Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003697.1 Hibiscus syriacus cultivar Beakdansim tig00007906_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: 129590
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2899 original size:20 final size:20
Alignment explanation
Indices: 2863--2910 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
2853 CAAAGTGACC
*
2863 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
2882 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
2902 TAATTTCAA
1 CAATTTCAA
2911 GCATAGTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:7976 original size:20 final size:20
Alignment explanation
Indices: 7933--7980 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
7923 CAAAGTGACC
* *
7933 CAATTTC-ACATTCTAGCAT
1 CAATTTCAACACTCTAACAT
7952 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
7972 TAATTTCAA
1 CAATTTCAA
7981 ACATAGTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:9376 original size:16 final size:16
Alignment explanation
Indices: 9353--9389 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
9343 GAAAAAAATG
*
9353 AGAAAATTTG-GAGAA
1 AGAAAAATTGAGAGAA
9368 AGAAAAATTGAGAGAA
1 AGAAAAATTGAGAGAA
9384 AGAAAA
1 AGAAAA
9390 GAGGATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (16 bp):
AGAAAAATTGAGAGAA
Found at i:13144 original size:20 final size:20
Alignment explanation
Indices: 13108--13155 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
13098 CAAAGTGACC
*
13108 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
13127 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
13147 TAATTTCAA
1 CAATTTCAA
13156 GCATAGTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:14737 original size:16 final size:16
Alignment explanation
Indices: 14714--14750 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
14704 GAAAAAAATG
*
14714 AGAAAATTTG-GAGAA
1 AGAAAAATTGAGAGAA
14729 AGAAAAATTGAGAGAA
1 AGAAAAATTGAGAGAA
14745 AGAAAA
1 AGAAAA
14751 GAGGATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (16 bp):
AGAAAAATTGAGAGAA
Found at i:14999 original size:2 final size:2
Alignment explanation
Indices: 14992--15021 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
14982 TAAATATAAC
14992 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
15022 TATGATTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16436 original size:49 final size:49
Alignment explanation
Indices: 16379--16490 Score: 224
Period size: 49 Copynumber: 2.3 Consensus size: 49
16369 GTTCTGTTGA
16379 ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
1 ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
16428 ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
1 ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
16477 ACAAAGAACTTGTT
1 ACAAAGAACTTGTT
16491 CTAACCGCTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 63 1.00
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.27
Consensus pattern (49 bp):
ACAAAGAACTTGTTATCAGAGTTATTCTACCAATTCAACAACTCAGAGC
Found at i:18551 original size:20 final size:20
Alignment explanation
Indices: 18515--18562 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
18505 CAAAGTGACC
*
18515 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
18534 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
18554 TAATTTCAA
1 CAATTTCAA
18563 GCATAGTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:23810 original size:20 final size:20
Alignment explanation
Indices: 23774--23821 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
23764 GAAAGTGACC
*
23774 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
23793 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
23813 TAATTTCAA
1 CAATTTCAA
23822 GCATAGTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:28092 original size:10 final size:10
Alignment explanation
Indices: 28077--28101 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28067 TATATATAAA
28077 AATTATTTTT
1 AATTATTTTT
28087 AATTATTTTT
1 AATTATTTTT
28097 AATTA
1 AATTA
28102 ATAATAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
AATTATTTTT
Found at i:29080 original size:20 final size:20
Alignment explanation
Indices: 29044--29091 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
29034 CGAAGTGACC
*
29044 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
29063 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
29083 TAATTTCAA
1 CAATTTCAA
29092 GCATAGTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:30677 original size:16 final size:16
Alignment explanation
Indices: 30654--30690 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
30644 AAAAAAAATG
*
30654 AGAAAATTTG-GAGAA
1 AGAAAAATTGAGAGAA
30669 AGAAAAATTGAGAGAA
1 AGAAAAATTGAGAGAA
30685 AGAAAA
1 AGAAAA
30691 GAGGATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (16 bp):
AGAAAAATTGAGAGAA
Found at i:31846 original size:23 final size:23
Alignment explanation
Indices: 31819--31874 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
31809 CTATAATTAA
31819 ATAAACAAATATTGGAACATGAC
1 ATAAACAAATATTGGAACATGAC
31842 ATAAACAAATATTGGAACATGAC
1 ATAAACAAATATTGGAACATGAC
31865 ATAAACAAAT
1 ATAAACAAAT
31875 TGCTAAAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.55, C:0.12, G:0.11, T:0.21
Consensus pattern (23 bp):
ATAAACAAATATTGGAACATGAC
Found at i:34228 original size:19 final size:20
Alignment explanation
Indices: 34204--34250 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
34194 CAAAGTGACC
*
34204 CAATTTCA-CATTCTAACAT
1 CAATTTCATCACTCTAACAT
34223 CAATTTCATCACTCTAACAT
1 CAATTTCATCACTCTAACAT
*
34243 TAATTTCA
1 CAATTTCA
34251 AGCATAGTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.36, C:0.26, G:0.00, T:0.38
Consensus pattern (20 bp):
CAATTTCATCACTCTAACAT
Found at i:35837 original size:16 final size:16
Alignment explanation
Indices: 35814--35850 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
35804 GAAAAAAATG
*
35814 AGAAAATTTG-GAGAA
1 AGAAAAATTGAGAGAA
35829 AGAAAAATTGAGAGAA
1 AGAAAAATTGAGAGAA
35845 AGAAAA
1 AGAAAA
35851 GAGGATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (16 bp):
AGAAAAATTGAGAGAA
Found at i:36341 original size:13 final size:13
Alignment explanation
Indices: 36323--36351 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
36313 ATATAGGGGT
36323 TTTAATATATAAA
1 TTTAATATATAAA
36336 TTTAATATATAAA
1 TTTAATATATAAA
36349 TTT
1 TTT
36352 CGATATAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTAATATATAAA
Found at i:38704 original size:20 final size:20
Alignment explanation
Indices: 38669--38715 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
38659 AAAGTGACCC
*
38669 AATTTC-ACATTCTAACATA
1 AATTTCAACACTCTAACATA
*
38688 AATTTCAACACTCTAACATT
1 AATTTCAACACTCTAACATA
38708 AATTTCAA
1 AATTTCAA
38716 GCATAGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTTCAACACTCTAACATA
Found at i:40492 original size:2 final size:2
Alignment explanation
Indices: 40485--40542 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
40475 TAAATATAAC
40485 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
40527 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
40543 GTAACCCCTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42122 original size:5 final size:5
Alignment explanation
Indices: 42112--42164 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
42102 AACGGTCAAC
* *
42112 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
42161 GGTC
1 GGTC
42165 AGACCCGGTC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:42127 original size:17 final size:17
Alignment explanation
Indices: 42105--42165 Score: 77
Period size: 17 Copynumber: 3.3 Consensus size: 17
42095 AACGGTCAAC
42105 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
42122 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAA----C-GGTCGGGTCG
42144 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
42161 GGTCA
1 GGTCA
42166 GACCCGGTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 21 0.54
18 1 0.03
21 1 0.03
22 16 0.41
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:42132 original size:7 final size:7
Alignment explanation
Indices: 42078--42115 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
42068 GTCAAAGAAA
42078 GTCAACG
1 GTCAACG
42085 GTCAACG
1 GTCAACG
42092 GTCAACG
1 GTCAACG
42099 GTCAACG
1 GTCAACG
42106 GTCAACG
1 GTCAACG
42113 GTC
1 GTC
42116 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:42140 original size:22 final size:22
Alignment explanation
Indices: 42098--42164 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
42088 AACGGTCAAC
*
42098 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCG
42122 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
42144 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
42165 AGACCCGGTC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
22 31 0.74
24 11 0.26
ACGTcount: A:0.12, C:0.24, G:0.46, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:42174 original size:10 final size:10
Alignment explanation
Indices: 42161--42211 Score: 63
Period size: 10 Copynumber: 5.3 Consensus size: 10
42151 GGTCGGGTCG
*
42161 GGTCAGACCC
1 GGTCAGAACC
42171 GGTCA-AACC
1 GGTCAGAACC
42180 GAGTCAG-ACC
1 G-GTCAGAACC
42190 GGTCA-AACC
1 GGTCAGAACC
42199 GGTCAGAACC
1 GGTCAGAACC
42209 GGT
1 GGT
42212 TGAAAACCGG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
9 16 0.44
10 20 0.56
ACGTcount: A:0.27, C:0.31, G:0.29, T:0.12
Consensus pattern (10 bp):
GGTCAGAACC
Found at i:42193 original size:19 final size:18
Alignment explanation
Indices: 42161--42211 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 18
42151 GGTCGGGTCG
42161 GGTCAGACCCGGTCAAACC
1 GGTCAGA-CCGGTCAAACC
42180 GAGTCAGACCGGTCAAACC
1 G-GTCAGACCGGTCAAACC
42199 GGTCAGAACCGGT
1 GGTCAG-ACCGGT
42212 TGAAAACCGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.17
19 19 0.63
20 6 0.20
ACGTcount: A:0.27, C:0.31, G:0.29, T:0.12
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:42199 original size:9 final size:9
Alignment explanation
Indices: 42169--42231 Score: 63
Period size: 9 Copynumber: 6.6 Consensus size: 9
42159 CGGGTCAGAC
42169 CCGGTCAAA
1 CCGGTCAAA
*
42178 CCGAGTCAGA
1 CCG-GTCAAA
42188 CCGGTCAAA
1 CCGGTCAAA
42197 CCGGTCAGAA
1 CCGGTCA-AA
*
42207 CCGGTTGAAAA
1 CCGG-T-CAAA
*
42218 CCGGTTAAA
1 CCGGTCAAA
42227 CCGGT
1 CCGGT
42232 TTCCAGCAGC
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
9 23 0.50
10 15 0.33
11 7 0.15
12 1 0.02
ACGTcount: A:0.30, C:0.29, G:0.27, T:0.14
Consensus pattern (9 bp):
CCGGTCAAA
Found at i:42230 original size:20 final size:21
Alignment explanation
Indices: 42194--42232 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
42184 CAGACCGGTC
42194 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
*
42215 AAACCGGTTA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
42233 TCCAGCAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:48476 original size:32 final size:31
Alignment explanation
Indices: 48440--48516 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
48430 CGGGGCCGTG
*
48440 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
48472 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
48503 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
48517 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:48499 original size:63 final size:63
Alignment explanation
Indices: 48393--48516 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
48383 CCCTAAGGGA
* * ** *
48393 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
48456 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
48517 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:49423 original size:5 final size:5
Alignment explanation
Indices: 49413--49465 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
49403 AACGGTCAAC
* *
49413 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
49462 GGTC
1 GGTC
49466 AGACCGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:49428 original size:17 final size:17
Alignment explanation
Indices: 49406--49466 Score: 77
Period size: 17 Copynumber: 3.3 Consensus size: 17
49396 AACGGTCAAC
49406 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
49423 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAA----C-GGTCGGGTCG
49445 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
49462 GGTCA
1 GGTCA
49467 GACCGGTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 21 0.54
18 1 0.03
21 1 0.03
22 16 0.41
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:49433 original size:7 final size:7
Alignment explanation
Indices: 49386--49416 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
49376 GTCAAAGAAA
49386 GTCAACG
1 GTCAACG
49393 GTCAACG
1 GTCAACG
49400 GTCAACG
1 GTCAACG
49407 GTCAACG
1 GTCAACG
49414 GTC
1 GTC
49417 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:49441 original size:22 final size:22
Alignment explanation
Indices: 49399--49465 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
49389 AACGGTCAAC
*
49399 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCG
49423 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
49445 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
49466 AGACCGGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
22 31 0.74
24 11 0.26
ACGTcount: A:0.12, C:0.24, G:0.46, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:49480 original size:9 final size:9
Alignment explanation
Indices: 49462--49580 Score: 94
Period size: 9 Copynumber: 12.3 Consensus size: 9
49452 GGTCGGGTCG
*
49462 GGTCAGACC
1 GGTCAAACC
49471 GGTCAAACC
1 GGTCAAACC
*
49480 GAGTCAGACC
1 G-GTCAAACC
49490 GGTCAAACC
1 GGTCAAACC
*
49499 GGTTCGAACC
1 GG-TCAAACC
*
49509 GGTTGAAACC
1 GG-TCAAACC
49519 GGTCAAACC
1 GGTCAAACC
49528 GGTCAGAACC
1 GGTCA-AACC
*
49538 GGTTGAAAACC
1 GG-T-CAAACC
*
49549 GGTTAAACC
1 GGTCAAACC
*
49558 GGTTGAAAACC
1 GG-T-CAAACC
*
49569 GGTTAAACC
1 GGTCAAACC
49578 GGT
1 GGT
49581 TTCCAGCAGC
Statistics
Matches: 92, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
9 44 0.48
10 33 0.36
11 14 0.15
12 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.28, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:49485 original size:19 final size:18
Alignment explanation
Indices: 49462--49540 Score: 88
Period size: 19 Copynumber: 4.2 Consensus size: 18
49452 GGTCGGGTCG
49462 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
49480 GAGTCAGACCGGTCAAACC
1 G-GTCAGACCGGTCAAACC
*
49499 GGTTC-GAACCGGTTGAAACC
1 GG-TCAG-ACCGG-TCAAACC
*
49519 GGTCAAACCGGTCAGAACC
1 GGTCAGACCGGTCA-AACC
49538 GGT
1 GGT
49541 TGAAAACCGG
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
18 5 0.10
19 39 0.75
20 8 0.15
ACGTcount: A:0.28, C:0.29, G:0.29, T:0.14
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:49519 original size:20 final size:19
Alignment explanation
Indices: 49487--49581 Score: 104
Period size: 20 Copynumber: 4.8 Consensus size: 19
49477 ACCGAGTCAG
*
49487 ACCGGTCAAACCGGTTCG-A
1 ACCGGTTAAACCGGTT-GAA
*
49506 ACCGGTTGAAACCGG-TCAA
1 ACCGGTT-AAACCGGTTGAA
*
49525 ACCGGTCAGAACCGGTTGAAA
1 ACCGGTTA-AACCGGTTG-AA
49546 ACCGGTTAAACCGGTTGAAA
1 ACCGGTTAAACCGGTTG-AA
49566 ACCGGTTAAACCGGTT
1 ACCGGTTAAACCGGTT
49582 TCCAGCAGCC
Statistics
Matches: 66, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
18 1 0.02
19 20 0.30
20 36 0.55
21 9 0.14
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.18
Consensus pattern (19 bp):
ACCGGTTAAACCGGTTGAA
Found at i:49519 original size:29 final size:29
Alignment explanation
Indices: 49487--49580 Score: 122
Period size: 29 Copynumber: 3.2 Consensus size: 29
49477 ACCGAGTCAG
49487 ACCGGTCAAACCGGTTCGAACCGGTTGAA
1 ACCGGTCAAACCGGTTCGAACCGGTTGAA
49516 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
*
49546 ACCGGTTAAACCGGTT-GAAAACCGGTT-AA
1 ACCGGTCAAACCGGTTCG--AACCGGTTGAA
49575 ACCGGT
1 ACCGGT
49581 TTCCAGCAGC
Statistics
Matches: 59, Mismatches: 1, Indels: 10
0.84 0.01 0.14
Matches are distributed among these distances:
28 2 0.03
29 33 0.56
30 15 0.25
31 9 0.15
ACGTcount: A:0.31, C:0.26, G:0.27, T:0.17
Consensus pattern (29 bp):
ACCGGTCAAACCGGTTCGAACCGGTTGAA
Found at i:53692 original size:20 final size:20
Alignment explanation
Indices: 53649--53696 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
53639 CAAAGTGCCC
*
53649 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
*
53668 CAATTTCAACACTCTAGCAT
1 CAATTTCAACACTCTAACAT
*
53688 TAATTTCAA
1 CAATTTCAA
53697 GCATAGTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:62848 original size:31 final size:31
Alignment explanation
Indices: 62813--62887 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
62803 CTAATGTGAC
*
62813 TCTTGGGTAGGATCTT-CGACCTCGAGATCAT
1 TCTTGGGTAGG-CCTTGCGACCTCGAGATCAT
* * **
62844 TCTTGGGTAGGCCTTGCGACCTTGGGATTTT
1 TCTTGGGTAGGCCTTGCGACCTCGAGATCAT
62875 TCTTGGGTAGGCC
1 TCTTGGGTAGGCC
62888 CCGTGGCCTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
30 3 0.08
31 35 0.92
ACGTcount: A:0.13, C:0.21, G:0.31, T:0.35
Consensus pattern (31 bp):
TCTTGGGTAGGCCTTGCGACCTCGAGATCAT
Found at i:62923 original size:23 final size:23
Alignment explanation
Indices: 62892--62944 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
62882 TAGGCCCCGT
*
62892 GGCCTTGAGATCATTATTGAATA
1 GGCCCTGAGATCATTATTGAATA
* * **
62915 GGCCCTGAGATCTTTCTTGGGTA
1 GGCCCTGAGATCATTATTGAATA
62938 GGCCCTG
1 GGCCCTG
62945 TGGCCCTGAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.32
Consensus pattern (23 bp):
GGCCCTGAGATCATTATTGAATA
Found at i:62981 original size:31 final size:31
Alignment explanation
Indices: 62914--62982 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
62904 ATTATTGAAT
* *
62914 AGGCCCTGAGATCTTTCTTGGGTAGGCCCTG
1 AGGCCCTGAGAACTTTCTTGGGTAGGCCCTC
* *
62945 TGGCCCTGAGAACTTTCTTGGGTAGGCTCTC
1 AGGCCCTGAGAACTTTCTTGGGTAGGCCCTC
62976 AGGCCCT
1 AGGCCCT
62983 AAGATGCTCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.13, C:0.28, G:0.30, T:0.29
Consensus pattern (31 bp):
AGGCCCTGAGAACTTTCTTGGGTAGGCCCTC
Found at i:64000 original size:20 final size:20
Alignment explanation
Indices: 63975--64014 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
63965 ATAGCGTGTA
*
63975 TGGTTAAAATATAACAGATT
1 TGGTTAAAATAGAACAGATT
63995 TGGTTAAAATAGAACAGATT
1 TGGTTAAAATAGAACAGATT
64015 CAGCTTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.05, G:0.17, T:0.33
Consensus pattern (20 bp):
TGGTTAAAATAGAACAGATT
Found at i:67260 original size:16 final size:16
Alignment explanation
Indices: 67237--67273 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
67227 AGAAAAAATG
*
67237 AGAAAATTTG-GAGAA
1 AGAAAAATTGAGAGAA
67252 AGAAAAATTGAGAGAA
1 AGAAAAATTGAGAGAA
67268 AGAAAA
1 AGAAAA
67274 GAGGAGTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (16 bp):
AGAAAAATTGAGAGAA
Found at i:73819 original size:19 final size:20
Alignment explanation
Indices: 73795--73838 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
73785 AAGTGGCCCG
*
73795 ATTTC-ACATTCTAACATCA
1 ATTTCAACACTCTAACATCA
*
73814 ATTTCAACACTCTAACATTA
1 ATTTCAACACTCTAACATCA
73834 ATTTC
1 ATTTC
73839 CAATATAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTTCAACACTCTAACATCA
Found at i:75410 original size:16 final size:16
Alignment explanation
Indices: 75389--75425 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
75379 GAAAACAATG
*
75389 AGAAAATTTG-GAGAA
1 AGAAAAATTGAGAGAA
75404 AGAAAAATTGAGAGAA
1 AGAAAAATTGAGAGAA
75420 AGAAAA
1 AGAAAA
75426 GAGGAGTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (16 bp):
AGAAAAATTGAGAGAA
Found at i:77650 original size:36 final size:35
Alignment explanation
Indices: 77605--77675 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 35
77595 TGGCAACTAA
77605 CTTTGAAAAATGTTTTTCAAAGTTTAGTAAATGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTAGTAAA-GTTT
*
77641 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAAGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTAGTAAAGTTT
77676 GGTAGATGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 4 0.12
36 30 0.88
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.46
Consensus pattern (35 bp):
CTTTGAAAAATGTTTTTCAAAGTTTAGTAAAGTTT
Found at i:78493 original size:12 final size:12
Alignment explanation
Indices: 78476--78503 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
78466 GGAAAAGACC
78476 ATGGCGGGTCTT
1 ATGGCGGGTCTT
78488 ATGGCGGGTCTT
1 ATGGCGGGTCTT
78500 ATGG
1 ATGG
78504 TAGCTCTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.11, C:0.14, G:0.43, T:0.32
Consensus pattern (12 bp):
ATGGCGGGTCTT
Found at i:82232 original size:21 final size:21
Alignment explanation
Indices: 82208--82268 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
82198 GGCAACCAAC
82208 TTTGAAAAATGTTTTTCAAAG
1 TTTGAAAAATGTTTTTCAAAG
**
82229 TTTGGTAAATG--TTTC----
1 TTTGAAAAATGTTTTTCAAAG
82244 TTTGAAAAATGTTTTTCAAAG
1 TTTGAAAAATGTTTTTCAAAG
82265 TTTG
1 TTTG
82269 GTAAAGTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
15 9 0.30
17 4 0.13
19 4 0.13
21 13 0.43
ACGTcount: A:0.31, C:0.05, G:0.16, T:0.48
Consensus pattern (21 bp):
TTTGAAAAATGTTTTTCAAAG
Found at i:82253 original size:36 final size:35
Alignment explanation
Indices: 82207--82277 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 35
82197 TGGCAACCAA
82207 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAA-GTTT
82243 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAAGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAAGTTT
82278 GGTAGATGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 4 0.11
36 31 0.89
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (35 bp):
CTTTGAAAAATGTTTTTCAAAGTTTGGTAAAGTTT
Found at i:84129 original size:19 final size:20
Alignment explanation
Indices: 84105--84148 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
84095 AAGTTGTCCG
*
84105 ATTTC-ACATTCTAAAATCA
1 ATTTCAACACTCTAAAATCA
* *
84124 ATTTCAACACTCTAACATTA
1 ATTTCAACACTCTAAAATCA
84144 ATTTC
1 ATTTC
84149 CAGCTTAGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTTCAACACTCTAAAATCA
Found at i:91800 original size:18 final size:18
Alignment explanation
Indices: 91779--91813 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
91769 ATAGCGTGTA
91779 TGGTTAAAATAGAACATT
1 TGGTTAAAATAGAACATT
91797 TGGTTAAAATAGAACAT
1 TGGTTAAAATAGAACAT
91814 ATTCAGCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.06, G:0.17, T:0.31
Consensus pattern (18 bp):
TGGTTAAAATAGAACATT
Found at i:113566 original size:20 final size:20
Alignment explanation
Indices: 113541--113621 Score: 90
Period size: 20 Copynumber: 4.0 Consensus size: 20
113531 GAAATTATTA
*
113541 TAAAGCCTTCGGGTCATTTG
1 TAAAGCCTTTGGGTCATTTG
* *
113561 TAAAGCCTTTAGGTTATTTG
1 TAAAGCCTTTGGGTCATTTG
* ** *
113581 TAAAACCTTTGCATAATTTG
1 TAAAGCCTTTGGGTCATTTG
*
113601 TAAATCCTTTGGGTCATTTG
1 TAAAGCCTTTGGGTCATTTG
113621 T
1 T
113622 CAGTCATTCA
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.42
Consensus pattern (20 bp):
TAAAGCCTTTGGGTCATTTG
Found at i:118190 original size:20 final size:20
Alignment explanation
Indices: 118165--118204 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
118155 ATAGCGTGCA
118165 TGGTTAAAATAGAACAGATT
1 TGGTTAAAATAGAACAGATT
118185 TGGTTAAAATAGAACAGATT
1 TGGTTAAAATAGAACAGATT
118205 CAGCTTATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (20 bp):
TGGTTAAAATAGAACAGATT
Found at i:119059 original size:13 final size:13
Alignment explanation
Indices: 119043--119070 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
119033 ACATTAAACC
119043 AGTTTTATAAATT
1 AGTTTTATAAATT
119056 AGTTTTATAAATT
1 AGTTTTATAAATT
119069 AG
1 AG
119071 CTTAATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (13 bp):
AGTTTTATAAATT
Found at i:124909 original size:20 final size:21
Alignment explanation
Indices: 124884--124923 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
124874 AATTTCATAT
124884 TCTAACATCAATTT-CAACAC
1 TCTAACATCAATTTCCAACAC
*
124904 TCTAACATTAATTTCCAACA
1 TCTAACATCAATTTCCAACA
124924 TGGTACATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.33
Consensus pattern (21 bp):
TCTAACATCAATTTCCAACAC
Found at i:127800 original size:31 final size:31
Alignment explanation
Indices: 127765--127834 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
127755 TAGGTTCTGC
* **
127765 GGCCCTGAGATCATTCTCGGGTAGGCCCTGT
1 GGCCCTGAGATCATTCTCAGGTAGGCCCCAT
* ** *
127796 GGCCCTGTGATTTTTCTTAGGTAGGCCCCAT
1 GGCCCTGAGATCATTCTCAGGTAGGCCCCAT
127827 GGCCCTGA
1 GGCCCTGA
127835 AACTTTCTTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.13, C:0.29, G:0.30, T:0.29
Consensus pattern (31 bp):
GGCCCTGAGATCATTCTCAGGTAGGCCCCAT
Done.