Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007528.1 Hibiscus syriacus cultivar Beakdansim tig00021011_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: 73374
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1188 original size:13 final size:13
Alignment explanation
Indices: 1172--1196 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1162 CAAATTTAAC
1172 AATCAAAGTCAAT
1 AATCAAAGTCAAT
1185 AATCAAAGTCAA
1 AATCAAAGTCAA
1197 CGGTCACAAT
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:0.56, C:0.16, G:0.08, T:0.20
Consensus pattern (13 bp):
AATCAAAGTCAAT
Found at i:7965 original size:20 final size:21
Alignment explanation
Indices: 7942--7980 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
7932 TATTATTTTG
7942 TAATGATTTAATAA-ATTTAA
1 TAATGATTTAATAATATTTAA
* *
7962 TAATTATTTTATAATATTT
1 TAATGATTTAATAATATTT
7981 GAAAGTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (21 bp):
TAATGATTTAATAATATTTAA
Found at i:7968 original size:31 final size:29
Alignment explanation
Indices: 7933--7993 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 29
7923 TCATTAAGGT
*
7933 ATTATTTTGTAATGATTTAATAAATTTAATA
1 ATTATTTTATAAT-ATTTAA-AAATTTAATA
* *
7964 ATTATTTTATAATATTTGAAAGTTTAATA
1 ATTATTTTATAATATTTAAAAATTTAATA
7993 A
1 A
7994 CCAAAAAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 10 0.37
30 5 0.19
31 12 0.44
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.51
Consensus pattern (29 bp):
ATTATTTTATAATATTTAAAAATTTAATA
Found at i:8510 original size:20 final size:20
Alignment explanation
Indices: 8478--8531 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 20
8468 AATTAATGTT
8478 AAATAATAATAAAAAT-ATGAA
1 AAATAA-AATAAAAATAAT-AA
8499 AAATAAAATAAAAATAAATAA
1 AAATAAAATAAAAAT-AATAA
8520 AAAT-AAATAAAA
1 AAATAAAATAAAA
8532 TTAAAGAGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 17 0.55
21 12 0.39
22 2 0.06
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (20 bp):
AAATAAAATAAAAATAATAA
Found at i:8530 original size:10 final size:10
Alignment explanation
Indices: 8485--8536 Score: 63
Period size: 10 Copynumber: 5.2 Consensus size: 10
8475 GTTAAATAAT
8485 AATAAAAAT-
1 AATAAAAATA
8494 -ATGAAAAATAA
1 AAT-AAAAAT-A
8505 AATAAAAATA
1 AATAAAAATA
8515 AATAAAAATA
1 AATAAAAATA
*
8525 AATAAAATTA
1 AATAAAAATA
8535 AA
1 AA
8537 GAGGGATTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
8 2 0.05
9 6 0.16
10 22 0.58
11 6 0.16
12 2 0.05
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (10 bp):
AATAAAAATA
Found at i:9781 original size:7 final size:7
Alignment explanation
Indices: 9756--9873 Score: 54
Period size: 7 Copynumber: 16.9 Consensus size: 7
9746 GACCTGAAAT
9756 AATAATTA
1 AATAA-TA
*
9764 AATCATA
1 AATAATA
9771 AATAAATA
1 AAT-AATA
9779 ATATAATA
1 A-ATAATA
9787 AATAAT-
1 AATAATA
9793 AAT-AT-
1 AATAATA
*
9798 TATAATA
1 AATAATA
9805 AATAATA
1 AATAATA
9812 ACAT-AT-
1 A-ATAATA
9818 AAT-ATA
1 AATAATA
*
9824 TAATAGTA
1 -AATAATA
9832 AATATATA
1 AATA-ATA
* *
9840 TATACTA
1 AATAATA
9847 TAAT-ATA
1 -AATAATA
9854 AAT-ATA
1 AATAATA
9860 TAATAATA
1 -AATAATA
*
9868 TATAAT
1 AATAAT
9874 GTATAAATAC
Statistics
Matches: 87, Mismatches: 11, Indels: 25
0.71 0.09 0.20
Matches are distributed among these distances:
5 8 0.09
6 12 0.14
7 38 0.44
8 27 0.31
9 2 0.02
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (7 bp):
AATAATA
Found at i:9838 original size:2 final size:2
Alignment explanation
Indices: 9814--9945 Score: 65
Period size: 2 Copynumber: 70.0 Consensus size: 2
9804 AAATAATAAC
* *
9814 AT AT A- AT AT AT A- AT AGT AA AT AT AT AT AT ACT AT A- AT AT AA
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT
* *
9855 AT AT AT A- AT A- AT AT AT A- AT GT AT AA AT ACT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* * *
9894 AT A- AT ACC AT AT CAT AT A- AT AT AT GT -T AT AT AA AT A- AT AT
1 AT AT AT A-T AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9934 AT A- AT AT A- AT AT
1 AT AT AT AT AT AT AT
9946 GATTTAATAA
Statistics
Matches: 99, Mismatches: 13, Indels: 36
0.67 0.09 0.24
Matches are distributed among these distances:
1 13 0.13
2 77 0.78
3 9 0.09
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (2 bp):
AT
Found at i:9842 original size:18 final size:17
Alignment explanation
Indices: 9776--9942 Score: 87
Period size: 18 Copynumber: 9.5 Consensus size: 17
9766 TCATAAATAA
*
9776 ATAATAT-AATAAATA-
1 ATAATATAAATATATAT
*
9791 ATAATATTATAATAAATA-
1 ATAATA-TA-AATATATAT
*
9809 ATAACATATAATATATAAT
1 ATAATATA-AATATAT-AT
*
9828 AGTAA-ATATATATATACT
1 A-TAATATAAATATATA-T
9846 ATAATATAAATATATA-
1 ATAATATAAATATATAT
* *
9862 ATAATATATAATGTATAA
1 ATAATATA-AATATATAT
*
9880 ATACTAT-AATATATAT
1 ATAATATAAATATATAT
*
9896 AATACCATATCATATAATATAT
1 -ATA--ATAT-AAAT-ATATAT
* *
9918 GTTATATAAATA-ATAT
1 ATAATATAAATATATAT
9934 ATAATATAA
1 ATAATATAA
9943 TATGATTTAA
Statistics
Matches: 121, Mismatches: 15, Indels: 31
0.72 0.09 0.19
Matches are distributed among these distances:
15 6 0.05
16 27 0.22
17 24 0.20
18 41 0.34
19 11 0.09
20 3 0.02
21 3 0.02
22 6 0.05
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (17 bp):
ATAATATAAATATATAT
Found at i:9878 original size:7 final size:7
Alignment explanation
Indices: 9779--9941 Score: 88
Period size: 7 Copynumber: 22.4 Consensus size: 7
9769 TAAATAAATA
9779 ATATAAT
1 ATATAAT
*
9786 AAATAAT
1 ATATAAT
*
9793 A-ATATT
1 ATATAAT
9799 ATAATAA-
1 AT-ATAAT
*
9806 ATAATAAC
1 AT-ATAAT
9814 ATATAAT
1 ATATAAT
9821 ATATAAT
1 ATATAAT
9828 AGTA-AAT
1 A-TATAAT
9835 ATATATAT
1 ATATA-AT
9843 ACTATAAT
1 A-TATAAT
*
9851 ATAAATAT
1 ATATA-AT
9859 ATAATAAT
1 AT-ATAAT
9867 ATATAAT
1 ATATAAT
*
9874 GTATAAAT
1 ATAT-AAT
9882 ACTATAAT
1 A-TATAAT
9890 ATAT-AT
1 ATATAAT
*
9896 AATACCATAT
1 -ATA-TA-AT
9906 CATATAAT
1 -ATATAAT
*
9914 ATAT-GT
1 ATATAAT
9920 -TAT-AT
1 ATATAAT
*
9925 AAATAAT
1 ATATAAT
9932 ATATAAT
1 ATATAAT
9939 ATA
1 ATA
9942 ATATGATTTA
Statistics
Matches: 124, Mismatches: 15, Indels: 34
0.72 0.09 0.20
Matches are distributed among these distances:
5 4 0.03
6 12 0.10
7 63 0.51
8 30 0.24
9 10 0.08
10 5 0.04
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (7 bp):
ATATAAT
Found at i:9943 original size:30 final size:30
Alignment explanation
Indices: 9772--9945 Score: 139
Period size: 30 Copynumber: 5.8 Consensus size: 30
9762 TAAATCATAA
9772 ATAAATAATATAATAA-ATAATA-ATATTAT
1 ATAAATAATAT-ATAATATAATATATATTAT
*
9801 AATAAATAATA-A-CATATAATATATA--AT
1 -ATAAATAATATATAATATAATATATATTAT
* *
9828 AGTAAATATATATATACTATAATATA-AATAT
1 A-TAAATA-ATATATAATATAATATATATTAT
*
9859 AT-AATAATATATAATGTATAAATACTATAATAT
1 ATAAATAATATATAA--TAT-AATA-TATATTAT
** * *
9892 ATATAATACCATATCATATAATATATGTTAT
1 ATA-AATAATATATAATATAATATATATTAT
9923 ATAAATAATATATAATATAATAT
1 ATAAATAATATATAATATAATAT
9946 GATTTAATAA
Statistics
Matches: 117, Mismatches: 12, Indels: 30
0.74 0.08 0.19
Matches are distributed among these distances:
26 1 0.01
27 9 0.08
28 17 0.15
29 9 0.08
30 40 0.34
31 16 0.14
32 6 0.05
33 10 0.09
35 9 0.08
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (30 bp):
ATAAATAATATATAATATAATATATATTAT
Found at i:11495 original size:30 final size:30
Alignment explanation
Indices: 11461--11522 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
11451 TTCACACAAG
*
11461 TGAAGATTCCCTAAATACCTATTATTTTCT
1 TGAAGATTCCCTAAATACCCATTATTTTCT
*
11491 TGAAGATTCCCTAAATACCCATTGTTTTCT
1 TGAAGATTCCCTAAATACCCATTATTTTCT
11521 TG
1 TG
11523 TCCAGGATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (30 bp):
TGAAGATTCCCTAAATACCCATTATTTTCT
Found at i:15658 original size:15 final size:15
Alignment explanation
Indices: 15638--15674 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
15628 CCAATTTCGT
15638 GGGCAACTACAATTG
1 GGGCAACTACAATTG
15653 GGGCAACTACAATTG
1 GGGCAACTACAATTG
*
15668 GAGCAAC
1 GGGCAAC
15675 AATAACCCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.35, C:0.22, G:0.27, T:0.16
Consensus pattern (15 bp):
GGGCAACTACAATTG
Found at i:29125 original size:20 final size:19
Alignment explanation
Indices: 29061--29112 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
29051 AAAATGTTTT
29061 TATGAATAGTACTATAATG
1 TATGAATAGTACTATAATG
* * *
29080 TATGAATAATATCTATATTT
1 TATGAATAGTA-CTATAATG
29100 TATGAATAGTACT
1 TATGAATAGTACT
29113 GATACTGTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (19 bp):
TATGAATAGTACTATAATG
Found at i:37850 original size:34 final size:35
Alignment explanation
Indices: 37791--37858 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 35
37781 GAATGTAAAG
37791 AGGGTACTGATACCCCCCCAAGGGTATCAATACCT
1 AGGGTACTGATACCCCCCCAAGGGTATCAATACCT
* *
37826 AGGGTA-TCGATA-CCCCCCAGGGGTATCTATACC
1 AGGGTACT-GATACCCCCCCAAGGGTATCAATACC
37859 CCCTGGCTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 20 0.67
35 10 0.33
ACGTcount: A:0.26, C:0.31, G:0.22, T:0.21
Consensus pattern (35 bp):
AGGGTACTGATACCCCCCCAAGGGTATCAATACCT
Found at i:40287 original size:18 final size:18
Alignment explanation
Indices: 40264--40321 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
40254 CAACAATTGG
*
40264 TAACAAATGGTATCTTTT
1 TAACAATTGGTATCTTTT
*
40282 TAACAATTGATATCCTTTTGT
1 TAACAATTGGTAT-C-TTT-T
*
40303 TAATAATTGGTATCTTTT
1 TAACAATTGGTATCTTTT
40321 T
1 T
40322 CATTAAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 13 0.39
19 4 0.12
20 4 0.12
21 12 0.36
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.50
Consensus pattern (18 bp):
TAACAATTGGTATCTTTT
Found at i:40310 original size:21 final size:21
Alignment explanation
Indices: 40281--40321 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40271 TGGTATCTTT
40281 TTAACAATTGATATCCTTTTG
1 TTAACAATTGATATCCTTTTG
* * *
40302 TTAATAATTGGTATCTTTTT
1 TTAACAATTGATATCCTTTT
40322 CATTAAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.54
Consensus pattern (21 bp):
TTAACAATTGATATCCTTTTG
Found at i:40630 original size:18 final size:17
Alignment explanation
Indices: 40607--40656 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 17
40597 AAATGCAAAG
40607 AGGGTATCGATACCCCC
1 AGGGTATCGATACCCCC
*
40624 TAGGGTATCCATA--CCC
1 -AGGGTATCGATACCCCC
*
40640 AGGGTACCGATACCCCC
1 AGGGTATCGATACCCCC
40657 CCAAGGGTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 10 0.37
16 3 0.11
17 3 0.11
18 11 0.41
ACGTcount: A:0.24, C:0.36, G:0.22, T:0.18
Consensus pattern (17 bp):
AGGGTATCGATACCCCC
Found at i:47369 original size:12 final size:11
Alignment explanation
Indices: 47358--47391 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
47348 AAATAGAAAT
47358 TAAAATTAAAA
1 TAAAATTAAAA
47369 TAATAATTAAAA
1 TAA-AATTAAAA
47381 TAAAA-TAAAA
1 TAAAATTAAAA
47391 T
1 T
47392 TCCTACCCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.27
11 5 0.23
12 11 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
TAAAATTAAAA
Found at i:47369 original size:18 final size:16
Alignment explanation
Indices: 47346--47392 Score: 67
Period size: 18 Copynumber: 2.8 Consensus size: 16
47336 AATAAGTTAG
47346 TAAAATAGAAATTAAAA
1 TAAAATA-AAATTAAAA
47363 TTAAAATAATAATTAAAA
1 -TAAAATAA-AATTAAAA
47381 TAAAATAAAATT
1 TAAAATAAAATT
47393 CCTACCCCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.14
17 9 0.32
18 15 0.54
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (16 bp):
TAAAATAAAATTAAAA
Found at i:49663 original size:12 final size:12
Alignment explanation
Indices: 49646--49712 Score: 56
Period size: 12 Copynumber: 6.0 Consensus size: 12
49636 TATTAAATAT
49646 ATATATACTATA
1 ATATATACTATA
*
49658 ATATATA--ATC
1 ATATATACTATA
*
49668 CTATAT-CATATA
1 ATATATAC-TATA
49680 ATATATACTAT-
1 ATATATACTATA
*
49691 ATAT-CA-TATA
1 ATATATACTATA
49701 ATATATACTATA
1 ATATATACTATA
49713 GAAAATAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
9 3 0.07
10 12 0.29
11 5 0.12
12 21 0.50
13 1 0.02
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATATACTATA
Found at i:49695 original size:21 final size:21
Alignment explanation
Indices: 49669--49744 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
49659 TATATAATCC
49669 TATATCATATAATATATACTA
1 TATATCATATAATATATACTA
49690 TATATCATATAATATATACTA
1 TATATCATATAATATATACTA
* * *
49711 TAGA--AAATAATATATAATA
1 TATATCATATAATATATACTA
*
49730 TAATATGATATAATA
1 T-ATATCATATAATA
49745 AAAAGGAACG
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 14 0.30
20 2 0.04
21 24 0.51
22 7 0.15
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (21 bp):
TATATCATATAATATATACTA
Found at i:49727 original size:7 final size:7
Alignment explanation
Indices: 49641--49744 Score: 74
Period size: 7 Copynumber: 14.6 Consensus size: 7
49631 TGAAATATTA
49641 AATATAT
1 AATATAT
49648 ATATACTAT
1 A-ATA-TAT
49657 AATATAT
1 AATATAT
*
49664 AATCCTAT
1 AAT-ATAT
49672 -ATCATAT
1 AAT-ATAT
49679 AATATAT
1 AATATAT
*
49686 ACTATAT
1 AATATAT
49693 -ATCATAT
1 AAT-ATAT
49700 AATATAT
1 AATATAT
* *
49707 ACTATAG
1 AATATAT
49714 AA-A-AT
1 AATATAT
49719 AATATAT
1 AATATAT
49726 AATATA-
1 AATATAT
49732 ATATGATAT
1 A-AT-ATAT
49741 AATA
1 AATA
49745 AAAAGGAACG
Statistics
Matches: 78, Mismatches: 8, Indels: 22
0.72 0.07 0.20
Matches are distributed among these distances:
5 3 0.04
6 4 0.05
7 48 0.62
8 18 0.23
9 5 0.06
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (7 bp):
AATATAT
Found at i:49976 original size:12 final size:12
Alignment explanation
Indices: 49961--49998 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
49951 GTTATTTAAA
49961 CGGGTATTGGGC
1 CGGGTATTGGGC
*
49973 CGGGTATTGGGT
1 CGGGTATTGGGC
49985 CGGGTATTGGGC
1 CGGGTATTGGGC
49997 CG
1 CG
49999 AGAATCGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.08, C:0.16, G:0.50, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:49988 original size:24 final size:24
Alignment explanation
Indices: 49961--50015 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
49951 GTTATTTAAA
* * *
49961 CGGGTATTGGGCCGGGTATTGGGT
1 CGGGTATTGGGCCGAGAATCGGGT
49985 CGGGTATTGGGCCGAGAATCGGGT
1 CGGGTATTGGGCCGAGAATCGGGT
50009 CGGGTAT
1 CGGGTAT
50016 ATATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.13, C:0.15, G:0.47, T:0.25
Consensus pattern (24 bp):
CGGGTATTGGGCCGAGAATCGGGT
Found at i:50218 original size:6 final size:6
Alignment explanation
Indices: 50207--50231 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
50197 AAATGGGTTT
50207 TCCCCG TCCCCG TCCCCG TCCCCG T
1 TCCCCG TCCCCG TCCCCG TCCCCG T
50232 TTATCATCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.64, G:0.16, T:0.20
Consensus pattern (6 bp):
TCCCCG
Found at i:52281 original size:43 final size:43
Alignment explanation
Indices: 52125--52401 Score: 177
Period size: 43 Copynumber: 6.3 Consensus size: 43
52115 TACGTTTCAT
* * *
52125 CTTTATAATTGACGCC-CTTAATATTTTGTCAATCTCATTTTTTTC
1 CTTTATAATTGAGGCCAC-TAAT-TTTT-TCAATCTCAATTTTTAC
* ** * * **
52170 ATTTATAATTGATGATC-CTAAGTTTTTCAATCTCACTTTGAAC
1 CTTTATAATTGA-GGCCACTAATTTTTTCAATCTCAATTTTTAC
* * * * * * *
52213 CTTTATAGTTAAGGTC-TTGATTTTTTCCAATCTGAATTTTTAT
1 CTTTATAATTGAGGCCACTAATTTTTT-CAATCTCAATTTTTAC
* *
52256 CTTTATAATTGAGGCCACTAATTTTTTCAATCCCAAGTTTTAC
1 CTTTATAATTGAGGCCACTAATTTTTTCAATCTCAATTTTTAC
* * *
52299 CTATATAATTTA-GCCACCTAATTTTATTCAATCTCACTTTTTAC
1 CTTTATAATTGAGGCCA-CTAATTTT-TTCAATCTCAATTTTTAC
* * * *
52343 CTTTGA-AATTGAGGCCCCTAAATTTTTTTTAATCTCACTTTTAAC
1 CTTT-ATAATTGAGGCCACT-AA-TTTTTTCAATCTCAATTTTTAC
* *
52388 TTTTAGAATTGAGG
1 CTTTATAATTGAGG
52402 TCTCAATCAC
Statistics
Matches: 181, Mismatches: 41, Indels: 20
0.75 0.17 0.08
Matches are distributed among these distances:
42 14 0.08
43 76 0.42
44 38 0.21
45 47 0.26
46 6 0.03
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.47
Consensus pattern (43 bp):
CTTTATAATTGAGGCCACTAATTTTTTCAATCTCAATTTTTAC
Found at i:53714 original size:26 final size:26
Alignment explanation
Indices: 53691--53755 Score: 121
Period size: 26 Copynumber: 2.5 Consensus size: 26
53681 CATATATTCG
53691 GGTCGGGTCGGGTGAAACTTTATTTT
1 GGTCGGGTCGGGTGAAACTTTATTTT
53717 GGTCGGGTCGGGTGAAACTTTATTTT
1 GGTCGGGTCGGGTGAAACTTTATTTT
*
53743 GGTCGGGTTGGGT
1 GGTCGGGTCGGGT
53756 CATTTTTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.12, C:0.11, G:0.40, T:0.37
Consensus pattern (26 bp):
GGTCGGGTCGGGTGAAACTTTATTTT
Found at i:54068 original size:38 final size:38
Alignment explanation
Indices: 54007--54095 Score: 135
Period size: 38 Copynumber: 2.3 Consensus size: 38
53997 TTTATTCGGC
*
54007 TCGGGTCGAG-TTTTTTAAGTGTGATATTAGGGTCGAG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTAGGGTCGAG
* *
54044 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTAGGGTCGAG
54082 TCGGGTTCGGGTTT
1 TCGGG-TCGGGTTT
54096 AGGGTGAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
37 9 0.19
38 30 0.64
39 8 0.17
ACGTcount: A:0.12, C:0.10, G:0.38, T:0.39
Consensus pattern (38 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATATTAGGGTCGAG
Found at i:54688 original size:17 final size:18
Alignment explanation
Indices: 54663--54709 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
54653 TATGGAATTG
54663 GATTCCAATTCC-TAACA
1 GATTCCAATTCCTTAACA
* *
54680 GATTTCAATTCCTTCACA
1 GATTCCAATTCCTTAACA
54698 GATTCCAATTCC
1 GATTCCAATTCC
54710 CTCATAAACG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.34
Consensus pattern (18 bp):
GATTCCAATTCCTTAACA
Found at i:55037 original size:20 final size:20
Alignment explanation
Indices: 55014--55065 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
55004 CCCTCTCATC
55014 AGTATCAATACCCTACCTAA
1 AGTATCAATACCCTACCTAA
55034 AGTATCAATACCCTACCTAA
1 AGTATCAATACCCTACCTAA
* *
55054 GGTATCGATACC
1 AGTATCAATACC
55066 TGGTGTTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.29, G:0.10, T:0.25
Consensus pattern (20 bp):
AGTATCAATACCCTACCTAA
Found at i:57194 original size:2 final size:2
Alignment explanation
Indices: 57182--57226 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
57172 TATTATTATC
57182 AT AT AT CAT 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
57225 AT
1 AT
57227 TTAAATAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:63383 original size:15 final size:16
Alignment explanation
Indices: 63358--63387 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
63348 TATACTTGAA
63358 GAAAGAAAGAAAAAAG
1 GAAAGAAAGAAAAAAG
63374 GAAA-AAAGAAAAAA
1 GAAAGAAAGAAAAAA
63388 ATTGAATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
GAAAGAAAGAAAAAAG
Found at i:67582 original size:54 final size:54
Alignment explanation
Indices: 67518--67655 Score: 179
Period size: 54 Copynumber: 2.6 Consensus size: 54
67508 ACAAAAAAAT
*
67518 GATGAATGTGTTGTCAAATGCTTTACGAACATCTGGCCAGAAGCCA-TAAGAAAG
1 GATGAATGTGTTATCAAATGCTTTACGAACATCTGGCCAGAAGCCACT-AGAAAG
* * * *
67572 GATGAATGTGTTATCAAAAGCTTTACGAAAATCTGGGCAGAAGCCACTAGAAAT
1 GATGAATGTGTTATCAAATGCTTTACGAACATCTGGCCAGAAGCCACTAGAAAG
* * * *
67626 GATGAATGTATTTTCACATGTTTTACGAAC
1 GATGAATGTGTTATCAAATGCTTTACGAAC
67656 CAGTGATTAT
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
54 71 0.99
55 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.28
Consensus pattern (54 bp):
GATGAATGTGTTATCAAATGCTTTACGAACATCTGGCCAGAAGCCACTAGAAAG
Found at i:68075 original size:22 final size:22
Alignment explanation
Indices: 68017--68076 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
68007 ATTATATCTA
*
68017 CACTCTTCAAAGATAATAAATT
1 CACTCTTCAAAGATGATAAATT
*
68039 CACTCTTCAAAGATGATAGATT
1 CACTCTTCAAAGATGATAAATT
* *
68061 CTCTTTTCAAAGATGA
1 CACTCTTCAAAGATGA
68077 AAGCTTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (22 bp):
CACTCTTCAAAGATGATAAATT
Found at i:68873 original size:74 final size:74
Alignment explanation
Indices: 68741--69432 Score: 894
Period size: 74 Copynumber: 9.3 Consensus size: 74
68731 ACTATTTCCC
* * * *
68741 TCATCCGTAAGAACTGCAGTGCAGGATGTTTTCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTT
1 TCATCTGTAAGACCTACAGTGCATGATG-TTTC-AAAAAGCCTTCGGGAGCTTTTTGAT-TTTTT
68806 AAAGCCTCCGGG
63 AAAGCCTCCGGG
* *
68818 TCATCTGTAAGACCTACAGTGCATGATG-TTCAAAAAGCCTTCGGGAGCCTTTTGATATTTTAAA
1 TCATCTGTAAGACCTACAGTGCATGATGTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTTTAAA
68882 GCCTCCGGG
66 GCCTCCGGG
* * * *
68891 TCATCCGTAAGACCTACAGTGCAAGAAGTTTTCGAAAAGCCTTCGGGAG-TTTTTGATATTTTTA
1 TCATCTGTAAGACCTACAGTGCATGATG-TTTCAAAAAGCCTTCGGGAGCTTTTTGAT-TTTTTA
68955 AAGCCTCCGGG
64 AAGCCTCCGGG
*
68966 TCATCTGTAAGACCTACAGTGCATGATG-TTCAAAAAGCCTTCGGGAGCTTGTTGATGTTTTTAA
1 TCATCTGTAAGACCTACAGTGCATGATGTTTCAAAAAGCCTTCGGGAGCTTTTTGAT-TTTTTAA
69030 AGCCTCCGGG
65 AGCCTCCGGG
** * * * *
69040 TCATCCATAAGCCCTAAAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTTA-TTTTTAA
1 TCATCTGTAAGACCTACAGTGCATGATG-TTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTTTAA
*
69104 AGCCTCCAGG
65 AGCCTCCGGG
* * *
69114 TCATCTGTAAGACCTACAGTGCATAATG-TTCAAAAAGCCTTCGGGAGCTTTTTGATATTTCAAA
1 TCATCTGTAAGACCTACAGTGCATGATGTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTTTAAA
*
69178 GCCTCTGGG
66 GCCTCCGGG
* *
69187 TCATCTGTAAGACCTACAGTGCATGATGTTTTAAAAAAAGCCTTCGGAAGCTTTTTGA-TTTTTA
1 TCATCTGTAAGACCTACAGTGCATGATG-TTT-CAAAAAGCCTTCGGGAGCTTTTTGATTTTTTA
* *
69251 AAGCCTCTGGA
64 AAGCCTCCGGG
* *
69262 TCATCTGTAAGACCTACAATGCATGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTTA
1 TCATCTGTAAGACCTACAGTGCATGATG-TTTCAAAAAGCCTTCGGGAGCTTTTTGAT-TTTTTA
69327 AAGCCTCCGGG
64 AAGCCTCCGGG
** * * * *
69338 TCATCCATAAGCCCTACAGTGCAGGATGTTTTCAAAGAGCCTTCGGGAGCTTTTTGA-TATTTAA
1 TCATCTGTAAGACCTACAGTGCATGATG-TTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTTTAA
* *
69402 ATCCTTCGGG
65 AGCCTCCGGG
*
69412 TCATCTGTAATACCTACAGTG
1 TCATCTGTAAGACCTACAGTG
69433 AAAGATGATA
Statistics
Matches: 540, Mismatches: 63, Indels: 27
0.86 0.10 0.04
Matches are distributed among these distances:
72 26 0.05
73 99 0.18
74 169 0.31
75 109 0.20
76 113 0.21
77 24 0.04
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.32
Consensus pattern (74 bp):
TCATCTGTAAGACCTACAGTGCATGATGTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTTTAAA
GCCTCCGGG
Found at i:69011 original size:148 final size:150
Alignment explanation
Indices: 68741--69432 Score: 990
Period size: 148 Copynumber: 4.6 Consensus size: 150
68731 ACTATTTCCC
* * *
68741 TCATCCGTAAGAACTGCAGTGCAGGATGTTTTCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTT
1 TCATCCGTAAGACCTACAGTGCAGGATGTTTTC-AAAAAGCCTTCGGGAGCTTTTTGATATTTTT
68806 AAAGCCTCCGGGTCATCTGTAAGACCTACAGTGCATGATGTTCAAAAAGCCTTCGGGAGCCTTTT
65 AAAGCCTCCGGGTCATCTGTAAGACCTACAGTGCATGATGTTCAAAAAGCCTTCGGGAGCCTTTT
68871 GAT-ATTTTAAAGCCTCCGGG
130 GATGATTTTAAAGCCTCCGGG
* * *
68891 TCATCCGTAAGACCTACAGTGCAAGAAGTTTTCGAAAAGCCTTCGGGAG-TTTTTGATATTTTTA
1 TCATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTTA
68955 AAGCCTCCGGGTCATCTGTAAGACCTACAGTGCATGATGTTCAAAAAGCCTTCGGGAG-CTTGTT
66 AAGCCTCCGGGTCATCTGTAAGACCTACAGTGCATGATGTTCAAAAAGCCTTCGGGAGCCTT-TT
*
69019 GATGTTTTTAAAGCCTCCGGG
130 GATGATTTTAAAGCCTCCGGG
* * *
69040 TCATCCATAAGCCCTAAAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTT--TATTTTTA
1 TCATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTTA
* * *
69103 AAGCCTCCAGGTCATCTGTAAGACCTACAGTGCATAATGTTCAAAAAGCCTTCGGGAGCTTTTTG
66 AAGCCTCCGGGTCATCTGTAAGACCTACAGTGCATGATGTTCAAAAAGCCTTCGGGAGCCTTTTG
* *
69168 AT-ATTTCAAAGCCTCTGGG
131 ATGATTTTAAAGCCTCCGGG
* * * *
69187 TCATCTGTAAGACCTACAGTGCATGATGTTTTAAAAAAAGCCTTCGGAAGCTTTTTG--ATTTTT
1 TCATCCGTAAGACCTACAGTGCAGGATGTTTT-CAAAAAGCCTTCGGGAGCTTTTTGATATTTTT
* * * * *
69250 AAAGCCTCTGGATCATCTGTAAGACCTACAATGCATGATGTTTTCAAAAAGCCTTCAGGAGCTTT
65 AAAGCCTCCGGGTCATCTGTAAGACCTACAGTGCATGATG--TTCAAAAAGCCTTCGGGAGCCTT
*
69315 TTGATGTTTTTAAAGCCTCCGGG
128 TTGATGATTTTAAAGCCTCCGGG
* * *
69338 TCATCCATAAGCCCTACAGTGCAGGATGTTTTCAAAGAGCCTTCGGGAGCTTTTTGATA--TTTA
1 TCATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTTA
* * *
69401 AATCCTTCGGGTCATCTGTAATACCTACAGTG
66 AAGCCTCCGGGTCATCTGTAAGACCTACAGTG
69433 AAAGATGATA
Statistics
Matches: 483, Mismatches: 48, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
147 44 0.09
148 208 0.43
149 76 0.16
150 112 0.23
151 42 0.09
152 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.32
Consensus pattern (150 bp):
TCATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTTA
AAGCCTCCGGGTCATCTGTAAGACCTACAGTGCATGATGTTCAAAAAGCCTTCGGGAGCCTTTTG
ATGATTTTAAAGCCTCCGGG
Found at i:69623 original size:3 final size:3
Alignment explanation
Indices: 69615--69687 Score: 96
Period size: 3 Copynumber: 24.7 Consensus size: 3
69605 TCATTTCATT
** *
69615 TTA TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA -TA ATA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
69661 TATA TTA TTA TTA TTA TTA TTA TTA TT
1 T-TA TTA TTA TTA TTA TTA TTA TTA TT
69688 TAATAAATAA
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
2 4 0.06
3 55 0.89
4 3 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Done.