Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003227.1 Hibiscus syriacus cultivar Beakdansim tig00006794_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: 64240
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Found at i:348 original size:17 final size:17
Alignment explanation
Indices: 321--360 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
311 AATTTACAAT
321 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
337 TAATTATAAATAATATC
1 TAATTATAAATAATATC
354 TAATTAT
1 TAATTAT
361 TCAAACATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:8171 original size:20 final size:20
Alignment explanation
Indices: 8146--8337 Score: 323
Period size: 20 Copynumber: 9.6 Consensus size: 20
8136 TGATTCAATC
* *
8146 AGTATCGATATCGAAGGCAG
1 AGTATCGATACCGAAGGGAG
8166 AGTATCGATACCGAAGGGAG
1 AGTATCGATACCGAAGGGAG
*
8186 AGTATCGATACTGAAGGGAG
1 AGTATCGATACCGAAGGGAG
8206 AGTATCGATACCGAAGGGAG
1 AGTATCGATACCGAAGGGAG
8226 AGTATCGATACCGAAGGGAG
1 AGTATCGATACCGAAGGGAG
8246 AGTATCGATACCGAAGGGAG
1 AGTATCGATACCGAAGGGAG
8266 AGTATCGATACCGAAGGGAG
1 AGTATCGATACCGAAGGGAG
8286 AGTATCGATACCGAAGGGAG
1 AGTATCGATACCGAAGGGAG
* *
8306 AGTATTGATACCGAAGAGA-
1 AGTATCGATACCGAAGGGAG
8325 ATGTATCGATACC
1 A-GTATCGATACC
8338 ATTCAAAAGA
Statistics
Matches: 164, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
19 1 0.01
20 163 0.99
ACGTcount: A:0.35, C:0.15, G:0.32, T:0.18
Consensus pattern (20 bp):
AGTATCGATACCGAAGGGAG
Found at i:8406 original size:22 final size:22
Alignment explanation
Indices: 8378--8431 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
8368 TACCATAGCA
8378 TAGTATCGATACCATAGTATGG
1 TAGTATCGATACCATAGTATGG
* * *
8400 TAGTATCAATTCCATGGTATGG
1 TAGTATCGATACCATAGTATGG
8422 --GTATCGATAC
1 TAGTATCGATAC
8432 TGAAGAGCCA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 8 0.30
22 19 0.70
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (22 bp):
TAGTATCGATACCATAGTATGG
Found at i:8837 original size:54 final size:54
Alignment explanation
Indices: 8755--9361 Score: 761
Period size: 54 Copynumber: 11.3 Consensus size: 54
8745 TACCAAATAA
* * *
8755 GCACTAAGTGTGCATTTCACGGAATTCATCCTGTGTAGATGAATAATCGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
* *
8809 GCACTAAGTGTGCACTACACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
** * * * * **
8863 ATAATAAGTGTACATCTCACAGAATTCATCCTATGTGGATGAATAACCGTTTTA
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
* * *
8917 ACACTAAGTGTGCATCTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
* * * ** *
8971 ACACTAAGTATGCATTTCAAGGAATTCATGTTATGTTGATGAATAACCGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
* * * *
9025 ACACTAAGTATGCATTTCACGGAATTTATCCTATGTAGATGAATAACCGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
*
9079 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCC
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
* * *
9133 GCACTAAGTGTGCATTTAATGAAATTCATCCTA--TGGATGAATAACCGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
*
9185 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAATCGTTTC-
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
* * * *
9238 GCACTAAGTGTGCATTTCACGAAATTTATCCTATGTGGATGAATAATCATTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
* *** * ** ** * *
9292 GCACTATGTGTGCAAACCACGAAATTCATAATATGTTTATGAATAACCGTATGG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
* *
9346 GCACTACGGGTGCATT
1 GCACTAAGTGTGCATT
9362 ATAAAGAAAT
Statistics
Matches: 485, Mismatches: 65, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
52 48 0.10
53 50 0.10
54 387 0.80
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (54 bp):
GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
Found at i:12719 original size:20 final size:20
Alignment explanation
Indices: 12696--12746 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
12686 TGAGTATTGG
*
12696 TACTGGATGAACAGTATCGA
1 TACTAGATGAACAGTATCGA
12716 TACTAGATGAACAGTATCGA
1 TACTAGATGAACAGTATCGA
12736 TACTAGATGAA
1 TACTAGATGAA
12747 TTGGGATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (20 bp):
TACTAGATGAACAGTATCGA
Found at i:13461 original size:30 final size:30
Alignment explanation
Indices: 13427--13485 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
13417 TAATAAACCC
*
13427 TTGTATAATGTTCTAGATAAGATAACGAGA
1 TTGTATAATGTTCTAGATAAGAGAACGAGA
13457 TTGTATAATGTTCTAGATAAGAGAACGAG
1 TTGTATAATGTTCTAGATAAGAGAACGAG
13486 CGAGATTGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (30 bp):
TTGTATAATGTTCTAGATAAGAGAACGAGA
Found at i:28757 original size:16 final size:16
Alignment explanation
Indices: 28736--28766 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28726 TTACCAGACC
28736 TGTTTTAAACCTGACA
1 TGTTTTAAACCTGACA
*
28752 TGTTTTTAACCTGAC
1 TGTTTTAAACCTGAC
28767 CTGTAAATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (16 bp):
TGTTTTAAACCTGACA
Found at i:28811 original size:16 final size:16
Alignment explanation
Indices: 28789--28826 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
28779 CGACTTGTTA
28789 ATTACCTGATCTGATAT
1 ATTACCTGA-CTGATAT
*
28806 -TTACCTGACTTATAT
1 ATTACCTGACTGATAT
28821 ATTACC
1 ATTACC
28827 ATGGACGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (16 bp):
ATTACCTGACTGATAT
Found at i:29031 original size:14 final size:14
Alignment explanation
Indices: 29009--29055 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
28999 TGCAAAGGAA
*
29009 AATTAATATAGTTT
1 AATTTATATAGTTT
29023 AATTTATATA----
1 AATTTATATAGTTT
29033 AA-TTATATAGTTT
1 AATTTATATAGTTT
29046 AATTTATATA
1 AATTTATATA
29056 AAGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:29042 original size:23 final size:24
Alignment explanation
Indices: 29008--29057 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
28998 ATGCAAAGGA
29008 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
29032 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
29055 AAA
1 AAA
29058 GAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:29569 original size:30 final size:30
Alignment explanation
Indices: 29532--29600 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
29522 GGCAGTAGGT
29532 AGCAGGCAGCAACAGGCAACAACAGGCAGC
1 AGCAGGCAGCAACAGGCAACAACAGGCAGC
* * *
29562 AGTAGGCAACAACAGGCAGCAACAGGCAGC
1 AGCAGGCAGCAACAGGCAACAACAGGCAGC
*
29592 TGCAGGCAG
1 AGCAGGCAG
29601 AATTTCTGCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.38, C:0.28, G:0.32, T:0.03
Consensus pattern (30 bp):
AGCAGGCAGCAACAGGCAACAACAGGCAGC
Found at i:29600 original size:10 final size:10
Alignment explanation
Indices: 29534--29591 Score: 80
Period size: 10 Copynumber: 5.8 Consensus size: 10
29524 CAGTAGGTAG
29534 CAGGCAGCAA
1 CAGGCAGCAA
*
29544 CAGGCAACAA
1 CAGGCAGCAA
*
29554 CAGGCAGCAG
1 CAGGCAGCAA
* *
29564 TAGGCAACAA
1 CAGGCAGCAA
29574 CAGGCAGCAA
1 CAGGCAGCAA
29584 CAGGCAGC
1 CAGGCAGC
29592 TGCAGGCAGA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 40 1.00
ACGTcount: A:0.40, C:0.29, G:0.29, T:0.02
Consensus pattern (10 bp):
CAGGCAGCAA
Found at i:29600 original size:20 final size:20
Alignment explanation
Indices: 29534--29589 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
29524 CAGTAGGTAG
29534 CAGGCAGCAACAGGCAACAA
1 CAGGCAGCAACAGGCAACAA
**
29554 CAGGCAGCAGTAGGCAACAA
1 CAGGCAGCAACAGGCAACAA
29574 CAGGCAGCAACAGGCA
1 CAGGCAGCAACAGGCA
29590 GCTGCAGGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.41, C:0.29, G:0.29, T:0.02
Consensus pattern (20 bp):
CAGGCAGCAACAGGCAACAA
Found at i:31758 original size:13 final size:13
Alignment explanation
Indices: 31740--31787 Score: 78
Period size: 13 Copynumber: 3.7 Consensus size: 13
31730 TGCGTCATAA
31740 ATTTATGACGCGC
1 ATTTATGACGCGC
*
31753 ATTTATGACACGC
1 ATTTATGACGCGC
*
31766 ATTTATGACGCGT
1 ATTTATGACGCGC
31779 ATTTATGAC
1 ATTTATGAC
31788 ACTCATTGCG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:31769 original size:26 final size:26
Alignment explanation
Indices: 31740--31794 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
31730 TGCGTCATAA
31740 ATTTATGACGCGCATTTATGACACGC
1 ATTTATGACGCGCATTTATGACACGC
* *
31766 ATTTATGACGCGTATTTATGACACTC
1 ATTTATGACGCGCATTTATGACACGC
31792 ATT
1 ATT
31795 GCGCATCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.36
Consensus pattern (26 bp):
ATTTATGACGCGCATTTATGACACGC
Found at i:31871 original size:85 final size:85
Alignment explanation
Indices: 31766--31930 Score: 201
Period size: 85 Copynumber: 1.9 Consensus size: 85
31756 TATGACACGC
* * * *
31766 ATTTATGACGCGTATTTATGACACT-CATTGCGCATCATTGAAGCCCCCGTCA-TA-AATGAAGA
1 ATTTATGACACGCATTTATGAC-CTACATTGCGCATCATTGAAGCACACGTCATTAGAA--AAGA
*
31828 CGACACACATTTGTGTGTAATAA
63 CGACACACATTCGTGTGTAATAA
* ** *
31851 ATTTATGACACGCATTTATGACTTACATTGCGTGTCATTGAAGCACACGTCATTAGAAAAGATGA
1 ATTTATGACACGCATTTATGACCTACATTGCGCATCATTGAAGCACACGTCATTAGAAAAGACGA
31916 CACACATTCGTGTGT
66 CACACATTCGTGTGT
31931 CGTGATTGTA
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
84 1 0.01
85 63 0.93
86 2 0.03
87 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (85 bp):
ATTTATGACACGCATTTATGACCTACATTGCGCATCATTGAAGCACACGTCATTAGAAAAGACGA
CACACATTCGTGTGTAATAA
Found at i:33906 original size:15 final size:15
Alignment explanation
Indices: 33866--33906 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
33856 GAATGAAGAA
*
33866 AAACTTAATTATGAC
1 AAACTTAATTGTGAC
33881 AAACTTAATTGTGAC
1 AAACTTAATTGTGAC
33896 AAACTTAATTG
1 AAACTTAATTG
33907 GAATTCCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (15 bp):
AAACTTAATTGTGAC
Found at i:34840 original size:17 final size:17
Alignment explanation
Indices: 34818--34851 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
34808 CCAACAGAAG
*
34818 TATAGATTAATGTGAAA
1 TATAGATTAATGGGAAA
34835 TATAGATTAATGGGAAA
1 TATAGATTAATGGGAAA
34852 GATAAATGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (17 bp):
TATAGATTAATGGGAAA
Found at i:35203 original size:2 final size:2
Alignment explanation
Indices: 35196--35257 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
35186 AATGAAATCA
35196 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
35238 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
35258 TTCTAATATC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35890 original size:16 final size:15
Alignment explanation
Indices: 35864--35893 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
35854 CATTTTGGAC
35864 AAAGGGAAAAAGGGA
1 AAAGGGAAAAAGGGA
35879 AAAGGTGAAAAAGGG
1 AAAGG-GAAAAAGGG
35894 GAAGCATGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.03
Consensus pattern (15 bp):
AAAGGGAAAAAGGGA
Found at i:36827 original size:120 final size:120
Alignment explanation
Indices: 36614--36871 Score: 453
Period size: 120 Copynumber: 2.1 Consensus size: 120
36604 GTAAAAATTA
*
36614 AACAGTAGCTACAAATTAAACAGTTTATTTAAATCTTAAATAAAGGAAACTAACAACCTTATACA
1 AACAGTAGCTACAAATTAAACAGTTTATTTAAATCCTAAATAAAGGAAACTAACAACCTTATACA
*
36679 ACCAATCCGAATAAACAACCAACAACACAAACAATGACTACAGAGGAAACAAATC
66 ACCAATCCGAATAAACAACCAACAACACAAACAAAGACTACAGAGGAAACAAATC
* *
36734 AACAGTAGCTACAAATTAAACAGTTTATTTAAATCCTAAATAAAGGTAGCTAACAACCTTATACA
1 AACAGTAGCTACAAATTAAACAGTTTATTTAAATCCTAAATAAAGGAAACTAACAACCTTATACA
* *
36799 AGCAATCCGAATGAACAACCAACAACACAAACAAAGACTACAGAGGAAACAAATC
66 ACCAATCCGAATAAACAACCAACAACACAAACAAAGACTACAGAGGAAACAAATC
*
36854 AACAGTAGCTATAAATTA
1 AACAGTAGCTACAAATTA
36872 TAGAATATTT
Statistics
Matches: 131, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 131 1.00
ACGTcount: A:0.51, C:0.20, G:0.10, T:0.19
Consensus pattern (120 bp):
AACAGTAGCTACAAATTAAACAGTTTATTTAAATCCTAAATAAAGGAAACTAACAACCTTATACA
ACCAATCCGAATAAACAACCAACAACACAAACAAAGACTACAGAGGAAACAAATC
Found at i:37145 original size:6 final size:6
Alignment explanation
Indices: 37136--37200 Score: 94
Period size: 6 Copynumber: 10.8 Consensus size: 6
37126 AGGTTTTGTA
* *
37136 TTCGGG TTCGGT TTCGGG TTCGGG TTTGGG TTCGGG TTCGGG TTCGGG
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG
* *
37184 TTCAGG TTCGAG TTCGG
1 TTCGGG TTCGGG TTCGG
37201 ATTCAGATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.03, C:0.15, G:0.45, T:0.37
Consensus pattern (6 bp):
TTCGGG
Found at i:37205 original size:18 final size:18
Alignment explanation
Indices: 37136--37244 Score: 94
Period size: 18 Copynumber: 6.1 Consensus size: 18
37126 AGGTTTTGTA
* *
37136 TTCGGGTTCGGTTTCGGG
1 TTCGGGTTCGGGTTCAGG
* *
37154 TTCGGGTTTGGGTTCGGG
1 TTCGGGTTCGGGTTCAGG
37172 TTCGGGTTCGGGTTCAGG
1 TTCGGGTTCGGGTTCAGG
* * *
37190 TTCGAGTTCGGATTCAGA
1 TTCGGGTTCGGGTTCAGG
** *
37208 TTTAGGTTC-AGTTCAGG
1 TTCGGGTTCGGGTTCAGG
* * *
37225 TTTGGGTTTGGGTTCGGG
1 TTCGGGTTCGGGTTCAGG
37243 TT
1 TT
37245 AGGTTTTAGG
Statistics
Matches: 73, Mismatches: 17, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
17 12 0.16
18 61 0.84
ACGTcount: A:0.07, C:0.13, G:0.40, T:0.39
Consensus pattern (18 bp):
TTCGGGTTCGGGTTCAGG
Found at i:37234 original size:6 final size:6
Alignment explanation
Indices: 37223--37293 Score: 61
Period size: 6 Copynumber: 11.8 Consensus size: 6
37213 GTTCAGTTCA
* * * * * *
37223 GGTTTG GGTTTG GGTTCG GGTTAG GTTTTA GGTTTG GGTTAG GGTTAG
1 GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG
* * *
37271 GGTTAG GGTTTG AGTTTG AGTTT
1 GGTTTG GGTTTG GGTTTG GGTTT
37294 ACATTTGAGT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.10, C:0.01, G:0.44, T:0.45
Consensus pattern (6 bp):
GGTTTG
Found at i:37243 original size:12 final size:12
Alignment explanation
Indices: 37139--37282 Score: 85
Period size: 12 Copynumber: 12.1 Consensus size: 12
37129 TTTTGTATTC
37139 GGGTTC-GGTTT
1 GGGTTCGGGTTT
37150 CGGGTTCGGGTTT
1 -GGGTTCGGGTTT
*
37163 GGGTTCGGGTTC
1 GGGTTCGGGTTT
*
37175 GGGTTCGGGTTC
1 GGGTTCGGGTTT
* * *
37187 AGGTTCGAGTTC
1 GGGTTCGGGTTT
* * *
37199 GGATTCAGATTT
1 GGGTTCGGGTTT
* * *
37211 AGGTTC-AGTTC
1 GGGTTCGGGTTT
* *
37222 AGGTTTGGGTTT
1 GGGTTCGGGTTT
*
37234 GGGTTCGGGTTA
1 GGGTTCGGGTTT
* **
37246 GGTTTTAGGTTT
1 GGGTTCGGGTTT
* *
37258 GGGTTAGGGTTA
1 GGGTTCGGGTTT
*
37270 GGGTTAGGGTTT
1 GGGTTCGGGTTT
37282 G
1 G
37283 AGTTTGAGTT
Statistics
Matches: 101, Mismatches: 29, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
11 7 0.07
12 89 0.88
13 5 0.05
ACGTcount: A:0.09, C:0.09, G:0.42, T:0.40
Consensus pattern (12 bp):
GGGTTCGGGTTT
Found at i:37288 original size:30 final size:30
Alignment explanation
Indices: 37222--37288 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
37212 GGTTCAGTTC
* * *
37222 AGGTTTGGGTTTGGGTTCGGGTTAGGTTTT
1 AGGTTTGGGTTAGGGTTAGGGTTAGGTTTG
37252 AGGTTTGGGTTAGGGTTAGGGTTAGGGTTTG
1 AGGTTTGGGTTAGGGTTAGGGTTA-GGTTTG
37283 A-GTTTG
1 AGGTTTG
37289 AGTTTACATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 27 0.82
31 6 0.18
ACGTcount: A:0.10, C:0.01, G:0.45, T:0.43
Consensus pattern (30 bp):
AGGTTTGGGTTAGGGTTAGGGTTAGGTTTG
Found at i:37723 original size:18 final size:19
Alignment explanation
Indices: 37681--37736 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
37671 GATGAACTTC
37681 TAGAGAGAAGACAGAGAAT
1 TAGAGAGAAGACAGAGAAT
* * *
37700 TTGAGAGAA-ACGGAGAGT
1 TAGAGAGAAGACAGAGAAT
*
37718 TAGAGAGAGAGAGAGAGAA
1 TAGAGAGA-AGACAGAGAA
37737 CAAAATGAGA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
18 14 0.50
19 9 0.32
20 5 0.18
ACGTcount: A:0.48, C:0.04, G:0.38, T:0.11
Consensus pattern (19 bp):
TAGAGAGAAGACAGAGAAT
Found at i:38019 original size:6 final size:6
Alignment explanation
Indices: 38010--38056 Score: 64
Period size: 6 Copynumber: 8.3 Consensus size: 6
38000 ATAGATTATA
*
38010 ATTAAT ATTAAT ATTAAT ATTAAT ATTAA- CTT-AT ATTAAT A-TAAT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT
38055 AT
1 AT
38057 AGTTTATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
4 1 0.03
5 9 0.25
6 26 0.72
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (6 bp):
ATTAAT
Found at i:38025 original size:34 final size:32
Alignment explanation
Indices: 37982--38091 Score: 95
Period size: 34 Copynumber: 3.4 Consensus size: 32
37972 ACTATTTATA
37982 ATTAATATTAAAATAATTATAGATTATAATTAAT
1 ATTAATA-TAAAATAATTATA-ATTATAATTAAT
* *
38016 ATTAATAT-TAAT-ATTA-ATATTA-ACTT-AT
1 ATTAATATAAAATAATTATA-ATTATAATTAAT
* * *
38044 ATTAATATAATATAGTTTATAATTTGTAATTAAT
1 ATTAATATAAAATA-ATTATAA-TTATAATTAAT
38078 ATTAATATAAAATA
1 ATTAATATAAAATA
38092 TAGTCTATAA
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
28 10 0.17
29 5 0.08
30 5 0.08
31 8 0.13
32 6 0.10
33 4 0.07
34 22 0.37
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (32 bp):
ATTAATATAAAATAATTATAATTATAATTAAT
Found at i:38031 original size:18 final size:17
Alignment explanation
Indices: 38004--38056 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
37994 ATAATTATAG
38004 ATTATAATTAATATTAAT
1 ATTAT-ATTAATATTAAT
38022 ATTAATATTAATATTAA-
1 ATT-ATATTAATATTAAT
*
38039 CTTATATTAATA-TAAT
1 ATTATATTAATATTAAT
38055 AT
1 AT
38057 AGTTTATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 3 0.10
16 10 0.32
17 2 0.06
18 14 0.45
19 2 0.06
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTATATTAATATTAAT
Found at i:38110 original size:31 final size:31
Alignment explanation
Indices: 38072--38132 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
38062 ATAATTTGTA
38072 ATTAATATTAATATAAAATATA-GTCTATAAC
1 ATTAATATTAATATAAAATATATGT-TATAAC
*
38103 ATTAATATTAATATAAACTATATGTTATAA
1 ATTAATATTAATATAAAATATATGTTATAA
38133 ACTATATAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (31 bp):
ATTAATATTAATATAAAATATATGTTATAAC
Found at i:38123 original size:24 final size:25
Alignment explanation
Indices: 38078--38124 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
38068 TGTAATTAAT
**
38078 ATTAATATAAAATATAGTCTATAAC
1 ATTAATATAAAATATAAACTATAAC
*
38103 ATTAATAT-TAATATAAACTATA
1 ATTAATATAAAATATAAACTATA
38125 TGTTATAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTAATATAAAATATAAACTATAAC
Found at i:38189 original size:29 final size:30
Alignment explanation
Indices: 37979--38245 Score: 90
Period size: 31 Copynumber: 8.5 Consensus size: 30
37969 TTTACTATTT
* *
37979 ATAATTAATATTAAAATAATTATAGATT---
1 ATAATTAATATTAATATAAGTATAG-TTAAA
*
38007 ATAATTAATATTAATATTA--ATA-TTAATA
1 ATAATTAATATTAATATAAGTATAGTTAA-A
*
38035 TTAACTT-ATATTAATATAA-TATAGTTTATAA
1 ATAA-TTAATATTAATATAAGTATAG-TTA-AA
* * *
38066 TTTGTAATTAATATTAATATAAAATATAGTCTATA
1 ---ATAATTAATATTAATAT-AAGTATAGT-TAAA
* *
38101 A-CATTAATATTAATATAAACTATATGTTATAA
1 ATAATTAATATTAATAT-AAGTATA-GTTA-AA
* * *
38133 ACT-ATATAGTATAGTTTATA-AACTATAGTTAAT
1 A-TAAT-TA--ATA-TTAATATAAGTATAGTTAAA
38166 ATAATTAATATTAATAT-AGTATAGTTTATAA
1 ATAATTAATATTAATATAAGTATAG-TTA-AA
* * *
38197 ACAATATACTATATTAATATAAATTATAGTTAAG
1 ATAAT-TA--ATATTAATAT-AAGTATAGTTAAA
*
38231 ATAATTAACATTAAT
1 ATAATTAATATTAAT
38246 GTAAACTATA
Statistics
Matches: 186, Mismatches: 20, Indels: 63
0.69 0.07 0.23
Matches are distributed among these distances:
24 2 0.01
26 3 0.02
28 31 0.17
29 16 0.09
30 6 0.03
31 39 0.21
32 10 0.05
33 10 0.05
34 34 0.18
35 14 0.08
36 16 0.09
37 5 0.03
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.43
Consensus pattern (30 bp):
ATAATTAATATTAATATAAGTATAGTTAAA
Found at i:38204 original size:21 final size:21
Alignment explanation
Indices: 38127--38209 Score: 69
Period size: 21 Copynumber: 3.9 Consensus size: 21
38117 AAACTATATG
*
38127 TTATAAACTATATAGTATAGT
1 TTATAAACAATATAGTATAGT
* * *
38148 TTATAAACTATAGTTAATATAAT
1 TTATAAACAATA--TAGTATAGT
* **
38171 TAAT-ATTAATATAGTATAGT
1 TTATAAACAATATAGTATAGT
*
38191 TTATAAACAATATACTATA
1 TTATAAACAATATAGTATA
38210 TTAATATAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
20 10 0.21
21 23 0.49
22 4 0.09
23 10 0.21
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (21 bp):
TTATAAACAATATAGTATAGT
Found at i:38296 original size:21 final size:21
Alignment explanation
Indices: 38267--38319 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
38257 AGTACATTAA
*
38267 TATAAACTATAGTTTAT-AAG
1 TATAAACTATAGGTTATAAAG
*
38287 TTATATACTATAGGTTATAAAG
1 -TATAAACTATAGGTTATAAAG
38309 TATAAACTATA
1 TATAAACTATA
38320 TAGTACACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (21 bp):
TATAAACTATAGGTTATAAAG
Found at i:38413 original size:24 final size:20
Alignment explanation
Indices: 38362--38420 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 20
38352 TATAGGTTAC
38362 ATATATAGTTTATATAACAT
1 ATATATAGTTTATATAACAT
*
38382 ATAAATAGATTGTATATATACAT
1 ATATATAG-TT-TATATA-ACAT
*
38405 ATACTATAGGTTATAT
1 ATA-TATAGTTTATAT
38421 GTATATAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
20 7 0.22
21 2 0.06
22 11 0.34
23 8 0.25
24 4 0.12
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.42
Consensus pattern (20 bp):
ATATATAGTTTATATAACAT
Found at i:38450 original size:20 final size:21
Alignment explanation
Indices: 38359--38482 Score: 79
Period size: 20 Copynumber: 6.1 Consensus size: 21
38349 AACTATAGGT
38359 TACATAT--ATAGTTTATATA
1 TACATATACATAGTTTATATA
*
38378 -ACATATAAATAGATTGTATATA
1 TACATATACATAG-TT-TATATA
*
38400 TACATATACTATAG-GT-TATA
1 TACATATAC-ATAGTTTATATA
*
38420 T--GTAT--ATAGTTTATATA
1 TACATATACATAGTTTATATA
*
38437 TAC-TATACATAGTTTATAAA
1 TACATATACATAGTTTATATA
*
38457 TACATGTACTATAAGTTATATATA
1 TACATATAC-AT-AGTT-TATATA
38481 TA
1 TA
38483 TAGTTTATGT
Statistics
Matches: 82, Mismatches: 7, Indels: 27
0.71 0.06 0.23
Matches are distributed among these distances:
15 4 0.05
16 1 0.01
17 5 0.06
18 12 0.15
20 23 0.28
21 7 0.09
22 8 0.10
23 11 0.13
24 11 0.13
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (21 bp):
TACATATACATAGTTTATATA
Found at i:38483 original size:57 final size:59
Alignment explanation
Indices: 38362--38490 Score: 183
Period size: 57 Copynumber: 2.2 Consensus size: 59
38352 TATAGGTTAC
* *
38362 ATATATAGTTTATATAACATATAAATAGATTGTATATATACATATACTATAGGTTATAT
1 ATATATAGTTTATATAACATATAAATAGATTGTATAAATACATATACTATAAGTTATAT
* * *
38421 GTATATAGTTTATATATAC-TATACATAG-TT-TATAAATACATGTACTATAAGTTATAT
1 ATATATAGTTTATATA-ACATATAAATAGATTGTATAAATACATATACTATAAGTTATAT
38478 ATATATAGTTTAT
1 ATATATAGTTTAT
38491 GTGTATACAT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
57 36 0.57
58 2 0.03
59 23 0.37
60 2 0.03
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (59 bp):
ATATATAGTTTATATAACATATAAATAGATTGTATAAATACATATACTATAAGTTATAT
Found at i:38549 original size:13 final size:13
Alignment explanation
Indices: 38531--38555 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38521 TAACTATTGT
38531 TTAGGGTTTAGGG
1 TTAGGGTTTAGGG
38544 TTAGGGTTTAGG
1 TTAGGGTTTAGG
38556 ATTTTTATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.44, T:0.40
Consensus pattern (13 bp):
TTAGGGTTTAGGG
Found at i:38685 original size:20 final size:21
Alignment explanation
Indices: 38645--38689 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
38635 ATATGGTTTA
*
38645 TATATATATATATATATAGTT
1 TATATATATATATACATAGTT
*
38666 TATATATAT-TGTACATAGTT
1 TATATATATATATACATAGTT
38686 TATA
1 TATA
38690 CATACATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (21 bp):
TATATATATATATACATAGTT
Found at i:38720 original size:35 final size:36
Alignment explanation
Indices: 38680--38750 Score: 99
Period size: 37 Copynumber: 2.0 Consensus size: 36
38670 TATATTGTAC
*
38680 ATAGTTT-ATACATACATGTACTATAAGTTACATAT
1 ATAGTTTAATACATACATATACTATAAGTTACATAT
**
38715 ATAGTTTACATGTATACATATACTATAAGTTACATA
1 ATAGTTTA-ATACATACATATACTATAAGTTACATA
38751 AATTAACTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 7 0.23
37 24 0.77
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.39
Consensus pattern (36 bp):
ATAGTTTAATACATACATATACTATAAGTTACATAT
Found at i:38953 original size:2 final size:2
Alignment explanation
Indices: 38946--39083 Score: 53
Period size: 2 Copynumber: 71.5 Consensus size: 2
38936 TGTTTCTTTA
* * *
38946 AT AT AT AT AT AT AT AT -T AT AT TT CT -T AT AT -T AGT -T AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* *
38985 AT AC AT AT AT AT ACT AT AT -T A- AT AT AA AT -T AT A- AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
39024 AA ACT AT AT AT -T TT AT AT A- AT TT AT AC AT AT AT AGT TT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* *
39066 AC AT AGT TT AT AT AT AT A
1 AT AT A-T AT AT AT AT AT A
39084 GTTCACATAA
Statistics
Matches: 100, Mismatches: 21, Indels: 30
0.66 0.14 0.20
Matches are distributed among these distances:
1 10 0.10
2 84 0.84
3 6 0.06
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39080 original size:26 final size:26
Alignment explanation
Indices: 39040--39119 Score: 88
Period size: 28 Copynumber: 2.9 Consensus size: 26
39030 TATATTTTAT
*
39040 ATAATTTATACATATATAGTTTATATAC
1 ATAATTTAT--ATATATAGTTTATAAAC
* *
39068 ATAGTTTATATATATAGTTCACATAAAC
1 ATAATTTATATATATAGTT--TATAAAC
*
39096 ATAATTTATATATATAGCTTATAA
1 ATAATTTATATATATAGTTTATAA
39120 TAATTATATA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
26 14 0.32
28 30 0.68
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (26 bp):
ATAATTTATATATATAGTTTATAAAC
Found at i:39146 original size:18 final size:18
Alignment explanation
Indices: 39102--39160 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
39092 AAACATAATT
* *
39102 TATATATATAGCTTATAA
1 TATAAATATAGTTTATAA
*
39120 TA-ATTATATAGTTTATAA
1 TATA-AATATAGTTTATAA
39138 TATAAATATAGTTTAT-A
1 TATAAATATAGTTTATAA
39155 TATAAA
1 TATAAA
39161 CTTATATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
17 8 0.22
18 28 0.76
19 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (18 bp):
TATAAATATAGTTTATAA
Found at i:39185 original size:13 final size:13
Alignment explanation
Indices: 38949--39185 Score: 71
Period size: 13 Copynumber: 17.4 Consensus size: 13
38939 TTCTTTAATA
38949 TATATATATATAT
1 TATATATATATAT
* *
38962 TATATTTCTTATAT
1 TATATAT-ATATAT
* *
38976 TAGT-TATACATACA
1 TA-TATATATATA-T
38990 TATATATACTATAT
1 TATATATA-TATAT
*
39004 TAATATAAATTATAAT
1 T-ATATATA-TAT-AT
*
39020 ATATAAACTATATAT
1 -TATATA-TATATAT
*
39035 TTTATATA-AT-T
1 TATATATATATAT
*
39046 TATACATATATAGT
1 TATATATATATA-T
*
39060 T-TATATACATAGT
1 TATATATATATA-T
39073 T-TATATATATAGT
1 TATATATATATA-T
* * *
39086 TCACATAAACATAAT
1 T-ATATATATAT-AT
*
39101 T-TATATATATAGC
1 TATATATATATA-T
39114 T-TATA-ATA-AT
1 TATATATATATAT
* *
39124 TATATAGTTTATAA
1 TATATA-TATATAT
*
39138 TATAAATATAGT-T
1 TATATATATA-TAT
39151 TATATATAAACTTATAT
1 TATATAT--A--TATAT
39168 TATATATATATAT
1 TATATATATATAT
39181 TATAT
1 TATAT
39186 TTTTTCAATT
Statistics
Matches: 165, Mismatches: 33, Indels: 52
0.66 0.13 0.21
Matches are distributed among these distances:
10 1 0.01
11 12 0.07
12 8 0.05
13 67 0.41
14 29 0.18
15 25 0.15
16 11 0.07
17 12 0.07
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (13 bp):
TATATATATATAT
Found at i:45274 original size:19 final size:19
Alignment explanation
Indices: 45244--45290 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 19
45234 ATTGGAAATC
45244 GACAAAATCGGTTGAAATTT
1 GACAAAA-CGGTTGAAATTT
*
45264 GACAAAACGGTTTAAATTT
1 GACAAAACGGTTGAAATTT
45283 GACAAAAC
1 GACAAAAC
45291 CGGTAAAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.26
Consensus pattern (19 bp):
GACAAAACGGTTGAAATTT
Found at i:45497 original size:199 final size:193
Alignment explanation
Indices: 45253--45772 Score: 541
Period size: 193 Copynumber: 2.7 Consensus size: 193
45243 CGACAAAATC
* * *
45253 GGTTGAAATTTGACAAAA-CGGTTTAAATTTGACAAAACCGGTAAAGAGCTATCAT-AATTTTTG
1 GGTTGAAATTTGACAAAACCGGTTTCAATTTGACAAAACCGGTAAAGAGCTA-CATGAAGTCTTG
* * *
45316 A-AATTTGTATCGATACTTTTATAAGTATATGTAGCAAAGTATCGGTACTG-AGGAATTTAAAAG
65 ACAA----TATCGATACTTTTATAAGTATATGTACCAAAGTATAGGTACTGTAGGAATTGAAAAG
* * * **
45379 AAATGAA-AAAAGGAAAATGTCTCGAAAATATCGATACCATACACACATGTATCGATACATGATG
126 AAATGAATAAAA-G----CGCCTAGAAAATATCGATACCATACACACATGTATCGATACATGACA
45443 ATATAACA
186 ATATAACA
*
45451 GGTTGAAATTTGACAAAACCGGTTTCAATTTGACAAAACCGGTAAAGAGCTACCTGAAGTCTTGA
1 GGTTGAAATTTGACAAAACCGGTTTCAATTTGACAAAACCGGTAAAGAGCTACATGAAGTCTTGA
* * * *
45516 CAATATCTATACTTTTATAAGTATGTGTACCAAAGTATATGTACTGTAGGAATTGAAAAGAATTG
66 CAATATCGATACTTTTATAAGTATATGTACCAAAGTATAGGTACTGTAGGAATTGAAAAGAAATG
* * * * *
45581 AATAATAGCGCCTATAAAGTATCGATACCTTAGACACATGTATCGATACATGACAATATAACA
131 AATAAAAGCGCCTAGAAAATATCGATACCATACACACATGTATCGATACATGACAATATAACA
* * * ** * * * *
45644 AGTTAAAATCTGACAAAACAAGTTTCAATTTGAAAAAACCAGTAAAGCGCTAC-TGGATA-TGTT
1 GGTTGAAATTTGACAAAACCGGTTTCAATTTGACAAAACCGGTAAAGAGCTACAT-GA-AGTCTT
** * * * * * *
45707 GACGCTATCGATACTTTTAGAAATATATGTACCATAGTATTGGTACTTTAAGAATTGAAAAGAAA
64 GACAATATCGATACTTTTATAAGTATATGTACCAAAGTATAGGTACTGTAGGAATTGAAAAGAAA
45772 T
129 T
45773 AAAAAAATGA
Statistics
Matches: 273, Mismatches: 42, Indels: 19
0.82 0.13 0.06
Matches are distributed among these distances:
192 1 0.00
193 150 0.55
194 1 0.00
196 38 0.14
197 19 0.07
198 23 0.08
199 39 0.14
200 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (193 bp):
GGTTGAAATTTGACAAAACCGGTTTCAATTTGACAAAACCGGTAAAGAGCTACATGAAGTCTTGA
CAATATCGATACTTTTATAAGTATATGTACCAAAGTATAGGTACTGTAGGAATTGAAAAGAAATG
AATAAAAGCGCCTAGAAAATATCGATACCATACACACATGTATCGATACATGACAATATAACA
Found at i:52980 original size:21 final size:21
Alignment explanation
Indices: 52956--53015 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
52946 CGTAAACATA
52956 AAGTATCGATACTTATTATAT
1 AAGTATCGATACTTATTATAT
52977 AAGTATCGATACTTATTATAT
1 AAGTATCGATACTTATTATAT
52998 AAGTATCGATACTT-TTAT
1 AAGTATCGATACTTATTAT
53016 TCCAGTATGC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
20 4 0.10
21 35 0.90
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (21 bp):
AAGTATCGATACTTATTATAT
Found at i:53078 original size:221 final size:221
Alignment explanation
Indices: 52756--53216 Score: 592
Period size: 221 Copynumber: 2.1 Consensus size: 221
52746 GAAAATGTCC
* * ** * * **
52756 AAGTTTCGATACTTTTTATATCCGTATTGATACTTTTATTCTAGTATGGTTCTCAAACAACTTTC
1 AAGTATCGATACTTATTATATAAGTATCGATACTTTTATTCCAGTATGCATCTCAAACAACTTTC
* * * * * *
52821 CCGCTACAAAGTATTGATACCCATATATAAAGTATCGATACTTGGAATTTCAAAACCTATTACTT
66 ACGCAAAAAAATATCGATA-CCATATATAAAGTATCGATACTTAGAATTTCAAAACCTATTACTT
* **
52886 TAAAGTAACATGTAAATTTACAATG-AGAACAATAAAAATCTAT-GGTTTAATGATAATAGGCGT
130 TAAAGTAACAGGTAAATTTACAATGTA-AACAATAAAAATCTATCAATTTAATGATAATAGGCGT
*
52949 AAACATAAAGTATCGATAC-TTATTATAT
194 AAACATAAAGTATCGATACGTT-TAATAT
52977 AAGTATCGATACTTATTATATAAGTATCGATACTTTTATTCCAGTATGCATCTCAAACAA-TTTG
1 AAGTATCGATACTTATTATATAAGTATCGATACTTTTATTCCAGTATGCATCTCAAACAACTTT-
* *
53041 CACGCAAAAAAATATCGATA-CATATATAACAAGTATCGATACTTAGAATTTCGAAACCTTTTAC
65 CACGCAAAAAAATATCGATACCATATAT-A-AAGTATCGATACTTAGAATTTCAAAACCTATTAC
* ***
53105 TTTAAAGTAATAGGTAAATTTACAATGTAAATGGTAAAAATCTATCAATTTAATGATAATAGGCG
128 TTTAAAGTAACAGGTAAATTTACAATGTAAACAATAAAAATCTATCAATTTAATGATAATAGGCG
53170 TAAACATAAAGTATCGATACGTTTAATAT
193 TAAACATAAAGTATCGATACGTTTAATAT
* *
53199 AGGTATCAATAC-TATTAT
1 AAGTATCGATACTTATTAT
53217 TCCAGTATGC
Statistics
Matches: 208, Mismatches: 26, Indels: 12
0.85 0.11 0.05
Matches are distributed among these distances:
219 7 0.03
220 4 0.02
221 142 0.68
222 53 0.25
223 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (221 bp):
AAGTATCGATACTTATTATATAAGTATCGATACTTTTATTCCAGTATGCATCTCAAACAACTTTC
ACGCAAAAAAATATCGATACCATATATAAAGTATCGATACTTAGAATTTCAAAACCTATTACTTT
AAAGTAACAGGTAAATTTACAATGTAAACAATAAAAATCTATCAATTTAATGATAATAGGCGTAA
ACATAAAGTATCGATACGTTTAATAT
Found at i:53321 original size:200 final size:199
Alignment explanation
Indices: 52977--54740 Score: 1442
Period size: 200 Copynumber: 9.1 Consensus size: 199
52967 CTTATTATAT
*
52977 AAGTATCGATACTTATTATATAAGTATCGATACTT-TTATTCCAGTATGCATCTCAAACAATTTG
1 AAGTATCGATACTTATTATATAGGTATCGATA-TTGTTATTCCAGTATGCATCTCAAACAATTTG
** * * * *
53041 CACGCAAAAAAATATCGATACATATATAACAAGTATCGATACTTAGAATTTCGAAACCTTTTACT
65 CACGCAAAAGCATA--GATACACATATAACAAGTATCGATACTTGGACTTTCGAAACCTATTACT
* * **
53106 TTAAAGTAATAGGTAAATTTACAATGTAAATGGTAAAAATCTATCAATTTAATGATAATAGGCGT
128 TTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAATAGGCGT
53171 AAACATA
193 AAACATA
* * * * * *
53178 AAGTATCGATACGTT-TAATATAGGTATCAATACTATTATTCCAGTATGCTTCTTAAACAATTTG
1 AAGTATCGATAC-TTATTATATAGGTATCGATATTGTTATTCCAGTATGCATCTCAAACAATTTG
* * *
53242 CTCGTCAAAAGCATAGATACACATGT-ACAAAGTATTGATACTTGGACTTTCGAAACCTATTACT
65 CACG-CAAAAGCATAGATACACATATAAC-AAGTATCGATACTTGGACTTTCGAAACCTATTACT
*
53306 TTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAAATCTACC-GTTTAATGATAATGGGCG
128 TTAAAGTAATAGGTAAATTTACAATGTAAACGGT-AAAAATCTACCGGTTTAATGATAATAGGCG
*
53370 TAAATATA
192 TAAACATA
* * * *
53378 AAGTATCGATACTTATTATATAGGCATCGCTATTGTTATTCCAGTATGTATCTCAAACAATTTGT
1 AAGTATCGATACTTATTATATAGGTATCGATATTGTTATTCCAGTATGCATCTCAAACAATTTGC
* * * ** * * * *
53443 TCGCAAAAAGTATCGAT--ACAT-GGAC---TTTCGAAACCTAT-TACTTT--AAA-GTA--A--
66 ACGC-AAAAGCATAGATACACATATAACAAGTATCGATA-CT-TGGACTTTCGAAACCTATTACT
* ** * * *
53494 -T-AGGTAA-ATTTACAATGTA-AA--T----GGTAAAAATCTATCGGGTTAATGATAATAGGCG
128 TTAAAGTAATAGGTA-AATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAATAGGCG
*
53549 TAAATATA
192 TAAACATA
* ** * *
53557 AAGTATCGATAATTATTATATAGGTATCGATATTGTTATTCCAGTATAAATATCAAACAATTTAC
1 AAGTATCGATACTTATTATATAGGTATCGATATTGTTATTCCAGTATGCATCTCAAACAATTTGC
* * *
53622 A-GAAAAAGTATCGATACACATATAACAAGTATCGATACTTGGACTTTCGAAACCTATTACTTTA
66 ACGCAAAAGCATAGATACACATATAACAAGTATCGATACTTGGACTTTCGAAACCTATTACTTTA
* * * ** *
53686 AAGTAATAGGTAAATTTACACTATAATA--AT-AAAATCTACCTTTTTAATGATAATGGGCGTAA
131 AAGTAATAGGTAAATTTACAATGTAA-ACGGTAAAAATCTACCGGTTTAATGATAATAGGCGTAA
53748 ACATA
195 ACATA
* * * *
53753 AAGTATTGATACTTATTATATACGTATCGATAATGTTATTCTAGTATGCATCTCAAACAATTTGC
1 AAGTATCGATACTTATTATATAGGTATCGATATTGTTATTCCAGTATGCATCTCAAACAATTTGC
* * * * * *
53818 TCGCAAAAAGTATCA-CTACACATATAACAAGTATCAATACTTGGAATTTCAAAACCTATTACTT
66 ACGC-AAAAGCAT-AGATACACATATAACAAGTATCGATACTTGGACTTTCGAAACCTATTACTT
* * * *
53882 TAAAGTAATAGGTAAATTTACAATGTAAACAGTAAAAATCTACCGGTGTAATGATAATATGCATA
129 TAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAATAGGCGTA
53947 AACATA
194 AACATA
* * *
53953 AAATATGGATACTTATTATATAGGTATCGATATTGTTATAAT-CGGTATGCATCTCAAACAATTT
1 AAGTATCGATACTTATTATATAGGTATCGATATTGTTAT--TCCAGTATGCATCTCAAACAATTT
* * *
54017 GCACGCAAAAAGTC-TCGATACACATATAACAAGTATCAATACTTGGACTTTTGAAACCTATTAC
64 GCACGC-AAAAG-CATAGATACACATATAACAAGTATCGATACTTGGACTTTCGAAACCTATTAC
* * * *
54081 TTTAAAGTAATAGGTAAATTAACAATGTAAACGCTAAAAAT-TACCGATTTAATGATAATAGGCA
127 TTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAATAGGCG
54145 TAAACATA
192 TAAACATA
* * *
54153 AAGTATCAATACATT-TAATATAGGTATCGATACTT-TTATTCCAGTATGCTTCTCAAACAATTT
1 AAGTATCGATAC-TTATTATATAGGTATCGATA-TTGTTATTCCAGTATGCATCTCAAACAATTT
* * * * * * *
54216 GCACGTCAAAAGCATTGTTACATATGT-ACAAAGTATCGATGCTTGGAATTTTC-AAAACTATTA
64 GCACG-CAAAAGCATAGATACACATATAAC-AAGTATCGATACTTGG-ACTTTCGAAACCTATTA
* * * * * *
54279 CTATAAAGTAATAGGTAAATTAACAATGTAAAGGGTAAAAGTTTTACCGGTATAATGATAATAGG
126 CTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAA-ATCTACCGGTTTAATGATAATAGG
* *
54344 TGTATATACCT-
190 CGTA-A-ACATA
* *
54355 -AGTATCGATACTT-TATATATAGGTATCGATATTGTTAGTCCAGTATGCTTCTC-AACAATTTG
1 AAGTATCGATACTTAT-TATATAGGTATCGATATTGTTATTCCAGTATGCATCTCAAACAATTTG
* * * * * * * * *
54417 CGCGCTAAAGGTATCGATAC-C--GT---AA-TTTCGAAAC-TGATTACTTT--AAA-GTA--A-
65 CACGC-AAAAGCATAGATACACATATAACAAGTATCGATACTTG--GACTTTCGAAACCTATTAC
* ** * * * * *
54468 --T-AGGTAA-ATTTACAATGT--AA---A--CGGTAAAAGTCTACCAGTATATTGATAATAGGC
127 TTTAAAGTAATAGGTA-AATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAATAGGC
* **
54522 GTAAATACC
191 GTAAACATA
* * * * *
54531 AAGTATCGATACTGT-CTATATAGGTATCGATACTT-TCATTACAGTATGCTTCTCAAGCAATTT
1 AAGTATCGATACT-TATTATATAGGTATCGATA-TTGTTATTCCAGTATGCATCTCAAACAATTT
* * ** *
54594 GCACGCAAAAGGTATCGATACACATATATA-AAGTATCGATACTTATAATTTCGAAACCTATTAC
64 GCACGCAAAA-GCATAGATACACATATA-ACAAGTATCGATACTTGGACTTTCGAAACCTATTAC
* * * * * * **
54658 TTTAAAGTAATAAGTTAATTTACAATGAAAATGGTAAAAGTATA-AAGTTATAATGATAATAGGC
127 TTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTT-TAATGATAATAGGC
*
54722 GTAAACATC
191 GTAAACATA
54731 AAGTATCGAT
1 AAGTATCGAT
54741 TCGTGGAATT
Statistics
Matches: 1273, Mismatches: 195, Indels: 191
0.77 0.12 0.12
Matches are distributed among these distances:
175 1 0.00
176 1 0.00
177 82 0.06
178 43 0.03
179 89 0.07
180 3 0.00
181 2 0.00
182 7 0.01
183 9 0.01
184 13 0.01
185 22 0.02
186 15 0.01
187 4 0.00
189 2 0.00
190 2 0.00
191 12 0.01
192 12 0.01
193 22 0.02
194 10 0.01
195 9 0.01
196 88 0.07
197 5 0.00
198 90 0.07
199 109 0.09
200 359 0.28
201 247 0.19
202 12 0.01
203 3 0.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (199 bp):
AAGTATCGATACTTATTATATAGGTATCGATATTGTTATTCCAGTATGCATCTCAAACAATTTGC
ACGCAAAAGCATAGATACACATATAACAAGTATCGATACTTGGACTTTCGAAACCTATTACTTTA
AAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAATAGGCGTAAA
CATA
Found at i:53575 original size:179 final size:177
Alignment explanation
Indices: 53270--53639 Score: 573
Period size: 179 Copynumber: 2.1 Consensus size: 177
53260 ACACATGTAC
* *
53270 AAAGTATTGATACTTGGACTTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAA
1 AAAGTATCGATACATGGACTTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAA
* * *
53335 ACGGTAAAAAATCTACCGTTTAATGATAATGGGCGTAAATATAAAGTATCGATACTTATTATATA
66 ACGGTAAAAAATCTACCGGTTAATGATAATAGGCGTAAATATAAAGTATCGATAATTATTATATA
* ** * *
53400 GGCATCGCTATTGTTATTCCAGTATGTATCTCAAACAATTTGTTC-GCAA
131 GGCATCGATATTGTTATTCCAGTATAAATATCAAACAA-TT-TACAG-AA
53449 AAAGTATCGATACATGGACTTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAA
1 AAAGTATCGATACATGGACTTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAA
* *
53514 ATGGT-AAAAATCTATCGGGTTAATGATAATAGGCGTAAATATAAAGTATCGATAATTATTATAT
66 ACGGTAAAAAATCTA-CCGGTTAATGATAATAGGCGTAAATATAAAGTATCGATAATTATTATAT
*
53578 AGGTATCGATATTGTTATTCCAGTATAAATATCAAACAATTTACAGAA
130 AGGCATCGATATTGTTATTCCAGTATAAATATCAAACAATTTACAGAA
53626 AAAGTATCGATACA
1 AAAGTATCGATACA
53640 CATATAACAA
Statistics
Matches: 176, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
177 18 0.10
178 12 0.07
179 146 0.83
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.34
Consensus pattern (177 bp):
AAAGTATCGATACATGGACTTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAA
ACGGTAAAAAATCTACCGGTTAATGATAATAGGCGTAAATATAAAGTATCGATAATTATTATATA
GGCATCGATATTGTTATTCCAGTATAAATATCAAACAATTTACAGAA
Found at i:54050 original size:201 final size:200
Alignment explanation
Indices: 53450--54436 Score: 1148
Period size: 201 Copynumber: 5.0 Consensus size: 200
53440 TGTTCGCAAA
*
53450 AAGTATCGATACATGGACTTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAA
1 AAGTATCGATACTTGGACTTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAA
** * * * *
53515 TGGTAAAAATCTATCGG-GTTAATGATAATAGGCGTAAATATAAAGTATCGATAATTATTATATA
66 CAGTAAAAATCTACCGGTG-TAATGATAATAGGCATAAACATAAAGTATCGATACTTATTATATA
** * *
53579 GGTATCGATATTGTTATTCCAGTATAAATATCAAACAATTTACA-G-AAAAAGTATCGATACACA
130 GGTATCGATATTGTTATTCCAGTATGCATCTCAAACAATTTGCACGCAAAAAGTATCGATACACA
53642 TATAAC
195 TATAAC
* *
53648 AAGTATCGATACTTGGACTTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACACTATAAT
1 AAGTATCGATACTTGGACTTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAA-
** * * * *
53713 A-A-T-AAAATCTACCTTTTTAATGATAATGGGCGTAAACATAAAGTATTGATACTTATTATATA
65 ACAGTAAAAATCTACCGGTGTAATGATAATAGGCATAAACATAAAGTATCGATACTTATTATATA
* * * *
53775 CGTATCGATAATGTTATTCTAGTATGCATCTCAAACAATTTGCTCGCAAAAAGTATC-ACTACAC
130 GGTATCGATATTGTTATTCCAGTATGCATCTCAAACAATTTGCACGCAAAAAGTATCGA-TACAC
53839 ATATAAC
194 ATATAAC
* * *
53846 AAGTATCAATACTTGGAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAA
1 AAGTATCGATACTTGGACTTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAA
* * *
53911 CAGTAAAAATCTACCGGTGTAATGATAATATGCATAAACATAAAATATGGATACTTATTATATAG
66 CAGTAAAAATCTACCGGTGTAATGATAATAGGCATAAACATAAAGTATCGATACTTATTATATAG
* *
53976 GTATCGATATTGTTATAAT-CGGTATGCATCTCAAACAATTTGCACGCAAAAAGTCTCGATACAC
131 GTATCGATATTGTTAT--TCCAGTATGCATCTCAAACAATTTGCACGCAAAAAGTATCGATACAC
54040 ATATAAC
194 ATATAAC
* * *
54047 AAGTATCAATACTTGGACTTTTGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAA
1 AAGTATCGATACTTGGACTTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAA
* * * *
54112 C-GCTAAAAAT-TACCGATTTAATGATAATAGGCATAAACATAAAGTATCAATACATT-TAATAT
66 CAG-TAAAAATCTACCGGTGTAATGATAATAGGCATAAACATAAAGTATCGATAC-TTATTATAT
* * * *
54174 AGGTATCGATACTT-TTATTCCAGTATGCTTCTCAAACAATTTGCACGTC-AAAAGCATTGTTAC
129 AGGTATCGATA-TTGTTATTCCAGTATGCATCTCAAACAATTTGCACG-CAAAAAGTATCGATAC
* *
54237 ATATGT-AC
192 ACATATAAC
* * * * *
54245 AAAGTATCGATGCTTGGAATTTTC-AAAACTATTACTATAAAGTAATAGGTAAATTAACAATGTA
1 -AAGTATCGATACTTGG-ACTTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTA
** * * * * * *
54309 AAGGGTAAAAGTTTTACCGGTATAATGATAATAGGTGTATATACCT--AGTATCGATACTT-TAT
64 AACAGTAAAA-ATCTACCGGTGTAATGATAATA-G-GCATAAACATAAAGTATCGATACTTAT-T
* * * * *
54371 ATATAGGTATCGATATTGTTAGTCCAGTATGCTTCTC-AACAATTTGCGCGCTAAAGGTATCGAT
125 ATATAGGTATCGATATTGTTATTCCAGTATGCATCTCAAACAATTTGCACGCAAAAAGTATCGAT
54435 AC
190 AC
54437 CGTAATTTCG
Statistics
Matches: 684, Mismatches: 79, Indels: 50
0.84 0.10 0.06
Matches are distributed among these distances:
196 86 0.13
197 4 0.01
198 146 0.21
199 101 0.15
200 158 0.23
201 179 0.26
202 3 0.00
203 7 0.01
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (200 bp):
AAGTATCGATACTTGGACTTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAA
CAGTAAAAATCTACCGGTGTAATGATAATAGGCATAAACATAAAGTATCGATACTTATTATATAG
GTATCGATATTGTTATTCCAGTATGCATCTCAAACAATTTGCACGCAAAAAGTATCGATACACAT
ATAAC
Found at i:54579 original size:177 final size:178
Alignment explanation
Indices: 54265--54614 Score: 508
Period size: 177 Copynumber: 2.0 Consensus size: 178
54255 TGCTTGGAAT
* * *
54265 TTTCAAAACTATTACTATAAAGTAATAGGTAAATTAACAATGTAAAGGGTAAAAGTTTTACCGGT
1 TTTCAAAACTATTACTATAAAGTAATAGGTAAATTAACAATGTAAACGGTAAAAGTTCTACCAGT
* * * * * *
54330 ATAATGATAATAGGTGTATATACCTAGTATCGATACTTTATATATAGGTATCGATATTGTTAGTC
66 ATAATGATAATAGGCGTAAATACCAAGTATCGATACTGTATATATAGGTATCGATATTGTCAGTA
* *
54395 CAGTATGCTTCTCAA-CAATTTGCGCGCTAAAGGTATCGATACCGTAA
131 CAGTATGCTTCTCAAGCAATTTGCACGCAAAAGGTATCGATACCGTAA
* * *
54442 TTTCGAAACTGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAG-TCTACCAG
1 TTTCAAAACT-ATTACTATAAAGTAATAGGTAAATTAACAATGTAAACGGTAAAAGTTCTACCAG
* * *
54506 TATATTGATAATAGGCGTAAATACCAAGTATCGATACTGTCTATATAGGTATCGATACTT-TCAT
65 TATAATGATAATAGGCGTAAATACCAAGTATCGATACTGTATATATAGGTATCGATA-TTGTCAG
54570 TACAGTATGCTTCTCAAGCAATTTGCACGCAAAAGGTATCGATAC
129 TACAGTATGCTTCTCAAGCAATTTGCACGCAAAAGGTATCGATAC
54615 ACATATATAA
Statistics
Matches: 153, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
177 84 0.55
178 69 0.45
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (178 bp):
TTTCAAAACTATTACTATAAAGTAATAGGTAAATTAACAATGTAAACGGTAAAAGTTCTACCAGT
ATAATGATAATAGGCGTAAATACCAAGTATCGATACTGTATATATAGGTATCGATATTGTCAGTA
CAGTATGCTTCTCAAGCAATTTGCACGCAAAAGGTATCGATACCGTAA
Found at i:54621 original size:976 final size:986
Alignment explanation
Indices: 52763--54681 Score: 2549
Period size: 976 Copynumber: 1.9 Consensus size: 986
52753 TCCAAGTTTC
* * * * * ** *
52763 GATACTTTTTATATCCGTATTGATACTTTTATTCTAGTATGGTTCTCAAACAACTTTCCCGCTAC
1 GATACTTATTATATACGTATCGATAATGTTATTCTAGTATGCATCTCAAACAACTTTCCCGCTAA
* * *
52828 AAAGTATTGATACCCATATATAAAGTATCGATACTTGGAATTTCAAAACCTATTACTTTAAAGTA
66 AAAGTATTCATACACATATATAAAGTATCAATACTTGGAATTTCAAAACCTATTACTTTAAAGTA
* * * *
52893 ACATGTAAATTTACAATGAGAACAATAAAAATCTATGGTTTAATGATAATAGGCGTAAACATAAA
131 ACAGGTAAATTTACAATGAGAACAATAAAAATCTACGGTGTAATGATAATAGGCATAAACATAAA
*
52958 GTATCGATACTTATTATATAAGTATCGATACTTATTATATAAGTATCGATACTTTTATTCCAGTA
196 ATATCGATACTTATTATATAAGTATCG-----TATTATAT-AGTATC-ATA----TATTCCAGTA
* *
53023 TGCATCTCAAACAATTTGCACGCAAAAAAATATCGATACATATATAACAAGTATCGATACTTAGA
250 TGCATCTCAAACAATTTGCACGCAAAAAAATATCGATACACATATAACAAGTATCAATACTTAGA
* * * * *
53088 ATTTCGAAACCTTTTACTTTAAAGTAATAGGTAAATTTACAATGTAAATGGTAAAAATCTATCAA
315 ATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAACGCTAAAAATCTACCAA
* * *
53153 TTTAATGATAATAGGCGTAAACATAAAGTATCGATACGTTTAATATAGGTATCAATACTATTATT
380 TTTAATGATAATAGGCATAAACATAAAGTATCAATACATTTAATATAGGTATCAATACTATTATT
* * *
53218 CCAGTATGCTTCTTAAACAATTTGCTCGTCAAAAGCATAGATACACATGTACAAAGTATTGATAC
445 CCAGTATGCTTCTCAAACAATTTGCACGTCAAAAGCATAGATACACATGTACAAAGTATCGATAC
* * *
53283 TTGGACTTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAAATC
510 TTGGACTTTCGAAAACTATTACTATAAAGTAATAGGTAAATTAACAATGTAAACGGTAAAAAATC
* * * *
53348 TACCGTTTAATGATAATGGGCGTAAATATAAAGTATCGATACTTATTATATAGGCATCGCTATTG
575 TACCGTATAATGATAATAGGCGTAAATACAAAGTATCGATACTTATTATATAGGCATCGATATTG
* ** * *
53413 TTATTCCAGTATGTATCTCAAACAATTTGTTCGCAAAAAGTATCGATACATGGACTTTCGAAACC
640 TTAGTCCAGTATGTATCTCAAACAATTTGCGCGCAAAAAGTATCGATACACGGAATTTCGAAACC
* **
53478 TATTACTTTAAAGTAATAGGTAAATTTACAATGTAAATGGTAAAAATCTATCGGGTTAATGATAA
705 TATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTATCCAGTTAATGATAA
* * * *
53543 TAGGCGTAAATATAAAGTATCGATAATTATTATATAGGTATCGATATTGTTATTCCAGTATAAAT
770 TAGGCGTAAATACAAAGTATCGATAATTACTATATAGGTATCGATATTGTCATTACAGTATAAAT
* *
53608 ATCAAACAATTTACAGAAAAAGTATCGATACACATATA-ACAAGTATCGATACTTGGACTTTCGA
835 ATCAAACAATTTACAGAAAAAGTATCGATACACATATATA-AAGTATCGATACTTAGAATTTCGA
*
53672 AACCTATTACTTTAAAGTAATAGGTAAATTTACACTATAATAATAAAATCTACCTTTTTAATGAT
899 AACCTATTACTTTAAAGTAATAAGTAAATTTACACTATAATAATAAAATCTACCTTTTTAATGAT
53737 AATGGGCGTAAACATAAAGTATT
964 AATGGGCGTAAACATAAAGTATT
*
53760 GATACTTATTATATACGTATCGATAATGTTATTCTAGTATGCATCTCAAACAA-TTTGCTCGC-A
1 GATACTTATTATATACGTATCGATAATGTTATTCTAGTATGCATCTCAAACAACTTT-CCCGCTA
53823 AAAAGTA-TCACTACACATATA-ACAAGTATCAATACTTGGAATTTCAAAACCTATTACTTTAAA
65 AAAAGTATTCA-TACACATATATA-AAGTATCAATACTTGGAATTTCAAAACCTATTACTTTAAA
* * *
53886 GTAATAGGTAAATTTACAATGTA-AACAGTAAAAATCTACCGGTGTAATGATAATATGCATAAAC
128 GTAACAGGTAAATTTACAATG-AGAACAATAAAAATCTA-CGGTGTAATGATAATAGGCATAAAC
* * *
53950 ATAAAATATGGATACTTATTATATAGGTATCG-A-TAT-T-GT-T-ATA-A-T-CGGTATGCATC
191 ATAAAATATCGATACTTATTATATAAGTATCGTATTATATAGTATCATATATTCCAGTATGCATC
* * * * *
54006 TCAAACAATTTGCACGC-AAAAAGTCTCGATACACATATAACAAGTATCAATACTTGGACTTTTG
256 TCAAACAATTTGCACGCAAAAAAATATCGATACACATATAACAAGTATCAATACTTAGAATTTCG
*
54070 AAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAACGCTAAAAAT-TACCGATTTAAT
321 AAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAACGCTAAAAATCTACCAATTTAAT
* *
54134 GATAATAGGCATAAACATAAAGTATCAATACATTTAATATAGGTATCGATACTTTTATTCCAGTA
386 GATAATAGGCATAAACATAAAGTATCAATACATTTAATATAGGTATCAATACTATTATTCCAGTA
* * * *
54199 TGCTTCTCAAACAATTTGCACGTCAAAAGCATTGTTACATATGTACAAAGTATCGATGCTTGGAA
451 TGCTTCTCAAACAATTTGCACGTCAAAAGCATAGATACACATGTACAAAGTATCGATACTTGG-A
* * ** *
54264 TTTTC-AAAACTATTACTATAAAGTAATAGGTAAATTAACAATGTAAAGGGTAAAAGTTTTACCG
515 CTTTCGAAAACTATTACTATAAAGTAATAGGTAAATTAACAATGTAAACGGTAAAAAATCTACC-
* * ** *
54328 GTATAATGATAATAGGTGTATATACCTAGTATCGATACTT-TATATATAGGTATCGATATTGTTA
579 GTATAATGATAATAGGCGTAAATACAAAGTATCGATACTTAT-TATATAGGCATCGATATTGTTA
* * *
54392 GTCCAGTATGCT-TCTC-AACAATTTGCGCGCTAAAGGTATCGATAC-CGTAATTTCGAAA-CTG
643 GTCCAGTATG-TATCTCAAACAATTTGCGCGCAAAAAGTATCGATACACGGAATTTCGAAACCT-
* *
54453 ATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAGTCTA-CCAGTATATTGATAA
706 ATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTATCCAGT-TAATGATAA
* * **
54517 TAGGCGTAAATACCAAGTATCGATACTGT-CTATATAGGTATCGATACTT-TCATTACAGTATGC
770 TAGGCGTAAATACAAAGTATCGATAAT-TACTATATAGGTATCGATA-TTGTCATTACAGTATAA
* * * * * *
54580 TTCTCAAGCAATTTGCACGCAAAAGGTATCGATACACATATATAAAGTATCGATACTTATAATTT
833 ATATCAAACAATTTACA-G-AAAAAGTATCGATACACATATATAAAGTATCGATACTTAGAATTT
*
54645 CGAAACCTATTACTTTAAAGTAATAAGTTAATTTACA
896 CGAAACCTATTACTTTAAAGTAATAAGTAAATTTACA
54682 ATGAAAATGG
Statistics
Matches: 810, Mismatches: 96, Indels: 53
0.84 0.10 0.06
Matches are distributed among these distances:
973 5 0.01
974 128 0.16
975 207 0.26
976 233 0.29
977 29 0.04
978 1 0.00
979 1 0.00
984 3 0.00
986 1 0.00
987 2 0.00
989 1 0.00
990 3 0.00
991 1 0.00
995 3 0.00
996 91 0.11
997 101 0.12
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (986 bp):
GATACTTATTATATACGTATCGATAATGTTATTCTAGTATGCATCTCAAACAACTTTCCCGCTAA
AAAGTATTCATACACATATATAAAGTATCAATACTTGGAATTTCAAAACCTATTACTTTAAAGTA
ACAGGTAAATTTACAATGAGAACAATAAAAATCTACGGTGTAATGATAATAGGCATAAACATAAA
ATATCGATACTTATTATATAAGTATCGTATTATATAGTATCATATATTCCAGTATGCATCTCAAA
CAATTTGCACGCAAAAAAATATCGATACACATATAACAAGTATCAATACTTAGAATTTCGAAACC
TATTACTTTAAAGTAATAGGTAAATTAACAATGTAAACGCTAAAAATCTACCAATTTAATGATAA
TAGGCATAAACATAAAGTATCAATACATTTAATATAGGTATCAATACTATTATTCCAGTATGCTT
CTCAAACAATTTGCACGTCAAAAGCATAGATACACATGTACAAAGTATCGATACTTGGACTTTCG
AAAACTATTACTATAAAGTAATAGGTAAATTAACAATGTAAACGGTAAAAAATCTACCGTATAAT
GATAATAGGCGTAAATACAAAGTATCGATACTTATTATATAGGCATCGATATTGTTAGTCCAGTA
TGTATCTCAAACAATTTGCGCGCAAAAAGTATCGATACACGGAATTTCGAAACCTATTACTTTAA
AGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTATCCAGTTAATGATAATAGGCGTAAAT
ACAAAGTATCGATAATTACTATATAGGTATCGATATTGTCATTACAGTATAAATATCAAACAATT
TACAGAAAAAGTATCGATACACATATATAAAGTATCGATACTTAGAATTTCGAAACCTATTACTT
TAAAGTAATAAGTAAATTTACACTATAATAATAAAATCTACCTTTTTAATGATAATGGGCGTAAA
CATAAAGTATT
Found at i:58030 original size:30 final size:31
Alignment explanation
Indices: 57994--58054 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
57984 ATCTTTCTGG
*
57994 TACTAACTCGTTT-TTCTCTTTTGTTTGTGT
1 TACTAACTCATTTCTTCTCTTTTGTTTGTGT
* *
58024 TACTAACTTATTTCTTTTCTTTTGTTTGTGT
1 TACTAACTCATTTCTTCTCTTTTGTTTGTGT
58055 CATTTTTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.11, C:0.15, G:0.11, T:0.62
Consensus pattern (31 bp):
TACTAACTCATTTCTTCTCTTTTGTTTGTGT
Found at i:60901 original size:32 final size:32
Alignment explanation
Indices: 60860--60929 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
60850 TGAAGCAAGA
* *
60860 AACATCGAATGTTGGGGCATCTTTGGAGATTC
1 AACATCGAATATTGGAGCATCTTTGGAGATTC
*
60892 AACATCGAATATTGGAGCATCTTTGGGGATTC
1 AACATCGAATATTGGAGCATCTTTGGAGATTC
60924 AACATC
1 AACATC
60930 CTGATGCGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (32 bp):
AACATCGAATATTGGAGCATCTTTGGAGATTC
Found at i:61165 original size:64 final size:60
Alignment explanation
Indices: 60998--61165 Score: 223
Period size: 60 Copynumber: 2.7 Consensus size: 60
60988 TTATCAGTAT
60998 TCTTTGAGTTGTTTCTCTAGAAACAAATTTTGTCTCTTGAGACAATTTCTTTTAAAAAAA
1 TCTTTGAGTTGTTTCTCTAGAAACAAATTTTGTCTCTTGAGACAATTTCTTTTAAAAAAA
* * * *
61058 -ATATGAGTCTGTTTCTCTGGAAACAAATTTTGTCTCTTCAGACAATTTCTTTTGAGAAAAAA
1 TCTTTGAGT-TGTTTCTCTAGAAACAAATTTTGTCTCTTGAGACAATTTCTTTT-A-AAAAAA
*
61120 TCTTTGAGATTGTTTC-CTTTGAAACAAAATTTTGTCTCTTGAGACA
1 TCTTTGAG-TTGTTTCTC-TAGAAAC-AAATTTTGTCTCTTGAGACA
61166 GCTTTTCTTG
Statistics
Matches: 93, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
59 6 0.06
60 42 0.45
61 1 0.01
62 7 0.08
63 17 0.18
64 20 0.22
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (60 bp):
TCTTTGAGTTGTTTCTCTAGAAACAAATTTTGTCTCTTGAGACAATTTCTTTTAAAAAAA
Found at i:61446 original size:131 final size:131
Alignment explanation
Indices: 61213--61493 Score: 352
Period size: 131 Copynumber: 2.1 Consensus size: 131
61203 TGAAACCATA
* * * * *
61213 ATCCCTAAAGATGGCCAGTCATCCTCATCGCGTAGGAACTGTGTCATCCCCGACCAGACCTCCTC
1 ATCCCTAAAGATGGCCAGTCATCCTCATCACATAAGAACCGTCTCATCCCCGACCAGACCTCCTC
* *
61278 ATAATGTAGGAGCCGTGTCATCCCTAGATAATCAGCCGTCCTCATCACGTAGGAA-TCGTGCTAT
66 ATAACGTAGGAGCCGTGTCATCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACT-GTGCTAT
61342 -C
130 AC
*** * *
61343 ATCCCTAAAGATGGTTTGTCATCCTCATCACATAAGAACCGTCTTATTCCCCGACCATACCTCCT
1 ATCCCTAAAGATGGCCAGTCATCCTCATCACATAAGAACCGTCTCA-TCCCCGACCAGACCTCCT
* ** *
61408 CATCACGTAGGAGCCGTGTCA-CCCTTAGATAACCAGCCGTCCTCATCGGGTAGGAACTGTGTTA
65 CATAACGTAGGAGCCGTGTCATCCC-TAGATAACCAGCCGTCCTCATCACGTAGGAACTGTGCTA
61472 TCAC
129 T-AC
61476 ATTCCCTAAAGATGGCCA
1 A-TCCCTAAAGATGGCCA
61494 AAACTCTTCA
Statistics
Matches: 126, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
130 40 0.32
131 70 0.56
132 1 0.01
133 2 0.02
134 13 0.10
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (131 bp):
ATCCCTAAAGATGGCCAGTCATCCTCATCACATAAGAACCGTCTCATCCCCGACCAGACCTCCTC
ATAACGTAGGAGCCGTGTCATCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACTGTGCTATA
C
Found at i:61775 original size:3 final size:3
Alignment explanation
Indices: 61758--61791 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
61748 TCTACAAAAA
*
61758 TAT TAT TAA TA- TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
61792 ATACATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Done.