Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008242.1 Hibiscus syriacus cultivar Beakdansim tig00110890_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 16962412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 58 of 73
Found at i:13535799 original size:25 final size:25
Alignment explanation
Indices: 13535766--13535826 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 25
13535756 TTTGAAAATA
13535766 TTTTTAAAATATATATAATATATAG
1 TTTTTAAAATATATATAATATATAG
* * *
13535791 TTTTGAAAACATTTATATATTATATAG
1 TTTT-TAAA-ATATATATAATATATAG
13535818 TTTTTAAAA
1 TTTTTAAAA
13535827 CATTTTGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
25 5 0.17
26 6 0.20
27 19 0.63
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (25 bp):
TTTTTAAAATATATATAATATATAG
Found at i:13535815 original size:27 final size:27
Alignment explanation
Indices: 13535777--13535831 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
13535767 TTTTAAAATA
13535777 TATATAATATATAGTTTTGAAAACATT
1 TATATAATATATAGTTTTGAAAACATT
* *
13535804 TATATATTATATAGTTTTTAAAACATT
1 TATATAATATATAGTTTTGAAAACATT
13535831 T
1 T
13535832 TGAAAACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (27 bp):
TATATAATATATAGTTTTGAAAACATT
Found at i:13535833 original size:38 final size:37
Alignment explanation
Indices: 13535791--13536052 Score: 233
Period size: 38 Copynumber: 7.1 Consensus size: 37
13535781 TAATATATAG
* *
13535791 TTTTGAAAACATTTATATATTATATAGTTTTTAAAACA
1 TTTTGAAAACA-TTATATAATATATAGTTTTAAAAACA
* *
13535829 TTTTGAAAAC-TTATATAGTATATAGTTTTTTTAAAACAA
1 TTTTGAAAACATTATATAATATATAG--TTTTAAAAAC-A
* **
13535868 TTTTGAAAA-ATTATATAATATATAATTTTAAAAATGTTT
1 TTTTGAAAACATTATATAATATATAGTTTTAAAAA---CA
* **
13535907 TTTTGAAAA-ATTATATAACATATAACTTTAAAAACA
1 TTTTGAAAACATTATATAATATATAGTTTTAAAAACA
13535943 TTTTTGGAAAA-ATTATATAATATATAGTTTTAAAAACA
1 -TTTT-GAAAACATTATATAATATATAGTTTTAAAAACA
13535981 TTTTTTGAAAAC-TTATAT-A-ATAT--TTTT-AAAACA
1 --TTTTGAAAACATTATATAATATATAGTTTTAAAAACA
* *
13536014 TTTTGAAAAC--TATATAATATATAGTTTTGAAAACT
1 TTTTGAAAACATTATATAATATATAGTTTTAAAAACA
13536049 TTTT
1 TTTT
13536053 TAAATATAAT
Statistics
Matches: 194, Mismatches: 14, Indels: 35
0.80 0.06 0.14
Matches are distributed among these distances:
30 5 0.03
31 11 0.06
32 4 0.02
33 6 0.03
34 8 0.04
35 9 0.05
36 18 0.09
37 13 0.07
38 60 0.31
39 60 0.31
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (37 bp):
TTTTGAAAACATTATATAATATATAGTTTTAAAAACA
Found at i:13535882 original size:39 final size:37
Alignment explanation
Indices: 13535791--13536047 Score: 233
Period size: 39 Copynumber: 6.9 Consensus size: 37
13535781 TAATATATAG
* *
13535791 TTTTGAAAACATTTATATATTATATAGTTTTTAAAAC-A
1 TTTTGAAAA-A-TTATATAATATATAGTTTTAAAAACAA
* * *
13535829 TTTTGAAAACTTATATAGTATATAGTTTTTTTAAAACAA
1 TTTTGAAAAATTATATAATATATAG--TTTTAAAAACAA
* ***
13535868 TTTTGAAAAATTATATAATATATAATTTTAAAAATGTTT
1 TTTTGAAAAATTATATAATATATAGTTTTAAAAA--CAA
* ** *
13535907 TTTTGAAAAATTATATAACATATAACTTTAAAAACAT
1 TTTTGAAAAATTATATAATATATAGTTTTAAAAACAA
*
13535944 TTTTGGAAAAATTATATAATATATAGTTTTAAAAACATT
1 TTTT-GAAAAATTATATAATATATAGTTTTAAAAACA-A
*
13535983 TTTTGAAAACTTATAT-A-ATAT--TTTT-AAAAC-A
1 TTTTGAAAAATTATATAATATATAGTTTTAAAAACAA
* *
13536014 TTTTG-AAAACTATATAATATATAGTTTTGAAAAC
1 TTTTGAAAAATTATATAATATATAGTTTTAAAAAC
13536048 TTTTTTAAAT
Statistics
Matches: 187, Mismatches: 20, Indels: 27
0.80 0.09 0.12
Matches are distributed among these distances:
30 8 0.04
31 6 0.03
32 4 0.02
33 5 0.03
34 8 0.04
35 5 0.03
36 18 0.10
37 14 0.07
38 59 0.32
39 60 0.32
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (37 bp):
TTTTGAAAAATTATATAATATATAGTTTTAAAAACAA
Found at i:13536085 original size:68 final size:68
Alignment explanation
Indices: 13535861--13536077 Score: 181
Period size: 77 Copynumber: 3.1 Consensus size: 68
13535851 TAGTTTTTTT
* * ** * *
13535861 AAAACAATTTTGAAAAATTATATAATATATAATTTTAAAAATGTTTTTTTGAAAAATTATATAAC
1 AAAAC-ATTTTG-AAAACTATATAATATATAGTTTTAAAAA-CATTTTTTGAAAACTAATAT-A-
*
13535926 ATATAACTTTA
61 ATAT---TTAA
* *
13535937 AAAACATTTTTGGAAAAATTATATAATATATAGTTTTAAAAACATTTTTTGAAAACTTATATAAT
1 AAAACA-TTTT-G-AAAACTATATAATATATAGTTTTAAAAACATTTTTTGAAAACTAATATAAT
**
13536002 ATTTTT
63 ATTTAA
*
13536008 AAAACATTTTGAAAACTATATAATATATAGTTTTGAAAAC-TTTTTT-AAATA-TAATAT-ATAG
1 AAAACATTTTGAAAACTATATAATATATAGTTTTAAAAACATTTTTTGAAA-ACTAATATAATA-
13536069 TTTAA
64 TTTAA
13536074 AAAA
1 AAAA
13536078 AATATTTTTG
Statistics
Matches: 127, Mismatches: 10, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
65 3 0.02
66 15 0.12
67 7 0.06
68 27 0.21
69 1 0.01
70 4 0.03
71 9 0.07
74 4 0.03
75 2 0.02
76 26 0.20
77 29 0.23
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.42
Consensus pattern (68 bp):
AAAACATTTTGAAAACTATATAATATATAGTTTTAAAAACATTTTTTGAAAACTAATATAATATT
TAA
Found at i:13536086 original size:33 final size:32
Alignment explanation
Indices: 13535957--13536099 Score: 94
Period size: 33 Copynumber: 4.3 Consensus size: 32
13535947 TGGAAAAATT
*
13535957 ATATAATATATAGTTTTAAAAACATTTTTTGAA
1 ATATAATATATAG-TTTAAAAAAATTTTTTGAA
* * * * ***
13535990 A-ACTTATATAATATTTTTAAAACATTTTGAAAA
1 ATA-TAATAT-ATAGTTTAAAAAAATTTTTTGAA
** *
13536023 CTATATAATATATAGTTTTGAAAACTTTTTT-AA
1 --ATATAATATATAGTTTAAAAAAATTTTTTGAA
13536056 ATATAATATATAGTTTAAAAAAAATATTTTTGAA
1 ATATAATATATAGTTT-AAAAAAAT-TTTTTGAA
*
13536090 GTAT-ATATAT
1 ATATAATATAT
13536100 TTATATAATT
Statistics
Matches: 85, Mismatches: 17, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
31 16 0.19
32 6 0.07
33 34 0.40
34 22 0.26
35 6 0.07
36 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (32 bp):
ATATAATATATAGTTTAAAAAAATTTTTTGAA
Found at i:13536125 original size:3 final size:3
Alignment explanation
Indices: 13536112--13536156 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
13536102 ATATAATTTA
13536112 TAT TA- TAT TAT TAT TAT TAT TATT TAT TCAT T-T TAT T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT T-AT TAT TAT TAT TAT TAT
13536156 T
1 T
13536157 TTCTTTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
2 6 0.16
3 25 0.68
4 6 0.16
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:13536157 original size:13 final size:13
Alignment explanation
Indices: 13536108--13536163 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
13536098 ATTTATATAA
*
13536108 TTTA-TATTATAT
1 TTTATTATTTTAT
13536120 TATTATTATTATTA-
1 T-TTATTATT-TTAT
13536134 TTTATTCATTTTAT
1 TTTATT-ATTTTAT
*
13536148 TTTATTATTTTCT
1 TTTATTATTTTAT
13536161 TTT
1 TTT
13536164 TATGTTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
12 1 0.03
13 20 0.54
14 14 0.38
15 2 0.05
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATTATTTTAT
Found at i:13543147 original size:37 final size:37
Alignment explanation
Indices: 13543106--13543218 Score: 154
Period size: 37 Copynumber: 3.1 Consensus size: 37
13543096 AACATAACGT
* * *
13543106 TAGAGTTTTACTAGGATTCGAACTCCTAAAAGTAAGA
1 TAGAGTTCTACTAGGATTCAAACTCCTAAAAATAAGA
* *
13543143 TAGAGTTCTACTAGGACTCAAACTCCTAAAAATAGGA
1 TAGAGTTCTACTAGGATTCAAACTCCTAAAAATAAGA
** *
13543180 TAGAGTTCTACTAAAATTCAAACTCCTAAAAATATGA
1 TAGAGTTCTACTAGGATTCAAACTCCTAAAAATAAGA
13543217 TA
1 TA
13543219 CACAAGCATT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (37 bp):
TAGAGTTCTACTAGGATTCAAACTCCTAAAAATAAGA
Found at i:13543817 original size:48 final size:46
Alignment explanation
Indices: 13543762--13543894 Score: 161
Period size: 45 Copynumber: 2.9 Consensus size: 46
13543752 AGATTACATA
13543762 TATATATATATATATATATATTACTTTTTATTATCTGTTTTATTAAT
1 TATATATATATATATATATATTACTTTTTATTAT-TGTTTTATTAAT
*
13543809 T-TATATATATATATATATA-TACTATTTT-TTA-TGTCTTTATTTAT
1 TATATATATATATATATATATTACT-TTTTATTATTGT-TTTATTAAT
* *
13543853 TATATATATATAT-TAT-TTTTACTTTTTTATTATTATTTTATT
1 TATATATATATATATATATATTAC-TTTTTATTATTGTTTTATT
13543895 TATATATTTT
Statistics
Matches: 76, Mismatches: 3, Indels: 16
0.80 0.03 0.17
Matches are distributed among these distances:
43 4 0.05
44 19 0.25
45 28 0.37
46 24 0.32
47 1 0.01
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.63
Consensus pattern (46 bp):
TATATATATATATATATATATTACTTTTTATTATTGTTTTATTAAT
Found at i:13543932 original size:33 final size:35
Alignment explanation
Indices: 13543820--13543962 Score: 113
Period size: 35 Copynumber: 4.1 Consensus size: 35
13543810 TATATATATA
* *
13543820 TATATATATACTATTTTTTA-TGTCTTTA-T-TTATTA
1 TATATATATA-T-TTTTTTACT-TTTTTATTATTATTT
13543855 TATATATATATTATTTTTACTTTTTTATTATTATTT
1 TATATATATATT-TTTTTACTTTTTTATTATTATTT
* *
13543891 TATTTATATATTTTTCTT-CTTTTTCT-TTATTTTTT
1 TATATATATATTTTT-TTACTTTTT-TATTATTATTT
*
13543926 TATATATAT-TTTTATTTA--TTTTTACTTACTATTT
1 TATATATATATTTT-TTTACTTTTTTA-TTATTATTT
13543960 TAT
1 TAT
13543963 CTTTGCTTTC
Statistics
Matches: 91, Mismatches: 7, Indels: 21
0.76 0.06 0.18
Matches are distributed among these distances:
32 1 0.01
33 5 0.05
34 28 0.31
35 38 0.42
36 19 0.21
ACGTcount: A:0.24, C:0.06, G:0.01, T:0.69
Consensus pattern (35 bp):
TATATATATATTTTTTTACTTTTTTATTATTATTT
Found at i:13543961 original size:34 final size:33
Alignment explanation
Indices: 13543822--13543962 Score: 108
Period size: 34 Copynumber: 4.1 Consensus size: 33
13543812 TATATATATA
* * *
13543822 TATATATACTATTTTTTATGTCTTTATTTATTA-TA
1 TATATATA-TTTTTTTTAT-T-TTTACTTATTATTT
*
13543857 TATATATATTATTTTTACTTTTTTA-TTATTATTT
1 TATATATATTTTTTTTA--TTTTTACTTATTATTT
* * *
13543891 TATTTATATATTTTTCTTCTTTTT-CTTTATTTTTT
1 TA--TATATATTTTTTTTATTTTTAC-TTATTATTT
*
13543926 TATATATATTTTTATTTATTTTTACTTACTATTT
1 TATATATATTTTT-TTTATTTTTACTTATTATTT
13543960 TAT
1 TAT
13543963 CTTTGCTTTC
Statistics
Matches: 86, Mismatches: 11, Indels: 19
0.74 0.09 0.16
Matches are distributed among these distances:
33 17 0.20
34 36 0.42
35 20 0.23
36 13 0.15
ACGTcount: A:0.24, C:0.06, G:0.01, T:0.70
Consensus pattern (33 bp):
TATATATATTTTTTTTATTTTTACTTATTATTT
Found at i:13546396 original size:27 final size:27
Alignment explanation
Indices: 13546366--13546459 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 27
13546356 AATATTAAAT
13546366 GAATTAAGGATTCTTTTAATTCTTCAA
1 GAATTAAGGATTCTTTTAATTCTTCAA
*
13546393 GAATTATA-GA-T-TTTTAGTTCTTCGAATATTAAA
1 GAATTA-AGGATTCTTTTAATTCTTC--------AA
13546426 TGAATTAAGGATTCTTTTAATTCTTCAA
1 -GAATTAAGGATTCTTTTAATTCTTCAA
13546454 GAATTA
1 GAATTA
13546460 TAGATTTTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 26
0.65 0.03 0.32
Matches are distributed among these distances:
25 11 0.21
26 1 0.02
27 14 0.27
28 3 0.06
33 3 0.06
34 8 0.15
35 1 0.02
36 11 0.21
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.45
Consensus pattern (27 bp):
GAATTAAGGATTCTTTTAATTCTTCAA
Found at i:13546414 original size:61 final size:61
Alignment explanation
Indices: 13546344--13546468 Score: 241
Period size: 61 Copynumber: 2.0 Consensus size: 61
13546334 AATTTTAATC
13546344 TTTAGTTCTTAGAATATTAAATGAATTAAGGATTCTTTTAATTCTTCAAGAATTATAGATT
1 TTTAGTTCTTAGAATATTAAATGAATTAAGGATTCTTTTAATTCTTCAAGAATTATAGATT
*
13546405 TTTAGTTCTTCGAATATTAAATGAATTAAGGATTCTTTTAATTCTTCAAGAATTATAGATT
1 TTTAGTTCTTAGAATATTAAATGAATTAAGGATTCTTTTAATTCTTCAAGAATTATAGATT
13546466 TTT
1 TTT
13546469 GACATATGGC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.47
Consensus pattern (61 bp):
TTTAGTTCTTAGAATATTAAATGAATTAAGGATTCTTTTAATTCTTCAAGAATTATAGATT
Found at i:13547151 original size:12 final size:13
Alignment explanation
Indices: 13547136--13547177 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
13547126 AAAAAGATTA
13547136 AAAAAACAAAG-G
1 AAAAAACAAAGAG
*
13547148 AAAAAGCAAAGAG
1 AAAAAACAAAGAG
*
13547161 AAAATAAAAAAGAG
1 AAAA-AACAAAGAG
13547175 AAA
1 AAA
13547178 CAAAAACCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 10 0.40
13 5 0.20
14 10 0.40
ACGTcount: A:0.76, C:0.05, G:0.17, T:0.02
Consensus pattern (13 bp):
AAAAAACAAAGAG
Found at i:13548330 original size:32 final size:32
Alignment explanation
Indices: 13548257--13548333 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
13548247 ATGAGGAACA
*
13548257 ATTGGGGCACCTTTGAAGATTCAACATCAAAT
1 ATTGGGGCATCTTTGAAGATTCAACATCAAAT
* * *
13548289 GTTGGGGCATTTTTGGAA-ATTCAACATCGAAT
1 ATTGGGGCATCTTT-GAAGATTCAACATCAAAT
13548321 ATTGGGGCATCTT
1 ATTGGGGCATCTT
13548334 CGGGGATTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 35 0.92
33 3 0.08
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (32 bp):
ATTGGGGCATCTTTGAAGATTCAACATCAAAT
Found at i:13548343 original size:32 final size:32
Alignment explanation
Indices: 13548257--13548344 Score: 95
Period size: 32 Copynumber: 2.8 Consensus size: 32
13548247 ATGAGGAACA
* * *
13548257 ATTGGGGCACCTTTGAAGATTCAACATCAAAT
1 ATTGGGGCATCTTCGGAGATTCAACATCAAAT
* * * * *
13548289 GTTGGGGCATTTTTGGAAATTCAACATCGAAT
1 ATTGGGGCATCTTCGGAGATTCAACATCAAAT
*
13548321 ATTGGGGCATCTTCGGGGATTCAA
1 ATTGGGGCATCTTCGGAGATTCAA
13548345 AATCCTGATA
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (32 bp):
ATTGGGGCATCTTCGGAGATTCAACATCAAAT
Found at i:13548704 original size:110 final size:110
Alignment explanation
Indices: 13548578--13548864 Score: 450
Period size: 110 Copynumber: 2.6 Consensus size: 110
13548568 TTTGAGAAAA
*
13548578 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGAT
1 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAAGAT
* *
13548643 ATTGGACTCGAGACAACACAAACTCAACTTCACTGCGAAGGGGAG
66 ATTGGACTCGAGACAACACAAACTCAACTTCACAGCGAAAGGGAG
* * * *
13548688 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAATTTCACAGCAAAATAT
1 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAAGAT
* *
13548753 ATTGGACTCGAGACAACACAAGCTCAACTTCACAGTGAAAGGGAG
66 ATTGGACTCGAGACAACACAAACTCAACTTCACAGCGAAAGGGAG
* * *
13548798 AATGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT-AGATTTCAACTTCACGACGAATGA
1 ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCA-ATTTCAACTTCACAACGAAAGA
13548862 TAT
65 TAT
13548865 CTACTTCAAA
Statistics
Matches: 160, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
109 1 0.01
110 159 0.99
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (110 bp):
ACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAAGAT
ATTGGACTCGAGACAACACAAACTCAACTTCACAGCGAAAGGGAG
Found at i:13550006 original size:37 final size:37
Alignment explanation
Indices: 13549824--13550005 Score: 283
Period size: 37 Copynumber: 4.9 Consensus size: 37
13549814 AATATAACGT
* * * * *
13549824 TAGAGTTTTACTATGATTCGAACTCCTAAAAATAAGA
1 TAGAGTTCTACTAGGACTCAAACTCCTAAAAATAGGA
13549861 TAGAGTTCTACTAGGACTCAAACTCCTAAAAATAGGA
1 TAGAGTTCTACTAGGACTCAAACTCCTAAAAATAGGA
13549898 TAGAGTTCTACTAGGACTCAAACTCCTAAAAATAGGA
1 TAGAGTTCTACTAGGACTCAAACTCCTAAAAATAGGA
*
13549935 TAGAGTTCTACTAGGACTCAAACTCCTAAAAATATGA
1 TAGAGTTCTACTAGGACTCAAACTCCTAAAAATAGGA
* * *
13549972 TAGAGTTATACTATGATTCAAACTCCTAAAAATA
1 TAGAGTTCTACTAGGACTCAAACTCCTAAAAATA
13550006 TAATACATAA
Statistics
Matches: 136, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 136 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (37 bp):
TAGAGTTCTACTAGGACTCAAACTCCTAAAAATAGGA
Found at i:13550553 original size:27 final size:26
Alignment explanation
Indices: 13550485--13550556 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
13550475 TCATGTAATA
* *
13550485 TTTTTTTACATT-TTATGTATTTTCT
1 TTTTTTTACATTAATATATATTTTCT
*
13550510 TTTTTTTACTTTAATATATATTTT-T
1 TTTTTTTACATTAATATATATTTTCT
*
13550535 ATTTTTTTAGATTACATATATA
1 -TTTTTTTACATTA-ATATATA
13550557 AATATATGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
25 12 0.31
26 20 0.51
27 7 0.18
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.67
Consensus pattern (26 bp):
TTTTTTTACATTAATATATATTTTCT
Found at i:13550602 original size:46 final size:44
Alignment explanation
Indices: 13550550--13550707 Score: 131
Period size: 46 Copynumber: 3.4 Consensus size: 44
13550540 TTTAGATTAC
*
13550550 ATATATAAATATATGTTACTTTTTATTATCTGTTTTATTAATTTAT
1 ATATATAAATATATTTTACTTTTTATTAT-T-TTTTATTAATTTAT
*
13550596 ATATATATATATATATATTTACTATTTT-TTATGTTTTTATTTA-TTAT
1 ATATATA-A-ATATAT-TTTACT-TTTTATTAT-TTTTTATTAATTTAT
* * * *
13550643 ATATATATATATTATTTTTACTTTTTTTTATTATTATATTTATTATAT
1 ATATATAAATA-TA-TTTTACTTTTTATTATT-TTTTATTAATT-TAT
* *
13550691 TTATATATATATATTTT
1 ATATATAAATATATTTT
13550708 TTCTTTATTT
Statistics
Matches: 96, Mismatches: 6, Indels: 20
0.79 0.05 0.16
Matches are distributed among these distances:
45 8 0.08
46 31 0.32
47 16 0.17
48 27 0.28
49 10 0.10
50 4 0.04
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (44 bp):
ATATATAAATATATTTTACTTTTTATTATTTTTTATTAATTTAT
Found at i:13550650 original size:37 final size:34
Alignment explanation
Indices: 13550603--13550681 Score: 97
Period size: 37 Copynumber: 2.3 Consensus size: 34
13550593 TATATATATA
* *
13550603 TATATATATATTTACTATTTTTTATGTTTTTATTTAT
1 TATATATATATATACTA-TTTTTA-CTTTTT-TTTAT
*
13550640 TATATATATATATATTATTTTTACTTTTTTTTAT
1 TATATATATATATACTATTTTTACTTTTTTTTAT
13550674 TAT-TATAT
1 TATATATAT
13550682 TTATTATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
33 5 0.13
34 8 0.21
35 5 0.13
36 6 0.15
37 15 0.38
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (34 bp):
TATATATATATATACTATTTTTACTTTTTTTTAT
Found at i:13550677 original size:22 final size:22
Alignment explanation
Indices: 13550652--13550751 Score: 89
Period size: 22 Copynumber: 4.4 Consensus size: 22
13550642 TATATATATA
*
13550652 TATTATTTTTACTTTTTTTTAT
1 TATTATTTTTACTTTATTTTAT
*
13550674 TATTATATTTA-TTATATTTATAT
1 TATTATTTTTACTT-TATTT-TAT
*
13550697 ATATATATTTTTTCTTTATTTTAT
1 -TAT-TATTTTTACTTTATTTTAT
13550721 T-TATATTTTT-CTTTATTTTACT
1 TAT-TATTTTTACTTTATTTTA-T
*
13550743 TACTATTTT
1 TATTATTTT
13550752 ATATTTGCTT
Statistics
Matches: 66, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
21 12 0.18
22 31 0.47
23 4 0.06
24 6 0.09
25 11 0.17
26 2 0.03
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (22 bp):
TATTATTTTTACTTTATTTTAT
Found at i:13550714 original size:21 final size:20
Alignment explanation
Indices: 13550664--13550737 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 20
13550654 TTATTTTTAC
13550664 TTTTT-TTTATTAT-TATAT
1 TTTTTCTTTATTATATATAT
*
13550682 TTATTATATTTATATATATATAT
1 TT-TT-TCTTTAT-TATATATAT
* *
13550705 TTTTTCTTTATTTTATTTAT
1 TTTTTCTTTATTATATATAT
13550725 ATTTTTCTTTATT
1 -TTTTTCTTTATT
13550738 TTACTTACTA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
18 2 0.04
19 2 0.04
20 8 0.17
21 23 0.49
22 5 0.11
23 7 0.15
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTTCTTTATTATATATAT
Found at i:13550738 original size:21 final size:22
Alignment explanation
Indices: 13550688--13550815 Score: 73
Period size: 21 Copynumber: 5.7 Consensus size: 22
13550678 ATATTTATTA
*
13550688 TATTTATATATATATATTTTTTCTT
1 TATTT-TATTTATAT-TTTT-TCTT
13550713 TATTTTATTTATA-TTTTTCTT
1 TATTTTATTTATATTTTTTCTT
* * *
13550734 TATTTTACTTACTATTTTATATT
1 TATTTTATTTA-TATTTTTTCTT
** * * * *
13550757 TGCTTTCTTTATCTTATCT-TT
1 TATTTTATTTATATTTTTTCTT
* *
13550778 TATTTAATTTATTTTTTTTCTT
1 TATTTTATTTATATTTTTTCTT
*
13550800 CATTTTAATTTA-ATTT
1 TATTTT-ATTTATATTT
13550816 ATTGATTTAT
Statistics
Matches: 78, Mismatches: 21, Indels: 11
0.71 0.19 0.10
Matches are distributed among these distances:
21 28 0.36
22 20 0.26
23 18 0.23
24 7 0.09
25 5 0.06
ACGTcount: A:0.22, C:0.08, G:0.01, T:0.70
Consensus pattern (22 bp):
TATTTTATTTATATTTTTTCTT
Found at i:13552131 original size:15 final size:15
Alignment explanation
Indices: 13552111--13552188 Score: 138
Period size: 15 Copynumber: 5.2 Consensus size: 15
13552101 ATATTTAGTT
*
13552111 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
13552126 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
*
13552141 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
13552156 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
13552171 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
13552186 GGG
1 GGG
13552189 TGGATAATGT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 60 1.00
ACGTcount: A:0.06, C:0.17, G:0.68, T:0.09
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:13553891 original size:2 final size:2
Alignment explanation
Indices: 13553886--13553957 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
13553876 ACAAACAAAT
13553886 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
13553928 TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13553958 GATGAGAAGC
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13555596 original size:18 final size:17
Alignment explanation
Indices: 13555573--13555653 Score: 99
Period size: 18 Copynumber: 4.6 Consensus size: 17
13555563 TGTTCCTGAG
13555573 GGAATTGGAATATGTGAA
1 GGAATTGGAATATGT-AA
* * *
13555591 GGAATTAGAATCTGTCA
1 GGAATTGGAATATGTAA
13555608 GGAATTGGAATATGTGAA
1 GGAATTGGAATATGT-AA
* *
13555626 GGAATTGGAATCTGTCA
1 GGAATTGGAATATGTAA
13555643 GGAATTGGAAT
1 GGAATTGGAAT
13555654 CTGAATCTGA
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
17 26 0.48
18 28 0.52
ACGTcount: A:0.36, C:0.05, G:0.31, T:0.28
Consensus pattern (17 bp):
GGAATTGGAATATGTAA
Found at i:13555612 original size:17 final size:17
Alignment explanation
Indices: 13555573--13555656 Score: 105
Period size: 17 Copynumber: 4.8 Consensus size: 17
13555563 TGTTCCTGAG
* *
13555573 GGAATTGGAATATGTGAA
1 GGAATTGGAATCTGT-CA
*
13555591 GGAATTAGAATCTGTCA
1 GGAATTGGAATCTGTCA
* *
13555608 GGAATTGGAATATGTGAA
1 GGAATTGGAATCTGT-CA
13555626 GGAATTGGAATCTGTCA
1 GGAATTGGAATCTGTCA
13555643 GGAATTGGAATCTG
1 GGAATTGGAATCTG
13555657 AATCTGAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
17 29 0.51
18 28 0.49
ACGTcount: A:0.35, C:0.06, G:0.31, T:0.29
Consensus pattern (17 bp):
GGAATTGGAATCTGTCA
Found at i:13555612 original size:35 final size:35
Alignment explanation
Indices: 13555573--13555653 Score: 153
Period size: 35 Copynumber: 2.3 Consensus size: 35
13555563 TGTTCCTGAG
13555573 GGAATTGGAATATGTGAAGGAATTAGAATCTGTCA
1 GGAATTGGAATATGTGAAGGAATTAGAATCTGTCA
*
13555608 GGAATTGGAATATGTGAAGGAATTGGAATCTGTCA
1 GGAATTGGAATATGTGAAGGAATTAGAATCTGTCA
13555643 GGAATTGGAAT
1 GGAATTGGAAT
13555654 CTGAATCTGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.36, C:0.05, G:0.31, T:0.28
Consensus pattern (35 bp):
GGAATTGGAATATGTGAAGGAATTAGAATCTGTCA
Found at i:13556287 original size:22 final size:21
Alignment explanation
Indices: 13556249--13556303 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
13556239 AAACTAAAGA
*
13556249 AAAATAAA-ATAAAGGAAATA-
1 AAAATAAAGAAAAAGGAAA-AT
13556269 AAAATAAATGAAAAAGGAAAAT
1 AAAATAAA-GAAAAAGGAAAAT
13556291 AAAATAAAGAAAA
1 AAAATAAAGAAAA
13556304 GATATAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 8 0.26
21 6 0.19
22 17 0.55
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (21 bp):
AAAATAAAGAAAAAGGAAAAT
Found at i:13556299 original size:15 final size:15
Alignment explanation
Indices: 13556235--13556282 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
13556225 CAATGAAAAT
* *
13556235 AAATAAACTAAAGAA
1 AAATAAAATAAAGGA
13556250 AAATAAAATAAAGG-
1 AAATAAAATAAAGGA
*
13556264 AAATAAAAATAAATGA
1 AAAT-AAAATAAAGGA
13556280 AAA
1 AAA
13556283 AGGAAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 4 0.14
15 21 0.75
16 3 0.11
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (15 bp):
AAATAAAATAAAGGA
Found at i:13556314 original size:20 final size:19
Alignment explanation
Indices: 13556230--13556397 Score: 76
Period size: 19 Copynumber: 8.7 Consensus size: 19
13556220 AAAGACAATG
* *
13556230 AAAATAAATAAACTAAAGA-
1 AAAAAAAATAAA-AAAAGAT
**
13556249 AAAATAAAATAAAGGAA-AT
1 AAAA-AAAATAAAAAAAGAT
* *
13556268 AAAAATAAATGAAAAAGGA-
1 AAAAA-AAATAAAAAAAGAT
*
13556287 AAATAAAATAAAGAAAAGAT
1 AAAAAAAATAAA-AAAAGAT
* *
13556307 ATAAAAAATAACATAAAGAT
1 AAAAAAAATAA-AAAAAGAT
* *
13556327 AAAAAAAACT-AAATAACAT
1 AAAAAAAA-TAAAAAAAGAT
* * *
13556346 AAAGAACAT-AAAAAACAT
1 AAAAAAAATAAAAAAAGAT
* * *
13556364 AAAAAAATTAAAAAATGAAG
1 AAAAAAAATAAAAAAAG-AT
13556384 AAAAATAAATAAAA
1 AAAAA-AAATAAAA
13556398 TAACCAAAAT
Statistics
Matches: 111, Mismatches: 27, Indels: 20
0.70 0.17 0.13
Matches are distributed among these distances:
18 23 0.21
19 42 0.38
20 37 0.33
21 9 0.08
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.15
Consensus pattern (19 bp):
AAAAAAAATAAAAAAAGAT
Found at i:13556322 original size:25 final size:22
Alignment explanation
Indices: 13556286--13556365 Score: 70
Period size: 25 Copynumber: 3.3 Consensus size: 22
13556276 ATGAAAAAGG
*
13556286 AAAATAAAATAAAGAAAAGATATAA
1 AAAATAACATAAAGAAAA-A-A-AA
13556311 AAAATAACATAAAGATAAAAAAA
1 AAAATAACATAAAGA-AAAAAAA
*
13556334 ACTAAATAACATAAAGAACATAAAA
1 A--AAATAACATAAAGAA-AAAAAA
*
13556359 AACATAA
1 AAAATAA
13556366 AAAAATTAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
23 8 0.17
24 2 0.04
25 35 0.73
26 3 0.06
ACGTcount: A:0.74, C:0.06, G:0.05, T:0.15
Consensus pattern (22 bp):
AAAATAACATAAAGAAAAAAAA
Found at i:13556397 original size:9 final size:9
Alignment explanation
Indices: 13556230--13556571 Score: 69
Period size: 9 Copynumber: 35.9 Consensus size: 9
13556220 AAAGACAATG
13556230 AAAATAAAT
1 AAAATAAAT
* *
13556239 AAACTAAAGA
1 AAAATAAA-T
13556249 AAAATAAAAT
1 AAAAT-AAAT
**
13556259 AAAGGAAAT
1 AAAATAAAT
13556268 AAAAATAAAT
1 -AAAATAAAT
*
13556278 GAAAAAGGAAAAT
1 --AAAA--TAAAT
*
13556291 AAAATAAAGA
1 AAAATAAA-T
13556301 AAAGATATAA-
1 AAA-ATA-AAT
13556311 AAAATAACAT
1 AAAATAA-AT
*
13556321 AAAGATAAAA
1 AAA-ATAAAT
13556331 AAAACTAAAT
1 AAAA-TAAAT
* *
13556341 AACATAAAG
1 AAAATAAAT
*
13556350 AACATAAA-
1 AAAATAAAT
13556358 AAACATAAA-
1 AAA-ATAAAT
*
13556367 AAAATTAA-
1 AAAATAAAT
13556375 AAAATGAAGA-
1 AAAAT-AA-AT
13556385 AAAATAAAT
1 AAAATAAAT
**
13556394 AAAATAACC
1 AAAATAAAT
*
13556403 AAAATAAAG
1 AAAATAAAT
* * **
13556412 ATAATGAGC
1 AAAATAAAT
13556421 AAAATAAAAT
1 AAAAT-AAAT
13556431 AAAAATAAGAAT
1 -AAAAT-A-AAT
*
13556443 AAAATAAAG
1 AAAATAAAT
13556452 AACAATACTAAT
1 AA-AATA--AAT
** *
13556464 AATTGTATAT
1 AA-AATAAAT
13556474 ACATAATAAAT
1 A-A-AATAAAT
13556485 AGAAA-AAAT
1 A-AAATAAAT
*
13556494 AAGAA-GAA-
1 AA-AATAAAT
* *
13556502 AATACAAAT
1 AAAATAAAT
13556511 GAAAATAAAT
1 -AAAATAAAT
*
13556521 -ATATAAAT
1 AAAATAAAT
13556529 AAAACTAATAT
1 AAAA-TAA-AT
13556540 AAAA-AAAT
1 AAAATAAAT
*
13556548 AAAAT-AAG
1 AAAATAAAT
*
13556556 AAAAGAAA-
1 AAAATAAAT
13556564 AAAATAAA
1 AAAATAAA
13556572 AGAAAAGAAA
Statistics
Matches: 250, Mismatches: 50, Indels: 67
0.68 0.14 0.18
Matches are distributed among these distances:
7 1 0.00
8 44 0.18
9 84 0.34
10 61 0.24
11 45 0.18
12 11 0.04
13 4 0.02
ACGTcount: A:0.72, C:0.04, G:0.07, T:0.17
Consensus pattern (9 bp):
AAAATAAAT
Found at i:13556553 original size:5 final size:5
Alignment explanation
Indices: 13556489--13556615 Score: 59
Period size: 5 Copynumber: 24.8 Consensus size: 5
13556479 ATAAATAGAA
* *
13556489 AAAAT AAGAAG AAAAT ACAAAT GAAAAT AAATAT ATAAAT AAAACT AATAT
1 AAAAT AA-AAT AAAAT A-AAAT -AAAAT AAA-AT A-AAAT AAAA-T AAAAT
* * * *
13556540 -AAA- AAAAT AAAAT AAGAA- AAGAAA AAAAT AAAAG AAAAG AAAA- GAAA-
1 AAAAT AAAAT AAAAT AA-AAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT
* *
13556587 AAAAT AAGAAA AAAAT AAGA- AAAAT AAAA
1 AAAAT AA-AAT AAAAT AAAAT AAAAT AAAA
13556616 AGTAAATATA
Statistics
Matches: 97, Mismatches: 12, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
4 14 0.14
5 50 0.52
6 30 0.31
7 3 0.03
ACGTcount: A:0.77, C:0.02, G:0.08, T:0.13
Consensus pattern (5 bp):
AAAAT
Found at i:13556566 original size:23 final size:22
Alignment explanation
Indices: 13556540--13556610 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 22
13556530 AAACTAATAT
*
13556540 AAAAAAAT-AAAATAAGAAAAG
1 AAAAAAATAAAAAAAAGAAAAG
13556561 AAAAAAATAAAAGAAAAGAAAAG
1 AAAAAAATAAAA-AAAAGAAAAG
*
13556584 AAAAAAATAAGAAAAAA-ATAAG
1 AAAAAAATAA-AAAAAAGAAAAG
13556606 AAAAA
1 AAAAA
13556611 TAAAAAGTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
21 8 0.18
22 12 0.27
23 23 0.51
24 2 0.04
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (22 bp):
AAAAAAATAAAAAAAAGAAAAG
Found at i:13556574 original size:18 final size:18
Alignment explanation
Indices: 13556553--13556604 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
13556543 AAAATAAAAT
13556553 AAGAAAAGAAAAAAATAA
1 AAGAAAAGAAAAAAATAA
*
13556571 AAGAAAAGAAAAGAA-AA
1 AAGAAAAGAAAAAAATAA
*
13556588 AA-ATAAGAAAAAAATAA
1 AAGAAAAGAAAAAAATAA
13556605 GAAAAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 10 0.33
17 6 0.20
18 14 0.47
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.06
Consensus pattern (18 bp):
AAGAAAAGAAAAAAATAA
Found at i:13556588 original size:11 final size:11
Alignment explanation
Indices: 13556540--13556610 Score: 76
Period size: 11 Copynumber: 6.5 Consensus size: 11
13556530 AAACTAATAT
13556540 AAAAAAATAA-
1 AAAAAAATAAG
*
13556550 AATAAGAA-AAG
1 AA-AAAAATAAG
13556561 AAAAAAATAA-
1 AAAAAAATAAG
*
13556571 AAGAAAAGAAAAG
1 AA-AAAA-ATAAG
13556584 AAAAAAATAAG
1 AAAAAAATAAG
13556595 AAAAAAATAAG
1 AAAAAAATAAG
13556606 AAAAA
1 AAAAA
13556611 TAAAAAGTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
10 10 0.20
11 32 0.63
12 7 0.14
13 2 0.04
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (11 bp):
AAAAAAATAAG
Found at i:13556631 original size:44 final size:44
Alignment explanation
Indices: 13556536--13556632 Score: 101
Period size: 44 Copynumber: 2.2 Consensus size: 44
13556526 AATAAAACTA
*
13556536 ATAT-AAAAAAATAAAATAAGAAAAGAAAAAAATAAAAGAAAAG
1 ATATGAAAAAAATAAAATAAAAAAAGAAAAAAATAAAAGAAAAG
* * * * *
13556579 AAAAGAAAAAAATAAGAA-AAAAATAAGAAAAATA-AAAAGTAAAT
1 ATATGAAAAAAATAA-AATAAAAA-AAGAAAAAAATAAAAGAAAAG
13556623 ATATGAAAAA
1 ATATGAAAAA
13556633 TAATGATGAG
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
43 2 0.05
44 30 0.70
45 11 0.26
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.12
Consensus pattern (44 bp):
ATATGAAAAAAATAAAATAAAAAAAGAAAAAAATAAAAGAAAAG
Found at i:13556996 original size:16 final size:15
Alignment explanation
Indices: 13556975--13557022 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
13556965 TTAAAAATAA
13556975 TAATTTGATTTAATGT
1 TAATTTGATTTAAT-T
**
13556991 TAATTTTTTTTAATT
1 TAATTTGATTTAATT
**
13557006 TGGTTTGATTTAATT
1 TAATTTGATTTAATT
13557021 TA
1 TA
13557023 TAGTTTTATA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.62
Consensus pattern (15 bp):
TAATTTGATTTAATT
Found at i:13557015 original size:31 final size:31
Alignment explanation
Indices: 13556977--13557047 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
13556967 AAAAATAATA
* * *
13556977 ATTTGATTTAATGTTA-ATTTTTTTTAATTTG
1 ATTTGATTTAAT-TTATAGTTTTATAAATTTG
*
13557008 GTTTGATTTAATTTATAGTTTTATAAATTTG
1 ATTTGATTTAATTTATAGTTTTATAAATTTG
13557039 ATTTGATTT
1 ATTTGATTT
13557048 GAAAAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 3 0.09
31 31 0.91
ACGTcount: A:0.27, C:0.00, G:0.11, T:0.62
Consensus pattern (31 bp):
ATTTGATTTAATTTATAGTTTTATAAATTTG
Found at i:13557686 original size:31 final size:31
Alignment explanation
Indices: 13557645--13557750 Score: 167
Period size: 31 Copynumber: 3.4 Consensus size: 31
13557635 ATGGTTGTCA
13557645 TGTTTGGGTGTATAAGGTATTTATTTTATTG
1 TGTTTGGGTGTATAAGGTATTTATTTTATTG
* *
13557676 TGTTTAGGTGTATAAGGTATTAATTTTATTG
1 TGTTTGGGTGTATAAGGTATTTATTTTATTG
* *
13557707 TGTTTGGGTGTTTAAGGTATTTATTTTTTTG
1 TGTTTGGGTGTATAAGGTATTTATTTTATTG
*
13557738 CGTTTGGGTGTAT
1 TGTTTGGGTGTAT
13557751 GAGATTTAAG
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 67 1.00
ACGTcount: A:0.18, C:0.01, G:0.26, T:0.55
Consensus pattern (31 bp):
TGTTTGGGTGTATAAGGTATTTATTTTATTG
Found at i:13562904 original size:3 final size:3
Alignment explanation
Indices: 13562891--13562969 Score: 113
Period size: 3 Copynumber: 26.0 Consensus size: 3
13562881 GTAATATTTA
* *
13562891 AAT AAT AAAT AAT ATT ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
13562937 AAT AAT AAT AAT AAT AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
13562970 TTAAAATGAA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
3 65 0.96
4 3 0.04
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:13563443 original size:3 final size:3
Alignment explanation
Indices: 13563435--13563478 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
13563425 CAATATTTTA
*
13563435 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTT TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
13563479 TTTTAAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:13569568 original size:2 final size:2
Alignment explanation
Indices: 13569563--13569598 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
13569553 ATTTTAGTTT
13569563 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
13569599 AGTTCATCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13569826 original size:20 final size:21
Alignment explanation
Indices: 13569801--13569852 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
13569791 TTTTCCCAAT
*
13569801 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
13569821 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
13569842 TCGCAATGCGA
1 TCGCAATGCGA
13569853 TATTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:13569866 original size:20 final size:20
Alignment explanation
Indices: 13569841--13569894 Score: 92
Period size: 20 Copynumber: 2.7 Consensus size: 20
13569831 AATTGGGAAA
13569841 ATCGCAATGCGATA-TTGACT
1 ATCGCAATGCGATACTT-ACT
13569861 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTTACT
13569881 ATCGCAATGCGATA
1 ATCGCAATGCGATA
13569895 ATACAAAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 31 0.94
21 2 0.06
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (20 bp):
ATCGCAATGCGATACTTACT
Found at i:13569903 original size:61 final size:62
Alignment explanation
Indices: 13569838--13569955 Score: 159
Period size: 61 Copynumber: 1.9 Consensus size: 62
13569828 GCGAATTGGG
* * * * *
13569838 AAAATCGCAATGCGATATTGACTATCGCAATGCGATACTTAC-T-ATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA-ATACATAATCGCAATGCGATAATAC
*
13569899 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATAATACATAATCGCAATGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATACATAATCGCAATGCGAT
13569956 TTTCAAAGCG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
60 3 0.06
61 33 0.67
62 13 0.27
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (62 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATACATAATCGCAATGCGATAATAC
Found at i:13569906 original size:41 final size:41
Alignment explanation
Indices: 13569861--13569955 Score: 136
Period size: 41 Copynumber: 2.3 Consensus size: 41
13569851 GATATTGACT
* *
13569861 ATCGCAATGCGATACTTACTATCGCAATGCGATAATACAAA
1 ATCGCAATGCGATACTGACTATCGCAACGCGATAATACAAA
* * * *
13569902 ATCGCAACGAGATACTGACTTTCGCAACGCGATAATACATA
1 ATCGCAATGCGATACTGACTATCGCAACGCGATAATACAAA
13569943 ATCGCAATGCGAT
1 ATCGCAATGCGAT
13569956 TTTCAAAGCG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (41 bp):
ATCGCAATGCGATACTGACTATCGCAACGCGATAATACAAA
Found at i:13570151 original size:22 final size:22
Alignment explanation
Indices: 13570123--13570166 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
13570113 CACTCTCTCA
13570123 CCCATCTCC-GACGAAATCCGTC
1 CCCATCTCCAG-CGAAATCCGTC
13570145 CCCATCTCCAGCGAAATCCGTC
1 CCCATCTCCAGCGAAATCCGTC
13570167 TATCTCCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCAGCGAAATCCGTC
Found at i:13570173 original size:20 final size:21
Alignment explanation
Indices: 13570123--13570174 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
13570113 CACTCTCTCA
13570123 CCCATCTCC-GACGAAATCCGT
1 CCCATCTCCAG-CGAAATCCGT
13570144 CCCCATCTCCAGCGAAATCCGT
1 -CCCATCTCCAGCGAAATCCGT
*
13570166 -CTATCTCCA
1 CCCATCTCCA
13570175 TCTCTCAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 8 0.29
22 19 0.68
23 1 0.04
ACGTcount: A:0.23, C:0.44, G:0.12, T:0.21
Consensus pattern (21 bp):
CCCATCTCCAGCGAAATCCGT
Found at i:13570439 original size:20 final size:20
Alignment explanation
Indices: 13570410--13570453 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
13570400 GCGATTTTAG
13570410 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
13570430 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
13570450 TTTC
1 TTTC
13570454 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:13571713 original size:18 final size:18
Alignment explanation
Indices: 13571692--13571736 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
13571682 TCCACTTCGG
*
13571692 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
13571710 GAGCTATCACCTCATCCA
1 GAGCCATCACCTCACCCA
13571728 GAGCCATCA
1 GAGCCATCA
13571737 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:13572243 original size:20 final size:20
Alignment explanation
Indices: 13572218--13572263 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
13572208 TAGTTTACTT
13572218 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
** * *
13572238 TCGCAATGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
13572258 TCGCAA
1 TCGCAA
13572264 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:13572272 original size:19 final size:20
Alignment explanation
Indices: 13572229--13572273 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
13572219 CGCAACACGA
13572229 AAATGACTATCGCAATGCGG
1 AAATGACTATCGCAATGCGG
*
13572249 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAATGCGG
13572268 AAATGA
1 AAATGA
13572274 AAATCGCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (20 bp):
AAATGACTATCGCAATGCGG
Found at i:13572279 original size:19 final size:19
Alignment explanation
Indices: 13572237--13572352 Score: 92
Period size: 19 Copynumber: 6.6 Consensus size: 19
13572227 GAAAATGACT
***
13572237 ATCGCAATGCGGAAATGGCT
1 ATCGCAATGC-GAAATGAAA
13572257 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
13572276 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
13572290 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
13572308 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
13572322 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
13572341 ATCGCAATGCGA
1 ATCGCAATGCGA
13572353 TTTGTGTTTC
Statistics
Matches: 77, Mismatches: 8, Indels: 23
0.71 0.07 0.21
Matches are distributed among these distances:
14 20 0.26
15 1 0.01
16 6 0.08
17 2 0.03
18 11 0.14
19 27 0.35
20 10 0.13
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:13572292 original size:14 final size:14
Alignment explanation
Indices: 13572273--13572330 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
13572263 ATGCGAAATG
13572273 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
13572287 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
13572303 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
13572319 AAAATCGCAACG
1 AAAATCGCAACG
13572331 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:13572315 original size:32 final size:33
Alignment explanation
Indices: 13572257--13572347 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
13572247 GGAAATGGCT
13572257 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
13572290 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
13572322 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
13572348 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:13572383 original size:14 final size:14
Alignment explanation
Indices: 13572364--13572435 Score: 99
Period size: 14 Copynumber: 4.9 Consensus size: 14
13572354 TTGTGTTTCG
13572364 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
13572378 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
13572394 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
13572410 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
13572424 CGTTGCGATTTT
1 CGTTGCGATTTT
13572436 CATTTCGCAT
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
14 35 0.67
16 8 0.15
18 9 0.17
ACGTcount: A:0.10, C:0.17, G:0.25, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:13572402 original size:32 final size:32
Alignment explanation
Indices: 13572359--13572420 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
13572349 GCGATTTGTG
*
13572359 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTCA
13572391 TTTCGCATTGCGATTTTGTCGTTGCGATTT
1 TTTCGCATTGCGATTTTGTCGTTGCGATTT
13572421 TGTCGTTGCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.10, C:0.18, G:0.24, T:0.48
Consensus pattern (32 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTCA
Found at i:13572470 original size:20 final size:20
Alignment explanation
Indices: 13572436--13572491 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
13572426 TTGCGATTTT
*
13572436 CATTTC-GCATTGCGATAGC
1 CATTTCTGCGTTGCGATAGC
*
13572455 CATTTCTGCGTTGCGATAGT
1 CATTTCTGCGTTGCGATAGC
13572475 CATTT-TCGCGTTGCGAT
1 CATTTCT-GCGTTGCGAT
13572492 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 7 0.21
20 26 0.79
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (20 bp):
CATTTCTGCGTTGCGATAGC
Found at i:13574456 original size:20 final size:20
Alignment explanation
Indices: 13574431--13574469 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
13574421 ATATTGAAGG
13574431 CAAAACAGACTATCGCAACA
1 CAAAACAGACTATCGCAACA
*
13574451 CAAAACTGACTATCGCAAC
1 CAAAACAGACTATCGCAAC
13574470 GAGAGAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.31, G:0.10, T:0.13
Consensus pattern (20 bp):
CAAAACAGACTATCGCAACA
Found at i:13574499 original size:19 final size:19
Alignment explanation
Indices: 13574475--13574519 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
13574465 GCAACGAGAG
13574475 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
13574494 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
13574513 AATCGCA
1 AATCGCA
13574520 GTGAATTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:13574589 original size:20 final size:20
Alignment explanation
Indices: 13574550--13574639 Score: 173
Period size: 20 Copynumber: 4.5 Consensus size: 20
13574540 GCGATTTTGT
13574550 CGTTGCGATAGCCA-TTTCG
1 CGTTGCGATAGCCATTTTCG
13574569 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
13574589 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
13574609 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
13574629 CGTTGCGATAG
1 CGTTGCGATAG
13574640 TCAAATGAAT
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
19 14 0.20
20 56 0.80
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:13574764 original size:20 final size:20
Alignment explanation
Indices: 13574725--13574814 Score: 173
Period size: 20 Copynumber: 4.5 Consensus size: 20
13574715 GCGATTTTGT
13574725 CGTTGCGATAGCCA-TTTCG
1 CGTTGCGATAGCCATTTTCG
13574744 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
13574764 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
13574784 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
13574804 CGTTGCGATAG
1 CGTTGCGATAG
13574815 TCAAATGAAT
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
19 14 0.20
20 56 0.80
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:13574787 original size:175 final size:176
Alignment explanation
Indices: 13574496--13574846 Score: 695
Period size: 175 Copynumber: 2.0 Consensus size: 176
13574486 GAAATGAAAA
13574496 TCGCAATGCGAAATGAAAATCGCAGTGAATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATAG
1 TCGCAATGCGAAATGAAAATCGCAGTGAATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATAG
13574561 CCATTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGCCATTT
66 CCATTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGCCATTT
13574626 TCGCGTTGCGATAGTCAAATGAATGTCTAATAA-TGATAACAACTG
131 TCGCGTTGCGATAGTCAAATGAATGTCTAATAAGTGATAACAACTG
13574671 TCGCAATGCGAAATGAAAATCGCAGTGAATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATAG
1 TCGCAATGCGAAATGAAAATCGCAGTGAATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATAG
13574736 CCATTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGCCATTT
66 CCATTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGCCATTT
13574801 TCGCGTTGCGATAGTCAAATGAATGTCTAATAAGTGATAACAACTG
131 TCGCGTTGCGATAGTCAAATGAATGTCTAATAAGTGATAACAACTG
13574847 AACAGATCAT
Statistics
Matches: 175, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
175 163 0.93
176 12 0.07
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (176 bp):
TCGCAATGCGAAATGAAAATCGCAGTGAATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATAG
CCATTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGCCATTT
TCGCGTTGCGATAGTCAAATGAATGTCTAATAAGTGATAACAACTG
Found at i:13575052 original size:20 final size:20
Alignment explanation
Indices: 13575027--13575077 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
13575017 AAATGATTGC
13575027 CTTTCGCAACGCGATTCTGA
1 CTTTCGCAACGCGATTCTGA
13575047 CTTTCGCAACGCGATTCTGA
1 CTTTCGCAACGCGATTCTGA
13575067 CTTTCGCAACG
1 CTTTCGCAACG
13575078 AGATAATACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.20, C:0.31, G:0.20, T:0.29
Consensus pattern (20 bp):
CTTTCGCAACGCGATTCTGA
Found at i:13575856 original size:24 final size:24
Alignment explanation
Indices: 13575822--13575875 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
13575812 GTATTCGAAA
*
13575822 TTTGATCTTGGACAATACCCGGAC
1 TTTGATATTGGACAATACCCGGAC
* * *
13575846 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGACAATACCCGGAC
13575870 TTTGAT
1 TTTGAT
13575876 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGACAATACCCGGAC
Found at i:13576067 original size:12 final size:12
Alignment explanation
Indices: 13576050--13576074 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13576040 ATATAATCCT
13576050 GAAGAAGAAAAA
1 GAAGAAGAAAAA
13576062 GAAGAAGAAAAA
1 GAAGAAGAAAAA
13576074 G
1 G
13576075 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:13578214 original size:20 final size:20
Alignment explanation
Indices: 13578184--13578240 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
13578174 CAATCATCTT
*
13578184 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGCGGA
* *
13578204 AATTACTATCGCAATGC-GA
1 AATGACTATCGCAACGCGGA
**
13578223 AATGAAAATCGCAACGCG
1 AATGACTATCGCAACGCG
13578241 AATTTAATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (20 bp):
AATGACTATCGCAACGCGGA
Found at i:13578289 original size:33 final size:33
Alignment explanation
Indices: 13578238--13578327 Score: 135
Period size: 33 Copynumber: 2.7 Consensus size: 33
13578228 AAATCGCAAC
* *
13578238 GCGAATTTAATTTCGCGTTGCGATTATCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTATCTCGTT
* *
13578271 GCGCTTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTATCTCGTT
*
13578304 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
13578328 AGTACTTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.43
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTATCTCGTT
Found at i:13578326 original size:19 final size:18
Alignment explanation
Indices: 13578269--13578327 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
13578259 GATTATCTCG
*
13578269 TTGCGCTTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
*
13578287 GTTGCGA--TTC-TCTCG-
1 -TTGCGATTTTCATTTCGC
13578302 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
13578320 ATTGCGAT
1 -TTGCGAT
13578328 AGTACTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 6 0.19
16 7 0.22
17 7 0.22
19 12 0.38
ACGTcount: A:0.10, C:0.24, G:0.20, T:0.46
Consensus pattern (18 bp):
TTGCGATTTTCATTTCGC
Found at i:13578455 original size:14 final size:14
Alignment explanation
Indices: 13578436--13578470 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
13578426 TCAATTAAAA
13578436 AAATCAACTTTTAC
1 AAATCAACTTTTAC
*
13578450 AAATCACCTTTTAC
1 AAATCAACTTTTAC
13578464 AAATCAA
1 AAATCAA
13578471 TTAAACAATA
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:0.23, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATCAACTTTTAC
Found at i:13579890 original size:21 final size:21
Alignment explanation
Indices: 13579824--13579890 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
13579814 GTGAATCGGG
*
13579824 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
13579844 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
13579866 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
13579887 CTCT
1 CTCT
13579891 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:13579909 original size:42 final size:41
Alignment explanation
Indices: 13579824--13579946 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
13579814 GTGAATCGGG
* * * *
13579824 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
13579866 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
13579908 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
13579947 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:13580340 original size:91 final size:90
Alignment explanation
Indices: 13580164--13580348 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
13580154 ATTTCAAACT
*
13580164 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
13580229 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
13580257 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
**
13580321 GTTTTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
13580348 T
1 T
13580349 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 41 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:13582069 original size:20 final size:19
Alignment explanation
Indices: 13582044--13582176 Score: 79
Period size: 19 Copynumber: 7.4 Consensus size: 19
13582034 TTGAAATAAA
*
13582044 AATCGCAACGAGATAATGAG
1 AATCGCAACGAGA-AATGAC
*
13582064 AATCGCAACGCGGAAATGAC
1 AATCGCAACG-AGAAATGAC
*
13582084 TATCGCAACGAG--A-G--
1 AATCGCAACGAGAAATGAC
*
13582098 AATCGCAACGCGAAATGAC
1 AATCGCAACGAGAAATGAC
* *
13582117 TATCGCGACGAG--A-G--
1 AATCGCAACGAGAAATGAC
* * *
13582131 AATCGTAACGCGAAATGAA
1 AATCGCAACGAGAAATGAC
* *
13582150 AATCGCAACGCGAAATGAA
1 AATCGCAACGAGAAATGAC
13582169 AATCGCAA
1 AATCGCAA
13582177 TGCGATTTTG
Statistics
Matches: 88, Mismatches: 14, Indels: 23
0.70 0.11 0.18
Matches are distributed among these distances:
14 18 0.20
16 4 0.05
17 4 0.05
19 36 0.41
20 24 0.27
21 2 0.02
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (19 bp):
AATCGCAACGAGAAATGAC
Found at i:13582118 original size:33 final size:33
Alignment explanation
Indices: 13582061--13582159 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 33
13582051 ACGAGATAAT
13582061 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
13582095 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
* **
13582128 GAGAATCGTAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
13582160 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
33 46 0.77
34 14 0.23
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:13582153 original size:19 final size:19
Alignment explanation
Indices: 13582131--13582181 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
13582121 GCGACGAGAG
*
13582131 AATCGTAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
13582150 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
13582169 AATCGCAATGCGA
1 AATCGCAACGCGA
13582182 TTTTGGTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:13582199 original size:19 final size:19
Alignment explanation
Indices: 13582177--13582221 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
13582167 AAAATCGCAA
*
13582177 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
* *
13582196 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
13582215 TGCGATT
1 TGCGATT
13582222 CTCTCGTCGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.07, C:0.16, G:0.27, T:0.51
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:13582793 original size:20 final size:20
Alignment explanation
Indices: 13582768--13582820 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
13582758 GCGCTATGTA
13582768 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
13582788 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
13582808 TATCTCGTTGCGA
1 AATCGCGTTGCGA
13582821 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:13582882 original size:20 final size:20
Alignment explanation
Indices: 13582829--13582882 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
13582819 GATTTTGTAT
*
13582829 TATCGCATTGCAATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
13582849 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
*
13582869 TATCGCATTACGAT
1 TATCGCATTGCGAT
13582883 TTTCCCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:13582993 original size:21 final size:21
Alignment explanation
Indices: 13582953--13582993 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
13582943 ACTGTAGACC
**
13582953 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
13582974 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
13582994 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:13583316 original size:7 final size:7
Alignment explanation
Indices: 13583304--13583331 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
13583294 CTAGGGTTTT
13583304 GAAGAAA
1 GAAGAAA
13583311 GAAGAAA
1 GAAGAAA
13583318 GAAGAAA
1 GAAGAAA
13583325 GAAGAAA
1 GAAGAAA
13583332 TAAAGGACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (7 bp):
GAAGAAA
Found at i:13585578 original size:17 final size:17
Alignment explanation
Indices: 13585558--13585640 Score: 53
Period size: 17 Copynumber: 4.8 Consensus size: 17
13585548 TATAAATGAA
13585558 TATAATAAATAAAATAT
1 TATAATAAATAAAATAT
*
13585575 TATAAT-AATAATAAATAA
1 TATAATAAAT-A-AAATAT
* *
13585593 TATTAAT-TATTAAATAT
1 TA-TAATAAATAAAATAT
* *
13585610 AATAAATAATTAAAATAT
1 TAT-AATAAATAAAATAT
* *
13585628 AATAATATATAAA
1 TATAATAAATAAA
13585641 TATAGTAATT
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
16 4 0.08
17 24 0.47
18 17 0.33
19 6 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TATAATAAATAAAATAT
Found at i:13585589 original size:23 final size:24
Alignment explanation
Indices: 13585559--13585642 Score: 84
Period size: 25 Copynumber: 3.4 Consensus size: 24
13585549 ATAAATGAAT
13585559 ATAATAAATAA-AATATTATAATA
1 ATAATAAATAATAATATTATAATA
*
13585582 ATAATAAATAATATTAATTATTAA-A
1 ATAATAAATAATAAT-ATTA-TAATA
*
13585607 TATAATAAATAATTAA-AATATAATA
1 -ATAATAAATAA-TAATATTATAATA
13585632 ATATATAAATA
1 ATA-ATAAATA
13585643 TAGTAATTAC
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
23 11 0.22
24 8 0.16
25 16 0.31
26 14 0.27
27 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
ATAATAAATAATAATATTATAATA
Found at i:13585611 original size:26 final size:23
Alignment explanation
Indices: 13585556--13585642 Score: 79
Period size: 23 Copynumber: 3.6 Consensus size: 23
13585546 AATATAAATG
13585556 AATATAATAAATAA-AATATTAT
1 AATATAATAAATAATAATATTAT
*
13585578 AATAATAATAAATAATATTAATTATT
1 AAT-ATAATAAATAATAAT-ATTA-T
*
13585604 AAATATAATAAATAATTAA-AATAT
1 -AATATAATAAATAA-TAATATTAT
13585628 AATAATATATAAATA
1 AAT-ATA-ATAAATA
13585643 TAGTAATTAC
Statistics
Matches: 54, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
22 3 0.06
23 14 0.26
24 6 0.11
25 14 0.26
26 12 0.22
27 5 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AATATAATAAATAATAATATTAT
Found at i:13587616 original size:81 final size:82
Alignment explanation
Indices: 13587449--13587618 Score: 184
Period size: 81 Copynumber: 2.1 Consensus size: 82
13587439 TTTTTTTCTT
* * * * * * * *
13587449 CAACAAATGCCGTAAAAGAGAGTACTTTAGCTACGTTTTTATACAAATGTCATAATAAGGTTCAT
1 CAACAAAAGCCGCAAAAGAGAGTACTTTAACGACGTTTTAATACAAACGCCACAATAAGGTTCAT
* ** *
13587514 ATATAGTGACTTTTTTT
66 ATATAGTGACGTCGTTA
13587531 CAACAAAAGCCGCAATAA-AGAGTACTTTAACGACG-TTTAATACAAACGCCACAAT-AGTGTTC
1 CAACAAAAGCCGCAA-AAGAGAGTACTTTAACGACGTTTTAATACAAACGCCACAATAAG-GTTC
*
13587593 ATATATAGTGGCGTCGTTA
64 ATATATAGTGACGTCGTTA
13587612 CAACAAA
1 CAACAAA
13587619 CGCCATAATA
Statistics
Matches: 73, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
80 2 0.03
81 41 0.56
82 28 0.38
83 2 0.03
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (82 bp):
CAACAAAAGCCGCAAAAGAGAGTACTTTAACGACGTTTTAATACAAACGCCACAATAAGGTTCAT
ATATAGTGACGTCGTTA
Found at i:13587869 original size:41 final size:41
Alignment explanation
Indices: 13587812--13587928 Score: 117
Period size: 41 Copynumber: 2.9 Consensus size: 41
13587802 TGTTTTTATA
* **
13587812 AAACGCCGTAAAATACTCTTACGTTAGTGGCGTTTGTAAAC
1 AAACGCCGCAAAATACTAATACGTTAGTGGCGTTTGTAAAC
* * *
13587853 AAACGTCGCAAAATACTAATACTTTCGTGGCGTTTGTAAAC
1 AAACGCCGCAAAATACTAATACGTTAGTGGCGTTTGTAAAC
* * * * * **
13587894 AAATGCCACTATAGACTTGTACGTTAGTGGCGTTT
1 AAACGCCGCAAAATACTAATACGTTAGTGGCGTTT
13587929 TTGTTCGAAA
Statistics
Matches: 60, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (41 bp):
AAACGCCGCAAAATACTAATACGTTAGTGGCGTTTGTAAAC
Found at i:13588275 original size:2 final size:2
Alignment explanation
Indices: 13588268--13588292 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13588258 AAGAACCTAC
13588268 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
13588293 TATTACTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13588840 original size:21 final size:21
Alignment explanation
Indices: 13588814--13588882 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
13588804 ATATAGAATA
*
13588814 TCCCAAAGGACCACATATATG
1 TCCCAAAGGACCTCATATATG
* * *
13588835 TCCCAAATGACCTCGTAGATTTG
1 TCCCAAAGGACCTC--ATATATG
* *
13588858 TCCCGAAGGACCTCATATATC
1 TCCCAAAGGACCTCATATATG
13588879 TCCC
1 TCCC
13588883 GAATGACCGC
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
21 20 0.54
23 17 0.46
ACGTcount: A:0.29, C:0.32, G:0.14, T:0.25
Consensus pattern (21 bp):
TCCCAAAGGACCTCATATATG
Found at i:13588888 original size:44 final size:44
Alignment explanation
Indices: 13588814--13588897 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
13588804 ATATAGAATA
* *
13588814 TCCCAAAGGACCACATATATGTCCCAAATGACCTCGTAGATTTG
1 TCCCAAAGGACCACATATATCTCCCAAATGACCGCGTAGATTTG
* * *
13588858 TCCCGAAGGACCTCATATATCTCCCGAATGACCGCGTAGA
1 TCCCAAAGGACCACATATATCTCCCAAATGACCGCGTAGA
13588898 ACCCTCGACT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.23
Consensus pattern (44 bp):
TCCCAAAGGACCACATATATCTCCCAAATGACCGCGTAGATTTG
Found at i:13597549 original size:18 final size:18
Alignment explanation
Indices: 13597526--13597564 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
13597516 AACAACACAC
*
13597526 GGAACAAGCACCACCAGA
1 GGAACAAGCACCAACAGA
*
13597544 GGAACAAGCACGAACAGA
1 GGAACAAGCACCAACAGA
13597562 GGA
1 GGA
13597565 TCAAATGCCT
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:0.46, C:0.26, G:0.28, T:0.00
Consensus pattern (18 bp):
GGAACAAGCACCAACAGA
Found at i:13604809 original size:23 final size:21
Alignment explanation
Indices: 13604755--13604816 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
13604745 TTTTGGTGCA
13604755 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAATCGATTCCCCCCTT
* *
13604775 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGATTCCCCCCTT
13604796 GAAGGGGAATCGATTCCCCCC
1 G-A-GGGAATCGATTCCCCCC
13604817 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 10 0.29
21 9 0.26
22 1 0.03
23 15 0.43
ACGTcount: A:0.21, C:0.34, G:0.26, T:0.19
Consensus pattern (21 bp):
GAGGGAATCGATTCCCCCCTT
Found at i:13604842 original size:20 final size:20
Alignment explanation
Indices: 13604757--13604842 Score: 75
Period size: 21 Copynumber: 4.1 Consensus size: 20
13604747 TTGGTGCAGA
13604757 GGGAATCGATCCCCCCTT-G
1 GGGAATCGATCCCCCCTTAG
* *
13604776 AGGGAACCGATTCCCCCTTTGAAG
1 -GGGAATCGA-TCCCCCCTT--AG
**
13604800 GGGAATCGATTCCCCCCACAG
1 GGGAATCGA-TCCCCCCTTAG
*
13604821 GGGAATCGATACCCCCTTAG
1 GGGAATCGATCCCCCCTTAG
13604841 GG
1 GG
13604843 TTCTGGTTAT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
20 18 0.34
21 19 0.36
23 15 0.28
24 1 0.02
ACGTcount: A:0.22, C:0.33, G:0.27, T:0.19
Consensus pattern (20 bp):
GGGAATCGATCCCCCCTTAG
Found at i:13609645 original size:28 final size:28
Alignment explanation
Indices: 13609605--13609667 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
13609595 CAACGACAAC
*
13609605 CATCACACTGAAGTCACCCCCAGGCCAT
1 CATCACACCGAAGTCACCCCCAGGCCAT
*
13609633 CATCACACCGAAGTCACCCCCGGGCCAT
1 CATCACACCGAAGTCACCCCCAGGCCAT
13609661 CATCACA
1 CATCACA
13609668 AGTGCAACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.29, C:0.44, G:0.14, T:0.13
Consensus pattern (28 bp):
CATCACACCGAAGTCACCCCCAGGCCAT
Found at i:13619273 original size:2 final size:2
Alignment explanation
Indices: 13619266--13619290 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13619256 AGTTTCGATC
13619266 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
13619291 CTTATTAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13621339 original size:29 final size:30
Alignment explanation
Indices: 13621280--13621364 Score: 91
Period size: 29 Copynumber: 2.8 Consensus size: 30
13621270 TTAAGTGTTT
*
13621280 AAATAGCAAAAAACAGAAACTTAAATAACTA
1 AAATAG-AAAAAACAGAAACTTAAAGAACTA
* * *
13621311 AAATAGAAAAAATAGAAACTT-AGGGACTA
1 AAATAGAAAAAACAGAAACTTAAAGAACTA
* * *
13621340 AAATAGATAAAACATAAAGTTAAAG
1 AAATAGAAAAAACAGAAACTTAAAG
13621365 GATTGAAATG
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 22 0.50
30 16 0.36
31 6 0.14
ACGTcount: A:0.62, C:0.08, G:0.12, T:0.18
Consensus pattern (30 bp):
AAATAGAAAAAACAGAAACTTAAAGAACTA
Found at i:13622884 original size:3 final size:3
Alignment explanation
Indices: 13622876--13622910 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
13622866 AAAAAATTTG
*
13622876 TAA TAA TAA TAA TTAA TAA TAA TAA TAA TGA TAA T
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA T
13622911 TAAATGGCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:13623326 original size:134 final size:133
Alignment explanation
Indices: 13623107--13623464 Score: 457
Period size: 134 Copynumber: 2.7 Consensus size: 133
13623097 GTTCTAGTCG
** ** * *
13623107 TCTAAGGGTGACACGATTCCTACGTGATGAGGAAATCTGGTCGTGGGATGACAT-TGCTCATGCA
1 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCG-GGGATGAC-TCGGCTCATACA
* * * *
13623171 TGATGAAGAGTTATGGTCATCTTTAGGAAGGTTGATAACTCGGTTCCTACGCGATGAGGACGACT
64 TGATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGACGAGGACGACT
13623236 GGTTA
129 GGTTA
* * *
13623241 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTTTGGTCGGAGGATGACTCGGCTCATACGT
1 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGG-GGATGACTCGGCTCATACAT
* * * *
13623306 GATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTTGGTTCCTACGTGACGAGGATGTCTG
65 GATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGACGAGGACGACTG
13623371 GTTA
130 GTTA
* * ** * * *
13623375 TCTATGGTTGACATTGCTCCTACGTGATGAGGAGGTCTGTTCGGTGGATGACACGGCTCATACTT
1 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGG-GGATGACTCGGCTCATACAT
13623440 GATGAAGAGTTCTGGCCATCTTTAG
65 GATGAAGAGTTCTGGCCATCTTTAG
13623465 TGATTATGGT
Statistics
Matches: 196, Mismatches: 26, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
133 2 0.01
134 194 0.99
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.29
Consensus pattern (133 bp):
TCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGATGACTCGGCTCATACATG
ATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGACGAGGACGACTGG
TTA
Found at i:13624003 original size:91 final size:87
Alignment explanation
Indices: 13623896--13624101 Score: 243
Period size: 91 Copynumber: 2.3 Consensus size: 87
13623886 TGATTTTGTT
* * *
13623896 AAAAGACACAATCTCAAAGATTTTTCAAAAGGAATAGACTCAAAGATTTTTCTCAAGAAAAACTG
1 AAAAGAAACAAACTCAAAGATTTTTCAAAAGAAAT-GACTCAAAGATTTTT-TCAAG--AAACTG
* *
13623961 TCTCAAGAGAGACAAAACTTTGTTTC
62 TCTCAAGAGAAACAAAACTTTGGTTC
* * *
13623987 AAAAGAAACAAACTCAAAAATTTTGGTTTCAAAAGAAATGACTCAAAGATTTTTTCACGAAATTG
1 AAAAGAAACAAACTCAAAGA--TT--TTTCAAAAGAAATGACTCAAAGATTTTTTCAAGAAACTG
*
13624052 TCTTAAGAGAAACAAAACTTTGGTTC
62 TCTCAAGAGAAACAAAACTTTGGTTC
*
13624078 AAAAGAAA-TAACTCAAAGATTTTT
1 AAAAGAAACAAACTCAAAGATTTTT
13624102 ATTTCAAAAG
Statistics
Matches: 100, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
86 3 0.03
88 2 0.02
90 9 0.09
91 53 0.53
93 6 0.06
94 15 0.15
95 12 0.12
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.28
Consensus pattern (87 bp):
AAAAGAAACAAACTCAAAGATTTTTCAAAAGAAATGACTCAAAGATTTTTTCAAGAAACTGTCTC
AAGAGAAACAAAACTTTGGTTC
Found at i:13624030 original size:29 final size:29
Alignment explanation
Indices: 13623974--13624243 Score: 103
Period size: 29 Copynumber: 9.1 Consensus size: 29
13623964 CAAGAGAGAC
*
13623974 AAAACTTTGTTTCAAAAGAAACAAACTCA
1 AAAATTTTGTTTCAAAAGAAACAAACTCA
**
13624003 AAAATTTTGGTTTCAAAAGAAA-TGACTCA
1 AAAATTTT-GTTTCAAAAGAAACAAACTCA
* *
13624032 AAGA-TTT-TTTCACGAAATTGTCTTAAGAGAAA--C-
1 AAAATTTTGTTTCA--AAA--G----AA-ACAAACTCA
* * *
13624065 AAAACTTTGGTTCAAAAGAAA-TAACTCA
1 AAAATTTTGTTTCAAAAGAAACAAACTCA
* *
13624093 AAGATTTTTATTTCAAAAGAAAC-AACTCA
1 AA-AATTTTGTTTCAAAAGAAACAAACTCA
* * *
13624122 CAGATTTTTATTTCAAAAGAAAC-AACTCA
1 -AAAATTTTGTTTCAAAAGAAACAAACTCA
* * *
13624151 CAGATTTTTATTTCAAAAGAAAC-AACTCA
1 -AAAATTTTGTTTCAAAAGAAACAAACTCA
* * *
13624180 CAGATTTTTATTTCAAAAGAAAC-AACTCA
1 -AAAATTTTGTTTCAAAAGAAACAAACTCA
** *
13624209 AAGATAGGTTTTGTTTCAAGGGAAACAATCTCA
1 AA-A-A--TTTTGTTTCAAAAGAAACAAACTCA
13624242 AA
1 AA
13624244 GATGTTTATT
Statistics
Matches: 197, Mismatches: 20, Indels: 44
0.75 0.08 0.17
Matches are distributed among these distances:
25 2 0.01
26 6 0.03
27 3 0.02
28 9 0.05
29 121 0.61
30 15 0.08
31 1 0.01
32 15 0.08
33 13 0.07
34 6 0.03
35 5 0.03
36 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (29 bp):
AAAATTTTGTTTCAAAAGAAACAAACTCA
Found at i:13624127 original size:90 final size:93
Alignment explanation
Indices: 13623918--13624130 Score: 270
Period size: 90 Copynumber: 2.3 Consensus size: 93
13623908 CTCAAAGATT
* *
13623918 TTTCAAAAGGAATAGACTCAAAGATTTTTCTCAAGAAAAACTGTCTCAAGAGAGACAAAACTTTG
1 TTTCAAAAGAAATA-ACTCAAAGATTTTTCTCAAG-AAAACTGTCTCAAGAGAAACAAAACTTTG
* *
13623983 TTTCAAAAGAAACAAACTCAAAAATTTTGG
64 GTTCAAAAGAAACAAACTCAAAAATTTTGA
* * * *
13624013 TTTCAAAAGAAATGACTCAAAGATTTTT-TCACG-AAATTGTCTTAAGAGAAACAAAACTTTGGT
1 TTTCAAAAGAAATAACTCAAAGATTTTTCTCAAGAAAACTGTCTCAAGAGAAACAAAACTTTGGT
* * *
13624076 TCAAAAGAAA-TAACTCAAAGATTTTTA
66 TCAAAAGAAACAAACTCAAAAATTTTGA
* *
13624103 TTTCAAAAGAAACAACTCACAGATTTTT
1 TTTCAAAAGAAATAACTCAAAGATTTTT
13624131 ATTTCAAAAG
Statistics
Matches: 104, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
90 38 0.37
91 36 0.35
93 4 0.04
94 14 0.13
95 12 0.12
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (93 bp):
TTTCAAAAGAAATAACTCAAAGATTTTTCTCAAGAAAACTGTCTCAAGAGAAACAAAACTTTGGT
TCAAAAGAAACAAACTCAAAAATTTTGA
Found at i:13624149 original size:58 final size:58
Alignment explanation
Indices: 13624075--13624263 Score: 261
Period size: 58 Copynumber: 3.2 Consensus size: 58
13624065 AAAACTTTGG
*
13624075 TTCAAAAGAAATAACTCAAAGATTTTTATTTCAAAAGAAACAACTCACAGATTTTTAT
1 TTCAAAAGAAACAACTCAAAGATTTTTATTTCAAAAGAAACAACTCACAGATTTTTAT
*
13624133 TTCAAAAGAAACAACTCACAGATTTTTATTTCAAAAGAAACAACTCACAGATTTTTAT
1 TTCAAAAGAAACAACTCAAAGATTTTTATTTCAAAAGAAACAACTCACAGATTTTTAT
* ** * *
13624191 TTCAAAAGAAACAACTCAAAGATAGGTTTTGTTTCAAGGGAAACAATCTCAAAGATGTTTAT
1 TTCAAAAGAAACAACTCAAAGAT---TTTTATTTCAAAAGAAACAA-CTCACAGATTTTTAT
* *
13624253 TTTAAGAGAAA
1 TTCAAAAGAAA
13624264 TTGTCTTAAA
Statistics
Matches: 117, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
58 78 0.67
61 17 0.15
62 22 0.19
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.31
Consensus pattern (58 bp):
TTCAAAAGAAACAACTCAAAGATTTTTATTTCAAAAGAAACAACTCACAGATTTTTAT
Found at i:13624190 original size:87 final size:89
Alignment explanation
Indices: 13624075--13624263 Score: 256
Period size: 87 Copynumber: 2.1 Consensus size: 89
13624065 AAAACTTTGG
* *
13624075 TTCAAAAGAAATAACTCAAAGATTTTTATTTCAAAAGAAACAACTCACAGAT-TTTTATTTCAAA
1 TTCAAAAGAAACAACTCAAAGATTTTTATTTCAAAAGAAACAACTCAAAGATGTTTTATTTCAAA
* *
13624139 AGAAACAA-CTCACAGATTTTTAT
66 AGAAACAATCTCAAAGATGTTTAT
* *
13624162 TTCAAAAGAAACAACTCACAGATTTTTATTTCAAAAGAAACAACTCAAAGATAGGTTTTGTTTCA
1 TTCAAAAGAAACAACTCAAAGATTTTTATTTCAAAAGAAACAACTCAAAGAT--GTTTTATTTCA
**
13624227 AGGGAAACAATCTCAAAGATGTTTAT
64 AAAGAAACAATCTCAAAGATGTTTAT
* *
13624253 TTTAAGAGAAA
1 TTCAAAAGAAA
13624264 TTGTCTTAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
87 49 0.56
90 17 0.19
91 22 0.25
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.31
Consensus pattern (89 bp):
TTCAAAAGAAACAACTCAAAGATTTTTATTTCAAAAGAAACAACTCAAAGATGTTTTATTTCAAA
AGAAACAATCTCAAAGATGTTTAT
Found at i:13624412 original size:64 final size:64
Alignment explanation
Indices: 13624319--13624439 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 64
13624309 AAGATTTTTC
* * *
13624319 TTCAAAAGGAACAGTCTCAAAAGTGACAAAATCTTGTT-TCCAAAGAAACATACTCAATGATTCT
1 TTCAAAAGAAACAGTCTAAAAAGAGACAAAATCTTGTTAT-CAAAGAAACATACTCAATGATTCT
** *
13624383 TTCAAAAGAAACTTTCTAAAAAGAGACAAAATTTTGTTATCAAAGAAACATACTCAA
1 TTCAAAAGAAACAGTCTAAAAAGAGACAAAATCTTGTTATCAAAGAAACATACTCAA
13624440 ATATTTTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
64 49 0.98
65 1 0.02
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (64 bp):
TTCAAAAGAAACAGTCTAAAAAGAGACAAAATCTTGTTATCAAAGAAACATACTCAATGATTCT
Found at i:13624570 original size:30 final size:31
Alignment explanation
Indices: 13624516--13624574 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
13624506 GAGACAAAGT
13624516 TTTGTTTCAAAAGAAATAGACTCAAAGATCA
1 TTTGTTTCAAAAGAAATAGACTCAAAGATCA
*
13624547 TTTGTTTCAAAAGAAA-CGACTCAAAGAT
1 TTTGTTTCAAAAGAAATAGACTCAAAGAT
13624575 GATGTTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.29
Consensus pattern (31 bp):
TTTGTTTCAAAAGAAATAGACTCAAAGATCA
Found at i:13624652 original size:36 final size:35
Alignment explanation
Indices: 13624612--13624721 Score: 121
Period size: 36 Copynumber: 3.1 Consensus size: 35
13624602 ATAATTTGGA
*
13624612 AAATTGTCTCAAGTGAGACAACATTTGTTTTAAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTT-AGAG
* * * * **
13624648 AAATTGTCTCAAACAACACAAAAAATGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTG-TTTTAGAG
* *
13624684 AAATTGTCTCAAGCGAGACAACGTTTGTTTTTGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTAGAG
13624719 AAA
1 AAA
13624722 ACGATCTCAA
Statistics
Matches: 58, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
35 10 0.17
36 44 0.76
37 4 0.07
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (35 bp):
AAATTGTCTCAAGCGAGACAACATTTGTTTTAGAG
Found at i:13624749 original size:36 final size:36
Alignment explanation
Indices: 13624617--13624737 Score: 91
Period size: 36 Copynumber: 3.4 Consensus size: 36
13624607 TTGGAAAATT
* * * **
13624617 GTCTCAAGTGAGACAACATTTGTTTTAAGAGAAATT
1 GTCTCAAGCGAGACAACGTTTGTTTTTAGAGAAAAC
* * * **** **
13624653 GTCTCAAACAACACAAAAAATGTTTTTAGAGAAATT
1 GTCTCAAGCGAGACAACGTTTGTTTTTAGAGAAAAC
13624689 GTCTCAAGCGAGACAACGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGCGAGACAACGTTTGTTTTTAGAGAAAAC
*
13624724 GATCTCAAGTGAGA
1 G-TCTCAAGCGAGA
13624738 TCAGCTTTGT
Statistics
Matches: 66, Mismatches: 18, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
35 7 0.11
36 59 0.89
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (36 bp):
GTCTCAAGCGAGACAACGTTTGTTTTTAGAGAAAAC
Found at i:13624845 original size:107 final size:105
Alignment explanation
Indices: 13624717--13625033 Score: 344
Period size: 108 Copynumber: 3.0 Consensus size: 105
13624707 TTTGTTTTTG
*
13624717 AGAA-AACGATCTCAAGTGAGATCAGCTTTGTTTAATATGAAAACAAATTTGAAATTTGTATTCT
1 AGAATAACGATCTCAAGTGAGATCAACTTTGTTTAATATG-AAACAAATTTGAAATTTGTA-TCT
*
13624781 CAAAGAAAAAATGTTTCAAACGAGACGAAATTTGTTTTGAAA
64 CAAAGAAAAAATGTCTCAAACGAGACGAAATTTGTTTTGAAA
* * * * * *
13624823 AGAATAACAATCTCAAGTGAGATTAATTTTTGTTTCAA-ATGAATCAAATTCGAAATTT-TATAT
1 AGAATAACGATCTCAAGTGAGATCAA-CTTTGTTT-AATATGAAACAAATTTGAAATTTGTATCT
* * * *
13624886 CAAAGGAAAAAAAATGTCTCAAGCAATACGAAGTTTGTTTT-AAGA
64 CAAA-G--AAAAAATGTCTCAAACGAGACGAAATTTGTTTTGAA-A
* * *
13624931 A-AAT-ACGATCTCAAATGAGATCAACTTTGTTTAATGTGAAACAAA-TTCAAATTTTGTATCTC
1 AGAATAACGATCTCAAGTGAGATCAACTTTGTTTAATATGAAACAAATTTGAAA-TTTGTATCTC
*
13624993 AAA-AGAAAAATGTCTCAAATGAGACGAAATTTGTTTTGAAA
65 AAAGA-AAAAATGTCTCAAACGAGACGAAATTTGTTTTGAAA
13625034 GAAATTGTCT
Statistics
Matches: 173, Mismatches: 26, Indels: 27
0.77 0.12 0.12
Matches are distributed among these distances:
102 1 0.01
103 28 0.16
104 8 0.05
105 24 0.14
106 32 0.18
107 38 0.22
108 40 0.23
109 2 0.01
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.32
Consensus pattern (105 bp):
AGAATAACGATCTCAAGTGAGATCAACTTTGTTTAATATGAAACAAATTTGAAATTTGTATCTCA
AAGAAAAAATGTCTCAAACGAGACGAAATTTGTTTTGAAA
Found at i:13625043 original size:36 final size:37
Alignment explanation
Indices: 13624994--13625063 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 37
13624984 TTGTATCTCA
* *
13624994 AAAGAAAAATGTCTCAAATGAGACGAAATTTGTTTTG
1 AAAGAAAAATGTCTCAAACGAGACAAAATTTGTTTTG
* *
13625031 AAAG-AAATTGTCTCAAGCGAGACAAAATTTGTT
1 AAAGAAAAATGTCTCAAACGAGACAAAATTTGTT
13625064 GTTAGAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 25 0.86
37 4 0.14
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.29
Consensus pattern (37 bp):
AAAGAAAAATGTCTCAAACGAGACAAAATTTGTTTTG
Found at i:13626649 original size:11 final size:11
Alignment explanation
Indices: 13626635--13626682 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
13626625 TGCTTTTGTC
13626635 TTCTTTTTCTT
1 TTCTTTTTCTT
13626646 TTCTTTTTCTTT
1 TTCTTTTTC-TT
13626658 TTCTATTTTTCTT
1 TTC--TTTTTCTT
**
13626671 TGATTTTTCTT
1 TTCTTTTTCTT
13626682 T
1 T
13626683 GTACTCTGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 18 0.56
12 5 0.16
13 3 0.09
14 6 0.19
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:13627291 original size:20 final size:20
Alignment explanation
Indices: 13627253--13627291 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13627243 GGATAAATGC
*
13627253 AATGTTTCAATGTCACAAAG
1 AATGTTTCAAGGTCACAAAG
*
13627273 AATGTTTCAAGGTCTCAAA
1 AATGTTTCAAGGTCACAAA
13627292 AAGAGGGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (20 bp):
AATGTTTCAAGGTCACAAAG
Found at i:13630384 original size:22 final size:21
Alignment explanation
Indices: 13630359--13630400 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13630349 ATTTAAGTGT
*
13630359 TTAAATAGCAAAAAATAGAAAC
1 TTAAATAAC-AAAAATAGAAAC
*
13630381 TTAAATAACTAAAATAGAAA
1 TTAAATAACAAAAATAGAAA
13630401 AAATAGAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (21 bp):
TTAAATAACAAAAATAGAAAC
Found at i:13630420 original size:29 final size:30
Alignment explanation
Indices: 13630361--13630454 Score: 100
Period size: 30 Copynumber: 3.1 Consensus size: 30
13630351 TTAAGTGTTT
*
13630361 AAATAGCAAAAAATAGAAACTTAAATAACTA
1 AAATAG-AAAAAATAGAAACTTAAAGAACTA
* *
13630392 AAATAGAAAAAATAGAAACTT-AGGGACTA
1 AAATAGAAAAAATAGAAACTTAAAGAACTA
* * * * *
13630421 AAATAGATAAAACAGAAAGTTAAAGGACTG
1 AAATAGAAAAAATAGAAACTTAAAGAACTA
13630451 AAAT
1 AAAT
13630455 GGTATTAACA
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
29 23 0.43
30 25 0.46
31 6 0.11
ACGTcount: A:0.61, C:0.07, G:0.14, T:0.18
Consensus pattern (30 bp):
AAATAGAAAAAATAGAAACTTAAAGAACTA
Found at i:13631898 original size:3 final size:3
Alignment explanation
Indices: 13631890--13631921 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
13631880 AAAAAATTTG
13631890 TAA TAA TAA TAA TTAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA T
13631922 TAAATGGCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:13632151 original size:21 final size:23
Alignment explanation
Indices: 13632108--13632152 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
13632098 CAAGATTCAG
13632108 AAAACAACAAAGAAAAATGTAAAA
1 AAAACAACAAAGAAAAA-GTAAAA
*
13632132 AAAACAA-AAATAAAAA-TAAAA
1 AAAACAACAAAGAAAAAGTAAAA
13632153 GGTTTCATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
23 8 0.40
24 7 0.35
ACGTcount: A:0.80, C:0.07, G:0.04, T:0.09
Consensus pattern (23 bp):
AAAACAACAAAGAAAAAGTAAAA
Found at i:13634509 original size:39 final size:39
Alignment explanation
Indices: 13634429--13634527 Score: 107
Period size: 39 Copynumber: 2.6 Consensus size: 39
13634419 ACTATTTAGA
* *
13634429 AAAT-AAA-AGAATAAAGTTATAGTTAATCTAAACTACT
1 AAATCAAATAGAATAGAGTTATAGTTAATCTAAACAACT
* *
13634466 AAATCAAATA-AGATAGAGTTATGGTTAATCTAAA-AAGT
1 AAATCAAATAGA-ATAGAGTTATAGTTAATCTAAACAACT
*
13634504 CAAATCAAATAGAATAGAGATATA
1 -AAATCAAATAGAATAGAGTTATA
13634528 ATTTGTAACA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
37 4 0.08
38 6 0.12
39 40 0.78
40 1 0.02
ACGTcount: A:0.54, C:0.07, G:0.12, T:0.27
Consensus pattern (39 bp):
AAATCAAATAGAATAGAGTTATAGTTAATCTAAACAACT
Found at i:13635462 original size:20 final size:19
Alignment explanation
Indices: 13635437--13635486 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
13635427 AGTCCCTCTA
* *
13635437 TATCGATACTAACCTTTGG
1 TATCGATACTAACATCTGG
*
13635456 CTATCGATAATAACATCTGG
1 -TATCGATACTAACATCTGG
13635476 TATCGATACTA
1 TATCGATACTA
13635487 CTACCTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (19 bp):
TATCGATACTAACATCTGG
Done.