Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 120 of 198
Found at i:38565315 original size:46 final size:46
Alignment explanation
Indices: 38565212--38565603 Score: 621
Period size: 46 Copynumber: 8.6 Consensus size: 46
38565202 CACTTATGAT
*
38565212 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-A-GACTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATG-CTAC
**
38565255 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAACTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
* * **
38565301 CACTTATCACTTTGTCACTTGACCAGATAAGTGTAGTTAAAACTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
* *
38565347 CACTTATCACTTTATCACTTGATCAGATAAGTGCAGCTAATGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
38565393 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
* *
38565439 CACTTATCACTTTCTCACTTGATCAGATAAGTGCAGCTAATGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
*
38565485 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
*
38565531 CACTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
*
38565577 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
38565604 AGTACTCAAA
Statistics
Matches: 329, Mismatches: 16, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
43 10 0.03
44 5 0.02
45 20 0.06
46 294 0.89
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.33
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
Found at i:38565887 original size:19 final size:21
Alignment explanation
Indices: 38565847--38565893 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
38565837 TTTTATTATC
38565847 ATTTCATCAATAAATATATAT
1 ATTTCATCAATAAATATATAT
*
38565868 ATTTCATC-ATACAT-TATAT
1 ATTTCATCAATAAATATATAT
*
38565887 AATTCAT
1 ATTTCAT
38565894 GAAATTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.46
20 5 0.21
21 8 0.33
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTCATCAATAAATATATAT
Found at i:38567368 original size:11 final size:13
Alignment explanation
Indices: 38567348--38567379 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
38567338 AATAAATTAA
38567348 TAAAATATCAT-T
1 TAAAATATCATAT
38567360 TAAAA-ATCATAT
1 TAAAATATCATAT
38567372 TAAAATAT
1 TAAAATAT
38567380 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCATAT
Found at i:38570607 original size:53 final size:53
Alignment explanation
Indices: 38570527--38570633 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
38570517 TCAAAAAGAA
38570527 AGAAAGAAGTCGGATTTATAAATTTTTTTCATAACACTTCCAGATTCGACCAT
1 AGAAAGAAGTCGGATTTATAAATTTTTTTCATAACACTTCCAGATTCGACCAT
38570580 AGAAAGAAGTCGGATTTATAAATTTTTTTCATAACACTTCCAGATTCGACCAT
1 AGAAAGAAGTCGGATTTATAAATTTTTTTCATAACACTTCCAGATTCGACCAT
38570633 A
1 A
38570634 ATGTCTACGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (53 bp):
AGAAAGAAGTCGGATTTATAAATTTTTTTCATAACACTTCCAGATTCGACCAT
Found at i:38571273 original size:4 final size:4
Alignment explanation
Indices: 38571264--38571310 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
38571254 ACTTCAATAC
38571264 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
38571311 AATAACTCCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:38572092 original size:16 final size:16
Alignment explanation
Indices: 38572067--38572113 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
38572057 AAAACTCAAG
38572067 GGTGTACTCTTTCTTA
1 GGTGTACTCTTTCTTA
* *
38572083 GGTGTGCTCTTTCTTG
1 GGTGTACTCTTTCTTA
* *
38572099 GGCGTAATCTTTCTT
1 GGTGTACTCTTTCTT
38572114 CACTTAAAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.09, C:0.19, G:0.23, T:0.49
Consensus pattern (16 bp):
GGTGTACTCTTTCTTA
Found at i:38578276 original size:18 final size:20
Alignment explanation
Indices: 38578243--38578293 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 20
38578233 ACATGATGAA
*
38578243 TATTATTTTAATTATATT-TT
1 TATTATATT-ATTATATTATT
38578263 TA-TATATTATTATATTAATT
1 TATTATATTATTATATT-ATT
38578283 TATTATATTAT
1 TATTATATTAT
38578294 ATCACCTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 8 0.30
19 5 0.19
20 6 0.22
21 8 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TATTATATTATTATATTATT
Found at i:38578285 original size:13 final size:13
Alignment explanation
Indices: 38578243--38578292 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
38578233 ACATGATGAA
*
38578243 TATTATTTTAATT
1 TATTATATTAATT
38578256 ATATT-T-TTATATAT
1 -TATTATATTA-AT-T
38578270 TATTATATTAATT
1 TATTATATTAATT
38578283 TATTATATTA
1 TATTATATTA
38578293 TATCACCTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
12 3 0.09
13 18 0.56
14 8 0.25
15 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTATATTAATT
Found at i:38578688 original size:140 final size:140
Alignment explanation
Indices: 38578420--38578700 Score: 474
Period size: 140 Copynumber: 2.0 Consensus size: 140
38578410 AATTTAATTG
*
38578420 TTATTTTTTCTAACTAAATTTGACCCTCAACCTTTAAAAAAAAAGTCTAATTTAATCATTAATCT
1 TTATTTTTTCTAACTAAATTTGACCCTCAACCTTT-AAAAAAAAGTATAATTTAATCATTAATCT
* *
38578485 TTGAAAAAGAGTTAAATTGTTGTTCTTTTGACGAAAATACTGACTAAGGGTCCCTTTGAATGGGA
65 TTCAAAAAGAGTTAAATTGTTGTTCTTTTGACGAAAATACCGACTAAGGGTCCCTTTGAATGGGA
38578550 GATGCAATTAC
130 GATGCAATTAC
* *
38578561 TTATTTTATTTTAACTAAATTTGACCCTCAACCTTT-AAAAAAATTATAATTTAATCATTAATCT
1 TTATTTT-TTCTAACTAAATTTGACCCTCAACCTTTAAAAAAAAGTATAATTTAATCATTAATCT
*
38578625 TTCAAAAAGAGTTAAATTGTTGTTCTTTTGACGAAAATACCGACTAAGGGTCCCTTTGGATGGGA
65 TTCAAAAAGAGTTAAATTGTTGTTCTTTTGACGAAAATACCGACTAAGGGTCCCTTTGAATGGGA
*
38578690 GATGCATTTAC
130 GATGCAATTAC
38578701 CTGCAGTTAG
Statistics
Matches: 132, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
140 98 0.74
141 7 0.05
142 27 0.20
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (140 bp):
TTATTTTTTCTAACTAAATTTGACCCTCAACCTTTAAAAAAAAGTATAATTTAATCATTAATCTT
TCAAAAAGAGTTAAATTGTTGTTCTTTTGACGAAAATACCGACTAAGGGTCCCTTTGAATGGGAG
ATGCAATTAC
Found at i:38578906 original size:19 final size:19
Alignment explanation
Indices: 38578879--38578916 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
38578869 CGAATTTGTA
38578879 TGAAC-TTTTTATTATTTTT
1 TGAACTTTTTTA-TATTTTT
*
38578898 TGAATTTTTTTATATTTTT
1 TGAACTTTTTTATATTTTT
38578917 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.71
Consensus pattern (19 bp):
TGAACTTTTTTATATTTTT
Found at i:38579158 original size:27 final size:27
Alignment explanation
Indices: 38579120--38579202 Score: 166
Period size: 27 Copynumber: 3.1 Consensus size: 27
38579110 GTTGATCTAA
38579120 GAAACTGTAGCCTTCATTTAATTTCGG
1 GAAACTGTAGCCTTCATTTAATTTCGG
38579147 GAAACTGTAGCCTTCATTTAATTTCGG
1 GAAACTGTAGCCTTCATTTAATTTCGG
38579174 GAAACTGTAGCCTTCATTTAATTTCGG
1 GAAACTGTAGCCTTCATTTAATTTCGG
38579201 GA
1 GA
38579203 CTTTTACAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (27 bp):
GAAACTGTAGCCTTCATTTAATTTCGG
Found at i:38579378 original size:27 final size:27
Alignment explanation
Indices: 38579340--38579408 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 27
38579330 GAGGAGGGTA
*
38579340 TCCCATGGGCGGCACCAAAGGTGCCTT
1 TCCCATGGGCGGCACCAAAGGTGCCAT
* * *
38579367 TCCCATAGGCGGCACCGATGGTGCCAT
1 TCCCATGGGCGGCACCAAAGGTGCCAT
38579394 TCCCATGGGCGGCAC
1 TCCCATGGGCGGCAC
38579409 TGCCCATATA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.17, C:0.35, G:0.30, T:0.17
Consensus pattern (27 bp):
TCCCATGGGCGGCACCAAAGGTGCCAT
Found at i:38586394 original size:27 final size:27
Alignment explanation
Indices: 38586330--38586397 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
38586320 ATGACACAAG
*
38586330 TGGTGCCGCCAATGGGAAAGGCACCTT
1 TGGTGCCGCCTATGGGAAAGGCACCTT
*
38586357 CGGTGCCGCCTATGGGAAAGGCACCTT
1 TGGTGCCGCCTATGGGAAAGGCACCTT
38586384 TGGTGCCGCCTATG
1 TGGTGCCGCCTATG
38586398 AGATACCCTC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.18, C:0.28, G:0.34, T:0.21
Consensus pattern (27 bp):
TGGTGCCGCCTATGGGAAAGGCACCTT
Found at i:38595749 original size:38 final size:37
Alignment explanation
Indices: 38595679--38595751 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 37
38595669 CTTTCATAAT
*
38595679 TTCACTTTTTCACTTTCAATCACAATTCAATTCAAAA
1 TTCACTTTTCCACTTTCAATCACAATTCAATTCAAAA
38595716 TTCACTTTTCCA-TTTCTAAGTCA-ATATTCAATTCAA
1 TTCACTTTTCCACTTTC-AA-TCACA-ATTCAATTCAA
38595752 TTCCACACCT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 4 0.12
37 14 0.44
38 14 0.44
ACGTcount: A:0.33, C:0.23, G:0.01, T:0.42
Consensus pattern (37 bp):
TTCACTTTTCCACTTTCAATCACAATTCAATTCAAAA
Found at i:38595958 original size:51 final size:51
Alignment explanation
Indices: 38595878--38596009 Score: 169
Period size: 51 Copynumber: 2.6 Consensus size: 51
38595868 TATGCCGGTT
* *
38595878 CACATAGTAGCATGCACATAGTACTACACAGGTGAAC-ATCA-CTATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACAAGTGAACGA--AGCTATCCGATA
* * * *
38595929 CACGTAGTAGCCTTCACATAGTACTACACAAGTGATCGAAGCTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACAAGTGAACGAAGCTATCCGATA
*
38595980 CGCATAGTAGCCTGCACATAGTACTACACA
1 CACATAGTAGCCTGCACATAGTACTACACA
38596010 TGCGACCTAT
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
50 1 0.01
51 68 0.97
52 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTACACAAGTGAACGAAGCTATCCGATA
Found at i:38596144 original size:51 final size:50
Alignment explanation
Indices: 38596033--38596303 Score: 271
Period size: 51 Copynumber: 5.3 Consensus size: 50
38596023 TCTGATACAT
* * *
38596033 ATAGTACTACACACGTGATC-AAGTTTTATGGTTCACGA-AGTAGCCTTCAC
1 ATAGTACTACACACGTGACCAAAGTTTT-CGGTACAC-ATAGTAGCCTTCAC
*
38596083 ATAGTACTACACACGTGATCAAAGCTTTTCGGTACACATAGTAGCCTTCAC
1 ATAGTACTACACACGTGACCAAAG-TTTTCGGTACACATAGTAGCCTTCAC
* * * * *
38596134 TTAGTACTACACATGTGACCATTA-TTTATCGATACACGTAGTAGCCTTCAC
1 ATAGTACTACACACGTGACCA-AAGTTT-TCGGTACACATAGTAGCCTTCAC
* * * *
38596185 ACAGTACTACACAAGTGACCAAAGCTTCTCGGTACACATTGTAGCCTTCAC
1 ATAGTACTACACACGTGACCAAAG-TTTTCGGTACACATAGTAGCCTTCAC
* * * * *
38596236 TTAGTACTACACATGTGACCATTA-TTTATCGATACACGTAGTAGCCTTCAC
1 ATAGTACTACACACGTGACCA-AAGTTT-TCGGTACACATAGTAGCCTTCAC
*
38596287 ACAGTACTACACACGTG
1 ATAGTACTACACACGTG
38596304 TTCATTGATA
Statistics
Matches: 185, Mismatches: 27, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
50 27 0.15
51 150 0.81
52 8 0.04
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (50 bp):
ATAGTACTACACACGTGACCAAAGTTTTCGGTACACATAGTAGCCTTCAC
Found at i:38596209 original size:102 final size:102
Alignment explanation
Indices: 38596066--38596299 Score: 414
Period size: 102 Copynumber: 2.3 Consensus size: 102
38596056 TTTTATGGTT
* * * * *
38596066 CACGAAGTAGCCTTCACATAGTACTACACACGTGATCAAAGCTTTTCGGTACACATAGTAGCCTT
1 CACGTAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCGGTACACATAGTAGCCTT
38596131 CACTTAGTACTACACATGTGACCATTATTTATCGATA
66 CACTTAGTACTACACATGTGACCATTATTTATCGATA
*
38596168 CACGTAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCGGTACACATTGTAGCCTT
1 CACGTAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCGGTACACATAGTAGCCTT
38596233 CACTTAGTACTACACATGTGACCATTATTTATCGATA
66 CACTTAGTACTACACATGTGACCATTATTTATCGATA
38596270 CACGTAGTAGCCTTCACACAGTACTACACA
1 CACGTAGTAGCCTTCACACAGTACTACACA
38596300 CGTGTTCATT
Statistics
Matches: 126, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 126 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (102 bp):
CACGTAGTAGCCTTCACACAGTACTACACAAGTGACCAAAGCTTCTCGGTACACATAGTAGCCTT
CACTTAGTACTACACATGTGACCATTATTTATCGATA
Found at i:38600986 original size:23 final size:23
Alignment explanation
Indices: 38600942--38600987 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
38600932 ACATTGTTCG
* *
38600942 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
38600965 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
38600988 CAAATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:38614838 original size:35 final size:35
Alignment explanation
Indices: 38614799--38614873 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
38614789 TGTGAAGGGT
*
38614799 ATGGATGAATTGGTATGTTTTGCATGTGTAAAAGG
1 ATGGATGAATTGGTATGTTTGGCATGTGTAAAAGG
38614834 ATGGATGAATTGGTATGTTTGGCATGTGTAAAAGG
1 ATGGATGAATTGGTATGTTTGGCATGTGTAAAAGG
*
38614869 TTGGA
1 ATGGA
38614874 ACTTCTTGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.28, C:0.03, G:0.33, T:0.36
Consensus pattern (35 bp):
ATGGATGAATTGGTATGTTTGGCATGTGTAAAAGG
Found at i:38616032 original size:28 final size:28
Alignment explanation
Indices: 38616001--38616084 Score: 91
Period size: 28 Copynumber: 3.0 Consensus size: 28
38615991 CATGACAGTT
*
38616001 AAGAAAAGCCTTTGTGGTGAACTCT-AA
1 AAGAAAAGCCTTTGTGGCGAACTCTGAA
*
38616028 GAAGAATAA-CCTTTGTGGCGAATTCTGAA
1 -AAGAA-AAGCCTTTGTGGCGAACTCTGAA
* * *
38616057 AAGAATAGCCTATGTGGCAAACTCTGAA
1 AAGAAAAGCCTTTGTGGCGAACTCTGAA
38616085 TGGATCGCTT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
27 1 0.02
28 42 0.89
29 4 0.09
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (28 bp):
AAGAAAAGCCTTTGTGGCGAACTCTGAA
Found at i:38618853 original size:69 final size:68
Alignment explanation
Indices: 38618780--38618914 Score: 209
Period size: 68 Copynumber: 2.0 Consensus size: 68
38618770 TGATTAAACT
*
38618780 TAATCACTTTAATATTAAATTAATATA-ATATTTATCAAGATAAACATTAAATTAAATTTAATAT
1 TAATCACTTTAATATTAAATTAATA-ACATA-CTATCAAGATAAACATTAAATTAAATTTAATAT
38618844 TAAGA
64 TAAGA
* * *
38618849 TAATCACTTTAATATTAAATTAATAACATACTATTAATATAAGCATTAAATTAAATTTAATATTA
1 TAATCACTTTAATATTAAATTAATAACATACTATCAAGATAAACATTAAATTAAATTTAATATTA
38618914 A
66 A
38618915 ACTATTAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
68 33 0.54
69 28 0.46
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (68 bp):
TAATCACTTTAATATTAAATTAATAACATACTATCAAGATAAACATTAAATTAAATTTAATATTA
AGA
Found at i:38618872 original size:20 final size:18
Alignment explanation
Indices: 38618772--38618873 Score: 63
Period size: 20 Copynumber: 5.7 Consensus size: 18
38618762 TTCAACTGTG
38618772 ATTAAACTTAATCACTTTAAT
1 ATTAAA-TTAAT-A-TTTAAT
38618793 ATTAAATTAATA--TAAT
1 ATTAAATTAATATTTAAT
* * * * *
38618809 ATT-TATCAAGA-TAAAC
1 ATTAAATTAATATTTAAT
38618825 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
38618842 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
38618862 ATTAAATTAATA
1 ATTAAATTAATA
38618874 ACATACTATT
Statistics
Matches: 64, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
15 5 0.08
16 13 0.20
17 15 0.23
18 1 0.02
19 4 0.06
20 20 0.31
21 6 0.09
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:38627590 original size:9 final size:9
Alignment explanation
Indices: 38627576--38627604 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
38627566 TTCGTACCTA
38627576 GTGAATCGG
1 GTGAATCGG
38627585 GTGAATCGG
1 GTGAATCGG
38627594 GTGAATCGG
1 GTGAATCGG
38627603 GT
1 GT
38627605 TGGGTTGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.45, T:0.24
Consensus pattern (9 bp):
GTGAATCGG
Found at i:38629650 original size:22 final size:22
Alignment explanation
Indices: 38629614--38629658 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
38629604 TTGATGTTCT
38629614 AGTTGGAATTGTAATGTGTCTAA
1 AGTTGGAATTGTAATGTGT-TAA
*
38629637 AGTTGGTA-TGTAATGTGTTAA
1 AGTTGGAATTGTAATGTGTTAA
38629658 A
1 A
38629659 CTTAATGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 10 0.48
23 7 0.33
ACGTcount: A:0.31, C:0.02, G:0.27, T:0.40
Consensus pattern (22 bp):
AGTTGGAATTGTAATGTGTTAA
Found at i:38634594 original size:22 final size:21
Alignment explanation
Indices: 38634566--38634610 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
38634556 ACAAATAATT
38634566 AAAAGAA-CTTAGAAATTTATAA
1 AAAAGAATCTTA-AAA-TTATAA
*
38634588 AAAAGAATTTTAAAATTATAA
1 AAAAGAATCTTAAAATTATAA
38634609 AA
1 AA
38634611 GAACTCAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 10 0.48
23 3 0.14
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (21 bp):
AAAAGAATCTTAAAATTATAA
Found at i:38635592 original size:22 final size:22
Alignment explanation
Indices: 38635538--38635580 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
38635528 TTTATTGTTC
38635538 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
38635560 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
38635581 TAGCCATGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:38637311 original size:2 final size:2
Alignment explanation
Indices: 38637269--38637298 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
38637259 TTGCATGTCC
*
38637269 AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38637299 TTTATGAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38637311 original size:15 final size:14
Alignment explanation
Indices: 38637277--38637318 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
38637267 CCATATATCT
*
38637277 ATATATATATATAT-
1 ATATATAT-TTTATG
38637291 ATATATATTTTATG
1 ATATATATTTTATG
38637305 A-ATATATTTTATG
1 ATATATATTTTATG
38637318 A
1 A
38637319 ATTGGTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 17 0.65
14 9 0.35
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (14 bp):
ATATATATTTTATG
Found at i:38637329 original size:15 final size:13
Alignment explanation
Indices: 38637293--38637320 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
38637283 ATATATATAT
38637293 ATATATTTTATGA
1 ATATATTTTATGA
38637306 ATATATTTTATGA
1 ATATATTTTATGA
38637319 AT
1 AT
38637321 TGGTATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (13 bp):
ATATATTTTATGA
Found at i:38637692 original size:108 final size:109
Alignment explanation
Indices: 38637494--38637912 Score: 668
Period size: 108 Copynumber: 3.9 Consensus size: 109
38637484 AAATTGTTCC
* *
38637494 AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTACCCTAAGGTACTGGGTTTTGATT
1 AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATT
38637559 TCTCGTTCGACCAAATAGCTAAATATCC-TTTAAAAACTTTTCA
66 TCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCA
38637602 AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATT
1 AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATT
* *
38637667 TCTCGTTCCACCAAAT-GACTTAATATCCTTTTCAAAAA-TTTTC-
66 TCTCGTTCGACCAAATAG-CTAAATATCCTTTT-AAAAACTTTTCA
*
38637710 AAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATT
1 AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATT
38637775 TCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCA
66 TCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCA
* * *
38637819 AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAACGTGCCCTAAGGTGCTAGGTTTCGATT
1 AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATT
* * * *
38637884 TCACGTT-TAGGCAAATTGCTAAATATCCT
66 TCTCGTTCGA-CCAAATAGCTAAATATCCT
38637913 CTTGAATTTT
Statistics
Matches: 289, Mismatches: 15, Indels: 13
0.91 0.05 0.04
Matches are distributed among these distances:
107 6 0.02
108 185 0.64
109 93 0.32
110 5 0.02
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (109 bp):
AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATT
TCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCA
Found at i:38640121 original size:59 final size:60
Alignment explanation
Indices: 38640056--38640186 Score: 147
Period size: 60 Copynumber: 2.2 Consensus size: 60
38640046 AAAACTTTGA
*
38640056 CAAGTACCAAATCCAA-CAAAAAAAAGATTAAGTACCAAATTAGGAAAAAGAGTCAAGTT
1 CAAGTACCAAATCCAACCAAAAAAAAGATTAAGTACCAAATTAAGAAAAAGAGTCAAGTT
** *** * * * *
38640115 CAAGTACCAAATTGAACCCTCAAAAAGTTTAAGTACCAACTTAAGAAAAAGTGTTAAGTT
1 CAAGTACCAAATCCAACCAAAAAAAAGATTAAGTACCAAATTAAGAAAAAGAGTCAAGTT
* *
38640175 TAGGTACCAAAT
1 CAAGTACCAAAT
38640187 TAGGAAAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
59 14 0.24
60 45 0.76
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.21
Consensus pattern (60 bp):
CAAGTACCAAATCCAACCAAAAAAAAGATTAAGTACCAAATTAAGAAAAAGAGTCAAGTT
Found at i:38640123 original size:31 final size:31
Alignment explanation
Indices: 38640085--38640218 Score: 94
Period size: 31 Copynumber: 4.4 Consensus size: 31
38640075 AAAAAAGATT
38640085 AAGTACCAAATTAGGAAAAAGAGTCAAGTTC
1 AAGTACCAAATTAGGAAAAAGAGTCAAGTTC
**** ** *
38640116 AAGTACCAAATT--GAACCCTCA-AAAAGTTT
1 AAGTACCAAATTAGGAA-AAAGAGTCAAGTTC
* * * * *
38640145 AAGTACCAACTTAAGAAAAAGTGTTAAGTTT
1 AAGTACCAAATTAGGAAAAAGAGTCAAGTTC
* *
38640176 AGGTACCAAATTAGGAAAAAAGTGTCAAGTTC
1 AAGTACCAAATTAGG-AAAAAGAGTCAAGTTC
*
38640208 AGGTACCAAAT
1 AAGTACCAAAT
38640219 GTTATATTAA
Statistics
Matches: 78, Mismatches: 20, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
29 19 0.24
30 1 0.01
31 33 0.42
32 25 0.32
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.23
Consensus pattern (31 bp):
AAGTACCAAATTAGGAAAAAGAGTCAAGTTC
Found at i:38640206 original size:32 final size:31
Alignment explanation
Indices: 38640139--38640218 Score: 106
Period size: 32 Copynumber: 2.5 Consensus size: 31
38640129 AACCCTCAAA
* * *
38640139 AAGTTTAAGTACCAACTTAAGAAAAAGTGTT
1 AAGTTTAGGTACCAAATTAAGAAAAAGTGTC
*
38640170 AAGTTTAGGTACCAAATTAGGAAAAAAGTGTC
1 AAGTTTAGGTACCAAATTAAG-AAAAAGTGTC
*
38640202 AAGTTCAGGTACCAAAT
1 AAGTTTAGGTACCAAAT
38640219 GTTATATTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 18 0.42
32 25 0.58
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (31 bp):
AAGTTTAGGTACCAAATTAAGAAAAAGTGTC
Found at i:38644211 original size:2 final size:2
Alignment explanation
Indices: 38644206--38644247 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
38644196 TCAGAGAGTT
38644206 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38644248 ATTTCTTTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38647864 original size:3 final size:3
Alignment explanation
Indices: 38647856--38647934 Score: 142
Period size: 3 Copynumber: 26.7 Consensus size: 3
38647846 TTTCATTCTG
*
38647856 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
38647904 AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
38647935 TCTGCATTCC
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 71 0.97
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:38649090 original size:19 final size:19
Alignment explanation
Indices: 38649066--38649106 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
38649056 TGATTTATTC
38649066 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
*
38649085 TAAGATTTATCTACTTAAA
1 TAAGATTTATCTACCTAAA
38649104 TAA
1 TAA
38649107 CTTTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (19 bp):
TAAGATTTATCTACCTAAA
Found at i:38652863 original size:41 final size:42
Alignment explanation
Indices: 38652771--38652863 Score: 138
Period size: 42 Copynumber: 2.2 Consensus size: 42
38652761 AACTGAATTT
*
38652771 AAATAATTCAT-TTATTCTAATAAACTACTAAAAAGATAAGAA
1 AAATAATTC-TCTTATTCTAATAAACTACTAAAAAGATAAAAA
38652813 AAATAATTCTCTTATTCTAATAAACTACT-AAAAGATAAAATA
1 AAATAATTCTCTTATTCTAATAAACTACTAAAAAGATAAAA-A
38652855 AAAT-ATTCT
1 AAATAATTCT
38652864 TAGAATATTT
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
41 16 0.33
42 32 0.67
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.33
Consensus pattern (42 bp):
AAATAATTCTCTTATTCTAATAAACTACTAAAAAGATAAAAA
Found at i:38652916 original size:23 final size:24
Alignment explanation
Indices: 38652890--38652937 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
38652880 ATTTATTCTA
38652890 AGATTTATCTAC-TAAATAAATTT
1 AGATTTATCTACTTAAATAAATTT
*
38652913 AGATTTATCTACTTAAATAACTTT
1 AGATTTATCTACTTAAATAAATTT
38652937 A
1 A
38652938 AAATATATCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (24 bp):
AGATTTATCTACTTAAATAAATTT
Found at i:38653746 original size:2 final size:2
Alignment explanation
Indices: 38653739--38653765 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38653729 ATTGATTATA
38653739 GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT G
38653766 GAAGCAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:38654012 original size:7 final size:7
Alignment explanation
Indices: 38654000--38654033 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
38653990 TTTCTGAAGT
38654000 AAAAATA
1 AAAAATA
38654007 AAAAATA
1 AAAAATA
38654014 AAAAATA
1 AAAAATA
38654021 AAAAATA
1 AAAAATA
38654028 AAAAAT
1 AAAAAT
38654034 GTAATATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAATA
Found at i:38661582 original size:20 final size:18
Alignment explanation
Indices: 38661535--38661583 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
38661525 CAAGATAAAC
38661535 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
38661552 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
38661572 ATTAAATTAATA
1 ATTAAATTAATA
38661584 AAATACTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:38676170 original size:38 final size:37
Alignment explanation
Indices: 38676082--38676172 Score: 112
Period size: 37 Copynumber: 2.4 Consensus size: 37
38676072 GACCCATTGC
* *
38676082 GTGGTGTGTAGGGTGGATGGGCCTATCATGGTCCTAT
1 GTGGTGTGTAGGGTGGATAGGCCTATCATAGTCCTAT
* *
38676119 GTGGTGTGTAGGGTTGATAGGCTTATCATAG-CCTAT
1 GTGGTGTGTAGGGTGGATAGGCCTATCATAGTCCTAT
*
38676155 AAGTGGTGTGCAGGGTGG
1 --GTGGTGTGTAGGGTGG
38676173 TCGGAGTGGC
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
36 5 0.11
37 27 0.59
38 14 0.30
ACGTcount: A:0.16, C:0.11, G:0.41, T:0.32
Consensus pattern (37 bp):
GTGGTGTGTAGGGTGGATAGGCCTATCATAGTCCTAT
Found at i:38678650 original size:28 final size:30
Alignment explanation
Indices: 38678594--38678650 Score: 73
Period size: 28 Copynumber: 1.9 Consensus size: 30
38678584 TAATTTCAGT
*
38678594 TTTAGGGATTAAATTGAACAAAGTGTAAAAG
1 TTTAGGGA-TAAATTGAACAAAGTATAAAAG
*
38678625 TTTAGGGA-AAATTG-ATAAAGTATAAA
1 TTTAGGGATAAATTGAACAAAGTATAAA
38678651 TTATAAGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 10 0.42
29 6 0.25
31 8 0.33
ACGTcount: A:0.47, C:0.02, G:0.21, T:0.30
Consensus pattern (30 bp):
TTTAGGGATAAATTGAACAAAGTATAAAAG
Found at i:38678936 original size:28 final size:27
Alignment explanation
Indices: 38678904--38678975 Score: 67
Period size: 28 Copynumber: 2.6 Consensus size: 27
38678894 ATTATTAATA
38678904 TTGAATTGAGGATATTAATTG-TTTACGG
1 TTGAATTGAGGATATTAA--GATTTACGG
* * *
38678932 TTGAATGTAAGG-TGAGTGAGATTTACGG
1 TTGAAT-TGAGGAT-ATTAAGATTTACGG
38678960 TTGAATTGAGGATATT
1 TTGAATTGAGGATATT
38678976 GTGGAAGTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
27 7 0.20
28 21 0.60
29 7 0.20
ACGTcount: A:0.29, C:0.03, G:0.29, T:0.39
Consensus pattern (27 bp):
TTGAATTGAGGATATTAAGATTTACGG
Found at i:38679116 original size:20 final size:20
Alignment explanation
Indices: 38679092--38679187 Score: 111
Period size: 20 Copynumber: 4.8 Consensus size: 20
38679082 TTGTATGGAT
*
38679092 TTGCACTTCGGTGCCTCTGT
1 TTGCACTTCGGTGCCTCTGA
38679112 TTGCACTTCGGTGCCTCTGA
1 TTGCACTTCGGTGCCTCTGA
* **
38679132 TTGCAGTTCTATGCCTCTGA
1 TTGCACTTCGGTGCCTCTGA
* ** * *
38679152 TTCCACTTCAATGCCCCTAA
1 TTGCACTTCGGTGCCTCTGA
38679172 TTGCACTTCGGTGCCT
1 TTGCACTTCGGTGCCT
38679188 TTGTTATTAT
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.12, C:0.31, G:0.20, T:0.36
Consensus pattern (20 bp):
TTGCACTTCGGTGCCTCTGA
Found at i:38697736 original size:20 final size:21
Alignment explanation
Indices: 38697711--38697793 Score: 81
Period size: 20 Copynumber: 4.1 Consensus size: 21
38697701 GCAACCCAAT
38697711 TTTTATTTTATTTATTA-TTA
1 TTTTATTTTATTTATTACTTA
38697731 TTTTATTATTA-TTATT--TT-
1 TTTTATT-TTATTTATTACTTA
*
38697749 TCTTTACTTTATTTATTACTTTA
1 T-TTTATTTTATTTATTAC-TTA
38697772 TTTTA--TTATTTATTACTTA
1 TTTTATTTTATTTATTACTTA
38697791 TTT
1 TTT
38697794 GGATATTAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 15
0.77 0.01 0.21
Matches are distributed among these distances:
18 4 0.07
19 18 0.33
20 23 0.42
21 3 0.05
22 6 0.11
23 1 0.02
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTATTTTATTTATTACTTA
Found at i:38697760 original size:35 final size:34
Alignment explanation
Indices: 38697717--38697782 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 34
38697707 CAATTTTTAT
*
38697717 TTTATTTA-TTATTATTTTATTATTATTATTTTTC
1 TTTATTTATTTATTACTTTATT-TTATTATTTTTC
38697751 TTTACTTTATTTATTACTTTATTTTATTATTT
1 TTTA-TTTATTTATTACTTTATTTTATTATTT
38697783 ATTACTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 4 0.14
35 13 0.45
36 12 0.41
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (34 bp):
TTTATTTATTTATTACTTTATTTTATTATTTTTC
Found at i:38697769 original size:12 final size:12
Alignment explanation
Indices: 38697752--38697785 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
38697742 TTATTTTTCT
38697752 TTACTTTATTTA
1 TTACTTTATTTA
38697764 TTACTTTATTTTA
1 TTACTTTA-TTTA
38697777 TTA-TTTATT
1 TTACTTTATT
38697786 ACTTATTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.10
12 12 0.57
13 7 0.33
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (12 bp):
TTACTTTATTTA
Found at i:38699951 original size:9 final size:9
Alignment explanation
Indices: 38699937--38699961 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
38699927 CCTAAAGTAA
38699937 AAAAAAAAG
1 AAAAAAAAG
38699946 AAAAAAAAG
1 AAAAAAAAG
38699955 AAAAAAA
1 AAAAAAA
38699962 TAATAATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:38705197 original size:25 final size:25
Alignment explanation
Indices: 38705169--38705216 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
38705159 AGATAGTACG
*
38705169 CCAAAAAGGCTTTTCAGAGAATTTT
1 CCAAAAAGGCTTCTCAGAGAATTTT
*
38705194 CCAAAAAGTCTTCTCAGAGAATT
1 CCAAAAAGGCTTCTCAGAGAATT
38705217 CACCACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.29
Consensus pattern (25 bp):
CCAAAAAGGCTTCTCAGAGAATTTT
Found at i:38711364 original size:21 final size:22
Alignment explanation
Indices: 38711338--38711378 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
38711328 AATATAAACA
38711338 TATACTATATT-A-TAAAAATAG
1 TATACT-TATTCATTAAAAATAG
38711359 TATACTTATTCATTAAAAAT
1 TATACTTATTCATTAAAAAT
38711379 TGTTATATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (22 bp):
TATACTTATTCATTAAAAATAG
Found at i:38713196 original size:18 final size:18
Alignment explanation
Indices: 38713157--38713199 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
38713147 GTTATTTCAT
* *
38713157 TTATACAATTTCTTTTTT
1 TTATTCAATTTCTTTTTG
38713175 TTATTCAATTT-TTTTTGG
1 TTATTCAATTTCTTTTT-G
38713193 TTATTCA
1 TTATTCA
38713200 CTCATGTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.21, C:0.09, G:0.05, T:0.65
Consensus pattern (18 bp):
TTATTCAATTTCTTTTTG
Found at i:38717227 original size:7 final size:7
Alignment explanation
Indices: 38717215--38717244 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
38717205 TTTAAAAATA
38717215 TTTTTAT
1 TTTTTAT
38717222 TTTTTA-
1 TTTTTAT
38717228 TTTTTAT
1 TTTTTAT
38717235 TTTTTAT
1 TTTTTAT
38717242 TTT
1 TTT
38717245 AAATTTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTAT
Found at i:38717231 original size:13 final size:13
Alignment explanation
Indices: 38717213--38717244 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
38717203 ACTTTAAAAA
38717213 TATTTTTATTTTT
1 TATTTTTATTTTT
38717226 TATTTTTATTTTT
1 TATTTTTATTTTT
38717239 TATTTT
1 TATTTT
38717245 AAATTTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TATTTTTATTTTT
Found at i:38717250 original size:20 final size:20
Alignment explanation
Indices: 38717215--38717252 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
38717205 TTTAAAAATA
**
38717215 TTTTTATTTTTTATTTTTAT
1 TTTTTATTTTAAATTTTTAT
38717235 TTTTTATTTTAAATTTTT
1 TTTTTATTTTAAATTTTT
38717253 TGTAAAAATC
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:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTATTTTAAATTTTTAT
Found at i:38717474 original size:17 final size:18
Alignment explanation
Indices: 38717443--38717484 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
38717433 TATCCTAGAA
*
38717443 TATTTG-GATAAATTA-T
1 TATTTGAGAAAAATTAGT
38717459 TATTTGAGAAAAATTAGT
1 TATTTGAGAAAAATTAGT
38717477 TGATTTGA
1 T-ATTTGA
38717485 TAGAGTAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 8 0.36
18 2 0.09
19 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (18 bp):
TATTTGAGAAAAATTAGT
Found at i:38717916 original size:24 final size:24
Alignment explanation
Indices: 38717869--38717916 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
38717859 TTGTTTTGTG
***
38717869 GCAAAGGATGAATTGACTGTAAAT
1 GCAAAGGATGAATTGACAAAAAAT
*
38717893 GCAAAGGATGAATTGGCAAAAAAT
1 GCAAAGGATGAATTGACAAAAAAT
38717917 AACCAAAGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.46, C:0.08, G:0.25, T:0.21
Consensus pattern (24 bp):
GCAAAGGATGAATTGACAAAAAAT
Found at i:38718016 original size:21 final size:21
Alignment explanation
Indices: 38717992--38718036 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
38717982 ACAAGCTTCT
38717992 GTTTAACTCA-TATGAGTTTCC
1 GTTTAAC-CATTATGAGTTTCC
*
38718013 GTTTAACCATTATGGGTTTCC
1 GTTTAACCATTATGAGTTTCC
38718034 GTT
1 GTT
38718037 CAGTTCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.44
Consensus pattern (21 bp):
GTTTAACCATTATGAGTTTCC
Found at i:38718074 original size:42 final size:42
Alignment explanation
Indices: 38718015--38718097 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
38718005 GAGTTTCCGT
* * * **
38718015 TTAACCATTATGGGTTTCCGTTCAGTTCTTTTGAGCTTCTGA
1 TTAACCATTATGAGTTTCCATTCAGCTCTGATGAGCTTCTGA
*
38718057 TTAACCCTTATGAGTTTCCATTCAGCTCTGATGAGCTTCTG
1 TTAACCATTATGAGTTTCCATTCAGCTCTGATGAGCTTCTG
38718098 TTCAACCTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (42 bp):
TTAACCATTATGAGTTTCCATTCAGCTCTGATGAGCTTCTGA
Found at i:38724823 original size:25 final size:24
Alignment explanation
Indices: 38724770--38724824 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
38724760 TATTTACTTT
* *
38724770 AATATTTAAAAATTTTAAATGAAT
1 AATATTAAAAAATTTTAAATGAAA
*
38724794 GATATTAAATAAATTTTAAAT-ATAA
1 AATATTAAA-AAATTTTAAATGA-AA
38724819 AATATT
1 AATATT
38724825 TATCAATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
AATATTAAAAAATTTTAAATGAAA
Found at i:38724851 original size:20 final size:20
Alignment explanation
Indices: 38724813--38724851 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38724803 TAAATTTTAA
* * *
38724813 ATATAAAATATTTATCAATT
1 ATATAAAATACTCACCAATT
38724833 ATATAAAATACTCACCAAT
1 ATATAAAATACTCACCAAT
38724852 AAACTCTAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (20 bp):
ATATAAAATACTCACCAATT
Found at i:38727418 original size:9 final size:9
Alignment explanation
Indices: 38727399--38727441 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
38727389 CAAAGTAAAT
38727399 ATTAA-TTA
1 ATTAATTTA
38727407 ATTAATTTA
1 ATTAATTTA
*
38727416 ATTAATCTA
1 ATTAATTTA
* *
38727425 ATTAACTAA
1 ATTAATTTA
38727434 ATTAATTT
1 ATTAATTT
38727442 CTCAATTAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
8 5 0.18
9 23 0.82
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (9 bp):
ATTAATTTA
Found at i:38727418 original size:13 final size:13
Alignment explanation
Indices: 38727400--38727441 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
38727390 AAAGTAAATA
38727400 TTAATTAATTAAT
1 TTAATTAATTAAT
38727413 TTAATTAATCTAA-
1 TTAATTAAT-TAAT
*
38727426 TTAACTAAATTAAT
1 TTAA-TTAATTAAT
38727440 TT
1 TT
38727442 CTCAATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAATTAATTAAT
Found at i:38730125 original size:23 final size:21
Alignment explanation
Indices: 38730099--38730142 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
38730089 CTAATTATTT
*
38730099 TAAAAGGTTAATTAGTAATTAAA
1 TAAAAGGTAAATTA--AATTAAA
*
38730122 TAAATGGTAAATTAAATTAAA
1 TAAAAGGTAAATTAAATTAAA
38730143 GGATGGTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
23 12 0.63
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (21 bp):
TAAAAGGTAAATTAAATTAAA
Found at i:38730702 original size:30 final size:30
Alignment explanation
Indices: 38730668--38730730 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
38730658 ACGGGTTGTC
*
38730668 ACACGGCCGTGTACTACACACGGTATCTGT
1 ACACGGCCGTGTACTACACACGATATCTGT
* *
38730698 ACACGGTCGTGTACTACACACGATCTCTGT
1 ACACGGCCGTGTACTACACACGATATCTGT
38730728 ACA
1 ACA
38730731 TGGTCTTGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (30 bp):
ACACGGCCGTGTACTACACACGATATCTGT
Found at i:38740749 original size:23 final size:24
Alignment explanation
Indices: 38740723--38740774 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
38740713 TTAAAATGAC
*
38740723 TAAATATCATAAAGAAG-ATAA-AA
1 TAAAAATCA-AAAGAAGCATAATAA
*
38740746 TAAAAATCAAATGAAGCATAATAA
1 TAAAAATCAAAAGAAGCATAATAA
38740770 TAAAA
1 TAAAA
38740775 TAAATAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.24
23 12 0.48
24 7 0.28
ACGTcount: A:0.65, C:0.06, G:0.08, T:0.21
Consensus pattern (24 bp):
TAAAAATCAAAAGAAGCATAATAA
Found at i:38740750 original size:5 final size:5
Alignment explanation
Indices: 38740740--38740836 Score: 72
Period size: 5 Copynumber: 18.0 Consensus size: 5
38740730 CATAAAGAAG
* *
38740740 ATAAA ATAAAA ATCAA ATGAAGC ATAATA ATAAA AT-AA ATAAA ATAAAA
1 ATAAA AT-AAA ATAAA AT-AA-A ATAA-A ATAAA ATAAA ATAAA AT-AAA
*
38740789 ATAATTA ATAAA ATACTAA AT-AA ATAAA ATAGA ATAAA ATAAA ATAAA
1 ATAA--A ATAAA ATA--AA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
38740837 TGAAGGCAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 20
0.74 0.07 0.20
Matches are distributed among these distances:
4 8 0.11
5 39 0.52
6 17 0.23
7 11 0.15
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (5 bp):
ATAAA
Found at i:38740779 original size:22 final size:21
Alignment explanation
Indices: 38740731--38740788 Score: 59
Period size: 23 Copynumber: 2.8 Consensus size: 21
38740721 ACTAAATATC
38740731 ATAAA-GAAGATAAAATAAAA
1 ATAAATGAAGATAAAATAAAA
38740751 ATCAAATGAAGCATAATAAT-AAA
1 AT-AAATGAAG-ATAA-AATAAAA
*
38740774 ATAAAT-AAAATAAAA
1 ATAAATGAAGATAAAA
38740789 ATAATTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
19 2 0.06
20 6 0.18
21 5 0.15
22 8 0.24
23 9 0.27
24 3 0.09
ACGTcount: A:0.71, C:0.03, G:0.07, T:0.19
Consensus pattern (21 bp):
ATAAATGAAGATAAAATAAAA
Found at i:38740789 original size:15 final size:13
Alignment explanation
Indices: 38740768--38740837 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 13
38740758 GAAGCATAAT
38740768 AATAAAATAAATAA
1 AATAAAATAAAT-A
*
38740782 AATAAAA-ATAATT
1 AATAAAATA-AATA
38740795 AATAAAATACTAAATA
1 AAT-AAA-A-TAAATA
38740811 AATAAAATAGAATAA
1 AATAAAATA-AAT-A
38740826 AATAAAATAAAT
1 AATAAAATAAAT
38740838 GAAGGCAAAC
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
13 6 0.13
14 20 0.43
15 14 0.30
16 6 0.13
17 1 0.02
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.24
Consensus pattern (13 bp):
AATAAAATAAATA
Found at i:38740810 original size:34 final size:31
Alignment explanation
Indices: 38740772--38740834 Score: 90
Period size: 34 Copynumber: 1.9 Consensus size: 31
38740762 CATAATAATA
38740772 AAATAAATAAAATAAAAATAATTAATAAAATACT
1 AAATAAATAAAAT-AAAATAA--AATAAAATACT
*
38740806 AAATAAATAAAATAGAATAAAATAAAATA
1 AAATAAATAAAATAAAATAAAATAAAATA
38740835 AATGAAGGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 9 0.32
33 6 0.21
34 13 0.46
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (31 bp):
AAATAAATAAAATAAAATAAAATAAAATACT
Found at i:38745344 original size:37 final size:37
Alignment explanation
Indices: 38745294--38745369 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
38745284 AACATGGTAA
* *
38745294 CTGCATCTAAATTAAAGACACTGGTTGTTTTCATTGG
1 CTGCATCTAAATTAAAGACACTGGCTGTTTTCATCGG
38745331 CTGCATCTAAATTAAAGACACTGGCTGTTTTCATCGG
1 CTGCATCTAAATTAAAGACACTGGCTGTTTTCATCGG
38745368 CT
1 CT
38745370 TCGTCCTCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (37 bp):
CTGCATCTAAATTAAAGACACTGGCTGTTTTCATCGG
Found at i:38751137 original size:16 final size:16
Alignment explanation
Indices: 38751116--38751159 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
38751106 AATGAAAAGG
*
38751116 TTGAAAAGGATGCCAA
1 TTGAAAAGGATACCAA
38751132 TTGAAAAGGATACCAA
1 TTGAAAAGGATACCAA
*
38751148 ATGAAAAGGATA
1 TTGAAAAGGATA
38751160 TCATTGGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.50, C:0.09, G:0.23, T:0.18
Consensus pattern (16 bp):
TTGAAAAGGATACCAA
Found at i:38754832 original size:22 final size:22
Alignment explanation
Indices: 38754777--38754829 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
38754767 ATTTTATGAA
*
38754777 AATTATGTGTGAATTAATTAGTT
1 AATTAAGT-TGAATTAATTAGTT
* *
38754800 AATTGAGTTGAATTTATTAGTT
1 AATTAAGTTGAATTAATTAGTT
38754822 AA-TAAGTT
1 AATTAAGTT
38754830 TGAGTTGAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 5 0.19
22 15 0.58
23 6 0.23
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (22 bp):
AATTAAGTTGAATTAATTAGTT
Found at i:38767224 original size:16 final size:16
Alignment explanation
Indices: 38767203--38767233 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38767193 ATCGGGTTGA
*
38767203 GAAAATTATTTAATTG
1 GAAAATTAATTAATTG
38767219 GAAAATTAATTAATT
1 GAAAATTAATTAATT
38767234 AATTAAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (16 bp):
GAAAATTAATTAATTG
Found at i:38767229 original size:20 final size:18
Alignment explanation
Indices: 38767206--38767247 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
38767196 GGGTTGAGAA
*
38767206 AATTATTTAATTGGAAAATT
1 AATTAATTAATT--AAAATT
38767226 AATTAATTAATTAAAATT
1 AATTAATTAATTAAAATT
38767244 AATT
1 AATT
38767248 TATGATGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
20 11 0.52
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTAATTAATTAAAATT
Found at i:38772318 original size:17 final size:17
Alignment explanation
Indices: 38772296--38772352 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
38772286 AATAAATAAC
38772296 AATAAAGACTATAACTA
1 AATAAAGACTATAACTA
*
38772313 AATAAAAACTA-AA-TAA
1 AATAAAGACTATAACT-A
38772329 CAATAAAGACTATAACTA
1 -AATAAAGACTATAACTA
38772347 AATAAA
1 AATAAA
38772353 AACCTAGGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
15 1 0.03
16 3 0.09
17 26 0.76
18 3 0.09
19 1 0.03
ACGTcount: A:0.65, C:0.11, G:0.04, T:0.21
Consensus pattern (17 bp):
AATAAAGACTATAACTA
Found at i:38772331 original size:34 final size:34
Alignment explanation
Indices: 38772288--38772355 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
38772278 ATTAACTAAA
38772288 TAAATAACAATAAAGACTATAACTAAATAAAAAC
1 TAAATAACAATAAAGACTATAACTAAATAAAAAC
38772322 TAAATAACAATAAAGACTATAACTAAATAAAAAC
1 TAAATAACAATAAAGACTATAACTAAATAAAAAC
38772356 CTAGGAAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.65, C:0.12, G:0.03, T:0.21
Consensus pattern (34 bp):
TAAATAACAATAAAGACTATAACTAAATAAAAAC
Found at i:38778500 original size:20 final size:21
Alignment explanation
Indices: 38778461--38778502 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
38778451 AGTATATAAT
*
38778461 TATATTTTAAAGAATAAAATA
1 TATATCTTAAAGAATAAAATA
*
38778482 TATATCTTAAA-ATTAAAATA
1 TATATCTTAAAGAATAAAATA
38778502 T
1 T
38778503 TATTAGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
TATATCTTAAAGAATAAAATA
Found at i:38779358 original size:17 final size:16
Alignment explanation
Indices: 38779325--38779364 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
38779315 TAAGTTATCA
38779325 AATAAAA-ATCATCTC
1 AATAAAATATCATCTC
*
38779340 AATTAAAATATCATTTC
1 AA-TAAAATATCATCTC
38779357 AATAAAAT
1 AATAAAAT
38779365 GTTTAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 2 0.09
16 11 0.50
17 9 0.41
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAAAATATCATCTC
Found at i:38779550 original size:4 final size:4
Alignment explanation
Indices: 38779541--38779580 Score: 71
Period size: 4 Copynumber: 9.8 Consensus size: 4
38779531 ATAACTCACG
38779541 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA A-TTA ATT
38779581 TGACAACTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 31 0.89
5 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (4 bp):
ATTA
Found at i:38779893 original size:29 final size:31
Alignment explanation
Indices: 38779838--38779905 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 31
38779828 TTTATTATGG
*
38779838 TGTACTTGTACTTTTGTAAAATGTTTAACGT
1 TGTACTTGTACTTTAGTAAAATGTTTAACGT
*
38779869 TGTACTTGTA-TTTAG-AAAATGTTTAATGT
1 TGTACTTGTACTTTAGTAAAATGTTTAACGT
*
38779898 AGTACTTG
1 TGTACTTG
38779906 AATTATCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 20 0.59
30 4 0.12
31 10 0.29
ACGTcount: A:0.28, C:0.07, G:0.18, T:0.47
Consensus pattern (31 bp):
TGTACTTGTACTTTAGTAAAATGTTTAACGT
Found at i:38779916 original size:29 final size:29
Alignment explanation
Indices: 38779855--38779919 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
38779845 GTACTTTTGT
* * *
38779855 AAAATGTTTAACGTTGTACTTGTATTTAG
1 AAAATGTTTAACGTAGTACTTGAATTTAC
*
38779884 AAAATGTTTAATGTAGTACTTGAA-TTATC
1 AAAATGTTTAACGTAGTACTTGAATTTA-C
38779913 AAAATGT
1 AAAATGT
38779920 GTTTTATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 3 0.10
29 28 0.90
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.42
Consensus pattern (29 bp):
AAAATGTTTAACGTAGTACTTGAATTTAC
Found at i:38788053 original size:56 final size:56
Alignment explanation
Indices: 38787903--38788056 Score: 220
Period size: 56 Copynumber: 2.8 Consensus size: 56
38787893 GGTGTCACAG
* *
38787903 TAGGAATCAAATTGCTAAAAGATAATA-CCCAGTAATAATATCCTATAATATCCCAT
1 TAGGAATCAAATTGCTAAAAGATAATATCCCA-TAATAATATCCTATAACATCCAAT
* * *
38787959 TAGGAATCAAATTGCTAAGAGATCATATCTCATAATAATATCCTATAACATCCAAT
1 TAGGAATCAAATTGCTAAAAGATAATATCCCATAATAATATCCTATAACATCCAAT
* * *
38788015 TAGGAATCAAATTGCTAAAAGTTAACATCCCATGATAATATC
1 TAGGAATCAAATTGCTAAAAGATAATATCCCATAATAATATC
38788057 TTAACAACTA
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
56 83 0.97
57 3 0.03
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.29
Consensus pattern (56 bp):
TAGGAATCAAATTGCTAAAAGATAATATCCCATAATAATATCCTATAACATCCAAT
Found at i:38788878 original size:21 final size:22
Alignment explanation
Indices: 38788854--38788896 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
38788844 TTCCTAATAT
* *
38788854 AATTGGTTGGTATTT-AATTTA
1 AATTGATTGCTATTTAAATTTA
*
38788875 AATTTATTGCTATTTAAATTTA
1 AATTGATTGCTATTTAAATTTA
38788897 TATTTATTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (22 bp):
AATTGATTGCTATTTAAATTTA
Found at i:38788901 original size:22 final size:21
Alignment explanation
Indices: 38788864--38788904 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
38788854 AATTGGTTGG
38788864 TATTTAATTTAAATTTATTGC
1 TATTTAATTTAAATTTATTGC
*
38788885 TATTTAAATTTATATTTATT
1 TATTT-AATTTAAATTTATT
38788905 AAATTAGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
TATTTAATTTAAATTTATTGC
Found at i:38788904 original size:16 final size:16
Alignment explanation
Indices: 38788864--38788909 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
38788854 AATTGGTTGG
38788864 TATTTAATTTAAATTTA
1 TATTT-ATTTAAATTTA
*
38788881 T-TGCTATTTAAATTTA
1 TAT-TTATTTAAATTTA
38788897 TATTTA-TTAAATT
1 TATTTATTTAAATT
38788910 AGACTAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 7 0.28
16 15 0.60
17 3 0.12
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (16 bp):
TATTTATTTAAATTTA
Found at i:38809408 original size:31 final size:32
Alignment explanation
Indices: 38809359--38809429 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
38809349 AGATATTTTA
* *
38809359 AGCTTGAAATTATCCAAATCTAAAAA-AATGG
1 AGCTTGAGATTATCCAAATCCAAAAATAATGG
* * * *
38809390 AGCTTGAGTTTATTCAAATCCAAAAATATTTG
1 AGCTTGAGATTATCCAAATCCAAAAATAATGG
38809422 AGCTTGAG
1 AGCTTGAG
38809430 CTTAAGCTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 22 0.67
32 11 0.33
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (32 bp):
AGCTTGAGATTATCCAAATCCAAAAATAATGG
Found at i:38813348 original size:51 final size:50
Alignment explanation
Indices: 38813290--38813429 Score: 212
Period size: 51 Copynumber: 2.8 Consensus size: 50
38813280 CTGGTTAAAA
38813290 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACT-TCCGATACACG
* * *
38813341 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCAC-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACC-ATCACTTCCGATACACG
*
38813391 TAGTA-CCTGCACATAGTACTACACACGTGACCATCACTT
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTT
38813430 TCACTTTCAC
Statistics
Matches: 82, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
48 5 0.06
49 26 0.32
50 14 0.17
51 32 0.39
52 5 0.06
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTTCCGATACACG
Found at i:38815378 original size:19 final size:19
Alignment explanation
Indices: 38815354--38815391 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
38815344 CAGGTGCGAT
38815354 ACCCTTACAGCACCCCGAG
1 ACCCTTACAGCACCCCGAG
**
38815373 ACCCTTATGGCACCCCGAG
1 ACCCTTACAGCACCCCGAG
38815392 CCAATTCGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.45, G:0.18, T:0.13
Consensus pattern (19 bp):
ACCCTTACAGCACCCCGAG
Found at i:38815644 original size:19 final size:19
Alignment explanation
Indices: 38815611--38815650 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
38815601 AAAATATCAT
*
38815611 ATTAATTTTAATTTATTTG
1 ATTAATTTTAATTTACTTG
38815630 ATTAA-TTTAATTTTACTTG
1 ATTAATTTTAA-TTTACTTG
38815649 AT
1 AT
38815651 CAAAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (19 bp):
ATTAATTTTAATTTACTTG
Found at i:38821941 original size:22 final size:22
Alignment explanation
Indices: 38821913--38821973 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
38821903 TTTATTGTTC
38821913 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
*
38821935 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTG
**
38821957 AGCCATGAGAGCTTAGT
1 AAACATGAGAGCTTAGT
38821974 CACACGAACG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:38835604 original size:17 final size:16
Alignment explanation
Indices: 38835576--38835613 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
38835566 ATCTACAAAG
38835576 GAAAGGGAAAGAAAAT
1 GAAAGGGAAAGAAAAT
38835592 GAAAGGCGAAAGAAAAT
1 GAAAGG-GAAAGAAAAT
38835609 GAAAG
1 GAAAG
38835614 AAAGAATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.61, C:0.03, G:0.32, T:0.05
Consensus pattern (16 bp):
GAAAGGGAAAGAAAAT
Found at i:38839005 original size:22 final size:22
Alignment explanation
Indices: 38838977--38839018 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
38838967 GCTTGTACGG
*
38838977 GTTTAACACTTCTGTGCTCTCT
1 GTTTAACACTTCGGTGCTCTCT
38838999 GTTTAACACTTCGGTGCTCT
1 GTTTAACACTTCGGTGCTCT
38839019 TTGGTATGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.26, G:0.17, T:0.43
Consensus pattern (22 bp):
GTTTAACACTTCGGTGCTCTCT
Found at i:38852460 original size:2 final size:2
Alignment explanation
Indices: 38852453--38852490 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
38852443 TTCAAAGTTA
38852453 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38852491 TCAAATGCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38853380 original size:87 final size:87
Alignment explanation
Indices: 38853267--38853442 Score: 343
Period size: 87 Copynumber: 2.0 Consensus size: 87
38853257 CATGTTGTCT
*
38853267 CATGTCTCGAGATAATCAACAAATTGTCTCGAGACAATTGGGGTTGTCTTGAGACAAGAGGCACC
1 CATGTCTCGAGATAATCAACAAATTGTCTCGAGACAATTGGGGTTGTCTTGAGACAAAAGGCACC
38853332 AAATGACTATTTTGCTTCGACC
66 AAATGACTATTTTGCTTCGACC
38853354 CATGTCTCGAGATAATCAACAAATTGTCTCGAGACAATTGGGGTTGTCTTGAGACAAAAGGCACC
1 CATGTCTCGAGATAATCAACAAATTGTCTCGAGACAATTGGGGTTGTCTTGAGACAAAAGGCACC
38853419 AAATGACTATTTTGCTTCGACC
66 AAATGACTATTTTGCTTCGACC
38853441 CA
1 CA
38853443 ATCTTAAGAC
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (87 bp):
CATGTCTCGAGATAATCAACAAATTGTCTCGAGACAATTGGGGTTGTCTTGAGACAAAAGGCACC
AAATGACTATTTTGCTTCGACC
Found at i:38860566 original size:40 final size:40
Alignment explanation
Indices: 38860490--38860571 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
38860480 CACAGAAAAT
* * ** *
38860490 TCAATCTAGAAAAATAAAGGAAGAACTGTAGGAAGTTAAC
1 TCAATCTAGAAAAATAAAGAAAGAAATACAGAAAGTTAAC
38860530 TCAATCTAGAAAAATAAAGAAAGAAATACAGAAAGTTAAC
1 TCAATCTAGAAAAATAAAGAAAGAAATACAGAAAGTTAAC
38860570 TC
1 TC
38860572 CACACTCTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.54, C:0.11, G:0.16, T:0.20
Consensus pattern (40 bp):
TCAATCTAGAAAAATAAAGAAAGAAATACAGAAAGTTAAC
Found at i:38860783 original size:20 final size:21
Alignment explanation
Indices: 38860758--38860801 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
38860748 TCTCACGCTG
38860758 ATTCTTCTCTCCCCTT-TTTT
1 ATTCTTCTCTCCCCTTCTTTT
*
38860778 ATTCTTCTCTCTCCTTCTTTT
1 ATTCTTCTCTCCCCTTCTTTT
38860799 ATT
1 ATT
38860802 GGGTAGATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.07, C:0.32, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTCTTCTCTCCCCTTCTTTT
Found at i:38860987 original size:9 final size:9
Alignment explanation
Indices: 38860973--38861000 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
38860963 TTTCTTTCTA
38860973 CATCCTCTT
1 CATCCTCTT
38860982 CATCCTCTT
1 CATCCTCTT
38860991 CATCCTCTT
1 CATCCTCTT
38861000 C
1 C
38861001 TTCTACCTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.11, C:0.46, G:0.00, T:0.43
Consensus pattern (9 bp):
CATCCTCTT
Found at i:38862781 original size:27 final size:27
Alignment explanation
Indices: 38862734--38862875 Score: 117
Period size: 27 Copynumber: 5.2 Consensus size: 27
38862724 GCGAATGGCC
*
38862734 TTGTAGCGATAATCATGAAAGAAAAACCT
1 TTGTGGCGA-AAT-ATGAAAGAAAAACCT
* * **
38862763 TTGTGGCAAAATATAAAAGAAAATTCT
1 TTGTGGCGAAATATGAAAGAAAAACCT
*
38862790 TTGTGGC-CAATCATGAAAGAAAATA-CT
1 TTGTGGCGAAAT-ATGAAAGAAAA-ACCT
* * * *
38862817 TTGTAGCGAAACATGAAAGAAAAATCG
1 TTGTGGCGAAATATGAAAGAAAAACCT
** *
38862844 TTGTAACGAAATATGAAAGAAAAACTT
1 TTGTGGCGAAATATGAAAGAAAAACCT
38862871 TTGTG
1 TTGTG
38862876 ATGAATTATA
Statistics
Matches: 91, Mismatches: 18, Indels: 10
0.76 0.15 0.08
Matches are distributed among these distances:
26 4 0.04
27 75 0.82
28 5 0.05
29 7 0.08
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (27 bp):
TTGTGGCGAAATATGAAAGAAAAACCT
Found at i:38862806 original size:54 final size:55
Alignment explanation
Indices: 38862734--38862875 Score: 146
Period size: 54 Copynumber: 2.6 Consensus size: 55
38862724 GCGAATGGCC
* * * *
38862734 TTGTAGCGATAATCATGAAAGAAAAACCTTTGTGGCAAAATATAAAAGAAAATTCT
1 TTGTAACGA-AATCATGAAAGAAAAACCTTTGTGGCAAAACATAAAAGAAAAATCG
** * * * *
38862790 TTGTGGC-CAATCATGAAAGAAAATA-CTTTGTAGCGAAACATGAAAGAAAAATCG
1 TTGTAACGAAATCATGAAAGAAAA-ACCTTTGTGGCAAAACATAAAAGAAAAATCG
*
38862844 TTGTAACGAAAT-ATGAAAGAAAAACTTTTGTG
1 TTGTAACGAAATCATGAAAGAAAAACCTTTGTG
38862876 ATGAATTATA
Statistics
Matches: 70, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
53 1 0.01
54 59 0.84
55 4 0.06
56 6 0.09
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (55 bp):
TTGTAACGAAATCATGAAAGAAAAACCTTTGTGGCAAAACATAAAAGAAAAATCG
Found at i:38865344 original size:21 final size:22
Alignment explanation
Indices: 38865318--38865358 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
38865308 AAATAAAATA
*
38865318 ATAAATTTTAATTAT-TTGCAT
1 ATAAATTTAAATTATATTGCAT
38865339 ATAAATTTAAATTATATTGC
1 ATAAATTTAAATTATATTGC
38865359 TTTTCGGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (22 bp):
ATAAATTTAAATTATATTGCAT
Found at i:38870179 original size:8 final size:8
Alignment explanation
Indices: 38870166--38870194 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
38870156 CAATAAATAA
38870166 AAAATATT
1 AAAATATT
38870174 AAAATATT
1 AAAATATT
38870182 -AAATATT
1 AAAATATT
38870189 AAAATA
1 AAAATA
38870195 AATCATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AAAATATT
Found at i:38874203 original size:20 final size:20
Alignment explanation
Indices: 38874139--38874203 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
38874129 TCCTCTTATT
*
38874139 TAAACATTGAGGATTTATCA
1 TAAACGTTGAGGATTTATCA
* * *
38874159 TAAACGTCGAGTA-ATAT--
1 TAAACGTTGAGGATTTATCA
38874176 TCAAACGTTGAGGATTTATCA
1 T-AAACGTTGAGGATTTATCA
38874197 TAAACGT
1 TAAACGT
38874204 CGGTATTCTT
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
17 1 0.03
18 10 0.29
19 6 0.18
20 16 0.47
21 1 0.03
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.32
Consensus pattern (20 bp):
TAAACGTTGAGGATTTATCA
Found at i:38883657 original size:25 final size:25
Alignment explanation
Indices: 38883629--38883683 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
38883619 CAAAATAGAT
38883629 ATACTCTTAATTTTGATTTGAAAAC
1 ATACTCTTAATTTTGATTTGAAAAC
38883654 ATACTCTTAATTTTGATTTGAAAAC
1 ATACTCTTAATTTTGATTTGAAAAC
38883679 ATACT
1 ATACT
38883684 TGAAGGAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (25 bp):
ATACTCTTAATTTTGATTTGAAAAC
Found at i:38883802 original size:44 final size:43
Alignment explanation
Indices: 38883754--38883891 Score: 102
Period size: 44 Copynumber: 3.1 Consensus size: 43
38883744 AATATTAATT
38883754 ATTTTAAATTATACAAATTCATATAAGAAAATTTATTATCAAGA
1 ATTTTAAATTATACAAATTCATATAAGAAAATTTATTAT-AAGA
* * * * * **
38883798 ATTTTATGAAATCATATATTATT-AT-TAA-ATTATATTTAATAATAATT
1 A-TTT-T-AAATTATACA-AATTCATATAAGA--AAATTT-ATTATAAGA
*
38883845 ATTTTAAATTATACAAATTCATATAAGAAAATTTATTAGTAATA
1 ATTTTAAATTATACAAATTCATATAAGAAAATTTATTA-TAAGA
38883889 ATT
1 ATT
38883892 ANNNNNNNNN
Statistics
Matches: 70, Mismatches: 13, Indels: 22
0.67 0.12 0.21
Matches are distributed among these distances:
43 6 0.09
44 23 0.33
45 8 0.11
46 8 0.11
47 18 0.26
48 7 0.10
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (43 bp):
ATTTTAAATTATACAAATTCATATAAGAAAATTTATTATAAGA
Found at i:38886729 original size:50 final size:50
Alignment explanation
Indices: 38886637--38886822 Score: 239
Period size: 50 Copynumber: 3.7 Consensus size: 50
38886627 AAGTCCCTGT
* * *
38886637 CACAAAGGCTTTATA-GCGACTCGCCACAAAGGTTTCCCAAATAGATCGC
1 CACAAAGGCTTTATAGGAGACTCGCCACAAAGGCTTCCCAAATAAATCGC
* * * *
38886686 CACAAAGGCTTTATAGGGGACTTGCCACAGAGGCTTCCCAAATAAATCAC
1 CACAAAGGCTTTATAGGAGACTCGCCACAAAGGCTTCCCAAATAAATCGC
** *
38886736 CACAAAGGCTTTATAGGAGACTCGTTATAAAGGCTTCCCAAATAAATCGC
1 CACAAAGGCTTTATAGGAGACTCGCCACAAAGGCTTCCCAAATAAATCGC
* * * *
38886786 CACAAAGGCTTTACAGGTGACTCGCTACAAAAGCTTC
1 CACAAAGGCTTTATAGGAGACTCGCCACAAAGGCTTC
38886823 ACATAAACTT
Statistics
Matches: 118, Mismatches: 18, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
49 15 0.13
50 103 0.87
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.22
Consensus pattern (50 bp):
CACAAAGGCTTTATAGGAGACTCGCCACAAAGGCTTCCCAAATAAATCGC
Found at i:38886810 original size:25 final size:25
Alignment explanation
Indices: 38886611--38886821 Score: 70
Period size: 25 Copynumber: 8.5 Consensus size: 25
38886601 TAAACATTTT
* * **
38886611 GCCACATAGGCTTTTCAAGTCCCT-
1 GCCACAAAGGCTTTACAAGTGACTC
* * *
38886635 GTCACAAAGGCTTTA-TAGCGACTC
1 GCCACAAAGGCTTTACAAGTGACTC
* *
38886659 GCCACAAAGG-TTTCCCAAATAGA-TC
1 GCCACAAAGGCTTT-ACAAGT-GACTC
* * * *
38886684 GCCACAAAGGCTTTATAGGGGACTT
1 GCCACAAAGGCTTTACAAGTGACTC
* ** * * *
38886709 GCCACAGAGGCTTCCCAAATAAATC
1 GCCACAAAGGCTTTACAAGTGACTC
* * * *
38886734 ACCACAAAGGCTTTATAGGAGACTC
1 GCCACAAAGGCTTTACAAGTGACTC
** * ** * * *
38886759 GTTATAAAGGCTTCCCAAATAAATC
1 GCCACAAAGGCTTTACAAGTGACTC
*
38886784 GCCACAAAGGCTTTACAGGTGACTC
1 GCCACAAAGGCTTTACAAGTGACTC
* *
38886809 GCTACAAAAGCTT
1 GCCACAAAGGCTT
38886822 CACATAAACT
Statistics
Matches: 120, Mismatches: 61, Indels: 11
0.62 0.32 0.06
Matches are distributed among these distances:
23 7 0.06
24 23 0.19
25 85 0.71
26 5 0.04
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (25 bp):
GCCACAAAGGCTTTACAAGTGACTC
Found at i:38900902 original size:34 final size:34
Alignment explanation
Indices: 38900845--38900911 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
38900835 AATAATAGAG
* * *
38900845 AAATAAACTAGGTGAATTGCTCAATCATGAAAAT
1 AAATAAACAACGTGAATTGCTCAACCATGAAAAT
*
38900879 AAATAAACAACGTGAATCT-CTCAACCTTGAAAA
1 AAATAAACAACGTGAAT-TGCTCAACCATGAAAA
38900912 GAAAAGTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 27 0.96
35 1 0.04
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (34 bp):
AAATAAACAACGTGAATTGCTCAACCATGAAAAT
Found at i:38906052 original size:21 final size:22
Alignment explanation
Indices: 38906015--38906055 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
38906005 AAATAGGTAG
*
38906015 AAAACAATAAGAAAATAACACT
1 AAAACAACAAGAAAATAACACT
38906037 AAAACAACAA-AAAATAACA
1 AAAACAACAAGAAAATAACA
38906056 TATTTTTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.73, C:0.15, G:0.02, T:0.10
Consensus pattern (22 bp):
AAAACAACAAGAAAATAACACT
Found at i:38913689 original size:24 final size:25
Alignment explanation
Indices: 38913659--38913718 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
38913649 ATTGCACCAA
*
38913659 AAGTGCCACATTTT-GATTGCA-CTG
1 AAGTGCCACATTTTCAATTGCATC-G
38913683 AAGTGCCAC-TTTTCAATTGCATCG
1 AAGTGCCACATTTTCAATTGCATCG
*
38913707 AAGTGTCACATT
1 AAGTGCCACATT
38913719 CATTTGTGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 4 0.13
24 24 0.77
25 3 0.10
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (25 bp):
AAGTGCCACATTTTCAATTGCATCG
Found at i:38914334 original size:60 final size:64
Alignment explanation
Indices: 38914234--38914356 Score: 182
Period size: 60 Copynumber: 2.0 Consensus size: 64
38914224 TCACATTGAT
*
38914234 ATTAAATTAATAAAATATTATCTAGATAAACATTTAATTTAATTTAATTTAATATCTCATATTCA
1 ATTAAATTAATAAAATACTATCTA-ATAAACA-TTAATTTAATTTAATTTAATATCTCATATTCA
38914299 A
64 A
*
38914300 ATTAAATTAATAAAATACTATCT-ATTAA-A-T-ATTTAATTTAATTTAATATCTCATATT
1 ATTAAATTAATAAAATACTATCTAATAAACATTAATTTAATTTAATTTAATATCTCATATT
38914357 AATATCTAGA
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
60 27 0.49
61 1 0.02
63 1 0.02
64 4 0.07
66 22 0.40
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.46
Consensus pattern (64 bp):
ATTAAATTAATAAAATACTATCTAATAAACATTAATTTAATTTAATTTAATATCTCATATTCAA
Found at i:38914824 original size:19 final size:20
Alignment explanation
Indices: 38914797--38914843 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
38914787 TAATATTTAT
*
38914797 TTTAA-TTTATTTGATT-AA
1 TTTAATTTTACTTGATTAAA
38914815 TTTAATTTTACTTGATTAAA
1 TTTAATTTTACTTGATTAAA
*
38914835 ATTAATTTT
1 TTTAATTTT
38914844 TGCAGAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 5 0.20
19 10 0.40
20 10 0.40
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTAATTTTACTTGATTAAA
Found at i:38923193 original size:20 final size:21
Alignment explanation
Indices: 38923170--38923212 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
38923160 GCTGAAGCTT
38923170 TAGAA-TTTCCATTATTTAGC
1 TAGAAGTTTCCATTATTTAGC
38923190 TAGAAGTTTCCATTATTTAGC
1 TAGAAGTTTCCATTATTTAGC
38923211 TA
1 TA
38923213 ACACCGTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (21 bp):
TAGAAGTTTCCATTATTTAGC
Found at i:38926794 original size:20 final size:20
Alignment explanation
Indices: 38926757--38926794 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38926747 ATGGTGCCTT
*
38926757 TGTTTGCACATTTGTGCCAC
1 TGTTTGCACATTCGTGCCAC
38926777 TGTTTGCAC-TTCGATGCC
1 TGTTTGCACATTCG-TGCC
38926795 CCTATTATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.13, C:0.26, G:0.21, T:0.39
Consensus pattern (20 bp):
TGTTTGCACATTCGTGCCAC
Found at i:38926948 original size:7 final size:7
Alignment explanation
Indices: 38926936--38926964 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
38926926 AAGACATTAG
38926936 TAAATGT
1 TAAATGT
38926943 TAAATGT
1 TAAATGT
38926950 TAAATGT
1 TAAATGT
38926957 TAAATGT
1 TAAATGT
38926964 T
1 T
38926965 CGATGAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (7 bp):
TAAATGT
Found at i:38931039 original size:12 final size:12
Alignment explanation
Indices: 38931022--38931047 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
38931012 AAATCCCTCC
38931022 TAGCAGATACAA
1 TAGCAGATACAA
38931034 TAGCAGATACAA
1 TAGCAGATACAA
38931046 TA
1 TA
38931048 TCAAGTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.19
Consensus pattern (12 bp):
TAGCAGATACAA
Found at i:38952191 original size:18 final size:17
Alignment explanation
Indices: 38952165--38952203 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
38952155 ATTTTCCTTC
38952165 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
38952182 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
38952200 CACA
1 CACA
38952204 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:38954839 original size:15 final size:15
Alignment explanation
Indices: 38954808--38954840 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
38954798 AAAATGTGGT
38954808 TAAAAAATTTTATAA
1 TAAAAAATTTTATAA
38954823 TAAAATAATTTTA-AA
1 TAAAA-AATTTTATAA
38954838 TAA
1 TAA
38954841 GTAAAAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAAAAAATTTTATAA
Found at i:38972361 original size:45 final size:44
Alignment explanation
Indices: 38972292--38972466 Score: 140
Period size: 45 Copynumber: 3.9 Consensus size: 44
38972282 ACCGAAGATG
* * *
38972292 ACAAATCTTATCTCCCTAAAGTTGCAATGGAGTAGATTAAAGCCA
1 ACAAGTCTTATCTCCCTGAAGTTGCAATGGAGTAGATTAAAG-AA
* *
38972337 ACAAGTCTTATCTCCCTGAAGTTGCAGA-AGAGTAGACTGACTAA-AA
1 ACAAGTCTTATCTCCCTGAAGTTGCA-ATGGAGTAGA-TTA--AAGAA
* * * * **
38972383 TCAA-TCTTATCTCCCTGAAGTTCCAGTGGAGTAGATTGAAGTT
1 ACAAGTCTTATCTCCCTGAAGTTGCAATGGAGTAGATTAAAGAA
* * * **
38972426 ACTAGTCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA
1 ACAAGTCTTATCTCCCTGAAGTTGCAATGGAGTAGATTAAA
38972467 ATGATGAATC
Statistics
Matches: 103, Mismatches: 20, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
42 2 0.02
43 2 0.02
44 32 0.31
45 58 0.56
46 7 0.07
48 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (44 bp):
ACAAGTCTTATCTCCCTGAAGTTGCAATGGAGTAGATTAAAGAA
Found at i:38972482 original size:44 final size:44
Alignment explanation
Indices: 38972289--38972497 Score: 140
Period size: 44 Copynumber: 4.7 Consensus size: 44
38972279 CAGACCGAAG
* * * *
38972289 ATGACAAATCTTATCTCCCTAAAGTTGCAATGGAGTAGATTAAA
1 ATGACTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
*** * * *
38972333 GCCAAC-AAGTCTTATCTCCCTGAAGTTGCAGAAGAGTAGACTGACTAAA
1 -ATGACTAA-TCTTATCTCCCTGAAGTTGCAG-TG-G-AG-CAGATTAAA
* * *
38972382 AT--C-AATCTTATCTCCCTGAAGTTCCAGTGGAGTAGATTGAA
1 ATGACTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
* * * * *
38972423 GTTACTAGTCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA
1 ATGACTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
**
38972467 ATGA-TGAATCTTATCTCTTTGAAGTTGCAGT
1 ATGACT-AATCTTATCTCCCTGAAGTTGCAGT
38972498 AAAGTAGATC
Statistics
Matches: 125, Mismatches: 30, Indels: 19
0.72 0.17 0.11
Matches are distributed among these distances:
41 6 0.05
42 2 0.02
43 3 0.02
44 58 0.46
45 43 0.34
46 4 0.03
47 1 0.01
48 2 0.02
49 6 0.05
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (44 bp):
ATGACTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
Done.