Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167827.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_10, 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: 24162007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 47000 characters in sequence are not A, C, G, or T
File 14 of 131
Found at i:3613005 original size:16 final size:15
Alignment explanation
Indices: 3612945--3612993 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
3612935 TTCAAAAATC
*
3612945 AATAATTTAAATTTGA
1 AATAATTCAAATTT-A
3612961 AATAATTCAAACTTTA
1 AATAATTCAAA-TTTA
*
3612977 ATTAATTCAAATTTA
1 AATAATTCAAATTTA
3612992 AA
1 AA
3612994 ATAACTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 5 0.17
16 21 0.72
17 3 0.10
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (15 bp):
AATAATTCAAATTTA
Found at i:3613089 original size:15 final size:16
Alignment explanation
Indices: 3613071--3613103 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3613061 AAAATTAATA
*
3613071 ATTTAGATT-AAAATG
1 ATTTAAATTCAAAATG
3613086 ATTTAAATTCAAAATG
1 ATTTAAATTCAAAATG
3613102 AT
1 AT
3613104 CCAAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.39
Consensus pattern (16 bp):
ATTTAAATTCAAAATG
Found at i:3616563 original size:2 final size:2
Alignment explanation
Indices: 3616558--3616586 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3616548 TATATATATA
3616558 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3616587 CACGTAGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3618101 original size:24 final size:24
Alignment explanation
Indices: 3618055--3618102 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3618045 TTTTAATTTG
* *
3618055 ATAAATTAAATCAATATATAATTA
1 ATAAATTAAATAAATATACAATTA
3618079 ATAAATT-AATAAATACTACAATTA
1 ATAAATTAAATAAATA-TACAATTA
3618103 CAATTATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (24 bp):
ATAAATTAAATAAATATACAATTA
Found at i:3621241 original size:3 final size:3
Alignment explanation
Indices: 3621233--3621294 Score: 67
Period size: 3 Copynumber: 21.3 Consensus size: 3
3621223 TATATATCAG
* *
3621233 TAT TAT TAT TAT TACT T-T TAT TAT TAT TAT T-T TAT TAC TCT TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
3621277 T-G TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
3621295 TTTTCTTTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 42 0.86
4 2 0.04
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3621267 original size:14 final size:14
Alignment explanation
Indices: 3621235--3621291 Score: 78
Period size: 14 Copynumber: 4.0 Consensus size: 14
3621225 TATATCAGTA
3621235 TTATTATTATTACTT
1 TTATTATTATTA-TT
3621250 TTATTATTATTATT
1 TTATTATTATTATT
* *
3621264 TTATTACTCTTATT
1 TTATTATTATTATT
*
3621278 GTATTATTATTATT
1 TTATTATTATTATT
3621292 ATTTTTTCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
14 25 0.68
15 12 0.32
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (14 bp):
TTATTATTATTATT
Found at i:3622075 original size:5 final size:5
Alignment explanation
Indices: 3622056--3622139 Score: 53
Period size: 5 Copynumber: 15.8 Consensus size: 5
3622046 AGGTTTCTTT
* * ** *
3622056 TTTTA TTTTA GTTTTA TTTTGA TTTGA TTTGA TTTTA TTTTTA GCTCA
1 TTTTA TTTTA -TTTTA TTTT-A TTTTA TTTTA TTTTA -TTTTA TTTTA
*
3622104 TTTTA TTTTTA GTTTTA TTATT- TTTTG TTTTA TTTT
1 TTTTA -TTTTA -TTTTA TT-TTA TTTTA TTTTA TTTT
3622140 TGAAAAATTT
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
4 2 0.03
5 35 0.56
6 26 0.41
ACGTcount: A:0.17, C:0.02, G:0.08, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:3622179 original size:17 final size:17
Alignment explanation
Indices: 3622133--3622182 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
3622123 ATTTTTTGTT
3622133 TTATTTTTGAAAAATTTA
1 TTATTTTT-AAAAATTTA
3622151 TTATTTTGTAAAAATTGT-
1 TTATTTT-TAAAAATT-TA
*
3622169 TTCTTTTTAAAAAT
1 TTATTTTTAAAAAT
3622183 AAAGGAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 7 0.24
18 20 0.69
19 2 0.07
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (17 bp):
TTATTTTTAAAAATTTA
Found at i:3625183 original size:35 final size:35
Alignment explanation
Indices: 3625144--3625220 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
3625134 AAGGAACATC
* *
3625144 TTAAATTTTAAGTATGTTCCTTTAATTAACAAACT
1 TTAAATTCTAAATATGTTCCTTTAATTAACAAACT
* * *
3625179 TTAAATTCTAAATCTGTTTCTTTAATTACCAAACT
1 TTAAATTCTAAATATGTTCCTTTAATTAACAAACT
3625214 TTAAATT
1 TTAAATT
3625221 ATTATTTGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (35 bp):
TTAAATTCTAAATATGTTCCTTTAATTAACAAACT
Found at i:3630384 original size:20 final size:20
Alignment explanation
Indices: 3630347--3630396 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
3630337 ATTTAATCTA
3630347 ATTATAT-TTAT-A-ATATT
1 ATTATATCTTATAATATATT
3630364 ATCT-TATCTTATAATATATT
1 AT-TATATCTTATAATATATT
3630384 ATTATATCTTATA
1 ATTATATCTTATA
3630397 TATCAAACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
17 5 0.18
18 5 0.18
19 2 0.07
20 16 0.57
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTATATCTTATAATATATT
Found at i:3632266 original size:210 final size:209
Alignment explanation
Indices: 3631984--3632379 Score: 503
Period size: 210 Copynumber: 1.9 Consensus size: 209
3631974 TTGAAGGCGA
3631984 CAAAAAATGCCTTGAATAATCTATTAACAAAAACACTAGAGCAGTTCAATCAGTTAGAACATACG
1 CAAAAAATGCCTTGAATAATCTATTAACAAAAACACTAGAGCAGTTCAATCAGTTAGAACATACG
* * * * * *
3632049 ATTATTAACCATTAGGTCATAGGTTCGATCTTTTACTCCAGCATTTTGAGGGTTTTTCAAGGGAT
66 ATTATTAACCATAAAGTCATAGGTTCGATC-CTCACTCCAGCATTTTAAGGGTTTTTCAAAGGAT
* * *
3632114 TATTAAAAGCGTTTTTAGCCATAAACAT-C-TTGAATAATCTCTTACAAAAAATTGAATATGATT
130 TATTAAAAGCGTTTTT-GACA-AAA-ATGCTTTGAATAATCCCTTACAAAAAATTAAATATGATT
3632177 ATTCAAGGTGTTTTTGAC
192 ATTCAAGGTGTTTTTGAC
* * * * ** *
3632195 CAAAAACT-CCTTGAATAAT-TCATTAACAAAAACACTTGAGTAGTTCAGTTGGTTAGAGCATAC
1 CAAAAAATGCCTTGAATAATCT-ATTAACAAAAACACTAGAGCAGTTCAATCAGTTAGAACATAC
* * * * * **
3632258 GGTTATTAATCATAAAGTCGTAGGTTTGATCCTCCCTTTAGCATTTTAAGGGTTTTTCAAAGGAT
65 GATTATTAACCATAAAGTCATAGGTTCGATCCTCACTCCAGCATTTTAAGGGTTTTTCAAAGGAT
*
3632323 TATTAAAGGCGTTTTTGACAAAAATGCTTTGAATAATCCCTTACAAAAAATTAAATA
130 TATTAAAAGCGTTTTTGACAAAAATGCTTTGAATAATCCCTTACAAAAAATTAAATA
3632380 ACCAAAAATG
Statistics
Matches: 158, Mismatches: 24, Indels: 9
0.83 0.13 0.05
Matches are distributed among these distances:
206 2 0.01
207 4 0.03
208 30 0.19
209 43 0.27
210 72 0.46
211 7 0.04
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (209 bp):
CAAAAAATGCCTTGAATAATCTATTAACAAAAACACTAGAGCAGTTCAATCAGTTAGAACATACG
ATTATTAACCATAAAGTCATAGGTTCGATCCTCACTCCAGCATTTTAAGGGTTTTTCAAAGGATT
ATTAAAAGCGTTTTTGACAAAAATGCTTTGAATAATCCCTTACAAAAAATTAAATATGATTATTC
AAGGTGTTTTTGAC
Found at i:3632658 original size:60 final size:60
Alignment explanation
Indices: 3632497--3633043 Score: 225
Period size: 60 Copynumber: 8.9 Consensus size: 60
3632487 ACTCCAGTGT
* * * * * * *
3632497 TTTTGTTAATGGATTATTCAAGTCATTTTTAGTC-AAAA-ACCTTTAAATAATCTTATTTAATTT
1 TTTT-TTAAAGGATTATTCAAGGCATTTTTGGCCAAAAATACC-TTGAATAATCCTA-TTAA--A
* * * ** *
3632560 TTTTTATAAAGGATTATTCAAGG-AGTTGTTAGCTAAAAACGCCTTGAATAATCCTATTCAA
1 TTTTT-TAAAGGATTATTCAAGGCA-TTTTTGGCCAAAAATACCTTGAATAATCCTATTAAA
*
3632621 TTTTTTAAAGGATTATTCAAGGCATTTTTGGCCAAAAATACCTTGAATAATCCCTA-AAAA
1 TTTTTTAAAGGATTATTCAAGGCATTTTTGGCCAAAAATACCTTGAATAAT-CCTATTAAA
*** *** * * * * * * * *
3632681 GAATGGCATGGATTATTTAATGCATTTTTAGCTAGAAATGCCTTGAATAA-CCTCATTTAA
1 TTTTTTAAAGGATTATTCAAGGCATTTTTGGCCAAAAATACCTTGAATAATCCT-ATTAAA
* * * *
3632741 -TTTTTATGAGGAGGTTATTCAAAGCATTTTTGGTCAAAAACACCTTGAATAAT-CT-TTAAAAA
1 TTTTTTA-AAGGA--TTATTCAAGGCATTTTTGGCCAAAAATACCTTGAATAATCCTATT--AAA
** ** * * * * * *
3632803 AATAGTAAAGGATTATTCAAAGCATTTTTGGCTAGAAATGCATTAAATAA-CCTTATTAAA
1 TTTTTTAAAGGATTATTCAAGGCATTTTTGGCCAAAAATACCTTGAATAATCC-TATTAAA
* * * ** * * * *
3632863 TTTTTTGTAATA-AATTATTAAAGGTATTTTTGGTGAAAAACACTTTAAATAATCTCTCATAAAA
1 -TTTTT-TAA-AGGATTATTCAAGGCATTTTTGGCCAAAAATACCTTGAATAATC-CT-ATTAAA
* * * *
3632927 TTTTATTAAGAGGATTATTCAAGCCGA-TTTTGACCAAAAATACCTTGAATAATCCCATTGAA
1 TTTT-TTAA-AGGATTATTCAAGGC-ATTTTTGGCCAAAAATACCTTGAATAATCCTATTAAA
* * * ** * * *
3632989 TTTTTTGTAAGAAATTATTTAAGATATTTTTGACAAAAAATGCCTTGAATAATCC
1 TTTTTT-AAAG-GATTATTCAAGGCATTTTTGGCCAAAAATACCTTGAATAATCC
3633044 AACAAGAAAT
Statistics
Matches: 359, Mismatches: 95, Indels: 61
0.70 0.18 0.12
Matches are distributed among these distances:
58 3 0.01
59 2 0.01
60 120 0.33
61 17 0.05
62 119 0.33
63 43 0.12
64 52 0.14
65 3 0.01
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.38
Consensus pattern (60 bp):
TTTTTTAAAGGATTATTCAAGGCATTTTTGGCCAAAAATACCTTGAATAATCCTATTAAA
Found at i:3632790 original size:122 final size:119
Alignment explanation
Indices: 3632567--3632868 Score: 331
Period size: 122 Copynumber: 2.5 Consensus size: 119
3632557 TTTTTTTTAT
* * * * *
3632567 AAAGGATTATTC-AAGGAGTTGTTAGCTAAAAACGCCTTGAATAATCCTATTCAATTTTTTAAAG
1 AAAGGATTATTCAAAGCA-TTTTTAGCTAGAAATGCCTTGAATAA-CCTATTAAATTTTTTAAAG
* *
3632631 GATTATTCAAGGCATTTTTGGCCAAAAATACCTTGAATAATCCCTAAAAAGAAT-GG
64 GATTATTCAAAGCATTTTTGGCCAAAAACACCTTGAATAATCCCTAAAAA-AATAGG
* * * * * *
3632687 CATGGATTATTTAATGCATTTTTAGCTAGAAATGCCTTGAATAACCTCATTTAA-TTTTTATGAG
1 AAAGGATTATTCAAAGCATTTTTAGCTAGAAATGCCTTGAATAACCT-ATTAAATTTTTTA-AAG
* ** *
3632751 GAGGTTATTCAAAGCATTTTTGGTCAAAAACACCTTGAATAATCTTTAAAAAAATAGT
64 GA--TTATTCAAAGCATTTTTGGCCAAAAACACCTTGAATAATCCCTAAAAAAATAGG
* * *
3632809 AAAGGATTATTCAAAGCATTTTTGGCTAGAAATGCATTAAATAACCTTATTAAATTTTTT
1 AAAGGATTATTCAAAGCATTTTTAGCTAGAAATGCCTTGAATAACC-TATTAAATTTTTT
3632869 GTAATAAATT
Statistics
Matches: 150, Mismatches: 24, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
119 9 0.06
120 41 0.27
121 6 0.04
122 88 0.59
123 6 0.04
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (119 bp):
AAAGGATTATTCAAAGCATTTTTAGCTAGAAATGCCTTGAATAACCTATTAAATTTTTTAAAGGA
TTATTCAAAGCATTTTTGGCCAAAAACACCTTGAATAATCCCTAAAAAAATAGG
Found at i:3632881 original size:122 final size:122
Alignment explanation
Indices: 3632567--3632919 Score: 324
Period size: 122 Copynumber: 2.9 Consensus size: 122
3632557 TTTTTTTTAT
* * * * * * * *
3632567 AAAGGATTATTC-AAGGAGTTGTTAGCTAAAAACGCCTTGAATAATCCT-ATTCAATTTTT-TAA
1 AAAGGATTATTCAAAGCA-TTTTTAGCTAGAAATGCATTAAATAA-CCTCATTAAATTTTTATGA
* * * * *
3632629 AG-GATTATTCAAGGCATTTTTGGCCAAAAATACCTTGAATAATCCCTAAAAAGAATGG
64 AGAAATTATTCAAAGCATTTTTGGTCAAAAACACCTTGAATAATCTCTAAAAAGAATGG
* * * * * * * *
3632687 CATGGATTATTTAATGCATTTTTAGCTAGAAATGCCTTGAATAACCTCATTTAATTTTTATGAGG
1 AAAGGATTATTCAAAGCATTTTTAGCTAGAAATGCATTAAATAACCTCATTAAATTTTTATGAAG
** * *
3632752 AGGTTATTCAAAGCATTTTTGGTCAAAAACACCTTGAATAATCTTTAAAAA-AATAGT
66 AAATTATTCAAAGCATTTTTGGTCAAAAACACCTTGAATAATCTCTAAAAAGAAT-GG
* *
3632809 AAAGGATTATTCAAAGCATTTTTGGCTAGAAATGCATTAAATAACCTTATTAAATTTTT-TGTAA
1 AAAGGATTATTCAAAGCATTTTTAGCTAGAAATGCATTAAATAACCTCATTAAATTTTTATG-AA
* * * * *
3632873 TAAATTATT-AAAGGTATTTTTGGTGAAAAACACTTTAAATAATCTCT
65 GAAATTATTCAAA-GCATTTTTGGTCAAAAACACCTTGAATAATCTCT
3632920 CATAAAATTT
Statistics
Matches: 190, Mismatches: 36, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
119 3 0.02
120 42 0.22
121 14 0.07
122 131 0.69
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (122 bp):
AAAGGATTATTCAAAGCATTTTTAGCTAGAAATGCATTAAATAACCTCATTAAATTTTTATGAAG
AAATTATTCAAAGCATTTTTGGTCAAAAACACCTTGAATAATCTCTAAAAAGAATGG
Found at i:3633971 original size:17 final size:18
Alignment explanation
Indices: 3633937--3633971 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3633927 TGTTATTAAA
*
3633937 TATTTTTACTATTTTATG
1 TATTTTTACTATTATATG
3633955 TATTTTTACT-TTATATG
1 TATTTTTACTATTATATG
3633972 AAATCATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.66
Consensus pattern (18 bp):
TATTTTTACTATTATATG
Found at i:3635200 original size:43 final size:43
Alignment explanation
Indices: 3635138--3635267 Score: 120
Period size: 43 Copynumber: 3.0 Consensus size: 43
3635128 GAACAACTTT
3635138 AAATATAG-AAGCTCCTCTAAACAAAAGTTCAATAACTTTAAA
1 AAATATAGAAAGCTCCTCTAAACAAAAGTTCAATAACTTTAAA
** ** * *
3635180 AAATATAGAAAGCTTTTCTAAACGGAAGCTCAACAACTTTAAA
1 AAATATAGAAAGCTCCTCTAAACAAAAGTTCAATAACTTTAAA
* * * * * *
3635223 GAACATGGAAGGCTCGTCTAAATAAAA-TCTCAATAACTTCTAAA
1 AAATATAGAAAGCTCCTCTAAACAAAAGT-TCAATAACTT-TAAA
3635267 A
1 A
3635268 TAAATACCCA
Statistics
Matches: 67, Mismatches: 18, Indels: 4
0.75 0.20 0.04
Matches are distributed among these distances:
42 8 0.12
43 55 0.82
44 4 0.06
ACGTcount: A:0.47, C:0.17, G:0.11, T:0.25
Consensus pattern (43 bp):
AAATATAGAAAGCTCCTCTAAACAAAAGTTCAATAACTTTAAA
Found at i:3636371 original size:15 final size:16
Alignment explanation
Indices: 3636351--3636384 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
3636341 AGTCCTCTTA
3636351 TTTCATTTTTTT-ATT
1 TTTCATTTTTTTCATT
3636366 TTTCATTTTTTTCATT
1 TTTCATTTTTTTCATT
3636382 TTT
1 TTT
3636385 TTAAGTGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCATTTTTTTCATT
Found at i:3636376 original size:9 final size:9
Alignment explanation
Indices: 3636351--3636386 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
3636341 AGTCCTCTTA
3636351 TTTCATTTT
1 TTTCATTTT
3636360 TTT-A--TT
1 TTTCATTTT
3636366 TTTCATTTT
1 TTTCATTTT
3636375 TTTCATTTT
1 TTTCATTTT
3636384 TTT
1 TTT
3636387 AAGTGTAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
6 5 0.21
7 1 0.04
8 1 0.04
9 17 0.71
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTCATTTT
Found at i:3642606 original size:3 final size:3
Alignment explanation
Indices: 3642594--3642663 Score: 90
Period size: 3 Copynumber: 24.0 Consensus size: 3
3642584 ACCATAGTAC
* *
3642594 ATT A-T ATT ATT ATC ATT -GT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
3642640 ATT GTT ATT ACT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT
3642664 TTTTTATTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
2 3 0.05
3 54 0.95
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:3643168 original size:12 final size:12
Alignment explanation
Indices: 3643151--3643175 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3643141 TCTGGGTTTA
3643151 GATGAATTTTTT
1 GATGAATTTTTT
3643163 GATGAATTTTTT
1 GATGAATTTTTT
3643175 G
1 G
3643176 GTGGGGTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (12 bp):
GATGAATTTTTT
Found at i:3643505 original size:19 final size:19
Alignment explanation
Indices: 3643481--3643518 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3643471 CAAAGTTTCC
3643481 TTTTTTCATTTTATTTTTA
1 TTTTTTCATTTTATTTTTA
*
3643500 TTTTTTGATTTTATTTTTA
1 TTTTTTCATTTTATTTTTA
3643519 ACTCATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.79
Consensus pattern (19 bp):
TTTTTTCATTTTATTTTTA
Found at i:3643645 original size:34 final size:35
Alignment explanation
Indices: 3643605--3643688 Score: 100
Period size: 37 Copynumber: 2.4 Consensus size: 35
3643595 ATAATTACAT
3643605 AAAAAAACTTTTTCAAATAAG-TCAAAAAAAAAAA
1 AAAAAAACTTTTTCAAATAAGTTCAAAAAAAAAAA
* *
3643639 AAAAAAA-TCTTTTCAAATAAGTTTTCAAAATAATAAA
1 AAAAAAACT-TTTTCAAATAAG--TTCAAAAAAAAAAA
*
3643676 AAAAAATCTTTTT
1 AAAAAAACTTTTT
3643689 AAGTTTTCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
33 1 0.02
34 19 0.45
37 21 0.50
38 1 0.02
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (35 bp):
AAAAAAACTTTTTCAAATAAGTTCAAAAAAAAAAA
Found at i:3643677 original size:36 final size:34
Alignment explanation
Indices: 3643605--3643687 Score: 98
Period size: 36 Copynumber: 2.4 Consensus size: 34
3643595 ATAATTACAT
*
3643605 AAAAAAACT-TTTTCAAATAAGTCAAAAAAAAAA
1 AAAAAAAATCTTTTCAAATAAGTCAAAAAAAAAA
* *
3643638 AAAAAAAATCTTTTCAAATAAGTTTTC-AAAATAATA
1 AAAAAAAATCTTTTCAAATAAG---TCAAAAAAAAAA
3643674 AAAAAAAATCTTTT
1 AAAAAAAATCTTTT
3643688 TAAGTTTTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
33 8 0.19
34 12 0.28
36 21 0.49
37 2 0.05
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.29
Consensus pattern (34 bp):
AAAAAAAATCTTTTCAAATAAGTCAAAAAAAAAA
Found at i:3643692 original size:32 final size:32
Alignment explanation
Indices: 3643630--3643704 Score: 98
Period size: 36 Copynumber: 2.2 Consensus size: 32
3643620 AATAAGTCAA
*
3643630 AAAAAAAAAAAAAAAATCTTTTCAAATAAGTTTTC
1 AAAAAATAAAAAAAAATCTTTT---ATAAGTTTTC
3643665 AAAATAATAAAAAAAAATCTTTT-TAAGTTTTC
1 AAAA-AATAAAAAAAAATCTTTTATAAGTTTTC
3643697 AAAAAATA
1 AAAAAATA
3643705 TTTATAAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
31 4 0.11
32 13 0.34
35 4 0.11
36 17 0.45
ACGTcount: A:0.60, C:0.07, G:0.03, T:0.31
Consensus pattern (32 bp):
AAAAAATAAAAAAAAATCTTTTATAAGTTTTC
Found at i:3643738 original size:17 final size:16
Alignment explanation
Indices: 3643716--3643769 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
3643706 TTATAAAACA
3643716 AAAAAAAAATCCTTTC
1 AAAAAAAAATCCTTTC
*
3643732 AATAAAAAAATCTTTTTC
1 AA-AAAAAAATC-CTTTC
* *
3643750 AAATAAAAATCCTTAC
1 AAAAAAAAATCCTTTC
3643766 AAAA
1 AAAA
3643770 TAAATTCGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 8 0.26
17 17 0.55
18 6 0.19
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAAAAAAATCCTTTC
Found at i:3643770 original size:17 final size:17
Alignment explanation
Indices: 3643713--3643773 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
3643703 TATTTATAAA
*
3643713 ACAAAAAAAAAATCCTT
1 ACAAAATAAAAATCCTT
* *
3643730 TCAATAA-AAAAATCTTTT
1 ACAA-AATAAAAATC-CTT
*
3643748 TC-AAATAAAAATCCTT
1 ACAAAATAAAAATCCTT
3643764 ACAAAATAAA
1 ACAAAATAAA
3643774 TTCGTAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
16 5 0.14
17 25 0.69
18 6 0.17
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (17 bp):
ACAAAATAAAAATCCTT
Found at i:3647740 original size:19 final size:19
Alignment explanation
Indices: 3647718--3647755 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3647708 CAAAAAGATT
3647718 GCAAAAAAAAAAAAGAGAA
1 GCAAAAAAAAAAAAGAGAA
*
3647737 GCAAAAAAAAAAATGAGAA
1 GCAAAAAAAAAAAAGAGAA
3647756 AAAAAGGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.76, C:0.05, G:0.16, T:0.03
Consensus pattern (19 bp):
GCAAAAAAAAAAAAGAGAA
Found at i:3649467 original size:120 final size:119
Alignment explanation
Indices: 3649284--3649613 Score: 326
Period size: 119 Copynumber: 2.8 Consensus size: 119
3649274 ATTCAATCTC
* * ** * * * * * *
3649284 GATTTC-AT-CAGATCATTTTCTAACTCATGATTTTATCCCGATCAACCATATTCTATCTTGACT
1 GATTTCTATCCAGATCATTTCCTGACTCACAATTTCATCCCGATCAATCATCTTCAACCTCGACT
* * * *
3649347 CGATCTTAGTCATTTTATCTTTTTGACTCGTAGTTTCATCTCAATTATTCGATAT
66 CGATCTTAGTCACTTTATCTTTTTGACTCGAAGTTT-ATCCCAATCATTCGATAT
* * ** *
3649402 CGATTT-TGTCCAGATCATTTCCTGACTTACAATTTCATCTTGATCAGTCATCTTCAACCTCGAC
1 -GATTTCTATCCAGATCATTTCCTGACTCACAATTTCATCCCGATCAATCATCTTCAACCTCGAC
* * * * *
3649466 TCGATCCTGGTCACTTTATCTTTTTGACTTGAAGTTTATCCCGATCATTCGATCT
65 TCGATCTTAGTCACTTTATCTTTTTGACTCGAAGTTTATCCCAATCATTCGATAT
* * * * *
3649521 TATTTCTATCCAGATCATTTCCTGACTCGCAGTTTCATCCCGATCAATCATCTTCGACCTTGACT
1 GATTTCTATCCAGATCATTTCCTGACTCACAATTTCATCCCGATCAATCATCTTCAACCTCGACT
* *
3649586 C-AGCCTTAGTCGCTTTATCTTTTTGACT
66 CGA-TCTTAGTCACTTTATCTTTTTGACT
3649614 TGTGATTTTA
Statistics
Matches: 169, Mismatches: 38, Indels: 8
0.79 0.18 0.04
Matches are distributed among these distances:
118 5 0.03
119 92 0.54
120 72 0.43
ACGTcount: A:0.22, C:0.25, G:0.11, T:0.42
Consensus pattern (119 bp):
GATTTCTATCCAGATCATTTCCTGACTCACAATTTCATCCCGATCAATCATCTTCAACCTCGACT
CGATCTTAGTCACTTTATCTTTTTGACTCGAAGTTTATCCCAATCATTCGATAT
Found at i:3649566 original size:119 final size:118
Alignment explanation
Indices: 3649318--3649674 Score: 326
Period size: 120 Copynumber: 3.0 Consensus size: 118
3649308 TCATGATTTT
* * * * * * * * *
3649318 ATCCCGATCAACCATATTCTATCTTGACTCGATCTTAGTCATTTTATCTTTTTGACTCGTAGTTT
1 ATCCCGATCAATCATCTTCAACCTCGACTCGATCCTAGTCACTTTATCTTTTTGACTTGAAGTTT
* * * * * *
3649383 CATCTCAATTATTCGATATCGATTT-TGTCCAGATCATTTCCTGACTTA-CAATTTC
66 -ATC-CCATCATTCGATCT-TATTTCTATCCAGATCATTTCCTGAC-TAGCAGTTTC
** * *
3649438 ATCTTGATCAGTCATCTTCAACCTCGACTCGATCCTGGTCACTTTATCTTTTTGACTTGAAGTTT
1 ATCCCGATCAATCATCTTCAACCTCGACTCGATCCTAGTCACTTTATCTTTTTGACTTGAAGTTT
*
3649503 ATCCCGATCATTCGATCTTATTTCTATCCAGATCATTTCCTGACTCGCAGTTTC
66 ATCCC-ATCATTCGATCTTATTTCTATCCAGATCATTTCCTGACTAGCAGTTTC
* * * * * *
3649557 ATCCCGATCAATCATCTTCGACCTTGACTC-AGCCTTAGTCGCTTTATCTTTTTGACTTGTGATT
1 ATCCCGATCAATCATCTTCAACCTCGACTCGATCC-TAGTCACTTTATCTTTTTGACTTG-AAGT
* * * **
3649621 TTATCCCAGTCATTTGATCTTGA-TTCCATCTAGATCATTTTTTGACTAGCAGTT
64 TTATCCCA-TCATTCGATCTT-ATTTCTATCCAGATCATTTCCTGACTAGCAGTT
3649675 CTATCCCAAT
Statistics
Matches: 194, Mismatches: 36, Indels: 14
0.80 0.15 0.06
Matches are distributed among these distances:
118 9 0.05
119 86 0.44
120 98 0.51
121 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.12, T:0.42
Consensus pattern (118 bp):
ATCCCGATCAATCATCTTCAACCTCGACTCGATCCTAGTCACTTTATCTTTTTGACTTGAAGTTT
ATCCCATCATTCGATCTTATTTCTATCCAGATCATTTCCTGACTAGCAGTTTC
Found at i:3649693 original size:120 final size:119
Alignment explanation
Indices: 3649410--3649697 Score: 280
Period size: 119 Copynumber: 2.4 Consensus size: 119
3649400 ATCGATTTTG
* *** ** * * *
3649410 TCCAGATCATTTCCTGACTTA-CAATTTCATCTTGATCAGTCATCTTCAACCTCGACTCGATCC-
1 TCCAGATCATTTCCTGAC-TAGCAGTTTCATCCCAATCAACCATCTTCGACCTTGACTC-AGCCT
* * *
3649473 TGGTCACTTTATCTTTTTGACTTGAAGTTTATCCCGATCATTCGATCTTATTTCTA
64 TAGTCGCTTTATCTTTTTGACTTGAAGTTTATCCCGATCATTCGATCTTATTTCCA
* * *
3649529 TCCAGATCATTTCCTGACTCGCAGTTTCATCCCGATCAATCATCTTCGACCTTGACTCAGCCTTA
1 TCCAGATCATTTCCTGACTAGCAGTTTCATCCCAATCAACCATCTTCGACCTTGACTCAGCCTTA
* * *
3649594 GTCGCTTTATCTTTTTGACTTGTGATTTTATCCC-AGTCATTTGATCTTGA-TTCCA
66 GTCGCTTTATCTTTTTGACTTG-AAGTTTATCCCGA-TCATTCGATCTT-ATTTCCA
* ** * *
3649649 TCTAGATCATTTTTTGACTAGCAG-TTCTATCCCAATTAGCCATCTTCGA
1 TCCAGATCATTTCCTGACTAGCAGTTTC-ATCCCAATCAACCATCTTCGA
3649698 TCTCAACTCA
Statistics
Matches: 141, Mismatches: 22, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
118 4 0.03
119 75 0.53
120 61 0.43
121 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.40
Consensus pattern (119 bp):
TCCAGATCATTTCCTGACTAGCAGTTTCATCCCAATCAACCATCTTCGACCTTGACTCAGCCTTA
GTCGCTTTATCTTTTTGACTTGAAGTTTATCCCGATCATTCGATCTTATTTCCA
Found at i:3649978 original size:3 final size:3
Alignment explanation
Indices: 3649961--3650106 Score: 105
Period size: 3 Copynumber: 52.0 Consensus size: 3
3649951 ACCATAGTAC
* * * * * *
3649961 ATT A-T ATT A-T ATT ATT ATC ATT -GT ACT ATT TTT ATT ATC ATT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
3650006 ATT ATT ACT ATT GTT A-T ATT A-T ATT A-T ATT A-T ATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
3650049 ATA ATT A-T ATT GTT ATT ATT ATA ATT ATT -TT AGT ATT ATT ATT ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3650095 ATT ATT ATT ATT
1 ATT ATT ATT ATT
3650107 TTTTCATTTT
Statistics
Matches: 108, Mismatches: 25, Indels: 20
0.71 0.16 0.13
Matches are distributed among these distances:
2 19 0.18
3 89 0.82
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:3650040 original size:29 final size:29
Alignment explanation
Indices: 3649962--3650104 Score: 118
Period size: 29 Copynumber: 4.8 Consensus size: 29
3649952 CCATAGTACA
* *
3649962 TTATATTATATTATTATCATT-GTACTATT
1 TTATATTATATTA-TATTATTATTACTATT
3649991 TT-TATTATCATTA-A-TATTATTACTATT
1 TTATATTAT-ATTATATTATTATTACTATT
3650018 GTTATATTATATTATATTA-TATTA-TATT
1 -TTATATTATATTATATTATTATTACTATT
* * *
3650046 ATTATAATTATATTGTTATTATTATAATTATT
1 -TTAT-ATTATATT-ATATTATTATTACTATT
3650078 TTAGTATTATTATTACTATTATTATTA
1 TTA-TATTA-TATTA-TATTATTATTA
3650105 TTTTTTCATT
Statistics
Matches: 94, Mismatches: 7, Indels: 23
0.76 0.06 0.19
Matches are distributed among these distances:
26 3 0.03
27 8 0.09
28 20 0.21
29 26 0.28
30 7 0.07
31 11 0.12
32 19 0.20
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (29 bp):
TTATATTATATTATATTATTATTACTATT
Found at i:3650044 original size:20 final size:20
Alignment explanation
Indices: 3649961--3650105 Score: 70
Period size: 20 Copynumber: 7.0 Consensus size: 20
3649951 ACCATAGTAC
3649961 ATTATATTATA-T-TATTAT
1 ATTATATTATATTATATTAT
* * *
3649979 CATTGTACTAT-TTTTATTAT
1 -ATTATATTATATTATATTAT
* *
3649999 CATTAATATTATTACTATTGTTAT
1 -ATT-ATATTA-TATTA-TATTAT
3650023 ATTATATTATATTATATTAT
1 ATTATATTATATTATATTAT
3650043 A-T-TATTATAATTATA-T-T
1 ATTATATTAT-ATTATATTAT
* *
3650060 GTTATTATTATAATTATTTTAGT
1 ATTA-TATTAT-ATTATATTA-T
3650083 ATTATTATTACTATTATTATTAT
1 ATTA-TATTA-TATTA-TATTAT
3650106 TTTTTCATTT
Statistics
Matches: 98, Mismatches: 13, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
17 1 0.01
18 8 0.08
19 16 0.16
20 28 0.29
21 9 0.09
22 7 0.07
23 19 0.19
24 10 0.10
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (20 bp):
ATTATATTATATTATATTAT
Found at i:3650611 original size:13 final size:12
Alignment explanation
Indices: 3650580--3650607 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3650570 TCTAGGTTTG
3650580 GATGAATTTTTT
1 GATGAATTTTTT
3650592 GATGAATTTTTT
1 GATGAATTTTTT
3650604 GATG
1 GATG
3650608 GAATATGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.21, T:0.54
Consensus pattern (12 bp):
GATGAATTTTTT
Found at i:3651054 original size:34 final size:34
Alignment explanation
Indices: 3650991--3651065 Score: 107
Period size: 33 Copynumber: 2.2 Consensus size: 34
3650981 ACAATTGTAA
3650991 AAAAAAAAACTTTTCAAATAAGTCCAAAAA-AAC
1 AAAAAAAAACTTTTCAAATAAGTCCAAAAATAAC
** *
3651024 AAAAAAAAACTTTTCAAATAAGTTTTAAAAATAAT
1 AAAAAAAAACTTTTCAAATAAG-TCCAAAAATAAC
3651059 AAAAAAA
1 AAAAAAA
3651066 TCTTTTTAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 22 0.59
34 6 0.16
35 9 0.24
ACGTcount: A:0.65, C:0.09, G:0.03, T:0.23
Consensus pattern (34 bp):
AAAAAAAAACTTTTCAAATAAGTCCAAAAATAAC
Found at i:3651120 original size:17 final size:17
Alignment explanation
Indices: 3651100--3651132 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3651090 TTATAAACAA
3651100 AAAAAAATACTTTCAAT
1 AAAAAAATACTTTCAAT
*
3651117 AAAAAAATATTTTCAA
1 AAAAAAATACTTTCAA
3651133 ATAAGTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAAAAATACTTTCAAT
Found at i:3651132 original size:92 final size:95
Alignment explanation
Indices: 3651024--3651224 Score: 318
Period size: 94 Copynumber: 2.1 Consensus size: 95
3651014 CCAAAAAAAC
*
3651024 AAAAAAAAACTTTTCAAATAAGTTTTAAAAATAAT-AAAAAAA-TCTTTTTAAGTTTTCAAAAAA
1 AAAAAAATA-TTTTCAAATAAGTTTTAAAAATAATAAAAAAAACTCTTTTTAAGTTTTCAAAAAA
*
3651087 TATTTATAAACA-AAAAAAAATACTTTCAAT
65 TATTTATAAAAACAAAAAAAATACTTTCAAT
* *
3651117 AAAAAAATATTTTCAAATAAGTTTTCAAAATAATAAAAAAAACTGTTTTTAAGTTTTCAAAAAAT
1 AAAAAAATATTTTCAAATAAGTTTTAAAAATAATAAAAAAAACTCTTTTTAAGTTTTCAAAAAAT
**
3651182 ATTTATAAAAACAAAAAAAATGTTTTCAAT
66 ATTTATAAAAACAAAAAAAATACTTTCAAT
3651212 AAAAAAATATTTT
1 AAAAAAATATTTT
3651225 TTAAATAAAA
Statistics
Matches: 99, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
92 24 0.24
93 15 0.15
94 31 0.31
95 29 0.29
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.34
Consensus pattern (95 bp):
AAAAAAATATTTTCAAATAAGTTTTAAAAATAATAAAAAAAACTCTTTTTAAGTTTTCAAAAAAT
ATTTATAAAAACAAAAAAAATACTTTCAAT
Found at i:3651215 original size:18 final size:19
Alignment explanation
Indices: 3651175--3651235 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
3651165 TTAAGTTTTC
* *
3651175 AAAAAATAT-TTATAAAAA
1 AAAAAATATGTTTTAAATA
* *
3651193 CAAAAAAAATGTTTTCAATA
1 -AAAAAATATGTTTTAAATA
*
3651213 AAAAAATATTTTTTAAATA
1 AAAAAATATGTTTTAAATA
3651232 AAAA
1 AAAA
3651236 TCCTTATAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 28 0.82
20 6 0.18
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAAAATATGTTTTAAATA
Found at i:3664783 original size:2 final size:2
Alignment explanation
Indices: 3664776--3664807 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3664766 TGTCCATCTT
3664776 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3664808 TTCAAATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 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):
TA
Found at i:3681921 original size:10 final size:10
Alignment explanation
Indices: 3681906--3681956 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
3681896 TTTGAAAAAA
3681906 TAAAAAATTT
1 TAAAAAATTT
*
3681916 TAAAAAATTG
1 TAAAAAATTT
3681926 TAAAAAATTAT
1 TAAAAAATT-T
** *
3681937 TTTAAAATTA
1 TAAAAAATTT
3681947 T-AAAAATTT
1 TAAAAAATTT
3681956 T
1 T
3681957 CATTTTTTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
9 7 0.21
10 19 0.58
11 7 0.21
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (10 bp):
TAAAAAATTT
Found at i:3681943 original size:21 final size:20
Alignment explanation
Indices: 3681905--3681956 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
3681895 TTTTGAAAAA
3681905 ATAAAAAATTTTAAAAAATT
1 ATAAAAAATTTTAAAAAATT
* **
3681925 GTAAAAAATTATTTTAAAATT
1 ATAAAAAATT-TTAAAAAATT
3681946 AT-AAAAATTTT
1 ATAAAAAATTTT
3681957 CATTTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.07
20 16 0.59
21 9 0.33
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
ATAAAAAATTTTAAAAAATT
Found at i:3682084 original size:41 final size:43
Alignment explanation
Indices: 3682039--3682128 Score: 116
Period size: 39 Copynumber: 2.2 Consensus size: 43
3682029 CATTAAATTT
* * *
3682039 TTTTTTATTTTTATTTTTCAGAATTTTTT-A-AAAATTTTAAA
1 TTTTTTATTATAATTTTTAAGAATTTTTTGATAAAATTTTAAA
3682080 -TTTTT-TTATAATTTTTAAGAATTTTTTGATAAAATTTTAAA
1 TTTTTTATTATAATTTTTAAGAATTTTTTGATAAAATTTTAAA
3682121 TCTTTTTA
1 T-TTTTTA
3682129 AAAATTTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
39 19 0.46
40 6 0.15
41 11 0.27
43 5 0.12
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.62
Consensus pattern (43 bp):
TTTTTTATTATAATTTTTAAGAATTTTTTGATAAAATTTTAAA
Found at i:3682136 original size:10 final size:10
Alignment explanation
Indices: 3682063--3682138 Score: 50
Period size: 10 Copynumber: 7.6 Consensus size: 10
3682053 TTTTCAGAAT
3682063 TTTTTAAAAA
1 TTTTTAAAAA
*
3682073 -TTTT-AAAT
1 TTTTTAAAAA
* *
3682081 TTTTTTATAA
1 TTTTTAAAAA
*
3682091 TTTTTAAGAAT
1 TTTTTAA-AAA
3682102 TTTTTGATAAAA
1 TTTTT-A-AAAA
**
3682114 -TTTTAAATC
1 TTTTTAAAAA
3682123 TTTTTAAAAA
1 TTTTTAAAAA
3682133 TTTTTA
1 TTTTTA
3682139 TTTTTTAATT
Statistics
Matches: 49, Mismatches: 11, Indels: 12
0.68 0.15 0.17
Matches are distributed among these distances:
8 3 0.06
9 10 0.20
10 22 0.45
11 10 0.20
12 3 0.06
13 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (10 bp):
TTTTTAAAAA
Found at i:3682288 original size:17 final size:17
Alignment explanation
Indices: 3682268--3682312 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
3682258 AATTTGAGAT
*
3682268 TTTTTTAATTTTTTAAG
1 TTTTATAATTTTTTAAG
3682285 TTTTAATAA-TTTTTAAG
1 TTTT-ATAATTTTTTAAG
3682302 TTTTATAATTT
1 TTTTATAATTT
3682313 CCAAAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 4 0.16
17 18 0.72
18 3 0.12
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (17 bp):
TTTTATAATTTTTTAAG
Found at i:3688680 original size:61 final size:62
Alignment explanation
Indices: 3688457--3688758 Score: 390
Period size: 61 Copynumber: 4.9 Consensus size: 62
3688447 TTTTTTGTAG
* * *
3688457 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA---TTTTTTGGAAATTTCGATTTTC-GA
1 GGAAAATTGATACTTTCAACTTTT-CCCAAAAATATTTTTTTTTTGAAATTTTGATTTTCTAA
* *** * *
3688516 GGAAAATTGATACTTTCAACTTTTCCTCGAAAA-CCCTTTTTTTTGAAAATTT-A-TTGCTAA
1 GGAAAATTGATACTTTCAACTTTTCC-CAAAAATATTTTTTTTTTGAAATTTTGATTTTCTAA
3688576 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTTGAAATTTTGATTTTC-AA
1 GGAAAATTGATACTTTCAACTTTT-CCCAAAAATATTTTTTTTTTGAAATTTTGATTTTCTAA
3688638 GGAAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTTTTTGAAATTTT-A-TTTCTAA
1 GGAAAATTGATACTTTCAACTTTTC-CCAAAAATATTTTTTTTTTGAAATTTTGATTTTCTAA
*
3688699 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTGGAAAATTTGATTTT
1 GGAAAATTGATACTTTCAACTTTTCCC-AAAAATATTTTTTTTTT-GAAATTTTGATTTT
3688759 TATTTGAAGA
Statistics
Matches: 214, Mismatches: 14, Indels: 25
0.85 0.06 0.10
Matches are distributed among these distances:
58 2 0.01
59 32 0.15
60 37 0.17
61 75 0.35
62 61 0.29
63 4 0.02
64 3 0.01
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.45
Consensus pattern (62 bp):
GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTTTTGAAATTTTGATTTTCTAA
Found at i:3688719 original size:123 final size:122
Alignment explanation
Indices: 3688457--3688758 Score: 450
Period size: 123 Copynumber: 2.5 Consensus size: 122
3688447 TTTTTTGTAG
* * *
3688457 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA---TTTTTTGGAAATTTCGATTTTCGAGGA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTTGAAATTTTGATTTTCAAGGA
* *
3688519 AAATTGATACTTTCAACTTTTCCTCGAAAACCCTTTTTTTTGAAAATTTATTGCTAA
66 AAATTGATACTTTCAACTTTTCCTCAAAAAACCTTTTTTTTGAAAATTTATTGCTAA
3688576 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTTGAAATTTTGATTTTCAAGGA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTTGAAATTTTGATTTTCAAGGA
** * *
3688641 AAATTGATACTTTCAACTTTT-CTCCAAAAATATTTTTTTTTTGAAATTTTATTTCTAA
66 AAATTGATACTTTCAACTTTTCCT-CAAAAA-ACCTTTTTTTTGAAAATTTATTGCTAA
* *
3688699 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTTGGAAAATTTGATTTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTT-GAAATTTTGATTTT
3688759 TATTTGAAGA
Statistics
Matches: 166, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
119 35 0.21
121 2 0.01
122 50 0.30
123 66 0.40
124 13 0.08
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.45
Consensus pattern (122 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTTGAAATTTTGATTTTCAAGGA
AAATTGATACTTTCAACTTTTCCTCAAAAAACCTTTTTTTTGAAAATTTATTGCTAA
Found at i:3688800 original size:20 final size:21
Alignment explanation
Indices: 3688769--3688808 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3688759 TATTTGAAGA
3688769 AAATAGAATAATAAAAAATAT
1 AAATAGAATAATAAAAAATAT
*
3688790 AAATA-AATAATAAAGAATA
1 AAATAGAATAATAAAAAATA
3688809 AAGAAAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (21 bp):
AAATAGAATAATAAAAAATAT
Found at i:3688867 original size:26 final size:27
Alignment explanation
Indices: 3688817--3688872 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
3688807 TAAAGAAAAG
3688817 TAAAACAAAAATTAAAAAAAACTAAGA
1 TAAAACAAAAATTAAAAAAAACTAAGA
* * * *
3688844 TAAAA-AAATATTAAATAAACCTAATA
1 TAAAACAAAAATTAAAAAAAACTAAGA
3688870 TAA
1 TAA
3688873 TAAATAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.21
Consensus pattern (27 bp):
TAAAACAAAAATTAAAAAAAACTAAGA
Found at i:3689384 original size:31 final size:31
Alignment explanation
Indices: 3689346--3689404 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
3689336 CCGAAAACTG
* *
3689346 GCCGAAAACTTC-AATGTTCGTCGGAATTGTT
1 GCCGAAAAATTCAAATG-TCGCCGGAATTGTT
3689377 GCCGAAAAATTCAAATGTCGCCGGAATT
1 GCCGAAAAATTCAAATGTCGCCGGAATT
3689405 TTCGTCGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (31 bp):
GCCGAAAAATTCAAATGTCGCCGGAATTGTT
Found at i:3689870 original size:17 final size:18
Alignment explanation
Indices: 3689848--3689881 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3689838 TAGATAAGTA
*
3689848 AAAATACAAAA-ATAAAT
1 AAAATAAAAAAGATAAAT
3689865 AAAATAAAAAAGATAAA
1 AAAATAAAAAAGATAAA
3689882 AAATATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (18 bp):
AAAATAAAAAAGATAAAT
Found at i:3690651 original size:16 final size:16
Alignment explanation
Indices: 3690624--3690665 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
3690614 AAAAATTACT
* *
3690624 ATTCAGATTTTATTAAA
1 ATTCACATTTTA-AAAA
3690641 ATTC-CATTTTAAAAA
1 ATTCACATTTTAAAAA
3690656 ATTCACATTT
1 ATTCACATTT
3690666 ATTTTTTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 7 0.32
16 11 0.50
17 4 0.18
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.45
Consensus pattern (16 bp):
ATTCACATTTTAAAAA
Found at i:3692221 original size:3 final size:3
Alignment explanation
Indices: 3692215--3692241 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3692205 AAAACTTAAT
3692215 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
3692242 ACCCATTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3694469 original size:19 final size:19
Alignment explanation
Indices: 3694442--3694485 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
3694432 TCTTTCCAAA
*
3694442 ATTTATATTATAGATTTA-T
1 ATTTTTATTATA-ATTTACT
*
3694461 ATTTTTATTTTAATTTACT
1 ATTTTTATTATAATTTACT
3694480 ATTTTT
1 ATTTTT
3694486 CCTTTTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTTTATTATAATTTACT
Found at i:3701068 original size:1 final size:1
Alignment explanation
Indices: 3701062--3701087 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
3701052 TCCTTAGTTG
3701062 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
3701088 CACACTCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3701502 original size:297 final size:297
Alignment explanation
Indices: 3700905--3701502 Score: 993
Period size: 308 Copynumber: 2.0 Consensus size: 297
3700895 ACAAAGACTT
3700905 GAATTAATCTCCAAACAAATTTTAAACAAATGCTTGGAAGCAATCAAAGAAAAACTAGCTAGGAA
1 GAATTAATCTCCAAACAAATTTTAAACAAATGCTTGGAAGCAATCAAAGAAAAACTAGCTAGGAA
* *
3700970 TAATCTTATCAATCACTAATAGCGTGTTTGGTTCGCTGGAATAATCTTTCCATTCAGGTCATTTT
66 TAATCTTATAAATCACTAATAGCGTGTTTGGTTCGCTGGAATAATCTTTCCATTCAGGTAATTTT
*
3701035 TTGGGAGAGATAGCAATTCCTTAGTTGTTTTTTTTTTTTTTTTTTTTTTTTTTCACACTCAGAAT
131 TTGGGAGAGATAGCAATTCCTTAGTTG-----------TTTTATTTTTTTTTTCACACTCAGAAT
*
3701100 ACAAATTCCATAAAATCAGCTATTCCTTTAAACAAGGAATCACCGTTCGGAACTTCACCCTAAGA
185 ACAAATTCCATAAAATCAGCTATTCCTTAAAACAAGGAATCACCGTTCGGAACTTCACCCTAAGA
3701165 ATGGTTATTCCGAGACTATCAGGATTACAGCCAATAATTTACAGCCAA
250 ATGGTTATTCCGAGACTATCAGGATTACAGCCAATAATTTACAGCCAA
* *
3701213 GAATTAATCTCCAAACAAATTTTTAACAAATGCTTGGAAGCCATCAAAGAAAAACTAGC-ATGGA
1 GAATTAATCTCCAAACAAATTTTAAACAAATGCTTGGAAGCAATCAAAGAAAAACTAGCTA-GGA
*
3701277 ATAATCTTATAAATCACTAATAGTGTGTTTGGTTCGCTGGAATAATCTTTCCATTCAGGTAATTT
65 ATAATCTTATAAATCACTAATAGCGTGTTTGGTTCGCTGGAATAATCTTTCCATTCAGGTAATTT
*
3701342 TTTGGGAGAGATAGCAATTCCTTAGTTG-TTTATTTTTTTTTTGACACTCAGAATACAAATTCCA
130 TTTGGGAGAGATAGCAATTCCTTAGTTGTTTTATTTTTTTTTTCACACTCAGAATACAAATTCCA
3701406 TAAAATCAGCTATTCCTTGAAAACAAGGAATCACCGTTCGGAACTTCACCCTAAGAATGGTTATT
195 TAAAATCAGCTATTCCTT-AAAACAAGGAATCACCGTTCGGAACTTCACCCTAAGAATGGTTATT
3701471 CCGAGACTATCAGGATTACAGCCAATAATTTA
259 CCGAGACTATCAGGATTACAGCCAATAATTTA
3701503 TGAGCCATTT
Statistics
Matches: 280, Mismatches: 8, Indels: 15
0.92 0.03 0.05
Matches are distributed among these distances:
296 52 0.19
297 77 0.28
307 1 0.00
308 150 0.54
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Consensus pattern (297 bp):
GAATTAATCTCCAAACAAATTTTAAACAAATGCTTGGAAGCAATCAAAGAAAAACTAGCTAGGAA
TAATCTTATAAATCACTAATAGCGTGTTTGGTTCGCTGGAATAATCTTTCCATTCAGGTAATTTT
TTGGGAGAGATAGCAATTCCTTAGTTGTTTTATTTTTTTTTTCACACTCAGAATACAAATTCCAT
AAAATCAGCTATTCCTTAAAACAAGGAATCACCGTTCGGAACTTCACCCTAAGAATGGTTATTCC
GAGACTATCAGGATTACAGCCAATAATTTACAGCCAA
Found at i:3702698 original size:24 final size:24
Alignment explanation
Indices: 3702645--3702698 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
3702635 AAAATTTAAA
*
3702645 ATTTAAATTTTAATATCTGTAATTT
1 ATTT-AATTTTAATATCTATAATTT
* *
3702670 TTTTAATTTTTATAT-TATAACTTT
1 ATTTAATTTTAATATCTATAA-TTT
3702694 ATTTA
1 ATTTA
3702699 TAAAATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 4 0.17
24 17 0.71
25 3 0.12
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (24 bp):
ATTTAATTTTAATATCTATAATTT
Found at i:3704265 original size:25 final size:26
Alignment explanation
Indices: 3704227--3704275 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
3704217 AACTTACAAT
* *
3704227 TAAATTAATCAATAATCATGCAAAAA
1 TAAATTAATAAATAACCATGCAAAAA
3704253 TAAA-TAATAAATAACCATGCAAA
1 TAAATTAATAAATAACCATGCAAA
3704276 TAAATATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.59, C:0.12, G:0.04, T:0.24
Consensus pattern (26 bp):
TAAATTAATAAATAACCATGCAAAAA
Found at i:3704347 original size:36 final size:36
Alignment explanation
Indices: 3704268--3704349 Score: 137
Period size: 36 Copynumber: 2.3 Consensus size: 36
3704258 AATAAATAAC
* * *
3704268 CATGCAAATAAATATATTAATTATGAGAATATTAAT
1 CATGCAAGTAAATATAATAATTATGAAAATATTAAT
3704304 CATGCAAGTAAATATAATAATTATGAAAATATTAAT
1 CATGCAAGTAAATATAATAATTATGAAAATATTAAT
3704340 CATGCAAGTA
1 CATGCAAGTA
3704350 TTAATAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (36 bp):
CATGCAAGTAAATATAATAATTATGAAAATATTAAT
Found at i:3704503 original size:17 final size:15
Alignment explanation
Indices: 3704483--3704535 Score: 54
Period size: 17 Copynumber: 3.3 Consensus size: 15
3704473 CAAATAGAAC
3704483 AAAAATAATTCAAAAAT
1 AAAAATAATT--AAAAT
3704500 AAAAATAATTAAAAT
1 AAAAATAATTAAAAT
*
3704515 AAATTAA-AATCAAAAT
1 AAA--AATAATTAAAAT
3704531 AAAAA
1 AAAAA
3704536 AAGAGAAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
14 2 0.06
15 8 0.24
16 11 0.33
17 12 0.36
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAATAATTAAAAT
Found at i:3705451 original size:19 final size:19
Alignment explanation
Indices: 3705427--3705495 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
3705417 CCTTTTTCCA
*
3705427 AAAAATTAAAAGTAAAAAT
1 AAAAATTAAAATTAAAAAT
*
3705446 AAAAA-TAAAATTGAAAAT
1 AAAAATTAAAATTAAAAAT
* *
3705464 CAAAACTAAAATTAAAAAT
1 AAAAATTAAAATTAAAAAT
* *
3705483 CAAAATCAAAATT
1 AAAAATTAAAATT
3705496 TCACTTAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
18 15 0.35
19 28 0.65
ACGTcount: A:0.70, C:0.06, G:0.03, T:0.22
Consensus pattern (19 bp):
AAAAATTAAAATTAAAAAT
Found at i:3705509 original size:6 final size:6
Alignment explanation
Indices: 3705428--3705530 Score: 71
Period size: 6 Copynumber: 16.7 Consensus size: 6
3705418 CTTTTTCCAA
* * * * *
3705428 AAAATT AAAAGT AAAAAT AAAAAT AAAATT GAAAATC AAAACT AAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT -AAAATT AAAATT AAAATT
* * ** * * *
3705477 AAAAATC AAAATC AAAATT TCACTT AAAATT AAGAATC AAAATT AAAAAT
1 -AAAATT AAAATT AAAATT AAAATT AAAATT AA-AATT AAAATT AAAATT
3705527 AAAA
1 AAAA
3705531 GTACAATTAG
Statistics
Matches: 76, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
6 61 0.80
7 15 0.20
ACGTcount: A:0.67, C:0.07, G:0.03, T:0.23
Consensus pattern (6 bp):
AAAATT
Found at i:3705529 original size:25 final size:24
Alignment explanation
Indices: 3705428--3705530 Score: 91
Period size: 25 Copynumber: 4.2 Consensus size: 24
3705418 CTTTTTCCAA
*
3705428 AAAATTAAAAGT-AAAAATAAAAAT
1 AAAATTAAAA-TCAAAATTAAAAAT
* *
3705452 AAAATTGAAAATCAAAACTAAAATT
1 AAAATT-AAAATCAAAATTAAAAAT
* ** **
3705477 AAAAATCAAAATCAAAATTTCACTT
1 -AAAATTAAAATCAAAATTAAAAAT
3705502 AAAATTAAGAATCAAAATTAAAAAT
1 AAAATTAA-AATCAAAATTAAAAAT
3705527 AAAA
1 AAAA
3705531 GTACAATTAG
Statistics
Matches: 63, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
24 14 0.22
25 44 0.70
26 5 0.08
ACGTcount: A:0.67, C:0.07, G:0.03, T:0.23
Consensus pattern (24 bp):
AAAATTAAAATCAAAATTAAAAAT
Found at i:3705867 original size:43 final size:43
Alignment explanation
Indices: 3705797--3705904 Score: 155
Period size: 43 Copynumber: 2.5 Consensus size: 43
3705787 CAGAGGTTTA
* * *
3705797 AAACTTTTGAAAAAAATAAAATACTCCCTTACAACTAAGGTTTTG
1 AAACTTTTG--AAAAATAAAATGCTCCCCTACAACTAAGGCTTTG
*
3705842 AAACTTTTGAAAAATAAAATGCTCCCCTACAACTAGGGCTTTG
1 AAACTTTTGAAAAATAAAATGCTCCCCTACAACTAAGGCTTTG
3705885 AAACTTTT-AAAAATAAAATG
1 AAACTTTTGAAAAATAAAATG
3705905 AGATCATTCT
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
42 12 0.20
43 38 0.64
45 9 0.15
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (43 bp):
AAACTTTTGAAAAATAAAATGCTCCCCTACAACTAAGGCTTTG
Found at i:3711810 original size:18 final size:18
Alignment explanation
Indices: 3711789--3711829 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3711779 TTATTTTATT
3711789 TTTAATTTT-TAATTTTAC
1 TTTAATTTTCT-ATTTTAC
*
3711807 TTTAATTTTCTATTTTAT
1 TTTAATTTTCTATTTTAC
3711825 TTTAA
1 TTTAA
3711830 ATGATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTAATTTTCTATTTTAC
Found at i:3718074 original size:21 final size:21
Alignment explanation
Indices: 3718049--3718101 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3718039 GTTAGTTAAC
* *
3718049 ATAATATAATATATACAAGAA
1 ATAATATAAAATACACAAGAA
*
3718070 ATAATATAAAATACACAAGGA
1 ATAATATAAAATACACAAGAA
*
3718091 ACAATATAAAA
1 ATAATATAAAA
3718102 GGTTAGTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.64, C:0.08, G:0.06, T:0.23
Consensus pattern (21 bp):
ATAATATAAAATACACAAGAA
Found at i:3719287 original size:20 final size:20
Alignment explanation
Indices: 3719171--3719288 Score: 63
Period size: 20 Copynumber: 6.0 Consensus size: 20
3719161 AAGAATGTCC
*
3719171 TGCAAATATATTAATTATCA
1 TGCAAATATATTAATAATCA
* *
3719191 TACAATAATAATAATAATAATCA
1 TGC-A-AAT-ATATTAATAATCA
* * *
3719214 TGTAGATATA-TAA-CATCA
1 TGCAAATATATTAATAATCA
3719232 TGCAAATATA-T--T-ATCA
1 TGCAAATATATTAATAATCA
* *
3719248 TTC-AATA-ATTAAAAATATCA
1 TGCAAATATATT-AATA-ATCA
3719268 TGCAAATATATTAATAATCA
1 TGCAAATATATTAATAATCA
3719288 T
1 T
3719289 TCATGCAAAT
Statistics
Matches: 73, Mismatches: 13, Indels: 24
0.66 0.12 0.22
Matches are distributed among these distances:
14 1 0.01
15 5 0.07
16 6 0.08
18 13 0.18
19 3 0.04
20 16 0.22
21 10 0.14
22 7 0.10
23 12 0.16
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.36
Consensus pattern (20 bp):
TGCAAATATATTAATAATCA
Found at i:3719325 original size:25 final size:27
Alignment explanation
Indices: 3719271--3719365 Score: 78
Period size: 25 Copynumber: 3.7 Consensus size: 27
3719261 AATATCATGC
*
3719271 AAATATATTAATAATCATTCATGCAAAT
1 AAATATATTAATAATCATGCATGC-AAT
3719299 AAATATATTAATAA-CATGCAAT-C-AT
1 AAATATATTAATAATCATGC-ATGCAAT
* *
3719324 AAATATATTAGGTAATCATACA---AAT
1 AAATATATTA-ATAATCATGCATGCAAT
*
3719349 AAATATA-AAATAATCAT
1 AAATATATTAATAATCAT
3719366 ACAAGTAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
23 7 0.12
24 1 0.02
25 21 0.36
26 4 0.07
27 9 0.16
28 16 0.28
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (27 bp):
AAATATATTAATAATCATGCATGCAAT
Found at i:3719362 original size:23 final size:23
Alignment explanation
Indices: 3719336--3719379 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
3719326 ATATATTAGG
3719336 TAATCATACAAATAAATATAAAA
1 TAATCATACAAATAAATATAAAA
*
3719359 TAATCATACAAGTAAATATAA
1 TAATCATACAAATAAATATAA
3719380 TAATTTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.27
Consensus pattern (23 bp):
TAATCATACAAATAAATATAAAA
Found at i:3719431 original size:20 final size:21
Alignment explanation
Indices: 3719395--3719443 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
3719385 TTCATGCAAA
* *
3719395 CATGCAATTAAATATAT-TAT
1 CATGCAAATAAATATATAAAT
3719415 CATGCAAAT-AATAATATAAAT
1 CATGCAAATAAAT-ATATAAAT
3719436 CATGCAAA
1 CATGCAAA
3719444 CAAACTTGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 12 0.48
21 10 0.40
ACGTcount: A:0.51, C:0.12, G:0.06, T:0.31
Consensus pattern (21 bp):
CATGCAAATAAATATATAAAT
Found at i:3720610 original size:19 final size:20
Alignment explanation
Indices: 3720588--3720625 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
3720578 TGATTTTCTG
3720588 TCTTTTTTTTTTA-CTTTTC
1 TCTTTTTTTTTTACCTTTTC
3720607 TCTTTTTTTTTTACCTTTT
1 TCTTTTTTTTTTACCTTTT
3720626 TTCTAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (20 bp):
TCTTTTTTTTTTACCTTTTC
Found at i:3720666 original size:13 final size:13
Alignment explanation
Indices: 3720650--3720699 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
3720640 AAGTAAAAAC
3720650 AAAATCAAAATTT
1 AAAATCAAAATTT
*
3720663 AAAATCAAAA-CT
1 AAAATCAAAATTT
* * *
3720675 AAAATTAAAAATC
1 AAAATCAAAATTT
3720688 AAAATCAAAATT
1 AAAATCAAAATT
3720700 CCATTTAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATCAAAATTT
Found at i:3720671 original size:19 final size:19
Alignment explanation
Indices: 3720643--3720699 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
3720633 AAATTAAAAG
*
3720643 TAAAAACAAAATCAAAATT
1 TAAAATCAAAATCAAAATT
3720662 TAAAATCAAAA-CTAAAATT
1 TAAAATCAAAATC-AAAATT
*
3720681 AAAAATCAAAATCAAAATT
1 TAAAATCAAAATCAAAATT
3720700 CCATTTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.03
19 32 0.94
20 1 0.03
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.23
Consensus pattern (19 bp):
TAAAATCAAAATCAAAATT
Found at i:3720713 original size:6 final size:6
Alignment explanation
Indices: 3720632--3720734 Score: 53
Period size: 6 Copynumber: 16.7 Consensus size: 6
3720622 TTTTTTCTAG
* ** * * *
3720632 AAAATT AAAAGT AAAAAC AAAATC AAAATTT AAAATC AAAACT AAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAA-TT AAAATT AAAATT AAAATT
* * ** * * * *
3720681 AAAAATC AAAATC AAAATT CCATTT AAAATT AAGAGTC AAAATT AAAAAT
1 -AAAATT AAAATT AAAATT AAAATT AAAATT AA-AATT AAAATT AAAATT
3720731 AAAA
1 AAAA
3720735 GTACAATTAG
Statistics
Matches: 72, Mismatches: 22, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
6 58 0.81
7 14 0.19
ACGTcount: A:0.65, C:0.09, G:0.03, T:0.23
Consensus pattern (6 bp):
AAAATT
Found at i:3721137 original size:16 final size:16
Alignment explanation
Indices: 3721116--3721156 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
3721106 ATTTTTTACT
3721116 ATAAATATGTAAAAA-A
1 ATAAATAT-TAAAAACA
3721132 ATAAATAATTAAAAACA
1 ATAAAT-ATTAAAAACA
3721149 A-AAATATT
1 ATAAATATT
3721157 CTCTTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 3 0.13
16 16 0.70
17 4 0.17
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (16 bp):
ATAAATATTAAAAACA
Found at i:3723487 original size:34 final size:35
Alignment explanation
Indices: 3723429--3723498 Score: 90
Period size: 34 Copynumber: 2.0 Consensus size: 35
3723419 ATAAAAAATA
* *
3723429 ACTTTTTTTCTTCTCTTTTGTTTTTT-GTTTCCTC
1 ACTTATTTTCTTCTCTTATGTTTTTTCGTTTCCTC
*
3723463 ACTTATTTTCTTCTCTTCAT-TTTTTTCTTTTCCTC
1 ACTTATTTTCTTCTCTT-ATGTTTTTTCGTTTCCTC
3723498 A
1 A
3723499 ACTAATTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 22 0.71
35 9 0.29
ACGTcount: A:0.07, C:0.23, G:0.03, T:0.67
Consensus pattern (35 bp):
ACTTATTTTCTTCTCTTATGTTTTTTCGTTTCCTC
Found at i:3723488 original size:17 final size:17
Alignment explanation
Indices: 3723431--3723491 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
3723421 AAAAAATAAC
*
3723431 TTTTTTTCTTCTCTT-T
1 TTTTTTTCTTCTCTTCA
* *
3723447 TGTTTTTTGTT-TCCTCA
1 T-TTTTTTCTTCTCTTCA
*
3723464 CTTATTTTCTTCTCTTCA
1 -TTTTTTTCTTCTCTTCA
3723482 TTTTTTTCTT
1 TTTTTTTCTT
3723492 TTCCTCAACT
Statistics
Matches: 34, Mismatches: 7, Indels: 7
0.71 0.15 0.15
Matches are distributed among these distances:
16 4 0.12
17 24 0.71
18 6 0.18
ACGTcount: A:0.05, C:0.20, G:0.03, T:0.72
Consensus pattern (17 bp):
TTTTTTTCTTCTCTTCA
Found at i:3723508 original size:35 final size:34
Alignment explanation
Indices: 3723435--3723514 Score: 85
Period size: 35 Copynumber: 2.3 Consensus size: 34
3723425 AATAACTTTT
*
3723435 TTTCTTCTCTTTTGTTTTTTGTTTCCTCACTTAT
1 TTTCTTCTCTTTTGTTTTTTGTTTCCTCACTTAA
3723469 TTTCTTCTCTTCATT-TTTTTCT-TTTCCTCAAC-TAA
1 TTTCTTCTCTT--TTGTTTTT-TGTTTCCTC-ACTTAA
3723504 TTTCTTTCTCT
1 TTTC-TTCTCT
3723515 ATAGTGTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
34 11 0.28
35 18 0.45
36 11 0.28
ACGTcount: A:0.09, C:0.24, G:0.03, T:0.65
Consensus pattern (34 bp):
TTTCTTCTCTTTTGTTTTTTGTTTCCTCACTTAA
Found at i:3732147 original size:13 final size:13
Alignment explanation
Indices: 3732129--3732157 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3732119 TTTCAATCTA
3732129 TTAATTTTAATTT
1 TTAATTTTAATTT
3732142 TTAATTTTAATTT
1 TTAATTTTAATTT
3732155 TTA
1 TTA
3732158 TTTACTCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTAATTTTAATTT
Found at i:3755777 original size:62 final size:63
Alignment explanation
Indices: 3755677--3755805 Score: 163
Period size: 62 Copynumber: 2.1 Consensus size: 63
3755667 TATTTTCTTG
* *
3755677 TTTTGAATTTCTAAATTCTCCACCATTTGGGCCTATTTAGAAATTTT-ATTTATTTATTTATTT
1 TTTTGAATTTCTAAATTCTCCACAATTTGGGCCAATTTA-AAATTTTCATTTATTTATTTATTT
* * * * * *
3755740 TTTTGAATTT-TATATTTTCCACAATTTGGGTCAATTTAAAATTTTCTTTTATTTTTTTCTTT
1 TTTTGAATTTCTAAATTCTCCACAATTTGGGCCAATTTAAAATTTTCATTTATTTATTTATTT
3755802 TTTT
1 TTTT
3755806 CGGAAAGAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
61 7 0.12
62 40 0.70
63 10 0.18
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.59
Consensus pattern (63 bp):
TTTTGAATTTCTAAATTCTCCACAATTTGGGCCAATTTAAAATTTTCATTTATTTATTTATTT
Found at i:3756266 original size:26 final size:24
Alignment explanation
Indices: 3756237--3756308 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 24
3756227 AAATTTAGAT
3756237 AAAATTTCTCATCTAGAAATTTTATA
1 AAAATTTCTCAT-TAGAAATTTT-TA
*
3756263 AAAATTTAC-CATTTGAAATTTTTA
1 AAAATTT-CTCATTAGAAATTTTTA
*
3756287 TAAATTTCATCATTAGATAATT
1 AAAATTTC-TCATTAGA-AATT
3756309 AATATTTACT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 1 0.03
24 8 0.21
25 15 0.38
26 14 0.36
27 1 0.03
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (24 bp):
AAAATTTCTCATTAGAAATTTTTA
Found at i:3756329 original size:184 final size:186
Alignment explanation
Indices: 3756004--3756348 Score: 441
Period size: 184 Copynumber: 1.9 Consensus size: 186
3755994 CAATTACTTC
* * *
3756004 TATTAAAATTTCATCTAAATTATTCCACCATTTGGGACAAATTTAAAGAAAAATTTTTCAACTAA
1 TATTAAAATTTCATCTAAATCATTCAACCATTTGGGACAAATTT-AAGAAAAATTTCTCAACTAA
* * * * **
3756069 AAATTTCTTAAAAATTTATCATTTGACATTTCTAAGAATCTCATCCTTAGGTAATTTGTATTTAA
65 AAATTTCTTAAAAATTTACCATTTGAAATTTCTAAGAATCTCATCATTAGATAATTAATATTTAA
*
3756134 TTCCAAAA-TTTTTATA-TTTTATATTTTTATTTTGAAAATAAATATTAATTATTGT
130 TCCCAAAATTTTTTATATTTTTATATTTTTATTTTGAAAATAAATATTAATTATTGT
* *
3756189 TATTAAAACTTT-ATCTAAATCATTCAACCATTTTGGACAAATTT-AGATAAAATTTCTCATCTA
1 TATTAAAA-TTTCATCTAAATCATTCAACCATTTGGGACAAATTTAAGA-AAAATTTCTCAACTA
* * *
3756252 GAAATTT-TATAAAAATTTACCATTTGAAATTTTTATA-AATTTCATCATTAGATAATTAATATT
64 AAAATTTCT-TAAAAATTTACCATTTGAAATTTCTA-AGAATCTCATCATTAGATAATTAATATT
* *
3756315 TACTCCCAAAATTTTTTTTTATTTTTATATTTTT
127 TAATCCCAAAA-TTTTTTATATTTTTATATTTTT
3756349 TTCTAAATTT
Statistics
Matches: 136, Mismatches: 17, Indels: 12
0.82 0.10 0.07
Matches are distributed among these distances:
183 4 0.03
184 72 0.53
185 38 0.28
186 10 0.07
187 12 0.09
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (186 bp):
TATTAAAATTTCATCTAAATCATTCAACCATTTGGGACAAATTTAAGAAAAATTTCTCAACTAAA
AATTTCTTAAAAATTTACCATTTGAAATTTCTAAGAATCTCATCATTAGATAATTAATATTTAAT
CCCAAAATTTTTTATATTTTTATATTTTTATTTTGAAAATAAATATTAATTATTGT
Found at i:3756405 original size:21 final size:19
Alignment explanation
Indices: 3756375--3756417 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
3756365 GCAAAAATAC
3756375 TAAA-AAATACATAAAATAAA
1 TAAATAAATACA-AAAA-AAA
3756395 TAAATAAATACAAAAAAAA
1 TAAATAAATACAAAAAAAA
3756414 -AAAT
1 TAAAT
3756418 GAAACGGCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.18
19 3 0.14
20 8 0.36
21 7 0.32
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.19
Consensus pattern (19 bp):
TAAATAAATACAAAAAAAA
Found at i:3756692 original size:13 final size:13
Alignment explanation
Indices: 3756674--3756718 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 13
3756664 CAGATCCCCC
*
3756674 TTCTTCCCTCTCT
1 TTCTTCTCTCTCT
3756687 TTCTTCTCT-TCT
1 TTCTTCTCTCTCT
*
3756699 TT-TTCTCTCCCT
1 TTCTTCTCTCTCT
3756711 TTC-TCTCT
1 TTCTTCTCT
3756719 AACAACCTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 6 0.21
12 14 0.50
13 8 0.29
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (13 bp):
TTCTTCTCTCTCT
Found at i:3757382 original size:17 final size:17
Alignment explanation
Indices: 3757360--3757396 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
3757350 AACTTTTGAA
3757360 AAATAAAATGCTCCTCT
1 AAATAAAATGCTCCTCT
*
3757377 AAATAAAATGCTTCTCT
1 AAATAAAATGCTCCTCT
3757394 AAA
1 AAA
3757397 CAGAGGCACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.19, G:0.05, T:0.30
Consensus pattern (17 bp):
AAATAAAATGCTCCTCT
Found at i:3757469 original size:51 final size:51
Alignment explanation
Indices: 3757414--3757512 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
3757404 ACCACAACTT
* * *
3757414 TTAAAAAATAAAATACTCCTCTAAATAGAGGCACCACAACTTTAAAAAATA
1 TTAAAAAATAAAATACTCATCTAAACAGAAGCACCACAACTTTAAAAAATA
**
3757465 TTAAAAAATAAAATGTTCATCTAAACAGAAGCACCACAACTTTAAAAA
1 TTAAAAAATAAAATACTCATCTAAACAGAAGCACCACAACTTTAAAAA
3757513 TTAAAATGCT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.54, C:0.17, G:0.06, T:0.23
Consensus pattern (51 bp):
TTAAAAAATAAAATACTCATCTAAACAGAAGCACCACAACTTTAAAAAATA
Found at i:3757510 original size:41 final size:41
Alignment explanation
Indices: 3757465--3757764 Score: 345
Period size: 41 Copynumber: 7.4 Consensus size: 41
3757455 TTAAAAAATA
* * *
3757465 TTAAAAAATAAAATGTTCATCTAAACAGAAGCACCACAACT
1 TTAAAAAATAAAATGCTCCTCTAAACAGAGGCACCACAACT
* * *
3757506 TTAAAAATTAAAATGCTCCTCTAAATAGAGACACCACAACTT
1 TTAAAAAATAAAATGCTCCTCTAAACAGAGGCACCACAAC-T
* * *
3757548 TTGAAAAATAAAATACTCCTCTAAACA-AGGCACCATAACT
1 TTAAAAAATAAAATGCTCCTCTAAACAGAGGCACCACAACT
* * * *
3757588 TTAAAAAAT-AAATGCTCCTTTAAATATAGACACCACAACT
1 TTAAAAAATAAAATGCTCCTCTAAACAGAGGCACCACAACT
* * *
3757628 TTAAAAAATAAATTGCTCTTCTAAACAGAGGTACCACAACT
1 TTAAAAAATAAAATGCTCCTCTAAACAGAGGCACCACAACT
* *
3757669 TTGAAAAAT-AAATGCTCATCTAAACAGAGGCACCACAACT
1 TTAAAAAATAAAATGCTCCTCTAAACAGAGGCACCACAACT
* * * * * *
3757709 TTGAAAAATAAAGTGCTCTTCTAAATATAGGCACTACAACT
1 TTAAAAAATAAAATGCTCCTCTAAACAGAGGCACCACAACT
*
3757750 TTGAAAAATAAAATG
1 TTAAAAAATAAAATG
3757765 TTTATTGACA
Statistics
Matches: 220, Mismatches: 35, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
39 14 0.06
40 66 0.30
41 116 0.53
42 24 0.11
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.25
Consensus pattern (41 bp):
TTAAAAAATAAAATGCTCCTCTAAACAGAGGCACCACAACT
Found at i:3757628 original size:81 final size:81
Alignment explanation
Indices: 3757468--3757761 Score: 374
Period size: 81 Copynumber: 3.6 Consensus size: 81
3757458 AAAAATATTA
* * * *
3757468 AAAAATAAAATGTTCATCTAAACAGAAGCACCACAACTTTAAAAATTAAAATGCTCCTCTAAATA
1 AAAAATAAAATGCTCTTCTAAACAGAGGCACCACAACTTTAAAAAAT-AAATGCTCCTCTAAATA
3757533 GAGACACCACAACTTTTG
65 GAGACACCACAAC-TTTG
* * * * *
3757551 AAAAATAAAATACTCCTCTAAACA-AGGCACCATAACTTTAAAAAATAAATGCTCCTTTAAATAT
1 AAAAATAAAATGCTCTTCTAAACAGAGGCACCACAACTTTAAAAAATAAATGCTCCTCTAAATAG
*
3757615 AGACACCACAACTTTA
66 AGACACCACAACTTTG
* * * * *
3757631 AAAAATAAATTGCTCTTCTAAACAGAGGTACCACAACTTTGAAAAATAAATGCTCATCTAAACAG
1 AAAAATAAAATGCTCTTCTAAACAGAGGCACCACAACTTTAAAAAATAAATGCTCCTCTAAATAG
*
3757696 AGGCACCACAACTTTG
66 AGACACCACAACTTTG
* * * * *
3757712 AAAAATAAAGTGCTCTTCTAAATATAGGCACTACAACTTTGAAAAATAAA
1 AAAAATAAAATGCTCTTCTAAACAGAGGCACCACAACTTTAAAAAATAAA
3757762 ATGTTTATTG
Statistics
Matches: 184, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
80 24 0.13
81 120 0.65
82 19 0.10
83 21 0.11
ACGTcount: A:0.47, C:0.20, G:0.09, T:0.24
Consensus pattern (81 bp):
AAAAATAAAATGCTCTTCTAAACAGAGGCACCACAACTTTAAAAAATAAATGCTCCTCTAAATAG
AGACACCACAACTTTG
Found at i:3757664 original size:122 final size:122
Alignment explanation
Indices: 3757465--3757764 Score: 374
Period size: 122 Copynumber: 2.5 Consensus size: 122
3757455 TTAAAAAATA
* * * * * *
3757465 TTAAAAAATAAAATGTTCATCTAAACAGA-AGCACCACAACTTTAAAAATTAAAATGCTCCTCTA
1 TTAAAAAATAAAGTGCTCTTCTAAATATAGA-CACCACAACTTTAAAAAATAAAATGCTCCTCTA
* * *
3757529 AATAGAGACACCACAACTTTTGAAAAATAAAATACTCCTCTAAACA-AGGCACCATAACT
65 AACAGAGACACCACAAC-TTTGAAAAAT-AAATACTCATCTAAACAGAGGCACCACAACT
* *
3757588 TTAAAAAATAAA-TGCTCCTT-TAAATATAGACACCACAACTTTAAAAAATAAATTGCTCTTCTA
1 TTAAAAAATAAAGTGCT-CTTCTAAATATAGACACCACAACTTTAAAAAATAAAATGCTCCTCTA
** *
3757651 AACAGAGGTACCACAACTTTGAAAAATAAATGCTCATCTAAACAGAGGCACCACAACT
65 AACAGAGACACCACAACTTTGAAAAATAAATACTCATCTAAACAGAGGCACCACAACT
* * * *
3757709 TTGAAAAATAAAGTGCTCTTCTAAATATAGGCACTACAACTTTGAAAAATAAAATG
1 TTAAAAAATAAAGTGCTCTTCTAAATATAGACACCACAACTTTAAAAAATAAAATG
3757765 TTTATTGACA
Statistics
Matches: 154, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
120 15 0.10
121 36 0.23
122 88 0.57
123 15 0.10
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.25
Consensus pattern (122 bp):
TTAAAAAATAAAGTGCTCTTCTAAATATAGACACCACAACTTTAAAAAATAAAATGCTCCTCTAA
ACAGAGACACCACAACTTTGAAAAATAAATACTCATCTAAACAGAGGCACCACAACT
Found at i:3758788 original size:11 final size:10
Alignment explanation
Indices: 3758758--3758854 Score: 83
Period size: 10 Copynumber: 9.4 Consensus size: 10
3758748 GACTTGAGTC
3758758 TTTCTTTTTAT
1 TTTCTTTTT-T
3758769 TATTCTTTTTT
1 T-TTCTTTTTT
*
3758780 TCTC-TTTTT
1 TTTCTTTTTT
3758789 TTTCTTTTTTT
1 TTTC-TTTTTT
3758800 TTTCTTTTGCTT
1 TTTCTTTT--TT
*
3758812 TTT-TCTTTCT
1 TTTCT-TTTTT
3758822 TTT-TTTTTT
1 TTTCTTTTTT
**
3758831 TAACTTTTTT
1 TTTCTTTTTT
3758841 TTTCTTTTTT
1 TTTCTTTTTT
3758851 TTTC
1 TTTC
3758855 AAGCATAGTA
Statistics
Matches: 71, Mismatches: 8, Indels: 15
0.76 0.09 0.16
Matches are distributed among these distances:
9 13 0.18
10 29 0.41
11 13 0.18
12 16 0.23
ACGTcount: A:0.04, C:0.12, G:0.01, T:0.82
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:3758801 original size:24 final size:25
Alignment explanation
Indices: 3758774--3758847 Score: 62
Period size: 25 Copynumber: 2.8 Consensus size: 25
3758764 TTTATTATTC
* *
3758774 TTTTTTTCTCTTTTTTTTCTTTTTTT
1 TTTTTTTCT-TTTTTTTTCTTTATCT
3758800 TTTCTTTTGCTTTTTTCTTTCTTT-T-T
1 TTT-TTTT-CTTTTTT-TTTCTTTATCT
*
3758826 TTTTTTAACTTTTTTTTTCTTT
1 TTTTTT-TCTTTTTTTTTCTTT
3758848 TTTTTTCAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
24 7 0.16
25 10 0.23
26 7 0.16
27 10 0.23
28 9 0.21
ACGTcount: A:0.03, C:0.12, G:0.01, T:0.84
Consensus pattern (25 bp):
TTTTTTTCTTTTTTTTTCTTTATCT
Found at i:3758848 original size:24 final size:24
Alignment explanation
Indices: 3758774--3758853 Score: 88
Period size: 26 Copynumber: 3.2 Consensus size: 24
3758764 TTTATTATTC
** *
3758774 TTTTTTTCTCTTTTTTTTCTTTTTT
1 TTTTTTTAACTTTTTTTT-TCTTTT
**
3758799 TTTTCTTTTGCTTTTTTCTTTCTTTT
1 TTTT-TTTAACTTTTTT-TTTCTTTT
3758825 TTTTTTTAACTTTTTTTTTCTTTT
1 TTTTTTTAACTTTTTTTTTCTTTT
3758849 TTTTT
1 TTTTT
3758854 CAAGCATAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.27
25 14 0.29
26 19 0.40
27 2 0.04
ACGTcount: A:0.03, C:0.11, G:0.01, T:0.85
Consensus pattern (24 bp):
TTTTTTTAACTTTTTTTTTCTTTT
Found at i:3758870 original size:1 final size:1
Alignment explanation
Indices: 3758774--3758853 Score: 52
Period size: 1 Copynumber: 80.0 Consensus size: 1
3758764 TTTATTATTC
* * * * ** * * ***
3758774 TTTTTTTCTCTTTTTTTTCTTTTTTTTTTCTTTTGCTTTTTTCTTTCTTTTTTTTTTTAACTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
3758839 TTTTTCTTTTTTTTT
1 TTTTTTTTTTTTTTT
3758854 CAAGCATAGT
Statistics
Matches: 59, Mismatches: 20, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.03, C:0.11, G:0.01, T:0.85
Consensus pattern (1 bp):
T
Found at i:3758886 original size:19 final size:17
Alignment explanation
Indices: 3758848--3758886 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
3758838 TTTTTTCTTT
*
3758848 TTTTTTCAAGCATAGTA
1 TTTTTTCAAGCATAGAA
3758865 TTTTTTCATAGCATTAGAA
1 TTTTTTCA-AGCA-TAGAA
3758884 TTT
1 TTT
3758887 ATAGGATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 4 0.21
19 7 0.37
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.51
Consensus pattern (17 bp):
TTTTTTCAAGCATAGAA
Found at i:3764547 original size:2 final size:2
Alignment explanation
Indices: 3764540--3764565 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3764530 GTCAATGTCA
3764540 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
3764566 TGAAGTGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3772438 original size:18 final size:19
Alignment explanation
Indices: 3772387--3772455 Score: 60
Period size: 17 Copynumber: 3.9 Consensus size: 19
3772377 TAAAAAATTA
* *
3772387 TTAAAAAAAT-TAAATAT-
1 TTAAAAAATTATAAAAATC
*
3772404 TTAAAAAATTATGAAAA-C
1 TTAAAAAATTATAAAAATC
3772422 TTAAAAAATTCA-AAAAATC
1 TTAAAAAATT-ATAAAAATC
3772441 TT--AAAATTATAAAAA
1 TTAAAAAATTATAAAAA
3772456 ATCCAAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
16 1 0.02
17 20 0.47
18 18 0.42
19 4 0.09
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.30
Consensus pattern (19 bp):
TTAAAAAATTATAAAAATC
Found at i:3772482 original size:27 final size:27
Alignment explanation
Indices: 3772406--3772484 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
3772396 TTAAATATTT
* ** *
3772406 AAAAAATTATGAAAACTTAAAAAATTC
1 AAAAAATTTTGAAATTTTAAAAAATCC
* * *
3772433 AAAAAATCTTAAAATTATAAAAAATCC
1 AAAAAATTTTGAAATTTTAAAAAATCC
3772460 AAAAAATTTTGAAATTTTCAAAAAA
1 AAAAAATTTTGAAATTTT-AAAAAA
3772485 AAATAAAAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
27 35 0.85
28 6 0.15
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.28
Consensus pattern (27 bp):
AAAAAATTTTGAAATTTTAAAAAATCC
Found at i:3772691 original size:27 final size:27
Alignment explanation
Indices: 3772656--3772720 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
3772646 TTTTTTAATC
3772656 TTGAA-ATTTTA-A-TTTTTACATATTTT
1 TTGAATATTTTATATTTTTTA-A-ATTTT
3772682 TTGAATATTTTATATTTTTTAAATTTT
1 TTGAATATTTTATATTTTTTAAATTTT
3772709 TTGAAT-TTTTAT
1 TTGAATATTTTAT
3772721 TAAAATTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
26 11 0.31
27 17 0.47
28 2 0.06
29 6 0.17
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.65
Consensus pattern (27 bp):
TTGAATATTTTATATTTTTTAAATTTT
Found at i:3772692 original size:9 final size:9
Alignment explanation
Indices: 3772677--3772718 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
3772667 ATTTTTACAT
3772677 ATTTTTTGA
1 ATTTTTTGA
*
3772686 ATATTTT-A
1 ATTTTTTGA
*
3772694 TATTTTTTAA
1 -ATTTTTTGA
3772704 ATTTTTTGA
1 ATTTTTTGA
3772713 ATTTTT
1 ATTTTT
3772719 ATTAAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
8 1 0.04
9 26 0.93
10 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (9 bp):
ATTTTTTGA
Found at i:3772710 original size:18 final size:17
Alignment explanation
Indices: 3772662--3772710 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
3772652 AATCTTGAAA
*
3772662 TTTTAATTTTTACATATT
1 TTTTAATTTTT-TATATT
*
3772680 TTTTGAATATTTTATATT
1 TTTT-AATTTTTTATATT
3772698 TTTTAAATTTTTT
1 TTTT-AATTTTTT
3772711 GAATTTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 20 0.77
19 6 0.23
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTTAATTTTTTATATT
Found at i:3772733 original size:27 final size:27
Alignment explanation
Indices: 3772677--3772731 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
3772667 ATTTTTACAT
**
3772677 ATTTTTTGAATATTTTATATTTTTTAA
1 ATTTTTTGAATATTTTATAAATTTTAA
3772704 ATTTTTTGAAT-TTTTATTAAAATTTTAA
1 ATTTTTTGAATATTTTA-T-AAATTTTAA
3772732 TTATTCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.21
27 12 0.50
28 7 0.29
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.64
Consensus pattern (27 bp):
ATTTTTTGAATATTTTATAAATTTTAA
Found at i:3772745 original size:15 final size:15
Alignment explanation
Indices: 3772717--3772764 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
3772707 TTTTGAATTT
3772717 TTATTAAAATTTTAA
1 TTATTAAAATTTTAA
3772732 TTATTCAAAATTTATAA
1 TTATT-AAAATTT-TAA
* *
3772749 TTTTTATAATTTTAA
1 TTATTAAAATTTTAA
3772764 T
1 T
3772765 AATATTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 9 0.31
16 13 0.45
17 7 0.24
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
TTATTAAAATTTTAA
Found at i:3772851 original size:34 final size:33
Alignment explanation
Indices: 3772779--3772875 Score: 81
Period size: 34 Copynumber: 2.8 Consensus size: 33
3772769 TTTAATGATT
*
3772779 TTTTTTAAATTTTAGAATTTTCAAAAAAAAATTT
1 TTTTTT-AATTTTAGAATTTTCAAAAAAAAATTA
* *
3772813 TTTTTTGAATTTTATATATTTT--AAAAAATATATA
1 TTTTTT-AATTTTAGA-ATTTTCAAAAAAAAAT-TA
* * *
3772847 TTTTTTAATTGTCAAAATTTTTAAAAAAA
1 TTTTTTAATT-TTAGAATTTTCAAAAAAA
3772876 TTTAGATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
33 17 0.33
34 24 0.46
35 11 0.21
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (33 bp):
TTTTTTAATTTTAGAATTTTCAAAAAAAAATTA
Found at i:3772886 original size:34 final size:32
Alignment explanation
Indices: 3772831--3772902 Score: 74
Period size: 34 Copynumber: 2.2 Consensus size: 32
3772821 ATTTTATATA
*
3772831 TTTTAAAAAATATATATTTTTTAATTGTCAAAAT
1 TTTTAAAAAATATATAATTTTTAATTGTC--AAT
* * *
3772865 TTTTAAAAAA-ATTTAGATTTTTTATTTTCAAT
1 TTTTAAAAAATATATA-ATTTTTAATTGTCAAT
3772897 TTTTAA
1 TTTTAA
3772903 GTTTTTGTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
32 9 0.27
33 4 0.12
34 20 0.61
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (32 bp):
TTTTAAAAAATATATAATTTTTAATTGTCAAT
Found at i:3772985 original size:21 final size:20
Alignment explanation
Indices: 3772943--3772988 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
3772933 GAACATTTTG
***
3772943 TTTTTATTAATTTTTTTTAT
1 TTTTTATTAATTTTTGAGAT
3772963 TTTTTATTAAATTTTTGAGAT
1 TTTTTATT-AATTTTTGAGAT
3772984 TTTTT
1 TTTTT
3772989 GAATTTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (20 bp):
TTTTTATTAATTTTTGAGAT
Found at i:3773057 original size:9 final size:9
Alignment explanation
Indices: 3772943--3773027 Score: 50
Period size: 9 Copynumber: 9.3 Consensus size: 9
3772933 GAACATTTTG
3772943 TTTTTATTAA
1 TTTTT-TTAA
*
3772953 TTTTTTTTAT
1 -TTTTTTTAA
3772963 TTTTTATTAA
1 TTTTT-TTAA
* *
3772973 ATTTTTGAGA
1 TTTTTTTA-A
*
3772983 TTTTTTGAA
1 TTTTTTTAA
3772992 -TTTTTTAA
1 TTTTTTTAA
* *
3773000 --GTTTTCA
1 TTTTTTTAA
3773007 TTTTTTTAA
1 TTTTTTTAA
*
3773016 TTTTTATAA
1 TTTTTTTAA
3773025 TTT
1 TTT
3773028 CTAAAAATAT
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
7 5 0.08
8 7 0.12
9 24 0.41
10 18 0.31
11 5 0.08
ACGTcount: A:0.24, C:0.01, G:0.05, T:0.71
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:3773057 original size:37 final size:37
Alignment explanation
Indices: 3773007--3773079 Score: 121
Period size: 38 Copynumber: 2.0 Consensus size: 37
3772997 TAAGTTTTCA
3773007 TTTTTTTAATTTTTATAATTTC-TAAAAATATTTAAT
1 TTTTTTTAATTTTTATAATTTCTTAAAAATATTTAAT
*
3773043 TTTTTTTAATTTTTTATATTTTCTTAAAAATATTTAA
1 TTTTTTTAA-TTTTTATAATTTCTTAAAAATATTTAA
3773080 AATTTTATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 9 0.26
37 12 0.35
38 13 0.38
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (37 bp):
TTTTTTTAATTTTTATAATTTCTTAAAAATATTTAAT
Found at i:3773095 original size:38 final size:36
Alignment explanation
Indices: 3773008--3773096 Score: 115
Period size: 38 Copynumber: 2.4 Consensus size: 36
3772998 AAGTTTTCAT
**
3773008 TTTTTTAATTTTTATAATTTCTAAAAATATTTAATT
1 TTTTTTAATTTTTATAATTTCTAAAAATATTTAAAA
*
3773044 TTTTTTAATTTTTTATATTTTCTTAAAAATATTTAAAA
1 TTTTTTAA-TTTTTATAATTTC-TAAAAATATTTAAAA
*
3773082 TTTTATAACTTTTTA
1 TTTTTTAA-TTTTTA
3773097 AAAAATGTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
36 8 0.17
37 12 0.26
38 26 0.57
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (36 bp):
TTTTTTAATTTTTATAATTTCTAAAAATATTTAAAA
Found at i:3774064 original size:15 final size:16
Alignment explanation
Indices: 3774033--3774072 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
3774023 ATTGATATTT
3774033 AAAAATTATAAATTTAA
1 AAAAATT-TAAATTTAA
3774050 AAAAATTTAAA-TTAA
1 AAAAATTTAAATTTAA
*
3774065 TAAAATTT
1 AAAAATTT
3774073 TTTTATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.50
16 4 0.18
17 7 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAAATTTAAATTTAA
Found at i:3782935 original size:2 final size:2
Alignment explanation
Indices: 3782930--3782964 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3782920 CTCTCTACTC
3782930 TA TA 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 TA TA T
3782965 CCACATAAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3786740 original size:29 final size:30
Alignment explanation
Indices: 3786708--3786780 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
3786698 TATTTTATTT
* *
3786708 AAATAAATTTTTATATTTTTA-TTATA-TCC-
1 AAATAAATTTTTA-ACTTTTACTT-TACACCA
3786737 AAATAAATTTTTAACTTTTACTTTACACCA
1 AAATAAATTTTTAACTTTTACTTTACACCA
3786767 AAATAAATTTTTAA
1 AAATAAATTTTTAA
3786781 ACATTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
28 8 0.21
29 17 0.44
30 14 0.36
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (30 bp):
AAATAAATTTTTAACTTTTACTTTACACCA
Found at i:3789289 original size:35 final size:36
Alignment explanation
Indices: 3789241--3789308 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
3789231 ACAAAAACTA
*
3789241 GTTGACATAAGAGAGGCTCATCACTC-TCCTCGGTG
1 GTTGACATAAGAGAGGATCATCACTCTTCCTCGGTG
* *
3789276 GTTGACATGAGAGAGGATCATCATTCTTCCTCG
1 GTTGACATAAGAGAGGATCATCACTCTTCCTCG
3789309 ATCATAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 23 0.79
36 6 0.21
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.28
Consensus pattern (36 bp):
GTTGACATAAGAGAGGATCATCACTCTTCCTCGGTG
Found at i:3796344 original size:52 final size:51
Alignment explanation
Indices: 3796263--3796410 Score: 199
Period size: 52 Copynumber: 2.8 Consensus size: 51
3796253 ACAAATTTAT
* *
3796263 CTATTAAGAATCTCTCTTCTCTTAAAATTCTTCTATTGTAAGTTAAACTTAC
1 CTATTAAGAATCTCT-TTCTTTTAGAATTCTTCTATTGTAAGTTAAACTTAC
* * *
3796315 CTATTAAGAATCTCTTTCCTTTTAGAATTCTTCTCTTGCAAGTCAAACTTAC
1 CTATTAAGAATCTCTTT-CTTTTAGAATTCTTCTATTGTAAGTTAAACTTAC
*
3796367 CTATTAAGAATCTCTTTTCTTTTAGAAATT-TTCTTTTGTAAGTT
1 CTATTAAGAATCTC-TTTCTTTTAG-AATTCTTCTATTGTAAGTT
3796411 TTTTTGTCCA
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
51 2 0.02
52 76 0.89
53 7 0.08
ACGTcount: A:0.28, C:0.18, G:0.07, T:0.47
Consensus pattern (51 bp):
CTATTAAGAATCTCTTTCTTTTAGAATTCTTCTATTGTAAGTTAAACTTAC
Found at i:3796778 original size:25 final size:25
Alignment explanation
Indices: 3796707--3796784 Score: 95
Period size: 25 Copynumber: 3.1 Consensus size: 25
3796697 AAACCATGCA
* *
3796707 CTTTCCACATCTTAAACTTTTAGCT
1 CTTTTCACATCTTAAACTTTTAACT
* *
3796732 TTTTTCACATCTCAAACTTTTAACT
1 CTTTTCACATCTTAAACTTTTAACT
*
3796757 CTTTTCACATCTTGAA-TCTTTAACT
1 CTTTTCACATCTTAAACT-TTTAACT
3796782 CTT
1 CTT
3796785 CTCATGTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
24 1 0.02
25 44 0.98
ACGTcount: A:0.24, C:0.26, G:0.03, T:0.47
Consensus pattern (25 bp):
CTTTTCACATCTTAAACTTTTAACT
Found at i:3797409 original size:52 final size:52
Alignment explanation
Indices: 3797339--3797495 Score: 206
Period size: 52 Copynumber: 3.0 Consensus size: 52
3797329 TATAACTATA
* * * *
3797339 CAAACTTACCCATTAAGAATCTATTTTCTCTTAGAATTCTTCTATTATAAGT
1 CAAACTTACCTATTAAGAATCTCTTTTCTTTTAGAATTCTTCTATTACAAGT
* * * * *
3797391 TAAACTTACCTATTAAGAATCTCTTTCCTTTTAGACTTCTTCTCTTACCAGT
1 CAAACTTACCTATTAAGAATCTCTTTTCTTTTAGAATTCTTCTATTACAAGT
* * *
3797443 CAAACTTACCTATTAAGAATCTCTTTTCTTTTAAAATTCTTCTTTTGCAAGT
1 CAAACTTACCTATTAAGAATCTCTTTTCTTTTAGAATTCTTCTATTACAAGT
3797495 C
1 C
3797496 TTCTTATCCA
Statistics
Matches: 89, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 89 1.00
ACGTcount: A:0.29, C:0.22, G:0.06, T:0.44
Consensus pattern (52 bp):
CAAACTTACCTATTAAGAATCTCTTTTCTTTTAGAATTCTTCTATTACAAGT
Found at i:3797536 original size:11 final size:11
Alignment explanation
Indices: 3797520--3797560 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
3797510 GCAATATCTG
3797520 ACAAATCTCAA
1 ACAAATCTCAA
* **
3797531 ACAAATTTTTA
1 ACAAATCTCAA
3797542 ACAAATCTCAA
1 ACAAATCTCAA
3797553 ACAAATCT
1 ACAAATCT
3797561 TTTATGAGAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:3797545 original size:22 final size:23
Alignment explanation
Indices: 3797520--3797564 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
3797510 GCAATATCTG
3797520 ACAAATCTCAAACAAAT-TTTTA
1 ACAAATCTCAAACAAATCTTTTA
3797542 ACAAATCTCAAACAAATCTTTTA
1 ACAAATCTCAAACAAATCTTTTA
3797565 TGAGATTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (23 bp):
ACAAATCTCAAACAAATCTTTTA
Found at i:3802508 original size:22 final size:21
Alignment explanation
Indices: 3802460--3802510 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
3802450 ATAATTTTTA
*
3802460 AATTTTAATAAAAATTATAAAT
1 AATTTTAAT-AAAATTAAAAAT
3802482 AATTTTAAT-AAATTAAAATAT
1 AATTTTAATAAAATTAAAA-AT
3802503 ATATTTTA
1 A-ATTTTA
3802511 TATTTTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 8 0.31
21 3 0.12
22 15 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTTTAATAAAATTAAAAAT
Found at i:3804089 original size:30 final size:31
Alignment explanation
Indices: 3804054--3804117 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
3804044 TAAGTTCCTA
*
3804054 TTTTATTATTT-GTATATAA-AATTATAAATT
1 TTTTATTATTTCTTA-ATAATAATTATAAATT
* *
3804084 TTTTATTTTTTCTTAATAATTATTATAAATT
1 TTTTATTATTTCTTAATAATAATTATAAATT
3804115 TTT
1 TTT
3804118 AAAATCAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 14 0.48
31 15 0.52
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (31 bp):
TTTTATTATTTCTTAATAATAATTATAAATT
Found at i:3807327 original size:4 final size:4
Alignment explanation
Indices: 3807320--3807364 Score: 67
Period size: 4 Copynumber: 11.8 Consensus size: 4
3807310 CATGCATACA
*
3807320 TATG TATG TATG TATA TATG TATG TA-- TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
3807365 ATAATGCAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
4 35 0.95
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:3807351 original size:18 final size:18
Alignment explanation
Indices: 3807319--3807366 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
3807309 ACATGCATAC
3807319 ATATGTATG--TATGTAT
1 ATATGTATGTATATGTAT
3807335 ATATGTATGTATATGTAT
1 ATATGTATGTATATGTAT
*
3807353 GTATGTATGTATAT
1 ATATGTATGTATAT
3807367 AATGCAAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 9 0.31
18 20 0.69
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (18 bp):
ATATGTATGTATATGTAT
Done.