Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008216.1 Hibiscus syriacus cultivar Beakdansim tig00110844_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: 118781
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:57 original size:40 final size:38
Alignment explanation
Indices: 2--129 Score: 180
Period size: 35 Copynumber: 3.5 Consensus size: 38
1 A
2 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTG-AGAA-GAAGAAG
42 AAGTTCATAATGAGAAGAACTCATCT--GAAGAA-AAG
1 AAGTTCATAATGAGAAGAACTCATCTGAGAAGAAGAAG
*
77 AATTTCATAATGAGAAGAACTCATCTGA-AAGAAG-A-
1 AAGTTCATAATGAGAAGAACTCATCTGAGAAGAAGAAG
112 AA-TTCATAATGAGAAGAA
1 AAGTTCATAATGAGAAGAA
130 TTTGTTCAAC
Statistics
Matches: 84, Mismatches: 1, Indels: 12
0.87 0.01 0.12
Matches are distributed among these distances:
34 16 0.19
35 30 0.36
36 9 0.11
37 3 0.04
40 26 0.31
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.20
Consensus pattern (38 bp):
AAGTTCATAATGAGAAGAACTCATCTGAGAAGAAGAAG
Found at i:59 original size:17 final size:16
Alignment explanation
Indices: 37--131 Score: 68
Period size: 17 Copynumber: 5.6 Consensus size: 16
27 TGAAGAAGGA
37 AGAAGAAGTTCATAATG
1 AGAAGAA-TTCATAATG
*
54 AGAAGAACTCATCTGAA-G
1 AGAAGAATTCA--T-AATG
*
72 AAAAGAATTTCATAATG
1 AGAAGAA-TTCATAATG
* *
89 AGAAGAACTCAT-CTG
1 AGAAGAATTCATAATG
104 AAAGAAGAAATTCATAATG
1 --AGAAG-AATTCATAATG
123 AGAAGAATT
1 AGAAGAATT
132 TGTTCAACCT
Statistics
Matches: 61, Mismatches: 8, Indels: 19
0.69 0.09 0.22
Matches are distributed among these distances:
15 2 0.03
16 13 0.21
17 25 0.41
18 14 0.23
19 7 0.11
ACGTcount: A:0.49, C:0.09, G:0.19, T:0.22
Consensus pattern (16 bp):
AGAAGAATTCATAATG
Found at i:84 original size:35 final size:35
Alignment explanation
Indices: 5--129 Score: 180
Period size: 40 Copynumber: 3.5 Consensus size: 35
1 AAAG
5 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
1 TTCATAATGAGAAGAACTCATCTGAAGAA--AAG-A-AA
*
44 GTTCATAATGAGAAGAACTCATCTGAAGAAAAGAAT
1 -TTCATAATGAGAAGAACTCATCTGAAGAAAAGAAA
*
80 TTCATAATGAGAAGAACTCATCTGAA-AGAAGAAA
1 TTCATAATGAGAAGAACTCATCTGAAGAAAAGAAA
114 TTCATAATGAGAAGAA
1 TTCATAATGAGAAGAA
130 TTTGTTCAAC
Statistics
Matches: 82, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
34 22 0.27
35 26 0.32
36 1 0.01
37 1 0.01
38 3 0.04
40 29 0.35
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.21
Consensus pattern (35 bp):
TTCATAATGAGAAGAACTCATCTGAAGAAAAGAAA
Found at i:497 original size:16 final size:16
Alignment explanation
Indices: 476--530 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 16
466 CATTTTAATG
476 TTATTATATATAATAA
1 TTATTATATATAATAA
492 TTATTATTAATTATAATAA
1 TTATTA-T-A-TATAATAA
511 TTATTAT-TATTAAT-A
1 TTATTATATA-TAATAA
526 TTATT
1 TTATT
531 TAATATTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
15 8 0.23
16 10 0.29
17 1 0.03
18 2 0.06
19 14 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATTATATATAATAA
Found at i:500 original size:19 final size:20
Alignment explanation
Indices: 476--520 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
466 CATTTTAATG
476 TTATTATA-TATAATAATTA
1 TTATTATATTATAATAATTA
495 TTATTA-ATTATAATAATTA
1 TTATTATATTATAATAATTA
514 TTATTAT
1 TTATTAT
521 TAATATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 1 0.04
19 23 0.96
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTATTATATTATAATAATTA
Found at i:537 original size:16 final size:15
Alignment explanation
Indices: 470--538 Score: 50
Period size: 16 Copynumber: 4.2 Consensus size: 15
460 TTTTTTCATT
*
470 TTAATGTTATTATATA
1 TTAATATTATTA-ATA
486 TAATAATTATTATTAAT-
1 T--TAA-TATTATTAATA
*
503 TATAATAATTATTATTA
1 T-TAAT-ATTATTAATA
520 TTAATATTATTTAATA
1 TTAATATTA-TTAATA
536 TTA
1 TTA
539 CAAAACCCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
15 5 0.11
16 25 0.57
17 2 0.05
18 5 0.11
19 7 0.16
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (15 bp):
TTAATATTATTAATA
Found at i:1000 original size:18 final size:19
Alignment explanation
Indices: 959--994 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
949 GGAGAGACAG
959 AAACAGAGCAAAAACAACA
1 AAACAGAGCAAAAACAACA
*
978 AAACAGAG-AACAACAAC
1 AAACAGAGCAAAAACAAC
995 CCAACAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.67, C:0.22, G:0.11, T:0.00
Consensus pattern (19 bp):
AAACAGAGCAAAAACAACA
Found at i:12947 original size:29 final size:28
Alignment explanation
Indices: 12909--12966 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
12899 TTAGATGTTA
* *
12909 TATCATTTATACCATTAAATTTTTAATTT
1 TATCAATTATACCACTAAATTTTT-ATTT
* *
12938 TATCAATTATAGCACTGAATTTTTATTT
1 TATCAATTATACCACTAAATTTTTATTT
12966 T
1 T
12967 CGTTTTAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.53
Consensus pattern (28 bp):
TATCAATTATACCACTAAATTTTTATTT
Found at i:17596 original size:36 final size:36
Alignment explanation
Indices: 17556--17686 Score: 190
Period size: 36 Copynumber: 3.6 Consensus size: 36
17546 ATCCATTATT
*
17556 AGCTTTGATACATTTGTGTATCAATGTTATCATATC
1 AGCTTTGATACATTCGTGTATCAATGTTATCATATC
* * * *
17592 AGCTTTGGTATATTCATATATCAATGTTATCATATC
1 AGCTTTGATACATTCGTGTATCAATGTTATCATATC
17628 AGCTTTGATACATTCGTGTATCAATGTTATCATATC
1 AGCTTTGATACATTCGTGTATCAATGTTATCATATC
* * *
17664 AGCTTTGGTATATTTGTGTATCA
1 AGCTTTGATACATTCGTGTATCA
17687 GTGTCCAGCA
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 83 1.00
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (36 bp):
AGCTTTGATACATTCGTGTATCAATGTTATCATATC
Found at i:18314 original size:14 final size:14
Alignment explanation
Indices: 18295--18327 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
18285 TAGAACTATT
18295 TTAGTTTA-TTTTA
1 TTAGTTTAGTTTTA
18308 CTTAGTTTAGTTTTA
1 -TTAGTTTAGTTTTA
18323 TTAGT
1 TTAGT
18328 ATCTATGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.21, C:0.03, G:0.12, T:0.64
Consensus pattern (14 bp):
TTAGTTTAGTTTTA
Found at i:25884 original size:18 final size:18
Alignment explanation
Indices: 25861--25965 Score: 174
Period size: 18 Copynumber: 5.8 Consensus size: 18
25851 ATTCTTAAGG
*
25861 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCGGGACAT
*
25879 AGTGGTCCTTCGGGACAA
1 AGTGGTCCTTCGGGACAT
25897 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
25915 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
25933 AGTGGTCCTTCGGGATAA
1 AGTGGTCCTTCGGGACAT
25951 AGTGGTCCTTCGGGA
1 AGTGGTCCTTCGGGA
25966 TAAGTGTTAA
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 82 1.00
ACGTcount: A:0.19, C:0.21, G:0.33, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:25920 original size:54 final size:54
Alignment explanation
Indices: 25861--25965 Score: 192
Period size: 54 Copynumber: 1.9 Consensus size: 54
25851 ATTCTTAAGG
25861 AGTGGTCCTTCAGGACATAGTGGTCCTTCGGGACAAAGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCAGGACATAGTGGTCCTTCGGGACAAAGTGGTCCTTCGGGACAT
* *
25915 AGTGGTCCTTCGGGACATAGTGGTCCTTCGGGATAAAGTGGTCCTTCGGGA
1 AGTGGTCCTTCAGGACATAGTGGTCCTTCGGGACAAAGTGGTCCTTCGGGA
25966 TAAGTGTTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.19, C:0.21, G:0.33, T:0.27
Consensus pattern (54 bp):
AGTGGTCCTTCAGGACATAGTGGTCCTTCGGGACAAAGTGGTCCTTCGGGACAT
Found at i:27858 original size:18 final size:18
Alignment explanation
Indices: 27835--27878 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
27825 TATGACTCAA
27835 AGAGGAAGGGGTAGAGGT
1 AGAGGAAGGGGTAGAGGT
27853 AGAGGAAGGGGTAGAGGT
1 AGAGGAAGGGGTAGAGGT
27871 AGAGGAAG
1 AGAGGAAG
27879 AAGTCAGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.55, T:0.09
Consensus pattern (18 bp):
AGAGGAAGGGGTAGAGGT
Found at i:30669 original size:19 final size:22
Alignment explanation
Indices: 30639--30696 Score: 77
Period size: 19 Copynumber: 2.8 Consensus size: 22
30629 AGAATGTTCG
*
30639 AATGGTACCGATACCCCC-TA-
1 AATGGTATCGATACCCCCATAC
*
30659 TA-GGTATCGATACCCCCATAC
1 AATGGTATCGATACCCCCATAC
30680 AATGGTATCGATACCCC
1 AATGGTATCGATACCCC
30697 TCAGATGGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 14 0.44
20 3 0.09
21 1 0.03
22 14 0.44
ACGTcount: A:0.29, C:0.33, G:0.16, T:0.22
Consensus pattern (22 bp):
AATGGTATCGATACCCCCATAC
Found at i:38495 original size:25 final size:25
Alignment explanation
Indices: 38467--38526 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
38457 TTTGAATGCT
*
38467 TTTGGATTTTTTTATTTTGAGTTTG
1 TTTGGATTTTTTTACTTTGAGTTTG
*
38492 TTTGGATTGTTTTACTTTGAGTTTG
1 TTTGGATTTTTTTACTTTGAGTTTG
38517 TTTGGATTTT
1 TTTGGATTTT
38527 GGATGTTCGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.12, C:0.02, G:0.22, T:0.65
Consensus pattern (25 bp):
TTTGGATTTTTTTACTTTGAGTTTG
Found at i:38858 original size:26 final size:26
Alignment explanation
Indices: 38825--38892 Score: 118
Period size: 28 Copynumber: 2.5 Consensus size: 26
38815 TAACAAAAAG
38825 GGGGAGAAGTGTTAAAGTGTTTTAAA
1 GGGGAGAAGTGTTAAAGTGTTTTAAA
38851 GGGGAGAAAAGTGTTAAAGTGTTTTAAA
1 GGGGAG--AAGTGTTAAAGTGTTTTAAA
38879 GGGGAGAAGTGTTA
1 GGGGAGAAGTGTTA
38893 GAGTAAGGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
26 14 0.35
28 26 0.65
ACGTcount: A:0.35, C:0.00, G:0.37, T:0.28
Consensus pattern (26 bp):
GGGGAGAAGTGTTAAAGTGTTTTAAA
Found at i:39379 original size:20 final size:19
Alignment explanation
Indices: 39313--39386 Score: 69
Period size: 22 Copynumber: 3.7 Consensus size: 19
39303 GAATGCTCGA
*
39313 ATGGTACCGATACCCCC-T
1 ATGGTACCGATACCCCCAG
*
39331 ATAGGTATCGATACCCCCATG
1 AT-GGTACCGATACCCCCA-G
*
39352 CAATGGTATCGATACCCCTCAG
1 --ATGGTACCGATACCCC-CAG
39374 ATGGTACCGATAC
1 ATGGTACCGATAC
39387 TCTAAGGCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
18 2 0.04
19 14 0.30
20 12 0.26
22 15 0.32
23 4 0.09
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (19 bp):
ATGGTACCGATACCCCCAG
Found at i:39460 original size:21 final size:21
Alignment explanation
Indices: 39430--39484 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
39420 TTACACTACA
*
39430 GGTACCGATACCCTATAAAGG
1 GGTACTGATACCCTATAAAGG
39451 GGTACTGATACCCTATAAAGG
1 GGTACTGATACCCTATAAAGG
39472 GGTACTGATACCC
1 GGTACTGATACCC
39485 CCCCACGCTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.22
Consensus pattern (21 bp):
GGTACTGATACCCTATAAAGG
Found at i:41916 original size:35 final size:35
Alignment explanation
Indices: 41877--41947 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
41867 ATGCGGTTCT
* *
41877 TCGGGACACATATTTGGTCCTTTGGAATATATATG
1 TCGGGACACATATTTGGTCATTCGGAATATATATG
41912 TCGGGACACATATTTGGTCATTCGGAATATATATG
1 TCGGGACACATATTTGGTCATTCGGAATATATATG
41947 T
1 T
41948 GATTCTTAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (35 bp):
TCGGGACACATATTTGGTCATTCGGAATATATATG
Found at i:41986 original size:18 final size:18
Alignment explanation
Indices: 41963--42056 Score: 143
Period size: 18 Copynumber: 5.2 Consensus size: 18
41953 TTAAGGAGTA
*
41963 GTCCTTCAGGACATAGTG
1 GTCCTTCGGGACATAGTG
41981 GTCCTTCGGGACATAGTG
1 GTCCTTCGGGACATAGTG
*
41999 GTCCTTCGGGACATAATG
1 GTCCTTCGGGACATAGTG
42017 GTCCTTCGGGACATAGTG
1 GTCCTTCGGGACATAGTG
* *
42035 GTCCTTCAGGGAAAAAGTG
1 GTCCTTC-GGGACATAGTG
42054 GTC
1 GTC
42057 ATTTGGGATA
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
18 58 0.83
19 12 0.17
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (18 bp):
GTCCTTCGGGACATAGTG
Found at i:44799 original size:20 final size:20
Alignment explanation
Indices: 44764--44808 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
44754 TTTTGCAGAG
44764 AAAACATCCCCAAACGGCTA
1 AAAACATCCCCAAACGGCTA
44784 AAAATCATCCCC-AACGGCTA
1 AAAA-CATCCCCAAACGGCTA
*
44804 TAAAC
1 AAAAC
44809 GGCCACAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 15 0.65
21 7 0.30
ACGTcount: A:0.44, C:0.33, G:0.09, T:0.13
Consensus pattern (20 bp):
AAAACATCCCCAAACGGCTA
Found at i:58654 original size:146 final size:146
Alignment explanation
Indices: 58390--58678 Score: 578
Period size: 146 Copynumber: 2.0 Consensus size: 146
58380 CTCTATAATC
58390 GTAACTATTTGAGTCTAAATATTTTTTTAATCATTGAGTTTATTTAATGGATTAGATGTAACATA
1 GTAACTATTTGAGTCTAAATATTTTTTTAATCATTGAGTTTATTTAATGGATTAGATGTAACATA
58455 TTAAATCCATAAATAACGTAACTGATAAGTTTGTATTATTTGAAGCAGGTAGGGCTCGGTCCTAT
66 TTAAATCCATAAATAACGTAACTGATAAGTTTGTATTATTTGAAGCAGGTAGGGCTCGGTCCTAT
58520 GCAATATCGACAGAGA
131 GCAATATCGACAGAGA
58536 GTAACTATTTGAGTCTAAATATTTTTTTAATCATTGAGTTTATTTAATGGATTAGATGTAACATA
1 GTAACTATTTGAGTCTAAATATTTTTTTAATCATTGAGTTTATTTAATGGATTAGATGTAACATA
58601 TTAAATCCATAAATAACGTAACTGATAAGTTTGTATTATTTGAAGCAGGTAGGGCTCGGTCCTAT
66 TTAAATCCATAAATAACGTAACTGATAAGTTTGTATTATTTGAAGCAGGTAGGGCTCGGTCCTAT
58666 GCAATATCGACAG
131 GCAATATCGACAG
58679 TTGGTAGGCC
Statistics
Matches: 143, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
146 143 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (146 bp):
GTAACTATTTGAGTCTAAATATTTTTTTAATCATTGAGTTTATTTAATGGATTAGATGTAACATA
TTAAATCCATAAATAACGTAACTGATAAGTTTGTATTATTTGAAGCAGGTAGGGCTCGGTCCTAT
GCAATATCGACAGAGA
Found at i:63718 original size:152 final size:153
Alignment explanation
Indices: 63500--63806 Score: 438
Period size: 152 Copynumber: 2.0 Consensus size: 153
63490 AATATTTTAG
* * * * * *
63500 TGTCTAAAGAATTTTTCGCTAAAAATAGGTGTTTAATGTTTTATCGGTTATATTTTTAGGGGCCT
1 TGTCTAAAGAATTTTTAGCTAAAAATA-GTGTATAACGTTTTATCGATTATACTTTTAGGGACCT
**
63565 ACAATTTATTTTTTTGGTTTTT-TAATAATAAAAATATTATTTTTAATTAAAAAAGAAAAAAGTT
65 ACAATTTA-TTTTTTAATTTTTGTAATAATAAAAATATTATTTTTAATTAAAAAAGAAAAAAGTT
63629 TAATATATTTATAAAAAAAACTAAC
129 TAATATATTTATAAAAAAAACTAAC
* * * * *
63654 TGTCTAAATAATTTTTAGTTAAAAATA-TGTATAACGTTTTCTTGATTATACTTTTAGGTACCTA
1 TGTCTAAAGAATTTTTAGCTAAAAATAGTGTATAACGTTTTATCGATTATACTTTTAGGGACCTA
*
63718 CAGTTTATTTTTTAATTTTTGTAATAATAAAAATATTATTTTTAATTAAAAAAGAAAAAAGTTTA
66 CAATTTATTTTTTAATTTTTGTAATAATAAAAATATTATTTTTAATTAAAAAAGAAAAAAGTTTA
* *
63783 ATCTATTTATAAAAAGAACTAAC
131 ATATATTTATAAAAAAAACTAAC
63806 T
1 T
63807 TTTTACTGAA
Statistics
Matches: 136, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
151 11 0.08
152 101 0.74
154 24 0.18
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.44
Consensus pattern (153 bp):
TGTCTAAAGAATTTTTAGCTAAAAATAGTGTATAACGTTTTATCGATTATACTTTTAGGGACCTA
CAATTTATTTTTTAATTTTTGTAATAATAAAAATATTATTTTTAATTAAAAAAGAAAAAAGTTTA
ATATATTTATAAAAAAAACTAAC
Found at i:64906 original size:55 final size:56
Alignment explanation
Indices: 64789--64914 Score: 148
Period size: 55 Copynumber: 2.3 Consensus size: 56
64779 TTTATTTTTT
* * * *
64789 TAGATAAATTCGATTTCAAAATCTCTATAAATATGCTTCTTAATAGCAACAACTGA
1 TAGATATATTCGATTTCAAAATCTCTATAAATATACTTATTAATAGCAACAACTAA
* * **
64845 TAGATATATTCGATTTCGAGATCTCTAT-TTTATACTTATTAAT-GACAACAACTAA
1 TAGATATATTCGATTTCAAAATCTCTATAAATATACTTATTAATAG-CAACAACTAA
*
64900 TAGATATATTTGATT
1 TAGATATATTCGATT
64915 CGGACCATTA
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
54 1 0.02
55 34 0.57
56 25 0.42
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (56 bp):
TAGATATATTCGATTTCAAAATCTCTATAAATATACTTATTAATAGCAACAACTAA
Found at i:71303 original size:3 final size:3
Alignment explanation
Indices: 71297--71323 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
71287 AAAAAAGCAA
71297 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
71324 TTCCCCTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:72268 original size:43 final size:43
Alignment explanation
Indices: 72182--72273 Score: 105
Period size: 43 Copynumber: 2.1 Consensus size: 43
72172 TTAATCGAAA
**
72182 AGAAAAGTAATAAGAATCTGAAATTTTGATAGATTGATTGAAT
1 AGAAAAGTAATAAGAATCTGAAATTTTGATAGATTGAGAGAAT
* * * *
72225 AGAAAAGTATTAGGAATCATGAAA-TTTGATTGTTTGAGAGAAT
1 AGAAAAGTAATAAGAATC-TGAAATTTTGATAGATTGAGAGAAT
*
72268 AAAAAA
1 AGAAAA
72274 AATTAACCCT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 36 0.88
44 5 0.12
ACGTcount: A:0.48, C:0.02, G:0.20, T:0.30
Consensus pattern (43 bp):
AGAAAAGTAATAAGAATCTGAAATTTTGATAGATTGAGAGAAT
Found at i:72977 original size:62 final size:61
Alignment explanation
Indices: 72874--72997 Score: 178
Period size: 62 Copynumber: 2.0 Consensus size: 61
72864 CTAAAACTTT
* *
72874 CAAGCATAAACAATTTCAACTTATCGACTTCGAAGCAGTAGGCTT-TACATTCAATAATTTG
1 CAAGCATAAACAATTTCAAATCATCGACTTCGAAGCAGTAGGCTTCT-CATTCAATAATTTG
* * *
72935 CAAGCTTAAACAATTTCAAATCATTCGACTTTGAAGCAGTAGGCTTCTCATTCCATAATTTG
1 CAAGCATAAACAATTTCAAATCA-TCGACTTCGAAGCAGTAGGCTTCTCATTCAATAATTTG
72997 C
1 C
72998 TTTGAATCTT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
61 20 0.36
62 35 0.62
63 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (61 bp):
CAAGCATAAACAATTTCAAATCATCGACTTCGAAGCAGTAGGCTTCTCATTCAATAATTTG
Found at i:77096 original size:62 final size:61
Alignment explanation
Indices: 76982--77103 Score: 158
Period size: 62 Copynumber: 2.0 Consensus size: 61
76972 ACAAACTTTT
* * * *
76982 AAGGATAAACAATTTCAAATTATTGGCTTCGAAGCAGTAGGCTTTACGTTCAATAATTTGC
1 AAGGATAAACAATTTCAAATCATTGACCTCGAAGCAGTAGGCTTTACATTCAATAATTTGC
*
77043 AAGGTTAAACAATTTCAAATCATTTGACACT-GAAGCAGTAGGCTTCT-CATTCAATAATTTG
1 AAGGATAAACAATTTCAAATCA-TTGAC-CTCGAAGCAGTAGGCTT-TACATTCAATAATTTG
77104 TTTTCAATCT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
61 20 0.38
62 31 0.58
63 2 0.04
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (61 bp):
AAGGATAAACAATTTCAAATCATTGACCTCGAAGCAGTAGGCTTTACATTCAATAATTTGC
Found at i:78600 original size:37 final size:36
Alignment explanation
Indices: 78541--78660 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
78531 ATCCCATTAT
* * *
78541 CATTTTTC-AACAAACATCTACCAAACTTTAAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTT-GAAAAC
*
78577 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
78613 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
78648 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
78661 TTGGTTATCA
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 35 0.46
36 13 0.17
37 28 0.37
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:78616 original size:21 final size:21
Alignment explanation
Indices: 78592--78652 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
78582 TTCAAAGAAA
78592 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
78613 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
78627 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
78648 CATTT
1 CATTT
78653 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:85694 original size:13 final size:14
Alignment explanation
Indices: 85676--85715 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
85666 TGTATTTGTA
85676 TTTAT-ATTAATAT
1 TTTATAATTAATAT
*
85689 TTTATAATTTA-AT
1 TTTATAATTAATAT
85702 TTTATAATTAATAT
1 TTTATAATTAATAT
85716 CAGATAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 17 0.74
14 6 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTATAATTAATAT
Found at i:90843 original size:21 final size:23
Alignment explanation
Indices: 90819--90862 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
90809 AGTAAGAGGG
*
90819 GGAGG-GC-GAAGAGAGGGGTGA
1 GGAGGCGCTGAAGAGAGCGGTGA
90840 GGAGGCCGCTGAAGAGAGCGGTG
1 GGAGG-CGCTGAAGAGAGCGGTG
90863 GCGGAGTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
23 2 0.11
24 12 0.63
ACGTcount: A:0.25, C:0.11, G:0.57, T:0.07
Consensus pattern (23 bp):
GGAGGCGCTGAAGAGAGCGGTGA
Found at i:91045 original size:23 final size:23
Alignment explanation
Indices: 91014--91068 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
91004 TCATTTTTTA
*
91014 TTTT-TTAATTATTAACTTAAAC
1 TTTTATTAATTATCAACTTAAAC
91036 TTTTATTAATTATCAACTTAAAC
1 TTTTATTAATTATCAACTTAAAC
91059 TTTTATTAAT
1 TTTTATTAAT
91069 AGGTTAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 4 0.13
23 27 0.87
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTTATTAATTATCAACTTAAAC
Found at i:91397 original size:62 final size:61
Alignment explanation
Indices: 91292--91414 Score: 158
Period size: 62 Copynumber: 2.0 Consensus size: 61
91282 GCTAACCCTA
* * * * *
91292 AAGCATAAACAATTTCAAATTATTGGCTTCGAAGCAGTAGGCTT-TACGTTCGATAATTTGC
1 AAGCATAAACAATCTCAAATCATTGACTTCGAAGCAGTAGGCTTCT-CATTCAATAATTTGC
* *
91353 AAGCTTAAACAATCTCAAATCATTTGACTTTGAAGCAGTAGGCTTCTCATTCAATAATTTGC
1 AAGCATAAACAATCTCAAATCA-TTGACTTCGAAGCAGTAGGCTTCTCATTCAATAATTTGC
91415 TTTCAATCTT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
61 19 0.36
62 33 0.62
63 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (61 bp):
AAGCATAAACAATCTCAAATCATTGACTTCGAAGCAGTAGGCTTCTCATTCAATAATTTGC
Found at i:94947 original size:12 final size:12
Alignment explanation
Indices: 94926--94954 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
94916 GGCATCGGAC
94926 TAGC-AATAATA
1 TAGCAAATAATA
94937 TAGCAAATAATA
1 TAGCAAATAATA
94949 TAGCAA
1 TAGCAA
94955 GTGCTCAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.24
Consensus pattern (12 bp):
TAGCAAATAATA
Found at i:96398 original size:18 final size:19
Alignment explanation
Indices: 96369--96404 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
96359 TTATTTATTT
96369 AAATATTATATTTAATTAC
1 AAATATTATATTTAATTAC
*
96388 AAATA-TATATTTTATTA
1 AAATATTATATTTAATTA
96405 TTATTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
AAATATTATATTTAATTAC
Found at i:99557 original size:15 final size:15
Alignment explanation
Indices: 99539--99573 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
99529 CGAGGGTTCT
99539 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
99554 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
99569 GTAGT
1 GTAGT
99574 GGTCCTACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:101102 original size:3 final size:3
Alignment explanation
Indices: 101058--101087 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
101048 TTATATTAAA
101058 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
101088 ATGTTACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:103077 original size:2 final size:2
Alignment explanation
Indices: 103064--103099 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
103054 ATCTTTTGTT
103064 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
103100 TCATACGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:115569 original size:53 final size:53
Alignment explanation
Indices: 115508--115675 Score: 230
Period size: 53 Copynumber: 3.1 Consensus size: 53
115498 GTGATGTTTC
*
115508 TATACTCCCTAGAGAAAGAGGGAGCGAACCCATTTGAAGAAGATGTCCGAGTT
1 TATACTCCCTAGAGAAAGAGGGAGCGAACCCATTTGAAGAAGATGTTCGAGTT
* ** *
115561 TATACTCCCTAGAGAAAGAGGGAGCAAACCTGTTTGAAGAAGATATTCGAGTT
1 TATACTCCCTAGAGAAAGAGGGAGCGAACCCATTTGAAGAAGATGTTCGAGTT
* **
115614 CTATACTCTCT-GAGAAAGAGGGAGCGAACCCATAAGAAGAAGATTGTTCGAGTCT
1 -TATACTCCCTAGAGAAAGAGGGAGCGAACCCATTTGAAGAAGA-TGTTCGAGT-T
115669 TATACTC
1 TATACTC
115676 TGAAGGAATA
Statistics
Matches: 100, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
53 75 0.75
54 24 0.24
55 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (53 bp):
TATACTCCCTAGAGAAAGAGGGAGCGAACCCATTTGAAGAAGATGTTCGAGTT
Found at i:115842 original size:54 final size:53
Alignment explanation
Indices: 115652--115842 Score: 189
Period size: 54 Copynumber: 3.5 Consensus size: 53
115642 CCCATAAGAA
*
115652 GAAGATTGTTCGAGTCT-TA-TACTCTGAAGGAATAGGGAGCAGACACGATAGTT
1 GAAGATTGTTCGAGTCTATACT-CTCTGAAGGAATAGGGAACAGACACGAT-GTT
* *
115705 GAAGATTGTTCGAGTCTTTACTCTCTAAAATAGG-ATAGGGAGA-AG--ACGATTGTT
1 GAAGATTGTTCGAGTCTATACTCTCT--GA-AGGAATAGGGA-ACAGACACGA-TGTT
*
115759 GAAGATTGTTCAAGTCTTATACTCTCTGAAGGAATAGGGAACAGACACGAGTGTT
1 GAAGATTGTTCGAGTC-TATACTCTCTGAAGGAATAGGGAACAGACACGA-TGTT
* *
115814 GAAGA-TGTTTGAGTTCTATACTCCCTGAA
1 GAAGATTGTTCGAG-TCTATACTCTCTGAA
115843 AGAAAAAGGG
Statistics
Matches: 116, Mismatches: 9, Indels: 25
0.77 0.06 0.17
Matches are distributed among these distances:
52 4 0.03
53 27 0.23
54 46 0.40
55 26 0.22
56 10 0.09
57 3 0.03
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (53 bp):
GAAGATTGTTCGAGTCTATACTCTCTGAAGGAATAGGGAACAGACACGATGTT
Found at i:116188 original size:3 final size:3
Alignment explanation
Indices: 116141--116173 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
116131 TTATATTAAA
116141 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
116174 ATGTTACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:118087 original size:2 final size:2
Alignment explanation
Indices: 118074--118107 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
118064 ATCTTTTGTT
118074 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA T
118108 TCATACGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Done.