Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 17 of 182
Found at i:6993945 original size:59 final size:59
Alignment explanation
Indices: 6993859--6993972 Score: 167
Period size: 59 Copynumber: 1.9 Consensus size: 59
6993849 CGAGGGAAAG
*
6993859 TTGGTGTCGGCCATTGGTTGCCAAACACC-AAAAAAAATATTTTTTAATTCATATTTTTA
1 TTGGTGTCGGCCATTGCTTGCCAAACACCAAAAAAAAATATTTTTT-ATTCATATTTTTA
* * * *
6993918 TTGGTGTTGGCTATTGCTTGTCAAACACCAAAAAAAAATATTTTTTATTCTTATT
1 TTGGTGTCGGCCATTGCTTGCCAAACACCAAAAAAAAATATTTTTTATTCATATT
6993973 ATTTGTGGGT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
59 33 0.67
60 16 0.33
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (59 bp):
TTGGTGTCGGCCATTGCTTGCCAAACACCAAAAAAAAATATTTTTTATTCATATTTTTA
Found at i:6993984 original size:60 final size:59
Alignment explanation
Indices: 6993861--6993985 Score: 162
Period size: 59 Copynumber: 2.1 Consensus size: 59
6993851 AGGGAAAGTT
* *
6993861 GGTGTCGGCCATTGGTTGCCAAACACCAAAAAAAATATTTTTTAATTCATATTTTTATT
1 GGTGTCGGCCATTGCTTGCCAAACACCAAAAAAAATATTTTTTAATTCATATTTTTATG
* * * * *
6993920 GGTGTTGGCTATTGCTTGTCAAACACCAAAAAAAAATATTTTTT-ATTCTTATTATTTGTG
1 GGTGTCGGCCATTGCTTGCCAAACACC-AAAAAAAATATTTTTTAATTCATATT-TTTATG
6993980 GGTGTC
1 GGTGTC
6993986 AACCATTAGA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
59 31 0.55
60 25 0.45
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.41
Consensus pattern (59 bp):
GGTGTCGGCCATTGCTTGCCAAACACCAAAAAAAATATTTTTTAATTCATATTTTTATG
Found at i:6994180 original size:59 final size:58
Alignment explanation
Indices: 6994032--6994182 Score: 160
Period size: 58 Copynumber: 2.6 Consensus size: 58
6994022 TTTTATTTTC
* * *
6994032 GAGTGTCGACTATGGGTTGACAAACACCCAAAAAATATGTTTTTGGTATCTGAAAAAGG
1 GAGTGTCGACCATGGCTTGACAAACACCC-AAAAATATGTTTTTGATATCTGAAAAAGG
* * ** * * * *
6994091 G-GTATTGGTCATGGTTTGACAAACACCCAAAAATATCTTTTTTGATATTTGGAAAAGG
1 GAGTGTCGACCATGGCTTGACAAACACCCAAAAATAT-GTTTTTGATATCTGAAAAAGG
* *
6994149 GAGTGTCGACCATGGCTTGACAGACATCCAAAAA
1 GAGTGTCGACCATGGCTTGACAAACACCCAAAAA
6994183 AATAATTTTT
Statistics
Matches: 73, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
57 8 0.11
58 39 0.53
59 26 0.36
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (58 bp):
GAGTGTCGACCATGGCTTGACAAACACCCAAAAATATGTTTTTGATATCTGAAAAAGG
Found at i:6994192 original size:59 final size:58
Alignment explanation
Indices: 6994032--6994192 Score: 144
Period size: 59 Copynumber: 2.7 Consensus size: 58
6994022 TTTTATTTTC
* * * * *
6994032 GAGTGTCGACTATGGGTTGACAAACACCCAAAAAATATGTTTTTGGTATCTGAAAAAGG
1 GAGTGTCGACCATGGCTTGACAAACACCAAAAAAATA-ATTTTTGATATCTGAAAAAGG
* * ** * * ** * *
6994091 G-GTATTGGTCATGGTTTGACAAACACCCAAAAATATCTTTTTTGATATTTGGAAAAGG
1 GAGTGTCGACCATGGCTTGACAAACA-CCAAAAAAATAATTTTTGATATCTGAAAAAGG
*
6994149 GAGTGTCGACCATGGCTTGACAGACATCCAAAAAAATAATTTTT
1 GAGTGTCGACCATGGCTTGACAAACA-CCAAAAAAATAATTTTT
6994193 TATTCATATT
Statistics
Matches: 77, Mismatches: 23, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
58 36 0.47
59 41 0.53
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (58 bp):
GAGTGTCGACCATGGCTTGACAAACACCAAAAAAATAATTTTTGATATCTGAAAAAGG
Found at i:6998349 original size:17 final size:17
Alignment explanation
Indices: 6998310--6998353 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
6998300 TTTCAATCAT
*
6998310 TTAAAATTTATAAAAATA
1 TTAAAA-TTATTAAAATA
6998328 -T-AAATTATTAAAATA
1 TTAAAATTATTAAAATA
6998343 TTAAAATTATT
1 TTAAAATTATT
6998354 CTCCCAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 10 0.43
16 4 0.17
17 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAAATTATTAAAATA
Found at i:6999746 original size:51 final size:51
Alignment explanation
Indices: 6999653--6999756 Score: 140
Period size: 51 Copynumber: 2.0 Consensus size: 51
6999643 ATATTTTGAA
* * *
6999653 AAAAAAAATTTGTGTTTGGCAGCTAATGGTCAACATC-AAAAAACACTAAT
1 AAAAAAAATTTGTGTTTGGCAACTAATGATCAACATCAAAAAAACACGAAT
*
6999703 AAAAAAAATTTGGTGTTTGGCAACTAATGATCGACA-CAAAAAAAACACGAAT
1 AAAAAAAATTT-GTGTTTGGCAACTAATGATCAACATC-AAAAAAACACGAAT
6999755 AA
1 AA
6999757 TTTTTTTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
50 12 0.26
51 21 0.45
52 14 0.30
ACGTcount: A:0.49, C:0.13, G:0.14, T:0.23
Consensus pattern (51 bp):
AAAAAAAATTTGTGTTTGGCAACTAATGATCAACATCAAAAAAACACGAAT
Found at i:6999874 original size:18 final size:17
Alignment explanation
Indices: 6999844--6999877 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
6999834 TATATTTTTA
6999844 AATTTTATATAAATTTG
1 AATTTTATATAAATTTG
6999861 AATTTTATTATAAATTT
1 AATTTTA-TATAAATTT
6999878 TAATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
AATTTTATATAAATTTG
Found at i:6999889 original size:10 final size:10
Alignment explanation
Indices: 6999874--6999910 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
6999864 TTTATTATAA
6999874 ATTTTAATAT
1 ATTTTAATAT
6999884 ATTTTAATA-
1 ATTTTAATAT
6999893 ACTTTTAATAT
1 A-TTTTAATAT
6999904 ATTTTAA
1 ATTTTAA
6999911 AATAATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 1 0.04
10 23 0.92
11 1 0.04
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (10 bp):
ATTTTAATAT
Found at i:6999898 original size:20 final size:20
Alignment explanation
Indices: 6999845--6999910 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
6999835 ATATTTTTAA
*
6999845 ATTTTATATAAATTTGAAT-T
1 ATTTTA-ATAAATTTTAATAT
6999865 -TTATT-ATAAATTTTAATAT
1 ATT-TTAATAAATTTTAATAT
*
6999884 ATTTTAATAACTTTTAATAT
1 ATTTTAATAAATTTTAATAT
6999904 ATTTTAA
1 ATTTTAA
6999911 AATAATATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 11 0.28
19 5 0.12
20 24 0.60
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTTTAATAAATTTTAATAT
Found at i:7000216 original size:17 final size:18
Alignment explanation
Indices: 7000185--7000219 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
7000175 GAAATGCAAT
*
7000185 AAAATATATATTTTTTAA
1 AAAATATATAATTTTTAA
7000203 AAAATAT-TAATTTTTAA
1 AAAATATATAATTTTTAA
7000220 TAGATTTCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAAATATATAATTTTTAA
Found at i:7001837 original size:24 final size:22
Alignment explanation
Indices: 7001792--7001853 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 22
7001782 AAGGCATAGA
7001792 TAATAAAATAAAATAATAACAC
1 TAATAAAATAAAATAATAACAC
* *
7001814 TAATAATAGTAAAATTAGTAACAC
1 TAATAA-AATAAAA-TAATAACAC
7001838 -ACATAAAATGAAAATA
1 TA-ATAAAAT-AAAATA
7001854 TTAATAATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 6 0.18
23 11 0.33
24 16 0.48
ACGTcount: A:0.63, C:0.08, G:0.05, T:0.24
Consensus pattern (22 bp):
TAATAAAATAAAATAATAACAC
Found at i:7001976 original size:23 final size:23
Alignment explanation
Indices: 7001950--7001996 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
7001940 CATGAAGTAT
7001950 AAAAGATAAAAAATATAAATTAC
1 AAAAGATAAAAAATATAAATTAC
* * *
7001973 AAAATATAAATAATATAGATTAC
1 AAAAGATAAAAAATATAAATTAC
7001996 A
1 A
7001997 TATGCTGGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (23 bp):
AAAAGATAAAAAATATAAATTAC
Found at i:7004467 original size:23 final size:23
Alignment explanation
Indices: 7004441--7004531 Score: 66
Period size: 23 Copynumber: 4.0 Consensus size: 23
7004431 TTACCGTTCA
*
7004441 GCACTGTGTCTGCTTACTGTTTC
1 GCACTGTGTCTGCCTACTGTTTC
*
7004464 GCACT-TCGTGTGCCTACTGATTTGC
1 GCACTGT-GTCTGCCTACTG-TTT-C
*
7004489 GCTA-TGTG-C-GCCTACTGATT-
1 GC-ACTGTGTCTGCCTACTGTTTC
* *
7004509 GCACTGTGTGTGCTTACTGTTTC
1 GCACTGTGTCTGCCTACTGTTTC
7004532 CCCAGCACTT
Statistics
Matches: 52, Mismatches: 7, Indels: 18
0.68 0.09 0.23
Matches are distributed among these distances:
19 1 0.02
20 6 0.12
22 12 0.23
23 23 0.44
24 3 0.06
25 5 0.10
26 2 0.04
ACGTcount: A:0.11, C:0.25, G:0.24, T:0.40
Consensus pattern (23 bp):
GCACTGTGTCTGCCTACTGTTTC
Found at i:7005538 original size:13 final size:13
Alignment explanation
Indices: 7005520--7005544 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7005510 CCTAGATCCC
7005520 CTTTTCTTTTTTT
1 CTTTTCTTTTTTT
7005533 CTTTTCTTTTTT
1 CTTTTCTTTTTT
7005545 ACTGTTCGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
CTTTTCTTTTTTT
Found at i:7014215 original size:6 final size:6
Alignment explanation
Indices: 7014204--7014245 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
7014194 ATGTAAAACC
7014204 CCTTTT CCTTTT CCTTTT CCTTTT CCTTTT CCTTTT CCTTTT
1 CCTTTT CCTTTT CCTTTT CCTTTT CCTTTT CCTTTT CCTTTT
7014246 TTTTTTCAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (6 bp):
CCTTTT
Found at i:7015492 original size:12 final size:12
Alignment explanation
Indices: 7015475--7015505 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
7015465 TACTCAACGT
7015475 TACATCACAGAA
1 TACATCACAGAA
7015487 TACATCACAGAA
1 TACATCACAGAA
*
7015499 TAAATCA
1 TACATCA
7015506 ATATTCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.52, C:0.23, G:0.06, T:0.19
Consensus pattern (12 bp):
TACATCACAGAA
Found at i:7016749 original size:36 final size:36
Alignment explanation
Indices: 7016687--7016785 Score: 153
Period size: 36 Copynumber: 2.8 Consensus size: 36
7016677 AAGGTCATGC
* * *
7016687 TTACACCCTATTAACCAAAAGGTCATGATGCTCATT
1 TTACTCCCTATTGACCCAAAGGTCATGATGCTCATT
*
7016723 TTACTCCCTGTTGACCCAAAGGTCATGATGCTCATT
1 TTACTCCCTATTGACCCAAAGGTCATGATGCTCATT
*
7016759 TTACTCCCTATTGACCCAAAGATCATG
1 TTACTCCCTATTGACCCAAAGGTCATG
7016786 CTTGTTACCA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.31
Consensus pattern (36 bp):
TTACTCCCTATTGACCCAAAGGTCATGATGCTCATT
Found at i:7021812 original size:18 final size:18
Alignment explanation
Indices: 7021776--7021812 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
7021766 TGAGCTTTCG
*
7021776 AATTCGAATAACTCCAAT
1 AATTCGAATAAATCCAAT
*
7021794 AATTCGAATAAATCGAAT
1 AATTCGAATAAATCCAAT
7021812 A
1 A
7021813 TCAAACTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.16, G:0.08, T:0.27
Consensus pattern (18 bp):
AATTCGAATAAATCCAAT
Found at i:7025409 original size:14 final size:14
Alignment explanation
Indices: 7025390--7025418 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
7025380 TAAGGCCTTC
7025390 TTTTTTTT-CTTTT
1 TTTTTTTTCCTTTT
7025403 TTTTTTTTCCTTTT
1 TTTTTTTTCCTTTT
7025417 TT
1 TT
7025419 AACTTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTTTTTCCTTTT
Found at i:7025443 original size:17 final size:18
Alignment explanation
Indices: 7025423--7025456 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7025413 TTTTTTAACT
7025423 TTTAT-AAATAAAATACA
1 TTTATCAAATAAAATACA
*
7025440 TTTATCAAGTAAAATAC
1 TTTATCAAATAAAATAC
7025457 CCACATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.35
Consensus pattern (18 bp):
TTTATCAAATAAAATACA
Found at i:7026358 original size:185 final size:179
Alignment explanation
Indices: 7026068--7026408 Score: 411
Period size: 185 Copynumber: 1.9 Consensus size: 179
7026058 TAATCCTCAT
7026068 CATTTATATATTGTGTCAAATTAATCTTAATTATAAAAAATTAACTCTCAACTTTTTCACATTGT
1 CATTTATATATTGTGTCAAATTAATCTTAATTATAAAAAATTAACTCTCAACTTTTTCACATTGT
* * * * *
7026133 GTAATTTAACCTCTATTTTTTTTCAATTTTGCTTTTTTTTTGGGTGACCTTTTCACTTAAAA-AG
66 GTAATTTAACCTC-ATCTTTTCTC-A-TTTGCATTTTTTTT--ATGACCTTTTCACCTAAAATA-
* *
7026197 CTAAAAGAAACCAAATTTACCAACTAAATTGGCGTAATAAAAACATTAACCATCAA
125 CTAAAA-AAAACAAATCTACCAACTAAATTGGCGTAATAAAAACATTAACCATCAA
* * *
7026253 CATTTATATATTGTGTCAAATTAGTCTTGATTATAAAAAAAAATTTAACTCTCTA-TATTTTCAC
1 CATTTATATATTGTGTCAAATTAATCTTAATTAT---AAAAAA-TTAACTCTCAACT-TTTTCAC
** *
7026317 ATTGTGTAATTTGGCCTC-TCTTTTCTC-TTTGCAATTTTTTTTATGATCTTTTCACCTAAAATA
61 ATTGTGTAATTTAACCTCATCTTTTCTCATTTGC-ATTTTTTTTATGACCTTTTCACCTAAAATA
*
7026380 CTAAAAAAAACAAATCTACTAACTAAATT
125 CTAAAAAAAACAAATCTACCAACTAAATT
7026409 TGATAAAAAA
Statistics
Matches: 135, Mismatches: 14, Indels: 17
0.81 0.08 0.10
Matches are distributed among these distances:
182 20 0.15
183 22 0.16
184 6 0.04
185 40 0.30
187 7 0.05
188 7 0.05
189 33 0.24
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (179 bp):
CATTTATATATTGTGTCAAATTAATCTTAATTATAAAAAATTAACTCTCAACTTTTTCACATTGT
GTAATTTAACCTCATCTTTTCTCATTTGCATTTTTTTTATGACCTTTTCACCTAAAATACTAAAA
AAAACAAATCTACCAACTAAATTGGCGTAATAAAAACATTAACCATCAA
Found at i:7039026 original size:3 final size:3
Alignment explanation
Indices: 7039018--7039042 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
7039008 ATTTTTAAAT
7039018 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
7039043 CTTTATTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:7051521 original size:17 final size:15
Alignment explanation
Indices: 7051487--7051519 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
7051477 TCACTCAATG
7051487 TTTATATAAATATTT
1 TTTATATAAATATTT
*
7051502 TTTATATACATATTT
1 TTTATATAAATATTT
7051517 TTT
1 TTT
7051520 TTTTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTATATAAATATTT
Found at i:7053577 original size:29 final size:29
Alignment explanation
Indices: 7053521--7053577 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
7053511 GATTTAATGT
* * * *
7053521 GTAATTTTATATATTAAATTTGATTTTAC
1 GTAATTCTATACATGAAATTTGAATTTAC
*
7053550 GTAATTCTATACATGAAATTTTAATTTA
1 GTAATTCTATACATGAAATTTGAATTTA
7053578 ATCGAATCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (29 bp):
GTAATTCTATACATGAAATTTGAATTTAC
Found at i:7054019 original size:3 final size:3
Alignment explanation
Indices: 7054011--7054036 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
7054001 GAAAGGAGCA
7054011 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
7054037 GGTAAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:7056557 original size:16 final size:18
Alignment explanation
Indices: 7056536--7056575 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
7056526 TTTCGTGCAA
7056536 ATATAAATT-TAAAAA-T
1 ATATAAATTATAAAAAGT
7056552 ATATAAATTAATAAAAAGT
1 ATATAAATT-ATAAAAAGT
7056571 ATATA
1 ATATA
7056576 TTTTTCACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.43
18 6 0.29
19 6 0.29
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
ATATAAATTATAAAAAGT
Found at i:7057794 original size:11 final size:10
Alignment explanation
Indices: 7057770--7057820 Score: 54
Period size: 10 Copynumber: 5.2 Consensus size: 10
7057760 TATTCCTTTT
7057770 TTAATTA-G-
1 TTAATTATGA
7057778 TTAATTTATGA
1 TTAA-TTATGA
7057789 TTAATTATGA
1 TTAATTATGA
*
7057799 TTTATT-TGA
1 TTAATTATGA
7057808 TTAATTTATGA
1 TTAA-TTATGA
7057819 TT
1 TT
7057821 TTTTAAGATG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
8 4 0.11
9 9 0.25
10 14 0.39
11 9 0.25
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (10 bp):
TTAATTATGA
Found at i:7059512 original size:24 final size:25
Alignment explanation
Indices: 7059476--7059523 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
7059466 TTCAAAAGTT
* *
7059476 ATTTCTTTTAAAATTTGTAATAATA
1 ATTTCTTTTAAAAATTATAATAATA
7059501 ATTT-TTTTAAAAATTATAATAAT
1 ATTTCTTTTAAAAATTATAATAAT
7059524 TATTGTGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (25 bp):
ATTTCTTTTAAAAATTATAATAATA
Found at i:7059615 original size:116 final size:114
Alignment explanation
Indices: 7059400--7059630 Score: 257
Period size: 116 Copynumber: 2.0 Consensus size: 114
7059390 AGTGAAAGTA
* ** * * *
7059400 TATAAGAATTATTGTGATGTGAATTGAAATTAATATTAAAATCTAATTAATATATAAATTATTTA
1 TATAAGAATTATTGTGAAGTGAATTGAAAAAAATATTAAAATCTAATTAATAGACAAATTATTAA
* * * * ***
7059465 ATTCAAAAGTTATTTCTTTTAAAATTTGTAATAA-TAATTTTTTTAAAAAT
66 ACTCAAAAGCTAATTATTTTAAAAACAGTAATAATTAA--TTTTTAAAAAT
* * * *
7059515 TATAATAATTATTGTGAAGTGATTTGAAAAAAAATATTAAAATTTAATTAATAGACAAATTGTTA
1 TATAAGAATTATTGTGAAGTGAATTG-AAAAAAATATTAAAATCTAATTAATAGACAAATTATTA
* *
7059580 AACTGAAAAGCTAATTATTTTAAAAACAGTGATAATTAATTTTTAAAAAT
65 AACTCAAAAGCTAATTATTTTAAAAACAGTAATAATTAATTTTTAAAAAT
7059630 T
1 T
7059631 TTATTTTCAA
Statistics
Matches: 95, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
115 35 0.37
116 57 0.60
117 3 0.03
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (114 bp):
TATAAGAATTATTGTGAAGTGAATTGAAAAAAATATTAAAATCTAATTAATAGACAAATTATTAA
ACTCAAAAGCTAATTATTTTAAAAACAGTAATAATTAATTTTTAAAAAT
Found at i:7069200 original size:18 final size:18
Alignment explanation
Indices: 7069179--7069216 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
7069169 AAAATGTAGC
7069179 AAAAAAA-TAAAAAAACAA
1 AAAAAAACT-AAAAAACAA
*
7069197 AAAAAAACTAGAAAACAA
1 AAAAAAACTAAAAAACAA
7069215 AA
1 AA
7069217 TATCAAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.84, C:0.08, G:0.03, T:0.05
Consensus pattern (18 bp):
AAAAAAACTAAAAAACAA
Found at i:7086654 original size:7 final size:7
Alignment explanation
Indices: 7086637--7086666 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
7086627 CCAGGCAAAT
7086637 AAAAT-A
1 AAAATAA
7086643 AAAATAA
1 AAAATAA
7086650 AAAATAA
1 AAAATAA
7086657 AAAATAA
1 AAAATAA
7086664 AAA
1 AAA
7086667 GCAAAAGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAATAA
Found at i:7090817 original size:26 final size:27
Alignment explanation
Indices: 7090782--7090832 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
7090772 TTAAATTTCA
*
7090782 ATTTCAAATATCAAAT-TATAGTATGC
1 ATTTCAAATATCAAATCGATAGTATGC
* *
7090808 ATTTCTAATATTAAATCGATAGTAT
1 ATTTCAAATATCAAATCGATAGTAT
7090833 CTATTTGGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 14 0.67
27 7 0.33
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (27 bp):
ATTTCAAATATCAAATCGATAGTATGC
Found at i:7091282 original size:5 final size:5
Alignment explanation
Indices: 7091272--7091299 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
7091262 AAGCTGTACC
7091272 ATATA ATATA ATATA ATATA ATATA ATA
1 ATATA ATATA ATATA ATATA ATATA ATA
7091300 AACAAAGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:7092118 original size:6 final size:6
Alignment explanation
Indices: 7092109--7092138 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
7092099 ATAAAAAACT
7092109 TGAAGC TGAAGC TGAAGC TGAAGC TGAAGC
1 TGAAGC TGAAGC TGAAGC TGAAGC TGAAGC
7092139 CATCCATGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.33, T:0.17
Consensus pattern (6 bp):
TGAAGC
Found at i:7092349 original size:6 final size:6
Alignment explanation
Indices: 7092338--7092385 Score: 89
Period size: 6 Copynumber: 8.2 Consensus size: 6
7092328 AGGAGTGAGG
7092338 ACCAGC ACCAGC ACCAGC ACCAGC ACCAGC ACCAGC ACCAGC A-CAGC
1 ACCAGC ACCAGC ACCAGC ACCAGC ACCAGC ACCAGC ACCAGC ACCAGC
7092385 A
1 A
7092386 ATCACTCTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.12
6 37 0.88
ACGTcount: A:0.35, C:0.48, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCAGC
Found at i:7093294 original size:57 final size:57
Alignment explanation
Indices: 7093215--7093339 Score: 169
Period size: 57 Copynumber: 2.2 Consensus size: 57
7093205 ACAAACAATC
* *
7093215 AAAATATTTTTAAATATGGAAAAGGTAGTATAGACCATTAGAAGGCAAACACCCAAA
1 AAAATATTTTTAAATATCGAAAAGGTAGTATAGACCATTAGAAGACAAACACCCAAA
* * * * ** *
7093272 AAAATATTTTTAAATCTCGAAAATGTAGTGTAGGCCATTAGGTGACAAACATCCAAA
1 AAAATATTTTTAAATATCGAAAAGGTAGTATAGACCATTAGAAGACAAACACCCAAA
7093329 AAAATATTTTT
1 AAAATATTTTT
7093340 TTATTCATAT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (57 bp):
AAAATATTTTTAAATATCGAAAAGGTAGTATAGACCATTAGAAGACAAACACCCAAA
Found at i:7093408 original size:114 final size:115
Alignment explanation
Indices: 7093261--7093467 Score: 247
Period size: 114 Copynumber: 1.8 Consensus size: 115
7093251 ATTAGAAGGC
* *** * * * * *
7093261 AAACACCCAAAAAAATATTTTTAAATCTCGAAAATGTAGTGTAGGCCATTAGGTGACAAACATCC
1 AAACACCCAAAAAAATATTTTTAAACCTCGAAAAAAAAATGTAGACCATGACGTAACAAACATCC
*
7093326 AAAAAAATATTTTTTTATTCATATTTTTTGGTTTTAGGCCATGGCTTGAT
66 AAAAAAATAATTTTTTATTCATATTTTTTGGTTTTAGGCCATGGCTTGAT
* * * * *
7093376 AAACA-CCTAAAAAATATTTTTGAGACCT-GAAAAAAAAATGTTGATCATGACTTAACAAACATC
1 AAACACCCAAAAAAATATTTTT-AAACCTCGAAAAAAAAATGTAGACCATGACGTAACAAACATC
*
7093439 CAAAAAAATAATTTTTTATTCGTATTTTT
65 CAAAAAAATAATTTTTTATTCATATTTTT
7093468 ATGTGTCGAT
Statistics
Matches: 75, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
114 66 0.88
115 9 0.12
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.35
Consensus pattern (115 bp):
AAACACCCAAAAAAATATTTTTAAACCTCGAAAAAAAAATGTAGACCATGACGTAACAAACATCC
AAAAAAATAATTTTTTATTCATATTTTTTGGTTTTAGGCCATGGCTTGAT
Found at i:7093535 original size:113 final size:113
Alignment explanation
Indices: 7093316--7093536 Score: 254
Period size: 113 Copynumber: 1.9 Consensus size: 113
7093306 CCATTAGGTG
* * * *
7093316 ACAAACATCCAAAAAAATATTTTTTTATTCATATTTTTTGGTTTTAGGCCATGGCTTGATAAACA
1 ACAAACATCCAAAAAAATAATTTTTTATTCATATTTTTTGGTTGTAGACCATGGCTTGACAAACA
* *
7093381 CCTAAAAAATATTTTTGAGACCTGAAAAAAAAATGTTGATCATGACTTA
66 CCTAAAAAATATTTTTGAGA-CTGAAAAAAAAATATCGATCATGACTTA
* * **
7093430 ACAAACATCCAAAAAAATAATTTTTTATTCGTATTTTTAT-G-TGTCGATTATGGCTTGACAAAC
1 ACAAACATCCAAAAAAATAATTTTTTATTCATATTTTT-TGGTTGTAGACCATGGCTTGACAAAC
*
7093493 A-CTCAAAAAATATTTTTTA-A-TGTAAAAATAATAATATCGATCAT
65 ACCT-AAAAAATATTTTTGAGACTG-AAAAA-AA-AATATCGATCAT
7093537 AAGATGTCAA
Statistics
Matches: 91, Mismatches: 11, Indels: 11
0.81 0.10 0.10
Matches are distributed among these distances:
110 2 0.02
111 5 0.05
112 5 0.05
113 41 0.45
114 37 0.41
115 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.37
Consensus pattern (113 bp):
ACAAACATCCAAAAAAATAATTTTTTATTCATATTTTTTGGTTGTAGACCATGGCTTGACAAACA
CCTAAAAAATATTTTTGAGACTGAAAAAAAAATATCGATCATGACTTA
Found at i:7101929 original size:22 final size:22
Alignment explanation
Indices: 7101904--7101956 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
7101894 CTGTTGGAAG
*
7101904 TATCGCGATTCCAAAGTATGGA
1 TATCACGATTCCAAAGTATGGA
* *
7101926 TATCATGATTCCAAGGTATGGA
1 TATCACGATTCCAAAGTATGGA
7101948 TATCACGAT
1 TATCACGAT
7101957 AGCCTTTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (22 bp):
TATCACGATTCCAAAGTATGGA
Found at i:7103694 original size:38 final size:38
Alignment explanation
Indices: 7103652--7103726 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
7103642 CCCGTGTGTT
*
7103652 CAAGATCCATTCTAAGGATGATGTTTTGATAGAGGTGC
1 CAAGATCCATTCTAAGGATGATATTTTGATAGAGGTGC
*
7103690 CAAGATCTATTCTAAGGATGATATTTTGATAGAGGTG
1 CAAGATCCATTCTAAGGATGATATTTTGATAGAGGTG
7103727 AATCTAGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (38 bp):
CAAGATCCATTCTAAGGATGATATTTTGATAGAGGTGC
Found at i:7110344 original size:5 final size:6
Alignment explanation
Indices: 7110318--7110343 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
7110308 AATTCTAAAT
7110318 AAATTA AAATTA AAATTA AAATTA AA
1 AAATTA AAATTA AAATTA AAATTA AA
7110344 TTTTATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATTA
Found at i:7111024 original size:28 final size:29
Alignment explanation
Indices: 7110993--7111049 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
7110983 GAAGTTACAT
7110993 TTTAATCCGTTAAAAATAA-AAAATTATA
1 TTTAATCCGTTAAAAATAATAAAATTATA
*** *
7111021 TTTAATTTTTTAAAAATAATGAAATTATA
1 TTTAATCCGTTAAAAATAATAAAATTATA
7111050 AATTAAAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (29 bp):
TTTAATCCGTTAAAAATAATAAAATTATA
Found at i:7112309 original size:14 final size:14
Alignment explanation
Indices: 7112290--7112324 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
7112280 TGTTACACTG
*
7112290 AAAATGGTTTCCGA
1 AAAATGATTTCCGA
*
7112304 AAAATGATTTCTGA
1 AAAATGATTTCCGA
7112318 AAAATGA
1 AAAATGA
7112325 CTTACTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.29
Consensus pattern (14 bp):
AAAATGATTTCCGA
Found at i:7126200 original size:3 final size:3
Alignment explanation
Indices: 7126192--7126229 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
7126182 GTTTTTATTA
7126192 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
7126230 AGTTTGAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:7127699 original size:19 final size:19
Alignment explanation
Indices: 7127661--7127700 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
7127651 ATCCATTCAG
* *
7127661 AATTCAAGATTTGGGCTTC
1 AATTCAAGATTTGAGATTC
*
7127680 AATTCAAGGTTTGAGATTC
1 AATTCAAGATTTGAGATTC
7127699 AA
1 AA
7127701 AATAAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (19 bp):
AATTCAAGATTTGAGATTC
Found at i:7129043 original size:18 final size:17
Alignment explanation
Indices: 7129018--7129056 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
7129008 AATTAACCCC
*
7129018 AAAATCAAAAGAATATA
1 AAAATCAAAAAAATATA
7129035 AAAATTCAAAAAAATATA
1 AAAA-TCAAAAAAATATA
7129053 AAAA
1 AAAA
7129057 AAAATTGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAATCAAAAAAATATA
Found at i:7130205 original size:20 final size:18
Alignment explanation
Indices: 7130164--7130199 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
7130154 TTTGATGGTG
*
7130164 ATTTGATTTTTTATACTA
1 ATTTGATTTTTTAAACTA
7130182 ATTTGATTTTTTAAACTA
1 ATTTGATTTTTTAAACTA
7130200 GAATTTTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.58
Consensus pattern (18 bp):
ATTTGATTTTTTAAACTA
Found at i:7130926 original size:96 final size:97
Alignment explanation
Indices: 7130815--7131041 Score: 377
Period size: 96 Copynumber: 2.4 Consensus size: 97
7130805 GGAATAAATT
* * *
7130815 TTTTTTATTTCTTATGTACCAAATAATTAATCTTTTTTAAATACAACTTAACGATGCATGGTATG
1 TTTTCTATTTTTTATGTACCAAATAATTAATCTTTTTTAAATACAACTTAACGATGCATGGCATG
7130880 A-AAAAACTTAATATCGATTGTGGAGTTAAAA
66 ACAAAAACTTAATATCGATTGTGGAGTTAAAA
7130911 TTTTCTATTTTTTATGTACCAAATAATTAAAT-TTTTTTAAATACAACTTAACGATGCATGGCAT
1 TTTTCTATTTTTTATGTACCAAATAATT-AATCTTTTTTAAATACAACTTAACGATGCATGGCAT
7130975 GACAAAAACTTAATATCGATTGTGGAGTTAAAA
65 GACAAAAACTTAATATCGATTGTGGAGTTAAAA
* * *
7131008 TTTTCTATTTTTTTTGCACCAAATAATTATTCTT
1 TTTTCTATTTTTTATGTACCAAATAATTAATCTT
7131042 AAATTAATCA
Statistics
Matches: 122, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
96 61 0.50
97 61 0.50
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (97 bp):
TTTTCTATTTTTTATGTACCAAATAATTAATCTTTTTTAAATACAACTTAACGATGCATGGCATG
ACAAAAACTTAATATCGATTGTGGAGTTAAAA
Found at i:7131013 original size:97 final size:97
Alignment explanation
Indices: 7130815--7131036 Score: 376
Period size: 97 Copynumber: 2.3 Consensus size: 97
7130805 GGAATAAATT
* * *
7130815 TTTTTTATTTCTTATGTACCAAATAATT-AATCTTTTTTAAATACAACTTAACGATGCATGGTAT
1 TTTTCTATTTTTTATGTACCAAATAATTAAATCTTTTTTAAATACAACTTAACGATGCATGGCAT
7130879 GAAAAAACTTAATATCGATTGTGGAGTTAAAA
66 GAAAAAACTTAATATCGATTGTGGAGTTAAAA
7130911 TTTTCTATTTTTTATGTACCAAATAATTAAAT-TTTTTTAAATACAACTTAACGATGCATGGCAT
1 TTTTCTATTTTTTATGTACCAAATAATTAAATCTTTTTTAAATACAACTTAACGATGCATGGCAT
7130975 GACAAAAACTTAATATCGATTGTGGAGTTAAAA
66 GA-AAAAACTTAATATCGATTGTGGAGTTAAAA
* *
7131008 TTTTCTATTTTTTTTGCACCAAATAATTA
1 TTTTCTATTTTTTATGTACCAAATAATTA
7131037 TTCTTAAATT
Statistics
Matches: 119, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
96 59 0.50
97 60 0.50
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.42
Consensus pattern (97 bp):
TTTTCTATTTTTTATGTACCAAATAATTAAATCTTTTTTAAATACAACTTAACGATGCATGGCAT
GAAAAAACTTAATATCGATTGTGGAGTTAAAA
Found at i:7132201 original size:5 final size:5
Alignment explanation
Indices: 7132191--7132240 Score: 91
Period size: 5 Copynumber: 10.0 Consensus size: 5
7132181 TTTTGGAAAG
*
7132191 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAG TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
7132241 GGAGAGTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:7134731 original size:22 final size:22
Alignment explanation
Indices: 7134688--7134729 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
7134678 TTTTTTTATT
7134688 TTTTAATATTTATATAATTTTA
1 TTTTAATATTTATATAATTTTA
7134710 TTTTAATATTTA-ATAATTTT
1 TTTTAATATTTATATAATTTT
7134730 TAAATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTAATATTTATATAATTTTA
Found at i:7135281 original size:16 final size:16
Alignment explanation
Indices: 7135262--7135297 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
7135252 TATAAATATT
* *
7135262 AATAATTATATGATTA
1 AATAATAATATGAGTA
7135278 AATAATAATATGAGTA
1 AATAATAATATGAGTA
7135294 AATA
1 AATA
7135298 GAAATGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (16 bp):
AATAATAATATGAGTA
Found at i:7135865 original size:4 final size:4
Alignment explanation
Indices: 7135856--7135881 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
7135846 TGAGTTCTGC
7135856 ATAA ATAA ATAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA AT
7135882 TTCTACACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:7146169 original size:3 final size:3
Alignment explanation
Indices: 7146161--7146192 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
7146151 AATCTAAAAT
7146161 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
7146193 GCATGAGCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:7162945 original size:6 final size:6
Alignment explanation
Indices: 7162928--7162960 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
7162918 GTGAATGCTG
*
7162928 CAGAGA CGGAGA CAGAGA CAGAGA CAGAGA CAG
1 CAGAGA CAGAGA CAGAGA CAGAGA CAGAGA CAG
7162961 CAGTGGCACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.45, C:0.18, G:0.36, T:0.00
Consensus pattern (6 bp):
CAGAGA
Found at i:7195443 original size:25 final size:25
Alignment explanation
Indices: 7195402--7195451 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
7195392 CTCATACAAA
*
7195402 AAAAAAATTAGTCTATTTTTATTTT
1 AAAAAAATTAGTCTATTTTAATTTT
*
7195427 AAAAAAATT-GCTTTATTTTAATTTT
1 AAAAAAATTAG-TCTATTTTAATTTT
7195452 TTTAATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (25 bp):
AAAAAAATTAGTCTATTTTAATTTT
Found at i:7201074 original size:5 final size:5
Alignment explanation
Indices: 7201064--7201100 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
7201054 TCCGTTATTT
*
7201064 AAAGA AAAGA AAAGAA AAAGA AAAAA AAAGA AAAGA A
1 AAAGA AAAGA AAAG-A AAAGA AAAGA AAAGA AAAGA A
7201101 GAAGGCCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:7201085 original size:16 final size:16
Alignment explanation
Indices: 7201064--7201097 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
7201054 TCCGTTATTT
*
7201064 AAAGAAAAGAAAAGAA
1 AAAGAAAAAAAAAGAA
7201080 AAAGAAAAAAAAAGAA
1 AAAGAAAAAAAAAGAA
7201096 AA
1 AA
7201098 GAAGAAGGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAAAAGAA
Found at i:7217394 original size:30 final size:28
Alignment explanation
Indices: 7217342--7217404 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
7217332 TGATACATAG
7217342 TAAAATTTTAATTTGACTTTT-AAAATGA
1 TAAAATTTTAATTTGACTTTTAAAAAT-A
*
7217370 TAAAATTTTAATTTAGTTCTTTTAAAAATA
1 TAAAATTTTAATTT-G-ACTTTTAAAAATA
7217400 TAAAA
1 TAAAA
7217405 ATATATGCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 14 0.45
29 1 0.03
30 11 0.35
31 5 0.16
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (28 bp):
TAAAATTTTAATTTGACTTTTAAAAATA
Found at i:7220755 original size:2 final size:2
Alignment explanation
Indices: 7220748--7220773 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7220738 ATATACTCAC
7220748 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
7220774 CTTGTAATCA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7221770 original size:6 final size:6
Alignment explanation
Indices: 7221759--7221784 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
7221749 TATCTCCAGG
7221759 ATGTCA ATGTCA ATGTCA ATGTCA AT
1 ATGTCA ATGTCA ATGTCA ATGTCA AT
7221785 TTGCAGACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (6 bp):
ATGTCA
Found at i:7224856 original size:19 final size:20
Alignment explanation
Indices: 7224813--7224865 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
7224803 AAAAAATACC
7224813 AAAATTATTGACTAAAGCATTA
1 AAAATT-TTGA-TAAAGCATTA
*
7224835 AAAATTTTGATAAAG-GTTA
1 AAAATTTTGATAAAGCATTA
*
7224854 AAAAATTTGATA
1 AAAATTTTGATA
7224866 TTGGTATACT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 14 0.48
20 5 0.17
21 4 0.14
22 6 0.21
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.34
Consensus pattern (20 bp):
AAAATTTTGATAAAGCATTA
Found at i:7228078 original size:15 final size:16
Alignment explanation
Indices: 7228058--7228091 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
7228048 AATTTTTTTA
7228058 AAATTATAAAAAT-AT
1 AAATTATAAAAATAAT
*
7228073 AAATTATTAAAATAAT
1 AAATTATAAAAATAAT
7228089 AAA
1 AAA
7228092 ATCATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATAAT
Found at i:7229179 original size:1 final size:1
Alignment explanation
Indices: 7229175--7229200 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
7229165 GTTCAAAAGC
7229175 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
7229201 GGTTTTTATT
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:7244169 original size:31 final size:31
Alignment explanation
Indices: 7244134--7244198 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
7244124 AGTGGTGAAT
7244134 TTATGTAAATAGAATTCTCGGCCAGAGCCAA
1 TTATGTAAATAGAATTCTCGGCCAGAGCCAA
7244165 TTATGTAAATAGAATTCTCGGCCAGAGCCAA
1 TTATGTAAATAGAATTCTCGGCCAGAGCCAA
7244196 TTA
1 TTA
7244199 CTTATTCGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (31 bp):
TTATGTAAATAGAATTCTCGGCCAGAGCCAA
Found at i:7248581 original size:46 final size:47
Alignment explanation
Indices: 7248514--7248608 Score: 140
Period size: 46 Copynumber: 2.0 Consensus size: 47
7248504 CAGTTGATAC
* * *
7248514 AATTACTTATTAAAATGATATTA-TT-TAAATTTTAATATGAGGTTAA
1 AATTACTTATGAAAATGATATTACTTGGAAA-TTTAATATGAGGCTAA
7248560 AATTACTTATGAAAATGATATTACTTGGAAATTTAATATGAGGCTAA
1 AATTACTTATGAAAATGATATTACTTGGAAATTTAATATGAGGCTAA
7248607 AA
1 AA
7248609 AATATCCAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
46 22 0.50
47 19 0.43
48 3 0.07
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.40
Consensus pattern (47 bp):
AATTACTTATGAAAATGATATTACTTGGAAATTTAATATGAGGCTAA
Found at i:7251642 original size:6 final size:6
Alignment explanation
Indices: 7251631--7251670 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
7251621 TATAAAATTA
7251631 TATATT TATATT TATA-- -ATATT TATATT TATA-T TATATT TA
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TA
7251671 AATAAATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
3 3 0.10
5 5 0.17
6 22 0.73
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TATATT
Found at i:7251643 original size:29 final size:25
Alignment explanation
Indices: 7251605--7251674 Score: 70
Period size: 29 Copynumber: 2.6 Consensus size: 25
7251595 ATTTGACGTA
7251605 ATATT-TATTTCAAATATATAAAATTAT
1 ATATTATATTT-AAATAT-TAAAATT-T
* *
7251632 ATATTTATATTTATAATATTTATATTT
1 ATA-TTATATTTA-AATATTAAAATTT
7251659 ATATTATATTTAAATA
1 ATATTATATTTAAATA
7251675 AATATTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
25 4 0.11
26 9 0.24
27 7 0.18
28 8 0.21
29 10 0.26
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (25 bp):
ATATTATATTTAAATATTAAAATTT
Found at i:7251652 original size:15 final size:15
Alignment explanation
Indices: 7251628--7251661 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
7251618 ATATATAAAA
7251628 TTAT-ATATTTATAT
1 TTATAATATTTATAT
7251642 TTATAATATTTATAT
1 TTATAATATTTATAT
7251657 TTATA
1 TTATA
7251662 TTATATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATAATATTTATAT
Found at i:7251863 original size:7 final size:7
Alignment explanation
Indices: 7251836--7251866 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
7251826 AATACAGCCC
*
7251836 AAGTGGC
1 AAGTGGT
7251843 AAGTGGT
1 AAGTGGT
7251850 AAGTGGT
1 AAGTGGT
7251857 AAGTGGT
1 AAGTGGT
7251864 AAG
1 AAG
7251867 AGGGATGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.32, C:0.03, G:0.42, T:0.23
Consensus pattern (7 bp):
AAGTGGT
Found at i:7257679 original size:42 final size:42
Alignment explanation
Indices: 7257622--7257753 Score: 221
Period size: 42 Copynumber: 3.1 Consensus size: 42
7257612 CCTTCTTCTT
7257622 CAGCCAAG-CCAGTGGCAACTACTGCCTCTGTTCCATCTTCCC
1 CAGCCAAGTCC-GTGGCAACTACTGCCTCTGTTCCATCTTCCC
7257664 CAGCCAAGTCCGTGGCAACTACTGCCTCTGTTCCATCTTCCC
1 CAGCCAAGTCCGTGGCAACTACTGCCTCTGTTCCATCTTCCC
* * *
7257706 CAGCCAAGTCCGTGGCAACTACGGCCTCTGTTCCAACTTCTC
1 CAGCCAAGTCCGTGGCAACTACTGCCTCTGTTCCATCTTCCC
7257748 CAGCCA
1 CAGCCA
7257754 GGACAGTTGC
Statistics
Matches: 86, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
42 84 0.98
43 2 0.02
ACGTcount: A:0.19, C:0.40, G:0.17, T:0.23
Consensus pattern (42 bp):
CAGCCAAGTCCGTGGCAACTACTGCCTCTGTTCCATCTTCCC
Found at i:7257777 original size:84 final size:84
Alignment explanation
Indices: 7257622--7257777 Score: 206
Period size: 84 Copynumber: 1.9 Consensus size: 84
7257612 CCTTCTTCTT
* * * * *
7257622 CAGCCAAGCCAGTGGCAACTACTGCCTCTGTTCCATCTTCCCCAGCCAAGTCCGTGGCAACTACT
1 CAGCCAAGCCAGTGGCAACTACGGCCTCTGTTCCAACTTCCCCAGCCAAGACAGTGGCAACCACT
7257687 GCCTCTGTTCCATCTTCCC
66 GCCTCTGTTCCATCTTCCC
* * * *
7257706 CAGCCAAGTCC-GTGGCAACTACGGCCTCTGTTCCAACTTCTCCAGCCAGGACAGTTGCAACCGC
1 CAGCCAAG-CCAGTGGCAACTACGGCCTCTGTTCCAACTTCCCCAGCCAAGACAGTGGCAACCAC
*
7257770 TGTCTCTG
65 TGCCTCTG
7257778 CACCAACTTC
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
84 59 0.97
85 2 0.03
ACGTcount: A:0.19, C:0.38, G:0.19, T:0.24
Consensus pattern (84 bp):
CAGCCAAGCCAGTGGCAACTACGGCCTCTGTTCCAACTTCCCCAGCCAAGACAGTGGCAACCACT
GCCTCTGTTCCATCTTCCC
Found at i:7262622 original size:18 final size:18
Alignment explanation
Indices: 7262599--7262634 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
7262589 TATAATACTT
*
7262599 TATATTATGTTATTTATA
1 TATATTATGTAATTTATA
7262617 TATATTATGTAATTTATA
1 TATATTATGTAATTTATA
7262635 ACACATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (18 bp):
TATATTATGTAATTTATA
Found at i:7263463 original size:18 final size:18
Alignment explanation
Indices: 7263425--7263463 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
7263415 GAAAATTTTG
*
7263425 AAATTAAAATTATTATAA
1 AAATTAAAATTATTAAAA
*
7263443 AAATTAAACTTATTAAAA
1 AAATTAAAATTATTAAAA
7263461 AAA
1 AAA
7263464 ACAAATTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATTAAAATTATTAAAA
Found at i:7269181 original size:18 final size:18
Alignment explanation
Indices: 7269158--7269227 Score: 88
Period size: 18 Copynumber: 3.9 Consensus size: 18
7269148 AAAATGCAGG
*
7269158 AAATGATGTTAACATTTT
1 AAATGATGTTAACATTTC
* * *
7269176 AAATGATATTAACACTGC
1 AAATGATGTTAACATTTC
7269194 AAATGATGTTCAA-ATTTC
1 AAATGATGTT-AACATTTC
7269212 AAATGATGTTAACATT
1 AAATGATGTTAACATT
7269228 GATGAACACG
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
17 2 0.05
18 39 0.91
19 2 0.05
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.37
Consensus pattern (18 bp):
AAATGATGTTAACATTTC
Found at i:7269747 original size:72 final size:72
Alignment explanation
Indices: 7269659--7269913 Score: 395
Period size: 72 Copynumber: 3.6 Consensus size: 72
7269649 AATGTTAAAC
7269659 TAGTTTTATCAATAGTTGTTTATGTTTGATTTTTGGATATTGAATTTATGTTCTACTTATTTATG
1 TAGTTTTATCAATAGTTGTTTATGTTTGATTTTTGGATATTGAATTTATGTTCTACTTATTTATG
7269724 TGTAATT
66 TGTAATT
* * * * *
7269731 TGGTTTTATCAATAGTTGTTTATGTTTGGTTCTTGAATATTGAATTTATATTCTACTTATTTATG
1 TAGTTTTATCAATAGTTGTTTATGTTTGATTTTTGGATATTGAATTTATGTTCTACTTATTTATG
* *
7269796 TGCAATC
66 TGTAATT
* * *
7269803 TAATTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTAAATTTATGTTCTACTTATTTATG
1 TAGTTTTATCAATAGTTGTTTATGTTTGATTTTTGGATATTGAATTTATGTTCTACTTATTTATG
*
7269868 TGTATTT
66 TGTAATT
*
7269875 TAGTTTTATCAATAGTTGTTTATATTTGA-TTTTGGATAT
1 TAGTTTTATCAATAGTTGTTTATGTTTGATTTTTGGATAT
7269914 AAAATTTGTT
Statistics
Matches: 164, Mismatches: 19, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
71 10 0.06
72 154 0.94
ACGTcount: A:0.24, C:0.05, G:0.15, T:0.56
Consensus pattern (72 bp):
TAGTTTTATCAATAGTTGTTTATGTTTGATTTTTGGATATTGAATTTATGTTCTACTTATTTATG
TGTAATT
Found at i:7273458 original size:21 final size:20
Alignment explanation
Indices: 7273434--7273515 Score: 62
Period size: 22 Copynumber: 4.0 Consensus size: 20
7273424 AAATTTATAA
7273434 AAATTTTAATGATATTTTTAT
1 AAATTTTAAT-ATATTTTTAT
*
7273455 AAATTTTAAAAATAATTTTTA-
1 AAATTTT-AATAT-ATTTTTAT
7273476 AATATTTT-ATA-ATTTTTAAT
1 AA-ATTTTAATATATTTTT-AT
**
7273496 AGCTTTTAATTATATTTTTA
1 AAATTTTAA-TATATTTTTA
7273516 CAATTTTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
18 6 0.12
19 5 0.10
20 4 0.08
21 14 0.29
22 20 0.41
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.56
Consensus pattern (20 bp):
AAATTTTAATATATTTTTAT
Found at i:7273475 original size:22 final size:21
Alignment explanation
Indices: 7273433--7273484 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
7273423 TAAATTTATA
**
7273433 AAAATTTTAATGAT-ATTTTT
1 AAAATTTTAAAAATAATTTTT
7273453 ATAAATTTTAAAAATAATTTTT
1 A-AAATTTTAAAAATAATTTTT
7273475 AAATATTTTA
1 AAA-ATTTTA
7273485 TAATTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 1 0.04
21 13 0.48
22 13 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
AAAATTTTAAAAATAATTTTT
Found at i:7273505 original size:17 final size:18
Alignment explanation
Indices: 7273466--7273506 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
7273456 AATTTTAAAA
*
7273466 ATAATTTTTAAATATTTT
1 ATAATTTTTAAATACTTT
7273484 ATAATTTTT-AATAGCTTT
1 ATAATTTTTAAATA-CTTT
7273502 -TAATT
1 ATAATT
7273507 ATATTTTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (18 bp):
ATAATTTTTAAATACTTT
Found at i:7273515 original size:31 final size:30
Alignment explanation
Indices: 7273437--7273524 Score: 81
Period size: 31 Copynumber: 2.8 Consensus size: 30
7273427 TTTATAAAAA
* *
7273437 TTTTAATGATATTTTTATAAATTTTAAAAATAAT
1 TTTTAAT-ATATTTTTAT-AATTTT--TAATAAC
*
7273471 TTTTAA-ATA-TTTTATAATTTTTAATAGC
1 TTTTAATATATTTTTATAATTTTTAATAAC
*
7273499 TTTTAATTATATTTTTACAATTTTTA
1 TTTTAA-TATATTTTTATAATTTTTA
7273525 TTTTAAAAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
28 10 0.21
30 9 0.19
31 19 0.40
32 3 0.06
34 6 0.13
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (30 bp):
TTTTAATATATTTTTATAATTTTTAATAAC
Found at i:7273805 original size:3 final size:3
Alignment explanation
Indices: 7273797--7273826 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
7273787 ATTATAAGAA
7273797 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
7273827 TTAAAAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:7273999 original size:8 final size:8
Alignment explanation
Indices: 7273986--7274029 Score: 52
Period size: 8 Copynumber: 5.1 Consensus size: 8
7273976 TATAATTGCA
7273986 ATAATTTT
1 ATAATTTT
7273994 ATAATTTTTT
1 ATAA--TTTT
*
7274004 ATAATTGTA
1 ATAATT-TT
7274013 ATAATTTT
1 ATAATTTT
7274021 ATAATTTT
1 ATAATTTT
7274029 A
1 A
7274030 AATAATTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
8 16 0.52
9 7 0.23
10 8 0.26
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (8 bp):
ATAATTTT
Found at i:7274022 original size:17 final size:18
Alignment explanation
Indices: 7274000--7274036 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
7273990 TTTTATAATT
7274000 TTTTATAATTGT-AATAA
1 TTTTATAATTGTAAATAA
*
7274017 TTTTATAATTTTAAATAA
1 TTTTATAATTGTAAATAA
7274035 TT
1 TT
7274037 ATTAAAAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TTTTATAATTGTAAATAA
Found at i:7274033 original size:18 final size:18
Alignment explanation
Indices: 7273986--7274036 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
7273976 TATAATTGCA
*
7273986 ATAATTTTATAAT-TTTTT
1 ATAATTTTA-AATAATTTT
*
7274004 ATAATTGT-AATAATTTT
1 ATAATTTTAAATAATTTT
7274021 ATAATTTTAAATAATT
1 ATAATTTTAAATAATT
7274037 ATTAAAAGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 3 0.11
17 11 0.39
18 14 0.50
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
ATAATTTTAAATAATTTT
Found at i:7274036 original size:27 final size:27
Alignment explanation
Indices: 7273963--7274028 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
7273953 AATTTCTTAT
7273963 ATTTT-TAATTTTTTATAATTGCAATA
1 ATTTTATAATTTTTTATAATTGCAATA
*
7273989 ATTTTATAATTTTTTATAATTGTAATA
1 ATTTTATAATTTTTTATAATTGCAATA
7274016 ATTTTATAATTTT
1 ATTTTATAATTTT
7274029 AAATAATTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 5 0.13
27 33 0.87
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.61
Consensus pattern (27 bp):
ATTTTATAATTTTTTATAATTGCAATA
Found at i:7279938 original size:16 final size:17
Alignment explanation
Indices: 7279917--7279949 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
7279907 TTGGTTAAAC
*
7279917 AATTTTTAATT-TTTAT
1 AATTTTAAATTATTTAT
7279933 AATTTTAAATTATTTAT
1 AATTTTAAATTATTTAT
7279950 TGATGTGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
AATTTTAAATTATTTAT
Found at i:7280417 original size:27 final size:27
Alignment explanation
Indices: 7280387--7280441 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
7280377 TTTTATAATA
7280387 TCATTCGTTGATTTGAAGGTATATATT
1 TCATTCGTTGATTTGAAGGTATATATT
7280414 TCATTCGTTGATTTGAAGGTATATATT
1 TCATTCGTTGATTTGAAGGTATATATT
7280441 T
1 T
7280442 TGAATTTGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.07, G:0.18, T:0.49
Consensus pattern (27 bp):
TCATTCGTTGATTTGAAGGTATATATT
Found at i:7286684 original size:2 final size:2
Alignment explanation
Indices: 7286679--7286720 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
7286669 AAATTAAAAA
7286679 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7286721 GTTACAAGAG
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):
AT
Found at i:7287365 original size:5 final size:5
Alignment explanation
Indices: 7287355--7287379 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
7287345 TCGCATGATC
7287355 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
7287380 ATATCTAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:7295286 original size:9 final size:9
Alignment explanation
Indices: 7295272--7295340 Score: 59
Period size: 9 Copynumber: 7.4 Consensus size: 9
7295262 TTGCTACTCC
*
7295272 TTTTATAGT
1 TTTTATAAT
7295281 TTTTATAAT
1 TTTTATAAT
*
7295290 TTTTGGAAAAT
1 TTTT--ATAAT
*
7295301 TTTAAT-AT
1 TTTTATAAT
*
7295309 TTTTATCAT
1 TTTTATAAT
*
7295318 TTTAATAATT
1 TTTTATAA-T
7295328 TTTTATAAT
1 TTTTATAAT
7295337 TTTT
1 TTTT
7295341 TTTGTAATCT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
8 7 0.15
9 26 0.54
10 8 0.17
11 7 0.15
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:7295481 original size:40 final size:41
Alignment explanation
Indices: 7295409--7295488 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 41
7295399 TTTATCATAT
* *
7295409 TTAATAAGTTTTCTACATTTTTTATATCATTTTAATAATTA
1 TTAATAAGTTTTCTACAATTTTTAAATCATTTTAATAATTA
* *
7295450 TTAATAA-TTTTCTATAATTTTTACAAT-ATTTTAGTAATT
1 TTAATAAGTTTTCTACAATTTTTA-AATCATTTTAATAATT
7295489 TTAGGCTTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 25 0.74
41 9 0.26
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (41 bp):
TTAATAAGTTTTCTACAATTTTTAAATCATTTTAATAATTA
Found at i:7297481 original size:14 final size:15
Alignment explanation
Indices: 7297462--7297490 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
7297452 GCATGAAGTA
7297462 AAACTTA-GATGCTT
1 AAACTTATGATGCTT
7297476 AAACTTATGATGCTT
1 AAACTTATGATGCTT
7297491 GTAAATACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (15 bp):
AAACTTATGATGCTT
Found at i:7299017 original size:16 final size:16
Alignment explanation
Indices: 7298997--7299028 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
7298987 AATTTTTTAC
7298997 ATTTTTT-TAATTTTT
1 ATTTTTTATAATTTTT
7299012 ATTTTTTATAATTTTT
1 ATTTTTTATAATTTTT
7299028 A
1 A
7299029 AATTATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
ATTTTTTATAATTTTT
Found at i:7299028 original size:9 final size:9
Alignment explanation
Indices: 7298985--7299032 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
7298975 GTAATTCTTG
7298985 ATAATTTTT
1 ATAATTTTT
7298994 -TACATTTTT
1 ATA-ATTTTT
*
7299003 TTAATTTTT
1 ATAATTTTT
7299012 AT--TTTTT
1 ATAATTTTT
7299019 ATAATTTTT
1 ATAATTTTT
7299028 A-AATT
1 ATAATT
7299033 ATTTTTTGAC
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
7 7 0.21
8 6 0.18
9 19 0.56
10 2 0.06
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (9 bp):
ATAATTTTT
Found at i:7302828 original size:26 final size:26
Alignment explanation
Indices: 7302792--7302872 Score: 144
Period size: 26 Copynumber: 3.1 Consensus size: 26
7302782 ACGACCGCAA
*
7302792 AATCTACTTCTCTTCTTCTAAATCTC
1 AATCTACTTCTCTTCATCTAAATCTC
7302818 AATCTACTTCTCTTCATCTAAATCTC
1 AATCTACTTCTCTTCATCTAAATCTC
*
7302844 AATCTACTTCTCTTCATCTAAATTTC
1 AATCTACTTCTCTTCATCTAAATCTC
7302870 AAT
1 AAT
7302873 GATACATAGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.27, C:0.28, G:0.00, T:0.44
Consensus pattern (26 bp):
AATCTACTTCTCTTCATCTAAATCTC
Found at i:7305758 original size:2 final size:2
Alignment explanation
Indices: 7305751--7305793 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
7305741 GTATTGCTAT
7305751 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
7305793 T
1 T
7305794 TCATTTAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7309316 original size:4 final size:4
Alignment explanation
Indices: 7309307--7309368 Score: 63
Period size: 4 Copynumber: 15.2 Consensus size: 4
7309297 AAATAAACGG
* * *
7309307 GAAA GAAA GAGAG GAAA GAAA GAAA GAAA GAAG GAGAG GAAA GAAA G-AA
1 GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA
*
7309356 GAAG GAAA GAAA G
1 GAAA GAAA GAAA G
7309369 GTAATGTGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
3 3 0.06
4 39 0.80
5 7 0.14
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:7309329 original size:17 final size:19
Alignment explanation
Indices: 7309307--7309368 Score: 83
Period size: 20 Copynumber: 3.3 Consensus size: 19
7309297 AAATAAACGG
7309307 GAAAGAAAG-AG-AGGAAA
1 GAAAGAAAGAAGAAGGAAA
*
7309324 GAAAGAAAGAAAGAAGGAGAG
1 GAAAGAAAG-AAGAAGGA-AA
7309345 GAAAGAAAGAAGAAGGAAA
1 GAAAGAAAGAAGAAGGAAA
7309364 GAAAG
1 GAAAG
7309369 GTAATGTGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
17 9 0.23
19 8 0.21
20 12 0.31
21 10 0.26
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (19 bp):
GAAAGAAAGAAGAAGGAAA
Found at i:7309335 original size:25 final size:24
Alignment explanation
Indices: 7309307--7309365 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 24
7309297 AAATAAACGG
7309307 GAAAGAAAGAGAGGAAAGAAAGAAA
1 GAAAGAAAGAGAGGAAAGAAAG-AA
*
7309332 GAAAGAAGGAGAGGAAAGAAAGAA
1 GAAAGAAAGAGAGGAAAGAAAGAA
*
7309356 GAAGGAAAGA
1 GAAAGAAAGA
7309366 AAGGTAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
24 10 0.32
25 21 0.68
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (24 bp):
GAAAGAAAGAGAGGAAAGAAAGAA
Found at i:7313382 original size:12 final size:12
Alignment explanation
Indices: 7313367--7313391 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7313357 ACAATTCATA
7313367 TCACTTTCAATT
1 TCACTTTCAATT
7313379 TCACTTTCAATT
1 TCACTTTCAATT
7313391 T
1 T
7313392 TGATCACAAA
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:0.24, G:0.00, T:0.52
Consensus pattern (12 bp):
TCACTTTCAATT
Found at i:7313564 original size:22 final size:22
Alignment explanation
Indices: 7313538--7313583 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
7313528 TAAACATATA
7313538 ATATTTCACATATACATTGTTC
1 ATATTTCACATATACATTGTTC
7313560 ATATTTCACATATACATTGTTC
1 ATATTTCACATATACATTGTTC
7313582 AT
1 AT
7313584 CACATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (22 bp):
ATATTTCACATATACATTGTTC
Found at i:7313588 original size:18 final size:20
Alignment explanation
Indices: 7313542--7313591 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
7313532 CATATAATAT
7313542 TTCACATATACATTGTTCATA
1 TTCACATATACATTGTTCA-A
7313563 TTTCACATATACATTGTTC-A
1 -TTCACATATACATTGTTCAA
7313583 -TCACATATA
1 TTCACATATA
7313592 TATCATCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.32
20 1 0.04
22 18 0.64
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (20 bp):
TTCACATATACATTGTTCAA
Found at i:7315331 original size:21 final size:21
Alignment explanation
Indices: 7315305--7315350 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
7315295 TTAGGGTCCA
*
7315305 ATTGCCCCGGAGGAGTAGAGT
1 ATTGCCCCGGAGGAGTAAAGT
**
7315326 ATTGCCTGGGAGGAGTAAAGT
1 ATTGCCCCGGAGGAGTAAAGT
7315347 ATTG
1 ATTG
7315351 TGGTGGCTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.13, G:0.37, T:0.24
Consensus pattern (21 bp):
ATTGCCCCGGAGGAGTAAAGT
Found at i:7317372 original size:16 final size:16
Alignment explanation
Indices: 7317351--7317400 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
7317341 TGATGGGGGT
7317351 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
7317367 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
7317382 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
7317397 ATTA
1 ATTA
7317401 GCTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:7317681 original size:4 final size:4
Alignment explanation
Indices: 7317674--7317710 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
7317664 CTTCCTTCTC
*
7317674 CTTT CTTT CTTT CTTT CTTT CTATT TTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CT-TT CTTT CTTT CTTT
7317711 TTCCCTCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 27 0.90
5 3 0.10
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.76
Consensus pattern (4 bp):
CTTT
Found at i:7318676 original size:9 final size:9
Alignment explanation
Indices: 7318664--7318698 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
7318654 AAAATTAAAA
7318664 AAAAATTAT
1 AAAAATTAT
7318673 AAAAATTAT
1 AAAAATTAT
7318682 AAAACATTAT
1 AAAA-ATTAT
*
7318692 TAAAATT
1 AAAAATT
7318699 TACTTATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:7330520 original size:82 final size:82
Alignment explanation
Indices: 7330381--7330539 Score: 282
Period size: 82 Copynumber: 1.9 Consensus size: 82
7330371 AATCCGGAAG
* * *
7330381 AATTCATGCTTATCAACAAAGAAAAGCATCGCCAGGTGTCAAGCTTCAAGAACATGAAGTGATGG
1 AATTCATGCTTATCAACAAAGAAAAGCATCGCCAGATGTCAAGCTTCAACAAAATGAAGTGATGG
7330446 CAGAGTTATCTGATAAA
66 CAGAGTTATCTGATAAA
7330463 AATTCATGCTTATCAACAAAGAAAAGCATCGCCAGATGTCAAGCTTCAACAAAATGAAGTGATGG
1 AATTCATGCTTATCAACAAAGAAAAGCATCGCCAGATGTCAAGCTTCAACAAAATGAAGTGATGG
*
7330528 CATAGTTATCTG
66 CAGAGTTATCTG
7330540 GAGGCATCCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 73 1.00
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (82 bp):
AATTCATGCTTATCAACAAAGAAAAGCATCGCCAGATGTCAAGCTTCAACAAAATGAAGTGATGG
CAGAGTTATCTGATAAA
Found at i:7332297 original size:24 final size:23
Alignment explanation
Indices: 7332219--7332300 Score: 94
Period size: 23 Copynumber: 3.5 Consensus size: 23
7332209 TAATGTTCAT
7332219 GAACATGTTCATTTAAC-TTAATC
1 GAACATGTTCA-TTAACATTAATC
* ** *
7332242 AAACATGTTCACAAACATTAAAC
1 GAACATGTTCATTAACATTAATC
*
7332265 GAACATGTTCATTAACATATAATT
1 GAACATGTTCATTAACAT-TAATC
7332289 GAACATGTTCAT
1 GAACATGTTCAT
7332301 GAATAATGTA
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
22 3 0.06
23 30 0.62
24 15 0.31
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (23 bp):
GAACATGTTCATTAACATTAATC
Found at i:7332315 original size:24 final size:24
Alignment explanation
Indices: 7332265--7332312 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
7332255 AACATTAAAC
* *
7332265 GAACATGTTCATTAACATATAATT
1 GAACATGTTCATGAAAATATAATT
*
7332289 GAACATGTTCATGAATAATGTAAT
1 GAACATGTTCATGAA-AATATAAT
7332313 GAATAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (24 bp):
GAACATGTTCATGAAAATATAATT
Found at i:7332348 original size:4 final size:4
Alignment explanation
Indices: 7332341--7332382 Score: 75
Period size: 4 Copynumber: 10.5 Consensus size: 4
7332331 CAAACAATAA
*
7332341 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ACAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
7332383 TATTTTGATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:7335375 original size:23 final size:24
Alignment explanation
Indices: 7335334--7335384 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
7335324 ATAAAGAGAG
*
7335334 AGAGAGAAAAAAAGTAGAATG-TT
1 AGAGAGAAAAAAAGTAGAAAGATT
*
7335357 AGAGAGTAATAAAAG-AGAAAGATT
1 AGAGAG-AAAAAAAGTAGAAAGATT
7335381 AGAG
1 AGAG
7335385 TGCAATTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.16
Consensus pattern (24 bp):
AGAGAGAAAAAAAGTAGAAAGATT
Found at i:7351447 original size:22 final size:22
Alignment explanation
Indices: 7351400--7351450 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
7351390 AAAAATTTTC
* * *
7351400 TAAAAATGAAAGTTACAATTAT
1 TAAAAATGAAAATTACAATAAA
7351422 TAAAAATGTAAAATTACAA-AAA
1 TAAAAATG-AAAATTACAATAAA
7351444 TAAAAAT
1 TAAAAAT
7351451 ATACTATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.27
Consensus pattern (22 bp):
TAAAAATGAAAATTACAATAAA
Found at i:7351449 original size:23 final size:22
Alignment explanation
Indices: 7351401--7351449 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
7351391 AAAATTTTCT
* ** *
7351401 AAAAATGAAAGTTACAATTATT
1 AAAAATGAAAATTACAAAAATA
7351423 AAAAATGTAAAATTACAAAAATA
1 AAAAATG-AAAATTACAAAAATA
7351446 AAAA
1 AAAA
7351450 TATACTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.24
Consensus pattern (22 bp):
AAAAATGAAAATTACAAAAATA
Found at i:7352273 original size:39 final size:39
Alignment explanation
Indices: 7352191--7352274 Score: 107
Period size: 39 Copynumber: 2.2 Consensus size: 39
7352181 TTTTTTCGAT
*
7352191 TTCTAATAATTTTTATAAAACTTTACAATATTTTACAAT
1 TTCTAATAATTTTTATAAAACTTTACAATATTTTACAAA
*** *
7352230 TTCTAATAATTTTTATAATTTTTTACAATTTATTTA-AAA
1 TTCTAATAATTTTTATAAAACTTTACAATAT-TTTACAAA
7352269 TTCTAA
1 TTCTAA
7352275 CATGTTTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 35 0.90
40 4 0.10
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.52
Consensus pattern (39 bp):
TTCTAATAATTTTTATAAAACTTTACAATATTTTACAAA
Found at i:7356632 original size:3 final size:3
Alignment explanation
Indices: 7356624--7356649 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
7356614 GCATTCTGTT
7356624 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
7356650 CTTTTTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:7361987 original size:12 final size:12
Alignment explanation
Indices: 7361951--7361979 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
7361941 AACCTAAAAT
7361951 TTTA-AGATATA
1 TTTATAGATATA
7361962 TTTATAGATATA
1 TTTATAGATATA
7361974 TTTATA
1 TTTATA
7361980 TATTTATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TTTATAGATATA
Found at i:7363352 original size:23 final size:23
Alignment explanation
Indices: 7363317--7363361 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
7363307 AAAATTTTGT
*
7363317 TTTTTAATATTATTATAGATTTAC
1 TTTTTAATATTA-TATAAATTTAC
*
7363341 TTTTT-ATGTTATATAAATTTA
1 TTTTTAATATTATATAAATTTA
7363362 ATAATATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 9 0.47
23 5 0.26
24 5 0.26
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTTAATATTATATAAATTTAC
Found at i:7368803 original size:24 final size:24
Alignment explanation
Indices: 7368767--7368828 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
7368757 CTTGGAACTA
*
7368767 AATATTAT-TTTTTATAATTTTA-T
1 AATATTATATTTTTA-ATTTTTATT
7368790 AATATTTATATTTTTAATTTTTATT
1 AATA-TTATATTTTTAATTTTTATT
*
7368815 AACATTATATTTTT
1 AATATTATATTTTT
7368829 TTGGTAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 4 0.12
24 20 0.59
25 10 0.29
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
AATATTATATTTTTAATTTTTATT
Found at i:7368807 original size:15 final size:17
Alignment explanation
Indices: 7368777--7368813 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
7368767 AATATTATTT
7368777 TTTATAATTTTATAATA
1 TTTATAATTTTATAATA
*
7368794 TTTAT-ATTTT-TAATT
1 TTTATAATTTTATAATA
7368809 TTTAT
1 TTTAT
7368814 TAACATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 9 0.47
16 5 0.26
17 5 0.26
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTATAATTTTATAATA
Found at i:7368828 original size:25 final size:24
Alignment explanation
Indices: 7368771--7368829 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
7368761 GAACTAAATA
*
7368771 TTATTTTTTATAATTTTATAATAT
1 TTATTTTTTATAATTTTATAACAT
*
7368795 TTATATTTTTA-ATTTTTATTAACAT
1 TTAT-TTTTTATAATTTTA-TAACAT
7368820 TATATTTTTT
1 T-TATTTTTT
7368830 TGGTAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 10 0.33
25 17 0.57
26 3 0.10
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (24 bp):
TTATTTTTTATAATTTTATAACAT
Done.