Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001017.1 Hibiscus syriacus cultivar Beakdansim tig00002029_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: 85813
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1152 original size:27 final size:27
Alignment explanation
Indices: 1111--1162 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1101 GCTCTTAGTT
1111 GTTTATATTTGTTTA-TTAGTCCCTAAA
1 GTTTATATTTGTTTATTTA-TCCCTAAA
* *
1138 GTTTCTATTTTTTTATTTATCCCTA
1 GTTTATATTTGTTTATTTATCCCTA
1163 GGTTTTCTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 19 0.86
28 3 0.14
ACGTcount: A:0.21, C:0.13, G:0.08, T:0.58
Consensus pattern (27 bp):
GTTTATATTTGTTTATTTATCCCTAAA
Found at i:4342 original size:20 final size:20
Alignment explanation
Indices: 4317--4377 Score: 97
Period size: 20 Copynumber: 3.0 Consensus size: 20
4307 ACATTCCCTC
4317 TCTTTGAGACCTTGAAACAT
1 TCTTTGAGACCTTGAAACAT
4337 TCTTTGAGACCTTGAAACAT
1 TCTTTGAGACCTTGAAACAT
*
4357 TCTTT-ACGGCCTTGAAACAT
1 TCTTTGA-GACCTTGAAACAT
4377 T
1 T
4378 GCATTTATCC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 1 0.03
20 38 0.97
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (20 bp):
TCTTTGAGACCTTGAAACAT
Found at i:5005 original size:12 final size:14
Alignment explanation
Indices: 4969--5016 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
4959 AGCGAAGAAC
4969 AAAGAAATCAAAGAG
1 AAAGAAA-CAAAGAG
4984 AAAGAAACAAAGAG
1 AAAGAAACAAAGAG
4998 -AA-AAAC-AAGCAG
1 AAAGAAACAAAG-AG
5010 AAAGAAA
1 AAAGAAA
5017 AGAAAAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 3 0.10
12 6 0.20
13 4 0.13
14 10 0.33
15 7 0.23
ACGTcount: A:0.71, C:0.08, G:0.19, T:0.02
Consensus pattern (14 bp):
AAAGAAACAAAGAG
Found at i:6249 original size:4 final size:4
Alignment explanation
Indices: 6240--8359 Score: 3592
Period size: 4 Copynumber: 543.0 Consensus size: 4
6230 ATACATCAAC
6240 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
6288 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
6336 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
6384 ACAT -CAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACCT AC-T
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
6430 ACAT --AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
6476 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * *
6524 ACAT ACAT ACAT -CAAC ACAT ACAT ACAT ACAT ACAT --AT ACAC ACAC
1 ACAT ACAT ACAT AC-AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
6570 ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT CACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT -ACAT ACAT
* * * *
6617 ACAT ACAT ACAC ATAC ACAT ACAT ACAT ACAC ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * *
6665 ATAT ACAC ACAC ACAT ACAT ACAT ACAT ACAT ACAT ACA- ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
6712 ACAT ACAT ACAT ACAT ACAT ACAT ACAT -CAT -CAC ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
6758 ACAT ACAT --AT ACAT AC-- ACAC ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
6802 ACAT ACAT ACAT ACAT ACAT ACAC ACAT ACAC ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * *
6850 ACAC ACAT ACAT ACAT ACAT ATAT ACAC ACAC ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
6898 ACAT ACAT ACAT ACAC ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
6946 ACAT ACAG AC-- ACAT ACAT -CAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
6991 ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
7037 ACAT ACAT --AT ACAT -CAC ACAT AC-- ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
7080 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
7128 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
7176 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
7224 ACAT ACAT ACAG ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
7272 ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT -CAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
7317 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
7365 -CAT ACAT ACAT ACAT --AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
7410 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
7458 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
7506 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT -CAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
7553 ACAT ACAT ACAG ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
7601 ACCT ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACA- ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
7646 ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
7693 ACAT ACAT ACAT AC-- ACAT ATAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
7739 ACAT -CAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACCT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
7786 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
7834 ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
7881 ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT AC-- ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
7925 ACAT ACAT ACAT ACAT ACAT ACCT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
7973 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
8021 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
8069 ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
8115 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
8162 ACAT ACAT ACAT ACAT ACAT A-AT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
8209 AC-- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
8255 ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
8302 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC--
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
8348 ACAT ACAT ACAT
1 ACAT ACAT ACAT
8360 GTTAAATGAG
Statistics
Matches: 2016, Mismatches: 45, Indels: 110
0.93 0.02 0.05
Matches are distributed among these distances:
2 36 0.02
3 50 0.02
4 1925 0.95
5 5 0.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:8805 original size:37 final size:36
Alignment explanation
Indices: 8713--8820 Score: 128
Period size: 37 Copynumber: 2.9 Consensus size: 36
8703 GTTTCGTTTG
8713 AAAAACAAATTTTGTCTCGCTTGAGACAATTTTCTAA
1 AAAAACAAA-TTTGTCTCGCTTGAGACAATTTTCTAA
* *
8750 AAAAACAAACGTTGTCTCGATTGAGACAATTTCTCT-A
1 AAAAACAAA-TTTGTCTCGCTTGAGACAATTT-TCTAA
* * *
8787 AAAAACAAATTATATCTCGCTTGATACATTTTTC
1 AAAAACAAATT-TGTCTCGCTTGAGACAATTTTC
8821 CGCAAATTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
36 3 0.05
37 55 0.90
38 3 0.05
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (36 bp):
AAAAACAAATTTGTCTCGCTTGAGACAATTTTCTAA
Found at i:9172 original size:28 final size:28
Alignment explanation
Indices: 9141--9242 Score: 111
Period size: 29 Copynumber: 3.6 Consensus size: 28
9131 ACAGTTTCTC
* *
9141 TTGAAACAAATCTTTGAGTATGTTCCTT
1 TTGAAAAAAATCTTTGAGTATGTTACTT
9169 TTGAATAAAAATCTTTGAGT-TGTTTAC-T
1 TTGAA-AAAAATCTTTGAGTATG-TTACTT
*
9197 TTGAGAAGAAAATCATTGAGTATGTTACTT
1 TTGA-AA-AAAATCTTTGAGTATGTTACTT
9227 TTGAAACAAAAT-TTTG
1 TTGAAA-AAAATCTTTG
9243 TCTTTCTTGA
Statistics
Matches: 63, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
28 16 0.25
29 40 0.63
30 7 0.11
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (28 bp):
TTGAAAAAAATCTTTGAGTATGTTACTT
Found at i:9288 original size:60 final size:59
Alignment explanation
Indices: 9205--9357 Score: 218
Period size: 60 Copynumber: 2.5 Consensus size: 59
9195 CTTTGAGAAG
* * *
9205 AAAATCATTGAGTATGTTACTTTTGAAACAAAATTTTGTCTTTCTTGAGACAATTTCGT-A
1 AAAATCTTTGAGT-TGTTTCTTTTGAAACAAAATTTTGTCTCTCTTGAGACAATTT-GTAA
*
9265 AAAATCTTTGAGTCTATTTCTTTTGAAACAAAATTTTGTCTCTCTTGAGACAATTTGTGAA
1 AAAATCTTTGAGT-TGTTTCTTTTGAAACAAAATTTTGTCTCTCTTGAGACAATTTGT-AA
*
9326 AAAATCTTTGAGTTGTTTCTTTTGAAAAAAAA
1 AAAATCTTTGAGTTGTTTCTTTTGAAACAAAA
9358 AACTTTGAGT
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
59 2 0.02
60 68 0.81
61 14 0.17
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (59 bp):
AAAATCTTTGAGTTGTTTCTTTTGAAACAAAATTTTGTCTCTCTTGAGACAATTTGTAA
Found at i:9363 original size:29 final size:30
Alignment explanation
Indices: 9324--9382 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
9314 ACAATTTGTG
* *
9324 AAAAAATCTTTGAGT-TGTTTCTTTTGAAA
1 AAAAAAACTTTGAGTATGTTTCTTTGGAAA
9353 AAAAAAACTTTGAGTATGTTTCTTTGGAAA
1 AAAAAAACTTTGAGTATGTTTCTTTGGAAA
9383 CAAATTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (30 bp):
AAAAAAACTTTGAGTATGTTTCTTTGGAAA
Found at i:9965 original size:133 final size:133
Alignment explanation
Indices: 9708--10049 Score: 443
Period size: 134 Copynumber: 2.6 Consensus size: 133
9698 AACCATCATC
* * * * *
9708 CCTAAAGATGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCTGACTAGACCTCTTCAT
1 CCTAAAGATGGCCAGCAGTCCTCATCACGTAGGAACCGTGTCATCCCC-GACCAGATCTCCTCAT
* * *
9773 CACGTAGGAGTCGTGTCAACCATAGATAACTAGTCGTCCTCATCACGTAGGAACCGAGTTATCAC
65 CACGTAGGAGCCGTATCAACCATAGATAACCAGTCGTCCTCATCACGTAGGAACCGAGTTATCAC
9838 CACT-
130 C-CTA
* * *
9842 CCTAAAGATGGCCAGCTGTCCTCATCACGTAGGAATCGTGTCATCCCCGACCAGGTCTCCTCATC
1 CCTAAAGATGGCCAGCAGTCCTCATCACGTAGGAACCGTGTCATCCCCGACCAGATCTCCTCATC
* * ** *
9907 ACGTAGGAGCCGTATCACCCTTAGATAACCAGTTTTCCTCATCACGTAGGAACTGAGTTATCACC
66 ACGTAGGAGCCGTATCAACCATAGATAACCAGTCGTCCTCATCACGTAGGAACCGAGTTATCACC
9972 CTA
131 CTA
* * * * * *
9975 CCTAAAGATGGCCACGAACTCTTCATCACGTATGAGCAGTGTCATCCCCGACCAGATCTCCTCAT
1 CCTAAAGATGGCCA-GCAGTCCTCATCACGTAGGAACCGTGTCATCCCCGACCAGATCTCCTCAT
*
10040 CAAGTAGGAG
65 CACGTAGGAG
10050 TCGTGTCTCC
Statistics
Matches: 181, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
132 2 0.01
133 84 0.46
134 95 0.52
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (133 bp):
CCTAAAGATGGCCAGCAGTCCTCATCACGTAGGAACCGTGTCATCCCCGACCAGATCTCCTCATC
ACGTAGGAGCCGTATCAACCATAGATAACCAGTCGTCCTCATCACGTAGGAACCGAGTTATCACC
CTA
Found at i:10083 original size:134 final size:133
Alignment explanation
Indices: 9708--10088 Score: 392
Period size: 134 Copynumber: 2.8 Consensus size: 133
9698 AACCATCATC
* * * * * *
9708 CCTAAAGATGGCCAG-CCGTCCTCATCATGTAGGAACCGTGTCATCCCCTGACTAGACCTCTTCA
1 CCTAAAGATGGCCAGAAC-TCCTCATCACGTAGGAAGCGTGTCATCCCC-GACCAGATCTCCTCA
* * * * * * * *
9772 TCACGTAGGAGTCGTGTCAACCATAGATAACTAGTCGTCCTCATCACGTAGGAACCGAGTTATCA
64 TCAAGTAGGAGCCGTATCACCCTTAGATAACCAGACCTCCTCATCACGTAGGAACCGAGTTATCA
9837 CCACT
129 CCACT
*** * *
9842 CCTAAAGATGGCCAGCTGTCCTCATCACGTAGGAATCGTGTCATCCCCGACCAGGTCTCCTCATC
1 CCTAAAGATGGCCAGAACTCCTCATCACGTAGGAAGCGTGTCATCCCCGACCAGATCTCCTCATC
* *** *
9907 ACGTAGGAGCCGTATCACCCTTAGATAACCAGTTTTCCTCATCACGTAGGAACTGAGTTATCACC
66 AAGTAGGAGCCGTATCACCCTTAGATAACCAGACCTCCTCATCACGTAGGAACCGAGTTATCACC
9972 -CT
131 ACT
* *
9974 ACCTAAAGATGGCCACGAACTCTTCATCACGTATG-AGCAGTGTCATCCCCGACCAGATCTCCTC
1 -CCTAAAGATGGCCA-GAACTCCTCATCACGTAGGAAGC-GTGTCATCCCCGACCAGATCTCCTC
* * * * * *
10038 ATCAAGTAGGAGTCGTGTCTCCTTTAG-TCGACCAGACCTCTTCATCACGTA
63 ATCAAGTAGGAGCCGTATCACCCTTAGAT-AACCAGACCTCCTCATCACGTA
10089 TGAGTAGTGT
Statistics
Matches: 209, Mismatches: 33, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
132 2 0.01
133 87 0.42
134 120 0.57
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (133 bp):
CCTAAAGATGGCCAGAACTCCTCATCACGTAGGAAGCGTGTCATCCCCGACCAGATCTCCTCATC
AAGTAGGAGCCGTATCACCCTTAGATAACCAGACCTCCTCATCACGTAGGAACCGAGTTATCACC
ACT
Found at i:10264 original size:3 final size:3
Alignment explanation
Indices: 10258--10315 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
10248 TTTTTTTAAT
* * * *
10258 TTA TTA TT- TTA TT- TTA TTA GTA TTA GTA TTA TTA TTA TTA GTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
10304 TTA TTA TTA TTA
1 TTA TTA TTA TTA
10316 ATTTACATGT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
2 4 0.09
3 42 0.91
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:11846 original size:30 final size:30
Alignment explanation
Indices: 11810--11881 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 30
11800 AGGTTTTCTA
*
11810 TTTTTGTTATTTGGATCCTTTAATTTTATG
1 TTTTTGTCATTTGGATCCTTTAATTTTATG
11840 TTTTTGTCATTTGGATCCTTTAATTTTATG
1 TTTTTGTCATTTGGATCCTTTAATTTTATG
*
11870 TTTTTGTGATTT
1 TTTTTGTCATTT
11882 TAGTCCTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.15, C:0.07, G:0.14, T:0.64
Consensus pattern (30 bp):
TTTTTGTCATTTGGATCCTTTAATTTTATG
Found at i:11889 original size:30 final size:30
Alignment explanation
Indices: 11810--11892 Score: 114
Period size: 30 Copynumber: 2.8 Consensus size: 30
11800 AGGTTTTCTA
* *
11810 TTTTTGTTATTTGGATCCTTTAATTTTATG
1 TTTTTGTCATTTAGATCCTTTAATTTTATG
*
11840 TTTTTGTCATTTGGATCCTTTAATTTTATG
1 TTTTTGTCATTTAGATCCTTTAATTTTATG
*
11870 TTTTTGTGATTTTAG-TCCTTTAA
1 TTTTTGTCA-TTTAGATCCTTTAA
11893 ACTTCTATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
30 45 0.92
31 4 0.08
ACGTcount: A:0.17, C:0.08, G:0.13, T:0.61
Consensus pattern (30 bp):
TTTTTGTCATTTAGATCCTTTAATTTTATG
Found at i:14932 original size:36 final size:36
Alignment explanation
Indices: 14881--15027 Score: 190
Period size: 36 Copynumber: 4.1 Consensus size: 36
14871 TGGCTAACAG
14881 AAAGAAGAACGAAAGGAAGCATC-AGCACTTTCGATTC
1 AAAG-AGAACGAAAGGAAGCATCGA-CACTTTCGATTC
*
14918 AATA-AGAACGAAAGGAAGTATCGACACTTTCGATTC
1 AA-AGAGAACGAAAGGAAGCATCGACACTTTCGATTC
* * *
14954 AAAGTGAACGGAAGGAAGCATCGACACTTTCGATTT
1 AAAGAGAACGAAAGGAAGCATCGACACTTTCGATTC
* * *
14990 AAAGTGAACGGAAGGAAGCATCGGCACTTTCGATTC
1 AAAGAGAACGAAAGGAAGCATCGACACTTTCGATTC
15026 AA
1 AA
15028 TTGTTTATCT
Statistics
Matches: 100, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
35 1 0.01
36 95 0.95
37 3 0.03
38 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (36 bp):
AAAGAGAACGAAAGGAAGCATCGACACTTTCGATTC
Found at i:16309 original size:36 final size:36
Alignment explanation
Indices: 16262--16330 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
16252 TGAGAAAGAA
* *
16262 GAACGAAAGGAAATATCAGTACTTTCGATTCAAAGT
1 GAACGAAAGGAAACATCAGCACTTTCGATTCAAAGT
* * *
16298 GAACGGAAGGAAGCATCGGCACTTTCGATTCAA
1 GAACGAAAGGAAACATCAGCACTTTCGATTCAA
16331 TTGTTCATCT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (36 bp):
GAACGAAAGGAAACATCAGCACTTTCGATTCAAAGT
Found at i:21238 original size:38 final size:38
Alignment explanation
Indices: 21144--21220 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
21134 GTGGACTTTC
*
21144 TATATCCTGTTCAATTTTCAGAGGAAGAATAAATTCTT
1 TATATCCTATTCAATTTTCAGAGGAAGAATAAATTCTT
21182 TATATCCTATTCAATTTTCAGAGGAAGAATAAATTCTT
1 TATATCCTATTCAATTTTCAGAGGAAGAATAAATTCTT
21220 T
1 T
21221 CTTCATCTCA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (38 bp):
TATATCCTATTCAATTTTCAGAGGAAGAATAAATTCTT
Found at i:34152 original size:20 final size:20
Alignment explanation
Indices: 34127--34200 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
34117 TTTTCCCAAT
*
34127 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
** *
34147 TCGCAACGCGAATTGGGAAA
1 TCGCAACGCGAATAAGTAAA
*
34167 TTCGCAATGCGAATAAGTAAA
1 -TCGCAACGCGAATAAGTAAA
34188 TCGCAACGCGAAT
1 TCGCAACGCGAAT
34201 TGGGAAAAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:34169 original size:41 final size:42
Alignment explanation
Indices: 34124--34220 Score: 178
Period size: 41 Copynumber: 2.3 Consensus size: 42
34114 CGATTTTCCC
34124 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGG-A
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
34165 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
*
34207 AAATCGCAATGCGA
1 AATTCGCAATGCGA
34221 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 40 0.74
42 14 0.26
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (42 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAA
Found at i:34234 original size:20 final size:20
Alignment explanation
Indices: 34209--34303 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
34199 ATTGGGAAAA
*
34209 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
34229 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
34250 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
34270 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
*
34290 TTCGCAACGCGATA
1 ATCGCAACGCGATA
34304 ATACATAATC
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
20 45 0.76
21 14 0.24
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:34283 original size:41 final size:41
Alignment explanation
Indices: 34205--34283 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
34195 GCGAATTGGG
* * **
34205 AAAAATCGCAATGCGATACTGACTATCGCAATGCGATAATA
1 AAAAATCGCAACGAGATACTGACTATCGCAACACGATAATA
* *
34246 AAAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAAATCGCAACGAGATACTGACTATCGCAACACGATA
34284 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAAATCGCAACGAGATACTGACTATCGCAACACGATAATA
Found at i:34519 original size:22 final size:22
Alignment explanation
Indices: 34491--34534 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
34481 CACTCTCTCA
34491 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
34513 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
34535 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:34823 original size:20 final size:20
Alignment explanation
Indices: 34798--34835 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
34788 CGATTCTCTC
34798 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
34818 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
34836 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:36174 original size:18 final size:18
Alignment explanation
Indices: 36153--36197 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
36143 TCCACTTCGG
*
36153 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
36171 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
*
36189 GAACCATCA
1 GAGCCATCA
36198 TCTGATCGAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.42, G:0.13, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:36749 original size:32 final size:33
Alignment explanation
Indices: 36705--36794 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
36695 GGAAATGGCT
*
36705 ATCGCAATGCGAAATGAAAATCGCAACGAC-AA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
36737 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
36769 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
36795 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
31 13 0.24
32 33 0.60
33 9 0.16
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:36788 original size:19 final size:19
Alignment explanation
Indices: 36667--36799 Score: 83
Period size: 19 Copynumber: 7.6 Consensus size: 19
36657 TAGTTTACTT
* **
36667 TCGCAACACGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
36686 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
36706 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
36725 TCGCAA--CG--A--CAAA
1 TCGCAACGCGAAATGAAAA
36738 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
36756 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
36770 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
36789 TCGCAATGCGA
1 TCGCAACGCGA
36800 TTTGTGTTTC
Statistics
Matches: 91, Mismatches: 10, Indels: 26
0.72 0.08 0.20
Matches are distributed among these distances:
13 9 0.10
14 10 0.11
15 3 0.03
16 4 0.04
17 3 0.03
18 10 0.11
19 35 0.38
20 17 0.19
ACGTcount: A:0.42, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:36851 original size:19 final size:19
Alignment explanation
Indices: 36825--36891 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
36815 GCGATTTTGT
**
36825 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
36844 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
36864 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
36883 CGTTGCGAT
1 CGTTGCGAT
36892 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:36871 original size:20 final size:19
Alignment explanation
Indices: 36837--36891 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
36827 TTGCGATTTT
*
36837 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
36856 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
36876 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
36892 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:38768 original size:14 final size:14
Alignment explanation
Indices: 38749--38784 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
38739 ATTGTTTAAT
38749 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
38763 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
38777 TGATTTGT
1 TGATTTGT
38785 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:38909 original size:14 final size:15
Alignment explanation
Indices: 38890--38966 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 15
38880 CGAAATGGCT
38890 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
*
38904 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
38922 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
38941 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
38955 ATCGCAATGCGA
1 ATCGCAA-GCGA
38967 TTTCATTTCG
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.13
17 2 0.04
18 13 0.25
19 9 0.17
20 1 0.02
21 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:38922 original size:19 final size:19
Alignment explanation
Indices: 38900--38966 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
38890 ATCGCAACGA
38900 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
38919 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
38937 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
38951 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
38967 TTTCATTTCG
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:39041 original size:20 final size:20
Alignment explanation
Indices: 38991--39041 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
38981 GCGATATTCT
* *
38991 CGTTGCGATAACCATTTTCG
1 CGTTGCGATAGCCATTTTCA
39011 CGTTGCGATAGCCATTTTCA
1 CGTTGCGATAGCCATTTTCA
39031 CGTTGCGATAG
1 CGTTGCGATAG
39042 TCAAATGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCA
Found at i:39423 original size:14 final size:14
Alignment explanation
Indices: 39404--39439 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
39394 ATTGTTTAAT
39404 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
39418 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
39432 TGATTTGT
1 TGATTTGT
39440 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:39859 original size:19 final size:18
Alignment explanation
Indices: 39837--39889 Score: 51
Period size: 19 Copynumber: 3.1 Consensus size: 18
39827 CTCGTTGCCT
39837 TTTTCATTTCGCATTGCGA
1 TTTTCA-TTCGCATTGCGA
39856 TTTT-A-TCG--TTGCGA
1 TTTTCATTCGCATTGCGA
*
39870 TTTGCAGTTCGCATTGCGA
1 TTTTCA-TTCGCATTGCGA
39889 T
1 T
39890 GGTCAAATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 10
0.72 0.03 0.26
Matches are distributed among these distances:
14 9 0.32
15 1 0.04
16 3 0.11
17 3 0.11
18 1 0.04
19 11 0.39
ACGTcount: A:0.15, C:0.19, G:0.21, T:0.45
Consensus pattern (18 bp):
TTTTCATTCGCATTGCGA
Found at i:40721 original size:24 final size:24
Alignment explanation
Indices: 40665--40723 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
40655 AGTCAGTATT
* *
40665 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
40689 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
40713 CGAATTTTGAT
1 CGAAATTTGAT
40724 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:40915 original size:12 final size:12
Alignment explanation
Indices: 40898--40922 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40888 ATATAATCCT
40898 GAAGAAGAAAAA
1 GAAGAAGAAAAA
40910 GAAGAAGAAAAA
1 GAAGAAGAAAAA
40922 G
1 G
40923 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:43238 original size:19 final size:19
Alignment explanation
Indices: 43196--43313 Score: 94
Period size: 19 Copynumber: 6.7 Consensus size: 19
43186 CTTAATGTCC
* **
43196 ATCGCAATGCGGAAATTACT
1 ATCGCAATGC-GAAATGAAA
43216 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
43235 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
43249 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
43268 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
43282 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
43301 ATCGCAACGCGAA
1 ATCGCAATGCGAA
43314 TTTAATTTCG
Statistics
Matches: 78, Mismatches: 10, Indels: 21
0.72 0.09 0.19
Matches are distributed among these distances:
14 19 0.24
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 37 0.47
20 10 0.13
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:43258 original size:33 final size:33
Alignment explanation
Indices: 43216--43309 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
43206 GGAAATTACT
43216 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
43249 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
43282 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
43310 CGAATTTAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:43331 original size:19 final size:20
Alignment explanation
Indices: 43309--43351 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
43299 AAATCGCAAC
43309 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
43328 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
43348 GCGA
1 GCGA
43352 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:43336 original size:14 final size:14
Alignment explanation
Indices: 43337--43370 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
43327 TGCGATTTTC
43337 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
43351 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
43365 ATTTTC
1 ATTTTC
43371 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:43511 original size:14 final size:14
Alignment explanation
Indices: 43492--43528 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
43482 CATCAATTAA
43492 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
43506 ACAAATCACCTTTT
1 ACAAATCAACTTTT
43520 ACAAATCAA
1 ACAAATCAA
43529 TTAAATAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:44920 original size:21 final size:21
Alignment explanation
Indices: 44854--44920 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
44844 GTGAATCGGG
*
44854 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
44874 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
44896 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
44917 CTCT
1 CTCT
44921 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:44939 original size:42 final size:41
Alignment explanation
Indices: 44854--44976 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
44844 GTGAATCGGG
* * * * *
44854 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
44896 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
44938 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
44977 CGAGTCGAGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:47007 original size:20 final size:19
Alignment explanation
Indices: 46976--47136 Score: 90
Period size: 20 Copynumber: 8.8 Consensus size: 19
46966 TCTTTTGGTT
46976 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
46995 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
47016 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
47035 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
47049 GAAATGACTATCG---CGA
1 GAAATGAAAATCGCAACGA
** * * *
47065 -CCA-GACAATCGCAATGC
1 GAAATGAAAATCGCAACGA
*
47082 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGA
* *
47102 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
47121 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
47137 TGCGATTTTG
Statistics
Matches: 109, Mismatches: 20, Indels: 26
0.70 0.13 0.17
Matches are distributed among these distances:
14 17 0.16
15 1 0.01
16 4 0.04
17 3 0.03
18 1 0.01
19 35 0.32
20 46 0.42
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:47058 original size:33 final size:33
Alignment explanation
Indices: 47001--47099 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
46991 ACGAGATAAT
*
47001 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
47035 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* * **
47068 GACAATCGCAATGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
47100 GCGAAATTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 44 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.25, G:0.23, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:47093 original size:19 final size:19
Alignment explanation
Indices: 47071--47141 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
47061 GCGACCAGAC
*
47071 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
47090 AATCGCAACCGCGAAATTAA
1 AATCGCAA-CGCGAAATGAA
47110 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
47129 AATCGCAATGCGA
1 AATCGCAACGCGA
47142 TTTTGGTTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
19 30 0.64
20 17 0.36
ACGTcount: A:0.45, C:0.21, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:47170 original size:19 final size:19
Alignment explanation
Indices: 47137--47181 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
47127 AAAATCGCAA
*
47137 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
47156 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
47175 TGCGATT
1 TGCGATT
47182 ATCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:47764 original size:20 final size:20
Alignment explanation
Indices: 47736--47787 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
47726 CGCTAAGTAA
* *
47736 ATCGCGTTGCGAAAGTCAGT
1 ATCGTGTTGCGAAAGTAAGT
47756 ATCGTGTTGCGAAAGTAAGT
1 ATCGTGTTGCGAAAGTAAGT
47776 ATC-TCGTTGCGA
1 ATCGT-GTTGCGA
47788 TTTTTTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (20 bp):
ATCGTGTTGCGAAAGTAAGT
Found at i:47842 original size:20 final size:20
Alignment explanation
Indices: 47798--47890 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
47788 TTTTTTATTA
* **
47798 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
47819 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
47839 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
47860 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
47880 TCGCATTGCGA
1 TCGCATTGCGA
47891 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:47843 original size:41 final size:41
Alignment explanation
Indices: 47780--47893 Score: 185
Period size: 41 Copynumber: 2.8 Consensus size: 41
47770 GTAAGTATCT
* *
47780 CGTTGCGATTT-TTTATTATCGCATTGCGATTTTCCCAATTCG
1 CGTTGCGATTTACTTA-T-TCGCATTGCGAATTTCCCAATTCG
47822 CGTTGCGATTTACTTATTCGCATTGCGAATTTCCCAATTCG
1 CGTTGCGATTTACTTATTCGCATTGCGAATTTCCCAATTCG
47863 CGTTGCGATTTACTTATTCGCATTGCGAATT
1 CGTTGCGATTTACTTATTCGCATTGCGAATT
47894 GGGAAAATCG
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
41 54 0.78
42 12 0.17
43 3 0.04
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (41 bp):
CGTTGCGATTTACTTATTCGCATTGCGAATTTCCCAATTCG
Found at i:64845 original size:10 final size:10
Alignment explanation
Indices: 64824--64868 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
64814 CGTCTGTTTT
*
64824 TCTGTTGTTC
1 TCTGTTGCTC
*
64834 TCCGTTGCTC
1 TCTGTTGCTC
* *
64844 TCTGTGGCTG
1 TCTGTTGCTC
64854 TCTGTTGCTC
1 TCTGTTGCTC
64864 TCTGT
1 TCTGT
64869 CCTTTTTTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.00, C:0.27, G:0.24, T:0.49
Consensus pattern (10 bp):
TCTGTTGCTC
Found at i:65326 original size:3 final size:3
Alignment explanation
Indices: 65318--65391 Score: 112
Period size: 3 Copynumber: 24.0 Consensus size: 3
65308 TTATTTATTA
* *
65318 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT ACT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
65365 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
65392 TTTAAATGAA
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
3 59 0.91
4 6 0.09
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:65807 original size:153 final size:152
Alignment explanation
Indices: 65516--66010 Score: 855
Period size: 153 Copynumber: 3.2 Consensus size: 152
65506 GATGGAAATG
* *
65516 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGC
* * *
65581 TCCCGAAGGCTTTTTGGAAACATCGTGCAATGAAGGACTTACAGATGACCCGAAGGTTTTGAAAA
65 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA
* * *
65646 CATCAAAAAGCTCCCGAAGGTTTT
130 TATTAAAAAGCTCCCGAAGG-CTT
* *
65670 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAATATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
65735 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAT
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAT
65800 ATTAAAAAGCTCCCGAAGGCTT
131 ATTAAAAAGCTCCCGAAGGCTT
65822 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
65887 CCCGAAGGTTTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA
66 CCCGAAGG-CTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA
*
65952 TATTAAAAAGCTCTCGAAGGCTT
130 TATTAAAAAGCTCCCGAAGGCTT
65975 TTTGGAAACATCATGCACTGAAGGACTTACAGATGA
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGA
66011 GGGAAATAGT
Statistics
Matches: 326, Mismatches: 14, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
152 73 0.22
153 210 0.64
154 43 0.13
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (152 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAT
ATTAAAAAGCTCCCGAAGGCTT
Found at i:65923 original size:229 final size:230
Alignment explanation
Indices: 65516--66010 Score: 911
Period size: 229 Copynumber: 2.2 Consensus size: 230
65506 GATGGAAATG
* *
65516 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTCTTTGAAAACATCAAAAAGC
* *
65581 TCCCGAAGGCTTTTTGGAAACATCGTGCAATGAAGGACTTACAGATGACCCGAAGGTTTTGAAAA
66 TCCCGAAGGCTTTTTGGAAACATCATGCAATGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA
65646 CATCAAAAAGCTCCCGAAGGTTTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGA
131 CATCAAAAAGCTCCCGAAGGTTTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGA
65711 AGGCTTTGAAAATATTAAAAAGCTCCCGAAGGCTT
196 AGGCTTTGAAAATATTAAAAAGCTCCCGAAGGCTT
* *
65746 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAATATTAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTCTTTGAAAACATCAAAAAGC
*
65810 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA
66 TCCCGAAGGCTTTTTGGAAACATCATGCAATGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA
65875 CATCAAAAAGCTCCCGAAGGTTTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGA
131 CATCAAAAAGCTCCCGAAGGTTTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGA
*
65940 AGGCTTTGAAAATATTAAAAAGCTCTCGAAGGCTT
196 AGGCTTTGAAAATATTAAAAAGCTCCCGAAGGCTT
65975 TTTGGAAACATCATGCACTGAAGGACTTACAGATGA
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGA
66011 GGGAAATAGT
Statistics
Matches: 257, Mismatches: 8, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
229 214 0.83
230 43 0.17
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (230 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTCTTTGAAAACATCAAAAAGC
TCCCGAAGGCTTTTTGGAAACATCATGCAATGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA
CATCAAAAAGCTCCCGAAGGTTTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGA
AGGCTTTGAAAATATTAAAAAGCTCCCGAAGGCTT
Found at i:66036 original size:76 final size:76
Alignment explanation
Indices: 65516--66010 Score: 837
Period size: 76 Copynumber: 6.5 Consensus size: 76
65506 GATGGAAATG
* * * *
65516 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAATATTAAAAAGC
65581 TCCCGAAGGCTT
65 TCCCGAAGGCTT
* * * * *
65593 TTTGGAAACATCGTGCAATGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAATATTAAAAAGCT
*
65658 CCCGAAGGTTTT
66 CCCGAAGG-CTT
65670 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAATATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAATATTAAAAAGCT
65735 CCCGAAGGCTT
66 CCCGAAGGCTT
65746 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAATATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAATATTAAAAAGCT
65811 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
65822 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAATATTAAAAAGCT
*
65887 CCCGAAGGTTTT
66 CCCGAAGG-CTT
65899 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAATATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAATATTAAAAAGCT
*
65964 CTCGAAGGCTT
66 CCCGAAGGCTT
65975 TTTGGAAACATCATGCACTGAAGGACTTACAGATGA
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGA
66011 GGGAAATAGT
Statistics
Matches: 399, Mismatches: 17, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
76 216 0.54
77 183 0.46
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAATATTAAAAAGCT
CCCGAAGGCTT
Found at i:67007 original size:343 final size:338
Alignment explanation
Indices: 66414--67193 Score: 1129
Period size: 343 Copynumber: 2.3 Consensus size: 338
66404 ATAGAATTAT
* *
66414 GCAAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * * *
66479 ATTATGAACTTCTCTGGAAAAGCTGCTCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGT
66 ATTATGAACTTCTCTGGAAAAGCTGATCCATCAAGTAATGAATTTAAGAAAAAGGTTGAACAAAT
*
66544 TCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGG
131 TCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTACTCTGG
* * *
66609 CAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACT
196 CAAAAATAATCCATCAAATGATGAATTAAGACAAAAAGTTGAACAAATTCTTCTCATTATGAACT
66674 TCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAA
261 TCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAA
66739 AT-ATTAGATTCAA
326 ATGA-TAGATTCAA
* * *
66752 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCCTTTAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
66817 ATTATGAACTTGAC-CTGGCAATGCTGATCCATTGAA-TAATGAATTTAAGTAAAAAGGTTGAAC
66 ATTATGAACTT--CTCTGGAAAAGCTGATCCA-TCAAGTAATGAATTTAAG-AAAAAGGTTGAAC
66880 AAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTC
127 AAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAAC-C
* ** * *
66945 TAC-CTGGTAATGATGATCCATCAAATGATGAATTTAAG-CAAAAAGTTGAACAAGTTCTTCTCA
188 TACTCTGGCAAAAATAATCCATCAAATGATGAA-TTAAGACAAAAAGTTGAACAAATTCTTCTCA
* *
67008 TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGCTG
252 TTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATG
* * **
67073 ATCCATCGAATGATGGATTTGA
317 ATCCATCAAATGATAGATTCAA
*
67095 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* **
67160 ATTATGAACTTTTTCTGGAAAAAATGATCCATCA
66 ATTATGAAC-TTCTCTGGAAAAGCTGATCCATCA
67194 TATGATGGAT
Statistics
Matches: 391, Mismatches: 39, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
338 71 0.18
339 24 0.06
340 55 0.14
342 2 0.01
343 229 0.59
344 10 0.03
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (338 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTCTCTGGAAAAGCTGATCCATCAAGTAATGAATTTAAGAAAAAGGTTGAACAAAT
TCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTACTCTGG
CAAAAATAATCCATCAAATGATGAATTAAGACAAAAAGTTGAACAAATTCTTCTCATTATGAACT
TCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAA
ATGATAGATTCAA
Found at i:67207 original size:113 final size:112
Alignment explanation
Indices: 66414--67205 Score: 1056
Period size: 113 Copynumber: 7.0 Consensus size: 112
66404 ATAGAATTAT
* *
66414 GCAAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
66479 ATTATGAAC-TTCTCTGGAAAAGCTGCTCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAATGATGATCCATCAA-TGATGGATTTAA
* *
66526 GCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * *
66591 ATTATGAACCTTCTCTGGCAAA-AATAATCCATCAAGTGAT-GAATTCA
66 ATTATGAACTTTCTCTGG-AAATGATGATCCATCAA-TGATGGATTTAA
*
66638 GACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCT
1 G-CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* *
66703 CATTATGAACTTTCTCTGGAAATGATGATCCATCAAAT-ATTAGATTCAA
65 CATTATGAACTTTCTCTGGAAATGATGATCCATC-AATGA-TGGATTTAA
* * *
66752 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCCTTTAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * * *
66817 ATTATGAACTTGAC-CTGGCAATGCTGATCCATTGAATAATGAATTTAA
66 ATTATGAACTT-TCTCTGGAAATGATGATCCA-TCAATGATGGATTTAA
* *
66865 GTAAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCT
1 G-CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCT
* * *
66930 TCTCATTATGAACTCTAC-CTGGTAATGATGATCCATCAAATGATGAATTTAA
62 TCTCATTATGAACT-TTCTCTGGAAATGATGATCCATC-AATGATGGATTTAA
* *
66982 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
67047 ATTATGAACTTTCTCTGGAAATGCTGATCCATCGAATGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAATGATGATCCATC-AATGATGGATTTAA
*
67095 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* **
67160 ATTATGAACTTTTTCTGGAAAAAATGATCCATCATATGATGGATTT
66 ATTATGAACTTTCTCTGGAAATGATGATCCATCA-ATGATGGATTT
67206 GAATCTTTGC
Statistics
Matches: 609, Mismatches: 53, Indels: 35
0.87 0.08 0.05
Matches are distributed among these distances:
112 85 0.14
113 359 0.59
114 62 0.10
116 50 0.08
117 52 0.09
118 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (112 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAATGATGATCCATCAATGATGGATTTAA
Found at i:67632 original size:22 final size:22
Alignment explanation
Indices: 67607--67661 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
67597 CATAAAGTTT
*
67607 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
67629 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
67651 CCATCTTTGAA
1 TCATCTTTGAA
67662 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:70328 original size:83 final size:83
Alignment explanation
Indices: 70189--70578 Score: 726
Period size: 83 Copynumber: 4.7 Consensus size: 83
70179 GGGGTTCATA
* * *
70189 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACAAATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAA
70254 ATTCAATGATTGGTTTTG
66 ATTCAATGATTGGTTTTG
70272 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAA
70337 ATTCAATGATTGGTTTTG
66 ATTCAATGATTGGTTTTG
*
70355 CCAAACCAGATCAGATGACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAA
70420 ATTCAATGATTGGTTTTG
66 ATTCAATGATTGGTTTTG
*
70438 CCAAACCAGATCAGATAACTCAAAGAACAATTCCAGAAGATGCTATGAGCACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAA
70503 ATTCAATGATTGGTTTTG
66 ATTCAATGATTGGTTTTG
*
70521 CCAAACCAGATCAGATAACTCAAAGAACAATTCCAGAAGATGCTATGAGCACATTCAT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCAT
70579 TTGTTCCATT
Statistics
Matches: 301, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 301 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAA
ATTCAATGATTGGTTTTG
Found at i:79819 original size:3 final size:3
Alignment explanation
Indices: 79811--79884 Score: 112
Period size: 3 Copynumber: 24.0 Consensus size: 3
79801 TTATTTATTA
* *
79811 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT ACT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
79858 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
79885 TTTAAATGAA
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
3 59 0.91
4 6 0.09
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:81790 original size:20 final size:20
Alignment explanation
Indices: 81761--81873 Score: 199
Period size: 20 Copynumber: 5.7 Consensus size: 20
81751 TTTTCCTAAT
81761 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
81781 TCGTAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
81801 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
81821 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
81841 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
81861 TCGCAAAGCGAAT
1 TCGCAATGCGAAT
81874 CTGACTATCG
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 88 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:81883 original size:20 final size:20
Alignment explanation
Indices: 81860--81926 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
81850 GAATACGTAA
* *
81860 ATCGCAAAGCGAATCTGACT
1 ATCGCAAAGAGATTCTGACT
*
81880 ATCGCAACGAGATTCTGACT
1 ATCGCAAAGAGATTCTGACT
* *
81900 ATTGCAATGAGATTCTGACT
1 ATCGCAAAGAGATTCTGACT
81920 ATCGCAA
1 ATCGCAA
81927 TACTGAATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAAAGAGATTCTGACT
Found at i:81884 original size:40 final size:40
Alignment explanation
Indices: 81761--81886 Score: 177
Period size: 40 Copynumber: 3.1 Consensus size: 40
81751 TTTTCCTAAT
*
81761 TCGCAATGCGAATACGTAAATCGTAATGCGAATACAT-AAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATAC-TGAAA
81801 TCGCAATGCGAATACGTAAATCGCAATGCGAATAC-GTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATACTG-AAA
* *
81841 TCGCAATGCGAATACGTAAATCGCAAAGCGAAT-CTGACTA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATACTGA-AA
81881 TCGCAA
1 TCGCAA
81887 CGAGATTCTG
Statistics
Matches: 79, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
39 2 0.03
40 77 0.97
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGAATACTGAAA
Found at i:81927 original size:20 final size:20
Alignment explanation
Indices: 81873--81927 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
81863 GCAAAGCGAA
*
81873 TCTGACTATCGCAACGAGAT
1 TCTGACTATCGCAATGAGAT
*
81893 TCTGACTATTGCAATGAGAT
1 TCTGACTATCGCAATGAGAT
81913 TCTGACTATCGCAAT
1 TCTGACTATCGCAAT
81928 ACTGAATTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (20 bp):
TCTGACTATCGCAATGAGAT
Found at i:82788 original size:24 final size:24
Alignment explanation
Indices: 82761--82814 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
82751 GTATTCGAAA
82761 TTTGATCTTGGTCAATAAC-CGGAC
1 TTTGATCTTGGTCAAT-ACTCGGAC
*
82785 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACTCGGAC
82809 TTTGAT
1 TTTGAT
82815 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 2 0.07
24 26 0.93
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCGGAC
Found at i:85238 original size:20 final size:20
Alignment explanation
Indices: 85213--85301 Score: 144
Period size: 20 Copynumber: 4.5 Consensus size: 20
85203 TAACGCGAAA
85213 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
85233 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
*
85253 ATCGCAACGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
85273 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
85293 ATCGCAACG
1 ATCGCAACG
85302 AGAGAATCGC
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
20 61 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:85323 original size:33 final size:33
Alignment explanation
Indices: 85273--85368 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
85263 GGAATTGACT
* **
85273 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
* *
85307 ATCGCAATGTGAAATGAAAATCGTAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
85340 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
85369 CGAATTTAGT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 30 0.56
34 24 0.44
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:85426 original size:34 final size:31
Alignment explanation
Indices: 85383--85477 Score: 109
Period size: 32 Copynumber: 2.9 Consensus size: 31
85373 TTTAGTTTCG
*
85383 CGTTGCGATTTTCATTTTTGCATTGCGATTCTCT
1 CGTTGCGATTTTCA-TTTCGCATTGCGA-T-TCT
85417 CGTTGCGATTTTTCATTTCGCATTGCGATTCT
1 CGTTGCGA-TTTTCATTTCGCATTGCGATTCT
** *
85449 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
85478 AGTCTGTTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
31 7 0.13
32 21 0.38
33 1 0.02
34 20 0.36
35 6 0.11
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (31 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCT
Found at i:85475 original size:32 final size:33
Alignment explanation
Indices: 85383--85477 Score: 97
Period size: 34 Copynumber: 2.9 Consensus size: 33
85373 TTTAGTTTCG
* *
85383 CGTTGCGATT-TTCATTTTTGCATTGCGATTCTCT
1 CGTTGCGATTAGTCA-TTTCGCATTGCGA-TCTCT
**
85417 CGTTGCGATTTTTCATTTCGCATTGCGAT-TCT
1 CGTTGCGATTAGTCATTTCGCATTGCGATCTCT
*
85449 CGTTGCGA-TAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTAGTCATTT-CGCATTGCGAT
85478 AGTCTGTTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
31 7 0.13
32 21 0.38
33 1 0.02
34 22 0.40
35 4 0.07
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTAGTCATTTCGCATTGCGATCTCT
Found at i:85598 original size:14 final size:14
Alignment explanation
Indices: 85579--85613 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
85569 ATCAATTAAA
85579 AAATCAACATTTAC
1 AAATCAACATTTAC
* *
85593 AAATCATCTTTTAC
1 AAATCAACATTTAC
85607 AAATCAA
1 AAATCAA
85614 TTAAACAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATCAACATTTAC
Done.