Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008408.1 Hibiscus syriacus cultivar Beakdansim tig00111177_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: 94065
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:1068 original size:13 final size:13
Alignment explanation
Indices: 1052--1084 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1042 GTCAACGGGT
*
1052 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
1065 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
1078 CGGGTCG
1 CGGGTCG
1085 TGACCGGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.21, G:0.48, T:0.15
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:1107 original size:10 final size:10
Alignment explanation
Indices: 1087--1141 Score: 78
Period size: 10 Copynumber: 5.6 Consensus size: 10
1077 ACGGGTCGTG
1087 ACCGGTC-AA
1 ACCGGTCAAA
1096 ACCGGTCAAA
1 ACCGGTCAAA
1106 ACCGGTTCAAA
1 ACCGG-TCAAA
*
1117 ACCGGT-TAA
1 ACCGGTCAAA
1126 ACCGGTCAAA
1 ACCGGTCAAA
1136 ACCGGT
1 ACCGGT
1142 TTCCAGCGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
9 15 0.37
10 16 0.39
11 10 0.24
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:1142 original size:19 final size:19
Alignment explanation
Indices: 1087--1142 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1077 ACGGGTCGTG
*
1087 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
1106 ACCGGTTCAAAACCGGTTAA
1 ACCGG-TCAAAACCGGTTAA
1126 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
1143 TCCAGCGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.50
20 9 0.26
21 8 0.24
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:8388 original size:10 final size:10
Alignment explanation
Indices: 8368--8422 Score: 78
Period size: 10 Copynumber: 5.6 Consensus size: 10
8358 ACGGGTCGTG
8368 ACCGGTC-AA
1 ACCGGTCAAA
8377 ACCGGTCAAA
1 ACCGGTCAAA
8387 ACCGGTTCAAA
1 ACCGG-TCAAA
*
8398 ACCGGT-TAA
1 ACCGGTCAAA
8407 ACCGGTCAAA
1 ACCGGTCAAA
8417 ACCGGT
1 ACCGGT
8423 TTCCAGCGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
9 15 0.37
10 16 0.39
11 10 0.24
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:8423 original size:19 final size:19
Alignment explanation
Indices: 8368--8423 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
8358 ACGGGTCGTG
*
8368 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
8387 ACCGGTTCAAAACCGGTTAA
1 ACCGG-TCAAAACCGGTTAA
8407 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
8424 TCCAGCGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.50
20 9 0.26
21 8 0.24
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:11941 original size:27 final size:29
Alignment explanation
Indices: 11883--11941 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
11873 ATTTATGTAC
*
11883 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
11912 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
11939 TTA
1 TTA
11942 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:23699 original size:27 final size:29
Alignment explanation
Indices: 23641--23699 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
23631 ATTTCTGTAC
*
23641 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
23670 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
23697 TTA
1 TTA
23700 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:28449 original size:27 final size:29
Alignment explanation
Indices: 28391--28449 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
28381 ATTTCTGTAC
*
28391 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
28420 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
28447 TTA
1 TTA
28450 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:30816 original size:25 final size:28
Alignment explanation
Indices: 30761--30816 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
30751 ATTTCTGTAC
*
30761 TTATTAAAACATATATGGTTAGTGTTTA
1 TTATTAAAACATATATGGTTAGTGTTGA
* *
30789 TTATTTAAA-ATATAT-TTTAG-GTTGA
1 TTATTAAAACATATATGGTTAGTGTTGA
30814 TTA
1 TTA
30817 ATCAATATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 7 0.28
26 4 0.16
27 6 0.24
28 8 0.32
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (28 bp):
TTATTAAAACATATATGGTTAGTGTTGA
Found at i:31765 original size:27 final size:29
Alignment explanation
Indices: 31707--31765 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
31697 ATTTATGTAC
*
31707 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
31736 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
31763 TTA
1 TTA
31766 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:32174 original size:951 final size:937
Alignment explanation
Indices: 30478--32375 Score: 3320
Period size: 951 Copynumber: 2.0 Consensus size: 937
30468 GCCAACTAAG
*
30478 TATTTTGATTCAATGATGCTTTTGTTATAAAAGGGAAAGACTCACTTTTCAATTTAAAGTACTTG
1 TATTTTGATTCAATGATGCTTTTGTTATAAAAGGGAAAGACTCACATTTCAATTTAAAGTACTTG
30543 TGTTCCATAGTAAGCAAGAATTATTTGAAATACAAAAAAATATGAAAGAATGTTGGTCTTAACAT
66 TGTTCCATAGTAAGCAAGAATTATTTGAAATACAAAAAAATATGAAAGAATGTTGGTCTTAACAT
30608 TTTTTCCCATATTATTTAACTAACTCGACGTTTGTAGTTTGATTTGTTTTAATAAACACAATTTT
131 TTTTTCCCATATTATTTAACTAACTCGACGTTTGTAGTTTGATTTGTTTTAATAAACACAATTTT
30673 TAACAAATAAATTATGTTTGTGATACAACGATTTACAAAATACGTTAACTTTTTTGTTCACCAAA
196 TAACAAATAAATTATGTTTGTGATACAACGATTTACAAAATACGTTAACTTTTTTGTTCACCAAA
*
30738 AGATTTAGTTTTAATTTCTGTACTTATTAAAACATATATGGTTAGTGTTTATTATTTAAAATATA
261 AGATTTAGTTTTAATTTATGTACTTATTAAAACATATATGGTTAGTGTTTATTATTTAAAATATA
30803 TTTTAGGTTGATTAATCAATATCAGACCAATGGAAAACCTATTAAAGGATCATTGAAACACTTCA
326 TTTTAGGTTGATTAATCAATATCAGACCAATGGAAAACCTATTAAAGGATCATTGAAACACTTCA
* *
30868 AAATAATTTTTTTGTAAAATAACTATTTCAATTCGAATTATTCAAATTGAGCGTAAAGTATTAAA
391 AAATAATTTTTTTGTAAAATAACTATTTCAATTCGAATTATTCAAATTGAGAGTAAAATATTAAA
* * *
30933 AATGGAAATTTTAAATACTAAAAGTTATTGACAGCTTTAAGCTTTTCTAATATTTAAATTAATTT
456 AATGGAAATTTTAAAAACTAAAAGTTATTGACAACTTTAAGCTTTTCTAATATTGAAATTAATTT
* *
30998 GCTTCCTAGACGATAAAATCATAATAATCGTTCTCGATATGACTGAAGGTCAAGATTAGTAAAGC
521 GCTTCCTAGAC-AT--AA-CATAATAATCGTTCTCAATATGACTGAAGCTCAAGATTAGTAAAGC
31063 ACGTTGGAATGAAAAGATAACATACATCTCATCTTATCCTGATAATAAAAGTTAAGTTAAGAGAA
582 ACGTTGGAATGAAAAGATAACATACATCTCATCTTATCCTGATAATAAAAGTTAAGTTAAGAGAA
* *
31128 AACAAAGTTTACTGATATAACGAGTTCCAATAACAATATATATAGGAATGCAGTATCTTATTTAG
647 AACAAAGTTTACTGATATAACGAGTTCCAATAACAATATATATAGCAATACAGTATCTTATTTAG
31193 AACTACTAAATTGACAATTCAAGTAAGTTCATCTTATATTCAAGTTTCCTTTACTATTTAAGATG
712 AACTACTAAATTGACAATTCAAGTAAGTTCATCTTATATTCAAGTTTCCTTTACTATTTAAGATG
* *
31258 AATTGGTTTCAAGTTTTAAAGTTCAAATTATAATTTTAATGAGGAAGATATGTTAA-TTTTACAA
777 AATTGGTTTCAAATTTTAAAGCTCAAATTATAATTTTAATGAGGAAGATATGTTAATTTTTACAA
* *
31322 TTAGTTCTAAATATAACTAAACATACATGATTTTATGTTTCACATTGTTTTTGAACATTATGTGG
842 TTAGTTCTAAAAATAACTAAACATACATGA-TTTATGCTTCACATTGTTTTTGAACATTATG-GG
31387 CATATTTTAAAGAAAATAGG-ACCCTAAAGAGAC
905 CATATTTTAAAGAAAATAGGTA-CCTAAAGAGAC
31420 TATTTTGATTCAATGATGCTTTTGTTATAAAAGGGAAAGACTCACATTTCAATTTAAAGTACTTG
1 TATTTTGATTCAATGATGCTTTTGTTATAAAAGGGAAAGACTCACATTTCAATTTAAAGTACTTG
31485 TGTTCCATAGTAAGCAAGAATTATTTGAAATACAAAAAAAATATGAAAGAATGTTGGTCTTAACA
66 TGTTCCATAGTAAGCAAGAATTATTTGAAATAC-AAAAAAATATGAAAGAATGTTGGTCTTAACA
*
31550 TTTTTTCCCATATTATTTAACTAACTCGACGTTTGTTGTTTGATTTGTTTTAATAAACACAATTT
130 TTTTTTCCCATATTATTTAACTAACTCGACGTTTGTAGTTTGATTTGTTTTAATAAACACAATTT
*
31615 TTAACAAATAAATTATGTTTGTGATACAATGATTTATACAAAATACGTTAACTTTTTTGTTCACC
195 TTAACAAATAAATTATGTTTGTGATACAACGA-TT-TACAAAATACGTTAACTTTTTTGTTCACC
* *
31680 AATAGTTTCTAGTTTTAATTTATGTACTTATTAAAAACATATATGGTTAGTGTTTATTATTTAAA
258 AAAAGATT-TAGTTTTAATTTATGTACTTATT-AAAACATATATGGTTAGTGTTTATTATTT-AA
31745 ATATATATTTTAGGTTGATTAATCAATATCAGACCAATGGAAAACCTATTAAAGGATCATTGAAA
320 A-ATATATTTTAGGTTGATTAATCAATATCAGACCAATGGAAAACCTATTAAAGGATCATTGAAA
*
31810 CACTTCAAAATAATTTTTTTTGTAAAATAACTATTTCAATTCGCATTATTCAAATTGAGAGTAAA
384 CACTTCAAAATAA-TTTTTTTGTAAAATAACTATTTCAATTCGAATTATTCAAATTGAGAGTAAA
31875 ATATTAAAAAATGGAAATTTTAAAAACTAAAAAGTTATTGACAACTTTAAGCTTTTCTAATATTG
448 ATATT-AAAAATGGAAATTTTAAAAACT-AAAAGTTATTGACAACTTTAAGCTTTTCTAATATTG
* *
31940 AAATTAATTTTCTTCCTAGAC-T-A-GTAATAATCGTTCTCAATATGACTGAAGCTCAAGATTAG
511 AAATTAATTTGCTTCCTAGACATAACATAATAATCGTTCTCAATATGACTGAAGCTCAAGATTAG
*
32002 TAAAGCACGTTGGAATGAAAAGATAACATACATCTCATCTTGTCCTGATAATAAAAAGTTAAGTT
576 TAAAGCACGTTGGAATGAAAAGATAACATACATCTCATCTTATCCTGATAAT-AAAAGTTAAGTT
*
32067 AAGTTAAGAGATAACAAAGTTTACTGATATAACGAGTTCCAATAACAATATATATATCAATACAG
640 AAG---AGA-A-AACAAAGTTTACTGATATAACGAGTTCCAATAACAATATATATAGCAATACAG
32132 TATCTTATTTAGAACTACTAAATTGACAATTCAAGTAAGTTCATCTTATATTCAAGTTTCCTTTA
700 TATCTTATTTAGAACTACTAAATTGACAATTCAAGTAAGTTCATCTTATATTCAAGTTTCCTTTA
*
32197 CTATTTAAGATGAATTGGTTTCAAATTTTGAAGCTCAAATTATAATTTTAATGAGGAAGATATGT
765 CTATTTAAGATGAATTGGTTTCAAATTTTAAAGCTCAAATTATAATTTTAATGAGGAAGATATGT
32262 TAATTTTTACAATTAGTTCTAAAAATAACTAAACATACATGATTTATGCTTCACATTGTTTTTGA
830 TAATTTTTACAATTAGTTCTAAAAATAACTAAACATACATGATTTATGCTTCACATTGTTTTTGA
*
32327 ACATTATGGGCATATTTTAATGAAAATAGGTACCTAAAGAGAC
895 ACATTATGGGCATATTTTAAAGAAAATAGGTACCTAAAGAGAC
32370 TATTTT
1 TATTTT
32376 TGTTTGGCGA
Statistics
Matches: 912, Mismatches: 26, Indels: 28
0.94 0.03 0.03
Matches are distributed among these distances:
942 97 0.11
943 126 0.14
944 2 0.00
945 122 0.13
946 37 0.04
947 30 0.03
948 3 0.00
949 79 0.09
950 93 0.10
951 232 0.25
952 91 0.10
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (937 bp):
TATTTTGATTCAATGATGCTTTTGTTATAAAAGGGAAAGACTCACATTTCAATTTAAAGTACTTG
TGTTCCATAGTAAGCAAGAATTATTTGAAATACAAAAAAATATGAAAGAATGTTGGTCTTAACAT
TTTTTCCCATATTATTTAACTAACTCGACGTTTGTAGTTTGATTTGTTTTAATAAACACAATTTT
TAACAAATAAATTATGTTTGTGATACAACGATTTACAAAATACGTTAACTTTTTTGTTCACCAAA
AGATTTAGTTTTAATTTATGTACTTATTAAAACATATATGGTTAGTGTTTATTATTTAAAATATA
TTTTAGGTTGATTAATCAATATCAGACCAATGGAAAACCTATTAAAGGATCATTGAAACACTTCA
AAATAATTTTTTTGTAAAATAACTATTTCAATTCGAATTATTCAAATTGAGAGTAAAATATTAAA
AATGGAAATTTTAAAAACTAAAAGTTATTGACAACTTTAAGCTTTTCTAATATTGAAATTAATTT
GCTTCCTAGACATAACATAATAATCGTTCTCAATATGACTGAAGCTCAAGATTAGTAAAGCACGT
TGGAATGAAAAGATAACATACATCTCATCTTATCCTGATAATAAAAGTTAAGTTAAGAGAAAACA
AAGTTTACTGATATAACGAGTTCCAATAACAATATATATAGCAATACAGTATCTTATTTAGAACT
ACTAAATTGACAATTCAAGTAAGTTCATCTTATATTCAAGTTTCCTTTACTATTTAAGATGAATT
GGTTTCAAATTTTAAAGCTCAAATTATAATTTTAATGAGGAAGATATGTTAATTTTTACAATTAG
TTCTAAAAATAACTAAACATACATGATTTATGCTTCACATTGTTTTTGAACATTATGGGCATATT
TTAAAGAAAATAGGTACCTAAAGAGAC
Found at i:40749 original size:27 final size:29
Alignment explanation
Indices: 40694--40749 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
40684 TTCTGTACTT
*
40694 TTTAAAACATATATGGTTAGTGTTTATTA
1 TTTAAAACATATATGGTTAGTGTTGATTA
* *
40723 TTTAAAATATATAT-TTTAG-GTTGATTA
1 TTTAAAACATATATGGTTAGTGTTGATTA
40750 ATCAGTATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 7 0.29
28 4 0.17
29 13 0.54
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (29 bp):
TTTAAAACATATATGGTTAGTGTTGATTA
Found at i:45385 original size:27 final size:29
Alignment explanation
Indices: 45327--45385 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
45317 ATTTATGTAC
*
45327 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
45356 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
45383 TTA
1 TTA
45386 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:47756 original size:27 final size:29
Alignment explanation
Indices: 47698--47756 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
47688 ATTTCTGTAC
*
47698 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
47727 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
47754 TTA
1 TTA
47757 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:50031 original size:27 final size:29
Alignment explanation
Indices: 49973--50031 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
49963 ATTTATGTAC
*
49973 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
50002 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
50029 TTA
1 TTA
50032 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:55019 original size:10 final size:9
Alignment explanation
Indices: 54984--55063 Score: 70
Period size: 10 Copynumber: 8.3 Consensus size: 9
54974 GCTGCTGGAA
*
54984 ACCGGTTTA
1 ACCGGTTTG
*
54993 ACCGGTTTTCA
1 ACCGG-TTT-G
55004 ACCGGTTCTG
1 ACCGGTT-TG
55014 ACCGGTTTG
1 ACCGGTTTG
*
55023 ACCGGTTTCA
1 ACCGGTTT-G
*
55033 ACCGGTTCG
1 ACCGGTTTG
55042 AACCGGTTTG
1 -ACCGGTTTG
*
55052 ACCGGTCTG
1 ACCGGTTTG
55061 ACC
1 ACC
55064 CGACCCGACC
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
9 26 0.43
10 27 0.45
11 7 0.12
ACGTcount: A:0.16, C:0.29, G:0.26, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:55046 original size:29 final size:30
Alignment explanation
Indices: 54983--55057 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
54973 GGCTGCTGGA
*
54983 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
55014 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
55042 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
55058 CTGACCCGAC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.67
30 13 0.31
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:55081 original size:17 final size:17
Alignment explanation
Indices: 55059--55097 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
55049 TTGACCGGTC
55059 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
*
55076 TGACCCGACCCGACTGT
1 TGACCCGACCCGACCGT
55093 TGACC
1 TGACC
55098 ATTGACTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.44, G:0.23, T:0.15
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:62344 original size:20 final size:20
Alignment explanation
Indices: 62319--62363 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
62309 GGCTGCTGGA
62319 AACCGGTT-TAACCAGTTTTC
1 AACCGGTTCTAACCAG-TTTC
*
62339 AACCGGTTCTGACCAGTTTC
1 AACCGGTTCTAACCAGTTTC
62359 AACCG
1 AACCG
62364 ATTCGAACTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (20 bp):
AACCGGTTCTAACCAGTTTC
Found at i:62390 original size:19 final size:19
Alignment explanation
Indices: 62368--62407 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
62358 CAACCGATTC
*
62368 GAACTGGTTTGACCGGTCT
1 GAACCGGTTTGACCGGTCT
62387 GAACCGGTTTGACCGGTCT
1 GAACCGGTTTGACCGGTCT
62406 GA
1 GA
62408 CCCGACCGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.23, G:0.33, T:0.28
Consensus pattern (19 bp):
GAACCGGTTTGACCGGTCT
Found at i:62441 original size:22 final size:21
Alignment explanation
Indices: 62406--62447 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
62396 TGACCGGTCT
62406 GACCCGACCGACCGTTGACCC
1 GACCCGACCGACCGTTGACCC
62427 GACCCGACCCGACCGTTGACC
1 GACCCGA-CCGACCGTTGACC
62448 GTTGACTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.19, C:0.48, G:0.24, T:0.10
Consensus pattern (21 bp):
GACCCGACCGACCGTTGACCC
Found at i:64580 original size:27 final size:29
Alignment explanation
Indices: 64522--64580 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
64512 ATTTATGTAC
*
64522 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
64551 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
64578 TTA
1 TTA
64581 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:66962 original size:27 final size:29
Alignment explanation
Indices: 66904--66962 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
66894 ATTTATGTAC
*
66904 TTATTTAAAACATATATGGTTAGTGTTTA
1 TTATTTAAAACATATATGGTTAGTGTTGA
* *
66933 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTTAAAACATATATGGTTAGTGTTGA
66960 TTA
1 TTA
66963 ATCAATATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 7 0.26
28 4 0.15
29 16 0.59
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.51
Consensus pattern (29 bp):
TTATTTAAAACATATATGGTTAGTGTTGA
Found at i:69338 original size:27 final size:29
Alignment explanation
Indices: 69280--69338 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
69270 ATTTCTGTAC
*
69280 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
69309 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
69336 TTA
1 TTA
69339 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:71710 original size:27 final size:29
Alignment explanation
Indices: 71652--71710 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
71642 ATTTATGTAC
*
71652 TTATTTAAAACATATATGGTTAGTGTTTA
1 TTATTTAAAACATATATGGTTAGTGTTGA
* *
71681 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTTAAAACATATATGGTTAGTGTTGA
71708 TTA
1 TTA
71711 ATCAATATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 7 0.26
28 4 0.15
29 16 0.59
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.51
Consensus pattern (29 bp):
TTATTTAAAACATATATGGTTAGTGTTGA
Found at i:72019 original size:5 final size:5
Alignment explanation
Indices: 72009--72036 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
71999 TGATAATAAA
72009 AAGTT AAGTT AAGTT AAGTT AAGTT AAG
1 AAGTT AAGTT AAGTT AAGTT AAGTT AAG
72037 AGAAAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (5 bp):
AAGTT
Found at i:74099 original size:27 final size:29
Alignment explanation
Indices: 74041--74099 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
74031 ATTTATGTAC
*
74041 TTATTTAAAACATATATGGTTAGTGTTTA
1 TTATTTAAAACATATATGGTTAGTGTTGA
* *
74070 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTTAAAACATATATGGTTAGTGTTGA
74097 TTA
1 TTA
74100 ATCAATATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 7 0.26
28 4 0.15
29 16 0.59
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.51
Consensus pattern (29 bp):
TTATTTAAAACATATATGGTTAGTGTTGA
Found at i:77163 original size:20 final size:20
Alignment explanation
Indices: 77135--77177 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
77125 GCAGCTGGAA
*
77135 AACCGGTTTGACCTGTTTTG
1 AACCAGTTTGACCTGTTTTG
77155 AACCAGTTTGACCTGTTTTG
1 AACCAGTTTGACCTGTTTTG
77175 AAC
1 AAC
77178 TGGTCTGACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (20 bp):
AACCAGTTTGACCTGTTTTG
Found at i:77186 original size:20 final size:20
Alignment explanation
Indices: 77143--77187 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
77133 AAAACCGGTT
*
77143 TGACCTGTTTTGAACCAGTT
1 TGACCTGTTTTGAACCAGTC
**
77163 TGACCTGTTTTGAACTGGTC
1 TGACCTGTTTTGAACCAGTC
77183 TGACC
1 TGACC
77188 CGACCCGACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
TGACCTGTTTTGAACCAGTC
Found at i:84242 original size:5 final size:5
Alignment explanation
Indices: 84232--84263 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
84222 AACTGGTTTT
84232 GACCC GACCC GACCC GA--C GACCC GACCC GACC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACC
84264 GTTGACTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
3 3 0.12
5 22 0.88
ACGTcount: A:0.22, C:0.56, G:0.22, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:84254 original size:13 final size:13
Alignment explanation
Indices: 84236--84262 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
84226 GGTTTTGACC
84236 CGACCCGACCCGA
1 CGACCCGACCCGA
84249 CGACCCGACCCGA
1 CGACCCGACCCGA
84262 C
1 C
84263 CGTTGACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.56, G:0.22, T:0.00
Consensus pattern (13 bp):
CGACCCGACCCGA
Found at i:88268 original size:27 final size:29
Alignment explanation
Indices: 88210--88268 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
88200 ATTTCTGTAC
*
88210 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
88239 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
88266 TTA
1 TTA
88269 ATCAATATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Done.