Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006670.1 Hibiscus syriacus cultivar Beakdansim tig00016531_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: 93626
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:2189 original size:131 final size:128
Alignment explanation
Indices: 1747--2188 Score: 485
Period size: 131 Copynumber: 3.4 Consensus size: 128
1737 GAGACATTAT
* *** * *
1747 CCCTAAAGATGGCCTGCCATCCTCATGGTGTAGGAACCGTGTCATCCACCGACCAAACCTCCTTA
1 CCCTAAAGATGGCCTGCCGTCCTCATCACGTAGGAACCATGTCATCC-CCGACCAAACCTCCTCA
* * * *
1812 TCATGTAGGAGCCGTGTCACTCCTAGATAACCAACCGTCCTCATCAC-GTAGGAACCATGTTATC
65 TCACGTAGAAGACGTGTCAC-CCCAGATAACC-ACCGTCCTCATCACAG-AGGAACCATGTTATC
*
1876 AT
127 AC
* * * * *
1878 TCCTAAAGATGGCCTAG-TGTCCTCATCACGTAGGAATCGTGTCATCCCCGACCAAATCTCCTCA
1 CCCTAAAGATGGCCT-GCCGTCCTCATCACGTAGGAACCATGTCATCCCCGACCAAACCTCCTCA
* * *
1942 TCACGTA-AGAGACGTGTCACCCCAGATAACGACCGTCCTAATCACATAGGAACCATGTTATCAC
65 TCACGTAGA-AGACGTGTCACCCCAGATAACCACCGTCCTCATCACAGAGGAACCATGTTATCAC
* * * * *
2006 CATTCCTAAAGATGGCTTGCCGTTCTCATCACGTAGGAACCATGCCATCCCCTGACTAGACCTCC
1 C---CCTAAAGATGGCCTGCCGTCCTCATCACGTAGGAACCATGTCATCCCC-GACCAAACCTCC
* *
2071 TCATCACGTAGAAGTCGTGTCACCCCAGATAACCAGCCGTCCTCATCACAGAGAAACCATGTTAT
62 TCATCACGTAGAAGACGTGTCACCCCAGATAACCA-CCGTCCTCATCACAGAGGAACCATGTTAT
2136 CAC
126 CAC
* * * *
2139 CCCTTAAAGATGGCATGTCGTCCTCATCGCGTAGAAACCATGTCATCCCC
1 CCC-TAAAGATGGCCTGCCGTCCTCATCACGTAGGAACCATGTCATCCCC
2189 TTAGATGACC
Statistics
Matches: 262, Mismatches: 38, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
128 29 0.11
129 9 0.03
130 34 0.13
131 118 0.45
132 41 0.16
133 31 0.12
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.23
Consensus pattern (128 bp):
CCCTAAAGATGGCCTGCCGTCCTCATCACGTAGGAACCATGTCATCCCCGACCAAACCTCCTCAT
CACGTAGAAGACGTGTCACCCCAGATAACCACCGTCCTCATCACAGAGGAACCATGTTATCAC
Found at i:3622 original size:30 final size:30
Alignment explanation
Indices: 3586--3648 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
3576 AAGTTATGAG
*
3586 CTATGTGATAAAGGTATAGAAATGATATGT
1 CTATGTGATAAAGGTATAGAAATAATATGT
*
3616 CTATGTGATAAAGGTATGGAAATAATATGT
1 CTATGTGATAAAGGTATAGAAATAATATGT
3646 CTA
1 CTA
3649 CGCGATATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (30 bp):
CTATGTGATAAAGGTATAGAAATAATATGT
Found at i:3924 original size:23 final size:23
Alignment explanation
Indices: 3890--3975 Score: 86
Period size: 23 Copynumber: 3.7 Consensus size: 23
3880 ACATATTATA
*
3890 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
3913 TGGCACTTCGGTGCATTTCTATG
1 TGGCACTTCGGTGCAATTCTACG
* *
3936 CTGTCA-TTCGAGAT-AAATTCTACG
1 -TGGCACTTCG-G-TGCAATTCTACG
3960 TGGCACTTCGGTGCAA
1 TGGCACTTCGGTGCAA
3976 ATTTATACGA
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
22 1 0.02
23 31 0.63
24 16 0.33
25 1 0.02
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:4527 original size:20 final size:20
Alignment explanation
Indices: 4502--4539 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4492 ATGCATCGAT
4502 GCACTGT-AGCACTGTTCATG
1 GCACTGTAAG-ACTGTTCATG
4522 GCACTGTAAGACTGTTCA
1 GCACTGTAAGACTGTTCA
4540 CTGTACTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (20 bp):
GCACTGTAAGACTGTTCATG
Found at i:13404 original size:101 final size:100
Alignment explanation
Indices: 13299--13494 Score: 286
Period size: 101 Copynumber: 1.9 Consensus size: 100
13289 ACATCTTGTA
*
13299 TTTTTCTTTTATATTAGTAAAATTAGTTTTCTATGT-GTAGTTGGTTTTTTCTGTTTAGGTTTTT
1 TTTTTCTTTTATATTAGTAAAATTAGTTTTCTATGTCATAGTTGGTTTTTTCTGTTTAGG-TTTT
**
13363 TTACGAAAATTTTGGTATCTTTTGTTCTTCTTATATT
65 TTACGAAAATTTTAAT-TCTTTTGTTCTTCTTATATT
* * * *
13400 TTTTTCTTTTATATTAGTAAAATTTGTTTTCTCTGTCATGGTTGGTTTTTTCTTTTTAGGTTTTT
1 TTTTTCTTTTATATTAGTAAAATTAGTTTTCTATGTCATAGTTGGTTTTTTCTGTTTAGGTTTTT
* *
13465 TACGTAAATTTTAATTTTTTTGTTCTTCTT
66 TACGAAAATTTTAATTCTTTTGTTCTTCTT
13495 TTTTCAATCA
Statistics
Matches: 85, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
100 14 0.16
101 51 0.60
102 20 0.24
ACGTcount: A:0.17, C:0.08, G:0.13, T:0.62
Consensus pattern (100 bp):
TTTTTCTTTTATATTAGTAAAATTAGTTTTCTATGTCATAGTTGGTTTTTTCTGTTTAGGTTTTT
TACGAAAATTTTAATTCTTTTGTTCTTCTTATATT
Found at i:13413 original size:15 final size:16
Alignment explanation
Indices: 13382--13414 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
13372 TTTTGGTATC
13382 TTTTGTTCTTCTTATA
1 TTTTGTTCTTCTTATA
*
13398 TTTTTTTCTT-TTATA
1 TTTTGTTCTTCTTATA
13413 TT
1 TT
13415 AGTAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTGTTCTTCTTATA
Found at i:16494 original size:16 final size:17
Alignment explanation
Indices: 16462--16517 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 17
16452 TATTAAGAAA
16462 AAAATAATAGAAAAAAT
1 AAAATAATAGAAAAAAT
*
16479 AAAATAA-AGTAAAAAT
1 AAAATAATAGAAAAAAT
* *
16495 ATAATATATATAAATAAAT
1 AAAATA-ATAGAAA-AAAT
16514 AAAA
1 AAAA
16518 ACAAAAATAG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 13 0.42
17 8 0.26
18 3 0.10
19 7 0.23
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (17 bp):
AAAATAATAGAAAAAAT
Found at i:16514 original size:47 final size:46
Alignment explanation
Indices: 16459--16572 Score: 110
Period size: 47 Copynumber: 2.4 Consensus size: 46
16449 TGATATTAAG
16459 AAAA-AAATAATAGAAAAAATA-AA-ATAAAGTAAAAATATAATATATA
1 AAAATAAATAATAGAAAAAATAGAATATAAAG--AAAATAT-ATATATA
* * *
16505 TAAATAAATAA-AAACAAAAATAGAATATTAAGAAAATATATATATA
1 AAAATAAATAATAGA-AAAAATAGAATATAAAGAAAATATATATATA
*
16551 AAAATATAATATTAAGAAAAAA
1 AAAATA-AATAAT-AGAAAAAA
16573 CATATACATA
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
46 17 0.31
47 24 0.44
48 7 0.13
49 7 0.13
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (46 bp):
AAAATAAATAATAGAAAAAATAGAATATAAAGAAAATATATATATA
Found at i:16540 original size:17 final size:16
Alignment explanation
Indices: 16451--16571 Score: 53
Period size: 16 Copynumber: 7.8 Consensus size: 16
16441 GATATACATG
16451 ATATTAAG-AAAA-AA
1 ATATTAAGAAAAATAA
*
16465 ATAAT-AGAAAAAATAA
1 ATATTAAG-AAAAATAA
*
16481 A-ATAAAGTAAAAATATA
1 ATATTAAG-AAAAATA-A
* *
16498 ATA-T-ATATAAATAA
1 ATATTAAGAAAAATAA
** *
16512 ATAAAAACAAAAATAGA
1 ATATTAAGAAAAATA-A
*
16529 ATATTAAG-AAAATAT
1 ATATTAAGAAAAATAA
*
16544 ATA-T-ATAAAAATATA
1 ATATTAAGAAAAATA-A
16559 ATATTAAGAAAAA
1 ATATTAAGAAAAA
16572 ACATATACAT
Statistics
Matches: 77, Mismatches: 17, Indels: 23
0.66 0.15 0.20
Matches are distributed among these distances:
13 3 0.04
14 15 0.19
15 17 0.22
16 27 0.35
17 14 0.18
18 1 0.01
ACGTcount: A:0.69, C:0.01, G:0.05, T:0.25
Consensus pattern (16 bp):
ATATTAAGAAAAATAA
Found at i:16577 original size:15 final size:14
Alignment explanation
Indices: 16528--16570 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
16518 ACAAAAATAG
16528 AATATTAAGAAAAT
1 AATATTAAGAAAAT
16542 ATATATATAA-AAATAT
1 A-ATAT-TAAGAAA-AT
16558 AATATTAAGAAAA
1 AATATTAAGAAAA
16571 AACATATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 5 0.20
15 14 0.56
16 6 0.24
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (14 bp):
AATATTAAGAAAAT
Found at i:16578 original size:30 final size:30
Alignment explanation
Indices: 16520--16578 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
16510 AAATAAAAAC
* *
16520 AAAAATAGAATATTAAGAAAATATATATAT
1 AAAAATAGAATATTAAGAAAAAACATATAT
*
16550 AAAAATATAATATTAAGAAAAAACATATA
1 AAAAATAGAATATTAAGAAAAAACATATA
16579 CATAGTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (30 bp):
AAAAATAGAATATTAAGAAAAAACATATAT
Found at i:16661 original size:23 final size:23
Alignment explanation
Indices: 16608--16702 Score: 68
Period size: 25 Copynumber: 4.0 Consensus size: 23
16598 TTAATACGTA
* *
16608 TATATATATATATATAATGATATAAG
1 TATATATA-ATA-AAAATAATAT-AG
16634 ATATATATAATAAAAATAATATAG
1 -TATATATAATAAAAATAATATAG
* * *
16658 TATAAATAAAAAAAGAGGAATATAG
1 TATATATAATAAAA-A-TAATATAG
*
16683 TAAATA-AATAAAAA-AATATA
1 TATATATAATAAAAATAATATA
16703 ATTAAAAATA
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
21 6 0.10
23 13 0.22
24 9 0.16
25 19 0.33
26 3 0.05
27 8 0.14
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (23 bp):
TATATATAATAAAAATAATATAG
Found at i:17843 original size:37 final size:37
Alignment explanation
Indices: 17793--17881 Score: 162
Period size: 37 Copynumber: 2.4 Consensus size: 37
17783 TGAGGGTTTG
17793 GTGTTTCAAGAGAAAC-ATCTTCAAAGGTTTTTTTTTT
1 GTGTTTCAAGAGAAACAAT-TTCAAAGGTTTTTTTTTT
17830 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTTT
17867 GTGTTTCAAGAGAAA
1 GTGTTTCAAGAGAAA
17882 TTGTATTCAA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
37 49 0.96
38 2 0.04
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (37 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTTT
Found at i:18050 original size:15 final size:15
Alignment explanation
Indices: 18026--18063 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
18016 AAAATATGCT
*
18026 TCAAGAGAAACTGTC
1 TCAAGAGAAACTATC
*
18041 TCAAGGGAAACTATC
1 TCAAGAGAAACTATC
18056 TCAAGAGA
1 TCAAGAGA
18064 GATAAAATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.18
Consensus pattern (15 bp):
TCAAGAGAAACTATC
Found at i:18160 original size:102 final size:102
Alignment explanation
Indices: 18054--18240 Score: 254
Period size: 102 Copynumber: 1.8 Consensus size: 102
18044 AGGGAAACTA
* * *
18054 TCTC-AAGAGAGATAAAATTCATTTCAATGGAAATG-TTTTC-AATGTTTATGTTTCAAGAGAAA
1 TCTCAAAG-GAGATAAAATTCATTTCAA-GGAAAAGATATTCAAATATTT-TGTTTCAAGAGAAA
18116 CTATCTCAAGAGAGATAAAACTTAGTTCCAAAAGAAAATG
63 CTATCTCAAGAGAGATAAAACTTAGTTCCAAAAGAAAATG
* ** * *
18156 TCTCAAAGGAGATGAAATTTGTTTCAAGGAAAAGATATTCAAATATTTTGTTTCAAGGGAAACTG
1 TCTCAAAGGAGATAAAATTCATTTCAAGGAAAAGATATTCAAATATTTTGTTTCAAGAGAAACTA
18221 TCTCAAGAGAGATAAAACTT
66 TCTCAAGAGAGATAAAACTT
18241 GGAAACTGTC
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
101 6 0.08
102 59 0.80
103 9 0.12
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.30
Consensus pattern (102 bp):
TCTCAAAGGAGATAAAATTCATTTCAAGGAAAAGATATTCAAATATTTTGTTTCAAGAGAAACTA
TCTCAAGAGAGATAAAACTTAGTTCCAAAAGAAAATG
Found at i:18579 original size:106 final size:106
Alignment explanation
Indices: 18388--18642 Score: 352
Period size: 106 Copynumber: 2.4 Consensus size: 106
18378 GTATTGTTCT
* *** * * *
18388 GAGTCCAATATCCTCCGCCATGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAACTGGAAAATTGTTTGTTGACAA
*
18453 CCAGCCATCCCTTTGATGTGAAGTAGAACTTGTGTTGTCTC
66 CCAGCCATCCCTTTGATGTGAAGTAGAACTTGTGTTATCTC
* * *
18494 GATTCCAATATCCTTC-ACTGTGAAGTTGAAATTGGTTTTGAAACTGGAAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGA-TGTGAAGTTGAAATTGGCTCTGAAACTGGAAAATTGTTTGTTGACA
* *
18558 ACCAGCCGTCCCTTT-ACTGTGAAGTTGAACTTGTGTTATCTC
65 ACCAGCCATCCCTTTGA-TGTGAAGTAGAACTTGTGTTATCTC
*
18600 GAGTCCAATATTCTTCGATGTGAAGTTGAAATTGGCTCTGAAA
1 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAA
18643 TTAGGAAGCC
Statistics
Matches: 129, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
105 1 0.01
106 127 0.98
107 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAACTGGAAAATTGTTTGTTGACAA
CCAGCCATCCCTTTGATGTGAAGTAGAACTTGTGTTATCTC
Found at i:19312 original size:32 final size:32
Alignment explanation
Indices: 19258--19370 Score: 129
Period size: 32 Copynumber: 3.5 Consensus size: 32
19248 TTTGCATCAG
* * * *
19258 GATGTTGAAT-TCCCAAAGATGCCCCAATATTC
1 GATGTTGAATCT-CAAAAAATGCCCCAACATTT
* *
19290 AATGTTGAATCTCAAAAAATGCCTCAACATTT
1 GATGTTGAATCTCAAAAAATGCCCCAACATTT
* *
19322 GATGTTAAATCTAAAAAAATGCCCCAACATTT
1 GATGTTGAATCTCAAAAAATGCCCCAACATTT
19354 GATGTTGAATCTTCAAA
1 GATGTTGAATC-TCAAA
19371 GATACCCTCA
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
32 62 0.93
33 5 0.07
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.30
Consensus pattern (32 bp):
GATGTTGAATCTCAAAAAATGCCCCAACATTT
Found at i:20480 original size:15 final size:13
Alignment explanation
Indices: 20438--20488 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
20428 TTTTCTTCAA
*
20438 TTTC-CTTTGTTT
1 TTTCTCTTTTTTT
*
20450 TTTCTCTTTTTAT
1 TTTCTCTTTTTTT
20463 TTTCTCTTTGCTTTT
1 TTTCTCTTT--TTTT
20478 TTTCTCTTTTT
1 TTTCTCTTTTT
20489 GTTCTGATTG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 4 0.12
13 17 0.52
15 12 0.36
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (13 bp):
TTTCTCTTTTTTT
Found at i:22237 original size:13 final size:14
Alignment explanation
Indices: 22208--22258 Score: 63
Period size: 13 Copynumber: 3.8 Consensus size: 14
22198 TTTTTCTTCA
22208 ATTTTC-CTTTGTT
1 ATTTTCTCTTTGTT
22221 -TTTTCTCTTT-TT
1 ATTTTCTCTTTGTT
22233 ATTTTCTCTTTGCTT
1 ATTTTCTCTTTG-TT
*
22248 TTTTTCTCTTT
1 ATTTTCTCTTT
22259 TTGTTCTGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 7 0.21
13 14 0.42
15 12 0.36
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.75
Consensus pattern (14 bp):
ATTTTCTCTTTGTT
Found at i:22243 original size:26 final size:26
Alignment explanation
Indices: 22208--22260 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 26
22198 TTTTTCTTCA
22208 ATTTTCCTTTG-TTTTTTCTCTTTTT
1 ATTTTCCTTTGCTTTTTTCTCTTTTT
22233 ATTTTCTCTTTGCTTTTTTTCTCTTTTT
1 ATTTTC-CTTTGC-TTTTTTCTCTTTTT
22261 GTTCTGATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
28 14 0.56
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.75
Consensus pattern (26 bp):
ATTTTCCTTTGCTTTTTTCTCTTTTT
Found at i:25379 original size:26 final size:27
Alignment explanation
Indices: 25330--25383 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
25320 TGCAAACAAG
25330 AGAATAATAAATAAAACAAGAAAAAAT
1 AGAATAATAAATAAAACAAGAAAAAAT
*
25357 AGAA-AAT-AATAAAACACGTAAAAAAT
1 AGAATAATAAATAAAACAAG-AAAAAAT
25383 A
1 A
25384 ATAAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 10 0.40
26 11 0.44
27 4 0.16
ACGTcount: A:0.72, C:0.06, G:0.07, T:0.15
Consensus pattern (27 bp):
AGAATAATAAATAAAACAAGAAAAAAT
Found at i:25393 original size:26 final size:25
Alignment explanation
Indices: 25332--25394 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
25322 CAAACAAGAG
*
25332 AATAATAAATAAAACAAGAAAAAAT
1 AATAAAAAATAAAACAAGAAAAAAT
* *
25357 AGA-AAATAATAAAACACGTAAAAAAT
1 A-ATAAAAAATAAAACAAG-AAAAAAT
25383 AATAAAAAATAA
1 AATAAAAAATAA
25395 TAAAAATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
25 14 0.45
26 17 0.55
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.16
Consensus pattern (25 bp):
AATAAAAAATAAAACAAGAAAAAAT
Found at i:25399 original size:19 final size:19
Alignment explanation
Indices: 25377--25418 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
25367 AAAACACGTA
25377 AAAAATAATAAAAAAT-AAT
1 AAAAATAA-AAAAAATGAAT
*
25396 AAAAATAAACAAAATGAAT
1 AAAAATAAAAAAAATGAAT
25415 AAAA
1 AAAA
25419 TGTTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (19 bp):
AAAAATAAAAAAAATGAAT
Found at i:25409 original size:9 final size:9
Alignment explanation
Indices: 25377--25418 Score: 50
Period size: 10 Copynumber: 4.4 Consensus size: 9
25367 AAAACACGTA
25377 AAAAATAAT
1 AAAAATAAT
25386 AAAAAATAAT
1 -AAAAATAAT
25396 AAAAATAA-
1 AAAAATAAT
25404 ACAAAATGAAT
1 A-AAAAT-AAT
25415 AAAA
1 AAAA
25419 TGTTAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 1 0.03
9 13 0.45
10 14 0.48
11 1 0.03
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (9 bp):
AAAAATAAT
Found at i:25409 original size:29 final size:28
Alignment explanation
Indices: 25332--25418 Score: 70
Period size: 29 Copynumber: 3.0 Consensus size: 28
25322 CAAACAAGAG
* * *
25332 AATAATAAATAAAACAAGAAAAAATAGAA
1 AATAATAAAAAAAACAA-AAATAATAAAA
**
25361 AATAATAAAACACGTA-AAAAATAATAAAA
1 AATAATAAAA-A-AAACAAAAATAATAAAA
25390 AATAATAAAAATAAAC-AAAATGAATAAAA
1 AATAATAAAAA-AAACAAAAAT-AATAAAA
25419 TGTTAAAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
28 7 0.15
29 35 0.76
30 3 0.07
31 1 0.02
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.16
Consensus pattern (28 bp):
AATAATAAAAAAAACAAAAATAATAAAA
Found at i:25495 original size:19 final size:18
Alignment explanation
Indices: 25462--25498 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
25452 AATTAATGGA
25462 GTAAAAAAATAAAAAAAG
1 GTAAAAAAATAAAAAAAG
*
25480 GTAAAAGAAATTAAAAAAG
1 GTAAAA-AAATAAAAAAAG
25499 AATAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (18 bp):
GTAAAAAAATAAAAAAAG
Found at i:25504 original size:20 final size:18
Alignment explanation
Indices: 25463--25506 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
25453 ATTAATGGAG
*
25463 TAAAAAAATAAAAAAAGG
1 TAAAAAAATAAAAAAAGA
*
25481 TAAAAGAAATTAAAAAAGAA
1 TAAAA-AAATAAAAAAAG-A
25501 TAAAAA
1 TAAAAA
25507 TAATGTGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 12 0.55
20 5 0.23
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (18 bp):
TAAAAAAATAAAAAAAGA
Found at i:25682 original size:32 final size:31
Alignment explanation
Indices: 25601--25714 Score: 83
Period size: 29 Copynumber: 3.6 Consensus size: 31
25591 GATATACATG
* *
25601 ATATTAAGAAAA-AAATAATAAAAAAAGTAAAA
1 ATATTAAGAAAATAAATAA-AAAAAAAAT-AGA
*
25633 ATATAATATATATAAATAAATAAAAACAAAAATAGA
1 ATAT--TA-AGA-AAATAAATAAAAA-AAAAATAGA
* * *
25669 ATATTAAGAAAAT--ATATATAAAAAATATA
1 ATATTAAGAAAATAAATAAAAAAAAAATAGA
25698 ATATTAAGAAAA-AAATA
1 ATATTAAGAAAATAAATA
25715 TATACATAGT
Statistics
Matches: 67, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
29 20 0.30
30 8 0.12
32 8 0.12
33 2 0.03
34 4 0.06
35 2 0.03
36 12 0.18
37 11 0.16
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.25
Consensus pattern (31 bp):
ATATTAAGAAAATAAATAAAAAAAAAATAGA
Found at i:25693 original size:29 final size:30
Alignment explanation
Indices: 25660--25718 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
25650 AAATAAAAAC
*
25660 AAAAATAGAATATTAAG-AAAATATATATA
1 AAAAATAGAATATTAAGAAAAAAATATATA
*
25689 AAAAATATAATATTAAGAAAAAAATATATA
1 AAAAATAGAATATTAAGAAAAAAATATATA
25719 CATAGTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (30 bp):
AAAAATAGAATATTAAGAAAAAAATATATA
Found at i:25751 original size:2 final size:2
Alignment explanation
Indices: 25746--25818 Score: 105
Period size: 2 Copynumber: 37.0 Consensus size: 2
25736 AATTAACACG
*
25746 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG 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
*
25788 TA TA TA TA TA TA -A TGA TA TA -A GA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA
25819 ATAAAAATAA
Statistics
Matches: 65, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.03
2 61 0.94
3 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:25836 original size:23 final size:23
Alignment explanation
Indices: 25783--25848 Score: 51
Period size: 25 Copynumber: 2.7 Consensus size: 23
25773 ATATATATGT
* *
25783 ATATATATATATATATAATGATATA
1 ATATATATA-ATA-AAAATAATATA
*
25808 AGATATATATAATAAAAATAATATA
1 ATATAT--ATAATAAAAATAATATA
* *
25833 ATATAAATAAAAAAAA
1 ATATATATAATAAAAA
25849 GAGGAATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
23 9 0.27
25 18 0.55
26 3 0.09
27 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (23 bp):
ATATATATAATAAAAATAATATA
Found at i:28429 original size:10 final size:10
Alignment explanation
Indices: 28414--28477 Score: 53
Period size: 10 Copynumber: 6.7 Consensus size: 10
28404 TTAACTTTAG
28414 TTTTTTAATT
1 TTTTTTAATT
28424 TTTTTTAA-T
1 TTTTTTAATT
**
28433 TTGATTAATT
1 TTTTTTAATT
* *
28443 TTTATT--TG
1 TTTTTTAATT
*
28451 TTTTTTAATA
1 TTTTTTAATT
*
28461 TTTTTTAATA
1 TTTTTTAATT
28471 TTTTTTA
1 TTTTTTA
28478 GATTGCACCA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
8 6 0.13
9 7 0.16
10 32 0.71
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (10 bp):
TTTTTTAATT
Found at i:30819 original size:57 final size:56
Alignment explanation
Indices: 30716--30852 Score: 141
Period size: 57 Copynumber: 2.4 Consensus size: 56
30706 AATTATGTGA
* * * * * *
30716 ATATGTTCTATGGGAAGAAATAATAATTTGAAGAATGGCATATGAAATGCTACGAGT
1 ATATG-TCTATGTGAACAAATGATAAGTTGAAGAAAGGCATATGAAATGCAACGAGT
* * *
30773 ATATGATCTATGTGAATAAATGATAAGTTG-AGAAAGGCTATGTGAAATGCAATGAGT
1 ATATG-TCTATGTGAACAAATGATAAGTTGAAGAAAGGC-ATATGAAATGCAACGAGT
*
30830 ATATGTTTGATGTGAACAAATGA
1 ATATGTCT-ATGTGAACAAATGA
30853 CAATTTGATT
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
56 9 0.13
57 58 0.87
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (56 bp):
ATATGTCTATGTGAACAAATGATAAGTTGAAGAAAGGCATATGAAATGCAACGAGT
Found at i:30999 original size:24 final size:24
Alignment explanation
Indices: 30972--31038 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
30962 CTTTGGTACG
30972 AATTCTATGTGGTCCTTCGAGACA
1 AATTCTATGTGGTCCTTCGAGACA
* * * *
30996 AATTCTACGCGGTCCTTCGGGATA
1 AATTCTATGTGGTCCTTCGAGACA
31020 AA-TCTATGTGG-CACTTCGA
1 AATTCTATGTGGTC-CTTCGA
31039 TGCATATTCT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
22 1 0.03
23 12 0.34
24 22 0.63
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (24 bp):
AATTCTATGTGGTCCTTCGAGACA
Found at i:31912 original size:36 final size:37
Alignment explanation
Indices: 31867--31939 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 37
31857 TTTATTTTTC
*
31867 ACAATTATTAATTTACTTTGTATTT-ATTTTTTTAAT
1 ACAATTATTAATTTACTTTGAATTTAATTTTTTTAAT
* *
31903 ACAATTATTATTTTTCTTTGAATTTGAATTTTTTTAA
1 ACAATTATTAATTTACTTTGAATTT-AATTTTTTTAA
31940 ATTTTATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 22 0.69
38 10 0.31
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.60
Consensus pattern (37 bp):
ACAATTATTAATTTACTTTGAATTTAATTTTTTTAAT
Found at i:36279 original size:20 final size:19
Alignment explanation
Indices: 36254--36307 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
36244 GCGAAATAAA
36254 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
36274 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
36294 AATCGCAACGCGAT
1 AATCGCAACGCGAT
36308 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:36367 original size:20 final size:20
Alignment explanation
Indices: 36342--36394 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
36332 ACAAATTCGC
* *
36342 AATCGCAATGCGAATATGA-A
1 AATCGCAACGCGAACAT-ATA
36362 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAACATATA
36382 AATCGCAACGCGA
1 AATCGCAACGCGA
36395 TTCTGACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.43, C:0.23, G:0.19, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCGAACATATA
Found at i:36429 original size:21 final size:21
Alignment explanation
Indices: 36403--36480 Score: 95
Period size: 21 Copynumber: 3.8 Consensus size: 21
36393 GATTCTGACT
36403 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGAGTATCCGTAAA
*
36424 ATCGCAACGCGTATCCGT-AA
1 ATCGCAACGAGTATCCGTAAA
* ** *
36444 ATCGCAATGACAATACGTAAA
1 ATCGCAACGAGTATCCGTAAA
*
36465 ATCGCAACGCGTATCC
1 ATCGCAACGAGTATCC
36481 TGAAGAATAG
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (21 bp):
ATCGCAACGAGTATCCGTAAA
Found at i:36448 original size:41 final size:41
Alignment explanation
Indices: 36403--36480 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
36393 GATTCTGACT
** *
36403 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
*
36444 ATCGCAATGACAATACGTAAAATCGCAACGCGTATCC
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCC
36481 TGAAGAATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (41 bp):
ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:37089 original size:26 final size:25
Alignment explanation
Indices: 37038--37091 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
37028 ATACCAAGTT
* *
37038 AGATATACCAAAAACTACACTGTGA
1 AGATATACCAAAAACTAAACTATGA
37063 AGATATACCAAAAACAATAAAC-ATGA
1 AGATATACCAAAAAC--TAAACTATGA
37089 AGA
1 AGA
37092 GTAGTAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 15 0.60
26 6 0.24
27 4 0.16
ACGTcount: A:0.56, C:0.17, G:0.11, T:0.17
Consensus pattern (25 bp):
AGATATACCAAAAACTAAACTATGA
Found at i:37179 original size:20 final size:20
Alignment explanation
Indices: 37154--37209 Score: 96
Period size: 20 Copynumber: 2.8 Consensus size: 20
37144 TGAAATAAAA
37154 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
37174 ATCGCAACGCAGA-AATGACT
1 ATCGCAACG-AGAGAATGACT
37194 ATCGCAACGAGAGAAT
1 ATCGCAACGAGAGAAT
37210 CGCAACACGA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.09
20 28 0.82
21 3 0.09
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.14
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:37231 original size:19 final size:19
Alignment explanation
Indices: 37145--37276 Score: 121
Period size: 19 Copynumber: 7.1 Consensus size: 19
37135 TCTTTTGGTT
* *
37145 GAAATAAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
37164 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
37184 AGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
* *
37202 G--A-GAGAATCGCAACAC
1 GAAATGAAAATCGCAACGC
37218 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
37237 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
37256 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
37275 GA
1 GA
37277 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
14 9 0.09
15 1 0.01
16 2 0.02
17 1 0.01
18 2 0.02
19 51 0.54
20 27 0.28
21 2 0.02
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:37323 original size:21 final size:20
Alignment explanation
Indices: 37299--37374 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
37289 GTTGCGATTA
37299 TCTCGTTGCGATTTTCATTT
1 TCTCGTTGCGATTTTCATTT
* **
37319 CTCTCGTTGCAATAGTCATTT
1 -TCTCGTTGCGATTTTCATTT
37340 TCGT-GTTGCGATTTTCATTTT
1 TC-TCGTTGCGATTTTCA-TTT
*
37361 TATC-TTGCGATTTT
1 TCTCGTTGCGATTTT
37375 AAGTTTAGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
20 23 0.51
21 22 0.49
ACGTcount: A:0.13, C:0.18, G:0.16, T:0.53
Consensus pattern (20 bp):
TCTCGTTGCGATTTTCATTT
Found at i:37957 original size:20 final size:20
Alignment explanation
Indices: 37932--38141 Score: 217
Period size: 20 Copynumber: 10.3 Consensus size: 20
37922 CTTTAAAAAT
37932 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
37952 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
37972 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
37993 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
38013 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* * *
38033 CACGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
38053 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
38073 CGTGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
38093 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
38114 CGCGTTGCGATTTTACTGATA
1 CGCGTTGCGA-TTTACGGATA
*
38135 CTCGTTG
1 CGCGTTG
38142 TGATAGTCAG
Statistics
Matches: 155, Mismatches: 28, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
20 107 0.69
21 48 0.31
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:38141 original size:41 final size:41
Alignment explanation
Indices: 37934--38129 Score: 324
Period size: 40 Copynumber: 4.8 Consensus size: 41
37924 TTAAAAATCG
*
37934 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
37975 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
38015 CGTTGCGATTTACAGATACACGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
38055 CGTTGCGATTTACGGATACGTGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
38096 CGTTGCGATTTACGGATACGCGTTGCGATTTTAC
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTAC
38130 TGATACTCGT
Statistics
Matches: 144, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
40 73 0.51
41 71 0.49
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:38177 original size:20 final size:20
Alignment explanation
Indices: 38154--38206 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
38144 ATAGTCAGAA
*
38154 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
38174 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
38194 TCGCGTTGCGATT
1 TCGCGTTGCGATT
38207 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:38198 original size:40 final size:39
Alignment explanation
Indices: 37931--38206 Score: 218
Period size: 40 Copynumber: 6.8 Consensus size: 39
37921 GCTTTAAAAA
*
37931 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGT
* * *
37970 ATTGTCGTTGCGATTTACGGATACGCATTGCGA-TTTACGTAT
1 -TCG-CGTTGCGATTTACGGATACGCGTTGCGATTTTA--TGT
* * * *
38012 TCTCGTTGCGATTTACAGATACACGTTGCGA-TTTACGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTA--TGT
* * *
38052 TCTCGTTGCGATTTACGGATACGTGTTGCGATTTTACGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGT
*
38091 ATTGTCGTTGCGATTTACGGATACGCGTTGCGATTTTACTGAT
1 -TCG-CGTTGCGATTTACGGATACGCGTTGCGATTTTA-TG-T
* * * * *
38134 ACTCGTTGTGATAGT-CAGA-ATCGCGTTGCGATTTATATGT
1 TCGCGTTGCGAT-TTACGGATA-CGCGTTGCGATTT-TATGT
* ** *
38174 TCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATT
38207 CTGGAAAATC
Statistics
Matches: 193, Mismatches: 30, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
39 2 0.01
40 95 0.49
41 90 0.47
42 5 0.03
43 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (39 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGT
Found at i:38305 original size:20 final size:19
Alignment explanation
Indices: 38256--38309 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
38246 ATTCTTCATA
38256 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
38275 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
38296 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
38310 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:49176 original size:31 final size:33
Alignment explanation
Indices: 49120--49182 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 33
49110 ATCGTGTCGT
* *
49120 TAAAATTTAACGTCTCAATACTATAATTGAAAC
1 TAAAATTTAAAGTCTCAAAACTATAATTGAAAC
49153 TAAAA-TTAAAGT-TCAAAACTATAATTGAAA
1 TAAAATTTAAAGTCTCAAAACTATAATTGAAA
49183 TAATTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 17 0.61
32 6 0.21
33 5 0.18
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.32
Consensus pattern (33 bp):
TAAAATTTAAAGTCTCAAAACTATAATTGAAAC
Found at i:52001 original size:2 final size:2
Alignment explanation
Indices: 51994--52034 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
51984 TTGCCGAGCA
51994 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT A
52035 AAAAGAGCGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53624 original size:35 final size:35
Alignment explanation
Indices: 53579--53699 Score: 163
Period size: 35 Copynumber: 3.4 Consensus size: 35
53569 GGCAACCAAC
53579 TTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 TTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
*
53615 TTTCG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 TTT-GAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
53650 CTTTGAAAAATAGTTTTTCAAAGTTTGGTATATGTTT
1 -TTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
53687 GTTGAAAAATGAT
1 TTTGAAAAATGAT
53700 AATGGATAAT
Statistics
Matches: 76, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
35 32 0.42
36 20 0.26
37 24 0.32
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.45
Consensus pattern (35 bp):
TTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:58162 original size:35 final size:36
Alignment explanation
Indices: 58116--58237 Score: 144
Period size: 35 Copynumber: 3.4 Consensus size: 36
58106 TGGCAACCAA
*
58116 CTTTGAAAAAATGATTTTCAAAGTTTCGTAAATGTTAT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTT-T
*
58154 -TTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
58188 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATG--T
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
58223 CTGTTGAAAAATGAT
1 CT-TTGAAAAATGAT
58238 AATGGGATAA
Statistics
Matches: 75, Mismatches: 5, Indels: 11
0.82 0.05 0.12
Matches are distributed among these distances:
34 1 0.01
35 36 0.48
36 14 0.19
37 24 0.32
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:59007 original size:30 final size:31
Alignment explanation
Indices: 58968--59030 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
58958 CAATTTTCAT
* * *
58968 TCCTAAAATTTTATAAA-TTTAAATTCGTCC
1 TCCTAAAATTATAAAAAGTTTAAATTCGCCC
*
58998 TCCTGAAATTATAAAAAGTTTAAATTCGCCC
1 TCCTAAAATTATAAAAAGTTTAAATTCGCCC
59029 TC
1 TC
59031 TAACATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 14 0.50
31 14 0.50
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.38
Consensus pattern (31 bp):
TCCTAAAATTATAAAAAGTTTAAATTCGCCC
Found at i:59918 original size:23 final size:23
Alignment explanation
Indices: 59886--59934 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
59876 TAATAGACAC
* **
59886 ATTTTTTGTGTAAAACGGATAAT
1 ATTTTCTGTGTAAAACCAATAAT
*
59909 ATTTTCTGTGTGAAACCAATAAT
1 ATTTTCTGTGTAAAACCAATAAT
59932 ATT
1 ATT
59935 ATGCTGGTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (23 bp):
ATTTTCTGTGTAAAACCAATAAT
Found at i:60189 original size:17 final size:16
Alignment explanation
Indices: 60167--60235 Score: 54
Period size: 15 Copynumber: 4.3 Consensus size: 16
60157 CCGTGTCCCG
*
60167 ACCCGGATGTTACGGGT
1 ACCCGGATATT-CGGGT
*
60184 ACCCGG-TAATCGGGT
1 ACCCGGATATTCGGGT
* *
60199 ATCCGGATTTTGCGGGT
1 ACCCGGATATT-CGGGT
60216 ACCCGGGA-A-TCGGGT
1 ACCC-GGATATTCGGGT
60231 ACCCG
1 ACCCG
60236 ATACCCGGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
14 1 0.02
15 19 0.45
16 5 0.12
17 14 0.33
18 3 0.07
ACGTcount: A:0.17, C:0.26, G:0.35, T:0.22
Consensus pattern (16 bp):
ACCCGGATATTCGGGT
Found at i:60199 original size:15 final size:15
Alignment explanation
Indices: 60179--60235 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
60169 CCGGATGTTA
60179 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
* **
60194 CGGGTATCCGGATTTT
1 CGGGTACCCGG-TAAT
*
60210 GCGGGTACCCGGGAAT
1 -CGGGTACCCGGTAAT
60226 CGGGTACCCG
1 CGGGTACCCG
60236 ATACCCGGTT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
15 20 0.61
16 3 0.09
17 10 0.30
ACGTcount: A:0.16, C:0.26, G:0.37, T:0.21
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:60205 original size:32 final size:32
Alignment explanation
Indices: 60169--60231 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
60159 GTGTCCCGAC
*
60169 CCGGATGTTACGGGTACCCGGTAATCGGGTAT
1 CCGGATGTTACGGGTACCCGGGAATCGGGTAT
* *
60201 CCGGATTTTGCGGGTACCCGGGAATCGGGTA
1 CCGGATGTTACGGGTACCCGGGAATCGGGTA
60232 CCCGATACCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.17, C:0.22, G:0.37, T:0.24
Consensus pattern (32 bp):
CCGGATGTTACGGGTACCCGGGAATCGGGTAT
Found at i:65547 original size:2 final size:2
Alignment explanation
Indices: 65540--65573 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
65530 GTATTCAATA
*
65540 AT AT AT AT AT AT TT 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
65574 GTATGCAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:67930 original size:2 final size:2
Alignment explanation
Indices: 67923--67978 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
67913 AATTATATTT
*
67923 CA CA CA CA CA CA CA CA AA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
67965 CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA
67979 TATATATATA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:67983 original size:2 final size:2
Alignment explanation
Indices: 67978--68039 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
67968 ACACACACAC
67978 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
68020 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
68040 TAAATTGCAG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68088 original size:26 final size:25
Alignment explanation
Indices: 68058--68108 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
68048 AGTTAATGAA
68058 ATATTTAAAAATAAAAATAATTTTTT
1 ATATTT-AAAATAAAAATAATTTTTT
* * *
68084 ATATTTTAAATTAAATTAATTTTTT
1 ATATTTAAAATAAAAATAATTTTTT
68109 TTAAATAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
ATATTTAAAATAAAAATAATTTTTT
Found at i:68395 original size:2 final size:2
Alignment explanation
Indices: 68388--68441 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
68378 TAATAATTTA
68388 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
68430 AT AT AT AT AT AT
1 AT AT AT AT AT AT
68442 TTGTGTGAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72568 original size:23 final size:23
Alignment explanation
Indices: 72520--72569 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
72510 ATCATGACTA
*
72520 TTCATGAAAAATAATTAAGTCTT
1 TTCATGAAAAATAATTAAGTCAT
* **
72543 TTCATGAAAAATAGTTATTTCAT
1 TTCATGAAAAATAATTAAGTCAT
72566 TTCA
1 TTCA
72570 CCCAAAAGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (23 bp):
TTCATGAAAAATAATTAAGTCAT
Found at i:80577 original size:21 final size:21
Alignment explanation
Indices: 80553--80593 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
80543 TATTATTTAT
*
80553 TTATTTAGTTGAATT-ATAATA
1 TTATTTAATT-AATTAATAATA
80574 TTATTTAATTAATTAATAAT
1 TTATTTAATTAATTAATAAT
80594 TATGTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (21 bp):
TTATTTAATTAATTAATAATA
Found at i:80577 original size:25 final size:24
Alignment explanation
Indices: 80518--80590 Score: 67
Period size: 25 Copynumber: 3.0 Consensus size: 24
80508 AGTTGAGGTA
* **
80518 TATAAT-TAATTTATTTAGTTTCT
1 TATAATATTATTTATTTAGTTAAT
*
80541 TATATTATTTATTTATTTAGTTGAAT
1 TATAATA-TTATTTATTTAGTT-AAT
* *
80567 TATAATATTATTTAATTAATTAAT
1 TATAATATTATTTATTTAGTTAAT
80591 AATTATGTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
23 5 0.12
24 3 0.08
25 25 0.62
26 7 0.17
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.59
Consensus pattern (24 bp):
TATAATATTATTTATTTAGTTAAT
Found at i:85165 original size:19 final size:18
Alignment explanation
Indices: 85129--85168 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
85119 TATCCTTGTA
85129 TATTTTAATTTTCTTTAT
1 TATTTTAATTTTCTTTAT
*
85147 TATTTTTA-TTT-TTTAT
1 TATTTTAATTTTCTTTAT
85163 TATTTT
1 TATTTT
85169 GTTTAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.52
17 3 0.14
18 7 0.33
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (18 bp):
TATTTTAATTTTCTTTAT
Found at i:93137 original size:14 final size:14
Alignment explanation
Indices: 93114--93145 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
93104 TCTTTGCATC
93114 ATATTATTTATTCT
1 ATATTATTTATTCT
*
93128 ATATTCTTTATTCT
1 ATATTATTTATTCT
93142 ATAT
1 ATAT
93146 AATATCCGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.62
Consensus pattern (14 bp):
ATATTATTTATTCT
Done.