Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002979.1 Hibiscus syriacus cultivar Beakdansim tig00006161_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: 127012
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:596 original size:31 final size:31
Alignment explanation
Indices: 527--584 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
517 TATGAGTATT
527 TTTAA-TTT-AATTTATTTATAAAATTAAAA
1 TTTAATTTTAAATTTATTTATAAAATTAAAA
556 TTTAATTTTAAATTTATTT-TAAAAATTAA
1 TTTAATTTTAAATTTATTTAT-AAAATTAA
585 CATATTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 5 0.19
30 4 0.15
31 17 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
TTTAATTTTAAATTTATTTATAAAATTAAAA
Found at i:10858 original size:21 final size:21
Alignment explanation
Indices: 10786--10859 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 21
10776 TGTTAAATAT
*
10786 TTTATATTTATTTTTAATTCAA
1 TTTATTTTTATTTTTAATT-AA
* *
10808 TTTTATATATTAATTTTGAGATT-A
1 -TTTAT-T-TTTATTTTTA-ATTAA
10832 TATTATTTTTATTTTTAATTAA
1 T-TTATTTTTATTTTTAATTAA
10854 TTTATT
1 TTTATT
10860 GTATCTTGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
21 8 0.20
22 10 0.24
23 7 0.17
24 5 0.12
25 8 0.20
26 3 0.07
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (21 bp):
TTTATTTTTATTTTTAATTAA
Found at i:11045 original size:31 final size:30
Alignment explanation
Indices: 10992--11052 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
10982 AGGGGAAATG
10992 ATCCTAACGTTATCAATCCGTTCAATTTTA
1 ATCCTAACGTTATCAATCCGTTCAATTTTA
* * * *
11022 ATCCATAATGTTATCCATTCGTTCGATTTTA
1 ATCC-TAACGTTATCAATCCGTTCAATTTTA
11053 GTTCCTTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.43
Consensus pattern (30 bp):
ATCCTAACGTTATCAATCCGTTCAATTTTA
Found at i:11319 original size:13 final size:13
Alignment explanation
Indices: 11303--11331 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
11293 GAAATCAATA
11303 TTGAATATATGGT
1 TTGAATATATGGT
11316 TTGAATATATGGT
1 TTGAATATATGGT
11329 TTG
1 TTG
11332 CCAATGGGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (13 bp):
TTGAATATATGGT
Found at i:15435 original size:33 final size:33
Alignment explanation
Indices: 15389--15492 Score: 156
Period size: 33 Copynumber: 3.2 Consensus size: 33
15379 ATACATGTCC
* * *
15389 GATCATTGAACTTGTAGTTCTATCCGAGGGTAT
1 GATCATCGGACTTGTAGTTCCATCCGAGGGTAT
*
15422 GATCATCGGACTTGTAGTTCCATCGGAGGGTAT
1 GATCATCGGACTTGTAGTTCCATCCGAGGGTAT
*
15455 GATCATCGGACTTGTAGTTCCGTCCGAGGGTAT
1 GATCATCGGACTTGTAGTTCCATCCGAGGGTAT
15488 G-TCAT
1 GATCAT
15493 TAGCTACTGT
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
32 4 0.06
33 61 0.94
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (33 bp):
GATCATCGGACTTGTAGTTCCATCCGAGGGTAT
Found at i:15447 original size:17 final size:17
Alignment explanation
Indices: 15425--15475 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
15415 AGGGTATGAT
15425 CATCGGACTTGTAGTTC
1 CATCGGACTTGTAGTTC
** *
15442 CATCGGA-GGGTATGAT-
1 CATCGGACTTGTA-GTTC
15458 CATCGGACTTGTAGTTC
1 CATCGGACTTGTAGTTC
15475 C
1 C
15476 GTCCGAGGGT
Statistics
Matches: 25, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (17 bp):
CATCGGACTTGTAGTTC
Found at i:15463 original size:16 final size:16
Alignment explanation
Indices: 15414--15464 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
15404 AGTTCTATCC
15414 GAGGGTATGATCATCG
1 GAGGGTATGATCATCG
** *
15430 GACTTGTA-GTTCCATCG
1 GA-GGGTATGAT-CATCG
15447 GAGGGTATGATCATCG
1 GAGGGTATGATCATCG
15463 GA
1 GA
15465 CTTGTAGTTC
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.24, C:0.16, G:0.33, T:0.27
Consensus pattern (16 bp):
GAGGGTATGATCATCG
Found at i:18179 original size:78 final size:78
Alignment explanation
Indices: 17942--18332 Score: 336
Period size: 78 Copynumber: 5.1 Consensus size: 78
17932 AGATTGGTCC
* *
17942 GAACCAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCATTGAAAGCCCTGAATCAACCC
1 GAACCAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAATCAACCC
*
18007 CAGATATTAGTTT
66 CAGAGATTAGTTT
* * * **** * * * * *
18020 GAACC------AGGTCTCATTCTCTGATGTTAAAAGTGCCATTATGGAAGACAC-CAAGCCGAA-
1 GAACCAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAA-TC-AAC
* * * **
18077 ACCGGAGATTGGTCC
64 CCCAGAGATTAGTTT
18092 GAACCAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAATCAACCC
1 GAACCAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAATCAACCC
18157 CAGAGATTAGTTT
66 CAGAGATTAGTTT
* * * ** * * ** ** * * **
18170 GAACC---AGAAGGTCTCATTCTCTGATGTTAAAAGTGTCATTACAGAAGATACCGAGTCAAAGC
1 GAACCAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAATCAACCC
* * **
18232 CGGAGATTGGTCC
66 CAGAGATTAGTTT
18245 GAACCAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAATCAACCC
1 GAACCAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAATCAACCC
18310 CAGAGATTAGTTT
66 CAGAGATTAGTTT
18323 GAACCAGAAG
1 GAACCAGAAG
18333 GTCTCATTCT
Statistics
Matches: 225, Mismatches: 75, Indels: 26
0.69 0.23 0.08
Matches are distributed among these distances:
71 2 0.01
72 46 0.20
73 2 0.01
75 56 0.25
77 2 0.01
78 115 0.51
79 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (78 bp):
GAACCAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAATCAACCC
CAGAGATTAGTTT
Found at i:18238 original size:75 final size:75
Alignment explanation
Indices: 18012--18392 Score: 284
Period size: 78 Copynumber: 5.0 Consensus size: 75
18002 AACCCCAGAT
* * * *
18012 ATTAGTTTGAACC---AGGTCTCATTCTCTGATGTTAAAAGTGCCATTATGGAAGACACCAAGCC
1 ATTAGTTTGAACCAGAAGGTCTCATTCTCTGATGTTAAAAGTGTCATTATAGAAGACACCGAGTC
18074 GAAA-CCGGAG
66 -AAACCCGGAG
* ** * * * ** * * * * *
18084 ATTGGTCCGAACCAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGA
1 ATTAGTTTGAACC---AGAAGGTCTCATTCTCTGATGTTAAAAGTGTCATTATAGAAGACACCGA
* * *
18149 ATCAACCCCAGAG
63 GTCAAACCCGGAG
* *
18162 ATTAGTTTGAACCAGAAGGTCTCATTCTCTGATGTTAAAAGTGTCATTACAGAAGATACCGAGTC
1 ATTAGTTTGAACCAGAAGGTCTCATTCTCTGATGTTAAAAGTGTCATTATAGAAGACACCGAGTC
*
18227 AAAGCCGGAG
66 AAACCCGGAG
* ** * * * ** * * * * *
18237 ATTGGTCCGAACCAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGA
1 ATTAGTTTGAACC---AGAAGGTCTCATTCTCTGATGTTAAAAGTGTCATTATAGAAGACACCGA
* * *
18302 ATCAACCCCAGAG
63 GTCAAACCCGGAG
* *
18315 ATTAGTTTGAACCAGAAGGTCTCATTCTCTGATGTTAAAAGTGTCATTAGAGAAGATACCGAGTC
1 ATTAGTTTGAACCAGAAGGTCTCATTCTCTGATGTTAAAAGTGTCATTATAGAAGACACCGAGTC
**
18380 AAAATCGGAG
66 AAACCCGGAG
18390 ATT
1 ATT
18393 TTTTCCAACC
Statistics
Matches: 222, Mismatches: 77, Indels: 17
0.70 0.24 0.05
Matches are distributed among these distances:
72 10 0.05
75 104 0.47
77 2 0.01
78 106 0.48
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.26
Consensus pattern (75 bp):
ATTAGTTTGAACCAGAAGGTCTCATTCTCTGATGTTAAAAGTGTCATTATAGAAGACACCGAGTC
AAACCCGGAG
Found at i:18254 original size:153 final size:153
Alignment explanation
Indices: 17921--18435 Score: 831
Period size: 153 Copynumber: 3.4 Consensus size: 153
17911 AAGATAATGG
17921 GTCAAAACCGGAGATTGGTCCGAACCAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCA
1 GTCAAAACCGGAGATTGGTCCGAACCAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCA
* * *
17986 TTGAAAGCCCTGAATCAACCCCAGATATTAGTTTGAACC---AGGTCTCATTCTCTGATGTTAAA
66 TTGAAGGCACTGAATCAACCCCAGAGATTAGTTTGAACCAGAAGGTCTCATTCTCTGATGTTAAA
* ** * *
18048 AGTGCCATTATGGAAGACACCAA
131 AGTGTCATTACAGAAGATACCGA
* *
18071 GCCGAAACCGGAGATTGGTCCGAACCAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCA
1 GTCAAAACCGGAGATTGGTCCGAACCAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCA
18136 TTGAAGGCACTGAATCAACCCCAGAGATTAGTTTGAACCAGAAGGTCTCATTCTCTGATGTTAAA
66 TTGAAGGCACTGAATCAACCCCAGAGATTAGTTTGAACCAGAAGGTCTCATTCTCTGATGTTAAA
18201 AGTGTCATTACAGAAGATACCGA
131 AGTGTCATTACAGAAGATACCGA
*
18224 GTCAAAGCCGGAGATTGGTCCGAACCAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCA
1 GTCAAAACCGGAGATTGGTCCGAACCAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCA
18289 TTGAAGGCACTGAATCAACCCCAGAGATTAGTTTGAACCAGAAGGTCTCATTCTCTGATGTTAAA
66 TTGAAGGCACTGAATCAACCCCAGAGATTAGTTTGAACCAGAAGGTCTCATTCTCTGATGTTAAA
*
18354 AGTGTCATTAGAGAAGATACCGA
131 AGTGTCATTACAGAAGATACCGA
* ** * * *
18377 GTCAAAATCGGAGATTTTTTCC-AACCAGAAGATGGTTTTGTTCTCCGATGTTGAAAGCA
1 GTCAAAACCGGAGA-TTGGTCCGAACCAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCA
18436 CTGAATCAAC
Statistics
Matches: 340, Mismatches: 21, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
150 99 0.29
153 236 0.69
154 5 0.01
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (153 bp):
GTCAAAACCGGAGATTGGTCCGAACCAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCA
TTGAAGGCACTGAATCAACCCCAGAGATTAGTTTGAACCAGAAGGTCTCATTCTCTGATGTTAAA
AGTGTCATTACAGAAGATACCGA
Found at i:18403 original size:75 final size:75
Alignment explanation
Indices: 18171--18407 Score: 208
Period size: 75 Copynumber: 3.1 Consensus size: 75
18161 GATTAGTTTG
*
18171 AACCAGAAGGTCTCATTCTCTGATGTTAAAAGTGTCATTACAGAAGATACCGAGTCAAAGCCGGA
1 AACCAGAAGGTCTCATTCTCTGATGTTAAAAGTGTCATTACAGAAGATACCGAGTCAAAACCGGA
**
18236 GA-TTGGTCC
66 GATTTTTTCC
* * * ** * * ** ** * * **
18245 GAACCAGAAGAAGGTTTCGTTCTCTGATGTTGAAAGCATAATCATTGAAGGCACTGAATCAACCC
1 -AACC---AGAAGGTCTCATTCTCTGATGTTAAAAGTGTCATTACAGAAGATACCGAGTCAAAAC
* * *
18310 CAGAGATTAGTTT-G
62 CGGAGATT-TTTTCC
* *
18324 AACCAGAAGGTCTCATTCTCTGATGTTAAAAGTGTCATTAGAGAAGATACCGAGTCAAAATCGGA
1 AACCAGAAGGTCTCATTCTCTGATGTTAAAAGTGTCATTACAGAAGATACCGAGTCAAAACCGGA
18389 GATTTTTTCC
66 GATTTTTTCC
18399 AACCAGAAG
1 AACCAGAAG
18408 ATGGTTTTGT
Statistics
Matches: 117, Mismatches: 39, Indels: 12
0.70 0.23 0.07
Matches are distributed among these distances:
74 3 0.03
75 61 0.52
78 51 0.44
79 1 0.01
80 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.26
Consensus pattern (75 bp):
AACCAGAAGGTCTCATTCTCTGATGTTAAAAGTGTCATTACAGAAGATACCGAGTCAAAACCGGA
GATTTTTTCC
Found at i:19945 original size:168 final size:168
Alignment explanation
Indices: 19667--20007 Score: 574
Period size: 168 Copynumber: 2.0 Consensus size: 168
19657 TAATCACACC
**
19667 GCAGGCTACTGAAATTCAACATGATAAACCTGAAACTGATGACCCCGAGGGTGGCTTGAACATCG
1 GCAGGCTACTGAAATTCAACATGATAAACCCAAAACTGATGACCCCGAGGGTGGCTTGAACATCG
* ** *
19732 TTGAAACGTTGTTCCCCGAAGAAGTGAAGTCTGAGGATCTCAAAACTGAAGATTCCATCGACGAC
66 TTGAAACGTTGTTCCCCAAAGAAGTGAAGTCTGAGGATCTCAAAACTGAAGATAACACCGACGAC
19797 TCTCAAAGTTCTGGAGATGTAGATATTACAATTAATGG
131 TCTCAAAGTTCTGGAGATGTAGATATTACAATTAATGG
* *
19835 GCAGGCTACTGAAATTCAACATGATAAACCCAAAACTGGTGACCCTGAGGGTGGCTTGAACATCG
1 GCAGGCTACTGAAATTCAACATGATAAACCCAAAACTGATGACCCCGAGGGTGGCTTGAACATCG
* *
19900 TTGAAACGTTTTTCCCCAAAGAAGTGAAGTCTGAGGATCTCAAAACTGAAGATAACACCGACGAT
66 TTGAAACGTTGTTCCCCAAAGAAGTGAAGTCTGAGGATCTCAAAACTGAAGATAACACCGACGAC
*
19965 TCTCAAAGTTCTGGAGCTGTAGATATTACAATTAATGG
131 TCTCAAAGTTCTGGAGATGTAGATATTACAATTAATGG
*
20003 ACAGG
1 GCAGG
20008 AAGAACAATT
Statistics
Matches: 161, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
168 161 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (168 bp):
GCAGGCTACTGAAATTCAACATGATAAACCCAAAACTGATGACCCCGAGGGTGGCTTGAACATCG
TTGAAACGTTGTTCCCCAAAGAAGTGAAGTCTGAGGATCTCAAAACTGAAGATAACACCGACGAC
TCTCAAAGTTCTGGAGATGTAGATATTACAATTAATGG
Found at i:24078 original size:2 final size:2
Alignment explanation
Indices: 24071--24116 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
24061 ACATACATAC
24071 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
24113 AT AT
1 AT AT
24117 GGAAAGTGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25520 original size:2 final size:2
Alignment explanation
Indices: 25513--25538 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25503 ACTGCAGATA
25513 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
25539 GAACTTTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26161 original size:8 final size:8
Alignment explanation
Indices: 26125--26166 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
26115 ATCTTATTAA
26125 ATAAATAT
1 ATAAATAT
26133 A-AAATAT
1 ATAAATAT
*
26140 ATAAAAAT
1 ATAAATAT
26148 GAATAAATAT
1 --ATAAATAT
26158 ATAAATAT
1 ATAAATAT
26166 A
1 A
26167 ATTATGGGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
7 7 0.24
8 15 0.52
10 7 0.24
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (8 bp):
ATAAATAT
Found at i:27990 original size:30 final size:31
Alignment explanation
Indices: 27956--28013 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
27946 TAAAAATGAG
* *
27956 TGACCTATTTGTA-TATTACTAATAATTGGC
1 TGACCCATTTATATTATTACTAATAATTGGC
* *
27986 TGACCCATTTATATTCTTACTTATAATT
1 TGACCCATTTATATTATTACTAATAATT
28014 AAATAATTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 11 0.48
31 12 0.52
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.47
Consensus pattern (31 bp):
TGACCCATTTATATTATTACTAATAATTGGC
Found at i:37599 original size:33 final size:33
Alignment explanation
Indices: 37562--37639 Score: 147
Period size: 33 Copynumber: 2.4 Consensus size: 33
37552 TTAATAAATT
37562 TAGAAATGGTTAATGACTTTATTTATTTTATTA
1 TAGAAATGGTTAATGACTTTATTTATTTTATTA
37595 TAGAAATGGTTAATGACTTTATTTATTTTATTA
1 TAGAAATGGTTAATGACTTTATTTATTTTATTA
*
37628 TAAAAATGGTTA
1 TAGAAATGGTTA
37640 TATATATATA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.36, C:0.03, G:0.13, T:0.49
Consensus pattern (33 bp):
TAGAAATGGTTAATGACTTTATTTATTTTATTA
Found at i:38696 original size:15 final size:15
Alignment explanation
Indices: 38676--38709 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
38666 ATATTTAGAT
*
38676 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
38691 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
38706 GGGC
1 GGGC
38710 AAGTAATGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.18, G:0.68, T:0.09
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:39086 original size:34 final size:34
Alignment explanation
Indices: 39043--39111 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
39033 AGATGAGCTT
*
39043 TACGACTTCTACTAGGGGAGGTCTTTGACTTTTC
1 TACGACTTCTACCAGGGGAGGTCTTTGACTTTTC
39077 TACGACTTCTACCAGGGGAGGTCTTTGACTTTTC
1 TACGACTTCTACCAGGGGAGGTCTTTGACTTTTC
39111 T
1 T
39112 TCAATTCTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (34 bp):
TACGACTTCTACCAGGGGAGGTCTTTGACTTTTC
Found at i:46723 original size:3 final size:3
Alignment explanation
Indices: 46715--46775 Score: 81
Period size: 3 Copynumber: 20.3 Consensus size: 3
46705 CTGTAATCAC
*
46715 TAT TAT TAT TAT TAG TATT TAT TAT TAT TAAT TAT TAT TA- TAT TA-
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT T-AT TAT TAT TAT TAT TAT
46760 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
46776 GATATTTGCA
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 4 0.08
3 43 0.83
4 5 0.10
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:46738 original size:13 final size:13
Alignment explanation
Indices: 46715--46772 Score: 75
Period size: 13 Copynumber: 4.5 Consensus size: 13
46705 CTGTAATCAC
46715 TATTA-TTATTAT
1 TATTATTTATTAT
*
46727 TAGTATTTATTAT
1 TATTATTTATTAT
*
46740 TATTAATTATTAT
1 TATTATTTATTAT
46753 TA-TATTATATTAT
1 TATTATT-TATTAT
46766 TATTATT
1 TATTATT
46773 ATTGATATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
12 7 0.18
13 28 0.72
14 4 0.10
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (13 bp):
TATTATTTATTAT
Found at i:46738 original size:16 final size:15
Alignment explanation
Indices: 46717--46774 Score: 68
Period size: 16 Copynumber: 3.9 Consensus size: 15
46707 GTAATCACTA
46717 TTATTATTATTAGTAT
1 TTATTATTATTA-TAT
46733 TTATTATTATTA-A-
1 TTATTATTATTATAT
46746 TTATTATTA-TATTAT
1 TTATTATTATTA-TAT
46761 ATTATTATTATTAT
1 -TTATTATTATTAT
46775 TGATATTTGC
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.05
13 9 0.24
14 2 0.05
16 22 0.59
17 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (15 bp):
TTATTATTATTATAT
Found at i:57585 original size:18 final size:18
Alignment explanation
Indices: 57562--57606 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 18
57552 CCAGTAATCC
*
57562 TATTCCCTGGTAATCTTT
1 TATTCCCTGATAATCTTT
57580 TATTCCCACTGATAATCTTT
1 TATT-CC-CTGATAATCTTT
57600 TATTCCC
1 TATTCCC
57607 ACAGATAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 5 0.21
19 4 0.17
20 15 0.62
ACGTcount: A:0.20, C:0.27, G:0.07, T:0.47
Consensus pattern (18 bp):
TATTCCCTGATAATCTTT
Found at i:57597 original size:20 final size:20
Alignment explanation
Indices: 57572--57618 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
57562 TATTCCCTGG
*
57572 TAATCTTTTATTCCCACTGA
1 TAATCTTTTATTCCCACAGA
57592 TAATCTTTTATTCCCACAGA
1 TAATCTTTTATTCCCACAGA
57612 TAATCTT
1 TAATCTT
57619 ACATTTCGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.23, G:0.04, T:0.45
Consensus pattern (20 bp):
TAATCTTTTATTCCCACAGA
Found at i:57802 original size:15 final size:15
Alignment explanation
Indices: 57782--57812 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
57772 TAATATCTTG
57782 TCTCGTTAATCCAAC
1 TCTCGTTAATCCAAC
57797 TCTCGTTAATCCAAC
1 TCTCGTTAATCCAAC
57812 T
1 T
57813 ATAGAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.32, G:0.06, T:0.35
Consensus pattern (15 bp):
TCTCGTTAATCCAAC
Found at i:60686 original size:55 final size:55
Alignment explanation
Indices: 60597--60905 Score: 276
Period size: 55 Copynumber: 5.7 Consensus size: 55
60587 TTGAATGACG
* *
60597 GGTCCGCTCCCTATTCGTTCAAGGAGTATAAGACTCGAATAATCTTCAACAAACA
1 GGTCCGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACA
* * * * ** *
60652 TGTCTGCTCCCTGTTTGTTCAGGGAGTATAAGACTCGAACAATCTTCAGTAAACG
1 GGTCCGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACA
* * *
60707 GGTCCGCTCCCTATTCATTCAGGGAGTAT-AGAACTCGAACAATCTT-AATAAAACG
1 GGTCCGCTCCCTATTCGTTCAGGGAGTATAAG-ACTCGAACAATCTTCAA-CAAACA
* * * **
60762 GGTCCGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCATA-AAATG
1 GGTCCGCTCCCTATTCGTTCAGGGAGTATAAG-ACTCGAACAATCTTCA-ACAAACA
* * * * *
60817 GGTCCGCTCTCTATTCCTTTAGAGAGTATAGGACTCG----ATCTTCAACAAAC-
1 GGTCCGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACA
* * * *
60867 GTGTCTGCTCCCTATTCATTCAGAGAGTATAGGACTCGA
1 G-GTCCGCTCCCTATTCGTTCAGGGAGTATAAGACTCGA
60906 TATTCATAAA
Statistics
Matches: 219, Mismatches: 27, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
50 2 0.01
51 42 0.19
54 3 0.01
55 169 0.77
56 2 0.01
57 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (55 bp):
GGTCCGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACA
Found at i:60745 original size:110 final size:109
Alignment explanation
Indices: 60594--60905 Score: 350
Period size: 110 Copynumber: 2.9 Consensus size: 109
60584 TTTTTGAATG
* * *
60594 ACGGGTCCGCTCCCTATTCGTTCAAGGAGTATA-AGACTCGAATAATCTTCAACAAACATGTCTG
1 ACGGGTCCGCTCCCTATTCATTCAGGGAGTATAGA-ACTCGAA-AATCTTCAACAAACGTGTCTG
* ** *
60658 CTCCCTGTTTGTTCAGGGAGTATAAGACTCGAACAATCTTCAGT-AA
64 CTCCCTATTCATTCAGAGAGTATAAGACTCGAACAATCTTCA-TAAA
* * *
60704 ACGGGTCCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTT-AATAAAACGGGTCCG
1 ACGGGTCCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAA-AATCTTCAA-CAAACGTGTCTG
* *
60768 CTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCATAAA
64 CTCCCTATTCATTCAGAGAGTATAAG-ACTCGAACAATCTTCATAAA
* * * * * *
60814 ATGGGTCCGCTCTCTATTCCTTTAGAGAGTATAGGACTCG---ATCTTCAACAAACGTGTCTGCT
1 ACGGGTCCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAAAATCTTCAACAAACGTGTCTGCT
*
60876 CCCTATTCATTCAGAGAGTATAGGACTCGA
66 CCCTATTCATTCAGAGAGTATAAGACTCGA
60906 TATTCATAAA
Statistics
Matches: 172, Mismatches: 24, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
106 41 0.24
107 3 0.02
109 5 0.03
110 122 0.71
111 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (109 bp):
ACGGGTCCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAAAATCTTCAACAAACGTGTCTGCT
CCCTATTCATTCAGAGAGTATAAGACTCGAACAATCTTCATAAA
Found at i:62172 original size:17 final size:17
Alignment explanation
Indices: 62152--62319 Score: 81
Period size: 17 Copynumber: 9.3 Consensus size: 17
62142 ATTTTTTTCA
62152 TTTTTTTCATTTTTCTTT
1 TTTTTTTCATTTTTC-TT
62170 TTTCTTTGTCATTTTTCTT
1 TTT-TTT-TCATTTTTCTT
***
62189 CCATTTTCTATTTTTTTCTTT
1 TTTTTTTC-A--TTTTTC-TT
**
62210 TTTCCTTTTCATTTTTCAC
1 TTT--TTTTCATTTTTCTT
** *
62229 CATTTTTCATTTTTTCTCA
1 TTTTTTTCA-TTTTTCT-T
*
62248 TTTTTTTCATTGTTTC-A
1 TTTTTTTCATT-TTTCTT
*
62265 TTTTTTTCATTTTT-TC
1 TTTTTTTCATTTTTCTT
* *
62281 ATTTTTTCATTTTTCAT
1 TTTTTTTCATTTTTCTT
*
62298 TTTTCTTC-TTTCTTCTT
1 TTTTTTTCATTT-TTCTT
62315 TTTTT
1 TTTTT
62320 AATTTTATTT
Statistics
Matches: 114, Mismatches: 22, Indels: 29
0.69 0.13 0.18
Matches are distributed among these distances:
16 19 0.17
17 34 0.30
18 15 0.13
19 17 0.15
20 21 0.18
21 2 0.02
22 1 0.01
23 5 0.04
ACGTcount: A:0.09, C:0.17, G:0.01, T:0.73
Consensus pattern (17 bp):
TTTTTTTCATTTTTCTT
Found at i:62183 original size:20 final size:19
Alignment explanation
Indices: 62155--62311 Score: 78
Period size: 20 Copynumber: 8.1 Consensus size: 19
62145 TTTTTCATTT
62155 TTTTCATTTTTCTTTTTTC
1 TTTTCATTTTTCTTTTTTC
62174 TTTGTCATTTTTCTTCCATTTTC
1 TTT-TCATTTTTCTT---TTTTC
*
62197 TATT--TTTTTCTTTTTTCC
1 TTTTCATTTTTCTTTTTT-C
****
62215 TTTTCATTTTTC-ACCAT-
1 TTTTCATTTTTCTTTTTTC
**
62232 TTTTCATTTTTTCTCATTT-
1 TTTTCA-TTTTTCTTTTTTC
*
62251 TTTTCATTGTTTC--ATTT-
1 TTTTCATT-TTTCTTTTTTC
62268 TTTTCATTTTTTCATTTTTTC
1 TTTTCA-TTTTTC-TTTTTTC
*
62289 ATTTTTCATTTTTCTTCTTTC
1 --TTTTCATTTTTCTTTTTTC
62310 TT
1 TT
62312 CTTTTTTTAA
Statistics
Matches: 109, Mismatches: 12, Indels: 34
0.70 0.08 0.22
Matches are distributed among these distances:
17 24 0.22
18 14 0.13
19 17 0.16
20 28 0.26
21 6 0.06
22 7 0.06
23 13 0.12
ACGTcount: A:0.10, C:0.17, G:0.01, T:0.72
Consensus pattern (19 bp):
TTTTCATTTTTCTTTTTTC
Found at i:62337 original size:8 final size:8
Alignment explanation
Indices: 62144--62301 Score: 102
Period size: 7 Copynumber: 19.6 Consensus size: 8
62134 TCTTATTTAT
62144 TTTTTTCA
1 TTTTTTCA
62152 TTTTTTTCA
1 -TTTTTTCA
62161 -TTTTTC-
1 TTTTTTCA
62167 TTTTTTC-
1 TTTTTTCA
*
62174 -TTTGTCA
1 TTTTTTCA
62181 TTTTTCTTCCA
1 -TTTT-TT-CA
*
62192 TTTTCT-A
1 TTTTTTCA
62199 TTTTTTTC-
1 -TTTTTTCA
62207 TTTTTTC-
1 TTTTTTCA
*
62214 -CTTTTCA
1 TTTTTTCA
62221 -TTTTTCA
1 TTTTTTCA
*
62228 CCATTTTTCA
1 --TTTTTTCA
62238 TTTTTTCTCA
1 -TTTTT-TCA
62248 TTTTTTTCA
1 -TTTTTTCA
*
62257 TTGTTTCA
1 TTTTTTCA
62265 TTTTTTTCA
1 -TTTTTTCA
62274 TTTTTTCA
1 TTTTTTCA
62282 TTTTTTCA
1 TTTTTTCA
62290 -TTTTTCA
1 TTTTTTCA
62297 TTTTT
1 TTTTT
62302 CTTCTTTCTT
Statistics
Matches: 124, Mismatches: 10, Indels: 31
0.75 0.06 0.19
Matches are distributed among these distances:
6 10 0.08
7 33 0.27
8 32 0.26
9 26 0.21
10 21 0.17
11 2 0.02
ACGTcount: A:0.10, C:0.16, G:0.01, T:0.73
Consensus pattern (8 bp):
TTTTTTCA
Found at i:73905 original size:51 final size:48
Alignment explanation
Indices: 73858--73948 Score: 132
Period size: 47 Copynumber: 1.9 Consensus size: 48
73848 CCATGCTTTG
73858 TTATTC-ACAAAAAGAAATCCTAACCACATGATATCTAATTCGCATGC
1 TTATTCAACAAAAAGAAATCCTAACCACATGATATCTAATTCGCATGC
* * * *
73905 TTATTCAAGAAAAATAAA-CCTAACCGCATGATATCTAGTTCGCA
1 TTATTCAACAAAAAGAAATCCTAACCACATGATATCTAATTCGCA
73949 AGCATTTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 30 0.77
48 9 0.23
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (48 bp):
TTATTCAACAAAAAGAAATCCTAACCACATGATATCTAATTCGCATGC
Found at i:73964 original size:47 final size:47
Alignment explanation
Indices: 73858--73970 Score: 131
Period size: 47 Copynumber: 2.4 Consensus size: 47
73848 CCATGCTTTG
* *
73858 TTATTCACAAAAAGAAATCCTAACCACATGATATCTAATTCGCATGC
1 TTATTCAGAAAAAGAAATCCTAACCACATGATATCTAATTCGCAAGC
* * *
73905 TTATTCAAGAAAAATAAA-CCTAACCGCATGATATCTAGTTCGCAAGC
1 TTATTC-AGAAAAAGAAATCCTAACCACATGATATCTAATTCGCAAGC
73952 ATTTATTC-GAAAAACGAAA
1 --TTATTCAGAAAAA-GAAA
73971 ATAAATGATT
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
47 38 0.68
48 12 0.21
49 6 0.11
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (47 bp):
TTATTCAGAAAAAGAAATCCTAACCACATGATATCTAATTCGCAAGC
Found at i:77076 original size:2 final size:2
Alignment explanation
Indices: 77069--77097 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
77059 GACATACATC
77069 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
77098 TATTCAATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:81458 original size:212 final size:212
Alignment explanation
Indices: 81091--81515 Score: 850
Period size: 212 Copynumber: 2.0 Consensus size: 212
81081 CGATGCTTCT
81091 TGCAGTTACTCTATGGGTCTGTGGGTAAGTCATAAGTGGCAGTTCATCATACCAGTTCACTTCTC
1 TGCAGTTACTCTATGGGTCTGTGGGTAAGTCATAAGTGGCAGTTCATCATACCAGTTCACTTCTC
81156 TTTCTATTTGAGTTGAGACATCGATATCTTTGCATCAAATGTTCGTGTGTACATGGAAATACTTC
66 TTTCTATTTGAGTTGAGACATCGATATCTTTGCATCAAATGTTCGTGTGTACATGGAAATACTTC
81221 ATTAGCTACCTTTACTTGTTACCCTCCCTTGTTAAGCTTTGCACATGCGAAGTCTACTGTCATGT
131 ATTAGCTACCTTTACTTGTTACCCTCCCTTGTTAAGCTTTGCACATGCGAAGTCTACTGTCATGT
81286 GAATGTTAAAATGAGTA
196 GAATGTTAAAATGAGTA
81303 TGCAGTTACTCTATGGGTCTGTGGGTAAGTCATAAGTGGCAGTTCATCATACCAGTTCACTTCTC
1 TGCAGTTACTCTATGGGTCTGTGGGTAAGTCATAAGTGGCAGTTCATCATACCAGTTCACTTCTC
81368 TTTCTATTTGAGTTGAGACATCGATATCTTTGCATCAAATGTTCGTGTGTACATGGAAATACTTC
66 TTTCTATTTGAGTTGAGACATCGATATCTTTGCATCAAATGTTCGTGTGTACATGGAAATACTTC
81433 ATTAGCTACCTTTACTTGTTACCCTCCCTTGTTAAGCTTTGCACATGCGAAGTCTACTGTCATGT
131 ATTAGCTACCTTTACTTGTTACCCTCCCTTGTTAAGCTTTGCACATGCGAAGTCTACTGTCATGT
81498 GAATGTTAAAATGAGTA
196 GAATGTTAAAATGAGTA
81515 T
1 T
81516 ACCATCTTGT
Statistics
Matches: 213, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
212 213 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.37
Consensus pattern (212 bp):
TGCAGTTACTCTATGGGTCTGTGGGTAAGTCATAAGTGGCAGTTCATCATACCAGTTCACTTCTC
TTTCTATTTGAGTTGAGACATCGATATCTTTGCATCAAATGTTCGTGTGTACATGGAAATACTTC
ATTAGCTACCTTTACTTGTTACCCTCCCTTGTTAAGCTTTGCACATGCGAAGTCTACTGTCATGT
GAATGTTAAAATGAGTA
Found at i:82013 original size:60 final size:60
Alignment explanation
Indices: 81927--82041 Score: 203
Period size: 60 Copynumber: 1.9 Consensus size: 60
81917 TGTGGTTTTG
*
81927 ATGTTTGCTTCAGAGCATATAATTGGTTACTTCTCTGATTTATTGATATTTCCGGTTTCA
1 ATGTTTGCTTCAGAACATATAATTGGTTACTTCTCTGATTTATTGATATTTCCGGTTTCA
* *
81987 ATGTTTGCTTCAGAACATATAATTGGTTACTTTTCTGATTTATTGGTATTTCCGG
1 ATGTTTGCTTCAGAACATATAATTGGTTACTTCTCTGATTTATTGATATTTCCGG
82042 AATCATATGC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.47
Consensus pattern (60 bp):
ATGTTTGCTTCAGAACATATAATTGGTTACTTCTCTGATTTATTGATATTTCCGGTTTCA
Found at i:92419 original size:20 final size:20
Alignment explanation
Indices: 92391--92443 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
92381 TATTCCCTAG
*
92391 TAATCTTACATTCCCACTAA
1 TAATTTTACATTCCCACTAA
* *
92411 TAATTTTACATTCCTACTGA
1 TAATTTTACATTCCCACTAA
92431 TAATTTTACATTC
1 TAATTTTACATTC
92444 TGCGAACCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.32, C:0.23, G:0.02, T:0.43
Consensus pattern (20 bp):
TAATTTTACATTCCCACTAA
Found at i:95900 original size:18 final size:18
Alignment explanation
Indices: 95859--95893 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
95849 TGATCATTAT
95859 AATTATTAAAATTTATCA
1 AATTATTAAAATTTATCA
95877 AATTATT-AAATTTATCA
1 AATTATTAAAATTTATCA
95894 TAGTTATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (18 bp):
AATTATTAAAATTTATCA
Found at i:99653 original size:28 final size:29
Alignment explanation
Indices: 99615--99673 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
99605 CATATGCCTA
*
99615 TTTTTTCAGTTTAGTGTTTAACGTTT-AT
1 TTTTTTCAGTTTAGTGCTTAACGTTTCAT
* *
99643 TTTTTTTAGTTTGGTGCTTAACGTTTCAT
1 TTTTTTCAGTTTAGTGCTTAACGTTTCAT
99672 TT
1 TT
99674 CATTACTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.61
Consensus pattern (29 bp):
TTTTTTCAGTTTAGTGCTTAACGTTTCAT
Found at i:100559 original size:2 final size:2
Alignment explanation
Indices: 100552--100602 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
100542 TATAAATCAA
100552 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
100594 AT AT AT AT A
1 AT AT AT AT A
100603 ATTACAAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:102782 original size:20 final size:20
Alignment explanation
Indices: 102757--102794 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
102747 TTTGGTTCAC
102757 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
102777 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
102795 GGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:102976 original size:35 final size:37
Alignment explanation
Indices: 102905--102977 Score: 107
Period size: 35 Copynumber: 2.0 Consensus size: 37
102895 GTTGTAAAAT
*
102905 ATTTATATATTTTCTTTAACAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAACAAAATTAAAATCATAAA
102942 ATTTATATATTTT-TTT-ACAAAATTAAAAAT-ATAAA
1 ATTTATATATTTTCTTTAACAAAATT-AAAATCATAAA
102977 A
1 A
102978 ACGTTTAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
35 14 0.41
36 7 0.21
37 13 0.38
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAACAAAATTAAAATCATAAA
Found at i:106438 original size:25 final size:25
Alignment explanation
Indices: 106410--106457 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
106400 GTCGCGGGCT
*
106410 TAAAATTTTAAAGCTCAAGTCGAAA
1 TAAAATATTAAAGCTCAAGTCGAAA
* *
106435 TAAAATATTGAAGCTCAATTCGA
1 TAAAATATTAAAGCTCAAGTCGA
106458 GCTCAAACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.29
Consensus pattern (25 bp):
TAAAATATTAAAGCTCAAGTCGAAA
Found at i:106777 original size:2 final size:2
Alignment explanation
Indices: 106770--106800 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
106760 ATTGTATTAA
106770 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 A
106801 AATGTTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:107253 original size:18 final size:18
Alignment explanation
Indices: 107230--107265 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
107220 TGGAAAGTGG
107230 CCACGAGAAACACGATTA
1 CCACGAGAAACACGATTA
107248 CCACGAGAAACACGATTA
1 CCACGAGAAACACGATTA
107266 TCTCTGCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.28, G:0.17, T:0.11
Consensus pattern (18 bp):
CCACGAGAAACACGATTA
Found at i:107399 original size:27 final size:28
Alignment explanation
Indices: 107342--107405 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
107332 TATATTTTTA
* * * *
107342 TTAAAAATATATTTTATCTCTTCAAATT
1 TTAAAATTTTATTTTATATCTTAAAATT
*
107370 TTATAATTTTATTTTATAT-TTAAAATT
1 TTAAAATTTTATTTTATATCTTAAAATT
107397 TTAAAATTT
1 TTAAAATTT
107406 ATTATTCTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 15 0.50
28 15 0.50
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (28 bp):
TTAAAATTTTATTTTATATCTTAAAATT
Found at i:107613 original size:16 final size:17
Alignment explanation
Indices: 107592--107624 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
107582 TTTATTTTAA
107592 TATTCAAAATT-TATTT
1 TATTCAAAATTATATTT
*
107608 TATTCATAATTATATTT
1 TATTCAAAATTATATTT
107625 AATTTTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTCAAAATTATATTT
Found at i:108560 original size:2 final size:2
Alignment explanation
Indices: 108553--108593 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
108543 TCATAGTCAA
108553 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
108594 ATAGTTGGAT
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:109302 original size:20 final size:20
Alignment explanation
Indices: 109262--109302 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
109252 TTTGATCATG
*
109262 ATATTTCAATATGCATGTAT
1 ATATTTCAATATGCATATAT
109282 ATATTTC-ATATGACATATAT
1 ATATTTCAATATG-CATATAT
109302 A
1 A
109303 ATCAAGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (20 bp):
ATATTTCAATATGCATATAT
Found at i:112664 original size:23 final size:25
Alignment explanation
Indices: 112607--112664 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 25
112597 ACTTTTAATA
* *
112607 AATTATTATTTTTATTTTATTTGAGT
1 AATTA-TATTTTTATTTTAGTTCAGT
*
112633 ATTTA-ATTTTTATTTT-GTTCA-T
1 AATTATATTTTTATTTTAGTTCAGT
112655 AATTATATTT
1 AATTATATTT
112665 AATTTTGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
22 5 0.19
23 7 0.26
24 11 0.41
26 4 0.15
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.66
Consensus pattern (25 bp):
AATTATATTTTTATTTTAGTTCAGT
Found at i:114062 original size:19 final size:19
Alignment explanation
Indices: 114038--114079 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
114028 ACAAAGAAAT
114038 GCAAACTGAAGGTAATCGA
1 GCAAACTGAAGGTAATCGA
114057 GCAAACTGAAGGTAATCGA
1 GCAAACTGAAGGTAATCGA
114076 GCAA
1 GCAA
114080 CCTAAATCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.26, T:0.14
Consensus pattern (19 bp):
GCAAACTGAAGGTAATCGA
Found at i:115934 original size:2 final size:2
Alignment explanation
Indices: 115923--115959 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
115913 TGTTAGTGAT
115923 TA TA -A 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
115960 AATTTTTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:116102 original size:24 final size:23
Alignment explanation
Indices: 116075--116142 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 23
116065 TGGGCAATAA
*
116075 ATTATTATGAAAATTATATATATT
1 ATTATTAT-AAAATAATATATATT
*
116099 ATTATTATACAAATAATAAAATATT
1 ATTATTATA-AAATAAT-ATATATT
*
116124 ATTTTTATAAAATAATATA
1 ATTATTATAAAATAATATA
116143 AGTAAATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
23 3 0.08
24 21 0.55
25 14 0.37
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (23 bp):
ATTATTATAAAATAATATATATT
Found at i:116454 original size:22 final size:20
Alignment explanation
Indices: 116420--116467 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
116410 ATAATTATTT
116420 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAA-ACC
*
116441 AAAAATATTTAATAAAAAACC
1 AAAAA-ATTAAATAAAAAACC
116462 AAAAAA
1 AAAAAA
116468 AAAATTAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 1 0.04
21 13 0.52
22 11 0.44
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (20 bp):
AAAAAATTAAATAAAAAACC
Found at i:116713 original size:7 final size:7
Alignment explanation
Indices: 116703--116770 Score: 54
Period size: 7 Copynumber: 10.1 Consensus size: 7
116693 TATAGTTTTC
116703 ATTTATA
1 ATTTATA
116710 ATTTA-A
1 ATTTATA
*
116716 TTTTATA
1 ATTTATA
*
116723 TTTTAT-
1 ATTTATA
116729 ATTTATA
1 ATTTATA
116736 ATTTATA
1 ATTTATA
116743 TATTT-TA
1 -ATTTATA
* *
116750 TTTTCTA
1 ATTTATA
*
116757 ATATA-A
1 ATTTATA
116763 ATTTATA
1 ATTTATA
116770 A
1 A
116771 CACTAATATA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
6 18 0.37
7 27 0.55
8 4 0.08
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTATA
Found at i:116718 original size:26 final size:26
Alignment explanation
Indices: 116689--116753 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
116679 ATTTGAATAT
116689 ATTTTATAGTTTT-CATTTATAATTTA
1 ATTTTATA-TTTTACATTTATAATTTA
*
116715 ATTTTATATTTTATATTTATAATTTA
1 ATTTTATATTTTACATTTATAATTTA
116741 TATATTT-TATTTT
1 -AT-TTTATATTTT
116754 CTAATATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
25 4 0.11
26 20 0.57
27 8 0.23
28 3 0.09
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (26 bp):
ATTTTATATTTTACATTTATAATTTA
Found at i:116720 original size:13 final size:14
Alignment explanation
Indices: 116703--116747 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 14
116693 TATAGTTTTC
116703 ATTTATAATTTAAT
1 ATTTATAATTTAAT
*
116717 -TTTAT-ATTTTAT
1 ATTTATAATTTAAT
116729 ATTTATAATTTATAT
1 ATTTATAATTTA-AT
116744 ATTT
1 ATTT
116748 TATTTTCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 6 0.23
13 10 0.38
14 4 0.15
15 6 0.23
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTTATAATTTAAT
Found at i:116727 original size:20 final size:22
Alignment explanation
Indices: 116704--116750 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
116694 ATAGTTTTCA
116704 TTTATAATT-TAATTT-TATAT
1 TTTATAATTATAATTTATATAT
*
116724 TTTATATTTATAATTTATATAT
1 TTTATAATTATAATTTATATAT
116746 TTTAT
1 TTTAT
116751 TTTCTAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 8 0.33
21 6 0.25
22 10 0.42
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTATAATTATAATTTATATAT
Found at i:121538 original size:21 final size:20
Alignment explanation
Indices: 121514--121575 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
121504 GGGTTAGGAA
121514 CTTTCGATGAAAGGACTTAAC
1 CTTT-GATGAAAGGACTTAAC
* * *
121535 CTTTAGATTAAATGACTTATC
1 CTTT-GATGAAAGGACTTAAC
*
121556 CTTATGATGAAAGGGCTTAA
1 CTT-TGATGAAAGGACTTAA
121576 TATTTTCATG
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 31 0.97
22 1 0.03
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Consensus pattern (20 bp):
CTTTGATGAAAGGACTTAAC
Found at i:121586 original size:21 final size:21
Alignment explanation
Indices: 121562--121608 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
121552 TATCCTTATG
*
121562 ATGAAAGGGCTTAATATTTTC
1 ATGAAAGGACTTAATATTTTC
*
121583 ATGAAAGGATTTAATATTTTC
1 ATGAAAGGACTTAATATTTTC
121604 ATGAA
1 ATGAA
121609 GAGAATTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (21 bp):
ATGAAAGGACTTAATATTTTC
Found at i:126843 original size:26 final size:27
Alignment explanation
Indices: 126807--126867 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
126797 CAAAACGCTG
126807 CTTAAGACTAT-GGTTGAATTCGAAAA
1 CTTAAGACTATGGGTTGAATTCGAAAA
126833 CTTAAGACTATGGGTTGAATTCGAAAA
1 CTTAAGACTATGGGTTGAATTCGAAAA
126860 CTATAAGA
1 CT-TAAGA
126868 TGCAAATAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 11 0.33
27 17 0.52
28 5 0.15
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (27 bp):
CTTAAGACTATGGGTTGAATTCGAAAA
Done.