Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008669.1 Hibiscus syriacus cultivar Beakdansim tig00111676_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: 41776
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.29
Found at i:374 original size:15 final size:15
Alignment explanation
Indices: 322--378 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
312 AAGGTTTGTT
*
322 TCAAGGGAAACTGTC
1 TCAAGAGAAACTGTC
* *
337 TCAAGATAACGAAATTGTT
1 TCAAG---A-GAAACTGTC
356 TCAAGAGAAACTGTC
1 TCAAGAGAAACTGTC
371 TCAAGAGA
1 TCAAGAGA
379 GACAAACTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 20 0.61
16 1 0.03
19 12 0.36
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (15 bp):
TCAAGAGAAACTGTC
Found at i:408 original size:36 final size:36
Alignment explanation
Indices: 316--587 Score: 268
Period size: 36 Copynumber: 7.9 Consensus size: 36
306 AATTCAAAGG
* *
316 TTTGTTTCAAGGGAAACTGTCTCAAGATA-ACGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
351 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* * * * *
385 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* *
422 -TTGTTTCAA-AGAAAACATAT-TC-----A-A--ATA
1 TTTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACGAAA
* *
449 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* * *
485 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
*
521 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
*
557 TTTGTTTCAAGGGAAACTGTCTC-AGAGAGAC
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
588 AAAACTCTTC
Statistics
Matches: 197, Mismatches: 23, Indels: 34
0.78 0.09 0.13
Matches are distributed among these distances:
27 3 0.02
28 15 0.08
29 2 0.01
30 1 0.01
33 1 0.01
34 32 0.16
35 23 0.12
36 118 0.60
37 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
Found at i:471 original size:99 final size:101
Alignment explanation
Indices: 351--536 Score: 270
Period size: 99 Copynumber: 1.9 Consensus size: 101
341 GATAACGAAA
*
351 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAACTTAGTTCCAAAAGAAACTGTCTCAAGGGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA-TTCCAAAAGAAACTGTCTCAAGAGA
*
415 GACGGAA-TTGTTTCAA-AGAAAACATATTCAAATAT
65 GACGAAATTTGTTTCAAGAGAAAACATATTCAAATAT
* * * ** *
450 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAG
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGAG
515 ACGAAATTTGTTTCAAGAGAAA
66 ACGAAATTTGTTTCAAGAGAAA
537 CTGTCTCAAG
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
99 56 0.74
100 15 0.20
101 5 0.07
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (101 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGAG
ACGAAATTTGTTTCAAGAGAAAACATATTCAAATAT
Found at i:1093 original size:18 final size:18
Alignment explanation
Indices: 1066--1101 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1056 TGTTGAATCC
* *
1066 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
1084 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
1102 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:1540 original size:22 final size:22
Alignment explanation
Indices: 1514--1562 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1504 TTGTGTTTGG
* *
1514 TCAAAGGTTTGGCATTTGATGA
1 TCAAAGGTTTGACATTGGATGA
*
1536 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGA
1558 TCAAA
1 TCAAA
1563 AGATTGATGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGA
Found at i:1569 original size:22 final size:22
Alignment explanation
Indices: 1526--1569 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1516 AAAGGTTTGG
* * *
1526 CATTTGATGATCAAAGGTTTGA
1 CATTGGATGATCAAAAGATTGA
*
1548 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGATCAAAAGATTGA
1570 TGGGGTAGCT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGATCAAAAGATTGA
Found at i:2218 original size:8 final size:8
Alignment explanation
Indices: 2207--2289 Score: 55
Period size: 8 Copynumber: 10.2 Consensus size: 8
2197 TCTTTTTGAT
*
2207 TTTTGCTC
1 TTTTGTTC
*
2215 TTTTTTTC
1 TTTTGTTC
2223 TTTTGTTC
1 TTTTGTTC
*
2231 TTGT-TTC
1 TTTTGTTC
2238 TTTTGTTTC
1 TTTTG-TTC
* *
2247 TTTGTTTTT
1 TTT-TGTTC
2256 TTTTGCTT-
1 TTTTG-TTC
2264 TTTTGCTTC
1 TTTTG-TTC
*
2273 TTTTCTT-
1 TTTTGTTC
2280 TTTTGTTC
1 TTTTGTTC
2288 TT
1 TT
2290 GATTGGATCT
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
7 12 0.20
8 29 0.49
9 17 0.29
10 1 0.02
ACGTcount: A:0.00, C:0.13, G:0.10, T:0.77
Consensus pattern (8 bp):
TTTTGTTC
Found at i:2227 original size:23 final size:23
Alignment explanation
Indices: 2194--2249 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
2184 TTTTTGTCCC
*
2194 TTTTCTTTTTGATTTTTG-CTCTTT
1 TTTTC-TTTTG-TTCTTGTCTCTTT
*
2218 TTTTCTTTTGTTCTTGTTTCTTT
1 TTTTCTTTTGTTCTTGTCTCTTT
2241 TGTTTCTTT
1 T-TTTCTTT
2250 GTTTTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 5 0.18
23 11 0.39
24 12 0.43
ACGTcount: A:0.02, C:0.12, G:0.09, T:0.77
Consensus pattern (23 bp):
TTTTCTTTTGTTCTTGTCTCTTT
Found at i:2237 original size:15 final size:17
Alignment explanation
Indices: 2213--2286 Score: 66
Period size: 16 Copynumber: 4.5 Consensus size: 17
2203 TGATTTTTGC
*
2213 TCTTTTTTTCTTTTG-T
1 TCTTTGTTTCTTTTGTT
2229 TC-TTGTTTCTTTTGTT
1 TCTTTGTTTCTTTTGTT
*
2245 TCTTTGTTTTTTTTTGCTT
1 TCTTTG-TTTCTTTTG-TT
* *
2264 T-TTTGCTTCTTTTCTT
1 TCTTTGTTTCTTTTGTT
2280 T-TTTGTT
1 TCTTTGTT
2287 CTTGATTGGA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
15 11 0.23
16 13 0.27
17 9 0.19
18 12 0.25
19 3 0.06
ACGTcount: A:0.00, C:0.12, G:0.09, T:0.78
Consensus pattern (17 bp):
TCTTTGTTTCTTTTGTT
Found at i:6959 original size:17 final size:16
Alignment explanation
Indices: 6933--6966 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6923 ATATAAAAAC
*
6933 ATAAATATAGGATAAAT
1 ATAAAAATA-GATAAAT
6950 ATAAAAATAGATAAAT
1 ATAAAAATAGATAAAT
6966 A
1 A
6967 AATGAGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (16 bp):
ATAAAAATAGATAAAT
Found at i:7582 original size:37 final size:36
Alignment explanation
Indices: 7539--7640 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
7529 ATAGTAGAAC
7539 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
7576 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
*
7610 TCTATCATATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
7641 TAGGACGAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
34 32 0.53
37 28 0.47
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:7692 original size:2 final size:2
Alignment explanation
Indices: 7685--7709 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7675 TTGTAAATAC
7685 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
7710 GAGAGAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8123 original size:12 final size:12
Alignment explanation
Indices: 8098--8136 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
8088 AATATATGGG
8098 TTTTTAAAATTTA
1 TTTTTAAAA-TTA
8111 TTTTTAAAATTA
1 TTTTTAAAATTA
* *
8123 TATTTAAAACTA
1 TTTTTAAAATTA
8135 TT
1 TT
8137 AGAAAAAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTTTAAAATTA
Found at i:8126 original size:14 final size:13
Alignment explanation
Indices: 8098--8131 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
8088 AATATATGGG
8098 TTTTTAAAATTTA
1 TTTTTAAAATTTA
8111 TTTTTAAAA-TTA
1 TTTTTAAAATTTA
*
8123 TATTTAAAA
1 TTTTTAAAA
8132 CTATTAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTTAAAATTTA
Found at i:9787 original size:42 final size:42
Alignment explanation
Indices: 9740--9823 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
9730 AGGAAATTAT
9740 CCAAAATATGTATTTAGTTTTTGGTTATAATTTTGAATATTC
1 CCAAAATATGTATTTAGTTTTTGGTTATAATTTTGAATATTC
*
9782 CCAAAATATGTATTTAGTTTTTTGTTATAATTTTGAATATTC
1 CCAAAATATGTATTTAGTTTTTGGTTATAATTTTGAATATTC
9824 TTATTTTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.31, C:0.07, G:0.11, T:0.51
Consensus pattern (42 bp):
CCAAAATATGTATTTAGTTTTTGGTTATAATTTTGAATATTC
Found at i:14882 original size:32 final size:31
Alignment explanation
Indices: 14846--14922 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
14836 CGGGGCCGTG
*
14846 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
14878 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
14909 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
14923 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:14905 original size:63 final size:63
Alignment explanation
Indices: 14799--14922 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
14789 CCCTAAGGGA
* * ** *
14799 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
14862 ACATCTTAGGGCC-GCAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTACCTAAGA
14923 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 48 0.92
64 3 0.06
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:15822 original size:5 final size:5
Alignment explanation
Indices: 15812--15857 Score: 65
Period size: 5 Copynumber: 8.8 Consensus size: 5
15802 AACGGTCAAC
*
15812 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTC
15858 AGACCGGTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
5 33 0.89
7 4 0.11
ACGTcount: A:0.04, C:0.22, G:0.54, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:15833 original size:22 final size:22
Alignment explanation
Indices: 15805--15852 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
15795 AACGGTCAAC
15805 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
15827 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
15849 GGTC
1 GGTC
15853 GGGTCAGACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.08, C:0.23, G:0.50, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:15849 original size:27 final size:28
Alignment explanation
Indices: 15798--15867 Score: 97
Period size: 27 Copynumber: 2.4 Consensus size: 28
15788 GAAAGTCAAC
15798 GGTCAACGGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTC-ACGGTCGGGTCGGGTCG
*
15827 GGTCAACGGTC-GGGTCGGGTCGGGTCG
1 GGTCAACGGTCACGGTCGGGTCGGGTCG
15854 GGTCAGACCGGTCA
1 GGTCA-A-CGGTCA
15868 AACCGATTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
27 20 0.54
28 1 0.03
29 16 0.43
ACGTcount: A:0.13, C:0.24, G:0.46, T:0.17
Consensus pattern (28 bp):
GGTCAACGGTCACGGTCGGGTCGGGTCG
Found at i:15872 original size:9 final size:9
Alignment explanation
Indices: 15854--15941 Score: 68
Period size: 9 Copynumber: 9.3 Consensus size: 9
15844 GGTCGGGTCG
*
15854 GGTCAGACC
1 GGTCAAACC
15863 GGTCAAACC
1 GGTCAAACC
* *
15872 GATTCAGACC
1 G-GTCAAACC
15882 GGTCAAACC
1 GGTCAAACC
*
15891 GGTTCGAACC
1 GG-TCAAACC
* * *
15901 AGTTGAAACT
1 -GGTCAAACC
15911 GGTCAAACC
1 GGTCAAACC
15920 GGTCAGAACC
1 GGTCA-AACC
*
15930 GGTTAAACC
1 GGTCAAACC
15939 GGT
1 GGT
15942 TTCCAGCAGC
Statistics
Matches: 61, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
9 35 0.57
10 25 0.41
11 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.26, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:15928 original size:29 final size:28
Alignment explanation
Indices: 15882--15937 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
15872 GATTCAGACC
15882 GGTCAAACCGGTTCGAACCAGTTGAAACT
1 GGTCAAACCGGTTCGAACCAGTT-AAACT
*
15911 GGTCAAACCGG-TCAGAACCGGTTAAAC
1 GGTCAAACCGGTTC-GAACCAGTTAAAC
15938 CGGTTTCCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (28 bp):
GGTCAAACCGGTTCGAACCAGTTAAACT
Found at i:22203 original size:32 final size:31
Alignment explanation
Indices: 22167--22243 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
22157 CGGGGCCGTG
*
22167 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
22199 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
22230 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
22244 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:22226 original size:63 final size:63
Alignment explanation
Indices: 22120--22243 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
22110 CCCTAAGGGA
* * ** *
22120 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
22183 ACATCTTAGGGCC-GCAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTACCTAAGA
22244 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 48 0.92
64 3 0.06
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:23143 original size:5 final size:5
Alignment explanation
Indices: 23133--23212 Score: 79
Period size: 5 Copynumber: 14.8 Consensus size: 5
23123 AACGGTCAAC
* *
23133 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
*
23182 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC
23213 AGACCGGTCA
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
5 51 0.81
7 12 0.19
ACGTcount: A:0.07, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:23154 original size:22 final size:22
Alignment explanation
Indices: 23126--23212 Score: 174
Period size: 22 Copynumber: 4.0 Consensus size: 22
23116 AACGGTCAAC
23126 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
23148 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
23170 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
23192 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
23213 AGACCGGTCA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 65 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:23158 original size:17 final size:16
Alignment explanation
Indices: 23138--23213 Score: 63
Period size: 17 Copynumber: 4.9 Consensus size: 16
23128 TCAACGGTCG
23138 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTC-AC
*
23155 GGTCGGGTCGGGTC-G
1 GGTCGGGTCGGGTCAC
** *
23170 GGTC--AAC-GGTC-G
1 GGTCGGGTCGGGTCAC
23182 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTC-AC
23199 GGTCGGGTCGGGTCA
1 GGTCGGGTCGGGTCA
23214 GACCGGTCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
12 9 0.19
13 1 0.02
14 1 0.02
15 8 0.17
16 1 0.02
17 28 0.58
ACGTcount: A:0.09, C:0.22, G:0.50, T:0.18
Consensus pattern (16 bp):
GGTCGGGTCGGGTCAC
Found at i:23227 original size:9 final size:9
Alignment explanation
Indices: 23209--23296 Score: 77
Period size: 9 Copynumber: 9.3 Consensus size: 9
23199 GGTCGGGTCG
*
23209 GGTCAGACC
1 GGTCAAACC
23218 GGTCAAACC
1 GGTCAAACC
* *
23227 GATTCAGACC
1 G-GTCAAACC
23237 GGTCAAACC
1 GGTCAAACC
*
23246 GGTTCGAACC
1 GG-TCAAACC
* *
23256 AGTTGAAACC
1 -GGTCAAACC
23266 GGTCAAACC
1 GGTCAAACC
23275 GGTCAGAACC
1 GGTCA-AACC
*
23285 GGTTAAACC
1 GGTCAAACC
23294 GGT
1 GGT
23297 TTCCAGCAGC
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
9 36 0.57
10 26 0.41
11 1 0.02
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:23284 original size:19 final size:19
Alignment explanation
Indices: 23209--23296 Score: 69
Period size: 19 Copynumber: 4.7 Consensus size: 19
23199 GGTCGGGTCG
23209 GGTCAG-ACCGGTCAAACC
1 GGTCAGAACCGGTCAAACC
*
23227 GATTCAG-ACCGGTCAAACC
1 G-GTCAGAACCGGTCAAACC
* *
23246 GGTTC-GAACCAGTTGAAACC
1 GG-TCAGAACC-GGTCAAACC
23266 GGTCA-AACCGGTCAGAACC
1 GGTCAGAACCGGTCA-AACC
*
23285 GGTTA-AACCGGT
1 GGTCAGAACCGGT
23297 TTCCAGCAGC
Statistics
Matches: 57, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
18 5 0.09
19 43 0.75
20 9 0.16
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (19 bp):
GGTCAGAACCGGTCAAACC
Found at i:29566 original size:32 final size:31
Alignment explanation
Indices: 29530--29606 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
29520 CGGGGCCGTG
*
29530 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
29562 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
29593 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
29607 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:29589 original size:63 final size:63
Alignment explanation
Indices: 29483--29606 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
29473 CCCTAAGGGA
* * ** *
29483 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
29546 ACATCTTAGGGCC-GCAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTACCTAAGA
29607 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 48 0.92
64 3 0.06
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:30506 original size:5 final size:5
Alignment explanation
Indices: 30496--30570 Score: 69
Period size: 5 Copynumber: 13.8 Consensus size: 5
30486 AACGGTCAAC
* *
30496 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
*
30545 GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTC--G GGTCG GGTCG GGTC
30571 AGACCGGTCA
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
5 46 0.79
7 12 0.21
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:30521 original size:17 final size:17
Alignment explanation
Indices: 30501--30571 Score: 97
Period size: 17 Copynumber: 3.9 Consensus size: 17
30491 TCAACGGTCG
30501 GGTCGGGTCGGGTCAACGGTC
1 GGTCGGGTCGGGTCAA----C
30522 GGGTCGGGTCGGGTCAAC
1 G-GTCGGGTCGGGTCAAC
30540 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
30557 GGTCGGGTCGGGTCA
1 GGTCGGGTCGGGTCA
30572 GACCGGTCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 31 0.63
18 2 0.04
21 1 0.02
22 15 0.31
ACGTcount: A:0.10, C:0.23, G:0.49, T:0.18
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAC
Found at i:30566 original size:22 final size:22
Alignment explanation
Indices: 30489--30553 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
30479 AACGGTCAAC
30489 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
30511 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
30533 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
30554 AACGGTCGGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:30585 original size:9 final size:9
Alignment explanation
Indices: 30567--30654 Score: 77
Period size: 9 Copynumber: 9.3 Consensus size: 9
30557 GGTCGGGTCG
*
30567 GGTCAGACC
1 GGTCAAACC
30576 GGTCAAACC
1 GGTCAAACC
* *
30585 GATTCAGACC
1 G-GTCAAACC
30595 GGTCAAACC
1 GGTCAAACC
*
30604 GGTTCGAACC
1 GG-TCAAACC
* *
30614 AGTTGAAACC
1 -GGTCAAACC
30624 GGTCAAACC
1 GGTCAAACC
30633 GGTCAGAACC
1 GGTCA-AACC
*
30643 GGTTAAACC
1 GGTCAAACC
30652 GGT
1 GGT
30655 TTCCAGCAGC
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
9 36 0.57
10 26 0.41
11 1 0.02
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:30642 original size:19 final size:19
Alignment explanation
Indices: 30567--30654 Score: 69
Period size: 19 Copynumber: 4.7 Consensus size: 19
30557 GGTCGGGTCG
30567 GGTCAG-ACCGGTCAAACC
1 GGTCAGAACCGGTCAAACC
*
30585 GATTCAG-ACCGGTCAAACC
1 G-GTCAGAACCGGTCAAACC
* *
30604 GGTTC-GAACCAGTTGAAACC
1 GG-TCAGAACC-GGTCAAACC
30624 GGTCA-AACCGGTCAGAACC
1 GGTCAGAACCGGTCA-AACC
*
30643 GGTTA-AACCGGT
1 GGTCAGAACCGGT
30655 TTCCAGCAGC
Statistics
Matches: 57, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
18 5 0.09
19 43 0.75
20 9 0.16
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (19 bp):
GGTCAGAACCGGTCAAACC
Found at i:36921 original size:32 final size:31
Alignment explanation
Indices: 36885--36961 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
36875 CGGGGCCGTG
*
36885 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
36917 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
36948 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
36962 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:36944 original size:63 final size:63
Alignment explanation
Indices: 36838--36961 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
36828 CCCTAAGGGA
* * ** *
36838 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
36901 ACATCTTAGGGCC-GCAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTACCTAAGA
36962 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 48 0.92
64 3 0.06
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:37889 original size:21 final size:21
Alignment explanation
Indices: 37840--37923 Score: 145
Period size: 21 Copynumber: 4.0 Consensus size: 21
37830 CAACGGTCAA
37840 CGGTCAACGGTCGGGTCGGGT
1 CGGTCAACGGTCGGGTCGGGT
37861 CGGGTCAACGGTCGGGTCGGGT
1 C-GGTCAACGGTCGGGTCGGGT
37883 CGGTCAACGGTCGGGTCGGGT
1 CGGTCAACGGTCGGGTCGGGT
37904 C-GTCAACGGTC-GGTCGGGT
1 CGGTCAACGGTCGGGTCGGGT
37923 C
1 C
37924 AGACCGGTCA
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
19 9 0.15
20 10 0.16
21 22 0.35
22 21 0.34
ACGTcount: A:0.10, C:0.25, G:0.46, T:0.19
Consensus pattern (21 bp):
CGGTCAACGGTCGGGTCGGGT
Found at i:37892 original size:43 final size:40
Alignment explanation
Indices: 37840--37923 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 40
37830 CAACGGTCAA
37840 CGGTCAACGGTCGGGTCGGGTCGGGTCAACGGTCGGGTCGGGT
1 CGGTCAACGGTCGGGTCGGGTC--GTCAACGGTC-GGTCGGGT
37883 CGGTCAACGGTCGGGTCGGGTCGTCAACGGTCGGTCGGGT
1 CGGTCAACGGTCGGGTCGGGTCGTCAACGGTCGGTCGGGT
37923 C
1 C
37924 AGACCGGTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
40 9 0.22
41 10 0.24
43 22 0.54
ACGTcount: A:0.10, C:0.25, G:0.46, T:0.19
Consensus pattern (40 bp):
CGGTCAACGGTCGGGTCGGGTCGTCAACGGTCGGTCGGGT
Found at i:37923 original size:5 final size:5
Alignment explanation
Indices: 37848--37905 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
37838 AACGGTCAAC
* *
37848 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC- GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
37896 GGTCG GGTCG
1 GGTCG GGTCG
37906 TCAACGGTCG
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
4 4 0.09
5 33 0.73
7 8 0.18
ACGTcount: A:0.07, C:0.22, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:37932 original size:9 final size:9
Alignment explanation
Indices: 37920--38007 Score: 77
Period size: 9 Copynumber: 9.3 Consensus size: 9
37910 CGGTCGGTCG
*
37920 GGTCAGACC
1 GGTCAAACC
37929 GGTCAAACC
1 GGTCAAACC
* *
37938 GATTCAGACC
1 G-GTCAAACC
37948 GGTCAAACC
1 GGTCAAACC
*
37957 GGTTCGAACC
1 GG-TCAAACC
* *
37967 AGTTGAAACC
1 -GGTCAAACC
37977 GGTCAAACC
1 GGTCAAACC
37986 GGTCAGAACC
1 GGTCA-AACC
*
37996 GGTTAAACC
1 GGTCAAACC
38005 GGT
1 GGT
38008 TTCCAGCAGC
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
9 36 0.57
10 26 0.41
11 1 0.02
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:37995 original size:19 final size:19
Alignment explanation
Indices: 37920--38007 Score: 69
Period size: 19 Copynumber: 4.7 Consensus size: 19
37910 CGGTCGGTCG
37920 GGTCAG-ACCGGTCAAACC
1 GGTCAGAACCGGTCAAACC
*
37938 GATTCAG-ACCGGTCAAACC
1 G-GTCAGAACCGGTCAAACC
* *
37957 GGTTC-GAACCAGTTGAAACC
1 GG-TCAGAACC-GGTCAAACC
37977 GGTCA-AACCGGTCAGAACC
1 GGTCAGAACCGGTCA-AACC
*
37996 GGTTA-AACCGGT
1 GGTCAGAACCGGT
38008 TTCCAGCAGC
Statistics
Matches: 57, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
18 5 0.09
19 43 0.75
20 9 0.16
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (19 bp):
GGTCAGAACCGGTCAAACC
Done.