAAAGTACTGGTCTTTAGCGGCGCTTTTTTCAA
Found at i:106029609 original size:38 final size:38
Alignment explanation
Indices: 106029566--106029643 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
106029556 GCATGCACAA
*
106029566 AAAATTTGTTTTAATAAATTATCAACATCAAATATGAT
1 AAAATTTGTTTTAATAAATTACCAACATCAAATATGAT
106029604 AAAATTTGTTTTAATAAATTACCAACATCAAATATGAT
1 AAAATTTGTTTTAATAAATTACCAACATCAAATATGAT
106029642 AA
1 AA
106029644 GTATTAGGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (38 bp):
AAAATTTGTTTTAATAAATTACCAACATCAAATATGAT
Found at i:106031241 original size:9 final size:9
Alignment explanation
Indices: 106031227--106031294 Score: 73
Period size: 9 Copynumber: 7.6 Consensus size: 9
106031217 ATAAGCATAA
106031227 AATTAACCG
1 AATTAACCG
*
106031236 AATTAATCG
1 AATTAACCG
106031245 AATTAACCG
1 AATTAACCG
*
106031254 AATTATCCG
1 AATTAACCG
* *
106031263 AATTATCCA
1 AATTAACCG
* *
106031272 AATTAATCT
1 AATTAACCG
*
106031281 AGTTAACCG
1 AATTAACCG
106031290 AATTA
1 AATTA
106031295 TTTGTATAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 48 1.00
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.31
Consensus pattern (9 bp):
AATTAACCG
Found at i:106031250 original size:18 final size:18
Alignment explanation
Indices: 106031227--106031294 Score: 84
Period size: 18 Copynumber: 3.8 Consensus size: 18
106031217 ATAAGCATAA
106031227 AATTAACCGAATTAATCG
1 AATTAACCGAATTAATCG
106031245 AATTAACCGAATT-ATCCG
1 AATTAACCGAATTAAT-CG
* * *
106031263 AATTATCCAAATTAATCT
1 AATTAACCGAATTAATCG
*
106031281 AGTTAACCGAATTA
1 AATTAACCGAATTA
106031295 TTTGTATAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
17 2 0.05
18 38 0.90
19 2 0.05
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.31
Consensus pattern (18 bp):
AATTAACCGAATTAATCG
Found at i:106031329 original size:5 final size:6
Alignment explanation
Indices: 106031314--106031354 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
106031304 AATTATATGT
*
106031314 TTTTTA TTTTTA TTTTTA GTTTTAGA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTT
106031355 ATTAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 22 0.71
7 8 0.26
8 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:106039772 original size:16 final size:17
Alignment explanation
Indices: 106039749--106039786 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
106039739 AATAAACAAT
106039749 TAAA-TAAATT-GGAAA
1 TAAATTAAATTGGGAAA
106039764 TAAATTAAATTGGGAAA
1 TAAATTAAATTGGGAAA
106039781 TAAATT
1 TAAATT
106039787 CGAATTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.19
16 6 0.29
17 11 0.52
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (17 bp):
TAAATTAAATTGGGAAA
Found at i:106042984 original size:10 final size:10
Alignment explanation
Indices: 106042969--106042993 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
106042959 TGGAGTCGTT
106042969 TTGGCGTATC
1 TTGGCGTATC
106042979 TTGGCGTATC
1 TTGGCGTATC
106042989 TTGGC
1 TTGGC
106042994 AGGGTCATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.20, G:0.32, T:0.40
Consensus pattern (10 bp):
TTGGCGTATC
Found at i:106043908 original size:15 final size:17
Alignment explanation
Indices: 106043882--106043915 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
106043872 TTTTAAAATT
106043882 ATAAAAATATTT-TAAA
1 ATAAAAATATTTGTAAA
106043898 ATAAAAA-ATTTGTAAA
1 ATAAAAATATTTGTAAA
106043914 AT
1 AT
106043916 TTATATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
ATAAAAATATTTGTAAA
Found at i:106043940 original size:22 final size:22
Alignment explanation
Indices: 106043898--106043959 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
106043888 ATATTTTAAA
106043898 ATAAAAAATTTGTAAAA-TTTAT
1 ATAAAAAATTT-TAAAATTTTAT
106043920 ATAAAAAATTTTAAAATTTTAT
1 ATAAAAAATTTTAAAATTTTAT
* * * *
106043942 TTTAAAAATATAAAAATT
1 ATAAAAAATTTTAAAATT
106043960 ATTGAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.14
22 30 0.86
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
ATAAAAAATTTTAAAATTTTAT
Found at i:106043948 original size:21 final size:22
Alignment explanation
Indices: 106043898--106043938 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
106043888 ATATTTTAAA
106043898 ATAAAAAATTTGTAAAATTTAT
1 ATAAAAAATTTGTAAAATTTAT
106043920 ATAAAAAATTT-TAAAATTT
1 ATAAAAAATTTGTAAAATTT
106043939 TATTTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
ATAAAAAATTTGTAAAATTTAT
Found at i:106044281 original size:18 final size:19
Alignment explanation
Indices: 106044260--106044296 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
106044250 AAATCATAAT
106044260 AATTTTAAAAT-ATTTTAA
1 AATTTTAAAATAATTTTAA
*
106044278 AATTTTATAATAATTTTAA
1 AATTTTAAAATAATTTTAA
106044297 TTTTTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AATTTTAAAATAATTTTAA
Found at i:106044565 original size:19 final size:19
Alignment explanation
Indices: 106044526--106044603 Score: 66
Period size: 19 Copynumber: 3.9 Consensus size: 19
106044516 ATAAAATAAA
* **
106044526 TTTTACAATTTTTAAGGAT
1 TTTTACAAATTTTAAATAT
*
106044545 TTTTACAACTTTTAAATAT
1 TTTTACAAATTTTAAATAT
*
106044564 TTTTAAATAAATTTTAAATAT
1 TTTT--ACAAATTTTAAATAT
* *
106044585 TTTTATATATATTTAAATA
1 TTTTACAAAT-TTTAAATA
106044604 AAATTTAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
19 25 0.50
20 8 0.16
21 17 0.34
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.54
Consensus pattern (19 bp):
TTTTACAAATTTTAAATAT
Found at i:106044567 original size:10 final size:10
Alignment explanation
Indices: 106044554--106044603 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
106044544 TTTTTACAAC
106044554 TTTTAAATAT
1 TTTTAAATAT
*
106044564 TTTTAAATAAA
1 TTTTAAAT-AT
106044575 TTTTAAATAT
1 TTTTAAATAT
*
106044585 TTTTATATAT
1 TTTTAAATAT
*
106044595 ATTTAAATA
1 TTTTAAATA
106044604 AAATTTAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
10 25 0.74
11 9 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTTAAATAT
Found at i:106044580 original size:21 final size:21
Alignment explanation
Indices: 106044554--106044603 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
106044544 TTTTTACAAC
106044554 TTTTAAATATTTTTAAATAAA
1 TTTTAAATATTTTTAAATAAA
* *
106044575 TTTTAAATATTTTTATATATA
1 TTTTAAATATTTTTAAATAAA
106044596 -TTTAAATA
1 TTTTAAATA
106044604 AAATTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTAAATATTTTTAAATAAA
Found at i:106044589 original size:31 final size:30
Alignment explanation
Indices: 106044554--106044622 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 30
106044544 TTTTTACAAC
* *
106044554 TTTTAAATATTTTTAAATAAATTTTAAATAT
1 TTTTAAATATATTTAAATAAAATTTAAA-AT
*
106044585 TTTTATATATATTTAAATAAAATTTAAAAT
1 TTTTAAATATATTTAAATAAAATTTAAAAT
106044615 TTTCTAAA
1 TTT-TAAA
106044623 CATTATTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 5 0.15
31 28 0.85
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (30 bp):
TTTTAAATATATTTAAATAAAATTTAAAAT
Found at i:106052336 original size:29 final size:27
Alignment explanation
Indices: 106052295--106052358 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 27
106052285 TGTTGCTCCC
*
106052295 AATAATTTTTATTTACTTT-TTATATTTTT
1 AATATTTTTTATTTA-TTTGTT-TA-TTTT
106052324 AATATTTTTTATTTATTTGTTTATTTT
1 AATATTTTTTATTTATTTGTTTATTTT
106052351 AA-ATTTTT
1 AATATTTTT
106052359 AAAAAATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
26 6 0.18
27 6 0.18
28 5 0.15
29 16 0.48
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (27 bp):
AATATTTTTTATTTATTTGTTTATTTT
Found at i:106061175 original size:104 final size:104
Alignment explanation
Indices: 106060995--106061261 Score: 455
Period size: 104 Copynumber: 2.6 Consensus size: 104
106060985 TTGTATATAA
** *
106060995 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
106061059 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
106061099 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
106061164 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
** *
106061203 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGCGGTGGTGCTAAGTGCGAGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
106061262 ATAACGGTTA
Statistics
Matches: 154, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
104 153 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.31, T:0.30
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:106064133 original size:10 final size:10
Alignment explanation
Indices: 106064126--106064158 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
106064116 GATTTTAATT
106064126 TTTTTTAAAA
1 TTTTTTAAAA
106064136 TTTTTTAAAA
1 TTTTTTAAAA
106064146 -TTTTTAAAA
1 TTTTTTAAAA
106064155 TTTT
1 TTTT
106064159 AAAAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTTTTAAAA
Found at i:106064164 original size:10 final size:9
Alignment explanation
Indices: 106064127--106064162 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
106064117 ATTTTAATTT
106064127 TTTTTAAAA
1 TTTTTAAAA
106064136 TTTTTTAAAA
1 -TTTTTAAAA
106064146 TTTTTAAAA
1 TTTTTAAAA
106064155 -TTTTAAAA
1 TTTTTAAAA
106064163 AAATTAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.31
9 9 0.35
10 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:106064288 original size:23 final size:22
Alignment explanation
Indices: 106064247--106064289 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
106064237 GAGTGATTTG
* *
106064247 ATAAAAAAATTAAATTTAAAGA
1 ATAAAAAAATAAAAATTAAAGA
106064269 ATAAAAAAATGAAAAATTAAA
1 ATAAAAAAAT-AAAAATTAAA
106064290 TGAAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (22 bp):
ATAAAAAAATAAAAATTAAAGA
Found at i:106075057 original size:12 final size:12
Alignment explanation
Indices: 106075040--106075070 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
106075030 GTTTTCTAAT
106075040 AAATTTAAAAAA
1 AAATTTAAAAAA
106075052 AAATTTAAAAAA
1 AAATTTAAAAAA
*
106075064 AACTTTA
1 AAATTTA
106075071 TACTTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (12 bp):
AAATTTAAAAAA
Found at i:106076026 original size:16 final size:17
Alignment explanation
Indices: 106076005--106076037 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
106075995 TATATAGAAA
106076005 AAAAATG-GACCGTTGG
1 AAAAATGTGACCGTTGG
106076021 AAAAATGTGACCGTTGG
1 AAAAATGTGACCGTTGG
106076038 TCCAATTAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.21
Consensus pattern (17 bp):
AAAAATGTGACCGTTGG
Found at i:106076086 original size:53 final size:53
Alignment explanation
Indices: 106076023--106076127 Score: 165
Period size: 53 Copynumber: 2.0 Consensus size: 53
106076013 ACCGTTGGAA
* * *
106076023 AAATGTGACCGTTGGTCCAATTAGCCGTTGGTTTCAATGGTTAGAAAATCAAG
1 AAATGTGACCGTTGGTCCAAGTAGCCGTTGGTCTCAACGGTTAGAAAATCAAG
* *
106076076 AAATGTGACCGTTGGTCTAAGTAGTCGTTGGTCTCAACGGTTAGAAAATCAA
1 AAATGTGACCGTTGGTCCAAGTAGCCGTTGGTCTCAACGGTTAGAAAATCAA
106076128 CGATGGTGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (53 bp):
AAATGTGACCGTTGGTCCAAGTAGCCGTTGGTCTCAACGGTTAGAAAATCAAG
Found at i:106078597 original size:14 final size:14
Alignment explanation
Indices: 106078578--106078608 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
106078568 TTTGATTGGT
*
106078578 GGAAAATATTTTCC
1 GGAAAATATTTTAC
106078592 GGAAAATATTTTAC
1 GGAAAATATTTTAC
106078606 GGA
1 GGA
106078609 TTTTCCAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (14 bp):
GGAAAATATTTTAC
Found at i:106078999 original size:13 final size:13
Alignment explanation
Indices: 106078981--106079005 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
106078971 CTTGTCTTGG
106078981 GCAGACTTTCTTC
1 GCAGACTTTCTTC
106078994 GCAGACTTTCTT
1 GCAGACTTTCTT
106079006 TAGAAAGGTA
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:0.16, C:0.28, G:0.16, T:0.40
Consensus pattern (13 bp):
GCAGACTTTCTTC
Done.